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Pass state Array4 in initdata instead of separate Array4 for each entry. #54

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merged 12 commits into from
Feb 22, 2022
Merged

Pass state Array4 in initdata instead of separate Array4 for each entry. #54

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23e6cf4
Update the Case/* pelelm_initdata to take in state Array4 instead of …
esclapez Feb 22, 2022
3f4e518
Update call to pelelm_initdata to take in state_arr instead of separa…
esclapez Feb 22, 2022
2731995
Update Efield folder.
esclapez Feb 22, 2022
6cde2ef
Update UnitTest folder.
esclapez Feb 22, 2022
d60bf55
Update RegTest/EB* cases.
esclapez Feb 22, 2022
68870b3
Update the remainder of the tests.
esclapez Feb 22, 2022
fe3e909
Activate fpe in HotBubble regtest 2D.
esclapez Feb 22, 2022
a1a4334
Add a couple of HoBubble regtests.
esclapez Feb 22, 2022
f8d3d86
Need to keep the aux Array4.
esclapez Feb 22, 2022
6ad1c84
Update submods.
esclapez Feb 22, 2022
a3919e0
Missing change to state Array4
esclapez Feb 22, 2022
777a7ba
Remove deprecated include of pmf.H
esclapez Feb 22, 2022
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62 changes: 62 additions & 0 deletions .github/workflows/linux.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -120,6 +120,68 @@ jobs:
run: |
./PeleLMeX2d.gnu.ex input.2d_CoVo amr.max_step=2 amr.plot_int=-1 amr.check_int=-1

# Build and Run the HoBubble RegTest with GNU7.5 and MPI support
HB2D_MPIRun:
name: GNU@7.5 MPI Run [HB2D]
runs-on: ubuntu-latest
env:
{CXXFLAGS: "-Werror -Wshadow -Woverloaded-virtual -Wunreachable-code"}
steps:
- name: Cancel previous runs
uses: styfle/cancel-workflow-action@0.6.0
with:
access_token: ${{github.token}}
- uses: actions/checkout@v2
- name: System Dependencies
run: .github/workflows/dependencies/dependencies.sh
- name: Repo Dependencies
run: Utils/CloneDeps.sh
- name: Build
env:
AMREX_HOME: ${GITHUB_WORKSPACE}/build/amrex
PELE_PHYSICS_HOME: ${GITHUB_WORKSPACE}/build/PelePhysics
PELELM_HOME: ${GITHUB_WORKSPACE}
AMREX_HYDRO_HOME: ${GITHUB_WORKSPACE}/build/AMReX-Hydro
working-directory: ./Exec/RegTests/HotBubble/
run: |
make TPL COMP=gnu USE_MPI=TRUE
make -j 2 COMP=gnu USE_MPI=TRUE
- name: Run
working-directory: ./Exec/RegTests/HotBubble/
run: |
./PeleLMeX2d.gnu.MPI.ex input.2d-regt amr.max_step=20 amr.plot_int=-1 amr.check_int=-1

# Build and Run the HoBubble RegTest with GNU7.5 in DEBUG
HB2D_DBGRun:
name: GNU@7.5 DEBUG Run [HB2DDBG]
runs-on: ubuntu-latest
env:
{CXXFLAGS: "-Werror -Wshadow -Woverloaded-virtual -Wunreachable-code"}
steps:
- name: Cancel previous runs
uses: styfle/cancel-workflow-action@0.6.0
with:
access_token: ${{github.token}}
- uses: actions/checkout@v2
- name: System Dependencies
run: .github/workflows/dependencies/dependencies.sh
- name: Repo Dependencies
run: Utils/CloneDeps.sh
- name: Build
env:
AMREX_HOME: ${GITHUB_WORKSPACE}/build/amrex
PELE_PHYSICS_HOME: ${GITHUB_WORKSPACE}/build/PelePhysics
PELELM_HOME: ${GITHUB_WORKSPACE}
AMREX_HYDRO_HOME: ${GITHUB_WORKSPACE}/build/AMReX-Hydro
working-directory: ./Exec/RegTests/HotBubble/
run: |
make TPL COMP=gnu DEBUG=TRUE USE_MPI=FALSE
make -j 2 COMP=gnu DEBUG=TRUE USE_MPI=FALSE
- name: Run
working-directory: ./Exec/RegTests/HotBubble/
run: |
./PeleLMeX2d.gnu.DEBUG.ex input.2d-regt amr.max_step=20 amr.plot_int=-1 amr.check_int=-1

# Build and Run the EnclosedFlame RegTest with GNU7.5 and MPI support
EF2D_MPIRun:
name: GNU@7.5 MPI Run [EF2D]
Expand Down
31 changes: 11 additions & 20 deletions Exec/Cases/CounterFlow/pelelm_prob.H
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Original file line number Diff line number Diff line change
Expand Up @@ -14,11 +14,7 @@ AMREX_GPU_DEVICE
AMREX_FORCE_INLINE
void pelelm_initdata(int i, int j, int k,
int is_incompressible,
amrex::Array4<amrex::Real> const& vel,
amrex::Array4<amrex::Real> const& rho,
amrex::Array4<amrex::Real> const& rhoY,
amrex::Array4<amrex::Real> const& rhoH,
amrex::Array4<amrex::Real> const& temp,
amrex::Array4<amrex::Real> const& state,
amrex::Array4<amrex::Real> const& aux,
amrex::GeometryData const& geomdata,
ProbParm const& prob_parm,
Expand All @@ -43,17 +39,12 @@ void pelelm_initdata(int i, int j, int k,
constexpr amrex::Real Pi = 3.14159265358979323846264338327950288;

auto eos = pele::physics::PhysicsType::eos();
amrex::GpuArray<amrex::Real, NUM_SPECIES + 4> pmf_vals = {0.0};
amrex::Real u[3] = {0.0};
amrex::Real molefrac[NUM_SPECIES] = {0.0};
amrex::Real massfrac[NUM_SPECIES] = {0.0};
amrex::Real y1, y2;
amrex::Real splitx = prob_lo[0] + 0.5 * Lx;

massfrac[N2_ID] = 0.767;
massfrac[O2_ID] = 0.233;

temp(i,j,k) = 298.0;
state(i,j,k,TEMP) = 298.0;

if (prob_parm.do_ignit) {
amrex::Real radiusSq = AMREX_D_TERM( (x-xc) * (x-xc),
Expand All @@ -62,31 +53,31 @@ void pelelm_initdata(int i, int j, int k,
amrex::Real radius = std::sqrt(radiusSq);
amrex::Real mixingWidth = 0.1*prob_parm.ignitSphereRad;
amrex::Real mixingFunction = 0.5 * ( 1.0 + std::tanh((prob_parm.ignitSphereRad - radius)/mixingWidth));
temp(i,j,k) = mixingFunction * prob_parm.ignitT + (1.0 - mixingFunction) * 298.0;
state(i,j,k,TEMP) = mixingFunction * prob_parm.ignitT + (1.0 - mixingFunction) * 298.0;
massfrac[CH4_ID] = 0.02;
massfrac[O2_ID] = 0.233 * (1.0 - massfrac[CH4_ID]);
massfrac[N2_ID] = 1.0 - massfrac[CH4_ID] - massfrac[O2_ID];
}

AMREX_D_TERM(vel(i,j,k,0) = 0.0;,
vel(i,j,k,1) = 0.1;,
vel(i,j,k,2) = 0.0);
AMREX_D_TERM(state(i,j,k,VELX) = 0.0;,
state(i,j,k,VELY) = 0.1;,
state(i,j,k,VELZ) = 0.0);

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

// Density
amrex::Real rho_cgs = 0.0;
eos.PYT2R(P_cgs, massfrac, temp(i,j,k), rho_cgs);
rho(i,j,k) = rho_cgs * 1.0e3;
eos.PYT2R(P_cgs, massfrac, state(i,j,k,TEMP), rho_cgs);
state(i,j,k,DENSITY) = rho_cgs * 1.0e3;

// Enthalpy
amrex::Real h_cgs = 0.0;
eos.TY2H(temp(i,j,k), massfrac, h_cgs);
rhoH(i,j,k) = h_cgs * 1.0e-4 * rho(i,j,k);
eos.TY2H(state(i,j,k,TEMP), massfrac, h_cgs);
state(i,j,k,RHOH) = h_cgs * 1.0e-4 * state(i,j,k,DENSITY);

// Species mass
for (int n = 0; n < NUM_SPECIES; n++) {
rhoY(i,j,k,n) = massfrac[n] * rho(i,j,k);
state(i,j,k,FIRSTSPEC+n) = massfrac[n] * state(i,j,k,DENSITY);
}
}

Expand Down
24 changes: 10 additions & 14 deletions Exec/Cases/NormalJet_OpenDomain/pelelm_prob.H
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Original file line number Diff line number Diff line change
Expand Up @@ -16,11 +16,7 @@ AMREX_FORCE_INLINE
void
pelelm_initdata (int i, int j, int k,
int is_incompressible,
amrex::Array4<amrex::Real> const& vel,
amrex::Array4<amrex::Real> const& rho,
amrex::Array4<amrex::Real> const& rhoY,
amrex::Array4<amrex::Real> const& rhoH,
amrex::Array4<amrex::Real> const& temp,
amrex::Array4<amrex::Real> const& state,
amrex::Array4<amrex::Real> const& aux,
amrex::GeometryData const& geomdata,
ProbParm const& prob_parm,
Expand All @@ -30,28 +26,28 @@ pelelm_initdata (int i, int j, int k,

amrex::Real massfrac[NUM_SPECIES] = {0.0};

temp(i,j,k) = prob_parm.T_ox;
state(i,j,k,TEMP) = prob_parm.T_ox;

for (int n = 0; n < NUM_SPECIES; n++)
{
massfrac[n] = prob_parm.Y_ox[n];
}

vel(i,j,k,0) = 0.0;
vel(i,j,k,1) = 0.0;
vel(i,j,k,2) = 1.0;
state(i,j,k,VELX) = 0.0;
state(i,j,k,VELY) = 0.0;
state(i,j,k,VELZ) = 1.0;

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

eos.PYT2R(P_cgs, massfrac, temp(i,j,k), rho_cgs);
rho(i,j,k) = rho_cgs * 1.0e3; // CGS -> MKS conversion
eos.PYT2R(P_cgs, massfrac, state(i,j,k,TEMP), rho_cgs);
state(i,j,k,DENSITY) = rho_cgs * 1.0e3; // CGS -> MKS conversion

eos.TY2H(temp(i,j,k), massfrac, rhoH(i,j,k));
rhoH(i,j,k) *= 1.0e-4 * rho(i,j,k); // CGS -> MKS conversion
eos.TY2H(state(i,j,k,TEMP), massfrac, state(i,j,k,RHOH));
state(i,j,k,RHOH) *= 1.0e-4 * state(i,j,k,DENSITY); // CGS -> MKS conversion

for (int n = 0; n < NUM_SPECIES; n++) {
rhoY(i,j,k,n) = massfrac[n] * rho(i,j,k);
state(i,j,k,FIRSTSPEC+n) = massfrac[n] * state(i,j,k,DENSITY);
}
}

Expand Down
28 changes: 12 additions & 16 deletions Exec/Cases/PremBunsen2D/pelelm_prob.H
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Original file line number Diff line number Diff line change
Expand Up @@ -15,11 +15,7 @@ AMREX_GPU_DEVICE
AMREX_FORCE_INLINE
void pelelm_initdata(int i, int j, int k,
int is_incompressible,
amrex::Array4<amrex::Real> const& vel,
amrex::Array4<amrex::Real> const& rho,
amrex::Array4<amrex::Real> const& rhoY,
amrex::Array4<amrex::Real> const& rhoH,
amrex::Array4<amrex::Real> const& temp,
amrex::Array4<amrex::Real> const& state,
amrex::Array4<amrex::Real> const& aux,
amrex::GeometryData const& geomdata,
ProbParm const& prob_parm,
Expand Down Expand Up @@ -50,7 +46,7 @@ void pelelm_initdata(int i, int j, int k,
massfrac[N2_ID] = 0.767;
massfrac[O2_ID] = 0.233;

temp(i,j,k) = 298.0;
state(i,j,k,TEMP) = 298.0;

if ( x >= splitx ) {
if ( (x-splitx) < ( std::sqrt((y+0.0009) / 0.01))/100.0) {
Expand All @@ -61,7 +57,7 @@ void pelelm_initdata(int i, int j, int k,
y2 += prob_parm.standoff;

pele::physics::PMF::pmf(pmf_data,y2, y2, pmf_vals);
temp(i,j,k) = pmf_vals[0];
state(i,j,k,TEMP) = pmf_vals[0];
for (int n = 0; n < NUM_SPECIES; n++){
massfrac[n] = pmf_vals[3 + n];
}
Expand All @@ -76,33 +72,33 @@ void pelelm_initdata(int i, int j, int k,
y2 += prob_parm.standoff;

pele::physics::PMF::pmf(pmf_data, y2, y2, pmf_vals);
temp(i,j,k) = pmf_vals[0];
state(i,j,k,TEMP) = pmf_vals[0];
for (int n = 0; n < NUM_SPECIES; n++){
massfrac[n] = pmf_vals[3 + n];
}
//eos.X2Y(molefrac, massfrac);
}
}

AMREX_D_TERM(vel(i,j,k,0) = 0.0;,
vel(i,j,k,1) = 0.1;,
vel(i,j,k,2) = 0.0);
AMREX_D_TERM(state(i,j,k,VELX) = 0.0;,
state(i,j,k,VELX) = 0.1;,
state(i,j,k,VELX) = 0.0);

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

// Density
amrex::Real rho_cgs = 0.0;
eos.PYT2R(P_cgs, massfrac, temp(i,j,k), rho_cgs);
rho(i,j,k) = rho_cgs * 1.0e3;
eos.PYT2R(P_cgs, massfrac, state(i,j,k,TEMP), rho_cgs);
state(i,j,k,DENSITY) = rho_cgs * 1.0e3;

// Enthalpy
amrex::Real h_cgs = 0.0;
eos.TY2H(temp(i,j,k), massfrac, h_cgs);
rhoH(i,j,k) = h_cgs * 1.0e-4 * rho(i,j,k);
eos.TY2H(state(i,j,k,TEMP), massfrac, h_cgs);
state(i,j,k,RHOH) = h_cgs * 1.0e-4 * state(i,j,k,DENSITY);

// Species mass
for (int n = 0; n < NUM_SPECIES; n++) {
rhoY(i,j,k,n) = massfrac[n] * rho(i,j,k);
state(i,j,k,FIRSTSPEC+n) = massfrac[n] * state(i,j,k,DENSITY);
}
}

Expand Down
26 changes: 11 additions & 15 deletions Exec/Cases/PremBunsen3D/pelelm_prob.H
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Original file line number Diff line number Diff line change
Expand Up @@ -15,11 +15,7 @@ AMREX_GPU_DEVICE
AMREX_FORCE_INLINE
void pelelm_initdata(int i, int j, int k,
int is_incompressible,
amrex::Array4<amrex::Real> const& vel,
amrex::Array4<amrex::Real> const& rho,
amrex::Array4<amrex::Real> const& rhoY,
amrex::Array4<amrex::Real> const& rhoH,
amrex::Array4<amrex::Real> const& temp,
amrex::Array4<amrex::Real> const& state,
amrex::Array4<amrex::Real> const& aux,
amrex::GeometryData const& geomdata,
ProbParm const& prob_parm,
Expand Down Expand Up @@ -52,7 +48,7 @@ void pelelm_initdata(int i, int j, int k,
massfrac[N2_ID] = 0.767;
massfrac[O2_ID] = 0.233;

temp(i,j,k) = 298.0;
state(i,j,k,TEMP) = 298.0;

if ( (rad_xy) < ( std::sqrt((z+0.0009) / 0.01))/100.0) {
amrex::Real pl1_angle = std::atan(0.01/prob_parm.slot_width);
Expand All @@ -62,32 +58,32 @@ void pelelm_initdata(int i, int j, int k,
y2 += prob_parm.standoff;

pele::physics::PMF::pmf(pmf_data,y2, y2, pmf_vals);
temp(i,j,k) = pmf_vals[0];
state(i,j,k,TEMP) = pmf_vals[0];
for (int n = 0; n < NUM_SPECIES; n++){
massfrac[n] = pmf_vals[3 + n];
}
//eos.X2Y(molefrac, massfrac);
}

AMREX_D_TERM(vel(i,j,k,0) = 0.0;,
vel(i,j,k,1) = 0.1;,
vel(i,j,k,2) = 0.0);
AMREX_D_TERM(state(i,j,k,VELX) = 0.0;,
state(i,j,k,VELY) = 0.1;,
state(i,j,k,VELZ) = 0.0);

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

// Density
amrex::Real rho_cgs = 0.0;
eos.PYT2R(P_cgs, massfrac, temp(i,j,k), rho_cgs);
rho(i,j,k) = rho_cgs * 1.0e3;
eos.PYT2R(P_cgs, massfrac, state(i,j,k,TEMP), rho_cgs);
state(i,j,k,DENSITY) = rho_cgs * 1.0e3;

// Enthalpy
amrex::Real h_cgs = 0.0;
eos.TY2H(temp(i,j,k), massfrac, h_cgs);
rhoH(i,j,k) = h_cgs * 1.0e-4 * rho(i,j,k);
eos.TY2H(state(i,j,k,TEMP), massfrac, h_cgs);
state(i,j,k,RHOH) = h_cgs * 1.0e-4 * state(i,j,k,DENSITY);

// Species mass
for (int n = 0; n < NUM_SPECIES; n++) {
rhoY(i,j,k,n) = massfrac[n] * rho(i,j,k);
state(i,j,k,FIRSTSPEC+n) = massfrac[n] * state(i,j,k,DENSITY);
}
}

Expand Down
22 changes: 9 additions & 13 deletions Exec/Cases/TripleFlame/pelelm_prob.H
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Original file line number Diff line number Diff line change
Expand Up @@ -49,11 +49,7 @@ AMREX_FORCE_INLINE
void
pelelm_initdata (int i, int j, int k,
int is_incompressible,
amrex::Array4<amrex::Real> const& vel,
amrex::Array4<amrex::Real> const& rho,
amrex::Array4<amrex::Real> const& rhoY,
amrex::Array4<amrex::Real> const& rhoH,
amrex::Array4<amrex::Real> const& temp,
amrex::Array4<amrex::Real> const& state,
amrex::Array4<amrex::Real> const& aux,
amrex::GeometryData const& geomdata,
ProbParm const& prob_parm,
Expand Down Expand Up @@ -94,28 +90,28 @@ pelelm_initdata (int i, int j, int k,

amrex::Real Gaussian_T = std::exp( - (rad*rad) / (2.0 * ( Gauss_T_width * ( 1.0 + (y - y_lo) / 0.03))
* ( Gauss_T_width * ( 1.0 + (y - y_lo) / 0.03)) ));
temp(i,j,k) = prob_parm.T_in + (Gauss_maxT-prob_parm.T_in) * Gaussian_T;
state(i,j,k,TEMP) = prob_parm.T_in + (Gauss_maxT-prob_parm.T_in) * Gaussian_T;

amrex::Real Gaussian_spec = std::exp( - (rad*rad) / (2.0 * ( Gauss_Spec_width * ( 1.0 + (y - y_lo) / 0.03))
* ( Gauss_Spec_width * ( 1.0 + (y - y_lo) / 0.03)) ));
for (int n = 0; n < NUM_SPECIES; ++n) {
massfrac[n] = (1.0 - Gaussian_spec) * massfrac[n] + Gaussian_spec * air_Y[n];
}

vel(i,j,k,0) = 0.0;
vel(i,j,k,1) = prob_parm.V_in;
state(i,j,k,VELX) = 0.0;
state(i,j,k,VELY) = prob_parm.V_in;

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

eos.PYT2R(P_cgs, massfrac, temp(i,j,k), rho_cgs);
rho(i,j,k) = rho_cgs * 1.0e3; // CGS -> MKS conversion
eos.PYT2R(P_cgs, massfrac, state(i,j,k,TEMP), rho_cgs);
state(i,j,k,DENSITY) = rho_cgs * 1.0e3; // CGS -> MKS conversion

eos.TY2H(temp(i,j,k), massfrac, rhoH(i,j,k));
rhoH(i,j,k) = rhoH(i,j,k) * 1.0e-4 * rho(i,j,k); // CGS -> MKS conversion
eos.TY2H(state(i,j,k,TEMP), massfrac, state(i,j,k,RHOH));
state(i,j,k,RHOH) *= 1.0e-4 * state(i,j,k,DENSITY); // CGS -> MKS conversion

for (int n = 0; n < NUM_SPECIES; n++) {
rhoY(i,j,k,n) = massfrac[n] * rho(i,j,k);
state(i,j,k,FIRSTSPEC+n) = massfrac[n] * state(i,j,k,DENSITY);
}
}

Expand Down
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