From e10fa236b4d8a481edd0177f02c20db5c0733a3b Mon Sep 17 00:00:00 2001 From: smithis7 Date: Wed, 2 Jun 2021 21:25:22 -0400 Subject: [PATCH 01/24] moving files --- .../components/atomic/atomic_data.rst | 0 .../components/atomic/atomic_data_description.rst | 0 .../components/atomic/current_public_table.rst | 0 .../configuration/components}/configuration.rst | 0 .../models}/Custom_TARDIS_Model_Tutorial.ipynb | 0 .../components/models/abundancecust/abund.dat | 0 .../models/abundancecust/abundancecust.rst | 0 .../tardis_configv1_abundance_cust_example.yml | 0 ...rdis_configv1_isotope_abundance_cust_example.yml | 0 .../models/abundancecust/tardis_model_abund.csv | 0 .../components/models/abundanceuni/abundanceuni.rst | 0 .../tardis_configv1_abundance_uniform_example.yml | 0 .../components/models}/converters/cmfgen.rst | 0 .../components/models}/converters/index.rst | 0 .../components/models}/converters/mesa.stella.dat | 0 .../models}/converters/stella_to_tardis.ipynb | 0 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docs/io/images/line_info_widget_demo.gif diff --git a/docs/io/images/images/sdec_ply_interaction.gif b/docs/io/images/sdec_ply_interaction.gif similarity index 100% rename from docs/io/images/images/sdec_ply_interaction.gif rename to docs/io/images/sdec_ply_interaction.gif diff --git a/docs/io/images/images/shell_info_widget_demo.gif b/docs/io/images/shell_info_widget_demo.gif similarity index 100% rename from docs/io/images/images/shell_info_widget_demo.gif rename to docs/io/images/shell_info_widget_demo.gif diff --git a/docs/physics/spectralsynthesis.rst b/docs/physics/spectralsynthesis.rst deleted file mode 100644 index fdc90f105f9..00000000000 --- a/docs/physics/spectralsynthesis.rst +++ /dev/null @@ -1,5 +0,0 @@ -*********************************** -Spectrum formation in SNe Ia ejecta -*********************************** - -Hopefully coming soon diff --git a/docs/physics/tardisprocedure.rst b/docs/physics/tardisprocedure.rst deleted file mode 100644 index 030435d30d4..00000000000 --- a/docs/physics/tardisprocedure.rst +++ /dev/null @@ -1,5 +0,0 @@ -*************************** -TARDIS simulation procedure -*************************** - -Hopefully coming soon. diff --git a/docs/using/components/index.rst b/docs/using/components/index.rst deleted file mode 100644 index 825c448c06b..00000000000 --- a/docs/using/components/index.rst +++ /dev/null @@ -1,17 +0,0 @@ -*********** -Components -*********** - -The TARDIS code needs three components to calculate spectra: - - -.. toctree:: - :maxdepth: 1 - - configuration/index - models/index - atomic/atomic_data - - -A quick start guide to run TARDIS can be found -`here <../../quickstart/quickstart.ipynb>`_. \ No newline at end of file diff --git a/docs/using/interaction/index.rst b/docs/using/interaction/index.rst deleted file mode 100644 index 38c9d7cff93..00000000000 --- a/docs/using/interaction/index.rst +++ /dev/null @@ -1,28 +0,0 @@ -Additional Interactivity -========================= - -To get more information from each run of TARDIS, one can run it interactively and -have full access to the model properties (as described in :ref:`physical_quantities`). - -.. toctree:: - :maxdepth: 1 - - - commandline - callback_example - converters/index - Custom_TARDIS_Model_Tutorial - custom_source - old_gui - access - init_trad_bug - integrator - isotope_pd_subclass - to_hdf.rst - hdf_writer - physical_quantities - using_formal_integral - -.. examples/run_simple_example.ipynb - - diff --git a/docs/using/visualization/tardis_example.yml b/docs/using/visualization/tardis_example.yml deleted file mode 120000 index 665fe53411f..00000000000 --- a/docs/using/visualization/tardis_example.yml +++ /dev/null @@ -1 +0,0 @@ -../../tardis_example.yml \ No newline at end of file From f53e4bdd258d5cde14f1e844fb4b23b925cbfac3 Mon Sep 17 00:00:00 2001 From: smithis7 Date: Fri, 4 Jun 2021 12:53:01 -0400 Subject: [PATCH 03/24] outdated section --- docs/outdated/index.rst | 24 ++++++++++++++++++++++++ docs/outdated/openmp.rst | 26 ++++++++++++++++++++++++++ 2 files changed, 50 insertions(+) create mode 100644 docs/outdated/index.rst create mode 100644 docs/outdated/openmp.rst diff --git a/docs/outdated/index.rst b/docs/outdated/index.rst new file mode 100644 index 00000000000..e77efcd1051 --- /dev/null +++ b/docs/outdated/index.rst @@ -0,0 +1,24 @@ +******************************* +Outdated Documentation Sections +******************************* + +The following pages are no longer relevant to the most recent release of TARDIS: + +.. warning:: Please update to a newer version of TARDIS. + +.. toctree:: + + commandline + old_gui + openmp + + +The following pages are no longer applicable to the TARDIS documentation in its current form, but will be edited +and incorporated back into the documentation in the future: + +.. toctree:: + + init_trad_bug + isotope_pd_subclass + integrator + using_formal_integral \ No newline at end of file diff --git a/docs/outdated/openmp.rst b/docs/outdated/openmp.rst new file mode 100644 index 00000000000..97f191712ff --- /dev/null +++ b/docs/outdated/openmp.rst @@ -0,0 +1,26 @@ +****************************** +Parallel execution with OpenMP +****************************** + +.. note:: TARDIS no longer uses C, and thus OpenMP is not relevant to TARDIS. + +Enabling parallel execution with OpenMP +======================================== + +Manually, cloning the repository enables other options such as running the code in parallel (enabling OpenMP). +In general, we encourage downloading the compilers from `conda` as we then can ensure that they work with TARDIS. +Within the TARDIS conda environment do:: + + conda install -c conda-forge compilers + +For macOS:: + + conda install -c conda-forge llvm-openmp + +For Linux:: + + conda install -c conda-forge openmp + +To compile TARDIS for parallel execution:: + + python setup.py install --with-openmp \ No newline at end of file From cd814f921889603a07944257cf2a101e03ef3117 Mon Sep 17 00:00:00 2001 From: smithis7 Date: Fri, 4 Jun 2021 16:40:14 -0400 Subject: [PATCH 04/24] creating new files --- docs/outdated/index.rst | 1 + docs/outdated/old_install.rst | 56 +++++++++++++++++++++++++++++ docs/physics/est_and_conv/index.rst | 3 ++ docs/physics/montecarlo/index.rst | 6 ++-- docs/physics/setup/index.rst | 3 ++ docs/physics/spectrum/index.rst | 3 ++ 6 files changed, 69 insertions(+), 3 deletions(-) create mode 100644 docs/outdated/old_install.rst create mode 100644 docs/physics/est_and_conv/index.rst create mode 100644 docs/physics/setup/index.rst create mode 100644 docs/physics/spectrum/index.rst diff --git a/docs/outdated/index.rst b/docs/outdated/index.rst index e77efcd1051..bff30781497 100644 --- a/docs/outdated/index.rst +++ b/docs/outdated/index.rst @@ -11,6 +11,7 @@ The following pages are no longer relevant to the most recent release of TARDIS: commandline old_gui openmp + old_install The following pages are no longer applicable to the TARDIS documentation in its current form, but will be edited diff --git a/docs/outdated/old_install.rst b/docs/outdated/old_install.rst new file mode 100644 index 00000000000..26bbea58ef5 --- /dev/null +++ b/docs/outdated/old_install.rst @@ -0,0 +1,56 @@ +************************** +Outdated Installation FAQs +************************** + +We highly encourage with any installation problems to try the recommended install +method because this often fixes problems. Here are some common problems when +installing and their fixes: + +**Problem:** While building TARDIS via ``python setup.py`` build you +may encounter the following error:: + + error: tardis/montecarlo/montecarlo.c: Could not find C file tardis/montecarlo/montecarlo.c for Cython file tardis/montecarlo/montecarlo.pyx when building extension tardis.montecarlo.montecarlo. Cython must be installed to build from a git checkout. + + +**Solution:** There are several solutions to this problem. A clean checkout will +help. To clean up your repository please try ``python setup.py clean`` and +then ``git clean -dfx`` (**WARNING** will delete any non-TARDIS file in that directory) +This will often clean this problem. If it still persists: + +Go into the tardis/montecarlo directory and build montecarlo.c by hand:: + + cython montecarlo.pyx + +Then, ``python setup.py build`` should run without problems. + + +**Problem:** when trying to set up CC=gcc python setup.py develop --with-openmp the following error popped up: +from tardis/_compiler.c:1: /Users/yssavo/miniconda2/envs/tardis-show2/lib/gcc/x86_64-apple-darwin13.4.0/5.2.0/include-fixed/limits.h:168:61: fatal error: limits.h: No such file or directory + +**Solution:** Run on terminal: + + open /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg + +**Problem:** Symbol not found: _GOMP_parallel when compiling with `--with-openmp` + +**Solution:** Install gcc8 from macports and then install with these flags: `link_args = ['-fopenmp','-Wl,-rpath,/opt/local/lib/gcc8/']` + +**Problem:** While building TARDIS (via python 2.7) via ``python setup.py`` build you +may encounter the following error:: + + TypeError: super() argument 1 must be type, not None + + ---------------------------------------- + Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-req-build-wPB39p/ + + +**Solution:** The cause for this problem is Sphinx or Sphinx version. It can be easily solved by installing Sphinx 1.5.6. + The command for the same is : + + pip install sphinx==1.5.6 + + or + + conda install sphinx==1.5.6 + +Then, ``python setup.py build install`` should run without problems. diff --git a/docs/physics/est_and_conv/index.rst b/docs/physics/est_and_conv/index.rst new file mode 100644 index 00000000000..7e4f6bf8b1e --- /dev/null +++ b/docs/physics/est_and_conv/index.rst @@ -0,0 +1,3 @@ +************************** +Estimators and Convergence +************************** \ No newline at end of file diff --git a/docs/physics/montecarlo/index.rst b/docs/physics/montecarlo/index.rst index 9f5c3faf8c5..ff20445dab0 100644 --- a/docs/physics/montecarlo/index.rst +++ b/docs/physics/montecarlo/index.rst @@ -1,6 +1,6 @@ -****************** -Monte Carlo Primer -****************** +********************* +Monte Carlo Iteration +********************* The following pages provide a very basic introduction to Monte Carlo radiative transfer techniques as they are used in TARDIS. All the information listed here diff --git a/docs/physics/setup/index.rst b/docs/physics/setup/index.rst new file mode 100644 index 00000000000..9e3cb3f2295 --- /dev/null +++ b/docs/physics/setup/index.rst @@ -0,0 +1,3 @@ +******************** +Setting Up SOMETHING +******************** \ No newline at end of file diff --git a/docs/physics/spectrum/index.rst b/docs/physics/spectrum/index.rst new file mode 100644 index 00000000000..568cb3fc96e --- /dev/null +++ b/docs/physics/spectrum/index.rst @@ -0,0 +1,3 @@ +******************* +Spectrum Generation +******************* \ No newline at end of file From 172e2108411cc216800c6cbda78700e46ca147e3 Mon Sep 17 00:00:00 2001 From: smithis7 Date: Mon, 7 Jun 2021 12:23:24 -0400 Subject: [PATCH 05/24] lots of file changes --- .../components/configuration.rst | 12 +- docs/io/configuration/components/index.rst | 197 +++ .../models}/tardis_example.yml | 0 .../configuration/components/schemas/schemas | 1 - .../tardis_example.rst => example.rst} | 20 +- .../examples/run_simple_example.ipynb | 1222 ----------------- docs/io/configuration/index.rst | 20 +- docs/io/configuration/tardis_example.yml | 1 + docs/io/optional/tardis_example.yml | 1 + docs/io/output/tardis_example.yml | 57 + 10 files changed, 279 insertions(+), 1252 deletions(-) create mode 100644 docs/io/configuration/components/index.rst rename docs/io/configuration/{examples => components/models}/tardis_example.yml (100%) delete mode 120000 docs/io/configuration/components/schemas/schemas rename docs/io/configuration/{examples/tardis_example.rst => example.rst} (69%) delete mode 100644 docs/io/configuration/examples/run_simple_example.ipynb create mode 120000 docs/io/configuration/tardis_example.yml create mode 120000 docs/io/optional/tardis_example.yml create mode 100644 docs/io/output/tardis_example.yml diff --git a/docs/io/configuration/components/configuration.rst b/docs/io/configuration/components/configuration.rst index cacf5f927ac..bbfc8cc04ab 100644 --- a/docs/io/configuration/components/configuration.rst +++ b/docs/io/configuration/components/configuration.rst @@ -1,8 +1,8 @@ -.. _config-file: +.. _config-components: -****************** -Configuration File -****************** +************************ +Configuration Components +************************ TARDIS uses the `YAML markup language `_ for its configuration files. There are several sections which allow different @@ -29,10 +29,10 @@ schemas to show what options are available. Our schema mark-up defines names in Configuration Schema ==================== -.. jsonschema:: schemas/base.yml +.. jsonschema:: schemas/schemas/base.yml -The base schema links to several other configuration parts +The base schema links to several other configuration parts. Supernova diff --git a/docs/io/configuration/components/index.rst b/docs/io/configuration/components/index.rst new file mode 100644 index 00000000000..6ba92382731 --- /dev/null +++ b/docs/io/configuration/components/index.rst @@ -0,0 +1,197 @@ +.. _config-components: + +***************************** +Configuration File Components +***************************** + +TARDIS uses the `YAML markup language `_ +for its configuration files. There are several sections which allow different +settings for the different aspects of the TARDIS calculation. An example +configuration file (with a small subset of the options that can be specified) can be downloaded at `example_yml`_. + +.. warning:: + One should note that currently floats in YAML need to be specified in a special format: + any pure floats need to have a +/- after the "e", e.g. 2e+5 + + +The TARDIS configuration consists of multiple sections that pertain to certain parts of the code. We will use the +schemas to show what options are available. Our schema mark-up defines names in bold-fat as required and can be seen here: + +.. note:: + + The following shows all the options (and their default settings) that are available for TARDIS. No other options + are allowed or available. + + +.. contents:: Overview + :local: + +Configuration Schema +==================== + +.. jsonschema:: schemas/base.yml + + +The base schema links to several other configuration parts + + +Supernova +--------- + +.. jsonschema:: schemas/supernova.yml + + +Model +----- + +The next sections, describing the model, are very hierarchical. The base level is ``model`` and contains two subsections: +``structure`` and ``abundances``. Both sections can either contain a ``file`` subsection that specifies a file and +file type where the information is stored or a number of other sections. + +.. jsonschema:: schemas/model.yml + +Abundances +^^^^^^^^^^ +The ``abundance`` section has a possible ``file`` parameter with ``type`` (currently only ``artis`` is allowed) +and a ``name`` parameter giving a path to a file containing the abundance information. + +.. warning:: + In contrast to the ``structure`` section, the ``abundance`` section will not ignore abundances set in the rest of + the section but merely will overwrite the abundances given in the file section. + +The rest of the section can be used to configure uniform abundances for all shells, by giving the atom name and a +relative abundance fraction. If it does not add up to 1., TARDIS will warn --- but normalize the numbers. + + +.. jsonschema:: schemas/model_definitions.yml#/definitions/abundances/file + +.. jsonschema:: schemas/model_definitions.yml#/definitions/abundances/uniform + +Structure +^^^^^^^^^ +All types of ``structure`` definitions have two keywords in common: ``v_inner_boundary`` and ``v_outer_boundary``. + +In the ``structure`` section, one can specify a ``file`` section containing a ``type`` parameter +(currently only ``artis`` is supported``) and a ``name`` parameter giving a path top a file. + +If one doesn't specify a ``file`` section, the code requires two sections (``velocities`` and ``densities``) and a +parameter ``no_of_shells``. ``no_of_shells`` is the requested number of shells for a model. The ``velocity`` section +requires a ``type``. Currently, only ``linear`` is supported. + +.. jsonschema:: schemas/model_definitions.yml#/definitions/structure/file + +.. jsonschema:: schemas/model_definitions.yml#/definitions/structure/specific + +Densities +""""""""" +In the ``densities`` section the ``type`` parameter again decides on the parameters. The type ``uniform`` only needs a +``value`` parameter with a density compatible quantity. The type ``branch85_w7`` uses a seven-order polynomial fit to +the W7 model and is parametrised by time since explosion. The parameters ``time_0`` and ``density_coefficient`` are set +to sensible defaults and should not be changed. + +.. jsonschema:: schemas/model_definitions.yml#/definitions/density/branch85_w7 + +.. jsonschema:: schemas/model_definitions.yml#/definitions/density/exponential + +.. jsonschema:: schemas/model_definitions.yml#/definitions/density/power_law + +.. jsonschema:: schemas/model_definitions.yml#/definitions/density/uniform + + +Plasma +------ + +.. jsonschema:: schemas/plasma.yml + +``inital_t_inner`` is initial temperature (will be updated for most modes of TARDIS --- see convergence section) of the black-body on the inner +boundary. ``initial_t_rad`` is the initial radiation temperature (will be updated for most modes of TARDIS - see convergence section). For debugging purposes and to compare to +:term:`synapps` calculations one can disable the electron scattering. TARDIS will issue a warning that this is not physical. +There are currently two ``plasma_type`` options available: ``nebular`` and ``lte``, which tell TARDIS how to run the +ionization equilibrium and level population calculations (see :ref:`plasma` for more information). +The radiative rates describe how to calculate the :math:`J_\textrm{blue}` needed for the :ref:`nlte` calculations and +:ref:`macroatom` calculations. There are three options for ``radiative_rates_type``: + +1) ``lte``, in which +:math:`J_\textrm{blue} = \textrm{Blackbody}(T_\textrm{rad})` + +2) ``nebular`` in which +:math:`J_\textrm{blue} = W \times \textrm{Blackbody}(T_\textrm{rad})` + +3) ``detailed`` in which the :math:`J_\textrm{blue}` +are calculated using an estimator (this is described in ??????). + +TARDIS currently supports three different kinds of line interaction: ``scatter`` --- a resonance scattering implementation, +``macroatom`` --- the most complex form of line interaction described in :ref:`macroatom` and ``downbranch`` a simplified +version of ``macroatom`` in which only downward transitions are allowed. + +Finally, ``w_epsilon`` describes the dilution factor to use to calculate :math:`J_\textrm{blue}` that are 0, which +causes problemsl with the code (so :math:`J_\textrm{blue}` are set to a very small number). + +NLTE +^^^^ + +.. code-block:: yaml + + nlte: + coronal_approximation: True + classical_nebular: False + +The NLTE configuration currently allows setting ``coronal_approximation``, which sets all :math:`J_\textrm{blue}` to 0. +This is useful for debugging with :term:`chianti` for example. Furthermore, one can enable 'classical_nebular' to set all +:math:`\beta_\textrm{Sobolev}` to 1. Both options are used for checking with other codes and should not be enabled in +normal operations. + + + +Monte Carlo +----------- + +The ``montecarlo`` section describes the parameters for the Monte Carlo radiation transport and convergence criteria: + +.. jsonschema:: schemas/montecarlo.yml + +.. jsonschema:: schemas/montecarlo_definitions.yml#/definitions/convergence_strategy/damped + +.. jsonschema:: schemas/montecarlo_definitions.yml#/definitions/convergence_strategy/custom + +The ``seed`` parameter seeds the random number generator first for the creation of the packets +(:math:`\nu` and :math:`\mu`) and then the interactions in the actual Monte Carlo process. +The ``no_of_packets`` parameter can take a float number for input convenience and gives the number of packets normally +used in each Monte Carlo loop. The parameters ``last_no_of_packets`` and ``no_of_virtual_packets`` influence the last run +of the Monte Carlo loop (which calculates the final spectrum!) when the radiation field should have converged. ``last_no_of_packets`` is normally higher than +``no_of_packets`` to create a less noisy output spectrum. ``no_of_virtual_packets`` can also be set to greater than 0 (a useful number is 3) to +use the Virtual Packet formalism. Increasing this number drastically increases computational costs (and memory requirements if they are logged). +The ``iterations`` parameter describes the maximum number of Monte Carlo loops executed in a simulation before it ends. Convergence criteria can be used to make the simulation stop +sooner when the convergence threshold has been reached. + +The ``convergence_criteria`` section again has a ``type`` keyword. Currently, one type is allowed: ``damped``. +All convergence criteria can be specified separately for the three variables for which convergence can be checked +(``t_inner``, ``t_rad``, ``ws``) by specifying subsections in the ``convergence_criteria`` of the same name. These then +override the defaults. + + +``damped`` only has one parameter ``damping-constant`` and does not check for convergence. This can be used to fix the +temperature of the inner boundary (by increasing the ``convergence_criteria`` and + + + +Spectrum +-------- + +.. jsonschema:: schemas/spectrum.yml + +``Start`` and ``end`` are given as Quantities with units. If they are given in +frequency space they are switched around if necessary. The number of bins is +just an integer. Finally, the method option selects the final spectral synthesis mode. Currently, there are three options: + +* real: construct spectrum from the real packet population alone +* virtual: use the :doc:`virtual packet scheme <../../../physics/montecarlo/virtualpackets>` for spectral synthesis +* integrated: use the :doc:`formal integral method <../../../physics/montecarlo/sourceintegration>` of Lucy 1999 + +.. warning:: + Currently, the "integrated" mode only works with the downbranching line + interaction mode. Note also the limitations listed at the bottom of the + dedicated page. + + +.. include:: ../../example_data.inc \ No newline at end of file diff --git a/docs/io/configuration/examples/tardis_example.yml b/docs/io/configuration/components/models/tardis_example.yml similarity index 100% rename from docs/io/configuration/examples/tardis_example.yml rename to docs/io/configuration/components/models/tardis_example.yml diff --git a/docs/io/configuration/components/schemas/schemas b/docs/io/configuration/components/schemas/schemas deleted file mode 120000 index 5bf8c07dd59..00000000000 --- a/docs/io/configuration/components/schemas/schemas +++ /dev/null @@ -1 +0,0 @@ -../../../../tardis/io/schemas \ No newline at end of file diff --git a/docs/io/configuration/examples/tardis_example.rst b/docs/io/configuration/example.rst similarity index 69% rename from docs/io/configuration/examples/tardis_example.rst rename to docs/io/configuration/example.rst index 5ab53d5435e..2e1b0b91d86 100644 --- a/docs/io/configuration/examples/tardis_example.rst +++ b/docs/io/configuration/example.rst @@ -1,11 +1,11 @@ -tardis_example --------------- +**************************** +Tardis Example Configuration +**************************** The simple and fast TARDIS setup is provided by ``tardis_example.yml`` which -may be obtained from `tardis-setups -`_ repository. It is located in -the ``tardis-setups/2014/2014_kerzendorf_sim/appendix_A1`` subfolder. We suggest every new user of TARDIS to run this -setup first. +may be obtained `here +`_. We suggest every new user of TARDIS to run this +setup first, which can be donw using the :ref:`quickstart guide `. It calculates a spectrum for a Type Ia supernova model 13 days after explosion, requesting a total output luminosity of @@ -30,11 +30,3 @@ The following YAML file summarizes the tardis_example setup: treatments and the reduced abundance set, this TARDIS setup serves for illustrative purposes and not for detailed SNe Ia spectral synthesis calculations. - -See the following link for an example of running TARDIS with this setup in a Jupyter notebook: - -.. toctree:: - :maxdepth: 1 - - run_simple_example - diff --git a/docs/io/configuration/examples/run_simple_example.ipynb b/docs/io/configuration/examples/run_simple_example.ipynb deleted file mode 100644 index 212e922e371..00000000000 --- a/docs/io/configuration/examples/run_simple_example.ipynb +++ /dev/null @@ -1,1222 +0,0 @@ -{ - "cells": [ - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "### Simple Jupyter TARDIS Example ###" - ] - }, - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "/Users/wkerzend/miniconda/envs/tardis3/lib/python3.6/site-packages/tqdm/autonotebook/__init__.py:14: TqdmExperimentalWarning: Using `tqdm.autonotebook.tqdm` in notebook mode. Use `tqdm.tqdm` instead to force console mode (e.g. in jupyter console)\n", - " \" (e.g. in jupyter console)\", TqdmExperimentalWarning)\n" - ] - } - ], - "source": [ - "from tardis import run_tardis\n", - "from tardis.io.atom_data.util import download_atom_data" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[\u001b[1mtardis.io.atom_data.atom_web_download\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Downloading atomic data from https://media.githubusercontent.com/media/tardis-sn/tardis-refdata/master/atom_data/kurucz_cd23_chianti_H_He.h5 to /Users/wkerzend/projects/tardis/tardis-data/kurucz_cd23_chianti_H_He.h5 (\u001b[1matom_web_download.py\u001b[0m:37)\n" - ] - }, - { - "data": { - "application/vnd.jupyter.widget-view+json": { - "model_id": "33dd6796be49474b81854df7f5cf0778", - "version_major": 2, - "version_minor": 0 - }, - "text/plain": [ - "HBox(children=(IntProgress(value=0, description='kurucz_cd23_chianti_H_He.h5', max=73704476, style=ProgressSty…" - ] - }, - "metadata": {}, - "output_type": "display_data" - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "\n" - ] - } - ], - "source": [ - "# the data is automatically downloaded\n", - "download_atom_data('kurucz_cd23_chianti_H_He')" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[\u001b[1mtardis.plasma.standard_plasmas\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Reading Atomic Data from kurucz_cd23_chianti_H_He.h5 (\u001b[1mstandard_plasmas.py\u001b[0m:76)\n", - "[\u001b[1mtardis.io.atom_data.util\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Atom Data kurucz_cd23_chianti_H_He.h5 not found in local path. Exists in TARDIS Data repo /Users/wkerzend/projects/tardis/tardis-data/kurucz_cd23_chianti_H_He.h5 (\u001b[1mutil.py\u001b[0m:29)\n", - "[\u001b[1mpy.warnings \u001b[0m][\u001b[1;33mWARNING\u001b[0m] /Users/wkerzend/miniconda/envs/tardis3/lib/python3.6/site-packages/IPython/core/interactiveshell.py:3267: PerformanceWarning: indexing past lexsort depth may impact performance.\n", - " exec(code_obj, self.user_global_ns, self.user_ns)\n", - " (\u001b[1mwarnings.py\u001b[0m:99)\n", - "[\u001b[1mtardis.io.atom_data.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Read Atom Data with UUID=6f7b09e887a311e7a06b246e96350010 and MD5=864f1753714343c41f99cb065710cace. (\u001b[1mbase.py\u001b[0m:175)\n", - "[\u001b[1mtardis.io.atom_data.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Non provided atomic data: synpp_refs, ion_cx_th_data, ion_cx_sp_data (\u001b[1mbase.py\u001b[0m:178)\n", - "[\u001b[1mpy.warnings \u001b[0m][\u001b[1;33mWARNING\u001b[0m] /Users/wkerzend/miniconda/envs/tardis3/lib/python3.6/site-packages/astropy/units/quantity.py:1067: AstropyDeprecationWarning: The truth value of a Quantity is ambiguous. In the future this will raise a ValueError.\n", - " AstropyDeprecationWarning)\n", - " (\u001b[1mwarnings.py\u001b[0m:99)\n", - "[\u001b[1mpy.warnings \u001b[0m][\u001b[1;33mWARNING\u001b[0m] /Users/wkerzend/python/tardis/tardis/plasma/properties/ion_population.py:59: FutureWarning: \n", - "Passing list-likes to .loc or [] with any missing label will raise\n", - "KeyError in the future, you can use .reindex() as an alternative.\n", - "\n", - "See the documentation here:\n", - "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", - " partition_function.index].dropna())\n", - " (\u001b[1mwarnings.py\u001b[0m:99)\n", - "[\u001b[1mpy.warnings \u001b[0m][\u001b[1;33mWARNING\u001b[0m] /Users/wkerzend/miniconda/envs/tardis3/lib/python3.6/site-packages/astropy/units/equivalencies.py:90: RuntimeWarning: divide by zero encountered in double_scalars\n", - " (si.m, si.Hz, lambda x: _si.c.value / x),\n", - " (\u001b[1mwarnings.py\u001b[0m:99)\n", - "[\u001b[1mpy.warnings \u001b[0m][\u001b[1;33mWARNING\u001b[0m] /Users/wkerzend/miniconda/envs/tardis3/lib/python3.6/site-packages/astropy/units/quantity.py:1067: AstropyDeprecationWarning: The truth value of a Quantity is ambiguous. In the future this will raise a ValueError.\n", - " AstropyDeprecationWarning)\n", - " (\u001b[1mwarnings.py\u001b[0m:99)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 1/20 (\u001b[1mbase.py\u001b[0m:266)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 7.96915e+42 erg / s Luminosity absorbed = 2.63370e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:357)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n", - "\t t_rad next_t_rad w next_w\n", - "\tShell \n", - "\t0 9926.501965 10171.209103 0.400392 0.500372\n", - "\t5 9852.611678 10306.111379 0.211205 0.191331\n", - "\t10 9779.813302 10174.379204 0.142695 0.116864\n", - "\t15 9708.082813 9910.442275 0.104556 0.085962\n", - "\n", - " (\u001b[1mbase.py\u001b[0m:348)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 9933.952 K -- next t_inner 11453.040 K (\u001b[1mbase.py\u001b[0m:350)\n", - "[\u001b[1mpy.warnings \u001b[0m][\u001b[1;33mWARNING\u001b[0m] /Users/wkerzend/python/tardis/tardis/plasma/properties/ion_population.py:59: FutureWarning: \n", - "Passing list-likes to .loc or [] with any missing label will raise\n", - "KeyError in the future, you can use .reindex() as an alternative.\n", - "\n", - "See the documentation here:\n", - "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", - " partition_function.index].dropna())\n", - " (\u001b[1mwarnings.py\u001b[0m:99)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 2/20 (\u001b[1mbase.py\u001b[0m:266)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 1.40398e+43 erg / s Luminosity absorbed = 4.68639e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:357)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n", - "\t t_rad next_t_rad w next_w\n", - "\tShell \n", - "\t0 10171.209103 11518.516702 0.500372 0.538298\n", - "\t5 10306.111379 11554.412119 0.191331 0.217946\n", - "\t10 10174.379204 11373.574056 0.116864 0.132935\n", - "\t15 9910.442275 11040.788763 0.085962 0.099700\n", - "\n", - " (\u001b[1mbase.py\u001b[0m:348)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 11453.040 K -- next t_inner 9948.201 K (\u001b[1mbase.py\u001b[0m:350)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 3/20 (\u001b[1mbase.py\u001b[0m:266)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 8.16814e+42 erg / s Luminosity absorbed = 2.50161e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:357)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n", - "\t t_rad next_t_rad w next_w\n", - "\tShell \n", - "\t0 11518.516702 10501.129902 0.538298 0.438591\n", - "\t5 11554.412119 10869.940791 0.217946 0.160809\n", - "\t10 11373.574056 10558.269547 0.132935 0.103807\n", - "\t15 11040.788763 10185.648701 0.099700 0.079165\n", - "\n", - " (\u001b[1mbase.py\u001b[0m:348)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 9948.201 K -- next t_inner 11328.896 K (\u001b[1mbase.py\u001b[0m:350)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 4/20 (\u001b[1mbase.py\u001b[0m:266)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 1.34487e+43 erg / s Luminosity absorbed = 4.47931e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:357)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n", - "\t t_rad next_t_rad w next_w\n", - "\tShell \n", - "\t0 10501.129902 11527.008679 0.438591 0.512509\n", - "\t5 10869.940791 11706.138980 0.160809 0.196458\n", - "\t10 10558.269547 11444.208532 0.103807 0.124092\n", - "\t15 10185.648701 11085.857161 0.079165 0.093694\n", - "\n", - " (\u001b[1mbase.py\u001b[0m:348)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 11328.896 K -- next t_inner 10054.300 K (\u001b[1mbase.py\u001b[0m:350)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 5/20 (\u001b[1mbase.py\u001b[0m:266)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 8.44348e+42 erg / s Luminosity absorbed = 2.68000e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:357)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n", - "\t t_rad next_t_rad w next_w\n", - "\tShell \n", - "\t0 11527.008679 10659.382763 0.512509 0.433573\n", - "\t5 11706.138980 11038.244897 0.196458 0.158494\n", - "\t10 11444.208532 10790.696726 0.124092 0.099660\n", - "\t15 11085.857161 10450.666394 0.093694 0.074550\n", - "\n", - " (\u001b[1mbase.py\u001b[0m:348)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 10054.300 K -- next t_inner 11261.489 K (\u001b[1mbase.py\u001b[0m:350)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 6/20 (\u001b[1mbase.py\u001b[0m:266)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 1.32492e+43 erg / s Luminosity absorbed = 4.26229e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:357)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n", - "\t t_rad next_t_rad w next_w\n", - "\tShell \n", - "\t0 10659.382763 11507.437689 0.433573 0.499441\n", - "\t5 11038.244897 11634.568776 0.158494 0.197953\n", - "\t10 10790.696726 11418.594559 0.099660 0.124085\n", - "\t15 10450.666394 10999.619473 0.074550 0.094676\n", - "\n", - " (\u001b[1mbase.py\u001b[0m:348)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 11261.489 K -- next t_inner 10069.444 K (\u001b[1mbase.py\u001b[0m:350)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 7/20 (\u001b[1mbase.py\u001b[0m:266)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 8.49858e+42 erg / s Luminosity absorbed = 2.69247e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:357)\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n", - "\t t_rad next_t_rad w next_w\n", - "\tShell \n", - "\t0 11507.437689 10679.650246 0.499441 0.431088\n", - "\t5 11634.568776 11048.266431 0.197953 0.157179\n", - "\t10 11418.594559 10825.714870 0.124085 0.098608\n", - "\t15 10999.619473 10506.321595 0.094676 0.073794\n", - "\n", - " (\u001b[1mbase.py\u001b[0m:348)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 10069.444 K -- next t_inner 11241.826 K (\u001b[1mbase.py\u001b[0m:350)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 8/20 (\u001b[1mbase.py\u001b[0m:266)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 1.30632e+43 erg / s Luminosity absorbed = 4.31719e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:357)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n", - "\t t_rad next_t_rad w next_w\n", - "\tShell \n", - "\t0 10679.650246 11459.828312 0.431088 0.506176\n", - "\t5 11048.266431 11688.139012 0.157179 0.193468\n", - "\t10 10825.714870 11441.768967 0.098608 0.122412\n", - "\t15 10506.321595 11099.449886 0.073794 0.090915\n", - "\n", - " (\u001b[1mbase.py\u001b[0m:348)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 11241.826 K -- next t_inner 10123.177 K (\u001b[1mbase.py\u001b[0m:350)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 9/20 (\u001b[1mbase.py\u001b[0m:266)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 8.68357e+42 erg / s Luminosity absorbed = 2.75015e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:357)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n", - "\t t_rad next_t_rad w next_w\n", - "\tShell \n", - "\t0 11459.828312 10666.223660 0.506176 0.445097\n", - "\t5 11688.139012 11000.288585 0.193468 0.163424\n", - "\t10 11441.768967 10822.884326 0.122412 0.101641\n", - "\t15 11099.449886 10384.181273 0.090915 0.078432\n", - "\n", - " (\u001b[1mbase.py\u001b[0m:348)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 10123.177 K -- next t_inner 11180.783 K (\u001b[1mbase.py\u001b[0m:350)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 10/20 (\u001b[1mbase.py\u001b[0m:266)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 1.28170e+43 erg / s Luminosity absorbed = 4.19511e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:357)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n", - "\t t_rad next_t_rad w next_w\n", - "\tShell \n", - "\t0 10666.223660 11427.410445 0.445097 0.500788\n", - "\t5 11000.288585 11612.349822 0.163424 0.193129\n", - "\t10 10822.884326 11373.245169 0.101641 0.121622\n", - "\t15 10384.181273 11047.955461 0.078432 0.090937\n", - "\n", - " (\u001b[1mbase.py\u001b[0m:348)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 11180.783 K -- next t_inner 10164.432 K (\u001b[1mbase.py\u001b[0m:350)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 11/20 (\u001b[1mbase.py\u001b[0m:266)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 8.79074e+42 erg / s Luminosity absorbed = 2.82804e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:357)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n", - "\t t_rad next_t_rad w next_w\n", - "\tShell \n", - "\t0 11427.410445 10741.337822 0.500788 0.439938\n", - "\t5 11612.349822 11230.515356 0.193129 0.153637\n", - "\t10 11373.245169 10870.696315 0.121622 0.101050\n", - "\t15 11047.955461 10538.170159 0.090937 0.074680\n", - "\n", - " (\u001b[1mbase.py\u001b[0m:348)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 10164.432 K -- next t_inner 11157.711 K (\u001b[1mbase.py\u001b[0m:350)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 12/20 (\u001b[1mbase.py\u001b[0m:266)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 1.27128e+43 erg / s Luminosity absorbed = 4.15415e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:357)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n", - "\t t_rad next_t_rad w next_w\n", - "\tShell \n", - "\t0 10741.337822 11507.877578 0.439938 0.483114\n", - "\t5 11230.515356 11808.852053 0.153637 0.181826\n", - "\t10 10870.696315 11557.412757 0.101050 0.113563\n", - "\t15 10538.170159 11117.762050 0.074680 0.087418\n", - "\n", - " (\u001b[1mbase.py\u001b[0m:348)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 11157.711 K -- next t_inner 10184.966 K (\u001b[1mbase.py\u001b[0m:350)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 13/20 (\u001b[1mbase.py\u001b[0m:266)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 8.90399e+42 erg / s Luminosity absorbed = 2.80864e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:357)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n", - "\t t_rad next_t_rad w next_w\n", - "\tShell \n", - "\t0 11507.877578 10727.217531 0.483114 0.443706\n", - "\t5 11808.852053 11171.758889 0.181826 0.160824\n", - "\t10 11557.412757 10971.722637 0.113563 0.098588\n", - "\t15 11117.762050 10574.916600 0.087418 0.075266\n", - "\n", - " (\u001b[1mbase.py\u001b[0m:348)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 10184.966 K -- next t_inner 11108.923 K (\u001b[1mbase.py\u001b[0m:350)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 14/20 (\u001b[1mbase.py\u001b[0m:266)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 1.25052e+43 erg / s Luminosity absorbed = 4.07335e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:357)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n", - "\t t_rad next_t_rad w next_w\n", - "\tShell \n", - "\t0 10727.217531 11413.626870 0.443706 0.489526\n", - "\t5 11171.758889 11697.006992 0.160824 0.184795\n", - "\t10 10971.722637 11424.445844 0.098588 0.116722\n", - "\t15 10574.916600 11047.434163 0.075266 0.088067\n", - "\n", - " (\u001b[1mbase.py\u001b[0m:348)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 11108.923 K -- next t_inner 10224.266 K (\u001b[1mbase.py\u001b[0m:350)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 15/20 (\u001b[1mbase.py\u001b[0m:266)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 9.00727e+42 erg / s Luminosity absorbed = 2.88724e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:357)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n", - "\t t_rad next_t_rad w next_w\n", - "\tShell \n", - "\t0 11413.626870 10712.622749 0.489526 0.455660\n", - "\t5 11697.006992 11125.894032 0.184795 0.164091\n", - "\t10 11424.445844 10816.390451 0.116722 0.104037\n", - "\t15 11047.434163 10421.687097 0.088067 0.080401\n", - "\n", - " (\u001b[1mbase.py\u001b[0m:348)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 10224.266 K -- next t_inner 11087.666 K (\u001b[1mbase.py\u001b[0m:350)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 16/20 (\u001b[1mbase.py\u001b[0m:266)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 1.23781e+43 erg / s Luminosity absorbed = 4.07435e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:357)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n", - "\t t_rad next_t_rad w next_w\n", - "\tShell \n", - "\t0 10712.622749 11352.158138 0.455660 0.500754\n", - "\t5 11125.894032 11644.968350 0.164091 0.185289\n", - "\t10 10816.390451 11320.695930 0.104037 0.119195\n", - "\t15 10421.687097 10965.228363 0.080401 0.089940\n", - "\n", - " (\u001b[1mbase.py\u001b[0m:348)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 11087.666 K -- next t_inner 10256.946 K (\u001b[1mbase.py\u001b[0m:350)\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 17/20 (\u001b[1mbase.py\u001b[0m:266)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 9.18956e+42 erg / s Luminosity absorbed = 2.86249e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:357)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n", - "\t t_rad next_t_rad w next_w\n", - "\tShell \n", - "\t0 11352.158138 10738.799194 0.500754 0.452965\n", - "\t5 11644.968350 11210.269586 0.185289 0.160945\n", - "\t10 11320.695930 10911.463205 0.119195 0.103910\n", - "\t15 10965.228363 10545.065525 0.089940 0.078433\n", - "\n", - " (\u001b[1mbase.py\u001b[0m:348)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 10256.946 K -- next t_inner 11012.230 K (\u001b[1mbase.py\u001b[0m:350)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 18/20 (\u001b[1mbase.py\u001b[0m:266)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 1.20741e+43 erg / s Luminosity absorbed = 3.93375e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:357)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n", - "\t t_rad next_t_rad w next_w\n", - "\tShell \n", - "\t0 10738.799194 11316.665617 0.452965 0.492135\n", - "\t5 11210.269586 11599.094127 0.160945 0.183929\n", - "\t10 10911.463205 11403.508986 0.103910 0.114400\n", - "\t15 10545.065525 10958.974248 0.078433 0.087415\n", - "\n", - " (\u001b[1mbase.py\u001b[0m:348)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 11012.230 K -- next t_inner 10314.623 K (\u001b[1mbase.py\u001b[0m:350)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 19/20 (\u001b[1mbase.py\u001b[0m:266)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 9.29848e+42 erg / s Luminosity absorbed = 3.02011e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:357)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n", - "\t t_rad next_t_rad w next_w\n", - "\tShell \n", - "\t0 11316.665617 10862.505720 0.492135 0.444495\n", - "\t5 11599.094127 11194.462074 0.183929 0.162842\n", - "\t10 11403.508986 11065.620645 0.114400 0.099372\n", - "\t15 10958.974248 10599.851144 0.087415 0.077690\n", - "\n", - " (\u001b[1mbase.py\u001b[0m:348)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 10314.623 K -- next t_inner 11009.102 K (\u001b[1mbase.py\u001b[0m:350)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 20/20 (\u001b[1mbase.py\u001b[0m:266)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 1.21062e+43 erg / s Luminosity absorbed = 3.88405e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:357)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Simulation finished in 20 iterations and took 23.02 s (\u001b[1mbase.py\u001b[0m:306)\n" - ] - } - ], - "source": [ - "#TARDIS now uses the data in the data repo\n", - "sim = run_tardis('tardis_example.yml')" - ] - }, - { - "cell_type": "code", - "execution_count": 5, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[\u001b[1mpy.warnings \u001b[0m][\u001b[1;33mWARNING\u001b[0m] /Users/wkerzend/miniconda/envs/tardis3/lib/python3.6/site-packages/matplotlib/style/core.py:167: UserWarning: In /Users/wkerzend/.matplotlib/stylelib/talk_default.mplstyle: \n", - "The text.latex.unicode rcparam was deprecated in Matplotlib 2.2 and will be removed in 3.1.\n", - " styles = read_style_directory(stylelib_path)\n", - " (\u001b[1mwarnings.py\u001b[0m:99)\n", - "Populating the interactive namespace from numpy and matplotlib\n", - "[\u001b[1mpy.warnings \u001b[0m][\u001b[1;33mWARNING\u001b[0m] /Users/wkerzend/miniconda/envs/tardis3/lib/python3.6/site-packages/astropy/units/quantity.py:1067: AstropyDeprecationWarning: The truth value of a Quantity is ambiguous. In the future this will raise a ValueError.\n", - " AstropyDeprecationWarning)\n", - " (\u001b[1mwarnings.py\u001b[0m:99)\n", - "[\u001b[1mpy.warnings \u001b[0m][\u001b[1;33mWARNING\u001b[0m] /Users/wkerzend/python/tardis/tardis/montecarlo/formal_integral.py:167: FutureWarning: Method .as_matrix will be removed in a future version. Use .values instead.\n", - " result = pd.DataFrame(att_S_ul.as_matrix(), index=transitions.transition_line_id.values)\n", - " (\u001b[1mwarnings.py\u001b[0m:99)\n" - ] - }, - { - "data": { - "application/javascript": [ - "/* Put everything inside the global mpl namespace */\n", - "window.mpl = {};\n", - "\n", - "\n", - "mpl.get_websocket_type = function() {\n", - " if (typeof(WebSocket) !== 'undefined') {\n", - " return WebSocket;\n", - " } else if (typeof(MozWebSocket) !== 'undefined') {\n", - " return MozWebSocket;\n", - " } else {\n", - " alert('Your browser does not have WebSocket support.' +\n", - " 'Please try Chrome, Safari or Firefox ≥ 6. ' +\n", - " 'Firefox 4 and 5 are also supported but you ' +\n", - " 'have to enable WebSockets in about:config.');\n", - " };\n", - "}\n", - "\n", - "mpl.figure = function(figure_id, websocket, ondownload, parent_element) {\n", - " this.id = figure_id;\n", - "\n", - " this.ws = websocket;\n", - "\n", - " this.supports_binary = (this.ws.binaryType != undefined);\n", - "\n", - " if (!this.supports_binary) {\n", - " var warnings = document.getElementById(\"mpl-warnings\");\n", - " if (warnings) {\n", - " warnings.style.display = 'block';\n", - " warnings.textContent = (\n", - " \"This browser does not support binary websocket messages. \" +\n", - " \"Performance may be slow.\");\n", - " }\n", - " }\n", - "\n", - " this.imageObj = new Image();\n", - "\n", - " this.context = undefined;\n", - " this.message = undefined;\n", - " this.canvas = undefined;\n", - " this.rubberband_canvas = undefined;\n", - " this.rubberband_context = undefined;\n", - " this.format_dropdown = undefined;\n", - "\n", - " this.image_mode = 'full';\n", - "\n", - " this.root = $('
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