From 3ad5687000a06fc128279657f4a4fd8331293a44 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Thu, 15 May 2008 20:49:38 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1805 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- src/pair_lj_gromacs.cpp | 425 +++++++++++++++++++++++ src/pair_lj_gromacs.h | 47 +++ src/pair_lj_gromacs_coul_gromacs.cpp | 491 +++++++++++++++++++++++++++ src/pair_lj_gromacs_coul_gromacs.h | 49 +++ src/style.h | 4 + 5 files changed, 1016 insertions(+) create mode 100644 src/pair_lj_gromacs.cpp create mode 100644 src/pair_lj_gromacs.h create mode 100644 src/pair_lj_gromacs_coul_gromacs.cpp create mode 100644 src/pair_lj_gromacs_coul_gromacs.h diff --git a/src/pair_lj_gromacs.cpp b/src/pair_lj_gromacs.cpp new file mode 100644 index 0000000000..81f9aa3b3d --- /dev/null +++ b/src/pair_lj_gromacs.cpp @@ -0,0 +1,425 @@ +/* ---------------------------------------------------------------------- + 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: Mark Stevens (SNL) +------------------------------------------------------------------------- */ + +#include "math.h" +#include "stdio.h" +#include "stdlib.h" +#include "string.h" +#include "pair_lj_gromacs.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)) + +/* ---------------------------------------------------------------------- */ + +PairLJGromacs::PairLJGromacs(LAMMPS *lmp) : Pair(lmp) {} + +/* ---------------------------------------------------------------------- */ + +PairLJGromacs::~PairLJGromacs() +{ + 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(cut_inner); + memory->destroy_2d_double_array(cut_inner_sq); + memory->destroy_2d_double_array(epsilon); + memory->destroy_2d_double_array(sigma); + memory->destroy_2d_double_array(lj1); + memory->destroy_2d_double_array(lj2); + memory->destroy_2d_double_array(lj3); + memory->destroy_2d_double_array(lj4); + memory->destroy_2d_double_array(ljsw1); + memory->destroy_2d_double_array(ljsw2); + memory->destroy_2d_double_array(ljsw3); + memory->destroy_2d_double_array(ljsw4); + memory->destroy_2d_double_array(ljsw5); + } +} + +/* ---------------------------------------------------------------------- */ + +void PairLJGromacs::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,forcelj,factor_lj; + double r,t,fswitch,eswitch; + 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; + double *q = atom->q; + 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; + forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]); + if (rsq > cut_inner_sq[itype][jtype]) { + r = sqrt(rsq); + t = r - cut_inner[itype][jtype]; + fswitch = r*t*t*(ljsw1[itype][jtype] + ljsw2[itype][jtype]*t); + forcelj += fswitch; + } + + fpair = 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) { + evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) + + ljsw5[itype][jtype]; + if (rsq > cut_inner_sq[itype][jtype]) { + eswitch = t*t*t*(ljsw3[itype][jtype] + ljsw4[itype][jtype]*t); + evdwl += eswitch; + } + 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 PairLJGromacs::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"); + cut_inner = memory->create_2d_double_array(n+1,n+1,"pair:cut_inner"); + cut_inner_sq = memory->create_2d_double_array(n+1,n+1,"pair:cut_inner_sq"); + epsilon = memory->create_2d_double_array(n+1,n+1,"pair:epsilon"); + sigma = memory->create_2d_double_array(n+1,n+1,"pair:sigma"); + lj1 = memory->create_2d_double_array(n+1,n+1,"pair:lj1"); + lj2 = memory->create_2d_double_array(n+1,n+1,"pair:lj2"); + lj3 = memory->create_2d_double_array(n+1,n+1,"pair:lj3"); + lj4 = memory->create_2d_double_array(n+1,n+1,"pair:lj4"); + ljsw1 = memory->create_2d_double_array(n+1,n+1,"pair:ljsw1"); + ljsw2 = memory->create_2d_double_array(n+1,n+1,"pair:ljsw2"); + ljsw3 = memory->create_2d_double_array(n+1,n+1,"pair:ljsw3"); + ljsw4 = memory->create_2d_double_array(n+1,n+1,"pair:ljsw4"); + ljsw5 = memory->create_2d_double_array(n+1,n+1,"pair:ljsw5"); +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairLJGromacs::settings(int narg, char **arg) +{ + if (narg != 2) error->all("Illegal pair_style command"); + + cut_inner_global = atof(arg[0]); + cut_global = atof(arg[1]); + + if (cut_inner_global <= 0.0 || cut_inner_global > cut_global) + error->all("Illegal pair_style command"); + + // 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_inner[i][j] = cut_inner_global; + cut[i][j] = cut_global; + } + } +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairLJGromacs::coeff(int narg, char **arg) +{ + if (narg != 4 && narg != 6) + 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 epsilon_one = atof(arg[2]); + double sigma_one = atof(arg[3]); + + double cut_inner_one = cut_inner_global; + double cut_one = cut_global; + if (narg == 6) { + cut_inner_one = atof(arg[4]); + cut_one = atof(arg[5]); + } + + if (cut_inner_one <= 0.0 || cut_inner_one > cut_one) + error->all("Incorrect args for pair coefficients"); + + 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_inner[i][j] = cut_inner_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 PairLJGromacs::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_inner[i][j] = mix_distance(cut_inner[i][i],cut_inner[j][j]); + cut[i][j] = mix_distance(cut[i][i],cut[j][j]); + } + + cut_inner_sq[i][j] = cut_inner[i][j]*cut_inner[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); + + double r6inv = 1.0/pow(cut[i][j],6.0); + double r8inv = 1.0/pow(cut[i][j],8.0); + double t = cut[i][j] - cut_inner[i][j]; + double t2inv = 1.0/(t*t); + double t3inv = t2inv/t; + double t3 = 1.0/t3inv; + double a6 = ( 7.0*cut_inner[i][j] - 10.0*cut[i][j])*r8inv*t2inv; + double b6 = ( 9.0*cut[i][j] - 7.0*cut_inner[i][j])*r8inv*t3inv; + double a12 = (13.0*cut_inner[i][j] - 16.0*cut[i][j])*r6inv*r8inv*t2inv; + double b12 = (15.0*cut[i][j] - 13.0*cut_inner[i][j])*r6inv*r8inv*t3inv; + double c6 = r6inv - t3*(a6/3.0 + b6*t/4.0); + double c12 = r6inv*r6inv - t3*(a12/3.0 + b12*t/4.0); + ljsw1[i][j] = lj1[i][j]*a12 - lj2[i][j]*a6; + ljsw2[i][j] = lj1[i][j]*b12 - lj2[i][j]*b6; + ljsw3[i][j] =-lj3[i][j]*a12/3.0 + lj4[i][j]*a6/3.0; + ljsw4[i][j] =-lj3[i][j]*b12/4.0 + lj4[i][j]*b6/4.0; + ljsw5[i][j] =-lj3[i][j]*c12 + lj4[i][j]*c6; + + cut_inner[j][i] = cut_inner[i][j]; + cut_inner_sq[j][i] = cut_inner_sq[i][j]; + lj1[j][i] = lj1[i][j]; + lj2[j][i] = lj2[i][j]; + lj3[j][i] = lj3[i][j]; + lj4[j][i] = lj4[i][j]; + ljsw1[j][i] = ljsw1[i][j]; + ljsw2[j][i] = ljsw2[i][j]; + ljsw3[j][i] = ljsw3[i][j]; + ljsw4[j][i] = ljsw4[i][j]; + ljsw5[j][i] = ljsw5[i][j]; + + return cut[i][j]; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairLJGromacs::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_inner[i][j],sizeof(double),1,fp); + fwrite(&cut[i][j],sizeof(double),1,fp); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairLJGromacs::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_inner[i][j],sizeof(double),1,fp); + fread(&cut[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_inner[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairLJGromacs::write_restart_settings(FILE *fp) +{ + fwrite(&cut_inner_global,sizeof(double),1,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 PairLJGromacs::read_restart_settings(FILE *fp) +{ + int me = comm->me; + if (me == 0) { + fread(&cut_inner_global,sizeof(double),1,fp); + fread(&cut_global,sizeof(double),1,fp); + fread(&offset_flag,sizeof(int),1,fp); + fread(&mix_flag,sizeof(int),1,fp); + } + MPI_Bcast(&cut_inner_global,1,MPI_DOUBLE,0,world); + 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 PairLJGromacs::single(int i, int j, int itype, int jtype, + double rsq, + double factor_coul, double factor_lj, + double &fforce) +{ + double r2inv,r6inv,forcelj,philj; + double r,t,fswitch,phiswitch; + + r2inv = 1.0/rsq; + r6inv = r2inv*r2inv*r2inv; + forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]); + if (rsq > cut_inner_sq[itype][jtype]) { + r = sqrt(rsq); + t = r - cut_inner[itype][jtype]; + fswitch = r*t*t*(ljsw1[itype][jtype] + ljsw2[itype][jtype]*t); + forcelj += fswitch; + } + fforce = factor_lj*forcelj*r2inv; + + philj = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) + + ljsw5[itype][jtype]; + if (rsq > cut_inner_sq[itype][jtype]) { + phiswitch = t*t*t*(ljsw3[itype][jtype] + ljsw4[itype][jtype]*t); + philj += phiswitch; + } + + return factor_lj*philj; +} diff --git a/src/pair_lj_gromacs.h b/src/pair_lj_gromacs.h new file mode 100644 index 0000000000..aad55f1e13 --- /dev/null +++ b/src/pair_lj_gromacs.h @@ -0,0 +1,47 @@ +/* ---------------------------------------------------------------------- + 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_LJ_GROMACS_H +#define PAIR_LJ_GROMACS_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairLJGromacs : public Pair { + public: + PairLJGromacs(class LAMMPS *); + virtual ~PairLJGromacs(); + virtual void compute(int, int); + virtual void settings(int, char **); + void coeff(int, char **); + double init_one(int, int); + void write_restart(FILE *); + void read_restart(FILE *); + virtual void write_restart_settings(FILE *); + virtual void read_restart_settings(FILE *); + virtual double single(int, int, int, int, double, double, double, double &); + + protected: + double cut_inner_global,cut_global; + double **cut,**cut_inner,**cut_inner_sq; + double **epsilon,**sigma; + double **lj1,**lj2,**lj3,**lj4; + double **ljsw1,**ljsw2,**ljsw3,**ljsw4,**ljsw5; + + void allocate(); +}; + +} + +#endif diff --git a/src/pair_lj_gromacs_coul_gromacs.cpp b/src/pair_lj_gromacs_coul_gromacs.cpp new file mode 100644 index 0000000000..83c3252633 --- /dev/null +++ b/src/pair_lj_gromacs_coul_gromacs.cpp @@ -0,0 +1,491 @@ +/* ---------------------------------------------------------------------- + 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: Mark Stevens (SNL) +------------------------------------------------------------------------- */ + +#include "math.h" +#include "stdio.h" +#include "stdlib.h" +#include "string.h" +#include "pair_lj_gromacs_coul_gromacs.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)) + +/* ---------------------------------------------------------------------- */ + +PairLJGromacsCoulGromacs::PairLJGromacsCoulGromacs(LAMMPS *lmp) : Pair(lmp) {} + +/* ---------------------------------------------------------------------- */ + +PairLJGromacsCoulGromacs::~PairLJGromacsCoulGromacs() +{ + if (allocated) { + memory->destroy_2d_int_array(setflag); + memory->destroy_2d_double_array(cutsq); + + memory->destroy_2d_double_array(epsilon); + memory->destroy_2d_double_array(sigma); + memory->destroy_2d_double_array(lj1); + memory->destroy_2d_double_array(lj2); + memory->destroy_2d_double_array(lj3); + memory->destroy_2d_double_array(lj4); + memory->destroy_2d_double_array(ljsw1); + memory->destroy_2d_double_array(ljsw2); + memory->destroy_2d_double_array(ljsw3); + memory->destroy_2d_double_array(ljsw4); + memory->destroy_2d_double_array(ljsw5); + } +} + +/* ---------------------------------------------------------------------- */ + +void PairLJGromacsCoulGromacs::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,forcelj,factor_coul,factor_lj; + double r,tlj,tc,fswitch,fswitchcoul,eswitch,ecoulswitch; + 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; + + if (rsq < cut_bothsq) { + r2inv = 1.0/rsq; + + // skip if qi or qj = 0.0 since this potential may be used as + // coarse-grain model with many uncharged atoms + + if (rsq < cut_coulsq && qtmp != 0.0 && q[j] != 0.0) { + forcecoul = qqrd2e * qtmp*q[j]*sqrt(r2inv); + if (rsq > cut_coul_innersq) { + r = sqrt(rsq); + tc = r - cut_coul_inner; + fswitchcoul = qqrd2e * qtmp*q[j]*r*tc*tc*(coulsw1 + coulsw2*tc); + forcecoul += fswitchcoul; + } + } else forcecoul = 0.0; + + if (rsq < cut_ljsq) { + r6inv = r2inv*r2inv*r2inv; + jtype = type[j]; + forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]); + if (rsq > cut_lj_innersq) { + r = sqrt(rsq); + tlj = r - cut_lj_inner; + fswitch = r*tlj*tlj*(ljsw1[itype][jtype] + + ljsw2[itype][jtype]*tlj); + forcelj += fswitch; + } + } else forcelj = 0.0; + + fpair = (factor_coul*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_coulsq) { + ecoul = qqrd2e * qtmp*q[j] * (sqrt(r2inv) - coulsw5); + if (rsq > cut_coul_innersq) { + ecoulswitch = tc*tc*tc * (coulsw3 + coulsw4*tc); + ecoul += qqrd2e*qtmp*q[j]*ecoulswitch; + } + ecoul *= factor_coul; + } else ecoul = 0.0; + if (rsq < cut_ljsq) { + evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) + + ljsw5[itype][jtype]; + if (rsq > cut_lj_innersq) { + eswitch = tlj*tlj*tlj * (ljsw3[itype][jtype] + + ljsw4[itype][jtype]*tlj); + evdwl += eswitch; + } + 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 PairLJGromacsCoulGromacs::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"); + + epsilon = memory->create_2d_double_array(n+1,n+1,"pair:epsilon"); + sigma = memory->create_2d_double_array(n+1,n+1,"pair:sigma"); + lj1 = memory->create_2d_double_array(n+1,n+1,"pair:lj1"); + lj2 = memory->create_2d_double_array(n+1,n+1,"pair:lj2"); + lj3 = memory->create_2d_double_array(n+1,n+1,"pair:lj3"); + lj4 = memory->create_2d_double_array(n+1,n+1,"pair:lj4"); + ljsw1 = memory->create_2d_double_array(n+1,n+1,"pair:ljsw1"); + ljsw2 = memory->create_2d_double_array(n+1,n+1,"pair:ljsw2"); + ljsw3 = memory->create_2d_double_array(n+1,n+1,"pair:ljsw3"); + ljsw4 = memory->create_2d_double_array(n+1,n+1,"pair:ljsw4"); + ljsw5 = memory->create_2d_double_array(n+1,n+1,"pair:ljsw5"); +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairLJGromacsCoulGromacs::settings(int narg, char **arg) +{ + if (narg != 2 && narg != 4) + error->all("Illegal pair_style command"); + + cut_lj_inner = atof(arg[0]); + cut_lj = atof(arg[1]); + if (narg == 2) { + cut_coul_inner = cut_lj_inner; + cut_coul = cut_lj; + } else { + cut_coul_inner = atof(arg[2]); + cut_coul = atof(arg[3]); + } + + if (cut_lj_inner <= 0.0 || cut_coul_inner < 0.0) + error->all("Illegal pair_style command"); + if (cut_lj_inner > cut_lj || cut_coul_inner > cut_coul) + error->all("Illegal pair_style command"); +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairLJGromacsCoulGromacs::coeff(int narg, char **arg) +{ + if (narg != 4) 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 epsilon_one = atof(arg[2]); + double sigma_one = atof(arg[3]); + + 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; + setflag[i][j] = 1; + count++; + } + } + + if (count == 0) error->all("Incorrect args for pair coefficients"); +} + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +void PairLJGromacsCoulGromacs::init_style() +{ + if (!atom->q_flag) + error->all("Pair style lj/gromacs/coul/gromacs requires atom attribute q"); + + int irequest = neighbor->request(this); + + cut_lj_innersq = cut_lj_inner * cut_lj_inner; + cut_ljsq = cut_lj * cut_lj; + cut_coul_innersq = cut_coul_inner * cut_coul_inner; + cut_coulsq = cut_coul * cut_coul; + cut_bothsq = MAX(cut_ljsq,cut_coulsq); +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairLJGromacsCoulGromacs::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]); + } + + double cut = MAX(cut_lj,cut_coul); + + 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); + + double r6inv = 1.0/pow(cut_lj,6.0); + double r8inv = 1.0/pow(cut_lj,8.0); + double t = cut_lj - cut_lj_inner; + double t2inv = 1.0/(t*t); + double t3inv = t2inv/t; + double t3 = 1.0/t3inv; + double a6 = (7.0*cut_lj_inner - 10.0*cut_lj)*r8inv*t2inv; + double b6 = (9.0*cut_lj - 7.0*cut_lj_inner)*r8inv*t3inv; + double a12 = (13.0*cut_lj_inner - 16.0*cut_lj)*r6inv*r8inv*t2inv; + double b12 = (15.0*cut_lj - 13.0*cut_lj_inner)*r6inv*r8inv*t3inv; + double c6 = r6inv - t3*(a6/3.0 + b6*t/4.0); + double c12 = r6inv*r6inv - t3*(a12/3.0 + b12*t/4.0); + ljsw1[i][j] = lj1[i][j]*a12 - lj2[i][j]*a6; + ljsw2[i][j] = lj1[i][j]*b12 - lj2[i][j]*b6; + ljsw3[i][j] = -lj3[i][j]*a12/3.0 + lj4[i][j]*a6/3.0; + ljsw4[i][j] = -lj3[i][j]*b12/4.0 + lj4[i][j]*b6/4.0; + ljsw5[i][j] = -lj3[i][j]*c12 + lj4[i][j]*c6; + + double r3inv = 1.0/pow(cut_coul,3.0); + t = cut_coul - cut_coul_inner; + t2inv = 1.0/(t*t); + t3inv = t2inv/t; + double a1 = (2.0*cut_coul_inner - 5.0*cut_coul) * r3inv*t2inv; + double b1 = (4.0*cut_coul - 2.0*cut_coul_inner) * r3inv*t3inv; + coulsw1 = a1; + coulsw2 = b1; + coulsw3 = -a1/3.0; + coulsw4 = -b1/4.0; + coulsw5 = 1.0/cut_coul - t*t*t*(a1/3.0 + b1*t/4.0); + + lj1[j][i] = lj1[i][j]; + lj2[j][i] = lj2[i][j]; + lj3[j][i] = lj3[i][j]; + lj4[j][i] = lj4[i][j]; + ljsw1[j][i] = ljsw1[i][j]; + ljsw2[j][i] = ljsw2[i][j]; + ljsw3[j][i] = ljsw3[i][j]; + ljsw4[j][i] = ljsw4[i][j]; + ljsw5[j][i] = ljsw5[i][j]; + + return cut; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairLJGromacsCoulGromacs::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); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairLJGromacsCoulGromacs::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); + } + MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairLJGromacsCoulGromacs::write_restart_settings(FILE *fp) +{ + fwrite(&cut_lj_inner,sizeof(double),1,fp); + fwrite(&cut_lj,sizeof(double),1,fp); + fwrite(&cut_coul_inner,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 PairLJGromacsCoulGromacs::read_restart_settings(FILE *fp) +{ + if (comm->me == 0) { + fread(&cut_lj_inner,sizeof(double),1,fp); + fread(&cut_lj,sizeof(double),1,fp); + fread(&cut_coul_inner,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_inner,1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_lj,1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_coul_inner,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 PairLJGromacsCoulGromacs::single(int i, int j, int itype, int jtype, + double rsq, + double factor_coul, double factor_lj, + double &fforce) +{ + double r2inv,r6inv,forcecoul,forcelj,phicoul,philj; + double r,tlj,tc,fswitch,phiswitch,fswitchcoul,phiswitchcoul; + + r2inv = 1.0/rsq; + if (rsq < cut_coulsq) { + forcecoul = force->qqrd2e * atom->q[i]*atom->q[j]*sqrt(r2inv); + if (rsq > cut_coul_innersq) { + r = sqrt(rsq); + tc = r - cut_coul_inner; + fswitchcoul = force->qqrd2e * + atom->q[i]*atom->q[j] * r*tc*tc * (coulsw1 + coulsw2*tcoul); + forcecoul += fswitchcoul; + } + } else forcecoul = 0.0; + + if (rsq < cut_ljsq) { + r6inv = r2inv*r2inv*r2inv; + forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]); + if (rsq > cut_lj_innersq) { + r = sqrt(rsq); + tlj = r - cut_lj_inner; + fswitch = r*tlj*tlj*(ljsw1[itype][jtype] + ljsw2[itype][jtype]*tlj); + forcelj += fswitch; + } + } else forcelj = 0.0; + + fforce = (factor_coul*forcecoul + factor_lj*forcelj) * r2inv; + + double eng = 0.0; + if (rsq < cut_coulsq) { + phicoul = force->qqrd2e * atom->q[i]*atom->q[j] * (sqrt(r2inv)-coulsw5); + if (rsq > cut_coul_innersq) { + phiswitchcoul = force->qqrd2e * atom->q[i]*atom->q[j] * + tc*tc*tc * (coulsw3 + coulsw4*tc); + phicoul += phiswitchcoul; + } + eng += factor_coul*phicoul; + } + + if (rsq < cut_ljsq) { + philj = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) + + ljsw5[itype][jtype]; + if (rsq > cut_lj_innersq) { + phiswitch = tlj*tlj*tlj * (ljsw3[itype][jtype] + + ljsw4[itype][jtype]*tlj); + philj += phiswitch; + } + eng += factor_lj*philj; + } + + return eng; +} diff --git a/src/pair_lj_gromacs_coul_gromacs.h b/src/pair_lj_gromacs_coul_gromacs.h new file mode 100644 index 0000000000..c7aafd7c49 --- /dev/null +++ b/src/pair_lj_gromacs_coul_gromacs.h @@ -0,0 +1,49 @@ +/* ---------------------------------------------------------------------- + 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_LJ_GROMACS_COUL_GROMACS_H +#define PAIR_LJ_GROMACS_COUL_GROMACS_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairLJGromacsCoulGromacs : public Pair { + public: + PairLJGromacsCoulGromacs(class LAMMPS *); + virtual ~PairLJGromacsCoulGromacs(); + virtual void compute(int, int); + virtual void settings(int, char **); + void coeff(int, char **); + void init_style(); + double init_one(int, int); + void write_restart(FILE *); + void read_restart(FILE *); + virtual void write_restart_settings(FILE *); + virtual void read_restart_settings(FILE *); + virtual double single(int, int, int, int, double, double, double, double &); + + protected: + double cut_lj_inner,cut_lj,cut_coul_inner,cut_coul; + double cut_lj_innersq,cut_ljsq,cut_coul_innersq,cut_coulsq,cut_bothsq; + double **epsilon,**sigma; + double **lj1,**lj2,**lj3,**lj4; + double **ljsw1,**ljsw2,**ljsw3,**ljsw4,**ljsw5; + double coulsw1,coulsw2,coulsw3,coulsw4,coulsw5; + + void allocate(); +}; + +} + +#endif diff --git a/src/style.h b/src/style.h index 7773ae2af1..fe84d72531 100644 --- a/src/style.h +++ b/src/style.h @@ -300,6 +300,8 @@ MinimizeStyle(sd,MinSD) #include "pair_lj_cut_coul_cut.h" #include "pair_lj_cut_coul_debye.h" #include "pair_lj_expand.h" +#include "pair_lj_gromacs.h" +#include "pair_lj_gromacs_coul_gromacs.h" #include "pair_lj_smooth.h" #include "pair_morse.h" #include "pair_soft.h" @@ -318,6 +320,8 @@ PairStyle(lj/cut,PairLJCut) PairStyle(lj/cut/coul/cut,PairLJCutCoulCut) PairStyle(lj/cut/coul/debye,PairLJCutCoulDebye) PairStyle(lj/expand,PairLJExpand) +PairStyle(lj/gromacs,PairLJGromacs) +PairStyle(lj/gromacs/coul/gromacs,PairLJGromacsCoulGromacs) PairStyle(lj/smooth,PairLJSmooth) PairStyle(morse,PairMorse) PairStyle(soft,PairSoft)