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Merge pull request #4182 from akohlmey/group-bitmap-accessor

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Refactor code to use group bitmap accessor
This commit is contained in:
Axel Kohlmeyer
2025-03-25 14:12:27 -04:00
committed by GitHub
parent 5dbeacb1e8 d5b82562bd
commit 9e241df062
20 changed files with 89 additions and 77 deletions
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2
src/atom.cpp
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@ -2301,7 +2301,7 @@ void Atom::first_reorder()
// nfirst = index of first atom not in firstgroup
// when find firstgroup atom out of place, swap it with atom nfirst
int bitmask = group->bitmask[firstgroup];
const int bitmask = group->get_bitmask_by_id(FLERR, firstgroupname, "Atom::first_reorder");
nfirst = 0;
while (nfirst < nlocal && mask[nfirst] & bitmask) nfirst++;

4
src/change_box.cpp
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@ -52,9 +52,7 @@ void ChangeBox::command(int narg, char **arg)
// group
int igroup = group->find(arg[0]);
if (igroup == -1) error->all(FLERR,"Could not find change_box group ID {}", arg[0]);
int groupbit = group->bitmask[igroup];
int groupbit = group->get_bitmask_by_id(FLERR, arg[0], "change_box");
// parse operation arguments
// allocate ops to max possible length

6
src/compute.cpp
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@ -48,11 +48,11 @@ Compute::Compute(LAMMPS *lmp, int narg, char **arg) :
id = utils::strdup(arg[0]);
if (!utils::is_id(id))
error->all(FLERR,"Compute ID must be alphanumeric or underscore characters");
error->all(FLERR,"Compute ID {} must only have alphanumeric or underscore characters", id);
groupbit = group->get_bitmask_by_id(FLERR, arg[1], fmt::format("compute {}", arg[2]));
igroup = group->find(arg[1]);
if (igroup == -1) error->all(FLERR,"Could not find compute group ID");
groupbit = group->bitmask[igroup];
if (igroup == -1) error->all(FLERR,"Could not find compute group ID {}", arg[1]);
style = utils::strdup(arg[2]);

8
src/compute_coord_atom.cpp
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@ -39,8 +39,7 @@ ComputeCoordAtom::ComputeCoordAtom(LAMMPS *lmp, int narg, char **arg) :
{
if (narg < 5) error->all(FLERR, "Illegal compute coord/atom command");
jgroup = group->find("all");
jgroupbit = group->bitmask[jgroup];
jgroupbit = group->get_bitmask_by_id(FLERR, "all", "compute coord/atom");
cstyle = NONE;
if (strcmp(arg[3], "cutoff") == 0) {
@ -50,11 +49,10 @@ ComputeCoordAtom::ComputeCoordAtom(LAMMPS *lmp, int narg, char **arg) :
int iarg = 5;
if ((narg > 6) && (strcmp(arg[5], "group") == 0)) {
delete[] group2;
group2 = utils::strdup(arg[6]);
iarg += 2;
jgroup = group->find(group2);
if (jgroup == -1) error->all(FLERR, "Compute coord/atom group2 ID does not exist");
jgroupbit = group->bitmask[jgroup];
jgroupbit = group->get_bitmask_by_id(FLERR, group2, "compute coord/atom");
}
ncol = narg - iarg + 1;

2
src/compute_coord_atom.h
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@ -46,7 +46,7 @@ class ComputeCoordAtom : public Compute {
double **carray;
char *group2;
int jgroup, jgroupbit;
int jgroupbit;
class ComputeOrientOrderAtom *c_orientorder;
char *id_orientorder;

8
src/compute_group_group.cpp
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@ -54,9 +54,7 @@ ComputeGroupGroup::ComputeGroupGroup(LAMMPS *lmp, int narg, char **arg) :
extvector = 1;
group2 = utils::strdup(arg[3]);
jgroup = group->find(group2);
if (jgroup == -1) error->all(FLERR, "Compute group/group group ID does not exist");
jgroupbit = group->bitmask[jgroup];
jgroupbit = group->get_bitmask_by_id(FLERR, group2, "compute group/group");
pairflag = 1;
kspaceflag = 0;
@ -147,9 +145,7 @@ void ComputeGroupGroup::init()
// recheck that group 2 has not been deleted
jgroup = group->find(group2);
if (jgroup == -1) error->all(FLERR, "Compute group/group group ID does not exist");
jgroupbit = group->bitmask[jgroup];
jgroupbit = group->get_bitmask_by_id(FLERR, group2, "compute group/group");
// need an occasional half neighbor list

2
src/compute_group_group.h
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@ -35,7 +35,7 @@ class ComputeGroupGroup : public Compute {
private:
char *group2;
int jgroup, jgroupbit, othergroupbit;
int jgroupbit;
double **cutsq;
double e_self, e_correction;
int pairflag, kspaceflag, boundaryflag, molflag;

8
src/create_bonds.cpp
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@ -59,12 +59,8 @@ void CreateBonds::command(int narg, char **arg)
if (strcmp(arg[0], "many") == 0) {
style = MANY;
if (narg != 6) error->all(FLERR, "No optional keywords allowed with create_bonds many");
igroup = group->find(arg[1]);
if (igroup == -1) error->all(FLERR, "Cannot find create_bonds first group ID {}", arg[1]);
group1bit = group->bitmask[igroup];
igroup = group->find(arg[2]);
if (igroup == -1) error->all(FLERR, "Cannot find create_bonds second group ID {}", arg[2]);
group2bit = group->bitmask[igroup];
group1bit = group->get_bitmask_by_id(FLERR, arg[1], "create_bonds");
group2bit = group->get_bitmask_by_id(FLERR, arg[2], "create_bonds");
btype = utils::inumeric(FLERR, arg[3], false, lmp);
rmin = utils::numeric(FLERR, arg[4], false, lmp);
rmax = utils::numeric(FLERR, arg[5], false, lmp);

2
src/create_bonds.h
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@ -30,7 +30,7 @@ class CreateBonds : public Command {
void command(int, char **) override;
private:
int igroup, group1bit, group2bit;
int group1bit, group2bit;
int btype, atype, dtype;
tagint batom1, batom2, aatom1, aatom2, aatom3, datom1, datom2, datom3, datom4;
double rmin, rmax;

25
src/delete_atoms.cpp
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@ -87,8 +87,8 @@ void DeleteAtoms::command(int narg, char **arg)
error->all(FLERR, "Unknown delete_atoms sub-command: {}", arg[0]);
if (allflag) {
int igroup = group->find("all");
if ((igroup >= 0) && modify->check_rigid_group_overlap(group->bitmask[igroup]))
int igroupbit = group->get_bitmask_by_id(FLERR, "all", "delete_atoms");
if (modify->check_rigid_group_overlap(igroupbit))
error->warning(FLERR, "Attempting to delete atoms in rigid bodies");
} else {
if (modify->check_rigid_list_overlap(dlist))
@ -216,8 +216,7 @@ void DeleteAtoms::delete_group(int narg, char **arg)
{
if (narg < 2) utils::missing_cmd_args(FLERR, "delete_atoms group", error);
int igroup = group->find(arg[1]);
if (igroup == -1) error->all(FLERR, "Could not find delete_atoms group ID {}", arg[1]);
int groupbit = group->get_bitmask_by_id(FLERR, arg[1], "delete_atoms");
options(narg - 2, &arg[2]);
// check for special case of group = all
@ -234,8 +233,6 @@ void DeleteAtoms::delete_group(int narg, char **arg)
for (int i = 0; i < nlocal; i++) dlist[i] = 0;
int *mask = atom->mask;
int groupbit = group->bitmask[igroup];
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) dlist[i] = 1;
}
@ -281,18 +278,11 @@ void DeleteAtoms::delete_overlap(int narg, char **arg)
const double cut = utils::numeric(FLERR, arg[1], false, lmp);
const double cutsq = cut * cut;
const int group1bit = group->get_bitmask_by_id(FLERR, arg[2], "delete_atoms");
const int group2bit = group->get_bitmask_by_id(FLERR, arg[3], "delete_atoms");
int igroup1 = group->find(arg[2]);
if (igroup1 < 0)
error->all(FLERR, "Could not find delete_atoms overlap first group ID {}", arg[2]);
int igroup2 = group->find(arg[3]);
if (igroup2 < 0)
error->all(FLERR, "Could not find delete_atoms overlap second group ID {}", arg[3]);
options(narg - 4, &arg[4]);
const int group1bit = group->bitmask[igroup1];
const int group2bit = group->bitmask[igroup2];
if (comm->me == 0) utils::logmesg(lmp, "System init for delete_atoms ...\n");
// request a full neighbor list for use by this command
@ -454,9 +444,7 @@ void DeleteAtoms::delete_random(int narg, char **arg)
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 random group ID {}", arg[4]);
int groupbit = group->get_bitmask_by_id(FLERR, arg[4], "delete_atoms");
auto region = domain->get_region_by_id(arg[5]);
if (!region && (strcmp(arg[5], "NULL") != 0))
error->all(FLERR, "Could not find delete_atoms random region ID {}", arg[5]);
@ -477,7 +465,6 @@ void DeleteAtoms::delete_random(int narg, char **arg)
double **x = atom->x;
int *mask = atom->mask;
int groupbit = group->bitmask[igroup];
if (region) region->prematch();
// delete approximate fraction of atoms in both group and region

6
src/delete_bonds.cpp
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@ -56,11 +56,9 @@ void DeleteBonds::command(int narg, char **arg)
if (comm->me == 0) utils::logmesg(lmp,"Deleting bonds ...\n");
// identify group
// get group bitmask
int igroup = group->find(arg[0]);
if (igroup == -1) error->all(FLERR,"Cannot find delete_bonds group ID");
int groupbit = group->bitmask[igroup];
int groupbit = group->get_bitmask_by_id(FLERR, arg[0], "delete_bonds");
// set style and which = type value

3
src/displace_atoms.cpp
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@ -74,8 +74,7 @@ void DisplaceAtoms::command(int narg, char **arg)
// group and style
igroup = group->find(arg[0]);
if (igroup == -1) error->all(FLERR,"Could not find displace_atoms group ID");
groupbit = group->bitmask[igroup];
groupbit = group->get_bitmask_by_id(FLERR, arg[0], "displace_atoms");
if (modify->check_rigid_group_overlap(groupbit))
error->warning(FLERR,"Attempting to displace atoms in rigid bodies");

3
src/dump.cpp
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@ -58,7 +58,7 @@ Dump::Dump(LAMMPS *lmp, int /*narg*/, char **arg) :
id = utils::strdup(arg[0]);
igroup = group->find(arg[1]);
groupbit = group->bitmask[igroup];
groupbit = group->get_bitmask_by_id(FLERR, arg[1], fmt::format("dump {}", arg[2]));
style = utils::strdup(arg[2]);
@ -311,6 +311,7 @@ void Dump::init()
int Dump::count()
{
// group all
if (igroup == 0) return atom->nlocal;
int *mask = atom->mask;

4
src/fix.cpp
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@ -48,8 +48,8 @@ Fix::Fix(LAMMPS *lmp, int /*narg*/, char **arg) :
error->all(FLERR,"Fix ID must be alphanumeric or underscore characters");
igroup = group->find(arg[1]);
if (igroup == -1) error->all(FLERR,"Could not find fix group ID");
groupbit = group->bitmask[igroup];
if (igroup == -1) error->all(FLERR,"Could not find fix {} group ID {}", arg[2], arg[1]);
groupbit = group->get_bitmask_by_id(FLERR, arg[1], fmt::format("fix {}",arg[2]));
style = utils::strdup(arg[2]);

10
src/fix_nh.cpp
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@ -271,7 +271,7 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) :
delete[] id_dilate;
id_dilate = utils::strdup(arg[iarg+1]);
int idilate = group->find(id_dilate);
if (idilate == -1)
if (idilate < 0)
error->all(FLERR,"Fix {} dilate group ID {} does not exist", style, id_dilate);
}
iarg += 2;
@ -629,12 +629,8 @@ void FixNH::init()
{
// recheck that dilate group has not been deleted
if (allremap == 0) {
int idilate = group->find(id_dilate);
if (idilate == -1)
error->all(FLERR,"Fix {} dilate group ID {} does not exist", style, id_dilate);
dilate_group_bit = group->bitmask[idilate];
}
if (allremap == 0)
dilate_group_bit = group->get_bitmask_by_id(FLERR, id_dilate, fmt::format("fix {}", style));
// ensure no conflict with fix deform

13
src/fix_recenter.cpp
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@ -41,7 +41,7 @@ enum{BOX,LATTICE,FRACTION};
FixRecenter::FixRecenter(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 6) error->all(FLERR,"Illegal fix recenter command");
if (narg < 6) utils::missing_cmd_args(FLERR,"fix recenter", error);
xcom = ycom = zcom = 0.0;
xflag = yflag = zflag = 1;
@ -74,17 +74,15 @@ FixRecenter::FixRecenter(LAMMPS *lmp, int narg, char **arg) :
int iarg = 6;
while (iarg < narg) {
if (strcmp(arg[iarg],"shift") == 0) {
int igroup2 = group->find(arg[iarg+1]);
if (igroup2 < 0) error->all(FLERR,"Could not find fix recenter group ID");
group2bit = group->bitmask[igroup2];
group2bit = group->get_bitmask_by_id(FLERR, arg[iarg+1], "fix recenter");
iarg += 2;
} else if (strcmp(arg[iarg],"units") == 0) {
if (strcmp(arg[iarg+1],"box") == 0) scaleflag = BOX;
else if (strcmp(arg[iarg+1],"lattice") == 0) scaleflag = LATTICE;
else if (strcmp(arg[iarg+1],"fraction") == 0) scaleflag = FRACTION;
else error->all(FLERR,"Illegal fix recenter command");
else error->all(FLERR,"Unknown fix recenter units argument {}", arg[iarg+1]);
iarg += 2;
} else error->all(FLERR,"Illegal fix recenter command");
} else error->all(FLERR,"Unknown fix recenter keyword {}", arg[iarg]);
}
// scale xcom,ycom,zcom
@ -103,8 +101,7 @@ FixRecenter::FixRecenter(LAMMPS *lmp, int narg, char **arg) :
// cannot have 0 atoms in group
if (group->count(igroup) == 0)
error->all(FLERR,"Fix recenter group has no atoms");
if (group->count(igroup) == 0) error->all(FLERR,"Fix recenter group {} has no atoms", arg[1]);
}
/* ---------------------------------------------------------------------- */

10
src/fix_spring.cpp
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@ -73,11 +73,9 @@ FixSpring::FixSpring(LAMMPS *lmp, int narg, char **arg) :
group2 = utils::strdup(arg[4]);
igroup2 = group->find(arg[4]);
if (igroup2 == -1)
error->all(FLERR,"Fix spring couple group ID does not exist");
if (igroup2 == igroup)
error->all(FLERR,"Two groups cannot be the same in fix spring couple");
group2bit = group->bitmask[igroup2];
error->all(FLERR,"The two groups cannot be the same in fix spring couple");
group2bit = group->get_bitmask_by_id(FLERR, arg[4], "fix spring");
k_spring = utils::numeric(FLERR,arg[5],false,lmp);
xflag = yflag = zflag = 1;
@ -121,9 +119,7 @@ void FixSpring::init()
if (group2) {
igroup2 = group->find(group2);
if (igroup2 == -1)
error->all(FLERR,"Fix spring couple group ID does not exist");
group2bit = group->bitmask[igroup2];
group2bit = group->get_bitmask_by_id(FLERR, group2, "fix spring");
}
masstotal = group->mass(igroup);

13
src/group.cpp
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@ -649,6 +649,19 @@ int Group::find_unused()
return -1;
}
/* ----------------------------------------------------------------------
return group bitmask for given group id. Error out if group is not found.
------------------------------------------------------------------------- */
int Group::get_bitmask_by_id(const std::string &file, int line, const std::string &name,
const std::string &caller)
{
int igroup = find(name);
if (igroup < 0)
error->all(file, line, "Group ID {} requested by {} does not exist", name, caller);
return bitmask[igroup];
}
/* ----------------------------------------------------------------------
add atoms to group that are in same molecules as atoms already in group
do not include molID = 0

2
src/group.h
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@ -31,11 +31,13 @@ class Group : protected Pointers {
Group(class LAMMPS *);
~Group() override;
void assign(int, char **); // assign atoms to a group
void assign(const std::string &); // convenience function
void create(const std::string &, int *); // add flagged atoms to a group
int find(const std::string &); // lookup name in list of groups
int find_or_create(const char *); // lookup name or create new group
int get_bitmask_by_id(const std::string &, int, const std::string &, const std::string &);
void write_restart(FILE *);
void read_restart(FILE *);

35
unittest/commands/test_groups.cpp
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@ -256,6 +256,41 @@ TEST_F(GroupTest, Molecular)
command("group three include xxx"););
}
TEST_F(GroupTest, Bitmap)
{
atomic_system();
BEGIN_HIDE_OUTPUT();
command("group one region left");
command("group two region right");
command("group three empty");
command("group four region left");
command("group four region right");
command("group six subtract four one");
END_HIDE_OUTPUT();
int bm_one = group->get_bitmask_by_id(FLERR, "one", "unittest 1");
int bm_two = group->get_bitmask_by_id(FLERR, "two", "unittest 2");
int bm_three = group->get_bitmask_by_id(FLERR, "three", "unittest 3");
int bm_four = group->get_bitmask_by_id(FLERR, "four", "unittest 4");
int bm_six = group->get_bitmask_by_id(FLERR, "six", "unittest 6");
int nlocal = lmp->atom->natoms;
auto mask = lmp->atom->mask;
for (int i = 0; i < nlocal; ++i) {
if ((mask[i] & bm_one) && (mask[i] & bm_two)) {
EXPECT_NE((mask[i] & bm_four), 0);
}
if (mask[i] & bm_two) {
EXPECT_NE((mask[i] & bm_six), 0);
}
EXPECT_EQ((mask[i] & bm_three), 0);
}
TEST_FAILURE(".*ERROR: Group ID five requested by unittest 5 does not exist.*",
group->get_bitmask_by_id(FLERR, "five", "unittest 5"););
}
TEST_F(GroupTest, Dynamic)
{
atomic_system();