From becdcdb27d35f552a5af1b594432fc1eb6a797cc Mon Sep 17 00:00:00 2001 From: sjplimp Date: Thu, 7 Oct 2010 21:40:10 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5010 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- src/pair_born.cpp | 404 +++++++++++++++++++++++++++++++++++++++++++++ src/pair_born.h | 54 ++++++ src/pair_gauss.cpp | 320 +++++++++++++++++++++++++++++++++++ src/pair_gauss.h | 52 ++++++ 4 files changed, 830 insertions(+) create mode 100644 src/pair_born.cpp create mode 100644 src/pair_born.h create mode 100644 src/pair_gauss.cpp create mode 100644 src/pair_gauss.h diff --git a/src/pair_born.cpp b/src/pair_born.cpp new file mode 100644 index 0000000000..5c8ab293cb --- /dev/null +++ b/src/pair_born.cpp @@ -0,0 +1,404 @@ +/* ---------------------------------------------------------------------- + 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: Sai Jayaraman (U Notre Dame) +------------------------------------------------------------------------- */ + +#include "math.h" +#include "stdio.h" +#include "stdlib.h" +#include "string.h" +#include "pair_born.h" +#include "atom.h" +#include "comm.h" +#include "force.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)) + +/* ---------------------------------------------------------------------- */ + +PairBorn::PairBorn(LAMMPS *lmp) : Pair(lmp) {} + +/* ---------------------------------------------------------------------- */ + +PairBorn::~PairBorn() +{ + if (allocated) { + memory->destroy_2d_int_array(setflag); + memory->destroy_2d_double_array(cutsq); + + memory->destroy_2d_double_array(cut); + 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 PairBorn::compute(int eflag, int vflag) +{ + int i,j,ii,jj,inum,jnum,itype,jtype; + double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair; + double rsq,r2inv,r6inv,force_tf,factor_lj; + double r,rexp; + int *ilist,*jlist,*numneigh,**firstneigh; + + evdwl = 0.0; + if (eflag || vflag) ev_setup(eflag,vflag); + else evflag = vflag_fdotr = 0; + + double **x = atom->x; + double **f = atom->f; + int *type = atom->type; + int nlocal = atom->nlocal; + int nall = nlocal + atom->nghost; + double *special_lj = force->special_lj; + int newton_pair = force->newton_pair; + + 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]; + 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_lj = 1.0; + else { + 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; + 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; + fpair = 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) { + evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv + + d[itype][jtype]*r6inv*r2inv - offset[itype][jtype]; + evdwl *= factor_lj; + } + + if (evflag) ev_tally(i,j,nlocal,newton_pair, + evdwl,0.0,fpair,delx,dely,delz); + } + } + } + + if (vflag_fdotr) virial_compute(); +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairBorn::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 = memory->create_2d_double_array(n+1,n+1,"pair:cut"); + 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 PairBorn::settings(int narg, char **arg) +{ + if (narg != 1) error->all("Illegal pair_style command"); + + cut_global = atof(arg[0]); + + // 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[i][j] = cut_global; + } +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairBorn::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 = force->numeric(arg[2]); + double rho_one = force->numeric(arg[3]); + double sigma_one = force->numeric(arg[4]); + if (rho_one <= 0) error->all("Incorrect args for pair coefficients"); + double c_one = force->numeric(arg[5]); + double d_one = force->numeric(arg[6]); + + double cut_one = cut_global; + if (narg == 8) cut_one = force->numeric(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[i][j] = cut_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 PairBorn::init_one(int i, int j) +{ + if (setflag[i][j] == 0) error->all("All pair coeffs are not set"); + + 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((sigma[i][j]-cut_lj[i][j])*rhoinv[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; + + 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]; + + // 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 PI = 4.0*atan(1.0); + double rho1 = rho[i][j]; + double rho2 = rho1*rho1; + double rho3 = rho2*rho1; + double rc = sigma[i][j] - cut[i][j]; + double rc2 = rc*rc; + double rc3 = rc2*rc; + double rc5 = rc3*rc2; + etail_ij = 2.0*PI*all[0]*all[1] * + (a[i][j]*exp(-rc/rho1)*rho1* (rc2 + 2.0*rho1*rc + 2.0*rho2) - + c[i][j]/(3.0*rc3) + d[i][j]/(5.0*rc5)); + ptail_ij = (-1/3.0)*2.0*PI*all[0]*all[1] * + (-a[i][j]*exp(-rc/rho1) * + (rc3 + 3.0*rho1*rc2 + 6.0*rho2*rc + 6.0*rho3) + + 2.0*c[i][j]/rc3 - 8.0*d[i][j]/(5.0*rc5)); + } + + return cut[i][j]; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairBorn::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[i][j],sizeof(double),1,fp); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairBorn::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[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[i][j],1,MPI_DOUBLE,0,world); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairBorn::write_restart_settings(FILE *fp) +{ + fwrite(&cut_global,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 PairBorn::read_restart_settings(FILE *fp) +{ + if (comm->me == 0) { + fread(&cut_global,sizeof(double),1,fp); + fread(&offset_flag,sizeof(int),1,fp); + fread(&mix_flag,sizeof(int),1,fp); + } + MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); + MPI_Bcast(&offset_flag,1,MPI_INT,0,world); + MPI_Bcast(&mix_flag,1,MPI_INT,0,world); +} + +/* ---------------------------------------------------------------------- */ + +double PairBorn::single(int i, int j, int itype, int jtype, + double rsq, double factor_coul, double factor_lj, + double &fforce) +{ + double r2inv,r6inv,r,rexp,forceborn,phiborn; + + r2inv = 1.0/rsq; + 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; + fforce = factor_lj*force_born*r2inv; + + phiborn = a[itype][jtype]*rexp - c[itype][jtype]*r6inv + + d[itype][jtype]*r2inv*r6inv - offset[itype][jtype]; + return factor_lj*phiborn; +} diff --git a/src/pair_born.h b/src/pair_born.h new file mode 100644 index 0000000000..a51cf0fba1 --- /dev/null +++ b/src/pair_born.h @@ -0,0 +1,54 @@ +/* ---------------------------------------------------------------------- + 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,PairBorn) + +#else + +#ifndef PAIR_BORN_H +#define PAIR_BORN_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairBorn : public Pair { + public: + PairBorn(class LAMMPS *); + ~PairBorn(); + void compute(int, int); + void settings(int, char **); + void coeff(int, char **); + 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 &); + + private: + double cut_global; + double **cut; + double **a,**rho,**sigma,**c, **d; + double **rhoinv,**tf1,**tf2,**tf3,**offset; + double **rhoinv,**born1,**born2,**born3,**offset; + + void allocate(); +}; + +} + +#endif +#endif diff --git a/src/pair_gauss.cpp b/src/pair_gauss.cpp new file mode 100644 index 0000000000..c9b2b18897 --- /dev/null +++ b/src/pair_gauss.cpp @@ -0,0 +1,320 @@ +/* ---------------------------------------------------------------------- + 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: Sai Jayaraman (University of Notre Dame) +------------------------------------------------------------------------- */ + +#include "math.h" +#include "stdio.h" +#include "stdlib.h" +#include "string.h" +#include "pair_gauss.h" +#include "atom.h" +#include "comm.h" +#include "force.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 EPSILON 1.0e-10 + +/* ---------------------------------------------------------------------- */ + +PairGauss::PairGauss(LAMMPS *lmp) :Pair(lmp) {} + +/* ---------------------------------------------------------------------- */ + +PairGauss::~PairGauss() +{ + if (allocated) { + memory->destroy_2d_int_array(setflag); + memory->destroy_2d_double_array(cutsq); + + memory->destroy_2d_double_array(cut); + memory->destroy_2d_double_array(a); + memory->destroy_2d_double_array(b); + memory->destroy_2d_double_array(offset); + } +} + +/* ---------------------------------------------------------------------- */ + +void PairGauss::compute(int eflag, int vflag) +{ + int i,j,ii,jj,inum,jnum,itype,jtype; + double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair; + double r,rsq,r2inv,r6inv,forcelj,rexp; + int *ilist,*jlist,*numneigh,**firstneigh; + + evdwl = 0.0; + if (eflag || vflag) ev_setup(eflag,vflag); + else evflag = vflag_fdotr = 0; + + double **x = atom->x; + double **f = atom->f; + int *type = atom->type; + int nlocal = atom->nlocal; + int nall = nlocal + atom->nghost; + int newton_pair = force->newton_pair; + + 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]; + 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]; + + 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; + r = sqrt(rsq); + forcelj = - 2.0*a[itype][jtype]*b[itype][jtype] * rsq * + exp(-b[itype][jtype]*rsq); + if (r < 0.00001) forcelj = 0.0; + fpair = 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) { + evdwl = -(a[itype][jtype]*exp(-b[itype][jtype]*rsq) - + offset[itype][jtype]); + evdwl *= MAX(EPSILON,latscale); + } + + if (evflag) ev_tally(i,j,nlocal,newton_pair, + evdwl,0.0,fpair,delx,dely,delz); + } + } + } + + if (vflag_fdotr) virial_compute(); +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairGauss::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 = 1; j <= n; j++) + setflag[i][j] = 0; + + cutsq = memory->create_2d_double_array(n+1,n+1,"pair:cutsq"); + + cut = memory->create_2d_double_array(n+1,n+1,"pair:cut_gauss"); + a = memory->create_2d_double_array(n+1,n+1,"pair:a"); + b = memory->create_2d_double_array(n+1,n+1,"pair:b"); + offset = memory->create_2d_double_array(n+1,n+1,"pair:offset"); +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairGauss::settings(int narg, char **arg) +{ + if (narg != 1) error->all("Illegal pair_style command"); + + cut_global = atof(arg[0]); + + // reset cutoffs that have been explicity 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[i][j] = cut_global; + } +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairGauss::coeff(int narg, char **arg) +{ + if (narg < 4 || narg > 5) 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 b_one = atof(arg[3]); + + double cut_one = cut_global; + if (narg == 5) cut_one = atof(arg[4]); + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo,i); j<=jhi; j++) { + a[i][j] = a_one; + b[i][j] = b_one; + cut[i][j] = cut_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 PairGauss::init_one(int i, int j) +{ + if (setflag[i][j] == 0) error->all("All pair coeffs are not set"); + + if (offset_flag) offset[i][j] = a[i][j]*exp(-b[i][j]*cut[i][j]*cut[i][j]); + else offset[i][j] = 0.0; + + a[j][i] = a[i][j]; + b[j][i] = b[i][j]; + offset[j][i] = offset[i][j]; + + return cut[i][j]; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairGauss::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(&b[i][j],sizeof(double),1,fp); + fwrite(&cut[i][j],sizeof(double),1,fp); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairGauss::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(&b[i][j],sizeof(double),1,fp); + fread(&cut[i][j],sizeof(double),1,fp); + } + MPI_Bcast(&a[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&b[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairGauss::write_restart_settings(FILE *fp) +{ + fwrite(&cut_global,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 PairGauss::read_restart_settings(FILE *fp) +{ + if (comm->me == 0) { + fread(&cut_global,sizeof(double),1,fp); + fread(&offset_flag,sizeof(int),1,fp); + fread(&mix_flag,sizeof(int),1,fp); + } + MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); + MPI_Bcast(&offset_flag,1,MPI_INT,0,world); + MPI_Bcast(&mix_flag,1,MPI_INT,0,world); +} + +/* ---------------------------------------------------------------------- */ + +double PairGauss::single(int i, int j, int itype, int jtype, double rsq, + double factor_coul, double factor_lj, + double &fforce) +{ + double r2inv,r6inv,forcelj,philj,r; + + r = sqrt(rsq); + + r2inv = 1.0/rsq; + philj = -(a[itype][jtype]*exp(-b[itype][jtype]*rsq) - offset[itype][jtype]); + philj *= MAX(eps,latscale); + + forcelj = -2.0*a[itype][jtype]*b[itype][jtype]*rsq*exp(-b[itype][jtype]*rsq); + fforce = forcelj*r2inv; + return philj; +} diff --git a/src/pair_gauss.h b/src/pair_gauss.h new file mode 100644 index 0000000000..9598457dca --- /dev/null +++ b/src/pair_gauss.h @@ -0,0 +1,52 @@ +/* ---------------------------------------------------------------------- + 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(gauss,PairGauss) + +#else + +#ifndef PAIR_GAUSS_H +#define PAIR_GAUSS_H + +#include "pair.h" + +namespace LAMMPS_NS { + + class PairGauss : public Pair { + public: + PairGauss(class LAMMPS *); + ~PairGauss(); + void compute(int,int); + void settings(int, char **); + void coeff(int, char **); + 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 &); + + private: + double cut_global; + double **cut; + double **a,**b; + double **offset; + + void allocate(); + }; +} + +#endif +#endif