diff --git a/examples/DIFFUSE/README b/examples/DIFFUSE/README
index df2a675f73b778dd3d4fda1bafff791f2bebf4a6..e78ca2eacf1a109ec3aeb79b3b13e3444ed7d7a9 100644
--- a/examples/DIFFUSE/README
+++ b/examples/DIFFUSE/README
@@ -47,7 +47,7 @@ compute the diffusion coefficient. You can see that both measures
give roughly the same answer and rapidly become roughly constant for
the 100K step simulation.
-Dcoeff = 0.36
+Dcoeff = 0.33
(2) in.vacf.2d
@@ -58,4 +58,4 @@ that point in time, converted into the diffusion coefficient. You can
see the VACF approach gives a more noise, fluctuating value for the
diffusion coefficient, compared to the MSD approach.
-Dcoeff = 0.25 to 0.45
+Dcoeff = ~0.25
diff --git a/examples/DIFFUSE/log.13Oct16.msd.2d.g++.8 b/examples/DIFFUSE/log.13Oct16.msd.2d.g++.8
deleted file mode 100644
index 473aa565278ec6802b78373adcf4b510722c93da..0000000000000000000000000000000000000000
--- a/examples/DIFFUSE/log.13Oct16.msd.2d.g++.8
+++ /dev/null
@@ -1,245 +0,0 @@
-LAMMPS (13 Oct 2016)
-# sample LAMMPS input script for diffusion of 2d LJ liquid
-# mean-squared displacement via compute msd
-
-# settings
-
-variable x equal 40
-variable y equal 40
-
-variable rho equal 0.6
-variable t equal 1.0
-variable rc equal 2.5
-
-# problem setup
-
-units lj
-dimension 2
-atom_style atomic
-neigh_modify delay 0 every 1
-
-lattice sq2 ${rho}
-lattice sq2 0.6
-Lattice spacing in x,y,z = 1.82574 1.82574 1.82574
-region simbox block 0 $x 0 $y -0.1 0.1
-region simbox block 0 40 0 $y -0.1 0.1
-region simbox block 0 40 0 40 -0.1 0.1
-create_box 1 simbox
-Created orthogonal box = (0 0 -0.182574) to (73.0297 73.0297 0.182574)
- 4 by 2 by 1 MPI processor grid
-create_atoms 1 box
-Created 3200 atoms
-
-pair_style lj/cut ${rc}
-pair_style lj/cut 2.5
-pair_coeff * * 1 1
-
-mass * 1.0
-velocity all create $t 97287
-velocity all create 1 97287
-
-fix 1 all nve
-fix 2 all langevin $t $t 0.1 498094
-fix 2 all langevin 1 $t 0.1 498094
-fix 2 all langevin 1 1 0.1 498094
-fix 3 all enforce2d
-
-# equilibration run
-
-thermo 1000
-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 = 53 53 1
-Memory usage per processor = 2.478 Mbytes
-Step Temp E_pair E_mol TotEng Press
- 0 1 -1.56492 0 -0.5652325 -1.5346995
- 1000 0.97537833 -1.5723957 0 -0.5973222 0.92877783
- 2000 0.99008371 -1.5748206 0 -0.58504633 1.0809416
- 3000 1.0111412 -1.5848987 0 -0.57407352 1.0174297
- 4000 1.0055417 -1.5857581 0 -0.58053054 0.95647691
- 5000 0.97069905 -1.5851114 0 -0.61471567 0.90108287
-Loop time of 0.554412 on 8 procs for 5000 steps with 3200 atoms
-
-Performance: 3896017.421 tau/day, 9018.559 timesteps/s
-98.9% CPU use with 8 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.23992 | 0.24608 | 0.25161 | 0.7 | 44.39
-Neigh | 0.063106 | 0.064417 | 0.066279 | 0.4 | 11.62
-Comm | 0.072465 | 0.085066 | 0.094837 | 2.3 | 15.34
-Output | 0.00013208 | 0.00013691 | 0.00014591 | 0.0 | 0.02
-Modify | 0.11441 | 0.11621 | 0.11769 | 0.3 | 20.96
-Other | | 0.04251 | | | 7.67
-
-Nlocal: 400 ave 406 max 394 min
-Histogram: 1 1 0 1 0 2 1 0 1 1
-Nghost: 202.5 ave 212 max 191 min
-Histogram: 1 0 0 0 3 1 0 2 0 1
-Neighs: 2800.88 ave 2903 max 2690 min
-Histogram: 1 1 0 0 1 2 1 0 1 1
-
-Total # of neighbors = 22407
-Ave neighs/atom = 7.00219
-Neighbor list builds = 599
-Dangerous builds = 0
-
-unfix 2
-
-# data gathering run
-
-reset_timestep 0
-
-# factor of 4 in 2 variables is for 2d
-
-compute msd all msd com yes
-variable twopoint equal c_msd[4]/4/(step*dt+1.0e-6)
-fix 9 all vector 10 c_msd[4]
-variable fitslope equal slope(f_9)/4/(10*dt)
-
-thermo_style custom step temp c_msd[4] v_twopoint v_fitslope
-
-# only need to run for 10K steps to make a good 100-frame movie
-
-#dump 1 all custom 1 tmp.dump id type vx vy vz
-
-#dump 2 all image 100 image.*.jpg type type zoom 1.6 adiam 1.2
-
-thermo 1000
-run 100000
-Memory usage per processor = 2.853 Mbytes
-Step Temp c_msd[4] v_twopoint v_fitslope
- 0 0.97069905 0 0 5e+20
- 1000 0.98138076 4.0484996 0.20242494 0.18046446
- 2000 0.97606079 9.2121392 0.23030346 0.2091528
- 3000 0.97924866 14.815034 0.24691721 0.22619184
- 4000 0.98568451 20.516817 0.25646019 0.23715506
- 5000 0.97551815 27.33922 0.27339219 0.24709999
- 6000 0.98482252 34.37734 0.28647782 0.25735178
- 7000 0.9672559 41.696689 0.29783348 0.26654059
- 8000 0.9836541 48.340277 0.30212673 0.27440308
- 9000 0.99087147 56.042692 0.31134828 0.28113047
- 10000 0.99663166 63.69663 0.31848314 0.28767921
- 11000 0.97776688 71.144109 0.32338231 0.29344527
- 12000 0.98246011 78.301774 0.32625739 0.29849471
- 13000 0.98788732 85.061923 0.32716124 0.3026655
- 14000 0.96872483 91.1658 0.32559214 0.30601023
- 15000 0.98955796 97.278388 0.32426129 0.3084275
- 16000 0.99855196 104.23997 0.3257499 0.31049883
- 17000 0.98600861 110.66055 0.3254722 0.31220348
- 18000 0.98696963 116.90111 0.32472531 0.31352676
- 19000 0.9881192 124.21305 0.32687644 0.31480062
- 20000 0.98527319 131.09874 0.32774685 0.31596198
- 21000 0.99015191 137.89263 0.32831579 0.31705324
- 22000 0.97972418 146.68982 0.33338595 0.31833889
- 23000 0.98911012 155.1264 0.33723129 0.31979515
- 24000 0.98810498 162.88634 0.33934653 0.32131187
- 25000 0.96961962 170.37907 0.34075814 0.32276215
- 26000 0.99118408 179.26511 0.34474059 0.32427111
- 27000 0.98515159 185.90764 0.3442734 0.32574529
- 28000 0.98951677 192.12183 0.34307469 0.32700292
- 29000 0.9832026 196.99457 0.33964581 0.32799023
- 30000 0.98449493 203.48475 0.33914124 0.3287171
- 31000 0.96585993 210.06193 0.33880956 0.32935775
- 32000 0.98758117 218.94174 0.34209646 0.33001591
- 33000 0.98875584 225.96489 0.34237104 0.33072947
- 34000 0.98007229 233.5792 0.34349882 0.3314385
- 35000 0.98415295 241.98148 0.34568783 0.33216634
- 36000 0.98101154 250.30876 0.34765106 0.33295272
- 37000 0.97606878 258.2127 0.34893608 0.33377673
- 38000 0.97220293 266.40464 0.35053242 0.33459273
- 39000 0.979783 272.8578 0.34981769 0.33539728
- 40000 0.98375673 279.87598 0.34984497 0.33609699
- 41000 0.97506523 288.07676 0.35131312 0.33677708
- 42000 0.97106749 296.11647 0.3525196 0.33751312
- 43000 0.97717259 304.46747 0.35403194 0.33823441
- 44000 0.98541435 312.57228 0.35519578 0.3389771
- 45000 0.97678287 321.82674 0.35758527 0.33973306
- 46000 0.98169719 329.78197 0.35845866 0.34051748
- 47000 0.99471466 337.11283 0.35863066 0.34127239
- 48000 0.98332437 346.0754 0.3604952 0.34202442
- 49000 0.98126947 356.11859 0.36338631 0.34282132
- 50000 0.98809751 365.65248 0.36565248 0.34368171
- 51000 0.95919516 373.91833 0.36658659 0.34454516
- 52000 0.98097913 381.26492 0.36660089 0.34538506
- 53000 0.97774072 388.81031 0.36680218 0.34618232
- 54000 0.99096915 395.56767 0.36626636 0.3469296
- 55000 0.97652739 401.72735 0.36520668 0.34760374
- 56000 0.99185306 407.28834 0.3636503 0.34819906
- 57000 0.96289342 414.75298 0.3638184 0.34871992
- 58000 0.97871716 424.69443 0.36611588 0.34927986
- 59000 0.98637393 433.14205 0.36706953 0.34986296
- 60000 0.98009845 438.14533 0.36512111 0.35040349
- 61000 0.99416712 446.08007 0.3656394 0.35088379
- 62000 0.97612483 450.90846 0.36363585 0.35132647
- 63000 0.97786531 455.36749 0.36140277 0.35167458
- 64000 0.99080668 458.04873 0.35785057 0.3519105
- 65000 0.97952497 461.31241 0.3548557 0.3520506
- 66000 0.98095955 463.91727 0.35145248 0.35207764
- 67000 0.98370788 468.93 0.34994776 0.35204043
- 68000 0.96931818 471.07765 0.34638063 0.35192685
- 69000 0.98512552 474.59146 0.34390685 0.35174053
- 70000 0.98065743 478.66071 0.3419005 0.35149002
- 71000 0.98971283 482.57357 0.33984054 0.35119434
- 72000 0.99890324 485.32018 0.3370279 0.35084345
- 73000 0.98649924 490.19497 0.33574998 0.35043722
- 74000 0.98723422 496.04991 0.33516886 0.35003351
- 75000 1.0025633 501.6313 0.33442087 0.34962094
- 76000 0.97859959 505.97813 0.33288035 0.34921013
- 77000 0.97973006 510.55334 0.33152814 0.3487692
- 78000 0.9903944 515.06966 0.33017286 0.34830833
- 79000 0.96847518 518.76483 0.32833217 0.3478214
- 80000 0.99171112 524.18127 0.32761329 0.34733349
- 81000 0.97202573 529.09959 0.32660468 0.3468315
- 82000 0.99368438 535.80271 0.32670897 0.34633058
- 83000 0.97932483 543.08233 0.32715803 0.34586259
- 84000 0.99078651 547.57861 0.32593965 0.34540839
- 85000 0.98973457 552.24581 0.32485048 0.34493584
- 86000 0.9835873 557.3493 0.32404029 0.34446152
- 87000 0.97180564 564.93434 0.32467491 0.34400358
- 88000 0.99743353 571.39837 0.32465817 0.3435667
- 89000 0.98993437 577.81703 0.32461631 0.3431411
- 90000 0.9926071 583.39378 0.32410765 0.342724
- 91000 0.98800458 591.08741 0.3247733 0.34232767
- 92000 0.98501879 596.10133 0.32396811 0.34193949
- 93000 0.98810082 604.02652 0.32474544 0.3415681
- 94000 0.97563748 609.43676 0.32416849 0.341209
- 95000 0.97283448 615.15754 0.32376713 0.34084828
- 96000 0.9883071 622.30912 0.32411933 0.34049871
- 97000 0.97717678 628.84457 0.32414669 0.34016355
- 98000 0.97190208 634.37377 0.32366009 0.3398341
- 99000 0.98687379 640.66666 0.32356902 0.33950845
- 100000 0.97559757 646.96406 0.32348203 0.33919036
-Loop time of 9.58779 on 8 procs for 100000 steps with 3200 atoms
-
-Performance: 4505729.040 tau/day, 10429.928 timesteps/s
-99.4% CPU use with 8 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 4.8572 | 4.9363 | 4.9822 | 1.7 | 51.49
-Neigh | 1.3583 | 1.376 | 1.3991 | 1.2 | 14.35
-Comm | 1.5192 | 1.7079 | 1.8264 | 7.2 | 17.81
-Output | 0.0085125 | 0.0086059 | 0.0089455 | 0.1 | 0.09
-Modify | 0.77663 | 0.7903 | 0.81378 | 1.3 | 8.24
-Other | | 0.7686 | | | 8.02
-
-Nlocal: 400 ave 413 max 391 min
-Histogram: 2 1 0 2 0 0 1 1 0 1
-Nghost: 204.75 ave 213 max 197 min
-Histogram: 1 1 0 1 0 3 0 1 0 1
-Neighs: 2800.62 ave 2959 max 2661 min
-Histogram: 1 1 1 2 0 0 0 1 1 1
-
-Total # of neighbors = 22405
-Ave neighs/atom = 7.00156
-Neighbor list builds = 12728
-Dangerous builds = 0
-Total wall time: 0:00:10
diff --git a/examples/DIFFUSE/log.3Aug18.msd.2d.g++.8 b/examples/DIFFUSE/log.3Aug18.msd.2d.g++.8
new file mode 100644
index 0000000000000000000000000000000000000000..113da9040d8a8eb37b84a4245ce3d904e219db3c
--- /dev/null
+++ b/examples/DIFFUSE/log.3Aug18.msd.2d.g++.8
@@ -0,0 +1,251 @@
+LAMMPS (2 Aug 2018)
+# sample LAMMPS input script for diffusion of 2d LJ liquid
+# mean-squared displacement via compute msd
+
+# settings
+
+variable x equal 40
+variable y equal 40
+
+variable rho equal 0.6
+variable t equal 1.0
+variable rc equal 2.5
+
+# problem setup
+
+units lj
+dimension 2
+atom_style atomic
+neigh_modify delay 0 every 1
+
+lattice sq2 ${rho}
+lattice sq2 0.6
+Lattice spacing in x,y,z = 1.82574 1.82574 1.82574
+region simbox block 0 $x 0 $y -0.1 0.1
+region simbox block 0 40 0 $y -0.1 0.1
+region simbox block 0 40 0 40 -0.1 0.1
+create_box 1 simbox
+Created orthogonal box = (0 0 -0.182574) to (73.0297 73.0297 0.182574)
+ 4 by 2 by 1 MPI processor grid
+create_atoms 1 box
+Created 3200 atoms
+ Time spent = 0.000706911 secs
+
+pair_style lj/cut ${rc}
+pair_style lj/cut 2.5
+pair_coeff * * 1 1
+
+mass * 1.0
+velocity all create $t 97287
+velocity all create 1 97287
+
+fix 1 all nve
+fix 2 all langevin $t $t 0.1 498094
+fix 2 all langevin 1 $t 0.1 498094
+fix 2 all langevin 1 1 0.1 498094
+fix 3 all enforce2d
+
+# equilibration run
+
+thermo 1000
+run 5000
+Neighbor list info ...
+ 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 = 53 53 1
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/2d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.052 | 3.052 | 3.052 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1 -1.56492 0 -0.5652325 -1.5346995
+ 1000 0.97537833 -1.5723957 0 -0.5973222 0.92877783
+ 2000 0.99008371 -1.5748206 0 -0.58504633 1.0809416
+ 3000 1.0111412 -1.5848987 0 -0.57407352 1.0174297
+ 4000 1.0055417 -1.5857581 0 -0.58053054 0.95647691
+ 5000 0.97069905 -1.5851114 0 -0.61471567 0.90108287
+Loop time of 0.667446 on 8 procs for 5000 steps with 3200 atoms
+
+Performance: 3236214.756 tau/day, 7491.238 timesteps/s
+99.9% CPU use with 8 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.22913 | 0.24877 | 0.28382 | 3.6 | 37.27
+Neigh | 0.064419 | 0.071256 | 0.080013 | 1.7 | 10.68
+Comm | 0.103 | 0.14054 | 0.17204 | 5.5 | 21.06
+Output | 0.00010705 | 0.00013995 | 0.00021911 | 0.0 | 0.02
+Modify | 0.13457 | 0.14973 | 0.16887 | 2.6 | 22.43
+Other | | 0.05701 | | | 8.54
+
+Nlocal: 400 ave 406 max 394 min
+Histogram: 1 1 0 1 0 2 1 0 1 1
+Nghost: 202.5 ave 212 max 191 min
+Histogram: 1 0 0 0 3 1 0 2 0 1
+Neighs: 2800.88 ave 2903 max 2690 min
+Histogram: 1 1 0 0 1 2 1 0 1 1
+
+Total # of neighbors = 22407
+Ave neighs/atom = 7.00219
+Neighbor list builds = 599
+Dangerous builds = 0
+
+unfix 2
+
+# data gathering run
+
+reset_timestep 0
+
+# factor of 4 in 2 variables is for 2d
+
+compute msd all msd com yes
+variable twopoint equal c_msd[4]/4/(step*dt+1.0e-6)
+fix 9 all vector 10 c_msd[4]
+variable fitslope equal slope(f_9)/4/(10*dt)
+
+thermo_style custom step temp c_msd[4] v_twopoint v_fitslope
+
+# only need to run for 10K steps to make a good 100-frame movie
+
+#dump 1 all custom 1 tmp.dump id type vx vy vz
+
+#dump 2 all image 100 image.*.jpg type type zoom 1.6 adiam 1.2
+
+thermo 1000
+run 100000
+Per MPI rank memory allocation (min/avg/max) = 3.427 | 3.427 | 3.427 Mbytes
+Step Temp c_msd[4] v_twopoint v_fitslope
+ 0 0.97069905 0 0 5e+20
+ 1000 0.98138076 4.0484996 0.20242494 0.20685564
+ 2000 0.97606079 9.2121392 0.23030346 0.23687918
+ 3000 0.97924866 14.815034 0.24691721 0.25405247
+ 4000 0.98568451 20.516817 0.25646019 0.26353644
+ 5000 0.97551815 27.33922 0.27339219 0.27544492
+ 6000 0.98482252 34.37734 0.28647782 0.28966619
+ 7000 0.9672559 41.696689 0.29783348 0.30165524
+ 8000 0.9836541 48.340277 0.30212673 0.31085371
+ 9000 0.99087147 56.042692 0.31134828 0.31811489
+ 10000 0.99663166 63.69663 0.31848314 0.32589374
+ 11000 0.97776688 71.144109 0.32338231 0.33219745
+ 12000 0.98246011 78.301774 0.32625739 0.33723
+ 13000 0.98788732 85.061923 0.32716124 0.34053027
+ 14000 0.96872483 91.1658 0.32559214 0.34231162
+ 15000 0.98955796 97.278388 0.32426129 0.34229511
+ 16000 0.99855196 104.23997 0.3257499 0.34217252
+ 17000 0.98600861 110.66055 0.3254722 0.34172446
+ 18000 0.98696963 116.90111 0.32472531 0.3408227
+ 19000 0.9881192 124.21305 0.32687644 0.34036538
+ 20000 0.98527319 131.09874 0.32774685 0.34003478
+ 21000 0.99015191 137.89263 0.32831579 0.33987868
+ 22000 0.97972418 146.68982 0.33338595 0.34060035
+ 23000 0.98911012 155.1264 0.33723129 0.34201036
+ 24000 0.98810498 162.88634 0.33934653 0.34371488
+ 25000 0.96961962 170.37907 0.34075814 0.34531409
+ 26000 0.99118408 179.26511 0.34474059 0.34717195
+ 27000 0.98515159 185.90764 0.3442734 0.34898035
+ 28000 0.98951677 192.12183 0.34307469 0.35021808
+ 29000 0.9832026 196.99457 0.33964581 0.35075459
+ 30000 0.98449493 203.48475 0.33914124 0.35066186
+ 31000 0.96585993 210.06193 0.33880956 0.35046715
+ 32000 0.98758117 218.94174 0.34209646 0.35046623
+ 33000 0.98875584 225.96489 0.34237104 0.35073944
+ 34000 0.98007229 233.5792 0.34349882 0.35109188
+ 35000 0.98415295 241.98148 0.34568783 0.35157879
+ 36000 0.98101154 250.30876 0.34765106 0.3523013
+ 37000 0.97606878 258.2127 0.34893608 0.35318097
+ 38000 0.97220293 266.40464 0.35053242 0.3540743
+ 39000 0.979783 272.8578 0.34981769 0.35496561
+ 40000 0.98375673 279.87598 0.34984497 0.35558182
+ 41000 0.97506523 288.07676 0.35131312 0.35618259
+ 42000 0.97106749 296.11647 0.3525196 0.35698571
+ 43000 0.97717259 304.46747 0.35403194 0.3577736
+ 44000 0.98541435 312.57228 0.35519578 0.35865003
+ 45000 0.97678287 321.82674 0.35758527 0.35958623
+ 46000 0.98169719 329.78197 0.35845866 0.36062236
+ 47000 0.99471466 337.11283 0.35863066 0.36158322
+ 48000 0.98332437 346.0754 0.3604952 0.36255042
+ 49000 0.98126947 356.11859 0.36338631 0.3636628
+ 50000 0.98809751 365.65248 0.36565248 0.36496809
+ 51000 0.95919516 373.91833 0.36658659 0.36628073
+ 52000 0.98097913 381.26492 0.36660089 0.36752237
+ 53000 0.97774072 388.81031 0.36680218 0.36863962
+ 54000 0.99096915 395.56767 0.36626636 0.36961521
+ 55000 0.97652739 401.72735 0.36520668 0.37038579
+ 56000 0.99185306 407.28834 0.3636503 0.37094092
+ 57000 0.96289342 414.75298 0.3638184 0.37130039
+ 58000 0.97871716 424.69443 0.36611588 0.37180428
+ 59000 0.98637393 433.14205 0.36706953 0.37239862
+ 60000 0.98009845 438.14533 0.36512111 0.37288487
+ 61000 0.99416712 446.08007 0.3656394 0.37321496
+ 62000 0.97612483 450.90846 0.36363585 0.37345792
+ 63000 0.97786531 455.36749 0.36140277 0.37344803
+ 64000 0.99080668 458.04873 0.35785057 0.37313914
+ 65000 0.97952497 461.31241 0.3548557 0.3725875
+ 66000 0.98095955 463.91727 0.35145248 0.37174735
+ 67000 0.98370788 468.93 0.34994776 0.37076942
+ 68000 0.96931818 471.07765 0.34638063 0.36961868
+ 69000 0.98512552 474.59146 0.34390685 0.36830908
+ 70000 0.98065743 478.66071 0.3419005 0.36686789
+ 71000 0.98971283 482.57357 0.33984054 0.36535224
+ 72000 0.99890324 485.32018 0.3370279 0.36373174
+ 73000 0.98649924 490.19497 0.33574998 0.36200692
+ 74000 0.98723422 496.04991 0.33516886 0.36034919
+ 75000 1.0025633 501.6313 0.33442087 0.35872052
+ 76000 0.97859959 505.97813 0.33288035 0.35714939
+ 77000 0.97973006 510.55334 0.33152814 0.35553808
+ 78000 0.9903944 515.06966 0.33017286 0.35391584
+ 79000 0.96847518 518.76483 0.32833217 0.35226287
+ 80000 0.99171112 524.18127 0.32761329 0.35065267
+ 81000 0.97202573 529.09959 0.32660468 0.34904364
+ 82000 0.99368438 535.80271 0.32670897 0.34747913
+ 83000 0.97932483 543.08233 0.32715803 0.34605097
+ 84000 0.99078651 547.57861 0.32593965 0.34469765
+ 85000 0.98973457 552.24581 0.32485048 0.34332115
+ 86000 0.9835873 557.3493 0.32404029 0.34197018
+ 87000 0.97180564 564.93434 0.32467491 0.34069702
+ 88000 0.99743353 571.39837 0.32465817 0.33951258
+ 89000 0.98993437 577.81703 0.32461631 0.33838511
+ 90000 0.9926071 583.39378 0.32410765 0.33730429
+ 91000 0.98800458 591.08741 0.3247733 0.33630505
+ 92000 0.98501879 596.10133 0.32396811 0.33534725
+ 93000 0.98810082 604.02652 0.32474544 0.33445545
+ 94000 0.97563748 609.43676 0.32416849 0.33361404
+ 95000 0.97283448 615.15754 0.32376713 0.33278044
+ 96000 0.9883071 622.30912 0.32411933 0.33199212
+ 97000 0.97717678 628.84457 0.32414669 0.33125729
+ 98000 0.97190208 634.37377 0.32366009 0.33054877
+ 99000 0.98687379 640.66666 0.32356902 0.32986014
+ 100000 0.97559757 646.96406 0.32348203 0.32920186
+Loop time of 7.61838 on 8 procs for 100000 steps with 3200 atoms
+
+Performance: 5670494.518 tau/day, 13126.145 timesteps/s
+100.0% CPU use with 8 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 3.5458 | 3.6709 | 3.8234 | 4.3 | 48.19
+Neigh | 1.1363 | 1.1513 | 1.1753 | 1.0 | 15.11
+Comm | 1.5901 | 1.7017 | 1.8664 | 6.9 | 22.34
+Output | 0.0041966 | 0.0043583 | 0.0050626 | 0.4 | 0.06
+Modify | 0.63816 | 0.65537 | 0.68918 | 2.0 | 8.60
+Other | | 0.4348 | | | 5.71
+
+Nlocal: 400 ave 413 max 391 min
+Histogram: 2 1 0 2 0 0 1 1 0 1
+Nghost: 204.75 ave 213 max 197 min
+Histogram: 1 1 0 1 0 3 0 1 0 1
+Neighs: 2800.62 ave 2959 max 2661 min
+Histogram: 1 1 1 2 0 0 0 1 1 1
+
+Total # of neighbors = 22405
+Ave neighs/atom = 7.00156
+Neighbor list builds = 12728
+Dangerous builds = 0
+Total wall time: 0:00:08
diff --git a/examples/DIFFUSE/log.13Oct16.vacf.2d.g++.8 b/examples/DIFFUSE/log.3Aug18.vacf.2d.g++.8
similarity index 84%
rename from examples/DIFFUSE/log.13Oct16.vacf.2d.g++.8
rename to examples/DIFFUSE/log.3Aug18.vacf.2d.g++.8
index 458315bc29de64e5a2102de7e98ed958e591252c..80c57ada9c31b8e299944689fd1cba2f6afb95f4 100644
--- a/examples/DIFFUSE/log.13Oct16.vacf.2d.g++.8
+++ b/examples/DIFFUSE/log.3Aug18.vacf.2d.g++.8
@@ -1,4 +1,4 @@
-LAMMPS (13 Oct 2016)
+LAMMPS (2 Aug 2018)
# sample LAMMPS input script for diffusion of 2d LJ liquid
# mean-squared displacement via compute msd
@@ -29,6 +29,7 @@ Created orthogonal box = (0 0 -0.182574) to (73.0297 73.0297 0.182574)
4 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 3200 atoms
+ Time spent = 0.000712872 secs
pair_style lj/cut ${rc}
pair_style lj/cut 2.5
@@ -49,13 +50,18 @@ fix 3 all enforce2d
thermo 1000
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 = 53 53 1
-Memory usage per processor = 2.478 Mbytes
+ binsize = 1.4, bins = 53 53 1
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/2d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.052 | 3.052 | 3.052 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -1.56492 0 -0.5652325 -1.5346995
1000 0.97537833 -1.5723957 0 -0.5973222 0.92877783
@@ -63,20 +69,20 @@ Step Temp E_pair E_mol TotEng Press
3000 1.0111412 -1.5848987 0 -0.57407352 1.0174297
4000 1.0055417 -1.5857581 0 -0.58053054 0.95647691
5000 0.97069905 -1.5851114 0 -0.61471567 0.90108287
-Loop time of 0.557588 on 8 procs for 5000 steps with 3200 atoms
+Loop time of 0.648098 on 8 procs for 5000 steps with 3200 atoms
-Performance: 3873826.669 tau/day, 8967.191 timesteps/s
-99.1% CPU use with 8 MPI tasks x no OpenMP threads
+Performance: 3332829.949 tau/day, 7714.884 timesteps/s
+99.9% CPU use with 8 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.23784 | 0.24683 | 0.25594 | 1.0 | 44.27
-Neigh | 0.062975 | 0.06439 | 0.0662 | 0.4 | 11.55
-Comm | 0.083826 | 0.092564 | 0.1035 | 2.1 | 16.60
-Output | 0.00011778 | 0.00012615 | 0.00014257 | 0.1 | 0.02
-Modify | 0.11466 | 0.11648 | 0.1187 | 0.4 | 20.89
-Other | | 0.0372 | | | 6.67
+Pair | 0.22614 | 0.24602 | 0.27481 | 2.8 | 37.96
+Neigh | 0.066875 | 0.07135 | 0.077825 | 1.2 | 11.01
+Comm | 0.098293 | 0.12744 | 0.1569 | 5.6 | 19.66
+Output | 0.0001049 | 0.00012228 | 0.00014496 | 0.0 | 0.02
+Modify | 0.13725 | 0.14919 | 0.16903 | 2.4 | 23.02
+Other | | 0.05398 | | | 8.33
Nlocal: 400 ave 406 max 394 min
Histogram: 1 1 0 1 0 2 1 0 1 1
@@ -114,7 +120,7 @@ thermo_style custom step temp c_vacf[4] v_vacf
thermo 1000
run 100000
-Memory usage per processor = 2.853 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 3.427 | 3.427 | 3.427 Mbytes
Step Temp c_vacf[4] v_vacf
0 0.97069905 1.9407914 0
1000 0.98138076 0.029239763 0.22157396
@@ -217,20 +223,20 @@ Step Temp c_vacf[4] v_vacf
98000 0.97190208 0.015065013 0.20906937
99000 0.98687379 -0.036869401 0.22993959
100000 0.97559757 0.045464091 0.23369283
-Loop time of 10.8346 on 8 procs for 100000 steps with 3200 atoms
+Loop time of 8.16691 on 8 procs for 100000 steps with 3200 atoms
-Performance: 3987213.825 tau/day, 9229.662 timesteps/s
-99.5% CPU use with 8 MPI tasks x no OpenMP threads
+Performance: 5289636.190 tau/day, 12244.528 timesteps/s
+100.0% CPU use with 8 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 4.8486 | 4.9469 | 5.0248 | 2.8 | 45.66
-Neigh | 1.3613 | 1.374 | 1.3916 | 0.8 | 12.68
-Comm | 1.8181 | 1.9534 | 2.0665 | 5.7 | 18.03
-Output | 0.016565 | 0.016701 | 0.017039 | 0.1 | 0.15
-Modify | 1.8395 | 1.9053 | 1.9704 | 2.8 | 17.59
-Other | | 0.6383 | | | 5.89
+Pair | 3.5668 | 3.6612 | 3.7867 | 4.0 | 44.83
+Neigh | 1.1409 | 1.1555 | 1.1804 | 1.4 | 14.15
+Comm | 1.581 | 1.711 | 1.8239 | 7.1 | 20.95
+Output | 0.016626 | 0.016831 | 0.017569 | 0.2 | 0.21
+Modify | 1.225 | 1.2594 | 1.3008 | 2.0 | 15.42
+Other | | 0.363 | | | 4.45
Nlocal: 400 ave 413 max 391 min
Histogram: 2 1 0 2 0 0 1 1 0 1
@@ -243,4 +249,4 @@ Total # of neighbors = 22405
Ave neighs/atom = 7.00156
Neighbor list builds = 12728
Dangerous builds = 0
-Total wall time: 0:00:11
+Total wall time: 0:00:08
diff --git a/src/variable.cpp b/src/variable.cpp
index 86296b4b402e4c066d2692d5362d579be635c54d..f005221400509f76fd5887f0323fa11cc8f30a32 100644
--- a/src/variable.cpp
+++ b/src/variable.cpp
@@ -1576,7 +1576,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
newtree->nextra = 0;
treestack[ntreestack++] = newtree;
- } else print_var_error(FLERR,"Mismatched compute in variable formula",ivar);
+ } else print_var_error(FLERR,
+ "Mismatched compute in variable formula",ivar);
// ----------------
// fix
@@ -1584,7 +1585,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
} else if (strncmp(word,"f_",2) == 0 || strncmp(word,"F_",2) == 0) {
if (domain->box_exist == 0)
- print_var_error(FLERR,"Variable evaluation before simulation box is defined",ivar);
+ print_var_error(FLERR,"Variable evaluation before "
+ "simulation box is defined",ivar);
// uppercase used to force access of
// global vector vs global scalar, and global array vs global vector
@@ -1667,11 +1669,14 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
if (index1 > fix->size_array_rows &&
fix->size_array_rows_variable == 0)
- print_var_error(FLERR,"Variable formula fix array is accessed out-of-range",ivar);
+ print_var_error(FLERR,"Variable formula fix array is "
+ "accessed out-of-range",ivar);
if (index2 > fix->size_array_cols)
- print_var_error(FLERR,"Variable formula fix array is accessed out-of-range",ivar);
+ print_var_error(FLERR,"Variable formula fix array is "
+ "accessed out-of-range",ivar);
if (update->whichflag > 0 && update->ntimestep % fix->global_freq)
- print_var_error(FLERR,"Fix in variable not computed at a compatible time",ivar);
+ print_var_error(FLERR,"Fix in variable not computed at a "
+ "compatible time",ivar);
value1 = fix->compute_array(index1-1,index2-1);
if (tree) {
@@ -1688,13 +1693,17 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
} else if (nbracket == 0 && fix->vector_flag) {
if (update->whichflag > 0 && update->ntimestep % fix->global_freq)
- print_var_error(FLERR,"Fix in variable not computed at compatible time",ivar);
+ print_var_error(FLERR,"Fix in variable not computed at "
+ "compatible time",ivar);
if (tree == NULL)
- print_var_error(FLERR,"Fix global vector in ""equal-style variable formula",ivar);
+ print_var_error(FLERR,"Fix global vector in "
+ "equal-style variable formula",ivar);
if (treetype == ATOM)
- print_var_error(FLERR,"Fix global vector in ""atom-style variable formula",ivar);
+ print_var_error(FLERR,"Fix global vector in "
+ "atom-style variable formula",ivar);
if (fix->size_vector == 0)
- print_var_error(FLERR,"Variable formula fix vector is zero length",ivar);
+ print_var_error(FLERR,"Variable formula "
+ "fix vector is zero length",ivar);
int nvec = fix->size_vector;
double *vec;
@@ -1726,7 +1735,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
print_var_error(FLERR,"Fix global vector in "
"atom-style variable formula",ivar);
if (fix->size_array_rows == 0)
- print_var_error(FLERR,"Variable formula fix array is zero length",ivar);
+ print_var_error(FLERR,"Variable formula fix array is "
+ "zero length",ivar);
int nvec = fix->size_array_rows;
double *vec;
@@ -1785,10 +1795,12 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
fix->size_peratom_cols == 0) {
if (tree == NULL)
- print_var_error(FLERR,"Per-atom fix in equal-style variable formula",ivar);
+ print_var_error(FLERR,"Per-atom fix in "
+ "equal-style variable formula",ivar);
if (update->whichflag > 0 &&
update->ntimestep % fix->peratom_freq)
- print_var_error(FLERR,"Fix in variable not computed at compatible time",ivar);
+ print_var_error(FLERR,"Fix in variable not computed at "
+ "compatible time",ivar);
Tree *newtree = new Tree();
newtree->type = ATOMARRAY;
@@ -1805,13 +1817,15 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
fix->size_peratom_cols > 0) {
if (tree == NULL)
- print_var_error(FLERR,"Per-atom fix in equal-style variable formula",ivar);
+ print_var_error(FLERR,"Per-atom fix in "
+ "equal-style variable formula",ivar);
if (index1 > fix->size_peratom_cols)
print_var_error(FLERR,"Variable formula fix array "
"is accessed out-of-range",ivar);
if (update->whichflag > 0 &&
update->ntimestep % fix->peratom_freq)
- print_var_error(FLERR,"Fix in variable not computed at compatible time",ivar);
+ print_var_error(FLERR,"Fix in variable not computed at "
+ "compatible time",ivar);
Tree *newtree = new Tree();
newtree->type = ATOMARRAY;
@@ -1878,7 +1892,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
char *var = retrieve(word+2);
if (var == NULL)
- print_var_error(FLERR,"Invalid variable evaluation in variable formula",ivar);
+ print_var_error(FLERR,"Invalid variable evaluation in "
+ "variable formula",ivar);
if (tree) {
Tree *newtree = new Tree();
newtree->type = VALUE;
@@ -1977,7 +1992,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
double *vec;
int nvec = compute_vector(ivar,&vec);
if (index <= 0 || index > nvec)
- print_var_error(FLERR,"Invalid index into vector-style variable",ivar);
+ print_var_error(FLERR,"Invalid index into "
+ "vector-style variable",ivar);
int m = index; // convert from tagint to int
if (tree) {
@@ -1989,7 +2005,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
treestack[ntreestack++] = newtree;
} else argstack[nargstack++] = vec[m-1];
- } else print_var_error(FLERR,"Mismatched variable in variable formula",ivar);
+ } else print_var_error(FLERR,"Mismatched variable in "
+ "variable formula",ivar);
// ----------------
// math/group/special function or atom value/vector or
@@ -2194,7 +2211,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
if (value2 == 0.0)
argstack[nargstack++] = 1.0;
else if ((value1 == 0.0) && (value2 < 0.0))
- print_var_error(FLERR,"Invalid power expression in variable formula",ivar);
+ print_var_error(FLERR,"Invalid power expression in "
+ "variable formula",ivar);
else argstack[nargstack++] = pow(value1,value2);
} else if (opprevious == UNARY) {
argstack[nargstack++] = -value2;
@@ -3368,7 +3386,8 @@ int Variable::math_function(char *word, char *contents, Tree **tree,
if (tree) newtree->type = LN;
else {
if (value1 <= 0.0)
- print_var_error(FLERR,"Log of zero/negative value in variable formula",ivar);
+ print_var_error(FLERR,"Log of zero/negative value in "
+ "variable formula",ivar);
argstack[nargstack++] = log(value1);
}
} else if (strcmp(word,"log") == 0) {
@@ -3377,7 +3396,8 @@ int Variable::math_function(char *word, char *contents, Tree **tree,
if (tree) newtree->type = LOG;
else {
if (value1 <= 0.0)
- print_var_error(FLERR,"Log of zero/negative value in variable formula",ivar);
+ print_var_error(FLERR,"Log of zero/negative value in "
+ "variable formula",ivar);
argstack[nargstack++] = log10(value1);
}
} else if (strcmp(word,"abs") == 0) {
@@ -3482,7 +3502,8 @@ int Variable::math_function(char *word, char *contents, Tree **tree,
if (narg != 2)
print_var_error(FLERR,"Invalid math function in variable formula",ivar);
if (update->whichflag == 0)
- print_var_error(FLERR,"Cannot use ramp in variable formula between runs",ivar);
+ print_var_error(FLERR,"Cannot use ramp in "
+ "variable formula between runs",ivar);
if (tree) newtree->type = RAMP;
else {
double delta = update->ntimestep - update->beginstep;
@@ -3617,7 +3638,8 @@ int Variable::math_function(char *word, char *contents, Tree **tree,
if (narg != 2)
print_var_error(FLERR,"Invalid math function in variable formula",ivar);
if (update->whichflag == 0)
- print_var_error(FLERR,"Cannot use vdisplace in variable formula between runs",ivar);
+ print_var_error(FLERR,"Cannot use vdisplace in "
+ "variable formula between runs",ivar);
if (tree) newtree->type = VDISPLACE;
else {
double delta = update->ntimestep - update->beginstep;
@@ -3629,7 +3651,8 @@ int Variable::math_function(char *word, char *contents, Tree **tree,
if (narg != 3)
print_var_error(FLERR,"Invalid math function in variable formula",ivar);
if (update->whichflag == 0)
- print_var_error(FLERR,"Cannot use swiggle in variable formula between runs",ivar);
+ print_var_error(FLERR,"Cannot use swiggle in "
+ "variable formula between runs",ivar);
if (tree) newtree->type = CWIGGLE;
else {
if (values[0] == 0.0)
@@ -3644,7 +3667,8 @@ int Variable::math_function(char *word, char *contents, Tree **tree,
if (narg != 3)
print_var_error(FLERR,"Invalid math function in variable formula",ivar);
if (update->whichflag == 0)
- print_var_error(FLERR,"Cannot use cwiggle in variable formula between runs",ivar);
+ print_var_error(FLERR,"Cannot use cwiggle in "
+ "variable formula between runs",ivar);
if (tree) newtree->type = CWIGGLE;
else {
if (values[0] == 0.0)
@@ -3709,7 +3733,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
if (strcmp(word,"count") == 0) {
if (narg == 1) value = group->count(igroup);
- else if (narg == 2) value = group->count(igroup,region_function(args[1],ivar));
+ else if (narg == 2)
+ value = group->count(igroup,region_function(args[1],ivar));
else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
} else if (strcmp(word,"mass") == 0) {
@@ -3719,7 +3744,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
} else if (strcmp(word,"charge") == 0) {
if (narg == 1) value = group->charge(igroup);
- else if (narg == 2) value = group->charge(igroup,region_function(args[1],ivar));
+ else if (narg == 2)
+ value = group->charge(igroup,region_function(args[1],ivar));
else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
} else if (strcmp(word,"xcm") == 0) {
@@ -3732,7 +3758,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
int iregion = region_function(args[2],ivar);
double masstotal = group->mass(igroup,iregion);
group->xcm(igroup,masstotal,xcm,iregion);
- } else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
+ } else print_var_error(FLERR,"Invalid group function in "
+ "variable formula",ivar);
if (strcmp(args[1],"x") == 0) value = xcm[0];
else if (strcmp(args[1],"y") == 0) value = xcm[1];
else if (strcmp(args[1],"z") == 0) value = xcm[2];
@@ -3748,7 +3775,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
int iregion = region_function(args[2],ivar);
double masstotal = group->mass(igroup,iregion);
group->vcm(igroup,masstotal,vcm,iregion);
- } else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
+ } else print_var_error(FLERR,"Invalid group function in "
+ "variable formula",ivar);
if (strcmp(args[1],"x") == 0) value = vcm[0];
else if (strcmp(args[1],"y") == 0) value = vcm[1];
else if (strcmp(args[1],"z") == 0) value = vcm[2];
@@ -3767,7 +3795,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
} else if (strcmp(word,"bound") == 0) {
double minmax[6];
if (narg == 2) group->bounds(igroup,minmax);
- else if (narg == 3) group->bounds(igroup,minmax,region_function(args[2],ivar));
+ else if (narg == 3)
+ group->bounds(igroup,minmax,region_function(args[2],ivar));
else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
if (strcmp(args[1],"xmin") == 0) value = minmax[0];
else if (strcmp(args[1],"xmax") == 0) value = minmax[1];
@@ -3789,7 +3818,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
double masstotal = group->mass(igroup,iregion);
group->xcm(igroup,masstotal,xcm,iregion);
value = group->gyration(igroup,masstotal,xcm,iregion);
- } else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
+ } else print_var_error(FLERR,"Invalid group function in "
+ "variable formula",ivar);
} else if (strcmp(word,"ke") == 0) {
if (narg == 1) value = group->ke(igroup);
@@ -3808,7 +3838,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
double masstotal = group->mass(igroup,iregion);
group->xcm(igroup,masstotal,xcm,iregion);
group->angmom(igroup,xcm,lmom,iregion);
- } else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
+ } else print_var_error(FLERR,"Invalid group function in "
+ "variable formula",ivar);
if (strcmp(args[1],"x") == 0) value = lmom[0];
else if (strcmp(args[1],"y") == 0) value = lmom[1];
else if (strcmp(args[1],"z") == 0) value = lmom[2];
@@ -3826,7 +3857,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
double masstotal = group->mass(igroup,iregion);
group->xcm(igroup,masstotal,xcm,iregion);
group->torque(igroup,xcm,tq,iregion);
- } else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
+ } else print_var_error(FLERR,"Invalid group function in "
+ "variable formula",ivar);
if (strcmp(args[1],"x") == 0) value = tq[0];
else if (strcmp(args[1],"y") == 0) value = tq[1];
else if (strcmp(args[1],"z") == 0) value = tq[2];
@@ -3844,7 +3876,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
double masstotal = group->mass(igroup,iregion);
group->xcm(igroup,masstotal,xcm,iregion);
group->inertia(igroup,xcm,inertia,iregion);
- } else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
+ } else print_var_error(FLERR,"Invalid group function in "
+ "variable formula",ivar);
if (strcmp(args[1],"xx") == 0) value = inertia[0][0];
else if (strcmp(args[1],"yy") == 0) value = inertia[1][1];
else if (strcmp(args[1],"zz") == 0) value = inertia[2][2];
@@ -3869,7 +3902,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
group->angmom(igroup,xcm,angmom,iregion);
group->inertia(igroup,xcm,inertia,iregion);
group->omega(angmom,inertia,omega);
- } else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
+ } else print_var_error(FLERR,"Invalid group function in "
+ "variable formula",ivar);
if (strcmp(args[1],"x") == 0) value = omega[0];
else if (strcmp(args[1],"y") == 0) value = omega[1];
else if (strcmp(args[1],"z") == 0) value = omega[2];
@@ -3924,7 +3958,8 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
Tree **treestack, int &ntreestack,
double *argstack, int &nargstack, int ivar)
{
- double value,xvalue,sx,sy,sxx,sxy;
+ bigint sx,sxx;
+ double value,xvalue,sy,sxy;
// word not a match to any special function
@@ -4020,11 +4055,13 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
} else index = 0;
int ifix = modify->find_fix(&args[0][2]);
- if (ifix < 0) print_var_error(FLERR,"Invalid fix ID in variable formula",ivar);
+ if (ifix < 0)
+ print_var_error(FLERR,"Invalid fix ID in variable formula",ivar);
fix = modify->fix[ifix];
if (index == 0 && fix->vector_flag) {
if (update->whichflag > 0 && update->ntimestep % fix->global_freq)
- print_var_error(FLERR,"Fix in variable not computed at compatible time",ivar);
+ print_var_error(FLERR,"Fix in variable not computed at "
+ "compatible time",ivar);
nvec = fix->size_vector;
nstride = 1;
} else if (index && fix->array_flag) {
@@ -4032,7 +4069,8 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
print_var_error(FLERR,"Variable formula fix array "
"is accessed out-of-range",ivar);
if (update->whichflag > 0 && update->ntimestep % fix->global_freq)
- print_var_error(FLERR,"Fix in variable not computed at compatible time",ivar);
+ print_var_error(FLERR,"Fix in variable not computed at "
+ "compatible time",ivar);
nvec = fix->size_array_rows;
nstride = fix->size_array_cols;
} else print_var_error(FLERR,"Mismatched fix in variable formula",ivar);
@@ -4048,10 +4086,12 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
} else index = 0;
if (index)
- print_var_error(FLERR,"Invalid special function in variable formula",ivar);
+ print_var_error(FLERR,"Invalid special function in "
+ "variable formula",ivar);
ivar = find(&args[0][2]);
if (ivar < 0)
- print_var_error(FLERR,"Invalid special function in variable formula",ivar);
+ print_var_error(FLERR,"Invalid special function in "
+ "variable formula",ivar);
if (style[ivar] != VECTOR)
print_var_error(FLERR,"Mis-matched special function variable "
"in variable formula",ivar);
@@ -4062,12 +4102,16 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
nvec = compute_vector(ivar,&vec);
nstride = 1;
- } else print_var_error(FLERR,"Invalid special function in variable formula",ivar);
+ } else print_var_error(FLERR,"Invalid special function in "
+ "variable formula",ivar);
value = 0.0;
- if (method == SLOPE) sx = sy = sxx = sxy = 0.0;
- if (method == XMIN) value = BIG;
- if (method == XMAX) value = -BIG;
+ if (method == SLOPE) {
+ sx = sxx = 0;
+ sy = sxy = 0.0;
+ }
+ else if (method == XMIN) value = BIG;
+ else if (method == XMAX) value = -BIG;
if (compute) {
double *vec;
@@ -4084,12 +4128,10 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
else if (method == AVE) value += vec[j];
else if (method == TRAP) value += vec[j];
else if (method == SLOPE) {
- if (nvec > 1) xvalue = (double) i / (nvec-1);
- else xvalue = 0.0;
- sx += xvalue;
+ sx += i;
sy += vec[j];
- sxx += xvalue*xvalue;
- sxy += xvalue*vec[j];
+ sxx += i*i;
+ sxy += i*vec[j];
}
j += nstride;
}
@@ -4107,12 +4149,10 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
else if (method == AVE) value += one;
else if (method == TRAP) value += one;
else if (method == SLOPE) {
- if (nvec > 1) xvalue = (double) i / (nvec-1);
- else xvalue = 0.0;
- sx += xvalue;
+ sx += i;
sy += one;
- sxx += xvalue*xvalue;
- sxy += xvalue*one;
+ sxx += i*i;
+ sxy += i*one;
}
}
if (method == TRAP) {
@@ -4134,12 +4174,10 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
else if (method == AVE) value += one;
else if (method == TRAP) value += one;
else if (method == SLOPE) {
- if (nvec > 1) xvalue = (double) i / (nvec-1);
- else xvalue = 0.0;
- sx += xvalue;
+ sx += i;
sy += one;
- sxx += xvalue*xvalue;
- sxy += xvalue*one;
+ sxx += i*i;
+ sxy += i*one;
}
}
if (method == TRAP) value -= 0.5*vec[0] + 0.5*vec[nvec-1];
@@ -4148,9 +4186,9 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
if (method == AVE) value /= nvec;
if (method == SLOPE) {
- double numerator = sxy - sx*sy;
- double denominator = sxx - sx*sx;
- if (denominator != 0.0) value = numerator/denominator / nvec;
+ double numerator = nvec*sxy - sx*sy;
+ double denominator = nvec*sxx - sx*sx;
+ if (denominator != 0.0) value = numerator/denominator;
else value = BIG;
}
@@ -4169,7 +4207,8 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
} else if (strcmp(word,"gmask") == 0) {
if (tree == NULL)
- print_var_error(FLERR,"Gmask function in equal-style variable formula",ivar);
+ print_var_error(FLERR,"Gmask function in equal-style "
+ "variable formula",ivar);
if (narg != 1)
print_var_error(FLERR,"Invalid special function in variable formula",ivar);
@@ -4186,7 +4225,8 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
} else if (strcmp(word,"rmask") == 0) {
if (tree == NULL)
- print_var_error(FLERR,"Rmask function in equal-style variable formula",ivar);
+ print_var_error(FLERR,"Rmask function in equal-style "
+ "variable formula",ivar);
if (narg != 1)
print_var_error(FLERR,"Invalid special function in variable formula",ivar);
@@ -4202,7 +4242,8 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
} else if (strcmp(word,"grmask") == 0) {
if (tree == NULL)
- print_var_error(FLERR,"Grmask function in equal-style variable formula",ivar);
+ print_var_error(FLERR,"Grmask function in equal-style "
+ "variable formula",ivar);
if (narg != 2)
print_var_error(FLERR,"Invalid special function in variable formula",ivar);
@@ -4228,7 +4269,8 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
int ivar = find(args[0]);
if (ivar < 0)
- print_var_error(FLERR,"Variable ID in variable formula does not exist",ivar);
+ print_var_error(FLERR,"Variable ID in "
+ "variable formula does not exist",ivar);
// SCALARFILE has single current value, read next one
// save value in tree or on argstack
@@ -4253,7 +4295,8 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
} else if (style[ivar] == ATOMFILE) {
if (tree == NULL)
- print_var_error(FLERR,"Atomfile variable in equal-style variable formula",ivar);
+ print_var_error(FLERR,"Atomfile variable in "
+ "equal-style variable formula",ivar);
double *result;
memory->create(result,atom->nlocal,"variable:result");
@@ -4271,11 +4314,13 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
newtree->nextra = 0;
treestack[ntreestack++] = newtree;
- } else print_var_error(FLERR,"Invalid variable style in special function next",ivar);
+ } else print_var_error(FLERR,"Invalid variable style in "
+ "special function next",ivar);
} else if (strcmp(word,"is_active") == 0) {
if (narg != 2)
- print_var_error(FLERR,"Invalid is_active() function in variable formula",ivar);
+ print_var_error(FLERR,"Invalid is_active() function in "
+ "variable formula",ivar);
Info info(lmp);
value = (info.is_active(args[0],args[1])) ? 1.0 : 0.0;
@@ -4293,7 +4338,8 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
} else if (strcmp(word,"is_available") == 0) {
if (narg != 2)
- print_var_error(FLERR,"Invalid is_available() function in variable formula",ivar);
+ print_var_error(FLERR,"Invalid is_available() function in "
+ "variable formula",ivar);
Info info(lmp);
value = (info.is_available(args[0],args[1])) ? 1.0 : 0.0;
@@ -4311,7 +4357,8 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
} else if (strcmp(word,"is_defined") == 0) {
if (narg != 2)
- print_var_error(FLERR,"Invalid is_defined() function in variable formula",ivar);
+ print_var_error(FLERR,"Invalid is_defined() function in "
+ "variable formula",ivar);
Info info(lmp);
value = (info.is_defined(args[0],args[1])) ? 1.0 : 0.0;