first few pieces of pair style python

examples/python/in.pair_python_hybrid

@@ -0,0 +1,60 @@
+# 3d Lennard-Jones hybrid
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+region		box block 0 10 0 10 0 10
+create_box	2 box
+create_atoms	1 box
+mass		* 1.0
+
+velocity	all create 3.0 87287
+
+pair_style	hybrid lj/cut 2.5 python 2.5
+pair_coeff	* * python lj-melt-potential.py lj NULL
+pair_coeff      * 2 lj/cut 1.0 1.0
+
+neighbor	0.3 bin
+neigh_modify	every 10 delay 0 check no
+
+fix		1 all nve
+
+thermo		50
+run		250
+
+write_data      hybrid.data
+write_restart   hybrid.restart
+
+clear
+
+read_restart    hybrid.restart
+
+pair_style	hybrid lj/cut 2.5 python 2.5
+pair_coeff	* * python lj-melt-potential.py lj NULL
+pair_coeff      * 2 lj/cut 1.0 1.0
+
+fix		1 all nve
+
+thermo		50
+run		250
+
+clear
+
+units		lj
+atom_style	atomic
+
+read_data       hybrid.data
+
+pair_style	hybrid lj/cut 2.5 python 2.5
+pair_coeff	* * python lj-melt-potential.py lj NULL
+pair_coeff      * 2 lj/cut 1.0 1.0
+
+neighbor	0.3 bin
+neigh_modify	every 10 delay 0 check no
+
+fix		1 all nve
+
+thermo		50
+run		250
+

examples/python/in.pair_python_melt

@@ -0,0 +1,57 @@
+# 3d Lennard-Jones melt
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+region		box block 0 10 0 10 0 10
+create_box	1 box
+create_atoms	1 box
+mass		1 1.0
+
+velocity	all create 3.0 87287
+
+pair_style	python 2.5
+pair_coeff	* * lj-melt-potential.py lj
+
+neighbor	0.3 bin
+neigh_modify	every 10 delay 0 check no
+
+fix		1 all nve
+
+thermo		50
+run		250
+
+write_data      melt.data
+write_restart   melt.restart
+
+clear
+
+read_restart    melt.restart
+
+pair_style	python 2.5
+pair_coeff	* * lj-melt-potential.py lj
+
+fix		1 all nve
+
+thermo		50
+run		250
+
+clear
+
+units		lj
+atom_style	atomic
+
+read_data       melt.data
+
+pair_style	python 2.5
+pair_coeff	* * lj-melt-potential.py lj
+
+neighbor	0.3 bin
+neigh_modify	every 10 delay 0 check no
+
+fix		1 all nve
+
+thermo		50
+run		250
+

examples/python/lj-melt-potential.py

@@ -0,0 +1,28 @@
+from __future__ import print_function
+
+class LAMMPSLJCutPotential(object):
+
+    def __init__(self):
+        self.pmap=dict()
+        # coefficients: epsilon, sigma
+        self.coeff = {'lj'  : {'lj'  : (1.0,1.0),
+                               'NULL': (0.0,1.0)},
+                      'NULL': {'lj'  : (0.0,1.0),
+                               'NULL': (0.0,1.0)}}
+
+    def map_coeff(self,type,name):
+        if self.coeff.has_key(name):
+           print("map type %d to name %s" % (type,name))
+           self.pmap[type] = name
+        else:
+           print("cannot match atom type",name)
+
+    def compute_force(self,r,itype,jtype,factor_lj):
+        return 0.0
+
+    def compute_energy(self,r,itype,jtype,factor_lj):
+        return 0.0
+
+lammps_pair_style = LAMMPSLJCutPotential()
+print ("lj-melt potential file loaded")
+

src/PYTHON/pair_python.cpp

@@ -0,0 +1,220 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Contributing author: Axel Kohlmeyer and Richard Berger (Temple U)
+------------------------------------------------------------------------- */
+
+#include <Python.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include "pair_python.h"
+#include "atom.h"
+#include "comm.h"
+#include "force.h"
+#include "memory.h"
+#include "neigh_list.h"
+#include "python.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+PairPython::PairPython(LAMMPS *lmp) : Pair(lmp) {
+  respa_enable = 0;
+  single_enable = 0;
+  writedata = 0;
+  restartinfo = 0;
+  one_coeff = 1;
+  reinitflag = 0;
+
+  python->init();
+}
+
+/* ---------------------------------------------------------------------- */
+
+PairPython::~PairPython()
+{
+  if (allocated) {
+    memory->destroy(setflag);
+    memory->destroy(cutsq);
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairPython::compute(int eflag, int vflag)
+{
+  int i,j,ii,jj,inum,jnum,itype,jtype;
+  double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
+  double rsq,factor_lj;
+  int *ilist,*jlist,*numneigh,**firstneigh;
+
+  evdwl = 0.0;
+  if (eflag || vflag) ev_setup(eflag,vflag);
+  else evflag = vflag_fdotr = 0;
+
+  double **x = atom->x;
+  double **f = atom->f;
+  int *type = atom->type;
+  int nlocal = atom->nlocal;
+  double *special_lj = force->special_lj;
+  int newton_pair = force->newton_pair;
+
+  inum = list->inum;
+  ilist = list->ilist;
+  numneigh = list->numneigh;
+  firstneigh = list->firstneigh;
+
+  // loop over neighbors of my atoms
+
+  for (ii = 0; ii < inum; ii++) {
+    i = ilist[ii];
+    xtmp = x[i][0];
+    ytmp = x[i][1];
+    ztmp = x[i][2];
+    itype = type[i];
+    jlist = firstneigh[i];
+    jnum = numneigh[i];
+
+    for (jj = 0; jj < jnum; jj++) {
+      j = jlist[jj];
+      factor_lj = special_lj[sbmask(j)];
+      j &= NEIGHMASK;
+
+      delx = xtmp - x[j][0];
+      dely = ytmp - x[j][1];
+      delz = ztmp - x[j][2];
+      rsq = delx*delx + dely*dely + delz*delz;
+      jtype = type[j];
+
+      if (rsq < cutsq[itype][jtype]) {
+        const double r = sqrt(rsq);
+        printf("compute f at r=%g for types %d,%d with factor %g\n",
+               r,itype,jtype,factor_lj);
+        fpair = 0.0;
+        fpair *= factor_lj;
+
+        f[i][0] += delx*fpair;
+        f[i][1] += dely*fpair;
+        f[i][2] += delz*fpair;
+        if (newton_pair || j < nlocal) {
+          f[j][0] -= delx*fpair;
+          f[j][1] -= dely*fpair;
+          f[j][2] -= delz*fpair;
+        }
+
+        if (eflag) {
+          printf("compute e at r=%g for types %d,%d with factor %g\n",
+                 r,itype,jtype,factor_lj);
+          evdwl = 0.0;
+          evdwl *= factor_lj;
+        }
+
+        if (evflag) ev_tally(i,j,nlocal,newton_pair,
+                             evdwl,0.0,fpair,delx,dely,delz);
+      }
+    }
+  }
+}
+
+/* ----------------------------------------------------------------------
+   allocate all arrays
+------------------------------------------------------------------------- */
+
+void PairPython::allocate()
+{
+  allocated = 1;
+  int n = atom->ntypes;
+
+  memory->create(setflag,n+1,n+1,"pair:setflag");
+  for (int i = 1; i <= n; i++)
+    for (int j = i; j <= n; j++)
+      setflag[i][j] = 0;
+
+  memory->create(cutsq,n+1,n+1,"pair:cutsq");
+}
+
+/* ----------------------------------------------------------------------
+   global settings
+------------------------------------------------------------------------- */
+
+void PairPython::settings(int narg, char **arg)
+{
+  if (narg != 1)
+    error->all(FLERR,"Illegal pair_style command");
+
+  cut_global = force->numeric(FLERR,arg[0]);
+}
+
+/* ----------------------------------------------------------------------
+   set coeffs for all type pairs
+------------------------------------------------------------------------- */
+
+void PairPython::coeff(int narg, char **arg)
+{
+  const int ntypes = atom->ntypes;
+
+  if (narg != 3+ntypes)
+    error->all(FLERR,"Incorrect args for pair coefficients");
+
+  if (!allocated) allocate();
+
+  // make sure I,J args are * *
+
+  if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0)
+    error->all(FLERR,"Incorrect args for pair coefficients");
+
+  // check if potential python file exists
+
+  FILE *fp = fopen(arg[2],"r");
+  if (fp == NULL)
+    error->all(FLERR,"Cannot open python pair potential class file");
+
+  PyGILState_STATE gstate = PyGILState_Ensure();
+  PyObject *pModule = PyImport_AddModule("__main__");
+  if (!pModule) error->all(FLERR,"Could not initialize embedded Python");
+
+  int err = PyRun_SimpleFile(fp,arg[2]);
+  if (err) error->all(FLERR,"Loading python pair style class failure");
+  fclose(fp);
+
+  PyObject *py_pair_instance =
+    PyObject_GetAttrString(pModule,"lammps_pair_style");
+
+  if (!py_pair_instance) {
+    PyGILState_Release(gstate);
+    error->all(FLERR,"Could not find 'lammps_pair_style instance'");
+  }
+
+
+  for (int i = 1; i <= ntypes ; i++) {
+    for (int j = i; j <= ntypes ; j++) {
+      if (strcmp(arg[2+i],"NULL") != 0) {
+        setflag[i][j] = 1;
+        cutsq[i][j] = cut_global*cut_global;
+      }
+    }
+  }
+  PyGILState_Release(gstate);
+}
+
+/* ---------------------------------------------------------------------- */
+
+double PairPython::init_one(int, int)
+{
+  return cut_global;
+}
+

src/PYTHON/pair_python.h

@@ -0,0 +1,74 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+
+   Pair zero is a dummy pair interaction useful for requiring a
+   force cutoff distance in the absense of pair-interactions or
+   with hybrid/overlay if a larger force cutoff distance is required.
+
+   This can be used in conjunction with bond/create to create bonds
+   that are longer than the cutoff of a given force field, or to
+   calculate radial distribution functions for models without
+   pair interactions.
+
+------------------------------------------------------------------------- */
+
+#ifdef PAIR_CLASS
+
+PairStyle(python,PairPython)
+
+#else
+
+#ifndef LMP_PAIR_PYTHON_H
+#define LMP_PAIR_PYTHON_H
+
+#include "pair.h"
+
+namespace LAMMPS_NS {
+
+class PairPython : public Pair {
+ public:
+  PairPython(class LAMMPS *);
+  virtual ~PairPython();
+  virtual void compute(int, int);
+  void settings(int, char **);
+  void coeff(int, char **);
+  double init_one(int, int);
+
+ protected:
+  double cut_global;
+
+  virtual void allocate();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+Self-explanatory.  Check the input script syntax and compare to the
+documentation for the command.  You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+E: Incorrect args for pair coefficients
+
+Self-explanatory.  Check the input script or data file.
+
+E: Pair cutoff < Respa interior cutoff
+
+One or more pairwise cutoffs are too short to use with the specified
+rRESPA cutoffs.
+
+*/

src/PYTHON/python_impl.cpp

@@ -51,7 +51,7 @@ PythonImpl::PythonImpl(LAMMPS *lmp) : Pointers(lmp)
   pfuncs = NULL;
 
   // one-time initialization of Python interpreter
-  // pymain stores pointer to main module
+  // pyMain stores pointer to main module
   external_interpreter = Py_IsInitialized();
 
   Py_Initialize();
@@ -63,7 +63,6 @@ PythonImpl::PythonImpl(LAMMPS *lmp) : Pointers(lmp)
   if (!pModule) error->all(FLERR,"Could not initialize embedded Python");
 
   pyMain = (void *) pModule;
-
   PyGILState_Release(gstate);
 }