New pair style lj/relres
This commit is contained in:
Mark Chaimovich
37075
examples/relres/Data.22DMH.in.relres
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37075
examples/relres/Data.22DMH.in.relres
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5
examples/relres/README
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5
examples/relres/README
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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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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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31
examples/relres/in.22DMH.relres
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examples/relres/in.22DMH.relres
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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 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 6 6 1.21585e-21 0.3905e-9 0 0.3905e-9 0.575e-9 0.625e-9 1.2e-9 1.4e-9
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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
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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
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pair_coeff 5 5 1.00742E-21 0.396E-9 0 0.396E-9
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pair_coeff 3 3 0.819828e-21 0.3905e-9 0 0.3905e-9
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pair_coeff 1 1 0.347385E-21 0.38E-9 20.2372E-21 0.39309E-9
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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 1.0e-15
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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-13
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run 1000
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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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121
examples/relres/log.relres
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examples/relres/log.relres
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LAMMPS (24 Dec 2020)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
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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 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 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 = 0.003 seconds
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read_data CPU = 0.062 seconds
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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
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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
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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
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pair_coeff 5 5 1.00742E-21 0.396E-9 0 0.396E-9
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pair_coeff 3 3 0.819828e-21 0.3905e-9 0 0.3905e-9
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pair_coeff 1 1 0.347385E-21 0.38E-9 20.2372E-21 0.39309E-9
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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 1.0e-15
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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-13
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run 1000
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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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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) = 19.53 | 19.53 | 19.53 Mbytes
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Step Temp Press PotEng KinEng TotEng E_pair E_mol Volume
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0 286.85659 -21390710 2.6345656e-17 4.7519899e-17 7.3865555e-17 -3.3260066e-17 5.9605722e-17 2.685318e-25
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100 292.25165 10716172 2.5245584e-17 4.841363e-17 7.3659214e-17 -3.2561964e-17 5.7807548e-17 2.685318e-25
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200 291.6011 48774461 2.4897987e-17 4.8305863e-17 7.320385e-17 -3.3268705e-17 5.8166692e-17 2.685318e-25
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300 291.50656 37655969 2.4389062e-17 4.8290201e-17 7.2679262e-17 -3.3428236e-17 5.7817297e-17 2.685318e-25
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400 287.23427 25920755 2.4747225e-17 4.7582464e-17 7.2329689e-17 -3.3065908e-17 5.7813133e-17 2.685318e-25
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500 288.56911 -9297451 2.4379025e-17 4.7803591e-17 7.2182615e-17 -3.3515426e-17 5.7894451e-17 2.685318e-25
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600 291.82949 20083719 2.3686904e-17 4.8343696e-17 7.2030599e-17 -3.3468666e-17 5.7155569e-17 2.685318e-25
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700 290.64445 60535932 2.3704156e-17 4.8147386e-17 7.1851542e-17 -3.3299994e-17 5.700415e-17 2.685318e-25
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800 293.01243 38119194 2.3163674e-17 4.8539659e-17 7.1703333e-17 -3.3641284e-17 5.6804958e-17 2.685318e-25
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900 289.1191 32514067 2.3608264e-17 4.7894701e-17 7.1502965e-17 -3.3787865e-17 5.7396129e-17 2.685318e-25
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1000 292.45834 -714652.68 2.2885394e-17 4.8447871e-17 7.1333265e-17 -3.3864138e-17 5.6749532e-17 2.685318e-25
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Loop time of 7.07676 on 2 procs for 1000 steps with 8000 atoms
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99.7% CPU use with 2 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 | 5.1275 | 5.1852 | 5.243 | 2.5 | 73.27
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Bond | 1.0056 | 1.0072 | 1.0087 | 0.2 | 14.23
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Neigh | 0.38261 | 0.38263 | 0.38266 | 0.0 | 5.41
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Comm | 0.25513 | 0.31266 | 0.37018 | 10.3 | 4.42
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Output | 0.00042391 | 0.00044036 | 0.00045681 | 0.0 | 0.01
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Modify | 0.14501 | 0.14643 | 0.14785 | 0.4 | 2.07
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Other | | 0.04219 | | | 0.60
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Nlocal: 4000.00 ave 4000 max 4000 min
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Histogram: 2 0 0 0 0 0 0 0 0 0
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Nghost: 13887.5 ave 13896 max 13879 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Neighs: 217142.0 ave 217471 max 216812 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Total # of neighbors = 434283
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Ave neighs/atom = 54.285375
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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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Creating table file potential.relres with DATE: 2021-02-05
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pair_write 2 2 1201 r 0.2e-9 1.4e-9 potential.relres LJ22
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Appending to table file potential.relres with DATE: 2021-02-05
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pair_write 1 2 1201 r 0.2e-9 1.4e-9 potential.relres LJ12
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Appending to table file potential.relres with DATE: 2021-02-05
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Please see the log.cite file for references relevant to this simulation
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Total wall time: 0:00:07
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3619
examples/relres/potential.relres
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3619
examples/relres/potential.relres
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File diff suppressed because it is too large
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