Absorb athena updates (#117)

- Athena upstream adds chemistry, lots of changes involved
- Fully absorbed the changes
- Mac does not pass because of the firewall. Will Fix later.

.github/workflows/main.yml

@@ -347,7 +347,7 @@ jobs:
 
       - name: combile outputs
         working-directory: ${{github.workspace}}/build/bin
-        run: ./combine.py -o test
+        run: python3 combine.py -o test
 
       - name: compare result
         run: >
@@ -400,7 +400,7 @@ jobs:
 
       - name: combile outputs
         working-directory: ${{github.workspace}}/build/bin
-        run: ./combine.py -o test
+        run: python3 combine.py -o test
 
       - name: compare result
         run: >
@@ -453,7 +453,7 @@ jobs:
 
       - name: combile outputs
         working-directory: ${{github.workspace}}/build/bin
-        run: ./combine.py -o test
+        run: python3 combine.py -o test
 
       - name: compare result
         run: >
@@ -504,7 +504,7 @@ jobs:
 
       - name: combile outputs
         working-directory: ${{github.workspace}}/build/bin
-        run: ./combine.py -o test
+        run: python3 combine.py -o test
 
       - name: compare result
         run: >
@@ -555,7 +555,7 @@ jobs:
 
       - name: combile outputs
         working-directory: ${{github.workspace}}/build/bin
-        run: ./combine.py -o test
+        run: python3 combine.py -o test
 
       - name: compare result
         run: >
@@ -608,7 +608,7 @@ jobs:
 
       - name: combile outputs
         working-directory: ${{github.workspace}}/build/bin
-        run: ./combine.py -o test
+        run: python3 combine.py -o test
 
       - name: compare result
         run: >
@@ -654,7 +654,7 @@ jobs:
 
       - name: combile outputs
         working-directory: ${{github.workspace}}/build/bin
-        run: ./combine.py -o test
+        run: python3 combine.py -o test
 
       - name: Test
         working-directory: ${{github.workspace}}/examples/2023-jupiter-mwr-eq

Brewfile

@@ -1,5 +1,4 @@
 tap "homebrew/bundle"
-tap "homebrew/core"
 brew "cfitsio"
 brew "ctags"
 brew "hdf5"

examples/2024-XZhang-cloud-rt/hywater.cpp

@@ -178,7 +178,7 @@ void MeshBlock::ProblemGenerator(ParameterInput *pin) {
       int i = is;
       for (; i <= ie; ++i) {
         if (air.w[IDN] < Tmin) break;
-        air.w[IVX] = 1. * sin(2. * M_PI * rand() / RAND_MAX);
+        air.w[IVX] = 0.1 * sin(2. * M_PI * rand() / RAND_MAX);
         AirParcelHelper::distribute_to_conserved(this, k, j, i, air);
         pthermo->Extrapolate(&air, pcoord->dx1f(i),
                              Thermodynamics::Method::PseudoAdiabat, grav,

external/install_cantera.sh

@@ -1,21 +1,21 @@
-#! /usr/bin/bash
+#! /bin/bash
 
 CXX=g++
 CC=gcc
-cxx_flags=-std=c++14
+cxx_flags=-std=c++17
 prefix=${HOME}/opt/
 python_package=n
 f90_interface=n
 system_eigen=y
-extra_inc_dirs=${HOME}/opt/include/eigen3
+extra_inc_dirs=/opt/homebrew/Cellar/eigen/3.4.0_1/include
 system_blas_lapack=n
-boost_inc_dir=`pwd`/cliboost/
+boost_inc_dir=`pwd`/ext/cliboost/
 
 cd cantera
 scons build CXX=${CXX} CC=${CC} cxx_flags=${cxx_flags} prefix=${prefix} \
   python_package=${python_package} f90_interface=${f90_interface} \
   system_eigen=${system_eigen} extra_inc_dirs=${extra_inc_dirs} \
   system_blas_lapack=${system_blas_lapack} \
-  boost_inc_dir=${boost_inc_dir}
+  boost_inc_dir=${boost_inc_dir} -j8
 scons install
 cd ..

external/install_pnetcdf.sh

@@ -16,7 +16,7 @@ tar -xvzf "$TARFILE"
 cd pnetcdf-1.12.3
 
 # Configure, make and install
-./configure --prefix="$DESTDIR"
+FFLAGS="-fPIC -g -O2" FCFLAGS="-fPIC -g -O2" CFLAGS="-fPIC -g -O3" CXXFLAGS="-fPIC -g -O2" ./configure --prefix="$DESTDIR"
 make
 make install
 

src/opacity/Giants/microwave/attenuation_electron.cpp

@@ -8,8 +8,8 @@
 #include <harp/radiation.hpp>
 
 // cli, 190801
-inline double SQUARE(double x) { return x * x; }
-inline double CUBE(double x) { return x * x * x; }
+inline double _SQUARE(double x) { return x * x; }
+inline double _CUBE(double x) { return x * x * x; }
 // end
 
 // From F. Oyafuso
@@ -26,17 +26,17 @@ double attenuation_freefree_Reference(double freq, double P, double T)
   double hbar_omega =
       4.13566733e-15 * freq * 1e9;  // eV (.6GHz) -- check that freq is in GHz
 
-  double debroglie_thermal = sqrt(2.0 * M_PI * SQUARE(hbarc) / (mc2 * kT));
+  double debroglie_thermal = sqrt(2.0 * M_PI * _SQUARE(hbarc) / (mc2 * kT));
   double E_ionization = 5.986;  // eV
   double n_Al = 1.6e-6 * (P * 1e5) / (kT * 1.609e-19) * 1e-6;
 
   double ni =
       sqrt(2 * n_Al / pow(debroglie_thermal, 3) * exp(-E_ionization / kT));
 
   double kludge = 0.5;
-  double alpha_ff = kludge * sqrt(32 * CUBE(M_PI) / 3.0) *
-                    (SQUARE(Z) * fine_struct) * sqrt(mc2 / kT) *
-                    (ni * CUBE(hbarc / hbar_omega)) * ni * sigma_T *
+  double alpha_ff = kludge * sqrt(32 * _CUBE(M_PI) / 3.0) *
+                    (_SQUARE(Z) * fine_struct) * sqrt(mc2 / kT) *
+                    (ni * _CUBE(hbarc / hbar_omega)) * ni * sigma_T *
                     (1.0 - exp(-hbar_omega / kT));
   return alpha_ff;
 }