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pair_list.cpp
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Fri, Nov 1, 11:05

pair_list.cpp
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/* ----------------------------------------------------------------------
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: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
#include "pair_list.h"
#include "atom.h"
#include "comm.h"
#include "domain.h"
#include "force.h"
#include "memory.h"
#include "error.h"
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <math.h>
using namespace LAMMPS_NS;
static const char * const stylename[] = {
"none", "harmonic", "morse", "lj126", NULL
};
// fast power function for integer exponent > 0
static double mypow(double x, int n) {
double yy;
if (x == 0.0) return 0.0;
for (yy = 1.0; n != 0; n >>= 1, x *=x)
if (n & 1) yy *= x;
return yy;
}
typedef struct { double x,y,z; } dbl3_t;
/* ---------------------------------------------------------------------- */
PairList::PairList(LAMMPS *lmp) : Pair(lmp)
{
single_enable = 0;
respa_enable = 0;
cut_global = 0.0;
style = NULL;
params = NULL;
check_flag = 1;
}
/* ---------------------------------------------------------------------- */
PairList::~PairList()
{
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(style);
memory->destroy(params);
}
/* ----------------------------------------------------------------------
in this pair style we don't use a neighbor list, but loop through
a list of pairwise interactions, determines the corresponding local
atom indices and compute those forces.
------------------------------------------------------------------------- */
void PairList::compute(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = eflag_global =
vflag_global = eflag_atom = vflag_atom = 0;
const int nlocal = atom->nlocal;
const int newton_pair = force->newton_pair;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) atom->f[0];
double fpair,epair;
int i,j;
int pc = 0;
for (int n=0; n < npairs; ++n) {
const list_parm_t &par = params[n];
i = atom->map(par.id1);
j = atom->map(par.id2);
// if one of the two atoms is missing on the node skip
if ((i < 0) || (j < 0)) continue;
// both atoms are ghosts -> skip
if ((i >= nlocal) && (j >= nlocal)) continue;
// with newton pair and one ghost we have to skip half the cases.
// if id1 is a ghost, we skip if the sum of both ids is even.
// if id2 is a ghost, we skip if the sum of both ids is odd.
if (newton_pair) {
if ((i >= nlocal) && ((par.id1+par.id2) & 1) == 0) continue;
if ((j >= nlocal) && ((par.id1+par.id2) & 1) == 1) continue;
}
const double dx = x[i].x - x[j].x;
const double dy = x[i].y - x[j].y;
const double dz = x[i].z - x[j].z;
const double rsq = dx*dx + dy*dy + dz*dz;
fpair = epair = 0.0;
if (check_flag) {
if (newton_pair || i < nlocal) ++pc;
if (newton_pair || j < nlocal) ++pc;
}
if (rsq < par.cutsq) {
const double r2inv = 1.0/rsq;
if (style[n] == HARM) {
const double r = sqrt(rsq);
const double dr = par.parm.harm.r0 - r;
fpair = 2.0*par.parm.harm.k*dr/r;
if (eflag_either)
epair = par.parm.harm.k*dr*dr - par.offset;
} else if (style[n] == MORSE) {
const double r = sqrt(rsq);
const double dr = par.parm.morse.r0 - r;
const double dexp = exp(par.parm.morse.alpha * dr);
fpair = 2.0*par.parm.morse.d0*par.parm.morse.alpha
* (dexp*dexp - dexp) / r;
if (eflag_either)
epair = par.parm.morse.d0 * (dexp*dexp - 2.0*dexp) - par.offset;
} else if (style[n] == LJ126) {
const double r6inv = r2inv*r2inv*r2inv;
const double sig6 = mypow(par.parm.lj126.sigma,6);
fpair = 24.0*par.parm.lj126.epsilon*r6inv
* (2.0*sig6*sig6*r6inv - sig6) * r2inv;
if (eflag_either)
epair = 4.0*par.parm.lj126.epsilon*r6inv
* (sig6*sig6*r6inv - sig6) - par.offset;
}
if (newton_pair || i < nlocal) {
f[i].x += dx*fpair;
f[i].y += dy*fpair;
f[i].z += dz*fpair;
}
if (newton_pair || j < nlocal) {
f[j].x -= dx*fpair;
f[j].y -= dy*fpair;
f[j].z -= dz*fpair;
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,epair,0.0,fpair,dx,dy,dz);
}
}
if (vflag_fdotr) virial_fdotr_compute();
if (check_flag) {
int tmp;
MPI_Allreduce(&pc,&tmp,1,MPI_INT,MPI_SUM,world);
if (tmp != 2*npairs)
error->all(FLERR,"Not all pairs processed in pair_style list");
}
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairList::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");
}
/* ----------------------------------------------------------------------
create one pair style for each arg in list
------------------------------------------------------------------------- */
void PairList::settings(int narg, char **arg)
{
if (narg < 2)
error->all(FLERR,"Illegal pair_style command");
cut_global = force->numeric(FLERR,arg[1]);
if (narg > 2) {
if (strcmp(arg[2],"nocheck") == 0) check_flag = 0;
if (strcmp(arg[2],"check") == 0) check_flag = 1;
}
FILE *fp = force->open_potential(arg[0]);
char line[1024];
if (fp == NULL)
error->all(FLERR,"Cannot open pair list file");
// count lines in file for upper limit of storage needed
int num = 1;
while(fgets(line,1024,fp)) ++num;
rewind(fp);
memory->create(style,num,"pair_list:style");
memory->create(params,num,"pair_list:params");
// now read and parse pair list file for real
npairs = 0;
char *ptr;
tagint id1, id2;
int nharm=0, nmorse=0, nlj126=0;
while(fgets(line,1024,fp)) {
ptr = strtok(line," \t\n\r\f");
// skip empty lines
if (!ptr) continue;
// skip comment lines starting with #
if (*ptr == '#') continue;
// get atom ids of pair
id1 = ATOTAGINT(ptr);
ptr = strtok(NULL," \t\n\r\f");
if (!ptr)
error->all(FLERR,"Incorrectly formatted pair list file");
id2 = ATOTAGINT(ptr);
// get potential type
ptr = strtok(NULL," \t\n\r\f");
if (!ptr)
error->all(FLERR,"Incorrectly formatted pair list file");
style[npairs] = NONE;
list_parm_t &par = params[npairs];
par.id1 = id1;
par.id2 = id2;
// harmonic potential
if (strcmp(ptr,stylename[HARM]) == 0) {
style[npairs] = HARM;
ptr = strtok(NULL," \t\n\r\f");
if ((ptr == NULL) || (*ptr == '#'))
error->all(FLERR,"Incorrectly formatted harmonic pair parameters");
par.parm.harm.k = force->numeric(FLERR,ptr);
ptr = strtok(NULL," \t\n\r\f");
if ((ptr == NULL) || (*ptr == '#'))
error->all(FLERR,"Incorrectly formatted harmonic pair parameters");
par.parm.harm.r0 = force->numeric(FLERR,ptr);
++nharm;
// morse potential
} else if (strcmp(ptr,stylename[MORSE]) == 0) {
style[npairs] = MORSE;
ptr = strtok(NULL," \t\n\r\f");
if (!ptr)
error->all(FLERR,"Incorrectly formatted morse pair parameters");
par.parm.morse.d0 = force->numeric(FLERR,ptr);
ptr = strtok(NULL," \t\n\r\f");
if (!ptr)
error->all(FLERR,"Incorrectly formatted morse pair parameters");
par.parm.morse.alpha = force->numeric(FLERR,ptr);
ptr = strtok(NULL," \t\n\r\f");
if (!ptr)
error->all(FLERR,"Incorrectly formatted morse pair parameters");
par.parm.morse.r0 = force->numeric(FLERR,ptr);
++nmorse;
} else if (strcmp(ptr,stylename[LJ126]) == 0) {
// 12-6 lj potential
style[npairs] = LJ126;
ptr = strtok(NULL," \t\n\r\f");
if (!ptr)
error->all(FLERR,"Incorrectly formatted 12-6 LJ pair parameters");
par.parm.lj126.epsilon = force->numeric(FLERR,ptr);
ptr = strtok(NULL," \t\n\r\f");
if (!ptr)
error->all(FLERR,"Incorrectly formatted 12-6 LJ pair parameters");
par.parm.lj126.sigma = force->numeric(FLERR,ptr);
++nlj126;
} else {
error->all(FLERR,"Unknown pair list potential style");
}
// optional cutoff parameter. if not specified use global value
ptr = strtok(NULL," \t\n\r\f");
if ((ptr != NULL) && (*ptr != '#')) {
double cut = force->numeric(FLERR,ptr);
par.cutsq = cut*cut;
} else {
par.cutsq = cut_global*cut_global;
}
// count complete entry
++npairs;
}
fclose(fp);
// informative output
if (comm->me == 0) {
if (screen)
fprintf(screen,"Read %d (%d/%d/%d) interacting pairs from %s\n",
npairs, nharm, nmorse, nlj126, arg[0]);
if (logfile)
fprintf(logfile,"Read %d (%d/%d/%d) interacting pairs from %s\n",
npairs, nharm, nmorse, nlj126, arg[0]);
}
}
/* ----------------------------------------------------------------------
there are no coeffs to be set, but we need to update setflag and pretend
------------------------------------------------------------------------- */
void PairList::coeff(int narg, char **arg)
{
if (narg < 2) error->all(FLERR,"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 count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
setflag[i][j] = 1;
count++;
}
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init specific to this pair style: compute energy offset at cutoff
------------------------------------------------------------------------- */
void PairList::init_style()
{
if (atom->tag_enable == 0)
error->all(FLERR,"Pair style list requires atom IDs");
if (atom->map_style == 0)
error->all(FLERR,"Pair style list requires an atom map");
if (offset_flag) {
for (int n=0; n < npairs; ++n) {
list_parm_t &par = params[n];
if (style[n] == HARM) {
const double dr = sqrt(par.cutsq) - par.parm.harm.r0;
par.offset = par.parm.harm.k*dr*dr;
} else if (style[n] == MORSE) {
const double dr = par.parm.morse.r0 - sqrt(par.cutsq);
const double dexp = exp(par.parm.morse.alpha * dr);
par.offset = par.parm.morse.d0 * (dexp*dexp - 2.0*dexp);
} else if (style[n] == LJ126) {
const double r6inv = par.cutsq*par.cutsq*par.cutsq;
const double sig6 = mypow(par.parm.lj126.sigma,6);
par.offset = 4.0*par.parm.lj126.epsilon*r6inv * (sig6*sig6*r6inv - sig6);
}
}
}
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
since we don't use atom types or neighbor lists, this is a NOP.
------------------------------------------------------------------------- */
double PairList::init_one(int, int)
{
return cut_global;
}
/* ----------------------------------------------------------------------
memory usage of each sub-style
------------------------------------------------------------------------- */
double PairList::memory_usage()
{
double bytes = npairs * sizeof(int);
bytes += npairs * sizeof(list_parm_t);
const int n = atom->ntypes+1;
bytes += n*(n*sizeof(int) + sizeof(int *));
bytes += n*(n*sizeof(double) + sizeof(double *));
return bytes;
}

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