Commit fdaa3f48 authored by Mingjian Wen's avatar Mingjian Wen
Browse files

Modify all methods other than compute

parent 2bdd9b75

src/USER-MISC/pair_drip.cpp

+69 −100
Original line number Diff line number Diff line
@@ -54,9 +54,9 @@ PairDRIP::PairDRIP(LAMMPS *lmp) : Pair(lmp) 
  nparams = maxparam = 0;

  params = NULL;

  elem2param = NULL;

  cutDRIPsq = NULL;

  map = NULL;



  cutmax = 0.0;

  nmax = 0;

  maxlocal = 0;

  DRIP_numneigh = NULL;
@@ -68,9 +68,6 @@ PairDRIP::PairDRIP(LAMMPS *lmp) : Pair(lmp) 
  dnormal = NULL;

  dnormdri = NULL;



  // always compute energy offset

  offset_flag = 1;



  // set comm size needed by this Pair

  comm_forward = 39;

  tap_flag = 0;
@@ -90,8 +87,6 @@ PairDRIP::~PairDRIP() 
  if (allocated) {

    memory->destroy(setflag);

    memory->destroy(cutsq);

    memory->destroy(cut);

    memory->destroy(offset);

  }



  if (elements)
@@ -99,7 +94,6 @@ PairDRIP::~PairDRIP() 
  delete [] elements;

  memory->destroy(params);

  memory->destroy(elem2param);

  memory->destroy(cutDRIPsq);

  if (allocated) delete [] map;

}
@@ -300,7 +294,7 @@ void PairDRIP::compute(int eflag, int vflag) 


        if (eflag) {

          if (tap_flag) evdwl = Tap*Vkc;

          else  evdwl = Vkc - offset[itype][jtype];

          else  evdwl = Vkc;

        }



        if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,evdwl,0,fkcx,fkcy,fkcz,delx,dely,delz);
@@ -641,44 +635,6 @@ void PairDRIP::calc_normal() 


}



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

   init specific to this pair style

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



void PairDRIP::init_style()

{

  if (force->newton_pair == 0)

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

  if (!atom->molecule_flag)

    error->all(FLERR,"Pair style drip requires atom attribute molecule");



  // need a full neighbor list, including neighbors of ghosts



  int irequest = neighbor->request(this,instance_me);

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

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

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



  // local DRIP neighbor list

  // create pages if first time or if neighbor pgsize/oneatom has changed



  int create = 0;

  if (ipage == NULL) create = 1;

  if (pgsize != neighbor->pgsize) create = 1;

  if (oneatom != neighbor->oneatom) create = 1;



  if (create) {

    delete [] ipage;

    pgsize = neighbor->pgsize;

    oneatom = neighbor->oneatom;



    int nmypage= comm->nthreads;

    ipage = new MyPage<int>[nmypage];

    for (int i = 0; i < nmypage; i++)

      ipage[i].init(oneatom,pgsize,PGDELTA);

  }

}





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

 create neighbor list from main neighbor list for calculating the normals
@@ -735,7 +691,11 @@ void PairDRIP::DRIP_neigh() 
      delz = ztmp - x[j][2];

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



      if (rsq != 0 && rsq < cutDRIPsq[itype][jtype] && atom->molecule[i] == atom->molecule[j]) {



      int iparam_ij = elem2param[itype][jtype];

      double rcutsq = params[iparam_ij].rcutsq;



      if (rsq != 0 && rsq < rcutsq && atom->molecule[i] == atom->molecule[j]) {

        neighptr[n++] = j;

      }

    }
@@ -749,6 +709,43 @@ void PairDRIP::DRIP_neigh() 
  }

}



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

   init specific to this pair style

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



void PairDRIP::init_style()

{

  if (force->newton_pair == 0)

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

  if (!atom->molecule_flag)

    error->all(FLERR,"Pair style drip requires atom attribute molecule");



  // need a full neighbor list, including neighbors of ghosts



  int irequest = neighbor->request(this,instance_me);

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

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

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



  // local DRIP neighbor list

  // create pages if first time or if neighbor pgsize/oneatom has changed



  int create = 0;

  if (ipage == NULL) create = 1;

  if (pgsize != neighbor->pgsize) create = 1;

  if (oneatom != neighbor->oneatom) create = 1;



  if (create) {

    delete [] ipage;

    pgsize = neighbor->pgsize;

    oneatom = neighbor->oneatom;



    int nmypage= comm->nthreads;

    ipage = new MyPage<int>[nmypage];

    for (int i = 0; i < nmypage; i++)

      ipage[i].init(oneatom,pgsize,PGDELTA);

  }

}



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

   allocate all arrays
@@ -759,14 +756,13 @@ void PairDRIP::allocate() 
  allocated = 1;

  int n = atom->ntypes;



  // MOVE init of setflag ot other places; se pair_sw

  memory->create(setflag,n+1,n+1,"pair:setflag");

  for (int i = 1; i <= n; i++)

    for (int j = i; j <= n; j++)

      setflag[i][j] = 0;



  memory->create(cutsq,n+1,n+1,"pair:cutsq");

  memory->create(cut,n+1,n+1,"pair:cut");

  memory->create(offset,n+1,n+1,"pair:offset");

  map = new int[atom->ntypes+1];

}
@@ -776,21 +772,9 @@ void PairDRIP::allocate() 


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

{

  if (narg < 1 || narg > 2) error->all(FLERR,"Illegal pair_style command");

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

  if (strcmp(force->pair_style,"hybrid/overlay")!=0)

    error->all(FLERR,"ERROR: requires hybrid/overlay pair_style");



  cut_global = force->numeric(FLERR,arg[0]);

  if (narg == 2) tap_flag = force->numeric(FLERR,arg[1]);



  // reset cutoffs that have been explicitly set



  if (allocated) {

    int i,j;

    for (i = 1; i <= atom->ntypes; i++)

      for (j = i; j <= atom->ntypes; j++)

        if (setflag[i][j]) cut[i][j] = cut_global;

  }

}



/* ----------------------------------------------------------------------
@@ -841,12 +825,9 @@ void PairDRIP::coeff(int narg, char **arg) 


  read_file(arg[2]);



  double cut_one = cut_global;



  int count = 0;

  for (int i = ilo; i <= ihi; i++) {

    for (int j = MAX(jlo,i); j <= jhi; j++) {

      cut[i][j] = cut_one;

      setflag[i][j] = 1;

      count++;

    }
@@ -864,14 +845,7 @@ double PairDRIP::init_one(int i, int j) 
{

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



  if (offset_flag && (cut[i][j] > 0.0)) {

    int iparam_ij = elem2param[map[i]][map[j]];

    Param& p = params[iparam_ij];

    offset[i][j] = -p.A*pow(p.z0/cut[i][j],6);

  } else offset[i][j] = 0.0;

  offset[j][i] = offset[i][j];



  return cut[i][j];

  return cutmax;

}



/* ----------------------------------------------------------------------
@@ -880,7 +854,7 @@ double PairDRIP::init_one(int i, int j) 


void PairDRIP::read_file(char *filename)

{

  int params_per_line = 12;

  int params_per_line = 14;

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

  memory->sfree(params);

  params = NULL;
@@ -973,37 +947,33 @@ void PairDRIP::read_file(char *filename) 


    params[nparams].ielement = ielement;

    params[nparams].jelement = jelement;

    params[nparams].z0       = atof(words[2]);

    params[nparams].C0       = atof(words[3]);

    params[nparams].C2       = atof(words[4]);

    params[nparams].C4       = atof(words[5]);

    params[nparams].C        = atof(words[6]);

    params[nparams].delta    = atof(words[7]);

    params[nparams].lambda   = atof(words[8]);

    params[nparams].A        = atof(words[9]);

    // S provides a convenient scaling of all energies

    params[nparams].S        = atof(words[10]);

    params[nparams].rcut     = atof(words[11]);



    // energies in meV further scaled by S

    double meV = 1.0e-3*params[nparams].S;

    params[nparams].C *= meV;

    params[nparams].A *= meV;

    params[nparams].C0 *= meV;

    params[nparams].C2 *= meV;

    params[nparams].C4 *= meV;



    // precompute some quantities

    params[nparams].delta2inv = pow(params[nparams].delta,-2);

    params[nparams].z06 = pow(params[nparams].z0,6);

    params[nparams].C0       = atof(words[2]);

    params[nparams].C2       = atof(words[3]);

    params[nparams].C4       = atof(words[4]);

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

    params[nparams].delta    = atof(words[6]);

    params[nparams].lambda   = atof(words[7]);

    params[nparams].A        = atof(words[8]);

    params[nparams].z0       = atof(words[9]);

    params[nparams].B        = atof(words[10]);

    params[nparams].eta      = atof(words[11]);

    params[nparams].rhocut   = atof(words[12]);

    params[nparams].rcut     = atof(words[13]);



    // convenient precomputations

    params[nparams].rhocutsq = params[nparams].rhocut * params[nparams].rhocut;

    params[nparams].rcutsq   = params[nparams].rcut * params[nparams].rcut;



    // set max cutoff

    if(params[nparams].rcut > cutmax) cutmax = params[nparams].rcut;





    nparams++;

    //if(nparams >= pow(atom->ntypes,3)) break;

  }



  memory->destroy(elem2param);

  memory->destroy(cutDRIPsq);

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

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

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

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

      n = -1;
@@ -1015,7 +985,6 @@ void PairDRIP::read_file(char *filename) 
      }

      if (n < 0) error->all(FLERR,"Potential file is missing an entry");

      elem2param[i][j] = n;

      cutDRIPsq[i][j] = params[n].rcut*params[n].rcut;

    }

  }

  delete [] words;

src/USER-MISC/pair_drip.h

+4 −6
Original line number Diff line number Diff line
@@ -41,6 +41,7 @@ class PairDRIP : public Pair { 
  void unpack_forward_comm(int, int, double *);



 protected:

  double cutmax;                   // max cutoff for all species

  int me;

  int maxlocal;                    // size of numneigh, firstneigh arrays

  int pgsize;                      // size of neighbor page
@@ -52,9 +53,10 @@ class PairDRIP : public Pair { 




  struct Param {

    double z0,C0,C2,C4,C,delta,lambda,A,S;

    double delta2inv,z06,rcut;

    int ielement,jelement;

    double C0,C2,C4,C,delta,lambda,A,z0,B,eta,rhocut,rcut;

    double rhocutsq, rcutsq;

    double delta2inv,z06;

  };

  Param *params;       // parameter set for I-J interactions

  char **elements;     // names of unique elements
@@ -65,11 +67,7 @@ class PairDRIP : public Pair { 
  int maxparam;        // max # of parameter sets

  int nmax;            // max # of atoms



  double cut_global;

  double cut_normal;

  double **cut;

  double **cutDRIPsq;

  double **offset;

  double **normal;

  double ***dnormdri;

  double ****dnormal;

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