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Revamping atom data storage in fixes

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This commit is contained in:
jtclemm
2023-02-20 12:47:51 -07:00
parent 560bd90e11
commit 4ac7a228b5
4 changed files with 88 additions and 26 deletions
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84
src/RHEO/fix_rheo.cpp
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@ -21,6 +21,7 @@
#include "compute_rheo_vshift.h"
#include "domain.h"
#include "error.h"
#include "fix_store_peratom.h"
#include "force.h"
#include "modify.h"
#include "update.h"
@ -33,15 +34,30 @@ using namespace FixConst;
FixRHEO::FixRHEO(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg), compute_grad(nullptr), compute_kernel(nullptr),
compute_interface(nullptr), compute_rhosum(nullptr), compute_vshift(nullptr)
compute_interface(nullptr), compute_rhosum(nullptr), compute_vshift(nullptr),
fix_store_visc(nullptr), fix_store_pres(nullptr), fix_store_cond(nullptr),
fix_store_surf(nullptr), fix_store_fp(nullptr), surface(nullptr), conductivity(nullptr),
viscosity(nullptr), pressure(nullptr), f_pressure(nullptr)
{
time_integrate = 1;
viscosity_fix_defined = 0;
pressure_fix_defined = 0;
thermal_fix_defined = 0;
surface_fix_defined = 0;
thermal_flag = 0;
rhosum_flag = 0;
shift_flag = 0;
solid_flag = 0;
interface_flag = 0;
surface_flag = 0;
rho0 = 1.0;
csq = 1.0;
if (igroup != 0)
error->all(FLERR,"fix rheo command requires group all");
if (atom->rho_flag != 1)
error->all(FLERR,"fix rheo command requires atom_style with density");
if (atom->status_flag != 1)
@ -68,6 +84,10 @@ FixRHEO::FixRHEO(LAMMPS *lmp, int narg, char **arg) :
shift_flag = 1;
} else if (strcmp(arg[iarg],"thermal") == 0) {
thermal_flag = 1;
} else if (strcmp(arg[iarg],"surface/detection") == 0) {
surface_flag = 1;
} else if (strcmp(arg[iarg],"interface/reconstruction") == 0) {
interface_flag = 1;
} else if (strcmp(arg[iarg],"rhosum") == 0) {
rhosum_flag = 1;
if(iarg + 1 >= narg) error->all(FLERR,"Illegal rhosum option in fix rheo");
@ -86,17 +106,18 @@ FixRHEO::FixRHEO(LAMMPS *lmp, int narg, char **arg) :
}
iarg += 1;
}
time_integrate = 1;
thermal_fix_defined = 0;
viscosity_fix_defined = 0;
pressure_fix_defined = 0;
}
/* ---------------------------------------------------------------------- */
FixRHEO::~FixRHEO()
{
if (fix_store_visc) modify->delete_fix("rheo_store_visc");
if (fix_store_pres) modify->delete_fix("rheo_store_pres");
if (fix_store_surf) modify->delete_fix("rheo_store_surf");
if (fix_store_cond) modify->delete_fix("rheo_store_cond");
if (fix_store_fp) modify->delete_fix("rheo_store_fp");
if (compute_kernel) modify->delete_compute("rheo_kernel");
if (compute_grad) modify->delete_compute("rheo_grad");
if (compute_interface) modify->delete_compute("rheo_interface");
@ -110,13 +131,18 @@ void FixRHEO::post_constructor()
{
compute_kernel = dynamic_cast<ComputeRHEOKernel *>(modify->add_compute(fmt::format("rheo_kernel all rheo/kernel {} {} {}", kernel_style, zmin_kernel, cut)));
if (thermal_flag)
compute_grad = dynamic_cast<ComputeRHEOGrad *>(modify->add_compute(fmt::format("rheo_grad all rheo/grad {} velocity rho viscosity temprature", cut)));
else
compute_grad = dynamic_cast<ComputeRHEOGrad *>(modify->add_compute(fmt::format("rheo_grad all rheo/grad {} velocity rho viscosity", cut)));
compute_grad->fix_rheo = this;
fix_store_visc = dynamic_cast<FixStorePeratom *>(modify->add_fix("rheo_store_visc all STORE/PERATOM 0 1"))
fix_store_visc->disable = 1;
viscosity = fix_store_visc->vstore;
fix_store_pres = dynamic_cast<FixStorePeratom *>(modify->add_fix("rheo_store_pres all STORE/PERATOM 0 1"))
pressure = fix_store_pres->vstore;
fix_store_pres->disable = 1;
compute_interface = dynamic_cast<ComputeRHEOInterface *>(modify->add_compute(fmt::format("rheo_interface all rheo/interface {}", cut)));
std::string cmd = "rheo_grad all rheo/grad {} velocity rho viscosity";
if (thermal_flag) cmd += "temperature";
compute_grad = dynamic_cast<ComputeRHEOGrad *>(modify->add_compute(fmt::format(cmd, cut)));
compute_grad->fix_rheo = this;
if (rhosum_flag)
compute_rhosum = dynamic_cast<ComputeRHEORhoSum *>(modify->add_compute(fmt::format("rheo_rhosum all rheo/rho/sum {} {}", cut, zmin_rhosum)));
@ -124,11 +150,25 @@ void FixRHEO::post_constructor()
if (shift_flag)
compute_vshift = dynamic_cast<ComputeRHEOVShift *>(modify->add_compute(fmt::format("rheo_vshift all rheo/vshift {}", cut)));
if (surface_flag) {
fix_store_surf = dynamic_cast<FixStorePeratom *>(modify->add_fix("rheo_store_surf all STORE/PERATOM 0 1"))
surface = fix_store_surf->vstore;
fix_store_surf->disable = 1;
}
//todo here
//allocate memory for viscosity, pressure, etc
//don't want to save to restart/datafiles (could disable fix store/state)
//but do want it available for dupm files
if (thermal_flag) {
fix_store_cond = dynamic_cast<FixStorePeratom *>(modify->add_fix("rheo_store_cond all STORE/PERATOM 0 1"))
conductivity = fix_store_cond->vstore;
fix_store_cond->disable = 1;
}
if (interface_flag) {
compute_interface = dynamic_cast<ComputeRHEOInterface *>(modify->add_compute(fmt::format("rheo_interface all rheo/interface {}", cut)));
fix_store_fp = dynamic_cast<FixStorePeratom *>(modify->add_fix("rheo_store_fp all STORE/PERATOM 0 3"))
f_pressure = fix_store_fp->astore;
fix_store_fp->disable = 1;
}
}
/* ---------------------------------------------------------------------- */
@ -158,19 +198,23 @@ void FixRHEO::init()
void FixRHEO::setup_pre_force(int /*vflag*/)
{
// Check to confirm all accessory fixes are defined
if(!thermal_fix_defined && thermal_flag)
error->all(FLERR, "Missing fix rheo/thermal");
if (!viscosity_fix_defined)
error->all(FLERR, "Missing fix rheo/viscosity");
if (!pressure_fix_defined)
error->all(FLERR, "Missing fix rheo/pressure");
if(!thermal_fix_defined && thermal_flag)
error->all(FLERR, "Missing fix rheo/thermal");
if(!surface_fix_defined && surface_flag)
error->all(FLERR, "Missing fix rheo/surface");
// Reset to zero for next run
thermal_fix_defined = 0;
viscosity_fix_defined = 0;
pressure_fix_defined = 0;
surface_fix_defined = 0;
pre_force(0);
}

14
src/RHEO/fix_rheo.h
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@ -41,17 +41,25 @@ class FixRHEO : public Fix {
int thermal_flag;
int rhosum_flag;
int shift_flag;
int solid_flag;
int interface_flag;
int surface_flag;
int thermal_fix_defined;
int viscosity_fix_defined;
int pressure_fix_defined;
int thermal_fix_defined;
int surface_fix_defined;
// Non-persistent per-atom arrays are initialized here
// Non-persistent per-atom arrays
int *surface;
double *conductivity, *viscosity, *pressure;
double **f_pressure;
class FixStorePeratom *fix_store_visc;
class FixStorePeratom *fix_store_pres;
class FixStorePeratom *fix_store_cond;
class FixStorePeratom *fix_store_surf;
class FixStorePeratom *fix_store_fp;
class ComputeRHEOGrad *compute_grad;
class ComputeRHEOKernel *compute_kernel;
class ComputeRHEOInterface *compute_interface;

13
src/RHEO/fix_rheo_viscosity.cpp
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@ -39,6 +39,7 @@ FixRHEOViscosity::FixRHEOViscosity(LAMMPS *lmp, int narg, char **arg) :
viscosity_style = NONE;
comm_forward = 1;
nmax = atom->nmax;
int ntypes = atom->ntypes;
int iarg = 3;
@ -107,8 +108,10 @@ void FixRHEOViscosity::init()
void FixRHEOViscosity::setup_pre_force(int /*vflag*/)
{
// Identify whether this is the last instance of fix viscosity
// Will handle communication
// Identify whether this is the first/last instance of fix viscosity
// First will handle growing arrays
// Last will handle communication
first_flag = 0
last_flag = 0;
int i = 0;
@ -118,6 +121,7 @@ void FixRHEOViscosity::setup_pre_force(int /*vflag*/)
i++;
}
if (i == 0) first_flag = 1;
if ((i + 1) == fixlist.size()) last_flag = 1;
pre_force(0);
@ -138,6 +142,11 @@ void FixRHEOViscosity::pre_force(int /*vflag*/)
int nlocal = atom->nlocal;
int dim = domain->dimension;
if (first_flag & nmax < atom->nmax) {
nmax = atom->nmax;
fix_rheo->fix_store_visc->grow_arrays(nmax);
}
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
if (viscosity_style == CONSTANT) {

3
src/RHEO/fix_rheo_viscosity.h
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@ -38,7 +38,8 @@ class FixRHEOViscosity : public Fix {
double *eta_type, eta;
double npow, K, gd0, tau0;
int viscosity_style;
int last_flag;
int first_flag, last_flag;
int nmax;
class FixRHEO *fix_rheo;
class ComputeRHEOGrad *compute_grad;
};