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lammps/examples/comb/log.comb.Cu2O.elastic.9Jan12.linux.1
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LAMMPS (10 Jan 2012)
# 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
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
Memory usage per processor = 492.454 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
0 1 -5.307041 -5.3071702 -2.6165358 -2.6906344 0.65426811 -1.3085362 25.62 25.62 25.62 16816.568
1 1.0009873 -5.3550555 -5.3551848 -2.9567646 -2.3984202 0.65426879 -1.3085376 25.62 25.62 25.62 16816.568
2 1.0026929 -5.3550537 -5.3551832 -2.9567602 -2.3984231 0.65426936 -1.3085387 25.62 25.62 25.62 16816.568
Loop time of 0.759578 on 1 procs for 2 steps with 1296 atoms
Pair time (%) = 0.101777 (13.3992)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00014329 (0.0188644)
Outpt time (%) = 6.62804e-05 (0.00872595)
Other time (%) = 0.657591 (86.5732)
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:167)
Memory usage per processor = 493.751 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
2 1.0026929 -5.3334035 -5.333533 -2.9696799 -2.3638531 0.65426936 -1.3085387 25.62 25.62 25.62 16816.568
3 1.0026929 -5.3366561 -5.3367856 -2.9701261 -2.3666596 0.65426936 -1.3085387 25.594382 25.59438 25.59438 16766.17
4 1.0026929 -5.3398622 -5.3399917 -2.9705203 -2.3694714 0.65426936 -1.3085387 25.568763 25.56876 25.56876 16715.873
5 1.0026929 -5.3430214 -5.3431509 -2.9708622 -2.3722886 0.65426936 -1.3085387 25.543145 25.543141 25.54314 16665.677
6 1.0026929 -5.346133 -5.3462625 -2.9711512 -2.3751113 0.65426936 -1.3085387 25.517527 25.517521 25.51752 16615.581
7 1.0026929 -5.3491964 -5.349326 -2.9713866 -2.3779393 0.65426936 -1.3085387 25.491909 25.491901 25.4919 16565.585
8 1.0026929 -5.3522113 -5.3523408 -2.971568 -2.3807728 0.65426936 -1.3085387 25.46629 25.466281 25.46628 16515.69
9 1.0026929 -5.3660227 -5.3661522 -2.9825701 -2.3835821 0.65426936 -1.3085387 25.440672 25.440662 25.44066 16465.896
10 1.0026929 -5.4362377 -5.4363673 -3.0499986 -2.3863686 0.65426936 -1.3085387 25.415054 25.415042 25.41504 16416.201
11 1.0026929 -5.5662016 -5.5663312 -3.1771711 -2.3891601 0.65426936 -1.3085387 25.389436 25.389422 25.38942 16366.607
12 1.0026929 -5.7519309 -5.7520604 -3.360104 -2.3919564 0.65426936 -1.3085387 25.363818 25.363802 25.3638 16317.113
13 1.0026929 -5.9874068 -5.9875363 -3.5927786 -2.3947577 0.65426936 -1.3085387 25.3382 25.338183 25.33818 16267.718
14 1.0026929 -6.2647792 -6.2649087 -3.8673448 -2.3975639 0.65426936 -1.3085387 25.312582 25.312563 25.31256 16218.423
15 1.0026929 -6.5746359 -6.5747654 -4.1743903 -2.400375 0.65426936 -1.3085387 25.286963 25.286943 25.28694 16169.228
16 1.0026929 -6.9063303 -6.9064598 -4.5032687 -2.4031911 0.65426936 -1.3085387 25.261343 25.261323 25.26132 16120.131
17 1.0026929 -7.2483579 -7.2484874 -4.8424753 -2.4060121 0.65426936 -1.3085387 25.235723 25.235703 25.2357 16071.134
18 1.0026929 -7.5887656 -7.5888951 -5.1800571 -2.408838 0.65426936 -1.3085387 25.210104 25.210083 25.21008 16022.236
19 1.0026929 -7.9155773 -7.9157068 -5.504038 -2.4116688 0.65426936 -1.3085387 25.184484 25.184463 25.18446 15973.438
20 1.0026929 -8.217244 -8.2173735 -5.8028522 -2.4145213 0.65426936 -1.3085387 25.158864 25.158844 25.15884 15924.739
21 1.0026929 -8.4831885 -8.483318 -6.0657645 -2.4175535 0.65426936 -1.3085387 25.133244 25.133224 25.133221 15876.139
22 1.0026929 -8.7037271 -8.7038566 -6.2832612 -2.4205954 0.65426936 -1.3085387 25.107624 25.107605 25.107602 15827.639
23 1.0026929 -8.8709155 -8.8710451 -6.4474006 -2.4236444 0.65426936 -1.3085387 25.082004 25.081986 25.081984 15779.238
24 1.0026929 -8.978681 -8.9788105 -6.55211 -2.4267005 0.65426936 -1.3085387 25.056384 25.056368 25.056366 15730.937
25 1.0026929 -9.0230511 -9.0231807 -6.593417 -2.4297637 0.65426936 -1.3085387 25.030764 25.030751 25.030749 15682.736
26 1.0026929 -9.0240292 -9.0241587 -6.5940118 -2.430147 0.65426936 -1.3085387 25.027561 25.027551 25.027549 15676.72
27 1.0026929 -9.0241357 -9.0242652 -6.5939267 -2.4303385 0.65426936 -1.3085387 25.02596 25.025952 25.025951 15673.715
28 1.0026929 -9.0241365 -9.024266 -6.5939394 -2.4303265 0.65426936 -1.3085387 25.026059 25.026052 25.026051 15673.902
29 1.0026929 -9.0241365 -9.024266 -6.5939394 -2.4303265 0.65426936 -1.3085387 25.026059 25.026052 25.026051 15673.902
Loop time of 5.88834 on 1 procs for 27 steps with 1296 atoms
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-5.33353304985 -9.02426597894 -9.02426597894
Force two-norm initial, final = 2433.53 179.132
Force max component initial, final = 1405.03 103.699
Final line search alpha, max atom move = 2.94289e-10 3.05176e-08
Iterations, force evaluations = 27 57
Pair time (%) = 5.50607 (93.508)
Neigh time (%) = 0.363057 (6.16569)
Comm time (%) = 0.00463033 (0.0786355)
Outpt time (%) = 0.000666857 (0.011325)
Other time (%) = 0.0139146 (0.236307)
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: 862272 ave 862272 max 862272 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 862272
Ave neighs/atom = 665.333
Neighbor list builds = 4
Dangerous builds = 0
min_modify dmax 0.2 line quadratic
unfix 1
fix 1 all nve
run 1
Memory usage per processor = 492.631 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
29 1.0026929 -9.0241365 -9.024266 -6.5939394 -2.4303265 0.63678555 -1.2735711 25.026059 25.026052 25.026051 15673.902
30 0.88741647 -9.0386219 -9.0387365 -6.7151088 -2.3236278 0.63678579 -1.2735716 25.026059 25.026052 25.026051 15673.902
Loop time of 0.476254 on 1 procs for 1 steps with 1296 atoms
Pair time (%) = 0.100822 (21.1698)
Neigh time (%) = 0 (0)
Comm time (%) = 6.79493e-05 (0.0142674)
Outpt time (%) = 2.69413e-05 (0.00565692)
Other time (%) = 0.375337 (78.8103)
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: 862272 ave 862272 max 862272 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 862272
Ave neighs/atom = 665.333
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 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:471)
run 10
Memory usage per processor = 492.89 Mbytes
Step Lx Ly Lz Xy Xz Yz fx[1] fx[2] fx[3] fx[4] fx[5] fx[6]
30 25.026059 25.026052 25.026051 0 0 0 -1.504334e+08 -1.5326204e+08 -1.5372549e+08 1064068.9 -599765.62 414723.34
31 25.026309 25.026052 25.026051 0 0 0 -1.504334e+08 -1.5326204e+08 -1.5372549e+08 1064068.9 -599765.62 414723.34
32 25.026559 25.026052 25.026051 0 0 0 65979938 -45173439 -45636876 1064082.2 -599660.21 414715.59
33 25.02681 25.026052 25.026051 0 0 0 2.8240082e+08 62914604 62451183 1064095.4 -599554.81 414707.84
34 25.02706 25.026052 25.026051 0 0 0 4.98829e+08 1.7100197e+08 1.7053856e+08 1064108.6 -599449.41 414700.08
35 25.02731 25.026052 25.026051 0 0 0 7.1526424e+08 2.7908854e+08 2.7862515e+08 1064121.9 -599344.01 414692.33
36 25.02756 25.026052 25.026051 0 0 0 9.3170631e+08 3.8717419e+08 3.8671082e+08 1064135.1 -599238.61 414684.58
37 25.027811 25.026052 25.026051 0 0 0 1.148155e+09 4.9525881e+08 4.9479545e+08 1064148.4 -599133.22 414676.83
38 25.028061 25.026052 25.026051 0 0 0 1.36461e+09 6.0334227e+08 6.0287893e+08 1064161.6 -599027.84 414669.08
39 25.028311 25.026052 25.026051 0 0 0 1.5810711e+09 7.1142446e+08 7.1096114e+08 1064174.9 -598922.45 414661.33
40 25.028561 25.026052 25.026051 0 0 0 1.7975381e+09 8.1950525e+08 8.1904196e+08 1064188.2 -598817.07 414653.58
Loop time of 1.1738 on 1 procs for 10 steps with 1296 atoms
Pair time (%) = 1.16988 (99.6661)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000679731 (0.0579088)
Outpt time (%) = 0.00296259 (0.252394)
Other time (%) = 0.000277042 (0.0236022)
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: 862272 ave 862272 max 862272 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 862272
Ave neighs/atom = 665.333
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 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 = 493.407 Mbytes
Step Lx Ly Lz Xy Xz Yz fz[1] fz[2] fz[3] fz[4] fz[5] fz[6]
40 25.028561 25.026052 25.026051 0 0 0 2.0140107e+09 9.2758454e+08 9.2712126e+08 1064201.4 -598711.69 414645.83
41 25.028561 25.026052 25.026302 0 0 0 2.0140107e+09 9.2758454e+08 9.2712126e+08 1064201.4 -598711.69 414645.83
42 25.028561 25.026052 25.026552 0 0 0 2.1220992e+09 1.0356731e+09 1.1435342e+09 1064179.7 -598601.58 414637.81
43 25.028561 25.026052 25.026802 0 0 0 2.2301859e+09 1.1437611e+09 1.3599535e+09 1064158 -598491.46 414629.79
44 25.028561 25.026052 25.027052 0 0 0 2.3382708e+09 1.2518485e+09 1.576379e+09 1064136.3 -598381.35 414621.77
45 25.028561 25.026052 25.027303 0 0 0 2.4463536e+09 1.359935e+09 1.7928103e+09 1064114.7 -598271.25 414613.74
46 25.028561 25.026052 25.027553 0 0 0 2.5544344e+09 1.4680207e+09 2.0092472e+09 1064093 -598161.15 414605.7
47 25.028561 25.026052 25.027803 0 0 0 2.662513e+09 1.5761053e+09 2.2256896e+09 1064071.3 -598051.06 414597.67
48 25.028561 25.026052 25.028053 0 0 0 2.7705891e+09 1.6841887e+09 2.4421371e+09 1064049.6 -597940.97 414589.63
49 25.028561 25.026052 25.028304 0 0 0 2.8786629e+09 1.7922709e+09 2.6585895e+09 1064027.9 -597830.89 414581.58
50 25.028561 25.026052 25.028554 0 0 0 2.986734e+09 1.9003517e+09 2.8750466e+09 1064006.2 -597720.81 414573.53
Loop time of 1.17224 on 1 procs for 10 steps with 1296 atoms
Pair time (%) = 1.16836 (99.6691)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000671864 (0.0573147)
Outpt time (%) = 0.00293803 (0.250635)
Other time (%) = 0.000269175 (0.0229625)
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: 862272 ave 862272 max 862272 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 862272
Ave neighs/atom = 665.333
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 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 = 493.924 Mbytes
Step Lx Ly Lz Xy Xz Yz fyz[1] fyz[2] fyz[3] fyz[4] fyz[5] fyz[6]
50 25.028561 25.026052 25.028554 0 0 0 3.0948025e+09 2.008431e+09 3.0915082e+09 1063984.5 -597610.74 414565.48
51 25.028561 25.026052 25.028554 0 0 5.0057108e-07 3.0948025e+09 2.008431e+09 3.0915082e+09 1063984.5 -597610.74 414565.48
52 25.028561 25.026052 25.028554 0 0 1.0011422e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 1063984.5 -597610.79 631065.93
53 25.028561 25.026052 25.028554 0 0 1.5017132e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 1063984.5 -597610.83 847566.39
54 25.028561 25.026052 25.028554 0 0 2.0022843e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 1063984.5 -597610.88 1064066.8
55 25.028561 25.026052 25.028554 0 0 2.5028554e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 1063984.6 -597610.93 1280567.3
56 25.028561 25.026052 25.028554 0 0 3.0034265e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 1063984.6 -597610.97 1497067.7
57 25.028561 25.026052 25.028554 0 0 3.5039975e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 1063984.6 -597611.02 1713568.2
58 25.028561 25.026052 25.028554 0 0 4.0045686e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 1063984.6 -597611.06 1930068.7
59 25.028561 25.026052 25.028554 0 0 4.5051397e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 1063984.6 -597611.11 2146569.1
60 25.028561 25.026052 25.028554 0 0 5.0057108e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 1063984.6 -597611.16 2363069.6
Loop time of 1.17218 on 1 procs for 10 steps with 1296 atoms
Pair time (%) = 1.16831 (99.6701)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000669956 (0.0571549)
Outpt time (%) = 0.00293446 (0.250342)
Other time (%) = 0.000262737 (0.0224145)
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: 862272 ave 862272 max 862272 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 862272
Ave neighs/atom = 665.333
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 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 = 494.441 Mbytes
Step Lx Ly Lz Xy Xz Yz fxy[1] fxy[2] fxy[3] fxy[4] fxy[5] fxy[6]
60 25.028561 25.026052 25.028554 0 0 5.0057108e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 1063984.6 -597611.2 2579570
61 25.028561 25.026052 25.028554 5.0052105e-07 0 5.0057108e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 1063984.6 -597611.2 2579570
62 25.028561 25.026052 25.028554 1.0010421e-06 0 5.0057108e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 1280463.3 -597611.17 2579570
63 25.028561 25.026052 25.028554 1.5015631e-06 0 5.0057108e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 1496942 -597611.15 2579570
64 25.028561 25.026052 25.028554 2.0020842e-06 0 5.0057108e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 1713420.7 -597611.12 2579570.1
65 25.028561 25.026052 25.028554 2.5026052e-06 0 5.0057108e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 1929899.5 -597611.09 2579570.1
66 25.028561 25.026052 25.028554 3.0031263e-06 0 5.0057108e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 2146378.2 -597611.06 2579570.1
67 25.028561 25.026052 25.028554 3.5036473e-06 0 5.0057108e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 2362856.9 -597611.03 2579570.1
68 25.028561 25.026052 25.028554 4.0041684e-06 0 5.0057108e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 2579335.6 -597611 2579570.1
69 25.028561 25.026052 25.028554 4.5046894e-06 0 5.0057108e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 2795814.4 -597610.97 2579570.1
70 25.028561 25.026052 25.028554 5.0052105e-06 0 5.0057108e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 3012293.1 -597610.95 2579570.1
Loop time of 1.17232 on 1 procs for 10 steps with 1296 atoms
Pair time (%) = 1.16846 (99.6703)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000672817 (0.0573919)
Outpt time (%) = 0.00292802 (0.249763)
Other time (%) = 0.000264168 (0.0225338)
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: 862272 ave 862272 max 862272 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 862272
Ave neighs/atom = 665.333
Neighbor list builds = 0
Dangerous builds = 0
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