From 34cc3946b8d94c7c1a38782fab0b6f141fea7b65 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sun, 14 May 2017 18:29:06 -0400
Subject: [PATCH] first few pieces of pair style python
---
examples/python/in.pair_python_hybrid | 60 +++++++
examples/python/in.pair_python_melt | 57 +++++++
examples/python/lj-melt-potential.py | 28 ++++
src/PYTHON/pair_python.cpp | 220 ++++++++++++++++++++++++++
src/PYTHON/pair_python.h | 74 +++++++++
src/PYTHON/python_impl.cpp | 3 +-
6 files changed, 440 insertions(+), 2 deletions(-)
create mode 100644 examples/python/in.pair_python_hybrid
create mode 100644 examples/python/in.pair_python_melt
create mode 100644 examples/python/lj-melt-potential.py
create mode 100644 src/PYTHON/pair_python.cpp
create mode 100644 src/PYTHON/pair_python.h
diff --git a/examples/python/in.pair_python_hybrid b/examples/python/in.pair_python_hybrid
new file mode 100644
index 0000000000..e4ea3eb99e
--- /dev/null
+++ b/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
+
diff --git a/examples/python/in.pair_python_melt b/examples/python/in.pair_python_melt
new file mode 100644
index 0000000000..ad6a84c494
--- /dev/null
+++ b/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
+
diff --git a/examples/python/lj-melt-potential.py b/examples/python/lj-melt-potential.py
new file mode 100644
index 0000000000..b1360e0ded
--- /dev/null
+++ b/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")
+
diff --git a/src/PYTHON/pair_python.cpp b/src/PYTHON/pair_python.cpp
new file mode 100644
index 0000000000..d951a11d77
--- /dev/null
+++ b/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;
+}
+
diff --git a/src/PYTHON/pair_python.h b/src/PYTHON/pair_python.h
new file mode 100644
index 0000000000..acb96de5e3
--- /dev/null
+++ b/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.
+
+*/
diff --git a/src/PYTHON/python_impl.cpp b/src/PYTHON/python_impl.cpp
index 1b9eef9ea6..c66e003228 100644
--- a/src/PYTHON/python_impl.cpp
+++ b/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);
}
--
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