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update examples and log files for cases affected by the fix_modify changes

This commit is contained in:
Axel Kohlmeyer 2021-02-08 21:17:52 -05:00
parent 72ce5c6238
commit 82dc03ab3d
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15 changed files with 1644 additions and 2237 deletions
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30
examples/hugoniostat/in.hugoniostat
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@ -1,16 +1,16 @@
# This script reproduces stress trajectories from Fig. 1 in
# Ravelo, Holian, Germann, and Lomdahl, PRB 70 014103 (2004)
#
# Three thermostatting scenarios are visited: undamped (nodrag),
# Three thermostatting scenarios are visited: undamped (nodrag),
# damped (drag) and Nose-Hoover chain (nhchains).
#
# The axial and shear stress trajectories are printed to the
# file "stress_vs_t.dat". For the damped case, the original figure
# seems to be a plot of 2*tau, rather than tau.
#
# The script also demonstrates how to
# The script also demonstrates how to
# orient a crystal along <110>,
# and how to use the lj/cubic pair style.
# and how to use the lj/cubic pair style.
units lj
boundary p p p
@ -39,7 +39,7 @@ pair_coeff * * 1.0 0.8908987
fix 3 all box/relax aniso 0.0 vmax 1.0e-4 nreset 100
thermo 100
thermo_style custom step temp pe etotal pxx pyy pzz lx ly lz
thermo_style custom step temp pe etotal pxx pyy pzz lx ly lz
min_modify line quadratic
minimize 0.0 1.0e-6 10000 100000
@ -61,16 +61,12 @@ reset_timestep 0
# Pzz = 40.0, drag/damping term off
fix myhug all nphug temp 1.0 1.0 10.0 z 40.0 40.0 70.0 drag 0.0 tchain 1 pchain 0
fix myhug all nphug temp 1.0 1.0 10.0 z 40.0 40.0 70.0 drag 0.0 tchain 1 pchain 0
# Specify reference state from paper, times 1000 atoms
fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
# Add fix energy to output etotal
fix_modify myhug energy yes
# Define output
variable dele equal f_myhug[1] # energy delta [temperature]
@ -81,7 +77,7 @@ variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress
variable time equal dt*step
thermo 1000
thermo_style custom step temp ke epair etotal pzz v_tau lz f_myhug v_dele v_us v_up
thermo_style custom step temp ke epair econserve pzz v_tau lz f_myhug v_dele v_us v_up
fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (no drag)'
@ -109,16 +105,12 @@ reset_timestep 0
# Pzz = 40.0, drag/damping term on
fix myhug all nphug temp 1.0 1.0 1.0 z 40.0 40.0 70.0 drag 200.0 tchain 1 pchain 0
fix myhug all nphug temp 1.0 1.0 1.0 z 40.0 40.0 70.0 drag 200.0 tchain 1 pchain 0
# Specify reference state from paper, times 1000 atoms
fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
# Add fix energy to output etotal
fix_modify myhug energy yes
# Define output
variable dele equal f_myhug[1] # energy delta [temperature]
@ -129,7 +121,7 @@ variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress
variable time equal dt*step
thermo 1000
thermo_style custom step temp ke epair etotal pzz v_tau lz f_myhug v_dele v_us v_up
thermo_style custom step temp ke epair econserve pzz v_tau lz f_myhug v_dele v_us v_up
fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (with drag)'
@ -153,10 +145,6 @@ fix myhug all nphug temp 1.0 1.0 1.0 z 40.0 40.0 70.0
fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
# Add fix energy to output etotal
fix_modify myhug energy yes
# Define output
variable dele equal f_myhug[1] # energy delta [temperature]
@ -167,7 +155,7 @@ variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress
variable time equal dt*step
thermo 1000
thermo_style custom step temp ke epair etotal pzz v_tau lz f_myhug v_dele v_us v_up
thermo_style custom step temp ke epair econserve pzz v_tau lz f_myhug v_dele v_us v_up
fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (Nose-Hoover chain)'

399
examples/hugoniostat/log.08Feb21.hugoniostat.g++.1 Normal file
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@ -0,0 +1,399 @@
LAMMPS (24 Dec 2020)
using 1 OpenMP thread(s) per MPI task
# This script reproduces stress trajectories from Fig. 1 in
# Ravelo, Holian, Germann, and Lomdahl, PRB 70 014103 (2004)
#
# Three thermostatting scenarios are visited: undamped (nodrag),
# damped (drag) and Nose-Hoover chain (nhchains).
#
# The axial and shear stress trajectories are printed to the
# file "stress_vs_t.dat". For the damped case, the original figure
# seems to be a plot of 2*tau, rather than tau.
#
# The script also demonstrates how to
# orient a crystal along <110>,
# and how to use the lj/cubic pair style.
units lj
boundary p p p
atom_style atomic
# Set up FCC lattice with z axis along <110>
lattice fcc 1.4142136 orient x 0 0 1 orient y 1 -1 0 orient z 1 1 0
Lattice spacing in x,y,z = 1.4142135 2.0000000 2.0000000
region mycell block 0.0 5.0 0.0 5.0 0.0 5.0 units lattice
create_box 1 mycell
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (7.0710677 9.9999999 9.9999999)
1 by 1 by 1 MPI processor grid
mass * 1.0
create_atoms 1 box
Created 1000 atoms
create_atoms CPU = 0.001 seconds
# Using units of Rmin, so sigma = 2^-1/6 = 0.8908987
pair_style lj/cubic
pair_coeff * * 1.0 0.8908987
# Relax box dimensions
fix 3 all box/relax aniso 0.0 vmax 1.0e-4 nreset 100
thermo 100
thermo_style custom step temp pe etotal pxx pyy pzz lx ly lz
min_modify line quadratic
minimize 0.0 1.0e-6 10000 100000
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:188)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.8475372
ghost atom cutoff = 1.8475372
binsize = 0.92376862, bins = 8 11 11
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cubic, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.247 | 4.247 | 4.247 Mbytes
Step Temp PotEng TotEng Pxx Pyy Pzz Lx Ly Lz
0 0 -6.2937536 -6.2937536 -2.7722424 -2.7722424 -2.7722424 7.0710677 9.9999999 9.9999999
100 0 -6.3319014 -6.3319014 -0.75971257 -0.75971257 -0.75971257 7.0003571 9.8999999 9.8999999
134 0 -6.3344253 -6.3344253 -4.3330648e-13 -4.7530261e-13 -4.7130069e-13 6.9780267 9.8684199 9.8684199
Loop time of 0.200013 on 1 procs for 134 steps with 1000 atoms
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = force tolerance
Energy initial, next-to-last, final =
-6.29375358358557 -6.33442531515503 -6.33442531515503
Force two-norm initial, final = 3395.2895 5.5740327e-10
Force max component initial, final = 1960.2713 3.2730334e-10
Final line search alpha, max atom move = 1.0000000 3.2730334e-10
Iterations, force evaluations = 134 137
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.14357 | 0.14357 | 0.14357 | 0.0 | 71.78
Neigh | 0.0017562 | 0.0017562 | 0.0017562 | 0.0 | 0.88
Comm | 0.0049057 | 0.0049057 | 0.0049057 | 0.0 | 2.45
Output | 5.126e-05 | 5.126e-05 | 5.126e-05 | 0.0 | 0.03
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.04973 | | | 24.86
Nlocal: 1000.00 ave 1000 max 1000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1724.00 ave 1724 max 1724 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 21000.0 ave 21000 max 21000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 21000
Ave neighs/atom = 21.000000
Neighbor list builds = 1
Dangerous builds = 0
# Define initial velocity
velocity all create 0.01 87287 mom yes rot yes dist gaussian
write_restart restart.equil
System init for write_restart ...
# Start Run #1
clear
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
Reading restart file ...
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
restoring atom style atomic from restart
orthogonal box = (0.046520549 0.065789991 0.065789991) to (7.0245472 9.9342099 9.9342099)
1 by 1 by 1 MPI processor grid
restoring pair style lj/cubic from restart
1000 atoms
read_restart CPU = 0.001 seconds
neighbor 0.2 bin
neigh_modify every 1 delay 0 check yes
timestep 0.001
reset_timestep 0
# Pzz = 40.0, drag/damping term off
fix myhug all nphug temp 1.0 1.0 10.0 z 40.0 40.0 70.0 drag 0.0 tchain 1 pchain 0
# Specify reference state from paper, times 1000 atoms
fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
# Define output
variable dele equal f_myhug[1] # energy delta [temperature]
variable us equal f_myhug[2] # shock velocity [distance/time]
variable up equal f_myhug[3] # particle velocity [distance/time]
variable pzz equal pzz # axial stress
variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress
variable time equal dt*step
thermo 1000
thermo_style custom step temp ke epair econserve pzz v_tau lz f_myhug v_dele v_us v_up
fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (no drag)'
#dump id all atom 500 dump.hugoniostat
#dump 2 all image 500 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 500 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
run 10000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.7475372
ghost atom cutoff = 1.7475372
binsize = 0.87376862, bins = 8 12 12
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cubic, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.124 | 3.124 | 3.124 Mbytes
Step Temp KinEng E_pair Econserve Pzz v_tau Lz f_myhug v_dele v_us v_up
0 0.01 0.014985 -6.3344253 -6.3194403 0.014381062 -0.00023971829 9.8684199 0 -0.004855267 2.3814248 0.0041108563
1000 0.0093381492 0.013993217 -2.1704431 -4183.8284 129.15284 58.544409 8.3142517 -4.1816719 0.93744212 23.519052 3.7381985
2000 0.24794859 0.37155095 -5.8915826 -528.38691 8.3849811 1.3744297 9.5938806 -0.52286688 -0.24350394 13.910493 0.41033425
3000 0.3892042 0.5832225 -3.7686896 -3442.3257 72.742382 28.486576 8.6238082 -3.4391402 0.0038227739 19.697354 2.5139569
4000 0.67010303 1.0041494 -4.2080956 -2935.8105 35.596234 3.9346859 8.7508489 -2.9326065 -0.58038927 14.529876 1.6677093
5000 0.41845028 0.62704774 -4.8392822 -1894.6664 30.624319 4.6370699 8.7827304 -1.8904542 -0.31998377 13.670423 1.5249748
6000 0.22409652 0.33580864 -3.7653422 -2666.4156 50.804071 7.220865 8.25496 -2.6629861 -0.017448126 14.48017 2.3883779
7000 0.094832866 0.14210705 -4.5432169 -2337.0271 35.853414 3.4750842 8.4475655 -2.332626 -0.052659776 12.95347 1.8841809
8000 0.043338745 0.06494311 -4.6249403 -1687.4892 39.679004 6.7256868 8.4321684 -1.6829292 0.070571417 13.554654 1.9927395
9000 0.018233343 0.027322664 -4.425909 -1916.4941 41.680023 5.9079935 8.3470382 -1.9120955 0.090887676 13.502397 2.1013348
10000 0.0082616415 0.01238007 -4.6221264 -1723.6542 39.842157 6.5678795 8.41093 -1.7190444 0.099616538 13.484322 2.0113699
Loop time of 15.2001 on 1 procs for 10000 steps with 1000 atoms
Performance: 56841.813 tau/day, 657.891 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 11.69 | 11.69 | 11.69 | 0.0 | 76.91
Neigh | 0.34087 | 0.34087 | 0.34087 | 0.0 | 2.24
Comm | 0.41211 | 0.41211 | 0.41211 | 0.0 | 2.71
Output | 0.001153 | 0.001153 | 0.001153 | 0.0 | 0.01
Modify | 2.6404 | 2.6404 | 2.6404 | 0.0 | 17.37
Other | | 0.1158 | | | 0.76
Nlocal: 1000.00 ave 1000 max 1000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1886.00 ave 1886 max 1886 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 20874.0 ave 20874 max 20874 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 20874
Ave neighs/atom = 20.874000
Neighbor list builds = 188
Dangerous builds = 0
# Start Run #2
clear
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
Reading restart file ...
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
restoring atom style atomic from restart
orthogonal box = (0.046520549 0.065789991 0.065789991) to (7.0245472 9.9342099 9.9342099)
1 by 1 by 1 MPI processor grid
restoring pair style lj/cubic from restart
1000 atoms
read_restart CPU = 0.001 seconds
neighbor 0.2 bin
neigh_modify every 1 delay 0 check yes
timestep 0.001
reset_timestep 0
# Pzz = 40.0, drag/damping term on
fix myhug all nphug temp 1.0 1.0 1.0 z 40.0 40.0 70.0 drag 200.0 tchain 1 pchain 0
# Specify reference state from paper, times 1000 atoms
fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
# Define output
variable dele equal f_myhug[1] # energy delta [temperature]
variable us equal f_myhug[2] # shock velocity [distance/time]
variable up equal f_myhug[3] # particle velocity [distance/time]
variable pzz equal pzz # axial stress
variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress
variable time equal dt*step
thermo 1000
thermo_style custom step temp ke epair econserve pzz v_tau lz f_myhug v_dele v_us v_up
fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (with drag)'
run 10000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.7475372
ghost atom cutoff = 1.7475372
binsize = 0.87376862, bins = 8 12 12
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cubic, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.124 | 3.124 | 3.124 Mbytes
Step Temp KinEng E_pair Econserve Pzz v_tau Lz f_myhug v_dele v_us v_up
0 0.01 0.014985 -6.3344253 -6.3194403 0.014381062 -0.00023971829 9.8684199 0 -0.004855267 2.3814248 0.0041108563
1000 0.0062572988 0.0093765623 -5.989087 -1670.9191 18.918118 7.5844401 9.2338165 -1.6649394 0.023419337 13.976997 0.92138738
2000 0.0068451081 0.010257394 -5.456581 -2537.81 37.064253 15.537266 8.9496405 -2.5323637 0.10230605 16.325406 1.5455016
3000 0.0073276099 0.010980423 -5.3663421 -2643.8751 39.907292 16.807489 8.9154852 -2.6385198 0.11818116 16.63905 1.6326832
4000 0.0069296906 0.010384141 -5.36234 -2655.7228 40.010742 16.851482 8.9144328 -2.6503709 0.11868137 16.651571 1.6356847
5000 0.0076142461 0.011409948 -5.3631443 -2664.4499 39.997648 16.846756 8.9145416 -2.6590982 0.1184114 16.649779 1.6353254
6000 0.0077053831 0.011546517 -5.3628538 -2673.2444 39.991598 16.840314 8.9145803 -2.667893 0.11818361 16.648852 1.6351691
7000 0.0077405663 0.011599239 -5.3623531 -2682.1589 40.000448 16.844009 8.9145774 -2.6768081 0.11809899 16.650669 1.6353525
8000 0.0080673569 0.012088934 -5.3623755 -2691.0104 39.995327 16.840134 8.9146099 -2.6856601 0.11787103 16.649882 1.6352204
9000 0.0083223083 0.012470979 -5.3622988 -2699.8929 40.00571 16.847764 8.9146503 -2.6945431 0.11781523 16.652389 1.6353987
10000 0.0091249116 0.01367368 -5.3630138 -2708.966 39.987197 16.837314 8.9146848 -2.7036167 0.11743014 16.648832 1.6349911
Loop time of 13.6753 on 1 procs for 10000 steps with 1000 atoms
Performance: 63179.754 tau/day, 731.247 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 10.568 | 10.568 | 10.568 | 0.0 | 77.28
Neigh | 0.019792 | 0.019792 | 0.019792 | 0.0 | 0.14
Comm | 0.33708 | 0.33708 | 0.33708 | 0.0 | 2.46
Output | 0.0011928 | 0.0011928 | 0.0011928 | 0.0 | 0.01
Modify | 2.639 | 2.639 | 2.639 | 0.0 | 19.30
Other | | 0.1101 | | | 0.81
Nlocal: 1000.00 ave 1000 max 1000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1724.00 ave 1724 max 1724 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 21000.0 ave 21000 max 21000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 21000
Ave neighs/atom = 21.000000
Neighbor list builds = 11
Dangerous builds = 0
# Start Run #3
clear
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
Reading restart file ...
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
restoring atom style atomic from restart
orthogonal box = (0.046520549 0.065789991 0.065789991) to (7.0245472 9.9342099 9.9342099)
1 by 1 by 1 MPI processor grid
restoring pair style lj/cubic from restart
1000 atoms
read_restart CPU = 0.001 seconds
neighbor 0.2 bin
neigh_modify every 1 delay 0 check yes
timestep 0.001
reset_timestep 0
# Pzz = 40.0, drag/damping term off, Nose-Hoover chains
fix myhug all nphug temp 1.0 1.0 1.0 z 40.0 40.0 70.0
# Specify reference state from paper, times 1000 atoms
fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
# Define output
variable dele equal f_myhug[1] # energy delta [temperature]
variable us equal f_myhug[2] # shock velocity [distance/time]
variable up equal f_myhug[3] # particle velocity [distance/time]
variable pzz equal pzz # axial stress
variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress
variable time equal dt*step
thermo 1000
thermo_style custom step temp ke epair econserve pzz v_tau lz f_myhug v_dele v_us v_up
fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (Nose-Hoover chain)'
run 10000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.7475372
ghost atom cutoff = 1.7475372
binsize = 0.87376862, bins = 8 12 12
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cubic, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.124 | 3.124 | 3.124 Mbytes
Step Temp KinEng E_pair Econserve Pzz v_tau Lz f_myhug v_dele v_us v_up
0 0.01 0.014985 -6.3344253 -6.3194403 0.014381062 -0.00023971829 9.8684199 0 -0.004855267 2.3814248 0.0041108563
1000 0.0083300318 0.012482553 -5.5023183 -838.99233 35.610078 14.886668 8.9677982 -0.83350249 0.093761717 16.159482 1.500112
2000 0.020386436 0.030549075 -5.294934 -1021.4347 41.760404 17.563313 8.8960328 -1.0161703 0.1178086 16.852842 1.6868239
3000 0.049693082 0.074465084 -5.3469418 -982.1922 39.030412 16.123502 8.9325589 -0.97691972 0.073097533 16.601991 1.6003728
4000 0.11859524 0.17771497 -5.207074 -1299.948 40.941639 16.507821 8.9213137 -1.2949186 0.018189971 16.904165 1.6487306
5000 0.130146 0.19502378 -5.261025 -1208.3405 39.059595 15.609328 8.9431689 -1.2032745 -0.00023811036 16.701434 1.5920334
6000 0.13812959 0.20698719 -5.1710048 -1334.1421 40.904888 16.242199 8.9222846 -1.329178 -0.0044756362 16.90509 1.6471606
7000 0.12107441 0.18143001 -5.2602562 -1170.0585 39.060849 15.577606 8.9397535 -1.1649797 0.005587398 16.671517 1.5949415
8000 0.14333426 0.21478639 -5.1717109 -1352.635 40.876285 16.205871 8.9218128 -1.3476781 -0.0069373292 16.895041 1.6469877
9000 0.12159783 0.18221435 -5.2591928 -1186.8604 39.22852 15.6778 8.9376658 -1.1817834 0.0077335044 16.68885 1.6001243
10000 0.15321647 0.22959488 -5.188176 -1391.2245 40.666599 16.146259 8.9228489 -1.3862659 -0.0091900905 16.860718 1.6418747
Loop time of 13.963 on 1 procs for 10000 steps with 1000 atoms
Performance: 61877.846 tau/day, 716.179 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 10.667 | 10.667 | 10.667 | 0.0 | 76.40
Neigh | 0.16763 | 0.16763 | 0.16763 | 0.0 | 1.20
Comm | 0.36182 | 0.36182 | 0.36182 | 0.0 | 2.59
Output | 0.0011809 | 0.0011809 | 0.0011809 | 0.0 | 0.01
Modify | 2.6516 | 2.6516 | 2.6516 | 0.0 | 18.99
Other | | 0.1135 | | | 0.81
Nlocal: 1000.00 ave 1000 max 1000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1724.00 ave 1724 max 1724 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 20654.0 ave 20654 max 20654 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 20654
Ave neighs/atom = 20.654000
Neighbor list builds = 94
Dangerous builds = 0
Total wall time: 0:00:43

399
examples/hugoniostat/log.08Feb21.hugoniostat.g++.4 Normal file
View File

@ -0,0 +1,399 @@
LAMMPS (24 Dec 2020)
using 1 OpenMP thread(s) per MPI task
# This script reproduces stress trajectories from Fig. 1 in
# Ravelo, Holian, Germann, and Lomdahl, PRB 70 014103 (2004)
#
# Three thermostatting scenarios are visited: undamped (nodrag),
# damped (drag) and Nose-Hoover chain (nhchains).
#
# The axial and shear stress trajectories are printed to the
# file "stress_vs_t.dat". For the damped case, the original figure
# seems to be a plot of 2*tau, rather than tau.
#
# The script also demonstrates how to
# orient a crystal along <110>,
# and how to use the lj/cubic pair style.
units lj
boundary p p p
atom_style atomic
# Set up FCC lattice with z axis along <110>
lattice fcc 1.4142136 orient x 0 0 1 orient y 1 -1 0 orient z 1 1 0
Lattice spacing in x,y,z = 1.4142135 2.0000000 2.0000000
region mycell block 0.0 5.0 0.0 5.0 0.0 5.0 units lattice
create_box 1 mycell
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (7.0710677 9.9999999 9.9999999)
1 by 2 by 2 MPI processor grid
mass * 1.0
create_atoms 1 box
Created 1000 atoms
create_atoms CPU = 0.105 seconds
# Using units of Rmin, so sigma = 2^-1/6 = 0.8908987
pair_style lj/cubic
pair_coeff * * 1.0 0.8908987
# Relax box dimensions
fix 3 all box/relax aniso 0.0 vmax 1.0e-4 nreset 100
thermo 100
thermo_style custom step temp pe etotal pxx pyy pzz lx ly lz
min_modify line quadratic
minimize 0.0 1.0e-6 10000 100000
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:188)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.8475372
ghost atom cutoff = 1.8475372
binsize = 0.92376862, bins = 8 11 11
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cubic, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.211 | 4.211 | 4.211 Mbytes
Step Temp PotEng TotEng Pxx Pyy Pzz Lx Ly Lz
0 0 -6.2937536 -6.2937536 -2.7722424 -2.7722424 -2.7722424 7.0710677 9.9999999 9.9999999
100 0 -6.3319014 -6.3319014 -0.75971257 -0.75971257 -0.75971257 7.0003571 9.8999999 9.8999999
134 0 -6.3344253 -6.3344253 -4.303004e-13 -4.72443e-13 -4.7038971e-13 6.9780267 9.8684199 9.8684199
Loop time of 0.38554 on 4 procs for 134 steps with 1000 atoms
75.8% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = force tolerance
Energy initial, next-to-last, final =
-6.29375358358589 -6.33442531515435 -6.33442531515435
Force two-norm initial, final = 3395.2895 5.5617370e-10
Force max component initial, final = 1960.2713 3.2533415e-10
Final line search alpha, max atom move = 1.0000000 3.2533415e-10
Iterations, force evaluations = 134 137
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.031873 | 0.042436 | 0.055233 | 4.3 | 11.01
Neigh | 0.0004189 | 0.00049466 | 0.00058317 | 0.0 | 0.13
Comm | 0.085755 | 0.095315 | 0.10484 | 2.7 | 24.72
Output | 2.8372e-05 | 3.0637e-05 | 3.6955e-05 | 0.0 | 0.01
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.2473 | | | 64.13
Nlocal: 250.000 ave 305 max 205 min
Histogram: 1 0 0 0 2 0 0 0 0 1
Nghost: 829.000 ave 874 max 774 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 5250.00 ave 6445 max 4305 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 21000
Ave neighs/atom = 21.000000
Neighbor list builds = 1
Dangerous builds = 0
# Define initial velocity
velocity all create 0.01 87287 mom yes rot yes dist gaussian
write_restart restart.equil
System init for write_restart ...
# Start Run #1
clear
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
Reading restart file ...
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
restoring atom style atomic from restart
orthogonal box = (0.046520549 0.065789991 0.065789991) to (7.0245472 9.9342099 9.9342099)
1 by 2 by 2 MPI processor grid
restoring pair style lj/cubic from restart
1000 atoms
read_restart CPU = 0.006 seconds
neighbor 0.2 bin
neigh_modify every 1 delay 0 check yes
timestep 0.001
reset_timestep 0
# Pzz = 40.0, drag/damping term off
fix myhug all nphug temp 1.0 1.0 10.0 z 40.0 40.0 70.0 drag 0.0 tchain 1 pchain 0
# Specify reference state from paper, times 1000 atoms
fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
# Define output
variable dele equal f_myhug[1] # energy delta [temperature]
variable us equal f_myhug[2] # shock velocity [distance/time]
variable up equal f_myhug[3] # particle velocity [distance/time]
variable pzz equal pzz # axial stress
variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress
variable time equal dt*step
thermo 1000
thermo_style custom step temp ke epair econserve pzz v_tau lz f_myhug v_dele v_us v_up
fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (no drag)'
#dump id all atom 500 dump.hugoniostat
#dump 2 all image 500 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 500 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
run 10000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.7475372
ghost atom cutoff = 1.7475372
binsize = 0.87376862, bins = 8 12 12
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cubic, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.086 | 3.086 | 3.086 Mbytes
Step Temp KinEng E_pair Econserve Pzz v_tau Lz f_myhug v_dele v_us v_up
0 0.01 0.014985 -6.3344253 -6.3194403 0.014347835 -0.00026463907 9.8684199 0 -0.0048552735 2.378672 0.0041061045
1000 0.010586669 0.015864123 -2.1721826 -4183.9265 129.03333 58.456619 8.3141284 -4.1817701 0.93542364 23.507245 3.7366151
2000 0.33213628 0.49770621 -5.5847928 -972.65689 12.097176 1.2026574 9.4616027 -0.9675698 -0.35714344 13.85823 0.59422982
3000 0.46981589 0.70401911 -3.9208694 -3177.4622 63.005615 22.559014 8.6828715 -3.1742453 -0.16959033 18.776506 2.284245
4000 0.5486246 0.82211396 -4.170224 -2897.9717 38.4091 4.9062274 8.6573154 -2.8946236 -0.45434723 14.506949 1.8023381
5000 0.30607733 0.45865688 -4.73528 -1914.3534 35.002193 6.2096608 8.6658138 -1.9100768 -0.19602135 13.896788 1.714585
6000 0.13928238 0.20871465 -4.3038564 -1672.0118 50.372856 12.190245 8.3966652 -1.6679166 0.11455965 15.089171 2.2725288
7000 0.055325106 0.082904671 -5.2030895 -1689.3101 30.859753 6.5561993 8.6850199 -1.6841899 0.020593532 13.15254 1.5972063
8000 0.02793065 0.041854078 -4.5281755 -966.55101 48.144696 12.229149 8.4107035 -0.96206469 0.19920754 14.821718 2.2112004
9000 0.018182543 0.02724654 -4.9847463 -1618.778 37.347471 8.7290944 8.5607031 -1.6138205 0.10912671 13.773572 1.8458347
10000 0.0082850143 0.012415094 -5.0129769 -1686.404 36.462176 8.3390717 8.5689886 -1.6814034 0.10655037 13.652105 1.8181142
Loop time of 22.212 on 4 procs for 10000 steps with 1000 atoms
Performance: 38897.956 tau/day, 450.208 timesteps/s
76.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.4702 | 3.5904 | 3.684 | 4.4 | 16.16
Neigh | 0.1001 | 0.10727 | 0.11784 | 2.0 | 0.48
Comm | 5.1418 | 5.2862 | 5.3573 | 3.7 | 23.80
Output | 0.083086 | 0.095493 | 0.11021 | 4.0 | 0.43
Modify | 11.789 | 11.841 | 11.967 | 2.1 | 53.31
Other | | 1.292 | | | 5.82
Nlocal: 250.000 ave 260 max 240 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 927.500 ave 934 max 921 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 5049.00 ave 5203 max 4889 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Total # of neighbors = 20196
Ave neighs/atom = 20.196000
Neighbor list builds = 175
Dangerous builds = 0
# Start Run #2
clear
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
Reading restart file ...
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
restoring atom style atomic from restart
orthogonal box = (0.046520549 0.065789991 0.065789991) to (7.0245472 9.9342099 9.9342099)
1 by 2 by 2 MPI processor grid
restoring pair style lj/cubic from restart
1000 atoms
read_restart CPU = 0.001 seconds
neighbor 0.2 bin
neigh_modify every 1 delay 0 check yes
timestep 0.001
reset_timestep 0
# Pzz = 40.0, drag/damping term on
fix myhug all nphug temp 1.0 1.0 1.0 z 40.0 40.0 70.0 drag 200.0 tchain 1 pchain 0
# Specify reference state from paper, times 1000 atoms
fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
# Define output
variable dele equal f_myhug[1] # energy delta [temperature]
variable us equal f_myhug[2] # shock velocity [distance/time]
variable up equal f_myhug[3] # particle velocity [distance/time]
variable pzz equal pzz # axial stress
variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress
variable time equal dt*step
thermo 1000
thermo_style custom step temp ke epair econserve pzz v_tau lz f_myhug v_dele v_us v_up
fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (with drag)'
run 10000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.7475372
ghost atom cutoff = 1.7475372
binsize = 0.87376862, bins = 8 12 12
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cubic, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.086 | 3.086 | 3.086 Mbytes
Step Temp KinEng E_pair Econserve Pzz v_tau Lz f_myhug v_dele v_us v_up
0 0.01 0.014985 -6.3344253 -6.3194403 0.014347835 -0.00026463907 9.8684199 0 -0.0048552735 2.378672 0.0041061045
1000 0.0063089135 0.0094539069 -5.9892322 -1671.0142 18.914957 7.5823225 9.2337797 -1.6650344 0.02342632 13.975435 0.92133641
2000 0.006881368 0.01031173 -5.4566762 -2537.9852 37.064191 15.537213 8.9495783 -2.5325389 0.1023455 16.32485 1.5455517
3000 0.0072427308 0.010853232 -5.3662814 -2644.0227 39.906002 16.80569 8.9154322 -2.6386673 0.1182133 16.638326 1.6327015
4000 0.0070936511 0.010629836 -5.362616 -2655.9513 40.007995 16.850321 8.9143648 -2.6505993 0.11869211 16.650416 1.6356858
5000 0.0074091959 0.01110268 -5.3628939 -2664.5927 39.998199 16.845204 8.9144816 -2.6592409 0.11846407 16.649379 1.6353872
6000 0.0077388568 0.011596677 -5.362926 -2673.502 39.995216 16.842807 8.9145056 -2.6681507 0.11826568 16.648964 1.635306
7000 0.0076023299 0.011392091 -5.3621079 -2682.3942 39.998343 16.839762 8.9144789 -2.6770435 0.1181081 16.649386 1.6353924
8000 0.0076916892 0.011525996 -5.3617056 -2691.2334 40.000701 16.839078 8.9144843 -2.6858832 0.11795298 16.649924 1.635436
9000 0.0082153298 0.012310672 -5.3620895 -2700.1796 40.006134 16.845865 8.914544 -2.6948298 0.11785245 16.651566 1.6354968
10000 0.0088368733 0.013242055 -5.3625353 -2709.138 39.989575 16.835079 8.914577 -2.7037887 0.11749055 16.648403 1.6351305
Loop time of 19.325 on 4 procs for 10000 steps with 1000 atoms
Performance: 44708.822 tau/day, 517.463 timesteps/s
77.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.3012 | 3.4003 | 3.584 | 5.9 | 17.60
Neigh | 0.0047636 | 0.0054044 | 0.0072584 | 1.5 | 0.03
Comm | 4.5282 | 4.5961 | 4.651 | 2.1 | 23.78
Output | 0.00071692 | 0.0062424 | 0.0086811 | 4.1 | 0.03
Modify | 10.133 | 10.215 | 10.287 | 1.7 | 52.86
Other | | 1.102 | | | 5.70
Nlocal: 250.000 ave 258 max 239 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Nghost: 829.000 ave 840 max 821 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Neighs: 5250.00 ave 5360 max 5090 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Total # of neighbors = 21000
Ave neighs/atom = 21.000000
Neighbor list builds = 10
Dangerous builds = 0
# Start Run #3
clear
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
Reading restart file ...
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
restoring atom style atomic from restart
orthogonal box = (0.046520549 0.065789991 0.065789991) to (7.0245472 9.9342099 9.9342099)
1 by 2 by 2 MPI processor grid
restoring pair style lj/cubic from restart
1000 atoms
read_restart CPU = 0.001 seconds
neighbor 0.2 bin
neigh_modify every 1 delay 0 check yes
timestep 0.001
reset_timestep 0
# Pzz = 40.0, drag/damping term off, Nose-Hoover chains
fix myhug all nphug temp 1.0 1.0 1.0 z 40.0 40.0 70.0
# Specify reference state from paper, times 1000 atoms
fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
# Define output
variable dele equal f_myhug[1] # energy delta [temperature]
variable us equal f_myhug[2] # shock velocity [distance/time]
variable up equal f_myhug[3] # particle velocity [distance/time]
variable pzz equal pzz # axial stress
variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress
variable time equal dt*step
thermo 1000
thermo_style custom step temp ke epair econserve pzz v_tau lz f_myhug v_dele v_us v_up
fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (Nose-Hoover chain)'
run 10000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.7475372
ghost atom cutoff = 1.7475372
binsize = 0.87376862, bins = 8 12 12
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cubic, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.086 | 3.086 | 3.086 Mbytes
Step Temp KinEng E_pair Econserve Pzz v_tau Lz f_myhug v_dele v_us v_up
0 0.01 0.014985 -6.3344253 -6.3194403 0.014347835 -0.00026463907 9.8684199 0 -0.0048552735 2.378672 0.0041061045
1000 0.0078345757 0.011740112 -5.5017136 -838.78091 35.616593 14.888102 8.9677603 -0.83329094 0.093891841 16.160627 1.5002802
2000 0.019260442 0.028861773 -5.2936038 -1018.9574 41.771461 17.563025 8.8958988 -1.0136927 0.11811776 16.853931 1.6871615
3000 0.04811126 0.072094723 -5.3454068 -976.69826 39.061528 16.137201 8.9322605 -0.97142494 0.073850795 16.606008 1.6012612
4000 0.11854637 0.17764173 -5.2071392 -1296.5766 40.843143 16.426195 8.9202981 -1.2915471 0.017621672 16.874934 1.6476132
5000 0.13634185 0.20430827 -5.2645154 -1258.4101 39.098283 15.627986 8.9407719 -1.2533499 -0.00067591716 16.688492 1.5948462
6000 0.14222512 0.21312434 -5.1774698 -1369.5986 40.888661 16.260803 8.9214848 -1.3646342 -0.0041700902 16.894723 1.6475174
7000 0.12683772 0.19006633 -5.2679854 -1210.973 39.084165 15.633846 8.9393379 -1.2058951 0.00572464 16.672829 1.595768
8000 0.14531337 0.21775209 -5.1737911 -1372.667 40.861256 16.19118 8.9199953 -1.367711 -0.0065459838 16.876028 1.648237
9000 0.12123505 0.18167072 -5.2546764 -1189.0875 39.276006 15.677923 8.9363537 -1.1840145 0.0075170176 16.687402 1.6022003
10000 0.1477113 0.22134539 -5.1833959 -1353.4057 40.578404 16.080238 8.9245614 -1.3484436 -0.0098061873 16.857426 1.6386338
Loop time of 18.9651 on 4 procs for 10000 steps with 1000 atoms
Performance: 45557.373 tau/day, 527.284 timesteps/s
77.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.1152 | 3.3473 | 3.5591 | 10.0 | 17.65
Neigh | 0.045731 | 0.056706 | 0.066921 | 3.7 | 0.30
Comm | 3.9563 | 4.1638 | 4.4413 | 9.7 | 21.96
Output | 0.00067329 | 0.0033167 | 0.011241 | 7.9 | 0.02
Modify | 10.321 | 10.425 | 10.482 | 2.0 | 54.97
Other | | 0.9693 | | | 5.11
Nlocal: 250.000 ave 257 max 244 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Nghost: 832.250 ave 840 max 822 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 5144.25 ave 5282 max 4949 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Total # of neighbors = 20577
Ave neighs/atom = 20.577000
Neighbor list builds = 95
Dangerous builds = 0
Total wall time: 0:01:01

401
examples/hugoniostat/log.27Nov18.hugoniostat.g++.1
View File

@ -1,401 +0,0 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# This script reproduces stress trajectories from Fig. 1 in
# Ravelo, Holian, Germann, and Lomdahl, PRB 70 014103 (2004)
#
# Three thermostatting scenarios are visited: undamped (nodrag),
# damped (drag) and Nose-Hoover chain (nhchains).
#
# The axial and shear stress trajectories are printed to the
# file "stress_vs_t.dat". For the damped case, the original figure
# seems to be a plot of 2*tau, rather than tau.
#
# The script also demonstrates how to
# orient a crystal along <110>,
# and how to use the lj/cubic pair style.
units lj
boundary p p p
atom_style atomic
# Set up FCC lattice with z axis along <110>
lattice fcc 1.4142136 orient x 0 0 1 orient y 1 -1 0 orient z 1 1 0
Lattice spacing in x,y,z = 1.41421 2 2
region mycell block 0.0 5.0 0.0 5.0 0.0 5.0 units lattice
create_box 1 mycell
Created orthogonal box = (0 0 0) to (7.07107 10 10)
1 by 1 by 1 MPI processor grid
mass * 1.0
create_atoms 1 box
Created 1000 atoms
Time spent = 0.000465155 secs
# Using units of Rmin, so sigma = 2^-1/6 = 0.8908987
pair_style lj/cubic
pair_coeff * * 1.0 0.8908987
# Relax box dimensions
fix 3 all box/relax aniso 0.0 vmax 1.0e-4 nreset 100
thermo 100
thermo_style custom step temp pe etotal pxx pyy pzz lx ly lz
min_modify line quadratic
minimize 0.0 1.0e-6 10000 100000
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.84754
ghost atom cutoff = 1.84754
binsize = 0.923769, bins = 8 11 11
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cubic, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.247 | 4.247 | 4.247 Mbytes
Step Temp PotEng TotEng Pxx Pyy Pzz Lx Ly Lz
0 0 -6.2937539 -6.2937539 -2.7722431 -2.7722431 -2.7722431 7.0710677 9.9999999 9.9999999
100 0 -6.3319018 -6.3319018 -0.75971321 -0.75971321 -0.75971321 7.0003571 9.8999999 9.8999999
134 0 -6.3344257 -6.3344257 -4.5005818e-13 -4.9677973e-13 -4.9219424e-13 6.9780266 9.8684199 9.8684199
Loop time of 0.0724094 on 1 procs for 134 steps with 1000 atoms
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = force tolerance
Energy initial, next-to-last, final =
-6.2937539309 -6.33442568056 -6.33442568056
Force two-norm initial, final = 3395.29 5.83329e-10
Force max component initial, final = 1960.27 3.42093e-10
Final line search alpha, max atom move = 1 3.42093e-10
Iterations, force evaluations = 134 137
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.054599 | 0.054599 | 0.054599 | 0.0 | 75.40
Neigh | 0.0011106 | 0.0011106 | 0.0011106 | 0.0 | 1.53
Comm | 0.002012 | 0.002012 | 0.002012 | 0.0 | 2.78
Output | 1.955e-05 | 1.955e-05 | 1.955e-05 | 0.0 | 0.03
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.01467 | | | 20.26
Nlocal: 1000 ave 1000 max 1000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1724 ave 1724 max 1724 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 21000 ave 21000 max 21000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 21000
Ave neighs/atom = 21
Neighbor list builds = 1
Dangerous builds = 0
# Define initial velocity
velocity all create 0.01 87287 mom yes rot yes dist gaussian
write_restart restart.equil
# Start Run #1
clear
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
restoring atom style atomic from restart
orthogonal box = (0.0465206 0.06579 0.06579) to (7.02455 9.93421 9.93421)
1 by 1 by 1 MPI processor grid
restoring pair style lj/cubic from restart
1000 atoms
neighbor 0.2 bin
neigh_modify every 1 delay 0 check yes
timestep 0.001
reset_timestep 0
# Pzz = 40.0, drag/damping term off
fix myhug all nphug temp 1.0 1.0 10.0 z 40.0 40.0 70.0 drag 0.0 tchain 1 pchain 0
# Specify reference state from paper, times 1000 atoms
fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
# Add fix energy to output etotal
fix_modify myhug energy yes
# Define output
variable dele equal f_myhug[1] # energy delta [temperature]
variable us equal f_myhug[2] # shock velocity [distance/time]
variable up equal f_myhug[3] # particle velocity [distance/time]
variable pzz equal pzz # axial stress
variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress
variable time equal dt*step
thermo 1000
thermo_style custom step temp ke epair etotal pzz v_tau lz f_myhug v_dele v_us v_up
fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (no drag)'
#dump id all atom 500 dump.hugoniostat
#dump 2 all image 500 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 500 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
run 10000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.74754
ghost atom cutoff = 1.74754
binsize = 0.873769, bins = 8 12 12
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cubic, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.771 | 2.771 | 2.771 Mbytes
Step Temp KinEng E_pair TotEng Pzz v_tau Lz f_myhug v_dele v_us v_up
0 0.01 0.014985 -6.3344257 -6.3194407 0.014381062 -0.0002397183 9.8684199 0 -0.0048551451 2.3814196 0.0041108654
1000 0.0093381489 0.013993216 -2.170443 -6.3381216 129.15286 58.544417 8.3142516 -4.1816719 0.93744258 23.519053 3.7381989
2000 0.24794909 0.37155171 -5.8915802 -6.0429087 8.3850692 1.3744507 9.5938765 -0.5228803 -0.2435043 13.910468 0.4103393
3000 0.38920701 0.5832267 -3.768677 -6.6246124 72.742761 28.486747 8.623805 -3.439162 0.003825459 19.697379 2.5139668
4000 0.67009971 1.0041444 -4.2080644 -6.1365367 35.596179 3.9344133 8.7508422 -2.9326167 -0.58039603 14.529822 1.6677129
5000 0.41848975 0.62710689 -4.8393088 -6.1026724 30.626544 4.6387208 8.7827245 -1.8904705 -0.31996439 13.670884 1.5250343
6000 0.22410139 0.33581594 -3.7652941 -6.0923259 50.807437 7.2229456 8.2549488 -2.6628477 -0.017396966 14.4806 2.3884652
7000 0.095001485 0.14235972 -4.5436753 -6.7307217 35.8743 3.4938089 8.4476287 -2.3294061 -0.052272192 12.957528 1.8846881
8000 0.043277437 0.064851239 -4.6264096 -6.2447456 39.658659 6.7266325 8.4327483 -1.6831873 0.070488482 13.553882 1.9918311
9000 0.018271956 0.027380526 -4.4239627 -6.3085661 41.708324 5.9081923 8.3463321 -1.9119839 0.091057512 13.503882 2.1025305
10000 0.0082840001 0.012413574 -4.622252 -6.3316699 39.830379 6.5596321 8.4109569 -1.7218314 0.099435465 13.482451 2.0110543
Loop time of 6.20702 on 1 procs for 10000 steps with 1000 atoms
Performance: 139197.321 tau/day, 1611.080 timesteps/s
98.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.0198 | 5.0198 | 5.0198 | 0.0 | 80.87
Neigh | 0.21405 | 0.21405 | 0.21405 | 0.0 | 3.45
Comm | 0.16164 | 0.16164 | 0.16164 | 0.0 | 2.60
Output | 0.00053501 | 0.00053501 | 0.00053501 | 0.0 | 0.01
Modify | 0.7419 | 0.7419 | 0.7419 | 0.0 | 11.95
Other | | 0.06911 | | | 1.11
Nlocal: 1000 ave 1000 max 1000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1886 ave 1886 max 1886 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 20874 ave 20874 max 20874 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 20874
Ave neighs/atom = 20.874
Neighbor list builds = 188
Dangerous builds = 0
# Start Run #2
clear
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
restoring atom style atomic from restart
orthogonal box = (0.0465206 0.06579 0.06579) to (7.02455 9.93421 9.93421)
1 by 1 by 1 MPI processor grid
restoring pair style lj/cubic from restart
1000 atoms
neighbor 0.2 bin
neigh_modify every 1 delay 0 check yes
timestep 0.001
reset_timestep 0
# Pzz = 40.0, drag/damping term on
fix myhug all nphug temp 1.0 1.0 1.0 z 40.0 40.0 70.0 drag 200.0 tchain 1 pchain 0
# Specify reference state from paper, times 1000 atoms
fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
# Add fix energy to output etotal
fix_modify myhug energy yes
# Define output
variable dele equal f_myhug[1] # energy delta [temperature]
variable us equal f_myhug[2] # shock velocity [distance/time]
variable up equal f_myhug[3] # particle velocity [distance/time]
variable pzz equal pzz # axial stress
variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress
variable time equal dt*step
thermo 1000
thermo_style custom step temp ke epair etotal pzz v_tau lz f_myhug v_dele v_us v_up
fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (with drag)'
run 10000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.74754
ghost atom cutoff = 1.74754
binsize = 0.873769, bins = 8 12 12
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cubic, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.771 | 2.771 | 2.771 Mbytes
Step Temp KinEng E_pair TotEng Pzz v_tau Lz f_myhug v_dele v_us v_up
0 0.01 0.014985 -6.3344257 -6.3194407 0.014381062 -0.0002397183 9.8684199 0 -0.0048551451 2.3814196 0.0041108654
1000 0.0062572991 0.0093765627 -5.9890874 -7.64465 18.918117 7.5844397 9.2338165 -1.6649392 0.02341947 13.976996 0.92138738
2000 0.006845108 0.010257394 -5.4565813 -7.9786876 37.064254 15.537266 8.9496404 -2.5323637 0.1023062 16.325405 1.5455017
3000 0.0073276109 0.010980425 -5.3663425 -7.9938818 39.907292 16.807488 8.9154852 -2.6385197 0.11818131 16.639049 1.6326833
4000 0.0069296915 0.010384143 -5.3623404 -8.0023271 40.010741 16.851482 8.9144328 -2.6503708 0.11868152 16.651571 1.6356847
5000 0.0076142476 0.01140995 -5.3631447 -8.0108329 39.997648 16.846756 8.9145416 -2.6590981 0.11841154 16.649778 1.6353255
6000 0.0077053839 0.011546518 -5.3628542 -8.0192007 39.991597 16.840313 8.9145803 -2.6678931 0.11818376 16.648851 1.6351691
7000 0.0077405662 0.011599239 -5.3623534 -8.0275624 40.000448 16.844008 8.9145774 -2.6768081 0.11809914 16.650669 1.6353525
8000 0.008067359 0.012088937 -5.3623759 -8.0359471 39.995327 16.840134 8.9146099 -2.6856601 0.11787118 16.649881 1.6352204
9000 0.0083223114 0.012470984 -5.3622992 -8.0443714 40.00571 16.847763 8.9146503 -2.6945431 0.11781538 16.652389 1.6353987
10000 0.0091249143 0.013673684 -5.3630142 -8.0529573 39.987196 16.837314 8.9146848 -2.7036168 0.11743028 16.648831 1.6349911
Loop time of 5.48047 on 1 procs for 10000 steps with 1000 atoms
Performance: 157650.687 tau/day, 1824.661 timesteps/s
98.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.5166 | 4.5166 | 4.5166 | 0.0 | 82.41
Neigh | 0.012162 | 0.012162 | 0.012162 | 0.0 | 0.22
Comm | 0.14168 | 0.14168 | 0.14168 | 0.0 | 2.59
Output | 0.00053787 | 0.00053787 | 0.00053787 | 0.0 | 0.01
Modify | 0.74394 | 0.74394 | 0.74394 | 0.0 | 13.57
Other | | 0.06553 | | | 1.20
Nlocal: 1000 ave 1000 max 1000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1724 ave 1724 max 1724 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 21000 ave 21000 max 21000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 21000
Ave neighs/atom = 21
Neighbor list builds = 11
Dangerous builds = 0
# Start Run #3
clear
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
restoring atom style atomic from restart
orthogonal box = (0.0465206 0.06579 0.06579) to (7.02455 9.93421 9.93421)
1 by 1 by 1 MPI processor grid
restoring pair style lj/cubic from restart
1000 atoms
neighbor 0.2 bin
neigh_modify every 1 delay 0 check yes
timestep 0.001
reset_timestep 0
# Pzz = 40.0, drag/damping term off, Nose-Hoover chains
fix myhug all nphug temp 1.0 1.0 1.0 z 40.0 40.0 70.0
# Specify reference state from paper, times 1000 atoms
fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
# Add fix energy to output etotal
fix_modify myhug energy yes
# Define output
variable dele equal f_myhug[1] # energy delta [temperature]
variable us equal f_myhug[2] # shock velocity [distance/time]
variable up equal f_myhug[3] # particle velocity [distance/time]
variable pzz equal pzz # axial stress
variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress
variable time equal dt*step
thermo 1000
thermo_style custom step temp ke epair etotal pzz v_tau lz f_myhug v_dele v_us v_up
fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (Nose-Hoover chain)'
run 10000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.74754
ghost atom cutoff = 1.74754
binsize = 0.873769, bins = 8 12 12
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cubic, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.771 | 2.771 | 2.771 Mbytes
Step Temp KinEng E_pair TotEng Pzz v_tau Lz f_myhug v_dele v_us v_up
0 0.01 0.014985 -6.3344257 -6.3194407 0.014381062 -0.0002397183 9.8684199 0 -0.0048551451 2.3814196 0.0041108654
1000 0.0083300394 0.012482564 -5.5023188 -6.3233387 35.610076 14.886667 8.9677982 -0.83350251 0.093761848 16.159481 1.500112
2000 0.020386462 0.030549113 -5.2949349 -6.2805556 41.760388 17.563305 8.896033 -1.0161699 0.11780863 16.85284 1.6868235
3000 0.049693152 0.074465188 -5.3469434 -6.2493961 39.030372 16.123483 8.9325594 -0.9769179 0.073097387 16.601986 1.6003716
4000 0.11859514 0.17771482 -5.207077 -6.3242752 40.941558 16.507785 8.9213147 -1.2949131 0.018189678 16.904156 1.6487282
5000 0.13014573 0.19502337 -5.2610248 -6.269279 39.059628 15.609345 8.9431685 -1.2032776 -0.00023747376 16.701437 1.5920344
6000 0.1381307 0.20698886 -5.171005 -6.2931942 40.904837 16.242165 8.9222854 -1.3291781 -0.0044770368 16.905086 1.6471589
7000 0.12107326 0.18142828 -5.2602554 -6.2438099 39.060928 15.57765 8.9397525 -1.1649827 0.0055890257 16.671524 1.594944
8000 0.14333636 0.21478954 -5.1717123 -6.304602 40.876188 16.205815 8.9218142 -1.3476793 -0.0069396327 16.895033 1.6469846
9000 0.12159663 0.18221255 -5.2591911 -6.2587685 39.228648 15.677869 8.9376641 -1.18179 0.0077357066 16.688862 1.6001283
10000 0.15321883 0.22959841 -5.1881787 -6.3448453 40.666451 16.146177 8.922851 -1.386265 -0.0091929687 16.860705 1.6418699
Loop time of 5.6426 on 1 procs for 10000 steps with 1000 atoms
Performance: 153120.907 tau/day, 1772.233 timesteps/s
98.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.5653 | 4.5653 | 4.5653 | 0.0 | 80.91
Neigh | 0.10885 | 0.10885 | 0.10885 | 0.0 | 1.93
Comm | 0.14695 | 0.14695 | 0.14695 | 0.0 | 2.60
Output | 0.00055218 | 0.00055218 | 0.00055218 | 0.0 | 0.01
Modify | 0.75364 | 0.75364 | 0.75364 | 0.0 | 13.36
Other | | 0.0673 | | | 1.19
Nlocal: 1000 ave 1000 max 1000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1724 ave 1724 max 1724 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 20654 ave 20654 max 20654 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 20654
Ave neighs/atom = 20.654
Neighbor list builds = 94
Dangerous builds = 0
Total wall time: 0:00:17

401
examples/hugoniostat/log.27Nov18.hugoniostat.g++.4
View File

@ -1,401 +0,0 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# This script reproduces stress trajectories from Fig. 1 in
# Ravelo, Holian, Germann, and Lomdahl, PRB 70 014103 (2004)
#
# Three thermostatting scenarios are visited: undamped (nodrag),
# damped (drag) and Nose-Hoover chain (nhchains).
#
# The axial and shear stress trajectories are printed to the
# file "stress_vs_t.dat". For the damped case, the original figure
# seems to be a plot of 2*tau, rather than tau.
#
# The script also demonstrates how to
# orient a crystal along <110>,
# and how to use the lj/cubic pair style.
units lj
boundary p p p
atom_style atomic
# Set up FCC lattice with z axis along <110>
lattice fcc 1.4142136 orient x 0 0 1 orient y 1 -1 0 orient z 1 1 0
Lattice spacing in x,y,z = 1.41421 2 2
region mycell block 0.0 5.0 0.0 5.0 0.0 5.0 units lattice
create_box 1 mycell
Created orthogonal box = (0 0 0) to (7.07107 10 10)
1 by 2 by 2 MPI processor grid
mass * 1.0
create_atoms 1 box
Created 1000 atoms
Time spent = 0.0003438 secs
# Using units of Rmin, so sigma = 2^-1/6 = 0.8908987
pair_style lj/cubic
pair_coeff * * 1.0 0.8908987
# Relax box dimensions
fix 3 all box/relax aniso 0.0 vmax 1.0e-4 nreset 100
thermo 100
thermo_style custom step temp pe etotal pxx pyy pzz lx ly lz
min_modify line quadratic
minimize 0.0 1.0e-6 10000 100000
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.84754
ghost atom cutoff = 1.84754
binsize = 0.923769, bins = 8 11 11
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cubic, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.211 | 4.211 | 4.211 Mbytes
Step Temp PotEng TotEng Pxx Pyy Pzz Lx Ly Lz
0 0 -6.2937539 -6.2937539 -2.7722431 -2.7722431 -2.7722431 7.0710677 9.9999999 9.9999999
100 0 -6.3319018 -6.3319018 -0.75971321 -0.75971321 -0.75971321 7.0003571 9.8999999 9.8999999
134 0 -6.3344257 -6.3344257 -4.5046204e-13 -4.92206e-13 -4.9610344e-13 6.9780266 9.8684199 9.8684199
Loop time of 0.0269771 on 4 procs for 134 steps with 1000 atoms
94.3% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = force tolerance
Energy initial, next-to-last, final =
-6.2937539309 -6.33442568056 -6.33442568056
Force two-norm initial, final = 3395.29 5.80609e-10
Force max component initial, final = 1960.27 3.41627e-10
Final line search alpha, max atom move = 1 3.41627e-10
Iterations, force evaluations = 134 137
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.011534 | 0.013897 | 0.016008 | 1.3 | 51.51
Neigh | 0.00024176 | 0.00029498 | 0.00035191 | 0.0 | 1.09
Comm | 0.0029764 | 0.0050126 | 0.0073018 | 2.2 | 18.58
Output | 1.8835e-05 | 1.9968e-05 | 2.2888e-05 | 0.0 | 0.07
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.007753 | | | 28.74
Nlocal: 250 ave 305 max 205 min
Histogram: 1 0 0 0 2 0 0 0 0 1
Nghost: 829 ave 874 max 774 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 5250 ave 6445 max 4305 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 21000
Ave neighs/atom = 21
Neighbor list builds = 1
Dangerous builds = 0
# Define initial velocity
velocity all create 0.01 87287 mom yes rot yes dist gaussian
write_restart restart.equil
# Start Run #1
clear
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
restoring atom style atomic from restart
orthogonal box = (0.0465206 0.06579 0.06579) to (7.02455 9.93421 9.93421)
1 by 2 by 2 MPI processor grid
restoring pair style lj/cubic from restart
1000 atoms
neighbor 0.2 bin
neigh_modify every 1 delay 0 check yes
timestep 0.001
reset_timestep 0
# Pzz = 40.0, drag/damping term off
fix myhug all nphug temp 1.0 1.0 10.0 z 40.0 40.0 70.0 drag 0.0 tchain 1 pchain 0
# Specify reference state from paper, times 1000 atoms
fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
# Add fix energy to output etotal
fix_modify myhug energy yes
# Define output
variable dele equal f_myhug[1] # energy delta [temperature]
variable us equal f_myhug[2] # shock velocity [distance/time]
variable up equal f_myhug[3] # particle velocity [distance/time]
variable pzz equal pzz # axial stress
variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress
variable time equal dt*step
thermo 1000
thermo_style custom step temp ke epair etotal pzz v_tau lz f_myhug v_dele v_us v_up
fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (no drag)'
#dump id all atom 500 dump.hugoniostat
#dump 2 all image 500 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 500 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
run 10000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.74754
ghost atom cutoff = 1.74754
binsize = 0.873769, bins = 8 12 12
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cubic, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.717 | 2.809 | 3.086 Mbytes
Step Temp KinEng E_pair TotEng Pzz v_tau Lz f_myhug v_dele v_us v_up
0 0.01 0.014985 -6.3344257 -6.3194407 0.014347835 -0.00026463907 9.8684199 0 -0.0048551516 2.3786668 0.0041061135
1000 0.010586668 0.015864122 -2.1721826 -6.3380886 129.03334 58.456626 8.3141284 -4.1817701 0.93542408 23.507246 3.7366154
2000 0.3321368 0.49770699 -5.584787 -6.0546694 12.097343 1.2026972 9.4615963 -0.96758935 -0.3571439 13.858218 0.5942385
3000 0.46981685 0.70402055 -3.9208474 -6.3911005 63.005989 22.559106 8.6828663 -3.1742737 -0.16958917 18.776521 2.2842567
4000 0.54866493 0.82217439 -4.1703408 -6.2427645 38.408608 4.9066022 8.6573289 -2.894598 -0.45434132 14.506935 1.8023166
5000 0.30625495 0.45892304 -4.7355785 -6.186448 35.000599 6.2097986 8.6658098 -1.9097925 -0.19603125 13.896448 1.7145489
6000 0.13938196 0.20886386 -4.303964 -5.7629121 50.370681 12.189231 8.3966581 -1.6678119 0.11451271 15.088809 2.2724852
7000 0.055349516 0.082941249 -5.2031342 -6.8043199 30.859256 6.5562297 8.6850282 -1.684127 0.020586458 13.152479 1.5971879
8000 0.027926794 0.0418483 -4.5281656 -5.4484008 48.145681 12.229919 8.4107051 -0.96208352 0.19922201 14.821877 2.2112219
9000 0.018195086 0.027265336 -4.9847444 -6.5712684 37.347655 8.7291385 8.5606968 -1.6137894 0.10912534 13.773573 1.8458438
10000 0.0082893467 0.012421586 -5.0130076 -6.6821423 36.46118 8.3386716 8.5689995 -1.6815563 0.1065388 13.651975 1.8180818
Loop time of 2.01177 on 4 procs for 10000 steps with 1000 atoms
Performance: 429472.539 tau/day, 4970.747 timesteps/s
98.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.2437 | 1.2651 | 1.2843 | 1.7 | 62.89
Neigh | 0.051696 | 0.052503 | 0.053247 | 0.3 | 2.61
Comm | 0.24826 | 0.26724 | 0.28867 | 3.5 | 13.28
Output | 0.00058603 | 0.00085759 | 0.0016623 | 0.0 | 0.04
Modify | 0.37363 | 0.37671 | 0.38189 | 0.5 | 18.73
Other | | 0.04935 | | | 2.45
Nlocal: 250 ave 260 max 240 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 927.5 ave 934 max 921 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 5048.5 ave 5203 max 4889 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Total # of neighbors = 20194
Ave neighs/atom = 20.194
Neighbor list builds = 175
Dangerous builds = 0
# Start Run #2
clear
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
restoring atom style atomic from restart
orthogonal box = (0.0465206 0.06579 0.06579) to (7.02455 9.93421 9.93421)
1 by 2 by 2 MPI processor grid
restoring pair style lj/cubic from restart
1000 atoms
neighbor 0.2 bin
neigh_modify every 1 delay 0 check yes
timestep 0.001
reset_timestep 0
# Pzz = 40.0, drag/damping term on
fix myhug all nphug temp 1.0 1.0 1.0 z 40.0 40.0 70.0 drag 200.0 tchain 1 pchain 0
# Specify reference state from paper, times 1000 atoms
fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
# Add fix energy to output etotal
fix_modify myhug energy yes
# Define output
variable dele equal f_myhug[1] # energy delta [temperature]
variable us equal f_myhug[2] # shock velocity [distance/time]
variable up equal f_myhug[3] # particle velocity [distance/time]
variable pzz equal pzz # axial stress
variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress
variable time equal dt*step
thermo 1000
thermo_style custom step temp ke epair etotal pzz v_tau lz f_myhug v_dele v_us v_up
fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (with drag)'
run 10000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.74754
ghost atom cutoff = 1.74754
binsize = 0.873769, bins = 8 12 12
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cubic, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.717 | 2.809 | 3.086 Mbytes
Step Temp KinEng E_pair TotEng Pzz v_tau Lz f_myhug v_dele v_us v_up
0 0.01 0.014985 -6.3344257 -6.3194407 0.014347835 -0.00026463907 9.8684199 0 -0.0048551516 2.3786668 0.0041061135
1000 0.0063089138 0.0094539073 -5.9892326 -7.6448129 18.914956 7.5823222 9.2337797 -1.6650342 0.023426454 13.975434 0.92133642
2000 0.0068813683 0.01031173 -5.4566765 -7.9789037 37.064192 15.537213 8.9495783 -2.5325388 0.10234565 16.32485 1.5455517
3000 0.0072427316 0.010853233 -5.3662818 -7.9940958 39.906002 16.80569 8.9154322 -2.6386672 0.11821344 16.638326 1.6327015
4000 0.0070936522 0.010629838 -5.3626164 -8.0025859 40.007994 16.850321 8.9143648 -2.6505993 0.11869226 16.650416 1.6356859
5000 0.0074091958 0.01110268 -5.3628943 -8.0110325 39.998199 16.845204 8.9144816 -2.6592409 0.11846422 16.649379 1.6353872
6000 0.0077388573 0.011596678 -5.3629264 -8.0194804 39.995216 16.842807 8.9145056 -2.6681507 0.11826582 16.648964 1.635306
7000 0.0076023298 0.011392091 -5.3621083 -8.0277598 39.998343 16.839762 8.9144789 -2.6770435 0.11810824 16.649386 1.6353924
8000 0.007691692 0.011526001 -5.361706 -8.0360632 40.000701 16.839078 8.9144843 -2.6858833 0.11795313 16.649923 1.6354361
9000 0.0082153298 0.012310672 -5.3620899 -8.0446091 40.006134 16.845865 8.914544 -2.6948299 0.11785259 16.651566 1.6354969
10000 0.0088368792 0.013242063 -5.3625357 -8.0530825 39.989575 16.835079 8.914577 -2.7037888 0.1174907 16.648402 1.6351306
Loop time of 1.80214 on 4 procs for 10000 steps with 1000 atoms
Performance: 479429.980 tau/day, 5548.958 timesteps/s
98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.1353 | 1.1591 | 1.1787 | 1.5 | 64.32
Neigh | 0.0028975 | 0.0029137 | 0.0029218 | 0.0 | 0.16
Comm | 0.20882 | 0.22752 | 0.25213 | 3.4 | 12.62
Output | 0.00058103 | 0.0007953 | 0.0014329 | 0.0 | 0.04
Modify | 0.36598 | 0.36908 | 0.37078 | 0.3 | 20.48
Other | | 0.04277 | | | 2.37
Nlocal: 250 ave 258 max 239 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Nghost: 829 ave 840 max 821 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Neighs: 5250 ave 5360 max 5090 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Total # of neighbors = 21000
Ave neighs/atom = 21
Neighbor list builds = 10
Dangerous builds = 0
# Start Run #3
clear
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
restoring atom style atomic from restart
orthogonal box = (0.0465206 0.06579 0.06579) to (7.02455 9.93421 9.93421)
1 by 2 by 2 MPI processor grid
restoring pair style lj/cubic from restart
1000 atoms
neighbor 0.2 bin
neigh_modify every 1 delay 0 check yes
timestep 0.001
reset_timestep 0
# Pzz = 40.0, drag/damping term off, Nose-Hoover chains
fix myhug all nphug temp 1.0 1.0 1.0 z 40.0 40.0 70.0
# Specify reference state from paper, times 1000 atoms
fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
# Add fix energy to output etotal
fix_modify myhug energy yes
# Define output
variable dele equal f_myhug[1] # energy delta [temperature]
variable us equal f_myhug[2] # shock velocity [distance/time]
variable up equal f_myhug[3] # particle velocity [distance/time]
variable pzz equal pzz # axial stress
variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress
variable time equal dt*step
thermo 1000
thermo_style custom step temp ke epair etotal pzz v_tau lz f_myhug v_dele v_us v_up
fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (Nose-Hoover chain)'
run 10000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.74754
ghost atom cutoff = 1.74754
binsize = 0.873769, bins = 8 12 12
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cubic, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.717 | 2.809 | 3.086 Mbytes
Step Temp KinEng E_pair TotEng Pzz v_tau Lz f_myhug v_dele v_us v_up
0 0.01 0.014985 -6.3344257 -6.3194407 0.014347835 -0.00026463907 9.8684199 0 -0.0048551516 2.3786668 0.0041061135
1000 0.0078345827 0.011740122 -5.501714 -6.3232649 35.616592 14.888101 8.9677603 -0.833291 0.093891974 16.160626 1.5002802
2000 0.019260469 0.028861813 -5.2936047 -6.2784351 41.771445 17.563018 8.895899 -1.0136922 0.11811779 16.853929 1.687161
3000 0.048111305 0.072094791 -5.3454082 -6.2447367 39.061491 16.137184 8.932261 -0.97142325 0.073850675 16.606004 1.6012602
4000 0.11854629 0.17764161 -5.2071426 -6.3210422 40.843054 16.426156 8.9202992 -1.2915412 0.017621345 16.874925 1.6476105
5000 0.13634167 0.204308 -5.2645153 -6.3135608 39.098316 15.628006 8.9407716 -1.2533534 -0.00067532215 16.688495 1.5948471
6000 0.14222646 0.21312635 -5.1774703 -6.3289809 40.888616 16.260775 8.9214855 -1.3646369 -0.0041713956 16.89472 1.6475159
7000 0.12683662 0.19006468 -5.2679846 -6.2838171 39.084233 15.633883 8.939337 -1.2058972 0.0057260888 16.672835 1.5957701
8000 0.14531516 0.21775476 -5.1737923 -6.3237483 40.861161 16.191124 8.9199968 -1.3677107 -0.0065481979 16.876021 1.6482339
9000 0.12123357 0.18166851 -5.2546748 -6.2570254 39.276123 15.677988 8.9363522 -1.1840191 0.0075191856 16.687414 1.6022039
10000 0.14771416 0.22134967 -5.1833988 -6.3104954 40.578265 16.080163 8.9245634 -1.3484463 -0.0098090911 16.857414 1.6386293
Loop time of 1.8702 on 4 procs for 10000 steps with 1000 atoms
Performance: 461983.152 tau/day, 5347.027 timesteps/s
98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.1723 | 1.1812 | 1.1956 | 0.9 | 63.16
Neigh | 0.028221 | 0.030409 | 0.035555 | 1.7 | 1.63
Comm | 0.22963 | 0.24139 | 0.25155 | 1.6 | 12.91
Output | 0.00055218 | 0.00077897 | 0.0014515 | 0.0 | 0.04
Modify | 0.37165 | 0.37241 | 0.3732 | 0.1 | 19.91
Other | | 0.04404 | | | 2.35
Nlocal: 250 ave 257 max 244 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Nghost: 832.25 ave 840 max 822 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 5144.25 ave 5282 max 4949 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Total # of neighbors = 20577
Ave neighs/atom = 20.577
Neighbor list builds = 95
Dangerous builds = 0
Total wall time: 0:00:05

110
examples/hugoniostat/log.5Oct16.hugoniostat.g++.1
View File

@ -1,110 +0,0 @@
LAMMPS (5 Oct 2016)
# This script reproduces stress trajectories from Fig. 1 in
# Ravelo, Holian, Germann, and Lomdahl, PRB 70 014103 (2004)
#
# Three thermostatting scenarios are visited: undamped (nodrag),
# damped (drag) and Nose-Hoover chain (nhchains).
#
# The axial and shear stress trajectories are printed to the
# file "stress_vs_t.dat". For the damped case, the original figure
# seems to be a plot of 2*tau, rather than tau.
#
# The script also demonstrates how to
# orient a crystal along <110>,
# and how to use the lj/cubic pair style.
units lj
boundary p p p
atom_style atomic
# Set up FCC lattice with z axis along <110>
lattice fcc 1.4142136 orient x 0 0 1 orient y 1 -1 0 orient z 1 1 0
Lattice spacing in x,y,z = 1.41421 2 2
region mycell block 0.0 5.0 0.0 5.0 0.0 5.0 units lattice
create_box 1 mycell
Created orthogonal box = (0 0 0) to (7.07107 10 10)
1 by 1 by 1 MPI processor grid
mass * 1.0
create_atoms 1 box
Created 1000 atoms
# Using units of Rmin, so sigma = 2^-1/6 = 0.8908987
pair_style lj/cubic
pair_coeff * * 1.0 0.8908987
# Relax box dimensions
fix 3 all box/relax aniso 0.0 vmax 1.0e-4 nreset 100
thermo 100
thermo_style custom step temp pe etotal pxx pyy pzz lx ly lz
min_modify line quadratic
minimize 0.0 1.0e-6 10000 100000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.84754
ghost atom cutoff = 1.84754
binsize = 0.923769 -> bins = 8 11 11
Memory usage per processor = 3.65406 Mbytes
Step Temp PotEng TotEng Pxx Pyy Pzz Lx Ly Lz
0 0 -6.2937539 -6.2937539 -2.7722431 -2.7722431 -2.7722431 7.0710677 9.9999999 9.9999999
100 0 -6.3319018 -6.3319018 -0.75971321 -0.75971321 -0.75971321 7.0003571 9.8999999 9.8999999
134 0 -6.3344257 -6.3344257 -4.5005818e-13 -4.9677973e-13 -4.9219424e-13 6.9780266 9.8684199 9.8684199
Loop time of 0.0817621 on 1 procs for 134 steps with 1000 atoms
100.3% CPU use with 1 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = force tolerance
Energy initial, next-to-last, final =
-6.2937539309 -6.33442568056 -6.33442568056
Force two-norm initial, final = 3395.29 5.83329e-10
Force max component initial, final = 1960.27 3.42093e-10
Final line search alpha, max atom move = 1 3.42093e-10
Iterations, force evaluations = 134 137
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.066955 | 0.066955 | 0.066955 | 0.0 | 81.89
Neigh | 0.001004 | 0.001004 | 0.001004 | 0.0 | 1.23
Comm | 0.0014298 | 0.0014298 | 0.0014298 | 0.0 | 1.75
Output | 1.5974e-05 | 1.5974e-05 | 1.5974e-05 | 0.0 | 0.02
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.01236 | | | 15.11
Nlocal: 1000 ave 1000 max 1000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1724 ave 1724 max 1724 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 21000 ave 21000 max 21000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 21000
Ave neighs/atom = 21
Neighbor list builds = 1
Dangerous builds = 0
# Define initial velocity
velocity all create 0.01 87287 mom yes rot yes dist gaussian
write_restart restart.equil
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 = 1.84754
ghost atom cutoff = 1.84754
binsize = 0.923769 -> bins = 8 11 11
# Start Run #1
log log.nodrag

110
examples/hugoniostat/log.5Oct16.hugoniostat.g++.4
View File

@ -1,110 +0,0 @@
LAMMPS (5 Oct 2016)
# This script reproduces stress trajectories from Fig. 1 in
# Ravelo, Holian, Germann, and Lomdahl, PRB 70 014103 (2004)
#
# Three thermostatting scenarios are visited: undamped (nodrag),
# damped (drag) and Nose-Hoover chain (nhchains).
#
# The axial and shear stress trajectories are printed to the
# file "stress_vs_t.dat". For the damped case, the original figure
# seems to be a plot of 2*tau, rather than tau.
#
# The script also demonstrates how to
# orient a crystal along <110>,
# and how to use the lj/cubic pair style.
units lj
boundary p p p
atom_style atomic
# Set up FCC lattice with z axis along <110>
lattice fcc 1.4142136 orient x 0 0 1 orient y 1 -1 0 orient z 1 1 0
Lattice spacing in x,y,z = 1.41421 2 2
region mycell block 0.0 5.0 0.0 5.0 0.0 5.0 units lattice
create_box 1 mycell
Created orthogonal box = (0 0 0) to (7.07107 10 10)
1 by 2 by 2 MPI processor grid
mass * 1.0
create_atoms 1 box
Created 1000 atoms
# Using units of Rmin, so sigma = 2^-1/6 = 0.8908987
pair_style lj/cubic
pair_coeff * * 1.0 0.8908987
# Relax box dimensions
fix 3 all box/relax aniso 0.0 vmax 1.0e-4 nreset 100
thermo 100
thermo_style custom step temp pe etotal pxx pyy pzz lx ly lz
min_modify line quadratic
minimize 0.0 1.0e-6 10000 100000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.84754
ghost atom cutoff = 1.84754
binsize = 0.923769 -> bins = 8 11 11
Memory usage per processor = 3.63062 Mbytes
Step Temp PotEng TotEng Pxx Pyy Pzz Lx Ly Lz
0 0 -6.2937539 -6.2937539 -2.7722431 -2.7722431 -2.7722431 7.0710677 9.9999999 9.9999999
100 0 -6.3319018 -6.3319018 -0.75971321 -0.75971321 -0.75971321 7.0003571 9.8999999 9.8999999
134 0 -6.3344257 -6.3344257 -4.5046204e-13 -4.92206e-13 -4.9610344e-13 6.9780266 9.8684199 9.8684199
Loop time of 0.0299768 on 4 procs for 134 steps with 1000 atoms
98.4% CPU use with 4 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = force tolerance
Energy initial, next-to-last, final =
-6.2937539309 -6.33442568056 -6.33442568056
Force two-norm initial, final = 3395.29 5.80609e-10
Force max component initial, final = 1960.27 3.41627e-10
Final line search alpha, max atom move = 1 3.41627e-10
Iterations, force evaluations = 134 137
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.01485 | 0.017638 | 0.020133 | 1.4 | 58.84
Neigh | 0.00022697 | 0.00027376 | 0.00033092 | 0.2 | 0.91
Comm | 0.0026414 | 0.0050641 | 0.0078235 | 2.6 | 16.89
Output | 1.502e-05 | 1.6749e-05 | 2.0027e-05 | 0.0 | 0.06
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.006985 | | | 23.30
Nlocal: 250 ave 305 max 205 min
Histogram: 1 0 0 0 2 0 0 0 0 1
Nghost: 829 ave 874 max 774 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 5250 ave 6445 max 4305 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 21000
Ave neighs/atom = 21
Neighbor list builds = 1
Dangerous builds = 0
# Define initial velocity
velocity all create 0.01 87287 mom yes rot yes dist gaussian
write_restart restart.equil
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 = 1.84754
ghost atom cutoff = 1.84754
binsize = 0.923769 -> bins = 8 11 11
# Start Run #1
log log.nodrag

5
examples/msst/in.msst
View File

@ -36,15 +36,12 @@ unfix 2
# MSST fix
fix msst all msst z 28.0 q 200 mu 3e2 tscale 0.01
# 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 &
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
#dump id all atom 50 dump.msst

87
examples/msst/log.30Jun20.msst.g++.1 → examples/msst/log.08Feb21.msst.g++.1
View File

@ -1,4 +1,4 @@
LAMMPS (30 Jun 2020)
LAMMPS (24 Dec 2020)
using 1 OpenMP thread(s) per MPI task
# LJ test of msst shock dynamics
@ -10,18 +10,18 @@ atom_style atomic
timestep 1e-03
lattice fcc 5.3589
Lattice spacing in x,y,z = 5.3589 5.3589 5.3589
Lattice spacing in x,y,z = 5.3589000 5.3589000 5.3589000
## 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)
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (96.460200 96.460200 96.460200)
1 by 1 by 1 MPI processor grid
create_atoms 1 region box1
Created 23328 atoms
create_atoms CPU = 0.007 seconds
create_atoms CPU = 0.012 seconds
mass 1 40.00
@ -63,30 +63,30 @@ Step Temp E_pair E_mol TotEng Press
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 3.62419 on 1 procs for 100 steps with 23328 atoms
Loop time of 8.29437 on 1 procs for 100 steps with 23328 atoms
Performance: 4.768 ns/day, 5.034 hours/ns, 27.592 timesteps/s
Performance: 2.083 ns/day, 11.520 hours/ns, 12.056 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.4606 | 3.4606 | 3.4606 | 0.0 | 95.49
Neigh | 0.065469 | 0.065469 | 0.065469 | 0.0 | 1.81
Comm | 0.030757 | 0.030757 | 0.030757 | 0.0 | 0.85
Output | 0.0024359 | 0.0024359 | 0.0024359 | 0.0 | 0.07
Modify | 0.049582 | 0.049582 | 0.049582 | 0.0 | 1.37
Other | | 0.01537 | | | 0.42
Pair | 7.9896 | 7.9896 | 7.9896 | 0.0 | 96.33
Neigh | 0.13503 | 0.13503 | 0.13503 | 0.0 | 1.63
Comm | 0.053102 | 0.053102 | 0.053102 | 0.0 | 0.64
Output | 0.0035691 | 0.0035691 | 0.0035691 | 0.0 | 0.04
Modify | 0.091417 | 0.091417 | 0.091417 | 0.0 | 1.10
Other | | 0.02167 | | | 0.26
Nlocal: 23328.0 ave 23328.0 max 23328.0 min
Nlocal: 23328.0 ave 23328 max 23328 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 22235.0 ave 22235.0 max 22235.0 min
Nghost: 22235.0 ave 22235 max 22235 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2183715.0 ave 2183715.0 max 2183715.0 min
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 = 93.60918209876543
Ave neighs/atom = 93.609182
Neighbor list builds = 1
Dangerous builds = 0
unfix 2
@ -102,15 +102,12 @@ MSST parameters:
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
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
#dump id all atom 50 dump.msst
@ -126,42 +123,42 @@ Fix MSST p0 = 8106.7886
Fix MSST e0 = -151.14112
Fix MSST initial strain rate of -0.032011238 established by reducing temperature by factor of 0.01
Per MPI rank memory allocation (min/avg/max) = 18.98 | 18.98 | 18.98 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 7.9807 on 1 procs for 100 steps with 23328 atoms
Step Temp KinEng PotEng Lx Ly Lz Pxx Pyy Pzz Econserve v_dhug v_dray v_lgr_vel v_lgr_pos f_msst
100 301.02788 907.67474 -1067.9843 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 -1054.6195 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 -1045.1008 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 -1043.0623 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 -1046.5151 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 -1051.6141 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 -1056.2049 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 -1058.0632 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 -1055.6732 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 -1053.3767 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 -1054.8236 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 13.2508 on 1 procs for 100 steps with 23328 atoms
Performance: 2.165 ns/day, 11.084 hours/ns, 12.530 timesteps/s
Performance: 1.304 ns/day, 18.404 hours/ns, 7.547 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 6.8295 | 6.8295 | 6.8295 | 0.0 | 85.58
Neigh | 0.13211 | 0.13211 | 0.13211 | 0.0 | 1.66
Comm | 0.032946 | 0.032946 | 0.032946 | 0.0 | 0.41
Output | 0.02301 | 0.02301 | 0.02301 | 0.0 | 0.29
Modify | 0.94857 | 0.94857 | 0.94857 | 0.0 | 11.89
Other | | 0.01452 | | | 0.18
Pair | 11.716 | 11.716 | 11.716 | 0.0 | 88.41
Neigh | 0.26843 | 0.26843 | 0.26843 | 0.0 | 2.03
Comm | 0.056694 | 0.056694 | 0.056694 | 0.0 | 0.43
Output | 0.029758 | 0.029758 | 0.029758 | 0.0 | 0.22
Modify | 1.1599 | 1.1599 | 1.1599 | 0.0 | 8.75
Other | | 0.02035 | | | 0.15
Nlocal: 23328.0 ave 23328.0 max 23328.0 min
Nlocal: 23328.0 ave 23328 max 23328 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 22205.0 ave 22205.0 max 22205.0 min
Nghost: 22205.0 ave 22205 max 22205 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2183494.0 ave 2183494.0 max 2183494.0 min
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 = 93.5997085048011
Ave neighs/atom = 93.599709
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:11
Total wall time: 0:00:22

91
examples/msst/log.30Jun20.msst.g++.4 → examples/msst/log.08Feb21.msst.g++.4
View File

@ -1,4 +1,4 @@
LAMMPS (30 Jun 2020)
LAMMPS (24 Dec 2020)
using 1 OpenMP thread(s) per MPI task
# LJ test of msst shock dynamics
@ -10,18 +10,18 @@ atom_style atomic
timestep 1e-03
lattice fcc 5.3589
Lattice spacing in x,y,z = 5.3589 5.3589 5.3589
Lattice spacing in x,y,z = 5.3589000 5.3589000 5.3589000
## 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)
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (96.460200 96.460200 96.460200)
1 by 2 by 2 MPI processor grid
create_atoms 1 region box1
Created 23328 atoms
create_atoms CPU = 0.003 seconds
create_atoms CPU = 0.080 seconds
mass 1 40.00
@ -63,30 +63,30 @@ Step Temp E_pair E_mol TotEng Press
80 299.37658 -1053.8476 0 -151.1519 8352.9467
90 304.24026 -1068.4941 0 -151.13319 8218.1594
100 301.9683 -1061.6332 0 -151.12284 8244.1277
Loop time of 0.995305 on 4 procs for 100 steps with 23328 atoms
Loop time of 5.66225 on 4 procs for 100 steps with 23328 atoms
Performance: 17.362 ns/day, 1.382 hours/ns, 100.472 timesteps/s
98.2% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 3.052 ns/day, 7.864 hours/ns, 17.661 timesteps/s
78.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.88957 | 0.90144 | 0.91686 | 1.1 | 90.57
Neigh | 0.016824 | 0.016945 | 0.017106 | 0.1 | 1.70
Comm | 0.039949 | 0.054853 | 0.068734 | 4.8 | 5.51
Output | 0.00076342 | 0.0010425 | 0.0018687 | 1.5 | 0.10
Modify | 0.012839 | 0.012946 | 0.013153 | 0.1 | 1.30
Other | | 0.008074 | | | 0.81
Pair | 2.6416 | 2.7792 | 2.9335 | 6.4 | 49.08
Neigh | 0.029522 | 0.037458 | 0.054701 | 5.3 | 0.66
Comm | 2.1998 | 2.4099 | 2.5822 | 8.8 | 42.56
Output | 0.10457 | 0.10816 | 0.11265 | 1.0 | 1.91
Modify | 0.023462 | 0.033517 | 0.044696 | 4.9 | 0.59
Other | | 0.294 | | | 5.19
Nlocal: 5832.0 ave 5850.0 max 5813.0 min
Nlocal: 5832.00 ave 5850 max 5813 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Nghost: 10571.0 ave 10590.0 max 10553.0 min
Nghost: 10571.0 ave 10590 max 10553 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Neighs: 545761.75 ave 548069.0 max 543643.0 min
Neighs: 545762.0 ave 548069 max 543643 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Total # of neighbors = 2183047
Ave neighs/atom = 93.58054698216735
Ave neighs/atom = 93.580547
Neighbor list builds = 1
Dangerous builds = 0
unfix 2
@ -102,15 +102,12 @@ MSST parameters:
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
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
#dump id all atom 50 dump.msst
@ -126,42 +123,42 @@ Fix MSST p0 = 8186.2393
Fix MSST e0 = -151.12284
Fix MSST initial strain rate of -0.031900492 established by reducing temperature by factor of 0.01
Per MPI rank memory allocation (min/avg/max) = 8.535 | 8.535 | 8.535 Mbytes
Step Temp KinEng PotEng Lx Ly Lz Pxx Pyy Pzz TotEng v_dhug v_dray v_lgr_vel v_lgr_pos f_msst
100 298.94862 901.40524 -1052.5281 96.4602 96.4602 96.4602 8270.9151 8253.4662 8175.4946 -151.12284 1.5098415 -10.744684 0 0 9.1051034
110 296.49826 894.01679 -1045.224 96.4602 96.4602 96.399609 8338.4937 8340.5504 8294.9909 -151.20723 1.4327442 23.73173 0.017588167 -0.55980562 5.6560557
120 295.97607 892.44225 -1043.7239 96.4602 96.4602 96.340904 8377.6797 8385.921 8378.3042 -151.28169 1.3584606 24.672199 0.034628719 -1.1192655 2.2953307
130 297.34893 896.58179 -1047.945 96.4602 96.4602 96.284029 8379.2516 8394.8806 8416.2669 -151.36322 1.2881444 -17.170168 0.051138087 -1.6783905 -0.96527961
140 299.71946 903.72952 -1055.1787 96.4602 96.4602 96.22888 8357.0358 8388.6743 8424.3188 -151.44922 1.221125 -86.501161 0.067146366 -2.2371908 -4.1195182
150 301.79241 909.97998 -1061.4976 96.4602 96.4602 96.175327 8332.7118 8393.7027 8434.6177 -151.51765 1.1560248 -151.34689 0.082691635 -2.7956762 -7.172084
160 303.18249 914.17141 -1065.7667 96.4602 96.4602 96.123244 8321.1154 8413.1248 8454.5596 -151.59527 1.0977348 -204.4864 0.097810061 -3.3538554 -10.134387
170 304.34089 917.66428 -1069.3198 96.4602 96.4602 96.072522 8327.6227 8431.1177 8467.92 -151.65554 1.0390628 -262.29751 0.11253339 -3.9117366 -13.01442
180 305.86343 922.25514 -1073.9633 96.4602 96.4602 96.023049 8345.1853 8432.5201 8461.3276 -151.70813 0.97863988 -338.30793 0.12689398 -4.4693274 -15.815462
190 307.44054 927.01052 -1078.7892 96.4602 96.4602 95.9747 8368.4081 8427.5109 8450.584 -151.77867 0.92329631 -416.89333 0.1409285 -5.0266346 -18.541801
200 308.43619 930.01265 -1081.8521 96.4602 96.4602 95.927349 8393.2058 8443.1265 8454.6733 -151.83947 0.8723277 -479.24592 0.1546734 -5.5836644 -21.20378
Loop time of 2.16596 on 4 procs for 100 steps with 23328 atoms
Step Temp KinEng PotEng Lx Ly Lz Pxx Pyy Pzz Econserve v_dhug v_dray v_lgr_vel v_lgr_pos f_msst
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
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
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
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
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
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
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
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
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
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
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
Loop time of 11.445 on 4 procs for 100 steps with 23328 atoms
Performance: 7.978 ns/day, 3.008 hours/ns, 46.169 timesteps/s
98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 1.510 ns/day, 15.896 hours/ns, 8.737 timesteps/s
77.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.7569 | 1.7822 | 1.8059 | 1.6 | 82.28
Neigh | 0.034235 | 0.03546 | 0.037677 | 0.7 | 1.64
Comm | 0.065427 | 0.091172 | 0.11833 | 7.4 | 4.21
Output | 0.0062776 | 0.0065615 | 0.0074117 | 0.6 | 0.30
Modify | 0.24069 | 0.2423 | 0.24655 | 0.5 | 11.19
Other | | 0.008271 | | | 0.38
Pair | 3.7358 | 4.0193 | 4.3315 | 10.5 | 35.12
Neigh | 0.05921 | 0.078071 | 0.089958 | 4.1 | 0.68
Comm | 2.3136 | 2.683 | 3.054 | 16.3 | 23.44
Output | 0.038525 | 0.040035 | 0.044559 | 1.3 | 0.35
Modify | 4.2814 | 4.3709 | 4.4749 | 4.1 | 38.19
Other | | 0.2537 | | | 2.22
Nlocal: 5832.0 ave 5874.0 max 5803.0 min
Nlocal: 5832.00 ave 5874 max 5803 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Nghost: 10563.75 ave 10588.0 max 10526.0 min
Nghost: 10563.8 ave 10588 max 10526 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Neighs: 545708.5 ave 550787.0 max 542668.0 min
Neighs: 545708.0 ave 550787 max 542668 min
Histogram: 2 0 0 0 1 0 0 0 0 1
Total # of neighbors = 2182834
Ave neighs/atom = 93.57141632373114
Ave neighs/atom = 93.571416
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:03
Total wall time: 0:00:17

8
examples/threebody/in.threebody
View File

@ -53,9 +53,9 @@ velocity all create $t 5287287 loop geom
pair_style sw
pair_coeff * * Si.sw Si Si Si Si Si Si Si Si
thermo_style custom step temp epair etotal econserve press
thermo 10
fix 1 all nvt temp $t $t 0.1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
@ -71,9 +71,9 @@ read_restart restart.equil
pair_style sw
pair_coeff * * CdTeZnSeHgS0.sw Cd Zn Hg Cd Te S Se Te
thermo_style custom step temp epair etotal econserve press
thermo 10
fix 1 all nvt temp $t $t 0.1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
@ -87,9 +87,9 @@ read_restart restart.equil
pair_style vashishta
pair_coeff * * InP.vashishta In In In In P P P P
thermo_style custom step temp epair etotal econserve press
thermo 10
fix 1 all nvt temp $t $t 0.1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
@ -106,9 +106,9 @@ change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap
pair_style tersoff
pair_coeff * * BNC.tersoff N N N C B B C B
thermo_style custom step temp epair etotal econserve press
thermo 10
fix 1 all nvt temp $t $t 0.1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes

373
examples/threebody/log.08Feb21.threebody.g++.1 Normal file
View File

@ -0,0 +1,373 @@
LAMMPS (24 Dec 2020)
using 1 OpenMP thread(s) per MPI task
# Simple regression tests for threebody potentials
# NOTE: These are not intended to represent real materials
units metal
atom_style atomic
atom_modify map array
boundary p p p
atom_modify sort 0 0.0
# temperature
variable t equal 1800.0
# cubic diamond unit cell
variable a equal 5.431
lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
lattice custom 5.431 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
Lattice spacing in x,y,z = 5.4310000 5.4310000 5.4310000
region myreg block 0 4 0 4 0 4
create_box 8 myreg
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
1 by 1 by 1 MPI processor grid
create_atoms 1 region myreg basis 1 1 basis 2 2 basis 3 3 basis 4 4 basis 5 5 basis 6 6 basis 7 7 basis 8 8
Created 512 atoms
create_atoms CPU = 0.001 seconds
mass * 28.06
velocity all create $t 5287287 loop geom
velocity all create 1800 5287287 loop geom
# Equilibrate using Stillinger-Weber model for silicon
pair_style sw
pair_coeff * * Si.sw Si Si Si Si Si Si Si Si
Reading sw potential file Si.sw with DATE: 2007-06-11
thermo_style custom step temp epair etotal econserve press
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.77118
ghost atom cutoff = 4.77118
binsize = 2.38559, bins = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair sw, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.983 | 2.983 | 2.983 Mbytes
Step Temp E_pair TotEng Econserve Press
0 1800 -2220.3392 -2101.4457 -2101.4457 12358.626
10 1006.0192 -2167.7053 -2101.2558 -2101.3286 13892.426
20 588.26396 -2139.7132 -2100.8573 -2101.3117 11295.566
30 990.55956 -2165.2164 -2099.788 -2101.3931 6279.0239
40 700.12917 -2144.4279 -2098.183 -2101.3427 5594.2388
50 523.64239 -2131.7796 -2097.192 -2101.3122 6013.0994
60 989.47092 -2161.3716 -2096.0152 -2101.3839 5819.2688
70 877.27433 -2152.4432 -2094.4975 -2101.3461 9116.6569
80 800.80221 -2146.1371 -2093.2426 -2101.313 11995.66
90 1293.9689 -2176.9021 -2091.4329 -2101.3848 11692.45
100 1112.9699 -2162.7259 -2089.2121 -2101.3478 12263.758
Loop time of 0.157871 on 1 procs for 100 steps with 512 atoms
Performance: 54.728 ns/day, 0.439 hours/ns, 633.430 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.14704 | 0.14704 | 0.14704 | 0.0 | 93.14
Neigh | 0.00247 | 0.00247 | 0.00247 | 0.0 | 1.56
Comm | 0.0024729 | 0.0024729 | 0.0024729 | 0.0 | 1.57
Output | 0.0002656 | 0.0002656 | 0.0002656 | 0.0 | 0.17
Modify | 0.0050237 | 0.0050237 | 0.0050237 | 0.0 | 3.18
Other | | 0.0006011 | | | 0.38
Nlocal: 512.000 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1017.00 ave 1017 max 1017 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 13988.0 ave 13988 max 13988 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 13988
Ave neighs/atom = 27.320312
Neighbor list builds = 2
Dangerous builds = 0
write_restart restart.equil
System init for write_restart ...
# Test Stillinger-Weber model for Cd/Te/Zn/Se/Hg/S
clear
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
Reading restart file ...
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
restoring atom style atomic from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
1 by 1 by 1 MPI processor grid
pair style sw stores no restart info
512 atoms
read_restart CPU = 0.001 seconds
pair_style sw
pair_coeff * * CdTeZnSeHgS0.sw Cd Zn Hg Cd Te S Se Te
Reading sw potential file CdTeZnSeHgS0.sw with DATE: 2013-08-09
thermo_style custom step temp epair etotal econserve press
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
Resetting global fix info from restart file:
fix style: nvt, fix ID: 1
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
All restart file global fix info was re-assigned
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.6320004
ghost atom cutoff = 5.6320004
binsize = 2.8160002, bins = 8 8 8
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair sw, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.001 | 3.001 | 3.001 Mbytes
Step Temp E_pair TotEng Econserve Press
100 1112.9699 -625.76163 -552.24781 -564.38354 462129.66
110 1502.8461 -649.55768 -550.29179 -564.45814 463413.45
120 1926.4523 -674.71265 -547.46675 -564.53612 486338.88
130 1152.6663 -621.47264 -545.33681 -564.37203 514892.2
140 1762.244 -659.86941 -543.46979 -564.4985 488159.88
150 1767.8665 -657.67178 -540.90078 -564.48386 466721.31
160 1075.2874 -610.12809 -539.10328 -564.36709 470151.9
170 1697.9313 -649.3684 -537.21675 -564.47207 467953.71
180 1856.1197 -657.14338 -534.54309 -564.48754 488372.27
190 1346.1107 -621.42431 -532.5111 -564.38065 511750.04
200 1919.5266 -657.26587 -530.47743 -564.47797 488684.56
Loop time of 0.455825 on 1 procs for 100 steps with 512 atoms
Performance: 18.955 ns/day, 1.266 hours/ns, 219.382 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.44091 | 0.44091 | 0.44091 | 0.0 | 96.73
Neigh | 0.0054555 | 0.0054555 | 0.0054555 | 0.0 | 1.20
Comm | 0.0035784 | 0.0035784 | 0.0035784 | 0.0 | 0.79
Output | 0.00024486 | 0.00024486 | 0.00024486 | 0.0 | 0.05
Modify | 0.0050471 | 0.0050471 | 0.0050471 | 0.0 | 1.11
Other | | 0.000592 | | | 0.13
Nlocal: 512.000 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1428.00 ave 1428 max 1428 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 17344.0 ave 17344 max 17344 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 17344
Ave neighs/atom = 33.875000
Neighbor list builds = 3
Dangerous builds = 0
# Test Vashishta model for In/P
clear
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
Reading restart file ...
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
restoring atom style atomic from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
1 by 1 by 1 MPI processor grid
pair style sw stores no restart info
512 atoms
read_restart CPU = 0.001 seconds
pair_style vashishta
pair_coeff * * InP.vashishta In In In In P P P P
Reading vashishta potential file InP.vashishta with DATE: 2015-10-14
thermo_style custom step temp epair etotal econserve press
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
Resetting global fix info from restart file:
fix style: nvt, fix ID: 1
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
All restart file global fix info was re-assigned
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 7
ghost atom cutoff = 7
binsize = 3.5, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair vashishta, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.025 | 3.025 | 3.025 Mbytes
Step Temp E_pair TotEng Econserve Press
100 1112.9699 -1497.2988 -1423.785 -1435.9207 355619.19
110 1250.545 -1504.5795 -1421.9785 -1435.9786 345188.52
120 1360.2275 -1509.3443 -1419.4986 -1435.9801 333306.3
130 1066.4516 -1487.9076 -1417.4664 -1435.9076 334465.11
140 1481.0477 -1513.0511 -1415.2251 -1435.988 308725.1
150 1216.1167 -1493.0774 -1412.7505 -1435.9217 304249.09
160 1211.4398 -1490.7459 -1410.728 -1435.9164 288897.09
170 1542.2025 -1510.0774 -1408.212 -1435.9608 260104.14
180 1302.9041 -1491.7765 -1405.7172 -1435.8971 249514.04
190 1332.3326 -1491.5271 -1403.524 -1435.9213 227537.99
200 1352.1813 -1490.4513 -1401.1371 -1435.9049 207626.42
Loop time of 0.217808 on 1 procs for 100 steps with 512 atoms
Performance: 39.668 ns/day, 0.605 hours/ns, 459.121 timesteps/s
98.2% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.19635 | 0.19635 | 0.19635 | 0.0 | 90.15
Neigh | 0.01054 | 0.01054 | 0.01054 | 0.0 | 4.84
Comm | 0.0051923 | 0.0051923 | 0.0051923 | 0.0 | 2.38
Output | 0.00027919 | 0.00027919 | 0.00027919 | 0.0 | 0.13
Modify | 0.0048637 | 0.0048637 | 0.0048637 | 0.0 | 2.23
Other | | 0.0005858 | | | 0.27
Nlocal: 512.000 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1838.00 ave 1838 max 1838 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 36482.0 ave 36482 max 36482 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 36482
Ave neighs/atom = 71.253906
Neighbor list builds = 4
Dangerous builds = 0
# Test Tersoff model for B/N/C
clear
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
Reading restart file ...
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
restoring atom style atomic from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
1 by 1 by 1 MPI processor grid
pair style sw stores no restart info
512 atoms
read_restart CPU = 0.001 seconds
variable fac equal 0.6
change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap
change_box all x scale 0.6 y scale ${fac} z scale ${fac} remap
change_box all x scale 0.6 y scale 0.6 z scale ${fac} remap
change_box all x scale 0.6 y scale 0.6 z scale 0.6 remap
Changing box ...
orthogonal box = (4.3448000 0.0000000 0.0000000) to (17.379200 21.724000 21.724000)
orthogonal box = (4.3448000 4.3448000 0.0000000) to (17.379200 17.379200 21.724000)
orthogonal box = (4.3448000 4.3448000 4.3448000) to (17.379200 17.379200 17.379200)
pair_style tersoff
pair_coeff * * BNC.tersoff N N N C B B C B
Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
thermo_style custom step temp epair etotal econserve press
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
Resetting global fix info from restart file:
fix style: nvt, fix ID: 1
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
All restart file global fix info was re-assigned
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.1
ghost atom cutoff = 3.1
binsize = 1.55, bins = 9 9 9
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.982 | 2.982 | 2.982 Mbytes
Step Temp E_pair TotEng Econserve Press
100 1112.9699 -3259.7676 -3186.2538 -3198.3895 1912461.3
110 1772.8268 -3301.5479 -3184.4493 -3198.8218 1885295.6
120 1169.7287 -3258.74 -3181.4772 -3197.9294 1898705.2
130 1308.5623 -3265.1338 -3178.7007 -3197.5922 1894187.5
140 1486.0361 -3274.951 -3176.7954 -3197.776 1871927.6
150 1419.0362 -3267.7302 -3174.0002 -3197.2296 1925234.6
160 1196.6689 -3250.1492 -3171.1069 -3196.7078 1902235.1
170 1707.5846 -3281.7658 -3168.9766 -3196.9721 1863047.3
180 1337.4358 -3254.9844 -3166.6442 -3196.8222 1880420.9
190 1441.8052 -3259.0364 -3163.8023 -3196.3556 1904512.1
200 1569.0317 -3265.0089 -3161.3714 -3196.3328 1899462.7
Loop time of 0.487425 on 1 procs for 100 steps with 512 atoms
Performance: 17.726 ns/day, 1.354 hours/ns, 205.160 timesteps/s
99.1% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.47762 | 0.47762 | 0.47762 | 0.0 | 97.99
Neigh | 0.0014286 | 0.0014286 | 0.0014286 | 0.0 | 0.29
Comm | 0.0024068 | 0.0024068 | 0.0024068 | 0.0 | 0.49
Output | 0.00028992 | 0.00028992 | 0.00028992 | 0.0 | 0.06
Modify | 0.0050635 | 0.0050635 | 0.0050635 | 0.0 | 1.04
Other | | 0.0006182 | | | 0.13
Nlocal: 512.000 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1028.00 ave 1028 max 1028 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 14604.0 ave 14604 max 14604 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 14604
Ave neighs/atom = 28.523438
Neighbor list builds = 1
Dangerous builds = 0
Total wall time: 0:00:01

373
examples/threebody/log.08Feb21.threebody.g++.4 Normal file
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LAMMPS (24 Dec 2020)
using 1 OpenMP thread(s) per MPI task
# Simple regression tests for threebody potentials
# NOTE: These are not intended to represent real materials
units metal
atom_style atomic
atom_modify map array
boundary p p p
atom_modify sort 0 0.0
# temperature
variable t equal 1800.0
# cubic diamond unit cell
variable a equal 5.431
lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
lattice custom 5.431 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
Lattice spacing in x,y,z = 5.4310000 5.4310000 5.4310000
region myreg block 0 4 0 4 0 4
create_box 8 myreg
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
1 by 2 by 2 MPI processor grid
create_atoms 1 region myreg basis 1 1 basis 2 2 basis 3 3 basis 4 4 basis 5 5 basis 6 6 basis 7 7 basis 8 8
Created 512 atoms
create_atoms CPU = 0.074 seconds
mass * 28.06
velocity all create $t 5287287 loop geom
velocity all create 1800 5287287 loop geom
# Equilibrate using Stillinger-Weber model for silicon
pair_style sw
pair_coeff * * Si.sw Si Si Si Si Si Si Si Si
Reading sw potential file Si.sw with DATE: 2007-06-11
thermo_style custom step temp epair etotal econserve press
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.77118
ghost atom cutoff = 4.77118
binsize = 2.38559, bins = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair sw, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.958 | 2.958 | 2.958 Mbytes
Step Temp E_pair TotEng Econserve Press
0 1800 -2220.3392 -2101.4457 -2101.4457 12358.626
10 1006.0192 -2167.7053 -2101.2558 -2101.3286 13892.426
20 588.26396 -2139.7132 -2100.8573 -2101.3117 11295.566
30 990.55956 -2165.2164 -2099.788 -2101.3931 6279.0239
40 700.12917 -2144.4279 -2098.183 -2101.3427 5594.2388
50 523.64239 -2131.7796 -2097.192 -2101.3122 6013.0994
60 989.47092 -2161.3716 -2096.0152 -2101.3839 5819.2688
70 877.27433 -2152.4432 -2094.4975 -2101.3461 9116.6569
80 800.80221 -2146.1371 -2093.2426 -2101.313 11995.66
90 1293.9689 -2176.9021 -2091.4329 -2101.3848 11692.45
100 1112.9699 -2162.7259 -2089.2121 -2101.3478 12263.758
Loop time of 0.0998364 on 4 procs for 100 steps with 512 atoms
Performance: 86.542 ns/day, 0.277 hours/ns, 1001.639 timesteps/s
81.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.037337 | 0.049389 | 0.069239 | 5.9 | 49.47
Neigh | 0.00067854 | 0.00068814 | 0.00070286 | 0.0 | 0.69
Comm | 0.025239 | 0.04504 | 0.056869 | 6.1 | 45.11
Output | 0.00015712 | 0.00082219 | 0.0028148 | 0.0 | 0.82
Modify | 0.0014369 | 0.0015754 | 0.0016632 | 0.2 | 1.58
Other | | 0.002321 | | | 2.33
Nlocal: 128.000 ave 132 max 125 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Nghost: 525.000 ave 528 max 521 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 3497.00 ave 3619 max 3397 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Total # of neighbors = 13988
Ave neighs/atom = 27.320312
Neighbor list builds = 2
Dangerous builds = 0
write_restart restart.equil
System init for write_restart ...
# Test Stillinger-Weber model for Cd/Te/Zn/Se/Hg/S
clear
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
Reading restart file ...
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
restoring atom style atomic from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
1 by 2 by 2 MPI processor grid
pair style sw stores no restart info
512 atoms
read_restart CPU = 0.001 seconds
pair_style sw
pair_coeff * * CdTeZnSeHgS0.sw Cd Zn Hg Cd Te S Se Te
Reading sw potential file CdTeZnSeHgS0.sw with DATE: 2013-08-09
thermo_style custom step temp epair etotal econserve press
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
Resetting global fix info from restart file:
fix style: nvt, fix ID: 1
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
All restart file global fix info was re-assigned
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.6320004
ghost atom cutoff = 5.6320004
binsize = 2.8160002, bins = 8 8 8
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair sw, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.967 | 2.967 | 2.968 Mbytes
Step Temp E_pair TotEng Econserve Press
100 1112.9699 -625.76163 -552.24782 -564.38354 462129.66
110 1502.8461 -649.55768 -550.29179 -564.45814 463413.45
120 1926.4523 -674.71265 -547.46675 -564.53613 486338.88
130 1152.6663 -621.47265 -545.33681 -564.37203 514892.19
140 1762.244 -659.86941 -543.46979 -564.4985 488159.88
150 1767.8665 -657.67179 -540.90079 -564.48386 466721.31
160 1075.2874 -610.1281 -539.10328 -564.36709 470151.9
170 1697.9313 -649.3684 -537.21676 -564.47208 467953.7
180 1856.1197 -657.14338 -534.54309 -564.48754 488372.26
190 1346.1107 -621.42432 -532.5111 -564.38065 511750.03
200 1919.5266 -657.26587 -530.47743 -564.47797 488684.56
Loop time of 0.286556 on 4 procs for 100 steps with 512 atoms
Performance: 30.151 ns/day, 0.796 hours/ns, 348.971 timesteps/s
81.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.11093 | 0.139 | 0.16864 | 5.8 | 48.51
Neigh | 0.0014305 | 0.0014756 | 0.0015156 | 0.1 | 0.51
Comm | 0.10154 | 0.12374 | 0.16907 | 7.8 | 43.18
Output | 0.0001862 | 0.00030428 | 0.0006578 | 0.0 | 0.11
Modify | 0.0038164 | 0.019159 | 0.034146 | 10.8 | 6.69
Other | | 0.002872 | | | 1.00
Nlocal: 128.000 ave 135 max 122 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Nghost: 759.750 ave 770 max 751 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 4336.00 ave 4563 max 4128 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Total # of neighbors = 17344
Ave neighs/atom = 33.875000
Neighbor list builds = 3
Dangerous builds = 0
# Test Vashishta model for In/P
clear
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
Reading restart file ...
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
restoring atom style atomic from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
1 by 2 by 2 MPI processor grid
pair style sw stores no restart info
512 atoms
read_restart CPU = 0.001 seconds
pair_style vashishta
pair_coeff * * InP.vashishta In In In In P P P P
Reading vashishta potential file InP.vashishta with DATE: 2015-10-14
thermo_style custom step temp epair etotal econserve press
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
Resetting global fix info from restart file:
fix style: nvt, fix ID: 1
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
All restart file global fix info was re-assigned
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 7
ghost atom cutoff = 7
binsize = 3.5, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair vashishta, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.988 | 2.988 | 2.988 Mbytes
Step Temp E_pair TotEng Econserve Press
100 1112.9699 -1497.2988 -1423.785 -1435.9207 355619.19
110 1250.545 -1504.5795 -1421.9785 -1435.9786 345188.52
120 1360.2275 -1509.3443 -1419.4986 -1435.9801 333306.3
130 1066.4516 -1487.9076 -1417.4664 -1435.9076 334465.11
140 1481.0477 -1513.0511 -1415.2251 -1435.988 308725.1
150 1216.1167 -1493.0774 -1412.7505 -1435.9217 304249.09
160 1211.4398 -1490.7459 -1410.728 -1435.9164 288897.09
170 1542.2025 -1510.0774 -1408.212 -1435.9608 260104.14
180 1302.9041 -1491.7765 -1405.7172 -1435.8971 249514.04
190 1332.3326 -1491.5271 -1403.524 -1435.9213 227537.99
200 1352.1813 -1490.4513 -1401.1371 -1435.9049 207626.42
Loop time of 0.14468 on 4 procs for 100 steps with 512 atoms
Performance: 59.718 ns/day, 0.402 hours/ns, 691.179 timesteps/s
81.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.047903 | 0.058669 | 0.086091 | 6.6 | 40.55
Neigh | 0.0027876 | 0.002852 | 0.0028808 | 0.1 | 1.97
Comm | 0.034642 | 0.066142 | 0.078599 | 7.1 | 45.72
Output | 0.00018477 | 0.0049147 | 0.019101 | 11.7 | 3.40
Modify | 0.0015709 | 0.0022651 | 0.0029545 | 1.4 | 1.57
Other | | 0.009837 | | | 6.80
Nlocal: 128.000 ave 131 max 124 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Nghost: 1013.25 ave 1025 max 1002 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 9120.50 ave 9356 max 8868 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Total # of neighbors = 36482
Ave neighs/atom = 71.253906
Neighbor list builds = 4
Dangerous builds = 0
# Test Tersoff model for B/N/C
clear
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
Reading restart file ...
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
restoring atom style atomic from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
1 by 2 by 2 MPI processor grid
pair style sw stores no restart info
512 atoms
read_restart CPU = 0.005 seconds
variable fac equal 0.6
change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap
change_box all x scale 0.6 y scale ${fac} z scale ${fac} remap
change_box all x scale 0.6 y scale 0.6 z scale ${fac} remap
change_box all x scale 0.6 y scale 0.6 z scale 0.6 remap
Changing box ...
orthogonal box = (4.3448000 0.0000000 0.0000000) to (17.379200 21.724000 21.724000)
orthogonal box = (4.3448000 4.3448000 0.0000000) to (17.379200 17.379200 21.724000)
orthogonal box = (4.3448000 4.3448000 4.3448000) to (17.379200 17.379200 17.379200)
pair_style tersoff
pair_coeff * * BNC.tersoff N N N C B B C B
Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
thermo_style custom step temp epair etotal econserve press
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
Resetting global fix info from restart file:
fix style: nvt, fix ID: 1
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
All restart file global fix info was re-assigned
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.1
ghost atom cutoff = 3.1
binsize = 1.55, bins = 9 9 9
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.948 | 2.948 | 2.948 Mbytes
Step Temp E_pair TotEng Econserve Press
100 1112.9699 -3259.7676 -3186.2538 -3198.3895 1912461.3
110 1772.8268 -3301.5479 -3184.4493 -3198.8218 1885295.6
120 1169.7287 -3258.74 -3181.4772 -3197.9294 1898705.2
130 1308.5623 -3265.1338 -3178.7007 -3197.5922 1894187.5
140 1486.0361 -3274.951 -3176.7954 -3197.776 1871927.6
150 1419.0362 -3267.7302 -3174.0002 -3197.2296 1925234.6
160 1196.6689 -3250.1492 -3171.1069 -3196.7078 1902235.1
170 1707.5846 -3281.7658 -3168.9766 -3196.9721 1863047.3
180 1337.4358 -3254.9844 -3166.6442 -3196.8222 1880420.9
190 1441.8052 -3259.0364 -3163.8023 -3196.3556 1904512.1
200 1569.0317 -3265.0089 -3161.3714 -3196.3328 1899462.7
Loop time of 0.348631 on 4 procs for 100 steps with 512 atoms
Performance: 24.783 ns/day, 0.968 hours/ns, 286.836 timesteps/s
81.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.13281 | 0.15657 | 0.20106 | 6.9 | 44.91
Neigh | 0.00037527 | 0.00039309 | 0.00040412 | 0.0 | 0.11
Comm | 0.12177 | 0.16672 | 0.19154 | 6.8 | 47.82
Output | 0.00019097 | 0.000462 | 0.0012722 | 0.0 | 0.13
Modify | 0.018353 | 0.020198 | 0.02302 | 1.3 | 5.79
Other | | 0.004286 | | | 1.23
Nlocal: 128.000 ave 132 max 123 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Nghost: 529.500 ave 533 max 524 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 3651.00 ave 3783 max 3494 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Total # of neighbors = 14604
Ave neighs/atom = 28.523438
Neighbor list builds = 1
Dangerous builds = 0
Total wall time: 0:00:01

547
examples/threebody/log.13Jan21.threebody.g++.1
View File

@ -1,547 +0,0 @@
LAMMPS (30 Nov 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
# Simple regression tests for threebody potentials
# NOTE: These are not intended to represent real materials
units metal
atom_style atomic
atom_modify map array
boundary p p p
atom_modify sort 0 0.0
# temperature
variable t equal 1800.0
# cubic diamond unit cell
variable a equal 5.431
lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
lattice custom 5.431 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
Lattice spacing in x,y,z = 5.4310000 5.4310000 5.4310000
region myreg block 0 4 0 4 0 4
create_box 8 myreg
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
1 by 1 by 1 MPI processor grid
create_atoms 1 region myreg basis 1 1 basis 2 2 basis 3 3 basis 4 4 basis 5 5 basis 6 6 basis 7 7 basis 8 8
Created 512 atoms
create_atoms CPU = 0.000 seconds
mass * 28.06
velocity all create $t 5287287 loop geom
velocity all create 1800 5287287 loop geom
# Equilibrate using Stillinger-Weber model for silicon
pair_style sw
pair_coeff * * Si.sw Si Si Si Si Si Si Si Si
Reading sw potential file Si.sw with DATE: 2007-06-11
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.77118
ghost atom cutoff = 4.77118
binsize = 2.38559, bins = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair sw, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.983 | 2.983 | 2.983 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1800 -2220.3392 0 -2101.4457 12358.626
10 1006.0192 -2167.7053 0 -2101.3286 13892.426
20 588.26396 -2139.7132 0 -2101.3117 11295.566
30 990.55956 -2165.2164 0 -2101.3931 6279.0239
40 700.12917 -2144.4279 0 -2101.3427 5594.2388
50 523.64239 -2131.7796 0 -2101.3122 6013.0994
60 989.47092 -2161.3716 0 -2101.3839 5819.2688
70 877.27433 -2152.4432 0 -2101.3461 9116.6569
80 800.80221 -2146.1371 0 -2101.313 11995.66
90 1293.9689 -2176.9021 0 -2101.3848 11692.45
100 1112.9699 -2162.7259 0 -2101.3478 12263.758
Loop time of 0.092666 on 1 procs for 100 steps with 512 atoms
Performance: 93.238 ns/day, 0.257 hours/ns, 1079.144 timesteps/s
99.1% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.089633 | 0.089633 | 0.089633 | 0.0 | 96.73
Neigh | 0.001474 | 0.001474 | 0.001474 | 0.0 | 1.59
Comm | 0.00041 | 0.00041 | 0.00041 | 0.0 | 0.44
Output | 0.000153 | 0.000153 | 0.000153 | 0.0 | 0.17
Modify | 0.000782 | 0.000782 | 0.000782 | 0.0 | 0.84
Other | | 0.000214 | | | 0.23
Nlocal: 512.000 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1017.00 ave 1017 max 1017 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 13988.0 ave 13988 max 13988 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 13988
Ave neighs/atom = 27.320312
Neighbor list builds = 2
Dangerous builds = 0
write_restart restart.equil
System init for write_restart ...
# Test Stillinger-Weber model for Cd/Te/Zn/Se/Hg/S
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
Reading restart file ...
restart file = 30 Nov 2020, LAMMPS = 30 Nov 2020
restoring atom style atomic from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
1 by 1 by 1 MPI processor grid
pair style sw stores no restart info
512 atoms
read_restart CPU = 0.002 seconds
pair_style sw
pair_coeff * * CdTeZnSeHgS0.sw Cd Zn Hg Cd Te S Se Te
Reading sw potential file CdTeZnSeHgS0.sw with DATE: 2013-08-09
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
Resetting global fix info from restart file:
fix style: nvt, fix ID: 1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
All restart file global fix info was re-assigned
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.6320004
ghost atom cutoff = 5.6320004
binsize = 2.8160002, bins = 8 8 8
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair sw, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.001 | 3.001 | 3.001 Mbytes
Step Temp E_pair E_mol TotEng Press
100 1112.9699 -625.76163 0 -564.38354 462129.66
110 1502.8461 -649.55768 0 -564.45814 463413.45
120 1926.4523 -674.71265 0 -564.53612 486338.88
130 1152.6663 -621.47264 0 -564.37203 514892.2
140 1762.244 -659.86941 0 -564.4985 488159.88
150 1767.8665 -657.67178 0 -564.48386 466721.31
160 1075.2874 -610.12809 0 -564.36709 470151.9
170 1697.9313 -649.3684 0 -564.47207 467953.71
180 1856.1197 -657.14338 0 -564.48754 488372.27
190 1346.1107 -621.42431 0 -564.38065 511750.04
200 1919.5266 -657.26587 0 -564.47797 488684.56
Loop time of 0.289193 on 1 procs for 100 steps with 512 atoms
Performance: 29.876 ns/day, 0.803 hours/ns, 345.790 timesteps/s
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.28463 | 0.28463 | 0.28463 | 0.0 | 98.42
Neigh | 0.002821 | 0.002821 | 0.002821 | 0.0 | 0.98
Comm | 0.000605 | 0.000605 | 0.000605 | 0.0 | 0.21
Output | 0.000176 | 0.000176 | 0.000176 | 0.0 | 0.06
Modify | 0.000769 | 0.000769 | 0.000769 | 0.0 | 0.27
Other | | 0.000188 | | | 0.07
Nlocal: 512.000 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1428.00 ave 1428 max 1428 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 17344.0 ave 17344 max 17344 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 17344
Ave neighs/atom = 33.875000
Neighbor list builds = 3
Dangerous builds = 0
# Test Vashishta model for In/P
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
Reading restart file ...
restart file = 30 Nov 2020, LAMMPS = 30 Nov 2020
restoring atom style atomic from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
1 by 1 by 1 MPI processor grid
pair style sw stores no restart info
512 atoms
read_restart CPU = 0.001 seconds
pair_style vashishta
pair_coeff * * InP.vashishta In In In In P P P P
Reading vashishta potential file InP.vashishta with DATE: 2015-10-14
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
Resetting global fix info from restart file:
fix style: nvt, fix ID: 1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
All restart file global fix info was re-assigned
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 7
ghost atom cutoff = 7
binsize = 3.5, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair vashishta, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.025 | 3.025 | 3.025 Mbytes
Step Temp E_pair E_mol TotEng Press
100 1112.9699 -1497.2988 0 -1435.9207 355619.19
110 1250.545 -1504.5795 0 -1435.9786 345188.52
120 1360.2275 -1509.3443 0 -1435.9801 333306.3
130 1066.4516 -1487.9076 0 -1435.9076 334465.11
140 1481.0477 -1513.0511 0 -1435.988 308725.1
150 1216.1167 -1493.0774 0 -1435.9217 304249.09
160 1211.4398 -1490.7459 0 -1435.9164 288897.09
170 1542.2025 -1510.0774 0 -1435.9608 260104.14
180 1302.9041 -1491.7765 0 -1435.8971 249514.04
190 1332.3326 -1491.5271 0 -1435.9213 227537.99
200 1352.1813 -1490.4513 0 -1435.9049 207626.42
Loop time of 0.126684 on 1 procs for 100 steps with 512 atoms
Performance: 68.201 ns/day, 0.352 hours/ns, 789.366 timesteps/s
99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.11981 | 0.11981 | 0.11981 | 0.0 | 94.57
Neigh | 0.004903 | 0.004903 | 0.004903 | 0.0 | 3.87
Comm | 0.000846 | 0.000846 | 0.000846 | 0.0 | 0.67
Output | 0.000145 | 0.000145 | 0.000145 | 0.0 | 0.11
Modify | 0.000772 | 0.000772 | 0.000772 | 0.0 | 0.61
Other | | 0.000207 | | | 0.16
Nlocal: 512.000 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1838.00 ave 1838 max 1838 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 36482.0 ave 36482 max 36482 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 36482
Ave neighs/atom = 71.253906
Neighbor list builds = 4
Dangerous builds = 0
# Test Tersoff model for B/N/C
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
Reading restart file ...
restart file = 30 Nov 2020, LAMMPS = 30 Nov 2020
restoring atom style atomic from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
1 by 1 by 1 MPI processor grid
pair style sw stores no restart info
512 atoms
read_restart CPU = 0.001 seconds
variable fac equal 0.6
change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap
change_box all x scale 0.6 y scale ${fac} z scale ${fac} remap
change_box all x scale 0.6 y scale 0.6 z scale ${fac} remap
change_box all x scale 0.6 y scale 0.6 z scale 0.6 remap
Changing box ...
orthogonal box = (4.3448000 0.0000000 0.0000000) to (17.379200 21.724000 21.724000)
orthogonal box = (4.3448000 4.3448000 0.0000000) to (17.379200 17.379200 21.724000)
orthogonal box = (4.3448000 4.3448000 4.3448000) to (17.379200 17.379200 17.379200)
pair_style tersoff
pair_coeff * * BNC.tersoff N N N C B B C B
Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
Resetting global fix info from restart file:
fix style: nvt, fix ID: 1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
All restart file global fix info was re-assigned
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.1
ghost atom cutoff = 3.1
binsize = 1.55, bins = 9 9 9
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.982 | 2.982 | 2.982 Mbytes
Step Temp E_pair E_mol TotEng Press
100 1112.9699 -3259.7676 0 -3198.3895 1912461.3
110 1772.8268 -3301.5479 0 -3198.8218 1885295.6
120 1169.7287 -3258.74 0 -3197.9294 1898705.2
130 1308.5623 -3265.1338 0 -3197.5922 1894187.5
140 1486.0361 -3274.951 0 -3197.776 1871927.6
150 1419.0362 -3267.7302 0 -3197.2296 1925234.6
160 1196.6689 -3250.1492 0 -3196.7078 1902235.1
170 1707.5846 -3281.7658 0 -3196.9721 1863047.3
180 1337.4358 -3254.9844 0 -3196.8222 1880420.9
190 1441.8052 -3259.0364 0 -3196.3556 1904512.1
200 1569.0317 -3265.0089 0 -3196.3328 1899462.7
Loop time of 0.114312 on 1 procs for 100 steps with 512 atoms
Performance: 75.583 ns/day, 0.318 hours/ns, 874.799 timesteps/s
99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.1121 | 0.1121 | 0.1121 | 0.0 | 98.06
Neigh | 0.000773 | 0.000773 | 0.000773 | 0.0 | 0.68
Comm | 0.000415 | 0.000415 | 0.000415 | 0.0 | 0.36
Output | 0.000136 | 0.000136 | 0.000136 | 0.0 | 0.12
Modify | 0.000703 | 0.000703 | 0.000703 | 0.0 | 0.61
Other | | 0.000186 | | | 0.16
Nlocal: 512.000 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1028.00 ave 1028 max 1028 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 14604.0 ave 14604 max 14604 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 14604
Ave neighs/atom = 28.523438
Neighbor list builds = 1
Dangerous builds = 0
# Test Tersoff/Mod model for Si
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
Reading restart file ...
restart file = 30 Nov 2020, LAMMPS = 30 Nov 2020
restoring atom style atomic from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
1 by 1 by 1 MPI processor grid
pair style sw stores no restart info
512 atoms
read_restart CPU = 0.001 seconds
pair_style tersoff/mod
pair_coeff * * Si.tersoff.mod Si Si Si Si Si Si Si Si
Reading tersoff/mod potential file Si.tersoff.mod with DATE: 2013-07-26
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
Resetting global fix info from restart file:
fix style: nvt, fix ID: 1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
All restart file global fix info was re-assigned
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.3
ghost atom cutoff = 4.3
binsize = 2.15, bins = 11 11 11
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff/mod, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.986 | 2.986 | 2.986 Mbytes
Step Temp E_pair E_mol TotEng Press
100 1112.9699 -2309.6047 0 -2248.2266 17662.891
110 835.77436 -2289.6119 0 -2248.1918 19964.211
120 1067.0735 -2303.0587 0 -2248.2414 13767.101
130 957.60664 -2293.7047 0 -2248.2139 14850.338
140 865.12471 -2285.7774 0 -2248.1971 17101.553
150 1104.7368 -2299.5468 0 -2248.2286 13031.988
160 1077.1682 -2295.3841 0 -2248.2227 13615.019
170 843.8591 -2277.9713 0 -2248.1911 18966.532
180 1008.7412 -2286.922 0 -2248.2075 17275.649
190 1237.9346 -2299.5487 0 -2248.2305 14334.006
200 1060.2161 -2285.3352 0 -2248.1952 18999.834
Loop time of 0.12412 on 1 procs for 100 steps with 512 atoms
Performance: 69.610 ns/day, 0.345 hours/ns, 805.672 timesteps/s
99.2% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.12079 | 0.12079 | 0.12079 | 0.0 | 97.32
Neigh | 0.001821 | 0.001821 | 0.001821 | 0.0 | 1.47
Comm | 0.000407 | 0.000407 | 0.000407 | 0.0 | 0.33
Output | 0.000159 | 0.000159 | 0.000159 | 0.0 | 0.13
Modify | 0.000736 | 0.000736 | 0.000736 | 0.0 | 0.59
Other | | 0.000203 | | | 0.16
Nlocal: 512.000 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1007.00 ave 1007 max 1007 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 8884.00 ave 8884 max 8884 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 8884
Ave neighs/atom = 17.351562
Neighbor list builds = 3
Dangerous builds = 0
# Test Tersoff/Mod/C model for Si
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
Reading restart file ...
restart file = 30 Nov 2020, LAMMPS = 30 Nov 2020
restoring atom style atomic from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
1 by 1 by 1 MPI processor grid
pair style sw stores no restart info
512 atoms
read_restart CPU = 0.001 seconds
newton on on
pair_style tersoff/mod/c
pair_coeff * * Si.tersoff.modc Si Si Si Si Si Si Si Si
Reading tersoff/mod/c potential file Si.tersoff.modc with DATE: 2016-11-09
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
Resetting global fix info from restart file:
fix style: nvt, fix ID: 1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
All restart file global fix info was re-assigned
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.205694
ghost atom cutoff = 4.205694
binsize = 2.102847, bins = 11 11 11
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff/mod/c, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.980 | 2.980 | 2.980 Mbytes
Step Temp E_pair E_mol TotEng Press
100 1112.9699 -2309.1331 0 -2247.755 20346.718
110 831.93715 -2288.8853 0 -2247.7187 21758.195
120 1077.6698 -2303.2846 0 -2247.7693 16036.053
130 972.43247 -2294.1847 0 -2247.7467 16614.835
140 815.76148 -2282.0495 0 -2247.7194 18310.116
150 1072.7096 -2297.0491 0 -2247.7574 13896.767
160 1061.8824 -2294.0028 0 -2247.7522 13663.179
170 787.17244 -2273.8946 0 -2247.7175 18586.606
180 932.5662 -2281.6828 0 -2247.7315 18154.167
190 1205.7299 -2297.2769 0 -2247.7608 14504.136
200 1022.5285 -2282.7039 0 -2247.7245 18710.495
Loop time of 0.12973 on 1 procs for 100 steps with 512 atoms
Performance: 66.600 ns/day, 0.360 hours/ns, 770.832 timesteps/s
99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.12643 | 0.12643 | 0.12643 | 0.0 | 97.45
Neigh | 0.001798 | 0.001798 | 0.001798 | 0.0 | 1.39
Comm | 0.000421 | 0.000421 | 0.000421 | 0.0 | 0.32
Output | 0.00016 | 0.00016 | 0.00016 | 0.0 | 0.12
Modify | 0.000733 | 0.000733 | 0.000733 | 0.0 | 0.57
Other | | 0.000192 | | | 0.15
Nlocal: 512.000 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 958.000 ave 958 max 958 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 8416.00 ave 8416 max 8416 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 8416
Ave neighs/atom = 16.437500
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:00

547
examples/threebody/log.13Jan21.threebody.g++.4
View File

@ -1,547 +0,0 @@
LAMMPS (30 Nov 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
# Simple regression tests for threebody potentials
# NOTE: These are not intended to represent real materials
units metal
atom_style atomic
atom_modify map array
boundary p p p
atom_modify sort 0 0.0
# temperature
variable t equal 1800.0
# cubic diamond unit cell
variable a equal 5.431
lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
lattice custom 5.431 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
Lattice spacing in x,y,z = 5.4310000 5.4310000 5.4310000
region myreg block 0 4 0 4 0 4
create_box 8 myreg
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
1 by 2 by 2 MPI processor grid
create_atoms 1 region myreg basis 1 1 basis 2 2 basis 3 3 basis 4 4 basis 5 5 basis 6 6 basis 7 7 basis 8 8
Created 512 atoms
create_atoms CPU = 0.001 seconds
mass * 28.06
velocity all create $t 5287287 loop geom
velocity all create 1800 5287287 loop geom
# Equilibrate using Stillinger-Weber model for silicon
pair_style sw
pair_coeff * * Si.sw Si Si Si Si Si Si Si Si
Reading sw potential file Si.sw with DATE: 2007-06-11
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.77118
ghost atom cutoff = 4.77118
binsize = 2.38559, bins = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair sw, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.958 | 2.958 | 2.958 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1800 -2220.3392 0 -2101.4457 12358.626
10 1006.0192 -2167.7053 0 -2101.3286 13892.426
20 588.26396 -2139.7132 0 -2101.3117 11295.566
30 990.55956 -2165.2164 0 -2101.3931 6279.0239
40 700.12917 -2144.4279 0 -2101.3427 5594.2388
50 523.64239 -2131.7796 0 -2101.3122 6013.0994
60 989.47092 -2161.3716 0 -2101.3839 5819.2688
70 877.27433 -2152.4432 0 -2101.3461 9116.6569
80 800.80221 -2146.1371 0 -2101.313 11995.66
90 1293.9689 -2176.9021 0 -2101.3848 11692.45
100 1112.9699 -2162.7259 0 -2101.3478 12263.758
Loop time of 0.0284905 on 4 procs for 100 steps with 512 atoms
Performance: 303.259 ns/day, 0.079 hours/ns, 3509.942 timesteps/s
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.022257 | 0.023383 | 0.025192 | 0.7 | 82.07
Neigh | 0.00036 | 0.00037475 | 0.000387 | 0.0 | 1.32
Comm | 0.002084 | 0.0039075 | 0.005034 | 1.8 | 13.72
Output | 9.9e-05 | 0.00011525 | 0.00016 | 0.0 | 0.40
Modify | 0.000428 | 0.00043675 | 0.000443 | 0.0 | 1.53
Other | | 0.0002728 | | | 0.96
Nlocal: 128.000 ave 132 max 125 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Nghost: 525.000 ave 528 max 521 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 3497.00 ave 3619 max 3397 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Total # of neighbors = 13988
Ave neighs/atom = 27.320312
Neighbor list builds = 2
Dangerous builds = 0
write_restart restart.equil
System init for write_restart ...
# Test Stillinger-Weber model for Cd/Te/Zn/Se/Hg/S
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
Reading restart file ...
restart file = 30 Nov 2020, LAMMPS = 30 Nov 2020
restoring atom style atomic from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
1 by 2 by 2 MPI processor grid
pair style sw stores no restart info
512 atoms
read_restart CPU = 0.000 seconds
pair_style sw
pair_coeff * * CdTeZnSeHgS0.sw Cd Zn Hg Cd Te S Se Te
Reading sw potential file CdTeZnSeHgS0.sw with DATE: 2013-08-09
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
Resetting global fix info from restart file:
fix style: nvt, fix ID: 1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
All restart file global fix info was re-assigned
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.6320004
ghost atom cutoff = 5.6320004
binsize = 2.8160002, bins = 8 8 8
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair sw, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.967 | 2.967 | 2.968 Mbytes
Step Temp E_pair E_mol TotEng Press
100 1112.9699 -625.76163 0 -564.38354 462129.66
110 1502.8461 -649.55768 0 -564.45814 463413.45
120 1926.4523 -674.71265 0 -564.53613 486338.88
130 1152.6663 -621.47265 0 -564.37203 514892.19
140 1762.244 -659.86941 0 -564.4985 488159.88
150 1767.8665 -657.67179 0 -564.48386 466721.31
160 1075.2874 -610.1281 0 -564.36709 470151.9
170 1697.9313 -649.3684 0 -564.47208 467953.7
180 1856.1197 -657.14338 0 -564.48754 488372.26
190 1346.1107 -621.42432 0 -564.38065 511750.03
200 1919.5266 -657.26587 0 -564.47797 488684.56
Loop time of 0.084576 on 4 procs for 100 steps with 512 atoms
Performance: 102.157 ns/day, 0.235 hours/ns, 1182.369 timesteps/s
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.072089 | 0.074912 | 0.076672 | 0.7 | 88.57
Neigh | 0.000745 | 0.0008125 | 0.000883 | 0.0 | 0.96
Comm | 0.006054 | 0.0077975 | 0.010598 | 2.1 | 9.22
Output | 0.000129 | 0.00015525 | 0.000219 | 0.0 | 0.18
Modify | 0.000523 | 0.000578 | 0.000641 | 0.0 | 0.68
Other | | 0.0003213 | | | 0.38
Nlocal: 128.000 ave 135 max 122 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Nghost: 759.750 ave 770 max 751 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 4336.00 ave 4563 max 4128 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Total # of neighbors = 17344
Ave neighs/atom = 33.875000
Neighbor list builds = 3
Dangerous builds = 0
# Test Vashishta model for In/P
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
Reading restart file ...
restart file = 30 Nov 2020, LAMMPS = 30 Nov 2020
restoring atom style atomic from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
1 by 2 by 2 MPI processor grid
pair style sw stores no restart info
512 atoms
read_restart CPU = 0.001 seconds
pair_style vashishta
pair_coeff * * InP.vashishta In In In In P P P P
Reading vashishta potential file InP.vashishta with DATE: 2015-10-14
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
Resetting global fix info from restart file:
fix style: nvt, fix ID: 1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
All restart file global fix info was re-assigned
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 7
ghost atom cutoff = 7
binsize = 3.5, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair vashishta, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.988 | 2.988 | 2.988 Mbytes
Step Temp E_pair E_mol TotEng Press
100 1112.9699 -1497.2988 0 -1435.9207 355619.19
110 1250.545 -1504.5795 0 -1435.9786 345188.52
120 1360.2275 -1509.3443 0 -1435.9801 333306.3
130 1066.4516 -1487.9076 0 -1435.9076 334465.11
140 1481.0477 -1513.0511 0 -1435.988 308725.1
150 1216.1167 -1493.0774 0 -1435.9217 304249.09
160 1211.4398 -1490.7459 0 -1435.9164 288897.09
170 1542.2025 -1510.0774 0 -1435.9608 260104.14
180 1302.9041 -1491.7765 0 -1435.8971 249514.04
190 1332.3326 -1491.5271 0 -1435.9213 227537.99
200 1352.1813 -1490.4513 0 -1435.9049 207626.42
Loop time of 0.0404882 on 4 procs for 100 steps with 512 atoms
Performance: 213.395 ns/day, 0.112 hours/ns, 2469.852 timesteps/s
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.032713 | 0.033094 | 0.033544 | 0.2 | 81.74
Neigh | 0.001251 | 0.0012875 | 0.001308 | 0.1 | 3.18
Comm | 0.004788 | 0.005204 | 0.00557 | 0.4 | 12.85
Output | 0.000123 | 0.0001385 | 0.000182 | 0.0 | 0.34
Modify | 0.000492 | 0.00050725 | 0.000533 | 0.0 | 1.25
Other | | 0.0002565 | | | 0.63
Nlocal: 128.000 ave 131 max 124 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Nghost: 1013.25 ave 1025 max 1002 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 9120.50 ave 9356 max 8868 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Total # of neighbors = 36482
Ave neighs/atom = 71.253906
Neighbor list builds = 4
Dangerous builds = 0
# Test Tersoff model for B/N/C
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
Reading restart file ...
restart file = 30 Nov 2020, LAMMPS = 30 Nov 2020
restoring atom style atomic from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
1 by 2 by 2 MPI processor grid
pair style sw stores no restart info
512 atoms
read_restart CPU = 0.001 seconds
variable fac equal 0.6
change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap
change_box all x scale 0.6 y scale ${fac} z scale ${fac} remap
change_box all x scale 0.6 y scale 0.6 z scale ${fac} remap
change_box all x scale 0.6 y scale 0.6 z scale 0.6 remap
Changing box ...
orthogonal box = (4.3448000 0.0000000 0.0000000) to (17.379200 21.724000 21.724000)
orthogonal box = (4.3448000 4.3448000 0.0000000) to (17.379200 17.379200 21.724000)
orthogonal box = (4.3448000 4.3448000 4.3448000) to (17.379200 17.379200 17.379200)
pair_style tersoff
pair_coeff * * BNC.tersoff N N N C B B C B
Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
Resetting global fix info from restart file:
fix style: nvt, fix ID: 1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
All restart file global fix info was re-assigned
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.1
ghost atom cutoff = 3.1
binsize = 1.55, bins = 9 9 9
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.948 | 2.948 | 2.948 Mbytes
Step Temp E_pair E_mol TotEng Press
100 1112.9699 -3259.7676 0 -3198.3895 1912461.3
110 1772.8268 -3301.5479 0 -3198.8218 1885295.6
120 1169.7287 -3258.74 0 -3197.9294 1898705.2
130 1308.5623 -3265.1338 0 -3197.5922 1894187.5
140 1486.0361 -3274.951 0 -3197.776 1871927.6
150 1419.0362 -3267.7302 0 -3197.2296 1925234.6
160 1196.6689 -3250.1492 0 -3196.7078 1902235.1
170 1707.5846 -3281.7658 0 -3196.9721 1863047.3
180 1337.4358 -3254.9844 0 -3196.8222 1880420.9
190 1441.8052 -3259.0364 0 -3196.3556 1904512.1
200 1569.0317 -3265.0089 0 -3196.3328 1899462.7
Loop time of 0.03452 on 4 procs for 100 steps with 512 atoms
Performance: 250.290 ns/day, 0.096 hours/ns, 2896.871 timesteps/s
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.029269 | 0.029729 | 0.030688 | 0.3 | 86.12
Neigh | 0.000203 | 0.00023375 | 0.000271 | 0.0 | 0.68
Comm | 0.00275 | 0.0036492 | 0.004132 | 0.9 | 10.57
Output | 0.000104 | 0.000121 | 0.000165 | 0.0 | 0.35
Modify | 0.000456 | 0.0004605 | 0.000463 | 0.0 | 1.33
Other | | 0.000326 | | | 0.94
Nlocal: 128.000 ave 132 max 123 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Nghost: 529.500 ave 533 max 524 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 3651.00 ave 3783 max 3494 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Total # of neighbors = 14604
Ave neighs/atom = 28.523438
Neighbor list builds = 1
Dangerous builds = 0
# Test Tersoff/Mod model for Si
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
Reading restart file ...
restart file = 30 Nov 2020, LAMMPS = 30 Nov 2020
restoring atom style atomic from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
1 by 2 by 2 MPI processor grid
pair style sw stores no restart info
512 atoms
read_restart CPU = 0.001 seconds
pair_style tersoff/mod
pair_coeff * * Si.tersoff.mod Si Si Si Si Si Si Si Si
Reading tersoff/mod potential file Si.tersoff.mod with DATE: 2013-07-26
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
Resetting global fix info from restart file:
fix style: nvt, fix ID: 1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
All restart file global fix info was re-assigned
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.3
ghost atom cutoff = 4.3
binsize = 2.15, bins = 11 11 11
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff/mod, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.950 | 2.950 | 2.950 Mbytes
Step Temp E_pair E_mol TotEng Press
100 1112.9699 -2309.6047 0 -2248.2266 17662.891
110 835.77436 -2289.6119 0 -2248.1918 19964.211
120 1067.0735 -2303.0587 0 -2248.2414 13767.101
130 957.60664 -2293.7047 0 -2248.2139 14850.338
140 865.12471 -2285.7774 0 -2248.1971 17101.553
150 1104.7368 -2299.5468 0 -2248.2286 13031.988
160 1077.1682 -2295.3841 0 -2248.2227 13615.019
170 843.8591 -2277.9713 0 -2248.1911 18966.532
180 1008.7412 -2286.922 0 -2248.2075 17275.649
190 1237.9346 -2299.5487 0 -2248.2305 14334.006
200 1060.2161 -2285.3352 0 -2248.1952 18999.834
Loop time of 0.043388 on 4 procs for 100 steps with 512 atoms
Performance: 199.133 ns/day, 0.121 hours/ns, 2304.785 timesteps/s
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.033874 | 0.036197 | 0.037433 | 0.7 | 83.43
Neigh | 0.000538 | 0.00055575 | 0.000575 | 0.0 | 1.28
Comm | 0.004381 | 0.0055505 | 0.007783 | 1.8 | 12.79
Output | 0.000141 | 0.0001635 | 0.000228 | 0.0 | 0.38
Modify | 0.000532 | 0.000615 | 0.000692 | 0.0 | 1.42
Other | | 0.000306 | | | 0.71
Nlocal: 128.000 ave 135 max 121 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Nghost: 515.000 ave 518 max 508 min
Histogram: 1 0 0 0 0 0 0 0 1 2
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 2221.00 ave 2328 max 2103 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Total # of neighbors = 8884
Ave neighs/atom = 17.351562
Neighbor list builds = 3
Dangerous builds = 0
# Test Tersoff/Mod/C model for Si
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
Reading restart file ...
restart file = 30 Nov 2020, LAMMPS = 30 Nov 2020
restoring atom style atomic from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
1 by 2 by 2 MPI processor grid
pair style sw stores no restart info
512 atoms
read_restart CPU = 0.001 seconds
newton on on
pair_style tersoff/mod/c
pair_coeff * * Si.tersoff.modc Si Si Si Si Si Si Si Si
Reading tersoff/mod/c potential file Si.tersoff.modc with DATE: 2016-11-09
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
Resetting global fix info from restart file:
fix style: nvt, fix ID: 1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
All restart file global fix info was re-assigned
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.205694
ghost atom cutoff = 4.205694
binsize = 2.102847, bins = 11 11 11
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff/mod/c, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.950 | 2.950 | 2.950 Mbytes
Step Temp E_pair E_mol TotEng Press
100 1112.9699 -2309.1331 0 -2247.755 20346.718
110 831.93715 -2288.8853 0 -2247.7187 21758.195
120 1077.6698 -2303.2846 0 -2247.7693 16036.053
130 972.43247 -2294.1847 0 -2247.7467 16614.835
140 815.76148 -2282.0495 0 -2247.7194 18310.116
150 1072.7096 -2297.0491 0 -2247.7574 13896.767
160 1061.8824 -2294.0028 0 -2247.7522 13663.179
170 787.17244 -2273.8946 0 -2247.7175 18586.606
180 932.5662 -2281.6828 0 -2247.7315 18154.167
190 1205.7299 -2297.2769 0 -2247.7608 14504.136
200 1022.5285 -2282.7039 0 -2247.7245 18710.495
Loop time of 0.0526065 on 4 procs for 100 steps with 512 atoms
Performance: 164.238 ns/day, 0.146 hours/ns, 1900.906 timesteps/s
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.044962 | 0.045875 | 0.046737 | 0.3 | 87.20
Neigh | 0.000603 | 0.00062075 | 0.000646 | 0.0 | 1.18
Comm | 0.003882 | 0.0047085 | 0.005598 | 1.0 | 8.95
Output | 0.000159 | 0.0001995 | 0.000321 | 0.0 | 0.38
Modify | 0.000767 | 0.0007775 | 0.000792 | 0.0 | 1.48
Other | | 0.0004255 | | | 0.81
Nlocal: 128.000 ave 131 max 122 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 483.000 ave 485 max 479 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 2104.00 ave 2169 max 2008 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Total # of neighbors = 8416
Ave neighs/atom = 16.437500
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:00