Restore old model

.github/workflows/mac.yml

@@ -22,6 +22,9 @@ jobs:
         with:
           lfs: false
 
+      - name: set up python libraries
+        run: pip3 install -r requirements.txt
+
       - name: check if artifact exists
         run: echo "ARTIFACT_EXISTS=$(./tools/check_artifact.sh straka_output.nc)" >> $GITHUB_ENV
 
@@ -222,6 +225,9 @@ jobs:
         with:
           lfs: false
 
+      - name: set up python libraries
+        run: pip3 install -r requirements.txt
+
       - name: check if artifact exists
         run: echo "ARTIFACT_EXISTS=$(./tools/check_artifact.sh swxy_output.nc)" >> $GITHUB_ENV
 
@@ -338,7 +344,7 @@ jobs:
         run: brew bundle
 
       - name: install python modules
-        run: sudo pip3 install -r requirements.txt
+        run: pip3 install -r requirements.txt
 
       - name: create build directory
         # Configure CMake in a 'build' subdirectory. `CMAKE_BUILD_TYPE` is only required if you are using a single-configuration generator such as make.
@@ -369,6 +375,9 @@ jobs:
         with:
           lfs: false
 
+      - name: install python modules
+        run: pip3 install -r requirements.txt
+
       - name: check if artifact exists
         run: echo "ARTIFACT_EXISTS=$(./tools/check_artifact.sh test_blast_output.nc)" >> $GITHUB_ENV
 

.github/workflows/main.yml

@@ -25,7 +25,7 @@ jobs:
       - run: echo "🖥️ The workspace, ${{ github.workspace }}, is now ready to test your code on the runner."
 
       - name: Install cpplint
-        run: sudo pip install cpplint
+        run: pip install cpplint
 
       - uses: actions/checkout@v3
         with:
@@ -49,6 +49,9 @@ jobs:
         with:
           lfs: false
 
+      - name: install python modules
+        run: pip install -r requirements.txt
+
       - name: create build directory
         # Configure CMake in a 'build' subdirectory. `CMAKE_BUILD_TYPE` is only required if you are using a single-configuration generator such as make.
         # See https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html?highlight=cmake_build_type
@@ -73,6 +76,9 @@ jobs:
         with:
           lfs: false
 
+      - name: install python modules
+        run: pip install -r requirements.txt
+
       - name: create build directory
         # Configure CMake in a 'build' subdirectory. `CMAKE_BUILD_TYPE` is only required if you are using a single-configuration generator such as make.
         # See https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html?highlight=cmake_build_type
@@ -100,6 +106,9 @@ jobs:
         with:
           lfs: false
 
+      - name: install python modules
+        run: pip install -r requirements.txt
+
       - name: create build directory
         # Configure CMake in a 'build' subdirectory. `CMAKE_BUILD_TYPE` is only required if you are using a single-configuration generator such as make.
         # See https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html?highlight=cmake_build_type
@@ -146,7 +155,7 @@ jobs:
           lfs: false
 
       - name: install python modules
-        run: sudo pip install -r requirements.txt
+        run: pip install -r requirements.txt
 
       - name: create build directory
         # Configure CMake in a 'build' subdirectory. `CMAKE_BUILD_TYPE` is only required if you are using a single-configuration generator such as make.
@@ -194,6 +203,9 @@ jobs:
         with:
           lfs: false
 
+      - name: install python modules
+        run: pip install -r requirements.txt
+
       - name: create build directory
         # Configure CMake in a 'build' subdirectory. `CMAKE_BUILD_TYPE` is only required if you are using a single-configuration generator such as make.
         # See https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html?highlight=cmake_build_type
@@ -241,6 +253,9 @@ jobs:
         with:
           lfs: false
 
+      - name: install python modules
+        run: pip install -r requirements.txt
+
       - name: create build directory
         # Configure CMake in a 'build' subdirectory. `CMAKE_BUILD_TYPE` is only required if you are using a single-configuration generator such as make.
         # See https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html?highlight=cmake_build_type
@@ -288,6 +303,9 @@ jobs:
         with:
           lfs: false
 
+      - name: install python modules
+        run: pip install -r requirements.txt
+
       - name: create build directory
         # Configure CMake in a 'build' subdirectory. `CMAKE_BUILD_TYPE` is only required if you are using a single-configuration generator such as make.
         # See https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html?highlight=cmake_build_type
@@ -335,7 +353,7 @@ jobs:
           lfs: false
 
       - name: install python modules
-        run: sudo pip install -r requirements.txt
+        run: pip install -r requirements.txt
 
       - name: create build directory
         # Configure CMake in a 'build' subdirectory. `CMAKE_BUILD_TYPE` is only required if you are using a single-configuration generator such as make.
@@ -367,6 +385,9 @@ jobs:
         with:
           lfs: false
 
+      - name: install python modules
+        run: pip install -r requirements.txt
+
       - name: check if artifact exists
         run: echo "ARTIFACT_EXISTS=$(./tools/check_artifact.sh robert_output.nc)" >> $GITHUB_ENV
 
@@ -380,9 +401,6 @@ jobs:
         if: env.ARTIFACT_EXISTS == 'false'
         run: git lfs pull -I examples/2019-Li-snap/straka_output.nc
 
-      - name: set up python libraries
-        run: pip3 install -r requirements.txt
-
       - name: create build directory
         run: cmake -B ${{github.workspace}}/build -DCMAKE_BUILD_TYPE=${{env.BUILD_TYPE}} -DTASK=straka
 
@@ -685,7 +703,7 @@ jobs:
           lfs: false
 
       - name: install python modules
-        run: sudo pip3 install -r requirements.txt
+        run: pip3 install -r requirements.txt
 
       - name: create build directory
         # Configure CMake in a 'build' subdirectory. `CMAKE_BUILD_TYPE` is only required if you are using a single-configuration generator such as make.
@@ -717,6 +735,9 @@ jobs:
         with:
           lfs: false
 
+      - name: install python modules
+        run: pip3 install -r requirements.txt
+
       - name: check if artifact exists
         run: echo "ARTIFACT_EXISTS=$(./tools/check_artifact.sh test_blast_output.nc)" >> $GITHUB_ENV
 

CMakeLists.txt

@@ -58,13 +58,12 @@ endif()
 message(STATUS "Include ${CMAKE_CURRENT_SOURCE_DIR}/cmake/parameters.cmake")
 include(${CMAKE_CURRENT_SOURCE_DIR}/cmake/parameters.cmake)
 find_package(Eigen3 REQUIRED)
-find_package(Cantera REQUIRED)
-find_package(Torch REQUIRED)
+find_package(Cantera)
+#find_package(Torch)
 
 ## 3. set up project system libraries ##
 message(STATUS "3. Set up system libraries")
-#message(STATUS "Include ${CMAKE_SOURCE_DIR}/cmake/athena.cmake")
-if (NOT ${CANTERA_FOUND} STREQUAL "TRUE")
+if (NOT ${CANTERA_FOUND})
   include(${CMAKE_SOURCE_DIR}/cmake/yamlpp.cmake)
 endif()
 include(${CMAKE_SOURCE_DIR}/cmake/gtest.cmake)

cmake/modules/FindCantera.cmake

@@ -49,4 +49,9 @@ if(CANTERA_INCLUDE_DIR)
     message(STATUS "Symbolic link created: ${LINK_PATH} -> ${SOURCE_PATH}")
   endif()
   include_directories(${CMAKE_CURRENT_BINARY_DIR}/ext1)
+else()
+  message(STATUS "Not using Cantera library")
+  set(CANTERA_INCLUDE_DIR "")
+  set(CANTERA_LIBRARY "")
+  set(CANTERA_FOUND FALSE)
 endif()

cmake/yamlpp.cmake

@@ -19,3 +19,5 @@ endif()
 
 # Where yaml-cpp's .h files can be found.
 include_directories(${yaml-cpp_SOURCE_DIR}/include)
+
+set(YAML_CPP_LIBRARIES yaml-cpp)

examples/2023-Li-saturn-vla/saturn_radio.cpp

@@ -14,7 +14,6 @@
 #include <athena/outputs/outputs.hpp>
 #include <athena/parameter_input.hpp>
 #include <athena/scalars/scalars.hpp>
-#include <athena/stride_iterator.hpp>
 
 // application
 #include <application/application.hpp>
@@ -32,6 +31,7 @@
 #include <climath/interpolation.h>
 
 // snap
+#include <snap/stride_iterator.hpp>
 #include <snap/thermodynamics/molecules.hpp>
 #include <snap/thermodynamics/thermodynamics.hpp>
 #include <snap/thermodynamics/vapors/sodium_vapors.hpp>

examples/2023-Li-uranus/uranus_mwr.cpp

@@ -14,7 +14,6 @@
 #include <athena/outputs/outputs.hpp>
 #include <athena/parameter_input.hpp>
 #include <athena/scalars/scalars.hpp>
-#include <athena/stride_iterator.hpp>
 
 // application
 #include <application/application.hpp>
@@ -32,6 +31,7 @@
 #include <climath/interpolation.h>
 
 // snap
+#include <snap/stride_iterator.hpp>
 #include <snap/thermodynamics/molecules.hpp>
 #include <snap/thermodynamics/thermodynamics.hpp>
 #include <snap/thermodynamics/vapors/sodium_vapors.hpp>

examples/2024-JHu-juno-mwr/juno_mwr.cpp

@@ -14,7 +14,6 @@
 #include <athena/outputs/outputs.hpp>
 #include <athena/parameter_input.hpp>
 #include <athena/scalars/scalars.hpp>
-#include <athena/stride_iterator.hpp>
 
 // application
 #include <application/application.hpp>
@@ -32,6 +31,7 @@
 #include <climath/interpolation.h>
 
 // snap
+#include <snap/stride_iterator.hpp>
 #include <snap/thermodynamics/atm_thermodynamics.hpp>
 #include <snap/thermodynamics/vapors/sodium_vapors.hpp>
 

src/CMakeLists.txt

@@ -33,6 +33,11 @@ add_library(${namel}_${buildl}
     ${src_files}
     )
 
+target_include_directories(${namel}_${buildl}
+    PRIVATE
+    ${EIGEN3_INCLUDE_DIR}
+    )
+
 set_target_properties(${namel}_${buildl}
     PROPERTIES
     COMPILE_FLAGS ${CMAKE_CXX_FLAGS_${buildu}}
@@ -56,9 +61,17 @@ add_subdirectory(special)
 add_subdirectory(single_column)
 add_subdirectory(diagnostics)
 add_subdirectory(forcing)
-add_subdirectory(modules)
+
+if (${Torch_FOUND})
+  add_subdirectory(torch)
+  add_subdirectory(modules)
+endif()
 #add_subdirectory(nbody)
 
+if(UNIX AND NOT APPLE)
+  set(EXTRA_LIBS dl stdc++fs)
+endif()
+
 set(CANOE_LIBRARY_${buildu}
   "canoe_${buildl}"
   "athenapp_${buildl}"
@@ -81,8 +94,8 @@ set(CANOE_LIBRARY_${buildu}
   "scm_${buildl}"
   "diagnostics_${buildl}"
   "forcing_${buildl}"
-  "modules_${buildl}"
-  #"yaml-cpp"
+  #"modules_${buildl}"
+  ${YAML_CPP_LIBRARIES}
   ${CPPDISORT_LIBRARY_${buildu}}
   ${PYTHON_LIBRARY_RELEASE}
   ${NETCDF_LIBRARIES}
@@ -94,6 +107,7 @@ set(CANOE_LIBRARY_${buildu}
   ${TORCH_LIBRARY}
   ${TORCH_CPU_LIBRARY}
   ${C10_LIBRARY}
+  ${EXTRA_LIBS}
   CACHE INTERNAL "canoe library")
 
 set(CANOE_INCLUDE_DIR

src/diagnostics/todo/convective_heat_flx.cpp

@@ -8,9 +8,9 @@
 #include <athena/athena_arrays.hpp>
 #include <athena/coordinates/coordinates.hpp>
 #include <athena/reconstruct/interpolation.hpp>
-#include <athena/stride_iterator.hpp>
 
 // snap
+#include <snap/stride_iterator.hpp>
 #include <snap/thermodynamics/thermodynamics.hpp>
 
 // canoe

src/exchanger/exchanger.hpp

@@ -1,6 +1,10 @@
 #ifndef SRC_EXCHANGER_EXCHANGER_HPP_
 #define SRC_EXCHANGER_EXCHANGER_HPP_
 
+// C/C++
+#include <array>
+#include <vector>
+
 // Athena++
 #include <athena/athena.hpp>
 #include <athena/bvals/bvals.hpp>

src/modules/eos_equilibrate_tp.cpp_

@@ -0,0 +1,76 @@
+// cantera
+#include <cantera/kinetics.h>
+#include <cantera/kinetics/Condensation.h>
+#include <cantera/thermo.h>
+
+// canoe
+#include <air_parcel.hpp>
+
+// snap
+#include "atm_thermodynamics.hpp"
+
+void Thermodynamics::EquilibrateTP(AirParcel* air) const {
+  air->ToMassFraction();
+  Real pres = air->w[IPR];
+  for (int n = IVX; n < IVX + NCLOUD; ++n) air->w[n] = air->c[n - IVX];
+  auto& thermo = kinetics_->thermo();
+  thermo.setMassFractionsPartial(&air->w[1]);
+  thermo.setDensity(air->w[IDN]);
+  thermo.setPressure(air->w[IPR]);
+
+  EquilibrateTP();
+
+  for (int n = 0; n < NCLOUD; ++n) air->c[n] = air->w[IVX + n];
+  air->w[IPR] = pres;
+  air->ToMoleFraction();
+}
+
+void Thermodynamics::EquilibrateTP() const {
+  std::static_pointer_cast<Cantera::Condensation>(kinetics_)
+      ->setQuantityMoleFraction();
+
+  std::vector<Real> rates(kinetics_->nTotalSpecies());
+  std::vector<Real> mfrac(kinetics_->nTotalSpecies());
+
+  auto& thermo = kinetics_->thermo();
+  Real temp = thermo.temperature();
+  Real pres = thermo.pressure();
+
+  int iter = 0, max_iter = 3;
+
+  while (iter++ < max_iter) {
+    // std::cout << "Iteration " << iter << std::endl;
+
+    // get mole fraction
+    kinetics_->getActivityConcentrations(mfrac.data());
+
+    /* print initial conditions
+    std::cout << "Mole fractions" << std::endl;
+    for (size_t i = 0; i < mfrac.size(); ++i) {
+      std::cout << "Mole fraction " << i << ": " << mfrac[i] << std::endl;
+    }*/
+
+    kinetics_->getNetProductionRates(rates.data());
+    /*for (size_t i = 0; i < rates.size(); ++i) {
+      std::cout << "NET Production " << i << ": " << rates[i] << std::endl;
+    }*/
+
+    // update mole fraction
+    for (size_t i = 1; i < rates.size(); ++i) {
+      mfrac[i] += rates[i];
+    }
+
+    thermo.setMoleFractions(mfrac.data());
+    thermo.setTemperature(temp);
+    thermo.setPressure(pres);
+
+    /* print again
+    std::cout << "After Mole fractions" << std::endl;
+    for (size_t i = 0; i < mfrac.size(); ++i) {
+      std::cout << "Mole fraction " << i << ": " << mfrac[i] << std::endl;
+    }
+    std::cout << "T = " << thermo.temperature() << std::endl;
+    std::cout << "P = " << thermo.pressure() << std::endl;
+    std::cout << "D = " << thermo.density() << std::endl;*/
+  }
+}