398 lines
11 KiB
C++
398 lines
11 KiB
C++
// clang-format off
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://www.lammps.org/, Sandia National Laboratories
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LAMMPS development team: developers@lammps.org
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributing author: Mike Parks (SNL)
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------------------------------------------------------------------------- */
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#include "pair_peri_pmb.h"
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#include "atom.h"
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#include "comm.h"
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#include "domain.h"
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#include "error.h"
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#include "fix_peri_neigh.h"
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#include "force.h"
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#include "lattice.h"
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#include "memory.h"
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#include "neigh_list.h"
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#include <cfloat>
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#include <cmath>
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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PairPeriPMB::PairPeriPMB(LAMMPS *_lmp) : PairPeri(_lmp)
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{
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single_enable = 1;
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}
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/* ---------------------------------------------------------------------- */
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void PairPeriPMB::compute(int eflag, int vflag)
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{
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int i,j,ii,jj,inum,jnum,itype,jtype;
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double xtmp,ytmp,ztmp,delx,dely,delz;
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double xtmp0,ytmp0,ztmp0,delx0,dely0,delz0,rsq0;
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double rsq,r,dr,rk,evdwl,fpair,fbond;
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int *ilist,*jlist,*numneigh,**firstneigh;
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double d_ij,delta,stretch;
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evdwl = 0.0;
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ev_init(eflag,vflag);
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double **f = atom->f;
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double **x = atom->x;
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int *type = atom->type;
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int nlocal = atom->nlocal;
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double *vfrac = atom->vfrac;
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double *s0 = atom->s0;
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double **x0 = atom->x0;
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double **r0 = fix_peri_neigh->r0;
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tagint **partner = fix_peri_neigh->partner;
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int *npartner = fix_peri_neigh->npartner;
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// lc = lattice constant
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// init_style guarantees it's the same in x, y, and z
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double lc = domain->lattice->xlattice;
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double half_lc = 0.5*lc;
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double vfrac_scale = 1.0;
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// short-range forces
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int newton_pair = force->newton_pair;
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int periodic = (domain->xperiodic || domain->yperiodic || domain->zperiodic);
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inum = list->inum;
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ilist = list->ilist;
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numneigh = list->numneigh;
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firstneigh = list->firstneigh;
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// loop over neighbors of my atoms
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// need minimg() for x0 difference since not ghosted
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for (ii = 0; ii < inum; ii++) {
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i = ilist[ii];
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xtmp = x[i][0];
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ytmp = x[i][1];
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ztmp = x[i][2];
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xtmp0 = x0[i][0];
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ytmp0 = x0[i][1];
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ztmp0 = x0[i][2];
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itype = type[i];
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jlist = firstneigh[i];
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jnum = numneigh[i];
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for (jj = 0; jj < jnum; jj++) {
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j = jlist[jj];
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j &= NEIGHMASK;
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delx = xtmp - x[j][0];
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dely = ytmp - x[j][1];
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delz = ztmp - x[j][2];
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rsq = delx*delx + dely*dely + delz*delz;
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delx0 = xtmp0 - x0[j][0];
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dely0 = ytmp0 - x0[j][1];
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delz0 = ztmp0 - x0[j][2];
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if (periodic) domain->minimum_image(delx0,dely0,delz0);
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rsq0 = delx0*delx0 + dely0*dely0 + delz0*delz0;
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jtype = type[j];
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r = sqrt(rsq);
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// short-range interaction distance based on initial particle position
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// 0.9 and 1.35 are constants
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d_ij = MIN(0.9*sqrt(rsq0),1.35*lc);
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// short-range contact forces
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// 15 is constant taken from the EMU Theory Manual
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// Silling, 12 May 2005, p 18
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if (r < d_ij) {
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dr = r - d_ij;
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rk = (15.0 * kspring[itype][jtype] * vfrac[j]) *
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(dr / cut[itype][jtype]);
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if (r > 0.0) fpair = -(rk/r);
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else fpair = 0.0;
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f[i][0] += delx*fpair;
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f[i][1] += dely*fpair;
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f[i][2] += delz*fpair;
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if (newton_pair || j < nlocal) {
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f[j][0] -= delx*fpair;
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f[j][1] -= dely*fpair;
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f[j][2] -= delz*fpair;
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}
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if (eflag) evdwl = 0.5*rk*dr;
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if (evflag) ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,
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fpair*vfrac[i],delx,dely,delz);
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}
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}
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}
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// grow bond forces array if necessary
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if (atom->nmax > nmax) {
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memory->destroy(s0_new);
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nmax = atom->nmax;
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memory->create(s0_new,nmax,"pair:s0_new");
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}
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// loop over my particles and their partners
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// partner list contains all bond partners, so I-J appears twice
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// if bond already broken, skip this partner
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// first = true if this is first neighbor of particle i
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bool first;
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for (i = 0; i < nlocal; i++) {
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xtmp = x[i][0];
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ytmp = x[i][1];
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ztmp = x[i][2];
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itype = type[i];
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jnum = npartner[i];
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s0_new[i] = DBL_MAX;
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first = true;
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for (jj = 0; jj < jnum; jj++) {
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if (partner[i][jj] == 0) continue;
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j = atom->map(partner[i][jj]);
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// check if lost a partner without first breaking bond
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if (j < 0) {
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partner[i][jj] = 0;
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continue;
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}
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// compute force density, add to PD equation of motion
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delx = xtmp - x[j][0];
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dely = ytmp - x[j][1];
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delz = ztmp - x[j][2];
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if (periodic) domain->minimum_image(delx,dely,delz);
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rsq = delx*delx + dely*dely + delz*delz;
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jtype = type[j];
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delta = cut[itype][jtype];
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r = sqrt(rsq);
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dr = r - r0[i][jj];
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// avoid roundoff errors
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if (fabs(dr) < NEAR_ZERO) dr = 0.0;
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// scale vfrac[j] if particle j near the horizon
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if ((fabs(r0[i][jj] - delta)) <= half_lc)
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vfrac_scale = (-1.0/(2*half_lc))*(r0[i][jj]) +
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(1.0 + ((delta - half_lc)/(2*half_lc) ) );
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else vfrac_scale = 1.0;
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stretch = dr / r0[i][jj];
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rk = (kspring[itype][jtype] * vfrac[j]) * vfrac_scale * stretch;
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if (r > 0.0) fbond = -(rk/r);
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else fbond = 0.0;
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f[i][0] += delx*fbond;
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f[i][1] += dely*fbond;
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f[i][2] += delz*fbond;
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// since I-J is double counted, set newton off & use 1/2 factor and I,I
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if (eflag) evdwl = 0.5*rk*dr;
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if (evflag) ev_tally(i,i,nlocal,0,0.5*evdwl,0.0,0.5*fbond*vfrac[i],delx,dely,delz);
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// find stretch in bond I-J and break if necessary
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// use s0 from previous timestep
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if (stretch > MIN(s0[i],s0[j])) partner[i][jj] = 0;
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// update s0 for next timestep
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if (first)
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s0_new[i] = s00[itype][jtype] - (alpha[itype][jtype] * stretch);
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else
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s0_new[i] = MAX(s0_new[i],s00[itype][jtype] - (alpha[itype][jtype] * stretch));
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first = false;
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}
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}
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// store new s0
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for (i = 0; i < nlocal; i++) s0[i] = s0_new[i];
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}
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/* ----------------------------------------------------------------------
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set coeffs for one or more type pairs
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------------------------------------------------------------------------- */
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void PairPeriPMB::coeff(int narg, char **arg)
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{
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if (narg != 6) error->all(FLERR,"Incorrect args for pair coefficients");
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if (!allocated) allocate();
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int ilo,ihi,jlo,jhi;
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utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error);
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utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error);
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double kspring_one = utils::numeric(FLERR,arg[2],false,lmp);
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double cut_one = utils::numeric(FLERR,arg[3],false,lmp);
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double s00_one = utils::numeric(FLERR,arg[4],false,lmp);
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double alpha_one = utils::numeric(FLERR,arg[5],false,lmp);
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int count = 0;
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for (int i = ilo; i <= ihi; i++) {
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for (int j = MAX(jlo,i); j <= jhi; j++) {
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kspring[i][j] = kspring_one;
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s00[i][j] = s00_one;
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alpha[i][j] = alpha_one;
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cut[i][j] = cut_one;
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setflag[i][j] = 1;
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count++;
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}
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}
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if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
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}
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/* ----------------------------------------------------------------------
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init for one type pair i,j and corresponding j,i
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------------------------------------------------------------------------- */
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double PairPeriPMB::init_one(int i, int j)
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{
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if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
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kspring[j][i] = kspring[i][j];
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alpha[j][i] = alpha[i][j];
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s00[j][i] = s00[i][j];
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cut[j][i] = cut[i][j];
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return cut[i][j];
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}
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/* ----------------------------------------------------------------------
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proc 0 writes to restart file
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------------------------------------------------------------------------- */
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void PairPeriPMB::write_restart(FILE *fp)
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{
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int i,j;
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for (i = 1; i <= atom->ntypes; i++)
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for (j = i; j <= atom->ntypes; j++) {
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fwrite(&setflag[i][j],sizeof(int),1,fp);
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if (setflag[i][j]) {
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fwrite(&kspring[i][j],sizeof(double),1,fp);
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fwrite(&s00[i][j],sizeof(double),1,fp);
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fwrite(&alpha[i][j],sizeof(double),1,fp);
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fwrite(&cut[i][j],sizeof(double),1,fp);
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}
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}
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}
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/* ----------------------------------------------------------------------
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proc 0 reads from restart file, bcasts
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------------------------------------------------------------------------- */
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void PairPeriPMB::read_restart(FILE *fp)
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{
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allocate();
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int i,j;
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int me = comm->me;
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for (i = 1; i <= atom->ntypes; i++)
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for (j = i; j <= atom->ntypes; j++) {
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if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,nullptr,error);
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MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
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if (setflag[i][j]) {
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if (me == 0) {
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utils::sfread(FLERR,&kspring[i][j],sizeof(double),1,fp,nullptr,error);
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utils::sfread(FLERR,&s00[i][j],sizeof(double),1,fp,nullptr,error);
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utils::sfread(FLERR,&alpha[i][j],sizeof(double),1,fp,nullptr,error);
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utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,nullptr,error);
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}
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MPI_Bcast(&kspring[i][j],1,MPI_DOUBLE,0,world);
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MPI_Bcast(&s00[i][j],1,MPI_DOUBLE,0,world);
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MPI_Bcast(&alpha[i][j],1,MPI_DOUBLE,0,world);
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MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
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}
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}
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}
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/* ---------------------------------------------------------------------- */
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double PairPeriPMB::single(int i, int j, int itype, int jtype, double rsq,
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double /*factor_coul*/, double /*factor_lj*/,
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double &fforce)
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{
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double delx0,dely0,delz0,rsq0;
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double d_ij,r,dr,rk,vfrac_scale;
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double *vfrac = atom->vfrac;
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double **x0 = atom->x0;
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double **r0 = fix_peri_neigh->r0;
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tagint **partner = fix_peri_neigh->partner;
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int *npartner = fix_peri_neigh->npartner;
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double lc = domain->lattice->xlattice;
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double half_lc = 0.5*lc;
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delx0 = x0[i][0] - x0[j][0];
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dely0 = x0[i][1] - x0[j][1];
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delz0 = x0[i][2] - x0[j][2];
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int periodic = domain->xperiodic || domain->yperiodic || domain->zperiodic;
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if (periodic) domain->minimum_image(delx0,dely0,delz0);
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rsq0 = delx0*delx0 + dely0*dely0 + delz0*delz0;
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d_ij = MIN(0.9*sqrt(rsq0),1.35*lc);
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r = sqrt(rsq);
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double energy = 0.0;
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fforce = 0.0;
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if (r < d_ij) {
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dr = r - d_ij;
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rk = (15.0 * kspring[itype][jtype] * vfrac[j]) *
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(dr / sqrt(cutsq[itype][jtype]));
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if (r > 0.0) fforce += -(rk/r);
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energy += 0.5*rk*dr;
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}
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int jnum = npartner[i];
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for (int jj = 0; jj < jnum; jj++) {
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if (partner[i][jj] == 0) continue;
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if (j < 0) continue;
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if (j == atom->map(partner[i][jj])) {
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dr = r - r0[i][jj];
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if (fabs(dr) < NEAR_ZERO) dr = 0.0;
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if ( (fabs(r0[i][jj] - sqrt(cutsq[itype][jtype]))) <= half_lc)
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vfrac_scale = (-1.0/(2*half_lc))*(r0[i][jj]) +
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(1.0 + ((sqrt(cutsq[itype][jtype]) - half_lc)/(2*half_lc)));
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else vfrac_scale = 1.0;
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rk = (kspring[itype][jtype] * vfrac[j] * vfrac_scale) *
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(dr / r0[i][jj]);
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if (r > 0.0) fforce += -(rk/r);
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energy += 0.5*rk*dr;
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}
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}
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return energy;
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}
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