pair_style lj/sf, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11

pair_style meam/spline, Alexander Stukowski (LLNL), alex at stukowski.com, 1 Feb 12

pair_style meam/sw/spline, Robert Rudd (LLNL), robert.rudd at llnl.gov, 1 Oct 12

pair_style nb3b/harmonic, Todd R. Zeitler, todd.zeitler at gmail.com, 6 Apr 13

pair_style tersoff/table, Luca Ferraro, luca.ferraro@caspur.it, 1 Dec 11

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

   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: Todd R. Zeitler (SNL)

   (based on Stillinger-Weber pair style)

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

#include "math.h"

#include "stdio.h"

#include "stdlib.h"

#include "string.h"

#include "pair_nb3b_harmonic.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"

using namespace LAMMPS_NS;

#define MAXLINE 1024

#define DELTA 4

#define SMALL 0.001

#define PI 3.141592653589793238462643383279 

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

PairNb3bHarmonic::PairNb3bHarmonic(LAMMPS *lmp) : Pair(lmp)

{

  single_enable = 0;

  one_coeff = 1;

  nelements = 0;

  elements = NULL;

  nparams = maxparam = 0;

  params = NULL;

  elem2param = NULL;

}

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

   check if allocated, since class can be destructed when incomplete

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

PairNb3bHarmonic::~PairNb3bHarmonic()

{

  if (elements)

    for (int i = 0; i < nelements; i++) delete [] elements[i];

  delete [] elements;

  memory->destroy(params);

  memory->destroy(elem2param);

  if (allocated) {

    memory->destroy(setflag);

    memory->destroy(cutsq);

    delete [] map;

  }

}

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

void PairNb3bHarmonic::compute(int eflag, int vflag)

{

  int i,j,k,ii,jj,kk,inum,jnum,jnumm1,itag,jtag;

  int itype,jtype,ktype,ijparam,ikparam,ijkparam;

  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;

  int *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;

  // 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];

    // two-body interactions, skip half of them

    jlist = firstneigh[i];

    jnum = numneigh[i];

    for (jj = 0; jj < jnum; jj++) {

      j = jlist[jj];

      j &= NEIGHMASK;

      jtag = tag[j];

      if (itag > jtag) {

	if ((itag+jtag) % 2 == 0) continue;

      } else if (itag < jtag) {

	if ((itag+jtag) % 2 == 1) continue;

      } else {

	if (x[j][2] < ztmp) continue;

	if (x[j][2] == ztmp && x[j][1] < ytmp) continue;

	if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;

      }

      jtype = map[type[j]];

      delx = xtmp - x[j][0];

      dely = ytmp - x[j][1];

      delz = ztmp - x[j][2];

      rsq = delx*delx + dely*dely + delz*delz;

      ijparam = elem2param[itype][jtype][jtype];

      if (rsq > params[ijparam].cutsq) continue;

    }

    jnumm1 = jnum - 1;

    for (jj = 0; jj < jnumm1; jj++) {

      j = jlist[jj];

      j &= NEIGHMASK;

      jtype = map[type[j]];

      ijparam = elem2param[itype][jtype][jtype];

      delr1[0] = x[j][0] - xtmp;

      delr1[1] = x[j][1] - ytmp;

      delr1[2] = x[j][2] - ztmp;

      rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2];

      if (rsq1 > params[ijparam].cutsq) continue;

      for (kk = jj+1; kk < jnum; kk++) {

	k = jlist[kk];

	k &= NEIGHMASK;

	ktype = map[type[k]];

	ikparam = elem2param[itype][ktype][ktype];

	ijkparam = elem2param[itype][jtype][ktype];

	delr2[0] = x[k][0] - xtmp;

	delr2[1] = x[k][1] - ytmp;

	delr2[2] = x[k][2] - ztmp;

	rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];

	if (rsq2 > params[ikparam].cutsq) continue;

        threebody(&params[ijparam],&params[ikparam],&params[ijkparam],

                  rsq1,rsq2,delr1,delr2,fj,fk,eflag,evdwl);

	f[i][0] -= fj[0] + fk[0];

	f[i][1] -= fj[1] + fk[1];

	f[i][2] -= fj[2] + fk[2];

	f[j][0] += fj[0];

	f[j][1] += fj[1];

	f[j][2] += fj[2];

	f[k][0] += fk[0];

	f[k][1] += fk[1];

	f[k][2] += fk[2];

	if (evflag) ev_tally3(i,j,k,evdwl,0.0,fj,fk,delr1,delr2);

      }

    }

  }

  if (vflag_fdotr) virial_fdotr_compute();

}

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

void PairNb3bHarmonic::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 PairNb3bHarmonic::settings(int narg, char **arg)

{

  if (narg != 0) error->all(FLERR,"Illegal pair_style command");

}

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

   set coeffs for one or more type pairs

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

void PairNb3bHarmonic::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();

  // 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 PairNb3bHarmonic::init_style()

{

  if (atom->tag_enable == 0)

    error->all(FLERR,"Pair style nb3b/harmonic requires atom IDs");

  if (force->newton_pair == 0)

    error->all(FLERR,"Pair style nb3b/harmonic requires newton pair on");

  // need a full neighbor list

  int irequest = neighbor->request(this);

  neighbor->requests[irequest]->half = 0;

  neighbor->requests[irequest]->full = 1;

}

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

   init for one type pair i,j and corresponding j,i

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

double PairNb3bHarmonic::init_one(int i, int j)

{

  if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");

  return cutmax;

}

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

void PairNb3bHarmonic::read_file(char *file)

{

  int params_per_line = 6;

  char **words = new char*[params_per_line+1];

  memory->sfree(params);

  params = NULL;

  nparams = maxparam = 0;

  // open file on proc 0

  FILE *fp;

  if (comm->me == 0) {

    fp = fopen(file,"r");

    if (fp == NULL) {

      char str[128];

      sprintf(str,"Cannot open nb3b/harmonic 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 nb3b/harmonic 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

    if (nparams == maxparam) {

      maxparam += DELTA;

      params = (Param *) memory->srealloc(params,maxparam*sizeof(Param),

					  "pair:params");

    }

    params[nparams].ielement = ielement;

    params[nparams].jelement = jelement;

    params[nparams].kelement = kelement;

    params[nparams].k_theta = atof(words[3]);

    params[nparams].theta0 = atof(words[4]);

    params[nparams].cutoff = atof(words[5]);

    if (params[nparams].k_theta < 0.0 || params[nparams].theta0 < 0.0 ||

        params[nparams].cutoff < 0.0) 

      error->all(FLERR,"Illegal nb3b/harmonic parameter");

    nparams++;

  }

  delete [] words;

}

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

void PairNb3bHarmonic::setup()

{

  int i,j,k,m,n;

  double rtmp;

  // 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].cutoff;

    params[m].cutsq = params[m].cut * params[m].cut;

    params[m].theta0 = params[m].theta0 / 180.0 * PI;

  }

  // 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;

  }

}  

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

void PairNb3bHarmonic::threebody(Param *paramij, Param *paramik, 

                                 Param *paramijk,

                                 double rsq1, double rsq2,

                                 double *delr1, double *delr2,

                                 double *fj, double *fk, int eflag, double &eng)

{

  double dtheta,tk;

  double r1,r2,c,s,a,a11,a12,a22;

  // angle (cos and sin)

  r1 = sqrt(rsq1);

  r2 = sqrt(rsq2);

  c = delr1[0]*delr2[0] + delr1[1]*delr2[1] + delr1[2]*delr2[2];

  c /= r1*r2;

  if (c > 1.0) c = 1.0;

  if (c < -1.0) c = -1.0;

  s = sqrt(1.0 - c*c);

  if (s < SMALL) s = SMALL;

  s = 1.0/s;

  // force & energy

  dtheta = acos(c) - paramijk->theta0;

  tk = paramijk->k_theta * dtheta;

  if (eflag) eng = tk*dtheta;

  a = -2.0 * tk * s;

  a11 = a*c / rsq1;

  a12 = -a / (r1*r2);

  a22 = a*c / rsq2;

  fj[0] = a11*delr1[0] + a12*delr2[0];

  fj[1] = a11*delr1[1] + a12*delr2[1];

  fj[2] = a11*delr1[2] + a12*delr2[2];

  fk[0] = a22*delr2[0] + a12*delr1[0];

  fk[1] = a22*delr2[1] + a12*delr1[1];

  fk[2] = a22*delr2[2] + a12*delr1[2];

}

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

   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(nb3b/harmonic,PairNb3bHarmonic)

#else

#ifndef LMP_PAIR_NB3B_HARMONIC_H

#define LMP_PAIR_NB3B_HARMONIC_H

#include "pair.h"

namespace LAMMPS_NS {

class PairNb3bHarmonic : public Pair {

 public:

  PairNb3bHarmonic(class LAMMPS *);

  ~PairNb3bHarmonic();

  void compute(int, int);

  void settings(int, char **);

  void coeff(int, char **);

  double init_one(int, int);

  void init_style();

 private:

  struct Param {

    double k_theta, theta0, cutoff;

    double cut,cutsq;

    int ielement,jelement,kelement;

  };

  double cutmax;                // max cutoff for all elements

  int nelements;                // # of unique elements

  char **elements;              // names of unique elements

  int ***elem2param;            // mapping from element triplets to parameters

  int *map;                     // mapping from atom types to elements

  int nparams;                  // # of stored parameter sets

  int maxparam;                 // max # of parameter sets

  Param *params;                // parameter set for an I-J-K interaction

  void allocate();

  void read_file(char *);

  void setup();

  void twobody(Param *, double, double &, int, double &);

  void threebody(Param *, Param *, Param *, double, double, double *, double *,

		 double *, double *, int, double &);

};

}

#endif

#endif