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new fix wall/gran/region command, REBO bug fix, new example log files

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This commit is contained in:
Steve Plimpton
2016-10-06 15:47:41 -06:00
parent c213457550
commit b3d2fb91bb
63 changed files with 6354 additions and 490 deletions
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71
src/region_intersect.cpp
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@ -43,7 +43,7 @@ RegIntersect::RegIntersect(LAMMPS *lmp, int narg, char **arg) :
idsub[nregion] = new char[m];
strcpy(idsub[nregion],arg[iarg+3]);
iregion = domain->find_region(idsub[nregion]);
if (iregion == -1)
if (iregion == -1)
error->all(FLERR,"Region intersect region ID does not exist");
list[nregion++] = iregion;
}
@ -88,11 +88,21 @@ RegIntersect::RegIntersect(LAMMPS *lmp, int narg, char **arg) :
}
// 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++)
size_restart = 0;
for (int ilist = 0; ilist < nregion; ilist++){
cmax += regions[list[ilist]]->cmax;
size_restart += regions[list[ilist]]->size_restart;
}
contact = new Contact[cmax];
tmax = 0;
for (int ilist = 0; ilist < nregion; ilist++) {
if (interior) tmax += regions[list[ilist]]->tmax;
else tmax++;
}
}
/* ---------------------------------------------------------------------- */
@ -117,7 +127,7 @@ void RegIntersect::init()
int iregion;
for (int ilist = 0; ilist < nregion; ilist++) {
iregion = domain->find_region(idsub[ilist]);
if (iregion == -1)
if (iregion == -1)
error->all(FLERR,"Region union region ID does not exist");
list[ilist] = iregion;
}
@ -159,6 +169,7 @@ int RegIntersect::surface_interior(double *x, double cutoff)
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);
@ -173,12 +184,18 @@ int RegIntersect::surface_interior(double *x, double cutoff)
}
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;
@ -218,9 +235,12 @@ int RegIntersect::surface_exterior(double *x, double cutoff)
}
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].varflag = regions[iregion]->contact[m].varflag;
n++;
}
}
@ -253,3 +273,48 @@ void RegIntersect::pretransform()
for (int ilist = 0; ilist < nregion; ilist++)
regions[list[ilist]]->pretransform();
}
/* ----------------------------------------------------------------------
get translational/angular velocities of all subregions
------------------------------------------------------------------------- */
void RegIntersect::set_velocity()
{
Region **regions = domain->regions;
for (int ilist = 0; ilist < nregion; ilist++)
regions[list[ilist]]->set_velocity();
}
/* ----------------------------------------------------------------------
region writes its current position/angle
needed by fix/wall/gran/region to compute velocity by differencing scheme
------------------------------------------------------------------------- */
void RegIntersect::write_restart(FILE *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 RegIntersect::restart(char *buf, int n)
{
for (int ilist = 0; ilist < nregion; ilist++)
n = domain->regions[list[ilist]]->restart(buf, n);
return n;
}
/* ----------------------------------------------------------------------
set prev vector to zero
------------------------------------------------------------------------- */
void RegIntersect::reset_vel()
{
for (int ilist = 0; ilist < nregion; ilist++)
domain->regions[list[ilist]]->reset_vel();
}