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Add full manifold model capability (#415)
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* basics of having eos_parm in PeleLMeX

* add eosparm to PeleLMeX_K functions

* more eosparm: now everywhere except Efield & BCs

* eosparm in BC stuff

* re-order functions for template

* remove manifold-specfic changes, will go in later PR

* gnu make changes for manifold

* create manifold version of adjust fluxes function

* Add abort for Closed Chamber + Manifold

* Better setup chackes for Manifold + wbar, closed chamber, mixfrac/prog

* advection of rho corrections for manifold models

* manifold-specific transport, derives, divu

* remove divide by zero

* go to templated EOS functions to use cellData

* fix oops in pelephysics

* fix compile errors for Manifold derives

* fix compile condition for transparm initialization

* fix missing RY2RRinvY conversion

* use PelePhysics that free manfunc shared pointer

* clang-formatting

* fux derives for manifold

* add flamesheet test case for manifold

* remove extraneous changes in file

* Update Source/PeleLMeX_Setup.cpp

Co-authored-by: Marc T. Henry de Frahan <[email protected]>

* address Marc HdF's comments with minor formatting

* remove copied line

* update PP for merged RY2R stuff

---------

Co-authored-by: Marc T. Henry de Frahan <[email protected]>
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@baperry2 @marchdf
baperry2 and marchdf authored Nov 6, 2024
1 parent 0919032 commit 86c4721
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Showing 14 changed files with 539 additions and 207 deletions.
16 changes: 16 additions & 0 deletions Exec/Make.PeleLMeX
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Original file line number Diff line number Diff line change
Expand Up @@ -77,6 +77,19 @@ endif
ifeq ($(Eos_Model),$(filter $(Eos_Model),Soave-Redlich-Kwong))
DEFINES += -DUSE_SRK_EOS
endif
ifeq ($(Eos_Model),$(filter $(Eos_Model),Manifold))
DEFINES += -DUSE_MANIFOLD_EOS
DEFINES += -DMANIFOLD_DIM=$(Manifold_Dim)
ifeq ($(Manifold_Type),Table)
DEFINES += -DMANIFOLD_EOS_TYPE=1
else
ifeq ($(Manifold_Type),Network)
DEFINES += -DMANIFOLD_EOS_TYPE=2
else
DEFINES += -DMANIFOLD_EOS_TYPE=0
endif
endif
endif

# Transport model switches
ifeq ($(Transport_Model), Simple)
Expand All @@ -92,6 +105,9 @@ endif
ifeq ($(Transport_Model), Sutherland)
DEFINES += -DUSE_SUTHERLAND_TRANSPORT
endif
ifeq ($(Transport_Model), Manifold)
DEFINES += -DUSE_MANIFOLD_TRANSPORT
endif

ifeq ($(PELE_USE_KLU), TRUE)
DEFINES += -DPELE_USE_KLU
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15 changes: 12 additions & 3 deletions Exec/RegTests/FlameSheet/GNUmakefile
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Expand Up @@ -29,9 +29,18 @@ THREAD_SANITIZER = FALSE
USE_EFIELD = FALSE

# PelePhysics
Chemistry_Model = drm19
Eos_Model = Fuego
Transport_Model = Simple
USE_MANIFOLD = FALSE
ifeq ($(USE_MANIFOLD), TRUE)
Eos_Model = Manifold
Chemistry_Model = Null
Transport_Model = Manifold
Manifold_Dim = 1
# Manifold_Type = Table
else
Chemistry_Model = drm19
Eos_Model = Fuego
Transport_Model = Simple
endif

PELE_HOME ?= ../../..
include $(PELE_HOME)/Exec/Make.PeleLMeX
85 changes: 85 additions & 0 deletions Exec/RegTests/FlameSheet/input.manifold
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@@ -0,0 +1,85 @@
#----------------------DOMAIN DEFINITION------------------------
geometry.is_periodic = 0 0 # For each dir, 0: non-perio, 1: periodic
geometry.coord_sys = 0 # 0 => cart, 1 => RZ
geometry.prob_lo = 0.0 0.0 0.0 # x_lo y_lo (z_lo)
geometry.prob_hi = 0.003 0.012 0.016 # x_hi y_hi (z_hi)

# >>>>>>>>>>>>> BC FLAGS <<<<<<<<<<<<<<<<
# Interior, Inflow, Outflow, Symmetry,
# SlipWallAdiab, NoSlipWallAdiab, SlipWallIsotherm, NoSlipWallIsotherm
peleLM.lo_bc = Interior Inflow
peleLM.hi_bc = Interior Outflow
peleLM.lo_bc = SlipWallAdiab Inflow
peleLM.hi_bc = SlipWallAdiab Outflow


#-------------------------AMR CONTROL----------------------------
amr.n_cell = 64 256 32 # Level 0 number of cells in each direction
amr.v = 1 # AMR verbose
amr.max_level = 0 # maximum level number allowed
amr.ref_ratio = 2 2 2 2 # refinement ratio
amr.regrid_int = 5 # how often to regrid
amr.n_error_buf = 1 1 2 2 # number of buffer cells in error est
amr.grid_eff = 0.7 # what constitutes an efficient grid
amr.blocking_factor = 16 # block factor in grid generation (min box size)
amr.max_grid_size = 64 # max box size


#--------------------------- Problem -------------------------------
prob.P_mean = 101325.0
prob.standoff = -.03
prob.pertmag = 0.0000
pmf.datafile = "prem_drm19_phi1_p1_t298_mani.dat"

#-------------------------PeleLM CONTROL----------------------------
peleLM.v = 3
peleLM.incompressible = 0
peleLM.rho = 1.17
peleLM.mu = 0.0
peleLM.sdc_iterMax = 1
peleLM.floor_species = 0

peleLM.do_temporals = 1
peleLM.temporal_int = 2
peleLM.mass_balance = 1

#amr.restart = chk00005
#amr.check_int = 20
amr.plot_int = 1
amr.max_step = 10
amr.dt_shrink = 0.01
amr.stop_time = 0.01
#amr.stop_time = 1.00
amr.cfl = 0.5
amr.derive_plot_vars = avg_pressure mag_vort mass_fractions maniout

# ------------------- INPUTS DERIVED DIAGS ------------------
peleLM.fuel_name = CH4

# --------------- INPUTS TO CHEMISTRY REACTOR ---------------
peleLM.chem_integrator = "ReactorRK64"

mac_proj.verbose = 0
nodal_proj.verbose = 0

#--------------------REFINEMENT CONTROL------------------------
amr.refinement_indicators = temp
amr.temp.max_level = 3
amr.temp.adjacent_difference_greater = 10
amr.temp.field_name = temp

#amrex.fpe_trap_invalid = 1
#amrex.fpe_trap_zero = 1
#amrex.fpe_trap_overflow = 1

#----------------------- Manifold Stuff ----------------------------
manifold.model = Table
manifold.table.v = 1
manifold.table.filename = prem_drm19_phi1_p1_t298.ctb
manifold.nominal_pressure_cgs = 1013250.0
manifold.compute_temperature = 1
manifold.density_lookup_type = log
peleLM.use_wbar = 0
peleLM.chi_correction_type = DivuFirstIter
#peleLM.chi_correction_type = NoDivu
peleLM.print_chi_convergence = 1
60 changes: 38 additions & 22 deletions Exec/RegTests/FlameSheet/pelelmex_prob.H
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Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,6 @@ pelelmex_initdata(
amrex::Real pert = 0.0;

if (prob_parm.pertmag > 0.0) {

#if (AMREX_SPACEDIM == 2)
amrex::GpuArray<amrex::Real, AMREX_SPACEDIM - 1> lpert{Lx};
if (prob_parm.pertlength > 0.0) {
Expand All @@ -58,10 +57,8 @@ pelelmex_initdata(
1.017 * std::sin(2 * Pi * 5 * (x - 0.0033) / lpert[0]) +
0.982 * std::sin(2 * Pi * 5 * (x - 0.014234) / lpert[0]));
}

amrex::Real y1 = (y - prob_parm.standoff - 0.5 * dx[1] + pert) * 100;
amrex::Real y2 = (y - prob_parm.standoff + 0.5 * dx[1] + pert) * 100;

#elif (AMREX_SPACEDIM == 3)
amrex::GpuArray<amrex::Real, AMREX_SPACEDIM - 1> lpert{Lx, Ly};
if (prob_parm.pertlength > 0.0) {
Expand All @@ -80,29 +77,36 @@ pelelmex_initdata(
std::sin(2 * Pi * 6 * (y - 0.018) / lpert[1]) +
0.982 * std::sin(2 * Pi * 5 * (x - 0.014234) / lpert[0]));
}

amrex::Real y1 = (z - prob_parm.standoff - 0.5 * dx[2] + pert) * 100;
amrex::Real y2 = (z - prob_parm.standoff + 0.5 * dx[2] + pert) * 100;
#endif

pele::physics::PMF::pmf(pmf_data, y1, y2, pmf_vals);

state(i, j, k, TEMP) = pmf_vals[0];
;
for (int dim = 0; dim < AMREX_SPACEDIM - 1; dim++) {
state(i, j, k, VELX + dim) = 0.0;
}
state(i, j, k, VELX + AMREX_SPACEDIM - 1) = pmf_vals[1] * 1e-2;

#ifdef USE_MANIFOLD_EOS
for (int n = 0; n < NUM_SPECIES - 1; n++) {
massfrac[n] = pmf_vals[3 + n];
}
amrex::Real rho_temp, tmp1, tmp2;
eos.PYT2R(tmp1, massfrac, tmp2, rho_temp);
rho_temp *= 1.0e3;
state(i, j, k, DENSITY) = rho_temp; // CGS -> MKS conversion
state(i, j, k, RHOH) = 0.0; // No RhoH transport in manifold model
for (int n = 0; n < NUM_SPECIES - 1; n++) {
state(i, j, k, FIRSTSPEC + n) = massfrac[n] * rho_temp;
}
state(i, j, k, FIRSTSPEC + NUM_SPECIES - 1) = rho_temp;
#else
for (int n = 0; n < NUM_SPECIES; n++) {
molefrac[n] = pmf_vals[3 + n];
}
eos.X2Y(molefrac, massfrac);

state(i, j, k, VELX) = 0.0;
#if (AMREX_SPACEDIM == 2)
state(i, j, k, VELY) = pmf_vals[1] * 1e-2;
#elif (AMREX_SPACEDIM == 3)
state(i, j, k, VELY) = 0.0;
state(i, j, k, VELZ) = pmf_vals[1] * 1e-2;
#endif

amrex::Real P_cgs = prob_parm.P_mean * 10.0;

// Density
Expand All @@ -119,6 +123,7 @@ pelelmex_initdata(
for (int n = 0; n < NUM_SPECIES; n++) {
state(i, j, k, FIRSTSPEC + n) = massfrac[n] * state(i, j, k, DENSITY);
}
#endif
}

AMREX_GPU_DEVICE
Expand All @@ -144,15 +149,25 @@ bcnormal(
if (sgn == 1) {
pele::physics::PMF::pmf(pmf_data, prob_lo[idir], prob_lo[idir], pmf_vals);

s_ext[VELX] = 0.0;
#if (AMREX_SPACEDIM == 2)
s_ext[VELY] = pmf_vals[1] * 1e-2;
#elif (AMREX_SPACEDIM == 3)
s_ext[VELY] = 0.0;
s_ext[VELZ] = pmf_vals[1] * 1e-2;
#endif

for (int dim = 0; dim < AMREX_SPACEDIM - 1; dim++) {
s_ext[VELX + dim] = 0.0;
}
s_ext[VELX + AMREX_SPACEDIM - 1] = pmf_vals[1] * 1e-2;
s_ext[TEMP] = pmf_vals[0];

#ifdef USE_MANIFOLD_EOS
for (int n = 0; n < NUM_SPECIES; n++) {
massfrac[n] = pmf_vals[3 + n];
}
amrex::Real P_dummy, rho_cgs;
eos.PYT2R(P_dummy, massfrac, s_ext[TEMP], rho_cgs);
s_ext[DENSITY] = rho_cgs * 1.0e3;
s_ext[RHOH] = 0.0;
for (int n = 0; n < NUM_SPECIES - 1; n++) {
s_ext[FIRSTSPEC + n] = massfrac[n] * s_ext[DENSITY];
}
s_ext[FIRSTSPEC + NUM_SPECIES - 1] = s_ext[DENSITY];
#else
for (int n = 0; n < NUM_SPECIES; n++) {
molefrac[n] = pmf_vals[3 + n];
}
Expand All @@ -170,6 +185,7 @@ bcnormal(
for (int n = 0; n < NUM_SPECIES; n++) {
s_ext[FIRSTSPEC + n] = massfrac[n] * s_ext[DENSITY];
}
#endif
}
}

Expand Down
1 change: 1 addition & 0 deletions Source/PeleLMeX.H
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Original file line number Diff line number Diff line change
Expand Up @@ -606,6 +606,7 @@ public:
* velocity, ensuring they sum up to zero. \param a_fluxes diffusion fluxes to
* be updated \param a_spec species rhoYs state data on all levels
*/
template <typename EOSType>
void adjustSpeciesFluxes(
const amrex::Vector<amrex::Array<amrex::MultiFab*, AMREX_SPACEDIM>>&
a_spfluxes,
Expand Down
19 changes: 7 additions & 12 deletions Source/PeleLMeX_Advection.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -488,9 +488,8 @@ PeleLM::computeScalarAdvTerms(std::unique_ptr<AdvanceAdvData>& advData)
afrac] AMREX_GPU_DEVICE(int i, int j, int k) noexcept {
rho_ed(i, j, k) = 0.0;
if (afrac(i, j, k) > 0.0) { // Uncovered faces
for (int n = 0; n < NUM_SPECIES; n++) {
rho_ed(i, j, k) += rhoY_ed(i, j, k, n);
}
pele::physics::PhysicsType::eos_type::RY2R(
rhoY_ed.cellData(i, j, k), rho_ed(i, j, k));
}
});
} else // Regular boxes
Expand All @@ -499,10 +498,8 @@ PeleLM::computeScalarAdvTerms(std::unique_ptr<AdvanceAdvData>& advData)
amrex::ParallelFor(
ebx,
[rho_ed, rhoY_ed] AMREX_GPU_DEVICE(int i, int j, int k) noexcept {
rho_ed(i, j, k) = 0.0;
for (int n = 0; n < NUM_SPECIES; n++) {
rho_ed(i, j, k) += rhoY_ed(i, j, k, n);
}
pele::physics::PhysicsType::eos_type::RY2R(
rhoY_ed.cellData(i, j, k), rho_ed(i, j, k));
});
}
}
Expand Down Expand Up @@ -751,11 +748,9 @@ PeleLM::computeScalarAdvTerms(std::unique_ptr<AdvanceAdvData>& advData)
amrex::ParallelFor(
advData->AofS[lev],
[=] AMREX_GPU_DEVICE(int box_no, int i, int j, int k) noexcept {
aofsma[box_no](i, j, k, DENSITY) = 0.0;
for (int n = 0; n < NUM_SPECIES; n++) {
aofsma[box_no](i, j, k, DENSITY) +=
aofsma[box_no](i, j, k, FIRSTSPEC + n);
}
pele::physics::PhysicsType::eos_type::RY2R(
aofsma[box_no].cellData(i, j, k), aofsma[box_no](i, j, k, DENSITY),
FIRSTSPEC);
});
}
Gpu::streamSynchronize();
Expand Down
16 changes: 16 additions & 0 deletions Source/PeleLMeX_DeriveFunc.H
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Original file line number Diff line number Diff line change
Expand Up @@ -290,6 +290,22 @@ void pelelmex_deruserdef(
const amrex::Vector<amrex::BCRec>& bcrec,
int level);

#ifdef USE_MANIFOLD_EOS
void pelelmex_dermaniout(
PeleLM* a_pelelm,
const amrex::Box& bx,
amrex::FArrayBox& derfab,
int dcomp,
int ncomp,
const amrex::FArrayBox& statefab,
const amrex::FArrayBox& reactfab,
const amrex::FArrayBox& pressfab,
const amrex::Geometry& geom,
amrex::Real time,
const amrex::Vector<amrex::BCRec>& bcrec,
int level);
#endif

#ifdef PELE_USE_EFIELD
#include <PeleLMeX_EFDeriveFunc.H>
#endif
Expand Down
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