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bug fixes from Doug Spearot

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This commit is contained in:
Steve Plimpton
2021-11-30 08:22:38 -07:00
parent 4d19895a88
commit 4a05628938
2 changed files with 20 additions and 19 deletions
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28
doc/src/delete_atoms.rst
View File

@ -81,9 +81,9 @@ be deleted when running on different numbers of processors.
For style *porosity* a specified *fraction* of atoms are deleted which
are both in the specified group and within the specified region. The
region-ID can be specified as NULL to only impose the group
criterion. Likewise, specifying the group-ID as *all* will only impose
the region criterion.
region-ID can be specified as NULL to only impose the group criterion.
Likewise, specifying the group-ID as *all* will only impose the region
criterion.
For example, if fraction is 0.1, then 10% of the eligible atoms will
be deleted. The atoms to delete are chosen randomly. There is no
@ -97,8 +97,8 @@ number of atoms in the system. Note that this is not done for
molecular systems (see the :doc:`atom_style <atom_style>` command),
regardless of the *compress* setting, since it would foul up the bond
connectivity that has already been assigned. However, the
:doc:`reset_atom_ids <reset_atom_ids>` command can be used after this command to
accomplish the same thing.
:doc:`reset_atom_ids <reset_atom_ids>` command can be used after this
command to accomplish the same thing.
Note that the re-assignment of IDs is not really a compression, where
gaps in atom IDs are removed by decrementing atom IDs that are larger.
@ -108,15 +108,15 @@ the :doc:`create_atoms <create_atoms>` command explains.
A molecular system with fixed bonds, angles, dihedrals, or improper
interactions, is one where the topology of the interactions is
typically defined in the data file read by the
:doc:`read_data <read_data>` command, and where the interactions
themselves are defined with the :doc:`bond_style <bond_style>`,
:doc:`angle_style <angle_style>`, etc commands. If you delete atoms
from such a system, you must be careful not to end up with bonded
interactions that are stored by remaining atoms but which include
deleted atoms. This will cause LAMMPS to generate a "missing atoms"
error when the bonded interaction is computed. The *bond* and *mol*
keywords offer two ways to do that.
typically defined in the data file read by the :doc:`read_data
<read_data>` command, and where the interactions themselves are
defined with the :doc:`bond_style <bond_style>`, :doc:`angle_style
<angle_style>`, etc commands. If you delete atoms from such a system,
you must be careful not to end up with bonded interactions that are
stored by remaining atoms but which include deleted atoms. This will
cause LAMMPS to generate a "missing atoms" error when the bonded
interaction is computed. The *bond* and *mol* keywords offer two ways
to do that.
It the *bond* keyword is set to *yes* then any bond or angle or
dihedral or improper interaction that includes a deleted atom is also

11
src/delete_atoms.cpp
View File

@ -431,7 +431,7 @@ void DeleteAtoms::delete_porosity(int narg, char **arg)
if (strcmp(arg[2],"NULL") == 0) regionflag = 0;
else {
regionflag = 1;
int iregion = domain->find_region(arg[2]);
iregion = domain->find_region(arg[2]);
if (iregion == -1) error->all(FLERR,"Could not find delete_atoms region ID");
domain->regions[iregion]->prematch();
}
@ -448,17 +448,18 @@ void DeleteAtoms::delete_porosity(int narg, char **arg)
memory->create(dlist,nlocal,"delete_atoms:dlist");
for (int i = 0; i < nlocal; i++) dlist[i] = 0;
// delete fraction of atoms in both group and region
// delete fraction of atoms which are in both group and region
double **x = atom->x;
int *mask = atom->mask;
int groupbit = group->bitmask[igroup];
for (int i = 0; i < nlocal; i++) {
for (int i = 0; i < nlocal; i++) {
if (!(mask[i] & groupbit)) continue;
if (regionflag && domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2]))
if (random->uniform() <= porosity_fraction) dlist[i] = 1;
if (regionflag &&
!domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2])) continue;
if (random->uniform() <= porosity_fraction) dlist[i] = 1;
}
delete random;