deploy: 9c6ac54

.gitignore

@@ -0,0 +1,2 @@
+.DS_Store
+docs/build

README.md

@@ -0,0 +1 @@
+# Chemistry Across Multiple Phases Configuration

_sources/aerosol_phases/index.rst.txt

@@ -0,0 +1,7 @@
+##############
+Aerosol Phases
+##############
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:

_sources/aerosol_representations/index.rst.txt

@@ -0,0 +1,7 @@
+######################
+Aerosol Representation
+######################
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:

_sources/bibliography.rst.txt

@@ -0,0 +1,6 @@
+############
+Bibliography
+############
+
+.. bibliography::
+   :all:

_sources/chemical_species/index.rst.txt

@@ -0,0 +1,56 @@
+.. _chemical-species:
+
+################
+Chemical Species
+################
+
+An object containing information about a chemical species has the following format:
+
+.. tab-set::
+
+   .. tab-item:: YAML
+
+      .. code-block:: yaml
+         :force:
+
+         camp-data:
+           - name: my species name
+             type: CHEM_SPEC
+           - name: my other species name
+             type: CHEM_SPEC
+             "molecular weight [kg mol-1]": 0.025
+             "diffusion coefficient [m2 s-1]": 2.3e2
+
+
+   .. tab-item:: JSON
+
+      .. code-block:: json
+         :force:
+
+         {
+           "camp-data": [
+             {
+               "name": "my species name",
+               "type": "CHEM_SPEC"
+             },
+             {
+               "name": "my other species name",
+               "type": "CHEM_SPEC",
+               "molecular weight [kg mol-1]": 0.025,
+               "diffusion coefficient [m2 s-1]": 2.3e2
+             }
+           ]
+         }
+
+
+The key-value pair ``name`` is required and must contain the unique name used for this
+species.
+The key-value pair ``type`` is also required, and must be ``CHEM_SPEC``.
+Optional key-value pairs are used to define physical and chemical properties.
+These include:
+
+- ``"molecular weight [kg mol-1]"``
+- ``"diffusion coefficient [m2 s-1]"``
+
+These optional properties are only required when a species participates in a
+reaction that requires that a particular property be defined (e.g., surface reactions).

_sources/examples/index.rst.txt

@@ -0,0 +1,69 @@
+##########
+Examples
+##########
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+
+Chapman
+=======
+
+Top Level Config
+----------------
+
+.. raw:: html
+
+    <div class="download-div">
+    <a href="../_static/examples/yaml/chapman/chapman.zip" download>
+       <button class="download-button">Download yaml ZIP</button>
+    </a>
+    <a href="../_static/examples/json/chapman/chapman.zip" download>
+       <button class="download-button">Download json ZIP</button>
+    </a>
+    </div>
+
+
+.. tab-set::
+
+    .. tab-item:: YAML
+
+        .. literalinclude:: ../_static/examples/yaml/chapman/config.yaml
+            :language: yaml
+
+    .. tab-item:: JSON
+
+        .. literalinclude:: ../_static/examples/json/chapman/config.json
+            :language: json
+
+
+Reactions
+---------
+
+.. tab-set::
+
+    .. tab-item:: YAML
+
+        .. literalinclude:: ../_static/examples/yaml/chapman/reactions.yaml
+            :language: yaml
+
+    .. tab-item:: JSON
+
+        .. literalinclude:: ../_static/examples/json/chapman/reactions.json
+            :language: json
+
+Species
+---------
+
+.. tab-set::
+
+    .. tab-item:: YAML
+
+        .. literalinclude:: ../_static/examples/yaml/chapman/species.yaml
+            :language: yaml
+
+    .. tab-item:: JSON
+
+        .. literalinclude:: ../_static/examples/json/chapman/species.json
+            :language: json

_sources/index.rst.txt

@@ -0,0 +1,39 @@
+.. OpenAtmos Mechanism Configuration documentation master file, created by
+   sphinx-quickstart on Fri Jul 21 21:05:33 2023.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+.. open atmos mechanism configuration documentation HTML titles
+..
+.. # (over and under) for module headings
+.. = for sections
+.. - for subsections
+.. ^ for subsubsections
+.. ~ for subsubsubsections
+.. " for paragraphs
+
+.. |project_version| replace:: 1.0.0
+
+###############################################################
+Welcome to the OpenAtmos Mechanism Configuration documentation!
+###############################################################
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   overview
+   chemical_species/index
+   mechanisms/index
+   reactions/index
+   examples/index
+   bibliography
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

_sources/mechanisms/index.rst.txt

@@ -0,0 +1,50 @@
+.. _mechanisms:
+
+##########
+Mechanisms
+##########
+
+Mechanisms are collections of reactions and have the following format:
+
+.. tab-set::
+
+   .. tab-item:: YAML
+
+      .. code-block:: yaml
+         :force:
+
+         camp-data:
+           - name: my mechanism
+             type: MECHANISM 
+             reactions:
+               - type: RXN_ARRHENIUS
+                 ...
+               - type: RXN_TROE
+                 ...
+
+   .. tab-item:: JSON
+
+      .. code-block:: json
+         :force:
+
+         {
+           "camp-data": [
+             "name": "my mechanism",
+             "type": "MECHANISM",
+             "reactions": [
+               {
+                 "type": "RXN_ARRHENIUS",
+                 ...
+               },
+               {
+                 "type": "RXN_TROE",
+                 ...
+               }
+             ]
+           ]
+
+
+The ``name`` is required and must be unique.
+Mechanisms with the same name will be merged into a single mechanism.
+The ``type`` is also required and must be ``MECHANISM``.
+The ``reactions`` should be an array of :ref:`reactions`.

_sources/overview.rst.txt

@@ -0,0 +1,95 @@
+########
+Overview
+########
+
+Chemical mechnanisms can be organized across a number of files in
+whatever way makes sense for the specific user and application.
+Every configuration should include one top-level file that
+lists the relative or absolute path to every configuration
+file that includes mechanism configuration data.
+
+Individual mechanism configuration files are combined to
+collectively describe the chemical system and processes.
+The order of files in the list is arbitrary.
+
+The file list configuration has the following format:
+
+.. tab-set::
+
+  .. tab-item:: YAML
+
+    .. code-block:: yaml
+
+        camp-files:
+          - path/to/foo.yml
+          - path/to/bar.yml
+
+  .. tab-item:: JSON
+
+    .. code-block:: json
+
+      {
+        "camp-files": [
+          "path/to/foo.json",
+          "path/to/bar.json"
+        ]
+      }
+
+
+Individual configuration files have the following format:
+
+.. tab-set::
+
+  .. tab-item:: YAML
+
+    .. code-block:: yaml
+       :force:
+
+        camp-data:
+          - type: OBJECT_TYPE
+            ...
+          - type: OBJECT_TYPE
+            ...
+
+  .. tab-item:: JSON
+
+    .. code-block:: json
+       :force:
+
+        {
+          "camp-data": [
+            {
+              "type": "OBJECT_TYPE",
+              ...
+            },
+            {
+              "type": "OBJECT_TYPE",
+              ...
+            }
+          ]
+        }
+
+
+Each input file should contain exactly one object with a single key-value
+pair ``camp-data`` whose value is an array of objects.
+Additional top-level key-value pairs will be ignored.
+Each of the objects in the ``camp-data`` array must contain a key-value pair ``type``
+whose value is a string referencing a valid configuration class.
+
+The valid top-level configuration objects that can appear in the ``camp-data``
+array are described here:
+
+:ref:`chemical-species`
+
+:ref:`mechanisms`
+
+The arrangement of objects within the ``camp-data`` array and between input files is arbitrary.
+Additionally, some objects, such as chemical species and mechanisms may be split into
+multiple objects within the ``camp-data`` array and/or between files,
+and will be combined based on their unique name.
+This flexibility is provided so that the chemical mechanism data can be organized
+in a way that makes sense to the designer of the mechanism.
+For example, files could be split based on species source (biogenic, fossil fuel, etc.)
+or based on properties (molecular weight, density, etc.) or any combination of criteria.
+However, if a single property of an object (e.g., the molecular weight of a chemical species)
+is set in more than one location, this should cause an error.