Added Model Doc Page (#26)

* Added Model Doc Page

* Added files for new CSVY doc page

docs/models/examples/abundancecust.rst

@@ -1,3 +1,5 @@
+.. _abundancecust:
+
 *************************************
 Using a custom stratified composition
 *************************************

docs/models/examples/csvy_full_rad.csvy

@@ -0,0 +1,30 @@
+---
+name: csvy_full
+model_density_time_0: 1 day
+description: Example csvy config file for TARDIS.
+tardis_model_config_version: v1.0
+datatype:
+  fields:
+    -  name: velocity
+       unit: km/s
+       desc: velocities of shell outer bounderies.
+    -  name: density
+       unit: g/cm^3
+       desc: density of shell.
+    -  name: t_rad
+       unit: K
+       desc: radiative temperature.
+    -  name: H
+       desc: fractional H abundance
+    -  name: He
+       desc: fractional He abundance
+    -  name: Ni56
+       desc: fractional Ni56 abundance
+
+v_inner_boundary: 9000 km/s
+v_outer_boundary: 12000 km/s
+---
+velocity,density,t_rad,H,He,Ni56
+9000, 5e-10, 7000, 1.0, 1.0, 1.0
+10500, 2.0e-10, 7000, 0.0, 0.99, 0.01
+12000, 9e-11, 7000, 0.4, 0.58, 0.02

docs/models/examples/densitycust.rst

@@ -1,3 +1,5 @@
+.. _densitycust:
+
 ******************************
 Using a custom density profile
 ******************************

docs/models/examples/modelconfig.rst

@@ -1,3 +1,5 @@
+.. _modelconfig:
+
 **************************
 Ejecta Model Configuration
 **************************

docs/models/index.rst

@@ -2,4 +2,47 @@
 Model
 *****
 
+TARDIS requires a model of the homologously expanding ejecta in order to run a simulation.
+A model will include information like the velocity shell structure, abundances, density, etc.
+TARDIS offers two ways of specifying the model: either directly in the configuration yaml file
+or separately in a model.csvy file. See `here <https://csvy.org/>`_ for an explanation of
+the csvy file format and :ref:`here <../running/configuration/config-file>` for a link to the csvy_model schema.
 
+.. note::
+    We highly recommend using the cleaner csvy format.
+
+CSVY Model
+==========
+
+The TARDIS YAML delimiter for csvy files is ``---``. This means that each csvy model
+file has the following structure: The first line of the file is the YAML delimiter,
+followed by the YAML portion of the csvy model. A line consisting of only the YAML
+delimiter separates the YAML portion of the csvy file from the csv part. The YAML part
+of the csvy file is for setting model parameters like **v_inner_boundary** or
+**model_density_time_0** while the csv part of the file is for setting profiles of
+physical parameters of the model (e.g. abundances, radiative temperature, dilution factor, etc).
+If you use the csvy model, then you will need to specify the path to the csvy model file
+in the main TARDIS configuration file:
+
+.. code-block::
+
+    csvy_model: /path/to/model.csvy
+
+Example CSVY Model
+==================
+
+Below we provide an example model.csvy file.
+
+.. literalinclude:: examples/csvy_full_rad.csvy
+
+Using the Config Model
+======================
+
+Although we strongly recommend using the CSVY Model, TARDIS also allows the user
+to define custom density and abundance profiles in separate files and reference
+these files directly in the main TARDIS configuration file. For further details,
+see the following links:
+
+* For general information: :ref:`modelconfig`
+* For defining a custom density file: :ref:`densitycust`
+* For defining a custom abundance file: :ref:`abundancecust`

docs/running/configuration/schemas/csvy_model.yml

@@ -0,0 +1,152 @@
+$schema: http://json-schema.org/draft-04/schema#
+type: object
+additionalProperties: false
+properties:
+  name: 
+    type: string
+    description: name of the model being run
+
+  model_density_time_0:
+    type: quantity
+    description: Initial time for the density in the model
+
+  model_isotope_time_0:
+    type: quantity
+    default: -1 day
+    description: initial time for isotope decay
+
+  description:
+    type: string
+    description: description of the model being run
+
+  tardis_model_config_version:
+    type: string
+    description: Version of the configuration file
+
+# datatype name used for consistency with astropy ecsv files.
+  datatype:
+    type: object
+    description: fields found in csv part of csvy file
+    additionalProperties: False
+    properties:
+      fields:
+        type: array
+
+  v_inner_boundary:
+    type: quantity
+    description: velocity of the inner boundary
+
+  v_outer_boundary:
+    type: quantity
+    description: velocity of the outer boundary of the last shell
+
+  velocity:
+    type: object
+    properties:
+      start:
+        type: quantity
+      stop:
+        type: quantity
+      num:
+        type: number
+        multipleOf: 1.0
+
+  density:
+    oneOf:
+    - $ref: '#/definitions/density/branch85_w7'
+    - $ref: '#/definitions/density/exponential'
+    - $ref: '#/definitions/density/power_law'
+    - $ref: '#/definitions/density/uniform'
+
+  abundance:
+    $ref: '#/definitions/abundance/uniform'
+
+required:
+- tardis_model_config_version
+
+definitions:
+  density:
+    branch85_w7:
+      type: object
+      additionalProperties: false
+      properties:
+        type:
+          enum:
+          - branch85_w7
+        w7_time_0:
+          type: quantity
+          default: 0.000231481 day
+          description: This needs no change - DO NOT TOUCH
+        w7_rho_0:
+          type: quantity
+          default: 3e29 g/cm^3
+          description: This needs no change - DO NOT TOUCH
+        w7_v_0:
+          type: quantity
+          default: 1 km/s
+          description: This needs no change - DO NOT TOUCH
+    exponential:
+      type: object
+      additionalProperties: false
+      properties:
+        type:
+          enum:
+          - exponential
+        time_0:
+          type: quantity
+          description: Time at which the pure model densities are right
+        rho_0:
+          type: quantity
+          description: density at time_0
+        v_0:
+          type: quantity
+          description: at what velocity the density rho_0 applies
+      required:
+      - rho_0
+      - v_0
+    power_law:
+      type: object
+      additionalProperties: false
+      properties:
+        type:
+          enum:
+          - power_law
+        time_0:
+          type: quantity
+          description: Time at which the pure model densities are right
+        rho_0:
+          type: quantity
+          description: density at time_0
+        v_0:
+          type: quantity
+          description: at what velocity the density rho_0 applies
+        exponent:
+          type: number
+          description: exponent for exponential density profile
+      required:
+      - rho_0
+      - v_0
+      - exponent
+    uniform:
+      type: object
+      additionalProperties: false
+      properties:
+        type:
+          enum:
+          - uniform
+        time_0:
+          type: quantity
+          description: Time at which the pure model densities are right
+        value:
+          type: quantity
+          description: value for uniform density
+      required:
+      - value
+  abundance:
+    uniform:
+      type: object
+      additionalProperties: true
+      properties:
+        type:
+          enum:
+          - uniform

tardis/io/schemas/base.yml

@@ -5,9 +5,6 @@ properties:
   tardis_config_version:
     type: string
     description: Version of the configuration file. The current version is 1.0 and no other versions are allowed
-  csvy_model:
-    type: string
-    description: Path to the csvy model file.
   supernova:
     $ref: supernova.yml
     description: a section pertaining to observations of the supernova
@@ -17,9 +14,13 @@ properties:
   plasma:
     $ref: plasma.yml
     description: configuration of the plasma microphysics
+  csvy_model:
+    type: string
+    $ref: csvy_model.yml
+    description: defining the model using csvy format
   model:
     $ref: model.yml
-    description: defining the model
+    description: defining the model in the config yaml file
   montecarlo:
     $ref: montecarlo.yml
     description: configuring the physics of the monte carlo radiative transfer