Update pelephysics submod (#968)

marchdf · web-flow · commit 2a001f023ef0 · 2025-07-22T10:35:44.000-06:00
diff --git a/CMake/BuildPeleExe.cmake b/CMake/BuildPeleExe.cmake
@@ -78,7 +78,7 @@ function(build_pele_exe pele_exe_name pele_physics_lib_name)
        ${SRC_DIR}/Tagging.cpp
        ${SRC_DIR}/Timestep.H
        ${SRC_DIR}/TransCoeff.H
-       ${SRC_DIR}/Utilities.H
+       ${SRC_DIR}/PeleCUtilities.H
        ${SRC_DIR}/Utilities.cpp
        ${SRC_DIR}/WENO.H
        ${SRC_DIR}/RotSource.cpp
diff --git a/CMake/BuildPelePhysicsLib.cmake b/CMake/BuildPelePhysicsLib.cmake
@@ -57,6 +57,12 @@ function(build_pele_physics_lib pele_physics_lib_name)
       ${PELE_PHYSICS_UTILITY_DIR}/BlackBoxFunction/Table.H)
     target_include_directories(${pele_physics_lib_name} PUBLIC ${PELE_PHYSICS_UTILITY_DIR}/BlackBoxFunction)
 
+    target_sources(${pele_physics_lib_name}
+      PRIVATE
+      ${PELE_PHYSICS_UTILITY_DIR}/Utilities/Utilities.H
+      ${PELE_PHYSICS_UTILITY_DIR}/Utilities/UnitConversions.H)
+    target_include_directories(${pele_physics_lib_name} PUBLIC ${PELE_PHYSICS_UTILITY_DIR}/Utilities)
+
     target_sources(${pele_physics_lib_name}
       PRIVATE
       ${PELE_PHYSICS_UTILITY_DIR}/Filter/Filter.cpp
diff --git a/Docs/sphinx/Equations.rst b/Docs/sphinx/Equations.rst
@@ -74,7 +74,7 @@ Primitive Forms
 PeleC uses the primitive form of the inviscid fluid equations, defined in terms of
 the state :math:`\mathbf{Q} = (\rho, \mathbf{u}, p, \rho e, Y_k, A_k, B_k)`, to construct the
 interface states that are input to the Riemann problem. All of the primitive variables are derived from the conservative state
-vector. This task is performed in the function ``pc_ctoprim`` located in ``Source/Utilities.H``.
+vector. This task is performed in the function ``pc_ctoprim`` located in ``Source/PeleCUtilities.H``.
 
 The inviscid equations for primitive variables namely density, velocity, and pressure are:
 
diff --git a/Exec/Make.PeleC b/Exec/Make.PeleC
@@ -44,6 +44,9 @@ Blocs += $(UTILITY_HOME)/Filter
 Bpack += $(UTILITY_HOME)/BlackBoxFunction/Make.package
 Blocs += $(UTILITY_HOME)/BlackBoxFunction
 
+Bpack += $(UTILITY_HOME)/Utilities/Make.package
+Blocs += $(UTILITY_HOME)/Utilities
+
 all: $(executable)
 ifneq ($(KEEP_BUILDINFO_CPP),TRUE)
 	$(SILENT) $(RM) AMReX_buildInfo.cpp
diff --git a/Exec/Production/CavityFlame/prob.H b/Exec/Production/CavityFlame/prob.H
@@ -20,7 +20,7 @@
 
 #include "ProblemSpecificFunctions.H"
 #include "prob_parm.H"
-#include "Utilities.H"
+#include "PeleCUtilities.H"
 #include "turbinflow.H"
 
 AMREX_GPU_DEVICE
diff --git a/Exec/Production/ChallengeProblem/prob.H b/Exec/Production/ChallengeProblem/prob.H
@@ -20,7 +20,7 @@
 #include "ProblemSpecificFunctions.H"
 #include "Tagging.H"
 #include "Transport.H"
-#include "Utilities.H"
+#include "PeleCUtilities.H"
 #include "prob_parm.H"
 #include "Geometry.H"
 
@@ -97,7 +97,8 @@ pc_initdata(
     amrex::Real slp[3] = {0.0};
     for (int cnt = 0; cnt < 3; cnt++) {
       mod[cnt] = std::fmod(x[cnt], prob_parm.Linput);
-      locate(prob_parm.d_xarray, prob_parm.inres, mod[cnt], idx[cnt]);
+      pele::physics::utilities::locate(
+        prob_parm.d_xarray, prob_parm.inres, mod[cnt], idx[cnt]);
       idxp1[cnt] = (idx[cnt] + 1) % prob_parm.inres;
       slp[cnt] =
         (mod[cnt] - prob_parm.d_xarray[idx[cnt]]) / prob_parm.d_xdiff[idx[cnt]];
diff --git a/Exec/Production/JetFlame/prob.H b/Exec/Production/JetFlame/prob.H
@@ -20,7 +20,7 @@
 
 #include "ProblemSpecificFunctions.H"
 #include "prob_parm.H"
-#include "Utilities.H"
+#include "PeleCUtilities.H"
 #include "turbinflow.H"
 
 AMREX_GPU_DEVICE
diff --git a/Exec/Production/PistonBowl/prob.H b/Exec/Production/PistonBowl/prob.H
@@ -20,7 +20,7 @@
 #include "ProblemSpecificFunctions.H"
 #include "Tagging.H"
 #include "Transport.H"
-#include "Utilities.H"
+#include "PeleCUtilities.H"
 #include "prob_parm.H"
 #include "Geometry.H"
 
@@ -70,17 +70,19 @@ InterpolateVelInflow(
   amrex::Real radSI = radius * 0.01;
   // Get radius location for interpolation
   int idR = 0;
-  locate(prob_parm.d_rM, prob_parm.nr, radSI, idR);
+  pele::physics::utilities::locate(prob_parm.d_rM, prob_parm.nr, radSI, idR);
   int idRp1 = idR + 1;
 
   theta = std::fmod(theta, prob_parm.thetaMax);
   int idT = 0;
-  locate(prob_parm.d_thetaM, prob_parm.nt, theta, idT);
+  pele::physics::utilities::locate(
+    prob_parm.d_thetaM, prob_parm.nt, theta, idT);
   const int idTp1 = idT + 1;
 
   amrex::Real timeInflow = std::fmod(timeInp, prob_parm.timeInflowMax);
   int indxTime = 0;
-  locate(prob_parm.d_timeInput, prob_parm.inflowNtime, timeInflow, indxTime);
+  pele::physics::utilities::locate(
+    prob_parm.d_timeInput, prob_parm.inflowNtime, timeInflow, indxTime);
   const int indxTimeP1 = indxTime + 1;
 
   // Interpolate in space
@@ -250,7 +252,8 @@ pc_initdata(
     amrex::Real slp[3] = {0.0};
     for (int cnt = 0; cnt < 3; cnt++) {
       mod[cnt] = std::fmod(x[cnt], prob_parm.Linput);
-      locate(prob_parm.d_xarray, prob_parm.inres, mod[cnt], idx[cnt]);
+      pele::physics::utilities::locate(
+        prob_parm.d_xarray, prob_parm.inres, mod[cnt], idx[cnt]);
       idxp1[cnt] = (idx[cnt] + 1) % prob_parm.inres;
       slp[cnt] =
         (mod[cnt] - prob_parm.d_xarray[idx[cnt]]) / prob_parm.d_xdiff[idx[cnt]];
diff --git a/Exec/RegTests/EB-ConvergingNozzle/prob.H b/Exec/RegTests/EB-ConvergingNozzle/prob.H
@@ -17,7 +17,7 @@
 #include "prob_parm.H"
 #include "EB.H"
 #include <AMReX_EB2_IF_Rotation.H>
-#include "Utilities.H"
+#include "PeleCUtilities.H"
 #include "Geometry.H"
 
 void parse_params(std::unique_ptr<ProbParmDevice>& prob_parm_device);
diff --git a/Exec/RegTests/EB-EnclosedVortex/prob.H b/Exec/RegTests/EB-EnclosedVortex/prob.H
@@ -18,7 +18,7 @@
 #include "prob_parm.H"
 #include "EB.H"
 #include <AMReX_EB2_IF_Rotation.H>
-#include "Utilities.H"
+#include "PeleCUtilities.H"
 #include "Geometry.H"
 
 void parse_params(std::unique_ptr<ProbParmDevice>& prob_parm_device);
diff --git a/Exec/RegTests/EB-InflowBC/prob.H b/Exec/RegTests/EB-InflowBC/prob.H
@@ -16,7 +16,7 @@
 #include "Tagging.H"
 #include "ProblemSpecificFunctions.H"
 #include "prob_parm.H"
-#include "Utilities.H"
+#include "PeleCUtilities.H"
 
 AMREX_GPU_DEVICE
 AMREX_FORCE_INLINE
diff --git a/Exec/RegTests/EB-Rotor4Blade/prob.H b/Exec/RegTests/EB-Rotor4Blade/prob.H
@@ -21,7 +21,7 @@
 #include "prob_parm.H"
 #include "EB.H"
 #include <AMReX_EB2_IF_Rotation.H>
-#include "Utilities.H"
+#include "PeleCUtilities.H"
 #include "Geometry.H"
 
 class EBConcCylinders : public pele::pelec::Geometry::Register<EBConcCylinders>
diff --git a/Exec/RegTests/EB-TaylorCouette/prob.H b/Exec/RegTests/EB-TaylorCouette/prob.H
@@ -21,7 +21,7 @@
 #include "prob_parm.H"
 #include "EB.H"
 #include <AMReX_EB2_IF_Rotation.H>
-#include "Utilities.H"
+#include "PeleCUtilities.H"
 #include "Geometry.H"
 
 class EBConcCylinders : public pele::pelec::Geometry::Register<EBConcCylinders>
diff --git a/Exec/RegTests/HIT/prob.H b/Exec/RegTests/HIT/prob.H
@@ -17,6 +17,7 @@
 #include "ProblemSpecificFunctions.H"
 #include "prob_parm.H"
 #include "Utilities.H"
+#include "PeleCUtilities.H"
 
 AMREX_GPU_DEVICE
 AMREX_FORCE_INLINE
@@ -58,7 +59,8 @@ pc_initdata(
   amrex::Real slp[3] = {0.0};
   for (int cnt = 0; cnt < 3; cnt++) {
     mod[cnt] = std::fmod(x[cnt], prob_parm.Linput);
-    locate(prob_parm.d_xarray, prob_parm.inres, mod[cnt], idx[cnt]);
+    pele::physics::utilities::locate(
+      prob_parm.d_xarray, prob_parm.inres, mod[cnt], idx[cnt]);
     idxp1[cnt] = (idx[cnt] + 1) % prob_parm.inres;
     slp[cnt] =
       (mod[cnt] - prob_parm.d_xarray[idx[cnt]]) / prob_parm.d_xdiff[idx[cnt]];
diff --git a/Exec/RegTests/TGReact/prob.H b/Exec/RegTests/TGReact/prob.H
@@ -2,19 +2,23 @@
 #define PROB_H
 
 #include <AMReX_Print.H>
-#include <AMReX_ParmParse.H>
 #include <AMReX_Geometry.H>
 #include <AMReX_FArrayBox.H>
+#include <AMReX_REAL.H>
+#include <AMReX_GpuMemory.H>
+#include <AMReX_ParmParse.H>
 
 #include "mechanism.H"
 
+#include "PeleC.H"
 #include "IndexDefines.H"
-#include "Constants.H"
-#include "EOS.H"
+#include "PelePhysics.H"
 #include "Tagging.H"
-#include "Transport.H"
 #include "ProblemSpecificFunctions.H"
 #include "prob_parm.H"
+#include "Utilities.H"
+#include "PeleCUtilities.H"
+#include "Constants.H"
 
 AMREX_GPU_DEVICE
 AMREX_FORCE_INLINE
@@ -51,7 +55,7 @@ pc_initdata(
   if ((prob_parm.case_type_int == 1) || (prob_parm.case_type_int == 2)) {
     amrex::Real xmod = std::fmod(x, prob_parm.L_x);
     int m = 0;
-    locate(prob_parm.d_xarray, prob_parm.nx, xmod, m);
+    pele::physics::utilities::locate(prob_parm.d_xarray, prob_parm.nx, xmod, m);
     const int mp1 = (m + 1) % prob_parm.nx;
     const amrex::Real fact =
       (x - prob_parm.d_input[prob_parm.input_x + m * prob_parm.nvars]) /
diff --git a/Source/Derive.H b/Source/Derive.H
@@ -9,7 +9,7 @@ using namespace MASA;
 #endif
 
 #include "EB.H"
-#include "Utilities.H"
+#include "PeleCUtilities.H"
 
 AMREX_GPU_DEVICE
 AMREX_FORCE_INLINE
diff --git a/Source/Derive.cpp b/Source/Derive.cpp
@@ -1,6 +1,6 @@
 #include "mechanism.H"
 
-#include "Utilities.H"
+#include "PeleCUtilities.H"
 #include "Derive.H"
 #include "PeleC.H"
 #include "IndexDefines.H"
diff --git a/Source/Diffterm.H b/Source/Diffterm.H
@@ -7,7 +7,7 @@
 #include "IndexDefines.H"
 #include "EBStencilTypes.H"
 #include "PelePhysics.H"
-#include "Utilities.H"
+#include "PeleCUtilities.H"
 #include "GradUtil.H"
 #include "TransCoeff.H"
 
diff --git a/Source/Diffusion.H b/Source/Diffusion.H
@@ -8,7 +8,7 @@
 #include <AMReX_FArrayBox.H>
 
 #include "PeleC.H"
-#include "Utilities.H"
+#include "PeleCUtilities.H"
 #include "GradUtil.H"
 #include "Diffterm.H"
 #include "MOL.H"
diff --git a/Source/EB.cpp b/Source/EB.cpp
@@ -1,5 +1,5 @@
 #include "EB.H"
-#include "Utilities.H"
+#include "PeleCUtilities.H"
 
 void
 pc_fill_sv_ebg(
diff --git a/Source/Geometry.H b/Source/Geometry.H
@@ -2,7 +2,7 @@
 #define GEOMETRY_H
 #include "Factory.H"
 #include "EB.H"
-#include "Utilities.H"
+#include "PeleCUtilities.H"
 
 namespace pele::pelec {
 
diff --git a/Source/Hydro.H b/Source/Hydro.H
@@ -4,7 +4,7 @@
 #include "PeleC.H"
 #include "IndexDefines.H"
 #include "PelePhysics.H"
-#include "Utilities.H"
+#include "PeleCUtilities.H"
 #include "Godunov.H"
 #include "AMReX_EB_Redistribution.H"
 
diff --git a/Source/InitEB.cpp b/Source/InitEB.cpp
@@ -3,7 +3,7 @@
 #include "AMReX_EB_Redistribution.H"
 #include "EB.H"
 #include "prob.H"
-#include "Utilities.H"
+#include "PeleCUtilities.H"
 #include "Geometry.H"
 
 inline bool
diff --git a/Source/LES.H b/Source/LES.H
@@ -2,7 +2,7 @@
 #define LES_H
 
 #include "PeleC.H"
-#include "Utilities.H"
+#include "PeleCUtilities.H"
 #include "Diffusion.H"
 #include "Diffterm.H"
 #include "GradUtil.H"
diff --git a/Source/Make.package b/Source/Make.package
@@ -43,7 +43,7 @@ CEXE_headers += GradUtil.H
 CEXE_headers += Godunov.H
 CEXE_headers += PLM.H
 CEXE_headers += PPM.H
-CEXE_headers += Utilities.H
+CEXE_headers += PeleCUtilities.H
 CEXE_headers += Transport.H
 CEXE_headers += MOL.H
 CEXE_headers += Riemann.H
diff --git a/Source/PeleC.H b/Source/PeleC.H
@@ -15,7 +15,7 @@
 #endif
 
 #include "Filter.H"
-#include "Utilities.H"
+#include "PeleCUtilities.H"
 #include "Tagging.H"
 #include "IndexDefines.H"
 #include "prob_parm.H"
diff --git a/Source/PeleC.cpp b/Source/PeleC.cpp
@@ -28,7 +28,7 @@ using namespace MASA;
 #include "Derive.H"
 #include "prob.H"
 #include "Timestep.H"
-#include "Utilities.H"
+#include "PeleCUtilities.H"
 #include "Tagging.H"
 #include "IndexDefines.H"
 
diff --git a/Source/PeleCUtilities.H b/Source/PeleCUtilities.H
@@ -1,5 +1,5 @@
-#ifndef UTILITIES_H
-#define UTILITIES_H
+#ifndef PELEC_UTILITIES_H
+#define PELEC_UTILITIES_H
 
 #include <AMReX_IArrayBox.H>
 #include <AMReX_FArrayBox.H>
@@ -428,48 +428,6 @@ void read_csv(
   const size_t nz,
   amrex::Vector<amrex::Real>& data);
 
-// -----------------------------------------------------------
-// Search for the closest index in an array to a given value
-// using the bisection technique.
-// INPUTS/OUTPUTS:
-// xtable(0:n-1) => array to search in (ascending order)
-// n             => array size
-// x             => x location
-// idxlo        <=> output st. xtable(idxlo) <= x < xtable(idxlo+1)
-// -----------------------------------------------------------
-AMREX_GPU_DEVICE
-AMREX_FORCE_INLINE
-void
-locate(const amrex::Real* xtable, const int n, const amrex::Real& x, int& idxlo)
-{
-  // If x is out of bounds, return boundary index
-  if (x >= xtable[n - 1]) {
-    idxlo = n - 1;
-    return;
-  }
-  if (x <= xtable[0]) {
-    idxlo = 0;
-    return;
-  }
-
-  // Do the bisection
-  idxlo = 0;
-  int idxhi = n - 1;
-  bool notdone = true;
-  while (notdone) {
-    if (idxhi - idxlo <= 1) {
-      notdone = false;
-    } else {
-      const int idxmid = (idxhi + idxlo) / 2;
-      if (x >= xtable[idxmid]) {
-        idxlo = idxmid;
-      } else {
-        idxhi = idxmid;
-      }
-    }
-  }
-}
-
 // Find position of element in vector
 template <typename T>
 int
diff --git a/Source/Timestep.H b/Source/Timestep.H
@@ -8,7 +8,7 @@
 #include "PelePhysics.H"
 #include "IndexDefines.H"
 #include "Constants.H"
-#include "Utilities.H"
+#include "PeleCUtilities.H"
 #include "TransCoeff.H"
 
 // EstDt routines
diff --git a/Source/Utilities.cpp b/Source/Utilities.cpp
@@ -1,4 +1,4 @@
-#include "Utilities.H"
+#include "PeleCUtilities.H"
 
 // -----------------------------------------------------------
 // Read a binary file
diff --git a/Submodules/PelePhysics b/Submodules/PelePhysics
@@ -1 +1 @@
-Subproject commit 4dd874584c2092c3b5c29ac3d833d0f1a911aa78
+Subproject commit 78d574c49bd280728fcc3fe086741a54b9857df9
