forked from lijiext/lammps
first few pieces of pair style python
This commit is contained in:
Axel Kohlmeyer
parent
06c151421c
commit
34cc3946b8
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@ -0,0 +1,60 @@
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# 3d Lennard-Jones hybrid
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units lj
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atom_style atomic
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lattice fcc 0.8442
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region box block 0 10 0 10 0 10
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create_box 2 box
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create_atoms 1 box
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mass * 1.0
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velocity all create 3.0 87287
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pair_style hybrid lj/cut 2.5 python 2.5
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pair_coeff * * python lj-melt-potential.py lj NULL
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pair_coeff * 2 lj/cut 1.0 1.0
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neighbor 0.3 bin
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neigh_modify every 10 delay 0 check no
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fix 1 all nve
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thermo 50
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run 250
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write_data hybrid.data
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write_restart hybrid.restart
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clear
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read_restart hybrid.restart
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pair_style hybrid lj/cut 2.5 python 2.5
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pair_coeff * * python lj-melt-potential.py lj NULL
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pair_coeff * 2 lj/cut 1.0 1.0
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fix 1 all nve
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thermo 50
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run 250
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clear
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units lj
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atom_style atomic
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read_data hybrid.data
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pair_style hybrid lj/cut 2.5 python 2.5
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pair_coeff * * python lj-melt-potential.py lj NULL
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pair_coeff * 2 lj/cut 1.0 1.0
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neighbor 0.3 bin
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neigh_modify every 10 delay 0 check no
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fix 1 all nve
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thermo 50
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run 250
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@ -0,0 +1,57 @@
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# 3d Lennard-Jones melt
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units lj
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atom_style atomic
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lattice fcc 0.8442
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region box block 0 10 0 10 0 10
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create_box 1 box
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create_atoms 1 box
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mass 1 1.0
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velocity all create 3.0 87287
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pair_style python 2.5
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pair_coeff * * lj-melt-potential.py lj
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neighbor 0.3 bin
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neigh_modify every 10 delay 0 check no
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fix 1 all nve
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thermo 50
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run 250
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write_data melt.data
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write_restart melt.restart
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clear
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read_restart melt.restart
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pair_style python 2.5
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pair_coeff * * lj-melt-potential.py lj
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fix 1 all nve
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thermo 50
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run 250
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clear
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units lj
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atom_style atomic
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read_data melt.data
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pair_style python 2.5
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pair_coeff * * lj-melt-potential.py lj
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neighbor 0.3 bin
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neigh_modify every 10 delay 0 check no
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fix 1 all nve
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thermo 50
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run 250
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@ -0,0 +1,28 @@
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from __future__ import print_function
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class LAMMPSLJCutPotential(object):
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def __init__(self):
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self.pmap=dict()
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# coefficients: epsilon, sigma
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self.coeff = {'lj' : {'lj' : (1.0,1.0),
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'NULL': (0.0,1.0)},
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'NULL': {'lj' : (0.0,1.0),
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'NULL': (0.0,1.0)}}
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def map_coeff(self,type,name):
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if self.coeff.has_key(name):
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print("map type %d to name %s" % (type,name))
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self.pmap[type] = name
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else:
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print("cannot match atom type",name)
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def compute_force(self,r,itype,jtype,factor_lj):
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return 0.0
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def compute_energy(self,r,itype,jtype,factor_lj):
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return 0.0
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lammps_pair_style = LAMMPSLJCutPotential()
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print ("lj-melt potential file loaded")
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@ -0,0 +1,220 @@
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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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@ -0,0 +1,74 @@
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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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Pair zero is a dummy pair interaction useful for requiring a
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force cutoff distance in the absense of pair-interactions or
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with hybrid/overlay if a larger force cutoff distance is required.
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This can be used in conjunction with bond/create to create bonds
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that are longer than the cutoff of a given force field, or to
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calculate radial distribution functions for models without
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pair interactions.
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------------------------------------------------------------------------- */
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#ifdef PAIR_CLASS
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PairStyle(python,PairPython)
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#else
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#ifndef LMP_PAIR_PYTHON_H
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#define LMP_PAIR_PYTHON_H
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#include "pair.h"
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namespace LAMMPS_NS {
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class PairPython : public Pair {
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public:
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PairPython(class LAMMPS *);
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virtual ~PairPython();
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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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protected:
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double cut_global;
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virtual 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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E: Pair cutoff < Respa interior cutoff
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One or more pairwise cutoffs are too short to use with the specified
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rRESPA cutoffs.
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*/
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@ -51,7 +51,7 @@ PythonImpl::PythonImpl(LAMMPS *lmp) : Pointers(lmp)
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pfuncs = NULL;
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// one-time initialization of Python interpreter
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// pymain stores pointer to main module
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// pyMain stores pointer to main module
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external_interpreter = Py_IsInitialized();
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Py_Initialize();
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@ -63,7 +63,6 @@ PythonImpl::PythonImpl(LAMMPS *lmp) : Pointers(lmp)
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if (!pModule) error->all(FLERR,"Could not initialize embedded Python");
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pyMain = (void *) pModule;
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PyGILState_Release(gstate);
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}
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