132 lines
4.6 KiB
Groff
132 lines
4.6 KiB
Groff
LAMMPS (8 Feb 2023)
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using 1 OpenMP thread(s) per MPI task
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# Interface
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newton off
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units lj
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atom_style dielectric
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atom_modify map array
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dimension 3
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boundary f f f
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variable method index gmres # gmres = BEM/GMRES
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# icc = BEM/ICC*
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# dof = Direct optimization of the functional
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# none
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variable data index data.sphere
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read_data ${data}
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read_data data.sphere
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Reading data file ...
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orthogonal box = (0 0 0) to (100 100 100)
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1 by 1 by 1 MPI processor grid
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WARNING: Atom style in data file differs from currently defined atom style (src/read_data.cpp:620)
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reading atoms ...
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643 atoms
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 0 0
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special bond factors coul: 0 0 0
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0 = max # of 1-2 neighbors
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0 = max # of 1-3 neighbors
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0 = max # of 1-4 neighbors
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1 = max # of special neighbors
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special bonds CPU = 0.000 seconds
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read_data CPU = 0.004 seconds
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group interface type 1
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642 atoms in group interface
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group ions type 2 3
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1 atoms in group ions
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pair_style lj/cut/coul/cut/dielectric 1.122 20.0
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pair_coeff * * 1.0 1.0
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pair_coeff 1 1 0.0 1.0
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neigh_modify one 5000
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#compute ef all efield/atom
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#dump 1 all custom 100 all.dump id mol type q x y z #c_ef[1] c_ef[2] c_ef[3]
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#
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#dump 2 interface custom 100 interface.dump id mol type q x y z #c_ef[1] c_ef[2] c_ef[3]
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#dump_modify 1 sort id
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fix 1 ions nve
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if "${method} == gmres" then "fix 3 interface polarize/bem/gmres 1 1.0e-4" elif "${method} == icc" "fix 3 interface polarize/bem/icc 1 1.0e-4" elif "${method} == dof" "fix 3 interface polarize/functional 1 1.0e-4" else "print 'Unsupported method for polarization' "
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fix 3 interface polarize/bem/gmres 1 1.0e-4
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thermo 1000
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thermo_style custom step evdwl ecoul elong epair
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thermo_modify flush yes
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run 0
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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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- DIELECTRIC package: doi:10.1016/j.cpc.2019.03.006
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@Article{TrungCPC19,
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author = {Trung Dac Nguyen and Honghao Li and Debarshee Bagchi and Francisco J. Solis and Olvera de la Cruz, Monica}
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title = {Incorporating Surface Polarization Effects Into Large-Scale
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Coarse-Grained Molecular Dynamics Simulation},
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journal = {Comput.\ Phys.\ Commun.},
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year = 2019,
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volume = 241,
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pages = {80--91}
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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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Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
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BEM/GMRES solver for 642 induced charges using maximum 641 q-vectors
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Neighbor list info ...
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update: every = 1 steps, delay = 0 steps, check = yes
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max neighbors/atom: 5000, page size: 100000
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master list distance cutoff = 20.3
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ghost atom cutoff = 20.3
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binsize = 10.15, bins = 10 10 10
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut/coul/cut/dielectric, perpetual
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attributes: full, newton off
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pair build: full/bin
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stencil: full/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 18.6 | 18.6 | 18.6 Mbytes
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Step E_vdwl E_coul E_long E_pair
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0 0 -0.011226675 0 -0.011226675
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Loop time of 1.659e-06 on 1 procs for 0 steps with 643 atoms
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120.6% 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 | 0 | 0 | 0 | 0.0 | 0.00
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Bond | 0 | 0 | 0 | 0.0 | 0.00
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0 | 0 | 0 | 0.0 | 0.00
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Output | 0 | 0 | 0 | 0.0 | 0.00
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Modify | 0 | 0 | 0 | 0.0 | 0.00
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Other | | 1.659e-06 | | |100.00
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Nlocal: 643 ave 643 max 643 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 0 ave 0 max 0 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 0 ave 0 max 0 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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FullNghs: 412806 ave 412806 max 412806 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 412806
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Ave neighs/atom = 642
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Ave special neighs/atom = 0
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Neighbor list builds = 0
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Dangerous builds = 0
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Total wall time: 0:00:00
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