165 lines
7.7 KiB
Groff
165 lines
7.7 KiB
Groff
LAMMPS (24 Dec 2020)
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using 1 OpenMP thread(s) per MPI task
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# LJ test of msst shock dynamics
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# Energy in eV, time in ps, distance in angstroms.
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units metal
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boundary p p p
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atom_style atomic
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timestep 1e-03
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lattice fcc 5.3589
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Lattice spacing in x,y,z = 5.3589000 5.3589000 5.3589000
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## Specify the box as a given number of unit cells.
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region box1 block 0 18 0 18 0 18 units lattice
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## Instantiate the system.
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create_box 1 box1
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Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (96.460200 96.460200 96.460200)
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1 by 2 by 2 MPI processor grid
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create_atoms 1 region box1
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Created 23328 atoms
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create_atoms CPU = 0.080 seconds
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mass 1 40.00
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# Initial velocities correspond to around 300K.
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velocity all create 600.0 9999
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pair_style lj/cut 10
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pair_coeff 1 1 0.01032 3.405
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timestep 2e-3
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# Equilibrate the system
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fix 2 all nve
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thermo 10
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run 100
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Neighbor list info ...
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 12
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ghost atom cutoff = 12
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binsize = 6, bins = 17 17 17
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 7.785 | 7.785 | 7.785 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 600 -1943.9014 0 -134.75058 992.06384
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10 586.47212 -1917.4465 0 -149.08565 1305.7368
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20 540.13678 -1779.3375 0 -150.68935 2488.8545
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30 450.11466 -1508.2891 0 -151.08028 4655.1306
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40 332.99843 -1155.1208 0 -151.04685 7357.5162
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50 259.2571 -932.72753 0 -151.0022 9086.2087
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60 256.22581 -923.67654 0 -151.0913 9257.1571
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70 281.12085 -998.79866 0 -151.14863 8759.7887
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80 299.37658 -1053.8476 0 -151.1519 8352.9467
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90 304.24026 -1068.4941 0 -151.13319 8218.1594
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100 301.9683 -1061.6332 0 -151.12284 8244.1277
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Loop time of 5.66225 on 4 procs for 100 steps with 23328 atoms
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Performance: 3.052 ns/day, 7.864 hours/ns, 17.661 timesteps/s
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78.0% CPU use with 4 MPI tasks x 1 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 | 2.6416 | 2.7792 | 2.9335 | 6.4 | 49.08
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Neigh | 0.029522 | 0.037458 | 0.054701 | 5.3 | 0.66
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Comm | 2.1998 | 2.4099 | 2.5822 | 8.8 | 42.56
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Output | 0.10457 | 0.10816 | 0.11265 | 1.0 | 1.91
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Modify | 0.023462 | 0.033517 | 0.044696 | 4.9 | 0.59
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Other | | 0.294 | | | 5.19
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Nlocal: 5832.00 ave 5850 max 5813 min
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Histogram: 1 0 0 0 1 1 0 0 0 1
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Nghost: 10571.0 ave 10590 max 10553 min
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Histogram: 1 0 0 0 1 1 0 0 0 1
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Neighs: 545762.0 ave 548069 max 543643 min
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Histogram: 1 0 0 1 0 1 0 0 0 1
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Total # of neighbors = 2183047
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Ave neighs/atom = 93.580547
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Neighbor list builds = 1
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Dangerous builds = 0
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unfix 2
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# MSST fix
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fix msst all msst z 28.0 q 200 mu 3e2 tscale 0.01
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MSST parameters:
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Shock in z direction
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Cell mass-like parameter qmass (units of mass^2/length^4) = 200
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Shock velocity = 28
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Artificial viscosity (units of mass/length/time) = 300
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Initial pressure calculated on first step
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Initial volume calculated on first step
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Initial energy calculated on first step
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variable dhug equal f_msst[1]
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variable dray equal f_msst[2]
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variable lgr_vel equal f_msst[3]
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variable lgr_pos equal f_msst[4]
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thermo_style custom step temp ke pe lx ly lz pxx pyy pzz econserve v_dhug v_dray v_lgr_vel v_lgr_pos f_msst
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#dump id all atom 50 dump.msst
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#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
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#dump_modify 2 pad 3
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#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
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#dump_modify 3 pad 3
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run 100
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Fix MSST v0 = 897520.7
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Fix MSST p0 = 8186.2393
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Fix MSST e0 = -151.12284
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Fix MSST initial strain rate of -0.031900492 established by reducing temperature by factor of 0.01
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Per MPI rank memory allocation (min/avg/max) = 8.535 | 8.535 | 8.535 Mbytes
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Step Temp KinEng PotEng Lx Ly Lz Pxx Pyy Pzz Econserve v_dhug v_dray v_lgr_vel v_lgr_pos f_msst
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100 298.94862 901.40524 -1061.6332 96.4602 96.4602 96.4602 8270.9151 8253.4662 8175.4946 -151.12284 1.5098415 -10.744684 0 0 9.1051034
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110 296.49826 894.01679 -1050.8801 96.4602 96.4602 96.399609 8338.4937 8340.5504 8294.9909 -151.20723 1.4327442 23.73173 0.017588167 -0.55980562 5.6560557
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120 295.97607 892.44225 -1046.0193 96.4602 96.4602 96.340904 8377.6797 8385.921 8378.3042 -151.28169 1.3584606 24.672199 0.034628719 -1.1192655 2.2953307
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130 297.34893 896.58179 -1046.9797 96.4602 96.4602 96.284029 8379.2516 8394.8806 8416.2669 -151.36322 1.2881444 -17.170168 0.051138087 -1.6783905 -0.96527961
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140 299.71946 903.72952 -1051.0592 96.4602 96.4602 96.22888 8357.0358 8388.6743 8424.3188 -151.44922 1.221125 -86.501161 0.067146366 -2.2371908 -4.1195182
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150 301.79241 909.97998 -1054.3256 96.4602 96.4602 96.175327 8332.7118 8393.7027 8434.6177 -151.51765 1.1560248 -151.34689 0.082691635 -2.7956762 -7.172084
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160 303.18249 914.17141 -1055.6323 96.4602 96.4602 96.123244 8321.1154 8413.1248 8454.5596 -151.59527 1.0977348 -204.4864 0.097810061 -3.3538554 -10.134387
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170 304.34089 917.66428 -1056.3054 96.4602 96.4602 96.072522 8327.6227 8431.1177 8467.92 -151.65554 1.0390628 -262.29751 0.11253339 -3.9117366 -13.01442
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180 305.86343 922.25514 -1058.1478 96.4602 96.4602 96.023049 8345.1853 8432.5201 8461.3276 -151.70813 0.97863988 -338.30793 0.12689398 -4.4693274 -15.815462
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190 307.44054 927.01052 -1060.2474 96.4602 96.4602 95.9747 8368.4081 8427.5109 8450.584 -151.77867 0.92329631 -416.89333 0.1409285 -5.0266346 -18.541801
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200 308.43619 930.01265 -1060.6483 96.4602 96.4602 95.927349 8393.2058 8443.1265 8454.6733 -151.83947 0.8723277 -479.24592 0.1546734 -5.5836644 -21.20378
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Loop time of 11.445 on 4 procs for 100 steps with 23328 atoms
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Performance: 1.510 ns/day, 15.896 hours/ns, 8.737 timesteps/s
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77.1% CPU use with 4 MPI tasks x 1 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 | 3.7358 | 4.0193 | 4.3315 | 10.5 | 35.12
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Neigh | 0.05921 | 0.078071 | 0.089958 | 4.1 | 0.68
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Comm | 2.3136 | 2.683 | 3.054 | 16.3 | 23.44
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Output | 0.038525 | 0.040035 | 0.044559 | 1.3 | 0.35
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Modify | 4.2814 | 4.3709 | 4.4749 | 4.1 | 38.19
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Other | | 0.2537 | | | 2.22
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Nlocal: 5832.00 ave 5874 max 5803 min
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Histogram: 2 0 0 0 0 1 0 0 0 1
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Nghost: 10563.8 ave 10588 max 10526 min
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Histogram: 1 0 0 0 1 0 0 0 0 2
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Neighs: 545708.0 ave 550787 max 542668 min
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Histogram: 2 0 0 0 1 0 0 0 0 1
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Total # of neighbors = 2182834
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Ave neighs/atom = 93.571416
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Neighbor list builds = 2
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Dangerous builds = 0
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Total wall time: 0:00:17
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