Merge e285394 into 7f31e2b

tardis-sn · Feb 9, 2021 · 8f204bc · 8f204bc
2 parents 7f31e2b + e285394
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diff --git a/...sing/components/models/examples/abund.dat → ...components/models/abundancecust/abund.dat b/...sing/components/models/examples/abund.dat → ...components/models/abundancecust/abund.dat
diff --git a/...ponents/models/examples/abundancecust.rst → ...ts/models/abundancecust/abundancecust.rst b/...ponents/models/examples/abundancecust.rst → ...ts/models/abundancecust/abundancecust.rst
@@ -9,7 +9,7 @@ ASCII Format
 
 To use a stratified ejecta composition in TARDIS, the elemental abundances may
 be specified on a per-cell basis via an external ASCII file (similar to setting
-up a :doc:`custom density <densitycust>` profile). An ASCII file that could
+up a :ref:`custom density <densitycust>` profile). An ASCII file that could
 work on a mesh with ten cells should be formatted like this:
 
 .. literalinclude:: abund.dat

diff --git a/...ardis_configv1_abundance_cust_example.yml → ...ardis_configv1_abundance_cust_example.yml b/...ardis_configv1_abundance_cust_example.yml → ...ardis_configv1_abundance_cust_example.yml
diff --git a/...nfigv1_isotope_abundance_cust_example.yml → ...nfigv1_isotope_abundance_cust_example.yml b/...nfigv1_isotope_abundance_cust_example.yml → ...nfigv1_isotope_abundance_cust_example.yml
diff --git a/...ts/models/examples/tardis_model_abund.csv → ...dels/abundancecust/tardis_model_abund.csv b/...ts/models/examples/tardis_model_abund.csv → ...dels/abundancecust/tardis_model_abund.csv
diff --git a/...mponents/models/examples/abundanceuni.rst → ...ents/models/abundanceuni/abundanceuni.rst b/...mponents/models/examples/abundanceuni.rst → ...ents/models/abundanceuni/abundanceuni.rst
diff --git a/...is_configv1_abundance_uniform_example.yml → ...is_configv1_abundance_uniform_example.yml b/...is_configv1_abundance_uniform_example.yml → ...is_configv1_abundance_uniform_example.yml
diff --git a/...onents/models/examples/csvy_full_rad.csvy → ...sing/components/models/csvy_full_rad.csvy b/...onents/models/examples/csvy_full_rad.csvy → ...sing/components/models/csvy_full_rad.csvy
diff --git a/docs/using/components/models/csy/csvy_test.ipynb b/docs/using/components/models/csy/csvy_test.ipynb
diff --git a/...tom_Density_And_Boundary_Velocities.ipynb → ...tom_Density_And_Boundary_Velocities.ipynb b/...tom_Density_And_Boundary_Velocities.ipynb → ...tom_Density_And_Boundary_Velocities.ipynb
diff --git a/...ng/components/models/examples/density.dat → ...components/models/densitycust/density.dat b/...ng/components/models/examples/density.dat → ...components/models/densitycust/density.dat
diff --git a/...omponents/models/examples/densitycust.rst → ...onents/models/densitycust/densitycust.rst b/...omponents/models/examples/densitycust.rst → ...onents/models/densitycust/densitycust.rst
diff --git a/.../tardis_configv1_density_cust_example.yml → .../tardis_configv1_density_cust_example.yml b/.../tardis_configv1_density_cust_example.yml → .../tardis_configv1_density_cust_example.yml
diff --git a/...components/models/examples/test_abund.dat → ...ponents/models/densitycust/test_abund.dat b/...components/models/examples/test_abund.dat → ...ponents/models/densitycust/test_abund.dat
diff --git a/docs/yml_files/densitycust/test_config.yml → ...onents/models/densitycust/test_config.yml b/docs/yml_files/densitycust/test_config.yml → ...onents/models/densitycust/test_config.yml
diff --git a/...yml_files/densitycust/test_config_ex1.yml → ...ts/models/densitycust/test_config_ex1.yml b/...yml_files/densitycust/test_config_ex1.yml → ...ts/models/densitycust/test_config_ex1.yml
diff --git a/...yml_files/densitycust/test_config_ex2.yml → ...ts/models/densitycust/test_config_ex2.yml b/...yml_files/densitycust/test_config_ex2.yml → ...ts/models/densitycust/test_config_ex2.yml
diff --git a/...yml_files/densitycust/test_config_ex3.yml → ...ts/models/densitycust/test_config_ex3.yml b/...yml_files/densitycust/test_config_ex3.yml → ...ts/models/densitycust/test_config_ex3.yml
diff --git a/...mponents/models/examples/test_density.txt → ...nents/models/densitycust/test_density.txt b/...mponents/models/examples/test_density.txt → ...nents/models/densitycust/test_density.txt
diff --git a/...components/models/examples/densityexp.rst → ...mponents/models/densityexp/densityexp.rst b/...components/models/examples/densityexp.rst → ...mponents/models/densityexp/densityexp.rst
diff --git a/..._configv1_density_exponential_example.yml → ..._configv1_density_exponential_example.yml b/..._configv1_density_exponential_example.yml → ..._configv1_density_exponential_example.yml
diff --git a/...components/models/examples/densitypow.rst → ...mponents/models/densitypow/densitypow.rst b/...components/models/examples/densitypow.rst → ...mponents/models/densitypow/densitypow.rst
diff --git a/...is_configv1_density_power_law_example.yml → ...is_configv1_density_power_law_example.yml b/...is_configv1_density_power_law_example.yml → ...is_configv1_density_power_law_example.yml
diff --git a/docs/using/components/models/examples/examples.rst b/docs/using/components/models/examples/examples.rst
diff --git a/docs/using/components/models/examples/index.rst b/docs/using/components/models/examples/index.rst
diff --git a/docs/using/components/models/examples/modelconfig.rst b/docs/using/components/models/examples/modelconfig.rst
diff --git a/docs/using/components/models/examples/run_simple_example.ipynb b/docs/using/components/models/examples/run_simple_example.ipynb
@@ -1214,7 +1214,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.8"
+   "version": "3.7.8"
   }
  },
  "nbformat": 4,

diff --git a/docs/using/components/models/examples/tardis_example.rst b/docs/using/components/models/examples/tardis_example.rst
@@ -30,3 +30,11 @@ The following YAML file summarizes the tardis_example setup:
     treatments and the reduced abundance set, this TARDIS setup serves for
     illustrative purposes and not for detailed SNe Ia spectral synthesis
     calculations.
+
+See the following link for an example of running TARDIS with this setup in a Jupyter notebook:
+
+.. toctree::
+    :maxdepth: 1
+
+    run_simple_example
+
diff --git a/docs/using/components/models/index.rst b/docs/using/components/models/index.rst
@@ -1,6 +1,6 @@
-*****
-Model
-*****
+******
+Models
+******
 
 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.
@@ -11,6 +11,37 @@ the CSVY file format and :ref:`here <config-file>` for a link to the csvy_model
 .. note::
     We highly recommend using the cleaner CSVY format.
 
+
+The following provides some example setups for a number of typical TARDIS use
+cases. You can use these examples as blueprints for your own TARDIS
+applications.
+
+
+Simple Parametrized Models
+==========================
+
+These setups specify the ejecta solely via the YAML configuration file:
+
+.. toctree::
+    :maxdepth: 2
+
+    examples/tardis_example
+
+
+API demonstrations
+==================
+
+An example on how to use the formal integrator with tardis:
+
+* :ref:`integrator`
+
+
+Detailed Explosion Models
+=========================
+
+Coming soon
+
+
 CSVY Model
 ==========
 
@@ -33,7 +64,7 @@ Example CSVY Model
 
 Below we provide an example model.csvy file.
 
-.. literalinclude:: examples/csvy_full_rad.csvy
+.. literalinclude:: csvy_full_rad.csvy
 
 Using the Config Model
 ======================
@@ -46,10 +77,9 @@ see the following links:
 .. toctree::
     :maxdepth: 1
 
-    examples/modelconfig
-    examples/densityexp
-    examples/densitypow
-    examples/densitycust
-    examples/abundanceuni
-    examples/abundancecust
+    densityexp/densityexp
+    densitypow/densitypow
+    densitycust/densitycust
+    abundanceuni/abundanceuni
+    abundancecust/abundancecust