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update reference log files for lj/relres

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Axel Kohlmeyer
2021-03-05 17:54:00 -05:00
parent b62a208f4a
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examples/relres/README
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The input script in.22DMH.relres provides an example of a molecular
simulation using the Relative Resolution (RelRes) algorithm. In this
example, 2,2-Dimethylhexane is the molecule in focus. This script
uses the data file Data.22DMH.in.relres, which consists of 8000
The input script in.22DMH.relres provides an example of a molecular
simulation using the Relative Resolution (RelRes) algorithm. In this
example, 2,2-Dimethylhexane is the molecule in focus. This script
uses the data file Data.22DMH.in.relres, which consists of 8000
molecules. It also generates the RelRes potential for the selected atom types.
The input script in.22DMH.respa demonstrates the use of the lj/relres pair
style with r-RESPA applying multi-timestepping between the appropriate atom
style with r-RESPA applying multi-timestepping between the appropriate atom
types (using a hybrid pair style configuration).
The input script in.22DMH.real demonstrates the use of the lj/relres pair
style with real units (the data file Data.22DMH.in.real). It performs
a set of molecular simulations with different switching distances. Finally,
it performs a molecular simulation with the lj/smooth pair style, allowing
comparison of the thermal characteristics and the running time between the
style with real units (the data file Data.22DMH.in.real). It performs
a set of molecular simulations with different switching distances. Finally,
it performs a molecular simulation with the lj/smooth pair style, allowing
comparison of the thermal characteristics and the running time between the
RelRes and the conventional approach.

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examples/relres/log.05Mar21.22DMH.real.g++.1 Normal file
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LAMMPS (10 Feb 2021)
using 1 OpenMP thread(s) per MPI task
# Example: use of lj/relres for simulation of 2,2-dimethylhexane: C3H7-C5H11
# with various Rso setting as well as run of reference system for time comparison (real units)
# The first run writes restart file that is used by all subsequent runs.
# Run relres with Rso=6.25
units real
atom_style molecular
boundary p p p
dielectric 1
special_bonds lj/coul 0.0 0.0 0.5
bond_style harmonic
angle_style harmonic
dihedral_style fourier
pair_style lj/relres 5.75 6.25 12.0 14.0
read_data Data.22DMH.in.real
Reading data file ...
orthogonal box = (3.7421629 3.7421629 3.7421629) to (68.257837 68.257837 68.257837)
1 by 1 by 1 MPI processor grid
reading atoms ...
8000 atoms
reading velocities ...
8000 velocities
scanning bonds ...
4 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
3 = max dihedrals/atom
reading bonds ...
7000 bonds
reading angles ...
9000 angles
reading dihedrals ...
5000 dihedrals
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0.5
special bond factors coul: 0 0 0.5
4 = max # of 1-2 neighbors
4 = max # of 1-3 neighbors
5 = max # of 1-4 neighbors
7 = max # of special neighbors
special bonds CPU = 0.003 seconds
read_data CPU = 0.036 seconds
pair_coeff 6 6 0.175 3.905 0.0 0.0
pair_coeff 4 4 0.118 3.905 0.0 0.0
pair_coeff 2 2 0.118 3.905 1.2218 3.905
pair_coeff 5 5 0.145 3.960 0.0 0.0
pair_coeff 3 3 0.118 3.905 0.0 0.0
pair_coeff 1 1 0.05 3.8 2.9128 3.9309
pair_modify shift yes
neighbor 2.0 bin
neigh_modify every 2 delay 4 check yes
timestep 1.0
thermo 100
thermo_style custom step temp press pe ke etotal epair emol vol
fix 2 all nvt temp 290 290 2.0e+02
run 1000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- Pair style lj/relres: doi:10.1021/acs.jctc.0c01003
@Article{Chaimovich1,
author = {A. Chaimovich, C. Peter, K. Kremer},
title = {Relative resolution: A hybrid formalism for fluid mixtures},
journal = {J.~Chem.~Phys.},
year = 2015,
volume = 143,
pages = {243107}
@Article{Chaimovich2,
author = {M. Chaimovich, A. Chaimovich},
title = {Relative Resolution: A Computationally Efficient Implementation in LAMMPS},
journal = {J.~Chem.~Theory~Comput.},
year = 2021,
volume = 17,
pages = {1045--1059}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 2 steps, delay 4 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 16
ghost atom cutoff = 16
binsize = 8, bins = 9 9 9
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/relres, 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) = 20.01 | 20.01 | 20.01 Mbytes
Step Temp Press PotEng KinEng TotEng E_pair E_mol Volume
0 286.85653 -328.51562 3703.8924 6839.6636 10543.556 -4875.3137 8579.2062 268531.8
100 293.231 -55.62132 3520.4874 6991.6533 10512.141 -4797.2633 8317.7507 268531.8
200 292.73476 332.40528 3456.3029 6979.8212 10436.124 -4914.7261 8371.0291 268531.8
300 292.56511 221.98408 3380.7472 6975.7762 10356.523 -4936.5552 8317.3024 268531.8
400 288.42948 117.72433 3428.113 6877.1681 10305.281 -4887.6852 8315.7982 268531.8
500 289.20503 -238.73381 3373.758 6895.6601 10269.418 -4947.3214 8321.0795 268531.8
600 292.02137 74.370782 3263.4324 6962.8115 10226.244 -4948.3906 8211.823 268531.8
700 290.20603 475.24398 3260.0754 6919.5273 10179.603 -4931.4093 8191.4846 268531.8
800 293.12504 175.54324 3156.6048 6989.1268 10145.732 -5006.7161 8163.3209 268531.8
900 287.78433 63.785361 3251.5393 6861.7855 10113.325 -5029.094 8280.6333 268531.8
1000 290.11974 -101.34839 3183.4817 6917.47 10100.952 -5002.9413 8186.423 268531.8
Loop time of 6.05162 on 1 procs for 1000 steps with 8000 atoms
Performance: 14.277 ns/day, 1.681 hours/ns, 165.245 timesteps/s
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.7637 | 4.7637 | 4.7637 | 0.0 | 78.72
Bond | 0.693 | 0.693 | 0.693 | 0.0 | 11.45
Neigh | 0.41311 | 0.41311 | 0.41311 | 0.0 | 6.83
Comm | 0.070843 | 0.070843 | 0.070843 | 0.0 | 1.17
Output | 0.00045886 | 0.00045886 | 0.00045886 | 0.0 | 0.01
Modify | 0.084814 | 0.084814 | 0.084814 | 0.0 | 1.40
Other | | 0.02564 | | | 0.42
Nlocal: 8000.00 ave 8000 max 8000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 18934.0 ave 18934 max 18934 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 371920.0 ave 371920 max 371920 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 371920
Ave neighs/atom = 46.490000
Ave special neighs/atom = 5.2500000
Neighbor list builds = 13
Dangerous builds = 0
write_restart restart.relres.real
System init for write_restart ...
# Run relres with Rso=7.25
clear
using 1 OpenMP thread(s) per MPI task
read_restart restart.relres.real
Reading restart file ...
restart file = 10 Feb 2021, LAMMPS = 10 Feb 2021
restoring atom style molecular from restart
orthogonal box = (3.7421629 3.7421629 3.7421629) to (68.257837 68.257837 68.257837)
1 by 1 by 1 MPI processor grid
restoring pair style lj/relres from restart
restoring bond style harmonic from restart
restoring angle style harmonic from restart
restoring dihedral style fourier from restart
8000 atoms
7000 bonds
9000 angles
5000 dihedrals
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0.5
special bond factors coul: 0 0 0.5
4 = max # of 1-2 neighbors
4 = max # of 1-3 neighbors
5 = max # of 1-4 neighbors
7 = max # of special neighbors
special bonds CPU = 0.002 seconds
read_restart CPU = 0.004 seconds
pair_style lj/relres 6.75 7.25 12.0 14.0
pair_coeff 6 6 0.175 3.905 0.0 0.0
pair_coeff 4 4 0.118 3.905 0.0 0.0
pair_coeff 2 2 0.118 3.905 1.2218 3.905
pair_coeff 5 5 0.145 3.960 0.0 0.0
pair_coeff 3 3 0.118 3.905 0.0 0.0
pair_coeff 1 1 0.05 3.8 2.9128 3.9309
pair_modify shift yes
neighbor 2.0 bin
neigh_modify every 2 delay 4 check yes
timestep 1.0
thermo 100
thermo_style custom step temp press pe ke etotal epair emol vol
fix 2 all nvt temp 290 290 2.0e+02
Resetting global fix info from restart file:
fix style: nvt, fix ID: 2
run 1000
All restart file global fix info was re-assigned
Neighbor list info ...
update every 2 steps, delay 4 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 16
ghost atom cutoff = 16
binsize = 8, bins = 9 9 9
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/relres, 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) = 20.51 | 20.51 | 20.51 Mbytes
Step Temp Press PotEng KinEng TotEng E_pair E_mol Volume
1000 290.11974 21.86402 3334.7257 6917.47 10252.196 -4851.6973 8186.423 268531.8
1100 289.71937 460.00291 3365.0978 6907.9236 10273.021 -4881.5513 8246.6491 268531.8
1200 293.0828 194.76483 3348.6267 6988.1197 10336.746 -4743.4894 8092.1162 268531.8
1300 291.27785 153.93026 3496.2858 6945.0834 10441.369 -4753.3325 8249.6183 268531.8
1400 292.69435 -51.690836 3516.6743 6978.8575 10495.532 -4774.0701 8290.7445 268531.8
1500 290.0279 149.43706 3578.8283 6915.2801 10494.108 -4815.5857 8394.414 268531.8
1600 292.89473 -109.05125 3487.6652 6983.6354 10471.301 -4839.1407 8326.8059 268531.8
1700 290.99802 -146.06465 3496.48 6938.4111 10434.891 -4868.0031 8364.4831 268531.8
1800 286.48455 -45.580207 3550.2611 6830.7943 10381.055 -4766.3336 8316.5947 268531.8
1900 287.0735 -157.60878 3488.4248 6844.8368 10333.262 -4853.6992 8342.124 268531.8
2000 287.38046 -429.32757 3435.8336 6852.1558 10287.989 -4878.4345 8314.2681 268531.8
Loop time of 7.46943 on 1 procs for 1000 steps with 8000 atoms
Performance: 11.567 ns/day, 2.075 hours/ns, 133.879 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 | 6.1145 | 6.1145 | 6.1145 | 0.0 | 81.86
Bond | 0.71392 | 0.71392 | 0.71392 | 0.0 | 9.56
Neigh | 0.45677 | 0.45677 | 0.45677 | 0.0 | 6.12
Comm | 0.072404 | 0.072404 | 0.072404 | 0.0 | 0.97
Output | 0.00036481 | 0.00036481 | 0.00036481 | 0.0 | 0.00
Modify | 0.085956 | 0.085956 | 0.085956 | 0.0 | 1.15
Other | | 0.02552 | | | 0.34
Nlocal: 8000.00 ave 8000 max 8000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 18846.0 ave 18846 max 18846 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 475557.0 ave 475557 max 475557 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 475557
Ave neighs/atom = 59.444625
Ave special neighs/atom = 5.2500000
Neighbor list builds = 14
Dangerous builds = 0
# Run relres with mixed Rso: 6.25 for C3H7 group and 7.25 for C5H11 group
clear
using 1 OpenMP thread(s) per MPI task
read_restart restart.relres.real
Reading restart file ...
restart file = 10 Feb 2021, LAMMPS = 10 Feb 2021
restoring atom style molecular from restart
orthogonal box = (3.7421629 3.7421629 3.7421629) to (68.257837 68.257837 68.257837)
1 by 1 by 1 MPI processor grid
restoring pair style lj/relres from restart
restoring bond style harmonic from restart
restoring angle style harmonic from restart
restoring dihedral style fourier from restart
8000 atoms
7000 bonds
9000 angles
5000 dihedrals
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0.5
special bond factors coul: 0 0 0.5
4 = max # of 1-2 neighbors
4 = max # of 1-3 neighbors
5 = max # of 1-4 neighbors
7 = max # of special neighbors
special bonds CPU = 0.002 seconds
read_restart CPU = 0.004 seconds
pair_style lj/relres 6.75 7.25 12.0 14.0
pair_coeff 6 6 0.175 3.905 0.0 0.0 5.75 6.25 12.0 14.0
pair_coeff 4 4 0.118 3.905 0.0 0.0 5.75 6.25 12.0 14.0
pair_coeff 2 2 0.118 3.905 1.2218 3.905 5.75 6.25 12.0 14.0
pair_coeff 5 5 0.145 3.960 0.0 0.0
pair_coeff 3 3 0.118 3.905 0.0 0.0
pair_coeff 1 1 0.05 3.8 2.9128 3.9309
pair_modify shift yes
neighbor 2.0 bin
neigh_modify every 2 delay 4 check yes
timestep 1.0
thermo 100
thermo_style custom step temp press pe ke etotal epair emol vol
fix 2 all nvt temp 290 290 2.0e+02
Resetting global fix info from restart file:
fix style: nvt, fix ID: 2
run 1000
All restart file global fix info was re-assigned
Neighbor list info ...
update every 2 steps, delay 4 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 16
ghost atom cutoff = 16
binsize = 8, bins = 9 9 9
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/relres, 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) = 20.51 | 20.51 | 20.51 Mbytes
Step Temp Press PotEng KinEng TotEng E_pair E_mol Volume
1000 290.11974 54.754001 3314.0966 6917.47 10231.567 -4872.3264 8186.423 268531.8
1100 289.78217 480.37221 3342.8765 6909.4211 10252.298 -4900.7266 8243.6032 268531.8
1200 293.25523 188.46596 3322.6257 6992.2308 10314.857 -4771.3485 8093.9742 268531.8
1300 291.59734 146.50303 3465.2113 6952.701 10417.912 -4782.9861 8248.1974 268531.8
1400 292.71873 -40.372074 3491.747 6979.4389 10471.186 -4790.7124 8282.4594 268531.8
1500 290.60378 120.25863 3539.5538 6929.0112 10468.565 -4849.9813 8389.5351 268531.8
1600 293.21218 -143.75501 3452.9516 6991.2046 10444.156 -4885.0192 8337.9708 268531.8
1700 291.02865 -207.34728 3465.4131 6939.1416 10404.555 -4887.363 8352.7761 268531.8
1800 286.00091 -91.017961 3530.3422 6819.2625 10349.605 -4807.6624 8338.0046 268531.8
1900 286.3006 -145.399 3485.1695 6826.4082 10311.578 -4848.263 8333.4325 268531.8
2000 288.43931 -469.99712 3409.0906 6877.4025 10286.493 -4905.9002 8314.9907 268531.8
Loop time of 6.78592 on 1 procs for 1000 steps with 8000 atoms
Performance: 12.732 ns/day, 1.885 hours/ns, 147.364 timesteps/s
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.4637 | 5.4637 | 5.4637 | 0.0 | 80.52
Bond | 0.68994 | 0.68994 | 0.68994 | 0.0 | 10.17
Neigh | 0.45166 | 0.45166 | 0.45166 | 0.0 | 6.66
Comm | 0.070376 | 0.070376 | 0.070376 | 0.0 | 1.04
Output | 0.000405 | 0.000405 | 0.000405 | 0.0 | 0.01
Modify | 0.084545 | 0.084545 | 0.084545 | 0.0 | 1.25
Other | | 0.02527 | | | 0.37
Nlocal: 8000.00 ave 8000 max 8000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 18820.0 ave 18820 max 18820 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 434269.0 ave 434269 max 434269 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 434269
Ave neighs/atom = 54.283625
Ave special neighs/atom = 5.2500000
Neighbor list builds = 14
Dangerous builds = 0
# Run reference system with lj/smooth
clear
using 1 OpenMP thread(s) per MPI task
read_restart restart.relres.real
Reading restart file ...
restart file = 10 Feb 2021, LAMMPS = 10 Feb 2021
restoring atom style molecular from restart
orthogonal box = (3.7421629 3.7421629 3.7421629) to (68.257837 68.257837 68.257837)
1 by 1 by 1 MPI processor grid
restoring pair style lj/relres from restart
restoring bond style harmonic from restart
restoring angle style harmonic from restart
restoring dihedral style fourier from restart
8000 atoms
7000 bonds
9000 angles
5000 dihedrals
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0.5
special bond factors coul: 0 0 0.5
4 = max # of 1-2 neighbors
4 = max # of 1-3 neighbors
5 = max # of 1-4 neighbors
7 = max # of special neighbors
special bonds CPU = 0.002 seconds
read_restart CPU = 0.004 seconds
pair_style lj/smooth 12.0 14.0
pair_coeff 6 6 0.175 3.905
pair_coeff 4 4 0.118 3.905
pair_coeff 2 2 0.118 3.905
pair_coeff 5 5 0.145 3.960
pair_coeff 3 3 0.118 3.905
pair_coeff 1 1 0.05 3.8
pair_modify shift yes
neighbor 2.0 bin
neigh_modify every 2 delay 4 check yes
timestep 1.0
thermo 100
thermo_style custom step temp press pe ke etotal epair emol vol
fix 2 all nvt temp 290 290 2.0e+02
Resetting global fix info from restart file:
fix style: nvt, fix ID: 2
run 1000
All restart file global fix info was re-assigned
Neighbor list info ...
update every 2 steps, delay 4 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 16
ghost atom cutoff = 16
binsize = 8, bins = 9 9 9
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/smooth, 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) = 26.62 | 26.62 | 26.62 Mbytes
Step Temp Press PotEng KinEng TotEng E_pair E_mol Volume
1000 290.11974 -80.648214 3258.0256 6917.47 10175.496 -4928.3973 8186.423 268531.8
1100 289.70919 358.20314 3288.412 6907.6811 10196.093 -4959.5166 8247.9285 268531.8
1200 292.84488 96.692992 3277.1296 6982.4468 10259.576 -4818.7374 8095.867 268531.8
1300 291.07262 65.629153 3425.4662 6940.1899 10365.656 -4828.0862 8253.5524 268531.8
1400 292.39722 -113.07286 3448.8088 6971.773 10420.582 -4841.3586 8290.1674 268531.8
1500 289.80998 90.176596 3510.6526 6910.0843 10420.737 -4884.6145 8395.2671 268531.8
1600 292.48452 -180.26543 3426.6967 6973.8544 10400.551 -4903.46 8330.1567 268531.8
1700 291.32152 -220.54923 3421.802 6946.1246 10367.927 -4946.101 8367.9031 268531.8
1800 286.77292 -101.26406 3475.3166 6837.6701 10312.987 -4830.565 8305.8816 268531.8
1900 286.6849 -161.65289 3428.0457 6835.5713 10263.617 -4909.5924 8337.6381 268531.8
2000 287.3785 -477.01298 3367.9719 6852.1091 10220.081 -4962.7001 8330.6719 268531.8
Loop time of 25.7415 on 1 procs for 1000 steps with 8000 atoms
Performance: 3.356 ns/day, 7.150 hours/ns, 38.848 timesteps/s
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 24.253 | 24.253 | 24.253 | 0.0 | 94.22
Bond | 0.72224 | 0.72224 | 0.72224 | 0.0 | 2.81
Neigh | 0.57723 | 0.57723 | 0.57723 | 0.0 | 2.24
Comm | 0.076624 | 0.076624 | 0.076624 | 0.0 | 0.30
Output | 0.00035693 | 0.00035693 | 0.00035693 | 0.0 | 0.00
Modify | 0.087599 | 0.087599 | 0.087599 | 0.0 | 0.34
Other | | 0.02479 | | | 0.10
Nlocal: 8000.00 ave 8000 max 8000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 18804.0 ave 18804 max 18804 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2.02600e+06 ave 2.026e+06 max 2.026e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2026005
Ave neighs/atom = 253.25063
Ave special neighs/atom = 5.2500000
Neighbor list builds = 13
Dangerous builds = 0
Total wall time: 0:00:46

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LAMMPS (10 Feb 2021)
using 1 OpenMP thread(s) per MPI task
# Example: use of lj/relres for simulation of 2,2-dimethylhexane: C3H7-C5H11
# with various Rso setting as well as run of reference system for time comparison (real units)
# The first run writes restart file that is used by all subsequent runs.
# Run relres with Rso=6.25
units real
atom_style molecular
boundary p p p
dielectric 1
special_bonds lj/coul 0.0 0.0 0.5
bond_style harmonic
angle_style harmonic
dihedral_style fourier
pair_style lj/relres 5.75 6.25 12.0 14.0
read_data Data.22DMH.in.real
Reading data file ...
orthogonal box = (3.7421629 3.7421629 3.7421629) to (68.257837 68.257837 68.257837)
2 by 1 by 2 MPI processor grid
reading atoms ...
8000 atoms
reading velocities ...
8000 velocities
scanning bonds ...
4 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
3 = max dihedrals/atom
reading bonds ...
7000 bonds
reading angles ...
9000 angles
reading dihedrals ...
5000 dihedrals
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0.5
special bond factors coul: 0 0 0.5
4 = max # of 1-2 neighbors
4 = max # of 1-3 neighbors
5 = max # of 1-4 neighbors
7 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.035 seconds
pair_coeff 6 6 0.175 3.905 0.0 0.0
pair_coeff 4 4 0.118 3.905 0.0 0.0
pair_coeff 2 2 0.118 3.905 1.2218 3.905
pair_coeff 5 5 0.145 3.960 0.0 0.0
pair_coeff 3 3 0.118 3.905 0.0 0.0
pair_coeff 1 1 0.05 3.8 2.9128 3.9309
pair_modify shift yes
neighbor 2.0 bin
neigh_modify every 2 delay 4 check yes
timestep 1.0
thermo 100
thermo_style custom step temp press pe ke etotal epair emol vol
fix 2 all nvt temp 290 290 2.0e+02
run 1000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- Pair style lj/relres: doi:10.1021/acs.jctc.0c01003
@Article{Chaimovich1,
author = {A. Chaimovich, C. Peter, K. Kremer},
title = {Relative resolution: A hybrid formalism for fluid mixtures},
journal = {J.~Chem.~Phys.},
year = 2015,
volume = 143,
pages = {243107}
@Article{Chaimovich2,
author = {M. Chaimovich, A. Chaimovich},
title = {Relative Resolution: A Computationally Efficient Implementation in LAMMPS},
journal = {J.~Chem.~Theory~Comput.},
year = 2021,
volume = 17,
pages = {1045--1059}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 2 steps, delay 4 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 16
ghost atom cutoff = 16
binsize = 8, bins = 9 9 9
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/relres, 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) = 9.953 | 9.953 | 9.953 Mbytes
Step Temp Press PotEng KinEng TotEng E_pair E_mol Volume
0 286.85653 -328.51562 3703.8924 6839.6636 10543.556 -4875.3137 8579.2062 268531.8
100 293.231 -55.62132 3520.4874 6991.6533 10512.141 -4797.2633 8317.7507 268531.8
200 292.73476 332.40528 3456.3029 6979.8212 10436.124 -4914.7261 8371.0291 268531.8
300 292.56511 221.98408 3380.7472 6975.7762 10356.523 -4936.5552 8317.3024 268531.8
400 288.42948 117.72433 3428.113 6877.1681 10305.281 -4887.6852 8315.7982 268531.8
500 289.20503 -238.73381 3373.758 6895.6601 10269.418 -4947.3214 8321.0795 268531.8
600 292.02137 74.370782 3263.4324 6962.8115 10226.244 -4948.3906 8211.823 268531.8
700 290.20603 475.24398 3260.0754 6919.5273 10179.603 -4931.4093 8191.4846 268531.8
800 293.12504 175.54324 3156.6048 6989.1268 10145.732 -5006.7161 8163.3209 268531.8
900 287.78433 63.785361 3251.5393 6861.7855 10113.325 -5029.094 8280.6333 268531.8
1000 290.11974 -101.34839 3183.4817 6917.47 10100.952 -5002.9413 8186.423 268531.8
Loop time of 2.12445 on 4 procs for 1000 steps with 8000 atoms
Performance: 40.669 ns/day, 0.590 hours/ns, 470.709 timesteps/s
91.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.2517 | 1.3228 | 1.4636 | 7.2 | 62.27
Bond | 0.18406 | 0.19356 | 0.20925 | 2.1 | 9.11
Neigh | 0.12468 | 0.125 | 0.12534 | 0.1 | 5.88
Comm | 0.25384 | 0.40233 | 0.4919 | 14.1 | 18.94
Output | 0.00034203 | 0.00061893 | 0.00088527 | 0.0 | 0.03
Modify | 0.052326 | 0.059507 | 0.066224 | 2.6 | 2.80
Other | | 0.02066 | | | 0.97
Nlocal: 2000.00 ave 2031 max 1964 min
Histogram: 1 0 0 0 1 0 0 1 0 1
Nghost: 9898.50 ave 9926 max 9869 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Neighs: 92980.0 ave 94819 max 90517 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Total # of neighbors = 371920
Ave neighs/atom = 46.490000
Ave special neighs/atom = 5.2500000
Neighbor list builds = 13
Dangerous builds = 0
write_restart restart.relres.real
System init for write_restart ...
# Run relres with Rso=7.25
clear
using 1 OpenMP thread(s) per MPI task
read_restart restart.relres.real
Reading restart file ...
restart file = 10 Feb 2021, LAMMPS = 10 Feb 2021
restoring atom style molecular from restart
orthogonal box = (3.7421629 3.7421629 3.7421629) to (68.257837 68.257837 68.257837)
2 by 1 by 2 MPI processor grid
restoring pair style lj/relres from restart
restoring bond style harmonic from restart
restoring angle style harmonic from restart
restoring dihedral style fourier from restart
8000 atoms
7000 bonds
9000 angles
5000 dihedrals
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0.5
special bond factors coul: 0 0 0.5
4 = max # of 1-2 neighbors
4 = max # of 1-3 neighbors
5 = max # of 1-4 neighbors
7 = max # of special neighbors
special bonds CPU = 0.002 seconds
read_restart CPU = 0.005 seconds
pair_style lj/relres 6.75 7.25 12.0 14.0
pair_coeff 6 6 0.175 3.905 0.0 0.0
pair_coeff 4 4 0.118 3.905 0.0 0.0
pair_coeff 2 2 0.118 3.905 1.2218 3.905
pair_coeff 5 5 0.145 3.960 0.0 0.0
pair_coeff 3 3 0.118 3.905 0.0 0.0
pair_coeff 1 1 0.05 3.8 2.9128 3.9309
pair_modify shift yes
neighbor 2.0 bin
neigh_modify every 2 delay 4 check yes
timestep 1.0
thermo 100
thermo_style custom step temp press pe ke etotal epair emol vol
fix 2 all nvt temp 290 290 2.0e+02
Resetting global fix info from restart file:
fix style: nvt, fix ID: 2
run 1000
All restart file global fix info was re-assigned
Neighbor list info ...
update every 2 steps, delay 4 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 16
ghost atom cutoff = 16
binsize = 8, bins = 9 9 9
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/relres, 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) = 10.34 | 10.34 | 10.34 Mbytes
Step Temp Press PotEng KinEng TotEng E_pair E_mol Volume
1000 290.11974 21.86402 3334.7257 6917.47 10252.196 -4851.6973 8186.423 268531.8
1100 289.71937 460.00291 3365.0978 6907.9236 10273.021 -4881.5513 8246.6491 268531.8
1200 293.0828 194.76483 3348.6267 6988.1197 10336.746 -4743.4894 8092.1162 268531.8
1300 291.27785 153.93026 3496.2858 6945.0834 10441.369 -4753.3325 8249.6183 268531.8
1400 292.69435 -51.690836 3516.6743 6978.8575 10495.532 -4774.0701 8290.7445 268531.8
1500 290.0279 149.43706 3578.8283 6915.2801 10494.108 -4815.5857 8394.414 268531.8
1600 292.89473 -109.05125 3487.6652 6983.6354 10471.301 -4839.1407 8326.8059 268531.8
1700 290.99802 -146.06465 3496.48 6938.4111 10434.891 -4868.0031 8364.4831 268531.8
1800 286.48455 -45.580207 3550.2611 6830.7943 10381.055 -4766.3336 8316.5947 268531.8
1900 287.0735 -157.60878 3488.4248 6844.8368 10333.262 -4853.6992 8342.124 268531.8
2000 287.38046 -429.32757 3435.8336 6852.1558 10287.989 -4878.4345 8314.2681 268531.8
Loop time of 2.6513 on 4 procs for 1000 steps with 8000 atoms
Performance: 32.588 ns/day, 0.736 hours/ns, 377.174 timesteps/s
89.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.5783 | 1.6371 | 1.7079 | 3.7 | 61.75
Bond | 0.18196 | 0.19132 | 0.20276 | 1.7 | 7.22
Neigh | 0.14093 | 0.14128 | 0.14156 | 0.1 | 5.33
Comm | 0.50333 | 0.5809 | 0.64199 | 6.6 | 21.91
Output | 0.00023452 | 0.00040924 | 0.00063279 | 0.0 | 0.02
Modify | 0.066524 | 0.076747 | 0.084331 | 2.5 | 2.89
Other | | 0.02354 | | | 0.89
Nlocal: 2000.00 ave 2009 max 1981 min
Histogram: 1 0 0 0 0 0 0 1 0 2
Nghost: 9892.50 ave 9923 max 9868 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Neighs: 118889.0 ave 120387 max 117552 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Total # of neighbors = 475557
Ave neighs/atom = 59.444625
Ave special neighs/atom = 5.2500000
Neighbor list builds = 14
Dangerous builds = 0
# Run relres with mixed Rso: 6.25 for C3H7 group and 7.25 for C5H11 group
clear
using 1 OpenMP thread(s) per MPI task
read_restart restart.relres.real
Reading restart file ...
restart file = 10 Feb 2021, LAMMPS = 10 Feb 2021
restoring atom style molecular from restart
orthogonal box = (3.7421629 3.7421629 3.7421629) to (68.257837 68.257837 68.257837)
2 by 1 by 2 MPI processor grid
restoring pair style lj/relres from restart
restoring bond style harmonic from restart
restoring angle style harmonic from restart
restoring dihedral style fourier from restart
8000 atoms
7000 bonds
9000 angles
5000 dihedrals
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0.5
special bond factors coul: 0 0 0.5
4 = max # of 1-2 neighbors
4 = max # of 1-3 neighbors
5 = max # of 1-4 neighbors
7 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_restart CPU = 0.004 seconds
pair_style lj/relres 6.75 7.25 12.0 14.0
pair_coeff 6 6 0.175 3.905 0.0 0.0 5.75 6.25 12.0 14.0
pair_coeff 4 4 0.118 3.905 0.0 0.0 5.75 6.25 12.0 14.0
pair_coeff 2 2 0.118 3.905 1.2218 3.905 5.75 6.25 12.0 14.0
pair_coeff 5 5 0.145 3.960 0.0 0.0
pair_coeff 3 3 0.118 3.905 0.0 0.0
pair_coeff 1 1 0.05 3.8 2.9128 3.9309
pair_modify shift yes
neighbor 2.0 bin
neigh_modify every 2 delay 4 check yes
timestep 1.0
thermo 100
thermo_style custom step temp press pe ke etotal epair emol vol
fix 2 all nvt temp 290 290 2.0e+02
Resetting global fix info from restart file:
fix style: nvt, fix ID: 2
run 1000
All restart file global fix info was re-assigned
Neighbor list info ...
update every 2 steps, delay 4 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 16
ghost atom cutoff = 16
binsize = 8, bins = 9 9 9
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/relres, 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) = 10.34 | 10.34 | 10.34 Mbytes
Step Temp Press PotEng KinEng TotEng E_pair E_mol Volume
1000 290.11974 54.754001 3314.0966 6917.47 10231.567 -4872.3264 8186.423 268531.8
1100 289.78217 480.37221 3342.8765 6909.4211 10252.298 -4900.7266 8243.6032 268531.8
1200 293.25523 188.46596 3322.6257 6992.2308 10314.857 -4771.3485 8093.9742 268531.8
1300 291.59734 146.50303 3465.2113 6952.701 10417.912 -4782.9861 8248.1974 268531.8
1400 292.71873 -40.372074 3491.747 6979.4389 10471.186 -4790.7124 8282.4594 268531.8
1500 290.60378 120.25863 3539.5538 6929.0112 10468.565 -4849.9813 8389.5351 268531.8
1600 293.21218 -143.75501 3452.9516 6991.2046 10444.156 -4885.0192 8337.9708 268531.8
1700 291.02865 -207.34728 3465.4131 6939.1416 10404.555 -4887.363 8352.7761 268531.8
1800 286.00091 -91.017961 3530.3422 6819.2625 10349.605 -4807.6624 8338.0046 268531.8
1900 286.3006 -145.399 3485.1695 6826.4082 10311.578 -4848.263 8333.4325 268531.8
2000 288.43931 -469.99712 3409.0906 6877.4025 10286.493 -4905.9002 8314.9907 268531.8
Loop time of 2.32221 on 4 procs for 1000 steps with 8000 atoms
Performance: 37.206 ns/day, 0.645 hours/ns, 430.624 timesteps/s
90.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.4451 | 1.5022 | 1.555 | 3.7 | 64.69
Bond | 0.18307 | 0.19206 | 0.20526 | 2.0 | 8.27
Neigh | 0.12827 | 0.12956 | 0.13074 | 0.3 | 5.58
Comm | 0.36752 | 0.42006 | 0.48825 | 8.1 | 18.09
Output | 0.00022658 | 0.00025297 | 0.0003292 | 0.0 | 0.01
Modify | 0.05223 | 0.057658 | 0.063373 | 2.1 | 2.48
Other | | 0.02044 | | | 0.88
Nlocal: 2000.00 ave 2016 max 1981 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Nghost: 9878.25 ave 9891 max 9868 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Neighs: 108567.0 ave 110532 max 107467 min
Histogram: 1 1 1 0 0 0 0 0 0 1
Total # of neighbors = 434269
Ave neighs/atom = 54.283625
Ave special neighs/atom = 5.2500000
Neighbor list builds = 14
Dangerous builds = 0
# Run reference system with lj/smooth
clear
using 1 OpenMP thread(s) per MPI task
read_restart restart.relres.real
Reading restart file ...
restart file = 10 Feb 2021, LAMMPS = 10 Feb 2021
restoring atom style molecular from restart
orthogonal box = (3.7421629 3.7421629 3.7421629) to (68.257837 68.257837 68.257837)
2 by 1 by 2 MPI processor grid
restoring pair style lj/relres from restart
restoring bond style harmonic from restart
restoring angle style harmonic from restart
restoring dihedral style fourier from restart
8000 atoms
7000 bonds
9000 angles
5000 dihedrals
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0.5
special bond factors coul: 0 0 0.5
4 = max # of 1-2 neighbors
4 = max # of 1-3 neighbors
5 = max # of 1-4 neighbors
7 = max # of special neighbors
special bonds CPU = 0.004 seconds
read_restart CPU = 0.007 seconds
pair_style lj/smooth 12.0 14.0
pair_coeff 6 6 0.175 3.905
pair_coeff 4 4 0.118 3.905
pair_coeff 2 2 0.118 3.905
pair_coeff 5 5 0.145 3.960
pair_coeff 3 3 0.118 3.905
pair_coeff 1 1 0.05 3.8
pair_modify shift yes
neighbor 2.0 bin
neigh_modify every 2 delay 4 check yes
timestep 1.0
thermo 100
thermo_style custom step temp press pe ke etotal epair emol vol
fix 2 all nvt temp 290 290 2.0e+02
Resetting global fix info from restart file:
fix style: nvt, fix ID: 2
run 1000
All restart file global fix info was re-assigned
Neighbor list info ...
update every 2 steps, delay 4 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 16
ghost atom cutoff = 16
binsize = 8, bins = 9 9 9
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/smooth, 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) = 11.86 | 11.86 | 11.86 Mbytes
Step Temp Press PotEng KinEng TotEng E_pair E_mol Volume
1000 290.11974 -80.648214 3258.0256 6917.47 10175.496 -4928.3973 8186.423 268531.8
1100 289.70919 358.20314 3288.412 6907.6811 10196.093 -4959.5166 8247.9285 268531.8
1200 292.84488 96.692992 3277.1296 6982.4468 10259.576 -4818.7374 8095.867 268531.8
1300 291.07262 65.629153 3425.4662 6940.1899 10365.656 -4828.0862 8253.5524 268531.8
1400 292.39722 -113.07286 3448.8088 6971.773 10420.582 -4841.3586 8290.1674 268531.8
1500 289.80998 90.176596 3510.6526 6910.0843 10420.737 -4884.6145 8395.2671 268531.8
1600 292.48452 -180.26543 3426.6967 6973.8544 10400.551 -4903.46 8330.1567 268531.8
1700 291.32152 -220.54923 3421.802 6946.1246 10367.927 -4946.101 8367.9031 268531.8
1800 286.77292 -101.26406 3475.3166 6837.6701 10312.987 -4830.565 8305.8816 268531.8
1900 286.6849 -161.65289 3428.0457 6835.5713 10263.617 -4909.5924 8337.6381 268531.8
2000 287.3785 -477.01298 3367.9719 6852.1091 10220.081 -4962.7001 8330.6719 268531.8
Loop time of 7.44371 on 4 procs for 1000 steps with 8000 atoms
Performance: 11.607 ns/day, 2.068 hours/ns, 134.342 timesteps/s
92.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 6.0092 | 6.1923 | 6.5395 | 8.2 | 83.19
Bond | 0.18292 | 0.18861 | 0.19918 | 1.5 | 2.53
Neigh | 0.16826 | 0.16868 | 0.1691 | 0.1 | 2.27
Comm | 0.47602 | 0.82734 | 1.0097 | 22.7 | 11.11
Output | 0.00023062 | 0.00025561 | 0.00032727 | 0.0 | 0.00
Modify | 0.040804 | 0.047642 | 0.054462 | 3.1 | 0.64
Other | | 0.01893 | | | 0.25
Nlocal: 2000.00 ave 2015 max 1972 min
Histogram: 1 0 0 0 0 0 0 1 1 1
Nghost: 9870.50 ave 9899 max 9855 min
Histogram: 1 1 1 0 0 0 0 0 0 1
Neighs: 506501.0 ave 514030 max 499023 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Total # of neighbors = 2026005
Ave neighs/atom = 253.25063
Ave special neighs/atom = 5.2500000
Neighbor list builds = 13
Dangerous builds = 0
Total wall time: 0:00:14

67
examples/relres/log.09Feb21.22DMH.relres.g++.1 → examples/relres/log.05Mar21.22DMH.relres.g++.1
View File

@ -1,5 +1,8 @@
LAMMPS (24 Dec 2020)
LAMMPS (10 Feb 2021)
using 1 OpenMP thread(s) per MPI task
# Example: use of lj/relres for simulation of 2,2-dimethylhexane: C3H7-C5H11
# with with mixed Rso: 0.625e-9 for C3H7 group and 0.725e-9 for C5H11 group (si units)
units si
atom_style molecular
boundary p p p
@ -37,13 +40,13 @@ Finding 1-2 1-3 1-4 neighbors ...
4 = max # of 1-3 neighbors
5 = max # of 1-4 neighbors
7 = max # of special neighbors
special bonds CPU = 0.019 seconds
read_data CPU = 0.168 seconds
pair_coeff 6 6 1.21585e-21 0.3905e-9 0 0.3905e-9 0.575e-9 0.625e-9 1.2e-9 1.4e-9
pair_coeff 4 4 0.819828e-21 0.3905e-9 0 0.3905e-9 0.575e-9 0.625e-9 1.2e-9 1.4e-9
pair_coeff 2 2 0.819828e-21 0.3905e-9 8.48872E-21 0.3905E-9 0.575e-9 0.625e-9 1.2e-9 1.4e-9
pair_coeff 5 5 1.00742E-21 0.396E-9 0 0.396E-9
pair_coeff 3 3 0.819828e-21 0.3905e-9 0 0.3905e-9
special bonds CPU = 0.003 seconds
read_data CPU = 0.035 seconds
pair_coeff 6 6 1.21585e-21 0.3905e-9 0.0 0.0 0.575e-9 0.625e-9 1.2e-9 1.4e-9
pair_coeff 4 4 0.819828e-21 0.3905e-9 0.0 0.0 0.575e-9 0.625e-9 1.2e-9 1.4e-9
pair_coeff 2 2 0.819828e-21 0.3905e-9 8.48872E-21 0.3905E-9 0.575e-9 0.625e-9 1.2e-9 1.4e-9
pair_coeff 5 5 1.00742E-21 0.396E-9 0.0 0.0
pair_coeff 3 3 0.819828e-21 0.3905e-9 0.0 0.0
pair_coeff 1 1 0.347385E-21 0.38E-9 20.2372E-21 0.39309E-9
pair_modify shift yes
neighbor 2.0e-10 bin
@ -55,6 +58,31 @@ thermo_style custom step temp press pe ke etotal epair emol vol
fix 2 all nvt temp 290 290 2.0e-13
run 1000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- Pair style lj/relres: doi:10.1021/acs.jctc.0c01003
@Article{Chaimovich1,
author = {A. Chaimovich, C. Peter, K. Kremer},
title = {Relative resolution: A hybrid formalism for fluid mixtures},
journal = {J.~Chem.~Phys.},
year = 2015,
volume = 143,
pages = {243107}
@Article{Chaimovich2,
author = {M. Chaimovich, A. Chaimovich},
title = {Relative Resolution: A Computationally Efficient Implementation in LAMMPS},
journal = {J.~Chem.~Theory~Comput.},
year = 2021,
volume = 17,
pages = {1045--1059}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 2 steps, delay 4 steps, check yes
max neighbors/atom: 2000, page size: 100000
@ -80,20 +108,20 @@ Step Temp Press PotEng KinEng TotEng E_pair E_mol Volume
800 293.01243 38119194 2.3163674e-17 4.8539659e-17 7.1703333e-17 -3.3641284e-17 5.6804958e-17 2.685318e-25
900 289.1191 32514067 2.3608264e-17 4.7894701e-17 7.1502965e-17 -3.3787865e-17 5.7396129e-17 2.685318e-25
1000 292.45834 -714652.68 2.2885394e-17 4.8447871e-17 7.1333265e-17 -3.3864138e-17 5.6749532e-17 2.685318e-25
Loop time of 20.1906 on 1 procs for 1000 steps with 8000 atoms
Loop time of 6.82188 on 1 procs for 1000 steps with 8000 atoms
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 15.751 | 15.751 | 15.751 | 0.0 | 78.01
Bond | 1.7612 | 1.7612 | 1.7612 | 0.0 | 8.72
Neigh | 1.4937 | 1.4937 | 1.4937 | 0.0 | 7.40
Comm | 0.404 | 0.404 | 0.404 | 0.0 | 2.00
Output | 0.0013139 | 0.0013139 | 0.0013139 | 0.0 | 0.01
Modify | 0.72282 | 0.72282 | 0.72282 | 0.0 | 3.58
Other | | 0.05691 | | | 0.28
Pair | 5.5321 | 5.5321 | 5.5321 | 0.0 | 81.09
Bond | 0.69427 | 0.69427 | 0.69427 | 0.0 | 10.18
Neigh | 0.4138 | 0.4138 | 0.4138 | 0.0 | 6.07
Comm | 0.070615 | 0.070615 | 0.070615 | 0.0 | 1.04
Output | 0.00037602 | 0.00037602 | 0.00037602 | 0.0 | 0.01
Modify | 0.084796 | 0.084796 | 0.084796 | 0.0 | 1.24
Other | | 0.02591 | | | 0.38
Nlocal: 8000.00 ave 8000 max 8000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -111,7 +139,4 @@ Dangerous builds = 0
#pair_write 1 1 1201 r 0.2e-9 1.4e-9 potential.relres LJ11
#pair_write 2 2 1201 r 0.2e-9 1.4e-9 potential.relres LJ22
#pair_write 1 2 1201 r 0.2e-9 1.4e-9 potential.relres LJ12
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:20
Total wall time: 0:00:06

67
examples/relres/log.09Feb21.22DMH.relres.g++.4 → examples/relres/log.05Mar21.22DMH.relres.g++.4
View File

@ -1,5 +1,8 @@
LAMMPS (24 Dec 2020)
LAMMPS (10 Feb 2021)
using 1 OpenMP thread(s) per MPI task
# Example: use of lj/relres for simulation of 2,2-dimethylhexane: C3H7-C5H11
# with with mixed Rso: 0.625e-9 for C3H7 group and 0.725e-9 for C5H11 group (si units)
units si
atom_style molecular
boundary p p p
@ -37,13 +40,13 @@ Finding 1-2 1-3 1-4 neighbors ...
4 = max # of 1-3 neighbors
5 = max # of 1-4 neighbors
7 = max # of special neighbors
special bonds CPU = 0.010 seconds
read_data CPU = 0.145 seconds
pair_coeff 6 6 1.21585e-21 0.3905e-9 0 0.3905e-9 0.575e-9 0.625e-9 1.2e-9 1.4e-9
pair_coeff 4 4 0.819828e-21 0.3905e-9 0 0.3905e-9 0.575e-9 0.625e-9 1.2e-9 1.4e-9
pair_coeff 2 2 0.819828e-21 0.3905e-9 8.48872E-21 0.3905E-9 0.575e-9 0.625e-9 1.2e-9 1.4e-9
pair_coeff 5 5 1.00742E-21 0.396E-9 0 0.396E-9
pair_coeff 3 3 0.819828e-21 0.3905e-9 0 0.3905e-9
special bonds CPU = 0.001 seconds
read_data CPU = 0.037 seconds
pair_coeff 6 6 1.21585e-21 0.3905e-9 0.0 0.0 0.575e-9 0.625e-9 1.2e-9 1.4e-9
pair_coeff 4 4 0.819828e-21 0.3905e-9 0.0 0.0 0.575e-9 0.625e-9 1.2e-9 1.4e-9
pair_coeff 2 2 0.819828e-21 0.3905e-9 8.48872E-21 0.3905E-9 0.575e-9 0.625e-9 1.2e-9 1.4e-9
pair_coeff 5 5 1.00742E-21 0.396E-9 0.0 0.0
pair_coeff 3 3 0.819828e-21 0.3905e-9 0.0 0.0
pair_coeff 1 1 0.347385E-21 0.38E-9 20.2372E-21 0.39309E-9
pair_modify shift yes
neighbor 2.0e-10 bin
@ -55,6 +58,31 @@ thermo_style custom step temp press pe ke etotal epair emol vol
fix 2 all nvt temp 290 290 2.0e-13
run 1000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- Pair style lj/relres: doi:10.1021/acs.jctc.0c01003
@Article{Chaimovich1,
author = {A. Chaimovich, C. Peter, K. Kremer},
title = {Relative resolution: A hybrid formalism for fluid mixtures},
journal = {J.~Chem.~Phys.},
year = 2015,
volume = 143,
pages = {243107}
@Article{Chaimovich2,
author = {M. Chaimovich, A. Chaimovich},
title = {Relative Resolution: A Computationally Efficient Implementation in LAMMPS},
journal = {J.~Chem.~Theory~Comput.},
year = 2021,
volume = 17,
pages = {1045--1059}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 2 steps, delay 4 steps, check yes
max neighbors/atom: 2000, page size: 100000
@ -80,20 +108,20 @@ Step Temp Press PotEng KinEng TotEng E_pair E_mol Volume
800 293.01243 38119194 2.3163674e-17 4.8539659e-17 7.1703333e-17 -3.3641284e-17 5.6804958e-17 2.685318e-25
900 289.1191 32514067 2.3608264e-17 4.7894701e-17 7.1502965e-17 -3.3787865e-17 5.7396129e-17 2.685318e-25
1000 292.45834 -714652.68 2.2885394e-17 4.8447871e-17 7.1333265e-17 -3.3864138e-17 5.6749532e-17 2.685318e-25
Loop time of 5.79033 on 4 procs for 1000 steps with 8000 atoms
Loop time of 2.33734 on 4 procs for 1000 steps with 8000 atoms
97.9% CPU use with 4 MPI tasks x 1 OpenMP threads
92.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.0309 | 4.0713 | 4.1247 | 1.7 | 70.31
Bond | 0.45193 | 0.46562 | 0.49307 | 2.4 | 8.04
Neigh | 0.40834 | 0.40848 | 0.40871 | 0.0 | 7.05
Comm | 0.48313 | 0.56787 | 0.60777 | 6.6 | 9.81
Output | 0.00049329 | 0.0010571 | 0.0020971 | 1.9 | 0.02
Modify | 0.22813 | 0.25523 | 0.27164 | 3.2 | 4.41
Other | | 0.02078 | | | 0.36
Pair | 1.474 | 1.5509 | 1.6662 | 5.7 | 66.35
Bond | 0.18735 | 0.19226 | 0.20418 | 1.6 | 8.23
Neigh | 0.11755 | 0.11806 | 0.11861 | 0.1 | 5.05
Comm | 0.28111 | 0.41325 | 0.49073 | 12.3 | 17.68
Output | 0.00020343 | 0.00056368 | 0.0016305 | 0.0 | 0.02
Modify | 0.038727 | 0.044364 | 0.050037 | 2.6 | 1.90
Other | | 0.01797 | | | 0.77
Nlocal: 2000.00 ave 2013 max 1987 min
Histogram: 1 0 0 0 1 1 0 0 0 1
@ -111,7 +139,4 @@ Dangerous builds = 0
#pair_write 1 1 1201 r 0.2e-9 1.4e-9 potential.relres LJ11
#pair_write 2 2 1201 r 0.2e-9 1.4e-9 potential.relres LJ22
#pair_write 1 2 1201 r 0.2e-9 1.4e-9 potential.relres LJ12
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:06
Total wall time: 0:00:02

60
examples/relres/log.09Feb21.22DMH.respa.g++.1 → examples/relres/log.05Mar21.22DMH.respa.g++.1
View File

@ -1,4 +1,4 @@
LAMMPS (24 Dec 2020)
LAMMPS (10 Feb 2021)
using 1 OpenMP thread(s) per MPI task
units si
atom_style molecular
@ -37,8 +37,8 @@ Finding 1-2 1-3 1-4 neighbors ...
4 = max # of 1-3 neighbors
5 = max # of 1-4 neighbors
7 = max # of special neighbors
special bonds CPU = 0.018 seconds
read_data CPU = 0.170 seconds
special bonds CPU = 0.002 seconds
read_data CPU = 0.035 seconds
pair_coeff 1 1 lj/relres 1 3.47385e-22 3.8e-10 2.02372e-20 3.9309e-10 6.75e-10 7.25e-10 1.2e-09 1.4e-09
pair_coeff 1 2 lj/relres 1 5.33663e-22 3.85214e-10 1.31068e-20 3.91793e-10 6.22997e-10 6.73146e-10 1.2e-09 1.4e-09
pair_coeff 1 3 lj/relres 2 5.33663e-22 3.85214e-10 0 3.91793e-10 6.75e-10 7.25e-10 7.25e-10 7.25e-10
@ -76,6 +76,31 @@ Respa levels:
2 = hybrid-2 kspace
run 500
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- Pair style lj/relres: doi:10.1021/acs.jctc.0c01003
@Article{Chaimovich1,
author = {A. Chaimovich, C. Peter, K. Kremer},
title = {Relative resolution: A hybrid formalism for fluid mixtures},
journal = {J.~Chem.~Phys.},
year = 2015,
volume = 143,
pages = {243107}
@Article{Chaimovich2,
author = {M. Chaimovich, A. Chaimovich},
title = {Relative Resolution: A Computationally Efficient Implementation in LAMMPS},
journal = {J.~Chem.~Theory~Comput.},
year = 2021,
volume = 17,
pages = {1045--1059}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 2 steps, delay 4 steps, check yes
max neighbors/atom: 2000, page size: 100000
@ -111,30 +136,30 @@ Step Temp Press PotEng KinEng TotEng E_pair E_mol Volume
400 293.0168 38268765 2.3173289e-17 4.8540384e-17 7.1713672e-17 -3.3633853e-17 5.6807142e-17 2.685318e-25
450 289.19195 33053376 2.36093e-17 4.7906769e-17 7.151607e-17 -3.3774223e-17 5.7383524e-17 2.685318e-25
500 292.43942 -684078.27 2.2898459e-17 4.8444735e-17 7.1343194e-17 -3.3856946e-17 5.6755405e-17 2.685318e-25
Loop time of 15.899 on 1 procs for 500 steps with 8000 atoms
Loop time of 4.85018 on 1 procs for 500 steps with 8000 atoms
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 11.067 | 11.067 | 11.067 | 0.0 | 69.61
Bond | 1.7933 | 1.7933 | 1.7933 | 0.0 | 11.28
Neigh | 1.5748 | 1.5748 | 1.5748 | 0.0 | 9.91
Comm | 0.50431 | 0.50431 | 0.50431 | 0.0 | 3.17
Output | 0.0013113 | 0.0013113 | 0.0013113 | 0.0 | 0.01
Modify | 0.69311 | 0.69311 | 0.69311 | 0.0 | 4.36
Other | | 0.2656 | | | 1.67
Pair | 3.4622 | 3.4622 | 3.4622 | 0.0 | 71.38
Bond | 0.68987 | 0.68987 | 0.68987 | 0.0 | 14.22
Neigh | 0.44102 | 0.44102 | 0.44102 | 0.0 | 9.09
Comm | 0.087413 | 0.087413 | 0.087413 | 0.0 | 1.80
Output | 0.00034455 | 0.00034455 | 0.00034455 | 0.0 | 0.01
Modify | 0.084174 | 0.084174 | 0.084174 | 0.0 | 1.74
Other | | 0.08514 | | | 1.76
Nlocal: 8000.00 ave 8000 max 8000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 18908.0 ave 18908 max 18908 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 126950.0 ave 126950 max 126950 min
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 126950
Ave neighs/atom = 15.868750
Total # of neighbors = 0
Ave neighs/atom = 0.0000000
Ave special neighs/atom = 5.2500000
Neighbor list builds = 13
Dangerous builds = 0
@ -142,7 +167,4 @@ Dangerous builds = 0
#pair_write 1 1 1201 r 0.2e-9 1.4e-9 potential.relres LJ11
#pair_write 2 2 1201 r 0.2e-9 1.4e-9 potential.relres LJ22
#pair_write 1 2 1201 r 0.2e-9 1.4e-9 potential.relres LJ12
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:16
Total wall time: 0:00:04

62
examples/relres/log.09Feb21.22DMH.respa.g++.4 → examples/relres/log.05Mar21.22DMH.respa.g++.4
View File

@ -1,4 +1,4 @@
LAMMPS (24 Dec 2020)
LAMMPS (10 Feb 2021)
using 1 OpenMP thread(s) per MPI task
units si
atom_style molecular
@ -37,8 +37,8 @@ Finding 1-2 1-3 1-4 neighbors ...
4 = max # of 1-3 neighbors
5 = max # of 1-4 neighbors
7 = max # of special neighbors
special bonds CPU = 0.005 seconds
read_data CPU = 0.135 seconds
special bonds CPU = 0.001 seconds
read_data CPU = 0.036 seconds
pair_coeff 1 1 lj/relres 1 3.47385e-22 3.8e-10 2.02372e-20 3.9309e-10 6.75e-10 7.25e-10 1.2e-09 1.4e-09
pair_coeff 1 2 lj/relres 1 5.33663e-22 3.85214e-10 1.31068e-20 3.91793e-10 6.22997e-10 6.73146e-10 1.2e-09 1.4e-09
pair_coeff 1 3 lj/relres 2 5.33663e-22 3.85214e-10 0 3.91793e-10 6.75e-10 7.25e-10 7.25e-10 7.25e-10
@ -76,6 +76,31 @@ Respa levels:
2 = hybrid-2 kspace
run 500
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- Pair style lj/relres: doi:10.1021/acs.jctc.0c01003
@Article{Chaimovich1,
author = {A. Chaimovich, C. Peter, K. Kremer},
title = {Relative resolution: A hybrid formalism for fluid mixtures},
journal = {J.~Chem.~Phys.},
year = 2015,
volume = 143,
pages = {243107}
@Article{Chaimovich2,
author = {M. Chaimovich, A. Chaimovich},
title = {Relative Resolution: A Computationally Efficient Implementation in LAMMPS},
journal = {J.~Chem.~Theory~Comput.},
year = 2021,
volume = 17,
pages = {1045--1059}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 2 steps, delay 4 steps, check yes
max neighbors/atom: 2000, page size: 100000
@ -111,30 +136,30 @@ Step Temp Press PotEng KinEng TotEng E_pair E_mol Volume
400 293.0168 38268765 2.3173289e-17 4.8540384e-17 7.1713672e-17 -3.3633853e-17 5.6807142e-17 2.685318e-25
450 289.19195 33053376 2.36093e-17 4.7906769e-17 7.151607e-17 -3.3774223e-17 5.7383524e-17 2.685318e-25
500 292.43942 -684078.27 2.2898459e-17 4.8444735e-17 7.1343194e-17 -3.3856946e-17 5.6755405e-17 2.685318e-25
Loop time of 4.45202 on 4 procs for 500 steps with 8000 atoms
Loop time of 1.76801 on 4 procs for 500 steps with 8000 atoms
98.0% CPU use with 4 MPI tasks x 1 OpenMP threads
91.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.6826 | 2.7363 | 2.7963 | 2.5 | 61.46
Bond | 0.45619 | 0.46186 | 0.46906 | 0.8 | 10.37
Neigh | 0.42817 | 0.42863 | 0.4292 | 0.1 | 9.63
Comm | 0.49036 | 0.56091 | 0.62185 | 6.5 | 12.60
Output | 0.00049472 | 0.0013556 | 0.0024905 | 2.0 | 0.03
Modify | 0.1831 | 0.18662 | 0.19193 | 0.8 | 4.19
Other | | 0.07637 | | | 1.72
Pair | 0.93397 | 0.97055 | 1.0377 | 4.0 | 54.89
Bond | 0.18914 | 0.19729 | 0.20727 | 1.5 | 11.16
Neigh | 0.12623 | 0.12644 | 0.12663 | 0.1 | 7.15
Comm | 0.31509 | 0.39593 | 0.44272 | 7.7 | 22.39
Output | 0.00031866 | 0.00034685 | 0.00041755 | 0.0 | 0.02
Modify | 0.035567 | 0.037833 | 0.039797 | 0.8 | 2.14
Other | | 0.03963 | | | 2.24
Nlocal: 2000.00 ave 2016 max 1985 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Nghost: 9883.00 ave 9895 max 9866 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Neighs: 31737.5 ave 32060 max 31459 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 126950
Ave neighs/atom = 15.868750
Total # of neighbors = 0
Ave neighs/atom = 0.0000000
Ave special neighs/atom = 5.2500000
Neighbor list builds = 13
Dangerous builds = 0
@ -142,7 +167,4 @@ Dangerous builds = 0
#pair_write 1 1 1201 r 0.2e-9 1.4e-9 potential.relres LJ11
#pair_write 2 2 1201 r 0.2e-9 1.4e-9 potential.relres LJ22
#pair_write 1 2 1201 r 0.2e-9 1.4e-9 potential.relres LJ12
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:04
Total wall time: 0:00:01