457 lines
19 KiB
Groff
457 lines
19 KiB
Groff
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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2 by 1 by 2 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 = 0.001 seconds
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read_data CPU = 0.035 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) = 9.953 | 9.953 | 9.953 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 2.12445 on 4 procs for 1000 steps with 8000 atoms
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Performance: 40.669 ns/day, 0.590 hours/ns, 470.709 timesteps/s
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91.7% CPU use with 4 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 | 1.2517 | 1.3228 | 1.4636 | 7.2 | 62.27
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Bond | 0.18406 | 0.19356 | 0.20925 | 2.1 | 9.11
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Neigh | 0.12468 | 0.125 | 0.12534 | 0.1 | 5.88
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Comm | 0.25384 | 0.40233 | 0.4919 | 14.1 | 18.94
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Output | 0.00034203 | 0.00061893 | 0.00088527 | 0.0 | 0.03
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Modify | 0.052326 | 0.059507 | 0.066224 | 2.6 | 2.80
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Other | | 0.02066 | | | 0.97
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Nlocal: 2000.00 ave 2031 max 1964 min
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Histogram: 1 0 0 0 1 0 0 1 0 1
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Nghost: 9898.50 ave 9926 max 9869 min
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Histogram: 1 0 0 0 1 0 1 0 0 1
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Neighs: 92980.0 ave 94819 max 90517 min
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Histogram: 1 0 0 1 0 0 0 0 0 2
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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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2 by 1 by 2 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 = 0.005 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) = 10.34 | 10.34 | 10.34 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 2.6513 on 4 procs for 1000 steps with 8000 atoms
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Performance: 32.588 ns/day, 0.736 hours/ns, 377.174 timesteps/s
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89.9% CPU use with 4 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 | 1.5783 | 1.6371 | 1.7079 | 3.7 | 61.75
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Bond | 0.18196 | 0.19132 | 0.20276 | 1.7 | 7.22
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Neigh | 0.14093 | 0.14128 | 0.14156 | 0.1 | 5.33
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Comm | 0.50333 | 0.5809 | 0.64199 | 6.6 | 21.91
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Output | 0.00023452 | 0.00040924 | 0.00063279 | 0.0 | 0.02
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Modify | 0.066524 | 0.076747 | 0.084331 | 2.5 | 2.89
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Other | | 0.02354 | | | 0.89
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Nlocal: 2000.00 ave 2009 max 1981 min
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Histogram: 1 0 0 0 0 0 0 1 0 2
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Nghost: 9892.50 ave 9923 max 9868 min
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Histogram: 2 0 0 0 0 0 0 1 0 1
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Neighs: 118889.0 ave 120387 max 117552 min
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Histogram: 1 0 0 1 0 1 0 0 0 1
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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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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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2 by 1 by 2 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 = 0.001 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 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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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) = 10.34 | 10.34 | 10.34 Mbytes
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Step Temp Press PotEng KinEng TotEng E_pair E_mol Volume
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1000 290.11974 54.754001 3314.0966 6917.47 10231.567 -4872.3264 8186.423 268531.8
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1100 289.78217 480.37221 3342.8765 6909.4211 10252.298 -4900.7266 8243.6032 268531.8
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1200 293.25523 188.46596 3322.6257 6992.2308 10314.857 -4771.3485 8093.9742 268531.8
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1300 291.59734 146.50303 3465.2113 6952.701 10417.912 -4782.9861 8248.1974 268531.8
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1400 292.71873 -40.372074 3491.747 6979.4389 10471.186 -4790.7124 8282.4594 268531.8
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1500 290.60378 120.25863 3539.5538 6929.0112 10468.565 -4849.9813 8389.5351 268531.8
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1600 293.21218 -143.75501 3452.9516 6991.2046 10444.156 -4885.0192 8337.9708 268531.8
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1700 291.02865 -207.34728 3465.4131 6939.1416 10404.555 -4887.363 8352.7761 268531.8
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1800 286.00091 -91.017961 3530.3422 6819.2625 10349.605 -4807.6624 8338.0046 268531.8
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1900 286.3006 -145.399 3485.1695 6826.4082 10311.578 -4848.263 8333.4325 268531.8
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2000 288.43931 -469.99712 3409.0906 6877.4025 10286.493 -4905.9002 8314.9907 268531.8
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Loop time of 2.32221 on 4 procs for 1000 steps with 8000 atoms
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Performance: 37.206 ns/day, 0.645 hours/ns, 430.624 timesteps/s
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90.9% CPU use with 4 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 | 1.4451 | 1.5022 | 1.555 | 3.7 | 64.69
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Bond | 0.18307 | 0.19206 | 0.20526 | 2.0 | 8.27
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Neigh | 0.12827 | 0.12956 | 0.13074 | 0.3 | 5.58
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Comm | 0.36752 | 0.42006 | 0.48825 | 8.1 | 18.09
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Output | 0.00022658 | 0.00025297 | 0.0003292 | 0.0 | 0.01
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Modify | 0.05223 | 0.057658 | 0.063373 | 2.1 | 2.48
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Other | | 0.02044 | | | 0.88
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Nlocal: 2000.00 ave 2016 max 1981 min
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Histogram: 1 0 0 0 0 1 1 0 0 1
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Nghost: 9878.25 ave 9891 max 9868 min
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Histogram: 1 0 1 0 0 1 0 0 0 1
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Neighs: 108567.0 ave 110532 max 107467 min
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Histogram: 1 1 1 0 0 0 0 0 0 1
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Total # of neighbors = 434269
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Ave neighs/atom = 54.283625
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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 reference system with lj/smooth
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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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2 by 1 by 2 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 = 0.004 seconds
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read_restart CPU = 0.007 seconds
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pair_style lj/smooth 12.0 14.0
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pair_coeff 6 6 0.175 3.905
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pair_coeff 4 4 0.118 3.905
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pair_coeff 2 2 0.118 3.905
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pair_coeff 5 5 0.145 3.960
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pair_coeff 3 3 0.118 3.905
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pair_coeff 1 1 0.05 3.8
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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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|
|
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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/smooth, 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) = 11.86 | 11.86 | 11.86 Mbytes
|
|
Step Temp Press PotEng KinEng TotEng E_pair E_mol Volume
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1000 290.11974 -80.648214 3258.0256 6917.47 10175.496 -4928.3973 8186.423 268531.8
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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
|