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lammps/examples/comb/log.comb.Si.elastic.15Jan10.linux.1
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LAMMPS (3 Sep 2010)
# Pure Si crystal, qeq off, calculates stress-strain, no out.*.cfg
units metal
atom_style charge
dimension 3
boundary p p p
lattice diamond 5.431
Lattice spacing in x,y,z = 5.431 5.431 5.431
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
1 by 1 by 1 processor grid
create_atoms 1 box
Created 512 atoms
mass 1 29.0
change_box triclinic
velocity all create 1.0 277387
pair_style comb
pair_coeff * * ffield.comb Si
neighbor 0.5 bin
neigh_modify every 20 delay 0 check no
fix 1 all box/relax aniso 0.0 vmax 0.001
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul #lx ly lz vol pxx pyy pzz
thermo_modify norm yes
thermo 1
minimize 1.0e-14 1.0e-20 1000 10000
Memory usage per processor = 3.48277 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul
0 1 -4.6295947 -4.6297237 -4.6297237 0
1 1 -4.6295963 -4.6297253 -4.6297253 0
2 1 -4.6295965 -4.6297255 -4.6297255 0
3 1 -4.6295965 -4.6297255 -4.6297255 0
Loop time of 0.767534 on 1 procs for 3 steps with 512 atoms
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-4.62972371535 -4.62972550036 -4.62972550036
Force two-norm initial, final = 5.86582 0.235602
Force max component initial, final = 3.38663 0.136025
Final line search alpha, max atom move = 0.000114869 1.5625e-05
Iterations, force evaluations = 3 16
Pair time (%) = 0.763441 (99.4668)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000983953 (0.128197)
Outpt time (%) = 3.40939e-05 (0.004442)
Other time (%) = 0.00307465 (0.400588)
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4861 ave 4861 max 4861 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 212992 ave 212992 max 212992 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0
min_modify dmax 0.2 line quadratic
unfix 1
run 1
Memory usage per processor = 2.56725 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul
3 1 -4.6295965 -4.6297255 -4.6297255 0
4 1 -4.6295965 -4.6297255 -4.6297255 0
Loop time of 0.0447631 on 1 procs for 1 steps with 512 atoms
Pair time (%) = 0.0446441 (99.7342)
Neigh time (%) = 0 (0)
Comm time (%) = 5.76973e-05 (0.128895)
Outpt time (%) = 4.41074e-05 (0.0985353)
Other time (%) = 1.71661e-05 (0.0383489)
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4861 ave 4861 max 4861 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 212992 ave 212992 max 212992 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0
### copy lines after this to any input script for elastic calculations ###
## Elastic constants calculations: strain box, measure box stress
## strain x, measure s_x, s_y, s_z, s_yz:
## calculates C11, C12, C13 and C14
fix 2 all deform 1 x scale 1.0001 remap x
compute perfx all stress/atom pair
compute fx all reduce sum c_perfx[1] c_perfx[2] c_perfx[3] c_perfx[4] c_perfx[5] c_perfx[6]
thermo_style custom step lx ly lz xy xz yz c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6]
run 10
Memory usage per processor = 3.02501 Mbytes
Step Lx Ly Lz Xy Xz Yz fx[1] fx[2] fx[3] fx[4] fx[5] fx[6]
4 21.728073 21.728073 21.728073 0 0 0 217976.4 217976.4 217976.4 1.9450404e-06 2.4752556e-06 -1.6071587e-06
5 21.728291 21.728073 21.728073 0 0 0 217976.4 217976.4 217976.4 1.8110987e-06 2.6015226e-06 -1.1358357e-06
6 21.728508 21.728073 21.728073 0 0 0 364177.1 295296.39 295296.39 -4.4966424e-06 1.848553e-07 -2.2958737e-06
7 21.728725 21.728073 21.728073 0 0 0 510377.09 372612.85 372612.85 2.4287963e-06 2.6615821e-06 -1.9832618e-06
8 21.728942 21.728073 21.728073 0 0 0 656576.36 449925.76 449925.76 2.4447348e-06 2.4469323e-06 -8.4990897e-07
9 21.72916 21.728073 21.728073 0 0 0 802774.92 527235.13 527235.13 4.0363922e-06 -5.9982754e-06 -2.3201799e-06
10 21.729377 21.728073 21.728073 0 0 0 948972.76 604540.97 604540.97 2.8253812e-06 2.5964234e-06 -8.931554e-07
11 21.729594 21.728073 21.728073 0 0 0 1095169.9 681843.26 681843.26 2.3933505e-06 2.283704e-06 -3.9266049e-07
12 21.729811 21.728073 21.728073 0 0 0 1241366.3 759142.02 759142.02 2.2037259e-06 2.6987214e-06 3.737462e-07
13 21.730029 21.728073 21.728073 0 0 0 1387562 836437.23 836437.23 2.6802555e-06 2.9969439e-06 1.7521287e-07
14 21.730246 21.728073 21.728073 0 0 0 1533757 913728.91 913728.91 4.4634386e-06 -4.2738918e-06 3.2367003e-07
Loop time of 0.482055 on 1 procs for 10 steps with 512 atoms
Pair time (%) = 0.478359 (99.2333)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000627995 (0.130274)
Outpt time (%) = 0.00278902 (0.578569)
Other time (%) = 0.00027895 (0.0578668)
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4861 ave 4861 max 4861 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 212992 ave 212992 max 212992 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0
## strain z, measure s_z: calculates C33
fix 2 all deform 1 z scale 1.0001 remap x
compute perfz all stress/atom pair
compute fz all reduce sum c_perfz[1] c_perfz[2] c_perfz[3] c_perfz[4] c_perfz[5] c_perfz[6]
thermo_style custom step lx ly lz xy xz yz c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6]
run 10
Memory usage per processor = 3.48277 Mbytes
Step Lx Ly Lz Xy Xz Yz fz[1] fz[2] fz[3] fz[4] fz[5] fz[6]
14 21.730246 21.728073 21.728073 0 0 0 1679951.2 991017.05 991017.05 1.3848713e-06 1.8198295e-06 -3.1488289e-06
15 21.730246 21.728073 21.728291 0 0 0 1679951.2 991017.05 991017.05 1.4477769e-06 2.1276907e-06 -2.7563351e-06
16 21.730246 21.728073 21.728508 0 0 0 1757243.6 1068312.4 1137190.1 2.1162843e-06 -3.0681281e-06 -1.8698946e-06
17 21.730246 21.728073 21.728725 0 0 0 1834532.4 1145604.2 1283362.4 1.5226892e-06 3.1081802e-06 -2.6821714e-06
18 21.730246 21.728073 21.728942 0 0 0 1911817.6 1222892.5 1429534 -7.5700513e-07 1.7188656e-06 4.1051196e-06
19 21.730246 21.728073 21.72916 0 0 0 1989099.3 1300177.3 1575704.9 -1.4391091e-06 2.0797417e-06 3.9123487e-06
20 21.730246 21.728073 21.729377 0 0 0 2066377.5 1377458.5 1721875.1 -1.5213551e-06 1.9181068e-06 -2.1773741e-06
21 21.730246 21.728073 21.729594 0 0 0 2143652.1 1454736.2 1868044.5 -1.4238005e-06 1.7984361e-06 -2.0333083e-06
22 21.730246 21.728073 21.729811 0 0 0 2220923.2 1532010.3 2014213.3 4.4088785e-06 2.5805071e-06 -2.1480169e-06
23 21.730246 21.728073 21.730029 0 0 0 2298190.7 1609280.9 2160381.3 -9.3407459e-07 2.1740278e-06 -1.3082692e-06
24 21.730246 21.728073 21.730246 0 0 0 2375454.8 1686547.9 2306548.6 -1.7972725e-06 2.108669e-06 -1.6910019e-06
Loop time of 0.482053 on 1 procs for 10 steps with 512 atoms
Pair time (%) = 0.478359 (99.2338)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000627756 (0.130226)
Outpt time (%) = 0.00281119 (0.583171)
Other time (%) = 0.000254631 (0.0528222)
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4861 ave 4861 max 4861 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 212992 ave 212992 max 212992 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0
## strain yz, measure s_yz: calculates C44
fix 2 all deform 1 yz erate 0.0001 remap x
compute perfyz all stress/atom pair
compute fyz all reduce sum c_perfyz[1] c_perfyz[2] c_perfyz[3] c_perfyz[4] c_perfyz[5] c_perfyz[6]
thermo_style custom step lx ly lz xy xz yz c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6]
run 10
Memory usage per processor = 3.94054 Mbytes
Step Lx Ly Lz Xy Xz Yz fyz[1] fyz[2] fyz[3] fyz[4] fyz[5] fyz[6]
24 21.730246 21.728073 21.730246 0 0 0 2452715.2 1763811.4 2452715.2 -1.7548117e-06 3.6087566e-06 -3.6198628e-06
25 21.730246 21.728073 21.730246 0 0 4.3460492e-07 2452715.2 1763811.4 2452715.2 -1.7167978e-06 3.4304272e-06 -2.9804569e-06
26 21.730246 21.728073 21.730246 0 0 8.6920984e-07 2452715.2 1763811.4 2452715.2 -1.8729445e-06 4.5840765e-06 243.65136
27 21.730246 21.728073 21.730246 0 0 1.3038148e-06 2452715.2 1763811.4 2452715.2 -1.2316967e-06 2.6286266e-06 487.30276
28 21.730246 21.728073 21.730246 0 0 1.7384197e-06 2452715.2 1763811.4 2452715.2 -1.3251453e-06 2.7225014e-06 730.95419
29 21.730246 21.728073 21.730246 0 0 2.1730246e-06 2452715.2 1763811.4 2452715.2 -8.5464495e-07 -6.3592996e-07 974.60551
30 21.730246 21.728073 21.730246 0 0 2.6076295e-06 2452715.2 1763811.4 2452715.2 -1.7272259e-06 2.0497545e-06 1218.2569
31 21.730246 21.728073 21.730246 0 0 3.0422344e-06 2452715.2 1763811.4 2452715.2 -4.6626464e-07 2.1955509e-06 1461.9083
32 21.730246 21.728073 21.730246 0 0 3.4768394e-06 2452715.2 1763811.4 2452715.2 -1.1296433e-06 2.2397275e-06 1705.5598
33 21.730246 21.728073 21.730246 0 0 3.9114443e-06 2452715.2 1763811.4 2452715.2 -1.388603e-06 1.2425658e-06 1949.2111
34 21.730246 21.728073 21.730246 0 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 -1.1793341e-06 1.7092936e-06 2192.8625
Loop time of 0.481734 on 1 procs for 10 steps with 512 atoms
Pair time (%) = 0.478086 (99.2427)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000612497 (0.127144)
Outpt time (%) = 0.00276494 (0.573956)
Other time (%) = 0.000270844 (0.0562226)
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4861 ave 4861 max 4861 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 212992 ave 212992 max 212992 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0
## strain xy, measure s_xy: calculates C66
fix 2 all deform 1 xy erate 0.0001 remap x
compute perfxy all stress/atom pair
compute fxy all reduce sum c_perfxy[1] c_perfxy[2] c_perfxy[3] c_perfxy[4] c_perfxy[5] c_perfxy[6]
thermo_style custom step lx ly lz xy xz yz c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6]
run 10
Memory usage per processor = 4.3983 Mbytes
Step Lx Ly Lz Xy Xz Yz fxy[1] fxy[2] fxy[3] fxy[4] fxy[5] fxy[6]
34 21.730246 21.728073 21.730246 0 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 -1.7294679e-06 4.8293026e-06 2436.5139
35 21.730246 21.728073 21.730246 4.3456146e-07 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 -1.4630595e-06 4.5052213e-06 2436.5139
36 21.730246 21.728073 21.730246 8.6912293e-07 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 243.63758 -0.00012576585 2436.5139
37 21.730246 21.728073 21.730246 1.3036844e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 487.27522 -0.00025542614 2436.5139
38 21.730246 21.728073 21.730246 1.7382459e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 730.91286 -0.00038565598 2436.5139
39 21.730246 21.728073 21.730246 2.1728073e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 974.55045 -0.00051669611 2436.5138
40 21.730246 21.728073 21.730246 2.6073688e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 1218.188 -0.00064706412 2436.5139
41 21.730246 21.728073 21.730246 3.0419303e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 1461.8257 -0.0007779958 2436.5139
42 21.730246 21.728073 21.730246 3.4764917e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 1705.4633 -0.00090716273 2436.5138
43 21.730246 21.728073 21.730246 3.9110532e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 1949.1009 -0.001038008 2436.5138
44 21.730246 21.728073 21.730246 4.3456146e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 2192.7385 -0.0011663311 2436.5138
Loop time of 0.482715 on 1 procs for 10 steps with 512 atoms
Pair time (%) = 0.479008 (99.2321)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000625372 (0.129553)
Outpt time (%) = 0.00280094 (0.580248)
Other time (%) = 0.00028038 (0.058084)
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4861 ave 4861 max 4861 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 212992 ave 212992 max 212992 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0
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