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‎.gitattributes‎

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/tests/**/* linguist-generated=true
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/toolchain/mechanisms/* linguist-generated=true

‎.github/workflows/cleanness.yml‎

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name: Cleanness
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on: [push, pull_request, workflow_dispatch]
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jobs:
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cleanness:
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name: Code Cleanness Test
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runs-on: "ubuntu-latest"
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env:
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pr_everything: 0
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master_everything: 0
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steps:
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- name: Clone - PR
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uses: actions/checkout@v3
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with:
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path: pr
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- name: Clone - Master
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uses: actions/checkout@v3
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with:
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repository: MFlowCode/MFC
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ref: master
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path: master
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- name: Setup Ubuntu
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run: |
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sudo apt update -y
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sudo apt install -y tar wget make cmake gcc g++ python3 python3-dev "openmpi-*" libopenmpi-dev
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- name: Build
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run: |
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(cd pr && /bin/bash mfc.sh build -j $(nproc) --debug 2> ../pr.txt)
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(cd master && /bin/bash mfc.sh build -j $(nproc) --debug 2> ../master.txt)
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sed -i '/\/pr\//d' pr.txt
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sed -i '/\/master\//d' master.txt
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- name: Unused Variables Diff
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run: |
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grep -F 'Wunused-variable' master.txt -B 4 > mUnused.txt
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grep -F 'Wunused-variable' pr.txt -B 4 > prUnused.txt
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diff prUnused.txt mUnused.txt || true
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- name: Unused Dummy Arguments Diff
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run: |
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grep -F 'Wunused-dummy-argument' pr.txt -B 4 > prDummy.txt
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grep -F 'Wunused-dummy-argument' master.txt -B 4 > mDummy.txt
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diff prDummy.txt mDummy.txt || true
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- name: Unused Value Diff
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run: |
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grep -F 'Wunused-value' pr.txt -B 4 > prUnused_val.txt
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grep -F 'Wunused-value' master.txt -B 4 > mUnused_val.txt
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diff prUnused_val.txt mUnused_val.txt || true
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- name: Maybe Uninitialized Variables Diff
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run: |
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grep -F 'Wmaybe-uninitialized' pr.txt -B 4 > prMaybe.txt
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grep -F 'Wmaybe-uninitialized' master.txt -B 4 > mMaybe.txt
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diff prMaybe.txt mMaybe.txt || true
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- name: Everything Diff
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run: |
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grep '\-W' pr.txt -B 4 > pr_every.txt
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grep '\-W' master.txt -B 4 > m_every.txt
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diff pr_every.txt m_every.txt || true
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- name: List of Warnings
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run: |
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cat pr_every.txt
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- name: Summary
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run: |
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pr_variable=$(grep -c -F 'Wunused-variable' pr.txt -B 4)
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pr_argument=$(grep -c -F 'Wunused-dummy-argument' pr.txt -B 4)
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pr_value=$(grep -c -F 'Wunused-value' pr.txt -B 4)
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pr_uninit=$(grep -c -F 'Wmaybe-uninitialized' pr.txt -B 4)
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pr_everything=$(grep -c '\-W' pr.txt -B 4)
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master_variable=$(grep -c -F 'Wunused-variable' master.txt -B 4)
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master_argument=$(grep -c -F 'Wunused-dummy-argument' master.txt -B 4)
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master_value=$(grep -c -F 'Wunused-value' master.txt -B 4)
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master_uninit=$(grep -c -F 'Wmaybe-uninitialized' master.txt -B 4)
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master_everything=$(grep -c '\-W' master.txt -B 4)
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echo "pr_everything=$pr_everything" >> $GITHUB_ENV
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echo "master_everything=$master_everything" >> $GITHUB_ENV
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echo "Difference is how many warnings were added or removed from master to pr, negative numbers are better since you are removing warnings"
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echo "Unused Variable Count: $pr_variable, Difference: $((pr_variable - master_variable))"
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echo "Unused Dummy Argument: $pr_argument, Difference: $((pr_argument - master_argument))"
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echo "Unused Value: $pr_value, Difference: $((pr_value - master_value))"
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echo "Maybe Uninitialized: $pr_uninit, Difference: $((pr_uninit - master_uninit))"
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echo "Everything: $pr_everything, Difference: $((pr_everything - master_everything))"
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- name: Check Differences
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if: env.pr_everything > env.master_everything
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run: |
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echo "Difference between warning count in PR is greater than in master."
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exit 1
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‎.github/workflows/docs.yml‎

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name: Documentation
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on:
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push:
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branches:
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- master
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workflow_dispatch:
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on: [push, pull_request, workflow_dispatch]
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jobs:
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docs:
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name: Build & Publish
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runs-on: ubuntu-latest
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if: github.repository == 'MFlowCode/MFC'
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concurrency:
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group: docs-publish
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cancel-in-progress: true
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echo "excluded-count = ${{ steps.sitemap.outputs.excluded-count }}"
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- name: Publish Documentation
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if: github.repository == 'MFlowCode/MFC' && github.ref == 'refs/heads/master' && github.event_name == 'push'
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run: |
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set +e
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git ls-remote "${{ secrets.DOC_PUSH_URL }}" -q

‎.github/workflows/test.yml‎

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- name: Setup MacOS
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if: matrix.os == 'macos'
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run: |
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brew install coreutils python cmake fftw hdf5 gcc@14 open-mpi
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brew install coreutils python cmake fftw hdf5 gcc@14 boost open-mpi
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echo "FC=gfortran-14" >> $GITHUB_ENV
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echo "BOOST_INCLUDE=/opt/homebrew/include/" >> $GITHUB_ENV
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- name: Setup Ubuntu
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if: matrix.os == 'ubuntu' && matrix.intel == false
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with:
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name: logs
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path: test-${{ matrix.device }}.out
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‎CMakeLists.txt‎

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-D MFC_${${target}_UPPER}
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-D MFC_COMPILER="${CMAKE_Fortran_COMPILER_ID}"
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-D MFC_CASE_OPTIMIZATION=False
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-D chemistry=False
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--line-numbering
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--no-folding
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"${fpp}" "${f90}"

‎README.md‎

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We'll give a brief intro. here for MacOS.
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Using [brew](https://brew.sh), install MFC's dependencies:
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```shell
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brew install coreutils python cmake fftw hdf5 gcc open-mpi
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brew install coreutils python cmake fftw hdf5 gcc boost open-mpi
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```
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You're now ready to build and test MFC!
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Put it to a convenient directory via
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```shell
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git clone https://github.com/MFlowCode/MFC
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cd MFC
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```
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and be sure MFC knows where to find Boost by appending to your dotfiles and sourcing them again
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```shell
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echo -e 'export BOOST_INCLUDE=/opt/homebrew/' | tee -a ~/.bash_profile ~/.zshrc
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. ~/.bash_profile 2>/dev/null || . ~/.zshrc 2>/dev/null
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! [ -z "${BOOST_INCLUDE+x}" ] && echo 'Environment is ready!' || echo 'Error: $BOOST_INCLUDE is unset. Please adjust the previous commands to fit with your environment.'
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```
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then you can build MFC and run the test suite!
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```shell
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./mfc.sh build -j $(nproc)

‎docs/documentation/case.md‎

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Some parameters, as described above, can be defined by analytical functions in the input file. For example, one can define the following patch:
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```shell
185-
'patch_icpp(2)%geometry' : 15,
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'patch_icpp(2)%geometry' : 1,
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'patch_icpp(2)%x_centroid' : 0.25,
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'patch_icpp(2)%length_x' : 9.5,
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'patch_icpp(2)%vel(1)' : 0.,
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and use `patch_icpp(i)%%geometry = 7` and `patch_icpp(i)%%hcid = 200` in the input file.
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Additional variables can be declared in `Hardcoded1[2,3]DVariables` and used in `hardcoded1[2,3]D`.
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As a convention, any hard coded patches that are part of the MFC master branch should be identified as 1[2,3]xx where the first digit indites the number of dimensions.
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As a convention, any hard coded patches that are part of the MFC master branch should be identified as 1[2,3]xx where the first digit indicates the number of dimensions.
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#### Parameter Descriptions
234234

@@ -353,9 +353,9 @@ Details of implementation of viscosity in MFC can be found in [Coralic (2015)](r
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| `mp_weno` | Logical | Monotonicity preserving WENO |
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| `riemann_solver` | Integer | Riemann solver algorithm: [1] HLL*; [2] HLLC; [3] Exact* |
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| `low_Mach` | Integer | Low Mach number correction for HLLC Riemann solver: [0] None; [1] Pressure (Chen et al. 2022); [2] Velocity (Thornber et al. 2008) |
356-
| `avg_state` | Integer | Averaged state evaluation method: [1] Roe averagen*; [2] Arithmetic mean |
356+
| `avg_state` | Integer | Averaged state evaluation method: [1] Roe average*; [2] Arithmetic mean |
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| `wave_speeds` | Integer | Wave-speed estimation: [1] Direct (Batten et al. 1997); [2] Pressure-velocity* (Toro 1999) |
358-
| `weno_Re_flux` | Logical | Compute velocity gradient using scaler divergence theorem |
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| `weno_Re_flux` | Logical | Compute velocity gradient using scalar divergence theorem |
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| `weno_avg` | Logical | Arithmetic mean of left and right, WENO-reconstructed, cell-boundary values |
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| `dt` | Real | Time step size |
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| `t_step_start` | Integer | Simulation starting time step |
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- `wave_speeds` specifies the choice of the method to compute the left, right, and middle wave speeds in the Riemann solver by an integer of 1 and 2.
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`wave_speeds = 1` and `2` correspond to the direct method ([Batten et al., 1997](references.md#Batten97)), and indirect method that approximates the pressures and velocity ([Toro, 2013](references.md#Toro13)), respectively.
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- `weno_Re_flux` activates the scaler divergence theorem in computing the velocity gradients using WENO-reconstructed cell boundary values.
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- `weno_Re_flux` activates the scalar divergence theorem in computing the velocity gradients using WENO-reconstructed cell boundary values.
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If this option is false, velocity gradient is computed using finite difference scheme of order 2 which is independent of the WENO order.
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- `weno_avg` it activates the arithmetic average of the left and right, WENO-reconstructed, cell-boundary values.
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- `%%element_on` specifies the element number of the transducer array that is on. The element number starts from 1. If all elements are on, set `%%element_on` to 0.
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595-
- `%%element_spacing_angle` specifies the spacing angle between adjacent transducer in radian. The total aperture (`%%aperture`) is set, so each transducer element is smaller if `%%element_spacing_angle` is larger.
595+
- `%%element_spacing_angle` specifies the spacing angle between adjacent transducer in radians. The total aperture (`%%aperture`) is set, so each transducer element is smaller if `%%element_spacing_angle` is larger.
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597597
- `%%element_polygon_ratio` specifies the ratio of the polygon side length to the aperture diameter of each transducer element in a circular 3D transducer array. The polygon side length is calculated by using the total aperture (`%%aperture`) as the circumcicle diameter, and `%%num_elements` as the number of sides of the polygon. The ratio is used specify the aperture size of each transducer element in the array, as a ratio of the total aperture.
598598

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679679
| Parameter | Type | Description |
680680
| ---: | :----: | :--- |
681-
| `perturb_flow` | Logical | Perturb the initlal velocity field by random noise |
681+
| `perturb_flow` | Logical | Perturb the initlial velocity field by random noise |
682682
| `perturb_flow_fluid` | Integer | Fluid density whose flow is to be perturbed |
683683
| `perturb_flow_mag` | Real | Set the magnitude of flow perturbations |
684684
| `perturb_sph` | Logical | Perturb the initial partial density by random noise |
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| 4 | Sweep line | 2 | Y | Not coordinate aligned. Requires `[x,y]_centroid` and `normal(i)`. |
790790
| 5 | Ellipse | 2 | Y | Requires `[x,y]_centroid` and `radii(i)`. |
791791
| 6 | N/A | 2 | N | No longer exists. Empty. |
792-
| 7 | 2D analytical | 2 | N | Assigns the primitive variables as analytical functions. |
792+
| 7 | 2D Hardcoded | 2 | N | Assigns the primitive variables as analytical functions. |
793793
| 8 | Sphere | 3 | Y | Requires `[x,y,z]_centroid` and `radius` |
794794
| 9 | Cuboid | 3 | N | Coordinate-aligned. Requires `[x,y,z]_centroid` and `length_[x,y,z]`. |
795795
| 10 | Cylinder | 3 | Y | Requires `[x,y,z]_centroid`, `radius`, and `length_[x,y,z]`. |
796796
| 11 | Sweep plane | 3 | Y | Not coordinate-aligned. Requires `x[y,z]_centroid` and `normal(i)`. |
797797
| 12 | Ellipsoid | 3 | Y | Requires `[x,y,z]_centroid` and `radii(i)`. |
798-
| 13 | 3D analytical | 3 | N | Assigns the primitive variables as analytical functions |
798+
| 13 | 3D Hardcoded | 3 | N | Assigns the primitive variables as analytical functions |
799799
| 14 | Spherical Harmonic | 3 | N | Requires `[x,y,z]_centroid`, `radius`, `epsilon`, `beta` |
800-
| 15 | 1D analytical | 1 | N | Assigns the primitive variables as analytical functions |
800+
| 15 | 1D Hardcoded | 1 | N | Assigns the primitive variables as analytical functions |
801801
| 16 | 1D bubble pulse | 1 | N | Requires `x_centroid`, `length_x` |
802802
| 17 | Spiral | 2 | N | Requires `[x,y]_centroid` |
803803
| 18 | 2D Varcircle | 2 | Y | Requires `[x,y]_centroid`, `radius`, and `thickness` |

‎docs/documentation/getting-started.md‎

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<details>
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<summary><h3>MacOS</h3></summary>
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104-
Using [Homebrew](https://brew.sh/) you can install the necessary dependencies:
104+
Using [Homebrew](https://brew.sh/) you can install the necessary dependencies
105+
before configuring your environment:
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106107
```shell
107-
brew install coreutils python cmake fftw hdf5 gcc open-mpi
108+
brew install coreutils python cmake fftw hdf5 gcc boost open-mpi
109+
echo -e 'export BOOST_INCLUDE=/opt/homebrew/' | tee -a ~/.bash_profile ~/.zshrc
110+
. ~/.bash_profile 2>/dev/null || . ~/.zshrc 2>/dev/null
111+
! [ -z "${BOOST_INCLUDE+x}" ] && echo 'Environment is ready!' || echo 'Error: $BOOST_INCLUDE is unset. Please adjust the previous commands to fit with your environment.'
108112
```
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They will download the dependencies MFC requires to build itself.

‎misc/fpp_to_fypp.sh‎

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#!/bin/bash
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for file in $(find src -type f | grep -Ev 'autogen' | grep -E '\.fpp$'); do
4+
echo "$file"
5+
mv "$file" "$(echo "$file" | sed s/\.fpp/\.fypp/)"
6+
done

‎src/common/include/macros.fpp‎

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140140
#endif
141141
#:enddef
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143-
#:def PROHIBIT(*args)
144-
#:set condition = args[0]
145-
#:if len(args) == 1
146-
#:set message = '""'
147-
#:else
148-
#:set message = args[1]
149-
#:endif
143+
#:def PROHIBIT(condition, message = None)
150144
if (${condition}$) then
151-
call s_prohibit_abort("${condition}$", ${message}$)
145+
call s_prohibit_abort("${condition}$", ${message or '""'}$)
152146
end if
153147
#:enddef
154148

155149
#define t_vec3 real(kind(0d0)), dimension(1:3)
156150
#define t_mat4x4 real(kind(0d0)), dimension(1:4,1:4)
151+
152+
#:def ASSERT(predicate, message = None)
153+
if (.not. (${predicate}$)) then
154+
call s_mpi_abort("${_FILE_.split('/')[-1]}$:${_LINE_}$: "// &
155+
"Assertion failed: ${predicate}$. " &
156+
//${message or '"No error description."'}$)
157+
end if
158+
#:enddef

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