forked from lijiext/lammps
316 lines
16 KiB
Groff
316 lines
16 KiB
Groff
LAMMPS (18 Feb 2013)
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# Cu2O crystal, qeq on, minimizes, then calculates elastic constants
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units metal
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atom_style charge
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dimension 3
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boundary p p p
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read_data data.Cu2O
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triclinic box = (0 0 0) to (25.62 25.62 25.62) with tilt (0 0 0)
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1 by 2 by 2 MPI processor grid
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1296 atoms
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mass 1 63.54
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group type1 type 1
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864 atoms in group type1
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compute charge1 type1 property/atom q
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compute q1 type1 reduce ave c_charge1
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mass 2 16.00
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group type2 type 2
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432 atoms in group type2
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compute charge2 type2 property/atom q
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compute q2 type2 reduce ave c_charge2
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velocity all create 1.0 277387
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pair_style comb
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pair_coeff * * ffield.comb Cu O
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neighbor 0.5 bin
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neigh_modify every 20 delay 0 check no
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timestep 0.00020
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thermo_style custom step temp etotal pe evdwl ecoul c_q1 c_q2 lx ly lz vol
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thermo_modify norm yes
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thermo 1
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fix 1 all nve
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fix 2 all qeq/comb 1 0.0001
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#dump 1 all cfg 1 *.cfg id type xs ys zs q f_2 vx vy vz fx fy fz
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#dump_modify 1 element Cu O
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run 2
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Memory usage per processor = 3.94168 Mbytes
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Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
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0 1 -3.8383547 -3.8384838 -1.1478494 -2.6906344 0.7228352 -1.4456704 25.62 25.62 25.62 16816.568
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1 0.99939067 -3.8453114 -3.8454405 -0.98378996 -2.8616505 0.72283606 -1.4456721 25.62 25.62 25.62 16816.568
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2 0.9975671 -3.8453114 -3.8454402 -0.98378316 -2.8616571 0.72283727 -1.4456745 25.62 25.62 25.62 16816.568
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Loop time of 0.0779197 on 4 procs for 2 steps with 1296 atoms
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Pair time (%) = 0.0256954 (32.9768)
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Neigh time (%) = 0 (0)
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Comm time (%) = 0.00067848 (0.870742)
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Outpt time (%) = 6.35386e-05 (0.0815436)
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Other time (%) = 0.0514823 (66.0709)
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Nlocal: 324 ave 324 max 324 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 4943 ave 4943 max 4943 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Neighs: 0 ave 0 max 0 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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FullNghs: 202608 ave 202608 max 202608 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 810432
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Ave neighs/atom = 625.333
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Neighbor list builds = 0
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Dangerous builds = 0
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unfix 1
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fix 1 all box/relax aniso 0.0 vmax 0.001
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minimize 1.0e-14 1.0e-20 1000 10000
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WARNING: Resetting reneighboring criteria during minimization (min.cpp:173)
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Memory usage per processor = 5.27942 Mbytes
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Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
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2 0.9975671 -3.8453114 -3.8454402 -0.98377395 -2.8616663 0.72283727 -1.4456745 25.62 25.62 25.62 16816.568
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3 0.9975671 -3.8453323 -3.8454611 -0.98048803 -2.8649731 0.72283727 -1.4456745 25.59438 25.59438 25.59438 16766.169
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4 0.9975671 -3.8453323 -3.8454611 -0.98048803 -2.8649731 0.72283727 -1.4456745 25.59438 25.59438 25.59438 16766.169
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Loop time of 0.202277 on 4 procs for 2 steps with 1296 atoms
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Minimization stats:
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Stopping criterion = linesearch alpha is zero
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Energy initial, next-to-last, final =
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-3.84544021729 -3.84546110694 -3.84546110694
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Force two-norm initial, final = 14.2445 25.7657
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Force max component initial, final = 8.22308 14.8753
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Final line search alpha, max atom move = 1.64125e-08 2.44141e-07
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Iterations, force evaluations = 2 14
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Pair time (%) = 0.194534 (96.1723)
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Neigh time (%) = 0 (0)
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Comm time (%) = 0.00576496 (2.85004)
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Outpt time (%) = 3.05772e-05 (0.0151165)
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Other time (%) = 0.00194705 (0.962565)
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Nlocal: 324 ave 331 max 321 min
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Histogram: 1 2 0 0 0 0 0 0 0 1
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Nghost: 4943 ave 4946 max 4936 min
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Histogram: 1 0 0 0 0 0 0 0 0 3
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Neighs: 0 ave 0 max 0 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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FullNghs: 202608 ave 207074 max 200694 min
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Histogram: 1 2 0 0 0 0 0 0 0 1
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Total # of neighbors = 810432
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Ave neighs/atom = 625.333
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Neighbor list builds = 0
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Dangerous builds = 0
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min_modify dmax 0.2 line quadratic
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unfix 1
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fix 1 all nve
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run 1
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Memory usage per processor = 4.25229 Mbytes
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Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
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4 0.9975671 -3.8453323 -3.8454611 -0.98048803 -2.8649731 0.72283983 -1.4456797 25.59438 25.59438 25.59438 16766.169
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5 0.99455526 -3.8453323 -3.8454607 -0.98046814 -2.8649926 0.72284124 -1.4456825 25.59438 25.59438 25.59438 16766.169
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Loop time of 0.0442772 on 4 procs for 1 steps with 1296 atoms
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Pair time (%) = 0.013078 (29.5366)
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Neigh time (%) = 0 (0)
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Comm time (%) = 0.000556648 (1.25719)
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Outpt time (%) = 3.05772e-05 (0.0690585)
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Other time (%) = 0.030612 (69.1372)
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Nlocal: 324 ave 331 max 321 min
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Histogram: 1 2 0 0 0 0 0 0 0 1
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Nghost: 4943 ave 4946 max 4936 min
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Histogram: 1 0 0 0 0 0 0 0 0 3
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Neighs: 0 ave 0 max 0 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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FullNghs: 202608 ave 207074 max 200694 min
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Histogram: 1 2 0 0 0 0 0 0 0 1
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Total # of neighbors = 810432
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Ave neighs/atom = 625.333
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Neighbor list builds = 0
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Dangerous builds = 0
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unfix 1
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unfix 2
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#undump 1
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### copy lines after this to any input script for elastic calculations ###
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## Elastic constants calculations: strain box, measure box stress
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## strain x, measure s_x, s_y, s_z, s_yz:
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## calculates C11, C12, C13 and C14
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fix 2 all deform 1 x scale 1.0001 remap x
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compute perfx all stress/atom pair
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compute fx all reduce sum c_perfx[1] c_perfx[2] c_perfx[3] c_perfx[4] c_perfx[5] c_perfx[6]
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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]
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WARNING: New thermo_style command, previous thermo_modify settings will be lost (output.cpp:663)
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run 10
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Memory usage per processor = 4.48932 Mbytes
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Step Lx Ly Lz Xy Xz Yz fx[1] fx[2] fx[3] fx[4] fx[5] fx[6]
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5 25.59438 25.59438 25.59438 0 0 0 -23809505 -23809514 -23809500 -57057.965 -66762.055 -48486.82
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6 25.594636 25.59438 25.59438 0 0 0 -23809505 -23809514 -23809500 -57057.965 -66762.055 -48486.82
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7 25.594892 25.59438 25.59438 0 0 0 -23480575 -23788468 -23788455 -57056.822 -66760.719 -48482.06
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8 25.595148 25.59438 25.59438 0 0 0 -23151645 -23767428 -23767415 -57055.68 -66759.384 -48477.299
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9 25.595404 25.59438 25.59438 0 0 0 -22822715 -23746393 -23746380 -57054.538 -66758.05 -48472.539
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10 25.59566 25.59438 25.59438 0 0 0 -22493785 -23725364 -23725351 -57053.397 -66756.716 -48467.778
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11 25.595916 25.59438 25.59438 0 0 0 -22164855 -23704340 -23704327 -57052.256 -66755.382 -48463.018
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12 25.596172 25.59438 25.59438 0 0 0 -21835925 -23683322 -23683309 -57051.116 -66754.048 -48458.258
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13 25.596428 25.59438 25.59438 0 0 0 -21506996 -23662310 -23662296 -57049.976 -66752.714 -48453.499
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14 25.596684 25.59438 25.59438 0 0 0 -21178067 -23641302 -23641289 -57048.836 -66751.379 -48448.74
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15 25.59694 25.59438 25.59438 0 0 0 -20849138 -23620300 -23620287 -57047.697 -66750.045 -48443.981
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Loop time of 0.166247 on 4 procs for 10 steps with 1296 atoms
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Pair time (%) = 0.157497 (94.7364)
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Neigh time (%) = 0 (0)
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Comm time (%) = 0.00575155 (3.45963)
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Outpt time (%) = 0.00286341 (1.72238)
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Other time (%) = 0.00013572 (0.0816372)
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Nlocal: 324 ave 331 max 321 min
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Histogram: 1 2 0 0 0 0 0 0 0 1
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Nghost: 4943 ave 4946 max 4936 min
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Histogram: 1 0 0 0 0 0 0 0 0 3
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Neighs: 0 ave 0 max 0 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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FullNghs: 202608 ave 207074 max 200694 min
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Histogram: 1 2 0 0 0 0 0 0 0 1
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Total # of neighbors = 810432
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Ave neighs/atom = 625.333
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Neighbor list builds = 0
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Dangerous builds = 0
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## strain z, measure s_z: calculates C33
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fix 2 all deform 1 z scale 1.0001 remap x
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compute perfz all stress/atom pair
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compute fz all reduce sum c_perfz[1] c_perfz[2] c_perfz[3] c_perfz[4] c_perfz[5] c_perfz[6]
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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]
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run 10
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Memory usage per processor = 4.96338 Mbytes
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Step Lx Ly Lz Xy Xz Yz fz[1] fz[2] fz[3] fz[4] fz[5] fz[6]
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15 25.59694 25.59438 25.59438 0 0 0 -20520209 -23599304 -23599291 -57046.557 -66748.711 -48439.223
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16 25.59694 25.59438 25.594636 0 0 0 -20520209 -23599304 -23599291 -57046.557 -66748.711 -48439.223
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17 25.59694 25.59438 25.594892 0 0 0 -20499216 -23578254 -23270413 -57040.958 -66747.376 -48438.253
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18 25.59694 25.59438 25.595148 0 0 0 -20478228 -23557209 -22941536 -57035.359 -66746.041 -48437.283
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19 25.59694 25.59438 25.595404 0 0 0 -20457246 -23536169 -22612658 -57029.76 -66744.706 -48436.313
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20 25.59694 25.59438 25.59566 0 0 0 -20436270 -23515135 -22283781 -57024.162 -66743.371 -48435.343
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21 25.59694 25.59438 25.595916 0 0 0 -20415299 -23494106 -21954904 -57018.563 -66742.035 -48434.374
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22 25.59694 25.59438 25.596172 0 0 0 -20394333 -23473083 -21626027 -57012.964 -66740.7 -48433.404
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23 25.59694 25.59438 25.596428 0 0 0 -20373373 -23452065 -21297150 -57007.366 -66739.366 -48432.435
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24 25.59694 25.59438 25.596684 0 0 0 -20352419 -23431053 -20968274 -57001.768 -66738.031 -48431.466
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25 25.59694 25.59438 25.59694 0 0 0 -20331470 -23410046 -20639397 -56996.17 -66736.696 -48430.497
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Loop time of 0.16598 on 4 procs for 10 steps with 1296 atoms
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Pair time (%) = 0.157451 (94.8617)
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Neigh time (%) = 0 (0)
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Comm time (%) = 0.00552714 (3.33001)
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Outpt time (%) = 0.00287336 (1.73115)
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Other time (%) = 0.00012809 (0.0771722)
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Nlocal: 324 ave 331 max 321 min
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Histogram: 1 2 0 0 0 0 0 0 0 1
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Nghost: 4943 ave 4946 max 4936 min
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Histogram: 1 0 0 0 0 0 0 0 0 3
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Neighs: 0 ave 0 max 0 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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FullNghs: 202608 ave 207074 max 200694 min
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Histogram: 1 2 0 0 0 0 0 0 0 1
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Total # of neighbors = 810432
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Ave neighs/atom = 625.333
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Neighbor list builds = 0
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Dangerous builds = 0
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## strain yz, measure s_yz: calculates C44
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fix 2 all deform 1 yz erate 0.0001 remap x
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compute perfyz all stress/atom pair
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compute fyz all reduce sum c_perfyz[1] c_perfyz[2] c_perfyz[3] c_perfyz[4] c_perfyz[5] c_perfyz[6]
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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]
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run 10
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Memory usage per processor = 5.43744 Mbytes
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Step Lx Ly Lz Xy Xz Yz fyz[1] fyz[2] fyz[3] fyz[4] fyz[5] fyz[6]
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25 25.59694 25.59438 25.59694 0 0 0 -20310526 -23389045 -20310521 -56990.572 -66735.361 -48429.528
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26 25.59694 25.59438 25.59694 0 0 5.1193879e-07 -20310526 -23389045 -20310521 -56990.572 -66735.361 -48429.528
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27 25.59694 25.59438 25.59694 0 0 1.0238776e-06 -20310526 -23389045 -20310521 -56990.566 -66735.355 -48165.06
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28 25.59694 25.59438 25.59694 0 0 1.5358164e-06 -20310526 -23389045 -20310521 -56990.561 -66735.349 -47900.593
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29 25.59694 25.59438 25.59694 0 0 2.0477552e-06 -20310526 -23389045 -20310521 -56990.555 -66735.343 -47636.125
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30 25.59694 25.59438 25.59694 0 0 2.559694e-06 -20310526 -23389045 -20310521 -56990.549 -66735.337 -47371.657
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31 25.59694 25.59438 25.59694 0 0 3.0716328e-06 -20310526 -23389045 -20310521 -56990.544 -66735.331 -47107.19
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32 25.59694 25.59438 25.59694 0 0 3.5835716e-06 -20310526 -23389045 -20310521 -56990.538 -66735.325 -46842.722
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33 25.59694 25.59438 25.59694 0 0 4.0955103e-06 -20310526 -23389045 -20310521 -56990.532 -66735.319 -46578.254
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34 25.59694 25.59438 25.59694 0 0 4.6074491e-06 -20310526 -23389045 -20310521 -56990.527 -66735.313 -46313.787
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35 25.59694 25.59438 25.59694 0 0 5.1193879e-06 -20310526 -23389045 -20310521 -56990.521 -66735.307 -46049.319
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Loop time of 0.166387 on 4 procs for 10 steps with 1296 atoms
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Pair time (%) = 0.158143 (95.0453)
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Neigh time (%) = 0 (0)
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Comm time (%) = 0.00517648 (3.11111)
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Outpt time (%) = 0.00292784 (1.75965)
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Other time (%) = 0.000139594 (0.0838971)
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Nlocal: 324 ave 331 max 321 min
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Histogram: 1 2 0 0 0 0 0 0 0 1
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Nghost: 4943 ave 4946 max 4936 min
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Histogram: 1 0 0 0 0 0 0 0 0 3
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Neighs: 0 ave 0 max 0 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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FullNghs: 202608 ave 207074 max 200694 min
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Histogram: 1 2 0 0 0 0 0 0 0 1
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Total # of neighbors = 810432
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Ave neighs/atom = 625.333
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Neighbor list builds = 0
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Dangerous builds = 0
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## strain xy, measure s_xy: calculates C66
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fix 2 all deform 1 xy erate 0.0001 remap x
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compute perfxy all stress/atom pair
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compute fxy all reduce sum c_perfxy[1] c_perfxy[2] c_perfxy[3] c_perfxy[4] c_perfxy[5] c_perfxy[6]
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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]
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run 10
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Memory usage per processor = 5.9115 Mbytes
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Step Lx Ly Lz Xy Xz Yz fxy[1] fxy[2] fxy[3] fxy[4] fxy[5] fxy[6]
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35 25.59694 25.59438 25.59694 0 0 5.1193879e-06 -20310526 -23389045 -20310521 -56990.515 -66735.301 -45784.851
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36 25.59694 25.59438 25.59694 5.118876e-07 0 5.1193879e-06 -20310526 -23389045 -20310521 -56990.515 -66735.301 -45784.851
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37 25.59694 25.59438 25.59694 1.0237752e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -56726.109 -66735.297 -45784.844
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38 25.59694 25.59438 25.59694 1.5356628e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -56461.703 -66735.293 -45784.837
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39 25.59694 25.59438 25.59694 2.0475504e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -56197.297 -66735.289 -45784.83
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40 25.59694 25.59438 25.59694 2.559438e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -55932.891 -66735.285 -45784.823
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41 25.59694 25.59438 25.59694 3.0713256e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -55668.485 -66735.281 -45784.816
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42 25.59694 25.59438 25.59694 3.5832132e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -55404.079 -66735.277 -45784.809
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43 25.59694 25.59438 25.59694 4.0951008e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -55139.672 -66735.273 -45784.802
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44 25.59694 25.59438 25.59694 4.6069884e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -54875.266 -66735.269 -45784.795
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45 25.59694 25.59438 25.59694 5.118876e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -54610.86 -66735.265 -45784.788
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Loop time of 0.166469 on 4 procs for 10 steps with 1296 atoms
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Pair time (%) = 0.160847 (96.6229)
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Neigh time (%) = 0 (0)
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Comm time (%) = 0.00259542 (1.5591)
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Outpt time (%) = 0.00287849 (1.72914)
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Other time (%) = 0.000147939 (0.0888686)
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Nlocal: 324 ave 331 max 321 min
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Histogram: 1 2 0 0 0 0 0 0 0 1
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Nghost: 4943 ave 4946 max 4936 min
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Histogram: 1 0 0 0 0 0 0 0 0 3
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Neighs: 0 ave 0 max 0 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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FullNghs: 202608 ave 207074 max 200694 min
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Histogram: 1 2 0 0 0 0 0 0 0 1
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Total # of neighbors = 810432
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Ave neighs/atom = 625.333
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Neighbor list builds = 0
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Dangerous builds = 0
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