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zingalezingale
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add jac_cell unit test (#1618)
this simply displays the analytic and numerical Jacobian elements for comparison
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‎.github/workflows/jac_cell.yml

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name: jac_cell
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on: [pull_request]
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jobs:
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nse_table:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- name: Get AMReX
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run: |
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mkdir external
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cd external
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git clone https://github.com/AMReX-Codes/amrex.git
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cd amrex
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git checkout development
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echo 'AMREX_HOME=$(GITHUB_WORKSPACE)/external/amrex' >> $GITHUB_ENV
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echo $AMREX_HOME
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if [[ -n "${AMREX_HOME}" ]]; then exit 1; fi
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cd ../..
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- name: Install dependencies
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run: |
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sudo apt-get update -y -qq
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sudo apt-get -qq -y install curl cmake jq clang g++>=9.3.0
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- name: Compile jac_cell
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run: |
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cd unit_test/jac_cell
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make -j 4
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- name: Run jac_cell
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run: |
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cd unit_test/jac_cell
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./main3d.gnu.ex inputs_aprox13 > test.out
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- name: Compare to stored output
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run: |
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cd unit_test/jac_cell
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diff -I "^Initializing AMReX" -I "^AMReX" test.out ci-benchmarks/jac_cell_aprox13.out
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‎sphinx_docs/source/unit_tests.rst

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given a $\rho$, $T$, and $X_k$, call the equation of state and print out
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the thermodynamic information.
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* ``jac_cell`` :
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for a single thermodynamic state, compute the analytic Jacobian
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(using the functions provided by the network) and a numerical
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finite-difference approximation to the Jacobian and output them,
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element-by-element, to the display.
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* ``nse_table_cell`` :
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given a $\rho$, $T$, and $Y_e$, evaluate the NSE state via table interpolation

‎unit_test/jac_cell/GNUmakefile

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PRECISION = DOUBLE
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PROFILE = FALSE
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DEBUG = FALSE
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DIM = 3
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COMP = gnu
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USE_MPI = FALSE
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USE_OMP = FALSE
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USE_REACT = TRUE
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EBASE = main
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BL_NO_FORT = TRUE
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# define the location of the Microphysics top directory
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MICROPHYSICS_HOME := ../..
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# This sets the EOS directory
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EOS_DIR := helmholtz
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# This sets the network directory
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NETWORK_DIR := aprox13
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CONDUCTIVITY_DIR := stellar
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INTEGRATOR_DIR = VODE
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EXTERN_SEARCH += . ..
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Bpack := ./Make.package
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Blocs := .
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include $(MICROPHYSICS_HOME)/unit_test/Make.unit_test
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‎unit_test/jac_cell/Make.package

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CEXE_sources += main.cpp
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CEXE_headers += jac_cell.H

‎unit_test/jac_cell/README.md

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# jac_cell
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For a single thermodynamic condition, evaluate the Jacobian using both
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the analytic version from the network and the finite-difference
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numerical approximation.

‎unit_test/jac_cell/_parameters

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@namespace: unit_test
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run_prefix string ""
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small_temp real 1.e5
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small_dens real 1.e5
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# the final time to integrate to
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tmax real 1.e-2
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# first output time -- we will output in nsteps logarithmically spaced steps between [tfirst, tmax]
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tfirst real 0.0
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# number of steps (logarithmically spaced)
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nsteps int 100
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density real 1.e7
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temperature real 3.e9
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skip_initial_normalization bool 0

‎unit_test/jac_cell/ci-benchmarks/jac_cell_aprox13.out

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Initializing AMReX (24.07-16-gdcb9cc0383dc)...
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AMReX (24.07-16-gdcb9cc0383dc) initialized
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starting the single zone burn...
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J( 1, 1) = -22.83252156 -22.76871089
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J( 1, 2) = -7074.184809 -7070.885902
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J( 1, 3) = -146332.0024 -146331.961
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J( 1, 4) = -2840218.246 -2840216.758
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J( 1, 5) = -1480087.416 -1480081.685
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J( 1, 6) = -150293.5967 -150288.8284
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J( 1, 7) = -155563.9558 -155558.7711
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J( 1, 8) = -90256.26203 -90254.79555
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J( 1, 9) = -4338.739586 -4338.971348
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J( 1, 10) = -1367.526773 -1364.641738
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J( 1, 11) = -754.4182788 -751.4739669
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J( 1, 12) = -164.8910475 -163.1314012
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J( 1, 13) = 0.177283612 8.045249939e-06
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J( 1, 14) = 2.036804679e-18 2.036804635e-18
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J( 2, 1) = 22.83252156 22.76871089
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J( 2, 2) = -21223.06355 -21215.80687
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J( 2, 3) = -0.1431906097 0.01577663496
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J( 2, 4) = -0.1527366503 0
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J( 2, 5) = -0.1591006774 0
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J( 2, 6) = -0.1636464111 0
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J( 2, 7) = -0.1670557113 0
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J( 2, 8) = -0.1697073892 0
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J( 2, 9) = -0.1718287316 0
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J( 2, 10) = -0.1735643754 0
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J( 2, 11) = -0.1750107452 0
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J( 2, 12) = -0.1762345965 0
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J( 2, 13) = -0.177283612 0
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J( 2, 14) = -2.036804679e-18 -2.036804635e-18
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J( 3, 1) = -5.632962675e-25 -5.570411722e-25
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J( 3, 2) = 28286.69277 28286.69277
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J( 3, 3) = -585327.8861 -585327.8861
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J( 3, 4) = 6128.217777 6128.217777
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J( 3, 5) = -1.739488553e-26 0
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J( 3, 6) = -1.789188226e-26 0
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J( 3, 7) = -1.826462981e-26 0
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J( 3, 8) = -1.855454457e-26 0
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J( 3, 9) = -1.878647638e-26 0
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J( 3, 10) = -1.897623876e-26 0
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J( 3, 11) = -1.913437409e-26 0
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J( 3, 12) = -1.92681809e-26 0
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J( 3, 13) = -1.938287245e-26 0
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J( 3, 14) = -2.226890848e-43 -2.226890927e-43
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J( 4, 1) = -1.366807088e-23 -1.347708423e-23
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J( 4, 2) = 4.753870727e-12 1.2621475e-25
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J( 4, 3) = 731659.8313 731659.8313
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J( 4, 4) = -14216404.34 -14216404.34
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J( 4, 5) = 0.003363940593 0.003363940593
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J( 4, 6) = -1.093051048e-24 0
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J( 4, 7) = -1.115822945e-24 0
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J( 4, 8) = -1.13353442e-24 0
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J( 4, 9) = -1.1477036e-24 0
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J( 4, 10) = -1.159296566e-24 0
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J( 4, 11) = -1.168957371e-24 0
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J( 4, 12) = -1.177131898e-24 0
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J( 4, 13) = -1.184138635e-24 0
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J( 4, 14) = -1.360452377e-41 -1.360452352e-41
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J( 5, 1) = 8.302657095e-24 8.170002764e-24
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J( 5, 2) = 3.153014201e-25 1.88760336e-28
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J( 5, 3) = 3.547140976e-25 1.88760336e-28
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J( 5, 4) = 17050492.88 17050492.88
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J( 5, 5) = -8880490.115 -8880490.115
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J( 5, 6) = 0.0001669112793 0.0001669112793
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J( 5, 7) = -5.810350496e-23 0
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J( 5, 8) = -5.809693618e-23 0
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J( 5, 9) = -5.809168116e-23 0
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J( 5, 10) = -5.808738159e-23 0
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J( 5, 11) = -5.808379862e-23 0
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J( 5, 12) = -5.808076688e-23 0
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J( 5, 13) = -5.807816824e-23 0
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J( 5, 14) = 5.045605543e-42 5.045605749e-42
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J( 6, 1) = 9.417373366e-24 9.308549997e-24
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J( 6, 2) = 7.540626412e-25 2.20220392e-28
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J( 6, 3) = 6.930014139e-18 2.204043829e-28
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J( 6, 4) = 5.942221324e-23 0
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J( 6, 5) = 10360571.8 10360571.8
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J( 6, 6) = -1052021.799 -1052021.799
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J( 6, 7) = 2.618223472 2.618223472
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J( 6, 8) = 5.952275493e-23 0
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J( 6, 9) = 5.953532264e-23 0
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J( 6, 10) = 5.954560531e-23 0
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J( 6, 11) = 5.955417421e-23 0
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J( 6, 12) = 5.956142481e-23 0
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J( 6, 13) = 5.956763961e-23 0
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J( 6, 14) = 1.206687442e-41 1.206687398e-41
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J( 7, 1) = -4.433213398e-26 -4.216253314e-26
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J( 7, 2) = -1.713032535e-26 0
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J( 7, 3) = 9.755839735e-19 2.590167837e-32
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J( 7, 4) = -2.055639042e-26 0
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J( 7, 5) = -2.141290668e-26 0
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J( 7, 6) = 1202310.628 1202310.628
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J( 7, 7) = -1244476.153 -1244476.153
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J( 7, 8) = 10.56270301 10.56270301
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J( 7, 9) = -2.312593922e-26 0
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J( 7, 10) = -2.335953456e-26 0
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J( 7, 11) = -2.355419735e-26 0
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J( 7, 12) = -2.371891202e-26 0
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J( 7, 13) = -2.386009602e-26 0
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J( 7, 14) = -2.741277362e-43 -2.741278343e-43
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J( 8, 1) = 5.935462112e-25 5.877272628e-25
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J( 8, 2) = 4.909905946e-26 0
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J( 8, 3) = 5.523644189e-26 0
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J( 8, 4) = 5.891887135e-26 0
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J( 8, 5) = 6.137382433e-26 0
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J( 8, 6) = 6.312736216e-26 0
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J( 8, 7) = 1400032.306 1400032.306
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J( 8, 8) = -812316.926 -812316.926
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J( 8, 9) = 1.524756764 1.524756764
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J( 8, 10) = 6.69532629e-26 0
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J( 8, 11) = 6.751120676e-26 0
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J( 8, 12) = 6.79833131e-26 0
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J( 8, 13) = 6.838797568e-26 0
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J( 8, 14) = 7.857068531e-43 7.857069044e-43
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J( 9, 1) = 8.75876269e-25 8.591697512e-25
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J( 9, 2) = 1.000399222e-25 0
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J( 9, 3) = 1.125449125e-25 0
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J( 9, 4) = 1.200479066e-25 0
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J( 9, 5) = 1.250499028e-25 0
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J( 9, 6) = 1.286227571e-25 0
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J( 9, 7) = 1.313023979e-25 0
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J( 9, 8) = 902561.1588 902561.1588
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J( 9, 9) = -43393.10183 -43393.10183
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J( 9, 10) = 136.1591093 136.1591093
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J( 9, 11) = 1.37554893e-25 0
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J( 9, 12) = 1.385168154e-25 0
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J( 9, 13) = 1.393413202e-25 0
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J( 9, 14) = 1.600887132e-42 1.600887039e-42
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J( 10, 1) = 3.341465689e-26 3.256971428e-26
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J( 10, 2) = 3.653921958e-27 0
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J( 10, 3) = 4.110662202e-27 0
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J( 10, 4) = 4.384706349e-27 0
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J( 10, 5) = 4.567402447e-27 0
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J( 10, 6) = 4.69789966e-27 0
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J( 10, 7) = 4.79577257e-27 0
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J( 10, 8) = 4.871895944e-27 0
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J( 10, 9) = 47730.54842 47730.54842
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J( 10, 10) = -15310.60916 -15310.60916
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J( 10, 11) = 0.002383888334 0.002383888334
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J( 10, 12) = 5.059276557e-27 0
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J( 10, 13) = 5.089391298e-27 0
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J( 10, 14) = 5.847182318e-44 5.847181188e-44
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J( 11, 1) = 7.727968776e-27 7.52140159e-27
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J( 11, 2) = 1.166347238e-27 0
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J( 11, 3) = 1.312140643e-27 0
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J( 11, 4) = 1.399616686e-27 0
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J( 11, 5) = 1.457934048e-27 0
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J( 11, 6) = 1.499589306e-27 0
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J( 11, 7) = 1.53083075e-27 0
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J( 11, 8) = 1.555129651e-27 0
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J( 11, 9) = 1.574568772e-27 0
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J( 11, 10) = 16539.09179 16539.09179
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J( 11, 11) = -9017.692804 -9017.692804
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J( 11, 12) = 0.000548515294 0.000548515294
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J( 11, 13) = 1.624555082e-27 0
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J( 11, 14) = 1.866445159e-44 1.866444877e-44
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J( 12, 1) = 7.899733031e-27 7.648455578e-27
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J( 12, 2) = 1.384355059e-27 0
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J( 12, 3) = 1.557399442e-27 0
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J( 12, 4) = 1.661226071e-27 0
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J( 12, 5) = 1.730443824e-27 0
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J( 12, 6) = 1.779885076e-27 0
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J( 12, 7) = 1.816966015e-27 0
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J( 12, 8) = 1.845806746e-27 0
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J( 12, 9) = 1.86887933e-27 0
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J( 12, 10) = 1.887756899e-27 0
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J( 12, 11) = 9769.164387 9769.164387
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J( 12, 12) = -2120.709403 -2120.709403
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J( 12, 13) = 0.0001045882492 0.0001045882492
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J( 12, 14) = 2.215311799e-44 2.215311465e-44
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J( 13, 1) = 2.36704737e-27 2.283840256e-27
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J( 13, 2) = 4.518871185e-28 0
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J( 13, 3) = 5.083730083e-28 0
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J( 13, 4) = 5.422645422e-28 0
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J( 13, 5) = 5.648588981e-28 0
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J( 13, 6) = 5.809977238e-28 0
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J( 13, 7) = 5.93101843e-28 0
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J( 13, 8) = 6.02516158e-28 0
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J( 13, 9) = 6.1004761e-28 0
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J( 13, 10) = 6.16209707e-28 0
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J( 13, 11) = 6.213447879e-28 0
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J( 13, 12) = 2283.840256 2283.840256
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J( 13, 13) = -0.0001126334991 -0.0001126334991
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J( 13, 14) = 7.231315828e-45 7.231315425e-45
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J( 14, 1) = 1.335535433e+19 1.331810907e+19
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J( 14, 2) = 1.672678172e+22 1.221628179e+22
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J( 14, 3) = 1.764169333e+23 1.669883326e+23
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J( 14, 4) = 6.38519349e+24 6.382691446e+24
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J( 14, 5) = 3.575435081e+24 3.56443165e+24
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J( 14, 6) = 2.522960852e+23 2.518972785e+23
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J( 14, 7) = 2.567887496e+23 2.492143743e+23
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J( 14, 8) = 1.63734141e+23 1.532779936e+23
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J( 14, 9) = 1.46197563e+22 5.363178614e+21
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J( 14, 10) = 1.41303877e+22 2.541660459e+21
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J( 14, 11) = 7.680250114e+21 1.43978686e+21
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J( 14, 12) = 6.72190453e+21 3.147552442e+20
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J( 14, 13) = -1.03705583e+17 -1.56260658e+13
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J( 14, 14) = -1.191469501 -1.191474366
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AMReX (24.07-16-gdcb9cc0383dc) finalized

‎unit_test/jac_cell/inputs_aprox13

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unit_test.run_prefix = "react_aprox13_"
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unit_test.small_temp = 1.e5
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unit_test.small_dens = 1.e5
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integrator.burner_verbose = 0
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# Set which jacobian to use
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# 1 = analytic jacobian
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# 2 = numerical jacobian
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integrator.jacobian = 2
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integrator.renormalize_abundances = 0
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integrator.rtol_spec = 1.0e-6
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integrator.rtol_enuc = 1.0e-6
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integrator.atol_spec = 1.0e-6
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integrator.atol_enuc = 1.0e-6
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unit_test.tmax = 1.e-2
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unit_test.density = 1.e6
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unit_test.temperature = 3.e9
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unit_test.X1 = 1.0
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unit_test.X2 = 0.0
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unit_test.X3 = 0.0
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unit_test.X4 = 0.0
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unit_test.X5 = 0.0
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unit_test.X6 = 0.0
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unit_test.X7 = 0.0
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unit_test.X8 = 0.0
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unit_test.X9 = 0.0
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unit_test.X10 = 0.0
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unit_test.X11 = 0.0
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unit_test.X12 = 0.0
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unit_test.X13 = 0.0

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