first few pieces of pair style python
This commit is contained in:
Axel Kohlmeyer
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src/PYTHON/pair_python.cpp
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src/PYTHON/pair_python.cpp
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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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/* ----------------------------------------------------------------------
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Contributing author: Axel Kohlmeyer and Richard Berger (Temple U)
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------------------------------------------------------------------------- */
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#include <Python.h>
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#include <stdio.h>
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#include <stdlib.h>
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#include <string.h>
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#include "pair_python.h"
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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 "memory.h"
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#include "neigh_list.h"
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#include "python.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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PairPython::PairPython(LAMMPS *lmp) : Pair(lmp) {
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respa_enable = 0;
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single_enable = 0;
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writedata = 0;
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restartinfo = 0;
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one_coeff = 1;
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reinitflag = 0;
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python->init();
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}
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/* ---------------------------------------------------------------------- */
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PairPython::~PairPython()
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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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}
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}
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/* ---------------------------------------------------------------------- */
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void PairPython::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 rsq,factor_lj;
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int *ilist,*jlist,*numneigh,**firstneigh;
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evdwl = 0.0;
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if (eflag || vflag) ev_setup(eflag,vflag);
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else evflag = vflag_fdotr = 0;
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double **x = atom->x;
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double **f = atom->f;
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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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const double r = sqrt(rsq);
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printf("compute f at r=%g for types %d,%d with factor %g\n",
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r,itype,jtype,factor_lj);
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fpair = 0.0;
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fpair *= factor_lj;
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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) {
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printf("compute e at r=%g for types %d,%d with factor %g\n",
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r,itype,jtype,factor_lj);
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evdwl = 0.0;
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evdwl *= factor_lj;
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}
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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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}
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/* ----------------------------------------------------------------------
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allocate all arrays
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------------------------------------------------------------------------- */
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void PairPython::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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}
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/* ----------------------------------------------------------------------
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global settings
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------------------------------------------------------------------------- */
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void PairPython::settings(int narg, char **arg)
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{
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if (narg != 1)
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error->all(FLERR,"Illegal pair_style command");
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cut_global = force->numeric(FLERR,arg[0]);
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}
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/* ----------------------------------------------------------------------
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set coeffs for all type pairs
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------------------------------------------------------------------------- */
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void PairPython::coeff(int narg, char **arg)
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{
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const int ntypes = atom->ntypes;
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if (narg != 3+ntypes)
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error->all(FLERR,"Incorrect args for pair coefficients");
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if (!allocated) allocate();
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// make sure I,J args are * *
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if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0)
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error->all(FLERR,"Incorrect args for pair coefficients");
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// check if potential python file exists
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FILE *fp = fopen(arg[2],"r");
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if (fp == NULL)
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error->all(FLERR,"Cannot open python pair potential class file");
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PyGILState_STATE gstate = PyGILState_Ensure();
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PyObject *pModule = PyImport_AddModule("__main__");
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if (!pModule) error->all(FLERR,"Could not initialize embedded Python");
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int err = PyRun_SimpleFile(fp,arg[2]);
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if (err) error->all(FLERR,"Loading python pair style class failure");
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fclose(fp);
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PyObject *py_pair_instance =
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PyObject_GetAttrString(pModule,"lammps_pair_style");
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if (!py_pair_instance) {
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PyGILState_Release(gstate);
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error->all(FLERR,"Could not find 'lammps_pair_style instance'");
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}
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for (int i = 1; i <= ntypes ; i++) {
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for (int j = i; j <= ntypes ; j++) {
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if (strcmp(arg[2+i],"NULL") != 0) {
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setflag[i][j] = 1;
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cutsq[i][j] = cut_global*cut_global;
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}
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}
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}
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PyGILState_Release(gstate);
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}
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/* ---------------------------------------------------------------------- */
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double PairPython::init_one(int, int)
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{
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return cut_global;
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}
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