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change partial to random

This commit is contained in:
Steve Plimpton 2022-05-17 11:02:42 -06:00
parent c0e5a03989
commit dbb3e75f24
3 changed files with 30 additions and 30 deletions
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26
doc/src/delete_atoms.rst
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@ -20,8 +20,8 @@ Syntax
cutoff = delete one atom from pairs of atoms within the cutoff (distance units)
group1-ID = one atom in pair must be in this group
group2-ID = other atom in pair must be in this group
*partial* args = pstyle value flag group-ID region-ID seed
pstyle = *fraction* or *count*
*random* args = ranstyle value flag group-ID region-ID seed
ranstyle = *fraction* or *count*
for *fraction*:
value = fraction (0.0 to 1.0) of eligible atoms to delete
flag = no/off for fast approximate deletion, yes/on for exact deletion
@ -52,9 +52,9 @@ Examples
delete_atoms region sphere compress no
delete_atoms overlap 0.3 all all
delete_atoms overlap 0.5 solvent colloid
delete_atoms partial fraction 0.1 1 all cube 482793 bond yes
delete_atoms partial fraction 0.3 0 polymer NULL 482793 bond yes
delete_atoms partial count 500 0 ions NULL 482793
delete_atoms random fraction 0.1 1 all cube 482793 bond yes
delete_atoms random fraction 0.3 0 polymer NULL 482793 bond yes
delete_atoms random count 500 0 ions NULL 482793
detele_atoms variable checkers
Description
@ -88,12 +88,12 @@ have occurred that no atom pairs within the cutoff will remain
minimum number of atoms will be deleted, or that the same atoms will
be deleted when running on different numbers of processors.
For style *partial* a subset of eligible atoms are deleted. Which
For style *random* a subset of eligible atoms are deleted. Which
atoms to delete are chosen randomly using the specified random number
*seed*. In all cases, which atoms are deleted may vary when running
on different numbers of processors.
For *pstyle* = *fraction*, the specified fraction *value*(0.0 to 1.0) of
For *ranstyle* = *fraction*, the specified fraction *value*(0.0 to 1.0) of
eligible atoms are deleted. If the *flag* is set to no/off/0, then the
number of deleted atoms will be approximate, but the operation will
always be fast. If instead the *flag* is set to yes/on/1, then the
@ -101,14 +101,14 @@ number deleted will be match the requested fraction as close as
possible, but for very large systems the selection of deleted atoms will
take additional time to determine.
For *pstyle* = *count*, the specified integer *value* is the number of
eligible atoms are deleted. If the *flag* is set to no/off/0, then
if the requested number is larger then the number of eligible atoms,
a warning is issued and only the eligible atoms are deleted instead of
For *ranstyle* = *count*, the specified integer *value* is the number
of eligible atoms are deleted. If the *flag* is set to no/off/0, then
if the requested number is larger then the number of eligible atoms, a
warning is issued and only the eligible atoms are deleted instead of
the requested *value*. If the *flag* is set to yes/on/1, an error is
triggered instead and LAMMPS will exit. For very large systems the
selection of atoms to delete may take additional time same as for requesting
the exact fraction with time as *pstyle* = *fraction*.
selection of atoms to delete may take additional time same as for
requesting the exact fraction with time as *pstyle* = *fraction*.
Which atoms are eligible for deletion for style *partial* is determined
by the specified *group-ID* and *region-ID*. To be eligible, an atom

32
src/delete_atoms.cpp
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@ -73,13 +73,13 @@ void DeleteAtoms::command(int narg, char **arg)
delete_region(narg, arg);
else if (strcmp(arg[0], "overlap") == 0)
delete_overlap(narg, arg);
else if (strcmp(arg[0], "partial") == 0)
delete_partial(narg, arg);
else if (strcmp(arg[0], "random") == 0)
delete_random(narg, arg);
// deprecated porosity option, now included in new partial option
else if (strcmp(arg[0], "porosity") == 0) {
error->all(FLERR,
"The delete_atoms 'porosity' keyword has been removed.\n"
"Please use: delete_atoms partial fraction frac exact group-ID region-ID seed\n");
"Please use: delete_atoms random fraction frac exact group-ID region-ID seed\n");
} else if (strcmp(arg[0], "variable") == 0)
delete_variable(narg, arg);
else
@ -422,38 +422,38 @@ void DeleteAtoms::delete_overlap(int narg, char **arg)
delete specified portion of atoms within group and/or region
------------------------------------------------------------------------- */
void DeleteAtoms::delete_partial(int narg, char **arg)
void DeleteAtoms::delete_random(int narg, char **arg)
{
if (narg < 7) utils::missing_cmd_args(FLERR, "delete_atoms partial", error);
if (narg < 7) utils::missing_cmd_args(FLERR, "delete_atoms random", error);
int partial_style = UNKNOWN;
int random_style = UNKNOWN;
bool exactflag = false;
bool errorflag = false;
bigint ncount = 0;
double fraction = 0.0;
if (strcmp(arg[1], "fraction") == 0) {
partial_style = FRACTION;
random_style = FRACTION;
fraction = utils::numeric(FLERR, arg[2], false, lmp);
exactflag = utils::logical(FLERR, arg[3], false, lmp);
if (fraction < 0.0 || fraction > 1.0)
error->all(FLERR, "Delete_atoms partial fraction has invalid value: {}", fraction);
error->all(FLERR, "Delete_atoms random fraction has invalid value: {}", fraction);
} else if (strcmp(arg[1], "count") == 0) {
partial_style = COUNT;
random_style = COUNT;
ncount = utils::bnumeric(FLERR, arg[2], false, lmp);
errorflag = utils::logical(FLERR, arg[3], false, lmp);
if (ncount < 0) error->all(FLERR, "Delete_atoms partial count has invalid value: {}", ncount);
if (ncount < 0) error->all(FLERR, "Delete_atoms random count has invalid value: {}", ncount);
exactflag = true;
} else {
error->all(FLERR, "Unknown delete_atoms partial style: {}", arg[1]);
error->all(FLERR, "Unknown delete_atoms random style: {}", arg[1]);
}
int igroup = group->find(arg[4]);
if (igroup == -1) error->all(FLERR, "Could not find delete_atoms partial group ID {}", arg[4]);
if (igroup == -1) error->all(FLERR, "Could not find delete_atoms random group ID {}", arg[4]);
auto region = domain->get_region_by_id(arg[5]);
if (!region && (strcmp(arg[5], "NULL") != 0))
error->all(FLERR, "Could not find delete_atoms partial region ID {}", arg[5]);
error->all(FLERR, "Could not find delete_atoms random region ID {}", arg[5]);
int seed = utils::inumeric(FLERR, arg[6], false, lmp);
options(narg - 7, &arg[7]);
@ -476,7 +476,7 @@ void DeleteAtoms::delete_partial(int narg, char **arg)
// delete approximate fraction of atoms in both group and region
if (partial_style == FRACTION && !exactflag) {
if (random_style == FRACTION && !exactflag) {
for (int i = 0; i < nlocal; i++) {
if (!(mask[i] & groupbit)) continue;
if (region && !region->match(x[i][0], x[i][1], x[i][2])) continue;
@ -504,9 +504,9 @@ void DeleteAtoms::delete_partial(int narg, char **arg)
bigint allcount;
MPI_Allreduce(&bcount, &allcount, 1, MPI_LMP_BIGINT, MPI_SUM, world);
if (partial_style == FRACTION) {
if (random_style == FRACTION) {
ncount = static_cast<bigint>(fraction * allcount);
} else if (partial_style == COUNT) {
} else if (random_style == COUNT) {
if (ncount > allcount) {
auto mesg = fmt::format("Delete_atoms count of {} exceeds number of eligible atoms {}",
ncount, allcount);

2
src/delete_atoms.h
View File

@ -38,7 +38,7 @@ class DeleteAtoms : public Command {
void delete_group(int, char **);
void delete_region(int, char **);
void delete_overlap(int, char **);
void delete_partial(int, char **);
void delete_random(int, char **);
void delete_variable(int, char **);
void delete_bond();