diff --git a/doc/src/pair_lj.txt b/doc/src/pair_lj.txt index 058d54fb5950aec706e4de4b4561cb23f924b5e9..e297d479bc3ae16d3054130ba67d9bb7fe3a0a97 100644 --- a/doc/src/pair_lj.txt +++ b/doc/src/pair_lj.txt @@ -32,6 +32,8 @@ pair_style lj/cut/coul/long/omp command :h3 pair_style lj/cut/coul/msm command :h3 pair_style lj/cut/coul/msm/gpu command :h3 pair_style lj/cut/coul/msm/omp command :h3 +pair_style lj/cut/coul/wolf command :h3 +pair_style lj/cut/coul/wolf/omp command :h3 pair_style lj/cut/tip4p/cut command :h3 pair_style lj/cut/tip4p/cut/omp command :h3 pair_style lj/cut/tip4p/long command :h3 @@ -63,6 +65,10 @@ args = list of arguments for a particular style :ul {lj/cut/coul/msm} args = cutoff (cutoff2) cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) cutoff2 = global cutoff for Coulombic (optional) (distance units) + {lj/cut/coul/wolf} args = alpha cutoff (cutoff2) + alpha = damping parameter (inverse distance units) + cutoff = global cutoff for LJ (and Coulombic if only 2 arg) (distance units) + cutoff2 = global cutoff for Coulombic (optional) (distance units) {lj/cut/tip4p/cut} args = otype htype btype atype qdist cutoff (cutoff2) otype,htype = atom types for TIP4P O and H btype,atype = bond and angle types for TIP4P waters @@ -115,6 +121,10 @@ pair_style lj/cut/tip4p/cut 1 2 7 8 0.15 12.0 10.0 pair_coeff * * 100.0 3.0 pair_coeff 1 1 100.0 3.5 9.0 :pre +pair_style lj/cut/coul/wolf 0.2 5. 10.0 +pair_coeff * * 1.0 1.0 +pair_coeff 1 1 1.0 1.0 2.5 :pre + pair_style lj/cut/tip4p/long 1 2 7 8 0.15 12.0 pair_style lj/cut/tip4p/long 1 2 7 8 0.15 12.0 10.0 pair_coeff * * 100.0 3.0 @@ -179,6 +189,24 @@ that a term is added for the "core/shell model"_Section_howto.html#howto_25 to allow charges on core and shell particles to be separated by r = 0.0. +Style {coul/wolf} adds a Coulombic pairwise interaction via the Wolf +summation method, described in "Wolf"_#Wolf1, given by: + +:c,image(Eqs/pair_coul_wolf.jpg) + +where {alpha} is the damping parameter, and erfc() is the +complementary error-function terms. This potential +is essentially a short-range, spherically-truncated, +charge-neutralized, shifted, pairwise {1/r} summation. With a +manipulation of adding and subtracting a self term (for i = j) to the +first and second term on the right-hand-side, respectively, and a +small enough {alpha} damping parameter, the second term shrinks and +the potential becomes a rapidly-converging real-space summation. With +a long enough cutoff and small enough alpha parameter, the energy and +forces calculated by the Wolf summation method approach those of the +Ewald sum. So it is a means of getting effective long-range +interactions with a short-range potential. + Styles {lj/cut/tip4p/cut} and {lj/cut/tip4p/long} implement the TIP4P water model of "(Jorgensen)"_#Jorgensen2, which introduces a massless site located a short distance away from the oxygen atom along the diff --git a/src/USER-OMP/pair_lj_cut_coul_wolf_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_wolf_omp.cpp new file mode 100644 index 0000000000000000000000000000000000000000..f5dc03e36828c60e1e68c509be24ee4d5c679ee2 --- /dev/null +++ b/src/USER-OMP/pair_lj_cut_coul_wolf_omp.cpp @@ -0,0 +1,204 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + This software is distributed under the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Axel Kohlmeyer (Temple U) +------------------------------------------------------------------------- */ + +#include <math.h> +#include "pair_lj_cut_coul_wolf_omp.h" +#include "atom.h" +#include "comm.h" +#include "force.h" +#include "neighbor.h" +#include "neigh_list.h" + +#include "suffix.h" +#include "math_const.h" +using namespace LAMMPS_NS; +using namespace MathConst; + +/* ---------------------------------------------------------------------- */ + +PairLJCutCoulWolfOMP::PairLJCutCoulWolfOMP(LAMMPS *lmp) : + PairLJCutCoulWolf(lmp), ThrOMP(lmp, THR_PAIR) +{ + suffix_flag |= Suffix::OMP; + respa_enable = 0; +} + +/* ---------------------------------------------------------------------- */ + +void PairLJCutCoulWolfOMP::compute(int eflag, int vflag) +{ + if (eflag || vflag) { + ev_setup(eflag,vflag); + } else evflag = vflag_fdotr = 0; + + const int nall = atom->nlocal + atom->nghost; + const int nthreads = comm->nthreads; + const int inum = list->inum; + +#if defined(_OPENMP) +#pragma omp parallel default(none) shared(eflag,vflag) +#endif + { + int ifrom, ito, tid; + + loop_setup_thr(ifrom, ito, tid, inum, nthreads); + ThrData *thr = fix->get_thr(tid); + thr->timer(Timer::START); + ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr); + + if (evflag) { + if (eflag) { + if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr); + else eval<1,1,0>(ifrom, ito, thr); + } else { + if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr); + else eval<1,0,0>(ifrom, ito, thr); + } + } else { + if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr); + else eval<0,0,0>(ifrom, ito, thr); + } + + thr->timer(Timer::PAIR); + reduce_thr(this, eflag, vflag, thr); + } // end of omp parallel region +} + +/* ---------------------------------------------------------------------- */ + +template <int EVFLAG, int EFLAG, int NEWTON_PAIR> +void PairLJCutCoulWolfOMP::eval(int iifrom, int iito, ThrData * const thr) +{ + int i,j,ii,jj,jnum,itype,jtype; + double qitmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair; + double r,rsq,r2inv,r6inv,forcecoul,forcelj,factor_coul,factor_lj; + double prefactor,erfcc,erfcd,v_sh,dvdrr,e_self,qisq; + int *ilist,*jlist,*numneigh,**firstneigh; + + evdwl = ecoul = 0.0; + + const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0]; + dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0]; + const double * _noalias const q = atom->q; + const int * _noalias const type = atom->type; + const int nlocal = atom->nlocal; + const double * _noalias const special_coul = force->special_coul; + const double * _noalias const special_lj = force->special_lj; + const double qqrd2e = force->qqrd2e; + double fxtmp,fytmp,fztmp; + + // self and shifted Coulombic energy + + e_self = v_sh = 0.0; + const double e_shift = erfc(alf*cut_coul)/cut_coul; + const double f_shift = -(e_shift+ 2.0*alf/MY_PIS + * exp(-alf*alf*cut_coul*cut_coul)) / cut_coul; + + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // loop over neighbors of my atoms + + for (ii = iifrom; ii < iito; ++ii) { + + i = ilist[ii]; + qitmp = q[i]; + xtmp = x[i].x; + ytmp = x[i].y; + ztmp = x[i].z; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + fxtmp=fytmp=fztmp=0.0; + + if (EFLAG) { + e_self = -(e_shift/2.0 + alf/MY_PIS) * qitmp*qitmp*qqrd2e; + ev_tally_thr(this,i,i,nlocal,0,0.0,e_self,0.0,0.0,0.0,0.0,thr); + } + + 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].x; + dely = ytmp - x[j].y; + delz = ztmp - x[j].z; + rsq = delx*delx + dely*dely + delz*delz; + jtype = type[j]; + + if (rsq < cutsq[itype][jtype]) { + r2inv = 1.0/rsq; + + if (rsq < cut_coulsq) { + r = sqrt(rsq); + prefactor = qqrd2e*qitmp*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; + forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]); + } else forcelj = 0.0; + + fpair = (forcecoul + factor_lj*forcelj) * r2inv; + + fxtmp += delx*fpair; + fytmp += dely*fpair; + fztmp += delz*fpair; + if (NEWTON_PAIR || j < nlocal) { + f[j].x -= delx*fpair; + f[j].y -= dely*fpair; + f[j].z -= delz*fpair; + } + + if (EFLAG) { + if (rsq < cut_ljsq[itype][jtype]) { + evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) - + offset[itype][jtype]; + evdwl *= factor_lj; + } else evdwl = 0.0; + + if (rsq < cut_coulsq) { + ecoul = v_sh; + if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor; + } else ecoul = 0.0; + } + + if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR, + evdwl,ecoul,fpair,delx,dely,delz,thr); + } + } + f[i].x += fxtmp; + f[i].y += fytmp; + f[i].z += fztmp; + } +} + +/* ---------------------------------------------------------------------- */ + +double PairLJCutCoulWolfOMP::memory_usage() +{ + double bytes = memory_usage_thr(); + bytes += PairLJCutCoulWolf::memory_usage(); + + return bytes; +} diff --git a/src/USER-OMP/pair_lj_cut_coul_wolf_omp.h b/src/USER-OMP/pair_lj_cut_coul_wolf_omp.h new file mode 100644 index 0000000000000000000000000000000000000000..4e56808c7bdb02350a8bce7a68faa5f42f98f8a5 --- /dev/null +++ b/src/USER-OMP/pair_lj_cut_coul_wolf_omp.h @@ -0,0 +1,48 @@ +/* -*- 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. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Axel Kohlmeyer (Temple U) +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(lj/cut/coul/wolf/omp,PairLJCutCoulWolfOMP) + +#else + +#ifndef LMP_PAIR_LJ_CUT_COUL_WOLF_OMP_H +#define LMP_PAIR_LJ_CUT_COUL_WOLF_OMP_H + +#include "pair_lj_cut_coul_wolf.h" +#include "thr_omp.h" + +namespace LAMMPS_NS { + +class PairLJCutCoulWolfOMP : public PairLJCutCoulWolf, public ThrOMP { + + public: + PairLJCutCoulWolfOMP(class LAMMPS *); + + virtual void compute(int, int); + virtual double memory_usage(); + + private: + template <int EVFLAG, int EFLAG, int NEWTON_PAIR> + void eval(int ifrom, int ito, ThrData * const thr); +}; + +} + +#endif +#endif diff --git a/src/pair_lj_cut_coul_wolf.cpp b/src/pair_lj_cut_coul_wolf.cpp new file mode 100644 index 0000000000000000000000000000000000000000..1527180eacfcbe92c99efa871bab7b4a12f9e2bc --- /dev/null +++ b/src/pair_lj_cut_coul_wolf.cpp @@ -0,0 +1,447 @@ +/* ---------------------------------------------------------------------- + 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. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Vishal Boddu (FAU) +------------------------------------------------------------------------- */ + +#include <math.h> +#include <stdio.h> +#include <stdlib.h> +#include <string.h> +#include "pair_lj_cut_coul_wolf.h" +#include "atom.h" +#include "comm.h" +#include "force.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "update.h" +#include "integrate.h" +#include "math_const.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; +using namespace MathConst; + +/* ---------------------------------------------------------------------- */ + +PairLJCutCoulWolf::PairLJCutCoulWolf(LAMMPS *lmp) : Pair(lmp) +{ + single_enable = 0; + writedata = 1; +} + +/* ---------------------------------------------------------------------- */ + +PairLJCutCoulWolf::~PairLJCutCoulWolf() +{ + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + + memory->destroy(cut_lj); + memory->destroy(cut_ljsq); + memory->destroy(epsilon); + memory->destroy(sigma); + memory->destroy(lj1); + memory->destroy(lj2); + memory->destroy(lj3); + memory->destroy(lj4); + memory->destroy(offset); + } +} + +/* ---------------------------------------------------------------------- */ + +void PairLJCutCoulWolf::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,forcelj,factor_lj,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; + + evdwl = 0.0; + 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_lj = force->special_lj; + 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]; + 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]) { + 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; + forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]); + } else forcelj = 0.0; + + fpair = (forcecoul + factor_lj*forcelj) * 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_ljsq[itype][jtype]) { + evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) - + offset[itype][jtype]; + evdwl *= factor_lj; + } else evdwl = 0.0; + + if (rsq < cut_coulsq) { + 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, + evdwl,ecoul,fpair,delx,dely,delz); + } + } + } + + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairLJCutCoulWolf::allocate() +{ + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag,n+1,n+1,"pair:setflag"); + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; + + memory->create(cutsq,n+1,n+1,"pair:cutsq"); + memory->create(cut_lj,n+1,n+1,"pair:cut"); + memory->create(cut_ljsq,n+1,n+1,"pair:cut_ljsq"); + memory->create(epsilon,n+1,n+1,"pair:epsilon"); + memory->create(sigma,n+1,n+1,"pair:sigma"); + memory->create(lj1,n+1,n+1,"pair:lj1"); + memory->create(lj2,n+1,n+1,"pair:lj2"); + memory->create(lj3,n+1,n+1,"pair:lj3"); + memory->create(lj4,n+1,n+1,"pair:lj4"); + memory->create(offset,n+1,n+1,"pair:offset"); +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairLJCutCoulWolf::settings(int narg, char **arg) +{ + if (narg < 2 || narg > 3) error->all(FLERR,"Illegal pair_style command"); + + alf = force->numeric(FLERR,arg[0]); + cut_lj_global = force->numeric(FLERR,arg[1]); + if (narg == 2) cut_coul = cut_lj_global; + + if (allocated) { + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) + if (setflag[i][j]) cut_lj[i][j] = cut_lj_global; + } +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairLJCutCoulWolf::coeff(int narg, char **arg) +{ + if (narg < 4 || narg > 5) + error->all(FLERR,"Incorrect args for pair coefficients"); + if (!allocated) allocate(); + + int ilo,ihi,jlo,jhi; + force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi); + force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi); + + double epsilon_one = force->numeric(FLERR,arg[2]); + double sigma_one = force->numeric(FLERR,arg[3]); + + double cut_lj_one = cut_lj_global; + if (narg == 5) cut_lj_one = force->numeric(FLERR,arg[4]); + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo,i); j <= jhi; j++) { + epsilon[i][j] = epsilon_one; + sigma[i][j] = sigma_one; + cut_lj[i][j] = cut_lj_one; + setflag[i][j] = 1; + count++; + } + } + + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); +} + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +void PairLJCutCoulWolf::init_style() +{ + if (!atom->q_flag) + error->all(FLERR,"Pair style lj/cut/coul/wolf requires atom attribute q"); + + cut_coulsq = cut_coul * cut_coul; + + // request regular or rRESPA neighbor list + + int irequest; + irequest = neighbor->request(this,instance_me); +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairLJCutCoulWolf::init_one(int i, int j) +{ + if (setflag[i][j] == 0) { + epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j], + sigma[i][i],sigma[j][j]); + sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]); + cut_lj[i][j] = mix_distance(cut_lj[i][i],cut_lj[j][j]); + } + + double cut = MAX(cut_lj[i][j],cut_coul); + cut_ljsq[i][j] = cut_lj[i][j] * cut_lj[i][j]; + + lj1[i][j] = 48.0 * epsilon[i][j] * pow(sigma[i][j],12.0); + lj2[i][j] = 24.0 * epsilon[i][j] * pow(sigma[i][j],6.0); + lj3[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],12.0); + lj4[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],6.0); + + if (offset_flag && (cut_lj[i][j] > 0.0)) { + double ratio = sigma[i][j] / cut_lj[i][j]; + offset[i][j] = 4.0 * epsilon[i][j] * (pow(ratio,12.0) - pow(ratio,6.0)); + } else offset[i][j] = 0.0; + + lj1[j][i] = lj1[i][j]; + lj2[j][i] = lj2[i][j]; + lj3[j][i] = lj3[i][j]; + lj4[j][i] = lj4[i][j]; + offset[j][i] = offset[i][j]; + + // compute I,J contribution to long-range tail correction + // count total # of atoms of type I and J via Allreduce + + if (tail_flag) { + int *type = atom->type; + int nlocal = atom->nlocal; + + double count[2],all[2]; + count[0] = count[1] = 0.0; + for (int k = 0; k < nlocal; k++) { + if (type[k] == i) count[0] += 1.0; + if (type[k] == j) count[1] += 1.0; + } + MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world); + + double sig2 = sigma[i][j]*sigma[i][j]; + double sig6 = sig2*sig2*sig2; + double rc3 = cut_lj[i][j]*cut_lj[i][j]*cut_lj[i][j]; + double rc6 = rc3*rc3; + double rc9 = rc3*rc6; + etail_ij = 8.0*MY_PI*all[0]*all[1]*epsilon[i][j] * + sig6 * (sig6 - 3.0*rc6) / (9.0*rc9); + ptail_ij = 16.0*MY_PI*all[0]*all[1]*epsilon[i][j] * + sig6 * (2.0*sig6 - 3.0*rc6) / (9.0*rc9); + } + + return cut; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairLJCutCoulWolf::write_restart(FILE *fp) +{ + write_restart_settings(fp); + + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + fwrite(&setflag[i][j],sizeof(int),1,fp); + if (setflag[i][j]) { + fwrite(&epsilon[i][j],sizeof(double),1,fp); + fwrite(&sigma[i][j],sizeof(double),1,fp); + fwrite(&cut_lj[i][j],sizeof(double),1,fp); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairLJCutCoulWolf::read_restart(FILE *fp) +{ + read_restart_settings(fp); + allocate(); + + int i,j; + int me = comm->me; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); + if (setflag[i][j]) { + if (me == 0) { + fread(&epsilon[i][j],sizeof(double),1,fp); + fread(&sigma[i][j],sizeof(double),1,fp); + fread(&cut_lj[i][j],sizeof(double),1,fp); + } + MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairLJCutCoulWolf::write_restart_settings(FILE *fp) +{ + fwrite(&alf,sizeof(double),1,fp); + fwrite(&cut_lj_global,sizeof(double),1,fp); + fwrite(&cut_coul,sizeof(double),1,fp); + fwrite(&offset_flag,sizeof(int),1,fp); + fwrite(&mix_flag,sizeof(int),1,fp); + fwrite(&tail_flag,sizeof(int),1,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairLJCutCoulWolf::read_restart_settings(FILE *fp) +{ + int me = comm->me; + if (me == 0) { + fread(&alf,sizeof(double),1,fp); + fread(&cut_lj_global,sizeof(double),1,fp); + fread(&cut_coul,sizeof(double),1,fp); + fread(&offset_flag,sizeof(int),1,fp); + fread(&mix_flag,sizeof(int),1,fp); + fread(&tail_flag,sizeof(int),1,fp); + } + MPI_Bcast(&alf,1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world); + MPI_Bcast(&offset_flag,1,MPI_INT,0,world); + MPI_Bcast(&mix_flag,1,MPI_INT,0,world); + MPI_Bcast(&tail_flag,1,MPI_INT,0,world); +} + +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void PairLJCutCoulWolf::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + fprintf(fp,"%d %g %g\n",i,epsilon[i][i],sigma[i][i]); +} + +/* ---------------------------------------------------------------------- + proc 0 writes all pairs to data file +------------------------------------------------------------------------- */ + +void PairLJCutCoulWolf::write_data_all(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + for (int j = i; j <= atom->ntypes; j++) + fprintf(fp,"%d %d %g %g %g\n",i,j,epsilon[i][j],sigma[i][j],cut_lj[i][j]); +} diff --git a/src/pair_lj_cut_coul_wolf.h b/src/pair_lj_cut_coul_wolf.h new file mode 100644 index 0000000000000000000000000000000000000000..aa4e08f9b79c8eae654a6cd13a5d77daada9c9a2 --- /dev/null +++ b/src/pair_lj_cut_coul_wolf.h @@ -0,0 +1,70 @@ +/* -*- 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(lj/cut/coul/wolf,PairLJCutCoulWolf) + +#else + +#ifndef LMP_PAIR_LJ_CUT_COUL_WOLF_H +#define LMP_PAIR_LJ_CUT_COUL_WOLF_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairLJCutCoulWolf : public Pair { + public: + PairLJCutCoulWolf(class LAMMPS *); + virtual ~PairLJCutCoulWolf(); + virtual void compute(int, int); + void settings(int, char **); + void coeff(int, char **); + void init_style(); + double init_one(int, int); + void write_restart(FILE *); + void read_restart(FILE *); + void write_restart_settings(FILE *); + void read_restart_settings(FILE *); + void write_data(FILE *); + void write_data_all(FILE *); + + protected: + double cut_lj_global; + double **cut_lj,**cut_ljsq; + double **epsilon,**sigma; + double **lj1,**lj2,**lj3,**lj4,**offset; + double cut_coul,cut_coulsq,alf; + + virtual void allocate(); +}; + +} + +#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. + +*/