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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12886 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2015-01-06 21:07:35 +00:00
parent 3c864bd317
commit f22314495c
2 changed files with 173 additions and 7 deletions
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175
src/delete_atoms.cpp
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@ -67,6 +67,9 @@ void DeleteAtoms::command(int narg, char **arg)
else if (strcmp(arg[0],"porosity") == 0) delete_porosity(narg,arg);
else error->all(FLERR,"Illegal delete_atoms command");
// optionally delete additional bonds or atoms in molecules
if (bond_flag) delete_bond();
if (mol_flag) delete_molecule();
// delete local atoms flagged in dlist
@ -124,7 +127,7 @@ void DeleteAtoms::command(int narg, char **arg)
fprintf(screen,"Deleted " BIGINT_FORMAT
" atoms, new total = " BIGINT_FORMAT "\n",
ndelete,atom->natoms);
if (mol_flag) {
if (bond_flag || mol_flag) {
if (nbonds_previous)
fprintf(screen,"Deleted " BIGINT_FORMAT
" bonds, new total = " BIGINT_FORMAT "\n",
@ -148,7 +151,7 @@ void DeleteAtoms::command(int narg, char **arg)
fprintf(logfile,"Deleted " BIGINT_FORMAT
" atoms, new total = " BIGINT_FORMAT "\n",
ndelete,atom->natoms);
if (mol_flag) {
if (bond_flag || mol_flag) {
if (nbonds_previous)
fprintf(logfile,"Deleted " BIGINT_FORMAT
" bonds, new total = " BIGINT_FORMAT "\n",
@ -403,6 +406,41 @@ void DeleteAtoms::delete_porosity(int narg, char **arg)
if (random->uniform() <= porosity_fraction) dlist[i] = 1;
}
/* ----------------------------------------------------------------------
delete all topology interactions that include deleted atoms
------------------------------------------------------------------------- */
void DeleteAtoms::delete_bond()
{
// hash = for atom IDs being deleted by one processor
// list of these IDs is sent around ring
// at each stage of ring pass, hash is re-populated with received IDs
hash = new std::map<tagint,int>();
// list = set of unique molecule IDs from which I deleted atoms
// pass list to all other procs via comm->ring()
tagint *tag = atom->tag;
int nlocal = atom->nlocal;
int n = 0;
for (int i = 0; i < nlocal; i++)
if (dlist[i]) n++;
tagint *list;
memory->create(list,n,"delete_atoms:list");
n = 0;
for (int i = 0; i < nlocal; i++)
if (dlist[i]) list[n++] = tag[i];
cptr = this;
comm->ring(n,sizeof(tagint),list,1,bondring,NULL);
delete hash;
memory->destroy(list);
}
/* ----------------------------------------------------------------------
delete atoms in molecules with any deletions
use dlist marked with atom deletions, and mark additional atoms
@ -505,9 +543,121 @@ void DeleteAtoms::recount_topology()
}
/* ----------------------------------------------------------------------
callback from comm->ring()
cbuf = list of N molecule IDs, put them in hash
loop over my atoms, if matches molecule ID in hash, delete that atom
callback from comm->ring() in delete_bond()
------------------------------------------------------------------------- */
void DeleteAtoms::bondring(int nbuf, char *cbuf)
{
tagint *list = (tagint *) cbuf;
std::map<tagint,int> *hash = cptr->hash;
int *num_bond = cptr->atom->num_bond;
int *num_angle = cptr->atom->num_angle;
int *num_dihedral = cptr->atom->num_dihedral;
int *num_improper = cptr->atom->num_improper;
int **bond_type = cptr->atom->bond_type;
int **bond_atom = cptr->atom->bond_atom;
int **angle_type = cptr->atom->angle_type;
int **angle_atom1 = cptr->atom->angle_atom1;
int **angle_atom2 = cptr->atom->angle_atom2;
int **angle_atom3 = cptr->atom->angle_atom3;
int **dihedral_type = cptr->atom->dihedral_type;
int **dihedral_atom1 = cptr->atom->dihedral_atom1;
int **dihedral_atom2 = cptr->atom->dihedral_atom2;
int **dihedral_atom3 = cptr->atom->dihedral_atom3;
int **dihedral_atom4 = cptr->atom->dihedral_atom4;
int **improper_type = cptr->atom->improper_type;
int **improper_atom1 = cptr->atom->improper_atom1;
int **improper_atom2 = cptr->atom->improper_atom2;
int **improper_atom3 = cptr->atom->improper_atom3;
int **improper_atom4 = cptr->atom->improper_atom4;
int nlocal = cptr->atom->nlocal;
// cbuf = list of N deleted atom IDs from other proc, put them in hash
hash->clear();
for (int i = 0; i < nbuf; i++) (*hash)[list[i]] = 1;
// loop over my atoms and their bond topology lists
// if any atom in an interaction matches atom ID in hash, delete interaction
int m,n;
for (int i = 0; i < nlocal; i++) {
if (num_bond) {
m = 0;
n = num_bond[i];
while (m < n) {
if (hash->find(bond_atom[i][m]) != hash->end()) {
bond_type[i][m] = bond_type[i][n-1];
bond_atom[i][m] = bond_atom[i][n-1];
n--;
} else m++;
}
num_bond[i] = n;
}
if (num_angle) {
m = 0;
n = num_angle[i];
while (m < n) {
if (hash->find(angle_atom1[i][m]) != hash->end() ||
hash->find(angle_atom2[i][m]) != hash->end() ||
hash->find(angle_atom3[i][m]) != hash->end()) {
angle_type[i][m] = angle_type[i][n-1];
angle_atom1[i][m] = angle_atom1[i][n-1];
angle_atom2[i][m] = angle_atom2[i][n-1];
angle_atom3[i][m] = angle_atom3[i][n-1];
n--;
} else m++;
}
num_angle[i] = n;
}
if (num_dihedral) {
m = 0;
n = num_dihedral[i];
while (m < n) {
if (hash->find(dihedral_atom1[i][m]) != hash->end() ||
hash->find(dihedral_atom2[i][m]) != hash->end() ||
hash->find(dihedral_atom3[i][m]) != hash->end()) {
dihedral_type[i][m] = dihedral_type[i][n-1];
dihedral_atom1[i][m] = dihedral_atom1[i][n-1];
dihedral_atom2[i][m] = dihedral_atom2[i][n-1];
dihedral_atom3[i][m] = dihedral_atom3[i][n-1];
dihedral_atom4[i][m] = dihedral_atom4[i][n-1];
n--;
} else m++;
}
num_dihedral[i] = n;
}
if (num_improper) {
m = 0;
n = num_improper[i];
while (m < n) {
if (hash->find(improper_atom1[i][m]) != hash->end() ||
hash->find(improper_atom2[i][m]) != hash->end() ||
hash->find(improper_atom3[i][m]) != hash->end()) {
improper_type[i][m] = improper_type[i][n-1];
improper_atom1[i][m] = improper_atom1[i][n-1];
improper_atom2[i][m] = improper_atom2[i][n-1];
improper_atom3[i][m] = improper_atom3[i][n-1];
improper_atom4[i][m] = improper_atom4[i][n-1];
n--;
} else m++;
}
num_improper[i] = n;
}
}
}
/* ----------------------------------------------------------------------
callback from comm->ring() in delete_molecule()
------------------------------------------------------------------------- */
void DeleteAtoms::molring(int n, char *cbuf)
@ -518,9 +668,13 @@ void DeleteAtoms::molring(int n, char *cbuf)
int nlocal = cptr->atom->nlocal;
tagint *molecule = cptr->atom->molecule;
// cbuf = list of N molecule IDs from other proc, put them in hash
hash->clear();
for (int i = 0; i < n; i++) (*hash)[list[i]] = 1;
// loop over my atoms, if matches molecule ID in hash, delete that atom
for (int i = 0; i < nlocal; i++)
if (hash->find(molecule[i]) != hash->end()) dlist[i] = 1;
}
@ -532,7 +686,7 @@ void DeleteAtoms::molring(int n, char *cbuf)
void DeleteAtoms::options(int narg, char **arg)
{
compress_flag = 1;
mol_flag = 0;
bond_flag = mol_flag = 0;
int iarg = 0;
while (iarg < narg) {
@ -542,6 +696,15 @@ void DeleteAtoms::options(int narg, char **arg)
else if (strcmp(arg[iarg+1],"no") == 0) compress_flag = 0;
else error->all(FLERR,"Illegal delete_atoms command");
iarg += 2;
} else if (strcmp(arg[iarg],"bond") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal delete_atoms command");
if (atom->molecular == 0)
error->all(FLERR,"Cannot delete_atoms bond yes for "
"non-molecular systems");
if (strcmp(arg[iarg+1],"yes") == 0) bond_flag = 1;
else if (strcmp(arg[iarg+1],"no") == 0) bond_flag = 0;
else error->all(FLERR,"Illegal delete_atoms command");
iarg += 2;
} else if (strcmp(arg[iarg],"mol") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal delete_atoms command");
if (atom->molecular == 0)