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complete region handling refactor

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This commit is contained in:
Axel Kohlmeyer
2022-04-16 00:12:43 -04:00
parent cbb4abc55c
commit aa4787f604
39 changed files with 1504 additions and 1664 deletions
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77
src/group.cpp
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@ -40,8 +40,8 @@
using namespace LAMMPS_NS;
#define MAX_GROUP 32
#define EPSILON 1.0e-6
static constexpr int MAX_GROUP = 32;
static constexpr double EPSILON = 1.0e-6;
enum{NONE,TYPE,MOLECULE,ID};
enum{LT,LE,GT,GE,EQ,NEQ,BETWEEN};
@ -176,13 +176,13 @@ void Group::assign(int narg, char **arg)
if (narg != 3) error->all(FLERR,"Illegal group command");
int iregion = domain->find_region(arg[2]);
if (iregion == -1) error->all(FLERR,"Group region ID does not exist");
domain->regions[iregion]->init();
domain->regions[iregion]->prematch();
auto region = domain->get_region_by_id(arg[2]);
if (!region) error->all(FLERR,"Group region {} does not exist", arg[2]);
region->init();
region->prematch();
for (i = 0; i < nlocal; i++)
if (domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2]))
if (region->match(x[i][0],x[i][1],x[i][2]))
mask[i] |= bit;
// create an empty group
@ -813,15 +813,6 @@ bigint Group::count(int igroup, Region *region)
return nall;
}
/* ----------------------------------------------------------------------
count atoms in group and region
------------------------------------------------------------------------- */
bigint Group::count(int igroup, int iregion)
{
return count(igroup, domain->regions[iregion]);
}
/* ----------------------------------------------------------------------
compute the total mass of group of atoms
use either per-type mass or per-atom rmass
@ -886,16 +877,6 @@ double Group::mass(int igroup, Region *region)
return all;
}
/* ----------------------------------------------------------------------
compute the total mass of group of atoms in region
use either per-type mass or per-atom rmass
------------------------------------------------------------------------- */
double Group::mass(int igroup, int iregion)
{
return mass(igroup, domain->regions[iregion]);
}
/* ----------------------------------------------------------------------
compute the total charge of group of atoms
------------------------------------------------------------------------- */
@ -921,10 +902,9 @@ double Group::charge(int igroup)
compute the total charge of group of atoms in region
------------------------------------------------------------------------- */
double Group::charge(int igroup, int iregion)
double Group::charge(int igroup, Region *region)
{
int groupbit = bitmask[igroup];
Region *region = domain->regions[iregion];
region->prematch();
double **x = atom->x;
@ -990,10 +970,9 @@ void Group::bounds(int igroup, double *minmax)
periodic images are not considered, so atoms are NOT unwrapped
------------------------------------------------------------------------- */
void Group::bounds(int igroup, double *minmax, int iregion)
void Group::bounds(int igroup, double *minmax, Region *region)
{
int groupbit = bitmask[igroup];
Region *region = domain->regions[iregion];
region->prematch();
double extent[6];
@ -1090,10 +1069,9 @@ void Group::xcm(int igroup, double masstotal, double *cm)
must unwrap atoms to compute center-of-mass correctly
------------------------------------------------------------------------- */
void Group::xcm(int igroup, double masstotal, double *cm, int iregion)
void Group::xcm(int igroup, double masstotal, double *cm, Region *region)
{
int groupbit = bitmask[igroup];
Region *region = domain->regions[iregion];
region->prematch();
double **x = atom->x;
@ -1232,17 +1210,6 @@ void Group::vcm(int igroup, double masstotal, double *cm, Region *region)
}
}
/* ----------------------------------------------------------------------
compute the center-of-mass velocity of group of atoms in region
masstotal = total mass
return center-of-mass velocity in cm[]
------------------------------------------------------------------------- */
void Group::vcm(int igroup, double masstotal, double *cm, int iregion)
{
vcm(igroup, masstotal, cm, domain->regions[iregion]);
}
/* ----------------------------------------------------------------------
compute the total force on group of atoms
------------------------------------------------------------------------- */
@ -1272,10 +1239,9 @@ void Group::fcm(int igroup, double *cm)
compute the total force on group of atoms in region
------------------------------------------------------------------------- */
void Group::fcm(int igroup, double *cm, int iregion)
void Group::fcm(int igroup, double *cm, Region *region)
{
int groupbit = bitmask[igroup];
Region *region = domain->regions[iregion];
region->prematch();
double **x = atom->x;
@ -1368,15 +1334,6 @@ double Group::ke(int igroup, Region *region)
return all;
}
/* ----------------------------------------------------------------------
compute the total kinetic energy of group of atoms in region and return it
------------------------------------------------------------------------- */
double Group::ke(int igroup, int iregion)
{
return ke(igroup, domain->regions[iregion]);
}
/* ----------------------------------------------------------------------
compute the radius-of-gyration of group of atoms
around center-of-mass cm
@ -1422,10 +1379,9 @@ double Group::gyration(int igroup, double masstotal, double *cm)
must unwrap atoms to compute Rg correctly
------------------------------------------------------------------------- */
double Group::gyration(int igroup, double masstotal, double *cm, int iregion)
double Group::gyration(int igroup, double masstotal, double *cm, Region *region)
{
int groupbit = bitmask[igroup];
Region *region = domain->regions[iregion];
region->prematch();
double **x = atom->x;
@ -1504,10 +1460,9 @@ void Group::angmom(int igroup, double *cm, double *lmom)
must unwrap atoms to compute L correctly
------------------------------------------------------------------------- */
void Group::angmom(int igroup, double *cm, double *lmom, int iregion)
void Group::angmom(int igroup, double *cm, double *lmom, Region *region)
{
int groupbit = bitmask[igroup];
Region *region = domain->regions[iregion];
region->prematch();
double **x = atom->x;
@ -1583,10 +1538,9 @@ void Group::torque(int igroup, double *cm, double *tq)
must unwrap atoms to compute T correctly
------------------------------------------------------------------------- */
void Group::torque(int igroup, double *cm, double *tq, int iregion)
void Group::torque(int igroup, double *cm, double *tq, Region *region)
{
int groupbit = bitmask[igroup];
Region *region = domain->regions[iregion];
region->prematch();
double **x = atom->x;
@ -1669,12 +1623,11 @@ void Group::inertia(int igroup, double *cm, double itensor[3][3])
must unwrap atoms to compute itensor correctly
------------------------------------------------------------------------- */
void Group::inertia(int igroup, double *cm, double itensor[3][3], int iregion)
void Group::inertia(int igroup, double *cm, double itensor[3][3], Region *region)
{
int i,j;
int groupbit = bitmask[igroup];
Region *region = domain->regions[iregion];
region->prematch();
double **x = atom->x;