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pair_peri_pmb.cpp
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Sun, Nov 10, 18:03

pair_peri_pmb.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: Mike Parks (SNL)
------------------------------------------------------------------------- */
#include <math.h>
#include <float.h>
#include <stdlib.h>
#include <string.h>
#include "pair_peri_pmb.h"
#include "atom.h"
#include "domain.h"
#include "lattice.h"
#include "force.h"
#include "update.h"
#include "modify.h"
#include "fix.h"
#include "fix_peri_neigh.h"
#include "comm.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairPeriPMB::PairPeriPMB(LAMMPS *lmp) : Pair(lmp)
{
for (int i = 0; i < 6; i++) virial[i] = 0.0;
no_virial_fdotr_compute=1;
ifix_peri = -1;
nmax = 0;
s0_new = NULL;
kspring = NULL;
s00 = NULL;
alpha = NULL;
cut = NULL;
}
/* ---------------------------------------------------------------------- */
PairPeriPMB::~PairPeriPMB()
{
if (ifix_peri >= 0) modify->delete_fix("PERI_NEIGH");
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(kspring);
memory->destroy(s00);
memory->destroy(alpha);
memory->destroy(cut);
memory->destroy(s0_new);
}
}
/* ---------------------------------------------------------------------- */
void PairPeriPMB::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz;
double xtmp0,ytmp0,ztmp0,delx0,dely0,delz0,rsq0;
double rsq,r,dr,rk,evdwl,fpair,fbond;
int *ilist,*jlist,*numneigh,**firstneigh;
double d_ij,delta,stretch;
evdwl = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
double **f = atom->f;
double **x = atom->x;
int *type = atom->type;
int nlocal = atom->nlocal;
double *vfrac = atom->vfrac;
double *s0 = atom->s0;
double **x0 = atom->x0;
double **r0 = ((FixPeriNeigh *) modify->fix[ifix_peri])->r0;
tagint **partner = ((FixPeriNeigh *) modify->fix[ifix_peri])->partner;
int *npartner = ((FixPeriNeigh *) modify->fix[ifix_peri])->npartner;
// lc = lattice constant
// init_style guarantees it's the same in x, y, and z
double lc = domain->lattice->xlattice;
double half_lc = 0.5*lc;
double vfrac_scale = 1.0;
// short-range forces
int newton_pair = force->newton_pair;
int periodic = (domain->xperiodic || domain->yperiodic || domain->zperiodic);
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
// need minimg() for x0 difference since not ghosted
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp0 = x0[i][0];
ytmp0 = x0[i][1];
ztmp0 = x0[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
delx0 = xtmp0 - x0[j][0];
dely0 = ytmp0 - x0[j][1];
delz0 = ztmp0 - x0[j][2];
if (periodic) domain->minimum_image(delx0,dely0,delz0);
rsq0 = delx0*delx0 + dely0*dely0 + delz0*delz0;
jtype = type[j];
r = sqrt(rsq);
// short-range interaction distance based on initial particle position
// 0.9 and 1.35 are constants
d_ij = MIN(0.9*sqrt(rsq0),1.35*lc);
// short-range contact forces
// 15 is constant taken from the EMU Theory Manual
// Silling, 12 May 2005, p 18
if (r < d_ij) {
dr = r - d_ij;
rk = (15.0 * kspring[itype][jtype] * vfrac[j]) *
(dr / cut[itype][jtype]);
if (r > 0.0) fpair = -(rk/r);
else fpair = 0.0;
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 = 0.5*rk*dr;
if (evflag) ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,
fpair*vfrac[i],delx,dely,delz);
}
}
}
// grow bond forces array if necessary
if (atom->nmax > nmax) {
memory->destroy(s0_new);
nmax = atom->nmax;
memory->create(s0_new,nmax,"pair:s0_new");
}
// loop over my particles and their partners
// partner list contains all bond partners, so I-J appears twice
// if bond already broken, skip this partner
// first = true if this is first neighbor of particle i
bool first;
for (i = 0; i < nlocal; i++) {
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jnum = npartner[i];
s0_new[i] = DBL_MAX;
first = true;
for (jj = 0; jj < jnum; jj++) {
if (partner[i][jj] == 0) continue;
j = atom->map(partner[i][jj]);
// check if lost a partner without first breaking bond
if (j < 0) {
partner[i][jj] = 0;
continue;
}
// compute force density, add to PD equation of motion
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
if (periodic) domain->minimum_image(delx,dely,delz);
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
delta = cut[itype][jtype];
r = sqrt(rsq);
dr = r - r0[i][jj];
// avoid roundoff errors
if (fabs(dr) < 2.2204e-016) dr = 0.0;
// scale vfrac[j] if particle j near the horizon
if ((fabs(r0[i][jj] - delta)) <= half_lc)
vfrac_scale = (-1.0/(2*half_lc))*(r0[i][jj]) +
(1.0 + ((delta - half_lc)/(2*half_lc) ) );
else vfrac_scale = 1.0;
stretch = dr / r0[i][jj];
rk = (kspring[itype][jtype] * vfrac[j]) * vfrac_scale * stretch;
if (r > 0.0) fbond = -(rk/r);
else fbond = 0.0;
f[i][0] += delx*fbond;
f[i][1] += dely*fbond;
f[i][2] += delz*fbond;
// since I-J is double counted, set newton off & use 1/2 factor and I,I
if (eflag) evdwl = 0.5*rk*dr;
if (evflag) ev_tally(i,i,nlocal,0,0.5*evdwl,0.0,0.5*fbond*vfrac[i],delx,dely,delz);
// find stretch in bond I-J and break if necessary
// use s0 from previous timestep
if (stretch > MIN(s0[i],s0[j])) partner[i][jj] = 0;
// update s0 for next timestep
if (first)
s0_new[i] = s00[itype][jtype] - (alpha[itype][jtype] * stretch);
else
s0_new[i] = MAX(s0_new[i],s00[itype][jtype] - (alpha[itype][jtype] * stretch));
first = false;
}
}
// store new s0
for (i = 0; i < nlocal; i++) s0[i] = s0_new[i];
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairPeriPMB::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(kspring,n+1,n+1,"pair:kspring");
memory->create(s00,n+1,n+1,"pair:s00");
memory->create(alpha,n+1,n+1,"pair:alpha");
memory->create(cut,n+1,n+1,"pair:cut");
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairPeriPMB::settings(int narg, char **arg)
{
if (narg) error->all(FLERR,"Illegal pair_style command");
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairPeriPMB::coeff(int narg, char **arg)
{
if (narg != 6) 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);
double kspring_one = force->numeric(FLERR,arg[2]);
double cut_one = force->numeric(FLERR,arg[3]);
double s00_one = force->numeric(FLERR,arg[4]);
double alpha_one = force->numeric(FLERR,arg[5]);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
kspring[i][j] = kspring_one;
s00[i][j] = s00_one;
alpha[i][j] = alpha_one;
cut[i][j] = cut_one;
setflag[i][j] = 1;
count++;
}
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairPeriPMB::init_one(int i, int j)
{
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
kspring[j][i] = kspring[i][j];
alpha[j][i] = alpha[i][j];
s00[j][i] = s00[i][j];
cut[j][i] = cut[i][j];
return cut[i][j];
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairPeriPMB::init_style()
{
// error checks
if (!atom->peri_flag)
error->all(FLERR,"Pair style peri requires atom style peri");
if (atom->map_style == 0)
error->all(FLERR,"Pair peri requires an atom map, see atom_modify");
if (domain->lattice->xlattice != domain->lattice->ylattice ||
domain->lattice->xlattice != domain->lattice->zlattice ||
domain->lattice->ylattice != domain->lattice->zlattice)
error->all(FLERR,"Pair peri lattice is not identical in x, y, and z");
// if first init, create Fix needed for storing fixed neighbors
if (ifix_peri == -1) {
char **fixarg = new char*[3];
fixarg[0] = (char *) "PERI_NEIGH";
fixarg[1] = (char *) "all";
fixarg[2] = (char *) "PERI_NEIGH";
modify->add_fix(3,fixarg);
delete [] fixarg;
}
// find associated PERI_NEIGH fix that must exist
// could have changed locations in fix list since created
for (int i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"PERI_NEIGH") == 0) ifix_peri = i;
if (ifix_peri == -1) error->all(FLERR,"Fix peri neigh does not exist");
neighbor->request(this,instance_me);
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairPeriPMB::write_restart(FILE *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(&kspring[i][j],sizeof(double),1,fp);
fwrite(&s00[i][j],sizeof(double),1,fp);
fwrite(&alpha[i][j],sizeof(double),1,fp);
fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairPeriPMB::read_restart(FILE *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(&kspring[i][j],sizeof(double),1,fp);
fread(&s00[i][j],sizeof(double),1,fp);
fread(&alpha[i][j],sizeof(double),1,fp);
fread(&cut[i][j],sizeof(double),1,fp);
}
MPI_Bcast(&kspring[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&s00[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&alpha[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
/* ---------------------------------------------------------------------- */
double PairPeriPMB::single(int i, int j, int itype, int jtype, double rsq,
double factor_coul, double factor_lj,
double &fforce)
{
double delx0,dely0,delz0,rsq0;
double d_ij,r,dr,rk,vfrac_scale;
double *vfrac = atom->vfrac;
double **x0 = atom->x0;
double **r0 = ((FixPeriNeigh *) modify->fix[ifix_peri])->r0;
tagint **partner = ((FixPeriNeigh *) modify->fix[ifix_peri])->partner;
int *npartner = ((FixPeriNeigh *) modify->fix[ifix_peri])->npartner;
double lc = domain->lattice->xlattice;
double half_lc = 0.5*lc;
delx0 = x0[i][0] - x0[j][0];
dely0 = x0[i][1] - x0[j][1];
delz0 = x0[i][2] - x0[j][2];
int periodic = domain->xperiodic || domain->yperiodic || domain->zperiodic;
if (periodic) domain->minimum_image(delx0,dely0,delz0);
rsq0 = delx0*delx0 + dely0*dely0 + delz0*delz0;
d_ij = MIN(0.9*sqrt(rsq0),1.35*lc);
r = sqrt(rsq);
double energy = 0.0;
fforce = 0.0;
if (r < d_ij) {
dr = r - d_ij;
rk = (15.0 * kspring[itype][jtype] * vfrac[j]) *
(dr / sqrt(cutsq[itype][jtype]));
if (r > 0.0) fforce += -(rk/r);
energy += 0.5*rk*dr;
}
int jnum = npartner[i];
for (int jj = 0; jj < jnum; jj++) {
if (partner[i][jj] == 0) continue;
if (j < 0) continue;
if (j == atom->map(partner[i][jj])) {
dr = r - r0[i][jj];
if (fabs(dr) < 2.2204e-016) dr = 0.0;
if ( (fabs(r0[i][jj] - sqrt(cutsq[itype][jtype]))) <= half_lc)
vfrac_scale = (-1.0/(2*half_lc))*(r0[i][jj]) +
(1.0 + ((sqrt(cutsq[itype][jtype]) - half_lc)/(2*half_lc)));
else vfrac_scale = 1.0;
rk = (kspring[itype][jtype] * vfrac[j] * vfrac_scale) *
(dr / r0[i][jj]);
if (r > 0.0) fforce += -(rk/r);
energy += 0.5*rk*dr;
}
}
return energy;
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double PairPeriPMB::memory_usage()
{
double bytes = nmax * sizeof(double);
return bytes;
}

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