From 93359cc7e926caa9b08ac47d43cdf6c9923b6480 Mon Sep 17 00:00:00 2001 From: Josh Shields Date: Fri, 14 Jun 2024 14:46:06 -0400 Subject: [PATCH 1/4] update installation instructions and small changes in physics_of_stardis --- docs/installation.rst | 8 +++++--- docs/physics/physics_of_stardis.rst | 4 ++-- 2 files changed, 7 insertions(+), 5 deletions(-) diff --git a/docs/installation.rst b/docs/installation.rst index 4fe6e16d..71886ae7 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -14,15 +14,16 @@ Setting Up the Environment * STARDIS packages and dependencies are distributed only through the `conda `__ package management system, therefore installation requires a conda distribution to be installed on your system. STARDIS uses `Miniconda `__ or `Mamba `__ by default. Other distributions are untested. STARDIS uses exclusively the packages in the TARDIS enviroment, as well -as using the TARDIS code itself. However, since STARDIS can be sensitive -to changes in TARDIS, we strongly suggest that users create a separate -environment for STARDIS that pins the TARDIS version. To do this, run +as using the TARDIS code itself. It uses a shared environment with TARDIS, +as well as the TARDIS code itself. We strongly suggest that users create a separate +environment for STARDIS. To do this, run the following in the terminal (replacing ``{platform}`` with ``linux-64``, ``linux-64-cuda``, or ``osx-64`` as applicable). .. code-block:: bash $ cd + $ wget -q https://raw.githubusercontent.com/tardis-sn/tardis/master/conda-{platform}.lock $ conda create --name stardis --file conda-{platform}.lock $ conda activate stardis $ pip install git+https://github.com/tardis-sn/tardis.git @@ -35,6 +36,7 @@ If you are using Mamba, the steps are similar: .. code-block:: bash $ cd + $ wget -q https://raw.githubusercontent.com/tardis-sn/tardis/master/conda-{platform}.lock $ mamba create --name stardis --file conda-{platform}.lock $ mamba activate stardis $ pip install git+https://github.com/tardis-sn/tardis.git diff --git a/docs/physics/physics_of_stardis.rst b/docs/physics/physics_of_stardis.rst index 8431d02a..68e544d9 100644 --- a/docs/physics/physics_of_stardis.rst +++ b/docs/physics/physics_of_stardis.rst @@ -6,7 +6,7 @@ Physics of STARDIS Model and Plasma ================ -STARDIS breaks down the stellar atmosphere into spherical shells as shown below and approximates that the plasma state is uniform throughout each shell. We rely on the MARCS code, a code that generates models of stellar atmospheres, to determine the temperatures, elemental abundances, and densities in each shell. The existing TARDIS plasma infrastructure determines the rest of the plasma state, namely the excitation and ionization properties and transition rates. +STARDIS breaks down the stellar atmosphere into spherically symmetric depth points as shown below and approximates that the plasma state is uniform at each radius or depth point. We ingest a model atmosphere from a third party such as the MARCS code, a code that generates models of stellar atmospheres, to initialize the temperatures, chemical abundances, and densities at each depth point. The existing TARDIS plasma infrastructure determines the rest of the plasma state, namely the excitation and ionization properties and transition rates of the plasma. .. image:: media/model_and_plasma-1.png :width: 500 px @@ -22,7 +22,7 @@ To determine an output spectrum, we need to understand how photons of light move Opacity Sources --------------- -The first four of these interactions are called continuum interactions, as they affect light at a large range of frequencies. Line interactions, on the other hand, only occur with light around specific frequencies, corresponding to the electron’s jump in energy. These are called *resonant frequencies*. +The first four of these interactions are called continuum interactions, as they affect light at a large range of frequencies. Line interactions, on the other hand, only occur with light around specific frequencies, corresponding to difference in potential energy of an electron before and after it transitions between states. These are called *resonant frequencies*. ^^^^^^^^^^^^^^^^^^^^^ Bound-Free Absorbtion From 3834faa73c1ad14e45aaa8d630cfbca1116bf280 Mon Sep 17 00:00:00 2001 From: Josh Shields Date: Fri, 14 Jun 2024 14:57:04 -0400 Subject: [PATCH 2/4] cleanup quickstart --- docs/quickstart/quickstart.ipynb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/quickstart/quickstart.ipynb b/docs/quickstart/quickstart.ipynb index c4665dcd..40b3fe2a 100644 --- a/docs/quickstart/quickstart.ipynb +++ b/docs/quickstart/quickstart.ipynb @@ -61,7 +61,7 @@ "\n", "from stardis.base import run_stardis\n", "\n", - "from astropy import units as u, constants as const" + "from astropy import units as u" ] }, { @@ -93,7 +93,7 @@ "source": [ "STARDIS uses [YAML](https://yaml.org/) files for the configuration. The configuration file called `stardis_example.yml` used here can be found\n", "[here](https://github.com/tardis-sn/stardis/tree/main/docs/quickstart),\n", - "along with any other files from this Quickstart. Below, we present an\n", + "along with the other files used in this Quickstart notebook. Below, we present an\n", "example for instructions for customizing the configuration for your\n", "needs.\n", "\n", @@ -102,7 +102,7 @@ "atom_data: \n", "model:\n", " type: marcs # more options will be available in the future\n", - " fname: \n", + " fname: \n", " final_atomic_number: # may be up to 30\n", "opacity:\n", " file: # reads a bound-free or free-free opacity file, omit if none\n", @@ -259,7 +259,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.17" + "version": "3.11.5" }, "toc": { "base_numbering": 1, From 34cbd56c990f622c217222c7cedafd034f14accb Mon Sep 17 00:00:00 2001 From: Josh Shields Date: Mon, 17 Jun 2024 11:18:06 -0400 Subject: [PATCH 3/4] update depth point description --- docs/physics/physics_of_stardis.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/physics/physics_of_stardis.rst b/docs/physics/physics_of_stardis.rst index 68e544d9..7b7473d1 100644 --- a/docs/physics/physics_of_stardis.rst +++ b/docs/physics/physics_of_stardis.rst @@ -6,7 +6,7 @@ Physics of STARDIS Model and Plasma ================ -STARDIS breaks down the stellar atmosphere into spherically symmetric depth points as shown below and approximates that the plasma state is uniform at each radius or depth point. We ingest a model atmosphere from a third party such as the MARCS code, a code that generates models of stellar atmospheres, to initialize the temperatures, chemical abundances, and densities at each depth point. The existing TARDIS plasma infrastructure determines the rest of the plasma state, namely the excitation and ionization properties and transition rates of the plasma. +STARDIS assumes that the stellar atmosphere is spherically symmetric and breaks down the stellar atmosphere into radial depth points, as shown below, and then solves the plasma state at those depth points. We ingest a model atmosphere from a third party such as the MARCS code, a code that generates models of stellar atmospheres, to initialize the temperatures, chemical abundances, and densities at each depth point. The existing TARDIS plasma infrastructure determines the rest of the plasma state, namely the excitation and ionization properties and transition rates of the plasma. .. image:: media/model_and_plasma-1.png :width: 500 px From 4a24777eabdd060cdd13beaac939786f6835b49e Mon Sep 17 00:00:00 2001 From: Josh Shields Date: Mon, 17 Jun 2024 11:57:11 -0400 Subject: [PATCH 4/4] further basic stardis explanation --- docs/physics/physics_of_stardis.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/physics/physics_of_stardis.rst b/docs/physics/physics_of_stardis.rst index 7b7473d1..cc95869e 100644 --- a/docs/physics/physics_of_stardis.rst +++ b/docs/physics/physics_of_stardis.rst @@ -6,7 +6,7 @@ Physics of STARDIS Model and Plasma ================ -STARDIS assumes that the stellar atmosphere is spherically symmetric and breaks down the stellar atmosphere into radial depth points, as shown below, and then solves the plasma state at those depth points. We ingest a model atmosphere from a third party such as the MARCS code, a code that generates models of stellar atmospheres, to initialize the temperatures, chemical abundances, and densities at each depth point. The existing TARDIS plasma infrastructure determines the rest of the plasma state, namely the excitation and ionization properties and transition rates of the plasma. +STARDIS assumes that the stellar atmosphere is spherically symmetric. It solves the state of the plasma at specific depth points throughout the atmosphere, as shown below, before moving light through the plasma. STARDIS ingests a model atmosphere from a third party such as the MARCS code, a code that generates models of stellar atmospheres, to initialize the temperatures, chemical abundances, and densities at each depth point. The code then determines the rest of the plasma, namely the states of the chemicals that compose the plasma, and uses that to understand how the plasma interacts with light. .. image:: media/model_and_plasma-1.png :width: 500 px