From 1597b1ccee655f8c0bf8acff0d9652d839f901f7 Mon Sep 17 00:00:00 2001 From: smithis7 Date: Sat, 5 Dec 2020 19:16:16 -0500 Subject: [PATCH 1/8] renaming running to using --- docs/{running => using}/components.rst | 0 .../configuration/schemas/csvy_model.yml | 0 docs/{running => using}/example_data.inc | 0 docs/{running => using}/images/LineInfo.png | Bin docs/{running => using}/images/OpeningScreen.png | Bin docs/{running => using}/images/ShellInfo.png | Bin .../images/line_info_spectrum_modebar.gif | Bin .../images/line_info_spectrum_rangeslider.gif | Bin .../images/line_info_spectrum_selection.gif | Bin .../images/line_info_widget_demo.gif | Bin .../images/shell_info_widget_demo.gif | Bin .../interaction/Custom_TARDIS_Model_Tutorial.ipynb | 0 docs/{running => using}/interaction/access.rst | 0 .../interaction/access_iterations.rst | 0 .../interaction/callback_example.ipynb | 0 docs/{running => using}/interaction/commandline.rst | 0 .../interaction/converters/cmfgen.rst | 0 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b/docs/using/interaction/isotope_pd_subclass.ipynb similarity index 100% rename from docs/running/interaction/isotope_pd_subclass.ipynb rename to docs/using/interaction/isotope_pd_subclass.ipynb diff --git a/docs/running/interaction/old_gui.rst b/docs/using/interaction/old_gui.rst similarity index 100% rename from docs/running/interaction/old_gui.rst rename to docs/using/interaction/old_gui.rst diff --git a/docs/running/interaction/physical_quantities.ipynb b/docs/using/interaction/physical_quantities.ipynb similarity index 100% rename from docs/running/interaction/physical_quantities.ipynb rename to docs/using/interaction/physical_quantities.ipynb diff --git a/docs/running/interaction/tardis_example.yml b/docs/using/interaction/tardis_example.yml similarity index 100% rename from docs/running/interaction/tardis_example.yml rename to docs/using/interaction/tardis_example.yml diff --git a/docs/running/interaction/to_hdf.ipynb b/docs/using/interaction/to_hdf.ipynb similarity index 100% rename from docs/running/interaction/to_hdf.ipynb rename to docs/using/interaction/to_hdf.ipynb diff --git a/docs/running/interaction/to_hdf.rst b/docs/using/interaction/to_hdf.rst similarity index 100% rename from docs/running/interaction/to_hdf.rst rename to docs/using/interaction/to_hdf.rst diff --git a/docs/running/interaction/using_formal_integral.rst b/docs/using/interaction/using_formal_integral.rst similarity index 100% rename from docs/running/interaction/using_formal_integral.rst rename to docs/using/interaction/using_formal_integral.rst diff --git a/docs/running/tardis_example.yml b/docs/using/tardis_example.yml similarity index 100% rename from docs/running/tardis_example.yml rename to docs/using/tardis_example.yml diff --git a/docs/running/tardis_widgets/generating_widgets.ipynb b/docs/using/tardis_widgets/generating_widgets.ipynb similarity index 100% rename from docs/running/tardis_widgets/generating_widgets.ipynb rename to docs/using/tardis_widgets/generating_widgets.ipynb diff --git a/docs/running/tardis_widgets/index.rst b/docs/using/tardis_widgets/index.rst similarity index 100% rename from docs/running/tardis_widgets/index.rst rename to docs/using/tardis_widgets/index.rst diff --git a/docs/running/tardis_widgets/using_widgets.rst b/docs/using/tardis_widgets/using_widgets.rst similarity index 100% rename from docs/running/tardis_widgets/using_widgets.rst rename to docs/using/tardis_widgets/using_widgets.rst From 8c5389496a28177fef1f5c06b8da92662aa0866d Mon Sep 17 00:00:00 2001 From: smithis7 Date: Sat, 5 Dec 2020 19:29:55 -0500 Subject: [PATCH 2/8] fixing merge conflict --- docs/index.rst | 8 ++++---- docs/physics/{old_physics.rst => old_physics/index.rst} | 2 +- docs/physics/{ => old_physics}/montecarlo_old.rst | 0 3 files changed, 5 insertions(+), 5 deletions(-) rename docs/physics/{old_physics.rst => old_physics/index.rst} (95%) rename docs/physics/{ => old_physics}/montecarlo_old.rst (100%) diff --git a/docs/index.rst b/docs/index.rst index 4994a38486e..b428d031bc6 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -57,9 +57,9 @@ Mission Statement :caption: Using TARDIS :hidden: - running/components - running/tardis_widgets/index - running/interaction/index + using/components + using/tardis_widgets/index + using/interaction/index .. toctree:: @@ -69,7 +69,7 @@ Mission Statement physics/montecarlo/index physics/plasma - physics/old_physics + physics/old_physics/index .. toctree:: diff --git a/docs/physics/old_physics.rst b/docs/physics/old_physics/index.rst similarity index 95% rename from docs/physics/old_physics.rst rename to docs/physics/old_physics/index.rst index 09588d3f53d..3367f4a4a4d 100644 --- a/docs/physics/old_physics.rst +++ b/docs/physics/old_physics/index.rst @@ -11,4 +11,4 @@ Old Physics Section (Outdated) .. toctree:: montecarlo_old - plasma/index \ No newline at end of file + ../plasma/index \ No newline at end of file diff --git a/docs/physics/montecarlo_old.rst b/docs/physics/old_physics/montecarlo_old.rst similarity index 100% rename from docs/physics/montecarlo_old.rst rename to docs/physics/old_physics/montecarlo_old.rst From 3ac370bdc53f2a525f0bd15193c62e92d3bfbae8 Mon Sep 17 00:00:00 2001 From: smithis7 Date: Sat, 5 Dec 2020 19:35:40 -0500 Subject: [PATCH 3/8] changing tardis_widgits to gui --- docs/using/{tardis_widgets => gui}/generating_widgets.ipynb | 0 docs/using/{tardis_widgets => gui}/index.rst | 0 docs/using/{tardis_widgets => gui}/using_widgets.rst | 0 3 files changed, 0 insertions(+), 0 deletions(-) rename docs/using/{tardis_widgets => gui}/generating_widgets.ipynb (100%) rename docs/using/{tardis_widgets => gui}/index.rst (100%) rename docs/using/{tardis_widgets => gui}/using_widgets.rst (100%) diff --git a/docs/using/tardis_widgets/generating_widgets.ipynb b/docs/using/gui/generating_widgets.ipynb similarity index 100% rename from docs/using/tardis_widgets/generating_widgets.ipynb rename to docs/using/gui/generating_widgets.ipynb diff --git a/docs/using/tardis_widgets/index.rst b/docs/using/gui/index.rst similarity index 100% rename from docs/using/tardis_widgets/index.rst rename to docs/using/gui/index.rst diff --git a/docs/using/tardis_widgets/using_widgets.rst b/docs/using/gui/using_widgets.rst similarity index 100% rename from docs/using/tardis_widgets/using_widgets.rst rename to docs/using/gui/using_widgets.rst From 002e635c3c6c7bd53f54b2e456a9c32c1b48cd59 Mon Sep 17 00:00:00 2001 From: smithis7 Date: Sat, 5 Dec 2020 22:44:29 -0500 Subject: [PATCH 4/8] turning tardis_widgits into gui on docs/index.rst --- docs/index.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/index.rst b/docs/index.rst index b428d031bc6..5cefa20d005 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -58,7 +58,7 @@ Mission Statement :hidden: using/components - using/tardis_widgets/index + using/gui/index using/interaction/index From 683d5d71dc9ef6ec7c78b5b631263e6b4c1ad986 Mon Sep 17 00:00:00 2001 From: smithis7 Date: Sun, 6 Dec 2020 22:04:26 -0500 Subject: [PATCH 5/8] putting models in using/components --- docs/index.rst | 2 +- ...y_And_Boundary_Velocities-checkpoint.ipynb | 810 ------------------ .../{components.rst => components/index.rst} | 8 +- .../components}/models/csy/csvy_test.ipynb | 0 ...stom_Density_And_Boundary_Velocities.ipynb | 0 .../components}/models/examples/abund.dat | 0 .../models/examples/abundancecust.rst | 0 .../models/examples/abundanceuni.rst | 0 .../models/examples/csvy_full_rad.csvy | 0 .../components}/models/examples/density.dat | 0 .../models/examples/densitycust.rst | 0 .../models/examples/densityexp.rst | 0 .../models/examples/densitypow.rst | 0 .../components}/models/examples/examples.rst | 0 .../components}/models/examples/index.rst | 0 .../models/examples/modelconfig.rst | 0 .../models/examples/run_simple_example.ipynb | 0 ...tardis_configv1_abundance_cust_example.yml | 0 ...dis_configv1_abundance_uniform_example.yml | 0 .../tardis_configv1_density_cust_example.yml | 0 ...s_configv1_density_exponential_example.yml | 0 ...dis_configv1_density_power_law_example.yml | 0 ...onfigv1_isotope_abundance_cust_example.yml | 0 .../models/examples/tardis_example.rst | 0 .../models/examples/tardis_example.yml | 0 .../models/examples/tardis_model_abund.csv | 0 .../models/examples/test_abund.dat | 0 .../models/examples/test_density.txt | 0 docs/{ => using/components}/models/index.rst | 0 29 files changed, 5 insertions(+), 815 deletions(-) delete mode 100644 docs/models/examples/.ipynb_checkpoints/Custom_Density_And_Boundary_Velocities-checkpoint.ipynb rename docs/using/{components.rst => components/index.rst} (60%) rename docs/{ => using/components}/models/csy/csvy_test.ipynb (100%) rename docs/{ => using/components}/models/examples/Custom_Density_And_Boundary_Velocities.ipynb (100%) rename docs/{ => using/components}/models/examples/abund.dat (100%) rename docs/{ => using/components}/models/examples/abundancecust.rst (100%) rename docs/{ => using/components}/models/examples/abundanceuni.rst (100%) rename docs/{ => using/components}/models/examples/csvy_full_rad.csvy (100%) rename docs/{ => using/components}/models/examples/density.dat (100%) rename docs/{ => using/components}/models/examples/densitycust.rst (100%) rename docs/{ => using/components}/models/examples/densityexp.rst (100%) rename docs/{ => using/components}/models/examples/densitypow.rst (100%) rename docs/{ => using/components}/models/examples/examples.rst (100%) rename docs/{ => using/components}/models/examples/index.rst (100%) rename docs/{ => using/components}/models/examples/modelconfig.rst (100%) rename docs/{ => using/components}/models/examples/run_simple_example.ipynb (100%) rename docs/{ => using/components}/models/examples/tardis_configv1_abundance_cust_example.yml (100%) rename docs/{ => using/components}/models/examples/tardis_configv1_abundance_uniform_example.yml (100%) rename docs/{ => using/components}/models/examples/tardis_configv1_density_cust_example.yml (100%) rename docs/{ => using/components}/models/examples/tardis_configv1_density_exponential_example.yml (100%) rename docs/{ => using/components}/models/examples/tardis_configv1_density_power_law_example.yml (100%) rename docs/{ => using/components}/models/examples/tardis_configv1_isotope_abundance_cust_example.yml (100%) rename docs/{ => using/components}/models/examples/tardis_example.rst (100%) rename docs/{ => using/components}/models/examples/tardis_example.yml (100%) rename docs/{ => using/components}/models/examples/tardis_model_abund.csv (100%) rename docs/{ => using/components}/models/examples/test_abund.dat (100%) rename docs/{ => using/components}/models/examples/test_density.txt (100%) rename docs/{ => using/components}/models/index.rst (100%) diff --git a/docs/index.rst b/docs/index.rst index 5cefa20d005..77dc411522e 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -57,7 +57,7 @@ Mission Statement :caption: Using TARDIS :hidden: - using/components + using/components/index using/gui/index using/interaction/index diff --git a/docs/models/examples/.ipynb_checkpoints/Custom_Density_And_Boundary_Velocities-checkpoint.ipynb b/docs/models/examples/.ipynb_checkpoints/Custom_Density_And_Boundary_Velocities-checkpoint.ipynb deleted file mode 100644 index 06804eac9d7..00000000000 --- a/docs/models/examples/.ipynb_checkpoints/Custom_Density_And_Boundary_Velocities-checkpoint.ipynb +++ /dev/null @@ -1,810 +0,0 @@ -{ - "cells": [ - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Specifying boundary velocities in addition to a custom density file\n", - "\n", - "This notebook will go through multiple detailed examples of how to properly run TARDIS with a custom ejecta profile specified by a custom density file and a custom abundance file. " - ] - }, - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [], - "source": [ - "import tardis\n", - "import matplotlib.pyplot as plt\n", - "import numpy as np" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "__Your custom density file__\n", - "\n", - "First, let's look at an example of a custom density file." - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "80 day\n", - "\n", - "0 9500 9e-16\n", - "\n", - "1 10500 6e-16\n", - "\n", - "2 12000 2e-17" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "* The first line specifies the time in days after the explosion\n", - "* After a skipped line, each row corresponds to a shell with index specified by the first column.\n", - "* The second column lists the velocities of the outer boundary of the cell in km/s.\n", - "* The third column lists the density of the cell.\n", - "\n", - "__IMPORTANT__\n", - "\n", - "The __default behavior__ of TARDIS is to use the first shell as the inner boundary. This means that v_inner_boundary = 9500, and the corresponding density 9e-16 is ignored because it is within the inner boundary. It can be replaced by an arbitrary number. The outer boundary of the last shell will be used as v_outer_boundary, so the default behavior will set v_outer_boundary = 12000." - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "__Your custom abundance file__\n", - "\n", - "Let's look at an example of a custom density file." - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "H He\n", - "\n", - "0.0 1.0\n", - "\n", - "0.4 0.6" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "* The first line indicates which elements (or isotopes) correspond to which columns.\n", - "* After a skipped line, each row specifies the chemical abundance of one shell. Therefore the numbers in a given row should sum to 1.0\n", - "\n", - "__IMPORTANT__\n", - "\n", - "Note that there are only 2 shells specified in this abundance file (despite the custom density file having 3 lines). This is because the custom density file specifies the boundaries of the shells, while the abundance file specifies the abundances within each shell." - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "__Running TARDIS with the custom files__\n", - "\n", - "Now let's run TARDIS using the example custom files." - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[\u001b[1mpy.warnings \u001b[0m][\u001b[1;33mWARNING\u001b[0m] /home/mew488/anaconda2/envs/tardis3/lib/python3.6/importlib/_bootstrap.py:219: QAWarning: pyne.data is not yet QA compliant.\n", - " return f(*args, **kwds)\n", - " (\u001b[1mwarnings.py\u001b[0m:99)\n", - "[\u001b[1mpy.warnings \u001b[0m][\u001b[1;33mWARNING\u001b[0m] /home/mew488/anaconda2/envs/tardis3/lib/python3.6/importlib/_bootstrap.py:219: QAWarning: pyne.material is not yet QA compliant.\n", - " return f(*args, **kwds)\n", - " (\u001b[1mwarnings.py\u001b[0m:99)\n", - "[\u001b[1mtardis.model.base \u001b[0m][\u001b[1;33mWARNING\u001b[0m] Abundances have not been normalized to 1. - normalizing (\u001b[1mbase.py\u001b[0m:367)\n", - "[\u001b[1mpy.warnings \u001b[0m][\u001b[1;33mWARNING\u001b[0m] /home/mew488/anaconda2/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.plasma.standard_plasmas\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Reading Atomic Data from /home/mew488/Research/TARDIS/tardis-refdata/atom_data/kurucz_cd23_chianti_H_He.h5 (\u001b[1mstandard_plasmas.py\u001b[0m:77)\n", - "[\u001b[1mpy.warnings \u001b[0m][\u001b[1;33mWARNING\u001b[0m] /home/mew488/anaconda2/envs/tardis3/lib/python3.6/site-packages/IPython/core/interactiveshell.py:3291: 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.atomic \u001b[0m][\u001b[1;37mINFO\u001b[0m ] Read Atom Data with UUID=6f7b09e887a311e7a06b246e96350010 and MD5=864f1753714343c41f99cb065710cace. (\u001b[1matomic.py\u001b[0m:173)\n", - "[\u001b[1mtardis.io.atomic \u001b[0m][\u001b[1;37mINFO\u001b[0m ] Non provided atomic data: synpp_refs, ion_cx_th_data, ion_cx_sp_data (\u001b[1matomic.py\u001b[0m:176)\n", - "[\u001b[1mpy.warnings \u001b[0m][\u001b[1;33mWARNING\u001b[0m] /home/mew488/src/dev/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] /home/mew488/anaconda2/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] /home/mew488/anaconda2/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 = 2.31327e+42 erg / s Luminosity absorbed = 3.85232e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 1/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6541.006187 6556.13016 0.343875 0.350118\n", - "\n", - " (\u001b[1mbase.py\u001b[0m:348)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6551.915 K -- next t_inner 6482.755 K (\u001b[1mbase.py\u001b[0m:350)\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 = 2.21734e+42 erg / s Luminosity absorbed = 2.64889e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 2/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6556.13016 6495.397989 0.350118 0.347789\n", - "\n", - " (\u001b[1mbase.py\u001b[0m:348)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6482.755 K -- next t_inner 6551.611 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 = 2.31324e+42 erg / s Luminosity absorbed = 2.21576e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 3/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6495.397989 6558.906259 0.347789 0.348258\n", - "\n", - " (\u001b[1mbase.py\u001b[0m:348)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6551.611 K -- next t_inner 6482.500 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 = 2.21685e+42 erg / s Luminosity absorbed = 3.70488e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 4/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6558.906259 6485.545593 0.348258 0.350397\n", - "\n", - " (\u001b[1mbase.py\u001b[0m:348)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6482.500 K -- next t_inner 6552.082 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 = 2.31359e+42 erg / s Luminosity absorbed = 2.20402e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 5/4 consecutive times. 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(\u001b[1mbase.py\u001b[0m:194)\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 6452.0629 6542.502642 0.358012 0.353289\n", - "\n", - " (\u001b[1mbase.py\u001b[0m:348)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6551.731 K -- next t_inner 6482.870 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 = 2.21734e+42 erg / s Luminosity absorbed = 3.17660e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 10/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6542.502642 6474.094395 0.353289 0.353484\n", - "\n", - " (\u001b[1mbase.py\u001b[0m:348)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6482.870 K -- next t_inner 6551.733 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 = 2.31318e+42 erg / s Luminosity absorbed = 2.21194e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 11/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6474.094395 6569.860807 0.353484 0.34756\n", - "\n", - " (\u001b[1mbase.py\u001b[0m:348)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6551.733 K -- next t_inner 6482.698 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 = 2.21741e+42 erg / s Luminosity absorbed = 1.59417e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 12/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6569.860807 6510.554611 0.34756 0.344308\n", - "\n", - " (\u001b[1mbase.py\u001b[0m:348)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6482.698 K -- next t_inner 6551.446 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 = 2.31272e+42 erg / s Luminosity absorbed = 2.20953e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 13/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6510.554611 6546.768598 0.344308 0.352781\n", - "\n", - " (\u001b[1mbase.py\u001b[0m:348)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6551.446 K -- next t_inner 6483.070 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 = 2.21777e+42 erg / s Luminosity absorbed = 2.64910e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 14/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6546.768598 6485.552351 0.352781 0.349363\n", - "\n", - " (\u001b[1mbase.py\u001b[0m:348)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6483.070 K -- next t_inner 6551.293 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 = 2.31237e+42 erg / s Luminosity absorbed = 2.76461e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 15/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6485.552351 6516.39366 0.349363 0.35982\n", - "\n", - " (\u001b[1mbase.py\u001b[0m:348)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6551.293 K -- next t_inner 6483.402 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 = 2.21811e+42 erg / s Luminosity absorbed = 2.64705e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 16/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6516.39366 6487.025434 0.35982 0.350732\n", - "\n", - " (\u001b[1mbase.py\u001b[0m:348)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6483.402 K -- next t_inner 6551.133 K (\u001b[1mbase.py\u001b[0m:350)\n", - "[\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 = 2.31225e+42 erg / s Luminosity absorbed = 2.21332e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 17/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6487.025434 6541.53332 0.350732 0.354308\n", - "\n", - " (\u001b[1mbase.py\u001b[0m:348)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6551.133 K -- next t_inner 6483.406 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" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 2.21806e+42 erg / s Luminosity absorbed = 3.18123e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 18/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6541.53332 6506.188917 0.354308 0.346155\n", - "\n", - " (\u001b[1mbase.py\u001b[0m:348)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6483.406 K -- next t_inner 6551.206 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 = 2.31238e+42 erg / s Luminosity absorbed = 2.76543e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 19/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6506.188917 6589.429688 0.346155 0.342891\n", - "\n", - " (\u001b[1mbase.py\u001b[0m:348)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6551.206 K -- next t_inner 6483.296 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 = 2.21775e+42 erg / s Luminosity absorbed = 5.09249e+38 erg / s Luminosity requested = 2.26469e+42 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 2.68 s (\u001b[1mbase.py\u001b[0m:306)\n" - ] - } - ], - "source": [ - "model = tardis.run_tardis('./test_config.yml')" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "You can check to make sure that the model loaded and used by TARDIS during the simulation is consistent with your expectations based on the custom files you provided:" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "v_inner_boundary = 950000000.0 cm / s\n", - "v_outer_boundary = 1200000000.0 cm / s\n", - "\n", - "\n", - "velocities of shell boundaries: \n", - "[9.50e+08 1.05e+09 1.20e+09] cm / s\n", - "\n", - "\n", - "densities loaded by TARDIS: (NOTE that the density in the first line of the file was ignored! Densities are also rescaled.)\n", - "[7.5e-14 2.5e-15] g / cm3\n" - ] - } - ], - "source": [ - "print('v_inner_boundary = ',model.model.v_boundary_inner)\n", - "print('v_outer_boundary = ',model.model.v_boundary_outer)\n", - "print('\\n')\n", - "print('velocities of shell boundaries: ')\n", - "print(model.model.velocity)\n", - "print('\\n')\n", - "print('densities loaded by TARDIS: (NOTE that the density in the first line of the file was ignored! Densities are also rescaled.)')\n", - "print(model.model.density)" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "## Specifying boundary velocities in the config file\n", - "\n", - "In addition to specifying custom density and abundance files, the user can set the v_inner_boundary and v_outer_boundary velocities in the YAML config file. This can cause some confusion, so we carefully go through some examples.\n", - "\n", - "__IMPORTANT__\n", - "\n", - "Boundary velocities set in the YAML config file must be __within__ the velocity range specified in the custom density file (if one is provided)." - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "## Example 1) v_inner_boundary lower than first velocity in density file\n", - "\n", - "In this example, the first velocity in the density file is 9500 km/s. The user can specify in the config file the velocity of the inner boundary to a lower velocity, say v_inner_boundary = 9000 km/s. This will cause TARDIS to raise an error." - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[\u001b[1mtardis.model.base \u001b[0m][\u001b[1;33mWARNING\u001b[0m] Abundances have not been normalized to 1. - normalizing (\u001b[1mbase.py\u001b[0m:367)\n" - ] - }, - { - "ename": "ValueError", - "evalue": "v_boundary_inner is lower than the lowest shell in the model.", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mValueError\u001b[0m Traceback (most recent call last)", - "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mmodel\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mtardis\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrun_tardis\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'./test_config_ex1.yml'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m", - "\u001b[0;32m~/src/dev/tardis/tardis/base.py\u001b[0m in \u001b[0;36mrun_tardis\u001b[0;34m(config, atom_data, simulation_callbacks)\u001b[0m\n\u001b[1;32m 35\u001b[0m \u001b[0mtardis_config\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mConfiguration\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfrom_config_dict\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mconfig\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 36\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 37\u001b[0;31m \u001b[0msimulation\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mSimulation\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfrom_config\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtardis_config\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0matom_data\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0matom_data\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 38\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mcb\u001b[0m \u001b[0;32min\u001b[0m \u001b[0msimulation_callbacks\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 39\u001b[0m \u001b[0msimulation\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0madd_callback\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mcb\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m~/src/dev/tardis/tardis/simulation/base.py\u001b[0m in \u001b[0;36mfrom_config\u001b[0;34m(cls, config, **kwargs)\u001b[0m\n\u001b[1;32m 430\u001b[0m \u001b[0mmodel\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mkwargs\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'model'\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 431\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 432\u001b[0;31m \u001b[0mmodel\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mRadial1DModel\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfrom_config\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mconfig\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 433\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0;34m'plasma'\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mkwargs\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 434\u001b[0m \u001b[0mplasma\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mkwargs\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'plasma'\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m~/src/dev/tardis/tardis/model/base.py\u001b[0m in \u001b[0;36mfrom_config\u001b[0;34m(cls, config)\u001b[0m\n\u001b[1;32m 383\u001b[0m \u001b[0mv_boundary_inner\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mstructure\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'v_inner_boundary'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 384\u001b[0m \u001b[0mv_boundary_outer\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mstructure\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'v_outer_boundary'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 385\u001b[0;31m electron_densities=electron_densities)\n\u001b[0m", - "\u001b[0;32m~/src/dev/tardis/tardis/model/base.py\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, velocity, homologous_density, abundance, isotope_abundance, time_explosion, t_inner, luminosity_requested, t_radiative, dilution_factor, v_boundary_inner, v_boundary_outer, electron_densities)\u001b[0m\n\u001b[1;32m 78\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_velocity\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 79\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mraw_velocity\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mvelocity\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 80\u001b[0;31m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mv_boundary_inner\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mv_boundary_inner\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 81\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mv_boundary_outer\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mv_boundary_outer\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 82\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mhomologous_density\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mhomologous_density\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m~/src/dev/tardis/tardis/model/base.py\u001b[0m in \u001b[0;36mv_boundary_inner\u001b[0;34m(self, value)\u001b[0m\n\u001b[1;32m 237\u001b[0m 'the model range.')\n\u001b[1;32m 238\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mvalue\u001b[0m \u001b[0;34m<\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mraw_velocity\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 239\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mValueError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'v_boundary_inner is lower than the lowest shell in the model.'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 240\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_v_boundary_inner\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mvalue\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 241\u001b[0m \u001b[0;31m# Invalidate the cached cut-down velocity array\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;31mValueError\u001b[0m: v_boundary_inner is lower than the lowest shell in the model." - ] - } - ], - "source": [ - "model = tardis.run_tardis('./test_config_ex1.yml')" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "## Example 2) v_outer_boundary larger than last velocity in density file\n", - "\n", - "In this example, the last velocity in the density file is 12000 km/s. The user can specify in the config file the velocity of the outer boundary to a larger velocity, say v_outer_boundary = 13000 km/s. This will cause TARDIS to raise an error." - ] - }, - { - "cell_type": "code", - "execution_count": 5, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[\u001b[1mtardis.model.base \u001b[0m][\u001b[1;33mWARNING\u001b[0m] Abundances have not been normalized to 1. - normalizing (\u001b[1mbase.py\u001b[0m:367)\n" - ] - }, - { - "ename": "ValueError", - "evalue": "v_boundary_outer is larger than the largest shell in the model.", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mValueError\u001b[0m Traceback (most recent call last)", - "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mmodel\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mtardis\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrun_tardis\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'./test_config_ex2.yml'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m", - "\u001b[0;32m~/src/dev/tardis/tardis/base.py\u001b[0m in \u001b[0;36mrun_tardis\u001b[0;34m(config, atom_data, simulation_callbacks)\u001b[0m\n\u001b[1;32m 35\u001b[0m \u001b[0mtardis_config\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mConfiguration\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfrom_config_dict\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mconfig\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 36\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 37\u001b[0;31m \u001b[0msimulation\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mSimulation\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfrom_config\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtardis_config\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0matom_data\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0matom_data\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 38\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mcb\u001b[0m \u001b[0;32min\u001b[0m \u001b[0msimulation_callbacks\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 39\u001b[0m \u001b[0msimulation\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0madd_callback\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mcb\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m~/src/dev/tardis/tardis/simulation/base.py\u001b[0m in \u001b[0;36mfrom_config\u001b[0;34m(cls, config, **kwargs)\u001b[0m\n\u001b[1;32m 430\u001b[0m \u001b[0mmodel\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mkwargs\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'model'\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 431\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 432\u001b[0;31m \u001b[0mmodel\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mRadial1DModel\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfrom_config\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mconfig\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 433\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0;34m'plasma'\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mkwargs\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 434\u001b[0m \u001b[0mplasma\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mkwargs\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'plasma'\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m~/src/dev/tardis/tardis/model/base.py\u001b[0m in \u001b[0;36mfrom_config\u001b[0;34m(cls, config)\u001b[0m\n\u001b[1;32m 383\u001b[0m \u001b[0mv_boundary_inner\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mstructure\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'v_inner_boundary'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 384\u001b[0m \u001b[0mv_boundary_outer\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mstructure\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'v_outer_boundary'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 385\u001b[0;31m electron_densities=electron_densities)\n\u001b[0m", - "\u001b[0;32m~/src/dev/tardis/tardis/model/base.py\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, velocity, homologous_density, abundance, isotope_abundance, time_explosion, t_inner, luminosity_requested, t_radiative, dilution_factor, v_boundary_inner, v_boundary_outer, electron_densities)\u001b[0m\n\u001b[1;32m 79\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mraw_velocity\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mvelocity\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 80\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mv_boundary_inner\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mv_boundary_inner\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 81\u001b[0;31m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mv_boundary_outer\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mv_boundary_outer\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 82\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mhomologous_density\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mhomologous_density\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 83\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_abundance\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mabundance\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m~/src/dev/tardis/tardis/model/base.py\u001b[0m in \u001b[0;36mv_boundary_outer\u001b[0;34m(self, value)\u001b[0m\n\u001b[1;32m 262\u001b[0m 'the model range.')\n\u001b[1;32m 263\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mvalue\u001b[0m \u001b[0;34m>\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mraw_velocity\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m-\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 264\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mValueError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'v_boundary_outer is larger than the largest shell in the model.'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 265\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_v_boundary_outer\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mvalue\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 266\u001b[0m \u001b[0;31m# Invalidate the cached cut-down velocity array\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;31mValueError\u001b[0m: v_boundary_outer is larger than the largest shell in the model." - ] - } - ], - "source": [ - "model = tardis.run_tardis('./test_config_ex2.yml')" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "## Example 3) v_boundaries in config file are within density file velocity range\n", - "\n", - "Here the user sets v_inner_boundary = 9700 and v_outer_boundary = 11500 in the config file. Both values fall within the velocity range specified by the custom density file." - ] - }, - { - "cell_type": "code", - "execution_count": 6, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[\u001b[1mtardis.model.base \u001b[0m][\u001b[1;33mWARNING\u001b[0m] Abundances have not been normalized to 1. - normalizing (\u001b[1mbase.py\u001b[0m:367)\n", - "[\u001b[1mtardis.plasma.standard_plasmas\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Reading Atomic Data from /home/mew488/Research/TARDIS/tardis-refdata/atom_data/kurucz_cd23_chianti_H_He.h5 (\u001b[1mstandard_plasmas.py\u001b[0m:77)\n", - "[\u001b[1mpy.warnings \u001b[0m][\u001b[1;33mWARNING\u001b[0m] /home/mew488/anaconda2/envs/tardis3/lib/python3.6/site-packages/IPython/core/interactiveshell.py:3291: 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.atomic \u001b[0m][\u001b[1;37mINFO\u001b[0m ] Read Atom Data with UUID=6f7b09e887a311e7a06b246e96350010 and MD5=864f1753714343c41f99cb065710cace. (\u001b[1matomic.py\u001b[0m:173)\n", - "[\u001b[1mtardis.io.atomic \u001b[0m][\u001b[1;37mINFO\u001b[0m ] Non provided atomic data: synpp_refs, ion_cx_th_data, ion_cx_sp_data (\u001b[1matomic.py\u001b[0m:176)\n", - "[\u001b[1mpy.warnings \u001b[0m][\u001b[1;33mWARNING\u001b[0m] /home/mew488/src/dev/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] /home/mew488/anaconda2/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] /home/mew488/anaconda2/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 = 2.31451e+42 erg / s Luminosity absorbed = 2.20992e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 1/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6475.378267 6488.637521 0.360681 0.366243\n", - "\n", - " (\u001b[1mbase.py\u001b[0m:348)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6484.018 K -- next t_inner 6413.863 K (\u001b[1mbase.py\u001b[0m:350)\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 = 2.21599e+42 erg / s Luminosity absorbed = 2.64272e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 2/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6488.637521 6427.216436 0.366243 0.363775\n", - "\n", - " (\u001b[1mbase.py\u001b[0m:348)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6413.863 K -- next t_inner 6483.959 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 = 2.31470e+42 erg / s Luminosity absorbed = 1.66285e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 3/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6427.216436 6492.265498 0.363775 0.364173\n", - "\n", - " (\u001b[1mbase.py\u001b[0m:348)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6483.959 K -- next t_inner 6413.533 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 = 2.21561e+42 erg / s Luminosity absorbed = 1.59276e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 4/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6492.265498 6417.052425 0.364173 0.366605\n", - "\n", - " (\u001b[1mbase.py\u001b[0m:348)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6413.533 K -- next t_inner 6484.185 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 = 2.31470e+42 erg / s Luminosity absorbed = 1.65313e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 5/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6417.052425 6482.377118 0.366605 0.368425\n", - "\n", - " (\u001b[1mbase.py\u001b[0m:348)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6484.185 K -- next t_inner 6413.755 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 = 2.21602e+42 erg / s Luminosity absorbed = 1.05695e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 6/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6482.377118 6394.506844 0.368425 0.371037\n", - "\n", - " (\u001b[1mbase.py\u001b[0m:348)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6413.755 K -- next t_inner 6483.813 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 = 2.31410e+42 erg / s Luminosity absorbed = 2.76180e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 7/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6394.506844 6519.309507 0.371037 0.36027\n", - "\n", - " (\u001b[1mbase.py\u001b[0m:348)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6483.813 K -- next t_inner 6414.228 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 = 2.21639e+42 erg / s Luminosity absorbed = 2.64764e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 8/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6519.309507 6383.889203 0.36027 0.374686\n", - "\n", - " (\u001b[1mbase.py\u001b[0m:348)\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6414.228 K -- next t_inner 6483.748 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 = 2.31428e+42 erg / s Luminosity absorbed = 5.54016e+37 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 9/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6383.889203 6473.974678 0.374686 0.369973\n", - "\n", - " (\u001b[1mbase.py\u001b[0m:348)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6483.748 K -- next t_inner 6413.915 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 = 2.21596e+42 erg / s Luminosity absorbed = 2.63810e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 10/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6473.974678 6406.611113 0.369973 0.369657\n", - "\n", - " (\u001b[1mbase.py\u001b[0m:348)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6413.915 K -- next t_inner 6484.063 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 = 2.31457e+42 erg / s Luminosity absorbed = 2.20714e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 11/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6406.611113 6501.97906 0.369657 0.363763\n", - "\n", - " (\u001b[1mbase.py\u001b[0m:348)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6484.063 K -- next t_inner 6413.825 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 = 2.21609e+42 erg / s Luminosity absorbed = 1.59204e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 12/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6501.97906 6442.380908 0.363763 0.360018\n", - "\n", - " (\u001b[1mbase.py\u001b[0m:348)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6413.825 K -- next t_inner 6483.774 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 = 2.31415e+42 erg / s Luminosity absorbed = 1.64927e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 13/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6442.380908 6479.130222 0.360018 0.369277\n", - "\n", - " (\u001b[1mbase.py\u001b[0m:348)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6483.774 K -- next t_inner 6414.121 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 = 2.21646e+42 erg / s Luminosity absorbed = 1.59283e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 14/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6479.130222 6416.085322 0.369277 0.365588\n", - "\n", - " (\u001b[1mbase.py\u001b[0m:348)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6414.121 K -- next t_inner 6483.538 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 = 2.31368e+42 erg / s Luminosity absorbed = 2.20875e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 15/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6416.085322 6449.419113 0.365588 0.376548\n", - "\n", - " (\u001b[1mbase.py\u001b[0m:348)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6483.538 K -- next t_inner 6414.538 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 = 2.21696e+42 erg / s Luminosity absorbed = 1.05743e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 16/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6449.419113 6417.878262 0.376548 0.367147\n", - "\n", - " (\u001b[1mbase.py\u001b[0m:348)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6414.538 K -- next t_inner 6483.218 K (\u001b[1mbase.py\u001b[0m:350)\n", - "[\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 = 2.31321e+42 erg / s Luminosity absorbed = 2.75526e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 17/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6417.878262 6473.045585 0.367147 0.371157\n", - "\n", - " (\u001b[1mbase.py\u001b[0m:348)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6483.218 K -- next t_inner 6414.863 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 = 2.21737e+42 erg / s Luminosity absorbed = 1.58484e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 18/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6473.045585 6436.504989 0.371157 0.362441\n", - "\n", - " (\u001b[1mbase.py\u001b[0m:348)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6414.863 K -- next t_inner 6482.959 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" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 2.31299e+42 erg / s Luminosity absorbed = 2.20411e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 19/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6436.504989 6520.140466 0.362441 0.358913\n", - "\n", - " (\u001b[1mbase.py\u001b[0m:348)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6482.959 K -- next t_inner 6414.912 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 = 2.21744e+42 erg / s Luminosity absorbed = 1.90600e+38 erg / s Luminosity requested = 2.26469e+42 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 2.44 s (\u001b[1mbase.py\u001b[0m:306)\n" - ] - } - ], - "source": [ - "model = tardis.run_tardis('./test_config_ex3.yml')" - ] - }, - { - "cell_type": "code", - "execution_count": 7, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "v_inner_boundary = 970000000.0 cm / s\n", - "v_outer_boundary = 1150000000.0 cm / s\n", - "\n", - "\n", - "velocities of shell boundaries: \n", - "[9.70e+08 1.05e+09 1.15e+09] cm / s\n", - "\n", - "\n", - "densities loaded by TARDIS: (NOTE that the density in the first line of the file was ignored! Densities are also rescaled.)\n", - "[7.5e-14 2.5e-15] g / cm3\n" - ] - } - ], - "source": [ - "print('v_inner_boundary = ',model.model.v_boundary_inner)\n", - "print('v_outer_boundary = ',model.model.v_boundary_outer)\n", - "print('\\n')\n", - "print('velocities of shell boundaries: ')\n", - "print(model.model.velocity)\n", - "print('\\n')\n", - "print('densities loaded by TARDIS: (NOTE that the density in the first line of the file was ignored! Densities are also rescaled.)')\n", - "print(model.model.density)" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "__IMPORTANT__\n", - "\n", - "Notice that the inner and outer boundary velocities are the ones specifically set by the user." - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.6.7" - } - }, - "nbformat": 4, - "nbformat_minor": 2 -} diff --git a/docs/using/components.rst b/docs/using/components/index.rst similarity index 60% rename from docs/using/components.rst rename to docs/using/components/index.rst index a9330fa36ec..26fb57d9a12 100644 --- a/docs/using/components.rst +++ b/docs/using/components/index.rst @@ -8,10 +8,10 @@ The TARDIS code needs three components to calculate spectra: .. toctree:: :maxdepth: 1 - ../configuration/index - ../models/index - ../atomic/atomic_data + ../../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 +`here <../../quickstart/quickstart.ipynb>`_. \ No newline at end of file diff --git a/docs/models/csy/csvy_test.ipynb b/docs/using/components/models/csy/csvy_test.ipynb similarity index 100% rename from docs/models/csy/csvy_test.ipynb rename to docs/using/components/models/csy/csvy_test.ipynb diff --git a/docs/models/examples/Custom_Density_And_Boundary_Velocities.ipynb b/docs/using/components/models/examples/Custom_Density_And_Boundary_Velocities.ipynb similarity index 100% rename from docs/models/examples/Custom_Density_And_Boundary_Velocities.ipynb rename to docs/using/components/models/examples/Custom_Density_And_Boundary_Velocities.ipynb diff --git a/docs/models/examples/abund.dat b/docs/using/components/models/examples/abund.dat similarity index 100% rename from docs/models/examples/abund.dat rename to docs/using/components/models/examples/abund.dat diff --git a/docs/models/examples/abundancecust.rst b/docs/using/components/models/examples/abundancecust.rst similarity index 100% rename from docs/models/examples/abundancecust.rst rename to docs/using/components/models/examples/abundancecust.rst diff --git a/docs/models/examples/abundanceuni.rst b/docs/using/components/models/examples/abundanceuni.rst similarity index 100% rename from docs/models/examples/abundanceuni.rst rename to docs/using/components/models/examples/abundanceuni.rst diff --git a/docs/models/examples/csvy_full_rad.csvy b/docs/using/components/models/examples/csvy_full_rad.csvy similarity index 100% rename from docs/models/examples/csvy_full_rad.csvy rename to docs/using/components/models/examples/csvy_full_rad.csvy diff --git a/docs/models/examples/density.dat b/docs/using/components/models/examples/density.dat similarity index 100% rename from docs/models/examples/density.dat rename to docs/using/components/models/examples/density.dat diff --git a/docs/models/examples/densitycust.rst b/docs/using/components/models/examples/densitycust.rst similarity index 100% rename from docs/models/examples/densitycust.rst rename to docs/using/components/models/examples/densitycust.rst diff --git a/docs/models/examples/densityexp.rst b/docs/using/components/models/examples/densityexp.rst similarity index 100% rename from docs/models/examples/densityexp.rst rename to docs/using/components/models/examples/densityexp.rst diff --git a/docs/models/examples/densitypow.rst b/docs/using/components/models/examples/densitypow.rst similarity index 100% rename from docs/models/examples/densitypow.rst rename to docs/using/components/models/examples/densitypow.rst diff --git a/docs/models/examples/examples.rst b/docs/using/components/models/examples/examples.rst similarity index 100% rename from docs/models/examples/examples.rst rename to docs/using/components/models/examples/examples.rst diff --git a/docs/models/examples/index.rst b/docs/using/components/models/examples/index.rst similarity index 100% rename from docs/models/examples/index.rst rename to docs/using/components/models/examples/index.rst diff --git a/docs/models/examples/modelconfig.rst b/docs/using/components/models/examples/modelconfig.rst similarity index 100% rename from docs/models/examples/modelconfig.rst rename to docs/using/components/models/examples/modelconfig.rst diff --git a/docs/models/examples/run_simple_example.ipynb b/docs/using/components/models/examples/run_simple_example.ipynb similarity index 100% rename from docs/models/examples/run_simple_example.ipynb rename to docs/using/components/models/examples/run_simple_example.ipynb diff --git a/docs/models/examples/tardis_configv1_abundance_cust_example.yml b/docs/using/components/models/examples/tardis_configv1_abundance_cust_example.yml similarity index 100% rename from docs/models/examples/tardis_configv1_abundance_cust_example.yml rename to docs/using/components/models/examples/tardis_configv1_abundance_cust_example.yml diff --git a/docs/models/examples/tardis_configv1_abundance_uniform_example.yml b/docs/using/components/models/examples/tardis_configv1_abundance_uniform_example.yml similarity index 100% rename from docs/models/examples/tardis_configv1_abundance_uniform_example.yml rename to docs/using/components/models/examples/tardis_configv1_abundance_uniform_example.yml diff --git a/docs/models/examples/tardis_configv1_density_cust_example.yml b/docs/using/components/models/examples/tardis_configv1_density_cust_example.yml similarity index 100% rename from docs/models/examples/tardis_configv1_density_cust_example.yml rename to docs/using/components/models/examples/tardis_configv1_density_cust_example.yml diff --git a/docs/models/examples/tardis_configv1_density_exponential_example.yml b/docs/using/components/models/examples/tardis_configv1_density_exponential_example.yml similarity index 100% rename from docs/models/examples/tardis_configv1_density_exponential_example.yml rename to docs/using/components/models/examples/tardis_configv1_density_exponential_example.yml diff --git a/docs/models/examples/tardis_configv1_density_power_law_example.yml b/docs/using/components/models/examples/tardis_configv1_density_power_law_example.yml similarity index 100% rename from docs/models/examples/tardis_configv1_density_power_law_example.yml rename to docs/using/components/models/examples/tardis_configv1_density_power_law_example.yml diff --git a/docs/models/examples/tardis_configv1_isotope_abundance_cust_example.yml b/docs/using/components/models/examples/tardis_configv1_isotope_abundance_cust_example.yml similarity index 100% rename from docs/models/examples/tardis_configv1_isotope_abundance_cust_example.yml rename to docs/using/components/models/examples/tardis_configv1_isotope_abundance_cust_example.yml diff --git a/docs/models/examples/tardis_example.rst b/docs/using/components/models/examples/tardis_example.rst similarity index 100% rename from docs/models/examples/tardis_example.rst rename to docs/using/components/models/examples/tardis_example.rst diff --git a/docs/models/examples/tardis_example.yml b/docs/using/components/models/examples/tardis_example.yml similarity index 100% rename from docs/models/examples/tardis_example.yml rename to docs/using/components/models/examples/tardis_example.yml diff --git a/docs/models/examples/tardis_model_abund.csv b/docs/using/components/models/examples/tardis_model_abund.csv similarity index 100% rename from docs/models/examples/tardis_model_abund.csv rename to docs/using/components/models/examples/tardis_model_abund.csv diff --git a/docs/models/examples/test_abund.dat b/docs/using/components/models/examples/test_abund.dat similarity index 100% rename from docs/models/examples/test_abund.dat rename to docs/using/components/models/examples/test_abund.dat diff --git a/docs/models/examples/test_density.txt b/docs/using/components/models/examples/test_density.txt similarity index 100% rename from docs/models/examples/test_density.txt rename to docs/using/components/models/examples/test_density.txt diff --git a/docs/models/index.rst b/docs/using/components/models/index.rst similarity index 100% rename from docs/models/index.rst rename to docs/using/components/models/index.rst From e3584119f59fabcc1569938633f27eeacc87a9ef Mon Sep 17 00:00:00 2001 From: smithis7 Date: Mon, 7 Dec 2020 23:40:37 -0500 Subject: [PATCH 6/8] adding configuration to docs/using/components --- .../components}/configuration/config_validator.rst | 0 docs/{ => using/components}/configuration/configuration.rst | 6 +++--- docs/{ => using/components}/configuration/index.rst | 0 .../components}/configuration/read_configuration.ipynb | 0 docs/{ => using/components}/configuration/schemas/base.yml | 0 docs/{ => using/components}/configuration/schemas/model.yml | 0 .../components}/configuration/schemas/montecarlo.yml | 0 .../{ => using/components}/configuration/schemas/plasma.yml | 0 .../components}/configuration/schemas/spectrum.yml | 0 .../components}/configuration/schemas/supernova.yml | 0 docs/using/components/index.rst | 2 +- 11 files changed, 4 insertions(+), 4 deletions(-) rename docs/{ => using/components}/configuration/config_validator.rst (100%) rename docs/{ => using/components}/configuration/configuration.rst (96%) rename docs/{ => using/components}/configuration/index.rst (100%) rename docs/{ => using/components}/configuration/read_configuration.ipynb (100%) rename docs/{ => using/components}/configuration/schemas/base.yml (100%) rename docs/{ => using/components}/configuration/schemas/model.yml (100%) rename docs/{ => using/components}/configuration/schemas/montecarlo.yml (100%) rename docs/{ => using/components}/configuration/schemas/plasma.yml (100%) rename docs/{ => using/components}/configuration/schemas/spectrum.yml (100%) rename docs/{ => using/components}/configuration/schemas/supernova.yml (100%) diff --git a/docs/configuration/config_validator.rst b/docs/using/components/configuration/config_validator.rst similarity index 100% rename from docs/configuration/config_validator.rst rename to docs/using/components/configuration/config_validator.rst diff --git a/docs/configuration/configuration.rst b/docs/using/components/configuration/configuration.rst similarity index 96% rename from docs/configuration/configuration.rst rename to docs/using/components/configuration/configuration.rst index 688d5df2e88..2eae7214c0d 100644 --- a/docs/configuration/configuration.rst +++ b/docs/using/components/configuration/configuration.rst @@ -158,8 +158,8 @@ 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 <../montecarlo/virtualpackets>` for spectral synthesis -* integrated: use the :doc:`formal integral method <../montecarlo/sourceintegration>` of Lucy 1999 +* 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:: @@ -168,4 +168,4 @@ just an integer. Finally, the method option selects the final spectral synthesis dedicated page. -.. include:: ../running/example_data.inc \ No newline at end of file +.. include:: ../../example_data.inc \ No newline at end of file diff --git a/docs/configuration/index.rst b/docs/using/components/configuration/index.rst similarity index 100% rename from docs/configuration/index.rst rename to docs/using/components/configuration/index.rst diff --git a/docs/configuration/read_configuration.ipynb b/docs/using/components/configuration/read_configuration.ipynb similarity index 100% rename from docs/configuration/read_configuration.ipynb rename to docs/using/components/configuration/read_configuration.ipynb diff --git a/docs/configuration/schemas/base.yml b/docs/using/components/configuration/schemas/base.yml similarity index 100% rename from docs/configuration/schemas/base.yml rename to docs/using/components/configuration/schemas/base.yml diff --git a/docs/configuration/schemas/model.yml b/docs/using/components/configuration/schemas/model.yml similarity index 100% rename from docs/configuration/schemas/model.yml rename to docs/using/components/configuration/schemas/model.yml diff --git a/docs/configuration/schemas/montecarlo.yml b/docs/using/components/configuration/schemas/montecarlo.yml similarity index 100% rename from docs/configuration/schemas/montecarlo.yml rename to docs/using/components/configuration/schemas/montecarlo.yml diff --git a/docs/configuration/schemas/plasma.yml b/docs/using/components/configuration/schemas/plasma.yml similarity index 100% rename from docs/configuration/schemas/plasma.yml rename to docs/using/components/configuration/schemas/plasma.yml diff --git a/docs/configuration/schemas/spectrum.yml b/docs/using/components/configuration/schemas/spectrum.yml similarity index 100% rename from docs/configuration/schemas/spectrum.yml rename to docs/using/components/configuration/schemas/spectrum.yml diff --git a/docs/configuration/schemas/supernova.yml b/docs/using/components/configuration/schemas/supernova.yml similarity index 100% rename from docs/configuration/schemas/supernova.yml rename to docs/using/components/configuration/schemas/supernova.yml diff --git a/docs/using/components/index.rst b/docs/using/components/index.rst index 26fb57d9a12..99c8a23a3e7 100644 --- a/docs/using/components/index.rst +++ b/docs/using/components/index.rst @@ -8,7 +8,7 @@ The TARDIS code needs three components to calculate spectra: .. toctree:: :maxdepth: 1 - ../../configuration/index + configuration/index models/index ../../atomic/atomic_data From 140d54067ed67989dee58671d2671f4664d8e44e Mon Sep 17 00:00:00 2001 From: smithis7 Date: Mon, 7 Dec 2020 23:58:47 -0500 Subject: [PATCH 7/8] adding atomic to docs/using/components --- docs/quickstart/quickstart.ipynb | 4 ++-- docs/{ => using/components}/atomic/atomic_data.rst | 0 .../{ => using/components}/atomic/atomic_data_description.rst | 0 docs/{ => using/components}/atomic/current_public_table.rst | 0 docs/using/components/index.rst | 2 +- 5 files changed, 3 insertions(+), 3 deletions(-) rename docs/{ => using/components}/atomic/atomic_data.rst (100%) rename docs/{ => using/components}/atomic/atomic_data_description.rst (100%) rename docs/{ => using/components}/atomic/current_public_table.rst (100%) diff --git a/docs/quickstart/quickstart.ipynb b/docs/quickstart/quickstart.ipynb index e4dde04ce84..609a43c7684 100644 --- a/docs/quickstart/quickstart.ipynb +++ b/docs/quickstart/quickstart.ipynb @@ -11,7 +11,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Every simulation run requires the atomic database (for more info refer to [atomic data](../atomic/atomic_data.rst) ) and a configuration file (more info at [configuration](../configuration/index.rst) ).\n", + "Every simulation run requires the atomic database (for more info refer to [atomic data](../using/components/atomic/atomic_data.rst) ) and a configuration file (more info at [configuration](../configuration/index.rst) ).\n", "You can obtain a copy of the atomic database from the\n", "(https://github.com/tardis-sn/tardis-refdata) repository\n", "(`atom_data` subfolder). We recommended to use the\n", @@ -444,7 +444,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.6.10" + "version": "3.7.8" }, "nbsphinx": { "execute": "always", diff --git a/docs/atomic/atomic_data.rst b/docs/using/components/atomic/atomic_data.rst similarity index 100% rename from docs/atomic/atomic_data.rst rename to docs/using/components/atomic/atomic_data.rst diff --git a/docs/atomic/atomic_data_description.rst b/docs/using/components/atomic/atomic_data_description.rst similarity index 100% rename from docs/atomic/atomic_data_description.rst rename to docs/using/components/atomic/atomic_data_description.rst diff --git a/docs/atomic/current_public_table.rst b/docs/using/components/atomic/current_public_table.rst similarity index 100% rename from docs/atomic/current_public_table.rst rename to docs/using/components/atomic/current_public_table.rst diff --git a/docs/using/components/index.rst b/docs/using/components/index.rst index 99c8a23a3e7..825c448c06b 100644 --- a/docs/using/components/index.rst +++ b/docs/using/components/index.rst @@ -10,7 +10,7 @@ The TARDIS code needs three components to calculate spectra: configuration/index models/index - ../../atomic/atomic_data + atomic/atomic_data A quick start guide to run TARDIS can be found From 9ffee87a07be0ca840e643391867173f6ebbeb7a Mon Sep 17 00:00:00 2001 From: smithis7 Date: Tue, 8 Dec 2020 00:06:20 -0500 Subject: [PATCH 8/8] fixing hyperlink in quickstart --- docs/quickstart/quickstart.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/quickstart/quickstart.ipynb b/docs/quickstart/quickstart.ipynb index 609a43c7684..b9523359c6a 100644 --- a/docs/quickstart/quickstart.ipynb +++ b/docs/quickstart/quickstart.ipynb @@ -11,7 +11,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Every simulation run requires the atomic database (for more info refer to [atomic data](../using/components/atomic/atomic_data.rst) ) and a configuration file (more info at [configuration](../configuration/index.rst) ).\n", + "Every simulation run requires the atomic database (for more info refer to [atomic data](../using/components/atomic/atomic_data.rst) ) and a configuration file (more info at [configuration](../using/components/configuration/index.rst) ).\n", "You can obtain a copy of the atomic database from the\n", "(https://github.com/tardis-sn/tardis-refdata) repository\n", "(`atom_data` subfolder). We recommended to use the\n",