From 688c433eb9983e9c42bef8bbca4aded12ebad291 Mon Sep 17 00:00:00 2001 From: athomps Date: Mon, 29 Aug 2011 18:54:51 +0000 Subject: [PATCH] Added pair_style lj/cubic git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@6855 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- src/pair_lj_cubic.cpp | 360 ++++++++++++++++++++++++++++++++++++++++++ src/pair_lj_cubic.h | 61 +++++++ 2 files changed, 421 insertions(+) create mode 100644 src/pair_lj_cubic.cpp create mode 100644 src/pair_lj_cubic.h diff --git a/src/pair_lj_cubic.cpp b/src/pair_lj_cubic.cpp new file mode 100644 index 0000000000..97f82b39c3 --- /dev/null +++ b/src/pair_lj_cubic.cpp @@ -0,0 +1,360 @@ + +/* ---------------------------------------------------------------------- + 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: Aidan Thompson (SNL) +------------------------------------------------------------------------- */ + +#include "math.h" +#include "stdio.h" +#include "stdlib.h" +#include "string.h" +#include "pair_lj_cubic.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)) + +/* ---------------------------------------------------------------------- */ + +PairLJCubic::PairLJCubic(LAMMPS *lmp) : Pair(lmp) {} + +/* ---------------------------------------------------------------------- */ + +PairLJCubic::~PairLJCubic() +{ + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + + memory->destroy(cut); + memory->destroy(cut_inner); + memory->destroy(cut_inner_sq); + memory->destroy(epsilon); + memory->destroy(sigma); + memory->destroy(lj1); + memory->destroy(lj2); + memory->destroy(lj3); + memory->destroy(lj4); + } +} + +/* ---------------------------------------------------------------------- */ + +void PairLJCubic::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,rmin; + 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; + 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]; + factor_lj = special_lj[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_inner_sq[itype][jtype]) { + r6inv = r2inv*r2inv*r2inv; + forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]); + } else { + r = sqrt(rsq); + rmin = sigma[itype][jtype]*rt6two; + t = (r - cut_inner[itype][jtype])/rmin; + forcelj = epsilon[itype][jtype]*(-dphids + a3*t*t/2.0)*r/rmin; + } + 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) { + if (rsq <= cut_inner_sq[itype][jtype]) + evdwl = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]); + else + evdwl = epsilon[itype][jtype]* + (phis + dphids*t - a3*t*t*t/6.0); + evdwl *= factor_lj; + + if (evflag) ev_tally(i,j,nlocal,newton_pair, + evdwl,0.0,fpair,delx,dely,delz); + } + } + } + } + + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairLJCubic::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,n+1,n+1,"pair:cut"); + memory->create(cut_inner,n+1,n+1,"pair:cut_inner"); + memory->create(cut_inner_sq,n+1,n+1,"pair:cut_inner_sq"); + 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"); +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairLJCubic::settings(int narg, char **arg) +{ + if (narg != 0) 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[i][j] = 0.0; + } +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairLJCubic::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 = force->numeric(arg[2]); + double sigma_one = force->numeric(arg[3]); + double rmin = sigma_one*rt6two; + + 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] = rmin*s; + cut[i][j] = rmin*sm; + 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 PairLJCubic::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); + + 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]; + + return cut[i][j]; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairLJCubic::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 PairLJCubic::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 PairLJCubic::write_restart_settings(FILE *fp) +{ + fwrite(&mix_flag,sizeof(int),1,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairLJCubic::read_restart_settings(FILE *fp) +{ + int me = comm->me; + if (me == 0) { + fread(&mix_flag,sizeof(int),1,fp); + } + MPI_Bcast(&mix_flag,1,MPI_INT,0,world); +} + +/* ---------------------------------------------------------------------- */ + +double PairLJCubic::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; + double rmin; + + r2inv = 1.0/rsq; + if (rsq <= cut_inner_sq[itype][jtype]) { + r6inv = r2inv*r2inv*r2inv; + forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]); + } else { + r = sqrt(rsq); + rmin = sigma[itype][jtype]*rt6two; + t = (r - cut_inner[itype][jtype])/rmin; + forcelj = epsilon[itype][jtype]*(-dphids + a3*t*t/2.0)*r/rmin; + } + fforce = factor_lj*forcelj*r2inv; + + if (rsq <= cut_inner_sq[itype][jtype]) + philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]); + else + philj = epsilon[itype][jtype]* + (phis + dphids*t - a3*t*t*t/6.0); + + return factor_lj*philj; +} diff --git a/src/pair_lj_cubic.h b/src/pair_lj_cubic.h new file mode 100644 index 0000000000..25b8d90344 --- /dev/null +++ b/src/pair_lj_cubic.h @@ -0,0 +1,61 @@ +/* ---------------------------------------------------------------------- + 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/cubic,PairLJCubic) + +#else + +#ifndef LMP_PAIR_LJ_CUBIC_H +#define LMP_PAIR_LJ_CUBIC_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairLJCubic : public Pair { + public: + PairLJCubic(class LAMMPS *); + virtual ~PairLJCubic(); + 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,**cut_inner,**cut_inner_sq; + double **epsilon,**sigma; + double **lj1,**lj2,**lj3,**lj4; + + // LJ quantities scaled by epsilon and rmin = sigma*2^1/6 + + static const double rt6two = 1.1224621; // 2^1/6 + static const double s = 1.1086834; // inflection point = (13/7)^1/6 + static const double phis = -0.7869823; // energy at s + static const double dphids = 2.6899009; // gradient at s + static const double a3 = 27.93357; // cubic coefficient + static const double sm = 1.5475375; // cubic cutoff = s*67/48 + + void allocate(); +}; + +} + +#endif +#endif