Page MenuHomec4science
Files F107376906

pair_cg_cmm_omp.cpp
No OneTemporary
Actions

File Metadata

Created
Mon, Apr 7, 14:26

pair_cg_cmm_omp.cpp
View Options

/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
CMM coarse grained MD potentials. Plain version w/o charges.
Contributing author: Axel Kohlmeyer <akohlmey@gmail.com>
------------------------------------------------------------------------- */
#include "pair_cg_cmm_omp.h"
#include "atom.h"
#include "comm.h"
#include "error.h"
#include "force.h"
#include "memory.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "stdlib.h"
#include "string.h"
#include "ctype.h"
#include "math.h"
using namespace LAMMPS_NS;
#define MAX(a,b) ((a) > (b) ? (a) : (b))
#define SMALL 1.0e-6
/* ---------------------------------------------------------------------- */
PairCGCMMOMP::PairCGCMMOMP(LAMMPS *lmp) : PairOMP(lmp)
{
respa_enable = 0;
single_enable = 1;
allocated = 0;
allocated_coul = 0;
ftable = NULL;
kappa = 0.0;
}
/* ---------------------------------------------------------------------- */
PairCGCMMOMP::~PairCGCMMOMP()
{
if (allocated) {
memory->destroy_2d_int_array(setflag);
memory->destroy_2d_int_array(cg_type);
memory->destroy_2d_double_array(cut);
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(offset);
allocated = 0;
}
}
/* ---------------------------------------------------------------------- */
void PairCGCMMOMP::compute(int eflag, int vflag)
{
if (eflag || vflag) {
ev_setup(eflag,vflag);
ev_setup_thr(eflag,vflag);
} else {
evflag = vflag_fdotr = 0;
}
if (evflag) {
if (eflag) {
if (force->newton_pair) {
return eval<1,1,1>();
} else {
return eval<1,1,0>();
}
} else {
if (force->newton_pair) {
return eval<1,0,1>();
} else {
return eval<1,0,0>();
}
}
} else {
if (force->newton_pair) {
return eval<0,0,1>();
} else {
return eval<0,0,0>();
}
}
}
template < int EVFLAG, int EFLAG, int NEWTON_PAIR >
void PairCGCMMOMP::eval() {
#if defined(_OPENMP)
#pragma omp parallel default(shared)
#endif
{
const int nlocal = atom->nlocal;
const int nall = nlocal + atom->nghost;
const int nthreads = comm->nthreads;
const int * const type = atom->type;
const double * const special_lj = force->special_lj;
const int inum = list->inum;
const int * const ilist = list->ilist;
const int * const numneigh = list->numneigh;
int * const * const firstneigh = list->firstneigh;
// loop over neighbors of my atoms
int ii, jj, iifrom, iito, tid;
const double * const * const x = atom->x;
double * const * const f = loop_setup_thr(atom->f, iifrom, iito, tid, inum, nall, nthreads);
for (ii = iifrom; ii < iito; ++ii) {
const int i = ilist[ii];
const double xtmp = x[i][0];
const double ytmp = x[i][1];
const double ztmp = x[i][2];
const int itype = type[i];
const int * const jlist = firstneigh[i];
const int jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
int j2 = jlist[jj];
double factor_lj = 1.0;
if (j2 >= nall) {
factor_lj = special_lj[j2/nall];
j2 %= nall;
}
const int j = j2;
const double delx = xtmp - x[j][0];
const double dely = ytmp - x[j][1];
const double delz = ztmp - x[j][2];
const double rsq = delx*delx + dely*dely + delz*delz;
const int jtype = type[j];
double evdwl = 0.0;
double fpair = 0.0;
const double r2inv = 1.0/rsq;
const int cgt=cg_type[itype][jtype];
if (rsq < cutsq[itype][jtype]) {
fpair=factor_lj;
if (EFLAG) evdwl=factor_lj;
if (cgt == CG_LJ12_4) {
const double r4inv=r2inv*r2inv;
fpair *= r4inv*(lj1[itype][jtype]*r4inv*r4inv
- lj2[itype][jtype]);
if (EFLAG) {
evdwl *= r4inv*(lj3[itype][jtype]*r4inv*r4inv
- lj4[itype][jtype]) - offset[itype][jtype];
}
} else if (cgt == CG_LJ9_6) {
const double r3inv = r2inv*sqrt(r2inv);
const double r6inv = r3inv*r3inv;
fpair *= r6inv*(lj1[itype][jtype]*r3inv
- lj2[itype][jtype]);
if (EFLAG) {
evdwl *= r6inv*(lj3[itype][jtype]*r3inv
- lj4[itype][jtype]) - offset[itype][jtype];
}
} else if (cgt == CG_LJ12_6) {
const double r6inv = r2inv*r2inv*r2inv;
fpair *= r6inv*(lj1[itype][jtype]*r6inv
- lj2[itype][jtype]);
if (EFLAG) {
evdwl *= r6inv*(lj3[itype][jtype]*r6inv
- lj4[itype][jtype]) - offset[itype][jtype];
}
} else {
/* do nothing. this is a "cannot happen(TM)" case */
;
}
fpair *= 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 (EVFLAG) ev_tally_thr(i,j,nlocal,NEWTON_PAIR,
evdwl,0.0,fpair,delx,dely,delz,tid);
}
}
}
// reduce per thread forces into global force array.
force_reduce_thr(atom->f, nall, nthreads, tid);
}
ev_reduce_thr();
if (vflag_fdotr) virial_compute();
}
/* ---------------------------------------------------------------------- */
void PairCGCMMOMP::allocate()
{
allocated = 1;
int n = atom->ntypes;
setflag = memory->create_2d_int_array(n+1,n+1,"paircg:setflag");
cg_type = memory->create_2d_int_array(n+1,n+1,"paircg:cg_type");
for (int i = 1; i <= n; i++) {
for (int j = i; j <= n; j++) {
setflag[i][j] = 0;
cg_type[i][j] = CG_NOT_SET;
}
}
cut = memory->create_2d_double_array(n+1,n+1,"paircg:cut");
cutsq = memory->create_2d_double_array(n+1,n+1,"paircg:cutsq");
epsilon = memory->create_2d_double_array(n+1,n+1,"paircg:epsilon");
sigma = memory->create_2d_double_array(n+1,n+1,"paircg:sigma");
offset = memory->create_2d_double_array(n+1,n+1,"paircg:offset");
lj1 = memory->create_2d_double_array(n+1,n+1,"paircg:lj1");
lj2 = memory->create_2d_double_array(n+1,n+1,"paircg:lj2");
lj3 = memory->create_2d_double_array(n+1,n+1,"paircg:lj3");
lj4 = memory->create_2d_double_array(n+1,n+1,"paircg:lj4");
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
// arguments to the pair_style command (global version)
// args = cutoff (cutoff2 (kappa))
void PairCGCMMOMP::settings(int narg, char **arg)
{
if ((narg < 1) || (narg > 2)) error->all("Illegal pair_style command");
cut_lj_global = force->numeric(arg[0]);
if (narg == 1) cut_coul_global = cut_lj_global;
else cut_coul_global = force->numeric(arg[1]);
cut_coulsq_global = cut_coul_global*cut_coul_global;
// 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_lj_global;
if (allocated_coul) {
cut[i][j] = MAX(cut_lj_global,cut_coul_global);
cut_lj[i][j] = cut_lj_global;
cut_coul[i][j] = cut_coul_global;
}
}
}
}
}
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairCGCMMOMP::coeff(int narg, char **arg)
{
if (narg < 5 || narg > 7) 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);
int cg_type_one=find_cg_type(arg[2]);
if (cg_type_one == CG_NOT_SET) error->all("Error reading CG type flag.");
double epsilon_one = force->numeric(arg[3]);
double sigma_one = force->numeric(arg[4]);
double cut_lj_one = cut_lj_global;
double cut_coul_one = cut_coul_global;
if (narg >= 6) cut_lj_one = force->numeric(arg[5]);
if (narg == 7) cut_coul_one = force->numeric(arg[6]);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
cg_type[i][j] = cg_type_one;
epsilon[i][j] = epsilon_one;
sigma[i][j] = sigma_one;
setflag[i][j] = 1;
if (allocated_coul) {
cut_lj[i][j] = cut_lj_one;
cut_coul[i][j] = cut_coul_one;
} else {
cut[i][j] = cut_lj_one;
}
count++;
}
}
if (count == 0) error->all("Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairCGCMMOMP::init_one(int i, int j)
{
if (setflag[i][j] == 0) {
error->all("for CG styles, epsilon and sigma need to be set explicitly for all pairs.");
}
const int cgt = cg_type[i][j];
if (cgt == CG_NOT_SET)
error->all("unrecognized LJ parameter flag");
lj1[i][j] = cg_prefact[cgt] * cg_pow1[cgt] * epsilon[i][j] * pow(sigma[i][j],cg_pow1[cgt]);
lj2[i][j] = cg_prefact[cgt] * cg_pow2[cgt] * epsilon[i][j] * pow(sigma[i][j],cg_pow2[cgt]);
lj3[i][j] = cg_prefact[cgt] * epsilon[i][j] * pow(sigma[i][j],cg_pow1[cgt]);
lj4[i][j] = cg_prefact[cgt] * epsilon[i][j] * pow(sigma[i][j],cg_pow2[cgt]);
double mycut = cut[i][j];
if (offset_flag) {
double ratio = sigma[i][j] / mycut;
offset[i][j] = cg_prefact[cgt] * epsilon[i][j] * (pow(ratio,cg_pow1[cgt]) - pow(ratio,cg_pow2[cgt]));
} else offset[i][j] = 0.0;
if (allocated_coul) {
mycut = MAX(cut_lj[i][j],cut_coul[i][j]);
cut[i][j] = mycut;
cut_ljsq[i][j]=cut_lj[i][j]*cut_lj[i][j];
cut_coulsq[i][j]=cut_coul[i][j]*cut_coul[i][j];
if (offset_flag) {
double ratio = sigma[i][j] / cut_lj[i][j];
offset[i][j] = cg_prefact[cgt] * epsilon[i][j] * (pow(ratio,cg_pow1[cgt]) - pow(ratio,cg_pow2[cgt]));
} else offset[i][j] = 0.0;
}
// make sure data is stored symmetrically
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];
cg_type[j][i] = cg_type[i][j];
cut[j][i] = mycut;
if (allocated_coul) {
cut_lj[j][i]=cut_lj[i][j];
cut_ljsq[j][i]=cut_ljsq[i][j];
cut_coul[j][i]=cut_coul[i][j];
cut_coulsq[j][i]=cut_coulsq[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) {
#if 1
error->all("tail correction not (yet) supported by CG potentials.");
#else
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 sig2 = sigma[i][j]*sigma[i][j];
double sig6 = sig2*sig2*sig2;
double rc3 = cut[i][j]*cut[i][j]*cut[i][j];
double rc6 = rc3*rc3;
double rc9 = rc3*rc6;
etail_ij = 8.0*PI*all[0]*all[1]*epsilon[i][j] *
sig6 * (sig6 - 3.0*rc6) / (9.0*rc9);
ptail_ij = 16.0*PI*all[0]*all[1]*epsilon[i][j] *
sig6 * (2.0*sig6 - 3.0*rc6) / (9.0*rc9);
#endif
}
return mycut;
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairCGCMMOMP::write_restart(FILE *fp)
{
int i,j;
write_restart_settings(fp);
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(&cg_type[i][j],sizeof(int),1,fp);
fwrite(&epsilon[i][j],sizeof(double),1,fp);
fwrite(&sigma[i][j],sizeof(double),1,fp);
fwrite(&cut[i][j],sizeof(double),1,fp);
if (allocated_coul) {
fwrite(&cut_lj[i][j],sizeof(double),1,fp);
fwrite(&cut_coul[i][j],sizeof(double),1,fp);
}
}
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairCGCMMOMP::read_restart(FILE *fp)
{
int i,j;
int me = comm->me;
read_restart_settings(fp);
allocate();
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(&cg_type[i][j],sizeof(int),1,fp);
fread(&epsilon[i][j],sizeof(double),1,fp);
fread(&sigma[i][j],sizeof(double),1,fp);
fread(&cut[i][j],sizeof(double),1,fp);
if(allocated_coul) {
fread(&cut_lj[i][j],sizeof(double),1,fp);
fread(&cut_coul[i][j],sizeof(double),1,fp);
}
}
MPI_Bcast(&cg_type[i][j],1,MPI_INT,0,world);
MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
if (allocated_coul) {
MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_coul[i][j],1,MPI_DOUBLE,0,world);
}
}
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairCGCMMOMP::write_restart_settings(FILE *fp)
{
fwrite(&cut_lj_global,sizeof(double),1,fp);
fwrite(&cut_coul_global,sizeof(double),1,fp);
fwrite(&kappa,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 PairCGCMMOMP::read_restart_settings(FILE *fp)
{
int me = comm->me;
if (me == 0) {
fread(&cut_lj_global,sizeof(double),1,fp);
fread(&cut_coul_global,sizeof(double),1,fp);
fread(&kappa,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_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&kappa,1,MPI_DOUBLE,0,world);
MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
cut_coulsq_global = cut_coul_global*cut_coul_global;
}
/* ---------------------------------------------------------------------- */
double PairCGCMMOMP::memory_usage()
{
double bytes=PairOMP::memory_usage();
int n = atom->ntypes;
// setflag/cg_type
bytes += (n+1)*(n+1)*sizeof(int)*2;
// cut/cutsq/epsilon/sigma/offset/lj1/lj2/lj3/lj4
bytes += (n+1)*(n+1)*sizeof(double)*9;
return bytes;
}
/* ---------------------------------------------------------------------- */
double PairCGCMMOMP::single(int i, int j, int itype, int jtype, double rsq,
double factor_coul, double factor_lj, double &fforce)
{
double lj_force, lj_erg;
lj_force=lj_erg=0.0;
if (rsq < cut_ljsq[itype][jtype]) {
const int cgt = cg_type[itype][jtype];
const double cgpow1 = cg_pow1[cgt];
const double cgpow2 = cg_pow2[cgt];
const double cgpref = cg_prefact[cgt];
const double ratio = sigma[itype][jtype]/sqrt(rsq);
const double eps = epsilon[itype][jtype];
lj_force = cgpref*eps * (cgpow1*pow(ratio,cgpow1)
- cgpow2*pow(ratio,cgpow2))/rsq;
lj_erg = cgpref*eps * (pow(ratio,cgpow1) - pow(ratio,cgpow2));
}
fforce = factor_lj*lj_force;
return factor_lj*lj_erg;
}
/* ------------------------------------------------------------------------ */

Event Timeline

c4science · Help