Homec4science
Diffusion lammps (lammm-devel) Browse

lammps/src/region_union.cpp
17c17ac40996lammm-devel

Last Change
Raw File

region_union.cpp
View Options

/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
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
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include <stdlib.h>
#include <string.h>
#include "region_union.h"
#include "domain.h"
#include "error.h"
#include "force.h"
using namespace LAMMPS_NS;
#define BIG 1.0e20
/* ---------------------------------------------------------------------- */
RegUnion::RegUnion(LAMMPS *lmp, int narg, char **arg) : Region(lmp, narg, arg),
idsub(NULL)
{
nregion = 0;
if (narg < 5) error->all(FLERR,"Illegal region command");
int n = force->inumeric(FLERR,arg[2]);
if (n < 2) error->all(FLERR,"Illegal region command");
options(narg-(n+3),&arg[n+3]);
// build list of region indices to union
// store sub-region IDs in idsub
idsub = new char*[n];
list = new int[n];
nregion = 0;
int m,iregion;
for (int iarg = 0; iarg < n; iarg++) {
m = strlen(arg[iarg+3]) + 1;
idsub[nregion] = new char[m];
strcpy(idsub[nregion],arg[iarg+3]);
iregion = domain->find_region(idsub[nregion]);
if (iregion == -1)
error->all(FLERR,"Region union region ID does not exist");
list[nregion++] = iregion;
}
// this region is variable shape or dynamic if any of sub-regions are
Region **regions = domain->regions;
for (int ilist = 0; ilist < nregion; ilist++) {
if (regions[list[ilist]]->varshape) varshape = 1;
if (regions[list[ilist]]->dynamic) dynamic = 1;
if (regions[list[ilist]]->moveflag) moveflag = 1;
if (regions[list[ilist]]->rotateflag) rotateflag = 1;
}
// extent of union of regions
// has bounding box if interior and all sub-regions have bounding box
bboxflag = 1;
for (int ilist = 0; ilist < nregion; ilist++)
if (regions[list[ilist]]->bboxflag == 0) bboxflag = 0;
if (!interior) bboxflag = 0;
if (bboxflag) {
extent_xlo = extent_ylo = extent_zlo = BIG;
extent_xhi = extent_yhi = extent_zhi = -BIG;
for (int ilist = 0; ilist < nregion; ilist++) {
extent_xlo = MIN(extent_xlo,regions[list[ilist]]->extent_xlo);
extent_ylo = MIN(extent_ylo,regions[list[ilist]]->extent_ylo);
extent_zlo = MIN(extent_zlo,regions[list[ilist]]->extent_zlo);
extent_xhi = MAX(extent_xhi,regions[list[ilist]]->extent_xhi);
extent_yhi = MAX(extent_yhi,regions[list[ilist]]->extent_yhi);
extent_zhi = MAX(extent_zhi,regions[list[ilist]]->extent_zhi);
}
}
// possible contacts = sum of possible contacts in all sub-regions
// for near contacts and touching contacts
cmax = 0;
for (int ilist = 0; ilist < nregion; ilist++)
cmax += regions[list[ilist]]->cmax;
contact = new Contact[cmax];
tmax = 0;
for (int ilist = 0; ilist < nregion; ilist++) {
if (interior) tmax += regions[list[ilist]]->tmax;
else tmax++;
}
}
/* ---------------------------------------------------------------------- */
RegUnion::~RegUnion()
{
for (int ilist = 0; ilist < nregion; ilist++) delete [] idsub[ilist];
delete [] idsub;
delete [] list;
delete [] contact;
}
/* ---------------------------------------------------------------------- */
void RegUnion::init()
{
Region::init();
// re-build list of sub-regions in case other regions were deleted
// error if a sub-region was deleted
int iregion;
for (int ilist = 0; ilist < nregion; ilist++) {
iregion = domain->find_region(idsub[ilist]);
if (iregion == -1)
error->all(FLERR,"Region union region ID does not exist");
list[ilist] = iregion;
}
// init the sub-regions
Region **regions = domain->regions;
for (int ilist = 0; ilist < nregion; ilist++)
regions[list[ilist]]->init();
}
/* ----------------------------------------------------------------------
inside = 1 if x,y,z is match() with any sub-region
else inside = 0
------------------------------------------------------------------------- */
int RegUnion::inside(double x, double y, double z)
{
int ilist;
Region **regions = domain->regions;
for (ilist = 0; ilist < nregion; ilist++)
if (regions[list[ilist]]->match(x,y,z)) break;
if (ilist == nregion) return 0;
return 1;
}
/* ----------------------------------------------------------------------
compute contacts with interior of union of sub-regions
(1) compute contacts in each sub-region
(2) only keep a contact if surface point is not match() to all other regions
------------------------------------------------------------------------- */
int RegUnion::surface_interior(double *x, double cutoff)
{
int m,ilist,jlist,iregion,jregion,ncontacts;
double xs,ys,zs;
Region **regions = domain->regions;
int n = 0;
int walloffset = 0 ;
for (ilist = 0; ilist < nregion; ilist++) {
iregion = list[ilist];
ncontacts = regions[iregion]->surface(x[0],x[1],x[2],cutoff);
for (m = 0; m < ncontacts; m++) {
xs = x[0] - regions[iregion]->contact[m].delx;
ys = x[1] - regions[iregion]->contact[m].dely;
zs = x[2] - regions[iregion]->contact[m].delz;
for (jlist = 0; jlist < nregion; jlist++) {
if (jlist == ilist) continue;
jregion = list[jlist];
if (regions[jregion]->match(xs,ys,zs) &&
!regions[jregion]->openflag) break;
}
if (jlist == nregion) {
contact[n].r = regions[iregion]->contact[m].r;
contact[n].radius = regions[iregion]->contact[m].radius;
contact[n].delx = regions[iregion]->contact[m].delx;
contact[n].dely = regions[iregion]->contact[m].dely;
contact[n].delz = regions[iregion]->contact[m].delz;
contact[n].iwall = regions[iregion]->contact[m].iwall + walloffset;
contact[n].varflag = regions[iregion]->contact[m].varflag;
n++;
}
}
// increment by cmax instead of tmax to insure
// possible wall IDs for sub-regions are non overlapping
walloffset += regions[iregion]->cmax;
}
return n;
}
/* ----------------------------------------------------------------------
compute contacts with exterior of union of sub-regions
(1) flip interior/exterior flag of each sub-region
(2) compute contacts in each sub-region
(3) only keep a contact if surface point is match() to all other regions
(4) flip interior/exterior flags back to original settings
this is effectively same algorithm as surface_interior() for RegIntersect
------------------------------------------------------------------------- */
int RegUnion::surface_exterior(double *x, double cutoff)
{
int m,ilist,jlist,iregion,jregion,ncontacts;
double xs,ys,zs;
Region **regions = domain->regions;
int n = 0;
for (ilist = 0; ilist < nregion; ilist++)
regions[list[ilist]]->interior ^= 1;
for (ilist = 0; ilist < nregion; ilist++) {
iregion = list[ilist];
ncontacts = regions[iregion]->surface(x[0],x[1],x[2],cutoff);
for (m = 0; m < ncontacts; m++) {
xs = x[0] - regions[iregion]->contact[m].delx;
ys = x[1] - regions[iregion]->contact[m].dely;
zs = x[2] - regions[iregion]->contact[m].delz;
for (jlist = 0; jlist < nregion; jlist++) {
if (jlist == ilist) continue;
jregion = list[jlist];
if (!regions[jregion]->match(xs,ys,zs)) break;
}
if (jlist == nregion) {
contact[n].r = regions[iregion]->contact[m].r;
contact[n].radius = regions[iregion]->contact[m].radius;
contact[n].delx = regions[iregion]->contact[m].delx;
contact[n].dely = regions[iregion]->contact[m].dely;
contact[n].delz = regions[iregion]->contact[m].delz;
contact[n].iwall = ilist;
contact[n].r = regions[iregion]->contact[m].varflag;
n++;
}
}
}
for (ilist = 0; ilist < nregion; ilist++)
regions[list[ilist]]->interior ^= 1;
return n;
}
/* ----------------------------------------------------------------------
change region shape of all sub-regions
------------------------------------------------------------------------- */
void RegUnion::shape_update()
{
Region **regions = domain->regions;
for (int ilist = 0; ilist < nregion; ilist++)
regions[list[ilist]]->shape_update();
}
/* ----------------------------------------------------------------------
move/rotate all sub-regions
------------------------------------------------------------------------- */
void RegUnion::pretransform()
{
Region **regions = domain->regions;
for (int ilist = 0; ilist < nregion; ilist++)
regions[list[ilist]]->pretransform();
}
/* ----------------------------------------------------------------------
get translational/angular velocities of all subregions
------------------------------------------------------------------------- */
void RegUnion::set_velocity()
{
Region **regions = domain->regions;
for (int ilist = 0; ilist < nregion; ilist++)
regions[list[ilist]]->set_velocity();
}
/* ----------------------------------------------------------------------
increment length of restart buffer based on region info
used by restart of fix/wall/gran/region
------------------------------------------------------------------------- */
void RegUnion::length_restart_string(int& n)
{
n += sizeof(int) + strlen(id)+1 +
sizeof(int) + strlen(style)+1 + sizeof(int);
for (int ilist = 0; ilist < nregion; ilist++)
domain->regions[list[ilist]]->length_restart_string(n);
}
/* ----------------------------------------------------------------------
region writes its current position/angle
needed by fix/wall/gran/region to compute velocity by differencing scheme
------------------------------------------------------------------------- */
void RegUnion::write_restart(FILE *fp)
{
int sizeid = (strlen(id)+1);
int sizestyle = (strlen(style)+1);
fwrite(&sizeid, sizeof(int), 1, fp);
fwrite(id, 1, sizeid, fp);
fwrite(&sizestyle, sizeof(int), 1, fp);
fwrite(style, 1, sizestyle, fp);
fwrite(&nregion,sizeof(int),1,fp);
for (int ilist = 0; ilist < nregion; ilist++)
domain->regions[list[ilist]]->write_restart(fp);
}
/* ----------------------------------------------------------------------
region reads its previous position/angle
needed by fix/wall/gran/region to compute velocity by differencing scheme
------------------------------------------------------------------------- */
int RegUnion::restart(char *buf, int &n)
{
int size = *((int *) (&buf[n]));
n += sizeof(int);
if ((size <= 0) || (strcmp(&buf[n],id) != 0)) return 0;
n += size;
size = *((int *) (&buf[n]));
n += sizeof(int);
if ((size <= 0) || (strcmp(&buf[n],style) != 0)) return 0;
n += size;
int restart_nreg = *((int *) (&buf[n]));
n += sizeof(int);
if (restart_nreg != nregion) return 0;
for (int ilist = 0; ilist < nregion; ilist++)
if (!domain->regions[list[ilist]]->restart(buf,n)) return 0;
return 1;
}
/* ----------------------------------------------------------------------
set prev vector to zero
------------------------------------------------------------------------- */
void RegUnion::reset_vel()
{
for (int ilist = 0; ilist < nregion; ilist++)
domain->regions[list[ilist]]->reset_vel();
}
c4science · Help