Merge branch 'master' of https://github.com/rudrakshnalbalwar/tardis

.gitignore

@@ -71,3 +71,9 @@ pip-wheel-metadata/
 
 # Mac OSX
 .DS_Store
+
+# Visual Studio Code
+*.code-workspace
+
+# Random files
+.hypothesis/unicode_data/11.0.0/charmap.json.gz

.mailmap

@@ -66,6 +66,9 @@ Dhruv Sondhi <dhruvsondhi05@gmail.com> DhruvSondhi <dhruvsondhi05@gmail.com>
 Epson Heringer <epson.heringer@gmail.com>
 Epson Heringer <epson.heringer@gmail.com> Heringer-Epson <epson.heringer@gmail.com>
 
+Erin Visser <erin.visser1@gmail.com>
+Erin Visser <erin.visser1@gmail.com> erinvisser <erin.visser1@gmail.com>
+
 Ezequiel Pássaro <epassaro15@gmail.com>
 
 Frederik Beaujean <beaujean@mpp.mpg.de>

.zenodo.json

@@ -113,28 +113,28 @@
       "orcid": "0000-0002-8310-0829"
     },
     {
-      "name": "Sondhi, Dhruv"
+      "name": "Shields, Joshua"
     },
     {
-      "name": "O'Brien, Jack"
+      "name": "Barbosa, Talytha"
     },
     {
-      "name": "Barbosa, Talytha"
+      "name": "Sondhi, Dhruv"
     },
     {
-      "name": "Yu, Jenny"
+      "name": "O'Brien, Jack"
     },
     {
-      "name": "Shields, Joshua"
+      "name": "Yu, Jenny"
     },
     {
       "name": "Patel, Maryam"
     },
     {
-      "name": "Varanasi, Kaushik"
+      "name": "Rathi, Shikha"
     },
     {
-      "name": "Rathi, Shikha"
+      "name": "Varanasi, Kaushik"
     },
     {
       "name": "Chitchyan, Sona"
@@ -154,48 +154,45 @@
       "name": "Reinecke, Martin"
     },
     {
-      "name": "Eweis, Youssef"
+      "name": "Holas, Alexander"
     },
     {
-      "name": "Holas, Alexander"
+      "name": "Eweis, Youssef"
     },
     {
       "name": "Bylund, Tomas"
     },
     {
-      "name": "Black, William"
+      "name": "Bentil, Laud"
     },
     {
-      "name": "Bentil, Laud"
+      "name": "Black, William"
     },
     {
       "name": "Eguren, Jordi",
       "orcid": "0000-0002-2328-8030"
     },
     {
-      "name": "Bartnik, Matthew"
+      "name": "Kumar, Ansh"
     },
     {
       "name": "Alam, Arib"
     },
     {
-      "name": "Kumar, Ansh"
+      "name": "Bartnik, Matthew"
     },
     {
-      "name": "Varma Buddaraju, Rohith"
+      "name": "Magee, Mark"
     },
     {
-      "name": "Magee, Mark"
+      "name": "Varma Buddaraju, Rohith"
     },
     {
       "name": "Kambham, Satwik"
     },
     {
       "name": "Livneh, Ran"
     },
-    {
-      "name": "Rajagopalan, Srinath"
-    },
     {
       "name": "Daksh, Ayushi"
     },
@@ -204,37 +201,46 @@
       "orcid": "0000-0001-8302-1584"
     },
     {
-      "name": "Dutta, Anirban"
+      "name": "Rajagopalan, Srinath"
     },
     {
-      "name": "Floers, Andreas"
+      "name": "Dutta, Anirban"
     },
     {
       "name": "Jain, Rinkle"
     },
     {
-      "name": "Reichenbach, John"
+      "name": "Actions, GitHub"
     },
     {
-      "name": "Actions, GitHub"
+      "name": "Floers, Andreas"
+    },
+    {
+      "name": "Reichenbach, John"
     },
     {
       "name": "Bhakar, Jayant"
     },
     {
-      "name": "Brar, Antreev"
+      "name": "Singh, Sourav"
     },
     {
       "name": "Chaumal, Aarya"
     },
     {
-      "name": "Singh, Sourav"
+      "name": "Brar, Antreev"
     },
     {
-      "name": "Selsing, Jonatan"
+      "name": "Lu, Jing"
     },
     {
-      "name": "Kowalski, Nathan"
+      "name": "Matsumura, Yuki"
+    },
+    {
+      "name": "Talegaonkar, Chinmay"
+    },
+    {
+      "name": "Patidar, Abhishek"
     },
     {
       "name": "Kumar, Aman"
@@ -243,22 +249,19 @@
       "name": "Gupta, Harshul"
     },
     {
-      "name": "Talegaonkar, Chinmay"
+      "name": "Kowalski, Nathan"
     },
     {
-      "name": "Matsumura, Yuki"
+      "name": "Selsing, Jonatan"
     },
     {
       "name": "Sofiatti, Caroline"
     },
     {
-      "name": "Patidar, Abhishek"
+      "name": "Visser, Erin"
     },
     {
-      "name": "Venkat, Shashank"
-    },
-    {
-      "name": "Buchner, Johannes"
+      "name": "Prasad, Shilpi"
     },
     {
       "name": "Yap, Kevin"
@@ -279,10 +282,10 @@
       "name": "Sarafina, Nance"
     },
     {
-      "name": "Volodin, Dmitry"
+      "name": "Patra, Nilesh"
     },
     {
-      "name": "Patra, Nilesh"
+      "name": "Singh Rathore, Parikshit"
     },
     {
       "name": "Patel, Pratik"
@@ -291,10 +294,10 @@
       "name": "Sharma, Sampark"
     },
     {
-      "name": "Lu, Jing"
+      "name": "Venkat, Shashank"
     },
     {
-      "name": "Prasad, Shilpi"
+      "name": "Buchner, Johannes"
     },
     {
       "name": "Gupta, Suyash"
@@ -309,7 +312,7 @@
       "name": "Aggarwal, Yash"
     },
     {
-      "name": "Singh Rathore, Parikshit"
+      "name": "Volodin, Dmitry"
     },
     {
       "name": "Dasgupta, Debajyoti"
@@ -324,10 +327,10 @@
       "name": "Kolliboyina, Chaitanya"
     },
     {
-      "name": "Kumar, Atul"
+      "name": "Kharkar, Atharwa"
     },
     {
-      "name": "Kharkar, Atharwa"
+      "name": "Kumar, Atul"
     }
   ]
 }

docs/installation.rst

@@ -30,7 +30,7 @@ this method by following the steps described below.
 
   ::
 
-    $ wget -q https://github.com/tardis-sn/tardis/releases/latest/download/conda-{platform}-64.lock
+    $ wget -q https://raw.githubusercontent.com/tardis-sn/tardis/master/conda-{platform}-64.lock
 
 2. Create and activate the ``tardis`` environment.
 
@@ -39,29 +39,7 @@ this method by following the steps described below.
     $ conda create --name tardis --file conda-{platform}-64.lock
     $ conda activate tardis
 
-3. a. Non-developers can install the latest release from ``conda-forge`` with the ``--no-deps`` flag,
-
-      .. warning::
-
-        Currently the conda forge installation doesn't work. It's recommended to install from the specific releases using pip-
-
-        `$ pip install git+https://github.com/tardis-sn/tardis.git@{tag}`
-
-        For example- 
-
-        `pip install git+https://github.com/tardis-sn/tardis.git@release-2023.09.17`
-
-      ::
-
-        $ conda install tardis-sn --channel conda-forge --no-deps
-
-      or trying the most recent, unreleased changes from upstream.
-
-      ::
-
-        $ pip install git+https://github.com/tardis-sn/tardis.git@master
-
-   b. Instead, developers should `fork the repository <https://github.com/tardis-sn/tardis/fork>`_, configure
+3. a. Developers should `fork the repository <https://github.com/tardis-sn/tardis/fork>`_, configure
       GitHub to `work with SSH keys <https://docs.github.com/en/authentication/connecting-to-github-with-ssh>`_,
       set up the `upstream remote <https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/working-with-forks/configuring-a-remote-for-a-fork>`_,
       and install the package in development mode.
@@ -78,7 +56,24 @@ this method by following the steps described below.
       .. note::
 
         The complete developer guidelines can be found :ref:`here <developer_guidelines>`.
+
+    b. Non-developers can install from specific releases using pip-
+
+      ::
+
+        $ pip install git+https://github.com/tardis-sn/tardis.git@{tag}
+
+      For example- 
+
+      ::
+      
+        $ pip install git+https://github.com/tardis-sn/tardis.git@release-latest
+
+      or trying the most recent, unreleased changes from upstream.
 
+      ::
+
+        $ pip install git+https://github.com/tardis-sn/tardis.git@master
 
 4. Once finished working, you can deactivate your environment.
 
@@ -111,6 +106,7 @@ To update the environment after a new release, download the latest lockfile and
 
 ::
 
+    $ wget -q https://github.com/tardis-sn/tardis/releases/latest/download/conda-{platform}-64.lock
     $ conda update --name tardis --file conda-{platform}-64.lock
 
 .. note::

docs/io/configuration/components/plasma.rst

@@ -72,6 +72,22 @@ NLTE Ionization
 
     plasma:
         nlte_ionization_species: [H I, H II, He I, He II]
+        nlte_solver: root
     
 This option allows the user to specify which species should be included in the NLTE ionization treatment. Note that the
 species must be present in the continuum interaction species as well.
+Here, ``nlte_solver`` can be set to ``root`` or ``lu``. ``root`` is the default and uses a root solver to calculate the
+NLTE populations. ``lu`` uses an iterative LU decomposition scheme to calculate the NLTE populations.
+
+.. note ::
+
+   ``lu`` iterates over the solutions up to a set tolerance. This tolerance is currently hard-coded to 1e-3. This
+   can be changed in the code by changing the ``NLTE_POPULATION_SOLVER_TOLERANCE`` constant in ``tardis/plasma/properties/nlte_rate_equation_solver.py``.
+   Furthermore, the maximum number of iterations is set to 1000. This can be changed in the code by changing the ``NLTE_POPULATION_SOLVER_MAX_ITERATIONS``
+   constant in ``tardis/plasma/properties/nlte_rate_equation_solver.py``.
+
+.. warning ::
+
+    ``lu`` is generally faster than ``root`` but does not solve explicitly for the electron density. Therefore, it is
+    not recommended to use ``lu`` for simulations where the electron density is important (e.g. for simulations where
+    NLTE excitation is important).

docs/physics/montecarlo/initialization.ipynb

@@ -237,7 +237,7 @@
     "def planck_function(nu):\n",
     "    return (\n",
     "        8\n",
-    "        * np.pi**2\n",
+    "        * np.pi\n",
     "        * r_boundary_inner**2\n",
     "        * h\n",
     "        * nu**3\n",

docs/physics/update_and_conv/update_and_conv.ipynb

@@ -311,7 +311,7 @@
    },
    "outputs": [],
    "source": [
-    "j_estimator = transport.transport_state.estimators.j_estimator * (u.erg * u.cm) \n",
+    "j_estimator = transport.transport_state.j_estimator * (u.erg * u.cm) \n",
     "j_estimator"
    ]
   },
@@ -324,7 +324,7 @@
    },
    "outputs": [],
    "source": [
-    "nu_bar_estimator = transport.transport_state.estimators.nu_bar_estimator * (u.erg * u.cm * u.Hz)\n",
+    "nu_bar_estimator = transport.transport_state.nu_bar_estimator * (u.erg * u.cm * u.Hz)\n",
     "nu_bar_estimator"
    ]
   },

tardis/energy_input/tests/test_energy_source.py

@@ -1,6 +1,6 @@
-import pytest
 import numpy as np
 import numpy.testing as npt
+import pytest
 
 from tardis.energy_input.samplers import (
     create_energy_cdf,