diff --git a/examples/colloid/log.colloid.21May08.linux.1 b/examples/colloid/log.colloid.21May08.linux.1
new file mode 100644
index 000000000..f097d2d11
--- /dev/null
+++ b/examples/colloid/log.colloid.21May08.linux.1
@@ -0,0 +1,120 @@
+LAMMPS (21 May 2008)
+# Big colloid particles and small LJ particles
+
+units lj
+atom_style atomic
+dimension 2
+
+lattice sq 0.01
+Lattice spacing in x,y,z = 10 10 10
+region box block 0 30 0 30 -0.5 0.5
+create_box 2 box
+Created orthogonal box = (0 0 -5) to (300 300 5)
+ 1 by 1 by 1 processor grid
+create_atoms 1 box
+Created 900 atoms
+
+set group all type/fraction 2 0.96 23984
+ 861 settings made for type/fraction
+
+mass 1 9
+mass 2 1
+
+velocity all create 1.44 87287 loop geom
+
+# multi neighbor and comm for efficiency
+
+neighbor 1 multi
+neigh_modify delay 0
+communicate multi
+
+# colloid potential
+
+pair_style colloid 12.5
+pair_coeff 1 1 1.0 1.0 5.0 5.0 12.5
+pair_coeff 1 2 5.0 1.0 5.0 0.0 7.0
+pair_coeff 2 2 10.0 1.0 0.0 0.0 2.5
+
+fix 1 all npt 2.0 2.0 1.0 xyz 0.0 1.0 10.0 drag 1.0
+fix 2 all enforce2d
+
+dump 1 all atom 200 dump.colloid
+
+thermo_style custom step temp epair etotal press vol
+thermo 1000
+
+timestep 0.005
+
+run 50000
+Memory usage per processor = 1.84805 Mbytes
+Step Temp E_pair TotEng Press Volume
+ 0 1.44 -2.2136534e-06 1.4383978 0.014383923 90000
+ 1000 1.7223559 0.00098929183 1.7214314 0.015437595 101049.21
+ 2000 1.9986757 0.00075885378 1.9972138 0.018605636 99044.305
+ 3000 2.117844 0.0022972154 2.1177881 0.0290761 68969.85
+ 4000 2.0898816 0.0057833635 2.0933428 0.047715809 41724.713
+ 5000 2.0439342 4.9494163e-05 2.0417126 0.068595136 27281.204
+ 6000 2.0064511 0.0044083308 2.0086301 0.099885102 20425.198
+ 7000 2.0093135 0.00030033275 2.0073813 0.1121452 16950.524
+ 8000 1.9916421 0.007621323 1.9970505 0.13964337 14953.142
+ 9000 1.9903947 0.01453264 2.0027158 0.15594249 13489.913
+ 10000 1.9988985 0.0052414174 2.0019189 0.17202156 12266.498
+ 11000 2.00691 0.01129961 2.0159797 0.1963436 11187.939
+ 12000 2.023487 0.002118289 2.023357 0.19929988 10338.246
+ 13000 1.9848513 0.023120894 2.0057668 0.27040057 9647.688
+ 14000 2.0010828 0.016195647 2.0150551 0.23608408 9076.0171
+ 15000 1.9851734 0.02269988 2.0056676 0.30152394 8550.0935
+ 16000 1.9911017 0.024538799 2.0134282 0.29719998 8065.2116
+ 17000 2.0092834 0.013074179 2.020125 0.33224922 7611.4535
+ 18000 2.0039464 0.015002702 2.0167225 0.34918313 7266.7936
+ 19000 2.0019869 0.030678635 2.0304411 0.35155001 6969.7731
+ 20000 2.0248332 0.023656323 2.0462397 0.35430625 6665.3958
+ 21000 2.0260129 0.011469083 2.0352308 0.37670894 6451.5167
+ 22000 1.9932271 0.02944517 2.0204576 0.44088832 6286.6382
+ 23000 1.9979731 0.022604615 2.0183578 0.40240249 6093.5172
+ 24000 2.0256254 0.014021814 2.0373965 0.43187961 5869.4093
+ 25000 1.9843937 0.046591133 2.0287799 0.44796375 5709.9348
+ 26000 2.0101586 0.017301084 2.0252262 0.51214936 5534.8985
+ 27000 1.9887979 0.042607087 2.0291953 0.5364801 5383.6677
+ 28000 2.0273894 0.010574688 2.0357114 0.53575221 5277.3504
+ 29000 2.0114853 0.026487843 2.0357382 0.5019495 5183.9253
+ 30000 1.9850719 0.036881749 2.019748 0.6029796 5083.5559
+ 31000 1.9896683 0.035584301 2.0230419 0.63219014 4941.787
+ 32000 1.9931863 0.045315686 2.0362874 0.59040131 4851.7745
+ 33000 1.9857406 0.047506524 2.0310408 0.67712512 4778.4773
+ 34000 1.9868172 0.057482705 2.0420923 0.71724066 4683.1331
+ 35000 2.0166361 0.039653294 2.0540487 0.65881549 4607.7207
+ 36000 1.9947118 0.057664381 2.0501599 0.73270964 4500.9296
+ 37000 2.0026862 0.056070861 2.0565318 0.75439865 4419.1699
+ 38000 2.0029796 0.058127694 2.0588818 0.75965407 4349.8826
+ 39000 2.0123422 0.051811215 2.0619175 0.73967495 4280.3846
+ 40000 1.979341 0.064620417 2.0417622 0.91817043 4210.1251
+ 41000 1.9987965 0.048789657 2.0453653 0.77100684 4156.1718
+ 42000 1.9941581 0.053682864 2.0456253 0.81849452 4093.031
+ 43000 2.0170196 0.047788852 2.0625674 0.80410205 4049.9079
+ 44000 2.0256856 0.039232233 2.062667 0.75599759 4004.6084
+ 45000 1.9948188 0.046497265 2.0390996 0.94849943 3947.7148
+ 46000 1.985315 0.080755658 2.0638648 0.88383148 3925.0434
+ 47000 2.0102018 0.055513279 2.0634815 0.89218971 3877.3667
+ 48000 1.9836965 0.073263577 2.054756 1.0335461 3819.6995
+ 49000 2.016596 0.049424893 2.0637802 0.89744695 3789.3397
+ 50000 2.0091046 0.054246496 2.0611188 0.97651208 3721.2095
+Loop time of 14.0034 on 1 procs for 50000 steps with 900 atoms
+
+Pair time (%) = 8.39301 (59.9356)
+Neigh time (%) = 1.62176 (11.5812)
+Comm time (%) = 0.390372 (2.7877)
+Outpt time (%) = 0.311517 (2.22459)
+Other time (%) = 3.28672 (23.4709)
+
+Nlocal: 900 ave 900 max 900 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 574 ave 574 max 574 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 6018 ave 6018 max 6018 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 6018
+Ave neighs/atom = 6.68667
+Neighbor list builds = 2802
+Dangerous builds = 0
diff --git a/examples/colloid/log.colloid.21May08.linux.4 b/examples/colloid/log.colloid.21May08.linux.4
new file mode 100644
index 000000000..3513781e3
--- /dev/null
+++ b/examples/colloid/log.colloid.21May08.linux.4
@@ -0,0 +1,120 @@
+LAMMPS (21 May 2008)
+# Big colloid particles and small LJ particles
+
+units lj
+atom_style atomic
+dimension 2
+
+lattice sq 0.01
+Lattice spacing in x,y,z = 10 10 10
+region box block 0 30 0 30 -0.5 0.5
+create_box 2 box
+Created orthogonal box = (0 0 -5) to (300 300 5)
+ 2 by 2 by 1 processor grid
+create_atoms 1 box
+Created 900 atoms
+
+set group all type/fraction 2 0.96 23984
+ 861 settings made for type/fraction
+
+mass 1 9
+mass 2 1
+
+velocity all create 1.44 87287 loop geom
+
+# multi neighbor and comm for efficiency
+
+neighbor 1 multi
+neigh_modify delay 0
+communicate multi
+
+# colloid potential
+
+pair_style colloid 12.5
+pair_coeff 1 1 1.0 1.0 5.0 5.0 12.5
+pair_coeff 1 2 5.0 1.0 5.0 0.0 7.0
+pair_coeff 2 2 10.0 1.0 0.0 0.0 2.5
+
+fix 1 all npt 2.0 2.0 1.0 xyz 0.0 1.0 10.0 drag 1.0
+fix 2 all enforce2d
+
+dump 1 all atom 200 dump.colloid
+
+thermo_style custom step temp epair etotal press vol
+thermo 1000
+
+timestep 0.005
+
+run 50000
+Memory usage per processor = 1.72729 Mbytes
+Step Temp E_pair TotEng Press Volume
+ 0 1.44 -2.2136534e-06 1.4383978 0.014383923 90000
+ 1000 1.7223559 0.00098929183 1.7214314 0.015437595 101049.21
+ 2000 1.9986757 0.00075885378 1.9972138 0.018605636 99044.305
+ 3000 2.117844 0.0022972154 2.1177881 0.0290761 68969.85
+ 4000 2.0898816 0.0057833635 2.0933428 0.047715809 41724.713
+ 5000 2.0439342 4.9493696e-05 2.0417126 0.068595137 27281.204
+ 6000 2.0064128 0.0044188137 2.0086023 0.099926529 20425.195
+ 7000 2.009238 0.00046917886 2.0074747 0.11213609 16950.59
+ 8000 1.9949838 0.0052143802 1.9979815 0.1425616 14958.04
+ 9000 2.0011383 0.0069562003 2.005871 0.14834553 13504.001
+ 10000 1.979696 0.02095102 1.9984473 0.19710313 12322.476
+ 11000 1.9924355 0.020996961 2.0112186 0.19380381 11317.61
+ 12000 2.0174806 0.0045044349 2.0197434 0.19561004 10406.802
+ 13000 2.0141962 0.012098292 2.0240564 0.23000265 9574.4324
+ 14000 2.0117821 0.011995258 2.0215421 0.24369426 8941.3844
+ 15000 2.0145336 0.0075091224 2.0198044 0.27014029 8427.7465
+ 16000 1.9951071 0.016297672 2.009188 0.29810761 8032.5886
+ 17000 1.9873425 0.017851879 2.0029862 0.37277713 7672.305
+ 18000 2.0113338 0.011550523 2.0206495 0.31040003 7349.9335
+ 19000 2.0042474 0.021677746 2.0236982 0.34923741 7038.9595
+ 20000 2.0132671 0.01770125 2.0287314 0.34219638 6788.2687
+ 21000 1.9990052 0.025514077 2.0222981 0.41034791 6511.8494
+ 22000 1.9920265 0.034234411 2.0240476 0.447435 6265.757
+ 23000 1.9785405 0.033612536 2.0099547 0.48855923 6083.2627
+ 24000 2.0072694 0.020012143 2.0250513 0.42997092 5921.4392
+ 25000 1.9999409 0.025903294 2.023622 0.48047026 5734.6208
+ 26000 1.9957819 0.025572875 2.0191372 0.51207606 5567.496
+ 27000 2.0045855 0.021594009 2.0239522 0.55039179 5429.0002
+ 28000 2.0095018 0.031277686 2.0385467 0.53154624 5292.7192
+ 29000 1.9973043 0.031158435 2.0262435 0.66732668 5135.6507
+ 30000 2.0052408 0.043659151 2.0466719 0.54053464 5006.0454
+ 31000 2.0054687 0.028869471 2.0321099 0.6486529 4917.9379
+ 32000 2.0014648 0.039097706 2.0383386 0.63590098 4830.9602
+ 33000 2.0109706 0.027207161 2.0359434 0.62127582 4737.6015
+ 34000 1.9926472 0.053463886 2.043897 0.70086128 4628.5249
+ 35000 2.0042786 0.043819947 2.0458716 0.70552776 4561.5216
+ 36000 2.0055993 0.032340095 2.035711 0.7089785 4483.1738
+ 37000 1.9884127 0.059230504 2.0454339 0.81716796 4421.5811
+ 38000 2.0051674 0.045925715 2.0488651 0.7107607 4384.2193
+ 39000 1.985589 0.050501548 2.0338844 0.85566246 4298.1153
+ 40000 1.9893789 0.06330525 2.0504737 0.80004664 4229.6943
+ 41000 2.0113301 0.036227311 2.0453226 0.87163382 4148.2176
+ 42000 1.9889787 0.05762879 2.0443975 0.76189797 4150.7988
+ 43000 2.0165757 0.042412435 2.0567475 0.7515161 4110.7711
+ 44000 2.0115095 0.047339399 2.0566139 0.80198372 4004.5573
+ 45000 2.0097681 0.061366139 2.0689011 0.84636277 3915.4567
+ 46000 1.9952706 0.065316805 2.0583704 0.84815375 3888.9886
+ 47000 2.0295555 0.04141762 2.0687181 0.85366092 3877.8183
+ 48000 2.0043454 0.064491592 2.0666099 0.93867902 3831.6649
+ 49000 1.995415 0.078541445 2.0717394 0.86534452 3757.6528
+ 50000 2.0184848 0.052970859 2.0692129 1.1246952 3732.4184
+Loop time of 30.607 on 4 procs for 50000 steps with 900 atoms
+
+Pair time (%) = 2.29298 (7.49168)
+Neigh time (%) = 0.420455 (1.37372)
+Comm time (%) = 15.7757 (51.5429)
+Outpt time (%) = 0.357466 (1.16792)
+Other time (%) = 11.7603 (38.4238)
+
+Nlocal: 225 ave 243 max 213 min
+Histogram: 1 1 0 0 1 0 0 0 0 1
+Nghost: 321.5 ave 334 max 315 min
+Histogram: 1 1 1 0 0 0 0 0 0 1
+Neighs: 1507.5 ave 1590 max 1436 min
+Histogram: 1 1 0 0 0 0 1 0 0 1
+
+Total # of neighbors = 6030
+Ave neighs/atom = 6.7
+Neighbor list builds = 2800
+Dangerous builds = 0
diff --git a/examples/colloid/log.colloid.22Jan08.linux.1 b/examples/colloid/log.colloid.22Jan08.linux.1
deleted file mode 100644
index 8e807276b..000000000
--- a/examples/colloid/log.colloid.22Jan08.linux.1
+++ /dev/null
@@ -1,120 +0,0 @@
-LAMMPS (22 Jan 2008)
-# Big colloid particles and small LJ particles
-
-units lj
-atom_style atomic
-dimension 2
-
-lattice sq 0.01
-Lattice spacing in x,y,z = 10 10 10
-region box block 0 30 0 30 -0.5 0.5
-create_box 2 box
-Created orthogonal box = (0 0 -5) to (300 300 5)
- 1 by 1 by 1 processor grid
-create_atoms 1 box
-Created 900 atoms
-
-set group all type/fraction 2 0.96 23984
- 861 settings made for type/fraction
-
-mass 1 9
-mass 2 1
-
-velocity all create 1.44 87287 loop geom
-
-# multi neighbor and comm for efficiency
-
-neighbor 1 multi
-neigh_modify delay 0
-communicate multi
-
-# colloid potential
-
-pair_style colloid 12.5
-pair_coeff 1 1 1.0 1.0 5.0 5.0 12.5
-pair_coeff 1 2 5.0 1.0 5.0 0.0 7.0
-pair_coeff 2 2 10.0 1.0 0.0 0.0 2.5
-
-fix 1 all npt 2.0 2.0 1.0 xyz 0.0 1.0 10.0 drag 1.0
-fix 2 all enforce2d
-
-dump 1 all atom 200 dump.colloid
-
-thermo_style custom step temp epair etotal press vol
-thermo 1000
-
-timestep 0.005
-
-run 50000
-Memory usage per processor = 1.84805 Mbytes
-Step Temp E_pair TotEng Press Volume
- 0 1.44 -2.2136534e-06 1.4375978 0.014375923 90000
- 1000 1.7223464 0.00099729506 1.7204731 0.015431199 101039.13
- 2000 1.9986619 0.00075906115 1.9960899 0.018607661 99018.745
- 3000 2.1174664 0.0023215952 2.1162589 0.029169081 68947.872
- 4000 2.0922515 0.0027117962 2.0914762 0.048247413 41709.954
- 5000 2.0457094 -0.0017934808 2.0405064 0.069440615 27252.713
- 6000 2.0094249 -0.0030357548 2.0030401 0.095318346 20437.896
- 7000 1.9791016 0.015378539 1.9911816 0.12201039 16963.981
- 8000 2.0037567 0.00087754405 2.0012947 0.13624715 14904.297
- 9000 1.9954986 0.0074776387 1.9996504 0.15437139 13466.422
- 10000 2.0017119 0.0090860936 2.0074618 0.15967653 12285.361
- 11000 1.9965885 0.020076864 2.0133378 0.20431975 11226.299
- 12000 1.9893265 0.029138936 2.0151499 0.22508119 10359.215
- 13000 2.0096277 0.0055549561 2.0118333 0.23118708 9650.1073
- 14000 1.9874756 0.025360954 2.009524 0.25223651 9022.125
- 15000 1.9818513 0.036888053 2.0154362 0.3116855 8475.2794
- 16000 1.9928816 0.018897335 2.0084574 0.30081232 8067.2389
- 17000 1.9990591 0.025240285 2.0209676 0.30592349 7632.1957
- 18000 2.0101337 0.01582473 2.0226082 0.35986446 7250.9935
- 19000 2.0091976 0.019233907 2.0250828 0.33919836 6974.9737
- 20000 2.0064131 0.017623877 2.020693 0.35420372 6745.1629
- 21000 1.9971779 0.023499432 2.0173487 0.40913112 6504.8686
- 22000 1.9899433 0.036716791 2.0233435 0.46792355 6249.486
- 23000 2.0165042 0.030701843 2.0438452 0.43797608 6047.9924
- 24000 2.0162136 0.034428645 2.0472819 0.45591758 5884.7421
- 25000 2.0127204 0.035477231 2.0448431 0.5131322 5698.5164
- 26000 2.0187252 0.017160139 2.0325208 0.43758584 5558.1903
- 27000 1.9830248 0.049563853 2.0292837 0.56069898 5409.6546
- 28000 2.0189391 0.019264404 2.0348386 0.48027834 5284.0336
- 29000 1.9713776 0.050692614 2.0187846 0.61025529 5173.3555
- 30000 1.9819168 0.039816462 2.0184301 0.63355537 5059.7477
- 31000 1.9957876 0.045223147 2.0376844 0.60945681 4940.036
- 32000 2.0208255 0.028176971 2.0456344 0.62584685 4820.4303
- 33000 2.0103751 0.039181534 2.046206 0.69487302 4753.2781
- 34000 1.9959594 0.061461733 2.0540945 0.611319 4671.1011
- 35000 1.9843152 0.063438307 2.0444463 0.67227839 4580.8853
- 36000 2.0187362 0.029117024 2.0444886 0.67437268 4451.5952
- 37000 1.9767721 0.064543976 2.0380214 0.75641695 4386.7451
- 38000 2.0054158 0.038665525 2.040739 0.75284861 4340.2087
- 39000 2.0190605 0.028863116 2.0445585 0.72515667 4322.6267
- 40000 1.99241 0.056203851 2.0452932 0.77541878 4240.6248
- 41000 1.9794314 0.06647082 2.0426031 0.91929985 4161.9926
- 42000 2.0137404 0.050868342 2.0612525 0.76319297 4112.588
- 43000 2.0251176 0.041454389 2.0631968 0.8153631 4098.5268
- 44000 1.9931653 0.058795109 2.0486384 0.83341834 4025.7567
- 45000 1.992498 0.059944502 2.0491217 0.9195581 3949.158
- 46000 1.950407 0.087564106 2.0347204 1.0730912 3904.5945
- 47000 1.9829495 0.079781556 2.0594262 0.99133843 3840.5951
- 48000 2.0085408 0.051200913 2.0563942 0.91558928 3817.7264
- 49000 1.9929984 0.063176682 2.0528534 0.97184545 3811.188
- 50000 1.9924895 0.066841874 2.0560106 1.0256436 3768.1172
-Loop time of 14.0171 on 1 procs for 50000 steps with 900 atoms
-
-Pair time (%) = 8.39109 (59.8632)
-Neigh time (%) = 1.62785 (11.6133)
-Comm time (%) = 0.380158 (2.7121)
-Outpt time (%) = 0.311819 (2.22456)
-Other time (%) = 3.3062 (23.5868)
-
-Nlocal: 900 ave 900 max 900 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 506 ave 506 max 506 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 6031 ave 6031 max 6031 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 6031
-Ave neighs/atom = 6.70111
-Neighbor list builds = 2778
-Dangerous builds = 0
diff --git a/examples/colloid/log.colloid.22Jan08.linux.4 b/examples/colloid/log.colloid.22Jan08.linux.4
deleted file mode 100644
index 65aa34a37..000000000
--- a/examples/colloid/log.colloid.22Jan08.linux.4
+++ /dev/null
@@ -1,120 +0,0 @@
-LAMMPS (22 Jan 2008)
-# Big colloid particles and small LJ particles
-
-units lj
-atom_style atomic
-dimension 2
-
-lattice sq 0.01
-Lattice spacing in x,y,z = 10 10 10
-region box block 0 30 0 30 -0.5 0.5
-create_box 2 box
-Created orthogonal box = (0 0 -5) to (300 300 5)
- 2 by 2 by 1 processor grid
-create_atoms 1 box
-Created 900 atoms
-
-set group all type/fraction 2 0.96 23984
- 861 settings made for type/fraction
-
-mass 1 9
-mass 2 1
-
-velocity all create 1.44 87287 loop geom
-
-# multi neighbor and comm for efficiency
-
-neighbor 1 multi
-neigh_modify delay 0
-communicate multi
-
-# colloid potential
-
-pair_style colloid 12.5
-pair_coeff 1 1 1.0 1.0 5.0 5.0 12.5
-pair_coeff 1 2 5.0 1.0 5.0 0.0 7.0
-pair_coeff 2 2 10.0 1.0 0.0 0.0 2.5
-
-fix 1 all npt 2.0 2.0 1.0 xyz 0.0 1.0 10.0 drag 1.0
-fix 2 all enforce2d
-
-dump 1 all atom 200 dump.colloid
-
-thermo_style custom step temp epair etotal press vol
-thermo 1000
-
-timestep 0.005
-
-run 50000
-Memory usage per processor = 1.72729 Mbytes
-Step Temp E_pair TotEng Press Volume
- 0 1.44 -2.2136534e-06 1.4375978 0.014375923 90000
- 1000 1.7223464 0.00099729506 1.7204731 0.015431199 101039.13
- 2000 1.9986619 0.00075906115 1.9960899 0.018607661 99018.745
- 3000 2.1174664 0.0023215952 2.1162589 0.029169081 68947.872
- 4000 2.0922515 0.0027117962 2.0914762 0.048247413 41709.954
- 5000 2.0457094 -0.0017934811 2.0405064 0.069440615 27252.713
- 6000 2.0094247 -0.0030357089 2.00304 0.095318361 20437.896
- 7000 1.9787517 0.015727213 1.991181 0.12210082 16963.98
- 8000 1.9983 0.0017433401 1.9967129 0.14165341 14903.677
- 9000 1.9927888 0.013406349 2.0028739 0.17008104 13468.549
- 10000 1.99929 0.011927067 2.0078849 0.18343491 12299.949
- 11000 2.0150846 0.00018121827 2.0119074 0.18478179 11314.797
- 12000 2.0039613 0.0083020972 2.0089234 0.22215222 10404.632
- 13000 2.0089431 0.00048942212 2.0060843 0.2159184 9598.2333
- 14000 1.9642202 0.03348398 1.9944305 0.29178119 8913.182
- 15000 1.9865717 0.028923917 2.0121846 0.29202685 8385.9226
- 16000 1.9824603 0.021603392 2.0007596 0.35043111 7979.2443
- 17000 2.0212495 0.0013151574 2.0191959 0.29445176 7613.1843
- 18000 2.00735 0.016693347 2.0206977 0.35537739 7292.1647
- 19000 1.9996379 0.025020058 2.0213252 0.35594894 6980.3692
- 20000 1.99304 0.035528694 2.025247 0.39068018 6690.3555
- 21000 1.9996323 0.017458241 2.0137578 0.39735127 6497.3837
- 22000 1.9949617 0.028866687 2.0205034 0.40527844 6223.7318
- 23000 2.0109325 0.017646321 2.0252272 0.4171507 5971.5878
- 24000 2.0065992 0.020958573 2.0242135 0.44285242 5811.3038
- 25000 2.0162034 0.013608049 2.0264511 0.44820753 5670.6039
- 26000 2.0155947 0.021613098 2.0338484 0.50646486 5560.9474
- 27000 1.9867282 0.061035788 2.0444527 0.52834033 5416.229
- 28000 2.0182277 0.027696843 2.0425608 0.50068529 5248.3423
- 29000 1.9969804 0.025362049 2.0190142 0.62372967 5114.3052
- 30000 1.9919721 0.031513314 2.0201654 0.58566807 5040.2167
- 31000 1.9717581 0.065297706 2.0337695 0.58587707 4925.982
- 32000 2.0031236 0.027941441 2.0277265 0.63718249 4800.1641
- 33000 2.009939 0.035745131 2.0423342 0.5565546 4716.8179
- 34000 2.0133737 0.032514079 2.0425322 0.59840543 4661.2112
- 35000 1.9946613 0.050844465 2.0421813 0.75006325 4544.451
- 36000 2.013397 0.0397056 2.0497469 0.65849841 4483.7497
- 37000 2.0006181 0.037963997 2.0352477 0.77598608 4414.6609
- 38000 1.9575408 0.06996425 2.0242425 0.86318741 4362.8063
- 39000 1.9858721 0.064218347 2.0467806 0.72824697 4313.8724
- 40000 2.0033244 0.046949963 2.0469355 0.71735138 4210.7464
- 41000 1.9841673 0.05811834 2.0389787 0.77792196 4140.5996
- 42000 2.0176912 0.035140169 2.0494686 0.72179939 4106.7454
- 43000 1.9910197 0.055696348 2.0433977 0.78813392 4042.2245
- 44000 1.9684218 0.090017002 2.0551581 0.89775094 3964.1659
- 45000 1.9934298 0.063845821 2.0539532 0.87564355 3943.1864
- 46000 2.0098408 0.043671419 2.0501625 0.9380022 3914.699
- 47000 2.0085323 0.055757448 2.0609422 0.83280289 3838.9374
- 48000 1.9935643 0.064908847 2.0551505 0.9287581 3822.0687
- 49000 2.0102242 0.045686005 2.0525598 0.92639038 3796.1209
- 50000 1.9866234 0.069280947 2.0525933 0.98907678 3713.7478
-Loop time of 36.2457 on 4 procs for 50000 steps with 900 atoms
-
-Pair time (%) = 2.46031 (6.78788)
-Neigh time (%) = 0.449679 (1.24064)
-Comm time (%) = 19.0279 (52.4971)
-Outpt time (%) = 0.376391 (1.03844)
-Other time (%) = 13.9313 (38.4359)
-
-Nlocal: 225 ave 253 max 182 min
-Histogram: 1 0 0 0 1 0 0 0 0 2
-Nghost: 297.5 ave 310 max 275 min
-Histogram: 1 0 0 0 0 0 1 0 0 2
-Neighs: 1518.5 ave 1657 max 1246 min
-Histogram: 1 0 0 0 0 0 1 0 0 2
-
-Total # of neighbors = 6074
-Ave neighs/atom = 6.74889
-Neighbor list builds = 2768
-Dangerous builds = 0
diff --git a/examples/crack/log.crack.21May08.linux.1 b/examples/crack/log.crack.21May08.linux.1
new file mode 100644
index 000000000..03a033f6e
--- /dev/null
+++ b/examples/crack/log.crack.21May08.linux.1
@@ -0,0 +1,129 @@
+LAMMPS (21 May 2008)
+# 2d LJ crack simulation
+
+dimension 2
+boundary s s p
+
+atom_style atomic
+neighbor 0.3 bin
+neigh_modify delay 5
+
+# create geometry
+
+lattice hex 0.93
+Lattice spacing in x,y,z = 1.11428 1.92998 1.11428
+region box block 0 100 0 40 -0.25 0.25
+create_box 5 box
+Created orthogonal box = (0 0 -0.278569) to (111.428 77.1994 0.278569)
+ 1 by 1 by 1 processor grid
+create_atoms 1 box
+Created 8141 atoms
+
+mass 1 1.0
+mass 2 1.0
+mass 3 1.0
+mass 4 1.0
+mass 5 1.0
+
+# LJ potentials
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0 2.5
+
+# define groups
+
+region 1 block INF INF INF 1.25 INF INF
+group lower region 1
+302 atoms in group lower
+region 2 block INF INF 38.75 INF INF INF
+group upper region 2
+302 atoms in group upper
+group boundary union lower upper
+604 atoms in group boundary
+group mobile subtract all boundary
+7537 atoms in group mobile
+
+region leftupper block INF 20 20 INF INF INF
+region leftlower block INF 20 INF 20 INF INF
+group leftupper region leftupper
+841 atoms in group leftupper
+group leftlower region leftlower
+841 atoms in group leftlower
+
+set group leftupper type 2
+ 841 settings made for type
+set group leftlower type 3
+ 841 settings made for type
+set group lower type 4
+ 302 settings made for type
+set group upper type 5
+ 302 settings made for type
+
+# initial velocities
+
+compute new mobile temp
+velocity mobile create 0.01 887723 temp new
+velocity upper set 0.0 0.3 0.0
+velocity mobile ramp vy 0.0 0.3 y 1.25 38.75 sum yes
+
+# fixes
+
+fix 1 all nve
+fix 2 boundary setforce NULL 0.0 0.0
+
+# run
+
+timestep 0.003
+thermo 200
+thermo_modify temp new
+
+neigh_modify exclude type 2 3
+dump 1 all atom 500 dump.crack
+run 5000
+Memory usage per processor = 1.98601 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 0.065651733 -3.2595015 0 -3.1987287 -0.03625351 8602.1883
+ 200 0.060086376 -3.2531936 0 -3.1975725 -0.23134158 8635.4
+ 400 0.060533553 -3.2509973 0 -3.1949623 -0.43071023 8675.8283
+ 600 0.06082965 -3.2466949 0 -3.1903858 -0.6030901 8713.3314
+ 800 0.061677224 -3.2413215 0 -3.1842278 -0.74856841 8752.7927
+ 1000 0.062383731 -3.2349273 0 -3.1771796 -0.87459354 8789.671
+ 1200 0.063709246 -3.2276094 0 -3.1686347 -0.98058454 8825.4386
+ 1400 0.065404552 -3.2196608 0 -3.1591168 -1.0699554 8863.034
+ 1600 0.067579602 -3.2110378 0 -3.1484804 -1.1460845 8897.2152
+ 1800 0.069324241 -3.2018536 0 -3.1376812 -1.2025669 8929.5485
+ 2000 0.071014927 -3.1921108 0 -3.1263733 -1.2434925 8960.5106
+ 2200 0.072992881 -3.1818701 0 -3.1143017 -1.2706212 9000.9309
+ 2400 0.075000723 -3.1712313 0 -3.1018043 -1.2835822 9031.5102
+ 2600 0.076843477 -3.1601004 0 -3.0889675 -1.2797332 9068.6361
+ 2800 0.078671706 -3.1487747 0 -3.0759495 -1.2664476 9100.45
+ 3000 0.080713586 -3.1373277 0 -3.0626123 -1.2445454 9131.0432
+ 3200 0.08309469 -3.1260242 0 -3.0491047 -1.2150129 9165.4844
+ 3400 0.085424766 -3.1146623 0 -3.0355859 -1.1843858 9203.3855
+ 3600 0.087396485 -3.1029493 0 -3.0220477 -1.1438492 9230.2539
+ 3800 0.089007987 -3.090822 0 -3.0084286 -1.1004992 9255.5005
+ 4000 0.089813071 -3.0794078 0 -2.9962692 -1.0632524 9278.281
+ 4200 0.08584753 -3.0668559 0 -2.9873882 -1.0383674 9305.2666
+ 4400 0.086197517 -3.0559678 0 -2.9761761 -1.0292345 9325.4174
+ 4600 0.086766447 -3.0437627 0 -2.9634443 -1.0212664 9358.4367
+ 4800 0.088195149 -3.0328502 0 -2.9512093 -1.0275959 9392.0495
+ 5000 0.089415266 -3.0228825 0 -2.9401122 -1.0219203 9432.5928
+Loop time of 12.8237 on 1 procs for 5000 steps with 8141 atoms
+
+Pair time (%) = 11.0154 (85.8987)
+Neigh time (%) = 0.39023 (3.04304)
+Comm time (%) = 0.00849199 (0.066221)
+Outpt time (%) = 0.114103 (0.889782)
+Other time (%) = 1.29548 (10.1022)
+
+Nlocal: 8141 ave 8141 max 8141 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 71389 ave 71389 max 71389 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 71389
+Ave neighs/atom = 8.76907
+Neighbor list builds = 100
+Dangerous builds = 0
diff --git a/examples/crack/log.crack.21May08.linux.4 b/examples/crack/log.crack.21May08.linux.4
new file mode 100644
index 000000000..794e29089
--- /dev/null
+++ b/examples/crack/log.crack.21May08.linux.4
@@ -0,0 +1,129 @@
+LAMMPS (21 May 2008)
+# 2d LJ crack simulation
+
+dimension 2
+boundary s s p
+
+atom_style atomic
+neighbor 0.3 bin
+neigh_modify delay 5
+
+# create geometry
+
+lattice hex 0.93
+Lattice spacing in x,y,z = 1.11428 1.92998 1.11428
+region box block 0 100 0 40 -0.25 0.25
+create_box 5 box
+Created orthogonal box = (0 0 -0.278569) to (111.428 77.1994 0.278569)
+ 2 by 2 by 1 processor grid
+create_atoms 1 box
+Created 8141 atoms
+
+mass 1 1.0
+mass 2 1.0
+mass 3 1.0
+mass 4 1.0
+mass 5 1.0
+
+# LJ potentials
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0 2.5
+
+# define groups
+
+region 1 block INF INF INF 1.25 INF INF
+group lower region 1
+302 atoms in group lower
+region 2 block INF INF 38.75 INF INF INF
+group upper region 2
+302 atoms in group upper
+group boundary union lower upper
+604 atoms in group boundary
+group mobile subtract all boundary
+7537 atoms in group mobile
+
+region leftupper block INF 20 20 INF INF INF
+region leftlower block INF 20 INF 20 INF INF
+group leftupper region leftupper
+841 atoms in group leftupper
+group leftlower region leftlower
+841 atoms in group leftlower
+
+set group leftupper type 2
+ 841 settings made for type
+set group leftlower type 3
+ 841 settings made for type
+set group lower type 4
+ 302 settings made for type
+set group upper type 5
+ 302 settings made for type
+
+# initial velocities
+
+compute new mobile temp
+velocity mobile create 0.01 887723 temp new
+velocity upper set 0.0 0.3 0.0
+velocity mobile ramp vy 0.0 0.3 y 1.25 38.75 sum yes
+
+# fixes
+
+fix 1 all nve
+fix 2 boundary setforce NULL 0.0 0.0
+
+# run
+
+timestep 0.003
+thermo 200
+thermo_modify temp new
+
+neigh_modify exclude type 2 3
+dump 1 all atom 500 dump.crack
+run 5000
+Memory usage per processor = 1.7559 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 0.065993465 -3.2595015 0 -3.1984123 -0.035954133 8602.1883
+ 200 0.060035253 -3.2531886 0 -3.1976149 -0.22766671 8635.1231
+ 400 0.06054278 -3.2510706 0 -3.1950271 -0.42828601 8674.411
+ 600 0.060576995 -3.246816 0 -3.1907408 -0.60041241 8714.1874
+ 800 0.060802753 -3.2413477 0 -3.1850635 -0.7452853 8753.0178
+ 1000 0.061812114 -3.2349942 0 -3.1777756 -0.87164178 8793.5161
+ 1200 0.06317147 -3.2277552 0 -3.1692783 -0.98048929 8819.7022
+ 1400 0.065125405 -3.2198031 0 -3.1595175 -1.0694348 8855.382
+ 1600 0.06725411 -3.2111272 0 -3.148871 -1.1445446 8889.2003
+ 1800 0.069389572 -3.2019689 0 -3.137736 -1.1995438 8930.2905
+ 2000 0.071276448 -3.1921621 0 -3.1261826 -1.2400335 8965.5706
+ 2200 0.073243486 -3.1818809 0 -3.1140805 -1.2653286 8994.1745
+ 2400 0.075063494 -3.1711703 0 -3.1016851 -1.2777211 9035.0036
+ 2600 0.076789207 -3.1600658 0 -3.0889832 -1.275987 9070.0031
+ 2800 0.07875979 -3.1487143 0 -3.0758075 -1.2642789 9102.7214
+ 3000 0.080591853 -3.1372361 0 -3.0626334 -1.2393582 9139.2757
+ 3200 0.08227693 -3.125423 0 -3.0492605 -1.2059907 9165.9163
+ 3400 0.084289444 -3.1136554 0 -3.03563 -1.1676892 9201.2975
+ 3600 0.086720297 -3.1021183 0 -3.0218427 -1.1268117 9229.7367
+ 3800 0.089264018 -3.0909262 0 -3.0082959 -1.0903935 9261.8789
+ 4000 0.091377688 -3.0795096 0 -2.9949227 -1.0584261 9294.1379
+ 4200 0.092665135 -3.0678736 0 -2.9820949 -1.0394077 9328.0647
+ 4400 0.09055434 -3.0560482 0 -2.9722234 -1.0327663 9358.6524
+ 4600 0.088763719 -3.0446018 0 -2.9624346 -1.0280829 9388.1338
+ 4800 0.089467982 -3.0337452 0 -2.950926 -1.0235966 9423.847
+ 5000 0.089910902 -3.0237571 0 -2.9405279 -1.0178644 9448.4573
+Loop time of 5.55919 on 4 procs for 5000 steps with 8141 atoms
+
+Pair time (%) = 2.79903 (50.3495)
+Neigh time (%) = 0.104656 (1.88258)
+Comm time (%) = 1.8012 (32.4004)
+Outpt time (%) = 0.109615 (1.97177)
+Other time (%) = 0.744692 (13.3957)
+
+Nlocal: 2035.25 ave 2064 max 2015 min
+Histogram: 1 1 0 0 0 1 0 0 0 1
+Nghost: 198 ave 248 max 150 min
+Histogram: 1 0 1 0 0 0 0 1 0 1
+Neighs: 17850 ave 18250 max 17601 min
+Histogram: 1 1 0 0 1 0 0 0 0 1
+
+Total # of neighbors = 71400
+Ave neighs/atom = 8.77042
+Neighbor list builds = 106
+Dangerous builds = 0
diff --git a/examples/crack/log.crack.22Jan08.linux.1 b/examples/crack/log.crack.22Jan08.linux.1
deleted file mode 100644
index 0721890db..000000000
--- a/examples/crack/log.crack.22Jan08.linux.1
+++ /dev/null
@@ -1,129 +0,0 @@
-LAMMPS (22 Jan 2008)
-# 2d LJ crack simulation
-
-dimension 2
-boundary s s p
-
-atom_style atomic
-neighbor 0.3 bin
-neigh_modify delay 5
-
-# create geometry
-
-lattice hex 0.93
-Lattice spacing in x,y,z = 1.11428 1.92998 1.11428
-region box block 0 100 0 40 -0.25 0.25
-create_box 5 box
-Created orthogonal box = (0 0 -0.278569) to (111.428 77.1994 0.278569)
- 1 by 1 by 1 processor grid
-create_atoms 1 box
-Created 8141 atoms
-
-mass 1 1.0
-mass 2 1.0
-mass 3 1.0
-mass 4 1.0
-mass 5 1.0
-
-# LJ potentials
-
-pair_style lj/cut 2.5
-pair_coeff * * 1.0 1.0 2.5
-
-# define groups
-
-region 1 block INF INF INF 1.25 INF INF
-group lower region 1
-302 atoms in group lower
-region 2 block INF INF 38.75 INF INF INF
-group upper region 2
-302 atoms in group upper
-group boundary union lower upper
-604 atoms in group boundary
-group mobile subtract all boundary
-7537 atoms in group mobile
-
-region leftupper block INF 20 20 INF INF INF
-region leftlower block INF 20 INF 20 INF INF
-group leftupper region leftupper
-841 atoms in group leftupper
-group leftlower region leftlower
-841 atoms in group leftlower
-
-set group leftupper type 2
- 841 settings made for type
-set group leftlower type 3
- 841 settings made for type
-set group lower type 4
- 302 settings made for type
-set group upper type 5
- 302 settings made for type
-
-# initial velocities
-
-compute new mobile temp
-velocity mobile create 0.01 887723 temp new
-velocity upper set 0.0 0.3 0.0
-velocity mobile ramp vy 0.0 0.3 y 1.25 38.75 sum yes
-
-# fixes
-
-fix 1 all nve
-fix 2 boundary setforce NULL 0.0 0.0
-
-# run
-
-timestep 0.003
-thermo 200
-thermo_modify temp new
-
-neigh_modify exclude type 2 3
-dump 1 all atom 500 dump.crack
-run 5000
-Memory usage per processor = 1.98601 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume
- 0 0.065655433 -3.2595015 0 -3.1987293 -0.036254085 8602.1883
- 200 0.060090071 -3.2531939 0 -3.1975731 -0.23134429 8635.3999
- 400 0.060537254 -3.2509976 0 -3.1949629 -0.4307124 8675.8282
- 600 0.060833381 -3.2466952 0 -3.1903864 -0.60309195 8713.3311
- 800 0.061681012 -3.2413218 0 -3.1842284 -0.74857006 8752.7925
- 1000 0.062387584 -3.2349276 0 -3.1771802 -0.87459498 8789.6707
- 1200 0.063713197 -3.2276097 0 -3.1686353 -0.98058579 8825.4383
- 1400 0.065408625 -3.2196611 0 -3.1591173 -1.0699564 8863.0337
- 1600 0.067583821 -3.2110381 0 -3.1484809 -1.1460853 8897.2148
- 1800 0.069328584 -3.2018539 0 -3.1376817 -1.2025675 8929.5481
- 2000 0.071019398 -3.192111 0 -3.1263738 -1.243493 8960.5103
- 2200 0.072997487 -3.1818704 0 -3.1143022 -1.2706215 9000.9304
- 2400 0.075005457 -3.1712316 0 -3.1018048 -1.2835823 9031.5099
- 2600 0.076848328 -3.1601006 0 -3.088968 -1.279733 9068.6358
- 2800 0.078676694 -3.148775 0 -3.07595 -1.2664473 9100.4495
- 3000 0.080718743 -3.137326 0 -3.0626108 -1.2445399 9131.0428
- 3200 0.083100049 -3.1260245 0 -3.0491051 -1.2150134 9165.484
- 3400 0.085430328 -3.1146626 0 -3.0355863 -1.1843864 9203.385
- 3600 0.087402049 -3.1029496 0 -3.0220482 -1.1438487 9230.2535
- 3800 0.089013695 -3.0908222 0 -3.0084291 -1.100499 9255.4996
- 4000 0.089818767 -3.079408 0 -2.9962696 -1.0632516 9278.2794
- 4200 0.085852921 -3.0668561 0 -2.9873886 -1.0383666 9305.2639
- 4400 0.086203112 -3.0559681 0 -2.9761765 -1.0292349 9325.4147
- 4600 0.086772028 -3.0437629 0 -2.9634447 -1.0212674 9358.4354
- 4800 0.088200815 -3.0328504 0 -2.9512097 -1.027596 9392.0468
- 5000 0.08942145 -3.0228831 0 -2.9401125 -1.0219214 9432.5895
-Loop time of 12.9137 on 1 procs for 5000 steps with 8141 atoms
-
-Pair time (%) = 11.1063 (86.0039)
-Neigh time (%) = 0.387242 (2.99868)
-Comm time (%) = 0.0083847 (0.0649286)
-Outpt time (%) = 0.112896 (0.874232)
-Other time (%) = 1.2989 (10.0583)
-
-Nlocal: 8141 ave 8141 max 8141 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 0 ave 0 max 0 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 71389 ave 71389 max 71389 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 71389
-Ave neighs/atom = 8.76907
-Neighbor list builds = 100
-Dangerous builds = 0
diff --git a/examples/crack/log.crack.22Jan08.linux.4 b/examples/crack/log.crack.22Jan08.linux.4
deleted file mode 100644
index 97b79a11c..000000000
--- a/examples/crack/log.crack.22Jan08.linux.4
+++ /dev/null
@@ -1,129 +0,0 @@
-LAMMPS (22 Jan 2008)
-# 2d LJ crack simulation
-
-dimension 2
-boundary s s p
-
-atom_style atomic
-neighbor 0.3 bin
-neigh_modify delay 5
-
-# create geometry
-
-lattice hex 0.93
-Lattice spacing in x,y,z = 1.11428 1.92998 1.11428
-region box block 0 100 0 40 -0.25 0.25
-create_box 5 box
-Created orthogonal box = (0 0 -0.278569) to (111.428 77.1994 0.278569)
- 2 by 2 by 1 processor grid
-create_atoms 1 box
-Created 8141 atoms
-
-mass 1 1.0
-mass 2 1.0
-mass 3 1.0
-mass 4 1.0
-mass 5 1.0
-
-# LJ potentials
-
-pair_style lj/cut 2.5
-pair_coeff * * 1.0 1.0 2.5
-
-# define groups
-
-region 1 block INF INF INF 1.25 INF INF
-group lower region 1
-302 atoms in group lower
-region 2 block INF INF 38.75 INF INF INF
-group upper region 2
-302 atoms in group upper
-group boundary union lower upper
-604 atoms in group boundary
-group mobile subtract all boundary
-7537 atoms in group mobile
-
-region leftupper block INF 20 20 INF INF INF
-region leftlower block INF 20 INF 20 INF INF
-group leftupper region leftupper
-841 atoms in group leftupper
-group leftlower region leftlower
-841 atoms in group leftlower
-
-set group leftupper type 2
- 841 settings made for type
-set group leftlower type 3
- 841 settings made for type
-set group lower type 4
- 302 settings made for type
-set group upper type 5
- 302 settings made for type
-
-# initial velocities
-
-compute new mobile temp
-velocity mobile create 0.01 887723 temp new
-velocity upper set 0.0 0.3 0.0
-velocity mobile ramp vy 0.0 0.3 y 1.25 38.75 sum yes
-
-# fixes
-
-fix 1 all nve
-fix 2 boundary setforce NULL 0.0 0.0
-
-# run
-
-timestep 0.003
-thermo 200
-thermo_modify temp new
-
-neigh_modify exclude type 2 3
-dump 1 all atom 500 dump.crack
-run 5000
-Memory usage per processor = 1.7559 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume
- 0 0.065997177 -3.2595015 0 -3.1984129 -0.035954718 8602.1883
- 200 0.060038948 -3.253189 0 -3.1976155 -0.22766954 8635.1229
- 400 0.060546481 -3.2510709 0 -3.1950277 -0.42828826 8674.4108
- 600 0.060580716 -3.2468162 0 -3.1907413 -0.60041431 8714.1872
- 800 0.060806514 -3.241348 0 -3.185064 -0.74528707 8753.0176
- 1000 0.06181595 -3.2349944 0 -3.1777762 -0.8716433 8793.5158
- 1200 0.063175404 -3.2277554 0 -3.1692788 -0.98049057 8819.7019
- 1400 0.065129472 -3.2198034 0 -3.159518 -1.0694359 8855.3817
- 1600 0.067258319 -3.2111274 0 -3.1488716 -1.1445455 8889.1999
- 1800 0.069393919 -3.2019692 0 -3.1377365 -1.1995445 8930.2901
- 2000 0.07128093 -3.1921624 0 -3.1261831 -1.2400341 8965.5702
- 2200 0.073248099 -3.1818812 0 -3.114081 -1.2653291 8994.1741
- 2400 0.075068232 -3.1711705 0 -3.1016856 -1.2777213 9035.0033
- 2600 0.076794061 -3.160066 0 -3.0889837 -1.2759869 9070.0027
- 2800 0.07876477 -3.1487145 0 -3.075808 -1.2642785 9102.721
- 3000 0.080596945 -3.1372363 0 -3.0626339 -1.2393574 9139.2753
- 3200 0.082282083 -3.1254232 0 -3.049261 -1.2059897 9165.9158
- 3400 0.084294646 -3.1136555 0 -3.0356304 -1.1676855 9201.297
- 3600 0.086725204 -3.102118 0 -3.0218431 -1.1268035 9229.7361
- 3800 0.089269145 -3.090924 0 -3.0082944 -1.0904239 9261.5209
- 4000 0.091383162 -3.0795096 0 -2.9949232 -1.0585032 9293.4417
- 4200 0.092671959 -3.0678751 0 -2.9820957 -1.0394459 9327.7894
- 4400 0.09056253 -3.0560492 0 -2.9722224 -1.0327842 9358.5052
- 4600 0.088770595 -3.0446045 0 -2.9624363 -1.0281074 9387.8048
- 4800 0.089473674 -3.0337454 0 -2.9509265 -1.023674 9423.1942
- 5000 0.089916902 -3.023759 0 -2.9405298 -1.0178836 9448.3239
-Loop time of 5.86098 on 4 procs for 5000 steps with 8141 atoms
-
-Pair time (%) = 2.87086 (48.9826)
-Neigh time (%) = 0.104604 (1.78475)
-Comm time (%) = 1.96126 (33.4629)
-Outpt time (%) = 0.111139 (1.89626)
-Other time (%) = 0.813119 (13.8734)
-
-Nlocal: 2035.25 ave 2064 max 2015 min
-Histogram: 1 1 0 0 0 1 0 0 0 1
-Nghost: 198.25 ave 249 max 150 min
-Histogram: 1 0 1 0 0 0 0 1 0 1
-Neighs: 17849.5 ave 18249 max 17601 min
-Histogram: 1 1 0 0 1 0 0 0 0 1
-
-Total # of neighbors = 71398
-Ave neighs/atom = 8.77018
-Neighbor list builds = 106
-Dangerous builds = 0
diff --git a/examples/dipole/log.dipole.21May08.linux.1 b/examples/dipole/log.dipole.21May08.linux.1
new file mode 100644
index 000000000..f318df191
--- /dev/null
+++ b/examples/dipole/log.dipole.21May08.linux.1
@@ -0,0 +1,84 @@
+LAMMPS (21 May 2008)
+# Point dipoles in a 2d box
+
+units lj
+atom_style dipole
+dimension 2
+
+lattice sq2 0.7
+Lattice spacing in x,y,z = 1.69031 1.69031 1.69031
+region box block 0 10 0 10 -0.5 0.5
+create_box 1 box
+Created orthogonal box = (0 0 -0.845154) to (16.9031 16.9031 0.845154)
+ 1 by 1 by 1 processor grid
+create_atoms 1 box
+Created 200 atoms
+
+mass 1 1.0
+shape 1 1 1 1
+dipole 1 0.75
+set group all dipole/random 98934
+ 200 settings made for dipole/random
+
+velocity all create 0.0 87287 mom no
+
+pair_style dipole/cut 2.5
+pair_coeff * * 1.0 1.0
+
+neighbor 0.3 bin
+neigh_modify delay 0
+
+fix 1 all nve/sphere update dipole
+fix 2 all enforce2d
+
+timestep 0.005
+
+compute erot all erotate/sphere
+thermo_style custom step temp epair c_erot etotal press
+thermo 500
+
+dump 1 all custom 200 dump.dipole tag type x y z mux muy muz
+
+run 10000
+Memory usage per processor = 2.56176 Mbytes
+Step Temp E_pair erot TotEng Press
+ 0 0 -2.1909822 0 -2.1909822 -2.5750971
+ 500 0.34147461 -2.7418258 0.19338547 -2.4020585 -0.8249727
+ 1000 0.40747968 -2.8229537 0.21834492 -2.4175114 -0.38840717
+ 1500 0.46154716 -2.8375913 0.18215373 -2.3783518 -0.53206048
+ 2000 0.4260216 -2.8138111 0.19511361 -2.3899196 0.25105158
+ 2500 0.46433558 -2.8605248 0.20450084 -2.3985109 -0.10749413
+ 3000 0.37036684 -2.7740526 0.22758113 -2.4055376 0.14916017
+ 3500 0.40204495 -2.7807076 0.21535453 -2.3806729 0.11443486
+ 4000 0.48414345 -2.8671661 0.22749713 -2.3854433 0.018686085
+ 4500 0.47100691 -2.824163 0.20797533 -2.3555111 -0.28502945
+ 5000 0.44520193 -2.8032518 0.21804415 -2.3602759 0.45640206
+ 5500 0.43822519 -2.8303277 0.26920423 -2.3942937 -0.38492346
+ 6000 0.42622278 -2.7949298 0.23879498 -2.3708381 -0.10124264
+ 6500 0.4806966 -2.8484234 0.24787183 -2.3701303 -0.12613324
+ 7000 0.4538584 -2.7937993 0.22316547 -2.3422102 -0.30300725
+ 7500 0.41925032 -2.76312 0.22603976 -2.3459659 -0.36661933
+ 8000 0.4445679 -2.8027613 0.24552024 -2.3604162 0.045204393
+ 8500 0.41376651 -2.7621404 0.23914419 -2.3504427 0.1157167
+ 9000 0.43955192 -2.7181551 0.19988038 -2.280801 -0.40091142
+ 9500 0.48346196 -2.7777386 0.22316491 -2.296694 -0.097144544
+ 10000 0.49780786 -2.7547088 0.2022762 -2.25939 0.077725534
+Loop time of 1.81301 on 1 procs for 10000 steps with 200 atoms
+
+Pair time (%) = 1.45147 (80.0584)
+Neigh time (%) = 0.0490155 (2.70354)
+Comm time (%) = 0.0771546 (4.25561)
+Outpt time (%) = 0.0313296 (1.72804)
+Other time (%) = 0.204043 (11.2544)
+
+Nlocal: 200 ave 200 max 200 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 147 ave 147 max 147 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 1657 ave 1657 max 1657 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1657
+Ave neighs/atom = 8.285
+Neighbor list builds = 693
+Dangerous builds = 0
diff --git a/examples/dipole/log.dipole.21May08.linux.4 b/examples/dipole/log.dipole.21May08.linux.4
new file mode 100644
index 000000000..046a4ac26
--- /dev/null
+++ b/examples/dipole/log.dipole.21May08.linux.4
@@ -0,0 +1,84 @@
+LAMMPS (21 May 2008)
+# Point dipoles in a 2d box
+
+units lj
+atom_style dipole
+dimension 2
+
+lattice sq2 0.7
+Lattice spacing in x,y,z = 1.69031 1.69031 1.69031
+region box block 0 10 0 10 -0.5 0.5
+create_box 1 box
+Created orthogonal box = (0 0 -0.845154) to (16.9031 16.9031 0.845154)
+ 2 by 2 by 1 processor grid
+create_atoms 1 box
+Created 200 atoms
+
+mass 1 1.0
+shape 1 1 1 1
+dipole 1 0.75
+set group all dipole/random 98934
+ 200 settings made for dipole/random
+
+velocity all create 0.0 87287 mom no
+
+pair_style dipole/cut 2.5
+pair_coeff * * 1.0 1.0
+
+neighbor 0.3 bin
+neigh_modify delay 0
+
+fix 1 all nve/sphere update dipole
+fix 2 all enforce2d
+
+timestep 0.005
+
+compute erot all erotate/sphere
+thermo_style custom step temp epair c_erot etotal press
+thermo 500
+
+dump 1 all custom 200 dump.dipole tag type x y z mux muy muz
+
+run 10000
+Memory usage per processor = 2.55191 Mbytes
+Step Temp E_pair erot TotEng Press
+ 0 0 -2.1909822 0 -2.1909822 -2.5750971
+ 500 0.34147461 -2.7418258 0.19338547 -2.4020585 -0.8249727
+ 1000 0.40747968 -2.8229537 0.21834492 -2.4175114 -0.38840717
+ 1500 0.46154713 -2.8375913 0.18215384 -2.3783519 -0.53206031
+ 2000 0.42597513 -2.8139804 0.19520391 -2.3901351 0.25133976
+ 2500 0.40224412 -2.8042036 0.20729219 -2.4039707 -0.13768351
+ 3000 0.44950081 -2.8607567 0.2163603 -2.4135034 -0.37718214
+ 3500 0.42561192 -2.8200273 0.20127716 -2.3965435 -0.2446625
+ 4000 0.38695908 -2.7984855 0.23451044 -2.4134612 -0.085904856
+ 4500 0.39315776 -2.7972983 0.24188008 -2.4061063 -0.1483928
+ 5000 0.43431963 -2.7938176 0.1924971 -2.3616696 0.16044322
+ 5500 0.53852608 -2.8823448 0.19537417 -2.3465113 0.14220621
+ 6000 0.50125727 -2.8270371 0.18662068 -2.3282861 -0.12637044
+ 6500 0.42401402 -2.7997548 0.24141194 -2.3778609 -0.016170475
+ 7000 0.40501108 -2.7515392 0.22505849 -2.3485531 -0.2059805
+ 7500 0.48308411 -2.8009045 0.19665048 -2.3202358 0.10495345
+ 8000 0.48408101 -2.8505581 0.24762262 -2.3688975 -0.092482458
+ 8500 0.40591248 -2.7151281 0.20375135 -2.3112452 -0.43234161
+ 9000 0.44299739 -2.7437233 0.20190578 -2.3029409 0.17321304
+ 9500 0.44248616 -2.7891931 0.26840058 -2.3489194 -0.34093083
+ 10000 0.46831122 -2.7619603 0.21675378 -2.2959906 0.06991871
+Loop time of 4.52779 on 4 procs for 10000 steps with 200 atoms
+
+Pair time (%) = 0.408237 (9.01626)
+Neigh time (%) = 0.0151789 (0.335238)
+Comm time (%) = 3.24156 (71.5926)
+Outpt time (%) = 0.0510209 (1.12684)
+Other time (%) = 0.811791 (17.9291)
+
+Nlocal: 50 ave 53 max 45 min
+Histogram: 1 0 0 0 0 0 1 0 1 1
+Nghost: 88.75 ave 92 max 84 min
+Histogram: 1 0 0 0 0 0 1 1 0 1
+Neighs: 411.5 ave 439 max 344 min
+Histogram: 1 0 0 0 0 0 0 0 1 2
+
+Total # of neighbors = 1646
+Ave neighs/atom = 8.23
+Neighbor list builds = 690
+Dangerous builds = 0
diff --git a/examples/dipole/log.dipole.22Jan08.linux.1 b/examples/dipole/log.dipole.22Jan08.linux.1
deleted file mode 100644
index 721c34def..000000000
--- a/examples/dipole/log.dipole.22Jan08.linux.1
+++ /dev/null
@@ -1,83 +0,0 @@
-LAMMPS (22 Jan 2008)
-# Point dipoles in a 2d box
-
-units lj
-atom_style dipole
-dimension 2
-
-lattice sq2 0.7
-Lattice spacing in x,y,z = 1.69031 1.69031 1.69031
-region box block 0 10 0 10 -0.5 0.5
-create_box 1 box
-Created orthogonal box = (0 0 -0.845154) to (16.9031 16.9031 0.845154)
- 1 by 1 by 1 processor grid
-create_atoms 1 box
-Created 200 atoms
-
-mass 1 1.0
-shape 1 1 1 1
-dipole 1 0.75
-set group all dipole/random 98934
- 200 settings made for dipole/random
-
-velocity all create 0.0 87287 mom no
-
-pair_style dipole/cut 2.5
-pair_coeff * * 1.0 1.0
-
-neighbor 0.3 bin
-neigh_modify delay 0
-
-fix 1 all nve/dipole
-fix 2 all enforce2d
-
-timestep 0.005
-
-thermo_style dipole
-thermo 500
-
-dump 1 all custom 200 dump.dipole tag type x y z mux muy muz
-
-run 10000
-Memory usage per processor = 2.56176 Mbytes
-Step Temp E_pair RotKEdip TotEng Press
- 0 0 -2.1909822 0 -2.1909822 -2.5750971
- 500 0.34233475 -2.7418258 0.24173184 -2.4020585 -0.8249727
- 1000 0.40850608 -2.8229537 0.27293115 -2.4175114 -0.38840717
- 1500 0.46270975 -2.8375913 0.22769216 -2.3783518 -0.53206048
- 2000 0.4270947 -2.8138111 0.24389202 -2.3899196 0.25105158
- 2500 0.46550519 -2.8605248 0.25562605 -2.3985109 -0.10749413
- 3000 0.37129975 -2.7740526 0.28447642 -2.4055376 0.14916017
- 3500 0.40305766 -2.7807076 0.26919316 -2.3806729 0.11443486
- 4000 0.48536295 -2.8671661 0.28437141 -2.3854433 0.018686085
- 4500 0.47219333 -2.824163 0.25996916 -2.3555111 -0.28502945
- 5000 0.44632334 -2.8032518 0.27255518 -2.3602759 0.45640206
- 5500 0.43932904 -2.8303277 0.33650528 -2.3942937 -0.38492346
- 6000 0.42729639 -2.7949298 0.29849372 -2.3708381 -0.10124264
- 6500 0.48190742 -2.8484234 0.30983979 -2.3701303 -0.12613324
- 7000 0.45500162 -2.7937993 0.27895684 -2.3422102 -0.30300725
- 7500 0.42030636 -2.76312 0.2825497 -2.3459659 -0.36661933
- 8000 0.44568772 -2.8027613 0.3069003 -2.3604162 0.045204393
- 8500 0.41480874 -2.7621404 0.29893023 -2.3504427 0.1157167
- 9000 0.44065911 -2.7181551 0.24985047 -2.280801 -0.40091142
- 9500 0.48467975 -2.7777386 0.27895614 -2.296694 -0.097144544
- 10000 0.49906178 -2.7547088 0.25284525 -2.25939 0.077725534
-Loop time of 1.88938 on 1 procs for 10000 steps with 200 atoms
-
-Pair time (%) = 1.46976 (77.7907)
-Neigh time (%) = 0.0489957 (2.59322)
-Comm time (%) = 0.0787163 (4.16625)
-Outpt time (%) = 0.0311885 (1.65073)
-Other time (%) = 0.260716 (13.7991)
-
-Nlocal: 200 ave 200 max 200 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 147 ave 147 max 147 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 1657 ave 1657 max 1657 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 1657
-Ave neighs/atom = 8.285
-Neighbor list builds = 693
-Dangerous builds = 0
diff --git a/examples/dipole/log.dipole.22Jan08.linux.4 b/examples/dipole/log.dipole.22Jan08.linux.4
deleted file mode 100644
index 5239cc80b..000000000
--- a/examples/dipole/log.dipole.22Jan08.linux.4
+++ /dev/null
@@ -1,83 +0,0 @@
-LAMMPS (22 Jan 2008)
-# Point dipoles in a 2d box
-
-units lj
-atom_style dipole
-dimension 2
-
-lattice sq2 0.7
-Lattice spacing in x,y,z = 1.69031 1.69031 1.69031
-region box block 0 10 0 10 -0.5 0.5
-create_box 1 box
-Created orthogonal box = (0 0 -0.845154) to (16.9031 16.9031 0.845154)
- 2 by 2 by 1 processor grid
-create_atoms 1 box
-Created 200 atoms
-
-mass 1 1.0
-shape 1 1 1 1
-dipole 1 0.75
-set group all dipole/random 98934
- 200 settings made for dipole/random
-
-velocity all create 0.0 87287 mom no
-
-pair_style dipole/cut 2.5
-pair_coeff * * 1.0 1.0
-
-neighbor 0.3 bin
-neigh_modify delay 0
-
-fix 1 all nve/dipole
-fix 2 all enforce2d
-
-timestep 0.005
-
-thermo_style dipole
-thermo 500
-
-dump 1 all custom 200 dump.dipole tag type x y z mux muy muz
-
-run 10000
-Memory usage per processor = 2.55191 Mbytes
-Step Temp E_pair RotKEdip TotEng Press
- 0 0 -2.1909822 0 -2.1909822 -2.5750971
- 500 0.34233475 -2.7418258 0.24173184 -2.4020585 -0.8249727
- 1000 0.40850608 -2.8229537 0.27293115 -2.4175114 -0.38840717
- 1500 0.46270972 -2.8375913 0.2276923 -2.3783519 -0.53206031
- 2000 0.42704811 -2.8139804 0.24400489 -2.3901351 0.25133976
- 2500 0.40325733 -2.8042036 0.25911523 -2.4039707 -0.13768351
- 3000 0.45063306 -2.8607567 0.27045037 -2.4135034 -0.37718214
- 3500 0.42668399 -2.8200273 0.25159644 -2.3965435 -0.2446625
- 4000 0.38793379 -2.7984855 0.29313805 -2.4134612 -0.085904856
- 4500 0.39414808 -2.7972983 0.3023501 -2.4061063 -0.1483928
- 5000 0.43541363 -2.7938176 0.24062138 -2.3616696 0.16044322
- 5500 0.53988257 -2.8823448 0.24421771 -2.3465113 0.14220621
- 6000 0.50251988 -2.8270371 0.23327585 -2.3282861 -0.12637044
- 6500 0.42508207 -2.7997548 0.30176493 -2.3778609 -0.016170475
- 7000 0.40603126 -2.7515392 0.28132311 -2.3485531 -0.2059805
- 7500 0.48430095 -2.8009045 0.2458131 -2.3202358 0.10495345
- 8000 0.48530036 -2.8505581 0.30952827 -2.3688975 -0.092482458
- 8500 0.40693493 -2.7151281 0.25468919 -2.3112452 -0.43234161
- 9000 0.44411326 -2.7437233 0.25238223 -2.3029409 0.17321304
- 9500 0.44360073 -2.7891931 0.33550072 -2.3489194 -0.34093083
- 10000 0.46949085 -2.7619603 0.27094222 -2.2959906 0.06991871
-Loop time of 4.8123 on 4 procs for 10000 steps with 200 atoms
-
-Pair time (%) = 0.457601 (9.50898)
-Neigh time (%) = 0.0173309 (0.360137)
-Comm time (%) = 3.3977 (70.6044)
-Outpt time (%) = 0.0532327 (1.10618)
-Other time (%) = 0.886439 (18.4203)
-
-Nlocal: 50 ave 53 max 45 min
-Histogram: 1 0 0 0 0 0 1 0 1 1
-Nghost: 88.75 ave 92 max 84 min
-Histogram: 1 0 0 0 0 0 1 1 0 1
-Neighs: 411.5 ave 439 max 344 min
-Histogram: 1 0 0 0 0 0 0 0 1 2
-
-Total # of neighbors = 1646
-Ave neighs/atom = 8.23
-Neighbor list builds = 690
-Dangerous builds = 0
diff --git a/examples/ellipse/log.ellipse.gayberne.21May08.linux.1 b/examples/ellipse/log.ellipse.gayberne.21May08.linux.1
new file mode 100644
index 000000000..8d0fcab50
--- /dev/null
+++ b/examples/ellipse/log.ellipse.gayberne.21May08.linux.1
@@ -0,0 +1,147 @@
+LAMMPS (21 May 2008)
+# GayBerne ellipsoids in LJ background fluid
+
+units lj
+atom_style ellipsoid
+dimension 2
+
+lattice sq 0.02
+Lattice spacing in x,y,z = 7.07107 7.07107 7.07107
+region box block 0 20 0 20 -0.5 0.5
+create_box 2 box
+Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553)
+ 1 by 1 by 1 processor grid
+create_atoms 1 box
+Created 400 atoms
+
+set group all type/fraction 2 0.1 95392
+ 45 settings made for type/fraction
+set group all quat/random 18238
+ 400 settings made for quat/random
+
+mass 1 1.0
+mass 2 1.5
+shape 1 1 1 1
+shape 2 3 1 1
+
+compute rot all temp/asphere
+velocity all create 2.4 87287 loop geom
+
+pair_style gayberne 1.0 3.0 1.0 4.0
+pair_coeff 1 1 3.0 1.0 1 1 1 1 1 1 2.5
+pair_coeff 1 2 3.0 1.0 1 1 1 0 0 0
+pair_coeff 2 2 1.0 1.0 1 1 0.2 0 0 0
+
+#pair_style resquared 4.0
+#pair_coeff 1 1 3.0 1 1 1 1 1 1 1 2.5
+#pair_coeff 1 2 3.0 1 1 1 1 0 0 0
+#pair_coeff 2 2 1.0 1 1 1 0.2 0 0 0
+
+neighbor 0.8 bin
+
+thermo_style custom step c_rot epair etotal press vol
+thermo 100
+
+timestep 0.002
+
+dump 1 all custom 100 dump.ellipse.gayberne tag type x y z quatw quati quatj quatk
+
+#dump 1 all custom 100 dump.ellipse.resquared # tag type x y z quatw quati quatj quatk
+
+fix 1 all npt/asphere 2.0 2.0 0.1 xyz 0.0 1.0 1.0
+fix 2 all enforce2d
+
+# equilibrate to shrink box around dilute system
+
+run 2000
+Memory usage per processor = 2.5914 Mbytes
+Step rot E_pair TotEng Press Volume
+ 0 2.2718861 0 2.394 0.04788 20000
+ 100 1.7442957 0 1.8380516 0.035762064 20558.675
+ 200 2.2770743 0 2.399467 0.046545738 20620.294
+ 300 1.8572884 0 1.9571177 0.042405959 18460.78
+ 400 2.1710835 -0.00050891124 2.2872701 0.06679187 13689.462
+ 500 1.9873905 -0.043659593 2.0341938 0.099193852 8475.4542
+ 600 2.0886735 -0.24318018 1.8272333 0.2239289 4674.8623
+ 700 2.2603303 -0.73326624 1.481118 0.57180409 2507.1015
+ 800 1.8732232 -1.6161321 0.22091752 1.3050105 1420.4282
+ 900 2.1404535 -3.0146811 -0.84038856 3.3565533 922.07286
+ 1000 1.5928029 -4.5754252 -2.9697801 2.5495232 743.19039
+ 1100 1.8380048 -4.8820036 -3.0604389 2.2950612 708.01399
+ 1200 2.0550725 -4.5701129 -2.4719895 1.4665076 753.52887
+ 1300 2.0004882 -4.075851 -2.0317412 0.35616813 842.13637
+ 1400 2.1055439 -3.7337832 -1.6632225 0.58520115 925.55921
+ 1500 1.9237101 -3.5796185 -1.638185 0.25036967 1006.9876
+ 1600 2.1423718 -3.4821215 -1.3475831 0.62921366 1061.9476
+ 1700 1.8831547 -3.3012167 -1.452471 0.55662052 1120.1928
+ 1800 2.0778263 -3.0986863 -1.0206119 1.0072124 1165.8323
+ 1900 1.8691514 -3.1095986 -1.2252585 0.8080875 1190.9616
+ 2000 1.9636929 -3.1701486 -1.2453089 1.1030872 1176.9149
+Loop time of 1.2504 on 1 procs for 2000 steps with 400 atoms
+
+Pair time (%) = 0.93252 (74.5778)
+Neigh time (%) = 0.0132384 (1.05874)
+Comm time (%) = 0.0220492 (1.76337)
+Outpt time (%) = 0.0338867 (2.71007)
+Other time (%) = 0.248705 (19.89)
+
+Nlocal: 400 ave 400 max 400 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 235 ave 235 max 235 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 2893 ave 2893 max 2893 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 2893
+Ave neighs/atom = 7.2325
+Neighbor list builds = 113
+Dangerous builds = 67
+
+# run dynamics on dense system
+
+unfix 1
+fix 1 all nve/asphere
+
+run 2000
+Memory usage per processor = 2.5919 Mbytes
+Step rot E_pair TotEng Press Volume
+ 2000 1.9636929 -3.1701486 -1.2453089 1.1030872 1176.9149
+ 2100 1.9786552 -3.1838438 -1.1881672 0.49856381 1176.9149
+ 2200 1.9734868 -3.180021 -1.1802031 0.79402856 1176.9149
+ 2300 1.9986019 -3.2105474 -1.2230998 0.74682866 1176.9149
+ 2400 2.0588205 -3.2718878 -1.1680024 0.65794795 1176.9149
+ 2500 2.0355464 -3.2470841 -1.2102204 0.72578641 1176.9149
+ 2600 2.0540796 -3.2674115 -1.1840972 0.60223605 1176.9149
+ 2700 2.0456166 -3.2583563 -1.177938 0.5998038 1176.9149
+ 2800 2.0424993 -3.2552445 -1.1893022 0.70082467 1176.9149
+ 2900 1.9846451 -3.1943095 -1.2115539 0.66453466 1176.9149
+ 3000 1.9581081 -3.1653173 -1.1986913 0.50999007 1176.9149
+ 3100 1.9857943 -3.1963058 -1.256007 0.37827202 1176.9149
+ 3200 2.0076052 -3.2177296 -1.2236764 0.483867 1176.9149
+ 3300 1.9802529 -3.1914149 -1.2047975 0.5938853 1176.9149
+ 3400 2.0450405 -3.2607288 -1.2259986 0.28609172 1176.9149
+ 3500 1.9999875 -3.2132498 -1.1854255 0.62924224 1176.9149
+ 3600 2.0631028 -3.2811837 -1.1722628 0.5970612 1176.9149
+ 3700 1.9794507 -3.1924321 -1.202882 0.82058842 1176.9149
+ 3800 2.0379967 -3.2512273 -1.1964393 0.40334248 1176.9149
+ 3900 2.1120245 -3.3297924 -1.2091066 0.51931911 1176.9149
+ 4000 2.0733971 -3.2925123 -1.2307427 0.56552238 1176.9149
+Loop time of 1.4074 on 1 procs for 2000 steps with 400 atoms
+
+Pair time (%) = 1.14031 (81.0225)
+Neigh time (%) = 0.00835967 (0.593981)
+Comm time (%) = 0.0250871 (1.78252)
+Outpt time (%) = 0.033994 (2.41538)
+Other time (%) = 0.199648 (14.1856)
+
+Nlocal: 400 ave 400 max 400 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 224 ave 224 max 224 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 2985 ave 2985 max 2985 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 2985
+Ave neighs/atom = 7.4625
+Neighbor list builds = 48
+Dangerous builds = 0
diff --git a/examples/ellipse/log.ellipse.gayberne.21May08.linux.4 b/examples/ellipse/log.ellipse.gayberne.21May08.linux.4
new file mode 100644
index 000000000..51b521654
--- /dev/null
+++ b/examples/ellipse/log.ellipse.gayberne.21May08.linux.4
@@ -0,0 +1,147 @@
+LAMMPS (21 May 2008)
+# GayBerne ellipsoids in LJ background fluid
+
+units lj
+atom_style ellipsoid
+dimension 2
+
+lattice sq 0.02
+Lattice spacing in x,y,z = 7.07107 7.07107 7.07107
+region box block 0 20 0 20 -0.5 0.5
+create_box 2 box
+Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553)
+ 2 by 2 by 1 processor grid
+create_atoms 1 box
+Created 400 atoms
+
+set group all type/fraction 2 0.1 95392
+ 45 settings made for type/fraction
+set group all quat/random 18238
+ 400 settings made for quat/random
+
+mass 1 1.0
+mass 2 1.5
+shape 1 1 1 1
+shape 2 3 1 1
+
+compute rot all temp/asphere
+velocity all create 2.4 87287 loop geom
+
+pair_style gayberne 1.0 3.0 1.0 4.0
+pair_coeff 1 1 3.0 1.0 1 1 1 1 1 1 2.5
+pair_coeff 1 2 3.0 1.0 1 1 1 0 0 0
+pair_coeff 2 2 1.0 1.0 1 1 0.2 0 0 0
+
+#pair_style resquared 4.0
+#pair_coeff 1 1 3.0 1 1 1 1 1 1 1 2.5
+#pair_coeff 1 2 3.0 1 1 1 1 0 0 0
+#pair_coeff 2 2 1.0 1 1 1 0.2 0 0 0
+
+neighbor 0.8 bin
+
+thermo_style custom step c_rot epair etotal press vol
+thermo 100
+
+timestep 0.002
+
+dump 1 all custom 100 dump.ellipse.gayberne tag type x y z quatw quati quatj quatk
+
+#dump 1 all custom 100 dump.ellipse.resquared # tag type x y z quatw quati quatj quatk
+
+fix 1 all npt/asphere 2.0 2.0 0.1 xyz 0.0 1.0 1.0
+fix 2 all enforce2d
+
+# equilibrate to shrink box around dilute system
+
+run 2000
+Memory usage per processor = 2.55985 Mbytes
+Step rot E_pair TotEng Press Volume
+ 0 2.2718861 0 2.394 0.04788 20000
+ 100 1.7442957 0 1.8380516 0.035762064 20558.675
+ 200 2.2770743 0 2.399467 0.046545738 20620.294
+ 300 1.8572884 0 1.9571177 0.042405959 18460.78
+ 400 2.1710835 -0.00050891124 2.2872701 0.06679187 13689.462
+ 500 1.9873905 -0.043659593 2.0341938 0.099193852 8475.4542
+ 600 2.0886735 -0.24318018 1.8272333 0.2239289 4674.8623
+ 700 2.2603303 -0.73326624 1.481118 0.57180409 2507.1015
+ 800 1.8732232 -1.6161321 0.22091752 1.3050105 1420.4282
+ 900 2.1404535 -3.0146811 -0.84038856 3.3565533 922.07286
+ 1000 1.5928029 -4.5754252 -2.9697801 2.5495232 743.19039
+ 1100 1.8380048 -4.8820036 -3.0604389 2.2950612 708.01399
+ 1200 2.0550725 -4.5701129 -2.4719895 1.4665076 753.52887
+ 1300 2.0004882 -4.075851 -2.0317412 0.35616813 842.13637
+ 1400 2.1055439 -3.7337832 -1.6632225 0.58520115 925.55921
+ 1500 1.9237101 -3.5796185 -1.638185 0.25036967 1006.9876
+ 1600 2.1423718 -3.4821215 -1.3475831 0.62921366 1061.9476
+ 1700 1.8831547 -3.3012167 -1.452471 0.55662052 1120.1928
+ 1800 2.0778263 -3.0986863 -1.0206119 1.0072124 1165.8323
+ 1900 1.8691514 -3.1095986 -1.2252585 0.80808749 1190.9616
+ 2000 1.9636929 -3.1701486 -1.2453089 1.1030871 1176.9149
+Loop time of 1.41726 on 4 procs for 2000 steps with 400 atoms
+
+Pair time (%) = 0.254874 (17.9836)
+Neigh time (%) = 0.00383508 (0.270599)
+Comm time (%) = 0.669287 (47.2241)
+Outpt time (%) = 0.0560044 (3.9516)
+Other time (%) = 0.433258 (30.5701)
+
+Nlocal: 100 ave 114 max 80 min
+Histogram: 1 0 0 0 0 1 0 1 0 1
+Nghost: 141.75 ave 153 max 131 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+Neighs: 723.25 ave 903 max 497 min
+Histogram: 1 0 0 0 0 1 0 1 0 1
+
+Total # of neighbors = 2893
+Ave neighs/atom = 7.2325
+Neighbor list builds = 113
+Dangerous builds = 67
+
+# run dynamics on dense system
+
+unfix 1
+fix 1 all nve/asphere
+
+run 2000
+Memory usage per processor = 2.56129 Mbytes
+Step rot E_pair TotEng Press Volume
+ 2000 1.9636929 -3.1701486 -1.2453089 1.1030871 1176.9149
+ 2100 1.9786552 -3.1838438 -1.1881672 0.49856382 1176.9149
+ 2200 1.9734867 -3.1800209 -1.1802031 0.79402882 1176.9149
+ 2300 1.9986018 -3.2105474 -1.2230998 0.74682898 1176.9149
+ 2400 2.0588206 -3.2718879 -1.1680027 0.65794654 1176.9149
+ 2500 2.0355453 -3.2470829 -1.2102212 0.72578578 1176.9149
+ 2600 2.0540797 -3.2674115 -1.1840971 0.60223907 1176.9149
+ 2700 2.0456165 -3.2583562 -1.1779378 0.59979597 1176.9149
+ 2800 2.0425097 -3.2552542 -1.189297 0.70076228 1176.9149
+ 2900 1.9846096 -3.1942735 -1.2115473 0.6646236 1176.9149
+ 3000 1.9581313 -3.1653426 -1.1986472 0.51000292 1176.9149
+ 3100 1.9853906 -3.1960037 -1.256084 0.37948337 1176.9149
+ 3200 2.0079056 -3.2180488 -1.2235777 0.48228921 1176.9149
+ 3300 1.9790253 -3.1899998 -1.2044075 0.59676043 1176.9149
+ 3400 2.0479977 -3.2638333 -1.2261703 0.27621482 1176.9149
+ 3500 2.0066637 -3.2203747 -1.1864954 0.62437852 1176.9149
+ 3600 2.0689199 -3.2865465 -1.1668082 0.58048934 1176.9149
+ 3700 1.9862678 -3.1988748 -1.207327 0.8353193 1176.9149
+ 3800 2.0401189 -3.2549146 -1.214896 0.34234416 1176.9149
+ 3900 2.0378699 -3.2539328 -1.1893919 0.66653795 1176.9149
+ 4000 2.0609507 -3.2820151 -1.2128386 0.64471907 1176.9149
+Loop time of 1.22293 on 4 procs for 2000 steps with 400 atoms
+
+Pair time (%) = 0.311134 (25.4416)
+Neigh time (%) = 0.00231725 (0.189483)
+Comm time (%) = 0.670141 (54.7979)
+Outpt time (%) = 0.0586291 (4.79414)
+Other time (%) = 0.180711 (14.7769)
+
+Nlocal: 100 ave 121 max 70 min
+Histogram: 1 0 0 0 0 0 1 1 0 1
+Nghost: 143 ave 155 max 129 min
+Histogram: 1 0 0 1 0 0 0 1 0 1
+Neighs: 750.5 ave 1001 max 418 min
+Histogram: 1 0 0 0 0 1 1 0 0 1
+
+Total # of neighbors = 3002
+Ave neighs/atom = 7.505
+Neighbor list builds = 47
+Dangerous builds = 0
diff --git a/examples/ellipse/log.ellipse.resquared.21May08.linux.1 b/examples/ellipse/log.ellipse.resquared.21May08.linux.1
new file mode 100644
index 000000000..94d9fd456
--- /dev/null
+++ b/examples/ellipse/log.ellipse.resquared.21May08.linux.1
@@ -0,0 +1,147 @@
+LAMMPS (21 May 2008)
+# RESquared ellipsoids in LJ background fluid
+
+units lj
+atom_style ellipsoid
+dimension 2
+
+lattice sq 0.02
+Lattice spacing in x,y,z = 7.07107 7.07107 7.07107
+region box block 0 20 0 20 -0.5 0.5
+create_box 2 box
+Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553)
+ 1 by 1 by 1 processor grid
+create_atoms 1 box
+Created 400 atoms
+
+set group all type/fraction 2 0.1 95392
+ 45 settings made for type/fraction
+set group all quat/random 18238
+ 400 settings made for quat/random
+
+mass 1 1.0
+mass 2 1.5
+shape 1 1 1 1
+shape 2 3 1 1
+
+compute rot all temp/asphere
+velocity all create 2.4 87287 loop geom
+
+#pair_style gayberne 1.0 3.0 1.0 4.0
+#pair_coeff 1 1 3.0 1.0 1 1 1 1 1 1 2.5
+#pair_coeff 1 2 3.0 1.0 1 1 1 0 0 0
+#pair_coeff 2 2 1.0 1.0 1 1 0.2 0 0 0
+
+pair_style resquared 4.0
+pair_coeff 1 1 3.0 1 1 1 1 1 1 1 2.5
+pair_coeff 1 2 3.0 1 1 1 1 0 0 0
+pair_coeff 2 2 1.0 1 1 1 0.2 0 0 0
+
+neighbor 0.8 bin
+
+thermo_style custom step c_rot epair etotal press vol
+thermo 100
+
+timestep 0.002
+
+#dump 1 all custom 100 dump.ellipse.gayberne # tag type x y z quatw quati quatj quatk
+
+dump 1 all custom 100 dump.ellipse.resquared tag type x y z quatw quati quatj quatk
+
+fix 1 all npt/asphere 2.0 2.0 0.1 xyz 0.0 1.0 1.0
+fix 2 all enforce2d
+
+# equilibrate to shrink box around dilute system
+
+run 2000
+Memory usage per processor = 2.5914 Mbytes
+Step rot E_pair TotEng Press Volume
+ 0 2.2718861 0 2.394 0.04788 20000
+ 100 1.7442957 0 1.8380516 0.035762064 20558.675
+ 200 2.2770743 0 2.399467 0.046545738 20620.294
+ 300 1.8572884 0 1.9571177 0.042405959 18460.78
+ 400 2.1709476 -2.7650868e-05 2.2876084 0.066840176 13689.499
+ 500 1.9974207 0.016918546 2.0563673 0.11517079 8482.9842
+ 600 2.0623605 0.078682156 2.0822655 0.2882877 4776.2504
+ 700 2.110577 0.19687352 2.3261907 0.85200625 2756.4677
+ 800 1.7458278 0.29268299 1.9788694 1.629108 1832.8121
+ 900 1.7925286 0.2406461 2.0272778 1.7295734 1516.7707
+ 1000 1.8280565 0.16642416 1.9844287 1.431503 1517.365
+ 1100 2.1579097 0.10561885 2.2607523 0.98798133 1744.9685
+ 1200 1.7966192 0.057740166 1.8308675 0.54361557 2182.8329
+ 1300 2.2982919 0.036420252 2.3349773 0.45727558 2731.1191
+ 1400 1.766633 0.038034214 1.7891558 0.32935291 3230.8068
+ 1500 2.3052769 0.08089522 2.3763972 0.45778471 3432.038
+ 1600 1.8587716 0.067481187 1.9188742 0.39446029 3276.3409
+ 1700 2.1802595 0.13974472 2.3397684 0.70931895 2829.789
+ 1800 1.9313351 0.14233089 2.0646735 0.83838184 2321.0971
+ 1900 2.0664832 0.16461014 2.1858936 1.1676882 1900.719
+ 2000 1.9340159 0.16879369 2.1186931 1.3526231 1658.4096
+Loop time of 2.3213 on 1 procs for 2000 steps with 400 atoms
+
+Pair time (%) = 1.99781 (86.0641)
+Neigh time (%) = 0.014091 (0.60703)
+Comm time (%) = 0.0165789 (0.714207)
+Outpt time (%) = 0.034477 (1.48524)
+Other time (%) = 0.258347 (11.1294)
+
+Nlocal: 400 ave 400 max 400 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 207 ave 207 max 207 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 1894 ave 1894 max 1894 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1894
+Ave neighs/atom = 4.735
+Neighbor list builds = 152
+Dangerous builds = 77
+
+# run dynamics on dense system
+
+unfix 1
+fix 1 all nve/asphere
+
+run 2000
+Memory usage per processor = 2.5919 Mbytes
+Step rot E_pair TotEng Press Volume
+ 2000 1.9340159 0.16879369 2.1186931 1.3526231 1658.4096
+ 2100 1.9499859 0.15215993 2.1113673 1.1823056 1658.4096
+ 2200 1.947135 0.15513968 2.1194838 1.2327003 1658.4096
+ 2300 1.9248051 0.17868446 2.099053 1.3075669 1658.4096
+ 2400 1.9130129 0.1909732 2.1178764 1.360918 1658.4096
+ 2500 1.923006 0.18047305 2.0814946 1.300819 1658.4096
+ 2600 1.9861146 0.11411525 2.0953259 1.0398086 1658.4096
+ 2700 1.9100096 0.19413009 2.0711987 1.3442038 1658.4096
+ 2800 1.9229156 0.18068077 2.0604436 1.3326936 1658.4096
+ 2900 1.9390668 0.16374522 2.084979 1.2648628 1658.4096
+ 3000 1.8823323 0.22349207 2.0853271 1.5182108 1658.4096
+ 3100 1.904216 0.2002807 2.0777595 1.3868716 1658.4096
+ 3200 1.9189112 0.18492983 2.069413 1.3303671 1658.4096
+ 3300 1.8823024 0.22351455 2.0549801 1.5696985 1658.4096
+ 3400 1.9062113 0.19834529 2.0909042 1.452763 1658.4096
+ 3500 1.9502985 0.15175121 2.0880307 1.2382766 1658.4096
+ 3600 1.9785887 0.12200393 2.1051591 1.0976058 1658.4096
+ 3700 1.8929677 0.21215454 2.0740511 1.4270618 1658.4096
+ 3800 1.9312361 0.17174214 2.0694738 1.30501 1658.4096
+ 3900 1.9552683 0.14654684 2.0903398 1.2082694 1658.4096
+ 4000 1.9147075 0.18935225 2.1044998 1.3672816 1658.4096
+Loop time of 4.08604 on 1 procs for 2000 steps with 400 atoms
+
+Pair time (%) = 3.80795 (93.1941)
+Neigh time (%) = 0.00631857 (0.154638)
+Comm time (%) = 0.0228438 (0.55907)
+Outpt time (%) = 0.0349987 (0.856542)
+Other time (%) = 0.213933 (5.23569)
+
+Nlocal: 400 ave 400 max 400 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 205 ave 205 max 205 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 1885 ave 1885 max 1885 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1885
+Ave neighs/atom = 4.7125
+Neighbor list builds = 46
+Dangerous builds = 0
diff --git a/examples/ellipse/log.ellipse.resquared.21May08.linux.4 b/examples/ellipse/log.ellipse.resquared.21May08.linux.4
new file mode 100644
index 000000000..4a3c404ae
--- /dev/null
+++ b/examples/ellipse/log.ellipse.resquared.21May08.linux.4
@@ -0,0 +1,147 @@
+LAMMPS (21 May 2008)
+# RESquared ellipsoids in LJ background fluid
+
+units lj
+atom_style ellipsoid
+dimension 2
+
+lattice sq 0.02
+Lattice spacing in x,y,z = 7.07107 7.07107 7.07107
+region box block 0 20 0 20 -0.5 0.5
+create_box 2 box
+Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553)
+ 2 by 2 by 1 processor grid
+create_atoms 1 box
+Created 400 atoms
+
+set group all type/fraction 2 0.1 95392
+ 45 settings made for type/fraction
+set group all quat/random 18238
+ 400 settings made for quat/random
+
+mass 1 1.0
+mass 2 1.5
+shape 1 1 1 1
+shape 2 3 1 1
+
+compute rot all temp/asphere
+velocity all create 2.4 87287 loop geom
+
+#pair_style gayberne 1.0 3.0 1.0 4.0
+#pair_coeff 1 1 3.0 1.0 1 1 1 1 1 1 2.5
+#pair_coeff 1 2 3.0 1.0 1 1 1 0 0 0
+#pair_coeff 2 2 1.0 1.0 1 1 0.2 0 0 0
+
+pair_style resquared 4.0
+pair_coeff 1 1 3.0 1 1 1 1 1 1 1 2.5
+pair_coeff 1 2 3.0 1 1 1 1 0 0 0
+pair_coeff 2 2 1.0 1 1 1 0.2 0 0 0
+
+neighbor 0.8 bin
+
+thermo_style custom step c_rot epair etotal press vol
+thermo 100
+
+timestep 0.002
+
+#dump 1 all custom 100 dump.ellipse.gayberne # tag type x y z quatw quati quatj quatk
+
+dump 1 all custom 100 dump.ellipse.resquared tag type x y z quatw quati quatj quatk
+
+fix 1 all npt/asphere 2.0 2.0 0.1 xyz 0.0 1.0 1.0
+fix 2 all enforce2d
+
+# equilibrate to shrink box around dilute system
+
+run 2000
+Memory usage per processor = 2.55985 Mbytes
+Step rot E_pair TotEng Press Volume
+ 0 2.2718861 0 2.394 0.04788 20000
+ 100 1.7442957 0 1.8380516 0.035762064 20558.675
+ 200 2.2770743 0 2.399467 0.046545738 20620.294
+ 300 1.8572884 0 1.9571177 0.042405959 18460.78
+ 400 2.1709476 -2.7650868e-05 2.2876084 0.066840176 13689.499
+ 500 1.9974207 0.016918546 2.0563673 0.11517079 8482.9842
+ 600 2.0623605 0.078682156 2.0822655 0.2882877 4776.2504
+ 700 2.110577 0.19687352 2.3261907 0.85200625 2756.4677
+ 800 1.7458278 0.29268299 1.9788694 1.629108 1832.8121
+ 900 1.7925286 0.2406461 2.0272778 1.7295734 1516.7707
+ 1000 1.8280565 0.16642416 1.9844287 1.431503 1517.365
+ 1100 2.1579097 0.10561885 2.2607523 0.98798133 1744.9685
+ 1200 1.7966192 0.057740166 1.8308675 0.54361557 2182.8329
+ 1300 2.2982919 0.036420252 2.3349773 0.45727558 2731.1191
+ 1400 1.766633 0.038034214 1.7891558 0.32935291 3230.8068
+ 1500 2.3052769 0.08089522 2.3763972 0.45778471 3432.038
+ 1600 1.8587716 0.067481187 1.9188742 0.39446029 3276.3409
+ 1700 2.1802595 0.13974472 2.3397684 0.70931895 2829.789
+ 1800 1.9313351 0.14233089 2.0646735 0.83838184 2321.0971
+ 1900 2.0664832 0.16461014 2.1858936 1.1676882 1900.719
+ 2000 1.9340159 0.16879369 2.1186931 1.3526231 1658.4096
+Loop time of 1.55915 on 4 procs for 2000 steps with 400 atoms
+
+Pair time (%) = 0.516469 (33.1252)
+Neigh time (%) = 0.00421089 (0.270077)
+Comm time (%) = 0.611745 (39.2359)
+Outpt time (%) = 0.0517598 (3.31975)
+Other time (%) = 0.37496 (24.0491)
+
+Nlocal: 100 ave 109 max 96 min
+Histogram: 2 0 1 0 0 0 0 0 0 1
+Nghost: 115.75 ave 120 max 108 min
+Histogram: 1 0 0 0 0 0 1 0 0 2
+Neighs: 473.5 ave 500 max 456 min
+Histogram: 1 0 1 1 0 0 0 0 0 1
+
+Total # of neighbors = 1894
+Ave neighs/atom = 4.735
+Neighbor list builds = 152
+Dangerous builds = 77
+
+# run dynamics on dense system
+
+unfix 1
+fix 1 all nve/asphere
+
+run 2000
+Memory usage per processor = 2.56081 Mbytes
+Step rot E_pair TotEng Press Volume
+ 2000 1.9340159 0.16879369 2.1186931 1.3526231 1658.4096
+ 2100 1.9499859 0.15215993 2.1113673 1.1823056 1658.4096
+ 2200 1.947135 0.15513969 2.1194838 1.2327003 1658.4096
+ 2300 1.9248051 0.17868446 2.099053 1.3075669 1658.4096
+ 2400 1.9130129 0.1909732 2.1178764 1.360918 1658.4096
+ 2500 1.923006 0.18047305 2.0814946 1.300819 1658.4096
+ 2600 1.9861146 0.11411525 2.0953259 1.0398086 1658.4096
+ 2700 1.9100096 0.1941301 2.0711987 1.3442038 1658.4096
+ 2800 1.9229156 0.1806807 2.0604436 1.3326933 1658.4096
+ 2900 1.9390667 0.16374526 2.0849791 1.264863 1658.4096
+ 3000 1.8823324 0.22349199 2.0853271 1.5182104 1658.4096
+ 3100 1.904216 0.20028063 2.0777596 1.3868713 1658.4096
+ 3200 1.9189114 0.18492962 2.069413 1.3303662 1658.4096
+ 3300 1.8823026 0.22351436 2.0549801 1.569697 1658.4096
+ 3400 1.9062107 0.1983459 2.0909008 1.4527662 1658.4096
+ 3500 1.9503014 0.15174814 2.0880308 1.2382499 1658.4096
+ 3600 1.9785903 0.12200228 2.1051589 1.0976001 1658.4096
+ 3700 1.8929681 0.21215409 2.0740513 1.4270612 1658.4096
+ 3800 1.9312505 0.17172697 2.0694714 1.3049156 1658.4096
+ 3900 1.9552504 0.14656576 2.0903398 1.2083612 1658.4096
+ 4000 1.9147153 0.18934405 2.1044888 1.3672132 1658.4096
+Loop time of 1.85192 on 4 procs for 2000 steps with 400 atoms
+
+Pair time (%) = 0.984376 (53.1543)
+Neigh time (%) = 0.00186694 (0.100811)
+Comm time (%) = 0.630368 (34.0385)
+Outpt time (%) = 0.0533838 (2.88262)
+Other time (%) = 0.181929 (9.82376)
+
+Nlocal: 100 ave 104 max 95 min
+Histogram: 1 0 0 1 0 0 0 0 1 1
+Nghost: 117 ave 121 max 110 min
+Histogram: 1 0 0 0 0 0 1 0 0 2
+Neighs: 471.25 ave 509 max 428 min
+Histogram: 1 0 1 0 0 0 0 0 1 1
+
+Total # of neighbors = 1885
+Ave neighs/atom = 4.7125
+Neighbor list builds = 46
+Dangerous builds = 0
diff --git a/examples/ellipse/log.gayberne.22Jan08.linux.1 b/examples/ellipse/log.gayberne.22Jan08.linux.1
deleted file mode 100644
index 09da4fee4..000000000
--- a/examples/ellipse/log.gayberne.22Jan08.linux.1
+++ /dev/null
@@ -1,147 +0,0 @@
-LAMMPS (22 Jan 2008)
-# GayBerne ellipsoids in LJ background fluid
-
-units lj
-atom_style ellipsoid
-dimension 2
-
-lattice sq 0.02
-Lattice spacing in x,y,z = 7.07107 7.07107 7.07107
-region box block 0 20 0 20 -0.5 0.5
-create_box 2 box
-Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553)
- 1 by 1 by 1 processor grid
-create_atoms 1 box
-Created 400 atoms
-
-set group all type/fraction 2 0.1 95392
- 45 settings made for type/fraction
-set group all quat/random 18238
- 400 settings made for quat/random
-
-mass 1 1.0
-mass 2 1.5
-shape 1 1 1 1
-shape 2 3 1 1
-
-compute rot all temp/asphere
-velocity all create 2.4 87287 loop geom
-
-pair_style gayberne 1.0 3.0 1.0 4.0
-pair_coeff 1 1 3.0 1.0 1 1 1 1 1 1 2.5
-pair_coeff 1 2 3.0 1.0 1 1 1 0 0 0
-pair_coeff 2 2 1.0 1.0 1 1 0.2 0 0 0
-
-#pair_style resquared 4.0
-#pair_coeff 1 1 3.0 1 1 1 1 1 1 1 2.5
-#pair_coeff 1 2 3.0 1 1 1 1 0 0 0
-#pair_coeff 2 2 1.0 1 1 1 0.2 0 0 0
-
-neighbor 0.8 bin
-
-thermo_style custom step c_rot epair etotal press vol
-thermo 100
-
-timestep 0.002
-
-dump 1 all custom 100 dump.gayberne tag type x y z quatw quati quatj quatk
-
-#dump 1 all custom 100 dump.resquared # tag type x y z quatw quati quatj quatk
-
-fix 1 all npt/asphere 2.0 2.0 0.1 xyz 0.0 1.0 1.0
-fix 2 all enforce2d
-
-# equilibrate to shrink box around dilute system
-
-run 2000
-Memory usage per processor = 2.5914 Mbytes
-Step rot E_pair TotEng Press Volume
- 0 2.1564825 0 2.391 0.04782 20000
- 100 1.838411 0 2.0383382 0.039613219 20582.404
- 200 2.1840926 0 2.4216127 0.046586295 20792.49
- 300 1.9277991 0 2.1374472 0.045558261 18766.715
- 400 2.1320898 -0.00053003398 2.3634243 0.067260787 14046.57
- 500 2.0125529 -0.044948035 2.1687617 0.10245426 8750.3467
- 600 2.0786425 -0.23406014 1.9442479 0.22613511 4851.3617
- 700 2.2133435 -0.69014988 1.5954372 0.54309778 2612.3736
- 800 1.9098353 -1.4850103 0.51347537 1.3704181 1483.4256
- 900 2.1260352 -2.8142501 -0.59067406 3.1656374 962.6457
- 1000 1.6045695 -4.3144152 -2.6174061 2.546312 768.15096
- 1100 1.8583682 -4.7215526 -2.7550345 2.2351608 721.1814
- 1200 2.0033979 -4.4224318 -2.3394492 1.497766 762.68534
- 1300 1.9444498 -3.9403965 -1.8821931 0.71183994 853.44376
- 1400 2.0389741 -3.5330024 -1.3903083 0.56027235 953.42519
- 1500 1.9557022 -3.3648518 -1.315844 0.5652338 1045.7045
- 1600 2.0224945 -3.2441781 -1.0982354 0.54437381 1120.6403
- 1700 2.0299156 -3.0845458 -0.92406001 0.48408419 1184.9462
- 1800 2.0251982 -2.9795387 -0.83247158 0.52149705 1215.081
- 1900 2.0206629 -3.159343 -1.0374344 0.72829367 1196.1151
- 2000 1.9665091 -3.2421939 -1.2158182 0.66817261 1162.3788
-Loop time of 1.24429 on 1 procs for 2000 steps with 400 atoms
-
-Pair time (%) = 0.909927 (73.1284)
-Neigh time (%) = 0.0135996 (1.09297)
-Comm time (%) = 0.0220442 (1.77163)
-Outpt time (%) = 0.0341184 (2.74201)
-Other time (%) = 0.264597 (21.2649)
-
-Nlocal: 400 ave 400 max 400 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 241 ave 241 max 241 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 2899 ave 2899 max 2899 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 2899
-Ave neighs/atom = 7.2475
-Neighbor list builds = 116
-Dangerous builds = 66
-
-# run dynamics on dense system
-
-unfix 1
-fix 1 all nve/asphere
-
-run 2000
-Memory usage per processor = 2.5924 Mbytes
-Step rot E_pair TotEng Press Volume
- 2000 1.9665091 -3.2421939 -1.2158182 0.66817261 1162.3788
- 2100 1.8708937 -3.1339765 -1.2087845 0.65485928 1162.3788
- 2200 1.9126691 -3.1751558 -1.1398886 0.64965308 1162.3788
- 2300 1.8486671 -3.106799 -1.1627689 0.7992831 1162.3788
- 2400 1.9064396 -3.1727593 -1.1529333 0.65253656 1162.3788
- 2500 1.9271407 -3.196764 -1.170919 0.69672634 1162.3788
- 2600 1.9128576 -3.1780462 -1.1737268 0.49259816 1162.3788
- 2700 1.8577605 -3.1183107 -1.1469431 0.69798298 1162.3788
- 2800 1.8968015 -3.1635109 -1.1706025 0.72238772 1162.3788
- 2900 1.9243377 -3.1936655 -1.2164049 0.71602441 1162.3788
- 3000 1.9744936 -3.2522509 -1.1675852 0.973599 1162.3788
- 3100 1.9958325 -3.2744643 -1.1947121 0.74284674 1162.3788
- 3200 1.970421 -3.2446567 -1.1999887 0.82553849 1162.3788
- 3300 2.0258625 -3.3090808 -1.1388773 0.92883543 1162.3788
- 3400 1.8890826 -3.1558929 -1.1949006 0.79651332 1162.3788
- 3500 1.995457 -3.2762027 -1.1679919 0.56633624 1162.3788
- 3600 1.931652 -3.2051941 -1.1993639 0.64332962 1162.3788
- 3700 1.9274391 -3.1996536 -1.1892997 0.30677766 1162.3788
- 3800 1.9107307 -3.1825901 -1.2150398 0.76019944 1162.3788
- 3900 2.0003232 -3.2826031 -1.2144381 0.69551187 1162.3788
- 4000 1.9971268 -3.2783688 -1.2104061 0.67606395 1162.3788
-Loop time of 1.41674 on 1 procs for 2000 steps with 400 atoms
-
-Pair time (%) = 1.12906 (79.6942)
-Neigh time (%) = 0.00786209 (0.554944)
-Comm time (%) = 0.0250032 (1.76484)
-Outpt time (%) = 0.0342295 (2.41608)
-Other time (%) = 0.220585 (15.5699)
-
-Nlocal: 400 ave 400 max 400 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 240 ave 240 max 240 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 2941 ave 2941 max 2941 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 2941
-Ave neighs/atom = 7.3525
-Neighbor list builds = 46
-Dangerous builds = 0
diff --git a/examples/ellipse/log.gayberne.22Jan08.linux.4 b/examples/ellipse/log.gayberne.22Jan08.linux.4
deleted file mode 100644
index 0f6d742fe..000000000
--- a/examples/ellipse/log.gayberne.22Jan08.linux.4
+++ /dev/null
@@ -1,147 +0,0 @@
-LAMMPS (22 Jan 2008)
-# GayBerne ellipsoids in LJ background fluid
-
-units lj
-atom_style ellipsoid
-dimension 2
-
-lattice sq 0.02
-Lattice spacing in x,y,z = 7.07107 7.07107 7.07107
-region box block 0 20 0 20 -0.5 0.5
-create_box 2 box
-Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553)
- 2 by 2 by 1 processor grid
-create_atoms 1 box
-Created 400 atoms
-
-set group all type/fraction 2 0.1 95392
- 45 settings made for type/fraction
-set group all quat/random 18238
- 400 settings made for quat/random
-
-mass 1 1.0
-mass 2 1.5
-shape 1 1 1 1
-shape 2 3 1 1
-
-compute rot all temp/asphere
-velocity all create 2.4 87287 loop geom
-
-pair_style gayberne 1.0 3.0 1.0 4.0
-pair_coeff 1 1 3.0 1.0 1 1 1 1 1 1 2.5
-pair_coeff 1 2 3.0 1.0 1 1 1 0 0 0
-pair_coeff 2 2 1.0 1.0 1 1 0.2 0 0 0
-
-#pair_style resquared 4.0
-#pair_coeff 1 1 3.0 1 1 1 1 1 1 1 2.5
-#pair_coeff 1 2 3.0 1 1 1 1 0 0 0
-#pair_coeff 2 2 1.0 1 1 1 0.2 0 0 0
-
-neighbor 0.8 bin
-
-thermo_style custom step c_rot epair etotal press vol
-thermo 100
-
-timestep 0.002
-
-dump 1 all custom 100 dump.gayberne tag type x y z quatw quati quatj quatk
-
-#dump 1 all custom 100 dump.resquared # tag type x y z quatw quati quatj quatk
-
-fix 1 all npt/asphere 2.0 2.0 0.1 xyz 0.0 1.0 1.0
-fix 2 all enforce2d
-
-# equilibrate to shrink box around dilute system
-
-run 2000
-Memory usage per processor = 2.55985 Mbytes
-Step rot E_pair TotEng Press Volume
- 0 2.1564825 0 2.391 0.04782 20000
- 100 1.838411 0 2.0383382 0.039613219 20582.404
- 200 2.1840926 0 2.4216127 0.046586295 20792.49
- 300 1.9277991 0 2.1374472 0.045558261 18766.715
- 400 2.1320898 -0.00053003398 2.3634243 0.067260787 14046.57
- 500 2.0125529 -0.044948035 2.1687617 0.10245426 8750.3467
- 600 2.0786425 -0.23406014 1.9442479 0.22613511 4851.3617
- 700 2.2133435 -0.69014988 1.5954372 0.54309778 2612.3736
- 800 1.9098353 -1.4850103 0.51347537 1.3704181 1483.4256
- 900 2.1260352 -2.8142501 -0.59067406 3.1656374 962.6457
- 1000 1.6045695 -4.3144152 -2.6174061 2.546312 768.15096
- 1100 1.8583682 -4.7215526 -2.7550345 2.2351608 721.1814
- 1200 2.0033979 -4.4224318 -2.3394492 1.497766 762.68534
- 1300 1.9444498 -3.9403965 -1.8821931 0.71183994 853.44376
- 1400 2.0389741 -3.5330024 -1.3903083 0.56027235 953.42519
- 1500 1.9557022 -3.3648518 -1.315844 0.5652338 1045.7045
- 1600 2.0224945 -3.2441781 -1.0982355 0.54437381 1120.6403
- 1700 2.0299156 -3.0845458 -0.92406001 0.48408419 1184.9462
- 1800 2.0251982 -2.9795387 -0.83247158 0.52149705 1215.081
- 1900 2.0206629 -3.159343 -1.0374344 0.72829366 1196.1151
- 2000 1.9665091 -3.2421939 -1.2158181 0.66817261 1162.3788
-Loop time of 1.46444 on 4 procs for 2000 steps with 400 atoms
-
-Pair time (%) = 0.262376 (17.9165)
-Neigh time (%) = 0.00438559 (0.299471)
-Comm time (%) = 0.695195 (47.4716)
-Outpt time (%) = 0.0550858 (3.76155)
-Other time (%) = 0.447401 (30.5509)
-
-Nlocal: 100 ave 114 max 89 min
-Histogram: 1 0 0 1 1 0 0 0 0 1
-Nghost: 143.75 ave 150 max 134 min
-Histogram: 1 0 0 0 1 0 0 0 0 2
-Neighs: 724.75 ave 888 max 603 min
-Histogram: 1 0 0 2 0 0 0 0 0 1
-
-Total # of neighbors = 2899
-Ave neighs/atom = 7.2475
-Neighbor list builds = 116
-Dangerous builds = 66
-
-# run dynamics on dense system
-
-unfix 1
-fix 1 all nve/asphere
-
-run 2000
-Memory usage per processor = 2.56108 Mbytes
-Step rot E_pair TotEng Press Volume
- 2000 1.9665091 -3.2421939 -1.2158181 0.66817261 1162.3788
- 2100 1.8708938 -3.1339766 -1.2087845 0.65485904 1162.3788
- 2200 1.9126692 -3.1751559 -1.1398886 0.64965265 1162.3788
- 2300 1.8486668 -3.1067986 -1.1627689 0.79928388 1162.3788
- 2400 1.9064384 -3.172758 -1.1529331 0.65253881 1162.3788
- 2500 1.9271407 -3.1967644 -1.170919 0.69672795 1162.3788
- 2600 1.9128672 -3.1780573 -1.173728 0.49255026 1162.3788
- 2700 1.8577651 -3.118316 -1.1469407 0.69794398 1162.3788
- 2800 1.896808 -3.1635198 -1.1706185 0.72233802 1162.3788
- 2900 1.9244369 -3.1937775 -1.2164447 0.71557304 1162.3788
- 3000 1.9743523 -3.2520956 -1.1675977 0.97482809 1162.3788
- 3100 1.996246 -3.2749273 -1.194868 0.74170535 1162.3788
- 3200 1.9705094 -3.2447603 -1.1997475 0.8278483 1162.3788
- 3300 2.0273054 -3.3108123 -1.1389432 0.92136684 1162.3788
- 3400 1.8906596 -3.1579072 -1.1949426 0.76619179 1162.3788
- 3500 1.9983053 -3.2795554 -1.1695681 0.60352395 1162.3788
- 3600 1.9635271 -3.2409899 -1.2167445 0.4863415 1162.3788
- 3700 1.9144359 -3.1843815 -1.2155475 0.42825617 1162.3788
- 3800 1.9125088 -3.1825738 -1.2078829 0.58850208 1162.3788
- 3900 1.9607643 -3.2375105 -1.2043099 0.50399343 1162.3788
- 4000 1.9199974 -3.1924774 -1.1937016 1.0992901 1162.3788
-Loop time of 1.30653 on 4 procs for 2000 steps with 400 atoms
-
-Pair time (%) = 0.327121 (25.0374)
-Neigh time (%) = 0.00245857 (0.188176)
-Comm time (%) = 0.719629 (55.0794)
-Outpt time (%) = 0.0561987 (4.30137)
-Other time (%) = 0.201123 (15.3937)
-
-Nlocal: 100 ave 112 max 86 min
-Histogram: 1 0 1 0 0 0 0 0 1 1
-Nghost: 152.5 ave 161 max 131 min
-Histogram: 1 0 0 0 0 0 0 0 0 3
-Neighs: 740.5 ave 888 max 623 min
-Histogram: 2 0 0 0 0 0 0 1 0 1
-
-Total # of neighbors = 2962
-Ave neighs/atom = 7.405
-Neighbor list builds = 46
-Dangerous builds = 0
diff --git a/examples/ellipse/log.resquared.22Jan08.linux.1 b/examples/ellipse/log.resquared.22Jan08.linux.1
deleted file mode 100644
index b71d262fd..000000000
--- a/examples/ellipse/log.resquared.22Jan08.linux.1
+++ /dev/null
@@ -1,147 +0,0 @@
-LAMMPS (22 Jan 2008)
-# RESquared ellipsoids in LJ background fluid
-
-units lj
-atom_style ellipsoid
-dimension 2
-
-lattice sq 0.02
-Lattice spacing in x,y,z = 7.07107 7.07107 7.07107
-region box block 0 20 0 20 -0.5 0.5
-create_box 2 box
-Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553)
- 1 by 1 by 1 processor grid
-create_atoms 1 box
-Created 400 atoms
-
-set group all type/fraction 2 0.1 95392
- 45 settings made for type/fraction
-set group all quat/random 18238
- 400 settings made for quat/random
-
-mass 1 1.0
-mass 2 1.5
-shape 1 1 1 1
-shape 2 3 1 1
-
-compute rot all temp/asphere
-velocity all create 2.4 87287 loop geom
-
-#pair_style gayberne 1.0 3.0 1.0 4.0
-#pair_coeff 1 1 3.0 1.0 1 1 1 1 1 1 2.5
-#pair_coeff 1 2 3.0 1.0 1 1 1 0 0 0
-#pair_coeff 2 2 1.0 1.0 1 1 0.2 0 0 0
-
-pair_style resquared 4.0
-pair_coeff 1 1 3.0 1 1 1 1 1 1 1 2.5
-pair_coeff 1 2 3.0 1 1 1 1 0 0 0
-pair_coeff 2 2 1.0 1 1 1 0.2 0 0 0
-
-neighbor 0.8 bin
-
-thermo_style custom step c_rot epair etotal press vol
-thermo 100
-
-timestep 0.002
-
-#dump 1 all custom 100 dump.gayberne # tag type x y z quatw quati quatj quatk
-
-dump 1 all custom 100 dump.resquared tag type x y z quatw quati quatj quatk
-
-fix 1 all npt/asphere 2.0 2.0 0.1 xyz 0.0 1.0 1.0
-fix 2 all enforce2d
-
-# equilibrate to shrink box around dilute system
-
-run 2000
-Memory usage per processor = 2.5914 Mbytes
-Step rot E_pair TotEng Press Volume
- 0 2.1564825 0 2.391 0.04782 20000
- 100 1.838411 0 2.0383382 0.039613219 20582.404
- 200 2.1840926 0 2.4216127 0.046586295 20792.49
- 300 1.9277991 0 2.1374472 0.045558261 18766.715
- 400 2.1319531 -2.8942919e-05 2.363774 0.067309702 14046.61
- 500 2.0159993 0.025003198 2.192142 0.12365516 8758.5309
- 600 2.0502951 0.082711121 2.1869989 0.2914997 4953.8346
- 700 2.1346857 0.19349894 2.4259271 0.83641851 2850.8843
- 800 1.7500542 0.31713085 2.1311843 1.7957167 1886.6112
- 900 1.7954476 0.2020433 2.0534119 1.5200892 1555.0105
- 1000 1.9617502 0.11559302 2.1882642 1.2192863 1547.216
- 1100 2.029642 0.11732822 2.28763 1.0329822 1776.5022
- 1200 1.932547 0.055745664 2.0771327 0.56592224 2220.4328
- 1300 2.1273555 0.022049267 2.2406619 0.39671812 2776.2006
- 1400 1.9348031 0.041576451 2.0680195 0.34763372 3284.7889
- 1500 2.145937 0.05819306 2.2958826 0.39414678 3503.5721
- 1600 1.925752 0.13306059 2.1690861 0.54488654 3303.1224
- 1700 2.1312499 0.14010948 2.3616269 0.69736084 2818.368
- 1800 1.9625036 0.1767238 2.2308375 0.96298372 2310.965
- 1900 1.9411448 0.23022702 2.301414 1.3620231 1895.482
- 2000 1.989287 0.23799274 2.3113674 1.6330055 1665.9849
-Loop time of 2.25316 on 1 procs for 2000 steps with 400 atoms
-
-Pair time (%) = 1.93077 (85.6918)
-Neigh time (%) = 0.0138793 (0.615992)
-Comm time (%) = 0.0163372 (0.725077)
-Outpt time (%) = 0.0341411 (1.51525)
-Other time (%) = 0.258029 (11.4518)
-
-Nlocal: 400 ave 400 max 400 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 208 ave 208 max 208 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 1896 ave 1896 max 1896 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 1896
-Ave neighs/atom = 4.74
-Neighbor list builds = 152
-Dangerous builds = 77
-
-# run dynamics on dense system
-
-unfix 1
-fix 1 all nve/asphere
-
-run 2000
-Memory usage per processor = 2.5924 Mbytes
-Step rot E_pair TotEng Press Volume
- 2000 1.989287 0.23799274 2.3113674 1.6330055 1665.9849
- 2100 2.0653748 0.15379429 2.3138055 1.2692328 1665.9849
- 2200 2.0296751 0.19333047 2.3431266 1.4194185 1665.9849
- 2300 2.031445 0.19134884 2.3346008 1.4455022 1665.9849
- 2400 2.0416873 0.17998527 2.3055585 1.3819478 1665.9849
- 2500 1.9732771 0.25585123 2.3498283 1.7058898 1665.9849
- 2600 2.0186547 0.2054707 2.2994266 1.5413429 1665.9849
- 2700 2.0300352 0.19285781 2.2682949 1.384344 1665.9849
- 2800 2.0258032 0.1974685 2.3003298 1.4218564 1665.9849
- 2900 2.0506397 0.16996513 2.3131175 1.3967849 1665.9849
- 3000 1.9768248 0.251823 2.3267822 1.6698709 1665.9849
- 3100 2.0005064 0.22563045 2.2868834 1.540767 1665.9849
- 3200 2.0309162 0.19193638 2.3082578 1.4597896 1665.9849
- 3300 2.0483286 0.17251967 2.3200717 1.3676295 1665.9849
- 3400 2.0019218 0.22424333 2.3467104 1.6024582 1665.9849
- 3500 2.0060182 0.21959616 2.3235298 1.582482 1665.9849
- 3600 2.0000757 0.22586393 2.3411772 1.5632004 1665.9849
- 3700 2.0293619 0.1936261 2.3426439 1.4262837 1665.9849
- 3800 2.0256136 0.19784063 2.3112499 1.5090404 1665.9849
- 3900 2.0554399 0.16475477 2.3129868 1.281966 1665.9849
- 4000 2.0845029 0.13253315 2.3282445 1.2142775 1665.9849
-Loop time of 4.02238 on 1 procs for 2000 steps with 400 atoms
-
-Pair time (%) = 3.74757 (93.1678)
-Neigh time (%) = 0.00655437 (0.162947)
-Comm time (%) = 0.0214994 (0.534494)
-Outpt time (%) = 0.0341754 (0.849631)
-Other time (%) = 0.212587 (5.2851)
-
-Nlocal: 400 ave 400 max 400 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 206 ave 206 max 206 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 1869 ave 1869 max 1869 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 1869
-Ave neighs/atom = 4.6725
-Neighbor list builds = 50
-Dangerous builds = 0
diff --git a/examples/ellipse/log.resquared.22Jan08.linux.4 b/examples/ellipse/log.resquared.22Jan08.linux.4
deleted file mode 100644
index f1be199d0..000000000
--- a/examples/ellipse/log.resquared.22Jan08.linux.4
+++ /dev/null
@@ -1,147 +0,0 @@
-LAMMPS (22 Jan 2008)
-# RESquared ellipsoids in LJ background fluid
-
-units lj
-atom_style ellipsoid
-dimension 2
-
-lattice sq 0.02
-Lattice spacing in x,y,z = 7.07107 7.07107 7.07107
-region box block 0 20 0 20 -0.5 0.5
-create_box 2 box
-Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553)
- 2 by 2 by 1 processor grid
-create_atoms 1 box
-Created 400 atoms
-
-set group all type/fraction 2 0.1 95392
- 45 settings made for type/fraction
-set group all quat/random 18238
- 400 settings made for quat/random
-
-mass 1 1.0
-mass 2 1.5
-shape 1 1 1 1
-shape 2 3 1 1
-
-compute rot all temp/asphere
-velocity all create 2.4 87287 loop geom
-
-#pair_style gayberne 1.0 3.0 1.0 4.0
-#pair_coeff 1 1 3.0 1.0 1 1 1 1 1 1 2.5
-#pair_coeff 1 2 3.0 1.0 1 1 1 0 0 0
-#pair_coeff 2 2 1.0 1.0 1 1 0.2 0 0 0
-
-pair_style resquared 4.0
-pair_coeff 1 1 3.0 1 1 1 1 1 1 1 2.5
-pair_coeff 1 2 3.0 1 1 1 1 0 0 0
-pair_coeff 2 2 1.0 1 1 1 0.2 0 0 0
-
-neighbor 0.8 bin
-
-thermo_style custom step c_rot epair etotal press vol
-thermo 100
-
-timestep 0.002
-
-#dump 1 all custom 100 dump.gayberne # tag type x y z quatw quati quatj quatk
-
-dump 1 all custom 100 dump.resquared tag type x y z quatw quati quatj quatk
-
-fix 1 all npt/asphere 2.0 2.0 0.1 xyz 0.0 1.0 1.0
-fix 2 all enforce2d
-
-# equilibrate to shrink box around dilute system
-
-run 2000
-Memory usage per processor = 2.55985 Mbytes
-Step rot E_pair TotEng Press Volume
- 0 2.1564825 0 2.391 0.04782 20000
- 100 1.838411 0 2.0383382 0.039613219 20582.404
- 200 2.1840926 0 2.4216127 0.046586295 20792.49
- 300 1.9277991 0 2.1374472 0.045558261 18766.715
- 400 2.1319531 -2.8942919e-05 2.363774 0.067309702 14046.61
- 500 2.0159993 0.025003198 2.192142 0.12365516 8758.5309
- 600 2.0502951 0.082711121 2.1869989 0.2914997 4953.8346
- 700 2.1346857 0.19349894 2.4259271 0.83641851 2850.8843
- 800 1.7500542 0.31713085 2.1311843 1.7957167 1886.6112
- 900 1.7954476 0.2020433 2.0534119 1.5200892 1555.0105
- 1000 1.9617502 0.11559302 2.1882642 1.2192863 1547.216
- 1100 2.029642 0.11732822 2.28763 1.0329822 1776.5022
- 1200 1.932547 0.055745664 2.0771327 0.56592224 2220.4328
- 1300 2.1273555 0.022049267 2.2406619 0.39671812 2776.2006
- 1400 1.9348031 0.041576451 2.0680195 0.34763372 3284.7889
- 1500 2.145937 0.05819306 2.2958826 0.39414678 3503.5721
- 1600 1.925752 0.13306059 2.1690861 0.54488654 3303.1224
- 1700 2.1312499 0.14010948 2.3616269 0.69736084 2818.368
- 1800 1.9625036 0.1767238 2.2308375 0.96298372 2310.965
- 1900 1.9411448 0.23022702 2.301414 1.3620231 1895.482
- 2000 1.989287 0.23799274 2.3113674 1.6330055 1665.9849
-Loop time of 1.70624 on 4 procs for 2000 steps with 400 atoms
-
-Pair time (%) = 0.53287 (31.2306)
-Neigh time (%) = 0.00461602 (0.270537)
-Comm time (%) = 0.702465 (41.1703)
-Outpt time (%) = 0.0564025 (3.30566)
-Other time (%) = 0.40989 (24.0229)
-
-Nlocal: 100 ave 103 max 98 min
-Histogram: 2 0 0 0 0 0 1 0 0 1
-Nghost: 118.25 ave 121 max 114 min
-Histogram: 1 0 0 0 1 0 0 0 0 2
-Neighs: 474 ave 509 max 460 min
-Histogram: 2 1 0 0 0 0 0 0 0 1
-
-Total # of neighbors = 1896
-Ave neighs/atom = 4.74
-Neighbor list builds = 152
-Dangerous builds = 77
-
-# run dynamics on dense system
-
-unfix 1
-fix 1 all nve/asphere
-
-run 2000
-Memory usage per processor = 2.56054 Mbytes
-Step rot E_pair TotEng Press Volume
- 2000 1.989287 0.23799274 2.3113674 1.6330055 1665.9849
- 2100 2.0653748 0.15379429 2.3138055 1.2692328 1665.9849
- 2200 2.0296751 0.19333047 2.3431266 1.4194185 1665.9849
- 2300 2.031445 0.19134884 2.3346008 1.4455022 1665.9849
- 2400 2.0416873 0.17998527 2.3055585 1.3819478 1665.9849
- 2500 1.9732771 0.25585123 2.3498283 1.7058898 1665.9849
- 2600 2.0186547 0.2054707 2.2994266 1.5413428 1665.9849
- 2700 2.0300352 0.19285781 2.2682949 1.384344 1665.9849
- 2800 2.0258032 0.19746848 2.3003298 1.4218563 1665.9849
- 2900 2.0506396 0.16996525 2.3131178 1.3967855 1665.9849
- 3000 1.9768248 0.25182299 2.3267824 1.6698709 1665.9849
- 3100 2.0005068 0.22563005 2.286884 1.5407669 1665.9849
- 3200 2.0309161 0.19193653 2.3082598 1.4597915 1665.9849
- 3300 2.0483373 0.1725101 2.3200665 1.3675732 1665.9849
- 3400 2.0019136 0.22425249 2.3467007 1.6025191 1665.9849
- 3500 2.0060157 0.21959893 2.3235339 1.5824949 1665.9849
- 3600 2.0000689 0.22587176 2.3411757 1.5633105 1665.9849
- 3700 2.0292856 0.19371118 2.342629 1.4266405 1665.9849
- 3800 2.0255614 0.19789877 2.3112561 1.5093285 1665.9849
- 3900 2.0554045 0.16479373 2.3130089 1.2821629 1665.9849
- 4000 2.0844571 0.13258442 2.3284091 1.2146999 1665.9849
-Loop time of 1.94966 on 4 procs for 2000 steps with 400 atoms
-
-Pair time (%) = 1.01464 (52.0418)
-Neigh time (%) = 0.00212574 (0.109032)
-Comm time (%) = 0.695318 (35.6636)
-Outpt time (%) = 0.0557072 (2.85728)
-Other time (%) = 0.181869 (9.32825)
-
-Nlocal: 100 ave 108 max 90 min
-Histogram: 1 0 0 0 0 0 2 0 0 1
-Nghost: 122.25 ave 128 max 114 min
-Histogram: 1 0 0 0 0 0 1 1 0 1
-Neighs: 467.25 ave 524 max 403 min
-Histogram: 1 0 0 0 0 1 1 0 0 1
-
-Total # of neighbors = 1869
-Ave neighs/atom = 4.6725
-Neighbor list builds = 50
-Dangerous builds = 0
diff --git a/examples/flow/in.flow.couette b/examples/flow/in.flow.couette
index 6eba1c0b3..542ce1eb7 100644
--- a/examples/flow/in.flow.couette
+++ b/examples/flow/in.flow.couette
@@ -1,69 +1,69 @@
# 2-d LJ flow simulation
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.7
region box block 0 20 0 10 -0.25 0.25
create_box 3 box
create_atoms 1 box
mass 1 1.0
mass 2 1.0
mass 3 1.0
# LJ potentials
pair_style lj/cut 1.12246
pair_coeff * * 1.0 1.0 1.12246
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
region 2 block INF INF 8.75 INF INF INF
group upper region 2
group boundary union lower upper
group flow subtract all boundary
set group lower type 2
set group upper type 3
# initial velocities
compute mobile flow temp
velocity flow create 1.0 482748 temp mobile
fix 1 all nve
fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
fix_modify 2 temp mobile
# Couette flow
velocity lower set 0.0 0.0 0.0
velocity upper set 3.0 0.0 0.0
fix 3 boundary setforce 0.0 0.0 0.0
fix 4 all enforce2d
-# Poiseuille flow
+# Poisseuille flow
#velocity boundary set 0.0 0.0 0.0
#fix 3 lower setforce 0.0 0.0 0.0
#fix 4 upper setforce 0.0 NULL 0.0
#fix 5 upper aveforce 0.0 -1.0 0.0
#fix 6 flow addforce 0.5 0.0 0.0
#fix 7 all enforce2d
# Run
timestep 0.003
thermo 500
thermo_modify temp mobile
dump 1 all atom 50 dump.flow
run 10000
diff --git a/examples/flow/in.flow.poiss b/examples/flow/in.flow.poiss
index 2fa4462c2..98de72953 100644
--- a/examples/flow/in.flow.poiss
+++ b/examples/flow/in.flow.poiss
@@ -1,69 +1,69 @@
# 2-d LJ flow simulation
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.7
region box block 0 20 0 10 -0.25 0.25
create_box 3 box
create_atoms 1 box
mass 1 1.0
mass 2 1.0
mass 3 1.0
# LJ potentials
pair_style lj/cut 1.12246
pair_coeff * * 1.0 1.0 1.12246
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
region 2 block INF INF 8.75 INF INF INF
group upper region 2
group boundary union lower upper
group flow subtract all boundary
set group lower type 2
set group upper type 3
# initial velocities
compute mobile flow temp
velocity flow create 1.0 482748 temp mobile
fix 1 all nve
fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
fix_modify 2 temp mobile
# Couette flow
#velocity lower set 0.0 0.0 0.0
#velocity upper set 3.0 0.0 0.0
#fix 3 boundary setforce 0.0 0.0 0.0
#fix 4 all enforce2d
-# Poiseuille flow
+# Poisseuille flow
velocity boundary set 0.0 0.0 0.0
fix 3 lower setforce 0.0 0.0 0.0
fix 4 upper setforce 0.0 NULL 0.0
fix 5 upper aveforce 0.0 -1.0 0.0
fix 6 flow addforce 0.5 0.0 0.0
fix 7 all enforce2d
# Run
timestep 0.003
thermo 500
thermo_modify temp mobile
dump 1 all atom 25 dump.flow
run 10000
diff --git a/examples/flow/log.flow.couette.21May08.linux.1 b/examples/flow/log.flow.couette.21May08.linux.1
new file mode 100644
index 000000000..2dc5cc7e7
--- /dev/null
+++ b/examples/flow/log.flow.couette.21May08.linux.1
@@ -0,0 +1,122 @@
+LAMMPS (21 May 2008)
+# 2-d LJ flow simulation
+
+dimension 2
+boundary p s p
+
+atom_style atomic
+neighbor 0.3 bin
+neigh_modify delay 5
+
+# create geometry
+
+lattice hex 0.7
+Lattice spacing in x,y,z = 1.28436 2.22457 1.28436
+region box block 0 20 0 10 -0.25 0.25
+create_box 3 box
+Created orthogonal box = (0 0 -0.321089) to (25.6871 22.2457 0.321089)
+ 1 by 1 by 1 processor grid
+create_atoms 1 box
+Created 420 atoms
+
+mass 1 1.0
+mass 2 1.0
+mass 3 1.0
+
+# LJ potentials
+
+pair_style lj/cut 1.12246
+pair_coeff * * 1.0 1.0 1.12246
+
+# define groups
+
+region 1 block INF INF INF 1.25 INF INF
+group lower region 1
+60 atoms in group lower
+region 2 block INF INF 8.75 INF INF INF
+group upper region 2
+60 atoms in group upper
+group boundary union lower upper
+120 atoms in group boundary
+group flow subtract all boundary
+300 atoms in group flow
+
+set group lower type 2
+ 60 settings made for type
+set group upper type 3
+ 60 settings made for type
+
+# initial velocities
+
+compute mobile flow temp
+velocity flow create 1.0 482748 temp mobile
+fix 1 all nve
+fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
+fix_modify 2 temp mobile
+
+# Couette flow
+
+velocity lower set 0.0 0.0 0.0
+velocity upper set 3.0 0.0 0.0
+fix 3 boundary setforce 0.0 0.0 0.0
+fix 4 all enforce2d
+
+# Poisseuille flow
+
+#velocity boundary set 0.0 0.0 0.0
+#fix 3 lower setforce 0.0 0.0 0.0
+#fix 4 upper setforce 0.0 NULL 0.0
+#fix 5 upper aveforce 0.0 -1.0 0.0
+#fix 6 flow addforce 0.5 0.0 0.0
+#fix 7 all enforce2d
+
+# Run
+
+timestep 0.003
+thermo 500
+thermo_modify temp mobile
+
+dump 1 all atom 50 dump.flow
+run 10000
+Memory usage per processor = 1.68525 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 1 0 0 0.71190476 0.5232453 571.43371
+ 500 1.0644427 -0.31382888 0 0.44395296 3.0018809 571.43371
+ 1000 1 -0.42965445 0 0.28225032 2.9617821 571.43371
+ 1500 1.0739874 -0.41189772 0 0.35267901 2.5626845 571.43371
+ 2000 1 -0.40814277 0 0.30376199 2.9235162 571.43371
+ 2500 1.1929962 -0.38734818 0 0.4619515 2.8343165 571.43371
+ 3000 1 -0.44746792 0 0.26443684 2.6627188 571.43371
+ 3500 1.010095 -0.40989137 0 0.30920005 2.5630541 571.43371
+ 4000 1 -0.41152442 0 0.30038034 2.6280421 571.43371
+ 4500 1.0014311 -0.38736161 0 0.32556193 2.4644773 571.43371
+ 5000 1 -0.39407987 0 0.31782489 2.4614403 571.43371
+ 5500 1.1069931 -0.45231944 0 0.3357542 2.4643506 571.43371
+ 6000 1 -0.45436915 0 0.25753561 2.5746902 571.43371
+ 6500 1.0330238 -0.38921069 0 0.34620389 2.7826579 571.43371
+ 7000 1 -0.44431846 0 0.2675863 2.5673807 571.43371
+ 7500 1.0140984 -0.46901787 0 0.25292361 2.3961693 571.43371
+ 8000 1 -0.45965057 0 0.2522542 2.1341657 571.43371
+ 8500 0.99284806 -0.43949501 0 0.26731825 2.3634229 571.43371
+ 9000 1 -0.46508823 0 0.24681654 2.3230725 571.43371
+ 9500 1.1114345 -0.4020811 0 0.3891544 2.559154 571.43371
+ 10000 1.0176833 -0.42582303 0 0.29867054 2.5282372 571.43371
+Loop time of 0.582808 on 1 procs for 10000 steps with 420 atoms
+
+Pair time (%) = 0.215462 (36.9697)
+Neigh time (%) = 0.0678575 (11.6432)
+Comm time (%) = 0.0175343 (3.00858)
+Outpt time (%) = 0.122674 (21.0489)
+Other time (%) = 0.15928 (27.3297)
+
+Nlocal: 420 ave 420 max 420 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 52 ave 52 max 52 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 957 ave 957 max 957 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 957
+Ave neighs/atom = 2.27857
+Neighbor list builds = 994
+Dangerous builds = 0
diff --git a/examples/flow/log.flow.couette.21May08.linux.4 b/examples/flow/log.flow.couette.21May08.linux.4
new file mode 100644
index 000000000..e8f669cb2
--- /dev/null
+++ b/examples/flow/log.flow.couette.21May08.linux.4
@@ -0,0 +1,122 @@
+LAMMPS (21 May 2008)
+# 2-d LJ flow simulation
+
+dimension 2
+boundary p s p
+
+atom_style atomic
+neighbor 0.3 bin
+neigh_modify delay 5
+
+# create geometry
+
+lattice hex 0.7
+Lattice spacing in x,y,z = 1.28436 2.22457 1.28436
+region box block 0 20 0 10 -0.25 0.25
+create_box 3 box
+Created orthogonal box = (0 0 -0.321089) to (25.6871 22.2457 0.321089)
+ 2 by 2 by 1 processor grid
+create_atoms 1 box
+Created 420 atoms
+
+mass 1 1.0
+mass 2 1.0
+mass 3 1.0
+
+# LJ potentials
+
+pair_style lj/cut 1.12246
+pair_coeff * * 1.0 1.0 1.12246
+
+# define groups
+
+region 1 block INF INF INF 1.25 INF INF
+group lower region 1
+60 atoms in group lower
+region 2 block INF INF 8.75 INF INF INF
+group upper region 2
+60 atoms in group upper
+group boundary union lower upper
+120 atoms in group boundary
+group flow subtract all boundary
+300 atoms in group flow
+
+set group lower type 2
+ 60 settings made for type
+set group upper type 3
+ 60 settings made for type
+
+# initial velocities
+
+compute mobile flow temp
+velocity flow create 1.0 482748 temp mobile
+fix 1 all nve
+fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
+fix_modify 2 temp mobile
+
+# Couette flow
+
+velocity lower set 0.0 0.0 0.0
+velocity upper set 3.0 0.0 0.0
+fix 3 boundary setforce 0.0 0.0 0.0
+fix 4 all enforce2d
+
+# Poisseuille flow
+
+#velocity boundary set 0.0 0.0 0.0
+#fix 3 lower setforce 0.0 0.0 0.0
+#fix 4 upper setforce 0.0 NULL 0.0
+#fix 5 upper aveforce 0.0 -1.0 0.0
+#fix 6 flow addforce 0.5 0.0 0.0
+#fix 7 all enforce2d
+
+# Run
+
+timestep 0.003
+thermo 500
+thermo_modify temp mobile
+
+dump 1 all atom 50 dump.flow
+run 10000
+Memory usage per processor = 1.67714 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 1 0 0 0.71190476 0.5232453 571.43371
+ 500 1.0951876 -0.33403931 0 0.44562996 3.2508527 571.43371
+ 1000 1 -0.3731019 0 0.33880286 2.856717 571.43371
+ 1500 1.0366879 -0.36031105 0 0.37771198 3.0202123 571.43371
+ 2000 1 -0.41052951 0 0.30137525 2.8657415 571.43371
+ 2500 1.1228466 -0.37043294 0 0.42892693 2.9450302 571.43371
+ 3000 1 -0.37926849 0 0.33263627 2.5756937 571.43371
+ 3500 1.0426371 -0.46446342 0 0.27779493 2.6309178 571.43371
+ 4000 1 -0.43996746 0 0.2719373 2.7108953 571.43371
+ 4500 0.97471021 -0.43234275 0 0.26155809 2.4118441 571.43371
+ 5000 1 -0.38709789 0 0.32480687 2.6100243 571.43371
+ 5500 1.0551901 -0.42334943 0 0.32784545 2.4333785 571.43371
+ 6000 1 -0.45014484 0 0.26175993 2.5188073 571.43371
+ 6500 1.0439428 -0.46442749 0 0.27876034 2.2352899 571.43371
+ 7000 1 -0.42616126 0 0.2857435 2.4560563 571.43371
+ 7500 1.0680429 -0.41282904 0 0.34751579 2.5532595 571.43371
+ 8000 1 -0.44461273 0 0.26729203 2.1838508 571.43371
+ 8500 1.0212571 -0.43065547 0 0.29638229 2.2193889 571.43371
+ 9000 1 -0.43364252 0 0.27826224 2.4244927 571.43371
+ 9500 1.1269004 -0.48721451 0 0.31503125 2.3601218 571.43371
+ 10000 1 -0.50814904 0 0.20375572 2.3234126 571.43371
+Loop time of 3.99854 on 4 procs for 10000 steps with 420 atoms
+
+Pair time (%) = 0.064626 (1.61624)
+Neigh time (%) = 0.0206351 (0.516066)
+Comm time (%) = 3.09756 (77.4671)
+Outpt time (%) = 0.163689 (4.0937)
+Other time (%) = 0.652038 (16.3069)
+
+Nlocal: 105 ave 116 max 93 min
+Histogram: 1 1 0 0 0 0 0 0 0 2
+Nghost: 40.25 ave 43 max 36 min
+Histogram: 1 0 0 0 1 0 0 0 0 2
+Neighs: 238.75 ave 307 max 175 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 955
+Ave neighs/atom = 2.27381
+Neighbor list builds = 967
+Dangerous builds = 0
diff --git a/examples/flow/log.flow.couette.22Jan08.linux.1 b/examples/flow/log.flow.couette.22Jan08.linux.1
deleted file mode 100644
index f46d0107e..000000000
--- a/examples/flow/log.flow.couette.22Jan08.linux.1
+++ /dev/null
@@ -1,122 +0,0 @@
-LAMMPS (22 Jan 2008)
-# 2-d LJ flow simulation
-
-dimension 2
-boundary p s p
-
-atom_style atomic
-neighbor 0.3 bin
-neigh_modify delay 5
-
-# create geometry
-
-lattice hex 0.7
-Lattice spacing in x,y,z = 1.28436 2.22457 1.28436
-region box block 0 20 0 10 -0.25 0.25
-create_box 3 box
-Created orthogonal box = (0 0 -0.321089) to (25.6871 22.2457 0.321089)
- 1 by 1 by 1 processor grid
-create_atoms 1 box
-Created 420 atoms
-
-mass 1 1.0
-mass 2 1.0
-mass 3 1.0
-
-# LJ potentials
-
-pair_style lj/cut 1.12246
-pair_coeff * * 1.0 1.0 1.12246
-
-# define groups
-
-region 1 block INF INF INF 1.25 INF INF
-group lower region 1
-60 atoms in group lower
-region 2 block INF INF 8.75 INF INF INF
-group upper region 2
-60 atoms in group upper
-group boundary union lower upper
-120 atoms in group boundary
-group flow subtract all boundary
-300 atoms in group flow
-
-set group lower type 2
- 60 settings made for type
-set group upper type 3
- 60 settings made for type
-
-# initial velocities
-
-compute mobile flow temp
-velocity flow create 1.0 482748 temp mobile
-fix 1 all nve
-fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
-fix_modify 2 temp mobile
-
-# Couette flow
-
-velocity lower set 0.0 0.0 0.0
-velocity upper set 3.0 0.0 0.0
-fix 3 boundary setforce 0.0 0.0 0.0
-fix 4 all enforce2d
-
-# Poisseuille flow
-
-#velocity boundary set 0.0 0.0 0.0
-#fix 3 lower setforce 0.0 0.0 0.0
-#fix 4 upper setforce 0.0 NULL 0.0
-#fix 5 upper aveforce 0.0 -1.0 0.0
-#fix 6 flow addforce 0.5 0.0 0.0
-#fix 7 all enforce2d
-
-# Run
-
-timestep 0.003
-thermo 500
-thermo_modify temp mobile
-
-dump 1 all atom 50 dump.flow
-run 10000
-Memory usage per processor = 1.68525 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume
- 0 1 0 0 0.71071429 0.5223703 571.43371
- 500 1.0604224 -0.31549525 0 0.4381621 3.006258 571.43371
- 1000 1 -0.34356865 0 0.36714563 2.9191962 571.43371
- 1500 1.1738082 -0.382026 0 0.45221625 2.8125373 571.43371
- 2000 1 -0.42682429 0 0.28389 2.7423533 571.43371
- 2500 1.0249762 -0.41630229 0 0.31216293 2.8311931 571.43371
- 3000 1 -0.415763 0 0.29495128 2.6837339 571.43371
- 3500 1.1483583 -0.44275044 0 0.37340417 2.5003955 571.43371
- 4000 1 -0.45903245 0 0.25168184 2.5138215 571.43371
- 4500 1.044392 -0.37885141 0 0.3634129 2.7980973 571.43371
- 5000 1 -0.45198477 0 0.25872952 2.3725427 571.43371
- 5500 1.1128857 -0.45615742 0 0.33478637 2.5476457 571.43371
- 6000 1 -0.44232084 0 0.26839344 2.6421628 571.43371
- 6500 1.1004439 -0.44788873 0 0.33421246 2.4753882 571.43371
- 7000 1 -0.44594794 0 0.26476635 2.1411957 571.43371
- 7500 0.96700164 -0.4037758 0 0.28348608 2.500408 571.43371
- 8000 1 -0.44011344 0 0.27060085 2.3472773 571.43371
- 8500 1.0317945 -0.42782829 0 0.30548278 2.6086809 571.43371
- 9000 1 -0.42662876 0 0.28408553 2.5753183 571.43371
- 9500 1.0439722 -0.43196226 0 0.3100037 2.4421759 571.43371
- 10000 1 -0.42551472 0 0.28519957 2.4293664 571.43371
-Loop time of 0.571892 on 1 procs for 10000 steps with 420 atoms
-
-Pair time (%) = 0.211723 (37.0215)
-Neigh time (%) = 0.0664635 (11.6217)
-Comm time (%) = 0.0170681 (2.98451)
-Outpt time (%) = 0.118025 (20.6376)
-Other time (%) = 0.158613 (27.7347)
-
-Nlocal: 420 ave 420 max 420 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 47 ave 47 max 47 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 958 ave 958 max 958 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 958
-Ave neighs/atom = 2.28095
-Neighbor list builds = 986
-Dangerous builds = 0
diff --git a/examples/flow/log.flow.couette.22Jan08.linux.4 b/examples/flow/log.flow.couette.22Jan08.linux.4
deleted file mode 100644
index f273d93cc..000000000
--- a/examples/flow/log.flow.couette.22Jan08.linux.4
+++ /dev/null
@@ -1,122 +0,0 @@
-LAMMPS (22 Jan 2008)
-# 2-d LJ flow simulation
-
-dimension 2
-boundary p s p
-
-atom_style atomic
-neighbor 0.3 bin
-neigh_modify delay 5
-
-# create geometry
-
-lattice hex 0.7
-Lattice spacing in x,y,z = 1.28436 2.22457 1.28436
-region box block 0 20 0 10 -0.25 0.25
-create_box 3 box
-Created orthogonal box = (0 0 -0.321089) to (25.6871 22.2457 0.321089)
- 2 by 2 by 1 processor grid
-create_atoms 1 box
-Created 420 atoms
-
-mass 1 1.0
-mass 2 1.0
-mass 3 1.0
-
-# LJ potentials
-
-pair_style lj/cut 1.12246
-pair_coeff * * 1.0 1.0 1.12246
-
-# define groups
-
-region 1 block INF INF INF 1.25 INF INF
-group lower region 1
-60 atoms in group lower
-region 2 block INF INF 8.75 INF INF INF
-group upper region 2
-60 atoms in group upper
-group boundary union lower upper
-120 atoms in group boundary
-group flow subtract all boundary
-300 atoms in group flow
-
-set group lower type 2
- 60 settings made for type
-set group upper type 3
- 60 settings made for type
-
-# initial velocities
-
-compute mobile flow temp
-velocity flow create 1.0 482748 temp mobile
-fix 1 all nve
-fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
-fix_modify 2 temp mobile
-
-# Couette flow
-
-velocity lower set 0.0 0.0 0.0
-velocity upper set 3.0 0.0 0.0
-fix 3 boundary setforce 0.0 0.0 0.0
-fix 4 all enforce2d
-
-# Poisseuille flow
-
-#velocity boundary set 0.0 0.0 0.0
-#fix 3 lower setforce 0.0 0.0 0.0
-#fix 4 upper setforce 0.0 NULL 0.0
-#fix 5 upper aveforce 0.0 -1.0 0.0
-#fix 6 flow addforce 0.5 0.0 0.0
-#fix 7 all enforce2d
-
-# Run
-
-timestep 0.003
-thermo 500
-thermo_modify temp mobile
-
-dump 1 all atom 50 dump.flow
-run 10000
-Memory usage per processor = 1.67714 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume
- 0 1 0 0 0.71071429 0.5223703 571.43371
- 500 1.0967867 -0.3465085 0 0.43299345 3.2514265 571.43371
- 1000 1 -0.36129869 0 0.3494156 3.1353617 571.43371
- 1500 1.1299217 -0.37859354 0 0.42445794 2.9270341 571.43371
- 2000 1 -0.34287506 0 0.36783923 3.0258649 571.43371
- 2500 1.0916596 -0.3872134 0 0.38864469 2.8426168 571.43371
- 3000 1 -0.42816199 0 0.2825523 2.7129793 571.43371
- 3500 0.94744822 -0.47483071 0 0.19853427 2.7259788 571.43371
- 4000 1 -0.3684736 0 0.34224069 2.6328623 571.43371
- 4500 0.99502131 -0.37808208 0 0.32909378 2.5909215 571.43371
- 5000 1 -0.41230276 0 0.29841152 2.9229369 571.43371
- 5500 1.0560855 -0.48401682 0 0.26655822 2.472482 571.43371
- 6000 1 -0.4068915 0 0.30382279 2.3428133 571.43371
- 6500 1.0437572 -0.41914338 0 0.32266981 2.6151758 571.43371
- 7000 1 -0.42595992 0 0.28475437 2.3109881 571.43371
- 7500 1.0600587 -0.336143 0 0.41725588 2.3511832 571.43371
- 8000 1 -0.40369591 0 0.30701838 2.6195769 571.43371
- 8500 1.0750756 -0.43763885 0 0.32643275 2.2469938 571.43371
- 9000 1 -0.44198063 0 0.26873366 2.5250617 571.43371
- 9500 1.0263815 -0.43395816 0 0.29550586 2.5922753 571.43371
- 10000 1 -0.47197889 0 0.23873539 2.4144186 571.43371
-Loop time of 4.11115 on 4 procs for 10000 steps with 420 atoms
-
-Pair time (%) = 0.0713452 (1.73541)
-Neigh time (%) = 0.0230771 (0.561329)
-Comm time (%) = 3.20043 (77.8475)
-Outpt time (%) = 0.163546 (3.9781)
-Other time (%) = 0.652753 (15.8776)
-
-Nlocal: 105 ave 116 max 95 min
-Histogram: 2 0 0 0 0 0 0 0 1 1
-Nghost: 41.75 ave 46 max 39 min
-Histogram: 1 0 2 0 0 0 0 0 0 1
-Neighs: 237.5 ave 301 max 178 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-
-Total # of neighbors = 950
-Ave neighs/atom = 2.2619
-Neighbor list builds = 973
-Dangerous builds = 0
diff --git a/examples/flow/log.flow.poiss.21May08.linux.1 b/examples/flow/log.flow.poiss.21May08.linux.1
new file mode 100644
index 000000000..65f97a5a7
--- /dev/null
+++ b/examples/flow/log.flow.poiss.21May08.linux.1
@@ -0,0 +1,122 @@
+LAMMPS (21 May 2008)
+# 2-d LJ flow simulation
+
+dimension 2
+boundary p s p
+
+atom_style atomic
+neighbor 0.3 bin
+neigh_modify delay 5
+
+# create geometry
+
+lattice hex 0.7
+Lattice spacing in x,y,z = 1.28436 2.22457 1.28436
+region box block 0 20 0 10 -0.25 0.25
+create_box 3 box
+Created orthogonal box = (0 0 -0.321089) to (25.6871 22.2457 0.321089)
+ 1 by 1 by 1 processor grid
+create_atoms 1 box
+Created 420 atoms
+
+mass 1 1.0
+mass 2 1.0
+mass 3 1.0
+
+# LJ potentials
+
+pair_style lj/cut 1.12246
+pair_coeff * * 1.0 1.0 1.12246
+
+# define groups
+
+region 1 block INF INF INF 1.25 INF INF
+group lower region 1
+60 atoms in group lower
+region 2 block INF INF 8.75 INF INF INF
+group upper region 2
+60 atoms in group upper
+group boundary union lower upper
+120 atoms in group boundary
+group flow subtract all boundary
+300 atoms in group flow
+
+set group lower type 2
+ 60 settings made for type
+set group upper type 3
+ 60 settings made for type
+
+# initial velocities
+
+compute mobile flow temp
+velocity flow create 1.0 482748 temp mobile
+fix 1 all nve
+fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
+fix_modify 2 temp mobile
+
+# Couette flow
+
+#velocity lower set 0.0 0.0 0.0
+#velocity upper set 3.0 0.0 0.0
+#fix 3 boundary setforce 0.0 0.0 0.0
+#fix 4 all enforce2d
+
+# Poisseuille flow
+
+velocity boundary set 0.0 0.0 0.0
+fix 3 lower setforce 0.0 0.0 0.0
+fix 4 upper setforce 0.0 NULL 0.0
+fix 5 upper aveforce 0.0 -1.0 0.0
+fix 6 flow addforce 0.5 0.0 0.0
+fix 7 all enforce2d
+
+# Run
+
+timestep 0.003
+thermo 500
+thermo_modify temp mobile
+
+dump 1 all atom 25 dump.flow
+run 10000
+Memory usage per processor = 1.68525 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 1 0 0 0.71190476 0.5232453 571.43371
+ 500 1.0990751 -0.36396768 0 0.41846911 2.5229954 575.44891
+ 1000 1 -0.34609791 0 0.36580685 1.9739861 584.56264
+ 1500 1.2112861 -0.39062708 0 0.47169327 1.5221639 587.13863
+ 2000 1 -0.39956949 0 0.31233527 1.2499009 582.89761
+ 2500 1.2236323 -0.40128446 0 0.46982521 1.4279626 569.92814
+ 3000 1 -0.48849341 0 0.22341135 1.5094342 553.53722
+ 3500 1.2404529 -0.63017441 0 0.25290988 1.7684925 535.11692
+ 4000 1 -0.71550459 0 -0.0035998233 2.2080667 516.62241
+ 4500 1.2252925 -0.76523375 0 0.10705778 2.6150526 503.09392
+ 5000 1 -0.79183795 0 -0.079933193 3.0396463 499.00782
+ 5500 1.2154662 -0.76641284 0 0.098883321 2.5749248 501.79835
+ 6000 1 -0.64579024 0 0.066114526 2.1632023 511.927
+ 6500 1.2040094 -0.67569325 0 0.18144675 1.988296 515.52367
+ 7000 1 -0.67495483 0 0.036949936 1.8145292 515.56679
+ 7500 1.224424 -0.70211643 0 0.16955688 1.9563915 513.39341
+ 8000 1 -0.68750419 0 0.024400573 2.2133264 508.15889
+ 8500 1.1991285 -0.81030024 0 0.04336508 2.5391079 501.58914
+ 9000 1 -0.79950245 0 -0.087597685 2.5700917 498.68874
+ 9500 1.2060053 -0.68460543 0 0.17395548 2.4774286 501.9809
+ 10000 1 -0.7187822 0 -0.0068774412 2.1346851 507.66533
+Loop time of 0.73335 on 1 procs for 10000 steps with 420 atoms
+
+Pair time (%) = 0.235934 (32.1721)
+Neigh time (%) = 0.0389028 (5.3048)
+Comm time (%) = 0.0151122 (2.0607)
+Outpt time (%) = 0.239849 (32.7059)
+Other time (%) = 0.203552 (27.7565)
+
+Nlocal: 420 ave 420 max 420 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 50 ave 50 max 50 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 1126 ave 1126 max 1126 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1126
+Ave neighs/atom = 2.68095
+Neighbor list builds = 560
+Dangerous builds = 0
diff --git a/examples/flow/log.flow.poiss.21May08.linux.4 b/examples/flow/log.flow.poiss.21May08.linux.4
new file mode 100644
index 000000000..18cd5fc7d
--- /dev/null
+++ b/examples/flow/log.flow.poiss.21May08.linux.4
@@ -0,0 +1,122 @@
+LAMMPS (21 May 2008)
+# 2-d LJ flow simulation
+
+dimension 2
+boundary p s p
+
+atom_style atomic
+neighbor 0.3 bin
+neigh_modify delay 5
+
+# create geometry
+
+lattice hex 0.7
+Lattice spacing in x,y,z = 1.28436 2.22457 1.28436
+region box block 0 20 0 10 -0.25 0.25
+create_box 3 box
+Created orthogonal box = (0 0 -0.321089) to (25.6871 22.2457 0.321089)
+ 2 by 2 by 1 processor grid
+create_atoms 1 box
+Created 420 atoms
+
+mass 1 1.0
+mass 2 1.0
+mass 3 1.0
+
+# LJ potentials
+
+pair_style lj/cut 1.12246
+pair_coeff * * 1.0 1.0 1.12246
+
+# define groups
+
+region 1 block INF INF INF 1.25 INF INF
+group lower region 1
+60 atoms in group lower
+region 2 block INF INF 8.75 INF INF INF
+group upper region 2
+60 atoms in group upper
+group boundary union lower upper
+120 atoms in group boundary
+group flow subtract all boundary
+300 atoms in group flow
+
+set group lower type 2
+ 60 settings made for type
+set group upper type 3
+ 60 settings made for type
+
+# initial velocities
+
+compute mobile flow temp
+velocity flow create 1.0 482748 temp mobile
+fix 1 all nve
+fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
+fix_modify 2 temp mobile
+
+# Couette flow
+
+#velocity lower set 0.0 0.0 0.0
+#velocity upper set 3.0 0.0 0.0
+#fix 3 boundary setforce 0.0 0.0 0.0
+#fix 4 all enforce2d
+
+# Poisseuille flow
+
+velocity boundary set 0.0 0.0 0.0
+fix 3 lower setforce 0.0 0.0 0.0
+fix 4 upper setforce 0.0 NULL 0.0
+fix 5 upper aveforce 0.0 -1.0 0.0
+fix 6 flow addforce 0.5 0.0 0.0
+fix 7 all enforce2d
+
+# Run
+
+timestep 0.003
+thermo 500
+thermo_modify temp mobile
+
+dump 1 all atom 25 dump.flow
+run 10000
+Memory usage per processor = 1.67714 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 1 0 0 0.71190476 0.5232453 571.43371
+ 500 1.0758737 -0.36090417 0 0.40501541 2.782759 574.95676
+ 1000 1 -0.35701441 0 0.35489035 2.0579148 585.60492
+ 1500 1.2368663 -0.37709732 0 0.50343367 1.4868643 587.08385
+ 2000 1 -0.39362939 0 0.31827537 1.4238684 578.83266
+ 2500 1.2272957 -0.423819 0 0.44989865 1.4547395 570.04942
+ 3000 1 -0.49143404 0 0.22047072 1.5348968 554.87718
+ 3500 1.2444907 -0.59761795 0 0.28834088 1.8757604 536.90691
+ 4000 1 -0.70134359 0 0.010561171 2.1398674 521.35908
+ 4500 1.2204821 -0.74251795 0 0.1263491 2.7628995 507.52799
+ 5000 1 -0.77812124 0 -0.066216477 2.9593453 500.99765
+ 5500 1.2036047 -0.76286922 0 0.093982666 2.6929974 506.25167
+ 6000 1 -0.77204718 0 -0.060142418 2.4240012 509.91665
+ 6500 1.2142987 -0.71937137 0 0.14509369 2.2503511 517.34969
+ 7000 1 -0.65416249 0 0.057742269 2.147319 518.76914
+ 7500 1.2280812 -0.68399882 0 0.19027806 2.0299907 517.0026
+ 8000 1 -0.71589339 0 -0.0039886296 2.2415408 513.76983
+ 8500 1.2274811 -0.70229467 0 0.17155497 2.1849604 512.25569
+ 9000 1 -0.75920668 0 -0.047301917 2.4592389 508.74337
+ 9500 1.2470681 -0.69158384 0 0.1962099 2.1530665 508.86868
+ 10000 1 -0.74646656 0 -0.034561799 2.3332271 509.78267
+Loop time of 4.49466 on 4 procs for 10000 steps with 420 atoms
+
+Pair time (%) = 0.0739097 (1.64439)
+Neigh time (%) = 0.0121227 (0.269713)
+Comm time (%) = 2.82285 (62.8044)
+Outpt time (%) = 0.281245 (6.25731)
+Other time (%) = 1.30454 (29.0242)
+
+Nlocal: 105 ave 107 max 103 min
+Histogram: 1 0 1 0 0 0 0 1 0 1
+Nghost: 44.75 ave 49 max 41 min
+Histogram: 1 1 0 0 0 0 0 1 0 1
+Neighs: 278 ave 296 max 259 min
+Histogram: 1 0 0 0 1 0 1 0 0 1
+
+Total # of neighbors = 1112
+Ave neighs/atom = 2.64762
+Neighbor list builds = 565
+Dangerous builds = 0
diff --git a/examples/flow/log.flow.poiss.22Jan08.linux.1 b/examples/flow/log.flow.poiss.22Jan08.linux.1
deleted file mode 100644
index 6d3486249..000000000
--- a/examples/flow/log.flow.poiss.22Jan08.linux.1
+++ /dev/null
@@ -1,122 +0,0 @@
-LAMMPS (22 Jan 2008)
-# 2-d LJ flow simulation
-
-dimension 2
-boundary p s p
-
-atom_style atomic
-neighbor 0.3 bin
-neigh_modify delay 5
-
-# create geometry
-
-lattice hex 0.7
-Lattice spacing in x,y,z = 1.28436 2.22457 1.28436
-region box block 0 20 0 10 -0.25 0.25
-create_box 3 box
-Created orthogonal box = (0 0 -0.321089) to (25.6871 22.2457 0.321089)
- 1 by 1 by 1 processor grid
-create_atoms 1 box
-Created 420 atoms
-
-mass 1 1.0
-mass 2 1.0
-mass 3 1.0
-
-# LJ potentials
-
-pair_style lj/cut 1.12246
-pair_coeff * * 1.0 1.0 1.12246
-
-# define groups
-
-region 1 block INF INF INF 1.25 INF INF
-group lower region 1
-60 atoms in group lower
-region 2 block INF INF 8.75 INF INF INF
-group upper region 2
-60 atoms in group upper
-group boundary union lower upper
-120 atoms in group boundary
-group flow subtract all boundary
-300 atoms in group flow
-
-set group lower type 2
- 60 settings made for type
-set group upper type 3
- 60 settings made for type
-
-# initial velocities
-
-compute mobile flow temp
-velocity flow create 1.0 482748 temp mobile
-fix 1 all nve
-fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
-fix_modify 2 temp mobile
-
-# Couette flow
-
-#velocity lower set 0.0 0.0 0.0
-#velocity upper set 3.0 0.0 0.0
-#fix 3 boundary setforce 0.0 0.0 0.0
-#fix 4 all enforce2d
-
-# Poisseuille flow
-
-velocity boundary set 0.0 0.0 0.0
-fix 3 lower setforce 0.0 0.0 0.0
-fix 4 upper setforce 0.0 NULL 0.0
-fix 5 upper aveforce 0.0 -1.0 0.0
-fix 6 flow addforce 0.5 0.0 0.0
-fix 7 all enforce2d
-
-# Run
-
-timestep 0.003
-thermo 500
-thermo_modify temp mobile
-
-dump 1 all atom 25 dump.flow
-run 10000
-Memory usage per processor = 1.68525 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume
- 0 1 0 0 0.71071429 0.5223703 571.43371
- 500 1.1036177 -0.37435595 0 0.4100009 2.5048411 575.42182
- 1000 1 -0.40278179 0 0.30793249 1.9811241 584.83497
- 1500 1.2346487 -0.41204291 0 0.46543956 1.5657713 586.36408
- 2000 1 -0.40773469 0 0.3029796 1.46174 583.54346
- 2500 1.2225527 -0.43831252 0 0.43057314 1.4819315 570.69513
- 3000 1 -0.49535278 0 0.21536151 1.5237868 553.26289
- 3500 1.2493782 -0.5997175 0 0.28823343 1.6851599 536.49066
- 4000 1 -0.67585271 0 0.034861579 2.0031708 518.19517
- 4500 1.1920623 -0.75096037 0 0.096255336 2.9347272 502.79894
- 5000 1 -0.82965482 0 -0.11894053 3.1069174 498.40593
- 5500 1.1922661 -0.78951149 0 0.057849031 3.0213496 502.16585
- 6000 1 -0.7308371 0 -0.020122809 2.394881 511.15935
- 6500 1.2295832 -0.71069261 0 0.16318977 1.971859 519.77333
- 7000 1 -0.64017925 0 0.070535035 2.0286235 520.82147
- 7500 1.2330112 -0.64928351 0 0.22703517 1.899572 518.70836
- 8000 1 -0.62643742 0 0.084276866 1.8527516 514.8535
- 8500 1.2117799 -0.71296056 0 0.14826876 2.280841 506.58294
- 9000 1 -0.72064639 0 -0.0099321068 2.2778589 504.4823
- 9500 1.2309735 -0.77916374 0 0.095706684 2.3907829 498.66444
- 10000 1 -0.7626132 0 -0.051898912 2.4826365 501.23793
-Loop time of 0.716502 on 1 procs for 10000 steps with 420 atoms
-
-Pair time (%) = 0.234028 (32.6626)
-Neigh time (%) = 0.0383184 (5.34798)
-Comm time (%) = 0.0147507 (2.05871)
-Outpt time (%) = 0.235236 (32.8312)
-Other time (%) = 0.194169 (27.0996)
-
-Nlocal: 420 ave 420 max 420 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 48 ave 48 max 48 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 1144 ave 1144 max 1144 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 1144
-Ave neighs/atom = 2.72381
-Neighbor list builds = 560
-Dangerous builds = 0
diff --git a/examples/flow/log.flow.poiss.22Jan08.linux.4 b/examples/flow/log.flow.poiss.22Jan08.linux.4
deleted file mode 100644
index fd7512a02..000000000
--- a/examples/flow/log.flow.poiss.22Jan08.linux.4
+++ /dev/null
@@ -1,122 +0,0 @@
-LAMMPS (22 Jan 2008)
-# 2-d LJ flow simulation
-
-dimension 2
-boundary p s p
-
-atom_style atomic
-neighbor 0.3 bin
-neigh_modify delay 5
-
-# create geometry
-
-lattice hex 0.7
-Lattice spacing in x,y,z = 1.28436 2.22457 1.28436
-region box block 0 20 0 10 -0.25 0.25
-create_box 3 box
-Created orthogonal box = (0 0 -0.321089) to (25.6871 22.2457 0.321089)
- 2 by 2 by 1 processor grid
-create_atoms 1 box
-Created 420 atoms
-
-mass 1 1.0
-mass 2 1.0
-mass 3 1.0
-
-# LJ potentials
-
-pair_style lj/cut 1.12246
-pair_coeff * * 1.0 1.0 1.12246
-
-# define groups
-
-region 1 block INF INF INF 1.25 INF INF
-group lower region 1
-60 atoms in group lower
-region 2 block INF INF 8.75 INF INF INF
-group upper region 2
-60 atoms in group upper
-group boundary union lower upper
-120 atoms in group boundary
-group flow subtract all boundary
-300 atoms in group flow
-
-set group lower type 2
- 60 settings made for type
-set group upper type 3
- 60 settings made for type
-
-# initial velocities
-
-compute mobile flow temp
-velocity flow create 1.0 482748 temp mobile
-fix 1 all nve
-fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
-fix_modify 2 temp mobile
-
-# Couette flow
-
-#velocity lower set 0.0 0.0 0.0
-#velocity upper set 3.0 0.0 0.0
-#fix 3 boundary setforce 0.0 0.0 0.0
-#fix 4 all enforce2d
-
-# Poisseuille flow
-
-velocity boundary set 0.0 0.0 0.0
-fix 3 lower setforce 0.0 0.0 0.0
-fix 4 upper setforce 0.0 NULL 0.0
-fix 5 upper aveforce 0.0 -1.0 0.0
-fix 6 flow addforce 0.5 0.0 0.0
-fix 7 all enforce2d
-
-# Run
-
-timestep 0.003
-thermo 500
-thermo_modify temp mobile
-
-dump 1 all atom 25 dump.flow
-run 10000
-Memory usage per processor = 1.67714 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume
- 0 1 0 0 0.71071429 0.5223703 571.43371
- 500 1.0778761 -0.35048279 0 0.41557918 2.7734524 574.92238
- 1000 1 -0.38740705 0 0.32330724 2.1851606 585.40362
- 1500 1.2052679 -0.37768559 0 0.47891551 1.5598219 585.77368
- 2000 1 -0.38060118 0 0.33011311 1.4422178 578.14206
- 2500 1.2211447 -0.39689947 0 0.47098548 1.5039485 566.96926
- 3000 1 -0.46632695 0 0.24438733 1.5055761 554.63863
- 3500 1.2338306 -0.57219064 0 0.30471041 1.750976 537.18508
- 4000 1 -0.70062676 0 0.01008753 2.2214089 518.64479
- 4500 1.2113785 -0.71432757 0 0.14661646 2.924362 503.68263
- 5000 1 -0.75295272 0 -0.042238438 3.0703778 500.62274
- 5500 1.2231978 -0.7326692 0 0.13667498 2.4722796 507.17803
- 6000 1 -0.69221877 0 0.018495519 2.1186078 514.07585
- 6500 1.2130182 -0.64829278 0 0.21381659 2.025108 517.78662
- 7000 1 -0.65011103 0 0.06060326 1.9907035 517.57821
- 7500 1.2244611 -0.68871579 0 0.1815262 2.1613555 512.52321
- 8000 1 -0.70033438 0 0.010379908 2.1994922 511.09769
- 8500 1.2325381 -0.73996991 0 0.13601255 2.2631942 507.50923
- 9000 1 -0.72281872 0 -0.012104437 2.4807895 504.20901
- 9500 1.2301783 -0.74960296 0 0.1247023 2.4156775 505.4057
- 10000 1 -0.76295913 0 -0.05224484 2.3054863 506.85774
-Loop time of 5.06933 on 4 procs for 10000 steps with 420 atoms
-
-Pair time (%) = 0.078612 (1.55074)
-Neigh time (%) = 0.0138444 (0.2731)
-Comm time (%) = 3.1048 (61.2466)
-Outpt time (%) = 0.311994 (6.15453)
-Other time (%) = 1.56009 (30.775)
-
-Nlocal: 105 ave 106 max 104 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Nghost: 44.5 ave 46 max 43 min
-Histogram: 1 0 0 1 0 0 1 0 0 1
-Neighs: 277.25 ave 292 max 254 min
-Histogram: 1 0 0 0 1 0 0 0 0 2
-
-Total # of neighbors = 1109
-Ave neighs/atom = 2.64048
-Neighbor list builds = 558
-Dangerous builds = 0
diff --git a/examples/friction/log.friction.22Jan08.linux.1 b/examples/friction/log.friction.21May08.linux.1
similarity index 51%
rename from examples/friction/log.friction.22Jan08.linux.1
rename to examples/friction/log.friction.21May08.linux.1
index b6cd125b1..08bac09db 100644
--- a/examples/friction/log.friction.22Jan08.linux.1
+++ b/examples/friction/log.friction.21May08.linux.1
@@ -1,140 +1,140 @@
-LAMMPS (22 Jan 2008)
+LAMMPS (21 May 2008)
# 2d friction simulation
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.9
Lattice spacing in x,y,z = 1.1327 1.96189 1.1327
region box block 0 50 0 22 -0.25 0.25
create_box 4 box
Created orthogonal box = (0 0 -0.283174) to (56.6348 43.1615 0.283174)
1 by 1 by 1 processor grid
mass 1 1.0
mass 2 1.0
mass 3 1.0
mass 4 1.0
# atom regions
region lo-fixed block INF INF INF 1.1 INF INF
region lo-slab block INF INF INF 7 INF INF
region above-lo block INF INF INF 7 INF INF side out
region hi-fixed block INF INF 20.9 INF INF INF
region hi-slab block INF INF 15 INF INF INF
region below-hi block INF INF 15 INF INF INF side out
region lo-asperity sphere 32 7 0 8
region hi-asperity sphere 18 15 0 8
region lo-half-sphere intersect 2 lo-asperity above-lo
region hi-half-sphere intersect 2 hi-asperity below-hi
# create 2 surfaces with asperities
create_atoms 1 region lo-slab
Created 750 atoms
create_atoms 1 region hi-slab
Created 750 atoms
create_atoms 2 region lo-half-sphere
Created 112 atoms
create_atoms 3 region hi-half-sphere
Created 112 atoms
# LJ potentials
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
# define groups
group lo region lo-slab
750 atoms in group lo
group lo type 2
862 atoms in group lo
group hi region hi-slab
750 atoms in group hi
group hi type 3
862 atoms in group hi
group lo-fixed region lo-fixed
150 atoms in group lo-fixed
group hi-fixed region hi-fixed
150 atoms in group hi-fixed
group boundary union lo-fixed hi-fixed
300 atoms in group boundary
group mobile subtract all boundary
1424 atoms in group mobile
set group lo-fixed type 4
150 settings made for type
set group hi-fixed type 4
150 settings made for type
# initial velocities
compute new mobile temp/partial 0 1 0
velocity mobile create 0.1 482748 temp new
velocity hi set 1.0 0.0 0.0 sum yes
# fixes
fix 1 all nve
fix 2 boundary setforce 0.0 0.0 0.0
fix 3 mobile temp/rescale 200 0.1 0.1 0.02 1.0
fix_modify 3 temp new
# Run
timestep 0.0025
thermo 1000
thermo_modify temp new
dump 1 all atom 500 dump.friction
run 20000
Memory usage per processor = 1.73539 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
- 0 0.1 -3.1333672 0 -3.0921549 -1.1440307 2444.4558
- 1000 0.085622556 -3.0583969 0 -3.0231098 0.033995503 2444.4558
- 2000 0.085921887 -3.0572271 0 -3.0218167 -0.51378547 2444.4558
- 3000 0.10739474 -3.0650606 0 -3.0208008 -0.035547438 2444.4558
- 4000 0.089682132 -3.04809 0 -3.01113 -0.19064505 2444.4558
- 5000 0.10934102 -3.0485926 0 -3.0035307 0.1034494 2444.4558
- 6000 0.10817011 -3.0584907 0 -3.0139113 -0.31026241 2444.4558
- 7000 0.10519386 -3.0511555 0 -3.0078027 -0.23777457 2444.4558
- 8000 0.11660726 -3.0348032 0 -2.9867467 -0.40191693 2444.4558
- 9000 0.1 -3.0308538 0 -2.9896415 -0.30056676 2444.4558
- 10000 0.10422874 -3.0468394 0 -3.0038843 -0.41010239 2444.4558
- 11000 0.10907653 -3.0470568 0 -3.0021038 -0.39779677 2444.4558
- 12000 0.10518096 -3.0467458 0 -3.0033983 -0.28073637 2444.4558
- 13000 0.1052846 -3.0424889 0 -2.9990987 -0.39335018 2444.4558
- 14000 0.10942544 -3.0462295 0 -3.0011328 -0.31177088 2444.4558
- 15000 0.10696705 -3.0423514 0 -2.9982679 -0.39759929 2444.4558
- 16000 0.11637773 -3.0496752 0 -3.0017132 -0.19541362 2444.4558
- 17000 0.11090878 -3.0452336 0 -2.9995256 -0.41097653 2444.4558
- 18000 0.11274493 -3.0471847 0 -3.0007199 -0.31516775 2444.4558
- 19000 0.1058703 -3.0463493 0 -3.0027177 -0.28413841 2444.4558
- 20000 0.11224126 -3.0475136 0 -3.0012564 -0.24520009 2444.4558
-Loop time of 10.8085 on 1 procs for 20000 steps with 1724 atoms
-
-Pair time (%) = 9.04044 (83.642)
-Neigh time (%) = 0.445875 (4.12523)
-Comm time (%) = 0.0687661 (0.636223)
-Outpt time (%) = 0.096189 (0.889939)
-Other time (%) = 1.15723 (10.7067)
+ 0 0.1 -3.1333672 0 -3.0921259 -1.1440102 2444.4558
+ 1000 0.1 -3.0915465 0 -3.0503052 0.010017516 2444.4558
+ 2000 0.1 -3.0826487 0 -3.0414074 -0.42021097 2444.4558
+ 3000 0.089819692 -3.07584 0 -3.0387972 -0.25257042 2444.4558
+ 4000 0.098489874 -3.0667093 0 -3.0260907 -0.25511521 2444.4558
+ 5000 0.11379986 -3.0557087 0 -3.0087762 -0.080886978 2444.4558
+ 6000 0.11269179 -3.04532 0 -2.9988445 -0.33387724 2444.4558
+ 7000 0.1 -3.0380598 0 -2.9968185 -0.32430283 2444.4558
+ 8000 0.1 -3.0346457 0 -2.9934044 -0.38023276 2444.4558
+ 9000 0.1 -3.0327792 0 -2.9915379 -0.43204961 2444.4558
+ 10000 0.11908329 -3.0384756 0 -2.9893641 -0.34377218 2444.4558
+ 11000 0.1 -3.0307666 0 -2.9895253 -0.46039249 2444.4558
+ 12000 0.11748666 -3.0410033 0 -2.9925503 -0.21956005 2444.4558
+ 13000 0.1 -3.0416003 0 -3.000359 -0.3651589 2444.4558
+ 14000 0.11069381 -3.0439855 0 -2.998334 -0.28704457 2444.4558
+ 15000 0.11218605 -3.0480708 0 -3.0018038 -0.32666261 2444.4558
+ 16000 0.11189162 -3.0483127 0 -3.0021671 -0.23171462 2444.4558
+ 17000 0.11423906 -3.0474938 0 -3.0003802 -0.34260897 2444.4558
+ 18000 0.11548632 -3.047828 0 -3.0002 -0.31060102 2444.4558
+ 19000 0.10034246 -3.0488263 0 -3.0074438 -0.2527683 2444.4558
+ 20000 0.10505024 -3.0494404 0 -3.0061164 -0.31791192 2444.4558
+Loop time of 10.9957 on 1 procs for 20000 steps with 1724 atoms
+
+Pair time (%) = 9.05434 (82.344)
+Neigh time (%) = 0.448596 (4.07973)
+Comm time (%) = 0.0685506 (0.623428)
+Outpt time (%) = 0.262556 (2.38779)
+Other time (%) = 1.1617 (10.565)
Nlocal: 1724 ave 1724 max 1724 min
Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 142 ave 142 max 142 min
+Nghost: 146 ave 146 max 146 min
Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 14388 ave 14388 max 14388 min
+Neighs: 14389 ave 14389 max 14389 min
Histogram: 1 0 0 0 0 0 0 0 0 0
-Total # of neighbors = 14388
-Ave neighs/atom = 8.34571
-Neighbor list builds = 736
+Total # of neighbors = 14389
+Ave neighs/atom = 8.34629
+Neighbor list builds = 723
Dangerous builds = 0
diff --git a/examples/friction/log.friction.21May08.linux.4 b/examples/friction/log.friction.21May08.linux.4
new file mode 100644
index 000000000..e1878f27c
--- /dev/null
+++ b/examples/friction/log.friction.21May08.linux.4
@@ -0,0 +1,140 @@
+LAMMPS (21 May 2008)
+# 2d friction simulation
+
+dimension 2
+boundary p s p
+
+atom_style atomic
+neighbor 0.3 bin
+neigh_modify delay 5
+
+# create geometry
+
+lattice hex 0.9
+Lattice spacing in x,y,z = 1.1327 1.96189 1.1327
+region box block 0 50 0 22 -0.25 0.25
+create_box 4 box
+Created orthogonal box = (0 0 -0.283174) to (56.6348 43.1615 0.283174)
+ 2 by 2 by 1 processor grid
+
+mass 1 1.0
+mass 2 1.0
+mass 3 1.0
+mass 4 1.0
+
+# atom regions
+
+region lo-fixed block INF INF INF 1.1 INF INF
+region lo-slab block INF INF INF 7 INF INF
+region above-lo block INF INF INF 7 INF INF side out
+region hi-fixed block INF INF 20.9 INF INF INF
+region hi-slab block INF INF 15 INF INF INF
+region below-hi block INF INF 15 INF INF INF side out
+region lo-asperity sphere 32 7 0 8
+region hi-asperity sphere 18 15 0 8
+region lo-half-sphere intersect 2 lo-asperity above-lo
+region hi-half-sphere intersect 2 hi-asperity below-hi
+
+# create 2 surfaces with asperities
+
+create_atoms 1 region lo-slab
+Created 750 atoms
+create_atoms 1 region hi-slab
+Created 750 atoms
+create_atoms 2 region lo-half-sphere
+Created 112 atoms
+create_atoms 3 region hi-half-sphere
+Created 112 atoms
+
+# LJ potentials
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0 2.5
+
+# define groups
+
+group lo region lo-slab
+750 atoms in group lo
+group lo type 2
+862 atoms in group lo
+group hi region hi-slab
+750 atoms in group hi
+group hi type 3
+862 atoms in group hi
+group lo-fixed region lo-fixed
+150 atoms in group lo-fixed
+group hi-fixed region hi-fixed
+150 atoms in group hi-fixed
+group boundary union lo-fixed hi-fixed
+300 atoms in group boundary
+group mobile subtract all boundary
+1424 atoms in group mobile
+
+set group lo-fixed type 4
+ 150 settings made for type
+set group hi-fixed type 4
+ 150 settings made for type
+
+# initial velocities
+
+compute new mobile temp/partial 0 1 0
+velocity mobile create 0.1 482748 temp new
+velocity hi set 1.0 0.0 0.0 sum yes
+
+# fixes
+
+fix 1 all nve
+fix 2 boundary setforce 0.0 0.0 0.0
+fix 3 mobile temp/rescale 200 0.1 0.1 0.02 1.0
+fix_modify 3 temp new
+
+# Run
+
+timestep 0.0025
+thermo 1000
+thermo_modify temp new
+
+dump 1 all atom 500 dump.friction
+run 20000
+Memory usage per processor = 1.69136 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 0.1 -3.1333672 0 -3.0921259 -1.1440102 2444.4558
+ 1000 0.081958665 -3.0927273 0 -3.0589265 -0.021850399 2444.4558
+ 2000 0.082641883 -3.0850764 0 -3.0509938 -0.44968978 2444.4558
+ 3000 0.092293442 -3.0748001 0 -3.0367371 -0.25358115 2444.4558
+ 4000 0.096012911 -3.0565129 0 -3.0169159 -0.027674947 2444.4558
+ 5000 0.1 -3.0465555 0 -3.0053142 -0.09934336 2444.4558
+ 6000 0.11642983 -3.0390782 0 -2.991061 -0.21038719 2444.4558
+ 7000 0.11597773 -3.0331763 0 -2.9853456 -0.46354951 2444.4558
+ 8000 0.11937916 -3.0305564 0 -2.9813229 -0.30779256 2444.4558
+ 9000 0.11110731 -3.0274253 0 -2.9816032 -0.5245514 2444.4558
+ 10000 0.11533593 -3.0167931 0 -2.969227 -0.3589085 2444.4558
+ 11000 0.11347587 -3.0130738 0 -2.9662749 -0.47723571 2444.4558
+ 12000 0.10688909 -3.0229092 0 -2.9788267 -0.31337183 2444.4558
+ 13000 0.11881914 -3.0191983 0 -2.9701958 -0.43871352 2444.4558
+ 14000 0.10970971 -3.0345115 0 -2.9892658 -0.26475254 2444.4558
+ 15000 0.10683593 -3.030202 0 -2.9861414 -0.37883026 2444.4558
+ 16000 0.11039182 -3.0315771 0 -2.9860501 -0.31830843 2444.4558
+ 17000 0.11294566 -3.0314496 0 -2.9848693 -0.34449141 2444.4558
+ 18000 0.11747267 -3.0330363 0 -2.984589 -0.21439976 2444.4558
+ 19000 0.11287946 -3.0392425 0 -2.9926895 -0.38778831 2444.4558
+ 20000 0.10942894 -3.0360473 0 -2.9909174 -0.3375786 2444.4558
+Loop time of 9.87621 on 4 procs for 20000 steps with 1724 atoms
+
+Pair time (%) = 2.4164 (24.4668)
+Neigh time (%) = 0.115138 (1.16582)
+Comm time (%) = 5.67421 (57.4533)
+Outpt time (%) = 0.102493 (1.03777)
+Other time (%) = 1.56798 (15.8763)
+
+Nlocal: 431 ave 494 max 376 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+Nghost: 95 ave 124 max 75 min
+Histogram: 1 1 0 0 1 0 0 0 0 1
+Neighs: 3578.5 ave 4170 max 3130 min
+Histogram: 1 1 0 0 0 1 0 0 0 1
+
+Total # of neighbors = 14314
+Ave neighs/atom = 8.30278
+Neighbor list builds = 703
+Dangerous builds = 0
diff --git a/examples/friction/log.friction.22Jan08.linux.4 b/examples/friction/log.friction.22Jan08.linux.4
deleted file mode 100644
index 49b29c499..000000000
--- a/examples/friction/log.friction.22Jan08.linux.4
+++ /dev/null
@@ -1,140 +0,0 @@
-LAMMPS (22 Jan 2008)
-# 2d friction simulation
-
-dimension 2
-boundary p s p
-
-atom_style atomic
-neighbor 0.3 bin
-neigh_modify delay 5
-
-# create geometry
-
-lattice hex 0.9
-Lattice spacing in x,y,z = 1.1327 1.96189 1.1327
-region box block 0 50 0 22 -0.25 0.25
-create_box 4 box
-Created orthogonal box = (0 0 -0.283174) to (56.6348 43.1615 0.283174)
- 2 by 2 by 1 processor grid
-
-mass 1 1.0
-mass 2 1.0
-mass 3 1.0
-mass 4 1.0
-
-# atom regions
-
-region lo-fixed block INF INF INF 1.1 INF INF
-region lo-slab block INF INF INF 7 INF INF
-region above-lo block INF INF INF 7 INF INF side out
-region hi-fixed block INF INF 20.9 INF INF INF
-region hi-slab block INF INF 15 INF INF INF
-region below-hi block INF INF 15 INF INF INF side out
-region lo-asperity sphere 32 7 0 8
-region hi-asperity sphere 18 15 0 8
-region lo-half-sphere intersect 2 lo-asperity above-lo
-region hi-half-sphere intersect 2 hi-asperity below-hi
-
-# create 2 surfaces with asperities
-
-create_atoms 1 region lo-slab
-Created 750 atoms
-create_atoms 1 region hi-slab
-Created 750 atoms
-create_atoms 2 region lo-half-sphere
-Created 112 atoms
-create_atoms 3 region hi-half-sphere
-Created 112 atoms
-
-# LJ potentials
-
-pair_style lj/cut 2.5
-pair_coeff * * 1.0 1.0 2.5
-
-# define groups
-
-group lo region lo-slab
-750 atoms in group lo
-group lo type 2
-862 atoms in group lo
-group hi region hi-slab
-750 atoms in group hi
-group hi type 3
-862 atoms in group hi
-group lo-fixed region lo-fixed
-150 atoms in group lo-fixed
-group hi-fixed region hi-fixed
-150 atoms in group hi-fixed
-group boundary union lo-fixed hi-fixed
-300 atoms in group boundary
-group mobile subtract all boundary
-1424 atoms in group mobile
-
-set group lo-fixed type 4
- 150 settings made for type
-set group hi-fixed type 4
- 150 settings made for type
-
-# initial velocities
-
-compute new mobile temp/partial 0 1 0
-velocity mobile create 0.1 482748 temp new
-velocity hi set 1.0 0.0 0.0 sum yes
-
-# fixes
-
-fix 1 all nve
-fix 2 boundary setforce 0.0 0.0 0.0
-fix 3 mobile temp/rescale 200 0.1 0.1 0.02 1.0
-fix_modify 3 temp new
-
-# Run
-
-timestep 0.0025
-thermo 1000
-thermo_modify temp new
-
-dump 1 all atom 500 dump.friction
-run 20000
-Memory usage per processor = 1.69136 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume
- 0 0.1 -3.1333672 0 -3.0921549 -1.1440307 2444.4558
- 1000 0.08936608 -3.060858 0 -3.0240282 0.015747058 2444.4558
- 2000 0.087353242 -3.0615115 0 -3.0255112 -0.49966222 2444.4558
- 3000 0.097185838 -3.0626106 0 -3.0225581 -0.084736345 2444.4558
- 4000 0.10514697 -3.0540883 0 -3.0107549 -0.34379432 2444.4558
- 5000 0.10965701 -3.0502726 0 -3.0050804 0.13242136 2444.4558
- 6000 0.1142368 -3.0461587 0 -2.9990791 -0.23407787 2444.4558
- 7000 0.1 -3.038824 0 -2.9976117 -0.3283908 2444.4558
- 8000 0.11116944 -3.0485104 0 -3.0026949 -0.42926135 2444.4558
- 9000 0.11429391 -3.0445555 0 -2.9974523 -0.39751757 2444.4558
- 10000 0.10617044 -3.050964 0 -3.0072087 -0.4320286 2444.4558
- 11000 0.10925063 -3.0492538 0 -3.0042291 -0.39877306 2444.4558
- 12000 0.11491574 -3.0511726 0 -3.0038132 -0.24990158 2444.4558
- 13000 0.10704872 -3.0467833 0 -3.0026661 -0.4272322 2444.4558
- 14000 0.10931685 -3.0488184 0 -3.0037664 -0.23385297 2444.4558
- 15000 0.103619 -3.0474073 0 -3.0047036 -0.39914954 2444.4558
- 16000 0.11669382 -3.0538214 0 -3.0057292 -0.29282079 2444.4558
- 17000 0.10983692 -3.0489199 0 -3.0036536 -0.30423885 2444.4558
- 18000 0.11157946 -3.0516854 0 -3.005701 -0.3165345 2444.4558
- 19000 0.11408792 -3.0522616 0 -3.0052433 -0.39019198 2444.4558
- 20000 0.10714842 -3.0629068 0 -3.0187485 -0.2392859 2444.4558
-Loop time of 11.275 on 4 procs for 20000 steps with 1724 atoms
-
-Pair time (%) = 2.6525 (23.5254)
-Neigh time (%) = 0.125193 (1.11036)
-Comm time (%) = 6.57651 (58.328)
-Outpt time (%) = 0.108834 (0.965266)
-Other time (%) = 1.81201 (16.071)
-
-Nlocal: 431 ave 483 max 383 min
-Histogram: 1 1 0 0 0 0 0 1 0 1
-Nghost: 100 ave 118 max 84 min
-Histogram: 1 0 0 1 0 1 0 0 0 1
-Neighs: 3600.5 ave 4171 max 3180 min
-Histogram: 2 0 0 0 0 0 1 0 0 1
-
-Total # of neighbors = 14402
-Ave neighs/atom = 8.35383
-Neighbor list builds = 724
-Dangerous builds = 0
diff --git a/examples/indent/log.indent.21May08.linux.1 b/examples/indent/log.indent.21May08.linux.1
new file mode 100644
index 000000000..9381804cc
--- /dev/null
+++ b/examples/indent/log.indent.21May08.linux.1
@@ -0,0 +1,169 @@
+LAMMPS (21 May 2008)
+# 2d indenter simulation
+
+dimension 2
+boundary p s p
+
+atom_style atomic
+neighbor 0.3 bin
+neigh_modify delay 5
+
+# create geometry
+
+lattice hex 0.9
+Lattice spacing in x,y,z = 1.1327 1.96189 1.1327
+region box block 0 20 0 10 -0.25 0.25
+create_box 2 box
+Created orthogonal box = (0 0 -0.283174) to (22.6539 19.6189 0.283174)
+ 1 by 1 by 1 processor grid
+create_atoms 1 box
+Created 420 atoms
+
+mass 1 1.0
+mass 2 1.0
+
+# LJ potentials
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0 2.5
+
+# define groups
+
+region 1 block INF INF INF 1.25 INF INF
+group lower region 1
+60 atoms in group lower
+group mobile subtract all lower
+360 atoms in group mobile
+set group lower type 2
+ 60 settings made for type
+
+# initial velocities
+
+compute new mobile temp
+velocity mobile create 0.2 482748 temp new
+fix 1 all nve
+fix 2 lower setforce 0.0 0.0 0.0
+fix 3 all temp/rescale 100 0.1 0.1 0.01 1.0
+
+# indenter
+
+fix 4 all indent 1000.0 sphere 10 13 0 5.0 vel 0.0 -0.02 0.0
+fix 5 all enforce2d
+
+# Run with indenter
+
+timestep 0.003
+thermo 1000
+thermo_modify temp new
+
+dump 1 all atom 250 dump.indent
+run 30000
+Memory usage per processor = 1.681 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 0.2 -3.1727576 0 -3.0018052 -1.4364576 444.44898
+ 1000 0.11974254 -3.0876892 0 -2.9853378 -0.037066341 440.70336
+ 2000 0.12086797 -3.0886512 0 -2.9853378 -0.39890862 444.27124
+ 3000 0.11671309 -3.0840074 0 -2.9842455 -0.34866631 442.86992
+ 4000 0.12339115 -3.1000529 0 -2.9945828 -0.049706317 438.90862
+ 5000 0.10860594 -3.0866045 0 -2.9937722 -0.47982999 443.91419
+ 6000 0.11839788 -3.0929689 0 -2.9917669 -0.033460572 442.61903
+ 7000 0.12194527 -3.0835584 0 -2.9793242 -0.13984271 443.27826
+ 8000 0.11671309 -3.0862884 0 -2.9865265 0.073966694 441.62891
+ 9000 0.12449823 -3.0880806 0 -2.9816643 0.286535 439.19731
+ 10000 0.12475263 -3.0830722 0 -2.9764384 0.38108755 440.41873
+ 11000 0.11198118 -3.0743549 0 -2.9786377 0.67596956 438.41816
+ 12000 0.10823034 -3.0621355 0 -2.9696244 0.66497739 441.05346
+ 13000 0.1194298 -3.0579575 0 -2.9558734 1.0886185 437.64369
+ 14000 0.12310404 -3.051382 0 -2.9461573 0.8709418 445.45576
+ 15000 0.11148459 -3.0402208 0 -2.944928 1.0042516 451.82353
+ 16000 0.12322327 -3.041552 0 -2.9362254 0.75832747 456.81933
+ 17000 0.12311088 -3.0300335 0 -2.924803 1.0485184 452.83217
+ 18000 0.12062516 -3.0261639 0 -2.9230581 1.3986189 451.63458
+ 19000 0.11958004 -3.0142969 0 -2.9120844 1.3964253 457.84108
+ 20000 0.12231468 -3.0015738 0 -2.8970239 1.1240498 470.04449
+ 21000 0.12075603 -3.0281424 0 -2.9249248 0.77047496 472.82097
+ 22000 0.1140902 -3.0149866 0 -2.9174666 0.59890761 475.27346
+ 23000 0.11660315 -3.022367 0 -2.9226991 0.86533578 474.33185
+ 24000 0.11788061 -3.0130282 0 -2.9122684 1.0089196 468.47962
+ 25000 0.11677694 -3.027 0 -2.9271835 0.95315571 470.28897
+ 26000 0.12227277 -3.0174852 0 -2.9129711 1.0595574 469.3955
+ 27000 0.11778994 -3.0019697 0 -2.9012873 1.2973295 472.846
+ 28000 0.10834261 -2.9909288 0 -2.8983217 1.4598621 471.38654
+ 29000 0.11506991 -2.9815688 0 -2.8832114 1.6220695 475.78184
+ 30000 0.1137611 -2.9910145 0 -2.8937758 1.5390363 476.49487
+Loop time of 4.35277 on 1 procs for 30000 steps with 420 atoms
+
+Pair time (%) = 3.3632 (77.2656)
+Neigh time (%) = 0.0964704 (2.2163)
+Comm time (%) = 0.056159 (1.29019)
+Outpt time (%) = 0.0744166 (1.70964)
+Other time (%) = 0.762532 (17.5183)
+
+Nlocal: 420 ave 420 max 420 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 110 ave 110 max 110 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 3704 ave 3704 max 3704 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 3704
+Ave neighs/atom = 8.81905
+Neighbor list builds = 620
+Dangerous builds = 0
+
+# Run without indenter
+
+unfix 4
+run 30000
+Memory usage per processor = 1.68109 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 30000 0.1137611 -2.9910145 0 -2.8937758 1.5390363 476.49487
+ 31000 0.11111993 -3.0361785 0 -2.9411974 -0.27734293 487.43496
+ 32000 0.12226168 -3.0352443 0 -2.9307397 -0.65334794 484.5377
+ 33000 0.12141332 -3.0559903 0 -2.9522108 0.2052495 480.86455
+ 34000 0.11608515 -3.0513192 0 -2.952094 -0.40452569 486.60815
+ 35000 0.12135397 -3.0431351 0 -2.9394063 -0.54073868 492.67492
+ 36000 0.11867423 -3.0517805 0 -2.9503423 0.17502223 481.35439
+ 37000 0.11592678 -3.0389976 0 -2.9399078 -0.45434566 489.41107
+ 38000 0.12303667 -3.0448814 0 -2.9397144 -0.37442535 488.51063
+ 39000 0.11824399 -3.0658885 0 -2.964818 -0.020875637 485.34869
+ 40000 0.10891424 -3.0684735 0 -2.9753777 -0.40194667 490.36569
+ 41000 0.11971963 -3.0777108 0 -2.975379 -0.31502752 485.70356
+ 42000 0.12242279 -3.0800244 0 -2.975382 -0.29154762 485.64123
+ 43000 0.11191041 -3.0710358 0 -2.9753791 -0.47381376 485.98823
+ 44000 0.11663432 -3.0750759 0 -2.9753813 -0.16155045 483.58595
+ 45000 0.11931527 -3.0773695 0 -2.9753833 -0.26683012 485.76005
+ 46000 0.11602561 -3.0745521 0 -2.9753778 -0.43504309 488.91425
+ 47000 0.11378336 -3.072636 0 -2.9753783 -0.065265912 485.31689
+ 48000 0.11466706 -3.0733926 0 -2.9753796 -0.34617216 489.24951
+ 49000 0.11892658 -3.0770335 0 -2.9753796 -0.34745886 486.45808
+ 50000 0.11518751 -3.0738396 0 -2.9753817 -0.13713339 483.56692
+ 51000 0.11924377 -3.0773057 0 -2.9753807 -0.46696512 487.41041
+ 52000 0.12732939 -3.084182 0 -2.9753457 -0.31430325 483.886
+ 53000 0.1184932 -3.0766623 0 -2.9753788 -0.22727456 485.05121
+ 54000 0.10979213 -3.0692247 0 -2.9753786 -0.46578194 487.22102
+ 55000 0.11813596 -3.0763601 0 -2.975382 -0.21269197 485.60016
+ 56000 0.11927788 -3.0820716 0 -2.9801174 -0.39257652 488.29363
+ 57000 0.11370876 -3.077309 0 -2.9801151 -0.42695354 487.36404
+ 58000 0.10977322 -3.0750653 0 -2.9812353 -0.13698023 483.43933
+ 59000 0.11837611 -3.0824237 0 -2.9812403 -0.42226934 488.24864
+ 60000 0.12513787 -3.0760063 0 -2.9690432 -0.27843098 488.02101
+Loop time of 4.04106 on 1 procs for 30000 steps with 420 atoms
+
+Pair time (%) = 3.33419 (82.5078)
+Neigh time (%) = 0.0975268 (2.4134)
+Comm time (%) = 0.0565064 (1.39831)
+Outpt time (%) = 0.0741966 (1.83607)
+Other time (%) = 0.478639 (11.8444)
+
+Nlocal: 420 ave 420 max 420 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 106 ave 106 max 106 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 3564 ave 3564 max 3564 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 3564
+Ave neighs/atom = 8.48571
+Neighbor list builds = 632
+Dangerous builds = 0
diff --git a/examples/indent/log.indent.21May08.linux.4 b/examples/indent/log.indent.21May08.linux.4
new file mode 100644
index 000000000..721086251
--- /dev/null
+++ b/examples/indent/log.indent.21May08.linux.4
@@ -0,0 +1,169 @@
+LAMMPS (21 May 2008)
+# 2d indenter simulation
+
+dimension 2
+boundary p s p
+
+atom_style atomic
+neighbor 0.3 bin
+neigh_modify delay 5
+
+# create geometry
+
+lattice hex 0.9
+Lattice spacing in x,y,z = 1.1327 1.96189 1.1327
+region box block 0 20 0 10 -0.25 0.25
+create_box 2 box
+Created orthogonal box = (0 0 -0.283174) to (22.6539 19.6189 0.283174)
+ 2 by 2 by 1 processor grid
+create_atoms 1 box
+Created 420 atoms
+
+mass 1 1.0
+mass 2 1.0
+
+# LJ potentials
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0 2.5
+
+# define groups
+
+region 1 block INF INF INF 1.25 INF INF
+group lower region 1
+60 atoms in group lower
+group mobile subtract all lower
+360 atoms in group mobile
+set group lower type 2
+ 60 settings made for type
+
+# initial velocities
+
+compute new mobile temp
+velocity mobile create 0.2 482748 temp new
+fix 1 all nve
+fix 2 lower setforce 0.0 0.0 0.0
+fix 3 all temp/rescale 100 0.1 0.1 0.01 1.0
+
+# indenter
+
+fix 4 all indent 1000.0 sphere 10 13 0 5.0 vel 0.0 -0.02 0.0
+fix 5 all enforce2d
+
+# Run with indenter
+
+timestep 0.003
+thermo 1000
+thermo_modify temp new
+
+dump 1 all atom 250 dump.indent
+run 30000
+Memory usage per processor = 1.67582 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 0.2 -3.1727576 0 -3.0018052 -1.4364576 444.44898
+ 1000 0.11573595 -3.0964873 0 -2.9975606 -0.20452577 441.75296
+ 2000 0.11519605 -3.0960246 0 -2.9975594 -0.38140765 442.24623
+ 3000 0.11367906 -3.0839597 0 -2.9867912 -0.42587846 444.50683
+ 4000 0.11618844 -3.0860897 0 -2.9867762 -0.041588892 439.76178
+ 5000 0.11327789 -3.0848614 0 -2.9880358 -0.48908114 446.10767
+ 6000 0.12058424 -3.0869438 0 -2.983873 0.011479332 440.48452
+ 7000 0.11772522 -3.0833477 0 -2.9827207 -0.090395475 442.48351
+ 8000 0.12533514 -3.0970033 0 -2.9898715 0.13265726 441.15042
+ 9000 0.1198683 -3.0867062 0 -2.9842473 0.340532 439.38624
+ 10000 0.12234014 -3.0835007 0 -2.9789291 0.28405153 441.85872
+ 11000 0.11082436 -3.0754796 0 -2.9807511 0.62206175 441.23576
+ 12000 0.10842719 -3.0646379 0 -2.9719584 0.65396033 442.56232
+ 13000 0.11686417 -3.0600388 0 -2.9601477 1.0043055 438.41699
+ 14000 0.12557378 -3.0570017 0 -2.949666 0.85725522 442.01753
+ 15000 0.11934083 -3.0498848 0 -2.9478768 1.0394141 451.6596
+ 16000 0.12576916 -3.0452181 0 -2.9377154 1.3482057 441.18585
+ 17000 0.11546551 -3.0348365 0 -2.9361409 1.6321334 439.4002
+ 18000 0.1214883 -3.0221153 0 -2.9182718 1.6092045 449.17018
+ 19000 0.11883751 -3.0036774 0 -2.9020996 1.5203993 447.04217
+ 20000 0.11165763 -3.0038239 0 -2.9083832 1.4080186 461.67014
+ 21000 0.11347925 -2.9899447 0 -2.8929469 1.1346232 473.86859
+ 22000 0.11913997 -3.0239282 0 -2.9220919 0.81021913 473.09495
+ 23000 0.1148535 -3.0126427 0 -2.9144703 1.1401379 470.54689
+ 24000 0.11671309 -3.016222 0 -2.9164601 0.84429095 472.7482
+ 25000 0.11161515 -3.0207137 0 -2.9253093 1.0597826 467.28214
+ 26000 0.11294692 -3.0085312 0 -2.9119885 1.0112464 469.64427
+ 27000 0.12828831 -3.010401 0 -2.9007451 1.0769835 473.94697
+ 28000 0.12123681 -3.0107629 0 -2.9071343 0.81020478 478.51729
+ 29000 0.12528058 -3.01932 0 -2.912235 1.0826534 472.26351
+ 30000 0.11527728 -3.0030382 0 -2.9045036 1.5931211 465.76942
+Loop time of 12.2538 on 4 procs for 30000 steps with 420 atoms
+
+Pair time (%) = 1.06251 (8.67087)
+Neigh time (%) = 0.0298207 (0.243358)
+Comm time (%) = 8.70494 (71.0387)
+Outpt time (%) = 0.0981069 (0.800624)
+Other time (%) = 2.35843 (19.2465)
+
+Nlocal: 105 ave 112 max 97 min
+Histogram: 1 0 1 0 0 0 0 0 1 1
+Nghost: 95.5 ave 100 max 92 min
+Histogram: 1 1 0 0 0 0 1 0 0 1
+Neighs: 914.75 ave 1023 max 810 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 3659
+Ave neighs/atom = 8.7119
+Neighbor list builds = 616
+Dangerous builds = 0
+
+# Run without indenter
+
+unfix 4
+run 30000
+Memory usage per processor = 1.67614 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 30000 0.11527728 -3.0030382 0 -2.9045036 1.5932587 465.72917
+ 31000 0.11671309 -3.0142211 0 -2.9144592 -0.37706203 481.50962
+ 32000 0.11671309 -3.0227063 0 -2.9229444 -0.58012876 480.95432
+ 33000 0.10635055 -3.0482223 0 -2.9573179 0.45560579 464.47424
+ 34000 0.11877148 -3.0703768 0 -2.9688555 -0.32968186 475.82732
+ 35000 0.1157547 -3.0679911 0 -2.9690484 -0.55386822 490.09322
+ 36000 0.12250126 -3.0847099 0 -2.9800005 0.16762425 482.76837
+ 37000 0.11211273 -3.076227 0 -2.9803973 -0.56416688 485.40738
+ 38000 0.12332877 -3.074982 0 -2.9695653 -0.35777769 490.47511
+ 39000 0.11065377 -3.0755102 0 -2.9809275 0.014347118 478.2741
+ 40000 0.10710169 -3.0724742 0 -2.9809278 -0.55516693 490.26814
+ 41000 0.1088162 -3.0739373 0 -2.9809254 -0.069868958 482.39533
+ 42000 0.12792219 -3.0902767 0 -2.9809336 -0.26461148 484.55637
+ 43000 0.11058857 -3.0754557 0 -2.9809288 -0.64800221 488.40619
+ 44000 0.11162461 -3.0763412 0 -2.9809287 0.075505051 482.91497
+ 45000 0.11497594 -3.0792046 0 -2.9809275 -0.38338131 485.15347
+ 46000 0.10637288 -3.0718511 0 -2.9809276 -0.47729139 489.49592
+ 47000 0.11706089 -3.0809897 0 -2.9809305 0.0034214827 482.52084
+ 48000 0.11104829 -3.075849 0 -2.9809292 -0.58552878 486.85862
+ 49000 0.11245495 -3.0770533 0 -2.9809311 -0.32773345 487.81722
+ 50000 0.11875403 -3.0824388 0 -2.9809324 -0.1284175 480.82151
+ 51000 0.10815089 -3.0733705 0 -2.9809273 -0.59528979 488.33208
+ 52000 0.11766627 -3.0713521 0 -2.9707755 -0.14820961 485.02169
+ 53000 0.12125512 -3.0857543 0 -2.98211 -0.27980304 483.66006
+ 54000 0.11567186 -3.0809806 0 -2.9821087 -0.51734052 487.77367
+ 55000 0.11215173 -3.0779718 0 -2.9821088 -0.13169059 482.81031
+ 56000 0.10952092 -3.0757199 0 -2.9821056 -0.35508967 485.28191
+ 57000 0.12592796 -3.0770934 0 -2.969455 -0.39550089 487.7802
+ 58000 0.11671309 -3.0836904 0 -2.9839285 -0.17868279 485.62136
+ 59000 0.10785966 -3.0761158 0 -2.9839215 -0.36413012 486.36951
+ 60000 0.12108723 -3.0736236 0 -2.9701228 -0.30955784 486.51342
+Loop time of 11.802 on 4 procs for 30000 steps with 420 atoms
+
+Pair time (%) = 0.984152 (8.33884)
+Neigh time (%) = 0.0291511 (0.247001)
+Comm time (%) = 8.40175 (71.1891)
+Outpt time (%) = 0.100835 (0.854389)
+Other time (%) = 2.28613 (19.3707)
+
+Nlocal: 105 ave 119 max 89 min
+Histogram: 1 1 0 0 0 0 0 0 0 2
+Nghost: 88 ave 91 max 84 min
+Histogram: 1 0 0 0 0 1 0 1 0 1
+Neighs: 891.5 ave 1073 max 705 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 3566
+Ave neighs/atom = 8.49048
+Neighbor list builds = 625
+Dangerous builds = 0
diff --git a/examples/indent/log.indent.22Jan08.linux.1 b/examples/indent/log.indent.22Jan08.linux.1
deleted file mode 100644
index b20395bf2..000000000
--- a/examples/indent/log.indent.22Jan08.linux.1
+++ /dev/null
@@ -1,169 +0,0 @@
-LAMMPS (22 Jan 2008)
-# 2d indenter simulation
-
-dimension 2
-boundary p s p
-
-atom_style atomic
-neighbor 0.3 bin
-neigh_modify delay 5
-
-# create geometry
-
-lattice hex 0.9
-Lattice spacing in x,y,z = 1.1327 1.96189 1.1327
-region box block 0 20 0 10 -0.25 0.25
-create_box 2 box
-Created orthogonal box = (0 0 -0.283174) to (22.6539 19.6189 0.283174)
- 1 by 1 by 1 processor grid
-create_atoms 1 box
-Created 420 atoms
-
-mass 1 1.0
-mass 2 1.0
-
-# LJ potentials
-
-pair_style lj/cut 2.5
-pair_coeff * * 1.0 1.0 2.5
-
-# define groups
-
-region 1 block INF INF INF 1.25 INF INF
-group lower region 1
-60 atoms in group lower
-group mobile subtract all lower
-360 atoms in group mobile
-set group lower type 2
- 60 settings made for type
-
-# initial velocities
-
-compute new mobile temp
-velocity mobile create 0.2 482748 temp new
-fix 1 all nve
-fix 2 lower setforce 0.0 0.0 0.0
-fix 3 all temp/rescale 100 0.1 0.1 0.01 1.0
-
-# indenter
-
-fix 4 all indent 1000.0 sphere 10 13 0 5.0 vel 0.0 -0.02 0.0
-fix 5 all enforce2d
-
-# Run with indenter
-
-timestep 0.003
-thermo 1000
-thermo_modify temp new
-
-dump 1 all atom 250 dump.indent
-run 30000
-Memory usage per processor = 1.681 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume
- 0 0.2 -3.1727576 0 -3.0020433 -1.4366826 444.44898
- 1000 0.11979027 -3.0878285 0 -2.9855789 -0.037115753 440.68307
- 2000 0.12095292 -3.0888211 0 -2.9855791 -0.39926994 444.26707
- 3000 0.1167364 -3.0841547 0 -2.9845118 -0.34877104 442.84444
- 4000 0.12249143 -3.1004175 0 -2.9958623 -0.051696807 438.73578
- 5000 0.10957873 -3.0886367 0 -2.9951034 -0.48968706 443.75021
- 6000 0.12346008 -3.0985964 0 -2.9932144 -0.061988469 442.24069
- 7000 0.10994736 -3.0850721 0 -2.9912241 -0.17265831 443.86094
- 8000 0.11557891 -3.086042 0 -2.9873871 0.19299422 440.53674
- 9000 0.12016755 -3.084536 0 -2.9819645 0.28219762 439.46924
- 10000 0.12659552 -3.0852403 0 -2.977182 0.34547052 440.85673
- 11000 0.12524777 -3.0736607 0 -2.9667528 0.65889968 439.12793
- 12000 0.11844672 -3.0571177 0 -2.9560149 0.65697119 441.00263
- 13000 0.12031568 -3.0583679 0 -2.9556699 1.0789051 437.17067
- 14000 0.1167364 -3.0548463 0 -2.9552034 0.92252944 441.75844
- 15000 0.1167364 -3.0549235 0 -2.9552806 1.104037 444.57625
- 16000 0.12471788 -3.052462 0 -2.9460064 1.3976876 440.83011
- 17000 0.12078165 -3.0356476 0 -2.9325518 1.6287355 437.90579
- 18000 0.11738015 -3.0294797 0 -2.9292874 1.685709 448.54282
- 19000 0.12273217 -3.0164912 0 -2.9117305 1.6952163 444.70626
- 20000 0.1254989 -3.0011836 0 -2.8940613 1.5120085 459.5423
- 21000 0.12037276 -2.9934283 0 -2.8906816 1.1633617 475.10793
- 22000 0.12303026 -3.0181561 0 -2.913141 0.80041224 476.32611
- 23000 0.12012255 -3.0180582 0 -2.915525 1.0242864 469.70124
- 24000 0.11834242 -3.011825 0 -2.9108113 0.91924231 471.07582
- 25000 0.11662147 -3.0266029 0 -2.9270581 1.2863229 465.94453
- 26000 0.10849743 -3.0122074 0 -2.9195971 1.0346219 471.89139
- 27000 0.11442546 -3.0195569 0 -2.9218866 0.95642369 472.17747
- 28000 0.12607822 -3.018653 0 -2.9110362 0.80288611 478.81533
- 29000 0.11485475 -3.0026613 0 -2.9046245 1.0162131 478.56821
- 30000 0.11957018 -3.007796 0 -2.9057344 1.1519595 473.32666
-Loop time of 4.36496 on 1 procs for 30000 steps with 420 atoms
-
-Pair time (%) = 3.38296 (77.5027)
-Neigh time (%) = 0.0948896 (2.17389)
-Comm time (%) = 0.055548 (1.27259)
-Outpt time (%) = 0.071348 (1.63456)
-Other time (%) = 0.760214 (17.4163)
-
-Nlocal: 420 ave 420 max 420 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 111 ave 111 max 111 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 3663 ave 3663 max 3663 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 3663
-Ave neighs/atom = 8.72143
-Neighbor list builds = 615
-Dangerous builds = 0
-
-# Run without indenter
-
-unfix 4
-run 30000
-Memory usage per processor = 1.68117 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume
- 30000 0.11957018 -3.007796 0 -2.9057344 1.1538424 472.55425
- 31000 0.10960776 -3.0320499 0 -2.9384919 -0.1111492 475.04939
- 32000 0.11696413 -3.017537 0 -2.9176998 -0.46118163 479.36156
- 33000 0.11881079 -3.0604548 0 -2.9590413 0.089398143 475.85863
- 34000 0.11291474 -3.0762007 0 -2.9798199 -0.53925844 467.63944
- 35000 0.12091623 -3.07146 0 -2.9682494 -0.30643332 465.79963
- 36000 0.11443202 -3.0773212 0 -2.9796453 -0.16930354 468.00022
- 37000 0.10847358 -3.0722351 0 -2.9796452 -0.40417498 466.35112
- 38000 0.12257573 -3.0842762 0 -2.979649 -0.3539779 464.74783
- 39000 0.10919826 -3.0728543 0 -2.9796458 -0.10190087 462.71616
- 40000 0.11592052 -3.0785918 0 -2.9796454 -0.56392258 466.79575
- 41000 0.1187654 -3.0810202 0 -2.9796454 -0.24959896 464.94494
- 42000 0.11065271 -3.0740978 0 -2.9796478 -0.13938683 463.95585
- 43000 0.11213075 -3.0753593 0 -2.9796477 -0.57295952 467.53433
- 44000 0.11851463 -3.0808118 0 -2.9796511 -0.072822043 462.69799
- 45000 0.11513293 -3.0779198 0 -2.9796456 -0.38690299 464.92762
- 46000 0.11802643 -3.0727964 0 -2.9720524 -0.41876651 467.61475
- 47000 0.10968445 -3.0767131 0 -2.9830896 0.00035992413 462.33575
- 48000 0.10986927 -3.0768658 0 -2.9830845 -0.50973722 466.84125
- 49000 0.11716516 -3.0730443 0 -2.9730355 -0.25528257 465.09708
- 50000 0.114152 -3.0811614 0 -2.9837245 -0.25131852 463.16554
- 51000 0.11151236 -3.0789097 0 -2.983726 -0.49587211 466.97181
- 52000 0.12287592 -3.0773446 0 -2.9724612 -0.23319519 466.44897
- 53000 0.12184618 -3.076465 0 -2.9724606 -0.32085107 465.19617
- 54000 0.11183696 -3.067917 0 -2.9724562 -0.31965796 465.50492
- 55000 0.11759344 -3.0728319 0 -2.9724575 -0.25579782 466.03182
- 56000 0.11864906 -3.0737344 0 -2.9724589 -0.21452862 465.36224
- 57000 0.12056652 -3.0753734 0 -2.9724613 -0.38889467 465.52022
- 58000 0.12467619 -3.0788817 0 -2.9724617 -0.25977738 463.35348
- 59000 0.1143898 -3.0802997 0 -2.9826599 -0.36709007 463.95776
- 60000 0.11996036 -3.0850555 0 -2.9826607 -0.43924518 465.21821
-Loop time of 4.03837 on 1 procs for 30000 steps with 420 atoms
-
-Pair time (%) = 3.33861 (82.6721)
-Neigh time (%) = 0.0961225 (2.38023)
-Comm time (%) = 0.0559936 (1.38654)
-Outpt time (%) = 0.071291 (1.76534)
-Other time (%) = 0.476356 (11.7957)
-
-Nlocal: 420 ave 420 max 420 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 107 ave 107 max 107 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 3565 ave 3565 max 3565 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 3565
-Ave neighs/atom = 8.4881
-Neighbor list builds = 620
-Dangerous builds = 0
diff --git a/examples/indent/log.indent.22Jan08.linux.4 b/examples/indent/log.indent.22Jan08.linux.4
deleted file mode 100644
index a99d82a10..000000000
--- a/examples/indent/log.indent.22Jan08.linux.4
+++ /dev/null
@@ -1,169 +0,0 @@
-LAMMPS (22 Jan 2008)
-# 2d indenter simulation
-
-dimension 2
-boundary p s p
-
-atom_style atomic
-neighbor 0.3 bin
-neigh_modify delay 5
-
-# create geometry
-
-lattice hex 0.9
-Lattice spacing in x,y,z = 1.1327 1.96189 1.1327
-region box block 0 20 0 10 -0.25 0.25
-create_box 2 box
-Created orthogonal box = (0 0 -0.283174) to (22.6539 19.6189 0.283174)
- 2 by 2 by 1 processor grid
-create_atoms 1 box
-Created 420 atoms
-
-mass 1 1.0
-mass 2 1.0
-
-# LJ potentials
-
-pair_style lj/cut 2.5
-pair_coeff * * 1.0 1.0 2.5
-
-# define groups
-
-region 1 block INF INF INF 1.25 INF INF
-group lower region 1
-60 atoms in group lower
-group mobile subtract all lower
-360 atoms in group mobile
-set group lower type 2
- 60 settings made for type
-
-# initial velocities
-
-compute new mobile temp
-velocity mobile create 0.2 482748 temp new
-fix 1 all nve
-fix 2 lower setforce 0.0 0.0 0.0
-fix 3 all temp/rescale 100 0.1 0.1 0.01 1.0
-
-# indenter
-
-fix 4 all indent 1000.0 sphere 10 13 0 5.0 vel 0.0 -0.02 0.0
-fix 5 all enforce2d
-
-# Run with indenter
-
-timestep 0.003
-thermo 1000
-thermo_modify temp new
-
-dump 1 all atom 250 dump.indent
-run 30000
-Memory usage per processor = 1.67582 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume
- 0 0.2 -3.1727576 0 -3.0020433 -1.4366826 444.44898
- 1000 0.11576832 -3.0966334 0 -2.9978168 -0.2046953 441.73683
- 2000 0.11528823 -3.0962223 0 -2.9978155 -0.38254021 442.23432
- 3000 0.11379051 -3.0840496 0 -2.9869213 -0.42664207 444.50384
- 4000 0.11595816 -3.085882 0 -2.9869034 -0.040632221 439.82253
- 5000 0.11272851 -3.0844605 0 -2.9882386 -0.48630294 445.8137
- 6000 0.12387775 -3.0900283 0 -2.9842898 0.0061789692 439.90649
- 7000 0.1113616 -3.0914902 0 -2.9964351 -0.10825389 441.94247
- 8000 0.1167364 -3.0879355 0 -2.9882926 0.17566419 441.73938
- 9000 0.11504768 -3.0918767 0 -2.9936753 0.29955458 440.3699
- 10000 0.11864876 -3.0776022 0 -2.976327 0.38844091 441.0787
- 11000 0.12749806 -3.0769801 0 -2.9681514 0.60370474 438.20684
- 12000 0.11068569 -3.0664256 0 -2.9719474 0.66212034 439.45966
- 13000 0.11341038 -3.0596733 0 -2.9628694 0.98257147 440.29995
- 14000 0.1176102 -3.058063 0 -2.9576743 1.0265509 439.75724
- 15000 0.12582685 -3.054119 0 -2.9467168 0.89411243 448.51929
- 16000 0.11716115 -3.0359807 0 -2.9359753 0.94392052 458.9918
- 17000 0.1183619 -3.0276207 0 -2.9265904 0.91928551 455.52056
- 18000 0.12271609 -3.017155 0 -2.9124081 1.2843751 467.90439
- 19000 0.11746036 -3.0102895 0 -2.9100287 1.3852631 472.51702
- 20000 0.12089249 -2.9967314 0 -2.893541 1.5300149 474.35237
- 21000 0.12575365 -2.9947646 0 -2.8874248 1.5751315 479.52718
- 22000 0.1167364 -2.9837589 0 -2.884116 1.2716662 486.91315
- 23000 0.12415934 -3.0113215 0 -2.9053426 1.0113981 485.76489
- 24000 0.12324594 -3.0224444 0 -2.9172451 1.1058302 484.29936
- 25000 0.12325265 -3.0115298 0 -2.9063249 0.95737324 492.3559
- 26000 0.1209802 -3.0094161 0 -2.9061509 0.72298537 503.98811
- 27000 0.12584652 -3.0019729 0 -2.8945539 1.1273224 494.9013
- 28000 0.1167364 -2.9910191 0 -2.8913762 1.2902722 496.61985
- 29000 0.1167364 -3.0029616 0 -2.9033188 0.89371934 502.82784
- 30000 0.1212253 -3.0101062 0 -2.9066317 0.66514457 508.68846
-Loop time of 14.6334 on 4 procs for 30000 steps with 420 atoms
-
-Pair time (%) = 1.07639 (7.3557)
-Neigh time (%) = 0.0313419 (0.214181)
-Comm time (%) = 10.5831 (72.3219)
-Outpt time (%) = 0.117674 (0.804145)
-Other time (%) = 2.82484 (19.3041)
-
-Nlocal: 105 ave 123 max 86 min
-Histogram: 1 1 0 0 0 0 0 0 0 2
-Nghost: 95.75 ave 103 max 88 min
-Histogram: 1 1 0 0 0 0 0 0 0 2
-Neighs: 905.25 ave 1127 max 678 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-
-Total # of neighbors = 3621
-Ave neighs/atom = 8.62143
-Neighbor list builds = 622
-Dangerous builds = 0
-
-# Run without indenter
-
-unfix 4
-run 30000
-Memory usage per processor = 1.67641 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume
- 30000 0.1212253 -3.0101062 0 -2.9066317 0.66472805 509.0072
- 31000 0.10753955 -3.0244479 0 -2.9326552 0.014150137 507.50974
- 32000 0.11147629 -3.0158355 0 -2.9206825 -0.28843033 519.21836
- 33000 0.11978091 -3.0365035 0 -2.9342619 -0.068567574 508.39504
- 34000 0.12177378 -3.0706615 0 -2.9667189 -0.21120889 505.55013
- 35000 0.12309818 -3.0718302 0 -2.9667571 -0.38249432 511.72908
- 36000 0.10844583 -3.0593175 0 -2.9667512 -0.2638784 503.54833
- 37000 0.11777916 -3.0777872 0 -2.9772543 -0.21323143 506.08932
- 38000 0.11033046 -3.0714259 0 -2.977251 -0.39909252 507.81232
- 39000 0.11215445 -3.0729827 0 -2.9772508 -0.23485622 509.16831
- 40000 0.11255907 -3.0733302 0 -2.977253 -0.2578202 504.01334
- 41000 0.11432059 -3.0748349 0 -2.9772541 -0.45901053 510.3073
- 42000 0.11170702 -3.0726007 0 -2.9772508 -0.15551038 504.69646
- 43000 0.11223315 -3.0730128 0 -2.9772138 -0.26797241 510.09817
- 44000 0.11243348 -3.0732228 0 -2.9772528 -0.38149257 508.55354
- 45000 0.1131438 -3.0738274 0 -2.9772511 -0.13310154 504.34955
- 46000 0.10933879 -3.0705795 0 -2.977251 -0.35927728 506.78452
- 47000 0.11758866 -3.0776231 0 -2.9772528 -0.27765047 506.95034
- 48000 0.11761342 -3.0776456 0 -2.9772542 -0.21700914 503.52997
- 49000 0.11471014 -3.0751668 0 -2.9772535 -0.44906884 508.46902
- 50000 0.11788451 -3.0778781 0 -2.9772553 -0.11247392 504.06984
- 51000 0.11837104 -3.0782917 0 -2.9772536 -0.27620472 505.52699
- 52000 0.10745291 -3.0689667 0 -2.9772479 -0.31961002 506.98322
- 53000 0.11244133 -3.0732297 0 -2.977253 -0.12156293 504.93407
- 54000 0.11314629 -3.0738292 0 -2.9772508 -0.4429982 506.82187
- 55000 0.11648474 -3.0766799 0 -2.9772519 -0.316804 507.16995
- 56000 0.12597906 -3.0847878 0 -2.9772557 -0.27802324 507.19137
- 57000 0.11827315 -3.0671955 0 -2.9662409 -0.32983726 508.50022
- 58000 0.12508397 -3.0730087 0 -2.9662406 -0.24866953 505.02704
- 59000 0.12079689 -3.0693502 0 -2.9662414 -0.23782258 505.35377
- 60000 0.1183543 -3.0672642 0 -2.9662403 -0.39709624 507.80337
-Loop time of 14.8577 on 4 procs for 30000 steps with 420 atoms
-
-Pair time (%) = 1.05365 (7.09162)
-Neigh time (%) = 0.0316316 (0.212898)
-Comm time (%) = 10.8588 (73.0857)
-Outpt time (%) = 0.117559 (0.791232)
-Other time (%) = 2.796 (18.8186)
-
-Nlocal: 105 ave 121 max 84 min
-Histogram: 1 0 0 1 0 0 0 0 0 2
-Nghost: 94.75 ave 104 max 87 min
-Histogram: 2 0 0 0 0 0 0 1 0 1
-Neighs: 889.75 ave 1087 max 662 min
-Histogram: 1 1 0 0 0 0 0 0 0 2
-
-Total # of neighbors = 3559
-Ave neighs/atom = 8.47381
-Neighbor list builds = 632
-Dangerous builds = 0
diff --git a/examples/indent/log.indent.min.21May08.linux.1 b/examples/indent/log.indent.min.21May08.linux.1
new file mode 100644
index 000000000..014bfa167
--- /dev/null
+++ b/examples/indent/log.indent.min.21May08.linux.1
@@ -0,0 +1,55 @@
+LAMMPS (21 May 2008)
+# 2d indenter simulation with minimization instead of dynamics
+
+dimension 2
+boundary p s p
+
+atom_style atomic
+neighbor 0.3 bin
+neigh_modify delay 5
+
+# create geometry
+
+lattice hex 0.9
+Lattice spacing in x,y,z = 1.1327 1.96189 1.1327
+region box block 0 20 0 10 -0.25 0.25
+create_box 2 box
+Created orthogonal box = (0 0 -0.283174) to (22.6539 19.6189 0.283174)
+ 1 by 1 by 1 processor grid
+create_atoms 1 box
+Created 420 atoms
+
+mass * 1.0
+
+# LJ potentials
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0 2.5
+
+# define groups
+
+region 1 block INF INF INF 1.25 INF INF
+group lower region 1
+60 atoms in group lower
+group mobile subtract all lower
+360 atoms in group mobile
+set group lower type 2
+ 60 settings made for type
+
+# initial velocities
+
+fix 2 lower setforce 0.0 0.0 0.0
+
+# indenter
+
+fix 5 all enforce2d
+
+# minimize with indenter
+
+thermo 10
+
+dump 1 all atom 10 dump.indent
+dump_modify 1 scale no
+
+minimize 1.0e-6 1000 1000
+ERROR: Illegal minimize command
diff --git a/examples/indent/log.indent.min.21May08.linux.4 b/examples/indent/log.indent.min.21May08.linux.4
new file mode 100644
index 000000000..d147ef090
--- /dev/null
+++ b/examples/indent/log.indent.min.21May08.linux.4
@@ -0,0 +1,55 @@
+LAMMPS (21 May 2008)
+# 2d indenter simulation with minimization instead of dynamics
+
+dimension 2
+boundary p s p
+
+atom_style atomic
+neighbor 0.3 bin
+neigh_modify delay 5
+
+# create geometry
+
+lattice hex 0.9
+Lattice spacing in x,y,z = 1.1327 1.96189 1.1327
+region box block 0 20 0 10 -0.25 0.25
+create_box 2 box
+Created orthogonal box = (0 0 -0.283174) to (22.6539 19.6189 0.283174)
+ 2 by 2 by 1 processor grid
+create_atoms 1 box
+Created 420 atoms
+
+mass * 1.0
+
+# LJ potentials
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0 2.5
+
+# define groups
+
+region 1 block INF INF INF 1.25 INF INF
+group lower region 1
+60 atoms in group lower
+group mobile subtract all lower
+360 atoms in group mobile
+set group lower type 2
+ 60 settings made for type
+
+# initial velocities
+
+fix 2 lower setforce 0.0 0.0 0.0
+
+# indenter
+
+fix 5 all enforce2d
+
+# minimize with indenter
+
+thermo 10
+
+dump 1 all atom 10 dump.indent
+dump_modify 1 scale no
+
+minimize 1.0e-6 1000 1000
+ERROR: Illegal minimize command
diff --git a/examples/indent/log.indent.min.22Jan08.linux.1 b/examples/indent/log.indent.min.22Jan08.linux.1
deleted file mode 100644
index 72088b8ab..000000000
--- a/examples/indent/log.indent.min.22Jan08.linux.1
+++ /dev/null
@@ -1,382 +0,0 @@
-LAMMPS (22 Jan 2008)
-# 2d indenter simulation with minimization instead of dynamics
-
-dimension 2
-boundary p s p
-
-atom_style atomic
-neighbor 0.3 bin
-neigh_modify delay 5
-
-# create geometry
-
-lattice hex 0.9
-Lattice spacing in x,y,z = 1.1327 1.96189 1.1327
-region box block 0 20 0 10 -0.25 0.25
-create_box 2 box
-Created orthogonal box = (0 0 -0.283174) to (22.6539 19.6189 0.283174)
- 1 by 1 by 1 processor grid
-create_atoms 1 box
-Created 420 atoms
-
-mass * 1.0
-
-# LJ potentials
-
-pair_style lj/cut 2.5
-pair_coeff * * 1.0 1.0 2.5
-
-# define groups
-
-region 1 block INF INF INF 1.25 INF INF
-group lower region 1
-60 atoms in group lower
-group mobile subtract all lower
-360 atoms in group mobile
-set group lower type 2
- 60 settings made for type
-
-# initial velocities
-
-fix 2 lower setforce 0.0 0.0 0.0
-
-# indenter
-
-fix 5 all enforce2d
-
-# minimize with indenter
-
-thermo 10
-
-dump 1 all atom 10 dump.indent
-dump_modify 1 scale no
-
-minimize 1.0e-6 1000 1000
-Memory usage per processor = 2.13877 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume
- 0 0 -3.1727576 0 -3.1727576 -1.5980059 444.44898
- 10 0 -3.1820434 0 -3.1820434 -1.1317017 440.97368
- 20 0 -3.1892762 0 -3.1892762 -0.875018 437.63427
- 30 0 -3.1906231 0 -3.1906231 -0.77012131 437.63427
- 38 0 -3.1909329 0 -3.1909329 -0.6923326 437.63427
-Loop time of 0.0332251 on 1 procs for 38 steps with 420 atoms
-
-Minimization stats:
- E initial, next-to-last, final = -3.17276 -3.19093 -3.19093
- Gradient 2-norm init/final= 6.74302 0.251767
- Gradient inf-norm init/final= 1.46877 0.0232337
- Iterations = 38
- Force evaluations = 148
-
-Pair time (%) = 0.0271435 (81.6958)
-Neigh time (%) = 0.00029707 (0.894113)
-Comm time (%) = 0.000262022 (0.788628)
-Outpt time (%) = 0.00231719 (6.97422)
-Other time (%) = 0.0032053 (9.64723)
-
-Nlocal: 420 ave 420 max 420 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 95 ave 95 max 95 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 3580 ave 3580 max 3580 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 3580
-Ave neighs/atom = 8.52381
-Neighbor list builds = 2
-Dangerous builds = 0
-
-fix 4 all indent 5000.0 sphere 10 13.0 0 6.0
-fix_modify 4 energy yes
-minimize 1.0e-6 1000 1000
-Memory usage per processor = 2.13877 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume
- 38 0 -3.1909329 0 -2.1718641 -0.69556621 435.59976
- 40 0 -3.169091 0 -2.8877594 -0.46675955 435.59973
- 50 0 -3.1711852 0 -3.1696057 -0.33713462 435.60143
- 60 0 -3.1780204 0 -3.1769046 -0.33322968 435.79292
- 70 0 -3.1800811 0 -3.1793038 -0.26556467 435.79292
- 80 0 -3.1809088 0 -3.1801828 -0.19926217 435.79292
- 90 0 -3.1811924 0 -3.1805002 -0.14442628 434.68835
- 100 0 -3.1812635 0 -3.1805822 -0.12227185 434.68835
- 103 0 -3.1812545 0 -3.180591 -0.12009024 434.68835
-Loop time of 0.0514102 on 1 procs for 65 steps with 420 atoms
-
-Minimization stats:
- E initial, next-to-last, final = -2.17186 -3.18059 -3.18059
- Gradient 2-norm init/final= 1621.12 0.469022
- Gradient inf-norm init/final= 1193.11 0.272199
- Iterations = 65
- Force evaluations = 211
-
-Pair time (%) = 0.0386546 (75.1885)
-Neigh time (%) = 0.000748396 (1.45573)
-Comm time (%) = 0.000388145 (0.754997)
-Outpt time (%) = 0.0052855 (10.281)
-Other time (%) = 0.00633359 (12.3197)
-
-Nlocal: 420 ave 420 max 420 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 95 ave 95 max 95 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 3586 ave 3586 max 3586 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 3586
-Ave neighs/atom = 8.5381
-Neighbor list builds = 5
-Dangerous builds = 0
-
-fix 4 all indent 1000.0 sphere 10 12.5 0 6.0
-fix_modify 4 energy yes
-minimize 1.0e-6 1000 1000
-Memory usage per processor = 2.13877 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume
- 103 0 -3.1812545 0 -0.21951029 -0.1202861 433.98055
- 110 0 -2.9284097 0 -2.6466557 2.0617709 433.9793
- 120 0 -3.0511214 0 -3.0267128 1.4983726 433.97719
- 130 0 -3.0919408 0 -3.0831141 1.2624464 434.23068
- 140 0 -3.1001312 0 -3.0930458 1.209277 434.23068
- 150 0 -3.102631 0 -3.0950311 1.2237232 434.73394
- 160 0 -3.1037978 0 -3.09648 1.3260564 431.60915
- 170 0 -3.1041785 0 -3.0969724 1.3941622 431.60915
- 180 0 -3.1042622 0 -3.0971039 1.4149115 431.60915
- 186 0 -3.1042077 0 -3.0971259 1.4187834 431.60915
-Loop time of 0.0678358 on 1 procs for 83 steps with 420 atoms
-
-Minimization stats:
- E initial, next-to-last, final = -0.21951 -3.09712 -3.09713
- Gradient 2-norm init/final= 1753.54 0.525185
- Gradient inf-norm init/final= 923.56 0.20363
- Iterations = 83
- Force evaluations = 279
-
-Pair time (%) = 0.0514042 (75.7774)
-Neigh time (%) = 0.00167418 (2.46798)
-Comm time (%) = 0.000550032 (0.810828)
-Outpt time (%) = 0.00602508 (8.88185)
-Other time (%) = 0.00818229 (12.0619)
-
-Nlocal: 420 ave 420 max 420 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 107 ave 107 max 107 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 3642 ave 3642 max 3642 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 3642
-Ave neighs/atom = 8.67143
-Neighbor list builds = 11
-Dangerous builds = 0
-
-fix 4 all indent 1000.0 sphere 10 12.0 0 6.0
-fix_modify 4 energy yes
-minimize 1.0e-6 1000 1000
-Memory usage per processor = 2.13877 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume
- 186 0 -3.1042077 0 1.9876467 1.4209266 430.95816
- 190 0 -2.7684954 0 -1.1554028 4.1104961 430.51479
- 200 0 -2.7738026 0 -2.6431045 4.5613937 435.03877
- 210 0 -2.892911 0 -2.863976 3.765261 442.55285
- 220 0 -2.9428319 0 -2.9275563 3.3111711 447.69227
- 230 0 -2.9566576 0 -2.9427828 3.183237 451.95964
- 240 0 -2.9622154 0 -2.9537038 3.0997525 453.12625
- 250 0 -2.9685121 0 -2.9588966 3.0016498 455.11967
- 260 0 -2.9851957 0 -2.9793281 2.7575287 455.75205
- 270 0 -3.0137593 0 -3.0035449 2.449694 453.80579
- 280 0 -3.0182039 0 -3.0121893 2.3442266 454.59869
- 290 0 -3.0271401 0 -3.0194953 2.053625 459.16264
- 300 0 -3.0332671 0 -3.0255652 2.059571 459.16264
- 310 0 -3.0346445 0 -3.0270706 2.0755976 456.56027
- 320 0 -3.0355796 0 -3.0277669 2.0482597 456.56027
- 330 0 -3.0359691 0 -3.0280778 2.0154636 456.56027
- 340 0 -3.0358963 0 -3.0281771 1.9966785 456.56027
- 350 0 -3.0359324 0 -3.0282261 1.9824739 456.56027
-Loop time of 0.141067 on 1 procs for 164 steps with 420 atoms
-
-Minimization stats:
- E initial, next-to-last, final = 1.98765 -3.02822 -3.02823
- Gradient 2-norm init/final= 2323.65 0.605548
- Gradient inf-norm init/final= 1037.31 0.149721
- Iterations = 164
- Force evaluations = 579
-
-Pair time (%) = 0.107919 (76.5017)
-Neigh time (%) = 0.00395179 (2.80135)
-Comm time (%) = 0.00117111 (0.830181)
-Outpt time (%) = 0.0119934 (8.50192)
-Other time (%) = 0.016032 (11.3648)
-
-Nlocal: 420 ave 420 max 420 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 109 ave 109 max 109 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 3789 ave 3789 max 3789 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 3789
-Ave neighs/atom = 9.02143
-Neighbor list builds = 25
-Dangerous builds = 0
-
-fix 4 all indent 1000.0 sphere 10 11.4 0 6.0
-fix_modify 4 energy yes
-minimize 1.0e-6 1000 1000
-Memory usage per processor = 2.13877 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume
- 350 0 -3.0359324 0 6.9766773 1.9786928 457.43272
- 360 0 -2.335093 0 -1.5707757 7.5510257 457.43998
- 370 0 -2.5599881 0 -2.4347598 6.4272916 457.91764
- 380 0 -2.7844216 0 -2.7584649 4.9001971 463.20184
- 390 0 -2.8656166 0 -2.8440742 4.2220788 464.98354
- 400 0 -2.9109956 0 -2.8923852 3.6096589 468.48088
- 410 0 -2.9467505 0 -2.9334194 3.210818 471.50863
- 420 0 -2.9744267 0 -2.9577148 3.1040552 470.74251
- 430 0 -2.9926456 0 -2.9736412 2.9546044 471.59618
- 440 0 -2.9975451 0 -2.9801205 2.8912377 471.28646
- 450 0 -2.9996109 0 -2.9820253 2.8472599 472.36332
- 460 0 -2.9987284 0 -2.9829306 2.8127874 472.36332
- 470 0 -2.9987247 0 -2.9846006 2.6439865 473.77264
- 480 0 -3.002881 0 -2.9903844 2.3001851 478.94935
- 490 0 -3.0065806 0 -2.9942666 2.1491834 481.91432
- 500 0 -3.0095236 0 -2.9964104 2.0319452 484.64425
- 510 0 -3.0114745 0 -2.9990245 1.9606412 485.51456
- 520 0 -3.0120857 0 -3.0020722 1.9278832 485.273
- 530 0 -3.0221073 0 -3.0141559 1.8289206 487.68636
- 540 0 -3.0307927 0 -3.0222342 1.7165806 489.75746
- 550 0 -3.0387697 0 -3.0286577 1.6073926 490.88326
- 560 0 -3.0423031 0 -3.0330395 1.586802 491.73724
- 570 0 -3.043509 0 -3.0343313 1.5673862 491.73724
- 580 0 -3.0440104 0 -3.0348575 1.558385 491.73724
- 590 0 -3.0439091 0 -3.0353446 1.5465643 490.86256
- 600 0 -3.0456641 0 -3.0369635 1.5266002 490.36123
- 610 0 -3.047406 0 -3.0381862 1.4944371 489.9176
- 620 0 -3.0502537 0 -3.0405998 1.4555164 491.15806
- 625 0 -3.0521001 0 -3.0423852 1.4492467 491.59747
-Loop time of 0.242592 on 1 procs for 275 steps with 420 atoms
-
-Minimization stats:
- E initial, next-to-last, final = 6.97668 -3.04203 -3.04239
- Gradient 2-norm init/final= 3559.61 9.34801
- Gradient inf-norm init/final= 1438.88 3.86075
- Iterations = 275
- Force evaluations = 1002
-
-Pair time (%) = 0.185928 (76.6423)
-Neigh time (%) = 0.0070498 (2.90603)
-Comm time (%) = 0.00214314 (0.883435)
-Outpt time (%) = 0.0202661 (8.35396)
-Other time (%) = 0.027205 (11.2143)
-
-Nlocal: 420 ave 420 max 420 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 115 ave 115 max 115 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 3678 ave 3678 max 3678 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 3678
-Ave neighs/atom = 8.75714
-Neighbor list builds = 44
-Dangerous builds = 0
-
-fix 4 all indent 1000.0 sphere 10 11.2 0 6.0
-fix_modify 4 energy yes
-minimize 1.0e-6 1000 1000
-Memory usage per processor = 2.13885 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume
- 625 0 -3.0521001 0 -2.6498801 1.4488549 491.7304
- 630 0 -2.9718737 0 -2.9110758 2.2436261 491.72959
- 640 0 -2.9788109 0 -2.9552133 2.2865455 491.95942
- 650 0 -2.9876288 0 -2.9678188 2.2441267 492.6284
- 660 0 -2.9897692 0 -2.9724888 2.2915736 492.03371
- 670 0 -2.9919535 0 -2.9762524 2.3486047 491.26568
- 680 0 -2.9958204 0 -2.9792159 2.3471087 490.11049
- 690 0 -3.0003811 0 -2.9827328 2.2999787 490.21162
- 700 0 -3.0023138 0 -2.9853549 2.2675318 491.33245
- 710 0 -3.0027659 0 -2.9867895 2.2883282 491.33245
- 720 0 -3.0031834 0 -2.9875047 2.3106077 489.42967
- 730 0 -3.0036556 0 -2.9876211 2.3088756 489.42967
- 740 0 -3.0038433 0 -2.9876825 2.3055494 489.42967
- 743 0 -3.0038605 0 -2.9876906 2.3053223 489.42967
-Loop time of 0.0952809 on 1 procs for 118 steps with 420 atoms
-
-Minimization stats:
- E initial, next-to-last, final = -2.64988 -2.98769 -2.98769
- Gradient 2-norm init/final= 391.935 0.735748
- Gradient inf-norm init/final= 174.478 0.254377
- Iterations = 118
- Force evaluations = 392
-
-Pair time (%) = 0.072511 (76.1023)
-Neigh time (%) = 0.0017426 (1.82891)
-Comm time (%) = 0.000789404 (0.828502)
-Outpt time (%) = 0.00900126 (9.44707)
-Other time (%) = 0.0112367 (11.7932)
-
-Nlocal: 420 ave 420 max 420 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 116 ave 116 max 116 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 3810 ave 3810 max 3810 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 3810
-Ave neighs/atom = 9.07143
-Neighbor list builds = 11
-Dangerous builds = 0
-
-fix 4 all indent 1000.0 sphere 10 11.0 0 6.0
-fix_modify 4 energy yes
-minimize 1.0e-6 1000 1000
-Memory usage per processor = 2.13885 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume
- 743 0 -3.0038605 0 -2.4096618 2.3078479 488.89405
- 750 0 -2.8899993 0 -2.8291939 3.4288679 488.89459
- 760 0 -2.8929447 0 -2.8576475 3.4739485 489.19553
- 770 0 -2.8951789 0 -2.8655275 3.4824252 489.19553
- 780 0 -2.8954908 0 -2.8692017 3.5158206 489.53759
- 790 0 -2.8987436 0 -2.8799874 3.417111 498.10919
- 800 0 -2.9103982 0 -2.8925867 3.1813363 505.60533
- 810 0 -2.923822 0 -2.9049543 2.7634162 510.69079
- 820 0 -2.9690464 0 -2.959277 2.1615844 511.87122
- 830 0 -3.0137954 0 -3.0063127 1.9411075 511.76042
- 840 0 -3.0263936 0 -3.018511 1.8625841 511.33281
- 850 0 -3.0332313 0 -3.0246203 1.785449 510.58928
- 860 0 -3.0400639 0 -3.0311608 1.660562 511.39199
- 870 0 -3.0490546 0 -3.0399986 1.5037912 513.99632
- 880 0 -3.0640791 0 -3.0552023 1.3477777 514.73114
- 890 0 -3.0696238 0 -3.0605878 1.3338106 514.97796
- 900 0 -3.072344 0 -3.0631492 1.3146094 515.21041
- 910 0 -3.0725478 0 -3.0638124 1.3020946 515.21041
- 920 0 -3.0733416 0 -3.0644345 1.2853311 516.14828
- 930 0 -3.0748377 0 -3.0658391 1.3067919 516.24534
- 940 0 -3.0750618 0 -3.066135 1.3077775 516.24534
- 950 0 -3.075108 0 -3.066207 1.3119176 516.24534
- 953 0 -3.0751175 0 -3.0662144 1.3125012 516.24534
-Loop time of 0.181291 on 1 procs for 210 steps with 420 atoms
-
-Minimization stats:
- E initial, next-to-last, final = -2.40966 -3.06621 -3.06621
- Gradient 2-norm init/final= 493.48 0.611378
- Gradient inf-norm init/final= 186.721 0.300913
- Iterations = 210
- Force evaluations = 750
-
-Pair time (%) = 0.13778 (75.9992)
-Neigh time (%) = 0.00535512 (2.95388)
-Comm time (%) = 0.00162768 (0.897829)
-Outpt time (%) = 0.0157762 (8.70211)
-Other time (%) = 0.0207524 (11.447)
-
-Nlocal: 420 ave 420 max 420 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 120 ave 120 max 120 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 3581 ave 3581 max 3581 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 3581
-Ave neighs/atom = 8.52619
-Neighbor list builds = 34
-Dangerous builds = 0
diff --git a/examples/indent/log.indent.min.22Jan08.linux.4 b/examples/indent/log.indent.min.22Jan08.linux.4
deleted file mode 100644
index 39afca64f..000000000
--- a/examples/indent/log.indent.min.22Jan08.linux.4
+++ /dev/null
@@ -1,384 +0,0 @@
-LAMMPS (22 Jan 2008)
-# 2d indenter simulation with minimization instead of dynamics
-
-dimension 2
-boundary p s p
-
-atom_style atomic
-neighbor 0.3 bin
-neigh_modify delay 5
-
-# create geometry
-
-lattice hex 0.9
-Lattice spacing in x,y,z = 1.1327 1.96189 1.1327
-region box block 0 20 0 10 -0.25 0.25
-create_box 2 box
-Created orthogonal box = (0 0 -0.283174) to (22.6539 19.6189 0.283174)
- 2 by 2 by 1 processor grid
-create_atoms 1 box
-Created 420 atoms
-
-mass * 1.0
-
-# LJ potentials
-
-pair_style lj/cut 2.5
-pair_coeff * * 1.0 1.0 2.5
-
-# define groups
-
-region 1 block INF INF INF 1.25 INF INF
-group lower region 1
-60 atoms in group lower
-group mobile subtract all lower
-360 atoms in group mobile
-set group lower type 2
- 60 settings made for type
-
-# initial velocities
-
-fix 2 lower setforce 0.0 0.0 0.0
-
-# indenter
-
-fix 5 all enforce2d
-
-# minimize with indenter
-
-thermo 10
-
-dump 1 all atom 10 dump.indent
-dump_modify 1 scale no
-
-minimize 1.0e-6 1000 1000
-Memory usage per processor = 2.13359 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume
- 0 0 -3.1727576 0 -3.1727576 -1.5980059 444.44898
- 10 0 -3.1820434 0 -3.1820434 -1.1317017 440.97368
- 20 0 -3.1892762 0 -3.1892762 -0.875018 437.63427
- 30 0 -3.1906231 0 -3.1906231 -0.77012131 437.63427
- 38 0 -3.1909329 0 -3.1909329 -0.6923326 437.63427
-Loop time of 0.116816 on 4 procs for 38 steps with 420 atoms
-
-Minimization stats:
- E initial, next-to-last, final = -3.17276 -3.19093 -3.19093
- Gradient 2-norm init/final= 6.74302 0.251767
- Gradient inf-norm init/final= 1.46877 0.0232337
- Iterations = 38
- Force evaluations = 148
-
-Pair time (%) = 0.00820065 (7.02014)
-Neigh time (%) = 9.92417e-05 (0.0849556)
-Comm time (%) = 0.052792 (45.1924)
-Outpt time (%) = 0.00496787 (4.25273)
-Other time (%) = 0.0507563 (43.4498)
-
-Nlocal: 105 ave 110 max 100 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Nghost: 84 ave 89 max 79 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Neighs: 895 ave 900 max 890 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-
-Total # of neighbors = 3580
-Ave neighs/atom = 8.52381
-Neighbor list builds = 2
-Dangerous builds = 0
-
-fix 4 all indent 5000.0 sphere 10 13.0 0 6.0
-fix_modify 4 energy yes
-minimize 1.0e-6 1000 1000
-Memory usage per processor = 2.13359 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume
- 38 0 -3.1909329 0 -2.1718641 -0.69556621 435.59976
- 40 0 -3.169091 0 -2.8877594 -0.46675955 435.59973
- 50 0 -3.1711852 0 -3.1696057 -0.33713462 435.60143
- 60 0 -3.1780204 0 -3.1769046 -0.33322968 435.79292
- 70 0 -3.1800811 0 -3.1793038 -0.26556467 435.79292
- 80 0 -3.1809088 0 -3.1801828 -0.19926217 435.79292
- 90 0 -3.1811924 0 -3.1805002 -0.14442628 434.68835
- 100 0 -3.1812635 0 -3.1805822 -0.12227185 434.68835
- 103 0 -3.1812545 0 -3.180591 -0.12009024 434.68835
-Loop time of 0.196576 on 4 procs for 65 steps with 420 atoms
-
-Minimization stats:
- E initial, next-to-last, final = -2.17186 -3.18059 -3.18059
- Gradient 2-norm init/final= 1621.12 0.469022
- Gradient inf-norm init/final= 1193.11 0.272199
- Iterations = 65
- Force evaluations = 211
-
-Pair time (%) = 0.0115743 (5.88792)
-Neigh time (%) = 0.000268996 (0.13684)
-Comm time (%) = 0.0783743 (39.8696)
-Outpt time (%) = 0.0115461 (5.87361)
-Other time (%) = 0.0948128 (48.232)
-
-Nlocal: 105 ave 112 max 100 min
-Histogram: 2 0 0 0 0 0 1 0 0 1
-Nghost: 87 ave 89 max 83 min
-Histogram: 1 0 0 0 0 0 1 0 0 2
-Neighs: 896.5 ave 1006 max 797 min
-Histogram: 2 0 0 0 0 0 0 0 1 1
-
-Total # of neighbors = 3586
-Ave neighs/atom = 8.5381
-Neighbor list builds = 5
-Dangerous builds = 0
-
-fix 4 all indent 1000.0 sphere 10 12.5 0 6.0
-fix_modify 4 energy yes
-minimize 1.0e-6 1000 1000
-Memory usage per processor = 2.13366 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume
- 103 0 -3.1812545 0 -0.21951029 -0.1202861 433.98055
- 110 0 -2.9284097 0 -2.6466557 2.0617709 433.9793
- 120 0 -3.0511214 0 -3.0267128 1.4983726 433.97719
- 130 0 -3.0919408 0 -3.0831141 1.2624464 434.23068
- 140 0 -3.1001312 0 -3.0930458 1.209277 434.23068
- 150 0 -3.102631 0 -3.0950311 1.2237232 434.73394
- 160 0 -3.1037978 0 -3.09648 1.3260564 431.60915
- 170 0 -3.1041785 0 -3.0969724 1.3941622 431.60915
- 180 0 -3.1042622 0 -3.0971039 1.4149115 431.60915
- 186 0 -3.1042077 0 -3.0971259 1.4187834 431.60915
-Loop time of 0.257513 on 4 procs for 83 steps with 420 atoms
-
-Minimization stats:
- E initial, next-to-last, final = -0.21951 -3.09712 -3.09713
- Gradient 2-norm init/final= 1753.54 0.525185
- Gradient inf-norm init/final= 923.56 0.20363
- Iterations = 83
- Force evaluations = 279
-
-Pair time (%) = 0.0152845 (5.93545)
-Neigh time (%) = 0.0005458 (0.211951)
-Comm time (%) = 0.105214 (40.8577)
-Outpt time (%) = 0.0132536 (5.14678)
-Other time (%) = 0.123215 (47.8481)
-
-Nlocal: 105 ave 110 max 99 min
-Histogram: 1 1 0 0 0 0 0 0 0 2
-Nghost: 95 ave 96 max 93 min
-Histogram: 1 0 0 0 0 0 1 0 0 2
-Neighs: 910.5 ave 990 max 829 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-
-Total # of neighbors = 3642
-Ave neighs/atom = 8.67143
-Neighbor list builds = 11
-Dangerous builds = 0
-
-fix 4 all indent 1000.0 sphere 10 12.0 0 6.0
-fix_modify 4 energy yes
-minimize 1.0e-6 1000 1000
-Memory usage per processor = 2.13366 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume
- 186 0 -3.1042077 0 1.9876467 1.4209266 430.95816
- 190 0 -2.7684954 0 -1.1554028 4.1104961 430.51479
- 200 0 -2.7738026 0 -2.6431045 4.5613937 435.03877
- 210 0 -2.892911 0 -2.863976 3.765261 442.55285
- 220 0 -2.9428319 0 -2.9275563 3.3111711 447.69227
- 230 0 -2.9566576 0 -2.9427828 3.183237 451.95964
- 240 0 -2.9622154 0 -2.9537038 3.0997525 453.12625
- 250 0 -2.9685121 0 -2.9588966 3.0016498 455.11967
- 260 0 -2.9851957 0 -2.9793281 2.7575287 455.75205
- 270 0 -3.0137593 0 -3.0035449 2.449694 453.80579
- 280 0 -3.0182039 0 -3.0121893 2.3442266 454.59869
- 290 0 -3.0271401 0 -3.0194953 2.053625 459.16264
- 300 0 -3.0332671 0 -3.0255652 2.059571 459.16264
- 310 0 -3.0346445 0 -3.0270706 2.0755976 456.56027
- 320 0 -3.0355796 0 -3.0277669 2.0482597 456.56027
- 330 0 -3.0359691 0 -3.0280778 2.0154636 456.56027
- 340 0 -3.0358963 0 -3.0281771 1.9966785 456.56027
- 350 0 -3.0359324 0 -3.0282261 1.9824739 456.56027
-Loop time of 0.532273 on 4 procs for 164 steps with 420 atoms
-
-Minimization stats:
- E initial, next-to-last, final = 1.98765 -3.02822 -3.02823
- Gradient 2-norm init/final= 2323.65 0.605548
- Gradient inf-norm init/final= 1037.31 0.149724
- Iterations = 164
- Force evaluations = 579
-
-Pair time (%) = 0.0322834 (6.06519)
-Neigh time (%) = 0.00126213 (0.23712)
-Comm time (%) = 0.218928 (41.1307)
-Outpt time (%) = 0.0269612 (5.0653)
-Other time (%) = 0.252839 (47.5017)
-
-Nlocal: 105 ave 110 max 100 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Nghost: 97.5 ave 103 max 92 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Neighs: 947.25 ave 1037 max 853 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-
-Total # of neighbors = 3789
-Ave neighs/atom = 9.02143
-Neighbor list builds = 25
-Dangerous builds = 0
-
-fix 4 all indent 1000.0 sphere 10 11.4 0 6.0
-fix_modify 4 energy yes
-minimize 1.0e-6 1000 1000
-Memory usage per processor = 2.1337 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume
- 350 0 -3.0359324 0 6.9766773 1.9786928 457.43272
- 360 0 -2.335093 0 -1.5707757 7.5510255 457.43998
- 370 0 -2.5599881 0 -2.4347597 6.4272915 457.91764
- 380 0 -2.7844215 0 -2.7584649 4.9001975 463.20184
- 390 0 -2.8656166 0 -2.8440742 4.2220787 464.98354
- 400 0 -2.9109956 0 -2.8923852 3.609659 468.48088
- 410 0 -2.9467505 0 -2.9334194 3.2108178 471.50864
- 420 0 -2.9744266 0 -2.9577148 3.1040552 470.74252
- 430 0 -2.9926466 0 -2.9736421 2.954598 471.59623
- 440 0 -2.9975379 0 -2.9801201 2.8913452 471.28684
- 450 0 -2.9996147 0 -2.9820225 2.8472573 472.36037
- 460 0 -2.9987772 0 -2.9829659 2.8129364 472.36037
- 470 0 -2.9988242 0 -2.984577 2.645832 473.75442
- 480 0 -3.0028611 0 -2.9903017 2.3005134 478.93214
- 490 0 -3.0065053 0 -2.994241 2.1434534 481.91632
- 500 0 -3.0101863 0 -2.997213 1.9981452 484.51804
- 510 0 -3.0141308 0 -3.0026782 1.8875017 486.09135
- 520 0 -3.016887 0 -3.0072286 1.8425613 486.25796
- 530 0 -3.0268257 0 -3.0179688 1.7806625 488.6896
- 540 0 -3.0327843 0 -3.0231488 1.7139694 488.6896
- 550 0 -3.0367114 0 -3.0272129 1.6635813 490.88644
- 560 0 -3.0416842 0 -3.0327314 1.6227923 491.57531
- 570 0 -3.0427518 0 -3.0338239 1.6110728 491.67857
- 580 0 -3.0441228 0 -3.0350202 1.5954365 490.32292
- 590 0 -3.0451747 0 -3.0365103 1.5821495 489.47103
- 600 0 -3.0459148 0 -3.0370886 1.5554566 489.47103
- 610 0 -3.0467598 0 -3.0376733 1.5248062 489.47103
- 620 0 -3.0478594 0 -3.0383087 1.4861327 491.72302
- 630 0 -3.049164 0 -3.0394832 1.4414188 492.07812
-Loop time of 0.908247 on 4 procs for 280 steps with 420 atoms
-
-Minimization stats:
- E initial, next-to-last, final = 6.97668 -3.03933 -3.03948
- Gradient 2-norm init/final= 3559.61 5.36456
- Gradient inf-norm init/final= 1438.88 1.92793
- Iterations = 280
- Force evaluations = 1001
-
-Pair time (%) = 0.0553258 (6.0915)
-Neigh time (%) = 0.00230616 (0.253914)
-Comm time (%) = 0.37568 (41.3632)
-Outpt time (%) = 0.0444704 (4.89629)
-Other time (%) = 0.430465 (47.3951)
-
-Nlocal: 105 ave 121 max 91 min
-Histogram: 2 0 0 0 0 0 0 0 1 1
-Nghost: 92.5 ave 100 max 85 min
-Histogram: 1 1 0 0 0 0 0 0 1 1
-Neighs: 926.25 ave 1120 max 713 min
-Histogram: 1 1 0 0 0 0 0 0 0 2
-
-Total # of neighbors = 3705
-Ave neighs/atom = 8.82143
-Neighbor list builds = 45
-Dangerous builds = 0
-
-fix 4 all indent 1000.0 sphere 10 11.2 0 6.0
-fix_modify 4 energy yes
-minimize 1.0e-6 1000 1000
-Memory usage per processor = 2.13417 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume
- 630 0 -3.049164 0 -2.6055395 1.4407137 492.31894
- 640 0 -2.9649975 0 -2.9343234 2.3582078 492.33219
- 650 0 -2.9752101 0 -2.9533487 2.332525 492.9171
- 660 0 -2.9831117 0 -2.9657992 2.3325621 491.8941
- 670 0 -2.9882854 0 -2.973258 2.3854087 491.08948
- 680 0 -2.9949851 0 -2.9787092 2.3588144 490.19902
- 690 0 -3.0018179 0 -2.9844849 2.3054542 489.23828
- 700 0 -3.0037328 0 -2.9866112 2.2732947 489.64495
- 710 0 -3.0036981 0 -2.9872548 2.2790001 489.64495
- 720 0 -3.0037586 0 -2.9874991 2.2976654 489.14253
- 730 0 -3.003966 0 -2.9876811 2.3010688 489.14253
- 740 0 -3.0042756 0 -2.9878462 2.3085029 489.14253
- 750 0 -3.0042803 0 -2.9882934 2.3139843 488.81187
- 760 0 -3.0045102 0 -2.9884423 2.311861 488.51868
- 770 0 -3.0045801 0 -2.9885408 2.3084529 488.51868
- 777 0 -3.0047746 0 -2.9886028 2.3027508 488.51868
-Loop time of 0.455153 on 4 procs for 147 steps with 420 atoms
-
-Minimization stats:
- E initial, next-to-last, final = -2.60554 -2.9886 -2.9886
- Gradient 2-norm init/final= 417.28 0.769176
- Gradient inf-norm init/final= 169.788 0.25824
- Iterations = 147
- Force evaluations = 497
-
-Pair time (%) = 0.0273476 (6.00845)
-Neigh time (%) = 0.00065726 (0.144404)
-Comm time (%) = 0.185723 (40.8046)
-Outpt time (%) = 0.0233747 (5.13558)
-Other time (%) = 0.21805 (47.907)
-
-Nlocal: 105 ave 121 max 88 min
-Histogram: 1 1 0 0 0 0 0 0 1 1
-Nghost: 93.75 ave 102 max 84 min
-Histogram: 1 0 1 0 0 0 0 0 1 1
-Neighs: 952.75 ave 1150 max 759 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-
-Total # of neighbors = 3811
-Ave neighs/atom = 9.07381
-Neighbor list builds = 13
-Dangerous builds = 0
-
-fix 4 all indent 1000.0 sphere 10 11.0 0 6.0
-fix_modify 4 energy yes
-minimize 1.0e-6 1000 1000
-Memory usage per processor = 2.13417 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume
- 777 0 -3.0047746 0 -2.4275389 2.30245 488.58251
- 780 0 -2.8947662 0 -2.7648906 3.2760992 488.58313
- 790 0 -2.8922178 0 -2.8552572 3.4749184 488.9907
- 800 0 -2.8997038 0 -2.8712066 3.4796289 489.36909
- 810 0 -2.902176 0 -2.8782065 3.4881184 489.89618
- 820 0 -2.9099852 0 -2.8915034 3.3342713 494.333
- 830 0 -2.9249749 0 -2.9075095 3.0348623 503.7551
- 840 0 -2.9421895 0 -2.9248611 2.5885038 511.66066
- 850 0 -2.9705134 0 -2.9566027 2.1604402 512.29096
- 860 0 -2.983166 0 -2.9715288 2.0550965 512.09303
- 870 0 -3.0022956 0 -2.9944909 2.0352125 509.02455
- 880 0 -3.0257602 0 -3.018125 1.8448712 510.86529
- 890 0 -3.0342452 0 -3.0255002 1.761039 510.97044
- 900 0 -3.0406548 0 -3.0316303 1.6443602 513.37976
- 910 0 -3.0517632 0 -3.0426532 1.4576879 514.63201
- 920 0 -3.0637404 0 -3.0545929 1.3334284 515.50851
- 930 0 -3.0683969 0 -3.0596546 1.3370449 515.29221
- 940 0 -3.0723501 0 -3.0632848 1.3237846 515.11444
- 950 0 -3.0738054 0 -3.0651295 1.3308782 515.95396
- 960 0 -3.0747293 0 -3.0657364 1.3207014 515.95396
- 970 0 -3.0750994 0 -3.0660707 1.3073068 516.11446
- 980 0 -3.0751645 0 -3.0661973 1.3050625 516.11446
- 985 0 -3.0751453 0 -3.0662144 1.3067705 516.11446
-Loop time of 0.708511 on 4 procs for 208 steps with 420 atoms
-
-Minimization stats:
- E initial, next-to-last, final = -2.42754 -3.06621 -3.06621
- Gradient 2-norm init/final= 483.567 0.68513
- Gradient inf-norm init/final= 212.61 0.339518
- Iterations = 208
- Force evaluations = 766
-
-Pair time (%) = 0.0414512 (5.85046)
-Neigh time (%) = 0.00191033 (0.269626)
-Comm time (%) = 0.294369 (41.5476)
-Outpt time (%) = 0.0348218 (4.91479)
-Other time (%) = 0.335958 (47.4175)
-
-Nlocal: 105 ave 128 max 80 min
-Histogram: 1 1 0 0 0 0 0 0 0 2
-Nghost: 94 ave 108 max 81 min
-Histogram: 2 0 0 0 0 0 0 0 1 1
-Neighs: 894.75 ave 1160 max 631 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-
-Total # of neighbors = 3579
-Ave neighs/atom = 8.52143
-Neighbor list builds = 38
-Dangerous builds = 0
diff --git a/examples/meam/log.meam.22Jan08.linux.1 b/examples/meam/log.meam.21May08.linux.1
similarity index 85%
rename from examples/meam/log.meam.22Jan08.linux.1
rename to examples/meam/log.meam.21May08.linux.1
index 7e8b26db0..946ea2688 100644
--- a/examples/meam/log.meam.22Jan08.linux.1
+++ b/examples/meam/log.meam.21May08.linux.1
@@ -1,60 +1,60 @@
-LAMMPS (22 Jan 2008)
+LAMMPS (21 May 2008)
# Test of MEAM potential for SiC system
units metal
boundary p p p
atom_style atomic
read_data data.meam
orthogonal box = (-6 -6 -6) to (5.97232 5.97232 5.97232)
1 by 1 by 1 processor grid
128 atoms
pair_style meam
pair_coeff * * library.meam Si C SiC.meam Si C
neighbor 0.3 bin
neigh_modify delay 10
fix 1 all nve
thermo 10
timestep 0.001
dump 1 all atom 10 dump.meam
run 100
Memory usage per processor = 4.62954 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -636.93784 0 -636.93784 -76401.859
10 1777.5718 -666.27518 0 -637.0945 -150596.32
20 1908.6646 -668.42203 0 -637.08932 -120846.06
30 1937.3373 -668.90047 0 -637.09706 -101367.81
40 2110.906 -671.75978 0 -637.10706 -110475.14
50 2057.8682 -670.89589 0 -637.11385 -107817.44
60 1887.9614 -668.08977 0 -637.09693 -108906.46
70 2036.4427 -670.53667 0 -637.10635 -113836.91
80 2111.2748 -671.75001 0 -637.09124 -100964.78
90 2087.3167 -671.34241 0 -637.07694 -95316.087
100 1990.2171 -669.74712 0 -637.07564 -97755.737
-Loop time of 0.127874 on 1 procs for 100 steps with 128 atoms
+Loop time of 0.127763 on 1 procs for 100 steps with 128 atoms
-Pair time (%) = 0.120988 (94.6152)
-Neigh time (%) = 0.00319433 (2.49803)
-Comm time (%) = 0.000864983 (0.676433)
-Outpt time (%) = 0.00216031 (1.6894)
-Other time (%) = 0.000666142 (0.520935)
+Pair time (%) = 0.120687 (94.4612)
+Neigh time (%) = 0.00334096 (2.61497)
+Comm time (%) = 0.000868797 (0.680007)
+Outpt time (%) = 0.00215125 (1.68378)
+Other time (%) = 0.000715494 (0.560017)
Nlocal: 128 ave 128 max 128 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 541 ave 541 max 541 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
FullNghs: 3074 ave 3074 max 3074 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3074
Ave neighs/atom = 24.0156
Neighbor list builds = 10
Dangerous builds = 10
diff --git a/examples/meam/log.meam.22Jan08.linux.4 b/examples/meam/log.meam.21May08.linux.4
similarity index 86%
rename from examples/meam/log.meam.22Jan08.linux.4
rename to examples/meam/log.meam.21May08.linux.4
index 36b974b90..3c1fe9907 100644
--- a/examples/meam/log.meam.22Jan08.linux.4
+++ b/examples/meam/log.meam.21May08.linux.4
@@ -1,60 +1,60 @@
-LAMMPS (22 Jan 2008)
+LAMMPS (21 May 2008)
# Test of MEAM potential for SiC system
units metal
boundary p p p
atom_style atomic
read_data data.meam
orthogonal box = (-6 -6 -6) to (5.97232 5.97232 5.97232)
1 by 2 by 2 processor grid
128 atoms
pair_style meam
pair_coeff * * library.meam Si C SiC.meam Si C
neighbor 0.3 bin
neigh_modify delay 10
fix 1 all nve
thermo 10
timestep 0.001
dump 1 all atom 10 dump.meam
run 100
Memory usage per processor = 4.51984 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -636.93784 0 -636.93784 -76401.859
10 1777.5718 -666.27518 0 -637.0945 -150596.32
20 1908.6646 -668.42203 0 -637.08932 -120846.06
30 1937.3373 -668.90047 0 -637.09706 -101367.81
40 2110.906 -671.75978 0 -637.10706 -110475.14
50 2057.8682 -670.89589 0 -637.11385 -107817.44
60 1887.9614 -668.08977 0 -637.09693 -108906.46
70 2036.4427 -670.53667 0 -637.10635 -113836.91
80 2111.2748 -671.75001 0 -637.09124 -100964.78
90 2087.3167 -671.34241 0 -637.07694 -95316.087
100 1990.2171 -669.74712 0 -637.07564 -97755.737
-Loop time of 0.164812 on 4 procs for 100 steps with 128 atoms
+Loop time of 0.143319 on 4 procs for 100 steps with 128 atoms
-Pair time (%) = 0.107879 (65.4556)
-Neigh time (%) = 0.00101417 (0.61535)
-Comm time (%) = 0.0441561 (26.7918)
-Outpt time (%) = 0.0102268 (6.20515)
-Other time (%) = 0.00153625 (0.932121)
+Pair time (%) = 0.100818 (70.3452)
+Neigh time (%) = 0.00115442 (0.805489)
+Comm time (%) = 0.0315838 (22.0374)
+Outpt time (%) = 0.00841707 (5.87294)
+Other time (%) = 0.00134581 (0.93903)
Nlocal: 32 ave 35 max 29 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Nghost: 292.25 ave 307 max 279 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs: 384.25 ave 432 max 327 min
Histogram: 1 0 0 0 1 0 0 1 0 1
FullNghs: 768.5 ave 859 max 657 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Total # of neighbors = 3074
Ave neighs/atom = 24.0156
Neighbor list builds = 10
Dangerous builds = 10
diff --git a/examples/meam/log.meam.shear.21May08.linux.1 b/examples/meam/log.meam.shear.21May08.linux.1
new file mode 100644
index 000000000..355b9613e
--- /dev/null
+++ b/examples/meam/log.meam.shear.21May08.linux.1
@@ -0,0 +1,163 @@
+LAMMPS (21 May 2008)
+# 3d metal shear simulation
+
+units metal
+boundary s s p
+
+atom_style atomic
+lattice fcc 3.52
+Lattice spacing in x,y,z = 3.52 3.52 3.52
+region box block 0 16.0 0 10.0 0 2.828427
+create_box 3 box
+Created orthogonal box = (0 0 0) to (56.32 35.2 9.95606)
+ 1 by 1 by 1 processor grid
+
+lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0
+Lattice spacing in x,y,z = 3.52 4.97803 4.97803
+create_atoms 1 box
+Created 1912 atoms
+
+pair_style meam
+pair_coeff * * library.meam Ni4 Ni.meam Ni4 Ni4 Ni4
+
+neighbor 0.3 bin
+neigh_modify delay 5
+
+region lower block INF INF INF 0.9 INF INF
+region upper block INF INF 6.1 INF INF INF
+group lower region lower
+264 atoms in group lower
+group upper region upper
+264 atoms in group upper
+group boundary union lower upper
+528 atoms in group boundary
+group mobile subtract all boundary
+1384 atoms in group mobile
+
+set group lower type 2
+ 264 settings made for type
+set group upper type 3
+ 264 settings made for type
+
+# void
+
+#region void cylinder z 8 5 2.5 INF INF
+#delete_atoms region void
+
+# temp controllers
+
+compute new3d mobile temp
+compute new2d mobile temp/partial 0 1 1
+
+# equilibrate
+
+velocity mobile create 300.0 5812775 temp new3d
+fix 1 all nve
+fix 2 boundary setforce 0.0 0.0 0.0
+
+fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
+fix_modify 3 temp new3d
+
+thermo 25
+thermo_modify temp new3d
+
+timestep 0.001
+run 100
+Memory usage per processor = 6.09291 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 300 -8232.7767 0 -8179.1466 1387.2089 19539.346
+ 25 222.78953 -8188.1215 0 -8148.2941 9099.4735 19539.346
+ 50 300 -8149.7654 0 -8096.1353 10637.302 19676.681
+ 75 304.80657 -8163.4557 0 -8108.9665 7048.2094 19752.029
+ 100 300 -8173.6884 0 -8120.0584 5954.839 19878.848
+Loop time of 2.46606 on 1 procs for 100 steps with 1912 atoms
+
+Pair time (%) = 2.43238 (98.6343)
+Neigh time (%) = 0.0218449 (0.885821)
+Comm time (%) = 0.00250888 (0.101736)
+Outpt time (%) = 0.00022912 (0.00929095)
+Other time (%) = 0.00909543 (0.368825)
+
+Nlocal: 1912 ave 1912 max 1912 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1672 ave 1672 max 1672 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 23806 ave 23806 max 23806 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs: 47612 ave 47612 max 47612 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 47612
+Ave neighs/atom = 24.9017
+Neighbor list builds = 5
+Dangerous builds = 0
+
+# shear
+
+velocity upper set 1.0 0 0
+velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes
+
+unfix 3
+fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
+fix_modify 3 temp new2d
+
+dump 1 all atom 100 dump.meam
+thermo 100
+thermo_modify temp new2d
+
+reset_timestep 0
+run 3000
+Memory usage per processor = 6.34243 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 300.50853 -8173.6884 0 -8137.8874 4994.9251 19886.554
+ 100 292.0799 -8177.7235 0 -8142.9266 2567.6871 19863.778
+ 200 306.71233 -8177.1504 0 -8140.6103 873.12617 20039.427
+ 300 295.7806 -8172.9505 0 -8137.7127 -1054.1773 20083.875
+ 400 309.18439 -8169.6374 0 -8132.8028 -1785.2352 20114.391
+ 500 304.51122 -8163.9147 0 -8127.6369 -160.33189 20175.64
+ 600 300 -8158.55 0 -8122.8096 1555.8342 20272.069
+ 700 304.32794 -8149.4746 0 -8113.2185 3702.0205 20422.656
+ 800 304.79621 -8138.8368 0 -8102.5249 3723.0289 20502.876
+ 900 303.87706 -8128.16 0 -8091.9576 4388.821 20631.103
+ 1000 300 -8113.4908 0 -8077.7503 6189.061 20747.117
+ 1100 306.13486 -8097.1731 0 -8060.7018 8908.048 20871.68
+ 1200 309.15672 -8081.8589 0 -8045.0276 10527.674 20988.916
+ 1300 304.48415 -8064.5597 0 -8028.2851 10066.833 21118.364
+ 1400 300 -8046.7607 0 -8011.0202 10976.597 21230.714
+ 1500 300 -8041.3546 0 -8005.6141 11944.044 21366.268
+ 1600 309.6032 -8035.2271 0 -7998.3426 11344.41 21522.036
+ 1700 300 -8029.1688 0 -7993.4283 11303.056 21627.406
+ 1800 300 -8034.2227 0 -7998.4823 9636.4113 21728.966
+ 1900 307.85809 -8037.1065 0 -8000.4299 6167.5234 21849.865
+ 2000 307.80945 -8029.9525 0 -7993.2817 3167.2857 22004.862
+ 2100 300 -8032.7568 0 -7997.0163 1297.8408 22098.991
+ 2200 300 -8042.2274 0 -8006.4869 1686.5561 22223.554
+ 2300 309.41797 -8041.3421 0 -8004.4797 3429.6069 22335.905
+ 2400 300 -8035.9622 0 -8000.2218 5397.5468 22461.689
+ 2500 300 -8037.3252 0 -8001.5848 7036.8769 22589.915
+ 2600 299.69899 -8035.7903 0 -8000.0857 9345.3265 22710.815
+ 2700 300 -8037.7061 0 -8001.9657 8732.1782 22834.156
+ 2800 300 -8039.9073 0 -8004.1669 8048.8501 22956.277
+ 2900 300 -8039.6401 0 -8003.8996 7057.3819 23069.849
+ 3000 300 -8038.195 0 -8002.4546 3400.007 23199.297
+Loop time of 78.1257 on 1 procs for 3000 steps with 1912 atoms
+
+Pair time (%) = 76.7401 (98.2264)
+Neigh time (%) = 0.942761 (1.20672)
+Comm time (%) = 0.0805891 (0.103153)
+Outpt time (%) = 0.0842321 (0.107816)
+Other time (%) = 0.27803 (0.355876)
+
+Nlocal: 1912 ave 1912 max 1912 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1657 ave 1657 max 1657 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 23426 ave 23426 max 23426 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs: 46852 ave 46852 max 46852 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 46852
+Ave neighs/atom = 24.5042
+Neighbor list builds = 221
+Dangerous builds = 0
diff --git a/examples/meam/log.meam.shear.21May08.linux.4 b/examples/meam/log.meam.shear.21May08.linux.4
new file mode 100644
index 000000000..d9068ad55
--- /dev/null
+++ b/examples/meam/log.meam.shear.21May08.linux.4
@@ -0,0 +1,163 @@
+LAMMPS (21 May 2008)
+# 3d metal shear simulation
+
+units metal
+boundary s s p
+
+atom_style atomic
+lattice fcc 3.52
+Lattice spacing in x,y,z = 3.52 3.52 3.52
+region box block 0 16.0 0 10.0 0 2.828427
+create_box 3 box
+Created orthogonal box = (0 0 0) to (56.32 35.2 9.95606)
+ 2 by 2 by 1 processor grid
+
+lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0
+Lattice spacing in x,y,z = 3.52 4.97803 4.97803
+create_atoms 1 box
+Created 1912 atoms
+
+pair_style meam
+pair_coeff * * library.meam Ni4 Ni.meam Ni4 Ni4 Ni4
+
+neighbor 0.3 bin
+neigh_modify delay 5
+
+region lower block INF INF INF 0.9 INF INF
+region upper block INF INF 6.1 INF INF INF
+group lower region lower
+264 atoms in group lower
+group upper region upper
+264 atoms in group upper
+group boundary union lower upper
+528 atoms in group boundary
+group mobile subtract all boundary
+1384 atoms in group mobile
+
+set group lower type 2
+ 264 settings made for type
+set group upper type 3
+ 264 settings made for type
+
+# void
+
+#region void cylinder z 8 5 2.5 INF INF
+#delete_atoms region void
+
+# temp controllers
+
+compute new3d mobile temp
+compute new2d mobile temp/partial 0 1 1
+
+# equilibrate
+
+velocity mobile create 300.0 5812775 temp new3d
+fix 1 all nve
+fix 2 boundary setforce 0.0 0.0 0.0
+
+fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
+fix_modify 3 temp new3d
+
+thermo 25
+thermo_modify temp new3d
+
+timestep 0.001
+run 100
+Memory usage per processor = 5.32801 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 300 -8232.7767 0 -8179.1466 1387.2089 19539.346
+ 25 223.02513 -8188.2962 0 -8148.4267 8998.4716 19539.346
+ 50 300 -8152.0635 0 -8098.4335 10060.658 19678.279
+ 75 308.13652 -8164.4552 0 -8109.3706 6520.8872 19773.8
+ 100 300 -8178.2806 0 -8124.6506 4001.6051 19951.128
+Loop time of 0.738111 on 4 procs for 100 steps with 1912 atoms
+
+Pair time (%) = 0.680541 (92.2004)
+Neigh time (%) = 0.00550801 (0.74623)
+Comm time (%) = 0.039358 (5.33226)
+Outpt time (%) = 0.00177252 (0.240143)
+Other time (%) = 0.0109315 (1.48101)
+
+Nlocal: 478 ave 486 max 469 min
+Histogram: 1 0 1 0 0 0 0 0 1 1
+Nghost: 809 ave 818 max 801 min
+Histogram: 1 1 0 0 0 0 0 1 0 1
+Neighs: 5932.75 ave 6076 max 5807 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+FullNghs: 11865.5 ave 12111 max 11653 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+
+Total # of neighbors = 47462
+Ave neighs/atom = 24.8232
+Neighbor list builds = 5
+Dangerous builds = 0
+
+# shear
+
+velocity upper set 1.0 0 0
+velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes
+
+unfix 3
+fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
+fix_modify 3 temp new2d
+
+dump 1 all atom 100 dump.meam
+thermo 100
+thermo_modify temp new2d
+
+reset_timestep 0
+run 3000
+Memory usage per processor = 5.38726 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 292.28828 -8178.2806 0 -8143.4589 2992.7013 19964.244
+ 100 301.02661 -8174.1628 0 -8138.3 441.39614 19947.951
+ 200 290.97251 -8175.7136 0 -8141.0487 -438.32628 19981.719
+ 300 304.4239 -8173.5555 0 -8137.288 -2447.7976 20067.185
+ 400 305.76192 -8168.2982 0 -8131.8713 -814.70984 20153.166
+ 500 304.73368 -8164.7296 0 -8128.4252 -963.99012 20227.497
+ 600 300.12426 -8157.4957 0 -8121.7405 39.926198 20299.368
+ 700 301.07583 -8150.7214 0 -8114.8528 2178.1731 20419.159
+ 800 297.37471 -8139.56 0 -8104.1323 4209.733 20518.203
+ 900 304.4007 -8127.6685 0 -8091.4038 6132.0576 20631.103
+ 1000 306.98916 -8112.2064 0 -8075.6333 8585.8087 20758.108
+ 1100 303.05268 -8097.0258 0 -8060.9217 9885.1628 20871.68
+ 1200 300.37461 -8081.159 0 -8045.3739 9988.7374 20999.907
+ 1300 307.55251 -8065.2275 0 -8028.5873 10516.036 21126.912
+ 1400 303.2639 -8051.2915 0 -8015.1623 11668.072 21235.599
+ 1500 300 -8039.6298 0 -8003.8893 12498.158 21361.383
+ 1600 300 -8032.3339 0 -7996.5935 13558.655 21487.167
+ 1700 300 -8021.6093 0 -7985.8689 13720.955 21608.067
+ 1800 300 -8013.5338 0 -7977.7933 10671.999 21727.745
+ 1900 300 -8014.5802 0 -7978.8398 6968.6003 21849.865
+ 2000 300 -8026.6569 0 -7990.9165 3269.3318 21974.428
+ 2100 300 -8033.1 0 -7997.3596 1537.5367 22102.655
+ 2200 307.34939 -8028.6438 0 -7992.0278 3817.2972 22222.333
+ 2300 300 -8027.8628 0 -7992.1223 3499.1613 22348.117
+ 2400 300 -8035.3356 0 -7999.5951 2942.2954 22465.353
+ 2500 303.62876 -8038.272 0 -8002.0993 1597.5261 22581.367
+ 2600 300 -8036.5107 0 -8000.7702 2079.386 22714.478
+ 2700 303.53313 -8037.4306 0 -8001.2693 1401.19 22832.935
+ 2800 300 -8036.0227 0 -8000.2823 686.67133 22953.834
+ 2900 300 -8033.2512 0 -7997.5108 76.040969 23067.406
+ 3000 300 -8032.7731 0 -7997.0327 -170.54788 23202.96
+Loop time of 23.4772 on 4 procs for 3000 steps with 1912 atoms
+
+Pair time (%) = 21.6076 (92.0366)
+Neigh time (%) = 0.240626 (1.02493)
+Comm time (%) = 1.2278 (5.22976)
+Outpt time (%) = 0.10237 (0.436041)
+Other time (%) = 0.298776 (1.27262)
+
+Nlocal: 478 ave 516 max 442 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+Nghost: 787.25 ave 825 max 752 min
+Histogram: 1 1 0 0 0 0 0 0 1 1
+Neighs: 5769.5 ave 6126 max 5446 min
+Histogram: 1 0 0 1 0 1 0 0 0 1
+FullNghs: 11539 ave 12266 max 10876 min
+Histogram: 1 0 0 1 0 1 0 0 0 1
+
+Total # of neighbors = 46156
+Ave neighs/atom = 24.1402
+Neighbor list builds = 222
+Dangerous builds = 0
diff --git a/examples/meam/log.meam.shear.22Jan08.linux.1 b/examples/meam/log.meam.shear.22Jan08.linux.1
deleted file mode 100644
index ee0e13a2a..000000000
--- a/examples/meam/log.meam.shear.22Jan08.linux.1
+++ /dev/null
@@ -1,163 +0,0 @@
-LAMMPS (22 Jan 2008)
-# 3d metal shear simulation
-
-units metal
-boundary s s p
-
-atom_style atomic
-lattice fcc 3.52
-Lattice spacing in x,y,z = 3.52 3.52 3.52
-region box block 0 16.0 0 10.0 0 2.828427
-create_box 3 box
-Created orthogonal box = (0 0 0) to (56.32 35.2 9.95606)
- 1 by 1 by 1 processor grid
-
-lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0
-Lattice spacing in x,y,z = 3.52 4.97803 4.97803
-create_atoms 1 box
-Created 1912 atoms
-
-pair_style meam
-pair_coeff * * library.meam Ni4 Ni.meam Ni4 Ni4 Ni4
-
-neighbor 0.3 bin
-neigh_modify delay 5
-
-region lower block INF INF INF 0.9 INF INF
-region upper block INF INF 6.1 INF INF INF
-group lower region lower
-264 atoms in group lower
-group upper region upper
-264 atoms in group upper
-group boundary union lower upper
-528 atoms in group boundary
-group mobile subtract all boundary
-1384 atoms in group mobile
-
-set group lower type 2
- 264 settings made for type
-set group upper type 3
- 264 settings made for type
-
-# void
-
-#region void cylinder z 8 5 2.5 INF INF
-#delete_atoms region void
-
-# temp controllers
-
-compute new3d mobile temp
-compute new2d mobile temp/partial 0 1 1
-
-# equilibrate
-
-velocity mobile create 300.0 5812775 temp new3d
-fix 1 all nve
-fix 2 boundary setforce 0.0 0.0 0.0
-
-fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
-fix_modify 3 temp new3d
-
-thermo 25
-thermo_modify temp new3d
-
-timestep 0.001
-run 100
-Memory usage per processor = 6.09291 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume
- 0 300 -8232.7767 0 -8179.1466 1387.2089 19539.346
- 25 222.78953 -8188.1215 0 -8148.2941 9099.4735 19539.346
- 50 300 -8149.7654 0 -8096.1353 10637.302 19676.681
- 75 304.80657 -8163.4557 0 -8108.9665 7048.2094 19752.029
- 100 300 -8173.6884 0 -8120.0584 5954.839 19878.848
-Loop time of 2.46093 on 1 procs for 100 steps with 1912 atoms
-
-Pair time (%) = 2.42762 (98.6468)
-Neigh time (%) = 0.0215614 (0.87615)
-Comm time (%) = 0.00257206 (0.104516)
-Outpt time (%) = 0.000188828 (0.00767303)
-Other time (%) = 0.00897908 (0.364866)
-
-Nlocal: 1912 ave 1912 max 1912 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 1672 ave 1672 max 1672 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 23806 ave 23806 max 23806 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-FullNghs: 47612 ave 47612 max 47612 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 47612
-Ave neighs/atom = 24.9017
-Neighbor list builds = 5
-Dangerous builds = 0
-
-# shear
-
-velocity upper set 1.0 0 0
-velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes
-
-unfix 3
-fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
-fix_modify 3 temp new2d
-
-dump 1 all atom 100 dump.meam
-thermo 100
-thermo_modify temp new2d
-
-reset_timestep 0
-run 3000
-Memory usage per processor = 6.34243 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume
- 0 300.50853 -8173.6884 0 -8137.8874 4994.9251 19886.554
- 100 292.43462 -8178.5214 0 -8143.6823 2595.8245 19846.142
- 200 302.79029 -8177.5966 0 -8141.5238 928.09995 20038.569
- 300 291.68573 -8173.4974 0 -8138.7474 -1202.8487 20113.221
- 400 300 -8170.0629 0 -8134.3225 -1617.1537 20115.738
- 500 308.49792 -8164.7324 0 -8127.9796 -346.62656 20250.005
- 600 308.95879 -8159.1257 0 -8122.3179 1160.1349 20280.432
- 700 303.02599 -8150.2418 0 -8114.1409 2807.9227 20434.583
- 800 305.36804 -8140.8077 0 -8104.4278 3218.2338 20500.434
- 900 305.593 -8128.943 0 -8092.5363 3121.7248 20628.661
- 1000 308.39114 -8113.6413 0 -8076.9012 5180.0491 20758.108
- 1100 304.62199 -8096.7999 0 -8060.5088 8173.3445 20874.123
- 1200 293.41155 -8082.676 0 -8047.7205 9884.2082 20987.695
- 1300 303.32764 -8066.7733 0 -8030.6364 10196.38 21108.594
- 1400 304.17524 -8049.5115 0 -8013.2736 11518.936 21249.033
- 1500 300 -8038.1747 0 -8002.4343 12554.565 21361.383
- 1600 304.95664 -8030.581 0 -7994.25 12166.265 21483.504
- 1700 302.82085 -8019.1918 0 -7983.1153 11726.892 21604.403
- 1800 300 -8010.2023 0 -7974.4619 11039.364 21737.514
- 1900 309.75521 -7999.8484 0 -7962.9457 10360.853 21859.635
- 2000 304.01114 -7995.6108 0 -7959.3925 11104.967 21974.428
- 2100 300 -7998.317 0 -7962.5766 9661.15 22094.106
- 2200 300 -8008.5986 0 -7972.8581 7070.9315 22225.996
- 2300 300 -8012.1558 0 -7976.4153 6974.7608 22346.896
- 2400 309.62904 -8011.7107 0 -7974.8232 9446.6153 22470.237
- 2500 295.33175 -8007.0125 0 -7971.8282 10709.603 22576.482
- 2600 300 -8012.3194 0 -7976.579 9761.1868 22698.603
- 2700 300.71244 -8007.8295 0 -7972.0042 12262.62 22821.944
- 2800 306.97204 -8005.1205 0 -7968.5494 12418.816 22950.171
- 2900 300 -8004.8006 0 -7969.0601 10851.969 23074.734
- 3000 300 -8004.2168 0 -7968.4764 10301.261 23202.96
-Loop time of 78.1421 on 1 procs for 3000 steps with 1912 atoms
-
-Pair time (%) = 76.7955 (98.2767)
-Neigh time (%) = 0.911251 (1.16615)
-Comm time (%) = 0.0806024 (0.103148)
-Outpt time (%) = 0.0821629 (0.105145)
-Other time (%) = 0.272587 (0.348835)
-
-Nlocal: 1912 ave 1912 max 1912 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 1661 ave 1661 max 1661 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 23451 ave 23451 max 23451 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-FullNghs: 46902 ave 46902 max 46902 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 46902
-Ave neighs/atom = 24.5303
-Neighbor list builds = 216
-Dangerous builds = 0
diff --git a/examples/meam/log.meam.shear.22Jan08.linux.4 b/examples/meam/log.meam.shear.22Jan08.linux.4
deleted file mode 100644
index 2a1681d19..000000000
--- a/examples/meam/log.meam.shear.22Jan08.linux.4
+++ /dev/null
@@ -1,163 +0,0 @@
-LAMMPS (22 Jan 2008)
-# 3d metal shear simulation
-
-units metal
-boundary s s p
-
-atom_style atomic
-lattice fcc 3.52
-Lattice spacing in x,y,z = 3.52 3.52 3.52
-region box block 0 16.0 0 10.0 0 2.828427
-create_box 3 box
-Created orthogonal box = (0 0 0) to (56.32 35.2 9.95606)
- 2 by 2 by 1 processor grid
-
-lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0
-Lattice spacing in x,y,z = 3.52 4.97803 4.97803
-create_atoms 1 box
-Created 1912 atoms
-
-pair_style meam
-pair_coeff * * library.meam Ni4 Ni.meam Ni4 Ni4 Ni4
-
-neighbor 0.3 bin
-neigh_modify delay 5
-
-region lower block INF INF INF 0.9 INF INF
-region upper block INF INF 6.1 INF INF INF
-group lower region lower
-264 atoms in group lower
-group upper region upper
-264 atoms in group upper
-group boundary union lower upper
-528 atoms in group boundary
-group mobile subtract all boundary
-1384 atoms in group mobile
-
-set group lower type 2
- 264 settings made for type
-set group upper type 3
- 264 settings made for type
-
-# void
-
-#region void cylinder z 8 5 2.5 INF INF
-#delete_atoms region void
-
-# temp controllers
-
-compute new3d mobile temp
-compute new2d mobile temp/partial 0 1 1
-
-# equilibrate
-
-velocity mobile create 300.0 5812775 temp new3d
-fix 1 all nve
-fix 2 boundary setforce 0.0 0.0 0.0
-
-fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
-fix_modify 3 temp new3d
-
-thermo 25
-thermo_modify temp new3d
-
-timestep 0.001
-run 100
-Memory usage per processor = 5.32801 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume
- 0 300 -8232.7767 0 -8179.1466 1387.2089 19539.346
- 25 223.02513 -8188.2962 0 -8148.4267 8998.4716 19539.346
- 50 300 -8152.0635 0 -8098.4335 10060.658 19678.279
- 75 308.13652 -8164.4552 0 -8109.3706 6520.8872 19773.8
- 100 300 -8178.2806 0 -8124.6506 4001.6051 19951.128
-Loop time of 0.743105 on 4 procs for 100 steps with 1912 atoms
-
-Pair time (%) = 0.686752 (92.4165)
-Neigh time (%) = 0.0055545 (0.747471)
-Comm time (%) = 0.0390352 (5.25299)
-Outpt time (%) = 0.00166398 (0.223923)
-Other time (%) = 0.0100994 (1.35907)
-
-Nlocal: 478 ave 486 max 469 min
-Histogram: 1 0 1 0 0 0 0 0 1 1
-Nghost: 809 ave 818 max 801 min
-Histogram: 1 1 0 0 0 0 0 1 0 1
-Neighs: 5932.75 ave 6076 max 5807 min
-Histogram: 2 0 0 0 0 0 0 0 1 1
-FullNghs: 11865.5 ave 12111 max 11653 min
-Histogram: 2 0 0 0 0 0 0 0 1 1
-
-Total # of neighbors = 47462
-Ave neighs/atom = 24.8232
-Neighbor list builds = 5
-Dangerous builds = 0
-
-# shear
-
-velocity upper set 1.0 0 0
-velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes
-
-unfix 3
-fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
-fix_modify 3 temp new2d
-
-dump 1 all atom 100 dump.meam
-thermo 100
-thermo_modify temp new2d
-
-reset_timestep 0
-run 3000
-Memory usage per processor = 5.38726 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume
- 0 292.28828 -8178.2806 0 -8143.4589 2992.7013 19964.244
- 100 304.48468 -8173.0606 0 -8136.7859 425.54216 19949.638
- 200 292.7057 -8176.0355 0 -8141.1641 -420.37567 19967.921
- 300 300 -8174.2457 0 -8138.5052 -2225.0957 20035.454
- 400 301.8783 -8169.8228 0 -8133.8586 -954.54062 20072.806
- 500 297.3529 -8163.9704 0 -8128.5453 -636.90863 20224.627
- 600 300.21575 -8158.4937 0 -8122.7275 426.04354 20300.212
- 700 294.62668 -8149.3419 0 -8114.2416 2914.3315 20397.69
- 800 297.68293 -8140.221 0 -8104.7566 4382.9813 20500.434
- 900 307.34872 -8129.6288 0 -8093.0129 6273.2975 20626.218
- 1000 299.54856 -8114.9745 0 -8079.2878 9036.1509 20758.108
- 1100 298.61047 -8098.7531 0 -8063.1782 10485.79 20872.901
- 1200 293.03092 -8082.1069 0 -8047.1967 11405.523 21004.792
- 1300 307.76804 -8065.4274 0 -8028.7615 11979.925 21120.806
- 1400 300 -8051.592 0 -8015.8516 12466.401 21238.042
- 1500 308.53325 -8037.7116 0 -8000.9546 15186.116 21363.826
- 1600 300 -8031.8572 0 -7996.1168 16229.517 21487.167
- 1700 300 -8022.9422 0 -7987.2018 18187.816 21605.624
- 1800 300 -8009.2383 0 -7973.4979 18721.492 21735.072
- 1900 300.25537 -7997.9537 0 -7962.1828 18854.857 21848.644
- 2000 300 -7987.6026 0 -7951.8622 18713.498 21976.871
- 2100 300 -7996.2028 0 -7960.4624 16426.801 22100.212
- 2200 306.21818 -8006.9292 0 -7970.448 13195.382 22211.342
- 2300 300 -8010.9873 0 -7975.2468 11233.26 22342.011
- 2400 300 -8015.0713 0 -7979.3308 12014.401 22456.804
- 2500 300 -8015.6198 0 -7979.8793 11824.876 22578.925
- 2600 305.67337 -8008.4547 0 -7972.0384 11729.677 22705.93
- 2700 304.98465 -8007.1197 0 -7970.7855 9757.3741 22832.935
- 2800 300 -8008.3745 0 -7972.6341 8658.7198 22953.834
- 2900 300 -8007.6958 0 -7971.9554 7167.5651 23068.628
- 3000 300 -8007.8744 0 -7972.134 6613.2779 23202.96
-Loop time of 23.8465 on 4 procs for 3000 steps with 1912 atoms
-
-Pair time (%) = 21.9333 (91.9771)
-Neigh time (%) = 0.240415 (1.00818)
-Comm time (%) = 1.26714 (5.31376)
-Outpt time (%) = 0.113929 (0.477759)
-Other time (%) = 0.291683 (1.22317)
-
-Nlocal: 478 ave 517 max 446 min
-Histogram: 2 0 0 0 0 0 0 1 0 1
-Nghost: 784.5 ave 838 max 736 min
-Histogram: 1 0 0 1 0 1 0 0 0 1
-Neighs: 5844.5 ave 6271 max 5655 min
-Histogram: 2 1 0 0 0 0 0 0 0 1
-FullNghs: 11689 ave 12514 max 11309 min
-Histogram: 2 0 1 0 0 0 0 0 0 1
-
-Total # of neighbors = 46756
-Ave neighs/atom = 24.454
-Neighbor list builds = 223
-Dangerous builds = 0
diff --git a/examples/melt/log.melt.22Jan08.linux.1 b/examples/melt/log.melt.21May08.linux.1
similarity index 83%
rename from examples/melt/log.melt.22Jan08.linux.1
rename to examples/melt/log.melt.21May08.linux.1
index f9a5ba5b4..4feeae69f 100644
--- a/examples/melt/log.melt.22Jan08.linux.1
+++ b/examples/melt/log.melt.21May08.linux.1
@@ -1,57 +1,57 @@
-LAMMPS (22 Jan 2008)
+LAMMPS (21 May 2008)
# 3d Lennard-Jones melt
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 10 0 10 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 1 by 1 processor grid
create_atoms 1 box
Created 4000 atoms
mass 1 1.0
velocity all create 3.0 87287
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
fix 1 all nve
dump id all atom 50 dump.melt
thermo 50
run 250
Memory usage per processor = 2.19355 Mbytes
Step Temp E_pair E_mol TotEng Press
0 3 -6.7733681 0 -2.2744931 -3.7033504
50 1.6758903 -4.7955425 0 -2.2823355 5.670064
100 1.6458363 -4.7492704 0 -2.2811332 5.8691042
150 1.6324555 -4.7286791 0 -2.280608 5.9589514
200 1.6630725 -4.7750988 0 -2.2811136 5.7364886
250 1.6275257 -4.7224992 0 -2.281821 5.9567365
-Loop time of 1.26243 on 1 procs for 250 steps with 4000 atoms
+Loop time of 1.2689 on 1 procs for 250 steps with 4000 atoms
-Pair time (%) = 1.06787 (84.5881)
-Neigh time (%) = 0.11483 (9.0959)
-Comm time (%) = 0.020905 (1.65593)
-Outpt time (%) = 0.028095 (2.22547)
-Other time (%) = 0.0307348 (2.43457)
+Pair time (%) = 1.07107 (84.4098)
+Neigh time (%) = 0.116847 (9.20853)
+Comm time (%) = 0.020932 (1.64962)
+Outpt time (%) = 0.0287478 (2.26557)
+Other time (%) = 0.0312967 (2.46645)
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5499 ave 5499 max 5499 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 151513 ave 151513 max 151513 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 151513
Ave neighs/atom = 37.8783
Neighbor list builds = 12
Dangerous builds = 0
diff --git a/examples/melt/log.melt.22Jan08.linux.4 b/examples/melt/log.melt.21May08.linux.4
similarity index 83%
rename from examples/melt/log.melt.22Jan08.linux.4
rename to examples/melt/log.melt.21May08.linux.4
index 84726e3bd..cd5be968b 100644
--- a/examples/melt/log.melt.22Jan08.linux.4
+++ b/examples/melt/log.melt.21May08.linux.4
@@ -1,57 +1,57 @@
-LAMMPS (22 Jan 2008)
+LAMMPS (21 May 2008)
# 3d Lennard-Jones melt
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 10 0 10 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 2 by 2 processor grid
create_atoms 1 box
Created 4000 atoms
mass 1 1.0
velocity all create 3.0 87287
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
fix 1 all nve
dump id all atom 50 dump.melt
thermo 50
run 250
Memory usage per processor = 1.60836 Mbytes
Step Temp E_pair E_mol TotEng Press
0 3 -6.7733681 0 -2.2744931 -3.7033504
50 1.6754119 -4.7947589 0 -2.2822693 5.6615925
100 1.6503357 -4.756014 0 -2.2811293 5.8050524
150 1.6596605 -4.7699432 0 -2.2810749 5.7830138
200 1.6371874 -4.7365462 0 -2.2813789 5.9246674
250 1.6323462 -4.7292021 0 -2.2812949 5.9762238
-Loop time of 0.504289 on 4 procs for 250 steps with 4000 atoms
+Loop time of 0.505746 on 4 procs for 250 steps with 4000 atoms
-Pair time (%) = 0.275774 (54.6857)
-Neigh time (%) = 0.029693 (5.88809)
-Comm time (%) = 0.153954 (30.5289)
-Outpt time (%) = 0.0334665 (6.63636)
-Other time (%) = 0.0114021 (2.26103)
+Pair time (%) = 0.277338 (54.8375)
+Neigh time (%) = 0.0297899 (5.89028)
+Comm time (%) = 0.156375 (30.9197)
+Outpt time (%) = 0.032173 (6.36149)
+Other time (%) = 0.0100698 (1.99108)
Nlocal: 1000 ave 1010 max 982 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 2703.75 ave 2713 max 2689 min
Histogram: 1 0 0 0 0 0 0 2 0 1
Neighs: 37915.5 ave 39239 max 36193 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Total # of neighbors = 151662
Ave neighs/atom = 37.9155
Neighbor list builds = 12
Dangerous builds = 0
diff --git a/examples/micelle/log.micelle.21May08.linux.1 b/examples/micelle/log.micelle.21May08.linux.1
new file mode 100644
index 000000000..355a183a4
--- /dev/null
+++ b/examples/micelle/log.micelle.21May08.linux.1
@@ -0,0 +1,200 @@
+LAMMPS (21 May 2008)
+# 2d micelle simulation
+
+dimension 2
+
+neighbor 0.3 bin
+neigh_modify delay 5
+
+atom_style bond
+
+# Soft potential push-off
+
+read_data data.micelle
+ 1 = max bonds/atom
+ orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
+ 1 by 1 by 1 processor grid
+ 1200 atoms
+ 300 bonds
+ 2 = max # of 1-2 neighbors
+ 1 = max # of 1-3 neighbors
+ 1 = max # of 1-4 neighbors
+ 2 = max # of special neighbors
+special_bonds 0 1 1
+ 2 = max # of 1-2 neighbors
+ 2 = max # of special neighbors
+
+pair_style soft 1.12246
+pair_coeff * * 1.0 20.0 1.12246
+
+bond_style harmonic
+bond_coeff 1 50.0 0.75
+
+velocity all create 0.45 2349852
+
+fix 1 all nve
+fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
+fix 3 all enforce2d
+
+thermo 50
+run 1000
+Memory usage per processor = 1.84502 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
+ 50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852
+ 100 0.45 0.73046745 0.054836584 1.234929 2.3196516
+ 150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416
+ 200 0.45 0.78481891 0.076931503 1.3113754 3.0412388
+ 250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024
+ 300 0.45 0.76820218 0.066727591 1.2845548 3.7861054
+ 350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621
+ 400 0.45 0.68527759 0.090724527 1.2256271 4.4725214
+ 450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211
+ 500 0.45 0.64883009 0.078376672 1.1768318 4.7919294
+ 550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705
+ 600 0.45 0.58193041 0.088386617 1.119942 5.131481
+ 650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294
+ 700 0.45 0.50856787 0.088471208 1.0466641 5.2550165
+ 750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763
+ 800 0.45 0.49926696 0.085958476 1.0348504 5.4665914
+ 850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932
+ 900 0.45 0.47785593 0.10150857 1.0289895 5.7765975
+ 950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245
+ 1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568
+Loop time of 0.300502 on 1 procs for 1000 steps with 1200 atoms
+
+Pair time (%) = 0.202995 (67.5518)
+Bond time (%) = 0.0206611 (6.87553)
+Neigh time (%) = 0.0275362 (9.16338)
+Comm time (%) = 0.00611711 (2.03563)
+Outpt time (%) = 0.000581026 (0.193352)
+Other time (%) = 0.0426121 (14.1803)
+
+Nlocal: 1200 ave 1200 max 1200 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 195 ave 195 max 195 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 3136 ave 3136 max 3136 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 3136
+Ave neighs/atom = 2.61333
+Ave special neighs/atom = 0.5
+Neighbor list builds = 92
+Dangerous builds = 0
+
+# Main run
+
+pair_style lj/cut 2.5
+
+# solvent/head - full-size and long-range
+
+pair_coeff 1 1 1.0 1.0 2.5
+pair_coeff 2 2 1.0 1.0 2.5
+pair_coeff 1 2 1.0 1.0 2.5
+
+# tail/tail - size-averaged and long-range
+
+pair_coeff 3 3 1.0 0.75 2.5
+pair_coeff 4 4 1.0 0.50 2.5
+pair_coeff 3 4 1.0 0.67 2.5
+
+# solvent/tail - full-size and repulsive
+
+pair_coeff 1 3 1.0 1.0 1.12246
+pair_coeff 1 4 1.0 1.0 1.12246
+
+# head/tail - size-averaged and repulsive
+
+pair_coeff 2 3 1.0 0.88 1.12246
+pair_coeff 2 4 1.0 0.75 1.12246
+
+thermo 1000
+dump 1 all atom 500 dump.micelle
+
+reset_timestep 0
+run 60000
+Memory usage per processor = 1.8908 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686
+ 1000 0.45 -1.9727615 0.058604601 -1.4645319 1.9982028
+ 2000 0.43716482 -1.9789902 0.064175291 -1.4780144 1.8178005
+ 3000 0.4652974 -2.0238585 0.067406181 -1.4915426 1.5369016
+ 4000 0.4450276 -2.0120252 0.05904261 -1.5083259 1.4795779
+ 5000 0.44249516 -2.0326528 0.06825332 -1.5222731 1.3463285
+ 6000 0.44359067 -2.0236106 0.05661929 -1.5237703 1.2336671
+ 7000 0.44829871 -2.053872 0.064049461 -1.5418974 1.2077943
+ 8000 0.43835338 -2.0295717 0.063594195 -1.5279894 1.2702884
+ 9000 0.46137509 -2.0331381 0.057420617 -1.5147269 1.293388
+ 10000 0.45864575 -2.0647458 0.061160344 -1.5453219 1.091648
+ 11000 0.43028298 -2.0528287 0.065356685 -1.5575476 1.0832846
+ 12000 0.43770429 -2.0600447 0.06341501 -1.5592902 1.0777045
+ 13000 0.46155652 -2.0506356 0.056176366 -1.5332873 1.2535564
+ 14000 0.45157492 -2.0609489 0.061187063 -1.5485632 1.0797813
+ 15000 0.46860396 -2.0810829 0.05900275 -1.5538667 1.0154193
+ 16000 0.44657573 -2.0585991 0.064727245 -1.5476683 0.98186948
+ 17000 0.43577692 -2.085853 0.064116312 -1.5863229 1.1138878
+ 18000 0.45579186 -2.0928391 0.052663191 -1.5847639 0.77972989
+ 19000 0.4638413 -2.1035558 0.05809772 -1.5820034 0.86184682
+ 20000 0.44419341 -2.0904971 0.062276482 -1.5843973 0.71988805
+ 21000 0.45600607 -2.097995 0.059849246 -1.5825197 0.78614854
+ 22000 0.45943121 -2.1073469 0.061572162 -1.5867264 0.9111383
+ 23000 0.45 -2.1088733 0.057406786 -1.6018415 0.68127639
+ 24000 0.45200935 -2.0902016 0.065206229 -1.5733627 0.99578038
+ 25000 0.45559026 -2.1000506 0.057458439 -1.5873816 0.76154574
+ 26000 0.46839853 -2.1048288 0.056806361 -1.5800142 0.72250339
+ 27000 0.45 -2.1126221 0.053370375 -1.6096267 0.78695915
+ 28000 0.43926352 -2.0999927 0.060587004 -1.6005082 0.90396399
+ 29000 0.44741081 -2.1167559 0.062267017 -1.6074509 0.72496134
+ 30000 0.46565548 -2.1194308 0.057631518 -1.5965319 0.73222696
+ 31000 0.46058458 -2.1102085 0.059770604 -1.5902371 0.79790524
+ 32000 0.45349363 -2.1192242 0.064718489 -1.60139 0.68868895
+ 33000 0.43945922 -2.1211684 0.056117328 -1.6259581 0.6127229
+ 34000 0.45789468 -2.111049 0.054210912 -1.599325 0.66682436
+ 35000 0.455467 -2.1261824 0.06685345 -1.6042415 0.54820231
+ 36000 0.46511205 -2.1208942 0.058276998 -1.5978928 0.59296374
+ 37000 0.44640964 -2.1143213 0.057944638 -1.610339 0.77242592
+ 38000 0.44596116 -2.0946988 0.062196767 -1.5869125 0.85606153
+ 39000 0.45745534 -2.1044294 0.054075498 -1.5932798 0.7490514
+ 40000 0.46774599 -2.1141735 0.055820661 -1.5909966 0.68263873
+ 41000 0.45209942 -2.1154203 0.069314198 -1.5943835 0.6331387
+ 42000 0.44276955 -2.115384 0.063045461 -1.6099379 0.65679589
+ 43000 0.44312295 -2.1028092 0.051688553 -1.608367 0.64527919
+ 44000 0.44136077 -2.1121431 0.06255545 -1.6085947 0.64301583
+ 45000 0.45549493 -2.1256992 0.054358465 -1.6162254 0.65053568
+ 46000 0.44968532 -2.1025103 0.064024111 -1.5891756 0.69878466
+ 47000 0.45751017 -2.1003604 0.054572612 -1.5886589 0.73343046
+ 48000 0.46590931 -2.1166285 0.052436194 -1.5986713 0.73090893
+ 49000 0.45210574 -2.1253492 0.058665633 -1.6149546 0.54736011
+ 50000 0.43629064 -2.1279448 0.069771465 -1.6222463 0.54429106
+ 51000 0.46639828 -2.1138965 0.061298663 -1.5865882 0.64577651
+ 52000 0.43831593 -2.1123621 0.057043795 -1.6173676 0.74662964
+ 53000 0.43501137 -2.1127324 0.075592639 -1.6024909 0.80359868
+ 54000 0.45696335 -2.1226029 0.062928151 -1.6030923 0.64671682
+ 55000 0.43593702 -2.127708 0.064441586 -1.6276927 0.62960269
+ 56000 0.44913808 -2.1093471 0.055492835 -1.6050905 0.85024228
+ 57000 0.44265459 -2.103588 0.054688319 -1.606614 0.71936833
+ 58000 0.46008975 -2.1189366 0.059119033 -1.6001112 0.6781833
+ 59000 0.45675715 -2.1231353 0.061231406 -1.6055274 0.62271773
+ 60000 0.45937135 -2.1293456 0.068515696 -1.6018413 0.52284735
+Loop time of 25.3203 on 1 procs for 60000 steps with 1200 atoms
+
+Pair time (%) = 17.7009 (69.908)
+Bond time (%) = 1.21589 (4.80203)
+Neigh time (%) = 3.06021 (12.086)
+Comm time (%) = 0.564598 (2.22982)
+Outpt time (%) = 0.203498 (0.803696)
+Other time (%) = 2.5752 (10.1705)
+
+Nlocal: 1200 ave 1200 max 1200 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 425 ave 425 max 425 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 9874 ave 9874 max 9874 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 9874
+Ave neighs/atom = 8.22833
+Ave special neighs/atom = 0.5
+Neighbor list builds = 4884
+Dangerous builds = 0
diff --git a/examples/micelle/log.micelle.21May08.linux.4 b/examples/micelle/log.micelle.21May08.linux.4
new file mode 100644
index 000000000..932b02bd5
--- /dev/null
+++ b/examples/micelle/log.micelle.21May08.linux.4
@@ -0,0 +1,200 @@
+LAMMPS (21 May 2008)
+# 2d micelle simulation
+
+dimension 2
+
+neighbor 0.3 bin
+neigh_modify delay 5
+
+atom_style bond
+
+# Soft potential push-off
+
+read_data data.micelle
+ 1 = max bonds/atom
+ orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
+ 2 by 2 by 1 processor grid
+ 1200 atoms
+ 300 bonds
+ 2 = max # of 1-2 neighbors
+ 1 = max # of 1-3 neighbors
+ 1 = max # of 1-4 neighbors
+ 2 = max # of special neighbors
+special_bonds 0 1 1
+ 2 = max # of 1-2 neighbors
+ 2 = max # of special neighbors
+
+pair_style soft 1.12246
+pair_coeff * * 1.0 20.0 1.12246
+
+bond_style harmonic
+bond_coeff 1 50.0 0.75
+
+velocity all create 0.45 2349852
+
+fix 1 all nve
+fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
+fix 3 all enforce2d
+
+thermo 50
+run 1000
+Memory usage per processor = 2.07665 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
+ 50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852
+ 100 0.45 0.73046745 0.054836584 1.234929 2.3196516
+ 150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416
+ 200 0.45 0.78481891 0.076931503 1.3113754 3.0412388
+ 250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024
+ 300 0.45 0.76820218 0.066727591 1.2845548 3.7861054
+ 350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621
+ 400 0.45 0.68527759 0.090724527 1.2256271 4.4725214
+ 450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211
+ 500 0.45 0.64883009 0.078376672 1.1768318 4.7919294
+ 550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705
+ 600 0.45 0.58193041 0.088386617 1.119942 5.131481
+ 650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294
+ 700 0.45 0.50856787 0.088471208 1.0466641 5.2550165
+ 750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763
+ 800 0.45 0.49926696 0.085958476 1.0348504 5.4665914
+ 850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932
+ 900 0.45 0.47785593 0.10150857 1.0289895 5.7765975
+ 950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245
+ 1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568
+Loop time of 0.451741 on 4 procs for 1000 steps with 1200 atoms
+
+Pair time (%) = 0.055 (12.1751)
+Bond time (%) = 0.0054844 (1.21406)
+Neigh time (%) = 0.00761467 (1.68563)
+Comm time (%) = 0.312935 (69.273)
+Outpt time (%) = 0.00906777 (2.0073)
+Other time (%) = 0.0616394 (13.6449)
+
+Nlocal: 300 ave 305 max 292 min
+Histogram: 1 0 0 0 0 0 1 0 1 1
+Nghost: 100.25 ave 108 max 93 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+Neighs: 784 ave 815 max 739 min
+Histogram: 1 0 0 0 0 0 1 1 0 1
+
+Total # of neighbors = 3136
+Ave neighs/atom = 2.61333
+Ave special neighs/atom = 0.5
+Neighbor list builds = 92
+Dangerous builds = 0
+
+# Main run
+
+pair_style lj/cut 2.5
+
+# solvent/head - full-size and long-range
+
+pair_coeff 1 1 1.0 1.0 2.5
+pair_coeff 2 2 1.0 1.0 2.5
+pair_coeff 1 2 1.0 1.0 2.5
+
+# tail/tail - size-averaged and long-range
+
+pair_coeff 3 3 1.0 0.75 2.5
+pair_coeff 4 4 1.0 0.50 2.5
+pair_coeff 3 4 1.0 0.67 2.5
+
+# solvent/tail - full-size and repulsive
+
+pair_coeff 1 3 1.0 1.0 1.12246
+pair_coeff 1 4 1.0 1.0 1.12246
+
+# head/tail - size-averaged and repulsive
+
+pair_coeff 2 3 1.0 0.88 1.12246
+pair_coeff 2 4 1.0 0.75 1.12246
+
+thermo 1000
+dump 1 all atom 500 dump.micelle
+
+reset_timestep 0
+run 60000
+Memory usage per processor = 2.08829 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686
+ 1000 0.45 -1.9727838 0.058618121 -1.4645407 1.9980741
+ 2000 0.45 -2.0008971 0.06046133 -1.4908107 1.7505633
+ 3000 0.46857989 -2.0062096 0.062600297 -1.4754199 1.4580464
+ 4000 0.46655193 -2.0452235 0.063633136 -1.5154273 1.2266944
+ 5000 0.44844443 -2.0305619 0.061707001 -1.5207842 1.2735298
+ 6000 0.45 -2.0580878 0.062213978 -1.5462488 1.0224016
+ 7000 0.4476022 -2.0378426 0.054638368 -1.535975 1.1284476
+ 8000 0.4468407 -2.0267685 0.06891916 -1.511381 1.3309425
+ 9000 0.45741983 -2.0597667 0.060064672 -1.5426633 1.0676372
+ 10000 0.45865753 -2.0646248 0.063101783 -1.5432477 1.0898972
+ 11000 0.4544539 -2.0523068 0.052930956 -1.5453006 1.0855721
+ 12000 0.4495638 -2.0587133 0.058599459 -1.5509247 1.0857171
+ 13000 0.46433272 -2.090385 0.059665091 -1.5667742 0.97090005
+ 14000 0.44532862 -2.0655988 0.059393868 -1.5612474 1.1164806
+ 15000 0.45523926 -2.0718246 0.056724666 -1.56024 1.0877035
+ 16000 0.46244762 -2.0767037 0.064385121 -1.5502564 0.98812624
+ 17000 0.46314908 -2.0857805 0.067070535 -1.5559468 0.94844275
+ 18000 0.45 -2.1004858 0.062440373 -1.5884204 0.7444894
+ 19000 0.45461444 -2.0745504 0.065328927 -1.5549859 0.9810655
+ 20000 0.43132218 -2.0810153 0.063878005 -1.5861745 1.0115249
+ 21000 0.45278155 -2.0976147 0.061040123 -1.5841704 0.87450921
+ 22000 0.4413178 -2.0849706 0.05514809 -1.5888725 0.86794005
+ 23000 0.4514062 -2.0698222 0.061531604 -1.5572605 1.0659691
+ 24000 0.44685643 -2.0970941 0.057566091 -1.593044 0.88412737
+ 25000 0.45304563 -2.1059193 0.067469611 -1.5857816 0.75590379
+ 26000 0.43665864 -2.0781503 0.060302863 -1.5815527 1.0518426
+ 27000 0.439842 -2.0820662 0.055355535 -1.5872352 1.02679
+ 28000 0.45421836 -2.0958012 0.068552595 -1.5734087 0.93876409
+ 29000 0.46710017 -2.0981517 0.054218079 -1.5772227 0.89764204
+ 30000 0.43140661 -2.0930753 0.05639766 -1.6056305 0.75868765
+ 31000 0.46278553 -2.1008921 0.05712374 -1.5813685 0.82007867
+ 32000 0.46400002 -2.1263545 0.063574225 -1.599167 0.67935923
+ 33000 0.43939072 -2.0940879 0.061376643 -1.5936867 0.78873715
+ 34000 0.45175636 -2.1132311 0.062639359 -1.5992119 0.71670369
+ 35000 0.44545357 -2.113453 0.065502953 -1.6028677 0.77337903
+ 36000 0.43878041 -2.1101296 0.067575973 -1.6041389 0.5702654
+ 37000 0.45726864 -2.0963464 0.063544674 -1.5759142 0.77408424
+ 38000 0.46058278 -2.0960925 0.060468593 -1.5754249 0.91253803
+ 39000 0.43612306 -2.088217 0.061585534 -1.5908718 0.80977481
+ 40000 0.45643431 -2.1078785 0.061223384 -1.5906012 0.90050763
+ 41000 0.45499013 -2.097803 0.060801097 -1.5823909 0.7724239
+ 42000 0.44008414 -2.1073806 0.059385138 -1.6082781 0.76677042
+ 43000 0.46520882 -2.1288778 0.053657089 -1.6103996 0.57206053
+ 44000 0.44575963 -2.0863972 0.055762678 -1.5852464 0.92852911
+ 45000 0.44272361 -2.1039527 0.05307631 -1.6085217 0.76464969
+ 46000 0.44274241 -2.100733 0.065427251 -1.5929323 0.74550533
+ 47000 0.44675956 -2.1111981 0.06130925 -1.6035016 0.72023447
+ 48000 0.46850415 -2.1097324 0.052877281 -1.5887414 0.5836148
+ 49000 0.46175146 -2.1056078 0.052122205 -1.5921189 0.73350989
+ 50000 0.46143089 -2.0950096 0.05966393 -1.5742993 0.79335455
+ 51000 0.44992091 -2.1092625 0.055443473 -1.604273 0.71374923
+ 52000 0.44053251 -2.0903005 0.054677072 -1.595458 0.7414373
+ 53000 0.44967972 -2.1071504 0.057337448 -1.6005079 0.63579953
+ 54000 0.45717923 -2.1109235 0.055545674 -1.5985796 0.60432994
+ 55000 0.4672155 -2.1209866 0.051378124 -1.6027823 0.70136422
+ 56000 0.44691536 -2.1207875 0.058716627 -1.615528 0.72583043
+ 57000 0.44378225 -2.1063669 0.056356727 -1.6065978 0.61593243
+ 58000 0.44119675 -2.1123324 0.061570128 -1.6099332 0.80512516
+ 59000 0.44879198 -2.0998451 0.052529358 -1.5988977 0.81118174
+ 60000 0.46206126 -2.1178369 0.06448607 -1.5916746 0.63817566
+Loop time of 30.5669 on 4 procs for 60000 steps with 1200 atoms
+
+Pair time (%) = 4.76739 (15.5966)
+Bond time (%) = 0.330764 (1.0821)
+Neigh time (%) = 0.83275 (2.72435)
+Comm time (%) = 20.1822 (66.0263)
+Outpt time (%) = 0.245281 (0.80244)
+Other time (%) = 4.20852 (13.7682)
+
+Nlocal: 300 ave 304 max 288 min
+Histogram: 1 0 0 0 0 0 0 0 0 3
+Nghost: 207.5 ave 213 max 199 min
+Histogram: 1 0 0 0 0 0 1 1 0 1
+Neighs: 2404.5 ave 2529 max 2304 min
+Histogram: 1 0 0 1 1 0 0 0 0 1
+
+Total # of neighbors = 9618
+Ave neighs/atom = 8.015
+Ave special neighs/atom = 0.5
+Neighbor list builds = 4886
+Dangerous builds = 0
diff --git a/examples/micelle/log.micelle.22Jan08.linux.1 b/examples/micelle/log.micelle.22Jan08.linux.1
deleted file mode 100644
index 594787a91..000000000
--- a/examples/micelle/log.micelle.22Jan08.linux.1
+++ /dev/null
@@ -1,200 +0,0 @@
-LAMMPS (22 Jan 2008)
-# 2d micelle simulation
-
-dimension 2
-
-neighbor 0.3 bin
-neigh_modify delay 5
-
-atom_style bond
-
-# Soft potential push-off
-
-read_data data.micelle
- 1 = max bonds/atom
- orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
- 1 by 1 by 1 processor grid
- 1200 atoms
- 300 bonds
- 2 = max # of 1-2 neighbors
- 1 = max # of 1-3 neighbors
- 1 = max # of 1-4 neighbors
- 2 = max # of special neighbors
-special_bonds 0 1 1
- 2 = max # of 1-2 neighbors
- 2 = max # of special neighbors
-
-pair_style soft 1.12246
-pair_coeff * * 1.0 20.0 1.12246
-
-bond_style harmonic
-bond_coeff 1 50.0 0.75
-
-velocity all create 0.45 2349852
-
-fix 1 all nve
-fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
-fix 3 all enforce2d
-
-thermo 50
-run 1000
-Memory usage per processor = 1.84502 Mbytes
-Step Temp E_pair E_mol TotEng Press
- 0 0.45 0.40003481 2.2200223e-06 0.84947453 0.78935018
- 50 0.47417944 0.67716204 0.057387153 1.2081359 1.3374428
- 100 0.45 0.73037684 0.054821983 1.2346363 2.3192865
- 150 0.67532546 0.72388376 0.043478036 1.4418431 2.8741848
- 200 0.45 0.78466058 0.076912805 1.3110109 3.0409372
- 250 0.66488946 0.69771453 0.081047682 1.4428206 3.6911924
- 300 0.45 0.76794745 0.066716745 1.2841017 3.7855266
- 350 0.67629601 0.62549506 0.072636862 1.3735826 4.2848322
- 400 0.45 0.68493339 0.090717081 1.225088 4.4713609
- 450 0.56732174 0.64322231 0.080690687 1.2905256 4.7372687
- 500 0.45 0.64764573 0.078468194 1.1755514 4.7911172
- 550 0.56476697 0.58160926 0.080519682 1.22619 4.9721793
- 600 0.45 0.58331363 0.088243449 1.1209946 5.131088
- 650 0.5229482 0.54530348 0.09321673 1.1608147 5.2637478
- 700 0.45 0.52374674 0.085166964 1.0583512 5.2922505
- 750 0.51528063 0.48974532 0.086434828 1.0908167 5.3858022
- 800 0.45 0.50467091 0.090255509 1.0443639 5.5801625
- 850 0.4950534 0.48512921 0.091950432 1.0715142 5.6661389
- 900 0.45 0.48352312 0.097223467 1.0301841 5.7149691
- 950 0.49451225 0.46619517 0.094098428 1.0541877 5.8766965
- 1000 0.45 0.46260893 0.10106179 1.0131082 5.8616912
-Loop time of 0.307229 on 1 procs for 1000 steps with 1200 atoms
-
-Pair time (%) = 0.209812 (68.2917)
-Bond time (%) = 0.0206535 (6.72251)
-Neigh time (%) = 0.0273674 (8.90781)
-Comm time (%) = 0.00643349 (2.09404)
-Outpt time (%) = 0.000555038 (0.18066)
-Other time (%) = 0.0424075 (13.8032)
-
-Nlocal: 1200 ave 1200 max 1200 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 193 ave 193 max 193 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 3176 ave 3176 max 3176 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 3176
-Ave neighs/atom = 2.64667
-Ave special neighs/atom = 0.5
-Neighbor list builds = 93
-Dangerous builds = 0
-
-# Main run
-
-pair_style lj/cut 2.5
-
-# solvent/head - full-size and long-range
-
-pair_coeff 1 1 1.0 1.0 2.5
-pair_coeff 2 2 1.0 1.0 2.5
-pair_coeff 1 2 1.0 1.0 2.5
-
-# tail/tail - size-averaged and long-range
-
-pair_coeff 3 3 1.0 0.75 2.5
-pair_coeff 4 4 1.0 0.50 2.5
-pair_coeff 3 4 1.0 0.67 2.5
-
-# solvent/tail - full-size and repulsive
-
-pair_coeff 1 3 1.0 1.0 1.12246
-pair_coeff 1 4 1.0 1.0 1.12246
-
-# head/tail - size-averaged and repulsive
-
-pair_coeff 2 3 1.0 0.88 1.12246
-pair_coeff 2 4 1.0 0.75 1.12246
-
-thermo 1000
-dump 1 all atom 500 dump.micelle
-
-reset_timestep 0
-run 60000
-Memory usage per processor = 1.8908 Mbytes
-Step Temp E_pair E_mol TotEng Press
- 0 0.45 -1.6864322 0.10106179 -1.1359329 3.7913551
- 1000 0.44913703 -1.9350593 0.071369049 -1.4151147 2.1470317
- 2000 0.46990408 -1.9863161 0.065077829 -1.4519216 1.6695179
- 3000 0.45096845 -2.0130162 0.061423646 -1.5011878 1.5489907
- 4000 0.4496134 -1.9991224 0.056693551 -1.4933774 1.5523766
- 5000 0.45935435 -2.0241729 0.065531769 -1.499861 1.3256492
- 6000 0.45626587 -2.0230661 0.060868899 -1.5065016 1.4541788
- 7000 0.46322362 -2.0578954 0.058349198 -1.5369017 1.2398016
- 8000 0.45253301 -2.0527631 0.069121572 -1.5316742 1.1230521
- 9000 0.45 -2.0616322 0.059639854 -1.5525549 1.0931151
- 10000 0.45473743 -2.0680168 0.062865722 -1.5509821 1.0393117
- 11000 0.46282597 -2.0645336 0.061660553 -1.5406256 1.0473486
- 12000 0.45729042 -2.0903864 0.053745705 -1.5799219 0.99522961
- 13000 0.45 -2.0993317 0.063786977 -1.5861073 0.81046383
- 14000 0.44464915 -2.0836131 0.061515258 -1.5780045 0.91036442
- 15000 0.45077322 -2.1026035 0.064321304 -1.5880724 0.72445371
- 16000 0.43806107 -2.0796558 0.056496971 -1.5856453 0.81980005
- 17000 0.44674015 -2.0942208 0.060106495 -1.5879326 0.88506041
- 18000 0.4517901 -2.0923656 0.051892418 -1.5892478 0.88650049
- 19000 0.45452903 -2.1066926 0.064413446 -1.5883183 0.70616051
- 20000 0.46590873 -2.1035695 0.049979109 -1.588264 0.68424889
- 21000 0.46952716 -2.1025765 0.05919241 -1.5744438 0.70616051
- 22000 0.4439583 -2.1004401 0.064237519 -1.5927993 0.70386205
- 23000 0.43508823 -2.0895563 0.067366868 -1.5876451 0.78908122
- 24000 0.43586625 -2.0944908 0.061850537 -1.5973188 0.75354904
- 25000 0.46055804 -2.0980569 0.057842949 -1.5802316 0.78832968
- 26000 0.44612123 -2.0803277 0.057849021 -1.5769151 0.88337838
- 27000 0.44546513 -2.0816879 0.060389445 -1.5763901 0.85808583
- 28000 0.43991361 -2.1030181 0.059409891 -1.6042445 0.71982555
- 29000 0.44356162 -2.1096901 0.052709226 -1.6139737 0.64555675
- 30000 0.43167655 -2.0778243 0.063810749 -1.5828766 0.94008105
- 31000 0.46020547 -2.0996246 0.055929654 -1.5840647 0.78413535
- 32000 0.44053792 -2.1146449 0.066783802 -1.6078738 0.80809122
- 33000 0.46051154 -2.1125835 0.054178744 -1.5984689 0.63733653
- 34000 0.4385451 -2.09542 0.058510448 -1.5989126 0.65064895
- 35000 0.44884027 -2.1147487 0.062438249 -1.6040312 0.74279786
- 36000 0.45524152 -2.1236253 0.056937704 -1.6120151 0.57159807
- 37000 0.45 -2.1085043 0.055110778 -1.603956 0.75114055
- 38000 0.43889198 -2.1102778 0.062986806 -1.6089476 0.63880845
- 39000 0.46777901 -2.1265214 0.053125894 -1.6062012 0.63053536
- 40000 0.45690015 -2.1199761 0.054748517 -1.6088985 0.68532972
- 41000 0.45311829 -2.0896266 0.051934484 -1.5851402 0.96365527
- 42000 0.45921622 -2.1034581 0.060948692 -1.5838672 0.73506328
- 43000 0.45 -2.1082479 0.056762774 -1.6020476 0.72674441
- 44000 0.4336231 -2.0956954 0.058341601 -1.6042727 0.74559009
- 45000 0.44994151 -2.1060939 0.057939004 -1.5987759 0.80070112
- 46000 0.44025695 -2.1197274 0.053721478 -1.6262993 0.6154191
- 47000 0.43248313 -2.1228046 0.062087253 -1.6287748 0.63193935
- 48000 0.44731445 -2.1105501 0.057531307 -1.6062635 0.67718731
- 49000 0.43994092 -2.1055833 0.05429976 -1.6118925 0.77492942
- 50000 0.44810318 -2.1233595 0.060967052 -1.6148494 0.59090715
- 51000 0.44881752 -2.102071 0.054986409 -1.5988281 0.59834463
- 52000 0.45426625 -2.1169037 0.058260039 -1.6049453 0.68188266
- 53000 0.45073048 -2.1230063 0.056513588 -1.6163256 0.62426353
- 54000 0.44959432 -2.1222829 0.063811706 -1.6094389 0.54386719
- 55000 0.45132261 -2.1279628 0.064303102 -1.6129012 0.64603693
- 56000 0.43984398 -2.1089368 0.073286695 -1.596356 0.68889946
- 57000 0.44087794 -2.1314477 0.062602042 -1.6285188 0.58345594
- 58000 0.45 -2.1366398 0.055525068 -1.6316773 0.46829877
- 59000 0.45897732 -2.1226343 0.055496441 -1.6087343 0.62440113
- 60000 0.46465277 -2.1313407 0.05734796 -1.6099208 0.4918466
-Loop time of 25.4217 on 1 procs for 60000 steps with 1200 atoms
-
-Pair time (%) = 17.848 (70.2078)
-Bond time (%) = 1.20659 (4.74631)
-Neigh time (%) = 3.04688 (11.9853)
-Comm time (%) = 0.550053 (2.16371)
-Outpt time (%) = 0.200696 (0.789469)
-Other time (%) = 2.56947 (10.1074)
-
-Nlocal: 1200 ave 1200 max 1200 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 402 ave 402 max 402 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 9819 ave 9819 max 9819 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 9819
-Ave neighs/atom = 8.1825
-Ave special neighs/atom = 0.5
-Neighbor list builds = 4883
-Dangerous builds = 0
diff --git a/examples/micelle/log.micelle.22Jan08.linux.4 b/examples/micelle/log.micelle.22Jan08.linux.4
deleted file mode 100644
index 79e0799c9..000000000
--- a/examples/micelle/log.micelle.22Jan08.linux.4
+++ /dev/null
@@ -1,200 +0,0 @@
-LAMMPS (22 Jan 2008)
-# 2d micelle simulation
-
-dimension 2
-
-neighbor 0.3 bin
-neigh_modify delay 5
-
-atom_style bond
-
-# Soft potential push-off
-
-read_data data.micelle
- 1 = max bonds/atom
- orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
- 2 by 2 by 1 processor grid
- 1200 atoms
- 300 bonds
- 2 = max # of 1-2 neighbors
- 1 = max # of 1-3 neighbors
- 1 = max # of 1-4 neighbors
- 2 = max # of special neighbors
-special_bonds 0 1 1
- 2 = max # of 1-2 neighbors
- 2 = max # of special neighbors
-
-pair_style soft 1.12246
-pair_coeff * * 1.0 20.0 1.12246
-
-bond_style harmonic
-bond_coeff 1 50.0 0.75
-
-velocity all create 0.45 2349852
-
-fix 1 all nve
-fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
-fix 3 all enforce2d
-
-thermo 50
-run 1000
-Memory usage per processor = 2.07665 Mbytes
-Step Temp E_pair E_mol TotEng Press
- 0 0.45 0.40003481 2.2200223e-06 0.84947453 0.78935018
- 50 0.47417944 0.67716204 0.057387153 1.2081359 1.3374428
- 100 0.45 0.73037684 0.054821983 1.2346363 2.3192865
- 150 0.67532546 0.72388376 0.043478036 1.4418431 2.8741848
- 200 0.45 0.78466058 0.076912805 1.3110109 3.0409372
- 250 0.66488946 0.69771453 0.081047682 1.4428206 3.6911924
- 300 0.45 0.76794745 0.066716745 1.2841017 3.7855266
- 350 0.67629601 0.62549506 0.072636862 1.3735826 4.2848322
- 400 0.45 0.68493339 0.090717081 1.225088 4.4713609
- 450 0.56732174 0.64322231 0.080690687 1.2905256 4.7372687
- 500 0.45 0.64764573 0.078468194 1.1755514 4.7911172
- 550 0.56476697 0.58160926 0.080519682 1.22619 4.9721793
- 600 0.45 0.58331363 0.088243449 1.1209946 5.131088
- 650 0.5229482 0.54530348 0.09321673 1.1608147 5.2637478
- 700 0.45 0.52374674 0.085166964 1.0583512 5.2922505
- 750 0.51528063 0.48974532 0.086434828 1.0908167 5.3858022
- 800 0.45 0.50467091 0.090255509 1.0443639 5.5801625
- 850 0.4950534 0.48512921 0.091950432 1.0715142 5.6661389
- 900 0.45 0.48352312 0.097223467 1.0301841 5.7149691
- 950 0.49451225 0.46619517 0.094098428 1.0541877 5.8766965
- 1000 0.45 0.46260893 0.10106179 1.0131082 5.8616912
-Loop time of 0.490955 on 4 procs for 1000 steps with 1200 atoms
-
-Pair time (%) = 0.0608874 (12.4018)
-Bond time (%) = 0.00615633 (1.25395)
-Neigh time (%) = 0.00803632 (1.63687)
-Comm time (%) = 0.342579 (69.7779)
-Outpt time (%) = 0.00870401 (1.77287)
-Other time (%) = 0.0645928 (13.1565)
-
-Nlocal: 300 ave 302 max 294 min
-Histogram: 1 0 0 0 0 0 0 0 0 3
-Nghost: 101.75 ave 105 max 100 min
-Histogram: 1 0 2 0 0 0 0 0 0 1
-Neighs: 794 ave 811 max 774 min
-Histogram: 1 0 0 0 1 0 0 1 0 1
-
-Total # of neighbors = 3176
-Ave neighs/atom = 2.64667
-Ave special neighs/atom = 0.5
-Neighbor list builds = 93
-Dangerous builds = 0
-
-# Main run
-
-pair_style lj/cut 2.5
-
-# solvent/head - full-size and long-range
-
-pair_coeff 1 1 1.0 1.0 2.5
-pair_coeff 2 2 1.0 1.0 2.5
-pair_coeff 1 2 1.0 1.0 2.5
-
-# tail/tail - size-averaged and long-range
-
-pair_coeff 3 3 1.0 0.75 2.5
-pair_coeff 4 4 1.0 0.50 2.5
-pair_coeff 3 4 1.0 0.67 2.5
-
-# solvent/tail - full-size and repulsive
-
-pair_coeff 1 3 1.0 1.0 1.12246
-pair_coeff 1 4 1.0 1.0 1.12246
-
-# head/tail - size-averaged and repulsive
-
-pair_coeff 2 3 1.0 0.88 1.12246
-pair_coeff 2 4 1.0 0.75 1.12246
-
-thermo 1000
-dump 1 all atom 500 dump.micelle
-
-reset_timestep 0
-run 60000
-Memory usage per processor = 2.08821 Mbytes
-Step Temp E_pair E_mol TotEng Press
- 0 0.45 -1.6864322 0.10106179 -1.1359329 3.7913551
- 1000 0.44913925 -1.9350607 0.071368027 -1.4151148 2.1469799
- 2000 0.46330233 -2.0109066 0.060062476 -1.4881209 1.5324898
- 3000 0.45558043 -2.0007635 0.059797299 -1.4859552 1.5702601
- 4000 0.45220563 -2.0072356 0.056527027 -1.4990682 1.638398
- 5000 0.44785006 -2.0311932 0.060134137 -1.5237688 1.230184
- 6000 0.45771088 -2.0463288 0.069315928 -1.5198741 1.2460547
- 7000 0.46138508 -2.0487713 0.057977884 -1.529985 1.2468528
- 8000 0.44559611 -2.0638065 0.062625272 -1.5561421 1.20002
- 9000 0.45 -2.061874 0.056615058 -1.5558214 1.1272832
- 10000 0.45166111 -2.0830577 0.057737309 -1.5742238 0.97887077
- 11000 0.44698685 -2.069784 0.055068221 -1.5682876 1.0177951
- 12000 0.46301669 -2.0580068 0.055605722 -1.5399631 1.1559766
- 13000 0.44484462 -2.0819608 0.061742828 -1.5759295 0.93700282
- 14000 0.44041342 -2.0635971 0.057739522 -1.5659947 1.0577447
- 15000 0.44729718 -2.0913481 0.065605983 -1.579004 0.87294698
- 16000 0.44435529 -2.0663697 0.060050789 -1.5625191 1.0631116
- 17000 0.44386777 -2.0903336 0.059516752 -1.587504 0.81739013
- 18000 0.45689902 -2.0971983 0.054107571 -1.5867628 0.71897374
- 19000 0.4472909 -2.0884034 0.058274968 -1.5833967 0.95673839
- 20000 0.44814664 -2.0845781 0.048930184 -1.5880615 0.80827939
- 21000 0.44928982 -2.1002512 0.053169424 -1.5983536 0.87819514
- 22000 0.44789387 -2.0897931 0.052822646 -1.5896365 0.98715706
- 23000 0.4433766 -2.0885794 0.066555201 -1.5792019 0.89898598
- 24000 0.44312667 -2.0861432 0.063151224 -1.5804193 0.95502225
- 25000 0.44098155 -2.0862551 0.059710845 -1.5861139 0.91917278
- 26000 0.45495856 -2.1061747 0.062767897 -1.5890169 0.77211421
- 27000 0.4594986 -2.0958799 0.055287838 -1.5816679 0.71488348
- 28000 0.4575183 -2.1105669 0.057934393 -1.5956861 0.73787599
- 29000 0.45421662 -2.0756975 0.057553024 -1.5644956 0.74039524
- 30000 0.4585136 -2.1105471 0.065985026 -1.5866216 0.73259472
- 31000 0.44753589 -2.0917336 0.063360868 -1.5813962 0.84906857
- 32000 0.44032392 -2.0946933 0.062048876 -1.5928709 0.85477256
- 33000 0.46201854 -2.1053574 0.05975115 -1.5841652 0.83818932
- 34000 0.44113983 -2.0919028 0.057435684 -1.5938787 0.85594396
- 35000 0.44618448 -2.1018231 0.067168229 -1.5890281 0.83395278
- 36000 0.44369159 -2.1069618 0.062019195 -1.6018056 0.78846571
- 37000 0.45 -2.1114624 0.058110601 -1.6039143 0.7636489
- 38000 0.4467252 -2.1236195 0.05737899 -1.6200737 0.66412548
- 39000 0.45340978 -2.0949326 0.064106121 -1.5779835 0.78205295
- 40000 0.45764316 -2.1083827 0.067605249 -1.5837063 0.52832333
- 41000 0.44990529 -2.1093636 0.060159079 -1.5998616 0.73739844
- 42000 0.43206581 -2.11498 0.0601205 -1.6233338 0.62095123
- 43000 0.45994792 -2.1258732 0.066327507 -1.6001727 0.65184873
- 44000 0.44630971 -2.1233109 0.060169292 -1.6173898 0.40001409
- 45000 0.46411804 -2.0884843 0.059218361 -1.5657281 0.79695879
- 46000 0.43537118 -2.0998107 0.059065989 -1.6059177 0.81031265
- 47000 0.43358801 -2.0923508 0.063011733 -1.5962931 0.80685805
- 48000 0.43269029 -2.1137973 0.064359382 -1.6172885 0.58880044
- 49000 0.45152462 -2.1061598 0.051956693 -1.6032429 0.60144086
- 50000 0.44478646 -2.1149128 0.061234138 -1.6094482 0.6469632
- 51000 0.45019705 -2.1220268 0.060861152 -1.6115313 0.64270507
- 52000 0.43441062 -2.1002627 0.061381281 -1.6050138 0.59292368
- 53000 0.45987875 -2.1235389 0.061089767 -1.6031452 0.63069651
- 54000 0.46481074 -2.1279595 0.064073893 -1.5996559 0.51751117
- 55000 0.44094766 -2.1099173 0.060438881 -1.609082 0.74322185
- 56000 0.46544759 -2.1154714 0.05368944 -1.5969162 0.69683289
- 57000 0.44210658 -2.1087889 0.061886033 -1.6053489 0.74955564
- 58000 0.44315581 -2.1143795 0.062404579 -1.609373 0.69155981
- 59000 0.44795459 -2.120618 0.061673573 -1.6115498 0.70340021
- 60000 0.44468469 -2.1226864 0.068304275 -1.6102533 0.67010695
-Loop time of 31.6764 on 4 procs for 60000 steps with 1200 atoms
-
-Pair time (%) = 5.20959 (16.4463)
-Bond time (%) = 0.359324 (1.13436)
-Neigh time (%) = 0.83879 (2.648)
-Comm time (%) = 20.8686 (65.8808)
-Outpt time (%) = 0.261901 (0.826802)
-Other time (%) = 4.13813 (13.0638)
-
-Nlocal: 300 ave 308 max 294 min
-Histogram: 2 0 0 0 0 0 0 1 0 1
-Nghost: 221.75 ave 228 max 206 min
-Histogram: 1 0 0 0 0 0 0 0 0 3
-Neighs: 2402.25 ave 2457 max 2258 min
-Histogram: 1 0 0 0 0 0 0 0 0 3
-
-Total # of neighbors = 9609
-Ave neighs/atom = 8.0075
-Ave special neighs/atom = 0.5
-Neighbor list builds = 4871
-Dangerous builds = 0
diff --git a/examples/min/in.min b/examples/min/in.min
index 73a71439f..5001f30ac 100644
--- a/examples/min/in.min
+++ b/examples/min/in.min
@@ -1,34 +1,35 @@
# 2d Lennard-Jones melt and subsequent energy minimization
units lj
dimension 2
-boundary s s p
atom_style atomic
lattice sq2 0.8442
region box block 0 20 0 20 -0.1 0.1
create_box 1 box
create_atoms 1 box
mass 1 1.0
velocity all create 5.0 87287 loop geom
pair_style lj/cut 2.5
-pair_coeff 1 1 1.0 1.0
+pair_coeff 1 1 1.0 1.0 2.5
pair_modify shift yes
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
-fix 2 all wall/reflect xlo xhi ylo yhi
-fix 3 all enforce2d
+fix 2 all enforce2d
-dump 1 all atom 50 dump.min
+dump 1 all atom 100 dump.min
thermo 100
-run 500
+run 1000
-min_style cg
-minimize 1.0e-16 1.0e-16 2000 20000
+neigh_modify delay 0 every 1 check yes
+
+dump_modify 1 every 25
+thermo 50
+minimize 1.0e-6 0.001 1000 10000
diff --git a/examples/min/log.min.21May08.linux.1 b/examples/min/log.min.21May08.linux.1
new file mode 100644
index 000000000..c1c6a8feb
--- /dev/null
+++ b/examples/min/log.min.21May08.linux.1
@@ -0,0 +1,113 @@
+LAMMPS (21 May 2008)
+# 2d Lennard-Jones melt and subsequent energy minimization
+
+units lj
+dimension 2
+atom_style atomic
+
+lattice sq2 0.8442
+Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
+region box block 0 20 0 20 -0.1 0.1
+create_box 1 box
+Created orthogonal box = (0 0 -0.153919) to (30.7838 30.7838 0.153919)
+ 1 by 1 by 1 processor grid
+create_atoms 1 box
+Created 800 atoms
+mass 1 1.0
+
+velocity all create 5.0 87287 loop geom
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+pair_modify shift yes
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nve
+fix 2 all enforce2d
+
+dump 1 all atom 100 dump.min
+
+thermo 100
+
+run 1000
+Memory usage per processor = 1.70423 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 5 -2.461717 0 2.532033 5.0190509
+ 100 3.2788864 -0.74311698 0 2.5316708 15.912832
+ 200 3.3041082 -0.77000277 0 2.5299752 15.602653
+ 300 3.3840228 -0.84859211 0 2.5312006 15.188203
+ 400 3.3916063 -0.85694601 0 2.5304208 15.383853
+ 500 3.3136052 -0.77935263 0 2.5301106 15.833296
+ 600 3.3888915 -0.85213741 0 2.532518 15.162759
+ 700 3.2123658 -0.67642058 0 2.5319297 16.31058
+ 800 3.3016845 -0.76574803 0 2.5318094 15.639063
+ 900 3.4631643 -0.92710879 0 2.5317266 14.770503
+ 1000 3.3142629 -0.77918518 0 2.5309349 15.655215
+Loop time of 0.347704 on 1 procs for 1000 steps with 800 atoms
+
+Pair time (%) = 0.232571 (66.8876)
+Neigh time (%) = 0.0642586 (18.4808)
+Comm time (%) = 0.00830054 (2.38724)
+Outpt time (%) = 0.0115886 (3.33289)
+Other time (%) = 0.0309854 (8.91142)
+
+Nlocal: 800 ave 800 max 800 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 316 ave 316 max 316 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 7741 ave 7741 max 7741 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 7741
+Ave neighs/atom = 9.67625
+Neighbor list builds = 203
+Dangerous builds = 0
+
+neigh_modify delay 0 every 1 check yes
+
+dump_modify 1 every 25
+thermo 50
+minimize 1.0e-6 0.001 1000 10000
+Memory usage per processor = 2.16199 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 1000 3.3142629 -0.77918518 0 2.5309349 15.655215
+ 1050 3.3142629 -2.8169324 0 0.49318768 1.6991832
+ 1100 3.3142629 -2.861172 0 0.4489481 1.6197458
+ 1150 3.3142629 -2.8697401 0 0.44037994 1.6413078
+ 1200 3.3142629 -2.8763859 0 0.4337342 1.5869118
+ 1250 3.3142629 -2.8934188 0 0.41670128 1.5990139
+ 1300 3.3142629 -2.8965883 0 0.41353175 1.654921
+ 1350 3.3142629 -2.8980407 0 0.41207941 1.6792847
+ 1400 3.3142629 -2.902264 0 0.40785611 1.6884403
+ 1450 3.3142629 -2.9064602 0 0.40365988 1.7024527
+ 1468 3.3142629 -2.9066747 0 0.40344535 1.7059968
+Loop time of 0.777846 on 1 procs for 468 steps with 800 atoms
+
+Minimization stats:
+ Stopping criterion = energy tolerance
+ Energy initial, next-to-last, final =
+ -0.779185181879 -2.90667292007 -2.90667472402
+ Force two-norm initial, final = 1916.37 0.710061
+ Force max component initial, final = 301.855 0.315889
+ Final line search alpha, max atom move = 0.00526935 0.00166453
+ Iterations, force evaluations = 468 1861
+
+Pair time (%) = 0.671168 (86.2855)
+Neigh time (%) = 0.0293589 (3.77438)
+Comm time (%) = 0.010078 (1.29562)
+Outpt time (%) = 0.0204384 (2.62757)
+Other time (%) = 0.0468025 (6.01694)
+
+Nlocal: 800 ave 800 max 800 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 319 ave 319 max 319 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 7004 ave 7004 max 7004 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 7004
+Ave neighs/atom = 8.755
+Neighbor list builds = 93
+Dangerous builds = 0
diff --git a/examples/min/log.min.21May08.linux.4 b/examples/min/log.min.21May08.linux.4
new file mode 100644
index 000000000..f798ad5d5
--- /dev/null
+++ b/examples/min/log.min.21May08.linux.4
@@ -0,0 +1,110 @@
+LAMMPS (21 May 2008)
+# 2d Lennard-Jones melt and subsequent energy minimization
+
+units lj
+dimension 2
+atom_style atomic
+
+lattice sq2 0.8442
+Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
+region box block 0 20 0 20 -0.1 0.1
+create_box 1 box
+Created orthogonal box = (0 0 -0.153919) to (30.7838 30.7838 0.153919)
+ 2 by 2 by 1 processor grid
+create_atoms 1 box
+Created 800 atoms
+mass 1 1.0
+
+velocity all create 5.0 87287 loop geom
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+pair_modify shift yes
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nve
+fix 2 all enforce2d
+
+dump 1 all atom 100 dump.min
+
+thermo 100
+
+run 1000
+Memory usage per processor = 1.67966 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 5 -2.461717 0 2.532033 5.0190509
+ 100 3.2788864 -0.74311698 0 2.5316708 15.912832
+ 200 3.3041082 -0.77000277 0 2.5299752 15.602653
+ 300 3.3840228 -0.84859211 0 2.5312006 15.188203
+ 400 3.3916063 -0.85694601 0 2.5304208 15.383853
+ 500 3.3136052 -0.77935264 0 2.5301106 15.833296
+ 600 3.3888915 -0.85213742 0 2.532518 15.162759
+ 700 3.2123644 -0.67641922 0 2.5319297 16.310586
+ 800 3.3016549 -0.7657205 0 2.5318073 15.639175
+ 900 3.4620767 -0.92601725 0 2.5317318 14.773629
+ 1000 3.287472 -0.75213644 0 2.5312262 15.801806
+Loop time of 0.540854 on 4 procs for 1000 steps with 800 atoms
+
+Pair time (%) = 0.0630118 (11.6504)
+Neigh time (%) = 0.017717 (3.27575)
+Comm time (%) = 0.35042 (64.7901)
+Outpt time (%) = 0.020339 (3.76053)
+Other time (%) = 0.089366 (16.5231)
+
+Nlocal: 200 ave 202 max 198 min
+Histogram: 1 0 1 0 0 0 0 1 0 1
+Nghost: 170.5 ave 177 max 167 min
+Histogram: 1 0 2 0 0 0 0 0 0 1
+Neighs: 1938 ave 1962 max 1890 min
+Histogram: 1 0 0 0 0 0 0 1 0 2
+
+Total # of neighbors = 7752
+Ave neighs/atom = 9.69
+Neighbor list builds = 203
+Dangerous builds = 0
+
+neigh_modify delay 0 every 1 check yes
+
+dump_modify 1 every 25
+thermo 50
+minimize 1.0e-6 0.001 1000 10000
+Memory usage per processor = 2.1377 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 1000 3.287472 -0.75213644 0 2.5312262 15.801806
+ 1050 3.287472 -2.8165208 0 0.46684181 1.6792079
+ 1100 3.287472 -2.8541112 0 0.42925141 1.6761282
+ 1150 3.287472 -2.8666373 0 0.4167253 1.6812573
+ 1200 3.287472 -2.8718121 0 0.41155051 1.6994149
+ 1250 3.287472 -2.8734488 0 0.40991379 1.7128405
+ 1300 3.287472 -2.877455 0 0.40590759 1.7118991
+ 1326 3.287472 -2.8781184 0 0.40524418 1.710365
+Loop time of 0.745146 on 4 procs for 326 steps with 800 atoms
+
+Minimization stats:
+ Stopping criterion = energy tolerance
+ Energy initial, next-to-last, final =
+ -0.752136436206 -2.87811588622 -2.8781184428
+ Force two-norm initial, final = 1981.45 0.760495
+ Force max component initial, final = 387.785 0.166498
+ Final line search alpha, max atom move = 0.00240665 0.000400702
+ Iterations, force evaluations = 326 1206
+
+Pair time (%) = 0.112617 (15.1134)
+Neigh time (%) = 0.00467056 (0.626798)
+Comm time (%) = 0.36602 (49.1206)
+Outpt time (%) = 0.019726 (2.64726)
+Other time (%) = 0.242112 (32.4919)
+
+Nlocal: 200 ave 204 max 197 min
+Histogram: 1 0 1 0 1 0 0 0 0 1
+Nghost: 172.25 ave 175 max 167 min
+Histogram: 1 0 0 0 0 0 0 1 1 1
+Neighs: 1760.5 ave 1791 max 1732 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+
+Total # of neighbors = 7042
+Ave neighs/atom = 8.8025
+Neighbor list builds = 54
+Dangerous builds = 0
diff --git a/examples/min/log.min.22Jan08.linux.1 b/examples/min/log.min.22Jan08.linux.1
deleted file mode 100644
index 794fde37f..000000000
--- a/examples/min/log.min.22Jan08.linux.1
+++ /dev/null
@@ -1,107 +0,0 @@
-LAMMPS (22 Jan 2008)
-# 2d Lennard-Jones melt and subsequent energy minimization
-
-units lj
-dimension 2
-boundary s s p
-atom_style atomic
-
-lattice sq2 0.8442
-Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
-region box block 0 20 0 20 -0.1 0.1
-create_box 1 box
-Created orthogonal box = (0 0 -0.153919) to (30.7838 30.7838 0.153919)
- 1 by 1 by 1 processor grid
-create_atoms 1 box
-Created 841 atoms
-mass 1 1.0
-
-velocity all create 5.0 87287 loop geom
-
-pair_style lj/cut 2.5
-pair_coeff 1 1 1.0 1.0
-pair_modify shift yes
-
-neighbor 0.3 bin
-neigh_modify delay 0 every 1 check yes
-
-fix 1 all nve
-fix 2 all wall/reflect xlo xhi ylo yhi
-fix 3 all enforce2d
-
-dump 1 all atom 50 dump.min
-
-thermo 100
-
-run 500
-Memory usage per processor = 1.69054 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume
- 0 5 -2.3392224 0 2.6518596 5.2514392 947.65505
- 100 3.3097379 -0.63883378 0 2.6650009 17.070807 943.40014
- 200 3.3080762 -0.6288886 0 2.6732874 17.04277 941.19268
- 300 3.3787956 -0.69098843 0 2.6817808 16.831266 939.23341
- 400 3.3724983 -0.65871066 0 2.7077725 17.321124 935.66558
- 500 3.2655218 -0.53947527 0 2.7202221 17.961553 933.59779
-Loop time of 0.178504 on 1 procs for 500 steps with 841 atoms
-
-Pair time (%) = 0.115572 (64.7446)
-Neigh time (%) = 0.0305917 (17.1378)
-Comm time (%) = 0.000834465 (0.467477)
-Outpt time (%) = 0.012027 (6.73768)
-Other time (%) = 0.019479 (10.9124)
-
-Nlocal: 841 ave 841 max 841 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: 7729 ave 7729 max 7729 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 7729
-Ave neighs/atom = 9.19025
-Neighbor list builds = 100
-Dangerous builds = 0
-
-min_style cg
-minimize 1.0e-16 1.0e-16 2000 20000
-Memory usage per processor = 2.1483 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume
- 500 3.2655218 -0.53947527 0 2.7202221 17.962424 933.55255
- 600 3.2655218 -2.7918184 0 0.467879 2.3687829 978.86967
- 700 3.2655218 -2.8484405 0 0.41125693 2.5617944 970.87845
- 800 3.2655218 -2.8653234 0 0.39437404 2.8341532 959.29931
- 900 3.2655218 -2.8709903 0 0.3887071 2.8615917 957.77926
- 1000 3.2655218 -2.875841 0 0.38385645 2.8424963 962.97893
- 1100 3.2655218 -2.8773559 0 0.38234149 2.8331831 966.27062
- 1200 3.2655218 -2.8779916 0 0.38170577 2.8383813 966.23993
- 1300 3.2655218 -2.877995 0 0.38170241 2.8377343 966.07015
- 1400 3.2655218 -2.8779951 0 0.38170231 2.8385866 965.76227
- 1500 3.2655218 -2.8779951 0 0.38170231 2.8358421 966.69888
-Loop time of 2.96182 on 1 procs for 1000 steps with 841 atoms
-
-Minimization stats:
- Stopping criterion = energy tolerance
- Energy initial, next-to-last, final =
- -0.5394752732 -2.87799510218 -2.87799510218
- Force two-norm initial, final = 2031.66 4.61875e-05
- Force max component initial, final = 297.987 7.7681e-06
- Final line search alpha, max atom move = 1.40663e-08 1.09269e-13
- Iterations, force evaluations = 1000 7616
-
-Pair time (%) = 2.67288 (90.2446)
-Neigh time (%) = 0.0491631 (1.65989)
-Comm time (%) = 0.00455403 (0.153758)
-Outpt time (%) = 0.0223653 (0.755121)
-Other time (%) = 0.212854 (7.18659)
-
-Nlocal: 841 ave 841 max 841 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: 7067 ave 7067 max 7067 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 7067
-Ave neighs/atom = 8.40309
-Neighbor list builds = 159
-Dangerous builds = 0
diff --git a/examples/min/log.min.22Jan08.linux.4 b/examples/min/log.min.22Jan08.linux.4
deleted file mode 100644
index 3453c2ff7..000000000
--- a/examples/min/log.min.22Jan08.linux.4
+++ /dev/null
@@ -1,115 +0,0 @@
-LAMMPS (22 Jan 2008)
-# 2d Lennard-Jones melt and subsequent energy minimization
-
-units lj
-dimension 2
-boundary s s p
-atom_style atomic
-
-lattice sq2 0.8442
-Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
-region box block 0 20 0 20 -0.1 0.1
-create_box 1 box
-Created orthogonal box = (0 0 -0.153919) to (30.7838 30.7838 0.153919)
- 2 by 2 by 1 processor grid
-create_atoms 1 box
-Created 841 atoms
-mass 1 1.0
-
-velocity all create 5.0 87287 loop geom
-
-pair_style lj/cut 2.5
-pair_coeff 1 1 1.0 1.0
-pair_modify shift yes
-
-neighbor 0.3 bin
-neigh_modify delay 0 every 1 check yes
-
-fix 1 all nve
-fix 2 all wall/reflect xlo xhi ylo yhi
-fix 3 all enforce2d
-
-dump 1 all atom 50 dump.min
-
-thermo 100
-
-run 500
-Memory usage per processor = 1.68047 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume
- 0 5 -2.3392224 0 2.6518596 5.2514392 947.65505
- 100 3.3097379 -0.63883378 0 2.6650009 17.070807 943.40014
- 200 3.3080762 -0.6288886 0 2.6732874 17.04277 941.19268
- 300 3.3787956 -0.69098843 0 2.6817808 16.831266 939.23341
- 400 3.3724983 -0.65871066 0 2.7077725 17.321124 935.66558
- 500 3.2655218 -0.53947532 0 2.7202221 17.961553 933.5978
-Loop time of 0.331249 on 4 procs for 500 steps with 841 atoms
-
-Pair time (%) = 0.0336406 (10.1557)
-Neigh time (%) = 0.00937784 (2.83105)
-Comm time (%) = 0.21005 (63.4114)
-Outpt time (%) = 0.0165854 (5.00693)
-Other time (%) = 0.0615957 (18.595)
-
-Nlocal: 210.25 ave 213 max 207 min
-Histogram: 1 0 0 1 0 0 0 0 1 1
-Nghost: 80.5 ave 85 max 78 min
-Histogram: 1 1 1 0 0 0 0 0 0 1
-Neighs: 1932.25 ave 2011 max 1878 min
-Histogram: 1 0 1 0 1 0 0 0 0 1
-
-Total # of neighbors = 7729
-Ave neighs/atom = 9.19025
-Neighbor list builds = 100
-Dangerous builds = 0
-
-min_style cg
-minimize 1.0e-16 1.0e-16 2000 20000
-Memory usage per processor = 2.13823 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume
- 500 3.2655218 -0.53947532 0 2.7202221 17.962423 933.55255
- 600 3.2655218 -2.7937912 0 0.46590627 2.3734536 977.59412
- 700 3.2655218 -2.8475351 0 0.41216236 2.6076008 966.90337
- 800 3.2655218 -2.8642481 0 0.39544933 2.8437164 954.79638
- 900 3.2655218 -2.8694679 0 0.39022957 2.8748519 952.24201
- 1000 3.2655218 -2.8750401 0 0.3846573 2.8381948 952.45791
- 1100 3.2655218 -2.8806997 0 0.37899774 2.8637062 955.32239
- 1200 3.2655218 -2.8828075 0 0.3768899 2.8570958 959.68528
- 1300 3.2655218 -2.8924026 0 0.36729488 2.8365883 960.6309
- 1400 3.2655218 -2.8930364 0 0.36666108 2.8441244 962.40489
- 1500 3.2655218 -2.9003629 0 0.35933455 2.8254524 962.68407
- 1600 3.2655218 -2.9070345 0 0.35266293 2.850024 963.46045
- 1700 3.2655218 -2.9075342 0 0.35216329 2.845873 963.37846
- 1800 3.2655218 -2.9075376 0 0.35215987 2.842893 964.32817
- 1900 3.2655218 -2.9075383 0 0.35215916 2.8397901 965.36065
- 2000 3.2655218 -2.9075383 0 0.35215911 2.8395142 965.44981
- 2100 3.2655218 -2.9075383 0 0.3521591 2.8436298 964.05174
- 2200 3.2655218 -2.9075383 0 0.3521591 2.842818 964.32681
- 2205 3.2655218 -2.9075383 0 0.3521591 2.842818 964.32681
-Loop time of 9.216 on 4 procs for 1705 steps with 841 atoms
-
-Minimization stats:
- Stopping criterion = energy tolerance
- Energy initial, next-to-last, final =
- -0.539475324067 -2.90753834001 -2.90753834001
- Force two-norm initial, final = 2031.66 2.66327e-05
- Force max component initial, final = 297.987 3.89961e-06
- Final line search alpha, max atom move = 7.28834e-10 2.84217e-15
- Iterations, force evaluations = 1705 13427
-
-Pair time (%) = 1.36367 (14.7968)
-Neigh time (%) = 0.031518 (0.341992)
-Comm time (%) = 4.829 (52.398)
-Outpt time (%) = 0.0586754 (0.636669)
-Other time (%) = 2.93313 (31.8265)
-
-Nlocal: 210.25 ave 216 max 203 min
-Histogram: 1 0 0 1 0 0 0 0 1 1
-Nghost: 85 ave 86 max 83 min
-Histogram: 1 0 0 0 0 0 1 0 0 2
-Neighs: 1762.75 ave 1856 max 1582 min
-Histogram: 1 0 0 0 0 0 1 0 0 2
-
-Total # of neighbors = 7051
-Ave neighs/atom = 8.38407
-Neighbor list builds = 333
-Dangerous builds = 0
diff --git a/examples/nemd/log.nemd.21May08.linux.1 b/examples/nemd/log.nemd.21May08.linux.1
new file mode 100644
index 000000000..a7dd5262d
--- /dev/null
+++ b/examples/nemd/log.nemd.21May08.linux.1
@@ -0,0 +1,109 @@
+LAMMPS (21 May 2008)
+# 2d NEMD simulation
+
+units lj
+atom_style atomic
+dimension 2d
+
+lattice sq2 0.8442
+Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
+region box prism 0 10 0 8 -0.5 0.5 0 0 0
+create_box 2 box
+Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
+ 1 by 1 by 1 processor grid
+create_atoms 1 box
+Created 160 atoms
+mass * 1.0
+
+velocity all create 1.44 87287 loop geom
+
+region slice block 4 6 INF INF INF INF
+set region slice type 2
+ 40 settings made for type
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0 1.0
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1
+
+fix 1 all nvt/sllod 1.0 1.0 1.0
+fix 2 all deform 1 xy erate 0.01 remap v
+
+dump 1 all custom 500 dump.nemd tag type x y z
+
+thermo 1000
+
+run 50000
+Memory usage per processor = 1.79413 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 1.44 0 0 1.431 1.2080502 189.52855
+ 1000 1.201216 0.22081306 0 1.4145215 5.812072 189.52855
+ 2000 1.1053634 0.34245325 0 1.4409081 7.2538039 189.52855
+ 3000 1.0369584 0.33062855 0 1.361106 6.660302 189.52855
+ 4000 1.0763793 0.2937252 0 1.3633772 6.8420884 189.52855
+ 5000 0.99089378 0.28590111 0 1.2706018 6.429982 189.52855
+ 6000 1.0307968 0.23016743 0 1.2545218 5.5964388 189.52855
+ 7000 0.88642282 0.28517029 0 1.166053 6.0559882 189.52855
+ 8000 0.95680641 0.19899612 0 1.1498225 4.9970284 189.52855
+ 9000 0.82948739 0.23322237 0 1.0575255 6.1567415 189.52855
+ 10000 0.8669664 0.21075772 0 1.0723056 5.530127 189.52855
+ 11000 0.82083041 0.23243452 0 1.0481347 5.755917 189.52855
+ 12000 0.87146711 0.19031553 0 1.056336 4.9189315 189.52855
+ 13000 0.87563025 0.23281315 0 1.1029707 5.3535722 189.52855
+ 14000 0.93356309 0.21105622 0 1.1387845 5.522022 189.52855
+ 15000 0.90866689 0.25933437 0 1.1623221 6.0137405 189.52855
+ 16000 1.0336736 0.24068668 0 1.2678999 6.0482803 189.52855
+ 17000 1.0277848 0.25504818 0 1.2764093 6.2722003 189.52855
+ 18000 1.0364869 0.26178553 0 1.2917944 5.7429124 189.52855
+ 19000 0.94527034 0.38926601 0 1.3286284 6.5023984 189.52855
+ 20000 1.0274028 0.31347493 0 1.3344564 7.0482764 189.52855
+ 21000 1.1191047 0.25917341 0 1.3712837 5.6562822 189.52855
+ 22000 1.0422655 0.34401979 0 1.3797711 6.3526729 189.52855
+ 23000 1.0321083 0.29206781 0 1.3177254 6.2154608 189.52855
+ 24000 1.0244771 0.32519735 0 1.3432715 6.6907816 189.52855
+ 25000 1.0657586 0.33274044 0 1.3918381 6.8894346 189.52855
+ 26000 1.1356479 0.23644778 0 1.3649979 5.4008811 189.52855
+ 27000 1.0630847 0.28714545 0 1.3435858 6.648475 189.52855
+ 28000 1.0803365 0.27113962 0 1.344724 6.7677826 189.52855
+ 29000 1.1410108 0.20529094 0 1.3391704 5.982283 189.52855
+ 30000 1.1917679 0.23409944 0 1.4184188 5.6963971 189.52855
+ 31000 1.0831878 0.36265238 0 1.4390702 7.2461956 189.52855
+ 32000 1.1345617 0.287766 0 1.4152367 6.4520365 189.52855
+ 33000 0.99110806 0.36761581 0 1.3525294 7.1366759 189.52855
+ 34000 1.078312 0.27340897 0 1.3449816 6.3911521 189.52855
+ 35000 0.99660085 0.36948608 0 1.3598582 7.5812397 189.52855
+ 36000 1.0144204 0.34392112 0 1.3520014 7.5639539 189.52855
+ 37000 0.98694344 0.28582689 0 1.2666019 6.6959949 189.52855
+ 38000 1.0024714 0.27282321 0 1.2690291 6.6264321 189.52855
+ 39000 0.97207374 0.25235501 0 1.2183533 6.4007459 189.52855
+ 40000 0.92812395 0.269067 0 1.1913902 6.3556929 189.52855
+ 41000 0.97149408 0.279107 0 1.2445292 6.0646852 189.52855
+ 42000 1.0134876 0.25321709 0 1.2603704 5.6813022 189.52855
+ 43000 0.92625362 0.25866794 0 1.1791325 5.5152806 189.52855
+ 44000 0.97786941 0.20193469 0 1.1736924 5.2346171 189.52855
+ 45000 0.92077813 0.20916856 0 1.1241918 5.3582525 189.52855
+ 46000 0.98568366 0.21767436 0 1.1971975 5.0698867 189.52855
+ 47000 0.98658256 0.24457963 0 1.224996 5.5310436 189.52855
+ 48000 1.0444714 0.24354858 0 1.281492 5.167352 189.52855
+ 49000 1.0009963 0.28263617 0 1.2773762 6.3125521 189.52855
+ 50000 1.0897606 0.2494605 0 1.3324101 6.4210283 189.52855
+Loop time of 1.6234 on 1 procs for 50000 steps with 160 atoms
+
+Pair time (%) = 0.317492 (19.5573)
+Neigh time (%) = 0.18852 (11.6127)
+Comm time (%) = 0.0984259 (6.06296)
+Outpt time (%) = 0.0293596 (1.80853)
+Other time (%) = 0.989599 (60.9585)
+
+Nlocal: 160 ave 160 max 160 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 61 ave 61 max 61 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 361 ave 361 max 361 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 361
+Ave neighs/atom = 2.25625
+Neighbor list builds = 5054
+Dangerous builds = 0
diff --git a/examples/nemd/log.nemd.21May08.linux.4 b/examples/nemd/log.nemd.21May08.linux.4
new file mode 100644
index 000000000..f3a045f07
--- /dev/null
+++ b/examples/nemd/log.nemd.21May08.linux.4
@@ -0,0 +1,109 @@
+LAMMPS (21 May 2008)
+# 2d NEMD simulation
+
+units lj
+atom_style atomic
+dimension 2d
+
+lattice sq2 0.8442
+Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
+region box prism 0 10 0 8 -0.5 0.5 0 0 0
+create_box 2 box
+Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
+ 2 by 2 by 1 processor grid
+create_atoms 1 box
+Created 160 atoms
+mass * 1.0
+
+velocity all create 1.44 87287 loop geom
+
+region slice block 4 6 INF INF INF INF
+set region slice type 2
+ 40 settings made for type
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0 1.0
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1
+
+fix 1 all nvt/sllod 1.0 1.0 1.0
+fix 2 all deform 1 xy erate 0.01 remap v
+
+dump 1 all custom 500 dump.nemd tag type x y z
+
+thermo 1000
+
+run 50000
+Memory usage per processor = 1.78793 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 1.44 0 0 1.431 1.2080502 189.52855
+ 1000 1.1697926 0.21325256 0 1.3757339 5.2080616 189.52855
+ 2000 1.0171912 0.29202538 0 1.3028591 6.2516963 189.52855
+ 3000 0.99202333 0.30099879 0 1.286822 7.1377169 189.52855
+ 4000 0.99232557 0.27498873 0 1.2611123 6.0634528 189.52855
+ 5000 0.97745735 0.29346168 0 1.2648099 6.6231602 189.52855
+ 6000 0.96324554 0.2806326 0 1.2378579 6.0791693 189.52855
+ 7000 0.99859204 0.21058692 0 1.2029378 5.312413 189.52855
+ 8000 1.0109566 0.19053005 0 1.1951682 5.114073 189.52855
+ 9000 0.95156948 0.32960966 0 1.2752318 6.5200852 189.52855
+ 10000 1.0191357 0.31557253 0 1.3283386 7.1244854 189.52855
+ 11000 1.1018622 0.26166595 0 1.3566415 6.0071258 189.52855
+ 12000 0.95953724 0.32378335 0 1.2773235 6.5580551 189.52855
+ 13000 0.99604838 0.28112532 0 1.2709484 5.8429234 189.52855
+ 14000 0.98563574 0.26169744 0 1.241173 6.4164311 189.52855
+ 15000 0.92737672 0.33493597 0 1.2565166 6.6062138 189.52855
+ 16000 0.95376077 0.33825777 0 1.2860575 7.4237304 189.52855
+ 17000 1.1011389 0.22545271 0 1.3197095 5.7483214 189.52855
+ 18000 0.99936019 0.34579596 0 1.3389102 6.5986774 189.52855
+ 19000 1.0385827 0.34139906 0 1.3734906 7.3725224 189.52855
+ 20000 1.0863768 0.25973407 0 1.3393211 5.719117 189.52855
+ 21000 1.0292233 0.27151556 0 1.2943062 6.2598972 189.52855
+ 22000 0.99429804 0.27141639 0 1.2595001 6.5580982 189.52855
+ 23000 0.94958875 0.21465821 0 1.158312 5.8037305 189.52855
+ 24000 0.88642624 0.20417299 0 1.0850591 5.4317389 189.52855
+ 25000 0.91450961 0.1677748 0 1.0765687 4.817349 189.52855
+ 26000 0.91751663 0.21347568 0 1.1252578 5.2020404 189.52855
+ 27000 0.92235414 0.2743999 0 1.1909893 5.9318744 189.52855
+ 28000 1.0147496 0.21738239 0 1.2257898 5.4243143 189.52855
+ 29000 1.0423796 0.2177307 0 1.2535955 5.9015198 189.52855
+ 30000 1.0918894 0.27418042 0 1.3592455 6.1376946 189.52855
+ 31000 1.0808038 0.34889063 0 1.4229394 6.7579123 189.52855
+ 32000 1.0621686 0.3810462 0 1.4365762 7.6754676 189.52855
+ 33000 1.2846684 0.24383496 0 1.5204741 6.0921751 189.52855
+ 34000 1.1516823 0.36346499 0 1.5079493 7.3192421 189.52855
+ 35000 1.1268604 0.35725077 0 1.4770683 7.0260174 189.52855
+ 36000 1.1843072 0.23214387 0 1.4090491 5.4136742 189.52855
+ 37000 1.0516345 0.32002698 0 1.3650888 6.7995753 189.52855
+ 38000 1.0383111 0.25289855 0 1.2847202 6.0240848 189.52855
+ 39000 0.98462749 0.28564014 0 1.2641137 6.3777186 189.52855
+ 40000 0.87538476 0.36557837 0 1.235492 6.8848323 189.52855
+ 41000 0.98587871 0.26116271 0 1.2408797 6.4161684 189.52855
+ 42000 0.97791927 0.27694735 0 1.2487546 6.3307714 189.52855
+ 43000 0.99292488 0.23856305 0 1.2252821 5.6251966 189.52855
+ 44000 0.84382228 0.3336851 0 1.1722335 6.706324 189.52855
+ 45000 0.97000203 0.24195557 0 1.2058951 5.9593224 189.52855
+ 46000 0.93260381 0.29811871 0 1.2248937 6.2647019 189.52855
+ 47000 0.98928475 0.24566783 0 1.2287695 5.6042505 189.52855
+ 48000 1.0089185 0.2711447 0 1.2737574 6.3042831 189.52855
+ 49000 1.0584424 0.28195041 0 1.3337776 6.5027698 189.52855
+ 50000 1.0404332 0.28577101 0 1.3197015 6.2419453 189.52855
+Loop time of 22.236 on 4 procs for 50000 steps with 160 atoms
+
+Pair time (%) = 0.117888 (0.530169)
+Neigh time (%) = 0.0656884 (0.295415)
+Comm time (%) = 14.7994 (66.5562)
+Outpt time (%) = 0.0774301 (0.34822)
+Other time (%) = 7.17555 (32.27)
+
+Nlocal: 40 ave 41 max 39 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost: 38 ave 39 max 36 min
+Histogram: 1 0 0 0 0 0 1 0 0 2
+Neighs: 88.25 ave 92 max 84 min
+Histogram: 1 0 0 0 0 1 1 0 0 1
+
+Total # of neighbors = 353
+Ave neighs/atom = 2.20625
+Neighbor list builds = 5077
+Dangerous builds = 0
diff --git a/examples/nemd/log.nemd.22Jan08.linux.1 b/examples/nemd/log.nemd.22Jan08.linux.1
deleted file mode 100644
index c65813312..000000000
--- a/examples/nemd/log.nemd.22Jan08.linux.1
+++ /dev/null
@@ -1,109 +0,0 @@
-LAMMPS (22 Jan 2008)
-# 2d NEMD simulation
-
-units lj
-atom_style atomic
-dimension 2d
-
-lattice sq2 0.8442
-Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
-region box prism 0 10 0 8 -0.5 0.5 0 0 0
-create_box 2 box
-Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
- 1 by 1 by 1 processor grid
-create_atoms 1 box
-Created 160 atoms
-mass * 1.0
-
-velocity all create 1.44 87287 loop geom
-
-region slice block 4 6 INF INF INF INF
-set region slice type 2
- 40 settings made for type
-
-pair_style lj/cut 2.5
-pair_coeff * * 1.0 1.0 1.0
-
-neighbor 0.3 bin
-neigh_modify delay 0 every 1
-
-fix 1 all nvt/sllod 1.0 1.0 1.0
-fix 2 all deform 1 xy erate 0.01 remap v
-
-dump 1 all custom 500 dump.nemd tag type x y z
-
-thermo 1000
-
-run 50000
-Memory usage per processor = 1.79413 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume
- 0 1.44 0 0 1.4265 1.2042513 189.52855
- 1000 1.1957714 0.24426867 0 1.4288297 5.6293729 189.52855
- 2000 1.0512544 0.36384346 0 1.4052424 7.4695343 189.52855
- 3000 1.1469734 0.23896893 0 1.3751894 5.6807214 189.52855
- 4000 1.0241419 0.33724993 0 1.3517905 7.6685283 189.52855
- 5000 1.0450738 0.3070054 0 1.3422817 6.5793804 189.52855
- 6000 1.0685486 0.28335604 0 1.341887 6.6844393 189.52855
- 7000 1.0897239 0.27389674 0 1.3534045 6.6481088 189.52855
- 8000 1.110529 0.22408733 0 1.3242051 5.6773903 189.52855
- 9000 1.0678619 0.29632567 0 1.3541763 6.3949916 189.52855
- 10000 1.1660924 0.22834951 0 1.3835098 5.5541843 189.52855
- 11000 1.0722384 0.27294548 0 1.3351317 6.4708617 189.52855
- 12000 1.0044103 0.32564577 0 1.3206397 7.2612801 189.52855
- 13000 0.99372325 0.28302395 0 1.2674311 6.7664165 189.52855
- 14000 0.92084625 0.35175684 0 1.2639702 6.8344289 189.52855
- 15000 1.0230407 0.23460993 0 1.2480596 5.8082977 189.52855
- 16000 1.0425501 0.2176758 0 1.250452 4.8674643 189.52855
- 17000 0.97012929 0.27885836 0 1.2398927 6.9865482 189.52855
- 18000 0.9831045 0.26127207 0 1.23516 6.3350937 189.52855
- 19000 0.98620312 0.21991389 0 1.1968714 5.5543736 189.52855
- 20000 1.01412 0.20446778 0 1.2090804 5.0827574 189.52855
- 21000 1.0010437 0.21376483 0 1.2054238 6.1091116 189.52855
- 22000 1.0127807 0.28721144 0 1.2904973 7.0634198 189.52855
- 23000 1.0813249 0.25976823 0 1.3309557 6.0306099 189.52855
- 24000 1.0802637 0.28544909 0 1.3555853 6.3827986 189.52855
- 25000 1.1518499 0.23206633 0 1.3731176 5.8921729 189.52855
- 26000 1.1108836 0.24930877 0 1.3497778 6.1708853 189.52855
- 27000 1.0607825 0.2234288 0 1.2742664 5.7632024 189.52855
- 28000 1.0391552 0.25691356 0 1.2863267 6.0416087 189.52855
- 29000 0.99095631 0.25778565 0 1.2394517 5.4705218 189.52855
- 30000 0.98637444 0.26105776 0 1.2381849 6.0167833 189.52855
- 31000 0.95692196 0.26393713 0 1.2118879 5.8106414 189.52855
- 32000 0.97151292 0.2510554 0 1.2134604 6.663016 189.52855
- 33000 1.0158087 0.26768531 0 1.2739708 6.5506448 189.52855
- 34000 0.95974388 0.31697173 0 1.267718 6.4849664 189.52855
- 35000 1.0527141 0.25903984 0 1.3018848 5.8715406 189.52855
- 36000 0.98256431 0.25872637 0 1.2320791 6.97778 189.52855
- 37000 1.0711558 0.2118975 0 1.2730112 5.5570897 189.52855
- 38000 1.0719782 0.21273864 0 1.274667 5.5745073 189.52855
- 39000 1.081957 0.20776531 0 1.279579 6.1207526 189.52855
- 40000 0.97959574 0.29250154 0 1.2629136 7.0039551 189.52855
- 41000 0.98177341 0.24070052 0 1.2132698 6.2770289 189.52855
- 42000 0.93713907 0.29565793 0 1.2240113 6.8009101 189.52855
- 43000 0.85994766 0.33876002 0 1.1906457 6.3808484 189.52855
- 44000 1.010351 0.24602983 0 1.2469088 6.0770182 189.52855
- 45000 0.98461752 0.25682126 0 1.232208 6.5865262 189.52855
- 46000 0.99366855 0.27489751 0 1.2592504 6.1331616 189.52855
- 47000 0.9723363 0.33478499 0 1.2980056 7.2892199 189.52855
- 48000 0.94450954 0.40945183 0 1.3451066 7.7632521 189.52855
- 49000 1.0821859 0.27329139 0 1.3453318 6.5206906 189.52855
- 50000 1.0229752 0.30045077 0 1.3138355 6.4390946 189.52855
-Loop time of 1.4216 on 1 procs for 50000 steps with 160 atoms
-
-Pair time (%) = 0.320149 (22.5203)
-Neigh time (%) = 0.19033 (13.3884)
-Comm time (%) = 0.0955777 (6.72324)
-Outpt time (%) = 0.0293758 (2.06639)
-Other time (%) = 0.78617 (55.3017)
-
-Nlocal: 160 ave 160 max 160 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 71 ave 71 max 71 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 357 ave 357 max 357 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 357
-Ave neighs/atom = 2.23125
-Neighbor list builds = 5054
-Dangerous builds = 0
diff --git a/examples/nemd/log.nemd.22Jan08.linux.4 b/examples/nemd/log.nemd.22Jan08.linux.4
deleted file mode 100644
index 5bc4a1473..000000000
--- a/examples/nemd/log.nemd.22Jan08.linux.4
+++ /dev/null
@@ -1,109 +0,0 @@
-LAMMPS (22 Jan 2008)
-# 2d NEMD simulation
-
-units lj
-atom_style atomic
-dimension 2d
-
-lattice sq2 0.8442
-Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
-region box prism 0 10 0 8 -0.5 0.5 0 0 0
-create_box 2 box
-Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
- 2 by 2 by 1 processor grid
-create_atoms 1 box
-Created 160 atoms
-mass * 1.0
-
-velocity all create 1.44 87287 loop geom
-
-region slice block 4 6 INF INF INF INF
-set region slice type 2
- 40 settings made for type
-
-pair_style lj/cut 2.5
-pair_coeff * * 1.0 1.0 1.0
-
-neighbor 0.3 bin
-neigh_modify delay 0 every 1
-
-fix 1 all nvt/sllod 1.0 1.0 1.0
-fix 2 all deform 1 xy erate 0.01 remap v
-
-dump 1 all custom 500 dump.nemd tag type x y z
-
-thermo 1000
-
-run 50000
-Memory usage per processor = 1.78793 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume
- 0 1.44 0 0 1.4265 1.2042513 189.52855
- 1000 1.1376326 0.2723749 0 1.3993422 6.0281618 189.52855
- 2000 1.1092867 0.30697161 0 1.4058587 6.5032573 189.52855
- 3000 1.1766842 0.22235709 0 1.3880098 5.8644335 189.52855
- 4000 1.0434686 0.34041502 0 1.3741011 7.0700722 189.52855
- 5000 1.1074638 0.22563765 0 1.322719 5.8819014 189.52855
- 6000 1.100945 0.2181433 0 1.3087669 6.0202699 189.52855
- 7000 0.97801661 0.33802096 0 1.3068687 7.5777517 189.52855
- 8000 1.0689837 0.23524351 0 1.2942054 5.85439 189.52855
- 9000 0.98697269 0.26366959 0 1.2413894 6.4300856 189.52855
- 10000 1.0108076 0.21921678 0 1.2205481 6.3955919 189.52855
- 11000 0.89800714 0.21444583 0 1.1040342 5.7539663 189.52855
- 12000 0.95992701 0.17693662 0 1.1278643 5.3022292 189.52855
- 13000 0.98389546 0.16326907 0 1.1379405 5.2203307 189.52855
- 14000 0.90861181 0.21504543 0 1.115139 4.9988336 189.52855
- 15000 0.85713034 0.19327642 0 1.0423712 5.3278582 189.52855
- 16000 0.8825445 0.23009835 0 1.104369 5.5304884 189.52855
- 17000 0.87611509 0.24874153 0 1.116643 6.43497 189.52855
- 18000 0.95591731 0.21548224 0 1.1624378 5.8740926 189.52855
- 19000 0.96623931 0.28660713 0 1.2437879 5.9965065 189.52855
- 20000 1.0307188 0.27291119 0 1.293967 6.2130706 189.52855
- 21000 1.058557 0.33094775 0 1.3795808 7.0034843 189.52855
- 22000 1.1038028 0.31323484 0 1.4066895 6.5357948 189.52855
- 23000 1.0332701 0.37233908 0 1.3959223 7.19646 189.52855
- 24000 1.1373415 0.2868604 0 1.4135393 6.512421 189.52855
- 25000 1.1251188 0.26998165 0 1.3845525 5.9383566 189.52855
- 26000 1.1495445 0.26242517 0 1.4011927 6.2097913 189.52855
- 27000 1.0710201 0.24813894 0 1.3091182 5.9469594 189.52855
- 28000 0.94089325 0.37721847 0 1.3092909 7.5991128 189.52855
- 29000 1.1245164 0.2012278 0 1.3152019 4.8980329 189.52855
- 30000 0.99392576 0.34334349 0 1.3279512 6.4315527 189.52855
- 31000 0.99011392 0.32648676 0 1.3073184 6.9984388 189.52855
- 32000 0.94636734 0.36450354 0 1.3019987 7.2324663 189.52855
- 33000 0.93907091 0.31264026 0 1.2429074 6.2071137 189.52855
- 34000 0.92196227 0.27866154 0 1.1919804 6.662139 189.52855
- 35000 0.9670411 0.25971717 0 1.2176923 5.8709837 189.52855
- 36000 0.94905466 0.30285469 0 1.243012 6.9870879 189.52855
- 37000 1.0027302 0.26550016 0 1.2588298 6.4022976 189.52855
- 38000 0.95341975 0.32978864 0 1.2742701 6.3304338 189.52855
- 39000 1.0930053 0.23648819 0 1.3192466 5.4154989 189.52855
- 40000 1.0943964 0.23898933 0 1.3231257 5.9056706 189.52855
- 41000 1.0267208 0.28983681 0 1.3069321 6.7084471 189.52855
- 42000 0.94374097 0.28271929 0 1.2176127 6.1336872 189.52855
- 43000 0.89703955 0.27637051 0 1.1650003 5.7892838 189.52855
- 44000 0.9145058 0.24114071 0 1.147073 5.7678354 189.52855
- 45000 0.98924374 0.24342035 0 1.2233899 5.8284458 189.52855
- 46000 0.97250668 0.23874128 0 1.2021307 6.56895 189.52855
- 47000 0.95124639 0.24487076 0 1.1871992 5.5045958 189.52855
- 48000 0.88977783 0.24482112 0 1.1262573 5.5189103 189.52855
- 49000 0.94390446 0.18400987 0 1.1190652 5.2014664 189.52855
- 50000 0.8982525 0.24633124 0 1.1361626 6.2422864 189.52855
-Loop time of 24.1271 on 4 procs for 50000 steps with 160 atoms
-
-Pair time (%) = 0.125436 (0.519896)
-Neigh time (%) = 0.0702366 (0.291111)
-Comm time (%) = 16.1323 (66.8637)
-Outpt time (%) = 0.0769518 (0.318944)
-Other time (%) = 7.72219 (32.0064)
-
-Nlocal: 40 ave 41 max 39 min
-Histogram: 1 0 0 0 0 2 0 0 0 1
-Nghost: 36.5 ave 38 max 34 min
-Histogram: 1 0 0 0 0 0 0 2 0 1
-Neighs: 87.5 ave 92 max 82 min
-Histogram: 1 0 0 1 0 0 0 0 0 2
-
-Total # of neighbors = 350
-Ave neighs/atom = 2.1875
-Neighbor list builds = 5057
-Dangerous builds = 0
diff --git a/examples/obstacle/in.obstacle b/examples/obstacle/in.obstacle
index e0c38695d..0c4b4fe5a 100644
--- a/examples/obstacle/in.obstacle
+++ b/examples/obstacle/in.obstacle
@@ -1,74 +1,74 @@
# 2d LJ obstacle flow
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.7
region box block 0 40 0 10 -0.25 0.25
create_box 3 box
create_atoms 1 box
mass 1 1.0
mass 2 1.0
mass 3 1.0
# LJ potentials
pair_style lj/cut 1.12246
pair_coeff * * 1.0 1.0 1.12246
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
region 2 block INF INF 8.75 INF INF INF
group upper region 2
group boundary union lower upper
group flow subtract all boundary
set group lower type 2
set group upper type 3
# initial velocities
compute mobile flow temp
velocity flow create 1.0 482748 temp mobile
fix 1 all nve
fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
fix_modify 2 temp mobile
-# Poisseuille flow
+# Poiselle flow
velocity boundary set 0.0 0.0 0.0
fix 3 lower setforce 0.0 0.0 0.0
fix 4 upper setforce 0.0 NULL 0.0
fix 5 upper aveforce 0.0 -0.5 0.0
fix 6 flow addforce 1.0 0.0 0.0
# 2 obstacles
region void1 sphere 10 4 0 3
delete_atoms region void1
region void2 sphere 20 7 0 3
delete_atoms region void2
fix 7 flow indent 100 sphere 10 4 0 4
fix 8 flow indent 100 sphere 20 7 0 4
fix 9 all enforce2d
# Run
timestep 0.003
thermo 1000
thermo_modify temp mobile
dump 1 all atom 100 dump.obstacle
#dump 1 all custom 100 dump.custom tag type x y z vx vy
run 25000
diff --git a/examples/obstacle/log.obstacle.21May08.linux.1 b/examples/obstacle/log.obstacle.21May08.linux.1
new file mode 100644
index 000000000..9061775d6
--- /dev/null
+++ b/examples/obstacle/log.obstacle.21May08.linux.1
@@ -0,0 +1,134 @@
+LAMMPS (21 May 2008)
+# 2d LJ obstacle flow
+
+dimension 2
+boundary p s p
+
+atom_style atomic
+neighbor 0.3 bin
+neigh_modify delay 5
+
+# create geometry
+
+lattice hex 0.7
+Lattice spacing in x,y,z = 1.28436 2.22457 1.28436
+region box block 0 40 0 10 -0.25 0.25
+create_box 3 box
+Created orthogonal box = (0 0 -0.321089) to (51.3743 22.2457 0.321089)
+ 1 by 1 by 1 processor grid
+create_atoms 1 box
+Created 840 atoms
+
+mass 1 1.0
+mass 2 1.0
+mass 3 1.0
+
+# LJ potentials
+
+pair_style lj/cut 1.12246
+pair_coeff * * 1.0 1.0 1.12246
+
+# define groups
+
+region 1 block INF INF INF 1.25 INF INF
+group lower region 1
+120 atoms in group lower
+region 2 block INF INF 8.75 INF INF INF
+group upper region 2
+120 atoms in group upper
+group boundary union lower upper
+240 atoms in group boundary
+group flow subtract all boundary
+600 atoms in group flow
+
+set group lower type 2
+ 120 settings made for type
+set group upper type 3
+ 120 settings made for type
+
+# initial velocities
+
+compute mobile flow temp
+velocity flow create 1.0 482748 temp mobile
+fix 1 all nve
+fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
+fix_modify 2 temp mobile
+
+# Poiselle flow
+
+velocity boundary set 0.0 0.0 0.0
+fix 3 lower setforce 0.0 0.0 0.0
+fix 4 upper setforce 0.0 NULL 0.0
+fix 5 upper aveforce 0.0 -0.5 0.0
+fix 6 flow addforce 1.0 0.0 0.0
+
+# 2 obstacles
+
+region void1 sphere 10 4 0 3
+delete_atoms region void1
+Deleted 36 atoms, new total = 804
+region void2 sphere 20 7 0 3
+delete_atoms region void2
+Deleted 35 atoms, new total = 769
+
+fix 7 flow indent 100 sphere 10 4 0 4
+fix 8 flow indent 100 sphere 20 7 0 4
+fix 9 all enforce2d
+
+# Run
+
+timestep 0.003
+thermo 1000
+thermo_modify temp mobile
+
+dump 1 all atom 100 dump.obstacle
+#dump 1 all custom 100 dump.custom tag type x y z vx vy
+
+run 25000
+Memory usage per processor = 1.70365 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 1.0027471 0 0 0.68849216 0.463265 1142.8674
+ 1000 1 -0.33974838 0 0.3468576 1.3038702 1270.08
+ 2000 1 -0.39015699 0 0.296449 1.3186607 1302.3377
+ 3000 1 -0.46396059 0 0.22264539 1.4481737 1319.6122
+ 4000 1 -0.5496054 0 0.13700058 1.4226554 1363.8627
+ 5000 1 -0.48050604 0 0.20609995 1.2559184 1407.1184
+ 6000 1 -0.48128066 0 0.20532532 1.269977 1433.5837
+ 7000 1 -0.40707539 0 0.2795306 1.1836577 1441.9606
+ 8000 1 -0.43843955 0 0.24816644 1.1680682 1445.6274
+ 9000 1 -0.37805786 0 0.30854812 1.0549192 1453.6089
+ 10000 1 -0.40408007 0 0.28252592 1.0810363 1446.2246
+ 11000 1 -0.42972416 0 0.25688183 1.1044938 1443.9994
+ 12000 1 -0.41545586 0 0.27115012 1.1307776 1447.7388
+ 13000 1 -0.36928332 0 0.31732266 0.97287103 1456.3013
+ 14000 1 -0.40912145 0 0.27748454 0.95493422 1459.6415
+ 15000 1 -0.37477252 0 0.31183347 1.0249663 1468.7959
+ 16000 1 -0.38531111 0 0.30129487 1.0220375 1462.2135
+ 17000 1 -0.37376992 0 0.31283607 0.97728961 1461.4028
+ 18000 1 -0.37434423 0 0.31226175 0.96886643 1463.9162
+ 19000 1 -0.36998688 0 0.3166191 0.91573344 1462.3663
+ 20000 1 -0.34624142 0 0.34036456 0.9870418 1458.2772
+ 21000 1 -0.39671499 0 0.28989099 1.0313285 1453.5442
+ 22000 1 -0.35842296 0 0.32818302 0.98937969 1454.5928
+ 23000 1 -0.36252176 0 0.32408422 0.98605146 1457.477
+ 24000 1 -0.38519815 0 0.30140784 1.0132503 1466.8342
+ 25000 1 -0.38889832 0 0.29770766 0.99272161 1462.2441
+Loop time of 3.01278 on 1 procs for 25000 steps with 769 atoms
+
+Pair time (%) = 0.867625 (28.7981)
+Neigh time (%) = 0.200178 (6.64429)
+Comm time (%) = 0.0479047 (1.59005)
+Outpt time (%) = 0.27641 (9.17456)
+Other time (%) = 1.62067 (53.793)
+
+Nlocal: 769 ave 769 max 769 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 45 ave 45 max 45 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 1615 ave 1615 max 1615 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1615
+Ave neighs/atom = 2.10013
+Neighbor list builds = 1636
+Dangerous builds = 0
diff --git a/examples/obstacle/log.obstacle.21May08.linux.4 b/examples/obstacle/log.obstacle.21May08.linux.4
new file mode 100644
index 000000000..756fb9f78
--- /dev/null
+++ b/examples/obstacle/log.obstacle.21May08.linux.4
@@ -0,0 +1,134 @@
+LAMMPS (21 May 2008)
+# 2d LJ obstacle flow
+
+dimension 2
+boundary p s p
+
+atom_style atomic
+neighbor 0.3 bin
+neigh_modify delay 5
+
+# create geometry
+
+lattice hex 0.7
+Lattice spacing in x,y,z = 1.28436 2.22457 1.28436
+region box block 0 40 0 10 -0.25 0.25
+create_box 3 box
+Created orthogonal box = (0 0 -0.321089) to (51.3743 22.2457 0.321089)
+ 4 by 1 by 1 processor grid
+create_atoms 1 box
+Created 840 atoms
+
+mass 1 1.0
+mass 2 1.0
+mass 3 1.0
+
+# LJ potentials
+
+pair_style lj/cut 1.12246
+pair_coeff * * 1.0 1.0 1.12246
+
+# define groups
+
+region 1 block INF INF INF 1.25 INF INF
+group lower region 1
+120 atoms in group lower
+region 2 block INF INF 8.75 INF INF INF
+group upper region 2
+120 atoms in group upper
+group boundary union lower upper
+240 atoms in group boundary
+group flow subtract all boundary
+600 atoms in group flow
+
+set group lower type 2
+ 120 settings made for type
+set group upper type 3
+ 120 settings made for type
+
+# initial velocities
+
+compute mobile flow temp
+velocity flow create 1.0 482748 temp mobile
+fix 1 all nve
+fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
+fix_modify 2 temp mobile
+
+# Poiselle flow
+
+velocity boundary set 0.0 0.0 0.0
+fix 3 lower setforce 0.0 0.0 0.0
+fix 4 upper setforce 0.0 NULL 0.0
+fix 5 upper aveforce 0.0 -0.5 0.0
+fix 6 flow addforce 1.0 0.0 0.0
+
+# 2 obstacles
+
+region void1 sphere 10 4 0 3
+delete_atoms region void1
+Deleted 36 atoms, new total = 804
+region void2 sphere 20 7 0 3
+delete_atoms region void2
+Deleted 35 atoms, new total = 769
+
+fix 7 flow indent 100 sphere 10 4 0 4
+fix 8 flow indent 100 sphere 20 7 0 4
+fix 9 all enforce2d
+
+# Run
+
+timestep 0.003
+thermo 1000
+thermo_modify temp mobile
+
+dump 1 all atom 100 dump.obstacle
+#dump 1 all custom 100 dump.custom tag type x y z vx vy
+
+run 25000
+Memory usage per processor = 1.6747 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 1.0004177 0 0 0.68689281 0.46218884 1142.8674
+ 1000 1 -0.31542378 0 0.3711822 1.175277 1269.5736
+ 2000 1 -0.41219854 0 0.27440745 1.1491113 1299.751
+ 3000 1 -0.47091634 0 0.21568964 1.5138975 1319.4646
+ 4000 1 -0.53218028 0 0.1544257 1.4947487 1368.5894
+ 5000 1 -0.46667863 0 0.21992736 1.2479263 1416.3743
+ 6000 1 -0.48435058 0 0.20225541 1.1547645 1435.6664
+ 7000 1 -0.45166298 0 0.23494301 1.2360154 1436.1059
+ 8000 1 -0.42767328 0 0.2589327 1.0669461 1445.2577
+ 9000 1 -0.3731244 0 0.31348158 1.0759192 1437.8863
+ 10000 1 -0.38390694 0 0.30269904 1.0086513 1433.1836
+ 11000 1 -0.38602215 0 0.30058383 0.97948448 1433.262
+ 12000 1 -0.39324632 0 0.29335966 1.0627957 1439.8189
+ 13000 1 -0.38406328 0 0.3025427 1.0506023 1450.2548
+ 14000 1 -0.39923996 0 0.28736602 1.0593743 1453.5768
+ 15000 1 -0.39243934 0 0.29416664 1.0295791 1451.2386
+ 16000 1 -0.39115558 0 0.2954504 0.99442342 1452.2425
+ 17000 1 -0.37672706 0 0.30987892 1.1334027 1446.7615
+ 18000 1 -0.39587578 0 0.2907302 1.0416836 1451.6676
+ 19000 1 -0.37159192 0 0.31501406 0.97004312 1453.7464
+ 20000 1 -0.37573625 0 0.31086973 1.0174394 1456.2812
+ 21000 1 -0.37788053 0 0.30872545 0.93039844 1468.4444
+ 22000 1 -0.38096917 0 0.30563681 1.0034608 1464.2511
+ 23000 1 -0.37098283 0 0.31562315 0.98141206 1460.3666
+ 24000 1 -0.37160721 0 0.31499877 0.98831948 1462.133
+ 25000 1 -0.39191532 0 0.29469067 1.0326092 1457.8187
+Loop time of 7.66898 on 4 procs for 25000 steps with 769 atoms
+
+Pair time (%) = 0.240548 (3.13664)
+Neigh time (%) = 0.0541248 (0.705762)
+Comm time (%) = 3.3025 (43.0631)
+Outpt time (%) = 0.277801 (3.6224)
+Other time (%) = 3.79401 (49.4721)
+
+Nlocal: 192.25 ave 235 max 157 min
+Histogram: 1 1 0 0 0 0 1 0 0 1
+Nghost: 42.25 ave 46 max 38 min
+Histogram: 1 0 0 0 0 1 1 0 0 1
+Neighs: 401.25 ave 540 max 283 min
+Histogram: 2 0 0 0 0 0 0 1 0 1
+
+Total # of neighbors = 1605
+Ave neighs/atom = 2.08713
+Neighbor list builds = 1636
+Dangerous builds = 0
diff --git a/examples/obstacle/log.obstacle.22Jan08.linux.1 b/examples/obstacle/log.obstacle.22Jan08.linux.1
deleted file mode 100644
index eaba87490..000000000
--- a/examples/obstacle/log.obstacle.22Jan08.linux.1
+++ /dev/null
@@ -1,134 +0,0 @@
-LAMMPS (22 Jan 2008)
-# 2d LJ obstacle flow
-
-dimension 2
-boundary p s p
-
-atom_style atomic
-neighbor 0.3 bin
-neigh_modify delay 5
-
-# create geometry
-
-lattice hex 0.7
-Lattice spacing in x,y,z = 1.28436 2.22457 1.28436
-region box block 0 40 0 10 -0.25 0.25
-create_box 3 box
-Created orthogonal box = (0 0 -0.321089) to (51.3743 22.2457 0.321089)
- 1 by 1 by 1 processor grid
-create_atoms 1 box
-Created 840 atoms
-
-mass 1 1.0
-mass 2 1.0
-mass 3 1.0
-
-# LJ potentials
-
-pair_style lj/cut 1.12246
-pair_coeff * * 1.0 1.0 1.12246
-
-# define groups
-
-region 1 block INF INF INF 1.25 INF INF
-group lower region 1
-120 atoms in group lower
-region 2 block INF INF 8.75 INF INF INF
-group upper region 2
-120 atoms in group upper
-group boundary union lower upper
-240 atoms in group boundary
-group flow subtract all boundary
-600 atoms in group flow
-
-set group lower type 2
- 120 settings made for type
-set group upper type 3
- 120 settings made for type
-
-# initial velocities
-
-compute mobile flow temp
-velocity flow create 1.0 482748 temp mobile
-fix 1 all nve
-fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
-fix_modify 2 temp mobile
-
-# Poiselle flow
-
-velocity boundary set 0.0 0.0 0.0
-fix 3 lower setforce 0.0 0.0 0.0
-fix 4 upper setforce 0.0 NULL 0.0
-fix 5 upper aveforce 0.0 -0.5 0.0
-fix 6 flow addforce 1.0 0.0 0.0
-
-# 2 obstacles
-
-region void1 sphere 10 4 0 3
-delete_atoms region void1
-Deleted 36 atoms, new total = 804
-region void2 sphere 20 7 0 3
-delete_atoms region void2
-Deleted 35 atoms, new total = 769
-
-fix 7 flow indent 100 sphere 10 4 0 4
-fix 8 flow indent 100 sphere 20 7 0 4
-fix 9 all enforce2d
-
-# Run
-
-timestep 0.003
-thermo 1000
-thermo_modify temp mobile
-
-dump 1 all atom 100 dump.obstacle
-#dump 1 all custom 100 dump.custom tag type x y z vx vy
-
-run 25000
-Memory usage per processor = 1.70365 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume
- 0 1.0028598 0 0 0.68791746 0.4628783 1142.8674
- 1000 1 -0.37328511 0 0.31267068 1.3684627 1268.502
- 2000 1 -0.37505949 0 0.3108963 1.1534403 1304.1442
- 3000 1 -0.47919489 0 0.20676089 1.4549832 1322.0606
- 4000 1 -0.48849092 0 0.19746486 1.4619445 1361.4653
- 5000 1 -0.5158306 0 0.17012519 1.3415433 1399.8571
- 6000 1 -0.46839183 0 0.21756396 1.1363632 1433.3799
- 7000 1 -0.4934634 0 0.19249239 1.1974639 1438.8597
- 8000 1 -0.43365481 0 0.25230098 1.1237932 1444.8858
- 9000 1 -0.38250014 0 0.30345564 1.0808676 1445.4458
- 10000 1 -0.41296265 0 0.27299313 1.0868711 1444.8934
- 11000 1 -0.3906263 0 0.29532949 1.0008831 1443.6394
- 12000 1 -0.41935827 0 0.26659752 1.0104839 1435.183
- 13000 1 -0.35477192 0 0.33118387 0.94488941 1440.5498
- 14000 1 -0.39497861 0 0.29097718 1.072787 1435.3595
- 15000 1 -0.38656691 0 0.29938888 1.05116 1442.1287
- 16000 1 -0.37132523 0 0.31463056 1.0827132 1450.8796
- 17000 1 -0.37146616 0 0.31448963 1.1724883 1450.3808
- 18000 1 -0.38747606 0 0.29847973 1.0753661 1455.6913
- 19000 1 -0.37206204 0 0.31389375 1.0665364 1450.8326
- 20000 1 -0.39878843 0 0.28716736 1.0958347 1453.0454
- 21000 1 -0.36006462 0 0.32589117 0.92452983 1459.3281
- 22000 1 -0.36787908 0 0.3180767 0.9659935 1465.6707
- 23000 1 -0.36909747 0 0.31685831 0.9769748 1470.1647
- 24000 1 -0.38163837 0 0.30431741 0.99582238 1458.5709
- 25000 1 -0.38524202 0 0.30071376 0.96693615 1458.596
-Loop time of 2.95816 on 1 procs for 25000 steps with 769 atoms
-
-Pair time (%) = 0.863224 (29.1811)
-Neigh time (%) = 0.197628 (6.68078)
-Comm time (%) = 0.0466022 (1.57538)
-Outpt time (%) = 0.271423 (9.17539)
-Other time (%) = 1.57928 (53.3874)
-
-Nlocal: 769 ave 769 max 769 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 43 ave 43 max 43 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 1642 ave 1642 max 1642 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 1642
-Ave neighs/atom = 2.13524
-Neighbor list builds = 1639
-Dangerous builds = 0
diff --git a/examples/obstacle/log.obstacle.22Jan08.linux.4 b/examples/obstacle/log.obstacle.22Jan08.linux.4
deleted file mode 100644
index 6d1adc8c2..000000000
--- a/examples/obstacle/log.obstacle.22Jan08.linux.4
+++ /dev/null
@@ -1,134 +0,0 @@
-LAMMPS (22 Jan 2008)
-# 2d LJ obstacle flow
-
-dimension 2
-boundary p s p
-
-atom_style atomic
-neighbor 0.3 bin
-neigh_modify delay 5
-
-# create geometry
-
-lattice hex 0.7
-Lattice spacing in x,y,z = 1.28436 2.22457 1.28436
-region box block 0 40 0 10 -0.25 0.25
-create_box 3 box
-Created orthogonal box = (0 0 -0.321089) to (51.3743 22.2457 0.321089)
- 4 by 1 by 1 processor grid
-create_atoms 1 box
-Created 840 atoms
-
-mass 1 1.0
-mass 2 1.0
-mass 3 1.0
-
-# LJ potentials
-
-pair_style lj/cut 1.12246
-pair_coeff * * 1.0 1.0 1.12246
-
-# define groups
-
-region 1 block INF INF INF 1.25 INF INF
-group lower region 1
-120 atoms in group lower
-region 2 block INF INF 8.75 INF INF INF
-group upper region 2
-120 atoms in group upper
-group boundary union lower upper
-240 atoms in group boundary
-group flow subtract all boundary
-600 atoms in group flow
-
-set group lower type 2
- 120 settings made for type
-set group upper type 3
- 120 settings made for type
-
-# initial velocities
-
-compute mobile flow temp
-velocity flow create 1.0 482748 temp mobile
-fix 1 all nve
-fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
-fix_modify 2 temp mobile
-
-# Poiselle flow
-
-velocity boundary set 0.0 0.0 0.0
-fix 3 lower setforce 0.0 0.0 0.0
-fix 4 upper setforce 0.0 NULL 0.0
-fix 5 upper aveforce 0.0 -0.5 0.0
-fix 6 flow addforce 1.0 0.0 0.0
-
-# 2 obstacles
-
-region void1 sphere 10 4 0 3
-delete_atoms region void1
-Deleted 36 atoms, new total = 804
-region void2 sphere 20 7 0 3
-delete_atoms region void2
-Deleted 35 atoms, new total = 769
-
-fix 7 flow indent 100 sphere 10 4 0 4
-fix 8 flow indent 100 sphere 20 7 0 4
-fix 9 all enforce2d
-
-# Run
-
-timestep 0.003
-thermo 1000
-thermo_modify temp mobile
-
-dump 1 all atom 100 dump.obstacle
-#dump 1 all custom 100 dump.custom tag type x y z vx vy
-
-run 25000
-Memory usage per processor = 1.6747 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume
- 0 1.0005301 0 0 0.68631944 0.46180304 1142.8674
- 1000 1 -0.2948784 0 0.39107738 1.1626002 1268.8767
- 2000 1 -0.34841619 0 0.3375396 1.1178514 1300.3744
- 3000 1 -0.45198006 0 0.23397572 1.5104251 1319.535
- 4000 1 -0.4930904 0 0.19286538 1.5054789 1359.7954
- 5000 1 -0.49437088 0 0.19158491 1.5038965 1397.2548
- 6000 1 -0.4538845 0 0.23207128 1.2100734 1429.6759
- 7000 1 -0.46715598 0 0.2187998 1.1832386 1441.9733
- 8000 1 -0.4490541 0 0.23690168 1.1504605 1441.328
- 9000 1 -0.41648732 0 0.26946847 1.1453723 1437.0673
- 10000 1 -0.3776725 0 0.30828328 1.080226 1434.3847
- 11000 1 -0.4189651 0 0.26699069 1.0496379 1435.2496
- 12000 1 -0.39688957 0 0.28906621 1.0443611 1440.7218
- 13000 1 -0.38977976 0 0.29617602 1.0309823 1460.2618
- 14000 1 -0.38124839 0 0.30470739 1.0195507 1463.0566
- 15000 1 -0.35208681 0 0.33386897 0.93784921 1466.2431
- 16000 1 -0.41112084 0 0.27483495 1.0717681 1465.3625
- 17000 1 -0.36742687 0 0.31852892 1.0452766 1466.8819
- 18000 1 -0.38418683 0 0.30176896 0.94933535 1464.1674
- 19000 1 -0.38168345 0 0.30427234 0.97892386 1457.3935
- 20000 1 -0.37778426 0 0.30817153 1.0205159 1452.8383
- 21000 1 -0.3778136 0 0.30814218 1.07933 1449.0972
- 22000 1 -0.36663586 0 0.31931993 0.93798261 1452.0117
- 23000 1 -0.39885464 0 0.28710115 1.0286456 1449.9107
- 24000 1 -0.40766765 0 0.27828813 1.138272 1451.4717
- 25000 1 -0.36180623 0 0.32414956 0.91494742 1464.0945
-Loop time of 9.24974 on 4 procs for 25000 steps with 769 atoms
-
-Pair time (%) = 0.269292 (2.91135)
-Neigh time (%) = 0.0605692 (0.654821)
-Comm time (%) = 4.36665 (47.2083)
-Outpt time (%) = 0.31033 (3.35502)
-Other time (%) = 4.2429 (45.8705)
-
-Nlocal: 192.25 ave 244 max 151 min
-Histogram: 1 1 0 0 0 1 0 0 0 1
-Nghost: 43 ave 45 max 41 min
-Histogram: 1 0 0 0 0 2 0 0 0 1
-Neighs: 399.25 ave 566 max 263 min
-Histogram: 1 1 0 0 0 0 1 0 0 1
-
-Total # of neighbors = 1597
-Ave neighs/atom = 2.07672
-Neighbor list builds = 1638
-Dangerous builds = 0
diff --git a/examples/peptide/log.peptide.22Jan08.linux.1 b/examples/peptide/log.peptide.21May08.linux.1
similarity index 85%
rename from examples/peptide/log.peptide.22Jan08.linux.1
rename to examples/peptide/log.peptide.21May08.linux.1
index 8fa2bb553..a29357477 100644
--- a/examples/peptide/log.peptide.22Jan08.linux.1
+++ b/examples/peptide/log.peptide.21May08.linux.1
@@ -1,155 +1,155 @@
-LAMMPS (22 Jan 2008)
+LAMMPS (21 May 2008)
# Solvated 5-mer peptide
units real
atom_style full
pair_style lj/charmm/coul/long 8.0 10.0 10.0
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
kspace_style pppm 0.0001
read_data data.peptide
3 = max bonds/atom
6 = max angles/atom
14 = max dihedrals/atom
1 = max impropers/atom
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
1 by 1 by 1 processor grid
2004 atoms
2004 velocities
1365 bonds
786 angles
207 dihedrals
12 impropers
4 = max # of 1-2 neighbors
7 = max # of 1-3 neighbors
14 = max # of 1-4 neighbors
18 = max # of special neighbors
neighbor 2.0 bin
neigh_modify delay 5
timestep 2.0
thermo_style multi
thermo 50
fix 1 all nvt 275.0 275.0 100.0
fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
19 = # of size 2 clusters
6 = # of size 3 clusters
3 = # of size 4 clusters
640 = # of frozen angles
group peptide type <= 12
84 atoms in group peptide
dump 1 peptide atom 10 dump.peptide
dump 2 peptide bond 300 dump.bond
run 300
PPPM initialization ...
G vector = 0.268721
grid = 15 15 15
RMS precision = 4.86052e-05
brick FFT buffer size/proc = 10648 3375 5808
SHAKE stats (type/ave/delta) on step 0
4 1.111 1.44264e-05
6 0.996998 7.26967e-06
8 1.08 1.32536e-05
10 1.111 1.22749e-05
12 1.08 1.11767e-05
14 0.96 0
18 0.957206 4.37979e-05
31 104.519 0.00396029
Memory usage per processor = 19.2806 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -5237.4580 KinEng = 1134.9186 Temp = 282.1005
PotEng = -6372.3765 E_bond = 16.5572 E_angle = 36.3726
E_dihed = 15.5190 E_impro = 1.9426 E_vdwl = 692.8945
E_coul = 26771.8055 E_long = -33907.4679 Press = -845.4767
----------------- Step 50 ----- CPU = 1.9580 (sec) ----------------
+---------------- Step 50 ----- CPU = 1.9220 (sec) ----------------
TotEng = -5247.5482 KinEng = 1132.4030 Temp = 281.4752
PotEng = -6379.9512 E_bond = 12.2118 E_angle = 31.7365
E_dihed = 18.8145 E_impro = 2.3612 E_vdwl = 658.1773
E_coul = 26803.9885 E_long = -33907.2410 Press = -1331.7941
SHAKE stats (type/ave/delta) on step 100
4 1.111 7.80751e-07
6 0.997 1.06201e-06
8 1.08 6.20437e-07
10 1.111 6.23402e-07
12 1.08 2.68046e-07
14 0.96 0
18 0.957201 5.38003e-06
31 104.52 0.000502302
----------------- Step 100 ----- CPU = 3.9176 (sec) ----------------
+---------------- Step 100 ----- CPU = 3.8466 (sec) ----------------
TotEng = -5257.9998 KinEng = 1078.0523 Temp = 267.9656
PotEng = -6336.0521 E_bond = 14.4828 E_angle = 43.4429
E_dihed = 15.2569 E_impro = 2.3160 E_vdwl = 708.3270
E_coul = 26786.2252 E_long = -33906.1028 Press = -648.6625
----------------- Step 150 ----- CPU = 5.9178 (sec) ----------------
+---------------- Step 150 ----- CPU = 5.8126 (sec) ----------------
TotEng = -5287.2845 KinEng = 1098.6038 Temp = 273.0740
PotEng = -6385.8884 E_bond = 17.4924 E_angle = 32.8594
E_dihed = 15.1624 E_impro = 1.6522 E_vdwl = 736.9699
E_coul = 26716.7972 E_long = -33906.8217 Press = -333.1793
SHAKE stats (type/ave/delta) on step 200
4 1.111 2.18836e-07
6 0.997 1.50912e-07
8 1.08 6.58565e-08
10 1.111 5.56675e-07
12 1.08 1.99343e-07
14 0.96 0
18 0.957201 3.59691e-06
31 104.52 0.000388135
----------------- Step 200 ----- CPU = 7.8301 (sec) ----------------
+---------------- Step 200 ----- CPU = 7.6880 (sec) ----------------
TotEng = -5308.4506 KinEng = 1100.5139 Temp = 273.5487
PotEng = -6408.9645 E_bond = 18.2714 E_angle = 33.3035
E_dihed = 16.8154 E_impro = 2.6052 E_vdwl = 686.3197
E_coul = 26735.6532 E_long = -33901.9330 Press = -1470.4759
----------------- Step 250 ----- CPU = 9.8341 (sec) ----------------
+---------------- Step 250 ----- CPU = 9.6620 (sec) ----------------
TotEng = -5294.1810 KinEng = 1071.1657 Temp = 266.2538
PotEng = -6365.3468 E_bond = 14.2024 E_angle = 39.1969
E_dihed = 19.4546 E_impro = 3.1388 E_vdwl = 753.6297
E_coul = 26713.2917 E_long = -33908.2610 Press = -187.7503
SHAKE stats (type/ave/delta) on step 300
4 1.111 3.78101e-06
6 0.997001 3.5121e-06
8 1.08 2.09172e-06
10 1.111 5.64083e-06
12 1.08 2.10195e-06
14 0.96 0
18 0.957202 7.62681e-06
31 104.52 0.000805945
----------------- Step 300 ----- CPU = 11.8338 (sec) ----------------
+---------------- Step 300 ----- CPU = 11.6334 (sec) ----------------
TotEng = -5251.4412 KinEng = 1123.4657 Temp = 279.2537
PotEng = -6374.9069 E_bond = 14.2235 E_angle = 38.4664
E_dihed = 18.1383 E_impro = 2.3705 E_vdwl = 715.5989
E_coul = 26744.9563 E_long = -33908.6606 Press = -467.2646
-Loop time of 11.8338 on 1 procs for 300 steps with 2004 atoms
+Loop time of 11.6334 on 1 procs for 300 steps with 2004 atoms
-Pair time (%) = 9.14838 (77.307)
-Bond time (%) = 0.0331497 (0.280127)
-Kspce time (%) = 1.27265 (10.7543)
-Neigh time (%) = 1.18564 (10.0191)
-Comm time (%) = 0.0640588 (0.541319)
-Outpt time (%) = 0.00577974 (0.0488409)
-Other time (%) = 0.124176 (1.04933)
+Pair time (%) = 8.95694 (76.9933)
+Bond time (%) = 0.0339992 (0.292255)
+Kspce time (%) = 1.24836 (10.7308)
+Neigh time (%) = 1.1949 (10.2713)
+Comm time (%) = 0.0653448 (0.5617)
+Outpt time (%) = 0.00594068 (0.0510657)
+Other time (%) = 0.127918 (1.09957)
-FFT time (% of Kspce) = 0.134997 (10.6076)
-FFT Gflps 3d 1d-only = 1.21865 1.86907
+FFT time (% of Kspce) = 0.136571 (10.94)
+FFT Gflps 3d 1d-only = 1.20461 1.854
Nlocal: 2004 ave 2004 max 2004 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11181 ave 11181 max 11181 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 708030 ave 708030 max 708030 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 708030
Ave neighs/atom = 353.308
Ave special neighs/atom = 2.34032
Neighbor list builds = 26
Dangerous builds = 0
diff --git a/examples/peptide/log.peptide.22Jan08.linux.4 b/examples/peptide/log.peptide.21May08.linux.4
similarity index 85%
rename from examples/peptide/log.peptide.22Jan08.linux.4
rename to examples/peptide/log.peptide.21May08.linux.4
index 538ef1a52..fde8fcd30 100644
--- a/examples/peptide/log.peptide.22Jan08.linux.4
+++ b/examples/peptide/log.peptide.21May08.linux.4
@@ -1,155 +1,155 @@
-LAMMPS (22 Jan 2008)
+LAMMPS (21 May 2008)
# Solvated 5-mer peptide
units real
atom_style full
pair_style lj/charmm/coul/long 8.0 10.0 10.0
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
kspace_style pppm 0.0001
read_data data.peptide
3 = max bonds/atom
6 = max angles/atom
14 = max dihedrals/atom
1 = max impropers/atom
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
1 by 2 by 2 processor grid
2004 atoms
2004 velocities
1365 bonds
786 angles
207 dihedrals
12 impropers
4 = max # of 1-2 neighbors
7 = max # of 1-3 neighbors
14 = max # of 1-4 neighbors
18 = max # of special neighbors
neighbor 2.0 bin
neigh_modify delay 5
timestep 2.0
thermo_style multi
thermo 50
fix 1 all nvt 275.0 275.0 100.0
fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
19 = # of size 2 clusters
6 = # of size 3 clusters
3 = # of size 4 clusters
640 = # of frozen angles
group peptide type <= 12
84 atoms in group peptide
dump 1 peptide atom 10 dump.peptide
dump 2 peptide bond 300 dump.bond
run 300
PPPM initialization ...
G vector = 0.268721
grid = 15 15 15
RMS precision = 4.86052e-05
brick FFT buffer size/proc = 4312 960 3696
SHAKE stats (type/ave/delta) on step 0
4 1.111 1.44264e-05
6 0.996998 7.26967e-06
8 1.08 1.32536e-05
10 1.111 1.22749e-05
12 1.08 1.11767e-05
14 0.96 0
18 0.957206 4.37979e-05
31 104.519 0.00396029
Memory usage per processor = 8.58908 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -5237.4580 KinEng = 1134.9186 Temp = 282.1005
PotEng = -6372.3765 E_bond = 16.5572 E_angle = 36.3726
E_dihed = 15.5190 E_impro = 1.9426 E_vdwl = 692.8945
E_coul = 26771.8055 E_long = -33907.4679 Press = -845.4767
----------------- Step 50 ----- CPU = 0.6428 (sec) ----------------
+---------------- Step 50 ----- CPU = 0.6366 (sec) ----------------
TotEng = -5247.5482 KinEng = 1132.4030 Temp = 281.4752
PotEng = -6379.9512 E_bond = 12.2118 E_angle = 31.7365
E_dihed = 18.8145 E_impro = 2.3612 E_vdwl = 658.1773
E_coul = 26803.9885 E_long = -33907.2410 Press = -1331.7941
SHAKE stats (type/ave/delta) on step 100
4 1.111 7.80751e-07
6 0.997 1.06201e-06
8 1.08 6.20437e-07
10 1.111 6.23402e-07
12 1.08 2.68046e-07
14 0.96 0
18 0.957201 5.38003e-06
31 104.52 0.000502302
----------------- Step 100 ----- CPU = 1.2863 (sec) ----------------
+---------------- Step 100 ----- CPU = 1.2804 (sec) ----------------
TotEng = -5257.9998 KinEng = 1078.0523 Temp = 267.9656
PotEng = -6336.0521 E_bond = 14.4828 E_angle = 43.4429
E_dihed = 15.2569 E_impro = 2.3160 E_vdwl = 708.3270
E_coul = 26786.2252 E_long = -33906.1028 Press = -648.6625
----------------- Step 150 ----- CPU = 1.9373 (sec) ----------------
+---------------- Step 150 ----- CPU = 1.9476 (sec) ----------------
TotEng = -5287.2845 KinEng = 1098.6039 Temp = 273.0740
PotEng = -6385.8883 E_bond = 17.4924 E_angle = 32.8594
E_dihed = 15.1624 E_impro = 1.6522 E_vdwl = 736.9699
E_coul = 26716.7972 E_long = -33906.8217 Press = -333.1793
SHAKE stats (type/ave/delta) on step 200
4 1.111 2.18836e-07
6 0.997 1.50913e-07
8 1.08 6.58567e-08
10 1.111 5.56674e-07
12 1.08 1.99344e-07
14 0.96 0
18 0.957201 3.59691e-06
31 104.52 0.000388135
----------------- Step 200 ----- CPU = 2.5714 (sec) ----------------
+---------------- Step 200 ----- CPU = 2.5921 (sec) ----------------
TotEng = -5308.4506 KinEng = 1100.5139 Temp = 273.5487
PotEng = -6408.9645 E_bond = 18.2714 E_angle = 33.3035
E_dihed = 16.8154 E_impro = 2.6052 E_vdwl = 686.3197
E_coul = 26735.6532 E_long = -33901.9330 Press = -1470.4761
----------------- Step 250 ----- CPU = 3.2272 (sec) ----------------
+---------------- Step 250 ----- CPU = 3.2541 (sec) ----------------
TotEng = -5294.1811 KinEng = 1071.1657 Temp = 266.2538
PotEng = -6365.3467 E_bond = 14.2024 E_angle = 39.1969
E_dihed = 19.4546 E_impro = 3.1388 E_vdwl = 753.6297
E_coul = 26713.2917 E_long = -33908.2610 Press = -187.7499
SHAKE stats (type/ave/delta) on step 300
4 1.111 3.78101e-06
6 0.997001 3.51215e-06
8 1.08 2.09172e-06
10 1.111 5.64082e-06
12 1.08 2.10195e-06
14 0.96 0
18 0.957202 7.62685e-06
31 104.52 0.000805946
----------------- Step 300 ----- CPU = 3.8863 (sec) ----------------
+---------------- Step 300 ----- CPU = 3.9119 (sec) ----------------
TotEng = -5251.4403 KinEng = 1123.4658 Temp = 279.2538
PotEng = -6374.9062 E_bond = 14.2235 E_angle = 38.4663
E_dihed = 18.1383 E_impro = 2.3705 E_vdwl = 715.5987
E_coul = 26744.9572 E_long = -33908.6606 Press = -467.2532
-Loop time of 3.88697 on 4 procs for 300 steps with 2004 atoms
+Loop time of 3.91243 on 4 procs for 300 steps with 2004 atoms
-Pair time (%) = 2.10925 (54.2645)
-Bond time (%) = 0.00993025 (0.255475)
-Kspce time (%) = 0.813088 (20.9183)
-Neigh time (%) = 0.259184 (6.66801)
-Comm time (%) = 0.390454 (10.0452)
-Outpt time (%) = 0.019382 (0.49864)
-Other time (%) = 0.285689 (7.34991)
+Pair time (%) = 2.14349 (54.7867)
+Bond time (%) = 0.0107697 (0.275269)
+Kspce time (%) = 0.751045 (19.1964)
+Neigh time (%) = 0.26354 (6.73596)
+Comm time (%) = 0.415519 (10.6205)
+Outpt time (%) = 0.0160949 (0.411378)
+Other time (%) = 0.31197 (7.97382)
-FFT time (% of Kspce) = 0.243359 (29.9302)
-FFT Gflps 3d 1d-only = 0.676015 5.55305
+FFT time (% of Kspce) = 0.2215 (29.4923)
+FFT Gflps 3d 1d-only = 0.742726 5.19614
Nlocal: 501 ave 508 max 490 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Nghost: 6586.25 ave 6628 max 6548 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs: 177008 ave 180557 max 170209 min
Histogram: 1 0 0 0 0 0 0 1 1 1
Total # of neighbors = 708030
Ave neighs/atom = 353.308
Ave special neighs/atom = 2.34032
Neighbor list builds = 26
Dangerous builds = 0
diff --git a/examples/pour/in.pour b/examples/pour/in.pour
index f3933cd41..cefac3513 100644
--- a/examples/pour/in.pour
+++ b/examples/pour/in.pour
@@ -1,39 +1,39 @@
# Pour granular particles into chute container, then induce flow
atom_style granular
boundary p p fm
newton off
region reg block -10 10 -10 10 -0.5 16 units box
create_box 1 reg
neighbor 0.2 bin
neigh_modify delay 0
# IMPORTANT NOTE: these values of stiffness (2000) and timestep (0.001)
# are used in this example file to produce a quick simulation and movie.
# More appropriate values for realistic simulations would be
# k = 2.0e5 and dt = 0.0001, as in bench/in.chute.
pair_style gran/history 2000.0 50.0 0.5 0
timestep 0.001
fix 1 all nve/sphere
fix 2 all gravity 1.0 spherical 0.0 -180.0
fix zlower all wall/gran zplane 0.0 2000.0 50.0 0.5
region slab block -9.0 9.0 -9.0 9.0 10.0 15.0 units box
fix ins all pour 3000 1 300719 vol 0.13 50 region slab
-compute erot all erotate/sphere
-thermo_style custom step atoms ke c_erot vol
+compute 1 all erotate/sphere
+thermo_style custom step atoms ke c_1 vol
thermo 1000
thermo_modify lost ignore norm no
compute_modify thermo_temp dynamic yes
dump id all atom 1000 dump.pour
run 25000
unfix ins
fix 2 all gravity 1.0 chute 26.0
run 25000
diff --git a/examples/pour/in.pour.2d b/examples/pour/in.pour.2d
index b3bc1c746..5f5f09284 100644
--- a/examples/pour/in.pour.2d
+++ b/examples/pour/in.pour.2d
@@ -1,40 +1,40 @@
# Pour 2d granular particles into container
dimension 2
atom_style granular
boundary f fm p
newton off
region reg block 0 100 0 50 -0.5 0.5 units box
create_box 1 reg
neighbor 0.2 bin
neigh_modify delay 0
# IMPORTANT NOTE: these values of stiffness (2000) and timestep (0.001)
# are used in this example file to produce a quick simulation and movie.
# More appropriate values for realistic simulations would be
# k = 2.0e5 and dt = 0.0001, as in bench/in.chute.
pair_style gran/hertzian 2000.0 50.0 0.5 0
timestep 0.001
fix 1 all nve/sphere
fix 2 all gravity 1.0 spherical 0.0 -180.0
fix xwalls all wall/gran xplane 0 100 50 0
fix ywalls all wall/gran yplane 0 NULL 50 0
region slab block 1.0 99.0 30 34.5 -0.5 0.5 units box
fix ins all pour 1000 1 4767548 vol 0.4 10 &
diam 0.5 1.0 region slab
fix 3 all enforce2d
-compute erot all erotate/sphere
-thermo_style custom step atoms ke c_erot vol
+compute 1 all erotate/sphere
+thermo_style custom step atoms ke c_1 vol
thermo 1000
thermo_modify lost ignore norm no
compute_modify thermo_temp dynamic yes
dump id all atom 250 dump.pour
run 25000
diff --git a/examples/pour/log.pour.22Jan08.linux.1 b/examples/pour/log.pour.21May08.linux.1
similarity index 86%
rename from examples/pour/log.pour.22Jan08.linux.1
rename to examples/pour/log.pour.21May08.linux.1
index 7c2c9d259..bc9a87874 100644
--- a/examples/pour/log.pour.22Jan08.linux.1
+++ b/examples/pour/log.pour.21May08.linux.1
@@ -1,136 +1,137 @@
-LAMMPS (22 Jan 2008)
+LAMMPS (21 May 2008)
# Pour granular particles into chute container, then induce flow
atom_style granular
boundary p p fm
newton off
region reg block -10 10 -10 10 -0.5 16 units box
create_box 1 reg
Created orthogonal box = (-10 -10 -0.5) to (10 10 16)
1 by 1 by 1 processor grid
neighbor 0.2 bin
neigh_modify delay 0
# IMPORTANT NOTE: these values of stiffness (2000) and timestep (0.001)
# are used in this example file to produce a quick simulation and movie.
# More appropriate values for realistic simulations would be
# k = 2.0e5 and dt = 0.0001, as in bench/in.chute.
pair_style gran/history 2000.0 50.0 0.5 0
timestep 0.001
-fix 1 all nve/gran
+fix 1 all nve/sphere
fix 2 all gravity 1.0 spherical 0.0 -180.0
fix zlower all wall/gran zplane 0.0 2000.0 50.0 0.5
region slab block -9.0 9.0 -9.0 9.0 10.0 15.0 units box
fix ins all pour 3000 1 300719 vol 0.13 50 region slab
Particle insertion: 402 every 3162 steps, 3000 by step 22135
-thermo_style granular
+compute 1 all erotate/sphere
+thermo_style custom step atoms ke c_1 vol
thermo 1000
-thermo_modify lost ignore
+thermo_modify lost ignore norm no
compute_modify thermo_temp dynamic yes
dump id all atom 1000 dump.pour
run 25000
Memory usage per processor = 3.27422 Mbytes
-Step Atoms KinEng RotKEgrn Volume
+Step Atoms KinEng 1 Volume
0 0 -0 0 6600
1000 402 779.98578 0 6600
2000 402 1424.4252 0 6600
3000 402 1424.6738 13.243803 6600
4000 804 1725.9135 47.193854 6600
5000 804 1605.9404 61.336034 6600
6000 804 1364.6108 67.554058 6600
7000 1206 1511.4113 74.376707 6600
8000 1206 1418.913 57.671895 6600
9000 1206 1255.7489 48.517269 6600
10000 1608 1395.1949 50.233076 6600
11000 1608 1231.4271 49.441618 6600
12000 1608 1178.1027 41.300781 6600
13000 2010 1318.0975 45.154764 6600
14000 2010 1168.906 45.046369 6600
15000 2010 991.83164 47.199522 6600
16000 2412 1030.5908 42.172928 6600
17000 2412 1040.764 42.35251 6600
18000 2412 915.48473 38.944011 6600
19000 2814 1004.7982 37.785123 6600
20000 2814 943.31525 40.195691 6600
21000 2814 775.08206 46.791635 6600
22000 2814 506.44822 40.426627 6600
23000 3000 422.1483 32.45423 6600
24000 3000 365.17401 21.632169 6600
25000 3000 220.87181 24.123943 6600
-Loop time of 20.7499 on 1 procs for 25000 steps with 3000 atoms
+Loop time of 20.231 on 1 procs for 25000 steps with 3000 atoms
-Pair time (%) = 13.5449 (65.2771)
-Neigh time (%) = 1.67646 (8.07935)
-Comm time (%) = 0.364293 (1.75563)
-Outpt time (%) = 0.0648448 (0.312507)
-Other time (%) = 5.09938 (24.5754)
+Pair time (%) = 13.4518 (66.4912)
+Neigh time (%) = 1.66174 (8.21387)
+Comm time (%) = 0.362025 (1.78946)
+Outpt time (%) = 0.066838 (0.330375)
+Other time (%) = 4.68855 (23.1751)
Nlocal: 3000 ave 3000 max 3000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 676 ave 676 max 676 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 13442 ave 13442 max 13442 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 13442
Ave neighs/atom = 4.48067
Neighbor list builds = 1152
Dangerous builds = 0
unfix ins
fix 2 all gravity 1.0 chute 26.0
run 25000
-Memory usage per processor = 10.1398 Mbytes
-Step Atoms KinEng RotKEgrn Volume
+Memory usage per processor = 9.91094 Mbytes
+Step Atoms KinEng 1 Volume
25000 3000 220.87181 24.123943 6600
26000 3000 108.79862 20.458515 6600
27000 3000 112.95727 12.664104 6600
28000 3000 215.54144 11.782398 6600
29000 3000 371.54504 14.420759 6600
30000 3000 566.41521 19.512827 6600
31000 3000 806.02711 27.02433 6600
32000 3000 1120.8523 29.184297 6600
33000 3000 1463.1136 39.128552 6600
34000 3000 1891.5244 40.587604 6600
35000 3000 2385.1262 50.786058 6600
36000 3000 3032.2477 61.683546 6600
37000 3000 3641.4351 73.734062 6600
38000 3000 4437.2989 80.156198 6600
39000 3000 5121.4213 91.975359 6600
40000 3000 6104.1682 107.37087 6600
41000 3000 7037.7666 111.54587 6600
42000 3000 8098.2378 127.03506 6600
43000 3000 9264.5588 136.68653 6600
44000 3000 10435.983 166.01939 6600
45000 3000 11791.776 174.23082 6600
46000 3000 13107.257 187.32711 6600
47000 3000 14573.417 198.76957 6600
48000 3000 16081.514 219.64212 6600
49000 3000 17731.002 236.51098 6600
50000 3000 19431.348 255.96964 6600
-Loop time of 40.4029 on 1 procs for 25000 steps with 3000 atoms
+Loop time of 39.3461 on 1 procs for 25000 steps with 3000 atoms
-Pair time (%) = 28.6386 (70.8825)
-Neigh time (%) = 2.64738 (6.55244)
-Comm time (%) = 0.784085 (1.94067)
-Outpt time (%) = 0.108553 (0.268677)
-Other time (%) = 8.22431 (20.3558)
+Pair time (%) = 28.4144 (72.2164)
+Neigh time (%) = 2.58973 (6.58193)
+Comm time (%) = 0.766247 (1.94745)
+Outpt time (%) = 0.107744 (0.273835)
+Other time (%) = 7.46804 (18.9804)
Nlocal: 3000 ave 3000 max 3000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 760 ave 760 max 760 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 14061 ave 14061 max 14061 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 14061
Ave neighs/atom = 4.687
Neighbor list builds = 826
Dangerous builds = 0
diff --git a/examples/pour/log.pour.22Jan08.linux.4 b/examples/pour/log.pour.21May08.linux.4
similarity index 86%
rename from examples/pour/log.pour.22Jan08.linux.4
rename to examples/pour/log.pour.21May08.linux.4
index f2cd9821f..1676e3e74 100644
--- a/examples/pour/log.pour.22Jan08.linux.4
+++ b/examples/pour/log.pour.21May08.linux.4
@@ -1,136 +1,137 @@
-LAMMPS (22 Jan 2008)
+LAMMPS (21 May 2008)
# Pour granular particles into chute container, then induce flow
atom_style granular
boundary p p fm
newton off
region reg block -10 10 -10 10 -0.5 16 units box
create_box 1 reg
Created orthogonal box = (-10 -10 -0.5) to (10 10 16)
2 by 2 by 1 processor grid
neighbor 0.2 bin
neigh_modify delay 0
# IMPORTANT NOTE: these values of stiffness (2000) and timestep (0.001)
# are used in this example file to produce a quick simulation and movie.
# More appropriate values for realistic simulations would be
# k = 2.0e5 and dt = 0.0001, as in bench/in.chute.
pair_style gran/history 2000.0 50.0 0.5 0
timestep 0.001
-fix 1 all nve/gran
+fix 1 all nve/sphere
fix 2 all gravity 1.0 spherical 0.0 -180.0
fix zlower all wall/gran zplane 0.0 2000.0 50.0 0.5
region slab block -9.0 9.0 -9.0 9.0 10.0 15.0 units box
fix ins all pour 3000 1 300719 vol 0.13 50 region slab
Particle insertion: 402 every 3162 steps, 3000 by step 22135
-thermo_style granular
+compute 1 all erotate/sphere
+thermo_style custom step atoms ke c_1 vol
thermo 1000
-thermo_modify lost ignore
+thermo_modify lost ignore norm no
compute_modify thermo_temp dynamic yes
dump id all atom 1000 dump.pour
run 25000
Memory usage per processor = 3.14935 Mbytes
-Step Atoms KinEng RotKEgrn Volume
+Step Atoms KinEng 1 Volume
0 0 -0 0 6600
1000 402 779.98578 0 6600
2000 402 1424.4252 0 6600
3000 402 1424.6738 13.243803 6600
4000 804 1725.4319 47.250762 6600
5000 804 1605.2015 60.084404 6600
6000 804 1371.3425 69.247899 6600
7000 1206 1524.3574 74.071529 6600
8000 1206 1418.8999 60.727347 6600
9000 1206 1258.0064 51.943448 6600
10000 1608 1391.6571 50.505619 6600
11000 1608 1232.8265 50.877674 6600
12000 1608 1195.2804 46.358334 6600
13000 2010 1315.8232 49.633638 6600
14000 2010 1171.0007 43.965336 6600
15000 2010 984.42685 42.714353 6600
16000 2412 1028.8418 41.732668 6600
17000 2412 1016.9257 44.039977 6600
18000 2412 911.33181 36.804113 6600
19000 2814 1002.0117 38.864202 6600
20000 2814 960.38825 45.167894 6600
21000 2814 747.55191 45.970768 6600
22000 2814 523.67155 43.946925 6600
23000 3000 438.80433 35.866677 6600
24000 3000 350.60693 23.380222 6600
25000 3000 232.00186 22.76523 6600
-Loop time of 13.1865 on 4 procs for 25000 steps with 3000 atoms
+Loop time of 12.3364 on 4 procs for 25000 steps with 3000 atoms
-Pair time (%) = 3.85555 (29.2386)
-Neigh time (%) = 0.421859 (3.19917)
-Comm time (%) = 5.00618 (37.9644)
-Outpt time (%) = 0.0909717 (0.689884)
-Other time (%) = 3.81195 (28.908)
+Pair time (%) = 3.62034 (29.3469)
+Neigh time (%) = 0.423409 (3.4322)
+Comm time (%) = 4.89279 (39.6614)
+Outpt time (%) = 0.0863795 (0.700201)
+Other time (%) = 3.31347 (26.8593)
Nlocal: 750 ave 763 max 730 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Nghost: 393.25 ave 404 max 387 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Neighs: 3584.25 ave 3654 max 3500 min
Histogram: 1 0 0 0 1 0 0 1 0 1
Total # of neighbors = 14337
Ave neighs/atom = 4.779
Neighbor list builds = 1151
Dangerous builds = 0
unfix ins
fix 2 all gravity 1.0 chute 26.0
run 25000
-Memory usage per processor = 9.90906 Mbytes
-Step Atoms KinEng RotKEgrn Volume
+Memory usage per processor = 9.68018 Mbytes
+Step Atoms KinEng 1 Volume
25000 3000 232.00186 22.76523 6600
26000 3000 106.03482 19.110968 6600
27000 3000 117.35702 11.863221 6600
28000 3000 210.16302 11.734546 6600
29000 3000 364.51031 13.978019 6600
30000 3000 615.67035 19.096214 6600
31000 3000 903.47015 29.320372 6600
32000 3000 1251.3923 32.674763 6600
33000 3000 1705.6441 43.39215 6600
34000 3000 2196.1688 50.259234 6600
35000 3000 2774.3046 56.750935 6600
36000 3000 3390.0639 66.826889 6600
37000 3000 4108.0306 80.340967 6600
38000 3000 4931.8421 82.362753 6600
39000 3000 5798.3775 99.330342 6600
40000 3000 6729.1245 110.92274 6600
41000 3000 7780.6383 123.43956 6600
42000 3000 8927.2592 135.00244 6600
43000 3000 10032.341 144.35759 6600
44000 3000 11220.512 163.73946 6600
45000 3000 12527.526 182.56044 6600
46000 3000 14021.788 208.42883 6600
47000 3000 15724.627 221.7706 6600
48000 3000 17394.628 231.95039 6600
49000 3000 19056.668 255.27889 6600
50000 3000 20908.007 287.26263 6600
-Loop time of 19.7873 on 4 procs for 25000 steps with 3000 atoms
+Loop time of 18.252 on 4 procs for 25000 steps with 3000 atoms
-Pair time (%) = 8.2543 (41.7152)
-Neigh time (%) = 0.681514 (3.44421)
-Comm time (%) = 5.89918 (29.813)
-Outpt time (%) = 0.13265 (0.670383)
-Other time (%) = 4.81962 (24.3572)
+Pair time (%) = 7.67562 (42.0535)
+Neigh time (%) = 0.668073 (3.66027)
+Comm time (%) = 5.45432 (29.8833)
+Outpt time (%) = 0.128624 (0.704711)
+Other time (%) = 4.3254 (23.6982)
Nlocal: 750 ave 760 max 743 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Nghost: 406 ave 408 max 402 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Neighs: 3714 ave 3765 max 3659 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Total # of neighbors = 14856
Ave neighs/atom = 4.952
Neighbor list builds = 850
Dangerous builds = 0
diff --git a/examples/pour/log.pour.2d.21May08.linux.1 b/examples/pour/log.pour.2d.21May08.linux.1
new file mode 100644
index 000000000..7cdb1b579
--- /dev/null
+++ b/examples/pour/log.pour.2d.21May08.linux.1
@@ -0,0 +1,90 @@
+LAMMPS (21 May 2008)
+# Pour 2d granular particles into container
+
+dimension 2
+atom_style granular
+boundary f fm p
+newton off
+
+region reg block 0 100 0 50 -0.5 0.5 units box
+create_box 1 reg
+Created orthogonal box = (0 0 -0.5) to (100 50 0.5)
+ 1 by 1 by 1 processor grid
+
+neighbor 0.2 bin
+neigh_modify delay 0
+
+# IMPORTANT NOTE: these values of stiffness (2000) and timestep (0.001)
+# are used in this example file to produce a quick simulation and movie.
+# More appropriate values for realistic simulations would be
+# k = 2.0e5 and dt = 0.0001, as in bench/in.chute.
+
+pair_style gran/hertzian 2000.0 50.0 0.5 0
+timestep 0.001
+
+fix 1 all nve/sphere
+fix 2 all gravity 1.0 spherical 0.0 -180.0
+fix xwalls all wall/gran xplane 0 100 50 0
+fix ywalls all wall/gran yplane 0 NULL 50 0
+
+region slab block 1.0 99.0 30 34.5 -0.5 0.5 units box
+fix ins all pour 1000 1 4767548 vol 0.4 10 diam 0.5 1.0 region slab
+Particle insertion: 224 every 3000 steps, 1000 by step 12001
+
+fix 3 all enforce2d
+
+compute 1 all erotate/sphere
+thermo_style custom step atoms ke c_1 vol
+thermo 1000
+thermo_modify lost ignore norm no
+compute_modify thermo_temp dynamic yes
+
+dump id all atom 250 dump.pour
+run 25000
+Memory usage per processor = 3.12551 Mbytes
+Step Atoms KinEng 1 Volume
+ 0 0 -0 0 5000
+ 1000 224 348.20549 0 5000
+ 2000 224 650.98655 0 5000
+ 3000 224 1056.0039 0 5000
+ 4000 448 1941.6817 0 5000
+ 5000 448 2869.092 0 5000
+ 6000 448 3244.0285 59.709037 5000
+ 7000 672 3381.9514 72.635418 5000
+ 8000 672 3209.9845 135.37739 5000
+ 9000 672 3037.2686 125.65507 5000
+ 10000 896 2983.0247 113.16927 5000
+ 11000 896 2808.8482 72.058343 5000
+ 12000 896 2750.718 73.383261 5000
+ 13000 1000 2726.6048 65.657144 5000
+ 14000 1000 2512.3122 60.161228 5000
+ 15000 1000 2081.7342 49.717007 5000
+ 16000 1000 1454.4989 55.593577 5000
+ 17000 1000 838.42356 47.392952 5000
+ 18000 1000 591.78268 31.70284 5000
+ 19000 1000 267.16614 26.169498 5000
+ 20000 1000 39.186825 15.992488 5000
+ 21000 1000 25.943515 7.3119929 5000
+ 22000 1000 15.094337 4.2244747 5000
+ 23000 1000 8.3263828 2.7944168 5000
+ 24000 1000 4.0127427 1.5742141 5000
+ 25000 1000 1.6900361 0.87976982 5000
+Loop time of 6.8258 on 1 procs for 25000 steps with 1000 atoms
+
+Pair time (%) = 3.86265 (56.5889)
+Neigh time (%) = 0.370904 (5.43385)
+Comm time (%) = 0.0147769 (0.216486)
+Outpt time (%) = 0.113987 (1.66994)
+Other time (%) = 2.46349 (36.0908)
+
+Nlocal: 1000 ave 1000 max 1000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 2475 ave 2475 max 2475 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 2475
+Ave neighs/atom = 2.475
+Neighbor list builds = 1627
+Dangerous builds = 0
diff --git a/examples/pour/log.pour.2d.21May08.linux.4 b/examples/pour/log.pour.2d.21May08.linux.4
new file mode 100644
index 000000000..9bd2737b6
--- /dev/null
+++ b/examples/pour/log.pour.2d.21May08.linux.4
@@ -0,0 +1,90 @@
+LAMMPS (21 May 2008)
+# Pour 2d granular particles into container
+
+dimension 2
+atom_style granular
+boundary f fm p
+newton off
+
+region reg block 0 100 0 50 -0.5 0.5 units box
+create_box 1 reg
+Created orthogonal box = (0 0 -0.5) to (100 50 0.5)
+ 2 by 2 by 1 processor grid
+
+neighbor 0.2 bin
+neigh_modify delay 0
+
+# IMPORTANT NOTE: these values of stiffness (2000) and timestep (0.001)
+# are used in this example file to produce a quick simulation and movie.
+# More appropriate values for realistic simulations would be
+# k = 2.0e5 and dt = 0.0001, as in bench/in.chute.
+
+pair_style gran/hertzian 2000.0 50.0 0.5 0
+timestep 0.001
+
+fix 1 all nve/sphere
+fix 2 all gravity 1.0 spherical 0.0 -180.0
+fix xwalls all wall/gran xplane 0 100 50 0
+fix ywalls all wall/gran yplane 0 NULL 50 0
+
+region slab block 1.0 99.0 30 34.5 -0.5 0.5 units box
+fix ins all pour 1000 1 4767548 vol 0.4 10 diam 0.5 1.0 region slab
+Particle insertion: 224 every 3000 steps, 1000 by step 12001
+
+fix 3 all enforce2d
+
+compute 1 all erotate/sphere
+thermo_style custom step atoms ke c_1 vol
+thermo 1000
+thermo_modify lost ignore norm no
+compute_modify thermo_temp dynamic yes
+
+dump id all atom 250 dump.pour
+run 25000
+Memory usage per processor = 3.09867 Mbytes
+Step Atoms KinEng 1 Volume
+ 0 0 -0 0 5000
+ 1000 224 348.20549 0 5000
+ 2000 224 650.98655 0 5000
+ 3000 224 1056.0039 0 5000
+ 4000 448 1941.6817 0 5000
+ 5000 448 2869.092 0 5000
+ 6000 448 3244.0285 59.709037 5000
+ 7000 672 3381.9514 72.635418 5000
+ 8000 672 3209.9845 135.37739 5000
+ 9000 672 3037.2686 125.65507 5000
+ 10000 896 2983.0247 113.16927 5000
+ 11000 896 2808.8482 72.058343 5000
+ 12000 896 2750.718 73.383261 5000
+ 13000 1000 2726.6044 65.656874 5000
+ 14000 1000 2512.4219 59.997862 5000
+ 15000 1000 2086.6017 51.808696 5000
+ 16000 1000 1465.7682 53.531804 5000
+ 17000 1000 830.37814 47.232643 5000
+ 18000 1000 598.17657 29.282204 5000
+ 19000 1000 253.30511 31.894452 5000
+ 20000 1000 37.347525 17.140954 5000
+ 21000 1000 20.803138 8.8531328 5000
+ 22000 1000 15.095346 4.8904454 5000
+ 23000 1000 8.7452294 2.3928721 5000
+ 24000 1000 5.0388199 1.1642031 5000
+ 25000 1000 3.4373452 0.74346362 5000
+Loop time of 9.49783 on 4 procs for 25000 steps with 1000 atoms
+
+Pair time (%) = 1.01844 (10.7229)
+Neigh time (%) = 0.101886 (1.07273)
+Comm time (%) = 3.84115 (40.4424)
+Outpt time (%) = 0.142735 (1.50282)
+Other time (%) = 4.39362 (46.2592)
+
+Nlocal: 250 ave 505 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost: 5.25 ave 11 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs: 627.25 ave 1265 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 2509
+Ave neighs/atom = 2.509
+Neighbor list builds = 1627
+Dangerous builds = 0
diff --git a/examples/pour/log.pour.2d.22Jan08.linux.1 b/examples/pour/log.pour.2d.22Jan08.linux.1
deleted file mode 100644
index 0b97aa134..000000000
--- a/examples/pour/log.pour.2d.22Jan08.linux.1
+++ /dev/null
@@ -1,89 +0,0 @@
-LAMMPS (22 Jan 2008)
-# Pour 2d granular particles into container
-
-dimension 2
-atom_style granular
-boundary f fm p
-newton off
-
-region reg block 0 100 0 50 -0.5 0.5 units box
-create_box 1 reg
-Created orthogonal box = (0 0 -0.5) to (100 50 0.5)
- 1 by 1 by 1 processor grid
-
-neighbor 0.2 bin
-neigh_modify delay 0
-
-# IMPORTANT NOTE: these values of stiffness (2000) and timestep (0.001)
-# are used in this example file to produce a quick simulation and movie.
-# More appropriate values for realistic simulations would be
-# k = 2.0e5 and dt = 0.0001, as in bench/in.chute.
-
-pair_style gran/hertzian 2000.0 50.0 0.5 0
-timestep 0.001
-
-fix 1 all nve/gran
-fix 2 all gravity 1.0 spherical 0.0 -180.0
-fix xwalls all wall/gran xplane 0 100 50 0
-fix ywalls all wall/gran yplane 0 NULL 50 0
-
-region slab block 1.0 99.0 30 34.5 -0.5 0.5 units box
-fix ins all pour 1000 1 4767548 vol 0.4 10 diam 0.5 1.0 region slab
-Particle insertion: 224 every 3000 steps, 1000 by step 12001
-
-fix 3 all enforce2d
-
-thermo_style granular
-thermo 1000
-thermo_modify lost ignore
-compute_modify thermo_temp dynamic yes
-
-dump id all atom 250 dump.pour
-run 25000
-Memory usage per processor = 3.12551 Mbytes
-Step Atoms KinEng RotKEgrn Volume
- 0 0 -0 0 5000
- 1000 224 348.20549 0 5000
- 2000 224 650.98655 0 5000
- 3000 224 1056.0039 0 5000
- 4000 448 1941.6817 0 5000
- 5000 448 2869.092 0 5000
- 6000 448 3240.26 51.002089 5000
- 7000 672 3375.857 86.854847 5000
- 8000 672 3218.9668 120.74194 5000
- 9000 672 3042.428 99.125781 5000
- 10000 896 2986.9987 88.589831 5000
- 11000 896 2829.33 66.164478 5000
- 12000 896 2741.8245 63.121028 5000
- 13000 1000 2712.5291 62.754703 5000
- 14000 1000 2476.3302 60.318998 5000
- 15000 1000 2074.2112 55.107868 5000
- 16000 1000 1441.07 57.502968 5000
- 17000 1000 837.81119 47.509652 5000
- 18000 1000 606.38794 34.97416 5000
- 19000 1000 267.8998 34.474186 5000
- 20000 1000 38.669262 19.982355 5000
- 21000 1000 21.342125 11.876372 5000
- 22000 1000 14.57957 5.6091923 5000
- 23000 1000 8.3300727 3.1535324 5000
- 24000 1000 5.3845351 1.4196696 5000
- 25000 1000 3.436019 0.90458586 5000
-Loop time of 7.10731 on 1 procs for 25000 steps with 1000 atoms
-
-Pair time (%) = 3.94757 (55.5425)
-Neigh time (%) = 0.374912 (5.27501)
-Comm time (%) = 0.0137208 (0.193051)
-Outpt time (%) = 0.114302 (1.60824)
-Other time (%) = 2.6568 (37.3812)
-
-Nlocal: 1000 ave 1000 max 1000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 0 ave 0 max 0 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 2464 ave 2464 max 2464 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 2464
-Ave neighs/atom = 2.464
-Neighbor list builds = 1615
-Dangerous builds = 0
diff --git a/examples/pour/log.pour.2d.22Jan08.linux.4 b/examples/pour/log.pour.2d.22Jan08.linux.4
deleted file mode 100644
index fb59cf25f..000000000
--- a/examples/pour/log.pour.2d.22Jan08.linux.4
+++ /dev/null
@@ -1,89 +0,0 @@
-LAMMPS (22 Jan 2008)
-# Pour 2d granular particles into container
-
-dimension 2
-atom_style granular
-boundary f fm p
-newton off
-
-region reg block 0 100 0 50 -0.5 0.5 units box
-create_box 1 reg
-Created orthogonal box = (0 0 -0.5) to (100 50 0.5)
- 2 by 2 by 1 processor grid
-
-neighbor 0.2 bin
-neigh_modify delay 0
-
-# IMPORTANT NOTE: these values of stiffness (2000) and timestep (0.001)
-# are used in this example file to produce a quick simulation and movie.
-# More appropriate values for realistic simulations would be
-# k = 2.0e5 and dt = 0.0001, as in bench/in.chute.
-
-pair_style gran/hertzian 2000.0 50.0 0.5 0
-timestep 0.001
-
-fix 1 all nve/gran
-fix 2 all gravity 1.0 spherical 0.0 -180.0
-fix xwalls all wall/gran xplane 0 100 50 0
-fix ywalls all wall/gran yplane 0 NULL 50 0
-
-region slab block 1.0 99.0 30 34.5 -0.5 0.5 units box
-fix ins all pour 1000 1 4767548 vol 0.4 10 diam 0.5 1.0 region slab
-Particle insertion: 224 every 3000 steps, 1000 by step 12001
-
-fix 3 all enforce2d
-
-thermo_style granular
-thermo 1000
-thermo_modify lost ignore
-compute_modify thermo_temp dynamic yes
-
-dump id all atom 250 dump.pour
-run 25000
-Memory usage per processor = 3.09867 Mbytes
-Step Atoms KinEng RotKEgrn Volume
- 0 0 -0 0 5000
- 1000 224 348.20549 0 5000
- 2000 224 650.98655 0 5000
- 3000 224 1056.0039 0 5000
- 4000 448 1941.6817 0 5000
- 5000 448 2869.092 0 5000
- 6000 448 3240.26 51.002089 5000
- 7000 672 3375.857 86.854847 5000
- 8000 672 3218.9668 120.74194 5000
- 9000 672 3042.428 99.125781 5000
- 10000 896 2986.9987 88.589831 5000
- 11000 896 2829.33 66.164478 5000
- 12000 896 2741.8245 63.121034 5000
- 13000 1000 2712.6085 62.756506 5000
- 14000 1000 2481.4123 60.427347 5000
- 15000 1000 2061.8464 56.399834 5000
- 16000 1000 1452.1851 54.458544 5000
- 17000 1000 833.03811 44.980618 5000
- 18000 1000 585.79885 36.672365 5000
- 19000 1000 276.7811 30.881939 5000
- 20000 1000 30.566489 17.571585 5000
- 21000 1000 18.21801 9.3358364 5000
- 22000 1000 11.354764 5.1520478 5000
- 23000 1000 7.4178622 2.1905651 5000
- 24000 1000 4.6531861 1.0674461 5000
- 25000 1000 2.6666049 0.68062336 5000
-Loop time of 9.60115 on 4 procs for 25000 steps with 1000 atoms
-
-Pair time (%) = 1.08202 (11.2697)
-Neigh time (%) = 0.110134 (1.14709)
-Comm time (%) = 3.93212 (40.9546)
-Outpt time (%) = 0.141791 (1.47682)
-Other time (%) = 4.33509 (45.1518)
-
-Nlocal: 250 ave 503 max 0 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Nghost: 6.25 ave 13 max 0 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Neighs: 621.75 ave 1244 max 0 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-
-Total # of neighbors = 2487
-Ave neighs/atom = 2.487
-Neighbor list builds = 1607
-Dangerous builds = 0
diff --git a/examples/rigid/log.rigid.22Jan08.linux.1 b/examples/rigid/log.rigid.21May08.linux.1
similarity index 98%
rename from examples/rigid/log.rigid.22Jan08.linux.1
rename to examples/rigid/log.rigid.21May08.linux.1
index eb4f29459..b720fc17a 100644
--- a/examples/rigid/log.rigid.22Jan08.linux.1
+++ b/examples/rigid/log.rigid.21May08.linux.1
@@ -1,306 +1,306 @@
-LAMMPS (22 Jan 2008)
+LAMMPS (21 May 2008)
# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 1 by 1 processor grid
81 atoms
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
fix 1 all rigid group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
9 rigid bodies with 81 atoms
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
dump 1 all atom 50 dump.rigid
timestep 0.0001
thermo 50
run 10000
Memory usage per processor = 1.62637 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.9722862e-05 0 5269.5046 14.510657
2650 16733.017 1.705148 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419351 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554428 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.059327511 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.846062 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663195 0 5269.4882 12.027009
3700 16738.602 -0.070934367 0 5269.4889 12.025288
3750 16737.731 0.20706556 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06942 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.00022115871 0 5269.5122 12.011687
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.0003969066 0 5269.5189 12.011706
8500 16738.481 -0.0034646801 0 5269.5182 12.011643
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
8600 16738.474 -0.00076532814 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.00037652441 0 5269.5216 12.011692
9550 16738.493 -0.0053156161 0 5269.5203 12.011611
9600 16738.549 -0.026814371 0 5269.5163 12.011415
9650 16738.765 -0.10191524 0 5269.5092 12.011013
9700 16735.041 1.0589895 0 5269.4979 12.062708
9750 16738.013 0.13550067 0 5269.5101 11.407245
9800 16738.512 -0.011620329 0 5269.5201 11.394973
9850 16738.489 -0.00067270563 0 5269.5237 11.395098
9900 16738.489 -0.00024984585 0 5269.5242 11.395084
9950 16738.49 0 0 5269.5245 11.395076
10000 16738.49 0 0 5269.5246 11.395075
-Loop time of 0.235085 on 1 procs for 10000 steps with 81 atoms
+Loop time of 0.236778 on 1 procs for 10000 steps with 81 atoms
-Pair time (%) = 0.0157146 (6.68466)
-Neigh time (%) = 0.0421674 (17.9371)
-Comm time (%) = 0.0163469 (6.95363)
-Outpt time (%) = 0.0261998 (11.1448)
-Other time (%) = 0.134656 (57.2798)
+Pair time (%) = 0.0151129 (6.38272)
+Neigh time (%) = 0.0427065 (18.0365)
+Comm time (%) = 0.0166826 (7.04568)
+Outpt time (%) = 0.0264668 (11.1779)
+Other time (%) = 0.135809 (57.3572)
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 84 ave 84 max 84 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 998
Dangerous builds = 997
diff --git a/examples/rigid/log.rigid.22Jan08.linux.4 b/examples/rigid/log.rigid.21May08.linux.4
similarity index 98%
rename from examples/rigid/log.rigid.22Jan08.linux.4
rename to examples/rigid/log.rigid.21May08.linux.4
index 9a58b581c..bc4d6dc23 100644
--- a/examples/rigid/log.rigid.22Jan08.linux.4
+++ b/examples/rigid/log.rigid.21May08.linux.4
@@ -1,306 +1,306 @@
-LAMMPS (22 Jan 2008)
+LAMMPS (21 May 2008)
# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 2 by 2 processor grid
81 atoms
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
fix 1 all rigid group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
9 rigid bodies with 81 atoms
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
dump 1 all atom 50 dump.rigid
timestep 0.0001
thermo 50
run 10000
Memory usage per processor = 1.59069 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.9722858e-05 0 5269.5046 14.510657
2650 16733.017 1.705148 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419351 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554428 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.059327511 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.846062 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663195 0 5269.4882 12.027009
3700 16738.602 -0.070934366 0 5269.4889 12.025288
3750 16737.731 0.20706556 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06942 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.00022115871 0 5269.5122 12.011687
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690659 0 5269.5189 12.011706
8500 16738.481 -0.0034646801 0 5269.5182 12.011643
8550 16738.483 -0.0045307409 0 5269.5178 12.01162
8600 16738.474 -0.00076532815 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.00037652443 0 5269.5216 12.011692
9550 16738.493 -0.0053156163 0 5269.5203 12.011611
9600 16738.549 -0.026814373 0 5269.5163 12.011415
9650 16738.765 -0.10191524 0 5269.5092 12.011013
9700 16735.041 1.0589901 0 5269.4979 12.062708
9750 16738.013 0.13550062 0 5269.5101 11.407245
9800 16738.512 -0.011620328 0 5269.5201 11.394973
9850 16738.489 -0.00067270547 0 5269.5237 11.395098
9900 16738.489 -0.00024984583 0 5269.5242 11.395084
9950 16738.49 0 0 5269.5245 11.395076
10000 16738.49 0 0 5269.5246 11.395075
-Loop time of 4.3193 on 4 procs for 10000 steps with 81 atoms
+Loop time of 4.06518 on 4 procs for 10000 steps with 81 atoms
-Pair time (%) = 0.00839633 (0.194391)
-Neigh time (%) = 0.0188292 (0.435933)
-Comm time (%) = 3.17395 (73.4829)
-Outpt time (%) = 0.168198 (3.89411)
-Other time (%) = 0.949927 (21.9926)
+Pair time (%) = 0.00766569 (0.18857)
+Neigh time (%) = 0.0178966 (0.440241)
+Comm time (%) = 2.97041 (73.0696)
+Outpt time (%) = 0.147557 (3.62977)
+Other time (%) = 0.921653 (22.6719)
Nlocal: 20.25 ave 38 max 3 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Nghost: 27.25 ave 48 max 13 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 998
Dangerous builds = 997
diff --git a/examples/rigid/log.rigid.poems.22Jan08.linux.1 b/examples/rigid/log.rigid.poems.21May08.linux.1
similarity index 98%
rename from examples/rigid/log.rigid.poems.22Jan08.linux.1
rename to examples/rigid/log.rigid.poems.21May08.linux.1
index 01b3247ed..c585f681f 100644
--- a/examples/rigid/log.rigid.poems.22Jan08.linux.1
+++ b/examples/rigid/log.rigid.poems.21May08.linux.1
@@ -1,306 +1,306 @@
-LAMMPS (22 Jan 2008)
+LAMMPS (21 May 2008)
# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 1 by 1 processor grid
81 atoms
velocity all create 100.0 4928459
# unconnected bodies
#group clump1 id <> 1 9
#group clump2 id <> 10 18
#group clump3 id <> 19 27
#group clump4 id <> 28 36
#group clump5 id <> 37 45
#group clump6 id <> 46 54
#group clump7 id <> 55 63
#group clump8 id <> 64 72
#group clump9 id <> 73 81
#fix 1 all rigid group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 1 chain of connected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 9 18
10 atoms in group clump2
group clump3 id <> 18 27
10 atoms in group clump3
group clump4 id <> 27 36
10 atoms in group clump4
group clump5 id <> 36 45
10 atoms in group clump5
group clump6 id <> 45 54
10 atoms in group clump6
group clump7 id <> 54 63
10 atoms in group clump7
group clump8 id <> 63 72
10 atoms in group clump8
group clump9 id <> 72 81
10 atoms in group clump9
fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
1 clusters, 9 bodies, 8 joints, 81 atoms
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
dump 1 all atom 50 dump.rigid
timestep 0.0001
thermo 50
run 10000
Memory usage per processor = 1.70328 Mbytes
Step Temp E_pair E_mol TotEng Press
0 217.7783 3430.3907 0 3466.6871 -2.7403788
50 13679.637 1404.2468 0 3684.1863 12.446066
100 16777.225 888.87665 0 3685.0808 -31.828677
150 19595.365 418.45042 0 3684.3446 40.709078
200 18524.188 596.47273 0 3683.8375 -0.8159371
250 21015.789 180.96521 0 3683.5967 -10.042469
300 20785.513 219.25314 0 3683.5053 2.6452719
350 21072.46 171.2554 0 3683.3321 7.0609024
400 19956.414 356.36381 0 3682.4328 19.320259
450 20724.42 227.73284 0 3681.8028 8.1259249
500 20152.578 322.71466 0 3681.4777 5.4929878
550 20017.022 345.29701 0 3681.4673 5.4661666
600 17897.743 698.72196 0 3681.6791 3.2854742
650 17297.758 796.60256 0 3679.5623 15.191113
700 18581.934 584.29715 0 3681.2861 5.1588289
750 21774.158 52.821062 0 3681.8474 -10.775664
800 21604.055 81.188546 0 3681.8644 -3.2045743
850 17821.483 711.53827 0 3681.7854 7.4384277
900 21033.292 175.98127 0 3681.5299 -16.345167
950 20968.166 186.59847 0 3681.2929 -2.330456
1000 20490.66 266.19375 0 3681.3037 11.787983
1050 20222.396 310.94072 0 3681.34 -8.3459539
1100 21321.687 127.61533 0 3681.2299 -1.2184717
1150 20849.582 206.01695 0 3680.9472 -0.86699149
1200 21815.003 45.317414 0 3681.1512 1.5988314
1250 18655.437 572.41453 0 3681.654 10.064078
1300 20780.781 217.36507 0 3680.8286 6.0538616
1350 20558.971 254.36482 0 3680.8601 -3.6773953
1400 21485.029 99.812921 0 3680.6511 -16.185473
1450 21771.107 52.15961 0 3680.6775 -2.4756673
1500 21520.948 93.503926 0 3680.3286 2.1023577
1550 21351.418 121.68137 0 3680.2511 5.5159947
1600 20778.805 216.92177 0 3680.0559 15.089188
1650 21477.638 100.21836 0 3679.8247 -1.1045742
1700 18501.339 596.47916 0 3680.0357 -15.679679
1750 18563.642 587.34789 0 3681.2882 33.53221
1800 19110.185 494.8234 0 3679.8543 18.024047
1850 21364.191 119.23543 0 3679.9339 2.5291097
1900 20146.627 322.14858 0 3679.9197 5.7313185
1950 20692.672 231.25332 0 3680.0319 4.2977747
2000 20943.904 189.11229 0 3679.7629 -22.645118
2050 19668.058 401.8298 0 3679.8394 3.6251799
2100 20280.442 299.76157 0 3679.8353 7.4807895
2150 19181.854 483.52299 0 3680.4987 22.620535
2200 21300.162 130.70525 0 3680.7322 4.7102567
2250 20486.948 266.63856 0 3681.1299 -8.645617
2300 18653.145 572.24428 0 3681.1018 -5.2637694
2350 21513.521 95.615166 0 3681.2021 -9.3621252
2400 21466.273 103.56429 0 3681.2765 -29.561439
2450 20100.086 332.27439 0 3682.2887 35.745178
2500 20764.384 221.6694 0 3682.4001 -12.469215
2550 20435.636 276.32104 0 3682.2603 -22.41345
2600 21466.443 104.54014 0 3682.2807 -10.078462
2650 20813.884 213.38106 0 3682.3617 5.1419485
2700 18565.501 588.40046 0 3682.6507 22.275657
2750 20769.76 220.59385 0 3682.2204 -7.9304099
2800 21014.35 179.80288 0 3682.1946 -7.0714386
2850 16780.444 885.71086 0 3682.4515 33.327109
2900 19301.711 465.19486 0 3682.1466 7.9488604
2950 20512.279 263.32376 0 3682.037 2.2691755
3000 20616.386 246.10536 0 3682.1698 -0.87560484
3050 18546.175 591.46309 0 3682.4922 -3.563201
3100 18589.568 584.13363 0 3682.395 -1.4433707
3150 20313.633 296.70715 0 3682.3127 5.0252684
3200 19324.457 461.67431 0 3682.4171 -0.29955759
3250 21515.748 96.273451 0 3682.2314 0.46353372
3300 20101.661 331.90071 0 3682.1776 4.3088543
3350 18503.393 597.99615 0 3681.8949 1.5805082
3400 19244.218 474.12808 0 3681.4977 9.9736162
3450 20440.714 275.18246 0 3681.9682 7.5888252
3500 19184.658 485.02691 0 3682.4699 1.080181
3550 20811.39 213.54898 0 3682.1141 -8.7881254
3600 18282.078 635.00903 0 3682.022 -13.693383
3650 17410.555 780.2866 0 3682.0458 -3.1631566
3700 15750.477 1057.3064 0 3682.3859 45.727704
3750 19562.836 421.07779 0 3681.5505 0.00056675794
3800 18898.305 530.58368 0 3680.3011 -15.039302
3850 20669.98 235.8331 0 3680.8298 -16.034069
3900 19680.004 401.17798 0 3681.1787 6.3384156
3950 18711.084 562.3823 0 3680.8962 0.68109414
4000 21192.725 149.74067 0 3681.8615 -3.6868572
4050 17818.626 712.22624 0 3681.9972 -23.806685
4100 16574.851 919.48098 0 3681.9562 -3.3600075
4150 21214.106 146.18774 0 3681.8721 2.7822122
4200 19709.923 397.26964 0 3682.2568 23.638764
4250 20988.614 184.16183 0 3682.2641 5.6467392
4300 21077.245 169.45414 0 3682.3284 -3.2759267
4350 18277.342 636.18259 0 3682.4062 1.1352386
4400 18488.177 600.07191 0 3681.4347 2.5369004
4450 19815.536 379.47225 0 3682.0615 -7.589101
4500 20535.901 259.16275 0 3681.8129 -1.1505361
4550 19480.188 435.47431 0 3682.1723 10.418166
4600 20163.968 321.1522 0 3681.8135 3.5491588
4650 21245.344 140.74399 0 3681.6346 -9.0022793
4700 19839.13 375.18705 0 3681.7087 6.9271776
4750 18390.547 616.78565 0 3681.8769 1.2873012
4800 19461.935 438.17504 0 3681.8308 -0.24779292
4850 18580.433 583.20736 0 3679.9462 10.15968
4900 21197.138 148.91446 0 3681.7708 1.4637295
4950 20624.65 244.13833 0 3681.5799 2.016093
5000 16136.434 992.86482 0 3682.2705 33.241782
5050 19460.401 437.60007 0 3681.0003 -25.703635
5100 20564.687 252.20769 0 3679.6556 6.2923966
5150 18775.592 551.99046 0 3681.2559 -19.910467
5200 17221.891 808.29471 0 3678.6098 -13.507697
5250 16826.206 876.56509 0 3680.9328 3.4329372
5300 20268.599 301.83666 0 3679.9366 13.804455
5350 20793.551 215.4013 0 3680.9931 4.6113121
5400 20835.003 208.24189 0 3680.7425 6.769571
5450 21231.898 142.36703 0 3681.0167 -9.1840288
5500 21770.447 52.883524 0 3681.2913 -15.581402
5550 20640.647 241.05037 0 3681.1582 7.1067478
5600 20334.25 292.48318 0 3681.5249 12.383931
5650 21918.294 28.527054 0 3681.5761 -11.715275
5700 19864.155 370.63971 0 3681.3321 -5.2498493
5750 19557.161 421.88326 0 3681.4101 10.266535
5800 21269.731 136.5163 0 3681.4715 -10.278869
5850 21217.567 144.87176 0 3681.133 -0.80004201
5900 20918.58 195.24343 0 3681.6734 -8.150687
5950 21562.393 87.966931 0 3681.6991 -7.0807503
6000 21737.026 58.960399 0 3681.798 0.35986633
6050 17665.146 736.87753 0 3681.0686 5.2353386
6100 21598.518 82.139112 0 3681.8921 -1.2295188
6150 18494 598.69844 0 3681.0318 -0.20557276
6200 21389.01 117.09447 0 3681.9295 -3.924552
6250 16832.48 875.20604 0 3680.6194 9.2758218
6300 20843.101 207.89957 0 3681.7497 -19.64557
6350 21327.871 127.43496 0 3682.0802 4.7716132
6400 21608.557 80.648525 0 3682.0746 -4.5491082
6450 21032.73 176.63135 0 3682.0864 3.6489024
6500 20344.987 290.8943 0 3681.7254 9.8516499
6550 19678.626 402.78527 0 3682.5563 -1.8297694
6600 17295.165 800.41146 0 3682.9389 3.6350738
6650 20548.144 257.97873 0 3682.6693 -42.05301
6700 21960.005 22.701541 0 3682.7024 -0.95498029
6750 21729.937 61.096002 0 3682.7522 4.8631652
6800 18818.035 546.40671 0 3682.7459 21.54246
6850 21180.871 152.66411 0 3682.8092 0.94209582
6900 21017.832 180.10147 0 3683.0734 -4.8512515
6950 20249.329 308.2243 0 3683.1124 -2.6970441
7000 16804.378 881.69654 0 3682.4261 1.8674304
7050 20279.639 302.9926 0 3682.9324 2.2882089
7100 21600.318 82.43581 0 3682.4888 -0.71486428
7150 16021.959 1012.5955 0 3682.9219 56.58285
7200 21585.896 84.669721 0 3682.319 1.060683
7250 21866.085 38.36431 0 3682.7118 -20.485419
7300 21718.518 62.967065 0 3682.7201 -15.805437
7350 18342.257 626.05933 0 3683.1022 -3.043995
7400 17585.563 752.4367 0 3683.3638 -15.498606
7450 14528.846 1262.5094 0 3683.9838 21.254966
7500 15820.666 1048.1264 0 3684.904 25.125876
7550 17630.095 744.07477 0 3682.4239 39.589015
7600 19755.97 390.01252 0 3682.6742 9.5527462
7650 21458.765 106.39492 0 3682.8557 -9.936815
7700 20195.194 317.14575 0 3683.0115 4.7293356
7750 18732.191 560.63272 0 3682.6646 29.587235
7800 19116.166 496.9194 0 3682.9471 8.01901
7850 20280.124 302.81132 0 3682.8321 -11.043326
7900 21584.811 85.465061 0 3682.9335 -20.236362
7950 19984.439 352.33839 0 3683.0782 -1.5496264
8000 18125.139 661.57474 0 3682.4312 -4.8267022
8050 19855.454 373.83997 0 3683.0824 -22.955733
8100 20400.376 282.70579 0 3682.7684 2.0217495
8150 20845.356 208.15672 0 3682.3827 -4.1597311
8200 20205.92 314.8131 0 3682.4664 -5.9347186
8250 18738.9 560.91355 0 3684.0635 2.0453533
8300 18607.944 580.69362 0 3682.0176 8.2163881
8350 16196.778 985.05148 0 3684.5144 8.3636546
8400 17585.741 752.82214 0 3683.779 -19.614442
8450 19511.86 430.32203 0 3682.2986 5.0608865
8500 20344.705 291.77489 0 3682.559 8.8918697
8550 19569.705 421.04089 0 3682.6585 8.4785194
8600 20289.223 300.95145 0 3682.4886 -3.9742259
8650 20379.787 286.55509 0 3683.1863 2.4827334
8700 21154.115 157.61851 0 3683.3043 -16.912866
8750 21472.217 104.41783 0 3683.1206 -21.300046
8800 21760.162 55.671759 0 3682.3654 -0.75786283
8850 20692.844 232.77873 0 3681.5861 6.3078965
8900 20153.783 322.18497 0 3681.1488 8.7099041
8950 19227.235 476.49095 0 3681.0302 7.8953617
9000 20017.406 344.69787 0 3680.9322 4.6812502
9050 21920.802 27.552335 0 3681.0194 -10.804625
9100 15935.584 1026.2618 0 3682.1926 22.793783
9150 21442.198 106.89206 0 3680.5917 -11.609027
9200 19035.95 507.80063 0 3680.459 -4.9227937
9250 20697.672 230.59419 0 3680.2062 -15.921697
9300 19859.816 369.18531 0 3679.1546 13.040337
9350 21181.669 149.7683 0 3680.0465 -15.76144
9400 20944.752 188.76152 0 3679.5535 -2.2751162
9450 20241.642 305.75441 0 3679.3615 4.6023616
9500 17745.73 721.6338 0 3679.2554 5.0753949
9550 18246.781 638.2829 0 3679.413 1.0522421
9600 20638.149 239.65443 0 3679.3459 4.3928288
9650 18215.957 643.21932 0 3679.2121 24.221766
9700 20328.363 290.95626 0 3679.0168 -0.15311046
9750 20900.251 195.40818 0 3678.7834 -7.254656
9800 20740.739 221.81279 0 3678.6027 -0.25607258
9850 21538.915 88.737884 0 3678.5571 1.9528485
9900 19690.077 396.95803 0 3678.6375 1.6169288
9950 20574.352 249.26902 0 3678.3277 5.9594646
10000 20861.51 201.85286 0 3678.7712 -0.64028741
-Loop time of 7.25136 on 1 procs for 10000 steps with 81 atoms
+Loop time of 7.26124 on 1 procs for 10000 steps with 81 atoms
-Pair time (%) = 0.280846 (3.87301)
-Neigh time (%) = 0.125411 (1.72948)
-Comm time (%) = 0.0173204 (0.238857)
-Outpt time (%) = 0.0274284 (0.378252)
-Other time (%) = 6.80035 (93.7804)
+Pair time (%) = 0.280442 (3.86218)
+Neigh time (%) = 0.121096 (1.6677)
+Comm time (%) = 0.0176237 (0.242709)
+Outpt time (%) = 0.0308731 (0.425176)
+Other time (%) = 6.8112 (93.8022)
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 72 ave 72 max 72 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1038 ave 1038 max 1038 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1038
Ave neighs/atom = 12.8148
Neighbor list builds = 991
Dangerous builds = 926
diff --git a/examples/rigid/log.rigid.poems.22Jan08.linux.4 b/examples/rigid/log.rigid.poems.21May08.linux.4
similarity index 98%
rename from examples/rigid/log.rigid.poems.22Jan08.linux.4
rename to examples/rigid/log.rigid.poems.21May08.linux.4
index f13e851eb..b8f4e123a 100644
--- a/examples/rigid/log.rigid.poems.22Jan08.linux.4
+++ b/examples/rigid/log.rigid.poems.21May08.linux.4
@@ -1,306 +1,306 @@
-LAMMPS (22 Jan 2008)
+LAMMPS (21 May 2008)
# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 2 by 2 processor grid
81 atoms
velocity all create 100.0 4928459
# unconnected bodies
#group clump1 id <> 1 9
#group clump2 id <> 10 18
#group clump3 id <> 19 27
#group clump4 id <> 28 36
#group clump5 id <> 37 45
#group clump6 id <> 46 54
#group clump7 id <> 55 63
#group clump8 id <> 64 72
#group clump9 id <> 73 81
#fix 1 all rigid group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 1 chain of connected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 9 18
10 atoms in group clump2
group clump3 id <> 18 27
10 atoms in group clump3
group clump4 id <> 27 36
10 atoms in group clump4
group clump5 id <> 36 45
10 atoms in group clump5
group clump6 id <> 45 54
10 atoms in group clump6
group clump7 id <> 54 63
10 atoms in group clump7
group clump8 id <> 63 72
10 atoms in group clump8
group clump9 id <> 72 81
10 atoms in group clump9
fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
1 clusters, 9 bodies, 8 joints, 81 atoms
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
dump 1 all atom 50 dump.rigid
timestep 0.0001
thermo 50
run 10000
Memory usage per processor = 1.66715 Mbytes
Step Temp E_pair E_mol TotEng Press
0 217.7783 3430.3907 0 3466.6871 -2.7403788
50 13679.637 1404.2468 0 3684.1863 12.446066
100 16777.225 888.87665 0 3685.0808 -31.828677
150 19595.365 418.45042 0 3684.3446 40.709078
200 18524.188 596.47273 0 3683.8375 -0.8159371
250 21015.789 180.96521 0 3683.5967 -10.042469
300 20785.513 219.25314 0 3683.5053 2.6452719
350 21072.46 171.2554 0 3683.3321 7.0609024
400 19956.414 356.36381 0 3682.4328 19.320259
450 20724.42 227.73284 0 3681.8028 8.1259249
500 20152.578 322.71466 0 3681.4777 5.4929878
550 20017.022 345.29701 0 3681.4673 5.4661666
600 17897.743 698.72196 0 3681.6791 3.2854742
650 17297.758 796.60256 0 3679.5623 15.191113
700 18581.934 584.29715 0 3681.2861 5.1588289
750 21774.158 52.821062 0 3681.8474 -10.775664
800 21604.055 81.188546 0 3681.8644 -3.2045743
850 17821.483 711.53827 0 3681.7854 7.4384277
900 21033.292 175.98127 0 3681.5299 -16.345167
950 20968.166 186.59847 0 3681.2929 -2.330456
1000 20490.66 266.19375 0 3681.3037 11.787983
1050 20222.396 310.94072 0 3681.34 -8.3459539
1100 21321.687 127.61533 0 3681.2299 -1.2184717
1150 20849.582 206.01695 0 3680.9472 -0.86699147
1200 21815.003 45.317414 0 3681.1512 1.5988314
1250 18655.437 572.41453 0 3681.654 10.064078
1300 20780.781 217.36507 0 3680.8286 6.0538616
1350 20558.971 254.36483 0 3680.8601 -3.6773951
1400 21485.029 99.812918 0 3680.6511 -16.185473
1450 21771.107 52.15961 0 3680.6775 -2.4756673
1500 21520.948 93.503924 0 3680.3286 2.1023577
1550 21351.418 121.68137 0 3680.2511 5.5159946
1600 20778.805 216.92178 0 3680.0559 15.089188
1650 21477.638 100.21838 0 3679.8247 -1.1045721
1700 18501.339 596.47923 0 3680.0357 -15.679684
1750 18563.642 587.34794 0 3681.2882 33.532214
1800 19110.185 494.82345 0 3679.8543 18.024048
1850 21364.191 119.23549 0 3679.9339 2.5291055
1900 20146.626 322.14873 0 3679.9197 5.7313299
1950 20692.671 231.25337 0 3680.0319 4.2977739
2000 20943.904 189.11223 0 3679.7629 -22.645065
2050 19668.05 401.83114 0 3679.8394 3.6251299
2100 20280.429 299.76377 0 3679.8353 7.4807724
2150 19181.824 483.52803 0 3680.4987 22.621058
2200 21300.2 130.69877 0 3680.7321 4.7101388
2250 20486.872 266.65126 0 3681.1298 -8.64606
2300 18652.975 572.27254 0 3681.1017 -5.2634974
2350 21513.607 95.600862 0 3681.202 -9.3630049
2400 21466.13 103.58801 0 3681.2764 -29.557768
2450 20100.368 332.22709 0 3682.2885 35.732014
2500 20764.657 221.62387 0 3682.4 -12.463862
2550 20438.076 275.91333 0 3682.2592 -22.425852
2600 21466.132 104.59173 0 3682.2805 -10.082268
2650 20822.428 211.95671 0 3682.3614 5.127481
2700 18565.278 588.44551 0 3682.6584 22.293432
2750 20797.862 215.91059 0 3682.2209 -8.1063144
2800 21059.469 172.28051 0 3682.1921 -7.0844003
2850 16872.586 870.34211 0 3682.4398 32.849964
2900 19328.831 460.66814 0 3682.1399 7.9281931
2950 20586.345 250.96712 0 3682.0246 1.7396391
3000 20611.491 246.91122 0 3682.1598 0.15773191
3050 18708.556 564.3119 0 3682.4045 -8.7956783
3100 19495.833 432.52761 0 3681.8332 -2.1653832
3150 19519.49 428.89092 0 3682.1393 4.0100548
3200 20944.893 191.20605 0 3682.0216 11.871543
3250 21146.02 157.83687 0 3682.1735 -4.7375853
3300 20265.669 304.00917 0 3681.6207 -17.157191
3350 21869.083 37.329716 0 3682.1769 1.4108575
3400 21255.354 139.32181 0 3681.8809 1.2422306
3450 20561.221 254.99337 0 3681.8635 -2.7886134
3500 19336.164 459.33327 0 3682.0272 -9.8731549
3550 18542.312 591.07728 0 3681.4627 15.77161
3600 18730.537 560.14948 0 3681.9057 10.217264
3650 20873.396 203.06221 0 3681.9616 -28.564248
3700 21436.606 109.16145 0 3681.9292 -21.061612
3750 18675.966 569.02439 0 3681.6855 11.64657
3800 20436.375 275.84131 0 3681.9038 -5.9290461
3850 18328.137 628.10932 0 3682.7989 14.246278
3900 19024.623 511.1793 0 3681.9498 14.007294
3950 19466.443 437.78895 0 3682.1961 12.682242
4000 21202.262 148.49308 0 3682.2035 0.47453452
4050 21732.696 60.300584 0 3682.4166 3.5393138
4100 21261.101 138.98135 0 3682.4981 -2.3688202
4150 21039.305 176.06896 0 3682.6198 -7.3850759
4200 20861.193 205.8717 0 3682.7372 -5.9549501
4250 20727.806 227.85881 0 3682.4931 -4.9378024
4300 21240.72 142.99909 0 3683.1191 6.0140859
4350 20278.96 303.68016 0 3683.5068 18.008787
4400 21571.464 89.217978 0 3684.462 -8.2541517
4450 20945.879 194.34119 0 3685.3211 -10.755909
4500 19357.576 459.20233 0 3685.4651 -1.1662243
4550 20070.673 340.02546 0 3685.1377 8.1832489
4600 18365.334 624.41217 0 3685.3011 11.456111
4650 21054.585 175.93533 0 3685.0329 4.0987465
4700 20453.567 274.95682 0 3683.8846 18.963024
4750 21099.159 168.60809 0 3685.1346 -11.855465
4800 21158.189 159.18204 0 3685.5469 -17.31802
4850 18094.578 669.72236 0 3685.4853 40.180964
4900 20034.808 346.31522 0 3685.45 4.1804507
4950 18429.609 611.87316 0 3683.4747 -8.6927733
5000 17101.392 834.83641 0 3685.0685 29.261971
5050 19972.453 356.73256 0 3685.4746 -23.478596
5100 20409.248 283.96903 0 3685.5103 -15.62688
5150 18619.464 582.41194 0 3685.656 27.596644
5200 21091.026 170.5616 0 3685.7327 -2.1985242
5250 19646.432 411.12533 0 3685.5307 5.3421684
5300 16532.264 929.93501 0 3685.3123 3.6084684
5350 18936.014 529.38477 0 3685.3872 5.7677833
5400 19076.138 505.98075 0 3685.337 -3.5638094
5450 18054.685 676.72364 0 3685.8378 -21.232447
5500 19888.218 369.90928 0 3684.6123 -7.2785968
5550 19490.999 436.65981 0 3685.1597 7.9038749
5600 19100.952 502.38941 0 3685.8814 14.985758
5650 21651.913 76.978971 0 3685.6312 -1.0194868
5700 21567.956 90.782103 0 3685.4415 -4.4649746
5750 20856.197 208.52372 0 3684.5565 4.8535252
5800 19843.284 377.984 0 3685.198 12.062532
5850 21790.829 54.281667 0 3686.0866 -3.2023915
5900 18902.646 535.37059 0 3685.8116 10.894118
5950 21829.087 48.387859 0 3686.5691 2.2039614
6000 21245.256 145.52299 0 3686.399 6.2974108
6050 21751.287 61.184407 0 3686.3988 -0.1980726
6100 19043.424 513.07185 0 3686.9759 9.8533553
6150 21901.252 36.150127 0 3686.3587 -7.0300867
6200 20949.233 194.29786 0 3685.8366 8.4342445
6250 20899.339 202.11234 0 3685.3354 -2.5050622
6300 21319.283 132.94251 0 3686.1564 -1.6810321
6350 21831.692 48.011342 0 3686.6267 -2.4722049
6400 21456.882 110.75974 0 3686.9068 -3.5310241
6450 21270.92 141.72151 0 3686.8749 -43.058347
6500 20362.334 292.29277 0 3686.0151 -4.4931124
6550 18532.916 596.57491 0 3685.3942 3.980097
6600 19297.139 470.28434 0 3686.4742 -2.9651136
6650 17192.426 820.51306 0 3685.9173 -12.722339
6700 20048.902 344.57156 0 3686.0552 5.4710406
6750 19514.781 433.21286 0 3685.6764 -2.1603719
6800 16180.331 990.63515 0 3687.357 39.735611
6850 19840.599 379.89398 0 3686.6604 2.2347728
6900 19953.112 361.20748 0 3686.7261 -0.46915334
6950 19137.537 497.33803 0 3686.9276 -1.4982013
7000 20429.395 281.81167 0 3686.7108 3.4039582
7050 20467.147 275.61561 0 3686.8067 2.9208489
7100 19080.701 505.64774 0 3685.7645 12.174506
7150 18840.308 545.83721 0 3685.8886 -6.6402164
7200 21125.322 165.63742 0 3686.5244 -12.447263
7250 21920.551 33.452671 0 3686.8779 -10.072614
7300 21189.411 155.39429 0 3686.9628 -4.8676358
7350 21124.285 166.49631 0 3687.2104 4.2436664
7400 20355.482 294.78497 0 3687.3653 4.6061221
7450 21093.692 171.68559 0 3687.301 6.0558915
7500 20270.87 308.63445 0 3687.1128 6.2719486
7550 19433.602 448.40677 0 3687.3404 -5.6016357
7600 20240.238 312.79173 0 3686.1647 -3.0011467
7650 19792.109 387.119 0 3685.8039 -10.580457
7700 14157.419 1328.0907 0 3687.6605 32.611071
7750 17338.754 796.44034 0 3686.2326 0.86175706
7800 19338.946 460.75469 0 3683.9123 -1.447495
7850 16030.091 1014.9705 0 3686.6524 14.019933
7900 19628.33 415.39423 0 3686.7825 20.701791
7950 18150.717 661.47911 0 3686.5986 -32.476748
8000 19007.599 520.08749 0 3688.0206 -28.168071
8050 17980.675 690.25759 0 3687.0368 4.4511504
8100 17755.592 727.97864 0 3687.244 14.484039
8150 19719.036 401.12252 0 3687.6285 10.139703
8200 20206.271 319.78443 0 3687.4963 2.6525333
8250 19142.437 497.06826 0 3687.4744 -6.9317419
8300 20331.241 299.00742 0 3687.5477 -0.95816396
8350 20774.563 225.32684 0 3687.754 4.8719815
8400 19985.962 356.99081 0 3687.9846 4.8325753
8450 20275.354 308.64721 0 3687.8729 -7.8397818
8500 21079.156 174.56708 0 3687.7598 -13.823972
8550 20709.01 236.36299 0 3687.8647 0.40092021
8600 19170.162 492.90906 0 3687.9361 -11.472935
8650 21372.968 125.61953 0 3687.7809 -10.410552
8700 18221.303 651.84494 0 3688.7287 8.2187226
8750 20642.357 247.40387 0 3687.7968 0.7210003
8800 16335.403 966.18976 0 3688.757 39.333007
8850 19371.075 459.85041 0 3688.3628 -3.8523819
8900 17301.339 805.68567 0 3689.2422 28.65235
8950 20681.779 241.47417 0 3688.4373 -4.118774
9000 20254.54 312.02857 0 3687.7852 -12.844695
9050 20345.188 297.61274 0 3688.4773 6.0688854
9100 21395.82 122.55534 0 3688.5253 -2.9714765
9150 20547.045 264.03422 0 3688.5417 7.9840299
9200 20458.955 278.89113 0 3688.717 -7.3675154
9250 21553.459 96.718566 0 3688.9617 -16.511845
9300 21791.079 57.139424 0 3688.9859 -9.7252419
9350 18105.817 667.20174 0 3684.8379 8.34612
9400 20716.075 235.60875 0 3688.2879 -3.6694637
9450 17323.793 800.75759 0 3688.0564 23.727483
9500 21699.072 71.60915 0 3688.1212 -20.010116
9550 20623.869 250.24107 0 3687.5526 -16.868229
9600 20926.325 199.40734 0 3687.1282 -7.6363545
9650 17859.603 709.98104 0 3686.5816 36.736527
9700 20198.022 319.33287 0 3685.6698 6.8254744
9750 20153.898 325.80574 0 3684.7887 -1.3328209
9800 17873.089 707.74921 0 3686.5973 45.940695
9850 20133.06 330.29907 0 3685.809 -10.579343
9900 20831.124 213.97543 0 3685.8294 -23.250883
9950 20257.767 308.71666 0 3685.0111 -9.1959081
10000 21123.35 164.53453 0 3685.0929 2.4217121
-Loop time of 11.8231 on 4 procs for 10000 steps with 81 atoms
+Loop time of 11.1702 on 4 procs for 10000 steps with 81 atoms
-Pair time (%) = 0.0847651 (0.716943)
-Neigh time (%) = 0.0420694 (0.355823)
-Comm time (%) = 3.50799 (29.6706)
-Outpt time (%) = 0.162343 (1.3731)
-Other time (%) = 8.02595 (67.8835)
+Pair time (%) = 0.0751896 (0.673126)
+Neigh time (%) = 0.0374737 (0.335479)
+Comm time (%) = 3.20709 (28.7111)
+Outpt time (%) = 0.17948 (1.60678)
+Other time (%) = 7.67097 (68.6735)
Nlocal: 20.25 ave 72 max 0 min
Histogram: 2 1 0 0 0 0 0 0 0 1
Nghost: 26.75 ave 67 max 1 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Neighs: 211.75 ave 845 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Total # of neighbors = 847
Ave neighs/atom = 10.4568
Neighbor list builds = 990
Dangerous builds = 919
diff --git a/examples/rigid/log.rigid.poems2.22Jan08.linux.1 b/examples/rigid/log.rigid.poems2.21May08.linux.1
similarity index 98%
rename from examples/rigid/log.rigid.poems2.22Jan08.linux.1
rename to examples/rigid/log.rigid.poems2.21May08.linux.1
index 48f01e7fa..ade359ec1 100644
--- a/examples/rigid/log.rigid.poems2.22Jan08.linux.1
+++ b/examples/rigid/log.rigid.poems2.21May08.linux.1
@@ -1,307 +1,307 @@
-LAMMPS (22 Jan 2008)
+LAMMPS (21 May 2008)
# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 1 by 1 processor grid
81 atoms
velocity all create 100.0 4928459
# unconnected bodies
#group clump1 id <> 1 9
#group clump2 id <> 10 18
#group clump3 id <> 19 27
#group clump4 id <> 28 36
#group clump5 id <> 37 45
#group clump6 id <> 46 54
#group clump7 id <> 55 63
#group clump8 id <> 64 72
#group clump9 id <> 73 81
#fix 1 all rigid group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 9 18
10 atoms in group clump2
group clump3 id <> 18 27
10 atoms in group clump3
group clump4 id <> 27 36
10 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 45 54
10 atoms in group clump6
group clump7 id <> 54 63
10 atoms in group clump7
group clump8 id <> 63 72
10 atoms in group clump8
group clump9 id <> 72 81
10 atoms in group clump9
fix 1 all poems group clump1 clump2 clump3 clump4
1 clusters, 4 bodies, 3 joints, 36 atoms
fix 2 all poems group clump5 clump6 clump7 clump8 clump9
1 clusters, 5 bodies, 4 joints, 45 atoms
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
dump 1 all atom 50 dump.rigid
timestep 0.0001
thermo 50
run 10000
Memory usage per processor = 2.04938 Mbytes
Step Temp E_pair E_mol TotEng Press
0 196.00047 3632.2347 0 3668.5311 -2.7403788
50 12167.633 1505.5478 0 3758.8133 35.125973
100 17556.978 512.66277 0 3763.9549 11.137534
150 19579.586 138.04942 0 3763.8987 -29.953971
200 19757.51 105.30542 0 3764.1036 -0.030645317
250 18218.374 390.10747 0 3763.8804 13.711001
300 19383.039 174.40688 0 3763.8586 5.7240693
350 20125.986 36.972611 0 3764.0071 1.9559205
400 18888.816 266.10975 0 3764.0386 9.6362168
450 19307.656 188.2511 0 3763.743 1.9326206
500 16331.197 738.56392 0 3762.8597 9.1715579
550 19318.722 186.16172 0 3763.7027 3.0115336
600 19455.268 161.20621 0 3764.0336 0.55208034
650 18487.011 340.03216 0 3763.5528 -8.0359122
700 17321.201 556.32471 0 3763.9545 -13.631751
750 18979.187 249.04389 0 3763.7082 -2.6072455
800 19342.456 181.85552 0 3763.7918 8.1918726
850 19070.641 232.19342 0 3763.7936 7.3148472
900 19478.873 156.65987 0 3763.8586 2.4284987
950 19912.415 76.437437 0 3763.9216 -1.4667227
1000 16003.749 802.39753 0 3766.0548 46.642188
1050 19859.583 86.64176 0 3764.3424 -2.1961943
1100 19229.575 203.61488 0 3764.6473 -10.632365
1150 18821.6 279.15861 0 3764.64 -0.89495035
1200 19392.695 173.59744 0 3764.8373 1.8508753
1250 16459.624 717.32104 0 3765.3995 33.478127
1300 19343.863 182.59043 0 3764.7874 0.75890736
1350 20019.643 57.503573 0 3764.8448 0.31444672
1400 18549.582 329.31436 0 3764.4221 10.738303
1450 15163.926 957.47584 0 3765.6103 -17.923459
1500 19223.688 204.15171 0 3764.0939 -1.6134537
1550 18147.996 404.12676 0 3764.8668 8.4194772
1600 18615.043 317.42465 0 3764.6548 -2.3288964
1650 20120.654 38.887931 0 3764.935 -8.7620234
1700 19450.906 162.98288 0 3765.0025 2.3254699
1750 19374.633 177.3795 0 3765.2744 8.9328779
1800 19424.403 167.93973 0 3765.0514 0.081235304
1850 17936.331 442.82718 0 3764.3699 6.6008391
1900 19982.596 64.40603 0 3764.8868 -2.9530194
1950 16215.981 761.88879 0 3764.8481 13.994088
2000 18584.381 322.128 0 3763.68 7.1655135
2050 20107.966 41.025597 0 3764.723 -0.31094122
2100 20002.35 60.589881 0 3764.7288 -6.7919416
2150 16949.562 626.63321 0 3765.441 3.5096306
2200 20010.952 58.808561 0 3764.5403 -10.86228
2250 18982.725 247.00987 0 3762.3292 -0.53791914
2300 18401.372 354.86612 0 3762.5275 1.0918754
2350 19390.489 172.94794 0 3763.7793 -3.3526861
2400 16081.953 786.17478 0 3764.3143 -16.196885
2450 18870.833 268.6722 0 3763.2708 11.190569
2500 19687.509 117.72716 0 3763.5621 4.3895758
2550 18872.588 268.46009 0 3763.3837 -5.65615
2600 17016.358 612.26248 0 3763.4398 6.3212358
2650 18770.003 287.95778 0 3763.8843 2.3918934
2700 19736.664 108.26363 0 3763.2014 -0.29985725
2750 19503.072 151.75954 0 3763.4396 -1.6107925
2800 18406.518 353.53932 0 3762.1537 21.011955
2850 18588.513 320.69227 0 3763.0095 3.8268039
2900 20117.999 37.673729 0 3763.2291 0.3860655
2950 15648.583 864.90426 0 3762.79 14.652139
3000 18110.003 409.12743 0 3762.8316 7.3046684
3050 18963.762 251.51142 0 3763.3192 8.8730034
3100 19360.233 177.87688 0 3763.1052 -3.0033938
3150 19397.488 171.24407 0 3763.3715 -8.1894526
3200 19861.487 85.443126 0 3763.4963 -7.9892279
3250 18129.617 406.07108 0 3763.4075 6.2227523
3300 18459.736 345.12838 0 3763.5981 -0.88498697
3350 18418.177 352.87007 0 3763.6435 5.1465625
3400 18198.837 393.573 0 3763.7281 17.906813
3450 19394.696 171.91336 0 3763.5237 2.3061791
3500 17989.508 431.57014 0 3762.9605 4.7721744
3550 19839.796 89.461378 0 3763.4977 0.7558346
3600 16651.367 679.91968 0 3763.5062 2.5921986
3650 19640.802 126.3709 0 3763.5565 3.8008774
3700 18760.791 289.23461 0 3763.4552 -0.23238761
3750 18422.908 351.84447 0 3763.494 -5.7068362
3800 19064.373 232.62149 0 3763.0609 1.9157181
3850 20028.174 54.865473 0 3763.7867 -2.0675059
3900 18363.88 363.15521 0 3763.8738 -0.83495509
3950 19144.012 218.22273 0 3763.4102 1.2543164
4000 17659.248 492.75853 0 3762.9896 12.60409
4050 19998.728 60.090184 0 3763.5584 0.64359974
4100 19023.135 240.33019 0 3763.133 -2.6947304
4150 18396.797 356.71902 0 3763.5332 15.109139
4200 18315.833 371.47968 0 3763.3006 -13.756621
4250 18854.397 272.12483 0 3763.6798 8.1077459
4300 18978.728 248.78988 0 3763.3692 -3.3208462
4350 18786.658 284.24444 0 3763.2551 -1.7398125
4400 18820.575 278.09291 0 3763.3846 6.4475568
4450 19690.377 117.11929 0 3763.4855 4.012577
4500 14617.737 1056.5845 0 3763.5729 7.0245567
4550 18625.243 314.21779 0 3763.3369 4.0564911
4600 19360.387 178.72404 0 3763.9809 0.33263149
4650 19620.797 130.21216 0 3763.693 -5.4726773
4700 19197.021 208.91339 0 3763.9173 -1.8042436
4750 19411.985 169.01841 0 3763.8304 -10.694251
4800 19056.192 234.93386 0 3763.8583 -2.7041261
4850 19709.453 113.94779 0 3763.8465 1.8599983
4900 19362.257 178.19337 0 3763.7966 5.1912208
4950 18337.767 368.49428 0 3764.377 18.140067
5000 19888.24 81.111906 0 3764.1194 2.5600957
5050 19611.529 132.35796 0 3764.1227 -3.3822641
5100 19566.081 140.69528 0 3764.0437 1.2449896
5150 19532.854 146.74524 0 3763.9404 3.8524377
5200 19373.811 176.3264 0 3764.0692 -4.3051482
5250 19698.182 116.23114 0 3764.0427 -5.0585702
5300 18474.212 342.91742 0 3764.0679 -1.6019006
5350 19635.571 127.66714 0 3763.884 3.7584612
5400 18607.657 318.08369 0 3763.9462 10.762902
5450 19588.259 136.49518 0 3763.9505 6.1172117
5500 19765.157 103.83083 0 3764.045 0.36918158
5550 18217.985 390.52967 0 3764.2305 18.816738
5600 19679.936 119.65589 0 3764.0885 1.7284717
5650 18768.785 288.29767 0 3763.9986 -1.7550105
5700 18474.924 342.54508 0 3763.8273 -0.47116767
5750 19654.098 123.76064 0 3763.4084 2.9224335
5800 19969.149 65.437823 0 3763.4283 1.5579018
5850 19197.889 208.36188 0 3763.5265 10.018565
5900 19069.242 232.23165 0 3763.5727 -2.3495992
5950 19171.042 213.33502 0 3763.5281 4.3208294
6000 19631.089 128.17938 0 3763.5662 5.1040226
6050 17777.019 470.94145 0 3762.9819 3.2383249
6100 19181.825 211.41374 0 3763.6035 3.2259341
6150 20185.733 25.759429 0 3763.8581 -4.4522835
6200 19874.491 83.403238 0 3763.8645 -8.6039321
6250 19768.708 102.9028 0 3763.7747 -8.5795285
6300 18936.55 256.8797 0 3763.6482 0.20667479
6350 19346.44 180.9489 0 3763.6229 7.6373366
6400 19167.283 214.16073 0 3763.6576 5.4329755
6450 19757 104.94544 0 3763.6491 1.9851548
6500 19641.69 126.44473 0 3763.7947 1.2730006
6550 18916.37 260.97919 0 3764.0107 1.6515332
6600 19431.157 165.31798 0 3763.6804 -7.8268121
6650 17535.67 516.82965 0 3764.176 7.7374819
6700 18820.205 278.4336 0 3763.6568 -11.297168
6750 19400.73 170.37067 0 3763.0984 0.79131515
6800 18455.468 345.88629 0 3763.5655 12.188053
6850 17800.169 467.12041 0 3763.448 12.916841
6900 18726.929 295.65024 0 3763.6 1.6289629
6950 19271.689 194.65896 0 3763.4902 -4.083701
7000 17981.935 433.45886 0 3763.4468 -6.3945803
7050 18276.81 378.6811 0 3763.2756 12.872885
7100 17861.241 455.74244 0 3763.3797 8.4221303
7150 20051.69 49.967954 0 3763.2438 -2.5498008
7200 19240.155 200.06954 0 3763.0612 11.392096
7250 19496.154 152.73815 0 3763.137 -0.040582106
7300 19647.869 124.5004 0 3762.9946 0.23514871
7350 19246.833 198.85412 0 3763.0825 -0.73645767
7400 19225.995 202.68281 0 3763.0522 3.0455791
7450 18020.098 426.17136 0 3763.2266 -6.5226863
7500 19214.283 204.97935 0 3763.1798 -0.2919171
7550 19705.287 114.13715 0 3763.2643 7.041629
7600 19178.956 211.59688 0 3763.2554 7.831605
7650 20037.443 52.751944 0 3763.3896 -0.77979354
7700 20016.2 56.704511 0 3763.4082 -1.8856173
7750 18697.512 300.96503 0 3763.4672 -5.3462105
7800 19937.068 71.362135 0 3763.4118 -0.91252014
7850 20102.546 40.714553 0 3763.4083 -3.1972795
7900 19480.106 155.99043 0 3763.4174 11.035723
7950 19885.239 80.923563 0 3763.3753 3.2874193
8000 19624.804 129.16452 0 3763.3874 -1.1516066
8050 19803.792 96.006636 0 3763.3755 1.9821101
8100 20011.845 57.495451 0 3763.3927 1.2382066
8150 19200.484 207.59204 0 3763.2373 6.0568259
8200 19827.269 91.624126 0 3763.3407 1.9883126
8250 19842.958 88.703224 0 3763.3251 -4.5756698
8300 18873.776 268.18104 0 3763.3247 -3.7359417
8350 19486.037 154.68335 0 3763.2087 0.8929882
8400 19934.053 71.48369 0 3762.975 0.08234901
8450 19683.678 117.78109 0 3762.9067 -11.54709
8500 18499.903 337.24598 0 3763.1539 -3.5045806
8550 19753.252 104.83934 0 3762.849 5.8791033
8600 20095.096 41.775811 0 3763.0899 -2.0563082
8650 19876.199 82.371224 0 3763.1489 -2.4348814
8700 15533.887 886.73227 0 3763.378 -6.6646724
8750 17890.913 450.07003 0 3763.202 9.4926975
8800 18705.916 298.95593 0 3763.0144 2.1309021
8850 19505.191 150.78385 0 3762.8563 3.9049146
8900 17389.794 540.29795 0 3760.6302 10.005241
8950 18715.055 297.10888 0 3762.8597 4.8803289
9000 19744.23 106.46616 0 3762.805 0.10287172
9050 19838.109 89.008308 0 3762.7321 -4.7062413
9100 17764.056 473.0557 0 3762.6957 3.8896676
9150 17181.335 580.10083 0 3761.8295 11.628818
9200 19223.407 202.50436 0 3762.3945 0.1590941
9250 15947.899 808.02603 0 3761.3407 12.151805
9300 19300.071 188.02038 0 3762.1075 -0.37927009
9350 18285.048 375.69389 0 3761.8139 -1.4254912
9400 19384.709 172.87653 0 3762.6374 0.95001481
9450 16817.179 648.70645 0 3762.9988 -1.3207316
9500 18964.068 250.55459 0 3762.419 1.6533798
9550 19754.429 103.95948 0 3762.1871 -4.5609305
9600 19811.139 93.102298 0 3761.8317 3.7563831
9650 19152.708 215.04016 0 3761.838 12.440802
9700 19963.416 65.083015 0 3762.0119 -3.0218611
9750 19895.404 77.764801 0 3762.0988 -5.3121454
9800 19008.238 242.21067 0 3762.2548 -3.8985859
9850 19681.717 117.48371 0 3762.2461 -4.3300452
9900 19741.039 106.38351 0 3762.1314 -0.15155351
9950 17199.878 577.88679 0 3763.0494 13.40024
10000 18985.433 246.5308 0 3762.3518 0.62625708
-Loop time of 7.54982 on 1 procs for 10000 steps with 81 atoms
+Loop time of 7.52498 on 1 procs for 10000 steps with 81 atoms
-Pair time (%) = 0.212344 (2.81257)
-Neigh time (%) = 0.0943768 (1.25005)
-Comm time (%) = 0.0214007 (0.283459)
-Outpt time (%) = 0.0292683 (0.387668)
-Other time (%) = 7.19243 (95.2663)
+Pair time (%) = 0.212854 (2.82864)
+Neigh time (%) = 0.0927372 (1.23239)
+Comm time (%) = 0.0216842 (0.288163)
+Outpt time (%) = 0.0303783 (0.4037)
+Other time (%) = 7.16732 (95.2471)
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 64 ave 64 max 64 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 621 ave 621 max 621 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 621
Ave neighs/atom = 7.66667
Neighbor list builds = 995
Dangerous builds = 967
diff --git a/examples/rigid/log.rigid.poems2.22Jan08.linux.4 b/examples/rigid/log.rigid.poems2.21May08.linux.4
similarity index 98%
rename from examples/rigid/log.rigid.poems2.22Jan08.linux.4
rename to examples/rigid/log.rigid.poems2.21May08.linux.4
index daa75fa21..e93b810dc 100644
--- a/examples/rigid/log.rigid.poems2.22Jan08.linux.4
+++ b/examples/rigid/log.rigid.poems2.21May08.linux.4
@@ -1,307 +1,307 @@
-LAMMPS (22 Jan 2008)
+LAMMPS (21 May 2008)
# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 2 by 2 processor grid
81 atoms
velocity all create 100.0 4928459
# unconnected bodies
#group clump1 id <> 1 9
#group clump2 id <> 10 18
#group clump3 id <> 19 27
#group clump4 id <> 28 36
#group clump5 id <> 37 45
#group clump6 id <> 46 54
#group clump7 id <> 55 63
#group clump8 id <> 64 72
#group clump9 id <> 73 81
#fix 1 all rigid group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 9 18
10 atoms in group clump2
group clump3 id <> 18 27
10 atoms in group clump3
group clump4 id <> 27 36
10 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 45 54
10 atoms in group clump6
group clump7 id <> 54 63
10 atoms in group clump7
group clump8 id <> 63 72
10 atoms in group clump8
group clump9 id <> 72 81
10 atoms in group clump9
fix 1 all poems group clump1 clump2 clump3 clump4
1 clusters, 4 bodies, 3 joints, 36 atoms
fix 2 all poems group clump5 clump6 clump7 clump8 clump9
1 clusters, 5 bodies, 4 joints, 45 atoms
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
dump 1 all atom 50 dump.rigid
timestep 0.0001
thermo 50
run 10000
Memory usage per processor = 2.01123 Mbytes
Step Temp E_pair E_mol TotEng Press
0 196.00047 3632.2347 0 3668.5311 -2.7403788
50 12167.633 1505.5478 0 3758.8133 35.125973
100 17556.978 512.66277 0 3763.9549 11.137534
150 19579.586 138.04942 0 3763.8987 -29.953971
200 19757.51 105.30542 0 3764.1036 -0.030645317
250 18218.374 390.10747 0 3763.8804 13.711001
300 19383.039 174.40688 0 3763.8586 5.7240693
350 20125.986 36.972611 0 3764.0071 1.9559205
400 18888.816 266.10975 0 3764.0386 9.6362168
450 19307.656 188.2511 0 3763.743 1.9326206
500 16331.197 738.56392 0 3762.8597 9.1715579
550 19318.722 186.16172 0 3763.7027 3.0115336
600 19455.268 161.20621 0 3764.0336 0.55208034
650 18487.011 340.03216 0 3763.5528 -8.0359122
700 17321.201 556.32471 0 3763.9545 -13.631751
750 18979.187 249.04389 0 3763.7082 -2.6072455
800 19342.456 181.85552 0 3763.7918 8.1918726
850 19070.641 232.19342 0 3763.7936 7.3148472
900 19478.873 156.65987 0 3763.8586 2.4284987
950 19912.415 76.437437 0 3763.9216 -1.4667227
1000 16003.749 802.39753 0 3766.0548 46.642188
1050 19859.583 86.64176 0 3764.3424 -2.1961943
1100 19229.575 203.61488 0 3764.6473 -10.632365
1150 18821.6 279.15861 0 3764.64 -0.89495035
1200 19392.695 173.59744 0 3764.8373 1.8508753
1250 16459.624 717.32104 0 3765.3995 33.478127
1300 19343.863 182.59043 0 3764.7874 0.75890736
1350 20019.643 57.503573 0 3764.8448 0.31444671
1400 18549.582 329.31436 0 3764.4221 10.738303
1450 15163.926 957.47584 0 3765.6103 -17.923459
1500 19223.688 204.15173 0 3764.0939 -1.6134533
1550 18147.996 404.12676 0 3764.8668 8.4194777
1600 18615.043 317.42467 0 3764.6548 -2.3288946
1650 20120.654 38.887921 0 3764.935 -8.762026
1700 19450.907 162.98278 0 3765.0025 2.3254718
1750 19374.632 177.37959 0 3765.2744 8.9328776
1800 19424.403 167.93969 0 3765.0514 0.081232329
1850 17936.282 442.8362 0 3764.3699 6.6009729
1900 19982.596 64.40613 0 3764.8868 -2.9529967
1950 16215.904 761.90316 0 3764.8484 13.994458
2000 18584.405 322.1235 0 3763.68 7.165446
2050 20107.966 41.025691 0 3764.723 -0.3109207
2100 20002.34 60.591745 0 3764.7288 -6.7919639
2150 16949.68 626.61132 0 3765.441 3.5092215
2200 20010.952 58.808395 0 3764.5403 -10.862215
2250 18982.727 247.0094 0 3762.3292 -0.53801024
2300 18401.329 354.87401 0 3762.5275 1.0919825
2350 19390.509 172.94434 0 3763.7793 -3.3525766
2400 16081.279 786.29986 0 3764.3144 -16.198999
2450 18870.586 268.71771 0 3763.2706 11.19479
2500 19687.968 117.64184 0 3763.5619 4.3854981
2550 18871.552 268.652 0 3763.3839 -5.6598123
2600 17018.095 611.94054 0 3763.4396 6.3151274
2650 18759.886 289.83493 0 3763.8878 2.4039285
2700 19740.164 107.62639 0 3763.2122 -0.31805782
2750 19516.266 149.31294 0 3763.4362 -1.6224242
2800 18358.662 362.49198 0 3762.2443 21.770839
2850 18467.52 343.09706 0 3763.0082 4.3423041
2900 20135.574 34.417701 0 3763.2277 0.85884412
2950 15515.162 889.21195 0 3762.3902 14.080582
3000 17723.38 481.44112 0 3763.5486 14.722181
3050 18381.135 359.45826 0 3763.3721 9.9835573
3100 18332.511 367.78446 0 3762.694 -7.3886751
3150 18614.425 316.10349 0 3763.2192 -7.7456785
3200 19729.937 109.55581 0 3763.2478 -7.7288745
3250 19571.827 138.77846 0 3763.1909 5.3260619
3300 19186.832 210.15314 0 3763.2701 7.0964224
3350 19051.087 235.32511 0 3763.3042 7.0039981
3400 17984.109 432.92549 0 3763.316 19.525696
3450 19816.122 93.46903 0 3763.1212 0.93406363
3500 16116.959 778.80017 0 3763.4223 -16.393122
3550 18360.763 362.74217 0 3762.8834 -1.6392609
3600 17932.893 442.36815 0 3763.2742 -4.5284033
3650 19361.757 177.48543 0 3762.996 2.9534892
3700 16171.988 768.78945 0 3763.6021 13.745857
3750 20139.429 33.883266 0 3763.4072 -3.2396898
3800 18827.574 276.59438 0 3763.1822 2.0190596
3850 19014.653 242.23251 0 3763.4646 2.3020369
3900 19035.411 238.45939 0 3763.5355 4.6373723
3950 19853.791 86.8932 0 3763.5212 4.0194756
4000 17410.265 538.42567 0 3762.5488 17.95381
4050 18206.278 391.36957 0 3762.9025 -13.769983
4100 18808.965 279.8479 0 3762.9896 6.0082648
4150 19232.014 202.09792 0 3763.582 -10.281477
4200 18792.127 283.21841 0 3763.242 -10.635301
4250 19145.491 217.48336 0 3762.9447 2.1471563
4300 19664.887 121.93826 0 3763.5839 -2.0730994
4350 19700.745 115.21856 0 3763.5047 2.8774214
4400 19578.899 137.66468 0 3763.3866 8.4984611
4450 18859.58 271.0341 0 3763.5489 5.2645569
4500 18464.886 343.87376 0 3763.2971 3.3130349
4550 19630.341 128.23266 0 3763.4811 4.2969524
4600 19437.701 164.00094 0 3763.5752 5.1130661
4650 19755.71 105.08536 0 3763.5503 -0.6517046
4700 19462.629 158.25383 0 3762.4444 -0.30468036
4750 19907.555 76.921174 0 3763.5055 3.4400883
4800 17463.04 529.62954 0 3763.5258 -18.109666
4850 18843.915 273.9062 0 3763.52 6.1277136
4900 19932.837 72.164658 0 3763.4308 3.8475873
4950 18789.577 283.59769 0 3763.149 11.854926
5000 19848.608 87.756004 0 3763.4242 -2.9271941
5050 19386.057 173.20964 0 3763.2202 -14.592158
5100 19562.287 140.98305 0 3763.6288 1.469574
5150 19768.169 102.77988 0 3763.5518 1.109855
5200 16491.44 708.59683 0 3762.5672 30.415205
5250 18348.29 365.43425 0 3763.2658 2.133794
5300 18310.805 372.23677 0 3763.1266 3.6232592
5350 19442.213 162.69223 0 3763.1021 -2.2352529
5400 19108.516 224.58431 0 3763.1983 -5.4827686
5450 19038.769 237.71604 0 3763.414 2.2536906
5500 18915.343 260.50945 0 3763.3508 6.4433856
5550 19806.543 95.410393 0 3763.2888 7.1573806
5600 19586.43 136.20593 0 3763.3226 4.2084232
5650 18934.674 256.87502 0 3763.296 1.0652817
5700 19379.411 174.63723 0 3763.4171 -16.099846
5750 17966.907 435.65528 0 3762.8602 15.573477
5800 18863.305 270.01624 0 3763.2208 3.2727217
5850 17928.61 443.11194 0 3763.2249 -0.37865943
5900 17379.69 544.76612 0 3763.2272 -5.7065719
5950 18361.744 362.60908 0 3762.932 -4.3958323
6000 18704.038 298.94878 0 3762.6594 6.898019
6050 15936.467 810.92728 0 3762.1249 18.422274
6100 17071.849 601.99083 0 3763.4443 4.2280601
6150 19822.301 92.132151 0 3762.9286 1.6855602
6200 19163.87 214.14753 0 3763.0124 5.3184996
6250 20161.078 29.407194 0 3762.9401 -0.67242018
6300 18796.357 282.07065 0 3762.8776 8.1775067
6350 19366.986 176.12874 0 3762.6076 -2.7479103
6400 19425.061 165.31052 0 3762.544 -12.916694
6450 17189.915 578.9515 0 3762.2691 4.9303412
6500 19875.308 81.917933 0 3762.5306 -0.93951735
6550 18302.585 372.46303 0 3761.8306 1.9560909
6600 19877.135 81.515781 0 3762.4668 -1.3991682
6650 19694.771 114.94067 0 3762.1205 -15.72083
6700 20049.45 49.38756 0 3762.2486 1.323048
6750 19113.647 222.15998 0 3761.7242 -6.1599285
6800 19405.364 168.71339 0 3762.2994 -4.3191765
6850 18441.771 346.66103 0 3761.8039 19.964057
6900 19544.094 143.03104 0 3762.3077 -3.41341
6950 19896.176 77.856807 0 3762.3338 0.11828835
7000 18710.926 297.28247 0 3762.2688 -0.59552027
7050 19226.752 202.05067 0 3762.5602 -1.8533644
7100 19320.172 184.76008 0 3762.5698 7.7909331
7150 19780.388 99.586065 0 3762.6209 8.2095401
7200 19088.724 227.32895 0 3762.2778 7.6855317
7250 19776.649 100.32237 0 3762.6648 0.94044622
7300 18507.22 335.55097 0 3762.814 -6.1662299
7350 17885.867 450.59261 0 3762.7901 1.2499902
7400 18262.199 380.80199 0 3762.6908 7.3392868
7450 19049.569 234.51188 0 3762.2099 5.1244012
7500 19553.726 141.36592 0 3762.4263 -3.8237895
7550 20185.751 24.610159 0 3762.7121 -10.932579
7600 17392.717 541.77079 0 3762.6442 -0.43384802
7650 20068.739 46.210036 0 3762.6432 -0.6828593
7700 17724.249 480.46375 0 3762.7321 4.6817369
7750 17343.196 551.13155 0 3762.8346 -2.1896616
7800 19879.224 81.449925 0 3762.7877 -5.5050054
7850 19447.49 161.05987 0 3762.4468 6.5551059
7900 19347.279 179.92264 0 3762.752 -0.22128912
7950 16111.259 779.90909 0 3763.4756 16.245065
8000 18793.831 282.55644 0 3762.8956 2.7542217
8050 17743.028 476.45151 0 3762.1974 27.194554
8100 19009.972 242.36714 0 3762.7324 1.2892353
8150 16678.474 674.54525 0 3763.1516 -10.118094
8200 17031.072 609.20451 0 3763.1067 -5.3547397
8250 19069.215 231.72951 0 3763.0656 11.653116
8300 18974.009 249.2464 0 3762.9518 8.5281104
8350 18258.716 381.94584 0 3763.1896 -2.3827747
8400 19159.557 215.19237 0 3763.2586 -10.596898
8450 18872.368 268.50254 0 3763.3856 -18.567827
8500 19220.617 203.86825 0 3763.2417 6.0196396
8550 19324.087 184.72918 0 3763.2639 -7.5202105
8600 19692.651 116.4876 0 3763.2748 -5.0995987
8650 19006.487 243.54291 0 3763.2627 -4.3110571
8700 18569.611 324.39458 0 3763.2114 9.70503
8750 18603.877 317.36329 0 3762.5258 11.849356
8800 19389.768 172.48258 0 3763.1803 10.449119
8850 19102.996 225.58959 0 3763.1815 0.71895877
8900 19585.652 135.95989 0 3762.9325 1.0242045
8950 19161.635 214.28295 0 3762.7338 2.1946644
9000 19724.587 110.24248 0 3762.9438 -1.4725699
9050 18898.222 263.31908 0 3762.9899 5.2519867
9100 18757.963 288.77375 0 3762.4706 6.6961009
9150 19828.253 91.178602 0 3763.0773 2.1940149
9200 19173.574 212.43267 0 3763.0944 -2.1554184
9250 19537.506 144.98302 0 3763.0396 0.49527878
9300 17573.062 508.41377 0 3762.6845 13.408224
9350 20041.904 51.66773 0 3763.1314 -1.4383526
9400 19788.001 98.546699 0 3762.9914 0.94893555
9450 19221.146 203.77535 0 3763.2469 -3.6082923
9500 19864.374 84.617003 0 3763.2048 -3.1142322
9550 18497.395 337.75311 0 3763.1966 5.8593905
9600 19968.433 65.464516 0 3763.3224 0.22354534
9650 19879.617 82.015812 0 3763.4264 -1.7947438
9700 19525.5 147.67058 0 3763.5039 0.9870726
9750 19387.903 173.04252 0 3763.3949 6.3543366
9800 18996.326 245.74232 0 3763.5804 10.384497
9850 19064.592 233.24533 0 3763.7253 -0.7632773
9900 19205.165 207.15936 0 3763.6714 7.5682042
9950 18962.217 252.13659 0 3763.6582 -1.4248706
10000 19978.362 63.931872 0 3763.6285 5.7744071
-Loop time of 12.4183 on 4 procs for 10000 steps with 81 atoms
+Loop time of 12.0971 on 4 procs for 10000 steps with 81 atoms
-Pair time (%) = 0.0675793 (0.54419)
-Neigh time (%) = 0.034472 (0.27759)
-Comm time (%) = 3.23596 (26.0579)
-Outpt time (%) = 0.162251 (1.30655)
-Other time (%) = 8.91806 (71.8137)
+Pair time (%) = 0.0632877 (0.523162)
+Neigh time (%) = 0.0323215 (0.267182)
+Comm time (%) = 3.17539 (26.2491)
+Outpt time (%) = 0.149343 (1.23453)
+Other time (%) = 8.6768 (71.726)
Nlocal: 20.25 ave 39 max 0 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 16.75 ave 39 max 1 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Neighs: 207.75 ave 533 max 0 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Total # of neighbors = 831
Ave neighs/atom = 10.2593
Neighbor list builds = 995
Dangerous builds = 965
diff --git a/examples/shear/log.shear.21May08.linux.1 b/examples/shear/log.shear.21May08.linux.1
new file mode 100644
index 000000000..c40e8a3d6
--- /dev/null
+++ b/examples/shear/log.shear.21May08.linux.1
@@ -0,0 +1,159 @@
+LAMMPS (21 May 2008)
+# 3d metal shear simulation
+
+units metal
+boundary s s p
+
+atom_style atomic
+lattice fcc 3.52
+Lattice spacing in x,y,z = 3.52 3.52 3.52
+region box block 0 16.0 0 10.0 0 2.828427
+create_box 3 box
+Created orthogonal box = (0 0 0) to (56.32 35.2 9.95606)
+ 1 by 1 by 1 processor grid
+
+lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0
+Lattice spacing in x,y,z = 3.52 4.97803 4.97803
+create_atoms 1 box
+Created 1912 atoms
+
+pair_style eam
+pair_coeff * * Ni_u3.eam
+
+neighbor 0.3 bin
+neigh_modify delay 5
+
+region lower block INF INF INF 0.9 INF INF
+region upper block INF INF 6.1 INF INF INF
+group lower region lower
+264 atoms in group lower
+group upper region upper
+264 atoms in group upper
+group boundary union lower upper
+528 atoms in group boundary
+group mobile subtract all boundary
+1384 atoms in group mobile
+
+set group lower type 2
+ 264 settings made for type
+set group upper type 3
+ 264 settings made for type
+
+# void
+
+#region void cylinder z 8 5 2.5 INF INF
+#delete_atoms region void
+
+# temp controllers
+
+compute new3d mobile temp
+compute new2d mobile temp/partial 0 1 1
+
+# equilibrate
+
+velocity mobile create 300.0 5812775 temp new3d
+fix 1 all nve
+fix 2 boundary setforce 0.0 0.0 0.0
+
+fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
+fix_modify 3 temp new3d
+
+thermo 25
+thermo_modify temp new3d
+
+timestep 0.001
+run 100
+Memory usage per processor = 1.98543 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 300 -8317.4367 0 -8263.8067 -7103.5557 19539.346
+ 25 220.34459 -8272.5701 0 -8233.1798 5170.6956 19539.346
+ 50 300 -8237.7876 0 -8184.1576 13746.642 19678.792
+ 75 292.67269 -8229.8093 0 -8177.4891 14324.984 19737.233
+ 100 300 -8245.8191 0 -8192.189 9038.4055 19770.872
+Loop time of 0.467599 on 1 procs for 100 steps with 1912 atoms
+
+Pair time (%) = 0.443526 (94.8517)
+Neigh time (%) = 0.0121951 (2.60803)
+Comm time (%) = 0.00291872 (0.624193)
+Outpt time (%) = 0.00022912 (0.0489993)
+Other time (%) = 0.00873041 (1.86707)
+
+Nlocal: 1912 ave 1912 max 1912 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 2122 ave 2122 max 2122 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 45975 ave 45975 max 45975 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 45975
+Ave neighs/atom = 24.0455
+Neighbor list builds = 4
+Dangerous builds = 0
+
+# shear
+
+velocity upper set 1.0 0 0
+velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes
+
+unfix 3
+fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
+fix_modify 3 temp new2d
+
+dump 1 all atom 100 dump.shear
+thermo 100
+thermo_modify temp new2d
+
+reset_timestep 0
+run 3000
+Memory usage per processor = 2.06028 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 298.53339 -8245.8191 0 -8210.2533 8059.4154 19778.399
+ 100 300 -8260.7953 0 -8225.0549 3177.3605 19809.773
+ 200 298.50746 -8257.8441 0 -8222.2815 1696.64 19926.446
+ 300 296.80999 -8250.2343 0 -8214.8739 -338.92466 20051.103
+ 400 306.47135 -8245.2265 0 -8208.7151 9.7606112 20134.594
+ 500 298.68843 -8240.244 0 -8204.6599 722.49284 20161.098
+ 600 302.37622 -8230.4652 0 -8194.4417 4007.3859 20279.478
+ 700 300 -8222.0223 0 -8186.2819 6769.4135 20405.698
+ 800 303.21952 -8210.998 0 -8174.874 8152.7988 20510.204
+ 900 297.74338 -8197.2403 0 -8161.7687 10764.828 20634.767
+ 1000 300 -8180.7508 0 -8145.0104 14227.468 20760.551
+ 1100 305.89822 -8166.6544 0 -8130.2113 18078.278 20875.344
+ 1200 295.27459 -8152.0699 0 -8116.8924 21328.094 21001.128
+ 1300 300 -8141.732 0 -8105.9916 22799.705 21115.921
+ 1400 300 -8130.0647 0 -8094.3243 23526.574 21246.59
+ 1500 300 -8125.4387 0 -8089.6983 22002.546 21356.499
+ 1600 300 -8128.9533 0 -8093.2128 18328.671 21485.946
+ 1700 300 -8151.4563 0 -8115.7159 11511.304 21600.74
+ 1800 300 -8160.1502 0 -8124.4098 7547.562 21724.081
+ 1900 309.29943 -8153.7122 0 -8116.8639 8409.7432 21858.414
+ 2000 307.15092 -8160.675 0 -8124.0826 5894.1343 21976.871
+ 2100 308.54207 -8156.5601 0 -8119.802 4916.8536 22095.327
+ 2200 300 -8157.4804 0 -8121.74 2411.8958 22217.448
+ 2300 300 -8162.7297 0 -8126.9893 -128.11671 22334.684
+ 2400 300 -8166.1396 0 -8130.3991 -1504.9194 22459.246
+ 2500 300 -8169.094 0 -8133.3536 -119.96486 22578.925
+ 2600 304.76063 -8162.5898 0 -8126.2822 2246.5398 22714.478
+ 2700 308.04872 -8167.1208 0 -8130.4215 77.151949 22834.156
+ 2800 300 -8167.1381 0 -8131.3977 -2885.907 22951.392
+ 2900 308.65071 -8164.1796 0 -8127.4086 -7537.8706 23075.955
+ 3000 302.42612 -8159.1684 0 -8123.139 -9974.9028 23189.527
+Loop time of 14.379 on 1 procs for 3000 steps with 1912 atoms
+
+Pair time (%) = 13.2702 (92.2892)
+Neigh time (%) = 0.67312 (4.68129)
+Comm time (%) = 0.0920188 (0.639955)
+Outpt time (%) = 0.081636 (0.567746)
+Other time (%) = 0.261964 (1.82186)
+
+Nlocal: 1912 ave 1912 max 1912 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 2104 ave 2104 max 2104 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 44986 ave 44986 max 44986 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 44986
+Ave neighs/atom = 23.5282
+Neighbor list builds = 221
+Dangerous builds = 0
diff --git a/examples/shear/log.shear.21May08.linux.4 b/examples/shear/log.shear.21May08.linux.4
new file mode 100644
index 000000000..0d6176246
--- /dev/null
+++ b/examples/shear/log.shear.21May08.linux.4
@@ -0,0 +1,159 @@
+LAMMPS (21 May 2008)
+# 3d metal shear simulation
+
+units metal
+boundary s s p
+
+atom_style atomic
+lattice fcc 3.52
+Lattice spacing in x,y,z = 3.52 3.52 3.52
+region box block 0 16.0 0 10.0 0 2.828427
+create_box 3 box
+Created orthogonal box = (0 0 0) to (56.32 35.2 9.95606)
+ 2 by 2 by 1 processor grid
+
+lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0
+Lattice spacing in x,y,z = 3.52 4.97803 4.97803
+create_atoms 1 box
+Created 1912 atoms
+
+pair_style eam
+pair_coeff * * Ni_u3.eam
+
+neighbor 0.3 bin
+neigh_modify delay 5
+
+region lower block INF INF INF 0.9 INF INF
+region upper block INF INF 6.1 INF INF INF
+group lower region lower
+264 atoms in group lower
+group upper region upper
+264 atoms in group upper
+group boundary union lower upper
+528 atoms in group boundary
+group mobile subtract all boundary
+1384 atoms in group mobile
+
+set group lower type 2
+ 264 settings made for type
+set group upper type 3
+ 264 settings made for type
+
+# void
+
+#region void cylinder z 8 5 2.5 INF INF
+#delete_atoms region void
+
+# temp controllers
+
+compute new3d mobile temp
+compute new2d mobile temp/partial 0 1 1
+
+# equilibrate
+
+velocity mobile create 300.0 5812775 temp new3d
+fix 1 all nve
+fix 2 boundary setforce 0.0 0.0 0.0
+
+fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
+fix_modify 3 temp new3d
+
+thermo 25
+thermo_modify temp new3d
+
+timestep 0.001
+run 100
+Memory usage per processor = 1.88566 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 300 -8317.4367 0 -8263.8067 -7103.5557 19539.346
+ 25 220.91849 -8272.7063 0 -8233.2134 5171.0015 19539.346
+ 50 300 -8239.0761 0 -8185.446 13404.703 19669.87
+ 75 295.11708 -8231.4059 0 -8178.6488 13741.993 19743.549
+ 100 300 -8250.5856 0 -8196.9555 6735.754 19818.526
+Loop time of 0.193502 on 4 procs for 100 steps with 1912 atoms
+
+Pair time (%) = 0.145985 (75.4434)
+Neigh time (%) = 0.00310105 (1.60259)
+Comm time (%) = 0.03407 (17.607)
+Outpt time (%) = 0.0012731 (0.657923)
+Other time (%) = 0.00907356 (4.68912)
+
+Nlocal: 478 ave 490 max 468 min
+Histogram: 2 0 0 0 0 0 0 1 0 1
+Nghost: 1033.75 ave 1043 max 1021 min
+Histogram: 1 0 0 0 0 1 0 1 0 1
+Neighs: 11508.8 ave 12218 max 10874 min
+Histogram: 1 0 0 0 2 0 0 0 0 1
+
+Total # of neighbors = 46035
+Ave neighs/atom = 24.0769
+Neighbor list builds = 4
+Dangerous builds = 0
+
+# shear
+
+velocity upper set 1.0 0 0
+velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes
+
+unfix 3
+fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
+fix_modify 3 temp new2d
+
+dump 1 all atom 100 dump.shear
+thermo 100
+thermo_modify temp new2d
+
+reset_timestep 0
+run 3000
+Memory usage per processor = 1.90439 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 292.46783 -8250.5856 0 -8215.7425 5714.7972 19847.781
+ 100 298.90147 -8254.2464 0 -8218.6368 1673.5647 19875.172
+ 200 292.67105 -8257.6816 0 -8222.8143 597.02209 19851.638
+ 300 304.83817 -8252.3996 0 -8216.0828 -1766.9124 19972.145
+ 400 304.67912 -8245.8917 0 -8209.5938 984.88656 20123.442
+ 500 304.19559 -8240.3464 0 -8204.1061 858.95575 20228.779
+ 600 300 -8228.866 0 -8193.1256 3277.69 20298.36
+ 700 301.21369 -8221.8851 0 -8186.0001 5982.9806 20420.849
+ 800 292.95939 -8207.7529 0 -8172.8512 9954.3357 20536.518
+ 900 301.91087 -8196.792 0 -8160.8239 12198.791 20621.333
+ 1000 304.47104 -8183.7675 0 -8147.4944 16413.662 20759.329
+ 1100 309.51789 -8171.7638 0 -8134.8895 19823.617 20871.68
+ 1200 300 -8162.1479 0 -8126.4075 21358.891 21002.349
+ 1300 306.82902 -8154.9346 0 -8118.3806 19922.78 21112.258
+ 1400 302.84766 -8146.0057 0 -8109.926 20387.683 21245.369
+ 1500 300 -8136.5305 0 -8100.7901 19767.587 21371.153
+ 1600 300 -8133.8687 0 -8098.1282 16820.721 21487.167
+ 1700 300 -8138.1712 0 -8102.4307 13421.303 21603.182
+ 1800 300 -8156.4639 0 -8120.7235 8511.6435 21732.63
+ 1900 300 -8171.1239 0 -8135.3835 5041.7586 21849.865
+ 2000 300 -8163.4848 0 -8127.7444 3694.8641 21970.765
+ 2100 308.72044 -8171.8831 0 -8135.1038 970.54577 22092.885
+ 2200 302.52995 -8169.1085 0 -8133.0666 52.192359 22216.227
+ 2300 300 -8170.9512 0 -8135.2107 -1542.8185 22335.905
+ 2400 300 -8172.0501 0 -8136.3097 -2043.706 22458.025
+ 2500 308.89262 -8175.1797 0 -8138.3798 -3806.7013 22581.367
+ 2600 308.78531 -8173.0575 0 -8136.2705 -3040.4487 22705.93
+ 2700 309.91867 -8169.3099 0 -8132.3878 -3733.9914 22819.502
+ 2800 300 -8170.4846 0 -8134.7442 -3811.1294 22953.834
+ 2900 298.97302 -8165.3476 0 -8129.7295 -4051.2587 23075.955
+ 3000 299.96914 -8161.4805 0 -8125.7437 -2883.9458 23201.739
+Loop time of 6.09161 on 4 procs for 3000 steps with 1912 atoms
+
+Pair time (%) = 4.41471 (72.4719)
+Neigh time (%) = 0.170875 (2.80508)
+Comm time (%) = 1.11289 (18.2692)
+Outpt time (%) = 0.104965 (1.7231)
+Other time (%) = 0.288174 (4.73068)
+
+Nlocal: 478 ave 512 max 446 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+Nghost: 1006 ave 1055 max 967 min
+Histogram: 2 0 0 0 0 0 0 1 0 1
+Neighs: 11265.2 ave 12221 max 10346 min
+Histogram: 1 0 1 0 0 0 0 1 0 1
+
+Total # of neighbors = 45061
+Ave neighs/atom = 23.5675
+Neighbor list builds = 223
+Dangerous builds = 0
diff --git a/examples/shear/log.shear.22Jan08.linux.1 b/examples/shear/log.shear.22Jan08.linux.1
deleted file mode 100644
index 33f2e3497..000000000
--- a/examples/shear/log.shear.22Jan08.linux.1
+++ /dev/null
@@ -1,159 +0,0 @@
-LAMMPS (22 Jan 2008)
-# 3d metal shear simulation
-
-units metal
-boundary s s p
-
-atom_style atomic
-lattice fcc 3.52
-Lattice spacing in x,y,z = 3.52 3.52 3.52
-region box block 0 16.0 0 10.0 0 2.828427
-create_box 3 box
-Created orthogonal box = (0 0 0) to (56.32 35.2 9.95606)
- 1 by 1 by 1 processor grid
-
-lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0
-Lattice spacing in x,y,z = 3.52 4.97803 4.97803
-create_atoms 1 box
-Created 1912 atoms
-
-pair_style eam
-pair_coeff * * Ni_u3.eam
-
-neighbor 0.3 bin
-neigh_modify delay 5
-
-region lower block INF INF INF 0.9 INF INF
-region upper block INF INF 6.1 INF INF INF
-group lower region lower
-264 atoms in group lower
-group upper region upper
-264 atoms in group upper
-group boundary union lower upper
-528 atoms in group boundary
-group mobile subtract all boundary
-1384 atoms in group mobile
-
-set group lower type 2
- 264 settings made for type
-set group upper type 3
- 264 settings made for type
-
-# void
-
-#region void cylinder z 8 5 2.5 INF INF
-#delete_atoms region void
-
-# temp controllers
-
-compute new3d mobile temp
-compute new2d mobile temp/partial 0 1 1
-
-# equilibrate
-
-velocity mobile create 300.0 5812775 temp new3d
-fix 1 all nve
-fix 2 boundary setforce 0.0 0.0 0.0
-
-fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
-fix_modify 3 temp new3d
-
-thermo 25
-thermo_modify temp new3d
-
-timestep 0.001
-run 100
-Memory usage per processor = 1.98543 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume
- 0 300 -8317.4367 0 -8263.8067 -7103.5557 19539.346
- 25 220.34459 -8272.5701 0 -8233.1798 5170.6956 19539.346
- 50 300 -8237.7876 0 -8184.1576 13746.642 19678.792
- 75 292.67269 -8229.8093 0 -8177.4891 14324.984 19737.233
- 100 300 -8245.8191 0 -8192.189 9038.4055 19770.872
-Loop time of 0.467166 on 1 procs for 100 steps with 1912 atoms
-
-Pair time (%) = 0.443394 (94.9114)
-Neigh time (%) = 0.0120709 (2.58386)
-Comm time (%) = 0.00285816 (0.611809)
-Outpt time (%) = 0.000116348 (0.0249051)
-Other time (%) = 0.0087266 (1.86799)
-
-Nlocal: 1912 ave 1912 max 1912 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 2122 ave 2122 max 2122 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 45975 ave 45975 max 45975 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 45975
-Ave neighs/atom = 24.0455
-Neighbor list builds = 4
-Dangerous builds = 0
-
-# shear
-
-velocity upper set 1.0 0 0
-velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes
-
-unfix 3
-fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
-fix_modify 3 temp new2d
-
-dump 1 all atom 100 dump.shear
-thermo 100
-thermo_modify temp new2d
-
-reset_timestep 0
-run 3000
-Memory usage per processor = 2.06028 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume
- 0 298.53339 -8245.8191 0 -8210.2533 8059.4154 19778.399
- 100 300 -8263.5777 0 -8227.8373 2795.3643 19788.083
- 200 295.48797 -8257.8787 0 -8222.6759 2179.0845 19913.732
- 300 292.48667 -8250.5584 0 -8215.7131 2.9847512 20043.736
- 400 304.93883 -8245.9033 0 -8209.5745 179.50544 20125.384
- 500 294.27283 -8241.2854 0 -8206.2272 829.41012 20145.713
- 600 302.25208 -8230.3821 0 -8194.3734 4273.5024 20285.46
- 700 300 -8223.3443 0 -8187.6038 6565.4269 20406.893
- 800 303.62781 -8211.0391 0 -8174.8665 8116.0638 20515.088
- 900 297.87427 -8197.7869 0 -8162.2997 10317.159 20621.333
- 1000 300 -8181.081 0 -8145.3406 13621.801 20748.339
- 1100 307.26338 -8166.9162 0 -8130.3105 17420.976 20877.786
- 1200 300.29796 -8153.8084 0 -8118.0325 20385.904 20986.474
- 1300 300 -8147.0071 0 -8111.2667 21178.857 21115.921
- 1400 300 -8137.1276 0 -8101.3872 21423.889 21246.59
- 1500 308.75316 -8131.6139 0 -8094.8306 20067.792 21365.047
- 1600 300 -8133.2906 0 -8097.5501 16682.824 21477.398
- 1700 308.52741 -8149.3473 0 -8112.5909 11697.908 21599.518
- 1800 300 -8152.6978 0 -8116.9573 9550.2281 21737.514
- 1900 308.57591 -8146.2494 0 -8109.4873 9662.4382 21859.635
- 2000 308.26812 -8146.4139 0 -8109.6884 9661.2057 21976.871
- 2100 302.17107 -8146.0627 0 -8110.0636 8521.2058 22094.106
- 2200 305.08447 -8151.7703 0 -8115.4241 4427.9711 22218.669
- 2300 300 -8166.2097 0 -8130.4693 -1334.8828 22346.896
- 2400 304.42128 -8165.4861 0 -8129.219 -931.52307 22464.131
- 2500 291.59698 -8160.1078 0 -8125.3684 2248.0287 22592.358
- 2600 304.33702 -8161.3244 0 -8125.0673 3566.8213 22704.709
- 2700 308.4539 -8163.6628 0 -8126.9152 1887.5801 22825.608
- 2800 309.42404 -8163.7723 0 -8126.9092 -395.06509 22946.507
- 2900 307.81471 -8165.3682 0 -8128.6967 -3460.652 23077.176
- 3000 299.7731 -8165.3688 0 -8129.6554 -5437.2745 23191.969
-Loop time of 14.364 on 1 procs for 3000 steps with 1912 atoms
-
-Pair time (%) = 13.2885 (92.5126)
-Neigh time (%) = 0.644948 (4.49003)
-Comm time (%) = 0.0909958 (0.633499)
-Outpt time (%) = 0.0792053 (0.551416)
-Other time (%) = 0.260347 (1.8125)
-
-Nlocal: 1912 ave 1912 max 1912 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 2089 ave 2089 max 2089 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 45088 ave 45088 max 45088 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 45088
-Ave neighs/atom = 23.5816
-Neighbor list builds = 216
-Dangerous builds = 0
diff --git a/examples/shear/log.shear.22Jan08.linux.4 b/examples/shear/log.shear.22Jan08.linux.4
deleted file mode 100644
index 21a86b856..000000000
--- a/examples/shear/log.shear.22Jan08.linux.4
+++ /dev/null
@@ -1,159 +0,0 @@
-LAMMPS (22 Jan 2008)
-# 3d metal shear simulation
-
-units metal
-boundary s s p
-
-atom_style atomic
-lattice fcc 3.52
-Lattice spacing in x,y,z = 3.52 3.52 3.52
-region box block 0 16.0 0 10.0 0 2.828427
-create_box 3 box
-Created orthogonal box = (0 0 0) to (56.32 35.2 9.95606)
- 2 by 2 by 1 processor grid
-
-lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0
-Lattice spacing in x,y,z = 3.52 4.97803 4.97803
-create_atoms 1 box
-Created 1912 atoms
-
-pair_style eam
-pair_coeff * * Ni_u3.eam
-
-neighbor 0.3 bin
-neigh_modify delay 5
-
-region lower block INF INF INF 0.9 INF INF
-region upper block INF INF 6.1 INF INF INF
-group lower region lower
-264 atoms in group lower
-group upper region upper
-264 atoms in group upper
-group boundary union lower upper
-528 atoms in group boundary
-group mobile subtract all boundary
-1384 atoms in group mobile
-
-set group lower type 2
- 264 settings made for type
-set group upper type 3
- 264 settings made for type
-
-# void
-
-#region void cylinder z 8 5 2.5 INF INF
-#delete_atoms region void
-
-# temp controllers
-
-compute new3d mobile temp
-compute new2d mobile temp/partial 0 1 1
-
-# equilibrate
-
-velocity mobile create 300.0 5812775 temp new3d
-fix 1 all nve
-fix 2 boundary setforce 0.0 0.0 0.0
-
-fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
-fix_modify 3 temp new3d
-
-thermo 25
-thermo_modify temp new3d
-
-timestep 0.001
-run 100
-Memory usage per processor = 1.88566 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume
- 0 300 -8317.4367 0 -8263.8067 -7103.5557 19539.346
- 25 220.91849 -8272.7063 0 -8233.2134 5171.0015 19539.346
- 50 300 -8239.0761 0 -8185.446 13404.703 19669.87
- 75 295.11708 -8231.4059 0 -8178.6488 13741.993 19743.549
- 100 300 -8250.5856 0 -8196.9555 6735.754 19818.526
-Loop time of 0.211954 on 4 procs for 100 steps with 1912 atoms
-
-Pair time (%) = 0.152662 (72.0261)
-Neigh time (%) = 0.0030964 (1.46088)
-Comm time (%) = 0.0420393 (19.8341)
-Outpt time (%) = 0.00200987 (0.948256)
-Other time (%) = 0.0121462 (5.7306)
-
-Nlocal: 478 ave 490 max 468 min
-Histogram: 2 0 0 0 0 0 0 1 0 1
-Nghost: 1033.75 ave 1043 max 1021 min
-Histogram: 1 0 0 0 0 1 0 1 0 1
-Neighs: 11508.8 ave 12218 max 10874 min
-Histogram: 1 0 0 0 2 0 0 0 0 1
-
-Total # of neighbors = 46035
-Ave neighs/atom = 24.0769
-Neighbor list builds = 4
-Dangerous builds = 0
-
-# shear
-
-velocity upper set 1.0 0 0
-velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes
-
-unfix 3
-fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
-fix_modify 3 temp new2d
-
-dump 1 all atom 100 dump.shear
-thermo 100
-thermo_modify temp new2d
-
-reset_timestep 0
-run 3000
-Memory usage per processor = 1.90439 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume
- 0 292.46783 -8250.5856 0 -8215.7425 5714.7972 19847.781
- 100 297.48776 -8255.7637 0 -8220.3225 1519.5936 19869.252
- 200 300 -8259.5191 0 -8223.7786 407.14026 19843.233
- 300 306.85093 -8252.9546 0 -8216.3979 -1452.8459 19987.791
- 400 303.87074 -8246.296 0 -8210.0945 1276.3308 20128.061
- 500 299.00581 -8241.6473 0 -8206.0253 943.44685 20226.281
- 600 300 -8228.0773 0 -8192.3369 3740.0009 20307.41
- 700 302.55478 -8222.4773 0 -8186.4325 6034.1752 20412.441
- 800 291.55934 -8208.4477 0 -8173.7129 9870.4071 20534.96
- 900 300.04405 -8197.8106 0 -8162.0649 11858.874 20635.988
- 1000 303.4363 -8185.1721 0 -8149.0223 15860.089 20755.666
- 1100 300 -8172.7372 0 -8136.9967 19064.863 20868.017
- 1200 300 -8163.6948 0 -8127.9543 20503.74 20997.464
- 1300 300 -8157.774 0 -8122.0336 19017.48 21108.594
- 1400 301.23169 -8148.1245 0 -8112.2373 19838.433 21245.369
- 1500 300 -8137.0376 0 -8101.2972 19618.234 21361.383
- 1600 300 -8129.5673 0 -8093.8269 17832.316 21493.274
- 1700 300 -8131.9086 0 -8096.1682 15651.56 21609.288
- 1800 300 -8154.2629 0 -8118.5225 9602.8973 21725.302
- 1900 300 -8166.6747 0 -8130.9342 7079.4166 21855.971
- 2000 297.56913 -8164.1963 0 -8128.7455 6008.7168 21970.765
- 2100 307.18117 -8162.4989 0 -8125.903 5339.1594 22100.212
- 2200 307.91443 -8165.8526 0 -8129.1693 4903.917 22218.669
- 2300 307.29809 -8166.6561 0 -8130.0463 4057.1866 22343.232
- 2400 306.14212 -8165.725 0 -8129.2529 4381.5236 22462.91
- 2500 306.62123 -8166.8443 0 -8130.3151 2924.8251 22583.809
- 2600 300 -8166.6003 0 -8130.8598 2179.9998 22701.045
- 2700 309.89171 -8168.2224 0 -8131.3035 3044.4626 22836.599
- 2800 305.74412 -8166.2652 0 -8129.8404 1099.7498 22952.613
- 2900 301.2671 -8170.7739 0 -8134.8825 -2699.4417 23073.512
- 3000 300 -8171.8299 0 -8136.0895 -3656.4591 23189.527
-Loop time of 6.35133 on 4 procs for 3000 steps with 1912 atoms
-
-Pair time (%) = 4.57768 (72.0743)
-Neigh time (%) = 0.167127 (2.63138)
-Comm time (%) = 1.18119 (18.5976)
-Outpt time (%) = 0.113077 (1.78037)
-Other time (%) = 0.312252 (4.91633)
-
-Nlocal: 478 ave 508 max 449 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Nghost: 1006.75 ave 1064 max 959 min
-Histogram: 1 1 0 0 0 0 0 1 0 1
-Neighs: 11284 ave 12171 max 10415 min
-Histogram: 1 0 0 1 0 0 1 0 0 1
-
-Total # of neighbors = 45136
-Ave neighs/atom = 23.6067
-Neighbor list builds = 216
-Dangerous builds = 0
diff --git a/examples/shear/log.shear.void.21May08.linux.1 b/examples/shear/log.shear.void.21May08.linux.1
new file mode 100644
index 000000000..a85083b16
--- /dev/null
+++ b/examples/shear/log.shear.void.21May08.linux.1
@@ -0,0 +1,160 @@
+LAMMPS (21 May 2008)
+# 3d metal shear simulation
+
+units metal
+boundary s s p
+
+atom_style atomic
+lattice fcc 3.52
+Lattice spacing in x,y,z = 3.52 3.52 3.52
+region box block 0 16.0 0 10.0 0 2.828427
+create_box 3 box
+Created orthogonal box = (0 0 0) to (56.32 35.2 9.95606)
+ 1 by 1 by 1 processor grid
+
+lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0
+Lattice spacing in x,y,z = 3.52 4.97803 4.97803
+create_atoms 1 box
+Created 1912 atoms
+
+pair_style eam
+pair_coeff * * Ni_u3.eam
+
+neighbor 0.3 bin
+neigh_modify delay 5
+
+region lower block INF INF INF 0.9 INF INF
+region upper block INF INF 6.1 INF INF INF
+group lower region lower
+264 atoms in group lower
+group upper region upper
+264 atoms in group upper
+group boundary union lower upper
+528 atoms in group boundary
+group mobile subtract all boundary
+1384 atoms in group mobile
+
+set group lower type 2
+ 264 settings made for type
+set group upper type 3
+ 264 settings made for type
+
+# void
+
+region void cylinder z 8 3.535534 2.5 INF INF
+delete_atoms region void
+Deleted 204 atoms, new total = 1708
+
+# temp controllers
+
+compute new3d mobile temp
+compute new2d mobile temp/partial 0 1 1
+
+# equilibrate
+
+velocity mobile create 300.0 5812775 temp new3d
+fix 1 all nve
+fix 2 boundary setforce 0.0 0.0 0.0
+
+fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
+fix_modify 3 temp new3d
+
+thermo 25
+thermo_modify temp new3d
+
+timestep 0.001
+run 100
+Memory usage per processor = 1.96813 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 300 -7358.6159 0 -7312.8966 -9604.6063 19539.346
+ 25 222.66197 -7321.4403 0 -7287.5071 562.50939 19539.346
+ 50 300 -7292.2273 0 -7246.508 7558.4629 19680.84
+ 75 292.67603 -7286.2016 0 -7241.5984 6828.0763 19738.503
+ 100 300 -7297.4174 0 -7251.698 1627.881 19767.928
+Loop time of 0.404765 on 1 procs for 100 steps with 1708 atoms
+
+Pair time (%) = 0.383371 (94.7145)
+Neigh time (%) = 0.0106142 (2.6223)
+Comm time (%) = 0.00265503 (0.655943)
+Outpt time (%) = 0.000173807 (0.0429402)
+Other time (%) = 0.00795102 (1.96435)
+
+Nlocal: 1708 ave 1708 max 1708 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1898 ave 1898 max 1898 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 39444 ave 39444 max 39444 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 39444
+Ave neighs/atom = 23.0937
+Neighbor list builds = 4
+Dangerous builds = 0
+
+# shear
+
+velocity upper set 1.0 0 0
+velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes
+
+unfix 3
+fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
+fix_modify 3 temp new2d
+
+dump 1 all atom 100 dump.shear
+thermo 100
+thermo_modify temp new2d
+
+reset_timestep 0
+run 3000
+Memory usage per processor = 2.03328 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 296.81549 -7297.4174 0 -7267.2741 786.10955 19771.704
+ 100 290.32156 -7309.73 0 -7280.2463 -5963.004 19831.09
+ 200 290.76236 -7306.4805 0 -7276.952 -7421.6375 19919.327
+ 300 293.25821 -7304.1086 0 -7274.3267 -11013.42 20035.976
+ 400 293.84766 -7299.0985 0 -7269.2567 -7886.1633 20097.992
+ 500 291.74499 -7299.9751 0 -7270.3468 -5636.1333 20137.736
+ 600 303.46664 -7291.5162 0 -7260.6975 -1010.2257 20269.626
+ 700 300 -7287.9569 0 -7257.4903 -2205.2748 20391.564
+ 800 300 -7280.4222 0 -7249.9555 -2876.2467 20512.915
+ 900 292.92463 -7272.7361 0 -7242.9881 -1776.974 20633.545
+ 1000 307.93499 -7265.1866 0 -7233.9141 -1238.6225 20750.781
+ 1100 300.17079 -7260.1229 0 -7229.6389 -1843.002 20881.45
+ 1200 302.06128 -7255.9277 0 -7225.2517 -1889.3058 21004.792
+ 1300 300 -7259.2664 0 -7228.7998 -3186.0907 21111.036
+ 1400 300 -7265.444 0 -7234.9774 -6109.5646 21244.148
+ 1500 308.79162 -7271.0073 0 -7239.6478 -6107.0978 21361.383
+ 1600 300 -7275.2324 0 -7244.7658 -8519.8045 21492.052
+ 1700 309.22602 -7278.5756 0 -7247.172 -13752.852 21610.509
+ 1800 300 -7284.3068 0 -7253.8402 -14337.648 21720.418
+ 1900 299.75827 -7283.413 0 -7252.9709 -14463.157 21846.202
+ 2000 297.70312 -7274.9007 0 -7244.6674 -20480.857 21978.092
+ 2100 304.09482 -7269.8328 0 -7238.9503 -19791.258 22092.885
+ 2200 299.66443 -7269.2566 0 -7238.8241 -16602.972 22216.227
+ 2300 299.27231 -7268.2781 0 -7237.8853 -15847.311 22337.126
+ 2400 300.69324 -7259.5316 0 -7228.9946 -14598.831 22462.91
+ 2500 297.44581 -7258.0006 0 -7227.7934 -17846.994 22581.367
+ 2600 300 -7253.3731 0 -7222.9065 -18557.919 22710.815
+ 2700 305.12651 -7253.1648 0 -7222.1775 -20331.834 22824.387
+ 2800 294.14063 -7249.1464 0 -7219.2748 -17541.566 22952.613
+ 2900 307.30441 -7249.4895 0 -7218.281 -17450.515 23071.07
+ 3000 304.44871 -7244.9559 0 -7214.0374 -15842.46 23199.297
+Loop time of 12.4157 on 1 procs for 3000 steps with 1708 atoms
+
+Pair time (%) = 11.4629 (92.3256)
+Neigh time (%) = 0.556271 (4.48038)
+Comm time (%) = 0.0828254 (0.667103)
+Outpt time (%) = 0.0738423 (0.59475)
+Other time (%) = 0.239896 (1.9322)
+
+Nlocal: 1708 ave 1708 max 1708 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1879 ave 1879 max 1879 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 38632 ave 38632 max 38632 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 38632
+Ave neighs/atom = 22.6183
+Neighbor list builds = 209
+Dangerous builds = 0
diff --git a/examples/shear/log.shear.void.21May08.linux.4 b/examples/shear/log.shear.void.21May08.linux.4
new file mode 100644
index 000000000..9162bdf5f
--- /dev/null
+++ b/examples/shear/log.shear.void.21May08.linux.4
@@ -0,0 +1,160 @@
+LAMMPS (21 May 2008)
+# 3d metal shear simulation
+
+units metal
+boundary s s p
+
+atom_style atomic
+lattice fcc 3.52
+Lattice spacing in x,y,z = 3.52 3.52 3.52
+region box block 0 16.0 0 10.0 0 2.828427
+create_box 3 box
+Created orthogonal box = (0 0 0) to (56.32 35.2 9.95606)
+ 2 by 2 by 1 processor grid
+
+lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0
+Lattice spacing in x,y,z = 3.52 4.97803 4.97803
+create_atoms 1 box
+Created 1912 atoms
+
+pair_style eam
+pair_coeff * * Ni_u3.eam
+
+neighbor 0.3 bin
+neigh_modify delay 5
+
+region lower block INF INF INF 0.9 INF INF
+region upper block INF INF 6.1 INF INF INF
+group lower region lower
+264 atoms in group lower
+group upper region upper
+264 atoms in group upper
+group boundary union lower upper
+528 atoms in group boundary
+group mobile subtract all boundary
+1384 atoms in group mobile
+
+set group lower type 2
+ 264 settings made for type
+set group upper type 3
+ 264 settings made for type
+
+# void
+
+region void cylinder z 8 3.535534 2.5 INF INF
+delete_atoms region void
+Deleted 204 atoms, new total = 1708
+
+# temp controllers
+
+compute new3d mobile temp
+compute new2d mobile temp/partial 0 1 1
+
+# equilibrate
+
+velocity mobile create 300.0 5812775 temp new3d
+fix 1 all nve
+fix 2 boundary setforce 0.0 0.0 0.0
+
+fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
+fix_modify 3 temp new3d
+
+thermo 25
+thermo_modify temp new3d
+
+timestep 0.001
+run 100
+Memory usage per processor = 1.87344 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 300 -7358.6159 0 -7312.8966 -9604.6063 19539.346
+ 25 221.73981 -7320.8381 0 -7287.0455 1130.0476 19599.582
+ 50 300 -7293.1759 0 -7247.4566 8052.1835 19662.062
+ 75 293.25753 -7287.1687 0 -7242.4769 7429.1313 19732.777
+ 100 300 -7300.0537 0 -7254.3344 1198.4581 19807.395
+Loop time of 0.176328 on 4 procs for 100 steps with 1708 atoms
+
+Pair time (%) = 0.1287 (72.9894)
+Neigh time (%) = 0.00338066 (1.91726)
+Comm time (%) = 0.033612 (19.0622)
+Outpt time (%) = 0.00139475 (0.790998)
+Other time (%) = 0.00923985 (5.24016)
+
+Nlocal: 427 ave 435 max 419 min
+Histogram: 1 0 1 0 0 0 0 1 0 1
+Nghost: 780.25 ave 792 max 769 min
+Histogram: 1 0 0 1 0 1 0 0 0 1
+Neighs: 9878.75 ave 10203 max 9534 min
+Histogram: 1 0 0 0 1 0 1 0 0 1
+
+Total # of neighbors = 39515
+Ave neighs/atom = 23.1352
+Neighbor list builds = 5
+Dangerous builds = 0
+
+# shear
+
+velocity upper set 1.0 0 0
+velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes
+
+unfix 3
+fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
+fix_modify 3 temp new2d
+
+dump 1 all atom 100 dump.shear
+thermo 100
+thermo_modify temp new2d
+
+reset_timestep 0
+run 3000
+Memory usage per processor = 1.89003 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 303.68338 -7300.0537 0 -7269.213 396.12256 19807.521
+ 100 309.43345 -7305.7349 0 -7274.3103 -4898.9067 19876.383
+ 200 292.09158 -7308.3924 0 -7278.7289 -9672.4555 19871.139
+ 300 297.20209 -7303.4054 0 -7273.2229 -10458.509 20026.545
+ 400 301.76624 -7298.9615 0 -7268.3155 -8311.9182 20057.341
+ 500 296.6739 -7299.7346 0 -7269.6058 -6648.1941 20142.621
+ 600 301.5451 -7294.6131 0 -7263.9896 -4525.1055 20268.839
+ 700 297.72688 -7285.6963 0 -7255.4605 -1774.5536 20391.147
+ 800 309.01491 -7279.9489 0 -7248.5668 -394.2912 20501.655
+ 900 307.05599 -7273.2334 0 -7242.0502 8.1721666 20633.545
+ 1000 299.45693 -7266.8728 0 -7236.4613 -2338.8876 20759.329
+ 1100 300 -7259.9532 0 -7229.4865 -3092.0664 20875.344
+ 1200 300 -7258.5089 0 -7228.0423 -5092.1152 20997.464
+ 1300 300 -7261.2914 0 -7230.8248 -5743.4972 21124.47
+ 1400 300 -7266.0446 0 -7235.578 -7828.4242 21233.157
+ 1500 307.13101 -7271.165 0 -7239.9741 -11309.87 21360.162
+ 1600 300 -7273.2378 0 -7242.7712 -13366.956 21484.725
+ 1700 301.7588 -7270.2824 0 -7239.6372 -14195.725 21609.288
+ 1800 300 -7271.2595 0 -7240.7929 -11929.424 21736.293
+ 1900 307.50197 -7274.3144 0 -7243.0859 -14024.738 21852.308
+ 2000 300 -7267.9904 0 -7237.5238 -19598.421 21965.88
+ 2100 300.69536 -7264.7536 0 -7234.2163 -20295.562 22090.443
+ 2200 301.08099 -7267.9694 0 -7237.393 -22833.972 22223.554
+ 2300 291.66065 -7261.6554 0 -7232.0357 -23125.705 22343.232
+ 2400 298.88457 -7257.9563 0 -7227.603 -25049.249 22470.237
+ 2500 304.37073 -7253.7601 0 -7222.8496 -25545.14 22589.915
+ 2600 300 -7246.4222 0 -7215.9556 -25051.428 22710.815
+ 2700 300 -7243.8917 0 -7213.4251 -28923.111 22826.829
+ 2800 300 -7239.3939 0 -7208.9273 -28323.168 22958.719
+ 2900 304.87485 -7235.3221 0 -7204.3604 -26726.42 23072.291
+ 3000 300 -7233.1367 0 -7202.6701 -27373.287 23200.518
+Loop time of 5.30706 on 4 procs for 3000 steps with 1708 atoms
+
+Pair time (%) = 3.79223 (71.4564)
+Neigh time (%) = 0.135778 (2.55845)
+Comm time (%) = 0.98511 (18.5623)
+Outpt time (%) = 0.097142 (1.83043)
+Other time (%) = 0.296796 (5.59247)
+
+Nlocal: 427 ave 441 max 411 min
+Histogram: 1 1 0 0 0 0 0 0 0 2
+Nghost: 777.25 ave 826 max 727 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs: 9559.25 ave 10062 max 9128 min
+Histogram: 1 0 0 0 2 0 0 0 0 1
+
+Total # of neighbors = 38237
+Ave neighs/atom = 22.387
+Neighbor list builds = 210
+Dangerous builds = 0
diff --git a/examples/shear/log.shear.void.22Jan08.linux.1 b/examples/shear/log.shear.void.22Jan08.linux.1
deleted file mode 100644
index ce2f6906a..000000000
--- a/examples/shear/log.shear.void.22Jan08.linux.1
+++ /dev/null
@@ -1,160 +0,0 @@
-LAMMPS (22 Jan 2008)
-# 3d metal shear simulation
-
-units metal
-boundary s s p
-
-atom_style atomic
-lattice fcc 3.52
-Lattice spacing in x,y,z = 3.52 3.52 3.52
-region box block 0 16.0 0 10.0 0 2.828427
-create_box 3 box
-Created orthogonal box = (0 0 0) to (56.32 35.2 9.95606)
- 1 by 1 by 1 processor grid
-
-lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0
-Lattice spacing in x,y,z = 3.52 4.97803 4.97803
-create_atoms 1 box
-Created 1912 atoms
-
-pair_style eam
-pair_coeff * * Ni_u3.eam
-
-neighbor 0.3 bin
-neigh_modify delay 5
-
-region lower block INF INF INF 0.9 INF INF
-region upper block INF INF 6.1 INF INF INF
-group lower region lower
-264 atoms in group lower
-group upper region upper
-264 atoms in group upper
-group boundary union lower upper
-528 atoms in group boundary
-group mobile subtract all boundary
-1384 atoms in group mobile
-
-set group lower type 2
- 264 settings made for type
-set group upper type 3
- 264 settings made for type
-
-# void
-
-region void cylinder z 8 3.535534 2.5 INF INF
-delete_atoms region void
-Deleted 204 atoms, new total = 1708
-
-# temp controllers
-
-compute new3d mobile temp
-compute new2d mobile temp/partial 0 1 1
-
-# equilibrate
-
-velocity mobile create 300.0 5812775 temp new3d
-fix 1 all nve
-fix 2 boundary setforce 0.0 0.0 0.0
-
-fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
-fix_modify 3 temp new3d
-
-thermo 25
-thermo_modify temp new3d
-
-timestep 0.001
-run 100
-Memory usage per processor = 1.96813 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume
- 0 300 -7358.6159 0 -7312.8966 -9604.6063 19539.346
- 25 222.66197 -7321.4403 0 -7287.5071 562.50939 19539.346
- 50 300 -7292.2273 0 -7246.508 7558.4629 19680.84
- 75 292.67603 -7286.2016 0 -7241.5984 6828.0763 19738.503
- 100 300 -7297.4174 0 -7251.698 1627.881 19767.928
-Loop time of 0.40687 on 1 procs for 100 steps with 1708 atoms
-
-Pair time (%) = 0.385552 (94.7605)
-Neigh time (%) = 0.0105622 (2.59596)
-Comm time (%) = 0.00262928 (0.646221)
-Outpt time (%) = 0.000127792 (0.0314086)
-Other time (%) = 0.0079987 (1.96591)
-
-Nlocal: 1708 ave 1708 max 1708 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 1898 ave 1898 max 1898 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 39444 ave 39444 max 39444 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 39444
-Ave neighs/atom = 23.0937
-Neighbor list builds = 4
-Dangerous builds = 0
-
-# shear
-
-velocity upper set 1.0 0 0
-velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes
-
-unfix 3
-fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
-fix_modify 3 temp new2d
-
-dump 1 all atom 100 dump.shear
-thermo 100
-thermo_modify temp new2d
-
-reset_timestep 0
-run 3000
-Memory usage per processor = 2.03328 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume
- 0 296.81549 -7297.4174 0 -7267.2741 786.10955 19771.704
- 100 300 -7311.9184 0 -7281.4518 -5944.573 19791.679
- 200 298.46333 -7306.5409 0 -7276.2304 -6669.0732 19903.341
- 300 298.05646 -7303.4774 0 -7273.2081 -10334.9 20033.654
- 400 297.71277 -7298.5998 0 -7268.3655 -7644.8753 20112.791
- 500 300 -7301.3145 0 -7270.8479 -6327.722 20143.842
- 600 306.29328 -7291.192 0 -7260.0863 -1482.3063 20281.66
- 700 308.44794 -7289.4349 0 -7258.1103 -3026.5046 20394.034
- 800 300 -7282.5733 0 -7252.1067 -3555.2034 20513.867
- 900 300 -7273.9966 0 -7243.53 -1850.9526 20622.554
- 1000 300 -7266.6095 0 -7236.1429 -1119.6046 20741.011
- 1100 301.26482 -7261.9024 0 -7231.3073 -1647.8612 20874.123
- 1200 299.17066 -7259.2281 0 -7228.8457 -1938.4437 20998.686
- 1300 300 -7263.9553 0 -7233.4887 -3376.9235 21112.258
- 1400 300 -7270.1139 0 -7239.6473 -5846.3511 21249.033
- 1500 307.98903 -7273.6991 0 -7242.4211 -6121.5944 21366.268
- 1600 300 -7278.9972 0 -7248.5306 -9389.2139 21484.725
- 1700 300 -7279.8403 0 -7249.3737 -14440.631 21615.394
- 1800 309.55921 -7284.1875 0 -7252.7501 -14795.954 21727.745
- 1900 299.29406 -7282.5749 0 -7252.18 -15392.232 21848.644
- 2000 299.964 -7271.7156 0 -7241.2526 -19451.05 21968.322
- 2100 308.54552 -7272.2334 0 -7240.8989 -23685.178 22100.212
- 2200 308.49102 -7271.1314 0 -7239.8025 -20630.136 22219.89
- 2300 290.31543 -7268.9828 0 -7239.4997 -19028.307 22342.011
- 2400 299.15433 -7259.7686 0 -7229.3878 -14272.769 22459.246
- 2500 299.15088 -7260.7963 0 -7230.4159 -14923.448 22576.482
- 2600 301.27999 -7258.5805 0 -7227.9839 -15706.203 22702.266
- 2700 307.83121 -7254.9828 0 -7223.7209 -19761.07 22830.493
- 2800 300 -7254.6086 0 -7224.142 -23849.892 22944.065
- 2900 303.23126 -7256.0886 0 -7225.2938 -23451.705 23080.84
- 3000 290.86402 -7255.5292 0 -7225.9904 -20678.136 23202.96
-Loop time of 12.3962 on 1 procs for 3000 steps with 1708 atoms
-
-Pair time (%) = 11.4662 (92.4971)
-Neigh time (%) = 0.539913 (4.35546)
-Comm time (%) = 0.0821109 (0.662385)
-Outpt time (%) = 0.0712039 (0.574399)
-Other time (%) = 0.23685 (1.91066)
-
-Nlocal: 1708 ave 1708 max 1708 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 1882 ave 1882 max 1882 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 38801 ave 38801 max 38801 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 38801
-Ave neighs/atom = 22.7172
-Neighbor list builds = 205
-Dangerous builds = 0
diff --git a/examples/shear/log.shear.void.22Jan08.linux.4 b/examples/shear/log.shear.void.22Jan08.linux.4
deleted file mode 100644
index 907e87205..000000000
--- a/examples/shear/log.shear.void.22Jan08.linux.4
+++ /dev/null
@@ -1,160 +0,0 @@
-LAMMPS (22 Jan 2008)
-# 3d metal shear simulation
-
-units metal
-boundary s s p
-
-atom_style atomic
-lattice fcc 3.52
-Lattice spacing in x,y,z = 3.52 3.52 3.52
-region box block 0 16.0 0 10.0 0 2.828427
-create_box 3 box
-Created orthogonal box = (0 0 0) to (56.32 35.2 9.95606)
- 2 by 2 by 1 processor grid
-
-lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0
-Lattice spacing in x,y,z = 3.52 4.97803 4.97803
-create_atoms 1 box
-Created 1912 atoms
-
-pair_style eam
-pair_coeff * * Ni_u3.eam
-
-neighbor 0.3 bin
-neigh_modify delay 5
-
-region lower block INF INF INF 0.9 INF INF
-region upper block INF INF 6.1 INF INF INF
-group lower region lower
-264 atoms in group lower
-group upper region upper
-264 atoms in group upper
-group boundary union lower upper
-528 atoms in group boundary
-group mobile subtract all boundary
-1384 atoms in group mobile
-
-set group lower type 2
- 264 settings made for type
-set group upper type 3
- 264 settings made for type
-
-# void
-
-region void cylinder z 8 3.535534 2.5 INF INF
-delete_atoms region void
-Deleted 204 atoms, new total = 1708
-
-# temp controllers
-
-compute new3d mobile temp
-compute new2d mobile temp/partial 0 1 1
-
-# equilibrate
-
-velocity mobile create 300.0 5812775 temp new3d
-fix 1 all nve
-fix 2 boundary setforce 0.0 0.0 0.0
-
-fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
-fix_modify 3 temp new3d
-
-thermo 25
-thermo_modify temp new3d
-
-timestep 0.001
-run 100
-Memory usage per processor = 1.87344 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume
- 0 300 -7358.6159 0 -7312.8966 -9604.6063 19539.346
- 25 221.73981 -7320.8381 0 -7287.0455 1130.0476 19599.582
- 50 300 -7293.1759 0 -7247.4566 8052.1835 19662.062
- 75 293.25753 -7287.1687 0 -7242.4769 7429.1313 19732.777
- 100 300 -7300.0537 0 -7254.3344 1198.4581 19807.395
-Loop time of 0.185206 on 4 procs for 100 steps with 1708 atoms
-
-Pair time (%) = 0.134434 (72.5863)
-Neigh time (%) = 0.00337529 (1.82245)
-Comm time (%) = 0.035861 (19.3627)
-Outpt time (%) = 0.00149727 (0.808433)
-Other time (%) = 0.0100384 (5.42011)
-
-Nlocal: 427 ave 435 max 419 min
-Histogram: 1 0 1 0 0 0 0 1 0 1
-Nghost: 780.25 ave 792 max 769 min
-Histogram: 1 0 0 1 0 1 0 0 0 1
-Neighs: 9878.75 ave 10203 max 9534 min
-Histogram: 1 0 0 0 1 0 1 0 0 1
-
-Total # of neighbors = 39515
-Ave neighs/atom = 23.1352
-Neighbor list builds = 5
-Dangerous builds = 0
-
-# shear
-
-velocity upper set 1.0 0 0
-velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes
-
-unfix 3
-fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
-fix_modify 3 temp new2d
-
-dump 1 all atom 100 dump.shear
-thermo 100
-thermo_modify temp new2d
-
-reset_timestep 0
-run 3000
-Memory usage per processor = 1.89003 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume
- 0 303.68338 -7300.0537 0 -7269.213 396.12256 19807.521
- 100 307.23986 -7307.219 0 -7276.0171 -5006.3499 19862.724
- 200 300 -7309.7515 0 -7279.2849 -9319.6187 19862.401
- 300 298.46847 -7303.3937 0 -7273.0826 -9727.416 20012.256
- 400 298.27255 -7299.2458 0 -7268.9546 -7916.7896 20056.15
- 500 297.5947 -7299.7495 0 -7269.5271 -6499.9287 20136.515
- 600 299.11571 -7294.7189 0 -7264.342 -4738.4592 20278.808
- 700 299.12204 -7285.1912 0 -7254.8138 -1900.5818 20396.287
- 800 300 -7279.6074 0 -7249.1408 -601.56409 20516.31
- 900 300 -7272.2062 0 -7241.7396 372.01695 20624.997
- 1000 297.17814 -7265.7734 0 -7235.5934 -1620.5152 20750.781
- 1100 300 -7257.7175 0 -7227.2509 -1422.3295 20870.459
- 1200 300 -7254.9538 0 -7224.4872 -2924.6246 20990.137
- 1300 300 -7257.9757 0 -7227.5091 -4069.1414 21123.248
- 1400 300 -7265.0693 0 -7234.6027 -6549.1146 21249.033
- 1500 305.40659 -7268.4 0 -7237.3844 -9980.0284 21360.162
- 1600 307.73328 -7272.8967 0 -7241.6447 -12845.156 21479.84
- 1700 308.89481 -7272.8308 0 -7241.4609 -14742.73 21599.518
- 1800 301.22537 -7272.7599 0 -7242.1688 -15363.965 21736.293
- 1900 294.08915 -7269.2219 0 -7239.3555 -17918.885 21854.75
- 2000 300 -7267.3723 0 -7236.9057 -22110.158 21970.765
- 2100 303.71749 -7266.6269 0 -7235.7828 -24452.593 22103.876
- 2200 305.09813 -7260.5568 0 -7229.5724 -22990.432 22219.89
- 2300 302.38637 -7258.8153 0 -7228.1063 -21646.154 22335.905
- 2400 305.66165 -7262.3039 0 -7231.2623 -21131.332 22458.025
- 2500 298.90421 -7257.9905 0 -7227.6352 -21269.206 22592.358
- 2600 300.16888 -7256.8469 0 -7226.3631 -23698.687 22699.824
- 2700 296.33302 -7251.3734 0 -7221.2792 -26655.74 22826.829
- 2800 296.22091 -7248.3427 0 -7218.2599 -30008.453 22947.728
- 2900 301.32756 -7250.3222 0 -7219.7207 -28370.97 23080.84
- 3000 300 -7252.9148 0 -7222.4482 -28938.171 23201.739
-Loop time of 5.54083 on 4 procs for 3000 steps with 1708 atoms
-
-Pair time (%) = 3.99282 (72.0617)
-Neigh time (%) = 0.141571 (2.55505)
-Comm time (%) = 1.02782 (18.55)
-Outpt time (%) = 0.102889 (1.85692)
-Other time (%) = 0.275728 (4.9763)
-
-Nlocal: 427 ave 441 max 415 min
-Histogram: 2 0 0 0 0 0 0 1 0 1
-Nghost: 784 ave 845 max 718 min
-Histogram: 1 1 0 0 0 0 0 0 0 2
-Neighs: 9597.25 ave 10151 max 9269 min
-Histogram: 1 0 2 0 0 0 0 0 0 1
-
-Total # of neighbors = 38389
-Ave neighs/atom = 22.476
-Neighbor list builds = 211
-Dangerous builds = 0