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Starting pair style, various clean ups

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This commit is contained in:
jtclemm
2023-02-21 19:41:52 -07:00
parent c715552f7e
commit 99e7673e8e
6 changed files with 126 additions and 115 deletions
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23
src/RHEO/fix_rheo.cpp
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@ -66,7 +66,7 @@ FixRHEO::FixRHEO(LAMMPS *lmp, int narg, char **arg) :
if (narg < 5)
error->all(FLERR,"Insufficient arguments for fix rheo command");
cut = utils::numeric(FLERR,arg[3],false,lmp);
h = utils::numeric(FLERR,arg[3],false,lmp);
if (strcmp(arg[4],"Quintic") == 0) {
kernel_style = QUINTIC;
} else if (strcmp(arg[4],"CRK0") == 0) {
@ -125,11 +125,14 @@ FixRHEO::~FixRHEO()
if (compute_vshift) modify->delete_compute("rheo_vshift");
}
/* ---------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Create necessary internal computes
------------------------------------------------------------------------- */
void FixRHEO::post_constructor()
{
compute_kernel = dynamic_cast<ComputeRHEOKernel *>(modify->add_compute(fmt::format("rheo_kernel all rheo/kernel {} {} {}", kernel_style, zmin_kernel, cut)));
compute_kernel = dynamic_cast<ComputeRHEOKernel *>(modify->add_compute(fmt::format("rheo_kernel all rheo/kernel {} {} {}", kernel_style, zmin_kernel, h)));
fix_store_visc = dynamic_cast<FixStorePeratom *>(modify->add_fix("rheo_store_visc all STORE/PERATOM 0 1"))
fix_store_visc->disable = 1;
@ -141,14 +144,14 @@ void FixRHEO::post_constructor()
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 = dynamic_cast<ComputeRHEOGrad *>(modify->add_compute(fmt::format(cmd, h)));
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)));
compute_rhosum = dynamic_cast<ComputeRHEORhoSum *>(modify->add_compute(fmt::format("rheo_rhosum all rheo/rho/sum {} {}", h, zmin_rhosum)));
if (shift_flag)
compute_vshift = dynamic_cast<ComputeRHEOVShift *>(modify->add_compute(fmt::format("rheo_vshift all rheo/vshift {}", cut)));
compute_vshift = dynamic_cast<ComputeRHEOVShift *>(modify->add_compute(fmt::format("rheo_vshift all rheo/vshift {}", h)));
if (surface_flag) {
fix_store_surf = dynamic_cast<FixStorePeratom *>(modify->add_fix("rheo_store_surf all STORE/PERATOM 0 1"))
@ -163,7 +166,7 @@ void FixRHEO::post_constructor()
}
if (interface_flag) {
compute_interface = dynamic_cast<ComputeRHEOInterface *>(modify->add_compute(fmt::format("rheo_interface all rheo/interface {}", cut)));
compute_interface = dynamic_cast<ComputeRHEOInterface *>(modify->add_compute(fmt::format("rheo_interface all rheo/interface {}", h)));
fix_store_fp = dynamic_cast<FixStorePeratom *>(modify->add_fix("rheo_store_fp all STORE/PERATOM 0 3"))
f_pressure = fix_store_fp->astore;
@ -197,8 +200,7 @@ void FixRHEO::init()
void FixRHEO::setup_pre_force(int /*vflag*/)
{
// Check to confirm no accessory fixes are yet defined
// FixRHEO must be the first fix
// Check to confirm accessory fixes do not preceed FixRHEO
// Note: these fixes set this flag in setup_pre_force()
if (viscosity_fix_defined || pressure_fix_defined || thermal_fix_defined || surface_fix_defined)
error->all(FLERR, "Fix RHEO must be defined before all other RHEO fixes");
@ -210,8 +212,7 @@ void FixRHEO::setup_pre_force(int /*vflag*/)
void FixRHEO::setup()
{
// Check to confirm all accessory fixes are defined
// Does not ensure fixes correctly cover all atoms (could be a subset group)
// Confirm all accessory fixes are defined, may not cover group all
// Note: these fixes set this flag in setup_pre_force()
if (!viscosity_fix_defined)
error->all(FLERR, "Missing fix rheo/viscosity");

63
src/RHEO/fix_rheo.h
View File

@ -32,12 +32,45 @@ class FixRHEO : public Fix {
void post_constructor() override;
void init() override;
void setup_pre_force(int) override;
void setup() override;
void pre_force(int) override;
void initial_integrate(int) override;
void final_integrate() override;
void reset_dt() override;
// Model parameters
double h, rho0, csq;
int zmin_kernel, rhosum_zmin;
int kernel_style;
enum {QUINTIC, CRK0, CRK1, CRK2};
// Non-persistent per-atom arrays
int *surface;
double *conductivity, *viscosity, *pressure;
double **f_pressure;
// Status variables
enum {
// Phase status
STATUS_FLUID = 1 << 0,
STATUS_REACTIVE = 1 << 1,
STATUS_SOLID = 1 << 2,
STATUS_FREEZING = 1 << 3
// Surface status
STATUS_BULK = 1 << 4,
STATUS_LAYER = 1 << 5,
STATUS_SURFACE = 1 << 6,
STATUS_SPLASH = 1 << 7,
// Temporary status options - reset in preforce
STATUS_SHIFT = 1 << 8,
STATUS_NO_FORCE = 1 << 9,
};
int phasemask = FFFFFFF0;
int surfacemask = FFFFFF0F;
// Accessory fixes/computes
int thermal_flag;
int rhosum_flag;
int shift_flag;
@ -47,13 +80,9 @@ class FixRHEO : public Fix {
int viscosity_fix_defined;
int pressure_fix_defined;
int thermal_fix_defined;
int interface_fix_defined;
int surface_fix_defined;
// 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;
@ -66,31 +95,7 @@ class FixRHEO : public Fix {
class ComputeRHEORhoSum *compute_rhosum;
class ComputeRHEOVShift *compute_vshift;
enum {QUINTIC, CRK0, CRK1, CRK2};
enum {LINEAR, CUBIC, TAITWATER};
enum {
// Phase status
STATUS_FLUID = 1 << 0, //Need to turn off other options
STATUS_REACTIVE = 1 << 1,
STATUS_SOLID = 1 << 2,
STATUS_FREEZING = 1 << 3
// Temporary status options - reset in preforce
STATUS_SHIFT = 1 << 4,
STATUS_NO_FORCE = 1 << 5,
// Surface status
STATUS_BULK = 1 << 6, //Need to turn off other options
STATUS_LAYER = 1 << 7,
STATUS_SURFACE = 1 << 8,
STATUS_SPLASH = 1 << 9,
};
protected:
double cut, rho0, csq;
int zmin_kernel, rhosum_zmin;
double dtv, dtf;
};

62
src/RHEO/fix_rheo_thermal.cpp
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@ -240,9 +240,11 @@ void FixRHEOThermal::post_integrate()
Tci = Tc_type[type[i]]);
}
if (Ti > Tci) { //Need to untoggle other phase options
if (Ti > Tci) {
status[i] &= phasemask;
status[i] |= FixRHEO::STATUS_FLUID;
} else if (!(status[i] & FixRHEO::STATUS_SOLID))
status[i] &= phasemask;
status[i] |= FixRHEO::STATUS_FREEZING;
}
}
@ -250,31 +252,59 @@ void FixRHEOThermal::post_integrate()
}
}
/* ----------------------------------------------------------------------
Only need to update non-evolving conductivity styles after atoms exchange
------------------------------------------------------------------------- */
add post neighbor then update preforce below
/* ---------------------------------------------------------------------- */
void FixRHEOThermal::pre_force(int /*vflag*/)
void FixRHEOThermal::post_neighbor()
{
double *conductivity = atom->conductivity;
int i;
int *type = atom->type;
double *conductivity = fix_rheo->conductivity;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
// Calculate non-persistent quantities before pairstyles
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
conductivity[i] = calc_kappa(i);
}
if (first_flag & nmax < atom->nmax) {
nmax = atom->nmax;
fix_rheo->fix_store_cond->grow_arrays(nmax);
}
if (conductivity_style == CONSTANT) {
return kappa;
for (i = 0; i < nall; i++)
if (mask[i] & groupbit) conductivity[i] = kappa;
} else if (conductivity_style == TYPE) {
int itype = atom->type[i];
return(kappa_type[itype]);
} else {
error->all(FLERR, "Invalid style");
for (i = 0; i < nall; i++)
if (mask[i] & groupbit) conductivity[i] = kappa_type[type[i]];
}
}
}
/* ----------------------------------------------------------------------
Update (and forward) evolving conductivity styles every timestep
------------------------------------------------------------------------- */
void FixRHEOThermal::pre_force(int /*vflag*/)
{
// So far, none exist
//int i;
//double *conductivity = fix_rheo->conductivity;
//int *mask = atom->mask;
//int nlocal = atom->nlocal;
//if (first_flag & nmax < atom->nmax) {
// nmax = atom->nmax;
// fix_rheo->fix_store_cond->grow_arrays(nmax);
//}
//if (conductivity_style == TBD) {
// for (i = 0; i < nlocal; i++) {
// if (mask[i] & groupbit) {
// }
// }
//}
//if (last_flag && comm_forward) comm->forward_comm(this);
}
/* ---------------------------------------------------------------------- */

12
src/RHEO/fix_rheo_viscosity.cpp
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@ -131,8 +131,9 @@ void FixRHEOViscosity::setup_pre_force(int /*vflag*/)
pre_force(0);
}
/* ---------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Only need to update non-evolving viscosity styles after atoms exchange
------------------------------------------------------------------------- */
void FixRHEOViscosity::post_neighbor()
{
@ -150,7 +151,6 @@ void FixRHEOViscosity::post_neighbor()
fix_rheo->fix_store_visc->grow_arrays(nmax);
}
// Update non-evolving viscosity styles only after atoms can exchange
if (viscosity_style == CONSTANT) {
for (i = 0; i < nall; i++)
if (mask[i] & groupbit) viscosity[i] = eta;
@ -161,14 +161,15 @@ void FixRHEOViscosity::post_neighbor()
}
}
/* ---------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Update (and forward) evolving viscosity styles every timestep
------------------------------------------------------------------------- */
void FixRHEOViscosity::pre_force(int /*vflag*/)
{
int i, a, b;
double tmp, gdot;
int *type = atom->type;
double *viscosity = fix_rheo->viscosity;
int *mask = atom->mask;
double **gradv = compute_grad->gradv;
@ -181,7 +182,6 @@ void FixRHEOViscosity::pre_force(int /*vflag*/)
fix_rheo->fix_store_visc->grow_arrays(nmax);
}
// Update viscosity styles that evolve in time every timestep
if (viscosity_style == POWER) {
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {

58
src/RHEO/pair_rheo.cpp
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@ -394,23 +394,23 @@ void PairRHEO::allocate()
void PairRHEO::settings(int narg, char **arg)
{
if(narg < 1) error->all(FLERR,"Illegal pair_style command");
if (narg < 1) error->all(FLERR,"Illegal pair_style command");
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg], "rho/damp") == 0) {
if (iarg+1 >= narg) error->all(FLERR,"Illegal pair_style command");
if (iarg + 1 >= narg) error->all(FLERR,"Illegal pair_style command");
rho_damp_flag = 1;
rho_damp = utils::numeric(FLERR,arg[iarg+1],false,lmp);
iarg ++;
rho_damp = utils::numeric(FLERR,arg[iarg + 1],false,lmp);
iarg++;
} else if (strcmp(arg[iarg], "artificial/visc") == 0) {
if (iarg+1 >= narg) error->all(FLERR,"Illegal pair_style command");
if (iarg + 1 >= narg) error->all(FLERR,"Illegal pair_style command");
artificial_visc_flag = 1;
av = utils::numeric(FLERR,arg[iarg+1],false,lmp);
iarg ++;
} else error->all(FLERR,"Illegal pair_style command");
iarg++;
} else error->all(FLERR,"Illegal pair_style command, {}", arg[iarg]);
iarg++;
}
}
@ -421,8 +421,8 @@ void PairRHEO::settings(int narg, char **arg)
void PairRHEO::coeff(int narg, char **arg)
{
if (narg != 4)
error->all(FLERR,"Incorrect number of args for pair_style llns coefficients");
if (narg != 2)
error->all(FLERR,"Incorrect number of args for pair_style rheo coefficients");
if (!allocated)
allocate();
@ -430,17 +430,8 @@ void PairRHEO::coeff(int narg, char **arg)
utils::bounds(FLERR,arg[0],1, atom->ntypes, ilo, ihi,error);
utils::bounds(FLERR,arg[1],1, atom->ntypes, jlo, jhi,error);
double rho0_one = utils::numeric(FLERR,arg[2],false,lmp);
double c_one = utils::numeric(FLERR,arg[3],false,lmp);
if (c_one != 1.0) error->warning(FLERR, "Need c = 1 for assumption in compute rheo/solids");
if (rho0_one != 1.0) error->warning(FLERR, "Need rho0 = 1 for assumption in compute rheo/solids");
int count = 0;
for (int i = ilo; i <= ihi; i++) {
rho0[i] = rho0_one;
csq[i] = c_one*c_one;
for (int j = 0; j <= atom->ntypes; j++) {
setflag[i][j] = 1;
count++;
@ -448,7 +439,7 @@ void PairRHEO::coeff(int narg, char **arg)
}
if (count == 0)
error->all(FLERR,"Incorrect args for pair llns coefficients");
error->all(FLERR,"Incorrect args for pair rheo coefficients");
}
/* ----------------------------------------------------------------------
@ -457,26 +448,21 @@ void PairRHEO::coeff(int narg, char **arg)
void PairRHEO::setup()
{
int flag;
int ifix = modify->find_fix_by_style("rheo");
if (ifix == -1) error->all(FLERR, "Using pair RHEO without fix RHEO");
fix_rheo = ((FixRHEO *) modify->fix[ifix]);
auto fixes = modify->get_fix_by_style("rheo");
if (fixes.size() == 0) error->all(FLERR, "Need to define fix rheo to use fix rheo/viscosity");
fix_rheo = dynamic_cast<FixRHEO *>(fixes[0]);
compute_kernel = fix_rheo->compute_kernel;
compute_grad = fix_rheo->compute_grad;
compute_sinterpolation = fix_rheo->compute_sinterpolation;
compute_interface = fix_rheo->compute_interface;
thermal_flag = fix_rheo->thermal_flag;
h = fix_rheo->h;
csq = fix_rheo->csq;
rho0 = fix_rheo->rho0;
h = utils::numeric(FLERR,arg[0],false,lmp);
if (h <= 0.0) error->all(FLERR,"Illegal pair_style command");
hinv = 1.0 / h;
hinv3 = 3.0 * hinv;
laplacian_order = -1;
if (comm->ghost_velocity == 0)
error->all(FLERR,"Pair RHEO requires ghost atoms store velocity");
@ -505,13 +491,3 @@ double PairRHEO::init_one(int i, int j)
return cut[i][j];
}
/* ---------------------------------------------------------------------- */
double PairRHEO::single(int /*i*/, int /*j*/, int /*itype*/, int /*jtype*/,
double /*rsq*/, double /*factor_coul*/, double /*factor_lj*/, double &fforce)
{
fforce = 0.0;
return 0.0;
}

15
src/RHEO/pair_rheo.h
View File

@ -12,9 +12,9 @@
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
// clang-format off
PairStyle(rheo,PairRHEO)
// clang-format on
#else
#ifndef LMP_PAIR_RHEO_H
@ -33,14 +33,13 @@ class PairRHEO : public Pair {
void coeff(int, char **) override;
void setup() override;
double init_one(int, int) override;
double single(int, int, int, int, double, double, double, double &) override;
protected:
int laplacian_order; // From fix RHEO
double h, csq*, rho0*; // From fix RHEO
double h, csq, rho0; // From fix RHEO
double hsq, hinv, rho0, av, rho_damp;
double hsq, hinv, av, rho_damp;
int laplacian_order;
int artificial_visc_flag;
int rho_damp_flag;
int thermal_flag;
@ -49,11 +48,11 @@ class PairRHEO : public Pair {
class ComputeRHEOKernel *compute_kernel;
class ComputeRHEOGrad *compute_grad;
class ComputeRHEOSolidInterpolation *compute_sinterpolation;
class ComputeRHEOInterface *compute_interface;
class FixRHEO *fix_rheo;
};
}
} // namespace LAMMPS_NS
#endif
#endif