ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Fixing compilation errors

Browse Source
This commit is contained in:
jtclemm
2023-04-24 19:46:27 -06:00
parent 35d1178cfa
commit 47b8cdc94f
21 changed files with 379 additions and 346 deletions
Download Patch File Download Diff File Expand all files Collapse all files

79
src/RHEO/fix_rheo.cpp
View File

@ -33,6 +33,7 @@
#include "utils.h"
using namespace LAMMPS_NS;
using namespace RHEO_NS;
using namespace FixConst;
/* ---------------------------------------------------------------------- */
@ -68,6 +69,7 @@ FixRHEO::FixRHEO(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR,"Insufficient arguments for fix rheo command");
h = utils::numeric(FLERR,arg[3],false,lmp);
cut = h;
if (strcmp(arg[4],"Quintic") == 0) {
kernel_style = QUINTIC;
} else if (strcmp(arg[4],"CRK0") == 0) {
@ -101,7 +103,7 @@ FixRHEO::FixRHEO(LAMMPS *lmp, int narg, char **arg) :
iarg += 2;
} else if (strcmp(arg[iarg],"interface/reconstruction") == 0) {
interface_flag = 1;
} else if (strcmp(arg[iarg],"rhosum") == 0) {
} else if (strcmp(arg[iarg],"rho/sum") == 0) {
rhosum_flag = 1;
} else if (strcmp(arg[iarg],"rho0") == 0) {
if(iarg + 1 >= narg) error->all(FLERR,"Illegal rho0 option in fix rheo");
@ -137,7 +139,8 @@ FixRHEO::~FixRHEO()
void FixRHEO::post_constructor()
{
compute_kernel = dynamic_cast<ComputeRHEOKernel *>(modify->add_compute("rheo_kernel all RHEO/KERNEL {}", kernel_style));
compute_kernel = dynamic_cast<ComputeRHEOKernel *>(modify->add_compute(
fmt::format("rheo_kernel all RHEO/KERNEL {}", kernel_style)));
compute_kernel->fix_rheo = this;
std::string cmd = "rheo_grad all RHEO/GRAD velocity rho viscosity";
@ -146,22 +149,26 @@ void FixRHEO::post_constructor()
compute_grad->fix_rheo = this;
if (rhosum_flag) {
compute_rhosum = dynamic_cast<ComputeRHEORhoSum *>(modify->add_compute("rheo_rho_sum all RHEO/RHO/SUM"));
compute_rhosum = dynamic_cast<ComputeRHEORhoSum *>(modify->add_compute(
"rheo_rho_sum all RHEO/RHO/SUM"));
compute_rhosum->fix_rheo = this;
}
if (shift_flag) {
compute_vshift = dynamic_cast<ComputeRHEOVShift *>(modify->add_compute("rheo_vshift all RHEO/VSHIFT"));
compute_vshift = dynamic_cast<ComputeRHEOVShift *>(modify->add_compute(
"rheo_vshift all RHEO/VSHIFT"));
compute_vshift->fix_rheo = this;
}
if (interface_flag) {
compute_interface = dynamic_cast<ComputeRHEOInterface *>(modify->add_compute(fmt::format("rheo_interface all RHEO/INTERFACE")));
compute_interface = dynamic_cast<ComputeRHEOInterface *>(modify->add_compute(
"rheo_interface all RHEO/INTERFACE"));
compute_interface->fix_rheo = this;
}
if (surface_flag) {
compute_surface = dynamic_cast<ComputeRHEOSurface *>(modify->add_compute(fmt::format("rheo_surface all RHEO/SURFACE")));
compute_surface = dynamic_cast<ComputeRHEOSurface *>(modify->add_compute(
"rheo_surface all RHEO/SURFACE"));
compute_surface->fix_rheo = this;
}
}
@ -193,7 +200,7 @@ void FixRHEO::init()
void FixRHEO::setup_pre_force(int /*vflag*/)
{
// Check to confirm accessory fixes do not preceed FixRHEO
// Note: these fixes set this flag in setup_pre_force()
// Note: fixes set this flag in setup_pre_force()
if (viscosity_fix_defined || pressure_fix_defined || thermal_fix_defined)
error->all(FLERR, "Fix RHEO must be defined before all other RHEO fixes");
@ -206,23 +213,23 @@ void FixRHEO::setup_pre_force(int /*vflag*/)
void FixRHEO::setup(int /*vflag*/)
{
// Confirm all accessory fixes are defined
// Note: these fixes set this flag in setup_pre_force()
// Note: fixes set this flag in setup_pre_force()
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)
if((!thermal_fix_defined) && thermal_flag)
error->all(FLERR, "Missing fix rheo/thermal");
// Reset to zero for next run
// Reset to zero for future runs
thermal_fix_defined = 0;
viscosity_fix_defined = 0;
pressure_fix_defined = 0;
// Check fixes cover all atoms (doesnt ensure user covers atoms created midrun)
// (pressure is currently required to be group all)
// Check fixes cover all atoms (may still fail if atoms are created)
// FixRHEOPressure currently requires group all
auto visc_fixes = modify->get_fix_by_style("rheo/viscosity");
auto therm_fixes = modify->get_fix_by_style("rheo/thermal");
@ -232,12 +239,12 @@ void FixRHEO::setup(int /*vflag*/)
int covered;
for (int i = 0; i < atom->nlocal; i++) {
covered = 0;
for (auto fix in visc_fixes)
for (auto fix : visc_fixes)
if (mask[i] & fix->groupbit) covered = 1;
if (!covered) v_coverage_flag = 0;
if (thermal_flag) {
covered = 0;
for (auto fix in therm_fixes)
for (auto fix : therm_fixes)
if (mask[i] & fix->groupbit) covered = 1;
if (!covered) v_coverage_flag = 0;
}
@ -253,11 +260,12 @@ void FixRHEO::setup(int /*vflag*/)
void FixRHEO::initial_integrate(int /*vflag*/)
{
// update v and x and rho of atoms in group
// update v, x and rho of atoms in group
int i, a, b;
double dtfm, divu;
int dim = domain->dimension;
int *type = atom->type;
int *mask = atom->mask;
int *status = atom->status;
double **x = atom->x;
double **v = atom->v;
@ -266,16 +274,14 @@ void FixRHEO::initial_integrate(int /*vflag*/)
double *drho = atom->drho;
double *mass = atom->mass;
double *rmass = atom->rmass;
int rmass_flag = atom->rmass_flag;
double **gradr = compute_grad->gradr;
double **gradv = compute_grad->gradv;
double **vshift;
if (shift_flag) compute_vshift->vshift;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int rmass_flag = atom->rmass_flag;
int dim = domain->dimension;
if (igroup == atom->firstgroup)
nlocal = atom->nfirst;
@ -333,7 +339,7 @@ void FixRHEO::initial_integrate(int /*vflag*/)
// Shifting atoms
if (shift_flag) {
compute_vshift->correct_surfaces(); // COuld this be moved to preforce after the surface fix runs?
compute_vshift->correct_surfaces(); // Could this be moved to preforce after the surface fix runs?
for (i = 0; i < nlocal; i++) {
if (!(status[i] & STATUS_SHIFT)) continue;
@ -376,6 +382,7 @@ void FixRHEO::pre_force(int /*vflag*/)
compute_vshift->compute_peratom();
// Remove extra shifting/no force options
int *mask = atom->mask;
int *status = atom->status;
int nall = atom->nlocal + atom->nghost;
for (int i = 0; i < nall; i++) {
@ -393,26 +400,28 @@ void FixRHEO::pre_force(int /*vflag*/)
/* ---------------------------------------------------------------------- */
void FixRHEO::final_integrate() {
int *status = atom->status;
double **gradv = compute_grad->gradv;
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
double *rho = atom->rho;
double *drho = atom->drho;
int *type = atom->type;
int *mask = atom->mask;
double *mass = atom->mass;
void FixRHEO::final_integrate()
{
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup)
nlocal = atom->nfirst;
double dtfm, divu;
double *rmass = atom->rmass;
int rmass_flag = atom->rmass_flag;
int i, a;
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
double **gradv = compute_grad->gradv;
double *rho = atom->rho;
double *drho = atom->drho;
double *mass = atom->mass;
double *rmass = atom->rmass;
int *type = atom->type;
int *mask = atom->mask;
int *status = atom->status;
int rmass_flag = atom->rmass_flag;
int dim = domain->dimension;
// Update velocity