AGN Triggering (#2)

* Added magnetic tower, agn triggering

* Finish rebase by updating input files

* Small changes

* Fixed cluster_hydro_agn_feedback python

* Changed to parthenon/develop

* Fixed hydro feedback test for Parthenon develop

* Fixed final output in regression tests

* Fixed magnetic tower ctest

* Zero masking divB when B^2==0

* Fixed Cluster restarts

* Cooling table T floor enforced

* WIP Adding AGN triggering to history

* Fixed std::max in tabular_cooling

* Debugging statements for tabular cooling

* Bug fixes in tabular cooling

* Bug fixes in AGN triggering

* Bug fixes in AGN Feedback

* AddParam fixes for upstream changes

* Fixed bug in jet precession

* Formatting

* Fixed AGN Triggering Mode in history dumps

* Removed DEBUGGING statements

* Fixed unyt unit error in testing

* Hack for tabular_cooling on DeltaGPUs

* Fixed MPI Reduction error for magnetized AGN jets

* Consolidated EOS ConsToPrim Functions

* cpp-py-formatter

* Cleanup inputs, move cooling tables

* Cooling table quick-fixes to run sims

* Cleaned up cooling cfl hack

* Thermal feedback fixes, Bondi fixes

* WIP docs for Clusters

* Adding equations to cluster docs

* Fix copyrights for cluster pgen

* Added Mathews BCG equation

* Fixed Mathews BCG profile to match reference

* Added citations to cluster docs

* Fixing formatting issues in cluster.md

* Added ipython notebook for generating cluster inputs

* Cleaned up cluster notebook

* HACK disable mass injection with thermal feedback

* Added optional AGN feedback mass fractions

* Moved gnat-sternberg.cooling

* Fixed Bondi Accretion mass removal

* Comments+Clarifications

* Fixed magnetic tower density bug

* Added Prim update to AGN Hydro feedback

* Removed Mathews BCG gravity, added density functions

* Added SNIA Feedback (no docs nor regression tests)

* Added SNIA feedback to docs and cluster input generator

* Added optional initial uniform B field

* Add optional dipole magnetic field

* Streamlined cluster_utils mass adding funcs

* Fixed number of hydro AGN feedback tests

* Fixed more add mass funcs

* Clarified HSE r-sampling parameter, removed maxdr

* Removed AGN triggering reductions from HST

* Removed defunct comment

* Avoid implicit casting of sign_jet

Co-authored-by: Philipp Grete <[email protected]>

* Removed defunct parameters from notebooks

* cpp-py-formatter

* Removed defunct `use_scratch`

* Disable SNIA feedback in cluster tests

* cpp-py-formatter

* Fixed bug in AGN power history output

* Fixed non-testing of hydro AGN feedback (still broken)

* cpp-py-formatter

* Fixed some coordinate issues in hydro_agn_feedback test

* Fixed bugs in jet coords, hydro AGN feedback

* Fixed coordinates in magnetic tower test

* cpp-py-formatter

* Cosmetic changes and enabling MPI CI for cluster tests

* Dont cool below the lower end of the cooling table

* Use Kokkos reductions

* Added checks for zero length scales, zero radii

* Add comment on theta for r=0 edge case in coord trans

* Fix temperature with kinetic feedback

* Added jet temperature and/or velocity

* Removing triggered gas conserves M,E

* cpp-py-formatter

* Updated documentation for new jet parameters

* Fixed compute jet temp from jet velocity

* Reverted triggering changes

* Fixed jet temperature and velocity check

* Fix typo

* Update var names

* Fix outdated magnetic field var names

* Fixed kinetic jet lower temp check when DEBUG

* Use mbar_over_kb for kinetic jet temp

* cpp-py-formatter

* Added header comments to cluster testing inputs

* Can change device mem in cluster notebook

* Jupyter notebbok with Precessing jet coord math

* Fixed AGN accretion to remove gas from entire grid

* cpp-py-formatter

---------

Co-authored-by: Philipp Grete <[email protected]>
Co-authored-by: Forrest Glines <[email protected]>
Co-authored-by: Forrest Glines <[email protected]>
Co-authored-by: Philipp Grete <[email protected]>
Co-authored-by: Forrest Glines <[email protected]>
Co-authored-by: par-hermes <[email protected]>

.gitignore

@@ -37,3 +37,7 @@ compile_commands.json
 
 # CMake Test files
 Testing
+
+# generate_cluster_input.ipynb files
+inputs/cluster/generate_cluster_input.ipynb
+inputs/cluster/my_cluster.input