forked from lijiext/lammps
334 lines
18 KiB
Groff
334 lines
18 KiB
Groff
LAMMPS (5 Oct 2016)
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# Pure Si crystal, qeq off, calculates stress-strain, no out.*.cfg
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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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lattice diamond 5.431
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Lattice spacing in x,y,z = 5.431 5.431 5.431
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region box block 0 4 0 4 0 4
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create_box 1 box
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Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
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1 by 1 by 1 MPI processor grid
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create_atoms 1 box
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Created 512 atoms
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mass 1 29.0
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change_box all triclinic
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triclinic box = (0 0 0) to (21.724 21.724 21.724) with tilt (0 0 0)
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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 Si
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Reading potential file ffield.comb with DATE: 2011-02-22
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neighbor 0.5 bin
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neigh_modify every 20 delay 0 check no
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fix 1 all box/relax aniso 0.0 vmax 0.001
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timestep 0.00020
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thermo_style custom step temp etotal pe evdwl ecoul #lx ly lz vol pxx pyy pzz
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thermo_modify norm yes
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thermo 1
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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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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 12.5
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ghost atom cutoff = 12.5
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binsize = 6.25 -> bins = 4 4 4
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Memory usage per processor = 7.60455 Mbytes
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Step Temp TotEng PotEng E_vdwl E_coul
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0 1 -4.6295947 -4.6297237 -4.6297237 0
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1 1 -4.6295965 -4.6297255 -4.6297255 0
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2 1 -4.6295965 -4.6297255 -4.6297255 0
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3 1 -4.6295965 -4.6297255 -4.6297255 0
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4 1 -4.6295965 -4.6297255 -4.6297255 0
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5 1 -4.6295965 -4.6297255 -4.6297255 0
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Loop time of 0.201077 on 1 procs for 5 steps with 512 atoms
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99.9% CPU use with 1 MPI tasks x no OpenMP threads
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Minimization stats:
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Stopping criterion = energy tolerance
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Energy initial, next-to-last, final =
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-4.62972371535 -4.62972550325 -4.62972550325
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Force two-norm initial, final = 5.86582 2.4862e-12
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Force max component initial, final = 3.38663 2.10283e-12
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Final line search alpha, max atom move = 1 2.10283e-12
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Iterations, force evaluations = 5 10
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.1996 | 0.1996 | 0.1996 | 0.0 | 99.27
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.00029564 | 0.00029564 | 0.00029564 | 0.0 | 0.15
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Output | 2.861e-05 | 2.861e-05 | 2.861e-05 | 0.0 | 0.01
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Modify | 0 | 0 | 0 | 0.0 | 0.00
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Other | | 0.001153 | | | 0.57
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Nlocal: 512 ave 512 max 512 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 4861 ave 4861 max 4861 min
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Histogram: 1 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: 1 0 0 0 0 0 0 0 0 0
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FullNghs: 212992 ave 212992 max 212992 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 212992
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Ave neighs/atom = 416
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Neighbor list builds = 0
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Dangerous builds not checked
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min_modify dmax 0.2 line quadratic
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unfix 1
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run 1
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WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
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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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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 12.5
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ghost atom cutoff = 12.5
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binsize = 6.25 -> bins = 4 4 4
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Memory usage per processor = 5.97955 Mbytes
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Step Temp TotEng PotEng E_vdwl E_coul
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5 1 -4.6295965 -4.6297255 -4.6297255 0
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6 1 -4.6295965 -4.6297255 -4.6297255 0
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Loop time of 0.018162 on 1 procs for 1 steps with 512 atoms
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Performance: 0.951 ns/day, 25.225 hours/ns, 55.060 timesteps/s
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99.1% CPU use with 1 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.018118 | 0.018118 | 0.018118 | 0.0 | 99.76
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 2.6941e-05 | 2.6941e-05 | 2.6941e-05 | 0.0 | 0.15
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Output | 8.1062e-06 | 8.1062e-06 | 8.1062e-06 | 0.0 | 0.04
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Modify | 2.1458e-06 | 2.1458e-06 | 2.1458e-06 | 0.0 | 0.01
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Other | | 6.914e-06 | | | 0.04
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Nlocal: 512 ave 512 max 512 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 4861 ave 4861 max 4861 min
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Histogram: 1 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: 1 0 0 0 0 0 0 0 0 0
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FullNghs: 212992 ave 212992 max 212992 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 212992
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Ave neighs/atom = 416
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Neighbor list builds = 0
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Dangerous builds not checked
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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:690)
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run 10
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Memory usage per processor = 6.72955 Mbytes
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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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6 21.727916 21.727916 21.727916 0 0 0 -4.5569391e-06 -9.3041736e-06 -3.863262e-06 5.3686749e-06 -1.5078216e-06 5.1674734e-06
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7 21.728133 21.727916 21.727916 0 0 0 -2.4800435e-06 -9.5067314e-06 -2.1562734e-06 5.5972954e-06 -2.3715124e-06 3.9555507e-06
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8 21.72835 21.727916 21.727916 0 0 0 146204.17 77325.788 77325.788 3.5125695e-06 -1.9487795e-06 5.2972201e-06
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9 21.728568 21.727916 21.727916 0 0 0 292407.63 154648.04 154648.04 5.6408383e-06 -2.4472325e-06 6.3046987e-06
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10 21.728785 21.727916 21.727916 0 0 0 438610.37 231966.74 231966.74 5.5704989e-06 -1.8785254e-06 -1.4083956e-06
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11 21.729002 21.727916 21.727916 0 0 0 584812.4 309281.91 309281.91 -1.2913749e-05 2.0544275e-06 7.547976e-06
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12 21.729219 21.727916 21.727916 0 0 0 731013.71 386593.54 386593.54 6.0987798e-06 -2.0790709e-06 7.8755963e-06
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13 21.729437 21.727916 21.727916 0 0 0 877214.3 463901.63 463901.63 5.2296156e-06 -2.2013505e-06 2.6034199e-06
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14 21.729654 21.727916 21.727916 0 0 0 1023414.2 541206.18 541206.18 5.6537455e-06 -1.9222461e-06 4.3649131e-06
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15 21.729871 21.727916 21.727916 0 0 0 1169613.3 618507.19 618507.19 5.5850663e-06 -2.204341e-06 6.1719985e-06
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16 21.730089 21.727916 21.727916 0 0 0 1315811.8 695804.66 695804.66 -1.3406996e-05 2.5348334e-06 6.2581356e-06
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Loop time of 0.199118 on 1 procs for 10 steps with 512 atoms
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Performance: 0.868 ns/day, 27.655 hours/ns, 50.221 timesteps/s
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99.9% CPU use with 1 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.19755 | 0.19755 | 0.19755 | 0.0 | 99.21
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.00027704 | 0.00027704 | 0.00027704 | 0.0 | 0.14
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Output | 0.0011551 | 0.0011551 | 0.0011551 | 0.0 | 0.58
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Modify | 7.8201e-05 | 7.8201e-05 | 7.8201e-05 | 0.0 | 0.04
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Other | | 5.865e-05 | | | 0.03
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Nlocal: 512 ave 512 max 512 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 4861 ave 4861 max 4861 min
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Histogram: 1 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: 1 0 0 0 0 0 0 0 0 0
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FullNghs: 212992 ave 212992 max 212992 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 212992
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Ave neighs/atom = 416
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Neighbor list builds = 0
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Dangerous builds not checked
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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 = 7.47955 Mbytes
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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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16 21.730089 21.727916 21.727916 0 0 0 1462009.5 773098.59 773098.59 4.2549849e-06 -8.3746497e-07 7.0310015e-06
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17 21.730089 21.727916 21.728133 0 0 0 1462009.5 773098.59 773098.59 5.1784721e-06 -2.3038152e-06 5.7172699e-06
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18 21.730089 21.727916 21.72835 0 0 0 1539307.6 850399.75 919275.09 9.5325273e-06 -6.4331187e-07 4.7453557e-06
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19 21.730089 21.727916 21.728568 0 0 0 1616602.2 927697.36 1065450.9 1.3298468e-05 -1.8936338e-06 4.6426389e-06
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20 21.730089 21.727916 21.728785 0 0 0 1693893.3 1004991.4 1211626 1.0653147e-05 -1.4284476e-06 6.3390661e-07
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21 21.730089 21.727916 21.729002 0 0 0 1771180.8 1082282 1357800.3 9.0018044e-06 -1.2309518e-06 5.565611e-06
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22 21.730089 21.727916 21.729219 0 0 0 1848464.7 1159569 1503974 7.5031694e-06 -2.7028978e-06 5.6324743e-06
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23 21.730089 21.727916 21.729437 0 0 0 1925745.2 1236852.4 1650146.9 4.3439607e-06 -2.4393614e-06 5.5564577e-06
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24 21.730089 21.727916 21.729654 0 0 0 2003022 1314132.4 1796319.1 2.3497113e-06 -2.3680104e-06 4.7932602e-06
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25 21.730089 21.727916 21.729871 0 0 0 2080295.4 1391408.8 1942490.6 6.941166e-06 -1.1601937e-06 4.9355658e-06
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26 21.730089 21.727916 21.730089 0 0 0 2157565.2 1468681.6 2088661.4 5.7633476e-06 -8.4264935e-07 4.0350137e-06
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Loop time of 0.199616 on 1 procs for 10 steps with 512 atoms
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Performance: 0.866 ns/day, 27.724 hours/ns, 50.096 timesteps/s
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100.2% CPU use with 1 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.19798 | 0.19798 | 0.19798 | 0.0 | 99.18
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.00028658 | 0.00028658 | 0.00028658 | 0.0 | 0.14
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Output | 0.0012088 | 0.0012088 | 0.0012088 | 0.0 | 0.61
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Modify | 7.987e-05 | 7.987e-05 | 7.987e-05 | 0.0 | 0.04
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Other | | 5.698e-05 | | | 0.03
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Nlocal: 512 ave 512 max 512 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 4861 ave 4861 max 4861 min
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Histogram: 1 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: 1 0 0 0 0 0 0 0 0 0
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FullNghs: 212992 ave 212992 max 212992 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 212992
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Ave neighs/atom = 416
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Neighbor list builds = 0
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Dangerous builds not checked
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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 = 8.24482 Mbytes
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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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26 21.730089 21.727916 21.730089 0 0 0 2234831.5 1545950.9 2234831.5 4.8476018e-06 4.2828413e-07 5.75372e-06
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27 21.730089 21.727916 21.730089 0 0 4.3460177e-07 2234831.5 1545950.9 2234831.5 5.088922e-06 -2.3012471e-06 5.6950612e-06
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28 21.730089 21.727916 21.730089 0 0 8.6920354e-07 2234831.5 1545950.9 2234831.5 4.7258447e-06 -1.3958256e-06 243.66105
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29 21.730089 21.727916 21.730089 0 0 1.3038053e-06 2234831.5 1545950.9 2234831.5 4.7492097e-06 -2.8958095e-06 487.32212
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30 21.730089 21.727916 21.730089 0 0 1.7384071e-06 2234831.5 1545950.9 2234831.5 4.8744538e-06 -2.3110563e-06 730.98324
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31 21.730089 21.727916 21.730089 0 0 2.1730089e-06 2234831.5 1545950.9 2234831.5 4.3760082e-06 -8.3074269e-07 974.64423
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32 21.730089 21.727916 21.730089 0 0 2.6076106e-06 2234831.5 1545950.9 2234831.5 4.7980741e-06 -5.7372478e-07 1218.3053
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33 21.730089 21.727916 21.730089 0 0 3.0422124e-06 2234831.5 1545950.9 2234831.5 4.8822804e-06 -2.3433596e-06 1461.9664
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34 21.730089 21.727916 21.730089 0 0 3.4768142e-06 2234831.5 1545950.9 2234831.5 4.8447261e-06 -1.9614792e-06 1705.6275
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35 21.730089 21.727916 21.730089 0 0 3.911416e-06 2234831.5 1545950.9 2234831.5 5.1297449e-06 -2.114135e-06 1949.2885
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36 21.730089 21.727916 21.730089 0 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 4.5571577e-06 -1.8415232e-06 2192.9496
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Loop time of 0.199427 on 1 procs for 10 steps with 512 atoms
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Performance: 0.866 ns/day, 27.698 hours/ns, 50.144 timesteps/s
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100.3% CPU use with 1 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.19785 | 0.19785 | 0.19785 | 0.0 | 99.21
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.00027561 | 0.00027561 | 0.00027561 | 0.0 | 0.14
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Output | 0.0011613 | 0.0011613 | 0.0011613 | 0.0 | 0.58
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Modify | 7.6056e-05 | 7.6056e-05 | 7.6056e-05 | 0.0 | 0.04
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Other | | 6.199e-05 | | | 0.03
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Nlocal: 512 ave 512 max 512 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 4861 ave 4861 max 4861 min
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Histogram: 1 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: 1 0 0 0 0 0 0 0 0 0
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FullNghs: 212992 ave 212992 max 212992 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 212992
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Ave neighs/atom = 416
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Neighbor list builds = 0
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Dangerous builds not checked
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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 = 8.99482 Mbytes
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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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36 21.730089 21.727916 21.730089 0 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 5.1293854e-06 -1.6748595e-06 2436.6106
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37 21.730089 21.727916 21.730089 4.3455832e-07 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 5.1236563e-06 -3.3624188e-06 2436.6106
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38 21.730089 21.727916 21.730089 8.6911663e-07 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 243.64727 -0.00013232165 2436.6106
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39 21.730089 21.727916 21.730089 1.3036749e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 487.29458 -0.0002652587 2436.6106
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40 21.730089 21.727916 21.730089 1.7382333e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 730.9419 -0.00039565085 2436.6106
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41 21.730089 21.727916 21.730089 2.1727916e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 974.58916 -0.00052768104 2436.6106
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42 21.730089 21.727916 21.730089 2.6073499e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 1218.2364 -0.00065822936 2436.6106
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|
43 21.730089 21.727916 21.730089 3.0419082e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 1461.8837 -0.0007889991 2436.6106
|
|
44 21.730089 21.727916 21.730089 3.4764665e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 1705.531 -0.00091806693 2436.6106
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|
45 21.730089 21.727916 21.730089 3.9110248e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 1949.1783 -0.001049945 2436.6106
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|
46 21.730089 21.727916 21.730089 4.3455832e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 2192.8256 -0.0011787861 2436.6106
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|
Loop time of 0.200513 on 1 procs for 10 steps with 512 atoms
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|
|
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Performance: 0.862 ns/day, 27.849 hours/ns, 49.872 timesteps/s
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100.2% CPU use with 1 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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|
---------------------------------------------------------------
|
|
Pair | 0.19893 | 0.19893 | 0.19893 | 0.0 | 99.21
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.00027752 | 0.00027752 | 0.00027752 | 0.0 | 0.14
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Output | 0.0011744 | 0.0011744 | 0.0011744 | 0.0 | 0.59
|
|
Modify | 7.4387e-05 | 7.4387e-05 | 7.4387e-05 | 0.0 | 0.04
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|
Other | | 6.08e-05 | | | 0.03
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|
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Nlocal: 512 ave 512 max 512 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 4861 ave 4861 max 4861 min
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Histogram: 1 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: 1 0 0 0 0 0 0 0 0 0
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FullNghs: 212992 ave 212992 max 212992 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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|
|
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Total # of neighbors = 212992
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Ave neighs/atom = 416
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|
Neighbor list builds = 0
|
|
Dangerous builds not checked
|
|
Total wall time: 0:00:01
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