Merge 3235867 into 52534dc

docs/conf.py

@@ -53,8 +53,7 @@
 ## get's rid of many toctree contains errors: see https://github.com/phn/pytpm/issues/3#issuecomment-12133978
 numpydoc_show_class_members = False
 extensions += ['matplotlib.sphinxext.plot_directive',
-               'sphinxcontrib.bibtex',
-               'sphinxcontrib.tikz']
+               'sphinxcontrib.bibtex']
 
 
 

docs/default_config_parser.rst → docs/configuration/config_validator.rst

@@ -1,13 +1,13 @@
+***********************
+Configuration Validator
+***********************
 
-Default Configuration Parser
-============================
-
-The default config parser takes a user configuration and a default configuration and creates a consistent and valid configuration for tardis based on the constraints given in the default configuration.  Both input data are normally given as a yaml dictionary with a consistent hierarchical structure i.e. for every item in the user configuration there has to be a declaration in the default configuration  at the same hierarchical level. This declaration can be either an unspecific empty level declaration like:
+The default config validator takes a user configuration and a default configuration and creates a consistent and valid configuration for tardis based on the constraints given in the default configuration.  Both input data are normally given as a yaml dictionary with a consistent hierarchical structure i.e. for every item in the user configuration there has to be a declaration in the default configuration  at the same hierarchical level. This declaration can be either an unspecific empty level declaration like:
 - Main_level:
 	- Second_level:
 		- Third_level:
 			…
-Or a declaration of  a configuration item like:
+or a declaration of  a configuration item like:
 - item:
         - property_type: int
         - default: 1
@@ -24,10 +24,12 @@ Quantity_range: Like property type range but with quantities as start and stop.
 Additionally to the four standard keywords the types integer, float, and quantity can have the keywords allowed_value and allowed_type. allowed_value specifies the allowed values in a list, whereas allowed_type specifies a range of allowed values like “x>10”.
 
 Container
----------
+^^^^^^^^^
 
 For more complex configurations with dependencies, you can use the containers which allow branching in the configuration. A container is declared in the default configuration file by setting the  property_type to container property and specifying the properties of the container with keyword type. The property_type of this section is container-declaration which allows you to specify the possible container items with the keyword container. For every specified container item, the code expects the declaration of all sub items. The keywords for this are “_“ + “name of the container item”.
 If the type declaration for this container is finished you can specify all container items like normal items. Here is an example for a container configuration with two branches
+
+..source: yaml
 - container_example:
         - property_type: container-property
         - type:
@@ -62,10 +64,12 @@ If the type declaration for this container is finished you can specify all conta
                 - help:  Like property type range but with quantities as start and stop. The consistency of the units is checked.
 
 How to use
-----------
+^^^^^^^^^^
 
-To use the default parser create a new config object form the class Config by either from a dictionaries or from yaml files. 
-- My_config = Config(default configuration dictionary, user configuration dictionary)
+To use the default parser create a new config object form the class Config by either from a dictionaries or from yaml files::
+
+    My_config = Config(default configuration dictionary, user configuration dictionary)
+
 or
 - My_config = Config.from_yaml(default configuration file, user configuration file)
 To access the configuration for tardis use the method get_config 

docs/configuration/configuration.rst

@@ -0,0 +1,6 @@
+******************
+Configuration File
+******************
+
+.. literalinclude:: ../../tardis/data/tardis_config_definition.yml
+    :language: yaml

docs/configuration.rst → docs/configuration/configuration_old.rst

@@ -260,7 +260,7 @@ parameter ``lum_density`` which sets the distance to :math:`\sqrt{\frac{1}{4 \pi
 Config Reader
 ^^^^^^^^^^^^^
 
-The YAML file is read by using a classmethod of the :meth:`~tardis.config_reader.TARDISConfiguration.from_yaml`.
+The YAML file is read by using a classmethod of the :meth:`~tardis.config_reader.Configuration.from_yaml`.
 
 
 

docs/configuration/index.rst

@@ -0,0 +1,16 @@
+********************
+TARDIS Configuration
+********************
+
+Most of the configuration for TARDIS uses the YAML format. If a YAML file is
+handed to TARDIS it is first checked using a configuration validator to
+see if the required keywords of the required type exist and produces a dictionary
+with that has the validated types as well as sensible defaults for missing values
+built-in. This validator uses a default validation file that already explains
+a lot about the required configuration items.
+
+.. toctree::
+    :maxdepth: 1
+
+    configuration
+    config_validator

docs/index.rst

@@ -17,6 +17,7 @@ rapid spectral modelling of supernovae. The code is described in this documentat
     installation
     running
     uses
+    configuration/index
     examples/examples
     testing
     atomic/atomic_data

docs/physics/physical_quantities.rst

@@ -30,7 +30,7 @@ and then run your calculation, which is based on your "my_config.yml" file
     import logging
     import warnings
 
-    tardis_config = config_reader.TARDISConfiguration.from_yaml("my_config.yml")
+    tardis_config = config_reader.Configuration.from_yaml("my_config.yml")
     radial1d = model.Radial1DModel(tardis_config)
     simulation.run_radial1d(radial1d)
 

docs/physics/plasma.rst

@@ -24,11 +24,7 @@ description of the BasePlasma (for details see :ref:`nebular_plasma`).
 All plasma calculations follow the same basic procedure in calculating the plasma state.
 This is always accomplished with the function ``update_radiationfield``. This block diagram shows the basic procedure
 
-.. blockdiag::
 
-    blockdiag update_radfield{
-      calculate_partition_functions -> "calculate ge" -> calculate_saha -> "iterate over calculate_ionization_balance" -> calculate_level_populations;
-    }
 
 Base Plasma
 -----------

docs/running.rst

@@ -43,7 +43,7 @@ Scripting TARDIS
     from tardis import model, simulation
     from tardis.io import config_reader
 
-    tardis_config = config_reader.TARDISConfiguration.from_yaml('myconfig.yml')
+    tardis_config = config_reader.Configuration.from_yaml('myconfig.yml')
     radial1d_mdl = model.Radial1DModel(tardis_config)
     simulation.run_radial1d(radial1d_mdl)
 

scripts/tardis

@@ -53,7 +53,7 @@ if args.packet_log_file:
     console_handler.setFormatter(packet_logging_formatter)
     logger.addHandler(packet_logging_handler)
 
-tardis_config = config_reader.TARDISConfiguration.from_yaml(args.config_fname)
+tardis_config = config_reader.Configuration.from_yaml(args.config_fname)
 
 radial1d_mdl = model.Radial1DModel(tardis_config)
 

setup.cfg

@@ -8,5 +8,7 @@ upload-dir = docs/_build/html
 show-response = 1
 
 [pytest]
+doctest_plus=disabled
+doctest_rst=disabled
 minversion = 2.2
 norecursedirs = build docs/_build

tardis/data/tardis_default_config_definition.yml → tardis/data/tardis_config_definition.yml

@@ -24,7 +24,18 @@ supernova:
         default: None
         help: distance to supernova
 
-
+    luminosity_wavelength_start:
+        property_type: quantity
+        mandatory: False
+        default: 0 angstrom
+        help: start of the integral needed for getting the luminosity right
+
+
+    luminosity_wavelength_end:
+        property_type: quantity
+        mandatory: False
+        default: inf angstrom
+        help: start of the integral needed for getting the luminosity right
 
 atom_data:
     property_type: string
@@ -116,71 +127,99 @@ plasma:
 
 model:
     structure:
-      property_type : container-property
-      type:
-          property_type: container-declaration
-          containers: ['file', 'specific']
-          _file: ['filename','filetype']
-          +file: ['v_inner_boundary','v_outer_boundary']
-          _specific: ['specific-property']
-
-
-      filename:
-        property_type: string
-        default: None
-        mandatory: True
-        help: file name (with path) to structure model
+        property_type : container-property
+        type:
+            property_type: container-declaration
+            containers: ['file', 'specific']
+            _file: ['filename','filetype']
+            +file: ['v_inner_boundary','v_outer_boundary']
+            _specific: ['velocity', 'density']
 
-      filetype:
-        property_type: string
-        default: None
-        mandatory: True
-        help: file type
-        #### there are only a handful of types available how do we validate that ####
 
-
+        filename:
+            property_type: string
+            default: None
+            mandatory: True
+            help: file name (with path) to structure model
+
+        filetype:
+            property_type: string
+            default: None
+            allowed_value: ['simple_ascii', 'artis']
+            mandatory: True
+            help: file type
+
+        v_inner_boundary:
+            property_type: quantity
+            default: 0 km/s
+            mandatory: False
+            help: location of the inner boundary chosen from the model
+
+        v_outer_boundary:
+            property_type: quantity
+            default: inf km/s
+            mandatory: False
+            help: location of the inner boundary chosen from the model
+
+
+        velocity:
+            property_type: quantity_range_sampled
+            default: None
+            mandatory: True
+            help: description of the boundaries of the shells
+
+        density:
+            property_type: container-property
+            type:
+                property_type: container-declaration
+                containers: ['branch85_w7','exponential','power_law']
+                _branch85_w7: []
+                +branch85_w7: ['w7_time_0', 'w7_rho_0', 'w7_v_0']
+                _power_law: ['time_0', 'rho_0', 'v_0', 'exponent']
+                _exponential: ['time_0', 'rho_0', 'v_0']
+
+            w7_time_0:
+                property_type: quantity
+                default: 0.000231481 day
+                mandatory: False
+                help: This needs no change - DO NOT TOUCH
+
+            w7_rho_0:
+                property_type: quantity
+                default: 29.37505157 g/cm^3
+                mandatory: False
+                help: This needs no change - DO NOT TOUCH
+
+            w7_v_0:
+                property_type: quantity
+                default: 1e4 km/s
+                mandatory: False
+                help: This needs no change - DO NOT TOUCH
+
+            time_0:
+                property_type: quantity
+                default: None
+                mandatory: True
+                help: Time at which the pure model densities are right
+
+            rho_0:
+                property_type: quantity
+                default: None
+                mandatory: True
+                help: density at time_0
+
+            v_0:
+                property_type: quantity
+                default: None
+                mandatory: True
+                help: at what velocity the density rho_0 applies
+
+            exponent:
+                property_type: float
+                default: None
+                mandatory: True
+                help: exponent for exponential density profile
 
-      v_inner_boundary:
-        property_type: quantity
-        default: 0 km/s
-        mandatory: False
-        help: location of the inner boundary chosen from the model
-
-      v_outer_boundary:
-          property_type: quantity
-          default: inf km/s
-          mandatory: False
-          help: location of the inner boundary chosen from the model
-
-      specific_property:
-          velocity:
-              property_type: quantity_range
-              default: None
-              mandatory: True
-              help: location of boundaries in the velocity field. There will be n-1 cells as this specifis both the inner and outer velocity components
-
-
-          density:
-              property_type: container-property
-              type:
-                  property_type: container-declaration
-                  containers: ['branch85_w7']
-
-                  _branch85_w7: ['branch85_w7-property'] # list
-
-              branch85_w7-property:
-                  time_0:
-                      property_type: quantity
-                      default: 19.9999584 s
-                      mandatory: False
-                      help: This needs no change - DO NOT TOUCH
-
-                  density_coefficient:
-                      property_type: float
-                      default: 3e29
-                      mandatory: False
-                      help: This needs no change - DO NOT TOUCH
-
     abundances:
         property_type: container-property
         type:
@@ -228,7 +267,7 @@ montecarlo:
 
     black_body_sampling:
         property_type: quantity_range_sampled
-        default: [1 angstrom, 1e6 angstrom, 1e6 angstrom]
+        default: [1 angstrom, 1e6 angstrom, 1000000]
         mandatory: False
         help: Sampling of the black-body for energy packet creation (giving maximum and minimum packet frequency)
 
@@ -262,8 +301,8 @@ montecarlo:
         type:
             property_type: container-declaration
             containers: ['damped', 'specific']
-            _damped: ['damping_constant']
-            +damped: ['t_inner', 't_rad', 'w']
+            _damped: []
+            +damped: ['damping_constant', 't_inner', 't_rad', 'w']
             _specific: ['damping_constant', 'threshold', 'fraction', 'hold-iterations']
             +specific: ['t_inner', 't_rad', 'w']