Combined Source Term lookups

…sport (AMReX-Combustion#492)

* manifold/table EOS support

* Convert tabs to spaces

* Initial framework for neural net based manifold EoS

Still need to generalize TabFuncParams and TabFuncData and work the neural net into the existing EoS framework

* Tentative start to NNFuncParams and NNFuncData

* Use generalize ManifoldFunc class instead of using TabFunc directly

* Migrate get_var_index; have TabFuncData inherit from ManFuncData

- Moved get_var_index to ManifoldFunc.H instead of EosParams.H
- Shortened get_var_index arglist

* Switch fully over to using generic ManFuncData struct when possible

* Mostly complete setup (I hope) for neural net manifold

- Still need to calculate source terms
- Still need to account for variables passed to input layer
- Maybe we can worry about GPUs later

* Set up neural net manifold to evaluate source terms

- This style of manifold will print all of the metadata properly, but SEGFAULTs at some point in EosEval/main.cpp

* Fixed SEGFAULT

* Non-crashing version of neural net manifold

* Switch manifold model selection to runtime parameter

* Add variable indices to NeuralNet manifold parameter defs

* Let manifold models read in mass fractions prefixed with Y-

* A few fixes to let IgnitionDelay run with neural net

* Make including training variables (mass fractions) in output variables optional

* Allow for reading of manifold biases from info file

* Fix an issue with calculating derivatives; add semicolon

* Switch to different initialization for iss

* Merge pull request #1 from baperry2/manifold

Combined Source Term lookups

* Use correct accessor dimension in loop bound

* Changes in Eos/ and Transport/ to permit home-rolled evaluation

* Add a few checks to ensure the input is valid

* Merge branch 'kiraneiden/manifold' of github.com:KiranEiden/PelePhysics into kiraneiden/manifold

* Avoid editing nnf_data, make indata_copy local again

* Implement 'get_all_values' function

* add inverse density option

* merge in updated pelephysics

* move new EOS files to Source/Eos

* other updates for EOS bringing in manifold

* constraints for physics combinations with manifold

* stuff for building with manifold transport

* bring in manifold transport

* changes to compile manifold stuff

* table lookup improvement

* EosEval test case

* clang-format new EOS stuff

* more formatting

* a few more missed files for formatting

* fix mangles make.package

* locate is a host device function

* address codespell issues

* move blackboxfunc to its own utility rather than part of eos

* gmake for moved blackboxfunc

* don't initialize idx_Wdot to avoid issues

* add some runtime gamma support, but warn because its risky

* dont compute wdot in test for gammalaw

* fix some bugs on cuda

* remove some hacks for manifold eos

* try running manifold in CI

* add_mani_src stuff change default in manifold EOS

* updates for Manifold in TranEval

* remove ProductionRateEval - EosEval tests the same thing

* partial removal of wdot stuff from black box funcs

* some sample network stuff

* new generic parameter stuff

* working template + Factory stuff

* updates to PeleParamsGeneric for templating

* move ManFuncData out of ManFuncParams

* improved GPU data management with templating

* remove old manfuncdata stuff

* remove a bunch of stupid test code

* start moving transport to new GPU data template

* trans stuff initialize using eos stuff

* clang-format and remove an old file

* remove unneeded file

* more clang-format

* fix spelling

* remove network evaluator using pytorch library for now

* clean up test cases; finish removing pytorch lib dep

* remove deprecated ManFuncParams class

* Add override tag to remove warning

* fix transport test in CI for manifold to use right chemistry

* add netork inputs file for transport

* no transparm in reacteval

* no transparm in ignition delay

* table dimensionality templates

* modify error checking in table

* compile time choice of network vs table for manifold

* add factory function for blackboxfunc

* move interpolation functions outside of table class for templating

* don't compile with Manifold for SYCL

final compilation change for no manifold with sycl

* rename ManifoldFunc to BlackBoxFunc

* 1D table if not manifold EOS

* revert some changes in ci workflow

* remove duplicate NUM_ELEMENTS in Null mech

* fix a bunch of compiler warnings

* fix a bunch more warnings

* streamline data storage for manifold models

* don't need changes in Make.package

* fix all clang-tidy stuff

* change species index from is to i in Eos loops

* style changes in EosParams

* use more verbose names in black box function stuff

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Co-authored-by: Kiran Eiden <[email protected]>
Co-authored-by: KiranEiden <[email protected]>

ceptr: Added functionality for reading and converting PLOG reactions.