large restructure

tardis-sn · Jul 19, 2019 · 7c699d6 · 7c699d6
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diff --git a/docs/atomic/atomic_data.rst b/docs/atomic/atomic_data.rst
@@ -1,8 +1,10 @@
 .. _atomic-data-download:
 
-**********************
-Atomic Data for TARDIS
-**********************
+***********
+Atomic Data
+***********
+
+The Atom Database for TARDIS is generated by the
 
 .. toctree::
     atomic_data_description

diff --git a/docs/index.rst b/docs/index.rst
@@ -59,7 +59,9 @@ Physics of TARDIS
     :maxdepth: 2
     :caption: The Physics of TARDIS
 
-    physics/index
+    Physics overview <physics/index>
+    physics/plasma/index
+    physics/montecarlo/index
 
 ====
 Team

diff --git a/..._And_Boundary_Velocities-checkpoint.ipynb → ..._And_Boundary_Velocities-checkpoint.ipynb b/..._And_Boundary_Velocities-checkpoint.ipynb → ..._And_Boundary_Velocities-checkpoint.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/docs/examples/abund.dat → docs/models/examples/abund.dat b/docs/examples/abund.dat → docs/models/examples/abund.dat
diff --git a/docs/examples/abundancecust.rst → docs/models/examples/abundancecust.rst b/docs/examples/abundancecust.rst → docs/models/examples/abundancecust.rst
diff --git a/docs/examples/abundanceuni.rst → docs/models/examples/abundanceuni.rst b/docs/examples/abundanceuni.rst → docs/models/examples/abundanceuni.rst
diff --git a/docs/examples/density.dat → docs/models/examples/density.dat b/docs/examples/density.dat → docs/models/examples/density.dat
diff --git a/docs/examples/densitycust.rst → docs/models/examples/densitycust.rst b/docs/examples/densitycust.rst → docs/models/examples/densitycust.rst
diff --git a/docs/examples/densityexp.rst → docs/models/examples/densityexp.rst b/docs/examples/densityexp.rst → docs/models/examples/densityexp.rst
diff --git a/docs/examples/densitypow.rst → docs/models/examples/densitypow.rst b/docs/examples/densitypow.rst → docs/models/examples/densitypow.rst
diff --git a/docs/examples/examples.rst → docs/models/examples/examples.rst b/docs/examples/examples.rst → docs/models/examples/examples.rst
diff --git a/docs/examples/index.rst → docs/models/examples/index.rst b/docs/examples/index.rst → docs/models/examples/index.rst
diff --git a/docs/examples/integrator.ipynb → docs/models/examples/integrator.ipynb b/docs/examples/integrator.ipynb → docs/models/examples/integrator.ipynb
diff --git a/docs/examples/mesa.stella.dat → docs/models/examples/mesa.stella.dat b/docs/examples/mesa.stella.dat → docs/models/examples/mesa.stella.dat
diff --git a/docs/examples/modelconfig.rst → docs/models/examples/modelconfig.rst b/docs/examples/modelconfig.rst → docs/models/examples/modelconfig.rst
diff --git a/docs/examples/run_simple_example.ipynb → .../models/examples/run_simple_example.ipynb b/docs/examples/run_simple_example.ipynb → .../models/examples/run_simple_example.ipynb
diff --git a/docs/examples/stella_to_tardis.ipynb → docs/models/examples/stella_to_tardis.ipynb b/docs/examples/stella_to_tardis.ipynb → docs/models/examples/stella_to_tardis.ipynb
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/...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/.../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/..._configv1_density_exponential_example.yml → ..._configv1_density_exponential_example.yml b/..._configv1_density_exponential_example.yml → ..._configv1_density_exponential_example.yml
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/...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/docs/examples/tardis_example.rst → docs/models/examples/tardis_example.rst b/docs/examples/tardis_example.rst → docs/models/examples/tardis_example.rst
diff --git a/docs/examples/tardis_example.yml → docs/models/examples/tardis_example.yml b/docs/examples/tardis_example.yml → docs/models/examples/tardis_example.yml
diff --git a/docs/examples/tardis_model_abund.csv → docs/models/examples/tardis_model_abund.csv b/docs/examples/tardis_model_abund.csv → docs/models/examples/tardis_model_abund.csv
diff --git a/docs/examples/test_abund.dat → docs/models/examples/test_abund.dat b/docs/examples/test_abund.dat → docs/models/examples/test_abund.dat
diff --git a/docs/examples/test_density.txt → docs/models/examples/test_density.txt b/docs/examples/test_density.txt → docs/models/examples/test_density.txt
diff --git a/docs/quickstart.rst b/docs/quickstart.rst
@@ -1,4 +1,4 @@
-.. _running:
+.. _quickstart:
 
 ****************
 Quickstart Guide

diff --git a/docs/running/index.rst b/docs/running/index.rst
@@ -4,7 +4,8 @@ Running TARDIS
 
 The TARDIS code needs three components to calculate spectra: 1) an Atom Database
 2) a model 3) a configuration file. The Atom Database is created by the
-`Carsus <https://tardis-sn.github.io/carsus/>`_ subpackage. A simple
+`Carsus <https://tardis-sn.github.io/carsus/>`_ subpackage. A quick start guide
+to run TARDIS can be found `here <quickstart>`
 
 Information regarding running and operating Tardis.