diff --git a/examples/colloid/log.colloid.22Jun07.liberty.4 b/examples/colloid/log.colloid.22Jun07.liberty.4 new file mode 100644 index 0000000000..373f90bca6 --- /dev/null +++ b/examples/colloid/log.colloid.22Jun07.liberty.4 @@ -0,0 +1,80 @@ +LAMMPS (22 June 2007) +# 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 + 868 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 10000 +Memory usage per processor = 1.45054 Mbytes +Step Temp E_pair TotEng Press Volume + 0 1.44 0 1.4376 0.0009584 900000 + 1000 1.8470142 0.0048357172 1.8487715 0.017163086 74830.331 + 2000 1.9719939 0.18486401 2.1535713 0.79205274 4710.4215 + 3000 1.8512583 0.19478206 2.0429549 1.2638229 3348.993 + 4000 2.0197762 0.085599862 2.1020098 0.44423307 6289.5217 + 5000 2.1100188 0.066582351 2.1730844 0.30071147 7797.8952 + 6000 2.122322 0.080537323 2.1993221 0.47114461 5829.3235 + 7000 2.0053017 0.17924225 2.1812018 0.82372251 4418.5393 + 8000 1.9850765 0.16081341 2.1425814 0.86380905 4218.1246 + 9000 2.0229633 0.14063325 2.1602249 0.8620141 4223.7169 + 10000 2.0133665 0.16380502 2.173816 0.95385436 3995.0006 +Loop time of 4.86636 on 4 procs for 10000 steps with 900 atoms + +Pair time (%) = 1.32706 (27.27) +Neigh time (%) = 0.274084 (5.63221) +Comm time (%) = 1.98481 (40.7863) +Outpt time (%) = 0.0898068 (1.84546) +Other time (%) = 1.1906 (24.466) + +Nlocal: 225 ave 232 max 218 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +Nghost: 411.5 ave 428 max 388 min +Histogram: 1 0 0 0 1 0 0 0 0 2 +Neighs: 2307 ave 2410 max 2183 min +Histogram: 1 0 1 0 0 0 0 0 0 2 + +Total # of neighbors = 9228 +Ave neighs/atom = 10.2533 +Neighbor list builds = 773 +Dangerous builds = 0 diff --git a/examples/colloid/log.colloid.22Jun07.linux.1 b/examples/colloid/log.colloid.22Jun07.linux.1 new file mode 100644 index 0000000000..a0b36dfc15 --- /dev/null +++ b/examples/colloid/log.colloid.22Jun07.linux.1 @@ -0,0 +1,80 @@ +LAMMPS (22 June 2007) +# 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 + 868 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 10000 +Memory usage per processor = 1.47629 Mbytes +Step Temp E_pair TotEng Press Volume + 0 1.44 0 1.4376 0.0009584 900000 + 1000 1.8470142 0.0048357172 1.8487715 0.017163086 74830.331 + 2000 1.9719939 0.18486401 2.1535713 0.79205271 4710.4215 + 3000 1.8760117 0.16888745 2.0417724 1.2866805 3349.4362 + 4000 2.0084889 0.10591744 2.1110589 0.41080478 6315.195 + 5000 2.0845189 0.074837406 2.1558821 0.32123703 7787.3569 + 6000 2.0635646 0.12699208 2.1871174 0.55212245 5811.0643 + 7000 2.0511741 0.13194486 2.1797003 0.75534937 4447.7483 + 8000 2.0057569 0.14524464 2.1476586 0.93321505 4260.455 + 9000 1.9863917 0.16294985 2.1460309 0.85687596 4264.0791 + 10000 1.9867944 0.17403524 2.1575183 1.019418 3985.5163 +Loop time of 13.1171 on 1 procs for 10000 steps with 900 atoms + +Pair time (%) = 8.49344 (64.7507) +Neigh time (%) = 1.7079 (13.0204) +Comm time (%) = 0.409296 (3.12032) +Outpt time (%) = 0.224203 (1.70924) +Other time (%) = 2.28229 (17.3993) + +Nlocal: 900 ave 900 max 900 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 648 ave 648 max 648 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 9057 ave 9057 max 9057 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 9057 +Ave neighs/atom = 10.0633 +Neighbor list builds = 777 +Dangerous builds = 0 diff --git a/examples/crack/log.crack.22Jun07.liberty.4 b/examples/crack/log.crack.22Jun07.liberty.4 new file mode 100644 index 0000000000..9a10a7a452 --- /dev/null +++ b/examples/crack/log.crack.22Jun07.liberty.4 @@ -0,0 +1,129 @@ +LAMMPS (22 June 2007) +# 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 +820 atoms in group leftupper +group leftlower region leftlower +841 atoms in group leftlower + +set group leftupper type 2 + 820 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 = 1.59725 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 0.065996472 -3.2595015 0 -3.1984136 -0.04302381 4792.6107 + 200 0.060047239 -3.2531973 0 -3.1976162 -0.27194148 4811.0322 + 400 0.060540328 -3.2510659 0 -3.1950283 -0.51122765 4832.8487 + 600 0.060577107 -3.2468136 0 -3.190742 -0.71796559 4855.0481 + 800 0.060812364 -3.241354 0 -3.1850647 -0.89095308 4876.899 + 1000 0.061815921 -3.2349951 0 -3.1777768 -1.0418483 4899.229 + 1200 0.063180751 -3.227761 0 -3.1692795 -1.1726472 4913.5762 + 1400 0.065132588 -3.2198103 0 -3.1595221 -1.279378 4933.6517 + 1600 0.067270882 -3.2111519 0 -3.1488844 -1.3695054 4952.9497 + 1800 0.0693778 -3.201954 0 -3.1377363 -1.4352657 4975.6762 + 2000 0.071252815 -3.1921529 0 -3.1261996 -1.4841334 4994.9699 + 2200 0.073149176 -3.181847 0 -3.1141384 -1.5151492 5011.4455 + 2400 0.074908709 -3.1710714 0 -3.1017341 -1.5320377 5034.0712 + 2600 0.076683014 -3.1599865 0 -3.0890069 -1.5392632 5049.8449 + 2800 0.078565789 -3.1486031 0 -3.0758808 -1.5361716 5070.8919 + 3000 0.080066913 -3.1368161 0 -3.0627043 -1.5207043 5089.9281 + 3200 0.081471767 -3.1247706 0 -3.0493584 -1.4971581 5105.9878 + 3400 0.08330546 -3.1128524 0 -3.035743 -1.4631308 5124.3294 + 3600 0.08531273 -3.1009259 0 -3.0219584 -1.4242782 5139.7334 + 3800 0.086420792 -3.0884931 0 -3.0085 -1.3812881 5151.9744 + 4000 0.085220498 -3.0759708 0 -2.9970887 -1.3501547 5163.5493 + 4200 0.08235554 -3.0634364 0 -2.9872062 -1.341062 5178.82 + 4400 0.08347755 -3.0521602 0 -2.9748914 -1.3473183 5192.4176 + 4600 0.084114334 -3.0389835 0 -2.9611253 -1.3384039 5209.5435 + 4800 0.085414901 -3.0273902 0 -2.9483282 -1.3365973 5232.9505 + 5000 0.087614902 -3.0176386 0 -2.9365402 -1.337001 5251.075 +Loop time of 7.15681 on 4 procs for 5000 steps with 8141 atoms + +Pair time (%) = 4.67775 (65.3608) +Neigh time (%) = 0.180912 (2.52784) +Comm time (%) = 1.1892 (16.6164) +Outpt time (%) = 0.174089 (2.4325) +Other time (%) = 0.934854 (13.0624) + +Nlocal: 2035.25 ave 2062 max 2008 min +Histogram: 1 0 0 0 1 1 0 0 0 1 +Nghost: 204.5 ave 246 max 175 min +Histogram: 2 0 0 0 0 0 1 0 0 1 +Neighs: 17860.5 ave 18270 max 17548 min +Histogram: 1 0 0 2 0 0 0 0 0 1 + +Total # of neighbors = 71442 +Ave neighs/atom = 8.77558 +Neighbor list builds = 98 +Dangerous builds = 0 diff --git a/examples/crack/log.crack.22Jun07.linux.1 b/examples/crack/log.crack.22Jun07.linux.1 new file mode 100644 index 0000000000..ed18b32560 --- /dev/null +++ b/examples/crack/log.crack.22Jun07.linux.1 @@ -0,0 +1,129 @@ +LAMMPS (22 June 2007) +# 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 +820 atoms in group leftupper +group leftlower region leftlower +841 atoms in group leftlower + +set group leftupper type 2 + 820 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 = 2.04243 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 0.065655433 -3.2595015 0 -3.1987293 -0.043381291 4792.6107 + 200 0.060090071 -3.2531939 0 -3.1975731 -0.27682436 4811.1142 + 400 0.060537254 -3.2509976 0 -3.1949629 -0.51538634 4833.6384 + 600 0.060833381 -3.2466952 0 -3.1903864 -0.72165405 4854.5327 + 800 0.061681012 -3.2413218 0 -3.1842284 -0.89573177 4876.5182 + 1000 0.062387584 -3.2349276 0 -3.1771802 -1.046532 4897.0644 + 1200 0.063713197 -3.2276097 0 -3.1686353 -1.1733596 4916.992 + 1400 0.065408625 -3.2196611 0 -3.1591173 -1.2802996 4937.9378 + 1600 0.067583821 -3.2110381 0 -3.1484809 -1.3713947 4956.9814 + 1800 0.069328584 -3.2018539 0 -3.1376817 -1.4389808 4974.9955 + 2000 0.071019398 -3.192111 0 -3.1263738 -1.4879518 4992.2457 + 2200 0.072997487 -3.1818704 0 -3.1143022 -1.5204135 5014.7654 + 2400 0.075005457 -3.1712316 0 -3.1018048 -1.5359222 5031.8024 + 2600 0.076848328 -3.1601006 0 -3.088968 -1.5313163 5052.4867 + 2800 0.078676694 -3.148775 0 -3.07595 -1.5154187 5070.2113 + 3000 0.080718743 -3.137326 0 -3.0626108 -1.4892046 5087.256 + 3200 0.083100049 -3.1260245 0 -3.0491051 -1.4538734 5106.4445 + 3400 0.085430328 -3.1146626 0 -3.0355863 -1.4172254 5127.5606 + 3600 0.087402049 -3.1029496 0 -3.0220482 -1.3687184 5142.5301 + 3800 0.089013695 -3.0908222 0 -3.0084291 -1.3168466 5156.5957 + 4000 0.089818767 -3.079408 0 -2.9962696 -1.2722766 5169.2872 + 4200 0.085852921 -3.0668561 0 -2.9873886 -1.2424995 5184.3213 + 4400 0.086203112 -3.0559681 0 -2.9761765 -1.2315726 5195.5481 + 4600 0.086772028 -3.0437629 0 -2.9634447 -1.2220387 5213.9452 + 4800 0.088200815 -3.0328504 0 -2.9512097 -1.2296115 5232.6714 + 5000 0.08942145 -3.0228831 0 -2.9401125 -1.2228214 5255.2593 +Loop time of 45.1427 on 1 procs for 5000 steps with 8141 atoms + +Pair time (%) = 36.1309 (80.0372) +Neigh time (%) = 1.29244 (2.86301) +Comm time (%) = 0.075937 (0.168216) +Outpt time (%) = 0.437291 (0.968687) +Other time (%) = 7.20605 (15.9628) + +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/dipole/log.dipole.22Jun07.liberty.4 b/examples/dipole/log.dipole.22Jun07.liberty.4 new file mode 100644 index 0000000000..409f739d65 --- /dev/null +++ b/examples/dipole/log.dipole.22Jun07.liberty.4 @@ -0,0 +1,83 @@ +LAMMPS (22 June 2007) +# 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 = 2.32239 Mbytes +Step Temp E_pair RotKEdip TotEng Press + 0 0 -2.1284412 0 -2.1284412 -0.98973217 + 500 0.38229437 -2.703408 0.24548268 -2.3239808 -0.073894217 + 1000 0.41156476 -2.7426733 0.25757681 -2.3341953 0.05919685 + 1500 0.43191585 -2.8089326 0.33203347 -2.3802561 -0.16059384 + 2000 0.43337741 -2.7836977 0.30755109 -2.3535707 -0.050258895 + 2500 0.41025746 -2.7704617 0.31976882 -2.3632812 -0.040387583 + 3000 0.4343462 -2.7853843 0.32540887 -2.3542957 -0.040773878 + 3500 0.4516216 -2.7378372 0.25848559 -2.2896027 0.01498558 + 4000 0.46812215 -2.7531454 0.25653816 -2.2885341 -0.015167924 + 4500 0.41857472 -2.7022096 0.27078871 -2.2867742 0.040384474 + 5000 0.42275097 -2.7173978 0.28129865 -2.2978174 0.08127607 + 5500 0.39689205 -2.6755268 0.28694074 -2.2816114 -0.063519745 + 6000 0.40712229 -2.6810855 0.29780556 -2.2770166 -0.010331415 + 6500 0.42401695 -2.7099716 0.32599472 -2.2891348 -0.080194492 + 7000 0.46557586 -2.7235207 0.277596 -2.2614366 -0.025483686 + 7500 0.4634213 -2.7520289 0.33385569 -2.2920833 -0.07670048 + 8000 0.44330991 -2.6937045 0.28515119 -2.2537194 0.063037221 + 8500 0.46501497 -2.7192191 0.31059999 -2.2576917 -0.12974997 + 9000 0.48895857 -2.7113963 0.27823171 -2.2261049 -0.032792109 + 9500 0.5206475 -2.7393465 0.2997953 -2.2226039 0.15436407 + 10000 0.47111871 -2.6818528 0.2936091 -2.2142675 -0.18366919 +Loop time of 2.70823 on 4 procs for 10000 steps with 200 atoms + +Pair time (%) = 0.644681 (23.8045) +Neigh time (%) = 0.0255789 (0.944486) +Comm time (%) = 1.55045 (57.2495) +Outpt time (%) = 0.0430555 (1.5898) +Other time (%) = 0.444467 (16.4117) + +Nlocal: 50 ave 53 max 46 min +Histogram: 1 0 0 0 0 1 0 1 0 1 +Nghost: 88.75 ave 91 max 86 min +Histogram: 1 0 0 0 1 0 0 0 1 1 +Neighs: 402.25 ave 443 max 365 min +Histogram: 1 0 0 1 0 1 0 0 0 1 + +Total # of neighbors = 1609 +Ave neighs/atom = 8.045 +Neighbor list builds = 700 +Dangerous builds = 0 diff --git a/examples/dipole/log.dipole.22Jun07.linux.1 b/examples/dipole/log.dipole.22Jun07.linux.1 new file mode 100644 index 0000000000..797d99423c --- /dev/null +++ b/examples/dipole/log.dipole.22Jun07.linux.1 @@ -0,0 +1,83 @@ +LAMMPS (22 June 2007) +# 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 = 2.33154 Mbytes +Step Temp E_pair RotKEdip TotEng Press + 0 0 -2.1284412 0 -2.1284412 -0.98973217 + 500 0.38229437 -2.703408 0.24548268 -2.3239808 -0.073894217 + 1000 0.41156476 -2.7426733 0.25757681 -2.3341953 0.05919685 + 1500 0.43191583 -2.8089326 0.33203347 -2.3802561 -0.16059384 + 2000 0.43342192 -2.7837445 0.30758527 -2.3535733 -0.050298945 + 2500 0.40678173 -2.7608212 0.32070295 -2.3570903 -0.066209676 + 3000 0.44085008 -2.7740637 0.3050664 -2.33652 -0.033394791 + 3500 0.44821249 -2.7478981 0.27867563 -2.3030472 0.0084562338 + 4000 0.45333935 -2.7563404 0.3084146 -2.3064011 -0.10934119 + 4500 0.45156284 -2.723795 0.27757494 -2.2756189 -0.23949041 + 5000 0.48926457 -2.7653696 0.29559023 -2.2797745 0.038474281 + 5500 0.47000827 -2.7286039 0.28271513 -2.2621207 -0.01679705 + 6000 0.49865525 -2.7247669 0.24383453 -2.2298516 -0.028697894 + 6500 0.46877605 -2.6998151 0.25730063 -2.2345548 -0.034887111 + 7000 0.38249447 -2.6298198 0.31407559 -2.250194 0.010153416 + 7500 0.4674564 -2.667655 0.25360513 -2.2037046 -0.14832 + 8000 0.46214985 -2.6953164 0.31284004 -2.2366327 -0.13077442 + 8500 0.45348969 -2.6629085 0.30178085 -2.21282 0.014011681 + 9000 0.45748811 -2.6903116 0.33394285 -2.2362547 -0.093496105 + 9500 0.49014698 -2.7127804 0.32910939 -2.2263096 -0.013973624 + 10000 0.39914132 -2.6368493 0.35529835 -2.2407016 -0.12272941 +Loop time of 6.7855 on 1 procs for 10000 steps with 200 atoms + +Pair time (%) = 5.39439 (79.4989) +Neigh time (%) = 0.164115 (2.41861) +Comm time (%) = 0.264522 (3.89834) +Outpt time (%) = 0.1165 (1.7169) +Other time (%) = 0.845967 (12.4673) + +Nlocal: 200 ave 200 max 200 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 144 ave 144 max 144 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 = 8.075 +Neighbor list builds = 697 +Dangerous builds = 0 diff --git a/examples/ellipse/log.ellipse.22Jun07.liberty.4 b/examples/ellipse/log.ellipse.22Jun07.liberty.4 new file mode 100644 index 0000000000..1093fc277f --- /dev/null +++ b/examples/ellipse/log.ellipse.22Jun07.liberty.4 @@ -0,0 +1,141 @@ +LAMMPS (22 June 2007) +# 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 + 38 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 + +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 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 = 2.3262 Mbytes +Step rot E_pair TotEng Press Volume + 0 2.1910653 0 2.391 0.0045085128 141421.36 + 100 1.9478792 0 2.1256232 0.004563496 124210.22 + 200 2.3700495 -3.3319106e-05 2.5862832 0.013268829 51975.461 + 300 1.8455677 -0.099549795 1.8705975 0.043367291 11254.795 + 400 4.7673362 -0.63680144 4.1000403 2.5967285 2117.5435 + 500 2.0914283 -3.1875966 -0.98127813 15.054185 716.60631 + 600 0.16670993 -6.5302264 -6.3521489 -1.2408868 763.95532 + 700 0.61510434 -6.2651546 -5.6130844 -1.7391671 850.63471 + 800 4.2400887 -4.7665917 -0.37668829 4.3628579 893.62251 + 900 0.56540605 -4.0704259 -3.4850161 -1.2625042 1339.0962 + 1000 4.1072215 -3.5049913 0.78871853 1.3994916 1581.8306 + 1100 1.002839 -3.4270693 -2.3625765 -0.34931088 2002.5983 + 1200 2.3739586 -3.2294296 -0.73953462 0.47928761 2137.475 + 1300 1.755069 -3.2886568 -1.4395111 0.24365268 2147.7339 + 1400 1.4374762 -3.597546 -2.0874512 0.26707014 1976.8436 + 1500 2.7207484 -3.4893404 -0.67636594 1.4873069 1672.6682 + 1600 1.0385312 -4.3747776 -3.2807384 0.10681629 1506.5847 + 1700 3.3252787 -4.3839001 -0.91852241 1.7513361 1235.5246 + 1800 1.2745712 -4.7993978 -3.4903396 0.16468564 1129.5996 + 1900 2.2642602 -4.906129 -2.5944276 2.1651713 988.12263 + 2000 1.807468 -5.0525829 -3.1803091 0.86237508 964.0263 +Loop time of 1.6379 on 4 procs for 2000 steps with 400 atoms + +Pair time (%) = 0.785513 (47.9584) +Neigh time (%) = 0.00847417 (0.517379) +Comm time (%) = 0.494713 (30.204) +Outpt time (%) = 0.0563657 (3.44133) +Other time (%) = 0.292839 (17.8789) + +Nlocal: 100 ave 109 max 89 min +Histogram: 1 0 0 0 0 1 1 0 0 1 +Nghost: 188.5 ave 199 max 184 min +Histogram: 2 1 0 0 0 0 0 0 0 1 +Neighs: 1116 ave 1233 max 921 min +Histogram: 1 0 0 0 0 0 1 0 1 1 + +Total # of neighbors = 4464 +Ave neighs/atom = 11.16 +Neighbor list builds = 106 +Dangerous builds = 43 + +# run dynamics on dense system + +unfix 1 +fix 1 all nve/asphere + +run 2000 +Memory usage per processor = 2.3271 Mbytes +Step rot E_pair TotEng Press Volume + 2000 1.807468 -5.0525829 -3.1803091 0.86237508 964.0263 + 2100 1.8124564 -5.0575946 -3.1482012 0.70216467 964.0263 + 2200 1.7626774 -5.0023408 -3.1505535 0.895245 964.0263 + 2300 1.7196825 -4.9521 -3.1438517 1.0459072 964.0263 + 2400 1.7461817 -4.9798462 -3.1713534 0.81729653 964.0263 + 2500 1.7613354 -4.9981109 -3.1720957 0.75962477 964.0263 + 2600 1.7938723 -5.0329298 -3.1542958 0.6834629 964.0263 + 2700 1.6845575 -4.9156511 -3.1602763 1.018788 964.0263 + 2800 1.8106845 -5.0514857 -3.1552486 0.82016251 964.0263 + 2900 1.7106648 -4.9415742 -3.172624 0.9661594 964.0263 + 3000 1.7191328 -4.9501009 -3.1633969 0.68191191 964.0263 + 3100 1.7105373 -4.9420092 -3.17246 0.54874965 964.0263 + 3200 1.7495364 -4.9843342 -3.1275575 0.77248303 964.0263 + 3300 1.7698509 -5.0087562 -3.1389426 0.8145502 964.0263 + 3400 1.7335983 -4.9691262 -3.1854084 0.79184554 964.0263 + 3500 1.7048596 -4.9344286 -3.1656937 0.81686942 964.0263 + 3600 1.759633 -4.9973343 -3.1654564 0.82451312 964.0263 + 3700 1.8497696 -5.0949098 -3.1884636 0.78672739 964.0263 + 3800 1.7619814 -4.997269 -3.1385271 1.0176047 964.0263 + 3900 1.7634023 -5.0041064 -3.1775639 1.058629 964.0263 + 4000 1.8327776 -5.0805738 -3.2201943 0.76054519 964.0263 +Loop time of 1.88218 on 4 procs for 2000 steps with 400 atoms + +Pair time (%) = 1.11996 (59.5032) +Neigh time (%) = 0.00454992 (0.241736) +Comm time (%) = 0.533296 (28.3339) +Outpt time (%) = 0.0546536 (2.90374) +Other time (%) = 0.169724 (9.01738) + +Nlocal: 100 ave 105 max 90 min +Histogram: 1 0 0 0 0 0 0 1 0 2 +Nghost: 188.75 ave 201 max 182 min +Histogram: 2 0 0 1 0 0 0 0 0 1 +Neighs: 1128.75 ave 1184 max 1035 min +Histogram: 1 0 0 0 0 0 0 2 0 1 + +Total # of neighbors = 4515 +Ave neighs/atom = 11.2875 +Neighbor list builds = 43 +Dangerous builds = 0 + diff --git a/examples/ellipse/log.ellipse.22Jun07.linux.1 b/examples/ellipse/log.ellipse.22Jun07.linux.1 new file mode 100644 index 0000000000..d371ce190e --- /dev/null +++ b/examples/ellipse/log.ellipse.22Jun07.linux.1 @@ -0,0 +1,141 @@ +LAMMPS (22 June 2007) +# 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 + 38 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 + +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 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 = 2.3468 Mbytes +Step rot E_pair TotEng Press Volume + 0 2.1910653 0 2.391 0.0045085128 141421.36 + 100 1.9478792 0 2.1256232 0.004563496 124210.22 + 200 2.3700495 -3.3319106e-05 2.5862832 0.013268829 51975.461 + 300 1.8455677 -0.099549795 1.8705975 0.043367291 11254.795 + 400 4.7673362 -0.63680144 4.1000403 2.5967285 2117.5435 + 500 2.0914283 -3.1875966 -0.98127813 15.054185 716.60631 + 600 0.16670993 -6.5302264 -6.3521489 -1.2408868 763.95532 + 700 0.61510434 -6.2651546 -5.6130844 -1.7391671 850.63471 + 800 4.2400887 -4.7665917 -0.37668829 4.3628579 893.62251 + 900 0.56540605 -4.0704259 -3.4850161 -1.2625042 1339.0962 + 1000 4.1072215 -3.5049913 0.78871853 1.3994916 1581.8306 + 1100 1.002839 -3.4270693 -2.3625765 -0.34931088 2002.5983 + 1200 2.3739586 -3.2294296 -0.73953462 0.47928761 2137.475 + 1300 1.755069 -3.2886568 -1.4395111 0.24365268 2147.7339 + 1400 1.4374762 -3.597546 -2.0874512 0.26707014 1976.8436 + 1500 2.7207484 -3.4893404 -0.67636594 1.4873069 1672.6682 + 1600 1.0385312 -4.3747776 -3.2807384 0.10681629 1506.5847 + 1700 3.3252787 -4.3839001 -0.91852241 1.7513361 1235.5246 + 1800 1.2745711 -4.7993978 -3.4903396 0.16468567 1129.5996 + 1900 2.2642603 -4.9061291 -2.5944276 2.1651712 988.12263 + 2000 1.8074681 -5.0525831 -3.180309 0.86237472 964.0263 +Loop time of 5.79084 on 1 procs for 2000 steps with 400 atoms + +Pair time (%) = 4.47783 (77.3261) +Neigh time (%) = 0.055152 (0.9524) +Comm time (%) = 0.092337 (1.59453) +Outpt time (%) = 0.101419 (1.75137) +Other time (%) = 1.0641 (18.3756) + +Nlocal: 400 ave 400 max 400 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 345 ave 345 max 345 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 4464 ave 4464 max 4464 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 4464 +Ave neighs/atom = 11.16 +Neighbor list builds = 106 +Dangerous builds = 43 + +# run dynamics on dense system + +unfix 1 +fix 1 all nve/asphere + +run 2000 +Memory usage per processor = 2.35512 Mbytes +Step rot E_pair TotEng Press Volume + 2000 1.8074681 -5.0525831 -3.180309 0.86237472 964.0263 + 2100 1.8124563 -5.0575946 -3.1482012 0.70216509 964.0263 + 2200 1.7626781 -5.0023416 -3.1505538 0.89524393 964.0263 + 2300 1.7196822 -4.9520998 -3.1438526 1.045906 964.0263 + 2400 1.7461825 -4.9798453 -3.1713506 0.81731176 964.0263 + 2500 1.7613208 -4.9980929 -3.1720863 0.75968573 964.0263 + 2600 1.7938507 -5.0328997 -3.1542798 0.68355324 964.0263 + 2700 1.6845018 -4.9157085 -3.1604062 1.0187342 964.0263 + 2800 1.8107758 -5.0515881 -3.1552159 0.8201522 964.0263 + 2900 1.7106214 -4.9415299 -3.1727682 0.96607251 964.0263 + 3000 1.7174173 -4.9483503 -3.1634164 0.68480916 964.0263 + 3100 1.713011 -4.9449497 -3.1743883 0.5448844 964.0263 + 3200 1.7540834 -4.988469 -3.1263823 0.78165991 964.0263 + 3300 1.7916136 -5.0322754 -3.1513102 0.74578197 964.0263 + 3400 1.7470198 -4.9834088 -3.1838699 0.74098826 964.0263 + 3500 1.6950853 -4.9232007 -3.1647376 0.96347072 964.0263 + 3600 1.7317637 -4.9664612 -3.1496825 0.91204136 964.0263 + 3700 1.7217782 -4.9544926 -3.1343126 1.0385551 964.0263 + 3800 1.8248397 -5.0685779 -3.172072 0.96728742 964.0263 + 3900 1.7621697 -4.9966809 -3.1392953 0.99972394 964.0263 + 4000 1.6909581 -4.9165496 -3.1646954 0.85776161 964.0263 +Loop time of 7.49334 on 1 procs for 2000 steps with 400 atoms + +Pair time (%) = 6.37188 (85.0339) +Neigh time (%) = 0.030365 (0.405227) +Comm time (%) = 0.110936 (1.48046) +Outpt time (%) = 0.100005 (1.33459) +Other time (%) = 0.880153 (11.7458) + +Nlocal: 400 ave 400 max 400 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 334 ave 334 max 334 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 4415 ave 4415 max 4415 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 4415 +Ave neighs/atom = 11.0375 +Neighbor list builds = 44 +Dangerous builds = 0 + diff --git a/examples/flow/log.flow.couette.22Jun07.liberty.4 b/examples/flow/log.flow.couette.22Jun07.liberty.4 new file mode 100644 index 0000000000..498380a003 --- /dev/null +++ b/examples/flow/log.flow.couette.22Jun07.liberty.4 @@ -0,0 +1,122 @@ +LAMMPS (22 June 2007) +# 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 = 1.44615 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 1 0 0 0.71071429 0.54228995 366.96236 + 500 1.0967867 -0.3465085 0 0.43299345 3.3754137 366.96236 + 1000 1 -0.36129869 0 0.3494156 3.254923 366.96236 + 1500 1.1299217 -0.37859354 0 0.42445794 3.0386512 366.96236 + 2000 1 -0.34287549 0 0.3678388 3.1412475 366.96236 + 2500 1.0894638 -0.38358068 0 0.3907168 2.9575357 366.96236 + 3000 1 -0.38250431 0 0.32820997 2.9128345 366.96236 + 3500 1.1577825 -0.41389292 0 0.40895962 3.0892503 366.96236 + 4000 1 -0.42306155 0 0.28765273 2.5216835 366.96236 + 4500 1.0340697 -0.39435146 0 0.34057665 2.5709158 366.96236 + 5000 1 -0.43445662 0 0.27625767 2.7074512 366.96236 + 5500 1.1091102 -0.45430683 0 0.33395366 2.451199 366.96236 + 6000 1 -0.41166346 0 0.29905082 2.7464633 366.96236 + 6500 1.0003563 -0.40533723 0 0.30563029 2.5834633 366.96236 + 7000 1 -0.3904519 0 0.32026238 2.5201459 366.96236 + 7500 1.1170747 -0.40190088 0 0.39202009 2.6487896 366.96236 + 8000 1 -0.46477384 0 0.24594045 2.6442771 366.96236 + 8500 1.1344912 -0.38276439 0 0.4235347 2.7888644 366.96236 + 9000 1 -0.39709912 0 0.31361516 2.4730908 366.96236 + 9500 0.99852413 -0.45682444 0 0.25284093 2.3290285 366.96236 + 10000 1 -0.45069251 0 0.26002177 2.5361799 366.96236 +Loop time of 1.99299 on 4 procs for 10000 steps with 420 atoms + +Pair time (%) = 0.0893506 (4.48324) +Neigh time (%) = 0.0427105 (2.14304) +Comm time (%) = 1.34109 (67.2904) +Outpt time (%) = 0.165156 (8.28685) +Other time (%) = 0.354682 (17.7964) + +Nlocal: 105 ave 115 max 96 min +Histogram: 2 0 0 0 0 0 0 0 1 1 +Nghost: 40.25 ave 44 max 37 min +Histogram: 1 0 1 0 0 1 0 0 0 1 +Neighs: 237.5 ave 296 max 179 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 950 +Ave neighs/atom = 2.2619 +Neighbor list builds = 984 +Dangerous builds = 0 diff --git a/examples/flow/log.flow.couette.22Jun07.linux.1 b/examples/flow/log.flow.couette.22Jun07.linux.1 new file mode 100644 index 0000000000..84038bd2a9 --- /dev/null +++ b/examples/flow/log.flow.couette.22Jun07.linux.1 @@ -0,0 +1,122 @@ +LAMMPS (22 June 2007) +# 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 = 1.45035 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 1 0 0 0.71071429 0.54228995 366.96236 + 500 1.0604224 -0.31549525 0 0.4381621 3.1208962 366.96236 + 1000 1 -0.34356865 0 0.36714563 3.0305145 366.96236 + 1500 1.1738082 -0.382026 0 0.45221626 2.9197883 366.96236 + 2000 1 -0.42682511 0 0.28388918 2.8469183 366.96236 + 2500 1.0256109 -0.41905835 0 0.30985794 2.9371918 366.96236 + 3000 1 -0.47521752 0 0.23549677 2.5062527 366.96236 + 3500 1.1314909 -0.4206347 0 0.38353207 2.7478302 366.96236 + 4000 1 -0.43576251 0 0.27495178 2.6141195 366.96236 + 4500 1.0005992 -0.42588084 0 0.28525931 2.7421664 366.96236 + 5000 1 -0.42282912 0 0.28788516 2.7688981 366.96236 + 5500 1.0686835 -0.4761288 0 0.28339982 2.5689028 366.96236 + 6000 1 -0.42978507 0 0.28092922 2.6551983 366.96236 + 6500 1.0786904 -0.43713715 0 0.3295035 2.5141669 366.96236 + 7000 1 -0.4121221 0 0.29859218 2.594973 366.96236 + 7500 1.0939854 -0.40293252 0 0.37457856 2.6974983 366.96236 + 8000 1 -0.45181425 0 0.25890004 2.6049049 366.96236 + 8500 1.0257333 -0.400669 0 0.32833428 2.5577387 366.96236 + 9000 1 -0.42858125 0 0.28213304 2.5725646 366.96236 + 9500 1.0823613 -0.38920599 0 0.38004366 2.6543624 366.96236 + 10000 1 -0.42341732 0 0.28729697 2.4806728 366.96236 +Loop time of 2.27165 on 1 procs for 10000 steps with 420 atoms + +Pair time (%) = 0.707011 (31.1232) +Neigh time (%) = 0.278071 (12.2409) +Comm time (%) = 0.108514 (4.77687) +Outpt time (%) = 0.425657 (18.7377) +Other time (%) = 0.752402 (33.1213) + +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: 955 ave 955 max 955 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 955 +Ave neighs/atom = 2.27381 +Neighbor list builds = 1003 +Dangerous builds = 0 diff --git a/examples/flow/log.flow.poiss.22Jun07.liberty.4 b/examples/flow/log.flow.poiss.22Jun07.liberty.4 new file mode 100644 index 0000000000..9476c0d8b1 --- /dev/null +++ b/examples/flow/log.flow.poiss.22Jun07.liberty.4 @@ -0,0 +1,122 @@ +LAMMPS (22 June 2007) +# 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 = 1.44615 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 1 0 0 0.71071429 0.54228995 366.96236 + 500 1.0778761 -0.35048279 0 0.41557918 2.8792129 369.20271 + 1000 1 -0.38740705 0 0.32330724 2.2684877 375.93354 + 1500 1.2052679 -0.37768559 0 0.47891551 1.6193029 376.17118 + 2000 1 -0.38060118 0 0.33011311 1.4972142 371.27032 + 2500 1.2211446 -0.39689946 0 0.47098548 1.5612989 364.09539 + 3000 1 -0.46394625 0 0.24676803 1.5629864 356.17691 + 3500 1.2338136 -0.5721878 0 0.30470115 1.8177807 344.96808 + 4000 1 -0.69530976 0 0.015404522 2.3144776 333.06418 + 4500 1.2279548 -0.72662695 0 0.14609808 2.9985939 323.55709 + 5000 1 -0.81185506 0 -0.10114077 3.1833009 321.19482 + 5500 1.2171627 -0.73966198 0 0.12539291 2.711954 325.39659 + 6000 1 -0.66983997 0 0.040874311 2.1579634 329.73937 + 6500 1.2267682 -0.66743744 0 0.20444422 2.1114545 331.88829 + 7000 1 -0.64509348 0 0.065620807 1.9028431 332.49532 + 7500 1.2202538 -0.6816503 0 0.18560148 2.1227978 329.88213 + 8000 1 -0.72110847 0 -0.010394181 2.3587956 327.78501 + 8500 1.2103845 -0.76502979 0 0.095207788 2.5823624 325.21722 + 9000 1 -0.75191645 0 -0.041202164 2.4020904 324.81713 + 9500 1.2094179 -0.74196652 0 0.11758403 2.5289414 326.12345 + 10000 1 -0.7568777 0 -0.046163412 2.5601376 326.60462 +Loop time of 2.41079 on 4 procs for 10000 steps with 420 atoms + +Pair time (%) = 0.099645 (4.13329) +Neigh time (%) = 0.0237269 (0.984194) +Comm time (%) = 1.25536 (52.0723) +Outpt time (%) = 0.306114 (12.6977) +Other time (%) = 0.725951 (30.1125) + +Nlocal: 105 ave 106 max 103 min +Histogram: 1 0 0 0 0 0 1 0 0 2 +Nghost: 43.75 ave 45 max 41 min +Histogram: 1 0 0 0 0 0 0 1 0 2 +Neighs: 276.5 ave 291 max 256 min +Histogram: 1 0 0 1 0 0 0 0 0 2 + +Total # of neighbors = 1106 +Ave neighs/atom = 2.63333 +Neighbor list builds = 553 +Dangerous builds = 0 diff --git a/examples/flow/log.flow.poiss.22Jun07.linux.1 b/examples/flow/log.flow.poiss.22Jun07.linux.1 new file mode 100644 index 0000000000..b63502dd29 --- /dev/null +++ b/examples/flow/log.flow.poiss.22Jun07.linux.1 @@ -0,0 +1,122 @@ +LAMMPS (22 June 2007) +# 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 = 1.45035 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 1 0 0 0.71071429 0.54228995 366.96236 + 500 1.1036177 -0.37435595 0 0.4100009 2.6003586 369.52344 + 1000 1 -0.40278179 0 0.30793249 2.0566706 375.56836 + 1500 1.2346487 -0.41204291 0 0.46543956 1.6254791 376.55032 + 2000 1 -0.40773469 0 0.3029796 1.5174808 374.73899 + 2500 1.2225527 -0.43831258 0 0.43057311 1.538442 366.48806 + 3000 1 -0.49535282 0 0.21536146 1.5818917 355.29347 + 3500 1.2493993 -0.59973642 0 0.28822953 1.7491905 344.52279 + 4000 1 -0.67338979 0 0.037324493 2.0787539 332.81149 + 4500 1.1956948 -0.72693321 0 0.12286419 3.0234335 322.85596 + 5000 1 -0.74958096 0 -0.038866674 3.2864093 320.05477 + 5500 1.1735028 -0.73256028 0 0.10146491 2.7725647 321.70778 + 6000 1 -0.68197653 0 0.028737759 2.4161345 328.01856 + 6500 1.1989708 -0.63163198 0 0.2204937 2.0979387 331.80767 + 7000 1 -0.65810386 0 0.052610422 2.1889649 331.12128 + 7500 1.2335065 -0.65237655 0 0.22429412 2.1016554 330.36358 + 8000 1 -0.68661166 0 0.024102628 2.1253504 327.99967 + 8500 1.2297323 -0.72995326 0 0.14403503 2.4289517 324.51364 + 9000 1 -0.72767623 0 -0.016961948 2.4354045 323.49316 + 9500 1.2252226 -0.75893761 0 0.1118456 2.5476916 324.00783 + 10000 1 -0.73637225 0 -0.025657963 2.3491973 324.64848 +Loop time of 2.80857 on 1 procs for 10000 steps with 420 atoms + +Pair time (%) = 0.736941 (26.239) +Neigh time (%) = 0.15112 (5.38067) +Comm time (%) = 0.100391 (3.57445) +Outpt time (%) = 1.02177 (36.3805) +Other time (%) = 0.798347 (28.4254) + +Nlocal: 420 ave 420 max 420 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 53 ave 53 max 53 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 1128 ave 1128 max 1128 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 1128 +Ave neighs/atom = 2.68571 +Neighbor list builds = 558 +Dangerous builds = 0 diff --git a/examples/friction/log.friction.22Jun07.liberty.4 b/examples/friction/log.friction.22Jun07.liberty.4 new file mode 100644 index 0000000000..5c897a58e4 --- /dev/null +++ b/examples/friction/log.friction.22Jun07.liberty.4 @@ -0,0 +1,140 @@ +LAMMPS (22 June 2007) +# 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 110 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 +860 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 +1422 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 = 1.46023 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 0.1 -3.1332695 0 -3.0920674 -1.3452097 1384.4128 + 1000 0.088860957 -3.0636883 0 -3.0270758 0.0047805196 1384.4128 + 2000 0.087112073 -3.066344 0 -3.030452 -0.63632956 1384.4128 + 3000 0.10058239 -3.0642114 0 -3.0227694 -0.25555813 1384.4128 + 4000 0.093260137 -3.0555323 0 -3.0171072 -0.40761447 1384.4128 + 5000 0.11067201 -3.0399212 0 -2.994322 0.066689705 1384.4128 + 6000 0.10526463 -3.0390544 0 -2.9956832 -0.51522958 1384.4128 + 7000 0.11541593 -3.0403447 0 -2.992791 -0.41397003 1384.4128 + 8000 0.10197576 -3.0347747 0 -2.9927585 -0.5486861 1384.4128 + 9000 0.11134064 -3.0333357 0 -2.9874611 -0.35496419 1384.4128 + 10000 0.11080628 -3.0436254 0 -2.9979709 -0.46700659 1384.4128 + 11000 0.11943821 -3.0413975 0 -2.9921865 -0.30699848 1384.4128 + 12000 0.10413208 -3.0510277 0 -3.0081231 -0.36572201 1384.4128 + 13000 0.099296169 -3.039397 0 -2.9984849 -0.4947437 1384.4128 + 14000 0.10330462 -3.0420671 0 -2.9995034 -0.39995589 1384.4128 + 15000 0.10870951 -3.038746 0 -2.9939554 -0.50477181 1384.4128 + 16000 0.11417657 -3.0464982 0 -2.9994551 -0.32657064 1384.4128 + 17000 0.10800189 -3.047902 0 -3.0034029 -0.41936081 1384.4128 + 18000 0.10829723 -3.0458306 0 -3.0012098 -0.41668893 1384.4128 + 19000 0.10404908 -3.0526816 0 -3.0098112 -0.41121519 1384.4128 + 20000 0.10691019 -3.0411759 0 -2.9971266 -0.23642395 1384.4128 +Loop time of 8.68844 on 4 procs for 20000 steps with 1722 atoms + +Pair time (%) = 3.88408 (44.704) +Neigh time (%) = 0.210725 (2.42535) +Comm time (%) = 3.2323 (37.2023) +Outpt time (%) = 0.152017 (1.74965) +Other time (%) = 1.20932 (13.9187) + +Nlocal: 430.5 ave 482 max 375 min +Histogram: 1 1 0 0 0 0 0 0 0 2 +Nghost: 92 ave 117 max 76 min +Histogram: 2 0 0 0 1 0 0 0 0 1 +Neighs: 3601.25 ave 4057 max 3129 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 14405 +Ave neighs/atom = 8.36527 +Neighbor list builds = 750 +Dangerous builds = 0 diff --git a/examples/friction/log.friction.22Jun07.linux.1 b/examples/friction/log.friction.22Jun07.linux.1 new file mode 100644 index 0000000000..472d0ffda5 --- /dev/null +++ b/examples/friction/log.friction.22Jun07.linux.1 @@ -0,0 +1,140 @@ +LAMMPS (22 June 2007) +# 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 110 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 +860 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 +1422 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 = 1.53816 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 0.1 -3.1332695 0 -3.0920674 -1.3452097 1384.4128 + 1000 0.088253389 -3.0560474 0 -3.0196852 0.050420633 1384.4128 + 2000 0.087864125 -3.0547262 0 -3.0185243 -0.67004561 1384.4128 + 3000 0.10557467 -3.0607837 0 -3.0172848 -0.221612 1384.4128 + 4000 0.085491315 -3.0478702 0 -3.012646 -0.42154648 1384.4128 + 5000 0.10534884 -3.051862 0 -3.0084561 -0.087935136 1384.4128 + 6000 0.10556767 -3.0559544 0 -3.0124583 -0.54210169 1384.4128 + 7000 0.098711954 -3.0590419 0 -3.0183705 -0.42838742 1384.4128 + 8000 0.11529691 -3.0366296 0 -2.9891248 -0.4457814 1384.4128 + 9000 0.1 -3.0333227 0 -2.9921206 -0.49174903 1384.4128 + 10000 0.11644796 -3.04181 0 -2.993831 -0.41991946 1384.4128 + 11000 0.1051652 -3.0340308 0 -2.9907005 -0.61535665 1384.4128 + 12000 0.10761127 -3.0351207 0 -2.9907826 -0.30937044 1384.4128 + 13000 0.11361189 -3.0354003 0 -2.9885898 -0.44289723 1384.4128 + 14000 0.11530172 -3.037545 0 -2.9900383 -0.31673329 1384.4128 + 15000 0.098629121 -3.0397602 0 -2.9991229 -0.44569024 1384.4128 + 16000 0.10525229 -3.0429476 0 -2.9995815 -0.29935796 1384.4128 + 17000 0.10467455 -3.0381932 0 -2.9950651 -0.48920299 1384.4128 + 18000 0.10817926 -3.0402364 0 -2.9956643 -0.37596363 1384.4128 + 19000 0.10816167 -3.0452456 0 -3.0006808 -0.35822139 1384.4128 + 20000 0.11364667 -3.0448494 0 -2.9980246 -0.40159119 1384.4128 +Loop time of 36.1633 on 1 procs for 20000 steps with 1722 atoms + +Pair time (%) = 28.7323 (79.4516) +Neigh time (%) = 1.38031 (3.81689) +Comm time (%) = 0.367905 (1.01734) +Outpt time (%) = 0.372357 (1.02965) +Other time (%) = 5.31041 (14.6845) + +Nlocal: 1722 ave 1722 max 1722 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 146 ave 146 max 146 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 14398 ave 14398 max 14398 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 14398 +Ave neighs/atom = 8.36121 +Neighbor list builds = 728 +Dangerous builds = 0 diff --git a/examples/indent/log.indent.22Jun07.liberty.4 b/examples/indent/log.indent.22Jun07.liberty.4 new file mode 100644 index 0000000000..4b344f2a94 --- /dev/null +++ b/examples/indent/log.indent.22Jun07.liberty.4 @@ -0,0 +1,169 @@ +LAMMPS (22 June 2007) +# 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 = 1.44615 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 0.2 -3.1727576 0 -3.0020433 -1.6911656 251.71282 + 1000 0.11576832 -3.0966334 0 -2.9978168 -0.24095347 250.17681 + 2000 0.11528823 -3.0962223 0 -2.9978155 -0.45030047 250.45856 + 3000 0.11379051 -3.0840496 0 -2.9869213 -0.5022142 251.7439 + 4000 0.11595816 -3.085882 0 -2.9869034 -0.047829504 249.09265 + 5000 0.11272851 -3.0844605 0 -2.9882386 -0.57244294 252.48573 + 6000 0.12387775 -3.0900283 0 -2.9842898 0.0072734648 249.1402 + 7000 0.1113616 -3.0914902 0 -2.9964351 -0.12742916 250.29327 + 8000 0.1167364 -3.0879355 0 -2.9882926 0.20678001 250.17825 + 9000 0.11504768 -3.0918767 0 -2.9936753 0.35261539 249.40265 + 10000 0.11864876 -3.0776022 0 -2.976327 0.45724638 249.80407 + 11000 0.12749806 -3.0769801 0 -2.9681514 0.7106404 248.1776 + 12000 0.11068569 -3.0664256 0 -2.9719474 0.77940328 248.88714 + 13000 0.11341039 -3.0596733 0 -2.9628694 1.1566167 249.36303 + 14000 0.1176102 -3.058063 0 -2.9576743 1.2083863 249.05567 + 15000 0.12582683 -3.054119 0 -2.9467168 1.052489 254.01804 + 16000 0.11716129 -3.0359809 0 -2.9359753 1.1111189 259.94912 + 17000 0.11836208 -3.0276209 0 -2.9265904 1.0821166 257.9832 + 18000 0.12271609 -3.0171547 0 -2.9124077 1.511924 264.99507 + 19000 0.11746326 -3.0102961 0 -2.9100328 1.6305608 267.60875 + 20000 0.12091083 -2.996777 0 -2.893571 1.7996398 268.87085 + 21000 0.1263182 -2.9950013 0 -2.8871797 1.8539429 271.55393 + 22000 0.12425331 -2.9761891 0 -2.87013 1.5415686 276.54337 + 23000 0.11563313 -2.9874945 0 -2.8887934 1.2018805 279.40748 + 24000 0.11553831 -2.9945403 0 -2.8959201 1.5305748 278.38798 + 25000 0.11085112 -2.9896742 0 -2.8950548 1.8815906 275.87487 + 26000 0.12077848 -2.986181 0 -2.883088 1.9122673 275.91918 + 27000 0.12399848 -2.9814354 0 -2.8755938 1.9167983 278.64025 + 28000 0.12143106 -3.0225278 0 -2.9188777 0.56589243 290.55803 + 29000 0.11959029 -3.0121799 0 -2.9101011 0.49660855 295.49221 + 30000 0.11931566 -3.0215043 0 -2.9196598 0.83146141 294.35452 +Loop time of 7.02654 on 4 procs for 30000 steps with 420 atoms + +Pair time (%) = 1.4371 (20.4525) +Neigh time (%) = 0.0463696 (0.659921) +Comm time (%) = 4.19698 (59.7304) +Outpt time (%) = 0.106641 (1.51768) +Other time (%) = 1.23945 (17.6395) + +Nlocal: 105 ave 125 max 79 min +Histogram: 1 0 0 1 0 0 0 0 0 2 +Nghost: 92.75 ave 104 max 77 min +Histogram: 1 0 0 0 1 0 0 0 0 2 +Neighs: 901 ave 1133 max 620 min +Histogram: 1 0 1 0 0 0 0 0 0 2 + +Total # of neighbors = 3604 +Ave neighs/atom = 8.58095 +Neighbor list builds = 622 +Dangerous builds = 0 + +# Run without indenter + +unfix 4 +run 30000 +Memory usage per processor = 1.4468 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 30000 0.11931566 -3.0215043 0 -2.9196598 0.83281489 293.87614 + 31000 0.1167364 -3.0429651 0 -2.9433222 -0.36091255 293.88145 + 32000 0.12641731 -3.0639714 0 -2.9560652 -0.46898184 290.09909 + 33000 0.10706313 -3.0741804 0 -2.9827944 0.00022078579 285.15883 + 34000 0.11367315 -3.0688054 0 -2.9717772 -0.76240201 289.87707 + 35000 0.10655807 -3.0627342 0 -2.9717793 -0.26051048 288.22641 + 36000 0.11703008 -3.0716705 0 -2.971777 -0.1853764 285.83663 + 37000 0.11221734 -3.0675632 0 -2.9717776 -0.73386022 290.12632 + 38000 0.11874224 -3.0731334 0 -2.9717784 -0.12687563 285.36376 + 39000 0.1189778 -3.0733361 0 -2.9717801 -0.25499323 287.084 + 40000 0.11898338 -3.0620885 0 -2.9605277 -0.62541843 288.73621 + 41000 0.1167364 -3.0735602 0 -2.9739173 -0.11692923 283.98124 + 42000 0.11266172 -3.0700831 0 -2.9739183 -0.39632943 286.59658 + 43000 0.11902827 -3.0755188 0 -2.9739196 -0.57312115 287.53858 + 44000 0.12554232 -3.0810812 0 -2.9739219 -0.070954433 286.20995 + 45000 0.11075688 -3.0684563 0 -2.9739174 -0.55071995 288.55119 + 46000 0.12586051 -3.0707391 0 -2.9633081 -0.48923571 289.30041 + 47000 0.11671697 -3.0736442 0 -2.9740179 -0.12378289 285.31819 + 48000 0.10853944 -3.0666634 0 -2.9740172 -0.57661015 289.17231 + 49000 0.1167364 -3.0679033 0 -2.9682604 -0.28913991 286.84813 + 50000 0.10777198 -3.0602483 0 -2.9682572 -0.2607135 286.76228 + 51000 0.10971818 -3.0619099 0 -2.9682576 -0.50602899 289.54807 + 52000 0.12283301 -3.0731069 0 -2.9682602 -0.17101974 286.39074 + 53000 0.11323492 -3.0762744 0 -2.9796203 -0.39853784 289.81061 + 54000 0.12076965 -3.0709553 0 -2.9678698 -0.3939254 288.24037 + 55000 0.12319168 -3.0730238 0 -2.9678709 -0.17986864 284.15611 + 56000 0.12040501 -3.0706451 0 -2.9678708 -0.34825544 286.68764 + 57000 0.12192823 -3.0719452 0 -2.9678707 -0.42539274 287.8374 + 58000 0.11878678 -3.0692629 0 -2.9678699 -0.24575165 286.73167 + 59000 0.11418711 -3.0653342 0 -2.9678674 -0.51388179 287.99512 + 60000 0.11462897 -3.0657114 0 -2.9678673 -0.4538483 288.11403 +Loop time of 6.86808 on 4 procs for 30000 steps with 420 atoms + +Pair time (%) = 1.4141 (20.5895) +Neigh time (%) = 0.0468405 (0.682003) +Comm time (%) = 4.16007 (60.5711) +Outpt time (%) = 0.107103 (1.55943) +Other time (%) = 1.13996 (16.5979) + +Nlocal: 105 ave 122 max 82 min +Histogram: 1 0 0 0 1 0 0 0 0 2 +Nghost: 92 ave 101 max 82 min +Histogram: 1 0 1 0 0 0 0 0 1 1 +Neighs: 888.5 ave 1097 max 643 min +Histogram: 1 0 1 0 0 0 0 0 0 2 + +Total # of neighbors = 3554 +Ave neighs/atom = 8.4619 +Neighbor list builds = 630 +Dangerous builds = 0 diff --git a/examples/indent/log.indent.22Jun07.linux.1 b/examples/indent/log.indent.22Jun07.linux.1 new file mode 100644 index 0000000000..84272d6373 --- /dev/null +++ b/examples/indent/log.indent.22Jun07.linux.1 @@ -0,0 +1,169 @@ +LAMMPS (22 June 2007) +# 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 = 1.45035 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 0.2 -3.1727576 0 -3.0020433 -1.6911656 251.71282 + 1000 0.11979027 -3.0878285 0 -2.9855789 -0.043690155 249.58001 + 2000 0.12095292 -3.0888211 0 -2.9855791 -0.46999358 251.6098 + 3000 0.1167364 -3.0841547 0 -2.9845118 -0.41054969 250.8041 + 4000 0.12249143 -3.1004175 0 -2.9958623 -0.060853986 248.47717 + 5000 0.10957873 -3.0886367 0 -2.9951034 -0.57642649 251.31708 + 6000 0.12346008 -3.0985964 0 -2.9932144 -0.072968634 250.46216 + 7000 0.10994736 -3.0850721 0 -2.9912241 -0.20324168 251.37979 + 8000 0.11557891 -3.086042 0 -2.9873871 0.22717975 249.49714 + 9000 0.12016755 -3.084536 0 -2.9819645 0.33218396 248.89256 + 10000 0.12659552 -3.0852403 0 -2.977182 0.40666454 249.67836 + 11000 0.12524777 -3.0736607 0 -2.9667528 0.77561215 248.69926 + 12000 0.11844672 -3.0571177 0 -2.9560149 0.77334207 249.761 + 13000 0.12031568 -3.0583679 0 -2.9556699 1.2700141 247.59077 + 14000 0.1167364 -3.0548463 0 -2.9552034 1.0859392 250.18904 + 15000 0.1167364 -3.0549235 0 -2.9552806 1.2995977 251.78491 + 16000 0.12471796 -3.0524621 0 -2.9460064 1.6452633 249.66328 + 17000 0.12078141 -3.0356474 0 -2.9325519 1.9172375 248.00713 + 18000 0.11737951 -3.0294793 0 -2.9292875 1.984307 254.03132 + 19000 0.12273273 -3.016492 0 -2.9117309 1.9954892 251.8583 + 20000 0.12551089 -3.0011944 0 -2.8940619 1.7797455 260.26155 + 21000 0.12037224 -2.9934253 0 -2.890679 1.3694744 269.07586 + 22000 0.12174807 -3.0193123 0 -2.9153916 0.94134986 270.00347 + 23000 0.12706029 -3.0244275 0 -2.9159725 1.1867392 266.05204 + 24000 0.11467621 -3.0095158 0 -2.9116314 0.73011254 267.48776 + 25000 0.11535618 -3.0158848 0 -2.91742 1.2611256 266.59514 + 26000 0.10710521 -3.0133947 0 -2.9219727 0.67441358 268.32045 + 27000 0.12422208 -3.0164988 0 -2.9104663 1.1543726 268.18532 + 28000 0.11139527 -3.0072089 0 -2.9121251 1.4607146 265.23157 + 29000 0.1167364 -3.0085086 0 -2.9088658 1.6594744 265.37526 + 30000 0.11102647 -3.0064551 0 -2.9116861 1.3943384 268.60718 +Loop time of 14.1353 on 1 procs for 30000 steps with 420 atoms + +Pair time (%) = 10.7241 (75.8675) +Neigh time (%) = 0.304084 (2.15125) +Comm time (%) = 0.321909 (2.27735) +Outpt time (%) = 0.401015 (2.83699) +Other time (%) = 2.38419 (16.867) + +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: 3655 ave 3655 max 3655 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 3655 +Ave neighs/atom = 8.70238 +Neighbor list builds = 616 +Dangerous builds = 0 + +# Run without indenter + +unfix 4 +run 30000 +Memory usage per processor = 1.45035 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 30000 0.11102647 -3.0064551 0 -2.9116861 1.3929673 268.87157 + 31000 0.12620212 -3.0510755 0 -2.943353 -0.18214813 273.9697 + 32000 0.11450566 -3.0412855 0 -2.9435467 -0.36947207 273.74363 + 33000 0.11300395 -3.0666261 0 -2.9701691 -0.36891232 262.29844 + 34000 0.11360641 -3.0910465 0 -2.9940753 -0.2930611 263.47461 + 35000 0.11792208 -3.0826962 0 -2.9820413 -0.53020156 264.92677 + 36000 0.1167364 -3.0791913 0 -2.9795484 -0.28901516 264.42654 + 37000 0.11195363 -3.075108 0 -2.9795476 -0.35271906 264.6512 + 38000 0.11608571 -3.0786363 0 -2.9795489 -0.5028598 264.60065 + 39000 0.1177969 -3.0800557 0 -2.9795076 -0.32434056 263.66269 + 40000 0.11466668 -3.0774252 0 -2.979549 -0.40950185 263.65927 + 41000 0.11118976 -3.0744545 0 -2.9795461 -0.58454381 264.39108 + 42000 0.11460312 -3.0773684 0 -2.9795464 -0.20755902 262.35795 + 43000 0.11677527 -3.0792261 0 -2.97955 -0.49949012 264.53893 + 44000 0.11158159 -3.0747894 0 -2.9795466 -0.37452501 263.88851 + 45000 0.12176422 -3.0834855 0 -2.979551 -0.16070447 262.66164 + 46000 0.11682005 -3.0792615 0 -2.9795472 -0.63716759 266.07809 + 47000 0.11262188 -3.0756805 0 -2.9795497 -0.15500292 263.19673 + 48000 0.12119234 -3.0829975 0 -2.9795512 -0.39672723 263.37224 + 49000 0.11784014 -3.0801322 0 -2.9795473 -0.42268487 265.07121 + 50000 0.11675902 -3.0792108 0 -2.9795486 -0.1111771 261.69863 + 51000 0.11170649 -3.0748959 0 -2.9795465 -0.46340258 263.55401 + 52000 0.12175858 -3.0834809 0 -2.9795513 -0.48539416 263.47789 + 53000 0.12074224 -3.0964747 0 -2.9934126 -0.4846085 262.58631 + 54000 0.11099551 -3.0767379 0 -2.9819953 -0.39099317 263.38816 + 55000 0.11519489 -3.0803219 0 -2.9819948 -0.38576064 263.5242 + 56000 0.11716036 -3.0820002 0 -2.9819954 -0.26199121 262.69272 + 57000 0.10872156 -3.0792099 0 -2.9864083 -0.49564243 267.348 + 58000 0.12397214 -3.0923068 0 -2.9864877 -0.37680531 262.14403 + 59000 0.11456625 -3.0842744 0 -2.9864839 -0.30718293 263.3254 + 60000 0.11413467 -3.0839074 0 -2.9864853 -0.54302442 263.54231 +Loop time of 13.6011 on 1 procs for 30000 steps with 420 atoms + +Pair time (%) = 10.6377 (78.2117) +Neigh time (%) = 0.311073 (2.28711) +Comm time (%) = 0.330723 (2.43159) +Outpt time (%) = 0.267656 (1.9679) +Other time (%) = 2.054 (15.1017) + +Nlocal: 420 ave 420 max 420 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 101 ave 101 max 101 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 3570 ave 3570 max 3570 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 3570 +Ave neighs/atom = 8.5 +Neighbor list builds = 630 +Dangerous builds = 0 diff --git a/examples/indent/log.indent.min.22Jun07.liberty.4 b/examples/indent/log.indent.min.22Jun07.liberty.4 new file mode 100644 index 0000000000..4225005876 --- /dev/null +++ b/examples/indent/log.indent.min.22Jun07.liberty.4 @@ -0,0 +1,382 @@ +LAMMPS (22 June 2007) +# 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 = 1.90392 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 0 -3.1727576 0 -3.1727576 -1.8810645 251.71282 + 10 0 -3.1820434 0 -3.1820434 -1.3321628 249.7446 + 20 0 -3.1892762 0 -3.1892762 -1.030012 247.85333 + 30 0 -3.1906231 0 -3.1906231 -0.90653473 247.85333 + 38 0 -3.1909329 0 -3.1909329 -0.81496712 247.85333 +Loop time of 0.05091 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 (%) = 0.00834811 (16.3978) +Neigh time (%) = 0.00015372 (0.301945) +Comm time (%) = 0.0218924 (43.0021) +Outpt time (%) = 0.00391895 (7.69779) +Other time (%) = 0.0165969 (32.6004) + +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 885 min +Histogram: 1 0 0 0 0 0 1 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 = 1.90395 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 38 0 -3.1909329 0 -2.1718641 -0.81877351 246.70109 + 40 0 -3.169091 0 -2.8877594 -0.54943778 246.70107 + 50 0 -3.1711852 0 -3.1696057 -0.39685207 246.70204 + 60 0 -3.1780204 0 -3.1769046 -0.39225544 246.81048 + 70 0 -3.1800811 0 -3.1793038 -0.31260477 246.81048 + 80 0 -3.1809088 0 -3.1801828 -0.23455796 246.81048 + 90 0 -3.1811924 0 -3.1805002 -0.17000885 246.18491 + 100 0 -3.1812635 0 -3.1805822 -0.14393015 246.18491 + 103 0 -3.1812545 0 -3.180591 -0.14136212 246.18491 +Loop time of 0.080998 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 (%) = 0.0118939 (14.6842) +Neigh time (%) = 0.000379205 (0.468166) +Comm time (%) = 0.0308498 (38.0871) +Outpt time (%) = 0.00909978 (11.2346) +Other time (%) = 0.0287753 (35.5259) + +Nlocal: 105 ave 111 max 98 min +Histogram: 1 0 0 1 0 0 0 0 1 1 +Nghost: 87 ave 91 max 84 min +Histogram: 1 0 1 0 1 0 0 0 0 1 +Neighs: 896.5 ave 999 max 789 min +Histogram: 1 1 0 0 0 0 0 0 0 2 + +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 = 1.90399 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 103 0 -3.1812545 0 -0.21951029 -0.14159267 245.78405 + 110 0 -2.9284097 0 -2.6466557 2.4269773 245.78334 + 120 0 -3.0511214 0 -3.0267128 1.7637829 245.78215 + 130 0 -3.0919408 0 -3.0831141 1.4860665 245.92571 + 140 0 -3.1001312 0 -3.0930458 1.4234791 245.92571 + 150 0 -3.102631 0 -3.0950311 1.4404842 246.21073 + 160 0 -3.1037978 0 -3.09648 1.5609439 244.44101 + 170 0 -3.1041785 0 -3.0969724 1.6411134 244.44101 + 180 0 -3.1042622 0 -3.0971039 1.6655381 244.44101 + 186 0 -3.1042077 0 -3.0971259 1.6700959 244.44101 +Loop time of 0.103969 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 (%) = 0.0159835 (15.3734) +Neigh time (%) = 0.000830472 (0.798769) +Comm time (%) = 0.039287 (37.7872) +Outpt time (%) = 0.0104416 (10.043) +Other time (%) = 0.0374264 (35.9976) + +Nlocal: 105 ave 111 max 98 min +Histogram: 1 0 0 1 0 0 0 0 1 1 +Nghost: 95 ave 97 max 92 min +Histogram: 1 0 0 0 0 0 1 0 1 1 +Neighs: 910.5 ave 1001 max 816 min +Histogram: 1 1 0 0 0 0 0 0 1 1 + +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 = 1.90399 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 186 0 -3.1042077 0 1.9876467 1.6726187 244.07233 + 190 0 -2.7684954 0 -1.1554028 4.8385981 243.82123 + 200 0 -2.7738026 0 -2.6431045 5.3693642 246.38337 + 210 0 -2.892911 0 -2.863976 4.4322106 250.63896 + 220 0 -2.9428319 0 -2.9275563 3.8976868 253.54966 + 230 0 -2.9566576 0 -2.9427828 3.7470914 255.96648 + 240 0 -2.9622154 0 -2.9537038 3.6488191 256.62718 + 250 0 -2.9685121 0 -2.9588966 3.5333392 257.75615 + 260 0 -2.9851957 0 -2.9793281 3.2459764 258.1143 + 270 0 -3.0137593 0 -3.0035449 2.8836141 257.01204 + 280 0 -3.0182039 0 -3.0121893 2.7594651 257.4611 + 290 0 -3.0271401 0 -3.0194953 2.4173885 260.04588 + 300 0 -3.0332671 0 -3.0255652 2.4243877 260.04588 + 310 0 -3.0346445 0 -3.0270706 2.4432531 258.57203 + 320 0 -3.0355796 0 -3.0277669 2.4110728 258.57203 + 330 0 -3.0359691 0 -3.0280778 2.3724675 258.57203 + 340 0 -3.0358963 0 -3.0281771 2.350355 258.57203 + 350 0 -3.0359324 0 -3.0282261 2.3336342 258.57203 +Loop time of 0.229392 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 0.605547 + Gradient inf-norm init/final= 1037.31 0.14972 + Iterations = 164 + Force evaluations = 579 + +Pair time (%) = 0.0342199 (14.9176) +Neigh time (%) = 0.00194269 (0.846887) +Comm time (%) = 0.0764942 (33.3465) +Outpt time (%) = 0.0237187 (10.3398) +Other time (%) = 0.0930168 (40.5492) + +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 857 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 = 1.90403 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 350 0 -3.0359324 0 6.9766773 2.3291833 259.06614 + 360 0 -2.335093 0 -1.5707757 8.8885569 259.07026 + 370 0 -2.5599881 0 -2.4347598 7.565773 259.34078 + 380 0 -2.7844216 0 -2.7584649 5.7681807 262.33347 + 390 0 -2.8656166 0 -2.8440742 4.9699457 263.34253 + 400 0 -2.9109956 0 -2.8923852 4.2490464 265.32325 + 410 0 -2.9467505 0 -2.9334194 3.7795578 267.03801 + 420 0 -2.9744267 0 -2.9577148 3.6538838 266.60412 + 430 0 -2.9926456 0 -2.9736412 3.47796 267.0876 + 440 0 -2.997545 0 -2.9801205 3.4033732 266.91219 + 450 0 -2.999611 0 -2.9820253 3.3516037 267.52197 + 460 0 -2.9987285 0 -2.9829306 3.3110334 267.52197 + 470 0 -2.9987287 0 -2.9846017 3.1122307 268.32025 + 480 0 -3.0028832 0 -2.9903847 2.7073161 271.2535 + 490 0 -3.0065428 0 -2.9942342 2.5293968 272.93505 + 500 0 -3.0095717 0 -2.996454 2.3893318 274.49155 + 510 0 -3.0115719 0 -2.9991889 2.3031093 274.994 + 520 0 -3.0127377 0 -3.0033432 2.2510198 275.25753 + 530 0 -3.0246486 0 -3.0155041 2.1233648 276.13644 + 540 0 -3.0313871 0 -3.0223311 2.0234035 276.99491 + 550 0 -3.0347292 0 -3.024608 1.9491149 277.7476 + 560 0 -3.0414445 0 -3.0318447 1.8709947 278.24973 + 570 0 -3.0430604 0 -3.0339769 1.8661497 278.31951 + 580 0 -3.0439059 0 -3.0348806 1.8551822 278.31951 + 590 0 -3.0447011 0 -3.0361812 1.8528222 277.66633 + 600 0 -3.0459159 0 -3.0371266 1.8221349 277.61268 + 610 0 -3.046738 0 -3.0376993 1.8002546 277.61268 + 620 0 -3.0485294 0 -3.0387662 1.7551062 278.38429 + 630 0 -3.0502895 0 -3.0409144 1.6978737 278.68446 + 631 0 -3.050959 0 -3.0413239 1.6846776 279.02342 +Loop time of 0.386644 on 4 procs for 281 steps with 420 atoms + +Minimization stats: + E initial, next-to-last, final = 6.97668 -3.04091 -3.04132 + Gradient 2-norm init/final= 3559.61 8.94131 + Gradient inf-norm init/final= 1438.88 3.48783 + Iterations = 281 + Force evaluations = 1001 + +Pair time (%) = 0.0592298 (15.3189) +Neigh time (%) = 0.00355858 (0.920375) +Comm time (%) = 0.141013 (36.4711) +Outpt time (%) = 0.0428388 (11.0797) +Other time (%) = 0.140004 (36.2099) + +Nlocal: 105 ave 121 max 91 min +Histogram: 2 0 0 0 0 0 0 0 1 1 +Nghost: 93 ave 100 max 86 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 918.5 ave 1110 max 728 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 3674 +Ave neighs/atom = 8.74762 +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 = 1.90445 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 631 0 -3.050959 0 -2.6512973 1.6846776 279.02342 + 640 0 -2.9724763 0 -2.9385365 2.6808269 279.01768 + 650 0 -2.9831473 0 -2.9603508 2.6529278 279.3157 + 660 0 -2.9883088 0 -2.9688882 2.6455144 279.19287 + 670 0 -2.9901301 0 -2.9719337 2.6833537 279.19287 + 680 0 -2.9901469 0 -2.973945 2.7672171 278.35898 + 690 0 -2.9914393 0 -2.9758977 2.8347562 277.52757 + 700 0 -2.9948972 0 -2.9783768 2.8254108 276.61918 + 710 0 -2.998313 0 -2.9811357 2.6879262 278.27732 + 720 0 -3.0011637 0 -2.9837006 2.6342646 278.77996 + 730 0 -3.0018221 0 -2.9859645 2.6867882 278.53266 + 740 0 -3.0027142 0 -2.9869511 2.7039706 278.53266 + 750 0 -3.0033059 0 -2.9872782 2.703748 278.53266 + 760 0 -3.0033193 0 -2.9872481 2.6988534 278.53266 + 766 0 -3.0034118 0 -2.987267 2.6950367 278.53266 +Loop time of 0.177757 on 4 procs for 135 steps with 420 atoms + +Minimization stats: + E initial, next-to-last, final = -2.6513 -2.98727 -2.98727 + Gradient 2-norm init/final= 390.148 0.682374 + Gradient inf-norm init/final= 173.709 0.209763 + Iterations = 135 + Force evaluations = 454 + +Pair time (%) = 0.0266486 (14.9915) +Neigh time (%) = 0.000991344 (0.557695) +Comm time (%) = 0.0658523 (37.0461) +Outpt time (%) = 0.0170659 (9.60066) +Other time (%) = 0.0671993 (37.804) + +Nlocal: 105 ave 120 max 90 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 93.25 ave 101 max 84 min +Histogram: 1 1 0 0 0 0 0 0 0 2 +Neighs: 951.75 ave 1140 max 744 min +Histogram: 1 1 0 0 0 0 0 0 0 2 + +Total # of neighbors = 3807 +Ave neighs/atom = 9.06429 +Neighbor list builds = 12 +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 = 1.90445 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 766 0 -3.0034118 0 -2.4108045 2.7094764 277.04827 + 770 0 -2.8791192 0 -2.7876589 4.0283682 277.04934 + 780 0 -2.8893782 0 -2.8546005 4.1023299 277.26539 + 790 0 -2.89497 0 -2.8651108 4.0749194 277.26539 + 800 0 -2.8939699 0 -2.8709228 4.1282326 277.3396 + 810 0 -2.9013871 0 -2.8864339 3.9178823 283.50328 + 820 0 -2.9229391 0 -2.9084604 3.5302579 287.65327 + 830 0 -2.9466199 0 -2.9297134 3.0931452 288.09455 + 840 0 -2.9731215 0 -2.9592738 2.6847913 287.70955 + 850 0 -2.9914172 0 -2.9815521 2.4955367 287.80661 + 860 0 -3.0193833 0 -3.0131192 2.2721938 289.11983 + 870 0 -3.0346779 0 -3.0266442 2.0697315 289.28859 + 880 0 -3.0438692 0 -3.0351998 1.9227994 289.55602 + 890 0 -3.0586749 0 -3.0486877 1.6182639 291.71842 + 900 0 -3.0709615 0 -3.0616412 1.451258 292.90302 + 910 0 -3.0739192 0 -3.0643475 1.4689297 293.25346 + 920 0 -3.0744679 0 -3.064872 1.4814698 293.25346 + 930 0 -3.0745289 0 -3.0654103 1.5231812 293.25346 + 940 0 -3.0747725 0 -3.0657629 1.563189 292.6074 + 950 0 -3.0747162 0 -3.0658229 1.5643522 292.6074 + 952 0 -3.0747117 0 -3.0658271 1.564168 292.6074 +Loop time of 0.265928 on 4 procs for 186 steps with 420 atoms + +Minimization stats: + E initial, next-to-last, final = -2.4108 -3.06583 -3.06583 + Gradient 2-norm init/final= 492.496 0.683919 + Gradient inf-norm init/final= 186.143 0.307738 + Iterations = 186 + Force evaluations = 690 + +Pair time (%) = 0.0411488 (15.4737) +Neigh time (%) = 0.00259405 (0.975474) +Comm time (%) = 0.104417 (39.2652) +Outpt time (%) = 0.0248856 (9.35804) +Other time (%) = 0.0928821 (34.9276) + +Nlocal: 105 ave 129 max 80 min +Histogram: 1 1 0 0 0 0 0 0 0 2 +Nghost: 95 ave 107 max 83 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 895 ave 1166 max 606 min +Histogram: 1 1 0 0 0 0 0 0 0 2 + +Total # of neighbors = 3580 +Ave neighs/atom = 8.52381 +Neighbor list builds = 33 +Dangerous builds = 0 diff --git a/examples/indent/log.indent.min.22Jun07.linux.1 b/examples/indent/log.indent.min.22Jun07.linux.1 new file mode 100644 index 0000000000..6c020f4579 --- /dev/null +++ b/examples/indent/log.indent.min.22Jun07.linux.1 @@ -0,0 +1,386 @@ +LAMMPS (22 June 2007) +# 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 = 1.90811 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 0 -3.1727576 0 -3.1727576 -1.8810645 251.71282 + 10 0 -3.1820434 0 -3.1820434 -1.3321628 249.7446 + 20 0 -3.1892762 0 -3.1892762 -1.030012 247.85333 + 30 0 -3.1906231 0 -3.1906231 -0.90653473 247.85333 + 38 0 -3.1909329 0 -3.1909329 -0.81496712 247.85333 +Loop time of 0.083943 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 (%) = 0.062235 (74.1396) +Neigh time (%) = 0.000978 (1.16508) +Comm time (%) = 0.001545 (1.84053) +Outpt time (%) = 0.006357 (7.573) +Other time (%) = 0.012828 (15.2818) + +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 = 1.90811 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 38 0 -3.1909329 0 -2.1718641 -0.81877351 246.70109 + 40 0 -3.169091 0 -2.8877594 -0.54943778 246.70107 + 50 0 -3.1711852 0 -3.1696057 -0.39685207 246.70204 + 60 0 -3.1780204 0 -3.1769046 -0.39225544 246.81048 + 70 0 -3.1800811 0 -3.1793038 -0.31260477 246.81048 + 80 0 -3.1809088 0 -3.1801828 -0.23455796 246.81048 + 90 0 -3.1811924 0 -3.1805002 -0.17000885 246.18491 + 100 0 -3.1812635 0 -3.1805822 -0.14393015 246.18491 + 103 0 -3.1812545 0 -3.180591 -0.14136212 246.18491 +Loop time of 0.130711 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 (%) = 0.089035 (68.1159) +Neigh time (%) = 0.002389 (1.8277) +Comm time (%) = 0.002298 (1.75808) +Outpt time (%) = 0.015673 (11.9906) +Other time (%) = 0.021316 (16.3077) + +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 = 1.90811 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 103 0 -3.1812545 0 -0.21951029 -0.14159267 245.78405 + 110 0 -2.9284097 0 -2.6466557 2.4269773 245.78334 + 120 0 -3.0511214 0 -3.0267128 1.7637829 245.78215 + 130 0 -3.0919408 0 -3.0831141 1.4860665 245.92571 + 140 0 -3.1001312 0 -3.0930458 1.4234791 245.92571 + 150 0 -3.102631 0 -3.0950311 1.4404842 246.21073 + 160 0 -3.1037978 0 -3.09648 1.5609439 244.44101 + 170 0 -3.1041785 0 -3.0969724 1.6411134 244.44101 + 180 0 -3.1042622 0 -3.0971039 1.6655381 244.44101 + 186 0 -3.1042077 0 -3.0971259 1.6700959 244.44101 +Loop time of 0.174012 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 (%) = 0.119678 (68.7757) +Neigh time (%) = 0.005353 (3.07622) +Comm time (%) = 0.003228 (1.85504) +Outpt time (%) = 0.017629 (10.1309) +Other time (%) = 0.028124 (16.1621) + +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 = 1.90811 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 186 0 -3.1042077 0 1.9876467 1.6726187 244.07233 + 190 0 -2.7684954 0 -1.1554028 4.8385981 243.82123 + 200 0 -2.7738026 0 -2.6431045 5.3693642 246.38337 + 210 0 -2.892911 0 -2.863976 4.4322106 250.63896 + 220 0 -2.9428319 0 -2.9275563 3.8976868 253.54966 + 230 0 -2.9566576 0 -2.9427828 3.7470914 255.96648 + 240 0 -2.9622154 0 -2.9537038 3.6488191 256.62718 + 250 0 -2.9685121 0 -2.9588966 3.5333392 257.75615 + 260 0 -2.9851957 0 -2.9793281 3.2459764 258.1143 + 270 0 -3.0137593 0 -3.0035449 2.8836141 257.01204 + 280 0 -3.0182039 0 -3.0121893 2.7594651 257.4611 + 290 0 -3.0271401 0 -3.0194953 2.4173885 260.04588 + 300 0 -3.0332671 0 -3.0255652 2.4243877 260.04588 + 310 0 -3.0346445 0 -3.0270706 2.4432531 258.57203 + 320 0 -3.0355796 0 -3.0277669 2.4110728 258.57203 + 330 0 -3.0359691 0 -3.0280778 2.3724675 258.57203 + 340 0 -3.0358963 0 -3.0281771 2.350355 258.57203 + 350 0 -3.0359324 0 -3.0282261 2.3336342 258.57203 +Loop time of 0.364823 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 0.605547 + Gradient inf-norm init/final= 1037.31 0.149722 + Iterations = 164 + Force evaluations = 579 + +Pair time (%) = 0.254752 (69.8289) +Neigh time (%) = 0.012437 (3.40905) +Comm time (%) = 0.007036 (1.92861) +Outpt time (%) = 0.035757 (9.80119) +Other time (%) = 0.054841 (15.0322) + +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 = 1.90811 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 350 0 -3.0359324 0 6.9766773 2.3291833 259.06614 + 360 0 -2.335093 0 -1.5707757 8.8885568 259.07026 + 370 0 -2.5599881 0 -2.4347598 7.565773 259.34078 + 380 0 -2.7844216 0 -2.7584649 5.7681809 262.33347 + 390 0 -2.8656166 0 -2.8440742 4.9699456 263.34254 + 400 0 -2.9109956 0 -2.8923852 4.2490464 265.32325 + 410 0 -2.9467505 0 -2.9334194 3.7795578 267.03801 + 420 0 -2.9744267 0 -2.9577148 3.6538839 266.60412 + 430 0 -2.9926459 0 -2.9736415 3.4779579 267.0876 + 440 0 -2.9975444 0 -2.9801207 3.4033949 266.91222 + 450 0 -2.9996115 0 -2.9820253 3.3516145 267.52149 + 460 0 -2.99873 0 -2.9829304 3.3110697 267.52149 + 470 0 -2.9987502 0 -2.984601 3.1122612 268.31993 + 480 0 -3.0028144 0 -2.990299 2.7066551 271.25603 + 490 0 -3.0064815 0 -2.9941922 2.5269217 272.94586 + 500 0 -3.0096474 0 -2.9965356 2.3795554 274.42313 + 510 0 -3.0123415 0 -2.999981 2.2773683 275.06513 + 520 0 -3.0153983 0 -3.0059828 2.2054397 275.17639 + 530 0 -3.0265326 0 -3.0171295 2.0959919 276.89139 + 540 0 -3.0324549 0 -3.0227829 2.0207038 276.89139 + 550 0 -3.0338293 0 -3.0240046 1.9861902 277.47265 + 560 0 -3.0373141 0 -3.027647 1.8982732 278.61063 + 570 0 -3.0418824 0 -3.0325541 1.8690028 278.55645 + 580 0 -3.0429662 0 -3.0340728 1.8795056 278.36003 + 590 0 -3.0447406 0 -3.0359543 1.8652644 277.68832 + 600 0 -3.045522 0 -3.0368802 1.8599157 277.68832 + 610 0 -3.0461885 0 -3.0374215 1.8228959 277.68832 + 620 0 -3.0469853 0 -3.0377678 1.7959291 277.9626 + 630 0 -3.0480444 0 -3.038612 1.7335705 278.37443 + 631 0 -3.0484588 0 -3.0387787 1.724502 278.37443 +Loop time of 0.627039 on 1 procs for 281 steps with 420 atoms + +Minimization stats: + E initial, next-to-last, final = 6.97668 -3.03861 -3.03878 + Gradient 2-norm init/final= 3559.61 6.9459 + Gradient inf-norm init/final= 1438.88 2.75216 + Iterations = 281 + Force evaluations = 1000 + +Pair time (%) = 0.440883 (70.3119) +Neigh time (%) = 0.02191 (3.4942) +Comm time (%) = 0.012146 (1.93704) +Outpt time (%) = 0.060133 (9.58999) +Other time (%) = 0.091967 (14.6669) + +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: 3702 ave 3702 max 3702 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 3702 +Ave neighs/atom = 8.81429 +Neighbor list builds = 43 +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 = 1.90811 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 631 0 -3.0484588 0 -2.604481 1.7235776 278.52373 + 640 0 -2.9643579 0 -2.928693 2.785548 278.5501 + 650 0 -2.9743774 0 -2.9520339 2.7702732 278.80038 + 660 0 -2.9814575 0 -2.9643711 2.777993 278.70742 + 670 0 -2.9873942 0 -2.9725414 2.8285795 277.74776 + 680 0 -2.9939115 0 -2.9787385 2.8153784 277.37112 + 690 0 -3.0030163 0 -2.9852712 2.7060285 277.07917 + 700 0 -3.0038477 0 -2.9869319 2.6884535 277.07917 + 710 0 -3.0038815 0 -2.9874213 2.6896219 277.07917 + 720 0 -3.0038761 0 -2.9875543 2.701217 277.07917 + 730 0 -3.003858 0 -2.9875861 2.7091036 277.07917 + 740 0 -3.00415 0 -2.987852 2.7243361 276.81523 + 750 0 -3.0041764 0 -2.9882589 2.7318353 276.72141 + 760 0 -3.0044009 0 -2.9883898 2.7254417 276.72141 + 770 0 -3.0045687 0 -2.9885435 2.7179258 276.72141 + 780 0 -3.00483 0 -2.988598 2.7038145 276.72141 + 784 0 -3.0048523 0 -2.9886088 2.7008904 276.72141 +Loop time of 0.341197 on 1 procs for 153 steps with 420 atoms + +Minimization stats: + E initial, next-to-last, final = -2.60448 -2.98861 -2.98861 + Gradient 2-norm init/final= 419.523 0.776857 + Gradient inf-norm init/final= 175.55 0.266814 + Iterations = 153 + Force evaluations = 523 + +Pair time (%) = 0.228625 (67.0067) +Neigh time (%) = 0.006238 (1.82827) +Comm time (%) = 0.006256 (1.83354) +Outpt time (%) = 0.050744 (14.8723) +Other time (%) = 0.049334 (14.4591) + +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: 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 = 12 +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 = 1.90811 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 784 0 -3.0048523 0 -2.4268246 2.7001678 276.79547 + 790 0 -2.8807915 0 -2.8212034 4.0892175 276.79878 + 800 0 -2.8950546 0 -2.8611291 4.082591 277.02332 + 810 0 -2.9005828 0 -2.8735631 4.0937007 277.23062 + 820 0 -2.9033388 0 -2.880864 4.0724241 277.48631 + 830 0 -2.9144679 0 -2.896527 3.8087147 281.95887 + 840 0 -2.9296668 0 -2.9129029 3.4437246 286.37863 + 850 0 -2.9523068 0 -2.9344645 2.7938894 290.46463 + 860 0 -2.9752409 0 -2.9623271 2.4497341 291.16741 + 870 0 -2.9878386 0 -2.9774613 2.3988152 288.45049 + 880 0 -3.0168937 0 -3.0094002 2.2534858 289.05328 + 890 0 -3.0298392 0 -3.0215958 2.118575 289.37008 + 900 0 -3.0361898 0 -3.0276031 2.0386889 289.68806 + 910 0 -3.0444205 0 -3.035322 1.8601706 291.35702 + 920 0 -3.0593366 0 -3.0505717 1.6181397 291.67077 + 930 0 -3.0654752 0 -3.0565939 1.571603 292.044 + 940 0 -3.0712476 0 -3.0620886 1.5718668 291.77651 + 950 0 -3.0727487 0 -3.0641228 1.5614938 291.98714 + 960 0 -3.0743601 0 -3.0655064 1.560509 292.20323 + 970 0 -3.0748867 0 -3.0659016 1.5496073 292.20323 + 980 0 -3.0752084 0 -3.0661516 1.5372769 292.25778 + 990 0 -3.0751243 0 -3.0662155 1.5394404 292.25778 + 991 0 -3.075136 0 -3.0662166 1.5393777 292.25778 +Loop time of 0.470478 on 1 procs for 207 steps with 420 atoms + +Minimization stats: + E initial, next-to-last, final = -2.42682 -3.06622 -3.06622 + Gradient 2-norm init/final= 483.942 0.629476 + Gradient inf-norm init/final= 212.858 0.27039 + Iterations = 207 + Force evaluations = 759 + +Pair time (%) = 0.325699 (69.2273) +Neigh time (%) = 0.01922 (4.08521) +Comm time (%) = 0.009439 (2.00626) +Outpt time (%) = 0.046274 (9.83553) +Other time (%) = 0.069846 (14.8458) + +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: 3579 ave 3579 max 3579 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 3579 +Ave neighs/atom = 8.52143 +Neighbor list builds = 38 +Dangerous builds = 0 diff --git a/examples/meam/log.meam.22Jun07.liberty.4 b/examples/meam/log.meam.22Jun07.liberty.4 new file mode 100644 index 0000000000..41d0a32c9e --- /dev/null +++ b/examples/meam/log.meam.22Jun07.liberty.4 @@ -0,0 +1,60 @@ +LAMMPS (22 June 2007) +# 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 = 4.55272 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 0.18309 on 4 procs for 100 steps with 128 atoms + +Pair time (%) = 0.155092 (84.7084) +Neigh time (%) = 0.00145948 (0.797139) +Comm time (%) = 0.0187557 (10.244) +Outpt time (%) = 0.00630403 (3.44313) +Other time (%) = 0.00147808 (0.807296) + +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.22Jun07.linux.1 b/examples/meam/log.meam.22Jun07.linux.1 new file mode 100644 index 0000000000..4585634b7e --- /dev/null +++ b/examples/meam/log.meam.22Jun07.linux.1 @@ -0,0 +1,60 @@ +LAMMPS (22 June 2007) +# 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 = 4.65579 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 0.447923 on 1 procs for 100 steps with 128 atoms + +Pair time (%) = 0.422714 (94.372) +Neigh time (%) = 0.008859 (1.9778) +Comm time (%) = 0.003976 (0.887653) +Outpt time (%) = 0.0087 (1.9423) +Other time (%) = 0.003674 (0.82023) + +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.shear.22Jun07.liberty.4 b/examples/meam/log.meam.shear.22Jun07.liberty.4 new file mode 100644 index 0000000000..381843d5e9 --- /dev/null +++ b/examples/meam/log.meam.shear.22Jun07.liberty.4 @@ -0,0 +1,163 @@ +LAMMPS (22 June 2007) +# 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 = 5.05583 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 1.74057 on 4 procs for 100 steps with 1912 atoms + +Pair time (%) = 1.69932 (97.6299) +Neigh time (%) = 0.00826591 (0.474896) +Comm time (%) = 0.022138 (1.27188) +Outpt time (%) = 0.000750303 (0.0431067) +Other time (%) = 0.0100996 (0.580245) + +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 = 5.10101 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 307.76805 -8065.4274 0 -8028.7615 11979.925 21120.806 + 1400 300 -8051.592 0 -8015.8516 12466.399 21238.042 + 1500 308.53314 -8037.7116 0 -8000.9546 15186.116 21363.826 + 1600 300 -8031.857 0 -7996.1166 16229.579 21487.167 + 1700 300 -8022.9424 0 -7987.202 18187.876 21605.624 + 1800 300 -8009.2389 0 -7973.4984 18721.834 21735.072 + 1900 300.26712 -7997.956 0 -7962.1837 18855.604 21848.644 + 2000 300 -7987.6035 0 -7951.8631 18711.312 21976.871 + 2100 300 -7996.1806 0 -7960.4401 16424.414 22100.212 + 2200 305.54436 -8006.7713 0 -7970.3703 13205.691 22211.342 + 2300 300 -8010.5965 0 -7974.8561 11455.319 22342.011 + 2400 300 -8012.9434 0 -7977.2029 12543.014 22469.016 + 2500 300 -8014.3999 0 -7978.6595 12003.377 22583.809 + 2600 296.98849 -8009.1337 0 -7973.7521 11080.253 22707.151 + 2700 300 -8002.4065 0 -7966.666 8890.8608 22836.599 + 2800 300 -8005.4907 0 -7969.7503 7724.8308 22956.277 + 2900 308.79197 -8003.0392 0 -7966.2514 8308.48 23072.291 + 3000 300 -8014.1797 0 -7978.4393 5468.9701 23199.297 +Loop time of 54.7884 on 4 procs for 3000 steps with 1912 atoms + +Pair time (%) = 53.2791 (97.2452) +Neigh time (%) = 0.365944 (0.667922) +Comm time (%) = 0.69469 (1.26795) +Outpt time (%) = 0.151946 (0.277333) +Other time (%) = 0.29672 (0.541574) + +Nlocal: 478 ave 521 max 447 min +Histogram: 1 1 0 0 0 1 0 0 0 1 +Nghost: 790.5 ave 838 max 745 min +Histogram: 1 0 1 0 0 0 0 1 0 1 +Neighs: 5842.25 ave 6343 max 5608 min +Histogram: 1 2 0 0 0 0 0 0 0 1 +FullNghs: 11684.5 ave 12654 max 11231 min +Histogram: 1 2 0 0 0 0 0 0 0 1 + +Total # of neighbors = 46738 +Ave neighs/atom = 24.4446 +Neighbor list builds = 225 +Dangerous builds = 0 diff --git a/examples/meam/log.meam.shear.22Jun07.linux.1 b/examples/meam/log.meam.shear.22Jun07.linux.1 new file mode 100644 index 0000000000..4e27c9fc4c --- /dev/null +++ b/examples/meam/log.meam.shear.22Jun07.linux.1 @@ -0,0 +1,163 @@ +LAMMPS (22 June 2007) +# 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 = 5.90372 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 8.49319 on 1 procs for 100 steps with 1912 atoms + +Pair time (%) = 8.38065 (98.6749) +Neigh time (%) = 0.058524 (0.68907) +Comm time (%) = 0.014651 (0.172503) +Outpt time (%) = 0.001071 (0.0126101) +Other time (%) = 0.038294 (0.450879) + +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 = 6.13252 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 8173.3442 20874.123 + 1200 293.41155 -8082.676 0 -8047.7205 9884.2077 20987.695 + 1300 303.32764 -8066.7733 0 -8030.6365 10196.38 21108.594 + 1400 304.17521 -8049.5115 0 -8013.2736 11518.937 21249.033 + 1500 300 -8038.1747 0 -8002.4342 12554.583 21361.383 + 1600 304.95273 -8030.5805 0 -7994.2501 12166.296 21483.504 + 1700 302.82122 -8019.1918 0 -7983.1152 11726.855 21604.403 + 1800 300 -8010.2021 0 -7974.4617 11039.327 21737.514 + 1900 309.75034 -7999.8523 0 -7962.9503 10360.771 21859.635 + 2000 303.95534 -7995.5876 0 -7959.3759 11106.855 21974.428 + 2100 300 -7998.4845 0 -7962.7441 9592.4431 22092.885 + 2200 300 -8010.3787 0 -7974.6383 7011.3257 22223.554 + 2300 300 -8013.8118 0 -7978.0714 7206.5123 22334.684 + 2400 300 -8016.5277 0 -7980.7872 8333.0814 22469.016 + 2500 309.73732 -8019.4133 0 -7982.5128 8734.2461 22586.252 + 2600 300 -8018.1897 0 -7982.4492 9088.9471 22702.266 + 2700 300.98484 -8016.4337 0 -7980.576 11358.168 22821.944 + 2800 309.26899 -8013.3976 0 -7976.5529 11582.101 22956.277 + 2900 305.82563 -8013.711 0 -7977.2765 8649.9858 23077.176 + 3000 309.93922 -8013.2879 0 -7976.3634 6488.7794 23187.085 +Loop time of 270.752 on 1 procs for 3000 steps with 1912 atoms + +Pair time (%) = 266.289 (98.3517) +Neigh time (%) = 2.51321 (0.928236) +Comm time (%) = 0.465902 (0.172077) +Outpt time (%) = 0.345781 (0.127711) +Other time (%) = 1.13779 (0.420235) + +Nlocal: 1912 ave 1912 max 1912 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1659 ave 1659 max 1659 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 23351 ave 23351 max 23351 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 46702 ave 46702 max 46702 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 46702 +Ave neighs/atom = 24.4257 +Neighbor list builds = 216 +Dangerous builds = 0 diff --git a/examples/melt/log.melt.22Jun07.liberty.4 b/examples/melt/log.melt.22Jun07.liberty.4 new file mode 100644 index 0000000000..0eee3c85d6 --- /dev/null +++ b/examples/melt/log.melt.22Jun07.liberty.4 @@ -0,0 +1,57 @@ +LAMMPS (22 June 2007) +# 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) + 2 by 1 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 = 1.52225 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 3 -6.7733681 0 -2.2744931 -3.7033504 + 50 1.6557237 -4.7655254 0 -2.2825608 5.7884064 + 100 1.6549846 -4.7636783 0 -2.281822 5.7819801 + 150 1.6390665 -4.7393685 0 -2.2813835 5.925551 + 200 1.6294936 -4.7247826 0 -2.2811533 5.9482013 + 250 1.6468354 -4.7510951 0 -2.2814595 5.8749319 +Loop time of 0.777116 on 4 procs for 250 steps with 4000 atoms + +Pair time (%) = 0.466133 (59.9824) +Neigh time (%) = 0.0471849 (6.0718) +Comm time (%) = 0.186014 (23.9365) +Outpt time (%) = 0.0529453 (6.81305) +Other time (%) = 0.0248383 (3.19622) + +Nlocal: 1000 ave 1005 max 995 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +Nghost: 2714.75 ave 2724 max 2701 min +Histogram: 1 0 0 0 0 0 1 1 0 1 +Neighs: 37856.2 ave 38434 max 37299 min +Histogram: 1 1 0 0 0 0 0 0 1 1 + +Total # of neighbors = 151425 +Ave neighs/atom = 37.8563 +Neighbor list builds = 12 +Dangerous builds = 0 diff --git a/examples/melt/log.melt.22Jun07.linux.1 b/examples/melt/log.melt.22Jun07.linux.1 new file mode 100644 index 0000000000..471112c63e --- /dev/null +++ b/examples/melt/log.melt.22Jun07.linux.1 @@ -0,0 +1,57 @@ +LAMMPS (22 June 2007) +# 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 = 2.28877 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 4.4047 on 1 procs for 250 steps with 4000 atoms + +Pair time (%) = 3.68702 (83.7066) +Neigh time (%) = 0.345328 (7.83999) +Comm time (%) = 0.110895 (2.51765) +Outpt time (%) = 0.095988 (2.17922) +Other time (%) = 0.165464 (3.75653) + +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/micelle/log.micelle.22Jun07.liberty.4 b/examples/micelle/log.micelle.22Jun07.liberty.4 new file mode 100644 index 0000000000..4aa65bc71d --- /dev/null +++ b/examples/micelle/log.micelle.22Jun07.liberty.4 @@ -0,0 +1,200 @@ +LAMMPS (22 June 2007) +# 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 = 1.84779 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0.45 0.40003481 2.2200223e-06 0.84947453 2.6311673 + 50 0.47417944 0.67716204 0.057387153 1.2081359 4.4581428 + 100 0.45 0.73037684 0.054821983 1.2346363 7.730955 + 150 0.67532546 0.72388376 0.043478036 1.4418431 9.580616 + 200 0.45 0.78466058 0.076912805 1.3110109 10.136457 + 250 0.66488946 0.69771453 0.081047682 1.4428206 12.303975 + 300 0.45 0.76794745 0.066716745 1.2841017 12.618422 + 350 0.67629601 0.62549506 0.072636862 1.3735826 14.282774 + 400 0.45 0.68493339 0.090717081 1.225088 14.904536 + 450 0.56732174 0.64322231 0.080690687 1.2905256 15.790896 + 500 0.45 0.64764573 0.078468194 1.1755514 15.970391 + 550 0.56476697 0.58160926 0.080519682 1.22619 16.573931 + 600 0.45 0.58331363 0.088243449 1.1209946 17.103627 + 650 0.5229482 0.54530348 0.09321673 1.1608147 17.545826 + 700 0.45 0.52374674 0.085166964 1.0583512 17.640835 + 750 0.51528063 0.48974532 0.086434828 1.0908167 17.952674 + 800 0.45 0.50467091 0.090255509 1.0443639 18.600542 + 850 0.4950534 0.48512921 0.091950432 1.0715142 18.88713 + 900 0.45 0.48352312 0.097223467 1.0301841 19.049897 + 950 0.49451225 0.46619517 0.094098428 1.0541877 19.588988 + 1000 0.45 0.46260893 0.10106179 1.0131082 19.538971 +Loop time of 0.292184 on 4 procs for 1000 steps with 1200 atoms + +Pair time (%) = 0.0816203 (27.9345) +Bond time (%) = 0.00599533 (2.0519) +Neigh time (%) = 0.015554 (5.32335) +Comm time (%) = 0.14458 (49.4825) +Outpt time (%) = 0.00397557 (1.36064) +Other time (%) = 0.040459 (13.8471) + +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 = 1.85934 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0.45 -1.6864322 0.10106179 -1.1359329 12.63785 + 1000 0.44914716 -1.9350719 0.071373764 -1.4151124 7.1568301 + 2000 0.45 -2.017979 0.070742172 -1.4977993 4.8375385 + 3000 0.46278827 -2.0089553 0.058330549 -1.488415 4.820275 + 4000 0.46714531 -2.0210549 0.057888529 -1.496605 4.2962188 + 5000 0.44804799 -2.0254175 0.06916971 -1.5087599 4.4157997 + 6000 0.45761629 -2.0368567 0.076990577 -1.5028219 4.6540238 + 7000 0.44640723 -2.0461339 0.064790763 -1.5354939 4.4179413 + 8000 0.45177284 -2.0324404 0.047705359 -1.5335269 4.54304 + 9000 0.43975305 -2.06401 0.069375126 -1.5554315 3.2833286 + 10000 0.45308355 -2.0423211 0.056575039 -1.5332289 4.1729746 + 11000 0.44229664 -2.0436958 0.065042761 -1.5369092 4.3783133 + 12000 0.4688876 -2.0591494 0.058270214 -1.5325777 3.6811782 + 13000 0.45151162 -2.0633938 0.053917641 -1.5585289 3.1767412 + 14000 0.44571931 -2.0503046 0.0570333 -1.5481092 3.5096724 + 15000 0.45 -2.0837399 0.060991769 -1.5733106 3.1370759 + 16000 0.45307444 -2.0804646 0.0670541 -1.5609024 3.2516824 + 17000 0.45880865 -2.072733 0.061534139 -1.5529637 3.3828133 + 18000 0.45650845 -2.0811023 0.057626785 -1.5675377 2.8631577 + 19000 0.45645839 -2.1137579 0.058378793 -1.5994913 2.6678277 + 20000 0.44760402 -2.109567 0.06512585 -1.5973966 2.3558292 + 21000 0.43651289 -2.0863769 0.057529291 -1.5928803 3.0018852 + 22000 0.43440649 -2.0950161 0.063482231 -1.5976704 2.3233803 + 23000 0.44572794 -2.0887627 0.061323772 -1.5822681 2.9579923 + 24000 0.44306777 -2.0843912 0.050176466 -1.5917008 2.8496622 + 25000 0.45 -2.1051658 0.061328265 -1.5944 2.1179388 + 26000 0.45552583 -2.119375 0.058663998 -1.6057546 2.2945202 + 27000 0.43912671 -2.1066914 0.051902852 -1.6162108 2.1491613 + 28000 0.45168054 -2.1078102 0.067816662 -1.5888776 2.4300025 + 29000 0.44173014 -2.0804191 0.05137384 -1.5878673 3.0500294 + 30000 0.44407338 -2.0998759 0.053922142 -1.6024355 2.7183453 + 31000 0.4431566 -2.1102821 0.061544598 -1.6061349 2.7379786 + 32000 0.45 -2.1163285 0.060739023 -1.606152 2.0727532 + 33000 0.46444105 -2.1050315 0.062866914 -1.5783041 1.9114822 + 34000 0.44581302 -2.0954209 0.063239112 -1.5869261 2.3525995 + 35000 0.45 -2.1261175 0.060452019 -1.616228 2.014967 + 36000 0.43470345 -2.1034119 0.063748152 -1.6055037 2.6086075 + 37000 0.44671396 -2.093898 0.057613863 -1.5901286 2.9715819 + 38000 0.45751276 -2.1085734 0.058845472 -1.592787 2.5044165 + 39000 0.44786323 -2.1130108 0.056041424 -1.609666 2.1432 + 40000 0.43937694 -2.1125665 0.04967594 -1.6240628 2.5594741 + 41000 0.45 -2.1083933 0.0547275 -1.6042283 2.4651511 + 42000 0.43287348 -2.1009617 0.054318981 -1.6143103 2.1496725 + 43000 0.44945469 -2.1285428 0.05863553 -1.6210144 2.2786034 + 44000 0.44737235 -2.0967009 0.058373014 -1.5915148 2.7502707 + 45000 0.45401167 -2.110646 0.059341015 -1.5978608 1.9203458 + 46000 0.43451455 -2.1077912 0.060728016 -1.6130918 2.3294588 + 47000 0.44822719 -2.1295807 0.061997031 -1.6199168 2.1463667 + 48000 0.43300738 -2.1029353 0.064025843 -1.6064433 2.1373309 + 49000 0.44657342 -2.1237489 0.060905756 -1.616828 2.0319341 + 50000 0.4677882 -2.1242266 0.059790209 -1.597233 2.5375996 + 51000 0.45536082 -2.0986081 0.052858152 -1.5909583 2.562239 + 52000 0.45919514 -2.1064277 0.057955 -1.5898515 2.3499751 + 53000 0.46449938 -2.1195508 0.060178993 -1.595453 2.5406265 + 54000 0.43682602 -2.1035311 0.069334917 -1.5979162 2.6919587 + 55000 0.45 -2.0965463 0.055320603 -1.5917882 2.5110927 + 56000 0.44913495 -2.1210973 0.058848556 -1.6136752 1.8246708 + 57000 0.44307699 -2.1361861 0.066761708 -1.6269012 2.4928119 + 58000 0.45181349 -2.1311357 0.05656415 -1.6233228 2.1515038 + 59000 0.45 -2.1345398 0.060573082 -1.6245292 1.715299 + 60000 0.45068289 -2.1230762 0.055943523 -1.6170131 2.1657885 +Loop time of 22.1561 on 4 procs for 60000 steps with 1200 atoms + +Pair time (%) = 7.33887 (33.1235) +Bond time (%) = 0.358887 (1.61981) +Neigh time (%) = 1.42228 (6.41939) +Comm time (%) = 10.1198 (45.675) +Outpt time (%) = 0.320405 (1.44613) +Other time (%) = 2.59584 (11.7162) + +Nlocal: 300 ave 308 max 291 min +Histogram: 1 0 1 0 0 0 0 0 1 1 +Nghost: 207 ave 218 max 195 min +Histogram: 1 0 0 0 1 0 1 0 0 1 +Neighs: 2467.25 ave 2570 max 2397 min +Histogram: 1 0 1 1 0 0 0 0 0 1 + +Total # of neighbors = 9869 +Ave neighs/atom = 8.22417 +Ave special neighs/atom = 0.5 +Neighbor list builds = 4885 +Dangerous builds = 0 diff --git a/examples/micelle/log.micelle.22Jun07.linux.1 b/examples/micelle/log.micelle.22Jun07.linux.1 new file mode 100644 index 0000000000..1ea310bc6e --- /dev/null +++ b/examples/micelle/log.micelle.22Jun07.linux.1 @@ -0,0 +1,200 @@ +LAMMPS (22 June 2007) +# 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 = 1.7704 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0.45 0.40003481 2.2200223e-06 0.84947453 2.6311673 + 50 0.47417944 0.67716204 0.057387153 1.2081359 4.4581428 + 100 0.45 0.73037684 0.054821983 1.2346363 7.730955 + 150 0.67532546 0.72388376 0.043478036 1.4418431 9.580616 + 200 0.45 0.78466058 0.076912805 1.3110109 10.136457 + 250 0.66488946 0.69771453 0.081047682 1.4428206 12.303975 + 300 0.45 0.76794745 0.066716745 1.2841017 12.618422 + 350 0.67629601 0.62549506 0.072636862 1.3735826 14.282774 + 400 0.45 0.68493339 0.090717081 1.225088 14.904536 + 450 0.56732174 0.64322231 0.080690687 1.2905256 15.790896 + 500 0.45 0.64764573 0.078468194 1.1755514 15.970391 + 550 0.56476697 0.58160926 0.080519682 1.22619 16.573931 + 600 0.45 0.58331363 0.088243449 1.1209946 17.103627 + 650 0.5229482 0.54530348 0.09321673 1.1608147 17.545826 + 700 0.45 0.52374674 0.085166964 1.0583512 17.640835 + 750 0.51528063 0.48974532 0.086434828 1.0908167 17.952674 + 800 0.45 0.50467091 0.090255509 1.0443639 18.600542 + 850 0.4950534 0.48512921 0.091950432 1.0715142 18.88713 + 900 0.45 0.48352312 0.097223467 1.0301841 19.049897 + 950 0.49451225 0.46619517 0.094098428 1.0541877 19.588988 + 1000 0.45 0.46260893 0.10106179 1.0131082 19.538971 +Loop time of 0.846992 on 1 procs for 1000 steps with 1200 atoms + +Pair time (%) = 0.503286 (59.4204) +Bond time (%) = 0.041896 (4.94645) +Neigh time (%) = 0.107992 (12.7501) +Comm time (%) = 0.026696 (3.15186) +Outpt time (%) = 0.00491 (0.579699) +Other time (%) = 0.162212 (19.1515) + +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 = 1.85432 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0.45 -1.6864322 0.10106179 -1.1359329 12.63785 + 1000 0.44914708 -1.9350711 0.071372351 -1.4151131 7.156807 + 2000 0.45270543 -2.0004904 0.066419058 -1.4819318 5.5702827 + 3000 0.46916283 -2.0213933 0.065872359 -1.4869445 5.0060597 + 4000 0.43945376 -2.0166598 0.067641209 -1.5101142 4.6396644 + 5000 0.45495437 -2.0447226 0.066285498 -1.5240515 3.9305266 + 6000 0.44963328 -2.056045 0.068450242 -1.5385235 3.8603798 + 7000 0.44856129 -2.0414287 0.058586674 -1.5348414 3.9952578 + 8000 0.43667749 -2.0567464 0.065334814 -1.5552799 4.2727683 + 9000 0.45682384 -2.0679034 0.060201786 -1.5514488 3.9267838 + 10000 0.45 -2.0518982 0.055746513 -1.5467142 4.0952215 + 11000 0.45708142 -2.0867219 0.069796539 -1.5604153 2.9408563 + 12000 0.45241478 -2.0660119 0.05984197 -1.5543207 3.1690286 + 13000 0.44107393 -2.0641661 0.05983938 -1.5638041 3.505816 + 14000 0.44110861 -2.097022 0.051901352 -1.6045634 3.1530067 + 15000 0.46350177 -2.0714176 0.060468155 -1.548027 3.1473645 + 16000 0.44655044 -2.1091366 0.063286789 -1.5998576 3.01513 + 17000 0.4669612 -2.0818303 0.06033586 -1.5551169 3.5882255 + 18000 0.46094826 -2.1157008 0.066505672 -1.5888231 2.3269852 + 19000 0.44560596 -2.0990576 0.065162589 -1.5888461 2.8984257 + 20000 0.44208903 -2.0909757 0.059515289 -1.589924 2.8119311 + 21000 0.45155589 -2.0997977 0.059798723 -1.5890075 2.8373688 + 22000 0.4454493 -2.1064356 0.057219664 -1.6043234 2.5646073 + 23000 0.44607005 -2.0965713 0.061416631 -1.5896422 2.4608998 + 24000 0.46538564 -2.1045166 0.05774363 -1.5819691 2.3150363 + 25000 0.45936625 -2.1067378 0.056323997 -1.5916218 2.048119 + 26000 0.44475849 -2.1039936 0.062084383 -1.5977067 2.6218634 + 27000 0.44698457 -2.0984145 0.055709014 -1.5962797 2.9317131 + 28000 0.43517932 -2.0913271 0.064117709 -1.5925741 2.8086074 + 29000 0.45647804 -2.1041742 0.062494065 -1.5857727 3.1137153 + 30000 0.46315669 -2.0956986 0.062535694 -1.5705852 2.7393652 + 31000 0.45 -2.1057734 0.06440468 -1.5919312 2.6231226 + 32000 0.45070852 -2.1035845 0.058447795 -1.5949916 2.4537766 + 33000 0.45666657 -2.1082739 0.062668872 -1.5895093 2.3000181 + 34000 0.45 -2.1016598 0.058047346 -1.594175 2.7045891 + 35000 0.45761633 -2.1166321 0.05661317 -1.6029746 2.4867114 + 36000 0.4472238 -2.1032503 0.058087856 -1.5984977 2.5708579 + 37000 0.45 -2.0862798 0.060216086 -1.5766262 3.0682877 + 38000 0.46457862 -2.111786 0.050899355 -1.5968888 2.3837735 + 39000 0.4461965 -2.0958328 0.065822692 -1.5843713 2.9356665 + 40000 0.44099466 -2.1082333 0.052068542 -1.6157214 2.7461117 + 41000 0.44708215 -2.1138114 0.061595428 -1.6056927 2.7512054 + 42000 0.45300055 -2.1160106 0.060484049 -1.6030923 2.1170549 + 43000 0.44584477 -2.1016681 0.065545873 -1.5908347 2.7168769 + 44000 0.44874855 -2.0962255 0.060190909 -1.587847 2.4701379 + 45000 0.43208001 -2.0985058 0.059429899 -1.607536 3.4135814 + 46000 0.43328324 -2.068705 0.062466255 -1.5734971 3.1729387 + 47000 0.46070055 -2.1056376 0.054706613 -1.5908063 2.4710329 + 48000 0.44818286 -2.1037138 0.060858877 -1.5952323 2.2822087 + 49000 0.43421688 -2.0920093 0.05524275 -1.6030924 2.9802749 + 50000 0.44919305 -2.118617 0.054774617 -1.6152108 2.1728215 + 51000 0.44744615 -2.1090016 0.059814306 -1.6023004 2.3189772 + 52000 0.45486735 -2.1082261 0.055067991 -1.5988594 2.2933516 + 53000 0.46483852 -2.1205596 0.059875293 -1.5964269 2.4109235 + 54000 0.43582273 -2.0939722 0.056892621 -1.6018017 2.9757336 + 55000 0.45654728 -2.1024753 0.062836674 -1.583662 2.3343503 + 56000 0.45942073 -2.0961849 0.053090528 -1.584248 2.8313158 + 57000 0.44650252 -2.092082 0.052991549 -1.5931461 3.0447824 + 58000 0.46418464 -2.1277093 0.060472378 -1.6036325 1.7271421 + 59000 0.45 -2.1304819 0.057808836 -1.6232356 1.6864115 + 60000 0.45599586 -2.1338576 0.053131762 -1.6253 2.201508 +Loop time of 81.32 on 1 procs for 60000 steps with 1200 atoms + +Pair time (%) = 56.0068 (68.8721) +Bond time (%) = 2.55027 (3.1361) +Neigh time (%) = 9.86523 (12.1314) +Comm time (%) = 2.19366 (2.69756) +Outpt time (%) = 0.727356 (0.894437) +Other time (%) = 9.97665 (12.2684) + +Nlocal: 1200 ave 1200 max 1200 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 396 ave 396 max 396 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 9650 ave 9650 max 9650 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 9650 +Ave neighs/atom = 8.04167 +Ave special neighs/atom = 0.5 +Neighbor list builds = 4890 +Dangerous builds = 0 diff --git a/examples/min/log.min.22Jun07.liberty.4 b/examples/min/log.min.22Jun07.liberty.4 new file mode 100644 index 0000000000..f3e3dca40d --- /dev/null +++ b/examples/min/log.min.22Jun07.liberty.4 @@ -0,0 +1,107 @@ +LAMMPS (22 June 2007) +# 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 + +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 = 1.44958 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 5 -2.6248859 0 2.3657391 10.863748 + 100 3.3056095 -0.90010417 0 2.3993073 34.161569 + 200 3.3179673 -0.91237776 0 2.3993683 33.885931 + 300 3.2898718 -0.88383768 0 2.3998656 34.100539 + 400 3.3040789 -0.8979868 0 2.3998969 33.870872 + 500 3.3858715 -0.98323293 0 2.39629 33.00502 + 600 3.3016075 -0.89577331 0 2.3996436 34.094211 + 700 3.3530103 -0.94642636 0 2.4002971 33.706321 + 800 3.2765339 -0.87171428 0 2.3986761 34.272397 + 900 3.4084164 -1.0031926 0 2.398833 32.606983 + 1000 3.3077995 -0.90272314 0 2.3988743 33.989676 +Loop time of 0.362762 on 4 procs for 1000 steps with 800 atoms + +Pair time (%) = 0.0987712 (27.2276) +Neigh time (%) = 0.0306859 (8.45897) +Comm time (%) = 0.164804 (45.4305) +Outpt time (%) = 0.0234722 (6.47043) +Other time (%) = 0.0450281 (12.4126) + +Nlocal: 200 ave 202 max 198 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +Nghost: 170.75 ave 175 max 167 min +Histogram: 1 0 0 1 0 1 0 0 0 1 +Neighs: 1943 ave 1984 max 1900 min +Histogram: 1 0 0 0 1 1 0 0 0 1 + +Total # of neighbors = 7772 +Ave neighs/atom = 9.715 +Neighbor list builds = 204 +Dangerous builds = 0 + +neigh_modify delay 0 every 1 check yes + +dump_modify 1 every 5 +thermo 5 +minimize 0.001 100 1000 +Memory usage per processor = 1.90765 Mbytes +Step Temp E_pair E_mol TotEng Press + 1000 3.3077995 -0.90272314 0 2.3988743 33.989676 + 1005 3.3077995 -2.4349846 0 0.86661284 12.143512 + 1010 3.3077995 -2.7077137 0 0.59388372 7.3653436 + 1015 3.3077995 -2.8095165 0 0.49208093 5.52331 + 1020 3.3077995 -2.8698628 0 0.43173457 4.5567353 + 1025 3.3077995 -2.9017222 0 0.3998752 4.1175547 + 1030 3.3077995 -2.9229662 0 0.37863118 3.8267031 + 1034 3.3077995 -2.9342146 0 0.36738284 3.7139314 +Loop time of 0.072973 on 4 procs for 34 steps with 800 atoms + +Minimization stats: + E initial, next-to-last, final = -0.902723 -2.93279 -2.93421 + Gradient 2-norm init/final= 1904.03 19.9961 + Gradient inf-norm init/final= 304.285 6.47018 + Iterations = 34 + Force evaluations = 140 + +Pair time (%) = 0.0167579 (22.9645) +Neigh time (%) = 0.00157726 (2.16143) +Comm time (%) = 0.0223088 (30.5713) +Outpt time (%) = 0.0142592 (19.5404) +Other time (%) = 0.0180699 (24.7624) + +Nlocal: 200 ave 202 max 198 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +Nghost: 171 ave 172 max 170 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 1828.5 ave 1839 max 1816 min +Histogram: 1 0 0 1 0 0 0 0 1 1 + +Total # of neighbors = 7314 +Ave neighs/atom = 9.1425 +Neighbor list builds = 10 +Dangerous builds = 0 diff --git a/examples/min/log.min.22Jun07.linux.1 b/examples/min/log.min.22Jun07.linux.1 new file mode 100644 index 0000000000..f044fb716c --- /dev/null +++ b/examples/min/log.min.22Jun07.linux.1 @@ -0,0 +1,107 @@ +LAMMPS (22 June 2007) +# 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 + +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 = 1.47247 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 5 -2.6248859 0 2.3657391 10.863748 + 100 3.3056095 -0.90010417 0 2.3993073 34.161569 + 200 3.3179673 -0.91237776 0 2.3993683 33.885931 + 300 3.2898718 -0.88383768 0 2.3998656 34.100539 + 400 3.3040789 -0.8979868 0 2.3998969 33.870872 + 500 3.3858715 -0.98323293 0 2.39629 33.00502 + 600 3.3016074 -0.89577327 0 2.3996436 34.094211 + 700 3.3530108 -0.94642681 0 2.4002971 33.706316 + 800 3.2765414 -0.87172188 0 2.398676 34.272332 + 900 3.4086632 -1.003472 0 2.3988 32.603903 + 1000 3.3011881 -0.89596181 0 2.3990365 34.054429 +Loop time of 1.1982 on 1 procs for 1000 steps with 800 atoms + +Pair time (%) = 0.771744 (64.4089) +Neigh time (%) = 0.216457 (18.0653) +Comm time (%) = 0.034888 (2.91171) +Outpt time (%) = 0.051374 (4.28762) +Other time (%) = 0.123732 (10.3265) + +Nlocal: 800 ave 800 max 800 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 314 ave 314 max 314 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 7777 ave 7777 max 7777 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 7777 +Ave neighs/atom = 9.72125 +Neighbor list builds = 204 +Dangerous builds = 0 + +neigh_modify delay 0 every 1 check yes + +dump_modify 1 every 5 +thermo 5 +minimize 0.001 100 1000 +Memory usage per processor = 1.96838 Mbytes +Step Temp E_pair E_mol TotEng Press + 1000 3.3011881 -0.89596181 0 2.3990365 34.054429 + 1005 3.3011881 -2.4401696 0 0.85482874 12.041862 + 1010 3.3011881 -2.7166328 0 0.5783655 7.1580172 + 1015 3.3011881 -2.8220746 0 0.47292374 5.2831538 + 1020 3.3011881 -2.8767531 0 0.41824521 4.4303385 + 1025 3.3011881 -2.9059245 0 0.3890739 4.0379055 + 1030 3.3011881 -2.9263769 0 0.36862144 3.7665159 + 1033 3.3011881 -2.9347626 0 0.3602357 3.6756741 +Loop time of 0.181051 on 1 procs for 33 steps with 800 atoms + +Minimization stats: + E initial, next-to-last, final = -0.895962 -2.93317 -2.93476 + Gradient 2-norm init/final= 1920.78 20.9248 + Gradient inf-norm init/final= 304.283 7.73109 + Iterations = 33 + Force evaluations = 134 + +Pair time (%) = 0.1206 (66.6111) +Neigh time (%) = 0.01161 (6.41256) +Comm time (%) = 0.003518 (1.9431) +Outpt time (%) = 0.025866 (14.2866) +Other time (%) = 0.019457 (10.7467) + +Nlocal: 800 ave 800 max 800 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 317 ave 317 max 317 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 7334 ave 7334 max 7334 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 7334 +Ave neighs/atom = 9.1675 +Neighbor list builds = 10 +Dangerous builds = 0 diff --git a/examples/nemd/log.nemd.22Jun07.liberty.4 b/examples/nemd/log.nemd.22Jun07.liberty.4 new file mode 100644 index 0000000000..29497ddcbc --- /dev/null +++ b/examples/nemd/log.nemd.22Jun07.liberty.4 @@ -0,0 +1,109 @@ +LAMMPS (22 June 2007) +# 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 = 1.55792 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 1.44 0 0 1.4265 0.52159515 291.72051 + 1000 1.0781851 0.3767373 0 1.4448145 3.341071 291.72051 + 2000 1.1353421 0.31826705 0 1.4429653 3.0572956 291.72051 + 3000 1.030567 0.33822461 0 1.35913 3.0754292 291.72051 + 4000 1.084434 0.22978281 0 1.3040503 2.9985039 291.72051 + 5000 1.0301138 0.29805878 0 1.3185153 2.9303247 291.72051 + 6000 1.0077497 0.25076216 0 1.2490642 2.6414909 291.72051 + 7000 0.94139392 0.25553029 0 1.1880986 2.5455354 291.72051 + 8000 0.99185449 0.20276353 0 1.1853194 2.3004842 291.72051 + 9000 0.98667899 0.19320088 0 1.1706297 2.3286929 291.72051 + 10000 0.8694539 0.30351063 0 1.1648134 2.8869823 291.72051 + 11000 0.91957626 0.26311283 0 1.1740681 2.482322 291.72051 + 12000 0.96816147 0.24842003 0 1.207505 2.5968204 291.72051 + 13000 0.99305932 0.27827402 0 1.2620234 2.6008086 291.72051 + 14000 0.96964013 0.32524077 0 1.2857905 2.7589889 291.72051 + 15000 1.0406234 0.27494524 0 1.3058128 2.9745583 291.72051 + 16000 1.0563876 0.30415531 0 1.3506393 2.9591999 291.72051 + 17000 1.1546609 0.26606543 0 1.4099014 2.6835151 291.72051 + 18000 1.1446667 0.23591973 0 1.3698552 2.5639461 291.72051 + 19000 1.0933319 0.32022608 0 1.403308 2.9400962 291.72051 + 20000 1.0496919 0.27302946 0 1.3128805 2.8111569 291.72051 + 21000 1.0045344 0.30920696 0 1.3043239 2.9781411 291.72051 + 22000 1.1738476 0.17013633 0 1.3329791 2.1044152 291.72051 + 23000 1.0772052 0.30975242 0 1.3768589 3.0931004 291.72051 + 24000 1.0736648 0.25699966 0 1.3205988 2.7170813 291.72051 + 25000 0.97012122 0.32820484 0 1.2892312 2.7960758 291.72051 + 26000 1.0135594 0.22519064 0 1.2292479 2.2619809 291.72051 + 27000 0.86643886 0.26495984 0 1.1232758 2.6357446 291.72051 + 28000 0.87485679 0.21153951 0 1.0781945 2.3944736 291.72051 + 29000 0.8794958 0.20903385 0 1.0802844 2.4996412 291.72051 + 30000 0.95021338 0.1785099 0 1.119815 2.1001022 291.72051 + 31000 0.89467667 0.30930983 0 1.1955989 2.7732651 291.72051 + 32000 0.9996451 0.27049753 0 1.260771 2.5230927 291.72051 + 33000 1.1456535 0.19262378 0 1.3275368 2.5191339 291.72051 + 34000 1.1172695 0.30009096 0 1.4068861 2.9083508 291.72051 + 35000 1.1782712 0.33658625 0 1.5038112 3.2710349 291.72051 + 36000 1.2175616 0.33888092 0 1.5450279 2.9095564 291.72051 + 37000 1.1251235 0.46373017 0 1.5783056 3.5548553 291.72051 + 38000 1.258536 0.33742417 0 1.5841613 2.9829523 291.72051 + 39000 1.1674319 0.35037031 0 1.5068575 3.4103837 291.72051 + 40000 1.1300951 0.30391857 0 1.4234191 2.9007945 291.72051 + 41000 1.0079916 0.33954008 0 1.3380817 2.7537688 291.72051 + 42000 0.98741084 0.28566374 0 1.2638176 2.7612619 291.72051 + 43000 0.97625215 0.22170786 0 1.1888077 2.4375962 291.72051 + 44000 0.93659924 0.23779606 0 1.1656147 2.4336161 291.72051 + 45000 0.95304289 0.25561996 0 1.1997281 2.6384297 291.72051 + 46000 1.0028816 0.2345278 0 1.2280074 2.0876811 291.72051 + 47000 0.93735189 0.28467325 0 1.2132375 2.7980605 291.72051 + 48000 0.94622747 0.24014997 0 1.1775066 2.307812 291.72051 + 49000 0.89706269 0.31167999 0 1.2003327 3.0336271 291.72051 + 50000 0.91583019 0.29328288 0 1.2005272 2.6667222 291.72051 +Loop time of 9.10519 on 4 procs for 50000 steps with 160 atoms + +Pair time (%) = 0.15942 (1.75087) +Neigh time (%) = 0.107759 (1.18349) +Comm time (%) = 5.86661 (64.4315) +Outpt time (%) = 0.052742 (0.579252) +Other time (%) = 2.91866 (32.0549) + +Nlocal: 40 ave 43 max 37 min +Histogram: 1 1 0 0 0 0 0 0 1 1 +Nghost: 36.75 ave 39 max 32 min +Histogram: 1 0 0 0 0 0 0 0 2 1 +Neighs: 86.75 ave 97 max 75 min +Histogram: 1 1 0 0 0 0 0 0 0 2 + +Total # of neighbors = 347 +Ave neighs/atom = 2.16875 +Neighbor list builds = 5065 +Dangerous builds = 0 diff --git a/examples/nemd/log.nemd.22Jun07.linux.1 b/examples/nemd/log.nemd.22Jun07.linux.1 new file mode 100644 index 0000000000..6afb053559 --- /dev/null +++ b/examples/nemd/log.nemd.22Jun07.linux.1 @@ -0,0 +1,109 @@ +LAMMPS (22 June 2007) +# 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 = 1.5625 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 1.44 0 0 1.4265 0.52159515 291.72051 + 1000 1.1192431 0.32152228 0 1.4302725 3.0849273 291.72051 + 2000 1.0722145 0.32792208 0 1.3900846 2.7359267 291.72051 + 3000 1.0803269 0.21497546 0 1.2851743 2.2834162 291.72051 + 4000 1.083557 0.23095583 0 1.3043545 2.5848777 291.72051 + 5000 1.0659096 0.23578138 0 1.2916981 2.7308093 291.72051 + 6000 0.97914922 0.28414151 0 1.2541112 2.8350724 291.72051 + 7000 0.94345331 0.24801991 0 1.1826283 2.2781061 291.72051 + 8000 0.91284482 0.21572014 0 1.120007 2.3373662 291.72051 + 9000 0.90773857 0.20179507 0 1.1010236 2.0423789 291.72051 + 10000 0.88145472 0.18125755 0 1.0544486 2.3362039 291.72051 + 11000 0.87571013 0.12262143 0 0.99012178 1.6880068 291.72051 + 12000 0.80074028 0.22956229 0 1.0227956 2.6468191 291.72051 + 13000 0.7825286 0.26841268 0 1.0436051 2.4945056 291.72051 + 14000 0.79211256 0.25282461 0 1.0375111 2.5466413 291.72051 + 15000 0.86932228 0.19819701 0 1.0593694 2.2687924 291.72051 + 16000 0.95832898 0.20737909 0 1.1567237 2.4392205 291.72051 + 17000 0.8874087 0.27245064 0 1.1515399 2.6651657 291.72051 + 18000 0.92215327 0.22555391 0 1.139062 2.3727549 291.72051 + 19000 0.93403801 0.28658997 0 1.2118714 2.6635906 291.72051 + 20000 1.0282451 0.28503838 0 1.3036437 2.8944077 291.72051 + 21000 1.1053745 0.30936149 0 1.4043731 3.050874 291.72051 + 22000 1.1681036 0.33179109 0 1.4889437 2.963996 291.72051 + 23000 1.0853893 0.39394314 0 1.4691569 3.1671499 291.72051 + 24000 1.1704699 0.35809955 0 1.5175963 2.8419242 291.72051 + 25000 1.1918317 0.37475072 0 1.5554089 3.0968822 291.72051 + 26000 1.168098 0.34965423 0 1.5068013 3.1272861 291.72051 + 27000 1.1354617 0.31857532 0 1.443392 3.0609084 291.72051 + 28000 1.1876004 0.23206863 0 1.4085352 2.7389154 291.72051 + 29000 1.079827 0.36142889 0 1.4311325 3.191018 291.72051 + 30000 1.0753913 0.33649265 0 1.4018022 3.0008887 291.72051 + 31000 1.0696975 0.24250732 0 1.3021764 2.5570239 291.72051 + 32000 0.98836403 0.27036659 0 1.2494647 2.6083143 291.72051 + 33000 0.88065423 0.36359233 0 1.2359904 3.1970968 291.72051 + 34000 0.98597162 0.25219858 0 1.2289267 2.498528 291.72051 + 35000 1.0112914 0.22672846 0 1.228539 2.493751 291.72051 + 36000 0.93127567 0.28243389 0 1.2049789 2.7373743 291.72051 + 37000 0.82187438 0.35141767 0 1.165587 3.1778458 291.72051 + 38000 0.9521639 0.25784465 0 1.201082 2.5899557 291.72051 + 39000 0.95037029 0.29516101 0 1.2366216 2.4676855 291.72051 + 40000 0.95260903 0.27577233 0 1.2194507 2.6339219 291.72051 + 41000 1.0486929 0.22025027 0 1.2591117 2.542758 291.72051 + 42000 1.0345116 0.25222001 0 1.2770331 2.4358793 291.72051 + 43000 0.98585285 0.26611246 0 1.2427229 2.5447851 291.72051 + 44000 0.97750213 0.28088531 0 1.2492234 2.7728279 291.72051 + 45000 0.89570157 0.3129666 0 1.200271 2.4704519 291.72051 + 46000 0.98786766 0.20874738 0 1.1873538 2.2601725 291.72051 + 47000 0.88635928 0.31043687 0 1.1884865 2.7900499 291.72051 + 48000 0.9178394 0.24146658 0 1.1507012 2.6352068 291.72051 + 49000 0.96622547 0.17283616 0 1.1300033 1.9782123 291.72051 + 50000 0.90751608 0.19739424 0 1.0964024 2.2519054 291.72051 +Loop time of 5.69224 on 1 procs for 50000 steps with 160 atoms + +Pair time (%) = 1.09039 (19.1556) +Neigh time (%) = 0.683712 (12.0113) +Comm time (%) = 0.57192 (10.0474) +Outpt time (%) = 0.09878 (1.73535) +Other time (%) = 3.24744 (57.0503) + +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: 348 ave 348 max 348 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 348 +Ave neighs/atom = 2.175 +Neighbor list builds = 5070 +Dangerous builds = 0 diff --git a/examples/obstacle/log.obstacle.22Jun07.liberty.4 b/examples/obstacle/log.obstacle.22Jun07.liberty.4 new file mode 100644 index 0000000000..a2dcb0161f --- /dev/null +++ b/examples/obstacle/log.obstacle.22Jun07.liberty.4 @@ -0,0 +1,134 @@ +LAMMPS (22 June 2007) +# 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 35 atoms, new total = 805 +region void2 sphere 20 7 0 3 +delete_atoms region void2 +Deleted 35 atoms, new total = 770 + +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 = 1.44234 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 1.0006918 0 0 0.68683847 0.48039951 733.92473 + 1000 1 -0.3603446 0 0.32601904 1.5725867 779.90508 + 2000 1 -0.42832732 0 0.25803632 1.3587382 813.11821 + 3000 1 -0.47232806 0 0.21403558 1.4341388 844.88084 + 4000 1 -0.52763648 0 0.15872716 1.5459739 875.13499 + 5000 1 -0.48314311 0 0.20322052 1.4357888 907.02154 + 6000 1 -0.472141 0 0.21422264 1.3030726 924.98416 + 7000 1 -0.44830722 0 0.23805641 1.2882909 928.95817 + 8000 1 -0.43371728 0 0.25264635 1.132775 927.35692 + 9000 1 -0.41463177 0 0.27173186 1.1209309 921.76003 + 10000 1 -0.38315652 0 0.30320712 1.0966664 922.24088 + 11000 1 -0.37156486 0 0.31479878 1.1423804 919.78903 + 12000 1 -0.3742195 0 0.31214414 1.0593775 928.05099 + 13000 1 -0.38124076 0 0.30512288 1.1256769 929.73097 + 14000 1 -0.38555026 0 0.30081337 1.0946739 933.53885 + 15000 1 -0.40703488 0 0.27932876 1.0764066 930.2934 + 16000 1 -0.3725232 0 0.31384044 1.0011147 931.1519 + 17000 1 -0.38470452 0 0.30165912 0.99838577 928.91833 + 18000 1 -0.40199729 0 0.28436634 1.0888096 932.68523 + 19000 1 -0.37259199 0 0.31377165 0.97032094 938.58622 + 20000 1 -0.44719826 0 0.23916537 1.0118322 936.68972 + 21000 1 -0.39518804 0 0.29117559 1.0584198 935.59526 + 22000 1 -0.36368989 0 0.32267374 1.0593392 935.25352 + 23000 1 -0.41084354 0 0.27552009 0.9952792 936.90123 + 24000 1 -0.39025763 0 0.29610601 1.014413 941.44567 + 25000 1 -0.36909647 0 0.31726717 0.9812463 940.90255 +Loop time of 4.74776 on 4 procs for 25000 steps with 770 atoms + +Pair time (%) = 0.368852 (7.76898) +Neigh time (%) = 0.124334 (2.6188) +Comm time (%) = 1.96391 (41.365) +Outpt time (%) = 0.360654 (7.59629) +Other time (%) = 1.93001 (40.6509) + +Nlocal: 192.5 ave 240 max 158 min +Histogram: 2 0 0 0 0 1 0 0 0 1 +Nghost: 42.5 ave 45 max 37 min +Histogram: 1 0 0 0 0 0 0 0 2 1 +Neighs: 401.25 ave 559 max 288 min +Histogram: 2 0 0 0 0 0 1 0 0 1 + +Total # of neighbors = 1605 +Ave neighs/atom = 2.08442 +Neighbor list builds = 1636 +Dangerous builds = 0 diff --git a/examples/obstacle/log.obstacle.22Jun07.linux.1 b/examples/obstacle/log.obstacle.22Jun07.linux.1 new file mode 100644 index 0000000000..79cae0716b --- /dev/null +++ b/examples/obstacle/log.obstacle.22Jun07.linux.1 @@ -0,0 +1,134 @@ +LAMMPS (22 June 2007) +# 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 35 atoms, new total = 805 +region void2 sphere 20 7 0 3 +delete_atoms region void2 +Deleted 35 atoms, new total = 770 + +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 = 1.4637 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 1.0087541 0 0 0.69237216 0.48426997 733.92473 + 1000 1 -0.37498059 0 0.31138304 1.5619007 780.16609 + 2000 1 -0.42018277 0 0.26618087 1.381975 813.7446 + 3000 1 -0.49158436 0 0.19477928 1.4950838 846.60042 + 4000 1 -0.50974647 0 0.17661717 1.6968335 877.90837 + 5000 1 -0.48739676 0 0.19896688 1.372862 906.72222 + 6000 1 -0.45489776 0 0.23146588 1.1850408 922.1588 + 7000 1 -0.44298261 0 0.24338103 1.2353271 922.55214 + 8000 1 -0.39106076 0 0.29530287 1.2129774 923.79013 + 9000 1 -0.36894699 0 0.31741665 1.1022787 925.88908 + 10000 1 -0.40366483 0 0.28269881 1.0425088 924.55991 + 11000 1 -0.37662826 0 0.30973537 1.0605386 924.15634 + 12000 1 -0.39748408 0 0.28887956 1.1069709 926.1591 + 13000 1 -0.40533845 0 0.28102518 1.0999422 931.71451 + 14000 1 -0.39364952 0 0.29271412 0.98434706 935.98322 + 15000 1 -0.38545757 0 0.30090607 1.0288972 936.10741 + 16000 1 -0.34970581 0 0.33665783 1.0686207 939.12879 + 17000 1 -0.35935376 0 0.32700987 0.96188021 939.41127 + 18000 1 -0.38218429 0 0.30417934 0.97219528 939.42804 + 19000 1 -0.35002145 0 0.33634218 0.96884865 941.93045 + 20000 1 -0.37936966 0 0.30699398 1.0604325 935.73258 + 21000 1 -0.3797544 0 0.30660924 1.0525308 936.59648 + 22000 1 -0.37015981 0 0.31620383 1.0908613 935.05927 + 23000 1 -0.39940438 0 0.28695925 1.0860163 932.28118 + 24000 1 -0.36738604 0 0.3189776 0.97212319 936.04359 + 25000 1 -0.36023241 0 0.32613123 1.0971047 938.21817 +Loop time of 9.91214 on 1 procs for 25000 steps with 770 atoms + +Pair time (%) = 3.48576 (35.1666) +Neigh time (%) = 0.841295 (8.48752) +Comm time (%) = 0.288146 (2.907) +Outpt time (%) = 0.994089 (10.029) +Other time (%) = 4.30285 (43.4099) + +Nlocal: 770 ave 770 max 770 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: 1637 ave 1637 max 1637 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 1637 +Ave neighs/atom = 2.12597 +Neighbor list builds = 1632 +Dangerous builds = 0 diff --git a/examples/peptide/log.peptide.22Jun07.liberty.4 b/examples/peptide/log.peptide.22Jun07.liberty.4 new file mode 100644 index 0000000000..48684ee46e --- /dev/null +++ b/examples/peptide/log.peptide.22Jun07.liberty.4 @@ -0,0 +1,155 @@ +LAMMPS (22 June 2007) +# 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 = 0.268725 + grid = 15 15 15 + RMS precision = 4.85953e-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 = 8.97394 Mbytes +---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- +TotEng = -5237.4579 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 = 26772.2794 E_long = -33907.9417 Press = -845.4771 +---------------- Step 50 ----- CPU = 1.0767 (sec) ---------------- +TotEng = -5247.5482 KinEng = 1132.4030 Temp = 281.4752 +PotEng = -6379.9511 E_bond = 12.2118 E_angle = 31.7365 +E_dihed = 18.8145 E_impro = 2.3612 E_vdwl = 658.1774 +E_coul = 26804.4624 E_long = -33907.7148 Press = -1331.7939 +SHAKE stats (type/ave/delta) on step 100 + 4 1.111 7.80748e-07 + 6 0.997 1.06201e-06 + 8 1.08 6.20434e-07 + 10 1.111 6.23399e-07 + 12 1.08 2.68045e-07 + 14 0.96 0 + 18 0.957201 5.38002e-06 + 31 104.52 0.000502303 +---------------- Step 100 ----- CPU = 2.1741 (sec) ---------------- +TotEng = -5257.9999 KinEng = 1078.0524 Temp = 267.9656 +PotEng = -6336.0523 E_bond = 14.4828 E_angle = 43.4429 +E_dihed = 15.2569 E_impro = 2.3160 E_vdwl = 708.3271 +E_coul = 26786.6988 E_long = -33906.5767 Press = -648.6634 +---------------- Step 150 ----- CPU = 3.3006 (sec) ---------------- +TotEng = -5287.2849 KinEng = 1098.6036 Temp = 273.0739 +PotEng = -6385.8885 E_bond = 17.4924 E_angle = 32.8594 +E_dihed = 15.1623 E_impro = 1.6522 E_vdwl = 736.9698 +E_coul = 26717.2709 E_long = -33907.2954 Press = -333.1851 +SHAKE stats (type/ave/delta) on step 200 + 4 1.111 2.18831e-07 + 6 0.997 1.50909e-07 + 8 1.08 6.58563e-08 + 10 1.111 5.56695e-07 + 12 1.08 1.99338e-07 + 14 0.96 0 + 18 0.957201 3.59689e-06 + 31 104.52 0.000388134 +---------------- Step 200 ----- CPU = 4.4047 (sec) ---------------- +TotEng = -5308.4508 KinEng = 1100.5108 Temp = 273.5480 +PotEng = -6408.9616 E_bond = 18.2713 E_angle = 33.3035 +E_dihed = 16.8154 E_impro = 2.6052 E_vdwl = 686.3209 +E_coul = 26736.1285 E_long = -33902.4064 Press = -1470.4571 +---------------- Step 250 ----- CPU = 5.5320 (sec) ---------------- +TotEng = -5294.1865 KinEng = 1071.1626 Temp = 266.2530 +PotEng = -6365.3492 E_bond = 14.2025 E_angle = 39.1972 +E_dihed = 19.4548 E_impro = 3.1389 E_vdwl = 753.6340 +E_coul = 26713.7586 E_long = -33908.7351 Press = -187.8153 +SHAKE stats (type/ave/delta) on step 300 + 4 1.111 3.78173e-06 + 6 0.997001 3.51761e-06 + 8 1.08 2.09202e-06 + 10 1.111 5.64179e-06 + 12 1.08 2.10252e-06 + 14 0.96 0 + 18 0.957202 7.62675e-06 + 31 104.52 0.00080599 +---------------- Step 300 ----- CPU = 6.6418 (sec) ---------------- +TotEng = -5251.4326 KinEng = 1123.4442 Temp = 279.2484 +PotEng = -6374.8768 E_bond = 14.2233 E_angle = 38.4644 +E_dihed = 18.1398 E_impro = 2.3706 E_vdwl = 715.6075 +E_coul = 26745.4484 E_long = -33909.1309 Press = -467.0013 +Loop time of 6.64219 on 4 procs for 300 steps with 2004 atoms + +Pair time (%) = 3.83138 (57.6825) +Bond time (%) = 0.0190526 (0.286843) +Kspce time (%) = 1.23672 (18.6191) +Neigh time (%) = 0.383302 (5.77072) +Comm time (%) = 0.699462 (10.5306) +Outpt time (%) = 0.0126947 (0.191122) +Other time (%) = 0.459581 (6.91913) + +FFT time (% of Kspce) = 0.217534 (17.5896) +FFT Gflps 3d 1d-only = 0.756267 3.92102 + +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 180559 max 170208 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/peptide/log.peptide.22Jun07.linux.1 b/examples/peptide/log.peptide.22Jun07.linux.1 new file mode 100644 index 0000000000..0f8e06d5e4 --- /dev/null +++ b/examples/peptide/log.peptide.22Jun07.linux.1 @@ -0,0 +1,155 @@ +LAMMPS (22 June 2007) +# 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 = 0.268725 + grid = 15 15 15 + RMS precision = 4.85953e-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 = 20.1003 Mbytes +---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- +TotEng = -5237.4579 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 = 26772.2794 E_long = -33907.9417 Press = -845.4771 +---------------- Step 50 ----- CPU = 7.7456 (sec) ---------------- +TotEng = -5247.5482 KinEng = 1132.4030 Temp = 281.4752 +PotEng = -6379.9511 E_bond = 12.2118 E_angle = 31.7365 +E_dihed = 18.8145 E_impro = 2.3612 E_vdwl = 658.1774 +E_coul = 26804.4624 E_long = -33907.7148 Press = -1331.7939 +SHAKE stats (type/ave/delta) on step 100 + 4 1.111 7.80748e-07 + 6 0.997 1.06201e-06 + 8 1.08 6.20434e-07 + 10 1.111 6.23399e-07 + 12 1.08 2.68045e-07 + 14 0.96 0 + 18 0.957201 5.38002e-06 + 31 104.52 0.000502303 +---------------- Step 100 ----- CPU = 15.4121 (sec) ---------------- +TotEng = -5257.9999 KinEng = 1078.0524 Temp = 267.9656 +PotEng = -6336.0523 E_bond = 14.4828 E_angle = 43.4429 +E_dihed = 15.2569 E_impro = 2.3160 E_vdwl = 708.3271 +E_coul = 26786.6988 E_long = -33906.5767 Press = -648.6634 +---------------- Step 150 ----- CPU = 23.2155 (sec) ---------------- +TotEng = -5287.2849 KinEng = 1098.6036 Temp = 273.0739 +PotEng = -6385.8885 E_bond = 17.4924 E_angle = 32.8594 +E_dihed = 15.1623 E_impro = 1.6522 E_vdwl = 736.9698 +E_coul = 26717.2709 E_long = -33907.2954 Press = -333.1851 +SHAKE stats (type/ave/delta) on step 200 + 4 1.111 2.18831e-07 + 6 0.997 1.50909e-07 + 8 1.08 6.58563e-08 + 10 1.111 5.56695e-07 + 12 1.08 1.99338e-07 + 14 0.96 0 + 18 0.957201 3.59689e-06 + 31 104.52 0.000388134 +---------------- Step 200 ----- CPU = 30.6635 (sec) ---------------- +TotEng = -5308.4508 KinEng = 1100.5108 Temp = 273.5480 +PotEng = -6408.9616 E_bond = 18.2713 E_angle = 33.3035 +E_dihed = 16.8154 E_impro = 2.6052 E_vdwl = 686.3209 +E_coul = 26736.1285 E_long = -33902.4064 Press = -1470.4571 +---------------- Step 250 ----- CPU = 38.4972 (sec) ---------------- +TotEng = -5294.1865 KinEng = 1071.1626 Temp = 266.2530 +PotEng = -6365.3492 E_bond = 14.2025 E_angle = 39.1972 +E_dihed = 19.4548 E_impro = 3.1389 E_vdwl = 753.6340 +E_coul = 26713.7586 E_long = -33908.7351 Press = -187.8153 +SHAKE stats (type/ave/delta) on step 300 + 4 1.111 3.78173e-06 + 6 0.997001 3.51761e-06 + 8 1.08 2.09202e-06 + 10 1.111 5.64179e-06 + 12 1.08 2.10252e-06 + 14 0.96 0 + 18 0.957202 7.62675e-06 + 31 104.52 0.00080599 +---------------- Step 300 ----- CPU = 46.2639 (sec) ---------------- +TotEng = -5251.4326 KinEng = 1123.4442 Temp = 279.2484 +PotEng = -6374.8768 E_bond = 14.2233 E_angle = 38.4644 +E_dihed = 18.1398 E_impro = 2.3706 E_vdwl = 715.6075 +E_coul = 26745.4484 E_long = -33909.1309 Press = -467.0013 +Loop time of 46.2643 on 1 procs for 300 steps with 2004 atoms + +Pair time (%) = 37.5374 (81.1369) +Bond time (%) = 0.079241 (0.171279) +Kspce time (%) = 3.3838 (7.31405) +Neigh time (%) = 4.46671 (9.65476) +Comm time (%) = 0.320268 (0.692257) +Outpt time (%) = 0.01816 (0.0392527) +Other time (%) = 0.458701 (0.991479) + +FFT time (% of Kspce) = 1.13484 (33.5375) +FFT Gflps 3d 1d-only = 0.144967 0.198071 + +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/pour/log.pour.22Jun07.liberty.4 b/examples/pour/log.pour.22Jun07.liberty.4 new file mode 100644 index 0000000000..9b55e0f6b7 --- /dev/null +++ b/examples/pour/log.pour.22Jun07.liberty.4 @@ -0,0 +1,136 @@ +LAMMPS (22 June 2007) +# 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 2 all gravity 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 +thermo 1000 +thermo_modify lost ignore +compute_modify thermo_temp dynamic yes + +dump id all atom 1000 dump.pour +run 25000 +Memory usage per processor = 0.335693 Mbytes +Step Atoms KinEng RotKEgrn 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 1418.8997 60.727536 6600 + 9000 1206 1258.0238 52.045974 6600 + 10000 1608 1387.2361 50.17452 6600 + 11000 1608 1226.8131 50.547962 6600 + 12000 1608 1195.97 41.951622 6600 + 13000 2010 1312.7197 51.888514 6600 + 14000 2010 1176.2242 43.086598 6600 + 15000 2010 972.7316 46.053358 6600 + 16000 2412 1040.0907 45.535472 6600 + 17000 2412 1033.3053 37.798831 6600 + 18000 2412 929.20314 37.574869 6600 + 19000 2814 1010.9926 38.716555 6600 + 20000 2814 953.49259 41.76949 6600 + 21000 2814 768.81045 45.76655 6600 + 22000 2814 501.98827 42.18076 6600 + 23000 3000 428.98535 35.914834 6600 + 24000 3000 365.81359 22.320118 6600 + 25000 3000 227.404 23.276402 6600 +Loop time of 12.9955 on 4 procs for 25000 steps with 3000 atoms + +Pair time (%) = 4.94591 (38.0586) +Neigh time (%) = 0.678777 (5.22316) +Comm time (%) = 3.9515 (30.4066) +Outpt time (%) = 0.122208 (0.940388) +Other time (%) = 3.29713 (25.3713) + +Nlocal: 750 ave 766 max 734 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +Nghost: 388.75 ave 395 max 386 min +Histogram: 1 2 0 0 0 0 0 0 0 1 +Neighs: 3588.5 ave 3661 max 3520 min +Histogram: 1 0 0 1 0 1 0 0 0 1 + +Total # of neighbors = 14354 +Ave neighs/atom = 4.78467 +Neighbor list builds = 1154 +Dangerous builds = 0 + +unfix ins +fix 2 all gravity chute 26.0 +run 25000 +Memory usage per processor = 6.82838 Mbytes +Step Atoms KinEng RotKEgrn Volume + 25000 3000 227.404 23.276402 6600 + 26000 3000 106.43826 18.101442 6600 + 27000 3000 113.05348 12.760864 6600 + 28000 3000 205.07328 11.584573 6600 + 29000 3000 358.43804 15.113582 6600 + 30000 3000 598.64933 20.578979 6600 + 31000 3000 873.5316 28.461109 6600 + 32000 3000 1170.5204 31.532882 6600 + 33000 3000 1527.4366 38.434515 6600 + 34000 3000 1984.9084 46.821444 6600 + 35000 3000 2510.0466 50.236977 6600 + 36000 3000 3115.8979 66.529363 6600 + 37000 3000 3828.8672 78.585843 6600 + 38000 3000 4614.202 90.003111 6600 + 39000 3000 5443.9784 97.5867 6600 + 40000 3000 6277.0696 109.40245 6600 + 41000 3000 7205.7543 116.90896 6600 + 42000 3000 8231.9822 123.54846 6600 + 43000 3000 9341.3262 139.91668 6600 + 44000 3000 10540.217 154.5832 6600 + 45000 3000 11634.026 163.89013 6600 + 46000 3000 12939.113 172.01293 6600 + 47000 3000 14117.982 183.04471 6600 + 48000 3000 15405.59 211.29982 6600 + 49000 3000 16780.191 197.48907 6600 + 50000 3000 18147.971 232.52213 6600 +Loop time of 23.7168 on 4 procs for 25000 steps with 3000 atoms + +Pair time (%) = 10.9603 (46.2134) +Neigh time (%) = 1.05963 (4.46785) +Comm time (%) = 5.99627 (25.2828) +Outpt time (%) = 0.196248 (0.827465) +Other time (%) = 5.5043 (23.2085) + +Nlocal: 750 ave 757 max 742 min +Histogram: 1 0 0 0 1 0 0 1 0 1 +Nghost: 401.5 ave 412 max 390 min +Histogram: 1 0 1 0 0 0 0 0 1 1 +Neighs: 3645.75 ave 3775 max 3584 min +Histogram: 1 2 0 0 0 0 0 0 0 1 + +Total # of neighbors = 14583 +Ave neighs/atom = 4.861 +Neighbor list builds = 825 +Dangerous builds = 0 diff --git a/examples/pour/log.pour.22Jun07.linux.1 b/examples/pour/log.pour.22Jun07.linux.1 new file mode 100644 index 0000000000..2173b67a66 --- /dev/null +++ b/examples/pour/log.pour.22Jun07.linux.1 @@ -0,0 +1,136 @@ +LAMMPS (22 June 2007) +# 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 2 all gravity 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 +thermo 1000 +thermo_modify lost ignore +compute_modify thermo_temp dynamic yes + +dump id all atom 1000 dump.pour +run 25000 +Memory usage per processor = 0.335693 Mbytes +Step Atoms KinEng RotKEgrn 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 1418.8901 57.72159 6600 + 9000 1206 1256.2845 48.910044 6600 + 10000 1608 1398.3246 51.447622 6600 + 11000 1608 1247.546 48.387594 6600 + 12000 1608 1182.5307 42.323247 6600 + 13000 2010 1308.4067 48.900862 6600 + 14000 2010 1184.2874 44.83509 6600 + 15000 2010 1005.943 39.943887 6600 + 16000 2412 1031.9872 47.786837 6600 + 17000 2412 1032.5851 40.540687 6600 + 18000 2412 919.78138 36.200329 6600 + 19000 2814 1017.0854 35.573349 6600 + 20000 2814 964.17268 41.63371 6600 + 21000 2814 748.30864 44.884418 6600 + 22000 2814 531.66082 40.886555 6600 + 23000 3000 415.96265 35.009259 6600 + 24000 3000 363.92132 18.910655 6600 + 25000 3000 223.50386 24.163325 6600 +Loop time of 75.6189 on 1 procs for 25000 steps with 3000 atoms + +Pair time (%) = 40.9621 (54.1691) +Neigh time (%) = 4.96025 (6.55953) +Comm time (%) = 2.47589 (3.27417) +Outpt time (%) = 0.225462 (0.298155) +Other time (%) = 26.9953 (35.6991) + +Nlocal: 3000 ave 3000 max 3000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 675 ave 675 max 675 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 13637 ave 13637 max 13637 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 13637 +Ave neighs/atom = 4.54567 +Neighbor list builds = 1153 +Dangerous builds = 0 + +unfix ins +fix 2 all gravity chute 26.0 +run 25000 +Memory usage per processor = 7.24008 Mbytes +Step Atoms KinEng RotKEgrn Volume + 25000 3000 223.50386 24.163325 6600 + 26000 3000 116.7995 18.613728 6600 + 27000 3000 122.40388 11.057402 6600 + 28000 3000 231.29589 11.189183 6600 + 29000 3000 394.03717 14.367314 6600 + 30000 3000 647.20427 22.016262 6600 + 31000 3000 908.91364 28.607326 6600 + 32000 3000 1271.4653 30.481316 6600 + 33000 3000 1667.4275 41.693229 6600 + 34000 3000 2165.6715 50.388564 6600 + 35000 3000 2742.9875 52.867314 6600 + 36000 3000 3313.9686 64.802217 6600 + 37000 3000 4043.4311 73.963901 6600 + 38000 3000 4826.4345 82.469868 6600 + 39000 3000 5665.19 95.419726 6600 + 40000 3000 6555.0312 105.12519 6600 + 41000 3000 7541.9934 121.4346 6600 + 42000 3000 8632.6663 129.37799 6600 + 43000 3000 9666.568 132.68521 6600 + 44000 3000 10825.138 153.12413 6600 + 45000 3000 12010.686 165.13241 6600 + 46000 3000 13364.225 184.80686 6600 + 47000 3000 14694.757 196.08109 6600 + 48000 3000 16083.771 220.53678 6600 + 49000 3000 17548.113 228.11249 6600 + 50000 3000 19103.087 244.48465 6600 +Loop time of 155.24 on 1 procs for 25000 steps with 3000 atoms + +Pair time (%) = 93.0545 (59.9425) +Neigh time (%) = 7.81717 (5.03555) +Comm time (%) = 5.47774 (3.52857) +Outpt time (%) = 0.403527 (0.259938) +Other time (%) = 48.4867 (31.2335) + +Nlocal: 3000 ave 3000 max 3000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 766 ave 766 max 766 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 13994 ave 13994 max 13994 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 13994 +Ave neighs/atom = 4.66467 +Neighbor list builds = 833 +Dangerous builds = 0 diff --git a/examples/pour/log.pour.2d.22Jun07.liberty.4 b/examples/pour/log.pour.2d.22Jun07.liberty.4 new file mode 100644 index 0000000000..d2d33d60c5 --- /dev/null +++ b/examples/pour/log.pour.2d.22Jun07.liberty.4 @@ -0,0 +1,89 @@ +LAMMPS (22 June 2007) +# 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 spherical 90.0 -90.0 +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 = 0.335693 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 99.125785 5000 + 10000 896 2986.9988 88.590035 5000 + 11000 896 2829.9982 65.795595 5000 + 12000 896 2742.1752 65.335529 5000 + 13000 1000 2701.7207 61.182084 5000 + 14000 1000 2478.5724 53.465798 5000 + 15000 1000 2079.7846 63.176195 5000 + 16000 1000 1440.481 54.982049 5000 + 17000 1000 809.4817 47.009446 5000 + 18000 1000 588.67412 33.215005 5000 + 19000 1000 259.55248 27.403802 5000 + 20000 1000 39.743003 14.941136 5000 + 21000 1000 20.085002 8.8303457 5000 + 22000 1000 11.861124 6.1014125 5000 + 23000 1000 11.065631 3.3946532 5000 + 24000 1000 5.1323063 2.011498 5000 + 25000 1000 2.6809517 1.3185775 5000 +Loop time of 7.24504 on 4 procs for 25000 steps with 1000 atoms + +Pair time (%) = 1.30585 (18.024) +Neigh time (%) = 0.24281 (3.35139) +Comm time (%) = 1.61472 (22.2872) +Outpt time (%) = 0.187656 (2.59012) +Other time (%) = 3.89401 (53.7472) + +Nlocal: 250 ave 501 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 5.75 ave 13 max 0 min +Histogram: 2 0 0 0 0 0 0 1 0 1 +Neighs: 620 ave 1246 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 2480 +Ave neighs/atom = 2.48 +Neighbor list builds = 1606 +Dangerous builds = 0 diff --git a/examples/pour/log.pour.2d.22Jun07.linux.1 b/examples/pour/log.pour.2d.22Jun07.linux.1 new file mode 100644 index 0000000000..bc958460b2 --- /dev/null +++ b/examples/pour/log.pour.2d.22Jun07.linux.1 @@ -0,0 +1,89 @@ +LAMMPS (22 June 2007) +# 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 spherical 90.0 -90.0 +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 = 0.320435 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 99.125785 5000 + 10000 896 2986.9988 88.590036 5000 + 11000 896 2829.9925 65.792313 5000 + 12000 896 2742.7084 65.819834 5000 + 13000 1000 2708.5986 57.322444 5000 + 14000 1000 2465.496 61.169722 5000 + 15000 1000 2053.8397 61.691032 5000 + 16000 1000 1462.2958 51.138602 5000 + 17000 1000 829.85835 42.214656 5000 + 18000 1000 598.95282 32.11476 5000 + 19000 1000 246.95726 30.259864 5000 + 20000 1000 36.390829 15.37906 5000 + 21000 1000 16.970773 8.7787109 5000 + 22000 1000 11.318963 5.9319445 5000 + 23000 1000 5.8086775 3.5214371 5000 + 24000 1000 4.5594534 2.588639 5000 + 25000 1000 2.1765737 0.75876888 5000 +Loop time of 24.7627 on 1 procs for 25000 steps with 1000 atoms + +Pair time (%) = 9.848 (39.7695) +Neigh time (%) = 1.90215 (7.68151) +Comm time (%) = 0.123851 (0.500152) +Outpt time (%) = 0.407864 (1.64709) +Other time (%) = 12.4808 (50.4017) + +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: 2469 ave 2469 max 2469 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 2469 +Ave neighs/atom = 2.469 +Neighbor list builds = 1600 +Dangerous builds = 0 diff --git a/examples/rigid/log.rigid.22Jun07.liberty.4 b/examples/rigid/log.rigid.22Jun07.liberty.4 new file mode 100644 index 0000000000..eb6f35203c --- /dev/null +++ b/examples/rigid/log.rigid.22Jun07.liberty.4 @@ -0,0 +1,306 @@ +LAMMPS (22 June 2007) +# 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 = 1.41797 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 -7.9722842e-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 1.2554429 0 5269.4841 11.963561 + 3300 16732.156 1.9585967 0 5269.4893 12.234024 + 3350 16738.655 -0.079693236 0 5269.497 12.092757 + 3400 16738.543 -0.042215005 0 5269.4991 12.092809 + 3450 16738.591 -0.059327511 0 5269.4972 12.092536 + 3500 16738.759 -0.11761245 0 5269.4918 12.09203 + 3550 16713.405 7.8460621 0 5269.4737 12.389816 + 3600 16734.939 1.0821936 0 5269.4891 12.173591 + 3650 16738.808 -0.13663194 0 5269.4882 12.027009 + 3700 16738.602 -0.070934368 0 5269.4889 12.025288 + 3750 16737.731 0.20706558 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 -0.0002211587 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 -0.00039690664 0 5269.5189 12.011706 + 8500 16738.481 -0.0034646803 0 5269.5182 12.011643 + 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 + 8600 16738.474 -0.00076532812 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 -0.00037652437 0 5269.5216 12.011692 + 9550 16738.493 -0.0053156161 0 5269.5203 12.011611 + 9600 16738.549 -0.02681437 0 5269.5163 12.011415 + 9650 16738.765 -0.10191523 0 5269.5092 12.011013 + 9700 16735.041 1.058989 0 5269.4979 12.062708 + 9750 16738.013 0.1355011 0 5269.5101 11.407245 + 9800 16738.512 -0.011620328 0 5269.5201 11.394974 + 9850 16738.489 -0.00067270524 0 5269.5237 11.395098 + 9900 16738.489 -0.00024984559 0 5269.5242 11.395085 + 9950 16738.49 0 0 5269.5245 11.395076 + 10000 16738.49 0 0 5269.5246 11.395075 +Loop time of 1.84118 on 4 procs for 10000 steps with 81 atoms + +Pair time (%) = 0.0128225 (0.696429) +Neigh time (%) = 0.0221436 (1.20268) +Comm time (%) = 1.1992 (65.1324) +Outpt time (%) = 0.0962372 (5.22693) +Other time (%) = 0.510773 (27.7416) + +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.22Jun07.linux.1 b/examples/rigid/log.rigid.22Jun07.linux.1 new file mode 100644 index 0000000000..c8f3add517 --- /dev/null +++ b/examples/rigid/log.rigid.22Jun07.linux.1 @@ -0,0 +1,306 @@ +LAMMPS (22 June 2007) +# 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 = 1.50411 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 -7.9722836e-05 0 5269.5046 14.510657 + 2650 16733.017 1.7051479 0 5269.5067 14.596295 + 2700 16738.761 -0.10614946 0 5269.5038 14.499584 + 2750 16733.973 1.4038179 0 5269.5064 14.598107 + 2800 16738.585 -0.046813448 0 5269.5076 14.511073 + 2850 16738.487 -0.012558719 0 5269.5111 14.510111 + 2900 16738.465 -0.0026252725 0 5269.514 14.510277 + 2950 16738.476 -0.0082220764 0 5269.512 14.510223 + 3000 16738.66 -0.071284779 0 5269.507 14.509758 + 3050 16715.332 7.2419352 0 5269.476 14.870305 + 3100 16653.226 26.818761 0 5269.5009 14.496764 + 3150 16739.351 -0.30690375 0 5269.4886 13.643904 + 3200 16733.238 1.6025328 0 5269.4737 12.016934 + 3250 16734.374 1.2554429 0 5269.4841 11.963561 + 3300 16732.156 1.9585967 0 5269.4893 12.234024 + 3350 16738.655 -0.079693236 0 5269.497 12.092757 + 3400 16738.543 -0.042215005 0 5269.4991 12.092809 + 3450 16738.591 -0.059327511 0 5269.4972 12.092536 + 3500 16738.759 -0.11761245 0 5269.4918 12.09203 + 3550 16713.405 7.8460621 0 5269.4737 12.389816 + 3600 16734.939 1.0821936 0 5269.4891 12.173591 + 3650 16738.808 -0.13663194 0 5269.4882 12.027009 + 3700 16738.602 -0.070934368 0 5269.4889 12.025288 + 3750 16737.731 0.20706558 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 -0.0002211587 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 -0.00039690665 0 5269.5189 12.011706 + 8500 16738.481 -0.0034646803 0 5269.5182 12.011643 + 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 + 8600 16738.474 -0.00076532811 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 -0.00037652435 0 5269.5216 12.011692 + 9550 16738.493 -0.0053156161 0 5269.5203 12.011611 + 9600 16738.549 -0.026814369 0 5269.5163 12.011415 + 9650 16738.765 -0.10191523 0 5269.5092 12.011013 + 9700 16735.041 1.0589887 0 5269.4979 12.062708 + 9750 16738.013 0.1355012 0 5269.5101 11.407246 + 9800 16738.512 -0.011620328 0 5269.5201 11.394974 + 9850 16738.489 -0.00067270518 0 5269.5237 11.395098 + 9900 16738.489 -0.00024984554 0 5269.5242 11.395085 + 9950 16738.49 0 0 5269.5245 11.395076 + 10000 16738.49 0 0 5269.5246 11.395075 +Loop time of 0.92229 on 1 procs for 10000 steps with 81 atoms + +Pair time (%) = 0.079705 (8.64208) +Neigh time (%) = 0.123638 (13.4055) +Comm time (%) = 0.108608 (11.7759) +Outpt time (%) = 0.176786 (19.1682) +Other time (%) = 0.433553 (47.0083) + +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.poems.22Jun07.liberty.4 b/examples/rigid/log.rigid.poems.22Jun07.liberty.4 new file mode 100644 index 0000000000..9d9e853858 --- /dev/null +++ b/examples/rigid/log.rigid.poems.22Jun07.liberty.4 @@ -0,0 +1,306 @@ +LAMMPS (22 June 2007) +# 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 = 1.49443 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 217.7783 3430.3907 0 3466.6871 -2.7403788 + 50 13679.637 1404.2468 0 3684.1863 12.446066 + 100 16777.225 888.87665 0 3685.0808 -31.828677 + 150 19595.365 418.45042 0 3684.3446 40.709078 + 200 18524.188 596.47273 0 3683.8375 -0.8159371 + 250 21015.789 180.96521 0 3683.5967 -10.042469 + 300 20785.513 219.25314 0 3683.5053 2.6452719 + 350 21072.46 171.2554 0 3683.3321 7.0609024 + 400 19956.414 356.36381 0 3682.4328 19.320259 + 450 20724.42 227.73284 0 3681.8028 8.1259249 + 500 20152.578 322.71466 0 3681.4777 5.4929878 + 550 20017.022 345.29701 0 3681.4673 5.4661666 + 600 17897.743 698.72196 0 3681.6791 3.2854742 + 650 17297.758 796.60256 0 3679.5623 15.191113 + 700 18581.934 584.29715 0 3681.2861 5.1588289 + 750 21774.158 52.821062 0 3681.8474 -10.775664 + 800 21604.055 81.188546 0 3681.8644 -3.2045743 + 850 17821.483 711.53827 0 3681.7854 7.4384276 + 900 21033.292 175.98127 0 3681.5299 -16.345167 + 950 20968.166 186.59847 0 3681.2929 -2.330456 + 1000 20490.66 266.19375 0 3681.3037 11.787983 + 1050 20222.396 310.94072 0 3681.34 -8.3459539 + 1100 21321.687 127.61533 0 3681.2299 -1.2184718 + 1150 20849.582 206.01695 0 3680.9472 -0.86699164 + 1200 21815.003 45.317416 0 3681.1512 1.5988314 + 1250 18655.437 572.41453 0 3681.654 10.064076 + 1300 20780.781 217.36505 0 3680.8286 6.0538621 + 1350 20558.972 254.3648 0 3680.8601 -3.6773984 + 1400 21485.029 99.812952 0 3680.6511 -16.185471 + 1450 21771.108 52.159597 0 3680.6775 -2.4756679 + 1500 21520.948 93.503946 0 3680.3286 2.1023577 + 1550 21351.418 121.68139 0 3680.2511 5.5159972 + 1600 20778.805 216.92173 0 3680.0559 15.089183 + 1650 21477.639 100.21821 0 3679.8247 -1.1045931 + 1700 18501.343 596.4785 0 3680.0357 -15.679631 + 1750 18563.643 587.3477 0 3681.2882 33.53217 + 1800 19110.189 494.82277 0 3679.8543 18.024037 + 1850 21364.196 119.23462 0 3679.9339 2.529149 + 1900 20146.64 322.14631 0 3679.9197 5.7311673 + 1950 20692.671 231.25338 0 3680.0319 4.2977687 + 2000 20943.903 189.11238 0 3679.7629 -22.645639 + 2050 19668.148 401.81475 0 3679.8394 3.6256063 + 2100 20280.572 299.73979 0 3679.8351 7.4809366 + 2150 19182.127 483.47805 0 3680.4992 22.615355 + 2200 21299.767 130.77158 0 3680.7327 4.7114063 + 2250 20487.762 266.50325 0 3681.1302 -8.6408345 + 2300 18655.048 571.92772 0 3681.1023 -5.266975 + 2350 21512.632 95.763771 0 3681.2025 -9.3526622 + 2400 21467.744 103.31997 0 3681.2773 -29.599491 + 2450 20097.033 332.78544 0 3682.291 35.886632 + 2500 20761.514 222.1498 0 3682.4021 -12.52654 + 2550 20410.179 280.57555 0 3682.272 -22.280218 + 2600 21469.95 103.95758 0 3682.2826 -10.039024 + 2650 20711.858 230.38535 0 3682.3616 5.3554349 + 2700 18584.052 585.19766 0 3682.5397 21.807604 + 2750 20511.368 263.53176 0 3682.0931 -4.7085799 + 2800 20592.991 249.9677 0 3682.1328 -6.5329985 + 2850 17078.939 835.43473 0 3681.9245 16.780854 + 2900 19704.624 397.94471 0 3682.0488 -0.87435077 + 2950 19282.968 468.43149 0 3682.2595 7.0271622 + 3000 20552.037 256.84085 0 3682.1804 -2.9282943 + 3050 20934.711 193.08576 0 3682.2043 3.8942358 + 3100 21703.768 64.8113 0 3682.106 0.063237279 + 3150 18722.82 561.7019 0 3682.172 -1.4520091 + 3200 18284.044 634.53317 0 3681.8739 6.3415584 + 3250 21255.255 139.48628 0 3682.0288 2.6455564 + 3300 20558.956 255.77083 0 3682.2636 -3.9152408 + 3350 20373.309 286.62048 0 3682.1719 4.5400971 + 3400 20618.175 245.81811 0 3682.1806 5.7100283 + 3450 19473.455 436.70128 0 3682.2771 11.870427 + 3500 18903.565 531.91776 0 3682.5119 -9.3476901 + 3550 21030.252 177.18619 0 3682.2282 -14.260278 + 3600 19942.611 357.98433 0 3681.7528 11.183792 + 3650 20388.541 283.86156 0 3681.9518 -8.2736257 + 3700 20724.985 226.58383 0 3680.748 -13.429981 + 3750 21586.121 84.456333 0 3682.1432 -2.7515188 + 3800 21478.159 102.70951 0 3682.4027 -2.5874121 + 3850 18107.437 665.11995 0 3683.0262 11.062091 + 3900 19602.682 415.48105 0 3682.5947 17.867347 + 3950 19208.319 480.73213 0 3682.1186 0.55405471 + 4000 20700.944 232.01332 0 3682.1706 4.2790356 + 4050 18241.028 641.65227 0 3681.8236 14.819974 + 4100 16330.098 961.03753 0 3682.7206 -8.1781858 + 4150 20507.949 263.34806 0 3681.3396 -5.2032219 + 4200 21620.592 79.051795 0 3682.4838 -11.796063 + 4250 20841.315 209.02052 0 3682.573 -5.781042 + 4300 21378.616 119.44038 0 3682.5431 -3.0055326 + 4350 21391.4 116.89963 0 3682.133 1.2620601 + 4400 20092.07 333.32793 0 3682.0062 11.429014 + 4450 19315.512 461.83055 0 3681.0825 1.3462703 + 4500 20839.628 208.21416 0 3681.4855 4.709479 + 4550 14522.388 1263.1063 0 3683.5043 -20.816537 + 4600 21284.581 134.21556 0 3681.6457 -4.8183612 + 4650 20126.198 327.1439 0 3681.5103 -5.5395838 + 4700 21764.236 54.44036 0 3681.813 3.4863656 + 4750 21095.836 165.90339 0 3681.876 6.1541649 + 4800 20619.747 245.94729 0 3682.5718 2.5595916 + 4850 20763.177 222.12286 0 3682.6523 -8.6266804 + 4900 20537.14 259.67462 0 3682.5313 -15.421035 + 4950 21422.584 112.253 0 3682.6837 -1.4727022 + 5000 16257.411 972.68578 0 3682.2542 2.3147962 + 5050 19857.171 373.56369 0 3683.0922 -15.300375 + 5100 15635.264 1076.6903 0 3682.5676 36.8946 + 5150 21553.911 90.645813 0 3682.9642 1.5400926 + 5200 21559.956 89.704166 0 3683.0302 2.0981184 + 5250 19117.968 496.85067 0 3683.1787 29.282193 + 5300 21330.342 127.91971 0 3682.9767 2.4699055 + 5350 21829.625 44.595903 0 3682.8667 -11.606558 + 5400 21789.041 51.183465 0 3682.6902 -3.8674971 + 5450 19143.18 491.7975 0 3682.3275 -0.6880826 + 5500 19773.011 386.55132 0 3682.0532 -0.39276859 + 5550 21170.746 153.72971 0 3682.1873 -0.039885143 + 5600 20634.546 243.05851 0 3682.1496 -10.510731 + 5650 18940.14 525.80138 0 3682.4913 -8.4026702 + 5700 18137.059 658.45807 0 3681.3012 1.8086854 + 5750 18402.492 614.81681 0 3681.8988 18.121726 + 5800 15725.316 1060.3153 0 3681.2013 32.3919 + 5850 21350.969 122.71085 0 3681.2057 1.6244497 + 5900 20596.373 248.09794 0 3680.8268 -10.287271 + 5950 19586.195 416.65918 0 3681.0251 7.1327258 + 6000 20566.394 252.63425 0 3680.3666 9.3309712 + 6050 18063.299 667.31886 0 3677.8687 -10.246241 + 6100 17305.121 797.2545 0 3681.4414 14.554146 + 6150 19696.433 395.50284 0 3678.2416 4.1990406 + 6200 20908.19 195.69314 0 3680.3915 -9.0297611 + 6250 20767.885 219.35847 0 3680.6727 -5.4239147 + 6300 20271.076 302.48547 0 3680.9981 7.5881011 + 6350 21510.748 96.348849 0 3681.4736 -0.28663642 + 6400 21731.982 60.504382 0 3682.5014 -3.5673143 + 6450 19495.709 434.28569 0 3683.5706 4.7979099 + 6500 18668.623 571.92754 0 3683.3647 1.5185672 + 6550 16004.711 1016.2903 0 3683.7422 8.1972253 + 6600 20629.015 244.44595 0 3682.615 3.8351386 + 6650 21647.055 75.493996 0 3683.3365 -0.10989704 + 6700 19793.226 384.41402 0 3683.2851 7.7597696 + 6750 20441.55 275.94512 0 3682.8702 3.6110747 + 6800 21623.66 79.350309 0 3683.2936 -6.3458991 + 6850 21644.786 75.922535 0 3683.3869 -22.166786 + 6900 18150.965 657.76117 0 3682.9219 -14.903565 + 6950 21192.162 150.83369 0 3682.8607 -7.6579085 + 7000 20481.657 268.91866 0 3682.5281 -10.728925 + 7050 19265.165 471.58584 0 3682.4467 -3.1547895 + 7100 20241.165 308.92052 0 3682.4479 10.770847 + 7150 20883.514 201.92495 0 3682.5106 12.276271 + 7200 20675.066 236.51208 0 3682.3564 4.0653811 + 7250 21464.099 105.01329 0 3682.3631 -4.2891409 + 7300 19279.539 469.63353 0 3682.89 19.415276 + 7350 20266.489 304.68631 0 3682.4344 -0.15439874 + 7400 18978.717 519.39579 0 3682.5153 19.185958 + 7450 20816.852 213.20924 0 3682.6845 18.435432 + 7500 20655.662 240.16805 0 3682.7785 -4.4996568 + 7550 19061.292 506.0418 0 3682.9238 -1.7545473 + 7600 20564.235 255.25251 0 3682.625 -5.3903401 + 7650 21273.693 137.41485 0 3683.0303 -6.9034645 + 7700 20999.106 183.2458 0 3683.0968 -5.9941062 + 7750 18886.194 534.2212 0 3681.9202 5.9891004 + 7800 20327.925 294.85306 0 3682.8405 -2.5902629 + 7850 19533.408 427.77688 0 3683.3448 -4.9977086 + 7900 20973.609 187.37509 0 3682.9765 0.11759117 + 7950 18164.635 654.02996 0 3681.4691 16.402128 + 8000 20938.276 193.48738 0 3683.2 -5.9311301 + 8050 20819.498 213.21616 0 3683.1324 1.3392987 + 8100 19553.561 424.27379 0 3683.2006 -2.5040641 + 8150 17524.659 759.26187 0 3680.0384 -37.279253 + 8200 21104.916 165.88837 0 3683.3744 -3.8952964 + 8250 19614.453 414.27984 0 3683.3553 -2.9352541 + 8300 13365.081 1457.0212 0 3684.5347 100.4608 + 8350 20920.925 197.0494 0 3683.8702 -11.661629 + 8400 19724.857 396.41163 0 3683.8878 0.74045509 + 8450 21751.144 58.967512 0 3684.1583 -4.095218 + 8500 21283.998 136.40954 0 3683.7425 -5.4781843 + 8550 19255.08 474.01022 0 3683.1903 0.61248835 + 8600 20786.099 219.06078 0 3683.4107 9.7864578 + 8650 20801.493 216.74923 0 3683.6647 7.1280503 + 8700 19893.433 368.11056 0 3683.6827 -9.5312543 + 8750 21072.739 171.47966 0 3683.6028 -17.222136 + 8800 18791.068 551.89466 0 3683.7394 -13.425301 + 8850 20323.723 296.58355 0 3683.8708 1.2544121 + 8900 19160.522 487.13728 0 3680.5575 7.5449432 + 8950 20247.9 309.46468 0 3684.1146 -11.397923 + 9000 20721.089 230.36979 0 3683.8846 11.354348 + 9050 21798.873 51.104409 0 3684.25 -9.645863 + 9100 21093.423 168.78605 0 3684.3565 -1.2127948 + 9150 20954.177 191.65626 0 3684.0191 0.61911701 + 9200 17054.376 842.546 0 3684.942 41.714389 + 9250 19253.515 475.58375 0 3684.5029 13.186069 + 9300 21681.124 71.036838 0 3684.5575 -4.139581 + 9350 21796.739 51.725799 0 3684.5157 -8.5902286 + 9400 21631.679 79.362722 0 3684.6425 -8.7541514 + 9450 18537.758 595.38459 0 3685.011 -6.2719267 + 9500 17152.352 824.77642 0 3683.5018 46.593524 + 9550 20928.938 196.82808 0 3684.9843 -1.5521829 + 9600 15991.62 1020.98 0 3686.25 -3.8314742 + 9650 19629.68 414.15513 0 3685.7685 32.867017 + 9700 20900.569 201.75492 0 3685.183 6.1694301 + 9750 17072.588 841.426 0 3686.8573 -4.0468499 + 9800 21939.049 29.032402 0 3685.5406 -9.1896877 + 9850 21261.674 141.7745 0 3685.3869 -13.02325 + 9900 19393.195 452.88226 0 3685.0814 1.4304574 + 9950 17226.824 814.05288 0 3685.1902 19.353254 + 10000 20630.15 245.97222 0 3684.3306 0.61583151 +Loop time of 16.3618 on 4 procs for 10000 steps with 81 atoms + +Pair time (%) = 0.125099 (0.764576) +Neigh time (%) = 0.0542815 (0.331757) +Comm time (%) = 1.68193 (10.2796) +Outpt time (%) = 0.102797 (0.628274) +Other time (%) = 14.3977 (87.9958) + +Nlocal: 20.25 ave 74 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 +Nghost: 42 ave 90 max 0 min +Histogram: 2 0 0 0 0 0 0 0 1 1 +Neighs: 211.25 ave 769 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 845 +Ave neighs/atom = 10.4321 +Neighbor list builds = 991 +Dangerous builds = 929 diff --git a/examples/rigid/log.rigid.poems.22Jun07.linux.1 b/examples/rigid/log.rigid.poems.22Jun07.linux.1 new file mode 100644 index 0000000000..75408c263e --- /dev/null +++ b/examples/rigid/log.rigid.poems.22Jun07.linux.1 @@ -0,0 +1,306 @@ +LAMMPS (22 June 2007) +# 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 = 1.58102 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 -0.86699156 + 1200 21815.003 45.317415 0 3681.1512 1.5988314 + 1250 18655.437 572.41453 0 3681.654 10.064077 + 1300 20780.781 217.36506 0 3680.8286 6.053862 + 1350 20558.972 254.36481 0 3680.8601 -3.6773966 + 1400 21485.029 99.812935 0 3680.6511 -16.185472 + 1450 21771.107 52.159605 0 3680.6775 -2.4756675 + 1500 21520.948 93.503934 0 3680.3286 2.1023577 + 1550 21351.418 121.68138 0 3680.2511 5.5159957 + 1600 20778.805 216.92176 0 3680.0559 15.089186 + 1650 21477.638 100.2183 0 3679.8247 -1.1045812 + 1700 18501.341 596.47889 0 3680.0357 -15.67966 + 1750 18563.642 587.34786 0 3681.2882 33.532195 + 1800 19110.187 494.82315 0 3679.8543 18.024044 + 1850 21364.193 119.2351 0 3679.9339 2.5291255 + 1900 20146.632 322.14766 0 3679.9197 5.7312569 + 1950 20692.671 231.25335 0 3680.0319 4.2977718 + 2000 20943.904 189.1123 0 3679.7629 -22.645328 + 2050 19668.094 401.82367 0 3679.8394 3.625351 + 2100 20280.495 299.75279 0 3679.8352 7.4808501 + 2150 19181.964 483.50484 0 3680.4989 22.618437 + 2200 21300.002 130.73207 0 3680.7324 4.7107204 + 2250 20487.278 266.58364 0 3681.13 -8.6436788 + 2300 18653.922 572.11506 0 3681.102 -5.2650803 + 2350 21513.162 95.675284 0 3681.2022 -9.358275 + 2400 21466.87 103.46516 0 3681.2768 -29.576898 + 2450 20098.852 332.48096 0 3682.2896 35.802574 + 2500 20763.224 221.86356 0 3682.401 -12.492465 + 2550 20425.308 278.04709 0 3682.265 -22.360414 + 2600 21467.742 104.32441 0 3682.2815 -10.062558 + 2650 20774.17 220.00066 0 3682.3623 5.2193436 + 2700 18569.233 587.73881 0 3682.6109 22.145192 + 2750 20654.466 239.78519 0 3682.1961 -6.9106068 + 2800 20814.792 213.06343 0 3682.1954 -6.9316614 + 2850 16353.471 956.9648 0 3682.5433 34.229058 + 2900 19519.089 429.00752 0 3682.189 8.7072031 + 2950 20171.665 320.18684 0 3682.1309 2.7223515 + 3000 20470.108 270.26106 0 3681.9457 -8.2674499 + 3050 20359.511 288.83368 0 3682.0856 -4.69092 + 3100 19856.099 372.69336 0 3682.0432 9.3653131 + 3150 20561.401 254.89391 0 3681.794 6.7807193 + 3200 18974.717 519.59328 0 3682.0462 14.028207 + 3250 17201.03 816.05668 0 3682.895 30.827229 + 3300 21032.748 176.57229 0 3682.0304 -8.8776478 + 3350 17299.203 798.82174 0 3682.0222 -6.5474977 + 3400 16871.128 870.67484 0 3682.5295 -23.235008 + 3450 19319.303 462.06051 0 3681.9443 -11.811901 + 3500 17860.126 705.48294 0 3682.1705 -15.992033 + 3550 21874.357 36.186306 0 3681.9124 -2.4098493 + 3600 21393.595 116.22067 0 3681.8199 -10.262929 + 3650 20544.718 257.71089 0 3681.8306 0.55484185 + 3700 20330.417 293.63761 0 3682.0404 16.661746 + 3750 21244.461 141.09081 0 3681.8343 4.9615754 + 3800 19958.592 355.64853 0 3682.0806 13.979713 + 3850 21497.423 98.927167 0 3681.8309 -6.621684 + 3900 21769.359 53.67612 0 3681.9026 -1.926207 + 3950 19975.772 352.52452 0 3681.8198 9.245817 + 4000 21113.483 163.03078 0 3681.9446 2.7569744 + 4050 19709.067 397.27579 0 3682.1202 -3.0811456 + 4100 21815.578 46.077634 0 3682.0073 -12.520188 + 4150 21642.428 74.997052 0 3682.0685 -1.1460009 + 4200 19928.01 360.19492 0 3681.53 8.857095 + 4250 17863.117 703.82283 0 3681.009 33.346649 + 4300 20382.848 284.9686 0 3682.1099 -7.0563493 + 4350 21589.546 83.691599 0 3681.9492 -6.3466935 + 4400 21561.341 88.259907 0 3681.8167 -0.05858595 + 4450 19016.303 512.39829 0 3681.7821 43.125503 + 4500 20065.798 337.40858 0 3681.7083 1.7677159 + 4550 19263.771 471.03594 0 3681.6644 -23.462523 + 4600 20845.688 207.74162 0 3682.023 0.16598388 + 4650 19646.643 407.84353 0 3682.2841 11.884842 + 4700 20692.329 233.43094 0 3682.1524 -14.265029 + 4750 17999.182 682.2895 0 3682.1531 -25.09426 + 4800 20585.117 251.43776 0 3682.2906 10.111397 + 4850 19368.488 453.98051 0 3682.0618 6.199069 + 4900 20416.868 279.66263 0 3682.474 7.5050136 + 4950 21376.045 119.55597 0 3682.2302 -9.6343892 + 5000 21346.337 124.42913 0 3682.1519 -3.6930357 + 5050 19787.72 384.70087 0 3682.6542 -5.855159 + 5100 20440.061 275.27592 0 3681.9528 1.7528745 + 5150 15625.189 1079.1543 0 3683.3525 19.539205 + 5200 20308.779 297.80498 0 3682.6014 8.9223119 + 5250 21044.849 175.43646 0 3682.9113 5.2785373 + 5300 20543.584 258.744 0 3682.6747 1.2007699 + 5350 21171.39 154.69163 0 3683.2566 -12.896011 + 5400 19626.405 409.45045 0 3680.518 16.150799 + 5450 20550.071 258.26489 0 3683.2766 -21.262685 + 5500 19104.84 499.01387 0 3683.1539 11.949545 + 5550 19559.267 422.41448 0 3682.2923 3.8829356 + 5600 20044.332 342.61709 0 3683.3391 -1.7700503 + 5650 21953.27 25.016694 0 3683.8951 -22.754979 + 5700 21639.986 77.352619 0 3684.017 -15.578393 + 5750 21144.414 159.81932 0 3683.8884 -9.0956708 + 5800 19267.59 472.68582 0 3683.9509 12.517057 + 5850 21221.184 146.53726 0 3683.4012 -0.35975116 + 5900 21141.226 159.83342 0 3683.371 0.79471018 + 5950 20417.806 280.84037 0 3683.808 -4.380384 + 6000 15946.467 1025.7528 0 3683.4973 -2.9233738 + 6050 20307.785 299.10545 0 3683.7362 -7.6865743 + 6100 18110.389 663.98174 0 3682.3799 4.1591862 + 6150 19958.364 357.9562 0 3684.3502 0.64161306 + 6200 18283.091 637.04273 0 3684.2246 1.3409324 + 6250 17081.956 837.9693 0 3684.962 -6.7113704 + 6300 21382.883 120.98513 0 3684.7989 -13.987822 + 6350 19952.702 359.01391 0 3684.4642 6.3550454 + 6400 20832.557 212.50673 0 3684.5995 -1.5787609 + 6450 18646.002 577.10671 0 3684.7738 7.7299342 + 6500 18261.033 641.30218 0 3684.8076 17.386854 + 6550 18426.877 613.53329 0 3684.6794 -3.3462219 + 6600 20349.993 293.18762 0 3684.8531 -12.422327 + 6650 21112.2 166.06059 0 3684.7606 -6.7451773 + 6700 20046.245 343.52129 0 3684.5621 -4.0057021 + 6750 20834.1 212.52233 0 3684.8724 -1.5556583 + 6800 21150.619 159.68754 0 3684.7908 -1.5850612 + 6850 20008.249 350.12255 0 3684.8308 6.4872768 + 6900 18654.888 575.51473 0 3684.6627 -17.992304 + 6950 19708.289 400.17932 0 3684.8942 7.0106327 + 7000 20437.426 278.17876 0 3684.4164 6.2019137 + 7050 19604.082 416.96446 0 3684.3114 -3.924055 + 7100 18301.87 633.03111 0 3683.3428 19.029745 + 7150 18558.782 591.49191 0 3684.6222 25.690348 + 7200 16746.788 894.4891 0 3685.6204 9.3897347 + 7250 19956.035 358.65844 0 3684.6642 2.9307876 + 7300 21612.74 82.596669 0 3684.7199 -6.0761772 + 7350 21082.361 170.97104 0 3684.6979 -1.6531911 + 7400 21447.623 110.03038 0 3684.6342 -9.6680921 + 7450 21815.262 48.645261 0 3684.5222 -2.4194461 + 7500 21586.807 86.513539 0 3684.3147 0.80475725 + 7550 21432.021 112.08344 0 3684.087 3.7213279 + 7600 18765.76 557.30844 0 3684.9351 25.566982 + 7650 19237.591 477.51887 0 3683.784 -0.93181342 + 7700 20058.61 340.75274 0 3683.8544 4.1984966 + 7750 21689.282 69.4903 0 3684.3707 -8.0484797 + 7800 21149.046 159.71259 0 3684.5537 7.1881243 + 7850 19334.412 461.23349 0 3683.6355 14.066324 + 7900 21263.983 140.83705 0 3684.8343 -14.739146 + 7950 20871.691 206.2356 0 3684.8508 -11.575259 + 8000 18916.496 531.93786 0 3684.6872 -20.395653 + 8050 20703.238 233.97858 0 3684.5183 4.2191304 + 8100 19544.399 426.74441 0 3684.1442 15.563275 + 8150 17578.916 755.02603 0 3684.8454 23.23474 + 8200 18121.828 663.35414 0 3683.6588 -23.277149 + 8250 19000.859 515.63274 0 3682.4425 8.1499185 + 8300 16312.856 965.20527 0 3684.0147 69.340264 + 8350 17908.285 699.50533 0 3684.2195 -13.64631 + 8400 19971.59 355.22033 0 3683.8187 6.2163041 + 8450 13617.129 1415.4014 0 3684.9229 -9.1829017 + 8500 20374.985 288.34097 0 3684.1719 1.0194401 + 8550 21452.212 108.96717 0 3684.3359 -8.0882838 + 8600 17196.613 818.7652 0 3684.8674 -2.1874477 + 8650 21510.389 99.326067 0 3684.3909 -3.5449392 + 8700 21446.623 109.76972 0 3684.2068 -0.76115037 + 8750 20700.162 234.50311 0 3684.5301 2.0551713 + 8800 21686.769 69.759974 0 3684.2215 -3.6322891 + 8850 20892.916 201.69594 0 3683.8486 0.57163157 + 8900 18095.714 668.44418 0 3684.3965 19.055292 + 8950 21325.044 129.56368 0 3683.7377 2.2916549 + 9000 20739.771 227.15562 0 3683.7842 -6.4759144 + 9050 20683.885 235.94003 0 3683.2543 1.8163478 + 9100 21432.386 111.08386 0 3683.1483 -9.5573949 + 9150 21686.43 69.315468 0 3683.7205 2.1854565 + 9200 16916.728 864.20897 0 3683.6636 7.2632357 + 9250 20122.374 329.80422 0 3683.5332 6.2589988 + 9300 20621.693 246.58967 0 3683.5386 -20.210043 + 9350 20343.792 292.92921 0 3683.5612 0.47974589 + 9400 20334.062 294.47957 0 3683.4899 -5.5269222 + 9450 20971.669 188.26826 0 3683.5464 1.5825497 + 9500 20948.938 191.99574 0 3683.4855 1.7294775 + 9550 21557.149 90.697719 0 3683.5559 4.5248095 + 9600 21121.109 162.83027 0 3683.0151 -3.8673505 + 9650 21306.551 132.27859 0 3683.3704 -0.05028404 + 9700 21064.24 172.82072 0 3683.5273 1.7248916 + 9750 18962.129 523.71798 0 3684.0729 17.93568 + 9800 21192.894 151.77036 0 3683.9193 -0.2514556 + 9850 20585.229 252.91402 0 3683.7855 9.2033197 + 9900 21584.165 86.429361 0 3683.7902 -5.4686156 + 9950 21190.652 151.98402 0 3683.7593 -3.5815764 + 10000 20061.072 340.24042 0 3683.7525 -2.2008049 +Loop time of 26.3326 on 1 procs for 10000 steps with 81 atoms + +Pair time (%) = 0.951727 (3.61425) +Neigh time (%) = 0.339969 (1.29106) +Comm time (%) = 0.117033 (0.444442) +Outpt time (%) = 0.166224 (0.631248) +Other time (%) = 24.7576 (94.019) + +Nlocal: 81 ave 81 max 81 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 60 ave 60 max 60 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 721 ave 721 max 721 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 721 +Ave neighs/atom = 8.90123 +Neighbor list builds = 989 +Dangerous builds = 911 diff --git a/examples/rigid/log.rigid.poems2.22Jun07.liberty.4 b/examples/rigid/log.rigid.poems2.22Jun07.liberty.4 new file mode 100644 index 0000000000..b39291f922 --- /dev/null +++ b/examples/rigid/log.rigid.poems2.22Jun07.liberty.4 @@ -0,0 +1,307 @@ +LAMMPS (22 June 2007) +# 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 = 1.83851 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 10.738304 + 1450 15163.926 957.47583 0 3765.6103 -17.923459 + 1500 19223.688 204.15164 0 3764.0939 -1.6134548 + 1550 18147.996 404.12675 0 3764.8668 8.419476 + 1600 18615.043 317.42462 0 3764.6548 -2.3289018 + 1650 20120.654 38.887963 0 3764.935 -8.7620159 + 1700 19450.904 162.98318 0 3765.0025 2.3254642 + 1750 19374.634 177.37922 0 3765.2744 8.932879 + 1800 19424.403 167.93984 0 3765.0514 0.081244414 + 1850 17936.476 442.80024 0 3764.3699 6.6004381 + 1900 19982.598 64.405734 0 3764.8868 -2.9530867 + 1950 16216.207 761.84618 0 3764.8475 13.99299 + 2000 18584.309 322.14125 0 3763.6799 7.1657135 + 2050 20107.968 41.025323 0 3764.723 -0.31100219 + 2100 20002.381 60.584283 0 3764.7288 -6.7918769 + 2150 16949.202 626.70007 0 3765.4412 3.5108751 + 2200 20010.949 58.809053 0 3764.5403 -10.862469 + 2250 18982.71 247.01257 0 3762.3292 -0.53760308 + 2300 18401.513 354.84007 0 3762.5277 1.0915424 + 2350 19390.418 172.96117 0 3763.7793 -3.3530683 + 2400 16084.09 785.7786 0 3764.3137 -16.190023 + 2450 18871.606 268.52952 0 3763.2713 11.177432 + 2500 19686.081 117.99211 0 3763.5626 4.4022105 + 2550 18875.819 267.86112 0 3763.3831 -5.644853 + 2600 17010.705 613.30983 0 3763.4405 6.339113 + 2650 18797.741 282.8114 0 3763.8745 2.3556876 + 2700 19726.505 110.11368 0 3763.1701 -0.24505394 + 2750 19436.803 164.0424 0 3763.4504 -1.5253044 + 2800 18357.485 362.53565 0 3762.0699 22.084345 + 2850 19004.145 243.73317 0 3763.0192 2.2627686 + 2900 20108.185 39.496053 0 3763.234 -0.48500324 + 2950 15919.562 814.90854 0 3762.9756 15.610955 + 3000 17654.881 493.61172 0 3763.0342 2.6630007 + 3050 18711.769 298.14871 0 3763.2911 2.9706053 + 3100 16038.72 793.07314 0 3763.2064 8.0214715 + 3150 19925.087 73.363563 0 3763.1945 -11.409754 + 3200 19305.94 187.89701 0 3763.0711 0.57287469 + 3250 19779.251 100.11507 0 3762.9394 -10.121237 + 3300 17922.539 444.12789 0 3763.1166 6.2204358 + 3350 18967.646 250.37413 0 3762.9011 6.3180053 + 3400 16940.148 625.60864 0 3762.673 35.103295 + 3450 19284.152 191.53891 0 3762.6781 2.3570968 + 3500 19321.512 184.58448 0 3762.6423 2.2709682 + 3550 19631.049 126.97845 0 3762.358 -0.65897943 + 3600 18494.976 337.74154 0 3762.7371 -2.419701 + 3650 19117.634 222.45812 0 3762.7607 0.050198383 + 3700 19400.367 170.05551 0 3762.716 -0.60552841 + 3750 19912.752 75.322358 0 3762.869 -3.6525006 + 3800 18564.109 325.06781 0 3762.8658 5.4109379 + 3850 19846.304 87.655562 0 3762.8971 2.5946736 + 3900 19476.444 156.1165 0 3762.8653 -8.9729351 + 3950 19647.738 124.43854 0 3762.9085 0.82844488 + 4000 18123.616 406.3511 0 3762.5762 8.2661512 + 4050 16574.617 693.99841 0 3763.372 0.84625476 + 4100 18946.287 254.50552 0 3763.0773 -0.39624245 + 4150 18466.555 343.35133 0 3763.0837 -10.151094 + 4200 19477.739 156.04727 0 3763.0359 -0.73208547 + 4250 19680.9 118.38024 0 3762.9913 1.4563423 + 4300 18320.329 369.90558 0 3762.5591 -1.1852345 + 4350 18767.214 286.789 0 3762.199 6.3326391 + 4400 16894.629 634.49312 0 3763.1281 10.255417 + 4450 17915.848 444.62515 0 3762.3748 -4.633212 + 4500 19487.927 154.02671 0 3762.9021 -2.8383574 + 4550 19880.496 81.301302 0 3762.8746 2.9361031 + 4600 19872.228 82.669863 0 3762.7122 -3.2788098 + 4650 15769.89 843.11924 0 3763.4693 8.5209519 + 4700 19720.045 110.85283 0 3762.7129 -0.52445088 + 4750 19764.607 102.5192 0 3762.6317 2.1798609 + 4800 17562.467 510.78691 0 3763.0956 7.3629583 + 4850 19463.538 158.32481 0 3762.6836 -3.9920666 + 4900 17932.952 441.75053 0 3762.6675 6.9598399 + 4950 19084.979 228.62301 0 3762.8785 6.4376261 + 5000 19472.38 156.9411 0 3762.9375 4.4983114 + 5050 19453.908 160.3778 0 3762.9533 4.6612574 + 5100 19521.287 147.96055 0 3763.0137 2.904162 + 5150 18128.471 405.81521 0 3762.9394 5.3809492 + 5200 17049.524 605.73212 0 3763.0514 -6.0390166 + 5250 19645.014 125.0255 0 3762.991 -6.8246205 + 5300 18281.054 377.45844 0 3762.8388 13.32637 + 5350 19457.083 159.77948 0 3762.9429 0.21762328 + 5400 18431.165 349.7041 0 3762.8827 -5.7191385 + 5450 19431.127 164.51144 0 3762.8682 -8.6635331 + 5500 19538.523 144.42775 0 3762.6727 -1.6610416 + 5550 16105.678 780.35525 0 3762.8882 48.462329 + 5600 20038.616 51.570638 0 3762.4254 -1.5590991 + 5650 19774.413 100.34213 0 3762.2704 -3.4571242 + 5700 19210.59 204.66324 0 3762.18 1.851606 + 5750 19146.331 216.47595 0 3762.0928 2.0721573 + 5800 19058.521 232.88706 0 3762.2428 -1.9839575 + 5850 19195.04 207.81355 0 3762.4506 -10.269192 + 5900 18304.113 372.73776 0 3762.3882 -5.7543087 + 5950 19936.776 70.443763 0 3762.4393 3.6659806 + 6000 19413.016 167.50961 0 3762.5125 2.5981288 + 6050 19169.847 212.36264 0 3762.3343 2.9324328 + 6100 19873.513 82.452317 0 3762.7325 -0.5468764 + 6150 18911.794 260.42784 0 3762.6119 -2.1216521 + 6200 19153.7 215.69884 0 3762.6802 -1.0975226 + 6250 18802.916 280.37164 0 3762.3932 4.7012709 + 6300 19385.046 172.8566 0 3762.6799 3.7637577 + 6350 20042.403 51.159768 0 3762.7159 -0.15040693 + 6400 17671.74 490.05042 0 3762.5948 9.0126067 + 6450 18092.22 412.77197 0 3763.1832 -2.8594764 + 6500 19953.711 67.838094 0 3762.9698 3.7323378 + 6550 19818.338 92.883562 0 3762.9461 -1.9994936 + 6600 19323.833 183.93088 0 3762.4184 -0.95695044 + 6650 18642.816 310.35894 0 3762.7323 15.264581 + 6700 16246.778 753.95834 0 3762.6209 26.618472 + 6750 19362.672 176.94037 0 3762.6204 -4.6442606 + 6800 18813.849 278.64468 0 3762.6908 2.5699369 + 6850 19386.278 172.79274 0 3762.8443 -10.400863 + 6900 19206.609 206.02588 0 3762.8054 -2.680536 + 6950 18068.847 416.85422 0 3762.9369 -9.0106209 + 7000 18369.805 360.43314 0 3762.249 13.735008 + 7050 18426.189 350.61688 0 3762.8741 8.3714758 + 7100 17656.982 492.79834 0 3762.6098 4.4583118 + 7150 18141.722 402.98387 0 3762.562 8.3258153 + 7200 18621.905 313.92925 0 3762.4301 -5.8742464 + 7250 18374.083 360.03493 0 3762.6429 -13.815946 + 7300 18040.277 421.82567 0 3762.6177 -4.6905029 + 7350 19146.198 217.01003 0 3762.6023 5.1451068 + 7400 18826.989 276.1892 0 3762.6686 6.5391972 + 7450 16067.243 787.1796 0 3762.5949 8.3754041 + 7500 18419.546 351.11771 0 3762.1448 7.7248275 + 7550 18446.346 346.8971 0 3762.8871 13.350672 + 7600 18944.672 254.13521 0 3762.4077 3.6554152 + 7650 18736.984 292.8881 0 3762.7 -14.958085 + 7700 18741.654 291.39068 0 3762.0673 -2.1933562 + 7750 18220.361 388.04072 0 3762.1816 9.7868422 + 7800 19348.223 178.96147 0 3761.9658 -0.26463817 + 7850 19401.949 169.04328 0 3761.9968 -1.5022009 + 7900 18577.957 321.63399 0 3761.9965 1.4151292 + 7950 17739.892 476.69976 0 3761.865 5.1996225 + 8000 17512.557 519.37266 0 3762.4387 5.2453534 + 8050 19168.123 212.38445 0 3762.0369 -3.9960482 + 8100 17916.044 443.46573 0 3761.2517 -5.9817899 + 8150 18601.23 316.95165 0 3761.6238 3.8327542 + 8200 17791.805 467.15931 0 3761.9381 -2.6931191 + 8250 18321.607 369.09405 0 3761.9843 1.4342349 + 8300 17334.957 552.06316 0 3762.2404 4.1774271 + 8350 17207.467 575.31923 0 3761.8872 1.1785558 + 8400 18225.217 387.22593 0 3762.2662 9.0197316 + 8450 19004.047 243.03694 0 3762.3048 7.664125 + 8500 18952.876 252.61597 0 3762.4078 -3.9713236 + 8550 19127.437 220.08856 0 3762.2066 -10.686924 + 8600 19542.154 143.35104 0 3762.2684 -1.9189815 + 8650 19294.525 189.17898 0 3762.2392 -1.4875507 + 8700 18832.532 274.05387 0 3761.5598 -1.9519412 + 8750 18591.931 318.93488 0 3761.885 9.928625 + 8800 18576.38 322.04174 0 3762.1121 -3.8846944 + 8850 19922.086 72.972833 0 3762.248 -0.56032546 + 8900 18892.839 263.55803 0 3762.2319 4.9733954 + 8950 16486.736 708.70288 0 3761.8022 37.965254 + 9000 18628.335 312.81773 0 3762.5094 6.0750689 + 9050 19286.823 190.4938 0 3762.1278 -2.2862927 + 9100 18973.378 247.96414 0 3761.5526 5.0771442 + 9150 17256.927 566.17648 0 3761.9038 5.7456977 + 9200 18507.288 334.66416 0 3761.9398 1.1406887 + 9250 18961.534 250.42427 0 3761.8194 -5.8909163 + 9300 19206.115 205.203 0 3761.8911 1.0922244 + 9350 19401.191 168.92055 0 3761.7336 -1.921044 + 9400 18069.392 415.54646 0 3761.7301 5.0565694 + 9450 18828.428 274.89551 0 3761.6415 10.024306 + 9500 18295.323 373.66825 0 3761.691 -1.4888703 + 9550 17709.338 482.22946 0 3761.7365 -9.028568 + 9600 19512.39 148.31281 0 3761.7184 -4.2133026 + 9650 19742.351 105.74048 0 3761.7315 -0.57801883 + 9700 19892.658 77.898869 0 3761.7245 1.2005091 + 9750 19035.044 236.65131 0 3761.6595 2.87911 + 9800 17443.415 531.71826 0 3761.9802 23.5179 + 9850 19545.912 141.99994 0 3761.6133 1.3493021 + 9900 19542.173 142.22929 0 3761.1503 3.087434 + 9950 19794.356 96.034607 0 3761.6561 -3.1844994 + 10000 19058.563 232.34496 0 3761.7085 -7.1466609 +Loop time of 17.168 on 4 procs for 10000 steps with 81 atoms + +Pair time (%) = 0.0928572 (0.540875) +Neigh time (%) = 0.0403583 (0.235079) +Comm time (%) = 1.50369 (8.75868) +Outpt time (%) = 0.0945153 (0.550533) +Other time (%) = 15.4366 (89.9148) + +Nlocal: 20.25 ave 42 max 0 min +Histogram: 2 0 0 0 0 0 0 0 1 1 +Nghost: 20.5 ave 37 max 9 min +Histogram: 2 0 0 0 0 0 1 0 0 1 +Neighs: 164.25 ave 401 max 0 min +Histogram: 2 0 0 0 0 0 1 0 0 1 + +Total # of neighbors = 657 +Ave neighs/atom = 8.11111 +Neighbor list builds = 991 +Dangerous builds = 930 diff --git a/examples/rigid/log.rigid.poems2.22Jun07.linux.1 b/examples/rigid/log.rigid.poems2.22Jun07.linux.1 new file mode 100644 index 0000000000..fcd95273b0 --- /dev/null +++ b/examples/rigid/log.rigid.poems2.22Jun07.linux.1 @@ -0,0 +1,307 @@ +LAMMPS (22 June 2007) +# 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 = 1.92712 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 10.738304 + 1450 15163.926 957.47582 0 3765.6103 -17.923459 + 1500 19223.689 204.15156 0 3764.0939 -1.6134559 + 1550 18147.996 404.12674 0 3764.8668 8.4194748 + 1600 18615.043 317.42458 0 3764.6548 -2.3289073 + 1650 20120.654 38.887996 0 3764.935 -8.7620081 + 1700 19450.903 162.98348 0 3765.0025 2.3254585 + 1750 19374.636 177.37893 0 3765.2744 8.93288 + 1800 19424.402 167.93995 0 3765.0514 0.081253537 + 1850 17936.625 442.77274 0 3764.3699 6.60003 + 1900 19982.599 64.405428 0 3764.8868 -2.9531558 + 1950 16216.44 761.80238 0 3764.8469 13.991862 + 2000 18584.234 322.15493 0 3763.6798 7.1659198 + 2050 20107.969 41.025039 0 3764.723 -0.31106422 + 2100 20002.411 60.57861 0 3764.7288 -6.7918086 + 2150 16948.844 626.76647 0 3765.4413 3.512116 + 2200 20010.946 58.809564 0 3764.5403 -10.862667 + 2250 18982.703 247.01388 0 3762.3292 -0.5373304 + 2300 18401.642 354.81637 0 3762.5279 1.0912175 + 2350 19390.361 172.97181 0 3763.7793 -3.3533924 + 2400 16086.125 785.40108 0 3764.3132 -16.183657 + 2450 18872.351 268.39211 0 3763.2718 11.164657 + 2500 19684.688 118.25055 0 3763.5632 4.4144806 + 2550 18878.925 267.2853 0 3763.3825 -5.6338978 + 2600 17005.407 614.29162 0 3763.441 6.3575302 + 2650 18827.389 277.31059 0 3763.8641 2.3182614 + 2700 19715.461 112.12451 0 3763.1358 -0.19109773 + 2750 19319.449 185.79269 0 3763.4684 -1.3550374 + 2800 18120.942 406.44184 0 3762.1719 26.654821 + 2850 19401.627 170.17075 0 3763.0647 0.73603491 + 2900 20106.157 39.874788 0 3763.2371 -1.1342032 + 2950 16814.814 649.4335 0 3763.288 12.415015 + 3000 16200.577 761.45184 0 3761.5588 21.599685 + 3050 18396.676 356.11264 0 3762.9044 7.6140431 + 3100 17582.958 506.67523 0 3762.7786 -14.766278 + 3150 18362.109 362.43838 0 3762.8289 3.2782729 + 3200 17008.785 613.88943 0 3763.6645 5.070376 + 3250 19614.194 130.81389 0 3763.072 1.1021521 + 3300 18995.955 245.31261 0 3763.0821 -8.6889904 + 3350 18215.815 389.87474 0 3763.1737 2.7550234 + 3400 18068.71 417.08655 0 3763.144 17.578891 + 3450 19352.914 179.0126 0 3762.8855 8.4058764 + 3500 18738.818 292.55665 0 3762.7082 3.8415777 + 3550 19469.912 157.36508 0 3762.9044 2.5399078 + 3600 18431.706 349.41269 0 3762.6916 2.3088878 + 3650 18819.962 277.76095 0 3762.9392 5.1521358 + 3700 19813.675 93.945731 0 3763.1449 -0.34475825 + 3750 18075.078 415.77801 0 3763.0146 -1.8968333 + 3800 19422.14 166.53886 0 3763.2315 -2.2150672 + 3850 18013.209 427.44475 0 3763.2243 -6.0428819 + 3900 19193.889 208.87526 0 3763.2991 -3.9692972 + 3950 16568.188 695.64549 0 3763.8284 13.243843 + 4000 17993.623 430.51008 0 3762.6626 5.0888559 + 4050 19625.511 128.63837 0 3762.9922 -0.70241793 + 4100 19069.298 231.35736 0 3762.7088 -5.6365968 + 4150 18033.877 424.02231 0 3763.6292 -6.8518969 + 4200 19950.626 68.482279 0 3763.0426 -1.8524059 + 4250 18786.19 284.10677 0 3763.0309 5.811473 + 4300 19526.067 146.81821 0 3762.7565 -9.5811432 + 4350 16343.335 736.72783 0 3763.2714 30.281083 + 4400 18759.668 288.81939 0 3762.8319 5.5918027 + 4450 18633.251 312.20135 0 3762.8033 3.8618473 + 4500 18079.31 414.80535 0 3762.8256 2.2481588 + 4550 18288.498 376.11039 0 3762.8693 4.1087615 + 4600 18315.887 371.16083 0 3762.9918 -3.5412078 + 4650 18901.901 262.59396 0 3762.9459 -7.3155419 + 4700 19311.704 186.85051 0 3763.092 -5.9856651 + 4750 19426.54 165.69302 0 3763.2005 -7.0519961 + 4800 18347.933 365.43611 0 3763.2015 5.0195241 + 4850 19952.067 68.477491 0 3763.3047 3.3126678 + 4900 19224.549 203.14962 0 3763.2513 -2.8437357 + 4950 19857.322 85.89601 0 3763.1779 -1.4381085 + 5000 19592.925 134.86246 0 3763.182 0.8610879 + 5050 19472.16 157.37877 0 3763.3343 -0.31578957 + 5100 19814.831 93.787624 0 3763.2008 5.3970415 + 5150 18211.407 390.82193 0 3763.3047 8.4423278 + 5200 18828.994 276.3271 0 3763.1778 10.441024 + 5250 20121.332 37.261735 0 3763.4344 -2.2672502 + 5300 17755.337 475.75071 0 3763.7761 3.3792401 + 5350 20033.05 53.761483 0 3763.5855 -3.031072 + 5400 19332.059 183.54479 0 3763.5557 6.0877875 + 5450 19964.421 66.56191 0 3763.677 0.034467069 + 5500 19838.257 89.969443 0 3763.7207 -3.5800893 + 5550 19202.804 207.40212 0 3763.4769 8.5123136 + 5600 19855.825 86.760789 0 3763.7654 1.3832846 + 5650 19060.478 234.22396 0 3763.9421 2.6116735 + 5700 20124.587 37.161564 0 3763.937 3.4519842 + 5750 19304.489 189.01672 0 3763.9221 -0.096371392 + 5800 18516.206 335.07659 0 3764.0036 -4.9526268 + 5850 18093.127 413.01533 0 3763.5945 -3.6663927 + 5900 17303.637 559.08088 0 3763.458 -4.805237 + 5950 19818.733 93.796285 0 3763.932 0.043875363 + 6000 18162.182 400.57864 0 3763.9457 7.4143797 + 6050 18439.177 349.30792 0 3763.9703 -0.92601434 + 6100 18899.456 263.84185 0 3763.741 8.018437 + 6150 17317.004 556.71789 0 3763.5704 10.764267 + 6200 18991.81 246.89696 0 3763.8989 -4.0990586 + 6250 19868.798 84.388048 0 3763.795 0.58061118 + 6300 18989.135 247.26992 0 3763.7763 12.682799 + 6350 15978.578 804.89 0 3763.8858 6.3163773 + 6400 18967.47 251.22915 0 3763.7236 1.3481515 + 6450 19294.369 190.87058 0 3763.9019 -8.5139829 + 6500 19826.451 92.014872 0 3763.5798 1.0125001 + 6550 17480.845 526.28717 0 3763.4807 5.9053655 + 6600 17806.087 465.8384 0 3763.262 21.004433 + 6650 17942.192 439.48981 0 3762.118 2.0212326 + 6700 16468.094 712.95472 0 3762.6018 6.6618901 + 6750 19305.119 188.34815 0 3763.3703 1.8765297 + 6800 19988.201 62.004452 0 3763.5231 -1.6652967 + 6850 20193.079 24.117041 0 3763.5761 -4.1748266 + 6900 20011.596 57.729546 0 3763.5806 -3.6774766 + 6950 18419.577 352.48285 0 3763.5157 -3.8710136 + 7000 19178.531 212.01179 0 3763.5917 5.2484112 + 7050 18754.875 289.8693 0 3762.9942 7.5083851 + 7100 19179.381 211.26035 0 3762.9975 1.8325782 + 7150 18221.392 388.75188 0 3763.0837 -9.4596464 + 7200 19508.765 150.73861 0 3763.4729 -8.4154341 + 7250 16779.268 656.19712 0 3763.4689 3.9284063 + 7300 19184.405 210.6069 0 3763.2744 -7.0049508 + 7350 17914.948 445.90458 0 3763.4876 1.9922265 + 7400 14040.559 1164.2709 0 3764.3744 -25.198045 + 7450 17680.643 489.04226 0 3763.2354 4.6678876 + 7500 15575.048 879.11471 0 3763.3829 5.3335325 + 7550 16738.339 663.36831 0 3763.0607 10.735452 + 7600 18927.126 258.2804 0 3763.3038 -1.3289622 + 7650 17033.929 610.18818 0 3764.6195 15.51609 + 7700 17800.589 463.84003 0 3760.2454 -9.8344679 + 7750 18337.643 367.47891 0 3763.3388 -3.4235631 + 7800 20102.521 40.465427 0 3763.1544 -2.5622118 + 7850 18854.307 271.72975 0 3763.2681 16.38529 + 7900 18769.869 287.08151 0 3762.9832 8.285443 + 7950 19530.556 146.69214 0 3763.4618 2.5699618 + 8000 17967.757 436.48149 0 3763.8439 -13.724493 + 8050 19995.451 60.489084 0 3763.3503 -6.7296549 + 8100 17668.554 491.39156 0 3763.346 -1.5877323 + 8150 17041.937 607.0112 0 3762.9255 29.132719 + 8200 19634.282 127.02828 0 3763.0064 5.4245146 + 8250 19464.43 158.26891 0 3762.7929 -1.0959737 + 8300 18262.088 380.75171 0 3762.6199 -9.5161603 + 8350 19154.678 214.95549 0 3762.118 1.4904442 + 8400 18631.904 312.04844 0 3762.4011 6.200446 + 8450 17326.79 552.9849 0 3761.6497 0.58133511 + 8500 18262.986 380.59746 0 3762.6319 -1.5859109 + 8550 16355.636 733.37813 0 3762.1995 -6.8040182 + 8600 17652.805 494.50385 0 3763.5419 2.9981184 + 8650 16589.75 690.94159 0 3763.1175 -0.61681982 + 8700 18767.632 287.52175 0 3763.0091 -0.15112824 + 8750 19530.676 145.40209 0 3762.194 3.6106484 + 8800 16209.935 760.89243 0 3762.7323 -12.504448 + 8850 19909.854 75.790768 0 3762.8008 1.4759603 + 8900 19162.868 213.40033 0 3762.0797 6.8118408 + 8950 17996.377 429.38719 0 3762.0496 11.126692 + 9000 17366.686 545.41384 0 3761.4667 -5.089277 + 9050 16976.454 618.54424 0 3762.332 -5.533809 + 9100 19419.965 166.18943 0 3762.4793 3.7595663 + 9150 17900.022 448.30981 0 3763.1287 -6.2299514 + 9200 18662.637 306.89813 0 3762.942 -2.0816787 + 9250 19806.478 95.487105 0 3763.3534 -19.715374 + 9300 19065.731 233.31844 0 3764.0093 0.66896622 + 9350 15347.66 921.21669 0 3763.3759 10.777468 + 9400 18056.449 416.32084 0 3760.1078 13.580271 + 9450 19104.743 225.75045 0 3763.6658 -0.57249212 + 9500 18193.488 394.55096 0 3763.7154 -3.8896144 + 9550 17005.07 614.383 0 3763.4701 20.544154 + 9600 18956.557 253.26137 0 3763.7349 1.0366132 + 9650 18278.345 379.38464 0 3764.2634 -11.945363 + 9700 19791.354 98.864736 0 3763.9303 1.0827422 + 9750 19840.264 89.82519 0 3763.9482 -2.1741548 + 9800 19120.304 222.91513 0 3763.7122 -3.392839 + 9850 15643.719 866.53246 0 3763.5175 1.2278747 + 9900 16998.456 616.53609 0 3764.3983 -8.3833815 + 9950 19670.981 121.07532 0 3763.8496 0.76591747 + 10000 16544.589 699.98952 0 3763.8022 -21.503512 +Loop time of 26.9591 on 1 procs for 10000 steps with 81 atoms + +Pair time (%) = 0.70095 (2.60005) +Neigh time (%) = 0.258285 (0.958063) +Comm time (%) = 0.131733 (0.488641) +Outpt time (%) = 0.175157 (0.649714) +Other time (%) = 25.693 (95.3035) + +Nlocal: 81 ave 81 max 81 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 71 ave 71 max 71 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 528 ave 528 max 528 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 528 +Ave neighs/atom = 6.51852 +Neighbor list builds = 993 +Dangerous builds = 946 diff --git a/examples/shear/log.shear.22Jun07.liberty.4 b/examples/shear/log.shear.22Jun07.liberty.4 new file mode 100644 index 0000000000..f21d560dbd --- /dev/null +++ b/examples/shear/log.shear.22Jun07.liberty.4 @@ -0,0 +1,159 @@ +LAMMPS (22 June 2007) +# 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 = 1.68686 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 0.207772 on 4 procs for 100 steps with 1912 atoms + +Pair time (%) = 0.172011 (82.7884) +Neigh time (%) = 0.0050208 (2.4165) +Comm time (%) = 0.0227784 (10.9632) +Outpt time (%) = 0.000707865 (0.340693) +Other time (%) = 0.00725383 (3.49125) + +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 = 1.70559 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 6.63055 on 4 procs for 3000 steps with 1912 atoms + +Pair time (%) = 5.21397 (78.6355) +Neigh time (%) = 0.273334 (4.12235) +Comm time (%) = 0.765037 (11.5381) +Outpt time (%) = 0.153763 (2.31901) +Other time (%) = 0.224447 (3.38504) + +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.22Jun07.linux.1 b/examples/shear/log.shear.22Jun07.linux.1 new file mode 100644 index 0000000000..8577f35527 --- /dev/null +++ b/examples/shear/log.shear.22Jun07.linux.1 @@ -0,0 +1,159 @@ +LAMMPS (22 June 2007) +# 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 = 1.92854 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 1.25061 on 1 procs for 100 steps with 1912 atoms + +Pair time (%) = 1.16404 (93.0782) +Neigh time (%) = 0.037578 (3.00478) +Comm time (%) = 0.012906 (1.03198) +Outpt time (%) = 0.001262 (0.100911) +Other time (%) = 0.034818 (2.78409) + +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 = 2.00339 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 -395.06508 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 41.7807 on 1 procs for 3000 steps with 1912 atoms + +Pair time (%) = 38.0687 (91.1155) +Neigh time (%) = 2.03169 (4.86276) +Comm time (%) = 0.401437 (0.960819) +Outpt time (%) = 0.279676 (0.66939) +Other time (%) = 0.999203 (2.39154) + +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.void.22Jun07.liberty.4 b/examples/shear/log.shear.void.22Jun07.liberty.4 new file mode 100644 index 0000000000..d77dc1ed0f --- /dev/null +++ b/examples/shear/log.shear.void.22Jun07.liberty.4 @@ -0,0 +1,160 @@ +LAMMPS (22 June 2007) +# 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 = 1.67464 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 0.17824 on 4 procs for 100 steps with 1708 atoms + +Pair time (%) = 0.14804 (83.0562) +Neigh time (%) = 0.00533068 (2.99073) +Comm time (%) = 0.0173439 (9.73062) +Outpt time (%) = 0.000686049 (0.384901) +Other time (%) = 0.00684005 (3.83754) + +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 = 1.69123 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 5.65794 on 4 procs for 3000 steps with 1708 atoms + +Pair time (%) = 4.48969 (79.352) +Neigh time (%) = 0.226591 (4.00482) +Comm time (%) = 0.582767 (10.3) +Outpt time (%) = 0.15564 (2.75081) +Other time (%) = 0.203256 (3.5924) + +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 diff --git a/examples/shear/log.shear.void.22Jun07.linux.1 b/examples/shear/log.shear.void.22Jun07.linux.1 new file mode 100644 index 0000000000..affc42b968 --- /dev/null +++ b/examples/shear/log.shear.void.22Jun07.linux.1 @@ -0,0 +1,160 @@ +LAMMPS (22 June 2007) +# 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 = 1.91124 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 1.06407 on 1 procs for 100 steps with 1708 atoms + +Pair time (%) = 0.989223 (92.9663) +Neigh time (%) = 0.030778 (2.89249) +Comm time (%) = 0.01177 (1.10613) +Outpt time (%) = 0.001512 (0.142096) +Other time (%) = 0.030783 (2.89296) + +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 = 1.97639 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 33.1295 on 1 procs for 3000 steps with 1708 atoms + +Pair time (%) = 29.994 (90.5356) +Neigh time (%) = 1.58958 (4.79809) +Comm time (%) = 0.381225 (1.15071) +Outpt time (%) = 0.25781 (0.778188) +Other time (%) = 0.906904 (2.73745) + +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