Commit 9b0987d8 authored by Axel Kohlmeyer's avatar Axel Kohlmeyer
Browse files

first complete implementation of AGNI pair style

parent e453adaf

src/USER-MISC/pair_agni.cpp

+70 −92
Original line number Diff line number Diff line
@@ -31,10 +31,11 @@ 
#include "memory.h"

#include "error.h"

#include "citeme.h"

#include "math_special.h"

#include "math_const.h"



using namespace LAMMPS_NS;



#define AGNI_VERSION 1

using namespace MathSpecial;



static const char cite_pair_agni[] =

  "pair agni command:\n\n"
@@ -61,10 +62,14 @@ static const char cite_pair_agni[] = 
  " publisher = {APS}\n"

  "}\n\n";





#define AGNI_VERSION 1

#define MAXLINE 10240

#define MAXWORD 40

#define DELTA 4



struct _3vec {

  double x,y,z;

};

typedef struct _3vec _3vec_t;



/* ---------------------------------------------------------------------- */
@@ -79,6 +84,7 @@ PairAGNI::PairAGNI(LAMMPS *lmp) : Pair(lmp) 


  nelements = 0;

  elements = NULL;

  elem2param = NULL;

  nparams = 0;

  params = NULL;

  map = NULL;
@@ -119,24 +125,17 @@ PairAGNI::~PairAGNI() 


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 i,j,k,ii,jj,inum,jnum,itype;

  double xtmp,ytmp,ztmp,delx,dely,delz;

  double rsq;

  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;
@@ -144,18 +143,22 @@ void PairAGNI::compute(int eflag, int vflag) 
  firstneigh = list->firstneigh;



  double fxtmp,fytmp,fztmp;

  _3vec_t *V;



  // 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;



    const Param &iparam = params[elem2param[itype]];

    V = new _3vec_t[iparam.numeta];

    memset(V,0,iparam.numeta *sizeof(_3vec_t));



    jlist = firstneigh[i];

    jnum = numneigh[i];
@@ -168,23 +171,42 @@ void PairAGNI::compute(int eflag, int vflag) 
      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) {

      if ((rsq > 0.0) && (rsq < iparam.cutsq)) {

        const double r = sqrt(rsq);

        const double cF = 0.5*(cos((MathConst::MY_PI*r)/iparam.cut)+1.0);

        const double wX = cF*delx/r;

        const double wY = cF*dely/r;

        const double wZ = cF*delz/r;

        

        // XXX compute force

        for (k = 0; k < iparam.numeta; ++k) {

          const double e = exp(-(iparam.eta[k]*rsq));

          V[k].x += wX*e;

          V[k].y += wY*e;

          V[k].z += wZ*e;

        }

      }

    }



        fxtmp += delx*fpair;

        fytmp += dely*fpair;

        fztmp += delz*fpair;

    for (j = 0; j < iparam.numtrain; ++j) {

      double kx = 0.0;

      double ky = 0.0;

      double kz = 0.0;    



        if (evflag) ev_tally(i,j,nlocal,newton_pair,

                             0,0.0,fpair,delx,dely,delz);

      for(int k = 0; k < iparam.numeta; ++k) {

        const double xu = iparam.xU[k][j];

        kx += square(V[k].x - xu);  

        ky += square(V[k].y - xu);

        kz += square(V[k].z - xu);        

      }

      const double e = -0.5/(square(iparam.sigma));

      fxtmp += iparam.alpha[j]*exp(kx*e);

      fytmp += iparam.alpha[j]*exp(ky*e);

      fztmp += iparam.alpha[j]*exp(kz*e);

    }

    f[i][0] += fxtmp;

    f[i][1] += fytmp;

    f[i][2] += fztmp;

    f[i][0] += fxtmp + iparam.b;

    f[i][1] += fytmp + iparam.b;

    f[i][2] += fztmp + iparam.b;

    delete [] V;

  }



  if (vflag_fdotr) virial_fdotr_compute();
@@ -315,7 +337,8 @@ void PairAGNI::read_file(char *file) 
  params = NULL;

  nparams = 0;



  // open file on proc 0

  // open file on proc 0 only

  // then read line by line and broadcast the line to all MPI ranks



  FILE *fp;

  if (comm->me == 0) {
@@ -327,11 +350,7 @@ void PairAGNI::read_file(char *file) 
    }

  }



  // 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 i,j,n,nwords,curparam,wantdata,numdata;

  int i,j,n,nwords,curparam,wantdata;

  char line[MAXLINE],*ptr;

  int eof = 0;

  char **words = new char*[MAXWORD+1];
@@ -386,8 +405,8 @@ void PairAGNI::read_file(char *file) 
      for (i = 0; i < nparams; ++i) {

        for (j = 0; j < nelements; ++j)

          if (strcmp(words[i+1],elements[j]) == 0) break;

        if (j == nelements) params[nparams].ielement = params[nparams].jelement = -1;

        else params[nparams].ielement = params[nparams].jelement = j;

        if (j == nelements) params[i].ielement = -1;

        else params[i].ielement = j;

      }

    } else if (params && (nwords == 2) && (strcmp(words[0],"interaction") == 0)) {

      for (i = 0; i < nparams; ++i)
@@ -443,78 +462,37 @@ void PairAGNI::read_file(char *file) 


void PairAGNI::setup_params()

{

  int i,j,k,m,n;

  int i,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

  // set elem2param for all elements



  memory->destroy(elem2param);

  memory->create(elem2param,nelements,nelements,nelements,"pair:elem2param");

  memory->create(elem2param,nelements,"pair:elem2param");



  for (i = 0; i < nelements; i++)

    for (j = 0; j < nelements; j++)

      for (k = 0; k < nelements; k++) {

  for (i = 0; i < nelements; i++) {

    n = -1;

    for (m = 0; m < nparams; m++) {

          if (i == params[m].ielement && j == params[m].jelement &&

              k == params[m].kelement) {

      if (i == params[m].ielement) {

        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;

    elem2param[i] = 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)



  cutmax = 0.0;

  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

+2 −2
Original line number Diff line number Diff line
@@ -38,14 +38,14 @@ class PairAGNI : public Pair { 
    double cut,cutsq;

    double *eta,**xU,*yU,*alpha;

    double sigma,lambda,b;

    int numeta,numtrain;

    int ielement,jelement;

    int numeta,numtrain,ielement;

  };



 protected:

  double cutmax;                // max cutoff for all elements

  int nelements;                // # of unique atom type labels

  char **elements;              // names of unique elements

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

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

  int nparams;                  // # of stored parameter sets

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

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