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update threebody example

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This commit is contained in:
Axel Kohlmeyer
2022-03-24 07:31:02 -04:00
parent d8d12ccf1c
commit 4278ff8205
4 changed files with 398 additions and 185 deletions
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1
examples/threebody/SiC.tersoff.zbl Symbolic link
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@ -0,0 +1 @@
../../potentials/SiC.tersoff.zbl

60
examples/threebody/in.threebody
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@ -7,7 +7,7 @@ units metal
atom_style atomic
atom_modify map array
boundary p p p
atom_modify sort 0 0.0
atom_modify sort 0 0.0
# temperature
@ -35,23 +35,23 @@ region myreg block 0 4 &
create_box 8 myreg
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
basis 1 1 &
basis 2 2 &
basis 3 3 &
basis 4 4 &
basis 5 5 &
basis 6 6 &
basis 7 7 &
basis 8 8
mass * 28.06
velocity all create $t 5287287 loop geom
velocity all create $t 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
pair_coeff * * Si.sw Si Si Si Si Si Si Si Si
thermo_style custom step temp epair etotal econserve press
thermo 10
@ -61,15 +61,15 @@ neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
write_restart restart.equil
write_restart restart.equil
# Test Stillinger-Weber model for Cd/Te/Zn/Se/Hg/S
clear
read_restart restart.equil
read_restart restart.equil
pair_style sw
pair_coeff * * CdTeZnSeHgS0.sw Cd Zn Hg Cd Te S Se Te
pair_coeff * * CdTeZnSeHgS0.sw Cd Zn Hg Cd Te S Se Te
thermo_style custom step temp epair etotal econserve press
thermo 10
@ -82,10 +82,10 @@ run 100
# Test Vashishta model for In/P
clear
read_restart restart.equil
read_restart restart.equil
pair_style vashishta
pair_coeff * * InP.vashishta In In In In P P P P
pair_coeff * * InP.vashishta In In In In P P P P
thermo_style custom step temp epair etotal econserve press
thermo 10
@ -98,13 +98,13 @@ run 100
# Test Tersoff model for B/N/C
clear
read_restart restart.equil
read_restart restart.equil
variable fac equal 0.6
change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap
variable fac equal 0.6
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
pair_coeff * * BNC.tersoff N N N C B B C B
thermo_style custom step temp epair etotal econserve press
thermo 10
@ -114,3 +114,23 @@ neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
# Test Tersoff/ZBL model for SiC
clear
read_restart restart.equil
variable fac equal 0.6
change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap
pair_style tersoff/zbl
pair_coeff * * SiC.tersoff.zbl C C C C Si Si Si Si
thermo_style custom step temp epair etotal econserve press
thermo 10
fix 1 all nvt temp $t $t 0.1
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
shell rm restart.equil

216
examples/threebody/log.08Feb21.threebody.g++.1 → examples/threebody/log.29Sep21.threebody.g++.1
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@ -1,4 +1,4 @@
LAMMPS (24 Dec 2020)
LAMMPS (29 Sep 2021 - Update 3)
using 1 OpenMP thread(s) per MPI task
# Simple regression tests for threebody potentials
@ -9,7 +9,7 @@ units metal
atom_style atomic
atom_modify map array
boundary p p p
atom_modify sort 0 0.0
atom_modify sort 0 0.0
# temperature
@ -27,19 +27,20 @@ region myreg block 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
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
using lattice units in orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
create_atoms CPU = 0.000 seconds
mass * 28.06
velocity all create $t 5287287 loop geom
velocity all create 1800 5287287 loop geom
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
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
@ -76,20 +77,20 @@ Step Temp E_pair TotEng Econserve Press
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
Loop time of 0.093281 on 1 procs for 100 steps with 512 atoms
Performance: 54.728 ns/day, 0.439 hours/ns, 633.430 timesteps/s
Performance: 92.623 ns/day, 0.259 hours/ns, 1072.029 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
Pair | 0.090256 | 0.090256 | 0.090256 | 0.0 | 96.76
Neigh | 0.0015078 | 0.0015078 | 0.0015078 | 0.0 | 1.62
Comm | 0.00045896 | 0.00045896 | 0.00045896 | 0.0 | 0.49
Output | 8.3447e-05 | 8.3447e-05 | 8.3447e-05 | 0.0 | 0.09
Modify | 0.00072384 | 0.00072384 | 0.00072384 | 0.0 | 0.78
Other | | 0.0002506 | | | 0.27
Nlocal: 512.000 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -105,25 +106,25 @@ Ave neighs/atom = 27.320312
Neighbor list builds = 2
Dangerous builds = 0
write_restart restart.equil
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
read_restart restart.equil
Reading restart file ...
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
restart file = 29 Sep 2021, LAMMPS = 29 Sep 2021
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
read_restart CPU = 0.000 seconds
pair_style sw
pair_coeff * * CdTeZnSeHgS0.sw Cd Zn Hg Cd Te S Se Te
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
@ -163,20 +164,20 @@ Step Temp E_pair TotEng Econserve Press
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
Loop time of 0.245572 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
Performance: 35.183 ns/day, 0.682 hours/ns, 407.212 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 | 0.44091 | 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
Pair | 0.24139 | 0.24139 | 0.24139 | 0.0 | 98.30
Neigh | 0.0027068 | 0.0027068 | 0.0027068 | 0.0 | 1.10
Comm | 0.00051188 | 0.00051188 | 0.00051188 | 0.0 | 0.21
Output | 0.00010395 | 0.00010395 | 0.00010395 | 0.0 | 0.04
Modify | 0.00059605 | 0.00059605 | 0.00059605 | 0.0 | 0.24
Other | | 0.0002608 | | | 0.11
Nlocal: 512.000 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -196,18 +197,18 @@ Dangerous builds = 0
clear
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
read_restart restart.equil
Reading restart file ...
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
restart file = 29 Sep 2021, LAMMPS = 29 Sep 2021
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
read_restart CPU = 0.000 seconds
pair_style vashishta
pair_coeff * * InP.vashishta In In In In P P P P
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
@ -247,20 +248,20 @@ Step Temp E_pair TotEng Econserve Press
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
Loop time of 0.111899 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
Performance: 77.212 ns/day, 0.311 hours/ns, 893.662 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 | 0.19635 | 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
Pair | 0.10539 | 0.10539 | 0.10539 | 0.0 | 94.18
Neigh | 0.0049229 | 0.0049229 | 0.0049229 | 0.0 | 4.40
Comm | 0.00068307 | 0.00068307 | 0.00068307 | 0.0 | 0.61
Output | 6.1989e-05 | 6.1989e-05 | 6.1989e-05 | 0.0 | 0.06
Modify | 0.00058532 | 0.00058532 | 0.00058532 | 0.0 | 0.52
Other | | 0.0002604 | | | 0.23
Nlocal: 512.000 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -280,28 +281,28 @@ Dangerous builds = 0
clear
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
read_restart restart.equil
Reading restart file ...
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
restart file = 29 Sep 2021, LAMMPS = 29 Sep 2021
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
read_restart CPU = 0.000 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
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
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
@ -341,20 +342,20 @@ Step Temp E_pair TotEng Econserve Press
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
Loop time of 0.097734 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
Performance: 88.403 ns/day, 0.271 hours/ns, 1023.186 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 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
Pair | 0.095481 | 0.095481 | 0.095481 | 0.0 | 97.69
Neigh | 0.000772 | 0.000772 | 0.000772 | 0.0 | 0.79
Comm | 0.00046158 | 0.00046158 | 0.00046158 | 0.0 | 0.47
Output | 6.7949e-05 | 6.7949e-05 | 6.7949e-05 | 0.0 | 0.07
Modify | 0.00068784 | 0.00068784 | 0.00068784 | 0.0 | 0.70
Other | | 0.0002635 | | | 0.27
Nlocal: 512.000 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -370,4 +371,99 @@ Ave neighs/atom = 28.523438
Neighbor list builds = 1
Dangerous builds = 0
# Test Tersoff/ZBL model for SiC
clear
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
Reading restart file ...
restart file = 29 Sep 2021, LAMMPS = 29 Sep 2021
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 = 0.000 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/zbl
pair_coeff * * SiC.tersoff.zbl C C C C Si Si Si Si
Reading tersoff/zbl potential file SiC.tersoff.zbl with DATE: 2009-04-15
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 = 4
ghost atom cutoff = 4
binsize = 2, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff/zbl, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.002 | 3.002 | 3.002 Mbytes
Step Temp E_pair TotEng Econserve Press
100 1112.9699 7067.9634 7141.4772 7129.3415 17683957
110 1676.669 7033.1458 7143.893 7128.6921 17837566
120 2450.2667 6982.2491 7144.094 7126.9524 18220027
130 2726.9659 6964.1219 7144.2432 7126.7678 18230324
140 2729.421 6962.7393 7143.0228 7127.2074 18176317
150 2738.5449 6959.1761 7140.0623 7127.6671 18068370
160 2687.2419 6958.1183 7135.6158 7127.8492 18156214
170 2697.7325 6952.1482 7130.3387 7127.7898 17978251
180 2577.9885 6954.5611 7124.8422 7127.5615 18068920
190 2502.6928 6954.4558 7119.7635 7127.67 18049652
200 2517.4866 6947.962 7114.2469 7127.1972 18209451
Loop time of 0.783169 on 1 procs for 100 steps with 512 atoms
Performance: 11.032 ns/day, 2.175 hours/ns, 127.686 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 | 0.78056 | 0.78056 | 0.78056 | 0.0 | 99.67
Neigh | 0.0011299 | 0.0011299 | 0.0011299 | 0.0 | 0.14
Comm | 0.00051332 | 0.00051332 | 0.00051332 | 0.0 | 0.07
Output | 9.2268e-05 | 9.2268e-05 | 9.2268e-05 | 0.0 | 0.01
Modify | 0.00060058 | 0.00060058 | 0.00060058 | 0.0 | 0.08
Other | | 0.0002706 | | | 0.03
Nlocal: 512.000 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1542.00 ave 1542 max 1542 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: 30142.0 ave 30142 max 30142 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 30142
Ave neighs/atom = 58.871094
Neighbor list builds = 1
Dangerous builds = 0
shell rm restart.equil
Total wall time: 0:00:01

306
examples/threebody/log.08Feb21.threebody.g++.4 → examples/threebody/log.29Sep21.threebody.g++.4
View File

@ -1,4 +1,4 @@
LAMMPS (24 Dec 2020)
LAMMPS (29 Sep 2021 - Update 3)
using 1 OpenMP thread(s) per MPI task
# Simple regression tests for threebody potentials
@ -9,7 +9,7 @@ units metal
atom_style atomic
atom_modify map array
boundary p p p
atom_modify sort 0 0.0
atom_modify sort 0 0.0
# temperature
@ -26,20 +26,21 @@ region myreg block 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
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 = 0.074 seconds
using lattice units in orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
create_atoms CPU = 0.000 seconds
mass * 28.06
velocity all create $t 5287287 loop geom
velocity all create 1800 5287287 loop geom
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
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
@ -63,7 +64,7 @@ Neighbor list info ...
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
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
@ -76,54 +77,54 @@ Step Temp E_pair TotEng Econserve Press
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
Loop time of 0.089642 on 1 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
Performance: 96.383 ns/day, 0.249 hours/ns, 1115.548 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 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
Pair | 0.086619 | 0.086619 | 0.086619 | 0.0 | 96.63
Neigh | 0.0015211 | 0.0015211 | 0.0015211 | 0.0 | 1.70
Comm | 0.000458 | 0.000458 | 0.000458 | 0.0 | 0.51
Output | 7.987e-05 | 7.987e-05 | 7.987e-05 | 0.0 | 0.09
Modify | 0.00073361 | 0.00073361 | 0.00073361 | 0.0 | 0.82
Other | | 0.0002301 | | | 0.26
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
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: 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
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
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
read_restart restart.equil
Reading restart file ...
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
restart file = 29 Sep 2021, LAMMPS = 29 Sep 2021
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
1 by 1 by 1 MPI processor grid
pair style sw stores no restart info
512 atoms
read_restart CPU = 0.001 seconds
read_restart CPU = 0.000 seconds
pair_style sw
pair_coeff * * CdTeZnSeHgS0.sw Cd Zn Hg Cd Te S Se Te
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
@ -150,42 +151,42 @@ Neighbor list info ...
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
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 -552.24782 -564.38354 462129.66
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 -564.53613 486338.88
130 1152.6663 -621.47265 -545.33681 -564.37203 514892.19
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 -657.67179 -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
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 0.286556 on 4 procs for 100 steps with 512 atoms
Loop time of 0.268183 on 1 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
Performance: 32.217 ns/day, 0.745 hours/ns, 372.880 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 | 0.11093 | 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
Pair | 0.26374 | 0.26374 | 0.26374 | 0.0 | 98.34
Neigh | 0.0027301 | 0.0027301 | 0.0027301 | 0.0 | 1.02
Comm | 0.00063014 | 0.00063014 | 0.00063014 | 0.0 | 0.23
Output | 8.4639e-05 | 8.4639e-05 | 8.4639e-05 | 0.0 | 0.03
Modify | 0.00072742 | 0.00072742 | 0.00072742 | 0.0 | 0.27
Other | | 0.0002725 | | | 0.10
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
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: 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
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
@ -196,18 +197,18 @@ Dangerous builds = 0
clear
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
read_restart restart.equil
Reading restart file ...
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
restart file = 29 Sep 2021, LAMMPS = 29 Sep 2021
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
1 by 1 by 1 MPI processor grid
pair style sw stores no restart info
512 atoms
read_restart CPU = 0.001 seconds
read_restart CPU = 0.000 seconds
pair_style vashishta
pair_coeff * * InP.vashishta In In In In P P P P
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
@ -234,7 +235,7 @@ Neighbor list info ...
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
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
@ -247,29 +248,29 @@ Step Temp E_pair TotEng Econserve Press
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
Loop time of 0.117875 on 1 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
Performance: 73.298 ns/day, 0.327 hours/ns, 848.357 timesteps/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.047903 | 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
Pair | 0.11085 | 0.11085 | 0.11085 | 0.0 | 94.04
Neigh | 0.005235 | 0.005235 | 0.005235 | 0.0 | 4.44
Comm | 0.00077152 | 0.00077152 | 0.00077152 | 0.0 | 0.65
Output | 7.9155e-05 | 7.9155e-05 | 7.9155e-05 | 0.0 | 0.07
Modify | 0.00065637 | 0.00065637 | 0.00065637 | 0.0 | 0.56
Other | | 0.0002811 | | | 0.24
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
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: 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
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
@ -280,28 +281,28 @@ Dangerous builds = 0
clear
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
read_restart restart.equil
Reading restart file ...
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
restart file = 29 Sep 2021, LAMMPS = 29 Sep 2021
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
1 by 1 by 1 MPI processor grid
pair style sw stores no restart info
512 atoms
read_restart CPU = 0.005 seconds
read_restart CPU = 0.000 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
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
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
@ -328,7 +329,7 @@ Neighbor list info ...
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
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
@ -341,33 +342,128 @@ Step Temp E_pair TotEng Econserve Press
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
Loop time of 0.098053 on 1 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
Performance: 88.116 ns/day, 0.272 hours/ns, 1019.857 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 | 0.13281 | 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
Pair | 0.096055 | 0.096055 | 0.096055 | 0.0 | 97.96
Neigh | 0.00079703 | 0.00079703 | 0.00079703 | 0.0 | 0.81
Comm | 0.00034523 | 0.00034523 | 0.00034523 | 0.0 | 0.35
Output | 6.8903e-05 | 6.8903e-05 | 6.8903e-05 | 0.0 | 0.07
Modify | 0.00060797 | 0.00060797 | 0.00060797 | 0.0 | 0.62
Other | | 0.0001793 | | | 0.18
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
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: 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
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/ZBL model for SiC
clear
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
Reading restart file ...
restart file = 29 Sep 2021, LAMMPS = 29 Sep 2021
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 = 0.000 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/zbl
pair_coeff * * SiC.tersoff.zbl C C C C Si Si Si Si
Reading tersoff/zbl potential file SiC.tersoff.zbl with DATE: 2009-04-15
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 = 4
ghost atom cutoff = 4
binsize = 2, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff/zbl, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.002 | 3.002 | 3.002 Mbytes
Step Temp E_pair TotEng Econserve Press
100 1112.9699 7067.9634 7141.4772 7129.3415 17683957
110 1676.669 7033.1458 7143.893 7128.6921 17837566
120 2450.2667 6982.2491 7144.094 7126.9524 18220027
130 2726.9659 6964.1219 7144.2432 7126.7678 18230324
140 2729.421 6962.7393 7143.0228 7127.2074 18176317
150 2738.5449 6959.1761 7140.0623 7127.6671 18068370
160 2687.2419 6958.1183 7135.6158 7127.8492 18156214
170 2697.7325 6952.1482 7130.3387 7127.7898 17978251
180 2577.9885 6954.5611 7124.8422 7127.5615 18068920
190 2502.6928 6954.4558 7119.7635 7127.67 18049652
200 2517.4866 6947.962 7114.2469 7127.1972 18209451
Loop time of 0.810948 on 1 procs for 100 steps with 512 atoms
Performance: 10.654 ns/day, 2.253 hours/ns, 123.312 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 | 0.8082 | 0.8082 | 0.8082 | 0.0 | 99.66
Neigh | 0.001195 | 0.001195 | 0.001195 | 0.0 | 0.15
Comm | 0.00054765 | 0.00054765 | 0.00054765 | 0.0 | 0.07
Output | 0.0001018 | 0.0001018 | 0.0001018 | 0.0 | 0.01
Modify | 0.00062656 | 0.00062656 | 0.00062656 | 0.0 | 0.08
Other | | 0.0002768 | | | 0.03
Nlocal: 512.000 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1542.00 ave 1542 max 1542 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: 30142.0 ave 30142 max 30142 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 30142
Ave neighs/atom = 58.871094
Neighbor list builds = 1
Dangerous builds = 0
shell rm restart.equil
Total wall time: 0:00:01