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lammps/examples/msst/log.5Oct16.msst.g++.1
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LAMMPS (5 Oct 2016)
# LJ test of msst shock dynamics
# Energy in eV, time in ps, distance in angstroms.
units metal
boundary p p p
atom_style atomic
timestep 1e-03
lattice fcc 5.3589
Lattice spacing in x,y,z = 5.3589 5.3589 5.3589
## Specify the box as a given number of unit cells.
region box1 block 0 18 0 18 0 18 units lattice
## Instantiate the system.
create_box 1 box1
Created orthogonal box = (0 0 0) to (96.4602 96.4602 96.4602)
1 by 1 by 1 MPI processor grid
create_atoms 1 region box1
Created 23328 atoms
mass 1 40.00
# Initial velocities correspond to around 300K.
velocity all create 600.0 9999
pair_style lj/cut 10
pair_coeff 1 1 0.01032 3.405
timestep 2e-3
# Equilibrate the system
fix 2 all nve
thermo 10
run 100
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6 -> bins = 17 17 17
Memory usage per processor = 8.03726 Mbytes
Step Temp E_pair E_mol TotEng Press
0 600 -1943.9014 0 -134.75058 992.06384
10 586.44651 -1917.3971 0 -149.11346 1306.17
20 539.94305 -1778.786 0 -150.72199 2492.7873
30 449.49509 -1506.4706 0 -151.12989 4667.6248
40 331.86049 -1151.7344 0 -151.09164 7379.764
50 258.27083 -929.8024 0 -151.05092 9103.558
60 256.1869 -923.58742 0 -151.1195 9252.9158
70 281.76061 -1000.7367 0 -151.1576 8739.2518
80 300.28534 -1056.589 0 -151.15321 8324.8812
90 305.83368 -1073.3097 0 -151.14426 8175.2478
100 304.06857 -1067.9843 0 -151.14112 8191.234
Loop time of 3.5066 on 1 procs for 100 steps with 23328 atoms
Performance: 4.928 ns/day, 4.870 hours/ns, 28.518 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.3534 | 3.3534 | 3.3534 | 0.0 | 95.63
Neigh | 0.066456 | 0.066456 | 0.066456 | 0.0 | 1.90
Comm | 0.01981 | 0.01981 | 0.01981 | 0.0 | 0.56
Output | 0.00096083 | 0.00096083 | 0.00096083 | 0.0 | 0.03
Modify | 0.037752 | 0.037752 | 0.037752 | 0.0 | 1.08
Other | | 0.02825 | | | 0.81
Nlocal: 23328 ave 23328 max 23328 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 22235 ave 22235 max 22235 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2.18372e+06 ave 2.18372e+06 max 2.18372e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2183715
Ave neighs/atom = 93.6092
Neighbor list builds = 1
Dangerous builds = 0
unfix 2
# MSST fix
fix msst all msst z 28.0 q 200 mu 3e2 tscale 0.01
MSST parameters:
Shock in z direction
Cell mass-like parameter qmass (units of mass^2/length^4) = 2.00000e+02
Shock velocity = 2.80000e+01
Artificial viscosity (units of mass/length/time) = 3.00000e+02
Initial pressure calculated on first step
Initial volume calculated on first step
Initial energy calculated on first step
# this is needed to make etotal equal the MSST conserved quantity
fix_modify msst energy yes
variable dhug equal f_msst[1]
variable dray equal f_msst[2]
variable lgr_vel equal f_msst[3]
variable lgr_pos equal f_msst[4]
thermo_style custom step temp ke pe lx ly lz pxx pyy pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos f_msst
#dump id all atom 50 dump.msst
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
run 100
Fix MSST v0 = 8.97521e+05
Fix MSST p0 = 8.10679e+03
Fix MSST e0 = to be -1.51141e+02
Fix MSST initial strain rate of -3.20112e-02 established by reducing temperature by factor of 1.00000e-02
Memory usage per processor = 8.04369 Mbytes
Step Temp KinEng PotEng Lx Ly Lz Pxx Pyy Pzz TotEng v_dhug v_dray v_lgr_vel v_lgr_pos f_msst
100 301.02788 907.67474 -1058.8159 96.4602 96.4602 96.4602 8242.1214 8202.9779 8095.8693 -151.14112 1.5203428 -10.919311 0 0 9.1684318
110 297.71411 897.68288 -1048.8859 96.4602 96.4602 96.399397 8347.6253 8303.7121 8220.7572 -151.20299 1.439058 28.652258 0.017649501 -0.55980494 5.7336721
120 295.64308 891.43821 -1042.72 96.4602 96.4602 96.340496 8431.6742 8379.2441 8331.5304 -151.28174 1.3655893 56.776734 0.034747125 -1.119263 2.3808018
130 296.02228 892.5816 -1043.9407 96.4602 96.4602 96.283468 8456.2492 8412.6368 8392.5853 -151.35912 1.2945465 37.811981 0.05130089 -1.6783851 -0.87840575
140 298.19024 899.11855 -1050.5482 96.4602 96.4602 96.228236 8430.5151 8415.6802 8414.2537 -151.42965 1.2243399 -18.01985 0.067333442 -2.2371818 -4.0330712
150 300.86421 907.18122 -1058.6966 96.4602 96.4602 96.174681 8399.4697 8396.2236 8420.9004 -151.51534 1.1598278 -86.5197 0.082879112 -2.7956634 -7.0824881
160 303.34119 914.64996 -1066.2388 96.4602 96.4602 96.122673 8388.3438 8360.5024 8428.751 -151.58881 1.0977647 -151.64553 0.097975827 -3.353839 -10.033902
170 304.87769 919.28288 -1070.961 96.4602 96.4602 96.072088 8408.8694 8333.4337 8449.5665 -151.67812 1.044322 -201.80899 0.11265931 -3.9117174 -12.897768
180 304.99 919.62151 -1071.3588 96.4602 96.4602 96.022824 8461.5542 8343.1436 8484.9824 -151.73733 0.99203387 -235.51793 0.12695926 -4.4693063 -15.685622
190 305.1148 919.99782 -1071.7807 96.4602 96.4602 95.9748 8498.7562 8371.4217 8514.4473 -151.78288 0.93937416 -273.43964 0.1408996 -5.0266132 -18.403999
200 306.45829 924.0488 -1075.8787 96.4602 96.4602 95.927931 8488.9509 8385.2408 8529.6443 -151.82991 0.88654815 -324.00777 0.15450451 -5.583645 -21.055149
Loop time of 4.74363 on 1 procs for 100 steps with 23328 atoms
Performance: 3.643 ns/day, 6.588 hours/ns, 21.081 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.366 | 3.366 | 3.366 | 0.0 | 70.96
Neigh | 0.13476 | 0.13476 | 0.13476 | 0.0 | 2.84
Comm | 0.017403 | 0.017403 | 0.017403 | 0.0 | 0.37
Output | 0.011465 | 0.011465 | 0.011465 | 0.0 | 0.24
Modify | 1.1866 | 1.1866 | 1.1866 | 0.0 | 25.01
Other | | 0.02743 | | | 0.58
Nlocal: 23328 ave 23328 max 23328 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 22205 ave 22205 max 22205 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2.18349e+06 ave 2.18349e+06 max 2.18349e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2183494
Ave neighs/atom = 93.5997
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:08
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