diff --git a/docs/atomic/atomic_data.rst b/docs/atomic/atomic_data.rst
index 8ac87a7aa72..7f46c848a7a 100644
--- 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
index abd9f095fe9..b15039158a4 100644
--- 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/docs/examples/.ipynb_checkpoints/Custom_Density_And_Boundary_Velocities-checkpoint.ipynb b/docs/models/examples/.ipynb_checkpoints/Custom_Density_And_Boundary_Velocities-checkpoint.ipynb
similarity index 100%
rename from docs/examples/.ipynb_checkpoints/Custom_Density_And_Boundary_Velocities-checkpoint.ipynb
rename to docs/models/examples/.ipynb_checkpoints/Custom_Density_And_Boundary_Velocities-checkpoint.ipynb
diff --git a/docs/examples/Custom_Density_And_Boundary_Velocities.ipynb b/docs/models/examples/Custom_Density_And_Boundary_Velocities.ipynb
similarity index 100%
rename from docs/examples/Custom_Density_And_Boundary_Velocities.ipynb
rename to docs/models/examples/Custom_Density_And_Boundary_Velocities.ipynb
diff --git a/docs/examples/abund.dat b/docs/models/examples/abund.dat
similarity index 100%
rename from docs/examples/abund.dat
rename to docs/models/examples/abund.dat
diff --git a/docs/examples/abundancecust.rst b/docs/models/examples/abundancecust.rst
similarity index 100%
rename from docs/examples/abundancecust.rst
rename to docs/models/examples/abundancecust.rst
diff --git a/docs/examples/abundanceuni.rst b/docs/models/examples/abundanceuni.rst
similarity index 100%
rename from docs/examples/abundanceuni.rst
rename to docs/models/examples/abundanceuni.rst
diff --git a/docs/examples/density.dat b/docs/models/examples/density.dat
similarity index 100%
rename from docs/examples/density.dat
rename to docs/models/examples/density.dat
diff --git a/docs/examples/densitycust.rst b/docs/models/examples/densitycust.rst
similarity index 100%
rename from docs/examples/densitycust.rst
rename to docs/models/examples/densitycust.rst
diff --git a/docs/examples/densityexp.rst b/docs/models/examples/densityexp.rst
similarity index 100%
rename from docs/examples/densityexp.rst
rename to docs/models/examples/densityexp.rst
diff --git a/docs/examples/densitypow.rst b/docs/models/examples/densitypow.rst
similarity index 100%
rename from docs/examples/densitypow.rst
rename to docs/models/examples/densitypow.rst
diff --git a/docs/examples/examples.rst b/docs/models/examples/examples.rst
similarity index 100%
rename from docs/examples/examples.rst
rename to docs/models/examples/examples.rst
diff --git a/docs/examples/index.rst b/docs/models/examples/index.rst
similarity index 100%
rename from docs/examples/index.rst
rename to docs/models/examples/index.rst
diff --git a/docs/examples/integrator.ipynb b/docs/models/examples/integrator.ipynb
similarity index 100%
rename from docs/examples/integrator.ipynb
rename to docs/models/examples/integrator.ipynb
diff --git a/docs/examples/mesa.stella.dat b/docs/models/examples/mesa.stella.dat
similarity index 100%
rename from docs/examples/mesa.stella.dat
rename to docs/models/examples/mesa.stella.dat
diff --git a/docs/examples/modelconfig.rst b/docs/models/examples/modelconfig.rst
similarity index 100%
rename from docs/examples/modelconfig.rst
rename to docs/models/examples/modelconfig.rst
diff --git a/docs/examples/run_simple_example.ipynb b/docs/models/examples/run_simple_example.ipynb
similarity index 100%
rename from docs/examples/run_simple_example.ipynb
rename to docs/models/examples/run_simple_example.ipynb
diff --git a/docs/examples/stella_to_tardis.ipynb b/docs/models/examples/stella_to_tardis.ipynb
similarity index 100%
rename from docs/examples/stella_to_tardis.ipynb
rename to docs/models/examples/stella_to_tardis.ipynb
diff --git a/docs/examples/tardis_configv1_abundance_cust_example.yml b/docs/models/examples/tardis_configv1_abundance_cust_example.yml
similarity index 100%
rename from docs/examples/tardis_configv1_abundance_cust_example.yml
rename to docs/models/examples/tardis_configv1_abundance_cust_example.yml
diff --git a/docs/examples/tardis_configv1_abundance_uniform_example.yml b/docs/models/examples/tardis_configv1_abundance_uniform_example.yml
similarity index 100%
rename from docs/examples/tardis_configv1_abundance_uniform_example.yml
rename to docs/models/examples/tardis_configv1_abundance_uniform_example.yml
diff --git a/docs/examples/tardis_configv1_density_cust_example.yml b/docs/models/examples/tardis_configv1_density_cust_example.yml
similarity index 100%
rename from docs/examples/tardis_configv1_density_cust_example.yml
rename to docs/models/examples/tardis_configv1_density_cust_example.yml
diff --git a/docs/examples/tardis_configv1_density_exponential_example.yml b/docs/models/examples/tardis_configv1_density_exponential_example.yml
similarity index 100%
rename from docs/examples/tardis_configv1_density_exponential_example.yml
rename to docs/models/examples/tardis_configv1_density_exponential_example.yml
diff --git a/docs/examples/tardis_configv1_density_power_law_example.yml b/docs/models/examples/tardis_configv1_density_power_law_example.yml
similarity index 100%
rename from docs/examples/tardis_configv1_density_power_law_example.yml
rename to docs/models/examples/tardis_configv1_density_power_law_example.yml
diff --git a/docs/examples/tardis_configv1_isotope_abundance_cust_example.yml b/docs/models/examples/tardis_configv1_isotope_abundance_cust_example.yml
similarity index 100%
rename from docs/examples/tardis_configv1_isotope_abundance_cust_example.yml
rename to docs/models/examples/tardis_configv1_isotope_abundance_cust_example.yml
diff --git a/docs/examples/tardis_example.rst b/docs/models/examples/tardis_example.rst
similarity index 100%
rename from docs/examples/tardis_example.rst
rename to docs/models/examples/tardis_example.rst
diff --git a/docs/examples/tardis_example.yml b/docs/models/examples/tardis_example.yml
similarity index 100%
rename from docs/examples/tardis_example.yml
rename to docs/models/examples/tardis_example.yml
diff --git a/docs/examples/tardis_model_abund.csv b/docs/models/examples/tardis_model_abund.csv
similarity index 100%
rename from docs/examples/tardis_model_abund.csv
rename to docs/models/examples/tardis_model_abund.csv
diff --git a/docs/examples/test_abund.dat b/docs/models/examples/test_abund.dat
similarity index 100%
rename from docs/examples/test_abund.dat
rename to docs/models/examples/test_abund.dat
diff --git a/docs/examples/test_density.txt b/docs/models/examples/test_density.txt
similarity index 100%
rename from docs/examples/test_density.txt
rename to docs/models/examples/test_density.txt
diff --git a/docs/quickstart.rst b/docs/quickstart.rst
index fb9e0177b0b..3f96fc3ab9b 100644
--- 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
index b35e0643c61..8a2c9616be6 100644
--- 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.