MUSICA Tutorial Chapter 2

docs/source/tutorial/chapter2.rst

@@ -0,0 +1,65 @@
+Chapter 2
+=========
+
+An MICM Box Model Fortran Example
+---------------------------------
+
+In this next MUSICA Fortran example,
+we will setup a MICM solver, starting with a set of MICM configuration files,
+and run the solver for a single integration time step.
+
+The MICM configuration is specified in a top-level ``config.json`` file,
+which simply lists the chemical species configuration file followed by
+the reactions configuration file.
+
+  .. literalinclude:: ../../../configs/analytical/config.json
+    :language: json
+
+For this example, we will have a system of three chemical species
+`A`, `B`, and `C`, defined in the JSON file ``species.json`` as follows:
+
+  .. literalinclude:: ../../../configs/analytical/species.json
+    :language: json
+
+The ``reactions.json`` specifies a mechanism, or a set of reactions for the system.
+Here, we will introduce two Arrhenius type reactions, the first
+with `B` evolving to `C`, and specifying all five reaction parameters,
+and the second reaction with `A` evolving to `B` and using only two reaction parameters. 
+The mechanism configuration might then be set up as:
+
+  .. literalinclude:: ../../../configs/analytical/reactions.json
+    :language: json
+
+More information on MICM configurations and reactions can be found in the MICM documentation
+at `https://ncar.github.io/micm/user_guide/`_
+
+The Fortran example code is shown below in full: 
+
+  .. literalinclude:: ../../../fortran/test/fetch_content_integration/test_micm_box_model.F90
+    :language: f90
+
+From the ``musica_util`` module we need the Fortran types
+``error_t``, ``string_t``, and ``mapping_t``.
+A pointer to a ``musica_micm::micm_t`` will serve as the interface to the MICM solver
+(in the example the pointer name is ``micm``).
+Note that the ``config_path`` in the code sample has been set to ``configs/analytical``,
+so that subdir should be created relative to the main program and contain
+the MICM JSON configuration files,
+or otherwise the ``config_path`` should be modified appropriately.
+The initial species concentrations are initialized in the ``concentrations`` array,
+which is an argument to the MICM solver.
+
+Finally, a single time step solution is obtained through a call to ``micm%solve``,
+after which the updated concentrations may be displayed.
+
+.. code-block:: bash
+
+  $ ./test_micm_box_model
+    Creating MICM solver...
+    Species Name:A, Index:           1
+    Species Name:B, Index:           2
+    Species Name:C, Index:           3
+    Solving starts...
+    After solving, concentrations  0.38  1.61E-009  2.62
+  $
+

docs/source/tutorial/tutorial.rst

@@ -7,3 +7,4 @@ Tutorial
    :caption: Contents:
 
    chapter1.rst
+   chapter2.rst

fortran/test/fetch_content_integration/CMakeLists.txt

@@ -65,6 +65,22 @@ if (MUSICA_ENABLE_MICM)
     COMMAND $<TARGET_FILE:test_get_micm_version>
     WORKING_DIRECTORY ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}
   )
+
+  target_link_libraries(test_micm_box_model
+    PRIVATE
+      musica::musica-fortran
+  )
+
+  set_target_properties(test_micm_box_model
+    PROPERTIES
+      LINKER_LANGUAGE Fortran
+  )
+
+  add_test(
+    NAME test_micm_box_model
+    COMMAND $<TARGET_FILE:test_micm_box_model>
+    WORKING_DIRECTORY ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}
+  )
 endif()
 
 # API Test

fortran/test/fetch_content_integration/test_micm_box_model.F90

@@ -0,0 +1,58 @@
+program test_micm_box_model
+
+    use, intrinsic :: iso_c_binding
+    use, intrinsic :: ieee_arithmetic
+
+    use musica_util, only: error_t, string_t, mapping_t
+    use musica_micm, only: micm_t
+
+    implicit none
+
+    call box_model()
+
+contains
+
+    subroutine box_model()
+
+        character(len=256) :: config_path
+
+        real(c_double) :: time_step
+        real(c_double) :: temperature
+        real(c_double) :: pressure
+
+        integer(c_int) :: num_concentrations = 3
+        real(c_double), dimension(3) :: concentrations
+
+        integer(c_int) :: num_user_defined_reaction_rates = 0
+        real(c_double), dimension(:), allocatable :: user_defined_reaction_rates 
+
+        type(error_t) :: error
+        type(micm_t), pointer :: micm
+
+        integer :: i
+
+        config_path = "configs/analytical"
+
+        time_step = 200
+        temperature = 273.0
+        pressure = 1.0e5
+
+        concentrations = (/ 1.0, 1.0, 1.0 /)
+
+        write(*,*) "Creating MICM solver..."
+        micm => micm_t(config_path, error)
+
+        do i = 1, size( micm%species_ordering )
+            associate(the_mapping => micm%species_ordering(i))
+            print *, "Species Name:", the_mapping%name(), ", Index:", the_mapping%index()
+            end associate
+        end do
+
+        write(*,*) "Solving starts..."
+        call micm%solve(time_step, temperature, pressure, num_concentrations, concentrations, &
+            num_user_defined_reaction_rates, user_defined_reaction_rates, error)
+        write(*,*) "After solving, concentrations", concentrations
+
+    end subroutine box_model
+
+end program test_micm_box_model

fortran/test/unit/CMakeLists.txt

@@ -5,6 +5,7 @@ create_standard_test_fortran(NAME fortran_util SOURCES util.F90)
 if (MUSICA_ENABLE_MICM)
   create_standard_test_fortran(NAME micm_fortran_api SOURCES ../fetch_content_integration/test_micm_api.F90)
   create_standard_test_fortran(NAME get_micm_version SOURCES ../fetch_content_integration/test_get_micm_version.F90)
+  create_standard_test_fortran(NAME micm_box_model SOURCES ../fetch_content_integration/test_micm_box_model.F90)
 endif()
 
 if (MUSICA_ENABLE_TUVX)

src/micm/micm.cpp

@@ -9,6 +9,7 @@
 #include <musica/micm.hpp>
 
 #include <micm/version.hpp>
+
 #include <micm/solver/rosenbrock_solver_parameters.hpp>
 #include <micm/system/species.hpp>