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Add more moisture state variables (#1350)
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* First pass. Took a step with Bubble in debug.

* Modify buoyancy and pert press. This touches uninitialized data; need to fix.

* It was an index issue on pert press, caused negative density.

* Fix plot file at time 0 and precompute the pressure in FE like Kessler.

* Fix index error in last commit and fix plotfile.

* No need to read/write qmoist to chk file now.

* Remove qmoist pert vars from init_custom_pert; these can be perturbed with state vars.

* Fix qv_for_p in slow rhs pre.

* Fix index issues and plotfile index divide by rho.

---------

Co-authored-by: Ann Almgren <[email protected]>
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@AMLattanzi @asalmgren
AMLattanzi and asalmgren authored Dec 30, 2023
1 parent b649ffb commit ed2a664
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Showing 89 changed files with 269 additions and 1,338 deletions.
3 changes: 0 additions & 3 deletions Exec/ABL/prob.H
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Expand Up @@ -62,9 +62,6 @@ public:
amrex::Array4<amrex::Real > const& p_hse,
amrex::Array4<amrex::Real const> const& z_nd,
amrex::Array4<amrex::Real const> const& z_cc,
amrex::Array4<amrex::Real > const& qv,
amrex::Array4<amrex::Real > const& qc,
amrex::Array4<amrex::Real > const& qi,
amrex::GeometryData const& geomdata,
amrex::Array4<amrex::Real const> const& mf_m,
amrex::Array4<amrex::Real const> const& mf_u,
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3 changes: 0 additions & 3 deletions Exec/ABL/prob.cpp
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Expand Up @@ -56,9 +56,6 @@ Problem::init_custom_pert(
amrex::Array4<amrex::Real > const& /*p_hse*/,
amrex::Array4<amrex::Real const> const& /*z_nd*/,
amrex::Array4<amrex::Real const> const& /*z_cc*/,
amrex::Array4<amrex::Real > const& /*qv*/,
amrex::Array4<amrex::Real > const& /*qc*/,
amrex::Array4<amrex::Real > const& /*qi*/,
amrex::GeometryData const& geomdata,
amrex::Array4<amrex::Real const> const& /*mf_m*/,
amrex::Array4<amrex::Real const> const& /*mf_u*/,
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3 changes: 0 additions & 3 deletions Exec/ABL_input_sounding/prob.H
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Expand Up @@ -61,9 +61,6 @@ public:
amrex::Array4<amrex::Real > const& p_hse,
amrex::Array4<amrex::Real const> const& z_nd,
amrex::Array4<amrex::Real const> const& z_cc,
amrex::Array4<amrex::Real > const& qv,
amrex::Array4<amrex::Real > const& qc,
amrex::Array4<amrex::Real > const& qi,
amrex::GeometryData const& geomdata,
amrex::Array4<amrex::Real const> const& mf_m,
amrex::Array4<amrex::Real const> const& mf_u,
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3 changes: 0 additions & 3 deletions Exec/ABL_input_sounding/prob.cpp
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Expand Up @@ -55,9 +55,6 @@ Problem::init_custom_pert(
amrex::Array4<amrex::Real > const& /*p_hse*/,
amrex::Array4<amrex::Real const> const& /*z_nd*/,
amrex::Array4<amrex::Real const> const& /*z_cc*/,
amrex::Array4<amrex::Real > const& /*qv*/,
amrex::Array4<amrex::Real > const& /*qc*/,
amrex::Array4<amrex::Real > const& /*qi*/,
amrex::GeometryData const& geomdata,
amrex::Array4<amrex::Real const> const& /*mf_m*/,
amrex::Array4<amrex::Real const> const& /*mf_u*/,
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3 changes: 0 additions & 3 deletions Exec/DevTests/MiguelDev/prob.H
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Expand Up @@ -51,9 +51,6 @@ public:
amrex::Array4<amrex::Real > const& p_hse,
amrex::Array4<amrex::Real const> const& z_nd,
amrex::Array4<amrex::Real const> const& z_cc,
amrex::Array4<amrex::Real > const& qv,
amrex::Array4<amrex::Real > const& qc,
amrex::Array4<amrex::Real > const& qi,
amrex::GeometryData const& geomdata,
amrex::Array4<amrex::Real const> const& mf_m,
amrex::Array4<amrex::Real const> const& mf_u,
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3 changes: 0 additions & 3 deletions Exec/DevTests/MiguelDev/prob.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -47,9 +47,6 @@ Problem::init_custom_pert(
Array4<Real> const&,
Array4<Real const> const&,
Array4<Real const> const&,
Array4<Real > const&,
Array4<Real > const&,
Array4<Real > const&,
amrex::GeometryData const& geomdata,
Array4<Real const> const&,
Array4<Real const> const&,
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3 changes: 0 additions & 3 deletions Exec/DevTests/MovingTerrain/prob.H
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Original file line number Diff line number Diff line change
Expand Up @@ -32,9 +32,6 @@ public:
amrex::Array4<amrex::Real > const& p_hse,
amrex::Array4<amrex::Real const> const& z_nd,
amrex::Array4<amrex::Real const> const& z_cc,
amrex::Array4<amrex::Real > const& qv,
amrex::Array4<amrex::Real > const& qc,
amrex::Array4<amrex::Real > const& qi,
amrex::GeometryData const& geomdata,
amrex::Array4<amrex::Real const> const& mf_m,
amrex::Array4<amrex::Real const> const& mf_u,
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3 changes: 0 additions & 3 deletions Exec/DevTests/MovingTerrain/prob.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -36,9 +36,6 @@ Problem::init_custom_pert(
Array4<Real > const& p_hse,
Array4<Real const> const& z_nd,
Array4<Real const> const& z_cc,
Array4<Real > const&,
Array4<Real > const&,
Array4<Real > const&,
GeometryData const& geomdata,
Array4<Real const> const& /*mf_m*/,
Array4<Real const> const& /*mf_u*/,
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3 changes: 0 additions & 3 deletions Exec/DevTests/MultiBlock/prob.H
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Original file line number Diff line number Diff line change
Expand Up @@ -40,9 +40,6 @@ public:
amrex::Array4<amrex::Real > const& p_hse,
amrex::Array4<amrex::Real const> const& z_nd,
amrex::Array4<amrex::Real const> const& z_cc,
amrex::Array4<amrex::Real > const& qv,
amrex::Array4<amrex::Real > const& qc,
amrex::Array4<amrex::Real > const& qi,
amrex::GeometryData const& geomdata,
amrex::Array4<amrex::Real const> const& mf_m,
amrex::Array4<amrex::Real const> const& mf_u,
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3 changes: 0 additions & 3 deletions Exec/DevTests/MultiBlock/prob.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -40,9 +40,6 @@ Problem::init_custom_pert(
Array4<Real > const& p_hse,
Array4<Real const> const&,
Array4<Real const> const&,
Array4<Real > const&,
Array4<Real > const&,
Array4<Real > const&,
GeometryData const& geomdata,
Array4<Real const> const& /*mf_m*/,
Array4<Real const> const& /*mf_u*/,
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3 changes: 0 additions & 3 deletions Exec/DevTests/ParticlesOverWoA/prob.H
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Original file line number Diff line number Diff line change
Expand Up @@ -40,9 +40,6 @@ public:
amrex::Array4<amrex::Real > const& p_hse,
amrex::Array4<amrex::Real const> const& z_nd,
amrex::Array4<amrex::Real const> const& z_cc,
amrex::Array4<amrex::Real > const& qv,
amrex::Array4<amrex::Real > const& qc,
amrex::Array4<amrex::Real > const& qi,
amrex::GeometryData const& geomdata,
amrex::Array4<amrex::Real const> const& mf_m,
amrex::Array4<amrex::Real const> const& mf_u,
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3 changes: 0 additions & 3 deletions Exec/DevTests/ParticlesOverWoA/prob.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -41,9 +41,6 @@ Problem::init_custom_pert(
Array4<Real > const& p_hse,
Array4<Real const> const& z_nd,
Array4<Real const> const& z_cc,
Array4<Real > const&,
Array4<Real > const&,
Array4<Real > const&,
GeometryData const& geomdata,
Array4<Real const> const& /*mf_m*/,
Array4<Real const> const& /*mf_u*/,
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3 changes: 0 additions & 3 deletions Exec/LLJ/prob.H
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Expand Up @@ -33,9 +33,6 @@ public:
amrex::Array4<amrex::Real > const& p_hse,
amrex::Array4<amrex::Real const> const& z_nd,
amrex::Array4<amrex::Real const> const& z_cc,
amrex::Array4<amrex::Real > const& qv,
amrex::Array4<amrex::Real > const& qc,
amrex::Array4<amrex::Real > const& qi,
amrex::GeometryData const& geomdata,
amrex::Array4<amrex::Real const> const& mf_m,
amrex::Array4<amrex::Real const> const& mf_u,
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3 changes: 0 additions & 3 deletions Exec/LLJ/prob.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -34,9 +34,6 @@ Problem::init_custom_pert(
Array4<Real > const&,
Array4<Real const> const&,
Array4<Real const> const&,
Array4<Real > const&,
Array4<Real > const&,
Array4<Real > const&,
GeometryData const&,
Array4<Real const> const&,
Array4<Real const> const&,
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3 changes: 0 additions & 3 deletions Exec/Radiation/prob.H
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Original file line number Diff line number Diff line change
Expand Up @@ -40,9 +40,6 @@ public:
amrex::Array4<amrex::Real > const& p_hse,
amrex::Array4<amrex::Real const> const& z_nd,
amrex::Array4<amrex::Real const> const& z_cc,
amrex::Array4<amrex::Real > const& qv,
amrex::Array4<amrex::Real > const& qc,
amrex::Array4<amrex::Real > const& qi,
amrex::GeometryData const& geomdata,
amrex::Array4<amrex::Real const> const& mf_m,
amrex::Array4<amrex::Real const> const& mf_u,
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10 changes: 0 additions & 10 deletions Exec/Radiation/prob.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -96,9 +96,6 @@ Problem::init_custom_pert(
Array4<Real > const& p_hse,
Array4<Real const> const& /*z_nd*/,
Array4<Real const> const& /*z_cc*/,
Array4<Real > const& qv,
Array4<Real > const& qc,
Array4<Real > const& qi,
GeometryData const& geomdata,
Array4<Real const> const& /*mf_m*/,
Array4<Real const> const& /*mf_u*/,
Expand Down Expand Up @@ -187,13 +184,6 @@ Problem::init_custom_pert(
if (use_moisture) {
state(i, j, k, RhoQ1_comp) = rho*qvapor;
state(i, j, k, RhoQ2_comp) = 0.0;
qv(i, j, k) = qvapor;
qc(i, j, k) = 0.0;
qi(i, j, k) = 0.0;
#if defined(ERF_USE_WARM_NO_PRECIP)
state(i, j, k, RhoQ1_comp) = rho*qvapor;
state(i, j, k, RhoQ2_comp) = 0.0;
#endif
}
});

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1 change: 1 addition & 0 deletions Exec/RegTests/Bubble/inputs_squall2d_x
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Expand Up @@ -47,6 +47,7 @@ erf.use_rayleigh_damping = false # TODO: enable
erf.les_type = "Deardorff"
erf.pbl_type = "None"
erf.moisture_model = "SAM"
erf.buoyancy_type = 1

erf.molec_diff_type = "Constant"
erf.rho0_trans = 1.0 # [kg/m^3], used to convert input diffusivities
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3 changes: 0 additions & 3 deletions Exec/RegTests/Bubble/prob.H
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Original file line number Diff line number Diff line change
Expand Up @@ -56,9 +56,6 @@ public:
amrex::Array4<amrex::Real > const& p_hse,
amrex::Array4<amrex::Real const> const& z_nd,
amrex::Array4<amrex::Real const> const& z_cc,
amrex::Array4<amrex::Real > const& qv,
amrex::Array4<amrex::Real > const& qc,
amrex::Array4<amrex::Real > const& qi,
amrex::GeometryData const& geomdata,
amrex::Array4<amrex::Real const> const& mf_m,
amrex::Array4<amrex::Real const> const& mf_u,
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3 changes: 0 additions & 3 deletions Exec/RegTests/Bubble/prob.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -47,9 +47,6 @@ Problem::init_custom_pert(
Array4<Real > const& p_hse,
Array4<Real const> const& /*z_nd*/,
Array4<Real const> const& z_cc,
Array4<Real > const&,
Array4<Real > const&,
Array4<Real > const&,
GeometryData const& geomdata,
Array4<Real const> const& /*mf_m*/,
Array4<Real const> const& /*mf_u*/,
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3 changes: 0 additions & 3 deletions Exec/RegTests/CouetteFlow/prob.H
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Original file line number Diff line number Diff line change
Expand Up @@ -35,9 +35,6 @@ public:
amrex::Array4<amrex::Real > const& p_hse,
amrex::Array4<amrex::Real const> const& z_nd,
amrex::Array4<amrex::Real const> const& z_cc,
amrex::Array4<amrex::Real > const& qv,
amrex::Array4<amrex::Real > const& qc,
amrex::Array4<amrex::Real > const& qi,
amrex::GeometryData const& geomdata,
amrex::Array4<amrex::Real const> const& mf_m,
amrex::Array4<amrex::Real const> const& mf_u,
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3 changes: 0 additions & 3 deletions Exec/RegTests/CouetteFlow/prob.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -37,9 +37,6 @@ Problem::init_custom_pert(
Array4<Real> const&,
Array4<Real const> const&,
Array4<Real const> const&,
Array4<Real > const&,
Array4<Real > const&,
Array4<Real > const&,
amrex::GeometryData const& geomdata,
Array4<Real const> const& /*mf_m*/,
Array4<Real const> const& /*mf_u*/,
Expand Down
3 changes: 0 additions & 3 deletions Exec/RegTests/DensityCurrent/prob.H
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Original file line number Diff line number Diff line change
Expand Up @@ -38,9 +38,6 @@ public:
amrex::Array4<amrex::Real > const& p_hse,
amrex::Array4<amrex::Real const> const& z_nd,
amrex::Array4<amrex::Real const> const& z_cc,
amrex::Array4<amrex::Real > const& qv,
amrex::Array4<amrex::Real > const& qc,
amrex::Array4<amrex::Real > const& qi,
amrex::GeometryData const& geomdata,
amrex::Array4<amrex::Real const> const& mf_m,
amrex::Array4<amrex::Real const> const& mf_u,
Expand Down
3 changes: 0 additions & 3 deletions Exec/RegTests/DensityCurrent/prob.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -40,9 +40,6 @@ Problem::init_custom_pert(
Array4<Real > const& p_hse,
Array4<Real const> const& /*z_nd*/,
Array4<Real const> const& z_cc,
Array4<Real > const&,
Array4<Real > const&,
Array4<Real > const&,
GeometryData const& geomdata,
Array4<Real const> const& /*mf_m*/,
Array4<Real const> const& /*mf_u*/,
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3 changes: 0 additions & 3 deletions Exec/RegTests/DynamicRefinement/prob.H
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Expand Up @@ -45,9 +45,6 @@ public:
amrex::Array4<amrex::Real > const& p_hse,
amrex::Array4<amrex::Real const> const& z_nd,
amrex::Array4<amrex::Real const> const& z_cc,
amrex::Array4<amrex::Real > const& qv,
amrex::Array4<amrex::Real > const& qc,
amrex::Array4<amrex::Real > const& qi,
amrex::GeometryData const& geomdata,
amrex::Array4<amrex::Real const> const& mf_m,
amrex::Array4<amrex::Real const> const& mf_u,
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3 changes: 0 additions & 3 deletions Exec/RegTests/DynamicRefinement/prob.cpp
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Expand Up @@ -84,9 +84,6 @@ Problem::init_custom_pert(
Array4<Real> const&,
Array4<Real const> const&,
Array4<Real const> const&,
Array4<Real > const&,
Array4<Real > const&,
Array4<Real > const&,
amrex::GeometryData const& geomdata,
Array4<Real const> const& /*mf_m*/,
Array4<Real const> const& /*mf_u*/,
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3 changes: 0 additions & 3 deletions Exec/RegTests/EkmanSpiral_custom/prob.H
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Original file line number Diff line number Diff line change
Expand Up @@ -33,9 +33,6 @@ public:
amrex::Array4<amrex::Real > const& p_hse,
amrex::Array4<amrex::Real const> const& z_nd,
amrex::Array4<amrex::Real const> const& z_cc,
amrex::Array4<amrex::Real > const& qv,
amrex::Array4<amrex::Real > const& qc,
amrex::Array4<amrex::Real > const& qi,
amrex::GeometryData const& geomdata,
amrex::Array4<amrex::Real const> const& mf_m,
amrex::Array4<amrex::Real const> const& mf_u,
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3 changes: 0 additions & 3 deletions Exec/RegTests/EkmanSpiral_custom/prob.cpp
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Expand Up @@ -34,9 +34,6 @@ Problem::init_custom_pert(
Array4<Real> const&,
Array4<Real const> const&,
Array4<Real const> const&,
Array4<Real > const&,
Array4<Real > const&,
Array4<Real > const&,
GeometryData const& geomdata,
Array4<Real const> const& /*mf_m*/,
Array4<Real const> const& /*mf_u*/,
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3 changes: 0 additions & 3 deletions Exec/RegTests/EkmanSpiral_ideal/prob.H
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Original file line number Diff line number Diff line change
Expand Up @@ -33,9 +33,6 @@ public:
amrex::Array4<amrex::Real > const& p_hse,
amrex::Array4<amrex::Real const> const& z_nd,
amrex::Array4<amrex::Real const> const& z_cc,
amrex::Array4<amrex::Real > const& qv,
amrex::Array4<amrex::Real > const& qc,
amrex::Array4<amrex::Real > const& qi,
amrex::GeometryData const& geomdata,
amrex::Array4<amrex::Real const> const& mf_m,
amrex::Array4<amrex::Real const> const& mf_u,
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3 changes: 0 additions & 3 deletions Exec/RegTests/EkmanSpiral_ideal/prob.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -34,9 +34,6 @@ Problem::init_custom_pert(
Array4<Real > const&,
Array4<Real const> const&,
Array4<Real const> const&,
Array4<Real > const&,
Array4<Real > const&,
Array4<Real > const&,
GeometryData const&,
Array4<Real const> const&,
Array4<Real const> const&,
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3 changes: 0 additions & 3 deletions Exec/RegTests/EkmanSpiral_input_sounding/prob.H
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Original file line number Diff line number Diff line change
Expand Up @@ -33,9 +33,6 @@ public:
amrex::Array4<amrex::Real > const& p_hse,
amrex::Array4<amrex::Real const> const& z_nd,
amrex::Array4<amrex::Real const> const& z_cc,
amrex::Array4<amrex::Real > const& qv,
amrex::Array4<amrex::Real > const& qc,
amrex::Array4<amrex::Real > const& qi,
amrex::GeometryData const& geomdata,
amrex::Array4<amrex::Real const> const& mf_m,
amrex::Array4<amrex::Real const> const& mf_u,
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3 changes: 0 additions & 3 deletions Exec/RegTests/EkmanSpiral_input_sounding/prob.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -34,9 +34,6 @@ Problem::init_custom_pert(
Array4<Real> const&,
Array4<Real const> const&,
Array4<Real const> const&,
Array4<Real > const&,
Array4<Real > const&,
Array4<Real > const&,
GeometryData const&,
Array4<Real const> const&,
Array4<Real const> const&,
Expand Down
3 changes: 0 additions & 3 deletions Exec/RegTests/GABLS1/prob.H
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Original file line number Diff line number Diff line change
Expand Up @@ -62,9 +62,6 @@ public:
amrex::Array4<amrex::Real > const& p_hse,
amrex::Array4<amrex::Real const> const& z_nd,
amrex::Array4<amrex::Real const> const& z_cc,
amrex::Array4<amrex::Real > const& qv,
amrex::Array4<amrex::Real > const& qc,
amrex::Array4<amrex::Real > const& qi,
amrex::GeometryData const& geomdata,
amrex::Array4<amrex::Real const> const& mf_m,
amrex::Array4<amrex::Real const> const& mf_u,
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3 changes: 0 additions & 3 deletions Exec/RegTests/GABLS1/prob.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -56,9 +56,6 @@ Problem::init_custom_pert(
amrex::Array4<amrex::Real > const& /*p_hse*/,
amrex::Array4<amrex::Real const> const& /*z_nd*/,
amrex::Array4<amrex::Real const> const& /*z_cc*/,
amrex::Array4<amrex::Real > const& /*qv*/,
amrex::Array4<amrex::Real > const& /*qc*/,
amrex::Array4<amrex::Real > const& /*qi*/,
amrex::GeometryData const& geomdata,
amrex::Array4<amrex::Real const> const& /*mf_m*/,
amrex::Array4<amrex::Real const> const& /*mf_u*/,
Expand Down
3 changes: 0 additions & 3 deletions Exec/RegTests/IsentropicVortex/prob.H
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Original file line number Diff line number Diff line change
Expand Up @@ -44,9 +44,6 @@ public:
amrex::Array4<amrex::Real > const& p_hse,
amrex::Array4<amrex::Real const> const& z_nd,
amrex::Array4<amrex::Real const> const& z_cc,
amrex::Array4<amrex::Real > const& qv,
amrex::Array4<amrex::Real > const& qc,
amrex::Array4<amrex::Real > const& qi,
amrex::GeometryData const& geomdata,
amrex::Array4<amrex::Real const> const& mf_m,
amrex::Array4<amrex::Real const> const& mf_u,
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3 changes: 0 additions & 3 deletions Exec/RegTests/IsentropicVortex/prob.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -86,9 +86,6 @@ Problem::init_custom_pert(
Array4<Real> const& p_hse,
Array4<Real const> const&,
Array4<Real const> const&,
Array4<Real > const&,
Array4<Real > const&,
Array4<Real > const&,
amrex::GeometryData const& geomdata,
Array4<Real const> const& /*mf_m*/,
Array4<Real const> const& /*mf_u*/,
Expand Down
3 changes: 0 additions & 3 deletions Exec/RegTests/PoiseuilleFlow/prob.H
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Original file line number Diff line number Diff line change
Expand Up @@ -34,9 +34,6 @@ public:
amrex::Array4<amrex::Real > const& p_hse,
amrex::Array4<amrex::Real const> const& z_nd,
amrex::Array4<amrex::Real const> const& z_cc,
amrex::Array4<amrex::Real > const& qv,
amrex::Array4<amrex::Real > const& qc,
amrex::Array4<amrex::Real > const& qi,
amrex::GeometryData const& geomdata,
amrex::Array4<amrex::Real const> const& mf_m,
amrex::Array4<amrex::Real const> const& mf_u,
Expand Down
3 changes: 0 additions & 3 deletions Exec/RegTests/PoiseuilleFlow/prob.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -36,9 +36,6 @@ Problem::init_custom_pert(
amrex::Array4<Real> const&,
amrex::Array4<Real const> const&,
amrex::Array4<Real const> const&,
Array4<Real > const&,
Array4<Real > const&,
Array4<Real > const&,
amrex::GeometryData const& geomdata,
Array4<Real const> const& /*mf_m*/,
Array4<Real const> const& /*mf_u*/,
Expand Down
3 changes: 0 additions & 3 deletions Exec/RegTests/ScalarAdvDiff/prob.H
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Expand Up @@ -46,9 +46,6 @@ public:
amrex::Array4<amrex::Real > const& p_hse,
amrex::Array4<amrex::Real const> const& z_nd,
amrex::Array4<amrex::Real const> const& z_cc,
amrex::Array4<amrex::Real > const& qv,
amrex::Array4<amrex::Real > const& qc,
amrex::Array4<amrex::Real > const& qi,
amrex::GeometryData const& geomdata,
amrex::Array4<amrex::Real const> const& mf_m,
amrex::Array4<amrex::Real const> const& mf_u,
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