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Cleaning up peratom variables, adding peratom variables to fix rheo/interface

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This commit is contained in:
jtclemm
2023-04-12 17:05:05 -06:00
parent 79ddd1445f
commit 986cfd6641
18 changed files with 184 additions and 180 deletions
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121
src/RHEO/compute_rheo_interface.cpp
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@ -18,24 +18,20 @@
#include "compute_rheo_interface.h"
#include "fix_rheo.h"
#include "compute_rheo_kernel.h"
#include "fix_store.h"
#include "fix.h"
#include <cmath>
#include <cstring>
#include "atom.h"
#include "update.h"
#include "modify.h"
#include "comm.h"
#include "domain.h"
#include "compute_rheo_kernel.h"
#include "error.h"
#include "force.h"
#include "fix_rheo.h"
#include "memory.h"
#include "modify.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "force.h"
#include "pair.h"
#include "comm.h"
#include "memory.h"
#include "error.h"
#include <cmath>
using namespace LAMMPS_NS;
@ -44,45 +40,29 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeRHEOInterface::ComputeRHEOInterface(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg),
id_fix_chi(nullptr)
Compute(lmp, narg, arg), fix_rheo(nullptr), compute_kernel(nullptr), fx_m_norm(nullptr),
norm(nullptr), normwf(nullptr), chi(nullptr), f_pressure(nullptr), id_fix_pa(nullptr)
{
if (narg != 4) error->all(FLERR,"Illegal compute RHEO/chi command");
cut = utils::numeric(FLERR,arg[3],false,lmp);
cutsq = cut*cut;
wall_max = sqrt(3)/12.0*cut;
if (narg != 3) error->all(FLERR,"Illegal compute rheo/interface command");
nmax = 0;
comm_forward = 3;
comm_reverse = 4;
fix_chi = nullptr;
norm = nullptr;
normwf = nullptr;
// new id = fix-ID + FIX_STORE_ATTRIBUTE
// new fix group = group for this fix
id_fix_chi = nullptr;
std::string fixcmd = id + std::string("_chi");
id_fix_chi = new char[fixcmd.size()+1];
strcpy(id_fix_chi,fixcmd.c_str());
fixcmd += fmt::format(" all STORE peratom 0 {}", 1);
modify->add_fix(fixcmd);
fix_chi = (FixStore *) modify->fix[modify->nfix-1];
chi = fix_chi->vstore;
}
/* ---------------------------------------------------------------------- */
ComputeRHEOInterface::~ComputeRHEOInterface()
{
if (id_fix_chi && modify->nfix) modify->delete_fix(id_fix_chi);
if (modify->nfix) modify->delete_fix("PROPERTY_ATOM_COMP_RHEO_SOLIDS");
// 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);
memory->destroy(fx_m_norm);
memory->destroy(norm);
memory->destroy(normwf);
}
@ -91,42 +71,40 @@ ComputeRHEOInterface::~ComputeRHEOInterface()
void ComputeRHEOInterface::init()
{
// need an occasional full neighbor list
int irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->compute = 1;
neighbor->requests[irequest]->half = 1;
neighbor->requests[irequest]->full = 0;
//neighbor->requests[irequest]->occasional = 1; //Anticipate needing regulalry
compute_kernel = fix_rheo->compute_kernel;
cut = fix_rheo->cut;
cutsq = cut * cut;
wall_max = sqrt(3.0) / 12.0 * cut;
int icompute = modify->find_compute("rheo_kernel");
if (icompute == -1) error->all(FLERR, "Using compute/RHEO/chi without compute/RHEO/kernel");
// 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_old exceeded
compute_kernel = ((ComputeRHEOKernel *) modify->compute[icompute]);
int create_flag = 0;
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);
nmax_old = nmax;
}
chi = atom->dvector[index];
//Store persistent per atom quantities - need to be exchanged
char **fixarg = new char*[8];
fixarg[0] = (char *) "PROPERTY_ATOM_COMP_RHEO_SOLIDS";
fixarg[1] = (char *) "all";
fixarg[2] = (char *) "property/atom";
fixarg[3] = (char *) "d_fx";
fixarg[4] = (char *) "d_fy";
fixarg[5] = (char *) "d_fz";
fixarg[6] = (char *) "ghost";
fixarg[7] = (char *) "yes";
modify->add_fix(8,fixarg,1);
delete [] fixarg;
// For fpressure, 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)
int temp_flag;
index_fx = atom->find_custom("fx", temp_flag);
if ((index_fx < 0) || (temp_flag != 1))
error->all(FLERR, "Compute rheo/solids can't find fix property/atom fx");
index_fy = atom->find_custom("fy", temp_flag);
if ((index_fy < 0) || (temp_flag != 1))
error->all(FLERR, "Compute rheo/solids can't find fix property/atom fy");
index_fz = atom->find_custom("fz", temp_flag);
if ((index_fz < 0) || (temp_flag != 1))
error->all(FLERR, "Compute rheo/solids can't find fix property/atom fz");
index = atom->find_custom("rheo_pressure", 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_f_pressure 3", id_fix_pa)));
index = atom->find_custom("rheo_pressure", tmp1, tmp2);
}
f_pressure = atom->darray[index];
// need an occasional half neighbor list
neighbor->add_request(this, NeighConst::REQ_HALF);
}
/* ---------------------------------------------------------------------- */
@ -138,6 +116,7 @@ void ComputeRHEOInterface::init_list(int /*id*/, NeighList *ptr)
/* ---------------------------------------------------------------------- */
// Left off here
void ComputeRHEOInterface::compute_peratom()
{
int i, j, ii, jj, jnum, itype, jtype, phase_match;