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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1422 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2008-01-24 22:30:58 +00:00
parent 32164786d0
commit d39a8de8ab
5 changed files with 72 additions and 72 deletions
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113
src/delete_atoms.cpp
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@ -24,8 +24,7 @@
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "comm.h"
#include "force.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
@ -55,15 +54,14 @@ void DeleteAtoms::command(int narg, char **arg)
// allocate and initialize deletion list
int nlocal = atom->nlocal;
int *dlist = new int[nlocal];
dlist = (int *) memory->smalloc(nlocal*sizeof(int),"delete_atoms:dlist");
for (int i = 0; i < nlocal; i++) dlist[i] = 0;
// delete the atoms
if (strcmp(arg[0],"group") == 0) delete_group(narg,arg,dlist);
else if (strcmp(arg[0],"region") == 0) delete_region(narg,arg,dlist);
else if (strcmp(arg[0],"overlap") == 0) delete_overlap(narg,arg,dlist);
if (strcmp(arg[0],"group") == 0) delete_group(narg,arg);
else if (strcmp(arg[0],"region") == 0) delete_region(narg,arg);
else if (strcmp(arg[0],"overlap") == 0) delete_overlap(narg,arg);
else error->all("Illegal delete_atoms command");
// delete local atoms in list
@ -80,7 +78,7 @@ void DeleteAtoms::command(int narg, char **arg)
} else i++;
}
atom->nlocal = nlocal;
delete [] dlist;
memory->sfree(dlist);
// if non-molecular system, reset atom tags to be contiguous
// set all atom IDs to 0, call tag_extend()
@ -122,7 +120,7 @@ void DeleteAtoms::command(int narg, char **arg)
group will still exist
------------------------------------------------------------------------- */
void DeleteAtoms::delete_group(int narg, char **arg, int *dlist)
void DeleteAtoms::delete_group(int narg, char **arg)
{
if (narg != 2) error->all("Illegal delete_atoms command");
@ -141,7 +139,7 @@ void DeleteAtoms::delete_group(int narg, char **arg, int *dlist)
delete all atoms in region
------------------------------------------------------------------------- */
void DeleteAtoms::delete_region(int narg, char **arg, int *dlist)
void DeleteAtoms::delete_region(int narg, char **arg)
{
if (narg != 2) error->all("Illegal delete_atoms command");
@ -162,34 +160,33 @@ void DeleteAtoms::delete_region(int narg, char **arg, int *dlist)
no guarantee that minimium number of atoms will be deleted
------------------------------------------------------------------------- */
void DeleteAtoms::delete_overlap(int narg, char **arg, int *dlist)
void DeleteAtoms::delete_overlap(int narg, char **arg)
{
if (narg < 2) error->all("Illegal delete_atoms command");
if (narg < 4) error->all("Illegal delete_atoms command");
// read args including optional type info
// read args
double cut = atof(arg[1]);
double cutsq = cut*cut;
int typeflag,type1,type2;
if (narg == 2) typeflag = 0;
else if (narg == 3) {
typeflag = 1;
type1 = atoi(arg[2]);
} else if (narg == 4) {
typeflag = 2;
type1 = atoi(arg[2]);
type2 = atoi(arg[3]);
} else error->all("Illegal delete_atoms command");
int igroup1 = group->find(arg[2]);
int igroup2 = group->find(arg[3]);
if (igroup1 < 0 || igroup2 < 0)
error->all("Could not find delete_atoms group ID");
int group1bit = group->bitmask[igroup1];
int group2bit = group->bitmask[igroup2];
if (comm->me == 0 && screen)
fprintf(screen,"System init for delete_atoms ...\n");
// request a half neighbor list for use by this command
// request a full neighbor list for use by this command
int irequest = neighbor->request((void *) this);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->command = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->occasional = 1;
// init entire system since comm->borders and neighbor->build is done
@ -218,30 +215,13 @@ void DeleteAtoms::delete_overlap(int narg, char **arg, int *dlist)
NeighList *list = neighbor->lists[irequest];
neighbor->build_one(irequest);
// create an atom map if one doesn't exist already
int mapflag = 0;
if (atom->map_style == 0) {
mapflag = 1;
atom->map_style = 1;
atom->map_init();
atom->map_set();
}
// double loop over owned atoms and their neighbors
// double loop over owned atoms and their full neighbor list
// at end of loop, there are no more overlaps
// criteria for i,j to undergo a deletion event:
// weighting factor != 0.0 for this pair
// could be 0 and still be in neigh list for long-range Coulombics
// local copy of j (map[tag[j]]) has not already been deleted
// distance between i,j is less than cutoff
// i,j are of valid types
// if all criteria met, delete i and skip to next i in outer loop
// unless j is ghost and newton_pair off and tag[j] < tag[i]
// then rely on other proc to delete
// only ever delete owned atom I, never J even if owned
int *tag = atom->tag;
int *type = atom->type;
int *mask = atom->mask;
double **x = atom->x;
int nlocal = atom->nlocal;
int nall = atom->nlocal + atom->nghost;
@ -270,17 +250,16 @@ void DeleteAtoms::delete_overlap(int narg, char **arg, int *dlist)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
// if weighting factors are 0, skip this pair
// could be 0 and still be in neigh list for long-range Coulombics
// want consistency with non-charged pairs which wouldn't be in list
if (j >= nall) {
if (special_coul[j/nall] == 0.0 && special_lj[j/nall] == 0.0) continue;
j %= nall;
}
if (j < nlocal) {
if (dlist[j]) continue;
} else {
m = atom->map(tag[j]);
if (m < nlocal && dlist[m]) continue;
}
// only consider deletion if I,J distance < cutoff
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
@ -288,24 +267,30 @@ void DeleteAtoms::delete_overlap(int narg, char **arg, int *dlist)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq >= cutsq) continue;
if (typeflag) {
jtype = type[j];
if (typeflag == 1 && itype != type1 && jtype != type1) continue;
if (typeflag == 2 && !(itype == type1 && jtype == type2) &&
!(itype == type2 && jtype == type1)) continue;
}
// only consider deletion if I,J are in groups 1,2 respectively
// true whether J is owned or ghost atom
if (j >= nlocal && newton_pair == 0 && tag[j] < tag[i]) continue;
if (!(mask[i] & group1bit)) continue;
if (!(mask[j] & group2bit)) continue;
// J is owned atom:
// delete atom I if atom J has not already been deleted
// J is ghost atom:
// delete atom I if J,I is not a candidate deletion pair
// due to being in groups 1,2 respectively
// if they are candidate pair, then either:
// another proc owns J and could delete J
// J is a ghost of another of my owned atoms, and I could delete J
// test on tags of I,J insures that only I or J is deleted
if (j < nlocal) {
if (dlist[j]) continue;
} else if ((mask[i] & group2bit) && (mask[j] & group1bit)) {
if (tag[i] > tag[j]) continue;
}
dlist[i] = 1;
break;
}
}
// delete temporary atom map
if (mapflag) {
atom->map_delete();
atom->map_style = 0;
}
}