From 71c4edda51da7a11287eab3ccb48ef2a00c6bfb9 Mon Sep 17 00:00:00 2001 From: vishalkenchan Date: Fri, 29 Sep 2017 15:52:34 +0200 Subject: [PATCH 1/2] add coul/wolf/cs and born/coul/wolf/cs pair styles for CORESHELL package --- src/CORESHELL/Install.sh | 24 ++-- src/CORESHELL/pair_born_coul_wolf_cs.cpp | 170 +++++++++++++++++++++++ src/CORESHELL/pair_born_coul_wolf_cs.h | 60 ++++++++ src/CORESHELL/pair_coul_wolf_cs.cpp | 145 +++++++++++++++++++ src/CORESHELL/pair_coul_wolf_cs.h | 54 +++++++ 5 files changed, 444 insertions(+), 9 deletions(-) create mode 100644 src/CORESHELL/pair_born_coul_wolf_cs.cpp create mode 100644 src/CORESHELL/pair_born_coul_wolf_cs.h create mode 100644 src/CORESHELL/pair_coul_wolf_cs.cpp create mode 100644 src/CORESHELL/pair_coul_wolf_cs.h diff --git a/src/CORESHELL/Install.sh b/src/CORESHELL/Install.sh index 7c0b7a02a2..93c8fe8132 100644 --- a/src/CORESHELL/Install.sh +++ b/src/CORESHELL/Install.sh @@ -30,13 +30,19 @@ action () { action compute_temp_cs.cpp action compute_temp_cs.h -action pair_born_coul_long_cs.cpp pair_born_coul_long.cpp -action pair_born_coul_dsf_cs.cpp pair_born_coul_dsf.cpp -action pair_buck_coul_long_cs.cpp pair_buck_coul_long.cpp -action pair_born_coul_long_cs.h pair_born_coul_long.h -action pair_born_coul_dsf_cs.h pair_born_coul_dsf.h -action pair_buck_coul_long_cs.h pair_buck_coul_long.h -action pair_coul_long_cs.cpp pair_coul_long.cpp -action pair_coul_long_cs.h pair_coul_long.h + +action pair_born_coul_long_cs.cpp pair_born_coul_long.cpp +action pair_born_coul_dsf_cs.cpp pair_born_coul_dsf.cpp +action pair_buck_coul_long_cs.cpp pair_buck_coul_long.cpp +action pair_born_coul_long_cs.h pair_born_coul_long.h +action pair_born_coul_dsf_cs.h pair_born_coul_dsf.h +action pair_buck_coul_long_cs.h pair_buck_coul_long.h +action pair_coul_long_cs.cpp pair_coul_long.cpp +action pair_coul_long_cs.h pair_coul_long.h action pair_lj_cut_coul_long_cs.cpp pair_lj_cut_coul_long.cpp -action pair_lj_cut_coul_long_cs.h pair_lj_cut_coul_long.h +action pair_lj_cut_coul_long_cs.h pair_lj_cut_coul_long.h + +action pair_born_coul_wolf_cs.cpp pair_born_coul_wolf.cpp +action pair_born_coul_wolf_cs.h pair_born_coul_wolf.h +action pair_coul_wolf_cs.cpp pair_coul_wolf.cpp +action pair_coul_wolf_cs.h pair_coul_wolf.h diff --git a/src/CORESHELL/pair_born_coul_wolf_cs.cpp b/src/CORESHELL/pair_born_coul_wolf_cs.cpp new file mode 100644 index 0000000000..c57e00cbd0 --- /dev/null +++ b/src/CORESHELL/pair_born_coul_wolf_cs.cpp @@ -0,0 +1,170 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + + +#include +#include +#include +#include +#include "pair_born_coul_wolf_cs.h" +#include "atom.h" +#include "comm.h" +#include "force.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "math_const.h" +#include "math_special.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; +using namespace MathConst; +using namespace MathSpecial; + +#define EPSILON 1.0e-20 + +/* ---------------------------------------------------------------------- */ + +PairBornCoulWolfCS::PairBornCoulWolfCS(LAMMPS *lmp) : PairBornCoulWolf(lmp) +{ + single_enable = 0; +} + +/* ---------------------------------------------------------------------- */ + +void PairBornCoulWolfCS::compute(int eflag, int vflag) +{ + int i,j,ii,jj,inum,jnum,itype,jtype; + double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair; + double rsq,r2inv,r6inv,forcecoul,forceborn,factor_coul,factor_lj; + double prefactor; + double r,rexp; + int *ilist,*jlist,*numneigh,**firstneigh; + double erfcc,erfcd,v_sh,dvdrr,e_self,e_shift,f_shift,qisq; + + evdwl = ecoul = 0.0; + if (eflag || vflag) ev_setup(eflag,vflag); + else evflag = vflag_fdotr = 0; + + double **x = atom->x; + double **f = atom->f; + double *q = atom->q; + int *type = atom->type; + int nlocal = atom->nlocal; + double *special_coul = force->special_coul; + double *special_lj = force->special_lj; + int newton_pair = force->newton_pair; + double qqrd2e = force->qqrd2e; + + // self and shifted coulombic energy + + e_self = v_sh = 0.0; + e_shift = erfc(alf*cut_coul)/cut_coul; + f_shift = -(e_shift+ 2.0*alf/MY_PIS * exp(-alf*alf*cut_coul*cut_coul)) / + cut_coul; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // loop over neighbors of my atoms + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + qtmp = q[i]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + qisq = qtmp*qtmp; + e_self = -(e_shift/2.0 + alf/MY_PIS) * qisq*qqrd2e; + if (eflag) ev_tally(i,i,nlocal,0,0.0,e_self,0.0,0.0,0.0,0.0); + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + factor_lj = special_lj[sbmask(j)]; + factor_coul = special_coul[sbmask(j)]; + j &= NEIGHMASK; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + jtype = type[j]; + + if (rsq < cutsq[itype][jtype]) { + rsq += EPSILON; + // Add EPISLON for case: r = 0; Interaction must be removed + // by special bond + r2inv = 1.0/rsq; + + if (rsq < cut_coulsq) { + r = sqrt(rsq); + prefactor = qqrd2e*qtmp*q[j]/r; + erfcc = erfc(alf*r); + erfcd = exp(-alf*alf*r*r); + v_sh = (erfcc - e_shift*r) * prefactor; + dvdrr = (erfcc/rsq + 2.0*alf/MY_PIS * erfcd/r) + f_shift; + forcecoul = dvdrr*rsq*prefactor; + if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor; + } else forcecoul = 0.0; + + if (rsq < cut_ljsq[itype][jtype]) { + r6inv = r2inv*r2inv*r2inv; + r = sqrt(rsq); + rexp = exp((sigma[itype][jtype]-r)*rhoinv[itype][jtype]); + forceborn = born1[itype][jtype]*r*rexp - born2[itype][jtype]*r6inv + + born3[itype][jtype]*r2inv*r6inv; + } else forceborn = 0.0; + + fpair = (forcecoul + factor_lj*forceborn) * r2inv; + + f[i][0] += delx*fpair; + f[i][1] += dely*fpair; + f[i][2] += delz*fpair; + if (newton_pair || j < nlocal) { + f[j][0] -= delx*fpair; + f[j][1] -= dely*fpair; + f[j][2] -= delz*fpair; + } + + if (eflag) { + if (rsq < cut_coulsq) { + ecoul = v_sh; + if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor; + } else ecoul = 0.0; + if (rsq < cut_ljsq[itype][jtype]) { + evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv + + d[itype][jtype]*r6inv*r2inv - offset[itype][jtype]; + evdwl *= factor_lj; + } else evdwl = 0.0; + } + + if (evflag) ev_tally(i,j,nlocal,newton_pair, + evdwl,ecoul,fpair,delx,dely,delz); + } + } + } + + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* +Using erfc and expmsq provided by math_special.h + +See: http://lammps.sandia.gov/threads/msg61934.html +*/ diff --git a/src/CORESHELL/pair_born_coul_wolf_cs.h b/src/CORESHELL/pair_born_coul_wolf_cs.h new file mode 100644 index 0000000000..00bbd5874c --- /dev/null +++ b/src/CORESHELL/pair_born_coul_wolf_cs.h @@ -0,0 +1,60 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(born/coul/wolf/cs,PairBornCoulWolfCS) + +#else + +#ifndef LMP_PAIR_BORN_COUL_WOLF_CS_H +#define LMP_PAIR_BORN_COUL_WOLF_CS_H + +#include "pair_born_coul_wolf.h" + +namespace LAMMPS_NS { + +class PairBornCoulWolfCS : public PairBornCoulWolf { + public: + PairBornCoulWolfCS(class LAMMPS *); + virtual void compute(int, int); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +E: All pair coeffs are not set + +All pair coefficients must be set in the data file or by the +pair_coeff command before running a simulation. + +E: Pair style born/coul/wolf/cs requires atom attribute q + +An atom style that defines this attribute must be used. + + +*/ diff --git a/src/CORESHELL/pair_coul_wolf_cs.cpp b/src/CORESHELL/pair_coul_wolf_cs.cpp new file mode 100644 index 0000000000..15de7c6777 --- /dev/null +++ b/src/CORESHELL/pair_coul_wolf_cs.cpp @@ -0,0 +1,145 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + + +#include +#include +#include +#include +#include "pair_coul_wolf_cs.h" +#include "atom.h" +#include "comm.h" +#include "force.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "math_const.h" +#include "math_special.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; +using namespace MathConst; +using namespace MathSpecial; + +#define EPSILON 1.0e-20 + +/* ---------------------------------------------------------------------- */ + +PairCoulWolfCS::PairCoulWolfCS(LAMMPS *lmp) : PairCoulWolf( lmp ) +{ + single_enable = 0; +} + +/* ---------------------------------------------------------------------- */ + +void PairCoulWolfCS::compute(int eflag, int vflag) +{ + int i,j,ii,jj,inum,jnum; + double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,ecoul,fpair; + double rsq,forcecoul,factor_coul; + double prefactor; + double r; + int *ilist,*jlist,*numneigh,**firstneigh; + double erfcc,erfcd,v_sh,dvdrr,e_self,e_shift,f_shift,qisq; + + ecoul = 0.0; + if (eflag || vflag) ev_setup(eflag,vflag); + else evflag = vflag_fdotr = 0; + + double **x = atom->x; + double **f = atom->f; + double *q = atom->q; + int nlocal = atom->nlocal; + double *special_coul = force->special_coul; + int newton_pair = force->newton_pair; + double qqrd2e = force->qqrd2e; + + // self and shifted coulombic energy + + e_self = v_sh = 0.0; + e_shift = erfc(alf*cut_coul)/cut_coul; + f_shift = -(e_shift+ 2.0*alf/MY_PIS * exp(-alf*alf*cut_coul*cut_coul)) / + cut_coul; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // loop over neighbors of my atoms + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + qtmp = q[i]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + qisq = qtmp*qtmp; + e_self = -(e_shift/2.0 + alf/MY_PIS) * qisq*qqrd2e; + if (evflag) ev_tally(i,i,nlocal,0,0.0,e_self,0.0,0.0,0.0,0.0); + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + factor_coul = special_coul[sbmask(j)]; + j &= NEIGHMASK; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq < cut_coulsq) { + rsq += EPSILON; + // Add EPISLON for case: r = 0; Interaction must be removed + // by special bond + r = sqrt(rsq); + prefactor = qqrd2e*qtmp*q[j]/r; + erfcc = erfc(alf*r); + erfcd = exp(-alf*alf*r*r); + v_sh = (erfcc - e_shift*r) * prefactor; + dvdrr = (erfcc/rsq + 2.0*alf/MY_PIS * erfcd/r) + f_shift; + forcecoul = dvdrr*rsq*prefactor; + if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor; + fpair = forcecoul / rsq; + + f[i][0] += delx*fpair; + f[i][1] += dely*fpair; + f[i][2] += delz*fpair; + if (newton_pair || j < nlocal) { + f[j][0] -= delx*fpair; + f[j][1] -= dely*fpair; + f[j][2] -= delz*fpair; + } + + if (eflag) { + ecoul = v_sh; + if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor; + } else ecoul = 0.0; + + if (evflag) ev_tally(i,j,nlocal,newton_pair, + 0.0,ecoul,fpair,delx,dely,delz); + } + } + } + + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* NOTES +Using erfc and expmsq provided by math_special.h + +See: http://lammps.sandia.gov/threads/msg61934.html +*/ diff --git a/src/CORESHELL/pair_coul_wolf_cs.h b/src/CORESHELL/pair_coul_wolf_cs.h new file mode 100644 index 0000000000..8d98b1bbc6 --- /dev/null +++ b/src/CORESHELL/pair_coul_wolf_cs.h @@ -0,0 +1,54 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(coul/wolf/cs,PairCoulWolfCS) + +#else + +#ifndef LMP_PAIR_COUL_WOLF_CS_H_ +#define LMP_PAIR_COUL_WOLF_CS_H_ + +#include "pair_coul_wolf.h" + +namespace LAMMPS_NS { + +class PairCoulWolfCS : public PairCoulWolf { + public: + PairCoulWolfCS( class LAMMPS *); + virtual void compute( int, int); +}; + +} + +#endif +#endif /* LMP_PAIR_COUL_WOLF_CS_H_ */ + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +E: Pair coul/wolf/cs requires atom attribute q + +The atom style defined does not have this attribute. + +*/ From e284545c5b996596cb49e03b8f5cd6c6c3604b8a Mon Sep 17 00:00:00 2001 From: vishalkenchan Date: Fri, 20 Oct 2017 12:03:22 +0200 Subject: [PATCH 2/2] added some documentation and reference example --- doc/src/pair_cs.txt | 21 +- examples/coreshell/in.coreshell.wolf | 71 +++++++ .../log.22Sep17.coreshell.wolf.g++.1 | 190 ++++++++++++++++++ .../log.22Sep17.coreshell.wolf.g++.4 | 190 ++++++++++++++++++ src/CORESHELL/pair_born_coul_wolf_cs.cpp | 9 +- 5 files changed, 474 insertions(+), 7 deletions(-) create mode 100644 examples/coreshell/in.coreshell.wolf create mode 100644 examples/coreshell/log.22Sep17.coreshell.wolf.g++.1 create mode 100644 examples/coreshell/log.22Sep17.coreshell.wolf.g++.4 diff --git a/doc/src/pair_cs.txt b/doc/src/pair_cs.txt index 64dfc20d47..c1084c6087 100644 --- a/doc/src/pair_cs.txt +++ b/doc/src/pair_cs.txt @@ -9,12 +9,13 @@ pair_style born/coul/long/cs command :h3 pair_style buck/coul/long/cs command :h3 pair_style born/coul/dsf/cs command :h3 +pair_style born/coul/wolf/cs command :h3 [Syntax:] pair_style style args :pre -style = {born/coul/long/cs} or {buck/coul/long/cs} or {born/coul/dsf/cs} +style = {born/coul/long/cs} or {buck/coul/long/cs} or {born/coul/dsf/cs} or {born/coul/wolf/cs} args = list of arguments for a particular style :ul {born/coul/long/cs} args = cutoff (cutoff2) cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units) @@ -26,6 +27,10 @@ args = list of arguments for a particular style :ul alpha = damping parameter (inverse distance units) cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units) cutoff2 = global cutoff for Coulombic (distance units) :pre + {born/coul/wolf/cs} args = alpha cutoff (cutoff2) + alpha = damping parameter (inverse distance units) + cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units) + cutoff2 = global cutoff for Coulombic (optional) (distance units) [Examples:] @@ -41,6 +46,10 @@ pair_style born/coul/dsf/cs 0.1 10.0 12.0 pair_coeff * * 0.0 1.00 0.00 0.00 0.00 pair_coeff 1 1 480.0 0.25 0.00 1.05 0.50 :pre +pair_style born/coul/wolf/cs 0.25 10.0 12.0 +pair_coeff * * 0.0 1.00 0.00 0.00 0.00 +pair_coeff 1 1 480.0 0.25 0.00 1.05 0.50 :pre + [Description:] These pair styles are designed to be used with the adiabatic @@ -73,13 +82,21 @@ the core and shell, epsilon is the dielectric constant and r_min is the minimal distance. The pair style {born/coul/dsf/cs} is identical to the -"pair_style born/coul/dsf"_pair_born.html style, which uses the +"pair_style born/coul/dsf"_pair_born.html style, which uses the damped shifted force model as in "coul/dsf"_pair_coul.html to compute the Coulomb contribution. This approach does not require a long-range solver, thus the only correction is the addition of a minimal distance to avoid the possible r = 0.0 case for a core/shell pair. +The pair style {born/coul/wolf/cs} is identical to the +"pair_style born/coul/wolf"_pair_born.html style, which uses +the Wolf summation as in "coul/wolf"_pair_coul.html to compute +the Coulomb contribution. This approach does not require +a long-range solver, thus the only correction is the addition of a +minimal distance to avoid the possible r = 0.0 case for a +core/shell pair. + [Restrictions:] These pair styles are part of the CORESHELL package. They are only diff --git a/examples/coreshell/in.coreshell.wolf b/examples/coreshell/in.coreshell.wolf new file mode 100644 index 0000000000..337057d0c8 --- /dev/null +++ b/examples/coreshell/in.coreshell.wolf @@ -0,0 +1,71 @@ +# Testsystem for core-shell model compared to Mitchel and Finchham +# Shamelessly copied from in.coreshell.dsf but this script uses Wolf summation. + +# ------------------------ INITIALIZATION ---------------------------- + +units metal +dimension 3 +boundary p p p +atom_style full + +# ----------------------- ATOM DEFINITION ---------------------------- + +fix csinfo all property/atom i_CSID +read_data data.coreshell fix csinfo NULL CS-Info + +group cores type 1 2 +group shells type 3 4 + +neighbor 2.0 bin +comm_modify vel yes + +# ------------------------ FORCE FIELDS ------------------------------ + +pair_style born/coul/wolf/cs 0.1 20.0 20.0 # A, rho, sigma=0, C, D +pair_coeff * * 0.0 1.000 0.00 0.00 0.00 +pair_coeff 3 3 487.0 0.23768 0.00 1.05 0.50 #Na-Na +pair_coeff 3 4 145134.0 0.23768 0.00 6.99 8.70 #Na-Cl +pair_coeff 4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl + +bond_style harmonic +bond_coeff 1 63.014 0.0 +bond_coeff 2 25.724 0.0 + +# ------------------------ Equilibration Run ------------------------------- + +reset_timestep 0 + +thermo 50 +thermo_style custom step etotal pe ke temp press & + epair evdwl ecoul elong ebond fnorm fmax vol + +compute CSequ all temp/cs cores shells + +# output via chunk method + +#compute prop all property/atom i_CSID +#compute cs_chunk all chunk/atom c_prop +#compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0 +#fix ave_chunk all ave/time 100 1 100 c_cstherm file chunk.dump mode vector + +thermo_modify temp CSequ + +# velocity bias option + +velocity all create 1427 134 dist gaussian mom yes rot no bias yes temp CSequ +velocity all scale 1427 temp CSequ + +fix thermoberendsen all temp/berendsen 1427 1427 0.4 +fix nve all nve +fix_modify thermoberendsen temp CSequ + +# 2 fmsec timestep + +timestep 0.002 +run 500 + +unfix thermoberendsen + +# ------------------------ Dynamic Run ------------------------------- + +run 1000 diff --git a/examples/coreshell/log.22Sep17.coreshell.wolf.g++.1 b/examples/coreshell/log.22Sep17.coreshell.wolf.g++.1 new file mode 100644 index 0000000000..35c30913fc --- /dev/null +++ b/examples/coreshell/log.22Sep17.coreshell.wolf.g++.1 @@ -0,0 +1,190 @@ +LAMMPS (22 Sep 2017) +# Testsystem for core-shell model compared to Mitchel and Finchham +# Shamelessly copied from in.coreshell.dsf but this script uses Wolf summation. + +# ------------------------ INITIALIZATION ---------------------------- + +units metal +dimension 3 +boundary p p p +atom_style full + +# ----------------------- ATOM DEFINITION ---------------------------- + +fix csinfo all property/atom i_CSID +read_data data.coreshell fix csinfo NULL CS-Info + orthogonal box = (0 0 0) to (24.096 24.096 24.096) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 432 atoms + scanning bonds ... + 1 = max bonds/atom + reading bonds ... + 216 bonds + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + +group cores type 1 2 +216 atoms in group cores +group shells type 3 4 +216 atoms in group shells + +neighbor 2.0 bin +comm_modify vel yes + +# ------------------------ FORCE FIELDS ------------------------------ + +pair_style born/coul/wolf/cs 0.1 20.0 20.0 # A, rho, sigma=0, C, D +pair_coeff * * 0.0 1.000 0.00 0.00 0.00 +pair_coeff 3 3 487.0 0.23768 0.00 1.05 0.50 #Na-Na +pair_coeff 3 4 145134.0 0.23768 0.00 6.99 8.70 #Na-Cl +pair_coeff 4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl + +bond_style harmonic +bond_coeff 1 63.014 0.0 +bond_coeff 2 25.724 0.0 + +# ------------------------ Equilibration Run ------------------------------- + +reset_timestep 0 + +thermo 50 +thermo_style custom step etotal pe ke temp press epair evdwl ecoul elong ebond fnorm fmax vol + +compute CSequ all temp/cs cores shells + +# output via chunk method + +#compute prop all property/atom i_CSID +#compute cs_chunk all chunk/atom c_prop +#compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0 +#fix ave_chunk all ave/time 100 1 100 c_cstherm file chunk.dump mode vector + +thermo_modify temp CSequ + +# velocity bias option + +velocity all create 1427 134 dist gaussian mom yes rot no bias yes temp CSequ +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 22 + ghost atom cutoff = 22 + binsize = 11, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair born/coul/wolf/cs, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +velocity all scale 1427 temp CSequ + +fix thermoberendsen all temp/berendsen 1427 1427 0.4 +fix nve all nve +fix_modify thermoberendsen temp CSequ + +# 2 fmsec timestep + +timestep 0.002 +run 500 +Per MPI rank memory allocation (min/avg/max) = 8.59 | 8.59 | 8.59 Mbytes +Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume + 0 -637.41039 -677.06805 39.657659 1427 -21302.622 -677.06805 1.6320365 -678.70009 0 0 1.2935454e-14 3.3306691e-15 13990.5 + 50 -635.62711 -667.67134 32.044236 1153.0465 -4533.0717 -669.45724 37.76997 -707.22721 0 1.7858939 9.6844521 2.2001656 13990.5 + 100 -632.76337 -662.83035 30.066977 1081.8989 -3492.8736 -664.98454 39.197093 -704.18164 0 2.1541967 11.063962 2.1543406 13990.5 + 150 -630.82538 -663.70056 32.875182 1182.9464 -74.330324 -666.12202 46.263665 -712.38569 0 2.4214607 11.739683 2.7558416 13990.5 + 200 -629.1541 -664.54637 35.39227 1273.5187 -1707.5508 -666.87772 41.796197 -708.67391 0 2.3313445 10.594804 3.0025376 13990.5 + 250 -627.86587 -662.60879 34.742918 1250.1531 -1258.7537 -665.21416 43.017024 -708.23118 0 2.6053655 10.576999 1.8400986 13990.5 + 300 -627.10755 -664.12897 37.021419 1332.1403 -1891.3466 -666.39618 40.769593 -707.16577 0 2.2672094 9.412943 1.2434258 13990.5 + 350 -626.27558 -665.04303 38.767448 1394.9676 -1436.8514 -667.47081 41.854746 -709.32556 0 2.4277827 10.304721 1.977594 13990.5 + 400 -625.55098 -661.86388 36.312896 1306.6455 -331.92076 -664.4632 44.426542 -708.88975 0 2.599325 11.081635 2.1734468 13990.5 + 450 -624.88626 -661.07359 36.187328 1302.1272 -2325.834 -663.6031 39.662697 -703.26579 0 2.5295037 9.9810051 1.3068929 13990.5 + 500 -623.87093 -660.24145 36.370525 1308.7192 410.85324 -662.86944 45.869201 -708.73864 0 2.6279856 10.592785 1.8162326 13990.5 +Loop time of 11.7065 on 1 procs for 500 steps with 432 atoms + +Performance: 7.381 ns/day, 3.252 hours/ns, 42.711 timesteps/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 11.535 | 11.535 | 11.535 | 0.0 | 98.54 +Bond | 0.001443 | 0.001443 | 0.001443 | 0.0 | 0.01 +Neigh | 0.10952 | 0.10952 | 0.10952 | 0.0 | 0.94 +Comm | 0.048796 | 0.048796 | 0.048796 | 0.0 | 0.42 +Output | 0.00038695 | 0.00038695 | 0.00038695 | 0.0 | 0.00 +Modify | 0.0067511 | 0.0067511 | 0.0067511 | 0.0 | 0.06 +Other | | 0.004243 | | | 0.04 + +Nlocal: 432 ave 432 max 432 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 9328 ave 9328 max 9328 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 297280 ave 297280 max 297280 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 297280 +Ave neighs/atom = 688.148 +Ave special neighs/atom = 1 +Neighbor list builds = 21 +Dangerous builds = 0 + +unfix thermoberendsen + +# ------------------------ Dynamic Run ------------------------------- + +run 1000 +Per MPI rank memory allocation (min/avg/max) = 8.59 | 8.59 | 8.59 Mbytes +Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume + 500 -623.87093 -660.24145 36.370525 1308.7192 410.85324 -662.86944 45.869201 -708.73864 0 2.6279856 10.592785 1.8162326 13990.5 + 550 -623.95762 -659.99899 36.041371 1296.8752 -442.62446 -662.68699 44.004419 -706.69141 0 2.6879934 10.936057 1.7358509 13990.5 + 600 -624.04214 -661.21748 37.175332 1337.6785 47.615854 -663.76133 45.009742 -708.77107 0 2.5438549 11.431366 2.1185464 13990.5 + 650 -623.98279 -661.85255 37.86976 1362.6661 -1708.3823 -664.31138 40.933446 -705.24482 0 2.4588298 9.7960191 1.4159904 13990.5 + 700 -624.02941 -661.57484 37.54543 1350.9958 -124.09512 -663.95322 44.666402 -708.61962 0 2.3783801 10.518712 2.0854584 13990.5 + 750 -624.03935 -661.11619 37.076837 1334.1344 -1163.2721 -663.82553 42.1219 -705.94743 0 2.7093404 10.634859 1.9381654 13990.5 + 800 -623.98709 -659.43647 35.44938 1275.5737 -285.65702 -662.23782 44.650233 -706.88805 0 2.8013482 11.83459 3.4506407 13990.5 + 850 -623.96081 -661.77923 37.818422 1360.8188 -814.33212 -664.38161 42.860208 -707.24181 0 2.6023728 10.766451 2.9211132 13990.5 + 900 -623.96136 -662.98419 39.022831 1404.157 308.13105 -665.65877 45.053188 -710.71195 0 2.6745786 11.028799 1.8494322 13990.5 + 950 -623.91048 -660.63828 36.7278 1321.575 -445.31526 -663.79806 43.94833 -707.74639 0 3.1597729 11.852051 1.8238458 13990.5 + 1000 -623.90541 -661.03474 37.129332 1336.0233 522.57958 -663.50212 45.863261 -709.36538 0 2.4673781 10.949291 1.8614095 13990.5 + 1050 -624.01134 -660.99076 36.979422 1330.6291 -1710.2829 -663.67762 41.056102 -704.73372 0 2.6868521 10.86533 2.2154165 13990.5 + 1100 -624.02639 -660.86661 36.840225 1325.6204 1151.0236 -663.5066 47.207185 -710.71378 0 2.6399847 11.298044 1.8900703 13990.5 + 1150 -624.04418 -661.29819 37.254006 1340.5094 161.09847 -663.73735 45.222561 -708.95991 0 2.4391651 11.261119 2.2245673 13990.5 + 1200 -624.08628 -662.39932 38.313043 1378.6168 -1405.0927 -664.93121 41.728112 -706.65933 0 2.5318927 10.458041 2.1153159 13990.5 + 1250 -624.03036 -661.25661 37.226248 1339.5106 63.407721 -663.72719 45.086961 -708.81415 0 2.4705832 11.766021 2.2297809 13990.5 + 1300 -623.97475 -661.55998 37.585229 1352.4278 -763.66781 -663.80645 42.870244 -706.6767 0 2.2464703 10.098322 1.7614596 13990.5 + 1350 -623.93123 -660.30786 36.376631 1308.9389 -2389.8052 -663.04725 39.749029 -702.79628 0 2.7393936 10.879364 2.6622521 13990.5 + 1400 -623.86468 -658.44644 34.581765 1244.3543 2262.7586 -660.95368 50.10608 -711.05976 0 2.5072434 11.528291 1.7861906 13990.5 + 1450 -623.85494 -661.47216 37.617217 1353.5789 -1435.0174 -664.13587 41.701767 -705.83764 0 2.6637191 11.297444 2.0038345 13990.5 + 1500 -623.79928 -659.70124 35.901959 1291.8588 -198.39562 -662.57415 44.358482 -706.93263 0 2.872907 11.075746 2.2821286 13990.5 +Loop time of 23.4119 on 1 procs for 1000 steps with 432 atoms + +Performance: 7.381 ns/day, 3.252 hours/ns, 42.713 timesteps/s +99.9% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 23.069 | 23.069 | 23.069 | 0.0 | 98.54 +Bond | 0.0029275 | 0.0029275 | 0.0029275 | 0.0 | 0.01 +Neigh | 0.22821 | 0.22821 | 0.22821 | 0.0 | 0.97 +Comm | 0.097941 | 0.097941 | 0.097941 | 0.0 | 0.42 +Output | 0.00074033 | 0.00074033 | 0.00074033 | 0.0 | 0.00 +Modify | 0.0042015 | 0.0042015 | 0.0042015 | 0.0 | 0.02 +Other | | 0.00865 | | | 0.04 + +Nlocal: 432 ave 432 max 432 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 9388 ave 9388 max 9388 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 297212 ave 297212 max 297212 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 297212 +Ave neighs/atom = 687.991 +Ave special neighs/atom = 1 +Neighbor list builds = 45 +Dangerous builds = 0 +Total wall time: 0:00:35 diff --git a/examples/coreshell/log.22Sep17.coreshell.wolf.g++.4 b/examples/coreshell/log.22Sep17.coreshell.wolf.g++.4 new file mode 100644 index 0000000000..84f854cf67 --- /dev/null +++ b/examples/coreshell/log.22Sep17.coreshell.wolf.g++.4 @@ -0,0 +1,190 @@ +LAMMPS (22 Sep 2017) +# Testsystem for core-shell model compared to Mitchel and Finchham +# Shamelessly copied from in.coreshell.dsf but this script uses Wolf summation. + +# ------------------------ INITIALIZATION ---------------------------- + +units metal +dimension 3 +boundary p p p +atom_style full + +# ----------------------- ATOM DEFINITION ---------------------------- + +fix csinfo all property/atom i_CSID +read_data data.coreshell fix csinfo NULL CS-Info + orthogonal box = (0 0 0) to (24.096 24.096 24.096) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 432 atoms + scanning bonds ... + 1 = max bonds/atom + reading bonds ... + 216 bonds + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + +group cores type 1 2 +216 atoms in group cores +group shells type 3 4 +216 atoms in group shells + +neighbor 2.0 bin +comm_modify vel yes + +# ------------------------ FORCE FIELDS ------------------------------ + +pair_style born/coul/wolf/cs 0.1 20.0 20.0 # A, rho, sigma=0, C, D +pair_coeff * * 0.0 1.000 0.00 0.00 0.00 +pair_coeff 3 3 487.0 0.23768 0.00 1.05 0.50 #Na-Na +pair_coeff 3 4 145134.0 0.23768 0.00 6.99 8.70 #Na-Cl +pair_coeff 4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl + +bond_style harmonic +bond_coeff 1 63.014 0.0 +bond_coeff 2 25.724 0.0 + +# ------------------------ Equilibration Run ------------------------------- + +reset_timestep 0 + +thermo 50 +thermo_style custom step etotal pe ke temp press epair evdwl ecoul elong ebond fnorm fmax vol + +compute CSequ all temp/cs cores shells + +# output via chunk method + +#compute prop all property/atom i_CSID +#compute cs_chunk all chunk/atom c_prop +#compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0 +#fix ave_chunk all ave/time 100 1 100 c_cstherm file chunk.dump mode vector + +thermo_modify temp CSequ + +# velocity bias option + +velocity all create 1427 134 dist gaussian mom yes rot no bias yes temp CSequ +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 22 + ghost atom cutoff = 22 + binsize = 11, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair born/coul/wolf/cs, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +velocity all scale 1427 temp CSequ + +fix thermoberendsen all temp/berendsen 1427 1427 0.4 +fix nve all nve +fix_modify thermoberendsen temp CSequ + +# 2 fmsec timestep + +timestep 0.002 +run 500 +Per MPI rank memory allocation (min/avg/max) = 6.881 | 6.881 | 6.881 Mbytes +Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume + 0 -637.41039 -677.06805 39.657659 1427 -21302.622 -677.06805 1.6320365 -678.70009 0 0 1.3530839e-14 3.6429193e-15 13990.5 + 50 -635.62704 -667.67108 32.044047 1153.0397 -4532.6842 -669.45828 37.771018 -707.2293 0 1.787201 9.6848095 2.2028349 13990.5 + 100 -632.76343 -662.83014 30.066711 1081.8893 -3493.0827 -664.98212 39.195967 -704.17809 0 2.151977 11.060773 2.1578583 13990.5 + 150 -630.82533 -663.70172 32.876385 1182.9897 -75.706974 -666.12608 46.261038 -712.38712 0 2.4243598 11.746728 2.7663319 13990.5 + 200 -629.15463 -664.55009 35.395466 1273.6337 -1707.9185 -666.88117 41.794868 -708.67604 0 2.331082 10.596229 3.0031523 13990.5 + 250 -627.86625 -662.60876 34.742511 1250.1384 -1263.5726 -665.214 43.005742 -708.21974 0 2.6052329 10.572641 1.841604 13990.5 + 300 -627.10829 -664.12159 37.013298 1331.8481 -1884.8587 -666.39136 40.786141 -707.1775 0 2.2697693 9.4160685 1.2472271 13990.5 + 350 -626.2729 -665.01858 38.745682 1394.1844 -1433.1302 -667.44315 41.864785 -709.30793 0 2.4245625 10.312641 1.9815612 13990.5 + 400 -625.54274 -661.84438 36.301638 1306.2404 -355.45544 -664.4483 44.370671 -708.81897 0 2.6039276 11.076154 2.1819703 13990.5 + 450 -624.88802 -661.12299 36.234964 1303.8413 -2356.6101 -663.6463 39.57847 -703.22477 0 2.523314 9.8995886 1.3113549 13990.5 + 500 -623.86344 -660.20235 36.338906 1307.5814 462.72862 -662.8515 45.983055 -708.83455 0 2.6491489 10.523732 1.6709561 13990.5 +Loop time of 4.63313 on 4 procs for 500 steps with 432 atoms + +Performance: 18.648 ns/day, 1.287 hours/ns, 107.919 timesteps/s +99.4% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.8133 | 3.5934 | 4.4255 | 36.3 | 77.56 +Bond | 0.00042245 | 0.00050305 | 0.00059825 | 0.0 | 0.01 +Neigh | 0.0411 | 0.041561 | 0.04202 | 0.2 | 0.90 +Comm | 0.15622 | 0.9884 | 1.7686 | 69.2 | 21.33 +Output | 0.00028311 | 0.00031345 | 0.00040011 | 0.0 | 0.01 +Modify | 0.0039899 | 0.00403 | 0.0040654 | 0.0 | 0.09 +Other | | 0.004911 | | | 0.11 + +Nlocal: 108 ave 112 max 106 min +Histogram: 2 0 0 1 0 0 0 0 0 1 +Nghost: 6531.75 ave 6611 max 6460 min +Histogram: 1 0 0 1 0 1 0 0 0 1 +Neighs: 74316.2 ave 75641 max 72780 min +Histogram: 1 0 0 1 0 0 0 0 1 1 + +Total # of neighbors = 297265 +Ave neighs/atom = 688.113 +Ave special neighs/atom = 1 +Neighbor list builds = 21 +Dangerous builds = 0 + +unfix thermoberendsen + +# ------------------------ Dynamic Run ------------------------------- + +run 1000 +Per MPI rank memory allocation (min/avg/max) = 6.884 | 7.01 | 7.138 Mbytes +Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume + 500 -623.86344 -660.20235 36.338906 1307.5814 462.72862 -662.8515 45.983055 -708.83455 0 2.6491489 10.523732 1.6709561 13990.5 + 550 -623.95339 -660.07946 36.126069 1299.9229 -362.67288 -662.8047 44.180832 -706.98553 0 2.725239 11.07199 2.0461377 13990.5 + 600 -624.04508 -661.27298 37.227902 1339.5701 110.39823 -663.90927 45.166569 -709.07584 0 2.6362911 11.747923 2.1846828 13990.5 + 650 -623.9608 -661.50573 37.544934 1350.9779 -1594.4701 -663.91531 41.226571 -705.14188 0 2.4095736 10.022027 1.6264014 13990.5 + 700 -624.00658 -663.55636 39.549777 1423.1181 -588.9804 -665.88666 43.124023 -709.01068 0 2.3302979 9.924587 2.1027837 13990.5 + 750 -623.99813 -659.97695 35.978816 1294.6243 -364.1415 -662.75959 43.973556 -706.73315 0 2.782646 11.487832 1.8799695 13990.5 + 800 -624.01235 -661.04908 37.036728 1332.6911 -85.655852 -663.49204 44.570117 -708.06215 0 2.4429547 11.213149 1.6792926 13990.5 + 850 -624.02581 -659.39933 35.373519 1272.844 -1090.9179 -662.11969 42.375064 -704.49476 0 2.7203673 11.214629 2.2907474 13990.5 + 900 -624.09244 -663.33386 39.241421 1412.0225 303.76207 -666.00593 45.332458 -711.33839 0 2.6720667 11.897188 2.0599033 13990.5 + 950 -624.04544 -661.11578 37.070341 1333.9007 1637.6438 -663.61305 48.65892 -712.27197 0 2.49727 12.343774 2.429225 13990.5 + 1000 -623.95457 -661.51816 37.563586 1351.6491 -851.77182 -663.83594 42.813468 -706.64941 0 2.317782 10.251422 1.6922864 13990.5 + 1050 -623.98731 -662.01988 38.032562 1368.5242 -2123.9075 -664.72609 39.917382 -704.64348 0 2.706218 9.600838 1.7365559 13990.5 + 1100 -623.9653 -659.32023 35.354929 1272.1751 -436.90576 -662.14454 44.057776 -706.20232 0 2.8243167 11.267546 2.6807602 13990.5 + 1150 -624.02273 -665.13902 41.116293 1479.486 -128.13268 -667.4769 44.013761 -711.49066 0 2.3378768 10.406604 1.5102324 13990.5 + 1200 -623.97328 -663.08042 39.107135 1407.1905 -539.63284 -665.67946 43.319308 -708.99877 0 2.599042 10.632657 1.4608707 13990.5 + 1250 -623.92529 -661.81902 37.893723 1363.5284 1708.0621 -664.63624 48.396874 -713.03311 0 2.8172251 11.369352 1.8836979 13990.5 + 1300 -623.99283 -662.19734 38.204509 1374.7114 -820.77291 -664.34556 42.656202 -707.00176 0 2.1482151 10.186898 1.7081329 13990.5 + 1350 -623.99798 -658.70752 34.709535 1248.9519 776.28486 -662.01647 46.925412 -708.94188 0 3.3089536 12.457581 2.5027978 13990.5 + 1400 -623.96941 -662.15959 38.190183 1374.1959 880.21756 -664.90452 46.628183 -711.5327 0 2.7449282 11.918894 3.0466188 13990.5 + 1450 -623.95068 -662.25435 38.303671 1378.2795 -391.56711 -664.7631 43.644066 -708.40716 0 2.5087493 10.465803 1.8744864 13990.5 + 1500 -624.00637 -661.48756 37.481185 1348.684 430.69453 -664.32151 45.704366 -710.02587 0 2.8339501 11.650821 2.0752813 13990.5 +Loop time of 6.7003 on 4 procs for 1000 steps with 432 atoms + +Performance: 25.790 ns/day, 0.931 hours/ns, 149.247 timesteps/s +99.1% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 5.9613 | 6.0752 | 6.2064 | 4.1 | 90.67 +Bond | 0.00087095 | 0.00088993 | 0.00091671 | 0.0 | 0.01 +Neigh | 0.06494 | 0.064964 | 0.064987 | 0.0 | 0.97 +Comm | 0.41743 | 0.54863 | 0.6626 | 13.8 | 8.19 +Output | 0.00053867 | 0.00059268 | 0.00074867 | 0.0 | 0.01 +Modify | 0.0013288 | 0.0013592 | 0.0013841 | 0.1 | 0.02 +Other | | 0.008613 | | | 0.13 + +Nlocal: 108 ave 116 max 102 min +Histogram: 2 0 0 0 0 0 0 1 0 1 +Nghost: 6504.5 ave 6624 max 6380 min +Histogram: 1 1 0 0 0 0 0 0 1 1 +Neighs: 74267 ave 79230 max 70993 min +Histogram: 2 0 0 0 0 1 0 0 0 1 + +Total # of neighbors = 297068 +Ave neighs/atom = 687.657 +Ave special neighs/atom = 1 +Neighbor list builds = 45 +Dangerous builds = 0 +Total wall time: 0:00:11 diff --git a/src/CORESHELL/pair_born_coul_wolf_cs.cpp b/src/CORESHELL/pair_born_coul_wolf_cs.cpp index c57e00cbd0..3c98f5bf77 100644 --- a/src/CORESHELL/pair_born_coul_wolf_cs.cpp +++ b/src/CORESHELL/pair_born_coul_wolf_cs.cpp @@ -70,8 +70,7 @@ void PairBornCoulWolfCS::compute(int eflag, int vflag) e_self = v_sh = 0.0; e_shift = erfc(alf*cut_coul)/cut_coul; - f_shift = -(e_shift+ 2.0*alf/MY_PIS * exp(-alf*alf*cut_coul*cut_coul)) / - cut_coul; + f_shift = -(e_shift+ 2.0*alf/MY_PIS * exp(-alf*alf*cut_coul*cut_coul)) / cut_coul; inum = list->inum; ilist = list->ilist; @@ -107,9 +106,9 @@ void PairBornCoulWolfCS::compute(int eflag, int vflag) jtype = type[j]; if (rsq < cutsq[itype][jtype]) { - rsq += EPSILON; - // Add EPISLON for case: r = 0; Interaction must be removed - // by special bond + rsq += EPSILON; + // Add EPISLON for case: r = 0; Interaction must be removed + // by special bond r2inv = 1.0/rsq; if (rsq < cut_coulsq) {