From d089e246b94ca8c3a16443519244a1696e97bc09 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Thu, 4 Jun 2009 16:53:17 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2853 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- src/KSPACE/pair_born_coul_long.cpp | 472 +++++++++++++++++++++++++++++ src/KSPACE/pair_born_coul_long.h | 50 +++ 2 files changed, 522 insertions(+) create mode 100644 src/KSPACE/pair_born_coul_long.cpp create mode 100644 src/KSPACE/pair_born_coul_long.h diff --git a/src/KSPACE/pair_born_coul_long.cpp b/src/KSPACE/pair_born_coul_long.cpp new file mode 100644 index 0000000000..edbe1a771c --- /dev/null +++ b/src/KSPACE/pair_born_coul_long.cpp @@ -0,0 +1,472 @@ +/* ---------------------------------------------------------------------- + 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: Ahmed Ismail (SNL) +------------------------------------------------------------------------- */ + +#include "math.h" +#include "stdio.h" +#include "stdlib.h" +#include "string.h" +#include "pair_born_coul_long.h" +#include "atom.h" +#include "comm.h" +#include "force.h" +#include "kspace.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; + +#define MIN(a,b) ((a) < (b) ? (a) : (b)) +#define MAX(a,b) ((a) > (b) ? (a) : (b)) + +#define EWALD_F 1.12837917 +#define EWALD_P 0.3275911 +#define A1 0.254829592 +#define A2 -0.284496736 +#define A3 1.421413741 +#define A4 -1.453152027 +#define A5 1.061405429 + +/* ---------------------------------------------------------------------- */ + +PairBornCoulLong::PairBornCoulLong(LAMMPS *lmp) : Pair(lmp) {} + +/* ---------------------------------------------------------------------- */ + +PairBornCoulLong::~PairBornCoulLong() +{ + if (allocated) { + memory->destroy_2d_int_array(setflag); + memory->destroy_2d_double_array(cutsq); + + memory->destroy_2d_double_array(cut_lj); + memory->destroy_2d_double_array(cut_ljsq); + memory->destroy_2d_double_array(a); + memory->destroy_2d_double_array(rho); + memory->destroy_2d_double_array(sigma); + memory->destroy_2d_double_array(c); + memory->destroy_2d_double_array(d); + memory->destroy_2d_double_array(rhoinv); + memory->destroy_2d_double_array(born1); + memory->destroy_2d_double_array(born2); + memory->destroy_2d_double_array(born3); + memory->destroy_2d_double_array(offset); + } +} + +/* ---------------------------------------------------------------------- */ + +void PairBornCoulLong::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 grij,expm2,prefactor,t,erfc; + double r,rexp; + int *ilist,*jlist,*numneigh,**firstneigh; + + 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; + int nall = nlocal + atom->nghost; + double *special_coul = force->special_coul; + double *special_lj = force->special_lj; + int newton_pair = force->newton_pair; + double qqrd2e = force->qqrd2e; + + 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]; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + + if (j < nall) factor_coul = factor_lj = 1.0; + else { + factor_coul = special_coul[j/nall]; + factor_lj = special_lj[j/nall]; + j %= nall; + } + + 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); + grij = g_ewald * r; + expm2 = exp(-grij*grij); + t = 1.0 / (1.0 + EWALD_P*grij); + erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2; + prefactor = qqrd2e * qtmp*q[j]/r; + forcecoul = prefactor * (erfc + EWALD_F*grij*expm2); + 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 = prefactor*erfc; + 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_compute(); +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairBornCoulLong::allocate() +{ + allocated = 1; + int n = atom->ntypes; + + setflag = memory->create_2d_int_array(n+1,n+1,"pair:setflag"); + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; + + cutsq = memory->create_2d_double_array(n+1,n+1,"pair:cutsq"); + + cut_lj = memory->create_2d_double_array(n+1,n+1,"pair:cut_lj"); + cut_ljsq = memory->create_2d_double_array(n+1,n+1,"pair:cut_ljsq"); + a = memory->create_2d_double_array(n+1,n+1,"pair:a"); + rho = memory->create_2d_double_array(n+1,n+1,"pair:rho"); + sigma = memory->create_2d_double_array(n+1,n+1,"pair:sigma"); + c = memory->create_2d_double_array(n+1,n+1,"pair:c"); + d = memory->create_2d_double_array(n+1,n+1,"pair:d"); + rhoinv = memory->create_2d_double_array(n+1,n+1,"pair:rhoinv"); + born1 = memory->create_2d_double_array(n+1,n+1,"pair:born1"); + born2 = memory->create_2d_double_array(n+1,n+1,"pair:born2"); + born3 = memory->create_2d_double_array(n+1,n+1,"pair:born3"); + offset = memory->create_2d_double_array(n+1,n+1,"pair:offset"); +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairBornCoulLong::settings(int narg, char **arg) +{ + if (narg < 1 || narg > 2) error->all("Illegal pair_style command"); + + cut_lj_global = atof(arg[0]); + if (narg == 1) cut_coul = cut_lj_global; + else cut_coul = atof(arg[1]); + + // reset cutoffs that have been explicitly set + + if (allocated) { + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i+1; j <= atom->ntypes; j++) + if (setflag[i][j]) cut_lj[i][j] = cut_lj_global; + } +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairBornCoulLong::coeff(int narg, char **arg) +{ + if (narg < 7 || narg > 8) error->all("Incorrect args for pair coefficients"); + if (!allocated) allocate(); + + int ilo,ihi,jlo,jhi; + force->bounds(arg[0],atom->ntypes,ilo,ihi); + force->bounds(arg[1],atom->ntypes,jlo,jhi); + + double a_one = atof(arg[2]); + double rho_one = atof(arg[3]); + double sigma_one = atof(arg[4]); + if (rho_one <= 0) error->all("Incorrect args for pair coefficients"); + double c_one = atof(arg[5]); + double d_one = atof(arg[6]); + + double cut_lj_one = cut_lj_global; + if (narg == 8) cut_lj_one = atof(arg[7]); + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo,i); j <= jhi; j++) { + a[i][j] = a_one; + rho[i][j] = rho_one; + sigma[i][j] = sigma_one; + c[i][j] = c_one; + d[i][j] = d_one; + cut_lj[i][j] = cut_lj_one; + setflag[i][j] = 1; + count++; + } + } + + if (count == 0) error->all("Incorrect args for pair coefficients"); +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairBornCoulLong::init_one(int i, int j) +{ + if (setflag[i][j] == 0) error->all("All pair coeffs are not set"); + + double cut = MAX(cut_lj[i][j],cut_coul); + cut_ljsq[i][j] = cut_lj[i][j] * cut_lj[i][j]; + + rhoinv[i][j] = 1.0/rho[i][j]; + born1[i][j] = a[i][j]/rho[i][j]; + born2[i][j] = 6.0*c[i][j]; + born3[i][j] = 8.0*d[i][j]; + + if (offset_flag) { + double rexp = exp(-cut_lj[i][j]/rho[i][j]); + offset[i][j] = a[i][j]*rexp - c[i][j]/pow(cut_lj[i][j],6.0) + + d[i][j]/pow(cut_lj[i][j],8.0); + } else offset[i][j] = 0.0; + + cut_ljsq[j][i] = cut_ljsq[i][j]; + a[j][i] = a[i][j]; + c[j][i] = c[i][j]; + d[j][i] = d[i][j]; + rhoinv[j][i] = rhoinv[i][j]; + sigma[j][i] = sigma[i][j]; + born1[j][i] = born1[i][j]; + born2[j][i] = born2[i][j]; + born3[j][i] = born3[i][j]; + offset[j][i] = offset[i][j]; + + return cut; +} + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +void PairBornCoulLong::init_style() +{ + if (!atom->q_flag) + error->all("Pair style born/coul/long requires atom attribute q"); + + cut_coulsq = cut_coul * cut_coul; + + // insure use of KSpace long-range solver, set g_ewald + + if (force->kspace == NULL) + error->all("Pair style is incompatible with KSpace style"); + g_ewald = force->kspace->g_ewald; + + int irequest = neighbor->request(this); +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairBornCoulLong::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(&a[i][j],sizeof(double),1,fp); + fwrite(&rho[i][j],sizeof(double),1,fp); + fwrite(&sigma[i][j],sizeof(double),1,fp); + fwrite(&c[i][j],sizeof(double),1,fp); + fwrite(&d[i][j],sizeof(double),1,fp); + fwrite(&cut_lj[i][j],sizeof(double),1,fp); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairBornCoulLong::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(&a[i][j],sizeof(double),1,fp); + fread(&rho[i][j],sizeof(double),1,fp); + fread(&sigma[i][j],sizeof(double),1,fp); + fread(&c[i][j],sizeof(double),1,fp); + fread(&d[i][j],sizeof(double),1,fp); + fread(&cut_lj[i][j],sizeof(double),1,fp); + } + MPI_Bcast(&a[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&rho[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&c[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&d[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 PairBornCoulLong::write_restart_settings(FILE *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); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairBornCoulLong::read_restart_settings(FILE *fp) +{ + if (comm->me == 0) { + 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); + } + 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); +} + +/* ---------------------------------------------------------------------- */ + +double PairBornCoulLong::single(int i, int j, int itype, int jtype, + double rsq, + double factor_coul, double factor_lj, + double &fforce) +{ + double r2inv,r6inv,r,rexp,grij,expm2,t,erfc,prefactor; + double forcecoul,forceborn,phicoul,phiborn; + + r2inv = 1.0/rsq; + if (rsq < cut_coulsq) { + r = sqrt(rsq); + grij = g_ewald * r; + expm2 = exp(-grij*grij); + t = 1.0 / (1.0 + EWALD_P*grij); + erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2; + prefactor = force->qqrd2e * atom->q[i]*atom->q[j]/r; + forcecoul = prefactor * (erfc + EWALD_F*grij*expm2); + 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(-r*rhoinv[itype][jtype]); + forceborn = born1[itype][jtype]*r*rexp - born2[itype][jtype]*r6inv + + born3[itype][jtype]*r2inv*r6inv; + } else forceborn = 0.0; + fforce = (forcecoul + factor_lj*forceborn) * r2inv; + + double eng = 0.0; + if (rsq < cut_coulsq) { + phicoul = prefactor*erfc; + if (factor_coul < 1.0) phicoul -= (1.0-factor_coul)*prefactor; + eng += phicoul; + } + if (rsq < cut_ljsq[itype][jtype]) { + phiborn = a[itype][jtype]*rexp - c[itype][jtype]*r6inv + + d[itype][jtype]*r2inv*r6inv - offset[itype][jtype]; + eng += factor_lj*phiborn; + } + return eng; +} + +/* ---------------------------------------------------------------------- */ + +void *PairBornCoulLong::extract(char *str) +{ + if (strcmp(str,"cut_coul") == 0) return (void *) &cut_coul; + return NULL; +} + diff --git a/src/KSPACE/pair_born_coul_long.h b/src/KSPACE/pair_born_coul_long.h new file mode 100644 index 0000000000..ea62b59e9e --- /dev/null +++ b/src/KSPACE/pair_born_coul_long.h @@ -0,0 +1,50 @@ +/* ---------------------------------------------------------------------- + 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. +------------------------------------------------------------------------- */ + +#ifndef PAIR_BORN_COUL_LONG_H +#define PAIR_BORN_COUL_LONG_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairBornCoulLong : public Pair { + public: + PairBornCoulLong(class LAMMPS *); + ~PairBornCoulLong(); + 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 *); + double single(int, int, int, int, double, double, double, double &); + void *extract(char *); + + private: + double cut_lj_global; + double **cut_lj,**cut_ljsq; + double cut_coul,cut_coulsq; + double **a,**rho,**sigma,**c,**d; + double **rhoinv,**born1,**born2,**born3,**offset; + double g_ewald; + + void allocate(); +}; + +} + +#endif