diff --git a/examples/balance/log.15Feb16.balance.bond.fast.g++.1 b/examples/balance/log.15Feb16.balance.bond.fast.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..3d87f5e0ed160e267dd9437f5f67d42ac2a36bbf
--- /dev/null
+++ b/examples/balance/log.15Feb16.balance.bond.fast.g++.1
@@ -0,0 +1,225 @@
+LAMMPS (15 Feb 2016)
+# 2d circle of particles inside a box with LJ walls
+
+variable b index 0
+
+variable x index 50
+variable y index 20
+variable d index 20
+variable v index 5
+variable w index 2
+
+units lj
+dimension 2
+atom_style bond
+boundary f f p
+
+lattice hex 0.85
+Lattice spacing in x,y,z = 1.16553 2.01877 1.16553
+region box block 0 $x 0 $y -0.5 0.5
+region box block 0 50 0 $y -0.5 0.5
+region box block 0 50 0 20 -0.5 0.5
+create_box 1 box bond/types 1 extra/bond/per/atom 6
+Created orthogonal box = (0 0 -0.582767) to (58.2767 40.3753 0.582767)
+ 1 by 1 by 1 MPI processor grid
+region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
+region circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
+region circle sphere 11 6.7735026918962581988 0.0 $(v_d/2)
+region circle sphere 11 6.7735026918962581988 0.0 10
+create_atoms 1 region circle
+Created 361 atoms
+mass 1 1.0
+
+velocity all create 0.5 87287 loop geom
+velocity all set $v $w 0 sum yes
+velocity all set 5 $w 0 sum yes
+velocity all set 5 2 0 sum yes
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 10.0 1.0 2.5
+
+bond_style harmonic
+bond_coeff 1 10.0 1.2
+
+# need to preserve 1-3, 1-4 pairwise interactions during hard collisions
+
+special_bonds lj/coul 0 1 1
+ 0 = max # of 1-2 neighbors
+ 1 = max # of special neighbors
+create_bonds all all 1 1.0 1.5
+Neighbor list info ...
+ 2 neighbor list requests
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4 -> bins = 42 29 1
+Added 1014 bonds, new total = 1014
+ 6 = max # of 1-2 neighbors
+ 6 = max # of special neighbors
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nve
+
+fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
+fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5
+fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
+fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5
+
+comm_style tiled
+comm_modify cutoff 7.5
+fix 10 all balance 50 0.9 rcb
+
+#compute 1 all property/atom proc
+#variable p atom (c_1%10)+1
+#dump 2 all custom 50 tmp.dump id v_p x y z
+
+#dump 3 all image 50 image.*.jpg v_p type bond atom 0.25 # adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
+#variable colors string # "red green blue yellow white # purple pink orange lime gray"
+#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
+
+thermo_style custom step temp epair press f_10[3] f_10
+thermo 100
+
+run 10000
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 7.5
+ binsize = 1.4 -> bins = 42 29 1
+Memory usage per processor = 4.44301 Mbytes
+Step Temp E_pair Press 10[3] 10
+ 0 25.701528 -2.2032569 3.1039469 1 1
+ 100 27.623422 -6.228166 2.6542136 1 1
+ 200 33.35302 -15.746749 3.2018248 1 1
+ 300 39.17734 -24.1557 4.9116986 1 1
+ 400 41.660701 -27.615203 8.6214678 1 1
+ 500 37.154935 -24.096962 3.2656162 1 1
+ 600 35.061294 -21.52655 2.3693223 1 1
+ 700 37.204395 -22.313267 2.7108913 1 1
+ 800 39.050704 -24.972147 5.5398741 1 1
+ 900 38.37275 -24.777769 3.9291488 1 1
+ 1000 39.147816 -26.003699 4.3586203 1 1
+ 1100 36.084337 -24.88638 4.5496174 1 1
+ 1200 32.404559 -20.810803 6.0760128 1 1
+ 1300 32.625538 -19.709411 4.3718289 1 1
+ 1400 32.246777 -18.785184 3.435959 1 1
+ 1500 29.174368 -17.434726 2.2702916 1 1
+ 1600 27.359273 -15.40756 1.033659 1 1
+ 1700 26.046626 -14.318045 0.87714473 1 1
+ 1800 24.540401 -13.017686 0.84464169 1 1
+ 1900 26.259688 -12.777739 0.80954004 1 1
+ 2000 27.491023 -13.363863 1.4519188 1 1
+ 2100 27.839831 -13.709118 3.0184763 1 1
+ 2200 26.669065 -12.710422 1.4560094 1 1
+ 2300 26.86742 -12.730386 0.16986139 1 1
+ 2400 26.375504 -12.476682 1.907352 1 1
+ 2500 26.581263 -12.530908 1.5507765 1 1
+ 2600 27.67091 -12.922702 2.0391206 1 1
+ 2700 27.158784 -13.306789 3.7355268 1 1
+ 2800 25.635671 -13.502047 2.9431633 1 1
+ 2900 24.648357 -12.388002 0.44910075 1 1
+ 3000 22.988768 -10.685349 0.37214853 1 1
+ 3100 21.788719 -10.171928 -0.95734833 1 1
+ 3200 22.707514 -9.6682633 -0.32868418 1 1
+ 3300 22.907772 -10.612766 -0.024319089 1 1
+ 3400 24.276426 -10.802246 0.44731188 1 1
+ 3500 25.086959 -10.797849 2.3218091 1 1
+ 3600 26.064365 -12.589537 1.2460738 1 1
+ 3700 24.656426 -11.956895 0.57862216 1 1
+ 3800 22.316856 -11.174148 -0.7567936 1 1
+ 3900 22.590299 -9.5928781 0.4127727 1 1
+ 4000 22.353461 -9.5887736 -0.34247396 1 1
+ 4100 24.103395 -9.76584 0.98989862 1 1
+ 4200 23.92261 -10.566828 -0.71536268 1 1
+ 4300 24.44409 -11.358378 0.37166197 1 1
+ 4400 24.772419 -11.324888 0.26732853 1 1
+ 4500 23.150748 -11.309892 -0.43134573 1 1
+ 4600 24.008361 -10.212365 0.43277527 1 1
+ 4700 25.107401 -9.5753673 0.020406689 1 1
+ 4800 23.658604 -8.9131426 0.46554745 1 1
+ 4900 22.530251 -9.023311 -0.014405315 1 1
+ 5000 23.110692 -9.6567397 0.9033234 1 1
+ 5100 23.760144 -9.7623416 0.32059726 1 1
+ 5200 25.048012 -9.6748253 0.66411561 1 1
+ 5300 24.09835 -9.7867216 0.61128267 1 1
+ 5400 22.984982 -9.9464053 0.28096544 1 1
+ 5500 22.502003 -9.9294451 -0.53666181 1 1
+ 5600 23.712298 -10.054318 0.64334761 1 1
+ 5700 23.350796 -10.217344 2.1979894 1 1
+ 5800 25.246549 -12.458753 0.055553025 1 1
+ 5900 24.422272 -10.641177 0.82506839 1 1
+ 6000 22.478315 -10.629525 -0.774321 1 1
+ 6100 22.970846 -10.218868 0.59819592 1 1
+ 6200 24.500063 -10.355481 0.55427078 1 1
+ 6300 22.358071 -9.9041539 0.89500518 1 1
+ 6400 23.924951 -11.121442 0.045999129 1 1
+ 6500 24.83773 -10.464191 2.0048038 1 1
+ 6600 24.752158 -9.9939162 0.53794465 1 1
+ 6700 23.073765 -9.3662561 0.38618685 1 1
+ 6800 21.940219 -8.4948475 -0.25184019 1 1
+ 6900 22.23783 -8.8668868 0.0072863367 1 1
+ 7000 25.667836 -10.473211 0.59852886 1 1
+ 7100 23.352123 -9.0862268 0.85289283 1 1
+ 7200 24.072107 -9.4020576 0.090222808 1 1
+ 7300 22.806746 -8.4687857 -0.46892989 1 1
+ 7400 24.798425 -9.1144357 -0.38738146 1 1
+ 7500 24.748499 -9.1560558 0.94929896 1 1
+ 7600 25.364753 -10.176533 0.2649225 1 1
+ 7700 25.137988 -9.6617897 1.3920543 1 1
+ 7800 25.502583 -10.320832 0.64812816 1 1
+ 7900 24.5208 -9.9466543 -0.084071026 1 1
+ 8000 24.653522 -10.312942 0.32535023 1 1
+ 8100 23.129565 -9.6250435 0.016356303 1 1
+ 8200 23.82421 -9.7608023 0.11631418 1 1
+ 8300 25.081262 -9.3510452 0.92337854 1 1
+ 8400 24.328205 -9.2875396 0.28266968 1 1
+ 8500 25.041711 -11.254976 -0.21368615 1 1
+ 8600 24.111473 -9.0389585 1.2102938 1 1
+ 8700 23.50066 -9.0926498 0.78819229 1 1
+ 8800 23.840962 -9.3434474 0.091313007 1 1
+ 8900 23.081841 -9.0635966 0.56672001 1 1
+ 9000 24.712103 -9.3243213 0.60301629 1 1
+ 9100 24.457422 -9.439298 -0.60457515 1 1
+ 9200 25.070662 -9.1945782 1.2399235 1 1
+ 9300 25.019869 -8.7910068 0.42340497 1 1
+ 9400 24.23662 -9.3111098 -0.75379175 1 1
+ 9500 24.836827 -8.7324281 0.81857501 1 1
+ 9600 24.901993 -8.6624128 0.84890877 1 1
+ 9700 24.936686 -8.9869503 1.9627894 1 1
+ 9800 25.393368 -9.8538595 0.45344428 1 1
+ 9900 25.942336 -9.7854728 0.68352091 1 1
+ 10000 24.636319 -9.3369442 0.62793231 1 1
+Loop time of 1.67474 on 1 procs for 10000 steps with 361 atoms
+
+Performance: 2579511.004 tau/day, 5971.090 timesteps/s
+99.8% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.47884 | 0.47884 | 0.47884 | 0.0 | 28.59
+Bond | 0.24918 | 0.24918 | 0.24918 | 0.0 | 14.88
+Neigh | 0.82974 | 0.82974 | 0.82974 | 0.0 | 49.54
+Comm | 0.01265 | 0.01265 | 0.01265 | 0.0 | 0.76
+Output | 0.00085878 | 0.00085878 | 0.00085878 | 0.0 | 0.05
+Modify | 0.075636 | 0.075636 | 0.075636 | 0.0 | 4.52
+Other | | 0.02783 | | | 1.66
+
+Nlocal: 361 ave 361 max 361 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 2421 ave 2421 max 2421 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 2421
+Ave neighs/atom = 6.70637
+Ave special neighs/atom = 5.61773
+Neighbor list builds = 4937
+Dangerous builds = 5
+Total wall time: 0:00:01
diff --git a/examples/balance/log.15Feb16.balance.bond.fast.g++.4 b/examples/balance/log.15Feb16.balance.bond.fast.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..cbc7bc0418c38b066b3a5e318251d5b3185de81e
--- /dev/null
+++ b/examples/balance/log.15Feb16.balance.bond.fast.g++.4
@@ -0,0 +1,225 @@
+LAMMPS (15 Feb 2016)
+# 2d circle of particles inside a box with LJ walls
+
+variable b index 0
+
+variable x index 50
+variable y index 20
+variable d index 20
+variable v index 5
+variable w index 2
+
+units lj
+dimension 2
+atom_style bond
+boundary f f p
+
+lattice hex 0.85
+Lattice spacing in x,y,z = 1.16553 2.01877 1.16553
+region box block 0 $x 0 $y -0.5 0.5
+region box block 0 50 0 $y -0.5 0.5
+region box block 0 50 0 20 -0.5 0.5
+create_box 1 box bond/types 1 extra/bond/per/atom 6
+Created orthogonal box = (0 0 -0.582767) to (58.2767 40.3753 0.582767)
+ 2 by 2 by 1 MPI processor grid
+region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
+region circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
+region circle sphere 11 6.7735026918962581988 0.0 $(v_d/2)
+region circle sphere 11 6.7735026918962581988 0.0 10
+create_atoms 1 region circle
+Created 361 atoms
+mass 1 1.0
+
+velocity all create 0.5 87287 loop geom
+velocity all set $v $w 0 sum yes
+velocity all set 5 $w 0 sum yes
+velocity all set 5 2 0 sum yes
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 10.0 1.0 2.5
+
+bond_style harmonic
+bond_coeff 1 10.0 1.2
+
+# need to preserve 1-3, 1-4 pairwise interactions during hard collisions
+
+special_bonds lj/coul 0 1 1
+ 0 = max # of 1-2 neighbors
+ 1 = max # of special neighbors
+create_bonds all all 1 1.0 1.5
+Neighbor list info ...
+ 2 neighbor list requests
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4 -> bins = 42 29 1
+Added 1014 bonds, new total = 1014
+ 6 = max # of 1-2 neighbors
+ 6 = max # of special neighbors
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nve
+
+fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
+fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5
+fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
+fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5
+
+comm_style tiled
+comm_modify cutoff 7.5
+fix 10 all balance 50 0.9 rcb
+
+#compute 1 all property/atom proc
+#variable p atom (c_1%10)+1
+#dump 2 all custom 50 tmp.dump id v_p x y z
+
+#dump 3 all image 50 image.*.jpg v_p type bond atom 0.25 # adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
+#variable colors string # "red green blue yellow white # purple pink orange lime gray"
+#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
+
+thermo_style custom step temp epair press f_10[3] f_10
+thermo 100
+
+run 10000
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 7.5
+ binsize = 1.4 -> bins = 42 29 1
+Memory usage per processor = 4.49421 Mbytes
+Step Temp E_pair Press 10[3] 10
+ 0 25.701528 -2.2032569 3.1039469 3.2354571 1.0526316
+ 100 27.623422 -6.228166 2.6542136 1.2631579 1.0083102
+ 200 33.35302 -15.746749 3.2018248 1.2963989 1.0193906
+ 300 39.17734 -24.1557 4.9116986 1.2963989 1.0193906
+ 400 41.660701 -27.615203 8.6214679 1.3518006 1.0083102
+ 500 37.154928 -24.096947 3.2656178 1.3296399 1.0193906
+ 600 35.059889 -21.524279 2.372849 1.3296399 1.0083102
+ 700 36.70516 -21.98396 3.2995108 1.3296399 1.0083102
+ 800 39.53521 -25.672748 4.3257712 1.3961219 1.0083102
+ 900 38.566797 -24.778382 4.1874914 1.3739612 1.0083102
+ 1000 37.506157 -25.381025 5.6634589 1.4182825 1.0193906
+ 1100 34.186888 -23.460558 5.2123037 1.2963989 1.0083102
+ 1200 33.302788 -22.509552 4.9394032 1.1745152 1.0193906
+ 1300 33.271956 -22.831342 4.5519649 1.1966759 1.0083102
+ 1400 30.344677 -20.654604 4.1641375 1.0969529 1.0193906
+ 1500 27.292624 -18.180523 1.0686706 1.1412742 1.0083102
+ 1600 26.787948 -15.907011 1.7236133 1.1745152 1.0193906
+ 1700 25.708419 -15.568774 0.73006531 1.1080332 1.0193906
+ 1800 26.523196 -14.641077 0.78443231 1.1301939 1.0083102
+ 1900 25.151151 -13.927975 1.1760729 1.1080332 1.0193906
+ 2000 27.637036 -15.055467 1.5903524 1.1301939 1.0083102
+ 2100 27.642772 -14.038356 2.4101976 1.2077562 1.0083102
+ 2200 27.178261 -13.277262 1.9252291 1.1745152 1.0193906
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+ 7900 22.897008 -10.849819 0.56424197 1.0415512 1.0083102
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+ 8100 22.726563 -9.8563277 0.30293638 1.0193906 1.0193906
+ 8200 23.424699 -10.687885 0.54222367 1.0415512 1.0083102
+ 8300 22.921826 -10.919492 0.55264172 1.0747922 1.0083102
+ 8400 23.220159 -9.7725217 1.2872547 1.1080332 1.0083102
+ 8500 23.606204 -9.7070499 1.0340181 1.0747922 1.0193906
+ 8600 23.008166 -10.451507 -0.42524326 1.0747922 1.0083102
+ 8700 22.4959 -10.278782 0.19535494 1.0858726 1.0083102
+ 8800 25.153658 -10.757 1.5966743 1.0193906 1.0193906
+ 8900 23.206798 -10.486994 1.2031737 1.0637119 1.0083102
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+ 9200 21.431928 -9.073801 0.3773795 1.0415512 1.0193906
+ 9300 23.596502 -11.045041 -0.3135787 1.0858726 1.0083102
+ 9400 25.308669 -11.931174 1.3143518 1.0526316 1.0193906
+ 9500 24.394499 -10.661499 0.82236963 1.0969529 1.0193906
+ 9600 21.987451 -9.5632699 0.30728292 1.0858726 1.0193906
+ 9700 22.150748 -9.5707928 -0.1239396 1.0526316 1.0193906
+ 9800 23.347328 -9.7899306 0.29737715 1.0193906 1.0083102
+ 9900 20.310207 -9.4839992 -1.2980277 1.0193906 1.0193906
+ 10000 22.978427 -9.9593786 -0.45943368 1.0526316 1.0083102
+Loop time of 0.815364 on 4 procs for 10000 steps with 361 atoms
+
+Performance: 5298244.819 tau/day, 12264.456 timesteps/s
+98.9% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.12547 | 0.13632 | 0.14796 | 2.6 | 16.72
+Bond | 0.05547 | 0.06023 | 0.064582 | 1.7 | 7.39
+Neigh | 0.28201 | 0.28972 | 0.298 | 1.1 | 35.53
+Comm | 0.16858 | 0.19467 | 0.22096 | 4.3 | 23.88
+Output | 0.0017931 | 0.0019639 | 0.0023253 | 0.5 | 0.24
+Modify | 0.039718 | 0.040559 | 0.041364 | 0.4 | 4.97
+Other | | 0.09189 | | | 11.27
+
+Nlocal: 90.25 ave 91 max 90 min
+Histogram: 3 0 0 0 0 0 0 0 0 1
+Nghost: 195.25 ave 202 max 185 min
+Histogram: 1 0 0 0 0 1 0 0 1 1
+Neighs: 629.5 ave 731 max 543 min
+Histogram: 1 1 0 0 0 0 1 0 0 1
+
+Total # of neighbors = 2518
+Ave neighs/atom = 6.97507
+Ave special neighs/atom = 5.61773
+Neighbor list builds = 4874
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/balance/log.15Feb16.balance.bond.slow.g++.1 b/examples/balance/log.15Feb16.balance.bond.slow.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..f794c76ffca7fff3ad06a93b79577d3a1be66773
--- /dev/null
+++ b/examples/balance/log.15Feb16.balance.bond.slow.g++.1
@@ -0,0 +1,524 @@
+LAMMPS (15 Feb 2016)
+# 2d circle of particles inside a box with LJ walls
+
+variable b index 0
+
+variable x index 50
+variable y index 20
+variable d index 20
+
+# careful not to slam into wall too hard
+
+variable v index 0.3
+variable w index 0.08
+
+units lj
+dimension 2
+atom_style bond
+boundary f f p
+
+lattice hex 0.85
+Lattice spacing in x,y,z = 1.16553 2.01877 1.16553
+region box block 0 $x 0 $y -0.5 0.5
+region box block 0 50 0 $y -0.5 0.5
+region box block 0 50 0 20 -0.5 0.5
+create_box 1 box bond/types 1 extra/bond/per/atom 6
+Created orthogonal box = (0 0 -0.582767) to (58.2767 40.3753 0.582767)
+ 1 by 1 by 1 MPI processor grid
+region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
+region circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
+region circle sphere 11 6.7735026918962581988 0.0 $(v_d/2)
+region circle sphere 11 6.7735026918962581988 0.0 10
+create_atoms 1 region circle
+Created 361 atoms
+mass 1 1.0
+
+velocity all create 0.5 87287 loop geom
+velocity all set $v $w 0 sum yes
+velocity all set 0.3 $w 0 sum yes
+velocity all set 0.3 0.08 0 sum yes
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 10.0 1.0 2.5
+
+bond_style harmonic
+bond_coeff 1 10.0 1.2
+
+create_bonds all all 1 1.0 1.5
+Neighbor list info ...
+ 2 neighbor list requests
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4 -> bins = 42 29 1
+Added 1014 bonds, new total = 1014
+ 6 = max # of 1-2 neighbors
+ 30 = max # of 1-3 neighbors
+ 180 = max # of 1-4 neighbors
+ 36 = max # of special neighbors
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nve
+
+fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
+fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5
+fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
+fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5
+
+comm_style tiled
+fix 10 all balance 50 0.9 rcb
+
+#compute 1 all property/atom proc
+#variable p atom (c_1%10)+1
+#dump 2 all custom 50 tmp.dump id v_p x y z
+
+#dump 3 all image 200 image.*.jpg v_p type bond atom 0.25 # adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
+#variable colors string # "red green blue yellow white # purple pink orange lime gray"
+#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
+
+thermo_style custom step temp epair press f_10[3] f_10
+thermo 100
+
+run 40000
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4 -> bins = 42 29 1
+Memory usage per processor = 6.31529 Mbytes
+Step Temp E_pair Press 10[3] 10
+ 0 0.57437856 0 0.26099453 1 1
+ 100 0.29756515 0 0.10149401 1 1
+ 200 0.35394813 0 0.075159099 1 1
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+ 400 0.34078347 0 -0.020825841 1 1
+ 500 0.35201095 0 -0.062637506 1 1
+ 600 0.34014717 0 -0.11122965 1 1
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+ 38600 0.32322402 0 0.053453832 1 1
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+ 39000 0.33775583 0 0.0788316 1 1
+ 39100 0.34256036 0 0.075874935 1 1
+ 39200 0.33128527 0 0.071610976 1 1
+ 39300 0.34519653 0 0.046257301 1 1
+ 39400 0.34351844 0 0.052422917 1 1
+ 39500 0.35716037 0 0.048916058 1 1
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+ 39700 0.34587892 0 0.021619621 1 1
+ 39800 0.34878036 0 0.0092881327 1 1
+ 39900 0.35225411 0 -0.011341599 1 1
+ 40000 0.36309266 0 0.0050869295 1 1
+Loop time of 1.94553 on 1 procs for 40000 steps with 361 atoms
+
+Performance: 8881898.790 tau/day, 20559.951 timesteps/s
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.068658 | 0.068658 | 0.068658 | 0.0 | 3.53
+Bond | 0.9979 | 0.9979 | 0.9979 | 0.0 | 51.29
+Neigh | 0.50428 | 0.50428 | 0.50428 | 0.0 | 25.92
+Comm | 0.015341 | 0.015341 | 0.015341 | 0.0 | 0.79
+Output | 0.0029466 | 0.0029466 | 0.0029466 | 0.0 | 0.15
+Modify | 0.28324 | 0.28324 | 0.28324 | 0.0 | 14.56
+Other | | 0.07317 | | | 3.76
+
+Nlocal: 361 ave 361 max 361 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Ave special neighs/atom = 31.0249
+Neighbor list builds = 3079
+Dangerous builds = 0
+Total wall time: 0:00:01
diff --git a/examples/balance/log.15Feb16.balance.bond.slow.g++.4 b/examples/balance/log.15Feb16.balance.bond.slow.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..f07d8e479e0a32eb96ab5413d35f289feaa43a8e
--- /dev/null
+++ b/examples/balance/log.15Feb16.balance.bond.slow.g++.4
@@ -0,0 +1,524 @@
+LAMMPS (15 Feb 2016)
+# 2d circle of particles inside a box with LJ walls
+
+variable b index 0
+
+variable x index 50
+variable y index 20
+variable d index 20
+
+# careful not to slam into wall too hard
+
+variable v index 0.3
+variable w index 0.08
+
+units lj
+dimension 2
+atom_style bond
+boundary f f p
+
+lattice hex 0.85
+Lattice spacing in x,y,z = 1.16553 2.01877 1.16553
+region box block 0 $x 0 $y -0.5 0.5
+region box block 0 50 0 $y -0.5 0.5
+region box block 0 50 0 20 -0.5 0.5
+create_box 1 box bond/types 1 extra/bond/per/atom 6
+Created orthogonal box = (0 0 -0.582767) to (58.2767 40.3753 0.582767)
+ 2 by 2 by 1 MPI processor grid
+region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
+region circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
+region circle sphere 11 6.7735026918962581988 0.0 $(v_d/2)
+region circle sphere 11 6.7735026918962581988 0.0 10
+create_atoms 1 region circle
+Created 361 atoms
+mass 1 1.0
+
+velocity all create 0.5 87287 loop geom
+velocity all set $v $w 0 sum yes
+velocity all set 0.3 $w 0 sum yes
+velocity all set 0.3 0.08 0 sum yes
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 10.0 1.0 2.5
+
+bond_style harmonic
+bond_coeff 1 10.0 1.2
+
+create_bonds all all 1 1.0 1.5
+Neighbor list info ...
+ 2 neighbor list requests
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4 -> bins = 42 29 1
+Added 1014 bonds, new total = 1014
+ 6 = max # of 1-2 neighbors
+ 30 = max # of 1-3 neighbors
+ 180 = max # of 1-4 neighbors
+ 36 = max # of special neighbors
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nve
+
+fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
+fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5
+fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
+fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5
+
+comm_style tiled
+fix 10 all balance 50 0.9 rcb
+
+#compute 1 all property/atom proc
+#variable p atom (c_1%10)+1
+#dump 2 all custom 50 tmp.dump id v_p x y z
+
+#dump 3 all image 200 image.*.jpg v_p type bond atom 0.25 # adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
+#variable colors string # "red green blue yellow white # purple pink orange lime gray"
+#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
+
+thermo_style custom step temp epair press f_10[3] f_10
+thermo 100
+
+run 40000
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4 -> bins = 42 29 1
+Memory usage per processor = 6.41878 Mbytes
+Step Temp E_pair Press 10[3] 10
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+ 40000 0.36309266 0 0.0050869295 1.0304709 1.0083102
+Loop time of 1.06031 on 4 procs for 40000 steps with 361 atoms
+
+Performance: 16297104.069 tau/day, 37724.778 timesteps/s
+99.2% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.019866 | 0.021036 | 0.024189 | 1.3 | 1.98
+Bond | 0.21436 | 0.24183 | 0.27259 | 5.1 | 22.81
+Neigh | 0.16022 | 0.16068 | 0.16101 | 0.1 | 15.15
+Comm | 0.2742 | 0.31331 | 0.3498 | 5.6 | 29.55
+Output | 0.0070348 | 0.0075188 | 0.0087383 | 0.8 | 0.71
+Modify | 0.14238 | 0.14861 | 0.15484 | 1.3 | 14.02
+Other | | 0.1673 | | | 15.78
+
+Nlocal: 90.25 ave 91 max 89 min
+Histogram: 1 0 0 0 0 1 0 0 0 2
+Nghost: 59.25 ave 61 max 56 min
+Histogram: 1 0 0 0 0 0 0 0 2 1
+Neighs: 0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Ave special neighs/atom = 31.0249
+Neighbor list builds = 3079
+Dangerous builds = 0
+Total wall time: 0:00:01
diff --git a/examples/balance/log.15Feb16.balance.g++.1 b/examples/balance/log.15Feb16.balance.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..d973de267e4c44938465b8040a930acc970b6e65
--- /dev/null
+++ b/examples/balance/log.15Feb16.balance.g++.1
@@ -0,0 +1,202 @@
+LAMMPS (15 Feb 2016)
+# 2d circle of particles inside a box with LJ walls
+
+variable b index 0
+
+variable x index 50
+variable y index 20
+variable d index 20
+variable v index 5
+variable w index 2
+
+units lj
+dimension 2
+atom_style atomic
+boundary f f p
+
+lattice hex 0.85
+Lattice spacing in x,y,z = 1.16553 2.01877 1.16553
+region box block 0 $x 0 $y -0.5 0.5
+region box block 0 50 0 $y -0.5 0.5
+region box block 0 50 0 20 -0.5 0.5
+create_box 1 box
+Created orthogonal box = (0 0 -0.582767) to (58.2767 40.3753 0.582767)
+ 1 by 1 by 1 MPI processor grid
+region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
+region circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
+region circle sphere 11 6.7735026918962581988 0.0 $(v_d/2)
+region circle sphere 11 6.7735026918962581988 0.0 10
+create_atoms 1 region circle
+Created 361 atoms
+mass 1 1.0
+
+velocity all create 0.5 87287 loop geom
+velocity all set $v $w 0 sum yes
+velocity all set 5 $w 0 sum yes
+velocity all set 5 2 0 sum yes
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 10.0 1.0 2.5
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nve
+
+fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
+fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5
+fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
+fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5
+
+comm_style tiled
+fix 10 all balance 50 0.9 rcb
+
+#compute 1 all property/atom proc
+#variable p atom c_1%10
+#dump 2 all custom 50 tmp.dump id v_p x y z
+
+#dump 3 all image 50 image.*.jpg v_p type # adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
+#variable colors string # "red green blue yellow white # purple pink orange lime gray"
+#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
+
+thermo_style custom step temp epair press f_10[3] f_10
+thermo 100
+
+run 10000
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4 -> bins = 42 29 1
+Memory usage per processor = 2.47688 Mbytes
+Step Temp E_pair Press 10[3] 10
+ 0 25.701528 -29.143179 -1.2407285 1 1
+ 100 26.269576 -29.713313 7.9052334 1 1
+ 200 26.368336 -29.809962 1.6412462 1 1
+ 300 26.479082 -29.920083 2.3678653 1 1
+ 400 26.522239 -29.965537 6.6787858 1 1
+ 500 25.725591 -29.168034 0.67065285 1 1
+ 600 26.247693 -29.692706 7.9887712 1 1
+ 700 26.237368 -29.676926 1.5987214 1 1
+ 800 25.889643 -29.431589 4.6160859 1 1
+ 900 23.635295 -27.372963 9.029962 1 1
+ 1000 22.571904 -25.87422 1.8936085 1 1
+ 1100 17.493795 -21.447274 9.502619 1 1
+ 1200 17.214459 -20.726964 6.3578933 1 1
+ 1300 16.424366 -19.75746 3.9025348 1 1
+ 1400 15.09282 -18.172384 1.7966088 1 1
+ 1500 13.669129 -16.736191 1.3320876 1 1
+ 1600 13.518191 -16.481254 2.2474968 1 1
+ 1700 13.840191 -16.808798 1.848689 1 1
+ 1800 12.705797 -15.654395 2.6658475 1 1
+ 1900 12.560112 -15.376796 1.6651246 1 1
+ 2000 12.11219 -14.943991 1.2347207 1 1
+ 2100 11.681161 -14.453803 1.1856253 1 1
+ 2200 11.380134 -14.15437 1.0983288 1 1
+ 2300 11.404137 -14.206989 1.0886428 1 1
+ 2400 11.267361 -14.00915 1.1353313 1 1
+ 2500 11.086288 -13.866685 1.5189761 1 1
+ 2600 11.241757 -14.031809 1.6088858 1 1
+ 2700 10.741715 -13.522752 1.2648051 1 1
+ 2800 10.594219 -13.461001 1.2068865 1 1
+ 2900 10.497917 -13.243311 0.90549881 1 1
+ 3000 9.8887944 -12.633322 1.2014467 1 1
+ 3100 10.046064 -12.757462 0.72911664 1 1
+ 3200 9.8202521 -12.544235 0.85793687 1 1
+ 3300 9.9932983 -12.729524 1.3692879 1 1
+ 3400 9.4389164 -12.132571 0.83559817 1 1
+ 3500 9.4456791 -12.154808 1.2415677 1 1
+ 3600 9.4291752 -12.13391 1.1892815 1 1
+ 3700 9.2656145 -11.994284 0.93597208 1 1
+ 3800 9.6833674 -12.407022 1.4696321 1 1
+ 3900 9.2075262 -11.996657 1.0201833 1 1
+ 4000 8.704708 -11.395839 1.5366945 1 1
+ 4100 8.496226 -11.160512 0.98385093 1 1
+ 4200 8.5566638 -11.241219 0.84428298 1 1
+ 4300 8.3079987 -10.963542 0.96552044 1 1
+ 4400 8.0878014 -10.695296 0.9598929 1 1
+ 4500 7.8974753 -10.510996 0.67253552 1 1
+ 4600 7.9008492 -10.511956 0.80200878 1 1
+ 4700 7.8469401 -10.46341 0.91408186 1 1
+ 4800 7.8237062 -10.478701 0.80709563 1 1
+ 4900 7.9248576 -10.569715 0.93955604 1 1
+ 5000 7.8285795 -10.450559 0.72760696 1 1
+ 5100 7.8176003 -10.433727 1.0046395 1 1
+ 5200 7.930586 -10.543139 1.1883254 1 1
+ 5300 7.4014327 -10.200353 1.2717149 1 1
+ 5400 7.3398704 -9.9377313 0.8277383 1 1
+ 5500 7.9323894 -10.544566 0.58409181 1 1
+ 5600 7.8256391 -10.452111 0.8371735 1 1
+ 5700 7.5744223 -10.225985 0.56633204 1 1
+ 5800 7.5149231 -10.128901 0.8877957 1 1
+ 5900 7.2696456 -9.868796 1.0183026 1 1
+ 6000 8.172964 -10.8046 0.82048799 1 1
+ 6100 7.569911 -10.224271 0.85335085 1 1
+ 6200 7.5498129 -10.158173 0.69550695 1 1
+ 6300 7.0906227 -9.664124 0.38267058 1 1
+ 6400 6.9720876 -9.556043 0.74772365 1 1
+ 6500 7.2708269 -9.8393843 0.87493485 1 1
+ 6600 7.0968522 -9.7557969 0.66499003 1 1
+ 6700 7.1122649 -9.7305659 1.3152794 1 1
+ 6800 6.9990684 -9.5808587 0.25569509 1 1
+ 6900 7.2436468 -9.8205382 0.94441711 1 1
+ 7000 7.0592104 -9.6306985 0.62683684 1 1
+ 7100 6.7457928 -9.3199995 0.92851433 1 1
+ 7200 7.0005278 -9.645515 0.79975493 1 1
+ 7300 7.0106928 -9.5922649 0.78131757 1 1
+ 7400 6.9425198 -9.5718261 0.3016744 1 1
+ 7500 7.4193009 -9.9953487 0.55537513 1 1
+ 7600 7.1870399 -9.7798145 0.94155142 1 1
+ 7700 6.8261504 -9.3693292 0.78601298 1 1
+ 7800 6.8794916 -9.4362689 0.9335562 1 1
+ 7900 7.0068635 -9.5490666 0.53210657 1 1
+ 8000 6.641609 -9.181226 0.80726821 1 1
+ 8100 6.9290677 -9.4788963 1.1195905 1 1
+ 8200 6.6497084 -9.197688 0.45616164 1 1
+ 8300 6.6000864 -9.207368 0.46307403 1 1
+ 8400 6.7434835 -9.3226196 0.78570419 1 1
+ 8500 7.0766248 -9.5981608 0.48778261 1 1
+ 8600 6.8206587 -9.3646115 0.76420951 1 1
+ 8700 7.2009315 -9.7629817 0.69026433 1 1
+ 8800 7.0581986 -9.636327 0.54467209 1 1
+ 8900 7.2337543 -9.8210795 0.61604427 1 1
+ 9000 6.7053026 -9.2552306 0.24196123 1 1
+ 9100 6.7919694 -9.3561383 0.34320213 1 1
+ 9200 6.8518231 -9.4142511 0.73735875 1 1
+ 9300 6.5891178 -9.1414615 0.45262773 1 1
+ 9400 6.4724853 -9.0217877 0.54837629 1 1
+ 9500 6.3569528 -8.9201793 0.19617724 1 1
+ 9600 6.3765498 -8.947548 0.85408461 1 1
+ 9700 6.5652079 -9.1101844 0.74478711 1 1
+ 9800 6.5099709 -9.0677449 0.69826809 1 1
+ 9900 6.1773299 -8.7085595 0.69981004 1 1
+ 10000 6.3999463 -8.9423632 0.42668066 1 1
+Loop time of 0.675636 on 1 procs for 10000 steps with 361 atoms
+
+Performance: 6393974.952 tau/day, 14800.868 timesteps/s
+99.7% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.29845 | 0.29845 | 0.29845 | 0.0 | 44.17
+Neigh | 0.26869 | 0.26869 | 0.26869 | 0.0 | 39.77
+Comm | 0.006007 | 0.006007 | 0.006007 | 0.0 | 0.89
+Output | 0.00076938 | 0.00076938 | 0.00076938 | 0.0 | 0.11
+Modify | 0.077204 | 0.077204 | 0.077204 | 0.0 | 11.43
+Other | | 0.02452 | | | 3.63
+
+Nlocal: 361 ave 361 max 361 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 1191 ave 1191 max 1191 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1191
+Ave neighs/atom = 3.29917
+Neighbor list builds = 3609
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/balance/log.15Feb16.balance.g++.4 b/examples/balance/log.15Feb16.balance.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..33381520cd9294c02dc0bd164ac1b67e83d563e8
--- /dev/null
+++ b/examples/balance/log.15Feb16.balance.g++.4
@@ -0,0 +1,202 @@
+LAMMPS (15 Feb 2016)
+# 2d circle of particles inside a box with LJ walls
+
+variable b index 0
+
+variable x index 50
+variable y index 20
+variable d index 20
+variable v index 5
+variable w index 2
+
+units lj
+dimension 2
+atom_style atomic
+boundary f f p
+
+lattice hex 0.85
+Lattice spacing in x,y,z = 1.16553 2.01877 1.16553
+region box block 0 $x 0 $y -0.5 0.5
+region box block 0 50 0 $y -0.5 0.5
+region box block 0 50 0 20 -0.5 0.5
+create_box 1 box
+Created orthogonal box = (0 0 -0.582767) to (58.2767 40.3753 0.582767)
+ 2 by 2 by 1 MPI processor grid
+region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
+region circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
+region circle sphere 11 6.7735026918962581988 0.0 $(v_d/2)
+region circle sphere 11 6.7735026918962581988 0.0 10
+create_atoms 1 region circle
+Created 361 atoms
+mass 1 1.0
+
+velocity all create 0.5 87287 loop geom
+velocity all set $v $w 0 sum yes
+velocity all set 5 $w 0 sum yes
+velocity all set 5 2 0 sum yes
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 10.0 1.0 2.5
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nve
+
+fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
+fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5
+fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
+fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5
+
+comm_style tiled
+fix 10 all balance 50 0.9 rcb
+
+#compute 1 all property/atom proc
+#variable p atom c_1%10
+#dump 2 all custom 50 tmp.dump id v_p x y z
+
+#dump 3 all image 50 image.*.jpg v_p type # adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
+#variable colors string # "red green blue yellow white # purple pink orange lime gray"
+#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
+
+thermo_style custom step temp epair press f_10[3] f_10
+thermo 100
+
+run 10000
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4 -> bins = 42 29 1
+Memory usage per processor = 2.48839 Mbytes
+Step Temp E_pair Press 10[3] 10
+ 0 25.701528 -29.143179 -1.2407285 3.2354571 1.0526316
+ 100 26.269576 -29.713313 7.9052334 1.2742382 1.0304709
+ 200 26.368336 -29.809962 1.6412462 1.2520776 1.0083102
+ 300 26.479082 -29.920083 2.3678653 1.2299169 1.0193906
+ 400 26.522239 -29.965537 6.6787858 1.1855956 1.0083102
+ 500 25.725591 -29.168034 0.67065285 1.2520776 1.0083102
+ 600 26.247693 -29.692706 7.9887712 1.3074792 1.0083102
+ 700 26.237368 -29.676926 1.5987214 1.2409972 1.0083102
+ 800 25.889643 -29.431589 4.6160859 1.2631579 1.0083102
+ 900 23.635295 -27.372963 9.029962 1.1634349 1.0083102
+ 1000 22.571904 -25.87422 1.8936085 1.1301939 1.0193906
+ 1100 17.493795 -21.447274 9.502619 1.0858726 1.0193906
+ 1200 17.214459 -20.726965 6.3578917 1.0304709 1.0193906
+ 1300 16.424154 -19.757386 3.9027133 1.1191136 1.0083102
+ 1400 15.04233 -18.126227 1.7539398 1.0858726 1.0193906
+ 1500 13.749022 -16.839766 1.4654778 1.0747922 1.0083102
+ 1600 13.888812 -16.855703 1.8972035 1.0858726 1.0304709
+ 1700 13.647879 -16.652436 1.5110481 1.0526316 1.0304709
+ 1800 12.61308 -15.580445 2.1861667 1.0083102 1.0083102
+ 1900 12.700272 -15.594505 1.6395684 1.0304709 1.0083102
+ 2000 12.204319 -15.16754 1.6302417 1.1080332 1.0083102
+ 2100 11.921129 -14.774621 1.4311256 1.0858726 1.0083102
+ 2200 11.959274 -14.797326 1.4920985 1.0415512 1.0083102
+ 2300 11.633606 -14.455284 1.4447243 1.1412742 1.0193906
+ 2400 12.180014 -14.719121 1.4582702 1.0304709 1.0083102
+ 2500 11.779995 -14.293633 1.2961686 1.0304709 1.0083102
+ 2600 11.86013 -14.272853 1.1970414 1.0415512 1.0193906
+ 2700 11.360658 -13.772549 1.192957 1.0526316 1.0083102
+ 2800 11.045632 -13.438591 1.2007074 1.0083102 1.0193906
+ 2900 10.689472 -13.127138 0.94544611 1.0193906 1.0193906
+ 3000 10.445298 -12.809325 1.3035047 1.0304709 1.0193906
+ 3100 10.22325 -12.599858 1.7838342 1.0304709 1.0083102
+ 3200 10.226845 -12.602391 0.91456469 1.0304709 1.0193906
+ 3300 9.8906692 -12.204654 1.4538962 1.0415512 1.0193906
+ 3400 9.0246858 -11.627057 1.1929498 1.0304709 1.0193906
+ 3500 9.4549317 -11.747347 0.92966653 1.0193906 1.0193906
+ 3600 9.2467281 -11.534358 0.94959796 1.0415512 1.0083102
+ 3700 9.1099307 -11.381318 1.2963887 1.0193906 1.0083102
+ 3800 9.2236074 -11.483205 1.3510186 1.1080332 1.0193906
+ 3900 8.6105519 -10.877844 1.3591509 1.0304709 1.0083102
+ 4000 8.588698 -10.846126 0.76473884 1.0415512 1.0083102
+ 4100 8.5960453 -10.831229 0.93758423 1.0747922 1.0193906
+ 4200 8.1049344 -10.436054 0.74947412 1.0526316 1.0083102
+ 4300 8.2606129 -10.471049 0.64465155 1.0193906 1.0193906
+ 4400 8.0777962 -10.288476 1.1145052 1.0193906 1.0083102
+ 4500 7.9202904 -10.10427 0.49016698 1.0304709 1.0083102
+ 4600 8.2366755 -10.434942 0.65930769 1.0193906 1.0083102
+ 4700 7.9313531 -10.13685 1.097861 1.0304709 1.0083102
+ 4800 7.8637296 -10.085957 0.56015483 1.0304709 1.0193906
+ 4900 7.3410322 -9.5357686 0.89340163 1.0304709 1.0193906
+ 5000 7.6647481 -9.8529515 0.8283225 1.0193906 1.0193906
+ 5100 7.4114006 -9.5917802 0.64812231 1.0083102 1.0193906
+ 5200 7.6261959 -9.8178843 0.90517452 1.0193906 1.0083102
+ 5300 7.6501619 -9.8428477 1.028077 1.0304709 1.0083102
+ 5400 7.4694373 -9.6434672 0.38259983 1.0193906 1.0083102
+ 5500 7.3111918 -9.4803007 0.47921149 1.0193906 1.0193906
+ 5600 7.2132446 -9.3694039 0.71282856 1.0193906 1.0083102
+ 5700 6.8349744 -9.0018958 0.85688618 1.0193906 1.0083102
+ 5800 7.1978042 -9.3667457 0.61717818 1.0304709 1.0193906
+ 5900 7.1441033 -9.3263118 0.32840394 1.0193906 1.0083102
+ 6000 7.0943691 -9.2621241 1.3099316 1.0083102 1.0083102
+ 6100 6.9547586 -9.1026607 0.44492974 1.0193906 1.0083102
+ 6200 7.0932682 -9.2934579 0.93444691 1.0415512 1.0083102
+ 6300 7.0536275 -9.2562193 0.57578551 1.0193906 1.0193906
+ 6400 6.8839921 -9.0513091 0.65690774 1.0193906 1.0083102
+ 6500 6.7618431 -8.9037814 0.6011838 1.0304709 1.0193906
+ 6600 6.6600729 -8.7979286 0.73495903 1.0193906 1.0193906
+ 6700 6.6544136 -8.8089155 0.41206297 1.0304709 1.0193906
+ 6800 6.7935502 -8.9405122 1.022055 1.0193906 1.0083102
+ 6900 6.6603594 -8.8085894 0.4271189 1.0526316 1.0193906
+ 7000 6.4894888 -8.6794785 0.64389173 1.0526316 1.0193906
+ 7100 6.6252776 -8.776746 1.3915989 1.0193906 1.0193906
+ 7200 6.6680717 -8.8468379 0.60275261 1.0193906 1.0193906
+ 7300 6.697874 -8.8458161 0.50887488 1.0637119 1.0083102
+ 7400 6.2112277 -8.340139 0.45211042 1.0415512 1.0193906
+ 7500 6.4923853 -8.6255862 0.79982162 1.0083102 1.0193906
+ 7600 6.2922271 -8.4027197 0.33603817 1.0304709 1.0083102
+ 7700 6.5744688 -8.7079756 0.51620003 1.0415512 1.0083102
+ 7800 6.6730316 -8.8278613 1.2334484 1.0304709 1.0083102
+ 7900 6.3831791 -8.4878853 0.49555781 1.0415512 1.0193906
+ 8000 6.690559 -8.7918607 0.88102021 1.0415512 1.0083102
+ 8100 6.5390375 -8.6612074 0.45605815 1.0304709 1.0193906
+ 8200 6.6957638 -8.8406262 0.45001955 1.0193906 1.0083102
+ 8300 6.8684401 -9.0293678 0.64215355 1.0083102 1.0083102
+ 8400 6.4416293 -8.5841829 0.53513285 1.0193906 1.0193906
+ 8500 6.6854101 -8.8269391 0.81750487 1.0637119 1.0083102
+ 8600 6.588469 -8.7315753 0.33201251 1.0083102 1.0083102
+ 8700 6.2974312 -8.4104697 0.57054382 1.0083102 1.0083102
+ 8800 6.4691853 -8.5985479 0.95554418 1.0415512 1.0083102
+ 8900 6.7437807 -8.8949865 0.69067866 1.0415512 1.0083102
+ 9000 6.5681473 -8.6984555 0.88464065 1.0193906 1.0083102
+ 9100 6.6158471 -8.7398687 0.72347757 1.0193906 1.0083102
+ 9200 6.4521137 -8.6048511 0.75093363 1.0193906 1.0193906
+ 9300 6.4179685 -8.5582051 1.0072192 1.0083102 1.0083102
+ 9400 6.580258 -8.7234535 0.56842466 1.0193906 1.0193906
+ 9500 6.4125418 -8.56348 0.36394135 1.0304709 1.0193906
+ 9600 6.6723409 -8.8402798 0.56711277 1.0304709 1.0193906
+ 9700 6.4522736 -8.594767 0.43495668 1.0193906 1.0083102
+ 9800 6.2127437 -8.3329761 0.68977311 1.0304709 1.0193906
+ 9900 6.4360513 -8.5839262 1.1702062 1.0304709 1.0193906
+ 10000 6.3393653 -8.4396274 0.46277884 1.0304709 1.0193906
+Loop time of 0.389322 on 4 procs for 10000 steps with 361 atoms
+
+Performance: 11096205.412 tau/day, 25685.661 timesteps/s
+98.7% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.061902 | 0.074659 | 0.098288 | 5.1 | 19.18
+Neigh | 0.061993 | 0.067136 | 0.078793 | 2.6 | 17.24
+Comm | 0.10335 | 0.13334 | 0.15511 | 5.6 | 34.25
+Output | 0.0017662 | 0.0020409 | 0.0027893 | 1.0 | 0.52
+Modify | 0.037374 | 0.038055 | 0.038669 | 0.2 | 9.77
+Other | | 0.07409 | | | 19.03
+
+Nlocal: 90.25 ave 92 max 88 min
+Histogram: 1 0 0 0 0 1 0 1 0 1
+Nghost: 36 ave 38 max 34 min
+Histogram: 1 0 0 0 0 2 0 0 0 1
+Neighs: 276.75 ave 448 max 153 min
+Histogram: 2 0 0 0 0 0 1 0 0 1
+
+Total # of neighbors = 1107
+Ave neighs/atom = 3.06648
+Neighbor list builds = 3472
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/body/log.15Feb16.body.g++.1 b/examples/body/log.15Feb16.body.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..150630405ad2ebf46a21917555bf2feaa1cb071d
--- /dev/null
+++ b/examples/body/log.15Feb16.body.g++.1
@@ -0,0 +1,86 @@
+LAMMPS (15 Feb 2016)
+# 2d polygon nparticle bodies
+
+units lj
+dimension 2
+atom_style body nparticle 2 6
+
+read_data data.body
+ orthogonal box = (-15.5322 -15.5322 -0.5) to (15.5322 15.5322 0.5)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 100 atoms
+ 100 bodies
+
+velocity all create 1.44 87287 loop geom
+
+pair_style body 5.0
+pair_coeff * * 1.0 1.0
+
+neighbor 0.3 bin
+
+fix 1 all nve/body
+fix 2 all enforce2d
+
+#compute 1 all body/local type 1 2 3
+#dump 1 all local 100 dump.body index c_1[1] c_1[2] c_1[3] c_1[4]
+
+thermo 500
+run 10000
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 5.3
+ ghost atom cutoff = 5.3
+ binsize = 2.65 -> bins = 12 12 1
+Memory usage per processor = 3.95249 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 -0.63799525 0 0.78760475 -0.15028724
+ 500 1.5681124 -1.6060641 0 -0.053632801 0.23819933
+ 1000 1.7596217 -1.7290976 0 0.012927885 0.12600944
+ 1500 1.5746717 -1.5427933 0 0.016131762 0.21832857
+ 2000 1.618761 -1.5563092 0 0.04626422 0.35910744
+ 2500 1.7204861 -1.6946681 0 0.0086130985 0.24678557
+ 3000 1.7361478 -1.7074239 0 0.011362383 0.28900802
+ 3500 1.6065118 -1.5857229 0 0.0047237772 0.43793842
+ 4000 1.8157912 -1.7310796 0 0.06655375 0.072835934
+ 4500 1.7986098 -1.74424 0 0.036383686 0.25507425
+ 5000 1.7182236 -1.7110892 0 -0.010047817 0.19846764
+ 5500 1.6246782 -1.5532517 0 0.055179713 0.38134959
+ 6000 1.5745671 -1.6393559 0 -0.08053447 0.52399765
+ 6500 1.7556697 -1.8091946 0 -0.071081574 0.25253905
+ 7000 1.6360783 -1.7317121 0 -0.11199463 0.19797181
+ 7500 1.7873556 -1.6976635 0 0.071818533 0.18343875
+ 8000 1.4168755 -1.5596513 0 -0.15694455 0.38638741
+ 8500 1.659868 -1.6673176 0 -0.024048309 0.17576797
+ 9000 1.7040724 -1.6906772 0 -0.0036454592 0.12467855
+ 9500 1.6305347 -1.7599864 0 -0.14575703 0.11285404
+ 10000 1.7422091 -1.8887509 0 -0.16396383 0.29065244
+Loop time of 2.35255 on 1 procs for 10000 steps with 100 atoms
+
+Performance: 1836307.682 tau/day, 4250.712 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 2.1426 | 2.1426 | 2.1426 | 0.0 | 91.08
+Neigh | 0.016685 | 0.016685 | 0.016685 | 0.0 | 0.71
+Comm | 0.026507 | 0.026507 | 0.026507 | 0.0 | 1.13
+Output | 0.00015068 | 0.00015068 | 0.00015068 | 0.0 | 0.01
+Modify | 0.16023 | 0.16023 | 0.16023 | 0.0 | 6.81
+Other | | 0.006348 | | | 0.27
+
+Nlocal: 100 ave 100 max 100 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 82 ave 82 max 82 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 428 ave 428 max 428 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 428
+Ave neighs/atom = 4.28
+Neighbor list builds = 776
+Dangerous builds = 65
+Total wall time: 0:00:02
diff --git a/examples/body/log.15Feb16.body.g++.4 b/examples/body/log.15Feb16.body.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..28c1f1ebe8595620cfe715567006be05eb96c2cb
--- /dev/null
+++ b/examples/body/log.15Feb16.body.g++.4
@@ -0,0 +1,86 @@
+LAMMPS (15 Feb 2016)
+# 2d polygon nparticle bodies
+
+units lj
+dimension 2
+atom_style body nparticle 2 6
+
+read_data data.body
+ orthogonal box = (-15.5322 -15.5322 -0.5) to (15.5322 15.5322 0.5)
+ 2 by 2 by 1 MPI processor grid
+ reading atoms ...
+ 100 atoms
+ 100 bodies
+
+velocity all create 1.44 87287 loop geom
+
+pair_style body 5.0
+pair_coeff * * 1.0 1.0
+
+neighbor 0.3 bin
+
+fix 1 all nve/body
+fix 2 all enforce2d
+
+#compute 1 all body/local type 1 2 3
+#dump 1 all local 100 dump.body index c_1[1] c_1[2] c_1[3] c_1[4]
+
+thermo 500
+run 10000
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 5.3
+ ghost atom cutoff = 5.3
+ binsize = 2.65 -> bins = 12 12 1
+Memory usage per processor = 3.93947 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 -0.63799525 0 0.78760475 -0.15028724
+ 500 1.5681124 -1.6060641 0 -0.053632801 0.23819933
+ 1000 1.7596217 -1.7290976 0 0.012927885 0.12600944
+ 1500 1.5746718 -1.5427933 0 0.016131767 0.21832856
+ 2000 1.6187614 -1.5563097 0 0.046264104 0.35910742
+ 2500 1.7210993 -1.6955088 0 0.0083794889 0.24522984
+ 3000 1.7893309 -1.752166 0 0.019271611 0.1013425
+ 3500 1.8922335 -1.7645965 0 0.10871463 0.51383163
+ 4000 1.7068531 -1.6754593 0 0.014325271 0.31615632
+ 4500 1.6924784 -1.7467381 0 -0.071184511 0.13138777
+ 5000 1.7693873 -1.7177224 0 0.033971031 0.15253256
+ 5500 1.6829564 -1.6729159 0 -0.0067890531 0.13745591
+ 6000 1.9528594 -1.8229135 0 0.11041735 0.21444568
+ 6500 1.8827185 -2.0037589 0 -0.13986752 0.044294616
+ 7000 1.4723386 -1.6538512 0 -0.19623597 0.23973507
+ 7500 1.7787216 -1.729955 0 0.030979334 0.15662931
+ 8000 1.8821398 -1.8913154 0 -0.027996988 0.26972798
+ 8500 1.7200393 -1.771927 0 -0.069088004 0.48600924
+ 9000 1.6731944 -1.702556 0 -0.046093535 0.1259234
+ 9500 1.7159449 -1.6430047 0 0.0557808 0.3620955
+ 10000 1.4879693 -1.5303732 0 -0.057283589 0.34668456
+Loop time of 0.853475 on 4 procs for 10000 steps with 100 atoms
+
+Performance: 5061659.129 tau/day, 11716.804 timesteps/s
+99.5% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.48406 | 0.55202 | 0.69789 | 11.6 | 64.68
+Neigh | 0.0044043 | 0.0046293 | 0.0049062 | 0.3 | 0.54
+Comm | 0.091245 | 0.24104 | 0.30869 | 18.0 | 28.24
+Output | 0.00033712 | 0.00036192 | 0.00039911 | 0.1 | 0.04
+Modify | 0.040754 | 0.042422 | 0.044837 | 0.7 | 4.97
+Other | | 0.013 | | | 1.52
+
+Nlocal: 25 ave 29 max 20 min
+Histogram: 1 0 0 0 0 1 1 0 0 1
+Nghost: 44 ave 45 max 43 min
+Histogram: 1 0 0 0 0 2 0 0 0 1
+Neighs: 104 ave 133 max 64 min
+Histogram: 1 0 0 1 0 0 0 0 0 2
+
+Total # of neighbors = 416
+Ave neighs/atom = 4.16
+Neighbor list builds = 773
+Dangerous builds = 31
+Total wall time: 0:00:00
diff --git a/examples/colloid/log.15Feb16.colloid.g++.1 b/examples/colloid/log.15Feb16.colloid.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..25075b2baffd312e02727fa8421af4c5d3a8aa67
--- /dev/null
+++ b/examples/colloid/log.15Feb16.colloid.g++.1
@@ -0,0 +1,146 @@
+LAMMPS (15 Feb 2016)
+# Big colloid particles and small LJ particles
+
+units lj
+atom_style sphere
+dimension 2
+
+lattice sq 0.01
+Lattice spacing in x,y,z = 10 10 10
+region box block 0 30 0 30 -0.5 0.5
+create_box 2 box
+Created orthogonal box = (0 0 -5) to (300 300 5)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 900 atoms
+
+set group all type/fraction 2 0.96 23984
+ 861 settings made for type/fraction
+
+set type 1 mass 9
+ 39 settings made for mass
+set type 2 mass 1
+ 861 settings made for mass
+
+velocity all create 1.44 87287 loop geom
+
+# multi neighbor and comm for efficiency
+
+neighbor 1 multi
+neigh_modify delay 0
+comm_modify mode multi
+
+# colloid potential
+
+pair_style colloid 12.5
+pair_coeff 1 1 1.0 1.0 5.0 5.0 12.5
+pair_coeff 1 2 5.0 1.0 5.0 0.0 7.0
+pair_coeff 2 2 10.0 1.0 0.0 0.0 2.5
+
+fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1
+fix 2 all enforce2d
+
+#dump 1 all atom 1000 dump.colloid
+
+#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5
+#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5
+
+#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5
+#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5
+
+thermo_style custom step temp epair etotal press vol
+thermo 1000
+
+timestep 0.005
+
+run 50000
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 13.5
+ ghost atom cutoff = 13.5
+ binsize = 1.75 -> bins = 172 172 6
+Memory usage per processor = 3.86192 Mbytes
+Step Temp E_pair TotEng Press Volume
+ 0 1.44 -2.2136534e-06 1.4383978 0.014383923 90000
+ 1000 1.9572355 -0.00037176804 1.954689 0.017979461 98945.011
+ 2000 2.0686234 -0.0010137498 2.0653112 0.01947028 96310.014
+ 3000 2.1785689 0.0049562211 2.1811045 0.029298361 68537.78
+ 4000 2.200053 0.00039100896 2.1979995 0.048071724 42672.579
+ 5000 2.1407629 0.016107912 2.1544922 0.076141728 28576.1
+ 6000 2.1131357 0.00050904012 2.1112969 0.095060602 21598.175
+ 7000 2.0717026 0.013639823 2.0830406 0.11782618 17864.757
+ 8000 2.0557671 0.015637275 2.0691201 0.13461012 15542.602
+ 9000 2.052181 0.011294709 2.0611955 0.15150744 13852.149
+ 10000 2.0531753 0.005995461 2.0568894 0.17005868 12487.961
+ 11000 2.0458212 0.013960278 2.0575083 0.18853479 11391.15
+ 12000 2.0405323 0.01846093 2.056726 0.20856764 10532.913
+ 13000 2.0169788 0.041436672 2.0561744 0.23593917 9743.2413
+ 14000 2.0381291 0.017030208 2.0528947 0.23907374 9093.804
+ 15000 2.0400498 0.010140701 2.0479238 0.27667462 8571.3248
+ 16000 2.0280005 0.024278921 2.0500261 0.31642444 8133.8701
+ 17000 2.0330813 0.018237365 2.0490597 0.30128788 7764.8228
+ 18000 2.0239878 0.02723825 2.0489771 0.30818234 7455.765
+ 19000 2.0213402 0.035515393 2.0546096 0.39654991 7096.9286
+ 20000 2.024466 0.032163441 2.0543801 0.37550172 6782.3498
+ 21000 2.033932 0.017240839 2.0489129 0.39674508 6520.0345
+ 22000 2.0204921 0.033630164 2.0518773 0.41617948 6306.7194
+ 23000 2.0103922 0.046109389 2.0542679 0.44503939 6108.8439
+ 24000 2.0063543 0.049507774 2.0536328 0.4949354 5923.2093
+ 25000 1.9953872 0.066107231 2.0592773 0.5424389 5746.6695
+ 26000 2.0416248 0.020853398 2.0602097 0.46642685 5593.8186
+ 27000 2.0280574 0.037040684 2.0628447 0.49730884 5433.376
+ 28000 2.0039648 0.055918617 2.0576568 0.56893257 5281.5584
+ 29000 2.0042398 0.056161548 2.0581744 0.55361133 5164.0991
+ 30000 2.031788 0.030776854 2.0603073 0.58478846 5056.2821
+ 31000 2.0220647 0.044025601 2.0638435 0.60571441 4939.9798
+ 32000 2.0115578 0.0548283 2.064151 0.62749615 4859.2601
+ 33000 1.9905768 0.071616735 2.0599817 0.64066244 4787.7818
+ 34000 2.0209823 0.052197269 2.0709341 0.68260584 4705.5825
+ 35000 1.995165 0.078611977 2.0715601 0.69333031 4599.9346
+ 36000 1.994471 0.079545726 2.0718006 0.7510532 4523.7494
+ 37000 1.9939754 0.083417982 2.0751779 0.73746747 4449.8485
+ 38000 1.9808613 0.098188975 2.0768493 0.89305039 4362.0588
+ 39000 2.0056223 0.070537588 2.0739314 0.75049166 4320.201
+ 40000 2.0490165 0.033488307 2.0802281 0.71809099 4259.8017
+ 41000 2.0170375 0.066555481 2.0813519 0.80145545 4165.276
+ 42000 2.034609 0.050123688 2.082472 0.7318767 4099.5342
+ 43000 2.027217 0.053657298 2.0786218 0.79779536 4050.1962
+ 44000 2.0107551 0.07427185 2.0827928 0.88949517 4022.2995
+ 45000 2.035579 0.054511708 2.087829 0.85058092 3982.0592
+ 46000 1.9855666 0.1079948 2.0913552 0.96268676 3937.279
+ 47000 1.9938397 0.095380271 2.0870046 0.94036115 3882.9266
+ 48000 2.0056151 0.087885527 2.0912722 0.94935203 3824.2309
+ 49000 2.0079615 0.089440768 2.0951712 0.97596247 3781.8079
+ 50000 1.9875181 0.10628651 2.0915963 1.1315334 3749.1501
+Loop time of 8.47628 on 1 procs for 50000 steps with 900 atoms
+
+Performance: 2548287.987 tau/day, 5898.815 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 4.0947 | 4.0947 | 4.0947 | 0.0 | 48.31
+Neigh | 1.3526 | 1.3526 | 1.3526 | 0.0 | 15.96
+Comm | 0.31602 | 0.31602 | 0.31602 | 0.0 | 3.73
+Output | 0.0005331 | 0.0005331 | 0.0005331 | 0.0 | 0.01
+Modify | 2.4242 | 2.4242 | 2.4242 | 0.0 | 28.60
+Other | | 0.2882 | | | 3.40
+
+Nlocal: 900 ave 900 max 900 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 548 ave 548 max 548 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 6073 ave 6073 max 6073 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 6073
+Ave neighs/atom = 6.74778
+Neighbor list builds = 3122
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:08
diff --git a/examples/colloid/log.15Feb16.colloid.g++.4 b/examples/colloid/log.15Feb16.colloid.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..2e5716b2bddd22ba5668e92ee08cfa9eab78bb85
--- /dev/null
+++ b/examples/colloid/log.15Feb16.colloid.g++.4
@@ -0,0 +1,146 @@
+LAMMPS (15 Feb 2016)
+# Big colloid particles and small LJ particles
+
+units lj
+atom_style sphere
+dimension 2
+
+lattice sq 0.01
+Lattice spacing in x,y,z = 10 10 10
+region box block 0 30 0 30 -0.5 0.5
+create_box 2 box
+Created orthogonal box = (0 0 -5) to (300 300 5)
+ 2 by 2 by 1 MPI processor grid
+create_atoms 1 box
+Created 900 atoms
+
+set group all type/fraction 2 0.96 23984
+ 861 settings made for type/fraction
+
+set type 1 mass 9
+ 39 settings made for mass
+set type 2 mass 1
+ 861 settings made for mass
+
+velocity all create 1.44 87287 loop geom
+
+# multi neighbor and comm for efficiency
+
+neighbor 1 multi
+neigh_modify delay 0
+comm_modify mode multi
+
+# colloid potential
+
+pair_style colloid 12.5
+pair_coeff 1 1 1.0 1.0 5.0 5.0 12.5
+pair_coeff 1 2 5.0 1.0 5.0 0.0 7.0
+pair_coeff 2 2 10.0 1.0 0.0 0.0 2.5
+
+fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1
+fix 2 all enforce2d
+
+#dump 1 all atom 1000 dump.colloid
+
+#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5
+#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5
+
+#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5
+#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5
+
+thermo_style custom step temp epair etotal press vol
+thermo 1000
+
+timestep 0.005
+
+run 50000
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 13.5
+ ghost atom cutoff = 13.5
+ binsize = 1.75 -> bins = 172 172 6
+Memory usage per processor = 3.76692 Mbytes
+Step Temp E_pair TotEng Press Volume
+ 0 1.44 -2.2136534e-06 1.4383978 0.014383923 90000
+ 1000 1.9572355 -0.00037176804 1.954689 0.017979461 98945.011
+ 2000 2.0686234 -0.0010137498 2.0653112 0.01947028 96310.014
+ 3000 2.1785689 0.0049562211 2.1811045 0.029298361 68537.78
+ 4000 2.200053 0.00039100896 2.1979995 0.048071724 42672.579
+ 5000 2.1407629 0.016107891 2.1544922 0.076141723 28576.1
+ 6000 2.1131348 0.00051000844 2.1112968 0.095061489 21598.174
+ 7000 2.0735911 0.011894403 2.0831815 0.11729552 17864.933
+ 8000 2.0619661 0.0060168177 2.0656919 0.1295732 15547.781
+ 9000 2.0595354 0.0024157411 2.0596627 0.14657861 13836.694
+ 10000 2.0425447 0.018278949 2.0585541 0.1740235 12474.354
+ 11000 2.0460068 0.012079252 2.0558127 0.19227728 11392.874
+ 12000 2.0372027 0.019110617 2.0540498 0.21648482 10523.896
+ 13000 2.0416804 0.015790699 2.0552026 0.24604625 9785.1314
+ 14000 2.0466943 0.0064454505 2.0508656 0.22777839 9165.8411
+ 15000 2.0436536 0.015576669 2.0569595 0.28266826 8582.5053
+ 16000 2.0335541 0.01998798 2.0512825 0.2894612 8114.5044
+ 17000 2.0109406 0.039132968 2.0478392 0.34665262 7758.9312
+ 18000 2.016964 0.038362354 2.0530852 0.37108874 7399.6774
+ 19000 2.0399584 0.012731426 2.0504232 0.32979629 7081.8066
+ 20000 2.0260154 0.027880228 2.0516445 0.36371005 6812.6037
+ 21000 2.0321966 0.023814364 2.053753 0.36376888 6556.4552
+ 22000 1.9850947 0.072749763 2.0556388 0.52542507 6293.5003
+ 23000 2.0360536 0.02395391 2.0577452 0.42540507 6061.6557
+ 24000 2.0237181 0.032711377 2.0541809 0.43998497 5883.2886
+ 25000 2.0145711 0.042376354 2.0547091 0.54706192 5715.4423
+ 26000 2.00533 0.049986982 2.0530888 0.55453953 5564.0132
+ 27000 2.0266398 0.035044901 2.0594329 0.51842026 5431.0259
+ 28000 2.0321757 0.029913711 2.0598314 0.49663872 5305.2909
+ 29000 1.9964359 0.066498777 2.0607164 0.56461185 5174.9947
+ 30000 1.982908 0.082624709 2.0633294 0.65815484 5046.1903
+ 31000 2.0141773 0.049027808 2.0609671 0.58512256 4980.1474
+ 32000 1.9938427 0.076695158 2.0683225 0.64309333 4844.0907
+ 33000 2.012869 0.054851302 2.0654838 0.63073652 4749.9868
+ 34000 1.9867827 0.083467738 2.0680429 0.7840696 4656.3038
+ 35000 2.0013706 0.067630614 2.0667775 0.72991936 4566.7052
+ 36000 2.0106349 0.063148106 2.071549 0.73927159 4495.7351
+ 37000 2.0245299 0.053399546 2.07568 0.7189467 4423.018
+ 38000 2.0133929 0.062427506 2.0735833 0.74002573 4351.9277
+ 39000 1.9874796 0.088021324 2.0732926 0.79349127 4293.1815
+ 40000 2.0240342 0.057908137 2.0796935 0.75182186 4235.9306
+ 41000 1.9973584 0.077969812 2.0731089 0.83868109 4218.8397
+ 42000 2.0034131 0.079826384 2.0810134 0.78010078 4179.2254
+ 43000 2.0438594 0.047617472 2.0892059 0.77402823 4089.0577
+ 44000 2.021871 0.066506327 2.0861308 0.82593265 3999.9932
+ 45000 2.0052391 0.07876379 2.0817748 0.84100298 3958.8163
+ 46000 2.0163501 0.073621087 2.0877308 0.8621767 3920.4982
+ 47000 2.020619 0.067706551 2.0860804 0.92651509 3885.827
+ 48000 2.0168306 0.082111421 2.0967011 0.9214563 3829.1155
+ 49000 2.0007804 0.098241181 2.0967985 0.93140657 3755.3901
+ 50000 2.0213773 0.071280328 2.0904116 0.9408025 3734.5105
+Loop time of 3.62754 on 4 procs for 50000 steps with 900 atoms
+
+Performance: 5954453.961 tau/day, 13783.458 timesteps/s
+99.4% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 1.0162 | 1.0554 | 1.0927 | 2.9 | 29.09
+Neigh | 0.33396 | 0.34264 | 0.35093 | 1.0 | 9.45
+Comm | 0.73343 | 0.79932 | 0.87689 | 5.7 | 22.03
+Output | 0.00097108 | 0.0010269 | 0.0011532 | 0.2 | 0.03
+Modify | 1.1624 | 1.1976 | 1.2436 | 3.2 | 33.01
+Other | | 0.2316 | | | 6.38
+
+Nlocal: 225 ave 234 max 208 min
+Histogram: 1 0 0 0 0 0 1 0 0 2
+Nghost: 305.25 ave 313 max 299 min
+Histogram: 1 0 0 1 1 0 0 0 0 1
+Neighs: 1501.75 ave 1627 max 1408 min
+Histogram: 1 0 1 0 1 0 0 0 0 1
+
+Total # of neighbors = 6007
+Ave neighs/atom = 6.67444
+Neighbor list builds = 3071
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:03
diff --git a/examples/comb/log.15Feb16.comb.Cu.g++.1 b/examples/comb/log.15Feb16.comb.Cu.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..8c9b051ed118454dd953f608a57c44055c8f5081
--- /dev/null
+++ b/examples/comb/log.15Feb16.comb.Cu.g++.1
@@ -0,0 +1,92 @@
+LAMMPS (15 Feb 2016)
+# Pure Cu crystal, structure created by LAMMPS, qeq off
+
+units metal
+atom_style charge
+dimension 3
+boundary p p p
+
+lattice fcc 3.615
+Lattice spacing in x,y,z = 3.615 3.615 3.615
+region box block 0 4 0 4 0 4
+create_box 1 box
+Created orthogonal box = (0 0 0) to (14.46 14.46 14.46)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 256 atoms
+mass 1 63.54
+
+pair_style comb
+pair_coeff * * ffield.comb Cu
+Reading potential file ffield.comb with DATE: 2011-02-22
+
+neighbor 0.5 bin
+neigh_modify every 1 delay 1 check yes
+
+fix 1 all nve
+timestep 0.00020
+
+thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz
+thermo_modify norm yes
+velocity all create 10.1 2398378
+thermo 1
+
+#dump 1 all custom 10 tmp.dump id type xs ys zs q vx vy vz fx fy fz
+#dump_modify 1 append yes element Cu
+
+#dump 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 2 element Cu
+
+#dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 2 element Cu
+
+run 10
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 1 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 12.5
+ ghost atom cutoff = 12.5
+ binsize = 6.25 -> bins = 3 3 3
+Memory usage per processor = 6.4805 Mbytes
+Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz
+ 0 10.1 -3.5063151 -3.5076155 -3.5076155 0 27.496055 3023.4645 14.46 14.46 14.46 0
+ 1 10.099643 -3.5063151 -3.5076155 -3.5076155 0 27.512983 3023.4645 14.46 14.46 14.46 0
+ 2 10.098572 -3.5063151 -3.5076153 -3.5076153 0 27.563765 3023.4645 14.46 14.46 14.46 0
+ 3 10.096788 -3.5063151 -3.5076151 -3.5076151 0 27.64839 3023.4645 14.46 14.46 14.46 0
+ 4 10.094291 -3.5063151 -3.5076148 -3.5076148 0 27.766843 3023.4645 14.46 14.46 14.46 0
+ 5 10.09108 -3.5063151 -3.5076144 -3.5076144 0 27.919101 3023.4645 14.46 14.46 14.46 0
+ 6 10.087158 -3.5063151 -3.5076139 -3.5076139 0 28.105138 3023.4645 14.46 14.46 14.46 0
+ 7 10.082524 -3.5063151 -3.5076133 -3.5076133 0 28.324919 3023.4645 14.46 14.46 14.46 0
+ 8 10.077179 -3.5063151 -3.5076126 -3.5076126 0 28.578403 3023.4645 14.46 14.46 14.46 0
+ 9 10.071123 -3.5063151 -3.5076118 -3.5076118 0 28.865545 3023.4645 14.46 14.46 14.46 0
+ 10 10.06436 -3.5063151 -3.5076109 -3.5076109 0 29.186292 3023.4645 14.46 14.46 14.46 0
+Loop time of 0.244377 on 1 procs for 10 steps with 256 atoms
+
+Performance: 0.707 ns/day, 33.941 hours/ns, 40.920 timesteps/s
+100.2% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.24393 | 0.24393 | 0.24393 | 0.0 | 99.82
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.00022697 | 0.00022697 | 0.00022697 | 0.0 | 0.09
+Output | 0.00011015 | 0.00011015 | 0.00011015 | 0.0 | 0.05
+Modify | 4.6968e-05 | 4.6968e-05 | 4.6968e-05 | 0.0 | 0.02
+Other | | 5.984e-05 | | | 0.02
+
+Nlocal: 256 ave 256 max 256 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 4375 ave 4375 max 4375 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs: 172544 ave 172544 max 172544 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 172544
+Ave neighs/atom = 674
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/comb/log.15Feb16.comb.Cu.g++.4 b/examples/comb/log.15Feb16.comb.Cu.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..c3847f85cf8667d70d764f92a64dc00284946b74
--- /dev/null
+++ b/examples/comb/log.15Feb16.comb.Cu.g++.4
@@ -0,0 +1,92 @@
+LAMMPS (15 Feb 2016)
+# Pure Cu crystal, structure created by LAMMPS, qeq off
+
+units metal
+atom_style charge
+dimension 3
+boundary p p p
+
+lattice fcc 3.615
+Lattice spacing in x,y,z = 3.615 3.615 3.615
+region box block 0 4 0 4 0 4
+create_box 1 box
+Created orthogonal box = (0 0 0) to (14.46 14.46 14.46)
+ 1 by 2 by 2 MPI processor grid
+create_atoms 1 box
+Created 256 atoms
+mass 1 63.54
+
+pair_style comb
+pair_coeff * * ffield.comb Cu
+Reading potential file ffield.comb with DATE: 2011-02-22
+
+neighbor 0.5 bin
+neigh_modify every 1 delay 1 check yes
+
+fix 1 all nve
+timestep 0.00020
+
+thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz
+thermo_modify norm yes
+velocity all create 10.1 2398378
+thermo 1
+
+#dump 1 all custom 10 tmp.dump id type xs ys zs q vx vy vz fx fy fz
+#dump_modify 1 append yes element Cu
+
+#dump 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 2 element Cu
+
+#dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 2 element Cu
+
+run 10
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 1 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 12.5
+ ghost atom cutoff = 12.5
+ binsize = 6.25 -> bins = 3 3 3
+Memory usage per processor = 6.35565 Mbytes
+Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz
+ 0 10.1 -3.5063151 -3.5076155 -3.5076155 0 27.496055 3023.4645 14.46 14.46 14.46 0
+ 1 10.099638 -3.5063151 -3.5076155 -3.5076155 0 27.513531 3023.4645 14.46 14.46 14.46 0
+ 2 10.098553 -3.5063151 -3.5076153 -3.5076153 0 27.565957 3023.4645 14.46 14.46 14.46 0
+ 3 10.096744 -3.5063151 -3.5076151 -3.5076151 0 27.653322 3023.4645 14.46 14.46 14.46 0
+ 4 10.094212 -3.5063151 -3.5076148 -3.5076148 0 27.775611 3023.4645 14.46 14.46 14.46 0
+ 5 10.090958 -3.5063151 -3.5076144 -3.5076144 0 27.932801 3023.4645 14.46 14.46 14.46 0
+ 6 10.086981 -3.5063151 -3.5076139 -3.5076139 0 28.124863 3023.4645 14.46 14.46 14.46 0
+ 7 10.082283 -3.5063151 -3.5076132 -3.5076132 0 28.351761 3023.4645 14.46 14.46 14.46 0
+ 8 10.076864 -3.5063151 -3.5076125 -3.5076125 0 28.613454 3023.4645 14.46 14.46 14.46 0
+ 9 10.070725 -3.5063151 -3.5076118 -3.5076118 0 28.909893 3023.4645 14.46 14.46 14.46 0
+ 10 10.063868 -3.5063151 -3.5076109 -3.5076109 0 29.241022 3023.4645 14.46 14.46 14.46 0
+Loop time of 0.0647703 on 4 procs for 10 steps with 256 atoms
+
+Performance: 2.668 ns/day, 8.996 hours/ns, 154.392 timesteps/s
+100.3% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.063009 | 0.063389 | 0.06358 | 0.1 | 97.87
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.00075269 | 0.00095391 | 0.001322 | 0.7 | 1.47
+Output | 0.00029755 | 0.00031668 | 0.00032735 | 0.1 | 0.49
+Modify | 1.5736e-05 | 1.7047e-05 | 1.8835e-05 | 0.0 | 0.03
+Other | | 9.34e-05 | | | 0.14
+
+Nlocal: 64 ave 64 max 64 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost: 2971 ave 2971 max 2971 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs: 43136 ave 43136 max 43136 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 172544
+Ave neighs/atom = 674
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/comb/log.15Feb16.comb.Cu2O.elastic.g++.1 b/examples/comb/log.15Feb16.comb.Cu2O.elastic.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..cd24d699cb15442a51d0ef65e8ff5a08e32de16e
--- /dev/null
+++ b/examples/comb/log.15Feb16.comb.Cu2O.elastic.g++.1
@@ -0,0 +1,409 @@
+LAMMPS (15 Feb 2016)
+# Cu2O crystal, qeq on, minimizes, then calculates elastic constants
+
+units metal
+atom_style charge
+dimension 3
+boundary p p p
+
+read_data data.Cu2O
+ triclinic box = (0 0 0) to (25.62 25.62 25.62) with tilt (0 0 0)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 1296 atoms
+mass 1 63.54
+group type1 type 1
+864 atoms in group type1
+compute charge1 type1 property/atom q
+compute q1 type1 reduce ave c_charge1
+mass 2 16.00
+group type2 type 2
+432 atoms in group type2
+compute charge2 type2 property/atom q
+compute q2 type2 reduce ave c_charge2
+
+velocity all create 1.0 277387
+
+pair_style comb
+pair_coeff * * ffield.comb Cu O
+Reading potential file ffield.comb with DATE: 2011-02-22
+
+neighbor 0.5 bin
+neigh_modify every 20 delay 0 check no
+
+timestep 0.00020
+
+thermo_style custom step temp etotal pe evdwl ecoul c_q1 c_q2 lx ly lz vol
+thermo_modify norm yes
+thermo 1
+fix 1 all nve
+fix 2 all qeq/comb 1 0.0001
+
+#dump 1 all cfg 1 *.cfg id type xs ys zs q f_2 vx vy vz fx fy fz
+#dump_modify 1 element Cu O
+
+run 2
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 20 steps, delay 0 steps, check no
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 12.5
+ ghost atom cutoff = 12.5
+ binsize = 6.25 -> bins = 5 5 5
+Memory usage per processor = 6.39852 Mbytes
+Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
+ 0 1 -2.9288959 -2.9290251 -0.23839068 -2.6906344 0.79666672 -1.5933334 25.62 25.62 25.62 16816.568
+ 1 1.0007128 -3.0464056 -3.0465348 0.40404394 -3.4505788 0.79666635 -1.5933327 25.62 25.62 25.62 16816.568
+ 2 1.0028587 -3.0464056 -3.0465351 0.40404056 -3.4505757 0.79666516 -1.5933303 25.62 25.62 25.62 16816.568
+Loop time of 0.690546 on 1 procs for 2 steps with 1296 atoms
+
+Performance: 0.050 ns/day, 479.546 hours/ns, 2.896 timesteps/s
+99.8% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.27005 | 0.27005 | 0.27005 | 0.0 | 39.11
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.00010324 | 0.00010324 | 0.00010324 | 0.0 | 0.01
+Output | 4.9114e-05 | 4.9114e-05 | 4.9114e-05 | 0.0 | 0.01
+Modify | 0.4203 | 0.4203 | 0.4203 | 0.0 | 60.86
+Other | | 4.387e-05 | | | 0.01
+
+Nlocal: 1296 ave 1296 max 1296 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 8243 ave 8243 max 8243 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs: 810432 ave 810432 max 810432 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 810432
+Ave neighs/atom = 625.333
+Neighbor list builds = 0
+Dangerous builds not checked
+
+unfix 1
+fix 1 all box/relax aniso 0.0 vmax 0.001
+minimize 1.0e-14 1.0e-20 1000 10000
+WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 12.5
+ ghost atom cutoff = 12.5
+ binsize = 6.25 -> bins = 5 5 5
+Memory usage per processor = 8.27781 Mbytes
+Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
+ 2 1.0028587 -3.0464056 -3.0465351 0.40403069 -3.4505658 0.79666516 -1.5933303 25.62 25.62 25.62 16816.568
+ 3 1.0028587 -3.0917245 -3.091854 0.36260063 -3.4544547 0.79642968 -1.5928594 25.59438 25.59438 25.59438 16766.169
+ 4 1.0028587 -3.1396788 -3.1398083 0.3165719 -3.4563802 0.7961845 -1.592369 25.56876 25.56876 25.56876 16715.871
+ 5 1.0028587 -3.1898661 -3.1899956 0.26823211 -3.4582277 0.79593359 -1.5918672 25.54314 25.54314 25.54314 16665.673
+ 6 1.0028587 -3.2418712 -3.2420007 0.21802935 -3.46003 0.79567997 -1.5913599 25.51752 25.51752 25.51752 16615.576
+ 7 1.0028587 -3.2952659 -3.2953954 0.16641718 -3.4618126 0.79542651 -1.590853 25.4919 25.4919 25.4919 16565.579
+ 8 1.0028587 -3.3496093 -3.3497388 0.11386046 -3.4635993 0.79517586 -1.5903517 25.46628 25.46628 25.46628 16515.683
+ 9 1.0028587 -3.4044042 -3.4045337 0.060834938 -3.4653687 0.7949272 -1.5898544 25.44066 25.44066 25.44066 16465.887
+ 10 1.0028587 -3.4591871 -3.4593166 0.0077994909 -3.4671161 0.79468287 -1.5893657 25.41504 25.41504 25.41504 16416.191
+ 11 1.0028587 -3.513522 -3.5136516 -0.044749471 -3.4689021 0.79444783 -1.5888957 25.38942 25.38942 25.38942 16366.595
+ 12 1.0028587 -3.5669229 -3.5670525 -0.096284014 -3.4707685 0.79422383 -1.5884477 25.3638 25.3638 25.3638 16317.099
+ 13 1.0028587 -3.6188974 -3.6190269 -0.14629696 -3.4727299 0.79401234 -1.5880247 25.33818 25.33818 25.33818 16267.704
+ 14 1.0028587 -3.6689504 -3.66908 -0.19428069 -3.4747993 0.79381468 -1.5876294 25.31256 25.31256 25.31256 16218.408
+ 15 1.0028587 -3.7165899 -3.7167195 -0.23973186 -3.4769876 0.79363192 -1.5872638 25.28694 25.28694 25.28694 16169.211
+ 16 1.0028587 -3.7613321 -3.7614616 -0.28215725 -3.4793044 0.79346499 -1.58693 25.26132 25.26132 25.26132 16120.114
+ 17 1.0028587 -3.8027083 -3.8028378 -0.32108032 -3.4817575 0.79331465 -1.5866293 25.2357 25.2357 25.2357 16071.117
+ 18 1.0028587 -3.8402726 -3.8404022 -0.35604832 -3.4843538 0.79318151 -1.586363 25.21008 25.21008 25.21008 16022.219
+ 19 1.0028587 -3.873609 -3.8737385 -0.38663966 -3.4870989 0.79306609 -1.5861322 25.18446 25.18446 25.18446 15973.421
+ 20 1.0028587 -3.9023636 -3.9024931 -0.41247128 -3.4900218 0.79297061 -1.5859412 25.15884 25.15884 25.15884 15924.721
+ 21 1.0028587 -3.9264347 -3.9265643 -0.43319004 -3.4933742 0.7929094 -1.5858188 25.13322 25.13322 25.13322 15876.121
+ 22 1.0028587 -3.9452897 -3.9454192 -0.44839149 -3.4970277 0.79287195 -1.5857439 25.1076 25.1076 25.1076 15827.62
+ 23 1.0028587 -3.958699 -3.9588285 -0.45793805 -3.5008905 0.79285787 -1.5857157 25.08198 25.08198 25.08198 15779.217
+ 24 1.0028587 -3.966498 -3.9666275 -0.4616679 -3.5049596 0.79285787 -1.5857157 25.05636 25.05636 25.05636 15730.913
+ 25 1.0028587 -3.9686392 -3.9687687 -0.46014255 -3.5086261 0.79286937 -1.5857387 25.034573 25.034573 25.034573 15689.914
+ 26 1.0028587 -3.9686392 -3.9687687 -0.46018211 -3.5085866 0.79286471 -1.5857294 25.034573 25.034573 25.034573 15689.914
+Loop time of 29.9485 on 1 procs for 24 steps with 1296 atoms
+
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+Minimization stats:
+ Stopping criterion = linesearch alpha is zero
+ Energy initial, next-to-last, final =
+ -3.04653512838 -3.96876869389 -3.96876869369
+ Force two-norm initial, final = 32801.4 117.257
+ Force max component initial, final = 18937.9 67.6917
+ Final line search alpha, max atom move = 9.01671e-10 6.10357e-08
+ Iterations, force evaluations = 24 53
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 7.6428 | 7.6428 | 7.6428 | 0.0 | 25.52
+Neigh | 0.072307 | 0.072307 | 0.072307 | 0.0 | 0.24
+Comm | 0.0033123 | 0.0033123 | 0.0033123 | 0.0 | 0.01
+Output | 0.00073075 | 0.00073075 | 0.00073075 | 0.0 | 0.00
+Modify | 22.217 | 22.217 | 22.217 | 0.0 | 74.18
+Other | | 0.01276 | | | 0.04
+
+Nlocal: 1296 ave 1296 max 1296 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 8243 ave 8243 max 8243 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs: 862272 ave 862272 max 862272 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 862272
+Ave neighs/atom = 665.333
+Neighbor list builds = 3
+Dangerous builds not checked
+min_modify dmax 0.2 line quadratic
+
+unfix 1
+fix 1 all nve
+run 1
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 20 steps, delay 0 steps, check no
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 12.5
+ ghost atom cutoff = 12.5
+ binsize = 6.25 -> bins = 5 5 5
+Memory usage per processor = 6.65281 Mbytes
+Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
+ 26 1.0028587 -3.9686392 -3.9687687 -0.46018211 -3.5085866 0.79286471 -1.5857294 25.034573 25.034573 25.034573 15689.914
+ 27 0.98924824 -3.9686392 -3.9687669 -0.46018036 -3.5085866 0.79286575 -1.5857315 25.034573 25.034573 25.034573 15689.914
+Loop time of 0.283693 on 1 procs for 1 steps with 1296 atoms
+
+Performance: 0.061 ns/day, 394.018 hours/ns, 3.525 timesteps/s
+100.1% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.14656 | 0.14656 | 0.14656 | 0.0 | 51.66
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 5.8889e-05 | 5.8889e-05 | 5.8889e-05 | 0.0 | 0.02
+Output | 2.8849e-05 | 2.8849e-05 | 2.8849e-05 | 0.0 | 0.01
+Modify | 0.13702 | 0.13702 | 0.13702 | 0.0 | 48.30
+Other | | 2.337e-05 | | | 0.01
+
+Nlocal: 1296 ave 1296 max 1296 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 8243 ave 8243 max 8243 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs: 862272 ave 862272 max 862272 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 862272
+Ave neighs/atom = 665.333
+Neighbor list builds = 0
+Dangerous builds not checked
+
+unfix 1
+unfix 2
+#undump 1
+
+### copy lines after this to any input script for elastic calculations ###
+## Elastic constants calculations: strain box, measure box stress
+## strain x, measure s_x, s_y, s_z, s_yz:
+## calculates C11, C12, C13 and C14
+
+fix 2 all deform 1 x scale 1.0001 remap x
+compute perfx all stress/atom NULL pair
+compute fx all reduce sum c_perfx[1] c_perfx[2] c_perfx[3] c_perfx[4] c_perfx[5] c_perfx[6]
+thermo_style custom step lx ly lz xy xz yz c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6]
+WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:680)
+run 10
+Memory usage per processor = 7.02781 Mbytes
+Step Lx Ly Lz Xy Xz Yz fx[1] fx[2] fx[3] fx[4] fx[5] fx[6]
+ 27 25.034573 25.034573 25.034573 0 0 0 -1.0598299e+08 -1.0598276e+08 -1.0598269e+08 -126504.69 -147668.13 -107881.81
+ 28 25.034823 25.034573 25.034573 0 0 0 -1.0598299e+08 -1.0598276e+08 -1.0598269e+08 -126504.69 -147668.13 -107881.81
+ 29 25.035074 25.034573 25.034573 0 0 0 -87059995 -96445744 -96445673 -126501.16 -147663.09 -107878.31
+ 30 25.035324 25.034573 25.034573 0 0 0 -68136799 -86908913 -86908841 -126497.63 -147658.05 -107874.8
+ 31 25.035574 25.034573 25.034573 0 0 0 -49213405 -77372273 -77372200 -126494.09 -147653.02 -107871.3
+ 32 25.035825 25.034573 25.034573 0 0 0 -30289818 -67835826 -67835753 -126490.56 -147647.98 -107867.79
+ 33 25.036075 25.034573 25.034573 0 0 0 -11366046 -58299575 -58299501 -126487.03 -147642.95 -107864.28
+ 34 25.036325 25.034573 25.034573 0 0 0 7557907.5 -48763524 -48763449 -126483.5 -147637.91 -107860.77
+ 35 25.036576 25.034573 25.034573 0 0 0 26482035 -39227675 -39227600 -126479.96 -147632.87 -107857.27
+ 36 25.036826 25.034573 25.034573 0 0 0 45406330 -29692031 -29691956 -126476.43 -147627.84 -107853.76
+ 37 25.037076 25.034573 25.034573 0 0 0 64330788 -20156596 -20156520 -126472.9 -147622.8 -107850.25
+Loop time of 1.61281 on 1 procs for 10 steps with 1296 atoms
+
+Performance: 0.107 ns/day, 224.001 hours/ns, 6.200 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 1.6096 | 1.6096 | 1.6096 | 0.0 | 99.80
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.00054646 | 0.00054646 | 0.00054646 | 0.0 | 0.03
+Output | 0.0023828 | 0.0023828 | 0.0023828 | 0.0 | 0.15
+Modify | 0.00019932 | 0.00019932 | 0.00019932 | 0.0 | 0.01
+Other | | 0.0001204 | | | 0.01
+
+Nlocal: 1296 ave 1296 max 1296 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 8243 ave 8243 max 8243 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs: 862272 ave 862272 max 862272 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 862272
+Ave neighs/atom = 665.333
+Neighbor list builds = 0
+Dangerous builds not checked
+
+## strain z, measure s_z: calculates C33
+
+fix 2 all deform 1 z scale 1.0001 remap x
+compute perfz all stress/atom NULL pair
+compute fz all reduce sum c_perfz[1] c_perfz[2] c_perfz[3] c_perfz[4] c_perfz[5] c_perfz[6]
+thermo_style custom step lx ly lz xy xz yz c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6]
+run 10
+Memory usage per processor = 7.77781 Mbytes
+Step Lx Ly Lz Xy Xz Yz fz[1] fz[2] fz[3] fz[4] fz[5] fz[6]
+ 37 25.037076 25.034573 25.034573 0 0 0 83255401 -10621373 -10621296 -126469.36 -147617.76 -107846.74
+ 38 25.037076 25.034573 25.034823 0 0 0 83255401 -10621373 -10621296 -126469.36 -147617.76 -107846.74
+ 39 25.037076 25.034573 25.035074 0 0 0 92791365 -1081679.6 8300643.1 -126464.81 -147612.37 -107844.24
+ 40 25.037076 25.034573 25.035324 0 0 0 1.0232711e+08 8457831.4 27222756 -126460.25 -147606.97 -107841.74
+ 41 25.037076 25.034573 25.035574 0 0 0 1.1186264e+08 17997157 46145038 -126455.7 -147601.57 -107839.24
+ 42 25.037076 25.034573 25.035825 0 0 0 1.2139794e+08 27536295 65067481 -126451.14 -147596.17 -107836.73
+ 43 25.037076 25.034573 25.036075 0 0 0 1.3093301e+08 37075242 83990081 -126446.58 -147590.78 -107834.23
+ 44 25.037076 25.034573 25.036325 0 0 0 1.4046786e+08 46613995 1.0291283e+08 -126442.03 -147585.38 -107831.73
+ 45 25.037076 25.034573 25.036576 0 0 0 1.5000248e+08 56152550 1.2183572e+08 -126437.47 -147579.98 -107829.23
+ 46 25.037076 25.034573 25.036826 0 0 0 1.5953685e+08 65690906 1.4075876e+08 -126432.91 -147574.58 -107826.72
+ 47 25.037076 25.034573 25.037076 0 0 0 1.69071e+08 75229058 1.5968192e+08 -126428.35 -147569.18 -107824.22
+Loop time of 1.56349 on 1 procs for 10 steps with 1296 atoms
+
+Performance: 0.111 ns/day, 217.151 hours/ns, 6.396 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 1.5603 | 1.5603 | 1.5603 | 0.0 | 99.79
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.0005424 | 0.0005424 | 0.0005424 | 0.0 | 0.03
+Output | 0.0023627 | 0.0023627 | 0.0023627 | 0.0 | 0.15
+Modify | 0.00018978 | 0.00018978 | 0.00018978 | 0.0 | 0.01
+Other | | 0.0001137 | | | 0.01
+
+Nlocal: 1296 ave 1296 max 1296 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 8243 ave 8243 max 8243 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs: 862272 ave 862272 max 862272 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 862272
+Ave neighs/atom = 665.333
+Neighbor list builds = 0
+Dangerous builds not checked
+
+## strain yz, measure s_yz: calculates C44
+
+fix 2 all deform 1 yz erate 0.0001 remap x
+compute perfyz all stress/atom NULL pair
+compute fyz all reduce sum c_perfyz[1] c_perfyz[2] c_perfyz[3] c_perfyz[4] c_perfyz[5] c_perfyz[6]
+thermo_style custom step lx ly lz xy xz yz c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6]
+run 10
+Memory usage per processor = 8.54308 Mbytes
+Step Lx Ly Lz Xy Xz Yz fyz[1] fyz[2] fyz[3] fyz[4] fyz[5] fyz[6]
+ 47 25.037076 25.034573 25.037076 0 0 0 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.79 -107821.72
+ 48 25.037076 25.034573 25.037076 0 0 5.0074153e-07 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.79 -107821.72
+ 49 25.037076 25.034573 25.037076 0 0 1.0014831e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.78 -88830.837
+ 50 25.037076 25.034573 25.037076 0 0 1.5022246e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.78 -69839.957
+ 51 25.037076 25.034573 25.037076 0 0 2.0029661e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.77 -50849.077
+ 52 25.037076 25.034573 25.037076 0 0 2.5037076e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.76 -31858.197
+ 53 25.037076 25.034573 25.037076 0 0 3.0044492e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.76 -12867.317
+ 54 25.037076 25.034573 25.037076 0 0 3.5051907e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.75 6123.563
+ 55 25.037076 25.034573 25.037076 0 0 4.0059322e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.75 25114.443
+ 56 25.037076 25.034573 25.037076 0 0 4.5066738e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.74 44105.323
+ 57 25.037076 25.034573 25.037076 0 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.74 63096.203
+Loop time of 1.55801 on 1 procs for 10 steps with 1296 atoms
+
+Performance: 0.111 ns/day, 216.390 hours/ns, 6.418 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 1.555 | 1.555 | 1.555 | 0.0 | 99.80
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.00052738 | 0.00052738 | 0.00052738 | 0.0 | 0.03
+Output | 0.0022299 | 0.0022299 | 0.0022299 | 0.0 | 0.14
+Modify | 0.00018501 | 0.00018501 | 0.00018501 | 0.0 | 0.01
+Other | | 0.0001023 | | | 0.01
+
+Nlocal: 1296 ave 1296 max 1296 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 8243 ave 8243 max 8243 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs: 862272 ave 862272 max 862272 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 862272
+Ave neighs/atom = 665.333
+Neighbor list builds = 0
+Dangerous builds not checked
+
+## strain xy, measure s_xy: calculates C66
+
+fix 2 all deform 1 xy erate 0.0001 remap x
+compute perfxy all stress/atom NULL pair
+compute fxy all reduce sum c_perfxy[1] c_perfxy[2] c_perfxy[3] c_perfxy[4] c_perfxy[5] c_perfxy[6]
+thermo_style custom step lx ly lz xy xz yz c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6]
+run 10
+Memory usage per processor = 9.29308 Mbytes
+Step Lx Ly Lz Xy Xz Yz fxy[1] fxy[2] fxy[3] fxy[4] fxy[5] fxy[6]
+ 57 25.037076 25.034573 25.037076 0 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.73 82087.083
+ 58 25.037076 25.034573 25.037076 5.0069146e-07 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.73 82087.083
+ 59 25.037076 25.034573 25.037076 1.0013829e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -107434.78 -147563.72 82087.087
+ 60 25.037076 25.034573 25.037076 1.5020744e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -88445.781 -147563.72 82087.09
+ 61 25.037076 25.034573 25.037076 2.0027658e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -69456.779 -147563.71 82087.094
+ 62 25.037076 25.034573 25.037076 2.5034573e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -50467.776 -147563.71 82087.098
+ 63 25.037076 25.034573 25.037076 3.0041488e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -31478.773 -147563.7 82087.101
+ 64 25.037076 25.034573 25.037076 3.5048402e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -12489.77 -147563.7 82087.105
+ 65 25.037076 25.034573 25.037076 4.0055317e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 6499.2334 -147563.69 82087.109
+ 66 25.037076 25.034573 25.037076 4.5062231e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 25488.236 -147563.69 82087.113
+ 67 25.037076 25.034573 25.037076 5.0069146e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 44477.239 -147563.68 82087.116
+Loop time of 1.56044 on 1 procs for 10 steps with 1296 atoms
+
+Performance: 0.111 ns/day, 216.728 hours/ns, 6.408 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 1.5574 | 1.5574 | 1.5574 | 0.0 | 99.80
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.00051975 | 0.00051975 | 0.00051975 | 0.0 | 0.03
+Output | 0.0022559 | 0.0022559 | 0.0022559 | 0.0 | 0.14
+Modify | 0.00019503 | 0.00019503 | 0.00019503 | 0.0 | 0.01
+Other | | 0.0001116 | | | 0.01
+
+Nlocal: 1296 ave 1296 max 1296 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 8243 ave 8243 max 8243 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs: 862272 ave 862272 max 862272 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 862272
+Ave neighs/atom = 665.333
+Neighbor list builds = 0
+Dangerous builds not checked
+Total wall time: 0:00:44
diff --git a/examples/comb/log.15Feb16.comb.Cu2O.elastic.g++.4 b/examples/comb/log.15Feb16.comb.Cu2O.elastic.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..01abbb40d61432b7f4f369259c7751d1c19c0825
--- /dev/null
+++ b/examples/comb/log.15Feb16.comb.Cu2O.elastic.g++.4
@@ -0,0 +1,409 @@
+LAMMPS (15 Feb 2016)
+# Cu2O crystal, qeq on, minimizes, then calculates elastic constants
+
+units metal
+atom_style charge
+dimension 3
+boundary p p p
+
+read_data data.Cu2O
+ triclinic box = (0 0 0) to (25.62 25.62 25.62) with tilt (0 0 0)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 1296 atoms
+mass 1 63.54
+group type1 type 1
+864 atoms in group type1
+compute charge1 type1 property/atom q
+compute q1 type1 reduce ave c_charge1
+mass 2 16.00
+group type2 type 2
+432 atoms in group type2
+compute charge2 type2 property/atom q
+compute q2 type2 reduce ave c_charge2
+
+velocity all create 1.0 277387
+
+pair_style comb
+pair_coeff * * ffield.comb Cu O
+Reading potential file ffield.comb with DATE: 2011-02-22
+
+neighbor 0.5 bin
+neigh_modify every 20 delay 0 check no
+
+timestep 0.00020
+
+thermo_style custom step temp etotal pe evdwl ecoul c_q1 c_q2 lx ly lz vol
+thermo_modify norm yes
+thermo 1
+fix 1 all nve
+fix 2 all qeq/comb 1 0.0001
+
+#dump 1 all cfg 1 *.cfg id type xs ys zs q f_2 vx vy vz fx fy fz
+#dump_modify 1 element Cu O
+
+run 2
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 20 steps, delay 0 steps, check no
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 12.5
+ ghost atom cutoff = 12.5
+ binsize = 6.25 -> bins = 5 5 5
+Memory usage per processor = 6.28094 Mbytes
+Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
+ 0 1 -2.9288959 -2.9290251 -0.23839068 -2.6906344 0.79666672 -1.5933334 25.62 25.62 25.62 16816.568
+ 1 1.0007128 -3.0464056 -3.0465348 0.40404394 -3.4505788 0.79666635 -1.5933327 25.62 25.62 25.62 16816.568
+ 2 1.0028587 -3.0464056 -3.0465351 0.40404056 -3.4505757 0.79666516 -1.5933303 25.62 25.62 25.62 16816.568
+Loop time of 0.174112 on 4 procs for 2 steps with 1296 atoms
+
+Performance: 0.198 ns/day, 120.911 hours/ns, 11.487 timesteps/s
+99.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.067018 | 0.067376 | 0.067552 | 0.1 | 38.70
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.00030375 | 0.00049108 | 0.00085974 | 1.0 | 0.28
+Output | 7.8678e-05 | 8.1301e-05 | 8.7023e-05 | 0.0 | 0.05
+Modify | 0.10611 | 0.10612 | 0.10613 | 0.0 | 60.95
+Other | | 4.166e-05 | | | 0.02
+
+Nlocal: 324 ave 324 max 324 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost: 4943 ave 4943 max 4943 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs: 202608 ave 202608 max 202608 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 810432
+Ave neighs/atom = 625.333
+Neighbor list builds = 0
+Dangerous builds not checked
+
+unfix 1
+fix 1 all box/relax aniso 0.0 vmax 0.001
+minimize 1.0e-14 1.0e-20 1000 10000
+WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 12.5
+ ghost atom cutoff = 12.5
+ binsize = 6.25 -> bins = 5 5 5
+Memory usage per processor = 8.15594 Mbytes
+Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
+ 2 1.0028587 -3.0464056 -3.0465351 0.40403069 -3.4505658 0.79666516 -1.5933303 25.62 25.62 25.62 16816.568
+ 3 1.0028587 -3.0917245 -3.091854 0.36260063 -3.4544547 0.79642968 -1.5928594 25.59438 25.59438 25.59438 16766.169
+ 4 1.0028587 -3.1396788 -3.1398083 0.3165719 -3.4563802 0.7961845 -1.592369 25.56876 25.56876 25.56876 16715.871
+ 5 1.0028587 -3.1898661 -3.1899956 0.26823211 -3.4582277 0.79593359 -1.5918672 25.54314 25.54314 25.54314 16665.673
+ 6 1.0028587 -3.2418712 -3.2420007 0.21802935 -3.46003 0.79567997 -1.5913599 25.51752 25.51752 25.51752 16615.576
+ 7 1.0028587 -3.2952659 -3.2953954 0.16641718 -3.4618126 0.79542651 -1.590853 25.4919 25.4919 25.4919 16565.579
+ 8 1.0028587 -3.3496093 -3.3497388 0.11386046 -3.4635993 0.79517586 -1.5903517 25.46628 25.46628 25.46628 16515.683
+ 9 1.0028587 -3.4044042 -3.4045337 0.060834938 -3.4653687 0.7949272 -1.5898544 25.44066 25.44066 25.44066 16465.887
+ 10 1.0028587 -3.4591871 -3.4593166 0.0077994909 -3.4671161 0.79468287 -1.5893657 25.41504 25.41504 25.41504 16416.191
+ 11 1.0028587 -3.513522 -3.5136516 -0.044749471 -3.4689021 0.79444783 -1.5888957 25.38942 25.38942 25.38942 16366.595
+ 12 1.0028587 -3.5669229 -3.5670525 -0.096284014 -3.4707685 0.79422383 -1.5884477 25.3638 25.3638 25.3638 16317.099
+ 13 1.0028587 -3.6188974 -3.6190269 -0.14629696 -3.4727299 0.79401234 -1.5880247 25.33818 25.33818 25.33818 16267.704
+ 14 1.0028587 -3.6689504 -3.66908 -0.19428069 -3.4747993 0.79381468 -1.5876294 25.31256 25.31256 25.31256 16218.408
+ 15 1.0028587 -3.7165899 -3.7167195 -0.23973186 -3.4769876 0.79363192 -1.5872638 25.28694 25.28694 25.28694 16169.211
+ 16 1.0028587 -3.7613321 -3.7614616 -0.28215725 -3.4793044 0.79346499 -1.58693 25.26132 25.26132 25.26132 16120.114
+ 17 1.0028587 -3.8027083 -3.8028378 -0.32108032 -3.4817575 0.79331465 -1.5866293 25.2357 25.2357 25.2357 16071.117
+ 18 1.0028587 -3.8402726 -3.8404022 -0.35604832 -3.4843538 0.79318151 -1.586363 25.21008 25.21008 25.21008 16022.219
+ 19 1.0028587 -3.873609 -3.8737385 -0.38663966 -3.4870989 0.79306609 -1.5861322 25.18446 25.18446 25.18446 15973.421
+ 20 1.0028587 -3.9023636 -3.9024931 -0.41247128 -3.4900218 0.79297061 -1.5859412 25.15884 25.15884 25.15884 15924.721
+ 21 1.0028587 -3.9264347 -3.9265643 -0.43319004 -3.4933742 0.7929094 -1.5858188 25.13322 25.13322 25.13322 15876.121
+ 22 1.0028587 -3.9452897 -3.9454192 -0.44839149 -3.4970277 0.79287195 -1.5857439 25.1076 25.1076 25.1076 15827.62
+ 23 1.0028587 -3.958699 -3.9588285 -0.45793805 -3.5008905 0.79285787 -1.5857157 25.08198 25.08198 25.08198 15779.217
+ 24 1.0028587 -3.966498 -3.9666275 -0.4616679 -3.5049596 0.79285787 -1.5857157 25.05636 25.05636 25.05636 15730.913
+ 25 1.0028587 -3.9686392 -3.9687687 -0.46014255 -3.5086261 0.79286937 -1.5857387 25.034573 25.034573 25.034573 15689.914
+ 26 1.0028587 -3.9686392 -3.9687687 -0.46018211 -3.5085866 0.79286471 -1.5857294 25.034573 25.034573 25.034573 15689.914
+Loop time of 7.73864 on 4 procs for 24 steps with 1296 atoms
+
+99.9% CPU use with 4 MPI tasks x no OpenMP threads
+
+Minimization stats:
+ Stopping criterion = linesearch alpha is zero
+ Energy initial, next-to-last, final =
+ -3.04653512838 -3.96876869389 -3.96876869369
+ Force two-norm initial, final = 32801.4 117.257
+ Force max component initial, final = 18937.9 67.6917
+ Final line search alpha, max atom move = 9.01671e-10 6.10357e-08
+ Iterations, force evaluations = 24 53
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 1.8982 | 1.9386 | 1.9643 | 1.8 | 25.05
+Neigh | 0.017612 | 0.017903 | 0.018068 | 0.1 | 0.23
+Comm | 0.011921 | 0.037696 | 0.078263 | 13.0 | 0.49
+Output | 0.00091124 | 0.00094914 | 0.0010424 | 0.2 | 0.01
+Modify | 5.736 | 5.7361 | 5.7362 | 0.0 | 74.12
+Other | | 0.007425 | | | 0.10
+
+Nlocal: 324 ave 328 max 318 min
+Histogram: 1 0 0 0 1 0 0 0 0 2
+Nghost: 4943 ave 4949 max 4939 min
+Histogram: 2 0 0 0 0 0 1 0 0 1
+Neighs: 0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs: 215568 ave 218192 max 211632 min
+Histogram: 1 0 0 0 1 0 0 0 0 2
+
+Total # of neighbors = 862272
+Ave neighs/atom = 665.333
+Neighbor list builds = 3
+Dangerous builds not checked
+min_modify dmax 0.2 line quadratic
+
+unfix 1
+fix 1 all nve
+run 1
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 20 steps, delay 0 steps, check no
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 12.5
+ ghost atom cutoff = 12.5
+ binsize = 6.25 -> bins = 5 5 5
+Memory usage per processor = 6.53094 Mbytes
+Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
+ 26 1.0028587 -3.9686392 -3.9687687 -0.46018211 -3.5085866 0.79286471 -1.5857294 25.034573 25.034573 25.034573 15689.914
+ 27 0.98924824 -3.9686392 -3.9687669 -0.46018036 -3.5085866 0.79286575 -1.5857315 25.034573 25.034573 25.034573 15689.914
+Loop time of 0.0716895 on 4 procs for 1 steps with 1296 atoms
+
+Performance: 0.241 ns/day, 99.569 hours/ns, 13.949 timesteps/s
+100.1% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.035934 | 0.036807 | 0.03732 | 0.3 | 51.34
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.00013494 | 0.00064868 | 0.0015209 | 2.1 | 0.90
+Output | 3.6955e-05 | 3.8445e-05 | 4.1962e-05 | 0.0 | 0.05
+Modify | 0.034179 | 0.034181 | 0.034182 | 0.0 | 47.68
+Other | | 1.472e-05 | | | 0.02
+
+Nlocal: 324 ave 328 max 318 min
+Histogram: 1 0 0 0 1 0 0 0 0 2
+Nghost: 4943 ave 4949 max 4939 min
+Histogram: 2 0 0 0 0 0 1 0 0 1
+Neighs: 0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs: 215568 ave 218192 max 211632 min
+Histogram: 1 0 0 0 1 0 0 0 0 2
+
+Total # of neighbors = 862272
+Ave neighs/atom = 665.333
+Neighbor list builds = 0
+Dangerous builds not checked
+
+unfix 1
+unfix 2
+#undump 1
+
+### copy lines after this to any input script for elastic calculations ###
+## Elastic constants calculations: strain box, measure box stress
+## strain x, measure s_x, s_y, s_z, s_yz:
+## calculates C11, C12, C13 and C14
+
+fix 2 all deform 1 x scale 1.0001 remap x
+compute perfx all stress/atom NULL pair
+compute fx all reduce sum c_perfx[1] c_perfx[2] c_perfx[3] c_perfx[4] c_perfx[5] c_perfx[6]
+thermo_style custom step lx ly lz xy xz yz c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6]
+WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:680)
+run 10
+Memory usage per processor = 6.90594 Mbytes
+Step Lx Ly Lz Xy Xz Yz fx[1] fx[2] fx[3] fx[4] fx[5] fx[6]
+ 27 25.034573 25.034573 25.034573 0 0 0 -1.0598299e+08 -1.0598276e+08 -1.0598269e+08 -126504.69 -147668.13 -107881.81
+ 28 25.034823 25.034573 25.034573 0 0 0 -1.0598299e+08 -1.0598276e+08 -1.0598269e+08 -126504.69 -147668.13 -107881.81
+ 29 25.035074 25.034573 25.034573 0 0 0 -87059995 -96445744 -96445673 -126501.16 -147663.09 -107878.31
+ 30 25.035324 25.034573 25.034573 0 0 0 -68136799 -86908913 -86908841 -126497.63 -147658.05 -107874.8
+ 31 25.035574 25.034573 25.034573 0 0 0 -49213405 -77372273 -77372200 -126494.09 -147653.02 -107871.3
+ 32 25.035825 25.034573 25.034573 0 0 0 -30289818 -67835826 -67835753 -126490.56 -147647.98 -107867.79
+ 33 25.036075 25.034573 25.034573 0 0 0 -11366046 -58299575 -58299501 -126487.03 -147642.95 -107864.28
+ 34 25.036325 25.034573 25.034573 0 0 0 7557907.5 -48763524 -48763449 -126483.5 -147637.91 -107860.77
+ 35 25.036576 25.034573 25.034573 0 0 0 26482035 -39227675 -39227600 -126479.96 -147632.87 -107857.27
+ 36 25.036826 25.034573 25.034573 0 0 0 45406330 -29692031 -29691956 -126476.43 -147627.84 -107853.76
+ 37 25.037076 25.034573 25.034573 0 0 0 64330788 -20156596 -20156520 -126472.9 -147622.8 -107850.25
+Loop time of 0.40881 on 4 procs for 10 steps with 1296 atoms
+
+Performance: 0.423 ns/day, 56.779 hours/ns, 24.461 timesteps/s
+99.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.38885 | 0.39776 | 0.40386 | 1.0 | 97.30
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.0020289 | 0.0081917 | 0.017143 | 7.1 | 2.00
+Output | 0.0026636 | 0.0027153 | 0.0027769 | 0.1 | 0.66
+Modify | 5.6982e-05 | 5.9664e-05 | 6.628e-05 | 0.0 | 0.01
+Other | | 8.208e-05 | | | 0.02
+
+Nlocal: 324 ave 328 max 318 min
+Histogram: 1 0 0 0 1 0 0 0 0 2
+Nghost: 4943 ave 4949 max 4939 min
+Histogram: 2 0 0 0 0 0 1 0 0 1
+Neighs: 0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs: 215568 ave 218192 max 211632 min
+Histogram: 1 0 0 0 1 0 0 0 0 2
+
+Total # of neighbors = 862272
+Ave neighs/atom = 665.333
+Neighbor list builds = 0
+Dangerous builds not checked
+
+## strain z, measure s_z: calculates C33
+
+fix 2 all deform 1 z scale 1.0001 remap x
+compute perfz all stress/atom NULL pair
+compute fz all reduce sum c_perfz[1] c_perfz[2] c_perfz[3] c_perfz[4] c_perfz[5] c_perfz[6]
+thermo_style custom step lx ly lz xy xz yz c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6]
+run 10
+Memory usage per processor = 7.65594 Mbytes
+Step Lx Ly Lz Xy Xz Yz fz[1] fz[2] fz[3] fz[4] fz[5] fz[6]
+ 37 25.037076 25.034573 25.034573 0 0 0 83255401 -10621373 -10621296 -126469.36 -147617.76 -107846.74
+ 38 25.037076 25.034573 25.034823 0 0 0 83255401 -10621373 -10621296 -126469.36 -147617.76 -107846.74
+ 39 25.037076 25.034573 25.035074 0 0 0 92791365 -1081679.6 8300643.1 -126464.81 -147612.37 -107844.24
+ 40 25.037076 25.034573 25.035324 0 0 0 1.0232711e+08 8457831.4 27222756 -126460.25 -147606.97 -107841.74
+ 41 25.037076 25.034573 25.035574 0 0 0 1.1186264e+08 17997157 46145038 -126455.7 -147601.57 -107839.24
+ 42 25.037076 25.034573 25.035825 0 0 0 1.2139794e+08 27536295 65067481 -126451.14 -147596.17 -107836.73
+ 43 25.037076 25.034573 25.036075 0 0 0 1.3093301e+08 37075242 83990081 -126446.58 -147590.78 -107834.23
+ 44 25.037076 25.034573 25.036325 0 0 0 1.4046786e+08 46613995 1.0291283e+08 -126442.03 -147585.38 -107831.73
+ 45 25.037076 25.034573 25.036576 0 0 0 1.5000248e+08 56152550 1.2183572e+08 -126437.47 -147579.98 -107829.23
+ 46 25.037076 25.034573 25.036826 0 0 0 1.5953685e+08 65690906 1.4075876e+08 -126432.91 -147574.58 -107826.72
+ 47 25.037076 25.034573 25.037076 0 0 0 1.69071e+08 75229058 1.5968192e+08 -126428.35 -147569.18 -107824.22
+Loop time of 0.407868 on 4 procs for 10 steps with 1296 atoms
+
+Performance: 0.424 ns/day, 56.648 hours/ns, 24.518 timesteps/s
+99.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.38874 | 0.39706 | 0.40377 | 0.9 | 97.35
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.001327 | 0.0080245 | 0.016345 | 6.6 | 1.97
+Output | 0.0026383 | 0.0026469 | 0.0026655 | 0.0 | 0.65
+Modify | 5.2929e-05 | 5.6744e-05 | 5.9128e-05 | 0.0 | 0.01
+Other | | 7.844e-05 | | | 0.02
+
+Nlocal: 324 ave 328 max 318 min
+Histogram: 1 0 0 0 1 0 0 0 0 2
+Nghost: 4943 ave 4949 max 4939 min
+Histogram: 2 0 0 0 0 0 1 0 0 1
+Neighs: 0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs: 215568 ave 218192 max 211632 min
+Histogram: 1 0 0 0 1 0 0 0 0 2
+
+Total # of neighbors = 862272
+Ave neighs/atom = 665.333
+Neighbor list builds = 0
+Dangerous builds not checked
+
+## strain yz, measure s_yz: calculates C44
+
+fix 2 all deform 1 yz erate 0.0001 remap x
+compute perfyz all stress/atom NULL pair
+compute fyz all reduce sum c_perfyz[1] c_perfyz[2] c_perfyz[3] c_perfyz[4] c_perfyz[5] c_perfyz[6]
+thermo_style custom step lx ly lz xy xz yz c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6]
+run 10
+Memory usage per processor = 8.42123 Mbytes
+Step Lx Ly Lz Xy Xz Yz fyz[1] fyz[2] fyz[3] fyz[4] fyz[5] fyz[6]
+ 47 25.037076 25.034573 25.037076 0 0 0 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.79 -107821.72
+ 48 25.037076 25.034573 25.037076 0 0 5.0074153e-07 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.79 -107821.72
+ 49 25.037076 25.034573 25.037076 0 0 1.0014831e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.78 -88830.837
+ 50 25.037076 25.034573 25.037076 0 0 1.5022246e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.78 -69839.957
+ 51 25.037076 25.034573 25.037076 0 0 2.0029661e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.77 -50849.077
+ 52 25.037076 25.034573 25.037076 0 0 2.5037076e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.76 -31858.197
+ 53 25.037076 25.034573 25.037076 0 0 3.0044492e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.76 -12867.317
+ 54 25.037076 25.034573 25.037076 0 0 3.5051907e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.75 6123.563
+ 55 25.037076 25.034573 25.037076 0 0 4.0059322e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.75 25114.443
+ 56 25.037076 25.034573 25.037076 0 0 4.5066738e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.74 44105.323
+ 57 25.037076 25.034573 25.037076 0 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.74 63096.203
+Loop time of 0.408682 on 4 procs for 10 steps with 1296 atoms
+
+Performance: 0.423 ns/day, 56.761 hours/ns, 24.469 timesteps/s
+99.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.38891 | 0.39738 | 0.40388 | 1.0 | 97.23
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.0019937 | 0.0084969 | 0.016969 | 6.6 | 2.08
+Output | 0.0026531 | 0.0026709 | 0.0026915 | 0.0 | 0.65
+Modify | 5.1975e-05 | 5.6446e-05 | 5.9366e-05 | 0.0 | 0.01
+Other | | 7.963e-05 | | | 0.02
+
+Nlocal: 324 ave 328 max 318 min
+Histogram: 1 0 0 0 1 0 0 0 0 2
+Nghost: 4943 ave 4949 max 4939 min
+Histogram: 2 0 0 0 0 0 1 0 0 1
+Neighs: 0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs: 215568 ave 218192 max 211632 min
+Histogram: 1 0 0 0 1 0 0 0 0 2
+
+Total # of neighbors = 862272
+Ave neighs/atom = 665.333
+Neighbor list builds = 0
+Dangerous builds not checked
+
+## strain xy, measure s_xy: calculates C66
+
+fix 2 all deform 1 xy erate 0.0001 remap x
+compute perfxy all stress/atom NULL pair
+compute fxy all reduce sum c_perfxy[1] c_perfxy[2] c_perfxy[3] c_perfxy[4] c_perfxy[5] c_perfxy[6]
+thermo_style custom step lx ly lz xy xz yz c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6]
+run 10
+Memory usage per processor = 9.17123 Mbytes
+Step Lx Ly Lz Xy Xz Yz fxy[1] fxy[2] fxy[3] fxy[4] fxy[5] fxy[6]
+ 57 25.037076 25.034573 25.037076 0 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.73 82087.083
+ 58 25.037076 25.034573 25.037076 5.0069146e-07 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.73 82087.083
+ 59 25.037076 25.034573 25.037076 1.0013829e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -107434.78 -147563.72 82087.087
+ 60 25.037076 25.034573 25.037076 1.5020744e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -88445.781 -147563.72 82087.09
+ 61 25.037076 25.034573 25.037076 2.0027658e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -69456.779 -147563.71 82087.094
+ 62 25.037076 25.034573 25.037076 2.5034573e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -50467.776 -147563.71 82087.098
+ 63 25.037076 25.034573 25.037076 3.0041488e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -31478.773 -147563.7 82087.101
+ 64 25.037076 25.034573 25.037076 3.5048402e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -12489.77 -147563.7 82087.105
+ 65 25.037076 25.034573 25.037076 4.0055317e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 6499.2334 -147563.69 82087.109
+ 66 25.037076 25.034573 25.037076 4.5062231e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 25488.236 -147563.69 82087.113
+ 67 25.037076 25.034573 25.037076 5.0069146e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 44477.239 -147563.68 82087.116
+Loop time of 0.411159 on 4 procs for 10 steps with 1296 atoms
+
+Performance: 0.420 ns/day, 57.105 hours/ns, 24.322 timesteps/s
+99.9% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.3889 | 0.39826 | 0.40584 | 1.1 | 96.86
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.0024002 | 0.010008 | 0.019374 | 6.8 | 2.43
+Output | 0.0027368 | 0.0027526 | 0.0027771 | 0.0 | 0.67
+Modify | 5.6028e-05 | 5.8174e-05 | 6.0081e-05 | 0.0 | 0.01
+Other | | 8.059e-05 | | | 0.02
+
+Nlocal: 324 ave 328 max 318 min
+Histogram: 1 0 0 0 1 0 0 0 0 2
+Nghost: 4943 ave 4949 max 4939 min
+Histogram: 2 0 0 0 0 0 1 0 0 1
+Neighs: 0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs: 215568 ave 218192 max 211632 min
+Histogram: 1 0 0 0 1 0 0 0 0 2
+
+Total # of neighbors = 862272
+Ave neighs/atom = 665.333
+Neighbor list builds = 0
+Dangerous builds not checked
+Total wall time: 0:00:11
diff --git a/examples/comb/log.15Feb16.comb.HfO2.g++.1 b/examples/comb/log.15Feb16.comb.HfO2.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..af1b5ff3aa50cab4978a0768776206eb02b59aaf
--- /dev/null
+++ b/examples/comb/log.15Feb16.comb.HfO2.g++.1
@@ -0,0 +1,235 @@
+LAMMPS (15 Feb 2016)
+units metal
+atom_style charge
+dimension 3
+boundary p p p
+
+read_data data.m-HfO2
+ triclinic box = (0 0 0) to (25.642 25.957 26.4845) with tilt (0 -4.46691 0)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 1500 atoms
+#read_data data.t-HfO2
+#read_data data.c-HfO2
+
+mass 1 178.0
+group type1 type 1
+500 atoms in group type1
+compute charge1 type1 property/atom q
+compute q1 type1 reduce ave c_charge1
+mass 2 16.00
+group type2 type 2
+1000 atoms in group type2
+compute charge2 type2 property/atom q
+compute q2 type2 reduce ave c_charge2
+
+pair_style comb
+pair_coeff * * ffield.comb Hf O
+Reading potential file ffield.comb with DATE: 2011-02-22
+
+neighbor 0.5 bin
+neigh_modify every 10 delay 10 check yes
+
+timestep 0.00020
+
+thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz c_q1 c_q2
+thermo_modify norm yes
+
+fix 1 all nvt temp 300.0 300.0 0.1
+thermo 1
+run 1
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 10 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 12.5
+ ghost atom cutoff = 12.5
+ binsize = 6.25 -> bins = 5 5 5
+Memory usage per processor = 6.13908 Mbytes
+Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
+ 0 0 -9.3995049 -9.3995049 5.256221 -14.655726 60985.254 17627.802 25.642 25.957 26.4845 -4.46691 3.6 -1.8
+ 1 0.039315732 -9.3995035 -9.3995086 5.2562201 -14.655729 60983.797 17627.802 25.642 25.957 26.4845 -4.46691 3.6 -1.8
+Loop time of 0.169538 on 1 procs for 1 steps with 1500 atoms
+
+Performance: 0.102 ns/day, 235.469 hours/ns, 5.898 timesteps/s
+99.7% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.16939 | 0.16939 | 0.16939 | 0.0 | 99.91
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 6.485e-05 | 6.485e-05 | 6.485e-05 | 0.0 | 0.04
+Output | 2.9802e-05 | 2.9802e-05 | 2.9802e-05 | 0.0 | 0.02
+Modify | 3.9101e-05 | 3.9101e-05 | 3.9101e-05 | 0.0 | 0.02
+Other | | 1.717e-05 | | | 0.01
+
+Nlocal: 1500 ave 1500 max 1500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 10100 ave 10100 max 10100 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs: 1.0375e+06 ave 1.0375e+06 max 1.0375e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1037500
+Ave neighs/atom = 691.667
+Neighbor list builds = 0
+Dangerous builds = 0
+fix 2 all qeq/comb 1 0.003 file fq.out
+run 5
+Memory usage per processor = 6.76408 Mbytes
+Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
+ 1 0.039315732 -9.3995035 -9.3995086 5.2562201 -14.655729 60983.797 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
+ 2 0.13734003 -10.041396 -10.041413 2.7214902 -12.762903 -130794.11 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
+ 3 0.2686308 -10.041388 -10.041423 2.7214912 -12.762914 -130800.39 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
+ 4 0.44445358 -10.041379 -10.041436 2.7214924 -12.762929 -130808.63 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
+ 5 0.66458606 -10.041367 -10.041453 2.7214941 -12.762947 -130818.84 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
+ 6 0.92875014 -10.041353 -10.041473 2.721496 -12.762969 -130831 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
+Loop time of 1.16742 on 1 procs for 5 steps with 1500 atoms
+
+Performance: 0.074 ns/day, 324.284 hours/ns, 4.283 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.85832 | 0.85832 | 0.85832 | 0.0 | 73.52
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.00033593 | 0.00033593 | 0.00033593 | 0.0 | 0.03
+Output | 0.00015116 | 0.00015116 | 0.00015116 | 0.0 | 0.01
+Modify | 0.30852 | 0.30852 | 0.30852 | 0.0 | 26.43
+Other | | 9.751e-05 | | | 0.01
+
+Nlocal: 1500 ave 1500 max 1500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 10100 ave 10100 max 10100 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs: 1.0375e+06 ave 1.0375e+06 max 1.0375e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1037500
+Ave neighs/atom = 691.667
+Neighbor list builds = 0
+Dangerous builds = 0
+
+unfix 1
+fix 1 all box/relax aniso 0.0 vmax 0.0002
+
+# should minimize to higher tolerance in practice
+
+#minimize 1.0e-12 1.0e-18 1000 10000
+minimize 1.0e-4 1.0e-6 1000 10000
+WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 12.5
+ ghost atom cutoff = 12.5
+ binsize = 6.25 -> bins = 5 5 5
+Memory usage per processor = 7.88908 Mbytes
+Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
+ 6 0.92875014 -10.041353 -10.041473 2.721496 -12.762969 -130831 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
+ 7 0.92875014 -10.041833 -10.041953 2.7196698 -12.761623 -130754.01 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
+Loop time of 0.64676 on 1 procs for 1 steps with 1500 atoms
+
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+Minimization stats:
+ Stopping criterion = energy tolerance
+ Energy initial, next-to-last, final =
+ -10.0414727016 -10.0414727016 -10.0419532985
+ Force two-norm initial, final = 2625.99 2625.45
+ Force max component initial, final = 1915.33 1916.61
+ Final line search alpha, max atom move = 1.04421e-07 0.000200134
+ Iterations, force evaluations = 1 1
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.34047 | 0.34047 | 0.34047 | 0.0 | 52.64
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.00012827 | 0.00012827 | 0.00012827 | 0.0 | 0.02
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0.30579 | 0.30579 | 0.30579 | 0.0 | 47.28
+Other | | 0.0003626 | | | 0.06
+
+Nlocal: 1500 ave 1500 max 1500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 10100 ave 10100 max 10100 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs: 1.0375e+06 ave 1.0375e+06 max 1.0375e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1037500
+Ave neighs/atom = 691.667
+Neighbor list builds = 0
+Dangerous builds = 0
+min_modify dmax 0.005 line quadratic
+
+#dump 1 all cfg 10 *.cfg id type xs ys zs q vx vy vz fx fy fz
+#dump_modify 1 element Hf O
+
+#dump 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 2 element Hf O
+
+#dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 2 element Hf O
+
+velocity all create 300.1 2398378
+run 10
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 10 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 12.5
+ ghost atom cutoff = 12.5
+ binsize = 6.25 -> bins = 5 5 5
+Memory usage per processor = 6.76408 Mbytes
+Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
+ 7 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
+ 8 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
+ 9 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
+ 10 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
+ 11 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
+ 12 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
+ 13 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
+ 14 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
+ 15 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
+ 16 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
+ 17 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
+Loop time of 2.31943 on 1 procs for 10 steps with 1500 atoms
+
+Performance: 0.075 ns/day, 322.143 hours/ns, 4.311 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 1.7064 | 1.7064 | 1.7064 | 0.0 | 73.57
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.00066495 | 0.00066495 | 0.00066495 | 0.0 | 0.03
+Output | 0.00035143 | 0.00035143 | 0.00035143 | 0.0 | 0.02
+Modify | 0.61178 | 0.61178 | 0.61178 | 0.0 | 26.38
+Other | | 0.0002165 | | | 0.01
+
+Nlocal: 1500 ave 1500 max 1500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 10100 ave 10100 max 10100 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs: 1.0375e+06 ave 1.0375e+06 max 1.0375e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1037500
+Ave neighs/atom = 691.667
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:10
diff --git a/examples/comb/log.15Feb16.comb.HfO2.g++.4 b/examples/comb/log.15Feb16.comb.HfO2.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..3841eeaee0d3c10d4feb177c11379e74c3ce48c9
--- /dev/null
+++ b/examples/comb/log.15Feb16.comb.HfO2.g++.4
@@ -0,0 +1,235 @@
+LAMMPS (15 Feb 2016)
+units metal
+atom_style charge
+dimension 3
+boundary p p p
+
+read_data data.m-HfO2
+ triclinic box = (0 0 0) to (25.642 25.957 26.4845) with tilt (0 -4.46691 0)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 1500 atoms
+#read_data data.t-HfO2
+#read_data data.c-HfO2
+
+mass 1 178.0
+group type1 type 1
+500 atoms in group type1
+compute charge1 type1 property/atom q
+compute q1 type1 reduce ave c_charge1
+mass 2 16.00
+group type2 type 2
+1000 atoms in group type2
+compute charge2 type2 property/atom q
+compute q2 type2 reduce ave c_charge2
+
+pair_style comb
+pair_coeff * * ffield.comb Hf O
+Reading potential file ffield.comb with DATE: 2011-02-22
+
+neighbor 0.5 bin
+neigh_modify every 10 delay 10 check yes
+
+timestep 0.00020
+
+thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz c_q1 c_q2
+thermo_modify norm yes
+
+fix 1 all nvt temp 300.0 300.0 0.1
+thermo 1
+run 1
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 10 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 12.5
+ ghost atom cutoff = 12.5
+ binsize = 6.25 -> bins = 5 5 5
+Memory usage per processor = 5.96686 Mbytes
+Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
+ 0 0 -9.3995049 -9.3995049 5.256221 -14.655726 60985.254 17627.802 25.642 25.957 26.4845 -4.46691 3.6 -1.8
+ 1 0.039315732 -9.3995035 -9.3995086 5.2562201 -14.655729 60983.797 17627.802 25.642 25.957 26.4845 -4.46691 3.6 -1.8
+Loop time of 0.0429993 on 4 procs for 1 steps with 1500 atoms
+
+Performance: 0.402 ns/day, 59.721 hours/ns, 23.256 timesteps/s
+99.4% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.042339 | 0.042613 | 0.042762 | 0.1 | 99.10
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.0001421 | 0.00029129 | 0.00056505 | 1.0 | 0.68
+Output | 3.7909e-05 | 4.0174e-05 | 4.6015e-05 | 0.1 | 0.09
+Modify | 2.4796e-05 | 2.4796e-05 | 2.4796e-05 | 0.0 | 0.06
+Other | | 3.028e-05 | | | 0.07
+
+Nlocal: 375 ave 375 max 375 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost: 6075 ave 6075 max 6075 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs: 259375 ave 259375 max 259375 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1037500
+Ave neighs/atom = 691.667
+Neighbor list builds = 0
+Dangerous builds = 0
+fix 2 all qeq/comb 1 0.003 file fq.out
+run 5
+Memory usage per processor = 6.59186 Mbytes
+Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
+ 1 0.039315732 -9.3995035 -9.3995086 5.2562201 -14.655729 60983.797 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
+ 2 0.13734003 -10.041396 -10.041413 2.7214902 -12.762903 -130794.11 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
+ 3 0.2686308 -10.041388 -10.041423 2.7214912 -12.762914 -130800.39 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
+ 4 0.44445358 -10.041379 -10.041436 2.7214924 -12.762929 -130808.63 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
+ 5 0.66458606 -10.041367 -10.041453 2.7214941 -12.762947 -130818.84 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
+ 6 0.92875014 -10.041353 -10.041473 2.721496 -12.762969 -130831 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
+Loop time of 0.290755 on 4 procs for 5 steps with 1500 atoms
+
+Performance: 0.297 ns/day, 80.765 hours/ns, 17.197 timesteps/s
+99.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.21107 | 0.21252 | 0.21354 | 0.2 | 73.09
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.00075912 | 0.001812 | 0.0032141 | 2.1 | 0.62
+Output | 0.00020814 | 0.00021452 | 0.00023079 | 0.1 | 0.07
+Modify | 0.07608 | 0.076133 | 0.076177 | 0.0 | 26.18
+Other | | 7.701e-05 | | | 0.03
+
+Nlocal: 375 ave 375 max 375 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost: 6075 ave 6075 max 6075 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs: 259375 ave 259375 max 259375 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1037500
+Ave neighs/atom = 691.667
+Neighbor list builds = 0
+Dangerous builds = 0
+
+unfix 1
+fix 1 all box/relax aniso 0.0 vmax 0.0002
+
+# should minimize to higher tolerance in practice
+
+#minimize 1.0e-12 1.0e-18 1000 10000
+minimize 1.0e-4 1.0e-6 1000 10000
+WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 12.5
+ ghost atom cutoff = 12.5
+ binsize = 6.25 -> bins = 5 5 5
+Memory usage per processor = 7.71686 Mbytes
+Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
+ 6 0.92875014 -10.041353 -10.041473 2.721496 -12.762969 -130831 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
+ 7 0.92875014 -10.041833 -10.041953 2.7196698 -12.761623 -130754.01 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
+Loop time of 0.161507 on 4 procs for 1 steps with 1500 atoms
+
+100.0% CPU use with 4 MPI tasks x no OpenMP threads
+
+Minimization stats:
+ Stopping criterion = energy tolerance
+ Energy initial, next-to-last, final =
+ -10.0414727016 -10.0414727016 -10.0419532985
+ Force two-norm initial, final = 2625.99 2625.45
+ Force max component initial, final = 1915.33 1916.61
+ Final line search alpha, max atom move = 1.04421e-07 0.000200134
+ Iterations, force evaluations = 1 1
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.084314 | 0.085016 | 0.085468 | 0.2 | 52.64
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.00030208 | 0.00076222 | 0.0014489 | 1.7 | 0.47
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0.075456 | 0.075471 | 0.07548 | 0.0 | 46.73
+Other | | 0.0002575 | | | 0.16
+
+Nlocal: 375 ave 375 max 375 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost: 6075 ave 6075 max 6075 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs: 259375 ave 259375 max 259375 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1037500
+Ave neighs/atom = 691.667
+Neighbor list builds = 0
+Dangerous builds = 0
+min_modify dmax 0.005 line quadratic
+
+#dump 1 all cfg 10 *.cfg id type xs ys zs q vx vy vz fx fy fz
+#dump_modify 1 element Hf O
+
+#dump 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 2 element Hf O
+
+#dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 2 element Hf O
+
+velocity all create 300.1 2398378
+run 10
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 10 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 12.5
+ ghost atom cutoff = 12.5
+ binsize = 6.25 -> bins = 5 5 5
+Memory usage per processor = 6.59186 Mbytes
+Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
+ 7 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
+ 8 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
+ 9 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
+ 10 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
+ 11 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
+ 12 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
+ 13 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
+ 14 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
+ 15 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
+ 16 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
+ 17 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
+Loop time of 0.581787 on 4 procs for 10 steps with 1500 atoms
+
+Performance: 0.297 ns/day, 80.804 hours/ns, 17.188 timesteps/s
+99.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.42265 | 0.42528 | 0.42704 | 0.2 | 73.10
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.0015607 | 0.0033906 | 0.0059152 | 2.7 | 0.58
+Output | 0.00046325 | 0.00046599 | 0.00046873 | 0.0 | 0.08
+Modify | 0.1524 | 0.15252 | 0.1526 | 0.0 | 26.22
+Other | | 0.0001305 | | | 0.02
+
+Nlocal: 375 ave 375 max 375 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost: 6075 ave 6075 max 6075 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs: 259375 ave 259375 max 259375 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1037500
+Ave neighs/atom = 691.667
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:02
diff --git a/examples/comb/log.15Feb16.comb.Si.elastic.g++.1 b/examples/comb/log.15Feb16.comb.Si.elastic.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..4287cb5e0633d1a9a0d40272f3ef8fef64fe0fe7
--- /dev/null
+++ b/examples/comb/log.15Feb16.comb.Si.elastic.g++.1
@@ -0,0 +1,333 @@
+LAMMPS (15 Feb 2016)
+# Pure Si crystal, qeq off, calculates stress-strain, no out.*.cfg
+
+units metal
+atom_style charge
+dimension 3
+boundary p p p
+
+lattice diamond 5.431
+Lattice spacing in x,y,z = 5.431 5.431 5.431
+region box block 0 4 0 4 0 4
+create_box 1 box
+Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 512 atoms
+mass 1 29.0
+change_box all triclinic
+ triclinic box = (0 0 0) to (21.724 21.724 21.724) with tilt (0 0 0)
+
+velocity all create 1.0 277387
+
+pair_style comb
+pair_coeff * * ffield.comb Si
+Reading potential file ffield.comb with DATE: 2011-02-22
+
+neighbor 0.5 bin
+neigh_modify every 20 delay 0 check no
+
+fix 1 all box/relax aniso 0.0 vmax 0.001
+timestep 0.00020
+
+thermo_style custom step temp etotal pe evdwl ecoul #lx ly lz vol pxx pyy pzz
+thermo_modify norm yes
+thermo 1
+minimize 1.0e-14 1.0e-20 1000 10000
+WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 12.5
+ ghost atom cutoff = 12.5
+ binsize = 6.25 -> bins = 4 4 4
+Memory usage per processor = 7.60455 Mbytes
+Step Temp TotEng PotEng E_vdwl E_coul
+ 0 1 -4.6295947 -4.6297237 -4.6297237 0
+ 1 1 -4.6295965 -4.6297255 -4.6297255 0
+ 2 1 -4.6295965 -4.6297255 -4.6297255 0
+ 3 1 -4.6295965 -4.6297255 -4.6297255 0
+ 4 1 -4.6295965 -4.6297255 -4.6297255 0
+ 5 1 -4.6295965 -4.6297255 -4.6297255 0
+Loop time of 0.206087 on 1 procs for 5 steps with 512 atoms
+
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+Minimization stats:
+ Stopping criterion = energy tolerance
+ Energy initial, next-to-last, final =
+ -4.62972371535 -4.62972550325 -4.62972550325
+ Force two-norm initial, final = 5.86582 2.4862e-12
+ Force max component initial, final = 3.38663 2.10283e-12
+ Final line search alpha, max atom move = 1 2.10283e-12
+ Iterations, force evaluations = 5 10
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.2046 | 0.2046 | 0.2046 | 0.0 | 99.28
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.00029564 | 0.00029564 | 0.00029564 | 0.0 | 0.14
+Output | 3.0041e-05 | 3.0041e-05 | 3.0041e-05 | 0.0 | 0.01
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 0.001161 | | | 0.56
+
+Nlocal: 512 ave 512 max 512 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 4861 ave 4861 max 4861 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs: 212992 ave 212992 max 212992 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 212992
+Ave neighs/atom = 416
+Neighbor list builds = 0
+Dangerous builds not checked
+min_modify dmax 0.2 line quadratic
+
+unfix 1
+run 1
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 20 steps, delay 0 steps, check no
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 12.5
+ ghost atom cutoff = 12.5
+ binsize = 6.25 -> bins = 4 4 4
+Memory usage per processor = 5.97955 Mbytes
+Step Temp TotEng PotEng E_vdwl E_coul
+ 5 1 -4.6295965 -4.6297255 -4.6297255 0
+ 6 1 -4.6295965 -4.6297255 -4.6297255 0
+Loop time of 0.018579 on 1 procs for 1 steps with 512 atoms
+
+Performance: 0.930 ns/day, 25.804 hours/ns, 53.824 timesteps/s
+102.2% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.018534 | 0.018534 | 0.018534 | 0.0 | 99.76
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 2.7895e-05 | 2.7895e-05 | 2.7895e-05 | 0.0 | 0.15
+Output | 9.0599e-06 | 9.0599e-06 | 9.0599e-06 | 0.0 | 0.05
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 7.868e-06 | | | 0.04
+
+Nlocal: 512 ave 512 max 512 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 4861 ave 4861 max 4861 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs: 212992 ave 212992 max 212992 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 212992
+Ave neighs/atom = 416
+Neighbor list builds = 0
+Dangerous builds not checked
+
+### copy lines after this to any input script for elastic calculations ###
+## Elastic constants calculations: strain box, measure box stress
+## strain x, measure s_x, s_y, s_z, s_yz:
+## calculates C11, C12, C13 and C14
+
+fix 2 all deform 1 x scale 1.0001 remap x
+compute perfx all stress/atom NULL pair
+compute fx all reduce sum c_perfx[1] c_perfx[2] c_perfx[3] c_perfx[4] c_perfx[5] c_perfx[6]
+thermo_style custom step lx ly lz xy xz yz c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6]
+WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:680)
+run 10
+Memory usage per processor = 6.72955 Mbytes
+Step Lx Ly Lz Xy Xz Yz fx[1] fx[2] fx[3] fx[4] fx[5] fx[6]
+ 6 21.727916 21.727916 21.727916 0 0 0 -4.5569391e-06 -9.3041736e-06 -3.863262e-06 5.3686749e-06 -1.5078216e-06 5.1674734e-06
+ 7 21.728133 21.727916 21.727916 0 0 0 -2.4800435e-06 -9.5067314e-06 -2.1562734e-06 5.5972954e-06 -2.3715124e-06 3.9555507e-06
+ 8 21.72835 21.727916 21.727916 0 0 0 146204.17 77325.788 77325.788 3.5125695e-06 -1.9487795e-06 5.2972201e-06
+ 9 21.728568 21.727916 21.727916 0 0 0 292407.63 154648.04 154648.04 5.6408383e-06 -2.4472325e-06 6.3046987e-06
+ 10 21.728785 21.727916 21.727916 0 0 0 438610.37 231966.74 231966.74 5.5704989e-06 -1.8785254e-06 -1.4083956e-06
+ 11 21.729002 21.727916 21.727916 0 0 0 584812.4 309281.91 309281.91 -1.2913749e-05 2.0544275e-06 7.547976e-06
+ 12 21.729219 21.727916 21.727916 0 0 0 731013.71 386593.54 386593.54 6.0987798e-06 -2.0790709e-06 7.8755963e-06
+ 13 21.729437 21.727916 21.727916 0 0 0 877214.3 463901.63 463901.63 5.2296156e-06 -2.2013505e-06 2.6034199e-06
+ 14 21.729654 21.727916 21.727916 0 0 0 1023414.2 541206.18 541206.18 5.6537455e-06 -1.9222461e-06 4.3649131e-06
+ 15 21.729871 21.727916 21.727916 0 0 0 1169613.3 618507.19 618507.19 5.5850663e-06 -2.204341e-06 6.1719985e-06
+ 16 21.730089 21.727916 21.727916 0 0 0 1315811.8 695804.66 695804.66 -1.3406996e-05 2.5348334e-06 6.2581356e-06
+Loop time of 0.203248 on 1 procs for 10 steps with 512 atoms
+
+Performance: 0.850 ns/day, 28.229 hours/ns, 49.201 timesteps/s
+99.4% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.20165 | 0.20165 | 0.20165 | 0.0 | 99.21
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.00027919 | 0.00027919 | 0.00027919 | 0.0 | 0.14
+Output | 0.0011773 | 0.0011773 | 0.0011773 | 0.0 | 0.58
+Modify | 8.1301e-05 | 8.1301e-05 | 8.1301e-05 | 0.0 | 0.04
+Other | | 5.889e-05 | | | 0.03
+
+Nlocal: 512 ave 512 max 512 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 4861 ave 4861 max 4861 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs: 212992 ave 212992 max 212992 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 212992
+Ave neighs/atom = 416
+Neighbor list builds = 0
+Dangerous builds not checked
+
+## strain z, measure s_z: calculates C33
+
+fix 2 all deform 1 z scale 1.0001 remap x
+compute perfz all stress/atom NULL pair
+compute fz all reduce sum c_perfz[1] c_perfz[2] c_perfz[3] c_perfz[4] c_perfz[5] c_perfz[6]
+thermo_style custom step lx ly lz xy xz yz c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6]
+run 10
+Memory usage per processor = 7.47955 Mbytes
+Step Lx Ly Lz Xy Xz Yz fz[1] fz[2] fz[3] fz[4] fz[5] fz[6]
+ 16 21.730089 21.727916 21.727916 0 0 0 1462009.5 773098.59 773098.59 4.2549849e-06 -8.3746497e-07 7.0310015e-06
+ 17 21.730089 21.727916 21.728133 0 0 0 1462009.5 773098.59 773098.59 5.1784721e-06 -2.3038152e-06 5.7172699e-06
+ 18 21.730089 21.727916 21.72835 0 0 0 1539307.6 850399.75 919275.09 9.5325273e-06 -6.4331187e-07 4.7453557e-06
+ 19 21.730089 21.727916 21.728568 0 0 0 1616602.2 927697.36 1065450.9 1.3298468e-05 -1.8936338e-06 4.6426389e-06
+ 20 21.730089 21.727916 21.728785 0 0 0 1693893.3 1004991.4 1211626 1.0653147e-05 -1.4284476e-06 6.3390661e-07
+ 21 21.730089 21.727916 21.729002 0 0 0 1771180.8 1082282 1357800.3 9.0018044e-06 -1.2309518e-06 5.565611e-06
+ 22 21.730089 21.727916 21.729219 0 0 0 1848464.7 1159569 1503974 7.5031694e-06 -2.7028978e-06 5.6324743e-06
+ 23 21.730089 21.727916 21.729437 0 0 0 1925745.2 1236852.4 1650146.9 4.3439607e-06 -2.4393614e-06 5.5564577e-06
+ 24 21.730089 21.727916 21.729654 0 0 0 2003022 1314132.4 1796319.1 2.3497113e-06 -2.3680104e-06 4.7932602e-06
+ 25 21.730089 21.727916 21.729871 0 0 0 2080295.4 1391408.8 1942490.6 6.941166e-06 -1.1601937e-06 4.9355658e-06
+ 26 21.730089 21.727916 21.730089 0 0 0 2157565.2 1468681.6 2088661.4 5.7633476e-06 -8.4264935e-07 4.0350137e-06
+Loop time of 0.206357 on 1 procs for 10 steps with 512 atoms
+
+Performance: 0.837 ns/day, 28.661 hours/ns, 48.460 timesteps/s
+100.3% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.20466 | 0.20466 | 0.20466 | 0.0 | 99.18
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.00027633 | 0.00027633 | 0.00027633 | 0.0 | 0.13
+Output | 0.0012765 | 0.0012765 | 0.0012765 | 0.0 | 0.62
+Modify | 7.7963e-05 | 7.7963e-05 | 7.7963e-05 | 0.0 | 0.04
+Other | | 6.175e-05 | | | 0.03
+
+Nlocal: 512 ave 512 max 512 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 4861 ave 4861 max 4861 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs: 212992 ave 212992 max 212992 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 212992
+Ave neighs/atom = 416
+Neighbor list builds = 0
+Dangerous builds not checked
+
+## strain yz, measure s_yz: calculates C44
+
+fix 2 all deform 1 yz erate 0.0001 remap x
+compute perfyz all stress/atom NULL pair
+compute fyz all reduce sum c_perfyz[1] c_perfyz[2] c_perfyz[3] c_perfyz[4] c_perfyz[5] c_perfyz[6]
+thermo_style custom step lx ly lz xy xz yz c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6]
+run 10
+Memory usage per processor = 8.24482 Mbytes
+Step Lx Ly Lz Xy Xz Yz fyz[1] fyz[2] fyz[3] fyz[4] fyz[5] fyz[6]
+ 26 21.730089 21.727916 21.730089 0 0 0 2234831.5 1545950.9 2234831.5 4.8476018e-06 4.2828413e-07 5.75372e-06
+ 27 21.730089 21.727916 21.730089 0 0 4.3460177e-07 2234831.5 1545950.9 2234831.5 5.088922e-06 -2.3012471e-06 5.6950612e-06
+ 28 21.730089 21.727916 21.730089 0 0 8.6920354e-07 2234831.5 1545950.9 2234831.5 4.7258447e-06 -1.3958256e-06 243.66105
+ 29 21.730089 21.727916 21.730089 0 0 1.3038053e-06 2234831.5 1545950.9 2234831.5 4.7492097e-06 -2.8958095e-06 487.32212
+ 30 21.730089 21.727916 21.730089 0 0 1.7384071e-06 2234831.5 1545950.9 2234831.5 4.8744538e-06 -2.3110563e-06 730.98324
+ 31 21.730089 21.727916 21.730089 0 0 2.1730089e-06 2234831.5 1545950.9 2234831.5 4.3760082e-06 -8.3074269e-07 974.64423
+ 32 21.730089 21.727916 21.730089 0 0 2.6076106e-06 2234831.5 1545950.9 2234831.5 4.7980741e-06 -5.7372478e-07 1218.3053
+ 33 21.730089 21.727916 21.730089 0 0 3.0422124e-06 2234831.5 1545950.9 2234831.5 4.8822804e-06 -2.3433596e-06 1461.9664
+ 34 21.730089 21.727916 21.730089 0 0 3.4768142e-06 2234831.5 1545950.9 2234831.5 4.8447261e-06 -1.9614792e-06 1705.6275
+ 35 21.730089 21.727916 21.730089 0 0 3.911416e-06 2234831.5 1545950.9 2234831.5 5.1297449e-06 -2.114135e-06 1949.2885
+ 36 21.730089 21.727916 21.730089 0 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 4.5571577e-06 -1.8415232e-06 2192.9496
+Loop time of 0.203569 on 1 procs for 10 steps with 512 atoms
+
+Performance: 0.849 ns/day, 28.273 hours/ns, 49.123 timesteps/s
+100.2% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.20196 | 0.20196 | 0.20196 | 0.0 | 99.21
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.00028515 | 0.00028515 | 0.00028515 | 0.0 | 0.14
+Output | 0.0011783 | 0.0011783 | 0.0011783 | 0.0 | 0.58
+Modify | 7.7724e-05 | 7.7724e-05 | 7.7724e-05 | 0.0 | 0.04
+Other | | 6.366e-05 | | | 0.03
+
+Nlocal: 512 ave 512 max 512 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 4861 ave 4861 max 4861 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs: 212992 ave 212992 max 212992 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 212992
+Ave neighs/atom = 416
+Neighbor list builds = 0
+Dangerous builds not checked
+
+## strain xy, measure s_xy: calculates C66
+
+fix 2 all deform 1 xy erate 0.0001 remap x
+compute perfxy all stress/atom NULL pair
+compute fxy all reduce sum c_perfxy[1] c_perfxy[2] c_perfxy[3] c_perfxy[4] c_perfxy[5] c_perfxy[6]
+thermo_style custom step lx ly lz xy xz yz c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6]
+run 10
+Memory usage per processor = 8.99482 Mbytes
+Step Lx Ly Lz Xy Xz Yz fxy[1] fxy[2] fxy[3] fxy[4] fxy[5] fxy[6]
+ 36 21.730089 21.727916 21.730089 0 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 5.1293854e-06 -1.6748595e-06 2436.6106
+ 37 21.730089 21.727916 21.730089 4.3455832e-07 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 5.1236563e-06 -3.3624188e-06 2436.6106
+ 38 21.730089 21.727916 21.730089 8.6911663e-07 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 243.64727 -0.00013232165 2436.6106
+ 39 21.730089 21.727916 21.730089 1.3036749e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 487.29458 -0.0002652587 2436.6106
+ 40 21.730089 21.727916 21.730089 1.7382333e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 730.9419 -0.00039565085 2436.6106
+ 41 21.730089 21.727916 21.730089 2.1727916e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 974.58916 -0.00052768104 2436.6106
+ 42 21.730089 21.727916 21.730089 2.6073499e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 1218.2364 -0.00065822936 2436.6106
+ 43 21.730089 21.727916 21.730089 3.0419082e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 1461.8837 -0.0007889991 2436.6106
+ 44 21.730089 21.727916 21.730089 3.4764665e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 1705.531 -0.00091806693 2436.6106
+ 45 21.730089 21.727916 21.730089 3.9110248e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 1949.1783 -0.001049945 2436.6106
+ 46 21.730089 21.727916 21.730089 4.3455832e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 2192.8256 -0.0011787861 2436.6106
+Loop time of 0.204484 on 1 procs for 10 steps with 512 atoms
+
+Performance: 0.845 ns/day, 28.401 hours/ns, 48.904 timesteps/s
+100.2% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.20272 | 0.20272 | 0.20272 | 0.0 | 99.14
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.00029564 | 0.00029564 | 0.00029564 | 0.0 | 0.14
+Output | 0.0013256 | 0.0013256 | 0.0013256 | 0.0 | 0.65
+Modify | 7.844e-05 | 7.844e-05 | 7.844e-05 | 0.0 | 0.04
+Other | | 6.27e-05 | | | 0.03
+
+Nlocal: 512 ave 512 max 512 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 4861 ave 4861 max 4861 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs: 212992 ave 212992 max 212992 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 212992
+Ave neighs/atom = 416
+Neighbor list builds = 0
+Dangerous builds not checked
+Total wall time: 0:00:01
diff --git a/examples/comb/log.15Feb16.comb.Si.elastic.g++.4 b/examples/comb/log.15Feb16.comb.Si.elastic.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..3023f450422da6f828e24d748ffbf590b139dce1
--- /dev/null
+++ b/examples/comb/log.15Feb16.comb.Si.elastic.g++.4
@@ -0,0 +1,331 @@
+LAMMPS (15 Feb 2016)
+# Pure Si crystal, qeq off, calculates stress-strain, no out.*.cfg
+
+units metal
+atom_style charge
+dimension 3
+boundary p p p
+
+lattice diamond 5.431
+Lattice spacing in x,y,z = 5.431 5.431 5.431
+region box block 0 4 0 4 0 4
+create_box 1 box
+Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
+ 1 by 2 by 2 MPI processor grid
+create_atoms 1 box
+Created 512 atoms
+mass 1 29.0
+change_box all triclinic
+ triclinic box = (0 0 0) to (21.724 21.724 21.724) with tilt (0 0 0)
+
+velocity all create 1.0 277387
+
+pair_style comb
+pair_coeff * * ffield.comb Si
+Reading potential file ffield.comb with DATE: 2011-02-22
+
+neighbor 0.5 bin
+neigh_modify every 20 delay 0 check no
+
+fix 1 all box/relax aniso 0.0 vmax 0.001
+timestep 0.00020
+
+thermo_style custom step temp etotal pe evdwl ecoul #lx ly lz vol pxx pyy pzz
+thermo_modify norm yes
+thermo 1
+minimize 1.0e-14 1.0e-20 1000 10000
+WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 12.5
+ ghost atom cutoff = 12.5
+ binsize = 6.25 -> bins = 4 4 4
+Memory usage per processor = 7.52233 Mbytes
+Step Temp TotEng PotEng E_vdwl E_coul
+ 0 1 -4.6295947 -4.6297237 -4.6297237 0
+ 1 1 -4.6295965 -4.6297255 -4.6297255 0
+ 2 1 -4.6295965 -4.6297255 -4.6297255 0
+ 3 1 -4.6295965 -4.6297255 -4.6297255 0
+Loop time of 0.0429027 on 4 procs for 3 steps with 512 atoms
+
+99.0% CPU use with 4 MPI tasks x no OpenMP threads
+
+Minimization stats:
+ Stopping criterion = energy tolerance
+ Energy initial, next-to-last, final =
+ -4.62972371535 -4.62972550325 -4.62972550325
+ Force two-norm initial, final = 5.86582 3.9583e-08
+ Force max component initial, final = 3.38663 2.28585e-08
+ Final line search alpha, max atom move = 1 2.28585e-08
+ Iterations, force evaluations = 3 6
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.026284 | 0.032657 | 0.041753 | 3.1 | 76.12
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.00052333 | 0.0096034 | 0.015953 | 5.7 | 22.38
+Output | 3.5048e-05 | 3.6538e-05 | 4.1008e-05 | 0.0 | 0.09
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 0.0006061 | | | 1.41
+
+Nlocal: 128 ave 164 max 100 min
+Histogram: 1 0 0 2 0 0 0 0 0 1
+Nghost: 3073 ave 3101 max 3037 min
+Histogram: 1 0 0 0 0 0 2 0 0 1
+Neighs: 0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs: 53248 ave 68224 max 41600 min
+Histogram: 1 0 0 2 0 0 0 0 0 1
+
+Total # of neighbors = 212992
+Ave neighs/atom = 416
+Neighbor list builds = 0
+Dangerous builds not checked
+min_modify dmax 0.2 line quadratic
+
+unfix 1
+run 1
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 20 steps, delay 0 steps, check no
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 12.5
+ ghost atom cutoff = 12.5
+ binsize = 6.25 -> bins = 4 4 4
+Memory usage per processor = 5.89733 Mbytes
+Step Temp TotEng PotEng E_vdwl E_coul
+ 3 1 -4.6295965 -4.6297255 -4.6297255 0
+ 4 1 -4.6295965 -4.6297255 -4.6297255 0
+Loop time of 0.00605559 on 4 procs for 1 steps with 512 atoms
+
+Performance: 2.854 ns/day, 8.411 hours/ns, 165.137 timesteps/s
+99.1% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0037332 | 0.0046489 | 0.00595 | 1.2 | 76.77
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 7.2002e-05 | 0.0013711 | 0.0022838 | 2.2 | 22.64
+Output | 2.0027e-05 | 2.3484e-05 | 2.5988e-05 | 0.0 | 0.39
+Modify | 0 | 2.3842e-07 | 9.5367e-07 | 0.1 | 0.00
+Other | | 1.186e-05 | | | 0.20
+
+Nlocal: 128 ave 164 max 100 min
+Histogram: 1 0 0 2 0 0 0 0 0 1
+Nghost: 3073 ave 3101 max 3037 min
+Histogram: 1 0 0 0 0 0 2 0 0 1
+Neighs: 0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs: 53248 ave 68224 max 41600 min
+Histogram: 1 0 0 2 0 0 0 0 0 1
+
+Total # of neighbors = 212992
+Ave neighs/atom = 416
+Neighbor list builds = 0
+Dangerous builds not checked
+
+### copy lines after this to any input script for elastic calculations ###
+## Elastic constants calculations: strain box, measure box stress
+## strain x, measure s_x, s_y, s_z, s_yz:
+## calculates C11, C12, C13 and C14
+
+fix 2 all deform 1 x scale 1.0001 remap x
+compute perfx all stress/atom NULL pair
+compute fx all reduce sum c_perfx[1] c_perfx[2] c_perfx[3] c_perfx[4] c_perfx[5] c_perfx[6]
+thermo_style custom step lx ly lz xy xz yz c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6]
+WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:680)
+run 10
+Memory usage per processor = 6.64733 Mbytes
+Step Lx Ly Lz Xy Xz Yz fx[1] fx[2] fx[3] fx[4] fx[5] fx[6]
+ 4 21.727916 21.727916 21.727916 0 0 0 0.036618297 0.036625051 0.036618342 -1.7136998e-07 -3.2302114e-06 -1.7543151e-06
+ 5 21.728133 21.727916 21.727916 0 0 0 0.036618988 0.036625612 0.036619564 -1.1309366e-06 -2.412817e-06 -2.6316468e-06
+ 6 21.72835 21.727916 21.727916 0 0 0 146204.21 77325.824 77325.824 2.3636154e-06 -2.6955085e-06 -5.4243912e-06
+ 7 21.728568 21.727916 21.727916 0 0 0 292407.66 154648.07 154648.07 -1.2891214e-06 -2.3607767e-06 -4.2545106e-06
+ 8 21.728785 21.727916 21.727916 0 0 0 438610.41 231966.78 231966.78 -1.7378096e-06 -2.0714741e-06 -3.8921893e-06
+ 9 21.729002 21.727916 21.727916 0 0 0 584812.43 309281.95 309281.95 2.5425006e-06 9.0454362e-06 -7.1598291e-06
+ 10 21.729219 21.727916 21.727916 0 0 0 731013.74 386593.58 386593.58 -1.6897864e-06 -2.6139147e-06 -5.4137742e-06
+ 11 21.729437 21.727916 21.727916 0 0 0 877214.34 463901.66 463901.66 -1.8806784e-06 -1.8704431e-06 -4.8350021e-06
+ 12 21.729654 21.727916 21.727916 0 0 0 1023414.2 541206.21 541206.21 -9.1665744e-07 -1.59238e-06 -7.7617215e-06
+ 13 21.729871 21.727916 21.727916 0 0 0 1169613.4 618507.22 618507.22 -1.1565806e-06 -2.0309366e-06 -6.6873647e-06
+ 14 21.730089 21.727916 21.727916 0 0 0 1315811.8 695804.69 695804.69 1.8915845e-06 7.7289624e-06 -6.2492306e-06
+Loop time of 0.0683999 on 4 procs for 10 steps with 512 atoms
+
+Performance: 2.526 ns/day, 9.500 hours/ns, 146.199 timesteps/s
+99.4% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.041408 | 0.051284 | 0.065623 | 3.9 | 74.98
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.0009675 | 0.015306 | 0.025153 | 7.1 | 22.38
+Output | 0.0016904 | 0.0017211 | 0.001745 | 0.1 | 2.52
+Modify | 2.4557e-05 | 2.9504e-05 | 3.4809e-05 | 0.1 | 0.04
+Other | | 5.972e-05 | | | 0.09
+
+Nlocal: 128 ave 164 max 100 min
+Histogram: 1 0 0 2 0 0 0 0 0 1
+Nghost: 3073 ave 3101 max 3037 min
+Histogram: 1 0 0 0 0 0 2 0 0 1
+Neighs: 0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs: 53248 ave 68224 max 41600 min
+Histogram: 1 0 0 2 0 0 0 0 0 1
+
+Total # of neighbors = 212992
+Ave neighs/atom = 416
+Neighbor list builds = 0
+Dangerous builds not checked
+
+## strain z, measure s_z: calculates C33
+
+fix 2 all deform 1 z scale 1.0001 remap x
+compute perfz all stress/atom NULL pair
+compute fz all reduce sum c_perfz[1] c_perfz[2] c_perfz[3] c_perfz[4] c_perfz[5] c_perfz[6]
+thermo_style custom step lx ly lz xy xz yz c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6]
+run 10
+Memory usage per processor = 7.39733 Mbytes
+Step Lx Ly Lz Xy Xz Yz fz[1] fz[2] fz[3] fz[4] fz[5] fz[6]
+ 14 21.730089 21.727916 21.727916 0 0 0 1462009.6 773098.62 773098.62 -6.2271887e-07 -3.134065e-06 -1.4448086e-06
+ 15 21.730089 21.727916 21.728133 0 0 0 1462009.6 773098.62 773098.62 -1.4749588e-06 -2.1972704e-06 -2.7974026e-06
+ 16 21.730089 21.727916 21.72835 0 0 0 1539307.7 850399.78 919275.13 -1.1741349e-06 8.1321584e-06 -2.1634811e-06
+ 17 21.730089 21.727916 21.728568 0 0 0 1616602.3 927697.4 1065450.9 9.2086349e-07 -2.6001292e-06 -2.9133823e-06
+ 18 21.730089 21.727916 21.728785 0 0 0 1693893.3 1004991.5 1211626 1.3356364e-06 -2.794764e-06 -9.2778033e-06
+ 19 21.730089 21.727916 21.729002 0 0 0 1771180.8 1082282 1357800.3 -8.7949961e-07 -3.4755821e-06 -7.1758788e-06
+ 20 21.730089 21.727916 21.729219 0 0 0 1848464.8 1159569 1503974 1.674426e-06 -2.898863e-06 -2.1520562e-06
+ 21 21.730089 21.727916 21.729437 0 0 0 1925745.2 1236852.5 1650146.9 -1.7524845e-06 -3.4851467e-06 -1.7806669e-06
+ 22 21.730089 21.727916 21.729654 0 0 0 2003022.1 1314132.4 1796319.1 -2.1981227e-06 -2.7285159e-06 -2.0486576e-06
+ 23 21.730089 21.727916 21.729871 0 0 0 2080295.4 1391408.8 1942490.6 -3.6986662e-06 -2.430512e-06 -2.6914988e-06
+ 24 21.730089 21.727916 21.730089 0 0 0 2157565.2 1468681.6 2088661.4 -7.1345705e-06 -2.6113355e-06 -1.261254e-06
+Loop time of 0.0679641 on 4 procs for 10 steps with 512 atoms
+
+Performance: 2.543 ns/day, 9.439 hours/ns, 147.137 timesteps/s
+100.0% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.041426 | 0.05157 | 0.065353 | 3.8 | 75.88
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.00090528 | 0.014692 | 0.024832 | 7.1 | 21.62
+Output | 0.0016062 | 0.0016239 | 0.0016341 | 0.0 | 2.39
+Modify | 1.9789e-05 | 2.6107e-05 | 3.4094e-05 | 0.1 | 0.04
+Other | | 5.156e-05 | | | 0.08
+
+Nlocal: 128 ave 164 max 100 min
+Histogram: 1 0 0 2 0 0 0 0 0 1
+Nghost: 3073 ave 3101 max 3037 min
+Histogram: 1 0 0 0 0 0 2 0 0 1
+Neighs: 0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs: 53248 ave 68224 max 41600 min
+Histogram: 1 0 0 2 0 0 0 0 0 1
+
+Total # of neighbors = 212992
+Ave neighs/atom = 416
+Neighbor list builds = 0
+Dangerous builds not checked
+
+## strain yz, measure s_yz: calculates C44
+
+fix 2 all deform 1 yz erate 0.0001 remap x
+compute perfyz all stress/atom NULL pair
+compute fyz all reduce sum c_perfyz[1] c_perfyz[2] c_perfyz[3] c_perfyz[4] c_perfyz[5] c_perfyz[6]
+thermo_style custom step lx ly lz xy xz yz c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6]
+run 10
+Memory usage per processor = 8.16262 Mbytes
+Step Lx Ly Lz Xy Xz Yz fyz[1] fyz[2] fyz[3] fyz[4] fyz[5] fyz[6]
+ 24 21.730089 21.727916 21.730089 0 0 0 2234831.5 1545950.9 2234831.5 -3.9610575e-06 -3.188829e-06 -5.7973926e-07
+ 25 21.730089 21.727916 21.730089 0 0 4.3460177e-07 2234831.5 1545950.9 2234831.5 -4.4960939e-06 -2.549801e-06 -1.5603844e-06
+ 26 21.730089 21.727916 21.730089 0 0 8.6920354e-07 2234831.5 1545950.9 2234831.5 -5.49227e-06 -4.2895969e-06 243.66104
+ 27 21.730089 21.727916 21.730089 0 0 1.3038053e-06 2234831.5 1545950.9 2234831.5 -6.5461301e-06 -6.5635547e-06 487.32212
+ 28 21.730089 21.727916 21.730089 0 0 1.7384071e-06 2234831.5 1545950.9 2234831.5 -6.2913987e-06 -6.8959666e-06 730.98323
+ 29 21.730089 21.727916 21.730089 0 0 2.1730089e-06 2234831.5 1545950.9 2234831.5 -6.1650242e-06 -6.374019e-06 974.64422
+ 30 21.730089 21.727916 21.730089 0 0 2.6076106e-06 2234831.5 1545950.9 2234831.5 -6.8112674e-06 -6.9206286e-06 1218.3053
+ 31 21.730089 21.727916 21.730089 0 0 3.0422124e-06 2234831.5 1545950.9 2234831.5 -6.5914369e-06 -8.6480249e-06 1461.9664
+ 32 21.730089 21.727916 21.730089 0 0 3.4768142e-06 2234831.5 1545950.9 2234831.5 -6.62009e-06 -8.621625e-06 1705.6275
+ 33 21.730089 21.727916 21.730089 0 0 3.911416e-06 2234831.5 1545950.9 2234831.5 -6.712501e-06 -8.7315457e-06 1949.2885
+ 34 21.730089 21.727916 21.730089 0 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 -6.3958831e-06 -7.1670331e-06 2192.9496
+Loop time of 0.0681064 on 4 procs for 10 steps with 512 atoms
+
+Performance: 2.537 ns/day, 9.459 hours/ns, 146.829 timesteps/s
+99.1% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.041511 | 0.051664 | 0.065403 | 3.8 | 75.86
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.00090647 | 0.014658 | 0.024812 | 7.1 | 21.52
+Output | 0.0016921 | 0.0017017 | 0.001713 | 0.0 | 2.50
+Modify | 2.2173e-05 | 2.7835e-05 | 3.0994e-05 | 0.1 | 0.04
+Other | | 5.496e-05 | | | 0.08
+
+Nlocal: 128 ave 164 max 100 min
+Histogram: 1 0 0 2 0 0 0 0 0 1
+Nghost: 3073 ave 3101 max 3037 min
+Histogram: 1 0 0 0 0 0 2 0 0 1
+Neighs: 0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs: 53248 ave 68224 max 41600 min
+Histogram: 1 0 0 2 0 0 0 0 0 1
+
+Total # of neighbors = 212992
+Ave neighs/atom = 416
+Neighbor list builds = 0
+Dangerous builds not checked
+
+## strain xy, measure s_xy: calculates C66
+
+fix 2 all deform 1 xy erate 0.0001 remap x
+compute perfxy all stress/atom NULL pair
+compute fxy all reduce sum c_perfxy[1] c_perfxy[2] c_perfxy[3] c_perfxy[4] c_perfxy[5] c_perfxy[6]
+thermo_style custom step lx ly lz xy xz yz c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6]
+run 10
+Memory usage per processor = 8.91262 Mbytes
+Step Lx Ly Lz Xy Xz Yz fxy[1] fxy[2] fxy[3] fxy[4] fxy[5] fxy[6]
+ 34 21.730089 21.727916 21.730089 0 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 -6.1581426e-06 -1.1350015e-05 2436.6106
+ 35 21.730089 21.727916 21.730089 4.3455832e-07 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 -6.7014652e-06 -1.1032048e-05 2436.6106
+ 36 21.730089 21.727916 21.730089 8.6911663e-07 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 243.64726 -0.00014128194 2436.6106
+ 37 21.730089 21.727916 21.730089 1.3036749e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 487.29457 -0.00027206674 2436.6106
+ 38 21.730089 21.727916 21.730089 1.7382333e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 730.94189 -0.00040462289 2436.6106
+ 39 21.730089 21.727916 21.730089 2.1727916e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 974.58915 -0.00053614117 2436.6106
+ 40 21.730089 21.727916 21.730089 2.6073499e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 1218.2364 -0.00066911336 2436.6106
+ 41 21.730089 21.727916 21.730089 3.0419082e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 1461.8837 -0.00080012128 2436.6106
+ 42 21.730089 21.727916 21.730089 3.4764665e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 1705.531 -0.00093156087 2436.6106
+ 43 21.730089 21.727916 21.730089 3.9110248e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 1949.1783 -0.0010618138 2436.6106
+ 44 21.730089 21.727916 21.730089 4.3455832e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 2192.8256 -0.0011926577 2436.6106
+Loop time of 0.0681901 on 4 procs for 10 steps with 512 atoms
+
+Performance: 2.534 ns/day, 9.471 hours/ns, 146.649 timesteps/s
+100.1% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.041675 | 0.051819 | 0.065549 | 3.8 | 75.99
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.00088024 | 0.014621 | 0.024764 | 7.2 | 21.44
+Output | 0.0016496 | 0.0016653 | 0.0016737 | 0.0 | 2.44
+Modify | 2.0027e-05 | 2.4855e-05 | 3.0756e-05 | 0.1 | 0.04
+Other | | 6.02e-05 | | | 0.09
+
+Nlocal: 128 ave 164 max 100 min
+Histogram: 1 0 0 2 0 0 0 0 0 1
+Nghost: 3073 ave 3101 max 3037 min
+Histogram: 1 0 0 0 0 0 2 0 0 1
+Neighs: 0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs: 53248 ave 68224 max 41600 min
+Histogram: 1 0 0 2 0 0 0 0 0 1
+
+Total # of neighbors = 212992
+Ave neighs/atom = 416
+Neighbor list builds = 0
+Dangerous builds not checked
+Total wall time: 0:00:00
diff --git a/examples/comb/log.15Feb16.comb.Si.g++.1 b/examples/comb/log.15Feb16.comb.Si.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..8bafc2cd99ccff7148537cc0672f36826ad20c69
--- /dev/null
+++ b/examples/comb/log.15Feb16.comb.Si.g++.1
@@ -0,0 +1,92 @@
+LAMMPS (15 Feb 2016)
+# Pure Si crystal, structure created by LAMMPS, qeq off
+
+units metal
+atom_style charge
+dimension 3
+boundary p p p
+
+lattice diamond 5.43
+Lattice spacing in x,y,z = 5.43 5.43 5.43
+region box block 0 4 0 4 0 4
+create_box 1 box
+Created orthogonal box = (0 0 0) to (21.72 21.72 21.72)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 512 atoms
+mass 1 29.0
+
+pair_style comb
+pair_coeff * * ffield.comb Si
+Reading potential file ffield.comb with DATE: 2011-02-22
+
+neighbor 0.5 bin
+neigh_modify every 1 delay 1 check yes
+
+fix 1 all nve
+timestep 0.00020
+
+thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz
+thermo_modify norm yes
+velocity all create 10.1 2398378
+thermo 1
+
+#dump 1 all cfg 10 *.cfg id type xs ys zs q vx vy vz fx fy fz
+#dump_modify 1 append yes element Si
+
+#dump 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 2 element Si
+
+#dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 2 element Si
+
+run 10
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 1 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 12.5
+ ghost atom cutoff = 12.5
+ binsize = 6.25 -> bins = 4 4 4
+Memory usage per processor = 6.47955 Mbytes
+Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz
+ 0 10.1 -4.6284152 -4.6297182 -4.6297182 0 1140.7851 10246.592 21.72 21.72 21.72 0
+ 1 10.097843 -4.6284152 -4.6297179 -4.6297179 0 1140.8131 10246.592 21.72 21.72 21.72 0
+ 2 10.091376 -4.6284152 -4.6297171 -4.6297171 0 1140.8972 10246.592 21.72 21.72 21.72 0
+ 3 10.080606 -4.6284152 -4.6297157 -4.6297157 0 1141.0373 10246.592 21.72 21.72 21.72 0
+ 4 10.065546 -4.6284152 -4.6297137 -4.6297137 0 1141.233 10246.592 21.72 21.72 21.72 0
+ 5 10.046214 -4.6284152 -4.6297113 -4.6297113 0 1141.4842 10246.592 21.72 21.72 21.72 0
+ 6 10.022634 -4.6284152 -4.6297082 -4.6297082 0 1141.7906 10246.592 21.72 21.72 21.72 0
+ 7 9.9948348 -4.6284152 -4.6297046 -4.6297046 0 1142.1515 10246.592 21.72 21.72 21.72 0
+ 8 9.9628496 -4.6284152 -4.6297005 -4.6297005 0 1142.5666 10246.592 21.72 21.72 21.72 0
+ 9 9.9267173 -4.6284152 -4.6296958 -4.6296958 0 1143.0353 10246.592 21.72 21.72 21.72 0
+ 10 9.8864817 -4.6284152 -4.6296906 -4.6296906 0 1143.5568 10246.592 21.72 21.72 21.72 0
+Loop time of 0.193527 on 1 procs for 10 steps with 512 atoms
+
+Performance: 0.893 ns/day, 26.879 hours/ns, 51.672 timesteps/s
+100.2% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.19296 | 0.19296 | 0.19296 | 0.0 | 99.71
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.00025725 | 0.00025725 | 0.00025725 | 0.0 | 0.13
+Output | 0.00012445 | 0.00012445 | 0.00012445 | 0.0 | 0.06
+Modify | 8.3208e-05 | 8.3208e-05 | 8.3208e-05 | 0.0 | 0.04
+Other | | 0.000104 | | | 0.05
+
+Nlocal: 512 ave 512 max 512 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 4861 ave 4861 max 4861 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs: 212992 ave 212992 max 212992 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 212992
+Ave neighs/atom = 416
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/comb/log.15Feb16.comb.Si.g++.4 b/examples/comb/log.15Feb16.comb.Si.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..2ef020552d9156c1b68b1af8a5e4434bd9d476a3
--- /dev/null
+++ b/examples/comb/log.15Feb16.comb.Si.g++.4
@@ -0,0 +1,92 @@
+LAMMPS (15 Feb 2016)
+# Pure Si crystal, structure created by LAMMPS, qeq off
+
+units metal
+atom_style charge
+dimension 3
+boundary p p p
+
+lattice diamond 5.43
+Lattice spacing in x,y,z = 5.43 5.43 5.43
+region box block 0 4 0 4 0 4
+create_box 1 box
+Created orthogonal box = (0 0 0) to (21.72 21.72 21.72)
+ 1 by 2 by 2 MPI processor grid
+create_atoms 1 box
+Created 512 atoms
+mass 1 29.0
+
+pair_style comb
+pair_coeff * * ffield.comb Si
+Reading potential file ffield.comb with DATE: 2011-02-22
+
+neighbor 0.5 bin
+neigh_modify every 1 delay 1 check yes
+
+fix 1 all nve
+timestep 0.00020
+
+thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz
+thermo_modify norm yes
+velocity all create 10.1 2398378
+thermo 1
+
+#dump 1 all cfg 10 *.cfg id type xs ys zs q vx vy vz fx fy fz
+#dump_modify 1 append yes element Si
+
+#dump 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 2 element Si
+
+#dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 2 element Si
+
+run 10
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 1 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 12.5
+ ghost atom cutoff = 12.5
+ binsize = 6.25 -> bins = 4 4 4
+Memory usage per processor = 6.39352 Mbytes
+Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz
+ 0 10.1 -4.6284152 -4.6297182 -4.6297182 0 1140.7851 10246.592 21.72 21.72 21.72 0
+ 1 10.097841 -4.6284152 -4.6297179 -4.6297179 0 1140.8134 10246.592 21.72 21.72 21.72 0
+ 2 10.091367 -4.6284152 -4.6297171 -4.6297171 0 1140.8983 10246.592 21.72 21.72 21.72 0
+ 3 10.080586 -4.6284152 -4.6297157 -4.6297157 0 1141.0397 10246.592 21.72 21.72 21.72 0
+ 4 10.065511 -4.6284152 -4.6297137 -4.6297137 0 1141.2373 10246.592 21.72 21.72 21.72 0
+ 5 10.046161 -4.6284152 -4.6297112 -4.6297112 0 1141.4909 10246.592 21.72 21.72 21.72 0
+ 6 10.02256 -4.6284152 -4.6297082 -4.6297082 0 1141.8001 10246.592 21.72 21.72 21.72 0
+ 7 9.9947353 -4.6284152 -4.6297046 -4.6297046 0 1142.1645 10246.592 21.72 21.72 21.72 0
+ 8 9.9627224 -4.6284152 -4.6297005 -4.6297005 0 1142.5835 10246.592 21.72 21.72 21.72 0
+ 9 9.9265602 -4.6284152 -4.6296958 -4.6296958 0 1143.0565 10246.592 21.72 21.72 21.72 0
+ 10 9.8862927 -4.6284152 -4.6296906 -4.6296906 0 1143.5829 10246.592 21.72 21.72 21.72 0
+Loop time of 0.0531193 on 4 procs for 10 steps with 512 atoms
+
+Performance: 3.253 ns/day, 7.378 hours/ns, 188.255 timesteps/s
+99.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.046737 | 0.048466 | 0.051893 | 1.0 | 91.24
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.00082636 | 0.0042595 | 0.0059838 | 3.2 | 8.02
+Output | 0.00026178 | 0.00027215 | 0.0002954 | 0.1 | 0.51
+Modify | 2.3842e-05 | 2.563e-05 | 2.8372e-05 | 0.0 | 0.05
+Other | | 9.644e-05 | | | 0.18
+
+Nlocal: 128 ave 128 max 128 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost: 3073 ave 3073 max 3073 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs: 53248 ave 53248 max 53248 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 212992
+Ave neighs/atom = 416
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/comb/log.15Feb16.comb3.g++.1 b/examples/comb/log.15Feb16.comb3.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..76f85b6525bcc5d3f2a6146024373dff70dbd5f5
--- /dev/null
+++ b/examples/comb/log.15Feb16.comb3.g++.1
@@ -0,0 +1,90 @@
+LAMMPS (15 Feb 2016)
+# Graphene-OH on Cu2O (110) surface
+
+units metal
+atom_style charge
+dimension 3
+boundary p p p
+
+read_data data.comb3-OHCCu
+ triclinic box = (0 0 0) to (21.3 24.6 33.8162) with tilt (0 0 0)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 682 atoms
+
+mass 1 16.0
+mass 2 63.5
+mass 3 1.00
+mass 4 12.0
+mass 5 12.0
+
+pair_style comb3 polar_off
+pair_coeff * * ffield.comb3 O Cu H C C
+Reading potential file lib.comb3 with DATE: 2014-02-01
+Reading potential file ffield.comb3 with DATE: 2014-02-01
+
+neighbor 2.0 bin
+neigh_modify every 1 delay 0 check yes
+
+#dump 1 all cfg 10 *.cfg mass type xs ys zs id type q
+#dump_modify 1 element O Cu H C C
+
+fix 1 all nve
+fix 2 all qeq/comb 10 1e-3 file fq.out
+
+timestep 0.00020
+
+thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz
+thermo_modify norm yes
+velocity all create 300.0 2398378
+thermo 10
+run 100
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 13
+ ghost atom cutoff = 13
+ binsize = 6.5 -> bins = 4 4 6
+Memory usage per processor = 4.47117 Mbytes
+Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz
+ 0 300 -4.5167776 -4.5554988 -3.9875717 -0.56792713 -19801.669 17719.012 21.3 24.6 33.8162
+ 10 467.10265 -4.5167723 -4.5770615 -4.0093169 -0.56774462 -15438.86 17719.012 21.3 24.6 33.8162
+ 20 732.82159 -4.5169309 -4.6115167 -4.0435338 -0.56798291 -12197.607 17719.012 21.3 24.6 33.8162
+ 30 906.42366 -4.517088 -4.6340807 -4.0657272 -0.56835345 -8825.2434 17719.012 21.3 24.6 33.8162
+ 40 957.57065 -4.5172533 -4.6408475 -4.0717295 -0.56911807 -12551.812 17719.012 21.3 24.6 33.8162
+ 50 920.31413 -4.517436 -4.6362215 -4.0660108 -0.57021068 -11911.093 17719.012 21.3 24.6 33.8162
+ 60 1003.2 -4.5176403 -4.647124 -4.0757679 -0.57135607 1337.5658 17719.012 21.3 24.6 33.8162
+ 70 1123.7779 -4.5178574 -4.6629041 -4.0904309 -0.57247327 7171.1488 17719.012 21.3 24.6 33.8162
+ 80 1188.3196 -4.518095 -4.6714721 -4.0978283 -0.57364387 12411.934 17719.012 21.3 24.6 33.8162
+ 90 1193.9207 -4.5183329 -4.672433 -4.0976379 -0.57479504 15405.848 17719.012 21.3 24.6 33.8162
+ 100 1197.343 -4.5185478 -4.6730896 -4.0971431 -0.57594648 17853.038 17719.012 21.3 24.6 33.8162
+Loop time of 45.764 on 1 procs for 100 steps with 682 atoms
+
+Performance: 0.038 ns/day, 635.612 hours/ns, 2.185 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 10.987 | 10.987 | 10.987 | 0.0 | 24.01
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.00317 | 0.00317 | 0.00317 | 0.0 | 0.01
+Output | 0.0001812 | 0.0001812 | 0.0001812 | 0.0 | 0.00
+Modify | 34.773 | 34.773 | 34.773 | 0.0 | 75.98
+Other | | 0.001366 | | | 0.00
+
+Nlocal: 682 ave 682 max 682 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 4154 ave 4154 max 4154 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs: 355216 ave 355216 max 355216 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 355216
+Ave neighs/atom = 520.845
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:48
diff --git a/examples/comb/log.15Feb16.comb3.g++.4 b/examples/comb/log.15Feb16.comb3.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..5f546737ec3221e68b49a96d683df31910ab4c4d
--- /dev/null
+++ b/examples/comb/log.15Feb16.comb3.g++.4
@@ -0,0 +1,90 @@
+LAMMPS (15 Feb 2016)
+# Graphene-OH on Cu2O (110) surface
+
+units metal
+atom_style charge
+dimension 3
+boundary p p p
+
+read_data data.comb3-OHCCu
+ triclinic box = (0 0 0) to (21.3 24.6 33.8162) with tilt (0 0 0)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 682 atoms
+
+mass 1 16.0
+mass 2 63.5
+mass 3 1.00
+mass 4 12.0
+mass 5 12.0
+
+pair_style comb3 polar_off
+pair_coeff * * ffield.comb3 O Cu H C C
+Reading potential file lib.comb3 with DATE: 2014-02-01
+Reading potential file ffield.comb3 with DATE: 2014-02-01
+
+neighbor 2.0 bin
+neigh_modify every 1 delay 0 check yes
+
+#dump 1 all cfg 10 *.cfg mass type xs ys zs id type q
+#dump_modify 1 element O Cu H C C
+
+fix 1 all nve
+fix 2 all qeq/comb 10 1e-3 file fq.out
+
+timestep 0.00020
+
+thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz
+thermo_modify norm yes
+velocity all create 300.0 2398378
+thermo 10
+run 100
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 13
+ ghost atom cutoff = 13
+ binsize = 6.5 -> bins = 4 4 6
+Memory usage per processor = 4.95436 Mbytes
+Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz
+ 0 300 -4.5167776 -4.5554988 -3.9875717 -0.56792713 -19801.669 17719.012 21.3 24.6 33.8162
+ 10 467.10265 -4.5167723 -4.5770615 -4.0093169 -0.56774462 -15438.86 17719.012 21.3 24.6 33.8162
+ 20 732.82159 -4.5169309 -4.6115167 -4.0435338 -0.56798291 -12197.607 17719.012 21.3 24.6 33.8162
+ 30 906.42366 -4.517088 -4.6340807 -4.0657272 -0.56835345 -8825.2434 17719.012 21.3 24.6 33.8162
+ 40 957.57065 -4.5172533 -4.6408475 -4.0717295 -0.56911807 -12551.812 17719.012 21.3 24.6 33.8162
+ 50 920.31413 -4.517436 -4.6362215 -4.0660108 -0.57021068 -11911.093 17719.012 21.3 24.6 33.8162
+ 60 1003.2 -4.5176403 -4.647124 -4.0757679 -0.57135607 1337.5658 17719.012 21.3 24.6 33.8162
+ 70 1123.7779 -4.5178574 -4.6629041 -4.0904309 -0.57247327 7171.1488 17719.012 21.3 24.6 33.8162
+ 80 1188.3196 -4.518095 -4.6714721 -4.0978283 -0.57364387 12411.934 17719.012 21.3 24.6 33.8162
+ 90 1193.9207 -4.5183329 -4.672433 -4.0976379 -0.57479504 15405.848 17719.012 21.3 24.6 33.8162
+ 100 1197.343 -4.5185478 -4.6730896 -4.0971431 -0.57594648 17853.038 17719.012 21.3 24.6 33.8162
+Loop time of 20.7745 on 4 procs for 100 steps with 682 atoms
+
+Performance: 0.083 ns/day, 288.534 hours/ns, 4.814 timesteps/s
+98.9% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 2.2393 | 3.5206 | 4.856 | 67.7 | 16.95
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.024316 | 1.3586 | 2.6388 | 108.8 | 6.54
+Output | 0.00034308 | 0.00036204 | 0.00038791 | 0.1 | 0.00
+Modify | 15.892 | 15.892 | 15.892 | 0.0 | 76.50
+Other | | 0.002505 | | | 0.01
+
+Nlocal: 170.5 ave 245 max 100 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost: 2872 ave 3583 max 2157 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs: 0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs: 88804 ave 131817 max 47999 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 355216
+Ave neighs/atom = 520.845
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:21
diff --git a/examples/crack/log.15Feb16.crack.g++.1 b/examples/crack/log.15Feb16.crack.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..242d690baf47f9f9736a134ee214f3aeb9dd0792
--- /dev/null
+++ b/examples/crack/log.15Feb16.crack.g++.1
@@ -0,0 +1,153 @@
+LAMMPS (15 Feb 2016)
+# 2d LJ crack simulation
+
+dimension 2
+boundary s s p
+
+atom_style atomic
+neighbor 0.3 bin
+neigh_modify delay 5
+
+# create geometry
+
+lattice hex 0.93
+Lattice spacing in x,y,z = 1.11428 1.92998 1.11428
+region box block 0 100 0 40 -0.25 0.25
+create_box 5 box
+Created orthogonal box = (0 0 -0.278569) to (111.428 77.1994 0.278569)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 8141 atoms
+
+mass 1 1.0
+mass 2 1.0
+mass 3 1.0
+mass 4 1.0
+mass 5 1.0
+
+# LJ potentials
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0 2.5
+
+# define groups
+
+region 1 block INF INF INF 1.25 INF INF
+group lower region 1
+302 atoms in group lower
+region 2 block INF INF 38.75 INF INF INF
+group upper region 2
+302 atoms in group upper
+group boundary union lower upper
+604 atoms in group boundary
+group mobile subtract all boundary
+7537 atoms in group mobile
+
+region leftupper block INF 20 20 INF INF INF
+region leftlower block INF 20 INF 20 INF INF
+group leftupper region leftupper
+841 atoms in group leftupper
+group leftlower region leftlower
+841 atoms in group leftlower
+
+set group leftupper type 2
+ 841 settings made for type
+set group leftlower type 3
+ 841 settings made for type
+set group lower type 4
+ 302 settings made for type
+set group upper type 5
+ 302 settings made for type
+
+# initial velocities
+
+compute new mobile temp
+velocity mobile create 0.01 887723 temp new
+velocity upper set 0.0 0.3 0.0
+velocity mobile ramp vy 0.0 0.3 y 1.25 38.75 sum yes
+
+# fixes
+
+fix 1 all nve
+fix 2 boundary setforce NULL 0.0 0.0
+
+# run
+
+timestep 0.003
+thermo 200
+thermo_modify temp new
+WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:445)
+
+neigh_modify exclude type 2 3
+
+#dump 1 all atom 500 dump.crack
+
+#dump 2 all image 250 image.*.jpg type type # zoom 1.6 adiam 1.5
+#dump_modify 2 pad 4
+
+#dump 3 all movie 250 movie.mpg type type # zoom 1.6 adiam 1.5
+#dump_modify 3 pad 4
+
+run 5000
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 5 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4 -> bins = 80 56 1
+Memory usage per processor = 2.48017 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 0.065651733 -3.2595015 0 -3.1987287 -0.036239172 8605.5917
+ 200 0.060086376 -3.2531936 0 -3.1975725 -0.23125026 8638.8101
+ 400 0.060533553 -3.2509973 0 -3.1949623 -0.4305406 8679.2464
+ 600 0.06082965 -3.2466949 0 -3.1903858 -0.6028531 8716.7569
+ 800 0.061677224 -3.2413215 0 -3.1842278 -0.7482749 8756.226
+ 1000 0.062383731 -3.2349273 0 -3.1771796 -0.87425132 8793.1116
+ 1200 0.063709246 -3.2276094 0 -3.1686347 -0.98020161 8828.8863
+ 1400 0.065404552 -3.2196608 0 -3.1591168 -1.0695384 8866.4893
+ 1600 0.067579602 -3.2110378 0 -3.1484804 -1.1456387 8900.6772
+ 1800 0.069324241 -3.2018536 0 -3.1376812 -1.2020999 8933.017
+ 2000 0.071014927 -3.1921108 0 -3.1263733 -1.2430105 8963.9853
+ 2200 0.072992881 -3.1818701 0 -3.1143017 -1.2701297 9004.4136
+ 2400 0.075000723 -3.1712313 0 -3.1018043 -1.2830866 9034.9991
+ 2600 0.076843477 -3.1601004 0 -3.0889675 -1.27924 9072.1325
+ 2800 0.078671706 -3.1487747 0 -3.0759495 -1.2659604 9103.9526
+ 3000 0.080713586 -3.1373277 0 -3.0626123 -1.2440673 9134.552
+ 3200 0.08309469 -3.1260242 0 -3.0491047 -1.214547 9169.0003
+ 3400 0.085424766 -3.1146623 0 -3.0355859 -1.1839326 9206.909
+ 3600 0.087396485 -3.1029493 0 -3.0220477 -1.143412 9233.783
+ 3800 0.089007987 -3.090822 0 -3.0084286 -1.1000791 9259.0348
+ 4000 0.089813071 -3.0794078 0 -2.9962692 -1.062847 9281.82
+ 4200 0.08584753 -3.0668559 0 -2.9873882 -1.037972 9308.8113
+ 4400 0.086197517 -3.0559678 0 -2.9761761 -1.028843 9328.9666
+ 4600 0.086766447 -3.0437627 0 -2.9634443 -1.0208785 9361.9925
+ 4800 0.088195149 -3.0328502 0 -2.9512093 -1.0272063 9395.6122
+ 5000 0.089415266 -3.0228825 0 -2.9401122 -1.0215336 9436.1637
+Loop time of 7.03796 on 1 procs for 5000 steps with 8141 atoms
+
+Performance: 184144.324 tau/day, 710.433 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 5.9472 | 5.9472 | 5.9472 | 0.0 | 84.50
+Neigh | 0.36178 | 0.36178 | 0.36178 | 0.0 | 5.14
+Comm | 0.0042093 | 0.0042093 | 0.0042093 | 0.0 | 0.06
+Output | 0.00080466 | 0.00080466 | 0.00080466 | 0.0 | 0.01
+Modify | 0.55 | 0.55 | 0.55 | 0.0 | 7.81
+Other | | 0.1739 | | | 2.47
+
+Nlocal: 8141 ave 8141 max 8141 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 71389 ave 71389 max 71389 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 71389
+Ave neighs/atom = 8.76907
+Neighbor list builds = 100
+Dangerous builds = 0
+Total wall time: 0:00:07
diff --git a/examples/crack/log.15Feb16.crack.g++.4 b/examples/crack/log.15Feb16.crack.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..eaae19666a92fef387079316f56ccf17aa74d8e5
--- /dev/null
+++ b/examples/crack/log.15Feb16.crack.g++.4
@@ -0,0 +1,153 @@
+LAMMPS (15 Feb 2016)
+# 2d LJ crack simulation
+
+dimension 2
+boundary s s p
+
+atom_style atomic
+neighbor 0.3 bin
+neigh_modify delay 5
+
+# create geometry
+
+lattice hex 0.93
+Lattice spacing in x,y,z = 1.11428 1.92998 1.11428
+region box block 0 100 0 40 -0.25 0.25
+create_box 5 box
+Created orthogonal box = (0 0 -0.278569) to (111.428 77.1994 0.278569)
+ 2 by 2 by 1 MPI processor grid
+create_atoms 1 box
+Created 8141 atoms
+
+mass 1 1.0
+mass 2 1.0
+mass 3 1.0
+mass 4 1.0
+mass 5 1.0
+
+# LJ potentials
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0 2.5
+
+# define groups
+
+region 1 block INF INF INF 1.25 INF INF
+group lower region 1
+302 atoms in group lower
+region 2 block INF INF 38.75 INF INF INF
+group upper region 2
+302 atoms in group upper
+group boundary union lower upper
+604 atoms in group boundary
+group mobile subtract all boundary
+7537 atoms in group mobile
+
+region leftupper block INF 20 20 INF INF INF
+region leftlower block INF 20 INF 20 INF INF
+group leftupper region leftupper
+841 atoms in group leftupper
+group leftlower region leftlower
+841 atoms in group leftlower
+
+set group leftupper type 2
+ 841 settings made for type
+set group leftlower type 3
+ 841 settings made for type
+set group lower type 4
+ 302 settings made for type
+set group upper type 5
+ 302 settings made for type
+
+# initial velocities
+
+compute new mobile temp
+velocity mobile create 0.01 887723 temp new
+velocity upper set 0.0 0.3 0.0
+velocity mobile ramp vy 0.0 0.3 y 1.25 38.75 sum yes
+
+# fixes
+
+fix 1 all nve
+fix 2 boundary setforce NULL 0.0 0.0
+
+# run
+
+timestep 0.003
+thermo 200
+thermo_modify temp new
+WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:445)
+
+neigh_modify exclude type 2 3
+
+#dump 1 all atom 500 dump.crack
+
+#dump 2 all image 250 image.*.jpg type type # zoom 1.6 adiam 1.5
+#dump_modify 2 pad 4
+
+#dump 3 all movie 250 movie.mpg type type # zoom 1.6 adiam 1.5
+#dump_modify 3 pad 4
+
+run 5000
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 5 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4 -> bins = 80 56 1
+Memory usage per processor = 2.48163 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 0.065993465 -3.2595015 0 -3.1984123 -0.035939913 8605.5917
+ 200 0.060035253 -3.2531886 0 -3.1976149 -0.22757684 8638.5331
+ 400 0.06054278 -3.2510706 0 -3.1950271 -0.42811733 8677.8288
+ 600 0.060576995 -3.246816 0 -3.1907408 -0.60017647 8717.6131
+ 800 0.060802753 -3.2413477 0 -3.1850635 -0.74499308 8756.4512
+ 1000 0.061812114 -3.2349942 0 -3.1777756 -0.87130079 8796.9575
+ 1200 0.06317147 -3.2277552 0 -3.1692783 -0.98010628 8823.1488
+ 1400 0.065125405 -3.2198031 0 -3.1595175 -1.0690179 8858.8358
+ 1600 0.06725411 -3.2111272 0 -3.148871 -1.1440993 8892.6607
+ 1800 0.069389572 -3.2019689 0 -3.137736 -1.199078 8933.7591
+ 2000 0.071276448 -3.1921621 0 -3.1261826 -1.239553 8969.0463
+ 2200 0.073243486 -3.1818809 0 -3.1140805 -1.264839 8997.6559
+ 2400 0.075063494 -3.1711703 0 -3.1016851 -1.2772278 9038.4932
+ 2600 0.076789207 -3.1600658 0 -3.0889832 -1.2754953 9073.4997
+ 2800 0.07875979 -3.1487143 0 -3.0758075 -1.2637926 9106.2245
+ 3000 0.080591853 -3.1372361 0 -3.0626334 -1.2388824 9142.7862
+ 3200 0.08227693 -3.125423 0 -3.0492605 -1.2055283 9169.4322
+ 3400 0.084289444 -3.1136554 0 -3.03563 -1.1672422 9204.8205
+ 3600 0.086720297 -3.1021183 0 -3.0218427 -1.126381 9233.2656
+ 3800 0.089264018 -3.0909262 0 -3.0082959 -1.0899774 9265.4143
+ 4000 0.091377688 -3.0795096 0 -2.9949227 -1.0580229 9297.6799
+ 4200 0.092665135 -3.0678736 0 -2.9820949 -1.0390124 9331.6135
+ 4400 0.09055434 -3.0560482 0 -2.9722234 -1.0323741 9362.2075
+ 4600 0.088763719 -3.0446018 0 -2.9624346 -1.027693 9391.6949
+ 4800 0.089467982 -3.0337452 0 -2.950926 -1.0232092 9427.4155
+ 5000 0.089910902 -3.0237571 0 -2.9405279 -1.0174796 9452.031
+Loop time of 1.91894 on 4 procs for 5000 steps with 8141 atoms
+
+Performance: 675373.090 tau/day, 2605.606 timesteps/s
+99.7% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 1.4786 | 1.5057 | 1.5343 | 2.0 | 78.47
+Neigh | 0.094529 | 0.099406 | 0.1061 | 1.4 | 5.18
+Comm | 0.071501 | 0.10352 | 0.13214 | 8.6 | 5.39
+Output | 0.00072479 | 0.00076115 | 0.00084186 | 0.2 | 0.04
+Modify | 0.13936 | 0.14058 | 0.14196 | 0.2 | 7.33
+Other | | 0.06895 | | | 3.59
+
+Nlocal: 2035.25 ave 2064 max 2015 min
+Histogram: 1 1 0 0 0 1 0 0 0 1
+Nghost: 198 ave 248 max 150 min
+Histogram: 1 0 1 0 0 0 0 1 0 1
+Neighs: 17850 ave 18247 max 17601 min
+Histogram: 1 1 0 0 1 0 0 0 0 1
+
+Total # of neighbors = 71400
+Ave neighs/atom = 8.77042
+Neighbor list builds = 106
+Dangerous builds = 0
+Total wall time: 0:00:01
diff --git a/examples/deposit/log.15Feb16.deposit.atom.g++.1 b/examples/deposit/log.15Feb16.deposit.atom.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..d9c3667bd96a0999e47a61015fca50b9d40f93b3
--- /dev/null
+++ b/examples/deposit/log.15Feb16.deposit.atom.g++.1
@@ -0,0 +1,193 @@
+LAMMPS (15 Feb 2016)
+# sample surface deposition script for atoms
+
+units lj
+atom_style atomic
+boundary p p f
+
+lattice fcc 1.0
+Lattice spacing in x,y,z = 1.5874 1.5874 1.5874
+region box block 0 5 0 5 0 10
+create_box 2 box
+Created orthogonal box = (0 0 0) to (7.93701 7.93701 15.874)
+ 1 by 1 by 1 MPI processor grid
+
+region substrate block INF INF INF INF INF 3
+create_atoms 1 region substrate
+Created 350 atoms
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0
+pair_coeff 1 2 1.0 1.0 5.0
+mass * 1.0
+
+neigh_modify delay 0
+
+group addatoms type 2
+0 atoms in group addatoms
+region mobile block 0 5 0 5 2 INF
+group mobile region mobile
+150 atoms in group mobile
+
+compute add addatoms temp
+compute_modify add dynamic yes extra 0
+
+fix 1 addatoms nve
+fix 2 mobile langevin 1.0 1.0 0.1 587283
+fix 3 mobile nve
+
+region slab block 0 5 0 5 8 9
+fix 4 addatoms deposit 100 2 100 12345 region slab near 1.0 vz -1.0 -1.0
+fix 5 addatoms wall/reflect zhi EDGE
+
+thermo_style custom step atoms temp epair etotal press
+thermo 100
+thermo_modify temp add
+WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:445)
+
+#dump 1 all atom 50 dump.deposit.atom
+
+#dump 2 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30
+#dump_modify 2 pad 5
+
+#dump 3 all movie 50 movie.mpg type type # axes yes 0.8 0.02 view 80 -30
+#dump_modify 3 pad 5
+
+run 10000
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 5.3
+ ghost atom cutoff = 5.3
+ binsize = 2.65 -> bins = 3 3 6
+Memory usage per processor = 2.54053 Mbytes
+Step Atoms Temp E_pair TotEng Press
+ 0 350 0 -6.9215833 -6.9215833 -1.0052629
+ 100 351 0.83994737 -6.3459678 -6.3423783 -0.12047746
+ 200 352 0.83994737 -6.2377119 -6.2305533 -0.3420432
+ 300 353 0.84063802 -6.102615 -6.0918986 -0.40610132
+ 400 354 0.84248131 -6.0284461 -6.0141667 -0.46041042
+ 500 355 0.84689832 -5.9201486 -5.9022564 -0.44565465
+ 600 356 0.86694405 -5.8676653 -5.8457482 -0.45310439
+ 700 357 0.93585062 -5.8080247 -5.7804997 -0.4235135
+ 800 358 0.87721962 -5.7667317 -5.7373277 -0.47514081
+ 900 359 0.98586832 -5.7397849 -5.7027118 -0.53506606
+ 1000 360 1.1977372 -5.7043822 -5.6544765 -0.5143915
+ 1100 361 0.86840339 -5.6974093 -5.6577177 -0.57133639
+ 1200 362 0.91410157 -5.6449104 -5.5994579 -0.54863872
+ 1300 363 1.0317704 -5.6108925 -5.5554668 -0.63480165
+ 1400 364 0.78937966 -5.5995247 -5.5539836 -0.54633211
+ 1500 365 1.0022364 -5.592367 -5.5305854 -0.61542058
+ 1600 366 1.36861 -5.5602006 -5.4704557 -0.5557092
+ 1700 367 1.2584928 -5.6125569 -5.5251139 -0.54474262
+ 1800 368 1.2395052 -5.5575635 -5.4666216 -0.39432632
+ 1900 369 1.4424114 -5.5511809 -5.4397751 -0.39219555
+ 2000 370 1.0355115 -5.5657056 -5.4817452 -0.42684751
+ 2100 371 1.0710232 -5.621664 -5.5307281 -0.60685079
+ 2200 372 1.1723348 -5.5425772 -5.4385798 -0.53815496
+ 2300 373 1.0854557 -5.6087637 -5.5083664 -0.6673737
+ 2400 374 1.1021474 -5.5084817 -5.4023926 -0.52097006
+ 2500 375 1.2269861 -5.4265984 -5.3038998 -0.49657196
+ 2600 376 1.0399561 -5.476211 -5.3683432 -0.62204748
+ 2700 377 1.0944051 -5.4078459 -5.2902772 -0.63977962
+ 2800 378 1.0323162 -5.3957488 -5.281047 -0.62614071
+ 2900 379 1.1065509 -5.3744068 -5.2474017 -0.57270098
+ 3000 380 1.0280773 -5.3681364 -5.2463904 -0.66444652
+ 3100 381 1.04368 -5.3317133 -5.2043351 -0.65414012
+ 3200 382 1.0449176 -5.3088894 -5.1775909 -0.63418281
+ 3300 383 1.1102316 -5.2604462 -5.1169568 -0.57913921
+ 3400 384 1.2757372 -5.2904271 -5.1209933 -0.56059979
+ 3500 385 1.0652825 -5.2267633 -5.0814975 -0.54269026
+ 3600 386 1.0229877 -5.2277887 -5.0846764 -0.61796376
+ 3700 387 0.96408893 -5.1769745 -5.0387137 -0.55113976
+ 3800 388 1.0505509 -5.2197338 -5.0654003 -0.70804854
+ 3900 389 0.95266837 -5.1605736 -5.017306 -0.52702995
+ 4000 390 1.0413134 -5.2352309 -5.0750288 -0.66067611
+ 4100 391 1.1486876 -5.2288717 -5.0481958 -0.65810366
+ 4200 392 1.042156 -5.2716813 -5.1041919 -0.66967821
+ 4300 393 0.9698966 -5.197189 -5.0380075 -0.46525386
+ 4400 394 0.77874089 -5.257629 -5.12718 -0.67739426
+ 4500 395 1.0157317 -5.2445238 -5.0709494 -0.5922696
+ 4600 396 1.1447586 -5.2710072 -5.0715417 -0.62651602
+ 4700 397 1.1902582 -5.311166 -5.0997978 -0.7459111
+ 4800 398 0.95725223 -5.2619858 -5.0888146 -0.49253005
+ 4900 399 1.0409188 -5.271542 -5.0797938 -0.56590831
+ 5000 400 1.0870091 -5.2619328 -5.0581186 -0.61273172
+ 5100 401 0.90909459 -5.3465255 -5.1730948 -0.61196826
+ 5200 402 0.86456113 -5.2535951 -5.0858445 -0.47565663
+ 5300 403 0.92212118 -5.27055 -5.0886427 -0.55555966
+ 5400 404 0.96914771 -5.2702613 -5.075952 -0.58082428
+ 5500 405 0.96828577 -5.263648 -5.0664046 -0.59818023
+ 5600 406 1.0567855 -5.2988668 -5.0802215 -0.76787404
+ 5700 407 1.0085537 -5.2053833 -4.9935127 -0.55232589
+ 5800 408 0.86382168 -5.2038339 -5.0196367 -0.58471077
+ 5900 409 0.98477929 -5.1862354 -4.9731475 -0.54570637
+ 6000 410 1.0777582 -5.2410631 -5.004482 -0.6711063
+ 6100 411 1.1113596 -5.1775001 -4.9300806 -0.54007427
+ 6200 412 0.86878402 -5.1939794 -4.9978704 -0.64766373
+ 6300 413 1.0174495 -5.2156346 -4.9828284 -0.60249161
+ 6400 414 1.1184824 -5.2250149 -4.9656567 -0.64875897
+ 6500 415 1.1607873 -5.2674286 -4.9947135 -0.65956525
+ 6600 416 0.98987615 -5.2384031 -5.0028316 -0.66246801
+ 6700 417 0.86291514 -5.2362314 -5.0282627 -0.56707491
+ 6800 418 0.97203041 -5.2323576 -4.9951636 -0.54330037
+ 6900 419 0.92972764 -5.2416508 -5.0119926 -0.58029478
+ 7000 420 1.1472637 -5.3052417 -5.0184258 -0.64366532
+ 7100 421 0.9275385 -5.3077824 -5.0731438 -0.54374736
+ 7200 422 0.91492781 -5.3012606 -5.0671084 -0.55376032
+ 7300 423 0.85621578 -5.3016071 -5.0799626 -0.56221777
+ 7400 424 0.94571335 -5.2212917 -4.9737111 -0.52202896
+ 7500 425 1.0819864 -5.2109452 -4.924537 -0.47511017
+ 7600 426 1.1449289 -5.2138905 -4.9075011 -0.62518982
+ 7700 427 0.98061711 -5.2129268 -4.9476779 -0.56003723
+ 7800 428 1.0450011 -5.1652647 -4.8795985 -0.51780393
+ 7900 429 0.98731276 -5.1520883 -4.879369 -0.46982802
+ 8000 430 1.058201 -5.2605391 -4.9652272 -0.69798004
+ 8100 431 1.1031976 -5.2428971 -4.9319029 -0.64564967
+ 8200 432 0.99653694 -5.2790505 -4.9953143 -0.70353076
+ 8300 433 1.2188348 -5.2664086 -4.9159584 -0.56779776
+ 8400 434 1.0610032 -5.2291848 -4.9211516 -0.44040649
+ 8500 435 0.88475193 -5.2938308 -5.034507 -0.70250793
+ 8600 436 0.98427323 -5.2350748 -4.9438564 -0.54824635
+ 8700 437 0.99048279 -5.2379591 -4.9421742 -0.68060327
+ 8800 438 0.92407001 -5.1922203 -4.9137335 -0.67045436
+ 8900 439 0.99630902 -5.1772321 -4.8742543 -0.66221601
+ 9000 440 0.95766319 -5.1605694 -4.8667409 -0.68216304
+ 9100 441 1.0231065 -5.1295203 -4.8128445 -0.52553274
+ 9200 442 0.87783667 -5.1084284 -4.8343527 -0.54144063
+ 9300 443 0.93581944 -5.1737089 -4.8790208 -0.68780812
+ 9400 444 0.99373921 -5.1548474 -4.839268 -0.57996189
+ 9500 445 0.95187515 -5.1408039 -4.8359899 -0.56491542
+ 9600 446 0.91625338 -5.1555381 -4.8597074 -0.62931435
+ 9700 447 0.9526195 -5.1025432 -4.7924624 -0.51046895
+ 9800 448 0.97167962 -5.185173 -4.8663406 -0.56989109
+ 9900 449 1.0038671 -5.1540302 -4.8220162 -0.56356384
+ 10000 450 0.95642062 -5.2046982 -4.8858913 -0.70500643
+Loop time of 5.66464 on 1 procs for 10000 steps with 450 atoms
+
+Performance: 762626.084 tau/day, 1765.338 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 3.2197 | 3.2197 | 3.2197 | 0.0 | 56.84
+Neigh | 2.1683 | 2.1683 | 2.1683 | 0.0 | 38.28
+Comm | 0.11987 | 0.11987 | 0.11987 | 0.0 | 2.12
+Output | 0.00085187 | 0.00085187 | 0.00085187 | 0.0 | 0.02
+Modify | 0.11944 | 0.11944 | 0.11944 | 0.0 | 2.11
+Other | | 0.03653 | | | 0.64
+
+Nlocal: 450 ave 450 max 450 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1973 ave 1973 max 1973 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 29176 ave 29176 max 29176 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 29176
+Ave neighs/atom = 64.8356
+Neighbor list builds = 1143
+Dangerous builds = 0
+Total wall time: 0:00:05
diff --git a/examples/deposit/log.15Feb16.deposit.atom.g++.4 b/examples/deposit/log.15Feb16.deposit.atom.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..9021c55effeea67aed467b1d5acae940d6a04b48
--- /dev/null
+++ b/examples/deposit/log.15Feb16.deposit.atom.g++.4
@@ -0,0 +1,193 @@
+LAMMPS (15 Feb 2016)
+# sample surface deposition script for atoms
+
+units lj
+atom_style atomic
+boundary p p f
+
+lattice fcc 1.0
+Lattice spacing in x,y,z = 1.5874 1.5874 1.5874
+region box block 0 5 0 5 0 10
+create_box 2 box
+Created orthogonal box = (0 0 0) to (7.93701 7.93701 15.874)
+ 1 by 1 by 4 MPI processor grid
+
+region substrate block INF INF INF INF INF 3
+create_atoms 1 region substrate
+Created 350 atoms
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0
+pair_coeff 1 2 1.0 1.0 5.0
+mass * 1.0
+
+neigh_modify delay 0
+
+group addatoms type 2
+0 atoms in group addatoms
+region mobile block 0 5 0 5 2 INF
+group mobile region mobile
+150 atoms in group mobile
+
+compute add addatoms temp
+compute_modify add dynamic yes extra 0
+
+fix 1 addatoms nve
+fix 2 mobile langevin 1.0 1.0 0.1 587283
+fix 3 mobile nve
+
+region slab block 0 5 0 5 8 9
+fix 4 addatoms deposit 100 2 100 12345 region slab near 1.0 vz -1.0 -1.0
+fix 5 addatoms wall/reflect zhi EDGE
+
+thermo_style custom step atoms temp epair etotal press
+thermo 100
+thermo_modify temp add
+WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:445)
+
+#dump 1 all atom 50 dump.deposit.atom
+
+#dump 2 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30
+#dump_modify 2 pad 5
+
+#dump 3 all movie 50 movie.mpg type type # axes yes 0.8 0.02 view 80 -30
+#dump_modify 3 pad 5
+
+run 10000
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 5.3
+ ghost atom cutoff = 5.3
+ binsize = 2.65 -> bins = 3 3 6
+Memory usage per processor = 2.60645 Mbytes
+Step Atoms Temp E_pair TotEng Press
+ 0 350 0 -6.9215833 -6.9215833 -1.0052629
+ 100 351 0.83994737 -6.3596932 -6.3561037 -0.10696131
+ 200 352 0.83994737 -6.3044678 -6.2973092 -0.38494392
+ 300 353 0.84063802 -6.164881 -6.1541646 -0.41223901
+ 400 354 0.84248131 -6.0388811 -6.0246018 -0.31496573
+ 500 355 0.84688124 -6.0084178 -5.990526 -0.37482638
+ 600 356 0.86681079 -6.0286531 -6.0067393 -0.54868509
+ 700 357 0.93465165 -5.9564751 -5.9289854 -0.48728319
+ 800 358 0.86905333 -5.8498868 -5.8207565 -0.4146325
+ 900 359 0.90267243 -5.7844092 -5.7504647 -0.38165702
+ 1000 360 0.92357983 -5.777549 -5.7390665 -0.38381524
+ 1100 361 1.3481334 -5.7713272 -5.7097089 -0.44738093
+ 1200 362 1.15494 -5.7155857 -5.6581577 -0.38961524
+ 1300 363 0.97329529 -5.6445379 -5.5922534 -0.37655267
+ 1400 364 1.2187161 -5.6818221 -5.6115115 -0.60238965
+ 1500 365 1.2026123 -5.66813 -5.5939963 -0.56317155
+ 1600 366 1.4012284 -5.6764268 -5.584543 -0.49098723
+ 1700 367 1.3618781 -5.6121414 -5.517515 -0.47893702
+ 1800 368 0.9670811 -5.5551479 -5.4841935 -0.3409573
+ 1900 369 1.002089 -5.6037307 -5.5263336 -0.45325785
+ 2000 370 1.3599869 -5.5793818 -5.4691126 -0.44566809
+ 2100 371 1.0007793 -5.585692 -5.5007201 -0.54221497
+ 2200 372 1.1061185 -5.5172265 -5.4191031 -0.46551381
+ 2300 373 0.99747278 -5.556485 -5.4642254 -0.55670256
+ 2400 374 1.0990419 -5.5538566 -5.4480664 -0.63197307
+ 2500 375 1.1415073 -5.5118583 -5.3977075 -0.51563393
+ 2600 376 1.010645 -5.5221148 -5.4172873 -0.5495753
+ 2700 377 1.0964314 -5.4985586 -5.3807722 -0.54042329
+ 2800 378 0.93010494 -5.4391153 -5.3357703 -0.52395276
+ 2900 379 0.93021935 -5.5144863 -5.4077197 -0.69409861
+ 3000 380 1.0264349 -5.4314217 -5.3098702 -0.55798648
+ 3100 381 1.1612003 -5.4088381 -5.2671168 -0.53167304
+ 3200 382 1.087873 -5.4402561 -5.30356 -0.71158961
+ 3300 383 1.048209 -5.4309208 -5.2954473 -0.67551183
+ 3400 384 1.0275111 -5.4536819 -5.3172156 -0.73761551
+ 3500 385 1.2716758 -5.4036871 -5.2302768 -0.63612803
+ 3600 386 1.2154857 -5.4003006 -5.2302586 -0.61641823
+ 3700 387 1.3376196 -5.4279619 -5.2361328 -0.59689863
+ 3800 388 1.2523858 -5.358924 -5.1749395 -0.55321551
+ 3900 389 1.1650111 -5.333714 -5.1585131 -0.55412715
+ 4000 390 0.98352817 -5.2980477 -5.1467357 -0.68167218
+ 4100 391 1.2779827 -5.297845 -5.0968324 -0.65191886
+ 4200 392 1.0255535 -5.2295551 -5.064734 -0.4761042
+ 4300 393 1.1237891 -5.2225392 -5.0381005 -0.52734107
+ 4400 394 0.97683493 -5.2029168 -5.0392846 -0.59056934
+ 4500 395 1.0041363 -5.1999674 -5.0283744 -0.72038887
+ 4600 396 1.180431 -5.1922463 -4.9865652 -0.55948152
+ 4700 397 1.0627588 -5.2298403 -5.0411136 -0.56208516
+ 4800 398 1.1202971 -5.2121979 -5.0095311 -0.46793143
+ 4900 399 1.2006424 -5.286657 -5.0654861 -0.63042465
+ 5000 400 1.0893045 -5.2512329 -5.0469883 -0.6377186
+ 5100 401 1.1454769 -5.2580965 -5.0395704 -0.59767673
+ 5200 402 0.9467869 -5.249752 -5.0660471 -0.71059143
+ 5300 403 0.96324471 -5.1724796 -4.9824599 -0.50261414
+ 5400 404 1.1634679 -5.1969879 -4.9637184 -0.5555004
+ 5500 405 0.99830529 -5.1678627 -4.9645042 -0.59796761
+ 5600 406 1.0065294 -5.1718443 -4.9635968 -0.59208276
+ 5700 407 0.97182891 -5.2110109 -5.0068552 -0.63948837
+ 5800 408 1.1234056 -5.167964 -4.9284143 -0.53293706
+ 5900 409 1.0124687 -5.1828555 -4.9637761 -0.4922831
+ 6000 410 1.0804251 -5.2275621 -4.9903956 -0.52329411
+ 6100 411 1.0772335 -5.26665 -5.0268279 -0.56252803
+ 6200 412 1.0954219 -5.2051974 -4.9579299 -0.42238433
+ 6300 413 1.0546562 -5.3045877 -5.0632681 -0.61171278
+ 6400 414 1.0985486 -5.335815 -5.0810791 -0.67859848
+ 6500 415 1.0416817 -5.2636237 -5.0188913 -0.61917889
+ 6600 416 0.86231375 -5.1755229 -4.9703088 -0.51453403
+ 6700 417 0.91939084 -5.2111481 -4.9895683 -0.5239181
+ 6800 418 1.1242247 -5.240558 -4.9662256 -0.50836149
+ 6900 419 1.0578099 -5.2020602 -4.9407635 -0.50665054
+ 7000 420 0.98040609 -5.1860531 -4.9409516 -0.63496783
+ 7100 421 0.99357521 -5.1989655 -4.9476216 -0.53673646
+ 7200 422 1.1168255 -5.1850834 -4.8992607 -0.59194739
+ 7300 423 1.0465199 -5.1485597 -4.877652 -0.4964202
+ 7400 424 0.91999946 -5.1379187 -4.8970698 -0.45185782
+ 7500 425 0.94098172 -5.2197403 -4.9706569 -0.6452508
+ 7600 426 0.92305237 -5.2489345 -5.0019205 -0.67135987
+ 7700 427 1.0692215 -5.2004352 -4.9112195 -0.60227676
+ 7800 428 0.98946072 -5.2168971 -4.9464137 -0.61326494
+ 7900 429 1.1578277 -5.2222386 -4.9024191 -0.6841757
+ 8000 430 1.1057865 -5.2447073 -4.9361157 -0.57784399
+ 8100 431 1.0527643 -5.2189715 -4.9221945 -0.5484357
+ 8200 432 1.058862 -5.2236909 -4.9222094 -0.66008275
+ 8300 433 1.0543331 -5.2105622 -4.907411 -0.60403808
+ 8400 434 1.204621 -5.193864 -4.8441353 -0.57011085
+ 8500 435 1.0247837 -5.1910294 -4.8906617 -0.6081565
+ 8600 436 1.0314146 -5.1732662 -4.8680999 -0.59109692
+ 8700 437 0.98196719 -5.144054 -4.8508121 -0.56483113
+ 8800 438 1.1013378 -5.1980036 -4.8660936 -0.60785883
+ 8900 439 1.1016903 -5.1251846 -4.7901603 -0.49838338
+ 9000 440 1.0926008 -5.1360049 -4.8007751 -0.54767492
+ 9100 441 1.1454324 -5.2217858 -4.8672472 -0.67308812
+ 9200 442 1.059963 -5.1945332 -4.8635945 -0.54419884
+ 9300 443 1.2168669 -5.2244149 -4.8412254 -0.49530257
+ 9400 444 1.0656851 -5.1556938 -4.8172667 -0.41869179
+ 9500 445 0.99794121 -5.2447091 -4.9251436 -0.638328
+ 9600 446 1.1717194 -5.247915 -4.869602 -0.65769093
+ 9700 447 1.2345494 -5.1717485 -4.7698985 -0.54917447
+ 9800 448 1.187781 -5.1672598 -4.7775192 -0.55482592
+ 9900 449 0.99538785 -5.1593424 -4.8301329 -0.5886329
+ 10000 450 0.95030539 -5.1408028 -4.8240344 -0.4992403
+Loop time of 4.67299 on 4 procs for 10000 steps with 450 atoms
+
+Performance: 924461.293 tau/day, 2139.957 timesteps/s
+98.4% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0024376 | 0.84903 | 2.165 | 97.5 | 18.17
+Neigh | 0.0053134 | 0.57645 | 1.783 | 95.1 | 12.34
+Comm | 0.54729 | 2.3753 | 4.0958 | 83.6 | 50.83
+Output | 0.0022168 | 0.00986 | 0.028065 | 10.7 | 0.21
+Modify | 0.0059755 | 0.037876 | 0.085638 | 16.4 | 0.81
+Other | | 0.8245 | | | 17.64
+
+Nlocal: 112.5 ave 250 max 9 min
+Histogram: 2 0 0 0 0 0 1 0 0 1
+Nghost: 1522.75 ave 2248 max 440 min
+Histogram: 1 0 0 0 1 0 0 0 1 1
+Neighs: 7415.25 ave 17049 max 23 min
+Histogram: 2 0 0 0 0 0 0 1 0 1
+
+Total # of neighbors = 29661
+Ave neighs/atom = 65.9133
+Neighbor list builds = 1164
+Dangerous builds = 0
+Total wall time: 0:00:04
diff --git a/examples/deposit/log.15Feb16.deposit.molecule.g++.1 b/examples/deposit/log.15Feb16.deposit.molecule.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..2a549c554c5979d99ba9b263316d1362b7e75443
--- /dev/null
+++ b/examples/deposit/log.15Feb16.deposit.molecule.g++.1
@@ -0,0 +1,205 @@
+LAMMPS (15 Feb 2016)
+# sample surface deposition script for molecules
+
+units lj
+atom_style bond
+boundary p p f
+
+lattice fcc 1.0
+Lattice spacing in x,y,z = 1.5874 1.5874 1.5874
+region box block 0 5 0 5 0 10
+create_box 3 box bond/types 1 extra/bond/per/atom 1
+Created orthogonal box = (0 0 0) to (7.93701 7.93701 15.874)
+ 1 by 1 by 1 MPI processor grid
+
+region substrate block INF INF INF INF INF 3
+create_atoms 1 region substrate
+Created 350 atoms
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0
+pair_coeff 1 2 1.0 1.0 5.0
+mass * 1.0
+
+bond_style harmonic
+bond_coeff 1 5.0 1.0
+
+neigh_modify delay 0
+
+group addatoms type 2
+0 atoms in group addatoms
+region mobile block 0 5 0 5 2 INF
+group mobile region mobile
+150 atoms in group mobile
+
+compute add addatoms temp
+compute_modify add dynamic yes extra 0
+
+fix 1 addatoms nve
+fix 2 mobile langevin 0.1 0.1 0.1 587283
+fix 3 mobile nve
+
+molecule dimer molecule.dimer
+Read molecule dimer:
+ 2 atoms with 3 types
+ 1 bonds with 1 types
+ 0 angles with 0 types
+ 0 dihedrals with 0 types
+ 0 impropers with 0 types
+region slab block 0 5 0 5 8 9
+fix 4 addatoms deposit 100 0 100 12345 region slab near 1.0 mol dimer vz -1.0 -1.0
+fix 5 addatoms wall/reflect zhi EDGE
+
+thermo_style custom step atoms temp epair etotal press
+thermo 100
+thermo_modify temp add lost/bond ignore lost warn
+WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:445)
+
+#dump 1 all atom 50 dump.deposit.atom
+
+#dump 2 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30
+#dump_modify 2 pad 5
+
+#dump 3 all movie 50 movie.mpg type type # axes yes 0.8 0.02 view 80 -30
+#dump_modify 3 pad 5
+
+run 10000
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 5.3
+ ghost atom cutoff = 5.3
+ binsize = 2.65 -> bins = 3 3 6
+Memory usage per processor = 3.56565 Mbytes
+Step Atoms Temp E_pair TotEng Press
+ 0 350 0 -6.9215833 -6.9215833 -1.0052629
+ 100 352 0.83994737 -6.8875167 -6.8803581 -0.73353914
+ 200 354 0.83994737 -6.8593854 -6.845149 -0.70414703
+ 300 356 0.84169616 -6.8174189 -6.7961324 -0.69200581
+ 400 358 0.84705847 -6.785416 -6.7570071 -0.70386101
+ 500 360 0.87562973 -6.7507562 -6.714217 -0.68491831
+ 600 362 0.89546097 -6.7133515 -6.6684358 -0.68373096
+ 700 364 0.86923875 -6.6724351 -6.6215093 -0.6663574
+ 800 366 0.93007871 -6.6448092 -6.5816911 -0.68706422
+ 900 368 1.0020611 -6.6164541 -6.540933 -0.66074734
+ 1000 370 1.0082042 -6.5845669 -6.5014101 -0.69453732
+ 1100 372 0.96783727 -6.5649235 -6.4753076 -0.6717256
+ 1200 374 0.97597749 -6.5935771 -6.4925926 -0.69360182
+ 1300 376 0.80208918 -6.5923852 -6.5033139 -0.64868248
+ 1400 378 0.66705029 -6.582928 -6.5082634 -0.6111322
+ 1500 380 0.67555528 -6.5640796 -6.4816473 -0.67638117
+ 1600 382 0.65916245 -6.551728 -6.4662574 -0.62833932
+ 1700 384 0.718469 -6.5624935 -6.4643654 -0.64737567
+ 1800 386 0.59257091 -6.5604373 -6.4675604 -0.61982866
+ 1900 388 0.63118529 -6.5638788 -6.467728 -0.63403973
+ 2000 390 0.6013361 -6.571937 -6.473428 -0.62753885
+ 2100 392 0.48508625 -6.5519559 -6.4663394 -0.66580902
+ 2200 394 0.50266444 -6.5357335 -6.4395422 -0.71780255
+ 2300 396 0.52557785 -6.5469569 -6.4355521 -0.65421156
+ 2400 398 0.66055178 -6.5509266 -6.4186172 -0.65273326
+ 2500 400 0.69210544 -6.5578062 -6.4211169 -0.68232818
+ 2600 402 0.64576434 -6.6050398 -6.4574266 -0.64849208
+ 2700 404 0.56298016 -6.6350083 -6.503562 -0.746185
+ 2800 406 0.49149694 -6.6482516 -6.5155551 -0.76320999
+ 2900 408 0.48366321 -6.6606024 -6.5257882 -0.65612432
+ 3000 410 0.47356141 -6.6756446 -6.5312692 -0.70811639
+ 3100 412 0.47568619 -6.6934709 -6.5474974 -0.72316681
+ 3200 414 0.38708973 -6.6932142 -6.5659264 -0.73056797
+ 3300 416 0.43665017 -6.6999962 -6.5567504 -0.75890315
+ 3400 418 0.34923989 -6.7185629 -6.5909531 -0.66986444
+ 3500 420 0.33999089 -6.6922536 -6.5729709 -0.70698979
+ 3600 422 0.37659 -6.6827522 -6.5521249 -0.68796169
+ 3700 424 0.34150483 -6.6973468 -6.5698573 -0.68312043
+ 3800 426 0.41110243 -6.7043016 -6.5510735 -0.71352712
+ 3900 428 0.40957994 -6.7172729 -6.5557011 -0.70233721
+ 4000 430 0.42723175 -6.7170007 -6.5537357 -0.7497547
+ 4100 432 0.37176212 -6.7218812 -6.5574518 -0.7098714
+ 4200 434 0.33265381 -6.7082458 -6.5637164 -0.70399102
+ 4300 436 0.43029564 -6.7142231 -6.5431037 -0.76230436
+ 4400 438 0.38216708 -6.7315576 -6.5614315 -0.6674734
+ 4500 440 0.35981631 -6.7496554 -6.583264 -0.73404044
+ 4600 442 0.36073617 -6.7479258 -6.5907772 -0.71067075
+ 4700 444 0.35705292 -6.7678184 -6.5973053 -0.75325156
+ 4800 446 0.37426281 -6.7869581 -6.6010006 -0.67542828
+ 4900 448 0.33524109 -6.7800476 -6.6026334 -0.66398211
+ 5000 450 0.31770101 -6.7884069 -6.6064017 -0.74655689
+ 5100 452 0.31791473 -6.7695361 -6.5901194 -0.77591531
+ 5200 454 0.37320367 -6.7756559 -6.5809165 -0.76247336
+ 5300 456 0.32228579 -6.7786007 -6.5856918 -0.67574614
+ 5400 458 0.31274193 -6.7828483 -6.5928063 -0.72466782
+ 5500 460 0.30708694 -6.7858555 -6.5973813 -0.76883863
+ 5600 462 0.32849848 -6.7983978 -6.6021343 -0.76855876
+ 5700 464 0.35124617 -6.8131288 -6.5975496 -0.78865946
+ 5800 466 0.35055399 -6.8184367 -6.6060092 -0.70530424
+ 5900 468 0.33326299 -6.8299034 -6.6095077 -0.68840817
+ 6000 470 0.40104727 -6.8633145 -6.6132375 -0.77187971
+ 6100 472 0.29105598 -6.8410097 -6.6311104 -0.7715889
+ 6200 474 0.30288813 -6.8634336 -6.6428858 -0.78760673
+ 6300 476 0.34293767 -6.9005784 -6.6534079 -0.74817698
+ 6400 478 0.34963015 -6.9292987 -6.666687 -0.71175243
+ 6500 480 0.319367 -6.9395521 -6.6743587 -0.76432283
+ 6600 482 0.29016877 -6.9324045 -6.679475 -0.90715919
+ 6700 484 0.35436305 -6.9551643 -6.6789059 -0.79939008
+ 6800 486 0.327512 -6.9608693 -6.687362 -0.70392295
+ 6900 488 0.32349315 -6.9513424 -6.6847712 -0.75205809
+ 7000 490 0.35355467 -6.9907283 -6.7038887 -0.80881264
+ 7100 492 0.32140685 -6.9979325 -6.7169278 -0.68673022
+ 7200 494 0.32242041 -7.0116346 -6.728848 -0.79432529
+ 7300 496 0.26266524 -6.9966902 -6.7334152 -0.86050198
+ 7400 498 0.31564904 -7.0133015 -6.7158904 -0.81615792
+ 7500 500 0.36973921 -7.0516561 -6.717083 -0.79423832
+ 7600 502 0.33599186 -7.0516408 -6.7296713 -0.83610882
+ 7700 504 0.29691416 -7.0495062 -6.738076 -0.83634675
+ 7800 506 0.3244215 -7.0434148 -6.7342677 -0.7170135
+ 7900 508 0.29167542 -7.0637209 -6.7576924 -0.78857188
+ 8000 510 0.34198998 -7.1041546 -6.7635656 -0.83376311
+ 8100 512 0.33068905 -7.1341746 -6.7960028 -0.78639771
+ 8200 514 0.29688969 -7.136245 -6.8093036 -0.85753154
+ 8300 516 0.29829676 -7.1313196 -6.8076328 -0.76960702
+ 8400 518 0.31096049 -7.1559166 -6.8202327 -0.72775356
+ 8500 520 0.26677854 -7.1413516 -6.8361967 -0.81908087
+ 8600 522 0.28811568 -7.1390821 -6.8248702 -0.88515896
+ 8700 524 0.27520272 -7.1501541 -6.8311651 -0.81462692
+ 8800 526 0.28763152 -7.1525343 -6.8281253 -0.74124759
+ 8900 528 0.29917883 -7.1547953 -6.8229151 -0.81440712
+ 9000 530 0.28474306 -7.1612717 -6.8236771 -0.79150099
+ 9100 532 0.29409713 -7.1748026 -6.8272211 -0.7916524
+ 9200 534 0.26767862 -7.1646362 -6.8313179 -0.79362392
+ 9300 536 0.27111075 -7.1719185 -6.8399556 -0.9578129
+ 9400 538 0.33952348 -7.207044 -6.8368639 -0.89888939
+ 9500 540 0.3284439 -7.2371916 -6.8625844 -0.7659201
+ 9600 542 0.31256223 -7.2266123 -6.8655682 -0.82722861
+ 9700 544 0.30268239 -7.2315617 -6.8705788 -0.81448482
+ 9800 546 0.26835398 -7.2214231 -6.8757262 -0.86029096
+ 9900 548 0.31676744 -7.264604 -6.884266 -0.74053962
+ 10000 550 0.31368419 -7.2759575 -6.8979611 -0.76153366
+Loop time of 6.58981 on 1 procs for 10000 steps with 550 atoms
+
+Performance: 655557.606 tau/day, 1517.494 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 4.1313 | 4.1313 | 4.1313 | 0.0 | 62.69
+Bond | 0.01234 | 0.01234 | 0.01234 | 0.0 | 0.19
+Neigh | 2.1423 | 2.1423 | 2.1423 | 0.0 | 32.51
+Comm | 0.13504 | 0.13504 | 0.13504 | 0.0 | 2.05
+Output | 0.0010068 | 0.0010068 | 0.0010068 | 0.0 | 0.02
+Modify | 0.12665 | 0.12665 | 0.12665 | 0.0 | 1.92
+Other | | 0.0411 | | | 0.62
+
+Nlocal: 550 ave 550 max 550 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 2349 ave 2349 max 2349 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 39710 ave 39710 max 39710 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 39710
+Ave neighs/atom = 72.2
+Ave special neighs/atom = 0.363636
+Neighbor list builds = 877
+Dangerous builds = 0
+Total wall time: 0:00:06
diff --git a/examples/deposit/log.15Feb16.deposit.molecule.g++.4 b/examples/deposit/log.15Feb16.deposit.molecule.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..b54adec62d26982d470ff9cb89cdf06c22946820
--- /dev/null
+++ b/examples/deposit/log.15Feb16.deposit.molecule.g++.4
@@ -0,0 +1,205 @@
+LAMMPS (15 Feb 2016)
+# sample surface deposition script for molecules
+
+units lj
+atom_style bond
+boundary p p f
+
+lattice fcc 1.0
+Lattice spacing in x,y,z = 1.5874 1.5874 1.5874
+region box block 0 5 0 5 0 10
+create_box 3 box bond/types 1 extra/bond/per/atom 1
+Created orthogonal box = (0 0 0) to (7.93701 7.93701 15.874)
+ 1 by 1 by 4 MPI processor grid
+
+region substrate block INF INF INF INF INF 3
+create_atoms 1 region substrate
+Created 350 atoms
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0
+pair_coeff 1 2 1.0 1.0 5.0
+mass * 1.0
+
+bond_style harmonic
+bond_coeff 1 5.0 1.0
+
+neigh_modify delay 0
+
+group addatoms type 2
+0 atoms in group addatoms
+region mobile block 0 5 0 5 2 INF
+group mobile region mobile
+150 atoms in group mobile
+
+compute add addatoms temp
+compute_modify add dynamic yes extra 0
+
+fix 1 addatoms nve
+fix 2 mobile langevin 0.1 0.1 0.1 587283
+fix 3 mobile nve
+
+molecule dimer molecule.dimer
+Read molecule dimer:
+ 2 atoms with 3 types
+ 1 bonds with 1 types
+ 0 angles with 0 types
+ 0 dihedrals with 0 types
+ 0 impropers with 0 types
+region slab block 0 5 0 5 8 9
+fix 4 addatoms deposit 100 0 100 12345 region slab near 1.0 mol dimer vz -1.0 -1.0
+fix 5 addatoms wall/reflect zhi EDGE
+
+thermo_style custom step atoms temp epair etotal press
+thermo 100
+thermo_modify temp add lost/bond ignore lost warn
+WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:445)
+
+#dump 1 all atom 50 dump.deposit.atom
+
+#dump 2 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30
+#dump_modify 2 pad 5
+
+#dump 3 all movie 50 movie.mpg type type # axes yes 0.8 0.02 view 80 -30
+#dump_modify 3 pad 5
+
+run 10000
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 5.3
+ ghost atom cutoff = 5.3
+ binsize = 2.65 -> bins = 3 3 6
+Memory usage per processor = 3.63985 Mbytes
+Step Atoms Temp E_pair TotEng Press
+ 0 350 0 -6.9215833 -6.9215833 -1.0052629
+ 100 352 0.83994737 -6.8946578 -6.8874992 -0.73775337
+ 200 354 0.83994737 -6.8644786 -6.8502422 -0.69623155
+ 300 356 0.84169616 -6.8219435 -6.800657 -0.69554978
+ 400 358 0.84705847 -6.7754627 -6.7470538 -0.67243811
+ 500 360 0.87562973 -6.7314753 -6.6949361 -0.6950742
+ 600 362 0.89546097 -6.710162 -6.6652463 -0.65981803
+ 700 364 0.86924248 -6.6786002 -6.6276742 -0.66815906
+ 800 366 0.93005193 -6.6524743 -6.5893578 -0.67112658
+ 900 368 1.0019234 -6.6197846 -6.5442728 -0.63787501
+ 1000 370 1.0088277 -6.5761382 -6.4929294 -0.68476387
+ 1100 372 0.95920389 -6.5674754 -6.4791094 -0.6514881
+ 1200 374 1.0580798 -6.5939034 -6.4854936 -0.64868897
+ 1300 376 0.86424162 -6.5983754 -6.5057565 -0.63699331
+ 1400 378 0.67483283 -6.5902961 -6.5114402 -0.65492911
+ 1500 380 0.75360589 -6.5780719 -6.4817845 -0.68120797
+ 1600 382 0.72620352 -6.569806 -6.4764019 -0.66989877
+ 1700 384 0.70645024 -6.5716163 -6.4726668 -0.6613115
+ 1800 386 0.69881235 -6.5763765 -6.4705405 -0.63092971
+ 1900 388 0.55849097 -6.5759885 -6.4828798 -0.66382981
+ 2000 390 0.61872265 -6.5695935 -6.4699984 -0.71796632
+ 2100 392 0.5081592 -6.5617458 -6.4722443 -0.63479779
+ 2200 394 0.48384274 -6.549079 -6.4615149 -0.66946296
+ 2300 396 0.58288701 -6.5480033 -6.4412303 -0.71651424
+ 2400 398 0.64008255 -6.5601944 -6.435487 -0.69102232
+ 2500 400 0.69425764 -6.5828171 -6.4479527 -0.69066043
+ 2600 402 0.64360746 -6.6331402 -6.4757801 -0.69090309
+ 2700 404 0.49461099 -6.6579388 -6.5307976 -0.64409671
+ 2800 406 0.55547146 -6.6714068 -6.5241964 -0.68541724
+ 2900 408 0.50073205 -6.686261 -6.5339011 -0.62669192
+ 3000 410 0.53038544 -6.6912316 -6.5383759 -0.66969696
+ 3100 412 0.50129241 -6.7018519 -6.5548588 -0.68883024
+ 3200 414 0.38030632 -6.6977772 -6.566269 -0.71750777
+ 3300 416 0.46068514 -6.727184 -6.5662475 -0.68188023
+ 3400 418 0.33822772 -6.7360772 -6.6016113 -0.72454552
+ 3500 420 0.36453111 -6.724924 -6.5850647 -0.64608093
+ 3600 422 0.36002968 -6.7121585 -6.5780413 -0.72223399
+ 3700 424 0.36475294 -6.7260042 -6.5866143 -0.67031145
+ 3800 426 0.36718557 -6.7217602 -6.5750235 -0.72937729
+ 3900 428 0.37814959 -6.7263989 -6.5726951 -0.71591892
+ 4000 430 0.40806996 -6.7375374 -6.5678266 -0.72678943
+ 4100 432 0.38045271 -6.7361841 -6.568644 -0.73821367
+ 4200 434 0.33066806 -6.7299457 -6.57638 -0.73722947
+ 4300 436 0.41794011 -6.7644169 -6.579351 -0.73641289
+ 4400 438 0.37024397 -6.7629482 -6.5884866 -0.71240322
+ 4500 440 0.40320567 -6.7752853 -6.5850469 -0.77279245
+ 4600 442 0.35772381 -6.7835099 -6.6013018 -0.73636644
+ 4700 444 0.3651311 -6.7990539 -6.6175275 -0.66854139
+ 4800 446 0.35091135 -6.802215 -6.6224615 -0.76162889
+ 4900 448 0.36081012 -6.7989512 -6.6125569 -0.76016221
+ 5000 450 0.31623339 -6.8039093 -6.6262913 -0.69115281
+ 5100 452 0.31543867 -6.7941532 -6.6159299 -0.72205584
+ 5200 454 0.36158004 -6.8038417 -6.5978895 -0.76776475
+ 5300 456 0.32434144 -6.793123 -6.6082355 -0.72624243
+ 5400 458 0.32124677 -6.793797 -6.6010261 -0.67741044
+ 5500 460 0.32879658 -6.8125027 -6.6145418 -0.77045881
+ 5600 462 0.33544185 -6.8282158 -6.6181936 -0.82298638
+ 5700 464 0.31929648 -6.8312019 -6.617542 -0.77506457
+ 5800 466 0.38513813 -6.8569307 -6.6094667 -0.72432147
+ 5900 468 0.36275508 -6.8784065 -6.6183826 -0.71794686
+ 6000 470 0.36550412 -6.8913174 -6.6280912 -0.73323549
+ 6100 472 0.31989948 -6.8850192 -6.653122 -0.770755
+ 6200 474 0.31533478 -6.8764261 -6.6470078 -0.81602846
+ 6300 476 0.33764472 -6.9058038 -6.6574918 -0.70233823
+ 6400 478 0.33629492 -6.9384728 -6.6676899 -0.750356
+ 6500 480 0.329134 -6.9539905 -6.6660118 -0.76780643
+ 6600 482 0.35893902 -6.9727388 -6.6687914 -0.79588633
+ 6700 484 0.35256839 -6.980576 -6.6800042 -0.67119736
+ 6800 486 0.3498406 -6.9854977 -6.6867156 -0.78135658
+ 6900 488 0.31757914 -6.9609817 -6.6859771 -0.78048643
+ 7000 490 0.40129918 -6.9903536 -6.6713072 -0.75727925
+ 7100 492 0.33833658 -7.0145206 -6.6977622 -0.7587661
+ 7200 494 0.35160231 -7.0237931 -6.7095634 -0.67933941
+ 7300 496 0.28084778 -7.024433 -6.7195845 -0.82825025
+ 7400 498 0.32213221 -7.0527945 -6.7230557 -0.84919299
+ 7500 500 0.40905237 -7.1021905 -6.7203497 -0.93185466
+ 7600 502 0.3609358 -7.1596615 -6.7690359 -0.64194099
+ 7700 504 0.29253629 -7.1428432 -6.796613 -0.6976599
+ 7800 506 0.31731365 -7.176045 -6.8068169 -0.87636485
+ 7900 508 0.2905957 -7.1788367 -6.8119013 -0.75756081
+ 8000 510 0.28404368 -7.1870361 -6.824287 -0.79842667
+ 8100 512 0.34219804 -7.222691 -6.8386818 -0.75369138
+ 8200 514 0.32055193 -7.2353127 -6.8551345 -0.78172901
+ 8300 516 0.30120879 -7.2446887 -6.8672024 -0.83621194
+ 8400 518 0.30883515 -7.2596909 -6.8762796 -0.71183282
+ 8500 520 0.26204254 -7.2431895 -6.8834311 -0.83712537
+ 8600 522 0.29103293 -7.2694658 -6.8867581 -0.82744948
+ 8700 524 0.26753583 -7.2593959 -6.889244 -0.78004892
+ 8800 526 0.26521096 -7.2599673 -6.8902608 -0.79408301
+ 8900 528 0.28003646 -7.2530274 -6.8808417 -0.8606495
+ 9000 530 0.26313192 -7.2628164 -6.8855381 -0.7707451
+ 9100 532 0.2646514 -7.2830171 -6.893178 -0.76585646
+ 9200 534 0.27846656 -7.2721664 -6.8861564 -0.89816607
+ 9300 536 0.30560594 -7.2964254 -6.8845198 -0.72034116
+ 9400 538 0.29262217 -7.3023252 -6.8913192 -0.62961985
+ 9500 540 0.29718418 -7.3048523 -6.8949946 -0.87394403
+ 9600 542 0.34146099 -7.349026 -6.9092212 -0.76789895
+ 9700 544 0.28703519 -7.3161372 -6.9121067 -0.84885733
+ 9800 546 0.28129876 -7.3140275 -6.9098746 -0.82726219
+ 9900 548 0.28891495 -7.3235633 -6.9092268 -0.88128702
+ 10000 550 0.29861445 -7.3507915 -6.9161229 -0.73192335
+Loop time of 5.52188 on 4 procs for 10000 steps with 550 atoms
+
+Performance: 782342.427 tau/day, 1810.978 timesteps/s
+98.3% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0013716 | 1.0723 | 3.0973 | 122.1 | 19.42
+Bond | 0.0012324 | 0.0039356 | 0.010944 | 6.5 | 0.07
+Neigh | 0.0033538 | 0.5728 | 1.8205 | 98.1 | 10.37
+Comm | 0.44758 | 2.8002 | 5.0381 | 103.8 | 50.71
+Output | 0.0021229 | 0.01519 | 0.050854 | 16.7 | 0.28
+Modify | 0.0069635 | 0.039662 | 0.076857 | 15.8 | 0.72
+Other | | 1.018 | | | 18.43
+
+Nlocal: 137.5 ave 299 max 2 min
+Histogram: 2 0 0 0 0 0 0 1 0 1
+Nghost: 1866.25 ave 2673 max 377 min
+Histogram: 1 0 0 0 0 0 1 0 0 2
+Neighs: 9891 ave 24535 max 0 min
+Histogram: 2 0 0 0 0 0 1 0 0 1
+
+Total # of neighbors = 39564
+Ave neighs/atom = 71.9345
+Ave special neighs/atom = 0.363636
+Neighbor list builds = 884
+Dangerous builds = 0
+Total wall time: 0:00:05
diff --git a/examples/deposit/log.15Feb16.deposit.molecule.shake.g++.1 b/examples/deposit/log.15Feb16.deposit.molecule.shake.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..63dcd59056bf2bee9e9c6232dad9f487ac9a7aea
--- /dev/null
+++ b/examples/deposit/log.15Feb16.deposit.molecule.shake.g++.1
@@ -0,0 +1,231 @@
+LAMMPS (15 Feb 2016)
+# sample surface deposition script for molecules
+
+units lj
+atom_style bond
+boundary p p f
+
+lattice fcc 1.0
+Lattice spacing in x,y,z = 1.5874 1.5874 1.5874
+region box block 0 5 0 5 0 10
+create_box 3 box bond/types 1 extra/bond/per/atom 1
+Created orthogonal box = (0 0 0) to (7.93701 7.93701 15.874)
+ 1 by 1 by 1 MPI processor grid
+
+region substrate block INF INF INF INF INF 3
+create_atoms 1 region substrate
+Created 350 atoms
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0
+pair_coeff 1 2 1.0 1.0 5.0
+mass * 1.0
+
+bond_style harmonic
+bond_coeff 1 5.0 1.0
+
+neigh_modify delay 0
+
+group addatoms type 2
+0 atoms in group addatoms
+region mobile block 0 5 0 5 2 INF
+group mobile region mobile
+150 atoms in group mobile
+
+compute add addatoms temp
+compute_modify add dynamic yes extra 0
+
+fix 1 addatoms nve
+fix 2 mobile langevin 0.1 0.1 0.1 587283
+fix 3 mobile nve
+
+molecule dimer molecule.dimer.shake
+Read molecule dimer:
+ 2 atoms with 3 types
+ 1 bonds with 1 types
+ 0 angles with 0 types
+ 0 dihedrals with 0 types
+ 0 impropers with 0 types
+region slab block 0 5 0 5 8 9
+fix 4 addatoms deposit 100 0 100 12345 region slab near 1.0 mol dimer vz -1.0 -1.0 shake 6
+fix 5 addatoms wall/reflect zhi EDGE
+fix 6 all shake 0.0001 20 1000 b 1 mol dimer
+ 0 = # of size 2 clusters
+ 0 = # of size 3 clusters
+ 0 = # of size 4 clusters
+ 0 = # of frozen angles
+
+thermo_style custom step atoms temp epair etotal press
+thermo 100
+thermo_modify temp add lost/bond ignore lost warn
+WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:445)
+
+#dump 1 all atom 50 dump.deposit.atom
+
+#dump 2 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30
+#dump_modify 2 pad 5
+
+#dump 3 all movie 50 tmp.mpg type type # axes yes 0.8 0.02 view 80 -30
+#dump_modify 3 pad 5
+
+run 10000
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 5.3
+ ghost atom cutoff = 5.3
+ binsize = 2.65 -> bins = 3 3 6
+SHAKE stats (type/ave/delta) on step 0
+Memory usage per processor = 4.44065 Mbytes
+Step Atoms Temp E_pair TotEng Press
+ 0 350 0 -6.9215833 -6.9215833 -1.0052629
+ 100 352 1.0079368 -6.8875167 -6.8803581 -0.73353914
+ 200 354 1.0079368 -6.8593854 -6.845149 -0.70414703
+ 300 356 1.0098741 -6.8174079 -6.7961324 -0.691981
+ 400 358 1.015821 -6.7853803 -6.7570054 -0.70383202
+ 500 360 1.0431742 -6.7504367 -6.7142154 -0.68490175
+ 600 362 1.0978772 -6.7139711 -6.6684789 -0.6851563
+ 700 364 1.0536935 -6.6722083 -6.62155 -0.66701737
+ 800 366 1.0615842 -6.6397391 -6.581729 -0.68874151
+ 900 368 1.1690777 -6.6124387 -6.5409597 -0.6631748
+SHAKE stats (type/ave/delta) on step 1000
+ 1 1 2.33147e-15
+ 1000 370 1.2238341 -6.5840994 -6.501408 -0.68752603
+ 1100 372 1.0648652 -6.557204 -6.4784841 -0.67502685
+ 1200 374 1.1172515 -6.5811189 -6.4914998 -0.67901522
+ 1300 376 0.90409242 -6.5843683 -6.506222 -0.63816276
+ 1400 378 0.7557157 -6.5929671 -6.5229934 -0.58917374
+ 1500 380 0.84878624 -6.5750822 -6.4913204 -0.68236463
+ 1600 382 0.7649257 -6.5590761 -6.4789792 -0.66149637
+ 1700 384 0.7158335 -6.5532553 -6.4740289 -0.59288863
+ 1800 386 0.71794608 -6.5599255 -6.4762271 -0.61004271
+ 1900 388 0.65121754 -6.5536032 -6.4738794 -0.64961438
+SHAKE stats (type/ave/delta) on step 2000
+ 1 1 2.9976e-15
+ 2000 390 0.69034633 -6.5451174 -6.4566114 -0.67204138
+ 2100 392 0.64581391 -6.5535183 -6.4670253 -0.65563645
+ 2200 394 0.65761022 -6.5431965 -6.4513982 -0.72677062
+ 2300 396 0.6528782 -6.554984 -6.4601848 -0.64557524
+ 2400 398 0.65836233 -6.5570075 -6.4577569 -0.69592521
+ 2500 400 0.6411519 -6.5498234 -6.4496434 -0.72785753
+ 2600 402 0.55292699 -6.5815848 -6.4921812 -0.64848109
+ 2700 404 0.49353048 -6.5774182 -6.4949596 -0.72662195
+ 2800 406 0.55912601 -6.5808134 -6.4844124 -0.75266257
+ 2900 408 0.51233032 -6.571748 -6.4807089 -0.67844491
+SHAKE stats (type/ave/delta) on step 3000
+ 1 1 1.9984e-15
+ 3000 410 0.47624368 -6.5904636 -6.5033458 -0.72887592
+ 3100 412 0.45076116 -6.5887249 -6.5039336 -0.67815331
+ 3200 414 0.50910708 -6.5995831 -6.501205 -0.78059594
+ 3300 416 0.45275554 -6.5991184 -6.5093291 -0.71529909
+ 3400 418 0.38977308 -6.6018891 -6.522629 -0.69785747
+ 3500 420 0.43625362 -6.6049671 -6.5140809 -0.69363556
+ 3600 422 0.48184349 -6.613181 -6.5104182 -0.72994587
+ 3700 424 0.39971995 -6.5997664 -6.5125634 -0.68093342
+ 3800 426 0.43158248 -6.6067065 -6.5104616 -0.7865976
+ 3900 428 0.39156456 -6.591465 -6.5022651 -0.72788973
+SHAKE stats (type/ave/delta) on step 4000
+ 1 1 1.66533e-15
+ 4000 430 0.45520202 -6.6043002 -6.4984393 -0.76339306
+ 4100 432 0.37804217 -6.5825484 -6.4928509 -0.677846
+ 4200 434 0.44408719 -6.6044968 -6.4970564 -0.72092913
+ 4300 436 0.45187505 -6.6214439 -6.5100298 -0.71003531
+ 4400 438 0.44634852 -6.6370982 -6.5250016 -0.7259646
+ 4500 440 0.44774369 -6.6482048 -6.5337249 -0.75067855
+ 4600 442 0.38004568 -6.6303883 -6.5315076 -0.70235189
+ 4700 444 0.39828448 -6.6228295 -6.5174277 -0.78272067
+ 4800 446 0.44085367 -6.6270343 -6.508419 -0.66562901
+ 4900 448 0.47288585 -6.660755 -6.5314503 -0.74826687
+SHAKE stats (type/ave/delta) on step 5000
+ 1 1 1.77636e-15
+ 5000 450 0.43761136 -6.6799555 -6.5583968 -0.78360367
+ 5100 452 0.411973 -6.678564 -6.5623548 -0.70194168
+ 5200 454 0.40797743 -6.6866303 -6.5698086 -0.80152835
+ 5300 456 0.34469092 -6.6716537 -6.5714968 -0.67613535
+ 5400 458 0.34013914 -6.6730911 -6.5728318 -0.76078338
+ 5500 460 0.34154783 -6.6605085 -6.5584154 -0.77667767
+ 5600 462 0.36897691 -6.659394 -6.5475828 -0.81373456
+ 5700 464 0.3540965 -6.6625103 -6.553763 -0.78251629
+ 5800 466 0.4082091 -6.6773565 -6.5503387 -0.70767517
+ 5900 468 0.447614 -6.7033749 -6.5623 -0.71623466
+SHAKE stats (type/ave/delta) on step 6000
+ 1 1 2.9976e-15
+ 6000 470 0.40113913 -6.679345 -6.5513219 -0.76250746
+ 6100 472 0.42232629 -6.6963163 -6.5598656 -0.86594326
+ 6200 474 0.39623605 -6.7100181 -6.5804473 -0.73732824
+ 6300 476 0.37197778 -6.7159803 -6.5928994 -0.77305419
+ 6400 478 0.33247467 -6.7128004 -6.6015118 -0.64546345
+ 6500 480 0.34120281 -6.7088232 -6.5933119 -0.90961564
+ 6600 482 0.3342529 -6.7056782 -6.5912555 -0.82385057
+ 6700 484 0.34349872 -6.7152033 -6.5963272 -0.73664697
+ 6800 486 0.33490767 -6.7243451 -6.6071963 -0.71978984
+ 6900 488 0.36292075 -6.7126402 -6.5843536 -0.74097013
+SHAKE stats (type/ave/delta) on step 7000
+ 1 1 2.55351e-15
+ 7000 490 0.37409279 -6.7221689 -6.5885643 -0.71570235
+ 7100 492 0.3742131 -6.7256916 -6.5906859 -0.70045361
+ 7200 494 0.35928736 -6.7227141 -6.5917997 -0.83125489
+ 7300 496 0.31306304 -6.7132829 -6.5980934 -0.80568965
+ 7400 498 0.381634 -6.7248419 -6.5830702 -0.81697798
+ 7500 500 0.36301318 -6.7268458 -6.5907159 -0.78210607
+ 7600 502 0.34015711 -6.7204559 -6.5917112 -0.81197949
+ 7700 504 0.33268221 -6.7140074 -6.5869413 -0.80133
+ 7800 506 0.32240031 -6.7139558 -6.5897106 -0.78091826
+ 7900 508 0.28597508 -6.7091152 -6.5979339 -0.80994821
+SHAKE stats (type/ave/delta) on step 8000
+ 1 1 2.44249e-15
+ 8000 510 0.3444676 -6.7275437 -6.5924583 -0.83444712
+ 8100 512 0.34432983 -6.7402771 -6.604092 -0.79667718
+ 8200 514 0.30652597 -6.7275717 -6.6053191 -0.79549578
+ 8300 516 0.34347028 -6.7383117 -6.6001914 -0.81425668
+ 8400 518 0.31465002 -6.7319759 -6.6044151 -0.77354562
+ 8500 520 0.32120885 -6.7340886 -6.6028253 -0.83177871
+ 8600 522 0.32040584 -6.71864 -6.5866721 -0.78525843
+ 8700 524 0.34513435 -6.7414459 -6.5981888 -0.8520753
+ 8800 526 0.32652464 -6.7316364 -6.5950672 -0.79191959
+ 8900 528 0.29931888 -6.723678 -6.5975445 -0.86587625
+SHAKE stats (type/ave/delta) on step 9000
+ 1 1 2.10942e-15
+ 9000 530 0.34199152 -6.7390429 -6.5938579 -0.8478443
+ 9100 532 0.32986081 -6.7434023 -6.6023434 -0.8020183
+ 9200 534 0.32008917 -6.7313919 -6.5935258 -0.73850848
+ 9300 536 0.31879033 -6.745493 -6.6072118 -0.88838081
+ 9400 538 0.31905323 -6.7359144 -6.596551 -0.90024213
+ 9500 540 0.30837753 -6.7292799 -6.5936509 -0.81564405
+ 9600 542 0.34603468 -6.7371426 -6.583917 -0.78921543
+ 9700 544 0.31957585 -6.7248739 -6.582416 -0.76240549
+ 9800 546 0.32315085 -6.7357573 -6.5907537 -0.92679394
+ 9900 548 0.34107078 -6.7519889 -6.5979469 -0.73569227
+SHAKE stats (type/ave/delta) on step 10000
+ 1 1 2.44249e-15
+ 10000 550 0.31059632 -6.7463923 -6.6052122 -0.75225652
+Loop time of 6.33784 on 1 procs for 10000 steps with 550 atoms
+
+Performance: 681620.330 tau/day, 1577.825 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 3.9751 | 3.9751 | 3.9751 | 0.0 | 62.72
+Bond | 0.012007 | 0.012007 | 0.012007 | 0.0 | 0.19
+Neigh | 2.0003 | 2.0003 | 2.0003 | 0.0 | 31.56
+Comm | 0.13159 | 0.13159 | 0.13159 | 0.0 | 2.08
+Output | 0.00095081 | 0.00095081 | 0.00095081 | 0.0 | 0.02
+Modify | 0.17719 | 0.17719 | 0.17719 | 0.0 | 2.80
+Other | | 0.04064 | | | 0.64
+
+Nlocal: 550 ave 550 max 550 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 2331 ave 2331 max 2331 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 36458 ave 36458 max 36458 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 36458
+Ave neighs/atom = 66.2873
+Ave special neighs/atom = 0.363636
+Neighbor list builds = 839
+Dangerous builds = 0
+Total wall time: 0:00:06
diff --git a/examples/deposit/log.15Feb16.deposit.molecule.shake.g++.4 b/examples/deposit/log.15Feb16.deposit.molecule.shake.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..fa79c2b20cebe32623fb89b66ef24e9bb776b793
--- /dev/null
+++ b/examples/deposit/log.15Feb16.deposit.molecule.shake.g++.4
@@ -0,0 +1,231 @@
+LAMMPS (15 Feb 2016)
+# sample surface deposition script for molecules
+
+units lj
+atom_style bond
+boundary p p f
+
+lattice fcc 1.0
+Lattice spacing in x,y,z = 1.5874 1.5874 1.5874
+region box block 0 5 0 5 0 10
+create_box 3 box bond/types 1 extra/bond/per/atom 1
+Created orthogonal box = (0 0 0) to (7.93701 7.93701 15.874)
+ 1 by 1 by 4 MPI processor grid
+
+region substrate block INF INF INF INF INF 3
+create_atoms 1 region substrate
+Created 350 atoms
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0
+pair_coeff 1 2 1.0 1.0 5.0
+mass * 1.0
+
+bond_style harmonic
+bond_coeff 1 5.0 1.0
+
+neigh_modify delay 0
+
+group addatoms type 2
+0 atoms in group addatoms
+region mobile block 0 5 0 5 2 INF
+group mobile region mobile
+150 atoms in group mobile
+
+compute add addatoms temp
+compute_modify add dynamic yes extra 0
+
+fix 1 addatoms nve
+fix 2 mobile langevin 0.1 0.1 0.1 587283
+fix 3 mobile nve
+
+molecule dimer molecule.dimer.shake
+Read molecule dimer:
+ 2 atoms with 3 types
+ 1 bonds with 1 types
+ 0 angles with 0 types
+ 0 dihedrals with 0 types
+ 0 impropers with 0 types
+region slab block 0 5 0 5 8 9
+fix 4 addatoms deposit 100 0 100 12345 region slab near 1.0 mol dimer vz -1.0 -1.0 shake 6
+fix 5 addatoms wall/reflect zhi EDGE
+fix 6 all shake 0.0001 20 1000 b 1 mol dimer
+ 0 = # of size 2 clusters
+ 0 = # of size 3 clusters
+ 0 = # of size 4 clusters
+ 0 = # of frozen angles
+
+thermo_style custom step atoms temp epair etotal press
+thermo 100
+thermo_modify temp add lost/bond ignore lost warn
+WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:445)
+
+#dump 1 all atom 50 dump.deposit.atom
+
+#dump 2 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30
+#dump_modify 2 pad 5
+
+#dump 3 all movie 50 tmp.mpg type type # axes yes 0.8 0.02 view 80 -30
+#dump_modify 3 pad 5
+
+run 10000
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 5.3
+ ghost atom cutoff = 5.3
+ binsize = 2.65 -> bins = 3 3 6
+SHAKE stats (type/ave/delta) on step 0
+Memory usage per processor = 4.51485 Mbytes
+Step Atoms Temp E_pair TotEng Press
+ 0 350 0 -6.9215833 -6.9215833 -1.0052629
+ 100 352 1.0079368 -6.8946578 -6.8874992 -0.73775337
+ 200 354 1.0079368 -6.8644786 -6.8502422 -0.69623155
+ 300 356 1.0098741 -6.8219324 -6.800657 -0.69552497
+ 400 358 1.015821 -6.775427 -6.7470521 -0.67240912
+ 500 360 1.0431742 -6.7311558 -6.6949345 -0.69505765
+ 600 362 1.0978772 -6.7107816 -6.6652895 -0.66124338
+ 700 364 1.0536993 -6.6818292 -6.6311706 -0.67789771
+ 800 366 1.0615655 -6.6354474 -6.5774383 -0.64710621
+ 900 368 1.1688557 -6.614281 -6.5428156 -0.64842218
+SHAKE stats (type/ave/delta) on step 1000
+ 1 1 1.22125e-15
+ 1000 370 1.2172009 -6.5772424 -6.4949991 -0.67942188
+ 1100 372 1.1031034 -6.55895 -6.4774034 -0.65896897
+ 1200 374 1.040192 -6.5874108 -6.503973 -0.62919433
+ 1300 376 0.94890463 -6.5897148 -6.5076952 -0.63346087
+ 1400 378 0.78945672 -6.5952649 -6.522167 -0.67613271
+ 1500 380 0.82876461 -6.5798609 -6.4980749 -0.65306056
+ 1600 382 0.73883758 -6.5591084 -6.4817432 -0.62749488
+ 1700 384 0.73539709 -6.5556021 -6.4742105 -0.66817567
+ 1800 386 0.67455206 -6.5535874 -6.474948 -0.57721026
+ 1900 388 0.66352723 -6.5469905 -6.4657597 -0.69276627
+SHAKE stats (type/ave/delta) on step 2000
+ 1 1 2.22045e-15
+ 2000 390 0.81013116 -6.5567994 -6.4529364 -0.71579948
+ 2100 392 0.72889872 -6.5689128 -6.4712924 -0.65504494
+ 2200 394 0.57901901 -6.552299 -6.4714715 -0.67723953
+ 2300 396 0.59157803 -6.5485081 -6.4626098 -0.66397554
+ 2400 398 0.70712699 -6.5593644 -6.4527623 -0.70641253
+ 2500 400 0.7569242 -6.576119 -6.4578496 -0.69907756
+ 2600 402 0.6662505 -6.6038869 -6.4961599 -0.66941055
+ 2700 404 0.51455113 -6.6038412 -6.5178704 -0.69578494
+ 2800 406 0.58401979 -6.6058664 -6.5051733 -0.70647457
+ 2900 408 0.50129416 -6.6138934 -6.5248154 -0.64390758
+SHAKE stats (type/ave/delta) on step 3000
+ 1 1 2.66454e-15
+ 3000 410 0.44807689 -6.6222658 -6.5403005 -0.68340233
+ 3100 412 0.45962393 -6.6204312 -6.5339728 -0.66309459
+ 3200 414 0.50182826 -6.6295842 -6.5326126 -0.74122586
+ 3300 416 0.48471205 -6.6424495 -6.5463227 -0.69764601
+ 3400 418 0.36856546 -6.6251783 -6.5502308 -0.76543921
+ 3500 420 0.4203509 -6.6198957 -6.5323226 -0.64154608
+ 3600 422 0.54795097 -6.6410801 -6.5242185 -0.7463818
+ 3700 424 0.51183952 -6.6521145 -6.5404514 -0.70304908
+ 3800 426 0.39414561 -6.6456807 -6.5577844 -0.74178922
+ 3900 428 0.40589341 -6.6564647 -6.5640007 -0.78327027
+SHAKE stats (type/ave/delta) on step 4000
+ 1 1 1.88738e-15
+ 4000 430 0.43166847 -6.6566443 -6.5562563 -0.73290988
+ 4100 432 0.40408931 -6.6500622 -6.5541845 -0.73057986
+ 4200 434 0.35377187 -6.6356255 -6.5500355 -0.76557381
+ 4300 436 0.4291929 -6.657321 -6.5514993 -0.78608144
+ 4400 438 0.43151668 -6.6494979 -6.5411262 -0.70820395
+ 4500 440 0.44315446 -6.6596739 -6.5463674 -0.82000058
+ 4600 442 0.41285261 -6.6553044 -6.547888 -0.76115447
+ 4700 444 0.38354616 -6.6502515 -6.54875 -0.6954286
+ 4800 446 0.39108666 -6.648355 -6.5431299 -0.72779836
+ 4900 448 0.3799768 -6.6517925 -6.5478926 -0.79771549
+SHAKE stats (type/ave/delta) on step 5000
+ 1 1 3.10862e-15
+ 5000 450 0.39260452 -6.6598567 -6.5507999 -0.76677324
+ 5100 452 0.41475009 -6.6627963 -6.5458038 -0.70468384
+ 5200 454 0.4115583 -6.6658575 -6.5480104 -0.78115993
+ 5300 456 0.3753641 -6.6631393 -6.5540696 -0.78711192
+ 5400 458 0.36565536 -6.6545908 -6.5468103 -0.74549556
+ 5500 460 0.33271655 -6.6418893 -6.542436 -0.76780862
+ 5600 462 0.36832168 -6.6440805 -6.5324679 -0.75143503
+ 5700 464 0.39059076 -6.6481163 -6.5281612 -0.78380485
+ 5800 466 0.36650802 -6.6430337 -6.5289916 -0.75502025
+ 5900 468 0.35914314 -6.6418801 -6.5286886 -0.67704807
+SHAKE stats (type/ave/delta) on step 6000
+ 1 1 2.22045e-15
+ 6000 470 0.39116517 -6.6612874 -6.5364474 -0.84800605
+ 6100 472 0.38421704 -6.6693489 -6.545211 -0.78734456
+ 6200 474 0.38216918 -6.6812774 -6.5563065 -0.81814647
+ 6300 476 0.34722048 -6.6730701 -6.5581809 -0.77616674
+ 6400 478 0.32907391 -6.6719973 -6.5618471 -0.7458085
+ 6500 480 0.31094699 -6.6715976 -6.566329 -0.83282406
+ 6600 482 0.35169592 -6.6680323 -6.5476384 -0.85138473
+ 6700 484 0.36350925 -6.6706468 -6.5448456 -0.71970784
+ 6800 486 0.38133383 -6.6922722 -6.5588839 -0.77339402
+ 6900 488 0.34810579 -6.6746177 -6.551568 -0.77360649
+SHAKE stats (type/ave/delta) on step 7000
+ 1 1 3.66374e-15
+ 7000 490 0.3590117 -6.683101 -6.5548825 -0.80004574
+ 7100 492 0.38269726 -6.688913 -6.5508464 -0.81445922
+ 7200 494 0.31934554 -6.6944357 -6.578075 -0.74069497
+ 7300 496 0.32758627 -6.6955862 -6.5750529 -0.78679117
+ 7400 498 0.3660502 -6.7111626 -6.5751801 -0.78104263
+ 7500 500 0.32569889 -6.6953555 -6.5732185 -0.74496853
+ 7600 502 0.33737271 -6.6971694 -6.5694785 -0.90240288
+ 7700 504 0.35222518 -6.7006509 -6.5661204 -0.86220892
+ 7800 506 0.31834385 -6.6988433 -6.5761614 -0.78723443
+ 7900 508 0.35977076 -6.7264843 -6.5866128 -0.8568963
+SHAKE stats (type/ave/delta) on step 8000
+ 1 1 2.22045e-15
+ 8000 510 0.35931856 -6.7266146 -6.5857054 -0.85544232
+ 8100 512 0.36797798 -6.739034 -6.5934958 -0.82062699
+ 8200 514 0.40277035 -6.7571847 -6.5965467 -0.82121365
+ 8300 516 0.32568144 -6.7419653 -6.6109984 -0.78580816
+ 8400 518 0.33705466 -6.7532799 -6.6166361 -0.83332745
+ 8500 520 0.30158673 -6.7342587 -6.6110142 -0.8578352
+ 8600 522 0.32525112 -6.7446972 -6.6107336 -0.96759
+ 8700 524 0.32985772 -6.7480971 -6.611181 -0.78464535
+ 8800 526 0.32397396 -6.7465569 -6.6110545 -0.81041129
+ 8900 528 0.33669589 -6.7543874 -6.6125032 -0.87866197
+SHAKE stats (type/ave/delta) on step 9000
+ 1 1 3.88578e-15
+ 9000 530 0.32538398 -6.7436298 -6.6054951 -0.79985713
+ 9100 532 0.3336509 -6.7541485 -6.6114688 -0.84449566
+ 9200 534 0.31516122 -6.7553334 -6.6195898 -0.88997909
+ 9300 536 0.30963064 -6.7627673 -6.6284593 -0.75349544
+ 9400 538 0.34228518 -6.7754099 -6.6258988 -0.77001741
+ 9500 540 0.29032769 -6.7737667 -6.6460763 -0.85854407
+ 9600 542 0.31033087 -6.7764458 -6.63903 -0.8553105
+ 9700 544 0.33657054 -6.7798228 -6.629789 -0.91356823
+ 9800 546 0.30235172 -6.7634263 -6.6277557 -0.92787364
+ 9900 548 0.3446797 -6.7794717 -6.6237998 -0.88766558
+SHAKE stats (type/ave/delta) on step 10000
+ 1 1 2.55351e-15
+ 10000 550 0.30296128 -6.7756768 -6.6379672 -0.84420968
+Loop time of 5.79101 on 4 procs for 10000 steps with 550 atoms
+
+Performance: 745983.597 tau/day, 1726.814 timesteps/s
+98.4% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0016487 | 1.0205 | 2.974 | 120.1 | 17.62
+Bond | 0.0012839 | 0.003953 | 0.010697 | 6.2 | 0.07
+Neigh | 0.0035315 | 0.52893 | 1.691 | 94.9 | 9.13
+Comm | 0.57816 | 2.7844 | 4.9123 | 99.7 | 48.08
+Output | 0.0024757 | 0.0037841 | 0.0065219 | 2.7 | 0.07
+Modify | 0.41353 | 1.2632 | 3.4168 | 111.3 | 21.81
+Other | | 0.1862 | | | 3.22
+
+Nlocal: 137.5 ave 300 max 2 min
+Histogram: 2 0 0 0 0 0 0 1 0 1
+Nghost: 1874.5 ave 2648 max 509 min
+Histogram: 1 0 0 0 0 0 1 0 0 2
+Neighs: 9185.75 ave 23231 max 0 min
+Histogram: 2 0 0 0 0 1 0 0 0 1
+
+Total # of neighbors = 36743
+Ave neighs/atom = 66.8055
+Ave special neighs/atom = 0.363636
+Neighbor list builds = 833
+Dangerous builds = 0
+Total wall time: 0:00:05
diff --git a/examples/dipole/log.15Feb16.dipole.g++.1 b/examples/dipole/log.15Feb16.dipole.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..cbda818619a45ecc12e4913807d02d8fa7ad7752
--- /dev/null
+++ b/examples/dipole/log.15Feb16.dipole.g++.1
@@ -0,0 +1,104 @@
+LAMMPS (15 Feb 2016)
+# Point dipoles in a 2d box
+
+units lj
+atom_style hybrid sphere dipole
+dimension 2
+
+lattice sq2 0.7
+Lattice spacing in x,y,z = 1.69031 1.69031 1.69031
+region box block 0 10 0 10 -0.5 0.5
+create_box 1 box
+Created orthogonal box = (0 0 -0.845154) to (16.9031 16.9031 0.845154)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 200 atoms
+
+# need both mass settings due to hybrid atom style
+
+mass 1 1.0
+set group all mass 1.0
+ 200 settings made for mass
+set group all dipole/random 98934 0.75
+ 200 settings made for dipole/random
+
+velocity all create 0.0 87287 mom no
+
+pair_style lj/cut/dipole/cut 2.5
+pair_coeff * * 1.0 1.0
+
+neighbor 0.3 bin
+neigh_modify delay 0
+
+fix 1 all nve/sphere update dipole
+fix 2 all enforce2d
+
+timestep 0.005
+
+compute erot all erotate/sphere
+thermo_style custom step temp epair c_erot etotal press
+thermo 500
+
+#dump 1 all custom 500 dump.dipole id type x y z mux muy
+
+#dump 1 all image 250 image.*.jpg mux type # zoom 1.6 adiam 1.2
+#dump_modify 1 pad 5
+
+run 10000
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4 -> bins = 13 13 2
+Memory usage per processor = 4.47689 Mbytes
+Step Temp E_pair erot TotEng Press
+ 0 0 -2.1909822 0 -2.1909822 -2.5750971
+ 500 0.39335419 -2.7940623 0.20683255 -2.4026749 -0.24768899
+ 1000 0.45259485 -2.8743423 0.22311811 -2.4240104 -0.14864606
+ 1500 0.42110221 -2.8019062 0.19532181 -2.3829095 0.18067141
+ 2000 0.39019964 -2.7914873 0.2240704 -2.4032387 -0.40914108
+ 2500 0.40258219 -2.8140936 0.24274448 -2.4135243 -0.33941924
+ 3000 0.41800133 -2.8282056 0.24466746 -2.4122942 -0.090527465
+ 3500 0.40116089 -2.7573067 0.18791549 -2.3581517 -0.10988473
+ 4000 0.44069383 -2.8320262 0.23306586 -2.3935358 -0.16090586
+ 4500 0.39984934 -2.7780055 0.2316558 -2.3801554 -0.060493508
+ 5000 0.38478499 -2.7506484 0.22192236 -2.3677873 -0.20522733
+ 5500 0.41563657 -2.7772758 0.21967501 -2.3637174 -0.21224098
+ 6000 0.4784307 -2.8050644 0.19178566 -2.3290259 -0.084370417
+ 6500 0.45915752 -2.8043874 0.21761744 -2.3475257 0.044744498
+ 7000 0.45492064 -2.7795535 0.20340455 -2.3269074 -0.027924625
+ 7500 0.41266295 -2.7515872 0.22903767 -2.3409876 -0.43730101
+ 8000 0.41905675 -2.7281536 0.19413869 -2.3111921 -0.020762772
+ 8500 0.42951176 -2.7616497 0.22863785 -2.3342855 -0.18867239
+ 9000 0.42532413 -2.748856 0.21378021 -2.3256584 0.015079949
+ 9500 0.42237159 -2.7266142 0.20255034 -2.3063545 -0.15538561
+ 10000 0.40758268 -2.778401 0.2746675 -2.3728562 -0.20811978
+Loop time of 1.04484 on 1 procs for 10000 steps with 200 atoms
+
+Performance: 4134616.221 tau/day, 9570.871 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.87532 | 0.87532 | 0.87532 | 0.0 | 83.78
+Neigh | 0.037165 | 0.037165 | 0.037165 | 0.0 | 3.56
+Comm | 0.034433 | 0.034433 | 0.034433 | 0.0 | 3.30
+Output | 0.00014114 | 0.00014114 | 0.00014114 | 0.0 | 0.01
+Modify | 0.083179 | 0.083179 | 0.083179 | 0.0 | 7.96
+Other | | 0.0146 | | | 1.40
+
+Nlocal: 200 ave 200 max 200 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 162 ave 162 max 162 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 1625 ave 1625 max 1625 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1625
+Ave neighs/atom = 8.125
+Neighbor list builds = 673
+Dangerous builds = 0
+Total wall time: 0:00:01
diff --git a/examples/dipole/log.15Feb16.dipole.g++.4 b/examples/dipole/log.15Feb16.dipole.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..62970b290dc9ac18b090134ca7166a0e3a5ae9a9
--- /dev/null
+++ b/examples/dipole/log.15Feb16.dipole.g++.4
@@ -0,0 +1,104 @@
+LAMMPS (15 Feb 2016)
+# Point dipoles in a 2d box
+
+units lj
+atom_style hybrid sphere dipole
+dimension 2
+
+lattice sq2 0.7
+Lattice spacing in x,y,z = 1.69031 1.69031 1.69031
+region box block 0 10 0 10 -0.5 0.5
+create_box 1 box
+Created orthogonal box = (0 0 -0.845154) to (16.9031 16.9031 0.845154)
+ 2 by 2 by 1 MPI processor grid
+create_atoms 1 box
+Created 200 atoms
+
+# need both mass settings due to hybrid atom style
+
+mass 1 1.0
+set group all mass 1.0
+ 200 settings made for mass
+set group all dipole/random 98934 0.75
+ 200 settings made for dipole/random
+
+velocity all create 0.0 87287 mom no
+
+pair_style lj/cut/dipole/cut 2.5
+pair_coeff * * 1.0 1.0
+
+neighbor 0.3 bin
+neigh_modify delay 0
+
+fix 1 all nve/sphere update dipole
+fix 2 all enforce2d
+
+timestep 0.005
+
+compute erot all erotate/sphere
+thermo_style custom step temp epair c_erot etotal press
+thermo 500
+
+#dump 1 all custom 500 dump.dipole id type x y z mux muy
+
+#dump 1 all image 250 image.*.jpg mux type # zoom 1.6 adiam 1.2
+#dump_modify 1 pad 5
+
+run 10000
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4 -> bins = 13 13 2
+Memory usage per processor = 4.47621 Mbytes
+Step Temp E_pair erot TotEng Press
+ 0 0 -2.1909822 0 -2.1909822 -2.5750971
+ 500 0.39335419 -2.7940623 0.20683255 -2.4026749 -0.24768899
+ 1000 0.45259485 -2.8743423 0.22311811 -2.4240104 -0.14864606
+ 1500 0.4211022 -2.8019061 0.19532181 -2.3829095 0.18067144
+ 2000 0.39019893 -2.7914865 0.22407024 -2.4032385 -0.4091294
+ 2500 0.40223098 -2.8137328 0.24270568 -2.4135129 -0.33712682
+ 3000 0.43134251 -2.8297507 0.23156863 -2.4005649 -0.03874002
+ 3500 0.4371177 -2.7992742 0.20071043 -2.3643421 -0.1177505
+ 4000 0.40172237 -2.783663 0.22854198 -2.3839493 -0.016498497
+ 4500 0.43131902 -2.8033297 0.22274751 -2.3741673 0.042304219
+ 5000 0.43199785 -2.8317062 0.25487137 -2.4018684 -0.13863416
+ 5500 0.45130496 -2.8225328 0.23220183 -2.3734843 0.11468611
+ 6000 0.45365193 -2.8417511 0.24954005 -2.3903675 -0.12276716
+ 6500 0.46129146 -2.8010207 0.21880638 -2.3420357 -0.13052608
+ 7000 0.41700962 -2.7768891 0.25189185 -2.3619645 -0.41894812
+ 7500 0.4156575 -2.7287605 0.21704468 -2.3151813 0.022065042
+ 8000 0.43032108 -2.7802305 0.2541409 -2.352061 0.018040465
+ 8500 0.47855371 -2.7877194 0.2130575 -2.3115585 -0.10958707
+ 9000 0.42318631 -2.7600929 0.25229644 -2.3390225 0.36820391
+ 9500 0.42857449 -2.6958592 0.18686752 -2.2694276 0.15379721
+ 10000 0.43323126 -2.71981 0.22185737 -2.2887449 0.038354509
+Loop time of 0.405458 on 4 procs for 10000 steps with 200 atoms
+
+Performance: 10654618.438 tau/day, 24663.469 timesteps/s
+99.3% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.17794 | 0.23423 | 0.25599 | 6.7 | 57.77
+Neigh | 0.0083153 | 0.010322 | 0.011204 | 1.2 | 2.55
+Comm | 0.086873 | 0.11001 | 0.17048 | 10.6 | 27.13
+Output | 0.00028467 | 0.00030136 | 0.00034618 | 0.1 | 0.07
+Modify | 0.021868 | 0.024962 | 0.026442 | 1.1 | 6.16
+Other | | 0.02564 | | | 6.32
+
+Nlocal: 50 ave 53 max 41 min
+Histogram: 1 0 0 0 0 0 0 0 0 3
+Nghost: 89.75 ave 94 max 83 min
+Histogram: 1 0 0 0 0 0 1 0 1 1
+Neighs: 411.25 ave 459 max 307 min
+Histogram: 1 0 0 0 0 0 0 0 2 1
+
+Total # of neighbors = 1645
+Ave neighs/atom = 8.225
+Neighbor list builds = 685
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/dreiding/log.15Feb16.dreiding.g++.1 b/examples/dreiding/log.15Feb16.dreiding.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..c7bb42325d193ee9c787417b115617452af95cbc
--- /dev/null
+++ b/examples/dreiding/log.15Feb16.dreiding.g++.1
@@ -0,0 +1,117 @@
+LAMMPS (15 Feb 2016)
+units real
+atom_style full
+boundary p p p
+dielectric 1
+special_bonds lj/coul 0.0 0.0 1.0
+
+pair_style hybrid/overlay hbond/dreiding/lj 2 6 6.5 90 lj/cut/coul/long 8.50000 11.5
+bond_style harmonic
+angle_style harmonic
+dihedral_style harmonic
+improper_style none
+kspace_style pppm 0.001
+
+read_data data.dreiding
+ orthogonal box = (0 0 0) to (19.9969 19.1282 19.4697)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 384 atoms
+ scanning bonds ...
+ 4 = max bonds/atom
+ scanning angles ...
+ 6 = max angles/atom
+ scanning dihedrals ...
+ 3 = max dihedrals/atom
+ reading bonds ...
+ 320 bonds
+ reading angles ...
+ 448 angles
+ reading dihedrals ...
+ 192 dihedrals
+ 4 = max # of 1-2 neighbors
+ 3 = max # of 1-3 neighbors
+ 5 = max # of special neighbors
+
+pair_coeff 1 1 lj/cut/coul/long 0.015200000256300 2.846421344984478
+pair_coeff 1 2 lj/cut/coul/long 0.001232882795416 2.846421344984478
+pair_coeff 1 3 lj/cut/coul/long 0.038019995160237 3.159705878878677
+pair_coeff 1 4 lj/cut/coul/long 0.038139744011598 2.939787518071103
+pair_coeff 2 2 lj/cut/coul/long 9.99999974737875e-05 2.846421344984478
+pair_coeff 2 3 lj/cut/coul/long 0.003083828758188 3.159705878878677
+pair_coeff 2 4 lj/cut/coul/long 0.003093541672406 2.939787518071103
+pair_coeff 3 3 lj/cut/coul/long 0.095100000500679 3.472990412772877
+pair_coeff 3 4 lj/cut/coul/long 0.095399530150179 3.253072051965302
+pair_coeff 4 4 lj/cut/coul/long 0.095700003206730 3.033153691157727
+pair_coeff 4 4 hbond/dreiding/lj 2 i 0.4000E+01 2.750000000000000 4
+pair_modify mix arithmetic
+neighbor 2.0 multi
+neigh_modify every 2 delay 4 check yes
+variable input index in.ch3oh.box.dreiding
+variable sname index ch3oh.box.dreiding
+
+compute hb all pair hbond/dreiding/lj
+variable C_hbond equal c_hb[1] #number hbonds
+variable E_hbond equal c_hb[2] #hbond energy
+thermo_style custom etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong v_E_hbond v_C_hbond press vol
+thermo_modify line multi format float %14.6f
+
+run 0
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+PPPM initialization ...
+WARNING: System is not charge neutral, net charge = -0.00064 (../kspace.cpp:297)
+ G vector (1/distance) = 0.142073
+ grid = 3 3 3
+ stencil order = 5
+ estimated absolute RMS force accuracy = 0.154715
+ estimated relative force accuracy = 0.00046592
+ using double precision FFTs
+ 3d grid and FFT values/proc = 512 27
+Neighbor list info ...
+ 3 neighbor list requests
+ update every 2 steps, delay 4 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 13.5
+ ghost atom cutoff = 13.5
+ binsize = 6.75 -> bins = 3 3 3
+Memory usage per processor = 8.70358 Mbytes
+---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
+TotEng = 113.723601 KinEng = 0.000000 Temp = 0.000000
+PotEng = 113.723601 E_bond = 0.535673 E_angle = 1.281880
+E_dihed = 1.232497 E_impro = 0.000000 E_vdwl = -125.381324
+E_coul = 597.219740 E_long = -361.164864 E_hbond = -69.322152
+C_hbond = 235.000000 Press = -328.847347 Volume = 7447.236335
+Loop time of 1.90735e-06 on 1 procs for 0 steps with 384 atoms
+
+0.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Bond | 0 | 0 | 0 | 0.0 | 0.00
+Kspace | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 1.907e-06 | | |100.00
+
+Nlocal: 384 ave 384 max 384 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 4637 ave 4637 max 4637 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 101854 ave 101854 max 101854 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs: 203708 ave 203708 max 203708 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 203708
+Ave neighs/atom = 530.49
+Ave special neighs/atom = 4
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:00
diff --git a/examples/dreiding/log.15Feb16.dreiding.g++.4 b/examples/dreiding/log.15Feb16.dreiding.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..2b04cf91fdc4c2c9f1b1f30980d3f092a37f70b9
--- /dev/null
+++ b/examples/dreiding/log.15Feb16.dreiding.g++.4
@@ -0,0 +1,117 @@
+LAMMPS (15 Feb 2016)
+units real
+atom_style full
+boundary p p p
+dielectric 1
+special_bonds lj/coul 0.0 0.0 1.0
+
+pair_style hybrid/overlay hbond/dreiding/lj 2 6 6.5 90 lj/cut/coul/long 8.50000 11.5
+bond_style harmonic
+angle_style harmonic
+dihedral_style harmonic
+improper_style none
+kspace_style pppm 0.001
+
+read_data data.dreiding
+ orthogonal box = (0 0 0) to (19.9969 19.1282 19.4697)
+ 2 by 1 by 2 MPI processor grid
+ reading atoms ...
+ 384 atoms
+ scanning bonds ...
+ 4 = max bonds/atom
+ scanning angles ...
+ 6 = max angles/atom
+ scanning dihedrals ...
+ 3 = max dihedrals/atom
+ reading bonds ...
+ 320 bonds
+ reading angles ...
+ 448 angles
+ reading dihedrals ...
+ 192 dihedrals
+ 4 = max # of 1-2 neighbors
+ 3 = max # of 1-3 neighbors
+ 5 = max # of special neighbors
+
+pair_coeff 1 1 lj/cut/coul/long 0.015200000256300 2.846421344984478
+pair_coeff 1 2 lj/cut/coul/long 0.001232882795416 2.846421344984478
+pair_coeff 1 3 lj/cut/coul/long 0.038019995160237 3.159705878878677
+pair_coeff 1 4 lj/cut/coul/long 0.038139744011598 2.939787518071103
+pair_coeff 2 2 lj/cut/coul/long 9.99999974737875e-05 2.846421344984478
+pair_coeff 2 3 lj/cut/coul/long 0.003083828758188 3.159705878878677
+pair_coeff 2 4 lj/cut/coul/long 0.003093541672406 2.939787518071103
+pair_coeff 3 3 lj/cut/coul/long 0.095100000500679 3.472990412772877
+pair_coeff 3 4 lj/cut/coul/long 0.095399530150179 3.253072051965302
+pair_coeff 4 4 lj/cut/coul/long 0.095700003206730 3.033153691157727
+pair_coeff 4 4 hbond/dreiding/lj 2 i 0.4000E+01 2.750000000000000 4
+pair_modify mix arithmetic
+neighbor 2.0 multi
+neigh_modify every 2 delay 4 check yes
+variable input index in.ch3oh.box.dreiding
+variable sname index ch3oh.box.dreiding
+
+compute hb all pair hbond/dreiding/lj
+variable C_hbond equal c_hb[1] #number hbonds
+variable E_hbond equal c_hb[2] #hbond energy
+thermo_style custom etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong v_E_hbond v_C_hbond press vol
+thermo_modify line multi format float %14.6f
+
+run 0
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+PPPM initialization ...
+WARNING: System is not charge neutral, net charge = -0.00064 (../kspace.cpp:297)
+ G vector (1/distance) = 0.142073
+ grid = 3 3 3
+ stencil order = 5
+ estimated absolute RMS force accuracy = 0.154715
+ estimated relative force accuracy = 0.00046592
+ using double precision FFTs
+ 3d grid and FFT values/proc = 392 12
+Neighbor list info ...
+ 3 neighbor list requests
+ update every 2 steps, delay 4 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 13.5
+ ghost atom cutoff = 13.5
+ binsize = 6.75 -> bins = 3 3 3
+Memory usage per processor = 8.55822 Mbytes
+---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
+TotEng = 113.723601 KinEng = 0.000000 Temp = 0.000000
+PotEng = 113.723601 E_bond = 0.535673 E_angle = 1.281880
+E_dihed = 1.232497 E_impro = 0.000000 E_vdwl = -125.381324
+E_coul = 597.219740 E_long = -361.164864 E_hbond = -69.322152
+C_hbond = 235.000000 Press = -328.847347 Volume = 7447.236335
+Loop time of 3.33786e-06 on 4 procs for 0 steps with 384 atoms
+
+0.0% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Bond | 0 | 0 | 0 | 0.0 | 0.00
+Kspace | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 3.338e-06 | | |100.00
+
+Nlocal: 96 ave 104 max 87 min
+Histogram: 1 1 0 0 0 0 0 0 0 2
+Nghost: 3063.25 ave 3108 max 3024 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+Neighs: 25463.5 ave 28799 max 22471 min
+Histogram: 1 0 0 1 0 1 0 0 0 1
+FullNghs: 50927 ave 55516 max 46073 min
+Histogram: 1 1 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 203708
+Ave neighs/atom = 530.49
+Ave special neighs/atom = 4
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:00
diff --git a/examples/eim/log.15Feb16.eim.g++.1 b/examples/eim/log.15Feb16.eim.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..f9e821679606bd61b821946f08507ef515cba0f0
--- /dev/null
+++ b/examples/eim/log.15Feb16.eim.g++.1
@@ -0,0 +1,88 @@
+LAMMPS (15 Feb 2016)
+# NaCl test problem for embedded atom method (EIM) potential
+
+units metal
+atom_style atomic
+
+boundary p p p
+
+lattice diamond 5.0
+Lattice spacing in x,y,z = 5 5 5
+read_data data.eim
+ orthogonal box = (-0.5 -0.5 -0.5) to (35.54 35.54 35.54)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 2000 atoms
+ reading velocities ...
+ 2000 velocities
+
+pair_style eim
+pair_coeff * * Na Cl ffield.eim Na Cl
+Reading potential file ffield.eim with DATE: 2010-08-31
+
+neighbor 0.3 bin
+neigh_modify delay 0
+
+timestep 0.001
+thermo_style custom step pe pxx pyy pzz temp
+thermo 50
+
+velocity all create 1400.0 43454 dist gaussian mom yes
+fix int all npt temp 1400.0 300.0 0.1 aniso 0.0 0.0 0.1
+
+#dump id all atom 100 dump.eim
+
+#dump 2 all image 25 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 3 element Na Cl
+
+#dump 3 all movie 25 movie.mpg element element # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 3 element Na Cl
+
+run 500
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 7.906
+ ghost atom cutoff = 7.906
+ binsize = 3.953 -> bins = 10 10 10
+Memory usage per processor = 2.33063 Mbytes
+Step PotEng Pxx Pyy Pzz Temp
+ 0 -5660.4738 -118151.29 -117613.39 -118064.41 1400
+ 50 -5773.8661 889.73924 898.43321 703.5365 891.68472
+ 100 -5742.8192 866.6183 817.86837 889.72898 838.77403
+ 150 -5738.752 -335.23317 -345.69716 -123.3196 900.54672
+ 200 -5704.2444 -172.01932 -508.83888 -654.45947 834.82705
+ 250 -5724.4679 375.50199 546.99196 405.29298 966.14585
+ 300 -5718.5442 428.47856 361.93998 752.00729 934.57116
+ 350 -5722.7694 -409.40162 -484.53168 42.702482 865.13075
+ 400 -5743.6862 173.43552 288.02324 107.96614 840.48912
+ 450 -5751.3366 -752.54635 -762.07316 -591.45022 743.42176
+ 500 -5780.5266 -157.23981 84.510897 -52.426827 712.64129
+Loop time of 5.98 on 1 procs for 500 steps with 2000 atoms
+
+Performance: 7.224 ns/day, 3.322 hours/ns, 83.612 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 5.5037 | 5.5037 | 5.5037 | 0.0 | 92.04
+Neigh | 0.38962 | 0.38962 | 0.38962 | 0.0 | 6.52
+Comm | 0.01958 | 0.01958 | 0.01958 | 0.0 | 0.33
+Output | 0.00030184 | 0.00030184 | 0.00030184 | 0.0 | 0.01
+Modify | 0.058852 | 0.058852 | 0.058852 | 0.0 | 0.98
+Other | | 0.007943 | | | 0.13
+
+Nlocal: 2000 ave 2000 max 2000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 4194 ave 4194 max 4194 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 99537 ave 99537 max 99537 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 99537
+Ave neighs/atom = 49.7685
+Neighbor list builds = 89
+Dangerous builds = 10
+Total wall time: 0:00:06
diff --git a/examples/eim/log.15Feb16.eim.g++.4 b/examples/eim/log.15Feb16.eim.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..7586427a7df9fe7645cb9ee413a73be714576c9d
--- /dev/null
+++ b/examples/eim/log.15Feb16.eim.g++.4
@@ -0,0 +1,88 @@
+LAMMPS (15 Feb 2016)
+# NaCl test problem for embedded atom method (EIM) potential
+
+units metal
+atom_style atomic
+
+boundary p p p
+
+lattice diamond 5.0
+Lattice spacing in x,y,z = 5 5 5
+read_data data.eim
+ orthogonal box = (-0.5 -0.5 -0.5) to (35.54 35.54 35.54)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 2000 atoms
+ reading velocities ...
+ 2000 velocities
+
+pair_style eim
+pair_coeff * * Na Cl ffield.eim Na Cl
+Reading potential file ffield.eim with DATE: 2010-08-31
+
+neighbor 0.3 bin
+neigh_modify delay 0
+
+timestep 0.001
+thermo_style custom step pe pxx pyy pzz temp
+thermo 50
+
+velocity all create 1400.0 43454 dist gaussian mom yes
+fix int all npt temp 1400.0 300.0 0.1 aniso 0.0 0.0 0.1
+
+#dump id all atom 100 dump.eim
+
+#dump 2 all image 25 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 3 element Na Cl
+
+#dump 3 all movie 25 movie.mpg element element # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 3 element Na Cl
+
+run 500
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 7.906
+ ghost atom cutoff = 7.906
+ binsize = 3.953 -> bins = 10 10 10
+Memory usage per processor = 2.21734 Mbytes
+Step PotEng Pxx Pyy Pzz Temp
+ 0 -5660.4738 -118151.29 -117613.39 -118064.41 1400
+ 50 -5773.8661 889.73924 898.43321 703.5365 891.68472
+ 100 -5742.8192 866.6183 817.86837 889.72898 838.77403
+ 150 -5738.752 -335.23317 -345.69716 -123.3196 900.54672
+ 200 -5704.2444 -172.01932 -508.83888 -654.45947 834.82705
+ 250 -5724.4679 375.50199 546.99196 405.29298 966.14585
+ 300 -5718.5442 428.47856 361.93998 752.00729 934.57116
+ 350 -5722.7694 -409.40162 -484.53168 42.702482 865.13075
+ 400 -5743.6862 173.43552 288.02324 107.96614 840.48912
+ 450 -5751.3366 -752.54635 -762.07316 -591.45022 743.42176
+ 500 -5780.5266 -157.23981 84.510897 -52.426827 712.64129
+Loop time of 1.57729 on 4 procs for 500 steps with 2000 atoms
+
+Performance: 27.389 ns/day, 0.876 hours/ns, 316.999 timesteps/s
+99.7% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 1.3994 | 1.4083 | 1.4269 | 0.9 | 89.29
+Neigh | 0.096567 | 0.096771 | 0.097035 | 0.1 | 6.14
+Comm | 0.02714 | 0.045477 | 0.054307 | 5.0 | 2.88
+Output | 0.00022769 | 0.0002473 | 0.00029278 | 0.2 | 0.02
+Modify | 0.021543 | 0.021803 | 0.022018 | 0.1 | 1.38
+Other | | 0.004696 | | | 0.30
+
+Nlocal: 500 ave 501 max 498 min
+Histogram: 1 0 0 0 0 0 1 0 0 2
+Nghost: 2179.25 ave 2182 max 2175 min
+Histogram: 1 0 0 0 0 1 0 0 1 1
+Neighs: 24884.2 ave 25164 max 24622 min
+Histogram: 1 0 0 1 0 1 0 0 0 1
+
+Total # of neighbors = 99537
+Ave neighs/atom = 49.7685
+Neighbor list builds = 89
+Dangerous builds = 10
+Total wall time: 0:00:01
diff --git a/examples/ellipse/log.15Feb16.ellipse.gayberne.g++.1 b/examples/ellipse/log.15Feb16.ellipse.gayberne.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..194175b2d8f610079cb5133541b7ce0927bb9519
--- /dev/null
+++ b/examples/ellipse/log.15Feb16.ellipse.gayberne.g++.1
@@ -0,0 +1,185 @@
+LAMMPS (15 Feb 2016)
+# GayBerne ellipsoids in LJ background fluid
+
+units lj
+atom_style ellipsoid
+dimension 2
+
+lattice sq 0.02
+Lattice spacing in x,y,z = 7.07107 7.07107 7.07107
+region box block 0 20 0 20 -0.5 0.5
+create_box 2 box
+Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 400 atoms
+
+set group all type/fraction 2 0.1 95392
+ 45 settings made for type/fraction
+set type 1 mass 1.0
+ 355 settings made for mass
+set type 2 mass 1.5
+ 45 settings made for mass
+set type 1 shape 1 1 1
+ 355 settings made for shape
+set type 2 shape 3 1 1
+ 45 settings made for shape
+set group all quat/random 18238
+ 400 settings made for quat/random
+
+compute rot all temp/asphere
+group spheroid type 1
+355 atoms in group spheroid
+variable dof equal count(spheroid)+2
+compute_modify rot extra ${dof}
+compute_modify rot extra 357
+
+velocity all create 2.4 87287 loop geom
+
+pair_style gayberne 1.0 3.0 1.0 4.0
+pair_coeff 1 1 3.0 1.0 1 1 1 1 1 1 2.5
+pair_coeff 1 2 3.0 1.0 1 1 1 0 0 0
+pair_coeff 2 2 1.0 1.0 1 1 0.2 0 0 0
+
+neighbor 0.8 bin
+
+thermo_style custom step c_rot epair etotal press vol
+thermo 100
+
+timestep 0.002
+
+compute q all property/atom quatw quati quatj quatk
+
+#dump 1 all custom 100 dump.ellipse.gayberne # id type x y z c_q[1] c_q[2] c_q[3] c_q[4]
+
+#dump 2 all image 100 image.*.jpg type type # zoom 1.6 center d 0.5 0.5 0.5
+#dump_modify 2 pad 4 adiam 1 1.0 adiam 2 2.0
+
+#dump 3 all movie 100 movie.mpg type type # zoom 1.6 center d 0.5 0.5 0.5
+#dump_modify 3 pad 4 adiam 1 1.0 adiam 2 2.0
+
+fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 mtk no pchain 0 tchain 1
+fix 2 all enforce2d
+
+compute_modify 1_temp extra ${dof}
+compute_modify 1_temp extra 357
+
+# equilibrate to shrink box around dilute system
+
+run 2000
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 4.8
+ ghost atom cutoff = 4.8
+ binsize = 2.4 -> bins = 59 59 3
+Memory usage per processor = 4.17878 Mbytes
+Step rot E_pair TotEng Press Volume
+ 0 2.2718861 0 2.394 0.04788 20000
+ 100 1.7443002 0 1.8380563 0.03576216 20558.672
+ 200 2.2770454 0 2.3994366 0.046545139 20620.298
+ 300 1.8573283 0 1.9571597 0.04240689 18460.771
+ 400 2.1709732 -0.00046172705 2.2872012 0.066791266 13689.473
+ 500 1.9712384 -0.014365021 2.0484832 0.12263116 8475.3548
+ 600 2.0811163 -0.21654179 1.8340664 0.22433913 4685.3955
+ 700 2.1578657 -0.68696192 1.3974517 0.60188995 2533.8873
+ 800 1.8843124 -1.6343111 0.2143696 1.105687 1440.5961
+ 900 2.1968489 -3.0749104 -0.92393949 3.2168763 924.62895
+ 1000 1.4196808 -4.3944118 -2.972349 3.1895485 744.95136
+ 1100 1.9354395 -4.9265904 -2.9959864 1.5434922 715.87574
+ 1200 2.1063417 -4.5664569 -2.4467911 1.2012289 760.07454
+ 1300 1.859493 -4.1043918 -2.2530918 0.35847277 846.54577
+ 1400 2.1430322 -3.7414541 -1.6163368 0.7461639 928.96639
+ 1500 1.9056885 -3.5118131 -1.5910333 0.35347839 1021.0387
+ 1600 2.1297675 -3.2577617 -1.119554 0.73265236 1087.6271
+ 1700 1.9341135 -3.2121534 -1.2832848 0.46406018 1140.8473
+ 1800 2.0861201 -3.2382735 -1.1460071 0.6058924 1161.1051
+ 1900 1.9976529 -3.2494581 -1.2698889 0.69257341 1151.4372
+ 2000 1.9791754 -3.3850065 -1.3653244 0.88473341 1121.7026
+Loop time of 1.034 on 1 procs for 2000 steps with 400 atoms
+
+Performance: 334235.078 tau/day, 1934.231 timesteps/s
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.82535 | 0.82535 | 0.82535 | 0.0 | 79.82
+Neigh | 0.01368 | 0.01368 | 0.01368 | 0.0 | 1.32
+Comm | 0.011166 | 0.011166 | 0.011166 | 0.0 | 1.08
+Output | 0.00032282 | 0.00032282 | 0.00032282 | 0.0 | 0.03
+Modify | 0.17955 | 0.17955 | 0.17955 | 0.0 | 17.36
+Other | | 0.003941 | | | 0.38
+
+Nlocal: 400 ave 400 max 400 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 249 ave 249 max 249 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 3031 ave 3031 max 3031 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 3031
+Ave neighs/atom = 7.5775
+Neighbor list builds = 140
+Dangerous builds = 80
+
+# run dynamics on dense system
+
+unfix 1
+fix 1 all nve/asphere
+
+run 2000
+Memory usage per processor = 4.18892 Mbytes
+Step rot E_pair TotEng Press Volume
+ 2000 1.9791754 -3.3850065 -1.3653244 0.88473341 1121.7026
+ 2100 2.0067383 -3.4164295 -1.402453 0.63163512 1121.7026
+ 2200 2.0298976 -3.4415998 -1.4231421 0.91861985 1121.7026
+ 2300 2.0418707 -3.4552616 -1.4277716 0.58834236 1121.7026
+ 2400 2.0126621 -3.424202 -1.3839096 0.80723942 1121.7026
+ 2500 1.9403964 -3.3489489 -1.3995215 0.79492719 1121.7026
+ 2600 2.0459304 -3.4600931 -1.4229608 0.69699402 1121.7026
+ 2700 2.0032293 -3.4126492 -1.429784 0.44210814 1121.7026
+ 2800 1.9367905 -3.345688 -1.4171068 0.6872734 1121.7026
+ 2900 1.9870908 -3.3983385 -1.4218501 0.42402247 1121.7026
+ 3000 1.9654849 -3.3767671 -1.3835149 0.6611643 1121.7026
+ 3100 1.9308462 -3.3343018 -1.3895992 0.45213534 1121.7026
+ 3200 1.8924656 -3.2956948 -1.4157919 0.56524685 1121.7026
+ 3300 1.8802888 -3.2822198 -1.4071878 0.86030365 1121.7026
+ 3400 1.8847013 -3.2852796 -1.4162404 0.91660541 1121.7026
+ 3500 1.9290452 -3.3332356 -1.3889879 0.70770119 1121.7026
+ 3600 1.9223314 -3.32413 -1.3896278 0.56763748 1121.7026
+ 3700 1.9185132 -3.3197222 -1.3913701 0.66889312 1121.7026
+ 3800 1.877321 -3.2796045 -1.4050964 0.67335591 1121.7026
+ 3900 1.9250447 -3.3313033 -1.3872185 0.64573122 1121.7026
+ 4000 1.8574113 -3.2592142 -1.3807543 0.46117918 1121.7026
+Loop time of 1.15469 on 1 procs for 2000 steps with 400 atoms
+
+Performance: 299301.907 tau/day, 1732.071 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 1.0251 | 1.0251 | 1.0251 | 0.0 | 88.77
+Neigh | 0.0063124 | 0.0063124 | 0.0063124 | 0.0 | 0.55
+Comm | 0.011792 | 0.011792 | 0.011792 | 0.0 | 1.02
+Output | 0.00035834 | 0.00035834 | 0.00035834 | 0.0 | 0.03
+Modify | 0.10537 | 0.10537 | 0.10537 | 0.0 | 9.13
+Other | | 0.005782 | | | 0.50
+
+Nlocal: 400 ave 400 max 400 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 219 ave 219 max 219 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 3046 ave 3046 max 3046 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 3046
+Ave neighs/atom = 7.615
+Neighbor list builds = 47
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:02
diff --git a/examples/ellipse/log.15Feb16.ellipse.gayberne.g++.4 b/examples/ellipse/log.15Feb16.ellipse.gayberne.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..2a1babaefc0f28239a7d3f1296740340e22b2443
--- /dev/null
+++ b/examples/ellipse/log.15Feb16.ellipse.gayberne.g++.4
@@ -0,0 +1,185 @@
+LAMMPS (15 Feb 2016)
+# GayBerne ellipsoids in LJ background fluid
+
+units lj
+atom_style ellipsoid
+dimension 2
+
+lattice sq 0.02
+Lattice spacing in x,y,z = 7.07107 7.07107 7.07107
+region box block 0 20 0 20 -0.5 0.5
+create_box 2 box
+Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553)
+ 2 by 2 by 1 MPI processor grid
+create_atoms 1 box
+Created 400 atoms
+
+set group all type/fraction 2 0.1 95392
+ 45 settings made for type/fraction
+set type 1 mass 1.0
+ 355 settings made for mass
+set type 2 mass 1.5
+ 45 settings made for mass
+set type 1 shape 1 1 1
+ 355 settings made for shape
+set type 2 shape 3 1 1
+ 45 settings made for shape
+set group all quat/random 18238
+ 400 settings made for quat/random
+
+compute rot all temp/asphere
+group spheroid type 1
+355 atoms in group spheroid
+variable dof equal count(spheroid)+2
+compute_modify rot extra ${dof}
+compute_modify rot extra 357
+
+velocity all create 2.4 87287 loop geom
+
+pair_style gayberne 1.0 3.0 1.0 4.0
+pair_coeff 1 1 3.0 1.0 1 1 1 1 1 1 2.5
+pair_coeff 1 2 3.0 1.0 1 1 1 0 0 0
+pair_coeff 2 2 1.0 1.0 1 1 0.2 0 0 0
+
+neighbor 0.8 bin
+
+thermo_style custom step c_rot epair etotal press vol
+thermo 100
+
+timestep 0.002
+
+compute q all property/atom quatw quati quatj quatk
+
+#dump 1 all custom 100 dump.ellipse.gayberne # id type x y z c_q[1] c_q[2] c_q[3] c_q[4]
+
+#dump 2 all image 100 image.*.jpg type type # zoom 1.6 center d 0.5 0.5 0.5
+#dump_modify 2 pad 4 adiam 1 1.0 adiam 2 2.0
+
+#dump 3 all movie 100 movie.mpg type type # zoom 1.6 center d 0.5 0.5 0.5
+#dump_modify 3 pad 4 adiam 1 1.0 adiam 2 2.0
+
+fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 mtk no pchain 0 tchain 1
+fix 2 all enforce2d
+
+compute_modify 1_temp extra ${dof}
+compute_modify 1_temp extra 357
+
+# equilibrate to shrink box around dilute system
+
+run 2000
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 4.8
+ ghost atom cutoff = 4.8
+ binsize = 2.4 -> bins = 59 59 3
+Memory usage per processor = 4.16784 Mbytes
+Step rot E_pair TotEng Press Volume
+ 0 2.2718861 0 2.394 0.04788 20000
+ 100 1.7443002 0 1.8380563 0.03576216 20558.672
+ 200 2.2770454 0 2.3994366 0.046545139 20620.298
+ 300 1.8573283 0 1.9571597 0.04240689 18460.771
+ 400 2.1709732 -0.00046172705 2.2872012 0.066791266 13689.473
+ 500 1.9712384 -0.014365021 2.0484832 0.12263116 8475.3548
+ 600 2.0811163 -0.21654179 1.8340664 0.22433913 4685.3955
+ 700 2.1578657 -0.68696192 1.3974517 0.60188995 2533.8873
+ 800 1.8843124 -1.6343111 0.2143696 1.105687 1440.5961
+ 900 2.1968489 -3.0749104 -0.92393949 3.2168763 924.62895
+ 1000 1.4196808 -4.3944118 -2.972349 3.1895485 744.95136
+ 1100 1.9354395 -4.9265904 -2.9959864 1.5434922 715.87574
+ 1200 2.1063417 -4.5664569 -2.4467911 1.2012289 760.07454
+ 1300 1.859493 -4.1043918 -2.2530918 0.35847277 846.54577
+ 1400 2.1430322 -3.7414541 -1.6163368 0.7461639 928.96639
+ 1500 1.9056885 -3.5118131 -1.5910333 0.35347839 1021.0387
+ 1600 2.1297675 -3.2577617 -1.119554 0.73265236 1087.6271
+ 1700 1.9341135 -3.2121534 -1.2832848 0.46406018 1140.8473
+ 1800 2.0861201 -3.2382735 -1.1460071 0.6058924 1161.1051
+ 1900 1.9976529 -3.2494581 -1.2698889 0.69257341 1151.4372
+ 2000 1.9791754 -3.3850065 -1.3653244 0.88473343 1121.7026
+Loop time of 0.513848 on 4 procs for 2000 steps with 400 atoms
+
+Performance: 672572.269 tau/day, 3892.201 timesteps/s
+88.1% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.19352 | 0.21426 | 0.23184 | 3.0 | 41.70
+Neigh | 0.0034561 | 0.0036583 | 0.0038161 | 0.3 | 0.71
+Comm | 0.10711 | 0.12693 | 0.14494 | 4.6 | 24.70
+Output | 0.0016916 | 0.0017142 | 0.0017467 | 0.1 | 0.33
+Modify | 0.14238 | 0.15759 | 0.16878 | 2.4 | 30.67
+Other | | 0.009694 | | | 1.89
+
+Nlocal: 100 ave 113 max 85 min
+Histogram: 1 0 0 1 0 0 0 1 0 1
+Nghost: 149.75 ave 160 max 141 min
+Histogram: 1 1 0 0 0 0 1 0 0 1
+Neighs: 757.75 ave 885 max 592 min
+Histogram: 1 0 0 1 0 0 0 0 1 1
+
+Total # of neighbors = 3031
+Ave neighs/atom = 7.5775
+Neighbor list builds = 140
+Dangerous builds = 80
+
+# run dynamics on dense system
+
+unfix 1
+fix 1 all nve/asphere
+
+run 2000
+Memory usage per processor = 4.16867 Mbytes
+Step rot E_pair TotEng Press Volume
+ 2000 1.9791754 -3.3850065 -1.3653244 0.88473343 1121.7026
+ 2100 2.0067383 -3.4164295 -1.402453 0.63163513 1121.7026
+ 2200 2.0298976 -3.4415998 -1.4231421 0.91861985 1121.7026
+ 2300 2.0418708 -3.4552617 -1.4277716 0.58834191 1121.7026
+ 2400 2.0126625 -3.4242024 -1.3839097 0.80723766 1121.7026
+ 2500 1.9403968 -3.3489494 -1.3995212 0.79492647 1121.7026
+ 2600 2.0459318 -3.4600945 -1.4229599 0.69698729 1121.7026
+ 2700 2.0032338 -3.4126541 -1.4297892 0.44208354 1121.7026
+ 2800 1.9367789 -3.3456765 -1.4171038 0.6873665 1121.7026
+ 2900 1.9870979 -3.3983434 -1.4218523 0.42398659 1121.7026
+ 3000 1.965491 -3.376773 -1.3835208 0.66112051 1121.7026
+ 3100 1.9307633 -3.3342121 -1.3895745 0.45224657 1121.7026
+ 3200 1.8918453 -3.2949278 -1.4157216 0.56825582 1121.7026
+ 3300 1.8824584 -3.2844031 -1.4066487 0.85795659 1121.7026
+ 3400 1.8871451 -3.2878452 -1.4156691 0.91410213 1121.7026
+ 3500 1.9297625 -3.3340904 -1.3901995 0.6754809 1121.7026
+ 3600 1.8994197 -3.3009141 -1.3964162 0.58676937 1121.7026
+ 3700 1.9181765 -3.3204193 -1.3956433 0.54632736 1121.7026
+ 3800 1.9278078 -3.3300748 -1.3999307 0.48904879 1121.7026
+ 3900 1.888321 -3.2896024 -1.3848249 0.49521159 1121.7026
+ 4000 1.8372182 -3.2347372 -1.4091759 0.61895915 1121.7026
+Loop time of 0.373834 on 4 procs for 2000 steps with 400 atoms
+
+Performance: 924475.349 tau/day, 5349.973 timesteps/s
+99.7% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.25404 | 0.26703 | 0.29737 | 3.4 | 71.43
+Neigh | 0.0014787 | 0.0016722 | 0.0018535 | 0.3 | 0.45
+Comm | 0.036186 | 0.068545 | 0.082895 | 7.2 | 18.34
+Output | 0.00050688 | 0.00052452 | 0.00055194 | 0.1 | 0.14
+Modify | 0.025374 | 0.027727 | 0.030269 | 1.1 | 7.42
+Other | | 0.008336 | | | 2.23
+
+Nlocal: 100 ave 106 max 92 min
+Histogram: 1 0 0 0 0 1 0 1 0 1
+Nghost: 148 ave 152 max 145 min
+Histogram: 1 1 0 0 0 1 0 0 0 1
+Neighs: 760.25 ave 815 max 713 min
+Histogram: 1 1 0 0 0 0 1 0 0 1
+
+Total # of neighbors = 3041
+Ave neighs/atom = 7.6025
+Neighbor list builds = 46
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:00
diff --git a/examples/ellipse/log.15Feb16.ellipse.resquared.g++.1 b/examples/ellipse/log.15Feb16.ellipse.resquared.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..6aaac2250741b9273101205ba184a5e791681af2
--- /dev/null
+++ b/examples/ellipse/log.15Feb16.ellipse.resquared.g++.1
@@ -0,0 +1,182 @@
+LAMMPS (15 Feb 2016)
+# RESquared ellipsoids in LJ background fluid
+
+units lj
+atom_style ellipsoid
+dimension 2
+
+lattice sq 0.02
+Lattice spacing in x,y,z = 7.07107 7.07107 7.07107
+region box block 0 20 0 20 -0.5 0.5
+create_box 2 box
+Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 400 atoms
+
+set group all type/fraction 2 0.1 95392
+ 45 settings made for type/fraction
+set type 1 mass 1.0
+ 355 settings made for mass
+set type 2 mass 1.5
+ 45 settings made for mass
+set type 1 shape 1 1 1
+ 355 settings made for shape
+set type 2 shape 3 1 1
+ 45 settings made for shape
+set group all quat/random 18238
+ 400 settings made for quat/random
+
+compute rot all temp/asphere
+group spheroid type 1
+355 atoms in group spheroid
+variable dof equal count(spheroid)+2
+compute_modify rot extra ${dof}
+compute_modify rot extra 357
+
+velocity all create 2.4 87287 loop geom
+
+pair_style resquared 4.0
+pair_coeff 1 1 3.0 1 1 1 1 1 1 1 2.5
+pair_coeff 1 2 3.0 1 1 1 1 0 0 0
+pair_coeff 2 2 1.0 1 1 1 0.2 0 0 0
+
+neighbor 0.8 bin
+
+thermo_style custom step c_rot epair etotal press vol
+thermo 100
+
+timestep 0.002
+
+compute q all property/atom quatw quati quatj quatk
+
+#dump 1 all custom 100 dump.ellipse.resquared # id type x y z c_q[1] c_q[2] c_q[3] c_q[4]
+
+#dump 2 all image 100 image.*.jpg type type # zoom 1.6 center d 0.5 0.5 0.5
+#dump_modify 2 pad 4 adiam 1 1.0 adiam 2 2.0
+
+#dump 3 all movie 100 movie.mpg type type # zoom 1.6 center d 0.5 0.5 0.5
+#dump_modify 3 pad 4 adiam 1 1.0 adiam 2 2.0
+
+fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 mtk no pchain 0 tchain 1
+fix 2 all enforce2d
+
+compute_modify 1_temp extra ${dof}
+compute_modify 1_temp extra 357
+
+# equilibrate to shrink box around dilute system
+
+run 2000
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 4.8
+ ghost atom cutoff = 4.8
+ binsize = 2.4 -> bins = 59 59 3
+Memory usage per processor = 4.17878 Mbytes
+Step rot E_pair TotEng Press Volume
+ 0 2.2718861 0 2.394 0.04788 20000
+ 100 1.7443002 0 1.8380563 0.03576216 20558.672
+ 200 2.2770454 0 2.3994366 0.046545139 20620.298
+ 300 1.8573283 0 1.9571597 0.04240689 18460.771
+ 400 2.1708593 -2.5387568e-05 2.2875176 0.066837565 13689.499
+ 500 2.012121 0.0083622744 2.0637959 0.10893231 8486.4241
+ 600 2.1416108 0.08602656 2.2040317 0.34087235 4775.2723
+ 700 2.0419962 0.17405962 2.1702488 0.78836378 2768.5757
+ 800 1.9520613 0.31921669 2.2528751 1.813059 1823.5943
+ 900 1.6291778 0.2415422 1.8569794 1.7008233 1518.2585
+ 1000 1.9412761 0.13859576 2.1184352 1.3019342 1521.7058
+ 1100 2.1016581 0.10912963 2.2356017 0.99454361 1756.0608
+ 1200 1.7849978 0.049963029 1.8591867 0.54025938 2204.358
+ 1300 2.3125867 0.046557089 2.3849986 0.47599584 2761.2014
+ 1400 1.757077 0.026326047 1.7889269 0.28604209 3309.8144
+ 1500 2.392565 0.048563131 2.4533846 0.37917665 3530.6855
+ 1600 1.7590832 0.050490264 1.8168201 0.33612171 3313.4472
+ 1700 2.252414 0.17372984 2.4394491 0.85851343 2716.0401
+ 1800 1.7966767 0.28338104 2.0779465 1.4326114 2152.4099
+ 1900 1.9682759 0.2168566 2.1183362 1.3383729 1806.7221
+ 2000 1.9694503 0.17559901 2.14777 1.3281701 1654.9587
+Loop time of 1.79538 on 1 procs for 2000 steps with 400 atoms
+
+Performance: 192494.490 tau/day, 1113.973 timesteps/s
+99.8% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 1.582 | 1.582 | 1.582 | 0.0 | 88.12
+Neigh | 0.013545 | 0.013545 | 0.013545 | 0.0 | 0.75
+Comm | 0.0087712 | 0.0087712 | 0.0087712 | 0.0 | 0.49
+Output | 0.00034428 | 0.00034428 | 0.00034428 | 0.0 | 0.02
+Modify | 0.18736 | 0.18736 | 0.18736 | 0.0 | 10.44
+Other | | 0.003359 | | | 0.19
+
+Nlocal: 400 ave 400 max 400 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 216 ave 216 max 216 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 1929 ave 1929 max 1929 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1929
+Ave neighs/atom = 4.8225
+Neighbor list builds = 177
+Dangerous builds = 146
+
+# run dynamics on dense system
+
+unfix 1
+fix 1 all nve/asphere
+
+run 2000
+Memory usage per processor = 4.18079 Mbytes
+Step rot E_pair TotEng Press Volume
+ 2000 1.9694503 0.17559901 2.14777 1.3281701 1654.9587
+ 2100 1.978918 0.16562152 2.1632874 1.3092233 1654.9587
+ 2200 1.9820406 0.16230289 2.1750657 1.2612976 1654.9587
+ 2300 1.9577019 0.18791066 2.1531422 1.3478385 1654.9587
+ 2400 2.0271146 0.11480565 2.1721336 1.0619428 1654.9587
+ 2500 1.9894838 0.1544598 2.1329407 1.2325572 1654.9587
+ 2600 1.998697 0.14468753 2.1485209 1.1903357 1654.9587
+ 2700 1.9608664 0.18459944 2.1483889 1.3461095 1654.9587
+ 2800 2.005755 0.13729992 2.1214078 1.1596182 1654.9587
+ 2900 1.9080687 0.24019772 2.1661723 1.5974752 1654.9587
+ 3000 1.9606374 0.18480425 2.1301691 1.3280548 1654.9587
+ 3100 1.9824235 0.16187644 2.1284432 1.2590072 1654.9587
+ 3200 1.9389485 0.20774117 2.106322 1.4587341 1654.9587
+ 3300 1.9849309 0.15929459 2.1301897 1.2415172 1654.9587
+ 3400 1.9596863 0.18578944 2.1215072 1.3738214 1654.9587
+ 3500 1.9671171 0.17804546 2.0934254 1.3147204 1654.9587
+ 3600 1.9702641 0.17471582 2.1569255 1.3331099 1654.9587
+ 3700 1.9103961 0.23792935 2.1305401 1.5832203 1654.9587
+ 3800 1.9129619 0.23512654 2.1445946 1.5657403 1654.9587
+ 3900 1.9868018 0.15725404 2.1658135 1.2582197 1654.9587
+ 4000 2.0058784 0.13726837 2.1534352 1.1351359 1654.9587
+Loop time of 3.05676 on 1 procs for 2000 steps with 400 atoms
+
+Performance: 113061.044 tau/day, 654.288 timesteps/s
+99.8% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 2.9201 | 2.9201 | 2.9201 | 0.0 | 95.53
+Neigh | 0.0051684 | 0.0051684 | 0.0051684 | 0.0 | 0.17
+Comm | 0.011668 | 0.011668 | 0.011668 | 0.0 | 0.38
+Output | 0.00038481 | 0.00038481 | 0.00038481 | 0.0 | 0.01
+Modify | 0.1134 | 0.1134 | 0.1134 | 0.0 | 3.71
+Other | | 0.00608 | | | 0.20
+
+Nlocal: 400 ave 400 max 400 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 204 ave 204 max 204 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 1857 ave 1857 max 1857 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1857
+Ave neighs/atom = 4.6425
+Neighbor list builds = 48
+Dangerous builds = 0
+Total wall time: 0:00:04
diff --git a/examples/ellipse/log.15Feb16.ellipse.resquared.g++.4 b/examples/ellipse/log.15Feb16.ellipse.resquared.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..49e3cda65f83516fb36ca63b5c47eeedf7ac2d4c
--- /dev/null
+++ b/examples/ellipse/log.15Feb16.ellipse.resquared.g++.4
@@ -0,0 +1,182 @@
+LAMMPS (15 Feb 2016)
+# RESquared ellipsoids in LJ background fluid
+
+units lj
+atom_style ellipsoid
+dimension 2
+
+lattice sq 0.02
+Lattice spacing in x,y,z = 7.07107 7.07107 7.07107
+region box block 0 20 0 20 -0.5 0.5
+create_box 2 box
+Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553)
+ 2 by 2 by 1 MPI processor grid
+create_atoms 1 box
+Created 400 atoms
+
+set group all type/fraction 2 0.1 95392
+ 45 settings made for type/fraction
+set type 1 mass 1.0
+ 355 settings made for mass
+set type 2 mass 1.5
+ 45 settings made for mass
+set type 1 shape 1 1 1
+ 355 settings made for shape
+set type 2 shape 3 1 1
+ 45 settings made for shape
+set group all quat/random 18238
+ 400 settings made for quat/random
+
+compute rot all temp/asphere
+group spheroid type 1
+355 atoms in group spheroid
+variable dof equal count(spheroid)+2
+compute_modify rot extra ${dof}
+compute_modify rot extra 357
+
+velocity all create 2.4 87287 loop geom
+
+pair_style resquared 4.0
+pair_coeff 1 1 3.0 1 1 1 1 1 1 1 2.5
+pair_coeff 1 2 3.0 1 1 1 1 0 0 0
+pair_coeff 2 2 1.0 1 1 1 0.2 0 0 0
+
+neighbor 0.8 bin
+
+thermo_style custom step c_rot epair etotal press vol
+thermo 100
+
+timestep 0.002
+
+compute q all property/atom quatw quati quatj quatk
+
+#dump 1 all custom 100 dump.ellipse.resquared # id type x y z c_q[1] c_q[2] c_q[3] c_q[4]
+
+#dump 2 all image 100 image.*.jpg type type # zoom 1.6 center d 0.5 0.5 0.5
+#dump_modify 2 pad 4 adiam 1 1.0 adiam 2 2.0
+
+#dump 3 all movie 100 movie.mpg type type # zoom 1.6 center d 0.5 0.5 0.5
+#dump_modify 3 pad 4 adiam 1 1.0 adiam 2 2.0
+
+fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 mtk no pchain 0 tchain 1
+fix 2 all enforce2d
+
+compute_modify 1_temp extra ${dof}
+compute_modify 1_temp extra 357
+
+# equilibrate to shrink box around dilute system
+
+run 2000
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 4.8
+ ghost atom cutoff = 4.8
+ binsize = 2.4 -> bins = 59 59 3
+Memory usage per processor = 4.16784 Mbytes
+Step rot E_pair TotEng Press Volume
+ 0 2.2718861 0 2.394 0.04788 20000
+ 100 1.7443002 0 1.8380563 0.03576216 20558.672
+ 200 2.2770454 0 2.3994366 0.046545139 20620.298
+ 300 1.8573283 0 1.9571597 0.04240689 18460.771
+ 400 2.1708593 -2.5387568e-05 2.2875176 0.066837565 13689.499
+ 500 2.012121 0.0083622744 2.0637959 0.10893231 8486.4241
+ 600 2.1416108 0.08602656 2.2040317 0.34087235 4775.2723
+ 700 2.0419962 0.17405962 2.1702488 0.78836378 2768.5757
+ 800 1.9520613 0.31921669 2.2528751 1.813059 1823.5943
+ 900 1.6291778 0.2415422 1.8569794 1.7008233 1518.2585
+ 1000 1.9412761 0.13859576 2.1184352 1.3019342 1521.7058
+ 1100 2.1016581 0.10912963 2.2356017 0.99454361 1756.0608
+ 1200 1.7849978 0.049963029 1.8591867 0.54025938 2204.358
+ 1300 2.3125867 0.046557089 2.3849986 0.47599584 2761.2014
+ 1400 1.757077 0.026326047 1.7889269 0.28604209 3309.8144
+ 1500 2.392565 0.048563131 2.4533846 0.37917665 3530.6855
+ 1600 1.7590832 0.050490264 1.8168201 0.33612171 3313.4472
+ 1700 2.252414 0.17372984 2.4394491 0.85851343 2716.0401
+ 1800 1.7966767 0.28338104 2.0779465 1.4326114 2152.4099
+ 1900 1.9682759 0.2168566 2.1183362 1.3383729 1806.7221
+ 2000 1.9694503 0.17559901 2.14777 1.3281701 1654.9587
+Loop time of 0.543654 on 4 procs for 2000 steps with 400 atoms
+
+Performance: 635698.342 tau/day, 3678.810 timesteps/s
+99.2% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.38532 | 0.40127 | 0.41984 | 2.3 | 73.81
+Neigh | 0.0035267 | 0.0035982 | 0.0036683 | 0.1 | 0.66
+Comm | 0.039163 | 0.057053 | 0.072538 | 5.9 | 10.49
+Output | 0.00048089 | 0.00050312 | 0.00056362 | 0.2 | 0.09
+Modify | 0.076422 | 0.077282 | 0.078008 | 0.2 | 14.22
+Other | | 0.003945 | | | 0.73
+
+Nlocal: 100 ave 108 max 95 min
+Histogram: 1 0 1 1 0 0 0 0 0 1
+Nghost: 125.75 ave 128 max 123 min
+Histogram: 1 0 1 0 0 0 0 0 0 2
+Neighs: 482.25 ave 535 max 442 min
+Histogram: 1 1 0 0 0 1 0 0 0 1
+
+Total # of neighbors = 1929
+Ave neighs/atom = 4.8225
+Neighbor list builds = 177
+Dangerous builds = 146
+
+# run dynamics on dense system
+
+unfix 1
+fix 1 all nve/asphere
+
+run 2000
+Memory usage per processor = 4.16867 Mbytes
+Step rot E_pair TotEng Press Volume
+ 2000 1.9694503 0.17559901 2.14777 1.3281701 1654.9587
+ 2100 1.978918 0.16562152 2.1632874 1.3092233 1654.9587
+ 2200 1.9820406 0.16230289 2.1750657 1.2612976 1654.9587
+ 2300 1.9577019 0.18791066 2.1531422 1.3478385 1654.9587
+ 2400 2.0271146 0.11480565 2.1721336 1.0619428 1654.9587
+ 2500 1.9894838 0.1544598 2.1329407 1.2325572 1654.9587
+ 2600 1.998697 0.14468753 2.1485209 1.1903357 1654.9587
+ 2700 1.9608664 0.18459944 2.1483889 1.3461096 1654.9587
+ 2800 2.005755 0.13729992 2.1214078 1.1596183 1654.9587
+ 2900 1.9080687 0.24019772 2.1661723 1.5974752 1654.9587
+ 3000 1.9606373 0.18480426 2.1301691 1.3280548 1654.9587
+ 3100 1.9824235 0.16187647 2.1284433 1.2590074 1654.9587
+ 3200 1.9389485 0.20774113 2.1063219 1.4587339 1654.9587
+ 3300 1.984931 0.15929453 2.1301897 1.2415169 1654.9587
+ 3400 1.9596864 0.18578934 2.1215072 1.3738204 1654.9587
+ 3500 1.9671165 0.17804604 2.0934256 1.3147236 1654.9587
+ 3600 1.9702644 0.17471548 2.156925 1.3331072 1654.9587
+ 3700 1.9104013 0.2379238 2.1305421 1.5831938 1654.9587
+ 3800 1.9129623 0.23512612 2.1445951 1.565741 1654.9587
+ 3900 1.9868116 0.15724371 2.1658058 1.2581725 1654.9587
+ 4000 2.0058633 0.13728433 2.1534403 1.1352037 1654.9587
+Loop time of 0.868601 on 4 procs for 2000 steps with 400 atoms
+
+Performance: 397881.371 tau/day, 2302.554 timesteps/s
+99.6% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.71894 | 0.74023 | 0.79323 | 3.6 | 85.22
+Neigh | 0.0012772 | 0.0013462 | 0.0014431 | 0.2 | 0.15
+Comm | 0.037097 | 0.089266 | 0.10999 | 10.2 | 10.28
+Output | 0.00050378 | 0.00052214 | 0.00055289 | 0.1 | 0.06
+Modify | 0.027847 | 0.028882 | 0.030547 | 0.6 | 3.33
+Other | | 0.008352 | | | 0.96
+
+Nlocal: 100 ave 103 max 96 min
+Histogram: 1 0 1 0 0 0 0 0 0 2
+Nghost: 118 ave 122 max 115 min
+Histogram: 1 0 1 0 1 0 0 0 0 1
+Neighs: 464.25 ave 489 max 449 min
+Histogram: 2 0 0 0 1 0 0 0 0 1
+
+Total # of neighbors = 1857
+Ave neighs/atom = 4.6425
+Neighbor list builds = 48
+Dangerous builds = 0
+Total wall time: 0:00:01
diff --git a/examples/flow/log.15Feb16.flow.couette.g++.1 b/examples/flow/log.15Feb16.flow.couette.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..b43e8cf64a301a93114727d972401e7a5fb70a7a
--- /dev/null
+++ b/examples/flow/log.15Feb16.flow.couette.g++.1
@@ -0,0 +1,145 @@
+LAMMPS (15 Feb 2016)
+# 2-d LJ flow simulation
+
+dimension 2
+boundary p s p
+
+atom_style atomic
+neighbor 0.3 bin
+neigh_modify delay 5
+
+# create geometry
+
+lattice hex 0.7
+Lattice spacing in x,y,z = 1.28436 2.22457 1.28436
+region box block 0 20 0 10 -0.25 0.25
+create_box 3 box
+Created orthogonal box = (0 0 -0.321089) to (25.6871 22.2457 0.321089)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 420 atoms
+
+mass 1 1.0
+mass 2 1.0
+mass 3 1.0
+
+# LJ potentials
+
+pair_style lj/cut 1.12246
+pair_coeff * * 1.0 1.0 1.12246
+
+# define groups
+
+region 1 block INF INF INF 1.25 INF INF
+group lower region 1
+60 atoms in group lower
+region 2 block INF INF 8.75 INF INF INF
+group upper region 2
+60 atoms in group upper
+group boundary union lower upper
+120 atoms in group boundary
+group flow subtract all boundary
+300 atoms in group flow
+
+set group lower type 2
+ 60 settings made for type
+set group upper type 3
+ 60 settings made for type
+
+# initial velocities
+
+compute mobile flow temp
+velocity flow create 1.0 482748 temp mobile
+fix 1 all nve
+fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
+fix_modify 2 temp mobile
+
+# Couette flow
+
+velocity lower set 0.0 0.0 0.0
+velocity upper set 3.0 0.0 0.0
+fix 3 boundary setforce 0.0 0.0 0.0
+fix 4 all enforce2d
+
+# Poiseuille flow
+
+#velocity boundary set 0.0 0.0 0.0
+#fix 3 lower setforce 0.0 0.0 0.0
+#fix 4 upper setforce 0.0 NULL 0.0
+#fix 5 upper aveforce 0.0 -1.0 0.0
+#fix 6 flow addforce 0.5 0.0 0.0
+#fix 7 all enforce2d
+
+# Run
+
+timestep 0.003
+thermo 500
+thermo_modify temp mobile
+WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:445)
+
+#dump 1 all atom 500 dump.flow
+
+#dump 2 all image 100 image.*.jpg type type # zoom 1.6 adiam 1.2
+#dump_modify 2 pad 5
+
+#dump 3 all movie 100 movie.mpg type type # zoom 1.6 adiam 1.2
+#dump_modify 3 pad 5
+
+run 10000
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 5 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 1.42246
+ ghost atom cutoff = 1.42246
+ binsize = 0.71123 -> bins = 37 32 1
+Memory usage per processor = 2.47395 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 1 0 0 0.71190476 0.52314537 571.54286
+ 500 1.0644427 -0.31382888 0 0.44395296 3.0013076 571.54286
+ 1000 1 -0.42965445 0 0.28225032 2.9612165 571.54286
+ 1500 1.0739874 -0.41189772 0 0.35267901 2.5621951 571.54286
+ 2000 1 -0.40814263 0 0.30376214 2.9229587 571.54286
+ 2500 1.1929729 -0.38735055 0 0.46193257 2.8337691 571.54286
+ 3000 1 -0.44542386 0 0.2664809 2.7214531 571.54286
+ 3500 1.1553179 -0.42687142 0 0.39560493 2.5109633 571.54286
+ 4000 1 -0.40604742 0 0.30585734 2.7055928 571.54286
+ 4500 1.1498154 -0.44055268 0 0.37800642 2.5561154 571.54286
+ 5000 1 -0.41742254 0 0.29448222 2.4788457 571.54286
+ 5500 1.014604 -0.42503236 0 0.29726906 2.579664 571.54286
+ 6000 1 -0.41264837 0 0.29925639 2.5861705 571.54286
+ 6500 1.1443238 -0.4392768 0 0.37537274 2.2801246 571.54286
+ 7000 1 -0.38852754 0 0.32337722 2.3294037 571.54286
+ 7500 1.0568142 -0.42350098 0 0.32885011 2.3953589 571.54286
+ 8000 1 -0.39343 0 0.31847477 2.5701342 571.54286
+ 8500 1.0872157 -0.46282796 0 0.3111661 2.2892446 571.54286
+ 9000 1 -0.402333 0 0.30957177 2.4852035 571.54286
+ 9500 0.99889786 -0.46870263 0 0.24241751 2.3763314 571.54286
+ 10000 1 -0.43338695 0 0.27851782 2.405424 571.54286
+Loop time of 0.271851 on 1 procs for 10000 steps with 420 atoms
+
+Performance: 9534632.580 tau/day, 36784.848 timesteps/s
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.12448 | 0.12448 | 0.12448 | 0.0 | 45.79
+Neigh | 0.054694 | 0.054694 | 0.054694 | 0.0 | 20.12
+Comm | 0.0075622 | 0.0075622 | 0.0075622 | 0.0 | 2.78
+Output | 0.00014329 | 0.00014329 | 0.00014329 | 0.0 | 0.05
+Modify | 0.067663 | 0.067663 | 0.067663 | 0.0 | 24.89
+Other | | 0.01731 | | | 6.37
+
+Nlocal: 420 ave 420 max 420 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 46 ave 46 max 46 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 952 ave 952 max 952 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 952
+Ave neighs/atom = 2.26667
+Neighbor list builds = 996
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/flow/log.15Feb16.flow.couette.g++.4 b/examples/flow/log.15Feb16.flow.couette.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..5f4fab63e9a749906a0f8dc0decaa0bb4e6d3849
--- /dev/null
+++ b/examples/flow/log.15Feb16.flow.couette.g++.4
@@ -0,0 +1,145 @@
+LAMMPS (15 Feb 2016)
+# 2-d LJ flow simulation
+
+dimension 2
+boundary p s p
+
+atom_style atomic
+neighbor 0.3 bin
+neigh_modify delay 5
+
+# create geometry
+
+lattice hex 0.7
+Lattice spacing in x,y,z = 1.28436 2.22457 1.28436
+region box block 0 20 0 10 -0.25 0.25
+create_box 3 box
+Created orthogonal box = (0 0 -0.321089) to (25.6871 22.2457 0.321089)
+ 2 by 2 by 1 MPI processor grid
+create_atoms 1 box
+Created 420 atoms
+
+mass 1 1.0
+mass 2 1.0
+mass 3 1.0
+
+# LJ potentials
+
+pair_style lj/cut 1.12246
+pair_coeff * * 1.0 1.0 1.12246
+
+# define groups
+
+region 1 block INF INF INF 1.25 INF INF
+group lower region 1
+60 atoms in group lower
+region 2 block INF INF 8.75 INF INF INF
+group upper region 2
+60 atoms in group upper
+group boundary union lower upper
+120 atoms in group boundary
+group flow subtract all boundary
+300 atoms in group flow
+
+set group lower type 2
+ 60 settings made for type
+set group upper type 3
+ 60 settings made for type
+
+# initial velocities
+
+compute mobile flow temp
+velocity flow create 1.0 482748 temp mobile
+fix 1 all nve
+fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
+fix_modify 2 temp mobile
+
+# Couette flow
+
+velocity lower set 0.0 0.0 0.0
+velocity upper set 3.0 0.0 0.0
+fix 3 boundary setforce 0.0 0.0 0.0
+fix 4 all enforce2d
+
+# Poiseuille flow
+
+#velocity boundary set 0.0 0.0 0.0
+#fix 3 lower setforce 0.0 0.0 0.0
+#fix 4 upper setforce 0.0 NULL 0.0
+#fix 5 upper aveforce 0.0 -1.0 0.0
+#fix 6 flow addforce 0.5 0.0 0.0
+#fix 7 all enforce2d
+
+# Run
+
+timestep 0.003
+thermo 500
+thermo_modify temp mobile
+WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:445)
+
+#dump 1 all atom 500 dump.flow
+
+#dump 2 all image 100 image.*.jpg type type # zoom 1.6 adiam 1.2
+#dump_modify 2 pad 5
+
+#dump 3 all movie 100 movie.mpg type type # zoom 1.6 adiam 1.2
+#dump_modify 3 pad 5
+
+run 10000
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 5 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 1.42246
+ ghost atom cutoff = 1.42246
+ binsize = 0.71123 -> bins = 37 32 1
+Memory usage per processor = 2.47768 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 1 0 0 0.71190476 0.52314537 571.54286
+ 500 1.0951876 -0.33403931 0 0.44562996 3.2502319 571.54286
+ 1000 1 -0.3731019 0 0.33880286 2.8561715 571.54286
+ 1500 1.0366879 -0.36031105 0 0.37771198 3.0196355 571.54286
+ 2000 1 -0.41052999 0 0.30137477 2.865191 571.54286
+ 2500 1.1227078 -0.37036396 0 0.42889708 2.944809 571.54286
+ 3000 1 -0.3831188 0 0.32878596 2.6840526 571.54286
+ 3500 1.0822111 -0.42234615 0 0.34808509 2.8119594 571.54286
+ 4000 1 -0.40805417 0 0.30385059 2.5977913 571.54286
+ 4500 1.0910738 -0.37103658 0 0.40570404 2.3742519 571.54286
+ 5000 1 -0.46702664 0 0.24487812 2.5666252 571.54286
+ 5500 1.0411533 -0.40531814 0 0.33588386 2.5125963 571.54286
+ 6000 1 -0.36183137 0 0.35007339 2.4382625 571.54286
+ 6500 1.0533061 -0.38887062 0 0.360983 2.6032319 571.54286
+ 7000 1 -0.49087253 0 0.22103223 2.4362009 571.54286
+ 7500 1.056871 -0.42142263 0 0.33096887 2.5406254 571.54286
+ 8000 1 -0.40440166 0 0.3075031 2.3664523 571.54286
+ 8500 1.0340789 -0.36193981 0 0.37422586 2.4461942 571.54286
+ 9000 1 -0.45171969 0 0.26018507 2.5525861 571.54286
+ 9500 1.0322994 -0.40989898 0 0.32499991 2.6021234 571.54286
+ 10000 1 -0.42489516 0 0.28700961 2.619505 571.54286
+Loop time of 0.131903 on 4 procs for 10000 steps with 420 atoms
+
+Performance: 19650813.964 tau/day, 75813.325 timesteps/s
+99.5% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.024203 | 0.030848 | 0.037153 | 3.6 | 23.39
+Neigh | 0.013397 | 0.014826 | 0.016212 | 1.1 | 11.24
+Comm | 0.039776 | 0.04867 | 0.05801 | 3.7 | 36.90
+Output | 0.00026822 | 0.00028723 | 0.00034046 | 0.2 | 0.22
+Modify | 0.018224 | 0.0192 | 0.020054 | 0.6 | 14.56
+Other | | 0.01807 | | | 13.70
+
+Nlocal: 105 ave 113 max 97 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost: 39.5 ave 43 max 36 min
+Histogram: 1 0 0 0 1 1 0 0 0 1
+Neighs: 236.75 ave 287 max 183 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 947
+Ave neighs/atom = 2.25476
+Neighbor list builds = 966
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/flow/log.15Feb16.flow.pois.g++.1 b/examples/flow/log.15Feb16.flow.pois.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..5f5feeb055868c823015c107d8c29a210ac80aa7
--- /dev/null
+++ b/examples/flow/log.15Feb16.flow.pois.g++.1
@@ -0,0 +1,145 @@
+LAMMPS (15 Feb 2016)
+# 2-d LJ flow simulation
+
+dimension 2
+boundary p s p
+
+atom_style atomic
+neighbor 0.3 bin
+neigh_modify delay 5
+
+# create geometry
+
+lattice hex 0.7
+Lattice spacing in x,y,z = 1.28436 2.22457 1.28436
+region box block 0 20 0 10 -0.25 0.25
+create_box 3 box
+Created orthogonal box = (0 0 -0.321089) to (25.6871 22.2457 0.321089)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 420 atoms
+
+mass 1 1.0
+mass 2 1.0
+mass 3 1.0
+
+# LJ potentials
+
+pair_style lj/cut 1.12246
+pair_coeff * * 1.0 1.0 1.12246
+
+# define groups
+
+region 1 block INF INF INF 1.25 INF INF
+group lower region 1
+60 atoms in group lower
+region 2 block INF INF 8.75 INF INF INF
+group upper region 2
+60 atoms in group upper
+group boundary union lower upper
+120 atoms in group boundary
+group flow subtract all boundary
+300 atoms in group flow
+
+set group lower type 2
+ 60 settings made for type
+set group upper type 3
+ 60 settings made for type
+
+# initial velocities
+
+compute mobile flow temp
+velocity flow create 1.0 482748 temp mobile
+fix 1 all nve
+fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
+fix_modify 2 temp mobile
+
+# Couette flow
+
+#velocity lower set 0.0 0.0 0.0
+#velocity upper set 3.0 0.0 0.0
+#fix 3 boundary setforce 0.0 0.0 0.0
+#fix 4 all enforce2d
+
+# Poiseuille flow
+
+velocity boundary set 0.0 0.0 0.0
+fix 3 lower setforce 0.0 0.0 0.0
+fix 4 upper setforce 0.0 NULL 0.0
+fix 5 upper aveforce 0.0 -1.0 0.0
+fix 6 flow addforce 0.5 0.0 0.0
+fix 7 all enforce2d
+
+# Run
+
+timestep 0.003
+thermo 500
+thermo_modify temp mobile
+WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:445)
+
+#dump 1 all atom 500 dump.flow
+
+#dump 2 all image 100 image.*.jpg type type # zoom 1.6 adiam 1.5
+#dump_modify 2 pad 5
+
+#dump 3 all movie 100 movie.mpg type type # zoom 1.6 adiam 1.5
+#dump_modify 3 pad 5
+
+run 10000
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 5 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 1.42246
+ ghost atom cutoff = 1.42246
+ binsize = 0.71123 -> bins = 37 32 1
+Memory usage per processor = 2.47395 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 1 0 0 0.71190476 0.52314537 571.54286
+ 500 1.0990751 -0.36396768 0 0.41846911 2.522517 575.55806
+ 1000 1 -0.34609791 0 0.36580685 1.9736175 584.67179
+ 1500 1.2112861 -0.39062708 0 0.47169327 1.521881 587.24778
+ 2000 1 -0.39956949 0 0.31233527 1.2496669 583.00676
+ 2500 1.2236323 -0.40128446 0 0.46982521 1.4276891 570.03729
+ 3000 1 -0.48849353 0 0.22341123 1.5091361 553.64637
+ 3500 1.2404547 -0.63017551 0 0.25291012 1.768107 535.22599
+ 4000 1 -0.71545964 0 -0.0035548789 2.2079822 516.73161
+ 4500 1.2270239 -0.78740977 0 0.086114399 2.6094706 503.17906
+ 5000 1 -0.8367971 0 -0.12489233 3.186175 498.73275
+ 5500 1.2257721 -0.77200456 0 0.10062844 2.6369599 502.75573
+ 6000 1 -0.6766551 0 0.035249665 2.2092944 512.08396
+ 6500 1.2201203 -0.67876788 0 0.18984154 1.8784541 517.92079
+ 7000 1 -0.68555696 0 0.026347797 1.8142356 516.44963
+ 7500 1.2482526 -0.7345934 0 0.15404357 2.0253109 511.4042
+ 8000 1 -0.70068231 0 0.011222455 2.1739831 504.55527
+ 8500 1.2151375 -0.77680457 0 0.088257564 2.6264947 498.00946
+ 9000 1 -0.74461165 0 -0.032706889 2.574656 498.14523
+ 9500 1.2047533 -0.75768848 0 0.09998113 2.4174997 501.8877
+ 10000 1 -0.67361996 0 0.038284798 2.2310948 507.57444
+Loop time of 0.308209 on 1 procs for 10000 steps with 420 atoms
+
+Performance: 8409879.284 tau/day, 32445.522 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.13686 | 0.13686 | 0.13686 | 0.0 | 44.40
+Neigh | 0.030894 | 0.030894 | 0.030894 | 0.0 | 10.02
+Comm | 0.0063944 | 0.0063944 | 0.0063944 | 0.0 | 2.07
+Output | 0.00016952 | 0.00016952 | 0.00016952 | 0.0 | 0.06
+Modify | 0.11606 | 0.11606 | 0.11606 | 0.0 | 37.66
+Other | | 0.01783 | | | 5.79
+
+Nlocal: 420 ave 420 max 420 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 48 ave 48 max 48 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 1124 ave 1124 max 1124 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1124
+Ave neighs/atom = 2.67619
+Neighbor list builds = 561
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/flow/log.15Feb16.flow.pois.g++.4 b/examples/flow/log.15Feb16.flow.pois.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..8aab95573b8a04360bc88617ffb705e347338458
--- /dev/null
+++ b/examples/flow/log.15Feb16.flow.pois.g++.4
@@ -0,0 +1,145 @@
+LAMMPS (15 Feb 2016)
+# 2-d LJ flow simulation
+
+dimension 2
+boundary p s p
+
+atom_style atomic
+neighbor 0.3 bin
+neigh_modify delay 5
+
+# create geometry
+
+lattice hex 0.7
+Lattice spacing in x,y,z = 1.28436 2.22457 1.28436
+region box block 0 20 0 10 -0.25 0.25
+create_box 3 box
+Created orthogonal box = (0 0 -0.321089) to (25.6871 22.2457 0.321089)
+ 2 by 2 by 1 MPI processor grid
+create_atoms 1 box
+Created 420 atoms
+
+mass 1 1.0
+mass 2 1.0
+mass 3 1.0
+
+# LJ potentials
+
+pair_style lj/cut 1.12246
+pair_coeff * * 1.0 1.0 1.12246
+
+# define groups
+
+region 1 block INF INF INF 1.25 INF INF
+group lower region 1
+60 atoms in group lower
+region 2 block INF INF 8.75 INF INF INF
+group upper region 2
+60 atoms in group upper
+group boundary union lower upper
+120 atoms in group boundary
+group flow subtract all boundary
+300 atoms in group flow
+
+set group lower type 2
+ 60 settings made for type
+set group upper type 3
+ 60 settings made for type
+
+# initial velocities
+
+compute mobile flow temp
+velocity flow create 1.0 482748 temp mobile
+fix 1 all nve
+fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
+fix_modify 2 temp mobile
+
+# Couette flow
+
+#velocity lower set 0.0 0.0 0.0
+#velocity upper set 3.0 0.0 0.0
+#fix 3 boundary setforce 0.0 0.0 0.0
+#fix 4 all enforce2d
+
+# Poiseuille flow
+
+velocity boundary set 0.0 0.0 0.0
+fix 3 lower setforce 0.0 0.0 0.0
+fix 4 upper setforce 0.0 NULL 0.0
+fix 5 upper aveforce 0.0 -1.0 0.0
+fix 6 flow addforce 0.5 0.0 0.0
+fix 7 all enforce2d
+
+# Run
+
+timestep 0.003
+thermo 500
+thermo_modify temp mobile
+WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:445)
+
+#dump 1 all atom 500 dump.flow
+
+#dump 2 all image 100 image.*.jpg type type # zoom 1.6 adiam 1.5
+#dump_modify 2 pad 5
+
+#dump 3 all movie 100 movie.mpg type type # zoom 1.6 adiam 1.5
+#dump_modify 3 pad 5
+
+run 10000
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 5 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 1.42246
+ ghost atom cutoff = 1.42246
+ binsize = 0.71123 -> bins = 37 32 1
+Memory usage per processor = 2.47768 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 1 0 0 0.71190476 0.52314537 571.54286
+ 500 1.0758737 -0.36090417 0 0.40501541 2.7822308 575.0659
+ 1000 1 -0.35701441 0 0.35489035 2.0575313 585.71407
+ 1500 1.2368663 -0.37709732 0 0.50343367 1.4865879 587.193
+ 2000 1 -0.39362939 0 0.31827537 1.4236 578.9418
+ 2500 1.2272957 -0.42381899 0 0.44989866 1.454461 570.15856
+ 3000 1 -0.49143418 0 0.22047058 1.5345944 554.98632
+ 3500 1.2444907 -0.59761906 0 0.28833979 1.8753537 537.01597
+ 4000 1 -0.70389808 0 0.008006681 2.1377407 521.46953
+ 4500 1.2086391 -0.73613601 0 0.12429994 2.8118471 507.60191
+ 5000 1 -0.82025509 0 -0.10835033 2.9561662 501.69891
+ 5500 1.2136337 -0.75490689 0 0.10908471 2.7434794 505.27439
+ 6000 1 -0.69627045 0 0.015634317 2.4524175 508.59669
+ 6500 1.207632 -0.68640835 0 0.17331064 2.2238608 515.69996
+ 7000 1 -0.69036919 0 0.02153557 2.2262384 515.59362
+ 7500 1.2071424 -0.70836083 0 0.15100956 2.1631657 513.88454
+ 8000 1 -0.72087298 0 -0.0089682187 2.2520771 509.87373
+ 8500 1.2046939 -0.75634562 0 0.10128171 2.2433251 505.69974
+ 9000 1 -0.8200207 0 -0.10811593 2.6210027 502.60511
+ 9500 1.2167146 -0.77385956 0 0.092325373 2.5938179 500.86068
+ 10000 1 -0.73082779 0 -0.018923029 2.735112 505.69856
+Loop time of 0.196428 on 4 procs for 10000 steps with 420 atoms
+
+Performance: 13195670.685 tau/day, 50909.223 timesteps/s
+99.3% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.033267 | 0.034629 | 0.035398 | 0.5 | 17.63
+Neigh | 0.0084751 | 0.0087134 | 0.0089035 | 0.2 | 4.44
+Comm | 0.063612 | 0.066345 | 0.06988 | 0.9 | 33.78
+Output | 0.00033164 | 0.00035477 | 0.00041437 | 0.2 | 0.18
+Modify | 0.056999 | 0.058513 | 0.061231 | 0.7 | 29.79
+Other | | 0.02787 | | | 14.19
+
+Nlocal: 105 ave 106 max 103 min
+Histogram: 1 0 0 0 0 0 1 0 0 2
+Nghost: 44.75 ave 47 max 44 min
+Histogram: 3 0 0 0 0 0 0 0 0 1
+Neighs: 277 ave 296 max 255 min
+Histogram: 1 0 1 0 0 0 0 0 0 2
+
+Total # of neighbors = 1108
+Ave neighs/atom = 2.6381
+Neighbor list builds = 564
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/friction/log.15Feb16.friction.g++.1 b/examples/friction/log.15Feb16.friction.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..ddf392c29f8ca07a4194d73c8c2c8e647f0e2d2a
--- /dev/null
+++ b/examples/friction/log.15Feb16.friction.g++.1
@@ -0,0 +1,164 @@
+LAMMPS (15 Feb 2016)
+# 2d friction simulation
+
+dimension 2
+boundary p s p
+
+atom_style atomic
+neighbor 0.3 bin
+neigh_modify delay 5
+
+# create geometry
+
+lattice hex 0.9
+Lattice spacing in x,y,z = 1.1327 1.96189 1.1327
+region box block 0 50 0 22 -0.25 0.25
+create_box 4 box
+Created orthogonal box = (0 0 -0.283174) to (56.6348 43.1615 0.283174)
+ 1 by 1 by 1 MPI processor grid
+
+mass 1 1.0
+mass 2 1.0
+mass 3 1.0
+mass 4 1.0
+
+# atom regions
+
+region lo-fixed block INF INF INF 1.1 INF INF
+region lo-slab block INF INF INF 7 INF INF
+region above-lo block INF INF INF 7 INF INF side out
+region hi-fixed block INF INF 20.9 INF INF INF
+region hi-slab block INF INF 15 INF INF INF
+region below-hi block INF INF 15 INF INF INF side out
+region lo-asperity sphere 32 7 0 8
+region hi-asperity sphere 18 15 0 8
+region lo-half-sphere intersect 2 lo-asperity above-lo
+region hi-half-sphere intersect 2 hi-asperity below-hi
+
+# create 2 surfaces with asperities
+
+create_atoms 1 region lo-slab
+Created 750 atoms
+create_atoms 1 region hi-slab
+Created 750 atoms
+create_atoms 2 region lo-half-sphere
+Created 112 atoms
+create_atoms 3 region hi-half-sphere
+Created 112 atoms
+
+# LJ potentials
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0 2.5
+
+# define groups
+
+group lo region lo-slab
+750 atoms in group lo
+group lo type 2
+862 atoms in group lo
+group hi region hi-slab
+750 atoms in group hi
+group hi type 3
+862 atoms in group hi
+group lo-fixed region lo-fixed
+150 atoms in group lo-fixed
+group hi-fixed region hi-fixed
+150 atoms in group hi-fixed
+group boundary union lo-fixed hi-fixed
+300 atoms in group boundary
+group mobile subtract all boundary
+1424 atoms in group mobile
+
+set group lo-fixed type 4
+ 150 settings made for type
+set group hi-fixed type 4
+ 150 settings made for type
+
+# initial velocities
+
+compute new mobile temp/partial 0 1 0
+velocity mobile create 0.1 482748 temp new
+velocity hi set 1.0 0.0 0.0 sum yes
+
+# fixes
+
+fix 1 all nve
+fix 2 boundary setforce 0.0 0.0 0.0
+fix 3 mobile temp/rescale 200 0.1 0.1 0.02 1.0
+fix_modify 3 temp new
+fix 4 all enforce2d
+
+# Run
+
+timestep 0.0025
+thermo 1000
+thermo_modify temp new
+WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:445)
+
+#dump 1 all atom 500 dump.friction
+
+#dump 2 all image 500 image.*.jpg type type # zoom 1.6 adiam 1.5
+#dump_modify 2 pad 5
+
+#dump 3 all movie 500 movie.mpg type type # zoom 1.6 adiam 1.5
+#dump_modify 3 pad 5
+
+run 20000
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 5 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4 -> bins = 41 31 1
+Memory usage per processor = 2.47434 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 0.1 -3.1333672 0 -3.0921259 -1.1437867 2444.9333
+ 1000 0.1 -3.0915465 0 -3.0503052 0.010015559 2444.9333
+ 2000 0.1 -3.0826487 0 -3.0414074 -0.42012889 2444.9333
+ 3000 0.089819692 -3.07584 0 -3.0387972 -0.25252108 2444.9333
+ 4000 0.098489874 -3.0667093 0 -3.0260907 -0.25506538 2444.9333
+ 5000 0.11379986 -3.0557087 0 -3.0087762 -0.080871179 2444.9333
+ 6000 0.11269179 -3.04532 0 -2.9988445 -0.33381202 2444.9333
+ 7000 0.1 -3.0380599 0 -2.9968186 -0.32423949 2444.9333
+ 8000 0.1 -3.0346451 0 -2.9934038 -0.38015467 2444.9333
+ 9000 0.1 -3.0328231 0 -2.9915818 -0.43229228 2444.9333
+ 10000 0.11715901 -3.0339975 0 -2.9856796 -0.32994136 2444.9333
+ 11000 0.11489931 -3.0347978 0 -2.9874118 -0.45189608 2444.9333
+ 12000 0.10977417 -3.0396002 0 -2.994328 -0.18902632 2444.9333
+ 13000 0.1 -3.0460576 0 -3.0048163 -0.30636366 2444.9333
+ 14000 0.10650444 -3.0498066 0 -3.0058827 -0.37168966 2444.9333
+ 15000 0.11262528 -3.053675 0 -3.0072269 -0.32295729 2444.9333
+ 16000 0.10822084 -3.0524308 0 -3.0077991 -0.25034257 2444.9333
+ 17000 0.10833465 -3.0487557 0 -3.0040771 -0.4048054 2444.9333
+ 18000 0.11599608 -3.0540506 0 -3.0062123 -0.30721348 2444.9333
+ 19000 0.11303674 -3.0521905 0 -3.0055727 -0.29399612 2444.9333
+ 20000 0.09925739 -3.0483895 0 -3.0074545 -0.34540139 2444.9333
+Loop time of 5.95865 on 1 procs for 20000 steps with 1724 atoms
+
+Performance: 724995.927 tau/day, 3356.463 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 4.8617 | 4.8617 | 4.8617 | 0.0 | 81.59
+Neigh | 0.33399 | 0.33399 | 0.33399 | 0.0 | 5.61
+Comm | 0.036682 | 0.036682 | 0.036682 | 0.0 | 0.62
+Output | 0.00041318 | 0.00041318 | 0.00041318 | 0.0 | 0.01
+Modify | 0.57978 | 0.57978 | 0.57978 | 0.0 | 9.73
+Other | | 0.1461 | | | 2.45
+
+Nlocal: 1724 ave 1724 max 1724 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 145 ave 145 max 145 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 14387 ave 14387 max 14387 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 14387
+Ave neighs/atom = 8.34513
+Neighbor list builds = 726
+Dangerous builds = 0
+Total wall time: 0:00:05
diff --git a/examples/friction/log.15Feb16.friction.g++.4 b/examples/friction/log.15Feb16.friction.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..224732305f3dc354316da995ec824c4df3730017
--- /dev/null
+++ b/examples/friction/log.15Feb16.friction.g++.4
@@ -0,0 +1,164 @@
+LAMMPS (15 Feb 2016)
+# 2d friction simulation
+
+dimension 2
+boundary p s p
+
+atom_style atomic
+neighbor 0.3 bin
+neigh_modify delay 5
+
+# create geometry
+
+lattice hex 0.9
+Lattice spacing in x,y,z = 1.1327 1.96189 1.1327
+region box block 0 50 0 22 -0.25 0.25
+create_box 4 box
+Created orthogonal box = (0 0 -0.283174) to (56.6348 43.1615 0.283174)
+ 2 by 2 by 1 MPI processor grid
+
+mass 1 1.0
+mass 2 1.0
+mass 3 1.0
+mass 4 1.0
+
+# atom regions
+
+region lo-fixed block INF INF INF 1.1 INF INF
+region lo-slab block INF INF INF 7 INF INF
+region above-lo block INF INF INF 7 INF INF side out
+region hi-fixed block INF INF 20.9 INF INF INF
+region hi-slab block INF INF 15 INF INF INF
+region below-hi block INF INF 15 INF INF INF side out
+region lo-asperity sphere 32 7 0 8
+region hi-asperity sphere 18 15 0 8
+region lo-half-sphere intersect 2 lo-asperity above-lo
+region hi-half-sphere intersect 2 hi-asperity below-hi
+
+# create 2 surfaces with asperities
+
+create_atoms 1 region lo-slab
+Created 750 atoms
+create_atoms 1 region hi-slab
+Created 750 atoms
+create_atoms 2 region lo-half-sphere
+Created 112 atoms
+create_atoms 3 region hi-half-sphere
+Created 112 atoms
+
+# LJ potentials
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0 2.5
+
+# define groups
+
+group lo region lo-slab
+750 atoms in group lo
+group lo type 2
+862 atoms in group lo
+group hi region hi-slab
+750 atoms in group hi
+group hi type 3
+862 atoms in group hi
+group lo-fixed region lo-fixed
+150 atoms in group lo-fixed
+group hi-fixed region hi-fixed
+150 atoms in group hi-fixed
+group boundary union lo-fixed hi-fixed
+300 atoms in group boundary
+group mobile subtract all boundary
+1424 atoms in group mobile
+
+set group lo-fixed type 4
+ 150 settings made for type
+set group hi-fixed type 4
+ 150 settings made for type
+
+# initial velocities
+
+compute new mobile temp/partial 0 1 0
+velocity mobile create 0.1 482748 temp new
+velocity hi set 1.0 0.0 0.0 sum yes
+
+# fixes
+
+fix 1 all nve
+fix 2 boundary setforce 0.0 0.0 0.0
+fix 3 mobile temp/rescale 200 0.1 0.1 0.02 1.0
+fix_modify 3 temp new
+fix 4 all enforce2d
+
+# Run
+
+timestep 0.0025
+thermo 1000
+thermo_modify temp new
+WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:445)
+
+#dump 1 all atom 500 dump.friction
+
+#dump 2 all image 500 image.*.jpg type type # zoom 1.6 adiam 1.5
+#dump_modify 2 pad 5
+
+#dump 3 all movie 500 movie.mpg type type # zoom 1.6 adiam 1.5
+#dump_modify 3 pad 5
+
+run 20000
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 5 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4 -> bins = 41 31 1
+Memory usage per processor = 2.47775 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 0.1 -3.1333672 0 -3.0921259 -1.1437867 2444.9333
+ 1000 0.081958665 -3.0927273 0 -3.0589265 -0.021846131 2444.9333
+ 2000 0.082641883 -3.0850764 0 -3.0509938 -0.44960195 2444.9333
+ 3000 0.092293442 -3.0748001 0 -3.0367371 -0.25353161 2444.9333
+ 4000 0.096012911 -3.0565129 0 -3.0169159 -0.027669541 2444.9333
+ 5000 0.1 -3.0465555 0 -3.0053142 -0.099323956 2444.9333
+ 6000 0.11642983 -3.0390782 0 -2.991061 -0.21034609 2444.9333
+ 7000 0.11597774 -3.0331763 0 -2.9853456 -0.46345898 2444.9333
+ 8000 0.11937908 -3.0305561 0 -2.9813227 -0.3077312 2444.9333
+ 9000 0.11110633 -3.0274042 0 -2.9815825 -0.52435329 2444.9333
+ 10000 0.11593138 -3.0164989 0 -2.9686873 -0.36943466 2444.9333
+ 11000 0.11066412 -3.0156369 0 -2.9699976 -0.46759658 2444.9333
+ 12000 0.10383247 -3.0199664 0 -2.9771445 -0.27390498 2444.9333
+ 13000 0.11288647 -3.027191 0 -2.9806352 -0.38261516 2444.9333
+ 14000 0.10587004 -3.0302799 0 -2.9866177 -0.20888958 2444.9333
+ 15000 0.11092262 -3.0308702 0 -2.9851243 -0.37310523 2444.9333
+ 16000 0.11258624 -3.0421958 0 -2.9957638 -0.27895709 2444.9333
+ 17000 0.10980848 -3.0388353 0 -2.9935488 -0.31492687 2444.9333
+ 18000 0.11125763 -3.0392991 0 -2.993415 -0.30414022 2444.9333
+ 19000 0.11673298 -3.0405242 0 -2.992382 -0.34902574 2444.9333
+ 20000 0.11753441 -3.0437232 0 -2.9952505 -0.31244935 2444.9333
+Loop time of 1.96189 on 4 procs for 20000 steps with 1724 atoms
+
+Performance: 2201963.286 tau/day, 10194.274 timesteps/s
+99.3% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 1.0666 | 1.2376 | 1.4382 | 12.1 | 63.08
+Neigh | 0.072524 | 0.085115 | 0.099557 | 3.4 | 4.34
+Comm | 0.16011 | 0.38337 | 0.56903 | 24.0 | 19.54
+Output | 0.00041413 | 0.00043744 | 0.0005033 | 0.2 | 0.02
+Modify | 0.12679 | 0.14438 | 0.15946 | 3.2 | 7.36
+Other | | 0.111 | | | 5.66
+
+Nlocal: 431 ave 495 max 377 min
+Histogram: 1 0 1 0 0 1 0 0 0 1
+Nghost: 96 ave 125 max 74 min
+Histogram: 1 1 0 0 0 1 0 0 0 1
+Neighs: 3597.75 ave 4233 max 3149 min
+Histogram: 1 1 0 0 0 1 0 0 0 1
+
+Total # of neighbors = 14391
+Ave neighs/atom = 8.34745
+Neighbor list builds = 704
+Dangerous builds = 0
+Total wall time: 0:00:01
diff --git a/examples/hugoniostat/log.15Feb16.hugoniostat.g++.1 b/examples/hugoniostat/log.15Feb16.hugoniostat.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..e3c3cae9afa4fd2ae929be6888ff7ad46aae766c
--- /dev/null
+++ b/examples/hugoniostat/log.15Feb16.hugoniostat.g++.1
@@ -0,0 +1,110 @@
+LAMMPS (15 Feb 2016)
+# This script reproduces stress trajectories from Fig. 1 in
+# Ravelo, Holian, Germann, and Lomdahl, PRB 70 014103 (2004)
+#
+# Three thermostatting scenarios are visited: undamped (nodrag),
+# damped (drag) and Nose-Hoover chain (nhchains).
+#
+# The axial and shear stress trajectories are printed to the
+# file "stress_vs_t.dat". For the damped case, the original figure
+# seems to be a plot of 2*tau, rather than tau.
+#
+# The script also demonstrates how to
+# orient a crystal along <110>,
+# and how to use the lj/cubic pair style.
+
+units lj
+boundary p p p
+
+atom_style atomic
+
+# Set up FCC lattice with z axis along <110>
+
+lattice fcc 1.4142136 orient x 0 0 1 orient y 1 -1 0 orient z 1 1 0
+Lattice spacing in x,y,z = 1.41421 2 2
+
+region mycell block 0.0 5.0 0.0 5.0 0.0 5.0 units lattice
+create_box 1 mycell
+Created orthogonal box = (0 0 0) to (7.07107 10 10)
+ 1 by 1 by 1 MPI processor grid
+mass * 1.0
+create_atoms 1 box
+Created 1000 atoms
+
+# Using units of Rmin, so sigma = 2^-1/6 = 0.8908987
+
+pair_style lj/cubic
+pair_coeff * * 1.0 0.8908987
+
+# Relax box dimensions
+
+fix 3 all box/relax aniso 0.0 vmax 1.0e-4 nreset 100
+
+thermo 100
+thermo_style custom step temp pe etotal pxx pyy pzz lx ly lz
+
+min_modify line quadratic
+minimize 0.0 1.0e-6 10000 100000
+WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 1.84754
+ ghost atom cutoff = 1.84754
+ binsize = 0.923769 -> bins = 8 11 11
+Memory usage per processor = 3.65406 Mbytes
+Step Temp PotEng TotEng Pxx Pyy Pzz Lx Ly Lz
+ 0 0 -6.2937539 -6.2937539 -2.7722431 -2.7722431 -2.7722431 7.0710677 9.9999999 9.9999999
+ 100 0 -6.3319018 -6.3319018 -0.75971321 -0.75971321 -0.75971321 7.0003571 9.8999999 9.8999999
+ 134 0 -6.3344257 -6.3344257 -4.5005818e-13 -4.9677973e-13 -4.9219424e-13 6.9780266 9.8684199 9.8684199
+Loop time of 0.083575 on 1 procs for 134 steps with 1000 atoms
+
+100.5% CPU use with 1 MPI tasks x no OpenMP threads
+
+Minimization stats:
+ Stopping criterion = force tolerance
+ Energy initial, next-to-last, final =
+ -6.2937539309 -6.33442568056 -6.33442568056
+ Force two-norm initial, final = 3395.29 5.83329e-10
+ Force max component initial, final = 1960.27 3.42093e-10
+ Final line search alpha, max atom move = 1 3.42093e-10
+ Iterations, force evaluations = 134 137
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.068495 | 0.068495 | 0.068495 | 0.0 | 81.96
+Neigh | 0.00106 | 0.00106 | 0.00106 | 0.0 | 1.27
+Comm | 0.0014729 | 0.0014729 | 0.0014729 | 0.0 | 1.76
+Output | 1.7166e-05 | 1.7166e-05 | 1.7166e-05 | 0.0 | 0.02
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 0.01253 | | | 14.99
+
+Nlocal: 1000 ave 1000 max 1000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1724 ave 1724 max 1724 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 21000 ave 21000 max 21000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 21000
+Ave neighs/atom = 21
+Neighbor list builds = 1
+Dangerous builds = 0
+
+# Define initial velocity
+
+velocity all create 0.01 87287 mom yes rot yes dist gaussian
+write_restart restart.equil
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 1.84754
+ ghost atom cutoff = 1.84754
+ binsize = 0.923769 -> bins = 8 11 11
+
+# Start Run #1
+
+log log.nodrag
diff --git a/examples/hugoniostat/log.15Feb16.hugoniostat.g++.4 b/examples/hugoniostat/log.15Feb16.hugoniostat.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..759c2b8c1ab2cc1b09f117a3eb55ee2bf9d3cd91
--- /dev/null
+++ b/examples/hugoniostat/log.15Feb16.hugoniostat.g++.4
@@ -0,0 +1,110 @@
+LAMMPS (15 Feb 2016)
+# This script reproduces stress trajectories from Fig. 1 in
+# Ravelo, Holian, Germann, and Lomdahl, PRB 70 014103 (2004)
+#
+# Three thermostatting scenarios are visited: undamped (nodrag),
+# damped (drag) and Nose-Hoover chain (nhchains).
+#
+# The axial and shear stress trajectories are printed to the
+# file "stress_vs_t.dat". For the damped case, the original figure
+# seems to be a plot of 2*tau, rather than tau.
+#
+# The script also demonstrates how to
+# orient a crystal along <110>,
+# and how to use the lj/cubic pair style.
+
+units lj
+boundary p p p
+
+atom_style atomic
+
+# Set up FCC lattice with z axis along <110>
+
+lattice fcc 1.4142136 orient x 0 0 1 orient y 1 -1 0 orient z 1 1 0
+Lattice spacing in x,y,z = 1.41421 2 2
+
+region mycell block 0.0 5.0 0.0 5.0 0.0 5.0 units lattice
+create_box 1 mycell
+Created orthogonal box = (0 0 0) to (7.07107 10 10)
+ 1 by 2 by 2 MPI processor grid
+mass * 1.0
+create_atoms 1 box
+Created 1000 atoms
+
+# Using units of Rmin, so sigma = 2^-1/6 = 0.8908987
+
+pair_style lj/cubic
+pair_coeff * * 1.0 0.8908987
+
+# Relax box dimensions
+
+fix 3 all box/relax aniso 0.0 vmax 1.0e-4 nreset 100
+
+thermo 100
+thermo_style custom step temp pe etotal pxx pyy pzz lx ly lz
+
+min_modify line quadratic
+minimize 0.0 1.0e-6 10000 100000
+WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 1.84754
+ ghost atom cutoff = 1.84754
+ binsize = 0.923769 -> bins = 8 11 11
+Memory usage per processor = 3.63062 Mbytes
+Step Temp PotEng TotEng Pxx Pyy Pzz Lx Ly Lz
+ 0 0 -6.2937539 -6.2937539 -2.7722431 -2.7722431 -2.7722431 7.0710677 9.9999999 9.9999999
+ 100 0 -6.3319018 -6.3319018 -0.75971321 -0.75971321 -0.75971321 7.0003571 9.8999999 9.8999999
+ 134 0 -6.3344257 -6.3344257 -4.5046204e-13 -4.92206e-13 -4.9610344e-13 6.9780266 9.8684199 9.8684199
+Loop time of 0.0294001 on 4 procs for 134 steps with 1000 atoms
+
+99.5% CPU use with 4 MPI tasks x no OpenMP threads
+
+Minimization stats:
+ Stopping criterion = force tolerance
+ Energy initial, next-to-last, final =
+ -6.2937539309 -6.33442568056 -6.33442568056
+ Force two-norm initial, final = 3395.29 5.80609e-10
+ Force max component initial, final = 1960.27 3.41627e-10
+ Final line search alpha, max atom move = 1 3.41627e-10
+ Iterations, force evaluations = 134 137
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.015008 | 0.017768 | 0.020491 | 1.5 | 60.43
+Neigh | 0.00022388 | 0.0002709 | 0.00032783 | 0.2 | 0.92
+Comm | 0.0022066 | 0.0049043 | 0.0076346 | 2.8 | 16.68
+Output | 1.5974e-05 | 1.6928e-05 | 1.9789e-05 | 0.0 | 0.06
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 0.00644 | | | 21.91
+
+Nlocal: 250 ave 305 max 205 min
+Histogram: 1 0 0 0 2 0 0 0 0 1
+Nghost: 829 ave 874 max 774 min
+Histogram: 1 0 0 0 0 0 2 0 0 1
+Neighs: 5250 ave 6445 max 4305 min
+Histogram: 1 0 0 2 0 0 0 0 0 1
+
+Total # of neighbors = 21000
+Ave neighs/atom = 21
+Neighbor list builds = 1
+Dangerous builds = 0
+
+# Define initial velocity
+
+velocity all create 0.01 87287 mom yes rot yes dist gaussian
+write_restart restart.equil
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 1.84754
+ ghost atom cutoff = 1.84754
+ binsize = 0.923769 -> bins = 8 11 11
+
+# Start Run #1
+
+log log.nodrag
diff --git a/examples/indent/log.15Feb16.indent.g++.1 b/examples/indent/log.15Feb16.indent.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..14327778951ccbcc837c76d77f33fa7737ec7c49
--- /dev/null
+++ b/examples/indent/log.15Feb16.indent.g++.1
@@ -0,0 +1,201 @@
+LAMMPS (15 Feb 2016)
+# 2d indenter simulation
+
+dimension 2
+boundary p s p
+
+atom_style atomic
+neighbor 0.3 bin
+neigh_modify delay 5
+
+# create geometry
+
+lattice hex 0.9
+Lattice spacing in x,y,z = 1.1327 1.96189 1.1327
+region box block 0 20 0 10 -0.25 0.25
+create_box 2 box
+Created orthogonal box = (0 0 -0.283174) to (22.6539 19.6189 0.283174)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 420 atoms
+
+mass 1 1.0
+mass 2 1.0
+
+# LJ potentials
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0 2.5
+
+# define groups
+
+region 1 block INF INF INF 1.25 INF INF
+group lower region 1
+60 atoms in group lower
+group mobile subtract all lower
+360 atoms in group mobile
+set group lower type 2
+ 60 settings made for type
+
+# initial velocities
+
+compute new mobile temp
+velocity mobile create 0.2 482748 temp new
+fix 1 all nve
+fix 2 lower setforce 0.0 0.0 0.0
+fix 3 all temp/rescale 100 0.1 0.1 0.01 1.0
+
+# run with indenter
+
+timestep 0.003
+variable k equal 1000.0/xlat
+variable y equal "13.0*ylat - step*dt*0.02*ylat"
+
+fix 4 all indent $k sphere 10 v_y 0 5.0
+fix 4 all indent 882.849286914813 sphere 10 v_y 0 5.0
+fix 5 all enforce2d
+
+thermo 1000
+thermo_modify temp new
+WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:445)
+
+#dump 1 all atom 250 dump.indent
+
+#dump 2 all image 1000 image.*.jpg type type # zoom 1.6 adiam 1.5
+#dump_modify 2 pad 5
+
+#dump 3 all movie 1000 movie.mpg type type # zoom 1.6 adiam 1.5
+#dump_modify 3 pad 5
+
+run 30000
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 5 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4 -> bins = 17 15 1
+Memory usage per processor = 2.4697 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 0.2 -3.1727576 0 -3.0018052 -1.436185 444.53333
+ 1000 0.11974254 -3.0876892 0 -2.9853378 -0.037059247 440.78771
+ 2000 0.12086797 -3.0886512 0 -2.9853378 -0.39883289 444.3556
+ 3000 0.11671309 -3.0840074 0 -2.9842455 -0.34859991 442.95428
+ 4000 0.12339115 -3.1000529 0 -2.9945828 -0.049696765 438.99297
+ 5000 0.10860594 -3.0866045 0 -2.9937722 -0.47973882 443.99855
+ 6000 0.11839788 -3.0929689 0 -2.9917669 -0.033454196 442.70339
+ 7000 0.12194527 -3.0835584 0 -2.9793242 -0.13981611 443.36261
+ 8000 0.11671309 -3.0862884 0 -2.9865265 0.073952568 441.71327
+ 9000 0.12449823 -3.0880806 0 -2.9816643 0.28647997 439.28167
+ 10000 0.12475263 -3.0830722 0 -2.9764384 0.38101457 440.50309
+ 11000 0.11198118 -3.0743549 0 -2.9786377 0.67583952 438.50252
+ 12000 0.10823034 -3.0621355 0 -2.9696244 0.66485023 441.13781
+ 13000 0.1194298 -3.0579575 0 -2.9558734 1.0884087 437.72805
+ 14000 0.12310404 -3.051382 0 -2.9461573 0.87077685 445.54012
+ 15000 0.11148458 -3.0402208 0 -2.944928 1.0040641 451.9079
+ 16000 0.12322323 -3.041552 0 -2.9362254 0.7581871 456.90367
+ 17000 0.12311085 -3.0300334 0 -2.9248029 1.0483261 452.91646
+ 18000 0.12062509 -3.0261636 0 -2.9230579 1.3983564 451.71896
+ 19000 0.11957854 -3.0142948 0 -2.9120836 1.3961883 457.92501
+ 20000 0.12230825 -3.0015681 0 -2.8970237 1.1238267 470.13177
+ 21000 0.1206722 -3.0280371 0 -2.9248911 0.77173089 472.88673
+ 22000 0.11522969 -3.0159631 0 -2.9174691 0.58945089 474.56136
+ 23000 0.1169292 -3.0257398 0 -2.9257932 0.90016236 473.58055
+ 24000 0.11814748 -3.0288882 0 -2.9279002 0.85469502 469.82134
+ 25000 0.11141357 -3.0218783 0 -2.9266463 1.0469177 471.01085
+ 26000 0.11159246 -3.0122701 0 -2.9168851 1.1216321 471.99194
+ 27000 0.10918089 -3.0045635 0 -2.9112398 1.2920286 474.41152
+ 28000 0.1183178 -3.0017823 0 -2.9006488 1.3477212 474.08453
+ 29000 0.118332 -2.9855957 0 -2.88445 1.4002777 478.49231
+ 30000 0.11691453 -2.9721091 0 -2.872175 1.6266108 479.0394
+Loop time of 2.46597 on 1 procs for 30000 steps with 420 atoms
+
+Performance: 3153322.983 tau/day, 12165.598 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 1.8479 | 1.8479 | 1.8479 | 0.0 | 74.94
+Neigh | 0.078045 | 0.078045 | 0.078045 | 0.0 | 3.16
+Comm | 0.026873 | 0.026873 | 0.026873 | 0.0 | 1.09
+Output | 0.00028443 | 0.00028443 | 0.00028443 | 0.0 | 0.01
+Modify | 0.44704 | 0.44704 | 0.44704 | 0.0 | 18.13
+Other | | 0.06581 | | | 2.67
+
+Nlocal: 420 ave 420 max 420 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 111 ave 111 max 111 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 3711 ave 3711 max 3711 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 3711
+Ave neighs/atom = 8.83571
+Neighbor list builds = 614
+Dangerous builds = 0
+
+# run without indenter
+
+unfix 4
+run 30000
+Memory usage per processor = 2.46978 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 30000 0.11691453 -2.9721091 0 -2.872175 1.6267079 479.0108
+ 31000 0.10925212 -3.0270482 0 -2.9336637 -0.33277278 488.93429
+ 32000 0.11439597 -2.9975157 0 -2.8997344 -0.41937391 489.30458
+ 33000 0.1202415 -3.0272086 0 -2.9244307 0.45435486 481.29876
+ 34000 0.12236916 -3.0291826 0 -2.9245861 0.060773047 480.57112
+ 35000 0.10701052 -3.0155083 0 -2.9240398 -0.32828426 491.34913
+ 36000 0.11671309 -3.0501978 0 -2.9504359 0.17774604 480.03548
+ 37000 0.11311041 -3.0472325 0 -2.9505501 -0.096250401 480.52043
+ 38000 0.11671309 -3.0386964 0 -2.9389345 -0.26914235 481.1656
+ 39000 0.127378 -3.0478959 0 -2.9390181 -0.11503417 478.38488
+ 40000 0.11422635 -3.0479185 0 -2.9502821 -0.11840551 479.29223
+ 41000 0.11339443 -3.0470107 0 -2.9500855 -0.36658233 484.33262
+ 42000 0.11750945 -3.0506884 0 -2.9502458 -0.18687218 482.18706
+ 43000 0.10968886 -3.0433967 0 -2.9496388 -0.23827778 483.87888
+ 44000 0.11163929 -3.0449886 0 -2.9495636 -0.2241347 482.09898
+ 45000 0.11726053 -3.0498339 0 -2.9496041 -0.03707734 480.27988
+ 46000 0.10971187 -3.0434544 0 -2.9496769 -0.311219 482.26813
+ 47000 0.11448154 -3.0476146 0 -2.9497602 -0.10374643 480.75372
+ 48000 0.11796515 -3.0503583 0 -2.9495262 -0.18534074 479.03433
+ 49000 0.11331324 -3.0464609 0 -2.9496051 -0.38382421 483.23363
+ 50000 0.1102072 -3.043921 0 -2.94972 -0.11678189 481.28121
+ 51000 0.11169997 -3.0449271 0 -2.9494503 -0.22869529 483.39421
+ 52000 0.1052379 -3.0396306 0 -2.9496773 -0.264831 479.77275
+ 53000 0.12170796 -3.0536766 0 -2.9496453 -0.14056206 482.58519
+ 54000 0.11347849 -3.0465613 0 -2.9495642 -0.23137478 481.27
+ 55000 0.115223 -3.0480538 0 -2.9495655 -0.32336031 485.15401
+ 56000 0.11115417 -3.044689 0 -2.9496787 -0.066353134 481.37281
+ 57000 0.10783414 -3.0418895 0 -2.949717 -0.20380917 482.14483
+ 58000 0.10703451 -3.04105 0 -2.949561 -0.2673909 482.03847
+ 59000 0.11041464 -3.0439806 0 -2.9496023 -0.17616699 481.33957
+ 60000 0.12014097 -3.05226 0 -2.949568 -0.21176633 481.15213
+Loop time of 2.13712 on 1 procs for 30000 steps with 420 atoms
+
+Performance: 3638544.822 tau/day, 14037.596 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 1.7832 | 1.7832 | 1.7832 | 0.0 | 83.44
+Neigh | 0.074649 | 0.074649 | 0.074649 | 0.0 | 3.49
+Comm | 0.02573 | 0.02573 | 0.02573 | 0.0 | 1.20
+Output | 0.00023127 | 0.00023127 | 0.00023127 | 0.0 | 0.01
+Modify | 0.19673 | 0.19673 | 0.19673 | 0.0 | 9.21
+Other | | 0.05655 | | | 2.65
+
+Nlocal: 420 ave 420 max 420 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 106 ave 106 max 106 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 3578 ave 3578 max 3578 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 3578
+Ave neighs/atom = 8.51905
+Neighbor list builds = 617
+Dangerous builds = 0
+Total wall time: 0:00:04
diff --git a/examples/indent/log.15Feb16.indent.g++.4 b/examples/indent/log.15Feb16.indent.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..7c8543fa8570ac721388fc46fa27860e996da59f
--- /dev/null
+++ b/examples/indent/log.15Feb16.indent.g++.4
@@ -0,0 +1,201 @@
+LAMMPS (15 Feb 2016)
+# 2d indenter simulation
+
+dimension 2
+boundary p s p
+
+atom_style atomic
+neighbor 0.3 bin
+neigh_modify delay 5
+
+# create geometry
+
+lattice hex 0.9
+Lattice spacing in x,y,z = 1.1327 1.96189 1.1327
+region box block 0 20 0 10 -0.25 0.25
+create_box 2 box
+Created orthogonal box = (0 0 -0.283174) to (22.6539 19.6189 0.283174)
+ 2 by 2 by 1 MPI processor grid
+create_atoms 1 box
+Created 420 atoms
+
+mass 1 1.0
+mass 2 1.0
+
+# LJ potentials
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0 2.5
+
+# define groups
+
+region 1 block INF INF INF 1.25 INF INF
+group lower region 1
+60 atoms in group lower
+group mobile subtract all lower
+360 atoms in group mobile
+set group lower type 2
+ 60 settings made for type
+
+# initial velocities
+
+compute new mobile temp
+velocity mobile create 0.2 482748 temp new
+fix 1 all nve
+fix 2 lower setforce 0.0 0.0 0.0
+fix 3 all temp/rescale 100 0.1 0.1 0.01 1.0
+
+# run with indenter
+
+timestep 0.003
+variable k equal 1000.0/xlat
+variable y equal "13.0*ylat - step*dt*0.02*ylat"
+
+fix 4 all indent $k sphere 10 v_y 0 5.0
+fix 4 all indent 882.849286914813 sphere 10 v_y 0 5.0
+fix 5 all enforce2d
+
+thermo 1000
+thermo_modify temp new
+WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:445)
+
+#dump 1 all atom 250 dump.indent
+
+#dump 2 all image 1000 image.*.jpg type type # zoom 1.6 adiam 1.5
+#dump_modify 2 pad 5
+
+#dump 3 all movie 1000 movie.mpg type type # zoom 1.6 adiam 1.5
+#dump_modify 3 pad 5
+
+run 30000
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 5 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4 -> bins = 17 15 1
+Memory usage per processor = 2.47636 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 0.2 -3.1727576 0 -3.0018052 -1.436185 444.53333
+ 1000 0.11573595 -3.0964873 0 -2.9975606 -0.20448672 441.83732
+ 2000 0.11519605 -3.0960246 0 -2.9975594 -0.38133491 442.33058
+ 3000 0.11367906 -3.0839597 0 -2.9867912 -0.42579765 444.59119
+ 4000 0.11618844 -3.0860897 0 -2.9867762 -0.041580916 439.84614
+ 5000 0.11327789 -3.0848614 0 -2.9880358 -0.48898867 446.19202
+ 6000 0.12058424 -3.0869438 0 -2.983873 0.011477134 440.56887
+ 7000 0.11772522 -3.0833477 0 -2.9827207 -0.090378245 442.56787
+ 8000 0.12533514 -3.0970033 0 -2.9898715 0.13263189 441.23478
+ 9000 0.1198683 -3.0867062 0 -2.9842473 0.34046664 439.4706
+ 10000 0.12234014 -3.0835007 0 -2.9789291 0.28399731 441.94307
+ 11000 0.11082436 -3.0754796 0 -2.9807511 0.62194284 441.32012
+ 12000 0.1084272 -3.0646379 0 -2.9719584 0.65383569 442.64668
+ 13000 0.11686417 -3.0600388 0 -2.9601477 1.0041123 438.50135
+ 14000 0.12557378 -3.0570017 0 -2.949666 0.85709169 442.10189
+ 15000 0.11934084 -3.0498848 0 -2.9478768 1.0392201 451.74396
+ 16000 0.12576913 -3.045218 0 -2.9377154 1.3479479 441.2702
+ 17000 0.11546579 -3.0348367 0 -2.9361409 1.631821 439.48441
+ 18000 0.12148869 -3.0221152 0 -2.9182713 1.6088855 449.25443
+ 19000 0.11883863 -3.0036777 0 -2.902099 1.5201108 447.12736
+ 20000 0.11163567 -3.0038144 0 -2.9083924 1.4078554 461.76339
+ 21000 0.11361999 -2.9900869 0 -2.8929688 1.1334192 473.91362
+ 22000 0.12696379 -3.0207381 0 -2.9122143 0.83288039 473.02925
+ 23000 0.1188706 -3.01731 0 -2.915704 1.1482286 468.57874
+ 24000 0.11820885 -3.0098527 0 -2.9088123 0.98884958 472.75675
+ 25000 0.11671309 -3.0101308 0 -2.9103689 1.2402973 469.77097
+ 26000 0.11965934 -3.0091118 0 -2.9068315 0.94844832 469.04458
+ 27000 0.12147721 -3.0085715 0 -2.9047374 1.2363584 474.98572
+ 28000 0.11718062 -2.993818 0 -2.8936565 1.143781 478.94786
+ 29000 0.10922042 -2.9873887 0 -2.8940313 1.6184815 473.13968
+ 30000 0.11475456 -2.9749758 0 -2.876888 1.8682946 472.49357
+Loop time of 1.12298 on 4 procs for 30000 steps with 420 atoms
+
+Performance: 6924409.691 tau/day, 26714.544 timesteps/s
+99.1% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.41457 | 0.4817 | 0.52191 | 6.4 | 42.89
+Neigh | 0.017548 | 0.01979 | 0.022012 | 1.5 | 1.76
+Comm | 0.22983 | 0.30219 | 0.38513 | 12.2 | 26.91
+Output | 0.00051403 | 0.00054651 | 0.00063753 | 0.2 | 0.05
+Modify | 0.1947 | 0.2007 | 0.20671 | 1.3 | 17.87
+Other | | 0.1181 | | | 10.51
+
+Nlocal: 105 ave 115 max 90 min
+Histogram: 1 0 0 0 1 0 0 0 0 2
+Nghost: 96.25 ave 104 max 87 min
+Histogram: 1 0 0 0 1 0 0 1 0 1
+Neighs: 931.25 ave 1078 max 743 min
+Histogram: 1 0 1 0 0 0 0 0 0 2
+
+Total # of neighbors = 3725
+Ave neighs/atom = 8.86905
+Neighbor list builds = 608
+Dangerous builds = 0
+
+# run without indenter
+
+unfix 4
+run 30000
+Memory usage per processor = 2.47641 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 30000 0.11475456 -2.9749758 0 -2.876888 1.8675667 472.67773
+ 31000 0.11574891 -3.0442299 0 -2.9452921 -0.72600606 489.16618
+ 32000 0.11316772 -3.0299575 0 -2.933226 -0.74912451 483.50803
+ 33000 0.12321675 -3.052617 0 -2.947296 0.29368262 473.07336
+ 34000 0.11671309 -3.0470741 0 -2.9473122 -0.46988097 480.59621
+ 35000 0.11671309 -3.0456501 0 -2.9458882 -0.74504498 475.07349
+ 36000 0.11980973 -3.0797043 0 -2.9772955 0.083053833 461.14624
+ 37000 0.10992033 -3.0712499 0 -2.9772942 -0.6447083 468.1598
+ 38000 0.11831288 -3.0676136 0 -2.9664842 -0.59676518 469.61724
+ 39000 0.11663782 -3.0775961 0 -2.9778985 0.21776888 460.87504
+ 40000 0.10805913 -3.0688733 0 -2.9765084 -0.59632811 469.15555
+ 41000 0.12118734 -3.0800988 0 -2.9765125 -0.32401944 466.81124
+ 42000 0.12373313 -3.0822746 0 -2.9765123 -0.0033603954 462.85792
+ 43000 0.1078275 -3.0686759 0 -2.976509 -0.71758451 469.60392
+ 44000 0.12315017 -3.0787716 0 -2.9735076 -0.05619902 463.06786
+ 45000 0.11564078 -3.0833684 0 -2.9845231 -0.36953273 465.92986
+ 46000 0.10640706 -3.0654913 0 -2.9745386 -0.53685976 469.3539
+ 47000 0.11810977 -3.0754985 0 -2.9745428 0.088083121 463.20699
+ 48000 0.11241387 -3.0828874 0 -2.9868003 -0.54828531 466.25548
+ 49000 0.11679121 -3.0748686 0 -2.9750399 -0.33781022 465.50451
+ 50000 0.11656344 -3.07471 0 -2.9750761 -0.054088803 461.22814
+ 51000 0.12060058 -3.0781622 0 -2.9750774 -0.55815121 468.81379
+ 52000 0.11936306 -3.0876851 0 -2.9856581 -0.34773758 464.10154
+ 53000 0.11032135 -3.0799138 0 -2.9856153 -0.1735616 465.533
+ 54000 0.12365261 -3.0737021 0 -2.9680086 -0.52954909 468.29003
+ 55000 0.12763641 -3.0771061 0 -2.9680074 -0.17884875 464.79749
+ 56000 0.12638245 -3.0879132 0 -2.9798863 -0.2754242 464.35767
+ 57000 0.11481136 -3.0780176 0 -2.9798812 -0.45547532 468.09393
+ 58000 0.11858604 -3.0812503 0 -2.9798874 -0.17502776 463.2168
+ 59000 0.11344551 -3.0768536 0 -2.9798847 -0.32382437 465.29204
+ 60000 0.11637998 -3.0793607 0 -2.9798836 -0.45942931 466.04868
+Loop time of 0.939672 on 4 procs for 30000 steps with 420 atoms
+
+Performance: 8275230.111 tau/day, 31926.042 timesteps/s
+99.1% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.40284 | 0.47452 | 0.51851 | 6.7 | 50.50
+Neigh | 0.017638 | 0.020592 | 0.023174 | 1.7 | 2.19
+Comm | 0.21243 | 0.28882 | 0.37711 | 12.8 | 30.74
+Output | 0.00049996 | 0.00052589 | 0.00059867 | 0.2 | 0.06
+Modify | 0.052075 | 0.056787 | 0.061078 | 1.7 | 6.04
+Other | | 0.09843 | | | 10.47
+
+Nlocal: 105 ave 112 max 98 min
+Histogram: 1 0 1 0 0 0 0 1 0 1
+Nghost: 92.5 ave 96 max 89 min
+Histogram: 1 0 1 0 0 0 0 1 0 1
+Neighs: 892.25 ave 1003 max 788 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+
+Total # of neighbors = 3569
+Ave neighs/atom = 8.49762
+Neighbor list builds = 634
+Dangerous builds = 0
+Total wall time: 0:00:02
diff --git a/examples/indent/log.15Feb16.indent.min.g++.1 b/examples/indent/log.15Feb16.indent.min.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..2eee0e8a74c1d88f7238c373e12e571aeeea6ab8
--- /dev/null
+++ b/examples/indent/log.15Feb16.indent.min.g++.1
@@ -0,0 +1,452 @@
+LAMMPS (15 Feb 2016)
+# 2d indenter simulation with minimization instead of dynamics
+
+dimension 2
+boundary p s p
+
+atom_style atomic
+neighbor 0.3 bin
+neigh_modify delay 5
+
+# create geometry
+
+lattice hex 0.9
+Lattice spacing in x,y,z = 1.1327 1.96189 1.1327
+region box block 0 20 0 10 -0.25 0.25
+create_box 2 box
+Created orthogonal box = (0 0 -0.283174) to (22.6539 19.6189 0.283174)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 420 atoms
+
+mass * 1.0
+
+# LJ potentials
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0 2.5
+
+# define groups
+
+region 1 block INF INF INF 1.25 INF INF
+group lower region 1
+60 atoms in group lower
+group mobile subtract all lower
+360 atoms in group mobile
+set group lower type 2
+ 60 settings made for type
+
+# initial velocities
+
+fix 2 lower setforce 0.0 0.0 0.0
+
+# indenter
+
+fix 5 all enforce2d
+
+# minimize with indenter
+
+thermo 10
+
+#dump 1 all atom 10 dump.indent
+
+#dump 2 all image 25 image.*.jpg type type # zoom 1.6 adiam 1.5
+#dump_modify 2 pad 4
+
+#dump 3 all movie 25 movie.mpg type type # zoom 1.6 adiam 1.5
+#dump_modify 3 pad 4
+
+minimize 1.0e-6 1.0e-6 1000 1000
+WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4 -> bins = 17 15 1
+Memory usage per processor = 3.5947 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 0 -3.1727576 0 -3.1727576 -1.5977027 444.53333
+ 10 0 -3.1815908 0 -3.1815908 -1.1226904 440.57558
+ 20 0 -3.1895471 0 -3.1895471 -0.86027602 436.93033
+ 30 0 -3.1908366 0 -3.1908366 -0.72179223 436.93033
+ 35 0 -3.1909386 0 -3.1909386 -0.69788745 433.53082
+Loop time of 0.00924516 on 1 procs for 35 steps with 420 atoms
+
+97.3% CPU use with 1 MPI tasks x no OpenMP threads
+
+Minimization stats:
+ Stopping criterion = energy tolerance
+ Energy initial, next-to-last, final =
+ -3.17275755126 -3.19093697812 -3.19093855395
+ Force two-norm initial, final = 6.74302 0.230475
+ Force max component initial, final = 1.46877 0.0236603
+ Final line search alpha, max atom move = 1 0.0236603
+ Iterations, force evaluations = 35 70
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0078757 | 0.0078757 | 0.0078757 | 0.0 | 85.19
+Neigh | 0.0004518 | 0.0004518 | 0.0004518 | 0.0 | 4.89
+Comm | 8.0109e-05 | 8.0109e-05 | 8.0109e-05 | 0.0 | 0.87
+Output | 2.5749e-05 | 2.5749e-05 | 2.5749e-05 | 0.0 | 0.28
+Modify | 0.00010729 | 0.00010729 | 0.00010729 | 0.0 | 1.16
+Other | | 0.0007045 | | | 7.62
+
+Nlocal: 420 ave 420 max 420 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 95 ave 95 max 95 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 3580 ave 3580 max 3580 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 3580
+Ave neighs/atom = 8.52381
+Neighbor list builds = 4
+Dangerous builds = 0
+
+variable k equal 5000.0/xlat
+variable k1 equal 1000.0/xlat
+
+fix 4 all indent $k sphere 10 13.0 0 6.0
+fix 4 all indent 4414.24643457407 sphere 10 13.0 0 6.0
+fix_modify 4 energy yes
+minimize 1.0e-6 1.0e-6 1000 1000
+WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
+Memory usage per processor = 3.5947 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 35 0 -3.1909386 0 -2.174369 -0.6944516 435.67574
+ 40 0 -3.1462704 0 -3.1261242 -0.20646557 435.67534
+ 50 0 -3.174757 0 -3.173603 -0.34916248 436.00326
+ 60 0 -3.1789904 0 -3.1780198 -0.31146423 436.06053
+ 70 0 -3.1800572 0 -3.1792392 -0.27664904 436.09293
+ 80 0 -3.1808315 0 -3.1799813 -0.24091474 435.00572
+ 90 0 -3.1810856 0 -3.1803991 -0.1771392 433.03804
+ 100 0 -3.1812307 0 -3.1805381 -0.15305004 434.96379
+ 110 0 -3.1812588 0 -3.1805938 -0.12504604 432.50683
+ 111 0 -3.1812728 0 -3.1805961 -0.12407116 432.50683
+Loop time of 0.0215449 on 1 procs for 76 steps with 420 atoms
+
+102.1% CPU use with 1 MPI tasks x no OpenMP threads
+
+Minimization stats:
+ Stopping criterion = energy tolerance
+ Energy initial, next-to-last, final =
+ -2.17436899358 -3.18059381924 -3.18059607055
+ Force two-norm initial, final = 1618.56 0.444006
+ Force max component initial, final = 1191.42 0.168708
+ Final line search alpha, max atom move = 0.428869 0.0723538
+ Iterations, force evaluations = 76 147
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.016444 | 0.016444 | 0.016444 | 0.0 | 76.33
+Neigh | 0.0022733 | 0.0022733 | 0.0022733 | 0.0 | 10.55
+Comm | 0.0001955 | 0.0001955 | 0.0001955 | 0.0 | 0.91
+Output | 5.7459e-05 | 5.7459e-05 | 5.7459e-05 | 0.0 | 0.27
+Modify | 0.00096774 | 0.00096774 | 0.00096774 | 0.0 | 4.49
+Other | | 0.001607 | | | 7.46
+
+Nlocal: 420 ave 420 max 420 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 95 ave 95 max 95 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 3596 ave 3596 max 3596 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 3596
+Ave neighs/atom = 8.5619
+Neighbor list builds = 19
+Dangerous builds = 0
+
+fix 4 all indent ${k1} sphere 10 12.5 0 6.0
+fix 4 all indent 882.849286914813 sphere 10 12.5 0 6.0
+fix_modify 4 energy yes
+minimize 1.0e-6 1.0e-6 1000 1000
+WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
+Memory usage per processor = 3.5947 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 111 0 -3.1812728 0 -0.21796953 -0.12362158 434.07977
+ 120 0 -2.9592755 0 -2.8003562 1.9418398 434.0832
+ 130 0 -3.0632093 0 -3.0453082 1.4275815 434.09622
+ 140 0 -3.0947739 0 -3.0852867 1.2276154 434.51983
+ 150 0 -3.1008901 0 -3.0931811 1.1938163 434.52998
+ 160 0 -3.1026159 0 -3.0950306 1.2229151 434.35672
+ 170 0 -3.1032959 0 -3.0962512 1.3134391 432.20445
+ 180 0 -3.1041304 0 -3.0969544 1.3751461 430.37017
+ 190 0 -3.1043441 0 -3.0970791 1.392095 430.37017
+ 193 0 -3.1043345 0 -3.0970891 1.3934777 430.37017
+Loop time of 0.022316 on 1 procs for 82 steps with 420 atoms
+
+103.1% CPU use with 1 MPI tasks x no OpenMP threads
+
+Minimization stats:
+ Stopping criterion = energy tolerance
+ Energy initial, next-to-last, final =
+ -0.217969533586 -3.09708660422 -3.09708908043
+ Force two-norm initial, final = 1754.38 0.648372
+ Force max component initial, final = 924.68 0.156564
+ Final line search alpha, max atom move = 0.961384 0.150518
+ Iterations, force evaluations = 82 156
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.017607 | 0.017607 | 0.017607 | 0.0 | 78.90
+Neigh | 0.0018115 | 0.0018115 | 0.0018115 | 0.0 | 8.12
+Comm | 0.00016046 | 0.00016046 | 0.00016046 | 0.0 | 0.72
+Output | 5.8413e-05 | 5.8413e-05 | 5.8413e-05 | 0.0 | 0.26
+Modify | 0.0010521 | 0.0010521 | 0.0010521 | 0.0 | 4.71
+Other | | 0.001626 | | | 7.29
+
+Nlocal: 420 ave 420 max 420 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 105 ave 105 max 105 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 3666 ave 3666 max 3666 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 3666
+Ave neighs/atom = 8.72857
+Neighbor list builds = 14
+Dangerous builds = 0
+
+fix 4 all indent ${k1} sphere 10 12.0 0 6.0
+fix 4 all indent 882.849286914813 sphere 10 12.0 0 6.0
+fix_modify 4 energy yes
+minimize 1.0e-6 1.0e-6 1000 1000
+WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
+Memory usage per processor = 3.5947 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 193 0 -3.1043345 0 2.0111862 1.3910056 431.13503
+ 200 0 -2.5918177 0 -1.931934 5.51119 430.91952
+ 210 0 -2.8122285 0 -2.7440908 4.2686845 440.18379
+ 220 0 -2.9102892 0 -2.8879734 3.5957736 444.98944
+ 230 0 -2.9492295 0 -2.9335905 3.2079493 451.92209
+ 240 0 -2.9611099 0 -2.9486963 3.1240398 452.59159
+ 250 0 -2.9644912 0 -2.9549723 3.0493724 455.54273
+ 260 0 -2.9716881 0 -2.9621479 2.8585653 458.29826
+ 270 0 -3.0142839 0 -3.0048107 2.1183076 462.48471
+ 280 0 -3.0666108 0 -3.0590819 1.4342986 470.61174
+ 290 0 -3.1004306 0 -3.0944504 1.1550298 472.70399
+ 300 0 -3.1107855 0 -3.1043751 1.0663324 470.76888
+ 310 0 -3.1124671 0 -3.1059633 1.0375877 473.02275
+ 316 0 -3.1126981 0 -3.1061297 1.0266662 473.02275
+Loop time of 0.0393021 on 1 procs for 123 steps with 420 atoms
+
+99.2% CPU use with 1 MPI tasks x no OpenMP threads
+
+Minimization stats:
+ Stopping criterion = linesearch alpha is zero
+ Energy initial, next-to-last, final =
+ 2.01118618013 -3.10612971775 -3.10612971775
+ Force two-norm initial, final = 2329.79 2.56384
+ Force max component initial, final = 1038.4 0.558457
+ Final line search alpha, max atom move = 6.21371e-07 3.47009e-07
+ Iterations, force evaluations = 123 270
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.030668 | 0.030668 | 0.030668 | 0.0 | 78.03
+Neigh | 0.0037498 | 0.0037498 | 0.0037498 | 0.0 | 9.54
+Comm | 0.00033641 | 0.00033641 | 0.00033641 | 0.0 | 0.86
+Output | 8.6069e-05 | 8.6069e-05 | 8.6069e-05 | 0.0 | 0.22
+Modify | 0.0017693 | 0.0017693 | 0.0017693 | 0.0 | 4.50
+Other | | 0.002692 | | | 6.85
+
+Nlocal: 420 ave 420 max 420 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 105 ave 105 max 105 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 3583 ave 3583 max 3583 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 3583
+Ave neighs/atom = 8.53095
+Neighbor list builds = 29
+Dangerous builds = 0
+
+fix 4 all indent ${k1} sphere 10 11.4 0 6.0
+fix 4 all indent 882.849286914813 sphere 10 11.4 0 6.0
+fix_modify 4 energy yes
+minimize 1.0e-6 1.0e-6 1000 1000
+WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
+Memory usage per processor = 3.5947 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 316 0 -3.1126981 0 5.3552772 1.0307152 471.16452
+ 320 0 -2.7131804 0 0.70918694 3.910187 471.16482
+ 330 0 -2.5180572 0 -2.2327154 5.9511047 472.82589
+ 340 0 -2.8183947 0 -2.790733 4.18655 477.34785
+ 350 0 -2.9132456 0 -2.8943586 3.4322048 481.94491
+ 360 0 -2.9337359 0 -2.9225123 3.2341233 484.63169
+ 370 0 -2.9463892 0 -2.9382426 3.0071366 485.20235
+ 380 0 -2.9682176 0 -2.9597318 2.6056737 490.5653
+ 390 0 -2.9878255 0 -2.974755 2.3632883 491.02616
+ 400 0 -3.0033473 0 -2.9915257 2.205124 490.20353
+ 410 0 -3.0130231 0 -3.001125 2.0531631 492.78365
+ 420 0 -3.0146089 0 -3.0030496 1.9865701 492.35543
+ 430 0 -3.0344603 0 -3.0225619 1.6795534 494.30371
+ 440 0 -3.03943 0 -3.0271752 1.64578 494.30371
+ 450 0 -3.0420658 0 -3.0294992 1.6461313 493.96169
+ 460 0 -3.0443144 0 -3.0312966 1.6701433 493.56812
+ 465 0 -3.0444584 0 -3.0313908 1.6713796 493.56812
+Loop time of 0.0470922 on 1 procs for 149 steps with 420 atoms
+
+99.8% CPU use with 1 MPI tasks x no OpenMP threads
+
+Minimization stats:
+ Stopping criterion = linesearch alpha is zero
+ Energy initial, next-to-last, final =
+ 5.35527716926 -3.03139082546 -3.03139082546
+ Force two-norm initial, final = 3151.59 4.64631
+ Force max component initial, final = 1384.28 2.19626
+ Final line search alpha, max atom move = 1.88135e-07 4.13193e-07
+ Iterations, force evaluations = 149 323
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.036967 | 0.036967 | 0.036967 | 0.0 | 78.50
+Neigh | 0.004194 | 0.004194 | 0.004194 | 0.0 | 8.91
+Comm | 0.00037503 | 0.00037503 | 0.00037503 | 0.0 | 0.80
+Output | 0.00010633 | 0.00010633 | 0.00010633 | 0.0 | 0.23
+Modify | 0.002212 | 0.002212 | 0.002212 | 0.0 | 4.70
+Other | | 0.003238 | | | 6.88
+
+Nlocal: 420 ave 420 max 420 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 113 ave 113 max 113 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 3693 ave 3693 max 3693 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 3693
+Ave neighs/atom = 8.79286
+Neighbor list builds = 33
+Dangerous builds = 0
+
+fix 4 all indent ${k1} sphere 10 11.2 0 6.0
+fix 4 all indent 882.849286914813 sphere 10 11.2 0 6.0
+fix_modify 4 energy yes
+minimize 1.0e-6 1.0e-6 1000 1000
+WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
+Memory usage per processor = 3.59478 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 465 0 -3.0444584 0 -2.5580192 1.6715946 493.50462
+ 470 0 -2.9426683 0 -2.8814986 2.6421083 493.54443
+ 480 0 -2.9569251 0 -2.9256743 2.6206554 493.55709
+ 490 0 -2.961805 0 -2.9376884 2.6095523 493.40001
+ 500 0 -2.9651536 0 -2.9450214 2.6314399 493.06356
+ 510 0 -2.9667772 0 -2.9489178 2.6710408 492.70775
+ 520 0 -2.9728188 0 -2.9566496 2.7182742 492.38186
+ 530 0 -2.9791224 0 -2.9651707 2.7038256 493.19977
+ 540 0 -2.9968316 0 -2.984276 2.5920672 495.29778
+ 550 0 -3.0029515 0 -2.9915532 2.4491025 500.52622
+ 560 0 -3.0160794 0 -3.0057787 2.0399831 513.34527
+ 570 0 -3.0363001 0 -3.0306173 1.6834763 520.40445
+ 580 0 -3.0548101 0 -3.0490935 1.501103 521.5353
+ 590 0 -3.0640876 0 -3.0585539 1.3888581 520.17883
+ 600 0 -3.0713144 0 -3.0649318 1.3341898 518.99349
+ 610 0 -3.0727361 0 -3.0662278 1.2983097 519.87058
+ 620 0 -3.0732598 0 -3.0671664 1.2611866 520.9829
+ 630 0 -3.076528 0 -3.069576 1.1930176 520.18857
+ 640 0 -3.0778611 0 -3.0710808 1.1946248 520.31492
+ 650 0 -3.0781525 0 -3.0715363 1.2031624 520.31492
+ 651 0 -3.0781525 0 -3.0715363 1.2031624 520.31492
+Loop time of 0.057997 on 1 procs for 186 steps with 420 atoms
+
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+Minimization stats:
+ Stopping criterion = linesearch alpha is zero
+ Energy initial, next-to-last, final =
+ -2.55801918976 -3.07153633363 -3.07153633363
+ Force two-norm initial, final = 440.856 1.45625
+ Force max component initial, final = 245.987 0.411517
+ Final line search alpha, max atom move = 1.25651e-06 5.17073e-07
+ Iterations, force evaluations = 186 403
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.045592 | 0.045592 | 0.045592 | 0.0 | 78.61
+Neigh | 0.0050173 | 0.0050173 | 0.0050173 | 0.0 | 8.65
+Comm | 0.00052071 | 0.00052071 | 0.00052071 | 0.0 | 0.90
+Output | 0.00014472 | 0.00014472 | 0.00014472 | 0.0 | 0.25
+Modify | 0.0027096 | 0.0027096 | 0.0027096 | 0.0 | 4.67
+Other | | 0.004013 | | | 6.92
+
+Nlocal: 420 ave 420 max 420 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 116 ave 116 max 116 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 3622 ave 3622 max 3622 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 3622
+Ave neighs/atom = 8.62381
+Neighbor list builds = 39
+Dangerous builds = 0
+
+fix 4 all indent ${k1} sphere 10 11.0 0 6.0
+fix 4 all indent 882.849286914813 sphere 10 11.0 0 6.0
+fix_modify 4 energy yes
+minimize 1.0e-6 1.0e-6 1000 1000
+WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
+Memory usage per processor = 3.59487 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 651 0 -3.0781525 0 -2.6488207 1.2032064 520.29591
+ 660 0 -3.0085949 0 -2.9796645 1.9715308 520.26872
+ 670 0 -3.014536 0 -2.9989599 2.0077209 520.35057
+ 680 0 -3.0193861 0 -3.0073499 2.0050119 520.52555
+ 690 0 -3.0214256 0 -3.0087927 2.0056587 520.37174
+ 700 0 -3.0218644 0 -3.0095894 2.0386389 520.05804
+ 710 0 -3.0262571 0 -3.0142277 2.1356802 520.14691
+ 720 0 -3.0325017 0 -3.0216037 2.1065924 521.43634
+ 730 0 -3.0400735 0 -3.0302631 2.0146233 523.09133
+ 740 0 -3.048476 0 -3.0386288 1.9305047 523.14231
+ 750 0 -3.0523937 0 -3.042131 1.9025403 522.0453
+ 760 0 -3.0544932 0 -3.044222 1.9106706 521.73287
+ 770 0 -3.0587698 0 -3.048907 1.9552463 521.6899
+ 780 0 -3.065994 0 -3.0566273 1.931796 521.52157
+ 790 0 -3.0675084 0 -3.0577936 1.9283059 520.99202
+ 799 0 -3.0677005 0 -3.057959 1.9288603 520.99202
+Loop time of 0.046221 on 1 procs for 148 steps with 420 atoms
+
+99.5% CPU use with 1 MPI tasks x no OpenMP threads
+
+Minimization stats:
+ Stopping criterion = linesearch alpha is zero
+ Energy initial, next-to-last, final =
+ -2.64882068661 -3.05795898949 -3.05795898949
+ Force two-norm initial, final = 420.333 1.17649
+ Force max component initial, final = 194.656 0.28552
+ Final line search alpha, max atom move = 1.95857e-06 5.5921e-07
+ Iterations, force evaluations = 148 327
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.036542 | 0.036542 | 0.036542 | 0.0 | 79.06
+Neigh | 0.0038009 | 0.0038009 | 0.0038009 | 0.0 | 8.22
+Comm | 0.00038958 | 0.00038958 | 0.00038958 | 0.0 | 0.84
+Output | 9.8705e-05 | 9.8705e-05 | 9.8705e-05 | 0.0 | 0.21
+Modify | 0.0021958 | 0.0021958 | 0.0021958 | 0.0 | 4.75
+Other | | 0.003194 | | | 6.91
+
+Nlocal: 420 ave 420 max 420 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 122 ave 122 max 122 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 3612 ave 3612 max 3612 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 3612
+Ave neighs/atom = 8.6
+Neighbor list builds = 30
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/indent/log.15Feb16.indent.min.g++.4 b/examples/indent/log.15Feb16.indent.min.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..a796c93ced88e1b8f9e8820cbe6464bf705442ba
--- /dev/null
+++ b/examples/indent/log.15Feb16.indent.min.g++.4
@@ -0,0 +1,445 @@
+LAMMPS (15 Feb 2016)
+# 2d indenter simulation with minimization instead of dynamics
+
+dimension 2
+boundary p s p
+
+atom_style atomic
+neighbor 0.3 bin
+neigh_modify delay 5
+
+# create geometry
+
+lattice hex 0.9
+Lattice spacing in x,y,z = 1.1327 1.96189 1.1327
+region box block 0 20 0 10 -0.25 0.25
+create_box 2 box
+Created orthogonal box = (0 0 -0.283174) to (22.6539 19.6189 0.283174)
+ 2 by 2 by 1 MPI processor grid
+create_atoms 1 box
+Created 420 atoms
+
+mass * 1.0
+
+# LJ potentials
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0 2.5
+
+# define groups
+
+region 1 block INF INF INF 1.25 INF INF
+group lower region 1
+60 atoms in group lower
+group mobile subtract all lower
+360 atoms in group mobile
+set group lower type 2
+ 60 settings made for type
+
+# initial velocities
+
+fix 2 lower setforce 0.0 0.0 0.0
+
+# indenter
+
+fix 5 all enforce2d
+
+# minimize with indenter
+
+thermo 10
+
+#dump 1 all atom 10 dump.indent
+
+#dump 2 all image 25 image.*.jpg type type # zoom 1.6 adiam 1.5
+#dump_modify 2 pad 4
+
+#dump 3 all movie 25 movie.mpg type type # zoom 1.6 adiam 1.5
+#dump_modify 3 pad 4
+
+minimize 1.0e-6 1.0e-6 1000 1000
+WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4 -> bins = 17 15 1
+Memory usage per processor = 3.60136 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 0 -3.1727576 0 -3.1727576 -1.5977027 444.53333
+ 10 0 -3.1815908 0 -3.1815908 -1.1226904 440.57558
+ 20 0 -3.1895471 0 -3.1895471 -0.86027602 436.93033
+ 30 0 -3.1908366 0 -3.1908366 -0.72179223 436.93033
+ 35 0 -3.1909386 0 -3.1909386 -0.69788745 433.53082
+Loop time of 0.00339699 on 4 procs for 35 steps with 420 atoms
+
+95.7% CPU use with 4 MPI tasks x no OpenMP threads
+
+Minimization stats:
+ Stopping criterion = energy tolerance
+ Energy initial, next-to-last, final =
+ -3.17275755126 -3.19093697812 -3.19093855395
+ Force two-norm initial, final = 6.74302 0.230475
+ Force max component initial, final = 1.46877 0.0236603
+ Final line search alpha, max atom move = 1 0.0236603
+ Iterations, force evaluations = 35 70
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0019855 | 0.002022 | 0.0020628 | 0.1 | 59.52
+Neigh | 0.00012016 | 0.00012463 | 0.00012922 | 0.0 | 3.67
+Comm | 0.00034857 | 0.00041682 | 0.00048089 | 0.3 | 12.27
+Output | 3.7909e-05 | 4.0412e-05 | 4.6968e-05 | 0.1 | 1.19
+Modify | 3.2663e-05 | 3.8743e-05 | 4.4823e-05 | 0.1 | 1.14
+Other | | 0.0007544 | | | 22.21
+
+Nlocal: 105 ave 111 max 99 min
+Histogram: 1 1 0 0 0 0 0 0 1 1
+Nghost: 84 ave 90 max 78 min
+Histogram: 1 1 0 0 0 0 0 0 1 1
+Neighs: 895 ave 999 max 798 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 3580
+Ave neighs/atom = 8.52381
+Neighbor list builds = 4
+Dangerous builds = 0
+
+variable k equal 5000.0/xlat
+variable k1 equal 1000.0/xlat
+
+fix 4 all indent $k sphere 10 13.0 0 6.0
+fix 4 all indent 4414.24643457407 sphere 10 13.0 0 6.0
+fix_modify 4 energy yes
+minimize 1.0e-6 1.0e-6 1000 1000
+WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
+Memory usage per processor = 3.60136 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 35 0 -3.1909386 0 -2.174369 -0.6944516 435.67574
+ 40 0 -3.1462704 0 -3.1261242 -0.20646557 435.67534
+ 50 0 -3.174757 0 -3.173603 -0.34916248 436.00326
+ 60 0 -3.1789904 0 -3.1780198 -0.31146423 436.06053
+ 70 0 -3.1800572 0 -3.1792392 -0.27664904 436.09293
+ 80 0 -3.1808315 0 -3.1799813 -0.24091474 435.00572
+ 90 0 -3.1810856 0 -3.1803991 -0.17713919 433.03804
+ 100 0 -3.1812307 0 -3.1805381 -0.15305002 434.96379
+ 110 0 -3.1812588 0 -3.1805938 -0.12504601 432.50683
+ 111 0 -3.1812728 0 -3.1805961 -0.12407115 432.50683
+Loop time of 0.00934356 on 4 procs for 76 steps with 420 atoms
+
+91.0% CPU use with 4 MPI tasks x no OpenMP threads
+
+Minimization stats:
+ Stopping criterion = energy tolerance
+ Energy initial, next-to-last, final =
+ -2.17436899358 -3.18059381928 -3.18059607058
+ Force two-norm initial, final = 1618.56 0.444005
+ Force max component initial, final = 1191.42 0.168709
+ Final line search alpha, max atom move = 0.428871 0.0723543
+ Iterations, force evaluations = 76 147
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0039222 | 0.0042289 | 0.0045605 | 0.5 | 45.26
+Neigh | 0.00056624 | 0.00060999 | 0.00065136 | 0.2 | 6.53
+Comm | 0.0011964 | 0.0017179 | 0.0022454 | 1.1 | 18.39
+Output | 0.00011611 | 0.0001232 | 0.000139 | 0.1 | 1.32
+Modify | 0.00025821 | 0.00028563 | 0.0003078 | 0.1 | 3.06
+Other | | 0.002378 | | | 25.45
+
+Nlocal: 105 ave 111 max 99 min
+Histogram: 1 1 0 0 0 0 0 0 1 1
+Nghost: 87 ave 90 max 84 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+Neighs: 899 ave 1001 max 797 min
+Histogram: 1 1 0 0 0 0 0 0 1 1
+
+Total # of neighbors = 3596
+Ave neighs/atom = 8.5619
+Neighbor list builds = 19
+Dangerous builds = 0
+
+fix 4 all indent ${k1} sphere 10 12.5 0 6.0
+fix 4 all indent 882.849286914813 sphere 10 12.5 0 6.0
+fix_modify 4 energy yes
+minimize 1.0e-6 1.0e-6 1000 1000
+WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
+Memory usage per processor = 3.60136 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 111 0 -3.1812728 0 -0.21796955 -0.12362156 434.07977
+ 120 0 -2.9592755 0 -2.8003562 1.9418398 434.0832
+ 130 0 -3.0632093 0 -3.0453082 1.4275815 434.09622
+ 140 0 -3.0947739 0 -3.0852867 1.2276154 434.51983
+ 150 0 -3.1008901 0 -3.0931811 1.1938163 434.52998
+ 160 0 -3.1026159 0 -3.0950306 1.2229151 434.35672
+ 170 0 -3.1032959 0 -3.0962512 1.3134388 432.20444
+ 180 0 -3.1041304 0 -3.0969544 1.3751455 430.37021
+ 190 0 -3.1043441 0 -3.0970791 1.3920926 430.37021
+ 193 0 -3.1043346 0 -3.0970891 1.3934753 430.37021
+Loop time of 0.0095458 on 4 procs for 82 steps with 420 atoms
+
+94.3% CPU use with 4 MPI tasks x no OpenMP threads
+
+Minimization stats:
+ Stopping criterion = energy tolerance
+ Energy initial, next-to-last, final =
+ -0.217969552445 -3.09708660005 -3.09708907864
+ Force two-norm initial, final = 1754.38 0.649535
+ Force max component initial, final = 924.68 0.156756
+ Final line search alpha, max atom move = 0.962047 0.150807
+ Iterations, force evaluations = 82 156
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0040784 | 0.0045295 | 0.00495 | 0.6 | 47.45
+Neigh | 0.00041556 | 0.00045681 | 0.0004952 | 0.2 | 4.79
+Comm | 0.0011504 | 0.0016876 | 0.0022304 | 1.2 | 17.68
+Output | 0.00012088 | 0.00012857 | 0.000144 | 0.1 | 1.35
+Modify | 0.00027156 | 0.00029528 | 0.00032377 | 0.1 | 3.09
+Other | | 0.002448 | | | 25.65
+
+Nlocal: 105 ave 112 max 98 min
+Histogram: 1 0 1 0 0 0 0 1 0 1
+Nghost: 94 ave 97 max 91 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+Neighs: 916.5 ave 1013 max 831 min
+Histogram: 1 1 0 0 0 0 0 1 0 1
+
+Total # of neighbors = 3666
+Ave neighs/atom = 8.72857
+Neighbor list builds = 14
+Dangerous builds = 0
+
+fix 4 all indent ${k1} sphere 10 12.0 0 6.0
+fix 4 all indent 882.849286914813 sphere 10 12.0 0 6.0
+fix_modify 4 energy yes
+minimize 1.0e-6 1.0e-6 1000 1000
+WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
+Memory usage per processor = 3.60136 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 193 0 -3.1043346 0 2.0111873 1.3910032 431.13505
+ 200 0 -2.5918062 0 -1.93191 5.511262 430.91953
+ 210 0 -2.8122299 0 -2.7440894 4.2686747 440.18337
+ 220 0 -2.910295 0 -2.8879715 3.5956981 444.98997
+ 230 0 -2.949231 0 -2.9335905 3.2079519 451.9225
+ 240 0 -2.9611012 0 -2.9486911 3.1241334 452.5907
+ 250 0 -2.9644798 0 -2.9549529 3.0499305 455.51712
+ 260 0 -2.9716705 0 -2.9621358 2.8593553 458.27346
+ 270 0 -3.0143454 0 -3.0048234 2.1158458 462.52748
+ 280 0 -3.0656896 0 -3.0590412 1.4428324 470.69566
+ 290 0 -3.1008608 0 -3.0951203 1.1487473 472.80734
+ 300 0 -3.1109522 0 -3.1046995 1.064904 470.50807
+ 310 0 -3.1123989 0 -3.105985 1.0430839 470.40952
+ 313 0 -3.1125022 0 -3.1060453 1.0390872 470.40952
+Loop time of 0.0165539 on 4 procs for 120 steps with 420 atoms
+
+92.1% CPU use with 4 MPI tasks x no OpenMP threads
+
+Minimization stats:
+ Stopping criterion = linesearch alpha is zero
+ Energy initial, next-to-last, final =
+ 2.01118731028 -3.10604533837 -3.10604533837
+ Force two-norm initial, final = 2329.79 2.39232
+ Force max component initial, final = 1038.4 0.571422
+ Final line search alpha, max atom move = 7.76258e-07 4.43571e-07
+ Iterations, force evaluations = 120 264
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0066144 | 0.0077118 | 0.0089424 | 1.2 | 46.59
+Neigh | 0.0008266 | 0.00094324 | 0.0010567 | 0.3 | 5.70
+Comm | 0.0018625 | 0.0032995 | 0.0045738 | 2.2 | 19.93
+Output | 0.00018287 | 0.00019288 | 0.00021982 | 0.1 | 1.17
+Modify | 0.00045705 | 0.00051093 | 0.00056267 | 0.2 | 3.09
+Other | | 0.003896 | | | 23.53
+
+Nlocal: 105 ave 123 max 90 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+Nghost: 91 ave 100 max 85 min
+Histogram: 2 0 0 0 0 0 1 0 0 1
+Neighs: 892.25 ave 1107 max 699 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+
+Total # of neighbors = 3569
+Ave neighs/atom = 8.49762
+Neighbor list builds = 28
+Dangerous builds = 0
+
+fix 4 all indent ${k1} sphere 10 11.4 0 6.0
+fix 4 all indent 882.849286914813 sphere 10 11.4 0 6.0
+fix_modify 4 energy yes
+minimize 1.0e-6 1.0e-6 1000 1000
+WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
+Memory usage per processor = 3.60136 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 313 0 -3.1125022 0 5.3341053 1.0377311 471.02427
+ 320 0 -2.402824 0 -0.86170235 6.1550233 471.02943
+ 330 0 -2.5964265 0 -2.4563494 5.5893601 473.87197
+ 340 0 -2.857458 0 -2.8325789 3.9156904 478.37268
+ 350 0 -2.923244 0 -2.9056267 3.3461026 481.81668
+ 360 0 -2.9355414 0 -2.924236 3.2437289 484.05209
+ 370 0 -2.9486011 0 -2.9405396 2.9295065 487.64545
+ 380 0 -2.9695687 0 -2.9616077 2.5116249 491.53648
+ 390 0 -2.991356 0 -2.9786736 2.2788393 491.056
+ 400 0 -3.0098108 0 -2.9963408 2.0798685 490.87751
+ 410 0 -3.0142937 0 -3.0017605 2.0015139 491.52711
+ 417 0 -3.0148998 0 -3.0024932 1.9909706 492.48053
+Loop time of 0.0134063 on 4 procs for 104 steps with 420 atoms
+
+95.1% CPU use with 4 MPI tasks x no OpenMP threads
+
+Minimization stats:
+ Stopping criterion = energy tolerance
+ Energy initial, next-to-last, final =
+ 5.33410533222 -3.00249023582 -3.00249317367
+ Force two-norm initial, final = 3147.64 2.97401
+ Force max component initial, final = 1384.36 0.679769
+ Final line search alpha, max atom move = 0.14124 0.0960107
+ Iterations, force evaluations = 104 200
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0046661 | 0.0059155 | 0.0071743 | 1.5 | 44.13
+Neigh | 0.00073218 | 0.00090402 | 0.0010717 | 0.5 | 6.74
+Comm | 0.001442 | 0.0029395 | 0.0044417 | 2.5 | 21.93
+Output | 0.00014901 | 0.00015819 | 0.00018287 | 0.1 | 1.18
+Modify | 0.0003469 | 0.00039375 | 0.0004406 | 0.2 | 2.94
+Other | | 0.003095 | | | 23.09
+
+Nlocal: 105 ave 121 max 89 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost: 93.5 ave 101 max 86 min
+Histogram: 1 1 0 0 0 0 0 0 1 1
+Neighs: 936 ave 1121 max 741 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 3744
+Ave neighs/atom = 8.91429
+Neighbor list builds = 27
+Dangerous builds = 0
+
+fix 4 all indent ${k1} sphere 10 11.2 0 6.0
+fix 4 all indent 882.849286914813 sphere 10 11.2 0 6.0
+fix_modify 4 energy yes
+minimize 1.0e-6 1.0e-6 1000 1000
+WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
+Memory usage per processor = 3.60141 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 417 0 -3.0148998 0 -2.4816986 1.9918498 492.26314
+ 420 0 -2.9209943 0 -2.7871779 2.8201475 492.26417
+ 430 0 -2.9210322 0 -2.8866221 3.0115293 492.22119
+ 440 0 -2.930174 0 -2.9072946 3.0289241 491.74253
+ 450 0 -2.9423694 0 -2.9251127 3.0269322 491.55578
+ 460 0 -2.9595882 0 -2.9424058 2.8769376 491.29122
+ 470 0 -2.9716874 0 -2.9531385 2.7820875 491.71167
+ 480 0 -2.9967793 0 -2.9798492 2.5135722 493.20335
+ 490 0 -3.0077594 0 -2.9927399 2.3652753 495.90598
+ 500 0 -3.0156527 0 -3.0064227 2.2002124 502.94121
+ 510 0 -3.0389075 0 -3.0316863 1.8518803 512.1298
+ 520 0 -3.0533374 0 -3.0444153 1.6968184 511.35747
+ 530 0 -3.0643133 0 -3.0573978 1.5165159 516.34223
+ 540 0 -3.0958216 0 -3.0905446 1.0627598 519.02979
+ 550 0 -3.1051578 0 -3.1009512 1.0050567 517.17039
+ 560 0 -3.1119271 0 -3.1069923 0.92711525 515.78315
+ 570 0 -3.114104 0 -3.1090684 0.9237051 515.34157
+ 580 0 -3.114576 0 -3.1094219 0.9181339 515.34157
+ 590 0 -3.114722 0 -3.1095528 0.90665975 515.99746
+ 600 0 -3.1149189 0 -3.1096744 0.88783587 515.99746
+ 605 0 -3.1149612 0 -3.1097106 0.88187936 515.99746
+Loop time of 0.0259686 on 4 procs for 188 steps with 420 atoms
+
+100.1% CPU use with 4 MPI tasks x no OpenMP threads
+
+Minimization stats:
+ Stopping criterion = linesearch alpha is zero
+ Energy initial, next-to-last, final =
+ -2.48169863396 -3.10971061979 -3.10971061979
+ Force two-norm initial, final = 470.636 1.194
+ Force max component initial, final = 222.162 0.376608
+ Final line search alpha, max atom move = 2.92234e-06 1.10058e-06
+ Iterations, force evaluations = 188 401
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0087585 | 0.011606 | 0.014545 | 2.6 | 44.69
+Neigh | 0.00098324 | 0.0012714 | 0.0015543 | 0.8 | 4.90
+Comm | 0.0028691 | 0.006242 | 0.0094991 | 4.1 | 24.04
+Output | 0.00028014 | 0.00029546 | 0.00033355 | 0.1 | 1.14
+Modify | 0.00066638 | 0.00077331 | 0.00089598 | 0.4 | 2.98
+Other | | 0.005781 | | | 22.26
+
+Nlocal: 105 ave 125 max 84 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost: 94.25 ave 104 max 84 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs: 895.75 ave 1159 max 648 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 3583
+Ave neighs/atom = 8.53095
+Neighbor list builds = 38
+Dangerous builds = 0
+
+fix 4 all indent ${k1} sphere 10 11.0 0 6.0
+fix 4 all indent 882.849286914813 sphere 10 11.0 0 6.0
+fix_modify 4 energy yes
+minimize 1.0e-6 1.0e-6 1000 1000
+WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
+Memory usage per processor = 3.60141 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 605 0 -3.1149612 0 -2.7562264 0.88153856 516.19694
+ 610 0 -3.0480145 0 -3.0046036 1.5377628 516.18952
+ 620 0 -3.0581364 0 -3.0393996 1.5790644 516.23694
+ 630 0 -3.058957 0 -3.0461523 1.6279637 515.82575
+ 640 0 -3.0608654 0 -3.0476936 1.631809 515.82575
+ 650 0 -3.059954 0 -3.0488507 1.7016953 514.58992
+ 660 0 -3.0601043 0 -3.0495387 1.7749452 513.2301
+ 670 0 -3.0600329 0 -3.0503272 1.8525614 512.87295
+ 680 0 -3.0618342 0 -3.0532875 1.9461671 512.7735
+ 690 0 -3.0681709 0 -3.0588644 1.8339583 513.83989
+ 700 0 -3.0723671 0 -3.0624663 1.7080165 515.99424
+ 710 0 -3.0738836 0 -3.0635305 1.6674853 516.40455
+ 720 0 -3.0744809 0 -3.0640016 1.6430059 516.40455
+ 729 0 -3.074692 0 -3.0641622 1.6351234 517.12194
+Loop time of 0.0175288 on 4 procs for 124 steps with 420 atoms
+
+99.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+Minimization stats:
+ Stopping criterion = linesearch alpha is zero
+ Energy initial, next-to-last, final =
+ -2.75622643697 -3.06416218566 -3.06416218566
+ Force two-norm initial, final = 387.971 1.75423
+ Force max component initial, final = 226.888 0.425447
+ Final line search alpha, max atom move = 9.47831e-07 4.03252e-07
+ Iterations, force evaluations = 124 275
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0053589 | 0.0078858 | 0.010479 | 2.7 | 44.99
+Neigh | 0.00037146 | 0.00052333 | 0.00067759 | 0.6 | 2.99
+Comm | 0.0017581 | 0.0046017 | 0.0073204 | 3.9 | 26.25
+Output | 0.00017619 | 0.00018531 | 0.00021076 | 0.1 | 1.06
+Modify | 0.00044012 | 0.00054049 | 0.00064754 | 0.4 | 3.08
+Other | | 0.003792 | | | 21.63
+
+Nlocal: 105 ave 131 max 78 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost: 97.25 ave 110 max 84 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs: 900.25 ave 1197 max 607 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 3601
+Ave neighs/atom = 8.57381
+Neighbor list builds = 16
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/meam/log.15Feb16.meam.icc.1 b/examples/meam/log.15Feb16.meam.icc.1
new file mode 100644
index 0000000000000000000000000000000000000000..0012964eb59f2b211a4c383564728252a22c340f
--- /dev/null
+++ b/examples/meam/log.15Feb16.meam.icc.1
@@ -0,0 +1,84 @@
+LAMMPS (15 Feb 2016)
+# Test of MEAM potential for SiC system
+
+units metal
+boundary p p p
+
+atom_style atomic
+
+read_data data.meam
+ orthogonal box = (-6 -6 -6) to (5.97232 5.97232 5.97232)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 128 atoms
+
+pair_style meam
+pair_coeff * * library.meam Si C SiC.meam Si C
+Reading potential file library.meam with DATE: 2012-06-29
+Reading potential file SiC.meam with DATE: 2007-06-11
+
+neighbor 0.3 bin
+neigh_modify delay 10
+
+fix 1 all nve
+thermo 10
+timestep 0.001
+
+#dump 1 all atom 50 dump.meam
+
+#dump 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 3 element Si C
+
+#dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 3 element Si C
+
+run 100
+Neighbor list info ...
+ 2 neighbor list requests
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 4.3
+ ghost atom cutoff = 4.3
+ binsize = 2.15 -> bins = 6 6 6
+Memory usage per processor = 6.89445 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 0 -636.38121 0 -636.38121 -76571.819
+ 10 1807.8862 -666.21959 0 -636.54126 -150571.49
+ 20 1932.4467 -668.2581 0 -636.53498 -120223.52
+ 30 1951.3652 -668.58139 0 -636.54771 -100508.4
+ 40 2172.5974 -672.22715 0 -636.5617 -110753.34
+ 50 2056.9149 -670.33108 0 -636.56468 -105418.07
+ 60 1947.9564 -668.52788 0 -636.55015 -111413.04
+ 70 1994.7712 -669.28849 0 -636.54225 -109645.76
+ 80 2126.0903 -671.43755 0 -636.53557 -97475.831
+ 90 2065.755 -670.4349 0 -636.52338 -95858.837
+ 100 2051.4553 -670.20799 0 -636.53122 -107068.9
+Loop time of 0.0991108 on 1 procs for 100 steps with 128 atoms
+
+Performance: 87.175 ns/day, 0.275 hours/ns, 1008.971 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.09579 | 0.09579 | 0.09579 | 0.0 | 96.65
+Neigh | 0.0022409 | 0.0022409 | 0.0022409 | 0.0 | 2.26
+Comm | 0.00058365 | 0.00058365 | 0.00058365 | 0.0 | 0.59
+Output | 9.6083e-05 | 9.6083e-05 | 9.6083e-05 | 0.0 | 0.10
+Modify | 0.000283 | 0.000283 | 0.000283 | 0.0 | 0.29
+Other | | 0.0001168 | | | 0.12
+
+Nlocal: 128 ave 128 max 128 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 543 ave 543 max 543 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 1526 ave 1526 max 1526 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs: 3052 ave 3052 max 3052 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 3052
+Ave neighs/atom = 23.8438
+Neighbor list builds = 10
+Dangerous builds = 10
+Total wall time: 0:00:00
diff --git a/examples/meam/log.15Feb16.meam.icc.4 b/examples/meam/log.15Feb16.meam.icc.4
new file mode 100644
index 0000000000000000000000000000000000000000..a01893c9a850f0607ced410236558982eb9c26f2
--- /dev/null
+++ b/examples/meam/log.15Feb16.meam.icc.4
@@ -0,0 +1,84 @@
+LAMMPS (15 Feb 2016)
+# Test of MEAM potential for SiC system
+
+units metal
+boundary p p p
+
+atom_style atomic
+
+read_data data.meam
+ orthogonal box = (-6 -6 -6) to (5.97232 5.97232 5.97232)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 128 atoms
+
+pair_style meam
+pair_coeff * * library.meam Si C SiC.meam Si C
+Reading potential file library.meam with DATE: 2012-06-29
+Reading potential file SiC.meam with DATE: 2007-06-11
+
+neighbor 0.3 bin
+neigh_modify delay 10
+
+fix 1 all nve
+thermo 10
+timestep 0.001
+
+#dump 1 all atom 50 dump.meam
+
+#dump 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 3 element Si C
+
+#dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 3 element Si C
+
+run 100
+Neighbor list info ...
+ 2 neighbor list requests
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 4.3
+ ghost atom cutoff = 4.3
+ binsize = 2.15 -> bins = 6 6 6
+Memory usage per processor = 6.82006 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 0 -636.38121 0 -636.38121 -76571.819
+ 10 1807.8862 -666.21959 0 -636.54126 -150571.49
+ 20 1932.4467 -668.2581 0 -636.53498 -120223.52
+ 30 1951.3652 -668.58139 0 -636.54771 -100508.4
+ 40 2172.5974 -672.22715 0 -636.5617 -110753.34
+ 50 2056.9149 -670.33108 0 -636.56468 -105418.07
+ 60 1947.9564 -668.52788 0 -636.55015 -111413.04
+ 70 1994.7712 -669.28849 0 -636.54225 -109645.76
+ 80 2126.0903 -671.43755 0 -636.53557 -97475.831
+ 90 2065.755 -670.4349 0 -636.52338 -95858.837
+ 100 2051.4553 -670.20799 0 -636.53122 -107068.9
+Loop time of 0.0386363 on 4 procs for 100 steps with 128 atoms
+
+Performance: 223.624 ns/day, 0.107 hours/ns, 2588.242 timesteps/s
+99.0% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.034338 | 0.034685 | 0.0351 | 0.1 | 89.77
+Neigh | 0.00057364 | 0.00061846 | 0.00071192 | 0.2 | 1.60
+Comm | 0.0023026 | 0.0027502 | 0.003161 | 0.6 | 7.12
+Output | 0.00025105 | 0.00029814 | 0.00041199 | 0.4 | 0.77
+Modify | 8.9169e-05 | 0.00010341 | 0.00012875 | 0.1 | 0.27
+Other | | 0.0001808 | | | 0.47
+
+Nlocal: 32 ave 36 max 30 min
+Histogram: 1 2 0 0 0 0 0 0 0 1
+Nghost: 293.75 ave 305 max 285 min
+Histogram: 2 0 0 0 0 0 0 1 0 1
+Neighs: 381.5 ave 413 max 334 min
+Histogram: 1 0 0 0 1 0 0 0 0 2
+FullNghs: 763 ave 866 max 678 min
+Histogram: 1 0 1 0 0 1 0 0 0 1
+
+Total # of neighbors = 3052
+Ave neighs/atom = 23.8438
+Neighbor list builds = 10
+Dangerous builds = 10
+Total wall time: 0:00:00
diff --git a/examples/meam/log.15Feb16.meam.shear.icc.1 b/examples/meam/log.15Feb16.meam.shear.icc.1
new file mode 100644
index 0000000000000000000000000000000000000000..5f7eff330a6b27745e5e37bbcfe1ea2329bbeb35
--- /dev/null
+++ b/examples/meam/log.15Feb16.meam.shear.icc.1
@@ -0,0 +1,196 @@
+LAMMPS (15 Feb 2016)
+# 3d metal shear simulation
+
+units metal
+boundary s s p
+
+atom_style atomic
+lattice fcc 3.52
+Lattice spacing in x,y,z = 3.52 3.52 3.52
+region box block 0 16.0 0 10.0 0 2.828427
+create_box 3 box
+Created orthogonal box = (0 0 0) to (56.32 35.2 9.95606)
+ 1 by 1 by 1 MPI processor grid
+
+lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0
+Lattice spacing in x,y,z = 3.52 4.97803 4.97803
+create_atoms 1 box
+Created 1912 atoms
+
+pair_style meam
+pair_coeff * * library.meam Ni4 Ni.meam Ni4 Ni4 Ni4
+Reading potential file library.meam with DATE: 2012-06-29
+Reading potential file Ni.meam with DATE: 2007-06-11
+
+neighbor 0.3 bin
+neigh_modify delay 5
+
+region lower block INF INF INF 0.9 INF INF
+region upper block INF INF 6.1 INF INF INF
+group lower region lower
+264 atoms in group lower
+group upper region upper
+264 atoms in group upper
+group boundary union lower upper
+528 atoms in group boundary
+group mobile subtract all boundary
+1384 atoms in group mobile
+
+set group lower type 2
+ 264 settings made for type
+set group upper type 3
+ 264 settings made for type
+
+# void
+
+#region void cylinder z 8 5 2.5 INF INF
+#delete_atoms region void
+
+# temp controllers
+
+compute new3d mobile temp
+compute new2d mobile temp/partial 0 1 1
+
+# equilibrate
+
+velocity mobile create 300.0 5812775 temp new3d
+fix 1 all nve
+fix 2 boundary setforce 0.0 0.0 0.0
+
+fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
+fix_modify 3 temp new3d
+
+thermo 25
+thermo_modify temp new3d
+WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:445)
+
+timestep 0.001
+run 100
+Neighbor list info ...
+ 2 neighbor list requests
+ update every 1 steps, delay 5 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 4.3
+ ghost atom cutoff = 4.3
+ binsize = 2.15 -> bins = 27 17 5
+Memory usage per processor = 8.55725 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 300 -8232.7767 0 -8179.1466 1386.6643 19547.02
+ 25 222.78953 -8188.1215 0 -8148.2941 9095.9008 19547.02
+ 50 300 -8149.7654 0 -8096.1353 10633.141 19684.382
+ 75 304.80657 -8163.4557 0 -8108.9665 7045.457 19759.745
+ 100 300 -8173.6884 0 -8120.0584 5952.521 19886.589
+Loop time of 1.81808 on 1 procs for 100 steps with 1912 atoms
+
+Performance: 4.752 ns/day, 5.050 hours/ns, 55.003 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 1.7962 | 1.7962 | 1.7962 | 0.0 | 98.80
+Neigh | 0.014991 | 0.014991 | 0.014991 | 0.0 | 0.82
+Comm | 0.0016303 | 0.0016303 | 0.0016303 | 0.0 | 0.09
+Output | 6.5804e-05 | 6.5804e-05 | 6.5804e-05 | 0.0 | 0.00
+Modify | 0.0041728 | 0.0041728 | 0.0041728 | 0.0 | 0.23
+Other | | 0.001022 | | | 0.06
+
+Nlocal: 1912 ave 1912 max 1912 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1672 ave 1672 max 1672 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 23806 ave 23806 max 23806 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs: 47612 ave 47612 max 47612 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 47612
+Ave neighs/atom = 24.9017
+Neighbor list builds = 5
+Dangerous builds = 0
+
+# shear
+
+velocity upper set 1.0 0 0
+velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes
+
+unfix 3
+fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
+fix_modify 3 temp new2d
+
+#dump 1 all atom 500 dump.meam.shear
+
+#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
+#dump_modify 2 pad 4
+
+#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
+#dump_modify 3 pad 4
+
+thermo 100
+thermo_modify temp new2d
+WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:445)
+
+reset_timestep 0
+run 3000
+Memory usage per processor = 8.73384 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 300.50853 -8173.6884 0 -8137.8874 4992.9811 19894.297
+ 100 292.0799 -8177.7235 0 -8142.9266 2566.6872 19871.516
+ 200 306.71233 -8177.1504 0 -8140.6103 872.78764 20047.2
+ 300 295.7806 -8172.9505 0 -8137.7127 -1053.769 20091.657
+ 400 309.18439 -8169.6374 0 -8132.8028 -1784.5443 20122.178
+ 500 304.51122 -8163.9147 0 -8127.6369 -160.26993 20183.44
+ 600 300 -8158.55 0 -8122.8096 1555.2344 20279.887
+ 700 304.32794 -8149.4746 0 -8113.2185 3700.5984 20430.504
+ 800 304.79621 -8138.8368 0 -8102.5249 3721.6015 20510.74
+ 900 303.87706 -8128.16 0 -8091.9576 4387.1435 20638.992
+ 1000 300 -8113.4908 0 -8077.7503 6186.7018 20755.029
+ 1100 306.13486 -8097.1731 0 -8060.7018 8904.6621 20879.616
+ 1200 309.15669 -8081.8589 0 -8045.0276 10523.683 20996.875
+ 1300 304.48415 -8064.5597 0 -8028.2851 10063.03 21126.348
+ 1400 300 -8046.7607 0 -8011.0203 10972.459 21238.721
+ 1500 300 -8041.3546 0 -8005.6142 11939.555 21374.301
+ 1600 309.60207 -8035.2265 0 -7998.3422 11340.176 21530.099
+ 1700 300 -8029.1685 0 -7993.4281 11298.745 21635.488
+ 1800 300 -8034.2271 0 -7998.4867 9629.3065 21738.292
+ 1900 307.84886 -8037.1066 0 -8000.4311 6166.9669 21857.993
+ 2000 307.82172 -8029.9182 0 -7993.246 3178.6607 22013.016
+ 2100 300 -8032.5982 0 -7996.8578 1354.4696 22107.168
+ 2200 300 -8040.9505 0 -8005.2101 1872.6686 22231.755
+ 2300 300 -8044.4439 0 -8008.7035 3214.7865 22355.121
+ 2400 304.60017 -8038.5216 0 -8002.2331 5092.8026 22477.266
+ 2500 308.48504 -8034.0394 0 -7997.2881 7280.4765 22596.967
+ 2600 308.46083 -8037.9984 0 -8001.25 9860.0578 22717.89
+ 2700 305.72597 -8038.4481 0 -8002.0255 10620.389 22837.592
+ 2800 308.33801 -8043.0579 0 -8006.3241 8184.9538 22957.293
+ 2900 300 -8042.671 0 -8006.9306 6691.6548 23085.545
+ 3000 305.66039 -8041.7651 0 -8005.3503 3816.3815 23204.025
+Loop time of 57.0164 on 1 procs for 3000 steps with 1912 atoms
+
+Performance: 4.546 ns/day, 5.279 hours/ns, 52.616 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 56.168 | 56.168 | 56.168 | 0.0 | 98.51
+Neigh | 0.64021 | 0.64021 | 0.64021 | 0.0 | 1.12
+Comm | 0.051842 | 0.051842 | 0.051842 | 0.0 | 0.09
+Output | 0.00062251 | 0.00062251 | 0.00062251 | 0.0 | 0.00
+Modify | 0.1245 | 0.1245 | 0.1245 | 0.0 | 0.22
+Other | | 0.03095 | | | 0.05
+
+Nlocal: 1912 ave 1912 max 1912 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1662 ave 1662 max 1662 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 23535 ave 23535 max 23535 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs: 47070 ave 47070 max 47070 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 47070
+Ave neighs/atom = 24.6182
+Neighbor list builds = 223
+Dangerous builds = 0
+Total wall time: 0:00:58
diff --git a/examples/meam/log.15Feb16.meam.shear.icc.4 b/examples/meam/log.15Feb16.meam.shear.icc.4
new file mode 100644
index 0000000000000000000000000000000000000000..4fca6eaf5d3fb10b4948b72402031c0dc7c279d7
--- /dev/null
+++ b/examples/meam/log.15Feb16.meam.shear.icc.4
@@ -0,0 +1,196 @@
+LAMMPS (15 Feb 2016)
+# 3d metal shear simulation
+
+units metal
+boundary s s p
+
+atom_style atomic
+lattice fcc 3.52
+Lattice spacing in x,y,z = 3.52 3.52 3.52
+region box block 0 16.0 0 10.0 0 2.828427
+create_box 3 box
+Created orthogonal box = (0 0 0) to (56.32 35.2 9.95606)
+ 2 by 2 by 1 MPI processor grid
+
+lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0
+Lattice spacing in x,y,z = 3.52 4.97803 4.97803
+create_atoms 1 box
+Created 1912 atoms
+
+pair_style meam
+pair_coeff * * library.meam Ni4 Ni.meam Ni4 Ni4 Ni4
+Reading potential file library.meam with DATE: 2012-06-29
+Reading potential file Ni.meam with DATE: 2007-06-11
+
+neighbor 0.3 bin
+neigh_modify delay 5
+
+region lower block INF INF INF 0.9 INF INF
+region upper block INF INF 6.1 INF INF INF
+group lower region lower
+264 atoms in group lower
+group upper region upper
+264 atoms in group upper
+group boundary union lower upper
+528 atoms in group boundary
+group mobile subtract all boundary
+1384 atoms in group mobile
+
+set group lower type 2
+ 264 settings made for type
+set group upper type 3
+ 264 settings made for type
+
+# void
+
+#region void cylinder z 8 5 2.5 INF INF
+#delete_atoms region void
+
+# temp controllers
+
+compute new3d mobile temp
+compute new2d mobile temp/partial 0 1 1
+
+# equilibrate
+
+velocity mobile create 300.0 5812775 temp new3d
+fix 1 all nve
+fix 2 boundary setforce 0.0 0.0 0.0
+
+fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
+fix_modify 3 temp new3d
+
+thermo 25
+thermo_modify temp new3d
+WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:445)
+
+timestep 0.001
+run 100
+Neighbor list info ...
+ 2 neighbor list requests
+ update every 1 steps, delay 5 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 4.3
+ ghost atom cutoff = 4.3
+ binsize = 2.15 -> bins = 27 17 5
+Memory usage per processor = 7.74146 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 300 -8232.7767 0 -8179.1466 1386.6643 19547.02
+ 25 221.59546 -8187.6813 0 -8148.0673 9100.4509 19547.02
+ 50 300 -8150.0685 0 -8096.4384 10317.407 19685.743
+ 75 307.76021 -8164.6669 0 -8109.6496 6289.7138 19757.814
+ 100 300 -8176.5141 0 -8122.884 4162.2559 19873.327
+Loop time of 0.491613 on 4 procs for 100 steps with 1912 atoms
+
+Performance: 17.575 ns/day, 1.366 hours/ns, 203.412 timesteps/s
+99.9% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.4688 | 0.47596 | 0.48111 | 0.7 | 96.82
+Neigh | 0.003762 | 0.003863 | 0.0039828 | 0.2 | 0.79
+Comm | 0.0044096 | 0.0096632 | 0.016901 | 5.3 | 1.97
+Output | 0.00011063 | 0.0001418 | 0.00019789 | 0.3 | 0.03
+Modify | 0.001152 | 0.0011944 | 0.0012844 | 0.2 | 0.24
+Other | | 0.0007868 | | | 0.16
+
+Nlocal: 478 ave 492 max 465 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+Nghost: 809 ave 822 max 795 min
+Histogram: 1 1 0 0 0 0 0 0 0 2
+Neighs: 5916 ave 6133 max 5658 min
+Histogram: 1 0 0 1 0 0 0 0 1 1
+FullNghs: 11832 ave 12277 max 11299 min
+Histogram: 1 0 0 1 0 0 0 0 1 1
+
+Total # of neighbors = 47328
+Ave neighs/atom = 24.7531
+Neighbor list builds = 5
+Dangerous builds = 0
+
+# shear
+
+velocity upper set 1.0 0 0
+velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes
+
+unfix 3
+fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
+fix_modify 3 temp new2d
+
+#dump 1 all atom 500 dump.meam.shear
+
+#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
+#dump_modify 2 pad 4
+
+#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
+#dump_modify 3 pad 4
+
+thermo 100
+thermo_modify temp new2d
+WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:445)
+
+reset_timestep 0
+run 3000
+Memory usage per processor = 7.78572 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 295.42794 -8176.5141 0 -8141.3183 3169.3113 19886.93
+ 100 292.02876 -8176.5475 0 -8141.7567 -826.45881 19918.758
+ 200 306.10676 -8176.7837 0 -8140.3158 -1371.1065 19948.794
+ 300 300 -8172.6378 0 -8136.8974 -1736.2602 20086.712
+ 400 306.48529 -8168.4581 0 -8131.9451 -957.8783 20111.985
+ 500 309.89005 -8166.3097 0 -8129.391 -1024.7828 20200.517
+ 600 302.35862 -8157.8008 0 -8121.7794 540.69714 20316.092
+ 700 292.46062 -8149.9463 0 -8115.1041 1709.248 20448.424
+ 800 306.03297 -8139.326 0 -8102.8669 4197.3195 20522.955
+ 900 302.01714 -8127.2712 0 -8091.2905 6337.0018 20634.106
+ 1000 300 -8112.4155 0 -8076.675 7383.2425 20759.915
+ 1100 303.06207 -8097.0321 0 -8060.9268 7921.3464 20879.616
+ 1200 300.99295 -8079.4118 0 -8043.5531 10534.001 20995.654
+ 1300 300 -8065.6269 0 -8029.8865 10683.83 21125.127
+ 1400 300 -8050.6108 0 -8014.8704 9586.4761 21255.821
+ 1500 300 -8041.9686 0 -8006.2281 9655.7305 21365.751
+ 1600 308.48003 -8031.9004 0 -7995.1497 10878.457 21496.446
+ 1700 300 -8018.8868 0 -7983.1463 11313.287 21610.04
+ 1800 300 -8011.8184 0 -7976.0779 11545.113 21730.963
+ 1900 300 -8008.9215 0 -7973.1811 9196.3325 21861.658
+ 2000 300 -8013.4567 0 -7977.7163 5843.9738 21977.695
+ 2100 300 -8023.8599 0 -7988.1195 1292.526 22107.168
+ 2200 300 -8036.0201 0 -8000.2797 711.97062 22221.984
+ 2300 300 -8041.9948 0 -8006.2544 898.57229 22344.128
+ 2400 300 -8048.658 0 -8012.9175 -389.36413 22478.487
+ 2500 300 -8050.0812 0 -8014.3408 -1981.1849 22592.082
+ 2600 307.46028 -8046.847 0 -8010.2178 -2034.1541 22713.005
+ 2700 293.56734 -8041.2081 0 -8006.2341 -2496.4019 22837.592
+ 2800 295.42272 -8035.3079 0 -8000.1128 -1331.5373 22953.629
+ 2900 300 -8033.3512 0 -7997.6107 -2171.4081 23089.209
+ 3000 300 -8029.6279 0 -7993.8875 -672.58255 23197.918
+Loop time of 15.7189 on 4 procs for 3000 steps with 1912 atoms
+
+Performance: 16.490 ns/day, 1.455 hours/ns, 190.853 timesteps/s
+99.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 15.034 | 15.188 | 15.303 | 2.8 | 96.62
+Neigh | 0.16167 | 0.16592 | 0.17044 | 0.8 | 1.06
+Comm | 0.19007 | 0.30646 | 0.46393 | 20.5 | 1.95
+Output | 0.00079918 | 0.00091255 | 0.0012419 | 0.6 | 0.01
+Modify | 0.033848 | 0.035817 | 0.037596 | 0.8 | 0.23
+Other | | 0.02219 | | | 0.14
+
+Nlocal: 478 ave 515 max 444 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+Nghost: 786.25 ave 835 max 748 min
+Histogram: 2 0 0 0 0 0 0 1 0 1
+Neighs: 5779.5 ave 6212 max 5416 min
+Histogram: 1 0 1 0 0 1 0 0 0 1
+FullNghs: 11559 ave 12371 max 10859 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+
+Total # of neighbors = 46236
+Ave neighs/atom = 24.182
+Neighbor list builds = 221
+Dangerous builds = 0
+Total wall time: 0:00:16
diff --git a/examples/melt/log.15Feb16.melt.g++.1 b/examples/melt/log.15Feb16.melt.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..cb40c5451ec385456ad16457642430cb3ab697cb
--- /dev/null
+++ b/examples/melt/log.15Feb16.melt.g++.1
@@ -0,0 +1,78 @@
+LAMMPS (15 Feb 2016)
+# 3d Lennard-Jones melt
+
+units lj
+atom_style atomic
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 10 0 10 0 10
+create_box 1 box
+Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 4000 atoms
+mass 1 1.0
+
+velocity all create 3.0 87287
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+
+neighbor 0.3 bin
+neigh_modify every 20 delay 0 check no
+
+fix 1 all nve
+
+#dump id all atom 50 dump.melt
+
+#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 3
+
+#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 3
+
+thermo 50
+run 250
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 20 steps, delay 0 steps, check no
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4 -> bins = 12 12 12
+Memory usage per processor = 2.19271 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 3 -6.7733681 0 -2.2744931 -3.7033504
+ 50 1.6758903 -4.7955425 0 -2.2823355 5.670064
+ 100 1.6458363 -4.7492704 0 -2.2811332 5.8691042
+ 150 1.6324555 -4.7286791 0 -2.280608 5.9589514
+ 200 1.6630725 -4.7750988 0 -2.2811136 5.7364886
+ 250 1.6275257 -4.7224992 0 -2.281821 5.9567365
+Loop time of 0.739 on 1 procs for 250 steps with 4000 atoms
+
+Performance: 146143.468 tau/day, 338.295 timesteps/s
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.62778 | 0.62778 | 0.62778 | 0.0 | 84.95
+Neigh | 0.083963 | 0.083963 | 0.083963 | 0.0 | 11.36
+Comm | 0.01149 | 0.01149 | 0.01149 | 0.0 | 1.55
+Output | 0.00010991 | 0.00010991 | 0.00010991 | 0.0 | 0.01
+Modify | 0.01251 | 0.01251 | 0.01251 | 0.0 | 1.69
+Other | | 0.003146 | | | 0.43
+
+Nlocal: 4000 ave 4000 max 4000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 5499 ave 5499 max 5499 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 151513 ave 151513 max 151513 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 151513
+Ave neighs/atom = 37.8783
+Neighbor list builds = 12
+Dangerous builds not checked
+Total wall time: 0:00:00
diff --git a/examples/melt/log.15Feb16.melt.g++.4 b/examples/melt/log.15Feb16.melt.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..24e6cfcdc9e563bcbeb232144d2748f8e064715c
--- /dev/null
+++ b/examples/melt/log.15Feb16.melt.g++.4
@@ -0,0 +1,78 @@
+LAMMPS (15 Feb 2016)
+# 3d Lennard-Jones melt
+
+units lj
+atom_style atomic
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 10 0 10 0 10
+create_box 1 box
+Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
+ 1 by 2 by 2 MPI processor grid
+create_atoms 1 box
+Created 4000 atoms
+mass 1 1.0
+
+velocity all create 3.0 87287
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+
+neighbor 0.3 bin
+neigh_modify every 20 delay 0 check no
+
+fix 1 all nve
+
+#dump id all atom 50 dump.melt
+
+#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 3
+
+#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 3
+
+thermo 50
+run 250
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 20 steps, delay 0 steps, check no
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4 -> bins = 12 12 12
+Memory usage per processor = 2.10344 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 3 -6.7733681 0 -2.2744931 -3.7033504
+ 50 1.6754119 -4.7947589 0 -2.2822693 5.6615925
+ 100 1.6503357 -4.756014 0 -2.2811293 5.8050524
+ 150 1.6596605 -4.7699432 0 -2.2810749 5.7830138
+ 200 1.6371874 -4.7365462 0 -2.2813789 5.9246674
+ 250 1.6323462 -4.7292021 0 -2.2812949 5.9762238
+Loop time of 0.214556 on 4 procs for 250 steps with 4000 atoms
+
+Performance: 503365.139 tau/day, 1165.197 timesteps/s
+98.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.16133 | 0.16562 | 0.1711 | 1.0 | 77.19
+Neigh | 0.021791 | 0.022137 | 0.022399 | 0.2 | 10.32
+Comm | 0.016056 | 0.022041 | 0.026695 | 2.9 | 10.27
+Output | 0.00012183 | 0.0001328 | 0.00014186 | 0.1 | 0.06
+Modify | 0.0032513 | 0.0033011 | 0.0033648 | 0.1 | 1.54
+Other | | 0.001321 | | | 0.62
+
+Nlocal: 1000 ave 1010 max 982 min
+Histogram: 1 0 0 0 0 0 1 0 0 2
+Nghost: 2703.75 ave 2713 max 2689 min
+Histogram: 1 0 0 0 0 0 0 2 0 1
+Neighs: 37915.5 ave 39239 max 36193 min
+Histogram: 1 0 0 0 0 1 1 0 0 1
+
+Total # of neighbors = 151662
+Ave neighs/atom = 37.9155
+Neighbor list builds = 12
+Dangerous builds not checked
+Total wall time: 0:00:00
diff --git a/examples/micelle/log.15Feb16.micelle.g++.1 b/examples/micelle/log.15Feb16.micelle.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..72a7853257f72f1cb4d3ab3f3724f3c0986349c9
--- /dev/null
+++ b/examples/micelle/log.15Feb16.micelle.g++.1
@@ -0,0 +1,244 @@
+LAMMPS (15 Feb 2016)
+# 2d micelle simulation
+
+dimension 2
+
+neighbor 0.3 bin
+neigh_modify delay 5
+
+atom_style bond
+
+# Soft potential push-off
+
+read_data data.micelle
+ orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 1200 atoms
+ scanning bonds ...
+ 1 = max bonds/atom
+ reading bonds ...
+ 300 bonds
+ 2 = max # of 1-2 neighbors
+ 1 = max # of 1-3 neighbors
+ 1 = max # of 1-4 neighbors
+ 2 = max # of special neighbors
+special_bonds fene
+ 2 = max # of 1-2 neighbors
+ 2 = max # of special neighbors
+
+pair_style soft 1.12246
+pair_coeff * * 0.0 1.12246
+
+bond_style harmonic
+bond_coeff 1 50.0 0.75
+
+velocity all create 0.45 2349852
+
+variable prefactor equal ramp(1.0,20.0)
+
+fix 1 all nve
+fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
+fix 3 all adapt 1 pair soft a * * v_prefactor
+fix 4 all enforce2d
+
+thermo 50
+run 1000
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 5 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 1.42246
+ ghost atom cutoff = 1.42246
+ binsize = 0.71123 -> bins = 51 51 1
+Memory usage per processor = 2.98958 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
+ 50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852
+ 100 0.45 0.73046745 0.054836584 1.234929 2.3196516
+ 150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416
+ 200 0.45 0.78481891 0.076931503 1.3113754 3.0412388
+ 250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024
+ 300 0.45 0.76820218 0.066727591 1.2845548 3.7861054
+ 350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621
+ 400 0.45 0.68527759 0.090724527 1.2256271 4.4725214
+ 450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211
+ 500 0.45 0.64883009 0.078376672 1.1768318 4.7919294
+ 550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705
+ 600 0.45 0.58193041 0.088386617 1.119942 5.131481
+ 650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294
+ 700 0.45 0.50856787 0.088471208 1.0466641 5.2550165
+ 750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763
+ 800 0.45 0.49926696 0.085958476 1.0348504 5.4665914
+ 850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932
+ 900 0.45 0.47785593 0.10150857 1.0289895 5.7765975
+ 950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245
+ 1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568
+Loop time of 0.188732 on 1 procs for 1000 steps with 1200 atoms
+
+Performance: 2288961.113 tau/day, 5298.521 timesteps/s
+100.1% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.13192 | 0.13192 | 0.13192 | 0.0 | 69.90
+Bond | 0.0065749 | 0.0065749 | 0.0065749 | 0.0 | 3.48
+Neigh | 0.021622 | 0.021622 | 0.021622 | 0.0 | 11.46
+Comm | 0.003341 | 0.003341 | 0.003341 | 0.0 | 1.77
+Output | 0.00019431 | 0.00019431 | 0.00019431 | 0.0 | 0.10
+Modify | 0.020563 | 0.020563 | 0.020563 | 0.0 | 10.90
+Other | | 0.004518 | | | 2.39
+
+Nlocal: 1200 ave 1200 max 1200 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 195 ave 195 max 195 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 3136 ave 3136 max 3136 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 3136
+Ave neighs/atom = 2.61333
+Ave special neighs/atom = 0.5
+Neighbor list builds = 92
+Dangerous builds = 0
+
+unfix 3
+
+# Main run
+
+pair_style lj/cut 2.5
+
+# solvent/head - full-size and long-range
+
+pair_coeff 1 1 1.0 1.0 2.5
+pair_coeff 2 2 1.0 1.0 2.5
+pair_coeff 1 2 1.0 1.0 2.5
+
+# tail/tail - size-averaged and long-range
+
+pair_coeff 3 3 1.0 0.75 2.5
+pair_coeff 4 4 1.0 0.50 2.5
+pair_coeff 3 4 1.0 0.67 2.5
+
+# solvent/tail - full-size and repulsive
+
+pair_coeff 1 3 1.0 1.0 1.12246
+pair_coeff 1 4 1.0 1.0 1.12246
+
+# head/tail - size-averaged and repulsive
+
+pair_coeff 2 3 1.0 0.88 1.12246
+pair_coeff 2 4 1.0 0.75 1.12246
+
+thermo 1000
+
+#dump 1 all atom 2000 dump.micelle
+
+#dump 2 all image 2000 image.*.jpg type type zoom 1.6
+#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
+
+#dump 3 all movie 2000 movie.mpg type type zoom 1.6
+#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
+
+reset_timestep 0
+run 60000
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 5 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4 -> bins = 26 26 1
+Memory usage per processor = 2.98958 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686
+ 1000 0.45 -1.9727655 0.058608718 -1.4645318 1.9982299
+ 2000 0.4661092 -1.9963233 0.067084121 -1.4635184 1.5676107
+ 3000 0.44946688 -2.0126501 0.070702998 -1.4928548 1.5636132
+ 4000 0.45269674 -1.9944702 0.05825464 -1.4838961 1.6015127
+ 5000 0.46281924 -2.0302807 0.058318349 -1.5095288 1.3929421
+ 6000 0.45409991 -2.0339156 0.061724414 -1.5184697 1.1978692
+ 7000 0.44058968 -2.0436374 0.060141133 -1.5432738 1.1877802
+ 8000 0.4429781 -2.0508103 0.061300632 -1.5469007 1.1825472
+ 9000 0.44909024 -2.0620769 0.063430248 -1.5499306 1.1841529
+ 10000 0.44709728 -2.0337047 0.059176633 -1.5278033 1.1906481
+ 11000 0.46222813 -2.0666276 0.053626157 -1.5511585 0.99322264
+ 12000 0.45722371 -2.0527602 0.062728903 -1.5331886 1.1135813
+ 13000 0.44844353 -2.0672473 0.07057216 -1.5486053 0.9416127
+ 14000 0.44211202 -2.0804052 0.056164487 -1.5824971 0.99700319
+ 15000 0.45659943 -2.0711771 0.059428792 -1.5555294 1.1123211
+ 16000 0.45113626 -2.0895625 0.057848795 -1.5809534 1.0015991
+ 17000 0.44423013 -2.0840859 0.06718595 -1.57304 0.92034012
+ 18000 0.45279338 -2.0644167 0.058541719 -1.5534589 1.1560585
+ 19000 0.44673847 -2.0729637 0.061474462 -1.565123 0.99627228
+ 20000 0.44428193 -2.0937135 0.066588799 -1.583213 0.86154418
+ 21000 0.45902797 -2.0821041 0.057286828 -1.5661718 0.76853595
+ 22000 0.45733559 -2.0962718 0.064103239 -1.5752141 0.90967955
+ 23000 0.44617227 -2.070896 0.061562573 -1.5635329 0.92864876
+ 24000 0.45569898 -2.0843503 0.061015469 -1.5680156 0.90170833
+ 25000 0.45952666 -2.0892064 0.058901296 -1.5711614 0.9123274
+ 26000 0.44773853 -2.0896169 0.065994021 -1.5762575 0.8887526
+ 27000 0.43541542 -2.0893237 0.060387783 -1.5938834 0.97604018
+ 28000 0.44025187 -2.0937721 0.066174764 -1.5877124 0.98394478
+ 29000 0.44695847 -2.0966733 0.064980967 -1.5851064 0.78278706
+ 30000 0.44848319 -2.1017012 0.053308469 -1.6002833 0.85185298
+ 31000 0.45215181 -2.0927324 0.057875178 -1.5830822 0.77068692
+ 32000 0.44586981 -2.0962193 0.056970051 -1.593751 0.85672441
+ 33000 0.43591379 -2.1069871 0.064934652 -1.6065019 0.87081371
+ 34000 0.44153683 -2.0967535 0.061537811 -1.5940468 0.75497708
+ 35000 0.45482946 -2.1045277 0.060250612 -1.5898266 0.80290163
+ 36000 0.45 -2.1154856 0.052206018 -1.6136546 0.67520748
+ 37000 0.44973679 -2.1076496 0.067371347 -1.5909163 0.83319072
+ 38000 0.45549751 -2.1044983 0.061863351 -1.587517 0.6786145
+ 39000 0.43927254 -2.1159446 0.057855173 -1.6191829 0.66483475
+ 40000 0.43711657 -2.0941837 0.063039594 -1.5943918 0.90680301
+ 41000 0.43992749 -2.0931285 0.063772204 -1.5897954 0.7538478
+ 42000 0.44374588 -2.1029745 0.061963499 -1.5976349 0.74793466
+ 43000 0.45 -2.0916744 0.055058096 -1.5869913 0.86069235
+ 44000 0.45381626 -2.0984483 0.059995477 -1.5850147 0.74948091
+ 45000 0.44547409 -2.1217483 0.058753101 -1.6178924 0.57348898
+ 46000 0.43283033 -2.1054695 0.059343099 -1.6136567 0.77490901
+ 47000 0.44310217 -2.1215687 0.066613901 -1.6122219 0.73014542
+ 48000 0.44611257 -2.118313 0.05944897 -1.6131232 0.59077782
+ 49000 0.44114725 -2.0911126 0.065639368 -1.5846936 0.78309201
+ 50000 0.44572124 -2.0892024 0.065540869 -1.5783117 0.87647821
+ 51000 0.4460699 -2.1142274 0.061090043 -1.6074391 0.61721581
+ 52000 0.44799203 -2.1122931 0.056821256 -1.6078531 0.70734576
+ 53000 0.44819437 -2.1098838 0.058117987 -1.6039449 0.71349136
+ 54000 0.45 -2.1384776 0.051012047 -1.6378405 0.4810217
+ 55000 0.43931842 -2.1053055 0.061275315 -1.6050778 0.58268948
+ 56000 0.44126963 -2.1133637 0.057474037 -1.6149877 0.68063945
+ 57000 0.45823746 -2.1205329 0.065224217 -1.5974531 0.73788456
+ 58000 0.437031 -2.0998724 0.051717885 -1.6114877 0.86071379
+ 59000 0.45070454 -2.1115874 0.053721754 -1.6075367 0.62358834
+ 60000 0.44181643 -2.1243164 0.060489492 -1.6223786 0.6992428
+Loop time of 13.7021 on 1 procs for 60000 steps with 1200 atoms
+
+Performance: 1891674.479 tau/day, 4378.876 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 9.5222 | 9.5222 | 9.5222 | 0.0 | 69.49
+Bond | 0.39977 | 0.39977 | 0.39977 | 0.0 | 2.92
+Neigh | 2.1261 | 2.1261 | 2.1261 | 0.0 | 15.52
+Comm | 0.26046 | 0.26046 | 0.26046 | 0.0 | 1.90
+Output | 0.00084543 | 0.00084543 | 0.00084543 | 0.0 | 0.01
+Modify | 1.1202 | 1.1202 | 1.1202 | 0.0 | 8.18
+Other | | 0.2726 | | | 1.99
+
+Nlocal: 1200 ave 1200 max 1200 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 417 ave 417 max 417 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 9495 ave 9495 max 9495 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 9495
+Ave neighs/atom = 7.9125
+Ave special neighs/atom = 0.5
+Neighbor list builds = 4885
+Dangerous builds = 0
+Total wall time: 0:00:13
diff --git a/examples/micelle/log.15Feb16.micelle.g++.4 b/examples/micelle/log.15Feb16.micelle.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..8fb710bec9920362ced7502e3657834ac73075fd
--- /dev/null
+++ b/examples/micelle/log.15Feb16.micelle.g++.4
@@ -0,0 +1,244 @@
+LAMMPS (15 Feb 2016)
+# 2d micelle simulation
+
+dimension 2
+
+neighbor 0.3 bin
+neigh_modify delay 5
+
+atom_style bond
+
+# Soft potential push-off
+
+read_data data.micelle
+ orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
+ 2 by 2 by 1 MPI processor grid
+ reading atoms ...
+ 1200 atoms
+ scanning bonds ...
+ 1 = max bonds/atom
+ reading bonds ...
+ 300 bonds
+ 2 = max # of 1-2 neighbors
+ 1 = max # of 1-3 neighbors
+ 1 = max # of 1-4 neighbors
+ 2 = max # of special neighbors
+special_bonds fene
+ 2 = max # of 1-2 neighbors
+ 2 = max # of special neighbors
+
+pair_style soft 1.12246
+pair_coeff * * 0.0 1.12246
+
+bond_style harmonic
+bond_coeff 1 50.0 0.75
+
+velocity all create 0.45 2349852
+
+variable prefactor equal ramp(1.0,20.0)
+
+fix 1 all nve
+fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
+fix 3 all adapt 1 pair soft a * * v_prefactor
+fix 4 all enforce2d
+
+thermo 50
+run 1000
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 5 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 1.42246
+ ghost atom cutoff = 1.42246
+ binsize = 0.71123 -> bins = 51 51 1
+Memory usage per processor = 3.55365 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
+ 50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852
+ 100 0.45 0.73046745 0.054836584 1.234929 2.3196516
+ 150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416
+ 200 0.45 0.78481891 0.076931503 1.3113754 3.0412388
+ 250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024
+ 300 0.45 0.76820218 0.066727591 1.2845548 3.7861054
+ 350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621
+ 400 0.45 0.68527759 0.090724527 1.2256271 4.4725214
+ 450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211
+ 500 0.45 0.64883009 0.078376672 1.1768318 4.7919294
+ 550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705
+ 600 0.45 0.58193041 0.088386617 1.119942 5.131481
+ 650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294
+ 700 0.45 0.50856787 0.088471208 1.0466641 5.2550165
+ 750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763
+ 800 0.45 0.49926696 0.085958476 1.0348504 5.4665914
+ 850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932
+ 900 0.45 0.47785593 0.10150857 1.0289895 5.7765975
+ 950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245
+ 1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568
+Loop time of 0.0662177 on 4 procs for 1000 steps with 1200 atoms
+
+Performance: 6523939.295 tau/day, 15101.711 timesteps/s
+98.9% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.03338 | 0.034415 | 0.035278 | 0.4 | 51.97
+Bond | 0.0016546 | 0.0017538 | 0.001863 | 0.2 | 2.65
+Neigh | 0.0062997 | 0.0064718 | 0.0066252 | 0.2 | 9.77
+Comm | 0.011654 | 0.012875 | 0.013857 | 0.8 | 19.44
+Output | 0.00039363 | 0.00041753 | 0.00046754 | 0.1 | 0.63
+Modify | 0.0067155 | 0.0069018 | 0.0072353 | 0.3 | 10.42
+Other | | 0.003383 | | | 5.11
+
+Nlocal: 300 ave 305 max 292 min
+Histogram: 1 0 0 0 0 0 1 0 1 1
+Nghost: 100.25 ave 108 max 93 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+Neighs: 784 ave 815 max 739 min
+Histogram: 1 0 0 0 0 0 1 1 0 1
+
+Total # of neighbors = 3136
+Ave neighs/atom = 2.61333
+Ave special neighs/atom = 0.5
+Neighbor list builds = 92
+Dangerous builds = 0
+
+unfix 3
+
+# Main run
+
+pair_style lj/cut 2.5
+
+# solvent/head - full-size and long-range
+
+pair_coeff 1 1 1.0 1.0 2.5
+pair_coeff 2 2 1.0 1.0 2.5
+pair_coeff 1 2 1.0 1.0 2.5
+
+# tail/tail - size-averaged and long-range
+
+pair_coeff 3 3 1.0 0.75 2.5
+pair_coeff 4 4 1.0 0.50 2.5
+pair_coeff 3 4 1.0 0.67 2.5
+
+# solvent/tail - full-size and repulsive
+
+pair_coeff 1 3 1.0 1.0 1.12246
+pair_coeff 1 4 1.0 1.0 1.12246
+
+# head/tail - size-averaged and repulsive
+
+pair_coeff 2 3 1.0 0.88 1.12246
+pair_coeff 2 4 1.0 0.75 1.12246
+
+thermo 1000
+
+#dump 1 all atom 2000 dump.micelle
+
+#dump 2 all image 2000 image.*.jpg type type zoom 1.6
+#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
+
+#dump 3 all movie 2000 movie.mpg type type zoom 1.6
+#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
+
+reset_timestep 0
+run 60000
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 5 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4 -> bins = 26 26 1
+Memory usage per processor = 3.55365 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686
+ 1000 0.45 -1.9727663 0.058608449 -1.4645328 1.9982389
+ 2000 0.45428051 -1.9704547 0.062434911 -1.4541178 1.7134222
+ 3000 0.46748648 -2.0088544 0.065086237 -1.4766712 1.4648627
+ 4000 0.45608936 -2.032563 0.057148422 -1.5197053 1.3833681
+ 5000 0.46134038 -2.0250107 0.061983009 -1.5020718 1.3378201
+ 6000 0.45254634 -2.0414745 0.071656389 -1.5176489 1.2670697
+ 7000 0.46380932 -2.0463598 0.060057501 -1.5228795 1.1029258
+ 8000 0.46495917 -2.0570216 0.058074076 -1.5343758 1.1187483
+ 9000 0.45771237 -2.0510911 0.061803881 -1.5319563 1.1540073
+ 10000 0.45 -2.0568306 0.06114562 -1.54606 1.128504
+ 11000 0.43977142 -2.0442503 0.061128391 -1.543717 1.2268919
+ 12000 0.4412548 -2.051046 0.065150223 -1.5450087 1.0681597
+ 13000 0.46384147 -2.0657072 0.064678941 -1.5375734 0.99078604
+ 14000 0.43330137 -2.0693058 0.06542588 -1.5709397 1.0252118
+ 15000 0.44825078 -2.078972 0.059800283 -1.5712944 0.76305383
+ 16000 0.45607271 -2.085101 0.058347214 -1.5710611 0.99903698
+ 17000 0.45329523 -2.0865426 0.057674526 -1.5759505 0.90245709
+ 18000 0.46719329 -2.076619 0.062698678 -1.5471164 0.95433376
+ 19000 0.45253889 -2.0741652 0.06154596 -1.5604575 1.0606446
+ 20000 0.43708811 -2.1005493 0.063453064 -1.6003723 0.65980174
+ 21000 0.43630563 -2.0780131 0.05595505 -1.586116 0.86690426
+ 22000 0.44050783 -2.0766368 0.057980992 -1.578515 0.99638367
+ 23000 0.44657992 -2.0731942 0.058890194 -1.5680963 0.92620975
+ 24000 0.45645869 -2.0957688 0.065464986 -1.5742255 0.88631971
+ 25000 0.46007071 -2.0928226 0.058133397 -1.5750019 0.75468418
+ 26000 0.46316546 -2.0945456 0.064110354 -1.5676557 0.84437166
+ 27000 0.44780223 -2.0966995 0.063284428 -1.585986 0.89645525
+ 28000 0.43945645 -2.0909433 0.062357411 -1.5894957 0.92336874
+ 29000 0.44332217 -2.0885003 0.063832997 -1.5817146 0.86508766
+ 30000 0.44865024 -2.0899642 0.057319345 -1.5843685 0.76862889
+ 31000 0.45702135 -2.0941006 0.059669304 -1.5777908 0.76171188
+ 32000 0.46630168 -2.1066612 0.051622888 -1.5891252 0.72214981
+ 33000 0.44966822 -2.1086408 0.061298737 -1.5980486 0.7056562
+ 34000 0.45599464 -2.11216 0.045835595 -1.6107098 0.75827582
+ 35000 0.44021366 -2.1082791 0.066290667 -1.6021416 0.85079438
+ 36000 0.46531913 -2.1228506 0.054779097 -1.6031402 0.60391389
+ 37000 0.44777064 -2.1193684 0.062074675 -1.6098962 0.68654583
+ 38000 0.46608897 -2.1243843 0.052889984 -1.6057938 0.6517974
+ 39000 0.44921432 -2.1050268 0.059790015 -1.5963968 0.74248261
+ 40000 0.44407222 -2.0930539 0.055687841 -1.5936639 0.69821332
+ 41000 0.4377755 -2.0929451 0.056403441 -1.599131 0.90040574
+ 42000 0.46403029 -2.1245032 0.058491534 -1.6023681 0.6984091
+ 43000 0.45456147 -2.0966395 0.055922733 -1.5865341 0.86499812
+ 44000 0.45619203 -2.1150101 0.054818604 -1.6043796 0.71197595
+ 45000 0.44806278 -2.1067617 0.057539822 -1.6015324 0.7644258
+ 46000 0.46326243 -2.1204997 0.060566953 -1.5970563 0.68822898
+ 47000 0.43464277 -2.1257611 0.069053137 -1.6224273 0.60024032
+ 48000 0.46986944 -2.1245871 0.058768355 -1.5963409 0.58191819
+ 49000 0.4428734 -2.1203847 0.059089451 -1.6187909 0.60806508
+ 50000 0.43813854 -2.12123 0.066218857 -1.6172377 0.42860822
+ 51000 0.4514578 -2.1304644 0.057932769 -1.62145 0.62355123
+ 52000 0.44155257 -2.1248047 0.062563155 -1.6210569 0.81276016
+ 53000 0.4467801 -2.1254575 0.056774655 -1.6222751 0.6115287
+ 54000 0.43972332 -2.1036785 0.061427338 -1.6028943 0.75225909
+ 55000 0.44933771 -2.104883 0.058556755 -1.5973629 0.75480805
+ 56000 0.45 -2.1212286 0.057392665 -1.614211 0.56759345
+ 57000 0.43127001 -2.0978236 0.04986292 -1.61705 0.71828346
+ 58000 0.43621486 -2.1097172 0.056706821 -1.617159 0.80497906
+ 59000 0.44446312 -2.1103931 0.055606397 -1.610694 0.79904859
+ 60000 0.43177211 -2.0985468 0.049687241 -1.6174473 0.81094066
+Loop time of 4.44409 on 4 procs for 60000 steps with 1200 atoms
+
+Performance: 5832469.978 tau/day, 13501.088 timesteps/s
+99.5% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 2.3453 | 2.4228 | 2.4713 | 3.0 | 54.52
+Bond | 0.084212 | 0.10413 | 0.11722 | 3.8 | 2.34
+Neigh | 0.61098 | 0.61843 | 0.62485 | 0.7 | 13.92
+Comm | 0.72832 | 0.81507 | 0.94114 | 9.7 | 18.34
+Output | 0.0012789 | 0.0013777 | 0.0016506 | 0.4 | 0.03
+Modify | 0.2745 | 0.28888 | 0.31551 | 3.0 | 6.50
+Other | | 0.1934 | | | 4.35
+
+Nlocal: 300 ave 305 max 293 min
+Histogram: 1 0 0 0 0 1 0 0 1 1
+Nghost: 211 ave 215 max 205 min
+Histogram: 1 0 0 0 0 0 1 0 1 1
+Neighs: 2448.75 ave 2531 max 2414 min
+Histogram: 2 1 0 0 0 0 0 0 0 1
+
+Total # of neighbors = 9795
+Ave neighs/atom = 8.1625
+Ave special neighs/atom = 0.5
+Neighbor list builds = 4880
+Dangerous builds = 0
+Total wall time: 0:00:04
diff --git a/examples/min/log.15Feb16.min.box.g++.1 b/examples/min/log.15Feb16.min.box.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..671ad77b7a6ba65cc22a21c0e94b4d9918c9b70d
--- /dev/null
+++ b/examples/min/log.15Feb16.min.box.g++.1
@@ -0,0 +1,553 @@
+LAMMPS (15 Feb 2016)
+# 2d Lennard-Jones melt and subsequent energy minimization,
+# followed by box relaxation to a target stress state
+#
+units lj
+dimension 2
+atom_style atomic
+
+lattice sq2 0.8442
+Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
+region box block 0 20 0 20 -0.1 0.1
+create_box 1 box
+Created orthogonal box = (0 0 -0.153919) to (30.7838 30.7838 0.153919)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 800 atoms
+mass 1 1.0
+
+velocity all create 5.0 87287 loop geom
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+pair_modify shift yes
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nve
+fix 2 all enforce2d
+
+#dump 1 all atom 500 dump.min
+
+#dump 2 all image 500 image.*.jpg type type # zoom 1.6 adiam 1.5
+#dump_modify 2 pad 4
+
+#dump 3 all movie 500 movie.mpg type type # zoom 1.6 adiam 1.5
+#dump_modify 3 pad 4
+
+thermo 100
+
+run 1000
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4 -> bins = 22 22 1
+Memory usage per processor = 2.47843 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 5 -2.461717 0 2.532033 5.0190509
+ 100 3.2788864 -0.74311698 0 2.5316708 15.912832
+ 200 3.3041082 -0.77000277 0 2.5299752 15.602653
+ 300 3.3840228 -0.84859211 0 2.5312006 15.188203
+ 400 3.3916063 -0.85694601 0 2.5304208 15.383853
+ 500 3.3136052 -0.77935263 0 2.5301106 15.833296
+ 600 3.3888915 -0.85213743 0 2.532518 15.162759
+ 700 3.2123675 -0.67642318 0 2.5319289 16.310565
+ 800 3.3016275 -0.76569171 0 2.5318087 15.639335
+ 900 3.4639203 -0.92788002 0 2.5317104 14.765912
+ 1000 3.3256788 -0.79078181 0 2.5307399 15.599298
+Loop time of 0.200459 on 1 procs for 1000 steps with 800 atoms
+
+Performance: 2155054.114 tau/day, 4988.551 timesteps/s
+99.3% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.12873 | 0.12873 | 0.12873 | 0.0 | 64.22
+Neigh | 0.050699 | 0.050699 | 0.050699 | 0.0 | 25.29
+Comm | 0.0045221 | 0.0045221 | 0.0045221 | 0.0 | 2.26
+Output | 8.5354e-05 | 8.5354e-05 | 8.5354e-05 | 0.0 | 0.04
+Modify | 0.011955 | 0.011955 | 0.011955 | 0.0 | 5.96
+Other | | 0.00447 | | | 2.23
+
+Nlocal: 800 ave 800 max 800 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 317 ave 317 max 317 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 7743 ave 7743 max 7743 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 7743
+Ave neighs/atom = 9.67875
+Neighbor list builds = 203
+Dangerous builds = 0
+
+# perform the box relaxation by progressively
+# adding more degrees of freedom, for smoother
+# convergence
+
+neigh_modify delay 0 every 1 check yes
+
+velocity all create 0.0 1
+thermo 50
+
+# atoms only
+
+minimize 1.0e-6 0.001 1000 10000
+Memory usage per processor = 3.60343 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 1000 0 -0.79078181 0 -0.79078181 12.79527
+ 1050 0 -2.8361415 0 -2.8361415 -1.1950285
+ 1100 0 -2.8661626 0 -2.8661626 -1.1864964
+ 1150 0 -2.8783275 0 -2.8783275 -1.1746571
+ 1200 0 -2.8838202 0 -2.8838202 -1.1647075
+ 1250 0 -2.8956657 0 -2.8956657 -1.1991876
+ 1300 0 -2.9039122 0 -2.9039122 -1.1445553
+ 1350 0 -2.9100776 0 -2.9100776 -1.1036121
+ 1400 0 -2.9131297 0 -2.9131297 -1.0962069
+ 1450 0 -2.9167506 0 -2.9167506 -1.0259809
+ 1475 0 -2.9169436 0 -2.9169436 -1.0125744
+Loop time of 0.239637 on 1 procs for 475 steps with 800 atoms
+
+100.1% CPU use with 1 MPI tasks x no OpenMP threads
+
+Minimization stats:
+ Stopping criterion = energy tolerance
+ Energy initial, next-to-last, final =
+ -0.790781812776 -2.9169407756 -2.91694356781
+ Force two-norm initial, final = 1905.47 0.794548
+ Force max component initial, final = 343.392 0.268404
+ Final line search alpha, max atom move = 0.347566 0.0932881
+ Iterations, force evaluations = 475 940
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.19656 | 0.19656 | 0.19656 | 0.0 | 82.02
+Neigh | 0.021103 | 0.021103 | 0.021103 | 0.0 | 8.81
+Comm | 0.0028365 | 0.0028365 | 0.0028365 | 0.0 | 1.18
+Output | 6.6996e-05 | 6.6996e-05 | 6.6996e-05 | 0.0 | 0.03
+Modify | 0.002048 | 0.002048 | 0.002048 | 0.0 | 0.85
+Other | | 0.01702 | | | 7.10
+
+Nlocal: 800 ave 800 max 800 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 329 ave 329 max 329 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 6957 ave 6957 max 6957 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 6957
+Ave neighs/atom = 8.69625
+Neighbor list builds = 85
+Dangerous builds = 0
+
+# isotropic volume relaxation to hydrostatic target
+
+fix 3 all box/relax iso 1.5 vmax 1.0e-3
+
+variable emin equal pe+f_3/atoms
+thermo_style custom step temp pe pxx pyy pxy f_3 v_emin
+
+# anisotropic volume relaxation to hydrostatic target
+
+minimize 0.0 10.0e0 10000 100000
+Memory usage per processor = 3.60343 Mbytes
+Step Temp PotEng Pxx Pyy Pxy 3 emin
+ 1475 0 -2.9169436 -1.0208231 -1.0043256 0.042048233 0 -2.9169436
+ 1500 0 -2.9112018 1.4420862 1.4721681 0.065929095 -0.087730988 -2.9989327
+ 1550 0 -2.9169778 1.5234769 1.5850923 0.063502312 -0.11432538 -3.0313032
+ 1600 0 -2.924265 1.4545702 1.5281333 0.053590255 -0.12032598 -3.044591
+ 1650 0 -2.9289538 1.4528452 1.5692678 0.038096542 -0.12516914 -3.054123
+ 1699 0 -2.9334511 1.4447667 1.5587557 0.044510608 -0.12731783 -3.060769
+Loop time of 0.112636 on 1 procs for 224 steps with 800 atoms
+
+100.3% CPU use with 1 MPI tasks x no OpenMP threads
+
+Minimization stats:
+ Stopping criterion = force tolerance
+ Energy initial, next-to-last, final =
+ -2.91694356781 -3.06076807543 -3.060768969
+ Force two-norm initial, final = 4762.05 8.66905
+ Force max component initial, final = 4762.05 3.21614
+ Final line search alpha, max atom move = 6.88085e-05 0.000221298
+ Iterations, force evaluations = 224 409
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.090125 | 0.090125 | 0.090125 | 0.0 | 80.01
+Neigh | 0.0039701 | 0.0039701 | 0.0039701 | 0.0 | 3.52
+Comm | 0.0010481 | 0.0010481 | 0.0010481 | 0.0 | 0.93
+Output | 9.6798e-05 | 9.6798e-05 | 9.6798e-05 | 0.0 | 0.09
+Modify | 0.00088024 | 0.00088024 | 0.00088024 | 0.0 | 0.78
+Other | | 0.01652 | | | 14.66
+
+Nlocal: 800 ave 800 max 800 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 338 ave 338 max 338 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 7313 ave 7313 max 7313 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 7313
+Ave neighs/atom = 9.14125
+Neighbor list builds = 16
+Dangerous builds = 0
+
+fix 3 all box/relax aniso 1.5 vmax 1.0e-3
+
+minimize 0.0 10.0 10000 100000
+Memory usage per processor = 3.60343 Mbytes
+Step Temp PotEng Pxx Pyy Pxy 3 emin
+ 1699 0 -2.9334511 1.4447667 1.5587557 0.044510608 0 -2.9334511
+ 1700 0 -2.9335996 1.4982915 1.4969508 0.044657372 9.09619e-05 -2.9335086
+Loop time of 0.000809908 on 1 procs for 1 steps with 800 atoms
+
+123.5% CPU use with 1 MPI tasks x no OpenMP threads
+
+Minimization stats:
+ Stopping criterion = force tolerance
+ Energy initial, next-to-last, final =
+ -2.93345114337 -2.93345114337 -2.93350862414
+ Force two-norm initial, final = 71.3983 8.74381
+ Force max component initial, final = 51.6897 2.68015
+ Final line search alpha, max atom move = 1.93462e-05 5.18508e-05
+ Iterations, force evaluations = 1 2
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.00066304 | 0.00066304 | 0.00066304 | 0.0 | 81.87
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 6.9141e-06 | 6.9141e-06 | 6.9141e-06 | 0.0 | 0.85
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 6.4373e-06 | 6.4373e-06 | 6.4373e-06 | 0.0 | 0.79
+Other | | 0.0001335 | | | 16.49
+
+Nlocal: 800 ave 800 max 800 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 338 ave 338 max 338 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 7301 ave 7301 max 7301 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 7301
+Ave neighs/atom = 9.12625
+Neighbor list builds = 0
+Dangerous builds = 0
+
+# anisotropic volume relaxation to non-hydrostatic target
+
+fix 3 all box/relax x 1.0 y 2.0 vmax 1.0e-3
+
+minimize 0.0 10.0 10000 100000
+Memory usage per processor = 3.60343 Mbytes
+Step Temp PotEng Pxx Pyy Pxy 3 emin
+ 1700 0 -2.9335996 1.4982915 1.4969508 0.044657372 -3.5527137e-17 -2.9335996
+ 1750 0 -2.9306696 0.95043712 1.984164 0.04474671 -0.014282691 -2.9449523
+ 1800 0 -2.9328947 1.0034263 1.9908351 0.043891947 -0.017255878 -2.9501506
+ 1850 0 -2.935585 0.98224846 1.9920507 0.047038767 -0.021070874 -2.9566559
+ 1900 0 -2.9380757 0.96811097 1.9677247 0.068809483 -0.024274947 -2.9623506
+ 1913 0 -2.9391305 0.98238419 1.9782761 0.074400364 -0.025108208 -2.9642387
+Loop time of 0.100323 on 1 procs for 213 steps with 800 atoms
+
+100.7% CPU use with 1 MPI tasks x no OpenMP threads
+
+Minimization stats:
+ Stopping criterion = force tolerance
+ Energy initial, next-to-last, final =
+ -2.93359958604 -2.96406714389 -2.96423867812
+ Force two-norm initial, final = 622.999 9.93502
+ Force max component initial, final = 442.577 5.00802
+ Final line search alpha, max atom move = 0.000369148 0.0018487
+ Iterations, force evaluations = 213 356
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.079344 | 0.079344 | 0.079344 | 0.0 | 79.09
+Neigh | 0.0028028 | 0.0028028 | 0.0028028 | 0.0 | 2.79
+Comm | 0.00087476 | 0.00087476 | 0.00087476 | 0.0 | 0.87
+Output | 0.00012708 | 0.00012708 | 0.00012708 | 0.0 | 0.13
+Modify | 0.00077343 | 0.00077343 | 0.00077343 | 0.0 | 0.77
+Other | | 0.0164 | | | 16.35
+
+Nlocal: 800 ave 800 max 800 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 337 ave 337 max 337 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 7344 ave 7344 max 7344 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 7344
+Ave neighs/atom = 9.18
+Neighbor list builds = 11
+Dangerous builds = 0
+
+minimize 0.0 1.0 10000 100000
+Memory usage per processor = 3.60343 Mbytes
+Step Temp PotEng Pxx Pyy Pxy 3 emin
+ 1913 0 -2.9391305 0.98238419 1.9782761 0.074400364 7.1054274e-17 -2.9391305
+ 1950 0 -2.9397224 0.98880561 2.0105792 0.10042798 -0.0026601558 -2.9423825
+ 2000 0 -2.9426513 0.99541675 1.9727175 0.13793826 -0.0055993834 -2.9482507
+ 2050 0 -2.9422932 1.0135462 2.062652 0.15208716 -0.0090986322 -2.9513919
+ 2100 0 -2.9452654 0.98891373 1.9917349 0.17178076 -0.0088814224 -2.9541468
+ 2150 0 -2.9479511 1.0054525 1.9938996 0.19677305 -0.012189723 -2.9601408
+ 2200 0 -2.9524854 0.92417794 1.9670411 0.21283803 -0.014527245 -2.9670127
+ 2250 0 -2.9546681 0.94388065 1.9485987 0.26294591 -0.016606496 -2.9712746
+ 2300 0 -2.9562108 0.97059342 2.0096507 0.26715603 -0.018777368 -2.9749882
+ 2350 0 -2.9568148 1.0327203 2.0192612 0.28381119 -0.019537293 -2.9763521
+ 2400 0 -2.9587001 1.0106008 1.9969503 0.30603661 -0.019408356 -2.9781085
+ 2450 0 -2.9590843 0.98958837 2.0224183 0.31018833 -0.020232067 -2.9793164
+ 2500 0 -2.9605371 1.0129369 2.0118845 0.31896899 -0.0206348 -2.9811719
+ 2550 0 -2.96203 1.0088756 1.9950565 0.31619508 -0.020741018 -2.982771
+ 2600 0 -2.9640352 1.0260949 1.9708112 0.32681194 -0.020520418 -2.9845557
+ 2650 0 -2.9660094 1.0023933 1.9418952 0.32890865 -0.020061429 -2.9860709
+ 2700 0 -2.9665094 0.99813752 1.9545648 0.33001828 -0.020784521 -2.9872939
+ 2750 0 -2.9670182 1.0109981 1.9548987 0.33172056 -0.021377228 -2.9883954
+ 2800 0 -2.9664869 1.0258673 2.0006802 0.31745442 -0.022943731 -2.9894306
+ 2850 0 -2.9667139 0.97403389 2.0113279 0.30412138 -0.023501638 -2.9902156
+ 2900 0 -2.9680973 0.9828473 1.9525815 0.28059505 -0.023126582 -2.9912239
+ 2950 0 -2.9682294 0.94859438 1.9938632 0.25025064 -0.024655342 -2.9928848
+ 3000 0 -2.969822 0.95834394 2.0063727 0.21932668 -0.025262588 -2.9950845
+ 3050 0 -2.9707839 1.0391399 2.0683958 0.16283029 -0.027043589 -2.9978275
+ 3100 0 -2.9758409 0.95391478 1.9747899 0.15833517 -0.025149181 -3.0009901
+ 3150 0 -2.9768939 0.97373082 2.0001007 0.15841842 -0.025677624 -3.0025715
+ 3200 0 -2.9777485 0.99736666 2.0198069 0.15135627 -0.025930613 -3.0036792
+ 3250 0 -2.9797804 1.0301449 1.9779232 0.14660973 -0.025016253 -3.0047966
+ 3300 0 -2.9820171 0.94285548 1.96158 0.13286429 -0.024090816 -3.0061079
+ 3350 0 -2.9817184 0.98345019 2.006374 0.11946654 -0.025223277 -3.0069417
+ 3400 0 -2.9812891 1.0291774 2.0523043 0.11233996 -0.026572014 -3.0078611
+ 3450 0 -2.9835185 1.0204667 2.0006849 0.10950044 -0.025913625 -3.0094321
+ 3500 0 -2.9846522 1.0357247 1.9956135 0.11397223 -0.02596945 -3.0106216
+ 3550 0 -2.9849965 1.0465415 2.0034542 0.10529073 -0.026768999 -3.0117655
+ 3600 0 -2.9854932 1.0100248 2.0061519 0.08830457 -0.027590513 -3.0130837
+ 3650 0 -2.9857647 0.98930272 2.0182283 0.087267346 -0.028614885 -3.0143796
+ 3700 0 -2.9858424 0.98968749 2.0513509 0.10976845 -0.030020766 -3.0158632
+ 3750 0 -2.9898376 1.0094545 1.9684317 0.12012512 -0.02962014 -3.0194577
+ 3800 0 -2.9909385 0.99283062 1.9564888 0.12537594 -0.030015407 -3.0209539
+ 3850 0 -2.9926048 0.98361678 1.9819742 0.16313881 -0.030948861 -3.0235536
+ 3900 0 -2.9932922 0.98225201 1.9919792 0.18301585 -0.031158418 -3.0244506
+ 3950 0 -2.993953 0.99909161 1.9914448 0.19489054 -0.03131767 -3.0252706
+ 4000 0 -2.9938341 0.98065126 2.0201506 0.19082331 -0.032058718 -3.0258928
+ 4050 0 -2.9950536 0.9785676 1.9774178 0.16443738 -0.031591517 -3.0266451
+ 4100 0 -2.9953218 1.0069483 1.9925044 0.14079031 -0.031936209 -3.027258
+ 4150 0 -2.9963656 0.97761728 1.9845911 0.11288389 -0.031595867 -3.0279614
+ 4200 0 -2.9964199 0.98359583 2.0139525 0.095496549 -0.032163052 -3.028583
+ 4250 0 -2.9972591 0.993874 2.0143705 0.091692668 -0.03194206 -3.0292011
+ 4300 0 -2.9982807 0.98492505 2.012554 0.11938807 -0.031454431 -3.0297351
+ 4350 0 -2.9999398 0.98784549 1.9881272 0.12507612 -0.031022256 -3.0309621
+ 4400 0 -3.0001304 0.99616457 1.9945789 0.12453613 -0.031177114 -3.0313075
+ 4450 0 -3.0004497 1.0000329 1.9931979 0.1270167 -0.031009688 -3.0314594
+ 4500 0 -3.0005789 0.99179213 1.9969317 0.13667693 -0.030980836 -3.0315598
+ 4550 0 -3.0007423 1.0041962 1.9941677 0.15252242 -0.031006633 -3.0317489
+ 4600 0 -3.0010569 1.0057204 1.9817944 0.15946073 -0.030819514 -3.0318765
+ 4650 0 -3.0014825 0.98469354 2.0019354 0.16598597 -0.030622748 -3.0321052
+ 4700 0 -3.0018368 1.0158862 2.0017724 0.17909232 -0.030557071 -3.0323939
+ 4750 0 -3.0024201 0.9960973 2.0134985 0.16196409 -0.030652485 -3.0330726
+ 4800 0 -3.0046547 0.99511822 1.9709749 0.11634573 -0.029985363 -3.03464
+ 4850 0 -3.0057898 0.9840066 2.0608646 0.10865238 -0.032240795 -3.0380306
+ 4900 0 -3.0073588 1.0457338 2.016365 0.11066013 -0.031987734 -3.0393466
+ 4950 0 -3.0090739 1.0131698 1.9782205 0.1141775 -0.031538332 -3.0406122
+ 5000 0 -3.0101274 1.0065972 1.9526686 0.11953597 -0.031347107 -3.0414745
+ 5050 0 -3.0102918 1.0154549 1.9752505 0.1220875 -0.031756469 -3.0420483
+ 5100 0 -3.0108263 1.0025509 2.0124654 0.13973674 -0.032101781 -3.0429281
+ 5150 0 -3.0148407 0.95927344 1.8896916 0.16214187 -0.030046018 -3.0448867
+ 5200 0 -3.0150313 0.95062265 2.0075523 0.17001319 -0.032059324 -3.0470906
+ 5250 0 -3.0175735 0.97218401 1.959978 0.14895932 -0.031263777 -3.0488372
+ 5300 0 -3.016581 1.0802252 2.05308 0.12479188 -0.034297458 -3.0508785
+ 5350 0 -3.0218616 0.92814595 1.9346365 0.11066894 -0.032101217 -3.0539628
+ 5400 0 -3.0230864 1.0009537 1.9581426 0.10072265 -0.033417491 -3.0565039
+ 5450 0 -3.0229488 0.97989404 2.0379675 0.085383544 -0.03507026 -3.0580191
+ 5500 0 -3.0253542 0.966137 1.971244 0.082518184 -0.033935405 -3.0592896
+ 5550 0 -3.0257839 1.0012734 2.0297929 0.088881743 -0.034859305 -3.0606432
+ 5600 0 -3.0285415 1.0069584 1.9971527 0.060161704 -0.034365808 -3.0629073
+ 5650 0 -3.0309829 1.0001688 2.0107095 0.042774249 -0.034976624 -3.0659595
+ 5700 0 -3.0346459 1.0148121 1.9812613 0.057797039 -0.034875301 -3.0695212
+ 5750 0 -3.034967 0.99889543 2.0007332 0.062522099 -0.035508727 -3.0704757
+ 5800 0 -3.0354193 0.99309448 1.9905175 0.058723802 -0.035599394 -3.0710187
+ 5850 0 -3.0377114 0.95244639 1.8862163 0.036564194 -0.034423714 -3.0721351
+ 5900 0 -3.0374037 0.9409737 1.9685026 0.020781029 -0.036371599 -3.0737753
+ 5950 0 -3.037355 1.0040584 1.9975884 0.029471446 -0.037134087 -3.0744891
+ 6000 0 -3.0377611 0.97903528 1.9912525 0.030018934 -0.036958151 -3.0747193
+ 6050 0 -3.0377435 1.0026599 1.9926518 0.03268008 -0.037097365 -3.0748408
+ 6100 0 -3.0376857 0.99774066 2.0011206 0.032339746 -0.037203823 -3.0748895
+ 6150 0 -3.0378018 0.99312254 1.9976029 0.033591679 -0.037118029 -3.0749198
+ 6200 0 -3.0378621 0.99757283 1.9947742 0.033965158 -0.037072763 -3.0749349
+ 6250 0 -3.0378032 0.99964291 1.9971778 0.033045048 -0.037140636 -3.0749439
+ 6300 0 -3.0377782 0.9965492 1.9980669 0.032201395 -0.037170252 -3.0749485
+ 6314 0 -3.0377854 0.99649081 1.9975871 0.032243768 -0.037163869 -3.0749493
+Loop time of 2.34844 on 1 procs for 4401 steps with 800 atoms
+
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+Minimization stats:
+ Stopping criterion = force tolerance
+ Energy initial, next-to-last, final =
+ -2.93913047033 -3.07494921994 -3.07494925979
+ Force two-norm initial, final = 25.9452 0.920316
+ Force max component initial, final = 19.0294 0.548784
+ Final line search alpha, max atom move = 0.000841982 0.000462066
+ Iterations, force evaluations = 4401 8540
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 1.9026 | 1.9026 | 1.9026 | 0.0 | 81.01
+Neigh | 0.027466 | 0.027466 | 0.027466 | 0.0 | 1.17
+Comm | 0.020059 | 0.020059 | 0.020059 | 0.0 | 0.85
+Output | 0.0028694 | 0.0028694 | 0.0028694 | 0.0 | 0.12
+Modify | 0.018381 | 0.018381 | 0.018381 | 0.0 | 0.78
+Other | | 0.3771 | | | 16.06
+
+Nlocal: 800 ave 800 max 800 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 342 ave 342 max 342 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 7244 ave 7244 max 7244 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 7244
+Ave neighs/atom = 9.055
+Neighbor list builds = 109
+Dangerous builds = 0
+
+minimize 0.0 1.0e-2 10000 100000
+Memory usage per processor = 3.60343 Mbytes
+Step Temp PotEng Pxx Pyy Pxy 3 emin
+ 6314 0 -3.0377854 0.99649081 1.9975871 0.032243768 3.5527137e-17 -3.0377854
+ 6350 0 -3.0377426 0.9995618 1.9997582 0.032364722 -4.5395813e-05 -3.037788
+ 6400 0 -3.0377432 0.99984154 1.9998786 0.032403541 -4.5666168e-05 -3.0377889
+ 6450 0 -3.0377267 0.99999473 2.0002343 0.032176487 -6.317327e-05 -3.0377899
+ 6500 0 -3.0377343 1.0000023 1.9999491 0.032228066 -5.6306704e-05 -3.0377906
+ 6550 0 -3.0377346 1.0001343 1.9999711 0.032298354 -5.6111747e-05 -3.0377907
+ 6600 0 -3.0377349 1.0002038 1.9999408 0.032324674 -5.5966675e-05 -3.0377908
+ 6650 0 -3.0377306 1.0004192 2.0000469 0.032324741 -6.0315852e-05 -3.0377909
+ 6700 0 -3.0377323 1.0000441 2.000009 0.032302097 -5.8641949e-05 -3.037791
+ 6750 0 -3.0377303 1.0000605 2.0000938 0.032293244 -6.0671758e-05 -3.037791
+ 6800 0 -3.0377231 1.0004525 2.0003454 0.032282004 -6.7960388e-05 -3.0377911
+ 6850 0 -3.0377314 0.99987595 1.9999542 0.032227371 -5.9796937e-05 -3.0377912
+ 6900 0 -3.0377256 0.99344819 2.0011607 0.031344595 -6.9303736e-05 -3.0377949
+ 6950 0 -3.0373578 0.99761743 2.0225249 0.030185311 -0.00050004148 -3.0378578
+ 7000 0 -3.0378367 1.0018764 1.9978072 0.032669355 -6.3346776e-05 -3.0379001
+ 7050 0 -3.037828 1.0008325 1.9993554 0.033274825 -7.6731821e-05 -3.0379047
+ 7100 0 -3.0378259 0.99929476 2.000522 0.033459662 -8.1578573e-05 -3.0379074
+ 7150 0 -3.0378481 1.0010779 1.9992842 0.0335711 -6.0551519e-05 -3.0379087
+ 7200 0 -3.0378388 0.99931209 2.0002124 0.033322503 -7.0644382e-05 -3.0379094
+ 7250 0 -3.0378359 1.0003652 1.9999793 0.033413223 -7.4037459e-05 -3.0379099
+ 7300 0 -3.0378373 0.99974121 2.0001941 0.03354157 -7.2831065e-05 -3.0379102
+ 7350 0 -3.0378405 1.000399 1.9998044 0.033708545 -6.9814263e-05 -3.0379103
+ 7400 0 -3.0378346 0.99989677 2.0001045 0.03373625 -7.5817257e-05 -3.0379104
+ 7450 0 -3.0378359 1.0001255 1.9999563 0.033756091 -7.4569461e-05 -3.0379105
+ 7500 0 -3.0378358 0.99994381 2.0000901 0.033790565 -7.4692471e-05 -3.0379105
+ 7550 0 -3.0378365 1.0001569 2.0000048 0.033810907 -7.3987385e-05 -3.0379105
+ 7600 0 -3.0378378 0.99995421 1.9999929 0.033778739 -7.2688901e-05 -3.0379105
+ 7650 0 -3.0378356 1.0000328 2.0000725 0.033750734 -7.4891228e-05 -3.0379105
+ 7700 0 -3.0378356 1.0000928 2.000025 0.033739518 -7.492587e-05 -3.0379105
+ 7750 0 -3.037836 1.000026 2.0000007 0.033743007 -7.4483428e-05 -3.0379105
+ 7800 0 -3.0378354 1.0000164 2.0000445 0.033752032 -7.5086586e-05 -3.0379105
+ 7850 0 -3.0378352 1.0000397 2.0000524 0.033753896 -7.5318252e-05 -3.0379105
+ 7900 0 -3.0378354 1.0000486 2.0000488 0.033742064 -7.5113089e-05 -3.0379105
+ 7904 0 -3.0378356 1.0000321 2.0000425 0.033740786 -7.491864e-05 -3.0379105
+Loop time of 0.858773 on 1 procs for 1590 steps with 800 atoms
+
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+Minimization stats:
+ Stopping criterion = force tolerance
+ Energy initial, next-to-last, final =
+ -3.03778539031 -3.0379105126 -3.03791051261
+ Force two-norm initial, final = 3.7074 0.00953997
+ Force max component initial, final = 3.0105 0.0052229
+ Final line search alpha, max atom move = 0.0789456 0.000412325
+ Iterations, force evaluations = 1590 3180
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.70479 | 0.70479 | 0.70479 | 0.0 | 82.07
+Neigh | 0.00049901 | 0.00049901 | 0.00049901 | 0.0 | 0.06
+Comm | 0.0068367 | 0.0068367 | 0.0068367 | 0.0 | 0.80
+Output | 0.00099421 | 0.00099421 | 0.00099421 | 0.0 | 0.12
+Modify | 0.0066617 | 0.0066617 | 0.0066617 | 0.0 | 0.78
+Other | | 0.139 | | | 16.19
+
+Nlocal: 800 ave 800 max 800 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 340 ave 340 max 340 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 7246 ave 7246 max 7246 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 7246
+Ave neighs/atom = 9.0575
+Neighbor list builds = 2
+Dangerous builds = 0
+
+# Final refinement uses nreset to eliminate stress offset
+
+fix 3 all box/relax x 1.0 y 2.0 vmax 1.0e-3 nreset 100
+
+minimize 0.0 1.0e-4 10000 100000
+Memory usage per processor = 3.60343 Mbytes
+Step Temp PotEng Pxx Pyy Pxy 3 emin
+ 7904 0 -3.0378356 1.0000321 2.0000425 0.033740786 0 -3.0378356
+ 7950 0 -3.0378364 1.000001 2.0000015 0.03373689 8.3404927e-07 -3.0378356
+ 8000 0 -3.0378364 0.99999791 2.0000025 0.033733241 8.1782018e-07 -3.0378356
+ 8050 0 -3.0378364 1.0000013 1.9999999 0.033727555 1.0952852e-07 -3.0378363
+ 8100 0 -3.0378364 0.99999975 1.9999993 0.03372457 1.1467852e-07 -3.0378363
+ 8150 0 -3.0378364 0.99999962 1.9999999 0.033723065 -1.6306321e-08 -3.0378364
+ 8200 0 -3.0378364 1.0000001 1.9999991 0.033723385 -9.8605362e-09 -3.0378364
+ 8250 0 -3.0378364 0.9999999 1.9999999 0.033724134 1.6533658e-08 -3.0378364
+ 8300 0 -3.0378364 0.99999987 1.9999999 0.033724908 2.416758e-08 -3.0378364
+ 8350 0 -3.0378364 1 1.9999991 0.0337256 1.2773347e-08 -3.0378364
+ 8400 0 -3.0378364 0.9999998 1.9999999 0.033725946 -1.1867813e-08 -3.0378364
+ 8450 0 -3.0378364 0.99999995 1.9999999 0.033726404 -1.3134768e-08 -3.0378364
+ 8500 0 -3.0378364 0.99999967 1.9999999 0.033726454 -1.1481639e-08 -3.0378364
+ 8550 0 -3.0378364 0.99999998 1.9999998 0.033726207 2.9756123e-09 -3.0378364
+ 8600 0 -3.0378364 0.99999979 1.9999999 0.033726113 4.7253467e-09 -3.0378364
+ 8650 0 -3.0378364 0.99999993 1.9999999 0.033725878 -1.9054681e-10 -3.0378364
+ 8700 0 -3.0378364 1 1.9999997 0.033725586 4.9116894e-09 -3.0378364
+ 8750 0 -3.0378364 0.99999991 2 0.033725386 7.3634181e-10 -3.0378364
+ 8753 0 -3.0378364 1 2 0.033725385 -1.0901182e-09 -3.0378364
+Loop time of 0.461345 on 1 procs for 849 steps with 800 atoms
+
+99.7% CPU use with 1 MPI tasks x no OpenMP threads
+
+Minimization stats:
+ Stopping criterion = force tolerance
+ Energy initial, next-to-last, final =
+ -3.03783559397 -3.03783642331 -3.03783642331
+ Force two-norm initial, final = 0.0462457 9.79399e-05
+ Force max component initial, final = 0.0364742 4.124e-05
+ Final line search alpha, max atom move = 1 4.124e-05
+ Iterations, force evaluations = 849 1698
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.37917 | 0.37917 | 0.37917 | 0.0 | 82.19
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.0035837 | 0.0035837 | 0.0035837 | 0.0 | 0.78
+Output | 0.00053287 | 0.00053287 | 0.00053287 | 0.0 | 0.12
+Modify | 0.0036094 | 0.0036094 | 0.0036094 | 0.0 | 0.78
+Other | | 0.07445 | | | 16.14
+
+Nlocal: 800 ave 800 max 800 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 342 ave 342 max 342 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 7245 ave 7245 max 7245 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 7245
+Ave neighs/atom = 9.05625
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Total wall time: 0:00:04
diff --git a/examples/min/log.15Feb16.min.box.g++.4 b/examples/min/log.15Feb16.min.box.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..d757f0c635513ea1c4df123e8f29a677cccd391e
--- /dev/null
+++ b/examples/min/log.15Feb16.min.box.g++.4
@@ -0,0 +1,542 @@
+LAMMPS (15 Feb 2016)
+# 2d Lennard-Jones melt and subsequent energy minimization,
+# followed by box relaxation to a target stress state
+#
+units lj
+dimension 2
+atom_style atomic
+
+lattice sq2 0.8442
+Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
+region box block 0 20 0 20 -0.1 0.1
+create_box 1 box
+Created orthogonal box = (0 0 -0.153919) to (30.7838 30.7838 0.153919)
+ 2 by 2 by 1 MPI processor grid
+create_atoms 1 box
+Created 800 atoms
+mass 1 1.0
+
+velocity all create 5.0 87287 loop geom
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+pair_modify shift yes
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nve
+fix 2 all enforce2d
+
+#dump 1 all atom 500 dump.min
+
+#dump 2 all image 500 image.*.jpg type type # zoom 1.6 adiam 1.5
+#dump_modify 2 pad 4
+
+#dump 3 all movie 500 movie.mpg type type # zoom 1.6 adiam 1.5
+#dump_modify 3 pad 4
+
+thermo 100
+
+run 1000
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4 -> bins = 22 22 1
+Memory usage per processor = 2.47676 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 5 -2.461717 0 2.532033 5.0190509
+ 100 3.2788864 -0.74311698 0 2.5316708 15.912832
+ 200 3.3041082 -0.77000277 0 2.5299752 15.602653
+ 300 3.3840228 -0.84859211 0 2.5312006 15.188203
+ 400 3.3916063 -0.85694601 0 2.5304208 15.383853
+ 500 3.3136053 -0.77935264 0 2.5301106 15.833296
+ 600 3.3888915 -0.85213737 0 2.532518 15.162759
+ 700 3.2123636 -0.67641846 0 2.5319297 16.31059
+ 800 3.3016408 -0.76570603 0 2.5318077 15.639259
+ 900 3.4621697 -0.92610292 0 2.5317391 14.773473
+ 1000 3.3058424 -0.77076863 0 2.5309414 15.708171
+Loop time of 0.0697336 on 4 procs for 1000 steps with 800 atoms
+
+Performance: 6195003.241 tau/day, 14340.285 timesteps/s
+100.0% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.033633 | 0.034047 | 0.03476 | 0.2 | 48.82
+Neigh | 0.01311 | 0.01343 | 0.013635 | 0.2 | 19.26
+Comm | 0.014188 | 0.014708 | 0.015157 | 0.4 | 21.09
+Output | 0.00019526 | 0.00020427 | 0.00022554 | 0.1 | 0.29
+Modify | 0.0031531 | 0.0032287 | 0.0034115 | 0.2 | 4.63
+Other | | 0.004116 | | | 5.90
+
+Nlocal: 200 ave 202 max 196 min
+Histogram: 1 0 0 0 0 0 0 0 2 1
+Nghost: 170.25 ave 174 max 167 min
+Histogram: 1 0 1 0 0 1 0 0 0 1
+Neighs: 1934.75 ave 1972 max 1873 min
+Histogram: 1 0 0 0 0 0 1 0 1 1
+
+Total # of neighbors = 7739
+Ave neighs/atom = 9.67375
+Neighbor list builds = 203
+Dangerous builds = 0
+
+# perform the box relaxation by progressively
+# adding more degrees of freedom, for smoother
+# convergence
+
+neigh_modify delay 0 every 1 check yes
+
+velocity all create 0.0 1
+thermo 50
+
+# atoms only
+
+minimize 1.0e-6 0.001 1000 10000
+Memory usage per processor = 3.60176 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 1000 0 -0.77076863 0 -0.77076863 12.920868
+ 1050 0 -2.8318266 0 -2.8318266 -1.1892931
+ 1100 0 -2.8658339 0 -2.8658339 -1.0859975
+ 1150 0 -2.8788056 0 -2.8788056 -1.1017533
+ 1200 0 -2.8831122 0 -2.8831122 -1.1004001
+ 1250 0 -2.8877971 0 -2.8877971 -1.0596414
+ 1300 0 -2.8887969 0 -2.8887969 -1.0448381
+Loop time of 0.0555401 on 4 procs for 300 steps with 800 atoms
+
+99.5% CPU use with 4 MPI tasks x no OpenMP threads
+
+Minimization stats:
+ Stopping criterion = energy tolerance
+ Energy initial, next-to-last, final =
+ -0.770768629298 -2.88879411525 -2.88879694984
+ Force two-norm initial, final = 1950.95 0.825241
+ Force max component initial, final = 374.098 0.224821
+ Final line search alpha, max atom move = 0.410301 0.0922441
+ Iterations, force evaluations = 300 595
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.032524 | 0.033133 | 0.033955 | 0.3 | 59.66
+Neigh | 0.0036891 | 0.0038166 | 0.0038748 | 0.1 | 6.87
+Comm | 0.0073385 | 0.0081375 | 0.0089004 | 0.6 | 14.65
+Output | 8.5831e-05 | 9.042e-05 | 0.0001018 | 0.1 | 0.16
+Modify | 0.00034714 | 0.0003776 | 0.00040054 | 0.1 | 0.68
+Other | | 0.009985 | | | 17.98
+
+Nlocal: 200 ave 202 max 196 min
+Histogram: 1 0 0 0 0 0 1 0 0 2
+Nghost: 172.5 ave 175 max 169 min
+Histogram: 1 0 0 1 0 0 0 0 0 2
+Neighs: 1757 ave 1793 max 1721 min
+Histogram: 1 0 1 0 0 0 0 1 0 1
+
+Total # of neighbors = 7028
+Ave neighs/atom = 8.785
+Neighbor list builds = 59
+Dangerous builds = 0
+
+# isotropic volume relaxation to hydrostatic target
+
+fix 3 all box/relax iso 1.5 vmax 1.0e-3
+
+variable emin equal pe+f_3/atoms
+thermo_style custom step temp pe pxx pyy pxy f_3 v_emin
+
+# anisotropic volume relaxation to hydrostatic target
+
+minimize 0.0 10.0e0 10000 100000
+Memory usage per processor = 3.60176 Mbytes
+Step Temp PotEng Pxx Pyy Pxy 3 emin
+ 1300 0 -2.8887969 -0.93904343 -1.1506328 -0.0037265764 0 -2.8887969
+ 1350 0 -2.889313 1.555657 1.4414453 -0.025585726 -0.10933729 -2.9986503
+ 1400 0 -2.8958621 1.5320803 1.476774 0.0041557664 -0.1208966 -3.0167587
+ 1403 0 -2.8962558 1.5290172 1.4743135 0.00471395 -0.12088872 -3.0171446
+Loop time of 0.0181124 on 4 procs for 103 steps with 800 atoms
+
+93.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+Minimization stats:
+ Stopping criterion = force tolerance
+ Energy initial, next-to-last, final =
+ -2.88879694984 -3.01714081772 -3.01714455432
+ Force two-norm initial, final = 4823.19 9.6427
+ Force max component initial, final = 4823.19 3.04698
+ Final line search alpha, max atom move = 2.87851e-05 8.77075e-05
+ Iterations, force evaluations = 103 161
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0093105 | 0.0095073 | 0.009722 | 0.1 | 52.49
+Neigh | 0.0010061 | 0.00104 | 0.0010571 | 0.1 | 5.74
+Comm | 0.0019989 | 0.0022128 | 0.0024509 | 0.3 | 12.22
+Output | 7.2956e-05 | 7.4506e-05 | 7.9155e-05 | 0.0 | 0.41
+Modify | 8.9645e-05 | 0.00010043 | 0.00010562 | 0.1 | 0.55
+Other | | 0.005177 | | | 28.58
+
+Nlocal: 200 ave 202 max 198 min
+Histogram: 1 0 0 0 0 2 0 0 0 1
+Nghost: 178.25 ave 181 max 175 min
+Histogram: 1 0 0 1 0 0 0 0 1 1
+Neighs: 1854.75 ave 1878 max 1822 min
+Histogram: 1 0 0 0 0 1 0 0 1 1
+
+Total # of neighbors = 7419
+Ave neighs/atom = 9.27375
+Neighbor list builds = 16
+Dangerous builds = 0
+
+fix 3 all box/relax aniso 1.5 vmax 1.0e-3
+
+minimize 0.0 10.0 10000 100000
+Memory usage per processor = 3.60176 Mbytes
+Step Temp PotEng Pxx Pyy Pxy 3 emin
+ 1403 0 -2.8962558 1.5290172 1.4743135 0.00471395 0 -2.8962558
+ 1404 0 -2.8963678 1.49615 1.499767 0.0037848845 9.6365079e-05 -2.8962714
+Loop time of 0.000356197 on 4 procs for 1 steps with 800 atoms
+
+0.0% CPU use with 4 MPI tasks x no OpenMP threads
+
+Minimization stats:
+ Stopping criterion = force tolerance
+ Energy initial, next-to-last, final =
+ -2.8962558314 -2.8962558314 -2.89627142801
+ Force two-norm initial, final = 35.4271 9.77898
+ Force max component initial, final = 25.6271 3.39863
+ Final line search alpha, max atom move = 3.90213e-05 0.000132619
+ Iterations, force evaluations = 1 2
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.00017381 | 0.0001772 | 0.00018167 | 0.0 | 49.75
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 3.314e-05 | 3.7372e-05 | 4.0054e-05 | 0.0 | 10.49
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 2.1458e-06 | 2.6226e-06 | 3.0994e-06 | 0.0 | 0.74
+Other | | 0.000139 | | | 39.02
+
+Nlocal: 200 ave 202 max 197 min
+Histogram: 1 0 0 0 0 0 1 0 1 1
+Nghost: 178.25 ave 180 max 176 min
+Histogram: 1 0 1 0 0 0 0 0 0 2
+Neighs: 1847 ave 1872 max 1822 min
+Histogram: 1 1 0 0 0 0 0 0 1 1
+
+Total # of neighbors = 7388
+Ave neighs/atom = 9.235
+Neighbor list builds = 0
+Dangerous builds = 0
+
+# anisotropic volume relaxation to non-hydrostatic target
+
+fix 3 all box/relax x 1.0 y 2.0 vmax 1.0e-3
+
+minimize 0.0 10.0 10000 100000
+Memory usage per processor = 3.60176 Mbytes
+Step Temp PotEng Pxx Pyy Pxy 3 emin
+ 1404 0 -2.8963678 1.49615 1.499767 0.0037848845 -7.1054274e-17 -2.8963678
+ 1450 0 -2.8925305 0.94584654 2.0945709 -0.029336194 -0.016086454 -2.9086169
+ 1500 0 -2.8975934 1.0123866 2.009477 -0.036498498 -0.01841842 -2.9160118
+ 1550 0 -2.903576 1.0046986 1.9380791 -0.037683327 -0.020970768 -2.9245468
+ 1592 0 -2.9061298 0.98518925 1.9835783 -0.048932212 -0.024234721 -2.9303646
+Loop time of 0.0329762 on 4 procs for 188 steps with 800 atoms
+
+100.1% CPU use with 4 MPI tasks x no OpenMP threads
+
+Minimization stats:
+ Stopping criterion = force tolerance
+ Energy initial, next-to-last, final =
+ -2.89636779309 -2.93027409874 -2.93036456323
+ Force two-norm initial, final = 622.345 9.97488
+ Force max component initial, final = 441.816 3.5534
+ Final line search alpha, max atom move = 4.49831e-05 0.000159843
+ Iterations, force evaluations = 188 295
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.017398 | 0.017577 | 0.017932 | 0.2 | 53.30
+Neigh | 0.00051427 | 0.00052792 | 0.00054002 | 0.0 | 1.60
+Comm | 0.0033214 | 0.0037473 | 0.0040131 | 0.4 | 11.36
+Output | 0.00013399 | 0.00013644 | 0.00014377 | 0.0 | 0.41
+Modify | 0.00018668 | 0.00020236 | 0.00021911 | 0.1 | 0.61
+Other | | 0.01079 | | | 32.71
+
+Nlocal: 200 ave 202 max 196 min
+Histogram: 1 0 0 0 0 0 0 0 2 1
+Nghost: 179.5 ave 183 max 176 min
+Histogram: 1 0 1 0 0 0 0 1 0 1
+Neighs: 1862.5 ave 1893 max 1821 min
+Histogram: 1 0 0 0 0 0 2 0 0 1
+
+Total # of neighbors = 7450
+Ave neighs/atom = 9.3125
+Neighbor list builds = 8
+Dangerous builds = 0
+
+minimize 0.0 1.0 10000 100000
+Memory usage per processor = 3.60176 Mbytes
+Step Temp PotEng Pxx Pyy Pxy 3 emin
+ 1592 0 -2.9061298 0.98518925 1.9835783 -0.048932212 3.5527137e-17 -2.9061298
+ 1600 0 -2.9046586 1.0529014 2.0593731 -0.050860896 -0.0020973121 -2.9067559
+ 1650 0 -2.9077781 0.98217454 2.0557227 -0.053762924 -0.0037318755 -2.91151
+ 1700 0 -2.911189 0.94319026 2.0024059 -0.048920328 -0.0038748811 -2.9150639
+ 1750 0 -2.9164651 0.94353792 1.9550633 -0.029155121 -0.0061062511 -2.9225713
+ 1800 0 -2.9184486 0.98650677 2.0009524 -0.0078670444 -0.0093780731 -2.9278267
+ 1850 0 -2.9212867 1.0498564 1.9603902 0.010111603 -0.010488406 -2.9317751
+ 1900 0 -2.9213403 0.99740355 2.0425934 0.026161958 -0.014050539 -2.9353909
+ 1950 0 -2.9266889 0.99152482 1.9933997 0.03409256 -0.015614063 -2.942303
+ 2000 0 -2.9285908 1.0350107 2.0275013 0.033065933 -0.019303075 -2.9478939
+ 2050 0 -2.9304105 0.96637822 1.9834345 0.026336793 -0.020013699 -2.9504242
+ 2100 0 -2.9330357 0.97845141 1.9025015 0.021574938 -0.019779787 -2.9528155
+ 2150 0 -2.9331851 0.99675158 2.0074323 -0.0065532256 -0.02481578 -2.9580009
+ 2200 0 -2.9368641 0.98438888 1.9246359 -0.019231932 -0.025247992 -2.962112
+ 2250 0 -2.939513 1.0279353 1.9269466 -0.023572931 -0.027689455 -2.9672025
+ 2300 0 -2.942156 0.94637839 2.0082098 -0.021822127 -0.031345014 -2.973501
+ 2350 0 -2.948735 0.93651267 1.9760466 -0.022735061 -0.032992594 -2.9817275
+ 2400 0 -2.9511278 0.99314345 1.9385123 -0.016972758 -0.032842878 -2.9839707
+ 2450 0 -2.9533012 0.97729639 2.0154201 -0.015641052 -0.035591247 -2.9888925
+ 2500 0 -2.954422 1.0349465 2.0120139 -0.019420841 -0.036210665 -2.9906327
+ 2550 0 -2.9575726 0.99530485 1.9284884 -0.016807344 -0.034822839 -2.9923955
+ 2600 0 -2.9573298 0.97329576 2.0164988 -0.01795058 -0.036637536 -2.9939673
+ 2650 0 -2.9593898 1.0203573 1.9464484 -0.020216394 -0.035748408 -2.9951382
+ 2700 0 -2.960177 0.96566571 2.0425296 0.0035371639 -0.037754691 -2.9979317
+ 2750 0 -2.9629231 1.0117643 1.9542228 0.02632338 -0.036929577 -2.9998526
+ 2800 0 -2.9657029 0.92990254 1.937087 0.017338918 -0.037267648 -3.0029706
+ 2850 0 -2.9658958 0.91635927 1.9894507 0.019284324 -0.038677428 -3.0045732
+ 2900 0 -2.965953 0.9735388 2.0220848 0.02052448 -0.040410779 -3.0063638
+ 2950 0 -2.9674506 1.0026034 1.9615451 0.018621661 -0.040233908 -3.0076845
+ 3000 0 -2.9681703 0.95627387 1.9536224 0.012057729 -0.041412351 -3.0095827
+ 3050 0 -2.9686102 0.94751435 1.9576194 0.0092272739 -0.042069932 -3.0106801
+ 3100 0 -2.9688024 0.94009207 1.9632077 0.00083680762 -0.04264597 -3.0114483
+ 3150 0 -2.9689839 0.94565802 1.967564 -0.00031007068 -0.0432371 -3.012221
+ 3200 0 -2.9694532 0.95670917 1.9517533 0.004846097 -0.043402976 -3.0128562
+ 3250 0 -2.9691757 0.98229076 1.944547 0.0041700186 -0.044427988 -3.0136037
+ 3300 0 -2.9688471 1.0032058 1.9262141 -0.026504883 -0.046396712 -3.0152438
+ 3350 0 -2.9696022 0.95533401 2.0105577 -0.025342982 -0.049074731 -3.0186769
+ 3400 0 -2.9731784 0.98985638 1.94557 -0.02748758 -0.050096034 -3.0232744
+ 3450 0 -2.974309 1.0513691 1.9998728 -0.020391151 -0.053374636 -3.0276836
+ 3500 0 -2.9765721 0.92595096 1.9633667 -0.020063084 -0.052822995 -3.0293951
+ 3550 0 -2.9777457 0.93450229 1.9995925 -0.013662027 -0.055309483 -3.0330551
+ 3600 0 -2.9806963 0.97640261 1.9283298 -0.0027545827 -0.05512979 -3.0358261
+ 3650 0 -2.9807118 0.93736872 1.9944251 0.0082873538 -0.056469091 -3.0371809
+ 3700 0 -2.9831586 1.0685131 2.0595128 0.06305966 -0.059015668 -3.0421743
+ 3750 0 -2.9875796 0.91547454 2.0024827 0.065982869 -0.058535211 -3.0461148
+ 3800 0 -2.9898449 0.93958431 1.9413764 0.05523992 -0.058407873 -3.0482528
+ 3850 0 -2.9903134 0.93830475 1.9849576 0.045612541 -0.059283499 -3.0495969
+ 3900 0 -2.9909848 0.9648608 1.994041 0.029853801 -0.059730698 -3.0507155
+ 3950 0 -2.9920567 1.0174164 1.9831331 0.02751284 -0.060321142 -3.0523778
+ 4000 0 -2.9931559 1.054449 2.0273684 0.025820071 -0.061814098 -3.05497
+ 4050 0 -2.9967814 1.0336441 1.9607185 0.0080753355 -0.061169081 -3.0579505
+ 4100 0 -2.996981 0.97811615 1.9997583 -0.0019083765 -0.062392266 -3.0593732
+ 4150 0 -2.9983301 0.991139 1.9758294 -0.016110953 -0.062441222 -3.0607713
+ 4200 0 -2.9995915 1.0106869 1.94477 -0.031095458 -0.062510217 -3.0621017
+ 4250 0 -3.0001063 1.0128218 1.9591959 -0.040593262 -0.063330573 -3.0634368
+ 4300 0 -3.0004474 1.0307974 2.0014391 -0.02845165 -0.064737002 -3.0651844
+ 4350 0 -3.0023551 0.94191501 1.9833078 -0.025720298 -0.064657395 -3.0670125
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+ 5150 0 -3.0177645 0.93541836 1.96018 -0.0071875906 -0.075709553 -3.0934741
+ 5200 0 -3.0178922 0.92272827 1.9365084 0.00055102294 -0.076432947 -3.0943251
+ 5250 0 -3.0196541 0.99625947 1.9913119 -0.031679622 -0.078732819 -3.0983869
+ 5300 0 -3.0244724 0.93077516 1.9153792 -0.028418358 -0.077643158 -3.1021155
+ 5350 0 -3.025691 0.95290818 1.9263259 0.0018721029 -0.078001949 -3.103693
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+ 5500 0 -3.0246542 0.95996989 1.9814976 -0.018179831 -0.080970098 -3.1056243
+ 5550 0 -3.0239232 0.98579742 1.9735322 -0.025560182 -0.082383595 -3.1063068
+ 5600 0 -3.0237848 0.9479909 2.0195426 0.0030195864 -0.084189849 -3.1079746
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+ 6050 0 -3.0313105 0.9590106 1.959899 0.10814531 -0.084790331 -3.1161008
+ 6100 0 -3.0313244 0.9580272 1.9605104 0.10879691 -0.08493735 -3.1162617
+ 6130 0 -3.0313384 0.95532497 1.9595324 0.10924759 -0.084945274 -3.1162837
+Loop time of 0.917613 on 4 procs for 4538 steps with 800 atoms
+
+99.6% CPU use with 4 MPI tasks x no OpenMP threads
+
+Minimization stats:
+ Stopping criterion = force tolerance
+ Energy initial, next-to-last, final =
+ -2.90612984251 -3.11628366855 -3.11628369961
+ Force two-norm initial, final = 21.7981 0.937604
+ Force max component initial, final = 14.4511 0.431389
+ Final line search alpha, max atom move = 0.000547499 0.000236185
+ Iterations, force evaluations = 4538 8462
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.49716 | 0.5033 | 0.51238 | 0.9 | 54.85
+Neigh | 0.0065906 | 0.0068512 | 0.0069604 | 0.2 | 0.75
+Comm | 0.094408 | 0.10467 | 0.11346 | 2.5 | 11.41
+Output | 0.0040958 | 0.0041735 | 0.0043962 | 0.2 | 0.45
+Modify | 0.0052106 | 0.0053825 | 0.0055635 | 0.2 | 0.59
+Other | | 0.2932 | | | 31.96
+
+Nlocal: 200 ave 203 max 197 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+Nghost: 181.5 ave 183 max 181 min
+Histogram: 3 0 0 0 0 0 0 0 0 1
+Neighs: 1814.25 ave 1838 max 1768 min
+Histogram: 1 0 0 0 0 0 0 1 0 2
+
+Total # of neighbors = 7257
+Ave neighs/atom = 9.07125
+Neighbor list builds = 104
+Dangerous builds = 0
+
+minimize 0.0 1.0e-2 10000 100000
+Memory usage per processor = 3.60176 Mbytes
+Step Temp PotEng Pxx Pyy Pxy 3 emin
+ 6130 0 -3.0313384 0.95532497 1.9595324 0.10924759 -3.5527137e-17 -3.0313384
+ 6150 0 -3.0304428 0.9947235 1.9969091 0.10935746 -0.00091797415 -3.0313608
+ 6200 0 -3.0303022 1.0001878 2.000297 0.10984247 -0.0010859161 -3.0313882
+ 6250 0 -3.0303474 0.99938469 1.9997606 0.10892851 -0.0010447278 -3.0313921
+ 6300 0 -3.030364 0.99909678 1.9994518 0.10814831 -0.0010293495 -3.0313933
+ 6350 0 -3.0303717 0.99985291 1.9992837 0.1079772 -0.0010221246 -3.0313938
+ 6400 0 -3.0303643 0.99996396 1.9996376 0.10768185 -0.0010298963 -3.0313942
+ 6450 0 -3.0303548 1.0000119 1.9998057 0.10740047 -0.0010396613 -3.0313944
+ 6500 0 -3.0303565 0.99994354 1.9997054 0.10745687 -0.0010380365 -3.0313945
+ 6550 0 -3.0303597 0.99997619 1.99973 0.10757709 -0.0010348341 -3.0313946
+ 6600 0 -3.0303627 0.99989601 1.9997112 0.10753202 -0.0010319717 -3.0313947
+ 6650 0 -3.0303601 0.99996966 1.9998692 0.10746847 -0.0010345994 -3.0313947
+ 6700 0 -3.0303593 0.9999198 1.9999738 0.10750063 -0.001035439 -3.0313948
+ 6750 0 -3.030358 0.99984873 1.9999385 0.10758609 -0.0010368344 -3.0313948
+ 6800 0 -3.0303557 0.99989034 1.999929 0.10766313 -0.0010390742 -3.0313948
+ 6850 0 -3.0303539 0.99997112 1.9999636 0.10767624 -0.0010409153 -3.0313948
+ 6900 0 -3.0303556 0.99996801 1.9998614 0.10770653 -0.0010392495 -3.0313948
+ 6950 0 -3.0303537 0.99999067 1.999933 0.10772838 -0.0010411386 -3.0313949
+ 7000 0 -3.0303521 0.99997861 1.9999979 0.1077447 -0.001042745 -3.0313949
+ 7050 0 -3.0303524 0.99996541 1.9999799 0.1077349 -0.0010424959 -3.0313949
+ 7100 0 -3.0303525 0.99999438 1.9999815 0.10775527 -0.0010423842 -3.0313949
+ 7150 0 -3.0303535 0.99998124 1.9999354 0.10775281 -0.0010413311 -3.0313949
+ 7200 0 -3.0303532 0.99999763 1.9999874 0.10772418 -0.001041638 -3.0313949
+ 7250 0 -3.0303539 0.99996105 1.9999842 0.10772361 -0.001041024 -3.0313949
+ 7300 0 -3.0303535 0.99998962 1.9999966 0.10770842 -0.001041396 -3.0313949
+ 7350 0 -3.0303535 1.0000095 1.9999958 0.10769735 -0.0010413981 -3.0313949
+ 7400 0 -3.0303541 1.0000005 1.9999858 0.1076965 -0.0010408177 -3.0313949
+ 7450 0 -3.030354 1.000003 1.9999931 0.10769929 -0.0010409352 -3.0313949
+ 7500 0 -3.0303537 1.0000034 1.9999885 0.10769864 -0.0010411458 -3.0313949
+ 7550 0 -3.0303533 1.0000018 1.9999949 0.10769873 -0.0010415749 -3.0313949
+ 7600 0 -3.0303529 1.0000017 2.0000034 0.10770161 -0.0010419517 -3.0313949
+ 7607 0 -3.0303527 1.0000104 2.0000131 0.10770259 -0.0010421819 -3.0313949
+Loop time of 0.320295 on 4 procs for 1477 steps with 800 atoms
+
+99.5% CPU use with 4 MPI tasks x no OpenMP threads
+
+Minimization stats:
+ Stopping criterion = force tolerance
+ Energy initial, next-to-last, final =
+ -3.03133842556 -3.03139488756 -3.03139488756
+ Force two-norm initial, final = 51.7975 0.00951208
+ Force max component initial, final = 38.3845 0.00429369
+ Final line search alpha, max atom move = 0.165786 0.000711832
+ Iterations, force evaluations = 1477 2954
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.16982 | 0.17493 | 0.18263 | 1.2 | 54.61
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.032802 | 0.041339 | 0.047369 | 2.7 | 12.91
+Output | 0.0013659 | 0.0013915 | 0.0014555 | 0.1 | 0.43
+Modify | 0.0018022 | 0.0019018 | 0.0019994 | 0.2 | 0.59
+Other | | 0.1007 | | | 31.45
+
+Nlocal: 200 ave 203 max 197 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+Nghost: 181.5 ave 183 max 181 min
+Histogram: 3 0 0 0 0 0 0 0 0 1
+Neighs: 1815.5 ave 1838 max 1771 min
+Histogram: 1 0 0 0 0 0 0 1 0 2
+
+Total # of neighbors = 7262
+Ave neighs/atom = 9.0775
+Neighbor list builds = 0
+Dangerous builds = 0
+
+# Final refinement uses nreset to eliminate stress offset
+
+fix 3 all box/relax x 1.0 y 2.0 vmax 1.0e-3 nreset 100
+
+minimize 0.0 1.0e-4 10000 100000
+Memory usage per processor = 3.60176 Mbytes
+Step Temp PotEng Pxx Pyy Pxy 3 emin
+ 7607 0 -3.0303527 1.0000104 2.0000131 0.10770259 3.5527137e-17 -3.0303527
+ 7650 0 -3.030353 0.9999904 2.0000076 0.10770145 2.9878713e-07 -3.0303527
+ 7700 0 -3.0303532 1.0000001 1.9999991 0.10770283 4.6315231e-07 -3.0303527
+ 7750 0 -3.0303531 1.0000061 2.0000052 0.10770517 2.2696958e-08 -3.0303531
+ 7800 0 -3.0303533 0.99999944 1.999999 0.10770496 1.5707701e-07 -3.0303531
+ 7850 0 -3.0303533 0.99999877 1.9999985 0.10770396 4.6999275e-08 -3.0303532
+ 7900 0 -3.0303533 0.99999936 2 0.10770371 6.8328929e-09 -3.0303532
+ 7950 0 -3.0303532 0.99999993 2.0000004 0.10770354 -1.6637037e-08 -3.0303533
+ 8000 0 -3.0303532 1.0000004 2.0000006 0.10770361 -2.6542248e-08 -3.0303533
+ 8050 0 -3.0303532 1.0000003 2.0000002 0.1077037 1.7569483e-10 -3.0303532
+ 8100 0 -3.0303532 1.0000002 2.0000001 0.10770386 3.0847712e-09 -3.0303532
+ 8150 0 -3.0303532 1.0000003 2.0000002 0.10770398 -1.4421314e-09 -3.0303532
+ 8200 0 -3.0303532 1.0000001 2.0000001 0.10770407 7.0744514e-10 -3.0303532
+ 8201 0 -3.0303532 0.99999993 2 0.10770406 3.9670625e-09 -3.0303532
+Loop time of 0.129254 on 4 procs for 594 steps with 800 atoms
+
+99.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+Minimization stats:
+ Stopping criterion = force tolerance
+ Energy initial, next-to-last, final =
+ -3.03035270564 -3.0303532347 -3.0303532347
+ Force two-norm initial, final = 0.0165847 8.42164e-05
+ Force max component initial, final = 0.0112809 5.39223e-05
+ Final line search alpha, max atom move = 1 5.39223e-05
+ Iterations, force evaluations = 594 1188
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.068712 | 0.07072 | 0.073833 | 0.7 | 54.71
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.01326 | 0.016652 | 0.019008 | 1.7 | 12.88
+Output | 0.00053024 | 0.00053924 | 0.00056386 | 0.1 | 0.42
+Modify | 0.00071311 | 0.00077671 | 0.00081825 | 0.2 | 0.60
+Other | | 0.04057 | | | 31.39
+
+Nlocal: 200 ave 203 max 197 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+Nghost: 181.5 ave 183 max 181 min
+Histogram: 3 0 0 0 0 0 0 0 0 1
+Neighs: 1816.25 ave 1841 max 1772 min
+Histogram: 1 0 0 0 0 0 1 0 1 1
+
+Total # of neighbors = 7265
+Ave neighs/atom = 9.08125
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Total wall time: 0:00:01
diff --git a/examples/min/log.15Feb16.min.g++.1 b/examples/min/log.15Feb16.min.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..478289285c8ff62824c63ddeef229b7961f1abcb
--- /dev/null
+++ b/examples/min/log.15Feb16.min.g++.1
@@ -0,0 +1,141 @@
+LAMMPS (15 Feb 2016)
+# 2d Lennard-Jones melt and subsequent energy minimization
+
+units lj
+dimension 2
+atom_style atomic
+
+lattice sq2 0.8442
+Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
+region box block 0 20 0 20 -0.1 0.1
+create_box 1 box
+Created orthogonal box = (0 0 -0.153919) to (30.7838 30.7838 0.153919)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 800 atoms
+mass 1 1.0
+
+velocity all create 5.0 87287 loop geom
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+pair_modify shift yes
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nve
+fix 2 all enforce2d
+
+#dump 1 all atom 100 dump.min
+
+#dump 2 all image 50 image.*.jpg type type # zoom 1.6 adiam 1.5
+#dump_modify 2 pad 4
+
+#dump 3 all movie 50 movie.mpg type type # zoom 1.6 adiam 1.5
+#dump_modify 3 pad 4
+
+thermo 100
+
+run 1000
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4 -> bins = 22 22 1
+Memory usage per processor = 2.47843 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 5 -2.461717 0 2.532033 5.0190509
+ 100 3.2788864 -0.74311698 0 2.5316708 15.912832
+ 200 3.3041082 -0.77000277 0 2.5299752 15.602653
+ 300 3.3840228 -0.84859211 0 2.5312006 15.188203
+ 400 3.3916063 -0.85694601 0 2.5304208 15.383853
+ 500 3.3136052 -0.77935263 0 2.5301106 15.833296
+ 600 3.3888915 -0.85213743 0 2.532518 15.162759
+ 700 3.2123675 -0.67642318 0 2.5319289 16.310565
+ 800 3.3016275 -0.76569171 0 2.5318087 15.639335
+ 900 3.4639203 -0.92788002 0 2.5317104 14.765912
+ 1000 3.3256788 -0.79078181 0 2.5307399 15.599298
+Loop time of 0.200054 on 1 procs for 1000 steps with 800 atoms
+
+Performance: 2159417.710 tau/day, 4998.652 timesteps/s
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.12834 | 0.12834 | 0.12834 | 0.0 | 64.15
+Neigh | 0.051023 | 0.051023 | 0.051023 | 0.0 | 25.50
+Comm | 0.0045159 | 0.0045159 | 0.0045159 | 0.0 | 2.26
+Output | 9.2268e-05 | 9.2268e-05 | 9.2268e-05 | 0.0 | 0.05
+Modify | 0.011642 | 0.011642 | 0.011642 | 0.0 | 5.82
+Other | | 0.004437 | | | 2.22
+
+Nlocal: 800 ave 800 max 800 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 317 ave 317 max 317 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 7743 ave 7743 max 7743 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 7743
+Ave neighs/atom = 9.67875
+Neighbor list builds = 203
+Dangerous builds = 0
+
+neigh_modify delay 0 every 1 check yes
+
+#dump_modify 1 every 25
+
+thermo 50
+minimize 1.0e-6 0.001 1000 10000
+Memory usage per processor = 3.60343 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 1000 3.3256788 -0.79078181 0 2.5307399 15.599298
+ 1050 3.3256788 -2.8361415 0 0.48538014 1.6090001
+ 1100 3.3256788 -2.8661626 0 0.45535906 1.6175322
+ 1150 3.3256788 -2.8783275 0 0.44319421 1.6293715
+ 1200 3.3256788 -2.8838202 0 0.43770144 1.6393211
+ 1250 3.3256788 -2.8956657 0 0.42585599 1.604841
+ 1300 3.3256788 -2.9039122 0 0.41760945 1.6594733
+ 1350 3.3256788 -2.9100776 0 0.4114441 1.7004165
+ 1400 3.3256788 -2.9131297 0 0.40839199 1.7078217
+ 1450 3.3256788 -2.9167506 0 0.40477104 1.7780477
+ 1475 3.3256788 -2.9169436 0 0.4045781 1.7914542
+Loop time of 0.241237 on 1 procs for 475 steps with 800 atoms
+
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+Minimization stats:
+ Stopping criterion = energy tolerance
+ Energy initial, next-to-last, final =
+ -0.790781812776 -2.9169407756 -2.91694356781
+ Force two-norm initial, final = 1905.47 0.794548
+ Force max component initial, final = 343.392 0.268404
+ Final line search alpha, max atom move = 0.347566 0.0932881
+ Iterations, force evaluations = 475 940
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.1979 | 0.1979 | 0.1979 | 0.0 | 82.04
+Neigh | 0.021076 | 0.021076 | 0.021076 | 0.0 | 8.74
+Comm | 0.0028479 | 0.0028479 | 0.0028479 | 0.0 | 1.18
+Output | 8.9169e-05 | 8.9169e-05 | 8.9169e-05 | 0.0 | 0.04
+Modify | 0.002037 | 0.002037 | 0.002037 | 0.0 | 0.84
+Other | | 0.01728 | | | 7.16
+
+Nlocal: 800 ave 800 max 800 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 329 ave 329 max 329 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 6957 ave 6957 max 6957 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 6957
+Ave neighs/atom = 8.69625
+Neighbor list builds = 85
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/min/log.15Feb16.min.g++.4 b/examples/min/log.15Feb16.min.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..ae22d29997a5409a70d6085282f7a3da06111bb1
--- /dev/null
+++ b/examples/min/log.15Feb16.min.g++.4
@@ -0,0 +1,137 @@
+LAMMPS (15 Feb 2016)
+# 2d Lennard-Jones melt and subsequent energy minimization
+
+units lj
+dimension 2
+atom_style atomic
+
+lattice sq2 0.8442
+Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
+region box block 0 20 0 20 -0.1 0.1
+create_box 1 box
+Created orthogonal box = (0 0 -0.153919) to (30.7838 30.7838 0.153919)
+ 2 by 2 by 1 MPI processor grid
+create_atoms 1 box
+Created 800 atoms
+mass 1 1.0
+
+velocity all create 5.0 87287 loop geom
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+pair_modify shift yes
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nve
+fix 2 all enforce2d
+
+#dump 1 all atom 100 dump.min
+
+#dump 2 all image 50 image.*.jpg type type # zoom 1.6 adiam 1.5
+#dump_modify 2 pad 4
+
+#dump 3 all movie 50 movie.mpg type type # zoom 1.6 adiam 1.5
+#dump_modify 3 pad 4
+
+thermo 100
+
+run 1000
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4 -> bins = 22 22 1
+Memory usage per processor = 2.47676 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 5 -2.461717 0 2.532033 5.0190509
+ 100 3.2788864 -0.74311698 0 2.5316708 15.912832
+ 200 3.3041082 -0.77000277 0 2.5299752 15.602653
+ 300 3.3840228 -0.84859211 0 2.5312006 15.188203
+ 400 3.3916063 -0.85694601 0 2.5304208 15.383853
+ 500 3.3136053 -0.77935264 0 2.5301106 15.833296
+ 600 3.3888915 -0.85213737 0 2.532518 15.162759
+ 700 3.2123636 -0.67641846 0 2.5319297 16.31059
+ 800 3.3016408 -0.76570603 0 2.5318077 15.639259
+ 900 3.4621697 -0.92610292 0 2.5317391 14.773473
+ 1000 3.3058424 -0.77076863 0 2.5309414 15.708171
+Loop time of 0.0792709 on 4 procs for 1000 steps with 800 atoms
+
+Performance: 5449666.950 tau/day, 12614.970 timesteps/s
+94.3% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.033109 | 0.03398 | 0.035743 | 0.6 | 42.87
+Neigh | 0.013423 | 0.013508 | 0.013607 | 0.1 | 17.04
+Comm | 0.019584 | 0.022177 | 0.023639 | 1.0 | 27.98
+Output | 0.0001688 | 0.00018328 | 0.00020313 | 0.1 | 0.23
+Modify | 0.0031462 | 0.0032172 | 0.0032594 | 0.1 | 4.06
+Other | | 0.006205 | | | 7.83
+
+Nlocal: 200 ave 202 max 196 min
+Histogram: 1 0 0 0 0 0 0 0 2 1
+Nghost: 170.25 ave 174 max 167 min
+Histogram: 1 0 1 0 0 1 0 0 0 1
+Neighs: 1934.75 ave 1972 max 1873 min
+Histogram: 1 0 0 0 0 0 1 0 1 1
+
+Total # of neighbors = 7739
+Ave neighs/atom = 9.67375
+Neighbor list builds = 203
+Dangerous builds = 0
+
+neigh_modify delay 0 every 1 check yes
+
+#dump_modify 1 every 25
+
+thermo 50
+minimize 1.0e-6 0.001 1000 10000
+Memory usage per processor = 3.60176 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 1000 3.3058424 -0.77076863 0 2.5309414 15.708171
+ 1050 3.3058424 -2.8318266 0 0.46988351 1.5980106
+ 1100 3.3058424 -2.8658339 0 0.43587618 1.7013061
+ 1150 3.3058424 -2.8788056 0 0.42290443 1.6855503
+ 1200 3.3058424 -2.8831122 0 0.41859789 1.6869035
+ 1250 3.3058424 -2.8877971 0 0.413913 1.7276622
+ 1300 3.3058424 -2.8887969 0 0.41291311 1.7424655
+Loop time of 0.053865 on 4 procs for 300 steps with 800 atoms
+
+98.4% CPU use with 4 MPI tasks x no OpenMP threads
+
+Minimization stats:
+ Stopping criterion = energy tolerance
+ Energy initial, next-to-last, final =
+ -0.770768629298 -2.88879411525 -2.88879694984
+ Force two-norm initial, final = 1950.95 0.825241
+ Force max component initial, final = 374.098 0.224821
+ Final line search alpha, max atom move = 0.410301 0.0922441
+ Iterations, force evaluations = 300 595
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.032029 | 0.032993 | 0.034442 | 0.5 | 61.25
+Neigh | 0.0037003 | 0.0038341 | 0.0038917 | 0.1 | 7.12
+Comm | 0.0051906 | 0.0071514 | 0.0082016 | 1.4 | 13.28
+Output | 8.1778e-05 | 8.5294e-05 | 9.5844e-05 | 0.1 | 0.16
+Modify | 0.00035262 | 0.00036818 | 0.00039029 | 0.1 | 0.68
+Other | | 0.009433 | | | 17.51
+
+Nlocal: 200 ave 202 max 196 min
+Histogram: 1 0 0 0 0 0 1 0 0 2
+Nghost: 172.5 ave 175 max 169 min
+Histogram: 1 0 0 1 0 0 0 0 0 2
+Neighs: 1757 ave 1793 max 1721 min
+Histogram: 1 0 1 0 0 0 0 1 0 1
+
+Total # of neighbors = 7028
+Ave neighs/atom = 8.785
+Neighbor list builds = 59
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/msst/log.15Feb16.msst.g++.1 b/examples/msst/log.15Feb16.msst.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..fa20c76530dcb6f81d01c3d682566b69ba7fa8df
--- /dev/null
+++ b/examples/msst/log.15Feb16.msst.g++.1
@@ -0,0 +1,160 @@
+LAMMPS (15 Feb 2016)
+# LJ test of msst shock dynamics
+
+# Energy in eV, time in ps, distance in angstroms.
+units metal
+boundary p p p
+
+atom_style atomic
+timestep 1e-03
+
+lattice fcc 5.3589
+Lattice spacing in x,y,z = 5.3589 5.3589 5.3589
+
+## Specify the box as a given number of unit cells.
+region box1 block 0 18 0 18 0 18 units lattice
+
+## Instantiate the system.
+create_box 1 box1
+Created orthogonal box = (0 0 0) to (96.4602 96.4602 96.4602)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 region box1
+Created 23328 atoms
+
+mass 1 40.00
+
+# Initial velocities correspond to around 300K.
+velocity all create 600.0 9999
+
+pair_style lj/cut 10
+pair_coeff 1 1 0.01032 3.405
+
+timestep 2e-3
+
+# Equilibrate the system
+fix 2 all nve
+thermo 10
+
+run 100
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 12
+ ghost atom cutoff = 12
+ binsize = 6 -> bins = 17 17 17
+Memory usage per processor = 7.53726 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 600 -1943.9014 0 -134.75058 992.06384
+ 10 586.44651 -1917.3971 0 -149.11346 1306.17
+ 20 539.94305 -1778.786 0 -150.72199 2492.7873
+ 30 449.49509 -1506.4706 0 -151.12989 4667.6248
+ 40 331.86049 -1151.7344 0 -151.09164 7379.764
+ 50 258.27083 -929.8024 0 -151.05092 9103.558
+ 60 256.1869 -923.58742 0 -151.1195 9252.9158
+ 70 281.76061 -1000.7367 0 -151.1576 8739.2518
+ 80 300.28534 -1056.589 0 -151.15321 8324.8812
+ 90 305.83368 -1073.3097 0 -151.14426 8175.2478
+ 100 304.06857 -1067.9843 0 -151.14112 8191.234
+Loop time of 3.56196 on 1 procs for 100 steps with 23328 atoms
+
+Performance: 4.851 ns/day, 4.947 hours/ns, 28.074 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 3.404 | 3.404 | 3.404 | 0.0 | 95.56
+Neigh | 0.069748 | 0.069748 | 0.069748 | 0.0 | 1.96
+Comm | 0.020276 | 0.020276 | 0.020276 | 0.0 | 0.57
+Output | 0.00094318 | 0.00094318 | 0.00094318 | 0.0 | 0.03
+Modify | 0.03792 | 0.03792 | 0.03792 | 0.0 | 1.06
+Other | | 0.02909 | | | 0.82
+
+Nlocal: 23328 ave 23328 max 23328 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 22235 ave 22235 max 22235 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 2.18372e+06 ave 2.18372e+06 max 2.18372e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 2183715
+Ave neighs/atom = 93.6092
+Neighbor list builds = 1
+Dangerous builds = 0
+unfix 2
+
+# MSST fix
+fix msst all msst z 28.0 q 200 mu 3e2 tscale 0.01
+MSST parameters:
+ Shock in z direction
+ Cell mass-like parameter qmass (units of mass^2/length^4) = 2.00000e+02
+ Shock velocity = 2.80000e+01
+ Artificial viscosity (units of mass/length/time) = 3.00000e+02
+ Initial pressure calculated on first step
+ Initial volume calculated on first step
+ Initial energy calculated on first step
+
+# this is needed to make etotal equal the MSST conserved quantity
+fix_modify msst energy yes
+
+variable dhug equal f_msst[1]
+variable dray equal f_msst[2]
+variable lgr_vel equal f_msst[3]
+variable lgr_pos equal f_msst[4]
+
+thermo_style custom step temp ke pe lx ly lz pxx pyy pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos f_msst
+
+#dump id all atom 50 dump.msst
+
+#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 3
+
+#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 3
+
+run 100
+Fix MSST v0 = 8.97521e+05
+Fix MSST p0 = 8.10679e+03
+Fix MSST e0 = to be -1.51141e+02
+Fix MSST initial strain rate of -3.20112e-02 established by reducing temperature by factor of 1.00000e-02
+Memory usage per processor = 7.54369 Mbytes
+Step Temp KinEng PotEng Lx Ly Lz Pxx Pyy Pzz TotEng dhug dray lgr_vel lgr_pos msst
+ 100 301.02788 907.67474 -1058.8159 96.4602 96.4602 96.4602 8242.1214 8202.9779 8095.8693 -151.14112 1.5203428 -10.919311 0 0 9.1684318
+ 110 297.71411 897.68288 -1048.8859 96.4602 96.4602 96.399397 8347.6253 8303.7121 8220.7572 -151.20299 1.439058 28.652258 0.017649501 -0.55980494 5.7336721
+ 120 295.64308 891.43821 -1042.72 96.4602 96.4602 96.340496 8431.6742 8379.2441 8331.5304 -151.28174 1.3655893 56.776734 0.034747125 -1.119263 2.3808018
+ 130 296.02228 892.5816 -1043.9407 96.4602 96.4602 96.283468 8456.2492 8412.6368 8392.5853 -151.35912 1.2945465 37.811981 0.05130089 -1.6783851 -0.87840575
+ 140 298.19024 899.11855 -1050.5482 96.4602 96.4602 96.228236 8430.5151 8415.6802 8414.2537 -151.42965 1.2243399 -18.01985 0.067333442 -2.2371818 -4.0330712
+ 150 300.86421 907.18122 -1058.6966 96.4602 96.4602 96.174681 8399.4697 8396.2236 8420.9004 -151.51534 1.1598278 -86.5197 0.082879112 -2.7956634 -7.0824881
+ 160 303.34119 914.64996 -1066.2388 96.4602 96.4602 96.122673 8388.3438 8360.5024 8428.751 -151.58881 1.0977647 -151.64553 0.097975827 -3.353839 -10.033902
+ 170 304.87769 919.28288 -1070.961 96.4602 96.4602 96.072088 8408.8694 8333.4337 8449.5665 -151.67812 1.044322 -201.80899 0.11265931 -3.9117174 -12.897768
+ 180 304.99 919.62151 -1071.3588 96.4602 96.4602 96.022824 8461.5542 8343.1436 8484.9824 -151.73733 0.99203387 -235.51793 0.12695926 -4.4693063 -15.685622
+ 190 305.1148 919.99782 -1071.7807 96.4602 96.4602 95.9748 8498.7562 8371.4217 8514.4473 -151.78288 0.93937416 -273.43964 0.1408996 -5.0266132 -18.403999
+ 200 306.45829 924.0488 -1075.8787 96.4602 96.4602 95.927931 8488.9509 8385.2408 8529.6443 -151.82991 0.88654815 -324.00777 0.15450451 -5.583645 -21.055149
+Loop time of 4.87683 on 1 procs for 100 steps with 23328 atoms
+
+Performance: 3.543 ns/day, 6.773 hours/ns, 20.505 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 3.4604 | 3.4604 | 3.4604 | 0.0 | 70.96
+Neigh | 0.13708 | 0.13708 | 0.13708 | 0.0 | 2.81
+Comm | 0.018285 | 0.018285 | 0.018285 | 0.0 | 0.37
+Output | 0.01176 | 0.01176 | 0.01176 | 0.0 | 0.24
+Modify | 1.219 | 1.219 | 1.219 | 0.0 | 25.00
+Other | | 0.03037 | | | 0.62
+
+Nlocal: 23328 ave 23328 max 23328 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 22205 ave 22205 max 22205 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 2.18349e+06 ave 2.18349e+06 max 2.18349e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 2183494
+Ave neighs/atom = 93.5997
+Neighbor list builds = 2
+Dangerous builds = 0
+Total wall time: 0:00:08
diff --git a/examples/msst/log.15Feb16.msst.g++.4 b/examples/msst/log.15Feb16.msst.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..7cbebcd5d3317f0fbbb7f71b6123ea1793e57142
--- /dev/null
+++ b/examples/msst/log.15Feb16.msst.g++.4
@@ -0,0 +1,160 @@
+LAMMPS (15 Feb 2016)
+# LJ test of msst shock dynamics
+
+# Energy in eV, time in ps, distance in angstroms.
+units metal
+boundary p p p
+
+atom_style atomic
+timestep 1e-03
+
+lattice fcc 5.3589
+Lattice spacing in x,y,z = 5.3589 5.3589 5.3589
+
+## Specify the box as a given number of unit cells.
+region box1 block 0 18 0 18 0 18 units lattice
+
+## Instantiate the system.
+create_box 1 box1
+Created orthogonal box = (0 0 0) to (96.4602 96.4602 96.4602)
+ 1 by 2 by 2 MPI processor grid
+create_atoms 1 region box1
+Created 23328 atoms
+
+mass 1 40.00
+
+# Initial velocities correspond to around 300K.
+velocity all create 600.0 9999
+
+pair_style lj/cut 10
+pair_coeff 1 1 0.01032 3.405
+
+timestep 2e-3
+
+# Equilibrate the system
+fix 2 all nve
+thermo 10
+
+run 100
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 12
+ ghost atom cutoff = 12
+ binsize = 6 -> bins = 17 17 17
+Memory usage per processor = 4.74184 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 600 -1943.9014 0 -134.75058 992.06384
+ 10 586.47212 -1917.4465 0 -149.08565 1305.7368
+ 20 540.13678 -1779.3375 0 -150.68935 2488.8545
+ 30 450.11466 -1508.2891 0 -151.08028 4655.1306
+ 40 332.99843 -1155.1208 0 -151.04685 7357.5162
+ 50 259.2571 -932.72753 0 -151.0022 9086.2087
+ 60 256.22581 -923.67654 0 -151.0913 9257.1571
+ 70 281.12085 -998.79866 0 -151.14863 8759.7887
+ 80 299.37658 -1053.8476 0 -151.1519 8352.9467
+ 90 304.24026 -1068.4941 0 -151.13319 8218.1594
+ 100 301.9683 -1061.6332 0 -151.12284 8244.1277
+Loop time of 0.933348 on 4 procs for 100 steps with 23328 atoms
+
+Performance: 18.514 ns/day, 1.296 hours/ns, 107.141 timesteps/s
+99.9% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.86277 | 0.86536 | 0.87057 | 0.3 | 92.72
+Neigh | 0.017456 | 0.017565 | 0.017691 | 0.1 | 1.88
+Comm | 0.026787 | 0.033015 | 0.037011 | 2.1 | 3.54
+Output | 0.00049233 | 0.00060636 | 0.00074911 | 0.4 | 0.06
+Modify | 0.0094292 | 0.0099058 | 0.010101 | 0.3 | 1.06
+Other | | 0.0069 | | | 0.74
+
+Nlocal: 5832 ave 5850 max 5813 min
+Histogram: 1 0 0 0 1 1 0 0 0 1
+Nghost: 10571 ave 10590 max 10553 min
+Histogram: 1 0 0 0 1 1 0 0 0 1
+Neighs: 545762 ave 548069 max 543643 min
+Histogram: 1 0 0 1 0 1 0 0 0 1
+
+Total # of neighbors = 2183047
+Ave neighs/atom = 93.5805
+Neighbor list builds = 1
+Dangerous builds = 0
+unfix 2
+
+# MSST fix
+fix msst all msst z 28.0 q 200 mu 3e2 tscale 0.01
+MSST parameters:
+ Shock in z direction
+ Cell mass-like parameter qmass (units of mass^2/length^4) = 2.00000e+02
+ Shock velocity = 2.80000e+01
+ Artificial viscosity (units of mass/length/time) = 3.00000e+02
+ Initial pressure calculated on first step
+ Initial volume calculated on first step
+ Initial energy calculated on first step
+
+# this is needed to make etotal equal the MSST conserved quantity
+fix_modify msst energy yes
+
+variable dhug equal f_msst[1]
+variable dray equal f_msst[2]
+variable lgr_vel equal f_msst[3]
+variable lgr_pos equal f_msst[4]
+
+thermo_style custom step temp ke pe lx ly lz pxx pyy pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos f_msst
+
+#dump id all atom 50 dump.msst
+
+#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 3
+
+#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 3
+
+run 100
+Fix MSST v0 = 8.97521e+05
+Fix MSST p0 = 8.18624e+03
+Fix MSST e0 = to be -1.51123e+02
+Fix MSST initial strain rate of -3.19005e-02 established by reducing temperature by factor of 1.00000e-02
+Memory usage per processor = 4.74184 Mbytes
+Step Temp KinEng PotEng Lx Ly Lz Pxx Pyy Pzz TotEng dhug dray lgr_vel lgr_pos msst
+ 100 298.94862 901.40524 -1052.5281 96.4602 96.4602 96.4602 8270.9151 8253.4662 8175.4946 -151.12284 1.5098415 -10.744684 0 0 9.1051034
+ 110 296.49826 894.01679 -1045.224 96.4602 96.4602 96.399609 8338.4937 8340.5504 8294.9909 -151.20723 1.4327442 23.73173 0.017588167 -0.55980562 5.6560557
+ 120 295.97607 892.44225 -1043.7239 96.4602 96.4602 96.340904 8377.6797 8385.921 8378.3042 -151.28169 1.3584606 24.672199 0.034628719 -1.1192655 2.2953307
+ 130 297.34893 896.58179 -1047.945 96.4602 96.4602 96.284029 8379.2516 8394.8806 8416.2669 -151.36322 1.2881444 -17.170168 0.051138087 -1.6783905 -0.96527961
+ 140 299.71946 903.72952 -1055.1787 96.4602 96.4602 96.22888 8357.0358 8388.6743 8424.3188 -151.44922 1.221125 -86.501161 0.067146366 -2.2371908 -4.1195182
+ 150 301.79241 909.97998 -1061.4976 96.4602 96.4602 96.175327 8332.7118 8393.7027 8434.6177 -151.51765 1.1560248 -151.34689 0.082691635 -2.7956762 -7.172084
+ 160 303.18249 914.17141 -1065.7667 96.4602 96.4602 96.123244 8321.1154 8413.1248 8454.5596 -151.59527 1.0977348 -204.4864 0.097810061 -3.3538554 -10.134387
+ 170 304.34089 917.66428 -1069.3198 96.4602 96.4602 96.072522 8327.6227 8431.1177 8467.92 -151.65554 1.0390628 -262.29751 0.11253339 -3.9117366 -13.01442
+ 180 305.86343 922.25514 -1073.9633 96.4602 96.4602 96.023049 8345.1853 8432.5201 8461.3276 -151.70813 0.97863988 -338.30793 0.12689398 -4.4693274 -15.815462
+ 190 307.44054 927.01052 -1078.7892 96.4602 96.4602 95.9747 8368.4081 8427.5109 8450.584 -151.77867 0.92329631 -416.89333 0.1409285 -5.0266346 -18.541801
+ 200 308.43619 930.01265 -1081.8521 96.4602 96.4602 95.927349 8393.2058 8443.1265 8454.6733 -151.83947 0.8723277 -479.24592 0.1546734 -5.5836644 -21.20378
+Loop time of 1.2639 on 4 procs for 100 steps with 23328 atoms
+
+Performance: 13.672 ns/day, 1.755 hours/ns, 79.120 timesteps/s
+99.9% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.86747 | 0.87285 | 0.87567 | 0.3 | 69.06
+Neigh | 0.035299 | 0.03557 | 0.035746 | 0.1 | 2.81
+Comm | 0.028839 | 0.031931 | 0.038177 | 2.0 | 2.53
+Output | 0.0037065 | 0.0037336 | 0.0038128 | 0.1 | 0.30
+Modify | 0.31184 | 0.31328 | 0.31455 | 0.2 | 24.79
+Other | | 0.006528 | | | 0.52
+
+Nlocal: 5832 ave 5874 max 5803 min
+Histogram: 2 0 0 0 0 1 0 0 0 1
+Nghost: 10563.8 ave 10588 max 10526 min
+Histogram: 1 0 0 0 1 0 0 0 0 2
+Neighs: 545708 ave 550787 max 542668 min
+Histogram: 2 0 0 0 1 0 0 0 0 1
+
+Total # of neighbors = 2182834
+Ave neighs/atom = 93.5714
+Neighbor list builds = 2
+Dangerous builds = 0
+Total wall time: 0:00:02
diff --git a/examples/nb3b/log.15Feb16.nb3b.g++.1 b/examples/nb3b/log.15Feb16.nb3b.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..2259aa3920b24525389fd1303f1cef225a98866b
--- /dev/null
+++ b/examples/nb3b/log.15Feb16.nb3b.g++.1
@@ -0,0 +1,173 @@
+LAMMPS (15 Feb 2016)
+# test of NB3B pair style with pair hybrid and KSpace solver
+
+units real
+atom_style full
+
+bond_style morse
+angle_style none
+dihedral_style none
+improper_style none
+
+read_data data.nb3b
+ orthogonal box = (0 0 0) to (22.5907 22.359 23.4708)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 1400 atoms
+ scanning bonds ...
+ 1 = max bonds/atom
+ reading bonds ...
+ 560 bonds
+ 1 = max # of 1-2 neighbors
+ 0 = max # of 1-3 neighbors
+ 0 = max # of 1-4 neighbors
+ 1 = max # of special neighbors
+
+pair_style hybrid/overlay nb3b/harmonic lj/cut/coul/long 10.0
+pair_coeff * * nb3b/harmonic MOH.nb3b.harmonic M O H
+Reading potential file MOH.nb3b.harmonic with DATE: 2013-06-28
+pair_modify mix arithmetic
+
+pair_coeff 1 1 lj/cut/coul/long 0.000000903 5.264325869
+pair_coeff 1 2 lj/cut/coul/long 0.000374621 4.214922978
+pair_coeff 1 3 lj/cut/coul/long 0 2.632162934
+pair_coeff 2 2 lj/cut/coul/long 0.155416412 3.165520088
+pair_coeff 2 3 lj/cut/coul/long 0 1.582760044
+pair_coeff 3 3 lj/cut/coul/long 0 0
+
+kspace_style ewald/disp 0.0001
+
+neighbor 2.0 bin
+neigh_modify delay 5
+special_bonds lj/coul 0.0 0.0 1.0
+ 1 = max # of 1-2 neighbors
+ 0 = max # of 1-3 neighbors
+ 1 = max # of special neighbors
+
+thermo_style custom step etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press lx ly lz xy xz yz vol
+
+timestep 1.0
+run_style respa 2 2 pair 1 kspace 2
+Respa levels:
+ 1 = bond angle dihedral improper pair
+ 2 = kspace
+
+thermo 50
+
+### Minimize forces in structure ###
+
+minimize 1.0e-06 1.0e-08 1000 10000
+WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
+EwaldDisp initialization ...
+WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:220)
+ G vector = 0.269426
+WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:220)
+Neighbor list info ...
+ 4 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 12
+ ghost atom cutoff = 12
+ binsize = 6 -> bins = 4 4 4
+ vectors: nbox = 6, nkvec = 478
+Memory usage per processor = 16.5817 Mbytes
+Step TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Lx Ly Lz Xy Xz Yz Volume
+ 0 -61505.983 0 0 -61505.983 198.11978 0 0 0 5426.6842 -20935.868 -46194.919 979.72809 22.5907 22.359 23.4708 0 0 0 11855.229
+ 4 -61506.604 0 0 -61506.604 198.69671 0 0 0 5460.0893 -20970.348 -46195.042 1657.4299 22.5907 22.359 23.4708 0 0 0 11855.229
+Loop time of 0.848486 on 1 procs for 4 steps with 1400 atoms
+
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+Minimization stats:
+ Stopping criterion = energy tolerance
+ Energy initial, next-to-last, final =
+ -61505.9829 -61506.5882212 -61506.6041431
+ Force two-norm initial, final = 17.893 3.40908
+ Force max component initial, final = 0.757547 0.131738
+ Final line search alpha, max atom move = 0.394559 0.0519786
+ Iterations, force evaluations = 4 8
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.77228 | 0.77228 | 0.77228 | 0.0 | 91.02
+Bond | 0.00031042 | 0.00031042 | 0.00031042 | 0.0 | 0.04
+Kspace | 0.074903 | 0.074903 | 0.074903 | 0.0 | 8.83
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.00057626 | 0.00057626 | 0.00057626 | 0.0 | 0.07
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 0.0004158 | | | 0.05
+
+Nlocal: 1400 ave 1400 max 1400 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 10804 ave 10804 max 10804 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 596960 ave 596960 max 596960 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs: 1.19392e+06 ave 1.19392e+06 max 1.19392e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1193920
+Ave neighs/atom = 852.8
+Ave special neighs/atom = 0.8
+Neighbor list builds = 0
+Dangerous builds = 0
+
+### Run NVE to equilibrate velocities ###
+
+velocity all create 298.0 4928459 mom yes rot yes dist gaussian
+
+fix 1 all nve
+fix 2 all temp/rescale 10 298.0 298.0 25.0 1.0
+
+run 100
+EwaldDisp initialization ...
+WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:220)
+ G vector = 0.269426
+WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:220)
+Neighbor list info ...
+ 4 neighbor list requests
+ update every 1 steps, delay 5 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 12
+ ghost atom cutoff = 12
+ binsize = 6 -> bins = 4 4 4
+Memory usage per processor = 16.2067 Mbytes
+Step TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Lx Ly Lz Xy Xz Yz Volume
+ 4 -60263.898 1242.7057 298 -61506.604 198.69671 0 0 0 5460.0893 -20970.348 -46195.042 6449.147 22.5907 22.359 23.4708 0 0 0 11855.229
+ 50 -58769.885 1186.4036 284.49881 -59956.289 309.92499 0 0 0 6168.8458 -20249.062 -46185.998 21737.807 22.5907 22.359 23.4708 0 0 0 11855.229
+ 100 -58865.196 1242.7057 298 -60107.902 371.56168 0 0 0 6422.4016 -20716.005 -46185.86 22887.006 22.5907 22.359 23.4708 0 0 0 11855.229
+ 104 -58865.334 1260.1244 302.177 -60125.458 386.24491 0 0 0 6377.3686 -20705.327 -46183.745 19154.01 22.5907 22.359 23.4708 0 0 0 11855.229
+Loop time of 17.467 on 1 procs for 100 steps with 1400 atoms
+
+Performance: 0.495 ns/day, 48.519 hours/ns, 5.725 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 16.477 | 16.477 | 16.477 | 0.0 | 94.33
+Bond | 0.0069525 | 0.0069525 | 0.0069525 | 0.0 | 0.04
+Kspace | 0.84704 | 0.84704 | 0.84704 | 0.0 | 4.85
+Neigh | 0.10518 | 0.10518 | 0.10518 | 0.0 | 0.60
+Comm | 0.015078 | 0.015078 | 0.015078 | 0.0 | 0.09
+Output | 0.00010085 | 0.00010085 | 0.00010085 | 0.0 | 0.00
+Modify | 0.0071354 | 0.0071354 | 0.0071354 | 0.0 | 0.04
+Other | | 0.008824 | | | 0.05
+
+Nlocal: 1400 ave 1400 max 1400 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 10843 ave 10843 max 10843 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 595307 ave 595307 max 595307 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs: 1.19061e+06 ave 1.19061e+06 max 1.19061e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1190614
+Ave neighs/atom = 850.439
+Ave special neighs/atom = 0.8
+Neighbor list builds = 2
+Dangerous builds = 0
+Total wall time: 0:00:18
diff --git a/examples/nb3b/log.15Feb16.nb3b.g++.4 b/examples/nb3b/log.15Feb16.nb3b.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..b51ea7379bbbbd951276037d577c32a2b79fa696
--- /dev/null
+++ b/examples/nb3b/log.15Feb16.nb3b.g++.4
@@ -0,0 +1,173 @@
+LAMMPS (15 Feb 2016)
+# test of NB3B pair style with pair hybrid and KSpace solver
+
+units real
+atom_style full
+
+bond_style morse
+angle_style none
+dihedral_style none
+improper_style none
+
+read_data data.nb3b
+ orthogonal box = (0 0 0) to (22.5907 22.359 23.4708)
+ 2 by 1 by 2 MPI processor grid
+ reading atoms ...
+ 1400 atoms
+ scanning bonds ...
+ 1 = max bonds/atom
+ reading bonds ...
+ 560 bonds
+ 1 = max # of 1-2 neighbors
+ 0 = max # of 1-3 neighbors
+ 0 = max # of 1-4 neighbors
+ 1 = max # of special neighbors
+
+pair_style hybrid/overlay nb3b/harmonic lj/cut/coul/long 10.0
+pair_coeff * * nb3b/harmonic MOH.nb3b.harmonic M O H
+Reading potential file MOH.nb3b.harmonic with DATE: 2013-06-28
+pair_modify mix arithmetic
+
+pair_coeff 1 1 lj/cut/coul/long 0.000000903 5.264325869
+pair_coeff 1 2 lj/cut/coul/long 0.000374621 4.214922978
+pair_coeff 1 3 lj/cut/coul/long 0 2.632162934
+pair_coeff 2 2 lj/cut/coul/long 0.155416412 3.165520088
+pair_coeff 2 3 lj/cut/coul/long 0 1.582760044
+pair_coeff 3 3 lj/cut/coul/long 0 0
+
+kspace_style ewald/disp 0.0001
+
+neighbor 2.0 bin
+neigh_modify delay 5
+special_bonds lj/coul 0.0 0.0 1.0
+ 1 = max # of 1-2 neighbors
+ 0 = max # of 1-3 neighbors
+ 1 = max # of special neighbors
+
+thermo_style custom step etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press lx ly lz xy xz yz vol
+
+timestep 1.0
+run_style respa 2 2 pair 1 kspace 2
+Respa levels:
+ 1 = bond angle dihedral improper pair
+ 2 = kspace
+
+thermo 50
+
+### Minimize forces in structure ###
+
+minimize 1.0e-06 1.0e-08 1000 10000
+WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
+EwaldDisp initialization ...
+WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:220)
+ G vector = 0.269426
+WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:220)
+Neighbor list info ...
+ 4 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 12
+ ghost atom cutoff = 12
+ binsize = 6 -> bins = 4 4 4
+ vectors: nbox = 6, nkvec = 478
+Memory usage per processor = 16.9507 Mbytes
+Step TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Lx Ly Lz Xy Xz Yz Volume
+ 0 -61505.983 0 0 -61505.983 198.11978 0 0 0 5426.6842 -20935.868 -46194.919 979.72809 22.5907 22.359 23.4708 0 0 0 11855.229
+ 4 -61506.604 0 0 -61506.604 198.69671 0 0 0 5460.0893 -20970.348 -46195.042 1657.4299 22.5907 22.359 23.4708 0 0 0 11855.229
+Loop time of 0.254354 on 4 procs for 4 steps with 1400 atoms
+
+99.0% CPU use with 4 MPI tasks x no OpenMP threads
+
+Minimization stats:
+ Stopping criterion = energy tolerance
+ Energy initial, next-to-last, final =
+ -61505.9829 -61506.5882212 -61506.6041431
+ Force two-norm initial, final = 17.893 3.40908
+ Force max component initial, final = 0.757547 0.131738
+ Final line search alpha, max atom move = 0.394559 0.0519786
+ Iterations, force evaluations = 4 8
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.07247 | 0.17424 | 0.22771 | 14.9 | 68.50
+Bond | 8.5115e-05 | 9.495e-05 | 0.0001049 | 0.1 | 0.04
+Kspace | 0.024093 | 0.07615 | 0.17696 | 22.2 | 29.94
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.0019753 | 0.0034024 | 0.0047915 | 2.0 | 1.34
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 0.0004643 | | | 0.18
+
+Nlocal: 350 ave 399 max 305 min
+Histogram: 1 1 0 0 0 0 0 0 1 1
+Nghost: 6602 ave 6647 max 6553 min
+Histogram: 1 1 0 0 0 0 0 0 1 1
+Neighs: 149240 ave 170954 max 129384 min
+Histogram: 1 1 0 0 0 0 0 1 0 1
+FullNghs: 298480 ave 340157 max 260160 min
+Histogram: 1 1 0 0 0 0 0 0 1 1
+
+Total # of neighbors = 1193920
+Ave neighs/atom = 852.8
+Ave special neighs/atom = 0.8
+Neighbor list builds = 0
+Dangerous builds = 0
+
+### Run NVE to equilibrate velocities ###
+
+velocity all create 298.0 4928459 mom yes rot yes dist gaussian
+
+fix 1 all nve
+fix 2 all temp/rescale 10 298.0 298.0 25.0 1.0
+
+run 100
+EwaldDisp initialization ...
+WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:220)
+ G vector = 0.269426
+WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:220)
+Neighbor list info ...
+ 4 neighbor list requests
+ update every 1 steps, delay 5 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 12
+ ghost atom cutoff = 12
+ binsize = 6 -> bins = 4 4 4
+Memory usage per processor = 16.5757 Mbytes
+Step TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Lx Ly Lz Xy Xz Yz Volume
+ 4 -60263.898 1242.7057 298 -61506.604 198.69671 0 0 0 5460.0893 -20970.348 -46195.042 6449.147 22.5907 22.359 23.4708 0 0 0 11855.229
+ 50 -58769.885 1186.4036 284.49881 -59956.289 309.92499 0 0 0 6168.8458 -20249.062 -46185.998 21737.807 22.5907 22.359 23.4708 0 0 0 11855.229
+ 100 -58865.196 1242.7057 298 -60107.902 371.56168 0 0 0 6422.4016 -20716.005 -46185.86 22887.006 22.5907 22.359 23.4708 0 0 0 11855.229
+ 104 -58865.334 1260.1244 302.177 -60125.458 386.24491 0 0 0 6377.3686 -20705.327 -46183.745 19154.01 22.5907 22.359 23.4708 0 0 0 11855.229
+Loop time of 4.80696 on 4 procs for 100 steps with 1400 atoms
+
+Performance: 1.797 ns/day, 13.353 hours/ns, 20.803 timesteps/s
+99.4% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 1.4587 | 3.5531 | 4.4418 | 64.9 | 73.91
+Bond | 0.0018251 | 0.0019184 | 0.0019794 | 0.1 | 0.04
+Kspace | 0.21553 | 0.22335 | 0.231 | 1.4 | 4.65
+Neigh | 0.026918 | 0.02694 | 0.026957 | 0.0 | 0.56
+Comm | 0.096146 | 0.98534 | 3.08 | 123.3 | 20.50
+Output | 0.00012541 | 0.00017965 | 0.00030398 | 0.5 | 0.00
+Modify | 0.0023086 | 0.0030754 | 0.0038064 | 1.2 | 0.06
+Other | | 0.0131 | | | 0.27
+
+Nlocal: 350 ave 357 max 340 min
+Histogram: 1 0 0 0 0 0 1 1 0 1
+Nghost: 6639.25 ave 6657 max 6627 min
+Histogram: 1 1 0 0 0 1 0 0 0 1
+Neighs: 148827 ave 152055 max 145212 min
+Histogram: 1 0 0 0 0 2 0 0 0 1
+FullNghs: 297654 ave 303283 max 288784 min
+Histogram: 1 0 0 0 0 0 1 1 0 1
+
+Total # of neighbors = 1190614
+Ave neighs/atom = 850.439
+Ave special neighs/atom = 0.8
+Neighbor list builds = 2
+Dangerous builds = 0
+Total wall time: 0:00:05
diff --git a/examples/neb/log.15Feb16.neb.hop1.g++.4 b/examples/neb/log.15Feb16.neb.hop1.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..c6d97c389a7a1932544acf8b9a8fc161473064e8
--- /dev/null
+++ b/examples/neb/log.15Feb16.neb.hop1.g++.4
@@ -0,0 +1,10 @@
+LAMMPS (15 Feb 2016)
+Running on 4 partitions of processors
+Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
+0 4327.2753 2746.3378 0.3387091 5.0075576 4514.5424 0.42933428 0.42323635 1.8941131 0 -3.0535948 0.33333333 -2.6242605 0.66666667 -2.7623811 1 -3.0474969
+100 0.10482184 0.085218486 0.014588241 0.066178594 0.19602237 0.0070900402 0.0022691875 2.3031875 0 -3.0535967 0.31839181 -3.0473647 0.63987598 -3.0465067 1 -3.0487759
+111 0.096708467 0.07803707 0.013922973 0.05417562 0.2023467 0.0070871172 0.0022668002 2.3052945 0 -3.0535968 0.31853431 -3.0473633 0.64178871 -3.0465096 1 -3.0487764
+Climbing replica = 3
+Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
+111 0.2023467 0.1777038 0.013922973 0.05417562 0.2023467 0.0070871172 0.0022668002 2.3052945 0 -3.0535968 0.31853431 -3.0473633 0.64178871 -3.0465096 1 -3.0487764
+179 0.096874474 0.090676856 0.01040177 0.023364005 0.096874474 0.0071047642 0.0022856172 2.3122768 0 -3.0535969 0.31577311 -3.0473955 0.61798541 -3.0464922 1 -3.0487778
diff --git a/examples/neb/log.15Feb16.neb.hop2.g++.4 b/examples/neb/log.15Feb16.neb.hop2.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..5ff6468fa402cf504543049d3b462910d29baf8d
--- /dev/null
+++ b/examples/neb/log.15Feb16.neb.hop2.g++.4
@@ -0,0 +1,18 @@
+LAMMPS (15 Feb 2016)
+Running on 4 partitions of processors
+Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
+0 14.104748 10.419633 0.24852044 5.0039071 8.2116049 0.0018276223 0.00064050211 0.98401186 0 -3.0514921 0.33333333 -3.0496673 0.66666667 -3.0496645 1 -3.050305
+100 0.24646695 0.10792196 0.01781018 0.098854684 0.63725646 0.001516756 0.0015151635 1.165391 0 -3.0514939 0.2890334 -3.0503533 0.59718494 -3.0499771 1 -3.0514923
+200 0.061777741 0.050288749 0.012466513 0.020420207 0.88741041 0.0014465772 0.0014462528 1.1692938 0 -3.0514941 0.29975094 -3.0503052 0.62768286 -3.0500476 1 -3.0514938
+300 0.056346766 0.030000618 0.0093152917 0.013765031 1.0101529 0.0014069751 0.0014068154 1.1699608 0 -3.0514942 0.30992449 -3.0502613 0.64174291 -3.0500873 1 -3.0514941
+400 0.025589489 0.015671005 0.0061287063 0.008588518 1.1136424 0.001370987 0.0013709154 1.1704204 0 -3.0514943 0.32016645 -3.0502198 0.65324019 -3.0501233 1 -3.0514943
+500 0.014778626 0.0092108366 0.0042668521 0.0059963914 1.1636579 0.0013527466 0.0013527072 1.1706283 0 -3.0514944 0.32550275 -3.0501993 0.65875414 -3.0501416 1 -3.0514943
+600 0.08786211 0.020876327 0.0031421548 0.0051657363 1.1898894 0.0013430848 0.0013430599 1.1707681 0 -3.0514944 0.32831927 -3.0501889 0.66160681 -3.0501513 1 -3.0514944
+633 0.0098132678 0.0055392541 0.0030063464 0.0043091323 1.1924486 0.0013420127 0.0013419893 1.1707818 0 -3.0514944 0.32862625 -3.0501878 0.66191769 -3.0501524 1 -3.0514944
+Climbing replica = 3
+Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
+633 1.1924486 1.1648685 0.0030063464 0.0043091323 1.1924486 0.0013420127 0.0013419893 1.1707818 0 -3.0514944 0.32862625 -3.0501878 0.66191769 -3.0501524 1 -3.0514944
+733 0.095331134 0.089136608 0.0021551441 0.0031844438 0.043042998 0.0016022317 0.0016022168 1.170789 0 -3.0514944 0.29157063 -3.0503375 0.50358402 -3.0498922 1 -3.0514944
+833 0.10539135 0.030724373 0.0013749699 0.002221013 0.10539135 0.0016019798 0.001601971 1.1732118 0 -3.0514944 0.26249002 -3.0504848 0.50415223 -3.0498924 1 -3.0514944
+933 0.01883894 0.011496399 0.0011058925 0.0018178041 0.014621806 0.0016018934 0.0016018865 1.173866 0 -3.0514944 0.25788763 -3.0505113 0.50466375 -3.0498925 1 -3.0514944
+996 0.0082457876 0.0036336551 0.00077325986 0.0013910671 0.0068823708 0.0016018293 0.0016018244 1.174511 0 -3.0514944 0.2544553 -3.0505324 0.50520462 -3.0498926 1 -3.0514944
diff --git a/examples/neb/log.15Feb16.neb.sivac.g++.3 b/examples/neb/log.15Feb16.neb.sivac.g++.3
new file mode 100644
index 0000000000000000000000000000000000000000..dbc2f08929b7b31de3bc2d927ac20d3e803906ea
--- /dev/null
+++ b/examples/neb/log.15Feb16.neb.sivac.g++.3
@@ -0,0 +1,14 @@
+LAMMPS (15 Feb 2016)
+Running on 3 partitions of processors
+Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
+0 7.5525391 1.6345605 0.16683659 7.5525391 7.5525391 1.5383951 0 1.6207355 0 -2213.3343 0.5 -2212.4096 1 -2211.7959
+10 0.27332818 0.040944923 0.039164338 0.27332818 0.17804882 0.51235911 0.497084 1.6790474 0 -2213.3364 0.49024121 -2212.824 1 -2213.3211
+20 0.1820396 0.018049916 0.024428411 0.1820396 0.08601739 0.51038174 0.5080746 1.7224961 0 -2213.337 0.49199582 -2212.8266 1 -2213.3347
+30 0.043288796 0.0068108825 0.017372479 0.043288796 0.049466709 0.51032316 0.5095943 1.7304745 0 -2213.3371 0.49553568 -2212.8268 1 -2213.3364
+40 0.042139318 0.0037035773 0.011737071 0.042139318 0.026104737 0.51022733 0.5100163 1.7366752 0 -2213.3373 0.49838067 -2212.8271 1 -2213.3371
+50 0.025904252 0.0022808801 0.008105847 0.025904252 0.016908971 0.5101712 0.51008591 1.7391431 0 -2213.3373 0.49923347 -2212.8272 1 -2213.3373
+Climbing replica = 2
+Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
+50 0.025904252 0.0044134315 0.008105847 0.025904252 0.016908971 0.5101712 0.51008591 1.7391431 0 -2213.3373 0.49923347 -2212.8272 1 -2213.3373
+60 0.011518317 0.0013089596 0.0054472815 0.011518317 0.0091629734 0.51014415 0.51010903 1.7406815 0 -2213.3374 0.50065207 -2212.8272 1 -2213.3373
+61 0.0089525108 0.0012703829 0.0052524345 0.0088142351 0.0089525108 0.51014321 0.51010962 1.7407173 0 -2213.3374 0.50065779 -2212.8272 1 -2213.3373
diff --git a/examples/nemd/log.15Feb16.nemd.g++.1 b/examples/nemd/log.15Feb16.nemd.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..1cd4fd5ef45bba8a747ba8bcbb13ed9737658a6e
--- /dev/null
+++ b/examples/nemd/log.15Feb16.nemd.g++.1
@@ -0,0 +1,130 @@
+LAMMPS (15 Feb 2016)
+# 2d NEMD simulation
+
+units lj
+atom_style atomic
+dimension 2
+
+lattice sq2 0.8442
+Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
+region box prism 0 10 0 8 -0.5 0.5 0 0 0
+create_box 2 box
+Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 160 atoms
+mass * 1.0
+
+velocity all create 1.44 87287 loop geom
+
+region slice block 4 6 INF INF INF INF
+set region slice type 2
+ 40 settings made for type
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0 1.0
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1
+
+fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1
+fix 2 all deform 1 xy erate 0.01 remap v
+
+#dump 1 all custom 5000 dump.nemd id type x y z
+
+#dump 2 all image 1000 image.*.jpg type type adiam 1.2
+#dump_modify 2 pad 5
+
+#dump 3 all movie 1000 movie.mpg type type adiam 1.2
+#dump_modify 3 pad 5
+
+thermo 1000
+
+run 50000
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 1.3
+ ghost atom cutoff = 1.3
+ binsize = 0.65 -> bins = 24 19 3
+Memory usage per processor = 2.49357 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 1.44 0 0 1.431 1.2080502 189.52855
+ 1000 1.1326992 0.25863754 0 1.3842573 6.0588079 189.52855
+ 2000 1.0158438 0.33502643 0 1.3445212 7.2638652 189.52855
+ 3000 1.0968167 0.3149227 0 1.4048843 7.0653223 189.52855
+ 4000 1.0070993 0.40611915 0 1.4069241 7.7283521 189.52855
+ 5000 1.1153133 0.2674828 0 1.3758254 6.2949171 189.52855
+ 6000 1.0170665 0.25843673 0 1.2691466 6.049412 189.52855
+ 7000 1.0224605 0.20974914 0 1.2258193 5.5104976 189.52855
+ 8000 0.96149374 0.24035439 0 1.1958388 5.4179146 189.52855
+ 9000 0.87759014 0.2590493 0 1.1311545 5.8711239 189.52855
+ 10000 0.83791968 0.23477897 0 1.0674617 5.666904 189.52855
+ 11000 0.87702487 0.22958877 0 1.1011322 5.9068062 189.52855
+ 12000 0.81507294 0.26375817 0 1.0737369 5.9166925 189.52855
+ 13000 0.85655284 0.24676491 0 1.0979643 5.6918734 189.52855
+ 14000 0.84369293 0.27818471 0 1.1166046 6.4146184 189.52855
+ 15000 0.90052173 0.19836095 0 1.0932544 5.2690913 189.52855
+ 16000 0.83836874 0.26921637 0 1.1023453 5.9579526 189.52855
+ 17000 0.90492897 0.21933098 0 1.1186041 5.6042194 189.52855
+ 18000 0.90113412 0.24880908 0 1.1443111 6.0634846 189.52855
+ 19000 1.0160445 0.17252962 0 1.1822239 5.3149334 189.52855
+ 20000 0.96217234 0.2414377 0 1.1975965 5.476653 189.52855
+ 21000 0.98229664 0.27569118 0 1.2518485 5.9340174 189.52855
+ 22000 1.0551763 0.26997615 0 1.3185576 6.2094112 189.52855
+ 23000 1.051999 0.34076639 0 1.3861904 7.082385 189.52855
+ 24000 1.1350071 0.23701844 0 1.3649317 6.1829742 189.52855
+ 25000 1.0946409 0.33366032 0 1.4214597 7.1907559 189.52855
+ 26000 1.1511799 0.24626808 0 1.3902531 5.8469984 189.52855
+ 27000 1.1009203 0.25653085 0 1.3505704 6.1504287 189.52855
+ 28000 1.0521302 0.2876798 0 1.3332342 5.9906187 189.52855
+ 29000 1.0518465 0.21853 0 1.2638025 5.6577549 189.52855
+ 30000 0.97264625 0.28758145 0 1.2541487 6.5769804 189.52855
+ 31000 1.0133579 0.31575837 0 1.3227828 6.6650893 189.52855
+ 32000 1.0714324 0.28757036 0 1.3523063 6.2682059 189.52855
+ 33000 1.0739451 0.28062459 0 1.3478575 6.6862746 189.52855
+ 34000 1.0056867 0.38289586 0 1.382297 7.1120131 189.52855
+ 35000 1.0911349 0.26370939 0 1.3480247 6.1476048 189.52855
+ 36000 1.0618618 0.28269593 0 1.3379211 6.9414608 189.52855
+ 37000 1.0704991 0.29974994 0 1.3635585 7.0834346 189.52855
+ 38000 1.1087507 0.2682201 0 1.3700411 5.8506019 189.52855
+ 39000 1.1303733 0.22362416 0 1.3469326 5.2500269 189.52855
+ 40000 1.0174248 0.28956571 0 1.3006316 6.4491571 189.52855
+ 41000 0.95981887 0.29162143 0 1.2454414 6.4658646 189.52855
+ 42000 0.88302144 0.30432252 0 1.1818251 6.7401923 189.52855
+ 43000 0.93164419 0.25110308 0 1.1769245 5.9067383 189.52855
+ 44000 0.98352598 0.23322873 0 1.2106077 5.5606585 189.52855
+ 45000 1.0247245 0.26503082 0 1.2833508 6.533394 189.52855
+ 46000 0.93004532 0.32277782 0 1.2470104 6.4689179 189.52855
+ 47000 1.0653176 0.29185413 0 1.3505135 6.9534569 189.52855
+ 48000 1.0401524 0.3420245 0 1.3756759 6.8016042 189.52855
+ 49000 1.0023407 0.31833091 0 1.314407 6.7385662 189.52855
+ 50000 1.0566272 0.28657142 0 1.3365947 6.261203 189.52855
+Loop time of 1.1489 on 1 procs for 50000 steps with 160 atoms
+
+Performance: 18800575.740 tau/day, 43519.851 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.20048 | 0.20048 | 0.20048 | 0.0 | 17.45
+Neigh | 0.16117 | 0.16117 | 0.16117 | 0.0 | 14.03
+Comm | 0.048121 | 0.048121 | 0.048121 | 0.0 | 4.19
+Output | 0.00054765 | 0.00054765 | 0.00054765 | 0.0 | 0.05
+Modify | 0.67693 | 0.67693 | 0.67693 | 0.0 | 58.92
+Other | | 0.06166 | | | 5.37
+
+Nlocal: 160 ave 160 max 160 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 71 ave 71 max 71 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 362 ave 362 max 362 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 362
+Ave neighs/atom = 2.2625
+Neighbor list builds = 5256
+Dangerous builds = 0
+Total wall time: 0:00:01
diff --git a/examples/nemd/log.15Feb16.nemd.g++.4 b/examples/nemd/log.15Feb16.nemd.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..c244e35e8085a8a7ab679122b488ac5570be4ac2
--- /dev/null
+++ b/examples/nemd/log.15Feb16.nemd.g++.4
@@ -0,0 +1,130 @@
+LAMMPS (15 Feb 2016)
+# 2d NEMD simulation
+
+units lj
+atom_style atomic
+dimension 2
+
+lattice sq2 0.8442
+Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
+region box prism 0 10 0 8 -0.5 0.5 0 0 0
+create_box 2 box
+Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
+ 2 by 2 by 1 MPI processor grid
+create_atoms 1 box
+Created 160 atoms
+mass * 1.0
+
+velocity all create 1.44 87287 loop geom
+
+region slice block 4 6 INF INF INF INF
+set region slice type 2
+ 40 settings made for type
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0 1.0
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1
+
+fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1
+fix 2 all deform 1 xy erate 0.01 remap v
+
+#dump 1 all custom 5000 dump.nemd id type x y z
+
+#dump 2 all image 1000 image.*.jpg type type adiam 1.2
+#dump_modify 2 pad 5
+
+#dump 3 all movie 1000 movie.mpg type type adiam 1.2
+#dump_modify 3 pad 5
+
+thermo 1000
+
+run 50000
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 1.3
+ ghost atom cutoff = 1.3
+ binsize = 0.65 -> bins = 24 19 3
+Memory usage per processor = 2.49198 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 1.44 0 0 1.431 1.2080502 189.52855
+ 1000 1.1682693 0.24486562 0 1.4058332 5.8092954 189.52855
+ 2000 1.0928734 0.27609364 0 1.3621366 6.2237017 189.52855
+ 3000 1.0895801 0.24812344 0 1.3308937 5.6987334 189.52855
+ 4000 1.0231536 0.23938192 0 1.2561408 5.6395384 189.52855
+ 5000 0.92980496 0.29549086 0 1.2194845 6.7361058 189.52855
+ 6000 0.94654468 0.27175873 0 1.2123875 6.1830354 189.52855
+ 7000 1.04513 0.19555104 0 1.234149 5.3099904 189.52855
+ 8000 0.90165043 0.33774203 0 1.2337571 6.8441345 189.52855
+ 9000 1.0559475 0.21527383 0 1.2646217 5.3936713 189.52855
+ 10000 1.0316023 0.25162907 0 1.2767839 6.0630699 189.52855
+ 11000 1.0057873 0.1929355 0 1.1924366 5.1939416 189.52855
+ 12000 0.95976424 0.23631857 0 1.1900843 5.1197849 189.52855
+ 13000 0.96228689 0.2359206 0 1.1921932 5.8485377 189.52855
+ 14000 0.92347491 0.28934379 0 1.207047 6.7279587 189.52855
+ 15000 0.98798195 0.25310368 0 1.2349107 5.5744542 189.52855
+ 16000 0.93800257 0.39455603 0 1.3266961 7.5939651 189.52855
+ 17000 1.1781148 0.21856228 0 1.3893138 5.8347428 189.52855
+ 18000 1.1292943 0.26429204 0 1.3865283 6.0510955 189.52855
+ 19000 1.1047406 0.37926848 0 1.4771045 8.1596576 189.52855
+ 20000 1.1716353 0.34662527 0 1.5109379 7.4616642 189.52855
+ 21000 1.1630831 0.35981763 0 1.5156314 7.1024447 189.52855
+ 22000 1.1249714 0.28308559 0 1.4010259 6.4004855 189.52855
+ 23000 1.1062056 0.28618757 0 1.3854794 6.4957851 189.52855
+ 24000 1.0588756 0.31727536 0 1.369533 6.987661 189.52855
+ 25000 1.0379506 0.30773124 0 1.3391947 6.3814122 189.52855
+ 26000 1.0316899 0.25596718 0 1.281209 6.4851096 189.52855
+ 27000 0.95909019 0.32282679 0 1.2759227 6.480673 189.52855
+ 28000 1.0224651 0.24795447 0 1.2640291 5.5846145 189.52855
+ 29000 0.98739892 0.24878333 0 1.230011 5.6749101 189.52855
+ 30000 1.0099165 0.22964407 0 1.2332486 5.3791167 189.52855
+ 31000 0.93350481 0.2879577 0 1.2156281 6.2148818 189.52855
+ 32000 0.99089487 0.22340991 0 1.2081117 5.639 189.52855
+ 33000 0.89519123 0.26943351 0 1.1590298 6.3869898 189.52855
+ 34000 0.891093 0.28473528 0 1.1702589 6.0284238 189.52855
+ 35000 0.83575157 0.25811245 0 1.0886406 6.4030425 189.52855
+ 36000 0.81108815 0.26558543 0 1.0716043 6.3037393 189.52855
+ 37000 0.92476501 0.18404704 0 1.1030323 5.3793557 189.52855
+ 38000 0.85121163 0.2792429 0 1.1251345 5.9668051 189.52855
+ 39000 0.90345348 0.2399627 0 1.1377696 6.1440023 189.52855
+ 40000 0.93871579 0.2217328 0 1.1545816 4.9454727 189.52855
+ 41000 1.0132854 0.25226008 0 1.2592124 6.2541531 189.52855
+ 42000 0.98600788 0.27213553 0 1.2519809 6.0321859 189.52855
+ 43000 1.0635948 0.27086236 0 1.3278097 6.6622232 189.52855
+ 44000 1.0332292 0.36613701 0 1.3929085 7.4935675 189.52855
+ 45000 1.1168224 0.3374366 0 1.4472788 7.3625776 189.52855
+ 46000 1.0725949 0.37916007 0 1.4450513 6.8897095 189.52855
+ 47000 1.0940234 0.35474661 0 1.4419324 7.4781317 189.52855
+ 48000 1.1093597 0.26705754 0 1.3694837 5.8401116 189.52855
+ 49000 1.0803976 0.29555751 0 1.3692026 6.4769008 189.52855
+ 50000 1.0150244 0.29822696 0 1.3069075 6.4417197 189.52855
+Loop time of 1.04457 on 4 procs for 50000 steps with 160 atoms
+
+Performance: 20678409.528 tau/day, 47866.689 timesteps/s
+99.1% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.049384 | 0.050257 | 0.051119 | 0.4 | 4.81
+Neigh | 0.043314 | 0.043914 | 0.044468 | 0.3 | 4.20
+Comm | 0.35483 | 0.40496 | 0.45232 | 5.9 | 38.77
+Output | 0.0010872 | 0.0012692 | 0.0017776 | 0.8 | 0.12
+Modify | 0.30946 | 0.35542 | 0.40435 | 6.0 | 34.03
+Other | | 0.1887 | | | 18.07
+
+Nlocal: 40 ave 42 max 38 min
+Histogram: 1 0 1 0 0 0 0 1 0 1
+Nghost: 35.5 ave 37 max 34 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+Neighs: 88.75 ave 96 max 79 min
+Histogram: 1 0 1 0 0 0 0 0 0 2
+
+Total # of neighbors = 355
+Ave neighs/atom = 2.21875
+Neighbor list builds = 5284
+Dangerous builds = 0
+Total wall time: 0:00:01
diff --git a/examples/obstacle/log.15Feb16.obstacle.g++.1 b/examples/obstacle/log.15Feb16.obstacle.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..448cdfcb73522e0a5ef3e230f495a0f5cd1594a1
--- /dev/null
+++ b/examples/obstacle/log.15Feb16.obstacle.g++.1
@@ -0,0 +1,155 @@
+LAMMPS (15 Feb 2016)
+# 2d LJ obstacle flow
+
+dimension 2
+boundary p s p
+
+atom_style atomic
+neighbor 0.3 bin
+neigh_modify delay 5
+
+# create geometry
+
+lattice hex 0.7
+Lattice spacing in x,y,z = 1.28436 2.22457 1.28436
+region box block 0 40 0 10 -0.25 0.25
+create_box 3 box
+Created orthogonal box = (0 0 -0.321089) to (51.3743 22.2457 0.321089)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 840 atoms
+
+mass 1 1.0
+mass 2 1.0
+mass 3 1.0
+
+# LJ potentials
+
+pair_style lj/cut 1.12246
+pair_coeff * * 1.0 1.0 1.12246
+
+# define groups
+
+region 1 block INF INF INF 1.25 INF INF
+group lower region 1
+120 atoms in group lower
+region 2 block INF INF 8.75 INF INF INF
+group upper region 2
+120 atoms in group upper
+group boundary union lower upper
+240 atoms in group boundary
+group flow subtract all boundary
+600 atoms in group flow
+
+set group lower type 2
+ 120 settings made for type
+set group upper type 3
+ 120 settings made for type
+
+# initial velocities
+
+compute mobile flow temp
+velocity flow create 1.0 482748 temp mobile
+fix 1 all nve
+fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
+fix_modify 2 temp mobile
+
+# Poiselle flow
+
+velocity boundary set 0.0 0.0 0.0
+fix 3 lower setforce 0.0 0.0 0.0
+fix 4 upper setforce 0.0 NULL 0.0
+fix 5 upper aveforce 0.0 -0.5 0.0
+fix 6 flow addforce 1.0 0.0 0.0
+
+# 2 obstacles
+
+region void1 sphere 10 4 0 3
+delete_atoms region void1
+Deleted 36 atoms, new total = 804
+region void2 sphere 20 7 0 3
+delete_atoms region void2
+Deleted 35 atoms, new total = 769
+
+fix 7 flow indent 100 sphere 10 4 0 4
+fix 8 flow indent 100 sphere 20 7 0 4
+fix 9 all enforce2d
+
+# Run
+
+timestep 0.003
+thermo 1000
+thermo_modify temp mobile
+WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:445)
+
+#dump 1 all atom 100 dump.obstacle
+
+#dump 2 all image 500 image.*.jpg type type # zoom 1.6 adiam 1.5
+#dump_modify 2 pad 5
+
+#dump 3 all movie 500 movie.mpg type type # zoom 1.6 adiam 1.5
+#dump_modify 3 pad 5
+
+run 25000
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 5 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 1.42246
+ ghost atom cutoff = 1.42246
+ binsize = 0.71123 -> bins = 73 32 1
+Memory usage per processor = 2.47903 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 1.0027471 0 0 0.68849216 0.46317653 1143.0857
+ 1000 1 -0.33689286 0 0.34971312 1.2905426 1286.7728
+ 2000 1 -0.36746164 0 0.31914434 1.1668828 1313.44
+ 3000 1 -0.52004759 0 0.16655839 1.417774 1324.489
+ 4000 1 -0.5052153 0 0.18139068 1.4877209 1370.8743
+ 5000 1 -0.49501138 0 0.1915946 1.2415582 1408.4993
+ 6000 1 -0.45834057 0 0.22826542 1.2577643 1433.2191
+ 7000 1 -0.44788351 0 0.23872247 1.1057853 1452.7011
+ 8000 1 -0.42511924 0 0.26148674 1.1445522 1453.2588
+ 9000 1 -0.35807547 0 0.32853051 1.0527564 1449.2608
+ 10000 1 -0.38692228 0 0.2996837 1.0338935 1447.9561
+ 11000 1 -0.38893457 0 0.29767141 1.0095645 1451.1231
+ 12000 1 -0.35706485 0 0.32954114 1.0796623 1453.0879
+ 13000 1 -0.39551125 0 0.29109474 1.0390286 1453.2992
+ 14000 1 -0.38153043 0 0.30507555 0.98105926 1452.5639
+ 15000 1 -0.38762689 0 0.29897909 1.1442417 1452.0174
+ 16000 1 -0.3685331 0 0.31807289 1.0032132 1458.431
+ 17000 1 -0.36299809 0 0.32360789 0.93727845 1460.2986
+ 18000 1 -0.35752931 0 0.32907667 0.98337283 1458.583
+ 19000 1 -0.38350344 0 0.30310254 1.0148373 1458.9749
+ 20000 1 -0.35659703 0 0.33000895 1.0264431 1460.0031
+ 21000 1 -0.36878002 0 0.31782596 1.0877739 1455.1053
+ 22000 1 -0.37986917 0 0.30673681 1.129754 1455.0258
+ 23000 1 -0.39249509 0 0.29411089 0.97187435 1459.6771
+ 24000 1 -0.33410442 0 0.35250156 0.93960021 1463.5903
+ 25000 1 -0.37437615 0 0.31222983 0.9644765 1464.9391
+Loop time of 1.65987 on 1 procs for 25000 steps with 769 atoms
+
+Performance: 3903929.372 tau/day, 15061.456 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.52106 | 0.52106 | 0.52106 | 0.0 | 31.39
+Neigh | 0.16143 | 0.16143 | 0.16143 | 0.0 | 9.73
+Comm | 0.023438 | 0.023438 | 0.023438 | 0.0 | 1.41
+Output | 0.00032663 | 0.00032663 | 0.00032663 | 0.0 | 0.02
+Modify | 0.87449 | 0.87449 | 0.87449 | 0.0 | 52.68
+Other | | 0.07912 | | | 4.77
+
+Nlocal: 769 ave 769 max 769 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 45 ave 45 max 45 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 1618 ave 1618 max 1618 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1618
+Ave neighs/atom = 2.10403
+Neighbor list builds = 1622
+Dangerous builds = 0
+Total wall time: 0:00:01
diff --git a/examples/obstacle/log.15Feb16.obstacle.g++.4 b/examples/obstacle/log.15Feb16.obstacle.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..e694d137cb1f10adf92f9a33a826cb9474aff098
--- /dev/null
+++ b/examples/obstacle/log.15Feb16.obstacle.g++.4
@@ -0,0 +1,155 @@
+LAMMPS (15 Feb 2016)
+# 2d LJ obstacle flow
+
+dimension 2
+boundary p s p
+
+atom_style atomic
+neighbor 0.3 bin
+neigh_modify delay 5
+
+# create geometry
+
+lattice hex 0.7
+Lattice spacing in x,y,z = 1.28436 2.22457 1.28436
+region box block 0 40 0 10 -0.25 0.25
+create_box 3 box
+Created orthogonal box = (0 0 -0.321089) to (51.3743 22.2457 0.321089)
+ 4 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 840 atoms
+
+mass 1 1.0
+mass 2 1.0
+mass 3 1.0
+
+# LJ potentials
+
+pair_style lj/cut 1.12246
+pair_coeff * * 1.0 1.0 1.12246
+
+# define groups
+
+region 1 block INF INF INF 1.25 INF INF
+group lower region 1
+120 atoms in group lower
+region 2 block INF INF 8.75 INF INF INF
+group upper region 2
+120 atoms in group upper
+group boundary union lower upper
+240 atoms in group boundary
+group flow subtract all boundary
+600 atoms in group flow
+
+set group lower type 2
+ 120 settings made for type
+set group upper type 3
+ 120 settings made for type
+
+# initial velocities
+
+compute mobile flow temp
+velocity flow create 1.0 482748 temp mobile
+fix 1 all nve
+fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
+fix_modify 2 temp mobile
+
+# Poiselle flow
+
+velocity boundary set 0.0 0.0 0.0
+fix 3 lower setforce 0.0 0.0 0.0
+fix 4 upper setforce 0.0 NULL 0.0
+fix 5 upper aveforce 0.0 -0.5 0.0
+fix 6 flow addforce 1.0 0.0 0.0
+
+# 2 obstacles
+
+region void1 sphere 10 4 0 3
+delete_atoms region void1
+Deleted 36 atoms, new total = 804
+region void2 sphere 20 7 0 3
+delete_atoms region void2
+Deleted 35 atoms, new total = 769
+
+fix 7 flow indent 100 sphere 10 4 0 4
+fix 8 flow indent 100 sphere 20 7 0 4
+fix 9 all enforce2d
+
+# Run
+
+timestep 0.003
+thermo 1000
+thermo_modify temp mobile
+WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:445)
+
+#dump 1 all atom 100 dump.obstacle
+
+#dump 2 all image 500 image.*.jpg type type # zoom 1.6 adiam 1.5
+#dump_modify 2 pad 5
+
+#dump 3 all movie 500 movie.mpg type type # zoom 1.6 adiam 1.5
+#dump_modify 3 pad 5
+
+run 25000
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 5 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 1.42246
+ ghost atom cutoff = 1.42246
+ binsize = 0.71123 -> bins = 73 32 1
+Memory usage per processor = 2.47142 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 1.0004177 0 0 0.68689281 0.46210058 1143.0857
+ 1000 1 -0.32494012 0 0.36166587 1.2240503 1282.5239
+ 2000 1 -0.37815616 0 0.30844982 1.0642877 1312.5691
+ 3000 1 -0.49062369 0 0.19598229 1.5239334 1322.2627
+ 4000 1 -0.50088987 0 0.18571611 1.4614192 1367.6511
+ 5000 1 -0.47747975 0 0.20912623 1.3417367 1405.501
+ 6000 1 -0.47477948 0 0.21182651 1.3061542 1432.0778
+ 7000 1 -0.44736042 0 0.23924556 1.1332701 1441.4911
+ 8000 1 -0.42748547 0 0.25912051 1.0531138 1443.7226
+ 9000 1 -0.41433123 0 0.27227475 1.0997172 1450.1414
+ 10000 1 -0.38722477 0 0.29938121 1.0652717 1456.2877
+ 11000 1 -0.40216239 0 0.28444359 1.1152975 1459.2764
+ 12000 1 -0.38520467 0 0.30140132 0.94109687 1463.6094
+ 13000 1 -0.38233942 0 0.30426656 1.0184283 1461.2151
+ 14000 1 -0.38106329 0 0.3055427 0.93372261 1459.276
+ 15000 1 -0.36896962 0 0.31763636 1.0015053 1456.4295
+ 16000 1 -0.38669413 0 0.29991185 0.99320514 1460.5925
+ 17000 1 -0.3879857 0 0.29862028 0.95908906 1461.1978
+ 18000 1 -0.37448688 0 0.3121191 0.96871256 1460.7159
+ 19000 1 -0.39700052 0 0.28960547 1.0770396 1458.2596
+ 20000 1 -0.36125976 0 0.32534622 0.86282353 1466.9129
+ 21000 1 -0.38882675 0 0.29777923 0.9877477 1457.4909
+ 22000 1 -0.38158333 0 0.30502266 1.0184682 1454.5247
+ 23000 1 -0.37327871 0 0.31332728 1.0623185 1453.1342
+ 24000 1 -0.40040333 0 0.28620265 0.94983886 1459.4461
+ 25000 1 -0.37645924 0 0.31014674 1.0526044 1458.7191
+Loop time of 0.801717 on 4 procs for 25000 steps with 769 atoms
+
+Performance: 8082654.578 tau/day, 31183.081 timesteps/s
+99.2% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.066442 | 0.13097 | 0.21239 | 16.1 | 16.34
+Neigh | 0.03235 | 0.042894 | 0.056734 | 4.4 | 5.35
+Comm | 0.14225 | 0.21218 | 0.28481 | 11.2 | 26.47
+Output | 0.0005331 | 0.00056887 | 0.00064301 | 0.2 | 0.07
+Modify | 0.27222 | 0.31224 | 0.33583 | 4.6 | 38.95
+Other | | 0.1029 | | | 12.83
+
+Nlocal: 192.25 ave 243 max 151 min
+Histogram: 1 1 0 0 0 0 1 0 0 1
+Nghost: 41.75 ave 43 max 39 min
+Histogram: 1 0 0 0 0 0 0 1 0 2
+Neighs: 408.5 ave 575 max 266 min
+Histogram: 1 1 0 0 0 0 0 1 0 1
+
+Total # of neighbors = 1634
+Ave neighs/atom = 2.12484
+Neighbor list builds = 1631
+Dangerous builds = 1
+Total wall time: 0:00:00
diff --git a/examples/peptide/log.15Feb16.peptide.g++.1 b/examples/peptide/log.15Feb16.peptide.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..fc3ec9ce4e6d5772fabfcb51e150e37f2ea22afd
--- /dev/null
+++ b/examples/peptide/log.15Feb16.peptide.g++.1
@@ -0,0 +1,189 @@
+LAMMPS (15 Feb 2016)
+# Solvated 5-mer peptide
+
+units real
+atom_style full
+
+pair_style lj/charmm/coul/long 8.0 10.0 10.0
+bond_style harmonic
+angle_style charmm
+dihedral_style charmm
+improper_style harmonic
+kspace_style pppm 0.0001
+
+read_data data.peptide
+ orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 2004 atoms
+ reading velocities ...
+ 2004 velocities
+ scanning bonds ...
+ 3 = max bonds/atom
+ scanning angles ...
+ 6 = max angles/atom
+ scanning dihedrals ...
+ 14 = max dihedrals/atom
+ scanning impropers ...
+ 1 = max impropers/atom
+ reading bonds ...
+ 1365 bonds
+ reading angles ...
+ 786 angles
+ reading dihedrals ...
+ 207 dihedrals
+ reading impropers ...
+ 12 impropers
+ 4 = max # of 1-2 neighbors
+ 7 = max # of 1-3 neighbors
+ 14 = max # of 1-4 neighbors
+ 18 = max # of special neighbors
+
+neighbor 2.0 bin
+neigh_modify delay 5
+
+timestep 2.0
+
+thermo_style multi
+thermo 50
+
+fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
+fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
+ 19 = # of size 2 clusters
+ 6 = # of size 3 clusters
+ 3 = # of size 4 clusters
+ 640 = # of frozen angles
+
+group peptide type <= 12
+84 atoms in group peptide
+
+#dump 1 peptide atom 10 dump.peptide
+
+#dump 2 peptide image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 bond atom 0.5
+#dump_modify 2 pad 3
+
+#dump 3 peptide movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 bond atom 0.5
+#dump_modify 3 pad 3
+
+#compute bnd all property/local btype batom1 batom2
+#dump 2 peptide local 300 dump.bond index c_bnd[1] c_bnd[2] c_bnd[3]
+
+run 300
+PPPM initialization ...
+ G vector (1/distance) = 0.268725
+ grid = 15 15 15
+ stencil order = 5
+ estimated absolute RMS force accuracy = 0.0228209
+ estimated relative force accuracy = 6.87243e-05
+ using double precision FFTs
+ 3d grid and FFT values/proc = 10648 3375
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 5 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 12
+ ghost atom cutoff = 12
+ binsize = 6 -> bins = 5 5 5
+SHAKE stats (type/ave/delta) on step 0
+ 4 1.111 1.44264e-05
+ 6 0.996998 7.26967e-06
+ 8 1.08 1.32536e-05
+ 10 1.111 1.22749e-05
+ 12 1.08 1.11767e-05
+ 14 0.96 0
+ 18 0.957206 4.37979e-05
+ 31 104.519 0.00396029
+Memory usage per processor = 15.1545 Mbytes
+---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
+TotEng = -5237.4580 KinEng = 1134.9186 Temp = 282.1005
+PotEng = -6372.3766 E_bond = 16.5572 E_angle = 36.3726
+E_dihed = 15.5190 E_impro = 1.9426 E_vdwl = 692.8945
+E_coul = 26772.2646 E_long = -33907.9271 Press = -845.4774
+---------------- Step 50 ----- CPU = 1.0068 (sec) ----------------
+TotEng = -5247.5490 KinEng = 1132.4011 Temp = 281.4748
+PotEng = -6379.9501 E_bond = 12.2118 E_angle = 31.7365
+E_dihed = 18.8145 E_impro = 2.3612 E_vdwl = 658.1771
+E_coul = 26804.4490 E_long = -33907.7002 Press = -1331.7980
+SHAKE stats (type/ave/delta) on step 100
+ 4 1.111 7.80799e-07
+ 6 0.997 1.06209e-06
+ 8 1.08 6.20485e-07
+ 10 1.111 6.23445e-07
+ 12 1.08 2.68063e-07
+ 14 0.96 0
+ 18 0.957201 5.38018e-06
+ 31 104.52 0.000502316
+---------------- Step 100 ----- CPU = 2.0247 (sec) ----------------
+TotEng = -5257.9972 KinEng = 1078.0556 Temp = 267.9664
+PotEng = -6336.0528 E_bond = 14.4828 E_angle = 43.4429
+E_dihed = 15.2569 E_impro = 2.3160 E_vdwl = 708.3266
+E_coul = 26786.6841 E_long = -33906.5620 Press = -648.6637
+---------------- Step 150 ----- CPU = 3.0615 (sec) ----------------
+TotEng = -5287.2845 KinEng = 1098.6036 Temp = 273.0739
+PotEng = -6385.8881 E_bond = 17.4924 E_angle = 32.8593
+E_dihed = 15.1623 E_impro = 1.6522 E_vdwl = 736.9686
+E_coul = 26717.2583 E_long = -33907.2812 Press = -333.1888
+SHAKE stats (type/ave/delta) on step 200
+ 4 1.111 2.18836e-07
+ 6 0.997 1.50855e-07
+ 8 1.08 6.58342e-08
+ 10 1.111 5.5535e-07
+ 12 1.08 1.99243e-07
+ 14 0.96 0
+ 18 0.957201 3.59666e-06
+ 31 104.52 0.000388186
+---------------- Step 200 ----- CPU = 4.0675 (sec) ----------------
+TotEng = -5308.4527 KinEng = 1100.5055 Temp = 273.5467
+PotEng = -6408.9582 E_bond = 18.2714 E_angle = 33.3035
+E_dihed = 16.8150 E_impro = 2.6053 E_vdwl = 686.3264
+E_coul = 26736.1130 E_long = -33902.3928 Press = -1470.3831
+---------------- Step 250 ----- CPU = 5.1252 (sec) ----------------
+TotEng = -5294.1807 KinEng = 1071.1619 Temp = 266.2529
+PotEng = -6365.3426 E_bond = 14.2022 E_angle = 39.1953
+E_dihed = 19.4555 E_impro = 3.1387 E_vdwl = 753.5416
+E_coul = 26713.8467 E_long = -33908.7226 Press = -188.8007
+SHAKE stats (type/ave/delta) on step 300
+ 4 1.111 3.78262e-06
+ 6 0.997001 3.50131e-06
+ 8 1.08 2.0932e-06
+ 10 1.111 5.64324e-06
+ 12 1.08 2.10399e-06
+ 14 0.96 0
+ 18 0.957202 7.67973e-06
+ 31 104.52 0.000806336
+---------------- Step 300 ----- CPU = 6.1883 (sec) ----------------
+TotEng = -5251.4333 KinEng = 1123.6266 Temp = 279.2937
+PotEng = -6375.0599 E_bond = 14.2249 E_angle = 38.4712
+E_dihed = 18.1324 E_impro = 2.3700 E_vdwl = 715.4550
+E_coul = 26745.4115 E_long = -33909.1249 Press = -469.5254
+Loop time of 6.18835 on 1 procs for 300 steps with 2004 atoms
+
+Performance: 8.377 ns/day, 2.865 hours/ns, 48.478 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 4.8942 | 4.8942 | 4.8942 | 0.0 | 79.09
+Bond | 0.015213 | 0.015213 | 0.015213 | 0.0 | 0.25
+Kspace | 0.49706 | 0.49706 | 0.49706 | 0.0 | 8.03
+Neigh | 0.67515 | 0.67515 | 0.67515 | 0.0 | 10.91
+Comm | 0.029536 | 0.029536 | 0.029536 | 0.0 | 0.48
+Output | 0.00019145 | 0.00019145 | 0.00019145 | 0.0 | 0.00
+Modify | 0.070009 | 0.070009 | 0.070009 | 0.0 | 1.13
+Other | | 0.006974 | | | 0.11
+
+Nlocal: 2004 ave 2004 max 2004 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 11181 ave 11181 max 11181 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 708029 ave 708029 max 708029 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 708029
+Ave neighs/atom = 353.308
+Ave special neighs/atom = 2.34032
+Neighbor list builds = 26
+Dangerous builds = 0
+
+Total wall time: 0:00:06
diff --git a/examples/peptide/log.15Feb16.peptide.g++.4 b/examples/peptide/log.15Feb16.peptide.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..b0196fbd915e5fce79bb165f74dd96946ad7046f
--- /dev/null
+++ b/examples/peptide/log.15Feb16.peptide.g++.4
@@ -0,0 +1,189 @@
+LAMMPS (15 Feb 2016)
+# Solvated 5-mer peptide
+
+units real
+atom_style full
+
+pair_style lj/charmm/coul/long 8.0 10.0 10.0
+bond_style harmonic
+angle_style charmm
+dihedral_style charmm
+improper_style harmonic
+kspace_style pppm 0.0001
+
+read_data data.peptide
+ orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 2004 atoms
+ reading velocities ...
+ 2004 velocities
+ scanning bonds ...
+ 3 = max bonds/atom
+ scanning angles ...
+ 6 = max angles/atom
+ scanning dihedrals ...
+ 14 = max dihedrals/atom
+ scanning impropers ...
+ 1 = max impropers/atom
+ reading bonds ...
+ 1365 bonds
+ reading angles ...
+ 786 angles
+ reading dihedrals ...
+ 207 dihedrals
+ reading impropers ...
+ 12 impropers
+ 4 = max # of 1-2 neighbors
+ 7 = max # of 1-3 neighbors
+ 14 = max # of 1-4 neighbors
+ 18 = max # of special neighbors
+
+neighbor 2.0 bin
+neigh_modify delay 5
+
+timestep 2.0
+
+thermo_style multi
+thermo 50
+
+fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
+fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
+ 19 = # of size 2 clusters
+ 6 = # of size 3 clusters
+ 3 = # of size 4 clusters
+ 640 = # of frozen angles
+
+group peptide type <= 12
+84 atoms in group peptide
+
+#dump 1 peptide atom 10 dump.peptide
+
+#dump 2 peptide image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 bond atom 0.5
+#dump_modify 2 pad 3
+
+#dump 3 peptide movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 bond atom 0.5
+#dump_modify 3 pad 3
+
+#compute bnd all property/local btype batom1 batom2
+#dump 2 peptide local 300 dump.bond index c_bnd[1] c_bnd[2] c_bnd[3]
+
+run 300
+PPPM initialization ...
+ G vector (1/distance) = 0.268725
+ grid = 15 15 15
+ stencil order = 5
+ estimated absolute RMS force accuracy = 0.0228209
+ estimated relative force accuracy = 6.87243e-05
+ using double precision FFTs
+ 3d grid and FFT values/proc = 4312 960
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 5 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 12
+ ghost atom cutoff = 12
+ binsize = 6 -> bins = 5 5 5
+SHAKE stats (type/ave/delta) on step 0
+ 4 1.111 1.44264e-05
+ 6 0.996998 7.26967e-06
+ 8 1.08 1.32536e-05
+ 10 1.111 1.22749e-05
+ 12 1.08 1.11767e-05
+ 14 0.96 0
+ 18 0.957206 4.37979e-05
+ 31 104.519 0.00396029
+Memory usage per processor = 14.4096 Mbytes
+---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
+TotEng = -5237.4580 KinEng = 1134.9186 Temp = 282.1005
+PotEng = -6372.3766 E_bond = 16.5572 E_angle = 36.3726
+E_dihed = 15.5190 E_impro = 1.9426 E_vdwl = 692.8945
+E_coul = 26772.2646 E_long = -33907.9271 Press = -845.4774
+---------------- Step 50 ----- CPU = 0.2819 (sec) ----------------
+TotEng = -5247.5490 KinEng = 1132.4011 Temp = 281.4748
+PotEng = -6379.9501 E_bond = 12.2118 E_angle = 31.7365
+E_dihed = 18.8145 E_impro = 2.3612 E_vdwl = 658.1771
+E_coul = 26804.4490 E_long = -33907.7002 Press = -1331.7981
+SHAKE stats (type/ave/delta) on step 100
+ 4 1.111 7.80799e-07
+ 6 0.997 1.06209e-06
+ 8 1.08 6.20484e-07
+ 10 1.111 6.23445e-07
+ 12 1.08 2.68063e-07
+ 14 0.96 0
+ 18 0.957201 5.38018e-06
+ 31 104.52 0.000502316
+---------------- Step 100 ----- CPU = 0.5649 (sec) ----------------
+TotEng = -5257.9973 KinEng = 1078.0556 Temp = 267.9664
+PotEng = -6336.0529 E_bond = 14.4828 E_angle = 43.4429
+E_dihed = 15.2569 E_impro = 2.3160 E_vdwl = 708.3266
+E_coul = 26786.6840 E_long = -33906.5620 Press = -648.6639
+---------------- Step 150 ----- CPU = 0.8549 (sec) ----------------
+TotEng = -5287.2844 KinEng = 1098.6036 Temp = 273.0739
+PotEng = -6385.8881 E_bond = 17.4924 E_angle = 32.8593
+E_dihed = 15.1623 E_impro = 1.6522 E_vdwl = 736.9685
+E_coul = 26717.2583 E_long = -33907.2812 Press = -333.1895
+SHAKE stats (type/ave/delta) on step 200
+ 4 1.111 2.18836e-07
+ 6 0.997 1.50856e-07
+ 8 1.08 6.58343e-08
+ 10 1.111 5.55349e-07
+ 12 1.08 1.99243e-07
+ 14 0.96 0
+ 18 0.957201 3.59666e-06
+ 31 104.52 0.000388184
+---------------- Step 200 ----- CPU = 1.1354 (sec) ----------------
+TotEng = -5308.4528 KinEng = 1100.5056 Temp = 273.5467
+PotEng = -6408.9584 E_bond = 18.2714 E_angle = 33.3035
+E_dihed = 16.8150 E_impro = 2.6053 E_vdwl = 686.3261
+E_coul = 26736.1131 E_long = -33902.3928 Press = -1470.3871
+---------------- Step 250 ----- CPU = 1.4311 (sec) ----------------
+TotEng = -5294.1809 KinEng = 1071.1623 Temp = 266.2530
+PotEng = -6365.3432 E_bond = 14.2022 E_angle = 39.1953
+E_dihed = 19.4555 E_impro = 3.1387 E_vdwl = 753.5412
+E_coul = 26713.8465 E_long = -33908.7226 Press = -188.8077
+SHAKE stats (type/ave/delta) on step 300
+ 4 1.111 3.78266e-06
+ 6 0.997001 3.50137e-06
+ 8 1.08 2.09322e-06
+ 10 1.111 5.64331e-06
+ 12 1.08 2.10401e-06
+ 14 0.96 0
+ 18 0.957202 7.67991e-06
+ 31 104.52 0.000806336
+---------------- Step 300 ----- CPU = 1.7306 (sec) ----------------
+TotEng = -5251.4350 KinEng = 1123.6256 Temp = 279.2935
+PotEng = -6375.0606 E_bond = 14.2249 E_angle = 38.4712
+E_dihed = 18.1324 E_impro = 2.3700 E_vdwl = 715.4557
+E_coul = 26745.4100 E_long = -33909.1249 Press = -469.5450
+Loop time of 1.73061 on 4 procs for 300 steps with 2004 atoms
+
+Performance: 29.955 ns/day, 0.801 hours/ns, 173.349 timesteps/s
+99.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 1.2122 | 1.2332 | 1.2511 | 1.6 | 71.26
+Bond | 0.0012589 | 0.0043506 | 0.007498 | 4.2 | 0.25
+Kspace | 0.1673 | 0.18692 | 0.20947 | 4.0 | 10.80
+Neigh | 0.17076 | 0.17102 | 0.17129 | 0.0 | 9.88
+Comm | 0.068879 | 0.070616 | 0.071993 | 0.5 | 4.08
+Output | 0.00030756 | 0.00032926 | 0.00038385 | 0.2 | 0.02
+Modify | 0.059337 | 0.059592 | 0.059881 | 0.1 | 3.44
+Other | | 0.004566 | | | 0.26
+
+Nlocal: 501 ave 508 max 490 min
+Histogram: 1 0 0 0 0 0 1 1 0 1
+Nghost: 6586.25 ave 6628 max 6548 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+Neighs: 177007 ave 180562 max 170212 min
+Histogram: 1 0 0 0 0 0 0 1 1 1
+
+Total # of neighbors = 708028
+Ave neighs/atom = 353.307
+Ave special neighs/atom = 2.34032
+Neighbor list builds = 26
+Dangerous builds = 0
+
+Total wall time: 0:00:01
diff --git a/examples/peri/log.15Feb16.peri.g++.1 b/examples/peri/log.15Feb16.peri.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..9189fade216884408de5bc53f86e338e8dd5713f
--- /dev/null
+++ b/examples/peri/log.15Feb16.peri.g++.1
@@ -0,0 +1,104 @@
+LAMMPS (15 Feb 2016)
+# small Peridynamic cylinder hit by projectile
+
+units si
+boundary s s s
+atom_style peri
+atom_modify map array
+neighbor 0.0010 bin
+
+# small target
+
+lattice sc 0.0005
+Lattice spacing in x,y,z = 0.0005 0.0005 0.0005
+region target cylinder y 0.0 0.0 0.0050 -0.0050 0.0 units box
+create_box 1 target
+Created orthogonal box = (-0.005 -0.005 -0.005) to (0.005 0 0.005)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 region target
+Created 3487 atoms
+
+pair_style peri/pmb
+pair_coeff * * 1.6863e22 0.0015001 0.0005 0.25
+set group all density 2200
+ 3487 settings made for density
+set group all volume 1.25e-10
+ 3487 settings made for volume
+velocity all set 0.0 0.0 0.0 sum no units box
+fix 1 all nve
+
+# spherical indenter to shatter target
+
+variable y0 equal 0.00155
+variable vy equal -100
+variable y equal "v_y0 + step*dt*v_vy"
+
+fix 2 all indent 1e17 sphere 0.0000 v_y 0.0000 0.0015 units box
+
+compute 1 all damage/atom
+timestep 1.0e-7
+thermo 100
+
+#dump 1 all custom 100 dump.peri id type x y z c_1
+
+#dump 2 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30 adiam 0.0006
+#dump_modify 2 pad 4
+
+#dump 3 all movie 50 movie.mpg type type # axes yes 0.8 0.02 view 80 -30 adiam 0.0006
+#dump_modify 3 pad 4
+
+run 1000
+Neighbor list info ...
+ 2 neighbor list requests
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 0.0025001
+ ghost atom cutoff = 0.0025001
+ binsize = 0.00125005 -> bins = 9 5 9
+Peridynamic bonds:
+ total # of bonds = 335966
+ bonds/atom = 96.3482
+Memory usage per processor = 26.6858 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 0 0 0 0 0 5.0030006e-07
+ 100 1.7890585e+24 552721.8 0 681881.47 1.7210968e+11 5.0030006e-07
+ 200 1.3549879e+27 3097027.6 0 1.0091931e+08 1.1829272e+14 5.5130066e-07
+ 300 3.3009625e+27 6331254.8 0 2.4464163e+08 1.9647265e+14 8.0862953e-07
+ 400 3.815184e+27 6225081.7 0 2.8165928e+08 1.8189267e+14 1.0095118e-06
+ 500 4.2580877e+27 20212686 0 3.2762196e+08 1.6249923e+14 1.2611723e-06
+ 600 5.5126512e+27 30861342 0 4.2884284e+08 1.7320038e+14 1.531873e-06
+ 700 1.1807414e+28 23119941 0 8.7554687e+08 2.9477434e+14 1.9278632e-06
+ 800 1.2424839e+28 2407361.6 0 8.994088e+08 2.3787786e+14 2.5138992e-06
+ 900 1.2358395e+28 4532520.6 0 8.9673706e+08 1.9097312e+14 3.1145903e-06
+ 1000 1.2341057e+28 3219939.5 0 8.9417279e+08 1.5968597e+14 3.7196039e-06
+Loop time of 20.9881 on 1 procs for 1000 steps with 3487 atoms
+
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 20.268 | 20.268 | 20.268 | 0.0 | 96.57
+Neigh | 0.59991 | 0.59991 | 0.59991 | 0.0 | 2.86
+Comm | 0.0019219 | 0.0019219 | 0.0019219 | 0.0 | 0.01
+Output | 0.0002439 | 0.0002439 | 0.0002439 | 0.0 | 0.00
+Modify | 0.10321 | 0.10321 | 0.10321 | 0.0 | 0.49
+Other | | 0.01511 | | | 0.07
+
+Nlocal: 3487 ave 3487 max 3487 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 567140 ave 567140 max 567140 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs: 1.20908e+06 ave 1.20908e+06 max 1.20908e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1209076
+Ave neighs/atom = 346.738
+Neighbor list builds = 46
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:21
diff --git a/examples/peri/log.15Feb16.peri.g++.4 b/examples/peri/log.15Feb16.peri.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..bdfa29a4cee2d2bda774053b1d49c91755ab7189
--- /dev/null
+++ b/examples/peri/log.15Feb16.peri.g++.4
@@ -0,0 +1,104 @@
+LAMMPS (15 Feb 2016)
+# small Peridynamic cylinder hit by projectile
+
+units si
+boundary s s s
+atom_style peri
+atom_modify map array
+neighbor 0.0010 bin
+
+# small target
+
+lattice sc 0.0005
+Lattice spacing in x,y,z = 0.0005 0.0005 0.0005
+region target cylinder y 0.0 0.0 0.0050 -0.0050 0.0 units box
+create_box 1 target
+Created orthogonal box = (-0.005 -0.005 -0.005) to (0.005 0 0.005)
+ 2 by 1 by 2 MPI processor grid
+create_atoms 1 region target
+Created 3487 atoms
+
+pair_style peri/pmb
+pair_coeff * * 1.6863e22 0.0015001 0.0005 0.25
+set group all density 2200
+ 3487 settings made for density
+set group all volume 1.25e-10
+ 3487 settings made for volume
+velocity all set 0.0 0.0 0.0 sum no units box
+fix 1 all nve
+
+# spherical indenter to shatter target
+
+variable y0 equal 0.00155
+variable vy equal -100
+variable y equal "v_y0 + step*dt*v_vy"
+
+fix 2 all indent 1e17 sphere 0.0000 v_y 0.0000 0.0015 units box
+
+compute 1 all damage/atom
+timestep 1.0e-7
+thermo 100
+
+#dump 1 all custom 100 dump.peri id type x y z c_1
+
+#dump 2 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30 adiam 0.0006
+#dump_modify 2 pad 4
+
+#dump 3 all movie 50 movie.mpg type type # axes yes 0.8 0.02 view 80 -30 adiam 0.0006
+#dump_modify 3 pad 4
+
+run 1000
+Neighbor list info ...
+ 2 neighbor list requests
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 0.0025001
+ ghost atom cutoff = 0.0025001
+ binsize = 0.00125005 -> bins = 9 5 9
+Peridynamic bonds:
+ total # of bonds = 335966
+ bonds/atom = 96.3482
+Memory usage per processor = 26.9049 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 0 0 0 0 0 5.0030006e-07
+ 100 1.7890585e+24 552721.8 0 681881.47 1.7210968e+11 5.0030006e-07
+ 200 1.3549879e+27 3097027.6 0 1.0091931e+08 1.1829272e+14 5.5130066e-07
+ 300 3.3009625e+27 6331254.8 0 2.4464163e+08 1.9647265e+14 8.0862953e-07
+ 400 3.815184e+27 6225081.7 0 2.8165928e+08 1.8189267e+14 1.0095118e-06
+ 500 4.2580877e+27 20212686 0 3.2762196e+08 1.6249923e+14 1.2611723e-06
+ 600 5.5126512e+27 30861342 0 4.2884284e+08 1.7320038e+14 1.531873e-06
+ 700 1.1807414e+28 23119941 0 8.7554687e+08 2.9477434e+14 1.9278632e-06
+ 800 1.2424839e+28 2407361.5 0 8.994088e+08 2.3787786e+14 2.5138992e-06
+ 900 1.2358395e+28 4532520.1 0 8.9673706e+08 1.9097312e+14 3.1145903e-06
+ 1000 1.2341057e+28 3219974.3 0 8.9417286e+08 1.5968598e+14 3.7196039e-06
+Loop time of 5.93611 on 4 procs for 1000 steps with 3487 atoms
+
+99.6% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 4.6969 | 5.0667 | 5.4557 | 15.1 | 85.35
+Neigh | 0.11722 | 0.15148 | 0.18695 | 8.1 | 2.55
+Comm | 0.24957 | 0.67644 | 1.083 | 45.2 | 11.40
+Output | 0.00026965 | 0.00032377 | 0.00040698 | 0.3 | 0.01
+Modify | 0.02939 | 0.029681 | 0.030176 | 0.2 | 0.50
+Other | | 0.01153 | | | 0.19
+
+Nlocal: 871.75 ave 920 max 824 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+Nghost: 1343.25 ave 1391 max 1295 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+Neighs: 141785 ave 170754 max 115891 min
+Histogram: 1 1 0 0 0 0 0 1 0 1
+FullNghs: 302269 ave 346070 max 260820 min
+Histogram: 1 0 0 0 2 0 0 0 0 1
+
+Total # of neighbors = 1209076
+Ave neighs/atom = 346.738
+Neighbor list builds = 46
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:05
diff --git a/examples/pour/log.15Feb16.pour.2d.g++.1 b/examples/pour/log.15Feb16.pour.2d.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..a440536edae430bff8dcee5ab8aceb2667e76f8c
--- /dev/null
+++ b/examples/pour/log.15Feb16.pour.2d.g++.1
@@ -0,0 +1,115 @@
+LAMMPS (15 Feb 2016)
+# Pour 2d granular particles into container
+
+dimension 2
+atom_style sphere
+boundary f fm p
+newton off
+comm_modify vel yes
+
+region reg block 0 100 0 50 -0.5 0.5 units box
+create_box 1 reg
+Created orthogonal box = (0 0 -0.5) to (100 50 0.5)
+ 1 by 1 by 1 MPI processor grid
+
+neighbor 0.2 bin
+neigh_modify delay 0
+
+# IMPORTANT NOTE: these values of stiffness (4000) and timestep (0.001)
+# are used in this example file to produce a quick simulation and movie.
+# More appropriate values for realistic simulations would be
+# k = 4.0e5 and dt = 0.0001, as in bench/in.chute (if it were Hertzian).
+
+pair_style gran/hertz/history 4000.0 NULL 100.0 NULL 0.5 0
+pair_coeff * *
+
+timestep 0.001
+
+fix 1 all nve/sphere
+fix 2 all gravity 1.0 spherical 0.0 -180.0
+fix xwalls all wall/gran 4000.0 NULL 100.0 NULL 0 1 xplane 0 100
+fix ywalls all wall/gran 4000.0 NULL 100.0 NULL 0 1 yplane 0 NULL
+
+region slab block 1.0 99.0 30 34.5 -0.5 0.5 units box
+fix ins all pour 1000 1 4767548 vol 0.4 10 diam range 0.5 1.0 region slab
+Particle insertion: 224 every 3000 steps, 1000 by step 12001
+
+fix 3 all enforce2d
+
+compute 1 all erotate/sphere
+thermo_style custom step atoms ke c_1 vol
+thermo 1000
+thermo_modify lost ignore norm no
+compute_modify thermo_temp dynamic yes
+
+#dump id all atom 250 dump.pour
+
+#dump 2 all image 500 image.*.jpg type type # zoom 1.6 adiam 1.5
+#dump_modify 2 pad 5
+
+#dump 3 all movie 500 movie.mpg type type # zoom 1.6 adiam 1.5
+#dump_modify 3 pad 5
+
+run 25000
+Neighbor list info ...
+ 2 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 1.2
+ ghost atom cutoff = 1.2
+ binsize = 0.6 -> bins = 167 84 2
+Memory usage per processor = 2.75187 Mbytes
+Step Atoms KinEng 1 Volume
+ 0 0 -0 0 5000
+ 1000 224 201.77464 0 5000
+ 2000 224 372.42868 0 5000
+ 3000 224 599.60221 0 5000
+ 4000 448 1084.3752 0 5000
+ 5000 448 1592.4543 0 5000
+ 6000 448 1763.3153 37.274939 5000
+ 7000 672 1805.206 89.331853 5000
+ 8000 672 1778.0015 111.58381 5000
+ 9000 672 1592.6805 97.550311 5000
+ 10000 896 1631.962 76.905078 5000
+ 11000 896 1590.1527 68.644552 5000
+ 12000 896 1564.4707 60.119562 5000
+ 13000 1000 1490.072 56.982972 5000
+ 14000 1000 1266.4669 57.579371 5000
+ 15000 1000 1034.1055 46.079374 5000
+ 16000 1000 748.70283 43.933154 5000
+ 17000 1000 462.65166 37.522016 5000
+ 18000 1000 327.40481 29.450285 5000
+ 19000 1000 223.24319 31.981144 5000
+ 20000 1000 54.792042 23.449101 5000
+ 21000 1000 25.805484 16.352528 5000
+ 22000 1000 20.617765 11.756965 5000
+ 23000 1000 16.115382 7.9435503 5000
+ 24000 1000 11.971003 5.9411126 5000
+ 25000 1000 10.404117 4.3811155 5000
+Loop time of 3.04462 on 1 procs for 25000 steps with 1000 atoms
+
+Performance: 709447.910 tau/day, 8211.203 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 1.2896 | 1.2896 | 1.2896 | 0.0 | 42.36
+Neigh | 0.40714 | 0.40714 | 0.40714 | 0.0 | 13.37
+Comm | 0.0080216 | 0.0080216 | 0.0080216 | 0.0 | 0.26
+Output | 0.00042129 | 0.00042129 | 0.00042129 | 0.0 | 0.01
+Modify | 1.2178 | 1.2178 | 1.2178 | 0.0 | 40.00
+Other | | 0.1217 | | | 4.00
+
+Nlocal: 1000 ave 1000 max 1000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 2374 ave 2374 max 2374 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 2374
+Ave neighs/atom = 2.374
+Neighbor list builds = 2089
+Dangerous builds = 0
+Total wall time: 0:00:03
diff --git a/examples/pour/log.15Feb16.pour.2d.g++.4 b/examples/pour/log.15Feb16.pour.2d.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..1145101b34f372c123e2dbb688ab5b174c6faea1
--- /dev/null
+++ b/examples/pour/log.15Feb16.pour.2d.g++.4
@@ -0,0 +1,115 @@
+LAMMPS (15 Feb 2016)
+# Pour 2d granular particles into container
+
+dimension 2
+atom_style sphere
+boundary f fm p
+newton off
+comm_modify vel yes
+
+region reg block 0 100 0 50 -0.5 0.5 units box
+create_box 1 reg
+Created orthogonal box = (0 0 -0.5) to (100 50 0.5)
+ 4 by 1 by 1 MPI processor grid
+
+neighbor 0.2 bin
+neigh_modify delay 0
+
+# IMPORTANT NOTE: these values of stiffness (4000) and timestep (0.001)
+# are used in this example file to produce a quick simulation and movie.
+# More appropriate values for realistic simulations would be
+# k = 4.0e5 and dt = 0.0001, as in bench/in.chute (if it were Hertzian).
+
+pair_style gran/hertz/history 4000.0 NULL 100.0 NULL 0.5 0
+pair_coeff * *
+
+timestep 0.001
+
+fix 1 all nve/sphere
+fix 2 all gravity 1.0 spherical 0.0 -180.0
+fix xwalls all wall/gran 4000.0 NULL 100.0 NULL 0 1 xplane 0 100
+fix ywalls all wall/gran 4000.0 NULL 100.0 NULL 0 1 yplane 0 NULL
+
+region slab block 1.0 99.0 30 34.5 -0.5 0.5 units box
+fix ins all pour 1000 1 4767548 vol 0.4 10 diam range 0.5 1.0 region slab
+Particle insertion: 224 every 3000 steps, 1000 by step 12001
+
+fix 3 all enforce2d
+
+compute 1 all erotate/sphere
+thermo_style custom step atoms ke c_1 vol
+thermo 1000
+thermo_modify lost ignore norm no
+compute_modify thermo_temp dynamic yes
+
+#dump id all atom 250 dump.pour
+
+#dump 2 all image 500 image.*.jpg type type # zoom 1.6 adiam 1.5
+#dump_modify 2 pad 5
+
+#dump 3 all movie 500 movie.mpg type type # zoom 1.6 adiam 1.5
+#dump_modify 3 pad 5
+
+run 25000
+Neighbor list info ...
+ 2 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 1.2
+ ghost atom cutoff = 1.2
+ binsize = 0.6 -> bins = 167 84 2
+Memory usage per processor = 2.71741 Mbytes
+Step Atoms KinEng 1 Volume
+ 0 0 -0 0 5000
+ 1000 224 201.77464 0 5000
+ 2000 224 372.42868 0 5000
+ 3000 224 599.60221 0 5000
+ 4000 448 1084.3752 0 5000
+ 5000 448 1592.4543 0 5000
+ 6000 448 1763.3153 37.274939 5000
+ 7000 672 1805.206 89.331853 5000
+ 8000 672 1778.0015 111.58381 5000
+ 9000 672 1592.6805 97.550311 5000
+ 10000 896 1630.8521 79.742572 5000
+ 11000 896 1593.1588 67.633788 5000
+ 12000 896 1562.2084 65.097236 5000
+ 13000 1000 1504.1203 63.468934 5000
+ 14000 1000 1266.5724 55.837334 5000
+ 15000 1000 1041.8665 48.938774 5000
+ 16000 1000 766.27305 43.846151 5000
+ 17000 1000 466.30103 43.206188 5000
+ 18000 1000 320.50154 26.84775 5000
+ 19000 1000 207.91453 29.183522 5000
+ 20000 1000 52.447982 19.30378 5000
+ 21000 1000 22.027641 10.395933 5000
+ 22000 1000 15.395099 6.7003289 5000
+ 23000 1000 11.97674 5.2548063 5000
+ 24000 1000 7.8974699 3.7396899 5000
+ 25000 1000 6.1288038 2.2056805 5000
+Loop time of 0.977215 on 4 procs for 25000 steps with 1000 atoms
+
+Performance: 2210364.086 tau/day, 25582.918 timesteps/s
+98.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.30766 | 0.33267 | 0.35001 | 3.1 | 34.04
+Neigh | 0.094669 | 0.1019 | 0.10693 | 1.6 | 10.43
+Comm | 0.060945 | 0.078421 | 0.097028 | 5.5 | 8.02
+Output | 0.00042653 | 0.00045699 | 0.00049639 | 0.1 | 0.05
+Modify | 0.2936 | 0.30701 | 0.31712 | 1.7 | 31.42
+Other | | 0.1568 | | | 16.04
+
+Nlocal: 250 ave 267 max 232 min
+Histogram: 1 0 0 0 1 1 0 0 0 1
+Nghost: 18 ave 23 max 14 min
+Histogram: 2 0 0 0 0 0 0 1 0 1
+Neighs: 606 ave 664 max 559 min
+Histogram: 1 0 1 0 0 1 0 0 0 1
+
+Total # of neighbors = 2424
+Ave neighs/atom = 2.424
+Neighbor list builds = 2060
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/pour/log.15Feb16.pour.2d.molecule.g++.1 b/examples/pour/log.15Feb16.pour.2d.molecule.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..bfe706ba9719a87dddf925ff8b5c0f150a17ae05
--- /dev/null
+++ b/examples/pour/log.15Feb16.pour.2d.molecule.g++.1
@@ -0,0 +1,136 @@
+LAMMPS (15 Feb 2016)
+# Pour 2d granular particles into container
+
+dimension 2
+atom_style sphere
+atom_modify map array
+boundary f fm p
+newton off
+comm_modify vel yes cutoff 2.5
+
+fix prop all property/atom mol ghost yes
+
+region reg block 0 100 0 50 -0.5 0.5 units box
+create_box 1 reg
+Created orthogonal box = (0 0 -0.5) to (100 50 0.5)
+ 1 by 1 by 1 MPI processor grid
+
+neighbor 0.2 bin
+neigh_modify delay 0
+
+# IMPORTANT NOTE: these values of stiffness (4000) and timestep (0.001)
+# are used in this example file to produce a quick simulation and movie.
+# More appropriate values for realistic simulations would be
+# k = 4.0e5 and dt = 0.0001, as in bench/in.chute (if it were Hertzian).
+
+pair_style gran/hertz/history 4000.0 NULL 100.0 NULL 0.5 0
+pair_coeff * *
+
+timestep 0.001
+
+fix 2 all gravity 1.0 spherical 0.0 -180.0
+fix xwalls all wall/gran 4000.0 NULL 100.0 NULL 0 1 xplane 0 100
+fix ywalls all wall/gran 4000.0 NULL 100.0 NULL 0 1 yplane 0 NULL
+
+molecule object molecule.vshape
+Read molecule object:
+ 5 atoms with 1 types
+ 0 bonds with 0 types
+ 0 angles with 0 types
+ 0 dihedrals with 0 types
+ 0 impropers with 0 types
+fix 3 all rigid/small molecule mol object
+0 rigid bodies with 0 atoms
+ 2.23607 = max distance from body owner to body atom
+
+# insure region size + molecule size does not overlap wall
+
+region slab block 3.0 97.0 30 34.5 -0.5 0.5 units box
+fix ins all pour 500 0 4767548 vol 0.8 10 region slab mol object rigid 3
+Particle insertion: 26 every 3000 steps, 500 by step 57001
+
+fix 4 all enforce2d
+
+compute 1 all erotate/sphere
+compute Tsphere all temp/sphere
+thermo_style custom step atoms ke c_1 vol
+thermo_modify lost ignore norm no temp Tsphere
+compute_modify Tsphere dynamic yes
+
+thermo 1000
+
+#dump id all atom 100 tmp.dump
+
+#variable colors string # "red green blue yellow white # purple pink orange lime gray"
+#variable mol2 atom mol%10
+#dump 2 all image 250 image.*.jpg v_mol2 type # zoom 1.6 adiam 1.5
+#dump_modify 2 pad 5 amap 0 10 sa 1 10 ${colors}
+
+#variable colors string # "red green blue yellow white # purple pink orange lime gray"
+#variable mol3 atom mol%10
+#dump 3 all movie 250 movie.mpg v_mol3 type # zoom 1.6 adiam 1.5
+#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
+
+run 25000
+Neighbor list info ...
+ 2 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 1.2
+ ghost atom cutoff = 2.5
+ binsize = 0.6 -> bins = 167 84 2
+Memory usage per processor = 2.75807 Mbytes
+Step Atoms KinEng 1 Volume
+ 0 0 -0 0 5000
+ 1000 130 259.24123 2.3772821e-30 5000
+ 2000 130 465.39775 9.5010246e-30 5000
+ 3000 130 736.55426 2.1365791e-29 5000
+ 4000 260 1274.295 6.045774e-05 5000
+ 5000 260 1855.4991 0.0021687846 5000
+ 6000 260 1936.8934 6.9705094 5000
+ 7000 390 1909.1519 11.402993 5000
+ 8000 390 1958.2549 10.910611 5000
+ 9000 390 1968.6293 14.080709 5000
+ 10000 520 2278.4559 8.2512574 5000
+ 11000 520 1952.4436 6.8525602 5000
+ 12000 520 1391.9826 3.6742003 5000
+ 13000 650 1608.9033 2.2121034 5000
+ 14000 650 1562.8758 2.9284792 5000
+ 15000 650 1549.101 2.432552 5000
+ 16000 780 1718.9486 2.339785 5000
+ 17000 780 1646.7053 5.1414663 5000
+ 18000 780 1441.0842 3.7040072 5000
+ 19000 910 1546.6435 2.5109623 5000
+ 20000 910 1379.5416 4.2028322 5000
+ 21000 910 1155.2864 2.05953 5000
+ 22000 1040 1237.0246 3.0494101 5000
+ 23000 1040 1160.8301 3.0040354 5000
+ 24000 1040 1192.673 1.6310726 5000
+ 25000 1170 1128.3916 3.3745733 5000
+Loop time of 3.24674 on 1 procs for 25000 steps with 1170 atoms
+
+Performance: 665282.302 tau/day, 7700.027 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.90701 | 0.90701 | 0.90701 | 0.0 | 27.94
+Neigh | 0.25099 | 0.25099 | 0.25099 | 0.0 | 7.73
+Comm | 0.010076 | 0.010076 | 0.010076 | 0.0 | 0.31
+Output | 0.00050974 | 0.00050974 | 0.00050974 | 0.0 | 0.02
+Modify | 1.9744 | 1.9744 | 1.9744 | 0.0 | 60.81
+Other | | 0.1038 | | | 3.20
+
+Nlocal: 1170 ave 1170 max 1170 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 1699 ave 1699 max 1699 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1699
+Ave neighs/atom = 1.45214
+Neighbor list builds = 1737
+Dangerous builds = 0
+Total wall time: 0:00:03
diff --git a/examples/pour/log.15Feb16.pour.2d.molecule.g++.4 b/examples/pour/log.15Feb16.pour.2d.molecule.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..dd002f2238a7e5659f0912268af5712ed8b27222
--- /dev/null
+++ b/examples/pour/log.15Feb16.pour.2d.molecule.g++.4
@@ -0,0 +1,136 @@
+LAMMPS (15 Feb 2016)
+# Pour 2d granular particles into container
+
+dimension 2
+atom_style sphere
+atom_modify map array
+boundary f fm p
+newton off
+comm_modify vel yes cutoff 2.5
+
+fix prop all property/atom mol ghost yes
+
+region reg block 0 100 0 50 -0.5 0.5 units box
+create_box 1 reg
+Created orthogonal box = (0 0 -0.5) to (100 50 0.5)
+ 4 by 1 by 1 MPI processor grid
+
+neighbor 0.2 bin
+neigh_modify delay 0
+
+# IMPORTANT NOTE: these values of stiffness (4000) and timestep (0.001)
+# are used in this example file to produce a quick simulation and movie.
+# More appropriate values for realistic simulations would be
+# k = 4.0e5 and dt = 0.0001, as in bench/in.chute (if it were Hertzian).
+
+pair_style gran/hertz/history 4000.0 NULL 100.0 NULL 0.5 0
+pair_coeff * *
+
+timestep 0.001
+
+fix 2 all gravity 1.0 spherical 0.0 -180.0
+fix xwalls all wall/gran 4000.0 NULL 100.0 NULL 0 1 xplane 0 100
+fix ywalls all wall/gran 4000.0 NULL 100.0 NULL 0 1 yplane 0 NULL
+
+molecule object molecule.vshape
+Read molecule object:
+ 5 atoms with 1 types
+ 0 bonds with 0 types
+ 0 angles with 0 types
+ 0 dihedrals with 0 types
+ 0 impropers with 0 types
+fix 3 all rigid/small molecule mol object
+0 rigid bodies with 0 atoms
+ 2.23607 = max distance from body owner to body atom
+
+# insure region size + molecule size does not overlap wall
+
+region slab block 3.0 97.0 30 34.5 -0.5 0.5 units box
+fix ins all pour 500 0 4767548 vol 0.8 10 region slab mol object rigid 3
+Particle insertion: 26 every 3000 steps, 500 by step 57001
+
+fix 4 all enforce2d
+
+compute 1 all erotate/sphere
+compute Tsphere all temp/sphere
+thermo_style custom step atoms ke c_1 vol
+thermo_modify lost ignore norm no temp Tsphere
+compute_modify Tsphere dynamic yes
+
+thermo 1000
+
+#dump id all atom 100 tmp.dump
+
+#variable colors string # "red green blue yellow white # purple pink orange lime gray"
+#variable mol2 atom mol%10
+#dump 2 all image 250 image.*.jpg v_mol2 type # zoom 1.6 adiam 1.5
+#dump_modify 2 pad 5 amap 0 10 sa 1 10 ${colors}
+
+#variable colors string # "red green blue yellow white # purple pink orange lime gray"
+#variable mol3 atom mol%10
+#dump 3 all movie 250 movie.mpg v_mol3 type # zoom 1.6 adiam 1.5
+#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
+
+run 25000
+Neighbor list info ...
+ 2 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 1.2
+ ghost atom cutoff = 2.5
+ binsize = 0.6 -> bins = 167 84 2
+Memory usage per processor = 2.72041 Mbytes
+Step Atoms KinEng 1 Volume
+ 0 0 -0 0 5000
+ 1000 130 259.24123 2.3773387e-30 5000
+ 2000 130 465.39775 9.5010816e-30 5000
+ 3000 130 736.55426 2.1365846e-29 5000
+ 4000 260 1274.295 6.045774e-05 5000
+ 5000 260 1855.4991 0.0021687846 5000
+ 6000 260 1936.8934 6.9705094 5000
+ 7000 390 1909.1519 11.402993 5000
+ 8000 390 1958.2549 10.910611 5000
+ 9000 390 1968.6293 14.080709 5000
+ 10000 520 2278.4559 8.2512574 5000
+ 11000 520 1952.4436 6.8525602 5000
+ 12000 520 1391.9826 3.6742003 5000
+ 13000 650 1608.8924 2.2123232 5000
+ 14000 650 1562.872 2.9306477 5000
+ 15000 650 1548.2428 2.4495128 5000
+ 16000 780 1712.8658 2.2773941 5000
+ 17000 780 1649.1423 4.9833774 5000
+ 18000 780 1421.6645 4.0064802 5000
+ 19000 910 1574.37 2.4833854 5000
+ 20000 910 1354.8838 5.1248395 5000
+ 21000 910 1156.7385 2.5239056 5000
+ 22000 1040 1233.7916 2.9364978 5000
+ 23000 1040 1150.2238 2.5059515 5000
+ 24000 1040 1224.372 1.6145537 5000
+ 25000 1170 1202.871 2.6775319 5000
+Loop time of 1.18423 on 4 procs for 25000 steps with 1170 atoms
+
+Performance: 1823968.216 tau/day, 21110.743 timesteps/s
+99.1% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.22024 | 0.23723 | 0.25431 | 2.6 | 20.03
+Neigh | 0.057575 | 0.064853 | 0.070241 | 1.8 | 5.48
+Comm | 0.068985 | 0.082663 | 0.097154 | 3.9 | 6.98
+Output | 0.00060296 | 0.00069225 | 0.0009203 | 0.5 | 0.06
+Modify | 0.67185 | 0.6862 | 0.69518 | 1.1 | 57.94
+Other | | 0.1126 | | | 9.51
+
+Nlocal: 292.5 ave 304 max 278 min
+Histogram: 1 0 1 0 0 0 0 0 0 2
+Nghost: 42.5 ave 58 max 27 min
+Histogram: 1 1 0 0 0 0 0 0 1 1
+Neighs: 427 ave 456 max 388 min
+Histogram: 1 0 0 1 0 0 0 0 0 2
+
+Total # of neighbors = 1708
+Ave neighs/atom = 1.45983
+Neighbor list builds = 1732
+Dangerous builds = 0
+Total wall time: 0:00:01
diff --git a/examples/pour/log.15Feb16.pour.g++.1 b/examples/pour/log.15Feb16.pour.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..6515c6178e6d61bbdf8473b2a1e21869a18dbd38
--- /dev/null
+++ b/examples/pour/log.15Feb16.pour.g++.1
@@ -0,0 +1,169 @@
+LAMMPS (15 Feb 2016)
+# Pour granular particles into chute container, then induce flow
+
+atom_style sphere
+boundary p p fm
+newton off
+comm_modify vel yes
+
+region reg block -10 10 -10 10 -0.5 16 units box
+create_box 1 reg
+Created orthogonal box = (-10 -10 -0.5) to (10 10 16)
+ 1 by 1 by 1 MPI processor grid
+
+neighbor 0.2 bin
+neigh_modify delay 0
+
+# IMPORTANT NOTE: these values of stiffness (2000) and timestep (0.001)
+# are used in this example file to produce a quick simulation and movie.
+# More appropriate values for realistic simulations would be
+# k = 2.0e5 and dt = 0.0001, as in bench/in.chute.
+
+pair_style gran/hooke/history 2000.0 NULL 50.0 NULL 0.5 0
+pair_coeff * *
+
+timestep 0.001
+
+fix 1 all nve/sphere
+fix 2 all gravity 1.0 spherical 0.0 -180.0
+fix zlower all wall/gran 2000.0 NULL 50.0 NULL 0.5 0 zplane 0.0 2000.0
+
+region slab block -9.0 9.0 -9.0 9.0 10.0 15.0 units box
+fix ins all pour 3000 1 300719 vol 0.13 50 region slab
+Particle insertion: 402 every 3162 steps, 3000 by step 22135
+
+compute 1 all erotate/sphere
+thermo_style custom step atoms ke c_1 vol
+thermo 1000
+thermo_modify lost ignore norm no
+compute_modify thermo_temp dynamic yes
+
+#dump id all atom 1000 dump.pour
+
+#dump 2 all image 1000 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30
+#dump_modify 2 pad 5
+
+#dump 3 all movie 1000 movie.mpg type type # axes yes 0.8 0.02 view 80 -30
+#dump_modify 3 pad 5
+
+run 25000
+Neighbor list info ...
+ 2 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 1.2
+ ghost atom cutoff = 1.2
+ binsize = 0.6 -> bins = 34 34 28
+Memory usage per processor = 2.90017 Mbytes
+Step Atoms KinEng 1 Volume
+ 0 0 -0 0 6600
+ 1000 402 768.04606 0 6600
+ 2000 402 1407.1714 0 6600
+ 3000 402 1373.819 15.59952 6600
+ 4000 804 1737.1399 39.311164 6600
+ 5000 804 1571.3184 67.501382 6600
+ 6000 804 1318.6439 77.636174 6600
+ 7000 1206 1522.1986 68.863683 6600
+ 8000 1206 1387.2223 64.067846 6600
+ 9000 1206 1265.9044 51.726525 6600
+ 10000 1608 1460.3212 48.844763 6600
+ 11000 1608 1310.2001 53.532609 6600
+ 12000 1608 1134.4592 48.567743 6600
+ 13000 2010 1182.5037 45.620614 6600
+ 14000 2010 1192.4303 39.066935 6600
+ 15000 2010 967.05968 42.363789 6600
+ 16000 2412 1119.8304 39.217157 6600
+ 17000 2412 1063.7921 45.71714 6600
+ 18000 2412 855.28326 42.745948 6600
+ 19000 2814 970.7019 40.155896 6600
+ 20000 2814 923.94347 34.590568 6600
+ 21000 2814 793.75092 36.707509 6600
+ 22000 2814 543.4546 37.669131 6600
+ 23000 3000 446.47658 39.719019 6600
+ 24000 3000 331.57201 24.034747 6600
+ 25000 3000 239.90493 18.457205 6600
+Loop time of 9.98164 on 1 procs for 25000 steps with 3000 atoms
+
+Performance: 216397.236 tau/day, 2504.598 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 5.5892 | 5.5892 | 5.5892 | 0.0 | 55.99
+Neigh | 1.5595 | 1.5595 | 1.5595 | 0.0 | 15.62
+Comm | 0.21001 | 0.21001 | 0.21001 | 0.0 | 2.10
+Output | 0.00055695 | 0.00055695 | 0.00055695 | 0.0 | 0.01
+Modify | 2.3514 | 2.3514 | 2.3514 | 0.0 | 23.56
+Other | | 0.271 | | | 2.71
+
+Nlocal: 3000 ave 3000 max 3000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 658 ave 658 max 658 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 13479 ave 13479 max 13479 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 13479
+Ave neighs/atom = 4.493
+Neighbor list builds = 1149
+Dangerous builds = 0
+
+unfix ins
+fix 2 all gravity 1.0 chute 26.0
+run 25000
+Memory usage per processor = 7.37566 Mbytes
+Step Atoms KinEng 1 Volume
+ 25000 3000 239.90493 18.457205 6600
+ 26000 3000 86.453151 19.990229 6600
+ 27000 3000 104.03763 12.243926 6600
+ 28000 3000 187.74939 11.703132 6600
+ 29000 3000 316.59921 14.610301 6600
+ 30000 3000 520.76149 18.82089 6600
+ 31000 3000 821.71283 25.266473 6600
+ 32000 3000 1153.8578 30.714985 6600
+ 33000 3000 1520.1476 38.247011 6600
+ 34000 3000 2006.3144 44.480026 6600
+ 35000 3000 2556.4751 55.768118 6600
+ 36000 3000 3160.9914 63.728696 6600
+ 37000 3000 3877.5537 71.484742 6600
+ 38000 3000 4675.4987 79.37485 6600
+ 39000 3000 5479.8489 94.281786 6600
+ 40000 3000 6350.6439 106.39353 6600
+ 41000 3000 7245.0837 113.40306 6600
+ 42000 3000 8227.1726 129.62268 6600
+ 43000 3000 9422.0189 144.63991 6600
+ 44000 3000 10616.036 149.84326 6600
+ 45000 3000 11908.182 169.96204 6600
+ 46000 3000 13257.313 184.73533 6600
+ 47000 3000 14765.4 201.20237 6600
+ 48000 3000 16184.643 202.00907 6600
+ 49000 3000 17573.204 215.30429 6600
+ 50000 3000 19117.749 232.28939 6600
+Loop time of 19.1635 on 1 procs for 25000 steps with 3000 atoms
+
+Performance: 112714.075 tau/day, 1304.561 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 12.221 | 12.221 | 12.221 | 0.0 | 63.77
+Neigh | 2.2719 | 2.2719 | 2.2719 | 0.0 | 11.86
+Comm | 0.44526 | 0.44526 | 0.44526 | 0.0 | 2.32
+Output | 0.00094628 | 0.00094628 | 0.00094628 | 0.0 | 0.00
+Modify | 3.7599 | 3.7599 | 3.7599 | 0.0 | 19.62
+Other | | 0.4643 | | | 2.42
+
+Nlocal: 3000 ave 3000 max 3000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 742 ave 742 max 742 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 13997 ave 13997 max 13997 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 13997
+Ave neighs/atom = 4.66567
+Neighbor list builds = 836
+Dangerous builds = 0
+Total wall time: 0:00:29
diff --git a/examples/pour/log.15Feb16.pour.g++.4 b/examples/pour/log.15Feb16.pour.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..f7063e5891c4c99f4e11a4fb01f40e0df386a9d5
--- /dev/null
+++ b/examples/pour/log.15Feb16.pour.g++.4
@@ -0,0 +1,169 @@
+LAMMPS (15 Feb 2016)
+# Pour granular particles into chute container, then induce flow
+
+atom_style sphere
+boundary p p fm
+newton off
+comm_modify vel yes
+
+region reg block -10 10 -10 10 -0.5 16 units box
+create_box 1 reg
+Created orthogonal box = (-10 -10 -0.5) to (10 10 16)
+ 2 by 2 by 1 MPI processor grid
+
+neighbor 0.2 bin
+neigh_modify delay 0
+
+# IMPORTANT NOTE: these values of stiffness (2000) and timestep (0.001)
+# are used in this example file to produce a quick simulation and movie.
+# More appropriate values for realistic simulations would be
+# k = 2.0e5 and dt = 0.0001, as in bench/in.chute.
+
+pair_style gran/hooke/history 2000.0 NULL 50.0 NULL 0.5 0
+pair_coeff * *
+
+timestep 0.001
+
+fix 1 all nve/sphere
+fix 2 all gravity 1.0 spherical 0.0 -180.0
+fix zlower all wall/gran 2000.0 NULL 50.0 NULL 0.5 0 zplane 0.0 2000.0
+
+region slab block -9.0 9.0 -9.0 9.0 10.0 15.0 units box
+fix ins all pour 3000 1 300719 vol 0.13 50 region slab
+Particle insertion: 402 every 3162 steps, 3000 by step 22135
+
+compute 1 all erotate/sphere
+thermo_style custom step atoms ke c_1 vol
+thermo 1000
+thermo_modify lost ignore norm no
+compute_modify thermo_temp dynamic yes
+
+#dump id all atom 1000 dump.pour
+
+#dump 2 all image 1000 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30
+#dump_modify 2 pad 5
+
+#dump 3 all movie 1000 movie.mpg type type # axes yes 0.8 0.02 view 80 -30
+#dump_modify 3 pad 5
+
+run 25000
+Neighbor list info ...
+ 2 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 1.2
+ ghost atom cutoff = 1.2
+ binsize = 0.6 -> bins = 34 34 28
+Memory usage per processor = 2.77531 Mbytes
+Step Atoms KinEng 1 Volume
+ 0 0 -0 0 6600
+ 1000 402 768.04606 0 6600
+ 2000 402 1407.1714 0 6600
+ 3000 402 1373.819 15.59952 6600
+ 4000 804 1737.1399 39.311164 6600
+ 5000 804 1571.3184 67.501382 6600
+ 6000 804 1318.6439 77.636174 6600
+ 7000 1206 1521.8348 69.010381 6600
+ 8000 1206 1391.0761 64.407583 6600
+ 9000 1206 1264.98 50.32567 6600
+ 10000 1608 1462.7175 49.903609 6600
+ 11000 1608 1317.5878 52.401196 6600
+ 12000 1608 1120.9416 46.067058 6600
+ 13000 2010 1200.1517 49.662302 6600
+ 14000 2010 1180.2805 38.850379 6600
+ 15000 2010 970.23519 39.121533 6600
+ 16000 2412 1101.3888 44.051087 6600
+ 17000 2412 1054.4967 43.489619 6600
+ 18000 2412 850.25959 42.296696 6600
+ 19000 2814 959.68841 42.757546 6600
+ 20000 2814 933.72206 42.668586 6600
+ 21000 2814 779.2842 42.116934 6600
+ 22000 2814 537.68477 35.113909 6600
+ 23000 3000 456.26221 36.394458 6600
+ 24000 3000 334.38331 26.256087 6600
+ 25000 3000 233.7217 18.768345 6600
+Loop time of 2.97699 on 4 procs for 25000 steps with 3000 atoms
+
+Performance: 725563.868 tau/day, 8397.730 timesteps/s
+99.6% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 1.3818 | 1.4161 | 1.4613 | 2.9 | 47.57
+Neigh | 0.39047 | 0.40059 | 0.40954 | 1.3 | 13.46
+Comm | 0.30601 | 0.31937 | 0.33453 | 2.2 | 10.73
+Output | 0.00056505 | 0.00065571 | 0.00070286 | 0.2 | 0.02
+Modify | 0.60454 | 0.61377 | 0.62323 | 1.1 | 20.62
+Other | | 0.2265 | | | 7.61
+
+Nlocal: 750 ave 765 max 730 min
+Histogram: 1 0 0 0 1 0 0 0 1 1
+Nghost: 390.75 ave 393 max 385 min
+Histogram: 1 0 0 0 0 0 0 0 1 2
+Neighs: 3548 ave 3643 max 3454 min
+Histogram: 1 0 1 0 0 0 0 1 0 1
+
+Total # of neighbors = 14192
+Ave neighs/atom = 4.73067
+Neighbor list builds = 1152
+Dangerous builds = 0
+
+unfix ins
+fix 2 all gravity 1.0 chute 26.0
+run 25000
+Memory usage per processor = 7.22932 Mbytes
+Step Atoms KinEng 1 Volume
+ 25000 3000 233.7217 18.768345 6600
+ 26000 3000 80.58756 21.114703 6600
+ 27000 3000 112.90794 11.760837 6600
+ 28000 3000 211.68857 11.667711 6600
+ 29000 3000 368.27114 15.483397 6600
+ 30000 3000 611.33941 21.023859 6600
+ 31000 3000 902.04662 29.663904 6600
+ 32000 3000 1188.6213 31.996848 6600
+ 33000 3000 1626.3144 38.244424 6600
+ 34000 3000 2068.1939 45.793779 6600
+ 35000 3000 2654.4292 55.900641 6600
+ 36000 3000 3212.0662 64.492942 6600
+ 37000 3000 3942.9079 73.557353 6600
+ 38000 3000 4710.2169 84.24051 6600
+ 39000 3000 5513.597 93.737814 6600
+ 40000 3000 6367.338 112.43633 6600
+ 41000 3000 7417.7889 130.70338 6600
+ 42000 3000 8428.2678 124.66302 6600
+ 43000 3000 9498.0121 136.37107 6600
+ 44000 3000 10680.269 149.21074 6600
+ 45000 3000 11852.03 154.67802 6600
+ 46000 3000 12896.699 167.10324 6600
+ 47000 3000 14218.465 196.70386 6600
+ 48000 3000 15555.796 204.40316 6600
+ 49000 3000 16694.338 208.98934 6600
+ 50000 3000 17936.665 192.19442 6600
+Loop time of 5.6096 on 4 procs for 25000 steps with 3000 atoms
+
+Performance: 385054.499 tau/day, 4456.649 timesteps/s
+99.5% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 3.0572 | 3.1012 | 3.1483 | 1.8 | 55.28
+Neigh | 0.57694 | 0.58054 | 0.5881 | 0.6 | 10.35
+Comm | 0.52065 | 0.53928 | 0.55884 | 1.8 | 9.61
+Output | 0.00074744 | 0.00090379 | 0.0011649 | 0.5 | 0.02
+Modify | 0.94697 | 0.95569 | 0.96864 | 0.9 | 17.04
+Other | | 0.432 | | | 7.70
+
+Nlocal: 750 ave 758 max 741 min
+Histogram: 1 0 0 0 0 2 0 0 0 1
+Nghost: 404 ave 417 max 395 min
+Histogram: 1 0 1 0 1 0 0 0 0 1
+Neighs: 3603.75 ave 3695 max 3528 min
+Histogram: 1 0 0 1 1 0 0 0 0 1
+
+Total # of neighbors = 14415
+Ave neighs/atom = 4.805
+Neighbor list builds = 827
+Dangerous builds = 0
+Total wall time: 0:00:08
diff --git a/examples/prd/log.15Feb16.prd.g++.4 b/examples/prd/log.15Feb16.prd.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..30e15d6fbf8ac10123b31eef4d6cbc384c7a44b1
--- /dev/null
+++ b/examples/prd/log.15Feb16.prd.g++.4
@@ -0,0 +1,22 @@
+LAMMPS (15 Feb 2016)
+Running on 4 partitions of processors
+Step CPU Clock Event Correlated Coincident Replica
+100 0.000 0 0 0 0 0
+100 0.539 0 0 0 0 0
+100 0.694 0 0 0 0 0
+100 0.850 0 0 0 0 0
+100 0.928 0 0 0 0 0
+200 1.555 400 1 0 4 1
+300 1.924 500 2 1 1 1
+500 3.495 772 3 0 2 2
+800 5.446 1328 4 0 2 2
+1000 7.037 1636 5 0 1 3
+1000 7.989 1636 5 0 1 3
+1200 8.838 1908 6 0 1 2
+1300 9.212 2008 7 1 1 2
+1900 12.291 4024 8 0 1 3
+1900 12.832 4024 8 0 1 3
+1900 13.157 4024 8 0 1 3
+1900 13.320 4024 8 0 1 3
+2100 14.090 4220 9 0 2 3
+Loop time of 14.0941 on 4 procs for 2000 steps with 511 atoms
diff --git a/examples/qeq/log.15Feb16.qeq.buck.g++.1 b/examples/qeq/log.15Feb16.qeq.buck.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..089ecf8571fd7437772bdff8f1c48160706085ff
--- /dev/null
+++ b/examples/qeq/log.15Feb16.qeq.buck.g++.1
@@ -0,0 +1,105 @@
+LAMMPS (15 Feb 2016)
+# This example demonstrates the use of various fix qeq variants with
+# that defines and uses charges, in this case pair_style buck/coul/long
+
+units metal
+atom_style charge
+
+read_data data.aC
+ orthogonal box = (0 0 0) to (25.1583 25.1583 28.0203)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 1200 atoms
+replicate 2 2 2
+ orthogonal box = (0 0 0) to (50.3166 50.3166 56.0405)
+ 1 by 1 by 1 MPI processor grid
+ 9600 atoms
+
+pair_style buck/coul/long 12.0
+pair_coeff 2 2 1388.77 .3623188 175.0
+pair_coeff 1 2 18003 .2052124 133.5381
+pair_coeff 1 1 0 .1 0
+kspace_style ewald 1e-6
+
+neighbor 1.0 bin
+neigh_modify delay 0 every 1 check yes
+
+group type1 type 1
+3200 atoms in group type1
+compute charge1 type1 property/atom q
+compute q1 type1 reduce ave c_charge1
+group type2 type 2
+6400 atoms in group type2
+compute charge2 type2 property/atom q
+compute q2 type2 reduce ave c_charge2
+variable qtot equal count(type1)*c_q1+count(type2)*c_q2
+
+thermo_style custom step pe c_q1 c_q2 v_qtot spcpu
+thermo 10
+
+timestep 0.0001
+
+velocity all create 300.0 1281937
+fix 1 all nve
+
+#fix 2 all qeq/point 1 10 1.0e-6 100 param.qeq2
+#fix 2 all qeq/shielded 1 10 1.0e-6 100 param.qeq2
+#fix 2 all qeq/slater 1 10 1.0e-6 100 param.qeq2
+#fix 2 all qeq/dynamic 1 10 1.0e-4 100 param.qeq2
+fix 2 all qeq/fire 1 10 1.0e-4 100 param.qeq2
+
+run 100
+Ewald initialization ...
+ G vector (1/distance) = 0.305064
+ estimated absolute RMS force accuracy = 2.07629e-05
+ estimated relative force accuracy = 1.44191e-06
+ KSpace vectors: actual max1d max3d = 13556 20 34460
+ kxmax kymax kzmax = 18 18 20
+Neighbor list info ...
+ 2 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 13
+ ghost atom cutoff = 13
+ binsize = 6.5 -> bins = 8 8 9
+Memory usage per processor = 70.3977 Mbytes
+Step PotEng q1 q2 qtot S/CPU
+ 0 -27457.219 0.85227886 -0.42613943 -2.1827873e-10 0
+ 10 -27626.057 0.85486228 -0.42743114 -2.14186e-10 0.65299981
+ 20 -27975.085 0.85968531 -0.42984266 -9.5496944e-11 0.55284542
+ 30 -28552.628 0.86755661 -0.4337783 -2.7284841e-11 0.52549773
+ 40 -29133.643 0.87426387 -0.43713193 -1.8098945e-10 0.52418671
+ 50 -29697.011 0.8794039 -0.43970195 -7.4578566e-11 0.51636783
+ 60 -30342.001 0.88478594 -0.44239297 -1.200533e-10 0.52492361
+ 70 -31081.138 0.8906973 -0.44534865 5.7752914e-11 0.56248275
+ 80 -31792.732 0.89506635 -0.44753317 2.2782842e-10 0.59687627
+ 90 -32424.749 0.89714841 -0.44857421 2.3510438e-10 0.58629238
+ 100 -32998.353 0.89755721 -0.44877861 1.5006663e-11 0.60415017
+Loop time of 178.066 on 1 procs for 100 steps with 9600 atoms
+
+Performance: 0.005 ns/day, 4946.280 hours/ns, 0.562 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 15.335 | 15.335 | 15.335 | 0.0 | 8.61
+Kspace | 96.45 | 96.45 | 96.45 | 0.0 | 54.17
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.022512 | 0.022512 | 0.022512 | 0.0 | 0.01
+Output | 0.0019941 | 0.0019941 | 0.0019941 | 0.0 | 0.00
+Modify | 66.247 | 66.247 | 66.247 | 0.0 | 37.20
+Other | | 0.01012 | | | 0.01
+
+Nlocal: 9600 ave 9600 max 9600 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 22125 ave 22125 max 22125 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 2.9408e+06 ave 2.9408e+06 max 2.9408e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 2940800
+Ave neighs/atom = 306.333
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:03:02
diff --git a/examples/qeq/log.15Feb16.qeq.buck.g++.4 b/examples/qeq/log.15Feb16.qeq.buck.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..9df7a88caadd8fca759cfe8250e430bb55214117
--- /dev/null
+++ b/examples/qeq/log.15Feb16.qeq.buck.g++.4
@@ -0,0 +1,105 @@
+LAMMPS (15 Feb 2016)
+# This example demonstrates the use of various fix qeq variants with
+# that defines and uses charges, in this case pair_style buck/coul/long
+
+units metal
+atom_style charge
+
+read_data data.aC
+ orthogonal box = (0 0 0) to (25.1583 25.1583 28.0203)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 1200 atoms
+replicate 2 2 2
+ orthogonal box = (0 0 0) to (50.3166 50.3166 56.0405)
+ 1 by 2 by 2 MPI processor grid
+ 9600 atoms
+
+pair_style buck/coul/long 12.0
+pair_coeff 2 2 1388.77 .3623188 175.0
+pair_coeff 1 2 18003 .2052124 133.5381
+pair_coeff 1 1 0 .1 0
+kspace_style ewald 1e-6
+
+neighbor 1.0 bin
+neigh_modify delay 0 every 1 check yes
+
+group type1 type 1
+3200 atoms in group type1
+compute charge1 type1 property/atom q
+compute q1 type1 reduce ave c_charge1
+group type2 type 2
+6400 atoms in group type2
+compute charge2 type2 property/atom q
+compute q2 type2 reduce ave c_charge2
+variable qtot equal count(type1)*c_q1+count(type2)*c_q2
+
+thermo_style custom step pe c_q1 c_q2 v_qtot spcpu
+thermo 10
+
+timestep 0.0001
+
+velocity all create 300.0 1281937
+fix 1 all nve
+
+#fix 2 all qeq/point 1 10 1.0e-6 100 param.qeq2
+#fix 2 all qeq/shielded 1 10 1.0e-6 100 param.qeq2
+#fix 2 all qeq/slater 1 10 1.0e-6 100 param.qeq2
+#fix 2 all qeq/dynamic 1 10 1.0e-4 100 param.qeq2
+fix 2 all qeq/fire 1 10 1.0e-4 100 param.qeq2
+
+run 100
+Ewald initialization ...
+ G vector (1/distance) = 0.305064
+ estimated absolute RMS force accuracy = 2.07629e-05
+ estimated relative force accuracy = 1.44191e-06
+ KSpace vectors: actual max1d max3d = 13556 20 34460
+ kxmax kymax kzmax = 18 18 20
+Neighbor list info ...
+ 2 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 13
+ ghost atom cutoff = 13
+ binsize = 6.5 -> bins = 8 8 9
+Memory usage per processor = 22.8544 Mbytes
+Step PotEng q1 q2 qtot S/CPU
+ 0 -27457.215 0.85227886 -0.42613943 2.1373125e-11 0
+ 10 -27626.057 0.85486228 -0.42743114 2.4556357e-11 2.5540579
+ 20 -27975.085 0.85968531 -0.42984266 6.0481398e-11 2.1404073
+ 30 -28552.627 0.86755661 -0.4337783 1.3278623e-10 2.0419173
+ 40 -29133.643 0.87426387 -0.43713193 6.3664629e-11 2.0338224
+ 50 -29697.01 0.8794039 -0.43970195 8.5492502e-11 2.0248457
+ 60 -30342 0.88478594 -0.44239297 1.3096724e-10 2.0459077
+ 70 -31081.139 0.89069733 -0.44534866 1.5188562e-10 2.1726062
+ 80 -31792.732 0.89506635 -0.44753317 1.3960744e-10 2.3350176
+ 90 -32424.752 0.89714841 -0.44857421 1.1641532e-10 2.2406318
+ 100 -32998.353 0.89755721 -0.44877861 8.0035534e-11 2.3247991
+Loop time of 45.8779 on 4 procs for 100 steps with 9600 atoms
+
+Performance: 0.019 ns/day, 1274.386 hours/ns, 2.180 timesteps/s
+99.9% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 3.9256 | 4.0039 | 4.0664 | 2.6 | 8.73
+Kspace | 24.225 | 24.347 | 24.445 | 1.6 | 53.07
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.12152 | 0.21473 | 0.28551 | 14.7 | 0.47
+Output | 0.0010197 | 0.0011217 | 0.0011744 | 0.2 | 0.00
+Modify | 17.303 | 17.304 | 17.304 | 0.0 | 37.72
+Other | | 0.007412 | | | 0.02
+
+Nlocal: 2400 ave 2400 max 2400 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost: 11550 ave 11550 max 11550 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs: 735200 ave 740758 max 729642 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 2940800
+Ave neighs/atom = 306.333
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:46
diff --git a/examples/qeq/log.15Feb16.qeq.reaxc.g++.1 b/examples/qeq/log.15Feb16.qeq.reaxc.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..f71a7f97ed07f602021a1ff01402ba214956e08d
--- /dev/null
+++ b/examples/qeq/log.15Feb16.qeq.reaxc.g++.1
@@ -0,0 +1,105 @@
+LAMMPS (15 Feb 2016)
+# This example demonstrates the use of various fix qeq variants with pair reax/c
+# You can comment in/out various versions below
+#
+# 1) Fix qeq/shielded generates the same results compared to fix qeq/reax when
+# used with pair_style reax/c, provided that the QEq parameters are the same.
+#
+# 2) Fix qeq/point and fix qeq/dynamic generate comparable results provided that
+# the QEq parameters are the same. These two styles can also be used with
+# pair_style reax/c.
+
+units real
+atom_style charge
+
+read_data data.CHO
+ orthogonal box = (0 0 0) to (25 25 25)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 105 atoms
+
+pair_style reax/c NULL checkqeq no
+pair_coeff * * ffield.reax.cho H C O
+Reading potential file ffield.reax.cho with DATE: 2011-02-18
+
+neighbor 1 bin
+neigh_modify every 1 delay 0 check yes
+
+group type1 type 1
+60 atoms in group type1
+compute charge1 type1 property/atom q
+compute q1 type1 reduce ave c_charge1
+group type2 type 2
+25 atoms in group type2
+compute charge2 type2 property/atom q
+compute q2 type2 reduce ave c_charge2
+group type3 type 3
+20 atoms in group type3
+compute charge3 type3 property/atom q
+compute q3 type3 reduce ave c_charge3
+variable qtot equal count(type1)*c_q1+count(type2)*c_q2+count(type3)*c_q3
+
+thermo_style custom step pe c_q1 c_q2 c_q3 v_qtot
+thermo 1
+
+velocity all create 300.0 1281937
+fix 1 all nve
+
+fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq.reax
+#fix 2 all qeq/shielded 1 10.0 1e-6 400 param.qeq1
+#fix 2 all qeq/point 1 10.0 1e-6 400 param.qeq1
+#fix 2 all qeq/dynamic 1 10.0 1e-3 100 param.qeq1
+
+timestep 0.25
+
+run 10
+Neighbor list info ...
+ 2 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 11
+ ghost atom cutoff = 11
+ binsize = 5.5 -> bins = 5 5 5
+Memory usage per processor = 15.3036 Mbytes
+Step PotEng q1 q2 q3 qtot
+ 0 -10226.557 0.095634063 -0.15658793 -0.091167279 4.4408921e-16
+ 1 -10225.799 0.095649584 -0.1566219 -0.091171371 7.1054274e-15
+ 2 -10223.656 0.095669731 -0.15666714 -0.091175264 -6.4392935e-15
+ 3 -10220.276 0.095691257 -0.15671597 -0.091178813 2.6645353e-15
+ 4 -10215.894 0.095714363 -0.15676887 -0.091182006 -3.1086245e-15
+ 5 -10210.804 0.095733863 -0.15681398 -0.09118412 6.6613381e-16
+ 6 -10205.342 0.095751253 -0.15685427 -0.091185918 -1.110223e-15
+ 7 -10199.848 0.095762028 -0.1568795 -0.091186707 8.8817842e-15
+ 8 -10194.646 0.095767243 -0.15689184 -0.091186932 -2.4424907e-15
+ 9 -10190.016 0.095760528 -0.15687664 -0.091185782 -4.4408921e-16
+ 10 -10186.168 0.095748006 -0.15684815 -0.09118383 1.110223e-15
+Loop time of 0.0423889 on 1 procs for 10 steps with 105 atoms
+
+Performance: 5.096 ns/day, 4.710 hours/ns, 235.911 timesteps/s
+99.1% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.037234 | 0.037234 | 0.037234 | 0.0 | 87.84
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 4.1485e-05 | 4.1485e-05 | 4.1485e-05 | 0.0 | 0.10
+Output | 0.00019646 | 0.00019646 | 0.00019646 | 0.0 | 0.46
+Modify | 0.0048897 | 0.0048897 | 0.0048897 | 0.0 | 11.54
+Other | | 2.766e-05 | | | 0.07
+
+Nlocal: 105 ave 105 max 105 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 512 ave 512 max 512 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 3417 ave 3417 max 3417 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 3417
+Ave neighs/atom = 32.5429
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:00
diff --git a/examples/qeq/log.15Feb16.qeq.reaxc.g++.4 b/examples/qeq/log.15Feb16.qeq.reaxc.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..ea1a7152a76009e80b4a0478d90a366172213ea3
--- /dev/null
+++ b/examples/qeq/log.15Feb16.qeq.reaxc.g++.4
@@ -0,0 +1,105 @@
+LAMMPS (15 Feb 2016)
+# This example demonstrates the use of various fix qeq variants with pair reax/c
+# You can comment in/out various versions below
+#
+# 1) Fix qeq/shielded generates the same results compared to fix qeq/reax when
+# used with pair_style reax/c, provided that the QEq parameters are the same.
+#
+# 2) Fix qeq/point and fix qeq/dynamic generate comparable results provided that
+# the QEq parameters are the same. These two styles can also be used with
+# pair_style reax/c.
+
+units real
+atom_style charge
+
+read_data data.CHO
+ orthogonal box = (0 0 0) to (25 25 25)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 105 atoms
+
+pair_style reax/c NULL checkqeq no
+pair_coeff * * ffield.reax.cho H C O
+Reading potential file ffield.reax.cho with DATE: 2011-02-18
+
+neighbor 1 bin
+neigh_modify every 1 delay 0 check yes
+
+group type1 type 1
+60 atoms in group type1
+compute charge1 type1 property/atom q
+compute q1 type1 reduce ave c_charge1
+group type2 type 2
+25 atoms in group type2
+compute charge2 type2 property/atom q
+compute q2 type2 reduce ave c_charge2
+group type3 type 3
+20 atoms in group type3
+compute charge3 type3 property/atom q
+compute q3 type3 reduce ave c_charge3
+variable qtot equal count(type1)*c_q1+count(type2)*c_q2+count(type3)*c_q3
+
+thermo_style custom step pe c_q1 c_q2 c_q3 v_qtot
+thermo 1
+
+velocity all create 300.0 1281937
+fix 1 all nve
+
+fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq.reax
+#fix 2 all qeq/shielded 1 10.0 1e-6 400 param.qeq1
+#fix 2 all qeq/point 1 10.0 1e-6 400 param.qeq1
+#fix 2 all qeq/dynamic 1 10.0 1e-3 100 param.qeq1
+
+timestep 0.25
+
+run 10
+Neighbor list info ...
+ 2 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 11
+ ghost atom cutoff = 11
+ binsize = 5.5 -> bins = 5 5 5
+Memory usage per processor = 11.1055 Mbytes
+Step PotEng q1 q2 q3 qtot
+ 0 -10226.557 0.095633919 -0.15658765 -0.091167194 1.7763568e-15
+ 1 -10225.799 0.0956503 -0.15662357 -0.09117143 2.8865799e-15
+ 2 -10223.656 0.095669684 -0.15666698 -0.091175327 1.110223e-15
+ 3 -10220.276 0.095691296 -0.15671615 -0.091178696 0
+ 4 -10215.894 0.09571384 -0.15676787 -0.091181678 8.8817842e-16
+ 5 -10210.804 0.095734178 -0.15681468 -0.09118418 1.3322676e-15
+ 6 -10205.342 0.095751126 -0.15685409 -0.091185769 4.4408921e-16
+ 7 -10199.848 0.095762403 -0.15688037 -0.091186751 0
+ 8 -10194.646 0.095766449 -0.15689014 -0.091186673 -4.4408921e-16
+ 9 -10190.016 0.095761078 -0.15687818 -0.09118551 -4.4408921e-16
+ 10 -10186.168 0.095747223 -0.15684634 -0.091183742 0
+Loop time of 0.0712105 on 4 procs for 10 steps with 105 atoms
+
+Performance: 3.033 ns/day, 7.912 hours/ns, 140.429 timesteps/s
+72.0% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.014191 | 0.015309 | 0.016687 | 0.7 | 21.50
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.0013485 | 0.010136 | 0.018539 | 7.8 | 14.23
+Output | 0.0023825 | 0.002628 | 0.0029249 | 0.4 | 3.69
+Modify | 0.035412 | 0.042747 | 0.050082 | 3.5 | 60.03
+Other | | 0.0003899 | | | 0.55
+
+Nlocal: 26.25 ave 35 max 15 min
+Histogram: 1 0 0 1 0 0 0 0 0 2
+Nghost: 300 ave 357 max 239 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs: 1025.25 ave 1468 max 405 min
+Histogram: 1 0 0 0 1 0 0 0 0 2
+
+Total # of neighbors = 4101
+Ave neighs/atom = 39.0571
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:00
diff --git a/examples/reax/log.15Feb16.reax.rdx.g++.1 b/examples/reax/log.15Feb16.reax.rdx.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..32e2f198d7b5c7df9e4111dc953894b658b622f7
--- /dev/null
+++ b/examples/reax/log.15Feb16.reax.rdx.g++.1
@@ -0,0 +1,101 @@
+LAMMPS (15 Feb 2016)
+# ReaxFF potential for RDX system
+
+units real
+
+atom_style charge
+read_data data.rdx
+ orthogonal box = (35 35 35) to (48 48 48)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 21 atoms
+
+# reax args: hbcut hbnewflag tripflag precision
+
+pair_style reax 6.0 1 1 1.0e-6
+WARNING: pair style reax is now deprecated and will soon be retired. Users should switch to pair_style reax/c (../pair_reax.cpp:48)
+pair_coeff * * ffield.reax 1 2 3 4
+
+compute reax all pair reax
+
+variable eb equal c_reax[1]
+variable ea equal c_reax[2]
+variable elp equal c_reax[3]
+variable emol equal c_reax[4]
+variable ev equal c_reax[5]
+variable epen equal c_reax[6]
+variable ecoa equal c_reax[7]
+variable ehb equal c_reax[8]
+variable et equal c_reax[9]
+variable eco equal c_reax[10]
+variable ew equal c_reax[11]
+variable ep equal c_reax[12]
+variable efi equal c_reax[13]
+variable eqeq equal c_reax[14]
+
+neighbor 2.5 bin
+neigh_modify every 10 delay 0 check no
+
+fix 1 all nve
+
+thermo 10
+thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
+
+timestep 1.0
+
+#dump 1 all custom 10 dump.reax.rdx id type q xs ys zs
+
+#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 3
+
+#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 3
+
+run 100
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 10 steps, delay 0 steps, check no
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 12.5
+ ghost atom cutoff = 12.5
+ binsize = 6.25 -> bins = 3 3 3
+Memory usage per processor = 2.95105 Mbytes
+Step Temp E_pair TotEng Press eb ea elp emol ev epen ecoa ehb et eco ew ep efi eqeq
+ 0 0 -1885.1268 -1885.1268 27233.074 -2958.4712 79.527715 0.31082031 0 97.771125 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79971 0 168.88435
+ 10 1281.7558 -1989.1322 -1912.7188 -19609.913 -2733.8828 -15.775275 0.20055725 0 55.020231 3.1070522 -77.710916 0 14.963568 -5.8082204 843.41939 -180.17724 0 107.5115
+ 20 516.83079 -1941.677 -1910.8655 -12525.41 -2801.8626 7.4107974 0.073134188 0 81.986982 0.2281551 -57.494871 0 30.656735 -10.102557 877.78696 -158.93385 0 88.574158
+ 30 467.2641 -1940.978 -1913.1215 -35957.487 -2755.021 -6.9179959 0.049322439 0 78.853175 0.13604392 -51.653634 0 19.862872 -9.7098575 853.79334 -151.232 0 80.861768
+ 40 647.45541 -1951.1994 -1912.6006 -5883.7147 -2798.3556 17.334807 0.15102863 0 63.23512 0.18070931 -54.598962 0 17.325008 -12.052277 883.01667 -164.21335 0 96.777422
+ 50 716.38057 -1949.4749 -1906.767 5473.2085 -2800.931 9.2056917 0.15413274 0 85.371449 3.2986106 -78.253597 0 34.861773 -8.5531236 882.01435 -193.85275 0 117.2096
+ 60 1175.2707 -1975.9611 -1905.8959 -1939.4971 -2726.5816 -11.651982 0.24296788 0 48.320663 7.1799636 -75.363641 0 16.520132 -4.8869463 844.754 -194.23296 0 119.73837
+ 70 1156.7 -1975.3486 -1906.3905 24628.344 -2880.5223 25.652478 0.26894312 0 83.724884 7.1049303 -68.700942 0 24.750744 -8.6338218 911.20067 -183.4058 0 113.21158
+ 80 840.23687 -1955.4768 -1905.3851 -17731.383 -2755.7295 -8.0168306 0.13867962 0 86.14748 2.2387306 -76.945841 0 23.595858 -7.2609645 853.6346 -167.88289 0 94.603895
+ 90 365.79169 -1926.406 -1904.5989 898.37155 -2842.183 47.368211 0.23109 0 92.288131 0.38031313 -61.361483 0 18.476377 -12.255472 900.24202 -186.48056 0 116.88831
+ 100 801.32078 -1953.4177 -1905.646 -2417.5518 -2802.7244 4.6676973 0.18046558 0 76.730114 5.4177372 -77.102556 0 24.997234 -7.7554179 898.67306 -196.8912 0 120.38952
+Loop time of 0.523648 on 1 procs for 100 steps with 21 atoms
+
+Performance: 16.500 ns/day, 1.455 hours/ns, 190.968 timesteps/s
+99.5% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.52205 | 0.52205 | 0.52205 | 0.0 | 99.70
+Neigh | 0.00072503 | 0.00072503 | 0.00072503 | 0.0 | 0.14
+Comm | 0.00039506 | 0.00039506 | 0.00039506 | 0.0 | 0.08
+Output | 0.00027037 | 0.00027037 | 0.00027037 | 0.0 | 0.05
+Modify | 7.2956e-05 | 7.2956e-05 | 7.2956e-05 | 0.0 | 0.01
+Other | | 0.0001328 | | | 0.03
+
+Nlocal: 21 ave 21 max 21 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 546 ave 546 max 546 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 1106 ave 1106 max 1106 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1106
+Ave neighs/atom = 52.6667
+Neighbor list builds = 10
+Dangerous builds not checked
+Total wall time: 0:00:00
diff --git a/examples/reax/log.15Feb16.reax.rdx.g++.4 b/examples/reax/log.15Feb16.reax.rdx.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..dbae3b9098615c6530321cb7ea657e3b69234b87
--- /dev/null
+++ b/examples/reax/log.15Feb16.reax.rdx.g++.4
@@ -0,0 +1,101 @@
+LAMMPS (15 Feb 2016)
+# ReaxFF potential for RDX system
+
+units real
+
+atom_style charge
+read_data data.rdx
+ orthogonal box = (35 35 35) to (48 48 48)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 21 atoms
+
+# reax args: hbcut hbnewflag tripflag precision
+
+pair_style reax 6.0 1 1 1.0e-6
+WARNING: pair style reax is now deprecated and will soon be retired. Users should switch to pair_style reax/c (../pair_reax.cpp:48)
+pair_coeff * * ffield.reax 1 2 3 4
+
+compute reax all pair reax
+
+variable eb equal c_reax[1]
+variable ea equal c_reax[2]
+variable elp equal c_reax[3]
+variable emol equal c_reax[4]
+variable ev equal c_reax[5]
+variable epen equal c_reax[6]
+variable ecoa equal c_reax[7]
+variable ehb equal c_reax[8]
+variable et equal c_reax[9]
+variable eco equal c_reax[10]
+variable ew equal c_reax[11]
+variable ep equal c_reax[12]
+variable efi equal c_reax[13]
+variable eqeq equal c_reax[14]
+
+neighbor 2.5 bin
+neigh_modify every 10 delay 0 check no
+
+fix 1 all nve
+
+thermo 10
+thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
+
+timestep 1.0
+
+#dump 1 all custom 10 dump.reax.rdx id type q xs ys zs
+
+#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 3
+
+#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 3
+
+run 100
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 10 steps, delay 0 steps, check no
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 12.5
+ ghost atom cutoff = 12.5
+ binsize = 6.25 -> bins = 3 3 3
+Memory usage per processor = 3.0718 Mbytes
+Step Temp E_pair TotEng Press eb ea elp emol ev epen ecoa ehb et eco ew ep efi eqeq
+ 0 0 -1885.1268 -1885.1268 27233.074 -2958.4712 79.527715 0.31082031 0 97.771125 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79972 0 168.8843
+ 10 1281.7558 -1989.1322 -1912.7188 -19609.913 -2733.8828 -15.775275 0.20055725 0 55.020231 3.1070523 -77.710916 0 14.963568 -5.8082204 843.41939 -180.17725 0 107.51148
+ 20 516.8308 -1941.677 -1910.8655 -12525.411 -2801.8626 7.4107973 0.07313419 0 81.986982 0.2281551 -57.494871 0 30.656735 -10.102557 877.78696 -158.93385 0 88.574155
+ 30 467.26411 -1940.978 -1913.1215 -35957.487 -2755.021 -6.9179966 0.049322437 0 78.853175 0.13604391 -51.653634 0 19.862872 -9.7098574 853.79333 -151.232 0 80.861765
+ 40 647.45584 -1951.1994 -1912.6006 -5883.7102 -2798.3557 17.334812 0.15102857 0 63.235124 0.18070914 -54.598951 0 17.325006 -12.052278 883.01674 -164.21335 0 96.777418
+ 50 716.38108 -1949.4679 -1906.76 5473.1803 -2800.9311 9.2057064 0.15413272 0 85.371443 3.2986124 -78.253597 0 34.861778 -8.5531235 882.01441 -193.85213 0 117.21596
+ 60 1175.2703 -1975.9632 -1905.898 -1939.6676 -2726.5815 -11.652032 0.24296779 0 48.320636 7.1799647 -75.363643 0 16.520124 -4.8869416 844.75396 -194.25563 0 119.75889
+ 70 1156.7016 -1975.3469 -1906.3887 24628.125 -2880.5225 25.65252 0.26894309 0 83.724869 7.1048931 -68.700978 0 24.750754 -8.6338341 911.20067 -183.41947 0 113.22722
+ 80 840.3323 -1955.4867 -1905.3893 -17732.956 -2755.7336 -8.0168615 0.13869303 0 86.143454 2.2388975 -76.946365 0 23.594977 -7.2608903 853.63682 -167.88599 0 94.604168
+ 90 365.75853 -1926.4192 -1904.6141 902.29004 -2842.1715 47.360077 0.23110905 0 92.28805 0.38040356 -61.364192 0 18.473252 -12.253964 900.23128 -186.47889 0 116.88518
+ 100 801.64661 -1953.4392 -1905.6481 -2464.5533 -2802.6922 4.6510183 0.18048786 0 76.715675 5.41849 -77.102069 0 24.987058 -7.7531389 898.65974 -196.87724 0 120.37303
+Loop time of 0.433318 on 4 procs for 100 steps with 21 atoms
+
+Performance: 19.939 ns/day, 1.204 hours/ns, 230.777 timesteps/s
+97.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.16821 | 0.25684 | 0.42837 | 20.0 | 59.27
+Neigh | 4.0293e-05 | 0.00022489 | 0.00054836 | 1.3 | 0.05
+Comm | 0.0036013 | 0.17559 | 0.26447 | 24.3 | 40.52
+Output | 0.00044513 | 0.00048918 | 0.00056028 | 0.2 | 0.11
+Modify | 3.4571e-05 | 6.1274e-05 | 8.2731e-05 | 0.2 | 0.01
+Other | | 0.0001184 | | | 0.03
+
+Nlocal: 5.25 ave 15 max 0 min
+Histogram: 1 0 2 0 0 0 0 0 0 1
+Nghost: 355.5 ave 432 max 282 min
+Histogram: 1 0 0 0 1 1 0 0 0 1
+Neighs: 301.25 ave 827 max 0 min
+Histogram: 1 0 2 0 0 0 0 0 0 1
+
+Total # of neighbors = 1205
+Ave neighs/atom = 57.381
+Neighbor list builds = 10
+Dangerous builds not checked
+Total wall time: 0:00:00
diff --git a/examples/reax/log.15Feb16.reax.tatb.g++.1 b/examples/reax/log.15Feb16.reax.tatb.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..8774ed30a8edb23e54c409e609f6f2181a63c3f3
--- /dev/null
+++ b/examples/reax/log.15Feb16.reax.tatb.g++.1
@@ -0,0 +1,97 @@
+LAMMPS (15 Feb 2016)
+# ReaxFF potential for TATB system
+
+units real
+
+atom_style charge
+read_data data.tatb
+ triclinic box = (0 0 0) to (13.624 17.1149 15.1826) with tilt (-5.75316 -6.32547 7.42573)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 384 atoms
+
+# reax args: hbcut hbnewflag tripflag precision
+pair_style reax 6.0 1 1 1.0e-6
+WARNING: pair style reax is now deprecated and will soon be retired. Users should switch to pair_style reax/c (../pair_reax.cpp:48)
+pair_coeff * * ffield.reax 1 2 3 4
+
+compute reax all pair reax
+
+variable eb equal c_reax[1]
+variable ea equal c_reax[2]
+variable elp equal c_reax[3]
+variable emol equal c_reax[4]
+variable ev equal c_reax[5]
+variable epen equal c_reax[6]
+variable ecoa equal c_reax[7]
+variable ehb equal c_reax[8]
+variable et equal c_reax[9]
+variable eco equal c_reax[10]
+variable ew equal c_reax[11]
+variable ep equal c_reax[12]
+variable efi equal c_reax[13]
+variable eqeq equal c_reax[14]
+
+neighbor 2.5 bin
+neigh_modify delay 0 every 5 check no
+
+fix 1 all nve
+
+thermo 5
+thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
+
+timestep 0.0625
+
+#dump 1 all custom 100 dump.reax.tatb id type q x y z
+
+#dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 3
+
+#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 3
+
+fix 2 all reax/bonds 25 bonds.reax.tatb
+
+run 25
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 5 steps, delay 0 steps, check no
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 12.5
+ ghost atom cutoff = 12.5
+ binsize = 6.25 -> bins = 5 4 3
+Memory usage per processor = 6.61277 Mbytes
+Step Temp E_pair TotEng Press eb ea elp emol ev epen ecoa ehb et eco ew ep efi eqeq
+ 0 0 -44767.08 -44767.08 7294.6353 -61120.591 486.4378 4.7236377 0 1568.024 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6378 0 6391.0231
+ 5 0.63682807 -44767.737 -44767.01 8391.5966 -61118.763 486.82916 4.723415 0 1567.835 20.768662 -278.20804 -1557.6962 252.64683 -655.74117 18859.328 -8738.2727 0 6388.8127
+ 10 2.4306957 -44769.41 -44766.635 11717.369 -61113.142 487.89093 4.7227063 0 1567.2936 20.705084 -274.37509 -1560.8546 252.87219 -655.43578 18850.19 -8731.0713 0 6381.7946
+ 15 5.0590478 -44772.63 -44766.854 17125.033 -61103.34 489.28007 4.7214008 0 1566.4744 20.590604 -268.28963 -1566.5961 252.97781 -654.93836 18835.335 -8719.3112 0 6370.4665
+ 20 8.0678579 -44775.923 -44766.713 24620.824 -61088.791 490.42346 4.7193467 0 1565.5541 20.415031 -260.38512 -1574.1001 253.39805 -654.26837 18815.312 -8703.3104 0 6355.1097
+ 25 10.975539 -44777.231 -44764.701 34381.278 -61068.889 490.53149 4.7164093 0 1566.5715 20.169755 -251.2311 -1582.8552 253.88696 -653.46042 18790.855 -8683.8362 0 6336.3099
+Loop time of 7.52359 on 1 procs for 25 steps with 384 atoms
+
+Performance: 0.018 ns/day, 1337.526 hours/ns, 3.323 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 7.4675 | 7.4675 | 7.4675 | 0.0 | 99.25
+Neigh | 0.052319 | 0.052319 | 0.052319 | 0.0 | 0.70
+Comm | 0.0021715 | 0.0021715 | 0.0021715 | 0.0 | 0.03
+Output | 0.00026178 | 0.00026178 | 0.00026178 | 0.0 | 0.00
+Modify | 0.0010068 | 0.0010068 | 0.0010068 | 0.0 | 0.01
+Other | | 0.000315 | | | 0.00
+
+Nlocal: 384 ave 384 max 384 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 7559 ave 7559 max 7559 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 286828 ave 286828 max 286828 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 286828
+Ave neighs/atom = 746.948
+Neighbor list builds = 5
+Dangerous builds not checked
+Total wall time: 0:00:07
diff --git a/examples/reax/log.15Feb16.reax.tatb.g++.4 b/examples/reax/log.15Feb16.reax.tatb.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..a72198bc960a645f39f86b1239665e617f41e715
--- /dev/null
+++ b/examples/reax/log.15Feb16.reax.tatb.g++.4
@@ -0,0 +1,97 @@
+LAMMPS (15 Feb 2016)
+# ReaxFF potential for TATB system
+
+units real
+
+atom_style charge
+read_data data.tatb
+ triclinic box = (0 0 0) to (13.624 17.1149 15.1826) with tilt (-5.75316 -6.32547 7.42573)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 384 atoms
+
+# reax args: hbcut hbnewflag tripflag precision
+pair_style reax 6.0 1 1 1.0e-6
+WARNING: pair style reax is now deprecated and will soon be retired. Users should switch to pair_style reax/c (../pair_reax.cpp:48)
+pair_coeff * * ffield.reax 1 2 3 4
+
+compute reax all pair reax
+
+variable eb equal c_reax[1]
+variable ea equal c_reax[2]
+variable elp equal c_reax[3]
+variable emol equal c_reax[4]
+variable ev equal c_reax[5]
+variable epen equal c_reax[6]
+variable ecoa equal c_reax[7]
+variable ehb equal c_reax[8]
+variable et equal c_reax[9]
+variable eco equal c_reax[10]
+variable ew equal c_reax[11]
+variable ep equal c_reax[12]
+variable efi equal c_reax[13]
+variable eqeq equal c_reax[14]
+
+neighbor 2.5 bin
+neigh_modify delay 0 every 5 check no
+
+fix 1 all nve
+
+thermo 5
+thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
+
+timestep 0.0625
+
+#dump 1 all custom 100 dump.reax.tatb id type q x y z
+
+#dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 3
+
+#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 3
+
+fix 2 all reax/bonds 25 bonds.reax.tatb
+
+run 25
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 5 steps, delay 0 steps, check no
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 12.5
+ ghost atom cutoff = 12.5
+ binsize = 6.25 -> bins = 5 4 3
+Memory usage per processor = 4.03843 Mbytes
+Step Temp E_pair TotEng Press eb ea elp emol ev epen ecoa ehb et eco ew ep efi eqeq
+ 0 0 -44767.08 -44767.08 7294.6353 -61120.591 486.4378 4.7236377 0 1568.024 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6378 0 6391.0231
+ 5 0.63682726 -44767.816 -44767.089 8391.165 -61118.763 486.82916 4.723415 0 1567.835 20.768662 -278.20804 -1557.6962 252.64683 -655.74117 18859.328 -8738.3995 0 6388.86
+ 10 2.4306905 -44769.408 -44766.633 11717.247 -61113.142 487.89094 4.7227063 0 1567.2936 20.705084 -274.3751 -1560.8546 252.87219 -655.43578 18850.19 -8731.0965 0 6381.8216
+ 15 5.0590422 -44772.626 -44766.85 17124.943 -61103.34 489.2801 4.7214008 0 1566.4744 20.590604 -268.28963 -1566.5961 252.97781 -654.93836 18835.335 -8719.3383 0 6370.4973
+ 20 8.0678512 -44775.934 -44766.723 24620.531 -61088.791 490.42349 4.7193467 0 1565.5541 20.415031 -260.38513 -1574.1001 253.39804 -654.26837 18815.312 -8703.4033 0 6355.1921
+ 25 10.97553 -44777.231 -44764.701 34381.242 -61068.889 490.53154 4.7164093 0 1566.5715 20.169755 -251.23111 -1582.8552 253.88696 -653.46042 18790.855 -8683.8451 0 6336.3185
+Loop time of 3.35853 on 4 procs for 25 steps with 384 atoms
+
+Performance: 0.040 ns/day, 597.072 hours/ns, 7.444 timesteps/s
+99.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 3.1029 | 3.2261 | 3.3401 | 5.3 | 96.06
+Neigh | 0.011399 | 0.011589 | 0.011772 | 0.1 | 0.35
+Comm | 0.0055692 | 0.11938 | 0.24261 | 27.6 | 3.55
+Output | 0.00039721 | 0.0005976 | 0.00081921 | 0.7 | 0.02
+Modify | 0.00036359 | 0.00061446 | 0.00086737 | 0.8 | 0.02
+Other | | 0.0002854 | | | 0.01
+
+Nlocal: 96 ave 96 max 96 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost: 5118 ave 5118 max 5118 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs: 79754 ave 79754 max 79754 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 319016
+Ave neighs/atom = 830.771
+Neighbor list builds = 5
+Dangerous builds not checked
+Total wall time: 0:00:03
diff --git a/examples/reax/log.15Feb16.reaxc.rdx.g++.1 b/examples/reax/log.15Feb16.reaxc.rdx.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..9915a2c5a22cb5d09ea55b9377826fd8995e7e86
--- /dev/null
+++ b/examples/reax/log.15Feb16.reaxc.rdx.g++.1
@@ -0,0 +1,104 @@
+LAMMPS (15 Feb 2016)
+# ReaxFF potential for RDX system
+# this run is equivalent to reax/in.reax.rdx
+
+units real
+
+atom_style charge
+read_data data.rdx
+ orthogonal box = (35 35 35) to (48 48 48)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 21 atoms
+
+pair_style reax/c control.reax_c.rdx
+pair_coeff * * ffield.reax C H O N
+Reading potential file ffield.reax with DATE: 2010-02-19
+
+compute reax all pair reax/c
+
+variable eb equal c_reax[1]
+variable ea equal c_reax[2]
+variable elp equal c_reax[3]
+variable emol equal c_reax[4]
+variable ev equal c_reax[5]
+variable epen equal c_reax[6]
+variable ecoa equal c_reax[7]
+variable ehb equal c_reax[8]
+variable et equal c_reax[9]
+variable eco equal c_reax[10]
+variable ew equal c_reax[11]
+variable ep equal c_reax[12]
+variable efi equal c_reax[13]
+variable eqeq equal c_reax[14]
+
+neighbor 2.5 bin
+neigh_modify every 10 delay 0 check no
+
+fix 1 all nve
+fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
+
+thermo 10
+thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
+
+timestep 1.0
+
+#dump 1 all atom 10 dump.reaxc.rdx
+
+#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 3
+
+#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 3
+
+run 100
+Neighbor list info ...
+ 2 neighbor list requests
+ update every 10 steps, delay 0 steps, check no
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 12.5
+ ghost atom cutoff = 12.5
+ binsize = 6.25 -> bins = 3 3 3
+Memory usage per processor = 14.4462 Mbytes
+Step Temp E_pair TotEng Press eb ea elp emol ev epen ecoa ehb et eco ew ep efi eqeq
+ 0 0 -1884.3081 -1884.3081 27186.181 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79931 0 168.88396
+ 10 1288.6116 -1989.6644 -1912.8422 -19456.353 -2734.6769 -15.607221 0.2017796 0 54.629557 3.125229 -77.7067 0 14.933901 -5.8108541 843.92073 -180.43321 0 107.75935
+ 20 538.95819 -1942.7037 -1910.5731 -10725.639 -2803.7394 7.9078269 0.07792668 0 81.610053 0.22951941 -57.557107 0 30.331207 -10.178049 878.99009 -159.68914 0 89.313379
+ 30 463.09535 -1933.5765 -1905.9686 -33255.546 -2749.859 -8.0154745 0.02762893 0 81.627395 0.11972413 -50.262293 0 20.820303 -9.6327015 851.88715 -149.49499 0 79.205727
+ 40 885.49171 -1958.9125 -1906.1229 -4814.6856 -2795.644 9.150669 0.13747498 0 70.947982 0.24360485 -57.862663 0 19.076496 -11.141218 873.73893 -159.99393 0 92.434096
+ 50 861.16578 -1954.4599 -1903.1205 -1896.7713 -2784.845 3.8270515 0.15793266 0 79.851823 3.3492142 -78.06613 0 32.629016 -7.956541 872.81838 -190.98567 0 114.75995
+ 60 1167.7852 -1971.8429 -1902.224 -3482.7305 -2705.863 -17.12171 0.22749077 0 44.507654 7.8560745 -74.788955 0 16.256483 -4.6046431 835.8304 -188.33691 0 114.19413
+ 70 1439.9966 -1989.3024 -1903.4553 23845.651 -2890.7895 31.958845 0.26671721 0 85.758695 3.1803544 -71.002903 0 24.357134 -10.31131 905.86775 -175.38471 0 106.79648
+ 80 502.39438 -1930.7544 -1900.8035 -20356.316 -2703.8115 -18.662467 0.11286011 0 99.804201 2.0329024 -76.171317 0 19.237028 -6.2786907 826.47451 -166.03125 0 92.539398
+ 90 749.08499 -1946.9838 -1902.3262 17798.51 -2863.7576 42.068717 0.2433807 0 96.181613 0.96184887 -69.955448 0 24.615302 -11.582765 903.68818 -190.13843 0 120.69141
+ 100 1109.6968 -1968.5874 -1902.4315 -4490.1018 -2755.8965 -7.1231014 0.21757699 0 61.806018 7.0827673 -75.645345 0 20.114997 -6.2371964 863.5635 -198.56976 0 122.09961
+Loop time of 0.372956 on 1 procs for 100 steps with 21 atoms
+
+Performance: 23.166 ns/day, 1.036 hours/ns, 268.128 timesteps/s
+99.7% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.35299 | 0.35299 | 0.35299 | 0.0 | 94.65
+Neigh | 0.008096 | 0.008096 | 0.008096 | 0.0 | 2.17
+Comm | 0.00043416 | 0.00043416 | 0.00043416 | 0.0 | 0.12
+Output | 0.00021172 | 0.00021172 | 0.00021172 | 0.0 | 0.06
+Modify | 0.011089 | 0.011089 | 0.011089 | 0.0 | 2.97
+Other | | 0.0001314 | | | 0.04
+
+Nlocal: 21 ave 21 max 21 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 546 ave 546 max 546 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 1096 ave 1096 max 1096 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1096
+Ave neighs/atom = 52.1905
+Neighbor list builds = 10
+Dangerous builds not checked
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:00
diff --git a/examples/reax/log.15Feb16.reaxc.rdx.g++.4 b/examples/reax/log.15Feb16.reaxc.rdx.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..1c0a7daf5942c73411892a82cb079c8c88e8a83a
--- /dev/null
+++ b/examples/reax/log.15Feb16.reaxc.rdx.g++.4
@@ -0,0 +1,104 @@
+LAMMPS (15 Feb 2016)
+# ReaxFF potential for RDX system
+# this run is equivalent to reax/in.reax.rdx
+
+units real
+
+atom_style charge
+read_data data.rdx
+ orthogonal box = (35 35 35) to (48 48 48)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 21 atoms
+
+pair_style reax/c control.reax_c.rdx
+pair_coeff * * ffield.reax C H O N
+Reading potential file ffield.reax with DATE: 2010-02-19
+
+compute reax all pair reax/c
+
+variable eb equal c_reax[1]
+variable ea equal c_reax[2]
+variable elp equal c_reax[3]
+variable emol equal c_reax[4]
+variable ev equal c_reax[5]
+variable epen equal c_reax[6]
+variable ecoa equal c_reax[7]
+variable ehb equal c_reax[8]
+variable et equal c_reax[9]
+variable eco equal c_reax[10]
+variable ew equal c_reax[11]
+variable ep equal c_reax[12]
+variable efi equal c_reax[13]
+variable eqeq equal c_reax[14]
+
+neighbor 2.5 bin
+neigh_modify every 10 delay 0 check no
+
+fix 1 all nve
+fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
+
+thermo 10
+thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
+
+timestep 1.0
+
+#dump 1 all atom 10 dump.reaxc.rdx
+
+#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 3
+
+#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 3
+
+run 100
+Neighbor list info ...
+ 2 neighbor list requests
+ update every 10 steps, delay 0 steps, check no
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 12.5
+ ghost atom cutoff = 12.5
+ binsize = 6.25 -> bins = 3 3 3
+Memory usage per processor = 12.531 Mbytes
+Step Temp E_pair TotEng Press eb ea elp emol ev epen ecoa ehb et eco ew ep efi eqeq
+ 0 0 -1884.3081 -1884.3081 27186.18 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79953 0 168.88418
+ 10 1288.6115 -1989.6644 -1912.8422 -19456.354 -2734.6769 -15.60722 0.2017796 0 54.629558 3.1252288 -77.7067 0 14.933901 -5.8108542 843.92073 -180.43321 0 107.75934
+ 20 538.95831 -1942.7037 -1910.5731 -10725.671 -2803.7395 7.9078306 0.077926651 0 81.610051 0.22951926 -57.557099 0 30.331204 -10.178049 878.99014 -159.69268 0 89.316921
+ 30 463.09502 -1933.5765 -1905.9685 -33255.512 -2749.8591 -8.015455 0.027628766 0 81.6274 0.11972393 -50.262275 0 20.820315 -9.6327041 851.88722 -149.49498 0 79.205714
+ 40 885.49378 -1958.9125 -1906.1228 -4814.644 -2795.644 9.1506485 0.13747497 0 70.948 0.24360511 -57.862677 0 19.076502 -11.141216 873.73898 -159.99393 0 92.43409
+ 50 861.16297 -1954.4602 -1903.1209 -1896.8002 -2784.8451 3.8270162 0.157933 0 79.851673 3.3492148 -78.066132 0 32.628944 -7.9565368 872.81852 -190.98572 0 114.76001
+ 60 1167.7835 -1971.8433 -1902.2245 -3482.8296 -2705.8635 -17.121613 0.2274909 0 44.507674 7.85602 -74.788998 0 16.256483 -4.6046575 835.83058 -188.33691 0 114.19414
+ 70 1439.9939 -1989.3026 -1903.4556 23846.042 -2890.7893 31.958672 0.26671708 0 85.758381 3.1804035 -71.002944 0 24.357195 -10.311284 905.8679 -175.38487 0 106.79661
+ 80 502.39535 -1930.7548 -1900.8039 -20356.194 -2703.8126 -18.662209 0.11286005 0 99.803849 2.0329206 -76.171278 0 19.23716 -6.2787147 826.47505 -166.03123 0 92.539386
+ 90 749.07874 -1946.9841 -1902.3269 17798.394 -2863.7576 42.068612 0.24338059 0 96.181423 0.96185061 -69.95542 0 24.615344 -11.582758 903.68812 -190.13826 0 120.69124
+ 100 1109.6904 -1968.5879 -1902.4323 -4490.0667 -2755.8991 -7.1224194 0.21757691 0 61.805857 7.0827218 -75.645383 0 20.115437 -6.23727 863.56487 -198.56975 0 122.09963
+Loop time of 0.301445 on 4 procs for 100 steps with 21 atoms
+
+Performance: 28.662 ns/day, 0.837 hours/ns, 331.736 timesteps/s
+99.2% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.2505 | 0.25132 | 0.25322 | 0.2 | 83.37
+Neigh | 0.0036662 | 0.0049902 | 0.006367 | 1.4 | 1.66
+Comm | 0.0030849 | 0.0049003 | 0.0058699 | 1.5 | 1.63
+Output | 0.00038004 | 0.00043535 | 0.00049639 | 0.2 | 0.14
+Modify | 0.038152 | 0.03968 | 0.041151 | 0.5 | 13.16
+Other | | 0.0001191 | | | 0.04
+
+Nlocal: 5.25 ave 15 max 0 min
+Histogram: 1 0 2 0 0 0 0 0 0 1
+Nghost: 355.5 ave 432 max 282 min
+Histogram: 1 0 0 0 1 1 0 0 0 1
+Neighs: 298.75 ave 822 max 0 min
+Histogram: 1 0 2 0 0 0 0 0 0 1
+
+Total # of neighbors = 1195
+Ave neighs/atom = 56.9048
+Neighbor list builds = 10
+Dangerous builds not checked
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:00
diff --git a/examples/reax/log.15Feb16.reaxc.tatb.g++.1 b/examples/reax/log.15Feb16.reaxc.tatb.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..7c330f0138eb652ca7f30d66530471f1a175bc39
--- /dev/null
+++ b/examples/reax/log.15Feb16.reaxc.tatb.g++.1
@@ -0,0 +1,102 @@
+LAMMPS (15 Feb 2016)
+# ReaxFF potential for TATB system
+# this run is equivalent to reax/in.reax.tatb,
+
+units real
+
+atom_style charge
+read_data data.tatb
+ triclinic box = (0 0 0) to (13.624 17.1149 15.1826) with tilt (-5.75316 -6.32547 7.42573)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 384 atoms
+
+pair_style reax/c control.reax_c.tatb
+pair_coeff * * ffield.reax C H O N
+Reading potential file ffield.reax with DATE: 2010-02-19
+
+compute reax all pair reax/c
+
+variable eb equal c_reax[1]
+variable ea equal c_reax[2]
+variable elp equal c_reax[3]
+variable emol equal c_reax[4]
+variable ev equal c_reax[5]
+variable epen equal c_reax[6]
+variable ecoa equal c_reax[7]
+variable ehb equal c_reax[8]
+variable et equal c_reax[9]
+variable eco equal c_reax[10]
+variable ew equal c_reax[11]
+variable ep equal c_reax[12]
+variable efi equal c_reax[13]
+variable eqeq equal c_reax[14]
+
+neighbor 2.5 bin
+neigh_modify delay 0 every 5 check no
+
+fix 1 all nve
+fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
+fix 4 all reax/c/bonds 5 bonds.reaxc
+
+thermo 5
+thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
+
+timestep 0.0625
+
+#dump 1 all custom 100 dump.reaxc.tatb id type q x y z
+
+#dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 3
+
+#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 3
+
+fix 3 all reax/c/species 1 5 5 species.tatb
+
+run 25
+Neighbor list info ...
+ 2 neighbor list requests
+ update every 5 steps, delay 0 steps, check no
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 12.5
+ ghost atom cutoff = 12.5
+ binsize = 6.25 -> bins = 5 4 3
+Memory usage per processor = 155.82 Mbytes
+Step Temp E_pair TotEng Press eb ea elp emol ev epen ecoa ehb et eco ew ep efi eqeq
+ 0 0 -44760.998 -44760.998 7827.7879 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6394 0 6391.0274
+ 5 0.61603942 -44761.698 -44760.994 8934.6281 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.193 0 6388.6691
+ 10 2.3525551 -44763.227 -44760.541 12288.607 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50358 -1560.7569 252.85309 -655.44063 18850.391 -8730.9688 0 6381.7066
+ 15 4.9013326 -44766.36 -44760.764 17717.015 -61103.434 489.14721 4.7213644 0 1572.6349 20.593139 -268.56847 -1566.3829 252.95174 -654.96611 18835.777 -8719.237 0 6370.4033
+ 20 7.829471 -44769.686 -44760.747 25205.558 -61089.006 490.21313 4.719302 0 1571.7022 20.420943 -260.85565 -1573.7378 253.3539 -654.31623 18816.07 -8703.5091 0 6355.2604
+ 25 10.697926 -44772.904 -44760.691 34232.793 -61069.308 490.25886 4.7163736 0 1570.7397 20.181346 -251.91377 -1582.3261 253.82253 -653.53184 18791.975 -8684.3608 0 6336.8416
+Loop time of 4.39835 on 1 procs for 25 steps with 384 atoms
+
+Performance: 0.031 ns/day, 781.929 hours/ns, 5.684 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 3.5683 | 3.5683 | 3.5683 | 0.0 | 81.13
+Neigh | 0.40996 | 0.40996 | 0.40996 | 0.0 | 9.32
+Comm | 0.0022433 | 0.0022433 | 0.0022433 | 0.0 | 0.05
+Output | 0.00019693 | 0.00019693 | 0.00019693 | 0.0 | 0.00
+Modify | 0.41718 | 0.41718 | 0.41718 | 0.0 | 9.49
+Other | | 0.0004306 | | | 0.01
+
+Nlocal: 384 ave 384 max 384 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 7559 ave 7559 max 7559 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 286828 ave 286828 max 286828 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 286828
+Ave neighs/atom = 746.948
+Neighbor list builds = 5
+Dangerous builds not checked
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:04
diff --git a/examples/reax/log.15Feb16.reaxc.tatb.g++.4 b/examples/reax/log.15Feb16.reaxc.tatb.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..38875723aeb9aa67d22f779597acdbb2c9a78040
--- /dev/null
+++ b/examples/reax/log.15Feb16.reaxc.tatb.g++.4
@@ -0,0 +1,102 @@
+LAMMPS (15 Feb 2016)
+# ReaxFF potential for TATB system
+# this run is equivalent to reax/in.reax.tatb,
+
+units real
+
+atom_style charge
+read_data data.tatb
+ triclinic box = (0 0 0) to (13.624 17.1149 15.1826) with tilt (-5.75316 -6.32547 7.42573)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 384 atoms
+
+pair_style reax/c control.reax_c.tatb
+pair_coeff * * ffield.reax C H O N
+Reading potential file ffield.reax with DATE: 2010-02-19
+
+compute reax all pair reax/c
+
+variable eb equal c_reax[1]
+variable ea equal c_reax[2]
+variable elp equal c_reax[3]
+variable emol equal c_reax[4]
+variable ev equal c_reax[5]
+variable epen equal c_reax[6]
+variable ecoa equal c_reax[7]
+variable ehb equal c_reax[8]
+variable et equal c_reax[9]
+variable eco equal c_reax[10]
+variable ew equal c_reax[11]
+variable ep equal c_reax[12]
+variable efi equal c_reax[13]
+variable eqeq equal c_reax[14]
+
+neighbor 2.5 bin
+neigh_modify delay 0 every 5 check no
+
+fix 1 all nve
+fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
+fix 4 all reax/c/bonds 5 bonds.reaxc
+
+thermo 5
+thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
+
+timestep 0.0625
+
+#dump 1 all custom 100 dump.reaxc.tatb id type q x y z
+
+#dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 3
+
+#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 3
+
+fix 3 all reax/c/species 1 5 5 species.tatb
+
+run 25
+Neighbor list info ...
+ 2 neighbor list requests
+ update every 5 steps, delay 0 steps, check no
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 12.5
+ ghost atom cutoff = 12.5
+ binsize = 6.25 -> bins = 5 4 3
+Memory usage per processor = 105.386 Mbytes
+Step Temp E_pair TotEng Press eb ea elp emol ev epen ecoa ehb et eco ew ep efi eqeq
+ 0 0 -44760.998 -44760.998 7827.7867 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6397 0 6391.0277
+ 5 0.61603967 -44761.698 -44760.994 8934.6339 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.1905 0 6388.6665
+ 10 2.3525545 -44763.227 -44760.541 12288.586 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50357 -1560.7569 252.85309 -655.44063 18850.391 -8730.9762 0 6381.714
+ 15 4.9013281 -44766.36 -44760.764 17716.982 -61103.434 489.14722 4.7213644 0 1572.6349 20.593139 -268.56847 -1566.3829 252.95174 -654.96611 18835.777 -8719.2476 0 6370.4138
+ 20 7.8294637 -44769.686 -44760.747 25205.512 -61089.006 490.21314 4.719302 0 1571.7022 20.420943 -260.85565 -1573.7378 253.3539 -654.31623 18816.07 -8703.518 0 6355.2692
+ 25 10.697905 -44772.904 -44760.691 34232.815 -61069.308 490.25887 4.7163736 0 1570.7397 20.181346 -251.91377 -1582.3261 253.82253 -653.53184 18791.975 -8684.3481 0 6336.829
+Loop time of 2.68044 on 4 procs for 25 steps with 384 atoms
+
+Performance: 0.050 ns/day, 476.523 hours/ns, 9.327 timesteps/s
+99.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 2.255 | 2.2552 | 2.2557 | 0.0 | 84.13
+Neigh | 0.22861 | 0.22899 | 0.22971 | 0.1 | 8.54
+Comm | 0.005641 | 0.006301 | 0.0065787 | 0.5 | 0.24
+Output | 0.00036383 | 0.002835 | 0.0036614 | 2.7 | 0.11
+Modify | 0.18515 | 0.18673 | 0.18977 | 0.4 | 6.97
+Other | | 0.0004016 | | | 0.01
+
+Nlocal: 96 ave 96 max 96 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost: 5118 ave 5118 max 5118 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs: 79754 ave 79754 max 79754 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 319016
+Ave neighs/atom = 830.771
+Neighbor list builds = 5
+Dangerous builds not checked
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:02
diff --git a/examples/rigid/log.15Feb16.rigid.g++.1 b/examples/rigid/log.15Feb16.rigid.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..437fb7c821680c859a98b8e343e59a9189da43e0
--- /dev/null
+++ b/examples/rigid/log.15Feb16.rigid.g++.1
@@ -0,0 +1,329 @@
+LAMMPS (15 Feb 2016)
+# Simple rigid body system
+
+units lj
+atom_style atomic
+
+pair_style lj/cut 2.5
+
+read_data data.rigid
+ orthogonal box = (-12 -12 -12) to (12 12 12)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 81 atoms
+
+velocity all create 100.0 4928459
+
+# unconnected bodies
+
+group clump1 id <> 1 9
+9 atoms in group clump1
+group clump2 id <> 10 18
+9 atoms in group clump2
+group clump3 id <> 19 27
+9 atoms in group clump3
+group clump4 id <> 28 36
+9 atoms in group clump4
+group clump5 id <> 37 45
+9 atoms in group clump5
+group clump6 id <> 46 54
+9 atoms in group clump6
+group clump7 id <> 55 63
+9 atoms in group clump7
+group clump8 id <> 64 72
+9 atoms in group clump8
+group clump9 id <> 73 81
+9 atoms in group clump9
+
+fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
+9 rigid bodies with 81 atoms
+
+# 1 chain of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 36 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
+
+# 2 chains of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 37 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4
+#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
+
+neigh_modify exclude group clump1 clump1
+neigh_modify exclude group clump2 clump2
+neigh_modify exclude group clump3 clump3
+neigh_modify exclude group clump4 clump4
+neigh_modify exclude group clump5 clump5
+neigh_modify exclude group clump6 clump6
+neigh_modify exclude group clump7 clump7
+neigh_modify exclude group clump8 clump8
+neigh_modify exclude group clump9 clump9
+
+thermo 100
+
+#dump 1 all atom 50 dump.rigid
+
+#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 5
+
+#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 5
+
+timestep 0.0001
+thermo 50
+run 10000
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4 -> bins = 18 18 18
+Memory usage per processor = 3.15778 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 115.29439 5235.9179 0 5272.2142 -2.7403788
+ 50 14910.685 571.71558 0 5265.82 32.006171
+ 100 16298.442 136.66184 0 5267.653 16.444229
+ 150 16682.606 17.490511 0 5269.4219 14.900344
+ 200 16733.929 1.372872 0 5269.4617 14.569267
+ 250 16738.853 -0.15252816 0 5269.4864 14.496404
+ 300 16738.588 -0.055171335 0 5269.5002 14.496025
+ 350 16738.492 -0.017444677 0 5269.5077 14.496446
+ 400 16738.464 -0.0060102023 0 5269.5104 14.496618
+ 450 16738.455 -0.0012713351 0 5269.5124 14.496701
+ 500 16738.455 -0.00081068621 0 5269.5128 14.496709
+ 550 16738.455 -0.00083203497 0 5269.5129 14.496707
+ 600 16738.455 -0.00058355356 0 5269.5131 14.496709
+ 650 16738.455 -0.00047226704 0 5269.5131 14.496708
+ 700 16738.455 0 0 5269.5136 14.496713
+ 750 16738.455 0 0 5269.5136 14.49671
+ 800 16738.455 0 0 5269.5137 14.496709
+ 850 16738.455 0 0 5269.5137 14.49671
+ 900 16738.456 0 0 5269.5138 14.496713
+ 950 16738.462 -0.0035323872 0 5269.5122 14.496671
+ 1000 16738.586 -0.051135144 0 5269.5036 14.496229
+ 1050 16737.358 0.32995057 0 5269.4981 14.525763
+ 1100 16737.892 0.16210246 0 5269.4984 14.531983
+ 1150 16738.703 -0.089235095 0 5269.5025 14.509899
+ 1200 16738.466 -0.0075446243 0 5269.5096 14.510615
+ 1250 16738.456 0 0 5269.514 14.510704
+ 1300 16738.457 0 0 5269.5141 14.510701
+ 1350 16738.457 0 0 5269.5141 14.510699
+ 1400 16738.457 -0.00044736511 0 5269.5138 14.510693
+ 1450 16738.458 -0.0010971179 0 5269.5134 14.510687
+ 1500 16738.458 -0.00057885428 0 5269.5139 14.510698
+ 1550 16738.457 0 0 5269.5143 14.51071
+ 1600 16738.457 0 0 5269.5144 14.510712
+ 1650 16738.457 0 0 5269.5144 14.510712
+ 1700 16738.458 0 0 5269.5144 14.51071
+ 1750 16738.458 0 0 5269.5145 14.510708
+ 1800 16738.458 0 0 5269.5145 14.510706
+ 1850 16738.458 0 0 5269.5146 14.510705
+ 1900 16738.458 0 0 5269.5146 14.510706
+ 1950 16738.465 -0.0031733615 0 5269.5134 14.510659
+ 2000 16738.491 -0.013255268 0 5269.5117 14.510532
+ 2050 16738.556 -0.0365811 0 5269.5087 14.51029
+ 2100 16738.633 -0.063209659 0 5269.5065 14.510219
+ 2150 16738.607 -0.05601761 0 5269.5055 14.510231
+ 2200 16738.557 -0.038423032 0 5269.5072 14.510404
+ 2250 16738.515 -0.023709918 0 5269.5088 14.510539
+ 2300 16738.489 -0.013249035 0 5269.5111 14.510621
+ 2350 16738.468 -0.0045563719 0 5269.5131 14.510714
+ 2400 16738.46 -0.00052194273 0 5269.5146 14.510771
+ 2450 16738.464 -0.0023259756 0 5269.514 14.510746
+ 2500 16738.468 -0.0051929186 0 5269.5127 14.510731
+ 2550 16738.581 -0.044940117 0 5269.5085 14.510315
+ 2600 16738.427 -7.972284e-05 0 5269.5046 14.510657
+ 2650 16733.017 1.7051479 0 5269.5067 14.596295
+ 2700 16738.761 -0.10614946 0 5269.5038 14.499584
+ 2750 16733.973 1.4038179 0 5269.5064 14.598107
+ 2800 16738.585 -0.046813448 0 5269.5076 14.511073
+ 2850 16738.487 -0.012558719 0 5269.5111 14.510111
+ 2900 16738.465 -0.0026252725 0 5269.514 14.510277
+ 2950 16738.476 -0.0082220764 0 5269.512 14.510223
+ 3000 16738.66 -0.071284779 0 5269.507 14.509758
+ 3050 16715.332 7.2419352 0 5269.476 14.870305
+ 3100 16653.226 26.818761 0 5269.5009 14.496764
+ 3150 16739.351 -0.30690375 0 5269.4886 13.643904
+ 3200 16733.238 1.6025328 0 5269.4737 12.016934
+ 3250 16734.374 1.2554429 0 5269.4841 11.963561
+ 3300 16732.156 1.9585967 0 5269.4893 12.234024
+ 3350 16738.655 -0.079693236 0 5269.497 12.092757
+ 3400 16738.543 -0.042215005 0 5269.4991 12.092809
+ 3450 16738.591 -0.059327511 0 5269.4972 12.092536
+ 3500 16738.759 -0.11761245 0 5269.4918 12.09203
+ 3550 16713.405 7.8460621 0 5269.4737 12.389816
+ 3600 16734.939 1.0821936 0 5269.4891 12.173591
+ 3650 16738.808 -0.13663194 0 5269.4882 12.027009
+ 3700 16738.602 -0.070934368 0 5269.4889 12.025288
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+ 9400 16738.48 0 0 5269.5215 12.011732
+ 9450 16738.48 0 0 5269.5216 12.011715
+ 9500 16738.481 -0.00037652434 0 5269.5216 12.011692
+ 9550 16738.493 -0.005315616 0 5269.5203 12.011611
+ 9600 16738.549 -0.026814368 0 5269.5163 12.011415
+ 9650 16738.765 -0.10191523 0 5269.5092 12.011013
+ 9700 16735.041 1.0589885 0 5269.4979 12.062708
+ 9750 16738.013 0.13550123 0 5269.5101 11.407245
+ 9800 16738.512 -0.011620328 0 5269.5201 11.394974
+ 9850 16738.489 -0.00067270523 0 5269.5237 11.395098
+ 9900 16738.489 -0.00024984554 0 5269.5242 11.395085
+ 9950 16738.49 0 0 5269.5245 11.395076
+ 10000 16738.49 0 0 5269.5246 11.395075
+Loop time of 0.122539 on 1 procs for 10000 steps with 81 atoms
+
+Performance: 705081.398 tau/day, 81606.643 timesteps/s
+100.4% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0094028 | 0.0094028 | 0.0094028 | 0.0 | 7.67
+Neigh | 0.03594 | 0.03594 | 0.03594 | 0.0 | 29.33
+Comm | 0.00758 | 0.00758 | 0.00758 | 0.0 | 6.19
+Output | 0.0011275 | 0.0011275 | 0.0011275 | 0.0 | 0.92
+Modify | 0.065143 | 0.065143 | 0.065143 | 0.0 | 53.16
+Other | | 0.003345 | | | 2.73
+
+Nlocal: 81 ave 81 max 81 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 84 ave 84 max 84 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 998
+Dangerous builds = 997
+Total wall time: 0:00:00
diff --git a/examples/rigid/log.15Feb16.rigid.g++.4 b/examples/rigid/log.15Feb16.rigid.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..0e8157316fcee3fc916de4d252d1928399ef1134
--- /dev/null
+++ b/examples/rigid/log.15Feb16.rigid.g++.4
@@ -0,0 +1,329 @@
+LAMMPS (15 Feb 2016)
+# Simple rigid body system
+
+units lj
+atom_style atomic
+
+pair_style lj/cut 2.5
+
+read_data data.rigid
+ orthogonal box = (-12 -12 -12) to (12 12 12)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 81 atoms
+
+velocity all create 100.0 4928459
+
+# unconnected bodies
+
+group clump1 id <> 1 9
+9 atoms in group clump1
+group clump2 id <> 10 18
+9 atoms in group clump2
+group clump3 id <> 19 27
+9 atoms in group clump3
+group clump4 id <> 28 36
+9 atoms in group clump4
+group clump5 id <> 37 45
+9 atoms in group clump5
+group clump6 id <> 46 54
+9 atoms in group clump6
+group clump7 id <> 55 63
+9 atoms in group clump7
+group clump8 id <> 64 72
+9 atoms in group clump8
+group clump9 id <> 73 81
+9 atoms in group clump9
+
+fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
+9 rigid bodies with 81 atoms
+
+# 1 chain of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 36 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
+
+# 2 chains of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 37 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4
+#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
+
+neigh_modify exclude group clump1 clump1
+neigh_modify exclude group clump2 clump2
+neigh_modify exclude group clump3 clump3
+neigh_modify exclude group clump4 clump4
+neigh_modify exclude group clump5 clump5
+neigh_modify exclude group clump6 clump6
+neigh_modify exclude group clump7 clump7
+neigh_modify exclude group clump8 clump8
+neigh_modify exclude group clump9 clump9
+
+thermo 100
+
+#dump 1 all atom 50 dump.rigid
+
+#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 5
+
+#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 5
+
+timestep 0.0001
+thermo 50
+run 10000
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4 -> bins = 18 18 18
+Memory usage per processor = 3.1287 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 115.29439 5235.9179 0 5272.2142 -2.7403788
+ 50 14910.685 571.71558 0 5265.82 32.006171
+ 100 16298.442 136.66184 0 5267.653 16.444229
+ 150 16682.606 17.490511 0 5269.4219 14.900344
+ 200 16733.929 1.372872 0 5269.4617 14.569267
+ 250 16738.853 -0.15252816 0 5269.4864 14.496404
+ 300 16738.588 -0.055171335 0 5269.5002 14.496025
+ 350 16738.492 -0.017444677 0 5269.5077 14.496446
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+ 8300 16738.471 0 0 5269.5187 12.011719
+ 8350 16738.472 0 0 5269.5189 12.011723
+ 8400 16738.472 0 0 5269.519 12.01172
+ 8450 16738.473 -0.00039690663 0 5269.5189 12.011706
+ 8500 16738.481 -0.0034646803 0 5269.5182 12.011643
+ 8550 16738.483 -0.0045307409 0 5269.5178 12.011621
+ 8600 16738.474 -0.00076532813 0 5269.5189 12.011681
+ 8650 16738.474 0 0 5269.5197 12.011699
+ 8700 16738.475 0 0 5269.5199 12.011715
+ 8750 16738.475 0 0 5269.52 12.011732
+ 8800 16738.475 0 0 5269.52 12.011743
+ 8850 16738.476 0 0 5269.5201 12.011744
+ 8900 16738.476 0 0 5269.5202 12.011735
+ 8950 16738.476 0 0 5269.5203 12.011719
+ 9000 16738.477 0 0 5269.5205 12.011698
+ 9050 16738.477 0 0 5269.5206 12.011683
+ 9100 16738.478 0 0 5269.5208 12.011684
+ 9150 16738.479 0 0 5269.521 12.011701
+ 9200 16738.479 0 0 5269.5212 12.011722
+ 9250 16738.479 0 0 5269.5213 12.011738
+ 9300 16738.48 0 0 5269.5214 12.011746
+ 9350 16738.48 0 0 5269.5214 12.011744
+ 9400 16738.48 0 0 5269.5215 12.011732
+ 9450 16738.48 0 0 5269.5216 12.011715
+ 9500 16738.481 -0.00037652438 0 5269.5216 12.011692
+ 9550 16738.493 -0.0053156163 0 5269.5203 12.011611
+ 9600 16738.549 -0.026814371 0 5269.5163 12.011415
+ 9650 16738.765 -0.10191523 0 5269.5092 12.011013
+ 9700 16735.041 1.0589894 0 5269.4979 12.062708
+ 9750 16738.013 0.13550109 0 5269.5101 11.407246
+ 9800 16738.512 -0.011620327 0 5269.5201 11.394974
+ 9850 16738.489 -0.00067270507 0 5269.5237 11.395098
+ 9900 16738.489 -0.00024984555 0 5269.5242 11.395085
+ 9950 16738.49 0 0 5269.5245 11.395076
+ 10000 16738.49 0 0 5269.5246 11.395075
+Loop time of 0.187163 on 4 procs for 10000 steps with 81 atoms
+
+Performance: 461628.979 tau/day, 53429.280 timesteps/s
+95.5% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0022814 | 0.0031556 | 0.0039577 | 1.1 | 1.69
+Neigh | 0.010708 | 0.011337 | 0.012736 | 0.8 | 6.06
+Comm | 0.084257 | 0.090435 | 0.10014 | 2.1 | 48.32
+Output | 0.003355 | 0.0035859 | 0.0039752 | 0.4 | 1.92
+Modify | 0.062852 | 0.072432 | 0.07759 | 2.1 | 38.70
+Other | | 0.006218 | | | 3.32
+
+Nlocal: 20.25 ave 38 max 3 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+Nghost: 27.25 ave 48 max 13 min
+Histogram: 1 0 1 1 0 0 0 0 0 1
+Neighs: 0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 998
+Dangerous builds = 997
+Total wall time: 0:00:00
diff --git a/examples/rigid/log.15Feb16.rigid.poems.g++.1 b/examples/rigid/log.15Feb16.rigid.poems.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..1aa3cd82be93493275da048c2e0c641b9b0344ea
--- /dev/null
+++ b/examples/rigid/log.15Feb16.rigid.poems.g++.1
@@ -0,0 +1,332 @@
+LAMMPS (15 Feb 2016)
+# Simple rigid body system
+
+units lj
+atom_style atomic
+
+pair_style lj/cut 2.5
+
+read_data data.rigid
+ orthogonal box = (-12 -12 -12) to (12 12 12)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 81 atoms
+
+velocity all create 100.0 4928459
+
+# unconnected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 10 18
+#group clump3 id <> 19 27
+#group clump4 id <> 28 36
+#group clump5 id <> 37 45
+#group clump6 id <> 46 54
+#group clump7 id <> 55 63
+#group clump8 id <> 64 72
+#group clump9 id <> 73 81
+
+#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
+
+# 1 chain of connected bodies
+
+group clump1 id <> 1 9
+9 atoms in group clump1
+group clump2 id <> 9 18
+10 atoms in group clump2
+group clump3 id <> 18 27
+10 atoms in group clump3
+group clump4 id <> 27 36
+10 atoms in group clump4
+group clump5 id <> 36 45
+10 atoms in group clump5
+group clump6 id <> 45 54
+10 atoms in group clump6
+group clump7 id <> 54 63
+10 atoms in group clump7
+group clump8 id <> 63 72
+10 atoms in group clump8
+group clump9 id <> 72 81
+10 atoms in group clump9
+
+fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
+1 clusters, 9 bodies, 8 joints, 81 atoms
+
+# 2 chains of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 37 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4
+#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
+
+neigh_modify exclude group clump1 clump1
+neigh_modify exclude group clump2 clump2
+neigh_modify exclude group clump3 clump3
+neigh_modify exclude group clump4 clump4
+neigh_modify exclude group clump5 clump5
+neigh_modify exclude group clump6 clump6
+neigh_modify exclude group clump7 clump7
+neigh_modify exclude group clump8 clump8
+neigh_modify exclude group clump9 clump9
+
+thermo 100
+
+#dump 1 all atom 50 dump.rigid.poems
+
+#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 5
+
+#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 5
+
+timestep 0.0001
+thermo 50
+run 10000
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4 -> bins = 18 18 18
+Memory usage per processor = 2.47028 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 217.7783 3430.3907 0 3466.6871 -2.7403788
+ 50 13679.637 1404.2468 0 3684.1863 12.446066
+ 100 16777.225 888.87665 0 3685.0808 -31.828677
+ 150 19595.365 418.45042 0 3684.3446 40.709078
+ 200 18524.188 596.47273 0 3683.8375 -0.8159371
+ 250 21015.789 180.96521 0 3683.5967 -10.042469
+ 300 20785.513 219.25314 0 3683.5053 2.6452719
+ 350 21072.46 171.2554 0 3683.3321 7.0609024
+ 400 19956.414 356.36381 0 3682.4328 19.320259
+ 450 20724.42 227.73284 0 3681.8028 8.1259249
+ 500 20152.578 322.71466 0 3681.4777 5.4929878
+ 550 20017.022 345.29701 0 3681.4673 5.4661666
+ 600 17897.743 698.72196 0 3681.6791 3.2854742
+ 650 17297.758 796.60256 0 3679.5623 15.191113
+ 700 18581.934 584.29715 0 3681.2861 5.1588289
+ 750 21774.158 52.821062 0 3681.8474 -10.775664
+ 800 21604.055 81.188546 0 3681.8644 -3.2045743
+ 850 17821.483 711.53827 0 3681.7854 7.4384277
+ 900 21033.292 175.98127 0 3681.5299 -16.345167
+ 950 20968.166 186.59847 0 3681.2929 -2.330456
+ 1000 20490.66 266.19375 0 3681.3037 11.787983
+ 1050 20222.396 310.94072 0 3681.34 -8.3459539
+ 1100 21321.687 127.61533 0 3681.2299 -1.2184717
+ 1150 20849.582 206.01695 0 3680.9472 -0.86699149
+ 1200 21815.003 45.317414 0 3681.1512 1.5988314
+ 1250 18655.437 572.41453 0 3681.654 10.064078
+ 1300 20780.781 217.36506 0 3680.8286 6.0538616
+ 1350 20558.971 254.36482 0 3680.8601 -3.6773952
+ 1400 21485.029 99.812921 0 3680.6511 -16.185473
+ 1450 21771.107 52.15961 0 3680.6775 -2.4756673
+ 1500 21520.948 93.503927 0 3680.3286 2.1023576
+ 1550 21351.418 121.68137 0 3680.2511 5.5159947
+ 1600 20778.805 216.92177 0 3680.0559 15.089188
+ 1650 21477.638 100.21836 0 3679.8247 -1.1045746
+ 1700 18501.339 596.47914 0 3680.0357 -15.679679
+ 1750 18563.642 587.34785 0 3681.2882 33.532209
+ 1800 19110.185 494.8234 0 3679.8543 18.024046
+ 1850 21364.191 119.23545 0 3679.9339 2.5291103
+ 1900 20146.626 322.14867 0 3679.9197 5.7313218
+ 1950 20692.672 231.25325 0 3680.0319 4.2977763
+ 2000 20943.904 189.11235 0 3679.7629 -22.645121
+ 2050 19668.057 401.82994 0 3679.8394 3.6251916
+ 2100 20280.442 299.76155 0 3679.8353 7.4807949
+ 2150 19181.86 483.522 0 3680.4987 22.620507
+ 2200 21300.161 130.70534 0 3680.7322 4.7102665
+ 2250 20486.943 266.63931 0 3681.1299 -8.6456512
+ 2300 18653.122 572.24819 0 3681.1018 -5.2637122
+ 2350 21513.523 95.614901 0 3681.2021 -9.3621767
+ 2400 21466.272 103.56446 0 3681.2765 -29.561368
+ 2450 20100.105 332.27123 0 3682.2887 35.744287
+ 2500 20764.395 221.6677 0 3682.4001 -12.468906
+ 2550 20435.699 276.31055 0 3682.2603 -22.413697
+ 2600 21466.467 104.53618 0 3682.2807 -10.078508
+ 2650 20814.737 213.23892 0 3682.3617 5.1390411
+ 2700 18565.761 588.3578 0 3682.6513 22.27664
+ 2750 20772.36 220.1607 0 3682.2206 -7.9448198
+ 2800 21018.563 179.10058 0 3682.1945 -7.0717829
+ 2850 16789.412 884.21472 0 3682.4501 33.279015
+ 2900 19304.363 464.75282 0 3682.1466 7.947554
+ 2950 20513.758 263.07578 0 3682.0355 2.2361434
+ 3000 20617.309 245.95251 0 3682.1706 -0.75213689
+ 3050 18567.52 587.90473 0 3682.4914 -4.0112006
+ 3100 18696.577 566.20617 0 3682.3023 -1.4814167
+ 3150 19864.606 371.56078 0 3682.3284 8.9362836
+ 3200 18902.643 532.04614 0 3682.4867 0.76630303
+ 3250 21110.454 163.86212 0 3682.271 -1.6253894
+ 3300 19369.939 454.05833 0 3682.3816 4.9066544
+ 3350 19082.603 501.69905 0 3682.133 3.5982292
+ 3400 19527.779 426.918 0 3681.5478 6.9612143
+ 3450 19892.953 366.19989 0 3681.6921 3.0050426
+ 3500 19708.981 396.84552 0 3681.6756 7.0757635
+ 3550 20256.096 306.23937 0 3682.2554 -1.752138
+ 3600 21289.889 133.93823 0 3682.253 -3.7462615
+ 3650 18333.877 627.18028 0 3682.8264 -15.276791
+ 3700 19829.133 377.33753 0 3682.1931 -6.269648
+ 3750 20771.635 220.07171 0 3682.0109 -28.479036
+ 3800 18373.813 619.79253 0 3682.0947 29.594781
+ 3850 19320.99 461.92786 0 3682.0928 -5.3212101
+ 3900 16119.825 995.68064 0 3682.3182 -8.4683118
+ 3950 15556.948 1091.3655 0 3684.1902 20.98273
+ 4000 20000.464 348.24891 0 3681.6596 7.1589745
+ 4050 18870.219 536.59924 0 3681.6358 -3.7997025
+ 4100 19889.518 367.49253 0 3682.4122 -14.091266
+ 4150 15789.623 1051.3399 0 3682.9438 -4.4152389
+ 4200 20548.889 256.83493 0 3681.6498 0.92234153
+ 4250 20681.925 235.46113 0 3682.4487 -11.515773
+ 4300 19330.404 460.80975 0 3682.5437 -22.351775
+ 4350 19369.443 453.35405 0 3681.5945 29.418242
+ 4400 20762.165 222.24133 0 3682.6021 2.6627047
+ 4450 19984.657 350.71294 0 3681.4891 28.88731
+ 4500 21167.58 154.25344 0 3682.1834 -3.0784322
+ 4550 18133.576 660.73671 0 3682.9995 2.5305835
+ 4600 19935.069 360.36826 0 3682.8798 2.4575034
+ 4650 21413.76 113.86464 0 3682.8246 -5.1271547
+ 4700 21716.333 63.609419 0 3682.9982 -2.4708049
+ 4750 21352.947 124.36961 0 3683.1941 -0.29026265
+ 4800 19043.788 508.8617 0 3682.8264 14.797006
+ 4850 20516.121 263.78758 0 3683.1411 7.1348281
+ 4900 20624.5 245.81827 0 3683.235 0.34708051
+ 4950 20317.197 296.68937 0 3682.8889 -0.55065946
+ 5000 18346.865 625.37246 0 3683.1832 7.3371413
+ 5050 18867.53 538.49153 0 3683.0799 1.9249866
+ 5100 18790.276 551.17224 0 3682.885 2.2333017
+ 5150 20241.365 311.84683 0 3685.4076 -3.998004
+ 5200 17685.058 739.76418 0 3687.2739 3.2835025
+ 5250 18496.626 604.58166 0 3687.3526 -10.185776
+ 5300 18420.042 617.82026 0 3687.8273 -16.392458
+ 5350 18767.338 559.0349 0 3686.9246 4.5320767
+ 5400 20423.245 284.90517 0 3688.7794 -8.6356656
+ 5450 21080.398 176.18494 0 3689.5846 -16.450038
+ 5500 16684.424 909.12643 0 3689.8637 49.94555
+ 5550 20132.31 335.03663 0 3690.4216 -16.018038
+ 5600 20430.923 285.17562 0 3690.3295 -5.0773675
+ 5650 20479.943 276.55962 0 3689.8834 5.4334564
+ 5700 20061.532 345.95553 0 3689.5441 -16.230658
+ 5750 20523.759 268.92217 0 3689.5487 -4.4128812
+ 5800 18900.356 537.65462 0 3687.7139 13.605549
+ 5850 20280.502 310.27193 0 3690.3556 -4.7884959
+ 5900 19050.26 515.66087 0 3690.7042 7.8864722
+ 5950 19566.917 430.2997 0 3691.4525 31.715268
+ 6000 18878.118 544.75449 0 3691.1076 -4.2415329
+ 6050 19308.682 471.70734 0 3689.821 -10.561614
+ 6100 18776.194 560.04764 0 3689.4133 -7.7286747
+ 6150 21475.064 110.1508 0 3689.3281 -3.6506391
+ 6200 19975 360.82675 0 3689.9934 10.282021
+ 6250 21396.341 123.5341 0 3689.5909 -5.7215163
+ 6300 18533.423 600.87422 0 3689.778 15.408027
+ 6350 20653.152 247.19253 0 3689.3846 8.5607784
+ 6400 19716.537 403.41487 0 3689.5044 13.165575
+ 6450 21120.66 168.79838 0 3688.9084 -0.50382728
+ 6500 19700.345 404.7155 0 3688.1064 13.941375
+ 6550 10818.393 1892.037 0 3695.1025 38.423155
+ 6600 18684.478 574.84755 0 3688.9273 5.9176985
+ 6650 19219.732 486.04269 0 3689.3314 18.287659
+ 6700 20058.587 344.88255 0 3687.9804 6.5372086
+ 6750 21279.318 142.77333 0 3689.3264 2.498188
+ 6800 20671.545 244.25024 0 3689.5078 -4.1356416
+ 6850 21203.598 155.82001 0 3689.753 -0.0083061182
+ 6900 21699.344 73.301497 0 3689.8588 -8.0309898
+ 6950 20951.212 197.19403 0 3689.0627 0.76668303
+ 7000 20166.275 329.02869 0 3690.0746 2.0083318
+ 7050 21554.944 97.465792 0 3689.9564 -3.2420086
+ 7100 20817.494 220.25476 0 3689.8372 0.17206182
+ 7150 21481.11 109.84029 0 3690.0253 -3.6814741
+ 7200 21266.824 145.53099 0 3690.0016 -2.060543
+ 7250 19434.684 450.81331 0 3689.9273 9.4822765
+ 7300 21246.525 148.96573 0 3690.0532 3.3208839
+ 7350 19749.269 398.60049 0 3690.1454 1.0929662
+ 7400 20354.792 297.70261 0 3690.168 1.547159
+ 7450 19996.859 357.16723 0 3689.977 -0.68412025
+ 7500 20179.628 326.53243 0 3689.8038 -2.4805507
+ 7550 18765.184 561.65039 0 3689.1811 -1.7976428
+ 7600 19457.496 447.04428 0 3689.9603 -1.9055522
+ 7650 18206.823 655.57276 0 3690.0433 1.2797964
+ 7700 19152.344 497.77422 0 3689.8315 18.145069
+ 7750 21387.484 125.48654 0 3690.0673 -2.9915772
+ 7800 18127.052 668.61425 0 3689.7896 9.044869
+ 7850 21419.557 120.08889 0 3690.015 6.2651717
+ 7900 21817.182 53.739819 0 3689.9368 -4.2387416
+ 7950 18215.195 654.15494 0 3690.0208 -54.628049
+ 8000 21523.503 102.58018 0 3689.8307 -4.84236
+ 8050 20720.799 236.28689 0 3689.7535 -9.3725225
+ 8100 21196.483 157.3232 0 3690.0704 -7.7222497
+ 8150 20869.667 211.65308 0 3689.9309 -6.8438295
+ 8200 17790.052 725.72497 0 3690.7336 -25.697688
+ 8250 19634.94 417.71929 0 3690.2094 8.861604
+ 8300 19135.784 500.92443 0 3690.2218 -3.1245167
+ 8350 20191.718 324.93312 0 3690.2195 6.5736107
+ 8400 20695.239 241.02378 0 3690.2302 -14.592221
+ 8450 21793.857 57.609525 0 3689.9191 -11.509747
+ 8500 21271.088 144.43102 0 3689.6124 -0.091587085
+ 8550 20064.337 345.21754 0 3689.2737 9.5058471
+ 8600 20282.86 308.2307 0 3688.7074 2.265529
+ 8650 21223.055 151.24306 0 3688.419 1.7296834
+ 8700 18875.342 542.42055 0 3688.3108 6.367148
+ 8750 20922.65 201.55122 0 3688.6595 3.4208578
+ 8800 21406.54 120.8539 0 3688.6106 1.8253729
+ 8850 19868.524 377.05623 0 3688.477 16.327796
+ 8900 20025.322 348.94892 0 3686.5025 17.063406
+ 8950 21224.374 151.3567 0 3688.7524 -0.11028753
+ 9000 21318.309 135.862 0 3688.9135 -0.50826819
+ 9050 17538.618 768.00136 0 3691.1043 37.978645
+ 9100 21247.861 147.84641 0 3689.1566 -6.7773259
+ 9150 18455.677 613.08767 0 3689.0339 -3.4844751
+ 9200 19486.859 441.03829 0 3688.8482 -18.602827
+ 9250 21774.926 59.710446 0 3688.8648 -13.379919
+ 9300 17628.877 750.72321 0 3688.8694 27.797974
+ 9350 19827.334 383.85708 0 3688.4128 6.5459021
+ 9400 20020.126 351.61742 0 3688.3051 -14.332562
+ 9450 21596.338 88.904175 0 3688.2939 1.5779716
+ 9500 18981.418 524.60141 0 3688.1711 5.4352409
+ 9550 18652.616 579.05144 0 3687.8208 25.600729
+ 9600 21198.037 155.23097 0 3688.2371 -3.3586596
+ 9650 19958.317 361.32544 0 3687.7115 4.2910178
+ 9700 19129.101 499.5993 0 3687.7828 13.267102
+ 9750 21913.967 35.689587 0 3688.0174 -7.3222905
+ 9800 21314.694 135.43794 0 3687.8869 -9.5613518
+ 9850 20899.743 204.82802 0 3688.1185 -2.6321428
+ 9900 20288.244 306.5013 0 3687.8753 3.6196618
+ 9950 19271.015 475.88527 0 3687.7211 -1.8196764
+ 10000 21122.24 167.82714 0 3688.2005 -3.8464842
+Loop time of 3.72277 on 1 procs for 10000 steps with 81 atoms
+
+Performance: 23208.538 tau/day, 2686.173 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.16199 | 0.16199 | 0.16199 | 0.0 | 4.35
+Neigh | 0.098636 | 0.098636 | 0.098636 | 0.0 | 2.65
+Comm | 0.010331 | 0.010331 | 0.010331 | 0.0 | 0.28
+Output | 0.0020616 | 0.0020616 | 0.0020616 | 0.0 | 0.06
+Modify | 3.4423 | 3.4423 | 3.4423 | 0.0 | 92.47
+Other | | 0.007444 | | | 0.20
+
+Nlocal: 81 ave 81 max 81 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 95 ave 95 max 95 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 744 ave 744 max 744 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 744
+Ave neighs/atom = 9.18519
+Neighbor list builds = 992
+Dangerous builds = 941
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:03
diff --git a/examples/rigid/log.15Feb16.rigid.poems.g++.4 b/examples/rigid/log.15Feb16.rigid.poems.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..ac89378ab709da4e93971624b866f322c2ffef52
--- /dev/null
+++ b/examples/rigid/log.15Feb16.rigid.poems.g++.4
@@ -0,0 +1,332 @@
+LAMMPS (15 Feb 2016)
+# Simple rigid body system
+
+units lj
+atom_style atomic
+
+pair_style lj/cut 2.5
+
+read_data data.rigid
+ orthogonal box = (-12 -12 -12) to (12 12 12)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 81 atoms
+
+velocity all create 100.0 4928459
+
+# unconnected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 10 18
+#group clump3 id <> 19 27
+#group clump4 id <> 28 36
+#group clump5 id <> 37 45
+#group clump6 id <> 46 54
+#group clump7 id <> 55 63
+#group clump8 id <> 64 72
+#group clump9 id <> 73 81
+
+#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
+
+# 1 chain of connected bodies
+
+group clump1 id <> 1 9
+9 atoms in group clump1
+group clump2 id <> 9 18
+10 atoms in group clump2
+group clump3 id <> 18 27
+10 atoms in group clump3
+group clump4 id <> 27 36
+10 atoms in group clump4
+group clump5 id <> 36 45
+10 atoms in group clump5
+group clump6 id <> 45 54
+10 atoms in group clump6
+group clump7 id <> 54 63
+10 atoms in group clump7
+group clump8 id <> 63 72
+10 atoms in group clump8
+group clump9 id <> 72 81
+10 atoms in group clump9
+
+fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
+1 clusters, 9 bodies, 8 joints, 81 atoms
+
+# 2 chains of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 37 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4
+#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
+
+neigh_modify exclude group clump1 clump1
+neigh_modify exclude group clump2 clump2
+neigh_modify exclude group clump3 clump3
+neigh_modify exclude group clump4 clump4
+neigh_modify exclude group clump5 clump5
+neigh_modify exclude group clump6 clump6
+neigh_modify exclude group clump7 clump7
+neigh_modify exclude group clump8 clump8
+neigh_modify exclude group clump9 clump9
+
+thermo 100
+
+#dump 1 all atom 50 dump.rigid.poems
+
+#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 5
+
+#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 5
+
+timestep 0.0001
+thermo 50
+run 10000
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4 -> bins = 18 18 18
+Memory usage per processor = 2.4412 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 217.7783 3430.3907 0 3466.6871 -2.7403788
+ 50 13679.637 1404.2468 0 3684.1863 12.446066
+ 100 16777.225 888.87665 0 3685.0808 -31.828677
+ 150 19595.365 418.45042 0 3684.3446 40.709078
+ 200 18524.188 596.47273 0 3683.8375 -0.8159371
+ 250 21015.789 180.96521 0 3683.5967 -10.042469
+ 300 20785.513 219.25314 0 3683.5053 2.6452719
+ 350 21072.46 171.2554 0 3683.3321 7.0609024
+ 400 19956.414 356.36381 0 3682.4328 19.320259
+ 450 20724.42 227.73284 0 3681.8028 8.1259249
+ 500 20152.578 322.71466 0 3681.4777 5.4929878
+ 550 20017.022 345.29701 0 3681.4673 5.4661666
+ 600 17897.743 698.72196 0 3681.6791 3.2854742
+ 650 17297.758 796.60256 0 3679.5623 15.191113
+ 700 18581.934 584.29715 0 3681.2861 5.1588289
+ 750 21774.158 52.821062 0 3681.8474 -10.775664
+ 800 21604.055 81.188546 0 3681.8644 -3.2045743
+ 850 17821.483 711.53827 0 3681.7854 7.4384276
+ 900 21033.292 175.98127 0 3681.5299 -16.345167
+ 950 20968.166 186.59847 0 3681.2929 -2.330456
+ 1000 20490.66 266.19375 0 3681.3037 11.787983
+ 1050 20222.396 310.94072 0 3681.34 -8.3459539
+ 1100 21321.687 127.61533 0 3681.2299 -1.2184718
+ 1150 20849.582 206.01695 0 3680.9472 -0.8669916
+ 1200 21815.003 45.317417 0 3681.1512 1.5988314
+ 1250 18655.437 572.41453 0 3681.654 10.064076
+ 1300 20780.781 217.36504 0 3680.8286 6.0538619
+ 1350 20558.972 254.3648 0 3680.8601 -3.6773987
+ 1400 21485.029 99.812949 0 3680.6511 -16.185471
+ 1450 21771.108 52.15959 0 3680.6775 -2.4756681
+ 1500 21520.948 93.503949 0 3680.3286 2.1023578
+ 1550 21351.418 121.6814 0 3680.2511 5.5159978
+ 1600 20778.805 216.92171 0 3680.0559 15.089182
+ 1650 21477.639 100.2182 0 3679.8247 -1.1045944
+ 1700 18501.343 596.47853 0 3680.0357 -15.67963
+ 1750 18563.643 587.34767 0 3681.2882 33.532167
+ 1800 19110.19 494.82264 0 3679.8543 18.024034
+ 1850 21364.196 119.23454 0 3679.9339 2.5291491
+ 1900 20146.643 322.14595 0 3679.9197 5.731152
+ 1950 20692.67 231.25357 0 3680.0319 4.2977641
+ 2000 20943.904 189.11223 0 3679.763 -22.645645
+ 2050 19668.152 401.81407 0 3679.8394 3.6255896
+ 2100 20280.572 299.73976 0 3679.8351 7.4809355
+ 2150 19182.121 483.47905 0 3680.4992 22.615309
+ 2200 21299.76 130.77281 0 3680.7327 4.7114154
+ 2250 20487.784 266.4995 0 3681.1302 -8.6406776
+ 2300 18655.125 571.91487 0 3681.1023 -5.2671669
+ 2350 21512.614 95.766913 0 3681.2025 -9.3523428
+ 2400 21467.773 103.31519 0 3681.2773 -29.600307
+ 2450 20096.937 332.80159 0 3682.2911 35.890912
+ 2500 20761.446 222.16118 0 3682.4022 -12.528127
+ 2550 20409.6 280.67234 0 3682.2723 -22.277373
+ 2600 21469.964 103.95529 0 3682.2826 -10.038267
+ 2650 20708.138 231.00516 0 3682.3615 5.3659502
+ 2700 18584.743 585.07862 0 3682.5357 21.785261
+ 2750 20503.019 264.91491 0 3682.0847 -4.5583917
+ 2800 20584.075 251.44664 0 3682.1258 -6.5084595
+ 2850 17277.076 802.33356 0 3681.8462 15.519513
+ 2900 19392.956 449.92915 0 3682.0885 -4.3829957
+ 2950 18371.786 620.29835 0 3682.2626 7.2117592
+ 3000 20412.015 280.25302 0 3682.2555 0.32492606
+ 3050 20858.248 205.65269 0 3682.0273 4.5055715
+ 3100 21561.094 88.438447 0 3681.9541 -3.7523733
+ 3150 15471.278 1103.4497 0 3681.9961 -14.576367
+ 3200 15386.973 1117.8815 0 3682.377 15.051163
+ 3250 19741.037 392.04755 0 3682.2204 -2.6610995
+ 3300 20870.191 203.58229 0 3681.9475 -4.7795545
+ 3350 16648.228 907.66571 0 3682.3704 -8.9242511
+ 3400 20104.016 331.58603 0 3682.2554 6.4783858
+ 3450 21421.316 112.28228 0 3682.5015 -8.3484987
+ 3500 19284.533 467.80739 0 3681.8962 -12.835452
+ 3550 20160.125 322.4476 0 3682.4684 1.6574827
+ 3600 16682.415 902.73752 0 3683.14 22.383296
+ 3650 16762.19 890.14636 0 3683.8446 16.119412
+ 3700 17858.568 707.37212 0 3683.8 -1.6582504
+ 3750 20029.881 345.15986 0 3683.4733 -3.1415889
+ 3800 20734 227.99158 0 3683.6582 -7.9580418
+ 3850 20741.089 226.39408 0 3683.2423 8.3055765
+ 3900 18671.251 571.42296 0 3683.2981 -3.7468858
+ 3950 19547.209 423.14256 0 3681.0108 5.8312279
+ 4000 19739.799 393.58799 0 3683.5544 18.604884
+ 4050 20014.121 347.8176 0 3683.5044 9.93387
+ 4100 20503.654 266.08691 0 3683.3626 8.1304118
+ 4150 18309.702 632.29807 0 3683.9151 -0.0021480359
+ 4200 20509.423 265.60353 0 3683.8408 -2.1658857
+ 4250 21805.541 50.325935 0 3684.5828 1.082842
+ 4300 21420.551 114.90431 0 3684.9962 -1.7985998
+ 4350 20256.928 308.74187 0 3684.8966 -11.669472
+ 4400 21633.488 79.629274 0 3685.2106 -0.96131785
+ 4450 20793.327 219.66955 0 3685.2241 1.3752349
+ 4500 18719.484 564.86754 0 3684.7816 2.6308699
+ 4550 20966.335 190.68308 0 3685.0722 -18.587627
+ 4600 19428.962 446.59618 0 3684.7565 -4.4051672
+ 4650 18408.956 616.85009 0 3685.0095 2.777272
+ 4700 19215.779 482.57562 0 3685.2054 19.441016
+ 4750 20155.927 326.13401 0 3685.4553 6.1734993
+ 4800 20918.085 199.31832 0 3685.6659 3.4407437
+ 4850 20236.958 312.07276 0 3684.899 3.2612893
+ 4900 21419.89 115.36879 0 3685.3505 -4.675951
+ 4950 19707.901 401.14828 0 3685.7985 -10.730734
+ 5000 19407.201 450.64394 0 3685.1775 17.518981
+ 5050 21527.598 97.655186 0 3685.5882 -9.2294707
+ 5100 21581.933 88.595517 0 3685.5843 -20.669485
+ 5150 21161.214 158.48503 0 3685.3541 -2.7587502
+ 5200 21166.679 157.24762 0 3685.0275 -18.180044
+ 5250 20909.576 200.23507 0 3685.1644 -16.617303
+ 5300 21911.746 33.236563 0 3685.1942 -5.8313967
+ 5350 20857.303 208.87453 0 3685.0916 12.176312
+ 5400 20958.96 191.96694 0 3685.1269 3.6116429
+ 5450 20433.179 279.61178 0 3685.1415 13.324529
+ 5500 19604.675 416.88499 0 3684.3308 21.536484
+ 5550 18171.145 655.92915 0 3684.4534 -9.2269804
+ 5600 19799.907 385.12116 0 3685.1056 22.202165
+ 5650 19711.882 399.30581 0 3684.6194 15.93063
+ 5700 17908.833 699.52405 0 3684.3295 0.35530356
+ 5750 18606.518 583.538 0 3684.6243 -4.4540843
+ 5800 21814.053 48.974627 0 3684.6501 -1.5206358
+ 5850 18029.107 679.9357 0 3684.7868 12.137677
+ 5900 21090.739 169.64502 0 3684.7682 -1.5051545
+ 5950 21086.26 170.29075 0 3684.6674 -2.8164474
+ 6000 21285.771 136.95608 0 3684.5846 -26.582739
+ 6050 21203.994 150.87822 0 3684.8772 -2.6617226
+ 6100 21481.553 104.57796 0 3684.8368 -16.524974
+ 6150 20354.4 292.57675 0 3684.9767 2.7960207
+ 6200 21326.591 130.75243 0 3685.1843 -1.5929194
+ 6250 21505.087 101.07817 0 3685.2593 -3.7821931
+ 6300 21296.273 135.6593 0 3685.0382 -0.55635908
+ 6350 21295.389 135.86485 0 3685.0964 5.6614093
+ 6400 16552.242 926.02655 0 3684.7336 14.177218
+ 6450 20148.951 327.1151 0 3685.2736 7.4561085
+ 6500 20962.151 191.79415 0 3685.486 -4.5436711
+ 6550 21710.328 67.433972 0 3685.8219 -5.7678572
+ 6600 20698.571 234.79099 0 3684.5528 -2.1984068
+ 6650 17892.287 704.05484 0 3686.1026 11.525836
+ 6700 21272.999 141.26589 0 3686.7657 0.44088069
+ 6750 19558.993 426.46448 0 3686.2966 -16.907401
+ 6800 20350.247 295.23951 0 3686.9474 1.1284348
+ 6850 18665.05 573.5326 0 3684.3742 17.088712
+ 6900 19769.199 392.1551 0 3687.0216 6.7562425
+ 6950 19439.159 446.99138 0 3686.8512 -6.0105763
+ 7000 19379.907 456.53471 0 3686.5192 -9.0505095
+ 7050 19983.754 356.02523 0 3686.651 -5.6274314
+ 7100 19867.737 375.47627 0 3686.7658 17.315482
+ 7150 19258.794 477.47344 0 3687.2724 14.316676
+ 7200 21282.428 139.96051 0 3687.0318 -0.77043459
+ 7250 19828.603 381.98919 0 3686.7564 6.5142869
+ 7300 20574.582 257.8245 0 3686.9215 -3.6547118
+ 7350 21613.467 84.771568 0 3687.0161 -7.5188826
+ 7400 21817.009 50.844944 0 3687.0131 -14.888864
+ 7450 14937.538 1197.4257 0 3687.0154 1.7540499
+ 7500 18326.914 632.40374 0 3686.8894 8.3397357
+ 7550 13611.007 1418.4727 0 3686.9739 -19.379482
+ 7600 19173.985 491.9482 0 3687.6123 17.229001
+ 7650 16911.504 867.33649 0 3685.9204 -21.042834
+ 7700 21752.116 61.143705 0 3686.4963 -10.344487
+ 7750 20208.337 318.26355 0 3686.3197 13.385814
+ 7800 21649.909 77.950987 0 3686.2692 -1.7911084
+ 7850 20139.64 329.50319 0 3686.1098 -5.5805093
+ 7900 21355.026 126.7642 0 3685.9352 -7.7062172
+ 7950 21336.178 129.88925 0 3685.9188 -2.059298
+ 8000 21047.596 177.71546 0 3685.6482 0.37963466
+ 8050 19217.351 482.62331 0 3685.5152 6.5582595
+ 8100 20499.057 268.7173 0 3685.2268 -1.1959737
+ 8150 21494.301 102.83829 0 3685.2219 -1.6427647
+ 8200 20074.928 339.19817 0 3685.0195 6.285123
+ 8250 17335.157 793.47566 0 3682.6685 22.877381
+ 8300 17340.544 794.62619 0 3684.7168 3.9147755
+ 8350 20529.345 262.51162 0 3684.0691 4.031768
+ 8400 18884.747 537.47827 0 3684.9361 22.853404
+ 8450 20341.86 293.10484 0 3683.4148 0.33856656
+ 8500 19300.282 467.58127 0 3684.2949 12.35507
+ 8550 21631.936 78.254534 0 3683.5772 -10.992959
+ 8600 20204.913 316.83233 0 3684.3178 20.74228
+ 8650 21018.189 181.32054 0 3684.352 1.8412068
+ 8700 20161.304 323.97907 0 3684.1964 -2.646629
+ 8750 19081.79 504.00155 0 3684.2998 -10.088053
+ 8800 20834.489 211.76247 0 3684.1773 14.896336
+ 8850 20929.355 196.18335 0 3684.4092 -1.2602398
+ 8900 21491.074 102.47788 0 3684.3235 -1.4696758
+ 8950 20474.735 271.69461 0 3684.1504 -6.9489258
+ 9000 21128.641 162.40732 0 3683.8474 -7.7928168
+ 9050 18421.801 614.46442 0 3684.7646 24.40313
+ 9100 19301.292 466.98873 0 3683.8707 4.4687046
+ 9150 21575.705 88.213763 0 3684.1646 -0.94696984
+ 9200 20004.776 350.05448 0 3684.1838 -7.3466605
+ 9250 21384.079 120.14472 0 3684.1578 -8.3773844
+ 9300 21980.599 20.702393 0 3684.1356 -12.666293
+ 9350 21686.606 69.517984 0 3683.9524 -8.8366533
+ 9400 20732.704 228.46247 0 3683.9131 -6.4080307
+ 9450 19798.859 384.34696 0 3684.1568 7.6198484
+ 9500 20270.695 305.22664 0 3683.6758 1.5862486
+ 9550 16496.156 935.28481 0 3684.6441 15.001468
+ 9600 20642.429 241.08853 0 3681.4934 -9.2159382
+ 9650 21292.587 135.4474 0 3684.2119 -0.54770976
+ 9700 18888.158 536.60518 0 3684.6315 5.3236926
+ 9750 18750.018 559.35922 0 3684.3623 -9.9424949
+ 9800 20544.772 259.71076 0 3683.8394 8.732202
+ 9850 16698.125 901.90076 0 3684.9216 9.9553329
+ 9900 21450.963 109.58687 0 3684.7474 -4.8001999
+ 9950 20664.461 240.66995 0 3684.7468 -3.4840781
+ 10000 18951.367 526.45428 0 3685.0155 21.512727
+Loop time of 3.8586 on 4 procs for 10000 steps with 81 atoms
+
+Performance: 22391.551 tau/day, 2591.615 timesteps/s
+99.6% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.014034 | 0.040794 | 0.089783 | 14.9 | 1.06
+Neigh | 0.012468 | 0.027018 | 0.055093 | 10.5 | 0.70
+Comm | 0.13187 | 0.18206 | 0.2474 | 11.1 | 4.72
+Output | 0.0053496 | 0.0060334 | 0.0076718 | 1.2 | 0.16
+Modify | 3.5463 | 3.5828 | 3.6347 | 2.0 | 92.85
+Other | | 0.01995 | | | 0.52
+
+Nlocal: 20.25 ave 81 max 0 min
+Histogram: 3 0 0 0 0 0 0 0 0 1
+Nghost: 46.25 ave 95 max 14 min
+Histogram: 2 0 0 0 0 1 0 0 0 1
+Neighs: 249.25 ave 997 max 0 min
+Histogram: 3 0 0 0 0 0 0 0 0 1
+
+Total # of neighbors = 997
+Ave neighs/atom = 12.3086
+Neighbor list builds = 993
+Dangerous builds = 943
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:03
diff --git a/examples/rigid/log.15Feb16.rigid.poems2.g++.1 b/examples/rigid/log.15Feb16.rigid.poems2.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..033fb06999594395eee92fb291aa2449dd8baf10
--- /dev/null
+++ b/examples/rigid/log.15Feb16.rigid.poems2.g++.1
@@ -0,0 +1,336 @@
+LAMMPS (15 Feb 2016)
+# Simple rigid body system
+
+units lj
+atom_style atomic
+
+pair_style lj/cut 2.5
+
+read_data data.rigid
+ orthogonal box = (-12 -12 -12) to (12 12 12)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 81 atoms
+
+velocity all create 100.0 4928459
+
+# unconnected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 10 18
+#group clump3 id <> 19 27
+#group clump4 id <> 28 36
+#group clump5 id <> 37 45
+#group clump6 id <> 46 54
+#group clump7 id <> 55 63
+#group clump8 id <> 64 72
+#group clump9 id <> 73 81
+
+#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
+
+# 1 chain of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 36 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
+
+# 2 chains of connected bodies
+
+group clump1 id <> 1 9
+9 atoms in group clump1
+group clump2 id <> 9 18
+10 atoms in group clump2
+group clump3 id <> 18 27
+10 atoms in group clump3
+group clump4 id <> 27 36
+10 atoms in group clump4
+group clump5 id <> 37 45
+9 atoms in group clump5
+group clump6 id <> 45 54
+10 atoms in group clump6
+group clump7 id <> 54 63
+10 atoms in group clump7
+group clump8 id <> 63 72
+10 atoms in group clump8
+group clump9 id <> 72 81
+10 atoms in group clump9
+
+fix 1 all poems group clump1 clump2 clump3 clump4
+1 clusters, 4 bodies, 3 joints, 36 atoms
+fix 2 all poems group clump5 clump6 clump7 clump8 clump9
+1 clusters, 5 bodies, 4 joints, 45 atoms
+
+neigh_modify exclude group clump1 clump1
+neigh_modify exclude group clump2 clump2
+neigh_modify exclude group clump3 clump3
+neigh_modify exclude group clump4 clump4
+neigh_modify exclude group clump5 clump5
+neigh_modify exclude group clump6 clump6
+neigh_modify exclude group clump7 clump7
+neigh_modify exclude group clump8 clump8
+neigh_modify exclude group clump9 clump9
+
+thermo 100
+
+#dump 1 all atom 50 dump.rigid.poems2
+
+#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 5
+
+#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 5
+
+timestep 0.0001
+thermo 50
+run 10000
+WARNING: More than one fix poems (../fix_poems.cpp:352)
+WARNING: More than one fix poems (../fix_poems.cpp:352)
+WARNING: One or more atoms are time integrated more than once (../modify.cpp:266)
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4 -> bins = 18 18 18
+Memory usage per processor = 3.03278 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 196.00047 3632.2347 0 3668.5311 -2.7403788
+ 50 12167.633 1505.5478 0 3758.8133 35.125973
+ 100 17556.978 512.66277 0 3763.9549 11.137534
+ 150 19579.586 138.04942 0 3763.8987 -29.953971
+ 200 19757.51 105.30542 0 3764.1036 -0.030645317
+ 250 18218.374 390.10747 0 3763.8804 13.711001
+ 300 19383.039 174.40688 0 3763.8586 5.7240693
+ 350 20125.986 36.972611 0 3764.0071 1.9559205
+ 400 18888.816 266.10975 0 3764.0386 9.6362168
+ 450 19307.656 188.2511 0 3763.743 1.9326206
+ 500 16331.197 738.56392 0 3762.8597 9.1715579
+ 550 19318.722 186.16172 0 3763.7027 3.0115336
+ 600 19455.268 161.20621 0 3764.0336 0.55208034
+ 650 18487.011 340.03216 0 3763.5528 -8.0359122
+ 700 17321.201 556.32471 0 3763.9545 -13.631751
+ 750 18979.187 249.04389 0 3763.7082 -2.6072455
+ 800 19342.456 181.85552 0 3763.7918 8.1918726
+ 850 19070.641 232.19342 0 3763.7936 7.3148472
+ 900 19478.873 156.65987 0 3763.8586 2.4284987
+ 950 19912.415 76.437437 0 3763.9216 -1.4667227
+ 1000 16003.749 802.39753 0 3766.0548 46.642188
+ 1050 19859.583 86.64176 0 3764.3424 -2.1961943
+ 1100 19229.575 203.61488 0 3764.6473 -10.632365
+ 1150 18821.6 279.15861 0 3764.64 -0.89495035
+ 1200 19392.695 173.59744 0 3764.8373 1.8508753
+ 1250 16459.624 717.32104 0 3765.3995 33.478127
+ 1300 19343.863 182.59043 0 3764.7874 0.75890736
+ 1350 20019.643 57.503573 0 3764.8448 0.31444671
+ 1400 18549.582 329.31436 0 3764.4221 10.738303
+ 1450 15163.926 957.47585 0 3765.6103 -17.923459
+ 1500 19223.688 204.15175 0 3764.0939 -1.6134531
+ 1550 18147.996 404.12677 0 3764.8668 8.4194779
+ 1600 18615.043 317.42467 0 3764.6548 -2.3288934
+ 1650 20120.654 38.887913 0 3764.935 -8.7620277
+ 1700 19450.907 162.98272 0 3765.0025 2.3254731
+ 1750 19374.632 177.37966 0 3765.2744 8.9328774
+ 1800 19424.404 167.93966 0 3765.0514 0.081230261
+ 1850 17936.249 442.84231 0 3764.3699 6.6010636
+ 1900 19982.595 64.406198 0 3764.8868 -2.9529813
+ 1950 16215.852 761.91287 0 3764.8485 13.994708
+ 2000 18584.422 322.12049 0 3763.68 7.1654003
+ 2050 20107.965 41.025754 0 3764.723 -0.3109069
+ 2100 20002.333 60.593017 0 3764.7288 -6.7919784
+ 2150 16949.762 626.59623 0 3765.441 3.508941
+ 2200 20010.953 58.808279 0 3764.5403 -10.862172
+ 2250 18982.73 247.00892 0 3762.3292 -0.53807815
+ 2300 18401.298 354.87973 0 3762.5274 1.0920554
+ 2350 19390.524 172.9415 0 3763.7793 -3.3524932
+ 2400 16080.801 786.38838 0 3764.3146 -16.200514
+ 2450 18870.412 268.74976 0 3763.2705 11.197736
+ 2500 19688.29 117.58223 0 3763.5618 4.382644
+ 2550 18870.825 268.78678 0 3763.384 -5.6623656
+ 2600 17019.35 611.70808 0 3763.4395 6.3109641
+ 2650 18753.285 291.0596 0 3763.8902 2.4120296
+ 2700 19742.456 107.20901 0 3763.2193 -0.33061303
+ 2750 19522.438 148.16759 0 3763.4339 -1.6254851
+ 2800 18304.801 372.55152 0 3762.3295 22.6368
+ 2850 18465.36 343.48495 0 3762.9961 4.4169272
+ 2900 20151.999 31.372926 0 3763.2245 1.2013699
+ 2950 15498.143 892.80071 0 3762.8272 13.263724
+ 3000 18728.301 294.65113 0 3762.855 8.1897838
+ 3050 18538.466 330.25223 0 3763.3015 8.5865739
+ 3100 19081.409 229.5907 0 3763.1849 -4.8573813
+ 3150 18498.802 337.11548 0 3762.8195 1.0555321
+ 3200 19925.897 73.358029 0 3763.339 -7.7325108
+ 3250 19780.108 100.23785 0 3763.2209 -5.5974972
+ 3300 19221.043 203.82387 0 3763.2763 4.2703251
+ 3350 19025.292 240.11329 0 3763.3156 5.7708328
+ 3400 18153.696 401.52086 0 3763.3164 21.076943
+ 3450 18611.375 316.50396 0 3763.0548 -3.5484945
+ 3500 19931.319 71.969274 0 3762.9543 1.8764978
+ 3550 19747.562 106.05439 0 3763.0103 -2.5506186
+ 3600 18491.39 338.4134 0 3762.7449 -4.0527808
+ 3650 19757.998 104.19207 0 3763.0806 1.4865598
+ 3700 20108.003 39.345514 0 3763.0498 0.062827129
+ 3750 19222.505 203.28065 0 3763.0039 0.33719277
+ 3800 19286.383 191.08831 0 3762.6406 -0.1826802
+ 3850 19450.083 161.09138 0 3762.9587 -0.2708263
+ 3900 18002.304 429.25655 0 3763.0166 -4.6832439
+ 3950 17186.829 582.26502 0 3765.0111 55.816834
+ 4000 16826.434 645.84974 0 3761.856 19.675962
+ 4050 19227.526 202.18151 0 3762.8344 -0.2596098
+ 4100 19908.792 76.084531 0 3762.8978 -2.796813
+ 4150 17821.329 462.63065 0 3762.8768 13.069155
+ 4200 19917.133 74.574998 0 3762.9329 -6.4181155
+ 4250 19012.618 241.96787 0 3762.823 4.0847974
+ 4300 19077.34 229.98133 0 3762.8221 4.324323
+ 4350 19361.128 177.47406 0 3762.8681 -7.377974
+ 4400 18565.044 324.95107 0 3762.9223 2.5229032
+ 4450 19352.406 178.98756 0 3762.7665 0.10862717
+ 4500 18482.218 340.15496 0 3762.788 12.518301
+ 4550 18359.732 362.83749 0 3762.7879 3.7500902
+ 4600 19623.618 128.71624 0 3762.7196 -1.1328521
+ 4650 17565.707 509.99904 0 3762.9078 1.7135935
+ 4700 19876.052 81.892814 0 3762.6431 0.32476108
+ 4750 19022.676 239.92262 0 3762.6403 -0.24613022
+ 4800 18862.685 269.24248 0 3762.3324 6.2733979
+ 4850 19899.174 77.426145 0 3762.4584 0.42535238
+ 4900 18250.865 382.72867 0 3762.5185 23.308462
+ 4950 18895.847 263.22651 0 3762.4575 8.0634675
+ 5000 19096.705 225.69358 0 3762.1204 3.6816481
+ 5050 16546.294 698.91312 0 3763.0416 17.453618
+ 5100 19501.208 151.20999 0 3762.5449 -1.1231291
+ 5150 19479.879 155.00669 0 3762.3917 -3.983378
+ 5200 17397.818 541.23039 0 3763.0485 6.1109992
+ 5250 18564.869 324.10557 0 3762.0442 9.2244762
+ 5300 16271.663 747.52374 0 3760.7947 -6.5256602
+ 5350 19831.418 89.851887 0 3762.3367 -2.3453958
+ 5400 18723.697 294.67435 0 3762.0256 4.6822081
+ 5450 19547.28 142.21934 0 3762.086 -5.5243408
+ 5500 19415.447 166.68729 0 3762.1404 -9.5658991
+ 5550 18492.721 337.54773 0 3762.1256 6.5184903
+ 5600 19391.389 171.14375 0 3762.1416 -0.53835361
+ 5650 18503.465 334.62751 0 3761.1951 4.6580363
+ 5700 18153.344 399.91064 0 3761.6409 12.851587
+ 5750 18342.297 365.14769 0 3761.8694 2.7148176
+ 5800 19583.241 135.64969 0 3762.1758 -1.089608
+ 5850 15967.283 804.18382 0 3761.088 11.278762
+ 5900 19040.271 235.35509 0 3761.3312 5.1352158
+ 5950 17920.962 443.17951 0 3761.8762 4.9621366
+ 6000 19100.92 224.3946 0 3761.602 -9.537589
+ 6050 17982.119 432.3251 0 3762.3472 -2.851617
+ 6100 16233.096 755.46191 0 3761.5908 25.113316
+ 6150 18316.543 370.01118 0 3761.9635 -1.7445703
+ 6200 18483.464 339.13282 0 3761.9966 -2.0857447
+ 6250 18609.406 315.56032 0 3761.7467 -12.289208
+ 6300 17167.919 582.68212 0 3761.9264 -3.8263397
+ 6350 17870.329 452.58116 0 3761.9013 -3.3843134
+ 6400 19309.717 186.11786 0 3761.9913 -4.9462739
+ 6450 17964.073 435.39924 0 3762.0794 12.272972
+ 6500 18772.847 285.61959 0 3762.0727 6.7928648
+ 6550 18915.116 259.41365 0 3762.213 -4.1449761
+ 6600 19446.628 161.18763 0 3762.415 -2.1906581
+ 6650 16348.787 734.99282 0 3762.546 -9.9624546
+ 6700 19066.684 231.43863 0 3762.3061 -5.362833
+ 6750 14890.323 1004.547 0 3762.0143 37.373013
+ 6800 18235.19 385.253 0 3762.1401 0.21012662
+ 6850 16447.997 716.11276 0 3762.0382 -9.2095411
+ 6900 18343.362 364.81902 0 3761.7379 10.417932
+ 6950 16014.084 797.13348 0 3762.7046 6.7906777
+ 7000 19120.393 221.29236 0 3762.1059 -1.3461375
+ 7050 18055.409 418.30136 0 3761.8957 1.5772317
+ 7100 18407.231 353.41868 0 3762.1652 0.61071769
+ 7150 18728.136 293.64021 0 3761.8136 5.1649654
+ 7200 17706.628 483.07628 0 3762.0815 18.000708
+ 7250 19349.505 178.89673 0 3762.1385 2.540201
+ 7300 20016.293 55.389159 0 3762.1101 -1.5793163
+ 7350 19398.573 169.86661 0 3762.1949 -5.060123
+ 7400 19466.526 157.37407 0 3762.2862 1.7158273
+ 7450 18440.348 347.09196 0 3761.9712 12.781963
+ 7500 19989.907 60.555934 0 3762.3906 -1.5033319
+ 7550 19667.28 120.27403 0 3762.363 -3.3502366
+ 7600 18497.707 336.15863 0 3761.66 1.7887539
+ 7650 17901.957 447.17282 0 3762.3501 0.016725252
+ 7700 19758.725 103.3129 0 3762.3361 -23.534448
+ 7750 19443.957 161.6532 0 3762.386 -10.323924
+ 7800 19776.178 100.1773 0 3762.4324 6.0854422
+ 7850 19242.512 198.86705 0 3762.2952 5.2823659
+ 7900 19499.929 151.30366 0 3762.4017 12.299911
+ 7950 19630.317 127.19541 0 3762.4393 8.0799632
+ 8000 19872.384 82.421129 0 3762.4923 2.2126691
+ 8050 17747.038 476.27982 0 3762.7683 -7.7042786
+ 8100 18832.654 274.78106 0 3762.3095 13.882157
+ 8150 19949.814 68.09711 0 3762.5072 -0.54410896
+ 8200 17555.866 511.02517 0 3762.1115 6.2471175
+ 8250 17800.1 465.9992 0 3762.314 13.583485
+ 8300 19755.224 103.89732 0 3762.2721 -1.487243
+ 8350 17583.61 506.17539 0 3762.3995 -9.7819128
+ 8400 18529.003 330.75623 0 3762.0532 14.731228
+ 8450 20155.902 29.797078 0 3762.3716 -8.5711085
+ 8500 18047.548 420.54645 0 3762.685 7.3875118
+ 8550 19790.794 97.493375 0 3762.4553 -3.3427911
+ 8600 19997.902 59.172074 0 3762.4874 3.3479688
+ 8650 19987.319 61.148363 0 3762.5037 -1.889232
+ 8700 19363.91 176.41833 0 3762.3276 -9.4291288
+ 8750 18712.689 296.3979 0 3761.7107 5.9221369
+ 8800 19783.17 98.860518 0 3762.4105 -3.5262066
+ 8850 18796.049 281.60057 0 3762.3504 -8.2913002
+ 8900 16738.277 662.62261 0 3762.3035 8.5838631
+ 8950 17869.613 452.25006 0 3761.4377 11.561101
+ 9000 18682.512 302.27997 0 3762.0043 3.8878724
+ 9050 17513.759 518.50265 0 3761.7914 23.05778
+ 9100 17500.686 521.57944 0 3762.4473 -2.8435751
+ 9150 19645.683 124.43597 0 3762.5254 -3.0193092
+ 9200 18898.897 262.76552 0 3762.5612 3.5891701
+ 9250 20114.279 37.614866 0 3762.4813 -0.58120871
+ 9300 19562.613 139.54073 0 3762.2468 -3.2630158
+ 9350 19679.811 118.05865 0 3762.468 -3.4644363
+ 9400 19297.384 188.84527 0 3762.4349 0.40498037
+ 9450 18267.029 379.52581 0 3762.309 -0.13762867
+ 9500 19951.072 67.63844 0 3762.2814 -7.575539
+ 9550 19134.562 218.46835 0 3761.9057 -1.9626244
+ 9600 19089.093 227.29178 0 3762.3089 -1.94158
+ 9650 16964.603 620.71289 0 3762.3061 16.987042
+ 9700 18846.881 271.3129 0 3761.4761 3.4458802
+ 9750 19309.225 186.0142 0 3761.7966 9.4048627
+ 9800 16359.704 733.51007 0 3763.0849 15.870164
+ 9850 19958.532 66.203725 0 3762.2282 6.0043645
+ 9900 19864.564 83.502384 0 3762.1253 -0.65360617
+ 9950 18996.789 244.25101 0 3762.1749 -2.4961826
+ 10000 17933.494 441.33587 0 3762.3532 -6.0731708
+Loop time of 3.92046 on 1 procs for 10000 steps with 81 atoms
+
+Performance: 22038.237 tau/day, 2550.722 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.11453 | 0.11453 | 0.11453 | 0.0 | 2.92
+Neigh | 0.076222 | 0.076222 | 0.076222 | 0.0 | 1.94
+Comm | 0.011672 | 0.011672 | 0.011672 | 0.0 | 0.30
+Output | 0.0017154 | 0.0017154 | 0.0017154 | 0.0 | 0.04
+Modify | 3.7089 | 3.7089 | 3.7089 | 0.0 | 94.60
+Other | | 0.007422 | | | 0.19
+
+Nlocal: 81 ave 81 max 81 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 71 ave 71 max 71 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 612 ave 612 max 612 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 612
+Ave neighs/atom = 7.55556
+Neighbor list builds = 989
+Dangerous builds = 906
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:03
diff --git a/examples/rigid/log.15Feb16.rigid.poems2.g++.4 b/examples/rigid/log.15Feb16.rigid.poems2.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..694e7988e720fc191871f571d31cf93b3fbb7867
--- /dev/null
+++ b/examples/rigid/log.15Feb16.rigid.poems2.g++.4
@@ -0,0 +1,336 @@
+LAMMPS (15 Feb 2016)
+# Simple rigid body system
+
+units lj
+atom_style atomic
+
+pair_style lj/cut 2.5
+
+read_data data.rigid
+ orthogonal box = (-12 -12 -12) to (12 12 12)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 81 atoms
+
+velocity all create 100.0 4928459
+
+# unconnected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 10 18
+#group clump3 id <> 19 27
+#group clump4 id <> 28 36
+#group clump5 id <> 37 45
+#group clump6 id <> 46 54
+#group clump7 id <> 55 63
+#group clump8 id <> 64 72
+#group clump9 id <> 73 81
+
+#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
+
+# 1 chain of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 36 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
+
+# 2 chains of connected bodies
+
+group clump1 id <> 1 9
+9 atoms in group clump1
+group clump2 id <> 9 18
+10 atoms in group clump2
+group clump3 id <> 18 27
+10 atoms in group clump3
+group clump4 id <> 27 36
+10 atoms in group clump4
+group clump5 id <> 37 45
+9 atoms in group clump5
+group clump6 id <> 45 54
+10 atoms in group clump6
+group clump7 id <> 54 63
+10 atoms in group clump7
+group clump8 id <> 63 72
+10 atoms in group clump8
+group clump9 id <> 72 81
+10 atoms in group clump9
+
+fix 1 all poems group clump1 clump2 clump3 clump4
+1 clusters, 4 bodies, 3 joints, 36 atoms
+fix 2 all poems group clump5 clump6 clump7 clump8 clump9
+1 clusters, 5 bodies, 4 joints, 45 atoms
+
+neigh_modify exclude group clump1 clump1
+neigh_modify exclude group clump2 clump2
+neigh_modify exclude group clump3 clump3
+neigh_modify exclude group clump4 clump4
+neigh_modify exclude group clump5 clump5
+neigh_modify exclude group clump6 clump6
+neigh_modify exclude group clump7 clump7
+neigh_modify exclude group clump8 clump8
+neigh_modify exclude group clump9 clump9
+
+thermo 100
+
+#dump 1 all atom 50 dump.rigid.poems2
+
+#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 5
+
+#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 5
+
+timestep 0.0001
+thermo 50
+run 10000
+WARNING: More than one fix poems (../fix_poems.cpp:352)
+WARNING: More than one fix poems (../fix_poems.cpp:352)
+WARNING: One or more atoms are time integrated more than once (../modify.cpp:266)
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4 -> bins = 18 18 18
+Memory usage per processor = 3.0037 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 196.00047 3632.2347 0 3668.5311 -2.7403788
+ 50 12167.633 1505.5478 0 3758.8133 35.125973
+ 100 17556.978 512.66277 0 3763.9549 11.137534
+ 150 19579.586 138.04942 0 3763.8987 -29.953971
+ 200 19757.51 105.30542 0 3764.1036 -0.030645317
+ 250 18218.374 390.10747 0 3763.8804 13.711001
+ 300 19383.039 174.40688 0 3763.8586 5.7240693
+ 350 20125.986 36.972611 0 3764.0071 1.9559205
+ 400 18888.816 266.10975 0 3764.0386 9.6362168
+ 450 19307.656 188.2511 0 3763.743 1.9326206
+ 500 16331.197 738.56392 0 3762.8597 9.1715579
+ 550 19318.722 186.16172 0 3763.7027 3.0115336
+ 600 19455.268 161.20621 0 3764.0336 0.55208034
+ 650 18487.011 340.03216 0 3763.5528 -8.0359122
+ 700 17321.201 556.32471 0 3763.9545 -13.631751
+ 750 18979.187 249.04389 0 3763.7082 -2.6072455
+ 800 19342.456 181.85552 0 3763.7918 8.1918726
+ 850 19070.641 232.19342 0 3763.7936 7.3148472
+ 900 19478.873 156.65987 0 3763.8586 2.4284987
+ 950 19912.415 76.437437 0 3763.9216 -1.4667227
+ 1000 16003.749 802.39753 0 3766.0548 46.642188
+ 1050 19859.583 86.64176 0 3764.3424 -2.1961943
+ 1100 19229.575 203.61488 0 3764.6473 -10.632365
+ 1150 18821.6 279.15861 0 3764.64 -0.89495035
+ 1200 19392.695 173.59744 0 3764.8373 1.8508753
+ 1250 16459.624 717.32104 0 3765.3995 33.478127
+ 1300 19343.863 182.59043 0 3764.7874 0.75890736
+ 1350 20019.643 57.503573 0 3764.8448 0.31444671
+ 1400 18549.582 329.31436 0 3764.4221 10.738303
+ 1450 15163.926 957.47585 0 3765.6103 -17.923459
+ 1500 19223.688 204.15176 0 3764.0939 -1.6134529
+ 1550 18147.996 404.12677 0 3764.8668 8.4194781
+ 1600 18615.043 317.42468 0 3764.6548 -2.3288926
+ 1650 20120.654 38.887908 0 3764.935 -8.7620288
+ 1700 19450.907 162.98267 0 3765.0025 2.3254739
+ 1750 19374.631 177.3797 0 3765.2744 8.9328773
+ 1800 19424.404 167.93965 0 3765.0514 0.081228843
+ 1850 17936.227 442.84645 0 3764.3699 6.6011251
+ 1900 19982.595 64.406244 0 3764.8868 -2.952971
+ 1950 16215.818 761.91942 0 3764.8486 13.994877
+ 2000 18584.433 322.11846 0 3763.6801 7.1653695
+ 2050 20107.965 41.025796 0 3764.723 -0.31089763
+ 2100 20002.329 60.593879 0 3764.7288 -6.7919882
+ 2150 16949.817 626.58598 0 3765.4409 3.5087505
+ 2200 20010.954 58.8082 0 3764.5403 -10.862143
+ 2250 18982.732 247.00854 0 3762.3293 -0.53812607
+ 2300 18401.276 354.88369 0 3762.5274 1.0921058
+ 2350 19390.535 172.93951 0 3763.7793 -3.3524354
+ 2400 16080.475 786.44896 0 3764.3146 -16.201558
+ 2450 18870.293 268.77171 0 3763.2704 11.199749
+ 2500 19688.508 117.54164 0 3763.5617 4.3806994
+ 2550 18870.328 268.87896 0 3763.3841 -5.6641099
+ 2600 17020.211 611.54841 0 3763.4394 6.3081434
+ 2650 18748.838 291.88478 0 3763.8917 2.4175163
+ 2700 19743.991 106.92945 0 3763.224 -0.33916964
+ 2750 19525.446 147.60906 0 3763.4324 -1.6251174
+ 2800 18257.411 381.40184 0 3762.4038 23.39495
+ 2850 18496.796 337.65425 0 3762.9868 4.3657735
+ 2900 20163.418 29.253902 0 3763.2203 1.4431917
+ 2950 16823.317 646.69817 0 3762.1273 4.9041552
+ 3000 19223.007 203.2529 0 3763.069 4.0414458
+ 3050 17391.02 542.93746 0 3763.4968 15.139863
+ 3100 19205.6 206.57791 0 3763.1705 4.8519241
+ 3150 19835.659 90.247763 0 3763.5179 -14.900053
+ 3200 18962.776 251.5838 0 3763.2089 -13.706561
+ 3250 19418.837 167.29058 0 3763.3716 -2.0866468
+ 3300 18628.291 313.69067 0 3763.3742 5.9919715
+ 3350 17465.974 529.14439 0 3763.5841 14.122593
+ 3400 18488.661 339.6186 0 3763.4448 21.526798
+ 3450 19163.152 214.26098 0 3762.9928 4.1888096
+ 3500 18000.27 429.81789 0 3763.2011 5.4734485
+ 3550 19582.423 136.71887 0 3763.0935 -2.5335675
+ 3600 19634.325 127.2219 0 3763.208 -1.9728322
+ 3650 19428.114 165.40707 0 3763.2059 -2.3318779
+ 3700 19861.116 85.356944 0 3763.3414 -3.9097609
+ 3750 19337.239 182.43992 0 3763.4102 -3.3559651
+ 3800 19493.146 153.40349 0 3763.2453 -0.71089657
+ 3850 18607.616 317.74889 0 3763.6037 3.475832
+ 3900 19719.59 111.5553 0 3763.3313 0.58876668
+ 3950 19756.661 104.5522 0 3763.1931 3.7526698
+ 4000 17904.708 447.1673 0 3762.854 12.270654
+ 4050 19588.087 135.80435 0 3763.2279 0.94578945
+ 4100 19065.901 232.38235 0 3763.1048 -2.7495195
+ 4150 18775.075 286.2257 0 3763.0915 -3.7039858
+ 4200 18800.725 281.46601 0 3763.0817 0.15619543
+ 4250 19732.687 108.90618 0 3763.1075 3.0865861
+ 4300 18278.151 377.63653 0 3762.4794 1.5768601
+ 4350 17915.757 445.4804 0 3763.2133 -3.7040484
+ 4400 15987.794 802.41575 0 3763.1183 22.252078
+ 4450 19302.37 188.69495 0 3763.2079 0.91081327
+ 4500 20039.32 52.304099 0 3763.2893 -2.0828905
+ 4550 19535.953 145.4374 0 3763.2064 -3.3804255
+ 4600 19700.723 114.79823 0 3763.0803 -1.1761163
+ 4650 17804.641 465.85788 0 3763.0136 7.5947192
+ 4700 19913.881 75.240289 0 3762.996 -2.1100557
+ 4750 19982.484 62.535995 0 3762.996 -4.5821237
+ 4800 17400.76 540.21707 0 3762.58 -5.8418778
+ 4850 19199.88 206.90989 0 3762.4433 3.4536341
+ 4900 19173.92 212.11327 0 3762.8392 5.0387071
+ 4950 19236.635 200.57537 0 3762.9152 -1.4932783
+ 5000 19077.616 230.04967 0 3762.9415 4.3742655
+ 5050 19893.763 78.909747 0 3762.94 -1.5796711
+ 5100 18884.746 265.68301 0 3762.8583 2.2767949
+ 5150 17417.096 537.54036 0 3762.9286 -2.8632555
+ 5200 18247.844 383.60092 0 3762.8312 10.384179
+ 5250 19494.107 152.60532 0 3762.6251 -4.7617287
+ 5300 18739.781 292.46206 0 3762.7919 23.210048
+ 5350 19310.938 186.62363 0 3762.7232 14.895327
+ 5400 19540.39 144.14287 0 3762.7336 6.094624
+ 5450 20074.459 45.247888 0 3762.7403 -2.0871835
+ 5500 19986.377 61.668045 0 3762.849 -2.4551918
+ 5550 19038.904 237.07578 0 3762.7987 5.4250813
+ 5600 19439.124 163.1438 0 3762.9816 4.1291468
+ 5650 19480.321 155.58325 0 3763.0501 -3.5308058
+ 5700 19869.291 83.651379 0 3763.1497 -7.8661592
+ 5750 19991.447 61.068554 0 3763.1884 -6.8473586
+ 5800 19454.072 160.36805 0 3762.9739 1.527662
+ 5850 17994.409 430.95597 0 3763.2539 -5.6078082
+ 5900 19209.794 205.74997 0 3763.1193 8.4113055
+ 5950 19046.427 236.06321 0 3763.1793 10.463356
+ 6000 19409.899 168.95271 0 3763.3785 2.542067
+ 6050 18068.174 417.35443 0 3763.3125 10.498199
+ 6100 19549.253 143.21885 0 3763.4509 2.3075797
+ 6150 18464.719 344.0303 0 3763.4228 0.46469762
+ 6200 19811.205 94.62725 0 3763.3689 1.2382763
+ 6250 18715.36 297.26445 0 3763.0718 -3.4541762
+ 6300 17115.664 594.09913 0 3763.6666 4.2065564
+ 6350 18155.927 400.71764 0 3762.9264 1.1521258
+ 6400 19873.093 83.169067 0 3763.3716 0.16383592
+ 6450 19991.88 61.13218 0 3763.3321 -1.3008128
+ 6500 19434.416 164.40698 0 3763.3728 -13.593422
+ 6550 19855.253 86.645329 0 3763.544 -0.85704037
+ 6600 19251.141 198.41152 0 3763.4376 4.3027745
+ 6650 19741.815 107.69047 0 3763.582 4.994835
+ 6700 19633.466 127.69333 0 3763.5203 6.3677145
+ 6750 16231.353 757.83705 0 3763.6431 -1.5978692
+ 6800 18863.396 270.1114 0 3763.3329 -11.915909
+ 6850 19644.779 125.29421 0 3763.2163 -1.151217
+ 6900 18883.642 266.06889 0 3763.0397 -4.3950749
+ 6950 19042.364 236.54144 0 3762.9052 5.5718878
+ 7000 18351.868 364.38028 0 3762.8743 7.8958273
+ 7050 19981.031 62.840667 0 3763.0316 -5.8572298
+ 7100 19796.372 97.073665 0 3763.0685 -3.5178361
+ 7150 19805.385 95.235221 0 3762.899 -2.5481726
+ 7200 18722.055 295.86113 0 3762.9084 13.826356
+ 7250 19537.304 144.54234 0 3762.5616 1.2288666
+ 7300 18787.328 283.49504 0 3762.6299 9.0044469
+ 7350 18886.005 265.52121 0 3762.9295 6.6791881
+ 7400 19891.864 79.239278 0 3762.9178 -2.3882842
+ 7450 18164.752 399.07065 0 3762.9137 3.9400481
+ 7500 18702.612 299.582 0 3763.0286 4.7987316
+ 7550 19884.986 80.231665 0 3762.6365 -0.75016515
+ 7600 19549.059 142.16243 0 3762.3586 -2.1035756
+ 7650 18223.668 387.9047 0 3762.658 -17.064339
+ 7700 19428.4 164.79531 0 3762.6473 -2.8342541
+ 7750 19239.584 199.93029 0 3762.8163 3.1746033
+ 7800 19458.005 159.46176 0 3762.7961 1.714515
+ 7850 18320.308 369.77051 0 3762.4202 2.1422976
+ 7900 18817.415 278.04812 0 3762.7546 0.94492621
+ 7950 19892.761 79.115928 0 3762.9606 1.4948501
+ 8000 19592.344 134.7639 0 3762.9758 -1.8520224
+ 8050 19316.109 185.70579 0 3762.7631 -4.8061205
+ 8100 19867.017 83.850395 0 3762.9277 -3.496391
+ 8150 19129.936 220.29802 0 3762.8789 -2.8357376
+ 8200 18449.554 346.30415 0 3762.8883 1.4417837
+ 8250 18405.197 354.49049 0 3762.8602 6.7020283
+ 8300 18310.437 372.25376 0 3763.0755 3.9043508
+ 8350 18842.702 273.55075 0 3762.94 -10.987272
+ 8400 18574.308 323.33378 0 3763.0204 12.008785
+ 8450 15368.628 918.21692 0 3764.2591 34.80292
+ 8500 18432.887 349.54013 0 3763.0378 0.00064258465
+ 8550 15777.73 841.79263 0 3763.5945 15.473699
+ 8600 17205.381 576.4515 0 3762.6331 2.3985544
+ 8650 19773.742 101.48276 0 3763.2869 2.3978892
+ 8700 19059.824 232.99716 0 3762.5941 5.2611349
+ 8750 19006.086 243.41125 0 3763.0568 4.7880403
+ 8800 19492.691 153.0188 0 3762.7763 1.9118755
+ 8850 19625.883 128.44474 0 3762.8675 3.4157389
+ 8900 19916.97 74.635094 0 3762.9629 -10.157254
+ 8950 16012.956 798.16801 0 3763.5302 16.904998
+ 9000 19364.051 177.00354 0 3762.9389 -13.373346
+ 9050 19133.929 219.61882 0 3762.9389 -7.3824392
+ 9100 18657.168 307.85939 0 3762.8905 9.3071421
+ 9150 17975.904 434.21548 0 3763.0867 6.9609506
+ 9200 19075.282 230.41699 0 3762.8767 7.0961232
+ 9250 20115.276 37.578674 0 3762.6298 1.8678552
+ 9300 18195.486 393.20682 0 3762.7413 13.272552
+ 9350 19617.155 129.85893 0 3762.6653 -2.0849447
+ 9400 19276.325 193.03425 0 3762.724 -2.8963555
+ 9450 18642.803 310.4759 0 3762.8467 3.407984
+ 9500 19175.951 211.72785 0 3762.8298 -0.39025564
+ 9550 17669.191 490.85942 0 3762.9319 5.3867954
+ 9600 18481.199 340.29485 0 3762.7391 8.9004886
+ 9650 20091.442 42.504743 0 3763.1422 -1.3206133
+ 9700 19651.405 124.04835 0 3763.1975 1.4000525
+ 9750 19138.245 219.03637 0 3763.1558 5.8352794
+ 9800 19189.146 209.67958 0 3763.2251 6.214691
+ 9850 19899.376 78.096337 0 3763.166 -0.75102404
+ 9900 19447.247 161.27279 0 3762.6149 -6.4166376
+ 9950 19807.083 95.152663 0 3763.1309 -0.88933698
+ 10000 18972.157 249.56342 0 3762.9258 1.9189241
+Loop time of 4.00036 on 4 procs for 10000 steps with 81 atoms
+
+Performance: 21598.043 tau/day, 2499.774 timesteps/s
+99.7% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0092638 | 0.031034 | 0.052506 | 8.9 | 0.78
+Neigh | 0.0083086 | 0.021315 | 0.035568 | 6.7 | 0.53
+Comm | 0.10259 | 0.1356 | 0.16345 | 6.8 | 3.39
+Output | 0.0045969 | 0.0049881 | 0.0056102 | 0.5 | 0.12
+Modify | 3.7245 | 3.7919 | 3.8593 | 2.5 | 94.79
+Other | | 0.01554 | | | 0.39
+
+Nlocal: 20.25 ave 37 max 0 min
+Histogram: 1 0 1 0 0 0 0 0 0 2
+Nghost: 17.75 ave 33 max 4 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+Neighs: 144.75 ave 356 max 0 min
+Histogram: 2 0 0 0 0 0 1 0 0 1
+
+Total # of neighbors = 579
+Ave neighs/atom = 7.14815
+Neighbor list builds = 994
+Dangerous builds = 958
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:04
diff --git a/examples/rigid/log.15Feb16.rigid.tnr.g++.1 b/examples/rigid/log.15Feb16.rigid.tnr.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..4c2010c1df51eba37b959105a0f73a53a91f9309
--- /dev/null
+++ b/examples/rigid/log.15Feb16.rigid.tnr.g++.1
@@ -0,0 +1,452 @@
+LAMMPS (15 Feb 2016)
+# Tethered nanorods
+
+atom_style molecular
+
+read_data data.rigid.tnr
+ orthogonal box = (-31.122 -31.122 -31.122) to (31.122 31.122 31.122)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 5600 atoms
+ scanning bonds ...
+ 1 = max bonds/atom
+ reading bonds ...
+ 1600 bonds
+ 2 = max # of 1-2 neighbors
+ 1 = max # of 1-3 neighbors
+ 1 = max # of 1-4 neighbors
+ 2 = max # of special neighbors
+
+# Specify bond parameters
+
+bond_style fene
+bond_coeff 1 30.0 1.5 1.0 1.0
+
+special_bonds fene
+ 2 = max # of 1-2 neighbors
+ 2 = max # of special neighbors
+
+# Specify initial velocities
+
+velocity all create 1.4 109345
+
+# Specify rigid components
+
+group rods type 2
+4000 atoms in group rods
+group tethers subtract all rods
+1600 atoms in group tethers
+
+neigh_modify exclude molecule rods delay 0 every 1
+
+# Specify the pair potentials
+
+pair_style lj/cut 2.5
+pair_modify shift yes
+pair_coeff * * 1.0 1.0 1.122
+pair_coeff 2 2 1.0 1.0 2.5
+
+# Specify output
+
+thermo 100
+thermo_style custom step temp pe etotal press enthalpy lx ly lz pxx pyy pzz
+thermo_modify flush yes lost warn
+
+timestep 0.005
+
+fix 1 rods rigid molecule
+800 rigid bodies with 4000 atoms
+fix 2 tethers nve
+fix 3 all langevin 1.4 1.4 1.0 437624
+
+run 5000
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4 -> bins = 45 45 45
+Memory usage per processor = 6.99131 Mbytes
+Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
+ 0 1.3963219 5.9478449 7.0445809 0.048565317 9.13595 62.244 62.244 62.244 0.0091983659 0.11850113 0.017996458
+ 100 1.3418512 5.9671777 7.0211299 0.025020362 8.0985822 62.244 62.244 62.244 0.02036076 0.038265078 0.016435248
+ 200 1.3730638 5.9750802 7.0535483 0.0053287535 7.2830205 62.244 62.244 62.244 -0.00054924195 0.0092396988 0.0072958036
+ 300 1.376262 5.9821642 7.0631443 0.0055536521 7.3023013 62.244 62.244 62.244 0.0033577704 0.0069111861 0.0063919998
+ 400 1.3782954 5.9983628 7.08094 0.0020507385 7.169251 62.244 62.244 62.244 -0.0060862717 0.0098998072 0.0023386801
+ 500 1.386863 6.0053312 7.0946377 -0.0009847031 7.0522334 62.244 62.244 62.244 -0.0038708372 0.0005697804 0.00034694745
+ 600 1.4069849 6.0035719 7.1086832 0.0047883912 7.3148858 62.244 62.244 62.244 0.001069365 0.0078059505 0.0054898581
+ 700 1.4423187 5.9982171 7.1310812 0.012141001 7.6539093 62.244 62.244 62.244 0.0094765272 0.011007593 0.015938883
+ 800 1.4303878 5.9968168 7.1203098 -0.00081349095 7.0852784 62.244 62.244 62.244 0.0011153812 0.00041597298 -0.0039718271
+ 900 1.4140538 5.9838168 7.0944803 0.00207609 7.183883 62.244 62.244 62.244 0.00043409671 0.0022778944 0.0035162788
+ 1000 1.3906567 5.988119 7.0804053 0.0022005856 7.1751692 62.244 62.244 62.244 0.0077268425 -0.0022042977 0.0010792119
+ 1100 1.3921992 5.9892203 7.0827181 0.0035041977 7.2336194 62.244 62.244 62.244 -0.0037576823 0.0040827951 0.01018748
+ 1200 1.3968803 5.9795846 7.0767592 -0.0031072146 6.9429532 62.244 62.244 62.244 -0.0077387449 0.0033056124 -0.0048885115
+ 1300 1.3755848 5.9739757 7.0544239 0.0092247106 7.4516677 62.244 62.244 62.244 0.0092788748 0.010737194 0.0076580625
+ 1400 1.3847985 5.9703631 7.0580481 0.0071703598 7.3668254 62.244 62.244 62.244 0.0080485848 0.012260474 0.001202021
+ 1500 1.4190051 5.956946 7.0714985 0.0035992903 7.2264948 62.244 62.244 62.244 -0.0055125437 0.01038369 0.0059267242
+ 1600 1.3980036 5.9671666 7.0652236 0.0061819851 7.3314385 62.244 62.244 62.244 0.0062429141 0.0035120077 0.0087910334
+ 1700 1.4276062 5.9610381 7.0823462 0.007832375 7.4196319 62.244 62.244 62.244 0.0083316819 0.0058394292 0.009326014
+ 1800 1.4112769 5.9630595 7.0715419 0.0068032101 7.3645087 62.244 62.244 62.244 0.0065502252 0.0062317255 0.0076276797
+ 1900 1.4276973 5.9489341 7.0703139 0.008397746 7.4319462 62.244 62.244 62.244 0.0148941 0.0032963108 0.0070028268
+ 2000 1.4056158 5.9564624 7.0604983 0.0090470732 7.4500926 62.244 62.244 62.244 0.011871718 0.0086681344 0.0066013673
+ 2100 1.3924778 5.9483611 7.0420778 0.0088893819 7.4248814 62.244 62.244 62.244 0.010247454 0.0097830093 0.0066376825
+ 2200 1.3760401 5.9435877 7.0243935 -0.0042972782 6.8393397 62.244 62.244 62.244 -0.0050064436 -0.0046216999 -0.0032636911
+ 2300 1.4191937 5.9334036 7.0481042 0.0047000032 7.2505006 62.244 62.244 62.244 0.0057709635 0.0044949165 0.0038341296
+ 2400 1.4213285 5.9472214 7.0635988 0.010197674 7.5027414 62.244 62.244 62.244 0.008373826 0.0090537939 0.013165402
+ 2500 1.4153808 5.9421661 7.0538718 0.00015906306 7.0607216 62.244 62.244 62.244 0.002351621 -0.0019814986 0.00010706677
+ 2600 1.4014223 5.9431386 7.0438807 0.0070733749 7.3484816 62.244 62.244 62.244 0.0054143871 0.010055843 0.0057498948
+ 2700 1.4138077 5.9369067 7.047377 0.0024268842 7.1518859 62.244 62.244 62.244 0.0052918436 0.0014960353 0.00049277371
+ 2800 1.432192 5.9347676 7.0596777 0.0077670448 7.3941501 62.244 62.244 62.244 0.012668421 0.0059113033 0.0047214106
+ 2900 1.3938659 5.921023 7.01583 0.0053751198 7.2472989 62.244 62.244 62.244 0.0020490372 0.0076566093 0.006419713
+ 3000 1.390221 5.9205014 7.0124455 -0.0010750977 6.9661485 62.244 62.244 62.244 0.0019519817 -0.0041878885 -0.00098938611
+ 3100 1.4205722 5.9178284 7.0336117 0.0098735475 7.4587965 62.244 62.244 62.244 0.0040973361 0.012167268 0.013356039
+ 3200 1.398418 5.9150349 7.0134173 0.0061541841 7.2784351 62.244 62.244 62.244 0.0067621815 0.011952563 -0.00025219251
+ 3300 1.4269859 5.9148727 7.0356937 0.0060623879 7.2967584 62.244 62.244 62.244 0.012956234 -2.4806661e-05 0.0052557362
+ 3400 1.434286 5.9356705 7.0622253 0.00027315892 7.0739884 62.244 62.244 62.244 -0.00054959866 0.0052526278 -0.0038835524
+ 3500 1.4416809 5.9228153 7.0551783 0.0083382977 7.4142506 62.244 62.244 62.244 0.007399393 0.0030328007 0.014582699
+ 3600 1.4136063 5.9039442 7.0142562 0.0019712004 7.0991421 62.244 62.244 62.244 -0.00032316149 0.0035029874 0.0027337752
+ 3700 1.4333819 5.9120101 7.0378548 0.0071287182 7.3448389 62.244 62.244 62.244 0.0064768218 0.0046765361 0.010232797
+ 3800 1.3659481 5.9032873 6.9761663 -0.0054033416 6.7434821 62.244 62.244 62.244 -0.0073943479 -0.0082831992 -0.00053247772
+ 3900 1.3963222 5.9042998 7.0010361 0.0053310264 7.2306062 62.244 62.244 62.244 0.0081855739 0.0048806019 0.0029269034
+ 4000 1.4125482 5.9060665 7.0155474 0.0028450296 7.138063 62.244 62.244 62.244 0.0052588294 0.00072395285 0.0025523065
+ 4100 1.3943951 5.9040875 6.9993102 0.0058050223 7.2492919 62.244 62.244 62.244 0.0060579697 0.0024782584 0.0088788387
+ 4200 1.4249768 5.8906371 7.0098801 0.0030210669 7.1399763 62.244 62.244 62.244 0.006174431 -0.002079586 0.0049683557
+ 4300 1.3899801 5.8966397 6.9883947 0.0057285402 7.2350829 62.244 62.244 62.244 0.0049048136 0.0021882328 0.010092574
+ 4400 1.4414352 5.898628 7.0307981 0.0050932552 7.2501291 62.244 62.244 62.244 0.0057941393 0.0037951842 0.0056904421
+ 4500 1.4092913 5.8922803 6.9992031 0.0012238869 7.0519073 62.244 62.244 62.244 0.0042907674 0.0014412643 -0.0020603711
+ 4600 1.3779868 5.8928757 6.9752105 0.0020701322 7.0643566 62.244 62.244 62.244 0.0029283254 -0.0031683908 0.006450462
+ 4700 1.4084635 5.9098782 7.0161508 -0.00052129502 6.9937023 62.244 62.244 62.244 -0.0018460523 -0.0018286314 0.0021107986
+ 4800 1.4393258 5.9148464 7.0453597 0.015311954 7.7047386 62.244 62.244 62.244 0.014718813 0.01801777 0.013199278
+ 4900 1.4500008 5.9076899 7.0465879 0.0075111779 7.3700419 62.244 62.244 62.244 0.0091865271 0.0080981174 0.0052488891
+ 5000 1.4279632 5.9111567 7.0327453 -0.0014189553 6.9716408 62.244 62.244 62.244 -0.0046013754 0.0019937576 -0.001649248
+Loop time of 6.61347 on 1 procs for 5000 steps with 5600 atoms
+
+Performance: 326606.103 tau/day, 756.033 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.53158 | 0.53158 | 0.53158 | 0.0 | 8.04
+Bond | 0.24987 | 0.24987 | 0.24987 | 0.0 | 3.78
+Neigh | 1.8367 | 1.8367 | 1.8367 | 0.0 | 27.77
+Comm | 0.17261 | 0.17261 | 0.17261 | 0.0 | 2.61
+Output | 0.0035651 | 0.0035651 | 0.0035651 | 0.0 | 0.05
+Modify | 3.6673 | 3.6673 | 3.6673 | 0.0 | 55.45
+Other | | 0.1519 | | | 2.30
+
+Nlocal: 5600 ave 5600 max 5600 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1351 ave 1351 max 1351 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 5254 ave 5254 max 5254 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 5254
+Ave neighs/atom = 0.938214
+Ave special neighs/atom = 0.571429
+Neighbor list builds = 766
+Dangerous builds = 0
+
+# Replace fix rigid and fix langevin with new ones
+
+unfix 1
+unfix 3
+
+fix 3 tethers langevin 1.4 1.4 1.0 198450
+
+# Test different integrators for rods
+
+fix 1 rods rigid/nve molecule
+800 rigid bodies with 4000 atoms
+print "rigid/nve"
+rigid/nve
+run 1000
+Memory usage per processor = 6.99131 Mbytes
+Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
+ 5000 1.4279632 5.9111567 7.0327453 0.027874409 8.2331015 62.244 62.244 62.244 0.018992956 0.039655696 0.024974575
+ 5100 1.439608 5.9052128 7.0359478 0.0060989863 7.2985885 62.244 62.244 62.244 0.0087364157 0.004022839 0.0055377041
+ 5200 1.4120672 5.9102569 7.01936 0.0064301432 7.2962614 62.244 62.244 62.244 0.0082738077 0.0038925667 0.0071240551
+ 5300 1.4452434 5.8842166 7.0193778 0.008172419 7.3713068 62.244 62.244 62.244 0.0077715647 0.0068924406 0.0098532518
+ 5400 1.4170243 5.887522 7.0005186 0.0008656658 7.0377968 62.244 62.244 62.244 -9.1800583e-05 -0.0020237513 0.0047125493
+ 5500 1.4209082 5.8758921 6.9919394 0.0093634084 7.395156 62.244 62.244 62.244 0.0088769348 0.0087092521 0.010504038
+ 5600 1.4132978 5.8798939 6.9899636 0.0014877766 7.0540317 62.244 62.244 62.244 -0.0023427923 0.004559371 0.002246751
+ 5700 1.4065053 5.887541 6.9922756 0.0028083452 7.1132114 62.244 62.244 62.244 0.0025188632 0.000510969 0.0053952035
+ 5800 1.4079051 5.8940739 6.999908 0.0015946158 7.0685769 62.244 62.244 62.244 0.0037830287 0.00021751956 0.00078329927
+ 5900 1.4076047 5.8941577 6.9997558 0.005189853 7.2232465 62.244 62.244 62.244 -0.00093244616 0.0096403542 0.0068616509
+ 6000 1.4322772 5.8903539 7.0153309 0.00029752476 7.0281432 62.244 62.244 62.244 0.001913333 -0.00073790796 -0.00028285075
+Loop time of 1.34998 on 1 procs for 1000 steps with 5600 atoms
+
+Performance: 320004.261 tau/day, 740.751 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.14397 | 0.14397 | 0.14397 | 0.0 | 10.66
+Bond | 0.049438 | 0.049438 | 0.049438 | 0.0 | 3.66
+Neigh | 0.39013 | 0.39013 | 0.39013 | 0.0 | 28.90
+Comm | 0.033965 | 0.033965 | 0.033965 | 0.0 | 2.52
+Output | 0.00092816 | 0.00092816 | 0.00092816 | 0.0 | 0.07
+Modify | 0.70139 | 0.70139 | 0.70139 | 0.0 | 51.96
+Other | | 0.03017 | | | 2.23
+
+Nlocal: 5600 ave 5600 max 5600 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1347 ave 1347 max 1347 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 5399 ave 5399 max 5399 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 5399
+Ave neighs/atom = 0.964107
+Ave special neighs/atom = 0.571429
+Neighbor list builds = 153
+Dangerous builds = 0
+unfix 1
+
+fix 1 rods rigid/nvt molecule temp 1.4 1.4 1.0
+800 rigid bodies with 4000 atoms
+print "rigid/nvt"
+rigid/nvt
+run 1000
+Memory usage per processor = 6.99131 Mbytes
+Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
+ 6000 1.4322772 5.8903539 7.0153309 0.012980585 7.574314 62.244 62.244 62.244 0.058317363 0.0073619377 -0.026737547
+ 6100 1.4199699 5.8764035 6.9917138 0.0054065567 7.2245364 62.244 62.244 62.244 0.0092276454 0.0019623806 0.005029644
+ 6200 1.3976825 5.8924426 6.9902474 0.0004390082 7.0091524 62.244 62.244 62.244 -0.0023073118 -0.00049925474 0.0041235912
+ 6300 1.4077283 5.8847362 6.9904313 0.0066398301 7.2763625 62.244 62.244 62.244 0.0058018933 0.0091933882 0.0049242089
+ 6400 1.3749203 5.8817073 6.9616336 0.0074967166 7.2844648 62.244 62.244 62.244 0.012281889 0.0039781604 0.0062301007
+ 6500 1.3467096 5.8881263 6.9458946 -0.00011926206 6.9407588 62.244 62.244 62.244 0.0030721983 -0.0013265855 -0.002103399
+ 6600 1.3646558 5.8739857 6.9458497 0.0056064173 7.1872789 62.244 62.244 62.244 0.0059660118 0.0057680329 0.0050852071
+ 6700 1.392725 5.8836119 6.9775228 0.0025583772 7.0876942 62.244 62.244 62.244 0.0030974509 0.0018499704 0.0027277104
+ 6800 1.4017002 5.9015884 7.0025488 0.0039067256 7.1707842 62.244 62.244 62.244 0.0068315449 0.0020054024 0.0028832295
+ 6900 1.4136756 5.8914708 7.0018372 0.005175385 7.2247049 62.244 62.244 62.244 0.0028462217 0.009405517 0.0032744161
+ 7000 1.4286618 5.8935692 7.0157065 0.0062967875 7.2868652 62.244 62.244 62.244 0.0047257503 0.0093417536 0.0048228587
+Loop time of 1.36768 on 1 procs for 1000 steps with 5600 atoms
+
+Performance: 315862.242 tau/day, 731.163 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.14502 | 0.14502 | 0.14502 | 0.0 | 10.60
+Bond | 0.049546 | 0.049546 | 0.049546 | 0.0 | 3.62
+Neigh | 0.38711 | 0.38711 | 0.38711 | 0.0 | 28.30
+Comm | 0.033742 | 0.033742 | 0.033742 | 0.0 | 2.47
+Output | 0.00089908 | 0.00089908 | 0.00089908 | 0.0 | 0.07
+Modify | 0.72137 | 0.72137 | 0.72137 | 0.0 | 52.74
+Other | | 0.03 | | | 2.19
+
+Nlocal: 5600 ave 5600 max 5600 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1284 ave 1284 max 1284 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 5677 ave 5677 max 5677 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 5677
+Ave neighs/atom = 1.01375
+Ave special neighs/atom = 0.571429
+Neighbor list builds = 151
+Dangerous builds = 0
+unfix 1
+
+compute myTemp all temp
+
+fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 iso 0.05 0.05 1.0 dilate all
+800 rigid bodies with 4000 atoms
+print "rigid/npt iso"
+rigid/npt iso
+fix_modify 1 temp myTemp
+
+run 1000
+Memory usage per processor = 6.99131 Mbytes
+Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
+ 7000 1.4286618 5.8935692 7.0157065 0.032107544 8.3983542 62.244 62.244 62.244 0.0040119822 0.040455544 0.051855105
+ 7100 1.4709107 5.8870981 7.0424197 0.019698532 7.6954221 57.045709 57.045709 57.045709 0.012930036 0.020495433 0.025670125
+ 7200 1.5163014 5.8421234 7.0330969 0.018918793 7.4624535 50.277182 50.277182 50.277182 0.017832308 0.02668088 0.012243191
+ 7300 1.5675512 5.7752788 7.0065063 0.02287049 7.3825189 45.15491 45.15491 45.15491 0.019317818 0.024266569 0.025027083
+ 7400 1.5432894 5.7512252 6.9633963 0.024351591 7.2723284 41.416611 41.416611 41.416611 0.032039305 0.022247464 0.018768005
+ 7500 1.5510339 5.7073864 6.9256404 0.030706866 7.2413185 38.612893 38.612893 38.612893 0.04157713 0.012507079 0.038036388
+ 7600 1.5435609 5.6657445 6.8781288 0.03187398 7.1535577 36.440727 36.440727 36.440727 0.036502896 0.022097075 0.037021969
+ 7700 1.5862733 5.6141666 6.8600993 0.053474714 7.2612259 34.762178 34.762178 34.762178 0.035691782 0.06016314 0.064569222
+ 7800 1.5106894 5.6005849 6.7871505 0.028896219 6.982719 33.59041 33.59041 33.59041 0.031167851 0.013090267 0.042430539
+ 7900 1.472566 5.5634394 6.7200611 0.092340877 7.2955261 32.679168 32.679168 32.679168 0.060527481 0.10093222 0.11556293
+ 8000 1.4805391 5.5132684 6.6761526 0.040035619 6.9105042 32.003919 32.003919 32.003919 0.04381615 0.023706176 0.052584532
+Loop time of 3.01539 on 1 procs for 1000 steps with 5600 atoms
+
+Performance: 143265.281 tau/day, 331.633 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.37256 | 0.37256 | 0.37256 | 0.0 | 12.36
+Bond | 0.072008 | 0.072008 | 0.072008 | 0.0 | 2.39
+Neigh | 1.3608 | 1.3608 | 1.3608 | 0.0 | 45.13
+Comm | 0.073025 | 0.073025 | 0.073025 | 0.0 | 2.42
+Output | 0.00085115 | 0.00085115 | 0.00085115 | 0.0 | 0.03
+Modify | 1.099 | 1.099 | 1.099 | 0.0 | 36.45
+Other | | 0.03715 | | | 1.23
+
+Nlocal: 5600 ave 5600 max 5600 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 2963 ave 2963 max 2963 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 25797 ave 25797 max 25797 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 25797
+Ave neighs/atom = 4.60661
+Ave special neighs/atom = 0.571429
+Neighbor list builds = 334
+Dangerous builds = 0
+unfix 1
+
+fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 x 0.05 0.05 1.0 dilate all
+800 rigid bodies with 4000 atoms
+print "rigid/npt x"
+rigid/npt x
+run 1000
+Memory usage per processor = 6.99518 Mbytes
+Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
+ 8000 1.4805391 5.5132684 6.6761526 0.10591497 7.2961342 32.003919 32.003919 32.003919 -0.0085253101 0.12196602 0.20430422
+ 8100 1.4629588 5.5087415 6.6578173 0.080159269 7.1245058 31.831354 32.003919 32.003919 0.078046473 0.088201582 0.074229751
+ 8200 1.4061729 5.5008938 6.6053673 0.038080967 6.8240633 31.398913 32.003919 32.003919 0.041554276 0.038085252 0.034603372
+ 8300 1.4225542 5.4730766 6.5904167 0.071241779 6.992772 30.878537 32.003919 32.003919 0.068190354 0.076631686 0.068903297
+ 8400 1.4344356 5.4772885 6.6039608 0.044141975 6.8495696 30.421029 32.003919 32.003919 0.031058774 0.039890974 0.061476178
+ 8500 1.4377845 5.4485066 6.5778092 0.04242205 6.8099428 29.91769 32.003919 32.003919 0.053013546 0.050003453 0.02424915
+ 8600 1.4339418 5.4280263 6.5543108 0.0048261176 6.58031 29.453954 32.003919 32.003919 -0.0020411927 0.005967365 0.010552181
+ 8700 1.4284879 5.4273043 6.549305 0.058717611 6.8609844 29.021604 32.003919 32.003919 0.09927212 0.02309782 0.053782894
+ 8800 1.3993066 5.4243917 6.5234721 0.030638337 6.683965 28.639961 32.003919 32.003919 0.08972583 0.0089328704 -0.0067436909
+ 8900 1.4429241 5.3850352 6.5183748 0.0053167016 6.5458205 28.223699 32.003919 32.003919 0.052590681 -0.031563606 -0.0050769701
+ 9000 1.41963 5.3772308 6.4922741 0.040105311 6.6961497 27.793622 32.003919 32.003919 0.070575176 0.0044551641 0.045285594
+Loop time of 3.0303 on 1 procs for 1000 steps with 5600 atoms
+
+Performance: 142560.181 tau/day, 330.000 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.59848 | 0.59848 | 0.59848 | 0.0 | 19.75
+Bond | 0.075771 | 0.075771 | 0.075771 | 0.0 | 2.50
+Neigh | 1.0984 | 1.0984 | 1.0984 | 0.0 | 36.25
+Comm | 0.055339 | 0.055339 | 0.055339 | 0.0 | 1.83
+Output | 0.00087357 | 0.00087357 | 0.00087357 | 0.0 | 0.03
+Modify | 1.1671 | 1.1671 | 1.1671 | 0.0 | 38.51
+Other | | 0.03439 | | | 1.13
+
+Nlocal: 5600 ave 5600 max 5600 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 3244 ave 3244 max 3244 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 30929 ave 30929 max 30929 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 30929
+Ave neighs/atom = 5.52304
+Ave special neighs/atom = 0.571429
+Neighbor list builds = 165
+Dangerous builds = 0
+unfix 1
+
+fix 1 rods rigid/nph molecule iso 0.05 0.05 1.0 dilate all
+800 rigid bodies with 4000 atoms
+print "rigid/nph iso"
+rigid/nph iso
+run 1000
+Memory usage per processor = 6.99518 Mbytes
+Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
+ 9000 1.41963 5.3772308 6.4922741 0.054032922 6.7669508 27.793622 32.003919 32.003919 0.36183473 -0.1011685 -0.098567468
+ 9100 1.468276 5.3693533 6.5226054 0.062009135 6.8364521 27.753087 31.957243 31.957243 0.072952506 0.067965393 0.045109506
+ 9200 1.4790176 5.3498933 6.5115824 0.068306349 6.8531758 27.642255 31.829623 31.829623 0.057719204 0.083928825 0.063271019
+ 9300 1.4685339 5.3439444 6.4973991 0.012381058 6.5578428 27.421331 31.575232 31.575232 0.018937907 0.0065076203 0.011697646
+ 9400 1.4675871 5.3321417 6.4848528 0.056515448 6.7525582 27.146928 31.259261 31.259261 0.035834387 0.047161137 0.086550819
+ 9500 1.4464119 5.3137665 6.4498455 0.043906827 6.6517871 26.881604 30.953745 30.953745 0.031891513 0.065507153 0.034321816
+ 9600 1.4541889 5.284445 6.4266325 0.046471589 6.6332098 26.578003 30.604153 30.604153 0.0041035598 0.071274602 0.064036606
+ 9700 1.4577034 5.2493866 6.3943346 0.045073503 6.5909605 26.41175 30.412715 30.412715 0.018293408 0.069031147 0.047895953
+ 9800 1.4701089 5.2202499 6.3749417 0.055758411 6.6108197 26.142656 30.102857 30.102857 0.045171706 0.039488766 0.082614761
+ 9900 1.4518855 5.2148116 6.3551898 0.011510897 6.4028899 25.963345 29.896384 29.896384 0.0060934464 0.010841773 0.017597473
+ 10000 1.4445828 5.2098073 6.3444498 0.075197507 6.654918 25.931556 29.859779 29.859779 0.08350416 0.066240185 0.075848177
+Loop time of 3.1675 on 1 procs for 1000 steps with 5600 atoms
+
+Performance: 136384.997 tau/day, 315.706 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.68944 | 0.68944 | 0.68944 | 0.0 | 21.77
+Bond | 0.074669 | 0.074669 | 0.074669 | 0.0 | 2.36
+Neigh | 1.1761 | 1.1761 | 1.1761 | 0.0 | 37.13
+Comm | 0.058399 | 0.058399 | 0.058399 | 0.0 | 1.84
+Output | 0.0006671 | 0.0006671 | 0.0006671 | 0.0 | 0.02
+Modify | 1.1339 | 1.1339 | 1.1339 | 0.0 | 35.80
+Other | | 0.03435 | | | 1.08
+
+Nlocal: 5600 ave 5600 max 5600 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 3635 ave 3635 max 3635 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 38235 ave 38235 max 38235 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 38235
+Ave neighs/atom = 6.82768
+Ave special neighs/atom = 0.571429
+Neighbor list builds = 165
+Dangerous builds = 0
+unfix 1
+
+fix 1 rods rigid/nph molecule x 0.05 0.05 1.0 y 0.05 0.05 1.0 couple xy dilate all
+800 rigid bodies with 4000 atoms
+print "rigid/nph xy couple"
+rigid/nph xy couple
+run 1000
+Memory usage per processor = 6.999 Mbytes
+Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
+ 10000 1.4445828 5.2098073 6.3444498 0.001962567 6.3525526 25.931556 29.859779 29.859779 0.18484796 -0.22902272 0.050062455
+ 10100 1.4368894 5.2096239 6.3382235 0.10403552 6.7662753 25.886842 29.808292 29.859779 0.12565247 0.094955776 0.091498324
+ 10200 1.4231669 5.2080497 6.3258711 0.086173671 6.682435 25.959905 29.892423 29.859779 0.11480457 0.12471881 0.018997629
+ 10300 1.4334516 5.1992954 6.3251949 -0.0076414301 6.2932457 26.095439 30.048488 29.859779 0.00870511 -0.0049134764 -0.026715924
+ 10400 1.4408912 5.1980613 6.3298041 0.070774329 6.6314048 26.345108 30.335978 29.859779 0.061559356 0.075929557 0.074834076
+ 10500 1.4299517 5.1990298 6.3221802 0.077553868 6.6569567 26.515356 30.532016 29.859779 0.11568876 0.063812738 0.053160106
+ 10600 1.439113 5.1937953 6.3241415 0.024333431 6.4286629 26.449816 30.456548 29.859779 0.035925567 0.023132021 0.013942706
+ 10700 1.4379108 5.1704548 6.2998567 0.06126476 6.5597578 26.285754 30.267632 29.859779 0.074214186 0.040233796 0.069346299
+ 10800 1.4358912 5.1798018 6.3076174 0.10549358 6.747456 26.058856 30.006363 29.859779 0.1992503 0.046346044 0.070884395
+ 10900 1.4470038 5.1528383 6.2893823 0.045720444 6.4780533 25.92502 29.852253 29.859779 0.041394051 0.026837211 0.068930071
+ 11000 1.437397 5.1841678 6.3131661 0.070020768 6.6023557 25.935798 29.864664 29.859779 0.11790932 0.072745235 0.019407746
+Loop time of 3.24668 on 1 procs for 1000 steps with 5600 atoms
+
+Performance: 133059.040 tau/day, 308.007 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.75941 | 0.75941 | 0.75941 | 0.0 | 23.39
+Bond | 0.075467 | 0.075467 | 0.075467 | 0.0 | 2.32
+Neigh | 1.1751 | 1.1751 | 1.1751 | 0.0 | 36.19
+Comm | 0.059018 | 0.059018 | 0.059018 | 0.0 | 1.82
+Output | 0.00065112 | 0.00065112 | 0.00065112 | 0.0 | 0.02
+Modify | 1.1432 | 1.1432 | 1.1432 | 0.0 | 35.21
+Other | | 0.03387 | | | 1.04
+
+Nlocal: 5600 ave 5600 max 5600 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 3799 ave 3799 max 3799 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 39646 ave 39646 max 39646 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 39646
+Ave neighs/atom = 7.07964
+Ave special neighs/atom = 0.571429
+Neighbor list builds = 158
+Dangerous builds = 0
+
+Total wall time: 0:00:21
diff --git a/examples/rigid/log.15Feb16.rigid.tnr.g++.4 b/examples/rigid/log.15Feb16.rigid.tnr.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..001a065823b13dc851d608e7f3a87b4af6f75677
--- /dev/null
+++ b/examples/rigid/log.15Feb16.rigid.tnr.g++.4
@@ -0,0 +1,452 @@
+LAMMPS (15 Feb 2016)
+# Tethered nanorods
+
+atom_style molecular
+
+read_data data.rigid.tnr
+ orthogonal box = (-31.122 -31.122 -31.122) to (31.122 31.122 31.122)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 5600 atoms
+ scanning bonds ...
+ 1 = max bonds/atom
+ reading bonds ...
+ 1600 bonds
+ 2 = max # of 1-2 neighbors
+ 1 = max # of 1-3 neighbors
+ 1 = max # of 1-4 neighbors
+ 2 = max # of special neighbors
+
+# Specify bond parameters
+
+bond_style fene
+bond_coeff 1 30.0 1.5 1.0 1.0
+
+special_bonds fene
+ 2 = max # of 1-2 neighbors
+ 2 = max # of special neighbors
+
+# Specify initial velocities
+
+velocity all create 1.4 109345
+
+# Specify rigid components
+
+group rods type 2
+4000 atoms in group rods
+group tethers subtract all rods
+1600 atoms in group tethers
+
+neigh_modify exclude molecule rods delay 0 every 1
+
+# Specify the pair potentials
+
+pair_style lj/cut 2.5
+pair_modify shift yes
+pair_coeff * * 1.0 1.0 1.122
+pair_coeff 2 2 1.0 1.0 2.5
+
+# Specify output
+
+thermo 100
+thermo_style custom step temp pe etotal press enthalpy lx ly lz pxx pyy pzz
+thermo_modify flush yes lost warn
+
+timestep 0.005
+
+fix 1 rods rigid molecule
+800 rigid bodies with 4000 atoms
+fix 2 tethers nve
+fix 3 all langevin 1.4 1.4 1.0 437624
+
+run 5000
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4 -> bins = 45 45 45
+Memory usage per processor = 6.96454 Mbytes
+Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
+ 0 1.3963219 5.9478449 7.0445809 0.048565317 9.13595 62.244 62.244 62.244 0.0091983659 0.11850113 0.017996458
+ 100 1.3999025 5.9707695 7.0703179 0.027293074 8.24564 62.244 62.244 62.244 0.017246307 0.04732529 0.017307624
+ 200 1.4245544 5.9878446 7.1067558 0.0072016369 7.41688 62.244 62.244 62.244 0.0071370801 0.0084066589 0.0060611719
+ 300 1.4212057 5.9942604 7.1105414 0.0023296933 7.210865 62.244 62.244 62.244 -0.0059197015 0.0040269953 0.008881786
+ 400 1.4030116 5.9953214 7.0973119 0.0055751834 7.3373961 62.244 62.244 62.244 -0.0026920847 0.013323321 0.0060943141
+ 500 1.4201338 5.9984777 7.1139168 -0.0018229523 7.035415 62.244 62.244 62.244 -0.0082217102 -0.00047319975 0.0032260529
+ 600 1.425173 5.9902537 7.1096508 0.013367744 7.6853062 62.244 62.244 62.244 0.012971415 0.016298595 0.010833222
+ 700 1.4181225 5.9840752 7.0979345 0.0014999758 7.1625279 62.244 62.244 62.244 -0.0015835387 0.0045967753 0.0014866907
+ 800 1.4084205 5.9778462 7.084085 0.0063728488 7.3585191 62.244 62.244 62.244 0.0036202744 0.005593586 0.0099046859
+ 900 1.3958301 5.9891019 7.0854517 0.0028974454 7.2102244 62.244 62.244 62.244 0.0087724642 0.0014508428 -0.001530971
+ 1000 1.3937374 5.9794855 7.0741916 0.0087158481 7.4495223 62.244 62.244 62.244 0.014424783 0.0034958881 0.0082268735
+ 1100 1.3729162 5.9916252 7.0699773 0.0030451966 7.2011127 62.244 62.244 62.244 0.00084635444 -0.00064448421 0.0089337195
+ 1200 1.4427374 5.9713589 7.1045519 0.0042680608 7.2883474 62.244 62.244 62.244 0.0030884628 0.0031576538 0.0065580658
+ 1300 1.3971469 5.9728674 7.0702514 0.0022809251 7.168475 62.244 62.244 62.244 0.00060902513 -0.00020572386 0.006439474
+ 1400 1.4194118 5.9672631 7.082135 0.012945844 7.6396221 62.244 62.244 62.244 0.0082418827 0.016256336 0.014339314
+ 1500 1.3866472 5.9728382 7.0619753 0.0010642438 7.1078049 62.244 62.244 62.244 0.0020316123 0.0020439035 -0.00088278432
+ 1600 1.4184955 5.9539591 7.0681113 0.0077605409 7.4023036 62.244 62.244 62.244 0.0033721722 0.0057827512 0.014126699
+ 1700 1.3612202 5.9676733 7.0368389 0.00016862131 7.0441002 62.244 62.244 62.244 0.0052525345 0.0007705269 -0.0055171975
+ 1800 1.3641041 5.9521837 7.0236144 0.0057884587 7.2728829 62.244 62.244 62.244 0.0038061044 0.0044032908 0.009155981
+ 1900 1.3594477 5.9646024 7.0323757 0.0044261926 7.2229809 62.244 62.244 62.244 0.0019417448 0.006871542 0.004465291
+ 2000 1.3776971 5.9431816 7.0252888 -0.0012460593 6.9716298 62.244 62.244 62.244 -0.0010913822 0.00098119436 -0.0036279901
+ 2100 1.3986245 5.9509735 7.0495181 0.007520633 7.3733792 62.244 62.244 62.244 0.008359824 0.0075919773 0.0066100978
+ 2200 1.4033594 5.9548158 7.0570794 0.0016804284 7.1294438 62.244 62.244 62.244 -0.001842641 0.0032876741 0.0035962521
+ 2300 1.4048926 5.9444129 7.0478808 0.0062444034 7.3167836 62.244 62.244 62.244 0.004383569 0.0065720464 0.007777595
+ 2400 1.4044043 5.9370822 7.0401666 0.0034562836 7.1890046 62.244 62.244 62.244 0.0068959298 0.0041111713 -0.00063825026
+ 2500 1.4200762 5.9359254 7.0513193 0.0028319649 7.1732722 62.244 62.244 62.244 -0.00030414203 0.0039571831 0.0048428538
+ 2600 1.3876469 5.9249124 7.0148347 -0.0017777224 6.9382806 62.244 62.244 62.244 -0.00047616392 -0.0025484917 -0.0023085116
+ 2700 1.4099941 5.916763 7.0242378 0.0070716263 7.3287634 62.244 62.244 62.244 0.012628756 0.0053812867 0.0032048359
+ 2800 1.4444643 5.9283432 7.0628925 0.0019400024 7.1464349 62.244 62.244 62.244 0.0014895079 0.0046367397 -0.00030624055
+ 2900 1.3902832 5.9152516 7.0072446 -0.002166221 6.9139606 62.244 62.244 62.244 -0.0012374412 -0.00056403267 -0.004697189
+ 3000 1.3711706 5.922146 6.9991271 0.011101505 7.4771914 62.244 62.244 62.244 0.011063833 0.012093026 0.010147657
+ 3100 1.3569137 5.9171753 6.9829583 -0.002826677 6.8612331 62.244 62.244 62.244 -0.0069507252 0.0010084399 -0.0025377458
+ 3200 1.4004275 5.905939 7.0058998 0.005439467 7.2401397 62.244 62.244 62.244 0.010352184 0.0057594148 0.00020680265
+ 3300 1.3641217 5.9145275 6.985972 -0.0027212811 6.8687855 62.244 62.244 62.244 -0.00065933677 -0.0057713008 -0.0017332057
+ 3400 1.3868722 5.9059546 6.9952684 0.0092591256 7.3939943 62.244 62.244 62.244 0.010690877 0.010752519 0.006333981
+ 3500 1.3939169 5.8992292 6.9940762 0.0074340028 7.3142068 62.244 62.244 62.244 0.010137307 0.0044252569 0.0077394447
+ 3600 1.3982507 5.9219461 7.0201971 0.005679459 7.2647718 62.244 62.244 62.244 0.0023367243 0.008059221 0.0066424317
+ 3700 1.4019908 5.9059957 7.0071843 0.0065915477 7.2910363 62.244 62.244 62.244 0.0049554109 0.010827005 0.0039922268
+ 3800 1.3960736 5.902079 6.99862 0.0027763588 7.1181784 62.244 62.244 62.244 -0.0015907217 0.0025862003 0.0073335977
+ 3900 1.4352825 5.8986215 7.025959 0.003498268 7.176605 62.244 62.244 62.244 0.0030416681 0.0027739509 0.0046791851
+ 4000 1.4121845 5.907903 7.0170983 0.005046232 7.2344043 62.244 62.244 62.244 0.0045542682 0.0064113499 0.0041730779
+ 4100 1.3989578 5.9082397 7.0070461 0.00042880001 7.0255115 62.244 62.244 62.244 0.0025735184 0.0025181486 -0.003805267
+ 4200 1.3998829 5.8998147 6.9993477 0.0042777376 7.18356 62.244 62.244 62.244 0.0013744091 0.00646996 0.0049888436
+ 4300 1.4076022 5.9044509 7.010047 0.0066789366 7.2976622 62.244 62.244 62.244 0.0073610616 0.0048139129 0.0078618353
+ 4400 1.4161075 5.9064331 7.0187096 -0.0011844267 6.9677046 62.244 62.244 62.244 -0.0019088313 -0.0037556503 0.0021112015
+ 4500 1.4292243 5.8980093 7.0205884 0.0018500416 7.1002567 62.244 62.244 62.244 0.0041144085 0.0010160497 0.00041966655
+ 4600 1.3958775 5.8943133 6.9907003 0.0041485723 7.1693504 62.244 62.244 62.244 0.0033999287 0.0041620406 0.0048837475
+ 4700 1.3856614 5.8886847 6.9770475 0.0013150314 7.0336767 62.244 62.244 62.244 -0.00051753674 0.0030875481 0.0013750828
+ 4800 1.401683 5.9023505 7.0032974 0.002504877 7.1111649 62.244 62.244 62.244 0.0016543718 -0.0001813413 0.0060416007
+ 4900 1.446628 5.9050553 7.0413042 -0.0026645902 6.9265589 62.244 62.244 62.244 -0.00069368076 -0.0073984763 9.8386402e-05
+ 5000 1.4387091 5.9077604 7.0377893 0.0049468048 7.2508137 62.244 62.244 62.244 0.0042902506 0.0046715523 0.0058786114
+Loop time of 3.13958 on 4 procs for 5000 steps with 5600 atoms
+
+Performance: 687990.006 tau/day, 1592.569 timesteps/s
+99.1% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.079872 | 0.12791 | 0.18245 | 13.2 | 4.07
+Bond | 0.038984 | 0.058535 | 0.077727 | 7.4 | 1.86
+Neigh | 0.63649 | 0.63904 | 0.64148 | 0.2 | 20.35
+Comm | 0.15118 | 0.22089 | 0.28197 | 13.0 | 7.04
+Output | 0.0019264 | 0.0028899 | 0.0034878 | 1.1 | 0.09
+Modify | 1.8465 | 1.9323 | 2.0081 | 5.4 | 61.55
+Other | | 0.158 | | | 5.03
+
+Nlocal: 1400 ave 1868 max 905 min
+Histogram: 1 1 0 0 0 0 0 0 0 2
+Nghost: 648.25 ave 688 max 598 min
+Histogram: 1 0 0 1 0 0 0 0 1 1
+Neighs: 1202.5 ave 1821 max 698 min
+Histogram: 2 0 0 0 0 0 0 1 0 1
+
+Total # of neighbors = 4810
+Ave neighs/atom = 0.858929
+Ave special neighs/atom = 0.571429
+Neighbor list builds = 759
+Dangerous builds = 0
+
+# Replace fix rigid and fix langevin with new ones
+
+unfix 1
+unfix 3
+
+fix 3 tethers langevin 1.4 1.4 1.0 198450
+
+# Test different integrators for rods
+
+fix 1 rods rigid/nve molecule
+800 rigid bodies with 4000 atoms
+print "rigid/nve"
+rigid/nve
+run 1000
+Memory usage per processor = 6.98553 Mbytes
+Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
+ 5000 1.4387091 5.9077604 7.0377893 0.0035977871 7.1927209 62.244 62.244 62.244 0.025518192 -0.016769871 0.0020450407
+ 5100 1.4449405 5.8876257 7.022549 0.0023104502 7.122044 62.244 62.244 62.244 0.0045960664 0.0036845954 -0.0013493113
+ 5200 1.4271652 5.9160022 7.036964 0.0020238904 7.1241189 62.244 62.244 62.244 -0.0022546188 0.00392213 0.0044041599
+ 5300 1.4143299 5.9052666 7.016147 0.0064054214 7.2919838 62.244 62.244 62.244 0.0090997079 0.0026363579 0.0074801984
+ 5400 1.4426441 5.9087558 7.0418754 0.0020465683 7.1300068 62.244 62.244 62.244 0.0043188307 3.0314417e-06 0.0018178427
+ 5500 1.4281065 5.9038871 7.0255883 0.00058665945 7.0508516 62.244 62.244 62.244 0.005898925 0.00066013177 -0.0047990784
+ 5600 1.4315628 5.902373 7.0267888 0.0096475978 7.4422435 62.244 62.244 62.244 0.0054175405 0.011780025 0.011745228
+ 5700 1.4075482 5.9075587 7.0131124 0.0052150708 7.2376891 62.244 62.244 62.244 0.0030069124 0.0036690785 0.0089692215
+ 5800 1.4215681 5.9048555 7.0214211 0.0015070444 7.086319 62.244 62.244 62.244 -5.6858344e-05 0.0023644208 0.0022135708
+ 5900 1.3992461 5.8949367 6.9939696 0.0062425817 7.262794 62.244 62.244 62.244 0.0056972212 0.0095293238 0.0035012003
+ 6000 1.385289 5.8972105 6.9852808 0.0043255163 7.1715506 62.244 62.244 62.244 0.0040215567 0.0026330714 0.0063219208
+Loop time of 0.745001 on 4 procs for 1000 steps with 5600 atoms
+
+Performance: 579865.026 tau/day, 1342.280 timesteps/s
+99.6% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.020505 | 0.033631 | 0.048735 | 7.0 | 4.51
+Bond | 0.0078509 | 0.011774 | 0.015532 | 3.2 | 1.58
+Neigh | 0.13791 | 0.13834 | 0.13874 | 0.1 | 18.57
+Comm | 0.029133 | 0.04799 | 0.064085 | 7.4 | 6.44
+Output | 0.0004046 | 0.00066173 | 0.00084162 | 0.6 | 0.09
+Modify | 0.46937 | 0.48315 | 0.4976 | 1.9 | 64.85
+Other | | 0.02945 | | | 3.95
+
+Nlocal: 1400 ave 1868 max 935 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost: 633.75 ave 695 max 541 min
+Histogram: 1 0 0 0 1 0 0 0 0 2
+Neighs: 1263 ave 1799 max 710 min
+Histogram: 1 1 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 5052
+Ave neighs/atom = 0.902143
+Ave special neighs/atom = 0.571429
+Neighbor list builds = 153
+Dangerous builds = 0
+unfix 1
+
+fix 1 rods rigid/nvt molecule temp 1.4 1.4 1.0
+800 rigid bodies with 4000 atoms
+print "rigid/nvt"
+rigid/nvt
+run 1000
+Memory usage per processor = 6.98553 Mbytes
+Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
+ 6000 1.385289 5.8972105 6.9852808 0.0029190017 7.1109818 62.244 62.244 62.244 0.026575922 -0.075631452 0.057812535
+ 6100 1.3829575 5.9055308 6.9917699 0.0022904847 7.0904051 62.244 62.244 62.244 -0.00045870152 0.004055647 0.0032745086
+ 6200 1.3942692 5.90506 7.0001838 0.0046406767 7.2000253 62.244 62.244 62.244 0.0042263478 0.0051632788 0.0045324035
+ 6300 1.4009885 5.902399 7.0028005 0.0077682485 7.3373247 62.244 62.244 62.244 0.0071636925 0.0098268465 0.0063142066
+ 6400 1.3627532 5.9075587 6.9779284 0.0093180812 7.3791931 62.244 62.244 62.244 0.0062401482 0.013022619 0.0086914761
+ 6500 1.3341203 5.9012967 6.9491767 0.010108056 7.3844601 62.244 62.244 62.244 0.0031876333 0.011099549 0.016036984
+ 6600 1.3572847 5.8915298 6.9576041 -0.00034416741 6.9427833 62.244 62.244 62.244 0.0025578983 -0.0011308804 -0.0024595201
+ 6700 1.3663741 5.8985276 6.9717412 0.002947281 7.09866 62.244 62.244 62.244 0.0022469396 -0.00042872124 0.0070236245
+ 6800 1.3816731 5.8909305 6.9761607 -9.1110394e-05 6.9722372 62.244 62.244 62.244 -0.0048195881 -0.00080983527 0.0053560922
+ 6900 1.4011479 5.8881921 6.9887187 0.0010084642 7.0321462 62.244 62.244 62.244 0.0012132523 -0.0025918018 0.0044039422
+ 7000 1.3973667 5.8867951 6.9843517 0.0070023833 7.2858955 62.244 62.244 62.244 0.0058928565 0.0076813429 0.0074329504
+Loop time of 0.760565 on 4 procs for 1000 steps with 5600 atoms
+
+Performance: 567998.937 tau/day, 1314.812 timesteps/s
+99.5% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.021564 | 0.034813 | 0.049583 | 6.9 | 4.58
+Bond | 0.0080154 | 0.011744 | 0.015375 | 3.2 | 1.54
+Neigh | 0.13546 | 0.13583 | 0.13616 | 0.1 | 17.86
+Comm | 0.029489 | 0.047668 | 0.06437 | 7.4 | 6.27
+Output | 0.00040579 | 0.00063974 | 0.00079918 | 0.6 | 0.08
+Modify | 0.48726 | 0.50088 | 0.51473 | 1.7 | 65.86
+Other | | 0.02899 | | | 3.81
+
+Nlocal: 1400 ave 1832 max 970 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost: 652.5 ave 749 max 561 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+Neighs: 1407.5 ave 2071 max 748 min
+Histogram: 1 1 0 0 0 0 0 0 1 1
+
+Total # of neighbors = 5630
+Ave neighs/atom = 1.00536
+Ave special neighs/atom = 0.571429
+Neighbor list builds = 149
+Dangerous builds = 0
+unfix 1
+
+compute myTemp all temp
+
+fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 iso 0.05 0.05 1.0 dilate all
+800 rigid bodies with 4000 atoms
+print "rigid/npt iso"
+rigid/npt iso
+fix_modify 1 temp myTemp
+
+run 1000
+Memory usage per processor = 6.98553 Mbytes
+Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
+ 7000 1.3973667 5.8867951 6.9843517 0.0026559416 7.0987246 62.244 62.244 62.244 0.033713637 -0.0068647989 -0.018881013
+ 7100 1.4639139 5.8611823 7.0110083 0.011521251 7.3924625 57.022152 57.022152 57.022152 0.010787531 0.0093708984 0.014405322
+ 7200 1.4950463 5.8177011 6.9919798 0.023101297 7.5163969 50.281647 50.281647 50.281647 0.023242216 0.018105116 0.02795656
+ 7300 1.5103331 5.7757714 6.9620571 0.022650056 7.3366292 45.243 45.243 45.243 0.023573421 0.022300241 0.022076507
+ 7400 1.5582095 5.7578511 6.9817412 0.028508467 7.3477691 41.582392 41.582392 41.582392 0.02740467 0.030003113 0.028117619
+ 7500 1.5992723 5.6927269 6.9488696 0.046538335 7.4419099 39.001967 39.001967 39.001967 0.057728057 0.030859627 0.05102732
+ 7600 1.5572154 5.6717168 6.894826 0.032055597 7.184009 36.967405 36.967405 36.967405 0.034785798 0.033408508 0.027972486
+ 7700 1.541013 5.6302838 6.840667 0.046629681 7.2052858 35.246953 35.246953 35.246953 0.051145184 0.022437926 0.066305932
+ 7800 1.4922447 5.6135845 6.7856627 0.066398531 7.2467615 33.879827 33.879827 33.879827 0.05766722 0.07643975 0.065088623
+ 7900 1.5126099 5.5498409 6.7379149 0.060758513 7.1190044 32.749346 32.749346 32.749346 0.045401188 0.069519167 0.067355184
+ 8000 1.498932 5.5307653 6.708096 0.0068958389 6.7481394 31.918601 31.918601 31.918601 0.004934357 -0.0067897493 0.022542909
+Loop time of 1.41333 on 4 procs for 1000 steps with 5600 atoms
+
+Performance: 305661.545 tau/day, 707.550 timesteps/s
+99.2% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.057705 | 0.096282 | 0.13813 | 11.4 | 6.81
+Bond | 0.012531 | 0.01785 | 0.023392 | 3.7 | 1.26
+Neigh | 0.50189 | 0.5024 | 0.50294 | 0.1 | 35.55
+Comm | 0.058384 | 0.10518 | 0.14841 | 12.2 | 7.44
+Output | 0.00038195 | 0.00049835 | 0.0007689 | 0.7 | 0.04
+Modify | 0.62292 | 0.64876 | 0.67248 | 2.8 | 45.90
+Other | | 0.04236 | | | 3.00
+
+Nlocal: 1400 ave 1820 max 1010 min
+Histogram: 1 1 0 0 0 0 0 0 1 1
+Nghost: 1576 ave 1694 max 1470 min
+Histogram: 1 1 0 0 0 0 0 1 0 1
+Neighs: 6543 ave 9989 max 3497 min
+Histogram: 1 1 0 0 0 0 0 1 0 1
+
+Total # of neighbors = 26172
+Ave neighs/atom = 4.67357
+Ave special neighs/atom = 0.571429
+Neighbor list builds = 337
+Dangerous builds = 0
+unfix 1
+
+fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 x 0.05 0.05 1.0 dilate all
+800 rigid bodies with 4000 atoms
+print "rigid/npt x"
+rigid/npt x
+run 1000
+Memory usage per processor = 7.00192 Mbytes
+Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
+ 8000 1.498932 5.5307653 6.708096 0.044418732 6.9660307 31.918601 31.918601 31.918601 0.033240642 0.090981355 0.0090341992
+ 8100 1.4932748 5.5104122 6.6832996 0.078824127 7.1379335 31.703188 31.918601 31.918601 0.046668046 0.090499077 0.099305258
+ 8200 1.4783774 5.4958482 6.6570345 0.024180825 6.7956092 31.500184 31.918601 31.918601 -0.01991799 0.022036912 0.070423554
+ 8300 1.4699766 5.468569 6.6231569 0.050331767 6.9062762 30.919162 31.918601 31.918601 0.030889484 0.091318073 0.028787743
+ 8400 1.4423945 5.4591749 6.5920985 0.034769472 6.7835475 30.266023 31.918601 31.918601 0.031838545 0.067297532 0.0051723374
+ 8500 1.4478469 5.4405027 6.5777089 0.061608005 6.9111775 29.752136 31.918601 31.918601 0.056987338 0.064105062 0.063731616
+ 8600 1.4216004 5.443144 6.5597349 0.031739807 6.7291722 29.343028 31.918601 31.918601 0.047008356 0.040197385 0.0080136813
+ 8700 1.3993468 5.4199487 6.5190607 0.055753353 6.8130189 28.981104 31.918601 31.918601 0.038071725 0.050746074 0.078442261
+ 8800 1.4272224 5.3956531 6.5166598 0.051937078 6.7855855 28.46133 31.918601 31.918601 0.038718856 0.054121272 0.062971108
+ 8900 1.430201 5.3881483 6.5114945 0.042705385 6.728515 27.933053 31.918601 31.918601 0.053090216 0.033892798 0.04113314
+ 9000 1.4147254 5.3571794 6.4683705 0.015474623 6.5454193 27.368213 31.918601 31.918601 0.018517547 0.023668345 0.0042379783
+Loop time of 1.40527 on 4 procs for 1000 steps with 5600 atoms
+
+Performance: 307413.312 tau/day, 711.605 timesteps/s
+99.1% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.09198 | 0.15293 | 0.22726 | 14.1 | 10.88
+Bond | 0.01415 | 0.01816 | 0.022801 | 2.8 | 1.29
+Neigh | 0.40174 | 0.40202 | 0.40228 | 0.0 | 28.61
+Comm | 0.053445 | 0.13222 | 0.19624 | 16.1 | 9.41
+Output | 0.00037909 | 0.00046462 | 0.00065279 | 0.5 | 0.03
+Modify | 0.6409 | 0.65867 | 0.6806 | 2.2 | 46.87
+Other | | 0.04081 | | | 2.90
+
+Nlocal: 1400 ave 1770 max 1095 min
+Histogram: 1 1 0 0 0 0 1 0 0 1
+Nghost: 1578.5 ave 1693 max 1493 min
+Histogram: 2 0 0 0 0 0 0 1 0 1
+Neighs: 7868 ave 12041 max 4579 min
+Histogram: 1 1 0 0 0 0 1 0 0 1
+
+Total # of neighbors = 31472
+Ave neighs/atom = 5.62
+Ave special neighs/atom = 0.571429
+Neighbor list builds = 167
+Dangerous builds = 0
+unfix 1
+
+fix 1 rods rigid/nph molecule iso 0.05 0.05 1.0 dilate all
+800 rigid bodies with 4000 atoms
+print "rigid/nph iso"
+rigid/nph iso
+run 1000
+Memory usage per processor = 7.00192 Mbytes
+Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
+ 9000 1.4147254 5.3571794 6.4683705 0.026540417 6.6005164 27.368213 31.918601 31.918601 -0.25291277 0.19881452 0.1337195
+ 9100 1.4143578 5.3349724 6.4458747 0.032533861 6.6070914 27.324726 31.867884 31.867884 0.031965858 0.023737907 0.041897818
+ 9200 1.4489265 5.3126352 6.4506893 0.020125553 6.5486389 27.161226 31.6772 31.6772 0.024138053 0.045983015 -0.0097444101
+ 9300 1.4434983 5.3100314 6.4438219 0.071722015 6.7864703 26.993744 31.481872 31.481872 0.081599435 0.059208723 0.074357889
+ 9400 1.4179009 5.3170886 6.4307738 0.020348306 6.5262516 26.832169 31.293432 31.293432 0.070733237 -0.0042808269 -0.0054074919
+ 9500 1.455947 5.2941589 6.4377273 0.0066330065 6.4680826 26.60963 31.033892 31.033892 -0.026145193 -0.017478757 0.06352297
+ 9600 1.4322198 5.2747171 6.399649 0.079157317 6.755508 26.452091 30.85016 30.85016 0.09770091 0.095143096 0.044627945
+ 9700 1.4366074 5.2650795 6.3934576 0.052444405 6.6264505 26.347873 30.728614 30.728614 0.043301655 0.043720535 0.070311026
+ 9800 1.4311568 5.268838 6.392935 0.056161789 6.637248 26.163729 30.513853 30.513853 0.071096045 0.048086199 0.049303122
+ 9900 1.4437347 5.2369801 6.3709564 0.11335968 6.8497267 25.907207 30.214681 30.214681 0.1259046 0.10149135 0.11268308
+ 10000 1.4627878 5.2272205 6.376162 0.082077049 6.7164073 25.746677 30.02746 30.02746 0.060839015 0.13885619 0.046535946
+Loop time of 1.41589 on 4 procs for 1000 steps with 5600 atoms
+
+Performance: 305107.630 tau/day, 706.268 timesteps/s
+99.1% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.11437 | 0.17662 | 0.24699 | 12.6 | 12.47
+Bond | 0.014617 | 0.018159 | 0.022451 | 2.4 | 1.28
+Neigh | 0.40766 | 0.40784 | 0.40799 | 0.0 | 28.80
+Comm | 0.054544 | 0.12898 | 0.19363 | 15.6 | 9.11
+Output | 0.00037289 | 0.00046611 | 0.00066733 | 0.6 | 0.03
+Modify | 0.62801 | 0.64468 | 0.6664 | 2.1 | 45.53
+Other | | 0.03915 | | | 2.76
+
+Nlocal: 1400 ave 1669 max 1139 min
+Histogram: 1 0 1 0 0 0 0 1 0 1
+Nghost: 1761.5 ave 1898 max 1632 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+Neighs: 9311.75 ave 12525 max 5959 min
+Histogram: 1 0 1 0 0 0 0 1 0 1
+
+Total # of neighbors = 37247
+Ave neighs/atom = 6.65125
+Ave special neighs/atom = 0.571429
+Neighbor list builds = 165
+Dangerous builds = 0
+unfix 1
+
+fix 1 rods rigid/nph molecule x 0.05 0.05 1.0 y 0.05 0.05 1.0 couple xy dilate all
+800 rigid bodies with 4000 atoms
+print "rigid/nph xy couple"
+rigid/nph xy couple
+run 1000
+Memory usage per processor = 7.00192 Mbytes
+Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
+ 10000 1.4627878 5.2272205 6.376162 0.087181735 6.7375684 25.746677 30.02746 30.02746 0.01077504 0.047196696 0.20357347
+ 10100 1.461932 5.2277217 6.3759909 0.045218386 6.5623932 25.674625 29.943429 30.02746 0.029664553 0.034940919 0.071049687
+ 10200 1.4394425 5.2183968 6.3490017 0.064139003 6.6129181 25.651225 29.916138 30.02746 0.063541799 0.099454655 0.029420554
+ 10300 1.445679 5.2124787 6.3479821 0.073611235 6.6513251 25.670301 29.938385 30.02746 0.09678342 0.1092442 0.01480609
+ 10400 1.4289478 5.2082727 6.3306346 -0.00091064043 6.3268902 25.642317 29.905748 30.02746 -0.021792005 0.043173882 -0.024113799
+ 10500 1.4138512 5.191318 6.3018224 0.051274311 6.5114152 25.566672 29.817526 30.02746 0.087657762 0.022098862 0.04406631
+ 10600 1.4101298 5.2048433 6.3124247 0.032021085 6.442127 25.450236 29.681731 30.02746 0.032483644 0.022737859 0.040841754
+ 10700 1.4527253 5.1827275 6.3237654 0.045295082 6.5054661 25.327296 29.53835 30.02746 0.082847312 0.0364514 0.016586533
+ 10800 1.4661732 5.1586918 6.3102923 0.084525247 6.6478976 25.272455 29.474391 30.02746 0.10699807 0.070825674 0.075751992
+ 10900 1.4301511 5.1743273 6.2976344 0.014007746 6.3539547 25.356203 29.572064 30.02746 -0.015258276 -0.0047253148 0.06200683
+ 11000 1.4346828 5.1625047 6.2893712 0.034027405 6.4273459 25.463687 29.697419 30.02746 0.041309225 0.014001823 0.046771165
+Loop time of 1.39005 on 4 procs for 1000 steps with 5600 atoms
+
+Performance: 310781.162 tau/day, 719.401 timesteps/s
+99.4% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.14204 | 0.19795 | 0.25554 | 10.2 | 14.24
+Bond | 0.015064 | 0.018318 | 0.021846 | 2.0 | 1.32
+Neigh | 0.37625 | 0.37681 | 0.37726 | 0.1 | 27.11
+Comm | 0.058424 | 0.11817 | 0.17563 | 13.6 | 8.50
+Output | 0.00036097 | 0.00047255 | 0.00073051 | 0.7 | 0.03
+Modify | 0.63824 | 0.64799 | 0.66001 | 1.1 | 46.62
+Other | | 0.03034 | | | 2.18
+
+Nlocal: 1400 ave 1607 max 1199 min
+Histogram: 1 0 1 0 0 0 0 1 0 1
+Nghost: 1819.25 ave 1940 max 1712 min
+Histogram: 1 1 0 0 0 0 0 1 0 1
+Neighs: 9882 ave 12628 max 7201 min
+Histogram: 1 0 1 0 0 0 0 1 0 1
+
+Total # of neighbors = 39528
+Ave neighs/atom = 7.05857
+Ave special neighs/atom = 0.571429
+Neighbor list builds = 156
+Dangerous builds = 0
+
+Total wall time: 0:00:10
diff --git a/examples/shear/log.15Feb16.shear.g++.1 b/examples/shear/log.15Feb16.shear.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..4643b05bdd8faea435f100a426ab72d0551dad73
--- /dev/null
+++ b/examples/shear/log.15Feb16.shear.g++.1
@@ -0,0 +1,191 @@
+LAMMPS (15 Feb 2016)
+# 3d metal shear simulation
+
+units metal
+boundary s s p
+
+atom_style atomic
+lattice fcc 3.52
+Lattice spacing in x,y,z = 3.52 3.52 3.52
+region box block 0 16.0 0 10.0 0 2.828427
+create_box 3 box
+Created orthogonal box = (0 0 0) to (56.32 35.2 9.95606)
+ 1 by 1 by 1 MPI processor grid
+
+lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0
+Lattice spacing in x,y,z = 3.52 4.97803 4.97803
+create_atoms 1 box
+Created 1912 atoms
+
+pair_style eam
+pair_coeff * * Ni_u3.eam
+Reading potential file Ni_u3.eam with DATE: 2007-06-11
+
+neighbor 0.3 bin
+neigh_modify delay 5
+
+region lower block INF INF INF 0.9 INF INF
+region upper block INF INF 6.1 INF INF INF
+group lower region lower
+264 atoms in group lower
+group upper region upper
+264 atoms in group upper
+group boundary union lower upper
+528 atoms in group boundary
+group mobile subtract all boundary
+1384 atoms in group mobile
+
+set group lower type 2
+ 264 settings made for type
+set group upper type 3
+ 264 settings made for type
+
+# void
+
+#region void cylinder z 8 5 2.5 INF INF
+#delete_atoms region void
+
+# temp controllers
+
+compute new3d mobile temp
+compute new2d mobile temp/partial 0 1 1
+
+# equilibrate
+
+velocity mobile create 300.0 5812775 temp new3d
+fix 1 all nve
+fix 2 boundary setforce 0.0 0.0 0.0
+
+fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
+fix_modify 3 temp new3d
+
+thermo 25
+thermo_modify temp new3d
+WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:445)
+
+timestep 0.001
+run 100
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 5 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 5.1
+ ghost atom cutoff = 5.1
+ binsize = 2.55 -> bins = 23 14 4
+Memory usage per processor = 2.88718 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 300 -8317.4367 0 -8263.8067 -7100.7667 19547.02
+ 25 220.34459 -8272.5701 0 -8233.1798 5168.6655 19547.02
+ 50 300 -8237.7876 0 -8184.1576 13741.264 19686.493
+ 75 292.67269 -8229.8093 0 -8177.4891 14319.387 19744.946
+ 100 300 -8245.8191 0 -8192.189 9034.8776 19778.592
+Loop time of 0.265527 on 1 procs for 100 steps with 1912 atoms
+
+Performance: 32.539 ns/day, 0.738 hours/ns, 376.610 timesteps/s
+100.2% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.25024 | 0.25024 | 0.25024 | 0.0 | 94.24
+Neigh | 0.0091426 | 0.0091426 | 0.0091426 | 0.0 | 3.44
+Comm | 0.0014474 | 0.0014474 | 0.0014474 | 0.0 | 0.55
+Output | 5.3644e-05 | 5.3644e-05 | 5.3644e-05 | 0.0 | 0.02
+Modify | 0.0034783 | 0.0034783 | 0.0034783 | 0.0 | 1.31
+Other | | 0.001166 | | | 0.44
+
+Nlocal: 1912 ave 1912 max 1912 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 2122 ave 2122 max 2122 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 45975 ave 45975 max 45975 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 45975
+Ave neighs/atom = 24.0455
+Neighbor list builds = 4
+Dangerous builds = 0
+
+# shear
+
+velocity upper set 1.0 0 0
+velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes
+
+unfix 3
+fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
+fix_modify 3 temp new2d
+
+#dump 1 all atom 100 dump.shear
+
+#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
+#dump_modify 2 pad 4
+
+#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
+#dump_modify 3 pad 4
+
+thermo 100
+thermo_modify temp new2d
+WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:445)
+
+reset_timestep 0
+run 3000
+Memory usage per processor = 2.88909 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 298.53339 -8245.8191 0 -8210.2533 8056.2702 19786.12
+ 100 300 -8260.7953 0 -8225.0549 3176.1215 19817.501
+ 200 298.50746 -8257.8441 0 -8222.2815 1695.9804 19934.196
+ 300 296.80999 -8250.2343 0 -8214.8739 -338.79329 20058.878
+ 400 306.47135 -8245.2265 0 -8208.7151 9.7568356 20142.386
+ 500 298.68843 -8240.244 0 -8204.6599 722.21355 20168.894
+ 600 302.37622 -8230.4652 0 -8194.4417 4005.8413 20287.297
+ 700 300 -8222.0223 0 -8186.2819 6766.8121 20413.543
+ 800 303.21952 -8210.998 0 -8174.874 8149.6736 20518.069
+ 900 297.74338 -8197.2403 0 -8161.7687 10760.713 20642.656
+ 1000 300 -8180.7508 0 -8145.0104 14222.046 20768.465
+ 1100 305.89822 -8166.6544 0 -8130.2113 18071.408 20883.281
+ 1200 295.27459 -8152.0699 0 -8116.8924 21320.011 21009.09
+ 1300 300 -8141.732 0 -8105.9916 22791.087 21123.905
+ 1400 300 -8130.0647 0 -8094.3243 23517.708 21254.6
+ 1500 300 -8125.4387 0 -8089.6983 21994.275 21364.53
+ 1600 300 -8128.9533 0 -8093.2128 18321.801 21494.003
+ 1700 300 -8151.4563 0 -8115.7159 11507 21608.819
+ 1800 300 -8160.1502 0 -8124.4098 7544.7477 21732.185
+ 1900 309.29943 -8153.7122 0 -8116.8639 8406.6165 21866.544
+ 2000 307.15092 -8160.675 0 -8124.0826 5891.9485 21985.024
+ 2100 308.54207 -8156.5601 0 -8119.802 4915.0348 22103.504
+ 2200 300 -8157.4804 0 -8121.74 2411.006 22225.648
+ 2300 300 -8162.7297 0 -8126.9893 -128.06955 22342.907
+ 2400 300 -8166.1396 0 -8130.3991 -1504.3669 22467.494
+ 2500 300 -8169.094 0 -8133.3536 -119.92093 22587.196
+ 2600 304.76063 -8162.5898 0 -8126.2822 2245.7194 22722.776
+ 2700 308.04872 -8167.1208 0 -8130.4215 77.123843 22842.478
+ 2800 300 -8167.1381 0 -8131.3977 -2884.8582 22959.736
+ 2900 308.65071 -8164.1796 0 -8127.4086 -7535.1379 23084.324
+ 3000 302.42612 -8159.1684 0 -8123.139 -9971.2947 23197.918
+Loop time of 8.08013 on 1 procs for 3000 steps with 1912 atoms
+
+Performance: 32.079 ns/day, 0.748 hours/ns, 371.281 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 7.3947 | 7.3947 | 7.3947 | 0.0 | 91.52
+Neigh | 0.50351 | 0.50351 | 0.50351 | 0.0 | 6.23
+Comm | 0.046209 | 0.046209 | 0.046209 | 0.0 | 0.57
+Output | 0.00058365 | 0.00058365 | 0.00058365 | 0.0 | 0.01
+Modify | 0.10414 | 0.10414 | 0.10414 | 0.0 | 1.29
+Other | | 0.03096 | | | 0.38
+
+Nlocal: 1912 ave 1912 max 1912 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 2104 ave 2104 max 2104 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 44986 ave 44986 max 44986 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 44986
+Ave neighs/atom = 23.5282
+Neighbor list builds = 221
+Dangerous builds = 0
+Total wall time: 0:00:08
diff --git a/examples/shear/log.15Feb16.shear.g++.4 b/examples/shear/log.15Feb16.shear.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..5b1c5a49476319a579916fc76f322c0bfb1c5bbc
--- /dev/null
+++ b/examples/shear/log.15Feb16.shear.g++.4
@@ -0,0 +1,191 @@
+LAMMPS (15 Feb 2016)
+# 3d metal shear simulation
+
+units metal
+boundary s s p
+
+atom_style atomic
+lattice fcc 3.52
+Lattice spacing in x,y,z = 3.52 3.52 3.52
+region box block 0 16.0 0 10.0 0 2.828427
+create_box 3 box
+Created orthogonal box = (0 0 0) to (56.32 35.2 9.95606)
+ 2 by 2 by 1 MPI processor grid
+
+lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0
+Lattice spacing in x,y,z = 3.52 4.97803 4.97803
+create_atoms 1 box
+Created 1912 atoms
+
+pair_style eam
+pair_coeff * * Ni_u3.eam
+Reading potential file Ni_u3.eam with DATE: 2007-06-11
+
+neighbor 0.3 bin
+neigh_modify delay 5
+
+region lower block INF INF INF 0.9 INF INF
+region upper block INF INF 6.1 INF INF INF
+group lower region lower
+264 atoms in group lower
+group upper region upper
+264 atoms in group upper
+group boundary union lower upper
+528 atoms in group boundary
+group mobile subtract all boundary
+1384 atoms in group mobile
+
+set group lower type 2
+ 264 settings made for type
+set group upper type 3
+ 264 settings made for type
+
+# void
+
+#region void cylinder z 8 5 2.5 INF INF
+#delete_atoms region void
+
+# temp controllers
+
+compute new3d mobile temp
+compute new2d mobile temp/partial 0 1 1
+
+# equilibrate
+
+velocity mobile create 300.0 5812775 temp new3d
+fix 1 all nve
+fix 2 boundary setforce 0.0 0.0 0.0
+
+fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
+fix_modify 3 temp new3d
+
+thermo 25
+thermo_modify temp new3d
+WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:445)
+
+timestep 0.001
+run 100
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 5 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 5.1
+ ghost atom cutoff = 5.1
+ binsize = 2.55 -> bins = 23 14 4
+Memory usage per processor = 2.78742 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 300 -8317.4367 0 -8263.8067 -7100.7667 19547.02
+ 25 219.81848 -8272.1577 0 -8232.8615 5206.8057 19547.02
+ 50 300 -8238.3413 0 -8184.7112 13308.809 19688.933
+ 75 294.78636 -8232.2217 0 -8179.5237 13192.782 19748.176
+ 100 300 -8248.1223 0 -8194.4923 7352.0246 19816.321
+Loop time of 0.0741301 on 4 procs for 100 steps with 1912 atoms
+
+Performance: 116.552 ns/day, 0.206 hours/ns, 1348.979 timesteps/s
+98.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.065906 | 0.066814 | 0.068289 | 0.3 | 90.13
+Neigh | 0.0022991 | 0.0023468 | 0.002413 | 0.1 | 3.17
+Comm | 0.0016782 | 0.0031904 | 0.0041595 | 1.7 | 4.30
+Output | 0.00010109 | 0.00011116 | 0.00013566 | 0.1 | 0.15
+Modify | 0.0009551 | 0.00096709 | 0.00098085 | 0.0 | 1.30
+Other | | 0.0007005 | | | 0.95
+
+Nlocal: 478 ave 490 max 466 min
+Histogram: 1 0 1 0 0 0 0 1 0 1
+Nghost: 1036.25 ave 1046 max 1027 min
+Histogram: 1 1 0 0 0 0 0 1 0 1
+Neighs: 11488 ave 11948 max 11157 min
+Histogram: 1 0 1 0 1 0 0 0 0 1
+
+Total # of neighbors = 45952
+Ave neighs/atom = 24.0335
+Neighbor list builds = 4
+Dangerous builds = 0
+
+# shear
+
+velocity upper set 1.0 0 0
+velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes
+
+unfix 3
+fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
+fix_modify 3 temp new2d
+
+#dump 1 all atom 100 dump.shear
+
+#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
+#dump_modify 2 pad 4
+
+#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
+#dump_modify 3 pad 4
+
+thermo 100
+thermo_modify temp new2d
+WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:445)
+
+reset_timestep 0
+run 3000
+Memory usage per processor = 2.78742 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 302.4034 -8248.1223 0 -8212.0956 6393.6774 19845.81
+ 100 291.62219 -8259.5645 0 -8224.8222 -1305.829 19874.353
+ 200 293.37436 -8257.0158 0 -8222.0647 -803.21007 19965.105
+ 300 305.94964 -8252.9337 0 -8216.4845 -1338.206 20062.042
+ 400 309.97419 -8247.5911 0 -8210.6624 -1064.8166 20094.42
+ 500 301.9509 -8239.3761 0 -8203.4033 794.43498 20172.617
+ 600 302.22577 -8230.7201 0 -8194.7145 3984.6172 20265.23
+ 700 296.33661 -8221.2208 0 -8185.9168 5407.761 20394.703
+ 800 291.23709 -8207.8855 0 -8173.1891 10664.616 20510.74
+ 900 297.90023 -8196.1342 0 -8160.6439 13966.21 20646.32
+ 1000 301.54908 -8182.0178 0 -8146.0928 17938.624 20752.586
+ 1100 309.01306 -8164.9485 0 -8128.1343 22821.748 20889.388
+ 1200 301.9299 -8153.5108 0 -8117.5405 25613.387 21000.539
+ 1300 300 -8143.4144 0 -8107.674 26662.495 21122.684
+ 1400 300 -8136.3101 0 -8100.5697 26322.787 21254.6
+ 1500 300 -8132.5702 0 -8096.8297 23577.661 21379.187
+ 1600 300 -8129.9485 0 -8094.2081 20683.092 21497.667
+ 1700 300 -8131.6622 0 -8095.9218 15384.841 21617.369
+ 1800 300 -8149.3274 0 -8113.587 9702.6228 21738.292
+ 1900 300 -8156.1594 0 -8120.419 9896.6056 21861.658
+ 2000 300 -8162.0579 0 -8126.3174 8370.0255 21987.467
+ 2100 300 -8164.32 0 -8128.5796 5207.4966 22105.947
+ 2200 309.50383 -8171.5055 0 -8134.6328 263.16699 22234.198
+ 2300 300 -8173.946 0 -8138.2056 -2861.1575 22346.571
+ 2400 300 -8184.1165 0 -8148.3761 -6684.5831 22471.159
+ 2500 308.09598 -8186.7631 0 -8150.0582 -8719.8136 22598.189
+ 2600 293.95252 -8179.2012 0 -8144.1813 -8299.1668 22720.333
+ 2700 300 -8173.1769 0 -8137.4365 -8570.4623 22831.485
+ 2800 307.83907 -8172.8218 0 -8136.1475 -10364.571 22959.736
+ 2900 299.48361 -8169.4289 0 -8133.75 -8567.3623 23079.438
+ 3000 300 -8167.764 0 -8132.0236 -11479.844 23206.468
+Loop time of 2.29026 on 4 procs for 3000 steps with 1912 atoms
+
+Performance: 113.175 ns/day, 0.212 hours/ns, 1309.896 timesteps/s
+99.7% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 1.9595 | 2.0004 | 2.0443 | 2.1 | 87.34
+Neigh | 0.12535 | 0.13213 | 0.1389 | 1.4 | 5.77
+Comm | 0.055656 | 0.10778 | 0.15512 | 10.7 | 4.71
+Output | 0.00081396 | 0.0008868 | 0.0010929 | 0.4 | 0.04
+Modify | 0.028605 | 0.029578 | 0.03042 | 0.4 | 1.29
+Other | | 0.01951 | | | 0.85
+
+Nlocal: 478 ave 510 max 443 min
+Histogram: 1 1 0 0 0 0 0 0 0 2
+Nghost: 1018.25 ave 1064 max 972 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs: 11225.8 ave 12344 max 10134 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+
+Total # of neighbors = 44903
+Ave neighs/atom = 23.4848
+Neighbor list builds = 226
+Dangerous builds = 0
+Total wall time: 0:00:02
diff --git a/examples/shear/log.15Feb16.shear.void.g++.1 b/examples/shear/log.15Feb16.shear.void.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..b8a32fb09c0f92b9f201d6a73b5f9ae9a28f9074
--- /dev/null
+++ b/examples/shear/log.15Feb16.shear.void.g++.1
@@ -0,0 +1,192 @@
+LAMMPS (15 Feb 2016)
+# 3d metal shear simulation
+
+units metal
+boundary s s p
+
+atom_style atomic
+lattice fcc 3.52
+Lattice spacing in x,y,z = 3.52 3.52 3.52
+region box block 0 16.0 0 10.0 0 2.828427
+create_box 3 box
+Created orthogonal box = (0 0 0) to (56.32 35.2 9.95606)
+ 1 by 1 by 1 MPI processor grid
+
+lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0
+Lattice spacing in x,y,z = 3.52 4.97803 4.97803
+create_atoms 1 box
+Created 1912 atoms
+
+pair_style eam
+pair_coeff * * Ni_u3.eam
+Reading potential file Ni_u3.eam with DATE: 2007-06-11
+
+neighbor 0.3 bin
+neigh_modify delay 5
+
+region lower block INF INF INF 0.9 INF INF
+region upper block INF INF 6.1 INF INF INF
+group lower region lower
+264 atoms in group lower
+group upper region upper
+264 atoms in group upper
+group boundary union lower upper
+528 atoms in group boundary
+group mobile subtract all boundary
+1384 atoms in group mobile
+
+set group lower type 2
+ 264 settings made for type
+set group upper type 3
+ 264 settings made for type
+
+# void
+
+region void cylinder z 8 3.535534 2.5 INF INF
+delete_atoms region void
+Deleted 204 atoms, new total = 1708
+
+# temp controllers
+
+compute new3d mobile temp
+compute new2d mobile temp/partial 0 1 1
+
+# equilibrate
+
+velocity mobile create 300.0 5812775 temp new3d
+fix 1 all nve
+fix 2 boundary setforce 0.0 0.0 0.0
+
+fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
+fix_modify 3 temp new3d
+
+thermo 25
+thermo_modify temp new3d
+WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:445)
+
+timestep 0.001
+run 100
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 5 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 5.1
+ ghost atom cutoff = 5.1
+ binsize = 2.55 -> bins = 23 14 4
+Memory usage per processor = 2.86988 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 300 -7358.6159 0 -7312.8966 -9600.8353 19547.02
+ 25 222.66197 -7321.4403 0 -7287.5071 562.28854 19547.02
+ 50 300 -7292.2273 0 -7246.508 7555.5059 19688.542
+ 75 292.67603 -7286.2016 0 -7241.5984 6825.409 19746.217
+ 100 300 -7297.4174 0 -7251.698 1627.2455 19775.648
+Loop time of 0.228758 on 1 procs for 100 steps with 1708 atoms
+
+Performance: 37.769 ns/day, 0.635 hours/ns, 437.143 timesteps/s
+99.7% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.21504 | 0.21504 | 0.21504 | 0.0 | 94.00
+Neigh | 0.0082476 | 0.0082476 | 0.0082476 | 0.0 | 3.61
+Comm | 0.0012808 | 0.0012808 | 0.0012808 | 0.0 | 0.56
+Output | 8.2016e-05 | 8.2016e-05 | 8.2016e-05 | 0.0 | 0.04
+Modify | 0.0031452 | 0.0031452 | 0.0031452 | 0.0 | 1.37
+Other | | 0.0009589 | | | 0.42
+
+Nlocal: 1708 ave 1708 max 1708 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1898 ave 1898 max 1898 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 39444 ave 39444 max 39444 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 39444
+Ave neighs/atom = 23.0937
+Neighbor list builds = 4
+Dangerous builds = 0
+
+# shear
+
+velocity upper set 1.0 0 0
+velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes
+
+unfix 3
+fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
+fix_modify 3 temp new2d
+
+#dump 1 all atom 100 dump.shear.void
+
+#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
+#dump_modify 2 pad 4
+
+#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
+#dump_modify 3 pad 4
+
+thermo 100
+thermo_modify temp new2d
+WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:445)
+
+reset_timestep 0
+run 3000
+Memory usage per processor = 2.86988 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 296.81549 -7297.4174 0 -7267.2741 785.80272 19779.424
+ 100 290.32156 -7309.73 0 -7280.2463 -5960.68 19838.822
+ 200 290.76236 -7306.4805 0 -7276.952 -7418.7514 19927.076
+ 300 293.25821 -7304.1086 0 -7274.3267 -11009.15 20043.748
+ 400 293.84766 -7299.0985 0 -7269.2567 -7883.11 20105.777
+ 500 291.74499 -7299.9751 0 -7270.3468 -5633.9534 20145.528
+ 600 303.46664 -7291.5162 0 -7260.6975 -1009.8362 20277.444
+ 700 300 -7287.9569 0 -7257.4903 -2204.427 20399.405
+ 800 300 -7280.4222 0 -7249.9555 -2875.1442 20520.781
+ 900 292.92463 -7272.7361 0 -7242.9881 -1776.2948 20641.435
+ 1000 307.93499 -7265.1866 0 -7233.9141 -1238.1504 20758.693
+ 1100 300.17079 -7260.1229 0 -7229.6389 -1842.3017 20889.388
+ 1200 302.06128 -7255.9277 0 -7225.2517 -1888.5899 21012.754
+ 1300 300 -7259.2664 0 -7228.7998 -3184.8863 21119.02
+ 1400 300 -7265.444 0 -7234.9774 -6107.2621 21252.157
+ 1500 308.79162 -7271.0073 0 -7239.6478 -6104.8023 21369.416
+ 1600 300 -7275.2324 0 -7244.7658 -8516.6115 21500.11
+ 1700 309.22602 -7278.5756 0 -7247.172 -13747.711 21618.59
+ 1800 300 -7284.3068 0 -7253.8402 -14332.302 21728.52
+ 1900 299.75827 -7283.413 0 -7252.9709 -14457.778 21854.329
+ 2000 297.70312 -7274.9007 0 -7244.6674 -20473.262 21986.245
+ 2100 304.09482 -7269.8328 0 -7238.9503 -19783.936 22101.061
+ 2200 299.66443 -7269.2566 0 -7238.8241 -16596.846 22224.427
+ 2300 299.27231 -7268.2781 0 -7237.8853 -15841.479 22345.35
+ 2400 300.69324 -7259.5316 0 -7228.9946 -14593.472 22471.159
+ 2500 297.44581 -7258.0006 0 -7227.7934 -17840.459 22589.639
+ 2600 300 -7253.3731 0 -7222.9065 -18551.141 22719.112
+ 2700 305.12651 -7253.1648 0 -7222.1775 -20324.426 22832.706
+ 2800 294.14063 -7249.1464 0 -7219.2748 -17535.191 22960.958
+ 2900 307.30441 -7249.4895 0 -7218.281 -17444.188 23079.438
+ 3000 304.44871 -7244.9559 0 -7214.0374 -15836.731 23207.69
+Loop time of 6.93892 on 1 procs for 3000 steps with 1708 atoms
+
+Performance: 37.355 ns/day, 0.642 hours/ns, 432.344 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 6.3414 | 6.3414 | 6.3414 | 0.0 | 91.39
+Neigh | 0.43388 | 0.43388 | 0.43388 | 0.0 | 6.25
+Comm | 0.041184 | 0.041184 | 0.041184 | 0.0 | 0.59
+Output | 0.00080252 | 0.00080252 | 0.00080252 | 0.0 | 0.01
+Modify | 0.093581 | 0.093581 | 0.093581 | 0.0 | 1.35
+Other | | 0.02807 | | | 0.40
+
+Nlocal: 1708 ave 1708 max 1708 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1879 ave 1879 max 1879 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 38632 ave 38632 max 38632 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 38632
+Ave neighs/atom = 22.6183
+Neighbor list builds = 209
+Dangerous builds = 0
+Total wall time: 0:00:07
diff --git a/examples/shear/log.15Feb16.shear.void.g++.4 b/examples/shear/log.15Feb16.shear.void.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..dc9a7b430993b1023985bb9dc292ec84591db7e5
--- /dev/null
+++ b/examples/shear/log.15Feb16.shear.void.g++.4
@@ -0,0 +1,192 @@
+LAMMPS (15 Feb 2016)
+# 3d metal shear simulation
+
+units metal
+boundary s s p
+
+atom_style atomic
+lattice fcc 3.52
+Lattice spacing in x,y,z = 3.52 3.52 3.52
+region box block 0 16.0 0 10.0 0 2.828427
+create_box 3 box
+Created orthogonal box = (0 0 0) to (56.32 35.2 9.95606)
+ 2 by 2 by 1 MPI processor grid
+
+lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0
+Lattice spacing in x,y,z = 3.52 4.97803 4.97803
+create_atoms 1 box
+Created 1912 atoms
+
+pair_style eam
+pair_coeff * * Ni_u3.eam
+Reading potential file Ni_u3.eam with DATE: 2007-06-11
+
+neighbor 0.3 bin
+neigh_modify delay 5
+
+region lower block INF INF INF 0.9 INF INF
+region upper block INF INF 6.1 INF INF INF
+group lower region lower
+264 atoms in group lower
+group upper region upper
+264 atoms in group upper
+group boundary union lower upper
+528 atoms in group boundary
+group mobile subtract all boundary
+1384 atoms in group mobile
+
+set group lower type 2
+ 264 settings made for type
+set group upper type 3
+ 264 settings made for type
+
+# void
+
+region void cylinder z 8 3.535534 2.5 INF INF
+delete_atoms region void
+Deleted 204 atoms, new total = 1708
+
+# temp controllers
+
+compute new3d mobile temp
+compute new2d mobile temp/partial 0 1 1
+
+# equilibrate
+
+velocity mobile create 300.0 5812775 temp new3d
+fix 1 all nve
+fix 2 boundary setforce 0.0 0.0 0.0
+
+fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
+fix_modify 3 temp new3d
+
+thermo 25
+thermo_modify temp new3d
+WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:445)
+
+timestep 0.001
+run 100
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 5 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 5.1
+ ghost atom cutoff = 5.1
+ binsize = 2.55 -> bins = 23 14 4
+Memory usage per processor = 2.7752 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 300 -7358.6159 0 -7312.8966 -9600.8353 19547.02
+ 25 220.57465 -7320.4003 0 -7286.7852 832.69858 19547.02
+ 50 300 -7292.1121 0 -7246.3928 7101.9213 19686.075
+ 75 295.2793 -7286.9013 0 -7241.9014 5282.1114 19746.39
+ 100 300 -7301.0026 0 -7255.2833 -1939.7714 19790.975
+Loop time of 0.0633137 on 4 procs for 100 steps with 1708 atoms
+
+Performance: 136.463 ns/day, 0.176 hours/ns, 1579.436 timesteps/s
+98.7% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.056509 | 0.057388 | 0.058275 | 0.3 | 90.64
+Neigh | 0.001965 | 0.0020149 | 0.0020759 | 0.1 | 3.18
+Comm | 0.0013819 | 0.0022985 | 0.003196 | 1.6 | 3.63
+Output | 9.8705e-05 | 0.0001052 | 0.00012016 | 0.1 | 0.17
+Modify | 0.00085497 | 0.00087214 | 0.00089121 | 0.1 | 1.38
+Other | | 0.0006346 | | | 1.00
+
+Nlocal: 427 ave 437 max 419 min
+Histogram: 1 1 0 0 0 0 1 0 0 1
+Nghost: 780 ave 788 max 774 min
+Histogram: 1 1 0 0 0 1 0 0 0 1
+Neighs: 9859.75 ave 10248 max 9544 min
+Histogram: 1 0 1 0 0 1 0 0 0 1
+
+Total # of neighbors = 39439
+Ave neighs/atom = 23.0907
+Neighbor list builds = 4
+Dangerous builds = 0
+
+# shear
+
+velocity upper set 1.0 0 0
+velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes
+
+unfix 3
+fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
+fix_modify 3 temp new2d
+
+#dump 1 all atom 100 dump.shear.void
+
+#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
+#dump_modify 2 pad 4
+
+#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
+#dump_modify 3 pad 4
+
+thermo 100
+thermo_modify temp new2d
+WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:445)
+
+reset_timestep 0
+run 3000
+Memory usage per processor = 2.7752 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 299.05825 -7301.0026 0 -7270.6316 -2766.8643 19799.958
+ 100 301.19116 -7308.1272 0 -7277.5397 -8905.8025 19851.046
+ 200 296.34396 -7306.2167 0 -7276.1214 -9976.4707 19977.676
+ 300 301.10727 -7303.6912 0 -7273.1122 -9863.5572 20024.08
+ 400 303.06413 -7299.743 0 -7268.9652 -7947.839 20095.051
+ 500 298.67442 -7297.287 0 -7266.955 -5764.8779 20168.374
+ 600 296.13094 -7292.6877 0 -7262.614 -1786.0615 20265.23
+ 700 305.86337 -7287.378 0 -7256.3159 -1049.7285 20413.77
+ 800 297.25967 -7280.2104 0 -7250.0221 -1484.4549 20516.847
+ 900 305.16151 -7272.5608 0 -7241.57 -808.36942 20629.22
+ 1000 303.28807 -7264.3771 0 -7233.5765 -2139.5907 20763.579
+ 1100 297.67659 -7258.2851 0 -7228.0544 -770.05741 20890.609
+ 1200 309.60751 -7254.7626 0 -7223.3203 819.60099 20995.654
+ 1300 300 -7251.8704 0 -7221.4038 -1919.6357 21121.462
+ 1400 300 -7258.7732 0 -7228.3066 -5164.6854 21253.378
+ 1500 304.51839 -7269.5164 0 -7238.5909 -8462.6306 21376.744
+ 1600 302.30135 -7270.4656 0 -7239.7653 -10283.715 21489.117
+ 1700 300 -7273.6082 0 -7243.1416 -11338.311 21616.147
+ 1800 306.59272 -7269.4364 0 -7238.3003 -14218.514 21740.735
+ 1900 306.24897 -7271.6064 0 -7240.5052 -19238.112 21854.329
+ 2000 302.17783 -7267.1183 0 -7236.4305 -20204.467 21975.252
+ 2100 308.30693 -7268.4528 0 -7237.1425 -25338.75 22097.397
+ 2200 306.39487 -7266.6795 0 -7235.5635 -27066.965 22230.534
+ 2300 300 -7262.1576 0 -7231.691 -24009.895 22351.457
+ 2400 300 -7261.5352 0 -7231.0686 -20454.104 22478.487
+ 2500 300.08812 -7260.6902 0 -7230.2146 -15315.132 22587.196
+ 2600 296.32147 -7257.4049 0 -7227.3118 -13410.947 22722.776
+ 2700 300 -7256.5862 0 -7226.1196 -15961.676 22830.263
+ 2800 298.83111 -7256.171 0 -7225.8231 -20667.094 22960.958
+ 2900 291.53879 -7248.9903 0 -7219.3829 -23968.563 23081.881
+ 3000 293.96302 -7243.6435 0 -7213.79 -25021.209 23200.361
+Loop time of 1.9353 on 4 procs for 3000 steps with 1708 atoms
+
+Performance: 133.933 ns/day, 0.179 hours/ns, 1550.145 timesteps/s
+99.7% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 1.6683 | 1.6925 | 1.736 | 2.0 | 87.46
+Neigh | 0.10491 | 0.10797 | 0.11187 | 0.8 | 5.58
+Comm | 0.041337 | 0.089808 | 0.11691 | 9.6 | 4.64
+Output | 0.00081921 | 0.00085014 | 0.00093603 | 0.2 | 0.04
+Modify | 0.025656 | 0.026361 | 0.027086 | 0.3 | 1.36
+Other | | 0.01777 | | | 0.92
+
+Nlocal: 427 ave 450 max 403 min
+Histogram: 1 1 0 0 0 0 0 0 1 1
+Nghost: 785 ave 843 max 722 min
+Histogram: 1 0 1 0 0 0 0 0 1 1
+Neighs: 9576.75 ave 10183 max 9094 min
+Histogram: 2 0 0 0 0 0 0 1 0 1
+
+Total # of neighbors = 38307
+Ave neighs/atom = 22.428
+Neighbor list builds = 215
+Dangerous builds = 0
+Total wall time: 0:00:02
diff --git a/examples/snap/log.15Feb16.snap.g++.1 b/examples/snap/log.15Feb16.snap.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..82f86edea23782440b30aa0337e36d8c35235be9
--- /dev/null
+++ b/examples/snap/log.15Feb16.snap.g++.1
@@ -0,0 +1,135 @@
+LAMMPS (15 Feb 2016)
+# Demonstrate SNAP Ta potential
+
+# Initialize simulation
+
+variable nsteps index 100
+variable nrep equal 4
+variable a equal 3.316
+units metal
+
+# generate the box and atom positions using a BCC lattice
+
+variable nx equal ${nrep}
+variable nx equal 4
+variable ny equal ${nrep}
+variable ny equal 4
+variable nz equal ${nrep}
+variable nz equal 4
+
+boundary p p p
+
+lattice bcc $a
+lattice bcc 3.316
+Lattice spacing in x,y,z = 3.316 3.316 3.316
+region box block 0 ${nx} 0 ${ny} 0 ${nz}
+region box block 0 4 0 ${ny} 0 ${nz}
+region box block 0 4 0 4 0 ${nz}
+region box block 0 4 0 4 0 4
+create_box 1 box
+Created orthogonal box = (0 0 0) to (13.264 13.264 13.264)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 128 atoms
+
+mass 1 180.88
+
+# choose potential
+
+include Ta06A_pot.snap
+# DATE: 2014-09-05 CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014)
+
+# Definition of SNAP potential Ta_Cand06A
+# Assumes 1 LAMMPS atom type
+
+variable zblcutinner equal 4
+variable zblcutouter equal 4.8
+variable zblz equal 73
+
+# Specify hybrid with SNAP, ZBL
+
+pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap
+pair_style hybrid/overlay zbl 4 ${zblcutouter} snap
+pair_style hybrid/overlay zbl 4 4.8 snap
+pair_coeff 1 1 zbl ${zblz} ${zblz}
+pair_coeff 1 1 zbl 73 ${zblz}
+pair_coeff 1 1 zbl 73 73
+pair_coeff * * snap Ta06A.snapcoeff Ta Ta06A.snapparam Ta
+Reading potential file Ta06A.snapcoeff with DATE: 2014-09-05
+SNAP Element = Ta, Radius 0.5, Weight 1
+Reading potential file Ta06A.snapparam with DATE: 2014-09-05
+SNAP keyword rcutfac 4.67637
+SNAP keyword twojmax 6
+SNAP keyword gamma 1
+SNAP keyword rfac0 0.99363
+SNAP keyword rmin0 0
+SNAP keyword diagonalstyle 3
+
+
+# Setup output
+
+thermo 10
+thermo_modify norm yes
+
+# Set up NVE run
+
+timestep 0.5e-3
+neighbor 1.0 bin
+neigh_modify once no every 1 delay 0 check yes
+
+# Run MD
+
+velocity all create 300.0 4928459
+fix 1 all nve
+run ${nsteps}
+run 100
+Neighbor list info ...
+ 2 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 5.8
+ ghost atom cutoff = 5.8
+ binsize = 2.9 -> bins = 5 5 5
+Memory usage per processor = 2.92823 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 300 -11.85157 0 -11.813095 2717.1661
+ 10 295.96579 -11.851053 0 -11.813095 2696.1559
+ 20 284.32535 -11.84956 0 -11.813095 2301.3713
+ 30 266.04602 -11.847215 0 -11.813095 1832.1745
+ 40 242.2862 -11.844168 0 -11.813095 1492.6765
+ 50 214.48968 -11.840603 0 -11.813094 1312.8908
+ 60 184.32523 -11.836734 0 -11.813094 1284.582
+ 70 153.58055 -11.832791 0 -11.813094 1374.4457
+ 80 124.04276 -11.829003 0 -11.813094 1537.703
+ 90 97.37622 -11.825582 0 -11.813094 1734.9662
+ 100 75.007873 -11.822714 0 -11.813094 1930.8005
+Loop time of 3.58062 on 1 procs for 100 steps with 128 atoms
+
+Performance: 1.206 ns/day, 19.892 hours/ns, 27.928 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 3.5795 | 3.5795 | 3.5795 | 0.0 | 99.97
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.00047183 | 0.00047183 | 0.00047183 | 0.0 | 0.01
+Output | 0.00010324 | 0.00010324 | 0.00010324 | 0.0 | 0.00
+Modify | 0.00026298 | 0.00026298 | 0.00026298 | 0.0 | 0.01
+Other | | 0.0003033 | | | 0.01
+
+Nlocal: 128 ave 128 max 128 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 727 ave 727 max 727 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 3712 ave 3712 max 3712 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs: 7424 ave 7424 max 7424 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 7424
+Ave neighs/atom = 58
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Total wall time: 0:00:03
diff --git a/examples/snap/log.15Feb16.snap.g++.4 b/examples/snap/log.15Feb16.snap.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..65b3be1eddaf778f8adec71842560787cfb15d69
--- /dev/null
+++ b/examples/snap/log.15Feb16.snap.g++.4
@@ -0,0 +1,135 @@
+LAMMPS (15 Feb 2016)
+# Demonstrate SNAP Ta potential
+
+# Initialize simulation
+
+variable nsteps index 100
+variable nrep equal 4
+variable a equal 3.316
+units metal
+
+# generate the box and atom positions using a BCC lattice
+
+variable nx equal ${nrep}
+variable nx equal 4
+variable ny equal ${nrep}
+variable ny equal 4
+variable nz equal ${nrep}
+variable nz equal 4
+
+boundary p p p
+
+lattice bcc $a
+lattice bcc 3.316
+Lattice spacing in x,y,z = 3.316 3.316 3.316
+region box block 0 ${nx} 0 ${ny} 0 ${nz}
+region box block 0 4 0 ${ny} 0 ${nz}
+region box block 0 4 0 4 0 ${nz}
+region box block 0 4 0 4 0 4
+create_box 1 box
+Created orthogonal box = (0 0 0) to (13.264 13.264 13.264)
+ 1 by 2 by 2 MPI processor grid
+create_atoms 1 box
+Created 128 atoms
+
+mass 1 180.88
+
+# choose potential
+
+include Ta06A_pot.snap
+# DATE: 2014-09-05 CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014)
+
+# Definition of SNAP potential Ta_Cand06A
+# Assumes 1 LAMMPS atom type
+
+variable zblcutinner equal 4
+variable zblcutouter equal 4.8
+variable zblz equal 73
+
+# Specify hybrid with SNAP, ZBL
+
+pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap
+pair_style hybrid/overlay zbl 4 ${zblcutouter} snap
+pair_style hybrid/overlay zbl 4 4.8 snap
+pair_coeff 1 1 zbl ${zblz} ${zblz}
+pair_coeff 1 1 zbl 73 ${zblz}
+pair_coeff 1 1 zbl 73 73
+pair_coeff * * snap Ta06A.snapcoeff Ta Ta06A.snapparam Ta
+Reading potential file Ta06A.snapcoeff with DATE: 2014-09-05
+SNAP Element = Ta, Radius 0.5, Weight 1
+Reading potential file Ta06A.snapparam with DATE: 2014-09-05
+SNAP keyword rcutfac 4.67637
+SNAP keyword twojmax 6
+SNAP keyword gamma 1
+SNAP keyword rfac0 0.99363
+SNAP keyword rmin0 0
+SNAP keyword diagonalstyle 3
+
+
+# Setup output
+
+thermo 10
+thermo_modify norm yes
+
+# Set up NVE run
+
+timestep 0.5e-3
+neighbor 1.0 bin
+neigh_modify once no every 1 delay 0 check yes
+
+# Run MD
+
+velocity all create 300.0 4928459
+fix 1 all nve
+run ${nsteps}
+run 100
+Neighbor list info ...
+ 2 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 5.8
+ ghost atom cutoff = 5.8
+ binsize = 2.9 -> bins = 5 5 5
+Memory usage per processor = 2.91109 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 300 -11.85157 0 -11.813095 2717.1661
+ 10 295.8664 -11.85104 0 -11.813095 2702.935
+ 20 283.95868 -11.849513 0 -11.813095 2301.3242
+ 30 265.29535 -11.847119 0 -11.813095 1870.3173
+ 40 241.09337 -11.844015 0 -11.813095 1568.1549
+ 50 212.86732 -11.840395 0 -11.813094 1409.2092
+ 60 182.35256 -11.836481 0 -11.813094 1389.0527
+ 70 151.38968 -11.83251 0 -11.813094 1474.9232
+ 80 121.80051 -11.828715 0 -11.813094 1627.6911
+ 90 95.262635 -11.825311 0 -11.813094 1812.9327
+ 100 73.194645 -11.822481 0 -11.813094 1995.2199
+Loop time of 0.899437 on 4 procs for 100 steps with 128 atoms
+
+Performance: 4.803 ns/day, 4.997 hours/ns, 111.181 timesteps/s
+99.9% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.87007 | 0.88069 | 0.8961 | 1.0 | 97.92
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.0022893 | 0.017643 | 0.02821 | 7.2 | 1.96
+Output | 0.00027275 | 0.00029993 | 0.00037384 | 0.2 | 0.03
+Modify | 9.203e-05 | 0.00010943 | 0.0001235 | 0.1 | 0.01
+Other | | 0.0006917 | | | 0.08
+
+Nlocal: 32 ave 32 max 32 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost: 431 ave 431 max 431 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs: 928 ave 928 max 928 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs: 1856 ave 1856 max 1856 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 7424
+Ave neighs/atom = 58
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Total wall time: 0:00:00
diff --git a/examples/srd/log.15Feb16.srd.mixture.g++.1 b/examples/srd/log.15Feb16.srd.mixture.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..bff83e4a9c0e1520e13f1ab708b4741d1eb1ddf0
--- /dev/null
+++ b/examples/srd/log.15Feb16.srd.mixture.g++.1
@@ -0,0 +1,269 @@
+LAMMPS (15 Feb 2016)
+# 2d SRD test: big + small particles
+
+units lj
+atom_style sphere
+atom_modify first big
+dimension 2
+
+# create big particles with sigma 1.0
+
+lattice sq 0.4
+Lattice spacing in x,y,z = 1.58114 1.58114 1.58114
+region box block 0 10 0 10 -0.5 0.5
+create_box 2 box
+Created orthogonal box = (0 0 -0.790569) to (15.8114 15.8114 0.790569)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 region box
+Created 100 atoms
+set type 1 mass 1.0
+ 100 settings made for mass
+set type 1 diameter 1.0
+ 100 settings made for diameter
+
+group big type 1
+100 atoms in group big
+velocity big create 1.44 87287 loop geom
+
+# equilibrate big particles
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0
+pair_coeff 2 2 0.0 1.0 0.0
+pair_coeff 1 2 0.0 1.0 0.0
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 big nve
+fix 2 all enforce2d
+
+run 1000
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4 -> bins = 12 12 2
+Memory usage per processor = 3.60175 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 -0.54272 0 0.88288 -0.041088
+ 1000 1.8791467 -0.97185784 0 0.8884974 0.61487656
+Loop time of 0.0150781 on 1 procs for 1000 steps with 100 atoms
+
+Performance: 28650885.930 tau/day, 66321.495 timesteps/s
+99.5% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0081143 | 0.0081143 | 0.0081143 | 0.0 | 53.82
+Neigh | 0.0028751 | 0.0028751 | 0.0028751 | 0.0 | 19.07
+Comm | 0.0014627 | 0.0014627 | 0.0014627 | 0.0 | 9.70
+Output | 7.1526e-06 | 7.1526e-06 | 7.1526e-06 | 0.0 | 0.05
+Modify | 0.0017178 | 0.0017178 | 0.0017178 | 0.0 | 11.39
+Other | | 0.000901 | | | 5.98
+
+Nlocal: 100 ave 100 max 100 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 88 ave 88 max 88 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 459 ave 459 max 459 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 459
+Ave neighs/atom = 4.59
+Neighbor list builds = 129
+Dangerous builds = 0
+
+unfix 1
+unfix 2
+
+# add small particles as hi density lattice
+
+lattice sq 0.4
+Lattice spacing in x,y,z = 1.58114 1.58114 1.58114
+region plane block 0 10 0 10 -0.001 0.001
+lattice sq 85.0
+Lattice spacing in x,y,z = 0.108465 0.108465 0.108465
+create_atoms 2 region plane
+Created 21316 atoms
+set type 2 mass 0.01
+ 21316 settings made for mass
+set type 2 diameter 0.0
+ 21316 settings made for diameter
+
+group small type 2
+21316 atoms in group small
+
+velocity small create 1.0 593849 loop geom
+
+# delete overlaps
+# must set 1-2 cutoff to non-zero value
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0
+pair_coeff 2 2 0.0 1.0 0.0
+pair_coeff 1 2 0.0 1.0 0.5
+
+delete_atoms overlap 0.5 small big
+Neighbor list info ...
+ 2 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4 -> bins = 12 12 2
+WARNING: Delete_atoms cutoff > minimum neighbor cutoff (../delete_atoms.cpp:277)
+Deleted 6700 atoms, new total = 14716
+
+# SRD run
+
+reset_timestep 0
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+comm_modify mode multi group big vel yes
+neigh_modify include big
+
+# no pairwise interactions with small particles
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0
+pair_coeff 2 2 0.0 1.0 0.0
+pair_coeff 1 2 0.0 1.0 0.0
+
+# use fix SRD to push small particles out from inside big ones
+
+timestep 0.001
+
+fix 1 big nve
+fix 2 small srd 20 big 1.0 0.25 49894 radius 0.88 search 0.2 collision slip
+fix 3 all enforce2d
+
+# diagnostics
+
+compute tbig big temp
+variable pebig equal pe*atoms/count(big)
+variable ebig equal etotal*atoms/count(big)
+thermo_style custom step temp f_2[7] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[8] f_2[9] f_2[10]
+
+thermo_modify temp tbig
+WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:445)
+thermo 100
+
+#dump 1 all atom 250 dump.srd.mixture
+
+#dump 2 all image 250 image.*.jpg type type zoom 1.6
+#dump_modify 2 pad 4 adiam 1 1 adiam 2 0.2
+
+#dump 3 all movie 250 movie.mpg type type zoom 1.6
+#dump_modify 3 pad 4 adiam 1 1 adiam 2 0.2
+
+run 5000
+SRD info:
+ SRD/big particles = 14616 100
+ big particle diameter max/min = 0.88 0.88
+ SRD temperature & lamda = 1 0.2
+ SRD max distance & max velocity = 0.8 40
+ SRD grid counts: 63 63 1
+ SRD grid size: request, actual (xyz) = 0.25, 0.250974 0.250974 1.58114
+ SRD per actual grid cell = 4.86648
+ SRD viscosity = 0.463448
+ big/SRD mass density ratio = 2.12808
+WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2884)
+ # of rescaled SRD velocities = 0
+ ave/max small velocity = 13.2944 24.262
+ ave/max big velocity = 1.69284 5.10989
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4 -> bins = 12 12 2
+Memory usage per processor = 14.7783 Mbytes
+Step Temp 2[7] TotEng pebig ebig Press 2[1] 2[2] 2[3] 2[4] 2[5] 2[6] 2[8] 2[9] 2[10]
+ 0 1.8791467 0 0.0060376284 -0.97185784 0.8884974 0.61487656 0 0 0 0 0 0 0 0 0
+ 100 1.1596877 3969 0.00179671 -0.88368701 0.26440385 0.85824547 7578 83 83 0 14 12996 3000 1.0041859 0
+ 200 1.2193132 3969 0.0018345215 -0.93715187 0.26996819 0.70474845 7511 90 90 0 53 12996 3022 1.0188815 0
+ 300 0.99431764 3969 -0.00029373076 -1.0275999 -0.043225419 0.17829084 7619 83 83 0 89 12996 3013 1.0200287 0
+ 400 1.0357776 3969 0.00051788234 -0.94920826 0.076211565 0.43014085 7571 85 85 0 120 12996 3004 1.0370684 0
+ 500 1.0481683 3969 0.0010184986 -0.88780442 0.14988225 0.70052984 7584 77 77 0 152 12996 3009 1.0142095 0
+ 600 1.1928825 3969 0.00095759759 -1.0400336 0.14092006 0.21451332 7494 69 69 0 195 12996 2993 1.0228103 0
+ 700 1.0524078 3969 0.00035360799 -0.9898468 0.052036951 0.42873114 7693 85 85 0 216 12996 3008 1.0054139 0
+ 800 0.90603094 3969 -0.00092639686 -1.0332992 -0.13632856 0.25916674 7671 99 99 0 247 12996 2966 1.0361445 0
+ 900 1.0636972 3969 0.00041617364 -0.99181615 0.061244113 0.58497843 7657 87 87 0 282 12996 2992 1.0161879 0
+ 1000 1.0507488 3969 -0.0001556117 -1.0631411 -0.022899818 0.47566195 7465 94 94 0 326 12996 3030 0.99530538 0
+ 1100 0.93006509 3969 -0.0003550828 -0.97301843 -0.052253985 0.77031309 7474 90 90 0 347 12996 3004 1.0214319 0
+ 1200 1.0402459 3969 -0.00046600382 -1.0984205 -0.068577122 0.31255586 7396 78 78 0 385 12996 3010 1.0176572 0
+ 1300 1.0520892 3969 -1.0354518e-06 -1.0417207 -0.00015237708 0.50280759 7529 81 81 0 415 12996 3000 1.0305024 0
+ 1400 1.0166314 3969 -0.00076800379 -1.1194845 -0.11301944 0.25711665 7525 93 93 0 443 12996 3001 1.031584 0
+ 1500 0.99218489 3969 -0.00098822242 -1.1276898 -0.14542681 0.25260367 7495 93 93 0 474 12996 2995 1.0242311 0
+ 1600 1.1064178 3969 -0.00017916094 -1.121719 -0.026365324 0.47764294 7505 94 94 0 506 12996 3022 1.0136332 0
+ 1700 1.1431125 3969 0.00094430031 -0.9927181 0.13896323 1.0995941 7474 88 88 0 539 12996 3003 1.0341733 0
+ 1800 1.0222823 3969 -0.00059038783 -1.098941 -0.086881473 0.62506101 7310 87 87 0 586 12996 2981 1.0382713 0
+ 1900 0.95084674 3969 -0.0015534806 -1.1699485 -0.22861021 0.2701615 7623 87 87 0 624 12996 3003 1.0181489 0
+ 2000 1.0861079 3969 -0.00065855134 -1.1721593 -0.096912415 0.34276301 7470 90 90 0 660 12996 3015 1.0268618 0
+ 2100 0.88345526 3969 -0.0016997139 -1.1247506 -0.2501299 0.43045597 7532 82 82 0 688 12996 3006 1.0124018 0
+ 2200 0.92745839 3969 -0.0010657957 -1.0750263 -0.15684249 0.67080961 7508 84 84 0 719 12996 3010 1.0232807 0
+ 2300 0.88367737 3969 -0.001454046 -1.088818 -0.21397742 0.63475334 7430 99 99 0 746 12996 2993 1.0344177 0
+ 2400 0.87359171 3969 -0.0012946593 -1.0553779 -0.19052207 0.58406648 7454 96 96 0 780 12996 2981 1.0343798 0
+ 2500 0.96618275 3969 -0.0010799782 -1.1154505 -0.1589296 0.32223081 7515 83 83 0 807 12996 3021 1.0142273 0
+ 2600 0.86458041 3969 -0.0015382749 -1.0823071 -0.22637254 0.25396199 7489 91 91 0 828 12996 2980 1.0291839 0
+ 2700 0.98390726 3969 -0.00079291155 -1.0907531 -0.11668486 0.30335914 7395 79 79 0 854 12996 3010 1.0120521 0
+ 2800 1.0033122 3969 -0.0001965439 -1.0222025 -0.0289234 0.66093465 7387 68 68 0 888 12996 2980 1.0251477 0
+ 2900 1.222899 3969 0.0012034132 -1.0335757 0.17709428 0.65880933 7386 85 85 0 919 12996 3004 1.0162822 0
+ 3000 1.002035 3969 -0.00054872208 -1.0727646 -0.080749941 0.34444254 7466 83 83 0 952 12996 3016 1.0122263 0
+ 3100 1.206972 3969 0.0011369559 -1.0275879 0.16731443 0.51852441 7468 84 84 0 992 12996 3025 1.0099007 0
+ 3200 1.0856646 3969 0.00014959203 -1.052794 0.022013964 0.3410219 7417 84 84 0 1032 12996 2976 1.0135289 0
+ 3300 1.3331295 3969 0.0019856133 -1.0275953 0.29220285 0.47025792 7524 69 69 0 1062 12996 3018 1.0255776 0
+ 3400 0.84929817 3969 -0.00098128795 -0.98521153 -0.14440633 0.36010527 7428 83 83 0 1101 12996 3014 1.0270963 0
+ 3500 1.1302394 3969 0.00036763215 -1.0648363 0.054100747 0.1522826 7572 90 90 0 1119 12996 3012 1.0289088 0
+ 3600 1.1936576 3969 0.00056858904 -1.0980475 0.083673563 0.23906343 7602 101 101 0 1158 12996 2995 1.0275146 0
+ 3700 1.1286007 3969 0.0010142941 -0.96805122 0.14926351 0.72687935 7415 84 84 0 1198 12996 3018 1.0256527 0
+ 3800 1.1244276 3969 0.00071868084 -1.0074222 0.10576107 0.44091142 7476 84 84 0 1231 12996 2984 1.0453126 0
+ 3900 0.98213284 3969 -0.0008786738 -1.1016171 -0.12930564 0.069507795 7445 88 88 0 1267 12996 3017 1.0203869 0
+ 4000 1.1632971 3969 0.00073199788 -1.0439433 0.10772081 0.50304552 7602 101 101 0 1301 12996 3021 1.0219416 0
+ 4100 1.060029 3969 -0.00023302512 -1.0837207 -0.034291977 0.36492957 7538 77 77 0 1326 12996 2997 1.017007 0
+ 4200 0.97057567 3969 -0.00052048968 -1.0374652 -0.076595262 0.3008083 7683 82 82 0 1363 12996 3010 1.0339142 0
+ 4300 1.0562211 3969 -0.00040298636 -1.1049624 -0.059303473 0.12322043 7511 84 84 0 1386 12996 2991 1.035082 0
+ 4400 0.97383798 3969 8.961738e-05 -0.95091151 0.013188094 0.68597762 7669 103 103 0 1420 12996 3010 1.0141431 0
+ 4500 0.94750799 3969 -0.00086783826 -1.065744 -0.12771108 0.2109101 7739 96 96 0 1452 12996 3012 1.0244541 0
+ 4600 1.1123048 3969 0.00016640454 -1.0766937 0.024488092 0.24736079 7615 75 75 0 1493 12996 3013 1.0013601 0
+ 4700 1.0624886 3969 -1.2753265e-05 -1.0537404 -0.0018767705 0.29324615 7568 91 91 0 1524 12996 2997 1.019485 0
+ 4800 1.2169028 3969 0.0010831546 -1.0453368 0.15939704 0.42728069 7444 80 80 0 1560 12996 2997 1.0300677 0
+ 4900 0.90968786 3969 -0.0010022199 -1.0480777 -0.14748667 0.37681568 7563 88 88 0 1592 12996 2997 1.0257714 0
+ 5000 1.0856525 3969 0.0001301746 -1.0556395 0.019156494 0.55496941 7439 78 78 0 1633 12996 3008 1.0343075 0
+Loop time of 3.01867 on 1 procs for 5000 steps with 14716 atoms
+
+Performance: 143109.526 tau/day, 1656.360 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.044753 | 0.044753 | 0.044753 | 0.0 | 1.48
+Neigh | 0.006125 | 0.006125 | 0.006125 | 0.0 | 0.20
+Comm | 0.028884 | 0.028884 | 0.028884 | 0.0 | 0.96
+Output | 0.002805 | 0.002805 | 0.002805 | 0.0 | 0.09
+Modify | 2.9085 | 2.9085 | 2.9085 | 0.0 | 96.35
+Other | | 0.02758 | | | 0.91
+
+Nlocal: 14716 ave 14716 max 14716 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 86 ave 86 max 86 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 467 ave 467 max 467 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 467
+Ave neighs/atom = 0.0317342
+Neighbor list builds = 250
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:03
diff --git a/examples/srd/log.15Feb16.srd.mixture.g++.4 b/examples/srd/log.15Feb16.srd.mixture.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..f41d3e0aaa2c21fe5fcf01dffa94719c586b4200
--- /dev/null
+++ b/examples/srd/log.15Feb16.srd.mixture.g++.4
@@ -0,0 +1,269 @@
+LAMMPS (15 Feb 2016)
+# 2d SRD test: big + small particles
+
+units lj
+atom_style sphere
+atom_modify first big
+dimension 2
+
+# create big particles with sigma 1.0
+
+lattice sq 0.4
+Lattice spacing in x,y,z = 1.58114 1.58114 1.58114
+region box block 0 10 0 10 -0.5 0.5
+create_box 2 box
+Created orthogonal box = (0 0 -0.790569) to (15.8114 15.8114 0.790569)
+ 2 by 2 by 1 MPI processor grid
+create_atoms 1 region box
+Created 100 atoms
+set type 1 mass 1.0
+ 100 settings made for mass
+set type 1 diameter 1.0
+ 100 settings made for diameter
+
+group big type 1
+100 atoms in group big
+velocity big create 1.44 87287 loop geom
+
+# equilibrate big particles
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0
+pair_coeff 2 2 0.0 1.0 0.0
+pair_coeff 1 2 0.0 1.0 0.0
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 big nve
+fix 2 all enforce2d
+
+run 1000
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4 -> bins = 12 12 2
+Memory usage per processor = 3.60121 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 -0.54272 0 0.88288 -0.041088
+ 1000 1.8791467 -0.97185784 0 0.8884974 0.61487657
+Loop time of 0.012567 on 4 procs for 1000 steps with 100 atoms
+
+Performance: 34375627.547 tau/day, 79573.212 timesteps/s
+87.5% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.001833 | 0.0021114 | 0.0025189 | 0.6 | 16.80
+Neigh | 0.00072002 | 0.00076324 | 0.0008471 | 0.2 | 6.07
+Comm | 0.0066237 | 0.0067103 | 0.0069342 | 0.2 | 53.40
+Output | 2.1935e-05 | 2.4259e-05 | 2.5988e-05 | 0.0 | 0.19
+Modify | 0.00064278 | 0.00070089 | 0.0008285 | 0.3 | 5.58
+Other | | 0.002257 | | | 17.96
+
+Nlocal: 25 ave 26 max 23 min
+Histogram: 1 0 0 0 0 0 1 0 0 2
+Nghost: 47 ave 48 max 46 min
+Histogram: 1 0 0 0 0 2 0 0 0 1
+Neighs: 114.75 ave 124 max 100 min
+Histogram: 1 0 0 0 0 1 0 0 0 2
+
+Total # of neighbors = 459
+Ave neighs/atom = 4.59
+Neighbor list builds = 129
+Dangerous builds = 0
+
+unfix 1
+unfix 2
+
+# add small particles as hi density lattice
+
+lattice sq 0.4
+Lattice spacing in x,y,z = 1.58114 1.58114 1.58114
+region plane block 0 10 0 10 -0.001 0.001
+lattice sq 85.0
+Lattice spacing in x,y,z = 0.108465 0.108465 0.108465
+create_atoms 2 region plane
+Created 21316 atoms
+set type 2 mass 0.01
+ 21316 settings made for mass
+set type 2 diameter 0.0
+ 21316 settings made for diameter
+
+group small type 2
+21316 atoms in group small
+
+velocity small create 1.0 593849 loop geom
+
+# delete overlaps
+# must set 1-2 cutoff to non-zero value
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0
+pair_coeff 2 2 0.0 1.0 0.0
+pair_coeff 1 2 0.0 1.0 0.5
+
+delete_atoms overlap 0.5 small big
+Neighbor list info ...
+ 2 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4 -> bins = 12 12 2
+WARNING: Delete_atoms cutoff > minimum neighbor cutoff (../delete_atoms.cpp:277)
+Deleted 6700 atoms, new total = 14716
+
+# SRD run
+
+reset_timestep 0
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+comm_modify mode multi group big vel yes
+neigh_modify include big
+
+# no pairwise interactions with small particles
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0
+pair_coeff 2 2 0.0 1.0 0.0
+pair_coeff 1 2 0.0 1.0 0.0
+
+# use fix SRD to push small particles out from inside big ones
+
+timestep 0.001
+
+fix 1 big nve
+fix 2 small srd 20 big 1.0 0.25 49894 radius 0.88 search 0.2 collision slip
+fix 3 all enforce2d
+
+# diagnostics
+
+compute tbig big temp
+variable pebig equal pe*atoms/count(big)
+variable ebig equal etotal*atoms/count(big)
+thermo_style custom step temp f_2[7] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[8] f_2[9] f_2[10]
+
+thermo_modify temp tbig
+WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:445)
+thermo 100
+
+#dump 1 all atom 250 dump.srd.mixture
+
+#dump 2 all image 250 image.*.jpg type type zoom 1.6
+#dump_modify 2 pad 4 adiam 1 1 adiam 2 0.2
+
+#dump 3 all movie 250 movie.mpg type type zoom 1.6
+#dump_modify 3 pad 4 adiam 1 1 adiam 2 0.2
+
+run 5000
+SRD info:
+ SRD/big particles = 14616 100
+ big particle diameter max/min = 0.88 0.88
+ SRD temperature & lamda = 1 0.2
+ SRD max distance & max velocity = 0.8 40
+ SRD grid counts: 63 63 1
+ SRD grid size: request, actual (xyz) = 0.25, 0.250974 0.250974 1.58114
+ SRD per actual grid cell = 4.86648
+ SRD viscosity = 0.463448
+ big/SRD mass density ratio = 2.12808
+WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2884)
+ # of rescaled SRD velocities = 0
+ ave/max small velocity = 13.2944 24.262
+ ave/max big velocity = 1.69284 5.10989
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4 -> bins = 12 12 2
+Memory usage per processor = 5.3246 Mbytes
+Step Temp 2[7] TotEng pebig ebig Press 2[1] 2[2] 2[3] 2[4] 2[5] 2[6] 2[8] 2[9] 2[10]
+ 0 1.8791467 0 0.0060376284 -0.97185784 0.8884974 0.61487657 0 0 0 0 0 0 0 0 0
+ 100 1.4044369 3969 0.0030633093 -0.93959598 0.4507966 0.78900119 7464 99 99 0 17 22500 3005 1.028131 0
+ 200 1.1569383 3969 0.0010543995 -0.99020352 0.15516543 0.50132981 7393 82 82 0 43 22500 2996 1.014347 0
+ 300 0.97802835 3969 -0.00019991154 -0.99766705 -0.029418982 0.35789515 7411 90 90 0 84 22500 3001 1.0213725 0
+ 400 1.0992982 3969 0.00055034756 -1.007316 0.080989146 0.35177983 7443 78 78 0 107 22500 2993 1.0451641 0
+ 500 1.0436705 3969 -7.4779704e-05 -1.0442384 -0.011004581 0.15132448 7504 94 94 0 141 22500 3007 1.0236992 0
+ 600 1.0216461 3969 -0.00032426678 -1.0591487 -0.047719099 0.2200765 7508 111 111 0 179 22500 3007 1.0304838 0
+ 700 1.1491339 3969 0.0012328743 -0.95621278 0.18142978 0.80670059 7448 95 95 0 201 22500 2978 1.0099113 0
+ 800 1.0332166 3969 -0.00040684239 -1.0827554 -0.059870926 0.35939225 7453 113 113 0 235 22500 3024 1.0141565 0
+ 900 1.0652211 3969 -6.1337025e-06 -1.0554715 -0.00090263566 0.51460169 7447 97 97 0 259 22500 2982 1.0192735 0
+ 1000 0.92834993 3969 -0.00067681883 -1.0186671 -0.09960066 0.738738 7328 78 78 0 286 22500 2999 1.023841 0
+ 1100 1.0386338 3969 -0.00018904027 -1.0560666 -0.027819166 0.57129719 7449 96 96 0 325 22500 3012 1.0373885 0
+ 1200 0.92218024 3969 -0.00077989365 -1.0277276 -0.11476915 0.48613467 7507 100 100 0 355 22500 3003 1.0254889 0
+ 1300 1.1835318 3969 0.00096836748 -1.0291915 0.14250496 0.62935386 7439 92 92 0 384 22500 2993 1.0289037 0
+ 1400 1.0895805 3969 0.00022072203 -1.0462033 0.032481455 0.49130771 7492 80 80 0 426 22500 3005 1.0083895 0
+ 1500 1.0713283 3969 0.00042008247 -0.99879571 0.061819337 0.63979877 7498 87 87 0 457 22500 3000 1.0009934 0
+ 1600 0.97815063 3969 -0.0005425653 -1.048213 -0.079843909 0.3604669 7533 105 105 0 492 22500 3004 1.0375508 0
+ 1700 1.1626991 3969 0.00048969594 -1.0790084 0.072063654 0.36261544 7493 87 87 0 519 22500 3014 1.0151507 0
+ 1800 0.91077626 3969 -0.001205934 -1.0791337 -0.17746525 0.14204132 7553 77 77 0 554 22500 3001 1.0393648 0
+ 1900 1.073632 3969 0.00048053229 -0.99218055 0.070715131 0.56468311 7660 96 96 0 579 22500 2990 1.0071005 0
+ 2000 1.0516743 3969 -0.00020689596 -1.0716044 -0.03044681 0.28030578 7561 96 96 0 631 22500 3020 1.0222307 0
+ 2100 1.141885 3969 0.00040167415 -1.0713558 0.059110368 0.32604475 7569 69 69 0 662 22500 2968 1.0125404 0
+ 2200 1.2228391 3969 0.0010327668 -1.0586288 0.15198196 0.36038619 7572 86 86 0 691 22500 2979 1.0235277 0
+ 2300 1.1087892 3969 0.00043721167 -1.0333612 0.06434007 0.39699935 7512 68 68 0 716 22500 3022 1.0515275 0
+ 2400 1.0637949 3969 0.00033715078 -1.0035418 0.049615108 0.47092535 7508 82 82 0 742 22500 2997 1.0295291 0
+ 2500 1.0345185 3969 0.00023374535 -0.98977538 0.034397966 0.57463578 7514 89 89 0 778 22500 2986 1.0252443 0
+ 2600 1.1040438 3969 0.00024293233 -1.0572534 0.035749922 0.38043986 7543 82 82 0 811 22500 2995 1.0181075 0
+ 2700 0.96252159 3969 -0.00081483156 -1.072807 -0.11991061 0.2771083 7555 97 97 0 842 22500 2990 1.0125575 0
+ 2800 0.98730039 3969 -0.00037330307 -1.0323627 -0.05493528 0.57796755 7359 88 88 0 866 22500 2981 1.0187945 0
+ 2900 1.056508 3969 0.0003868833 -0.98900914 0.056933747 0.63280739 7485 84 84 0 906 22500 3009 1.0260952 0
+ 3000 0.97367876 3969 -0.0002599408 -1.0021949 -0.038252888 0.66404419 7424 99 99 0 951 22500 2998 1.0143644 0
+ 3100 0.97186052 3969 -0.00084858744 -1.08702 -0.12487813 0.33835871 7502 88 88 0 983 22500 3016 1.0292976 0
+ 3200 0.97992936 3969 -0.0006672966 -1.0683294 -0.098199368 0.45138198 7326 72 72 0 1026 22500 3005 1.023367 0
+ 3300 0.96722828 3969 -0.00034604616 -1.0084802 -0.050924152 0.58525322 7383 70 70 0 1053 22500 2986 1.034213 0
+ 3400 1.1202892 3969 0.00043227098 -1.0454733 0.063612998 0.43718189 7364 85 85 0 1087 22500 2995 1.0158362 0
+ 3500 0.79750662 3969 -0.0014948003 -1.0095064 -0.21997481 0.41132937 7511 90 90 0 1116 22500 2993 1.0182386 0
+ 3600 1.0491778 3969 -0.00010433247 -1.0540396 -0.015353567 0.42315074 7489 95 95 0 1144 22500 2999 1.020922 0
+ 3700 0.9610381 3969 -0.00021690291 -0.98334715 -0.031919432 0.55752687 7496 80 80 0 1172 22500 3019 1.0303605 0
+ 3800 0.76471906 3969 -0.0017426239 -1.0135164 -0.25644453 0.32180761 7518 89 89 0 1213 22500 3008 1.0419804 0
+ 3900 1.086591 3969 0.00018698809 -1.0482079 0.027517167 0.26073092 7462 98 98 0 1246 22500 3005 1.0261112 0
+ 4000 0.82619819 3969 -0.0014452395 -1.0306176 -0.21268144 0.14915039 7545 98 98 0 1287 22500 3008 1.0352711 0
+ 4100 0.95064219 3969 -0.00053545528 -1.0199334 -0.0787976 0.39089361 7572 85 85 0 1318 22500 3001 1.0372179 0
+ 4200 0.90370321 3969 -0.0007185822 -1.0004127 -0.10574656 0.47384816 7460 61 61 0 1355 22500 2998 1.012362 0
+ 4300 0.97729216 3969 -0.00029144098 -1.0104077 -0.042888455 0.46030155 7533 70 70 0 1388 22500 3007 1.0223284 0
+ 4400 1.0140429 3969 4.720814e-06 -1.0032078 0.00069471498 0.55984871 7501 88 88 0 1412 22500 2995 1.0285533 0
+ 4500 1.0498677 3969 0.00022703142 -1.0059591 0.033409944 0.61932234 7461 82 82 0 1442 22500 2994 1.0292131 0
+ 4600 0.90182406 3969 -0.00092157839 -1.0284253 -0.13561948 0.59198635 7499 73 73 0 1483 22500 3020 1.0159894 0
+ 4700 1.0138009 3969 -0.00028404538 -1.045463 -0.041800118 0.53428422 7407 78 78 0 1507 22500 3011 1.0058816 0
+ 4800 1.0506575 3969 -0.00043345499 -1.1039381 -0.063787236 0.30643257 7543 87 87 0 1524 22500 2995 1.0210242 0
+ 4900 1.1479137 3969 -0.00019383126 -1.1649587 -0.028524208 0.28842185 7416 91 91 0 1557 22500 2988 1.0063463 0
+ 5000 0.9092746 3969 -0.00087214131 -1.0285262 -0.12834432 0.76635862 7389 85 85 0 1589 22500 3000 1.0157079 0
+Loop time of 0.924227 on 4 procs for 5000 steps with 14716 atoms
+
+Performance: 467417.396 tau/day, 5409.924 timesteps/s
+99.0% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0083485 | 0.011347 | 0.01386 | 1.9 | 1.23
+Neigh | 0.0014212 | 0.0017646 | 0.0020251 | 0.5 | 0.19
+Comm | 0.065314 | 0.072466 | 0.078769 | 2.0 | 7.84
+Output | 0.0028164 | 0.0031637 | 0.0035689 | 0.5 | 0.34
+Modify | 0.73464 | 0.78282 | 0.81577 | 3.4 | 84.70
+Other | | 0.05267 | | | 5.70
+
+Nlocal: 3679 ave 4013 max 3459 min
+Histogram: 1 0 1 1 0 0 0 0 0 1
+Nghost: 48.25 ave 54 max 44 min
+Histogram: 1 0 1 0 0 1 0 0 0 1
+Neighs: 117 ave 136 max 87 min
+Histogram: 1 0 0 0 0 0 1 1 0 1
+
+Total # of neighbors = 468
+Ave neighs/atom = 0.0318021
+Neighbor list builds = 250
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:01
diff --git a/examples/srd/log.15Feb16.srd.pure.g++.1 b/examples/srd/log.15Feb16.srd.pure.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..a33c1c7903763a1c636a4d44bd997c2438ae6734
--- /dev/null
+++ b/examples/srd/log.15Feb16.srd.pure.g++.1
@@ -0,0 +1,163 @@
+LAMMPS (15 Feb 2016)
+# 2d SRD only test
+
+units lj
+atom_style atomic
+atom_modify first empty
+dimension 2
+
+# create box with big lattice
+
+lattice sq 0.4
+Lattice spacing in x,y,z = 1.58114 1.58114 1.58114
+region box block 0 10 0 10 -0.5 0.5
+create_box 1 box
+Created orthogonal box = (0 0 -0.790569) to (15.8114 15.8114 0.790569)
+ 1 by 1 by 1 MPI processor grid
+
+# add SRD particles as hi density lattice
+
+lattice sq 0.4
+Lattice spacing in x,y,z = 1.58114 1.58114 1.58114
+region plane block 0 10 0 10 -0.001 0.001
+lattice sq 85.0
+Lattice spacing in x,y,z = 0.108465 0.108465 0.108465
+create_atoms 1 region plane
+Created 21316 atoms
+
+group empty type 2
+0 atoms in group empty
+
+mass 1 0.01
+velocity all create 1.0 593849 loop geom
+
+# settings - need dummy empty group to enable no communication
+
+neighbor 0.3 bin
+neigh_modify delay 1 every 1 check no
+
+comm_modify group empty
+
+# timestep is big and SRD frequency is 1
+
+timestep 0.02
+
+fix 1 all srd 1 NULL 1.0 0.25 49894 collision slip
+fix 2 all enforce2d
+
+# diagnostics
+
+thermo_style custom step temp f_1[7] etotal press f_1[3] f_1[4] f_1[6]
+thermo 100
+
+#dump 1 all atom 250 dump.srd.pure
+
+#dump 2 all image 250 image.*.jpg type type zoom 1.6 adiam 0.2
+#dump_modify 2 pad 4
+
+#dump 3 all movie 250 movie.mpg type type zoom 1.6 adiam 0.2
+#dump_modify 3 pad 4
+
+run 5000
+SRD info:
+ SRD/big particles = 21316 0
+ big particle diameter max/min = 0 1e+20
+ SRD temperature & lamda = 1 0.2
+ SRD max distance & max velocity = 0.8 40
+ SRD grid counts: 63 63 1
+ SRD grid size: request, actual (xyz) = 0.25, 0.250974 0.250974 1.58114
+ SRD per actual grid cell = 5.37062
+ SRD viscosity = 0.439647
+ big/SRD mass density ratio = 0
+ # of rescaled SRD velocities = 0
+ ave/max all velocity = 13.2735 24.2873
+Neighbor list info ...
+ 0 neighbor list requests
+ update every 1 steps, delay 1 steps, check no
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 0
+ ghost atom cutoff = 0
+ binsize = 15.8114 -> bins = 1 1 1
+Memory usage per processor = 5.16355 Mbytes
+Step Temp 1[7] TotEng Press 1[3] 1[4] 1[6]
+ 0 1 0 0.99995309 85.26 0 0 0
+ 100 0.97820615 3969 0.97816026 83.401857 0 0 0
+ 200 0.9609326 3969 0.96088752 81.929113 0 0 0
+ 300 0.94460302 3969 0.9445587 80.536853 0 0 0
+ 400 0.93098293 3969 0.93093925 79.375605 0 0 0
+ 500 0.91803208 3969 0.91798901 78.271415 0 0 0
+ 600 0.90779378 3969 0.90775119 77.398497 0 0 0
+ 700 0.89695247 3969 0.89691039 76.474168 0 0 0
+ 800 0.88637078 3969 0.88632919 75.571972 0 0 0
+ 900 0.87833669 3969 0.87829548 74.886986 0 0 0
+ 1000 0.87030089 3969 0.87026006 74.201854 0 0 0
+ 1100 0.86318709 3969 0.86314659 73.595331 0 0 0
+ 1200 0.85736665 3969 0.85732643 73.099081 0 0 0
+ 1300 0.85147901 3969 0.85143906 72.5971 0 0 0
+ 1400 0.84496088 3969 0.84492124 72.041365 0 0 0
+ 1500 0.83857476 3969 0.83853542 71.496884 0 0 0
+ 1600 0.8336916 3969 0.83365249 71.080546 0 0 0
+ 1700 0.82954371 3969 0.8295048 70.726897 0 0 0
+ 1800 0.82570979 3969 0.82567105 70.400016 0 0 0
+ 1900 0.82189413 3969 0.82185557 70.074693 0 0 0
+ 2000 0.81818525 3969 0.81814687 69.758475 0 0 0
+ 2100 0.81436257 3969 0.81432436 69.432552 0 0 0
+ 2200 0.80997949 3969 0.80994149 69.058851 0 0 0
+ 2300 0.80685831 3969 0.80682045 68.792739 0 0 0
+ 2400 0.80374622 3969 0.80370851 68.527402 0 0 0
+ 2500 0.80103773 3969 0.80100015 68.296477 0 0 0
+ 2600 0.79858358 3969 0.79854611 68.087236 0 0 0
+ 2700 0.79617295 3969 0.7961356 67.881706 0 0 0
+ 2800 0.79312496 3969 0.79308775 67.621834 0 0 0
+ 2900 0.79126456 3969 0.79122744 67.463216 0 0 0
+ 3000 0.78897033 3969 0.78893331 67.26761 0 0 0
+ 3100 0.78632296 3969 0.78628607 67.041895 0 0 0
+ 3200 0.78442284 3969 0.78438604 66.879892 0 0 0
+ 3300 0.78168316 3969 0.78164649 66.646306 0 0 0
+ 3400 0.7788658 3969 0.77882926 66.406098 0 0 0
+ 3500 0.77703408 3969 0.77699762 66.249925 0 0 0
+ 3600 0.77441139 3969 0.77437506 66.026315 0 0 0
+ 3700 0.7723528 3969 0.77231656 65.850799 0 0 0
+ 3800 0.77019626 3969 0.77016013 65.666933 0 0 0
+ 3900 0.76835687 3969 0.76832082 65.510107 0 0 0
+ 4000 0.76701071 3969 0.76697473 65.395333 0 0 0
+ 4100 0.76552115 3969 0.76548523 65.268333 0 0 0
+ 4200 0.76360426 3969 0.76356843 65.104899 0 0 0
+ 4300 0.76173186 3969 0.76169613 64.945259 0 0 0
+ 4400 0.75933463 3969 0.759299 64.74087 0 0 0
+ 4500 0.75806391 3969 0.75802835 64.632529 0 0 0
+ 4600 0.75692832 3969 0.75689281 64.535709 0 0 0
+ 4700 0.75569109 3969 0.75565564 64.430222 0 0 0
+ 4800 0.75446697 3969 0.75443157 64.325854 0 0 0
+ 4900 0.75276753 3969 0.75273221 64.180959 0 0 0
+ 5000 0.75113693 3969 0.75110169 64.041935 0 0 0
+Loop time of 7.49986 on 1 procs for 5000 steps with 21316 atoms
+
+Performance: 1152022.120 tau/day, 666.679 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0.0010734 | 0.0010734 | 0.0010734 | 0.0 | 0.01
+Comm | 0.39384 | 0.39384 | 0.39384 | 0.0 | 5.25
+Output | 0.0039084 | 0.0039084 | 0.0039084 | 0.0 | 0.05
+Modify | 6.4261 | 6.4261 | 6.4261 | 0.0 | 85.68
+Other | | 0.6749 | | | 9.00
+
+Nlocal: 21316 ave 21316 max 21316 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 5000
+Dangerous builds not checked
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:07
diff --git a/examples/srd/log.15Feb16.srd.pure.g++.4 b/examples/srd/log.15Feb16.srd.pure.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..67a86b20fe23fee0e48cc802384175e57d2230ae
--- /dev/null
+++ b/examples/srd/log.15Feb16.srd.pure.g++.4
@@ -0,0 +1,163 @@
+LAMMPS (15 Feb 2016)
+# 2d SRD only test
+
+units lj
+atom_style atomic
+atom_modify first empty
+dimension 2
+
+# create box with big lattice
+
+lattice sq 0.4
+Lattice spacing in x,y,z = 1.58114 1.58114 1.58114
+region box block 0 10 0 10 -0.5 0.5
+create_box 1 box
+Created orthogonal box = (0 0 -0.790569) to (15.8114 15.8114 0.790569)
+ 2 by 2 by 1 MPI processor grid
+
+# add SRD particles as hi density lattice
+
+lattice sq 0.4
+Lattice spacing in x,y,z = 1.58114 1.58114 1.58114
+region plane block 0 10 0 10 -0.001 0.001
+lattice sq 85.0
+Lattice spacing in x,y,z = 0.108465 0.108465 0.108465
+create_atoms 1 region plane
+Created 21316 atoms
+
+group empty type 2
+0 atoms in group empty
+
+mass 1 0.01
+velocity all create 1.0 593849 loop geom
+
+# settings - need dummy empty group to enable no communication
+
+neighbor 0.3 bin
+neigh_modify delay 1 every 1 check no
+
+comm_modify group empty
+
+# timestep is big and SRD frequency is 1
+
+timestep 0.02
+
+fix 1 all srd 1 NULL 1.0 0.25 49894 collision slip
+fix 2 all enforce2d
+
+# diagnostics
+
+thermo_style custom step temp f_1[7] etotal press f_1[3] f_1[4] f_1[6]
+thermo 100
+
+#dump 1 all atom 250 dump.srd.pure
+
+#dump 2 all image 250 image.*.jpg type type zoom 1.6 adiam 0.2
+#dump_modify 2 pad 4
+
+#dump 3 all movie 250 movie.mpg type type zoom 1.6 adiam 0.2
+#dump_modify 3 pad 4
+
+run 5000
+SRD info:
+ SRD/big particles = 21316 0
+ big particle diameter max/min = 0 1e+20
+ SRD temperature & lamda = 1 0.2
+ SRD max distance & max velocity = 0.8 40
+ SRD grid counts: 63 63 1
+ SRD grid size: request, actual (xyz) = 0.25, 0.250974 0.250974 1.58114
+ SRD per actual grid cell = 5.37062
+ SRD viscosity = 0.439647
+ big/SRD mass density ratio = 0
+ # of rescaled SRD velocities = 0
+ ave/max all velocity = 13.2735 24.2873
+Neighbor list info ...
+ 0 neighbor list requests
+ update every 1 steps, delay 1 steps, check no
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 0
+ ghost atom cutoff = 0
+ binsize = 15.8114 -> bins = 1 1 1
+Memory usage per processor = 2.29814 Mbytes
+Step Temp 1[7] TotEng Press 1[3] 1[4] 1[6]
+ 0 1 0 0.99995309 85.26 0 0 0
+ 100 0.97718565 3969 0.97713981 83.314849 0 0 0
+ 200 0.95953504 3969 0.95949002 81.809957 0 0 0
+ 300 0.94384163 3969 0.94379735 80.471937 0 0 0
+ 400 0.93018267 3969 0.93013903 79.307374 0 0 0
+ 500 0.9189656 3969 0.91892248 78.351007 0 0 0
+ 600 0.90794939 3969 0.9079068 77.411765 0 0 0
+ 700 0.899123 3969 0.89908081 76.659227 0 0 0
+ 800 0.89045828 3969 0.89041651 75.920473 0 0 0
+ 900 0.88189664 3969 0.88185527 75.190507 0 0 0
+ 1000 0.87511065 3969 0.87506959 74.611934 0 0 0
+ 1100 0.86844868 3969 0.86840794 74.043934 0 0 0
+ 1200 0.86236759 3969 0.86232713 73.52546 0 0 0
+ 1300 0.85644064 3969 0.85640047 73.020129 0 0 0
+ 1400 0.85088468 3969 0.85084476 72.546428 0 0 0
+ 1500 0.84573938 3969 0.8456997 72.107739 0 0 0
+ 1600 0.84169541 3969 0.84165592 71.76295 0 0 0
+ 1700 0.83686816 3969 0.8368289 71.351379 0 0 0
+ 1800 0.83199161 3969 0.83195258 70.935605 0 0 0
+ 1900 0.82774228 3969 0.82770345 70.573307 0 0 0
+ 2000 0.82446049 3969 0.82442181 70.293501 0 0 0
+ 2100 0.82065145 3969 0.82061295 69.968743 0 0 0
+ 2200 0.81761922 3969 0.81758087 69.710215 0 0 0
+ 2300 0.81355286 3969 0.8135147 69.363517 0 0 0
+ 2400 0.81040375 3969 0.81036573 69.095024 0 0 0
+ 2500 0.80651947 3969 0.80648164 68.76385 0 0 0
+ 2600 0.80304949 3969 0.80301181 68.467999 0 0 0
+ 2700 0.80027966 3969 0.80024211 68.231843 0 0 0
+ 2800 0.79726989 3969 0.79723248 67.97523 0 0 0
+ 2900 0.79526953 3969 0.79523222 67.80468 0 0 0
+ 3000 0.79213985 3969 0.79210268 67.537843 0 0 0
+ 3100 0.79008514 3969 0.79004808 67.362659 0 0 0
+ 3200 0.78760949 3969 0.78757254 67.151585 0 0 0
+ 3300 0.78482758 3969 0.78479077 66.9144 0 0 0
+ 3400 0.78225219 3969 0.7822155 66.694822 0 0 0
+ 3500 0.78019518 3969 0.78015858 66.519441 0 0 0
+ 3600 0.7782201 3969 0.77818359 66.351045 0 0 0
+ 3700 0.77626555 3969 0.77622913 66.184401 0 0 0
+ 3800 0.77429464 3969 0.77425832 66.016361 0 0 0
+ 3900 0.7728635 3969 0.77282724 65.894342 0 0 0
+ 4000 0.7712408 3969 0.77120462 65.75599 0 0 0
+ 4100 0.76928811 3969 0.76925202 65.589504 0 0 0
+ 4200 0.76768117 3969 0.76764516 65.452497 0 0 0
+ 4300 0.76576395 3969 0.76572802 65.289034 0 0 0
+ 4400 0.76375476 3969 0.76371893 65.117731 0 0 0
+ 4500 0.76222055 3969 0.76218479 64.986924 0 0 0
+ 4600 0.76007803 3969 0.76004237 64.804252 0 0 0
+ 4700 0.75921155 3969 0.75917594 64.730377 0 0 0
+ 4800 0.75699084 3969 0.75695533 64.541039 0 0 0
+ 4900 0.75590428 3969 0.75586882 64.448399 0 0 0
+ 5000 0.75435525 3969 0.75431986 64.316328 0 0 0
+Loop time of 1.79922 on 4 procs for 5000 steps with 21316 atoms
+
+Performance: 4802076.856 tau/day, 2778.980 timesteps/s
+99.6% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0.0014281 | 0.0015157 | 0.001564 | 0.1 | 0.08
+Comm | 0.23789 | 0.24253 | 0.25126 | 1.1 | 13.48
+Output | 0.0022333 | 0.0023788 | 0.0027263 | 0.4 | 0.13
+Modify | 1.37 | 1.3762 | 1.3788 | 0.3 | 76.49
+Other | | 0.1766 | | | 9.82
+
+Nlocal: 5329 ave 5410 max 5266 min
+Histogram: 1 0 0 2 0 0 0 0 0 1
+Nghost: 0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 5000
+Dangerous builds not checked
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:01
diff --git a/examples/streitz/log.15Feb16.streitz.ewald.g++.1 b/examples/streitz/log.15Feb16.streitz.ewald.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..87e7a660a9764d8ce7bf2f84a93094f3bf8dc225
--- /dev/null
+++ b/examples/streitz/log.15Feb16.streitz.ewald.g++.1
@@ -0,0 +1,118 @@
+LAMMPS (15 Feb 2016)
+# Streitz-Mintmire potential with alpha-alumina
+# option to use with Ewald or Wolf sum
+# EAM (AlO.eam.alloy) includes 1994 SM and 2004 Zhou versions
+# Streitz Mintmire (coul/streitz) does not include 2004 Zhou modifications
+# Contributing authors: Ray Shan, Chris Weinberger (Sandia)
+
+units metal
+atom_style charge
+dimension 3
+boundary p p p
+
+read_data data.streitz
+ orthogonal box = (0 0 0) to (24.7337 28.56 25.9798)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 2160 atoms
+
+group type1 type 1
+864 atoms in group type1
+compute charge1 type1 property/atom q
+compute q1 type1 reduce ave c_charge1
+group type2 type 2
+1296 atoms in group type2
+compute charge2 type2 property/atom q
+compute q2 type2 reduce ave c_charge2
+
+variable qcat equal 2.8
+variable qani equal -${qcat}*count(type1)/count(type2)
+variable qani equal -2.8*count(type1)/count(type2)
+set group type1 charge ${qcat}
+set group type1 charge 2.8
+ 864 settings made for charge
+set group type2 charge ${qani}
+set group type2 charge -1.86666666666667
+ 1296 settings made for charge
+variable qsum equal count(type1)*c_q1+count(type2)*c_q2
+
+# Ewald sum for coul/streitz
+pair_style hybrid/overlay coul/streitz 12.0 ewald eam/alloy
+kspace_style ewald 1e-6
+
+# Wolf sum for coul/streitz
+#pair_style hybrid/overlay coul/streitz 12.0 wolf 0.31 eam/alloy
+
+pair_coeff * * coul/streitz AlO.streitz Al O
+pair_coeff * * eam/alloy AlO.eam.alloy Al O
+Reading potential file AlO.eam.alloy with DATE: 2015-02-19
+
+neighbor 1.0 bin
+neigh_modify every 10 delay 0 check yes
+timestep 0.0004
+
+thermo_style custom step temp etotal pe evdwl ecoul elong c_q1 c_q2 v_qsum press spcpu
+thermo_modify norm yes
+thermo 10
+
+velocity all create 300.0 42128
+fix 1 all qeq/slater 1 12.0 1.0e-6 100 coul/streitz
+fix 2 all nve
+
+run 100
+Ewald initialization ...
+ G vector (1/distance) = 0.310132
+ estimated absolute RMS force accuracy = 1.9688e-05
+ estimated relative force accuracy = 1.36725e-06
+ KSpace vectors: actual max1d max3d = 2541 11 6083
+ kxmax kymax kzmax = 10 11 10
+Neighbor list info ...
+ 3 neighbor list requests
+ update every 10 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 13
+ ghost atom cutoff = 13
+ binsize = 6.5 -> bins = 4 5 4
+Memory usage per processor = 45.932 Mbytes
+Step Temp TotEng PotEng E_vdwl E_coul E_long q1 q2 qsum Press S/CPU
+ 0 300 -6.3402658 -6.3790259 -2.7952901 10.218189 -13.801924 2.8665317 -1.9110211 2.7284841e-12 -26072.585 0
+ 10 272.45428 -6.340306 -6.3755071 -2.790294 10.191122 -13.776335 2.8636996 -1.9091331 4.5474735e-13 -21774.211 0.98299564
+ 20 219.94294 -6.3402438 -6.3686605 -2.7790335 10.192017 -13.781644 2.8638745 -1.9092497 1.3642421e-12 -16693.959 1.0766305
+ 30 179.36108 -6.3401905 -6.363364 -2.7689124 10.190565 -13.785017 2.8639191 -1.9092794 1.0004442e-11 -12974.154 1.0788526
+ 40 162.68484 -6.340179 -6.3611979 -2.7652026 10.173296 -13.769291 2.8621763 -1.9081175 -3.6379788e-12 -12735.477 1.0766815
+ 50 152.76246 -6.3401898 -6.3599268 -2.7673924 10.132267 -13.724802 2.8575298 -1.9050198 6.3664629e-12 -14532.643 1.0788532
+ 60 138.38061 -6.340206 -6.3580848 -2.7714511 10.085334 -13.671967 2.8519579 -1.9013053 3.1832315e-12 -15656.278 1.0783423
+ 70 134.9572 -6.3401907 -6.3576272 -2.7740776 10.063528 -13.647077 2.849277 -1.899518 -2.7284841e-12 -14160.692 1.080689
+ 80 161.55083 -6.3401305 -6.3610029 -2.7741365 10.086552 -13.673419 2.8520585 -1.9013723 1.8189894e-12 -9666.5838 1.0803586
+ 90 207.33012 -6.3400321 -6.3668192 -2.7713864 10.144722 -13.740155 2.8591984 -1.9061323 -3.1832315e-12 -2530.8605 1.080603
+ 100 233.80619 -6.3399378 -6.3701456 -2.7659477 10.207141 -13.811339 2.8668083 -1.9112055 9.094947e-13 6120.857 1.0744946
+Loop time of 93.6311 on 1 procs for 100 steps with 2160 atoms
+
+Performance: 0.037 ns/day, 650.216 hours/ns, 1.068 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 40.728 | 40.728 | 40.728 | 0.0 | 43.50
+Kspace | 4.7191 | 4.7191 | 4.7191 | 0.0 | 5.04
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.010949 | 0.010949 | 0.010949 | 0.0 | 0.01
+Output | 0.00077391 | 0.00077391 | 0.00077391 | 0.0 | 0.00
+Modify | 48.171 | 48.171 | 48.171 | 0.0 | 51.45
+Other | | 0.002255 | | | 0.00
+
+Nlocal: 2160 ave 2160 max 2160 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 14994 ave 14994 max 14994 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 1.17893e+06 ave 1.17893e+06 max 1.17893e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs: 2.35786e+06 ave 2.35786e+06 max 2.35786e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 2357856
+Ave neighs/atom = 1091.6
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:01:34
diff --git a/examples/streitz/log.15Feb16.streitz.ewald.g++.4 b/examples/streitz/log.15Feb16.streitz.ewald.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..1fa646bb0877e4d4857676d599e9bd691a562ce2
--- /dev/null
+++ b/examples/streitz/log.15Feb16.streitz.ewald.g++.4
@@ -0,0 +1,118 @@
+LAMMPS (15 Feb 2016)
+# Streitz-Mintmire potential with alpha-alumina
+# option to use with Ewald or Wolf sum
+# EAM (AlO.eam.alloy) includes 1994 SM and 2004 Zhou versions
+# Streitz Mintmire (coul/streitz) does not include 2004 Zhou modifications
+# Contributing authors: Ray Shan, Chris Weinberger (Sandia)
+
+units metal
+atom_style charge
+dimension 3
+boundary p p p
+
+read_data data.streitz
+ orthogonal box = (0 0 0) to (24.7337 28.56 25.9798)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 2160 atoms
+
+group type1 type 1
+864 atoms in group type1
+compute charge1 type1 property/atom q
+compute q1 type1 reduce ave c_charge1
+group type2 type 2
+1296 atoms in group type2
+compute charge2 type2 property/atom q
+compute q2 type2 reduce ave c_charge2
+
+variable qcat equal 2.8
+variable qani equal -${qcat}*count(type1)/count(type2)
+variable qani equal -2.8*count(type1)/count(type2)
+set group type1 charge ${qcat}
+set group type1 charge 2.8
+ 864 settings made for charge
+set group type2 charge ${qani}
+set group type2 charge -1.86666666666667
+ 1296 settings made for charge
+variable qsum equal count(type1)*c_q1+count(type2)*c_q2
+
+# Ewald sum for coul/streitz
+pair_style hybrid/overlay coul/streitz 12.0 ewald eam/alloy
+kspace_style ewald 1e-6
+
+# Wolf sum for coul/streitz
+#pair_style hybrid/overlay coul/streitz 12.0 wolf 0.31 eam/alloy
+
+pair_coeff * * coul/streitz AlO.streitz Al O
+pair_coeff * * eam/alloy AlO.eam.alloy Al O
+Reading potential file AlO.eam.alloy with DATE: 2015-02-19
+
+neighbor 1.0 bin
+neigh_modify every 10 delay 0 check yes
+timestep 0.0004
+
+thermo_style custom step temp etotal pe evdwl ecoul elong c_q1 c_q2 v_qsum press spcpu
+thermo_modify norm yes
+thermo 10
+
+velocity all create 300.0 42128
+fix 1 all qeq/slater 1 12.0 1.0e-6 100 coul/streitz
+fix 2 all nve
+
+run 100
+Ewald initialization ...
+ G vector (1/distance) = 0.310132
+ estimated absolute RMS force accuracy = 1.9688e-05
+ estimated relative force accuracy = 1.36725e-06
+ KSpace vectors: actual max1d max3d = 2541 11 6083
+ kxmax kymax kzmax = 10 11 10
+Neighbor list info ...
+ 3 neighbor list requests
+ update every 10 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 13
+ ghost atom cutoff = 13
+ binsize = 6.5 -> bins = 4 5 4
+Memory usage per processor = 14.8576 Mbytes
+Step Temp TotEng PotEng E_vdwl E_coul E_long q1 q2 qsum Press S/CPU
+ 0 300 -6.3402658 -6.3790259 -2.7952901 10.218189 -13.801925 2.8665317 -1.9110211 4.5474735e-13 -26072.6 0
+ 10 272.45429 -6.340306 -6.3755071 -2.790294 10.191122 -13.776335 2.8636996 -1.9091331 4.5474735e-13 -21774.214 3.8580722
+ 20 219.94295 -6.3402438 -6.3686605 -2.7790335 10.192018 -13.781645 2.8638746 -1.9092497 -4.5474735e-13 -16694.015 4.0670146
+ 30 179.36109 -6.3401905 -6.363364 -2.7689124 10.190566 -13.785018 2.8639192 -1.9092795 9.094947e-13 -12974.238 4.0378837
+ 40 162.68485 -6.340179 -6.3611979 -2.7652026 10.173296 -13.769291 2.8621763 -1.9081175 -4.5474735e-13 -12735.472 4.0162158
+ 50 152.76249 -6.3401898 -6.3599268 -2.7673924 10.132267 -13.724801 2.8575297 -1.9050198 4.5474735e-13 -14532.583 4.1665957
+ 60 138.38062 -6.340206 -6.3580848 -2.7714511 10.085334 -13.671968 2.851958 -1.9013053 4.5474735e-13 -15656.298 4.1164274
+ 70 134.9572 -6.3401907 -6.3576272 -2.7740776 10.063527 -13.647077 2.8492769 -1.8995179 -1.3642421e-12 -14160.655 4.1602701
+ 80 161.55082 -6.3401305 -6.3610029 -2.7741365 10.086553 -13.673419 2.8520585 -1.9013723 0 -9666.5793 4.0929794
+ 90 207.3301 -6.3400321 -6.3668192 -2.7713864 10.144722 -13.740155 2.8591985 -1.9061323 0 -2530.8682 4.1414557
+ 100 233.80619 -6.3399378 -6.3701456 -2.7659477 10.207141 -13.811339 2.8668082 -1.9112055 -4.5474735e-13 6120.8881 4.0358738
+Loop time of 24.5859 on 4 procs for 100 steps with 2160 atoms
+
+Performance: 0.141 ns/day, 170.735 hours/ns, 4.067 timesteps/s
+99.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 10.584 | 10.594 | 10.604 | 0.2 | 43.09
+Kspace | 1.2174 | 1.2284 | 1.2348 | 0.6 | 5.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.030463 | 0.044712 | 0.054575 | 4.4 | 0.18
+Output | 0.00080562 | 0.00086939 | 0.00099111 | 0.3 | 0.00
+Modify | 12.716 | 12.716 | 12.716 | 0.0 | 51.72
+Other | | 0.001631 | | | 0.01
+
+Nlocal: 540 ave 540 max 540 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost: 8994 ave 8994 max 8994 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs: 294732 ave 294732 max 294732 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs: 589464 ave 589464 max 589464 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 2357856
+Ave neighs/atom = 1091.6
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:24
diff --git a/examples/streitz/log.15Feb16.streitz.wolf.g++.1 b/examples/streitz/log.15Feb16.streitz.wolf.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..1f299d7cf15bbee184e6f8519845b9107b388a2e
--- /dev/null
+++ b/examples/streitz/log.15Feb16.streitz.wolf.g++.1
@@ -0,0 +1,111 @@
+LAMMPS (15 Feb 2016)
+# Streitz-Mintmire potential with alpha-alumina
+# option to use with Ewald or Wolf sum
+# EAM (AlO.eam.alloy) includes 1994 SM and 2004 Zhou versions
+# Streitz Mintmire (coul/streitz) does not include 2004 Zhou modifications
+# Contributing authors: Ray Shan, Chris Weinberger (Sandia)
+
+units metal
+atom_style charge
+dimension 3
+boundary p p p
+
+read_data data.streitz
+ orthogonal box = (0 0 0) to (24.7337 28.56 25.9798)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 2160 atoms
+
+group type1 type 1
+864 atoms in group type1
+compute charge1 type1 property/atom q
+compute q1 type1 reduce ave c_charge1
+group type2 type 2
+1296 atoms in group type2
+compute charge2 type2 property/atom q
+compute q2 type2 reduce ave c_charge2
+
+variable qcat equal 2.8
+variable qani equal -${qcat}*count(type1)/count(type2)
+variable qani equal -2.8*count(type1)/count(type2)
+set group type1 charge ${qcat}
+set group type1 charge 2.8
+ 864 settings made for charge
+set group type2 charge ${qani}
+set group type2 charge -1.86666666666667
+ 1296 settings made for charge
+variable qsum equal count(type1)*c_q1+count(type2)*c_q2
+
+# Ewald sum for coul/streitz
+#pair_style hybrid/overlay coul/streitz 12.0 ewald eam/alloy
+#kspace_style ewald 1e-6
+
+# Wolf sum for coul/streitz
+pair_style hybrid/overlay coul/streitz 12.0 wolf 0.31 eam/alloy
+
+pair_coeff * * coul/streitz AlO.streitz Al O
+pair_coeff * * eam/alloy AlO.eam.alloy Al O
+Reading potential file AlO.eam.alloy with DATE: 2015-02-19
+
+neighbor 1.0 bin
+neigh_modify every 10 delay 0 check yes
+timestep 0.0004
+
+thermo_style custom step temp etotal pe evdwl ecoul elong c_q1 c_q2 v_qsum press spcpu
+thermo_modify norm yes
+thermo 10
+
+velocity all create 300.0 42128
+fix 1 all qeq/slater 1 12.0 1.0e-6 100 coul/streitz
+fix 2 all nve
+
+run 100
+Neighbor list info ...
+ 3 neighbor list requests
+ update every 10 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 13
+ ghost atom cutoff = 13
+ binsize = 6.5 -> bins = 4 5 4
+Memory usage per processor = 42.889 Mbytes
+Step Temp TotEng PotEng E_vdwl E_coul E_long q1 q2 qsum Press S/CPU
+ 0 300 -6.3403863 -6.3791464 -2.7952901 -3.5838563 0 2.8665317 -1.9110211 2.7284841e-12 -25874.942 0
+ 10 272.66671 -6.3403993 -6.375628 -2.7902909 -3.5853371 0 2.8636914 -1.9091276 -5.9117156e-12 -21564.556 0.78738346
+ 20 220.54622 -6.3402616 -6.3687562 -2.7790072 -3.589749 0 2.863852 -1.9092346 -2.7284841e-12 -16449.483 0.84086461
+ 30 180.22122 -6.3401053 -6.36339 -2.768798 -3.5945919 0 2.8639472 -1.9092981 -4.0927262e-12 -12688.515 0.84560968
+ 40 163.64074 -6.3399908 -6.3611332 -2.7648763 -3.5962569 0 2.8623043 -1.9082029 5.9117156e-12 -12334.208 0.86431685
+ 50 153.73808 -6.3399173 -6.3597803 -2.7667004 -3.5930799 0 2.8578231 -1.9052154 -1.3642421e-12 -13908.747 0.86273946
+ 60 139.1264 -6.3398818 -6.357857 -2.7702921 -3.5875649 0 2.8524119 -1.9016079 -2.7284841e-12 -14717.564 0.85607122
+ 70 134.93296 -6.3398533 -6.3572867 -2.7724725 -3.5848142 0 2.849924 -1.8999493 4.5474735e-13 -12982.145 0.8507753
+ 80 160.3429 -6.3398152 -6.3605315 -2.7722306 -3.5883009 0 2.8528608 -1.9019072 9.094947e-13 -8388.9494 0.86675264
+ 90 205.15419 -6.3397713 -6.3662773 -2.7693832 -3.596894 0 2.8599384 -1.9066256 -9.094947e-13 -1208.0269 0.86326407
+ 100 231.50843 -6.339741 -6.369652 -2.7640167 -3.6056353 0 2.8675277 -1.9116851 -1.8189894e-12 7331.3742 0.85574508
+Loop time of 117.822 on 1 procs for 100 steps with 2160 atoms
+
+Performance: 0.029 ns/day, 818.206 hours/ns, 0.849 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 69.35 | 69.35 | 69.35 | 0.0 | 58.86
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.011168 | 0.011168 | 0.011168 | 0.0 | 0.01
+Output | 0.00075531 | 0.00075531 | 0.00075531 | 0.0 | 0.00
+Modify | 48.457 | 48.457 | 48.457 | 0.0 | 41.13
+Other | | 0.002336 | | | 0.00
+
+Nlocal: 2160 ave 2160 max 2160 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 14994 ave 14994 max 14994 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 1.17893e+06 ave 1.17893e+06 max 1.17893e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs: 2.35786e+06 ave 2.35786e+06 max 2.35786e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 2357856
+Ave neighs/atom = 1091.6
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:01:59
diff --git a/examples/streitz/log.15Feb16.streitz.wolf.g++.4 b/examples/streitz/log.15Feb16.streitz.wolf.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..89d93fac715c6aa18254603d991726097dce71ae
--- /dev/null
+++ b/examples/streitz/log.15Feb16.streitz.wolf.g++.4
@@ -0,0 +1,111 @@
+LAMMPS (15 Feb 2016)
+# Streitz-Mintmire potential with alpha-alumina
+# option to use with Ewald or Wolf sum
+# EAM (AlO.eam.alloy) includes 1994 SM and 2004 Zhou versions
+# Streitz Mintmire (coul/streitz) does not include 2004 Zhou modifications
+# Contributing authors: Ray Shan, Chris Weinberger (Sandia)
+
+units metal
+atom_style charge
+dimension 3
+boundary p p p
+
+read_data data.streitz
+ orthogonal box = (0 0 0) to (24.7337 28.56 25.9798)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 2160 atoms
+
+group type1 type 1
+864 atoms in group type1
+compute charge1 type1 property/atom q
+compute q1 type1 reduce ave c_charge1
+group type2 type 2
+1296 atoms in group type2
+compute charge2 type2 property/atom q
+compute q2 type2 reduce ave c_charge2
+
+variable qcat equal 2.8
+variable qani equal -${qcat}*count(type1)/count(type2)
+variable qani equal -2.8*count(type1)/count(type2)
+set group type1 charge ${qcat}
+set group type1 charge 2.8
+ 864 settings made for charge
+set group type2 charge ${qani}
+set group type2 charge -1.86666666666667
+ 1296 settings made for charge
+variable qsum equal count(type1)*c_q1+count(type2)*c_q2
+
+# Ewald sum for coul/streitz
+#pair_style hybrid/overlay coul/streitz 12.0 ewald eam/alloy
+#kspace_style ewald 1e-6
+
+# Wolf sum for coul/streitz
+pair_style hybrid/overlay coul/streitz 12.0 wolf 0.31 eam/alloy
+
+pair_coeff * * coul/streitz AlO.streitz Al O
+pair_coeff * * eam/alloy AlO.eam.alloy Al O
+Reading potential file AlO.eam.alloy with DATE: 2015-02-19
+
+neighbor 1.0 bin
+neigh_modify every 10 delay 0 check yes
+timestep 0.0004
+
+thermo_style custom step temp etotal pe evdwl ecoul elong c_q1 c_q2 v_qsum press spcpu
+thermo_modify norm yes
+thermo 10
+
+velocity all create 300.0 42128
+fix 1 all qeq/slater 1 12.0 1.0e-6 100 coul/streitz
+fix 2 all nve
+
+run 100
+Neighbor list info ...
+ 3 neighbor list requests
+ update every 10 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 13
+ ghost atom cutoff = 13
+ binsize = 6.5 -> bins = 4 5 4
+Memory usage per processor = 13.4993 Mbytes
+Step Temp TotEng PotEng E_vdwl E_coul E_long q1 q2 qsum Press S/CPU
+ 0 300 -6.3403863 -6.3791464 -2.7952901 -3.5838563 0 2.8665317 -1.9110211 4.5474735e-13 -25874.956 0
+ 10 272.66671 -6.3403993 -6.375628 -2.7902909 -3.5853371 0 2.8636914 -1.9091276 -1.3642421e-12 -21564.555 2.9573751
+ 20 220.54623 -6.3402616 -6.3687562 -2.7790072 -3.589749 0 2.863852 -1.9092346 -1.3642421e-12 -16449.483 3.1648484
+ 30 180.22123 -6.3401053 -6.36339 -2.768798 -3.5945919 0 2.8639472 -1.9092981 1.3642421e-12 -12688.521 3.1669432
+ 40 163.64074 -6.3399908 -6.3611332 -2.7648763 -3.5962569 0 2.8623043 -1.9082029 -9.094947e-13 -12334.216 3.1612475
+ 50 153.73807 -6.3399173 -6.3597803 -2.7667004 -3.5930799 0 2.8578231 -1.9052154 4.5474735e-13 -13908.735 3.1540211
+ 60 139.12639 -6.3398818 -6.357857 -2.7702921 -3.5875649 0 2.8524119 -1.901608 0 -14717.582 3.1663976
+ 70 134.93296 -6.3398533 -6.3572867 -2.7724725 -3.5848142 0 2.849924 -1.8999493 -4.5474735e-13 -12982.152 3.1682565
+ 80 160.3429 -6.3398152 -6.3605315 -2.7722306 -3.5883009 0 2.8528608 -1.9019072 -4.5474735e-13 -8388.9691 3.158454
+ 90 205.15418 -6.3397713 -6.3662773 -2.7693832 -3.596894 0 2.8599384 -1.9066256 -1.3642421e-12 -1208.0315 3.1545482
+ 100 231.50843 -6.339741 -6.369652 -2.7640167 -3.6056353 0 2.8675276 -1.9116851 0 7331.4547 3.1731517
+Loop time of 31.8346 on 4 procs for 100 steps with 2160 atoms
+
+Performance: 0.109 ns/day, 221.074 hours/ns, 3.141 timesteps/s
+99.9% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 17.842 | 17.846 | 17.851 | 0.1 | 56.06
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.026919 | 0.032234 | 0.035781 | 2.1 | 0.10
+Output | 0.00069213 | 0.00072718 | 0.00081635 | 0.2 | 0.00
+Modify | 13.953 | 13.954 | 13.954 | 0.0 | 43.83
+Other | | 0.002242 | | | 0.01
+
+Nlocal: 540 ave 540 max 540 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost: 8994 ave 8994 max 8994 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs: 294732 ave 294732 max 294732 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs: 589464 ave 589464 max 589464 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 2357856
+Ave neighs/atom = 1091.6
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:32
diff --git a/examples/tad/log.15Feb16.tad.g++.3 b/examples/tad/log.15Feb16.tad.g++.3
new file mode 100644
index 0000000000000000000000000000000000000000..5258d0100ffd99eb4969f0f4b09d9f5df1e39fba
--- /dev/null
+++ b/examples/tad/log.15Feb16.tad.g++.3
@@ -0,0 +1,39 @@
+LAMMPS (15 Feb 2016)
+Running on 3 partitions of processors
+Step CPU N M Status Barrier Margin t_lo delt_lo
+1000 0.000 0 0 E 0.000 0.000 0.000 0.000
+1150 0.965 0 0 DF 2.957 0.000 0.000 17626.822
+1550 2.888 0 1 DF 0.510 0.049 0.000 1251.400
+1950 4.950 0 2 D 2.971 0.610 0.000 114049.526
+2350 6.900 0 3 D 0.510 0.867 0.000 3071.448
+2800 9.204 0 4 D 2.971 1.156 0.000 216079.482
+1550 9.204 1 1 E 0.510 0.000 1251.400 1251.400
+1650 9.815 1 0 DF 0.510 0.000 1251.400 227.525
+1750 10.426 1 1 D 0.510 0.461 1251.400 455.068
+1850 11.033 1 2 D 0.510 0.692 1251.400 682.575
+1950 11.656 1 3 D 0.510 0.923 1251.400 910.139
+2050 12.284 1 4 D 0.510 1.154 1251.400 1137.620
+1650 12.284 2 0 E 0.510 0.000 1478.925 227.525
+1850 13.368 2 0 DF 0.510 0.000 1478.925 455.069
+2050 14.444 2 1 D 0.510 0.549 1478.925 910.151
+2250 15.517 2 2 D 0.510 0.823 1478.925 1365.187
+2450 16.582 2 3 D 0.510 1.098 1478.925 1820.330
+1850 16.582 3 0 E 0.510 0.000 1933.994 455.069
+1950 17.221 3 0 DF 0.510 0.000 1933.994 227.535
+2050 17.845 3 1 D 0.510 0.461 1933.994 455.048
+2150 18.497 3 2 D 0.510 0.692 1933.994 682.547
+2250 19.121 3 3 D 0.510 0.923 1933.994 910.098
+2350 19.748 3 4 D 0.510 1.154 1933.994 1137.697
+1950 19.748 4 0 E 0.510 0.000 2161.529 227.535
+2100 20.642 4 0 DF 2.518 0.000 2161.529 8680.975
+2250 21.487 4 1 DF 0.510 0.045 2161.529 682.601
+2400 22.368 4 2 D 2.518 0.455 2161.529 26043.029
+2550 23.226 4 3 D 0.510 0.607 2161.529 1365.124
+2700 24.119 4 4 D 2.518 0.759 2161.529 43402.020
+2850 24.959 4 5 D 0.510 0.911 2161.529 2047.724
+3000 25.850 4 6 D 2.518 1.063 2161.529 60767.455
+2250 25.850 5 1 E 0.510 0.000 2844.130 682.601
+2450 26.916 5 0 DF 0.510 0.000 2844.130 455.061
+2700 28.212 5 1 D 0.510 0.617 2844.130 1023.896
+2950 29.505 5 2 D 0.510 0.960 2844.130 1592.629
+Loop time of 29.7303 on 3 procs for 2000 steps with 511 atoms
diff --git a/examples/voronoi/log.15Feb16.voronoi.2d.g++.1 b/examples/voronoi/log.15Feb16.voronoi.2d.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..d41da713c150b072295fe9fe205c16c8259f03ec
--- /dev/null
+++ b/examples/voronoi/log.15Feb16.voronoi.2d.g++.1
@@ -0,0 +1,130 @@
+LAMMPS (15 Feb 2016)
+# Test volume definitions for 2d and finite systems
+
+variable rcut equal 10.0
+variable rskin equal 2.0
+variable rcomm equal 20.0
+variable len equal 4.0
+variable lenz equal 10.0
+
+dimension 2
+units metal
+boundary p p p
+
+#lattice sq 1.0 origin 0.5 0.5 0.0
+lattice hex 1.0 origin 0.5 0.5 0.0
+Lattice spacing in x,y,z = 1 1.73205 1
+
+atom_style atomic
+
+region box block 0 ${len} 0 ${len} 0.0 ${lenz}
+region box block 0 4 0 ${len} 0.0 ${lenz}
+region box block 0 4 0 4 0.0 ${lenz}
+region box block 0 4 0 4 0.0 10
+region atoms block 0 ${len} 0 ${len} 0.0 0.0
+region atoms block 0 4 0 ${len} 0.0 0.0
+region atoms block 0 4 0 4 0.0 0.0
+create_box 1 box
+Created orthogonal box = (0 0 0) to (4 6.9282 10)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 region atoms
+Created 32 atoms
+
+mass 1 1.0
+
+pair_style lj/cut ${rcut}
+pair_style lj/cut 10
+pair_coeff 1 1 0.0 1.0
+
+neighbor ${rskin} nsq
+neighbor 2 nsq
+
+# set the minimum communication cut-off
+comm_modify cutoff ${rcomm}
+comm_modify cutoff 20
+
+compute v1 all voronoi/atom neighbors yes
+compute volvor all reduce sum c_v1[1]
+variable volsys equal lz*lx*ly
+variable err equal c_volvor-v_volsys
+thermo_style custom c_volvor v_volsys vol v_err
+thermo 1
+
+#
+# TEST 1: Volume check for 2d bulk system
+#
+
+run 0
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 12
+ ghost atom cutoff = 20
+Memory usage per processor = 2.37519 Mbytes
+volvor volsys Volume err
+ 277.12813 277.12813 27.712813 5.6843419e-14
+Loop time of 3.09944e-06 on 1 procs for 0 steps with 32 atoms
+
+0.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 3.099e-06 | | |100.00
+
+Nlocal: 32 ave 32 max 32 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 2415 ave 2415 max 2415 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 8256 ave 8256 max 8256 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 8256
+Ave neighs/atom = 258
+Neighbor list builds = 0
+Dangerous builds = 0
+
+#
+# TEST 2: Volume check for 2d finite system
+# add margins in x and y directions
+#
+
+change_box all boundary f f p
+run 0
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Memory usage per processor = 7.05652 Mbytes
+volvor volsys Volume err
+ 277.12813 277.12813 27.712813 3.4106051e-13
+Loop time of 0 on 1 procs for 0 steps with 32 atoms
+
+0.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 0 | | | 0.00
+
+Nlocal: 32 ave 32 max 32 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 496 ave 496 max 496 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 496
+Ave neighs/atom = 15.5
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/voronoi/log.15Feb16.voronoi.2d.g++.4 b/examples/voronoi/log.15Feb16.voronoi.2d.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..db3f2a8bc1ec7b26dbf6373c532897397f1c3756
--- /dev/null
+++ b/examples/voronoi/log.15Feb16.voronoi.2d.g++.4
@@ -0,0 +1,130 @@
+LAMMPS (15 Feb 2016)
+# Test volume definitions for 2d and finite systems
+
+variable rcut equal 10.0
+variable rskin equal 2.0
+variable rcomm equal 20.0
+variable len equal 4.0
+variable lenz equal 10.0
+
+dimension 2
+units metal
+boundary p p p
+
+#lattice sq 1.0 origin 0.5 0.5 0.0
+lattice hex 1.0 origin 0.5 0.5 0.0
+Lattice spacing in x,y,z = 1 1.73205 1
+
+atom_style atomic
+
+region box block 0 ${len} 0 ${len} 0.0 ${lenz}
+region box block 0 4 0 ${len} 0.0 ${lenz}
+region box block 0 4 0 4 0.0 ${lenz}
+region box block 0 4 0 4 0.0 10
+region atoms block 0 ${len} 0 ${len} 0.0 0.0
+region atoms block 0 4 0 ${len} 0.0 0.0
+region atoms block 0 4 0 4 0.0 0.0
+create_box 1 box
+Created orthogonal box = (0 0 0) to (4 6.9282 10)
+ 2 by 2 by 1 MPI processor grid
+create_atoms 1 region atoms
+Created 32 atoms
+
+mass 1 1.0
+
+pair_style lj/cut ${rcut}
+pair_style lj/cut 10
+pair_coeff 1 1 0.0 1.0
+
+neighbor ${rskin} nsq
+neighbor 2 nsq
+
+# set the minimum communication cut-off
+comm_modify cutoff ${rcomm}
+comm_modify cutoff 20
+
+compute v1 all voronoi/atom neighbors yes
+compute volvor all reduce sum c_v1[1]
+variable volsys equal lz*lx*ly
+variable err equal c_volvor-v_volsys
+thermo_style custom c_volvor v_volsys vol v_err
+thermo 1
+
+#
+# TEST 1: Volume check for 2d bulk system
+#
+
+run 0
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 12
+ ghost atom cutoff = 20
+Memory usage per processor = 2.41069 Mbytes
+volvor volsys Volume err
+ 277.12813 277.12813 27.712813 5.1159077e-13
+Loop time of 6.19888e-06 on 4 procs for 0 steps with 32 atoms
+
+0.0% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 6.199e-06 | | |100.00
+
+Nlocal: 8 ave 8 max 8 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost: 2159 ave 2159 max 2159 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs: 2064 ave 2077 max 2051 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+
+Total # of neighbors = 8256
+Ave neighs/atom = 258
+Neighbor list builds = 0
+Dangerous builds = 0
+
+#
+# TEST 2: Volume check for 2d finite system
+# add margins in x and y directions
+#
+
+change_box all boundary f f p
+run 0
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Memory usage per processor = 7.04625 Mbytes
+volvor volsys Volume err
+ 277.12813 277.12813 27.712813 3.4106051e-13
+Loop time of 2.86102e-06 on 4 procs for 0 steps with 32 atoms
+
+0.0% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 2.861e-06 | | |100.00
+
+Nlocal: 8 ave 8 max 8 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost: 24 ave 24 max 24 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs: 124 ave 124 max 124 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 496
+Ave neighs/atom = 15.5
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/voronoi/log.15Feb16.voronoi.data.g++.1 b/examples/voronoi/log.15Feb16.voronoi.data.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..01908e356c35ecdce16d42d7eb159c70543d1889
--- /dev/null
+++ b/examples/voronoi/log.15Feb16.voronoi.data.g++.1
@@ -0,0 +1,163 @@
+LAMMPS (15 Feb 2016)
+# Exercise different output data options
+
+variable len equal 4.0
+variable lenz equal 10.0
+
+dimension 2
+units metal
+boundary f f p
+
+lattice hex 1.0 origin 0.25 0.25 0.0
+Lattice spacing in x,y,z = 1 1.73205 1
+
+atom_style atomic
+
+region box block 0 ${len} 0 ${len} 0.0 ${lenz}
+region box block 0 4 0 ${len} 0.0 ${lenz}
+region box block 0 4 0 4 0.0 ${lenz}
+region box block 0 4 0 4 0.0 10
+region atoms block 0 ${len} 0 ${len} 0.0 0.0
+region atoms block 0 4 0 ${len} 0.0 0.0
+region atoms block 0 4 0 4 0.0 0.0
+create_box 1 box
+Created orthogonal box = (0 0 0) to (4 6.9282 10)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 region atoms
+Created 32 atoms
+
+mass 1 1.0
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 0.0 1.0
+
+neighbor 1.0 nsq
+
+#
+# TEST 1:
+#
+
+# This compute voronoi generates all three
+# types of quantity: per-atom, local, and global
+
+compute v1 all voronoi/atom neighbors yes edge_histo 6
+
+# write voronoi per-atom quantities to a file
+
+dump dperatom all custom 1 dump.voro id type x y z c_v1[1] c_v1[2]
+
+# writing voronoi local quantities to a file
+
+dump dlocal all local 1 dump.neighbors index c_v1[1] c_v1[2] c_v1[3]
+
+# sum up a voronoi per-atom quantity
+
+compute volvor all reduce sum c_v1[1]
+
+variable volsys equal lz*lx*ly
+variable err equal c_volvor-v_volsys
+
+# output voronoi global quantities
+
+thermo_style custom c_volvor v_volsys vol v_err c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7]
+thermo 1
+
+run 0
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 3.5
+ ghost atom cutoff = 3.5
+Memory usage per processor = 9.40674 Mbytes
+volvor volsys Volume err v1[3] v1[4] v1[5] v1[6] v1[7]
+ 277.12813 277.12813 27.712813 3.9790393e-13 0 186 12 36 0
+Loop time of 1.19209e-06 on 1 procs for 0 steps with 32 atoms
+
+0.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 1.192e-06 | | |100.00
+
+Nlocal: 32 ave 32 max 32 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 325 ave 325 max 325 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 325
+Ave neighs/atom = 10.1562
+Neighbor list builds = 0
+Dangerous builds = 0
+
+uncompute v1
+uncompute volvor
+undump dperatom
+undump dlocal
+
+#
+# TEST 2:
+#
+
+# This compute voronoi generates
+# local and global quantities, but
+# not per-atom quantities
+
+compute v2 all voronoi/atom neighbors yes edge_histo 6 peratom no
+
+# write voronoi local quantities to a file
+
+dump d2 all local 1 dump.neighbors2 index c_v2[1] c_v2[2] c_v2[3]
+
+# sum up a voronoi local quantity
+
+compute sumarea all reduce sum c_v2[3]
+
+# output voronoi global quantities
+
+thermo_style custom c_sumarea c_v2[3] c_v2[4] c_v2[5] c_v2[6] c_v2[7]
+thermo 1
+
+run 0
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Memory usage per processor = 8.15503 Mbytes
+sumarea v2[3] v2[4] v2[5] v2[6] v2[7]
+ 1215.0706 0 186 12 36 0
+Loop time of 0 on 1 procs for 0 steps with 32 atoms
+
+0.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 0 | | | 0.00
+
+Nlocal: 32 ave 32 max 32 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 325 ave 325 max 325 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 325
+Ave neighs/atom = 10.1562
+Neighbor list builds = 0
+Dangerous builds = 0
+
+
+
+Total wall time: 0:00:00
diff --git a/examples/voronoi/log.15Feb16.voronoi.data.g++.4 b/examples/voronoi/log.15Feb16.voronoi.data.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..45742da07d18c5027676e3f5e79271b9669138b0
--- /dev/null
+++ b/examples/voronoi/log.15Feb16.voronoi.data.g++.4
@@ -0,0 +1,163 @@
+LAMMPS (15 Feb 2016)
+# Exercise different output data options
+
+variable len equal 4.0
+variable lenz equal 10.0
+
+dimension 2
+units metal
+boundary f f p
+
+lattice hex 1.0 origin 0.25 0.25 0.0
+Lattice spacing in x,y,z = 1 1.73205 1
+
+atom_style atomic
+
+region box block 0 ${len} 0 ${len} 0.0 ${lenz}
+region box block 0 4 0 ${len} 0.0 ${lenz}
+region box block 0 4 0 4 0.0 ${lenz}
+region box block 0 4 0 4 0.0 10
+region atoms block 0 ${len} 0 ${len} 0.0 0.0
+region atoms block 0 4 0 ${len} 0.0 0.0
+region atoms block 0 4 0 4 0.0 0.0
+create_box 1 box
+Created orthogonal box = (0 0 0) to (4 6.9282 10)
+ 2 by 2 by 1 MPI processor grid
+create_atoms 1 region atoms
+Created 32 atoms
+
+mass 1 1.0
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 0.0 1.0
+
+neighbor 1.0 nsq
+
+#
+# TEST 1:
+#
+
+# This compute voronoi generates all three
+# types of quantity: per-atom, local, and global
+
+compute v1 all voronoi/atom neighbors yes edge_histo 6
+
+# write voronoi per-atom quantities to a file
+
+dump dperatom all custom 1 dump.voro id type x y z c_v1[1] c_v1[2]
+
+# writing voronoi local quantities to a file
+
+dump dlocal all local 1 dump.neighbors index c_v1[1] c_v1[2] c_v1[3]
+
+# sum up a voronoi per-atom quantity
+
+compute volvor all reduce sum c_v1[1]
+
+variable volsys equal lz*lx*ly
+variable err equal c_volvor-v_volsys
+
+# output voronoi global quantities
+
+thermo_style custom c_volvor v_volsys vol v_err c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7]
+thermo 1
+
+run 0
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 3.5
+ ghost atom cutoff = 3.5
+Memory usage per processor = 9.29039 Mbytes
+volvor volsys Volume err v1[3] v1[4] v1[5] v1[6] v1[7]
+ 277.12813 277.12813 27.712813 3.4106051e-13 0 186 12 36 0
+Loop time of 3.99351e-06 on 4 procs for 0 steps with 32 atoms
+
+0.0% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 3.994e-06 | | |100.00
+
+Nlocal: 8 ave 8 max 8 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost: 24 ave 24 max 24 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs: 81.25 ave 84 max 77 min
+Histogram: 1 0 0 0 1 0 0 0 0 2
+
+Total # of neighbors = 325
+Ave neighs/atom = 10.1562
+Neighbor list builds = 0
+Dangerous builds = 0
+
+uncompute v1
+uncompute volvor
+undump dperatom
+undump dlocal
+
+#
+# TEST 2:
+#
+
+# This compute voronoi generates
+# local and global quantities, but
+# not per-atom quantities
+
+compute v2 all voronoi/atom neighbors yes edge_histo 6 peratom no
+
+# write voronoi local quantities to a file
+
+dump d2 all local 1 dump.neighbors2 index c_v2[1] c_v2[2] c_v2[3]
+
+# sum up a voronoi local quantity
+
+compute sumarea all reduce sum c_v2[3]
+
+# output voronoi global quantities
+
+thermo_style custom c_sumarea c_v2[3] c_v2[4] c_v2[5] c_v2[6] c_v2[7]
+thermo 1
+
+run 0
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Memory usage per processor = 8.03996 Mbytes
+sumarea v2[3] v2[4] v2[5] v2[6] v2[7]
+ 1215.0706 0 186 12 36 0
+Loop time of 2.86102e-06 on 4 procs for 0 steps with 32 atoms
+
+0.0% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 2.861e-06 | | |100.00
+
+Nlocal: 8 ave 8 max 8 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost: 24 ave 24 max 24 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs: 81.25 ave 84 max 77 min
+Histogram: 1 0 0 0 1 0 0 0 0 2
+
+Total # of neighbors = 325
+Ave neighs/atom = 10.1562
+Neighbor list builds = 0
+Dangerous builds = 0
+
+
+
+Total wall time: 0:00:00
diff --git a/examples/voronoi/log.15Feb16.voronoi.g++.1 b/examples/voronoi/log.15Feb16.voronoi.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..a9b327aa07c84b5c7187c25dfdb612385b476c60
--- /dev/null
+++ b/examples/voronoi/log.15Feb16.voronoi.g++.1
@@ -0,0 +1,619 @@
+LAMMPS (15 Feb 2016)
+# Test of Kawasaki Dynamics on LJ test system
+
+units metal
+#newton off
+boundary p p p
+
+lattice fcc 1 origin 0.25 0.25 0.25
+Lattice spacing in x,y,z = 1 1 1
+atom_style atomic
+
+# indexed atom variables in test 5 need a map
+
+atom_modify sort 0 0.0 map hash
+
+region box block 0 10 0 10 0 10
+create_box 2 box
+Created orthogonal box = (0 0 0) to (10 10 10)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box basis 1 2
+Created 4000 atoms
+
+mass 1 50
+mass 2 50
+
+pair_style lj/cut 2.0
+pair_coeff 1 1 0.0 1.0
+pair_coeff 1 2 0.0 1.0
+pair_coeff 2 2 0.0 1.0
+
+neighbor 0.3 bin
+neigh_modify delay 10
+
+# set the cut-off to 2.5x the cutoff from the potential
+comm_modify cutoff 5.0
+
+# atom radii per type
+variable r atom (type==1)*0.1+(type==2)*0.3
+
+# groups
+group type1 type 1
+3000 atoms in group type1
+group type2 type 2
+1000 atoms in group type2
+
+thermo 1
+# reduce computes
+#compute r1 type1 reduce sum c_v1[1]
+#compute r2 type2 reduce sum c_v1[1]
+
+#compute v1 all voronoi/atom radius v_r
+
+#
+# TEST 1: Sum of all voronoi cells is the simulation cell volume
+#
+
+compute v1 all voronoi/atom
+dump d1 all custom 1 dump.voro id type x y z c_v1[1] c_v1[2]
+compute r0 all reduce sum c_v1[1]
+thermo_style custom c_r0
+variable t1 equal c_r0
+run 0
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.3
+ ghost atom cutoff = 5
+ binsize = 1.15 -> bins = 9 9 9
+Memory usage per processor = 8.24398 Mbytes
+r0
+ 1000
+Loop time of 1.90735e-06 on 1 procs for 0 steps with 4000 atoms
+
+0.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 1.907e-06 | | |100.00
+
+Nlocal: 4000 ave 4000 max 4000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 28000 ave 28000 max 28000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 400000 ave 400000 max 400000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 400000
+Ave neighs/atom = 100
+Neighbor list builds = 0
+Dangerous builds = 0
+print "TEST_1 $(round(abs(v_t1-1000)/10))% Error. Sum of all voronoi cells is the simulation cell volume"
+TEST_1 0% Error. Sum of all voronoi cells is the simulation cell volume
+uncompute v1
+uncompute r0
+undump d1
+
+#
+# TEST 2: Sum of all only_group voronoi cells is the simulation cell volume
+#
+
+compute v1 type2 voronoi/atom only_group
+dump d1 all custom 1 dump.voro id type x y z c_v1[1] c_v1[2]
+compute r0 type2 reduce sum c_v1[1]
+compute r1 type1 reduce sum c_v1[1]
+thermo_style custom c_r0 c_r1
+variable t2a equal c_r0
+variable t2b equal c_r1
+run 0
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Memory usage per processor = 8.24398 Mbytes
+r0 r1
+ 1000 0
+Loop time of 9.53674e-07 on 1 procs for 0 steps with 4000 atoms
+
+0.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 9.537e-07 | | |100.00
+
+Nlocal: 4000 ave 4000 max 4000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 28000 ave 28000 max 28000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 400000 ave 400000 max 400000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 400000
+Ave neighs/atom = 100
+Neighbor list builds = 0
+Dangerous builds = 0
+print "TEST_2a $(round(abs(v_t2a-1000)/10))% Error. Sum of all only_group voronoi cells is the simulation cell volume"
+TEST_2a 0% Error. Sum of all only_group voronoi cells is the simulation cell volume
+print "TEST_2b $(round(v_t2b/10))% Error. Sum of all only_group not included voronoi cells is zero"
+TEST_2b 0% Error. Sum of all only_group not included voronoi cells is zero
+uncompute v1
+uncompute r0
+uncompute r1
+undump d1
+
+#
+# TEST 3: Sum of all radius voronoi cells is the simulation cell volume
+#
+
+compute v1 all voronoi/atom radius v_r
+dump d1 all custom 1 dump.voro id type x y z c_v1[1] c_v1[2]
+compute r0 all reduce sum c_v1[1]
+thermo_style custom c_r0
+variable t3 equal c_r0
+run 0
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Memory usage per processor = 8.24398 Mbytes
+r0
+ 1000
+Loop time of 1.90735e-06 on 1 procs for 0 steps with 4000 atoms
+
+0.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 1.907e-06 | | |100.00
+
+Nlocal: 4000 ave 4000 max 4000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 28000 ave 28000 max 28000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 400000 ave 400000 max 400000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 400000
+Ave neighs/atom = 100
+Neighbor list builds = 0
+Dangerous builds = 0
+print "TEST_3 $(round(abs(v_t3-1000)/10))% Error. Sum of all radius voronoi cells is the simulation cell volume"
+TEST_3 0% Error. Sum of all radius voronoi cells is the simulation cell volume
+uncompute v1
+uncompute r0
+undump d1
+
+#
+# TEST 4: Edge histogram tests
+#
+
+compute v1 type2 voronoi/atom edge_histo 8
+thermo_style custom c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7]
+run 1
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Memory usage per processor = 6.03036 Mbytes
+v1[1] v1[2] v1[3] v1[4] v1[5] v1[6] v1[7]
+ 0 0 0 12000 0 0 0
+ 0 0 0 12000 0 0 0
+Loop time of 0.454023 on 1 procs for 1 steps with 4000 atoms
+
+Performance: 0.190 ns/day, 126.118 hours/ns, 2.203 timesteps/s
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0059121 | 0.0059121 | 0.0059121 | 0.0 | 1.30
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.00020099 | 0.00020099 | 0.00020099 | 0.0 | 0.04
+Output | 0.44782 | 0.44782 | 0.44782 | 0.0 | 98.63
+Modify | 9.5367e-07 | 9.5367e-07 | 9.5367e-07 | 0.0 | 0.00
+Other | | 8.702e-05 | | | 0.02
+
+Nlocal: 4000 ave 4000 max 4000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 28000 ave 28000 max 28000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 400000 ave 400000 max 400000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 400000
+Ave neighs/atom = 100
+Neighbor list builds = 0
+Dangerous builds = 0
+variable t4a equal (abs(c_v1[4]-12000)+c_v1[1]+c_v1[2]+c_v1[3]+c_v1[5]+c_v1[6]+c_v1[7])/120
+print "TEST_4a $(round(v_t4a))% Error. Edge histogram of a simple cubic lattice (6 sides. 4 edges per side)"
+TEST_4a 0% Error. Edge histogram of a simple cubic lattice (6 sides. 4 edges per side)
+uncompute v1
+compute v1 all voronoi/atom edge_histo 8
+thermo_style custom c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7]
+run 1
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Memory usage per processor = 6.03036 Mbytes
+v1[1] v1[2] v1[3] v1[4] v1[5] v1[6] v1[7]
+ 0 0 0 48000 0 0 0
+ 0 0 0 48000 0 0 0
+Loop time of 0.473173 on 1 procs for 1 steps with 4000 atoms
+
+Performance: 0.183 ns/day, 131.437 hours/ns, 2.113 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.005954 | 0.005954 | 0.005954 | 0.0 | 1.26
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.0002439 | 0.0002439 | 0.0002439 | 0.0 | 0.05
+Output | 0.46687 | 0.46687 | 0.46687 | 0.0 | 98.67
+Modify | 9.5367e-07 | 9.5367e-07 | 9.5367e-07 | 0.0 | 0.00
+Other | | 0.0001042 | | | 0.02
+
+Nlocal: 4000 ave 4000 max 4000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 28000 ave 28000 max 28000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 400000 ave 400000 max 400000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 400000
+Ave neighs/atom = 100
+Neighbor list builds = 0
+Dangerous builds = 0
+variable t4b equal (abs(c_v1[4]-48000)+c_v1[1]+c_v1[2]+c_v1[3]+c_v1[5]+c_v1[6]+c_v1[7])/480
+print "TEST_4b $(round(v_t4b))% Error. Edge histogram of a face centered cubic lattice (12 sides. 4 edges per side)"
+TEST_4b 0% Error. Edge histogram of a face centered cubic lattice (12 sides. 4 edges per side)
+uncompute v1
+
+# perturbed fcc lattice
+displace_atoms all random 0.01 0.01 0.01 31423
+compute v1 all voronoi/atom edge_histo 8 edge_threshold 0.1
+thermo_style custom c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7]
+run 1
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Memory usage per processor = 6.03036 Mbytes
+v1[1] v1[2] v1[3] v1[4] v1[5] v1[6] v1[7]
+ 0 0 0 48000 0 0 0
+ 0 0 0 48000 0 0 0
+Loop time of 0.471937 on 1 procs for 1 steps with 4000 atoms
+
+Performance: 0.183 ns/day, 131.094 hours/ns, 2.119 timesteps/s
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0062199 | 0.0062199 | 0.0062199 | 0.0 | 1.32
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.00022388 | 0.00022388 | 0.00022388 | 0.0 | 0.05
+Output | 0.46539 | 0.46539 | 0.46539 | 0.0 | 98.61
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 9.823e-05 | | | 0.02
+
+Nlocal: 4000 ave 4000 max 4000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 28000 ave 28000 max 28000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 400000 ave 400000 max 400000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 400000
+Ave neighs/atom = 100
+Neighbor list builds = 0
+Dangerous builds = 0
+variable t4c equal (abs(c_v1[4]-48000)+c_v1[1]+c_v1[2]+c_v1[3]+c_v1[5]+c_v1[6]+c_v1[7])/480
+print "TEST_4c $(round(v_t4c))% Error. Edge histogram of a perturbed face centered cubic lattice with edge_threshold"
+TEST_4c 0% Error. Edge histogram of a perturbed face centered cubic lattice with edge_threshold
+uncompute v1
+
+# bcc lattice
+delete_atoms group all
+Deleted 4000 atoms, new total = 0
+lattice bcc 1 origin 0.25 0.25 0.25
+Lattice spacing in x,y,z = 1 1 1
+create_atoms 1 box
+Created 2000 atoms
+compute v1 all voronoi/atom edge_histo 8
+thermo_style custom c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7]
+run 1
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Memory usage per processor = 6.03036 Mbytes
+v1[1] v1[2] v1[3] v1[4] v1[5] v1[6] v1[7]
+ 0 0 0 12000 0 16000 0
+ 0 0 0 12000 0 16000 0
+Loop time of 0.211795 on 1 procs for 1 steps with 2000 atoms
+
+Performance: 0.408 ns/day, 58.832 hours/ns, 4.722 timesteps/s
+100.1% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0014911 | 0.0014911 | 0.0014911 | 0.0 | 0.70
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 8.9884e-05 | 8.9884e-05 | 8.9884e-05 | 0.0 | 0.04
+Output | 0.21018 | 0.21018 | 0.21018 | 0.0 | 99.24
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 3.695e-05 | | | 0.02
+
+Nlocal: 2000 ave 2000 max 2000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 14000 ave 14000 max 14000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 112000 ave 112000 max 112000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 112000
+Ave neighs/atom = 56
+Neighbor list builds = 0
+Dangerous builds = 0
+variable t4d equal (abs(c_v1[4]-12000)+abs(c_v1[6]-16000)+c_v1[1]+c_v1[2]+c_v1[3]+c_v1[5]+c_v1[7])/280
+print "TEST_4d $(round(v_t4d))% Error. Edge histogram of a body centered cubic lattice (truncated octahedron, 6 sides with 4 edges, 8 sides with 6 edges)"
+TEST_4d 0% Error. Edge histogram of a body centered cubic lattice (truncated octahedron, 6 sides with 4 edges, 8 sides with 6 edges)
+uncompute v1
+
+# restore fcc lattice
+delete_atoms group all
+Deleted 2000 atoms, new total = 0
+lattice fcc 1 origin 0.25 0.25 0.25
+Lattice spacing in x,y,z = 1 1 1
+create_atoms 1 box basis 1 2
+Created 4000 atoms
+
+#
+# TEST 5: Occupation analysis
+#
+
+print "START5"
+START5
+
+# start with pristine lattice
+variable i1 equal 13
+variable i2 equal 257
+compute v1 all voronoi/atom occupation
+compute r0 all reduce sum c_v1[1]
+compute r1 all reduce sum c_v1[2]
+variable d5a equal c_v1[${i1}][1]
+variable d5a equal c_v1[13][1]
+variable d5b equal c_v1[${i2}][1]
+variable d5b equal c_v1[257][1]
+variable d5c equal c_v1[${i1}][2]
+variable d5c equal c_v1[13][2]
+variable d5d equal c_v1[${i2}][2]
+variable d5d equal c_v1[257][2]
+thermo_style custom c_r0 c_r1 v_d5a v_d5b v_d5c v_d5d
+
+run 0
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Memory usage per processor = 6.03036 Mbytes
+r0 r1 d5a d5b d5c d5d
+ 4000 4000 1 1 1 1
+Loop time of 1.19209e-06 on 1 procs for 0 steps with 4000 atoms
+
+0.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 1.192e-06 | | |100.00
+
+Nlocal: 4000 ave 4000 max 4000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 28000 ave 28000 max 28000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 400000 ave 400000 max 400000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 400000
+Ave neighs/atom = 100
+Neighbor list builds = 0
+Dangerous builds = 0
+# expect 1 1 1 1 (one atom per cell each)
+variable t5a equal abs(${d5a}-1)+abs(${d5b}-1)+abs(${d5c}-1)+abs(${d5d}-1)
+variable t5a equal abs(1-1)+abs(${d5b}-1)+abs(${d5c}-1)+abs(${d5d}-1)
+variable t5a equal abs(1-1)+abs(1-1)+abs(${d5c}-1)+abs(${d5d}-1)
+variable t5a equal abs(1-1)+abs(1-1)+abs(1-1)+abs(${d5d}-1)
+variable t5a equal abs(1-1)+abs(1-1)+abs(1-1)+abs(1-1)
+
+# move atom i1 next to atom i2
+variable oxd equal x[${i1}]
+variable oxd equal x[13]
+variable oyd equal y[${i1}]
+variable oyd equal y[13]
+variable ozd equal z[${i1}]
+variable ozd equal z[13]
+# we need to freeze this value
+variable ox equal ${oxd}
+variable ox equal 3.25
+variable oy equal ${oyd}
+variable oy equal 0.25
+variable oz equal ${ozd}
+variable oz equal 0.25
+# these coords dont change so dynamic evaluation is ok
+variable nx equal x[${i2}]
+variable nx equal x[257]
+variable ny equal y[${i2}]
+variable ny equal y[257]
+variable nz equal z[${i2}]
+variable nz equal z[257]
+set atom ${i1} x $(v_nx+0.2) y $(v_ny+0.2) z $(v_nz+0.2)
+set atom 13 x $(v_nx+0.2) y $(v_ny+0.2) z $(v_nz+0.2)
+set atom 13 x 4.4500000000000001776 y $(v_ny+0.2) z $(v_nz+0.2)
+set atom 13 x 4.4500000000000001776 y 6.4500000000000001776 z $(v_nz+0.2)
+set atom 13 x 4.4500000000000001776 y 6.4500000000000001776 z 0.4500000000000000111
+ 1 settings made for x
+ 1 settings made for y
+ 1 settings made for z
+
+run 0
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Memory usage per processor = 6.53036 Mbytes
+r0 r1 d5a d5b d5c d5d
+ 4000 4002 0 2 2 2
+Loop time of 1.19209e-06 on 1 procs for 0 steps with 4000 atoms
+
+0.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 1.192e-06 | | |100.00
+
+Nlocal: 4000 ave 4000 max 4000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 28000 ave 28000 max 28000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 399998 ave 399998 max 399998 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 399998
+Ave neighs/atom = 99.9995
+Neighbor list builds = 0
+Dangerous builds = 0
+# expect 0 2 2 2 (vacancy at the original i1 site, interstitial at i2 and both atoms are now sharing a site)
+variable t5b equal abs(${d5a}-0)+abs(${d5b}-2)+abs(${d5c}-2)+abs(${d5d}-2)
+variable t5b equal abs(0-0)+abs(${d5b}-2)+abs(${d5c}-2)+abs(${d5d}-2)
+variable t5b equal abs(0-0)+abs(2-2)+abs(${d5c}-2)+abs(${d5d}-2)
+variable t5b equal abs(0-0)+abs(2-2)+abs(2-2)+abs(${d5d}-2)
+variable t5b equal abs(0-0)+abs(2-2)+abs(2-2)+abs(2-2)
+
+# move atom back
+set atom ${i1} x ${ox} y ${oy} z ${oz}
+set atom 13 x ${ox} y ${oy} z ${oz}
+set atom 13 x 3.25 y ${oy} z ${oz}
+set atom 13 x 3.25 y 0.25 z ${oz}
+set atom 13 x 3.25 y 0.25 z 0.25
+ 1 settings made for x
+ 1 settings made for y
+ 1 settings made for z
+
+run 0
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Memory usage per processor = 6.53036 Mbytes
+r0 r1 d5a d5b d5c d5d
+ 4000 4000 1 1 1 1
+Loop time of 9.53674e-07 on 1 procs for 0 steps with 4000 atoms
+
+0.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 9.537e-07 | | |100.00
+
+Nlocal: 4000 ave 4000 max 4000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 28000 ave 28000 max 28000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 400000 ave 400000 max 400000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 400000
+Ave neighs/atom = 100
+Neighbor list builds = 0
+Dangerous builds = 0
+# expect 1 1 1 1 (restored to the initial state)
+variable t5c equal abs(${d5a}-1)+abs(${d5b}-1)+abs(${d5c}-1)+abs(${d5d}-1)
+variable t5c equal abs(1-1)+abs(${d5b}-1)+abs(${d5c}-1)+abs(${d5d}-1)
+variable t5c equal abs(1-1)+abs(1-1)+abs(${d5c}-1)+abs(${d5d}-1)
+variable t5c equal abs(1-1)+abs(1-1)+abs(1-1)+abs(${d5d}-1)
+variable t5c equal abs(1-1)+abs(1-1)+abs(1-1)+abs(1-1)
+
+print "TEST_5 $((v_t5a+v_t5b+v_t5c)*100)% Error. Detection of vacancies and interstitials using the {occupation} keyword."
+TEST_5 0% Error. Detection of vacancies and interstitials using the {occupation} keyword.
+
+uncompute v1
+uncompute r0
+uncompute r1
+
+#
+# TEST 6: Sum of all voronoi cells is the triclinic simulation cell volume
+#
+
+# switch to triclinic box
+change_box all triclinic
+ triclinic box = (0 0 0) to (10 10 10) with tilt (0 0 0)
+change_box all xy final 5.0 remap units box
+ triclinic box = (0 0 0) to (10 10 10) with tilt (5 0 0)
+
+compute v1 all voronoi/atom
+dump d1 all custom 1 dump.voro id type x y z c_v1[1] c_v1[2]
+compute r0 all reduce sum c_v1[1]
+thermo_style custom c_r0
+variable t6 equal c_r0
+run 0
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.3
+ ghost atom cutoff = 5
+ binsize = 1.15 -> bins = 14 9 9
+Memory usage per processor = 11.5794 Mbytes
+r0
+ 1000
+Loop time of 1.19209e-06 on 1 procs for 0 steps with 4000 atoms
+
+0.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 1.192e-06 | | |100.00
+
+Nlocal: 4000 ave 4000 max 4000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 29600 ave 29600 max 29600 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 432000 ave 432000 max 432000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 432000
+Ave neighs/atom = 108
+Neighbor list builds = 0
+Dangerous builds = 0
+print "TEST_6 $(round((v_t6-1000)/10))% Error. Sum of all voronoi cells is the triclinic simulation cell volume"
+TEST_6 0% Error. Sum of all voronoi cells is the triclinic simulation cell volume
+uncompute v1
+uncompute r0
+undump d1
+
+# All tests done
+
+print TEST_DONE
+TEST_DONE
+Total wall time: 0:00:30
diff --git a/examples/voronoi/log.15Feb16.voronoi.g++.4 b/examples/voronoi/log.15Feb16.voronoi.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..3421794483b707f4e7296ecf2fd832808d4f4a31
--- /dev/null
+++ b/examples/voronoi/log.15Feb16.voronoi.g++.4
@@ -0,0 +1,619 @@
+LAMMPS (15 Feb 2016)
+# Test of Kawasaki Dynamics on LJ test system
+
+units metal
+#newton off
+boundary p p p
+
+lattice fcc 1 origin 0.25 0.25 0.25
+Lattice spacing in x,y,z = 1 1 1
+atom_style atomic
+
+# indexed atom variables in test 5 need a map
+
+atom_modify sort 0 0.0 map hash
+
+region box block 0 10 0 10 0 10
+create_box 2 box
+Created orthogonal box = (0 0 0) to (10 10 10)
+ 1 by 2 by 2 MPI processor grid
+create_atoms 1 box basis 1 2
+Created 4000 atoms
+
+mass 1 50
+mass 2 50
+
+pair_style lj/cut 2.0
+pair_coeff 1 1 0.0 1.0
+pair_coeff 1 2 0.0 1.0
+pair_coeff 2 2 0.0 1.0
+
+neighbor 0.3 bin
+neigh_modify delay 10
+
+# set the cut-off to 2.5x the cutoff from the potential
+comm_modify cutoff 5.0
+
+# atom radii per type
+variable r atom (type==1)*0.1+(type==2)*0.3
+
+# groups
+group type1 type 1
+3000 atoms in group type1
+group type2 type 2
+1000 atoms in group type2
+
+thermo 1
+# reduce computes
+#compute r1 type1 reduce sum c_v1[1]
+#compute r2 type2 reduce sum c_v1[1]
+
+#compute v1 all voronoi/atom radius v_r
+
+#
+# TEST 1: Sum of all voronoi cells is the simulation cell volume
+#
+
+compute v1 all voronoi/atom
+dump d1 all custom 1 dump.voro id type x y z c_v1[1] c_v1[2]
+compute r0 all reduce sum c_v1[1]
+thermo_style custom c_r0
+variable t1 equal c_r0
+run 0
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.3
+ ghost atom cutoff = 5
+ binsize = 1.15 -> bins = 9 9 9
+Memory usage per processor = 7.70003 Mbytes
+r0
+ 1000
+Loop time of 5.96046e-06 on 4 procs for 0 steps with 4000 atoms
+
+0.0% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 5.96e-06 | | |100.00
+
+Nlocal: 1000 ave 1000 max 1000 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost: 17000 ave 17000 max 17000 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs: 100000 ave 100000 max 100000 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 400000
+Ave neighs/atom = 100
+Neighbor list builds = 0
+Dangerous builds = 0
+print "TEST_1 $(round(abs(v_t1-1000)/10))% Error. Sum of all voronoi cells is the simulation cell volume"
+TEST_1 0% Error. Sum of all voronoi cells is the simulation cell volume
+uncompute v1
+uncompute r0
+undump d1
+
+#
+# TEST 2: Sum of all only_group voronoi cells is the simulation cell volume
+#
+
+compute v1 type2 voronoi/atom only_group
+dump d1 all custom 1 dump.voro id type x y z c_v1[1] c_v1[2]
+compute r0 type2 reduce sum c_v1[1]
+compute r1 type1 reduce sum c_v1[1]
+thermo_style custom c_r0 c_r1
+variable t2a equal c_r0
+variable t2b equal c_r1
+run 0
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Memory usage per processor = 7.70003 Mbytes
+r0 r1
+ 1000 0
+Loop time of 3.09944e-06 on 4 procs for 0 steps with 4000 atoms
+
+0.0% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 3.099e-06 | | |100.00
+
+Nlocal: 1000 ave 1000 max 1000 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost: 17000 ave 17000 max 17000 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs: 100000 ave 100000 max 100000 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 400000
+Ave neighs/atom = 100
+Neighbor list builds = 0
+Dangerous builds = 0
+print "TEST_2a $(round(abs(v_t2a-1000)/10))% Error. Sum of all only_group voronoi cells is the simulation cell volume"
+TEST_2a 0% Error. Sum of all only_group voronoi cells is the simulation cell volume
+print "TEST_2b $(round(v_t2b/10))% Error. Sum of all only_group not included voronoi cells is zero"
+TEST_2b 0% Error. Sum of all only_group not included voronoi cells is zero
+uncompute v1
+uncompute r0
+uncompute r1
+undump d1
+
+#
+# TEST 3: Sum of all radius voronoi cells is the simulation cell volume
+#
+
+compute v1 all voronoi/atom radius v_r
+dump d1 all custom 1 dump.voro id type x y z c_v1[1] c_v1[2]
+compute r0 all reduce sum c_v1[1]
+thermo_style custom c_r0
+variable t3 equal c_r0
+run 0
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Memory usage per processor = 7.70003 Mbytes
+r0
+ 1000
+Loop time of 2.86102e-06 on 4 procs for 0 steps with 4000 atoms
+
+0.0% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 2.861e-06 | | |100.00
+
+Nlocal: 1000 ave 1000 max 1000 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost: 17000 ave 17000 max 17000 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs: 100000 ave 100000 max 100000 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 400000
+Ave neighs/atom = 100
+Neighbor list builds = 0
+Dangerous builds = 0
+print "TEST_3 $(round(abs(v_t3-1000)/10))% Error. Sum of all radius voronoi cells is the simulation cell volume"
+TEST_3 0% Error. Sum of all radius voronoi cells is the simulation cell volume
+uncompute v1
+uncompute r0
+undump d1
+
+#
+# TEST 4: Edge histogram tests
+#
+
+compute v1 type2 voronoi/atom edge_histo 8
+thermo_style custom c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7]
+run 1
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Memory usage per processor = 5.64663 Mbytes
+v1[1] v1[2] v1[3] v1[4] v1[5] v1[6] v1[7]
+ 0 0 0 12000 0 0 0
+ 0 0 0 12000 0 0 0
+Loop time of 0.262419 on 4 procs for 1 steps with 4000 atoms
+
+Performance: 0.329 ns/day, 72.894 hours/ns, 3.811 timesteps/s
+100.0% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0015318 | 0.0015455 | 0.0015759 | 0.0 | 0.59
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.00056005 | 0.00060356 | 0.00064278 | 0.2 | 0.23
+Output | 0.26013 | 0.26017 | 0.2602 | 0.0 | 99.14
+Modify | 0 | 1.2517e-06 | 2.1458e-06 | 0.1 | 0.00
+Other | | 9.871e-05 | | | 0.04
+
+Nlocal: 1000 ave 1000 max 1000 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost: 17000 ave 17000 max 17000 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs: 100000 ave 100000 max 100000 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 400000
+Ave neighs/atom = 100
+Neighbor list builds = 0
+Dangerous builds = 0
+variable t4a equal (abs(c_v1[4]-12000)+c_v1[1]+c_v1[2]+c_v1[3]+c_v1[5]+c_v1[6]+c_v1[7])/120
+print "TEST_4a $(round(v_t4a))% Error. Edge histogram of a simple cubic lattice (6 sides. 4 edges per side)"
+TEST_4a 0% Error. Edge histogram of a simple cubic lattice (6 sides. 4 edges per side)
+uncompute v1
+compute v1 all voronoi/atom edge_histo 8
+thermo_style custom c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7]
+run 1
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Memory usage per processor = 5.64663 Mbytes
+v1[1] v1[2] v1[3] v1[4] v1[5] v1[6] v1[7]
+ 0 0 0 48000 0 0 0
+ 0 0 0 48000 0 0 0
+Loop time of 0.27636 on 4 procs for 1 steps with 4000 atoms
+
+Performance: 0.313 ns/day, 76.767 hours/ns, 3.618 timesteps/s
+100.0% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0015159 | 0.001533 | 0.001559 | 0.0 | 0.55
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.00051785 | 0.00055867 | 0.00060701 | 0.1 | 0.20
+Output | 0.27416 | 0.2742 | 0.27422 | 0.0 | 99.22
+Modify | 0 | 1.0729e-06 | 1.9073e-06 | 0.1 | 0.00
+Other | | 6.926e-05 | | | 0.03
+
+Nlocal: 1000 ave 1000 max 1000 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost: 17000 ave 17000 max 17000 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs: 100000 ave 100000 max 100000 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 400000
+Ave neighs/atom = 100
+Neighbor list builds = 0
+Dangerous builds = 0
+variable t4b equal (abs(c_v1[4]-48000)+c_v1[1]+c_v1[2]+c_v1[3]+c_v1[5]+c_v1[6]+c_v1[7])/480
+print "TEST_4b $(round(v_t4b))% Error. Edge histogram of a face centered cubic lattice (12 sides. 4 edges per side)"
+TEST_4b 0% Error. Edge histogram of a face centered cubic lattice (12 sides. 4 edges per side)
+uncompute v1
+
+# perturbed fcc lattice
+displace_atoms all random 0.01 0.01 0.01 31423
+compute v1 all voronoi/atom edge_histo 8 edge_threshold 0.1
+thermo_style custom c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7]
+run 1
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Memory usage per processor = 5.64663 Mbytes
+v1[1] v1[2] v1[3] v1[4] v1[5] v1[6] v1[7]
+ 0 0 0 48000 0 0 0
+ 0 0 0 48000 0 0 0
+Loop time of 0.272119 on 4 procs for 1 steps with 4000 atoms
+
+Performance: 0.318 ns/day, 75.589 hours/ns, 3.675 timesteps/s
+99.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0015891 | 0.0015998 | 0.0016181 | 0.0 | 0.59
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.00053191 | 0.00055522 | 0.00059175 | 0.1 | 0.20
+Output | 0.26986 | 0.2699 | 0.26992 | 0.0 | 99.18
+Modify | 0 | 2.3842e-07 | 9.5367e-07 | 0.1 | 0.00
+Other | | 6.658e-05 | | | 0.02
+
+Nlocal: 1000 ave 1000 max 1000 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost: 17000 ave 17000 max 17000 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs: 100000 ave 100016 max 99984 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+
+Total # of neighbors = 400000
+Ave neighs/atom = 100
+Neighbor list builds = 0
+Dangerous builds = 0
+variable t4c equal (abs(c_v1[4]-48000)+c_v1[1]+c_v1[2]+c_v1[3]+c_v1[5]+c_v1[6]+c_v1[7])/480
+print "TEST_4c $(round(v_t4c))% Error. Edge histogram of a perturbed face centered cubic lattice with edge_threshold"
+TEST_4c 0% Error. Edge histogram of a perturbed face centered cubic lattice with edge_threshold
+uncompute v1
+
+# bcc lattice
+delete_atoms group all
+Deleted 4000 atoms, new total = 0
+lattice bcc 1 origin 0.25 0.25 0.25
+Lattice spacing in x,y,z = 1 1 1
+create_atoms 1 box
+Created 2000 atoms
+compute v1 all voronoi/atom edge_histo 8
+thermo_style custom c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7]
+run 1
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Memory usage per processor = 5.64663 Mbytes
+v1[1] v1[2] v1[3] v1[4] v1[5] v1[6] v1[7]
+ 0 0 0 12000 0 16000 0
+ 0 0 0 12000 0 16000 0
+Loop time of 0.120695 on 4 procs for 1 steps with 2000 atoms
+
+Performance: 0.716 ns/day, 33.526 hours/ns, 8.285 timesteps/s
+99.4% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.00037694 | 0.00038201 | 0.00039315 | 0.0 | 0.32
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.00030208 | 0.00031257 | 0.00033903 | 0.1 | 0.26
+Output | 0.11993 | 0.11996 | 0.11997 | 0.0 | 99.39
+Modify | 0 | 7.1526e-07 | 1.9073e-06 | 0.1 | 0.00
+Other | | 4.16e-05 | | | 0.03
+
+Nlocal: 500 ave 500 max 500 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost: 8500 ave 8500 max 8500 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs: 28000 ave 28000 max 28000 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 112000
+Ave neighs/atom = 56
+Neighbor list builds = 0
+Dangerous builds = 0
+variable t4d equal (abs(c_v1[4]-12000)+abs(c_v1[6]-16000)+c_v1[1]+c_v1[2]+c_v1[3]+c_v1[5]+c_v1[7])/280
+print "TEST_4d $(round(v_t4d))% Error. Edge histogram of a body centered cubic lattice (truncated octahedron, 6 sides with 4 edges, 8 sides with 6 edges)"
+TEST_4d 0% Error. Edge histogram of a body centered cubic lattice (truncated octahedron, 6 sides with 4 edges, 8 sides with 6 edges)
+uncompute v1
+
+# restore fcc lattice
+delete_atoms group all
+Deleted 2000 atoms, new total = 0
+lattice fcc 1 origin 0.25 0.25 0.25
+Lattice spacing in x,y,z = 1 1 1
+create_atoms 1 box basis 1 2
+Created 4000 atoms
+
+#
+# TEST 5: Occupation analysis
+#
+
+print "START5"
+START5
+
+# start with pristine lattice
+variable i1 equal 13
+variable i2 equal 257
+compute v1 all voronoi/atom occupation
+compute r0 all reduce sum c_v1[1]
+compute r1 all reduce sum c_v1[2]
+variable d5a equal c_v1[${i1}][1]
+variable d5a equal c_v1[13][1]
+variable d5b equal c_v1[${i2}][1]
+variable d5b equal c_v1[257][1]
+variable d5c equal c_v1[${i1}][2]
+variable d5c equal c_v1[13][2]
+variable d5d equal c_v1[${i2}][2]
+variable d5d equal c_v1[257][2]
+thermo_style custom c_r0 c_r1 v_d5a v_d5b v_d5c v_d5d
+
+run 0
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Memory usage per processor = 5.64663 Mbytes
+r0 r1 d5a d5b d5c d5d
+ 4000 4000 1 1 1 1
+Loop time of 2.86102e-06 on 4 procs for 0 steps with 4000 atoms
+
+0.0% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 2.861e-06 | | |100.00
+
+Nlocal: 1000 ave 1000 max 1000 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost: 17000 ave 17000 max 17000 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs: 100000 ave 100000 max 100000 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 400000
+Ave neighs/atom = 100
+Neighbor list builds = 0
+Dangerous builds = 0
+# expect 1 1 1 1 (one atom per cell each)
+variable t5a equal abs(${d5a}-1)+abs(${d5b}-1)+abs(${d5c}-1)+abs(${d5d}-1)
+variable t5a equal abs(1-1)+abs(${d5b}-1)+abs(${d5c}-1)+abs(${d5d}-1)
+variable t5a equal abs(1-1)+abs(1-1)+abs(${d5c}-1)+abs(${d5d}-1)
+variable t5a equal abs(1-1)+abs(1-1)+abs(1-1)+abs(${d5d}-1)
+variable t5a equal abs(1-1)+abs(1-1)+abs(1-1)+abs(1-1)
+
+# move atom i1 next to atom i2
+variable oxd equal x[${i1}]
+variable oxd equal x[13]
+variable oyd equal y[${i1}]
+variable oyd equal y[13]
+variable ozd equal z[${i1}]
+variable ozd equal z[13]
+# we need to freeze this value
+variable ox equal ${oxd}
+variable ox equal 3.25
+variable oy equal ${oyd}
+variable oy equal 0.25
+variable oz equal ${ozd}
+variable oz equal 0.25
+# these coords dont change so dynamic evaluation is ok
+variable nx equal x[${i2}]
+variable nx equal x[257]
+variable ny equal y[${i2}]
+variable ny equal y[257]
+variable nz equal z[${i2}]
+variable nz equal z[257]
+set atom ${i1} x $(v_nx+0.2) y $(v_ny+0.2) z $(v_nz+0.2)
+set atom 13 x $(v_nx+0.2) y $(v_ny+0.2) z $(v_nz+0.2)
+set atom 13 x 4.4500000000000001776 y $(v_ny+0.2) z $(v_nz+0.2)
+set atom 13 x 4.4500000000000001776 y 1.4499999999999999556 z $(v_nz+0.2)
+set atom 13 x 4.4500000000000001776 y 1.4499999999999999556 z 1.4499999999999999556
+ 1 settings made for x
+ 1 settings made for y
+ 1 settings made for z
+
+run 0
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Memory usage per processor = 6.14663 Mbytes
+r0 r1 d5a d5b d5c d5d
+ 4000 4002 0 2 2 2
+Loop time of 2.74181e-06 on 4 procs for 0 steps with 4000 atoms
+
+0.0% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 2.742e-06 | | |100.00
+
+Nlocal: 1000 ave 1000 max 1000 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost: 17000 ave 17000 max 17000 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs: 99999.2 ave 100075 max 99967 min
+Histogram: 2 1 0 0 0 0 0 0 0 1
+
+Total # of neighbors = 399997
+Ave neighs/atom = 99.9993
+Neighbor list builds = 0
+Dangerous builds = 0
+# expect 0 2 2 2 (vacancy at the original i1 site, interstitial at i2 and both atoms are now sharing a site)
+variable t5b equal abs(${d5a}-0)+abs(${d5b}-2)+abs(${d5c}-2)+abs(${d5d}-2)
+variable t5b equal abs(0-0)+abs(${d5b}-2)+abs(${d5c}-2)+abs(${d5d}-2)
+variable t5b equal abs(0-0)+abs(2-2)+abs(${d5c}-2)+abs(${d5d}-2)
+variable t5b equal abs(0-0)+abs(2-2)+abs(2-2)+abs(${d5d}-2)
+variable t5b equal abs(0-0)+abs(2-2)+abs(2-2)+abs(2-2)
+
+# move atom back
+set atom ${i1} x ${ox} y ${oy} z ${oz}
+set atom 13 x ${ox} y ${oy} z ${oz}
+set atom 13 x 3.25 y ${oy} z ${oz}
+set atom 13 x 3.25 y 0.25 z ${oz}
+set atom 13 x 3.25 y 0.25 z 0.25
+ 1 settings made for x
+ 1 settings made for y
+ 1 settings made for z
+
+run 0
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Memory usage per processor = 6.14663 Mbytes
+r0 r1 d5a d5b d5c d5d
+ 4000 4000 1 1 1 1
+Loop time of 2.6226e-06 on 4 procs for 0 steps with 4000 atoms
+
+0.0% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 2.623e-06 | | |100.00
+
+Nlocal: 1000 ave 1000 max 1000 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost: 17000 ave 17000 max 17000 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs: 100000 ave 100000 max 100000 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 400000
+Ave neighs/atom = 100
+Neighbor list builds = 0
+Dangerous builds = 0
+# expect 1 1 1 1 (restored to the initial state)
+variable t5c equal abs(${d5a}-1)+abs(${d5b}-1)+abs(${d5c}-1)+abs(${d5d}-1)
+variable t5c equal abs(1-1)+abs(${d5b}-1)+abs(${d5c}-1)+abs(${d5d}-1)
+variable t5c equal abs(1-1)+abs(1-1)+abs(${d5c}-1)+abs(${d5d}-1)
+variable t5c equal abs(1-1)+abs(1-1)+abs(1-1)+abs(${d5d}-1)
+variable t5c equal abs(1-1)+abs(1-1)+abs(1-1)+abs(1-1)
+
+print "TEST_5 $((v_t5a+v_t5b+v_t5c)*100)% Error. Detection of vacancies and interstitials using the {occupation} keyword."
+TEST_5 0% Error. Detection of vacancies and interstitials using the {occupation} keyword.
+
+uncompute v1
+uncompute r0
+uncompute r1
+
+#
+# TEST 6: Sum of all voronoi cells is the triclinic simulation cell volume
+#
+
+# switch to triclinic box
+change_box all triclinic
+ triclinic box = (0 0 0) to (10 10 10) with tilt (0 0 0)
+change_box all xy final 5.0 remap units box
+ triclinic box = (0 0 0) to (10 10 10) with tilt (5 0 0)
+
+compute v1 all voronoi/atom
+dump d1 all custom 1 dump.voro id type x y z c_v1[1] c_v1[2]
+compute r0 all reduce sum c_v1[1]
+thermo_style custom c_r0
+variable t6 equal c_r0
+run 0
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.3
+ ghost atom cutoff = 5
+ binsize = 1.15 -> bins = 14 9 9
+Memory usage per processor = 7.70784 Mbytes
+r0
+ 250
+Loop time of 4.29153e-06 on 4 procs for 0 steps with 4000 atoms
+
+0.0% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 4.292e-06 | | |100.00
+
+Nlocal: 1000 ave 1000 max 1000 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost: 17900 ave 17900 max 17900 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs: 108000 ave 108000 max 108000 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 432000
+Ave neighs/atom = 108
+Neighbor list builds = 0
+Dangerous builds = 0
+print "TEST_6 $(round((v_t6-1000)/10))% Error. Sum of all voronoi cells is the triclinic simulation cell volume"
+TEST_6 -75% Error. Sum of all voronoi cells is the triclinic simulation cell volume
+uncompute v1
+uncompute r0
+undump d1
+
+# All tests done
+
+print TEST_DONE
+TEST_DONE
+Total wall time: 0:00:11