update reference log files for lj/relres
This commit is contained in:
Axel Kohlmeyer
@ -1,16 +1,16 @@
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The input script in.22DMH.relres provides an example of a molecular
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The input script in.22DMH.relres provides an example of a molecular
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simulation using the Relative Resolution (RelRes) algorithm. In this
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simulation using the Relative Resolution (RelRes) algorithm. In this
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example, 2,2-Dimethylhexane is the molecule in focus. This script
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example, 2,2-Dimethylhexane is the molecule in focus. This script
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uses the data file Data.22DMH.in.relres, which consists of 8000
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uses the data file Data.22DMH.in.relres, which consists of 8000
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molecules. It also generates the RelRes potential for the selected atom types.
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molecules. It also generates the RelRes potential for the selected atom types.
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The input script in.22DMH.respa demonstrates the use of the lj/relres pair
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The input script in.22DMH.respa demonstrates the use of the lj/relres pair
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style with r-RESPA applying multi-timestepping between the appropriate atom
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style with r-RESPA applying multi-timestepping between the appropriate atom
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types (using a hybrid pair style configuration).
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types (using a hybrid pair style configuration).
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The input script in.22DMH.real demonstrates the use of the lj/relres pair
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The input script in.22DMH.real demonstrates the use of the lj/relres pair
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style with real units (the data file Data.22DMH.in.real). It performs
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style with real units (the data file Data.22DMH.in.real). It performs
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a set of molecular simulations with different switching distances. Finally,
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a set of molecular simulations with different switching distances. Finally,
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it performs a molecular simulation with the lj/smooth pair style, allowing
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it performs a molecular simulation with the lj/smooth pair style, allowing
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comparison of the thermal characteristics and the running time between the
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comparison of the thermal characteristics and the running time between the
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RelRes and the conventional approach.
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RelRes and the conventional approach.
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456
examples/relres/log.05Mar21.22DMH.real.g++.1
Normal file
456
examples/relres/log.05Mar21.22DMH.real.g++.1
Normal file
@ -0,0 +1,456 @@
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LAMMPS (10 Feb 2021)
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using 1 OpenMP thread(s) per MPI task
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# Example: use of lj/relres for simulation of 2,2-dimethylhexane: C3H7-C5H11
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# with various Rso setting as well as run of reference system for time comparison (real units)
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# The first run writes restart file that is used by all subsequent runs.
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# Run relres with Rso=6.25
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units real
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atom_style molecular
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boundary p p p
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dielectric 1
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special_bonds lj/coul 0.0 0.0 0.5
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bond_style harmonic
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angle_style harmonic
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dihedral_style fourier
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pair_style lj/relres 5.75 6.25 12.0 14.0
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read_data Data.22DMH.in.real
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Reading data file ...
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orthogonal box = (3.7421629 3.7421629 3.7421629) to (68.257837 68.257837 68.257837)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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8000 atoms
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reading velocities ...
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8000 velocities
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scanning bonds ...
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4 = max bonds/atom
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scanning angles ...
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6 = max angles/atom
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scanning dihedrals ...
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3 = max dihedrals/atom
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reading bonds ...
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7000 bonds
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reading angles ...
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9000 angles
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reading dihedrals ...
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5000 dihedrals
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 0 0.5
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special bond factors coul: 0 0 0.5
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4 = max # of 1-2 neighbors
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4 = max # of 1-3 neighbors
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5 = max # of 1-4 neighbors
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7 = max # of special neighbors
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special bonds CPU = 0.003 seconds
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read_data CPU = 0.036 seconds
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pair_coeff 6 6 0.175 3.905 0.0 0.0
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pair_coeff 4 4 0.118 3.905 0.0 0.0
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pair_coeff 2 2 0.118 3.905 1.2218 3.905
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pair_coeff 5 5 0.145 3.960 0.0 0.0
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pair_coeff 3 3 0.118 3.905 0.0 0.0
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pair_coeff 1 1 0.05 3.8 2.9128 3.9309
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pair_modify shift yes
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neighbor 2.0 bin
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neigh_modify every 2 delay 4 check yes
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timestep 1.0
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thermo 100
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thermo_style custom step temp press pe ke etotal epair emol vol
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fix 2 all nvt temp 290 290 2.0e+02
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run 1000
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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Your simulation uses code contributions which should be cited:
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- Pair style lj/relres: doi:10.1021/acs.jctc.0c01003
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@Article{Chaimovich1,
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author = {A. Chaimovich, C. Peter, K. Kremer},
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title = {Relative resolution: A hybrid formalism for fluid mixtures},
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journal = {J.~Chem.~Phys.},
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year = 2015,
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volume = 143,
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pages = {243107}
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@Article{Chaimovich2,
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author = {M. Chaimovich, A. Chaimovich},
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title = {Relative Resolution: A Computationally Efficient Implementation in LAMMPS},
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journal = {J.~Chem.~Theory~Comput.},
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year = 2021,
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volume = 17,
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pages = {1045--1059}
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}
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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Neighbor list info ...
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update every 2 steps, delay 4 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 16
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ghost atom cutoff = 16
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binsize = 8, bins = 9 9 9
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/relres, perpetual
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attributes: half, newton on
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pair build: half/bin/newton
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stencil: half/bin/3d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 20.01 | 20.01 | 20.01 Mbytes
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Step Temp Press PotEng KinEng TotEng E_pair E_mol Volume
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0 286.85653 -328.51562 3703.8924 6839.6636 10543.556 -4875.3137 8579.2062 268531.8
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100 293.231 -55.62132 3520.4874 6991.6533 10512.141 -4797.2633 8317.7507 268531.8
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200 292.73476 332.40528 3456.3029 6979.8212 10436.124 -4914.7261 8371.0291 268531.8
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300 292.56511 221.98408 3380.7472 6975.7762 10356.523 -4936.5552 8317.3024 268531.8
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400 288.42948 117.72433 3428.113 6877.1681 10305.281 -4887.6852 8315.7982 268531.8
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500 289.20503 -238.73381 3373.758 6895.6601 10269.418 -4947.3214 8321.0795 268531.8
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600 292.02137 74.370782 3263.4324 6962.8115 10226.244 -4948.3906 8211.823 268531.8
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700 290.20603 475.24398 3260.0754 6919.5273 10179.603 -4931.4093 8191.4846 268531.8
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800 293.12504 175.54324 3156.6048 6989.1268 10145.732 -5006.7161 8163.3209 268531.8
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900 287.78433 63.785361 3251.5393 6861.7855 10113.325 -5029.094 8280.6333 268531.8
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1000 290.11974 -101.34839 3183.4817 6917.47 10100.952 -5002.9413 8186.423 268531.8
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Loop time of 6.05162 on 1 procs for 1000 steps with 8000 atoms
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Performance: 14.277 ns/day, 1.681 hours/ns, 165.245 timesteps/s
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99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 4.7637 | 4.7637 | 4.7637 | 0.0 | 78.72
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Bond | 0.693 | 0.693 | 0.693 | 0.0 | 11.45
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Neigh | 0.41311 | 0.41311 | 0.41311 | 0.0 | 6.83
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Comm | 0.070843 | 0.070843 | 0.070843 | 0.0 | 1.17
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Output | 0.00045886 | 0.00045886 | 0.00045886 | 0.0 | 0.01
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Modify | 0.084814 | 0.084814 | 0.084814 | 0.0 | 1.40
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Other | | 0.02564 | | | 0.42
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Nlocal: 8000.00 ave 8000 max 8000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 18934.0 ave 18934 max 18934 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 371920.0 ave 371920 max 371920 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 371920
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Ave neighs/atom = 46.490000
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Ave special neighs/atom = 5.2500000
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Neighbor list builds = 13
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Dangerous builds = 0
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write_restart restart.relres.real
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System init for write_restart ...
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# Run relres with Rso=7.25
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clear
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using 1 OpenMP thread(s) per MPI task
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read_restart restart.relres.real
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Reading restart file ...
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restart file = 10 Feb 2021, LAMMPS = 10 Feb 2021
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restoring atom style molecular from restart
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orthogonal box = (3.7421629 3.7421629 3.7421629) to (68.257837 68.257837 68.257837)
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1 by 1 by 1 MPI processor grid
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restoring pair style lj/relres from restart
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restoring bond style harmonic from restart
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restoring angle style harmonic from restart
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restoring dihedral style fourier from restart
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8000 atoms
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7000 bonds
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9000 angles
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5000 dihedrals
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 0 0.5
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special bond factors coul: 0 0 0.5
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4 = max # of 1-2 neighbors
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4 = max # of 1-3 neighbors
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5 = max # of 1-4 neighbors
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7 = max # of special neighbors
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special bonds CPU = 0.002 seconds
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read_restart CPU = 0.004 seconds
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pair_style lj/relres 6.75 7.25 12.0 14.0
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pair_coeff 6 6 0.175 3.905 0.0 0.0
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pair_coeff 4 4 0.118 3.905 0.0 0.0
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pair_coeff 2 2 0.118 3.905 1.2218 3.905
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pair_coeff 5 5 0.145 3.960 0.0 0.0
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pair_coeff 3 3 0.118 3.905 0.0 0.0
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pair_coeff 1 1 0.05 3.8 2.9128 3.9309
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pair_modify shift yes
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neighbor 2.0 bin
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neigh_modify every 2 delay 4 check yes
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timestep 1.0
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thermo 100
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thermo_style custom step temp press pe ke etotal epair emol vol
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fix 2 all nvt temp 290 290 2.0e+02
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Resetting global fix info from restart file:
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fix style: nvt, fix ID: 2
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run 1000
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All restart file global fix info was re-assigned
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Neighbor list info ...
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update every 2 steps, delay 4 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 16
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ghost atom cutoff = 16
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binsize = 8, bins = 9 9 9
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/relres, perpetual
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attributes: half, newton on
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pair build: half/bin/newton
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stencil: half/bin/3d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 20.51 | 20.51 | 20.51 Mbytes
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Step Temp Press PotEng KinEng TotEng E_pair E_mol Volume
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1000 290.11974 21.86402 3334.7257 6917.47 10252.196 -4851.6973 8186.423 268531.8
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1100 289.71937 460.00291 3365.0978 6907.9236 10273.021 -4881.5513 8246.6491 268531.8
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1200 293.0828 194.76483 3348.6267 6988.1197 10336.746 -4743.4894 8092.1162 268531.8
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1300 291.27785 153.93026 3496.2858 6945.0834 10441.369 -4753.3325 8249.6183 268531.8
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1400 292.69435 -51.690836 3516.6743 6978.8575 10495.532 -4774.0701 8290.7445 268531.8
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1500 290.0279 149.43706 3578.8283 6915.2801 10494.108 -4815.5857 8394.414 268531.8
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1600 292.89473 -109.05125 3487.6652 6983.6354 10471.301 -4839.1407 8326.8059 268531.8
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1700 290.99802 -146.06465 3496.48 6938.4111 10434.891 -4868.0031 8364.4831 268531.8
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1800 286.48455 -45.580207 3550.2611 6830.7943 10381.055 -4766.3336 8316.5947 268531.8
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1900 287.0735 -157.60878 3488.4248 6844.8368 10333.262 -4853.6992 8342.124 268531.8
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2000 287.38046 -429.32757 3435.8336 6852.1558 10287.989 -4878.4345 8314.2681 268531.8
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Loop time of 7.46943 on 1 procs for 1000 steps with 8000 atoms
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Performance: 11.567 ns/day, 2.075 hours/ns, 133.879 timesteps/s
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99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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|
---------------------------------------------------------------
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Pair | 6.1145 | 6.1145 | 6.1145 | 0.0 | 81.86
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Bond | 0.71392 | 0.71392 | 0.71392 | 0.0 | 9.56
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Neigh | 0.45677 | 0.45677 | 0.45677 | 0.0 | 6.12
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Comm | 0.072404 | 0.072404 | 0.072404 | 0.0 | 0.97
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Output | 0.00036481 | 0.00036481 | 0.00036481 | 0.0 | 0.00
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Modify | 0.085956 | 0.085956 | 0.085956 | 0.0 | 1.15
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Other | | 0.02552 | | | 0.34
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Nlocal: 8000.00 ave 8000 max 8000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 18846.0 ave 18846 max 18846 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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||||||
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Neighs: 475557.0 ave 475557 max 475557 min
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||||||
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Histogram: 1 0 0 0 0 0 0 0 0 0
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||||||
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||||||
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Total # of neighbors = 475557
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Ave neighs/atom = 59.444625
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Ave special neighs/atom = 5.2500000
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Neighbor list builds = 14
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Dangerous builds = 0
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# Run relres with mixed Rso: 6.25 for C3H7 group and 7.25 for C5H11 group
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clear
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using 1 OpenMP thread(s) per MPI task
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read_restart restart.relres.real
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Reading restart file ...
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||||||
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restart file = 10 Feb 2021, LAMMPS = 10 Feb 2021
|
||||||
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restoring atom style molecular from restart
|
||||||
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orthogonal box = (3.7421629 3.7421629 3.7421629) to (68.257837 68.257837 68.257837)
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1 by 1 by 1 MPI processor grid
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||||||
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restoring pair style lj/relres from restart
|
||||||
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restoring bond style harmonic from restart
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||||||
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restoring angle style harmonic from restart
|
||||||
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restoring dihedral style fourier from restart
|
||||||
|
8000 atoms
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||||||
|
7000 bonds
|
||||||
|
9000 angles
|
||||||
|
5000 dihedrals
|
||||||
|
Finding 1-2 1-3 1-4 neighbors ...
|
||||||
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special bond factors lj: 0 0 0.5
|
||||||
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special bond factors coul: 0 0 0.5
|
||||||
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4 = max # of 1-2 neighbors
|
||||||
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4 = max # of 1-3 neighbors
|
||||||
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5 = max # of 1-4 neighbors
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||||||
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7 = max # of special neighbors
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||||||
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special bonds CPU = 0.002 seconds
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||||||
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read_restart CPU = 0.004 seconds
|
||||||
|
|
||||||
|
pair_style lj/relres 6.75 7.25 12.0 14.0
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||||||
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||||||
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pair_coeff 6 6 0.175 3.905 0.0 0.0 5.75 6.25 12.0 14.0
|
||||||
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pair_coeff 4 4 0.118 3.905 0.0 0.0 5.75 6.25 12.0 14.0
|
||||||
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pair_coeff 2 2 0.118 3.905 1.2218 3.905 5.75 6.25 12.0 14.0
|
||||||
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pair_coeff 5 5 0.145 3.960 0.0 0.0
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||||||
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pair_coeff 3 3 0.118 3.905 0.0 0.0
|
||||||
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pair_coeff 1 1 0.05 3.8 2.9128 3.9309
|
||||||
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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
|
||||||
456
examples/relres/log.05Mar21.22DMH.real.g++.4
Normal file
456
examples/relres/log.05Mar21.22DMH.real.g++.4
Normal file
@ -0,0 +1,456 @@
|
|||||||
|
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
|
||||||
@ -1,5 +1,8 @@
|
|||||||
LAMMPS (24 Dec 2020)
|
LAMMPS (10 Feb 2021)
|
||||||
using 1 OpenMP thread(s) per MPI task
|
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
|
units si
|
||||||
atom_style molecular
|
atom_style molecular
|
||||||
boundary p p p
|
boundary p p p
|
||||||
@ -37,13 +40,13 @@ Finding 1-2 1-3 1-4 neighbors ...
|
|||||||
4 = max # of 1-3 neighbors
|
4 = max # of 1-3 neighbors
|
||||||
5 = max # of 1-4 neighbors
|
5 = max # of 1-4 neighbors
|
||||||
7 = max # of special neighbors
|
7 = max # of special neighbors
|
||||||
special bonds CPU = 0.019 seconds
|
special bonds CPU = 0.003 seconds
|
||||||
read_data CPU = 0.168 seconds
|
read_data CPU = 0.035 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 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 0.3905e-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 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 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 5 5 1.00742E-21 0.396E-9 0.0 0.0
|
||||||
pair_coeff 3 3 0.819828e-21 0.3905e-9 0 0.3905e-9
|
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_coeff 1 1 0.347385E-21 0.38E-9 20.2372E-21 0.39309E-9
|
||||||
pair_modify shift yes
|
pair_modify shift yes
|
||||||
neighbor 2.0e-10 bin
|
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
|
fix 2 all nvt temp 290 290 2.0e-13
|
||||||
|
|
||||||
run 1000
|
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 ...
|
Neighbor list info ...
|
||||||
update every 2 steps, delay 4 steps, check yes
|
update every 2 steps, delay 4 steps, check yes
|
||||||
max neighbors/atom: 2000, page size: 100000
|
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
|
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
|
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
|
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:
|
MPI task timing breakdown:
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
---------------------------------------------------------------
|
---------------------------------------------------------------
|
||||||
Pair | 15.751 | 15.751 | 15.751 | 0.0 | 78.01
|
Pair | 5.5321 | 5.5321 | 5.5321 | 0.0 | 81.09
|
||||||
Bond | 1.7612 | 1.7612 | 1.7612 | 0.0 | 8.72
|
Bond | 0.69427 | 0.69427 | 0.69427 | 0.0 | 10.18
|
||||||
Neigh | 1.4937 | 1.4937 | 1.4937 | 0.0 | 7.40
|
Neigh | 0.4138 | 0.4138 | 0.4138 | 0.0 | 6.07
|
||||||
Comm | 0.404 | 0.404 | 0.404 | 0.0 | 2.00
|
Comm | 0.070615 | 0.070615 | 0.070615 | 0.0 | 1.04
|
||||||
Output | 0.0013139 | 0.0013139 | 0.0013139 | 0.0 | 0.01
|
Output | 0.00037602 | 0.00037602 | 0.00037602 | 0.0 | 0.01
|
||||||
Modify | 0.72282 | 0.72282 | 0.72282 | 0.0 | 3.58
|
Modify | 0.084796 | 0.084796 | 0.084796 | 0.0 | 1.24
|
||||||
Other | | 0.05691 | | | 0.28
|
Other | | 0.02591 | | | 0.38
|
||||||
|
|
||||||
Nlocal: 8000.00 ave 8000 max 8000 min
|
Nlocal: 8000.00 ave 8000 max 8000 min
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
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 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 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
|
#pair_write 1 2 1201 r 0.2e-9 1.4e-9 potential.relres LJ12
|
||||||
|
Total wall time: 0:00:06
|
||||||
Please see the log.cite file for references relevant to this simulation
|
|
||||||
|
|
||||||
Total wall time: 0:00:20
|
|
||||||
@ -1,5 +1,8 @@
|
|||||||
LAMMPS (24 Dec 2020)
|
LAMMPS (10 Feb 2021)
|
||||||
using 1 OpenMP thread(s) per MPI task
|
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
|
units si
|
||||||
atom_style molecular
|
atom_style molecular
|
||||||
boundary p p p
|
boundary p p p
|
||||||
@ -37,13 +40,13 @@ Finding 1-2 1-3 1-4 neighbors ...
|
|||||||
4 = max # of 1-3 neighbors
|
4 = max # of 1-3 neighbors
|
||||||
5 = max # of 1-4 neighbors
|
5 = max # of 1-4 neighbors
|
||||||
7 = max # of special neighbors
|
7 = max # of special neighbors
|
||||||
special bonds CPU = 0.010 seconds
|
special bonds CPU = 0.001 seconds
|
||||||
read_data CPU = 0.145 seconds
|
read_data CPU = 0.037 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 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 0.3905e-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 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 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 5 5 1.00742E-21 0.396E-9 0.0 0.0
|
||||||
pair_coeff 3 3 0.819828e-21 0.3905e-9 0 0.3905e-9
|
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_coeff 1 1 0.347385E-21 0.38E-9 20.2372E-21 0.39309E-9
|
||||||
pair_modify shift yes
|
pair_modify shift yes
|
||||||
neighbor 2.0e-10 bin
|
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
|
fix 2 all nvt temp 290 290 2.0e-13
|
||||||
|
|
||||||
run 1000
|
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 ...
|
Neighbor list info ...
|
||||||
update every 2 steps, delay 4 steps, check yes
|
update every 2 steps, delay 4 steps, check yes
|
||||||
max neighbors/atom: 2000, page size: 100000
|
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
|
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
|
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
|
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:
|
MPI task timing breakdown:
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
---------------------------------------------------------------
|
---------------------------------------------------------------
|
||||||
Pair | 4.0309 | 4.0713 | 4.1247 | 1.7 | 70.31
|
Pair | 1.474 | 1.5509 | 1.6662 | 5.7 | 66.35
|
||||||
Bond | 0.45193 | 0.46562 | 0.49307 | 2.4 | 8.04
|
Bond | 0.18735 | 0.19226 | 0.20418 | 1.6 | 8.23
|
||||||
Neigh | 0.40834 | 0.40848 | 0.40871 | 0.0 | 7.05
|
Neigh | 0.11755 | 0.11806 | 0.11861 | 0.1 | 5.05
|
||||||
Comm | 0.48313 | 0.56787 | 0.60777 | 6.6 | 9.81
|
Comm | 0.28111 | 0.41325 | 0.49073 | 12.3 | 17.68
|
||||||
Output | 0.00049329 | 0.0010571 | 0.0020971 | 1.9 | 0.02
|
Output | 0.00020343 | 0.00056368 | 0.0016305 | 0.0 | 0.02
|
||||||
Modify | 0.22813 | 0.25523 | 0.27164 | 3.2 | 4.41
|
Modify | 0.038727 | 0.044364 | 0.050037 | 2.6 | 1.90
|
||||||
Other | | 0.02078 | | | 0.36
|
Other | | 0.01797 | | | 0.77
|
||||||
|
|
||||||
Nlocal: 2000.00 ave 2013 max 1987 min
|
Nlocal: 2000.00 ave 2013 max 1987 min
|
||||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
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 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 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
|
#pair_write 1 2 1201 r 0.2e-9 1.4e-9 potential.relres LJ12
|
||||||
|
Total wall time: 0:00:02
|
||||||
Please see the log.cite file for references relevant to this simulation
|
|
||||||
|
|
||||||
Total wall time: 0:00:06
|
|
||||||
@ -1,4 +1,4 @@
|
|||||||
LAMMPS (24 Dec 2020)
|
LAMMPS (10 Feb 2021)
|
||||||
using 1 OpenMP thread(s) per MPI task
|
using 1 OpenMP thread(s) per MPI task
|
||||||
units si
|
units si
|
||||||
atom_style molecular
|
atom_style molecular
|
||||||
@ -37,8 +37,8 @@ Finding 1-2 1-3 1-4 neighbors ...
|
|||||||
4 = max # of 1-3 neighbors
|
4 = max # of 1-3 neighbors
|
||||||
5 = max # of 1-4 neighbors
|
5 = max # of 1-4 neighbors
|
||||||
7 = max # of special neighbors
|
7 = max # of special neighbors
|
||||||
special bonds CPU = 0.018 seconds
|
special bonds CPU = 0.002 seconds
|
||||||
read_data CPU = 0.170 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 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 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
|
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
|
2 = hybrid-2 kspace
|
||||||
|
|
||||||
run 500
|
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 ...
|
Neighbor list info ...
|
||||||
update every 2 steps, delay 4 steps, check yes
|
update every 2 steps, delay 4 steps, check yes
|
||||||
max neighbors/atom: 2000, page size: 100000
|
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
|
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
|
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
|
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:
|
MPI task timing breakdown:
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
---------------------------------------------------------------
|
---------------------------------------------------------------
|
||||||
Pair | 11.067 | 11.067 | 11.067 | 0.0 | 69.61
|
Pair | 3.4622 | 3.4622 | 3.4622 | 0.0 | 71.38
|
||||||
Bond | 1.7933 | 1.7933 | 1.7933 | 0.0 | 11.28
|
Bond | 0.68987 | 0.68987 | 0.68987 | 0.0 | 14.22
|
||||||
Neigh | 1.5748 | 1.5748 | 1.5748 | 0.0 | 9.91
|
Neigh | 0.44102 | 0.44102 | 0.44102 | 0.0 | 9.09
|
||||||
Comm | 0.50431 | 0.50431 | 0.50431 | 0.0 | 3.17
|
Comm | 0.087413 | 0.087413 | 0.087413 | 0.0 | 1.80
|
||||||
Output | 0.0013113 | 0.0013113 | 0.0013113 | 0.0 | 0.01
|
Output | 0.00034455 | 0.00034455 | 0.00034455 | 0.0 | 0.01
|
||||||
Modify | 0.69311 | 0.69311 | 0.69311 | 0.0 | 4.36
|
Modify | 0.084174 | 0.084174 | 0.084174 | 0.0 | 1.74
|
||||||
Other | | 0.2656 | | | 1.67
|
Other | | 0.08514 | | | 1.76
|
||||||
|
|
||||||
Nlocal: 8000.00 ave 8000 max 8000 min
|
Nlocal: 8000.00 ave 8000 max 8000 min
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
Nghost: 18908.0 ave 18908 max 18908 min
|
Nghost: 18908.0 ave 18908 max 18908 min
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
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
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
Total # of neighbors = 126950
|
Total # of neighbors = 0
|
||||||
Ave neighs/atom = 15.868750
|
Ave neighs/atom = 0.0000000
|
||||||
Ave special neighs/atom = 5.2500000
|
Ave special neighs/atom = 5.2500000
|
||||||
Neighbor list builds = 13
|
Neighbor list builds = 13
|
||||||
Dangerous builds = 0
|
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 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 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
|
#pair_write 1 2 1201 r 0.2e-9 1.4e-9 potential.relres LJ12
|
||||||
|
Total wall time: 0:00:04
|
||||||
Please see the log.cite file for references relevant to this simulation
|
|
||||||
|
|
||||||
Total wall time: 0:00:16
|
|
||||||
@ -1,4 +1,4 @@
|
|||||||
LAMMPS (24 Dec 2020)
|
LAMMPS (10 Feb 2021)
|
||||||
using 1 OpenMP thread(s) per MPI task
|
using 1 OpenMP thread(s) per MPI task
|
||||||
units si
|
units si
|
||||||
atom_style molecular
|
atom_style molecular
|
||||||
@ -37,8 +37,8 @@ Finding 1-2 1-3 1-4 neighbors ...
|
|||||||
4 = max # of 1-3 neighbors
|
4 = max # of 1-3 neighbors
|
||||||
5 = max # of 1-4 neighbors
|
5 = max # of 1-4 neighbors
|
||||||
7 = max # of special neighbors
|
7 = max # of special neighbors
|
||||||
special bonds CPU = 0.005 seconds
|
special bonds CPU = 0.001 seconds
|
||||||
read_data CPU = 0.135 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 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 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
|
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
|
2 = hybrid-2 kspace
|
||||||
|
|
||||||
run 500
|
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 ...
|
Neighbor list info ...
|
||||||
update every 2 steps, delay 4 steps, check yes
|
update every 2 steps, delay 4 steps, check yes
|
||||||
max neighbors/atom: 2000, page size: 100000
|
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
|
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
|
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
|
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:
|
MPI task timing breakdown:
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
---------------------------------------------------------------
|
---------------------------------------------------------------
|
||||||
Pair | 2.6826 | 2.7363 | 2.7963 | 2.5 | 61.46
|
Pair | 0.93397 | 0.97055 | 1.0377 | 4.0 | 54.89
|
||||||
Bond | 0.45619 | 0.46186 | 0.46906 | 0.8 | 10.37
|
Bond | 0.18914 | 0.19729 | 0.20727 | 1.5 | 11.16
|
||||||
Neigh | 0.42817 | 0.42863 | 0.4292 | 0.1 | 9.63
|
Neigh | 0.12623 | 0.12644 | 0.12663 | 0.1 | 7.15
|
||||||
Comm | 0.49036 | 0.56091 | 0.62185 | 6.5 | 12.60
|
Comm | 0.31509 | 0.39593 | 0.44272 | 7.7 | 22.39
|
||||||
Output | 0.00049472 | 0.0013556 | 0.0024905 | 2.0 | 0.03
|
Output | 0.00031866 | 0.00034685 | 0.00041755 | 0.0 | 0.02
|
||||||
Modify | 0.1831 | 0.18662 | 0.19193 | 0.8 | 4.19
|
Modify | 0.035567 | 0.037833 | 0.039797 | 0.8 | 2.14
|
||||||
Other | | 0.07637 | | | 1.72
|
Other | | 0.03963 | | | 2.24
|
||||||
|
|
||||||
Nlocal: 2000.00 ave 2016 max 1985 min
|
Nlocal: 2000.00 ave 2016 max 1985 min
|
||||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||||
Nghost: 9883.00 ave 9895 max 9866 min
|
Nghost: 9883.00 ave 9895 max 9866 min
|
||||||
Histogram: 1 0 0 0 0 1 0 1 0 1
|
Histogram: 1 0 0 0 0 1 0 1 0 1
|
||||||
Neighs: 31737.5 ave 32060 max 31459 min
|
Neighs: 0.00000 ave 0 max 0 min
|
||||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
Total # of neighbors = 126950
|
Total # of neighbors = 0
|
||||||
Ave neighs/atom = 15.868750
|
Ave neighs/atom = 0.0000000
|
||||||
Ave special neighs/atom = 5.2500000
|
Ave special neighs/atom = 5.2500000
|
||||||
Neighbor list builds = 13
|
Neighbor list builds = 13
|
||||||
Dangerous builds = 0
|
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 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 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
|
#pair_write 1 2 1201 r 0.2e-9 1.4e-9 potential.relres LJ12
|
||||||
|
Total wall time: 0:00:01
|
||||||
Please see the log.cite file for references relevant to this simulation
|
|
||||||
|
|
||||||
Total wall time: 0:00:04
|
|
||||||
Reference in New Issue
Block a user