forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11854 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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@ -117,8 +117,7 @@ void DeleteAtoms::command(int narg, char **arg)
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}
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/* ----------------------------------------------------------------------
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delete all atoms in group
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group will still exist
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delete all atoms in group, group will still exist
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------------------------------------------------------------------------- */
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void DeleteAtoms::delete_group(int narg, char **arg)
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@ -140,11 +139,12 @@ void DeleteAtoms::delete_group(int narg, char **arg)
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) dlist[i] = 1;
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if (mol_flag) delete_molecule();
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}
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/* ----------------------------------------------------------------------
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delete all atoms in region
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if mol_flag is set, also delete atoms in molecules with any deletions
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------------------------------------------------------------------------- */
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void DeleteAtoms::delete_region(int narg, char **arg)
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@ -166,53 +166,7 @@ void DeleteAtoms::delete_region(int narg, char **arg)
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for (int i = 0; i < nlocal; i++)
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if (domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2])) dlist[i] = 1;
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if (mol_flag == 0) return;
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// delete entire molecules if any atom in molecule was deleted
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// store list of molecule IDs I delete atoms from in list
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// pass list from proc to proc via ring communication
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hash = new std::map<tagint,int>();
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tagint *molecule = atom->molecule;
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for (int i = 0; i < nlocal; i++)
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if (dlist[i] && hash->find(molecule[i]) == hash->end())
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(*hash)[molecule[i]] = 1;
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int n = hash->size();
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tagint *list;
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memory->create(list,n,"delete_atoms:list");
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n = 0;
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std::map<tagint,int>::iterator pos;
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for (pos = hash->begin(); pos != hash->end(); ++pos) list[n++] = pos->first;
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cptr = this;
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comm->ring(n,sizeof(tagint),list,1,molring,NULL);
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delete hash;
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memory->destroy(list);
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}
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/* ----------------------------------------------------------------------
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callback from comm->ring()
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cbuf = list of N molecule IDs, put them in hash
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loop over my atoms, if matches molecule ID in hash, delete that atom
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------------------------------------------------------------------------- */
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void DeleteAtoms::molring(int n, char *cbuf)
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{
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tagint *list = (tagint *) cbuf;
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int *dlist = cptr->dlist;
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std::map<tagint,int> *hash = cptr->hash;
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int nlocal = cptr->atom->nlocal;
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tagint *molecule = cptr->atom->molecule;
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hash->clear();
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for (int i = 0; i < n; i++) (*hash)[list[i]] = 1;
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for (int i = 0; i < nlocal; i++)
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if (hash->find(molecule[i]) != hash->end()) dlist[i] = 1;
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if (mol_flag) delete_molecule();
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}
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/* ----------------------------------------------------------------------
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@ -364,6 +318,8 @@ void DeleteAtoms::delete_overlap(int narg, char **arg)
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break;
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}
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}
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if (mol_flag) delete_molecule();
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}
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/* ----------------------------------------------------------------------
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@ -394,6 +350,65 @@ void DeleteAtoms::delete_porosity(int narg, char **arg)
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for (int i = 0; i < nlocal; i++)
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if (domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2]))
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if (random->uniform() <= porosity_fraction) dlist[i] = 1;
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if (mol_flag) delete_molecule();
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}
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/* ----------------------------------------------------------------------
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delete atoms in molecules with any deletions
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use dlist marked with atom deletions, and mark additional atoms
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------------------------------------------------------------------------- */
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void DeleteAtoms::delete_molecule()
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{
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// hash = unique molecule IDs from which I deleted atoms
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hash = new std::map<tagint,int>();
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tagint *molecule = atom->molecule;
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int nlocal = atom->nlocal;
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for (int i = 0; i < nlocal; i++)
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if (dlist[i] && hash->find(molecule[i]) == hash->end())
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(*hash)[molecule[i]] = 1;
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// list = set of unique molecule IDs from which I deleted atoms
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// pass list to all other procs via comm->ring()
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int n = hash->size();
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tagint *list;
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memory->create(list,n,"delete_atoms:list");
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n = 0;
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std::map<tagint,int>::iterator pos;
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for (pos = hash->begin(); pos != hash->end(); ++pos) list[n++] = pos->first;
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cptr = this;
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comm->ring(n,sizeof(tagint),list,1,molring,NULL);
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delete hash;
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memory->destroy(list);
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}
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/* ----------------------------------------------------------------------
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callback from comm->ring()
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cbuf = list of N molecule IDs, put them in hash
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loop over my atoms, if matches molecule ID in hash, delete that atom
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------------------------------------------------------------------------- */
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void DeleteAtoms::molring(int n, char *cbuf)
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{
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tagint *list = (tagint *) cbuf;
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int *dlist = cptr->dlist;
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std::map<tagint,int> *hash = cptr->hash;
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int nlocal = cptr->atom->nlocal;
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tagint *molecule = cptr->atom->molecule;
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hash->clear();
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for (int i = 0; i < n; i++) (*hash)[list[i]] = 1;
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for (int i = 0; i < nlocal; i++)
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if (hash->find(molecule[i]) != hash->end()) dlist[i] = 1;
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}
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/* ----------------------------------------------------------------------
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@ -39,6 +39,7 @@ class DeleteAtoms : protected Pointers {
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void delete_region(int, char **);
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void delete_overlap(int, char **);
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void delete_porosity(int, char **);
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void delete_molecule();
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void options(int, char **);
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inline int sbmask(int j) {
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