Add the TaylorGreen vortex breakdown case from PeleC

Docs/source/Validation.rst

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+PeleLMeX validations
+====================
+
+This section is work-in-progress.
+
+Taylor-Green vortex breakdown
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The Taylor-Green vortex breakdown case is a classical CFD test case
+described in `here <>`
+
+Building and running
+####################
+
+.. code-block:: bash
+
+   $ make -j 16 DIM=3 USE_MPI=TRUE TPL
+   $ make -j 16 DIM=3 USE_MPI=TRUE
+   $ mpiexec -n 16 $EXECUTABLE inputs_3d amr.ncell=64 64 64
+
+The user can run a convergence study by varying ``amr.ncell``.
+
+Results
+#######
+
+The following figures shows the kinetic energy, the dissipation rate and 
+the enstrophy as function of time (all quantities are non-dimensional)
+for increasing resolutions (ranging from 64^3 to 512^3) and compared
+to the results of a high-order spectral solver with a 512^3 resolution.
+
+.. figure:: images/validations/TaylorGreen/KinEnergy.png
+   :align: center
+   :figwidth: 60%
+
+.. figure:: images/validations/TaylorGreen/Dissipation.png
+   :align: center
+   :figwidth: 60%
+
+.. figure:: images/validations/TaylorGreen/Enstrophy.png
+   :align: center
+   :figwidth: 60%

Docs/source/index.rst

@@ -28,6 +28,7 @@ point your web browser at the file ``${PELELMEX_HOME}/Docs/build/html/index.html
    :caption: Contents:
 
    Model.rst
+   Validation.rst
    LMeXControls.rst
    Troubleshooting.rst
 

Exec/RegTests/TaylorGreen/GNUmakefile

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+TOP = ../../../..
+AMREX_HOME         ?= ${TOP}/amrex
+PELELMEX_HOME      ?= ${TOP}/PeleLMeX
+PELE_PHYSICS_HOME  ?= ${TOP}/PelePhysics
+AMREX_HYDRO_HOME   ?= ${TOP}/AMReX-Hydro
+
+
+# AMReX
+DIM             = 3
+DEBUG           = FALSE
+PRECISION       = DOUBLE
+VERBOSE         = FALSE
+TINY_PROFILE    = FALSE
+
+# Compilation
+COMP            = llvm
+USE_MPI         = TRUE
+USE_OMP         = FALSE
+USE_CUDA        = FALSE
+USE_HIP         = FALSE
+
+# PeleLMeX
+
+# PelePhysics
+Chemistry_Model = air
+Eos_Model       = Fuego
+Transport_Model = Constant
+
+include $(PELELMEX_HOME)/Utils/Make.PeleLMeX

Exec/RegTests/TaylorGreen/Readme.md

@@ -0,0 +1,19 @@
+# Taylor-Green Vortex (pulled from PeleC)
+
+This setup is one of the test problems outlined by [the High-Order CFD workshop](https://www.grc.nasa.gov/hiocfd/).
+
+A complete description of the problem can be found 
+[here](https://www.grc.nasa.gov/hiocfd/wp-content/uploads/sites/22/case_c3.3.pdf) and
+the reference data is found
+[here](https://www.grc.nasa.gov/wp-content/uploads/sites/22/C3.3_datafiles.zip). More
+details of the problem and methods used to obtain the reference data
+can be found in Bull and Jameson (2014) 7th AIAA Theoretical Fluid
+Mechanics Conference (doi: 10.2514/6.2014-3210) and DeBonis (2013)
+51st AIAA Aerospace Sciences Meeting (doi:10.2514/6.2013-382).
+
+To directly plot the evolution of integrated kinetic energy and enstrophy, use
+the data provided in temporals/tempState with the help of the processTGdata.py
+script.
+
+Note that these commands provide adimentional results, with t\* = t/(L\_0/V\_0),
+E\_k\* = E\_k / ( rho\_0 * V\_0 * V\_0) and psi\* = psi / (V\_0/L\_0)^2

Exec/RegTests/TaylorGreen/input.3d_BDS

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+#----------------------DOMAIN DEFINITION------------------------
+geometry.is_periodic = 1 1 1              # For each dir, 0: non-perio, 1: periodic
+geometry.coord_sys   = 0                  # 0 => cart, 1 => RZ
+geometry.prob_lo     = -0.01 -0.01 -0.01        # x_lo y_lo (z_lo)
+geometry.prob_hi     =  0.01  0.01  0.01  # x_hi y_hi (z_hi)
+
+# >>>>>>>>>>>>>  BC FLAGS <<<<<<<<<<<<<<<<
+# Interior, Inflow, Outflow, Symmetry,
+# SlipWallAdiab, NoSlipWallAdiab, SlipWallIsotherm, NoSlipWallIsotherm
+peleLM.lo_bc = Interior Interior Interior
+peleLM.hi_bc = Interior Interior Interior
+
+
+#-------------------------AMR CONTROL----------------------------
+amr.n_cell          = 32 32 32         # Level 0 number of cells in each direction   
+amr.n_cell          = 64 64 64         # 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      = 2                # 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.T_mean = 351.59509
+prob.P_mean = 101325.0
+prob.reynolds = 1600.0
+prob.mach = 0.08
+prob.prandtl = 0.71
+
+#-------------------------PeleLM CONTROL----------------------------
+peleLM.v = 1
+peleLM.incompressible = 0
+peleLM.sdc_iterMax = 1
+peleLM.advection_scheme = "Godunov_BDS"
+
+peleLM.do_temporals = 1
+peleLM.temporal_int = 5
+
+amr.check_int = 100
+amr.plot_int = 100
+amr.max_step = 500
+amr.dt_shrink = 0.1
+amr.stop_time = 0.0021160148
+amr.cfl = 0.7
+amr.derive_plot_vars = avg_pressure mag_vort
+#amr.restart = chk00500
+
+#--------------------REFINEMENT CONTROL------------------------
+#amr.refinement_indicators = temp
+#amr.temp.max_level     = 2
+#amr.temp.value_greater = 305
+#amr.temp.field_name    = temp
+
+#amrex.fpe_trap_invalid = 1
+#amrex.fpe_trap_zero = 1
+#amrex.fpe_trap_overflow = 1

Exec/RegTests/TaylorGreen/input.3d_PLM

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+#----------------------DOMAIN DEFINITION------------------------
+geometry.is_periodic = 1 1 1              # For each dir, 0: non-perio, 1: periodic
+geometry.coord_sys   = 0                  # 0 => cart, 1 => RZ
+geometry.prob_lo     = -0.01 -0.01 -0.01        # x_lo y_lo (z_lo)
+geometry.prob_hi     =  0.01  0.01  0.01  # x_hi y_hi (z_hi)
+
+# >>>>>>>>>>>>>  BC FLAGS <<<<<<<<<<<<<<<<
+# Interior, Inflow, Outflow, Symmetry,
+# SlipWallAdiab, NoSlipWallAdiab, SlipWallIsotherm, NoSlipWallIsotherm
+peleLM.lo_bc = Interior Interior Interior
+peleLM.hi_bc = Interior Interior Interior
+
+
+#-------------------------AMR CONTROL----------------------------
+amr.n_cell          = 32 32 32         # Level 0 number of cells in each direction   
+#amr.n_cell          = 64 64 64         # 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      = 2                # 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.T_mean = 351.59509
+prob.P_mean = 101325.0
+prob.reynolds = 1600.0
+prob.mach = 0.08
+prob.prandtl = 0.71
+
+#-------------------------PeleLM CONTROL----------------------------
+peleLM.v = 1
+peleLM.incompressible = 0
+peleLM.sdc_iterMax = 1
+peleLM.advection_scheme = "Godunov_PPM"
+
+peleLM.do_temporals = 1
+peleLM.temporal_int = 5
+
+amr.check_int = 100
+amr.plot_int = 100
+amr.max_step = 500
+amr.dt_shrink = 0.1
+amr.stop_time = 0.0021160148
+amr.cfl = 0.7
+amr.derive_plot_vars = avg_pressure mag_vort
+#amr.restart = chk00500
+
+#--------------------REFINEMENT CONTROL------------------------
+#amr.refinement_indicators = temp
+#amr.temp.max_level     = 2
+#amr.temp.value_greater = 305
+#amr.temp.field_name    = temp
+
+#amrex.fpe_trap_invalid = 1
+#amrex.fpe_trap_zero = 1
+#amrex.fpe_trap_overflow = 1

Exec/RegTests/TaylorGreen/input.3d_PPM

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+#----------------------DOMAIN DEFINITION------------------------
+geometry.is_periodic = 1 1 1              # For each dir, 0: non-perio, 1: periodic
+geometry.coord_sys   = 0                  # 0 => cart, 1 => RZ
+geometry.prob_lo     = -0.01 -0.01 -0.01        # x_lo y_lo (z_lo)
+geometry.prob_hi     =  0.01  0.01  0.01  # x_hi y_hi (z_hi)
+
+# >>>>>>>>>>>>>  BC FLAGS <<<<<<<<<<<<<<<<
+# Interior, Inflow, Outflow, Symmetry,
+# SlipWallAdiab, NoSlipWallAdiab, SlipWallIsotherm, NoSlipWallIsotherm
+peleLM.lo_bc = Interior Interior Interior
+peleLM.hi_bc = Interior Interior Interior
+
+
+#-------------------------AMR CONTROL----------------------------
+amr.n_cell          = 32 32 32         # Level 0 number of cells in each direction   
+amr.n_cell          = 64 64 64         # 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      = 2                # 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.T_mean = 351.59509
+prob.P_mean = 101325.0
+prob.reynolds = 1600.0
+prob.mach = 0.08
+prob.prandtl = 0.71
+
+#-------------------------PeleLM CONTROL----------------------------
+peleLM.v = 1
+peleLM.incompressible = 0
+peleLM.sdc_iterMax = 1
+peleLM.advection_scheme = "Godunov_PPM"
+
+peleLM.do_temporals = 1
+peleLM.temporal_int = 5
+
+amr.check_int = 100
+amr.plot_int = 100
+amr.max_step = 500
+amr.dt_shrink = 0.1
+amr.stop_time = 0.0021160148
+amr.cfl = 0.7
+amr.derive_plot_vars = avg_pressure mag_vort
+#amr.restart = chk00500
+
+#--------------------REFINEMENT CONTROL------------------------
+#amr.refinement_indicators = temp
+#amr.temp.max_level     = 2
+#amr.temp.value_greater = 305
+#amr.temp.field_name    = temp
+
+#amrex.fpe_trap_invalid = 1
+#amrex.fpe_trap_zero = 1
+#amrex.fpe_trap_overflow = 1

Exec/RegTests/TaylorGreen/pelelm_prob.H

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+#ifndef PELELM_PROB_H_
+#define PELELM_PROB_H_
+
+#include <AMReX_Geometry.H>
+#include <AMReX_FArrayBox.H>
+#include <AMReX_SPACE.H>
+
+#include <PeleLM_Index.H>
+#include <pelelm_prob_parm.H>
+#include <PMFData.H>
+#include <PelePhysics.H>
+
+AMREX_GPU_DEVICE
+AMREX_FORCE_INLINE
+void pelelm_initdata(int i, int j, int k,
+                     int is_incompressible,
+                     amrex::Array4<amrex::Real> const& state,
+                     amrex::Array4<amrex::Real> const& aux,
+                     amrex::GeometryData const& geomdata,
+                     ProbParm const& prob_parm,
+                     pele::physics::PMF::PmfData::DataContainer const * /*pmf_data*/)
+{
+    const amrex::Real* prob_lo = geomdata.ProbLo();
+    const amrex::Real* prob_hi = geomdata.ProbHi();
+    const amrex::Real* dx      = geomdata.CellSize();
+
+    AMREX_D_TERM(const amrex::Real x = prob_lo[0] + (i+0.5)*dx[0];,
+                 const amrex::Real y = prob_lo[1] + (j+0.5)*dx[1];,
+                 const amrex::Real z = prob_lo[2] + (k+0.5)*dx[2];);
+
+    AMREX_D_TERM(const amrex::Real Lx = prob_hi[0] - prob_lo[0];,
+                 const amrex::Real Ly = prob_hi[1] - prob_lo[1];,
+                 const amrex::Real Lz = prob_hi[2] - prob_lo[2]);
+
+    auto eos = pele::physics::PhysicsType::eos();
+
+    amrex::Real massfrac[NUM_SPECIES] = {0.0};
+    massfrac[O2_ID] = 0.233;
+    massfrac[N2_ID] = 0.767;
+
+    // TG functions
+    amrex::Real u[3] = {0.0};
+    u[0] = prob_parm.v0 * AMREX_D_TERM( sin(prob_parm.omega_x * x / prob_parm.L),
+                                       *cos(prob_parm.omega_y * y / prob_parm.L),
+                                       *cos(prob_parm.omega_z * z / prob_parm.L));
+    u[1] = -prob_parm.v0 * AMREX_D_TERM( cos(prob_parm.omega_x * x / prob_parm.L),
+                                        *sin(prob_parm.omega_y * y / prob_parm.L),
+                                        *cos(prob_parm.omega_z * z / prob_parm.L));
+    if (prob_parm.convecting) {
+      u[0] += prob_parm.v0;
+      u[1] += prob_parm.v0;
+    }
+
+    AMREX_D_TERM(state(i,j,k,VELX) = u[0];,
+                 state(i,j,k,VELY) = u[1];,
+                 state(i,j,k,VELZ) = u[2]);
+
+    state(i,j,k,TEMP) = prob_parm.T_mean;
+
+    amrex::Real P_cgs = prob_parm.P_mean * 10.0;
+
+    // Density
+    amrex::Real rho_cgs = 0.0;
+    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(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++) {
+       state(i,j,k,FIRSTSPEC+n) = massfrac[n] * state(i,j,k,DENSITY);
+    }
+
+}
+
+AMREX_GPU_DEVICE
+AMREX_FORCE_INLINE
+void
+bcnormal(
+  const amrex::Real* /*x[AMREX_SPACEDIM]*/,
+  const int /*m_nAux*/,
+  amrex::Real* /*s_ext[NVAR]*/,
+  const int /*idir*/,
+  const int /*sgn*/,
+  const amrex::Real /*time*/,
+  amrex::GeometryData const& /*geomdata*/,
+  ProbParm const& /*prob_parm*/,
+  pele::physics::PMF::PmfData::DataContainer const * /*pmf_data*/)
+{
+}
+
+AMREX_GPU_DEVICE
+AMREX_FORCE_INLINE
+void
+zero_visc (int i, int j, int k,
+           amrex::Array4<amrex::Real> const& beta,
+           amrex::GeometryData const& geomdata,
+           amrex::Box const& domainBox,
+           const int  dir,
+           const int  beta_comp,
+           const int  nComp)
+{
+     amrex::ignore_unused(i,j,k,beta,geomdata,domainBox,dir,beta_comp,nComp);
+    // We treat species when beta_comp == 0 and nComp == NUM_SPECIES
+    // otherwise this routine could be called for other face diffusivity (Temp, velocity, ...)
+}
+#endif