forked from lijiext/lammps
330 lines
17 KiB
Groff
330 lines
17 KiB
Groff
LAMMPS (30 Apr 2015)
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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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reading atoms ...
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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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Neighbor list info ...
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1 neighbor list requests
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update every 20 steps, delay 0 steps, check no
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master list distance cutoff = 12.5
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Memory usage per processor = 6.28094 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 0.99954481 -3.8453114 -3.8454405 -0.98378999 -2.8616505 0.72283606 -1.4456721 25.62 25.62 25.62 16816.568
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2 0.99818299 -3.8453114 -3.8454403 -0.98378324 -2.8616571 0.72283727 -1.4456745 25.62 25.62 25.62 16816.568
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Loop time of 0.0905606 on 4 procs for 2 steps with 1296 atoms
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Pair time (%) = 0.0316537 (34.9531)
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Neigh time (%) = 0 (0)
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Comm time (%) = 0.000888228 (0.980812)
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Outpt time (%) = 7.83205e-05 (0.0864841)
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Other time (%) = 0.0579403 (63.9796)
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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:168)
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Neighbor list info ...
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1 neighbor list requests
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update every 1 steps, delay 0 steps, check yes
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master list distance cutoff = 12.5
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Memory usage per processor = 8.15594 Mbytes
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Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
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2 0.99818299 -3.8453114 -3.8454403 -0.98377404 -2.8616663 0.72283727 -1.4456745 25.62 25.62 25.62 16816.568
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3 0.99818299 -3.8453249 -3.8454539 -0.98259134 -2.8628625 0.72283983 -1.4456797 25.610878 25.610878 25.610878 16798.611
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4 0.99818299 -3.8453255 -3.8454544 -0.98248805 -2.8629664 0.7228394 -1.4456788 25.610392 25.610392 25.610392 16797.656
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5 0.99818299 -3.8453255 -3.8454544 -0.98252572 -2.8629287 0.7228403 -1.4456806 25.610392 25.610392 25.610392 16797.656
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Loop time of 6.28643 on 4 procs for 3 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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-3.84544029724 -3.84545440474 -3.84545441597
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Force two-norm initial, final = 14.244 0.733113
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Force max component initial, final = 8.22312 0.41081
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Final line search alpha, max atom move = 2.38596e-05 9.80177e-06
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Iterations, force evaluations = 3 27
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Pair time (%) = 0.459659 (7.31192)
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Neigh time (%) = 0 (0)
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Comm time (%) = 0.0115937 (0.184424)
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Outpt time (%) = 7.76052e-05 (0.00123449)
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Other time (%) = 5.8151 (92.5024)
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Nlocal: 324 ave 328 max 318 min
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Histogram: 1 0 0 0 1 0 0 0 0 2
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Nghost: 4943 ave 4949 max 4939 min
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Histogram: 2 0 0 0 0 0 1 0 0 1
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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 205160 max 198780 min
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Histogram: 1 0 0 0 1 0 0 0 0 2
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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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Neighbor list info ...
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1 neighbor list requests
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update every 20 steps, delay 0 steps, check no
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master list distance cutoff = 12.5
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Memory usage per processor = 6.53094 Mbytes
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Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
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5 0.99818299 -3.8453255 -3.8454544 -0.98252572 -2.8629287 0.7228403 -1.4456806 25.610392 25.610392 25.610392 16797.656
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6 0.99600405 -3.8453255 -3.8454541 -0.98252544 -2.8629287 0.72284035 -1.4456807 25.610392 25.610392 25.610392 16797.656
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Loop time of 0.0854127 on 4 procs for 1 steps with 1296 atoms
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Pair time (%) = 0.0163963 (19.1965)
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Neigh time (%) = 0 (0)
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Comm time (%) = 0.000354767 (0.415356)
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Outpt time (%) = 3.74913e-05 (0.0438943)
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Other time (%) = 0.0686242 (80.3442)
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Nlocal: 324 ave 329 max 320 min
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Histogram: 2 0 0 0 0 0 0 1 0 1
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Nghost: 4943 ave 4947 max 4938 min
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Histogram: 1 0 1 0 0 0 0 0 0 2
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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 205798 max 200056 min
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Histogram: 2 0 0 0 0 0 0 1 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 NULL 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:665)
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run 10
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Memory usage per processor = 6.90594 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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6 25.610392 25.610392 25.610392 0 0 0 -658401.77 -658419.97 -658392.44 -60685.043 -70926.603 -51580.218
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7 25.610648 25.610392 25.610392 0 0 0 -658401.77 -658419.97 -658392.44 -60685.043 -70926.603 -51580.218
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8 25.610904 25.610392 25.610392 0 0 0 -329933.78 -638001.39 -637973.86 -60683.825 -70925.179 -51575.113
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9 25.611161 25.610392 25.610392 0 0 0 -1465.9477 -617588.27 -617560.74 -60682.607 -70923.756 -51570.007
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10 25.611417 25.610392 25.610392 0 0 0 327001.72 -597180.62 -597153.09 -60681.389 -70922.332 -51564.902
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11 25.611673 25.610392 25.610392 0 0 0 655469.22 -576778.42 -576750.89 -60680.171 -70920.908 -51559.797
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12 25.611929 25.610392 25.610392 0 0 0 983936.56 -556381.67 -556354.15 -60678.953 -70919.485 -51554.692
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13 25.612185 25.610392 25.610392 0 0 0 1312403.7 -535990.39 -535962.87 -60677.735 -70918.061 -51549.588
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14 25.612441 25.610392 25.610392 0 0 0 1640870.7 -515604.56 -515577.05 -60676.517 -70916.637 -51544.483
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15 25.612697 25.610392 25.610392 0 0 0 1969337.6 -495224.2 -495196.68 -60675.299 -70915.213 -51539.378
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16 25.612953 25.610392 25.610392 0 0 0 2297804.2 -474849.28 -474821.77 -60674.082 -70913.79 -51534.274
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Loop time of 0.184534 on 4 procs for 10 steps with 1296 atoms
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Pair time (%) = 0.178071 (96.4977)
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Neigh time (%) = 0 (0)
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Comm time (%) = 0.00348192 (1.88687)
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Outpt time (%) = 0.0028165 (1.52628)
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Other time (%) = 0.000164449 (0.0891159)
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Nlocal: 324 ave 329 max 319 min
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Histogram: 1 0 1 0 0 0 0 0 1 1
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Nghost: 4943 ave 4948 max 4938 min
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Histogram: 1 0 1 0 0 0 0 0 1 1
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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 205798 max 199418 min
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Histogram: 1 0 1 0 0 0 0 0 1 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 NULL 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 = 7.65594 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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16 25.612953 25.610392 25.610392 0 0 0 2626270.7 -454479.82 -454452.32 -60672.864 -70912.366 -51529.17
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17 25.612953 25.610392 25.610648 0 0 0 2626270.7 -454479.82 -454452.32 -60672.864 -70912.366 -51529.17
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18 25.612953 25.610392 25.610904 0 0 0 2646636.7 -434056.14 -126036.92 -60666.856 -70910.942 -51528.134
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19 25.612953 25.610392 25.611161 0 0 0 2666997.3 -413637.91 202378.33 -60660.849 -70909.518 -51527.099
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20 25.612953 25.610392 25.611417 0 0 0 2687352.4 -393225.15 530793.41 -60654.842 -70908.094 -51526.063
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21 25.612953 25.610392 25.611673 0 0 0 2707702 -372817.84 859208.34 -60648.835 -70906.671 -51525.028
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22 25.612953 25.610392 25.611929 0 0 0 2728046.2 -352415.99 1187623.1 -60642.828 -70905.247 -51523.993
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23 25.612953 25.610392 25.612185 0 0 0 2748384.9 -332019.6 1516037.7 -60636.821 -70903.823 -51522.958
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24 25.612953 25.610392 25.612441 0 0 0 2768718.2 -311628.66 1844452.1 -60630.815 -70902.399 -51521.923
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25 25.612953 25.610392 25.612697 0 0 0 2789045.9 -291243.19 2172866.4 -60624.808 -70900.976 -51520.888
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26 25.612953 25.610392 25.612953 0 0 0 2809368.3 -270863.16 2501280.5 -60618.802 -70899.553 -51519.854
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Loop time of 0.185136 on 4 procs for 10 steps with 1296 atoms
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Pair time (%) = 0.17822 (96.2646)
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Neigh time (%) = 0 (0)
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Comm time (%) = 0.00373882 (2.0195)
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Outpt time (%) = 0.0030095 (1.62556)
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Other time (%) = 0.00016731 (0.0903717)
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Nlocal: 324 ave 329 max 319 min
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Histogram: 1 0 1 0 0 0 0 0 1 1
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Nghost: 4943 ave 4948 max 4938 min
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Histogram: 1 0 1 0 0 0 0 0 1 1
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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 205798 max 199418 min
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Histogram: 1 0 1 0 0 0 0 0 1 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 NULL 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 = 8.42123 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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26 25.612953 25.610392 25.612953 0 0 0 2829685.1 -250488.6 2829694.5 -60612.796 -70898.13 -51518.819
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27 25.612953 25.610392 25.612953 0 0 5.1225907e-07 2829685.1 -250488.6 2829694.5 -60612.796 -70898.13 -51518.819
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28 25.612953 25.610392 25.612953 0 0 1.0245181e-06 2829685.1 -250488.59 2829694.5 -60612.79 -70898.123 -51255.309
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29 25.612953 25.610392 25.612953 0 0 1.5367772e-06 2829685.1 -250488.59 2829694.5 -60612.784 -70898.117 -50991.8
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30 25.612953 25.610392 25.612953 0 0 2.0490363e-06 2829685.1 -250488.59 2829694.5 -60612.778 -70898.11 -50728.29
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31 25.612953 25.610392 25.612953 0 0 2.5612953e-06 2829685.2 -250488.59 2829694.5 -60612.772 -70898.104 -50464.78
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32 25.612953 25.610392 25.612953 0 0 3.0735544e-06 2829685.2 -250488.59 2829694.5 -60612.765 -70898.097 -50201.27
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33 25.612953 25.610392 25.612953 0 0 3.5858135e-06 2829685.2 -250488.59 2829694.5 -60612.759 -70898.091 -49937.76
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34 25.612953 25.610392 25.612953 0 0 4.0980725e-06 2829685.2 -250488.59 2829694.5 -60612.753 -70898.085 -49674.25
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35 25.612953 25.610392 25.612953 0 0 4.6103316e-06 2829685.2 -250488.59 2829694.5 -60612.747 -70898.078 -49410.741
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36 25.612953 25.610392 25.612953 0 0 5.1225907e-06 2829685.2 -250488.59 2829694.5 -60612.741 -70898.072 -49147.231
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Loop time of 0.184386 on 4 procs for 10 steps with 1296 atoms
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Pair time (%) = 0.177878 (96.4706)
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Neigh time (%) = 0 (0)
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Comm time (%) = 0.00345647 (1.87459)
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Outpt time (%) = 0.00290865 (1.57748)
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Other time (%) = 0.000142515 (0.0772917)
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Nlocal: 324 ave 329 max 319 min
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Histogram: 1 0 1 0 0 0 0 0 1 1
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Nghost: 4943 ave 4948 max 4938 min
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Histogram: 1 0 1 0 0 0 0 0 1 1
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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 205798 max 199418 min
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Histogram: 1 0 1 0 0 0 0 0 1 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 NULL 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 = 9.17123 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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36 25.612953 25.610392 25.612953 0 0 5.1225907e-06 2829685.2 -250488.59 2829694.5 -60612.735 -70898.065 -48883.721
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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
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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
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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
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40 25.612953 25.610392 25.612953 2.0488314e-06 0 5.1225907e-06 2829685.2 -250488.57 2829694.5 -59822.39 -70898.053 -48883.698
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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
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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
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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
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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
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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
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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
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Loop time of 0.184383 on 4 procs for 10 steps with 1296 atoms
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Pair time (%) = 0.177841 (96.4522)
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Neigh time (%) = 0 (0)
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Comm time (%) = 0.00349998 (1.89821)
|
|
Outpt time (%) = 0.00289482 (1.57)
|
|
Other time (%) = 0.000146747 (0.079588)
|
|
|
|
Nlocal: 324 ave 329 max 319 min
|
|
Histogram: 1 0 1 0 0 0 0 0 1 1
|
|
Nghost: 4943 ave 4948 max 4938 min
|
|
Histogram: 1 0 1 0 0 0 0 0 1 1
|
|
Neighs: 0 ave 0 max 0 min
|
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
FullNghs: 202608 ave 205798 max 199418 min
|
|
Histogram: 1 0 1 0 0 0 0 0 1 1
|
|
|
|
Total # of neighbors = 810432
|
|
Ave neighs/atom = 625.333
|
|
Neighbor list builds = 0
|
|
Dangerous builds = 0
|