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Adding output option for reorganized peratom values

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This commit is contained in:
jtclemm
2023-04-25 16:29:29 -06:00
parent 7fc916a1d4
commit be568d257d
27 changed files with 1443 additions and 449 deletions
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66
src/RHEO/compute_rheo_interface.cpp
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@ -46,24 +46,35 @@ ComputeRHEOInterface::ComputeRHEOInterface(LAMMPS *lmp, int narg, char **arg) :
{
if (narg != 3) error->all(FLERR,"Illegal compute rheo/interface command");
nmax_store = 0;
comm_forward = 3;
comm_reverse = 4;
nmax_store = atom->nmax;
memory->create(chi, nmax_store, "rheo:chi");
memory->create(norm, nmax_store, "rheo/interface:norm");
memory->create(normwf, nmax_store, "rheo/interface:normwf");
// For fp_store, create an instance of fix property atom
// Need restarts + exchanging with neighbors since it needs to persist
// between timesteps (fix property atom will handle callbacks)
int tmp1, tmp2;
int index = atom->find_custom("fp_store", tmp1, tmp2);
if (index == -1) {
id_fix_pa = utils::strdup(id + std::string("_fix_property_atom"));
modify->add_fix(fmt::format("{} all property/atom d2_fp_store 3", id_fix_pa));
index = atom->find_custom("fp_store", tmp1, tmp2);
}
fp_store = atom->darray[index];
}
/* ---------------------------------------------------------------------- */
ComputeRHEOInterface::~ComputeRHEOInterface()
{
// Remove custom property if it exists
int tmp1, tmp2, index;
index = atom->find_custom("rheo_chi", tmp1, tmp2);
if (index != -1) atom->remove_custom(index, 1, 0);
if (id_fix_pa && modify->nfix) modify->delete_fix(id_fix_pa);
delete[] id_fix_pa;
memory->destroy(chi);
memory->destroy(norm);
memory->destroy(normwf);
}
@ -80,37 +91,6 @@ void ComputeRHEOInterface::init()
cutsq = cut * cut;
wall_max = sqrt(3.0) / 12.0 * cut;
// Create chi array if it doesn't already exist
// Create a custom atom property so it works with compute property/atom
// Do not create grow callback as there's no reason to copy/exchange data
// Manually grow if nmax_store exceeded
int tmp1, tmp2;
int nmax = atom->nmax;
int index = atom->find_custom("rheo_chi", tmp1, tmp2);
if (index == -1) {
index = atom->add_custom("rheo_chi", 1, 0);
memory->destroy(norm);
memory->destroy(normwf);
memory->create(norm, nmax, "rheo/interface:norm");
memory->create(normwf, nmax, "rheo/interface:normwf");
nmax_store = nmax;
}
chi = atom->dvector[index];
// For fp_store, go ahead and create an instance of fix property atom
// Need restarts + exchanging with neighbors since it needs to persist
// between timesteps (fix property atom will handle callbacks)
index = atom->find_custom("fp_store", tmp1, tmp2);
if (index == -1) {
id_fix_pa = utils::strdup(id + std::string("_fix_property_atom"));
modify->add_fix(fmt::format("{} all property/atom d2_fp_store 3", id_fix_pa));
index = atom->find_custom("fp_store", tmp1, tmp2);
}
fp_store = atom->darray[index];
// need an occasional half neighbor list
neighbor->add_request(this, NeighConst::REQ_DEFAULT);
}
@ -145,11 +125,9 @@ void ComputeRHEOInterface::compute_peratom()
if (atom->nmax > nmax_store) {
nmax_store = atom->nmax;
memory->destroy(norm);
memory->destroy(normwf);
memory->create(norm, nmax_store, "rheo/interface:norm");
memory->create(normwf, nmax_store, "rheo/interface:normwf");
memory->grow(chi, nmax_store, "rheo/interface:chi");
memory->grow(norm, nmax_store, "rheo/interface:norm");
memory->grow(normwf, nmax_store, "rheo/interface:normwf");
memory->grow(chi, nmax_store, "rheo:chi");
}
for (i = 0; i < nall; i++) {