From c763916f9e8709774f16bd517a2aaa3c4e5bf90f Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 28 Nov 2018 21:21:54 -0500
Subject: [PATCH] update log files for granregion hugoniostat and indent
examples
---
.../log.27Nov18.granregion.box.g++.1 | 475 ++++++++++++++
.../log.27Nov18.granregion.box.g++.4 | 475 ++++++++++++++
.../log.27Nov18.granregion.funnel.g++.1 | 601 +++++++++++++++++
.../log.27Nov18.granregion.funnel.g++.4 | 601 +++++++++++++++++
.../log.27Nov18.granregion.mixer.g++.1 | 602 +++++++++++++++++
.../log.27Nov18.granregion.mixer.g++.4 | 602 +++++++++++++++++
.../log.6Oct16.granregion.box.g++.1 | 468 --------------
.../log.6Oct16.granregion.box.g++.4 | 468 --------------
.../log.6Oct16.granregion.funnel.g++.1 | 608 -----------------
.../log.6Oct16.granregion.funnel.g++.4 | 608 -----------------
.../log.6Oct16.granregion.mixer.g++.1 | 609 ------------------
.../log.6Oct16.granregion.mixer.g++.4 | 609 ------------------
examples/hugoniostat/in.hugoniostat | 32 +-
.../hugoniostat/log.27Nov18.hugoniostat.g++.1 | 401 ++++++++++++
.../hugoniostat/log.27Nov18.hugoniostat.g++.4 | 401 ++++++++++++
....indent.g++.1 => log.27Nov18.indent.g++.1} | 55 +-
....indent.g++.4 => log.27Nov18.indent.g++.4} | 57 +-
...min.g++.1 => log.27Nov18.indent.min.g++.1} | 153 ++---
...min.g++.4 => log.27Nov18.indent.min.g++.4} | 153 ++---
19 files changed, 4394 insertions(+), 3584 deletions(-)
create mode 100644 examples/granregion/log.27Nov18.granregion.box.g++.1
create mode 100644 examples/granregion/log.27Nov18.granregion.box.g++.4
create mode 100644 examples/granregion/log.27Nov18.granregion.funnel.g++.1
create mode 100644 examples/granregion/log.27Nov18.granregion.funnel.g++.4
create mode 100644 examples/granregion/log.27Nov18.granregion.mixer.g++.1
create mode 100644 examples/granregion/log.27Nov18.granregion.mixer.g++.4
delete mode 100644 examples/granregion/log.6Oct16.granregion.box.g++.1
delete mode 100644 examples/granregion/log.6Oct16.granregion.box.g++.4
delete mode 100644 examples/granregion/log.6Oct16.granregion.funnel.g++.1
delete mode 100644 examples/granregion/log.6Oct16.granregion.funnel.g++.4
delete mode 100644 examples/granregion/log.6Oct16.granregion.mixer.g++.1
delete mode 100644 examples/granregion/log.6Oct16.granregion.mixer.g++.4
create mode 100644 examples/hugoniostat/log.27Nov18.hugoniostat.g++.1
create mode 100644 examples/hugoniostat/log.27Nov18.hugoniostat.g++.4
rename examples/indent/{log.5Oct16.indent.g++.1 => log.27Nov18.indent.g++.1} (82%)
rename examples/indent/{log.5Oct16.indent.g++.4 => log.27Nov18.indent.g++.4} (82%)
rename examples/indent/{log.5Oct16.indent.min.g++.1 => log.27Nov18.indent.min.g++.1} (77%)
rename examples/indent/{log.5Oct16.indent.min.g++.4 => log.27Nov18.indent.min.g++.4} (76%)
diff --git a/examples/granregion/log.27Nov18.granregion.box.g++.1 b/examples/granregion/log.27Nov18.granregion.box.g++.1
new file mode 100644
index 0000000000..ef004b7398
--- /dev/null
+++ b/examples/granregion/log.27Nov18.granregion.box.g++.1
@@ -0,0 +1,475 @@
+LAMMPS (27 Nov 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+# pouring spheres into container box
+
+units lj
+atom_style sphere
+boundary f f f
+dimension 3
+comm_modify vel yes
+
+region box block -10 10 -10 10 -10 10 units box
+create_box 2 box
+Created orthogonal box = (-10 -10 -10) to (10 10 10)
+ 1 by 1 by 1 MPI processor grid
+
+pair_style hybrid gran/hooke 4000.0 NULL 100.0 NULL 0.5 1
+pair_coeff * * gran/hooke
+
+region container block -6 6 -6 6 -6 6 units box
+fix container all wall/gran/region hooke/history 4000.0 NULL 100.0 NULL 0.5 1 region container
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 2 all nve/sphere
+fix 3 all gravity 1.0 vector 0 0 -1
+
+region slab block -2 2 -2 2 -2 2 units box
+fix ins all pour 100 2 4767548 vol 0.4 10 diam one 1.0 region slab ignore
+Particle insertion: 48 every 566 steps, 100 by step 1133
+
+timestep 0.005
+
+compute 1 all temp
+compute_modify 1 dynamic/dof yes
+
+compute 2 all temp/sphere
+compute_modify 2 dynamic/dof yes
+
+thermo 100
+thermo_style custom step atoms temp c_1 c_2 press
+thermo_modify lost ignore
+compute_modify thermo_temp dynamic/dof yes
+
+#dump 2 all image 100 image.*.jpg type type # zoom 1.4 adiam 1.0 box no 0.0 axes yes 0.9 0.03
+#dump_modify 2 pad 5
+
+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 = 1.3
+ ghost atom cutoff = 1.3
+ binsize = 0.65, bins = 31 31 31
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair gran/hooke, perpetual
+ attributes: half, newton on, size
+ pair build: half/size/bin/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 0.5855 | 0.5855 | 0.5855 Mbytes
+Step Atoms Temp c_1 c_2 Press
+ 0 0 0 0 0 0
+ 100 21 0.54270729 0.54270729 0.26473526 0.0013567682
+ 200 21 0.87606961 0.87606961 0.42735103 0.002190174
+ 300 21 1.1428374 1.1428374 0.55748167 0.0028570936
+ 400 21 1.3543103 1.3543103 0.66829516 0.0033857758
+ 500 21 1.0677786 1.0677786 0.53582407 0.0045048164
+ 600 56 0.6744286 0.6744286 0.3502938 0.0047464584
+ 700 56 0.75569283 0.75569283 0.39779462 0.0051953882
+ 800 56 0.61597505 0.61597505 0.32943642 0.0086022783
+ 900 56 0.65260802 0.65260802 0.34474044 0.0059298996
+ 1000 56 0.51624952 0.51624952 0.28326898 0.0067827337
+ 1100 56 0.46050076 0.46050076 0.25656319 0.0061891094
+ 1200 81 0.39112346 0.39112346 0.21690172 0.0086559316
+ 1300 81 0.33302617 0.33302617 0.19109398 0.0033381104
+ 1400 81 0.3933533 0.3933533 0.21221692 0.004135078
+ 1500 81 0.35495297 0.35495297 0.19925984 0.0037374946
+ 1600 81 0.34150606 0.34150606 0.19025811 0.0053492835
+ 1700 100 0.2561647 0.2561647 0.14186278 0.0090767057
+ 1800 100 0.21124278 0.21124278 0.12154878 0.0028545759
+ 1900 100 0.21793955 0.21793955 0.12173867 0.0029049155
+ 2000 100 0.25530858 0.25530858 0.13892272 0.0035528009
+ 2100 100 0.24671808 0.24671808 0.13687783 0.0076812435
+ 2200 100 0.22465216 0.22465216 0.12513603 0.0042528715
+ 2300 100 0.19362854 0.19362854 0.10914305 0.0061173739
+ 2400 100 0.061627608 0.061627608 0.045907717 0.0010422721
+ 2500 100 0.052700901 0.052700901 0.038883014 0.0019341647
+ 2600 100 0.037332018 0.037332018 0.028357146 0.0028364476
+ 2700 100 0.033526602 0.033526602 0.024609055 0.00044524562
+ 2800 100 0.0194148 0.0194148 0.014491377 0.00056526591
+ 2900 100 0.012346108 0.012346108 0.009857017 0.00081855699
+ 3000 100 0.0107344 0.0107344 0.008669364 0.00040371396
+ 3100 100 0.0092678291 0.0092678291 0.0073003108 0.00033287397
+ 3200 100 0.0085847001 0.0085847001 0.0064045591 0.00023253547
+ 3300 100 0.0049475182 0.0049475182 0.0041173627 0.00019876269
+ 3400 100 0.0030471097 0.0030471097 0.0026940466 0.00013462604
+ 3500 100 0.0031188371 0.0031188371 0.002612223 0.00026148578
+ 3600 100 0.0017616584 0.0017616584 0.0017464137 0.00019049724
+ 3700 100 0.0015475923 0.0015475923 0.0015560356 0.00025062814
+ 3800 100 0.0012547887 0.0012547887 0.0012622678 0.00014132236
+ 3900 100 0.0010047282 0.0010047282 0.0010379262 9.7665594e-05
+ 4000 100 0.00080895307 0.00080895307 0.00088263027 8.1278842e-05
+ 4100 100 0.00079078739 0.00079078739 0.00085810727 8.1271694e-05
+ 4200 100 0.00075192318 0.00075192318 0.00083085046 8.9352453e-05
+ 4300 100 0.00063546457 0.00063546457 0.00073222177 8.9264255e-05
+ 4400 100 0.00062398391 0.00062398391 0.00071312118 8.4200615e-05
+ 4500 100 0.00056464934 0.00056464934 0.00066087801 9.2097641e-05
+ 4600 100 0.00066951894 0.00066951894 0.00071633313 8.2457941e-05
+ 4700 100 0.001128837 0.001128837 0.00095293877 0.00011716361
+ 4800 100 0.00049580391 0.00049580391 0.00056710488 0.00010718794
+ 4900 100 0.00054374371 0.00054374371 0.00058671699 5.6580257e-05
+ 5000 100 0.00043016232 0.00043016232 0.00050264172 2.8640786e-05
+Loop time of 0.0807264 on 1 procs for 5000 steps with 100 atoms
+
+Performance: 26757050.955 tau/day, 61937.618 timesteps/s
+97.4% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0089066 | 0.0089066 | 0.0089066 | 0.0 | 11.03
+Neigh | 0.017107 | 0.017107 | 0.017107 | 0.0 | 21.19
+Comm | 0.00091505 | 0.00091505 | 0.00091505 | 0.0 | 1.13
+Output | 0.00051451 | 0.00051451 | 0.00051451 | 0.0 | 0.64
+Modify | 0.047671 | 0.047671 | 0.047671 | 0.0 | 59.05
+Other | | 0.005612 | | | 6.95
+
+Nlocal: 100 ave 100 max 100 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: 158 ave 158 max 158 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 158
+Ave neighs/atom = 1.58
+Neighbor list builds = 310
+Dangerous builds = 0
+
+region container delete
+variable theta equal (step-5000)*(4.0*PI/5000)
+region container block -6 6 -6 6 -6 6 units box rotate v_theta 0 0 0 0 0 1
+run 5000
+Per MPI rank memory allocation (min/avg/max) = 5.836 | 5.836 | 5.836 Mbytes
+Step Atoms Temp c_1 c_2 Press
+ 5000 100 0.00043016232 0.00043016232 0.00050264172 2.8677624e-05
+ 5100 100 0.56489668 0.56489668 0.31137762 0.011848041
+ 5200 100 0.66068288 0.66068288 0.35915482 0.010199755
+ 5300 100 0.74068022 0.74068022 0.39643217 0.010806409
+ 5400 100 0.80913562 0.80913562 0.42748505 0.01190892
+ 5500 100 0.89409135 0.89409135 0.46135116 0.013093474
+ 5600 100 0.97585093 0.97585093 0.50021126 0.013588886
+ 5700 100 1.0151954 1.0151954 0.5174624 0.01601347
+ 5800 100 1.0452728 1.0452728 0.53122496 0.01879329
+ 5900 100 1.0881689 1.0881689 0.55152229 0.017120714
+ 6000 100 1.1133186 1.1133186 0.5638022 0.017284617
+ 6100 100 1.1532099 1.1532099 0.58310076 0.017031384
+ 6200 100 1.1798849 1.1798849 0.5959516 0.017971323
+ 6300 100 1.19387 1.19387 0.60173877 0.020140984
+ 6400 100 1.2126705 1.2126705 0.61086899 0.018426638
+ 6500 100 1.2137646 1.2137646 0.61284198 0.019127381
+ 6600 100 1.2339012 1.2339012 0.62199324 0.019378799
+ 6700 100 1.2439326 1.2439326 0.62488425 0.021049447
+ 6800 100 1.2489549 1.2489549 0.6278167 0.019552409
+ 6900 100 1.2733303 1.2733303 0.63898149 0.020237284
+ 7000 100 1.2835029 1.2835029 0.6440245 0.020798586
+ 7100 100 1.2866111 1.2866111 0.64522896 0.020355019
+ 7200 100 1.2886381 1.2886381 0.6467497 0.02062322
+ 7300 100 1.2885085 1.2885085 0.64617988 0.020350755
+ 7400 100 1.2912349 1.2912349 0.64691898 0.020197503
+ 7500 100 1.2963062 1.2963062 0.64926335 0.020349791
+ 7600 100 1.3016488 1.3016488 0.65150178 0.021001457
+ 7700 100 1.3009311 1.3009311 0.65106234 0.021546471
+ 7800 100 1.3016987 1.3016987 0.65143099 0.020994967
+ 7900 100 1.3028811 1.3028811 0.65164558 0.022200425
+ 8000 100 1.3087855 1.3087855 0.65439023 0.021310808
+ 8100 100 1.3102001 1.3102001 0.65514941 0.021177764
+ 8200 100 1.3133931 1.3133931 0.65681861 0.021591267
+ 8300 100 1.3148898 1.3148898 0.65775353 0.021335384
+ 8400 100 1.3160355 1.3160355 0.65845913 0.021238095
+ 8500 100 1.3171797 1.3171797 0.65934185 0.021172983
+ 8600 100 1.3176785 1.3176785 0.65964311 0.020747457
+ 8700 100 1.3180425 1.3180425 0.66019624 0.021275913
+ 8800 100 1.3287501 1.3287501 0.66444242 0.021832635
+ 8900 100 1.3249847 1.3249847 0.6625848 0.021337451
+ 9000 100 1.326216 1.326216 0.66297827 0.021470663
+ 9100 100 1.3261662 1.3261662 0.66303852 0.021423573
+ 9200 100 1.3312132 1.3312132 0.6653609 0.021385943
+ 9300 100 1.3300976 1.3300976 0.66504574 0.021489888
+ 9400 100 1.3377335 1.3377335 0.66820989 0.021565001
+ 9500 100 1.3421956 1.3421956 0.67027168 0.022402346
+ 9600 100 1.3464217 1.3464217 0.67228206 0.021991922
+ 9700 100 1.3470623 1.3470623 0.67258349 0.022035729
+ 9800 100 1.3446725 1.3446725 0.67135725 0.022295251
+ 9900 100 1.343146 1.343146 0.67066672 0.022049041
+ 10000 100 1.3435397 1.3435397 0.67093067 0.022451365
+Loop time of 0.247549 on 1 procs for 5000 steps with 100 atoms
+
+Performance: 8725560.044 tau/day, 20198.056 timesteps/s
+99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.031783 | 0.031783 | 0.031783 | 0.0 | 12.84
+Neigh | 0.038383 | 0.038383 | 0.038383 | 0.0 | 15.51
+Comm | 0.0012343 | 0.0012343 | 0.0012343 | 0.0 | 0.50
+Output | 0.00056028 | 0.00056028 | 0.00056028 | 0.0 | 0.23
+Modify | 0.1687 | 0.1687 | 0.1687 | 0.0 | 68.15
+Other | | 0.00689 | | | 2.78
+
+Nlocal: 100 ave 100 max 100 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: 199 ave 199 max 199 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 199
+Ave neighs/atom = 1.99
+Neighbor list builds = 621
+Dangerous builds = 0
+
+region container delete
+region container block -6 6 -6 6 -6 6 units box
+run 5000
+Per MPI rank memory allocation (min/avg/max) = 5.836 | 5.836 | 5.836 Mbytes
+Step Atoms Temp c_1 c_2 Press
+ 10000 100 1.3435397 1.3435397 0.67093067 0.022411116
+ 10100 100 0.31352763 0.31352763 0.18877908 0.01321582
+ 10200 100 0.13367611 0.13367611 0.090010637 0.0074171016
+ 10300 100 0.068195658 0.068195658 0.052632714 0.0019696287
+ 10400 100 0.053814936 0.053814936 0.043037586 0.0017121584
+ 10500 100 0.04032072 0.04032072 0.032944572 0.0011809154
+ 10600 100 0.029178161 0.029178161 0.023951873 0.0007804529
+ 10700 100 0.025978206 0.025978206 0.021045025 0.00099531465
+ 10800 100 0.023205036 0.023205036 0.01898502 0.00040036401
+ 10900 100 0.019994638 0.019994638 0.016451227 0.00027385559
+ 11000 100 0.017838131 0.017838131 0.014730762 0.00040399762
+ 11100 100 0.014863196 0.014863196 0.012314308 0.00019097464
+ 11200 100 0.012131256 0.012131256 0.010102122 0.00018514926
+ 11300 100 0.010881385 0.010881385 0.0090013541 0.00016579157
+ 11400 100 0.0076519814 0.0076519814 0.0064604568 0.00035399997
+ 11500 100 0.0067507315 0.0067507315 0.0057378868 0.00049116726
+ 11600 100 0.0053146649 0.0053146649 0.0047005938 0.00019625233
+ 11700 100 0.0044162463 0.0044162463 0.0039534657 0.00012548039
+ 11800 100 0.0037025387 0.0037025387 0.0033604103 6.2969827e-05
+ 11900 100 0.0032632211 0.0032632211 0.0030406641 8.1600622e-05
+ 12000 100 0.0028944057 0.0028944057 0.0026875858 6.6435833e-05
+ 12100 100 0.0027644728 0.0027644728 0.0025859762 5.5899271e-05
+ 12200 100 0.002480367 0.002480367 0.0023685117 6.0201418e-05
+ 12300 100 0.0024136475 0.0024136475 0.0023107986 4.4386874e-05
+ 12400 100 0.0021911567 0.0021911567 0.0021413262 5.0213175e-05
+ 12500 100 0.0019775905 0.0019775905 0.0019927698 0.00035250097
+ 12600 100 0.0017410363 0.0017410363 0.001830428 5.7885177e-05
+ 12700 100 0.0015749276 0.0015749276 0.0016816771 4.5530192e-05
+ 12800 100 0.0015187705 0.0015187705 0.0016218625 4.0589413e-05
+ 12900 100 0.0014778376 0.0014778376 0.001580232 4.0085455e-05
+ 13000 100 0.0014693491 0.0014693491 0.0015681809 4.0407656e-05
+ 13100 100 0.0014434495 0.0014434495 0.0015356278 5.7849212e-05
+ 13200 100 0.0014121959 0.0014121959 0.0015058758 3.2720737e-05
+ 13300 100 0.0012876041 0.0012876041 0.0013838998 3.7725702e-05
+ 13400 100 0.0012304951 0.0012304951 0.0013373457 3.6784546e-05
+ 13500 100 0.0011954303 0.0011954303 0.0012877627 3.6584963e-05
+ 13600 100 0.0011028947 0.0011028947 0.0011955404 2.3767582e-05
+ 13700 100 0.0010611762 0.0010611762 0.0011504675 3.485879e-05
+ 13800 100 0.0010080835 0.0010080835 0.0010997919 3.7905404e-05
+ 13900 100 0.00096495712 0.00096495712 0.0010530767 3.5273885e-05
+ 14000 100 0.00094945029 0.00094945029 0.0010409175 3.3718395e-05
+ 14100 100 0.00092386757 0.00092386757 0.0010217415 3.3313256e-05
+ 14200 100 0.00088928389 0.00088928389 0.000983023 3.290941e-05
+ 14300 100 0.00082696485 0.00082696485 0.00092690771 3.1651431e-05
+ 14400 100 0.00081086188 0.00081086188 0.00091681096 3.1845632e-05
+ 14500 100 0.00077732305 0.00077732305 0.00087592983 4.8087361e-05
+ 14600 100 0.00073386005 0.00073386005 0.00082546873 3.0892065e-05
+ 14700 100 0.00068701098 0.00068701098 0.00075953521 0.00010208859
+ 14800 100 0.00065860451 0.00065860451 0.00073738846 2.9272912e-05
+ 14900 100 0.00064706564 0.00064706564 0.00072748391 2.9817955e-05
+ 15000 100 0.00064227996 0.00064227996 0.00070964586 3.2547768e-05
+Loop time of 0.0840213 on 1 procs for 5000 steps with 100 atoms
+
+Performance: 25707757.817 tau/day, 59508.699 timesteps/s
+98.2% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.01004 | 0.01004 | 0.01004 | 0.0 | 11.95
+Neigh | 0.0057366 | 0.0057366 | 0.0057366 | 0.0 | 6.83
+Comm | 0.00086808 | 0.00086808 | 0.00086808 | 0.0 | 1.03
+Output | 0.00049472 | 0.00049472 | 0.00049472 | 0.0 | 0.59
+Modify | 0.060893 | 0.060893 | 0.060893 | 0.0 | 72.47
+Other | | 0.005989 | | | 7.13
+
+Nlocal: 100 ave 100 max 100 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: 151 ave 151 max 151 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 151
+Ave neighs/atom = 1.51
+Neighbor list builds = 92
+Dangerous builds = 0
+
+region container delete
+variable theta equal (step-15000)*(4.0*PI/5000)
+region container block -6 6 -6 6 -6 6 units box rotate v_theta 0 0 0 1 1 1
+run 5000
+Per MPI rank memory allocation (min/avg/max) = 5.836 | 5.836 | 5.836 Mbytes
+Step Atoms Temp c_1 c_2 Press
+ 15000 100 0.00064227996 0.00064227996 0.00070964586 3.2291286e-05
+ 15100 100 0.81230775 0.81230775 0.53266834 0.010948517
+ 15200 100 0.87957637 0.87957637 0.57559572 0.012401402
+ 15300 100 1.0262431 1.0262431 0.66535656 0.015239294
+ 15400 100 1.2863564 1.2863564 0.82026439 0.020115365
+ 15500 100 1.4721549 1.4721549 0.92138954 0.022400442
+ 15600 100 1.7140429 1.7140429 1.0103822 0.02558084
+ 15700 100 1.8963287 1.8963287 1.0916756 0.032032318
+ 15800 100 2.0741177 2.0741177 1.1706233 0.034251942
+ 15900 100 2.1434733 2.1434733 1.2054242 0.030132271
+ 16000 100 2.1409892 2.1409892 1.2019761 0.030914205
+ 16100 100 2.2496058 2.2496058 1.2476438 0.030939743
+ 16200 100 2.233356 2.233356 1.2499888 0.030097445
+ 16300 100 2.2673491 2.2673491 1.272321 0.030968524
+ 16400 100 2.3735648 2.3735648 1.3126117 0.034532377
+ 16500 100 2.4510087 2.4510087 1.3588349 0.036685351
+ 16600 100 2.497406 2.497406 1.3811443 0.032019982
+ 16700 100 2.6800518 2.6800518 1.4661941 0.037455527
+ 16800 100 2.8673997 2.8673997 1.5558303 0.03606532
+ 16900 100 3.1229488 3.1229488 1.6918439 0.039753213
+ 17000 100 3.117815 3.117815 1.6996841 0.046210837
+ 17100 100 3.3336225 3.3336225 1.7834517 0.047865361
+ 17200 100 3.1773164 3.1773164 1.7113961 0.047778334
+ 17300 100 3.4336759 3.4336759 1.8343073 0.049673718
+ 17400 100 3.3142326 3.3142326 1.7796613 0.055329946
+ 17500 100 3.3205493 3.3205493 1.7853946 0.043558145
+ 17600 100 3.2764553 3.2764553 1.7640702 0.051463316
+ 17700 100 3.1909643 3.1909643 1.7407995 0.043248948
+ 17800 100 3.1958324 3.1958324 1.735056 0.050123145
+ 17900 100 3.2431806 3.2431806 1.7380638 0.050838878
+ 18000 100 3.2967417 3.2967417 1.7705821 0.042176084
+ 18100 100 3.4270672 3.4270672 1.8459819 0.043589925
+ 18200 100 3.3638494 3.3638494 1.8159436 0.048949648
+ 18300 100 3.3192279 3.3192279 1.8122198 0.043629595
+ 18400 100 3.2627211 3.2627211 1.796316 0.045504529
+ 18500 100 3.5669172 3.5669172 1.9257062 0.048460393
+ 18600 100 3.5546411 3.5546411 1.9154318 0.046890968
+ 18700 100 3.7288485 3.7288485 2.011106 0.046906531
+ 18800 100 3.6800347 3.6800347 1.9936406 0.049985172
+ 18900 100 3.7151898 3.7151898 2.007659 0.050394561
+ 19000 100 3.9693368 3.9693368 2.1311549 0.053710204
+ 19100 100 3.6907732 3.6907732 1.9939387 0.05480136
+ 19200 100 3.8808777 3.8808777 2.0790125 0.055093552
+ 19300 100 3.8422142 3.8422142 2.0756951 0.058090774
+ 19400 100 3.7836875 3.7836875 2.0399805 0.06965907
+ 19500 100 4.0480195 4.0480195 2.169214 0.053420651
+ 19600 100 3.965917 3.965917 2.1245227 0.059077084
+ 19700 100 3.8980869 3.8980869 2.0956306 0.050857062
+ 19800 100 4.008079 4.008079 2.1501421 0.054938689
+ 19900 100 3.7244506 3.7244506 2.0080877 0.055481507
+ 20000 100 3.8146094 3.8146094 2.0541416 0.053187111
+Loop time of 0.210396 on 1 procs for 5000 steps with 100 atoms
+
+Performance: 10266363.999 tau/day, 23764.731 timesteps/s
+98.3% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.013991 | 0.013991 | 0.013991 | 0.0 | 6.65
+Neigh | 0.056947 | 0.056947 | 0.056947 | 0.0 | 27.07
+Comm | 0.0013928 | 0.0013928 | 0.0013928 | 0.0 | 0.66
+Output | 0.00054646 | 0.00054646 | 0.00054646 | 0.0 | 0.26
+Modify | 0.13027 | 0.13027 | 0.13027 | 0.0 | 61.92
+Other | | 0.007249 | | | 3.45
+
+Nlocal: 100 ave 100 max 100 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: 144 ave 144 max 144 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 144
+Ave neighs/atom = 1.44
+Neighbor list builds = 910
+Dangerous builds = 0
+
+region container delete
+region container block -6 6 -6 6 -6 6 units box
+run 5000
+Per MPI rank memory allocation (min/avg/max) = 5.836 | 5.836 | 5.836 Mbytes
+Step Atoms Temp c_1 c_2 Press
+ 20000 100 3.8146094 3.8146094 2.0541416 0.052956687
+ 20100 100 1.3848453 1.3848453 0.82244153 0.017544632
+ 20200 100 0.89469578 0.89469578 0.55929611 0.0111604
+ 20300 100 0.83962013 0.83962013 0.52665461 0.010396174
+ 20400 100 0.77264252 0.77264252 0.48961142 0.0095493901
+ 20500 100 0.78613208 0.78613208 0.48683715 0.012166835
+ 20600 100 0.88411633 0.88411633 0.52854942 0.011725323
+ 20700 100 0.89833225 0.89833225 0.52549693 0.012193413
+ 20800 100 0.90216089 0.90216089 0.51167019 0.014289685
+ 20900 100 0.98665057 0.98665057 0.5468893 0.013794318
+ 21000 100 0.7576342 0.7576342 0.42758791 0.011720156
+ 21100 100 0.3821563 0.3821563 0.23426423 0.005324458
+ 21200 100 0.17486973 0.17486973 0.12876582 0.0029726352
+ 21300 100 0.17940562 0.17940562 0.12400155 0.0026179917
+ 21400 100 0.15526876 0.15526876 0.10526802 0.002341177
+ 21500 100 0.079493361 0.079493361 0.062289324 0.0017379534
+ 21600 100 0.057299519 0.057299519 0.047939171 0.0020095941
+ 21700 100 0.056900097 0.056900097 0.045799124 0.0017782068
+ 21800 100 0.039847861 0.039847861 0.035138066 0.0018265057
+ 21900 100 0.03919167 0.03919167 0.031815619 0.0012160098
+ 22000 100 0.025499317 0.025499317 0.022126202 0.0010056809
+ 22100 100 0.018956113 0.018956113 0.017843095 0.0016109368
+ 22200 100 0.017337018 0.017337018 0.016063068 0.00042537508
+ 22300 100 0.014785686 0.014785686 0.013007571 0.00049466367
+ 22400 100 0.011754087 0.011754087 0.010399793 0.00042349151
+ 22500 100 0.010362474 0.010362474 0.009077435 0.00025198478
+ 22600 100 0.0089484896 0.0089484896 0.0079474121 0.00035239475
+ 22700 100 0.0089936432 0.0089936432 0.0077908763 0.00018548371
+ 22800 100 0.0068663718 0.0068663718 0.0064061667 0.00025641972
+ 22900 100 0.0050272392 0.0050272392 0.0046676214 0.00040466013
+ 23000 100 0.0049250142 0.0049250142 0.0044849467 0.00035704909
+ 23100 100 0.0050508148 0.0050508148 0.0043117775 0.00030051828
+ 23200 100 0.0037293467 0.0037293467 0.0033592517 0.00038108923
+ 23300 100 0.0032823722 0.0032823722 0.0030511575 0.00040421775
+ 23400 100 0.0026913866 0.0026913866 0.0025493429 9.2813733e-05
+ 23500 100 0.0025590632 0.0025590632 0.0024466447 8.4695125e-05
+ 23600 100 0.0025270441 0.0025270441 0.0024236554 8.4237376e-05
+ 23700 100 0.0026406527 0.0026406527 0.0024501963 0.00015009901
+ 23800 100 0.0024633391 0.0024633391 0.0023470594 3.8990761e-05
+ 23900 100 0.0029505606 0.0029505606 0.0025122613 4.9810757e-05
+ 24000 100 0.0019535519 0.0019535519 0.0019112421 3.5804751e-05
+ 24100 100 0.0017505151 0.0017505151 0.001726233 2.380737e-05
+ 24200 100 0.0015864857 0.0015864857 0.0015479949 1.963276e-05
+ 24300 100 0.0014535898 0.0014535898 0.0014221262 3.6607862e-05
+ 24400 100 0.0013744934 0.0013744934 0.0013523293 1.4522467e-05
+ 24500 100 0.0013286378 0.0013286378 0.0013097089 3.2389792e-05
+ 24600 100 0.0012093624 0.0012093624 0.0011617482 4.848694e-05
+ 24700 100 0.0011817062 0.0011817062 0.0011409092 3.8898899e-05
+ 24800 100 0.0011142524 0.0011142524 0.0010877723 1.4560662e-05
+ 24900 100 0.0010941199 0.0010941199 0.0010614415 7.0209336e-05
+ 25000 100 0.0010773559 0.0010773559 0.0010389783 1.3332279e-05
+Loop time of 0.0912137 on 1 procs for 5000 steps with 100 atoms
+
+Performance: 23680652.416 tau/day, 54816.325 timesteps/s
+99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.010053 | 0.010053 | 0.010053 | 0.0 | 11.02
+Neigh | 0.017597 | 0.017597 | 0.017597 | 0.0 | 19.29
+Comm | 0.00092912 | 0.00092912 | 0.00092912 | 0.0 | 1.02
+Output | 0.00049806 | 0.00049806 | 0.00049806 | 0.0 | 0.55
+Modify | 0.056085 | 0.056085 | 0.056085 | 0.0 | 61.49
+Other | | 0.006052 | | | 6.63
+
+Nlocal: 100 ave 100 max 100 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: 143 ave 143 max 143 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 143
+Ave neighs/atom = 1.43
+Neighbor list builds = 289
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/granregion/log.27Nov18.granregion.box.g++.4 b/examples/granregion/log.27Nov18.granregion.box.g++.4
new file mode 100644
index 0000000000..170c8be867
--- /dev/null
+++ b/examples/granregion/log.27Nov18.granregion.box.g++.4
@@ -0,0 +1,475 @@
+LAMMPS (27 Nov 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+# pouring spheres into container box
+
+units lj
+atom_style sphere
+boundary f f f
+dimension 3
+comm_modify vel yes
+
+region box block -10 10 -10 10 -10 10 units box
+create_box 2 box
+Created orthogonal box = (-10 -10 -10) to (10 10 10)
+ 1 by 2 by 2 MPI processor grid
+
+pair_style hybrid gran/hooke 4000.0 NULL 100.0 NULL 0.5 1
+pair_coeff * * gran/hooke
+
+region container block -6 6 -6 6 -6 6 units box
+fix container all wall/gran/region hooke/history 4000.0 NULL 100.0 NULL 0.5 1 region container
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 2 all nve/sphere
+fix 3 all gravity 1.0 vector 0 0 -1
+
+region slab block -2 2 -2 2 -2 2 units box
+fix ins all pour 100 2 4767548 vol 0.4 10 diam one 1.0 region slab ignore
+Particle insertion: 48 every 566 steps, 100 by step 1133
+
+timestep 0.005
+
+compute 1 all temp
+compute_modify 1 dynamic/dof yes
+
+compute 2 all temp/sphere
+compute_modify 2 dynamic/dof yes
+
+thermo 100
+thermo_style custom step atoms temp c_1 c_2 press
+thermo_modify lost ignore
+compute_modify thermo_temp dynamic/dof yes
+
+#dump 2 all image 100 image.*.jpg type type # zoom 1.4 adiam 1.0 box no 0.0 axes yes 0.9 0.03
+#dump_modify 2 pad 5
+
+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 = 1.3
+ ghost atom cutoff = 1.3
+ binsize = 0.65, bins = 31 31 31
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair gran/hooke, perpetual
+ attributes: half, newton on, size
+ pair build: half/size/bin/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 0.4834 | 0.4834 | 0.4834 Mbytes
+Step Atoms Temp c_1 c_2 Press
+ 0 0 0 0 0 0
+ 100 21 0.54270729 0.54270729 0.26473526 0.0013567682
+ 200 21 0.87606961 0.87606961 0.42735103 0.002190174
+ 300 21 1.1428374 1.1428374 0.55748167 0.0028570936
+ 400 21 1.3543103 1.3543103 0.66829516 0.0033857758
+ 500 21 1.0677786 1.0677786 0.53582407 0.0045048164
+ 600 56 0.6744286 0.6744286 0.3502938 0.0047464584
+ 700 56 0.75569283 0.75569283 0.39779462 0.0051953882
+ 800 56 0.61597505 0.61597505 0.32943642 0.0086022783
+ 900 56 0.65260802 0.65260802 0.34474044 0.0059298996
+ 1000 56 0.51624952 0.51624952 0.28326898 0.0067827337
+ 1100 56 0.46050076 0.46050076 0.25656319 0.0061891094
+ 1200 81 0.39112346 0.39112346 0.21690172 0.0086559316
+ 1300 81 0.33302617 0.33302617 0.19109398 0.0033381104
+ 1400 81 0.3933533 0.3933533 0.21221692 0.004135078
+ 1500 81 0.35495297 0.35495297 0.19925984 0.0037374946
+ 1600 81 0.34150606 0.34150606 0.19025811 0.0053492835
+ 1700 100 0.2561647 0.2561647 0.14186278 0.0090767057
+ 1800 100 0.21124278 0.21124278 0.12154878 0.002854576
+ 1900 100 0.21793955 0.21793955 0.12173867 0.0029049175
+ 2000 100 0.25530858 0.25530858 0.13892272 0.0035528022
+ 2100 100 0.24671805 0.24671805 0.13687782 0.0076812357
+ 2200 100 0.22465212 0.22465212 0.12513612 0.0042526344
+ 2300 100 0.19362805 0.19362805 0.10914275 0.0061175383
+ 2400 100 0.061626039 0.061626039 0.045905953 0.0010393593
+ 2500 100 0.052690575 0.052690575 0.038879745 0.0018543933
+ 2600 100 0.037256691 0.037256691 0.02833916 0.0027683815
+ 2700 100 0.033416362 0.033416362 0.024551243 0.00046725913
+ 2800 100 0.019617758 0.019617758 0.014619416 0.00064550316
+ 2900 100 0.012313874 0.012313874 0.0098188153 0.00033470181
+ 3000 100 0.010948455 0.010948455 0.0087981878 0.00034401243
+ 3100 100 0.009359431 0.009359431 0.0073642412 0.00045497356
+ 3200 100 0.008129885 0.008129885 0.0061460516 0.00029944201
+ 3300 100 0.0050682533 0.0050682533 0.0042692811 0.00026543293
+ 3400 100 0.0031539312 0.0031539312 0.0027256511 0.00012475748
+ 3500 100 0.0023621311 0.0023621311 0.0021691817 0.0001186392
+ 3600 100 0.0018305354 0.0018305354 0.0018004128 0.00015926282
+ 3700 100 0.0016522492 0.0016522492 0.0017231072 0.0002193159
+ 3800 100 0.0011715102 0.0011715102 0.0012739973 0.0001747857
+ 3900 100 0.0010607606 0.0010607606 0.0010974725 0.00012476088
+ 4000 100 0.00087570802 0.00087570802 0.00095828935 6.5544103e-05
+ 4100 100 0.00078598203 0.00078598203 0.00088068743 9.4560761e-05
+ 4200 100 0.00088317454 0.00088317454 0.00092784605 8.1108122e-05
+ 4300 100 0.0015013254 0.0015013254 0.0012069505 8.8289686e-05
+ 4400 100 0.00070054041 0.00070054041 0.00079451193 5.195712e-05
+ 4500 100 0.00096259073 0.00096259073 0.00091232511 3.4895669e-05
+ 4600 100 0.00056641848 0.00056641848 0.00069083146 3.9657253e-05
+ 4700 100 0.0005455099 0.0005455099 0.00064816699 2.8131762e-05
+ 4800 100 0.00048254366 0.00048254366 0.00057192255 4.7914432e-05
+ 4900 100 0.00037108125 0.00037108125 0.00048035333 6.4711817e-05
+ 5000 100 0.00031290399 0.00031290399 0.00042398478 4.6025975e-05
+Loop time of 0.075416 on 4 procs for 5000 steps with 100 atoms
+
+Performance: 28641126.336 tau/day, 66298.904 timesteps/s
+93.7% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0022948 | 0.0041364 | 0.0061705 | 2.8 | 5.48
+Neigh | 0.0043123 | 0.0057145 | 0.0070784 | 1.8 | 7.58
+Comm | 0.014259 | 0.018658 | 0.024313 | 3.3 | 24.74
+Output | 0.0011525 | 0.001404 | 0.0015383 | 0.4 | 1.86
+Modify | 0.0030508 | 0.014543 | 0.026602 | 9.5 | 19.28
+Other | | 0.03096 | | | 41.05
+
+Nlocal: 25 ave 51 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost: 5.5 ave 12 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+Neighs: 39.75 ave 84 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+
+Total # of neighbors = 159
+Ave neighs/atom = 1.59
+Neighbor list builds = 310
+Dangerous builds = 0
+
+region container delete
+variable theta equal (step-5000)*(4.0*PI/5000)
+region container block -6 6 -6 6 -6 6 units box rotate v_theta 0 0 0 0 0 1
+run 5000
+Per MPI rank memory allocation (min/avg/max) = 5.733 | 5.733 | 5.734 Mbytes
+Step Atoms Temp c_1 c_2 Press
+ 5000 100 0.00031290399 0.00031290399 0.00042398478 4.4282259e-05
+ 5100 100 0.62661084 0.62661084 0.33840611 0.012020153
+ 5200 100 0.67371678 0.67371678 0.36218522 0.0093514044
+ 5300 100 0.75892331 0.75892331 0.4000747 0.010693252
+ 5400 100 0.86207426 0.86207426 0.44630388 0.013540097
+ 5500 100 0.96205334 0.96205334 0.49432848 0.017375079
+ 5600 100 1.0261194 1.0261194 0.52203912 0.016045333
+ 5700 100 1.0584366 1.0584366 0.53794336 0.018621676
+ 5800 100 1.0881674 1.0881674 0.55300469 0.01930602
+ 5900 100 1.1214233 1.1214233 0.56613492 0.021141141
+ 6000 100 1.1666836 1.1666836 0.58759377 0.017655361
+ 6100 100 1.1785775 1.1785775 0.59365148 0.01829443
+ 6200 100 1.2092305 1.2092305 0.60798809 0.018752443
+ 6300 100 1.2331787 1.2331787 0.62003386 0.020291021
+ 6400 100 1.2561616 1.2561616 0.63143643 0.019899235
+ 6500 100 1.284432 1.284432 0.6460504 0.02083284
+ 6600 100 1.2678801 1.2678801 0.63882384 0.019456553
+ 6700 100 1.2662641 1.2662641 0.63676836 0.020235578
+ 6800 100 1.2785484 1.2785484 0.64129093 0.020335162
+ 6900 100 1.2916608 1.2916608 0.64764298 0.020154225
+ 7000 100 1.2907774 1.2907774 0.64724849 0.020550885
+ 7100 100 1.3074473 1.3074473 0.65460147 0.020847362
+ 7200 100 1.3124592 1.3124592 0.65641332 0.020897348
+ 7300 100 1.3206191 1.3206191 0.66011491 0.021444077
+ 7400 100 1.3273988 1.3273988 0.66350669 0.02129418
+ 7500 100 1.3343911 1.3343911 0.66707269 0.021337376
+ 7600 100 1.3368998 1.3368998 0.66869327 0.021415901
+ 7700 100 1.330658 1.330658 0.66535295 0.021500761
+ 7800 100 1.330801 1.330801 0.66555123 0.022806058
+ 7900 100 1.3392828 1.3392828 0.66926796 0.02194009
+ 8000 100 1.3432728 1.3432728 0.67142337 0.022393719
+ 8100 100 1.3411612 1.3411612 0.66989302 0.022366895
+ 8200 100 1.3427451 1.3427451 0.67054285 0.021966329
+ 8300 100 1.3418147 1.3418147 0.67023132 0.022513459
+ 8400 100 1.346493 1.346493 0.67247837 0.022705366
+ 8500 100 1.3513958 1.3513958 0.6749092 0.022834077
+ 8600 100 1.3520297 1.3520297 0.67506261 0.023227676
+ 8700 100 1.3517157 1.3517157 0.67485073 0.023043414
+ 8800 100 1.3530071 1.3530071 0.67547212 0.022933766
+ 8900 100 1.3550454 1.3550454 0.67657277 0.022744182
+ 9000 100 1.3554069 1.3554069 0.67673505 0.022802134
+ 9100 100 1.3556675 1.3556675 0.67698335 0.022868449
+ 9200 100 1.3534709 1.3534709 0.67600677 0.022537792
+ 9300 100 1.3525103 1.3525103 0.67569499 0.022687849
+ 9400 100 1.3612673 1.3612673 0.67967213 0.022703588
+ 9500 100 1.3649439 1.3649439 0.68147385 0.023498539
+ 9600 100 1.3629376 1.3629376 0.68063814 0.023515579
+ 9700 100 1.3648924 1.3648924 0.68137104 0.023641856
+ 9800 100 1.3662063 1.3662063 0.68196538 0.023576884
+ 9900 100 1.3689695 1.3689695 0.68326751 0.023572622
+ 10000 100 1.3701139 1.3701139 0.68383343 0.023720885
+Loop time of 0.174251 on 4 procs for 5000 steps with 100 atoms
+
+Performance: 12395939.906 tau/day, 28694.305 timesteps/s
+96.5% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0024631 | 0.010709 | 0.020461 | 8.0 | 6.15
+Neigh | 0.0078361 | 0.012368 | 0.016955 | 4.0 | 7.10
+Comm | 0.0059071 | 0.013641 | 0.023547 | 6.6 | 7.83
+Output | 0.0011749 | 0.0021775 | 0.0030091 | 1.4 | 1.25
+Modify | 0.015055 | 0.055709 | 0.097013 | 17.2 | 31.97
+Other | | 0.07965 | | | 45.71
+
+Nlocal: 25 ave 51 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost: 4.5 ave 10 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+Neighs: 49.25 ave 101 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 197
+Ave neighs/atom = 1.97
+Neighbor list builds = 627
+Dangerous builds = 0
+
+region container delete
+region container block -6 6 -6 6 -6 6 units box
+run 5000
+Per MPI rank memory allocation (min/avg/max) = 5.733 | 5.733 | 5.734 Mbytes
+Step Atoms Temp c_1 c_2 Press
+ 10000 100 1.3701139 1.3701139 0.68383343 0.023895921
+ 10100 100 0.25960098 0.25960098 0.15183967 0.0049554084
+ 10200 100 0.15017576 0.15017576 0.10081112 0.0045433238
+ 10300 100 0.10129671 0.10129671 0.078049099 0.0014012658
+ 10400 100 0.06742425 0.06742425 0.055603816 0.0010184792
+ 10500 100 0.053446366 0.053446366 0.045338293 0.00089291689
+ 10600 100 0.041898231 0.041898231 0.036081995 0.00060703885
+ 10700 100 0.03580041 0.03580041 0.031118724 0.00067731964
+ 10800 100 0.030933755 0.030933755 0.026372348 0.00039362325
+ 10900 100 0.027278004 0.027278004 0.022868898 0.0003680788
+ 11000 100 0.021566952 0.021566952 0.017994879 0.0013056062
+ 11100 100 0.019143625 0.019143625 0.015833865 0.00050998112
+ 11200 100 0.015659868 0.015659868 0.013119379 0.00012755696
+ 11300 100 0.013554605 0.013554605 0.01147808 0.00027393437
+ 11400 100 0.01204033 0.01204033 0.010273026 0.00033430792
+ 11500 100 0.010958991 0.010958991 0.0093924566 0.00049023273
+ 11600 100 0.01012553 0.01012553 0.0084556996 0.00021457333
+ 11700 100 0.0083584131 0.0083584131 0.0071118766 7.7149089e-05
+ 11800 100 0.007044883 0.007044883 0.0058675523 0.00036165381
+ 11900 100 0.0059875106 0.0059875106 0.0050610372 7.4095443e-05
+ 12000 100 0.0045180275 0.0045180275 0.0039006565 0.00014607704
+ 12100 100 0.0036631356 0.0036631356 0.0031154279 7.031064e-05
+ 12200 100 0.0034443424 0.0034443424 0.0029190637 0.00020974475
+ 12300 100 0.0030853504 0.0030853504 0.0026315266 3.4873541e-05
+ 12400 100 0.0025451749 0.0025451749 0.0022290833 0.00041551536
+ 12500 100 0.0021624857 0.0021624857 0.0019127734 2.6760761e-05
+ 12600 100 0.0020637862 0.0020637862 0.0018186641 4.9446655e-05
+ 12700 100 0.0019889538 0.0019889538 0.0017604689 3.326943e-05
+ 12800 100 0.0018706349 0.0018706349 0.0016669237 2.3327318e-05
+ 12900 100 0.0017472824 0.0017472824 0.001579469 8.816765e-05
+ 13000 100 0.0016034824 0.0016034824 0.0014549852 3.5407524e-05
+ 13100 100 0.00151798 0.00151798 0.0013826659 1.8754149e-05
+ 13200 100 0.0013049781 0.0013049781 0.0012137907 0.00015263775
+ 13300 100 0.0012270536 0.0012270536 0.0011590841 4.77636e-06
+ 13400 100 0.0011395128 0.0011395128 0.0010860297 2.5606328e-05
+ 13500 100 0.0010858414 0.0010858414 0.0010486713 5.8563931e-05
+ 13600 100 0.0010474389 0.0010474389 0.001015904 1.4319658e-05
+ 13700 100 0.00099241549 0.00099241549 0.00097825038 1.2281142e-05
+ 13800 100 0.00084449252 0.00084449252 0.00084141963 1.0451215e-05
+ 13900 100 0.00084004792 0.00084004792 0.00083755495 3.7174162e-05
+ 14000 100 0.00082183505 0.00082183505 0.00082027058 1.0170209e-05
+ 14100 100 0.00082377076 0.00082377076 0.00080489795 1.181976e-05
+ 14200 100 0.00076903208 0.00076903208 0.00076216608 4.4590341e-05
+ 14300 100 0.00075173269 0.00075173269 0.00074828209 2.2134371e-05
+ 14400 100 0.00074379148 0.00074379148 0.00074072001 1.5746014e-05
+ 14500 100 0.00072454029 0.00072454029 0.0007174429 8.9830398e-06
+ 14600 100 0.00072372648 0.00072372648 0.00071678769 9.1111512e-06
+ 14700 100 0.00071541587 0.00071541587 0.00070893868 7.8446375e-05
+ 14800 100 0.0006820307 0.0006820307 0.00066675502 8.4401299e-06
+ 14900 100 0.00067050627 0.00067050627 0.00065751846 0.0001228548
+ 15000 100 0.00064977132 0.00064977132 0.00062305247 7.8887775e-06
+Loop time of 0.0746691 on 4 procs for 5000 steps with 100 atoms
+
+Performance: 28927619.905 tau/day, 66962.083 timesteps/s
+96.6% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0021737 | 0.0042608 | 0.0063519 | 3.2 | 5.71
+Neigh | 0.0012126 | 0.0019009 | 0.0026193 | 1.6 | 2.55
+Comm | 0.0023425 | 0.0092477 | 0.016876 | 7.2 | 12.38
+Output | 0.0010619 | 0.0017995 | 0.0030522 | 1.8 | 2.41
+Modify | 0.00097013 | 0.017151 | 0.03415 | 12.3 | 22.97
+Other | | 0.04031 | | | 53.98
+
+Nlocal: 25 ave 55 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+Nghost: 3.75 ave 9 max 0 min
+Histogram: 2 0 0 0 0 0 1 0 0 1
+Neighs: 42.5 ave 88 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 170
+Ave neighs/atom = 1.7
+Neighbor list builds = 97
+Dangerous builds = 0
+
+region container delete
+variable theta equal (step-15000)*(4.0*PI/5000)
+region container block -6 6 -6 6 -6 6 units box rotate v_theta 0 0 0 1 1 1
+run 5000
+Per MPI rank memory allocation (min/avg/max) = 5.733 | 5.733 | 5.734 Mbytes
+Step Atoms Temp c_1 c_2 Press
+ 15000 100 0.00064977132 0.00064977132 0.00062305247 7.9405607e-06
+ 15100 100 1.0123899 1.0123899 0.66185504 0.014587215
+ 15200 100 1.0332828 1.0332828 0.67443308 0.014002815
+ 15300 100 1.0804076 1.0804076 0.72450056 0.016985272
+ 15400 100 1.2868163 1.2868163 0.8708132 0.022190597
+ 15500 100 1.5180471 1.5180471 0.99613124 0.026761866
+ 15600 100 1.5422016 1.5422016 1.0021746 0.024490139
+ 15700 100 1.7142241 1.7142241 1.0611146 0.0301368
+ 15800 100 1.8747057 1.8747057 1.1207858 0.027612699
+ 15900 100 1.9294819 1.9294819 1.1289025 0.027270228
+ 16000 100 1.953275 1.953275 1.1264475 0.031568811
+ 16100 100 2.0434228 2.0434228 1.1665365 0.026358952
+ 16200 100 2.2129393 2.2129393 1.2448327 0.029613382
+ 16300 100 2.2558224 2.2558224 1.2373264 0.028306021
+ 16400 100 2.367398 2.367398 1.293448 0.029659303
+ 16500 100 2.4221549 2.4221549 1.3198966 0.032541712
+ 16600 100 2.510283 2.510283 1.3618001 0.034740544
+ 16700 100 2.6776293 2.6776293 1.4508262 0.034556341
+ 16800 100 2.8095841 2.8095841 1.5190571 0.035183782
+ 16900 100 2.8485646 2.8485646 1.5344387 0.037153336
+ 17000 100 3.0298285 3.0298285 1.6321623 0.040745906
+ 17100 100 3.0218054 3.0218054 1.6187189 0.042082135
+ 17200 100 3.1981705 3.1981705 1.7090597 0.041770208
+ 17300 100 3.3178559 3.3178559 1.7723201 0.044604756
+ 17400 100 3.3940903 3.3940903 1.8229846 0.049231759
+ 17500 100 3.3274817 3.3274817 1.7870996 0.051649102
+ 17600 100 3.3204358 3.3204358 1.791527 0.043875639
+ 17700 100 3.2185649 3.2185649 1.7480866 0.049941218
+ 17800 100 3.2507826 3.2507826 1.7727758 0.048622479
+ 17900 100 3.2432767 3.2432767 1.7796296 0.044343902
+ 18000 100 3.0841272 3.0841272 1.6978832 0.045344433
+ 18100 100 3.0953909 3.0953909 1.699898 0.040070963
+ 18200 100 3.1405704 3.1405704 1.7316463 0.042528194
+ 18300 100 3.1904871 3.1904871 1.7555188 0.041141165
+ 18400 100 3.3256779 3.3256779 1.8243767 0.043908318
+ 18500 100 3.5161823 3.5161823 1.9150861 0.045165166
+ 18600 100 3.5668273 3.5668273 1.9217975 0.048127705
+ 18700 100 3.6648305 3.6648305 1.9685241 0.051205352
+ 18800 100 3.9000502 3.9000502 2.0886668 0.05262835
+ 18900 100 4.0217758 4.0217758 2.1465498 0.054502839
+ 19000 100 3.8431174 3.8431174 2.0581611 0.054852333
+ 19100 100 4.1721454 4.1721454 2.2221193 0.053831555
+ 19200 100 3.9061181 3.9061181 2.096323 0.058077678
+ 19300 100 4.0191085 4.0191085 2.1408069 0.05475437
+ 19400 100 3.8840871 3.8840871 2.0887677 0.061905092
+ 19500 100 3.8388062 3.8388062 2.0567095 0.051076414
+ 19600 100 3.6331742 3.6331742 1.9574769 0.04748008
+ 19700 100 3.6996954 3.6996954 1.9887285 0.053305043
+ 19800 100 3.8649872 3.8649872 2.0827424 0.060484008
+ 19900 100 3.8305733 3.8305733 2.0700281 0.052926584
+ 20000 100 3.7948463 3.7948463 2.0657301 0.048516953
+Loop time of 0.156359 on 4 procs for 5000 steps with 100 atoms
+
+Performance: 13814330.011 tau/day, 31977.616 timesteps/s
+94.9% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0040646 | 0.0058124 | 0.0074518 | 1.6 | 3.72
+Neigh | 0.014813 | 0.018389 | 0.020829 | 1.6 | 11.76
+Comm | 0.031892 | 0.034103 | 0.036658 | 1.0 | 21.81
+Output | 0.0013497 | 0.0019822 | 0.003484 | 2.0 | 1.27
+Modify | 0.031006 | 0.046878 | 0.056364 | 4.5 | 29.98
+Other | | 0.0492 | | | 31.46
+
+Nlocal: 25 ave 37 max 10 min
+Histogram: 1 0 0 0 0 1 0 1 0 1
+Nghost: 3.75 ave 6 max 2 min
+Histogram: 1 0 1 0 0 1 0 0 0 1
+Neighs: 36.25 ave 57 max 9 min
+Histogram: 1 0 0 0 0 0 2 0 0 1
+
+Total # of neighbors = 145
+Ave neighs/atom = 1.45
+Neighbor list builds = 921
+Dangerous builds = 0
+
+region container delete
+region container block -6 6 -6 6 -6 6 units box
+run 5000
+Per MPI rank memory allocation (min/avg/max) = 5.733 | 5.734 | 5.734 Mbytes
+Step Atoms Temp c_1 c_2 Press
+ 20000 100 3.7948463 3.7948463 2.0657301 0.048381317
+ 20100 100 1.1359931 1.1359931 0.70170151 0.015300556
+ 20200 100 0.87354617 0.87354617 0.55969299 0.012181983
+ 20300 100 0.84424484 0.84424484 0.52849351 0.017724782
+ 20400 100 0.82422562 0.82422562 0.50175766 0.0098154181
+ 20500 100 0.83731289 0.83731289 0.49814627 0.010465327
+ 20600 100 0.93125924 0.93125924 0.53803834 0.011624902
+ 20700 100 1.0810919 1.0810919 0.60974741 0.01425935
+ 20800 100 1.0646343 1.0646343 0.60037545 0.013418132
+ 20900 100 1.0608055 1.0608055 0.58353908 0.015119612
+ 21000 100 0.68173094 0.68173094 0.3941588 0.0099947535
+ 21100 100 0.35407592 0.35407592 0.21306735 0.0043859494
+ 21200 100 0.19247432 0.19247432 0.12989264 0.0031808422
+ 21300 100 0.13493768 0.13493768 0.093987634 0.0025990872
+ 21400 100 0.085735857 0.085735857 0.062091707 0.001434207
+ 21500 100 0.074307566 0.074307566 0.05224051 0.0022163094
+ 21600 100 0.069932382 0.069932382 0.045388838 0.0020296572
+ 21700 100 0.041749712 0.041749712 0.031422931 0.001211155
+ 21800 100 0.03378055 0.03378055 0.026248846 0.0020596463
+ 21900 100 0.030608528 0.030608528 0.022868294 0.0016282878
+ 22000 100 0.025632448 0.025632448 0.019606402 0.0011659657
+ 22100 100 0.013785062 0.013785062 0.011561769 0.00069006322
+ 22200 100 0.013139066 0.013139066 0.010559726 0.00038424576
+ 22300 100 0.01455318 0.01455318 0.011094558 0.00054735929
+ 22400 100 0.0096885414 0.0096885414 0.008012617 0.00055875777
+ 22500 100 0.0081193116 0.0081193116 0.006802973 0.00052914932
+ 22600 100 0.0057159621 0.0057159621 0.0048680253 0.00054864875
+ 22700 100 0.0052344376 0.0052344376 0.0045511708 0.00026333033
+ 22800 100 0.0054554177 0.0054554177 0.0045005479 0.0002085972
+ 22900 100 0.0039455776 0.0039455776 0.0035287888 0.00022514017
+ 23000 100 0.0042620461 0.0042620461 0.0035747729 0.00020030999
+ 23100 100 0.0035303095 0.0035303095 0.0031995108 0.00016007298
+ 23200 100 0.0029747457 0.0029747457 0.0027095904 0.00029775807
+ 23300 100 0.0032404433 0.0032404433 0.002769389 0.00019627995
+ 23400 100 0.0024965262 0.0024965262 0.0022343473 0.00018870133
+ 23500 100 0.00251617 0.00251617 0.0022533604 0.0002661237
+ 23600 100 0.0025923653 0.0025923653 0.0022887204 0.00018475201
+ 23700 100 0.0023016545 0.0023016545 0.0019829032 0.00014888334
+ 23800 100 0.0028358441 0.0028358441 0.0021790504 0.00064613131
+ 23900 100 0.0016682403 0.0016682403 0.0014930521 8.8407075e-05
+ 24000 100 0.0016341577 0.0016341577 0.0014597606 0.00011262081
+ 24100 100 0.0015433636 0.0015433636 0.0013981581 8.364568e-05
+ 24200 100 0.0015033978 0.0015033978 0.0013582013 8.4539006e-05
+ 24300 100 0.0014513098 0.0014513098 0.0012943981 0.00010546194
+ 24400 100 0.0013293352 0.0013293352 0.001206366 8.4967509e-05
+ 24500 100 0.0013732518 0.0013732518 0.001202532 0.00014787559
+ 24600 100 0.00091890041 0.00091890041 0.00084499923 0.00010080638
+ 24700 100 0.00083467915 0.00083467915 0.00077071316 5.3934025e-05
+ 24800 100 0.00080701934 0.00080701934 0.0007477161 5.3982095e-05
+ 24900 100 0.00080620771 0.00080620771 0.0007471026 5.3581294e-05
+ 25000 100 0.00080568604 0.00080568604 0.00074625735 5.3574637e-05
+Loop time of 0.0792506 on 4 procs for 5000 steps with 100 atoms
+
+Performance: 27255302.560 tau/day, 63090.978 timesteps/s
+95.0% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0023611 | 0.0047854 | 0.0077851 | 3.4 | 6.04
+Neigh | 0.0042653 | 0.005571 | 0.0067258 | 1.5 | 7.03
+Comm | 0.0077977 | 0.013373 | 0.019515 | 4.4 | 16.87
+Output | 0.0010924 | 0.0017727 | 0.0030222 | 1.8 | 2.24
+Modify | 0.0023608 | 0.015964 | 0.030545 | 10.5 | 20.14
+Other | | 0.03778 | | | 47.68
+
+Nlocal: 25 ave 50 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost: 5 ave 10 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs: 35.75 ave 78 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+
+Total # of neighbors = 143
+Ave neighs/atom = 1.43
+Neighbor list builds = 287
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/granregion/log.27Nov18.granregion.funnel.g++.1 b/examples/granregion/log.27Nov18.granregion.funnel.g++.1
new file mode 100644
index 0000000000..0268ed000a
--- /dev/null
+++ b/examples/granregion/log.27Nov18.granregion.funnel.g++.1
@@ -0,0 +1,601 @@
+LAMMPS (27 Nov 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+# pour particles into cone-shaped funnel, settle them, let them run out bottom
+
+variable name string funnel_pour
+
+thermo_modify flush yes
+units si
+variable PI equal 3.141592653589
+variable seed equal 14314
+
+###############################################
+# Geometry-related parameters
+###############################################
+
+variable xlo equal 10
+variable xhi equal 40
+variable ylo equal 10
+variable yhi equal 40
+variable zlo equal -20
+variable zhi equal 50
+
+variable xc equal 25
+variable yc equal 25
+
+variable zconehi equal 50
+variable zconelo equal 10
+variable zcyllo equal 0
+variable radconelo equal 2
+variable radconehi equal 20
+
+################################################
+# Particle sizes
+################################################
+
+variable rlo equal 0.25
+variable rhi equal 0.5
+variable dlo equal 2.0*${rlo}
+variable dlo equal 2.0*0.25
+variable dhi equal 2.0*${rhi}
+variable dhi equal 2.0*0.5
+
+variable skin equal ${rhi}
+variable skin equal 0.5
+
+###############################################
+# Granular contact parameters
+###############################################
+
+variable coeffRes equal 0.1
+variable coeffFric equal 0.5
+
+variable density equal 1.0
+variable EYoung equal 10^5
+variable Poisson equal 2.0/7.0
+variable GShear equal ${EYoung}/(2*(1+${Poisson}))
+variable GShear equal 100000/(2*(1+${Poisson}))
+variable GShear equal 100000/(2*(1+0.285714285714286))
+
+variable gravity equal 1.0
+
+variable reff equal 0.5*(${rhi}+${rlo})
+variable reff equal 0.5*(0.5+${rlo})
+variable reff equal 0.5*(0.5+0.25)
+variable meff equal ${density}*4.0/3.0*${PI}*${reff}^3
+variable meff equal 1*4.0/3.0*${PI}*${reff}^3
+variable meff equal 1*4.0/3.0*3.141592653589*${reff}^3
+variable meff equal 1*4.0/3.0*3.141592653589*0.375^3
+variable min_mass equal ${density}*4.0/3.0*${PI}*${rlo}*${rlo}*${rlo}
+variable min_mass equal 1*4.0/3.0*${PI}*${rlo}*${rlo}*${rlo}
+variable min_mass equal 1*4.0/3.0*3.141592653589*${rlo}*${rlo}*${rlo}
+variable min_mass equal 1*4.0/3.0*3.141592653589*0.25*${rlo}*${rlo}
+variable min_mass equal 1*4.0/3.0*3.141592653589*0.25*0.25*${rlo}
+variable min_mass equal 1*4.0/3.0*3.141592653589*0.25*0.25*0.25
+variable max_mass equal ${density}*4.0/3.0*${PI}*${rhi}*${rhi}*${rhi}
+variable max_mass equal 1*4.0/3.0*${PI}*${rhi}*${rhi}*${rhi}
+variable max_mass equal 1*4.0/3.0*3.141592653589*${rhi}*${rhi}*${rhi}
+variable max_mass equal 1*4.0/3.0*3.141592653589*0.5*${rhi}*${rhi}
+variable max_mass equal 1*4.0/3.0*3.141592653589*0.5*0.5*${rhi}
+variable max_mass equal 1*4.0/3.0*3.141592653589*0.5*0.5*0.5
+
+## Typical way to set kn, kt, etc.:
+variable kn equal 4.0*${GShear}/(3*(1-${Poisson}))
+variable kn equal 4.0*38888.8888888889/(3*(1-${Poisson}))
+variable kn equal 4.0*38888.8888888889/(3*(1-0.285714285714286))
+variable kt equal 4.0*${GShear}/(2-${Poisson})
+variable kt equal 4.0*38888.8888888889/(2-${Poisson})
+variable kt equal 4.0*38888.8888888889/(2-0.285714285714286)
+
+variable a equal (-2.0*log(${coeffRes})/${PI})^2
+variable a equal (-2.0*log(0.1)/${PI})^2
+variable a equal (-2.0*log(0.1)/3.141592653589)^2
+variable gamma_n equal sqrt($a*2*${kn}/${min_mass}/(1+0.25*$a))
+variable gamma_n equal sqrt(0.405284734569556*2*${kn}/${min_mass}/(1+0.25*$a))
+variable gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/${min_mass}/(1+0.25*$a))
+variable gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/0.0654498469497708/(1+0.25*$a))
+variable gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/0.0654498469497708/(1+0.25*0.405284734569556))
+variable gamma_t equal ${gamma_n}*0.5
+variable gamma_t equal 903.503751814138*0.5
+
+variable tcol equal ${PI}/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
+variable tcol equal 3.141592653589/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
+variable tcol equal 3.141592653589/sqrt(2*72592.5925925926/${min_mass}-${gamma_n}/4.0)
+variable tcol equal 3.141592653589/sqrt(2*72592.5925925926/0.0654498469497708-${gamma_n}/4.0)
+variable tcol equal 3.141592653589/sqrt(2*72592.5925925926/0.0654498469497708-903.503751814138/4.0)
+
+variable dt equal ${tcol}*0.05
+variable dt equal 0.00210943016014969*0.05
+timestep ${dt}
+timestep 0.000105471508007485
+
+###############################################
+variable dumpfreq equal 1000
+variable logfreq equal 1000
+
+newton off
+atom_style sphere
+
+boundary p p f
+
+region boxreg block ${xlo} ${xhi} ${ylo} ${yhi} ${zlo} ${zhi}
+region boxreg block 10 ${xhi} ${ylo} ${yhi} ${zlo} ${zhi}
+region boxreg block 10 40 ${ylo} ${yhi} ${zlo} ${zhi}
+region boxreg block 10 40 10 ${yhi} ${zlo} ${zhi}
+region boxreg block 10 40 10 40 ${zlo} ${zhi}
+region boxreg block 10 40 10 40 -20 ${zhi}
+region boxreg block 10 40 10 40 -20 50
+create_box 1 boxreg
+Created orthogonal box = (10 10 -20) to (40 40 50)
+ 1 by 1 by 1 MPI processor grid
+
+pair_style gran/hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
+pair_style gran/hertz/history 72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
+pair_style gran/hertz/history 72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1
+pair_style gran/hertz/history 72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1
+pair_style gran/hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1
+pair_style gran/hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1
+pair_coeff * *
+
+neighbor ${skin} bin
+neighbor 0.5 bin
+thermo ${logfreq}
+thermo 1000
+
+comm_style brick
+comm_modify mode multi group all vel yes
+balance 1.1 shift xyz 20 1.1
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 0
+ ghost atom cutoff = 0
+ binsize = 30, bins = 1 1 3
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair gran/hertz/history, perpetual
+ attributes: half, newton off, size, history
+ pair build: half/size/bin/newtoff
+ stencil: half/bin/3d/newtoff
+ bin: standard
+fix bal all balance 10000 1.1 shift xyz 20 1.01
+
+####################### Options specific to pouring #########################
+
+# insertion region for fix/pour
+
+region insreg cylinder z ${xc} ${yc} 10 30 50 side in units box
+region insreg cylinder z 25 ${yc} 10 30 50 side in units box
+region insreg cylinder z 25 25 10 30 50 side in units box
+
+# define cone and cylinder regions - see lammps doc on region command
+# note new open options
+
+region cylreg cylinder z ${xc} ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 2 #Top is open
+region cylreg cylinder z 25 ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 2
+region cylreg cylinder z 25 25 ${radconelo} ${zcyllo} ${zconelo} side in units box open 2
+region cylreg cylinder z 25 25 2 ${zcyllo} ${zconelo} side in units box open 2
+region cylreg cylinder z 25 25 2 0 ${zconelo} side in units box open 2
+region cylreg cylinder z 25 25 2 0 10 side in units box open 2
+
+region conereg cone z ${xc} ${yc} ${radconelo} ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2 #Bottom and top are open
+region conereg cone z 25 ${yc} ${radconelo} ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2
+region conereg cone z 25 25 ${radconelo} ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2
+region conereg cone z 25 25 2 ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2
+region conereg cone z 25 25 2 20 ${zconelo} ${zconehi} side in units box open 1 open 2
+region conereg cone z 25 25 2 20 10 ${zconehi} side in units box open 1 open 2
+region conereg cone z 25 25 2 20 10 50 side in units box open 1 open 2
+
+region hopreg union 2 conereg cylreg
+
+fix grav all gravity ${gravity} vector 0 0 -1
+fix grav all gravity 1 vector 0 0 -1
+fix 1 all nve/sphere
+
+
+fix hopper3 all wall/gran/region hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
+fix hopper3 all wall/gran/region hertz/history 72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
+fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
+fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1 region hopreg
+fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1 region hopreg
+fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1 region hopreg
+
+fix ins all pour 2000 1 42424 region insreg diam range ${dlo} ${dhi} dens ${density} ${density}
+fix ins all pour 2000 1 42424 region insreg diam range 0.5 ${dhi} dens ${density} ${density}
+fix ins all pour 2000 1 42424 region insreg diam range 0.5 1 dens ${density} ${density}
+fix ins all pour 2000 1 42424 region insreg diam range 0.5 1 dens 1 ${density}
+fix ins all pour 2000 1 42424 region insreg diam range 0.5 1 dens 1 1
+Particle insertion: 3000 every 59965 steps, 2000 by step 1
+
+#dump 1 all custom ${dumpfreq} ${name}.dump # id type mass diameter x y z
+
+#dump 2 all image 4000 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 zoom 3.0 # box no 0.0 axes no 0.0 0.0
+#dump_modify 2 pad 6
+
+thermo_style custom step cpu atoms ke
+WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:705)
+thermo_modify flush yes lost warn
+
+# Initial run to fill up the cone
+
+run 20000
+Per MPI rank memory allocation (min/avg/max) = 6.649 | 6.649 | 6.649 Mbytes
+Step CPU Atoms KinEng
+ 0 0 0 -0
+ 1000 0.63593698 2000 -0
+ 2000 1.0282419 2000 -0
+ 3000 1.4184453 2000 -0
+ 4000 1.8055785 2000 -0
+ 5000 2.1941335 2000 -0
+ 6000 2.5804653 2000 -0
+ 7000 2.9660621 2000 -0
+ 8000 3.3506265 2000 -0
+ 9000 3.7344413 2000 -0
+ 10000 4.1212304 2000 -0
+ 11000 4.5044594 2000 -0
+ 12000 4.8875456 2000 -0
+ 13000 5.2698007 2000 -0
+ 14000 5.6527214 2000 -0
+ 15000 6.0349295 2000 -0
+ 16000 6.4172938 2000 -0
+ 17000 6.8001184 2000 -0
+ 18000 7.1826644 2000 -0
+ 19000 7.5654378 2000 -0
+ 20000 7.9511659 2000 -0
+Loop time of 7.95118 on 1 procs for 20000 steps with 2000 atoms
+
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.6189 | 0.6189 | 0.6189 | 0.0 | 7.78
+Neigh | 0.09361 | 0.09361 | 0.09361 | 0.0 | 1.18
+Comm | 0.016098 | 0.016098 | 0.016098 | 0.0 | 0.20
+Output | 0.00048828 | 0.00048828 | 0.00048828 | 0.0 | 0.01
+Modify | 6.9973 | 6.9973 | 6.9973 | 0.0 | 88.00
+Other | | 0.2248 | | | 2.83
+
+Nlocal: 2000 ave 2000 max 2000 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: 1537 ave 1537 max 1537 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1537
+Ave neighs/atom = 0.7685
+Neighbor list builds = 69
+Dangerous builds = 0
+unfix ins
+run 150000
+Per MPI rank memory allocation (min/avg/max) = 12.77 | 12.77 | 12.77 Mbytes
+Step CPU Atoms KinEng
+ 20000 0 2000 6443.7665
+ 21000 0.3826313 2000 6572.3531
+ 22000 0.76688981 2000 6723.8376
+ 23000 1.1534231 2000 6853.1812
+ 24000 1.5391715 2000 6976.0209
+ 25000 1.9263508 2000 7096.9955
+ 26000 2.3168406 2000 7215.5795
+ 27000 2.7065961 2000 7349.2382
+ 28000 3.096664 2000 7471.8719
+ 29000 3.4905531 2000 7574.8228
+ 30000 3.8877606 2000 7659.3836
+ 31000 4.2839894 2000 7703.6856
+ 32000 4.6859732 2000 7644.279
+ 33000 5.0932801 2000 7526.6944
+ 34000 5.5045564 2000 7370.0821
+ 35000 5.9206297 2000 7193.0457
+ 36000 6.343729 2000 6990.9899
+ 37000 6.7719142 2000 6849.2841
+ 38000 7.2016783 2000 6701.7433
+ 39000 7.6354482 2000 6538.9557
+ 40000 8.078445 2000 6381.9346
+ 41000 8.5191586 2000 6217.5253
+ 42000 8.9630713 2000 6093.5344
+ 43000 9.4097741 2000 5943.0479
+ 44000 9.8652256 2000 5841.0782
+ 45000 10.331057 2000 5652.8319
+ 46000 10.803253 2000 5476.1466
+ 47000 11.278766 2000 5267.7855
+ 48000 11.759121 2000 5131.4036
+ 49000 12.248896 2000 4972.7696
+ 50000 12.747719 2000 4867.0868
+ 51000 13.246704 2000 4681.897
+ 52000 13.757842 2000 4506.8185
+ 53000 14.276078 2000 4346.8045
+ 54000 14.795933 2000 4193.8194
+ 55000 15.311241 2000 4058.2049
+ 56000 15.828737 2000 3879.0325
+ 57000 16.359453 2000 3696.3154
+ 58000 16.905406 2000 3504.0399
+ 59000 17.460454 2000 3284.6522
+ 60000 18.027276 2000 3061.0727
+ 61000 18.586931 2000 2874.2926
+ 62000 19.158563 2000 2653.0722
+ 63000 19.738442 2000 2437.4941
+ 64000 20.331411 2000 2124.1876
+ 65000 20.936204 2000 1864.5661
+ 66000 21.547443 2000 1610.2335
+ 67000 22.166888 2000 1390.0428
+ 68000 22.789106 2000 1163.7679
+ 69000 23.416016 2000 933.0928
+ 70000 24.038879 2000 745.66667
+ 71000 24.663115 2000 605.58458
+ 72000 25.294193 2000 444.31183
+ 73000 25.932019 2000 357.19162
+ 74000 26.568184 2000 291.16762
+ 75000 27.203393 2000 230.58362
+ 76000 27.836079 2000 197.59502
+ 77000 28.467344 2000 166.55702
+ 78000 29.099997 2000 139.89052
+ 79000 29.741694 2000 117.1145
+ 80000 30.388097 2000 100.12353
+ 81000 31.036193 2000 85.233155
+ 82000 31.688463 2000 71.145302
+ 83000 32.343411 2000 61.545348
+ 84000 32.999346 2000 54.099358
+ 85000 33.652976 2000 46.922028
+ 86000 34.306931 2000 41.606645
+ 87000 34.967787 2000 37.462793
+ 88000 35.633721 2000 33.698298
+ 89000 36.310035 2000 29.340455
+ 90000 36.995441 2000 26.072122
+ 91000 37.67904 2000 23.20848
+ 92000 38.367699 2000 21.015862
+ 93000 39.058641 2000 20.134175
+ 94000 39.749342 2000 19.196075
+ 95000 40.442651 2000 18.285127
+ 96000 41.140177 2000 17.476411
+ 97000 41.840761 2000 16.55882
+ 98000 42.543845 2000 15.444541
+ 99000 43.256415 2000 14.41642
+ 100000 43.97382 2000 13.818738
+ 101000 44.684596 2000 12.878373
+ 102000 45.401082 2000 12.11804
+ 103000 46.120936 2000 11.016885
+ 104000 46.83935 2000 10.531044
+ 105000 47.559419 2000 10.46735
+ 106000 48.286016 2000 10.246007
+ 107000 49.012266 2000 9.6423041
+ 108000 49.74013 2000 9.3948808
+ 109000 50.471961 2000 9.5178141
+ 110000 51.206152 2000 9.4143884
+ 111000 51.939123 2000 9.5058226
+ 112000 52.673443 2000 9.6911516
+ 113000 53.410485 2000 9.7756849
+ 114000 54.152537 2000 9.3876232
+ 115000 54.891784 2000 8.6725333
+ 116000 55.631474 2000 8.6691065
+ 117000 56.371762 2000 8.0156055
+ 118000 57.110131 2000 7.9150786
+ 119000 57.8533 2000 7.5310892
+ 120000 58.599064 2000 7.2940498
+ 121000 59.340753 2000 6.8347898
+ 122000 60.084676 2000 6.696484
+ 123000 60.826952 2000 6.7799146
+ 124000 61.569413 2000 6.7901567
+ 125000 62.316334 2000 6.7532108
+ 126000 63.061374 2000 6.762162
+ 127000 63.806385 2000 6.6317366
+ 128000 64.555969 2000 6.8246399
+ 129000 65.308131 2000 6.9130358
+ 130000 66.060967 2000 7.1750566
+ 131000 66.809725 2000 6.9507379
+ 132000 67.559796 2000 6.7987445
+ 133000 68.314249 2000 6.8535775
+ 134000 69.065513 2000 7.0255144
+ 135000 69.817604 2000 6.7381064
+ 136000 70.572079 2000 6.5567748
+ 137000 71.324444 2000 6.2655395
+ 138000 72.079147 2000 6.1923013
+ 139000 72.831323 2000 6.0958081
+ 140000 73.59117 2000 5.9185709
+ 141000 74.343753 2000 5.9151241
+ 142000 75.096509 2000 5.4743035
+ 143000 75.852151 2000 5.438642
+ 144000 76.605005 2000 4.6646664
+ 145000 77.357571 2000 4.6899837
+ 146000 78.113125 2000 4.5357917
+ 147000 78.867751 2000 4.5993842
+ 148000 79.625344 2000 4.7076884
+ 149000 80.37992 2000 4.8306642
+ 150000 81.143175 2000 4.8282147
+ 151000 81.899326 2000 4.546308
+ 152000 82.658645 2000 4.6700755
+ 153000 83.41837 2000 4.7557633
+ 154000 84.17509 2000 4.9004538
+ 155000 84.934161 2000 5.0552949
+ 156000 85.695466 2000 4.0672495
+ 157000 86.453115 2000 3.5819543
+ 158000 87.212663 2000 3.3533477
+ 159000 87.967768 2000 3.3281001
+ 160000 88.729631 2000 3.0831743
+ 161000 89.498983 2000 3.0519269
+ 162000 90.259424 2000 3.0951675
+ 163000 91.019656 2000 2.9868352
+ 164000 91.776359 2000 2.9195788
+ 165000 92.536374 2000 2.5637813
+ 166000 93.296332 2000 2.5553272
+ 167000 94.05653 2000 2.0752912
+ 168000 94.814559 2000 1.9689845
+ 169000 95.576005 2000 1.9117916
+ 170000 96.337863 2000 1.8568914
+Loop time of 96.3379 on 1 procs for 150000 steps with 2000 atoms
+
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 37.121 | 37.121 | 37.121 | 0.0 | 38.53
+Neigh | 0.8454 | 0.8454 | 0.8454 | 0.0 | 0.88
+Comm | 0.11506 | 0.11506 | 0.11506 | 0.0 | 0.12
+Output | 0.004431 | 0.004431 | 0.004431 | 0.0 | 0.00
+Modify | 56.517 | 56.517 | 56.517 | 0.0 | 58.67
+Other | | 1.735 | | | 1.80
+
+Nlocal: 2000 ave 2000 max 2000 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: 15524 ave 15524 max 15524 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 15524
+Ave neighs/atom = 7.762
+Neighbor list builds = 388
+Dangerous builds = 0
+
+# remove "plug" - need to redefine cylinder region & union
+
+region cylreg delete
+region hopreg delete
+region cylreg cylinder z ${xc} ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 1 open 2 #Bottom & top are open
+region cylreg cylinder z 25 ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 1 open 2
+region cylreg cylinder z 25 25 ${radconelo} ${zcyllo} ${zconelo} side in units box open 1 open 2
+region cylreg cylinder z 25 25 2 ${zcyllo} ${zconelo} side in units box open 1 open 2
+region cylreg cylinder z 25 25 2 0 ${zconelo} side in units box open 1 open 2
+region cylreg cylinder z 25 25 2 0 10 side in units box open 1 open 2
+
+region hopreg union 2 cylreg conereg
+
+unfix hopper3
+fix hopper3 all wall/gran/region hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
+fix hopper3 all wall/gran/region hertz/history 72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
+fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
+fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1 region hopreg
+fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1 region hopreg
+fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1 region hopreg
+
+run 100000
+Per MPI rank memory allocation (min/avg/max) = 18.64 | 18.64 | 18.64 Mbytes
+Step CPU Atoms KinEng
+ 170000 0 2000 1.8568914
+ 171000 0.75704765 2000 2.4011583
+ 172000 1.5101345 2000 3.176628
+ 173000 2.2556529 2000 4.5364486
+ 174000 2.9946566 2000 6.5494125
+ 175000 3.7253478 2000 9.1934319
+ 176000 4.4570525 2000 12.25765
+ 177000 5.1876664 2000 15.799657
+ 178000 5.9178619 2000 19.982558
+ 179000 6.6439464 2000 24.927165
+ 180000 7.3749168 2000 30.428362
+ 181000 8.1011977 2000 36.74232
+ 182000 8.8207343 2000 43.820448
+ 183000 9.5397925 2000 50.903222
+ 184000 10.253098 2000 59.425781
+ 185000 10.965505 2000 69.143119
+ 186000 11.673319 2000 79.210705
+ 187000 12.373966 2000 90.411346
+ 188000 13.075475 2000 102.35389
+ 189000 13.770632 2000 114.93888
+ 190000 14.469445 2000 128.63341
+ 191000 15.158381 2000 143.44526
+ 192000 15.846267 2000 159.04574
+ 193000 16.527754 2000 174.3114
+ 194000 17.204808 2000 190.42123
+ 195000 17.881059 2000 207.70459
+ 196000 18.556555 2000 224.90931
+ 197000 19.229818 2000 242.64914
+ 198000 19.905086 2000 261.48312
+ 199000 20.578518 2000 281.28308
+ 200000 21.25632 2000 302.95108
+ 201000 21.921347 2000 325.95534
+ 202000 22.583873 2000 350.6874
+ 203000 23.244724 2000 376.31773
+ 204000 23.904842 2000 404.21947
+ 205000 24.562788 2000 432.96116
+ 206000 25.217762 2000 462.4113
+ 207000 25.875814 2000 491.91207
+ 208000 26.531285 2000 522.15395
+ 209000 27.184766 2000 553.1024
+ 210000 27.842961 2000 585.7133
+ 211000 28.489339 2000 619.96357
+ 212000 29.139612 2000 653.96189
+ 213000 29.783866 2000 689.8027
+ 214000 30.426881 2000 727.28401
+ 215000 31.06706 2000 766.40354
+ 216000 31.706399 2000 805.65433
+ 217000 32.343033 2000 845.40981
+ 218000 32.989384 2000 884.24637
+ 219000 33.633664 2000 923.5998
+ 220000 34.285172 2000 965.01779
+ 221000 34.931959 2000 1009.1763
+ 222000 35.571624 2000 1054.7789
+ 223000 36.207868 2000 1101.9922
+ 224000 36.836062 2000 1151.1205
+ 225000 37.464514 2000 1201.3979
+ 226000 38.09746 2000 1252.4054
+ 227000 38.732507 1999 1296.6784
+ 228000 39.371367 1997 1342.3466
+ 229000 40.012553 1992 1368.8559
+ 230000 40.652111 1977 1360.2259
+ 231000 41.275478 1965 1340.3793
+ 232000 41.892734 1953 1318.8318
+ 233000 42.50588 1938 1295.5667
+ 234000 43.121427 1924 1270.0641
+ 235000 43.740727 1914 1258.296
+ 236000 44.359241 1902 1224.3945
+ 237000 44.979463 1899 1248.3905
+ 238000 45.597358 1885 1206.9229
+ 239000 46.210114 1875 1195.5429
+ 240000 46.818148 1861 1142.6591
+ 241000 47.411079 1851 1131.5523
+ 242000 48.002522 1841 1116.8741
+ 243000 48.594254 1830 1099.9978
+ 244000 49.191798 1822 1078.6068
+ 245000 49.791332 1814 1072.1498
+ 246000 50.389728 1803 1020.7842
+ 247000 50.984212 1794 1000.1936
+ 248000 51.571047 1781 942.02462
+ 249000 52.149428 1772 916.83697
+ 250000 52.726202 1758 825.10751
+ 251000 53.29913 1748 789.06351
+ 252000 53.871912 1739 753.92258
+ 253000 54.441009 1729 697.83686
+ 254000 55.010203 1718 648.98541
+ 255000 55.573602 1710 620.38129
+ 256000 56.134709 1705 622.43466
+ 257000 56.701827 1700 595.79102
+ 258000 57.264463 1698 608.49223
+ 259000 57.827817 1695 614.0119
+ 260000 58.398994 1690 601.50438
+ 261000 58.964611 1687 608.5892
+ 262000 59.526765 1683 597.07884
+ 263000 60.082729 1682 618.65041
+ 264000 60.640105 1678 615.47784
+ 265000 61.195717 1675 605.27658
+ 266000 61.751087 1671 583.69853
+ 267000 62.305546 1669 600.11043
+ 268000 62.86105 1666 598.79807
+ 269000 63.417551 1663 588.40338
+ 270000 63.974486 1660 579.59387
+Loop time of 63.9745 on 1 procs for 100000 steps with 1660 atoms
+
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 26.514 | 26.514 | 26.514 | 0.0 | 41.44
+Neigh | 0.60324 | 0.60324 | 0.60324 | 0.0 | 0.94
+Comm | 0.075881 | 0.075881 | 0.075881 | 0.0 | 0.12
+Output | 0.0029137 | 0.0029137 | 0.0029137 | 0.0 | 0.00
+Modify | 35.686 | 35.686 | 35.686 | 0.0 | 55.78
+Other | | 1.092 | | | 1.71
+
+Nlocal: 1660 ave 1660 max 1660 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: 11681 ave 11681 max 11681 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 11681
+Ave neighs/atom = 7.03675
+Neighbor list builds = 249
+Dangerous builds = 0
+Total wall time: 0:02:48
diff --git a/examples/granregion/log.27Nov18.granregion.funnel.g++.4 b/examples/granregion/log.27Nov18.granregion.funnel.g++.4
new file mode 100644
index 0000000000..67c307d212
--- /dev/null
+++ b/examples/granregion/log.27Nov18.granregion.funnel.g++.4
@@ -0,0 +1,601 @@
+LAMMPS (27 Nov 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+# pour particles into cone-shaped funnel, settle them, let them run out bottom
+
+variable name string funnel_pour
+
+thermo_modify flush yes
+units si
+variable PI equal 3.141592653589
+variable seed equal 14314
+
+###############################################
+# Geometry-related parameters
+###############################################
+
+variable xlo equal 10
+variable xhi equal 40
+variable ylo equal 10
+variable yhi equal 40
+variable zlo equal -20
+variable zhi equal 50
+
+variable xc equal 25
+variable yc equal 25
+
+variable zconehi equal 50
+variable zconelo equal 10
+variable zcyllo equal 0
+variable radconelo equal 2
+variable radconehi equal 20
+
+################################################
+# Particle sizes
+################################################
+
+variable rlo equal 0.25
+variable rhi equal 0.5
+variable dlo equal 2.0*${rlo}
+variable dlo equal 2.0*0.25
+variable dhi equal 2.0*${rhi}
+variable dhi equal 2.0*0.5
+
+variable skin equal ${rhi}
+variable skin equal 0.5
+
+###############################################
+# Granular contact parameters
+###############################################
+
+variable coeffRes equal 0.1
+variable coeffFric equal 0.5
+
+variable density equal 1.0
+variable EYoung equal 10^5
+variable Poisson equal 2.0/7.0
+variable GShear equal ${EYoung}/(2*(1+${Poisson}))
+variable GShear equal 100000/(2*(1+${Poisson}))
+variable GShear equal 100000/(2*(1+0.285714285714286))
+
+variable gravity equal 1.0
+
+variable reff equal 0.5*(${rhi}+${rlo})
+variable reff equal 0.5*(0.5+${rlo})
+variable reff equal 0.5*(0.5+0.25)
+variable meff equal ${density}*4.0/3.0*${PI}*${reff}^3
+variable meff equal 1*4.0/3.0*${PI}*${reff}^3
+variable meff equal 1*4.0/3.0*3.141592653589*${reff}^3
+variable meff equal 1*4.0/3.0*3.141592653589*0.375^3
+variable min_mass equal ${density}*4.0/3.0*${PI}*${rlo}*${rlo}*${rlo}
+variable min_mass equal 1*4.0/3.0*${PI}*${rlo}*${rlo}*${rlo}
+variable min_mass equal 1*4.0/3.0*3.141592653589*${rlo}*${rlo}*${rlo}
+variable min_mass equal 1*4.0/3.0*3.141592653589*0.25*${rlo}*${rlo}
+variable min_mass equal 1*4.0/3.0*3.141592653589*0.25*0.25*${rlo}
+variable min_mass equal 1*4.0/3.0*3.141592653589*0.25*0.25*0.25
+variable max_mass equal ${density}*4.0/3.0*${PI}*${rhi}*${rhi}*${rhi}
+variable max_mass equal 1*4.0/3.0*${PI}*${rhi}*${rhi}*${rhi}
+variable max_mass equal 1*4.0/3.0*3.141592653589*${rhi}*${rhi}*${rhi}
+variable max_mass equal 1*4.0/3.0*3.141592653589*0.5*${rhi}*${rhi}
+variable max_mass equal 1*4.0/3.0*3.141592653589*0.5*0.5*${rhi}
+variable max_mass equal 1*4.0/3.0*3.141592653589*0.5*0.5*0.5
+
+## Typical way to set kn, kt, etc.:
+variable kn equal 4.0*${GShear}/(3*(1-${Poisson}))
+variable kn equal 4.0*38888.8888888889/(3*(1-${Poisson}))
+variable kn equal 4.0*38888.8888888889/(3*(1-0.285714285714286))
+variable kt equal 4.0*${GShear}/(2-${Poisson})
+variable kt equal 4.0*38888.8888888889/(2-${Poisson})
+variable kt equal 4.0*38888.8888888889/(2-0.285714285714286)
+
+variable a equal (-2.0*log(${coeffRes})/${PI})^2
+variable a equal (-2.0*log(0.1)/${PI})^2
+variable a equal (-2.0*log(0.1)/3.141592653589)^2
+variable gamma_n equal sqrt($a*2*${kn}/${min_mass}/(1+0.25*$a))
+variable gamma_n equal sqrt(0.405284734569556*2*${kn}/${min_mass}/(1+0.25*$a))
+variable gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/${min_mass}/(1+0.25*$a))
+variable gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/0.0654498469497708/(1+0.25*$a))
+variable gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/0.0654498469497708/(1+0.25*0.405284734569556))
+variable gamma_t equal ${gamma_n}*0.5
+variable gamma_t equal 903.503751814138*0.5
+
+variable tcol equal ${PI}/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
+variable tcol equal 3.141592653589/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
+variable tcol equal 3.141592653589/sqrt(2*72592.5925925926/${min_mass}-${gamma_n}/4.0)
+variable tcol equal 3.141592653589/sqrt(2*72592.5925925926/0.0654498469497708-${gamma_n}/4.0)
+variable tcol equal 3.141592653589/sqrt(2*72592.5925925926/0.0654498469497708-903.503751814138/4.0)
+
+variable dt equal ${tcol}*0.05
+variable dt equal 0.00210943016014969*0.05
+timestep ${dt}
+timestep 0.000105471508007485
+
+###############################################
+variable dumpfreq equal 1000
+variable logfreq equal 1000
+
+newton off
+atom_style sphere
+
+boundary p p f
+
+region boxreg block ${xlo} ${xhi} ${ylo} ${yhi} ${zlo} ${zhi}
+region boxreg block 10 ${xhi} ${ylo} ${yhi} ${zlo} ${zhi}
+region boxreg block 10 40 ${ylo} ${yhi} ${zlo} ${zhi}
+region boxreg block 10 40 10 ${yhi} ${zlo} ${zhi}
+region boxreg block 10 40 10 40 ${zlo} ${zhi}
+region boxreg block 10 40 10 40 -20 ${zhi}
+region boxreg block 10 40 10 40 -20 50
+create_box 1 boxreg
+Created orthogonal box = (10 10 -20) to (40 40 50)
+ 1 by 1 by 4 MPI processor grid
+
+pair_style gran/hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
+pair_style gran/hertz/history 72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
+pair_style gran/hertz/history 72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1
+pair_style gran/hertz/history 72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1
+pair_style gran/hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1
+pair_style gran/hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1
+pair_coeff * *
+
+neighbor ${skin} bin
+neighbor 0.5 bin
+thermo ${logfreq}
+thermo 1000
+
+comm_style brick
+comm_modify mode multi group all vel yes
+balance 1.1 shift xyz 20 1.1
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 0
+ ghost atom cutoff = 0
+ binsize = 30, bins = 1 1 3
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair gran/hertz/history, perpetual
+ attributes: half, newton off, size, history
+ pair build: half/size/bin/newtoff
+ stencil: half/bin/3d/newtoff
+ bin: standard
+fix bal all balance 10000 1.1 shift xyz 20 1.01
+
+####################### Options specific to pouring #########################
+
+# insertion region for fix/pour
+
+region insreg cylinder z ${xc} ${yc} 10 30 50 side in units box
+region insreg cylinder z 25 ${yc} 10 30 50 side in units box
+region insreg cylinder z 25 25 10 30 50 side in units box
+
+# define cone and cylinder regions - see lammps doc on region command
+# note new open options
+
+region cylreg cylinder z ${xc} ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 2 #Top is open
+region cylreg cylinder z 25 ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 2
+region cylreg cylinder z 25 25 ${radconelo} ${zcyllo} ${zconelo} side in units box open 2
+region cylreg cylinder z 25 25 2 ${zcyllo} ${zconelo} side in units box open 2
+region cylreg cylinder z 25 25 2 0 ${zconelo} side in units box open 2
+region cylreg cylinder z 25 25 2 0 10 side in units box open 2
+
+region conereg cone z ${xc} ${yc} ${radconelo} ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2 #Bottom and top are open
+region conereg cone z 25 ${yc} ${radconelo} ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2
+region conereg cone z 25 25 ${radconelo} ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2
+region conereg cone z 25 25 2 ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2
+region conereg cone z 25 25 2 20 ${zconelo} ${zconehi} side in units box open 1 open 2
+region conereg cone z 25 25 2 20 10 ${zconehi} side in units box open 1 open 2
+region conereg cone z 25 25 2 20 10 50 side in units box open 1 open 2
+
+region hopreg union 2 conereg cylreg
+
+fix grav all gravity ${gravity} vector 0 0 -1
+fix grav all gravity 1 vector 0 0 -1
+fix 1 all nve/sphere
+
+
+fix hopper3 all wall/gran/region hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
+fix hopper3 all wall/gran/region hertz/history 72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
+fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
+fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1 region hopreg
+fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1 region hopreg
+fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1 region hopreg
+
+fix ins all pour 2000 1 42424 region insreg diam range ${dlo} ${dhi} dens ${density} ${density}
+fix ins all pour 2000 1 42424 region insreg diam range 0.5 ${dhi} dens ${density} ${density}
+fix ins all pour 2000 1 42424 region insreg diam range 0.5 1 dens ${density} ${density}
+fix ins all pour 2000 1 42424 region insreg diam range 0.5 1 dens 1 ${density}
+fix ins all pour 2000 1 42424 region insreg diam range 0.5 1 dens 1 1
+Particle insertion: 3000 every 59965 steps, 2000 by step 1
+
+#dump 1 all custom ${dumpfreq} ${name}.dump # id type mass diameter x y z
+
+#dump 2 all image 4000 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 zoom 3.0 # box no 0.0 axes no 0.0 0.0
+#dump_modify 2 pad 6
+
+thermo_style custom step cpu atoms ke
+WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:705)
+thermo_modify flush yes lost warn
+
+# Initial run to fill up the cone
+
+run 20000
+Per MPI rank memory allocation (min/avg/max) = 6.05 | 6.05 | 6.05 Mbytes
+Step CPU Atoms KinEng
+ 0 0 0 -0
+ 1000 0.63366675 2000 -0
+ 2000 1.0221362 2000 -0
+ 3000 1.3905275 2000 -0
+ 4000 1.7514329 2000 -0
+ 5000 2.1040537 2000 -0
+ 6000 2.4468088 2000 -0
+ 7000 2.7853072 2000 -0
+ 8000 3.1109948 2000 -0
+ 9000 3.4281557 2000 -0
+ 10000 3.7435207 2000 -0
+ 11000 3.8612552 2000 -0
+ 12000 3.9786677 2000 -0
+ 13000 4.0988154 2000 -0
+ 14000 4.2249811 2000 -0
+ 15000 4.3562138 2000 -0
+ 16000 4.4940333 2000 -0
+ 17000 4.6394637 2000 -0
+ 18000 4.7909062 2000 -0
+ 19000 4.9482198 2000 -0
+ 20000 5.1116607 2000 -0
+Loop time of 5.11176 on 4 procs for 20000 steps with 2000 atoms
+
+97.4% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.050997 | 0.14884 | 0.36048 | 32.0 | 2.91
+Neigh | 0.01374 | 0.025199 | 0.043743 | 7.0 | 0.49
+Comm | 0.063387 | 0.1781 | 0.29748 | 22.6 | 3.48
+Output | 0.0016627 | 0.0060938 | 0.015082 | 6.8 | 0.12
+Modify | 1.1198 | 1.987 | 3.7195 | 72.6 | 38.87
+Other | | 2.767 | | | 54.12
+
+Nlocal: 500 ave 505 max 493 min
+Histogram: 1 0 0 0 0 1 0 1 0 1
+Nghost: 159.25 ave 254 max 71 min
+Histogram: 1 0 0 1 0 1 0 0 0 1
+Neighs: 397.5 ave 616 max 214 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+
+Total # of neighbors = 1590
+Ave neighs/atom = 0.795
+Neighbor list builds = 69
+Dangerous builds = 0
+unfix ins
+run 150000
+Per MPI rank memory allocation (min/avg/max) = 12.37 | 12.51 | 12.7 Mbytes
+Step CPU Atoms KinEng
+ 20000 0 2000 6443.7665
+ 21000 0.11261106 2000 6572.3531
+ 22000 0.23091817 2000 6723.8376
+ 23000 0.35577631 2000 6853.1812
+ 24000 0.48790455 2000 6976.0209
+ 25000 0.63509274 2000 7096.9955
+ 26000 0.78251743 2000 7215.5795
+ 27000 0.93707466 2000 7349.2382
+ 28000 1.1032445 2000 7471.8719
+ 29000 1.2721858 2000 7574.8228
+ 30000 1.449265 2000 7659.3836
+ 31000 1.5742557 2000 7703.6856
+ 32000 1.7076068 2000 7644.279
+ 33000 1.8527873 2000 7526.6944
+ 34000 2.009855 2000 7370.0821
+ 35000 2.1766446 2000 7193.0459
+ 36000 2.3557482 2000 6990.9912
+ 37000 2.5468907 2000 6849.286
+ 38000 2.7480681 2000 6701.7548
+ 39000 2.9574037 2000 6538.6915
+ 40000 3.1807711 2000 6382.3209
+ 41000 3.3486595 2000 6216.424
+ 42000 3.5162592 2000 6091.29
+ 43000 3.687057 2000 5945.3256
+ 44000 3.8662596 2000 5840.875
+ 45000 4.0557241 2000 5649.763
+ 46000 4.2541051 2000 5476.2837
+ 47000 4.4571214 2000 5277.0701
+ 48000 4.6628008 2000 5123.9796
+ 49000 4.8686502 2000 4968.3344
+ 50000 5.0788848 2000 4869.5754
+ 51000 5.2552598 2000 4704.8517
+ 52000 5.4428713 2000 4522.8978
+ 53000 5.6520596 2000 4393.8047
+ 54000 5.8613031 2000 4235.438
+ 55000 6.0776098 2000 4082.3073
+ 56000 6.2998042 2000 3901.0483
+ 57000 6.5321434 2000 3718.0882
+ 58000 6.7745438 2000 3504.621
+ 59000 7.0237701 2000 3285.7484
+ 60000 7.2791855 2000 3047.3386
+ 61000 7.489058 2000 2875.4032
+ 62000 7.7044094 2000 2647.83
+ 63000 7.9194827 2000 2396.5343
+ 64000 8.1429474 2000 2107.2113
+ 65000 8.3745618 2000 1858.1977
+ 66000 8.610673 2000 1615.8096
+ 67000 8.8505244 2000 1416.5065
+ 68000 9.0955915 2000 1206.8534
+ 69000 9.3609676 2000 953.93974
+ 70000 9.6382594 2000 766.9148
+ 71000 9.8719468 2000 611.45063
+ 72000 10.095534 2000 464.94805
+ 73000 10.317962 2000 364.31415
+ 74000 10.547287 2000 298.77524
+ 75000 10.764052 2000 245.73022
+ 76000 10.978769 2000 207.8035
+ 77000 11.199921 2000 179.1305
+ 78000 11.410296 2000 151.21032
+ 79000 11.624499 2000 124.49675
+ 80000 11.849562 2000 106.71504
+ 81000 12.077449 2000 93.299034
+ 82000 12.306904 2000 81.220408
+ 83000 12.539016 2000 67.383955
+ 84000 12.773108 2000 57.287165
+ 85000 13.009487 2000 49.255887
+ 86000 13.252544 2000 44.082536
+ 87000 13.502564 2000 40.193574
+ 88000 13.747198 2000 36.903867
+ 89000 13.993028 2000 33.55332
+ 90000 14.240036 2000 30.730912
+ 91000 14.472719 2000 28.650574
+ 92000 14.708542 2000 26.377609
+ 93000 14.948106 2000 24.433165
+ 94000 15.186653 2000 22.933076
+ 95000 15.428022 2000 22.31788
+ 96000 15.676323 2000 20.829124
+ 97000 15.916326 2000 19.401354
+ 98000 16.160197 2000 18.943699
+ 99000 16.404796 2000 17.690599
+ 100000 16.659731 2000 17.215943
+ 101000 16.904498 2000 15.948087
+ 102000 17.150993 2000 15.140324
+ 103000 17.39584 2000 14.885674
+ 104000 17.643707 2000 14.414752
+ 105000 17.889343 2000 14.270676
+ 106000 18.136159 2000 13.943799
+ 107000 18.383653 2000 13.840145
+ 108000 18.630952 2000 12.826341
+ 109000 18.878218 2000 12.209012
+ 110000 19.125558 2000 11.916194
+ 111000 19.3726 2000 11.970849
+ 112000 19.621494 2000 11.56909
+ 113000 19.869978 2000 11.390562
+ 114000 20.123402 2000 11.276545
+ 115000 20.370963 2000 11.171298
+ 116000 20.619975 2000 11.686225
+ 117000 20.869585 2000 11.379805
+ 118000 21.118875 2000 10.539511
+ 119000 21.36837 2000 10.064595
+ 120000 21.629511 2000 10.003722
+ 121000 21.877867 2000 9.6974586
+ 122000 22.127922 2000 9.7156209
+ 123000 22.378215 2000 9.615256
+ 124000 22.630463 2000 8.8979008
+ 125000 22.882154 2000 8.2220003
+ 126000 23.135763 2000 8.3153866
+ 127000 23.392389 2000 8.0945497
+ 128000 23.645521 2000 7.8942467
+ 129000 23.89965 2000 7.4794776
+ 130000 24.153195 2000 7.3635341
+ 131000 24.406239 2000 7.5757743
+ 132000 24.66016 2000 7.7047492
+ 133000 24.914093 2000 8.0142133
+ 134000 25.173429 2000 8.1716714
+ 135000 25.433318 2000 7.7803343
+ 136000 25.692997 2000 6.3545482
+ 137000 25.947787 2000 6.313769
+ 138000 26.200427 2000 6.4948596
+ 139000 26.452514 2000 6.6183259
+ 140000 26.714963 2000 6.7922281
+ 141000 26.968235 2000 7.0752448
+ 142000 27.220962 2000 7.2328717
+ 143000 27.474819 2000 7.626453
+ 144000 27.728029 2000 7.4576787
+ 145000 27.981958 2000 7.124435
+ 146000 28.236591 2000 7.2581589
+ 147000 28.489842 2000 7.0622049
+ 148000 28.744432 2000 7.1672801
+ 149000 28.998739 2000 7.3248363
+ 150000 29.253511 2000 7.0092266
+ 151000 29.50567 2000 6.8124438
+ 152000 29.759836 2000 6.9808705
+ 153000 30.015359 2000 7.1516731
+ 154000 30.275488 2000 6.6245443
+ 155000 30.533407 2000 5.5867165
+ 156000 30.788683 2000 5.318949
+ 157000 31.043126 2000 5.1195805
+ 158000 31.297011 2000 5.2045485
+ 159000 31.551327 2000 5.24992
+ 160000 31.807728 2000 5.3270577
+ 161000 32.061371 2000 4.995281
+ 162000 32.315467 2000 5.0755874
+ 163000 32.57628 2000 5.0788135
+ 164000 32.83119 2000 4.5917317
+ 165000 33.085634 2000 4.6255452
+ 166000 33.344148 2000 4.2563299
+ 167000 33.599342 2000 3.3808566
+ 168000 33.853488 2000 3.218931
+ 169000 34.121464 2000 3.0839289
+ 170000 34.378727 2000 3.0358838
+Loop time of 34.3788 on 4 procs for 150000 steps with 2000 atoms
+
+98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 6.5861 | 10.058 | 12.152 | 68.4 | 29.26
+Neigh | 0.17612 | 0.25274 | 0.30005 | 9.2 | 0.74
+Comm | 1.5024 | 2.6626 | 3.4174 | 44.9 | 7.74
+Output | 0.006542 | 0.019532 | 0.046425 | 11.5 | 0.06
+Modify | 11.945 | 14.674 | 16.29 | 42.7 | 42.68
+Other | | 6.711 | | | 19.52
+
+Nlocal: 500 ave 508 max 489 min
+Histogram: 1 0 0 1 0 0 0 0 0 2
+Nghost: 446.75 ave 708 max 191 min
+Histogram: 1 0 0 1 0 1 0 0 0 1
+Neighs: 4498 ave 5441 max 3786 min
+Histogram: 1 1 0 0 0 0 1 0 0 1
+
+Total # of neighbors = 17992
+Ave neighs/atom = 8.996
+Neighbor list builds = 403
+Dangerous builds = 0
+
+# remove "plug" - need to redefine cylinder region & union
+
+region cylreg delete
+region hopreg delete
+region cylreg cylinder z ${xc} ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 1 open 2 #Bottom & top are open
+region cylreg cylinder z 25 ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 1 open 2
+region cylreg cylinder z 25 25 ${radconelo} ${zcyllo} ${zconelo} side in units box open 1 open 2
+region cylreg cylinder z 25 25 2 ${zcyllo} ${zconelo} side in units box open 1 open 2
+region cylreg cylinder z 25 25 2 0 ${zconelo} side in units box open 1 open 2
+region cylreg cylinder z 25 25 2 0 10 side in units box open 1 open 2
+
+region hopreg union 2 cylreg conereg
+
+unfix hopper3
+fix hopper3 all wall/gran/region hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
+fix hopper3 all wall/gran/region hertz/history 72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
+fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
+fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1 region hopreg
+fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1 region hopreg
+fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1 region hopreg
+
+run 100000
+Per MPI rank memory allocation (min/avg/max) = 13.68 | 15.35 | 16.59 Mbytes
+Step CPU Atoms KinEng
+ 170000 0 2000 3.0358838
+ 171000 0.25455499 2000 3.7725185
+ 172000 0.50768304 2000 4.727285
+ 173000 0.76122355 2000 5.9840449
+ 174000 1.0141416 2000 8.0335022
+ 175000 1.2750733 2000 10.177259
+ 176000 1.5277736 2000 13.655163
+ 177000 1.7810826 2000 17.987975
+ 178000 2.0348532 2000 23.266471
+ 179000 2.2915859 2000 29.266364
+ 180000 2.547174 2000 35.84089
+ 181000 2.8009758 2000 43.130989
+ 182000 3.0531759 2000 51.177142
+ 183000 3.3130636 2000 60.031831
+ 184000 3.5651338 2000 69.52374
+ 185000 3.8185399 2000 79.941907
+ 186000 4.070199 2000 91.195382
+ 187000 4.3204038 2000 102.1696
+ 188000 4.5699775 2000 112.73657
+ 189000 4.8184452 2000 123.57252
+ 190000 5.0653601 2000 135.59942
+ 191000 5.3119307 2000 147.37757
+ 192000 5.5574484 2000 159.12931
+ 193000 5.8029084 2000 170.90271
+ 194000 6.0463562 2000 185.71189
+ 195000 6.2883332 2000 201.83733
+ 196000 6.5281694 2000 218.30785
+ 197000 6.7682493 2000 236.05694
+ 198000 7.0084231 2000 255.23099
+ 199000 7.2519951 2000 273.94566
+ 200000 7.5010133 2000 293.91107
+ 201000 7.7396591 2000 316.52142
+ 202000 7.9784184 2000 340.91391
+ 203000 8.224021 2000 364.81801
+ 204000 8.4597676 2000 390.06478
+ 205000 8.6934731 2000 415.90918
+ 206000 8.9342225 2000 441.0995
+ 207000 9.1714027 2000 467.40314
+ 208000 9.4081488 2000 494.93631
+ 209000 9.6457636 2000 524.70539
+ 210000 9.8831718 2000 556.52058
+ 211000 10.118018 2000 589.36821
+ 212000 10.3541 2000 622.6887
+ 213000 10.587226 2000 657.05888
+ 214000 10.820744 2000 691.14292
+ 215000 11.055785 2000 726.94959
+ 216000 11.298702 2000 762.92802
+ 217000 11.534793 2000 801.23648
+ 218000 11.769849 2000 841.1559
+ 219000 12.000917 2000 882.4342
+ 220000 12.232812 2000 924.8466
+ 221000 12.461166 2000 968.86229
+ 222000 12.698451 2000 1013.1381
+ 223000 12.930287 2000 1058.2988
+ 224000 13.172862 2000 1105.2911
+ 225000 13.405001 2000 1152.8617
+ 226000 13.633187 1999 1197.6777
+ 227000 13.857126 1998 1243.1211
+ 228000 14.079622 1992 1262.1402
+ 229000 14.303362 1987 1281.9162
+ 230000 14.530392 1973 1264.0674
+ 231000 14.756486 1964 1277.8347
+ 232000 14.984495 1953 1266.7926
+ 233000 15.213102 1940 1244.0038
+ 234000 15.441666 1925 1206.4472
+ 235000 15.667547 1914 1193.33
+ 236000 15.895047 1901 1160.4096
+ 237000 16.120833 1890 1141.6816
+ 238000 16.346628 1883 1149.1584
+ 239000 16.573303 1877 1141.7514
+ 240000 16.801035 1871 1146.8662
+ 241000 17.024775 1866 1152.561
+ 242000 17.248651 1858 1148.2529
+ 243000 17.47241 1847 1114.7239
+ 244000 17.70222 1832 1070.9996
+ 245000 17.926477 1824 1066.7549
+ 246000 18.157588 1813 1027.1865
+ 247000 18.378868 1804 1011.5024
+ 248000 18.599988 1797 993.10451
+ 249000 18.819007 1787 951.89778
+ 250000 19.044634 1777 926.30475
+ 251000 19.254408 1764 875.07091
+ 252000 19.465788 1755 824.89358
+ 253000 19.676327 1742 742.51957
+ 254000 19.887648 1731 708.30958
+ 255000 20.094912 1722 690.09761
+ 256000 20.299963 1713 638.00218
+ 257000 20.506153 1705 596.86839
+ 258000 20.713994 1701 583.71937
+ 259000 20.919755 1691 549.0049
+ 260000 21.123122 1688 549.4278
+ 261000 21.332215 1684 535.35719
+ 262000 21.533673 1682 546.74031
+ 263000 21.737042 1678 532.69324
+ 264000 21.941306 1676 537.89254
+ 265000 22.15135 1676 559.50898
+ 266000 22.358371 1670 540.21452
+ 267000 22.563236 1668 557.19857
+ 268000 22.764648 1665 569.52869
+ 269000 22.96391 1658 543.77057
+ 270000 23.172415 1656 550.23716
+Loop time of 23.1725 on 4 procs for 100000 steps with 1656 atoms
+
+98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 3.3849 | 7.3002 | 10.192 | 91.3 | 31.50
+Neigh | 0.14271 | 0.16781 | 0.19054 | 4.5 | 0.72
+Comm | 1.086 | 1.9721 | 2.6157 | 42.7 | 8.51
+Output | 0.0018437 | 0.013918 | 0.041359 | 13.5 | 0.06
+Modify | 8.6598 | 9.3198 | 9.8874 | 16.6 | 40.22
+Other | | 4.399 | | | 18.98
+
+Nlocal: 414 ave 454 max 385 min
+Histogram: 2 0 0 0 0 0 1 0 0 1
+Nghost: 395.25 ave 645 max 157 min
+Histogram: 1 0 0 1 0 1 0 0 0 1
+Neighs: 3498.5 ave 4524 max 2034 min
+Histogram: 1 0 0 0 1 0 0 0 0 2
+
+Total # of neighbors = 13994
+Ave neighs/atom = 8.45048
+Neighbor list builds = 240
+Dangerous builds = 0
+Total wall time: 0:01:02
diff --git a/examples/granregion/log.27Nov18.granregion.mixer.g++.1 b/examples/granregion/log.27Nov18.granregion.mixer.g++.1
new file mode 100644
index 0000000000..f2ba9d7122
--- /dev/null
+++ b/examples/granregion/log.27Nov18.granregion.mixer.g++.1
@@ -0,0 +1,602 @@
+LAMMPS (27 Nov 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+variable name string mixer
+
+thermo_modify flush yes
+variable seed equal 14314
+
+###############################################
+# Particle parameters
+################################################
+
+variable rlo equal 0.3
+variable rhi equal 0.6
+variable dlo equal 2.0*${rlo}
+variable dlo equal 2.0*0.3
+variable dhi equal 2.0*${rhi}
+variable dhi equal 2.0*0.6
+variable skin equal ${rhi}
+variable skin equal 0.6
+
+variable coeffRes equal 0.1
+variable coeffFric equal 0.5
+
+variable kn equal 10^5
+variable kt equal 0.2*${kn}
+variable kt equal 0.2*100000
+
+variable gravity equal 1.0
+variable density equal 1.0
+
+variable min_mass equal ${density}*4.0/3.0*PI*${rlo}*${rlo}*${rlo}
+variable min_mass equal 1*4.0/3.0*PI*${rlo}*${rlo}*${rlo}
+variable min_mass equal 1*4.0/3.0*PI*0.3*${rlo}*${rlo}
+variable min_mass equal 1*4.0/3.0*PI*0.3*0.3*${rlo}
+variable min_mass equal 1*4.0/3.0*PI*0.3*0.3*0.3
+variable a equal (-2.0*log(${coeffRes})/PI)^2
+variable a equal (-2.0*log(0.1)/PI)^2
+variable gamma_n equal sqrt($a*2*${kn}/${min_mass}/(1+0.25*$a))
+variable gamma_n equal sqrt(0.405284734569351*2*${kn}/${min_mass}/(1+0.25*$a))
+variable gamma_n equal sqrt(0.405284734569351*2*100000/${min_mass}/(1+0.25*$a))
+variable gamma_n equal sqrt(0.405284734569351*2*100000/0.113097335529233/(1+0.25*$a))
+variable gamma_n equal sqrt(0.405284734569351*2*100000/0.113097335529233/(1+0.25*0.405284734569351))
+variable gamma_t equal ${gamma_n}*0.5
+variable gamma_t equal 806.699778405191*0.5
+
+variable tcol equal PI/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
+variable tcol equal PI/sqrt(2*100000/${min_mass}-${gamma_n}/4.0)
+variable tcol equal PI/sqrt(2*100000/0.113097335529233-${gamma_n}/4.0)
+variable tcol equal PI/sqrt(2*100000/0.113097335529233-806.699778405191/4.0)
+
+variable dt equal ${tcol}*0.02
+variable dt equal 0.00236257621510454*0.02
+timestep ${dt}
+timestep 4.72515243020908e-05
+
+###############################################
+
+variable dumpfreq equal 1000
+variable logfreq equal 1000
+
+newton on
+atom_style sphere
+
+boundary p p f
+
+region boxreg block 0 20 0 20 0 20
+create_box 1 boxreg
+Created orthogonal box = (0 0 0) to (20 20 20)
+ 1 by 1 by 1 MPI processor grid
+
+pair_style gran/hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
+pair_style gran/hertz/history 100000 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
+pair_style gran/hertz/history 100000 20000 ${gamma_n} ${gamma_t} ${coeffFric} 1
+pair_style gran/hertz/history 100000 20000 806.699778405191 ${gamma_t} ${coeffFric} 1
+pair_style gran/hertz/history 100000 20000 806.699778405191 403.349889202595 ${coeffFric} 1
+pair_style gran/hertz/history 100000 20000 806.699778405191 403.349889202595 0.5 1
+pair_coeff * *
+
+neighbor ${skin} bin
+neighbor 0.6 bin
+thermo ${logfreq}
+thermo 1000
+
+comm_style brick
+comm_modify mode multi group all vel yes
+balance 1.1 shift xyz 20 1.1
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 0
+ ghost atom cutoff = 0
+ binsize = 20, bins = 1 1 1
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair gran/hertz/history, perpetual
+ attributes: half, newton on, size, history
+ pair build: half/size/bin/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+fix bal all balance 10000 1.1 shift xyz 20 1.01
+
+####################### Options specific to pouring #########################
+
+region insreg cylinder z 10 10 8 10 18 side in units box
+region cylreg cylinder z 10 10 10 0 20 side in units box
+
+variable theta equal (step/400000)*2*PI
+
+region b1 block 2 18 9 11 0 4 side out rotate v_theta 10 10 0 0 0 1 units box
+region b2 block 9 11 2 18 0 3.99999 side out rotate v_theta 10 10 0 0 0 1 units box
+
+region mixer intersect 3 cylreg b1 b2 side in
+
+fix grav all gravity ${gravity} vector 0 0 -1
+fix grav all gravity 1 vector 0 0 -1
+fix 1 all nve/sphere
+
+fix mixwall all wall/gran/region hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
+fix mixwall all wall/gran/region hertz/history 100000 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
+fix mixwall all wall/gran/region hertz/history 100000 20000 ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
+fix mixwall all wall/gran/region hertz/history 100000 20000 806.699778405191 ${gamma_t} ${coeffFric} 1 region mixer
+fix mixwall all wall/gran/region hertz/history 100000 20000 806.699778405191 403.349889202595 ${coeffFric} 1 region mixer
+fix mixwall all wall/gran/region hertz/history 100000 20000 806.699778405191 403.349889202595 0.5 1 region mixer
+
+fix ins all pour 1000 1 42424 region insreg diam range ${dlo} ${dhi} dens ${density} ${density}
+fix ins all pour 1000 1 42424 region insreg diam range 0.6 ${dhi} dens ${density} ${density}
+fix ins all pour 1000 1 42424 region insreg diam range 0.6 1.2 dens ${density} ${density}
+fix ins all pour 1000 1 42424 region insreg diam range 0.6 1.2 dens 1 ${density}
+fix ins all pour 1000 1 42424 region insreg diam range 0.6 1.2 dens 1 1
+Particle insertion: 444 every 84653 steps, 1000 by step 169307
+
+#dump 1 all custom ${dumpfreq} ${name}_pour.dump # id type mass diameter x y z
+
+#dump 2 all image 4000 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 zoom 1.5 # box no 0.0 axes no 0.0 0.0
+#dump_modify 2 pad 6
+
+thermo_style custom step cpu atoms ke v_theta
+WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:705)
+thermo_modify flush yes lost warn
+
+run 200000
+Per MPI rank memory allocation (min/avg/max) = 5.862 | 5.862 | 5.862 Mbytes
+Step CPU Atoms KinEng v_theta
+ 0 0 0 -0 0
+ 1000 0.15327144 444 -0 0.015707963
+ 2000 0.30070925 444 -0 0.031415927
+ 3000 0.44653535 444 -0 0.04712389
+ 4000 0.59226131 444 -0 0.062831853
+ 5000 0.73794818 444 -0 0.078539816
+ 6000 0.88327622 444 -0 0.09424778
+ 7000 1.0286083 444 -0 0.10995574
+ 8000 1.1740625 444 -0 0.12566371
+ 9000 1.3224797 444 -0 0.14137167
+ 10000 1.4717772 444 -0 0.15707963
+ 11000 1.6204555 444 -0 0.1727876
+ 12000 1.7690799 444 -0 0.18849556
+ 13000 1.918304 444 -0 0.20420352
+ 14000 2.0670426 444 -0 0.21991149
+ 15000 2.2157068 444 -0 0.23561945
+ 16000 2.3642888 444 -0 0.25132741
+ 17000 2.5129776 444 -0 0.26703538
+ 18000 2.6614521 444 -0 0.28274334
+ 19000 2.8100598 444 -0 0.2984513
+ 20000 2.9591351 444 -0 0.31415927
+ 21000 3.1073661 444 -0 0.32986723
+ 22000 3.2557554 444 -0 0.34557519
+ 23000 3.4041324 444 -0 0.36128316
+ 24000 3.5526814 444 -0 0.37699112
+ 25000 3.700824 444 -0 0.39269908
+ 26000 3.8496137 444 -0 0.40840704
+ 27000 3.9986103 444 -0 0.42411501
+ 28000 4.1475384 444 -0 0.43982297
+ 29000 4.2963772 444 -0 0.45553093
+ 30000 4.4454341 444 -0 0.4712389
+ 31000 4.5942066 444 -0 0.48694686
+ 32000 4.7434044 444 -0 0.50265482
+ 33000 4.893549 444 -0 0.51836279
+ 34000 5.0427935 444 -0 0.53407075
+ 35000 5.1920972 444 -0 0.54977871
+ 36000 5.3411844 444 -0 0.56548668
+ 37000 5.4904606 444 -0 0.58119464
+ 38000 5.6397707 444 -0 0.5969026
+ 39000 5.7900345 444 -0 0.61261057
+ 40000 5.9405882 444 -0 0.62831853
+ 41000 6.089345 444 -0 0.64402649
+ 42000 6.2388933 444 -0 0.65973446
+ 43000 6.3888056 444 -0 0.67544242
+ 44000 6.5379841 444 -0 0.69115038
+ 45000 6.6875141 444 -0 0.70685835
+ 46000 6.8370855 444 -0 0.72256631
+ 47000 6.9866009 444 -0 0.73827427
+ 48000 7.1364653 444 -0 0.75398224
+ 49000 7.2859883 444 -0 0.7696902
+ 50000 7.4368248 444 -0 0.78539816
+ 51000 7.5870779 444 -0 0.80110613
+ 52000 7.7370813 444 -0 0.81681409
+ 53000 7.8879561 444 -0 0.83252205
+ 54000 8.0383027 444 -0 0.84823002
+ 55000 8.1916294 444 -0 0.86393798
+ 56000 8.3458471 444 -0 0.87964594
+ 57000 8.5010631 444 -0 0.89535391
+ 58000 8.6560545 444 -0 0.91106187
+ 59000 8.8110209 444 -0 0.92676983
+ 60000 8.9674675 444 -0 0.9424778
+ 61000 9.1231239 444 -0 0.95818576
+ 62000 9.2785382 444 -0 0.97389372
+ 63000 9.4343674 444 -0 0.98960169
+ 64000 9.5911541 444 -0 1.0053096
+ 65000 9.7477772 444 -0 1.0210176
+ 66000 9.9050307 444 -0 1.0367256
+ 67000 10.063978 444 -0 1.0524335
+ 68000 10.221835 444 -0 1.0681415
+ 69000 10.37944 444 -0 1.0838495
+ 70000 10.537409 444 -0 1.0995574
+ 71000 10.695649 444 -0 1.1152654
+ 72000 10.85453 444 -0 1.1309734
+ 73000 11.013438 444 -0 1.1466813
+ 74000 11.172689 444 -0 1.1623893
+ 75000 11.332172 444 -0 1.1780972
+ 76000 11.492824 444 -0 1.1938052
+ 77000 11.653915 444 -0 1.2095132
+ 78000 11.815798 444 -0 1.2252211
+ 79000 11.97868 444 -0 1.2409291
+ 80000 12.141392 444 -0 1.2566371
+ 81000 12.30536 444 -0 1.272345
+ 82000 12.468797 444 -0 1.288053
+ 83000 12.633028 444 -0 1.303761
+ 84000 12.797936 444 -0 1.3194689
+ 85000 13.019726 888 -0 1.3351769
+ 86000 13.333436 888 -0 1.3508848
+ 87000 13.648179 888 -0 1.3665928
+ 88000 13.962435 888 -0 1.3823008
+ 89000 14.276158 888 -0 1.3980087
+ 90000 14.590669 888 -0 1.4137167
+ 91000 14.904268 888 -0 1.4294247
+ 92000 15.216788 888 -0 1.4451326
+ 93000 15.529868 888 -0 1.4608406
+ 94000 15.843157 888 -0 1.4765485
+ 95000 16.156564 888 -0 1.4922565
+ 96000 16.469569 888 -0 1.5079645
+ 97000 16.784048 888 -0 1.5236724
+ 98000 17.100451 888 -0 1.5393804
+ 99000 17.416338 888 -0 1.5550884
+ 100000 17.733482 888 -0 1.5707963
+ 101000 18.052522 888 -0 1.5865043
+ 102000 18.371428 888 -0 1.6022123
+ 103000 18.690222 888 -0 1.6179202
+ 104000 19.009665 888 -0 1.6336282
+ 105000 19.328189 888 -0 1.6493361
+ 106000 19.647804 888 -0 1.6650441
+ 107000 19.96805 888 -0 1.6807521
+ 108000 20.286857 888 -0 1.69646
+ 109000 20.607965 888 -0 1.712168
+ 110000 20.931749 888 -0 1.727876
+ 111000 21.251903 888 -0 1.7435839
+ 112000 21.572158 888 -0 1.7592919
+ 113000 21.892612 888 -0 1.7749998
+ 114000 22.214408 888 -0 1.7907078
+ 115000 22.535498 888 -0 1.8064158
+ 116000 22.856752 888 -0 1.8221237
+ 117000 23.178885 888 -0 1.8378317
+ 118000 23.501127 888 -0 1.8535397
+ 119000 23.8241 888 -0 1.8692476
+ 120000 24.147258 888 -0 1.8849556
+ 121000 24.472969 888 -0 1.9006636
+ 122000 24.799108 888 -0 1.9163715
+ 123000 25.125275 888 -0 1.9320795
+ 124000 25.453866 888 -0 1.9477874
+ 125000 25.784766 888 -0 1.9634954
+ 126000 26.117013 888 -0 1.9792034
+ 127000 26.448734 888 -0 1.9949113
+ 128000 26.780032 888 -0 2.0106193
+ 129000 27.113678 888 -0 2.0263273
+ 130000 27.450001 888 -0 2.0420352
+ 131000 27.782047 888 -0 2.0577432
+ 132000 28.114287 888 -0 2.0734512
+ 133000 28.446648 888 -0 2.0891591
+ 134000 28.780438 888 -0 2.1048671
+ 135000 29.116443 888 -0 2.120575
+ 136000 29.451848 888 -0 2.136283
+ 137000 29.787778 888 -0 2.151991
+ 138000 30.12804 888 -0 2.1676989
+ 139000 30.46814 888 -0 2.1834069
+ 140000 30.808946 888 -0 2.1991149
+ 141000 31.147584 888 -0 2.2148228
+ 142000 31.486475 888 -0 2.2305308
+ 143000 31.826754 888 -0 2.2462387
+ 144000 32.165796 888 -0 2.2619467
+ 145000 32.506074 888 -0 2.2776547
+ 146000 32.847604 888 -0 2.2933626
+ 147000 33.188988 888 -0 2.3090706
+ 148000 33.532869 888 -0 2.3247786
+ 149000 33.876629 888 -0 2.3404865
+ 150000 34.221172 888 -0 2.3561945
+ 151000 34.562559 888 -0 2.3719025
+ 152000 34.904679 888 -0 2.3876104
+ 153000 35.247727 888 -0 2.4033184
+ 154000 35.591228 888 -0 2.4190263
+ 155000 35.949192 888 -0 2.4347343
+ 156000 36.320157 888 -0 2.4504423
+ 157000 36.693571 888 -0 2.4661502
+ 158000 37.069463 888 -0 2.4818582
+ 159000 37.44221 888 -0 2.4975662
+ 160000 37.81863 888 -0 2.5132741
+ 161000 38.195121 888 -0 2.5289821
+ 162000 38.573424 888 -0 2.54469
+ 163000 38.950044 888 -0 2.560398
+ 164000 39.331977 888 -0 2.576106
+ 165000 39.714367 888 -0 2.5918139
+ 166000 40.097099 888 -0 2.6075219
+ 167000 40.477443 888 -0 2.6232299
+ 168000 40.860404 888 -0 2.6389378
+ 169000 41.244357 888 -0 2.6546458
+ 170000 41.658126 1000 -0 2.6703538
+ 171000 42.082517 1000 -0 2.6860617
+ 172000 42.507502 1000 -0 2.7017697
+ 173000 42.93363 1000 -0 2.7174776
+ 174000 43.361133 1000 -0 2.7331856
+ 175000 43.792381 1000 -0 2.7488936
+ 176000 44.223827 1000 -0 2.7646015
+ 177000 44.656581 1000 -0 2.7803095
+ 178000 45.087615 1000 -0 2.7960175
+ 179000 45.521129 1000 -0 2.8117254
+ 180000 45.957808 1000 -0 2.8274334
+ 181000 46.391451 1000 -0 2.8431414
+ 182000 46.825486 1000 -0 2.8588493
+ 183000 47.26091 1000 -0 2.8745573
+ 184000 47.694263 1000 -0 2.8902652
+ 185000 48.123312 1000 -0 2.9059732
+ 186000 48.554081 1000 -0 2.9216812
+ 187000 48.982617 1000 -0 2.9373891
+ 188000 49.414355 1000 -0 2.9530971
+ 189000 49.84753 1000 -0 2.9688051
+ 190000 50.284462 1000 -0 2.984513
+ 191000 50.71899 1000 -0 3.000221
+ 192000 51.157278 1000 -0 3.0159289
+ 193000 51.586171 1000 -0 3.0316369
+ 194000 52.011691 1000 -0 3.0473449
+ 195000 52.437732 1000 -0 3.0630528
+ 196000 52.863703 1000 -0 3.0787608
+ 197000 53.290403 1000 -0 3.0944688
+ 198000 53.7191 1000 -0 3.1101767
+ 199000 54.147195 1000 -0 3.1258847
+ 200000 54.575967 1000 -0 3.1415927
+Loop time of 54.576 on 1 procs for 200000 steps with 1000 atoms
+
+Performance: 14960.907 tau/day, 3664.615 timesteps/s
+98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 3.7989 | 3.7989 | 3.7989 | 0.0 | 6.96
+Neigh | 0.067629 | 0.067629 | 0.067629 | 0.0 | 0.12
+Comm | 0.63734 | 0.63734 | 0.63734 | 0.0 | 1.17
+Output | 0.0049303 | 0.0049303 | 0.0049303 | 0.0 | 0.01
+Modify | 49.1 | 49.1 | 49.1 | 0.0 | 89.97
+Other | | 0.9668 | | | 1.77
+
+Nlocal: 1000 ave 1000 max 1000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 196 ave 196 max 196 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 3910 ave 3910 max 3910 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 3910
+Ave neighs/atom = 3.91
+Neighbor list builds = 219
+Dangerous builds = 0
+unfix ins
+run 200000
+Per MPI rank memory allocation (min/avg/max) = 12.65 | 12.65 | 12.65 Mbytes
+Step CPU Atoms KinEng v_theta
+ 200000 0 1000 0.93873133 3.1415927
+ 201000 0.4261198 1000 0.93239566 3.1573006
+ 202000 0.84928846 1000 0.90333835 3.1730086
+ 203000 1.2720087 1000 0.89351493 3.1887165
+ 204000 1.6929317 1000 0.87648478 3.2044245
+ 205000 2.114043 1000 0.86818482 3.2201325
+ 206000 2.5357664 1000 0.86033251 3.2358404
+ 207000 2.9579847 1000 0.85442625 3.2515484
+ 208000 3.3812878 1000 0.8517451 3.2672564
+ 209000 3.8124611 1000 0.84406987 3.2829643
+ 210000 4.2440236 1000 0.83964642 3.2986723
+ 211000 4.6781921 1000 0.82994066 3.3143802
+ 212000 5.1116509 1000 0.82908369 3.3300882
+ 213000 5.5468135 1000 0.83115482 3.3457962
+ 214000 5.9802556 1000 0.82680518 3.3615041
+ 215000 6.4107294 1000 0.8223909 3.3772121
+ 216000 6.8419023 1000 0.81872537 3.3929201
+ 217000 7.2763367 1000 0.82446065 3.408628
+ 218000 7.7160695 1000 0.82278874 3.424336
+ 219000 8.1540956 1000 0.83017397 3.440044
+ 220000 8.5917952 1000 0.82232305 3.4557519
+ 221000 9.0296218 1000 0.82584132 3.4714599
+ 222000 9.4719794 1000 0.82143909 3.4871678
+ 223000 9.9180939 1000 0.82925587 3.5028758
+ 224000 10.361852 1000 0.84546265 3.5185838
+ 225000 10.803539 1000 0.84436452 3.5342917
+ 226000 11.248456 1000 0.84849375 3.5499997
+ 227000 11.695092 1000 0.8409057 3.5657077
+ 228000 12.136044 1000 0.83139305 3.5814156
+ 229000 12.579807 1000 0.83098473 3.5971236
+ 230000 13.02219 1000 0.81335147 3.6128316
+ 231000 13.463863 1000 0.78946649 3.6285395
+ 232000 13.906293 1000 0.78807613 3.6442475
+ 233000 14.348807 1000 0.79086655 3.6599554
+ 234000 14.793175 1000 0.79358862 3.6756634
+ 235000 15.238316 1000 0.79444252 3.6913714
+ 236000 15.683342 1000 0.79392156 3.7070793
+ 237000 16.12611 1000 0.80416034 3.7227873
+ 238000 16.5711 1000 0.80365093 3.7384953
+ 239000 17.014355 1000 0.80860323 3.7542032
+ 240000 17.454467 1000 0.80245788 3.7699112
+ 241000 17.89162 1000 0.79602568 3.7856191
+ 242000 18.330859 1000 0.79023692 3.8013271
+ 243000 18.769301 1000 0.79066782 3.8170351
+ 244000 19.211293 1000 0.77671368 3.832743
+ 245000 19.651443 1000 0.77121874 3.848451
+ 246000 20.092102 1000 0.74658977 3.864159
+ 247000 20.532732 1000 0.73825017 3.8798669
+ 248000 20.975646 1000 0.7187986 3.8955749
+ 249000 21.418807 1000 0.71707058 3.9112829
+ 250000 21.862497 1000 0.72983635 3.9269908
+ 251000 22.311832 1000 0.7355358 3.9426988
+ 252000 22.75883 1000 0.74427811 3.9584067
+ 253000 23.203455 1000 0.74968093 3.9741147
+ 254000 23.651472 1000 0.75350303 3.9898227
+ 255000 24.102152 1000 0.75617916 4.0055306
+ 256000 24.554236 1000 0.74949839 4.0212386
+ 257000 25.008718 1000 0.73534118 4.0369466
+ 258000 25.461913 1000 0.73761942 4.0526545
+ 259000 25.916674 1000 0.75485851 4.0683625
+ 260000 26.373941 1000 0.77147511 4.0840704
+ 261000 26.832072 1000 0.76658917 4.0997784
+ 262000 27.28741 1000 0.76441563 4.1154864
+ 263000 27.742157 1000 0.74449444 4.1311943
+ 264000 28.192718 1000 0.7403314 4.1469023
+ 265000 28.642541 1000 0.74262656 4.1626103
+ 266000 29.09406 1000 0.74117022 4.1783182
+ 267000 29.547747 1000 0.73877643 4.1940262
+ 268000 29.998243 1000 0.75062626 4.2097342
+ 269000 30.449751 1000 0.74649396 4.2254421
+ 270000 30.901232 1000 0.75371324 4.2411501
+ 271000 31.354755 1000 0.75254842 4.256858
+ 272000 31.810717 1000 0.74245946 4.272566
+ 273000 32.265754 1000 0.73056023 4.288274
+ 274000 32.719719 1000 0.72004393 4.3039819
+ 275000 33.173929 1000 0.70665742 4.3196899
+ 276000 33.628581 1000 0.69417262 4.3353979
+ 277000 34.080936 1000 0.67343474 4.3511058
+ 278000 34.532053 1000 0.66922758 4.3668138
+ 279000 34.985569 1000 0.66239909 4.3825218
+ 280000 35.443496 1000 0.66406486 4.3982297
+ 281000 35.901536 1000 0.67123654 4.4139377
+ 282000 36.357765 1000 0.67660885 4.4296456
+ 283000 36.811956 1000 0.6809288 4.4453536
+ 284000 37.266937 1000 0.69561154 4.4610616
+ 285000 37.720866 1000 0.70874512 4.4767695
+ 286000 38.177032 1000 0.72957833 4.4924775
+ 287000 38.633109 1000 0.72891066 4.5081855
+ 288000 39.086933 1000 0.72673285 4.5238934
+ 289000 39.538699 1000 0.72583062 4.5396014
+ 290000 39.991294 1000 0.7209406 4.5553093
+ 291000 40.437987 1000 0.70642559 4.5710173
+ 292000 40.885753 1000 0.69074151 4.5867253
+ 293000 41.326601 1000 0.68041469 4.6024332
+ 294000 41.763719 1000 0.6712034 4.6181412
+ 295000 42.198532 1000 0.66140336 4.6338492
+ 296000 42.635139 1000 0.65458145 4.6495571
+ 297000 43.071132 1000 0.63884999 4.6652651
+ 298000 43.507309 1000 0.63182296 4.6809731
+ 299000 43.943936 1000 0.6324286 4.696681
+ 300000 44.383148 1000 0.62640427 4.712389
+ 301000 44.819379 1000 0.62138494 4.7280969
+ 302000 45.260834 1000 0.62902694 4.7438049
+ 303000 45.705719 1000 0.63308052 4.7595129
+ 304000 46.14622 1000 0.63266845 4.7752208
+ 305000 46.586693 1000 0.63464534 4.7909288
+ 306000 47.028768 1000 0.62941378 4.8066368
+ 307000 47.470183 1000 0.62801025 4.8223447
+ 308000 47.914518 1000 0.62291875 4.8380527
+ 309000 48.365654 1000 0.62529494 4.8537606
+ 310000 48.817185 1000 0.62504442 4.8694686
+ 311000 49.269423 1000 0.63074915 4.8851766
+ 312000 49.722869 1000 0.64292914 4.9008845
+ 313000 50.175859 1000 0.65319818 4.9165925
+ 314000 50.630132 1000 0.66755513 4.9323005
+ 315000 51.084836 1000 0.67585436 4.9480084
+ 316000 51.539391 1000 0.67676226 4.9637164
+ 317000 51.995233 1000 0.67394312 4.9794244
+ 318000 52.453581 1000 0.67299959 4.9951323
+ 319000 52.906322 1000 0.68074615 5.0108403
+ 320000 53.362206 1000 0.67696004 5.0265482
+ 321000 53.813824 1000 0.67899008 5.0422562
+ 322000 54.264433 1000 0.67901671 5.0579642
+ 323000 54.715627 1000 0.67620354 5.0736721
+ 324000 55.168 1000 0.67165541 5.0893801
+ 325000 55.620891 1000 0.67820953 5.1050881
+ 326000 56.073685 1000 0.67490808 5.120796
+ 327000 56.526012 1000 0.67238149 5.136504
+ 328000 56.977525 1000 0.66885914 5.152212
+ 329000 57.431088 1000 0.66876389 5.1679199
+ 330000 57.886694 1000 0.66879597 5.1836279
+ 331000 58.338381 1000 0.66577546 5.1993358
+ 332000 58.791084 1000 0.6602875 5.2150438
+ 333000 59.242965 1000 0.65879422 5.2307518
+ 334000 59.698559 1000 0.6581474 5.2464597
+ 335000 60.153261 1000 0.6521249 5.2621677
+ 336000 60.605605 1000 0.63371979 5.2778757
+ 337000 61.059824 1000 0.62373279 5.2935836
+ 338000 61.510606 1000 0.6212013 5.3092916
+ 339000 61.962049 1000 0.62303395 5.3249995
+ 340000 62.413564 1000 0.63183785 5.3407075
+ 341000 62.86366 1000 0.64387158 5.3564155
+ 342000 63.317623 1000 0.65045982 5.3721234
+ 343000 63.772034 1000 0.65401192 5.3878314
+ 344000 64.225206 1000 0.65181077 5.4035394
+ 345000 64.681317 1000 0.64098248 5.4192473
+ 346000 65.136483 1000 0.63163559 5.4349553
+ 347000 65.588996 1000 0.64182161 5.4506633
+ 348000 66.042215 1000 0.65528889 5.4663712
+ 349000 66.501687 1000 0.66603277 5.4820792
+ 350000 66.960896 1000 0.67362185 5.4977871
+ 351000 67.417316 1000 0.68867905 5.5134951
+ 352000 67.876742 1000 0.6907547 5.5292031
+ 353000 68.336836 1000 0.69043981 5.544911
+ 354000 68.797396 1000 0.68676964 5.560619
+ 355000 69.255062 1000 0.68019369 5.576327
+ 356000 69.711663 1000 0.66189875 5.5920349
+ 357000 70.172728 1000 0.65275709 5.6077429
+ 358000 70.632655 1000 0.64560617 5.6234508
+ 359000 71.091165 1000 0.63865266 5.6391588
+ 360000 71.548341 1000 0.6366388 5.6548668
+ 361000 72.006137 1000 0.63619567 5.6705747
+ 362000 72.466621 1000 0.63986167 5.6862827
+ 363000 72.928505 1000 0.656198 5.7019907
+ 364000 73.391876 1000 0.66522563 5.7176986
+ 365000 73.852366 1000 0.67330205 5.7334066
+ 366000 74.317924 1000 0.67997811 5.7491146
+ 367000 74.781431 1000 0.67734915 5.7648225
+ 368000 75.24363 1000 0.66811078 5.7805305
+ 369000 75.704319 1000 0.67232161 5.7962384
+ 370000 76.165294 1000 0.67262944 5.8119464
+ 371000 76.624971 1000 0.68614241 5.8276544
+ 372000 77.085918 1000 0.70293842 5.8433623
+ 373000 77.544679 1000 0.71889856 5.8590703
+ 374000 78.007103 1000 0.7170296 5.8747783
+ 375000 78.468913 1000 0.71258031 5.8904862
+ 376000 78.93354 1000 0.70758873 5.9061942
+ 377000 79.39396 1000 0.69486822 5.9219022
+ 378000 79.850685 1000 0.68311194 5.9376101
+ 379000 80.307228 1000 0.67317549 5.9533181
+ 380000 80.767418 1000 0.67691049 5.969026
+ 381000 81.227579 1000 0.69231691 5.984734
+ 382000 81.686924 1000 0.69998609 6.000442
+ 383000 82.145783 1000 0.69328258 6.0161499
+ 384000 82.604827 1000 0.69903908 6.0318579
+ 385000 83.056443 1000 0.69455744 6.0475659
+ 386000 83.507131 1000 0.68865933 6.0632738
+ 387000 83.95695 1000 0.68630439 6.0789818
+ 388000 84.404079 1000 0.6800564 6.0946897
+ 389000 84.851053 1000 0.66747339 6.1103977
+ 390000 85.298614 1000 0.65695883 6.1261057
+ 391000 85.744507 1000 0.65659359 6.1418136
+ 392000 86.191348 1000 0.65933663 6.1575216
+ 393000 86.632782 1000 0.65170236 6.1732296
+ 394000 87.074105 1000 0.65631817 6.1889375
+ 395000 87.5177 1000 0.66205838 6.2046455
+ 396000 87.963111 1000 0.65512694 6.2203535
+ 397000 88.408348 1000 0.65266011 6.2360614
+ 398000 88.854042 1000 0.64593806 6.2517694
+ 399000 89.298754 1000 0.64940473 6.2674773
+ 400000 89.745445 1000 0.66033435 6.2831853
+Loop time of 89.7455 on 1 procs for 200000 steps with 1000 atoms
+
+Performance: 9098.023 tau/day, 2228.525 timesteps/s
+98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 10.924 | 10.924 | 10.924 | 0.0 | 12.17
+Neigh | 0.10266 | 0.10266 | 0.10266 | 0.0 | 0.11
+Comm | 1.9424 | 1.9424 | 1.9424 | 0.0 | 2.16
+Output | 0.0056458 | 0.0056458 | 0.0056458 | 0.0 | 0.01
+Modify | 75.442 | 75.442 | 75.442 | 0.0 | 84.06
+Other | | 1.329 | | | 1.48
+
+Nlocal: 1000 ave 1000 max 1000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 272 ave 272 max 272 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 4933 ave 4933 max 4933 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 4933
+Ave neighs/atom = 4.933
+Neighbor list builds = 171
+Dangerous builds = 0
+Total wall time: 0:02:24
diff --git a/examples/granregion/log.27Nov18.granregion.mixer.g++.4 b/examples/granregion/log.27Nov18.granregion.mixer.g++.4
new file mode 100644
index 0000000000..be690a7df5
--- /dev/null
+++ b/examples/granregion/log.27Nov18.granregion.mixer.g++.4
@@ -0,0 +1,602 @@
+LAMMPS (27 Nov 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+variable name string mixer
+
+thermo_modify flush yes
+variable seed equal 14314
+
+###############################################
+# Particle parameters
+################################################
+
+variable rlo equal 0.3
+variable rhi equal 0.6
+variable dlo equal 2.0*${rlo}
+variable dlo equal 2.0*0.3
+variable dhi equal 2.0*${rhi}
+variable dhi equal 2.0*0.6
+variable skin equal ${rhi}
+variable skin equal 0.6
+
+variable coeffRes equal 0.1
+variable coeffFric equal 0.5
+
+variable kn equal 10^5
+variable kt equal 0.2*${kn}
+variable kt equal 0.2*100000
+
+variable gravity equal 1.0
+variable density equal 1.0
+
+variable min_mass equal ${density}*4.0/3.0*PI*${rlo}*${rlo}*${rlo}
+variable min_mass equal 1*4.0/3.0*PI*${rlo}*${rlo}*${rlo}
+variable min_mass equal 1*4.0/3.0*PI*0.3*${rlo}*${rlo}
+variable min_mass equal 1*4.0/3.0*PI*0.3*0.3*${rlo}
+variable min_mass equal 1*4.0/3.0*PI*0.3*0.3*0.3
+variable a equal (-2.0*log(${coeffRes})/PI)^2
+variable a equal (-2.0*log(0.1)/PI)^2
+variable gamma_n equal sqrt($a*2*${kn}/${min_mass}/(1+0.25*$a))
+variable gamma_n equal sqrt(0.405284734569351*2*${kn}/${min_mass}/(1+0.25*$a))
+variable gamma_n equal sqrt(0.405284734569351*2*100000/${min_mass}/(1+0.25*$a))
+variable gamma_n equal sqrt(0.405284734569351*2*100000/0.113097335529233/(1+0.25*$a))
+variable gamma_n equal sqrt(0.405284734569351*2*100000/0.113097335529233/(1+0.25*0.405284734569351))
+variable gamma_t equal ${gamma_n}*0.5
+variable gamma_t equal 806.699778405191*0.5
+
+variable tcol equal PI/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
+variable tcol equal PI/sqrt(2*100000/${min_mass}-${gamma_n}/4.0)
+variable tcol equal PI/sqrt(2*100000/0.113097335529233-${gamma_n}/4.0)
+variable tcol equal PI/sqrt(2*100000/0.113097335529233-806.699778405191/4.0)
+
+variable dt equal ${tcol}*0.02
+variable dt equal 0.00236257621510454*0.02
+timestep ${dt}
+timestep 4.72515243020908e-05
+
+###############################################
+
+variable dumpfreq equal 1000
+variable logfreq equal 1000
+
+newton on
+atom_style sphere
+
+boundary p p f
+
+region boxreg block 0 20 0 20 0 20
+create_box 1 boxreg
+Created orthogonal box = (0 0 0) to (20 20 20)
+ 1 by 2 by 2 MPI processor grid
+
+pair_style gran/hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
+pair_style gran/hertz/history 100000 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
+pair_style gran/hertz/history 100000 20000 ${gamma_n} ${gamma_t} ${coeffFric} 1
+pair_style gran/hertz/history 100000 20000 806.699778405191 ${gamma_t} ${coeffFric} 1
+pair_style gran/hertz/history 100000 20000 806.699778405191 403.349889202595 ${coeffFric} 1
+pair_style gran/hertz/history 100000 20000 806.699778405191 403.349889202595 0.5 1
+pair_coeff * *
+
+neighbor ${skin} bin
+neighbor 0.6 bin
+thermo ${logfreq}
+thermo 1000
+
+comm_style brick
+comm_modify mode multi group all vel yes
+balance 1.1 shift xyz 20 1.1
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 0
+ ghost atom cutoff = 0
+ binsize = 20, bins = 1 1 1
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair gran/hertz/history, perpetual
+ attributes: half, newton on, size, history
+ pair build: half/size/bin/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+fix bal all balance 10000 1.1 shift xyz 20 1.01
+
+####################### Options specific to pouring #########################
+
+region insreg cylinder z 10 10 8 10 18 side in units box
+region cylreg cylinder z 10 10 10 0 20 side in units box
+
+variable theta equal (step/400000)*2*PI
+
+region b1 block 2 18 9 11 0 4 side out rotate v_theta 10 10 0 0 0 1 units box
+region b2 block 9 11 2 18 0 3.99999 side out rotate v_theta 10 10 0 0 0 1 units box
+
+region mixer intersect 3 cylreg b1 b2 side in
+
+fix grav all gravity ${gravity} vector 0 0 -1
+fix grav all gravity 1 vector 0 0 -1
+fix 1 all nve/sphere
+
+fix mixwall all wall/gran/region hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
+fix mixwall all wall/gran/region hertz/history 100000 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
+fix mixwall all wall/gran/region hertz/history 100000 20000 ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
+fix mixwall all wall/gran/region hertz/history 100000 20000 806.699778405191 ${gamma_t} ${coeffFric} 1 region mixer
+fix mixwall all wall/gran/region hertz/history 100000 20000 806.699778405191 403.349889202595 ${coeffFric} 1 region mixer
+fix mixwall all wall/gran/region hertz/history 100000 20000 806.699778405191 403.349889202595 0.5 1 region mixer
+
+fix ins all pour 1000 1 42424 region insreg diam range ${dlo} ${dhi} dens ${density} ${density}
+fix ins all pour 1000 1 42424 region insreg diam range 0.6 ${dhi} dens ${density} ${density}
+fix ins all pour 1000 1 42424 region insreg diam range 0.6 1.2 dens ${density} ${density}
+fix ins all pour 1000 1 42424 region insreg diam range 0.6 1.2 dens 1 ${density}
+fix ins all pour 1000 1 42424 region insreg diam range 0.6 1.2 dens 1 1
+Particle insertion: 444 every 84653 steps, 1000 by step 169307
+
+#dump 1 all custom ${dumpfreq} ${name}_pour.dump # id type mass diameter x y z
+
+#dump 2 all image 4000 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 zoom 1.5 # box no 0.0 axes no 0.0 0.0
+#dump_modify 2 pad 6
+
+thermo_style custom step cpu atoms ke v_theta
+WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:705)
+thermo_modify flush yes lost warn
+
+run 200000
+Per MPI rank memory allocation (min/avg/max) = 5.817 | 5.817 | 5.817 Mbytes
+Step CPU Atoms KinEng v_theta
+ 0 0 0 -0 0
+ 1000 0.096722603 444 -0 0.015707963
+ 2000 0.18796778 444 -0 0.031415927
+ 3000 0.27916241 444 -0 0.04712389
+ 4000 0.37111688 444 -0 0.062831853
+ 5000 0.46224833 444 -0 0.078539816
+ 6000 0.55190682 444 -0 0.09424778
+ 7000 0.64120579 444 -0 0.10995574
+ 8000 0.73025131 444 -0 0.12566371
+ 9000 0.82121348 444 -0 0.14137167
+ 10000 0.91006637 444 -0 0.15707963
+ 11000 0.97034311 444 -0 0.1727876
+ 12000 1.030247 444 -0 0.18849556
+ 13000 1.0894752 444 -0 0.20420352
+ 14000 1.1483686 444 -0 0.21991149
+ 15000 1.2138393 444 -0 0.23561945
+ 16000 1.2744856 444 -0 0.25132741
+ 17000 1.3361425 444 -0 0.26703538
+ 18000 1.3998857 444 -0 0.28274334
+ 19000 1.4625463 444 -0 0.2984513
+ 20000 1.5255082 444 -0 0.31415927
+ 21000 1.5845048 444 -0 0.32986723
+ 22000 1.6437175 444 -0 0.34557519
+ 23000 1.7022173 444 -0 0.36128316
+ 24000 1.7614172 444 -0 0.37699112
+ 25000 1.8209105 444 -0 0.39269908
+ 26000 1.8818901 444 -0 0.40840704
+ 27000 1.9439991 444 -0 0.42411501
+ 28000 2.0067189 444 -0 0.43982297
+ 29000 2.0697014 444 -0 0.45553093
+ 30000 2.1327429 444 -0 0.4712389
+ 31000 2.1904151 444 -0 0.48694686
+ 32000 2.2478669 444 -0 0.50265482
+ 33000 2.3062997 444 -0 0.51836279
+ 34000 2.3723967 444 -0 0.53407075
+ 35000 2.4331915 444 -0 0.54977871
+ 36000 2.4937904 444 -0 0.56548668
+ 37000 2.5550685 444 -0 0.58119464
+ 38000 2.6170652 444 -0 0.5969026
+ 39000 2.6789875 444 -0 0.61261057
+ 40000 2.7414019 444 -0 0.62831853
+ 41000 2.799027 444 -0 0.64402649
+ 42000 2.8570235 444 -0 0.65973446
+ 43000 2.9140713 444 -0 0.67544242
+ 44000 2.9702985 444 -0 0.69115038
+ 45000 3.0274565 444 -0 0.70685835
+ 46000 3.0860338 444 -0 0.72256631
+ 47000 3.1450455 444 -0 0.73827427
+ 48000 3.2057948 444 -0 0.75398224
+ 49000 3.267339 444 -0 0.7696902
+ 50000 3.3300545 444 -0 0.78539816
+ 51000 3.3942592 444 -0 0.80110613
+ 52000 3.4522727 444 -0 0.81681409
+ 53000 3.5117693 444 -0 0.83252205
+ 54000 3.5717957 444 -0 0.84823002
+ 55000 3.6338761 444 -0 0.86393798
+ 56000 3.7006576 444 -0 0.87964594
+ 57000 3.7648654 444 -0 0.89535391
+ 58000 3.829128 444 -0 0.91106187
+ 59000 3.8930187 444 -0 0.92676983
+ 60000 3.9581499 444 -0 0.9424778
+ 61000 4.0213017 444 -0 0.95818576
+ 62000 4.0822632 444 -0 0.97389372
+ 63000 4.1443422 444 -0 0.98960169
+ 64000 4.2072315 444 -0 1.0053096
+ 65000 4.2711387 444 -0 1.0210176
+ 66000 4.3361402 444 -0 1.0367256
+ 67000 4.4031398 444 -0 1.0524335
+ 68000 4.4698064 444 -0 1.0681415
+ 69000 4.5374978 444 -0 1.0838495
+ 70000 4.6051283 444 -0 1.0995574
+ 71000 4.6694169 444 -0 1.1152654
+ 72000 4.7335079 444 -0 1.1309734
+ 73000 4.7967482 444 -0 1.1466813
+ 74000 4.8603547 444 -0 1.1623893
+ 75000 4.9250085 444 -0 1.1780972
+ 76000 4.9909372 444 -0 1.1938052
+ 77000 5.0578024 444 -0 1.2095132
+ 78000 5.1250138 444 -0 1.2252211
+ 79000 5.1929755 444 -0 1.2409291
+ 80000 5.2627637 444 -0 1.2566371
+ 81000 5.3280981 444 -0 1.272345
+ 82000 5.3957336 444 -0 1.288053
+ 83000 5.4648135 444 -0 1.303761
+ 84000 5.5368683 444 -0 1.3194689
+ 85000 5.6352935 888 -0 1.3351769
+ 86000 5.7708502 888 -0 1.3508848
+ 87000 5.9051492 888 -0 1.3665928
+ 88000 6.0384896 888 -0 1.3823008
+ 89000 6.1714747 888 -0 1.3980087
+ 90000 6.3042989 888 -0 1.4137167
+ 91000 6.4114611 888 -0 1.4294247
+ 92000 6.5164247 888 -0 1.4451326
+ 93000 6.6219602 888 -0 1.4608406
+ 94000 6.728405 888 -0 1.4765485
+ 95000 6.8411646 888 -0 1.4922565
+ 96000 6.9479821 888 -0 1.5079645
+ 97000 7.0569239 888 -0 1.5236724
+ 98000 7.1673372 888 -0 1.5393804
+ 99000 7.2778809 888 -0 1.5550884
+ 100000 7.398834 888 -0 1.5707963
+ 101000 7.5066864 888 -0 1.5865043
+ 102000 7.6158357 888 -0 1.6022123
+ 103000 7.725111 888 -0 1.6179202
+ 104000 7.8344197 888 -0 1.6336282
+ 105000 7.9532022 888 -0 1.6493361
+ 106000 8.0643187 888 -0 1.6650441
+ 107000 8.1765473 888 -0 1.6807521
+ 108000 8.2890661 888 -0 1.69646
+ 109000 8.4048562 888 -0 1.712168
+ 110000 8.5208168 888 -0 1.727876
+ 111000 8.6303153 888 -0 1.7435839
+ 112000 8.7401052 888 -0 1.7592919
+ 113000 8.8518219 888 -0 1.7749998
+ 114000 8.9638157 888 -0 1.7907078
+ 115000 9.0766122 888 -0 1.8064158
+ 116000 9.1908746 888 -0 1.8221237
+ 117000 9.306145 888 -0 1.8378317
+ 118000 9.4229569 888 -0 1.8535397
+ 119000 9.5407412 888 -0 1.8692476
+ 120000 9.6574531 888 -0 1.8849556
+ 121000 9.7683234 888 -0 1.9006636
+ 122000 9.8812008 888 -0 1.9163715
+ 123000 9.9952521 888 -0 1.9320795
+ 124000 10.111879 888 -0 1.9477874
+ 125000 10.228812 888 -0 1.9634954
+ 126000 10.347842 888 -0 1.9792034
+ 127000 10.47052 888 -0 1.9949113
+ 128000 10.593136 888 -0 2.0106193
+ 129000 10.718124 888 -0 2.0263273
+ 130000 10.844211 888 -0 2.0420352
+ 131000 10.959177 888 -0 2.0577432
+ 132000 11.075781 888 -0 2.0734512
+ 133000 11.191418 888 -0 2.0891591
+ 134000 11.313376 888 -0 2.1048671
+ 135000 11.432321 888 -0 2.120575
+ 136000 11.551893 888 -0 2.136283
+ 137000 11.672695 888 -0 2.151991
+ 138000 11.793487 888 -0 2.1676989
+ 139000 11.914089 888 -0 2.1834069
+ 140000 12.037441 888 -0 2.1991149
+ 141000 12.161974 888 -0 2.2148228
+ 142000 12.286641 888 -0 2.2305308
+ 143000 12.414012 888 -0 2.2462387
+ 144000 12.540939 888 -0 2.2619467
+ 145000 12.66985 888 -0 2.2776547
+ 146000 12.79975 888 -0 2.2933626
+ 147000 12.932702 888 -0 2.3090706
+ 148000 13.066088 888 -0 2.3247786
+ 149000 13.200814 888 -0 2.3404865
+ 150000 13.33565 888 -0 2.3561945
+ 151000 13.465995 888 -0 2.3719025
+ 152000 13.586622 888 -0 2.3876104
+ 153000 13.711423 888 -0 2.4033184
+ 154000 13.835058 888 -0 2.4190263
+ 155000 13.967661 888 -0 2.4347343
+ 156000 14.100609 888 -0 2.4504423
+ 157000 14.234485 888 -0 2.4661502
+ 158000 14.373325 888 -0 2.4818582
+ 159000 14.510608 888 -0 2.4975662
+ 160000 14.651416 888 -0 2.5132741
+ 161000 14.785767 888 -0 2.5289821
+ 162000 14.921569 888 -0 2.54469
+ 163000 15.058895 888 -0 2.560398
+ 164000 15.198786 888 -0 2.576106
+ 165000 15.341662 888 -0 2.5918139
+ 166000 15.487128 888 -0 2.6075219
+ 167000 15.649383 888 -0 2.6232299
+ 168000 15.795388 888 -0 2.6389378
+ 169000 15.942671 888 -0 2.6546458
+ 170000 16.091824 1000 -0 2.6703538
+ 171000 16.239863 1000 -0 2.6860617
+ 172000 16.391118 1000 -0 2.7017697
+ 173000 16.5417 1000 -0 2.7174776
+ 174000 16.69479 1000 -0 2.7331856
+ 175000 16.847412 1000 -0 2.7488936
+ 176000 17.000374 1000 -0 2.7646015
+ 177000 17.15471 1000 -0 2.7803095
+ 178000 17.31284 1000 -0 2.7960175
+ 179000 17.46991 1000 -0 2.8117254
+ 180000 17.629018 1000 -0 2.8274334
+ 181000 17.787736 1000 -0 2.8431414
+ 182000 17.946197 1000 -0 2.8588493
+ 183000 18.105271 1000 -0 2.8745573
+ 184000 18.263731 1000 -0 2.8902652
+ 185000 18.433277 1000 -0 2.9059732
+ 186000 18.594456 1000 -0 2.9216812
+ 187000 18.755532 1000 -0 2.9373891
+ 188000 18.918447 1000 -0 2.9530971
+ 189000 19.080359 1000 -0 2.9688051
+ 190000 19.243927 1000 -0 2.984513
+ 191000 19.395044 1000 -0 3.000221
+ 192000 19.546837 1000 -0 3.0159289
+ 193000 19.695827 1000 -0 3.0316369
+ 194000 19.843856 1000 -0 3.0473449
+ 195000 19.993821 1000 -0 3.0630528
+ 196000 20.145787 1000 -0 3.0787608
+ 197000 20.298114 1000 -0 3.0944688
+ 198000 20.45074 1000 -0 3.1101767
+ 199000 20.607595 1000 -0 3.1258847
+ 200000 20.760979 1000 -0 3.1415927
+Loop time of 20.7611 on 4 procs for 200000 steps with 1000 atoms
+
+Performance: 39328.699 tau/day, 9633.409 timesteps/s
+98.0% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.57172 | 0.93292 | 1.2995 | 37.1 | 4.49
+Neigh | 0.015648 | 0.018747 | 0.02175 | 2.1 | 0.09
+Comm | 3.17 | 3.6151 | 4.0856 | 23.0 | 17.41
+Output | 0.0051017 | 0.012686 | 0.033359 | 10.6 | 0.06
+Modify | 12.36 | 13.269 | 14.095 | 21.8 | 63.91
+Other | | 2.912 | | | 14.03
+
+Nlocal: 250 ave 270 max 230 min
+Histogram: 1 0 0 0 1 0 1 0 0 1
+Nghost: 297 ave 337 max 234 min
+Histogram: 1 0 0 0 0 1 0 0 0 2
+Neighs: 982.5 ave 1580 max 496 min
+Histogram: 2 0 0 0 0 0 0 1 0 1
+
+Total # of neighbors = 3930
+Ave neighs/atom = 3.93
+Neighbor list builds = 218
+Dangerous builds = 0
+unfix ins
+run 200000
+Per MPI rank memory allocation (min/avg/max) = 12 | 12.19 | 12.35 Mbytes
+Step CPU Atoms KinEng v_theta
+ 200000 0 1000 0.89289812 3.1415927
+ 201000 0.15554476 1000 0.90162438 3.1573006
+ 202000 0.31118774 1000 0.89175077 3.1730086
+ 203000 0.47266722 1000 0.88068523 3.1887165
+ 204000 0.64758801 1000 0.88775074 3.2044245
+ 205000 0.85137105 1000 0.89009449 3.2201325
+ 206000 1.0712745 1000 0.89031724 3.2358404
+ 207000 1.3620427 1000 0.90901476 3.2515484
+ 208000 1.6051998 1000 0.91977358 3.2672564
+ 209000 1.7975032 1000 0.92044257 3.2829643
+ 210000 1.9654117 1000 0.90550844 3.2986723
+ 211000 2.1186137 1000 0.90179135 3.3143802
+ 212000 2.2714169 1000 0.90474936 3.3300882
+ 213000 2.4236252 1000 0.9011002 3.3457962
+ 214000 2.5737655 1000 0.89619815 3.3615041
+ 215000 2.7326233 1000 0.89129064 3.3772121
+ 216000 2.8794787 1000 0.88785486 3.3929201
+ 217000 3.0264313 1000 0.89448821 3.408628
+ 218000 3.1743443 1000 0.89323746 3.424336
+ 219000 3.3225086 1000 0.88176869 3.440044
+ 220000 3.4717121 1000 0.86989815 3.4557519
+ 221000 3.6229391 1000 0.85900389 3.4714599
+ 222000 3.7768724 1000 0.85440461 3.4871678
+ 223000 3.9287963 1000 0.8604449 3.5028758
+ 224000 4.082505 1000 0.84537374 3.5185838
+ 225000 4.234731 1000 0.84526488 3.5342917
+ 226000 4.3872988 1000 0.85877362 3.5499997
+ 227000 4.5396216 1000 0.86762074 3.5657077
+ 228000 4.7092509 1000 0.86460359 3.5814156
+ 229000 4.8631954 1000 0.85409682 3.5971236
+ 230000 5.0194352 1000 0.83902718 3.6128316
+ 231000 5.1765387 1000 0.83908755 3.6285395
+ 232000 5.3335299 1000 0.83178808 3.6442475
+ 233000 5.4917257 1000 0.83369584 3.6599554
+ 234000 5.654233 1000 0.8530074 3.6756634
+ 235000 5.8163757 1000 0.86385009 3.6913714
+ 236000 5.9791231 1000 0.86453337 3.7070793
+ 237000 6.1401029 1000 0.86137572 3.7227873
+ 238000 6.300632 1000 0.8656285 3.7384953
+ 239000 6.4597898 1000 0.85993724 3.7542032
+ 240000 6.6216707 1000 0.8484153 3.7699112
+ 241000 6.7793672 1000 0.84624799 3.7856191
+ 242000 6.939244 1000 0.83739227 3.8013271
+ 243000 7.1013088 1000 0.83026469 3.8170351
+ 244000 7.267416 1000 0.81060567 3.832743
+ 245000 7.4318523 1000 0.81081038 3.848451
+ 246000 7.6077905 1000 0.80857771 3.864159
+ 247000 7.7763391 1000 0.80353315 3.8798669
+ 248000 7.9485247 1000 0.80191903 3.8955749
+ 249000 8.1208956 1000 0.79865102 3.9112829
+ 250000 8.2921841 1000 0.79407385 3.9269908
+ 251000 8.4614651 1000 0.7880275 3.9426988
+ 252000 8.6266186 1000 0.79212521 3.9584067
+ 253000 8.7913449 1000 0.78976714 3.9741147
+ 254000 8.9596558 1000 0.79720779 3.9898227
+ 255000 9.1278918 1000 0.79329363 4.0055306
+ 256000 9.3016815 1000 0.80851295 4.0212386
+ 257000 9.4701304 1000 0.82322071 4.0369466
+ 258000 9.6399531 1000 0.83042211 4.0526545
+ 259000 9.8090186 1000 0.82773068 4.0683625
+ 260000 9.9798045 1000 0.8246773 4.0840704
+ 261000 10.148952 1000 0.81374287 4.0997784
+ 262000 10.318855 1000 0.79936963 4.1154864
+ 263000 10.496092 1000 0.78124408 4.1311943
+ 264000 10.671031 1000 0.77790646 4.1469023
+ 265000 10.843052 1000 0.77212005 4.1626103
+ 266000 11.01867 1000 0.77977752 4.1783182
+ 267000 11.192151 1000 0.79237542 4.1940262
+ 268000 11.362491 1000 0.80631398 4.2097342
+ 269000 11.53223 1000 0.82380407 4.2254421
+ 270000 11.7123 1000 0.82477127 4.2411501
+ 271000 11.883593 1000 0.81655074 4.256858
+ 272000 12.052348 1000 0.80678676 4.272566
+ 273000 12.220196 1000 0.79162789 4.288274
+ 274000 12.395164 1000 0.78896081 4.3039819
+ 275000 12.569757 1000 0.77904648 4.3196899
+ 276000 12.748754 1000 0.78252999 4.3353979
+ 277000 12.91648 1000 0.78293295 4.3511058
+ 278000 13.086087 1000 0.78311337 4.3668138
+ 279000 13.260159 1000 0.77657634 4.3825218
+ 280000 13.428503 1000 0.76835711 4.3982297
+ 281000 13.596094 1000 0.75586438 4.4139377
+ 282000 13.763325 1000 0.74600306 4.4296456
+ 283000 13.932867 1000 0.73228762 4.4453536
+ 284000 14.098865 1000 0.72344939 4.4610616
+ 285000 14.269317 1000 0.72160289 4.4767695
+ 286000 14.441196 1000 0.71321619 4.4924775
+ 287000 14.614458 1000 0.72631772 4.5081855
+ 288000 14.783358 1000 0.74390396 4.5238934
+ 289000 14.953564 1000 0.77320352 4.5396014
+ 290000 15.12428 1000 0.77249469 4.5553093
+ 291000 15.283974 1000 0.7583723 4.5710173
+ 292000 15.449553 1000 0.74568347 4.5867253
+ 293000 15.611965 1000 0.74108034 4.6024332
+ 294000 15.770807 1000 0.72706174 4.6181412
+ 295000 15.927151 1000 0.71122597 4.6338492
+ 296000 16.086734 1000 0.70272297 4.6495571
+ 297000 16.245418 1000 0.6945394 4.6652651
+ 298000 16.406617 1000 0.69541258 4.6809731
+ 299000 16.568989 1000 0.71696092 4.696681
+ 300000 16.754911 1000 0.72939561 4.712389
+ 301000 16.919453 1000 0.73621801 4.7280969
+ 302000 17.07794 1000 0.72052605 4.7438049
+ 303000 17.234397 1000 0.71057318 4.7595129
+ 304000 17.39014 1000 0.70014814 4.7752208
+ 305000 17.550789 1000 0.68855925 4.7909288
+ 306000 17.718802 1000 0.68665019 4.8066368
+ 307000 17.874036 1000 0.6831349 4.8223447
+ 308000 18.029367 1000 0.67929468 4.8380527
+ 309000 18.188065 1000 0.67833006 4.8537606
+ 310000 18.348243 1000 0.67764037 4.8694686
+ 311000 18.512475 1000 0.68271978 4.8851766
+ 312000 18.676519 1000 0.69021026 4.9008845
+ 313000 18.836426 1000 0.68795473 4.9165925
+ 314000 18.997681 1000 0.68308892 4.9323005
+ 315000 19.158794 1000 0.68086977 4.9480084
+ 316000 19.318186 1000 0.67879169 4.9637164
+ 317000 19.479364 1000 0.68128526 4.9794244
+ 318000 19.645085 1000 0.68718719 4.9951323
+ 319000 19.806831 1000 0.68419901 5.0108403
+ 320000 19.97005 1000 0.68045269 5.0265482
+ 321000 20.130643 1000 0.68430036 5.0422562
+ 322000 20.291637 1000 0.68195368 5.0579642
+ 323000 20.457605 1000 0.67964011 5.0736721
+ 324000 20.621699 1000 0.67681293 5.0893801
+ 325000 20.78525 1000 0.67601868 5.1050881
+ 326000 20.950321 1000 0.67600265 5.120796
+ 327000 21.11346 1000 0.68484094 5.136504
+ 328000 21.276964 1000 0.68526189 5.152212
+ 329000 21.440971 1000 0.67602072 5.1679199
+ 330000 21.609791 1000 0.68222852 5.1836279
+ 331000 21.773574 1000 0.68825647 5.1993358
+ 332000 21.93854 1000 0.68168415 5.2150438
+ 333000 22.102281 1000 0.67460357 5.2307518
+ 334000 22.265741 1000 0.67747925 5.2464597
+ 335000 22.436954 1000 0.681763 5.2621677
+ 336000 22.614367 1000 0.67611867 5.2778757
+ 337000 22.779064 1000 0.66903217 5.2935836
+ 338000 22.945739 1000 0.6684293 5.3092916
+ 339000 23.111375 1000 0.66465194 5.3249995
+ 340000 23.278674 1000 0.66226848 5.3407075
+ 341000 23.444642 1000 0.66407188 5.3564155
+ 342000 23.614615 1000 0.65762812 5.3721234
+ 343000 23.785007 1000 0.66936507 5.3878314
+ 344000 23.956265 1000 0.67424224 5.4035394
+ 345000 24.129057 1000 0.684271 5.4192473
+ 346000 24.303073 1000 0.68294352 5.4349553
+ 347000 24.475812 1000 0.69795697 5.4506633
+ 348000 24.652771 1000 0.69818863 5.4663712
+ 349000 24.830973 1000 0.69578798 5.4820792
+ 350000 25.00923 1000 0.69377251 5.4977871
+ 351000 25.185421 1000 0.69638202 5.5134951
+ 352000 25.363647 1000 0.70115823 5.5292031
+ 353000 25.540517 1000 0.70891635 5.544911
+ 354000 25.718709 1000 0.70876639 5.560619
+ 355000 25.893633 1000 0.71130235 5.576327
+ 356000 26.068423 1000 0.69380913 5.5920349
+ 357000 26.243801 1000 0.67934899 5.6077429
+ 358000 26.418883 1000 0.67024516 5.6234508
+ 359000 26.594722 1000 0.66145645 5.6391588
+ 360000 26.770322 1000 0.65335546 5.6548668
+ 361000 26.946396 1000 0.65495192 5.6705747
+ 362000 27.12296 1000 0.64973833 5.6862827
+ 363000 27.298461 1000 0.64532381 5.7019907
+ 364000 27.473586 1000 0.64282855 5.7176986
+ 365000 27.653872 1000 0.64451862 5.7334066
+ 366000 27.830317 1000 0.64366439 5.7491146
+ 367000 28.007037 1000 0.64395479 5.7648225
+ 368000 28.184079 1000 0.65827587 5.7805305
+ 369000 28.376009 1000 0.66311341 5.7962384
+ 370000 28.557287 1000 0.66165026 5.8119464
+ 371000 28.736569 1000 0.66878374 5.8276544
+ 372000 28.91063 1000 0.66944548 5.8433623
+ 373000 29.084648 1000 0.66061945 5.8590703
+ 374000 29.258649 1000 0.65320954 5.8747783
+ 375000 29.433156 1000 0.64641195 5.8904862
+ 376000 29.611781 1000 0.64631388 5.9061942
+ 377000 29.78531 1000 0.64232398 5.9219022
+ 378000 29.955917 1000 0.63805257 5.9376101
+ 379000 30.126378 1000 0.63666047 5.9533181
+ 380000 30.297285 1000 0.63651856 5.969026
+ 381000 30.471635 1000 0.6377374 5.984734
+ 382000 30.644813 1000 0.64750107 6.000442
+ 383000 30.816208 1000 0.65655138 6.0161499
+ 384000 30.986444 1000 0.65408935 6.0318579
+ 385000 31.156501 1000 0.64437236 6.0475659
+ 386000 31.327665 1000 0.63862174 6.0632738
+ 387000 31.49731 1000 0.64133807 6.0789818
+ 388000 31.682031 1000 0.64174374 6.0946897
+ 389000 31.85148 1000 0.64480071 6.1103977
+ 390000 32.020336 1000 0.64982943 6.1261057
+ 391000 32.187634 1000 0.6461109 6.1418136
+ 392000 32.357282 1000 0.64044412 6.1575216
+ 393000 32.527796 1000 0.64662995 6.1732296
+ 394000 32.704323 1000 0.65330527 6.1889375
+ 395000 32.880643 1000 0.66026265 6.2046455
+ 396000 33.048614 1000 0.6718969 6.2203535
+ 397000 33.222059 1000 0.66481385 6.2360614
+ 398000 33.391738 1000 0.66685494 6.2517694
+ 399000 33.560431 1000 0.6612594 6.2674773
+ 400000 33.729715 1000 0.65289572 6.2831853
+Loop time of 33.7298 on 4 procs for 200000 steps with 1000 atoms
+
+Performance: 24207.249 tau/day, 5929.470 timesteps/s
+97.9% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 1.6748 | 2.6848 | 3.6646 | 58.4 | 7.96
+Neigh | 0.021206 | 0.026438 | 0.03191 | 3.1 | 0.08
+Comm | 6.133 | 7.3745 | 8.6652 | 45.0 | 21.86
+Output | 0.0053763 | 0.016101 | 0.044719 | 13.0 | 0.05
+Modify | 18.26 | 20.115 | 22.413 | 39.2 | 59.64
+Other | | 3.513 | | | 10.42
+
+Nlocal: 250 ave 266 max 230 min
+Histogram: 1 0 0 0 0 1 1 0 0 1
+Nghost: 401.5 ave 476 max 325 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs: 1264 ave 1634 max 895 min
+Histogram: 1 0 1 0 0 0 0 1 0 1
+
+Total # of neighbors = 5056
+Ave neighs/atom = 5.056
+Neighbor list builds = 160
+Dangerous builds = 0
+Total wall time: 0:00:54
diff --git a/examples/granregion/log.6Oct16.granregion.box.g++.1 b/examples/granregion/log.6Oct16.granregion.box.g++.1
deleted file mode 100644
index ae2ec694e9..0000000000
--- a/examples/granregion/log.6Oct16.granregion.box.g++.1
+++ /dev/null
@@ -1,468 +0,0 @@
-LAMMPS (5 Oct 2016)
-# pouring spheres into container box
-
-units lj
-atom_style sphere
-boundary f f f
-dimension 3
-comm_modify vel yes
-
-region box block -10 10 -10 10 -10 10 units box
-create_box 2 box
-Created orthogonal box = (-10 -10 -10) to (10 10 10)
- 1 by 1 by 1 MPI processor grid
-
-pair_style hybrid gran/hooke 4000.0 NULL 100.0 NULL 0.5 1
-pair_coeff * * gran/hooke
-
-region container block -6 6 -6 6 -6 6 units box
-fix container all wall/gran/region hooke/history 4000.0 NULL 100.0 NULL 0.5 1 region container
-
-neighbor 0.3 bin
-neigh_modify delay 0 every 1 check yes
-
-fix 2 all nve/sphere
-fix 3 all gravity 1.0 vector 0 0 -1
-
-region slab block -2 2 -2 2 -2 2 units box
-fix ins all pour 100 2 4767548 vol 0.4 10 diam one 1.0 region slab ignore
-Particle insertion: 48 every 566 steps, 100 by step 1133
-
-timestep 0.005
-
-compute 1 all temp
-compute_modify 1 dynamic yes
-
-compute 2 all temp/sphere
-compute_modify 2 dynamic yes
-
-thermo 100
-thermo_style custom step atoms temp c_1 c_2 press
-thermo_modify lost ignore
-compute_modify thermo_temp dynamic yes
-
-#dump 2 all image 100 image.*.jpg type type # zoom 1.4 adiam 1.0 box no 0.0 axes yes 0.9 0.03
-#dump_modify 2 pad 5
-
-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 = 1.3
- ghost atom cutoff = 1.3
- binsize = 0.65 -> bins = 31 31 31
-Memory usage per processor = 0.201172 Mbytes
-Step Atoms Temp c_1 c_2 Press
- 0 0 0 0 0 0
- 100 21 0.54270729 0.54270729 0.26473526 0.0013567682
- 200 21 0.87606961 0.87606961 0.42735103 0.002190174
- 300 21 1.1428374 1.1428374 0.55748167 0.0028570936
- 400 21 1.3543103 1.3543103 0.66829516 0.0033857758
- 500 21 1.0677786 1.0677786 0.53582407 0.0045048164
- 600 56 0.6744286 0.6744286 0.3502938 0.0047464584
- 700 56 0.75569283 0.75569283 0.39779462 0.0051953882
- 800 56 0.61597505 0.61597505 0.32943642 0.0086022783
- 900 56 0.65260802 0.65260802 0.34474044 0.0059298996
- 1000 56 0.51624952 0.51624952 0.28326898 0.0067827337
- 1100 56 0.46050076 0.46050076 0.25656319 0.0061891094
- 1200 81 0.39112377 0.39112377 0.21690744 0.0086559347
- 1300 81 0.33302801 0.33302801 0.19110222 0.0033381288
- 1400 81 0.39333146 0.39333146 0.21220965 0.0041348597
- 1500 81 0.35493951 0.35493951 0.19924958 0.00373736
- 1600 81 0.34154491 0.34154491 0.19031147 0.005349672
- 1700 100 0.25598828 0.25598828 0.14171498 0.0092236643
- 1800 100 0.2114074 0.2114074 0.12162965 0.0027213483
- 1900 100 0.21810423 0.21810423 0.12176698 0.0036436034
- 2000 100 0.2553198 0.2553198 0.13900087 0.0032844504
- 2100 100 0.24809937 0.24809937 0.13753654 0.0088764373
- 2200 100 0.22455642 0.22455642 0.12500977 0.0043517009
- 2300 100 0.19586874 0.19586874 0.11064996 0.0055178814
- 2400 100 0.059619074 0.059619074 0.045535036 0.00079051539
- 2500 100 0.052222462 0.052222462 0.038563852 0.00098981299
- 2600 100 0.036930777 0.036930777 0.027579114 0.0012285499
- 2700 100 0.027937818 0.027937818 0.020587353 0.00063085447
- 2800 100 0.02103783 0.02103783 0.015469157 0.00050316582
- 2900 100 0.010408128 0.010408128 0.0084894275 0.00035440391
- 3000 100 0.0077664382 0.0077664382 0.0068149074 0.0011153614
- 3100 100 0.0088789208 0.0088789208 0.0070143391 0.00032679783
- 3200 100 0.0077683432 0.0077683432 0.0059711038 0.00044762363
- 3300 100 0.00411 0.00411 0.00372409 0.00015328221
- 3400 100 0.0039192171 0.0039192171 0.0032409072 9.3603399e-05
- 3500 100 0.0023532199 0.0023532199 0.0020924799 0.00049044152
- 3600 100 0.0022544513 0.0022544513 0.0019545724 8.1086108e-05
- 3700 100 0.0012696379 0.0012696379 0.0013134108 5.0058058e-05
- 3800 100 0.0012035225 0.0012035225 0.0012490584 6.0331967e-05
- 3900 100 0.00080361803 0.00080361803 0.00094424552 6.7229227e-05
- 4000 100 0.00060715659 0.00060715659 0.00076521759 6.7029916e-05
- 4100 100 0.00058510487 0.00058510487 0.00073844578 5.5867098e-05
- 4200 100 0.00046832309 0.00046832309 0.00060848748 5.3853715e-05
- 4300 100 0.00045207186 0.00045207186 0.00057825336 4.8367831e-05
- 4400 100 0.00041874845 0.00041874845 0.00053103589 8.666037e-05
- 4500 100 0.00041136295 0.00041136295 0.00052246056 6.0456585e-05
- 4600 100 0.00041021147 0.00041021147 0.0005190668 4.8701604e-05
- 4700 100 0.00037176253 0.00037176253 0.00049156279 5.8874891e-05
- 4800 100 0.0003262417 0.0003262417 0.00045551846 5.0610728e-05
- 4900 100 0.00028093583 0.00028093583 0.00042099654 4.6558605e-05
- 5000 100 0.00027730599 0.00027730599 0.00041664922 4.7053044e-05
-Loop time of 0.081454 on 1 procs for 5000 steps with 100 atoms
-
-Performance: 26518022.146 tau/day, 61384.311 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 | 0.0085223 | 0.0085223 | 0.0085223 | 0.0 | 10.46
-Neigh | 0.01466 | 0.01466 | 0.01466 | 0.0 | 18.00
-Comm | 0.00076532 | 0.00076532 | 0.00076532 | 0.0 | 0.94
-Output | 0.00052285 | 0.00052285 | 0.00052285 | 0.0 | 0.64
-Modify | 0.05317 | 0.05317 | 0.05317 | 0.0 | 65.28
-Other | | 0.003814 | | | 4.68
-
-Nlocal: 100 ave 100 max 100 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: 158 ave 158 max 158 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 158
-Ave neighs/atom = 1.58
-Neighbor list builds = 306
-Dangerous builds = 0
-
-region container delete
-variable theta equal (step-5000)*(4.0*PI/5000)
-region container block -6 6 -6 6 -6 6 units box rotate v_theta 0 0 0 0 0 1
-run 5000
-Memory usage per processor = 5.26337 Mbytes
-Step Atoms Temp c_1 c_2 Press
- 5000 100 0.00027730599 0.00027730599 0.00041664922 4.705763e-05
- 5100 100 0.60717077 0.60717077 0.33118944 0.010686501
- 5200 100 0.64991179 0.64991179 0.35498767 0.011370453
- 5300 100 0.72038713 0.72038713 0.38745069 0.010507667
- 5400 100 0.81357499 0.81357499 0.42946808 0.012920419
- 5500 100 0.90488411 0.90488411 0.46803321 0.015077428
- 5600 100 0.99065617 0.99065617 0.50811954 0.015556572
- 5700 100 1.0701203 1.0701203 0.54641187 0.016464366
- 5800 100 1.1351242 1.1351242 0.57607707 0.017832476
- 5900 100 1.1883602 1.1883602 0.60022389 0.019571838
- 6000 100 1.2153421 1.2153421 0.61245652 0.020549414
- 6100 100 1.2369293 1.2369293 0.62229634 0.01827529
- 6200 100 1.2556883 1.2556883 0.63207905 0.020286322
- 6300 100 1.2618555 1.2618555 0.63610311 0.019844583
- 6400 100 1.2671678 1.2671678 0.63873131 0.019817249
- 6500 100 1.2875312 1.2875312 0.64728693 0.020097362
- 6600 100 1.3014055 1.3014055 0.65413071 0.020000886
- 6700 100 1.2904021 1.2904021 0.6485358 0.020009625
- 6800 100 1.2962767 1.2962767 0.65088367 0.021340143
- 6900 100 1.3056081 1.3056081 0.65490644 0.020455771
- 7000 100 1.3116731 1.3116731 0.65766216 0.020475061
- 7100 100 1.319457 1.319457 0.66105016 0.020937651
- 7200 100 1.3213585 1.3213585 0.66207982 0.02120792
- 7300 100 1.3232411 1.3232411 0.66392391 0.021040683
- 7400 100 1.3300163 1.3300163 0.66599805 0.021202273
- 7500 100 1.3350122 1.3350122 0.66894534 0.021161833
- 7600 100 1.3344633 1.3344633 0.6688403 0.020871936
- 7700 100 1.3492825 1.3492825 0.6751371 0.021415859
- 7800 100 1.3539647 1.3539647 0.67757279 0.021306442
- 7900 100 1.3527157 1.3527157 0.67722774 0.021793531
- 8000 100 1.3526931 1.3526931 0.67713399 0.022973395
- 8100 100 1.3568279 1.3568279 0.67936578 0.021422428
- 8200 100 1.3599258 1.3599258 0.68113142 0.021397012
- 8300 100 1.3601893 1.3601893 0.68165656 0.021643375
- 8400 100 1.3752164 1.3752164 0.68788213 0.022208765
- 8500 100 1.3821458 1.3821458 0.69165274 0.022015877
- 8600 100 1.3784691 1.3784691 0.68964478 0.022144188
- 8700 100 1.3801422 1.3801422 0.6904093 0.0220402
- 8800 100 1.3900051 1.3900051 0.6947875 0.02216362
- 8900 100 1.3897902 1.3897902 0.69427134 0.023078569
- 9000 100 1.3909918 1.3909918 0.69456955 0.022043699
- 9100 100 1.3925028 1.3925028 0.69519141 0.022180156
- 9200 100 1.3923277 1.3923277 0.69512657 0.022113729
- 9300 100 1.3945193 1.3945193 0.69625374 0.022344694
- 9400 100 1.3960782 1.3960782 0.69705144 0.022181158
- 9500 100 1.3932407 1.3932407 0.69560365 0.022129998
- 9600 100 1.3925489 1.3925489 0.69532399 0.022124653
- 9700 100 1.3935299 1.3935299 0.69581607 0.022258368
- 9800 100 1.3933949 1.3933949 0.69579137 0.022209028
- 9900 100 1.3934712 1.3934712 0.69587898 0.022214942
- 10000 100 1.3935828 1.3935828 0.69598655 0.022231414
-Loop time of 0.261407 on 1 procs for 5000 steps with 100 atoms
-
-Performance: 8262972.563 tau/day, 19127.251 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 | 0.042233 | 0.042233 | 0.042233 | 0.0 | 16.16
-Neigh | 0.035131 | 0.035131 | 0.035131 | 0.0 | 13.44
-Comm | 0.0010462 | 0.0010462 | 0.0010462 | 0.0 | 0.40
-Output | 0.00051785 | 0.00051785 | 0.00051785 | 0.0 | 0.20
-Modify | 0.17687 | 0.17687 | 0.17687 | 0.0 | 67.66
-Other | | 0.00561 | | | 2.15
-
-Nlocal: 100 ave 100 max 100 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: 187 ave 187 max 187 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 187
-Ave neighs/atom = 1.87
-Neighbor list builds = 634
-Dangerous builds = 0
-
-region container delete
-region container block -6 6 -6 6 -6 6 units box
-run 5000
-Memory usage per processor = 5.26337 Mbytes
-Step Atoms Temp c_1 c_2 Press
- 10000 100 1.3935828 1.3935828 0.69598655 0.02230659
- 10100 100 0.3402861 0.3402861 0.19584226 0.014767914
- 10200 100 0.19064555 0.19064555 0.12536788 0.0025413789
- 10300 100 0.13281358 0.13281358 0.10275768 0.002843208
- 10400 100 0.10124671 0.10124671 0.077914135 0.0017745353
- 10500 100 0.082636734 0.082636734 0.063857622 0.001419336
- 10600 100 0.066744462 0.066744462 0.051927437 0.0010830674
- 10700 100 0.060778462 0.060778462 0.047461784 0.0011418844
- 10800 100 0.043437178 0.043437178 0.032805669 0.0017050393
- 10900 100 0.036483219 0.036483219 0.027387805 0.00086936813
- 11000 100 0.027639076 0.027639076 0.021221241 0.00054920607
- 11100 100 0.023614696 0.023614696 0.018445634 0.00058724552
- 11200 100 0.020103248 0.020103248 0.015933089 0.00072830275
- 11300 100 0.018645345 0.018645345 0.014559759 0.0002319388
- 11400 100 0.015499672 0.015499672 0.01248828 0.00036020862
- 11500 100 0.013421296 0.013421296 0.010743248 0.00043093929
- 11600 100 0.011214892 0.011214892 0.0089653924 0.00059789544
- 11700 100 0.0086660806 0.0086660806 0.0070563902 0.00029684573
- 11800 100 0.0064777244 0.0064777244 0.0052946156 0.00046466386
- 11900 100 0.0059360881 0.0059360881 0.0048568813 8.361561e-05
- 12000 100 0.0045341025 0.0045341025 0.003883229 0.00016408047
- 12100 100 0.0042504415 0.0042504415 0.0036944958 6.5005147e-05
- 12200 100 0.0041367637 0.0041367637 0.0035928232 7.3025698e-05
- 12300 100 0.0037700129 0.0037700129 0.003283398 6.381318e-05
- 12400 100 0.0033494476 0.0033494476 0.0029274495 4.7731105e-05
- 12500 100 0.0030903175 0.0030903175 0.0027068073 6.797313e-05
- 12600 100 0.0026406999 0.0026406999 0.0023315387 0.0002371331
- 12700 100 0.0025020713 0.0025020713 0.0022367855 4.2787276e-05
- 12800 100 0.0022977381 0.0022977381 0.0020778307 3.9744567e-05
- 12900 100 0.002039634 0.002039634 0.0018862012 0.00011669223
- 13000 100 0.0018044702 0.0018044702 0.00171399 0.00013835538
- 13100 100 0.0016600965 0.0016600965 0.0015553191 3.2320019e-05
- 13200 100 0.0015596204 0.0015596204 0.001486374 1.9246911e-05
- 13300 100 0.001316505 0.001316505 0.0012105249 9.1469679e-05
- 13400 100 0.0012517536 0.0012517536 0.0011525753 4.815292e-05
- 13500 100 0.0010827608 0.0010827608 0.001038339 2.0913017e-05
- 13600 100 0.0009863908 0.0009863908 0.00095924929 9.7716736e-05
- 13700 100 0.00094543599 0.00094543599 0.00092425645 1.378887e-05
- 13800 100 0.00087893271 0.00087893271 0.00086801608 1.8981177e-05
- 13900 100 0.00080241572 0.00080241572 0.0007930026 5.0987122e-05
- 14000 100 0.00070705631 0.00070705631 0.00069238137 1.2900066e-05
- 14100 100 0.0006525032 0.0006525032 0.000637991 0.00010838464
- 14200 100 0.00059338444 0.00059338444 0.00057560454 7.3431324e-06
- 14300 100 0.00058641228 0.00058641228 0.00056944735 7.256852e-06
- 14400 100 0.00056221112 0.00056221112 0.00054625666 8.1343426e-06
- 14500 100 0.00055493127 0.00055493127 0.00053957583 1.1713058e-05
- 14600 100 0.00052854921 0.00052854921 0.00051816618 8.6527225e-06
- 14700 100 0.00052630581 0.00052630581 0.00051584277 6.4890475e-06
- 14800 100 0.00052563819 0.00052563819 0.00051493123 1.2687153e-05
- 14900 100 0.00052131364 0.00052131364 0.00050917244 7.4589995e-08
- 15000 100 0.00051902191 0.00051902191 0.00050725364 6.4228962e-06
-Loop time of 0.0895741 on 1 procs for 5000 steps with 100 atoms
-
-Performance: 24114113.723 tau/day, 55819.708 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 | 0.0098987 | 0.0098987 | 0.0098987 | 0.0 | 11.05
-Neigh | 0.0061045 | 0.0061045 | 0.0061045 | 0.0 | 6.81
-Comm | 0.00069976 | 0.00069976 | 0.00069976 | 0.0 | 0.78
-Output | 0.00049758 | 0.00049758 | 0.00049758 | 0.0 | 0.56
-Modify | 0.068435 | 0.068435 | 0.068435 | 0.0 | 76.40
-Other | | 0.003939 | | | 4.40
-
-Nlocal: 100 ave 100 max 100 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: 160 ave 160 max 160 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 160
-Ave neighs/atom = 1.6
-Neighbor list builds = 111
-Dangerous builds = 0
-
-region container delete
-variable theta equal (step-15000)*(4.0*PI/5000)
-region container block -6 6 -6 6 -6 6 units box rotate v_theta 0 0 0 1 1 1
-run 5000
-Memory usage per processor = 5.26337 Mbytes
-Step Atoms Temp c_1 c_2 Press
- 15000 100 0.00051902191 0.00051902191 0.00050725364 6.4228962e-06
- 15100 100 1.1235353 1.1235353 0.72003773 0.013686681
- 15200 100 1.0778556 1.0778556 0.69137925 0.013478363
- 15300 100 1.069015 1.069015 0.69798184 0.014165255
- 15400 100 1.2249943 1.2249943 0.79096059 0.020933395
- 15500 100 1.5225664 1.5225664 0.94822282 0.023932611
- 15600 100 1.5867194 1.5867194 0.98143504 0.024565132
- 15700 100 1.6595267 1.6595267 1.0203985 0.025152432
- 15800 100 1.8188027 1.8188027 1.0857586 0.031597641
- 15900 100 1.9234102 1.9234102 1.1099361 0.032381895
- 16000 100 2.039435 2.039435 1.1656948 0.032501981
- 16100 100 2.17315 2.17315 1.2265552 0.032675825
- 16200 100 2.2017279 2.2017279 1.23995 0.028634878
- 16300 100 2.3510902 2.3510902 1.3055642 0.03248003
- 16400 100 2.373932 2.373932 1.3059254 0.031292969
- 16500 100 2.5010862 2.5010862 1.3607219 0.032322054
- 16600 100 2.4815092 2.4815092 1.3524159 0.031223889
- 16700 100 2.6549226 2.6549226 1.4383508 0.033713507
- 16800 100 2.8087564 2.8087564 1.5261538 0.036598837
- 16900 100 2.8653588 2.8653588 1.5649123 0.035890231
- 17000 100 2.903748 2.903748 1.5907716 0.038038745
- 17100 100 2.9679376 2.9679376 1.6195577 0.051771432
- 17200 100 2.9632377 2.9632377 1.6233074 0.039825751
- 17300 100 3.0436883 3.0436883 1.6591248 0.042862982
- 17400 100 3.0969015 3.0969015 1.6811582 0.042104811
- 17500 100 3.0827135 3.0827135 1.691414 0.045839327
- 17600 100 3.0854805 3.0854805 1.689399 0.041770144
- 17700 100 3.07523 3.07523 1.6685518 0.045104715
- 17800 100 2.9610899 2.9610899 1.6349099 0.039060791
- 17900 100 2.8002989 2.8002989 1.5665223 0.037917927
- 18000 100 2.9139644 2.9139644 1.6206891 0.050841302
- 18100 100 3.0134757 3.0134757 1.6673916 0.040967255
- 18200 100 3.0731184 3.0731184 1.6777507 0.043503474
- 18300 100 3.0915242 3.0915242 1.6843452 0.040157898
- 18400 100 3.098896 3.098896 1.6904524 0.039629218
- 18500 100 3.1651814 3.1651814 1.7290259 0.042604953
- 18600 100 3.353247 3.353247 1.8236992 0.045132486
- 18700 100 3.540156 3.540156 1.9078363 0.046602063
- 18800 100 3.6395129 3.6395129 1.9578976 0.045659959
- 18900 100 3.7638134 3.7638134 2.0179445 0.051061068
- 19000 100 3.7603453 3.7603453 2.003355 0.057123184
- 19100 100 3.9218495 3.9218495 2.0968869 0.057671742
- 19200 100 3.9924222 3.9924222 2.1321955 0.051824898
- 19300 100 3.9690887 3.9690887 2.1270643 0.054832867
- 19400 100 3.9408481 3.9408481 2.1146593 0.057020024
- 19500 100 3.8313782 3.8313782 2.0610797 0.055164704
- 19600 100 3.8317496 3.8317496 2.0668123 0.049840804
- 19700 100 3.6068628 3.6068628 1.964227 0.05142407
- 19800 100 3.5477437 3.5477437 1.9314948 0.051076014
- 19900 100 3.6526881 3.6526881 1.9855353 0.047130029
- 20000 100 3.7243709 3.7243709 2.0380212 0.048446835
-Loop time of 0.206397 on 1 procs for 5000 steps with 100 atoms
-
-Performance: 10465265.522 tau/day, 24225.152 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 | 0.014297 | 0.014297 | 0.014297 | 0.0 | 6.93
-Neigh | 0.050213 | 0.050213 | 0.050213 | 0.0 | 24.33
-Comm | 0.0011115 | 0.0011115 | 0.0011115 | 0.0 | 0.54
-Output | 0.00051141 | 0.00051141 | 0.00051141 | 0.0 | 0.25
-Modify | 0.13415 | 0.13415 | 0.13415 | 0.0 | 65.00
-Other | | 0.006114 | | | 2.96
-
-Nlocal: 100 ave 100 max 100 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: 142 ave 142 max 142 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 142
-Ave neighs/atom = 1.42
-Neighbor list builds = 899
-Dangerous builds = 0
-
-region container delete
-region container block -6 6 -6 6 -6 6 units box
-run 5000
-Memory usage per processor = 5.26337 Mbytes
-Step Atoms Temp c_1 c_2 Press
- 20000 100 3.7243709 3.7243709 2.0380212 0.048156434
- 20100 100 1.1186527 1.1186527 0.69104385 0.014964891
- 20200 100 0.91445605 0.91445605 0.57005236 0.011324474
- 20300 100 0.8936601 0.8936601 0.55534411 0.011071843
- 20400 100 0.90773143 0.90773143 0.55999953 0.011254101
- 20500 100 0.91995508 0.91995508 0.55837916 0.011548541
- 20600 100 0.91682167 0.91682167 0.54095261 0.012563797
- 20700 100 0.97806337 0.97806337 0.56016442 0.012396925
- 20800 100 0.97778738 0.97778738 0.55606194 0.015441479
- 20900 100 0.77253213 0.77253213 0.44636799 0.011428992
- 21000 100 0.63053468 0.63053468 0.35995394 0.01005502
- 21100 100 0.25437539 0.25437539 0.16544433 0.004628738
- 21200 100 0.11828032 0.11828032 0.087911985 0.0037076362
- 21300 100 0.11219312 0.11219312 0.080957112 0.0015847347
- 21400 100 0.10765357 0.10765357 0.074676159 0.0022823419
- 21500 100 0.060787093 0.060787093 0.046135213 0.00091422949
- 21600 100 0.040447932 0.040447932 0.033050575 0.0013404194
- 21700 100 0.035227782 0.035227782 0.02916621 0.00138779
- 21800 100 0.03309101 0.03309101 0.026613861 0.00058184323
- 21900 100 0.031461843 0.031461843 0.024751985 0.0013090333
- 22000 100 0.021624144 0.021624144 0.017872639 0.0010893822
- 22100 100 0.016728267 0.016728267 0.01403934 0.00049128736
- 22200 100 0.016256915 0.016256915 0.013763903 0.00047288638
- 22300 100 0.01349256 0.01349256 0.011498343 0.0013508309
- 22400 100 0.010027007 0.010027007 0.0087924966 0.00030117996
- 22500 100 0.0107355 0.0107355 0.0088715062 0.001043188
- 22600 100 0.0095852245 0.0095852245 0.007965421 0.00028464236
- 22700 100 0.0072956464 0.0072956464 0.0062403843 0.00061636772
- 22800 100 0.0060874415 0.0060874415 0.0054788049 0.00021135824
- 22900 100 0.0059688159 0.0059688159 0.0049530273 0.00022094116
- 23000 100 0.0050218996 0.0050218996 0.0043518404 0.00022527705
- 23100 100 0.005022208 0.005022208 0.0043118432 0.00052482006
- 23200 100 0.0047096056 0.0047096056 0.0039698638 0.00026423471
- 23300 100 0.0039510068 0.0039510068 0.0034773285 0.0001891104
- 23400 100 0.0037308781 0.0037308781 0.0031763304 0.00027163016
- 23500 100 0.0036278619 0.0036278619 0.0030371899 0.00017961072
- 23600 100 0.0033598677 0.0033598677 0.0027586323 0.00015034494
- 23700 100 0.0028530843 0.0028530843 0.0024809444 0.00012294415
- 23800 100 0.0025388819 0.0025388819 0.0022812799 0.00018946676
- 23900 100 0.0021129272 0.0021129272 0.0019905358 0.00015816903
- 24000 100 0.0021010978 0.0021010978 0.0019864539 0.00017086049
- 24100 100 0.0022189886 0.0022189886 0.0020466911 0.00030932562
- 24200 100 0.0019226314 0.0019226314 0.0017933042 9.3246067e-05
- 24300 100 0.0016875781 0.0016875781 0.0015999656 9.9935458e-05
- 24400 100 0.0015929611 0.0015929611 0.001531011 9.7429139e-05
- 24500 100 0.0015143044 0.0015143044 0.0014044175 9.807117e-05
- 24600 100 0.0018595492 0.0018595492 0.0014740944 7.4734729e-05
- 24700 100 0.0011646988 0.0011646988 0.0010881356 6.1197025e-05
- 24800 100 0.0014641612 0.0014641612 0.0012316664 8.81462e-05
- 24900 100 0.001024996 0.001024996 0.00094311114 5.8776472e-05
- 25000 100 0.00097890442 0.00097890442 0.00090302317 3.3980657e-05
-Loop time of 0.0954661 on 1 procs for 5000 steps with 100 atoms
-
-Performance: 22625823.872 tau/day, 52374.592 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 | 0.01234 | 0.01234 | 0.01234 | 0.0 | 12.93
-Neigh | 0.015404 | 0.015404 | 0.015404 | 0.0 | 16.14
-Comm | 0.00077391 | 0.00077391 | 0.00077391 | 0.0 | 0.81
-Output | 0.000494 | 0.000494 | 0.000494 | 0.0 | 0.52
-Modify | 0.062222 | 0.062222 | 0.062222 | 0.0 | 65.18
-Other | | 0.004233 | | | 4.43
-
-Nlocal: 100 ave 100 max 100 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: 150 ave 150 max 150 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 150
-Ave neighs/atom = 1.5
-Neighbor list builds = 283
-Dangerous builds = 0
-Total wall time: 0:00:00
diff --git a/examples/granregion/log.6Oct16.granregion.box.g++.4 b/examples/granregion/log.6Oct16.granregion.box.g++.4
deleted file mode 100644
index daaae2019e..0000000000
--- a/examples/granregion/log.6Oct16.granregion.box.g++.4
+++ /dev/null
@@ -1,468 +0,0 @@
-LAMMPS (5 Oct 2016)
-# pouring spheres into container box
-
-units lj
-atom_style sphere
-boundary f f f
-dimension 3
-comm_modify vel yes
-
-region box block -10 10 -10 10 -10 10 units box
-create_box 2 box
-Created orthogonal box = (-10 -10 -10) to (10 10 10)
- 1 by 2 by 2 MPI processor grid
-
-pair_style hybrid gran/hooke 4000.0 NULL 100.0 NULL 0.5 1
-pair_coeff * * gran/hooke
-
-region container block -6 6 -6 6 -6 6 units box
-fix container all wall/gran/region hooke/history 4000.0 NULL 100.0 NULL 0.5 1 region container
-
-neighbor 0.3 bin
-neigh_modify delay 0 every 1 check yes
-
-fix 2 all nve/sphere
-fix 3 all gravity 1.0 vector 0 0 -1
-
-region slab block -2 2 -2 2 -2 2 units box
-fix ins all pour 100 2 4767548 vol 0.4 10 diam one 1.0 region slab ignore
-Particle insertion: 48 every 566 steps, 100 by step 1133
-
-timestep 0.005
-
-compute 1 all temp
-compute_modify 1 dynamic yes
-
-compute 2 all temp/sphere
-compute_modify 2 dynamic yes
-
-thermo 100
-thermo_style custom step atoms temp c_1 c_2 press
-thermo_modify lost ignore
-compute_modify thermo_temp dynamic yes
-
-#dump 2 all image 100 image.*.jpg type type # zoom 1.4 adiam 1.0 box no 0.0 axes yes 0.9 0.03
-#dump_modify 2 pad 5
-
-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 = 1.3
- ghost atom cutoff = 1.3
- binsize = 0.65 -> bins = 31 31 31
-Memory usage per processor = 0.0990257 Mbytes
-Step Atoms Temp c_1 c_2 Press
- 0 0 0 0 0 0
- 100 21 0.54270729 0.54270729 0.26473526 0.0013567682
- 200 21 0.87606961 0.87606961 0.42735103 0.002190174
- 300 21 1.1428374 1.1428374 0.55748167 0.0028570936
- 400 21 1.3543103 1.3543103 0.66829516 0.0033857758
- 500 21 1.0677786 1.0677786 0.53582407 0.0045048164
- 600 56 0.6744286 0.6744286 0.3502938 0.0047464584
- 700 56 0.75569283 0.75569283 0.39779462 0.0051953882
- 800 56 0.61597505 0.61597505 0.32943642 0.0086022783
- 900 56 0.65260802 0.65260802 0.34474044 0.0059298996
- 1000 56 0.51624952 0.51624952 0.28326898 0.0067827337
- 1100 56 0.46050076 0.46050076 0.25656319 0.0061891094
- 1200 81 0.39112377 0.39112377 0.21690744 0.0086559347
- 1300 81 0.33302801 0.33302801 0.19110222 0.0033381288
- 1400 81 0.39333146 0.39333146 0.21220965 0.0041348597
- 1500 81 0.35493951 0.35493951 0.19924958 0.00373736
- 1600 81 0.34154491 0.34154491 0.19031147 0.005349672
- 1700 100 0.25598828 0.25598828 0.14171498 0.0092236643
- 1800 100 0.2114074 0.2114074 0.12162965 0.0027213483
- 1900 100 0.21810423 0.21810423 0.12176698 0.0036436054
- 2000 100 0.2553198 0.2553198 0.13900087 0.0032844518
- 2100 100 0.24809936 0.24809936 0.13753654 0.0088764777
- 2200 100 0.22455625 0.22455625 0.12500973 0.0043515755
- 2300 100 0.19586871 0.19586871 0.11064996 0.0055176298
- 2400 100 0.059621411 0.059621411 0.045535517 0.00079910861
- 2500 100 0.052217518 0.052217518 0.038542594 0.0009759424
- 2600 100 0.036907358 0.036907358 0.027550263 0.0014047668
- 2700 100 0.027926944 0.027926944 0.020599405 0.00063362027
- 2800 100 0.020876282 0.020876282 0.015385856 0.00066161626
- 2900 100 0.010390963 0.010390963 0.0085038611 0.00026222195
- 3000 100 0.0080105974 0.0080105974 0.006995365 0.00059521652
- 3100 100 0.0087388005 0.0087388005 0.0069051613 0.00028045343
- 3200 100 0.0078828927 0.0078828927 0.0060159861 0.00014819289
- 3300 100 0.0039336821 0.0039336821 0.0036525886 0.0001439482
- 3400 100 0.0037684472 0.0037684472 0.0031531439 0.00010653386
- 3500 100 0.0023527874 0.0023527874 0.0020983632 6.3797052e-05
- 3600 100 0.0018768162 0.0018768162 0.0017248798 0.00014904114
- 3700 100 0.00135595 0.00135595 0.0013962044 6.2461444e-05
- 3800 100 0.0012673777 0.0012673777 0.0013074364 0.00028034063
- 3900 100 0.00081311806 0.00081311806 0.00095642595 7.9543605e-05
- 4000 100 0.00059774673 0.00059774673 0.00074849615 6.8190201e-05
- 4100 100 0.00052811986 0.00052811986 0.00067263919 5.012633e-05
- 4200 100 0.00049555855 0.00049555855 0.00061736675 4.9888372e-05
- 4300 100 0.00048274473 0.00048274473 0.00059050389 5.1381757e-05
- 4400 100 0.00047341333 0.00047341333 0.00058083446 5.02623e-05
- 4500 100 0.00046792237 0.00046792237 0.00057416894 4.9019652e-05
- 4600 100 0.00046035378 0.00046035378 0.00056694823 6.0353699e-05
- 4700 100 0.00038114933 0.00038114933 0.0004980117 6.5173515e-05
- 4800 100 0.0003783967 0.0003783967 0.00049488428 4.8463898e-05
- 4900 100 0.00027940611 0.00027940611 0.00041517649 5.0979155e-05
- 5000 100 0.00026071989 0.00026071989 0.00040045214 5.151673e-05
-Loop time of 0.0799825 on 4 procs for 5000 steps with 100 atoms
-
-Performance: 27005901.076 tau/day, 62513.660 timesteps/s
-96.6% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.00093961 | 0.0032012 | 0.0054553 | 3.8 | 4.00
-Neigh | 0.0032456 | 0.0046872 | 0.0061908 | 2.0 | 5.86
-Comm | 0.014328 | 0.02121 | 0.029619 | 4.7 | 26.52
-Output | 0.0011828 | 0.0014142 | 0.0015574 | 0.4 | 1.77
-Modify | 0.002455 | 0.013876 | 0.026567 | 9.6 | 17.35
-Other | | 0.03559 | | | 44.50
-
-Nlocal: 25 ave 51 max 0 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Nghost: 4.75 ave 11 max 0 min
-Histogram: 2 0 0 0 0 0 0 1 0 1
-Neighs: 39.5 ave 85 max 0 min
-Histogram: 2 0 0 0 0 0 0 0 1 1
-
-Total # of neighbors = 158
-Ave neighs/atom = 1.58
-Neighbor list builds = 305
-Dangerous builds = 0
-
-region container delete
-variable theta equal (step-5000)*(4.0*PI/5000)
-region container block -6 6 -6 6 -6 6 units box rotate v_theta 0 0 0 0 0 1
-run 5000
-Memory usage per processor = 5.16122 Mbytes
-Step Atoms Temp c_1 c_2 Press
- 5000 100 0.00026071989 0.00026071989 0.00040045214 5.1497323e-05
- 5100 100 0.66352492 0.66352492 0.35750241 0.015948709
- 5200 100 0.6922229 0.6922229 0.37176131 0.011025479
- 5300 100 0.76307067 0.76307067 0.40325027 0.010979511
- 5400 100 0.83871418 0.83871418 0.43756084 0.012600965
- 5500 100 0.93090048 0.93090048 0.4817574 0.012306942
- 5600 100 0.98338567 0.98338567 0.50374148 0.015434412
- 5700 100 1.0455442 1.0455442 0.53265847 0.017959409
- 5800 100 1.1081511 1.1081511 0.56112842 0.018832417
- 5900 100 1.1724309 1.1724309 0.59276447 0.019257973
- 6000 100 1.1914813 1.1914813 0.60201665 0.019694573
- 6100 100 1.2417733 1.2417733 0.62578893 0.019616524
- 6200 100 1.2612898 1.2612898 0.63503847 0.020442394
- 6300 100 1.2657345 1.2657345 0.63714395 0.020498843
- 6400 100 1.2678009 1.2678009 0.63828941 0.019900919
- 6500 100 1.284156 1.284156 0.64724666 0.020147256
- 6600 100 1.3090278 1.3090278 0.65925035 0.02136883
- 6700 100 1.3122075 1.3122075 0.66136807 0.020782325
- 6800 100 1.3147107 1.3147107 0.66026206 0.022887611
- 6900 100 1.3185295 1.3185295 0.66157265 0.021249838
- 7000 100 1.3232771 1.3232771 0.66334852 0.021738995
- 7100 100 1.3375003 1.3375003 0.67017176 0.021997185
- 7200 100 1.3349835 1.3349835 0.66895884 0.022149977
- 7300 100 1.3388711 1.3388711 0.67061163 0.021662545
- 7400 100 1.338676 1.338676 0.67074642 0.021076102
- 7500 100 1.3409052 1.3409052 0.67205098 0.021664853
- 7600 100 1.3499236 1.3499236 0.67612412 0.021653422
- 7700 100 1.3479719 1.3479719 0.67510646 0.021873569
- 7800 100 1.3489138 1.3489138 0.67563223 0.021419315
- 7900 100 1.357018 1.357018 0.6795804 0.022201202
- 8000 100 1.3540513 1.3540513 0.67843711 0.02275761
- 8100 100 1.3560429 1.3560429 0.67947065 0.022421723
- 8200 100 1.3590694 1.3590694 0.6806094 0.022004213
- 8300 100 1.3592154 1.3592154 0.68083948 0.021923269
- 8400 100 1.3601392 1.3601392 0.68121418 0.022155184
- 8500 100 1.3622149 1.3622149 0.6824182 0.022126924
- 8600 100 1.3651697 1.3651697 0.68397342 0.022195287
- 8700 100 1.3679254 1.3679254 0.68540978 0.023609651
- 8800 100 1.3686254 1.3686254 0.68559712 0.02242291
- 8900 100 1.3761277 1.3761277 0.68897201 0.023594162
- 9000 100 1.379968 1.379968 0.69045216 0.022516846
- 9100 100 1.3784732 1.3784732 0.68955121 0.022836115
- 9200 100 1.376848 1.376848 0.6885551 0.02279321
- 9300 100 1.3799231 1.3799231 0.68964009 0.023105818
- 9400 100 1.3817992 1.3817992 0.69057466 0.023062265
- 9500 100 1.3836544 1.3836544 0.69156755 0.024363244
- 9600 100 1.388032 1.388032 0.69348762 0.024930983
- 9700 100 1.3943738 1.3943738 0.6965703 0.024448451
- 9800 100 1.3963094 1.3963094 0.6971039 0.02341203
- 9900 100 1.3995489 1.3995489 0.69881652 0.023502542
- 10000 100 1.3974742 1.3974742 0.69765474 0.02340004
-Loop time of 0.18267 on 4 procs for 5000 steps with 100 atoms
-
-Performance: 11824571.055 tau/day, 27371.692 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 | 0.0010765 | 0.012038 | 0.023519 | 9.9 | 6.59
-Neigh | 0.0057316 | 0.010541 | 0.015351 | 4.6 | 5.77
-Comm | 0.0067229 | 0.017007 | 0.028509 | 7.8 | 9.31
-Output | 0.0011928 | 0.002021 | 0.0027668 | 1.6 | 1.11
-Modify | 0.009697 | 0.053707 | 0.098413 | 19.0 | 29.40
-Other | | 0.08736 | | | 47.82
-
-Nlocal: 25 ave 51 max 0 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Nghost: 3.25 ave 8 max 0 min
-Histogram: 2 0 0 0 0 0 1 0 0 1
-Neighs: 46.75 ave 104 max 0 min
-Histogram: 2 0 0 0 0 0 0 1 0 1
-
-Total # of neighbors = 187
-Ave neighs/atom = 1.87
-Neighbor list builds = 633
-Dangerous builds = 0
-
-region container delete
-region container block -6 6 -6 6 -6 6 units box
-run 5000
-Memory usage per processor = 5.16122 Mbytes
-Step Atoms Temp c_1 c_2 Press
- 10000 100 1.3974742 1.3974742 0.69765474 0.023347613
- 10100 100 0.34944285 0.34944285 0.20251378 0.019176827
- 10200 100 0.22524385 0.22524385 0.14368424 0.0033260831
- 10300 100 0.15243438 0.15243438 0.11070165 0.0064816535
- 10400 100 0.1143586 0.1143586 0.087867032 0.0024091961
- 10500 100 0.092025102 0.092025102 0.071291506 0.0030683413
- 10600 100 0.071051442 0.071051442 0.05700858 0.00100243
- 10700 100 0.058346771 0.058346771 0.04843626 0.0006073275
- 10800 100 0.048700232 0.048700232 0.039550383 0.00091511006
- 10900 100 0.036880936 0.036880936 0.029482183 0.0011698854
- 11000 100 0.028768807 0.028768807 0.023865852 0.0011980794
- 11100 100 0.022823005 0.022823005 0.018819891 0.0004639259
- 11200 100 0.016954703 0.016954703 0.014075803 0.00085142865
- 11300 100 0.015359685 0.015359685 0.01295219 0.00026241662
- 11400 100 0.012748378 0.012748378 0.011085291 0.00045626939
- 11500 100 0.010464459 0.010464459 0.0087024732 0.00029325411
- 11600 100 0.0099186727 0.0099186727 0.0080127406 0.00031388584
- 11700 100 0.0088308874 0.0088308874 0.0072317369 0.00017850972
- 11800 100 0.0081740195 0.0081740195 0.0066522963 0.00012282618
- 11900 100 0.0079005289 0.0079005289 0.0063346391 0.00010630403
- 12000 100 0.0066277573 0.0066277573 0.0054122601 5.4791661e-05
- 12100 100 0.00567928 0.00567928 0.0047331385 9.2668647e-05
- 12200 100 0.005282803 0.005282803 0.0043827202 8.7820361e-05
- 12300 100 0.0051590302 0.0051590302 0.0042806737 6.5433983e-05
- 12400 100 0.0049013329 0.0049013329 0.0040882737 6.2007733e-05
- 12500 100 0.0044725745 0.0044725745 0.0037535523 6.1132729e-05
- 12600 100 0.0043131884 0.0043131884 0.0035845765 5.3375706e-05
- 12700 100 0.0042020236 0.0042020236 0.0034902096 0.0001192142
- 12800 100 0.0041367453 0.0041367453 0.003433341 0.00011052418
- 12900 100 0.0039862367 0.0039862367 0.0033026224 5.2674711e-05
- 13000 100 0.0033163769 0.0033163769 0.0028118123 5.9042575e-05
- 13100 100 0.0030645983 0.0030645983 0.002571872 4.9521551e-05
- 13200 100 0.002808301 0.002808301 0.0023652684 3.4748246e-05
- 13300 100 0.002556475 0.002556475 0.0021699595 0.00042840611
- 13400 100 0.0023430405 0.0023430405 0.0019913198 2.2687303e-05
- 13500 100 0.0021422817 0.0021422817 0.0018017112 -6.7761855e-06
- 13600 100 0.0020993702 0.0020993702 0.001749657 2.5979707e-05
- 13700 100 0.0019871396 0.0019871396 0.0016647634 5.754995e-05
- 13800 100 0.0017311886 0.0017311886 0.0014696399 2.1585018e-05
- 13900 100 0.0016249641 0.0016249641 0.0013982224 2.0108931e-05
- 14000 100 0.0015874763 0.0015874763 0.0013613318 0.00018348921
- 14100 100 0.0013772541 0.0013772541 0.0012193388 1.9336869e-05
- 14200 100 0.0013587865 0.0013587865 0.0012054213 1.807845e-05
- 14300 100 0.0011824329 0.0011824329 0.0010348168 0.00017307518
- 14400 100 0.0011387278 0.0011387278 0.0010010725 1.4091757e-05
- 14500 100 0.0010441599 0.0010441599 0.00092205881 1.3630652e-05
- 14600 100 0.00096839518 0.00096839518 0.00086828535 1.2437299e-05
- 14700 100 0.00094215882 0.00094215882 0.00084418599 5.3989122e-05
- 14800 100 0.00077297853 0.00077297853 0.00070382005 8.5049867e-06
- 14900 100 0.00072181281 0.00072181281 0.00066110432 8.9324335e-06
- 15000 100 0.00070122327 0.00070122327 0.00063826734 3.4876262e-05
-Loop time of 0.0815294 on 4 procs for 5000 steps with 100 atoms
-
-Performance: 26493517.176 tau/day, 61327.586 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 | 0.00076294 | 0.0033154 | 0.0062585 | 4.3 | 4.07
-Neigh | 0.0010953 | 0.0020078 | 0.002914 | 2.0 | 2.46
-Comm | 0.0021389 | 0.012184 | 0.023433 | 9.1 | 14.94
-Output | 0.0011332 | 0.0014591 | 0.0017147 | 0.7 | 1.79
-Modify | 0.00083971 | 0.017889 | 0.035367 | 12.7 | 21.94
-Other | | 0.04467 | | | 54.79
-
-Nlocal: 25 ave 54 max 0 min
-Histogram: 2 0 0 0 0 0 0 0 1 1
-Nghost: 3.75 ave 8 max 0 min
-Histogram: 2 0 0 0 0 0 0 0 1 1
-Neighs: 37.5 ave 97 max 0 min
-Histogram: 2 0 0 0 0 1 0 0 0 1
-
-Total # of neighbors = 150
-Ave neighs/atom = 1.5
-Neighbor list builds = 120
-Dangerous builds = 0
-
-region container delete
-variable theta equal (step-15000)*(4.0*PI/5000)
-region container block -6 6 -6 6 -6 6 units box rotate v_theta 0 0 0 1 1 1
-run 5000
-Memory usage per processor = 5.16122 Mbytes
-Step Atoms Temp c_1 c_2 Press
- 15000 100 0.00070122327 0.00070122327 0.00063826734 3.4742207e-05
- 15100 100 1.1981004 1.1981004 0.74046013 0.017300203
- 15200 100 1.2197457 1.2197457 0.75847511 0.016724637
- 15300 100 1.1794198 1.1794198 0.77076582 0.017228755
- 15400 100 1.4027714 1.4027714 0.87950036 0.021028602
- 15500 100 1.5514702 1.5514702 0.95040716 0.019935207
- 15600 100 1.8360404 1.8360404 1.0987247 0.02494663
- 15700 100 2.0317625 2.0317625 1.2004001 0.029286087
- 15800 100 2.0478625 2.0478625 1.189893 0.031660426
- 15900 100 2.1289888 2.1289888 1.2083316 0.028754408
- 16000 100 2.2261493 2.2261493 1.2550891 0.030665647
- 16100 100 2.3005184 2.3005184 1.29238 0.036511242
- 16200 100 2.4515818 2.4515818 1.3563253 0.033787104
- 16300 100 2.4524614 2.4524614 1.3571527 0.031905963
- 16400 100 2.5592541 2.5592541 1.405001 0.035688651
- 16500 100 2.5311864 2.5311864 1.3918694 0.032451265
- 16600 100 2.6471904 2.6471904 1.4481739 0.034763978
- 16700 100 2.7024085 2.7024085 1.4785065 0.037514299
- 16800 100 2.8116979 2.8116979 1.5403269 0.03585152
- 16900 100 2.9095374 2.9095374 1.5962283 0.038244982
- 17000 100 2.9228985 2.9228985 1.5978628 0.037971615
- 17100 100 2.983589 2.983589 1.6205713 0.038332341
- 17200 100 3.1245984 3.1245984 1.6925827 0.042532223
- 17300 100 3.1060575 3.1060575 1.6713928 0.052589575
- 17400 100 3.2494904 3.2494904 1.7567188 0.044783721
- 17500 100 3.2313349 3.2313349 1.7549177 0.044959213
- 17600 100 3.3928412 3.3928412 1.822978 0.052512199
- 17700 100 3.3064729 3.3064729 1.7924768 0.046624738
- 17800 100 3.1907518 3.1907518 1.7406131 0.042864325
- 17900 100 3.0224556 3.0224556 1.6641648 0.040151025
- 18000 100 3.105271 3.105271 1.7045599 0.047137803
- 18100 100 3.0293425 3.0293425 1.6626024 0.04198758
- 18200 100 3.139773 3.139773 1.7310307 0.040137164
- 18300 100 2.9732894 2.9732894 1.6555933 0.03777758
- 18400 100 3.1250324 3.1250324 1.739812 0.038542298
- 18500 100 3.1687407 3.1687407 1.7593494 0.041591022
- 18600 100 3.2880821 3.2880821 1.8169373 0.042503015
- 18700 100 3.4877047 3.4877047 1.9049979 0.048156272
- 18800 100 3.7982973 3.7982973 2.055323 0.049805341
- 18900 100 3.9922267 3.9922267 2.1260665 0.062688073
- 19000 100 3.8620284 3.8620284 2.0652184 0.064418518
- 19100 100 3.8757665 3.8757665 2.0615465 0.058600317
- 19200 100 3.9425495 3.9425495 2.1030375 0.053714175
- 19300 100 3.8589133 3.8589133 2.0485568 0.05531747
- 19400 100 3.9202395 3.9202395 2.0904529 0.056324297
- 19500 100 3.9748628 3.9748628 2.1114492 0.055590699
- 19600 100 3.8876771 3.8876771 2.0918436 0.052415532
- 19700 100 3.8975921 3.8975921 2.0755799 0.050647718
- 19800 100 3.7488333 3.7488333 2.0024562 0.056966734
- 19900 100 3.7818574 3.7818574 2.00915 0.050079148
- 20000 100 3.4510736 3.4510736 1.8525818 0.053548452
-Loop time of 0.156607 on 4 procs for 5000 steps with 100 atoms
-
-Performance: 13792452.627 tau/day, 31926.974 timesteps/s
-98.5% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.0030923 | 0.0049732 | 0.0071678 | 2.1 | 3.18
-Neigh | 0.012225 | 0.015592 | 0.017859 | 1.7 | 9.96
-Comm | 0.034876 | 0.037526 | 0.040807 | 1.1 | 23.96
-Output | 0.0013812 | 0.0015668 | 0.0017419 | 0.3 | 1.00
-Modify | 0.026932 | 0.044011 | 0.054787 | 5.0 | 28.10
-Other | | 0.05294 | | | 33.80
-
-Nlocal: 25 ave 41 max 12 min
-Histogram: 1 0 0 1 1 0 0 0 0 1
-Nghost: 3.25 ave 6 max 1 min
-Histogram: 1 0 1 0 0 0 1 0 0 1
-Neighs: 35.75 ave 59 max 9 min
-Histogram: 1 0 0 0 0 1 1 0 0 1
-
-Total # of neighbors = 143
-Ave neighs/atom = 1.43
-Neighbor list builds = 917
-Dangerous builds = 0
-
-region container delete
-region container block -6 6 -6 6 -6 6 units box
-run 5000
-Memory usage per processor = 5.16122 Mbytes
-Step Atoms Temp c_1 c_2 Press
- 20000 100 3.4510736 3.4510736 1.8525818 0.053182767
- 20100 100 0.99241675 0.99241675 0.61590164 0.015233656
- 20200 100 0.92799489 0.92799489 0.55540992 0.011885237
- 20300 100 0.9171573 0.9171573 0.54477252 0.012926388
- 20400 100 0.86718407 0.86718407 0.5145422 0.011384414
- 20500 100 0.84470122 0.84470122 0.50181203 0.010482207
- 20600 100 0.93025469 0.93025469 0.53939952 0.011377044
- 20700 100 0.96631348 0.96631348 0.55772027 0.015287231
- 20800 100 0.90708015 0.90708015 0.52037018 0.014854537
- 20900 100 0.73319001 0.73319001 0.42824847 0.0092980012
- 21000 100 0.3371096 0.3371096 0.21272171 0.0061783554
- 21100 100 0.21771022 0.21771022 0.14128887 0.0082147558
- 21200 100 0.18133275 0.18133275 0.11945636 0.0055722731
- 21300 100 0.17117199 0.17117199 0.11048263 0.0027980106
- 21400 100 0.15741047 0.15741047 0.10346676 0.0023057723
- 21500 100 0.10045855 0.10045855 0.069905343 0.0023941181
- 21600 100 0.066094864 0.066094864 0.051285108 0.0022519002
- 21700 100 0.048622069 0.048622069 0.040662255 0.00073951939
- 21800 100 0.046829799 0.046829799 0.037431722 0.0015913976
- 21900 100 0.025308514 0.025308514 0.02092076 0.00064225773
- 22000 100 0.016326886 0.016326886 0.013588504 0.00087416572
- 22100 100 0.011892981 0.011892981 0.010417133 0.00080132313
- 22200 100 0.011974602 0.011974602 0.010342276 0.00044437732
- 22300 100 0.012567486 0.012567486 0.010294969 0.00048413872
- 22400 100 0.011676022 0.011676022 0.0091714238 0.00066567365
- 22500 100 0.0098737136 0.0098737136 0.0079252142 0.00024081335
- 22600 100 0.0052495523 0.0052495523 0.0047802341 0.00029167814
- 22700 100 0.0049396543 0.0049396543 0.0043570686 0.00019793167
- 22800 100 0.004469254 0.004469254 0.0038657445 0.00052965165
- 22900 100 0.0043837877 0.0043837877 0.0034611363 0.00045595698
- 23000 100 0.003439309 0.003439309 0.0028031344 0.00025784869
- 23100 100 0.0034805091 0.0034805091 0.0027537344 0.00012746906
- 23200 100 0.0045502061 0.0045502061 0.0032298328 0.00024006432
- 23300 100 0.0028553043 0.0028553043 0.0023107483 0.00012803066
- 23400 100 0.0022736412 0.0022736412 0.0018560302 0.0002706771
- 23500 100 0.0020966521 0.0020966521 0.0017106541 0.00014239612
- 23600 100 0.0018760993 0.0018760993 0.0015415318 0.00010892634
- 23700 100 0.0022362451 0.0022362451 0.0017014519 0.00012547256
- 23800 100 0.0017603403 0.0017603403 0.0014681398 0.00023372731
- 23900 100 0.0023396747 0.0023396747 0.0016700312 0.00017014305
- 24000 100 0.0012059144 0.0012059144 0.0009982224 3.6215959e-05
- 24100 100 0.0011739433 0.0011739433 0.00097155852 3.6169918e-05
- 24200 100 0.0011071139 0.0011071139 0.00092095478 8.8000847e-05
- 24300 100 0.0011078659 0.0011078659 0.00092073833 4.8706222e-05
- 24400 100 0.0011037562 0.0011037562 0.00091673546 3.7548502e-05
- 24500 100 0.00098422752 0.00098422752 0.00083054499 9.1151844e-05
- 24600 100 0.00097403646 0.00097403646 0.00082364881 5.0914687e-05
- 24700 100 0.00093082012 0.00093082012 0.00079047801 3.2230016e-05
- 24800 100 0.0009138973 0.0009138973 0.00075880177 2.8780789e-05
- 24900 100 0.0012881027 0.0012881027 0.00093025416 1.6385252e-05
- 25000 100 0.00076099168 0.00076099168 0.00065175575 9.417272e-06
-Loop time of 0.0846543 on 4 procs for 5000 steps with 100 atoms
-
-Performance: 25515528.493 tau/day, 59063.723 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 | 0.0010469 | 0.0037468 | 0.0067947 | 4.3 | 4.43
-Neigh | 0.0032442 | 0.0047541 | 0.0065064 | 2.0 | 5.62
-Comm | 0.0085762 | 0.016923 | 0.024509 | 5.8 | 19.99
-Output | 0.0011523 | 0.0014572 | 0.0016789 | 0.6 | 1.72
-Modify | 0.0017715 | 0.016296 | 0.031399 | 11.1 | 19.25
-Other | | 0.04148 | | | 49.00
-
-Nlocal: 25 ave 50 max 0 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Nghost: 6 ave 13 max 0 min
-Histogram: 2 0 0 0 0 0 0 0 1 1
-Neighs: 39 ave 80 max 0 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-
-Total # of neighbors = 156
-Ave neighs/atom = 1.56
-Neighbor list builds = 284
-Dangerous builds = 0
-Total wall time: 0:00:00
diff --git a/examples/granregion/log.6Oct16.granregion.funnel.g++.1 b/examples/granregion/log.6Oct16.granregion.funnel.g++.1
deleted file mode 100644
index 86faeb3401..0000000000
--- a/examples/granregion/log.6Oct16.granregion.funnel.g++.1
+++ /dev/null
@@ -1,608 +0,0 @@
-LAMMPS (5 Oct 2016)
-# pour particles into cone-shaped funnel, settle them, let them run out bottom
-
-variable name string funnel_pour
-
-thermo_modify flush yes
-units si
-variable PI equal 3.141592653589
-variable seed equal 14314
-
-###############################################
-# Geometry-related parameters
-###############################################
-
-variable xlo equal 10
-variable xhi equal 40
-variable ylo equal 10
-variable yhi equal 40
-variable zlo equal -20
-variable zhi equal 50
-
-variable xc equal 25
-variable yc equal 25
-
-variable zconehi equal 50
-variable zconelo equal 10
-variable zcyllo equal 0
-variable radconelo equal 2
-variable radconehi equal 20
-
-################################################
-# Particle sizes
-################################################
-
-variable rlo equal 0.25
-variable rhi equal 0.5
-variable dlo equal 2.0*${rlo}
-variable dlo equal 2.0*0.25
-variable dhi equal 2.0*${rhi}
-variable dhi equal 2.0*0.5
-
-variable skin equal ${rhi}
-variable skin equal 0.5
-
-###############################################
-# Granular contact parameters
-###############################################
-
-variable coeffRes equal 0.1
-variable coeffFric equal 0.5
-
-variable density equal 1.0
-variable EYoung equal 10^5
-variable Poisson equal 2.0/7.0
-variable GShear equal ${EYoung}/(2*(1+${Poisson}))
-variable GShear equal 100000/(2*(1+${Poisson}))
-variable GShear equal 100000/(2*(1+0.285714285714286))
-
-variable gravity equal 1.0
-
-variable reff equal 0.5*(${rhi}+${rlo})
-variable reff equal 0.5*(0.5+${rlo})
-variable reff equal 0.5*(0.5+0.25)
-variable meff equal ${density}*4.0/3.0*${PI}*${reff}^3
-variable meff equal 1*4.0/3.0*${PI}*${reff}^3
-variable meff equal 1*4.0/3.0*3.141592653589*${reff}^3
-variable meff equal 1*4.0/3.0*3.141592653589*0.375^3
-variable min_mass equal ${density}*4.0/3.0*${PI}*${rlo}*${rlo}*${rlo}
-variable min_mass equal 1*4.0/3.0*${PI}*${rlo}*${rlo}*${rlo}
-variable min_mass equal 1*4.0/3.0*3.141592653589*${rlo}*${rlo}*${rlo}
-variable min_mass equal 1*4.0/3.0*3.141592653589*0.25*${rlo}*${rlo}
-variable min_mass equal 1*4.0/3.0*3.141592653589*0.25*0.25*${rlo}
-variable min_mass equal 1*4.0/3.0*3.141592653589*0.25*0.25*0.25
-variable max_mass equal ${density}*4.0/3.0*${PI}*${rhi}*${rhi}*${rhi}
-variable max_mass equal 1*4.0/3.0*${PI}*${rhi}*${rhi}*${rhi}
-variable max_mass equal 1*4.0/3.0*3.141592653589*${rhi}*${rhi}*${rhi}
-variable max_mass equal 1*4.0/3.0*3.141592653589*0.5*${rhi}*${rhi}
-variable max_mass equal 1*4.0/3.0*3.141592653589*0.5*0.5*${rhi}
-variable max_mass equal 1*4.0/3.0*3.141592653589*0.5*0.5*0.5
-
-## Typical way to set kn, kt, etc.:
-variable kn equal 4.0*${GShear}/(3*(1-${Poisson}))
-variable kn equal 4.0*38888.8888888889/(3*(1-${Poisson}))
-variable kn equal 4.0*38888.8888888889/(3*(1-0.285714285714286))
-variable kt equal 4.0*${GShear}/(2-${Poisson})
-variable kt equal 4.0*38888.8888888889/(2-${Poisson})
-variable kt equal 4.0*38888.8888888889/(2-0.285714285714286)
-
-variable a equal (-2.0*log(${coeffRes})/${PI})^2
-variable a equal (-2.0*log(0.1)/${PI})^2
-variable a equal (-2.0*log(0.1)/3.141592653589)^2
-variable gamma_n equal sqrt($a*2*${kn}/${min_mass}/(1+0.25*$a))
-variable gamma_n equal sqrt(0.405284734569556*2*${kn}/${min_mass}/(1+0.25*$a))
-variable gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/${min_mass}/(1+0.25*$a))
-variable gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/0.0654498469497708/(1+0.25*$a))
-variable gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/0.0654498469497708/(1+0.25*0.405284734569556))
-variable gamma_t equal ${gamma_n}*0.5
-variable gamma_t equal 903.503751814138*0.5
-
-variable tcol equal ${PI}/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
-variable tcol equal 3.141592653589/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
-variable tcol equal 3.141592653589/sqrt(2*72592.5925925926/${min_mass}-${gamma_n}/4.0)
-variable tcol equal 3.141592653589/sqrt(2*72592.5925925926/0.0654498469497708-${gamma_n}/4.0)
-variable tcol equal 3.141592653589/sqrt(2*72592.5925925926/0.0654498469497708-903.503751814138/4.0)
-
-variable dt equal ${tcol}*0.05
-variable dt equal 0.00210943016014969*0.05
-timestep ${dt}
-timestep 0.000105471508007485
-
-###############################################
-variable dumpfreq equal 1000
-variable logfreq equal 1000
-
-newton off
-atom_style sphere
-
-boundary p p f
-
-region boxreg block ${xlo} ${xhi} ${ylo} ${yhi} ${zlo} ${zhi}
-region boxreg block 10 ${xhi} ${ylo} ${yhi} ${zlo} ${zhi}
-region boxreg block 10 40 ${ylo} ${yhi} ${zlo} ${zhi}
-region boxreg block 10 40 10 ${yhi} ${zlo} ${zhi}
-region boxreg block 10 40 10 40 ${zlo} ${zhi}
-region boxreg block 10 40 10 40 -20 ${zhi}
-region boxreg block 10 40 10 40 -20 50
-create_box 1 boxreg
-Created orthogonal box = (10 10 -20) to (40 40 50)
- 1 by 1 by 1 MPI processor grid
-
-pair_style gran/hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
-pair_style gran/hertz/history 72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
-pair_style gran/hertz/history 72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1
-pair_style gran/hertz/history 72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1
-pair_style gran/hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1
-pair_style gran/hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1
-pair_coeff * *
-
-neighbor ${skin} bin
-neighbor 0.5 bin
-thermo ${logfreq}
-thermo 1000
-
-comm_style brick
-comm_modify mode multi group all vel yes
-balance 1.1 shift xyz 20 1.1
-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
- ghost atom cutoff = 0
- binsize = 30 -> bins = 1 1 3
-fix bal all balance 10000 1.1 shift xyz 20 1.01
-
-####################### Options specific to pouring #########################
-
-# insertion region for fix/pour
-
-region insreg cylinder z ${xc} ${yc} 10 30 50 side in units box
-region insreg cylinder z 25 ${yc} 10 30 50 side in units box
-region insreg cylinder z 25 25 10 30 50 side in units box
-
-# define cone and cylinder regions - see lammps doc on region command
-# note new open options
-
-region cylreg cylinder z ${xc} ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 2 #Top is open
-region cylreg cylinder z 25 ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 2
-region cylreg cylinder z 25 25 ${radconelo} ${zcyllo} ${zconelo} side in units box open 2
-region cylreg cylinder z 25 25 2 ${zcyllo} ${zconelo} side in units box open 2
-region cylreg cylinder z 25 25 2 0 ${zconelo} side in units box open 2
-region cylreg cylinder z 25 25 2 0 10 side in units box open 2
-
-region conereg cone z ${xc} ${yc} ${radconelo} ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2 #Bottom and top are open
-region conereg cone z 25 ${yc} ${radconelo} ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2
-region conereg cone z 25 25 ${radconelo} ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2
-region conereg cone z 25 25 2 ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2
-region conereg cone z 25 25 2 20 ${zconelo} ${zconehi} side in units box open 1 open 2
-region conereg cone z 25 25 2 20 10 ${zconehi} side in units box open 1 open 2
-region conereg cone z 25 25 2 20 10 50 side in units box open 1 open 2
-
-region hopreg union 2 conereg cylreg
-
-fix grav all gravity ${gravity} vector 0 0 -1
-fix grav all gravity 1 vector 0 0 -1
-fix 1 all nve/sphere
-
-
-fix hopper3 all wall/gran/region hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
-fix hopper3 all wall/gran/region hertz/history 72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
-fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
-fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1 region hopreg
-fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1 region hopreg
-fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1 region hopreg
-
-fix ins all pour 2000 1 42424 region insreg diam range ${dlo} ${dhi} dens ${density} ${density}
-fix ins all pour 2000 1 42424 region insreg diam range 0.5 ${dhi} dens ${density} ${density}
-fix ins all pour 2000 1 42424 region insreg diam range 0.5 1 dens ${density} ${density}
-fix ins all pour 2000 1 42424 region insreg diam range 0.5 1 dens 1 ${density}
-fix ins all pour 2000 1 42424 region insreg diam range 0.5 1 dens 1 1
-Particle insertion: 3000 every 59965 steps, 2000 by step 1
-
-#dump 1 all custom ${dumpfreq} ${name}.dump # id type mass diameter x y z
-
-#dump 2 all image 4000 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 zoom 3.0 # box no 0.0 axes no 0.0 0.0
-#dump_modify 2 pad 6
-
-thermo_style custom step cpu atoms ke
-WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:690)
-thermo_modify flush yes lost warn
-
-# Initial run to fill up the cone
-
-run 20000
-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 = 1.5
- ghost atom cutoff = 1.5
- binsize = 0.75 -> bins = 40 40 94
-Memory usage per processor = 3.59417 Mbytes
-Step CPU Atoms KinEng
- 0 0 0 -0
- 1000 0.54582715 2000 -0
- 2000 0.93155909 2000 -0
- 3000 1.3159981 2000 -0
- 4000 1.697911 2000 -0
- 5000 2.080133 2000 -0
- 6000 2.461525 2000 -0
- 7000 2.842278 2000 -0
- 8000 3.222302 2000 -0
- 9000 3.6018171 2000 -0
- 10000 3.9843922 2000 -0
- 11000 4.363066 2000 -0
- 12000 4.743022 2000 -0
- 13000 5.121953 2000 -0
- 14000 5.5021431 2000 -0
- 15000 5.8807089 2000 -0
- 16000 6.2604752 2000 -0
- 17000 6.640244 2000 -0
- 18000 7.0199981 2000 -0
- 19000 7.40029 2000 -0
- 20000 7.7834539 2000 -0
-Loop time of 7.78348 on 1 procs for 20000 steps with 2000 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 | 0.64588 | 0.64588 | 0.64588 | 0.0 | 8.30
-Neigh | 0.097229 | 0.097229 | 0.097229 | 0.0 | 1.25
-Comm | 0.011505 | 0.011505 | 0.011505 | 0.0 | 0.15
-Output | 0.00041127 | 0.00041127 | 0.00041127 | 0.0 | 0.01
-Modify | 6.8117 | 6.8117 | 6.8117 | 0.0 | 87.51
-Other | | 0.2168 | | | 2.79
-
-Nlocal: 2000 ave 2000 max 2000 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: 1537 ave 1537 max 1537 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 1537
-Ave neighs/atom = 0.7685
-Neighbor list builds = 69
-Dangerous builds = 0
-unfix ins
-run 150000
-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 = 1.49993
- ghost atom cutoff = 1.49993
- binsize = 0.749963 -> bins = 41 41 94
-Memory usage per processor = 9.40639 Mbytes
-Step CPU Atoms KinEng
- 20000 0 2000 6443.7665
- 21000 0.37979388 2000 6572.3531
- 22000 0.76149178 2000 6723.8376
- 23000 1.1449339 2000 6853.1812
- 24000 1.529017 2000 6976.0209
- 25000 1.9145579 2000 7096.9955
- 26000 2.30124 2000 7215.5795
- 27000 2.6893978 2000 7349.2382
- 28000 3.0777299 2000 7471.8719
- 29000 3.4699018 2000 7574.7988
- 30000 3.8656738 2000 7660.2353
- 31000 4.2606828 2000 7703.5736
- 32000 4.6632309 2000 7643.5299
- 33000 5.0728998 2000 7520.14
- 34000 5.4878559 2000 7372.2247
- 35000 5.910604 2000 7192.1639
- 36000 6.340683 2000 6985.7075
- 37000 6.8159268 2000 6858.944
- 38000 7.2553098 2000 6717.0485
- 39000 7.699847 2000 6541.6874
- 40000 8.1524599 2000 6382.1661
- 41000 8.6083429 2000 6235.6681
- 42000 9.0669999 2000 6103.095
- 43000 9.5359929 2000 5951.0523
- 44000 10.012767 2000 5811.0158
- 45000 10.497891 2000 5627.7273
- 46000 10.988827 2000 5471.7262
- 47000 11.48741 2000 5299.1205
- 48000 11.990619 2000 5164.1642
- 49000 12.497663 2000 5006.5014
- 50000 13.020399 2000 4872.2336
- 51000 13.548012 2000 4694.5332
- 52000 14.082238 2000 4515.5164
- 53000 14.622731 2000 4384.7531
- 54000 15.170292 2000 4215.1354
- 55000 15.721908 2000 4063.0658
- 56000 16.285099 2000 3895.7872
- 57000 16.858606 2000 3693.0537
- 58000 17.440427 2000 3514.887
- 59000 18.03239 2000 3268.5625
- 60000 18.640969 2000 3049.7365
- 61000 19.245721 2000 2885.6786
- 62000 19.85574 2000 2652.9108
- 63000 20.47405 2000 2408.6484
- 64000 21.10165 2000 2126.9549
- 65000 21.743939 2000 1879.2829
- 66000 22.39462 2000 1645.0406
- 67000 23.059044 2000 1425.8023
- 68000 23.730976 2000 1160.2206
- 69000 24.410132 2000 961.78467
- 70000 25.096468 2000 785.64232
- 71000 25.778622 2000 626.09642
- 72000 26.474474 2000 468.40645
- 73000 27.171065 2000 358.58331
- 74000 27.860177 2000 299.43443
- 75000 28.544588 2000 246.40717
- 76000 29.226358 2000 206.30408
- 77000 29.902697 2000 176.97739
- 78000 30.577693 2000 144.25328
- 79000 31.269697 2000 115.11502
- 80000 31.977588 2000 97.780887
- 81000 32.685445 2000 82.593472
- 82000 33.397946 2000 72.226521
- 83000 34.114464 2000 62.978026
- 84000 34.831341 2000 55.350711
- 85000 35.545558 2000 51.162661
- 86000 36.266238 2000 46.100957
- 87000 36.99804 2000 41.19148
- 88000 37.743379 2000 36.31567
- 89000 38.499655 2000 32.456379
- 90000 39.270287 2000 30.16589
- 91000 40.035401 2000 27.36473
- 92000 40.799095 2000 25.488138
- 93000 41.564371 2000 23.674866
- 94000 42.335499 2000 22.219066
- 95000 43.114508 2000 20.982603
- 96000 43.897793 2000 19.840979
- 97000 44.685675 2000 19.092279
- 98000 45.483452 2000 18.20277
- 99000 46.282718 2000 17.512786
- 100000 47.085373 2000 16.921053
- 101000 47.888376 2000 16.228234
- 102000 48.698546 2000 15.958752
- 103000 49.51312 2000 15.640913
- 104000 50.330832 2000 14.016542
- 105000 51.146589 2000 13.484725
- 106000 51.96128 2000 13.369222
- 107000 52.781047 2000 12.965898
- 108000 53.604374 2000 12.268212
- 109000 54.424389 2000 11.492904
- 110000 55.253544 2000 11.110936
- 111000 56.077677 2000 10.05383
- 112000 56.904333 2000 10.159311
- 113000 57.729366 2000 10.071694
- 114000 58.559509 2000 9.820289
- 115000 59.391732 2000 9.4736012
- 116000 60.221045 2000 9.5616457
- 117000 61.052557 2000 8.6478552
- 118000 61.890195 2000 8.7425719
- 119000 62.726358 2000 8.4741204
- 120000 63.565646 2000 7.772287
- 121000 64.397804 2000 6.9466866
- 122000 65.231394 2000 6.7645153
- 123000 66.064887 2000 6.6568629
- 124000 66.901915 2000 6.7578346
- 125000 67.741833 2000 6.7845523
- 126000 68.582414 2000 6.8385357
- 127000 69.421944 2000 6.8984218
- 128000 70.262972 2000 7.031649
- 129000 71.108668 2000 6.5894805
- 130000 71.954121 2000 6.6452991
- 131000 72.795366 2000 6.7278453
- 132000 73.639866 2000 6.679577
- 133000 74.484945 2000 6.8049542
- 134000 75.326506 2000 6.9015567
- 135000 76.171268 2000 7.2052436
- 136000 77.015739 2000 7.5532841
- 137000 77.861613 2000 7.2577958
- 138000 78.706479 2000 7.5218509
- 139000 79.549466 2000 7.5221639
- 140000 80.398284 2000 7.6657717
- 141000 81.240794 2000 7.9761942
- 142000 82.087164 2000 8.2314258
- 143000 82.931215 2000 8.3019975
- 144000 83.777896 2000 8.0179905
- 145000 84.622383 2000 8.2517491
- 146000 85.469753 2000 6.9481522
- 147000 86.315756 2000 6.6131212
- 148000 87.164711 2000 6.7706881
- 149000 88.012004 2000 6.8104528
- 150000 88.861557 2000 6.7339102
- 151000 89.708494 2000 6.4777998
- 152000 90.558437 2000 6.3011889
- 153000 91.40365 2000 6.3101502
- 154000 92.249997 2000 6.5542552
- 155000 93.099774 2000 6.7687268
- 156000 93.945557 2000 6.7974687
- 157000 94.795065 2000 6.4615869
- 158000 95.645761 2000 6.5566144
- 159000 96.495711 2000 6.4371
- 160000 97.349979 2000 6.4540668
- 161000 98.19875 2000 6.6987231
- 162000 99.049934 2000 6.2464506
- 163000 99.902813 2000 4.7573102
- 164000 100.75416 2000 4.7782706
- 165000 101.60479 2000 4.9414064
- 166000 102.45183 2000 4.970526
- 167000 103.30172 2000 5.1492473
- 168000 104.15283 2000 5.3633229
- 169000 105.00583 2000 4.3464936
- 170000 105.85919 2000 3.6784016
-Loop time of 105.859 on 1 procs for 150000 steps with 2000 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 | 46.786 | 46.786 | 46.786 | -nan | 44.20
-Neigh | 0.88556 | 0.88556 | 0.88556 | 0.0 | 0.84
-Comm | 0.080127 | 0.080127 | 0.080127 | 0.0 | 0.08
-Output | 0.0033967 | 0.0033967 | 0.0033967 | 0.0 | 0.00
-Modify | 56.418 | 56.418 | 56.418 | 0.0 | 53.29
-Other | | 1.687 | | | 1.59
-
-Nlocal: 2000 ave 2000 max 2000 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: 15507 ave 15507 max 15507 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 15507
-Ave neighs/atom = 7.7535
-Neighbor list builds = 401
-Dangerous builds = 0
-
-# remove "plug" - need to redefine cylinder region & union
-
-region cylreg delete
-region hopreg delete
-region cylreg cylinder z ${xc} ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 1 open 2 #Bottom & top are open
-region cylreg cylinder z 25 ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 1 open 2
-region cylreg cylinder z 25 25 ${radconelo} ${zcyllo} ${zconelo} side in units box open 1 open 2
-region cylreg cylinder z 25 25 2 ${zcyllo} ${zconelo} side in units box open 1 open 2
-region cylreg cylinder z 25 25 2 0 ${zconelo} side in units box open 1 open 2
-region cylreg cylinder z 25 25 2 0 10 side in units box open 1 open 2
-
-region hopreg union 2 cylreg conereg
-
-unfix hopper3
-fix hopper3 all wall/gran/region hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
-fix hopper3 all wall/gran/region hertz/history 72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
-fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
-fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1 region hopreg
-fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1 region hopreg
-fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1 region hopreg
-
-run 100000
-Memory usage per processor = 9.40667 Mbytes
-Step CPU Atoms KinEng
- 170000 0 2000 3.6784016
- 171000 0.84847808 2000 4.3936331
- 172000 1.6901879 2000 5.5750342
- 173000 2.523411 2000 6.8205762
- 174000 3.3501492 2000 8.9700613
- 175000 4.1766891 2000 11.336633
- 176000 4.9954321 2000 14.225242
- 177000 5.814229 2000 17.653262
- 178000 6.630548 2000 21.796078
- 179000 7.4493361 2000 26.660801
- 180000 8.2656369 2000 32.428193
- 181000 9.069953 2000 39.229088
- 182000 9.8759181 2000 46.242732
- 183000 10.674972 2000 54.604245
- 184000 11.47082 2000 63.96931
- 185000 12.259916 2000 74.132316
- 186000 13.046788 2000 84.690798
- 187000 13.832446 2000 95.486707
- 188000 14.612976 2000 106.68052
- 189000 15.391779 2000 118.91376
- 190000 16.160107 2000 131.90023
- 191000 16.919573 2000 146.30664
- 192000 17.677855 2000 161.10142
- 193000 18.4352 2000 174.91947
- 194000 19.188156 2000 191.47629
- 195000 19.937255 2000 208.19912
- 196000 20.687716 2000 224.80045
- 197000 21.43754 2000 243.29637
- 198000 22.18579 2000 262.88685
- 199000 22.932473 2000 282.34797
- 200000 23.680828 2000 302.78689
- 201000 24.428559 2000 323.48767
- 202000 25.167341 2000 345.99414
- 203000 25.904465 2000 368.54389
- 204000 26.635727 2000 393.49643
- 205000 27.366891 2000 417.82722
- 206000 28.094282 2000 443.67976
- 207000 28.821021 2000 470.35934
- 208000 29.545596 2000 499.01368
- 209000 30.267439 2000 528.99746
- 210000 30.993287 2000 561.03931
- 211000 31.713729 2000 594.0482
- 212000 32.42933 2000 628.20118
- 213000 33.14608 2000 662.585
- 214000 33.863882 2000 697.41408
- 215000 34.580495 2000 733.36799
- 216000 35.302571 2000 770.46796
- 217000 36.023821 2000 806.72007
- 218000 36.74189 2000 844.06965
- 219000 37.460105 2000 884.31774
- 220000 38.177705 2000 926.23771
- 221000 38.886587 2000 970.02095
- 222000 39.594003 2000 1015.3938
- 223000 40.29579 2000 1061.1281
- 224000 41.001112 2000 1107.9962
- 225000 41.706489 2000 1155.3656
- 226000 42.417622 1998 1196.6939
- 227000 43.133238 1996 1240.8434
- 228000 43.844991 1990 1260.0436
- 229000 44.545565 1986 1280.0431
- 230000 45.246651 1974 1285.222
- 231000 45.934355 1970 1311.8189
- 232000 46.624066 1960 1300.7922
- 233000 47.310339 1943 1282.113
- 234000 47.993433 1932 1261.0871
- 235000 48.66937 1918 1211.0667
- 236000 49.332954 1911 1232.6411
- 237000 49.99742 1898 1209.112
- 238000 50.664096 1888 1189.4002
- 239000 51.336205 1875 1151.415
- 240000 52.010198 1863 1108.0821
- 241000 52.680788 1856 1090.2279
- 242000 53.343069 1843 1062.9726
- 243000 53.996768 1830 1016.0933
- 244000 54.635882 1825 1023.5568
- 245000 55.271259 1817 1012.2897
- 246000 55.902793 1811 1019.8355
- 247000 56.541437 1802 996.81934
- 248000 57.182244 1793 971.29353
- 249000 57.827453 1785 947.98166
- 250000 58.473311 1771 898.58408
- 251000 59.1075 1762 851.46342
- 252000 59.73473 1754 826.46301
- 253000 60.362094 1747 808.08292
- 254000 60.989489 1737 778.86892
- 255000 61.616293 1720 702.90046
- 256000 62.243096 1709 665.14293
- 257000 62.866596 1703 628.63036
- 258000 63.48969 1702 645.42118
- 259000 64.119075 1696 617.03362
- 260000 64.752187 1692 607.96874
- 261000 65.374973 1690 619.83155
- 262000 65.991365 1688 622.09585
- 263000 66.608686 1682 612.86762
- 264000 67.220696 1681 636.53769
- 265000 67.830797 1678 638.33305
- 266000 68.439964 1675 635.97419
- 267000 69.043459 1672 634.91103
- 268000 69.643043 1669 638.50196
- 269000 70.250146 1667 646.16045
- 270000 70.86361 1664 659.62209
-Loop time of 70.8636 on 1 procs for 100000 steps with 1664 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 | 33.501 | 33.501 | 33.501 | 0.0 | 47.27
-Neigh | 0.63279 | 0.63279 | 0.63279 | 0.0 | 0.89
-Comm | 0.055495 | 0.055495 | 0.055495 | 0.0 | 0.08
-Output | 0.0021648 | 0.0021648 | 0.0021648 | 0.0 | 0.00
-Modify | 35.602 | 35.602 | 35.602 | 0.0 | 50.24
-Other | | 1.07 | | | 1.51
-
-Nlocal: 1664 ave 1664 max 1664 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: 11687 ave 11687 max 11687 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 11687
-Ave neighs/atom = 7.02344
-Neighbor list builds = 261
-Dangerous builds = 0
-Total wall time: 0:03:04
diff --git a/examples/granregion/log.6Oct16.granregion.funnel.g++.4 b/examples/granregion/log.6Oct16.granregion.funnel.g++.4
deleted file mode 100644
index fcbd050b76..0000000000
--- a/examples/granregion/log.6Oct16.granregion.funnel.g++.4
+++ /dev/null
@@ -1,608 +0,0 @@
-LAMMPS (5 Oct 2016)
-# pour particles into cone-shaped funnel, settle them, let them run out bottom
-
-variable name string funnel_pour
-
-thermo_modify flush yes
-units si
-variable PI equal 3.141592653589
-variable seed equal 14314
-
-###############################################
-# Geometry-related parameters
-###############################################
-
-variable xlo equal 10
-variable xhi equal 40
-variable ylo equal 10
-variable yhi equal 40
-variable zlo equal -20
-variable zhi equal 50
-
-variable xc equal 25
-variable yc equal 25
-
-variable zconehi equal 50
-variable zconelo equal 10
-variable zcyllo equal 0
-variable radconelo equal 2
-variable radconehi equal 20
-
-################################################
-# Particle sizes
-################################################
-
-variable rlo equal 0.25
-variable rhi equal 0.5
-variable dlo equal 2.0*${rlo}
-variable dlo equal 2.0*0.25
-variable dhi equal 2.0*${rhi}
-variable dhi equal 2.0*0.5
-
-variable skin equal ${rhi}
-variable skin equal 0.5
-
-###############################################
-# Granular contact parameters
-###############################################
-
-variable coeffRes equal 0.1
-variable coeffFric equal 0.5
-
-variable density equal 1.0
-variable EYoung equal 10^5
-variable Poisson equal 2.0/7.0
-variable GShear equal ${EYoung}/(2*(1+${Poisson}))
-variable GShear equal 100000/(2*(1+${Poisson}))
-variable GShear equal 100000/(2*(1+0.285714285714286))
-
-variable gravity equal 1.0
-
-variable reff equal 0.5*(${rhi}+${rlo})
-variable reff equal 0.5*(0.5+${rlo})
-variable reff equal 0.5*(0.5+0.25)
-variable meff equal ${density}*4.0/3.0*${PI}*${reff}^3
-variable meff equal 1*4.0/3.0*${PI}*${reff}^3
-variable meff equal 1*4.0/3.0*3.141592653589*${reff}^3
-variable meff equal 1*4.0/3.0*3.141592653589*0.375^3
-variable min_mass equal ${density}*4.0/3.0*${PI}*${rlo}*${rlo}*${rlo}
-variable min_mass equal 1*4.0/3.0*${PI}*${rlo}*${rlo}*${rlo}
-variable min_mass equal 1*4.0/3.0*3.141592653589*${rlo}*${rlo}*${rlo}
-variable min_mass equal 1*4.0/3.0*3.141592653589*0.25*${rlo}*${rlo}
-variable min_mass equal 1*4.0/3.0*3.141592653589*0.25*0.25*${rlo}
-variable min_mass equal 1*4.0/3.0*3.141592653589*0.25*0.25*0.25
-variable max_mass equal ${density}*4.0/3.0*${PI}*${rhi}*${rhi}*${rhi}
-variable max_mass equal 1*4.0/3.0*${PI}*${rhi}*${rhi}*${rhi}
-variable max_mass equal 1*4.0/3.0*3.141592653589*${rhi}*${rhi}*${rhi}
-variable max_mass equal 1*4.0/3.0*3.141592653589*0.5*${rhi}*${rhi}
-variable max_mass equal 1*4.0/3.0*3.141592653589*0.5*0.5*${rhi}
-variable max_mass equal 1*4.0/3.0*3.141592653589*0.5*0.5*0.5
-
-## Typical way to set kn, kt, etc.:
-variable kn equal 4.0*${GShear}/(3*(1-${Poisson}))
-variable kn equal 4.0*38888.8888888889/(3*(1-${Poisson}))
-variable kn equal 4.0*38888.8888888889/(3*(1-0.285714285714286))
-variable kt equal 4.0*${GShear}/(2-${Poisson})
-variable kt equal 4.0*38888.8888888889/(2-${Poisson})
-variable kt equal 4.0*38888.8888888889/(2-0.285714285714286)
-
-variable a equal (-2.0*log(${coeffRes})/${PI})^2
-variable a equal (-2.0*log(0.1)/${PI})^2
-variable a equal (-2.0*log(0.1)/3.141592653589)^2
-variable gamma_n equal sqrt($a*2*${kn}/${min_mass}/(1+0.25*$a))
-variable gamma_n equal sqrt(0.405284734569556*2*${kn}/${min_mass}/(1+0.25*$a))
-variable gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/${min_mass}/(1+0.25*$a))
-variable gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/0.0654498469497708/(1+0.25*$a))
-variable gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/0.0654498469497708/(1+0.25*0.405284734569556))
-variable gamma_t equal ${gamma_n}*0.5
-variable gamma_t equal 903.503751814138*0.5
-
-variable tcol equal ${PI}/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
-variable tcol equal 3.141592653589/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
-variable tcol equal 3.141592653589/sqrt(2*72592.5925925926/${min_mass}-${gamma_n}/4.0)
-variable tcol equal 3.141592653589/sqrt(2*72592.5925925926/0.0654498469497708-${gamma_n}/4.0)
-variable tcol equal 3.141592653589/sqrt(2*72592.5925925926/0.0654498469497708-903.503751814138/4.0)
-
-variable dt equal ${tcol}*0.05
-variable dt equal 0.00210943016014969*0.05
-timestep ${dt}
-timestep 0.000105471508007485
-
-###############################################
-variable dumpfreq equal 1000
-variable logfreq equal 1000
-
-newton off
-atom_style sphere
-
-boundary p p f
-
-region boxreg block ${xlo} ${xhi} ${ylo} ${yhi} ${zlo} ${zhi}
-region boxreg block 10 ${xhi} ${ylo} ${yhi} ${zlo} ${zhi}
-region boxreg block 10 40 ${ylo} ${yhi} ${zlo} ${zhi}
-region boxreg block 10 40 10 ${yhi} ${zlo} ${zhi}
-region boxreg block 10 40 10 40 ${zlo} ${zhi}
-region boxreg block 10 40 10 40 -20 ${zhi}
-region boxreg block 10 40 10 40 -20 50
-create_box 1 boxreg
-Created orthogonal box = (10 10 -20) to (40 40 50)
- 1 by 1 by 4 MPI processor grid
-
-pair_style gran/hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
-pair_style gran/hertz/history 72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
-pair_style gran/hertz/history 72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1
-pair_style gran/hertz/history 72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1
-pair_style gran/hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1
-pair_style gran/hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1
-pair_coeff * *
-
-neighbor ${skin} bin
-neighbor 0.5 bin
-thermo ${logfreq}
-thermo 1000
-
-comm_style brick
-comm_modify mode multi group all vel yes
-balance 1.1 shift xyz 20 1.1
-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
- ghost atom cutoff = 0
- binsize = 30 -> bins = 1 1 3
-fix bal all balance 10000 1.1 shift xyz 20 1.01
-
-####################### Options specific to pouring #########################
-
-# insertion region for fix/pour
-
-region insreg cylinder z ${xc} ${yc} 10 30 50 side in units box
-region insreg cylinder z 25 ${yc} 10 30 50 side in units box
-region insreg cylinder z 25 25 10 30 50 side in units box
-
-# define cone and cylinder regions - see lammps doc on region command
-# note new open options
-
-region cylreg cylinder z ${xc} ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 2 #Top is open
-region cylreg cylinder z 25 ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 2
-region cylreg cylinder z 25 25 ${radconelo} ${zcyllo} ${zconelo} side in units box open 2
-region cylreg cylinder z 25 25 2 ${zcyllo} ${zconelo} side in units box open 2
-region cylreg cylinder z 25 25 2 0 ${zconelo} side in units box open 2
-region cylreg cylinder z 25 25 2 0 10 side in units box open 2
-
-region conereg cone z ${xc} ${yc} ${radconelo} ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2 #Bottom and top are open
-region conereg cone z 25 ${yc} ${radconelo} ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2
-region conereg cone z 25 25 ${radconelo} ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2
-region conereg cone z 25 25 2 ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2
-region conereg cone z 25 25 2 20 ${zconelo} ${zconehi} side in units box open 1 open 2
-region conereg cone z 25 25 2 20 10 ${zconehi} side in units box open 1 open 2
-region conereg cone z 25 25 2 20 10 50 side in units box open 1 open 2
-
-region hopreg union 2 conereg cylreg
-
-fix grav all gravity ${gravity} vector 0 0 -1
-fix grav all gravity 1 vector 0 0 -1
-fix 1 all nve/sphere
-
-
-fix hopper3 all wall/gran/region hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
-fix hopper3 all wall/gran/region hertz/history 72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
-fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
-fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1 region hopreg
-fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1 region hopreg
-fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1 region hopreg
-
-fix ins all pour 2000 1 42424 region insreg diam range ${dlo} ${dhi} dens ${density} ${density}
-fix ins all pour 2000 1 42424 region insreg diam range 0.5 ${dhi} dens ${density} ${density}
-fix ins all pour 2000 1 42424 region insreg diam range 0.5 1 dens ${density} ${density}
-fix ins all pour 2000 1 42424 region insreg diam range 0.5 1 dens 1 ${density}
-fix ins all pour 2000 1 42424 region insreg diam range 0.5 1 dens 1 1
-Particle insertion: 3000 every 59965 steps, 2000 by step 1
-
-#dump 1 all custom ${dumpfreq} ${name}.dump # id type mass diameter x y z
-
-#dump 2 all image 4000 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 zoom 3.0 # box no 0.0 axes no 0.0 0.0
-#dump_modify 2 pad 6
-
-thermo_style custom step cpu atoms ke
-WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:690)
-thermo_modify flush yes lost warn
-
-# Initial run to fill up the cone
-
-run 20000
-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 = 1.5
- ghost atom cutoff = 1.5
- binsize = 0.75 -> bins = 40 40 94
-Memory usage per processor = 2.99539 Mbytes
-Step CPU Atoms KinEng
- 0 0 0 -0
- 1000 0.53632808 2000 -0
- 2000 0.90599012 2000 -0
- 3000 1.2640941 2000 -0
- 4000 1.6225331 2000 -0
- 5000 1.9735272 2000 -0
- 6000 2.3156731 2000 -0
- 7000 2.6499262 2000 -0
- 8000 2.9751072 2000 -0
- 9000 3.2918322 2000 -0
- 10000 3.597712 2000 -0
- 11000 3.7157061 2000 -0
- 12000 3.833451 2000 -0
- 13000 3.9541111 2000 -0
- 14000 4.081727 2000 -0
- 15000 4.2142782 2000 -0
- 16000 4.3530872 2000 -0
- 17000 4.4987361 2000 -0
- 18000 4.6507492 2000 -0
- 19000 4.807373 2000 -0
- 20000 4.9710512 2000 -0
-Loop time of 4.97109 on 4 procs for 20000 steps with 2000 atoms
-
-98.5% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.067799 | 0.17326 | 0.37341 | 28.4 | 3.49
-Neigh | 0.013881 | 0.025808 | 0.045841 | 7.5 | 0.52
-Comm | 0.078163 | 0.1808 | 0.2915 | 21.0 | 3.64
-Output | 0.0011413 | 0.0027029 | 0.0036721 | 1.8 | 0.05
-Modify | 1.0146 | 1.8605 | 3.562 | 73.8 | 37.43
-Other | | 2.728 | | | 54.88
-
-Nlocal: 500 ave 505 max 493 min
-Histogram: 1 0 0 0 0 1 0 1 0 1
-Nghost: 159.25 ave 254 max 71 min
-Histogram: 1 0 0 1 0 1 0 0 0 1
-Neighs: 397.5 ave 616 max 214 min
-Histogram: 1 0 1 0 0 0 1 0 0 1
-
-Total # of neighbors = 1590
-Ave neighs/atom = 0.795
-Neighbor list builds = 69
-Dangerous builds = 0
-unfix ins
-run 150000
-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 = 1.49993
- ghost atom cutoff = 1.49993
- binsize = 0.749963 -> bins = 41 41 94
-Memory usage per processor = 9.39737 Mbytes
-Step CPU Atoms KinEng
- 20000 0 2000 6443.7665
- 21000 0.11240888 2000 6572.3531
- 22000 0.23014092 2000 6723.8376
- 23000 0.35371184 2000 6853.1812
- 24000 0.4838469 2000 6976.0209
- 25000 0.62193394 2000 7096.9955
- 26000 0.76781893 2000 7215.5795
- 27000 0.92212081 2000 7349.2382
- 28000 1.0841098 2000 7471.8719
- 29000 1.2593179 2000 7574.7988
- 30000 1.4459748 2000 7660.2353
- 31000 1.5759299 2000 7703.5736
- 32000 1.7189329 2000 7643.5299
- 33000 1.876133 2000 7520.14
- 34000 2.0453629 2000 7372.2247
- 35000 2.2281299 2000 7192.1638
- 36000 2.4208269 2000 6985.7056
- 37000 2.6258228 2000 6858.9422
- 38000 2.839473 2000 6717.0655
- 39000 3.065336 2000 6541.5809
- 40000 3.3090389 2000 6381.8513
- 41000 3.4969938 2000 6236.4297
- 42000 3.6888108 2000 6104.2528
- 43000 3.8874888 2000 5951.0314
- 44000 4.0956569 2000 5819.0972
- 45000 4.312974 2000 5620.6457
- 46000 4.5343778 2000 5479.332
- 47000 4.757262 2000 5295.328
- 48000 4.9850328 2000 5179.9559
- 49000 5.2210319 2000 5022.5562
- 50000 5.4699879 2000 4899.1332
- 51000 5.6774018 2000 4699.4456
- 52000 5.8900218 2000 4522.5719
- 53000 6.110677 2000 4402.8664
- 54000 6.3361218 2000 4256.1664
- 55000 6.5778289 2000 4093.6265
- 56000 6.8319149 2000 3933.0179
- 57000 7.0925779 2000 3738.4628
- 58000 7.3578169 2000 3535.7866
- 59000 7.6344049 2000 3298.4079
- 60000 7.9258108 2000 3058.9356
- 61000 8.1758959 2000 2888.0074
- 62000 8.4278228 2000 2652.4613
- 63000 8.6815088 2000 2435.0991
- 64000 8.9371588 2000 2147.9441
- 65000 9.208025 2000 1898.0657
- 66000 9.4795358 2000 1650.5794
- 67000 9.7519388 2000 1425.7284
- 68000 10.025867 2000 1193.3786
- 69000 10.313816 2000 940.55767
- 70000 10.610488 2000 761.5312
- 71000 10.879718 2000 599.1989
- 72000 11.154029 2000 453.25929
- 73000 11.424376 2000 345.73222
- 74000 11.697359 2000 273.72167
- 75000 11.966099 2000 222.44251
- 76000 12.230213 2000 190.79993
- 77000 12.481982 2000 157.71153
- 78000 12.73433 2000 131.99208
- 79000 12.986017 2000 111.10589
- 80000 13.243904 2000 96.736337
- 81000 13.500538 2000 81.24169
- 82000 13.765755 2000 66.640863
- 83000 14.032985 2000 53.07725
- 84000 14.308284 2000 45.942738
- 85000 14.586721 2000 38.811918
- 86000 14.861759 2000 34.59113
- 87000 15.135665 2000 31.04487
- 88000 15.417487 2000 27.659144
- 89000 15.698281 2000 24.596119
- 90000 15.97969 2000 22.004865
- 91000 16.266118 2000 20.541665
- 92000 16.557007 2000 18.938077
- 93000 16.846745 2000 17.293956
- 94000 17.133408 2000 16.443596
- 95000 17.42023 2000 15.518083
- 96000 17.709025 2000 14.264343
- 97000 18.001337 2000 13.410217
- 98000 18.292414 2000 13.036621
- 99000 18.583887 2000 12.523214
- 100000 18.880312 2000 12.371509
- 101000 19.176964 2000 11.828077
- 102000 19.474371 2000 11.510333
- 103000 19.770957 2000 11.289304
- 104000 20.070744 2000 10.370661
- 105000 20.372617 2000 10.217921
- 106000 20.673949 2000 9.3275222
- 107000 20.9765 2000 8.9156372
- 108000 21.276062 2000 8.5850821
- 109000 21.585305 2000 8.5326934
- 110000 21.89079 2000 8.0579504
- 111000 22.194207 2000 8.1084595
- 112000 22.501593 2000 7.9190174
- 113000 22.81251 2000 8.0127499
- 114000 23.118514 2000 8.1791911
- 115000 23.432862 2000 8.3333032
- 116000 23.735549 2000 8.4833817
- 117000 24.038329 2000 8.315498
- 118000 24.343247 2000 7.9460007
- 119000 24.643288 2000 7.5922134
- 120000 24.94731 2000 7.4089143
- 121000 25.253605 2000 7.5790659
- 122000 25.56672 2000 7.3778204
- 123000 25.870958 2000 7.1384456
- 124000 26.180729 2000 6.9151887
- 125000 26.493089 2000 6.4671685
- 126000 26.806734 2000 5.6773128
- 127000 27.10969 2000 5.5603057
- 128000 27.410973 2000 5.6376136
- 129000 27.712398 2000 5.5578044
- 130000 28.015943 2000 5.4632646
- 131000 28.319002 2000 4.9669466
- 132000 28.620558 2000 5.0191026
- 133000 28.923233 2000 4.7146653
- 134000 29.235178 2000 4.4835803
- 135000 29.542816 2000 4.5469703
- 136000 29.8518 2000 4.3349926
- 137000 30.159096 2000 4.423031
- 138000 30.464283 2000 4.3680646
- 139000 30.769279 2000 4.2461787
- 140000 31.074457 2000 4.4140001
- 141000 31.380334 2000 4.3991236
- 142000 31.683855 2000 4.572989
- 143000 31.987308 2000 4.7601702
- 144000 32.28998 2000 4.7790587
- 145000 32.594971 2000 4.8127728
- 146000 32.89855 2000 4.8750003
- 147000 33.205142 2000 4.9830109
- 148000 33.509096 2000 4.9960037
- 149000 33.812951 2000 5.2151503
- 150000 34.117585 2000 5.2745187
- 151000 34.420995 2000 4.8959892
- 152000 34.725788 2000 4.7600627
- 153000 35.032001 2000 4.6944719
- 154000 35.337093 2000 4.7647384
- 155000 35.645299 2000 4.312228
- 156000 35.953225 2000 3.8513036
- 157000 36.258107 2000 3.8798947
- 158000 36.570122 2000 3.7116749
- 159000 36.880424 2000 3.7246469
- 160000 37.187331 2000 3.8165318
- 161000 37.491939 2000 3.8954595
- 162000 37.806365 2000 4.0109691
- 163000 38.122006 2000 3.3864369
- 164000 38.437246 2000 3.4533589
- 165000 38.753073 2000 3.4967205
- 166000 39.068713 2000 3.5758702
- 167000 39.376388 2000 2.8913997
- 168000 39.685628 2000 2.507523
- 169000 39.99294 2000 2.4910068
- 170000 40.302393 2000 2.4992886
-Loop time of 40.3024 on 4 procs for 150000 steps with 2000 atoms
-
-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 | 7.9352 | 13.451 | 15.947 | 88.7 | 33.37
-Neigh | 0.15394 | 0.23292 | 0.28243 | 10.0 | 0.58
-Comm | 2.1471 | 3.534 | 4.4671 | 47.3 | 8.77
-Output | 0.0070386 | 0.011774 | 0.021483 | 5.4 | 0.03
-Modify | 10.816 | 14.404 | 16.047 | 55.2 | 35.74
-Other | | 8.669 | | | 21.51
-
-Nlocal: 500 ave 542 max 430 min
-Histogram: 1 0 0 0 0 0 1 0 1 1
-Nghost: 449.5 ave 679 max 208 min
-Histogram: 1 0 0 0 1 0 1 0 0 1
-Neighs: 4506.75 ave 5611 max 3508 min
-Histogram: 1 0 1 0 0 0 1 0 0 1
-
-Total # of neighbors = 18027
-Ave neighs/atom = 9.0135
-Neighbor list builds = 386
-Dangerous builds = 0
-
-# remove "plug" - need to redefine cylinder region & union
-
-region cylreg delete
-region hopreg delete
-region cylreg cylinder z ${xc} ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 1 open 2 #Bottom & top are open
-region cylreg cylinder z 25 ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 1 open 2
-region cylreg cylinder z 25 25 ${radconelo} ${zcyllo} ${zconelo} side in units box open 1 open 2
-region cylreg cylinder z 25 25 2 ${zcyllo} ${zconelo} side in units box open 1 open 2
-region cylreg cylinder z 25 25 2 0 ${zconelo} side in units box open 1 open 2
-region cylreg cylinder z 25 25 2 0 10 side in units box open 1 open 2
-
-region hopreg union 2 cylreg conereg
-
-unfix hopper3
-fix hopper3 all wall/gran/region hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
-fix hopper3 all wall/gran/region hertz/history 72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
-fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
-fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1 region hopreg
-fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1 region hopreg
-fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1 region hopreg
-
-run 100000
-Memory usage per processor = 9.41929 Mbytes
-Step CPU Atoms KinEng
- 170000 0 2000 2.4992886
- 171000 0.30864286 2000 3.6052039
- 172000 0.62273479 2000 4.8584577
- 173000 0.94411087 2000 6.5620833
- 174000 1.2588799 2000 8.8636423
- 175000 1.574302 2000 11.743197
- 176000 1.888201 2000 15.60405
- 177000 2.1948938 2000 20.29426
- 178000 2.508261 2000 25.069266
- 179000 2.8257489 2000 31.340924
- 180000 3.1444538 2000 38.454779
- 181000 3.4541628 2000 46.488676
- 182000 3.7632799 2000 55.279578
- 183000 4.0711808 2000 65.192327
- 184000 4.386853 2000 75.466011
- 185000 4.7000408 2000 86.06934
- 186000 5.00436 2000 97.157035
- 187000 5.3041189 2000 108.92242
- 188000 5.601872 2000 120.88599
- 189000 5.9027078 2000 134.09884
- 190000 6.2037618 2000 148.60143
- 191000 6.4879329 2000 163.96898
- 192000 6.7703898 2000 180.32931
- 193000 7.0603459 2000 198.83575
- 194000 7.3395619 2000 217.46631
- 195000 7.6245389 2000 235.34916
- 196000 7.911685 2000 253.61893
- 197000 8.1976559 2000 271.3908
- 198000 8.483418 2000 289.60064
- 199000 8.7664149 2000 309.44306
- 200000 9.0593698 2000 331.9367
- 201000 9.3373818 2000 354.86646
- 202000 9.612149 2000 380.56766
- 203000 9.8876739 2000 406.97399
- 204000 10.152671 2000 435.69917
- 205000 10.415859 2000 465.1954
- 206000 10.67967 2000 494.6045
- 207000 10.941435 2000 522.71704
- 208000 11.205367 2000 550.56072
- 209000 11.471415 2000 580.10547
- 210000 11.738137 2000 610.36222
- 211000 12.006432 2000 641.99128
- 212000 12.270102 2000 676.0736
- 213000 12.531937 2000 711.70118
- 214000 12.797442 2000 747.84561
- 215000 13.062646 2000 785.59575
- 216000 13.33019 2000 826.36549
- 217000 13.598467 2000 868.35085
- 218000 13.863022 2000 911.07041
- 219000 14.127777 2000 953.70251
- 220000 14.391496 2000 997.5717
- 221000 14.655347 2000 1043.5565
- 222000 14.923357 2000 1090.7944
- 223000 15.193349 2000 1140.1324
- 224000 15.462326 2000 1190.6956
- 225000 15.729748 1999 1238.1536
- 226000 15.996867 1998 1286.8076
- 227000 16.261762 1995 1326.9895
- 228000 16.527382 1989 1349.5997
- 229000 16.788356 1984 1370.593
- 230000 17.05426 1968 1344.3763
- 231000 17.320126 1962 1363.7958
- 232000 17.58387 1949 1340.1482
- 233000 17.850221 1940 1348.409
- 234000 18.116595 1929 1335.9703
- 235000 18.383276 1918 1328.201
- 236000 18.650066 1905 1309.6469
- 237000 18.916963 1896 1292.9758
- 238000 19.185209 1884 1266.3598
- 239000 19.453402 1872 1221.0069
- 240000 19.722178 1855 1166.1488
- 241000 19.98987 1842 1126.9482
- 242000 20.257783 1828 1107.128
- 243000 20.523743 1815 1060.6573
- 244000 20.793404 1805 1026.0259
- 245000 21.061462 1797 1009.4924
- 246000 21.325574 1790 995.26136
- 247000 21.587046 1782 976.04886
- 248000 21.840234 1778 989.11589
- 249000 22.09455 1762 903.62508
- 250000 22.356228 1748 852.03257
- 251000 22.602243 1738 807.41049
- 252000 22.852106 1722 738.82529
- 253000 23.097209 1712 706.05657
- 254000 23.341263 1696 626.53135
- 255000 23.58614 1692 613.89548
- 256000 23.83122 1686 598.9367
- 257000 24.076937 1683 589.27487
- 258000 24.321166 1681 591.42793
- 259000 24.566143 1678 595.25383
- 260000 24.820743 1677 617.50379
- 261000 25.057835 1675 623.39319
- 262000 25.294068 1673 627.08829
- 263000 25.526724 1669 623.52963
- 264000 25.766729 1667 626.44957
- 265000 26.005453 1664 631.58936
- 266000 26.244549 1660 605.22452
- 267000 26.478879 1657 611.76935
- 268000 26.71252 1655 611.73538
- 269000 26.951368 1652 624.58227
- 270000 27.186447 1648 625.97446
-Loop time of 27.1865 on 4 procs for 100000 steps with 1648 atoms
-
-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 | 4.6257 | 9.631 | 13.049 | 100.0 | 35.43
-Neigh | 0.1522 | 0.17549 | 0.19588 | 4.3 | 0.65
-Comm | 1.5797 | 2.7289 | 3.602 | 48.7 | 10.04
-Output | 0.0014181 | 0.007208 | 0.016675 | 6.8 | 0.03
-Modify | 7.7129 | 9.0949 | 10.256 | 31.9 | 33.45
-Other | | 5.549 | | | 20.41
-
-Nlocal: 412 ave 436 max 388 min
-Histogram: 1 1 0 0 0 0 0 0 1 1
-Nghost: 391 ave 629 max 158 min
-Histogram: 1 0 0 1 0 1 0 0 0 1
-Neighs: 3406 ave 4479 max 2040 min
-Histogram: 1 0 0 0 1 0 0 1 0 1
-
-Total # of neighbors = 13624
-Ave neighs/atom = 8.26699
-Neighbor list builds = 260
-Dangerous builds = 0
-Total wall time: 0:01:12
diff --git a/examples/granregion/log.6Oct16.granregion.mixer.g++.1 b/examples/granregion/log.6Oct16.granregion.mixer.g++.1
deleted file mode 100644
index 3cfa3eb0fc..0000000000
--- a/examples/granregion/log.6Oct16.granregion.mixer.g++.1
+++ /dev/null
@@ -1,609 +0,0 @@
-LAMMPS (5 Oct 2016)
-variable name string mixer
-
-thermo_modify flush yes
-variable seed equal 14314
-
-###############################################
-# Particle parameters
-################################################
-
-variable rlo equal 0.3
-variable rhi equal 0.6
-variable dlo equal 2.0*${rlo}
-variable dlo equal 2.0*0.3
-variable dhi equal 2.0*${rhi}
-variable dhi equal 2.0*0.6
-variable skin equal ${rhi}
-variable skin equal 0.6
-
-variable coeffRes equal 0.1
-variable coeffFric equal 0.5
-
-variable kn equal 10^5
-variable kt equal 0.2*${kn}
-variable kt equal 0.2*100000
-
-variable gravity equal 1.0
-variable density equal 1.0
-
-variable min_mass equal ${density}*4.0/3.0*PI*${rlo}*${rlo}*${rlo}
-variable min_mass equal 1*4.0/3.0*PI*${rlo}*${rlo}*${rlo}
-variable min_mass equal 1*4.0/3.0*PI*0.3*${rlo}*${rlo}
-variable min_mass equal 1*4.0/3.0*PI*0.3*0.3*${rlo}
-variable min_mass equal 1*4.0/3.0*PI*0.3*0.3*0.3
-variable a equal (-2.0*log(${coeffRes})/PI)^2
-variable a equal (-2.0*log(0.1)/PI)^2
-variable gamma_n equal sqrt($a*2*${kn}/${min_mass}/(1+0.25*$a))
-variable gamma_n equal sqrt(0.405284734569351*2*${kn}/${min_mass}/(1+0.25*$a))
-variable gamma_n equal sqrt(0.405284734569351*2*100000/${min_mass}/(1+0.25*$a))
-variable gamma_n equal sqrt(0.405284734569351*2*100000/0.113097335529233/(1+0.25*$a))
-variable gamma_n equal sqrt(0.405284734569351*2*100000/0.113097335529233/(1+0.25*0.405284734569351))
-variable gamma_t equal ${gamma_n}*0.5
-variable gamma_t equal 806.699778405191*0.5
-
-variable tcol equal PI/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
-variable tcol equal PI/sqrt(2*100000/${min_mass}-${gamma_n}/4.0)
-variable tcol equal PI/sqrt(2*100000/0.113097335529233-${gamma_n}/4.0)
-variable tcol equal PI/sqrt(2*100000/0.113097335529233-806.699778405191/4.0)
-
-variable dt equal ${tcol}*0.02
-variable dt equal 0.00236257621510454*0.02
-timestep ${dt}
-timestep 4.72515243020908e-05
-
-###############################################
-
-variable dumpfreq equal 1000
-variable logfreq equal 1000
-
-newton on
-atom_style sphere
-
-boundary p p f
-
-region boxreg block 0 20 0 20 0 20
-create_box 1 boxreg
-Created orthogonal box = (0 0 0) to (20 20 20)
- 1 by 1 by 1 MPI processor grid
-
-pair_style gran/hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
-pair_style gran/hertz/history 100000 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
-pair_style gran/hertz/history 100000 20000 ${gamma_n} ${gamma_t} ${coeffFric} 1
-pair_style gran/hertz/history 100000 20000 806.699778405191 ${gamma_t} ${coeffFric} 1
-pair_style gran/hertz/history 100000 20000 806.699778405191 403.349889202595 ${coeffFric} 1
-pair_style gran/hertz/history 100000 20000 806.699778405191 403.349889202595 0.5 1
-pair_coeff * *
-
-neighbor ${skin} bin
-neighbor 0.6 bin
-thermo ${logfreq}
-thermo 1000
-
-comm_style brick
-comm_modify mode multi group all vel yes
-balance 1.1 shift xyz 20 1.1
-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
- ghost atom cutoff = 0
- binsize = 20 -> bins = 1 1 1
-fix bal all balance 10000 1.1 shift xyz 20 1.01
-
-####################### Options specific to pouring #########################
-
-region insreg cylinder z 10 10 8 10 18 side in units box
-region cylreg cylinder z 10 10 10 0 20 side in units box
-
-variable theta equal (step/400000)*2*PI
-
-region b1 block 2 18 9 11 0 4 side out rotate v_theta 10 10 0 0 0 1 units box
-region b2 block 9 11 2 18 0 3.99999 side out rotate v_theta 10 10 0 0 0 1 units box
-
-region mixer intersect 3 cylreg b1 b2 side in
-
-fix grav all gravity ${gravity} vector 0 0 -1
-fix grav all gravity 1 vector 0 0 -1
-fix 1 all nve/sphere
-
-fix mixwall all wall/gran/region hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
-fix mixwall all wall/gran/region hertz/history 100000 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
-fix mixwall all wall/gran/region hertz/history 100000 20000 ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
-fix mixwall all wall/gran/region hertz/history 100000 20000 806.699778405191 ${gamma_t} ${coeffFric} 1 region mixer
-fix mixwall all wall/gran/region hertz/history 100000 20000 806.699778405191 403.349889202595 ${coeffFric} 1 region mixer
-fix mixwall all wall/gran/region hertz/history 100000 20000 806.699778405191 403.349889202595 0.5 1 region mixer
-
-fix ins all pour 1000 1 42424 region insreg diam range ${dlo} ${dhi} dens ${density} ${density}
-fix ins all pour 1000 1 42424 region insreg diam range 0.6 ${dhi} dens ${density} ${density}
-fix ins all pour 1000 1 42424 region insreg diam range 0.6 1.2 dens ${density} ${density}
-fix ins all pour 1000 1 42424 region insreg diam range 0.6 1.2 dens 1 ${density}
-fix ins all pour 1000 1 42424 region insreg diam range 0.6 1.2 dens 1 1
-Particle insertion: 444 every 84653 steps, 1000 by step 169307
-
-#dump 1 all custom ${dumpfreq} ${name}_pour.dump # id type mass diameter x y z
-
-#dump 2 all image 4000 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 zoom 1.5 # box no 0.0 axes no 0.0 0.0
-#dump_modify 2 pad 6
-
-thermo_style custom step cpu atoms ke v_theta
-WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:690)
-thermo_modify flush yes lost warn
-
-run 200000
-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 = 1.8
- ghost atom cutoff = 1.8
- binsize = 0.9 -> bins = 23 23 23
-Memory usage per processor = 2.80779 Mbytes
-Step CPU Atoms KinEng v_theta
- 0 0 0 -0 0
- 1000 0.16771817 444 -0 0.015707963
- 2000 0.33019304 444 -0 0.031415927
- 3000 0.4894321 444 -0 0.04712389
- 4000 0.64879322 444 -0 0.062831853
- 5000 0.80816507 444 -0 0.078539816
- 6000 0.96711302 444 -0 0.09424778
- 7000 1.1265812 444 -0 0.10995574
- 8000 1.286129 444 -0 0.12566371
- 9000 1.445487 444 -0 0.14137167
- 10000 1.6056392 444 -0 0.15707963
- 11000 1.7650061 444 -0 0.1727876
- 12000 1.9249642 444 -0 0.18849556
- 13000 2.0851831 444 -0 0.20420352
- 14000 2.244523 444 -0 0.21991149
- 15000 2.4043641 444 -0 0.23561945
- 16000 2.5638251 444 -0 0.25132741
- 17000 2.7155962 444 -0 0.26703538
- 18000 2.866904 444 -0 0.28274334
- 19000 3.0188181 444 -0 0.2984513
- 20000 3.17047 444 -0 0.31415927
- 21000 3.3214712 444 -0 0.32986723
- 22000 3.472692 444 -0 0.34557519
- 23000 3.6240032 444 -0 0.36128316
- 24000 3.7753551 444 -0 0.37699112
- 25000 3.926239 444 -0 0.39269908
- 26000 4.0782132 444 -0 0.40840704
- 27000 4.2301712 444 -0 0.42411501
- 28000 4.382267 444 -0 0.43982297
- 29000 4.5339992 444 -0 0.45553093
- 30000 4.6860211 444 -0 0.4712389
- 31000 4.8376751 444 -0 0.48694686
- 32000 4.989748 444 -0 0.50265482
- 33000 5.1418142 444 -0 0.51836279
- 34000 5.294476 444 -0 0.53407075
- 35000 5.4472861 444 -0 0.54977871
- 36000 5.5999811 444 -0 0.56548668
- 37000 5.7526181 444 -0 0.58119464
- 38000 5.9061031 444 -0 0.5969026
- 39000 6.0593271 444 -0 0.61261057
- 40000 6.2123802 444 -0 0.62831853
- 41000 6.3652351 444 -0 0.64402649
- 42000 6.5186551 444 -0 0.65973446
- 43000 6.672132 444 -0 0.67544242
- 44000 6.8245611 444 -0 0.69115038
- 45000 6.9778051 444 -0 0.70685835
- 46000 7.131258 444 -0 0.72256631
- 47000 7.2841291 444 -0 0.73827427
- 48000 7.4379101 444 -0 0.75398224
- 49000 7.5915 444 -0 0.7696902
- 50000 7.7461231 444 -0 0.78539816
- 51000 7.9047191 444 -0 0.80110613
- 52000 8.0634432 444 -0 0.81681409
- 53000 8.2226322 444 -0 0.83252205
- 54000 8.3817451 444 -0 0.84823002
- 55000 8.5419021 444 -0 0.86393798
- 56000 8.701194 444 -0 0.87964594
- 57000 8.8613491 444 -0 0.89535391
- 58000 9.0211501 444 -0 0.91106187
- 59000 9.180917 444 -0 0.92676983
- 60000 9.341964 444 -0 0.9424778
- 61000 9.5026722 444 -0 0.95818576
- 62000 9.6630561 444 -0 0.97389372
- 63000 9.8236201 444 -0 0.98960169
- 64000 9.9854801 444 -0 1.0053096
- 65000 10.148318 444 -0 1.0210176
- 66000 10.311267 444 -0 1.0367256
- 67000 10.476498 444 -0 1.0524335
- 68000 10.640768 444 -0 1.0681415
- 69000 10.804709 444 -0 1.0838495
- 70000 10.969271 444 -0 1.0995574
- 71000 11.133451 444 -0 1.1152654
- 72000 11.299253 444 -0 1.1309734
- 73000 11.463999 444 -0 1.1466813
- 74000 11.62903 444 -0 1.1623893
- 75000 11.795109 444 -0 1.1780972
- 76000 11.962154 444 -0 1.1938052
- 77000 12.1292 444 -0 1.2095132
- 78000 12.298106 444 -0 1.2252211
- 79000 12.46744 444 -0 1.2409291
- 80000 12.637916 444 -0 1.2566371
- 81000 12.808494 444 -0 1.272345
- 82000 12.97813 444 -0 1.288053
- 83000 13.149135 444 -0 1.303761
- 84000 13.32082 444 -0 1.3194689
- 85000 13.56205 888 -0 1.3351769
- 86000 13.908699 888 -0 1.3508848
- 87000 14.254615 888 -0 1.3665928
- 88000 14.600851 888 -0 1.3823008
- 89000 14.946295 888 -0 1.3980087
- 90000 15.291315 888 -0 1.4137167
- 91000 15.637396 888 -0 1.4294247
- 92000 15.981426 888 -0 1.4451326
- 93000 16.327519 888 -0 1.4608406
- 94000 16.675434 888 -0 1.4765485
- 95000 17.023515 888 -0 1.4922565
- 96000 17.372152 888 -0 1.5079645
- 97000 17.719346 888 -0 1.5236724
- 98000 18.067159 888 -0 1.5393804
- 99000 18.414599 888 -0 1.5550884
- 100000 18.764775 888 -0 1.5707963
- 101000 19.114239 888 -0 1.5865043
- 102000 19.464285 888 -0 1.6022123
- 103000 19.813956 888 -0 1.6179202
- 104000 20.163276 888 -0 1.6336282
- 105000 20.553808 888 -0 1.6493361
- 106000 20.904093 888 -0 1.6650441
- 107000 21.25918 888 -0 1.6807521
- 108000 21.615056 888 -0 1.69646
- 109000 21.971067 888 -0 1.712168
- 110000 22.326407 888 -0 1.727876
- 111000 22.68062 888 -0 1.7435839
- 112000 23.03653 888 -0 1.7592919
- 113000 23.39161 888 -0 1.7749998
- 114000 23.751273 888 -0 1.7907078
- 115000 24.106946 888 -0 1.8064158
- 116000 24.461182 888 -0 1.8221237
- 117000 24.797533 888 -0 1.8378317
- 118000 25.133924 888 -0 1.8535397
- 119000 25.472617 888 -0 1.8692476
- 120000 25.810786 888 -0 1.8849556
- 121000 26.147399 888 -0 1.9006636
- 122000 26.485868 888 -0 1.9163715
- 123000 26.82395 888 -0 1.9320795
- 124000 27.162345 888 -0 1.9477874
- 125000 27.501503 888 -0 1.9634954
- 126000 27.843318 888 -0 1.9792034
- 127000 28.183379 888 -0 1.9949113
- 128000 28.525406 888 -0 2.0106193
- 129000 28.869601 888 -0 2.0263273
- 130000 29.216232 888 -0 2.0420352
- 131000 29.562432 888 -0 2.0577432
- 132000 29.95624 888 -0 2.0734512
- 133000 30.308919 888 -0 2.0891591
- 134000 30.662184 888 -0 2.1048671
- 135000 31.015509 888 -0 2.120575
- 136000 31.366132 888 -0 2.136283
- 137000 31.71887 888 -0 2.151991
- 138000 32.0723 888 -0 2.1676989
- 139000 32.428657 888 -0 2.1834069
- 140000 32.781484 888 -0 2.1991149
- 141000 33.133593 888 -0 2.2148228
- 142000 33.487376 888 -0 2.2305308
- 143000 33.838656 888 -0 2.2462387
- 144000 34.188723 888 -0 2.2619467
- 145000 34.540083 888 -0 2.2776547
- 146000 34.895624 888 -0 2.2933626
- 147000 35.25153 888 -0 2.3090706
- 148000 35.607482 888 -0 2.3247786
- 149000 35.9642 888 -0 2.3404865
- 150000 36.321759 888 -0 2.3561945
- 151000 36.667172 888 -0 2.3719025
- 152000 37.013822 888 -0 2.3876104
- 153000 37.362735 888 -0 2.4033184
- 154000 37.712576 888 -0 2.4190263
- 155000 38.063528 888 -0 2.4347343
- 156000 38.414666 888 -0 2.4504423
- 157000 38.766119 888 -0 2.4661502
- 158000 39.115828 888 -0 2.4818582
- 159000 39.470874 888 -0 2.4975662
- 160000 39.827871 888 -0 2.5132741
- 161000 40.184885 888 -0 2.5289821
- 162000 40.543838 888 -0 2.54469
- 163000 40.901814 888 -0 2.560398
- 164000 41.258631 888 -0 2.576106
- 165000 41.619086 888 -0 2.5918139
- 166000 41.977332 888 -0 2.6075219
- 167000 42.33775 888 -0 2.6232299
- 168000 42.701344 888 -0 2.6389378
- 169000 43.067663 888 -0 2.6546458
- 170000 43.461687 1000 -0 2.6703538
- 171000 43.866086 1000 -0 2.6860617
- 172000 44.271406 1000 -0 2.7017697
- 173000 44.677085 1000 -0 2.7174776
- 174000 45.082441 1000 -0 2.7331856
- 175000 45.491593 1000 -0 2.7488936
- 176000 45.903002 1000 -0 2.7646015
- 177000 46.315031 1000 -0 2.7803095
- 178000 46.726531 1000 -0 2.7960175
- 179000 47.140818 1000 -0 2.8117254
- 180000 47.553784 1000 -0 2.8274334
- 181000 47.964021 1000 -0 2.8431414
- 182000 48.376739 1000 -0 2.8588493
- 183000 48.789612 1000 -0 2.8745573
- 184000 49.204073 1000 -0 2.8902652
- 185000 49.642401 1000 -0 2.9059732
- 186000 50.083479 1000 -0 2.9216812
- 187000 50.523357 1000 -0 2.9373891
- 188000 50.963685 1000 -0 2.9530971
- 189000 51.404166 1000 -0 2.9688051
- 190000 51.849094 1000 -0 2.984513
- 191000 52.291805 1000 -0 3.000221
- 192000 52.731855 1000 -0 3.0159289
- 193000 53.174104 1000 -0 3.0316369
- 194000 53.619739 1000 -0 3.0473449
- 195000 54.061019 1000 -0 3.0630528
- 196000 54.501149 1000 -0 3.0787608
- 197000 54.940486 1000 -0 3.0944688
- 198000 55.381843 1000 -0 3.1101767
- 199000 55.822243 1000 -0 3.1258847
- 200000 56.264319 1000 -0 3.1415927
-Loop time of 56.2643 on 1 procs for 200000 steps with 1000 atoms
-
-Performance: 14511.970 tau/day, 3554.650 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 | 4.6309 | 4.6309 | 4.6309 | 0.0 | 8.23
-Neigh | 0.071456 | 0.071456 | 0.071456 | 0.0 | 0.13
-Comm | 0.50064 | 0.50064 | 0.50064 | 0.0 | 0.89
-Output | 0.0039163 | 0.0039163 | 0.0039163 | 0.0 | 0.01
-Modify | 50.189 | 50.189 | 50.189 | 0.0 | 89.20
-Other | | 0.8688 | | | 1.54
-
-Nlocal: 1000 ave 1000 max 1000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 183 ave 183 max 183 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 3926 ave 3926 max 3926 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 3926
-Ave neighs/atom = 3.926
-Neighbor list builds = 217
-Dangerous builds = 0
-unfix ins
-run 200000
-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 = 1.79826
- ghost atom cutoff = 1.79826
- binsize = 0.899132 -> bins = 23 23 23
-Memory usage per processor = 8.62017 Mbytes
-Step CPU Atoms KinEng v_theta
- 200000 0 1000 0.90078559 3.1415927
- 201000 0.44072509 1000 0.90377135 3.1573006
- 202000 0.8800211 1000 0.89194106 3.1730086
- 203000 1.3210881 1000 0.8940532 3.1887165
- 204000 1.762887 1000 0.8967696 3.2044245
- 205000 2.2080901 1000 0.89758718 3.2201325
- 206000 2.6548181 1000 0.89434418 3.2358404
- 207000 3.1002531 1000 0.87633906 3.2515484
- 208000 3.547334 1000 0.86721615 3.2672564
- 209000 3.993988 1000 0.86214817 3.2829643
- 210000 4.4423161 1000 0.85463743 3.2986723
- 211000 4.889446 1000 0.85744914 3.3143802
- 212000 5.3357229 1000 0.84702799 3.3300882
- 213000 5.780273 1000 0.84375104 3.3457962
- 214000 6.2249129 1000 0.83820701 3.3615041
- 215000 6.670651 1000 0.83566708 3.3772121
- 216000 7.113143 1000 0.83620798 3.3929201
- 217000 7.5359521 1000 0.83581605 3.408628
- 218000 7.9623129 1000 0.84045719 3.424336
- 219000 8.3878851 1000 0.85410521 3.440044
- 220000 8.8153811 1000 0.84336839 3.4557519
- 221000 9.244349 1000 0.85145747 3.4714599
- 222000 9.6728511 1000 0.8476916 3.4871678
- 223000 10.104052 1000 0.8412701 3.5028758
- 224000 10.532736 1000 0.8390277 3.5185838
- 225000 10.959564 1000 0.8359107 3.5342917
- 226000 11.38617 1000 0.83920631 3.5499997
- 227000 11.814104 1000 0.83930526 3.5657077
- 228000 12.241758 1000 0.83152308 3.5814156
- 229000 12.67198 1000 0.81211079 3.5971236
- 230000 13.101597 1000 0.80395018 3.6128316
- 231000 13.532943 1000 0.79991397 3.6285395
- 232000 13.969412 1000 0.80828959 3.6442475
- 233000 14.403885 1000 0.80892923 3.6599554
- 234000 14.833452 1000 0.82048914 3.6756634
- 235000 15.266211 1000 0.8174713 3.6913714
- 236000 15.697822 1000 0.81898551 3.7070793
- 237000 16.133023 1000 0.82034714 3.7227873
- 238000 16.569559 1000 0.81950728 3.7384953
- 239000 17.006308 1000 0.82152915 3.7542032
- 240000 17.445493 1000 0.83217597 3.7699112
- 241000 17.885585 1000 0.83464253 3.7856191
- 242000 18.324268 1000 0.84326166 3.8013271
- 243000 18.763748 1000 0.84235055 3.8170351
- 244000 19.203869 1000 0.83325408 3.832743
- 245000 19.645 1000 0.82577315 3.848451
- 246000 20.08666 1000 0.83923456 3.864159
- 247000 20.530596 1000 0.84153419 3.8798669
- 248000 20.971984 1000 0.85768309 3.8955749
- 249000 21.413571 1000 0.86910799 3.9112829
- 250000 21.854153 1000 0.8775521 3.9269908
- 251000 22.302884 1000 0.87299296 3.9426988
- 252000 22.753789 1000 0.86613861 3.9584067
- 253000 23.202458 1000 0.85513456 3.9741147
- 254000 23.655372 1000 0.84629733 3.9898227
- 255000 24.108225 1000 0.84154885 4.0055306
- 256000 24.561535 1000 0.84162715 4.0212386
- 257000 25.012338 1000 0.83959672 4.0369466
- 258000 25.466506 1000 0.83577695 4.0526545
- 259000 25.919168 1000 0.83021368 4.0683625
- 260000 26.37215 1000 0.81106893 4.0840704
- 261000 26.823834 1000 0.79884608 4.0997784
- 262000 27.276505 1000 0.78360303 4.1154864
- 263000 27.728503 1000 0.77030843 4.1311943
- 264000 28.181969 1000 0.76127974 4.1469023
- 265000 28.636329 1000 0.75553065 4.1626103
- 266000 29.090593 1000 0.75332019 4.1783182
- 267000 29.549547 1000 0.74670528 4.1940262
- 268000 30.008774 1000 0.74216141 4.2097342
- 269000 30.463826 1000 0.74564756 4.2254421
- 270000 30.920159 1000 0.7416035 4.2411501
- 271000 31.377192 1000 0.73061389 4.256858
- 272000 31.836268 1000 0.71620113 4.272566
- 273000 32.291662 1000 0.70840181 4.288274
- 274000 32.743646 1000 0.70946906 4.3039819
- 275000 33.197723 1000 0.70418049 4.3196899
- 276000 33.651405 1000 0.69591327 4.3353979
- 277000 34.106289 1000 0.69499716 4.3511058
- 278000 34.564324 1000 0.69242545 4.3668138
- 279000 35.020887 1000 0.69690811 4.3825218
- 280000 35.478222 1000 0.70402124 4.3982297
- 281000 35.938226 1000 0.71936578 4.4139377
- 282000 36.39808 1000 0.72439386 4.4296456
- 283000 36.855587 1000 0.72221632 4.4453536
- 284000 37.309629 1000 0.70387029 4.4610616
- 285000 37.791869 1000 0.70505716 4.4767695
- 286000 38.277853 1000 0.70731734 4.4924775
- 287000 38.764774 1000 0.71149743 4.5081855
- 288000 39.24815 1000 0.70994023 4.5238934
- 289000 39.728005 1000 0.69794225 4.5396014
- 290000 40.206798 1000 0.6905751 4.5553093
- 291000 40.678802 1000 0.68652972 4.5710173
- 292000 41.147991 1000 0.6743341 4.5867253
- 293000 41.618836 1000 0.67357205 4.6024332
- 294000 42.08982 1000 0.66465346 4.6181412
- 295000 42.561323 1000 0.65587678 4.6338492
- 296000 43.034196 1000 0.65455827 4.6495571
- 297000 43.505748 1000 0.65135145 4.6652651
- 298000 43.975299 1000 0.65400349 4.6809731
- 299000 44.447556 1000 0.66186899 4.696681
- 300000 44.926073 1000 0.66844193 4.712389
- 301000 45.402658 1000 0.67720506 4.7280969
- 302000 45.880643 1000 0.68554918 4.7438049
- 303000 46.359444 1000 0.69321489 4.7595129
- 304000 46.841542 1000 0.70345329 4.7752208
- 305000 47.323539 1000 0.70172137 4.7909288
- 306000 47.809358 1000 0.70989191 4.8066368
- 307000 48.291664 1000 0.70546377 4.8223447
- 308000 48.770327 1000 0.70820389 4.8380527
- 309000 49.248974 1000 0.69637815 4.8537606
- 310000 49.72965 1000 0.68679532 4.8694686
- 311000 50.204503 1000 0.68824984 4.8851766
- 312000 50.683502 1000 0.68647935 4.9008845
- 313000 51.161407 1000 0.68289956 4.9165925
- 314000 51.638365 1000 0.68356788 4.9323005
- 315000 52.114341 1000 0.68269829 4.9480084
- 316000 52.590791 1000 0.67961769 4.9637164
- 317000 53.043198 1000 0.67437047 4.9794244
- 318000 53.499062 1000 0.66534726 4.9951323
- 319000 53.954004 1000 0.66052125 5.0108403
- 320000 54.409776 1000 0.65351962 5.0265482
- 321000 54.867935 1000 0.64155441 5.0422562
- 322000 55.324528 1000 0.63463177 5.0579642
- 323000 55.780399 1000 0.62945691 5.0736721
- 324000 56.239189 1000 0.63156746 5.0893801
- 325000 56.697767 1000 0.63883759 5.1050881
- 326000 57.155746 1000 0.64703516 5.120796
- 327000 57.618744 1000 0.65532057 5.136504
- 328000 58.083021 1000 0.66697061 5.152212
- 329000 58.547646 1000 0.66896271 5.1679199
- 330000 59.011518 1000 0.66551963 5.1836279
- 331000 59.478689 1000 0.65083894 5.1993358
- 332000 59.94887 1000 0.65171641 5.2150438
- 333000 60.416096 1000 0.65122777 5.2307518
- 334000 60.889826 1000 0.65844334 5.2464597
- 335000 61.363105 1000 0.66931264 5.2621677
- 336000 61.832482 1000 0.66847415 5.2778757
- 337000 62.300731 1000 0.65863495 5.2935836
- 338000 62.769011 1000 0.64977739 5.3092916
- 339000 63.232862 1000 0.6454395 5.3249995
- 340000 63.699228 1000 0.63484999 5.3407075
- 341000 64.165101 1000 0.62753448 5.3564155
- 342000 64.631118 1000 0.62781442 5.3721234
- 343000 65.099469 1000 0.63813963 5.3878314
- 344000 65.576568 1000 0.6485183 5.4035394
- 345000 66.054068 1000 0.67111606 5.4192473
- 346000 66.531747 1000 0.68435581 5.4349553
- 347000 67.007296 1000 0.69526046 5.4506633
- 348000 67.478242 1000 0.6876531 5.4663712
- 349000 67.944422 1000 0.67962108 5.4820792
- 350000 68.410281 1000 0.6800934 5.4977871
- 351000 68.862112 1000 0.67658657 5.5134951
- 352000 69.316476 1000 0.67043355 5.5292031
- 353000 69.76356 1000 0.66863154 5.544911
- 354000 70.212144 1000 0.65806572 5.560619
- 355000 70.658375 1000 0.6498301 5.576327
- 356000 71.103688 1000 0.64384284 5.5920349
- 357000 71.551545 1000 0.64228421 5.6077429
- 358000 72.001238 1000 0.6408188 5.6234508
- 359000 72.45158 1000 0.64388002 5.6391588
- 360000 72.906369 1000 0.64347896 5.6548668
- 361000 73.358316 1000 0.65055455 5.6705747
- 362000 73.814119 1000 0.65545061 5.6862827
- 363000 74.277034 1000 0.6667431 5.7019907
- 364000 74.737593 1000 0.6869856 5.7176986
- 365000 75.20209 1000 0.69651407 5.7334066
- 366000 75.667448 1000 0.70824091 5.7491146
- 367000 76.132389 1000 0.7144853 5.7648225
- 368000 76.596067 1000 0.71780876 5.7805305
- 369000 77.059749 1000 0.7159398 5.7962384
- 370000 77.519236 1000 0.70648968 5.8119464
- 371000 77.977404 1000 0.69796557 5.8276544
- 372000 78.434017 1000 0.69876891 5.8433623
- 373000 78.887217 1000 0.70908957 5.8590703
- 374000 79.341658 1000 0.70831124 5.8747783
- 375000 79.802381 1000 0.70631178 5.8904862
- 376000 80.265165 1000 0.70533876 5.9061942
- 377000 80.727821 1000 0.70097225 5.9219022
- 378000 81.187538 1000 0.70139806 5.9376101
- 379000 81.645627 1000 0.69691027 5.9533181
- 380000 82.105692 1000 0.69163881 5.969026
- 381000 82.56483 1000 0.68973183 5.984734
- 382000 83.025126 1000 0.68059207 6.000442
- 383000 83.482786 1000 0.68096466 6.0161499
- 384000 83.939808 1000 0.6698933 6.0318579
- 385000 84.418408 1000 0.66795846 6.0475659
- 386000 84.898757 1000 0.66153854 6.0632738
- 387000 85.376756 1000 0.66560025 6.0789818
- 388000 85.853575 1000 0.66671699 6.0946897
- 389000 86.32865 1000 0.66013733 6.1103977
- 390000 86.807772 1000 0.66181942 6.1261057
- 391000 87.290335 1000 0.66281334 6.1418136
- 392000 87.773899 1000 0.66657879 6.1575216
- 393000 88.248567 1000 0.66608992 6.1732296
- 394000 88.723817 1000 0.66128929 6.1889375
- 395000 89.200089 1000 0.65764538 6.2046455
- 396000 89.671826 1000 0.65073015 6.2203535
- 397000 90.142595 1000 0.64967355 6.2360614
- 398000 90.616654 1000 0.65193957 6.2517694
- 399000 91.093856 1000 0.64936977 6.2674773
- 400000 91.571678 1000 0.65849743 6.2831853
-Loop time of 91.5717 on 1 procs for 200000 steps with 1000 atoms
-
-Performance: 8916.580 tau/day, 2184.081 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 | 13.827 | 13.827 | 13.827 | 0.0 | 15.10
-Neigh | 0.097679 | 0.097679 | 0.097679 | 0.0 | 0.11
-Comm | 1.5668 | 1.5668 | 1.5668 | 0.0 | 1.71
-Output | 0.0042615 | 0.0042615 | 0.0042615 | 0.0 | 0.00
-Modify | 74.804 | 74.804 | 74.804 | 0.0 | 81.69
-Other | | 1.273 | | | 1.39
-
-Nlocal: 1000 ave 1000 max 1000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 289 ave 289 max 289 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 5091 ave 5091 max 5091 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 5091
-Ave neighs/atom = 5.091
-Neighbor list builds = 160
-Dangerous builds = 0
-Total wall time: 0:02:27
diff --git a/examples/granregion/log.6Oct16.granregion.mixer.g++.4 b/examples/granregion/log.6Oct16.granregion.mixer.g++.4
deleted file mode 100644
index 726b31f8fe..0000000000
--- a/examples/granregion/log.6Oct16.granregion.mixer.g++.4
+++ /dev/null
@@ -1,609 +0,0 @@
-LAMMPS (5 Oct 2016)
-variable name string mixer
-
-thermo_modify flush yes
-variable seed equal 14314
-
-###############################################
-# Particle parameters
-################################################
-
-variable rlo equal 0.3
-variable rhi equal 0.6
-variable dlo equal 2.0*${rlo}
-variable dlo equal 2.0*0.3
-variable dhi equal 2.0*${rhi}
-variable dhi equal 2.0*0.6
-variable skin equal ${rhi}
-variable skin equal 0.6
-
-variable coeffRes equal 0.1
-variable coeffFric equal 0.5
-
-variable kn equal 10^5
-variable kt equal 0.2*${kn}
-variable kt equal 0.2*100000
-
-variable gravity equal 1.0
-variable density equal 1.0
-
-variable min_mass equal ${density}*4.0/3.0*PI*${rlo}*${rlo}*${rlo}
-variable min_mass equal 1*4.0/3.0*PI*${rlo}*${rlo}*${rlo}
-variable min_mass equal 1*4.0/3.0*PI*0.3*${rlo}*${rlo}
-variable min_mass equal 1*4.0/3.0*PI*0.3*0.3*${rlo}
-variable min_mass equal 1*4.0/3.0*PI*0.3*0.3*0.3
-variable a equal (-2.0*log(${coeffRes})/PI)^2
-variable a equal (-2.0*log(0.1)/PI)^2
-variable gamma_n equal sqrt($a*2*${kn}/${min_mass}/(1+0.25*$a))
-variable gamma_n equal sqrt(0.405284734569351*2*${kn}/${min_mass}/(1+0.25*$a))
-variable gamma_n equal sqrt(0.405284734569351*2*100000/${min_mass}/(1+0.25*$a))
-variable gamma_n equal sqrt(0.405284734569351*2*100000/0.113097335529233/(1+0.25*$a))
-variable gamma_n equal sqrt(0.405284734569351*2*100000/0.113097335529233/(1+0.25*0.405284734569351))
-variable gamma_t equal ${gamma_n}*0.5
-variable gamma_t equal 806.699778405191*0.5
-
-variable tcol equal PI/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
-variable tcol equal PI/sqrt(2*100000/${min_mass}-${gamma_n}/4.0)
-variable tcol equal PI/sqrt(2*100000/0.113097335529233-${gamma_n}/4.0)
-variable tcol equal PI/sqrt(2*100000/0.113097335529233-806.699778405191/4.0)
-
-variable dt equal ${tcol}*0.02
-variable dt equal 0.00236257621510454*0.02
-timestep ${dt}
-timestep 4.72515243020908e-05
-
-###############################################
-
-variable dumpfreq equal 1000
-variable logfreq equal 1000
-
-newton on
-atom_style sphere
-
-boundary p p f
-
-region boxreg block 0 20 0 20 0 20
-create_box 1 boxreg
-Created orthogonal box = (0 0 0) to (20 20 20)
- 1 by 2 by 2 MPI processor grid
-
-pair_style gran/hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
-pair_style gran/hertz/history 100000 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
-pair_style gran/hertz/history 100000 20000 ${gamma_n} ${gamma_t} ${coeffFric} 1
-pair_style gran/hertz/history 100000 20000 806.699778405191 ${gamma_t} ${coeffFric} 1
-pair_style gran/hertz/history 100000 20000 806.699778405191 403.349889202595 ${coeffFric} 1
-pair_style gran/hertz/history 100000 20000 806.699778405191 403.349889202595 0.5 1
-pair_coeff * *
-
-neighbor ${skin} bin
-neighbor 0.6 bin
-thermo ${logfreq}
-thermo 1000
-
-comm_style brick
-comm_modify mode multi group all vel yes
-balance 1.1 shift xyz 20 1.1
-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
- ghost atom cutoff = 0
- binsize = 20 -> bins = 1 1 1
-fix bal all balance 10000 1.1 shift xyz 20 1.01
-
-####################### Options specific to pouring #########################
-
-region insreg cylinder z 10 10 8 10 18 side in units box
-region cylreg cylinder z 10 10 10 0 20 side in units box
-
-variable theta equal (step/400000)*2*PI
-
-region b1 block 2 18 9 11 0 4 side out rotate v_theta 10 10 0 0 0 1 units box
-region b2 block 9 11 2 18 0 3.99999 side out rotate v_theta 10 10 0 0 0 1 units box
-
-region mixer intersect 3 cylreg b1 b2 side in
-
-fix grav all gravity ${gravity} vector 0 0 -1
-fix grav all gravity 1 vector 0 0 -1
-fix 1 all nve/sphere
-
-fix mixwall all wall/gran/region hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
-fix mixwall all wall/gran/region hertz/history 100000 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
-fix mixwall all wall/gran/region hertz/history 100000 20000 ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
-fix mixwall all wall/gran/region hertz/history 100000 20000 806.699778405191 ${gamma_t} ${coeffFric} 1 region mixer
-fix mixwall all wall/gran/region hertz/history 100000 20000 806.699778405191 403.349889202595 ${coeffFric} 1 region mixer
-fix mixwall all wall/gran/region hertz/history 100000 20000 806.699778405191 403.349889202595 0.5 1 region mixer
-
-fix ins all pour 1000 1 42424 region insreg diam range ${dlo} ${dhi} dens ${density} ${density}
-fix ins all pour 1000 1 42424 region insreg diam range 0.6 ${dhi} dens ${density} ${density}
-fix ins all pour 1000 1 42424 region insreg diam range 0.6 1.2 dens ${density} ${density}
-fix ins all pour 1000 1 42424 region insreg diam range 0.6 1.2 dens 1 ${density}
-fix ins all pour 1000 1 42424 region insreg diam range 0.6 1.2 dens 1 1
-Particle insertion: 444 every 84653 steps, 1000 by step 169307
-
-#dump 1 all custom ${dumpfreq} ${name}_pour.dump # id type mass diameter x y z
-
-#dump 2 all image 4000 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 zoom 1.5 # box no 0.0 axes no 0.0 0.0
-#dump_modify 2 pad 6
-
-thermo_style custom step cpu atoms ke v_theta
-WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:690)
-thermo_modify flush yes lost warn
-
-run 200000
-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 = 1.8
- ghost atom cutoff = 1.8
- binsize = 0.9 -> bins = 23 23 23
-Memory usage per processor = 2.76258 Mbytes
-Step CPU Atoms KinEng v_theta
- 0 0 0 -0 0
- 1000 0.10398197 444 -0 0.015707963
- 2000 0.20485091 444 -0 0.031415927
- 3000 0.3069241 444 -0 0.04712389
- 4000 0.40875912 444 -0 0.062831853
- 5000 0.50989199 444 -0 0.078539816
- 6000 0.60949397 444 -0 0.09424778
- 7000 0.708915 444 -0 0.10995574
- 8000 0.80870605 444 -0 0.12566371
- 9000 0.90752602 444 -0 0.14137167
- 10000 1.0054469 444 -0 0.15707963
- 11000 1.072515 444 -0 0.1727876
- 12000 1.139096 444 -0 0.18849556
- 13000 1.2049479 444 -0 0.20420352
- 14000 1.2707851 444 -0 0.21991149
- 15000 1.3377919 444 -0 0.23561945
- 16000 1.405757 444 -0 0.25132741
- 17000 1.471797 444 -0 0.26703538
- 18000 1.538343 444 -0 0.28274334
- 19000 1.6035659 444 -0 0.2984513
- 20000 1.6690421 444 -0 0.31415927
- 21000 1.729399 444 -0 0.32986723
- 22000 1.7885301 444 -0 0.34557519
- 23000 1.8496239 444 -0 0.36128316
- 24000 1.913486 444 -0 0.37699112
- 25000 1.977428 444 -0 0.39269908
- 26000 2.04282 444 -0 0.40840704
- 27000 2.1089439 444 -0 0.42411501
- 28000 2.1759491 444 -0 0.43982297
- 29000 2.243813 444 -0 0.45553093
- 30000 2.312156 444 -0 0.4712389
- 31000 2.3742449 444 -0 0.48694686
- 32000 2.435447 444 -0 0.50265482
- 33000 2.495765 444 -0 0.51836279
- 34000 2.556865 444 -0 0.53407075
- 35000 2.6201291 444 -0 0.54977871
- 36000 2.6843281 444 -0 0.56548668
- 37000 2.7505059 444 -0 0.58119464
- 38000 2.817348 444 -0 0.5969026
- 39000 2.8837919 444 -0 0.61261057
- 40000 2.951216 444 -0 0.62831853
- 41000 3.012845 444 -0 0.64402649
- 42000 3.074688 444 -0 0.65973446
- 43000 3.13556 444 -0 0.67544242
- 44000 3.1965449 444 -0 0.69115038
- 45000 3.2582009 444 -0 0.70685835
- 46000 3.3201971 444 -0 0.72256631
- 47000 3.3819821 444 -0 0.73827427
- 48000 3.4455171 444 -0 0.75398224
- 49000 3.508738 444 -0 0.7696902
- 50000 3.5734961 444 -0 0.78539816
- 51000 3.6333289 444 -0 0.80110613
- 52000 3.694531 444 -0 0.81681409
- 53000 3.757041 444 -0 0.83252205
- 54000 3.820612 444 -0 0.84823002
- 55000 3.8852711 444 -0 0.86393798
- 56000 3.950211 444 -0 0.87964594
- 57000 4.015795 444 -0 0.89535391
- 58000 4.0818441 444 -0 0.91106187
- 59000 4.1476641 444 -0 0.92676983
- 60000 4.2141221 444 -0 0.9424778
- 61000 4.276612 444 -0 0.95818576
- 62000 4.339952 444 -0 0.97389372
- 63000 4.404351 444 -0 0.98960169
- 64000 4.4700999 444 -0 1.0053096
- 65000 4.5364759 444 -0 1.0210176
- 66000 4.605715 444 -0 1.0367256
- 67000 4.677629 444 -0 1.0524335
- 68000 4.7494669 444 -0 1.0681415
- 69000 4.8212609 444 -0 1.0838495
- 70000 4.894326 444 -0 1.0995574
- 71000 4.9639831 444 -0 1.1152654
- 72000 5.0345671 444 -0 1.1309734
- 73000 5.1048689 444 -0 1.1466813
- 74000 5.175498 444 -0 1.1623893
- 75000 5.2477591 444 -0 1.1780972
- 76000 5.3205409 444 -0 1.1938052
- 77000 5.394573 444 -0 1.2095132
- 78000 5.4685309 444 -0 1.2252211
- 79000 5.5431759 444 -0 1.2409291
- 80000 5.6212411 444 -0 1.2566371
- 81000 5.6890731 444 -0 1.272345
- 82000 5.7582159 444 -0 1.288053
- 83000 5.8298571 444 -0 1.303761
- 84000 5.9029069 444 -0 1.3194689
- 85000 6.0061591 888 -0 1.3351769
- 86000 6.1541281 888 -0 1.3508848
- 87000 6.3004079 888 -0 1.3665928
- 88000 6.4460659 888 -0 1.3823008
- 89000 6.591886 888 -0 1.3980087
- 90000 6.7376239 888 -0 1.4137167
- 91000 6.850734 888 -0 1.4294247
- 92000 6.9631939 888 -0 1.4451326
- 93000 7.0786369 888 -0 1.4608406
- 94000 7.1958089 888 -0 1.4765485
- 95000 7.3130219 888 -0 1.4922565
- 96000 7.430867 888 -0 1.5079645
- 97000 7.5498819 888 -0 1.5236724
- 98000 7.673686 888 -0 1.5393804
- 99000 7.7966969 888 -0 1.5550884
- 100000 7.921546 888 -0 1.5707963
- 101000 8.0396931 888 -0 1.5865043
- 102000 8.1583791 888 -0 1.6022123
- 103000 8.276613 888 -0 1.6179202
- 104000 8.3952639 888 -0 1.6336282
- 105000 8.514308 888 -0 1.6493361
- 106000 8.6361439 888 -0 1.6650441
- 107000 8.762326 888 -0 1.6807521
- 108000 8.8900061 888 -0 1.69646
- 109000 9.0179789 888 -0 1.712168
- 110000 9.1496761 888 -0 1.727876
- 111000 9.2728269 888 -0 1.7435839
- 112000 9.398078 888 -0 1.7592919
- 113000 9.519841 888 -0 1.7749998
- 114000 9.642343 888 -0 1.7907078
- 115000 9.7643859 888 -0 1.8064158
- 116000 9.8893411 888 -0 1.8221237
- 117000 10.01295 888 -0 1.8378317
- 118000 10.137574 888 -0 1.8535397
- 119000 10.263738 888 -0 1.8692476
- 120000 10.388673 888 -0 1.8849556
- 121000 10.507599 888 -0 1.9006636
- 122000 10.623901 888 -0 1.9163715
- 123000 10.740251 888 -0 1.9320795
- 124000 10.857467 888 -0 1.9477874
- 125000 10.975856 888 -0 1.9634954
- 126000 11.096002 888 -0 1.9792034
- 127000 11.217218 888 -0 1.9949113
- 128000 11.341925 888 -0 2.0106193
- 129000 11.467607 888 -0 2.0263273
- 130000 11.59517 888 -0 2.0420352
- 131000 11.71358 888 -0 2.0577432
- 132000 11.833024 888 -0 2.0734512
- 133000 11.954967 888 -0 2.0891591
- 134000 12.078482 888 -0 2.1048671
- 135000 12.202435 888 -0 2.120575
- 136000 12.327202 888 -0 2.136283
- 137000 12.453334 888 -0 2.151991
- 138000 12.583142 888 -0 2.1676989
- 139000 12.718396 888 -0 2.1834069
- 140000 12.854459 888 -0 2.1991149
- 141000 12.981024 888 -0 2.2148228
- 142000 13.108875 888 -0 2.2305308
- 143000 13.236802 888 -0 2.2462387
- 144000 13.36691 888 -0 2.2619467
- 145000 13.500126 888 -0 2.2776547
- 146000 13.633748 888 -0 2.2933626
- 147000 13.769077 888 -0 2.3090706
- 148000 13.90522 888 -0 2.3247786
- 149000 14.040417 888 -0 2.3404865
- 150000 14.176483 888 -0 2.3561945
- 151000 14.303389 888 -0 2.3719025
- 152000 14.432187 888 -0 2.3876104
- 153000 14.559857 888 -0 2.4033184
- 154000 14.691256 888 -0 2.4190263
- 155000 14.823413 888 -0 2.4347343
- 156000 14.956581 888 -0 2.4504423
- 157000 15.090666 888 -0 2.4661502
- 158000 15.228012 888 -0 2.4818582
- 159000 15.364569 888 -0 2.4975662
- 160000 15.501847 888 -0 2.5132741
- 161000 15.642772 888 -0 2.5289821
- 162000 15.783889 888 -0 2.54469
- 163000 15.926508 888 -0 2.560398
- 164000 16.07293 888 -0 2.576106
- 165000 16.221293 888 -0 2.5918139
- 166000 16.371738 888 -0 2.6075219
- 167000 16.523027 888 -0 2.6232299
- 168000 16.675525 888 -0 2.6389378
- 169000 16.830527 888 -0 2.6546458
- 170000 16.989955 1000 -0 2.6703538
- 171000 17.14772 1000 -0 2.6860617
- 172000 17.305565 1000 -0 2.7017697
- 173000 17.463517 1000 -0 2.7174776
- 174000 17.623862 1000 -0 2.7331856
- 175000 17.788165 1000 -0 2.7488936
- 176000 17.952028 1000 -0 2.7646015
- 177000 18.119269 1000 -0 2.7803095
- 178000 18.285714 1000 -0 2.7960175
- 179000 18.452439 1000 -0 2.8117254
- 180000 18.621119 1000 -0 2.8274334
- 181000 18.777982 1000 -0 2.8431414
- 182000 18.940248 1000 -0 2.8588493
- 183000 19.105385 1000 -0 2.8745573
- 184000 19.273934 1000 -0 2.8902652
- 185000 19.450922 1000 -0 2.9059732
- 186000 19.625563 1000 -0 2.9216812
- 187000 19.801329 1000 -0 2.9373891
- 188000 19.976869 1000 -0 2.9530971
- 189000 20.151134 1000 -0 2.9688051
- 190000 20.319214 1000 -0 2.984513
- 191000 20.485033 1000 -0 3.000221
- 192000 20.652254 1000 -0 3.0159289
- 193000 20.820876 1000 -0 3.0316369
- 194000 20.988597 1000 -0 3.0473449
- 195000 21.154705 1000 -0 3.0630528
- 196000 21.322634 1000 -0 3.0787608
- 197000 21.489394 1000 -0 3.0944688
- 198000 21.659512 1000 -0 3.1101767
- 199000 21.833228 1000 -0 3.1258847
- 200000 22.006487 1000 -0 3.1415927
-Loop time of 22.0065 on 4 procs for 200000 steps with 1000 atoms
-
-Performance: 37102.953 tau/day, 9088.222 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 | 0.67692 | 1.166 | 1.6704 | 44.4 | 5.30
-Neigh | 0.01562 | 0.018723 | 0.0222 | 2.3 | 0.09
-Comm | 3.845 | 4.4454 | 5.0282 | 26.1 | 20.20
-Output | 0.0043464 | 0.0052906 | 0.0056455 | 0.8 | 0.02
-Modify | 12.239 | 13.152 | 14.347 | 25.1 | 59.76
-Other | | 3.22 | | | 14.63
-
-Nlocal: 250 ave 257 max 244 min
-Histogram: 1 1 0 0 0 0 1 0 0 1
-Nghost: 305.75 ave 372 max 242 min
-Histogram: 1 0 0 1 0 1 0 0 0 1
-Neighs: 982.5 ave 1380 max 572 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-
-Total # of neighbors = 3930
-Ave neighs/atom = 3.93
-Neighbor list builds = 216
-Dangerous builds = 0
-unfix ins
-run 200000
-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 = 1.79826
- ghost atom cutoff = 1.79826
- binsize = 0.899132 -> bins = 23 23 23
-Memory usage per processor = 8.63577 Mbytes
-Step CPU Atoms KinEng v_theta
- 200000 0 1000 0.90316284 3.1415927
- 201000 0.16518497 1000 0.8867387 3.1573006
- 202000 0.33065486 1000 0.88745316 3.1730086
- 203000 0.4991529 1000 0.87793424 3.1887165
- 204000 0.6695168 1000 0.87009551 3.2044245
- 205000 0.83599901 1000 0.86431259 3.2201325
- 206000 1.001833 1000 0.85039776 3.2358404
- 207000 1.166487 1000 0.82897867 3.2515484
- 208000 1.3331649 1000 0.82069182 3.2672564
- 209000 1.5031869 1000 0.82349024 3.2829643
- 210000 1.6751509 1000 0.81859611 3.2986723
- 211000 1.846776 1000 0.82053992 3.3143802
- 212000 2.0198569 1000 0.82832647 3.3300882
- 213000 2.1932938 1000 0.82676865 3.3457962
- 214000 2.3676898 1000 0.82425781 3.3615041
- 215000 2.5424879 1000 0.83127148 3.3772121
- 216000 2.715348 1000 0.83925992 3.3929201
- 217000 2.8844988 1000 0.84390181 3.408628
- 218000 3.0485029 1000 0.85705713 3.424336
- 219000 3.211767 1000 0.85325946 3.440044
- 220000 3.3767338 1000 0.85641557 3.4557519
- 221000 3.5419538 1000 0.86922287 3.4714599
- 222000 3.710084 1000 0.89591143 3.4871678
- 223000 3.880873 1000 0.90395821 3.5028758
- 224000 4.054816 1000 0.91161431 3.5185838
- 225000 4.2260928 1000 0.92716425 3.5342917
- 226000 4.3996999 1000 0.91664886 3.5499997
- 227000 4.5679309 1000 0.9128853 3.5657077
- 228000 4.7353978 1000 0.91063998 3.5814156
- 229000 4.9045198 1000 0.90616712 3.5971236
- 230000 5.079206 1000 0.9042797 3.6128316
- 231000 5.252316 1000 0.91588137 3.6285395
- 232000 5.4218178 1000 0.92322871 3.6442475
- 233000 5.592988 1000 0.92370885 3.6599554
- 234000 5.753634 1000 0.91531408 3.6756634
- 235000 5.9159088 1000 0.91016621 3.6913714
- 236000 6.0817358 1000 0.89501073 3.7070793
- 237000 6.249059 1000 0.88504426 3.7227873
- 238000 6.4182718 1000 0.88268268 3.7384953
- 239000 6.5897119 1000 0.87811868 3.7542032
- 240000 6.758353 1000 0.88272663 3.7699112
- 241000 6.928581 1000 0.87751512 3.7856191
- 242000 7.0978079 1000 0.87017281 3.8013271
- 243000 7.268832 1000 0.86587613 3.8170351
- 244000 7.439904 1000 0.85157794 3.832743
- 245000 7.6105168 1000 0.8291738 3.848451
- 246000 7.7830069 1000 0.82315948 3.864159
- 247000 7.9578128 1000 0.81231703 3.8798669
- 248000 8.134944 1000 0.79931415 3.8955749
- 249000 8.3061719 1000 0.78877578 3.9112829
- 250000 8.476692 1000 0.78519942 3.9269908
- 251000 8.6525538 1000 0.78837716 3.9426988
- 252000 8.8288019 1000 0.79621044 3.9584067
- 253000 9.006846 1000 0.78744385 3.9741147
- 254000 9.1839809 1000 0.78810047 3.9898227
- 255000 9.3600328 1000 0.79053484 4.0055306
- 256000 9.538172 1000 0.79976932 4.0212386
- 257000 9.7188668 1000 0.81724577 4.0369466
- 258000 9.9032769 1000 0.81135963 4.0526545
- 259000 10.084928 1000 0.82017101 4.0683625
- 260000 10.266693 1000 0.82352898 4.0840704
- 261000 10.449515 1000 0.81662689 4.0997784
- 262000 10.630166 1000 0.82707216 4.1154864
- 263000 10.812056 1000 0.82001278 4.1311943
- 264000 10.991668 1000 0.81136264 4.1469023
- 265000 11.172162 1000 0.80507755 4.1626103
- 266000 11.353101 1000 0.80247583 4.1783182
- 267000 11.533476 1000 0.78870449 4.1940262
- 268000 11.716022 1000 0.77775428 4.2097342
- 269000 11.900351 1000 0.78170639 4.2254421
- 270000 12.083609 1000 0.78023258 4.2411501
- 271000 12.266298 1000 0.76257507 4.256858
- 272000 12.449454 1000 0.75871195 4.272566
- 273000 12.633748 1000 0.75909277 4.288274
- 274000 12.820916 1000 0.76329234 4.3039819
- 275000 13.004197 1000 0.76188557 4.3196899
- 276000 13.188507 1000 0.75974847 4.3353979
- 277000 13.372202 1000 0.75392834 4.3511058
- 278000 13.557712 1000 0.74837333 4.3668138
- 279000 13.747933 1000 0.74268307 4.3825218
- 280000 13.934871 1000 0.73840427 4.3982297
- 281000 14.11717 1000 0.73817851 4.4139377
- 282000 14.30208 1000 0.73666069 4.4296456
- 283000 14.485039 1000 0.74064713 4.4453536
- 284000 14.671087 1000 0.73916222 4.4610616
- 285000 14.863267 1000 0.73225442 4.4767695
- 286000 15.050005 1000 0.7312283 4.4924775
- 287000 15.234556 1000 0.72947519 4.5081855
- 288000 15.422593 1000 0.72469992 4.5238934
- 289000 15.609153 1000 0.70843645 4.5396014
- 290000 15.797906 1000 0.69731415 4.5553093
- 291000 15.983677 1000 0.69099822 4.5710173
- 292000 16.168935 1000 0.68855366 4.5867253
- 293000 16.355853 1000 0.69826256 4.6024332
- 294000 16.544831 1000 0.70211589 4.6181412
- 295000 16.733875 1000 0.7055847 4.6338492
- 296000 16.918698 1000 0.69692413 4.6495571
- 297000 17.100869 1000 0.68027227 4.6652651
- 298000 17.280404 1000 0.67254493 4.6809731
- 299000 17.46406 1000 0.67767946 4.696681
- 300000 17.652748 1000 0.68480172 4.712389
- 301000 17.84199 1000 0.67864643 4.7280969
- 302000 18.025759 1000 0.67656342 4.7438049
- 303000 18.208747 1000 0.67719641 4.7595129
- 304000 18.391225 1000 0.68049491 4.7752208
- 305000 18.576276 1000 0.68230722 4.7909288
- 306000 18.764125 1000 0.67985 4.8066368
- 307000 18.956063 1000 0.67790944 4.8223447
- 308000 19.147159 1000 0.6836647 4.8380527
- 309000 19.339173 1000 0.69705355 4.8537606
- 310000 19.530591 1000 0.69858847 4.8694686
- 311000 19.720214 1000 0.69448554 4.8851766
- 312000 19.907717 1000 0.68878539 4.9008845
- 313000 20.088793 1000 0.68810484 4.9165925
- 314000 20.268118 1000 0.68483484 4.9323005
- 315000 20.445564 1000 0.67732034 4.9480084
- 316000 20.627415 1000 0.67943319 4.9637164
- 317000 20.807826 1000 0.67326868 4.9794244
- 318000 20.983587 1000 0.67762092 4.9951323
- 319000 21.156655 1000 0.68914624 5.0108403
- 320000 21.331391 1000 0.69872806 5.0265482
- 321000 21.506313 1000 0.71510434 5.0422562
- 322000 21.679505 1000 0.71452122 5.0579642
- 323000 21.85396 1000 0.71765429 5.0736721
- 324000 22.02904 1000 0.72748838 5.0893801
- 325000 22.205191 1000 0.72974854 5.1050881
- 326000 22.38063 1000 0.73324928 5.120796
- 327000 22.555817 1000 0.72479525 5.136504
- 328000 22.729859 1000 0.71942855 5.152212
- 329000 22.903234 1000 0.71890587 5.1679199
- 330000 23.078575 1000 0.73495891 5.1836279
- 331000 23.252865 1000 0.74306733 5.1993358
- 332000 23.427175 1000 0.75274051 5.2150438
- 333000 23.604881 1000 0.75981346 5.2307518
- 334000 23.789045 1000 0.75410165 5.2464597
- 335000 23.971105 1000 0.74802374 5.2621677
- 336000 24.150954 1000 0.73111266 5.2778757
- 337000 24.331991 1000 0.72226021 5.2935836
- 338000 24.515157 1000 0.70866271 5.3092916
- 339000 24.69639 1000 0.70253496 5.3249995
- 340000 24.879524 1000 0.69381505 5.3407075
- 341000 25.061928 1000 0.68285569 5.3564155
- 342000 25.2437 1000 0.67262303 5.3721234
- 343000 25.423809 1000 0.67160137 5.3878314
- 344000 25.605531 1000 0.67658439 5.4035394
- 345000 25.78848 1000 0.67113748 5.4192473
- 346000 25.969866 1000 0.67506296 5.4349553
- 347000 26.152485 1000 0.67686518 5.4506633
- 348000 26.335445 1000 0.68878941 5.4663712
- 349000 26.522271 1000 0.70728493 5.4820792
- 350000 26.709942 1000 0.70870657 5.4977871
- 351000 26.889998 1000 0.71541489 5.5134951
- 352000 27.069872 1000 0.71827633 5.5292031
- 353000 27.249259 1000 0.7099127 5.544911
- 354000 27.428386 1000 0.70507946 5.560619
- 355000 27.607797 1000 0.70709703 5.576327
- 356000 27.788887 1000 0.70637714 5.5920349
- 357000 27.975344 1000 0.7088694 5.6077429
- 358000 28.164236 1000 0.70907948 5.6234508
- 359000 28.352999 1000 0.71504714 5.6391588
- 360000 28.539172 1000 0.71417205 5.6548668
- 361000 28.722691 1000 0.70716852 5.6705747
- 362000 28.906856 1000 0.70193967 5.6862827
- 363000 29.087598 1000 0.69786793 5.7019907
- 364000 29.268141 1000 0.68714789 5.7176986
- 365000 29.450765 1000 0.68170443 5.7334066
- 366000 29.633131 1000 0.67832571 5.7491146
- 367000 29.816219 1000 0.67809457 5.7648225
- 368000 29.999479 1000 0.66886004 5.7805305
- 369000 30.182675 1000 0.67233336 5.7962384
- 370000 30.36698 1000 0.67433369 5.8119464
- 371000 30.550787 1000 0.67478226 5.8276544
- 372000 30.736018 1000 0.67882814 5.8433623
- 373000 30.922576 1000 0.68494254 5.8590703
- 374000 31.107558 1000 0.69046765 5.8747783
- 375000 31.291329 1000 0.69398953 5.8904862
- 376000 31.474582 1000 0.68692367 5.9061942
- 377000 31.656979 1000 0.674184 5.9219022
- 378000 31.83851 1000 0.65899449 5.9376101
- 379000 32.019869 1000 0.65198402 5.9533181
- 380000 32.200375 1000 0.64366122 5.969026
- 381000 32.381651 1000 0.64443345 5.984734
- 382000 32.561897 1000 0.64655912 6.000442
- 383000 32.743947 1000 0.64894161 6.0161499
- 384000 32.927231 1000 0.65259561 6.0318579
- 385000 33.11882 1000 0.65230446 6.0475659
- 386000 33.311072 1000 0.64177598 6.0632738
- 387000 33.50435 1000 0.63900349 6.0789818
- 388000 33.695734 1000 0.64611067 6.0946897
- 389000 33.885915 1000 0.64943993 6.1103977
- 390000 34.076093 1000 0.66303716 6.1261057
- 391000 34.264909 1000 0.68916583 6.1418136
- 392000 34.45411 1000 0.71501556 6.1575216
- 393000 34.644116 1000 0.73685375 6.1732296
- 394000 34.834608 1000 0.74461041 6.1889375
- 395000 35.025693 1000 0.75251204 6.2046455
- 396000 35.217372 1000 0.75493054 6.2203535
- 397000 35.407008 1000 0.77028775 6.2360614
- 398000 35.594868 1000 0.7686439 6.2517694
- 399000 35.778411 1000 0.75167376 6.2674773
- 400000 35.962646 1000 0.73505917 6.2831853
-Loop time of 35.9627 on 4 procs for 200000 steps with 1000 atoms
-
-Performance: 22704.278 tau/day, 5561.323 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 | 2.0549 | 3.4094 | 4.9773 | 72.1 | 9.48
-Neigh | 0.022087 | 0.026923 | 0.032716 | 2.9 | 0.07
-Comm | 7.3555 | 9.2143 | 10.854 | 53.0 | 25.62
-Output | 0.0046289 | 0.0058927 | 0.0071292 | 1.4 | 0.02
-Modify | 17.504 | 19.601 | 22.342 | 44.9 | 54.50
-Other | | 3.705 | | | 10.30
-
-Nlocal: 250 ave 269 max 225 min
-Histogram: 1 0 0 0 0 1 0 1 0 1
-Nghost: 408.5 ave 500 max 320 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Neighs: 1262.25 ave 1665 max 880 min
-Histogram: 1 0 1 0 0 0 0 1 0 1
-
-Total # of neighbors = 5049
-Ave neighs/atom = 5.049
-Neighbor list builds = 166
-Dangerous builds = 0
-Total wall time: 0:00:57
diff --git a/examples/hugoniostat/in.hugoniostat b/examples/hugoniostat/in.hugoniostat
index affc97980c..01c2a246fc 100644
--- a/examples/hugoniostat/in.hugoniostat
+++ b/examples/hugoniostat/in.hugoniostat
@@ -15,7 +15,7 @@
units lj
boundary p p p
-atom_style atomic
+atom_style atomic
# Set up FCC lattice with z axis along <110>
@@ -39,10 +39,10 @@ pair_coeff * * 1.0 0.8908987
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
+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
+minimize 0.0 1.0e-6 10000 100000
# Define initial velocity
@@ -51,8 +51,6 @@ write_restart restart.equil
# Start Run #1
-log log.nodrag
-
clear
read_restart restart.equil
@@ -87,22 +85,20 @@ thermo_style custom step temp ke epair etotal pzz v_tau lz f_myhug v_dele v_us v
fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (no drag)'
-#dump id all atom 500 dump.hugoniostat
+#dump id all atom 500 dump.hugoniostat
-#dump 2 all image 500 image.*.jpg type type &
-# axes yes 0.8 0.02 view 60 -30
-#dump_modify 2 pad 5
+#dump 2 all image 500 image.*.jpg type type &
+# axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 5
-#dump 3 all movie 500 movie.mpg type type &
-# axes yes 0.8 0.02 view 60 -30
-#dump_modify 3 pad 5
+#dump 3 all movie 500 movie.mpg type type &
+# axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 5
-run 10000
+run 10000
# Start Run #2
-log log.drag
-
clear
read_restart restart.equil
@@ -137,12 +133,10 @@ thermo_style custom step temp ke epair etotal pzz v_tau lz f_myhug v_dele v_us v
fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (with drag)'
-run 10000
+run 10000
# Start Run #3
-log log.nhchains
-
clear
read_restart restart.equil
@@ -177,5 +171,5 @@ thermo_style custom step temp ke epair etotal pzz v_tau lz f_myhug v_dele v_us v
fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (Nose-Hoover chain)'
-run 10000
+run 10000
diff --git a/examples/hugoniostat/log.27Nov18.hugoniostat.g++.1 b/examples/hugoniostat/log.27Nov18.hugoniostat.g++.1
new file mode 100644
index 0000000000..2473641dea
--- /dev/null
+++ b/examples/hugoniostat/log.27Nov18.hugoniostat.g++.1
@@ -0,0 +1,401 @@
+LAMMPS (27 Nov 2018)
+ using 1 OpenMP thread(s) per MPI task
+# 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
+ Time spent = 0.000465155 secs
+
+# 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: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168)
+Neighbor list info ...
+ 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
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cubic, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.247 | 4.247 | 4.247 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 0.0724094 on 1 procs for 134 steps with 1000 atoms
+
+99.9% CPU use with 1 MPI tasks x 1 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 | 0.054599 | 0.054599 | 0.054599 | 0.0 | 75.40
+Neigh | 0.0011106 | 0.0011106 | 0.0011106 | 0.0 | 1.53
+Comm | 0.002012 | 0.002012 | 0.002012 | 0.0 | 2.78
+Output | 1.955e-05 | 1.955e-05 | 1.955e-05 | 0.0 | 0.03
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 0.01467 | | | 20.26
+
+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
+
+# Start Run #1
+
+clear
+ using 1 OpenMP thread(s) per MPI task
+read_restart restart.equil
+ restoring atom style atomic from restart
+ orthogonal box = (0.0465206 0.06579 0.06579) to (7.02455 9.93421 9.93421)
+ 1 by 1 by 1 MPI processor grid
+ restoring pair style lj/cubic from restart
+ 1000 atoms
+
+neighbor 0.2 bin
+neigh_modify every 1 delay 0 check yes
+timestep 0.001
+reset_timestep 0
+
+# Pzz = 40.0, drag/damping term off
+
+fix myhug all nphug temp 1.0 1.0 10.0 z 40.0 40.0 70.0 drag 0.0 tchain 1 pchain 0
+
+# Specify reference state from paper, times 1000 atoms
+
+fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
+
+# Add fix energy to ouput etotal
+
+fix_modify myhug energy yes
+
+# Define output
+
+variable dele equal f_myhug[1] # energy delta [temperature]
+variable us equal f_myhug[2] # shock velocity [distance/time]
+variable up equal f_myhug[3] # particle velocity [distance/time]
+variable pzz equal pzz # axial stress
+variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress
+variable time equal dt*step
+
+thermo 1000
+thermo_style custom step temp ke epair etotal pzz v_tau lz f_myhug v_dele v_us v_up
+
+fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (no drag)'
+
+#dump id all atom 500 dump.hugoniostat
+
+#dump 2 all image 500 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 5
+
+#dump 3 all movie 500 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 5
+
+run 10000
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 1.74754
+ ghost atom cutoff = 1.74754
+ binsize = 0.873769, bins = 8 12 12
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cubic, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 2.771 | 2.771 | 2.771 Mbytes
+Step Temp KinEng E_pair TotEng Pzz v_tau Lz f_myhug v_dele v_us v_up
+ 0 0.01 0.014985 -6.3344257 -6.3194407 0.014381062 -0.0002397183 9.8684199 0 -0.0048551451 2.3814196 0.0041108654
+ 1000 0.0093381489 0.013993216 -2.170443 -6.3381216 129.15286 58.544417 8.3142516 -4.1816719 0.93744258 23.519053 3.7381989
+ 2000 0.24794909 0.37155171 -5.8915802 -6.0429087 8.3850692 1.3744507 9.5938765 -0.5228803 -0.2435043 13.910468 0.4103393
+ 3000 0.38920701 0.5832267 -3.768677 -6.6246124 72.742761 28.486747 8.623805 -3.439162 0.003825459 19.697379 2.5139668
+ 4000 0.67009971 1.0041444 -4.2080644 -6.1365367 35.596179 3.9344133 8.7508422 -2.9326167 -0.58039603 14.529822 1.6677129
+ 5000 0.41848975 0.62710689 -4.8393088 -6.1026724 30.626544 4.6387208 8.7827245 -1.8904705 -0.31996439 13.670884 1.5250343
+ 6000 0.22410139 0.33581594 -3.7652941 -6.0923259 50.807437 7.2229456 8.2549488 -2.6628477 -0.017396966 14.4806 2.3884652
+ 7000 0.095001485 0.14235972 -4.5436753 -6.7307217 35.8743 3.4938089 8.4476287 -2.3294061 -0.052272192 12.957528 1.8846881
+ 8000 0.043277437 0.064851239 -4.6264096 -6.2447456 39.658659 6.7266325 8.4327483 -1.6831873 0.070488482 13.553882 1.9918311
+ 9000 0.018271956 0.027380526 -4.4239627 -6.3085661 41.708324 5.9081923 8.3463321 -1.9119839 0.091057512 13.503882 2.1025305
+ 10000 0.0082840001 0.012413574 -4.622252 -6.3316699 39.830379 6.5596321 8.4109569 -1.7218314 0.099435465 13.482451 2.0110543
+Loop time of 6.20702 on 1 procs for 10000 steps with 1000 atoms
+
+Performance: 139197.321 tau/day, 1611.080 timesteps/s
+98.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 5.0198 | 5.0198 | 5.0198 | 0.0 | 80.87
+Neigh | 0.21405 | 0.21405 | 0.21405 | 0.0 | 3.45
+Comm | 0.16164 | 0.16164 | 0.16164 | 0.0 | 2.60
+Output | 0.00053501 | 0.00053501 | 0.00053501 | 0.0 | 0.01
+Modify | 0.7419 | 0.7419 | 0.7419 | 0.0 | 11.95
+Other | | 0.06911 | | | 1.11
+
+Nlocal: 1000 ave 1000 max 1000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1886 ave 1886 max 1886 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 20874 ave 20874 max 20874 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 20874
+Ave neighs/atom = 20.874
+Neighbor list builds = 188
+Dangerous builds = 0
+
+# Start Run #2
+
+clear
+ using 1 OpenMP thread(s) per MPI task
+read_restart restart.equil
+ restoring atom style atomic from restart
+ orthogonal box = (0.0465206 0.06579 0.06579) to (7.02455 9.93421 9.93421)
+ 1 by 1 by 1 MPI processor grid
+ restoring pair style lj/cubic from restart
+ 1000 atoms
+
+neighbor 0.2 bin
+neigh_modify every 1 delay 0 check yes
+timestep 0.001
+reset_timestep 0
+
+# Pzz = 40.0, drag/damping term on
+
+fix myhug all nphug temp 1.0 1.0 1.0 z 40.0 40.0 70.0 drag 200.0 tchain 1 pchain 0
+
+# Specify reference state from paper, times 1000 atoms
+
+fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
+
+# Add fix energy to ouput etotal
+
+fix_modify myhug energy yes
+
+# Define output
+
+variable dele equal f_myhug[1] # energy delta [temperature]
+variable us equal f_myhug[2] # shock velocity [distance/time]
+variable up equal f_myhug[3] # particle velocity [distance/time]
+variable pzz equal pzz # axial stress
+variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress
+variable time equal dt*step
+
+thermo 1000
+thermo_style custom step temp ke epair etotal pzz v_tau lz f_myhug v_dele v_us v_up
+
+fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (with drag)'
+
+run 10000
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 1.74754
+ ghost atom cutoff = 1.74754
+ binsize = 0.873769, bins = 8 12 12
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cubic, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 2.771 | 2.771 | 2.771 Mbytes
+Step Temp KinEng E_pair TotEng Pzz v_tau Lz f_myhug v_dele v_us v_up
+ 0 0.01 0.014985 -6.3344257 -6.3194407 0.014381062 -0.0002397183 9.8684199 0 -0.0048551451 2.3814196 0.0041108654
+ 1000 0.0062572991 0.0093765627 -5.9890874 -7.64465 18.918117 7.5844397 9.2338165 -1.6649392 0.02341947 13.976996 0.92138738
+ 2000 0.006845108 0.010257394 -5.4565813 -7.9786876 37.064254 15.537266 8.9496404 -2.5323637 0.1023062 16.325405 1.5455017
+ 3000 0.0073276109 0.010980425 -5.3663425 -7.9938818 39.907292 16.807488 8.9154852 -2.6385197 0.11818131 16.639049 1.6326833
+ 4000 0.0069296915 0.010384143 -5.3623404 -8.0023271 40.010741 16.851482 8.9144328 -2.6503708 0.11868152 16.651571 1.6356847
+ 5000 0.0076142476 0.01140995 -5.3631447 -8.0108329 39.997648 16.846756 8.9145416 -2.6590981 0.11841154 16.649778 1.6353255
+ 6000 0.0077053839 0.011546518 -5.3628542 -8.0192007 39.991597 16.840313 8.9145803 -2.6678931 0.11818376 16.648851 1.6351691
+ 7000 0.0077405662 0.011599239 -5.3623534 -8.0275624 40.000448 16.844008 8.9145774 -2.6768081 0.11809914 16.650669 1.6353525
+ 8000 0.008067359 0.012088937 -5.3623759 -8.0359471 39.995327 16.840134 8.9146099 -2.6856601 0.11787118 16.649881 1.6352204
+ 9000 0.0083223114 0.012470984 -5.3622992 -8.0443714 40.00571 16.847763 8.9146503 -2.6945431 0.11781538 16.652389 1.6353987
+ 10000 0.0091249143 0.013673684 -5.3630142 -8.0529573 39.987196 16.837314 8.9146848 -2.7036168 0.11743028 16.648831 1.6349911
+Loop time of 5.48047 on 1 procs for 10000 steps with 1000 atoms
+
+Performance: 157650.687 tau/day, 1824.661 timesteps/s
+98.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 4.5166 | 4.5166 | 4.5166 | 0.0 | 82.41
+Neigh | 0.012162 | 0.012162 | 0.012162 | 0.0 | 0.22
+Comm | 0.14168 | 0.14168 | 0.14168 | 0.0 | 2.59
+Output | 0.00053787 | 0.00053787 | 0.00053787 | 0.0 | 0.01
+Modify | 0.74394 | 0.74394 | 0.74394 | 0.0 | 13.57
+Other | | 0.06553 | | | 1.20
+
+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 = 11
+Dangerous builds = 0
+
+# Start Run #3
+
+clear
+ using 1 OpenMP thread(s) per MPI task
+read_restart restart.equil
+ restoring atom style atomic from restart
+ orthogonal box = (0.0465206 0.06579 0.06579) to (7.02455 9.93421 9.93421)
+ 1 by 1 by 1 MPI processor grid
+ restoring pair style lj/cubic from restart
+ 1000 atoms
+
+neighbor 0.2 bin
+neigh_modify every 1 delay 0 check yes
+timestep 0.001
+reset_timestep 0
+
+# Pzz = 40.0, drag/damping term off, Nose-Hoover chains
+
+fix myhug all nphug temp 1.0 1.0 1.0 z 40.0 40.0 70.0
+
+# Specify reference state from paper, times 1000 atoms
+
+fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
+
+# Add fix energy to ouput etotal
+
+fix_modify myhug energy yes
+
+# Define output
+
+variable dele equal f_myhug[1] # energy delta [temperature]
+variable us equal f_myhug[2] # shock velocity [distance/time]
+variable up equal f_myhug[3] # particle velocity [distance/time]
+variable pzz equal pzz # axial stress
+variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress
+variable time equal dt*step
+
+thermo 1000
+thermo_style custom step temp ke epair etotal pzz v_tau lz f_myhug v_dele v_us v_up
+
+fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (Nose-Hoover chain)'
+
+run 10000
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 1.74754
+ ghost atom cutoff = 1.74754
+ binsize = 0.873769, bins = 8 12 12
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cubic, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 2.771 | 2.771 | 2.771 Mbytes
+Step Temp KinEng E_pair TotEng Pzz v_tau Lz f_myhug v_dele v_us v_up
+ 0 0.01 0.014985 -6.3344257 -6.3194407 0.014381062 -0.0002397183 9.8684199 0 -0.0048551451 2.3814196 0.0041108654
+ 1000 0.0083300394 0.012482564 -5.5023188 -6.3233387 35.610076 14.886667 8.9677982 -0.83350251 0.093761848 16.159481 1.500112
+ 2000 0.020386462 0.030549113 -5.2949349 -6.2805556 41.760388 17.563305 8.896033 -1.0161699 0.11780863 16.85284 1.6868235
+ 3000 0.049693152 0.074465188 -5.3469434 -6.2493961 39.030372 16.123483 8.9325594 -0.9769179 0.073097387 16.601986 1.6003716
+ 4000 0.11859514 0.17771482 -5.207077 -6.3242752 40.941558 16.507785 8.9213147 -1.2949131 0.018189678 16.904156 1.6487282
+ 5000 0.13014573 0.19502337 -5.2610248 -6.269279 39.059628 15.609345 8.9431685 -1.2032776 -0.00023747376 16.701437 1.5920344
+ 6000 0.1381307 0.20698886 -5.171005 -6.2931942 40.904837 16.242165 8.9222854 -1.3291781 -0.0044770368 16.905086 1.6471589
+ 7000 0.12107326 0.18142828 -5.2602554 -6.2438099 39.060928 15.57765 8.9397525 -1.1649827 0.0055890257 16.671524 1.594944
+ 8000 0.14333636 0.21478954 -5.1717123 -6.304602 40.876188 16.205815 8.9218142 -1.3476793 -0.0069396327 16.895033 1.6469846
+ 9000 0.12159663 0.18221255 -5.2591911 -6.2587685 39.228648 15.677869 8.9376641 -1.18179 0.0077357066 16.688862 1.6001283
+ 10000 0.15321883 0.22959841 -5.1881787 -6.3448453 40.666451 16.146177 8.922851 -1.386265 -0.0091929687 16.860705 1.6418699
+Loop time of 5.6426 on 1 procs for 10000 steps with 1000 atoms
+
+Performance: 153120.907 tau/day, 1772.233 timesteps/s
+98.7% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 4.5653 | 4.5653 | 4.5653 | 0.0 | 80.91
+Neigh | 0.10885 | 0.10885 | 0.10885 | 0.0 | 1.93
+Comm | 0.14695 | 0.14695 | 0.14695 | 0.0 | 2.60
+Output | 0.00055218 | 0.00055218 | 0.00055218 | 0.0 | 0.01
+Modify | 0.75364 | 0.75364 | 0.75364 | 0.0 | 13.36
+Other | | 0.0673 | | | 1.19
+
+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: 20654 ave 20654 max 20654 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 20654
+Ave neighs/atom = 20.654
+Neighbor list builds = 94
+Dangerous builds = 0
+
+Total wall time: 0:00:17
diff --git a/examples/hugoniostat/log.27Nov18.hugoniostat.g++.4 b/examples/hugoniostat/log.27Nov18.hugoniostat.g++.4
new file mode 100644
index 0000000000..30f1335ea9
--- /dev/null
+++ b/examples/hugoniostat/log.27Nov18.hugoniostat.g++.4
@@ -0,0 +1,401 @@
+LAMMPS (27 Nov 2018)
+ using 1 OpenMP thread(s) per MPI task
+# 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
+ Time spent = 0.0003438 secs
+
+# 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: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168)
+Neighbor list info ...
+ 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
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cubic, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.211 | 4.211 | 4.211 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 0.0269771 on 4 procs for 134 steps with 1000 atoms
+
+94.3% CPU use with 4 MPI tasks x 1 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 | 0.011534 | 0.013897 | 0.016008 | 1.3 | 51.51
+Neigh | 0.00024176 | 0.00029498 | 0.00035191 | 0.0 | 1.09
+Comm | 0.0029764 | 0.0050126 | 0.0073018 | 2.2 | 18.58
+Output | 1.8835e-05 | 1.9968e-05 | 2.2888e-05 | 0.0 | 0.07
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 0.007753 | | | 28.74
+
+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
+
+# Start Run #1
+
+clear
+ using 1 OpenMP thread(s) per MPI task
+read_restart restart.equil
+ restoring atom style atomic from restart
+ orthogonal box = (0.0465206 0.06579 0.06579) to (7.02455 9.93421 9.93421)
+ 1 by 2 by 2 MPI processor grid
+ restoring pair style lj/cubic from restart
+ 1000 atoms
+
+neighbor 0.2 bin
+neigh_modify every 1 delay 0 check yes
+timestep 0.001
+reset_timestep 0
+
+# Pzz = 40.0, drag/damping term off
+
+fix myhug all nphug temp 1.0 1.0 10.0 z 40.0 40.0 70.0 drag 0.0 tchain 1 pchain 0
+
+# Specify reference state from paper, times 1000 atoms
+
+fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
+
+# Add fix energy to ouput etotal
+
+fix_modify myhug energy yes
+
+# Define output
+
+variable dele equal f_myhug[1] # energy delta [temperature]
+variable us equal f_myhug[2] # shock velocity [distance/time]
+variable up equal f_myhug[3] # particle velocity [distance/time]
+variable pzz equal pzz # axial stress
+variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress
+variable time equal dt*step
+
+thermo 1000
+thermo_style custom step temp ke epair etotal pzz v_tau lz f_myhug v_dele v_us v_up
+
+fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (no drag)'
+
+#dump id all atom 500 dump.hugoniostat
+
+#dump 2 all image 500 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 5
+
+#dump 3 all movie 500 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 5
+
+run 10000
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 1.74754
+ ghost atom cutoff = 1.74754
+ binsize = 0.873769, bins = 8 12 12
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cubic, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 2.717 | 2.809 | 3.086 Mbytes
+Step Temp KinEng E_pair TotEng Pzz v_tau Lz f_myhug v_dele v_us v_up
+ 0 0.01 0.014985 -6.3344257 -6.3194407 0.014347835 -0.00026463907 9.8684199 0 -0.0048551516 2.3786668 0.0041061135
+ 1000 0.010586668 0.015864122 -2.1721826 -6.3380886 129.03334 58.456626 8.3141284 -4.1817701 0.93542408 23.507246 3.7366154
+ 2000 0.3321368 0.49770699 -5.584787 -6.0546694 12.097343 1.2026972 9.4615963 -0.96758935 -0.3571439 13.858218 0.5942385
+ 3000 0.46981685 0.70402055 -3.9208474 -6.3911005 63.005989 22.559106 8.6828663 -3.1742737 -0.16958917 18.776521 2.2842567
+ 4000 0.54866493 0.82217439 -4.1703408 -6.2427645 38.408608 4.9066022 8.6573289 -2.894598 -0.45434132 14.506935 1.8023166
+ 5000 0.30625495 0.45892304 -4.7355785 -6.186448 35.000599 6.2097986 8.6658098 -1.9097925 -0.19603125 13.896448 1.7145489
+ 6000 0.13938196 0.20886386 -4.303964 -5.7629121 50.370681 12.189231 8.3966581 -1.6678119 0.11451271 15.088809 2.2724852
+ 7000 0.055349516 0.082941249 -5.2031342 -6.8043199 30.859256 6.5562297 8.6850282 -1.684127 0.020586458 13.152479 1.5971879
+ 8000 0.027926794 0.0418483 -4.5281656 -5.4484008 48.145681 12.229919 8.4107051 -0.96208352 0.19922201 14.821877 2.2112219
+ 9000 0.018195086 0.027265336 -4.9847444 -6.5712684 37.347655 8.7291385 8.5606968 -1.6137894 0.10912534 13.773573 1.8458438
+ 10000 0.0082893467 0.012421586 -5.0130076 -6.6821423 36.46118 8.3386716 8.5689995 -1.6815563 0.1065388 13.651975 1.8180818
+Loop time of 2.01177 on 4 procs for 10000 steps with 1000 atoms
+
+Performance: 429472.539 tau/day, 4970.747 timesteps/s
+98.1% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 1.2437 | 1.2651 | 1.2843 | 1.7 | 62.89
+Neigh | 0.051696 | 0.052503 | 0.053247 | 0.3 | 2.61
+Comm | 0.24826 | 0.26724 | 0.28867 | 3.5 | 13.28
+Output | 0.00058603 | 0.00085759 | 0.0016623 | 0.0 | 0.04
+Modify | 0.37363 | 0.37671 | 0.38189 | 0.5 | 18.73
+Other | | 0.04935 | | | 2.45
+
+Nlocal: 250 ave 260 max 240 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost: 927.5 ave 934 max 921 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs: 5048.5 ave 5203 max 4889 min
+Histogram: 1 1 0 0 0 0 0 0 1 1
+
+Total # of neighbors = 20194
+Ave neighs/atom = 20.194
+Neighbor list builds = 175
+Dangerous builds = 0
+
+# Start Run #2
+
+clear
+ using 1 OpenMP thread(s) per MPI task
+read_restart restart.equil
+ restoring atom style atomic from restart
+ orthogonal box = (0.0465206 0.06579 0.06579) to (7.02455 9.93421 9.93421)
+ 1 by 2 by 2 MPI processor grid
+ restoring pair style lj/cubic from restart
+ 1000 atoms
+
+neighbor 0.2 bin
+neigh_modify every 1 delay 0 check yes
+timestep 0.001
+reset_timestep 0
+
+# Pzz = 40.0, drag/damping term on
+
+fix myhug all nphug temp 1.0 1.0 1.0 z 40.0 40.0 70.0 drag 200.0 tchain 1 pchain 0
+
+# Specify reference state from paper, times 1000 atoms
+
+fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
+
+# Add fix energy to ouput etotal
+
+fix_modify myhug energy yes
+
+# Define output
+
+variable dele equal f_myhug[1] # energy delta [temperature]
+variable us equal f_myhug[2] # shock velocity [distance/time]
+variable up equal f_myhug[3] # particle velocity [distance/time]
+variable pzz equal pzz # axial stress
+variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress
+variable time equal dt*step
+
+thermo 1000
+thermo_style custom step temp ke epair etotal pzz v_tau lz f_myhug v_dele v_us v_up
+
+fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (with drag)'
+
+run 10000
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 1.74754
+ ghost atom cutoff = 1.74754
+ binsize = 0.873769, bins = 8 12 12
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cubic, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 2.717 | 2.809 | 3.086 Mbytes
+Step Temp KinEng E_pair TotEng Pzz v_tau Lz f_myhug v_dele v_us v_up
+ 0 0.01 0.014985 -6.3344257 -6.3194407 0.014347835 -0.00026463907 9.8684199 0 -0.0048551516 2.3786668 0.0041061135
+ 1000 0.0063089138 0.0094539073 -5.9892326 -7.6448129 18.914956 7.5823222 9.2337797 -1.6650342 0.023426454 13.975434 0.92133642
+ 2000 0.0068813683 0.01031173 -5.4566765 -7.9789037 37.064192 15.537213 8.9495783 -2.5325388 0.10234565 16.32485 1.5455517
+ 3000 0.0072427316 0.010853233 -5.3662818 -7.9940958 39.906002 16.80569 8.9154322 -2.6386672 0.11821344 16.638326 1.6327015
+ 4000 0.0070936522 0.010629838 -5.3626164 -8.0025859 40.007994 16.850321 8.9143648 -2.6505993 0.11869226 16.650416 1.6356859
+ 5000 0.0074091958 0.01110268 -5.3628943 -8.0110325 39.998199 16.845204 8.9144816 -2.6592409 0.11846422 16.649379 1.6353872
+ 6000 0.0077388573 0.011596678 -5.3629264 -8.0194804 39.995216 16.842807 8.9145056 -2.6681507 0.11826582 16.648964 1.635306
+ 7000 0.0076023298 0.011392091 -5.3621083 -8.0277598 39.998343 16.839762 8.9144789 -2.6770435 0.11810824 16.649386 1.6353924
+ 8000 0.007691692 0.011526001 -5.361706 -8.0360632 40.000701 16.839078 8.9144843 -2.6858833 0.11795313 16.649923 1.6354361
+ 9000 0.0082153298 0.012310672 -5.3620899 -8.0446091 40.006134 16.845865 8.914544 -2.6948299 0.11785259 16.651566 1.6354969
+ 10000 0.0088368792 0.013242063 -5.3625357 -8.0530825 39.989575 16.835079 8.914577 -2.7037888 0.1174907 16.648402 1.6351306
+Loop time of 1.80214 on 4 procs for 10000 steps with 1000 atoms
+
+Performance: 479429.980 tau/day, 5548.958 timesteps/s
+98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 1.1353 | 1.1591 | 1.1787 | 1.5 | 64.32
+Neigh | 0.0028975 | 0.0029137 | 0.0029218 | 0.0 | 0.16
+Comm | 0.20882 | 0.22752 | 0.25213 | 3.4 | 12.62
+Output | 0.00058103 | 0.0007953 | 0.0014329 | 0.0 | 0.04
+Modify | 0.36598 | 0.36908 | 0.37078 | 0.3 | 20.48
+Other | | 0.04277 | | | 2.37
+
+Nlocal: 250 ave 258 max 239 min
+Histogram: 1 0 0 0 1 0 0 0 1 1
+Nghost: 829 ave 840 max 821 min
+Histogram: 1 1 0 0 0 1 0 0 0 1
+Neighs: 5250 ave 5360 max 5090 min
+Histogram: 1 0 0 0 1 0 0 0 0 2
+
+Total # of neighbors = 21000
+Ave neighs/atom = 21
+Neighbor list builds = 10
+Dangerous builds = 0
+
+# Start Run #3
+
+clear
+ using 1 OpenMP thread(s) per MPI task
+read_restart restart.equil
+ restoring atom style atomic from restart
+ orthogonal box = (0.0465206 0.06579 0.06579) to (7.02455 9.93421 9.93421)
+ 1 by 2 by 2 MPI processor grid
+ restoring pair style lj/cubic from restart
+ 1000 atoms
+
+neighbor 0.2 bin
+neigh_modify every 1 delay 0 check yes
+timestep 0.001
+reset_timestep 0
+
+# Pzz = 40.0, drag/damping term off, Nose-Hoover chains
+
+fix myhug all nphug temp 1.0 1.0 1.0 z 40.0 40.0 70.0
+
+# Specify reference state from paper, times 1000 atoms
+
+fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
+
+# Add fix energy to ouput etotal
+
+fix_modify myhug energy yes
+
+# Define output
+
+variable dele equal f_myhug[1] # energy delta [temperature]
+variable us equal f_myhug[2] # shock velocity [distance/time]
+variable up equal f_myhug[3] # particle velocity [distance/time]
+variable pzz equal pzz # axial stress
+variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress
+variable time equal dt*step
+
+thermo 1000
+thermo_style custom step temp ke epair etotal pzz v_tau lz f_myhug v_dele v_us v_up
+
+fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (Nose-Hoover chain)'
+
+run 10000
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 1.74754
+ ghost atom cutoff = 1.74754
+ binsize = 0.873769, bins = 8 12 12
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cubic, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 2.717 | 2.809 | 3.086 Mbytes
+Step Temp KinEng E_pair TotEng Pzz v_tau Lz f_myhug v_dele v_us v_up
+ 0 0.01 0.014985 -6.3344257 -6.3194407 0.014347835 -0.00026463907 9.8684199 0 -0.0048551516 2.3786668 0.0041061135
+ 1000 0.0078345827 0.011740122 -5.501714 -6.3232649 35.616592 14.888101 8.9677603 -0.833291 0.093891974 16.160626 1.5002802
+ 2000 0.019260469 0.028861813 -5.2936047 -6.2784351 41.771445 17.563018 8.895899 -1.0136922 0.11811779 16.853929 1.687161
+ 3000 0.048111305 0.072094791 -5.3454082 -6.2447367 39.061491 16.137184 8.932261 -0.97142325 0.073850675 16.606004 1.6012602
+ 4000 0.11854629 0.17764161 -5.2071426 -6.3210422 40.843054 16.426156 8.9202992 -1.2915412 0.017621345 16.874925 1.6476105
+ 5000 0.13634167 0.204308 -5.2645153 -6.3135608 39.098316 15.628006 8.9407716 -1.2533534 -0.00067532215 16.688495 1.5948471
+ 6000 0.14222646 0.21312635 -5.1774703 -6.3289809 40.888616 16.260775 8.9214855 -1.3646369 -0.0041713956 16.89472 1.6475159
+ 7000 0.12683662 0.19006468 -5.2679846 -6.2838171 39.084233 15.633883 8.939337 -1.2058972 0.0057260888 16.672835 1.5957701
+ 8000 0.14531516 0.21775476 -5.1737923 -6.3237483 40.861161 16.191124 8.9199968 -1.3677107 -0.0065481979 16.876021 1.6482339
+ 9000 0.12123357 0.18166851 -5.2546748 -6.2570254 39.276123 15.677988 8.9363522 -1.1840191 0.0075191856 16.687414 1.6022039
+ 10000 0.14771416 0.22134967 -5.1833988 -6.3104954 40.578265 16.080163 8.9245634 -1.3484463 -0.0098090911 16.857414 1.6386293
+Loop time of 1.8702 on 4 procs for 10000 steps with 1000 atoms
+
+Performance: 461983.152 tau/day, 5347.027 timesteps/s
+98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 1.1723 | 1.1812 | 1.1956 | 0.9 | 63.16
+Neigh | 0.028221 | 0.030409 | 0.035555 | 1.7 | 1.63
+Comm | 0.22963 | 0.24139 | 0.25155 | 1.6 | 12.91
+Output | 0.00055218 | 0.00077897 | 0.0014515 | 0.0 | 0.04
+Modify | 0.37165 | 0.37241 | 0.3732 | 0.1 | 19.91
+Other | | 0.04404 | | | 2.35
+
+Nlocal: 250 ave 257 max 244 min
+Histogram: 1 0 0 1 1 0 0 0 0 1
+Nghost: 832.25 ave 840 max 822 min
+Histogram: 1 0 0 0 0 0 2 0 0 1
+Neighs: 5144.25 ave 5282 max 4949 min
+Histogram: 1 0 0 0 0 1 0 1 0 1
+
+Total # of neighbors = 20577
+Ave neighs/atom = 20.577
+Neighbor list builds = 95
+Dangerous builds = 0
+
+Total wall time: 0:00:05
diff --git a/examples/indent/log.5Oct16.indent.g++.1 b/examples/indent/log.27Nov18.indent.g++.1
similarity index 82%
rename from examples/indent/log.5Oct16.indent.g++.1
rename to examples/indent/log.27Nov18.indent.g++.1
index 8c718d44b1..746f1322fb 100644
--- a/examples/indent/log.5Oct16.indent.g++.1
+++ b/examples/indent/log.27Nov18.indent.g++.1
@@ -1,4 +1,5 @@
-LAMMPS (5 Oct 2016)
+LAMMPS (27 Nov 2018)
+ using 1 OpenMP thread(s) per MPI task
# 2d indenter simulation
dimension 2
@@ -18,6 +19,7 @@ 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
+ Time spent = 0.000351191 secs
mass 1 1.0
mass 2 1.0
@@ -57,7 +59,7 @@ fix 5 all enforce2d
thermo 1000
thermo_modify temp new
-WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474)
+WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488)
#dump 1 all atom 250 dump.indent
@@ -69,13 +71,18 @@ WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474
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
+ binsize = 1.4, bins = 17 15 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) = 3.043 | 3.043 | 3.043 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
@@ -108,20 +115,20 @@ Step Temp E_pair E_mol TotEng Press Volume
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 2.36919 on 1 procs for 30000 steps with 420 atoms
+Loop time of 2.58797 on 1 procs for 30000 steps with 420 atoms
-Performance: 3282134.431 tau/day, 12662.556 timesteps/s
-99.9% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 3004676.853 tau/day, 11592.117 timesteps/s
+99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 1.7824 | 1.7824 | 1.7824 | 0.0 | 75.23
-Neigh | 0.073035 | 0.073035 | 0.073035 | 0.0 | 3.08
-Comm | 0.023414 | 0.023414 | 0.023414 | 0.0 | 0.99
-Output | 0.00027108 | 0.00027108 | 0.00027108 | 0.0 | 0.01
-Modify | 0.42744 | 0.42744 | 0.42744 | 0.0 | 18.04
-Other | | 0.06268 | | | 2.65
+Pair | 1.7803 | 1.7803 | 1.7803 | 0.0 | 68.79
+Neigh | 0.074505 | 0.074505 | 0.074505 | 0.0 | 2.88
+Comm | 0.038266 | 0.038266 | 0.038266 | 0.0 | 1.48
+Output | 0.00033927 | 0.00033927 | 0.00033927 | 0.0 | 0.01
+Modify | 0.61562 | 0.61562 | 0.61562 | 0.0 | 23.79
+Other | | 0.07897 | | | 3.05
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -139,7 +146,7 @@ Dangerous builds = 0
unfix 4
run 30000
-Memory usage per processor = 2.46978 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 3.043 | 3.043 | 3.043 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
@@ -172,20 +179,20 @@ Step Temp E_pair E_mol TotEng Press Volume
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 2.11008 on 1 procs for 30000 steps with 420 atoms
+Loop time of 2.20628 on 1 procs for 30000 steps with 420 atoms
-Performance: 3685166.663 tau/day, 14217.464 timesteps/s
-99.9% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 3524485.426 tau/day, 13597.552 timesteps/s
+99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 1.7612 | 1.7612 | 1.7612 | 0.0 | 83.46
-Neigh | 0.072587 | 0.072587 | 0.072587 | 0.0 | 3.44
-Comm | 0.023835 | 0.023835 | 0.023835 | 0.0 | 1.13
-Output | 0.00023365 | 0.00023365 | 0.00023365 | 0.0 | 0.01
-Modify | 0.19556 | 0.19556 | 0.19556 | 0.0 | 9.27
-Other | | 0.05669 | | | 2.69
+Pair | 1.7599 | 1.7599 | 1.7599 | 0.0 | 79.77
+Neigh | 0.074152 | 0.074152 | 0.074152 | 0.0 | 3.36
+Comm | 0.037216 | 0.037216 | 0.037216 | 0.0 | 1.69
+Output | 0.00033259 | 0.00033259 | 0.00033259 | 0.0 | 0.02
+Modify | 0.25688 | 0.25688 | 0.25688 | 0.0 | 11.64
+Other | | 0.07779 | | | 3.53
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
diff --git a/examples/indent/log.5Oct16.indent.g++.4 b/examples/indent/log.27Nov18.indent.g++.4
similarity index 82%
rename from examples/indent/log.5Oct16.indent.g++.4
rename to examples/indent/log.27Nov18.indent.g++.4
index 3d96cf6185..1f0556475b 100644
--- a/examples/indent/log.5Oct16.indent.g++.4
+++ b/examples/indent/log.27Nov18.indent.g++.4
@@ -1,4 +1,5 @@
-LAMMPS (5 Oct 2016)
+LAMMPS (27 Nov 2018)
+ using 1 OpenMP thread(s) per MPI task
# 2d indenter simulation
dimension 2
@@ -18,6 +19,7 @@ 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
+ Time spent = 0.00031352 secs
mass 1 1.0
mass 2 1.0
@@ -57,7 +59,7 @@ fix 5 all enforce2d
thermo 1000
thermo_modify temp new
-WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474)
+WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488)
#dump 1 all atom 250 dump.indent
@@ -69,13 +71,18 @@ WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474
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
+ binsize = 1.4, bins = 17 15 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) = 3.047 | 3.047 | 3.047 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
@@ -108,20 +115,20 @@ Step Temp E_pair E_mol TotEng Press Volume
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 1.05783 on 4 procs for 30000 steps with 420 atoms
+Loop time of 1.15893 on 4 procs for 30000 steps with 420 atoms
-Performance: 7350928.409 tau/day, 28360.063 timesteps/s
-99.2% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 6709635.246 tau/day, 25885.938 timesteps/s
+97.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.40826 | 0.46628 | 0.5198 | 6.6 | 44.08
-Neigh | 0.017807 | 0.019817 | 0.021682 | 1.1 | 1.87
-Comm | 0.22255 | 0.26884 | 0.31893 | 8.2 | 25.41
-Output | 0.0005722 | 0.00060749 | 0.00070214 | 0.2 | 0.06
-Modify | 0.18744 | 0.19364 | 0.20341 | 1.5 | 18.31
-Other | | 0.1086 | | | 10.27
+Pair | 0.39848 | 0.4603 | 0.53798 | 8.6 | 39.72
+Neigh | 0.018286 | 0.020391 | 0.022765 | 1.4 | 1.76
+Comm | 0.18903 | 0.27493 | 0.34712 | 13.2 | 23.72
+Output | 0.00055623 | 0.00077116 | 0.0014129 | 0.0 | 0.07
+Modify | 0.28166 | 0.29302 | 0.30362 | 1.5 | 25.28
+Other | | 0.1095 | | | 9.45
Nlocal: 105 ave 115 max 90 min
Histogram: 1 0 0 0 1 0 0 0 0 2
@@ -139,7 +146,7 @@ Dangerous builds = 0
unfix 4
run 30000
-Memory usage per processor = 2.47641 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 3.047 | 3.048 | 3.048 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
@@ -172,20 +179,20 @@ Step Temp E_pair E_mol TotEng Press Volume
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 0.87344 on 4 procs for 30000 steps with 420 atoms
+Loop time of 0.903556 on 4 procs for 30000 steps with 420 atoms
-Performance: 8902734.020 tau/day, 34346.968 timesteps/s
-99.3% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 8605992.311 tau/day, 33202.131 timesteps/s
+97.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.38824 | 0.45201 | 0.49914 | 6.9 | 51.75
-Neigh | 0.0175 | 0.020234 | 0.022472 | 1.5 | 2.32
-Comm | 0.21322 | 0.26426 | 0.33067 | 10.0 | 30.25
-Output | 0.00049305 | 0.00051773 | 0.00058699 | 0.2 | 0.06
-Modify | 0.04793 | 0.053404 | 0.05745 | 1.8 | 6.11
-Other | | 0.08302 | | | 9.50
+Pair | 0.3899 | 0.45567 | 0.53041 | 8.7 | 50.43
+Neigh | 0.017401 | 0.021048 | 0.024747 | 2.1 | 2.33
+Comm | 0.17915 | 0.26432 | 0.34168 | 13.8 | 29.25
+Output | 0.00051928 | 0.00093985 | 0.0021935 | 0.0 | 0.10
+Modify | 0.067609 | 0.075224 | 0.08228 | 2.4 | 8.33
+Other | | 0.08635 | | | 9.56
Nlocal: 105 ave 112 max 98 min
Histogram: 1 0 1 0 0 0 0 1 0 1
@@ -198,4 +205,4 @@ Total # of neighbors = 3569
Ave neighs/atom = 8.49762
Neighbor list builds = 634
Dangerous builds = 0
-Total wall time: 0:00:01
+Total wall time: 0:00:02
diff --git a/examples/indent/log.5Oct16.indent.min.g++.1 b/examples/indent/log.27Nov18.indent.min.g++.1
similarity index 77%
rename from examples/indent/log.5Oct16.indent.min.g++.1
rename to examples/indent/log.27Nov18.indent.min.g++.1
index e988892da1..ce5b0b1b61 100644
--- a/examples/indent/log.5Oct16.indent.min.g++.1
+++ b/examples/indent/log.27Nov18.indent.min.g++.1
@@ -1,4 +1,5 @@
-LAMMPS (5 Oct 2016)
+LAMMPS (27 Nov 2018)
+ using 1 OpenMP thread(s) per MPI task
# 2d indenter simulation with minimization instead of dynamics
dimension 2
@@ -18,6 +19,7 @@ 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
+ Time spent = 0.000453234 secs
mass * 1.0
@@ -57,24 +59,29 @@ thermo 10
#dump_modify 3 pad 4
minimize 1.0e-6 1.0e-6 1000 1000
-WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
+WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/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
+ binsize = 1.4, bins = 17 15 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) = 4.168 | 4.168 | 4.168 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 0.00874686 on 1 procs for 35 steps with 420 atoms
+Loop time of 0.00889349 on 1 procs for 35 steps with 420 atoms
-102.9% CPU use with 1 MPI tasks x no OpenMP threads
+98.1% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
@@ -88,12 +95,12 @@ Minimization stats:
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.0074182 | 0.0074182 | 0.0074182 | 0.0 | 84.81
-Neigh | 0.00042582 | 0.00042582 | 0.00042582 | 0.0 | 4.87
-Comm | 7.2718e-05 | 7.2718e-05 | 7.2718e-05 | 0.0 | 0.83
-Output | 2.2173e-05 | 2.2173e-05 | 2.2173e-05 | 0.0 | 0.25
-Modify | 0.00011134 | 0.00011134 | 0.00011134 | 0.0 | 1.27
-Other | | 0.0006967 | | | 7.96
+Pair | 0.0073352 | 0.0073352 | 0.0073352 | 0.0 | 82.48
+Neigh | 0.00039649 | 0.00039649 | 0.00039649 | 0.0 | 4.46
+Comm | 9.8944e-05 | 9.8944e-05 | 9.8944e-05 | 0.0 | 1.11
+Output | 2.718e-05 | 2.718e-05 | 2.718e-05 | 0.0 | 0.31
+Modify | 0.00016856 | 0.00016856 | 0.00016856 | 0.0 | 1.90
+Other | | 0.0008671 | | | 9.75
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -114,8 +121,8 @@ 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
+WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168)
+Per MPI rank memory allocation (min/avg/max) = 4.168 | 4.168 | 4.168 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
@@ -127,9 +134,9 @@ Step Temp E_pair E_mol TotEng Press Volume
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 0.02054 on 1 procs for 76 steps with 420 atoms
+Loop time of 0.0211506 on 1 procs for 76 steps with 420 atoms
-97.4% CPU use with 1 MPI tasks x no OpenMP threads
+99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
@@ -143,12 +150,12 @@ Minimization stats:
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.015534 | 0.015534 | 0.015534 | 0.0 | 75.63
-Neigh | 0.0021462 | 0.0021462 | 0.0021462 | 0.0 | 10.45
-Comm | 0.00019169 | 0.00019169 | 0.00019169 | 0.0 | 0.93
-Output | 6.2704e-05 | 6.2704e-05 | 6.2704e-05 | 0.0 | 0.31
-Modify | 0.00095463 | 0.00095463 | 0.00095463 | 0.0 | 4.65
-Other | | 0.001651 | | | 8.04
+Pair | 0.015347 | 0.015347 | 0.015347 | 0.0 | 72.56
+Neigh | 0.002106 | 0.002106 | 0.002106 | 0.0 | 9.96
+Comm | 0.00025511 | 0.00025511 | 0.00025511 | 0.0 | 1.21
+Output | 7.1287e-05 | 7.1287e-05 | 7.1287e-05 | 0.0 | 0.34
+Modify | 0.0013864 | 0.0013864 | 0.0013864 | 0.0 | 6.55
+Other | | 0.001985 | | | 9.38
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -166,8 +173,8 @@ 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
+WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168)
+Per MPI rank memory allocation (min/avg/max) = 4.168 | 4.168 | 4.168 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
@@ -179,9 +186,9 @@ Step Temp E_pair E_mol TotEng Press Volume
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 0.0210519 on 1 procs for 82 steps with 420 atoms
+Loop time of 0.0218823 on 1 procs for 82 steps with 420 atoms
-104.5% CPU use with 1 MPI tasks x no OpenMP threads
+99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
@@ -195,12 +202,12 @@ Minimization stats:
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.01655 | 0.01655 | 0.01655 | 0.0 | 78.62
-Neigh | 0.0016158 | 0.0016158 | 0.0016158 | 0.0 | 7.68
-Comm | 0.00016141 | 0.00016141 | 0.00016141 | 0.0 | 0.77
-Output | 5.4359e-05 | 5.4359e-05 | 5.4359e-05 | 0.0 | 0.26
-Modify | 0.0010245 | 0.0010245 | 0.0010245 | 0.0 | 4.87
-Other | | 0.001646 | | | 7.82
+Pair | 0.016445 | 0.016445 | 0.016445 | 0.0 | 75.15
+Neigh | 0.0015912 | 0.0015912 | 0.0015912 | 0.0 | 7.27
+Comm | 0.00024986 | 0.00024986 | 0.00024986 | 0.0 | 1.14
+Output | 7.1526e-05 | 7.1526e-05 | 7.1526e-05 | 0.0 | 0.33
+Modify | 0.0014741 | 0.0014741 | 0.0014741 | 0.0 | 6.74
+Other | | 0.002051 | | | 9.37
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -218,8 +225,8 @@ 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
+WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168)
+Per MPI rank memory allocation (min/avg/max) = 4.168 | 4.168 | 4.168 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
@@ -235,9 +242,9 @@ Step Temp E_pair E_mol TotEng Press Volume
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 0.0372601 on 1 procs for 123 steps with 420 atoms
+Loop time of 0.0387044 on 1 procs for 123 steps with 420 atoms
-99.3% CPU use with 1 MPI tasks x no OpenMP threads
+99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = linesearch alpha is zero
@@ -251,12 +258,12 @@ Minimization stats:
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.028822 | 0.028822 | 0.028822 | 0.0 | 77.35
-Neigh | 0.0035007 | 0.0035007 | 0.0035007 | 0.0 | 9.40
-Comm | 0.00031781 | 0.00031781 | 0.00031781 | 0.0 | 0.85
-Output | 8.1539e-05 | 8.1539e-05 | 8.1539e-05 | 0.0 | 0.22
-Modify | 0.0017815 | 0.0017815 | 0.0017815 | 0.0 | 4.78
-Other | | 0.002757 | | | 7.40
+Pair | 0.028596 | 0.028596 | 0.028596 | 0.0 | 73.88
+Neigh | 0.0035679 | 0.0035679 | 0.0035679 | 0.0 | 9.22
+Comm | 0.00047278 | 0.00047278 | 0.00047278 | 0.0 | 1.22
+Output | 0.0001111 | 0.0001111 | 0.0001111 | 0.0 | 0.29
+Modify | 0.0025539 | 0.0025539 | 0.0025539 | 0.0 | 6.60
+Other | | 0.003402 | | | 8.79
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -274,8 +281,8 @@ 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
+WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168)
+Per MPI rank memory allocation (min/avg/max) = 4.168 | 4.168 | 4.168 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
@@ -294,9 +301,9 @@ Step Temp E_pair E_mol TotEng Press Volume
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 0.0447221 on 1 procs for 149 steps with 420 atoms
+Loop time of 0.046638 on 1 procs for 149 steps with 420 atoms
-96.1% CPU use with 1 MPI tasks x no OpenMP threads
+99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = linesearch alpha is zero
@@ -310,12 +317,12 @@ Minimization stats:
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.034669 | 0.034669 | 0.034669 | 0.0 | 77.52
-Neigh | 0.0041096 | 0.0041096 | 0.0041096 | 0.0 | 9.19
-Comm | 0.00039029 | 0.00039029 | 0.00039029 | 0.0 | 0.87
-Output | 0.00010586 | 0.00010586 | 0.00010586 | 0.0 | 0.24
-Modify | 0.0021372 | 0.0021372 | 0.0021372 | 0.0 | 4.78
-Other | | 0.00331 | | | 7.40
+Pair | 0.034523 | 0.034523 | 0.034523 | 0.0 | 74.02
+Neigh | 0.0042307 | 0.0042307 | 0.0042307 | 0.0 | 9.07
+Comm | 0.00056744 | 0.00056744 | 0.00056744 | 0.0 | 1.22
+Output | 0.00013828 | 0.00013828 | 0.00013828 | 0.0 | 0.30
+Modify | 0.0030701 | 0.0030701 | 0.0030701 | 0.0 | 6.58
+Other | | 0.004109 | | | 8.81
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -333,8 +340,8 @@ 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
+WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168)
+Per MPI rank memory allocation (min/avg/max) = 4.168 | 4.168 | 4.168 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
@@ -357,9 +364,9 @@ Step Temp E_pair E_mol TotEng Press Volume
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 0.055048 on 1 procs for 186 steps with 420 atoms
+Loop time of 0.0571101 on 1 procs for 186 steps with 420 atoms
-99.9% CPU use with 1 MPI tasks x no OpenMP threads
+99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = linesearch alpha is zero
@@ -373,12 +380,12 @@ Minimization stats:
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.042811 | 0.042811 | 0.042811 | 0.0 | 77.77
-Neigh | 0.0048847 | 0.0048847 | 0.0048847 | 0.0 | 8.87
-Comm | 0.00049543 | 0.00049543 | 0.00049543 | 0.0 | 0.90
-Output | 0.00013161 | 0.00013161 | 0.00013161 | 0.0 | 0.24
-Modify | 0.0026782 | 0.0026782 | 0.0026782 | 0.0 | 4.87
-Other | | 0.004047 | | | 7.35
+Pair | 0.042337 | 0.042337 | 0.042337 | 0.0 | 74.13
+Neigh | 0.0050063 | 0.0050063 | 0.0050063 | 0.0 | 8.77
+Comm | 0.00071383 | 0.00071383 | 0.00071383 | 0.0 | 1.25
+Output | 0.00017142 | 0.00017142 | 0.00017142 | 0.0 | 0.30
+Modify | 0.0038519 | 0.0038519 | 0.0038519 | 0.0 | 6.74
+Other | | 0.005029 | | | 8.81
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -396,8 +403,8 @@ 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
+WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168)
+Per MPI rank memory allocation (min/avg/max) = 4.169 | 4.169 | 4.169 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
@@ -415,9 +422,9 @@ Step Temp E_pair E_mol TotEng Press Volume
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 0.043978 on 1 procs for 148 steps with 420 atoms
+Loop time of 0.0457094 on 1 procs for 148 steps with 420 atoms
-100.0% CPU use with 1 MPI tasks x no OpenMP threads
+99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = linesearch alpha is zero
@@ -431,12 +438,12 @@ Minimization stats:
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.034369 | 0.034369 | 0.034369 | 0.0 | 78.15
-Neigh | 0.0036526 | 0.0036526 | 0.0036526 | 0.0 | 8.31
-Comm | 0.00038934 | 0.00038934 | 0.00038934 | 0.0 | 0.89
-Output | 9.3699e-05 | 9.3699e-05 | 9.3699e-05 | 0.0 | 0.21
-Modify | 0.0021935 | 0.0021935 | 0.0021935 | 0.0 | 4.99
-Other | | 0.00328 | | | 7.46
+Pair | 0.03413 | 0.03413 | 0.03413 | 0.0 | 74.67
+Neigh | 0.0037162 | 0.0037162 | 0.0037162 | 0.0 | 8.13
+Comm | 0.00058603 | 0.00058603 | 0.00058603 | 0.0 | 1.28
+Output | 0.00012612 | 0.00012612 | 0.00012612 | 0.0 | 0.28
+Modify | 0.0031106 | 0.0031106 | 0.0031106 | 0.0 | 6.81
+Other | | 0.00404 | | | 8.84
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
diff --git a/examples/indent/log.5Oct16.indent.min.g++.4 b/examples/indent/log.27Nov18.indent.min.g++.4
similarity index 76%
rename from examples/indent/log.5Oct16.indent.min.g++.4
rename to examples/indent/log.27Nov18.indent.min.g++.4
index 4ea1a37d25..b0dca95501 100644
--- a/examples/indent/log.5Oct16.indent.min.g++.4
+++ b/examples/indent/log.27Nov18.indent.min.g++.4
@@ -1,4 +1,5 @@
-LAMMPS (5 Oct 2016)
+LAMMPS (27 Nov 2018)
+ using 1 OpenMP thread(s) per MPI task
# 2d indenter simulation with minimization instead of dynamics
dimension 2
@@ -18,6 +19,7 @@ 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
+ Time spent = 0.000312805 secs
mass * 1.0
@@ -57,24 +59,29 @@ thermo 10
#dump_modify 3 pad 4
minimize 1.0e-6 1.0e-6 1000 1000
-WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
+WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/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
+ binsize = 1.4, bins = 17 15 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) = 4.172 | 4.172 | 4.172 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 0.00329685 on 4 procs for 35 steps with 420 atoms
+Loop time of 0.00425965 on 4 procs for 35 steps with 420 atoms
-75.8% CPU use with 4 MPI tasks x no OpenMP threads
+91.0% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
@@ -88,12 +95,12 @@ Minimization stats:
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.0018942 | 0.0019329 | 0.0019758 | 0.1 | 58.63
-Neigh | 0.00011587 | 0.000121 | 0.00012612 | 0.0 | 3.67
-Comm | 0.00034523 | 0.00040966 | 0.00046587 | 0.3 | 12.43
-Output | 4.3869e-05 | 4.667e-05 | 5.2929e-05 | 0.1 | 1.42
-Modify | 2.4796e-05 | 3.7432e-05 | 5.0306e-05 | 0.2 | 1.14
-Other | | 0.0007492 | | | 22.73
+Pair | 0.0018404 | 0.0020409 | 0.002239 | 0.3 | 47.91
+Neigh | 0.00011182 | 0.00011867 | 0.00012565 | 0.0 | 2.79
+Comm | 0.00071144 | 0.0010059 | 0.0013125 | 0.7 | 23.62
+Output | 4.1723e-05 | 4.4882e-05 | 5.1022e-05 | 0.0 | 1.05
+Modify | 4.7445e-05 | 5.6326e-05 | 6.4611e-05 | 0.0 | 1.32
+Other | | 0.0009929 | | | 23.31
Nlocal: 105 ave 111 max 99 min
Histogram: 1 1 0 0 0 0 0 0 1 1
@@ -114,8 +121,8 @@ 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
+WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168)
+Per MPI rank memory allocation (min/avg/max) = 4.172 | 4.172 | 4.172 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
@@ -127,9 +134,9 @@ Step Temp E_pair E_mol TotEng Press Volume
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 0.00908947 on 4 procs for 76 steps with 420 atoms
+Loop time of 0.009408 on 4 procs for 76 steps with 420 atoms
-96.2% CPU use with 4 MPI tasks x no OpenMP threads
+98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
@@ -143,12 +150,12 @@ Minimization stats:
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.0037253 | 0.0040306 | 0.0043435 | 0.5 | 44.34
-Neigh | 0.00058532 | 0.00061685 | 0.00064421 | 0.1 | 6.79
-Comm | 0.0012383 | 0.0015994 | 0.0019143 | 0.8 | 17.60
-Output | 0.00012493 | 0.0001325 | 0.00015235 | 0.1 | 1.46
-Modify | 0.00026274 | 0.00028539 | 0.00030255 | 0.1 | 3.14
-Other | | 0.002425 | | | 26.68
+Pair | 0.0035956 | 0.0040194 | 0.0043173 | 0.5 | 42.72
+Neigh | 0.00058937 | 0.00061256 | 0.00065064 | 0.0 | 6.51
+Comm | 0.0012782 | 0.0017276 | 0.0023015 | 1.0 | 18.36
+Output | 0.00012088 | 0.00013882 | 0.00018907 | 0.0 | 1.48
+Modify | 0.00037575 | 0.00040001 | 0.00041938 | 0.0 | 4.25
+Other | | 0.00251 | | | 26.68
Nlocal: 105 ave 111 max 99 min
Histogram: 1 1 0 0 0 0 0 0 1 1
@@ -166,8 +173,8 @@ 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
+WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168)
+Per MPI rank memory allocation (min/avg/max) = 4.172 | 4.172 | 4.172 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
@@ -179,9 +186,9 @@ Step Temp E_pair E_mol TotEng Press Volume
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 0.00948715 on 4 procs for 82 steps with 420 atoms
+Loop time of 0.00970888 on 4 procs for 82 steps with 420 atoms
-100.1% CPU use with 4 MPI tasks x no OpenMP threads
+98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
@@ -195,12 +202,12 @@ Minimization stats:
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.0037739 | 0.0042151 | 0.0046482 | 0.6 | 44.43
-Neigh | 0.00041008 | 0.0004425 | 0.00048161 | 0.1 | 4.66
-Comm | 0.0013449 | 0.0018466 | 0.0023468 | 1.1 | 19.46
-Output | 0.00012422 | 0.00013196 | 0.00015044 | 0.1 | 1.39
-Modify | 0.00026131 | 0.00028855 | 0.00030518 | 0.1 | 3.04
-Other | | 0.002563 | | | 27.01
+Pair | 0.0038064 | 0.0043663 | 0.0049345 | 0.7 | 44.97
+Neigh | 0.00041938 | 0.00044787 | 0.00046825 | 0.0 | 4.61
+Comm | 0.0012298 | 0.0018778 | 0.0025084 | 1.2 | 19.34
+Output | 0.00010872 | 0.00013095 | 0.00019455 | 0.0 | 1.35
+Modify | 0.0003829 | 0.00042218 | 0.00045204 | 0.0 | 4.35
+Other | | 0.002464 | | | 25.38
Nlocal: 105 ave 112 max 98 min
Histogram: 1 0 1 0 0 0 0 1 0 1
@@ -218,8 +225,8 @@ 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
+WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168)
+Per MPI rank memory allocation (min/avg/max) = 4.172 | 4.172 | 4.172 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
@@ -235,9 +242,9 @@ Step Temp E_pair E_mol TotEng Press Volume
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 0.016437 on 4 procs for 120 steps with 420 atoms
+Loop time of 0.0169249 on 4 procs for 120 steps with 420 atoms
-95.8% CPU use with 4 MPI tasks x no OpenMP threads
+95.2% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = linesearch alpha is zero
@@ -251,12 +258,12 @@ Minimization stats:
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.0060949 | 0.0071945 | 0.008219 | 1.2 | 43.77
-Neigh | 0.00081253 | 0.00092614 | 0.0010352 | 0.3 | 5.63
-Comm | 0.0022275 | 0.0035025 | 0.0047491 | 2.1 | 21.31
-Output | 0.00018907 | 0.00019854 | 0.00022316 | 0.1 | 1.21
-Modify | 0.00045967 | 0.00049853 | 0.0005331 | 0.1 | 3.03
-Other | | 0.004117 | | | 25.05
+Pair | 0.0061595 | 0.0073055 | 0.0083787 | 1.2 | 43.16
+Neigh | 0.00085759 | 0.00095439 | 0.0010619 | 0.0 | 5.64
+Comm | 0.0020378 | 0.0032984 | 0.0046635 | 2.1 | 19.49
+Output | 0.00016832 | 0.00020832 | 0.00032616 | 0.0 | 1.23
+Modify | 0.0006628 | 0.00078654 | 0.00090957 | 0.0 | 4.65
+Other | | 0.004372 | | | 25.83
Nlocal: 105 ave 123 max 90 min
Histogram: 2 0 0 0 0 0 0 0 1 1
@@ -274,8 +281,8 @@ 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
+WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168)
+Per MPI rank memory allocation (min/avg/max) = 4.172 | 4.172 | 4.173 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
@@ -289,9 +296,9 @@ Step Temp E_pair E_mol TotEng Press Volume
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 0.0132418 on 4 procs for 104 steps with 420 atoms
+Loop time of 0.0135124 on 4 procs for 104 steps with 420 atoms
-94.4% CPU use with 4 MPI tasks x no OpenMP threads
+90.7% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
@@ -305,12 +312,12 @@ Minimization stats:
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.0043645 | 0.0054896 | 0.0065427 | 1.4 | 41.46
-Neigh | 0.00071716 | 0.00088716 | 0.0010509 | 0.5 | 6.70
-Comm | 0.0017078 | 0.0030243 | 0.0044179 | 2.3 | 22.84
-Output | 0.00015879 | 0.00016719 | 0.00018978 | 0.1 | 1.26
-Modify | 0.00033998 | 0.00038028 | 0.00042176 | 0.2 | 2.87
-Other | | 0.003293 | | | 24.87
+Pair | 0.0043001 | 0.0056325 | 0.0068884 | 1.5 | 41.68
+Neigh | 0.0007472 | 0.00091684 | 0.0010941 | 0.0 | 6.79
+Comm | 0.0015268 | 0.0030602 | 0.0046747 | 2.4 | 22.65
+Output | 0.00014591 | 0.00017387 | 0.00025606 | 0.0 | 1.29
+Modify | 0.00047064 | 0.00054699 | 0.00062537 | 0.0 | 4.05
+Other | | 0.003182 | | | 23.55
Nlocal: 105 ave 121 max 89 min
Histogram: 2 0 0 0 0 0 0 0 0 2
@@ -328,8 +335,8 @@ 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
+WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168)
+Per MPI rank memory allocation (min/avg/max) = 4.172 | 4.173 | 4.173 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
@@ -352,9 +359,9 @@ Step Temp E_pair E_mol TotEng Press Volume
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 0.0257494 on 4 procs for 188 steps with 420 atoms
+Loop time of 0.0262601 on 4 procs for 188 steps with 420 atoms
-98.0% CPU use with 4 MPI tasks x no OpenMP threads
+95.8% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = linesearch alpha is zero
@@ -368,12 +375,12 @@ Minimization stats:
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.0080748 | 0.010793 | 0.013608 | 2.6 | 41.91
-Neigh | 0.000983 | 0.0012598 | 0.0015397 | 0.8 | 4.89
-Comm | 0.003365 | 0.0064785 | 0.0095432 | 3.8 | 25.16
-Output | 0.0002985 | 0.00031477 | 0.00035667 | 0.1 | 1.22
-Modify | 0.00062346 | 0.0007531 | 0.00086522 | 0.4 | 2.92
-Other | | 0.00615 | | | 23.89
+Pair | 0.0080013 | 0.010975 | 0.013789 | 2.6 | 41.79
+Neigh | 0.001025 | 0.001315 | 0.0016329 | 0.8 | 5.01
+Comm | 0.0033126 | 0.0065627 | 0.010028 | 3.9 | 24.99
+Output | 0.00025845 | 0.00032175 | 0.00050783 | 0.0 | 1.23
+Modify | 0.00088954 | 0.0010915 | 0.0012805 | 0.6 | 4.16
+Other | | 0.005994 | | | 22.83
Nlocal: 105 ave 125 max 84 min
Histogram: 2 0 0 0 0 0 0 0 0 2
@@ -391,8 +398,8 @@ 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
+WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168)
+Per MPI rank memory allocation (min/avg/max) = 4.172 | 4.173 | 4.173 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
@@ -408,9 +415,9 @@ Step Temp E_pair E_mol TotEng Press Volume
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 0.017405 on 4 procs for 124 steps with 420 atoms
+Loop time of 0.0187363 on 4 procs for 124 steps with 420 atoms
-97.7% CPU use with 4 MPI tasks x no OpenMP threads
+94.5% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = linesearch alpha is zero
@@ -424,12 +431,12 @@ Minimization stats:
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.0049167 | 0.0073144 | 0.0095913 | 2.7 | 42.02
-Neigh | 0.00037408 | 0.00051659 | 0.00065827 | 0.6 | 2.97
-Comm | 0.0021894 | 0.0047411 | 0.0072858 | 3.6 | 27.24
-Output | 0.00018907 | 0.0001967 | 0.00021863 | 0.1 | 1.13
-Modify | 0.00040865 | 0.00051677 | 0.00060606 | 0.4 | 2.97
-Other | | 0.004119 | | | 23.67
+Pair | 0.0051301 | 0.0074221 | 0.0098505 | 2.6 | 39.61
+Neigh | 0.00038052 | 0.00054228 | 0.00068402 | 0.0 | 2.89
+Comm | 0.0018504 | 0.004572 | 0.007129 | 3.8 | 24.40
+Output | 0.00017834 | 0.00021213 | 0.00030828 | 0.0 | 1.13
+Modify | 0.00057554 | 0.00075471 | 0.00091839 | 0.0 | 4.03
+Other | | 0.005233 | | | 27.93
Nlocal: 105 ave 131 max 78 min
Histogram: 2 0 0 0 0 0 0 0 0 2
--
GitLab