From 7c699d68ee145e46f391c33c1273d66ca32c2065 Mon Sep 17 00:00:00 2001 From: Wolfgang Kerzendorf Date: Fri, 19 Jul 2019 16:11:54 -0400 Subject: [PATCH] large restructure --- docs/atomic/atomic_data.rst | 8 +++++--- docs/index.rst | 4 +++- ...ustom_Density_And_Boundary_Velocities-checkpoint.ipynb | 0 .../examples/Custom_Density_And_Boundary_Velocities.ipynb | 0 docs/{ => models}/examples/abund.dat | 0 docs/{ => models}/examples/abundancecust.rst | 0 docs/{ => models}/examples/abundanceuni.rst | 0 docs/{ => models}/examples/density.dat | 0 docs/{ => models}/examples/densitycust.rst | 0 docs/{ => models}/examples/densityexp.rst | 0 docs/{ => models}/examples/densitypow.rst | 0 docs/{ => models}/examples/examples.rst | 0 docs/{ => models}/examples/index.rst | 0 docs/{ => models}/examples/integrator.ipynb | 0 docs/{ => models}/examples/mesa.stella.dat | 0 docs/{ => models}/examples/modelconfig.rst | 0 docs/{ => models}/examples/run_simple_example.ipynb | 0 docs/{ => models}/examples/stella_to_tardis.ipynb | 0 .../examples/tardis_configv1_abundance_cust_example.yml | 0 .../tardis_configv1_abundance_uniform_example.yml | 0 .../examples/tardis_configv1_density_cust_example.yml | 0 .../tardis_configv1_density_exponential_example.yml | 0 .../tardis_configv1_density_power_law_example.yml | 0 .../tardis_configv1_isotope_abundance_cust_example.yml | 0 docs/{ => models}/examples/tardis_example.rst | 0 docs/{ => models}/examples/tardis_example.yml | 0 docs/{ => models}/examples/tardis_model_abund.csv | 0 docs/{ => models}/examples/test_abund.dat | 0 docs/{ => models}/examples/test_density.txt | 0 docs/quickstart.rst | 2 +- docs/running/index.rst | 3 ++- 31 files changed, 11 insertions(+), 6 deletions(-) rename docs/{ => models}/examples/.ipynb_checkpoints/Custom_Density_And_Boundary_Velocities-checkpoint.ipynb (100%) rename docs/{ => models}/examples/Custom_Density_And_Boundary_Velocities.ipynb (100%) rename docs/{ => models}/examples/abund.dat (100%) rename docs/{ => models}/examples/abundancecust.rst (100%) rename docs/{ => models}/examples/abundanceuni.rst (100%) rename docs/{ => models}/examples/density.dat (100%) rename docs/{ => models}/examples/densitycust.rst (100%) rename docs/{ => models}/examples/densityexp.rst (100%) rename docs/{ => models}/examples/densitypow.rst (100%) rename docs/{ => models}/examples/examples.rst (100%) rename docs/{ => models}/examples/index.rst (100%) rename docs/{ => models}/examples/integrator.ipynb (100%) rename docs/{ => models}/examples/mesa.stella.dat (100%) rename docs/{ => models}/examples/modelconfig.rst (100%) rename docs/{ => models}/examples/run_simple_example.ipynb (100%) rename docs/{ => models}/examples/stella_to_tardis.ipynb (100%) rename docs/{ => models}/examples/tardis_configv1_abundance_cust_example.yml (100%) rename docs/{ => models}/examples/tardis_configv1_abundance_uniform_example.yml (100%) rename docs/{ => models}/examples/tardis_configv1_density_cust_example.yml (100%) rename docs/{ => models}/examples/tardis_configv1_density_exponential_example.yml (100%) rename docs/{ => models}/examples/tardis_configv1_density_power_law_example.yml (100%) rename docs/{ => models}/examples/tardis_configv1_isotope_abundance_cust_example.yml (100%) rename docs/{ => models}/examples/tardis_example.rst (100%) rename docs/{ => models}/examples/tardis_example.yml (100%) rename docs/{ => models}/examples/tardis_model_abund.csv (100%) rename docs/{ => models}/examples/test_abund.dat (100%) rename docs/{ => models}/examples/test_density.txt (100%) 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/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 `_ subpackage. A simple +`Carsus `_ subpackage. A quick start guide +to run TARDIS can be found `here ` Information regarding running and operating Tardis.