dummy framework implementation for AGNI pair style

src/.gitignore

@@ -539,6 +539,8 @@
 
 /pair_adp.cpp
 /pair_adp.h
+/pair_agni.cpp
+/pair_agni.h
 /pair_airebo.cpp
 /pair_airebo.h
 /pair_airebo_morse.cpp

src/USER-MISC/pair_agni.cpp

+/* ----------------------------------------------------------------------
+   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 (Temple U)
+------------------------------------------------------------------------- */
+
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include "pair_agni.h"
+#include "atom.h"
+#include "neighbor.h"
+#include "neigh_request.h"
+#include "force.h"
+#include "comm.h"
+#include "memory.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "memory.h"
+#include "error.h"
+#include "citeme.h"
+
+using namespace LAMMPS_NS;
+
+static const char cite_pair_agni[] =
+  "pair agni command:\n\n"
+  "@article{botu2015adaptive,\n"
+  " author    = {Botu, Venkatesh and Ramprasad, Rampi},\n"
+  " title     = {Adaptive machine learning framework to"
+                " accelerate ab initio molecular dynamics},\n"
+  " journal   = {International Journal of Quantum Chemistry},\n"
+  " volume    = {115},\n"
+  " number    = {16},\n"
+  " pages     = {1074--1083},\n"
+  " year      = {2015},\n"
+  " publisher = {Wiley Online Library}\n"
+  "}\n\n"
+  "@article{botu2015learning,\n"
+  " author    = {Botu, Venkatesh and Ramprasad, Rampi},\n"
+  " title     = {Learning scheme to predict atomic forces"
+                " and accelerate materials simulations},\n"
+  " journal   = {Physical Review B},\n"
+  " volume    = {92},\n"
+  " number    = {9},\n"
+  " pages     = {094306},\n"
+  " year      = {2015},\n"
+  " publisher = {APS}\n"
+  "}\n\n";
+
+
+#define MAXLINE 1024
+#define DELTA 4
+
+/* ---------------------------------------------------------------------- */
+
+PairAGNI::PairAGNI(LAMMPS *lmp) : Pair(lmp)
+{
+  if (lmp->citeme) lmp->citeme->add(cite_pair_agni);
+
+  single_enable = 0;
+  restartinfo = 0;
+  one_coeff = 1;
+  manybody_flag = 1;
+
+  nelements = 0;
+  elements = NULL;
+  nparams = 0;
+  params = NULL;
+  map = NULL;
+}
+
+/* ----------------------------------------------------------------------
+   check if allocated, since class can be destructed when incomplete
+------------------------------------------------------------------------- */
+
+PairAGNI::~PairAGNI()
+{
+  if (elements)
+    for (int i = 0; i < nelements; i++) delete [] elements[i];
+  delete [] elements;
+  memory->destroy(params);
+
+  if (allocated) {
+    memory->destroy(setflag);
+    memory->destroy(cutsq);
+    delete [] map;
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairAGNI::compute(int eflag, int vflag)
+{
+  int i,j,k,ii,jj,kk,inum,jnum,jnumm1;
+  int itype,jtype,ktype,ijparam,ikparam,ijkparam;
+  tagint itag,jtag;
+  double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
+  double rsq,rsq1,rsq2;
+  double delr1[3],delr2[3],fj[3],fk[3];
+  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;
+  tagint *tag = atom->tag;
+  int *type = atom->type;
+  int nlocal = atom->nlocal;
+  int newton_pair = force->newton_pair;
+
+  inum = list->inum;
+  ilist = list->ilist;
+  numneigh = list->numneigh;
+  firstneigh = list->firstneigh;
+
+  double fxtmp,fytmp,fztmp;
+
+  // loop over full neighbor list of my atoms
+
+  for (ii = 0; ii < inum; ii++) {
+    i = ilist[ii];
+    itag = tag[i];
+    itype = map[type[i]];
+    xtmp = x[i][0];
+    ytmp = x[i][1];
+    ztmp = x[i][2];
+    fxtmp = fytmp = fztmp = 0.0;
+
+    jlist = firstneigh[i];
+    jnum = numneigh[i];
+
+    for (jj = 0; jj < jnum; jj++) {
+      j = jlist[jj];
+      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 = map[type[j]];
+      // ijparam = elem2param[itype][jtype];
+      if (rsq < params[ijparam].cutsq) {
+
+        // XXX compute force
+
+        fxtmp += delx*fpair;
+        fytmp += dely*fpair;
+        fztmp += delz*fpair;
+
+        if (evflag) ev_tally(i,j,nlocal,newton_pair,
+                             0,0.0,fpair,delx,dely,delz);
+      }
+    }
+    f[i][0] += fxtmp;
+    f[i][1] += fytmp;
+    f[i][2] += fztmp;
+  }
+
+  if (vflag_fdotr) virial_fdotr_compute();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairAGNI::allocate()
+{
+  allocated = 1;
+  int n = atom->ntypes;
+
+  memory->create(setflag,n+1,n+1,"pair:setflag");
+  memory->create(cutsq,n+1,n+1,"pair:cutsq");
+  map = new int[n+1];
+}
+
+/* ----------------------------------------------------------------------
+   global settings
+------------------------------------------------------------------------- */
+
+void PairAGNI::settings(int narg, char **arg)
+{
+  if (narg != 0) error->all(FLERR,"Illegal pair_style command");
+}
+
+/* ----------------------------------------------------------------------
+   set coeffs for one or more type pairs
+------------------------------------------------------------------------- */
+
+void PairAGNI::coeff(int narg, char **arg)
+{
+  int i,j,n;
+
+  if (!allocated) allocate();
+
+  if (narg != 3 + atom->ntypes)
+    error->all(FLERR,"Incorrect args for pair coefficients");
+
+  // insure I,J args are * *
+
+  if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0)
+    error->all(FLERR,"Incorrect args for pair coefficients");
+
+  // read args that map atom types to elements in potential file
+  // map[i] = which element the Ith atom type is, -1 if NULL
+  // nelements = # of unique elements
+  // elements = list of element names
+
+  if (elements) {
+    for (i = 0; i < nelements; i++) delete [] elements[i];
+    delete [] elements;
+  }
+  elements = new char*[atom->ntypes];
+  for (i = 0; i < atom->ntypes; i++) elements[i] = NULL;
+
+  nelements = 0;
+  for (i = 3; i < narg; i++) {
+    if (strcmp(arg[i],"NULL") == 0) {
+      map[i-2] = -1;
+      continue;
+    }
+    for (j = 0; j < nelements; j++)
+      if (strcmp(arg[i],elements[j]) == 0) break;
+    map[i-2] = j;
+    if (j == nelements) {
+      n = strlen(arg[i]) + 1;
+      elements[j] = new char[n];
+      strcpy(elements[j],arg[i]);
+      nelements++;
+    }
+  }
+
+  // read potential file and initialize potential parameters
+
+  read_file(arg[2]);
+  setup_params();
+
+  // clear setflag since coeff() called once with I,J = * *
+
+  n = atom->ntypes;
+  for (int i = 1; i <= n; i++)
+    for (int j = i; j <= n; j++)
+      setflag[i][j] = 0;
+
+  // set setflag i,j for type pairs where both are mapped to elements
+
+  int count = 0;
+  for (int i = 1; i <= n; i++)
+    for (int j = i; j <= n; j++)
+      if (map[i] >= 0 && map[j] >= 0) {
+        setflag[i][j] = 1;
+        count++;
+      }
+
+  if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
+}
+
+/* ----------------------------------------------------------------------
+   init specific to this pair style
+------------------------------------------------------------------------- */
+
+void PairAGNI::init_style()
+{
+  // need a full neighbor list
+
+  int irequest = neighbor->request(this,instance_me);
+  neighbor->requests[irequest]->half = 0;
+  neighbor->requests[irequest]->full = 1;
+}
+
+/* ----------------------------------------------------------------------
+   init for one type pair i,j and corresponding j,i
+------------------------------------------------------------------------- */
+
+double PairAGNI::init_one(int i, int j)
+{
+  if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
+
+  return cutmax;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairAGNI::read_file(char *file)
+{
+  int params_per_line = 14;
+  char **words = new char*[params_per_line+1];
+
+  memory->sfree(params);
+  params = NULL;
+  nparams = 0;
+
+  // open file on proc 0
+
+  FILE *fp;
+  if (comm->me == 0) {
+    fp = force->open_potential(file);
+    if (fp == NULL) {
+      char str[128];
+      sprintf(str,"Cannot open AGNI potential file %s",file);
+      error->one(FLERR,str);
+    }
+  }
+
+  // read each set of params from potential file
+  // one set of params can span multiple lines
+  // store params if all 3 element tags are in element list
+
+  int n,nwords,ielement,jelement,kelement;
+  char line[MAXLINE],*ptr;
+  int eof = 0;
+
+  while (1) {
+    if (comm->me == 0) {
+      ptr = fgets(line,MAXLINE,fp);
+      if (ptr == NULL) {
+        eof = 1;
+        fclose(fp);
+      } else n = strlen(line) + 1;
+    }
+    MPI_Bcast(&eof,1,MPI_INT,0,world);
+    if (eof) break;
+    MPI_Bcast(&n,1,MPI_INT,0,world);
+    MPI_Bcast(line,n,MPI_CHAR,0,world);
+
+    // strip comment, skip line if blank
+
+    if ((ptr = strchr(line,'#'))) *ptr = '\0';
+    nwords = atom->count_words(line);
+    if (nwords == 0) continue;
+
+    // concatenate additional lines until have params_per_line words
+
+    while (nwords < params_per_line) {
+      n = strlen(line);
+      if (comm->me == 0) {
+        ptr = fgets(&line[n],MAXLINE-n,fp);
+        if (ptr == NULL) {
+          eof = 1;
+          fclose(fp);
+        } else n = strlen(line) + 1;
+      }
+      MPI_Bcast(&eof,1,MPI_INT,0,world);
+      if (eof) break;
+      MPI_Bcast(&n,1,MPI_INT,0,world);
+      MPI_Bcast(line,n,MPI_CHAR,0,world);
+      if ((ptr = strchr(line,'#'))) *ptr = '\0';
+      nwords = atom->count_words(line);
+    }
+
+    if (nwords != params_per_line)
+      error->all(FLERR,"Incorrect format in Stillinger-Weber potential file");
+
+    // words = ptrs to all words in line
+
+    nwords = 0;
+    words[nwords++] = strtok(line," \t\n\r\f");
+    while ((words[nwords++] = strtok(NULL," \t\n\r\f"))) continue;
+
+    // ielement,jelement,kelement = 1st args
+    // if all 3 args are in element list, then parse this line
+    // else skip to next entry in file
+
+    for (ielement = 0; ielement < nelements; ielement++)
+      if (strcmp(words[0],elements[ielement]) == 0) break;
+    if (ielement == nelements) continue;
+    for (jelement = 0; jelement < nelements; jelement++)
+      if (strcmp(words[1],elements[jelement]) == 0) break;
+    if (jelement == nelements) continue;
+    for (kelement = 0; kelement < nelements; kelement++)
+      if (strcmp(words[2],elements[kelement]) == 0) break;
+    if (kelement == nelements) continue;
+
+    // load up parameter settings and error check their values
+
+    params[nparams].ielement = ielement;
+    params[nparams].jelement = jelement;
+    params[nparams].epsilon = atof(words[3]);
+    params[nparams].sigma = atof(words[4]);
+
+    if (params[nparams].epsilon < 0.0 || params[nparams].sigma < 0.0)
+      error->all(FLERR,"Illegal AGNI parameter");
+
+    nparams++;
+  }
+
+  delete [] words;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairAGNI::setup_params()
+{
+  int i,j,k,m,n;
+  double rtmp;
+
+#if 0
+  // set elem2param for all triplet combinations
+  // must be a single exact match to lines read from file
+  // do not allow for ACB in place of ABC
+
+  memory->destroy(elem2param);
+  memory->create(elem2param,nelements,nelements,nelements,"pair:elem2param");
+
+  for (i = 0; i < nelements; i++)
+    for (j = 0; j < nelements; j++)
+      for (k = 0; k < nelements; k++) {
+        n = -1;
+        for (m = 0; m < nparams; m++) {
+          if (i == params[m].ielement && j == params[m].jelement &&
+              k == params[m].kelement) {
+            if (n >= 0) error->all(FLERR,"Potential file has duplicate entry");
+            n = m;
+          }
+        }
+        if (n < 0) error->all(FLERR,"Potential file is missing an entry");
+        elem2param[i][j][k] = n;
+      }
+
+
+  // compute parameter values derived from inputs
+
+  // set cutsq using shortcut to reduce neighbor list for accelerated
+  // calculations. cut must remain unchanged as it is a potential parameter
+  // (cut = a*sigma)
+
+  for (m = 0; m < nparams; m++) {
+    params[m].cut = params[m].sigma*params[m].littlea;
+
+    rtmp = params[m].cut;
+    if (params[m].tol > 0.0) {
+      if (params[m].tol > 0.01) params[m].tol = 0.01;
+      if (params[m].gamma < 1.0)
+        rtmp = rtmp +
+          params[m].gamma * params[m].sigma / log(params[m].tol);
+      else rtmp = rtmp +
+             params[m].sigma / log(params[m].tol);
+    }
+    params[m].cutsq = rtmp * rtmp;
+
+    params[m].sigma_gamma = params[m].sigma*params[m].gamma;
+    params[m].lambda_epsilon = params[m].lambda*params[m].epsilon;
+    params[m].lambda_epsilon2 = 2.0*params[m].lambda*params[m].epsilon;
+    params[m].c1 = params[m].biga*params[m].epsilon *
+      params[m].powerp*params[m].bigb *
+      pow(params[m].sigma,params[m].powerp);
+    params[m].c2 = params[m].biga*params[m].epsilon*params[m].powerq *
+      pow(params[m].sigma,params[m].powerq);
+    params[m].c3 = params[m].biga*params[m].epsilon*params[m].bigb *
+      pow(params[m].sigma,params[m].powerp+1.0);
+    params[m].c4 = params[m].biga*params[m].epsilon *
+      pow(params[m].sigma,params[m].powerq+1.0);
+    params[m].c5 = params[m].biga*params[m].epsilon*params[m].bigb *
+      pow(params[m].sigma,params[m].powerp);
+    params[m].c6 = params[m].biga*params[m].epsilon *
+      pow(params[m].sigma,params[m].powerq);
+  }
+
+  // set cutmax to max of all params
+
+  cutmax = 0.0;
+  for (m = 0; m < nparams; m++) {
+    rtmp = sqrt(params[m].cutsq);
+    if (rtmp > cutmax) cutmax = rtmp;
+  }
+#endif
+}
+

src/USER-MISC/pair_agni.h

+/* -*- 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.
+------------------------------------------------------------------------- */
+
+#ifdef PAIR_CLASS
+
+PairStyle(agni,PairAGNI)
+
+#else
+
+#ifndef LMP_PAIR_AGNI_H
+#define LMP_PAIR_AGNI_H
+
+#include "pair.h"
+
+namespace LAMMPS_NS {
+
+class PairAGNI : public Pair {
+ public:
+  PairAGNI(class LAMMPS *);
+  virtual ~PairAGNI();
+  virtual void compute(int, int);
+  void settings(int, char **);
+  virtual void coeff(int, char **);
+  virtual double init_one(int, int);
+  virtual void init_style();
+
+  struct Param {
+    double epsilon,sigma;
+    double cut,cutsq;
+    int ielement,jelement;
+  };
+
+ protected:
+  double cutmax;                // max cutoff for all elements
+  int nelements;                // # of unique atom type labels
+  char **elements;              // names of unique elements
+  int *map;                     // mapping from atom types to elements
+  int nparams;                  // # of stored parameter sets
+  Param *params;                // parameter set for an I-J interaction
+
+  virtual void allocate();
+  void read_file(char *);
+  virtual void setup_params();
+};
+
+}
+
+#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: Cannot open AGNI potential file %s
+
+The specified AGNI potential file cannot be opened.  Check that the path
+and name are correct.
+
+E: Incorrect format in AGNI potential file
+
+The potential file is not compatible with the AGNI pair style
+implementation in this LAMMPS version.
+
+*/