dummy framework implementation for AGNI pair style

/pair_adp.cpp

/pair_adp.h

/pair_agni.cpp

/pair_agni.h

/pair_airebo.cpp

/pair_airebo.h

/pair_airebo_morse.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

}

/* -*- 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.

*/