Commit 73a87e79 authored by athomps's avatar athomps
Browse files

Added group keywords to fix gcmc 

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13452 f3b2605a-c512-4ea7-a41b-209d697bcdaa
parent 68295026

src/MC/fix_gcmc.cpp

+119 −5
Original line number Diff line number Diff line
@@ -226,6 +226,14 @@ void FixGCMC::options(int narg, char **arg) 
  charge_flag = false;

  full_flag = false;

  idshake = NULL;

  ngroups = 0;

  int ngroupsmax = 0;

  groupstrings = NULL;

  ngrouptypes = 0;

  int ngrouptypesmax = 0;

  grouptypestrings = NULL;

  grouptypes = NULL;

  grouptypebits = NULL;



  int iarg = 0;

  while (iarg < narg) {
@@ -281,6 +289,33 @@ void FixGCMC::options(int narg, char **arg) 
    } else if (strcmp(arg[iarg],"full_energy") == 0) {

      full_flag = true;

      iarg += 1;

    } else if (strcmp(arg[iarg],"group") == 0) {

      if (iarg+2 > narg) error->all(FLERR,"Illegal fix gcmc command");

      if (ngroups >= ngroupsmax) {

	ngroupsmax = ngroups+1;

	groupstrings = (char**) memory->srealloc(groupstrings,ngroupsmax*sizeof(char *),

			 "fix_gcmc:groupstrings");

      }

      int n = strlen(arg[iarg+1]) + 1;

      groupstrings[ngroups] = new char[n];

      strcpy(groupstrings[ngroups],arg[iarg+1]);

      ngroups++;

      iarg += 2;

    } else if (strcmp(arg[iarg],"grouptype") == 0) {

      if (iarg+3 > narg) error->all(FLERR,"Illegal fix gcmc command");

      if (ngrouptypes >= ngrouptypesmax) {

	ngrouptypesmax = ngrouptypes+1;

	grouptypes = (int*) memory->srealloc(grouptypes,ngrouptypesmax*sizeof(int),

			 "fix_gcmc:grouptypes");

	grouptypestrings = (char**) memory->srealloc(grouptypestrings,ngrouptypesmax*sizeof(char *),

			 "fix_gcmc:grouptypestrings");

      }

      grouptypes[ngrouptypes] = atoi(arg[iarg+1]);

      int n = strlen(arg[iarg+2]) + 1;

      grouptypestrings[ngrouptypes] = new char[n];

      strcpy(grouptypestrings[ngrouptypes],arg[iarg+2]);

      ngrouptypes++;

      iarg += 3;

    } else error->all(FLERR,"Illegal fix gcmc command");

  }

}
@@ -304,6 +339,8 @@ FixGCMC::~FixGCMC() 
    delete [] group_arg;

  } 



  // This seems to be causing seg-faults

  

  if (exclusion_group && (strcmp(group->names[0],"all") == 0)) {

    char **group_arg = new char*[2];

    group_arg[0] = group->names[exclusion_group];
@@ -318,6 +355,20 @@ FixGCMC::~FixGCMC() 
  memory->destroy(imageflags);

  

  delete [] idshake;



  if (ngroups > 0) {

    for (int igroup = 0; igroup < ngroups; igroup++)

      delete [] groupstrings[igroup];

    memory->destroy(groupstrings);

  }



  if (ngrouptypes > 0) {

    for (int igroup = 0; igroup < ngrouptypes; igroup++)

      delete [] grouptypestrings[igroup];

    memory->destroy(grouptypestrings);

    memory->destroy(grouptypes);

    memory->destroy(grouptypebits);

  }

}



/* ---------------------------------------------------------------------- */
@@ -515,6 +566,31 @@ void FixGCMC::init() 
  

  imagetmp = ((imageint) IMGMAX << IMG2BITS) | 

             ((imageint) IMGMAX << IMGBITS) | IMGMAX;



  // construct group bitmask for all new atoms

  // aggregated over all group keywords

 

  groupbitall = 1 | groupbit;

  for (int igroup = 0; igroup < ngroups; igroup++) {

    int jgroup = group->find(groupstrings[igroup]);

    if (jgroup == -1) 

      error->all(FLERR,"Could not find specified fix gcmc group ID");

    groupbitall |= group->bitmask[jgroup];

  }



  // construct group type bitmasks

  // not aggregated over all group keywords



  if (ngrouptypes > 0) {

    memory->create(grouptypebits,ngrouptypes,"fix_gcmc:grouptypebits");

    for (int igroup = 0; igroup < ngrouptypes; igroup++) {

      int jgroup = group->find(grouptypestrings[igroup]);

      if (jgroup == -1) 

	error->all(FLERR,"Could not find specified fix gcmc group ID");

      grouptypebits[igroup] = group->bitmask[jgroup];

    }

  }



}



/* ----------------------------------------------------------------------
@@ -750,7 +826,16 @@ void FixGCMC::attempt_atomic_insertion() 
        zz*volume*exp(-beta*insertion_energy)/(ngas+1)) {

      atom->avec->create_atom(ngcmc_type,coord);

      int m = atom->nlocal - 1;

      atom->mask[m] = 1 | groupbit;



      // add to groups

      // optionally add to type-based groups



      atom->mask[m] = groupbitall;

      for (int igroup = 0; igroup < ngrouptypes; igroup++) {

	if (ngcmc_type == grouptypes[igroup])

	  atom->mask[m] |= grouptypebits[igroup];

      }



      atom->v[m][0] = random_unequal->gaussian()*sigma;

      atom->v[m][1] = random_unequal->gaussian()*sigma;

      atom->v[m][2] = random_unequal->gaussian()*sigma;
@@ -1086,7 +1171,16 @@ void FixGCMC::attempt_molecule_insertion() 
      if (procflag[i]) {

        atom->avec->create_atom(ngcmc_type+onemols[imol]->type[i],atom_coord[i]);

        int m = atom->nlocal - 1;

        atom->mask[m] = 1 | groupbit;



	// add to groups

	// optionally add to type-based groups



	atom->mask[m] = groupbitall;

	for (int igroup = 0; igroup < ngrouptypes; igroup++) {

	  if (ngcmc_type == grouptypes[igroup])

	    atom->mask[m] |= grouptypebits[igroup];

	}



        atom->image[m] = imagetmp;

        domain->remap(atom->x[m],atom->image[m]);

        atom->molecule[m] = maxmol_all;
@@ -1347,7 +1441,16 @@ void FixGCMC::attempt_atomic_insertion_full() 
    proc_flag = 1;

    atom->avec->create_atom(ngcmc_type,coord);

    int m = atom->nlocal - 1;

    atom->mask[m] = 1 | groupbit;



    // add to groups

    // optionally add to type-based groups

    

    atom->mask[m] = groupbitall;

    for (int igroup = 0; igroup < ngrouptypes; igroup++) {

      if (ngcmc_type == grouptypes[igroup])

	atom->mask[m] |= grouptypebits[igroup];

    }



    atom->v[m][0] = random_unequal->gaussian()*sigma;

    atom->v[m][1] = random_unequal->gaussian()*sigma;

    atom->v[m][2] = random_unequal->gaussian()*sigma;
@@ -1696,7 +1799,18 @@ void FixGCMC::attempt_molecule_insertion_full() 


      atom->avec->create_atom(ngcmc_type+onemols[imol]->type[i],xtmp);

      int m = atom->nlocal - 1;

      atom->mask[m] = 1 | groupbit;



      // add to groups

      // optionally add to type-based groups



      atom->mask[m] = groupbitall;

      printf("ngrouptypes %d\n",ngrouptypes);

      for (int igroup = 0; igroup < ngrouptypes; igroup++) {

	printf("check type %d %d\n",ngcmc_type,grouptypes[igroup]);

	if (ngcmc_type == grouptypes[igroup])

	  atom->mask[m] |= grouptypebits[igroup];

      }



      atom->image[m] = imagetmp;

      domain->remap(atom->x[m],atom->image[m]);

      atom->molecule[m] = insertion_molecule;

src/MC/fix_gcmc.h

+8 −1
Original line number Diff line number Diff line
@@ -77,6 +77,13 @@ class FixGCMC : public Fix { 
 

  int natoms_per_molecule;  // number of atoms in each gas molecule



  int groupbitall;          // group bitmask for inserted atoms

  int ngroups;              // number of group-ids for inserted atoms

  char** groupstrings;      // list of group-ids for inserted atoms

  int ngrouptypes;          // number of type-based group-ids for inserted atoms

  char** grouptypestrings;  // list of type-based group-ids for inserted atoms

  int* grouptypebits;       // list of type-based group bitmasks 

  int* grouptypes;          // list of type-based group types 

  double ntranslation_attempts;

  double ntranslation_successes;

  double nrotation_attempts;

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