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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9901 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2013-05-23 22:45:11 +00:00
parent e85fdb8d63
commit 60b9a09f77
4 changed files with 79 additions and 9 deletions
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62
src/delete_atoms.cpp
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@ -28,8 +28,14 @@
#include "memory.h"
#include "error.h"
#include <map>
using namespace LAMMPS_NS;
// allocate space for static class variable
DeleteAtoms *DeleteAtoms::cptr;
/* ---------------------------------------------------------------------- */
DeleteAtoms::DeleteAtoms(LAMMPS *lmp) : Pointers(lmp) {}
@ -138,6 +144,7 @@ void DeleteAtoms::delete_group(int narg, char **arg)
/* ----------------------------------------------------------------------
delete all atoms in region
if mol_flag is set, also delete atoms in molecules with any deletions
------------------------------------------------------------------------- */
void DeleteAtoms::delete_region(int narg, char **arg)
@ -158,6 +165,54 @@ void DeleteAtoms::delete_region(int narg, char **arg)
for (int i = 0; i < nlocal; i++)
if (domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2])) dlist[i] = 1;
if (mol_flag == 0) return;
// delete entire molecules if any atom in molecule was deleted
// store list of molecule IDs I delete atoms from in list
// pass list from proc to proc via ring communication
hash = new std::map<int,int>();
int *molecule = atom->molecule;
for (int i = 0; i < nlocal; i++)
if (dlist[i] && hash->find(molecule[i]) == hash->end())
(*hash)[molecule[i]] = 1;
int n = hash->size();
int *list;
memory->create(list,n,"delete_atoms:list");
n = 0;
std::map<int,int>::iterator pos;
for (pos = hash->begin(); pos != hash->end(); ++pos) list[n++] = pos->first;
cptr = this;
comm->ring(n,sizeof(int),list,1,molring,NULL);
delete hash;
memory->destroy(list);
}
/* ----------------------------------------------------------------------
callback from comm->ring()
cbuf = list of N molecule IDs, put them in hash
loop over my atoms, if matches moleculed ID in hash, delete that atom
------------------------------------------------------------------------- */
void DeleteAtoms::molring(int n, char *cbuf)
{
int *list = (int *) cbuf;
int *dlist = cptr->dlist;
std::map<int,int> *hash = cptr->hash;
int nlocal = cptr->atom->nlocal;
int *molecule = cptr->atom->molecule;
hash->clear();
for (int i = 0; i < n; i++) (*hash)[list[i]] = 1;
for (int i = 0; i < nlocal; i++)
if (hash->find(molecule[i]) != hash->end()) dlist[i] = 1;
}
/* ----------------------------------------------------------------------
@ -346,6 +401,7 @@ void DeleteAtoms::delete_porosity(int narg, char **arg)
void DeleteAtoms::options(int narg, char **arg)
{
compress_flag = 1;
mol_flag = 0;
int iarg = 0;
while (iarg < narg) {
@ -355,6 +411,12 @@ void DeleteAtoms::options(int narg, char **arg)
else if (strcmp(arg[iarg+1],"no") == 0) compress_flag = 0;
else error->all(FLERR,"Illegal delete_bonds command");
iarg += 2;
} else if (strcmp(arg[iarg],"mol") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal delete_bonds command");
if (strcmp(arg[iarg+1],"yes") == 0) mol_flag = 1;
else if (strcmp(arg[iarg+1],"no") == 0) mol_flag = 0;
else error->all(FLERR,"Illegal delete_bonds command");
iarg += 2;
} else error->all(FLERR,"Illegal delete_bonds command");
}
}