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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8226 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2012-06-06 22:47:51 +00:00
parent f46eb9dedb
commit ef9e700545
1408 changed files with 58053 additions and 57983 deletions
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38
src/delete_atoms.cpp
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@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@ -38,7 +38,7 @@ DeleteAtoms::DeleteAtoms(LAMMPS *lmp) : Pointers(lmp) {}
void DeleteAtoms::command(int narg, char **arg)
{
if (domain->box_exist == 0)
if (domain->box_exist == 0)
error->all(FLERR,"Delete_atoms command before simulation box is defined");
if (narg < 1) error->all(FLERR,"Illegal delete_atoms command");
if (atom->tag_enable == 0)
@ -101,12 +101,12 @@ void DeleteAtoms::command(int narg, char **arg)
bigint ndelete = natoms_previous - atom->natoms;
if (comm->me == 0) {
if (screen) fprintf(screen,"Deleted " BIGINT_FORMAT
" atoms, new total = " BIGINT_FORMAT "\n",
ndelete,atom->natoms);
if (logfile) fprintf(logfile,"Deleted " BIGINT_FORMAT
" atoms, new total = " BIGINT_FORMAT "\n",
ndelete,atom->natoms);
if (screen) fprintf(screen,"Deleted " BIGINT_FORMAT
" atoms, new total = " BIGINT_FORMAT "\n",
ndelete,atom->natoms);
if (logfile) fprintf(logfile,"Deleted " BIGINT_FORMAT
" atoms, new total = " BIGINT_FORMAT "\n",
ndelete,atom->natoms);
}
}
@ -124,7 +124,7 @@ void DeleteAtoms::delete_group(int narg, char **arg)
options(narg-2,&arg[2]);
// allocate and initialize deletion list
int nlocal = atom->nlocal;
memory->create(dlist,nlocal,"delete_atoms:dlist");
for (int i = 0; i < nlocal; i++) dlist[i] = 0;
@ -143,13 +143,13 @@ void DeleteAtoms::delete_group(int narg, char **arg)
void DeleteAtoms::delete_region(int narg, char **arg)
{
if (narg < 2) error->all(FLERR,"Illegal delete_atoms command");
int iregion = domain->find_region(arg[1]);
if (iregion == -1) error->all(FLERR,"Could not find delete_atoms region ID");
options(narg-2,&arg[2]);
// allocate and initialize deletion list
int nlocal = atom->nlocal;
memory->create(dlist,nlocal,"delete_atoms:dlist");
for (int i = 0; i < nlocal; i++) dlist[i] = 0;
@ -170,7 +170,7 @@ void DeleteAtoms::delete_region(int narg, char **arg)
void DeleteAtoms::delete_overlap(int narg, char **arg)
{
if (narg < 4) error->all(FLERR,"Illegal delete_atoms command");
// read args
double cut = atof(arg[1]);
@ -199,7 +199,7 @@ void DeleteAtoms::delete_overlap(int narg, char **arg)
// init entire system since comm->borders and neighbor->build is done
// comm::init needs neighbor::init needs pair::init needs kspace::init, etc
lmp->init();
// error check on cutoff
@ -207,7 +207,7 @@ void DeleteAtoms::delete_overlap(int narg, char **arg)
if (force->pair == NULL)
error->all(FLERR,"Delete_atoms requires a pair style be defined");
if (cut > neighbor->cutneighmax)
if (cut > neighbor->cutneighmax)
error->all(FLERR,"Delete_atoms cutoff > neighbor cutoff");
// setup domain, communication and neighboring
@ -228,7 +228,7 @@ void DeleteAtoms::delete_overlap(int narg, char **arg)
// allocate and initialize deletion list
// must be after exchange potentially changes nlocal
int nlocal = atom->nlocal;
memory->create(dlist,nlocal,"delete_atoms:dlist");
for (int i = 0; i < nlocal; i++) dlist[i] = 0;
@ -298,9 +298,9 @@ void DeleteAtoms::delete_overlap(int narg, char **arg)
// test on tags of I,J insures that only I or J is deleted
if (j < nlocal) {
if (dlist[j]) continue;
if (dlist[j]) continue;
} else if ((mask[i] & group2bit) && (mask[j] & group1bit)) {
if (tag[i] > tag[j]) continue;
if (tag[i] > tag[j]) continue;
}
dlist[i] = 1;
@ -310,7 +310,7 @@ void DeleteAtoms::delete_overlap(int narg, char **arg)
}
/* ----------------------------------------------------------------------
create porosity by deleting atoms in a specified region
create porosity by deleting atoms in a specified region
------------------------------------------------------------------------- */
void DeleteAtoms::delete_porosity(int narg, char **arg)
@ -327,7 +327,7 @@ void DeleteAtoms::delete_porosity(int narg, char **arg)
RanMars *random = new RanMars(lmp,seed + comm->me);
// allocate and initialize deletion list
int nlocal = atom->nlocal;
memory->create(dlist,nlocal,"delete_atoms:dlist");
for (int i = 0; i < nlocal; i++) dlist[i] = 0;