Merge branch 'vof' of github.com:IFDL-WSU/incflo into vof

IFDL-WSU · Jun 22, 2024 · 39448dd · 39448dd
2 parents 6ee1d1c + 1356ac7
commit 39448dd
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diff --git a/.github/workflows/cleanup-cache-postpr.yml b/.github/workflows/cleanup-cache-postpr.yml
@@ -16,7 +16,7 @@ jobs:
     env:
       GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Clean up ccahe
         run: |
           gh extension install actions/gh-actions-cache

diff --git a/.github/workflows/cleanup-cache.yml b/.github/workflows/cleanup-cache.yml
@@ -16,7 +16,7 @@ jobs:
     env:
       GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Clean up ccahe
         run: |
           gh extension install actions/gh-actions-cache

diff --git a/.github/workflows/cuda.yml b/.github/workflows/cuda.yml
@@ -19,21 +19,21 @@ jobs:
     env: {CXXFLAGS: "-Werror -Wall -Wextra -Wpedantic -Wnull-dereference -Wfloat-conversion -Wshadow -Woverloaded-virtual -Wnon-virtual-dtor -Wlogical-op -Wmisleading-indentation -Wduplicated-cond -Wduplicated-branches -Wmissing-include-dirs"}
     steps:
     - name: Checkout incflo
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         path: incflo
     - name: Checkout AMReX-Hydro
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         repository: AMReX-Fluids/AMReX-Hydro
         path: AMReX-Hydro
     - name: Checkout AMReX
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         repository: AMReX-Codes/amrex
         path: amrex
     - name: Set Up Cache
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: ~/.cache/ccache
         key: ccache-${{ github.workflow }}-${{ github.job }}-git-${{ github.sha }}
@@ -85,21 +85,21 @@ jobs:
     env: {CXXFLAGS: "-Werror -Wall -Wextra -Wpedantic -Wnull-dereference -Wfloat-conversion -Wshadow -Woverloaded-virtual -Wnon-virtual-dtor -Wlogical-op -Wmisleading-indentation -Wduplicated-cond -Wduplicated-branches -Wmissing-include-dirs"}
     steps:
     - name: Checkout incflo
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         path: incflo
     - name: Checkout AMReX-Hydro
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         repository: AMReX-Fluids/AMReX-Hydro
         path: AMReX-Hydro
     - name: Checkout AMReX
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         repository: AMReX-Codes/amrex
         path: amrex
     - name: Set Up Cache
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: ~/.cache/ccache
         key: ccache-${{ github.workflow }}-${{ github.job }}-git-${{ github.sha }}
@@ -153,7 +153,7 @@ jobs:
           PR_NUMBER: ${{ github.event.number }}
         run: |
           echo $PR_NUMBER > pr_number.txt
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: pr_number
           path: pr_number.txt

diff --git a/.github/workflows/gcc.yml b/.github/workflows/gcc.yml
@@ -19,21 +19,21 @@ jobs:
     env: {CXXFLAGS: "-Werror -Wall -Wextra -Wpedantic -Wnull-dereference -Wfloat-conversion -Wshadow -Woverloaded-virtual -Wnon-virtual-dtor -Wlogical-op -Wmisleading-indentation -Wduplicated-cond -Wduplicated-branches -Wmissing-include-dirs"}
     steps:
     - name: Checkout incflo
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         path: incflo
     - name: Checkout AMReX-Hydro
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         repository: AMReX-Fluids/AMReX-Hydro
         path: AMReX-Hydro
     - name: Checkout AMReX
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         repository: AMReX-Codes/amrex
         path: amrex
     - name: Set Up Cache
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: ~/.cache/ccache
         key: ccache-${{ github.workflow }}-${{ github.job }}-git-${{ github.sha }}
@@ -89,21 +89,21 @@ jobs:
     env: {CXXFLAGS: "-Werror -Wall -Wextra -Wpedantic -Wnull-dereference -Wfloat-conversion -Wshadow -Woverloaded-virtual -Wnon-virtual-dtor -Wlogical-op -Wmisleading-indentation -Wduplicated-cond -Wduplicated-branches -Wmissing-include-dirs"}
     steps:
     - name: Checkout incflo
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         path: incflo
     - name: Checkout AMReX-Hydro
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         repository: AMReX-Fluids/AMReX-Hydro
         path: AMReX-Hydro
     - name: Checkout AMReX
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         repository: AMReX-Codes/amrex
         path: amrex
     - name: Set Up Cache
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: ~/.cache/ccache
         key: ccache-${{ github.workflow }}-${{ github.job }}-git-${{ github.sha }}
@@ -174,21 +174,21 @@ jobs:
     env: {CXXFLAGS: "-Werror -Wall -Wextra -Wpedantic -Wnull-dereference -Wfloat-conversion -Wshadow -Woverloaded-virtual -Wnon-virtual-dtor -Wlogical-op -Wmisleading-indentation -Wduplicated-cond -Wduplicated-branches -Wmissing-include-dirs"}
     steps:
     - name: Checkout incflo
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         path: incflo
     - name: Checkout AMReX-Hydro
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         repository: AMReX-Fluids/AMReX-Hydro
         path: AMReX-Hydro
     - name: Checkout AMReX
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         repository: AMReX-Codes/amrex
         path: amrex
     - name: Set Up Cache
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: ~/.cache/ccache
         key: ccache-${{ github.workflow }}-${{ github.job }}-git-${{ github.sha }}
@@ -259,21 +259,21 @@ jobs:
     env: {CXXFLAGS: "-Werror -Wall -Wextra -Wpedantic -Wnull-dereference -Wfloat-conversion -Wshadow -Woverloaded-virtual -Wnon-virtual-dtor -Wlogical-op -Wmisleading-indentation -Wduplicated-cond -Wduplicated-branches -Wmissing-include-dirs"}
     steps:
     - name: Checkout incflo
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         path: incflo
     - name: Checkout AMReX-Hydro
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         repository: AMReX-Fluids/AMReX-Hydro
         path: AMReX-Hydro
     - name: Checkout AMReX
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         repository: AMReX-Codes/amrex
         path: amrex
     - name: Set Up Cache
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: ~/.cache/ccache
         key: ccache-${{ github.workflow }}-${{ github.job }}-git-${{ github.sha }}
@@ -332,7 +332,7 @@ jobs:
           PR_NUMBER: ${{ github.event.number }}
         run: |
           echo $PR_NUMBER > pr_number.txt
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: pr_number
           path: pr_number.txt

diff --git a/.github/workflows/hip.yml b/.github/workflows/hip.yml
@@ -19,21 +19,21 @@ jobs:
     env: {CXXFLAGS: "-Werror -Wall -Wextra -Wpedantic -Wnull-dereference -Wfloat-conversion -Wshadow -Woverloaded-virtual -Wextra-semi -Wunreachable-code -Wnon-virtual-dtor -Wno-deprecated-declarations -Wno-gnu-zero-variadic-macro-arguments"}
     steps:
     - name: Checkout incflo
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         path: incflo
     - name: Checkout AMReX-Hydro
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         repository: AMReX-Fluids/AMReX-Hydro
         path: AMReX-Hydro
     - name: Checkout AMReX
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         repository: AMReX-Codes/amrex
         path: amrex
     - name: Set Up Cache
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: ~/.cache/ccache
         key: ccache-${{ github.workflow }}-${{ github.job }}-git-${{ github.sha }}
@@ -85,7 +85,7 @@ jobs:
           PR_NUMBER: ${{ github.event.number }}
         run: |
           echo $PR_NUMBER > pr_number.txt
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: pr_number
           path: pr_number.txt

diff --git a/.github/workflows/post-pr.yml b/.github/workflows/post-pr.yml
@@ -13,7 +13,7 @@ jobs:
           PR_NUMBER: ${{ github.event.number }}
         run: |
           echo $PR_NUMBER > pr_number.txt
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: pr_number
           path: pr_number.txt

diff --git a/.github/workflows/style.yml b/.github/workflows/style.yml
@@ -10,13 +10,13 @@ jobs:
   tabs:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Tabs
         run: .github/workflows/style/check_tabs.sh
 
   trailing_whitespaces:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Trailing Whitespaces
         run: .github/workflows/style/check_trailing_whitespaces.sh
diff --git a/.github/workflows/sycl.yml b/.github/workflows/sycl.yml
@@ -19,21 +19,21 @@ jobs:
     env: {CXXFLAGS: "-Werror -Wall -Wextra -Wpedantic -Wnull-dereference -Wfloat-conversion -Wshadow -Woverloaded-virtual -Wextra-semi -Wunreachable-code -Wnon-virtual-dtor -Wno-sign-compare -Wno-missing-braces"}
     steps:
     - name: Checkout incflo
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         path: incflo
     - name: Checkout AMReX-Hydro
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         repository: AMReX-Fluids/AMReX-Hydro
         path: AMReX-Hydro
     - name: Checkout AMReX
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         repository: AMReX-Codes/amrex
         path: amrex
     - name: Set Up Cache
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: ~/.cache/ccache
         key: ccache-${{ github.workflow }}-${{ github.job }}-git-${{ github.sha }}
@@ -84,7 +84,7 @@ jobs:
           PR_NUMBER: ${{ github.event.number }}
         run: |
           echo $PR_NUMBER > pr_number.txt
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: pr_number
           path: pr_number.txt

diff --git a/Docs/sphinx_documentation/source/InputsCheckpoint.rst b/Docs/sphinx_documentation/source/InputsCheckpoint.rst
@@ -5,14 +5,18 @@ Checkpoint/Restart
 
 The following inputs must be preceded by "amr" and control checkpoint/restart.
 
-+------------------+-----------------------------------------------------------------------+-------------+-----------+
-|                  | Description                                                           |   Type      | Default   |
-+==================+=======================================================================+=============+===========+
-| restart          | If present, then the name of file to restart from                     |    String   | None      |
-+------------------+-----------------------------------------------------------------------+-------------+-----------+
-| check_int        | Frequency of checkpoint output;                                       |    Int      | -1        |
-|                  | if -1 then no checkpoints will be written                             |             |           |
-+------------------+-----------------------------------------------------------------------+-------------+-----------+
-| check_file       | Prefix to use for checkpoint output                                   |  String     | chk       |
-+------------------+-----------------------------------------------------------------------+-------------+-----------+
++---------------------+-----------------------------------------------------------------------+-------------+-----------+
+|                     | Description                                                           |   Type      | Default   |
++=====================+=======================================================================+=============+===========+
+| restart             | If present, then the name of file to restart from                     |    String   | None      |
++---------------------+-----------------------------------------------------------------------+-------------+-----------+
+| plotfile_on_restart | Write a plotfile before taking a time step                            |    bool     | false     |
++---------------------+-----------------------------------------------------------------------+-------------+-----------+
+| regrid_on_restart   | Create new grids, including level 0, on restart                       |    bool     | false     |
++---------------------+-----------------------------------------------------------------------+-------------+-----------+
+| check_int           | Frequency of checkpoint output;                                       |    Int      | -1        |
+|                     | if -1 then no checkpoints will be written                             |             |           |
++---------------------+-----------------------------------------------------------------------+-------------+-----------+
+| check_file          | Prefix to use for checkpoint output                                   |  String     | chk       |
++---------------------+-----------------------------------------------------------------------+-------------+-----------+
 
diff --git a/Docs/sphinx_documentation/source/InputsTimeStepping.rst b/Docs/sphinx_documentation/source/InputsTimeStepping.rst
@@ -28,6 +28,10 @@ The inputs below must be preceded by "incflo."
 +----------------------+-----------------------------------------------------------------------+-------------+--------------+
 | cfl                  | CFL constraint (dt < cfl * dx / u) if fixed_dt not > 0                |    Real     |   0.5        |
 +----------------------+-----------------------------------------------------------------------+-------------+--------------+
+| dt_change_max        | maximum percentage dt can increase                                    |    Real     |   1.1        |
++----------------------+-----------------------------------------------------------------------+-------------+--------------+
+| init_shrink          | reduce the initial time step by this safety factor                    |    Real     |   0.1        |
++----------------------+-----------------------------------------------------------------------+-------------+--------------+
 
 Setting the Time Step
 ---------------------

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
@@ -11,8 +11,12 @@ target_sources(incflo
    incflo_correct_small_cells.cpp
    incflo_redistribute.cpp
    incflo_explicit_update.cpp
-   incflo_tagging.cpp
    incflo_regrid.cpp
+   incflo_tagging.cpp
+   incflo_update_density.cpp
+   incflo_update_tracer.cpp
+   incflo_update_velocity.cpp
+   incflo_utils.cpp
    main.cpp
    )
 

diff --git a/src/Make.package b/src/Make.package
@@ -5,8 +5,12 @@ CEXE_sources += incflo_apply_corrector.cpp
 CEXE_sources += incflo_compute_dt.cpp
 CEXE_sources += incflo_compute_forces.cpp
 CEXE_sources += incflo_explicit_update.cpp
-CEXE_sources += incflo_tagging.cpp
 CEXE_sources += incflo_regrid.cpp
+CEXE_sources += incflo_tagging.cpp
+CEXE_sources += incflo_update_density.cpp
+CEXE_sources += incflo_update_tracer.cpp
+CEXE_sources += incflo_update_velocity.cpp
+CEXE_sources += incflo_utils.cpp
 CEXE_sources += main.cpp
 
 ifeq ($(USE_EB), TRUE)