refactor group access, enable and apply clang-format
This commit is contained in:
Axel Kohlmeyer
@ -1,4 +1,3 @@
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// clang-format off
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://www.lammps.org/, Sandia National Laboratories
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@ -24,36 +23,35 @@ using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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RegIntersect::RegIntersect(LAMMPS *lmp, int narg, char **arg) :
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Region(lmp, narg, arg), idsub(nullptr)
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Region(lmp, narg, arg), idsub(nullptr)
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{
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nregion = 0;
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if (narg < 5) error->all(FLERR,"Illegal region command");
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int n = utils::inumeric(FLERR,arg[2],false,lmp);
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if (n < 2) error->all(FLERR,"Illegal region command");
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options(narg-(n+3),&arg[n+3]);
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if (narg < 5) error->all(FLERR, "Illegal region command");
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int n = utils::inumeric(FLERR, arg[2], false, lmp);
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if (n < 2) error->all(FLERR, "Illegal region command");
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options(narg - (n + 3), &arg[n + 3]);
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// build list of regions to intersect
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// store sub-region IDs in idsub
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idsub = new char*[n];
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list = new int[n];
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idsub = new char *[n];
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reglist = new Region *[n];
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nregion = 0;
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for (int iarg = 0; iarg < n; iarg++) {
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idsub[nregion] = utils::strdup(arg[iarg+3]);
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int iregion = domain->find_region(idsub[nregion]);
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if (iregion == -1)
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error->all(FLERR,"Region intersect region ID does not exist");
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list[nregion++] = iregion;
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idsub[nregion] = utils::strdup(arg[iarg + 3]);
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reglist[nregion] = domain->get_region_by_id(idsub[nregion]);
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if (!reglist[nregion])
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error->all(FLERR, "Region intersect region {} does not exist", idsub[nregion]);
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nregion++;
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}
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// this region is variable shape or dynamic if any of sub-regions are
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Region **regions = domain->regions;
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for (int ilist = 0; ilist < nregion; ilist++) {
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if (regions[list[ilist]]->varshape) varshape = 1;
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if (regions[list[ilist]]->dynamic) dynamic = 1;
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if (reglist[ilist]->varshape) varshape = 1;
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if (reglist[ilist]->dynamic) dynamic = 1;
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}
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// extent of intersection of regions
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@ -61,29 +59,29 @@ RegIntersect::RegIntersect(LAMMPS *lmp, int narg, char **arg) :
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bboxflag = 0;
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for (int ilist = 0; ilist < nregion; ilist++)
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if (regions[list[ilist]]->bboxflag == 1) bboxflag = 1;
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if (reglist[ilist]->bboxflag == 1) bboxflag = 1;
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if (!interior) bboxflag = 0;
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if (bboxflag) {
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int first = 1;
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for (int ilist = 0; ilist < nregion; ilist++) {
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if (regions[list[ilist]]->bboxflag == 0) continue;
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if (reglist[ilist]->bboxflag == 0) continue;
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if (first) {
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extent_xlo = regions[list[ilist]]->extent_xlo;
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extent_ylo = regions[list[ilist]]->extent_ylo;
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extent_zlo = regions[list[ilist]]->extent_zlo;
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extent_xhi = regions[list[ilist]]->extent_xhi;
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extent_yhi = regions[list[ilist]]->extent_yhi;
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extent_zhi = regions[list[ilist]]->extent_zhi;
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extent_xlo = reglist[ilist]->extent_xlo;
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extent_ylo = reglist[ilist]->extent_ylo;
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extent_zlo = reglist[ilist]->extent_zlo;
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extent_xhi = reglist[ilist]->extent_xhi;
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extent_yhi = reglist[ilist]->extent_yhi;
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extent_zhi = reglist[ilist]->extent_zhi;
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first = 0;
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}
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extent_xlo = MAX(extent_xlo,regions[list[ilist]]->extent_xlo);
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extent_ylo = MAX(extent_ylo,regions[list[ilist]]->extent_ylo);
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extent_zlo = MAX(extent_zlo,regions[list[ilist]]->extent_zlo);
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extent_xhi = MIN(extent_xhi,regions[list[ilist]]->extent_xhi);
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extent_yhi = MIN(extent_yhi,regions[list[ilist]]->extent_yhi);
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extent_zhi = MIN(extent_zhi,regions[list[ilist]]->extent_zhi);
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extent_xlo = MAX(extent_xlo, reglist[ilist]->extent_xlo);
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extent_ylo = MAX(extent_ylo, reglist[ilist]->extent_ylo);
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extent_zlo = MAX(extent_zlo, reglist[ilist]->extent_zlo);
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extent_xhi = MIN(extent_xhi, reglist[ilist]->extent_xhi);
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extent_yhi = MIN(extent_yhi, reglist[ilist]->extent_yhi);
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extent_zhi = MIN(extent_zhi, reglist[ilist]->extent_zhi);
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}
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}
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@ -91,14 +89,15 @@ RegIntersect::RegIntersect(LAMMPS *lmp, int narg, char **arg) :
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// for near contacts and touching contacts
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cmax = 0;
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for (int ilist = 0; ilist < nregion; ilist++)
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cmax += regions[list[ilist]]->cmax;
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for (int ilist = 0; ilist < nregion; ilist++) cmax += reglist[ilist]->cmax;
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contact = new Contact[cmax];
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tmax = 0;
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for (int ilist = 0; ilist < nregion; ilist++) {
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if (interior) tmax += regions[list[ilist]]->tmax;
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else tmax++;
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if (interior)
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tmax += reglist[ilist]->tmax;
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else
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tmax++;
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}
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}
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@ -106,10 +105,10 @@ RegIntersect::RegIntersect(LAMMPS *lmp, int narg, char **arg) :
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RegIntersect::~RegIntersect()
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{
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for (int ilist = 0; ilist < nregion; ilist++) delete [] idsub[ilist];
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delete [] idsub;
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delete [] list;
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delete [] contact;
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for (int ilist = 0; ilist < nregion; ilist++) delete[] idsub[ilist];
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delete[] idsub;
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delete[] reglist;
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delete[] contact;
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}
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/* ---------------------------------------------------------------------- */
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@ -122,17 +121,14 @@ void RegIntersect::init()
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// error if a sub-region was deleted
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for (int ilist = 0; ilist < nregion; ilist++) {
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int iregion = domain->find_region(idsub[ilist]);
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if (iregion == -1)
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error->all(FLERR,"Region union region ID does not exist");
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list[ilist] = iregion;
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reglist[ilist] = domain->get_region_by_id(idsub[ilist]);
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if (!reglist[ilist])
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error->all(FLERR, "Region intersect region {} does not exist", idsub[ilist]);
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}
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// init the sub-regions
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Region **regions = domain->regions;
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for (int ilist = 0; ilist < nregion; ilist++)
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regions[list[ilist]]->init();
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for (int ilist = 0; ilist < nregion; ilist++) reglist[ilist]->init();
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}
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/* ----------------------------------------------------------------------
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@ -143,9 +139,8 @@ void RegIntersect::init()
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int RegIntersect::inside(double x, double y, double z)
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{
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int ilist;
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Region **regions = domain->regions;
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for (ilist = 0; ilist < nregion; ilist++)
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if (!regions[list[ilist]]->match(x,y,z)) break;
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if (!reglist[ilist]->match(x, y, z)) break;
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if (ilist == nregion) return 1;
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return 0;
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@ -159,39 +154,36 @@ int RegIntersect::inside(double x, double y, double z)
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int RegIntersect::surface_interior(double *x, double cutoff)
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{
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int m,ilist,jlist,iregion,jregion,ncontacts;
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double xs,ys,zs;
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int m, ilist, jlist, ncontacts;
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double xs, ys, zs;
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Region **regions = domain->regions;
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int n = 0;
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int walloffset = 0;
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for (ilist = 0; ilist < nregion; ilist++) {
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iregion = list[ilist];
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ncontacts = regions[iregion]->surface(x[0],x[1],x[2],cutoff);
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auto region = reglist[ilist];
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ncontacts = region->surface(x[0], x[1], x[2], cutoff);
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for (m = 0; m < ncontacts; m++) {
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xs = x[0] - regions[iregion]->contact[m].delx;
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ys = x[1] - regions[iregion]->contact[m].dely;
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zs = x[2] - regions[iregion]->contact[m].delz;
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xs = x[0] - region->contact[m].delx;
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ys = x[1] - region->contact[m].dely;
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zs = x[2] - region->contact[m].delz;
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for (jlist = 0; jlist < nregion; jlist++) {
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if (jlist == ilist) continue;
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jregion = list[jlist];
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if (!regions[jregion]->match(xs,ys,zs)) break;
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if (!reglist[jlist]->match(xs, ys, zs)) break;
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}
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if (jlist == nregion) {
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contact[n].r = regions[iregion]->contact[m].r;
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contact[n].radius = regions[iregion]->contact[m].radius;
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contact[n].delx = regions[iregion]->contact[m].delx;
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contact[n].dely = regions[iregion]->contact[m].dely;
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contact[n].delz = regions[iregion]->contact[m].delz;
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contact[n].iwall = regions[iregion]->contact[m].iwall + walloffset;
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contact[n].varflag = regions[iregion]->contact[m].varflag;
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contact[n].r = region->contact[m].r;
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contact[n].radius = region->contact[m].radius;
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contact[n].delx = region->contact[m].delx;
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contact[n].dely = region->contact[m].dely;
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contact[n].delz = region->contact[m].delz;
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contact[n].iwall = region->contact[m].iwall + walloffset;
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contact[n].varflag = region->contact[m].varflag;
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n++;
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}
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}
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// increment by cmax instead of tmax to insure
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// possible wall IDs for sub-regions are non overlapping
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walloffset += regions[iregion]->cmax;
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walloffset += region->cmax;
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}
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return n;
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@ -208,42 +200,37 @@ int RegIntersect::surface_interior(double *x, double cutoff)
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int RegIntersect::surface_exterior(double *x, double cutoff)
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{
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int m,ilist,jlist,iregion,jregion,ncontacts;
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double xs,ys,zs;
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int m, ilist, jlist, ncontacts;
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double xs, ys, zs;
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Region **regions = domain->regions;
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int n = 0;
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for (ilist = 0; ilist < nregion; ilist++)
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regions[list[ilist]]->interior ^= 1;
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for (ilist = 0; ilist < nregion; ilist++) reglist[ilist]->interior ^= 1;
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for (ilist = 0; ilist < nregion; ilist++) {
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iregion = list[ilist];
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ncontacts = regions[iregion]->surface(x[0],x[1],x[2],cutoff);
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auto region = reglist[ilist];
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ncontacts = region->surface(x[0], x[1], x[2], cutoff);
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for (m = 0; m < ncontacts; m++) {
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xs = x[0] - regions[iregion]->contact[m].delx;
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ys = x[1] - regions[iregion]->contact[m].dely;
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zs = x[2] - regions[iregion]->contact[m].delz;
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xs = x[0] - region->contact[m].delx;
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ys = x[1] - region->contact[m].dely;
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zs = x[2] - region->contact[m].delz;
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for (jlist = 0; jlist < nregion; jlist++) {
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if (jlist == ilist) continue;
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jregion = list[jlist];
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if (regions[jregion]->match(xs,ys,zs)) break;
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if (reglist[jlist]->match(xs, ys, zs)) break;
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}
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if (jlist == nregion) {
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contact[n].r = regions[iregion]->contact[m].r;
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contact[n].radius = regions[iregion]->contact[m].radius;
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contact[n].delx = regions[iregion]->contact[m].delx;
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contact[n].dely = regions[iregion]->contact[m].dely;
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contact[n].delz = regions[iregion]->contact[m].delz;
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contact[n].r = region->contact[m].r;
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contact[n].radius = region->contact[m].radius;
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contact[n].delx = region->contact[m].delx;
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contact[n].dely = region->contact[m].dely;
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contact[n].delz = region->contact[m].delz;
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contact[n].iwall = ilist;
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contact[n].varflag = regions[iregion]->contact[m].varflag;
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contact[n].varflag = region->contact[m].varflag;
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n++;
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}
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}
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}
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for (ilist = 0; ilist < nregion; ilist++)
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regions[list[ilist]]->interior ^= 1;
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for (ilist = 0; ilist < nregion; ilist++) reglist[ilist]->interior ^= 1;
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return n;
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}
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@ -254,9 +241,7 @@ int RegIntersect::surface_exterior(double *x, double cutoff)
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void RegIntersect::shape_update()
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{
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Region **regions = domain->regions;
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for (int ilist = 0; ilist < nregion; ilist++)
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regions[list[ilist]]->shape_update();
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for (int ilist = 0; ilist < nregion; ilist++) reglist[ilist]->shape_update();
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}
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/* ----------------------------------------------------------------------
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@ -265,21 +250,16 @@ void RegIntersect::shape_update()
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void RegIntersect::pretransform()
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{
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Region **regions = domain->regions;
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for (int ilist = 0; ilist < nregion; ilist++)
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regions[list[ilist]]->pretransform();
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for (int ilist = 0; ilist < nregion; ilist++) reglist[ilist]->pretransform();
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}
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/* ----------------------------------------------------------------------
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get translational/angular velocities of all subregions
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------------------------------------------------------------------------- */
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void RegIntersect::set_velocity()
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{
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Region **regions = domain->regions;
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for (int ilist = 0; ilist < nregion; ilist++)
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regions[list[ilist]]->set_velocity();
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for (int ilist = 0; ilist < nregion; ilist++) reglist[ilist]->set_velocity();
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}
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/* ----------------------------------------------------------------------
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@ -287,13 +267,10 @@ void RegIntersect::set_velocity()
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used by restart of fix/wall/gran/region
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------------------------------------------------------------------------- */
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void RegIntersect::length_restart_string(int& n)
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void RegIntersect::length_restart_string(int &n)
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{
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n += sizeof(int) + strlen(id)+1 +
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sizeof(int) + strlen(style)+1 + sizeof(int);
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for (int ilist = 0; ilist < nregion; ilist++)
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domain->regions[list[ilist]]->length_restart_string(n);
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n += sizeof(int) + strlen(id) + 1 + sizeof(int) + strlen(style) + 1 + sizeof(int);
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for (int ilist = 0; ilist < nregion; ilist++) reglist[ilist]->length_restart_string(n);
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}
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/* ----------------------------------------------------------------------
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region writes its current position/angle
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@ -302,17 +279,15 @@ void RegIntersect::length_restart_string(int& n)
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void RegIntersect::write_restart(FILE *fp)
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{
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int sizeid = (strlen(id)+1);
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int sizestyle = (strlen(style)+1);
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int sizeid = (strlen(id) + 1);
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int sizestyle = (strlen(style) + 1);
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fwrite(&sizeid, sizeof(int), 1, fp);
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fwrite(id, 1, sizeid, fp);
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fwrite(&sizestyle, sizeof(int), 1, fp);
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fwrite(style, 1, sizestyle, fp);
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fwrite(&nregion,sizeof(int),1,fp);
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fwrite(&nregion, sizeof(int), 1, fp);
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for (int ilist = 0; ilist < nregion; ilist++) {
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domain->regions[list[ilist]]->write_restart(fp);
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}
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for (int ilist = 0; ilist < nregion; ilist++) { reglist[ilist]->write_restart(fp); }
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}
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/* ----------------------------------------------------------------------
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@ -324,12 +299,12 @@ int RegIntersect::restart(char *buf, int &n)
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{
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int size = *((int *) (&buf[n]));
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n += sizeof(int);
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if ((size <= 0) || (strcmp(&buf[n],id) != 0)) return 0;
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if ((size <= 0) || (strcmp(&buf[n], id) != 0)) return 0;
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n += size;
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size = *((int *) (&buf[n]));
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n += sizeof(int);
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if ((size <= 0) || (strcmp(&buf[n],style) != 0)) return 0;
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if ((size <= 0) || (strcmp(&buf[n], style) != 0)) return 0;
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n += size;
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int restart_nreg = *((int *) (&buf[n]));
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@ -337,7 +312,7 @@ int RegIntersect::restart(char *buf, int &n)
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if (restart_nreg != nregion) return 0;
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for (int ilist = 0; ilist < nregion; ilist++)
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if (!domain->regions[list[ilist]]->restart(buf,n)) return 0;
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if (!reglist[ilist]->restart(buf, n)) return 0;
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return 1;
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}
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@ -348,7 +323,5 @@ int RegIntersect::restart(char *buf, int &n)
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void RegIntersect::reset_vel()
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{
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for (int ilist = 0; ilist < nregion; ilist++)
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domain->regions[list[ilist]]->reset_vel();
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for (int ilist = 0; ilist < nregion; ilist++) reglist[ilist]->reset_vel();
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}
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