LAMMPS (8 Feb 2023) using 1 OpenMP thread(s) per MPI task # Interface newton off units lj atom_style dielectric atom_modify map array dimension 3 boundary f f f variable method index gmres # gmres = BEM/GMRES # icc = BEM/ICC* # dof = Direct optimization of the functional # none variable data index data.sphere read_data ${data} read_data data.sphere Reading data file ... orthogonal box = (0 0 0) to (100 100 100) 1 by 1 by 1 MPI processor grid WARNING: Atom style in data file differs from currently defined atom style (src/read_data.cpp:620) reading atoms ... 643 atoms Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 0 0 special bond factors coul: 0 0 0 0 = max # of 1-2 neighbors 0 = max # of 1-3 neighbors 0 = max # of 1-4 neighbors 1 = max # of special neighbors special bonds CPU = 0.000 seconds read_data CPU = 0.004 seconds group interface type 1 642 atoms in group interface group ions type 2 3 1 atoms in group ions pair_style lj/cut/coul/cut/dielectric 1.122 20.0 pair_coeff * * 1.0 1.0 pair_coeff 1 1 0.0 1.0 neigh_modify one 5000 #compute ef all efield/atom #dump 1 all custom 100 all.dump id mol type q x y z #c_ef[1] c_ef[2] c_ef[3] # #dump 2 interface custom 100 interface.dump id mol type q x y z #c_ef[1] c_ef[2] c_ef[3] #dump_modify 1 sort id fix 1 ions nve if "${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' " fix 3 interface polarize/bem/icc 1 1.0e-4 thermo 1000 thermo_style custom step evdwl ecoul elong epair thermo_modify flush yes run 0 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - DIELECTRIC package: doi:10.1016/j.cpc.2019.03.006 @Article{TrungCPC19, author = {Trung Dac Nguyen and Honghao Li and Debarshee Bagchi and Francisco J. Solis and Olvera de la Cruz, Monica} title = {Incorporating Surface Polarization Effects Into Large-Scale Coarse-Grained Molecular Dynamics Simulation}, journal = {Comput.\ Phys.\ Commun.}, year = 2019, volume = 241, pages = {80--91} } CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule BEM/ICC solver for 642 induced charges using pair style lj/cut/coul/cut/dielectric Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 5000, page size: 100000 master list distance cutoff = 20.3 ghost atom cutoff = 20.3 binsize = 10.15, bins = 10 10 10 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut/coul/cut/dielectric, perpetual attributes: full, newton off pair build: full/bin stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 8.898 | 8.898 | 8.898 Mbytes Step E_vdwl E_coul E_long E_pair 0 0 -0.011226707 0 -0.011226707 Loop time of 1.532e-06 on 1 procs for 0 steps with 643 atoms 130.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Bond | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 1.532e-06 | | |100.00 Nlocal: 643 ave 643 max 643 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 412806 ave 412806 max 412806 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 412806 Ave neighs/atom = 642 Ave special neighs/atom = 0 Neighbor list builds = 0 Dangerous builds = 0 Total wall time: 0:00:00