Adding todo note for comm, testing for full nlist
This commit is contained in:
Joel Clemmer
@ -243,6 +243,8 @@ void Comm::init()
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if (fix[i]->maxexchange_dynamic) maxexchange_fix_dynamic = 1;
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// Can't used multi2 communication with Newton off
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// TODO: need to somehow restrict this option with full neighbor lists
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// CANNOT use multi2 communication with full nlist
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if (force->newton == 0 && multi2)
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error->all(FLERR,"Cannot use multi2 communication with Newton off");
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}
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341
src/pair_full_print.cpp
Normal file
341
src/pair_full_print.cpp
Normal file
@ -0,0 +1,341 @@
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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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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#include "pair_full_print.h"
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#include <cmath>
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#include <cstring>
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#include "atom.h"
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#include "comm.h"
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#include "force.h"
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#include "neigh_list.h"
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#include "neigh_request.h"
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#include "neighbor.h"
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#include "math_const.h"
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#include "memory.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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using namespace MathConst;
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/* ---------------------------------------------------------------------- */
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PairFullPrint::PairFullPrint(LAMMPS *lmp) : Pair(lmp)
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{
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writedata = 1;
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}
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/* ---------------------------------------------------------------------- */
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PairFullPrint::~PairFullPrint()
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{
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if (allocated) {
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memory->destroy(setflag);
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memory->destroy(cutsq);
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memory->destroy(prefactor);
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memory->destroy(cut);
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}
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}
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/* ---------------------------------------------------------------------- */
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void PairFullPrint::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,evdwl,fpair;
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double r,rsq,arg,factor_lj;
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int *ilist,*jlist,*numneigh,**firstneigh;
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evdwl = 0.0;
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ev_init(eflag,vflag);
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double **x = atom->x;
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double **f = atom->f;
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tagint *tag = atom->tag;
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int *type = atom->type;
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int nlocal = atom->nlocal;
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double *special_lj = force->special_lj;
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int newton_pair = force->newton_pair;
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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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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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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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factor_lj = special_lj[sbmask(j)];
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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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jtype = type[j];
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if (rsq < cutsq[itype][jtype]) {
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printf("NLIST %d %d %d %d\n", tag[i], tag[j], type[i], type[j]);
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r = sqrt(rsq);
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arg = MY_PI*r/cut[itype][jtype];
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if (r > 0.0) fpair = factor_lj * prefactor[itype][jtype] *
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sin(arg) * MY_PI/cut[itype][jtype]/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 (eflag)
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evdwl = factor_lj * prefactor[itype][jtype] * (1.0+cos(arg));
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if (evflag) ev_tally(i,j,nlocal,newton_pair,
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evdwl,0.0,fpair,delx,dely,delz);
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}
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}
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}
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if (vflag_fdotr) virial_fdotr_compute();
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}
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/* ----------------------------------------------------------------------
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allocate all arrays
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------------------------------------------------------------------------- */
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void PairFullPrint::allocate()
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{
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allocated = 1;
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int n = atom->ntypes;
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memory->create(setflag,n+1,n+1,"pair:setflag");
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for (int i = 1; i <= n; i++)
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for (int j = i; j <= n; j++)
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setflag[i][j] = 0;
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memory->create(cutsq,n+1,n+1,"pair:cutsq");
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memory->create(prefactor,n+1,n+1,"pair:prefactor");
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memory->create(cut,n+1,n+1,"pair:cut");
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}
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/* ----------------------------------------------------------------------
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global settings
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------------------------------------------------------------------------- */
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void PairFullPrint::settings(int narg, char **arg)
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{
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if (narg != 1) error->all(FLERR,"Illegal pair_style command");
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cut_global = utils::numeric(FLERR,arg[0],false,lmp);
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// reset cutoffs that have been explicitly set
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if (allocated) {
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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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if (setflag[i][j]) cut[i][j] = cut_global;
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}
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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 PairFullPrint::coeff(int narg, char **arg)
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{
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if (narg < 3 || narg > 4)
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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 prefactor_one = utils::numeric(FLERR,arg[2],false,lmp);
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double cut_one = cut_global;
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if (narg == 4) cut_one = utils::numeric(FLERR,arg[3],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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prefactor[i][j] = prefactor_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 specific to this pair style
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------------------------------------------------------------------------- */
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void PairFullPrint::init_style() {
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// need a full neighbor list
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int irequest = neighbor->request(this,instance_me);
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neighbor->requests[irequest]->half = 0;
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neighbor->requests[irequest]->full = 1;
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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 PairFullPrint::init_one(int i, int j)
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{
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// always mix prefactors geometrically
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if (setflag[i][j] == 0) {
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prefactor[i][j] = sqrt(prefactor[i][i]*prefactor[j][j]);
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cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
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}
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prefactor[j][i] = prefactor[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 PairFullPrint::write_restart(FILE *fp)
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{
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write_restart_settings(fp);
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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(&prefactor[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 PairFullPrint::read_restart(FILE *fp)
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{
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read_restart_settings(fp);
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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,&prefactor[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(&prefactor[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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proc 0 writes to restart file
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------------------------------------------------------------------------- */
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void PairFullPrint::write_restart_settings(FILE *fp)
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{
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fwrite(&cut_global,sizeof(double),1,fp);
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fwrite(&mix_flag,sizeof(int),1,fp);
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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 PairFullPrint::read_restart_settings(FILE *fp)
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{
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if (comm->me == 0) {
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utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,nullptr,error);
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utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,nullptr,error);
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}
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MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
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MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
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}
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/* ----------------------------------------------------------------------
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proc 0 writes to data file
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------------------------------------------------------------------------- */
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void PairFullPrint::write_data(FILE *fp)
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{
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for (int i = 1; i <= atom->ntypes; i++)
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fprintf(fp,"%d %g\n",i,prefactor[i][i]);
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}
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/* ----------------------------------------------------------------------
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proc 0 writes all pairs to data file
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------------------------------------------------------------------------- */
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void PairFullPrint::write_data_all(FILE *fp)
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{
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for (int i = 1; i <= atom->ntypes; i++)
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for (int j = i; j <= atom->ntypes; j++)
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fprintf(fp,"%d %d %g %g\n",i,j,prefactor[i][j],cut[i][j]);
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}
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/* ---------------------------------------------------------------------- */
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double PairFullPrint::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 r,arg,philj;
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r = sqrt(rsq);
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arg = MY_PI*r/cut[itype][jtype];
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fforce = factor_lj * prefactor[itype][jtype] *
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sin(arg) * MY_PI/cut[itype][jtype]/r;
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philj = prefactor[itype][jtype] * (1.0+cos(arg));
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return factor_lj*philj;
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}
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/* ---------------------------------------------------------------------- */
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void *PairFullPrint::extract(const char *str, int &dim)
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{
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dim = 2;
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if (strcmp(str,"a") == 0) return (void *) prefactor;
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return nullptr;
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}
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72
src/pair_full_print.h
Normal file
72
src/pair_full_print.h
Normal file
@ -0,0 +1,72 @@
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/* -*- c++ -*- ----------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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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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#ifdef PAIR_CLASS
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PairStyle(full/print,PairFullPrint)
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#else
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#ifndef LMP_PAIR_FULL_PRINT_H
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#define LMP_PAIR_FULL_PRINT_H
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#include "pair.h"
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namespace LAMMPS_NS {
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class PairFullPrint : public Pair {
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friend class Pair;
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public:
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PairFullPrint(class LAMMPS *);
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virtual ~PairFullPrint();
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void init_style();
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virtual void compute(int, int);
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void settings(int, char **);
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void coeff(int, char **);
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double init_one(int, int);
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void write_restart(FILE *);
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void read_restart(FILE *);
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void write_restart_settings(FILE *);
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void read_restart_settings(FILE *);
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void write_data(FILE *);
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void write_data_all(FILE *);
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double single(int, int, int, int, double, double, double, double &);
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void *extract(const char *, int &);
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protected:
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double cut_global;
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double **prefactor;
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double **cut;
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void allocate();
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};
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}
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#endif
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#endif
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/* ERROR/WARNING messages:
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E: Illegal ... command
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Self-explanatory. Check the input script syntax and compare to the
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documentation for the command. You can use -echo screen as a
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command-line option when running LAMMPS to see the offending line.
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E: Incorrect args for pair coefficients
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Self-explanatory. Check the input script or data file.
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*/
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Reference in New Issue
Block a user