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Merge pull request #4574 from talinke/develop

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New Fix for GJF Langevin Dynamics
This commit is contained in:
Axel Kohlmeyer
2025-05-06 13:24:06 -04:00
committed by GitHub
parent 750cfbedd3 def38bf0f3
commit c1e9adbd80
23 changed files with 1839 additions and 532 deletions
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examples/gjf/README Normal file
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LAMMPS GJ THERMOSTAT EXAMPLE
Required LAMMPS packages: EXTRA-FIX, MOLECULE, EXTRA-PAIR
This directory contains the ingredients to run an NVT simulation using the
GJ thermostats.
Example:
NP=4 #number of processors
mpirun -np $NP lmp_mpi -in.gjf.vhalf
Compared to other thermostats, the GJ thermostat allows for larger timesteps
with the correct Boltzmann statistics. A comparison using averaged properties
from this example's input file is shown below. 'X' denotes a failed simulation.
The theoretical value for KE is 1.1168 eV.
POTENTIAL ENERGY (eV)
| Δt || 0.01 | 0.05 | 0.10 | 0.11 | 0.12 | 0.13 | 0.14 |
|===================||========|========|========|========|========|========|========|
| gjf half || -55.11 | -55.11 | -55.11 | -55.11 | -55.11 | -55.10 | -55.07 |
| gjf full || -55.11 | -55.11 | -55.11 | -55.11 | -55.11 | -55.10 | -55.07 |
| langevin || -55.11 | -55.07 | -54.87 | -54.79 | -54.65 | X | X |
| nvt (Nose-Hoover) || -55.14 | -55.07 | -54.90 | -54.84 | -54.76 | X | X |
|-------------------||--------|--------|--------|--------|--------|--------|--------|
KINETIC ENERGY (eV)
| Δt || 0.01 | 0.05 | 0.10 | 0.11 | 0.12 | 0.13 | 0.14 |
|===================||========|========|========|========|========|========|========|
| gjf half || 1.117 | 1.116 | 1.119 | 1.119 | 1.123 | 1.136 | 1.170 |
| gjf full || 1.116 | 1.071 | 0.938 | 0.898 | 0.858 | 0.817 | 0.780 |
| langevin || 1.110 | 1.113 | 1.121 | 1.129 | 1.157 | X | X |
| nvt (Nose-Hoover) || 1.083 | 1.109 | 1.112 | 1.113 | 1.114 | X | X |
|-------------------||--------|--------|--------|--------|--------|--------|--------|
Script Commands:
--
fix lang all gjf 10 10 1 26488
--
fix lang all gjf 10 10 1 26488 vel vfull
--
fix nve all nve
fix lang all langevin 10 10 1 26488
--
fix noho all nvt temp 10 10 1
--

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examples/gjf/README.md
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# LAMMPS GJF-2GJ THERMOSTAT EXAMPLE
## GJF-2GJ THERMOSTAT
This directory contains the ingredients to run an NVT simulation using the GJF-2GJ thermostat.
Example:
```
NP=4 #number of processors
mpirun -np $NP lmp_mpi -in.gjf.vhalf
```
## Required LAMMPS packages: MOLECULE package

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examples/gjf/in.gjf.vfull
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# GJF-2GJ thermostat
# GJ thermostat
units metal
atom_style full
boundary p p p
read_data argon.lmp
include ff-argon.lmp
velocity all create 10 2357 mom yes dist gaussian
neighbor 1 bin
timestep 0.1
fix lang all langevin 10 10 1 26488 gjf vfull
fix nve all nve
compute myKE all ke
compute myPE all pe
fix lang all gjf 10 10 1 26488 vel vfull method 1
thermo 200
run 5000
fix energies all ave/time 1 20000 20000 c_myKE c_myPE #file ave.out
thermo 2000
run 35000

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examples/gjf/in.gjf.vhalf
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# GJF-2GJ thermostat
# GJ thermostat
units metal
atom_style full
boundary p p p
read_data argon.lmp
include ff-argon.lmp
velocity all create 10 2357 mom yes dist gaussian
neighbor 1 bin
timestep 0.1
fix lang all langevin 10 10 1 26488 gjf vhalf
fix nve all nve
compute myKE all ke
compute myPE all pe
fix lang all gjf 10 10 1 26488
thermo 200
run 5000
fix energies all ave/time 1 20000 20000 c_myKE c_myPE #file ave.out
thermo 2000
run 35000

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examples/gjf/log.15Oct19.gjf.vfull.g++.1
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LAMMPS (19 Sep 2019)
using 1 OpenMP thread(s) per MPI task
# GJF-2GJ thermostat
units metal
atom_style full
boundary p p p
read_data argon.lmp
orthogonal box = (0 0 0) to (32.146 32.146 32.146)
1 by 1 by 1 MPI processor grid
reading atoms ...
864 atoms
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000150019 secs
read_data CPU = 0.001946 secs
include ff-argon.lmp
#############################
#Atoms types - mass - charge#
#############################
#@ 1 atom types #!THIS LINE IS NECESSARY DON'T SPEND HOURS FINDING THAT OUT!#
variable Ar equal 1
#############
#Atom Masses#
#############
mass ${Ar} 39.903
mass 1 39.903
###########################
#Pair Potentials - Tersoff#
###########################
pair_style lj/cubic
pair_coeff * * 0.0102701 3.42
velocity all create 10 2357 mom yes dist gaussian
neighbor 1 bin
timestep 0.1
fix lang all langevin 10 10 1 26488 gjf vfull
fix nve all nve
thermo 200
run 5000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.94072
ghost atom cutoff = 6.94072
binsize = 3.47036, bins = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cubic, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.875 | 6.875 | 6.875 Mbytes
Step Temp E_pair E_mol TotEng Press
0 11.080223 -56.207655 0 -54.97164 37.215524
200 8.2588471 -55.073602 0 -54.152316 339.80416
400 8.1427292 -55.072244 0 -54.16391 338.91883
600 8.7595618 -55.066739 0 -54.089596 344.25426
800 8.550633 -55.148315 0 -54.194479 318.9385
1000 8.5394337 -55.125709 0 -54.173122 326.59471
1200 8.565973 -55.114892 0 -54.159345 328.5193
1400 8.2092914 -55.109233 0 -54.193475 329.56161
1600 8.209495 -55.138161 0 -54.22238 321.39971
1800 8.4039924 -55.13355 0 -54.196072 322.64214
2000 8.4548937 -55.062994 0 -54.119838 343.29888
2200 8.3775139 -55.13364 0 -54.199116 323.63744
2400 8.537332 -55.163702 0 -54.21135 315.62864
2600 8.672488 -55.112054 0 -54.144625 330.1106
2800 8.3000218 -55.147275 0 -54.221396 318.73112
3000 8.3552421 -55.135164 0 -54.203124 323.53075
3200 8.4126798 -55.135753 0 -54.197306 321.48817
3400 8.4986413 -55.135408 0 -54.187372 323.42951
3600 8.38431 -55.103932 0 -54.16865 330.68929
3800 8.8262454 -55.103648 0 -54.119067 332.97779
4000 7.9658136 -55.120402 0 -54.231803 324.9595
4200 8.2265544 -55.129011 0 -54.211327 323.87069
4400 8.1253738 -55.153089 0 -54.246691 316.304
4600 8.2010823 -55.124053 0 -54.20921 325.98402
4800 8.5512149 -55.075877 0 -54.121976 338.30137
5000 8.4737659 -55.158604 0 -54.213343 316.22418
Loop time of 2.73236 on 1 procs for 5000 steps with 864 atoms
Performance: 15810.507 ns/day, 0.002 hours/ns, 1829.920 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 | 1.4262 | 1.4262 | 1.4262 | 0.0 | 52.20
Bond | 0.00042836 | 0.00042836 | 0.00042836 | 0.0 | 0.02
Neigh | 0.12819 | 0.12819 | 0.12819 | 0.0 | 4.69
Comm | 0.058611 | 0.058611 | 0.058611 | 0.0 | 2.15
Output | 0.00047283 | 0.00047283 | 0.00047283 | 0.0 | 0.02
Modify | 1.0924 | 1.0924 | 1.0924 | 0.0 | 39.98
Other | | 0.02605 | | | 0.95
Nlocal: 864 ave 864 max 864 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1593 ave 1593 max 1593 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 18143 ave 18143 max 18143 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 18143
Ave neighs/atom = 20.9988
Ave special neighs/atom = 0
Neighbor list builds = 158
Dangerous builds = 5
Total wall time: 0:00:02

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LAMMPS (19 Sep 2019)
using 1 OpenMP thread(s) per MPI task
# GJF-2GJ thermostat
units metal
atom_style full
boundary p p p
read_data argon.lmp
orthogonal box = (0 0 0) to (32.146 32.146 32.146)
1 by 2 by 2 MPI processor grid
reading atoms ...
864 atoms
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000556268 secs
read_data CPU = 0.003817 secs
include ff-argon.lmp
#############################
#Atoms types - mass - charge#
#############################
#@ 1 atom types #!THIS LINE IS NECESSARY DON'T SPEND HOURS FINDING THAT OUT!#
variable Ar equal 1
#############
#Atom Masses#
#############
mass ${Ar} 39.903
mass 1 39.903
###########################
#Pair Potentials - Tersoff#
###########################
pair_style lj/cubic
pair_coeff * * 0.0102701 3.42
velocity all create 10 2357 mom yes dist gaussian
neighbor 1 bin
timestep 0.1
fix lang all langevin 10 10 1 26488 gjf vfull
fix nve all nve
thermo 200
run 5000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.94072
ghost atom cutoff = 6.94072
binsize = 3.47036, bins = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cubic, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.808 | 6.808 | 6.808 Mbytes
Step Temp E_pair E_mol TotEng Press
0 11.080228 -56.207655 0 -54.971639 37.215541
200 8.4818184 -55.127334 0 -54.181174 324.96159
400 8.5960916 -55.09236 0 -54.133453 334.83136
600 8.1607556 -55.073136 0 -54.162791 339.035
800 8.8350489 -55.133382 0 -54.147819 324.48149
1000 8.5692704 -55.118463 0 -54.162548 327.26328
1200 8.4174147 -55.126297 0 -54.187322 324.4248
1400 8.6362603 -55.123075 0 -54.159688 326.7798
1600 8.222512 -55.153799 0 -54.236565 317.8147
1800 8.324523 -55.116698 0 -54.188085 327.35373
2000 7.9615959 -55.155825 0 -54.267697 315.37215
2200 8.495968 -55.083943 0 -54.136205 336.67775
2400 7.7926986 -55.044816 0 -54.175529 344.87758
2600 8.1551351 -55.069404 0 -54.159687 339.60901
2800 8.2593599 -55.084151 0 -54.162807 336.54935
3000 8.2860869 -55.110296 0 -54.185971 328.99074
3200 8.4074534 -55.123576 0 -54.185712 326.06823
3400 8.6694364 -55.128925 0 -54.161836 324.67512
3600 8.5718984 -55.129861 0 -54.173653 325.20586
3800 8.508102 -55.099093 0 -54.150001 333.91437
4000 8.2966658 -55.117782 0 -54.192276 327.13516
4200 8.7641728 -55.135792 0 -54.158136 324.00844
4400 8.8827909 -55.096369 0 -54.10548 335.08467
4600 8.7666577 -55.127213 0 -54.149279 326.15539
4800 8.6670762 -55.163395 0 -54.19657 316.48383
5000 8.1893094 -55.073756 0 -54.160226 337.95271
Loop time of 0.870594 on 4 procs for 5000 steps with 864 atoms
Performance: 49621.267 ns/day, 0.000 hours/ns, 5743.202 timesteps/s
96.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.33582 | 0.35125 | 0.3724 | 2.3 | 40.35
Bond | 0.00030267 | 0.00031316 | 0.00033538 | 0.0 | 0.04
Neigh | 0.034246 | 0.03479 | 0.035904 | 0.4 | 4.00
Comm | 0.15068 | 0.17419 | 0.19191 | 3.6 | 20.01
Output | 0.00044776 | 0.00054703 | 0.00083177 | 0.0 | 0.06
Modify | 0.27679 | 0.28079 | 0.28849 | 0.9 | 32.25
Other | | 0.02871 | | | 3.30
Nlocal: 216 ave 216 max 216 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 888.75 ave 899 max 876 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Neighs: 4536 ave 4737 max 4335 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 18144
Ave neighs/atom = 21
Ave special neighs/atom = 0
Neighbor list builds = 178
Dangerous builds = 11
Total wall time: 0:00:00

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LAMMPS (19 Sep 2019)
using 1 OpenMP thread(s) per MPI task
# GJF-2GJ thermostat
units metal
atom_style full
boundary p p p
read_data argon.lmp
orthogonal box = (0 0 0) to (32.146 32.146 32.146)
1 by 1 by 1 MPI processor grid
reading atoms ...
864 atoms
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000147804 secs
read_data CPU = 0.00194898 secs
include ff-argon.lmp
#############################
#Atoms types - mass - charge#
#############################
#@ 1 atom types #!THIS LINE IS NECESSARY DON'T SPEND HOURS FINDING THAT OUT!#
variable Ar equal 1
#############
#Atom Masses#
#############
mass ${Ar} 39.903
mass 1 39.903
###########################
#Pair Potentials - Tersoff#
###########################
pair_style lj/cubic
pair_coeff * * 0.0102701 3.42
velocity all create 10 2357 mom yes dist gaussian
neighbor 1 bin
timestep 0.1
fix lang all langevin 10 10 1 26488 gjf vhalf
fix nve all nve
thermo 200
run 5000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.94072
ghost atom cutoff = 6.94072
binsize = 3.47036, bins = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cubic, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.5 | 6.5 | 6.5 Mbytes
Step Temp E_pair E_mol TotEng Press
0 11.080223 -56.207655 0 -54.97164 37.215524
200 9.8808568 -55.073602 0 -53.971378 345.62207
400 9.8712816 -55.072244 0 -53.971088 345.11889
600 10.528988 -55.066739 0 -53.892214 350.60093
800 10.167171 -55.148315 0 -54.014152 324.73679
1000 10.029026 -55.125709 0 -54.006956 331.93766
1200 10.194424 -55.114892 0 -53.977688 334.36032
1400 9.3473846 -55.109233 0 -54.066518 333.64378
1600 9.7774071 -55.138161 0 -54.047477 327.02358
1800 9.9814275 -55.13355 0 -54.020107 328.30017
2000 10.2515 -55.062994 0 -53.919424 349.74304
2200 9.8126922 -55.13364 0 -54.039019 328.78521
2400 10.044314 -55.163702 0 -54.043244 321.03397
2600 10.543316 -55.112054 0 -53.935932 336.82099
2800 9.7874375 -55.147275 0 -54.055472 324.06626
3000 9.7703821 -55.135164 0 -54.045263 328.60665
3200 10.141958 -55.135753 0 -54.004402 327.69084
3400 10.160576 -55.135408 0 -54.00198 329.39063
3600 10.044652 -55.103932 0 -53.983436 336.64469
3800 10.662403 -55.103648 0 -53.914241 339.56382
4000 9.2921047 -55.120402 0 -54.083853 329.71671
4200 9.8744553 -55.129011 0 -54.027501 329.78147
4400 9.4085964 -55.153089 0 -54.103546 320.90673
4600 9.5463801 -55.124053 0 -54.05914 330.80941
4800 10.223884 -55.075877 0 -53.935387 344.30099
5000 9.6243338 -55.158604 0 -54.084996 320.3511
Loop time of 2.29551 on 1 procs for 5000 steps with 864 atoms
Performance: 18819.358 ns/day, 0.001 hours/ns, 2178.166 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 | 1.4393 | 1.4393 | 1.4393 | 0.0 | 62.70
Bond | 0.0004441 | 0.0004441 | 0.0004441 | 0.0 | 0.02
Neigh | 0.12136 | 0.12136 | 0.12136 | 0.0 | 5.29
Comm | 0.059342 | 0.059342 | 0.059342 | 0.0 | 2.59
Output | 0.00046968 | 0.00046968 | 0.00046968 | 0.0 | 0.02
Modify | 0.64937 | 0.64937 | 0.64937 | 0.0 | 28.29
Other | | 0.02522 | | | 1.10
Nlocal: 864 ave 864 max 864 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1593 ave 1593 max 1593 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 18143 ave 18143 max 18143 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 18143
Ave neighs/atom = 20.9988
Ave special neighs/atom = 0
Neighbor list builds = 158
Dangerous builds = 5
Total wall time: 0:00:02

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LAMMPS (19 Sep 2019)
using 1 OpenMP thread(s) per MPI task
# GJF-2GJ thermostat
units metal
atom_style full
boundary p p p
read_data argon.lmp
orthogonal box = (0 0 0) to (32.146 32.146 32.146)
1 by 2 by 2 MPI processor grid
reading atoms ...
864 atoms
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000315903 secs
read_data CPU = 0.0653752 secs
include ff-argon.lmp
#############################
#Atoms types - mass - charge#
#############################
#@ 1 atom types #!THIS LINE IS NECESSARY DON'T SPEND HOURS FINDING THAT OUT!#
variable Ar equal 1
#############
#Atom Masses#
#############
mass ${Ar} 39.903
mass 1 39.903
###########################
#Pair Potentials - Tersoff#
###########################
pair_style lj/cubic
pair_coeff * * 0.0102701 3.42
velocity all create 10 2357 mom yes dist gaussian
neighbor 1 bin
timestep 0.1
fix lang all langevin 10 10 1 26488 gjf vhalf
fix nve all nve
thermo 200
run 5000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.94072
ghost atom cutoff = 6.94072
binsize = 3.47036, bins = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cubic, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.433 | 6.433 | 6.433 Mbytes
Step Temp E_pair E_mol TotEng Press
0 11.080228 -56.207655 0 -54.971639 37.215541
200 9.8046716 -55.127334 0 -54.033608 329.70647
400 10.174622 -55.09236 0 -53.957366 340.49331
600 9.9812299 -55.073136 0 -53.959714 345.56477
800 10.512874 -55.133382 0 -53.960655 330.4996
1000 9.9587885 -55.118463 0 -54.007545 332.24728
1200 10.236607 -55.126297 0 -53.984388 330.94998
1400 10.134679 -55.123075 0 -53.992537 332.15441
1600 9.8934078 -55.153799 0 -54.050174 323.80795
1800 10.064966 -55.116698 0 -53.993936 333.59644
2000 9.6736107 -55.155825 0 -54.076719 321.5129
2200 10.264537 -55.083943 0 -53.938918 343.02135
2400 9.5640032 -55.044816 0 -53.977937 351.23099
2600 9.6581077 -55.069404 0 -53.992028 344.99996
2800 9.9622575 -55.084151 0 -53.972846 342.6574
3000 9.8724909 -55.110296 0 -54.009005 334.68094
3200 10.032027 -55.123576 0 -54.004488 331.89534
3400 10.221132 -55.128925 0 -53.988742 330.24082
3600 10.085802 -55.129861 0 -54.004774 330.63601
3800 10.098545 -55.099093 0 -53.972585 339.61905
4000 10.000257 -55.117782 0 -54.002238 333.24569
4200 10.20477 -55.135792 0 -53.997435 329.17565
4400 10.545132 -55.096369 0 -53.920044 341.04725
4600 10.376108 -55.127213 0 -53.969743 331.92825
4800 10.247392 -55.163395 0 -54.020283 322.15219
5000 9.7753102 -55.073756 0 -53.983305 343.64146
Loop time of 1.19785 on 4 procs for 5000 steps with 864 atoms
Performance: 36064.674 ns/day, 0.001 hours/ns, 4174.152 timesteps/s
88.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.36387 | 0.38652 | 0.44086 | 5.1 | 32.27
Bond | 0.00028847 | 0.00030833 | 0.000338 | 0.0 | 0.03
Neigh | 0.033934 | 0.034959 | 0.036917 | 0.6 | 2.92
Comm | 0.39292 | 0.47821 | 0.52198 | 7.3 | 39.92
Output | 0.00050343 | 0.0012343 | 0.0023338 | 1.9 | 0.10
Modify | 0.1605 | 0.17963 | 0.19457 | 2.9 | 15.00
Other | | 0.117 | | | 9.77
Nlocal: 216 ave 216 max 216 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 888.75 ave 899 max 876 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Neighs: 4536 ave 4737 max 4335 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 18144
Ave neighs/atom = 21
Ave special neighs/atom = 0
Neighbor list builds = 178
Dangerous builds = 11
Total wall time: 0:00:01

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LAMMPS (2 Apr 2025 - Development - d4867ab55e-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
# GJ thermostat
units metal
atom_style full
boundary p p p
read_data argon.lmp
Reading data file ...
orthogonal box = (0 0 0) to (32.146 32.146 32.146)
1 by 1 by 1 MPI processor grid
reading atoms ...
864 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.007 seconds
include ff-argon.lmp
#############################
#Atoms types - mass - charge#
#############################
#@ 1 atom types #!THIS LINE IS NECESSARY DON'T SPEND HOURS FINDING THAT OUT!#
variable Ar equal 1
#############
#Atom Masses#
#############
mass ${Ar} 39.903
mass 1 39.903
###########################
#Pair Potentials - Tersoff#
###########################
pair_style lj/cubic
pair_coeff * * 0.0102701 3.42
velocity all create 10 2357 mom yes dist gaussian
neighbor 1 bin
timestep 0.1
compute myKE all ke
compute myPE all pe
fix lang all gjf 10 10 1 26488 vel vfull method 1
run 5000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- GJ methods: doi:10.1080/00268976.2019.1662506
@Article{gronbech-jensen_complete_2020,
title = {Complete set of stochastic Verlet-type thermostats for correct Langevin simulations},
volume = {118},
number = {8},
url = {https://www.tandfonline.com/doi/full/10.1080/00268976.2019.1662506},
doi = {10.1080/00268976.2019.1662506},
journal = {Molecular Physics},
author = {Grønbech-Jensen, Niels},
year = {2020}
}
- GJ-I vfull method: doi:10.1080/00268976.2012.760055
@Article{gronbech-jensen_simple_2013,
title = {A simple and effective Verlet-type algorithm for simulating Langevin dynamics},
volume = {111},
url = {http://www.tandfonline.com/doi/abs/10.1080/00268976.2012.760055},
doi = {10.1080/00268976.2012.760055},
pages = {983-991},
number = {8},
journal = {Molecular Physics},
author = {Grønbech-Jensen, Niels and Farago, Oded},
year = {2013}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.9407173
ghost atom cutoff = 6.9407173
binsize = 3.4703587, bins = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cubic, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.481 | 6.481 | 6.481 Mbytes
Step Temp E_pair E_mol TotEng Press
0 10 -56.207652 0 -55.092137 33.341103
5000 8.4535562 -55.150518 0 -54.207511 318.20862
Loop time of 2.26831 on 1 procs for 5000 steps with 864 atoms
Performance: 19044.977 ns/day, 0.001 hours/ns, 2204.280 timesteps/s, 1.904 Matom-step/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 | 1.2802 | 1.2802 | 1.2802 | 0.0 | 56.44
Bond | 0.00051213 | 0.00051213 | 0.00051213 | 0.0 | 0.02
Neigh | 0.27007 | 0.27007 | 0.27007 | 0.0 | 11.91
Comm | 0.057527 | 0.057527 | 0.057527 | 0.0 | 2.54
Output | 6.3876e-05 | 6.3876e-05 | 6.3876e-05 | 0.0 | 0.00
Modify | 0.63364 | 0.63364 | 0.63364 | 0.0 | 27.93
Other | | 0.02635 | | | 1.16
Nlocal: 864 ave 864 max 864 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1593 ave 1593 max 1593 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 18143 ave 18143 max 18143 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 18143
Ave neighs/atom = 20.998843
Ave special neighs/atom = 0
Neighbor list builds = 258
Dangerous builds = 0
fix energies all ave/time 1 20000 20000 c_myKE c_myPE #file ave.out
thermo 2000
run 35000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 6.481 | 6.481 | 6.481 Mbytes
Step Temp E_pair E_mol TotEng Press
5000 8.4535562 -55.150518 0 -54.207511 318.20862
6000 8.4899401 -55.108242 0 -54.161176 331.10703
8000 8.3618893 -55.092171 0 -54.15939 334.11831
10000 8.8684311 -55.100316 0 -54.111029 334.09931
12000 8.4339192 -55.07343 0 -54.132614 340.00487
14000 8.072393 -55.115121 0 -54.214633 327.98965
16000 8.3420289 -55.077813 0 -54.147247 337.74926
18000 8.3803911 -55.12201 0 -54.187164 326.10485
20000 8.4676985 -55.176339 0 -54.231754 311.57092
22000 8.8560138 -55.110505 0 -54.122603 330.66179
24000 8.3187826 -55.120592 0 -54.192619 327.01148
26000 8.0327666 -55.116664 0 -54.220596 326.25179
28000 8.3672169 -55.130413 0 -54.197037 324.2368
30000 8.1669275 -55.057678 0 -54.146645 344.9168
32000 8.3819314 -55.08989 0 -54.154873 335.45317
34000 8.109088 -55.17222 0 -54.267639 310.83717
36000 8.3048574 -55.079475 0 -54.153056 338.04291
38000 8.8708544 -55.108991 0 -54.119434 330.70097
40000 8.4012779 -55.080817 0 -54.143642 338.54326
Loop time of 18.9699 on 1 procs for 35000 steps with 864 atoms
Performance: 15941.040 ns/day, 0.002 hours/ns, 1845.028 timesteps/s, 1.594 Matom-step/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 | 11.593 | 11.593 | 11.593 | 0.0 | 61.11
Bond | 0.0041801 | 0.0041801 | 0.0041801 | 0.0 | 0.02
Neigh | 2.2671 | 2.2671 | 2.2671 | 0.0 | 11.95
Comm | 0.42339 | 0.42339 | 0.42339 | 0.0 | 2.23
Output | 0.00062204 | 0.00062204 | 0.00062204 | 0.0 | 0.00
Modify | 4.4976 | 4.4976 | 4.4976 | 0.0 | 23.71
Other | | 0.1839 | | | 0.97
Nlocal: 864 ave 864 max 864 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1592 ave 1592 max 1592 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 18144 ave 18144 max 18144 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 18144
Ave neighs/atom = 21
Ave special neighs/atom = 0
Neighbor list builds = 2122
Dangerous builds = 0
Total wall time: 0:00:21

193
examples/gjf/log.2Apr25.gjf.vfull.g++.4 Normal file
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@ -0,0 +1,193 @@
LAMMPS (2 Apr 2025 - Development - d4867ab55e-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
# GJ thermostat
units metal
atom_style full
boundary p p p
read_data argon.lmp
Reading data file ...
orthogonal box = (0 0 0) to (32.146 32.146 32.146)
1 by 2 by 2 MPI processor grid
reading atoms ...
864 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.002 seconds
read_data CPU = 0.015 seconds
include ff-argon.lmp
#############################
#Atoms types - mass - charge#
#############################
#@ 1 atom types #!THIS LINE IS NECESSARY DON'T SPEND HOURS FINDING THAT OUT!#
variable Ar equal 1
#############
#Atom Masses#
#############
mass ${Ar} 39.903
mass 1 39.903
###########################
#Pair Potentials - Tersoff#
###########################
pair_style lj/cubic
pair_coeff * * 0.0102701 3.42
velocity all create 10 2357 mom yes dist gaussian
neighbor 1 bin
timestep 0.1
compute myKE all ke
compute myPE all pe
fix lang all gjf 10 10 1 26488 vel vfull method 1
run 5000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- GJ methods: doi:10.1080/00268976.2019.1662506
@Article{gronbech-jensen_complete_2020,
title = {Complete set of stochastic Verlet-type thermostats for correct Langevin simulations},
volume = {118},
number = {8},
url = {https://www.tandfonline.com/doi/full/10.1080/00268976.2019.1662506},
doi = {10.1080/00268976.2019.1662506},
journal = {Molecular Physics},
author = {Grønbech-Jensen, Niels},
year = {2020}
}
- GJ-I vfull method: doi:10.1080/00268976.2012.760055
@Article{gronbech-jensen_simple_2013,
title = {A simple and effective Verlet-type algorithm for simulating Langevin dynamics},
volume = {111},
url = {http://www.tandfonline.com/doi/abs/10.1080/00268976.2012.760055},
doi = {10.1080/00268976.2012.760055},
pages = {983-991},
number = {8},
journal = {Molecular Physics},
author = {Grønbech-Jensen, Niels and Farago, Oded},
year = {2013}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.9407173
ghost atom cutoff = 6.9407173
binsize = 3.4703587, bins = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cubic, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.427 | 6.427 | 6.427 Mbytes
Step Temp E_pair E_mol TotEng Press
0 10 -56.207652 0 -55.092137 33.341103
5000 7.946377 -55.076514 0 -54.190084 337.31999
Loop time of 2.0998 on 4 procs for 5000 steps with 864 atoms
Performance: 20573.405 ns/day, 0.001 hours/ns, 2381.181 timesteps/s, 2.057 Matom-step/s
65.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.53641 | 0.54389 | 0.54721 | 0.6 | 25.90
Bond | 0.00056487 | 0.0006195 | 0.00068462 | 0.0 | 0.03
Neigh | 0.10567 | 0.1086 | 0.11128 | 0.7 | 5.17
Comm | 0.96913 | 0.97758 | 0.98191 | 0.5 | 46.56
Output | 0.00025213 | 0.00025642 | 0.00026405 | 0.0 | 0.01
Modify | 0.25061 | 0.25105 | 0.25172 | 0.1 | 11.96
Other | | 0.2178 | | | 10.37
Nlocal: 216 ave 216 max 216 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 884.75 ave 885 max 884 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 4536 ave 4737 max 4335 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 18144
Ave neighs/atom = 21
Ave special neighs/atom = 0
Neighbor list builds = 273
Dangerous builds = 0
fix energies all ave/time 1 20000 20000 c_myKE c_myPE #file ave.out
thermo 2000
run 35000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 6.428 | 6.428 | 6.428 Mbytes
Step Temp E_pair E_mol TotEng Press
5000 7.946377 -55.076514 0 -54.190084 337.31999
6000 8.2565866 -55.129244 0 -54.208209 324.57967
8000 7.9942397 -55.101417 0 -54.209648 331.24127
10000 8.5413968 -55.083292 0 -54.130486 337.82599
12000 8.3682078 -55.090905 0 -54.157419 335.08066
14000 8.5082065 -55.085051 0 -54.135948 336.2765
16000 8.1944037 -55.090733 0 -54.176635 334.03786
18000 8.2607106 -55.030131 0 -54.108637 352.49892
20000 8.1154691 -55.104072 0 -54.198779 330.14203
22000 8.5592601 -55.152019 0 -54.197221 318.03507
24000 8.3182914 -55.115242 0 -54.187324 328.46084
26000 8.3691375 -55.125275 0 -54.191685 325.43673
28000 8.531632 -55.107097 0 -54.155381 331.42771
30000 8.1102222 -55.099011 0 -54.194304 332.04678
32000 8.5558571 -55.077016 0 -54.122598 339.87746
34000 8.4213946 -55.097068 0 -54.157649 333.34935
36000 8.0936615 -55.152202 0 -54.249342 316.20169
38000 7.999652 -55.048407 0 -54.156034 345.07945
40000 8.6699753 -55.087634 0 -54.120485 337.23709
Loop time of 17.6726 on 4 procs for 35000 steps with 864 atoms
Performance: 17111.263 ns/day, 0.001 hours/ns, 1980.470 timesteps/s, 1.711 Matom-step/s
65.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.0739 | 5.1178 | 5.1689 | 1.5 | 28.96
Bond | 0.0043764 | 0.004688 | 0.0051706 | 0.4 | 0.03
Neigh | 0.83797 | 0.85506 | 0.87554 | 1.8 | 4.84
Comm | 6.816 | 6.8932 | 6.9215 | 1.7 | 39.00
Output | 0.0043624 | 0.0045336 | 0.004998 | 0.4 | 0.03
Modify | 3.3008 | 3.3033 | 3.3066 | 0.1 | 18.69
Other | | 1.494 | | | 8.45
Nlocal: 216 ave 222 max 210 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 905.5 ave 911 max 899 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Neighs: 4535.75 ave 4837 max 4218 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Total # of neighbors = 18143
Ave neighs/atom = 20.998843
Ave special neighs/atom = 0
Neighbor list builds = 2140
Dangerous builds = 0
Total wall time: 0:00:19

192
examples/gjf/log.2Apr25.gjf.vhalf.g++.1 Normal file
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@ -0,0 +1,192 @@
LAMMPS (2 Apr 2025 - Development - d4867ab55e-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
# GJ thermostat
units metal
atom_style full
boundary p p p
read_data argon.lmp
Reading data file ...
orthogonal box = (0 0 0) to (32.146 32.146 32.146)
1 by 1 by 1 MPI processor grid
reading atoms ...
864 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.010 seconds
include ff-argon.lmp
#############################
#Atoms types - mass - charge#
#############################
#@ 1 atom types #!THIS LINE IS NECESSARY DON'T SPEND HOURS FINDING THAT OUT!#
variable Ar equal 1
#############
#Atom Masses#
#############
mass ${Ar} 39.903
mass 1 39.903
###########################
#Pair Potentials - Tersoff#
###########################
pair_style lj/cubic
pair_coeff * * 0.0102701 3.42
velocity all create 10 2357 mom yes dist gaussian
neighbor 1 bin
timestep 0.1
compute myKE all ke
compute myPE all pe
fix lang all gjf 10 10 1 26488
run 5000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- GJ methods: doi:10.1080/00268976.2019.1662506
@Article{gronbech-jensen_complete_2020,
title = {Complete set of stochastic Verlet-type thermostats for correct Langevin simulations},
volume = {118},
number = {8},
url = {https://www.tandfonline.com/doi/full/10.1080/00268976.2019.1662506},
doi = {10.1080/00268976.2019.1662506},
journal = {Molecular Physics},
author = {Grønbech-Jensen, Niels},
year = {2020}
}
- GJ-I vhalf method: doi:10.1080/00268976.2019.1570369
@Article{jensen_accurate_2019,
title = {Accurate configurational and kinetic statistics in discrete-time Langevin systems},
volume = {117},
url = {https://www.tandfonline.com/doi/full/10.1080/00268976.2019.1570369},
doi = {10.1080/00268976.2019.1570369},
number = {18},
journal = {Molecular Physics},
author = {Jensen, Lucas Frese Grønbech and Grønbech-Jensen, Niels},
year = {2019}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.9407173
ghost atom cutoff = 6.9407173
binsize = 3.4703587, bins = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cubic, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.481 | 6.481 | 6.481 Mbytes
Step Temp E_pair E_mol TotEng Press
0 10 -56.207652 0 -55.092137 33.341103
5000 9.7731898 -55.150518 0 -54.060304 322.94195
Loop time of 2.28421 on 1 procs for 5000 steps with 864 atoms
Performance: 18912.438 ns/day, 0.001 hours/ns, 2188.940 timesteps/s, 1.891 Matom-step/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 | 1.2715 | 1.2715 | 1.2715 | 0.0 | 55.66
Bond | 0.00057126 | 0.00057126 | 0.00057126 | 0.0 | 0.03
Neigh | 0.27008 | 0.27008 | 0.27008 | 0.0 | 11.82
Comm | 0.057938 | 0.057938 | 0.057938 | 0.0 | 2.54
Output | 6.1954e-05 | 6.1954e-05 | 6.1954e-05 | 0.0 | 0.00
Modify | 0.658 | 0.658 | 0.658 | 0.0 | 28.81
Other | | 0.0261 | | | 1.14
Nlocal: 864 ave 864 max 864 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1593 ave 1593 max 1593 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 18143 ave 18143 max 18143 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 18143
Ave neighs/atom = 20.998843
Ave special neighs/atom = 0
Neighbor list builds = 258
Dangerous builds = 0
fix energies all ave/time 1 20000 20000 c_myKE c_myPE #file ave.out
thermo 2000
run 35000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 6.481 | 6.481 | 6.481 Mbytes
Step Temp E_pair E_mol TotEng Press
5000 9.7731898 -55.150518 0 -54.060304 322.94195
6000 10.024842 -55.108242 0 -53.989956 336.6125
8000 10.118994 -55.092171 0 -53.963382 340.42078
10000 10.541359 -55.100316 0 -53.924412 340.09986
12000 10.023234 -55.07343 0 -53.955323 345.70551
14000 9.5912018 -55.115121 0 -54.045208 333.43739
16000 9.9450498 -55.077813 0 -53.968428 343.49906
18000 10.113744 -55.12201 0 -53.993806 332.32214
20000 9.9345204 -55.176339 0 -54.068128 316.83219
22000 10.585719 -55.110505 0 -53.929652 336.86599
24000 10.024757 -55.120592 0 -54.002315 333.13056
26000 9.7787474 -55.116664 0 -54.02583 332.51437
28000 9.6092087 -55.130413 0 -54.058491 328.69165
30000 9.8245787 -55.057678 0 -53.961731 350.86255
32000 10.066994 -55.08989 0 -53.966902 341.49724
34000 9.5677059 -55.17222 0 -54.104928 316.06902
36000 9.7252627 -55.079475 0 -53.994608 343.13769
38000 10.438984 -55.108991 0 -53.944506 336.32562
40000 10.238268 -55.080817 0 -53.938723 345.13228
Loop time of 19.138 on 1 procs for 35000 steps with 864 atoms
Performance: 15801.041 ns/day, 0.002 hours/ns, 1828.824 timesteps/s, 1.580 Matom-step/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 | 11.568 | 11.568 | 11.568 | 0.0 | 60.44
Bond | 0.0042372 | 0.0042372 | 0.0042372 | 0.0 | 0.02
Neigh | 2.2577 | 2.2577 | 2.2577 | 0.0 | 11.80
Comm | 0.42841 | 0.42841 | 0.42841 | 0.0 | 2.24
Output | 0.00060128 | 0.00060128 | 0.00060128 | 0.0 | 0.00
Modify | 4.694 | 4.694 | 4.694 | 0.0 | 24.53
Other | | 0.1852 | | | 0.97
Nlocal: 864 ave 864 max 864 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1592 ave 1592 max 1592 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 18144 ave 18144 max 18144 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 18144
Ave neighs/atom = 21
Ave special neighs/atom = 0
Neighbor list builds = 2122
Dangerous builds = 0
Total wall time: 0:00:21

192
examples/gjf/log.2Apr25.gjf.vhalf.g++.4 Normal file
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@ -0,0 +1,192 @@
LAMMPS (2 Apr 2025 - Development - d4867ab55e-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
# GJ thermostat
units metal
atom_style full
boundary p p p
read_data argon.lmp
Reading data file ...
orthogonal box = (0 0 0) to (32.146 32.146 32.146)
1 by 2 by 2 MPI processor grid
reading atoms ...
864 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.002 seconds
read_data CPU = 0.015 seconds
include ff-argon.lmp
#############################
#Atoms types - mass - charge#
#############################
#@ 1 atom types #!THIS LINE IS NECESSARY DON'T SPEND HOURS FINDING THAT OUT!#
variable Ar equal 1
#############
#Atom Masses#
#############
mass ${Ar} 39.903
mass 1 39.903
###########################
#Pair Potentials - Tersoff#
###########################
pair_style lj/cubic
pair_coeff * * 0.0102701 3.42
velocity all create 10 2357 mom yes dist gaussian
neighbor 1 bin
timestep 0.1
compute myKE all ke
compute myPE all pe
fix lang all gjf 10 10 1 26488
run 5000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- GJ methods: doi:10.1080/00268976.2019.1662506
@Article{gronbech-jensen_complete_2020,
title = {Complete set of stochastic Verlet-type thermostats for correct Langevin simulations},
volume = {118},
number = {8},
url = {https://www.tandfonline.com/doi/full/10.1080/00268976.2019.1662506},
doi = {10.1080/00268976.2019.1662506},
journal = {Molecular Physics},
author = {Grønbech-Jensen, Niels},
year = {2020}
}
- GJ-I vhalf method: doi:10.1080/00268976.2019.1570369
@Article{jensen_accurate_2019,
title = {Accurate configurational and kinetic statistics in discrete-time Langevin systems},
volume = {117},
url = {https://www.tandfonline.com/doi/full/10.1080/00268976.2019.1570369},
doi = {10.1080/00268976.2019.1570369},
number = {18},
journal = {Molecular Physics},
author = {Jensen, Lucas Frese Grønbech and Grønbech-Jensen, Niels},
year = {2019}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.9407173
ghost atom cutoff = 6.9407173
binsize = 3.4703587, bins = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cubic, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.427 | 6.427 | 6.427 Mbytes
Step Temp E_pair E_mol TotEng Press
0 10 -56.207652 0 -55.092137 33.341103
5000 9.3726166 -55.076514 0 -54.030985 342.43571
Loop time of 2.11818 on 4 procs for 5000 steps with 864 atoms
Performance: 20394.822 ns/day, 0.001 hours/ns, 2360.512 timesteps/s, 2.039 Matom-step/s
63.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.53987 | 0.54922 | 0.56044 | 1.2 | 25.93
Bond | 0.00058281 | 0.00063674 | 0.00075153 | 0.0 | 0.03
Neigh | 0.10821 | 0.10912 | 0.11017 | 0.2 | 5.15
Comm | 0.96075 | 0.97484 | 0.98645 | 1.1 | 46.02
Output | 0.00026318 | 0.00026575 | 0.00027192 | 0.0 | 0.01
Modify | 0.26142 | 0.2634 | 0.26465 | 0.2 | 12.44
Other | | 0.2207 | | | 10.42
Nlocal: 216 ave 216 max 216 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 884.75 ave 885 max 884 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 4536 ave 4737 max 4335 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 18144
Ave neighs/atom = 21
Ave special neighs/atom = 0
Neighbor list builds = 273
Dangerous builds = 0
fix energies all ave/time 1 20000 20000 c_myKE c_myPE #file ave.out
thermo 2000
run 35000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 6.428 | 6.428 | 6.428 Mbytes
Step Temp E_pair E_mol TotEng Press
5000 9.3726166 -55.076514 0 -54.030985 342.43571
6000 9.6911866 -55.129244 0 -54.048177 329.72537
8000 9.7296551 -55.101417 0 -54.016059 337.46595
10000 10.098808 -55.083292 0 -53.956755 343.4122
12000 10.114344 -55.090905 0 -53.962635 341.3438
14000 10.230012 -55.085051 0 -53.943878 342.45237
16000 9.5989709 -55.090733 0 -54.019954 339.07584
18000 10.016071 -55.030131 0 -53.912824 358.79514
20000 9.7197057 -55.104072 0 -54.019824 335.89619
22000 9.959647 -55.152019 0 -54.041005 323.05805
24000 10.075138 -55.115242 0 -53.991345 334.76239
26000 10.227192 -55.125275 0 -53.984416 332.10131
28000 10.177109 -55.107097 0 -53.971825 337.32979
30000 9.521036 -55.099011 0 -54.036925 337.10716
32000 10.265633 -55.077016 0 -53.93187 346.01018
34000 10.173978 -55.097068 0 -53.962146 339.63562
36000 9.6032778 -55.152202 0 -54.080942 321.61646
38000 9.8802995 -55.048407 0 -53.946245 351.82506
40000 10.372288 -55.087634 0 -53.93059 343.34304
Loop time of 17.867 on 4 procs for 35000 steps with 864 atoms
Performance: 16925.013 ns/day, 0.001 hours/ns, 1958.914 timesteps/s, 1.693 Matom-step/s
65.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.0932 | 5.1683 | 5.2256 | 2.5 | 28.93
Bond | 0.0044473 | 0.0048347 | 0.0058137 | 0.8 | 0.03
Neigh | 0.85262 | 0.8601 | 0.87438 | 0.9 | 4.81
Comm | 6.8164 | 6.8981 | 6.9859 | 2.6 | 38.61
Output | 0.0046884 | 0.0047093 | 0.0047322 | 0.0 | 0.03
Modify | 3.4107 | 3.4186 | 3.4248 | 0.3 | 19.13
Other | | 1.512 | | | 8.47
Nlocal: 216 ave 222 max 210 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 905.5 ave 911 max 899 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Neighs: 4535.75 ave 4837 max 4218 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Total # of neighbors = 18143
Ave neighs/atom = 20.998843
Ave special neighs/atom = 0
Neighbor list builds = 2140
Dangerous builds = 0
Total wall time: 0:00:21