lammps/src/SNAP/pair_snap.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.
------------------------------------------------------------------------- */

#include "pair_snap.h"
#include <mpi.h>
#include <cmath>
#include <cstdlib>
#include <cstring>
#include "atom.h"
#include "force.h"
#include "comm.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "sna.h"
#include "memory.h"
#include "error.h"
#include "utils.h"

using namespace LAMMPS_NS;

#define MAXLINE 1024
#define MAXWORD 3

/* ---------------------------------------------------------------------- */

PairSNAP::PairSNAP(LAMMPS *lmp) : Pair(lmp)
{
  single_enable = 0;
  restartinfo = 0;
  one_coeff = 1;
  manybody_flag = 1;

  nelements = 0;
  elements = NULL;
  radelem = NULL;
  wjelem = NULL;
  coeffelem = NULL;

  beta_max = 0;
  beta = NULL;
  bispectrum = NULL;
  snaptr = NULL;
}

/* ---------------------------------------------------------------------- */

PairSNAP::~PairSNAP()
{
  if (copymode) return;

  if (nelements) {
    for (int i = 0; i < nelements; i++)
      delete[] elements[i];
    delete[] elements;
    memory->destroy(radelem);
    memory->destroy(wjelem);
    memory->destroy(coeffelem);
  }

  memory->destroy(beta);
  memory->destroy(bispectrum);

  delete snaptr;

  if (allocated) {
    memory->destroy(setflag);
    memory->destroy(cutsq);
    memory->destroy(map);
  }

}

/* ----------------------------------------------------------------------
   This version is a straightforward implementation
   ---------------------------------------------------------------------- */

void PairSNAP::compute(int eflag, int vflag)
{
  int i,j,jnum,ninside;
  double delx,dely,delz,evdwl,rsq;
  double fij[3];
  int *jlist,*numneigh,**firstneigh;
  evdwl = 0.0;

  ev_init(eflag,vflag);

  double **x = atom->x;
  double **f = atom->f;
  int *type = atom->type;
  int nlocal = atom->nlocal;
  int newton_pair = force->newton_pair;

  if (beta_max < list->inum) {
    memory->grow(beta,list->inum,ncoeff,"PairSNAP:beta");
    memory->grow(bispectrum,list->inum,ncoeff,"PairSNAP:bispectrum");
    beta_max = list->inum;
  }

  // compute dE_i/dB_i = beta_i for all i in list

  if (quadraticflag || eflag)
    compute_bispectrum();
  compute_beta();

  numneigh = list->numneigh;
  firstneigh = list->firstneigh;

  for (int ii = 0; ii < list->inum; ii++) {
    i = list->ilist[ii];

    const double xtmp = x[i][0];
    const double ytmp = x[i][1];
    const double ztmp = x[i][2];
    const int itype = type[i];
    const int ielem = map[itype];
    const double radi = radelem[ielem];

    jlist = firstneigh[i];
    jnum = numneigh[i];

    // insure rij, inside, wj, and rcutij are of size jnum

    snaptr->grow_rij(jnum);

    // rij[][3] = displacements between atom I and those neighbors
    // inside = indices of neighbors of I within cutoff
    // wj = weights for neighbors of I within cutoff
    // rcutij = cutoffs for neighbors of I within cutoff
    // note Rij sign convention => dU/dRij = dU/dRj = -dU/dRi

    ninside = 0;
    for (int jj = 0; jj < jnum; jj++) {
      j = jlist[jj];
      j &= NEIGHMASK;
      delx = x[j][0] - xtmp;
      dely = x[j][1] - ytmp;
      delz = x[j][2] - ztmp;
      rsq = delx*delx + dely*dely + delz*delz;
      int jtype = type[j];
      int jelem = map[jtype];

      if (rsq < cutsq[itype][jtype]&&rsq>1e-20) {
        snaptr->rij[ninside][0] = delx;
        snaptr->rij[ninside][1] = dely;
        snaptr->rij[ninside][2] = delz;
        snaptr->inside[ninside] = j;
        snaptr->wj[ninside] = wjelem[jelem];
        snaptr->rcutij[ninside] = (radi + radelem[jelem])*rcutfac;
        ninside++;
      }
    }

    // compute Ui, Yi for atom I

    snaptr->compute_ui(ninside);

    // for neighbors of I within cutoff:
    // compute Fij = dEi/dRj = -dEi/dRi
    // add to Fi, subtract from Fj

    snaptr->compute_yi(beta[ii]);

    for (int jj = 0; jj < ninside; jj++) {
      int j = snaptr->inside[jj];
      snaptr->compute_duidrj(snaptr->rij[jj],
                             snaptr->wj[jj],snaptr->rcutij[jj],jj);

      snaptr->compute_deidrj(fij);

      f[i][0] += fij[0];
      f[i][1] += fij[1];
      f[i][2] += fij[2];
      f[j][0] -= fij[0];
      f[j][1] -= fij[1];
      f[j][2] -= fij[2];

      // tally per-atom virial contribution

      if (vflag)
        ev_tally_xyz(i,j,nlocal,newton_pair,0.0,0.0,
                     fij[0],fij[1],fij[2],
                     -snaptr->rij[jj][0],-snaptr->rij[jj][1],
                     -snaptr->rij[jj][2]);
    }

    // tally energy contribution

    if (eflag) {

      // evdwl = energy of atom I, sum over coeffs_k * Bi_k

      double* coeffi = coeffelem[ielem];
      evdwl = coeffi[0];

      // E = beta.B + 0.5*B^t.alpha.B

      // linear contributions

      for (int icoeff = 0; icoeff < ncoeff; icoeff++)
        evdwl += coeffi[icoeff+1]*bispectrum[ii][icoeff];

      // quadratic contributions

      if (quadraticflag) {
        int k = ncoeff+1;
        for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
          double bveci = bispectrum[ii][icoeff];
          evdwl += 0.5*coeffi[k++]*bveci*bveci;
          for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++) {
            double bvecj = bispectrum[ii][jcoeff];
            evdwl += coeffi[k++]*bveci*bvecj;
          }
        }
      }
      ev_tally_full(i,2.0*evdwl,0.0,0.0,0.0,0.0,0.0);
    }

  }

  if (vflag_fdotr) virial_fdotr_compute();
}

/* ----------------------------------------------------------------------
   compute beta
------------------------------------------------------------------------- */

void PairSNAP::compute_beta()
{
  int i;
  int *type = atom->type;

  for (int ii = 0; ii < list->inum; ii++) {
    i = list->ilist[ii];
    const int itype = type[i];
    const int ielem = map[itype];
    double* coeffi = coeffelem[ielem];

    for (int icoeff = 0; icoeff < ncoeff; icoeff++)
      beta[ii][icoeff] = coeffi[icoeff+1];

    if (quadraticflag) {
      int k = ncoeff+1;
      for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
        double bveci = bispectrum[ii][icoeff];
        beta[ii][icoeff] += coeffi[k]*bveci;
        k++;
        for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++) {
          double bvecj = bispectrum[ii][jcoeff];
          beta[ii][icoeff] += coeffi[k]*bvecj;
          beta[ii][jcoeff] += coeffi[k]*bveci;
          k++;
        }
      }
    }
  }
}

/* ----------------------------------------------------------------------
   compute bispectrum
------------------------------------------------------------------------- */

void PairSNAP::compute_bispectrum()
{
  int i,j,jnum,ninside;
  double delx,dely,delz,rsq;
  int *jlist;

  double **x = atom->x;
  int *type = atom->type;

  for (int ii = 0; ii < list->inum; ii++) {
    i = list->ilist[ii];

    const double xtmp = x[i][0];
    const double ytmp = x[i][1];
    const double ztmp = x[i][2];
    const int itype = type[i];
    const int ielem = map[itype];
    const double radi = radelem[ielem];

    jlist = list->firstneigh[i];
    jnum = list->numneigh[i];

    // insure rij, inside, wj, and rcutij are of size jnum

    snaptr->grow_rij(jnum);

    // rij[][3] = displacements between atom I and those neighbors
    // inside = indices of neighbors of I within cutoff
    // wj = weights for neighbors of I within cutoff
    // rcutij = cutoffs for neighbors of I within cutoff
    // note Rij sign convention => dU/dRij = dU/dRj = -dU/dRi

    ninside = 0;
    for (int jj = 0; jj < jnum; jj++) {
      j = jlist[jj];
      j &= NEIGHMASK;
      delx = x[j][0] - xtmp;
      dely = x[j][1] - ytmp;
      delz = x[j][2] - ztmp;
      rsq = delx*delx + dely*dely + delz*delz;
      int jtype = type[j];
      int jelem = map[jtype];

      if (rsq < cutsq[itype][jtype]&&rsq>1e-20) {
        snaptr->rij[ninside][0] = delx;
        snaptr->rij[ninside][1] = dely;
        snaptr->rij[ninside][2] = delz;
        snaptr->inside[ninside] = j;
        snaptr->wj[ninside] = wjelem[jelem];
        snaptr->rcutij[ninside] = (radi + radelem[jelem])*rcutfac;
        ninside++;
      }
    }

    snaptr->compute_ui(ninside);
    snaptr->compute_zi();
    snaptr->compute_bi();

    for (int icoeff = 0; icoeff < ncoeff; icoeff++)
      bispectrum[ii][icoeff] = snaptr->blist[icoeff];
  }
}

/* ----------------------------------------------------------------------
   allocate all arrays
------------------------------------------------------------------------- */

void PairSNAP::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");
  memory->create(map,n+1,"pair:map");
}

/* ----------------------------------------------------------------------
   global settings
------------------------------------------------------------------------- */

void PairSNAP::settings(int narg, char ** /* arg */)
{
  if (narg > 0)
    error->all(FLERR,"Illegal pair_style command");
}

/* ----------------------------------------------------------------------
   set coeffs for one or more type pairs
------------------------------------------------------------------------- */

void PairSNAP::coeff(int narg, char **arg)
{
  if (narg < 5) error->all(FLERR,"Incorrect args for pair coefficients");
  if (!allocated) allocate();

  if (nelements) {
    for (int i = 0; i < nelements; i++)
      delete[] elements[i];
    delete[] elements;
    memory->destroy(radelem);
    memory->destroy(wjelem);
    memory->destroy(coeffelem);
  }

  char* type1 = arg[0];
  char* type2 = arg[1];
  char* coefffilename = arg[2];
  char* paramfilename = arg[3];
  char** elemtypes = &arg[4];

  // insure I,J args are * *

  if (strcmp(type1,"*") != 0 || strcmp(type2,"*") != 0)
    error->all(FLERR,"Incorrect args for pair coefficients");

  // read snapcoeff and snapparam files

  read_files(coefffilename,paramfilename);

  if (!quadraticflag)
    ncoeff = ncoeffall - 1;
  else {

    // ncoeffall should be (ncoeff+2)*(ncoeff+1)/2
    // so, ncoeff = floor(sqrt(2*ncoeffall))-1

    ncoeff = sqrt(2*ncoeffall)-1;
    ncoeffq = (ncoeff*(ncoeff+1))/2;
    int ntmp = 1+ncoeff+ncoeffq;
    if (ntmp != ncoeffall) {
      printf("ncoeffall = %d ntmp = %d ncoeff = %d \n",ncoeffall,ntmp,ncoeff);
      error->all(FLERR,"Incorrect SNAP coeff file");
    }
  }

  // read args that map atom types to SNAP elements
  // map[i] = which element the Ith atom type is, -1 if not mapped
  // map[0] is not used

  for (int i = 1; i <= atom->ntypes; i++) {
    char* elemname = elemtypes[i-1];
    int jelem;
    for (jelem = 0; jelem < nelements; jelem++)
      if (strcmp(elemname,elements[jelem]) == 0)
        break;

    if (jelem < nelements)
      map[i] = jelem;
    else if (strcmp(elemname,"NULL") == 0) map[i] = -1;
    else error->all(FLERR,"Incorrect args for pair coefficients");
  }

  // clear setflag since coeff() called once with I,J = * *

  int 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");

  snaptr = new SNA(lmp,rfac0,twojmax,
                   rmin0,switchflag,bzeroflag);

  if (ncoeff != snaptr->ncoeff) {
    if (comm->me == 0)
      printf("ncoeff = %d snancoeff = %d \n",ncoeff,snaptr->ncoeff);
    error->all(FLERR,"Incorrect SNAP parameter file");
  }

  // Calculate maximum cutoff for all elements

  rcutmax = 0.0;
  for (int ielem = 0; ielem < nelements; ielem++)
    rcutmax = MAX(2.0*radelem[ielem]*rcutfac,rcutmax);

}

/* ----------------------------------------------------------------------
   init specific to this pair style
------------------------------------------------------------------------- */

void PairSNAP::init_style()
{
  if (force->newton_pair == 0)
    error->all(FLERR,"Pair style SNAP requires newton pair on");

  // need a full neighbor list

  int irequest = neighbor->request(this,instance_me);
  neighbor->requests[irequest]->half = 0;
  neighbor->requests[irequest]->full = 1;

  snaptr->init();

}

/* ----------------------------------------------------------------------
   init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */

double PairSNAP::init_one(int i, int j)
{
  if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
  return (radelem[map[i]] +
          radelem[map[j]])*rcutfac;
}

/* ---------------------------------------------------------------------- */

void PairSNAP::read_files(char *coefffilename, char *paramfilename)
{

  // open SNAP coefficient file on proc 0

  FILE *fpcoeff;
  if (comm->me == 0) {
    fpcoeff = force->open_potential(coefffilename);
    if (fpcoeff == NULL) {
      char str[128];
      snprintf(str,128,"Cannot open SNAP coefficient file %s",coefffilename);
      error->one(FLERR,str);
    }
  }

  char line[MAXLINE],*ptr;
  int eof = 0;

  int n;
  int nwords = 0;
  while (nwords == 0) {
    if (comm->me == 0) {
      ptr = fgets(line,MAXLINE,fpcoeff);
      if (ptr == NULL) {
        eof = 1;
        fclose(fpcoeff);
      } 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 = utils::count_words(line);
  }
  if (nwords != 2)
    error->all(FLERR,"Incorrect format in SNAP coefficient file");

  // words = ptrs to all words in line
  // strip single and double quotes from words

  char* words[MAXWORD];
  int iword = 0;
  words[iword] = strtok(line,"' \t\n\r\f");
  iword = 1;
  words[iword] = strtok(NULL,"' \t\n\r\f");

  nelements = atoi(words[0]);
  ncoeffall = atoi(words[1]);

  // set up element lists

  elements = new char*[nelements];
  memory->create(radelem,nelements,"pair:radelem");
  memory->create(wjelem,nelements,"pair:wjelem");
  memory->create(coeffelem,nelements,ncoeffall,"pair:coeffelem");

  // Loop over nelements blocks in the SNAP coefficient file

  for (int ielem = 0; ielem < nelements; ielem++) {

    if (comm->me == 0) {
      ptr = fgets(line,MAXLINE,fpcoeff);
      if (ptr == NULL) {
        eof = 1;
        fclose(fpcoeff);
      } else n = strlen(line) + 1;
    }
    MPI_Bcast(&eof,1,MPI_INT,0,world);
    if (eof)
      error->all(FLERR,"Incorrect format in SNAP coefficient file");
    MPI_Bcast(&n,1,MPI_INT,0,world);
    MPI_Bcast(line,n,MPI_CHAR,0,world);

    nwords = utils::trim_and_count_words(line);
    if (nwords != 3)
      error->all(FLERR,"Incorrect format in SNAP coefficient file");

    iword = 0;
    words[iword] = strtok(line,"' \t\n\r\f");
    iword = 1;
    words[iword] = strtok(NULL,"' \t\n\r\f");
    iword = 2;
    words[iword] = strtok(NULL,"' \t\n\r\f");

    char* elemtmp = words[0];
    int n = strlen(elemtmp) + 1;
    elements[ielem] = new char[n];
    strcpy(elements[ielem],elemtmp);

    radelem[ielem] = atof(words[1]);
    wjelem[ielem] = atof(words[2]);


    if (comm->me == 0) {
      if (screen) fprintf(screen,"SNAP Element = %s, Radius %g, Weight %g \n",
                          elements[ielem], radelem[ielem], wjelem[ielem]);
      if (logfile) fprintf(logfile,"SNAP Element = %s, Radius %g, Weight %g \n",
                          elements[ielem], radelem[ielem], wjelem[ielem]);
    }

    for (int icoeff = 0; icoeff < ncoeffall; icoeff++) {
      if (comm->me == 0) {
        ptr = fgets(line,MAXLINE,fpcoeff);
        if (ptr == NULL) {
          eof = 1;
          fclose(fpcoeff);
        } else n = strlen(line) + 1;
      }

      MPI_Bcast(&eof,1,MPI_INT,0,world);
      if (eof)
        error->all(FLERR,"Incorrect format in SNAP coefficient file");
      MPI_Bcast(&n,1,MPI_INT,0,world);
      MPI_Bcast(line,n,MPI_CHAR,0,world);

      nwords = utils::trim_and_count_words(line);
      if (nwords != 1)
        error->all(FLERR,"Incorrect format in SNAP coefficient file");

      iword = 0;
      words[iword] = strtok(line,"' \t\n\r\f");

      coeffelem[ielem][icoeff] = atof(words[0]);

    }
  }

  if (comm->me == 0) fclose(fpcoeff);

  // set flags for required keywords

  rcutfacflag = 0;
  twojmaxflag = 0;

  // Set defaults for optional keywords

  rfac0 = 0.99363;
  rmin0 = 0.0;
  switchflag = 1;
  bzeroflag = 1;
  quadraticflag = 0;
  chunksize = 2000;

  // open SNAP parameter file on proc 0

  FILE *fpparam;
  if (comm->me == 0) {
    fpparam = force->open_potential(paramfilename);
    if (fpparam == NULL) {
      char str[128];
      snprintf(str,128,"Cannot open SNAP parameter file %s",paramfilename);
      error->one(FLERR,str);
    }
  }

  eof = 0;
  while (1) {
    if (comm->me == 0) {
      ptr = fgets(line,MAXLINE,fpparam);
      if (ptr == NULL) {
        eof = 1;
        fclose(fpparam);
      } 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 = utils::count_words(line);
    if (nwords == 0) continue;

    if (nwords != 2)
      error->all(FLERR,"Incorrect format in SNAP parameter file");

    // words = ptrs to all words in line
    // strip single and double quotes from words

    char* keywd = strtok(line,"' \t\n\r\f");
    char* keyval = strtok(NULL,"' \t\n\r\f");

    if (comm->me == 0) {
      if (screen) fprintf(screen,"SNAP keyword %s %s \n",keywd,keyval);
      if (logfile) fprintf(logfile,"SNAP keyword %s %s \n",keywd,keyval);
    }

    if (strcmp(keywd,"rcutfac") == 0) {
      rcutfac = atof(keyval);
      rcutfacflag = 1;
    } else if (strcmp(keywd,"twojmax") == 0) {
      twojmax = atoi(keyval);
      twojmaxflag = 1;
    } else if (strcmp(keywd,"rfac0") == 0)
      rfac0 = atof(keyval);
    else if (strcmp(keywd,"rmin0") == 0)
      rmin0 = atof(keyval);
    else if (strcmp(keywd,"switchflag") == 0)
      switchflag = atoi(keyval);
    else if (strcmp(keywd,"bzeroflag") == 0)
      bzeroflag = atoi(keyval);
    else if (strcmp(keywd,"quadraticflag") == 0)
      quadraticflag = atoi(keyval);
    else if (strcmp(keywd,"chunksize") == 0)
      chunksize = atoi(keyval);
    else
      error->all(FLERR,"Incorrect SNAP parameter file");
  }

  if (rcutfacflag == 0 || twojmaxflag == 0)
    error->all(FLERR,"Incorrect SNAP parameter file");

}

/* ----------------------------------------------------------------------
   memory usage
------------------------------------------------------------------------- */

double PairSNAP::memory_usage()
{
  double bytes = Pair::memory_usage();

  int n = atom->ntypes+1;
  bytes += n*n*sizeof(int);      // setflag
  bytes += n*n*sizeof(double);   // cutsq
  bytes += n*sizeof(int);        // map
  bytes += beta_max*ncoeff*sizeof(double); // bispectrum
  bytes += beta_max*ncoeff*sizeof(double); // beta

  bytes += snaptr->memory_usage(); // SNA object

  return bytes;
}