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* Minor changes to the environment file * Remove old readthedocs files
* removing kwarg from MonteCarloConfiguration, as jitclass does not support them * need to pass enable_full_relativity to configuration_initialize, as removed kwarg in MonteCarloConfiguration * move_r_packet and trace_packet both require montecarlo_configuration arg * r_packet object used in distance calculation in place of r_packet.r value * the full_relativity bool was being passed as a different kwarg * added montecarlo_configuration to args of trace_vpacket_volley and trace_vpacket, so that relativity attribute continues to get passed down * making sure the vpacket funcs that now require montecarlo_configuration get called with this arg * Added random seed; does not work with numba * Changed to numpy random seed * Commented out MonteCarloException block; will test how this impacts output * Need the MonteCarloException block to be run, otherwise large discrepancies between numba branch and master branch * Adding custom seeds to vpackets; few line adjustments * changed from njit to jit to ease debugging * More descriptive montecarloexception, with optional printing beforehand * Changed njit to jit in single_loop to ease debugging * Added single-packet debugging capabilities to MonteCarloRunner. * Removing plotting funcs from montecarlo * Added basic logging capabilities to montecarlo_numba * Generalized logger to *args * Tweaking configuration of logging in module * Logger can now handle kwargs * Renamed logger * Make logging more in line with other TARDIS loggers. * Share global variable DEBUG_MODE across modules with montecarlo init. * No longer calling removed plot_single_packet; also referring to __init__ DEBUG_MODE * Now referring to montecarlo __init__ DEBUG_MODE global * Remove dangling else statement * no longer need plotting in montecarlo_numba base.py * Remove import of function that no longer exists. * No longer holding global variables in montecarlo init * Importing mc_logger for global variables now * Moving log_decorator from base.py * Adding logger to new montecarlo_logger file * Add new logger to, remove print statements from r_packet.py * Ensure that DEBUG_MODE is referenced within the montecarlo_logger file * Allow the function being decorated to take its kwargs. * Apply wraps correctly * Make else block logic more apparent * Get rid of extra blank line * Got rid of a few todos * Add note about why decorator behavior will not change according to config * removing reference to logger in base * Added crude buffer * Increase buffer; check DEBUG_MODE checked during call, not init * Set default buffer in montecarlo logger to stated default * Allow specification of buffer in montecarlo yml * Make sure logger_buffer is passed through to montecarlo logger * Remove todo, question from log_decorator * Adding better docstrings to log_decorator * Add newline at end of montecarlo_logger file * Make logger config happen outside of decorator * Moved print statement to exception; * Added logging to file * No longer profiling calculate_distance_line * Add functionality to profile incomplete packet runs * Rename previous debug mode, as it was not for single packets * Added single packet seed to yml * Propagate single_packet_seed throughout configurations * Reference single packet seed from montecarloconfiguration * Add bool type to single packet seed type * Catch exception better, catch extra random seed * Set whole index, including energies, not just random seed * Change where loop is broken. * Move close_line_threshold check past montecarloexception * Add single-packet debug documentation and script * Add jitclass arg for single packet seed in montecarloconfiguration * Now the default for single_packet_seed cannot be a bool * Added new debug page to developer part of documentation * Now the single_packet_seed has to be not 1, not not False * Pause using log_decorator, remove try/except for nopython * Vpacket jitclass now allows for an int64 index * Exceptions args must be compile-time constants in nopython mode * Allow 0 nu_diff to not throw exception. * v_packets should have the same random seed as their r_packet * Fix MonteCarloException throw * Fix estimator typos * Make sure return is not made before relativity block * Rename esitmators to keep them consistent * Also rename the estimators in montecarlo.pyx * Rename estimators in numba_interface * Clean up estimator typos; change back to njit * Include Doppler factor in energy calculation for full_relativity * Add back not statement * Added relativistic Doppler factor * Add in Doppler factor relativity for interaction * Add angle aberration * add angle aberration to interactions * Update numba version * Remove relativity branching * Logger no longer prints to console if printing to file * Initialize configuration with external module, not jitclass * Remove extra repr of logger.handlers * Ensure the angle aberration is called on vpacket, remove jitclass reference * Convert montecarloconfiguration refs from jitclass to module * Add more references to global module, complete relativistic branching * Pass r_packet.mu to angle aberration calculation * Clarify angle aberration calc, include doppler factor to distance calc * Remove reference to MonteCarloConfiguration * Trying to delete C tests * Remove C montecarlo * Remove references to C module * Alter formal integral tests for python version * Rewrite formal integral in python
* Change `pytestconfig` to `request.config` * Removed docstring by mistake. Fixed.
…ontributing Added better mission statement
* Moved and renamed coverage file * Omit astropy_init from coverage calculation * generalize omit of astropy_init to all file types
* Added roadmap link to main page * Added roadmap page Co-authored-by: Marc Williamson <marcwilliamson@Marcs-MacBook-Pro.local>
* Update team.rst - Add roles and descriptions Added roles and descriptions to the team page * Update team.rst - Added new GSoC students Update GSoC students section * Update team.rst - Added new roles Added new roles and minor style changes * add several nbsphinx related options * restructure the Governance model page * re-enabled nbsphinx * fix issues marked by @yssa Co-authored-by: Yssa Camacho <yssavo.camacho@gmail.com>
* Update team.rst - Add roles and descriptions Added roles and descriptions to the team page * Update team.rst - Added new GSoC students Update GSoC students section * Update team.rst - Added new roles Added new roles and minor style changes * add several nbsphinx related options * restructure the Governance model page * re-enabled nbsphinx * add adapted CoC * ammending code of conduct in the root * add code of conduct * getting upstream/master team.rst Co-authored-by: Yssa Camacho <yssavo.camacho@gmail.com>
* add code_of_conduct_symlink * add code of conduct link
* Added new contributing guidelines * Added symlink of Contributing.md to Contribting to TARDIS section * Fixed sym link * Update CONTRIBUTING.md Co-authored-by: Wolfgang Kerzendorf <wkerzendorf@gmail.com> * Update CONTRIBUTING.md Co-authored-by: Wolfgang Kerzendorf <wkerzendorf@gmail.com> Co-authored-by: Marc Williamson <marxwillia@gmail.com> Co-authored-by: Wolfgang Kerzendorf <wkerzendorf@gmail.com>
* testing mamba installation. Simply install mamba from conda and try to create env * added mamba after conda installation * check if mamba installation succesful * installing mamba before activating * fix syntax errors * Pin mamba to 0.4.0 and make pipelines exit on error with any bash command * move tardis_env.sh into pipelines file * fetch reference data fetching from bash scripts to azure pipelines file * fix syntax error * Added packet data * Adding variable shellopts to check * added shellopts=errexit so that build fails on non-zero error code * testing if pipeline fails * reverting changes, testing succesful * remove unused lines * testing, this should fail the pipeline * Made all single lines where necessary Added a step to fail build on error as suggested by epassaro improved documentation to steps * added back the git lfs pull code * removed git lfs codes * added git lfs to pipelines to make it faster
…tories (tardis-sn#1213) * Added directories to exclude in black configuration file * Added black to tardis environment file * Excluded setup related files from black configuration * Applied black formatting to remaining files
* Add governance document * Update docs/governance.rst Co-authored-by: Christian Vogl <cvogl@mpa-garching.mpg.de> * Added rules for Tardis-core Co-authored-by: Christian Vogl <cvogl@mpa-garching.mpg.de> Co-authored-by: Andreas Flörs <33418619+afloers@users.noreply.github.com>
capitalize TARDIS
add tardis core email
* Unpin packages * Pin numpy to 1.15 again * Pin numba to v0.50 * [skip-ci] Remove Git LFS directive * [skip-ci] (revert) Remove Git LFS directive * Pin pyne to v0.7 * Trying to find problem in macOS env * Trying to find problem in macOS env (2) * Trying to find problem in macOS env (3) * Trying to find problem in macOS env (4) * Remove all the pins * Add some pins * Add some pins (2) * Pin numpy to v1.16 * Pin numpy to v1.17 * Pin numpy to v1.16 and scipy to v1.5 * Pin numba to v0.50 * Pin pyne to v0.7 * [skip-ci] Remove Git LFS directive * [skip-ci] Remove Git LFS directive (2)
* add GIT_LFS_SMUDGE * fixed smudge command
* add GIT_LFS_SMUDGE * fixed smudge command * Minor changes * Fetch refdata from GDrive backup * Move fetch refdata steps to the top * Fix typo * Debugging pipeline * Move fetch refdata steps again. Install gdown within TARDIS env * [skip-ci] Minor changes * Update azure-pipelines/simple_test_framework.yml Co-authored-by: Wolfgang Kerzendorf <wkerzendorf@gmail.com> Co-authored-by: Kaushik Varanasi <kaushik.varanasi1@gmail.com> Co-authored-by: Wolfgang Kerzendorf <wkerzendorf@gmail.com>
* test for detecting error * files needed for tests * add test for csvy vs. hard coded data * add test fir config vs. hard coded data * make tests and test files more descriptive * remove condig model test and asociated files, remove unused files * make filenames more descriptive * remove more unused files * rename files for other test * fix filename join * fix errors in tests * Apply black and add descriptions to tests * make descriptions more uniform across files * restore line accidentaly removed * More docstrings and clarifications and PEP8 * rename files to make their purpose clearer * fix wrong extension for csvy file * change wording of comment * change abundance and density files names and changed references * restore base.py accidentally committed before * fix wording in docstring * Update tardis/model/tests/test_csvy_model.py Co-authored-by: Alice Harpole <harpolea@users.noreply.github.com> * Update tardis/model/tests/test_csvy_model.py Co-authored-by: Alice Harpole <harpolea@users.noreply.github.com> * Update tardis/model/tests/test_csvy_model.py Co-authored-by: Alice Harpole <harpolea@users.noreply.github.com> * Alice's corrections Co-authored-by: Alice Harpole <harpolea@users.noreply.github.com> * change wording of docstring * change filenames function name * fix typos, clarifications * change name to reference abundance and spellcheck docstring * Apply suggestions from code review add Christian's corrections Co-authored-by: Christian Vogl <cvogl@mpa-garching.mpg.de> * move reference data to fixtures * small clarification in file * delete duplicate tests * test for detecting error * files needed for tests * add test for csvy vs. hard coded data * add test fir config vs. hard coded data * make tests and test files more descriptive * remove condig model test and asociated files, remove unused files * make filenames more descriptive * remove more unused files * rename files for other test * fix filename join * fix errors in tests * Apply black and add descriptions to tests * make descriptions more uniform across files * restore line accidentaly removed * More docstrings and clarifications and PEP8 * rename files to make their purpose clearer * fix wrong extension for csvy file * change wording of comment * change abundance and density files names and changed references * restore base.py accidentally committed before * fix wording in docstring * change wording of docstring * Update tardis/model/tests/test_csvy_model.py Co-authored-by: Alice Harpole <harpolea@users.noreply.github.com> * Update tardis/model/tests/test_csvy_model.py Co-authored-by: Alice Harpole <harpolea@users.noreply.github.com> * Alice's corrections Co-authored-by: Alice Harpole <harpolea@users.noreply.github.com> * change filenames function name * fix typos, clarifications * change name to reference abundance and spellcheck docstring * Apply suggestions from code review add Christian's corrections Co-authored-by: Christian Vogl <cvogl@mpa-garching.mpg.de> * move reference data to fixtures * small clarification in file * delete duplicate tests * move docstring to fixture * fix issue-1228 Co-authored-by: Alice Harpole <harpolea@users.noreply.github.com> Co-authored-by: Christian Vogl <cvogl@mpa-garching.mpg.de>
Adding Plasma File in TOC
Reorganizing files in docs (2/2)
Fixing Quickstart Problem
epassaro
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Apr 8, 2022
* Add calculation of bound-free opacity for numba MC * Fix bound-free frequency sorting error * Add determination of macro atom activation level after bound-free absorption skip-checks: true * Fix sorting error in bound-free opacity interpolator * Calculate factor used in free-free cooling from fundamental constants * Add determination of macro atom activation level after continuum absorption * Fix renaming bug * Add calculation of free-free opacity * Add note about free-free Gaunt factor * Add function for combined bf and ff opacity calculation * Make it easier to retrieve the transition_idx of a MA deactivation channel * Swap level order in transition_idx references to deactivation * Reformat some lines * Add transition_types and idxs for MA deactivation by cooling * Add mask for retrieving transition probabilities of non continuum species * Combine the Markov chain and normal transition probabilities * Reformat some lines * Replace dummy k-packet idx in interaction handling * Change output name of combined continuum transition probabilities * Add block references for combined continuum transition probabilities * Activate macro atom by level idx instead of line idx * Make macro atom data a plasma property to enable modularity * Split transition probabilities and transition info * Fix macro atom test * Adapt transition types in plasma to match the ones in the numba macro atom * Make the macro atom return the transition type * Add individual fb cooling probabilities to MC transition probabilities * Make bound-free cross sections available in the MC calculation * Initialize the arrays for the continuum estimators * Convert continuum estimator arrays to DataFrames * Make t_electrons available in MC calculation * Propagate continuum estimators into plasma * Add continuum estimators to Numba estimators * Reformat some lines * Made path selection a little bit faster and simplifiedw * Add sorted list of threshold frequencies for photoionization to Numba MC * Added selection fucntion for continuum process, WIP * Moved continuum selection inside of tracepacket, still need a docstring * added plasma properties that perform the sampling of the free-free and free-bound emission processes * restrcited sampling range between continuum ids * Record bound-free estimators during Numba MC * Began work on Continuum jitclass * Implemented the Continuum as a jitclass which caches the state at a given shell_id and fequency * Added the continuum samplers to the attribute of the continuum processes file. Fixed implementation after merge * Added temporary change to make all continuum processes thomson scatter so that the simulation finished in a finite amount of time for testing during development * fixed the continuum samplers so they are now properly processed. Also fixed some bugs in the samplers * Reworked the continuum process selection function a little bit to work with the new continuum jitclass * started addition of free-free emission handler * Add calculation of bound-free opacity for numba MC * Fix bound-free frequency sorting error * Add determination of macro atom activation level after bound-free absorption skip-checks: true * Fix sorting error in bound-free opacity interpolator * Calculate factor used in free-free cooling from fundamental constants * Add determination of macro atom activation level after continuum absorption * Fix renaming bug * Add calculation of free-free opacity * Add note about free-free Gaunt factor * Add function for combined bf and ff opacity calculation * Make it easier to retrieve the transition_idx of a MA deactivation channel * Swap level order in transition_idx references to deactivation * Reformat some lines * Add transition_types and idxs for MA deactivation by cooling * Add mask for retrieving transition probabilities of non continuum species * Combine the Markov chain and normal transition probabilities * Reformat some lines * Replace dummy k-packet idx in interaction handling * Change output name of combined continuum transition probabilities * Add block references for combined continuum transition probabilities * Activate macro atom by level idx instead of line idx * Make macro atom data a plasma property to enable modularity * Split transition probabilities and transition info * Fix macro atom test * Adapt transition types in plasma to match the ones in the numba macro atom * Make the macro atom return the transition type * Add individual fb cooling probabilities to MC transition probabilities * Make bound-free cross sections available in the MC calculation * Initialize the arrays for the continuum estimators * Convert continuum estimator arrays to DataFrames * Make t_electrons available in MC calculation * Propagate continuum estimators into plasma * Add continuum estimators to Numba estimators * Reformat some lines * Add sorted list of threshold frequencies for photoionization to Numba MC * Record bound-free estimators during Numba MC * Add estimator for stimulated recombination cooling rate * Add column name to estimator DataFrames * updated interactions to work with new macroatom * Added continuum process frquency samplers to the continuum jitclass constructor * Fixed typo from merge conflict * Fixed spacing * small formatting updates to get the changes to track * propagated continuum through single packet loop * Cleaned up file, bound-free and free-free emission pathways should be in the correct place now * added fixture for a new continuum object * Added placeholder test for calculating the continuum opacities. I'm weary to put in exact values until we're done * reworked the contruction of the continuum class so that only a plasma object needs to be passed * Updated interaction to now get the macro activation level from the continuum object * refer to previous commit * Added the continuum_process into the single packet loop so packets can now actually interact with the contniuum * various small bugfixes to get the numba funcs to compile properly * Removed extra functions * Merge pull request #5 from chvogl/monte-carlo-continuum (#4) * Reworked the continuum process selection function a little bit to work with the new continuum jitclass * started addition of free-free emission handler * updated interactions to work with new macroatom * Added continuum process frquency samplers to the continuum jitclass constructor * Fixed typo from merge conflict * Fixed spacing * small formatting updates to get the changes to track * propagated continuum through single packet loop * Cleaned up file, bound-free and free-free emission pathways should be in the correct place now * added fixture for a new continuum object * Added placeholder test for calculating the continuum opacities. I'm weary to put in exact values until we're done * reworked the contruction of the continuum class so that only a plasma object needs to be passed * Updated interaction to now get the macro activation level from the continuum object * refer to previous commit * Added the continuum_process into the single packet loop so packets can now actually interact with the contniuum * various small bugfixes to get the numba funcs to compile properly * Removed extra functions * Fix bug in calculation of corrected photoionization rate coefficient * Format some lines * Update tardis/montecarlo/montecarlo_numba/interaction.py Co-authored-by: Christian Vogl <cvogl@mpa-garching.mpg.de> * No longer recalculate the local continuum opacities before interacting * Resolved comment from Christian, do the same process for BF cooling as BF emission * Minor formatting, currently we still don't actually run through any continuum processes because the new macroatom is not in * Resolved a couple of comments. (#5) * Reworked the continuum process selection function a little bit to work with the new continuum jitclass * started addition of free-free emission handler * updated interactions to work with new macroatom * Added continuum process frquency samplers to the continuum jitclass constructor * Fixed typo from merge conflict * Fixed spacing * small formatting updates to get the changes to track * propagated continuum through single packet loop * Cleaned up file, bound-free and free-free emission pathways should be in the correct place now * added fixture for a new continuum object * Added placeholder test for calculating the continuum opacities. I'm weary to put in exact values until we're done * reworked the contruction of the continuum class so that only a plasma object needs to be passed * Updated interaction to now get the macro activation level from the continuum object * refer to previous commit * Added the continuum_process into the single packet loop so packets can now actually interact with the contniuum * various small bugfixes to get the numba funcs to compile properly * Removed extra functions * No longer recalculate the local continuum opacities before interacting * Resolved comment from Christian, do the same process for BF cooling as BF emission * Minor formatting, currently we still don't actually run through any continuum processes because the new macroatom is not in * Switch to macro atom data and probabilities with continuum processes * Raise an exception if more than one two-photon decays are requested * Add transition info for two-photon decays to numba macro atom data * Add frequency sampler for two-photon emission * Updated the bound-free frequency sampler. Fixed an issue arising from the indexing * Now allows for continuum processes to occur * Added proper interaction type to r_packet for continuum processes * Added bound-free cooling and adiabatic cooling, debugging in progress. Current issue with macroatom running out of the block * fixed updatin gof distance_continuum in r_packet, set the chi_bf to zero when there's no cuirrent continuum * removed print statements for packet index * Removed excess print statements, added some comments for clarity * removed a couple commented-out print statements * added docstrings * fixed error from typo * Added conditional compilation of the Continuum jitclass such that normal methods are replaces with dummy methods when we are not worrying about the continuum opacities. Updated the conditional initialization of the plasma as well accordingly * updated docstring for montecarlo main loop, should be noted that passing a CPUDispatcher used as a constructor to the main loop function is slow according to numba docs, in the future a factory function should generate the main loop * added some fixed for running without continuum species * Added proper flag for adiabatic cooling * removed extra print statement to check for continuum processes in testing * removed commented out print statements * Added configuration parameter for inclusion of continuum processes and had it set during the initialization of the simulation object. Will be useful for future numba optimization as a compile-time constant * switched check for continuum processes to rely on config parameter * Added conditional paths for continuum interactions in the macroatom events based upon compile time constant * Fixed vpackets throwing a close line error * Implimented partial fixed for formal integral, development ongoing * Fixed merge issues * Fix treatment at end of line list * Updated continuum interactions to appropriately use comoving frequencies when exciting a macroatom * added copy method to continuum class * Added continuum interactions to vpacket * added continuum interactions to vpacket * Fixed arg ordering so args come before kwargs, removed conversion of lists to numpy arrays before concatenations * Vpackets now all share one continuum object since they go sequentially * decided to go with copies of continuum * Defer updating continuum if parameters have not changed since last call * removed check for updating continuum since vpackets always cross a shell boundary before updating * went back to single instance of continuum to share among vpackets since deffering updating of the continuum is unneccesary * realtivity check * Added a step to recompile the main_loop to make sure things get properly set on new runs * Removed reindexing of photoionization data to be compatable with carsus * Added fix from chvogl for handling duplicate lines * Removed the recompile since it caused issues with the lifetimes of some objects * Fixed bug introduced by relativity fix. Now recompiling the main loops works and the relativity flag has a namespace * fixed problems Co-authored-by: Andreas Flörs <afloers@users.noreply.github.com> Co-authored-by: Christian Vogl <cvogl@mpa-garching.mpg.de> * fixed tracker * Added Co-authored-by: Jack O'Brien <jobrien585@gmail.com> * trying to fix the tests Co-authored-by: Jack O'Brien <jobrien585@gmail.com> * remove recompile step due to some numba screwup related tardis-sn#1908 Co-authored-by Jack O'Brien <jobrien585@gmail.com> Co-authored-by: Christian Vogl <cvogl@mpa-garching.mpg.de> Co-authored-by: rodot- <jto33@drexel.edu> Co-authored-by: Jack O'Brien <jobrien585@gmail.com> Co-authored-by: Sona Chitchyan <chitchyan.sona@gmail.com>
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