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lammps/examples/comb/log.15May15.comb.Cu2O.elastic.g++.1
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LAMMPS (30 Apr 2015)
# Cu2O crystal, qeq on, minimizes, then calculates elastic constants
units metal
atom_style charge
dimension 3
boundary p p p
read_data data.Cu2O
triclinic box = (0 0 0) to (25.62 25.62 25.62) with tilt (0 0 0)
1 by 1 by 1 MPI processor grid
reading atoms ...
1296 atoms
mass 1 63.54
group type1 type 1
864 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
mass 2 16.00
group type2 type 2
432 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
velocity all create 1.0 277387
pair_style comb
pair_coeff * * ffield.comb Cu O
neighbor 0.5 bin
neigh_modify every 20 delay 0 check no
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul c_q1 c_q2 lx ly lz vol
thermo_modify norm yes
thermo 1
fix 1 all nve
fix 2 all qeq/comb 1 0.0001
#dump 1 all cfg 1 *.cfg id type xs ys zs q f_2 vx vy vz fx fy fz
#dump_modify 1 element Cu O
run 2
Neighbor list info ...
1 neighbor list requests
update every 20 steps, delay 0 steps, check no
master list distance cutoff = 12.5
Memory usage per processor = 6.39852 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
0 1 -3.8383547 -3.8384838 -1.1478494 -2.6906344 0.7228352 -1.4456704 25.62 25.62 25.62 16816.568
1 0.99954481 -3.8453114 -3.8454405 -0.98378999 -2.8616505 0.72283606 -1.4456721 25.62 25.62 25.62 16816.568
2 0.99818299 -3.8453114 -3.8454403 -0.98378324 -2.8616571 0.72283727 -1.4456745 25.62 25.62 25.62 16816.568
Loop time of 0.346024 on 1 procs for 2 steps with 1296 atoms
Pair time (%) = 0.123725 (35.7562)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000100136 (0.028939)
Outpt time (%) = 4.79221e-05 (0.0138494)
Other time (%) = 0.222151 (64.201)
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 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: 810432 ave 810432 max 810432 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
unfix 1
fix 1 all box/relax aniso 0.0 vmax 0.001
minimize 1.0e-14 1.0e-20 1000 10000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
master list distance cutoff = 12.5
Memory usage per processor = 8.27781 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
2 0.99818299 -3.8453114 -3.8454403 -0.98377404 -2.8616663 0.72283727 -1.4456745 25.62 25.62 25.62 16816.568
3 0.99818299 -3.8453249 -3.8454539 -0.98259134 -2.8628625 0.72283983 -1.4456797 25.610878 25.610878 25.610878 16798.611
4 0.99818299 -3.8453255 -3.8454544 -0.98248805 -2.8629664 0.7228394 -1.4456788 25.610392 25.610392 25.610392 16797.656
5 0.99818299 -3.8453255 -3.8454544 -0.98252572 -2.8629287 0.7228403 -1.4456806 25.610392 25.610392 25.610392 16797.656
Loop time of 24.2523 on 1 procs for 3 steps with 1296 atoms
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-3.84544029724 -3.84545440474 -3.84545441597
Force two-norm initial, final = 14.244 0.733113
Force max component initial, final = 8.22312 0.41081
Final line search alpha, max atom move = 2.38596e-05 9.80177e-06
Iterations, force evaluations = 3 27
Pair time (%) = 1.81002 (7.46331)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00140429 (0.00579032)
Outpt time (%) = 5.60284e-05 (0.000231023)
Other time (%) = 22.4408 (92.5307)
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 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: 810432 ave 810432 max 810432 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
min_modify dmax 0.2 line quadratic
unfix 1
fix 1 all nve
run 1
Neighbor list info ...
1 neighbor list requests
update every 20 steps, delay 0 steps, check no
master list distance cutoff = 12.5
Memory usage per processor = 6.65281 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
5 0.99818299 -3.8453255 -3.8454544 -0.98252572 -2.8629287 0.7228403 -1.4456806 25.610392 25.610392 25.610392 16797.656
6 0.99600405 -3.8453255 -3.8454541 -0.98252544 -2.8629287 0.72284035 -1.4456807 25.610392 25.610392 25.610392 16797.656
Loop time of 0.333947 on 1 procs for 1 steps with 1296 atoms
Pair time (%) = 0.0653648 (19.5734)
Neigh time (%) = 0 (0)
Comm time (%) = 5.126e-05 (0.0153497)
Outpt time (%) = 2.47955e-05 (0.00742499)
Other time (%) = 0.268506 (80.4038)
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 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: 810432 ave 810432 max 810432 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
unfix 1
unfix 2
#undump 1
### 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 NULL 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]
WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:665)
run 10
Memory usage per processor = 7.02781 Mbytes
Step Lx Ly Lz Xy Xz Yz fx[1] fx[2] fx[3] fx[4] fx[5] fx[6]
6 25.610392 25.610392 25.610392 0 0 0 -658401.77 -658419.97 -658392.44 -60685.043 -70926.603 -51580.218
7 25.610648 25.610392 25.610392 0 0 0 -658401.77 -658419.97 -658392.44 -60685.043 -70926.603 -51580.218
8 25.610904 25.610392 25.610392 0 0 0 -329933.78 -638001.39 -637973.86 -60683.825 -70925.179 -51575.113
9 25.611161 25.610392 25.610392 0 0 0 -1465.948 -617588.28 -617560.74 -60682.607 -70923.756 -51570.007
10 25.611417 25.610392 25.610392 0 0 0 327001.72 -597180.62 -597153.09 -60681.389 -70922.332 -51564.902
11 25.611673 25.610392 25.610392 0 0 0 655469.22 -576778.42 -576750.89 -60680.171 -70920.908 -51559.797
12 25.611929 25.610392 25.610392 0 0 0 983936.56 -556381.68 -556354.15 -60678.953 -70919.485 -51554.692
13 25.612185 25.610392 25.610392 0 0 0 1312403.7 -535990.39 -535962.87 -60677.735 -70918.061 -51549.588
14 25.612441 25.610392 25.610392 0 0 0 1640870.7 -515604.57 -515577.05 -60676.517 -70916.637 -51544.483
15 25.612697 25.610392 25.610392 0 0 0 1969337.6 -495224.2 -495196.68 -60675.299 -70915.213 -51539.378
16 25.612953 25.610392 25.610392 0 0 0 2297804.2 -474849.28 -474821.77 -60674.082 -70913.79 -51534.274
Loop time of 0.710404 on 1 procs for 10 steps with 1296 atoms
Pair time (%) = 0.707336 (99.5681)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000524282 (0.0738006)
Outpt time (%) = 0.00224686 (0.316279)
Other time (%) = 0.00029707 (0.041817)
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 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: 810432 ave 810432 max 810432 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 810432
Ave neighs/atom = 625.333
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 NULL 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 = 7.77781 Mbytes
Step Lx Ly Lz Xy Xz Yz fz[1] fz[2] fz[3] fz[4] fz[5] fz[6]
16 25.612953 25.610392 25.610392 0 0 0 2626270.7 -454479.83 -454452.32 -60672.864 -70912.366 -51529.17
17 25.612953 25.610392 25.610648 0 0 0 2626270.7 -454479.83 -454452.32 -60672.864 -70912.366 -51529.17
18 25.612953 25.610392 25.610904 0 0 0 2646636.7 -434056.14 -126036.92 -60666.856 -70910.942 -51528.134
19 25.612953 25.610392 25.611161 0 0 0 2666997.3 -413637.91 202378.33 -60660.849 -70909.518 -51527.099
20 25.612953 25.610392 25.611417 0 0 0 2687352.4 -393225.15 530793.41 -60654.842 -70908.094 -51526.063
21 25.612953 25.610392 25.611673 0 0 0 2707702 -372817.84 859208.34 -60648.835 -70906.671 -51525.028
22 25.612953 25.610392 25.611929 0 0 0 2728046.2 -352415.99 1187623.1 -60642.828 -70905.247 -51523.993
23 25.612953 25.610392 25.612185 0 0 0 2748384.9 -332019.6 1516037.7 -60636.821 -70903.823 -51522.958
24 25.612953 25.610392 25.612441 0 0 0 2768718.2 -311628.66 1844452.1 -60630.815 -70902.399 -51521.923
25 25.612953 25.610392 25.612697 0 0 0 2789045.9 -291243.19 2172866.4 -60624.808 -70900.976 -51520.888
26 25.612953 25.610392 25.612953 0 0 0 2809368.3 -270863.16 2501280.5 -60618.802 -70899.553 -51519.854
Loop time of 0.710274 on 1 procs for 10 steps with 1296 atoms
Pair time (%) = 0.707209 (99.5685)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000524759 (0.0738812)
Outpt time (%) = 0.00224233 (0.315699)
Other time (%) = 0.000298023 (0.0419589)
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 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: 810432 ave 810432 max 810432 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 810432
Ave neighs/atom = 625.333
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 NULL 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 = 8.54308 Mbytes
Step Lx Ly Lz Xy Xz Yz fyz[1] fyz[2] fyz[3] fyz[4] fyz[5] fyz[6]
26 25.612953 25.610392 25.612953 0 0 0 2829685.1 -250488.6 2829694.5 -60612.796 -70898.13 -51518.819
27 25.612953 25.610392 25.612953 0 0 5.1225907e-07 2829685.1 -250488.6 2829694.5 -60612.796 -70898.13 -51518.819
28 25.612953 25.610392 25.612953 0 0 1.0245181e-06 2829685.1 -250488.6 2829694.5 -60612.79 -70898.123 -51255.309
29 25.612953 25.610392 25.612953 0 0 1.5367772e-06 2829685.1 -250488.59 2829694.5 -60612.784 -70898.117 -50991.8
30 25.612953 25.610392 25.612953 0 0 2.0490363e-06 2829685.1 -250488.59 2829694.5 -60612.778 -70898.11 -50728.29
31 25.612953 25.610392 25.612953 0 0 2.5612953e-06 2829685.2 -250488.59 2829694.5 -60612.772 -70898.104 -50464.78
32 25.612953 25.610392 25.612953 0 0 3.0735544e-06 2829685.2 -250488.59 2829694.5 -60612.765 -70898.097 -50201.27
33 25.612953 25.610392 25.612953 0 0 3.5858135e-06 2829685.2 -250488.59 2829694.5 -60612.759 -70898.091 -49937.76
34 25.612953 25.610392 25.612953 0 0 4.0980725e-06 2829685.2 -250488.59 2829694.5 -60612.753 -70898.085 -49674.25
35 25.612953 25.610392 25.612953 0 0 4.6103316e-06 2829685.2 -250488.59 2829694.5 -60612.747 -70898.078 -49410.741
36 25.612953 25.610392 25.612953 0 0 5.1225907e-06 2829685.2 -250488.59 2829694.5 -60612.741 -70898.072 -49147.231
Loop time of 0.693701 on 1 procs for 10 steps with 1296 atoms
Pair time (%) = 0.69068 (99.5645)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00051713 (0.0745465)
Outpt time (%) = 0.00221395 (0.319151)
Other time (%) = 0.000290155 (0.0418272)
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 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: 810432 ave 810432 max 810432 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 810432
Ave neighs/atom = 625.333
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 NULL 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 = 9.29308 Mbytes
Step Lx Ly Lz Xy Xz Yz fxy[1] fxy[2] fxy[3] fxy[4] fxy[5] fxy[6]
36 25.612953 25.610392 25.612953 0 0 5.1225907e-06 2829685.2 -250488.59 2829694.5 -60612.735 -70898.065 -48883.721
37 25.612953 25.610392 25.612953 5.1220784e-07 0 5.1225907e-06 2829685.2 -250488.59 2829694.5 -60612.735 -70898.065 -48883.721
38 25.612953 25.610392 25.612953 1.0244157e-06 0 5.1225907e-06 2829685.2 -250488.58 2829694.5 -60349.287 -70898.061 -48883.713
39 25.612953 25.610392 25.612953 1.5366235e-06 0 5.1225907e-06 2829685.2 -250488.58 2829694.5 -60085.839 -70898.057 -48883.706
40 25.612953 25.610392 25.612953 2.0488314e-06 0 5.1225907e-06 2829685.2 -250488.58 2829694.5 -59822.39 -70898.053 -48883.698
41 25.612953 25.610392 25.612953 2.5610392e-06 0 5.1225907e-06 2829685.2 -250488.57 2829694.5 -59558.942 -70898.048 -48883.691
42 25.612953 25.610392 25.612953 3.0732471e-06 0 5.1225907e-06 2829685.2 -250488.57 2829694.5 -59295.494 -70898.044 -48883.683
43 25.612953 25.610392 25.612953 3.5854549e-06 0 5.1225907e-06 2829685.2 -250488.56 2829694.6 -59032.046 -70898.04 -48883.676
44 25.612953 25.610392 25.612953 4.0976627e-06 0 5.1225907e-06 2829685.2 -250488.56 2829694.6 -58768.597 -70898.035 -48883.668
45 25.612953 25.610392 25.612953 4.6098706e-06 0 5.1225907e-06 2829685.2 -250488.56 2829694.6 -58505.149 -70898.031 -48883.661
46 25.612953 25.610392 25.612953 5.1220784e-06 0 5.1225907e-06 2829685.2 -250488.55 2829694.6 -58241.701 -70898.027 -48883.653
Loop time of 0.710342 on 1 procs for 10 steps with 1296 atoms
Pair time (%) = 0.707279 (99.5688)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000520468 (0.07327)
Outpt time (%) = 0.00224543 (0.316105)
Other time (%) = 0.000297308 (0.0418542)
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 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: 810432 ave 810432 max 810432 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
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