add demonstration of using r-RESPA with a FG/CG sites split
This commit is contained in:
Axel Kohlmeyer
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The input script in.22DMH.relres provide example of simulation using Relative Resolution (RelRes) potential.
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In this example 2,2-Dimethylhexane is selected as simulated substance to give complete view of the RelRes utilization.
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The input script in.22DMH.relres provide example of simulation using
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Relative Resolution (RelRes) potential. In this example 2,2-Dimethylhexane
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is selected as simulated substance to give complete view of the RelRes
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utilization.
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This script uses data file Data.22DMH.in.relres consisting 8000 molecule of the substance. It also generates RelRes potential for selected atom types.
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This script uses data file Data.22DMH.in.relres consisting of 8000 molecules.
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It also generates RelRes potential for 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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style with r-RESPA using multi-timestepping between FG and CG sites using
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a hybrid pair style configuration.
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49
examples/relres/in.22DMH.respa
Normal file
49
examples/relres/in.22DMH.respa
Normal file
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units si
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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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pair_style hybrid lj/relres 0.675e-9 0.725e-9 1.2e-9 1.4e-9 lj/relres 0.675e-9 .725e-9 1.2e-9 1.4e-9
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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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read_data Data.22DMH.in.relres
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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
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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
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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
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pair_coeff 1 4 lj/relres 2 5.33663e-22 3.85214e-10 0 3.91793e-10 6.22997e-10 6.73146e-10 6.73146e-10 6.73146e-10
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pair_coeff 1 5 lj/relres 2 5.91576e-22 3.87918e-10 0 3.94542e-10 6.75e-10 7.25e-10 7.25e-10 7.25e-10
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pair_coeff 1 6 lj/relres 2 6.49898e-22 3.85214e-10 0 3.91793e-10 6.22997e-10 6.73146e-10 6.73146e-10 6.73146e-10
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pair_coeff 2 2 lj/relres 1 8.19828e-22 3.905e-10 8.48872e-21 3.905e-10 5.75e-10 6.25e-10 1.2e-09 1.4e-09
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pair_coeff 2 3 lj/relres 2 8.19828e-22 3.905e-10 0 3.905e-10 6.22997e-10 6.73146e-10 6.73146e-10 6.73146e-10
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pair_coeff 2 4 lj/relres 2 8.19828e-22 3.905e-10 0 3.905e-10 5.75e-10 6.25e-10 6.25e-10 6.25e-10
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pair_coeff 2 5 lj/relres 2 9.08797e-22 3.9324e-10 0 3.9324e-10 6.22997e-10 6.73146e-10 6.73146e-10 6.73146e-10
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pair_coeff 2 6 lj/relres 2 9.98393e-22 3.905e-10 0 3.905e-10 5.75e-10 6.25e-10 6.25e-10 6.25e-10
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pair_coeff 3 3 lj/relres 2 8.19828e-22 3.905e-10 0 3.905e-10 6.75e-10 7.25e-10 7.25e-10 7.25e-10
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pair_coeff 3 4 lj/relres 2 8.19828e-22 3.905e-10 0 3.905e-10 6.22997e-10 6.73146e-10 6.73146e-10 6.73146e-10
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pair_coeff 3 5 lj/relres 2 9.08797e-22 3.9324e-10 0 3.9324e-10 6.75e-10 7.25e-10 7.25e-10 7.25e-10
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pair_coeff 3 6 lj/relres 2 9.98393e-22 3.905e-10 0 3.905e-10 6.22997e-10 6.73146e-10 6.73146e-10 6.73146e-10
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pair_coeff 4 4 lj/relres 2 8.19828e-22 3.905e-10 0 3.905e-10 5.75e-10 6.25e-10 6.25e-10 6.25e-10
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pair_coeff 4 5 lj/relres 2 9.08797e-22 3.9324e-10 0 3.9324e-10 6.22997e-10 6.73146e-10 6.73146e-10 6.73146e-10
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pair_coeff 4 6 lj/relres 2 9.98393e-22 3.905e-10 0 3.905e-10 5.75e-10 6.25e-10 6.25e-10 6.25e-10
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pair_coeff 5 5 lj/relres 2 1.00742e-21 3.96e-10 0 3.96e-10 6.75e-10 7.25e-10 7.25e-10 7.25e-10
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pair_coeff 5 6 lj/relres 2 1.10674e-21 3.9324e-10 0 3.9324e-10 6.22997e-10 6.73146e-10 6.73146e-10 6.73146e-10
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pair_coeff 6 6 lj/relres 2 1.21585e-21 3.905e-10 0 3.905e-10 5.75e-10 6.25e-10 6.25e-10 6.25e-10
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pair_modify shift yes
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neighbor 2.0e-10 bin
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neigh_modify every 2 delay 4 check yes
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timestep 2.0e-15
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thermo 50
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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-13
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run_style respa 2 2 hybrid 1 2
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run 500
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#write_data Data.22DMH.out.relres pair ij
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#pair_write 1 1 1201 r 0.2e-9 1.4e-9 potential.relres LJ11
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#pair_write 2 2 1201 r 0.2e-9 1.4e-9 potential.relres LJ22
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#pair_write 1 2 1201 r 0.2e-9 1.4e-9 potential.relres LJ12
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148
examples/relres/log.09Feb21.22DMH.respa.g++.1
Normal file
148
examples/relres/log.09Feb21.22DMH.respa.g++.1
Normal file
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LAMMPS (24 Dec 2020)
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using 1 OpenMP thread(s) per MPI task
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units si
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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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pair_style hybrid lj/relres 0.675e-9 0.725e-9 1.2e-9 1.4e-9 lj/relres 0.675e-9 .725e-9 1.2e-9 1.4e-9
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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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read_data Data.22DMH.in.relres
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Reading data file ...
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orthogonal box = (3.7421629e-10 3.7421629e-10 3.7421629e-10) to (6.8257837e-09 6.8257837e-09 6.8257837e-09)
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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 = 0.018 seconds
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read_data CPU = 0.170 seconds
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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
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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
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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
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pair_coeff 1 4 lj/relres 2 5.33663e-22 3.85214e-10 0 3.91793e-10 6.22997e-10 6.73146e-10 6.73146e-10 6.73146e-10
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pair_coeff 1 5 lj/relres 2 5.91576e-22 3.87918e-10 0 3.94542e-10 6.75e-10 7.25e-10 7.25e-10 7.25e-10
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pair_coeff 1 6 lj/relres 2 6.49898e-22 3.85214e-10 0 3.91793e-10 6.22997e-10 6.73146e-10 6.73146e-10 6.73146e-10
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pair_coeff 2 2 lj/relres 1 8.19828e-22 3.905e-10 8.48872e-21 3.905e-10 5.75e-10 6.25e-10 1.2e-09 1.4e-09
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pair_coeff 2 3 lj/relres 2 8.19828e-22 3.905e-10 0 3.905e-10 6.22997e-10 6.73146e-10 6.73146e-10 6.73146e-10
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pair_coeff 2 4 lj/relres 2 8.19828e-22 3.905e-10 0 3.905e-10 5.75e-10 6.25e-10 6.25e-10 6.25e-10
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pair_coeff 2 5 lj/relres 2 9.08797e-22 3.9324e-10 0 3.9324e-10 6.22997e-10 6.73146e-10 6.73146e-10 6.73146e-10
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pair_coeff 2 6 lj/relres 2 9.98393e-22 3.905e-10 0 3.905e-10 5.75e-10 6.25e-10 6.25e-10 6.25e-10
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pair_coeff 3 3 lj/relres 2 8.19828e-22 3.905e-10 0 3.905e-10 6.75e-10 7.25e-10 7.25e-10 7.25e-10
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pair_coeff 3 4 lj/relres 2 8.19828e-22 3.905e-10 0 3.905e-10 6.22997e-10 6.73146e-10 6.73146e-10 6.73146e-10
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pair_coeff 3 5 lj/relres 2 9.08797e-22 3.9324e-10 0 3.9324e-10 6.75e-10 7.25e-10 7.25e-10 7.25e-10
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pair_coeff 3 6 lj/relres 2 9.98393e-22 3.905e-10 0 3.905e-10 6.22997e-10 6.73146e-10 6.73146e-10 6.73146e-10
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pair_coeff 4 4 lj/relres 2 8.19828e-22 3.905e-10 0 3.905e-10 5.75e-10 6.25e-10 6.25e-10 6.25e-10
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pair_coeff 4 5 lj/relres 2 9.08797e-22 3.9324e-10 0 3.9324e-10 6.22997e-10 6.73146e-10 6.73146e-10 6.73146e-10
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pair_coeff 4 6 lj/relres 2 9.98393e-22 3.905e-10 0 3.905e-10 5.75e-10 6.25e-10 6.25e-10 6.25e-10
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pair_coeff 5 5 lj/relres 2 1.00742e-21 3.96e-10 0 3.96e-10 6.75e-10 7.25e-10 7.25e-10 7.25e-10
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pair_coeff 5 6 lj/relres 2 1.10674e-21 3.9324e-10 0 3.9324e-10 6.22997e-10 6.73146e-10 6.73146e-10 6.73146e-10
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pair_coeff 6 6 lj/relres 2 1.21585e-21 3.905e-10 0 3.905e-10 5.75e-10 6.25e-10 6.25e-10 6.25e-10
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pair_modify shift yes
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neighbor 2.0e-10 bin
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neigh_modify every 2 delay 4 check yes
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timestep 2.0e-15
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thermo 50
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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-13
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run_style respa 2 2 hybrid 1 2
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Respa levels:
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1 = bond angle dihedral improper hybrid-1
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2 = hybrid-2 kspace
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run 500
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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 = 1.6e-09
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ghost atom cutoff = 1.6e-09
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binsize = 8e-10, bins = 9 9 9
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3 neighbor lists, perpetual/occasional/extra = 3 0 0
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(1) pair lj/relres, perpetual, skip from (3)
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attributes: half, newton on
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pair build: skip
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stencil: none
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bin: none
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(2) pair lj/relres, perpetual, skip from (3)
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attributes: half, newton on
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pair build: skip
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stencil: none
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bin: none
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(3) neighbor class addition, 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) = 24.68 | 24.68 | 24.68 Mbytes
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Step Temp Press PotEng KinEng TotEng E_pair E_mol Volume
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0 286.85659 -21399113 2.6345159e-17 4.7519899e-17 7.3865059e-17 -3.3260563e-17 5.9605722e-17 2.685318e-25
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50 292.22255 10509008 2.525105e-17 4.840881e-17 7.3659861e-17 -3.2554301e-17 5.7805351e-17 2.685318e-25
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100 291.58497 48053357 2.4902763e-17 4.8303191e-17 7.3205953e-17 -3.325361e-17 5.8156373e-17 2.685318e-25
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150 291.49413 37394583 2.4391667e-17 4.8288142e-17 7.2679809e-17 -3.3414422e-17 5.7806089e-17 2.685318e-25
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200 287.20382 26161531 2.4752701e-17 4.7577421e-17 7.2330122e-17 -3.3050943e-17 5.7803644e-17 2.685318e-25
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250 288.54952 -9191037 2.4382928e-17 4.7800345e-17 7.2183273e-17 -3.3506471e-17 5.78894e-17 2.685318e-25
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300 291.83353 19619708 2.369006e-17 4.8344366e-17 7.2034426e-17 -3.3461257e-17 5.7151317e-17 2.685318e-25
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350 290.64842 60193012 2.3711746e-17 4.8148044e-17 7.185979e-17 -3.3286381e-17 5.6998127e-17 2.685318e-25
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400 293.0168 38268765 2.3173289e-17 4.8540384e-17 7.1713672e-17 -3.3633853e-17 5.6807142e-17 2.685318e-25
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450 289.19195 33053376 2.36093e-17 4.7906769e-17 7.151607e-17 -3.3774223e-17 5.7383524e-17 2.685318e-25
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500 292.43942 -684078.27 2.2898459e-17 4.8444735e-17 7.1343194e-17 -3.3856946e-17 5.6755405e-17 2.685318e-25
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Loop time of 15.899 on 1 procs for 500 steps with 8000 atoms
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99.9% 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 | 11.067 | 11.067 | 11.067 | 0.0 | 69.61
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Bond | 1.7933 | 1.7933 | 1.7933 | 0.0 | 11.28
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Neigh | 1.5748 | 1.5748 | 1.5748 | 0.0 | 9.91
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Comm | 0.50431 | 0.50431 | 0.50431 | 0.0 | 3.17
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Output | 0.0013113 | 0.0013113 | 0.0013113 | 0.0 | 0.01
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Modify | 0.69311 | 0.69311 | 0.69311 | 0.0 | 4.36
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Other | | 0.2656 | | | 1.67
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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: 18908.0 ave 18908 max 18908 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 126950.0 ave 126950 max 126950 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 126950
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Ave neighs/atom = 15.868750
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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_data Data.22DMH.out.relres pair ij
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#pair_write 1 1 1201 r 0.2e-9 1.4e-9 potential.relres LJ11
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#pair_write 2 2 1201 r 0.2e-9 1.4e-9 potential.relres LJ22
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#pair_write 1 2 1201 r 0.2e-9 1.4e-9 potential.relres LJ12
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Please see the log.cite file for references relevant to this simulation
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Total wall time: 0:00:16
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148
examples/relres/log.09Feb21.22DMH.respa.g++.4
Normal file
148
examples/relres/log.09Feb21.22DMH.respa.g++.4
Normal file
@ -0,0 +1,148 @@
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LAMMPS (24 Dec 2020)
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using 1 OpenMP thread(s) per MPI task
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units si
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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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pair_style hybrid lj/relres 0.675e-9 0.725e-9 1.2e-9 1.4e-9 lj/relres 0.675e-9 .725e-9 1.2e-9 1.4e-9
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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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read_data Data.22DMH.in.relres
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Reading data file ...
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orthogonal box = (3.7421629e-10 3.7421629e-10 3.7421629e-10) to (6.8257837e-09 6.8257837e-09 6.8257837e-09)
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1 by 2 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 = 0.005 seconds
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read_data CPU = 0.135 seconds
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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
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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
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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
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pair_coeff 1 4 lj/relres 2 5.33663e-22 3.85214e-10 0 3.91793e-10 6.22997e-10 6.73146e-10 6.73146e-10 6.73146e-10
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pair_coeff 1 5 lj/relres 2 5.91576e-22 3.87918e-10 0 3.94542e-10 6.75e-10 7.25e-10 7.25e-10 7.25e-10
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pair_coeff 1 6 lj/relres 2 6.49898e-22 3.85214e-10 0 3.91793e-10 6.22997e-10 6.73146e-10 6.73146e-10 6.73146e-10
|
||||
pair_coeff 2 2 lj/relres 1 8.19828e-22 3.905e-10 8.48872e-21 3.905e-10 5.75e-10 6.25e-10 1.2e-09 1.4e-09
|
||||
pair_coeff 2 3 lj/relres 2 8.19828e-22 3.905e-10 0 3.905e-10 6.22997e-10 6.73146e-10 6.73146e-10 6.73146e-10
|
||||
pair_coeff 2 4 lj/relres 2 8.19828e-22 3.905e-10 0 3.905e-10 5.75e-10 6.25e-10 6.25e-10 6.25e-10
|
||||
pair_coeff 2 5 lj/relres 2 9.08797e-22 3.9324e-10 0 3.9324e-10 6.22997e-10 6.73146e-10 6.73146e-10 6.73146e-10
|
||||
pair_coeff 2 6 lj/relres 2 9.98393e-22 3.905e-10 0 3.905e-10 5.75e-10 6.25e-10 6.25e-10 6.25e-10
|
||||
pair_coeff 3 3 lj/relres 2 8.19828e-22 3.905e-10 0 3.905e-10 6.75e-10 7.25e-10 7.25e-10 7.25e-10
|
||||
pair_coeff 3 4 lj/relres 2 8.19828e-22 3.905e-10 0 3.905e-10 6.22997e-10 6.73146e-10 6.73146e-10 6.73146e-10
|
||||
pair_coeff 3 5 lj/relres 2 9.08797e-22 3.9324e-10 0 3.9324e-10 6.75e-10 7.25e-10 7.25e-10 7.25e-10
|
||||
pair_coeff 3 6 lj/relres 2 9.98393e-22 3.905e-10 0 3.905e-10 6.22997e-10 6.73146e-10 6.73146e-10 6.73146e-10
|
||||
pair_coeff 4 4 lj/relres 2 8.19828e-22 3.905e-10 0 3.905e-10 5.75e-10 6.25e-10 6.25e-10 6.25e-10
|
||||
pair_coeff 4 5 lj/relres 2 9.08797e-22 3.9324e-10 0 3.9324e-10 6.22997e-10 6.73146e-10 6.73146e-10 6.73146e-10
|
||||
pair_coeff 4 6 lj/relres 2 9.98393e-22 3.905e-10 0 3.905e-10 5.75e-10 6.25e-10 6.25e-10 6.25e-10
|
||||
pair_coeff 5 5 lj/relres 2 1.00742e-21 3.96e-10 0 3.96e-10 6.75e-10 7.25e-10 7.25e-10 7.25e-10
|
||||
pair_coeff 5 6 lj/relres 2 1.10674e-21 3.9324e-10 0 3.9324e-10 6.22997e-10 6.73146e-10 6.73146e-10 6.73146e-10
|
||||
pair_coeff 6 6 lj/relres 2 1.21585e-21 3.905e-10 0 3.905e-10 5.75e-10 6.25e-10 6.25e-10 6.25e-10
|
||||
|
||||
pair_modify shift yes
|
||||
neighbor 2.0e-10 bin
|
||||
neigh_modify every 2 delay 4 check yes
|
||||
|
||||
timestep 2.0e-15
|
||||
thermo 50
|
||||
thermo_style custom step temp press pe ke etotal epair emol vol
|
||||
fix 2 all nvt temp 290 290 2.0e-13
|
||||
|
||||
run_style respa 2 2 hybrid 1 2
|
||||
Respa levels:
|
||||
1 = bond angle dihedral improper hybrid-1
|
||||
2 = hybrid-2 kspace
|
||||
|
||||
run 500
|
||||
Neighbor list info ...
|
||||
update every 2 steps, delay 4 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.6e-09
|
||||
ghost atom cutoff = 1.6e-09
|
||||
binsize = 8e-10, bins = 9 9 9
|
||||
3 neighbor lists, perpetual/occasional/extra = 3 0 0
|
||||
(1) pair lj/relres, perpetual, skip from (3)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair lj/relres, perpetual, skip from (3)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) neighbor class addition, 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) = 12.35 | 12.35 | 12.35 Mbytes
|
||||
Step Temp Press PotEng KinEng TotEng E_pair E_mol Volume
|
||||
0 286.85659 -21399113 2.6345159e-17 4.7519899e-17 7.3865059e-17 -3.3260563e-17 5.9605722e-17 2.685318e-25
|
||||
50 292.22255 10509008 2.525105e-17 4.840881e-17 7.3659861e-17 -3.2554301e-17 5.7805351e-17 2.685318e-25
|
||||
100 291.58497 48053357 2.4902763e-17 4.8303191e-17 7.3205953e-17 -3.325361e-17 5.8156373e-17 2.685318e-25
|
||||
150 291.49413 37394583 2.4391667e-17 4.8288142e-17 7.2679809e-17 -3.3414422e-17 5.7806089e-17 2.685318e-25
|
||||
200 287.20382 26161531 2.4752701e-17 4.7577421e-17 7.2330122e-17 -3.3050943e-17 5.7803644e-17 2.685318e-25
|
||||
250 288.54952 -9191037 2.4382928e-17 4.7800345e-17 7.2183273e-17 -3.3506471e-17 5.78894e-17 2.685318e-25
|
||||
300 291.83353 19619708 2.369006e-17 4.8344366e-17 7.2034426e-17 -3.3461257e-17 5.7151317e-17 2.685318e-25
|
||||
350 290.64842 60193012 2.3711746e-17 4.8148044e-17 7.185979e-17 -3.3286381e-17 5.6998127e-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
|
||||
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
|
||||
|
||||
98.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.6826 | 2.7363 | 2.7963 | 2.5 | 61.46
|
||||
Bond | 0.45619 | 0.46186 | 0.46906 | 0.8 | 10.37
|
||||
Neigh | 0.42817 | 0.42863 | 0.4292 | 0.1 | 9.63
|
||||
Comm | 0.49036 | 0.56091 | 0.62185 | 6.5 | 12.60
|
||||
Output | 0.00049472 | 0.0013556 | 0.0024905 | 2.0 | 0.03
|
||||
Modify | 0.1831 | 0.18662 | 0.19193 | 0.8 | 4.19
|
||||
Other | | 0.07637 | | | 1.72
|
||||
|
||||
Nlocal: 2000.00 ave 2016 max 1985 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
Nghost: 9883.00 ave 9895 max 9866 min
|
||||
Histogram: 1 0 0 0 0 1 0 1 0 1
|
||||
Neighs: 31737.5 ave 32060 max 31459 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 126950
|
||||
Ave neighs/atom = 15.868750
|
||||
Ave special neighs/atom = 5.2500000
|
||||
Neighbor list builds = 13
|
||||
Dangerous builds = 0
|
||||
#write_data Data.22DMH.out.relres pair ij
|
||||
#pair_write 1 1 1201 r 0.2e-9 1.4e-9 potential.relres LJ11
|
||||
#pair_write 2 2 1201 r 0.2e-9 1.4e-9 potential.relres LJ22
|
||||
#pair_write 1 2 1201 r 0.2e-9 1.4e-9 potential.relres LJ12
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:04
|
||||
Reference in New Issue
Block a user