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/functional 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
Direct solver using a variational approach for 642 induced charges
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
  2 neighbor lists, perpetual/occasional/extra = 2 0 0
  (1) pair lj/cut/coul/cut/dielectric, perpetual
      attributes: full, newton off
      pair build: full/bin
      stencil: full/bin/3d
      bin: standard
  (2) fix polarize/functional, perpetual, copy from (1)
      attributes: full, newton off
      pair build: copy
      stencil: none
      bin: none
Per MPI rank memory allocation (min/avg/max) = 29.83 | 29.83 | 29.83 Mbytes
   Step         E_vdwl         E_coul         E_long         E_pair    
         0   0             -0.011053355    0             -0.011053355  
Loop time of 1.691e-06 on 1 procs for 0 steps with 643 atoms

177.4% 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   |            | 1.691e-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: 0:00:02
