[init]

.github/workflows/ci.yml

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+name: CI
+
+on:
+
+  push:
+    branches:
+      - main
+
+jobs:
+
+  extract-nd:
+    name: Compile sources and push 2d and 3d branches
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        dimension: [2, 3]
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@main
+        with:
+          repository: "NaokiHori/SpectralNSSolver1"
+          ref: ${{ github.ref_name }}
+          submodules: "recursive"
+      - name: Install dependencies
+        run: |
+          sudo apt-get -y update && \
+          sudo apt-get -y install make libopenmpi-dev libfftw3-dev
+      - name: Remove another dimension
+        run: |
+          python .github/workflows/extract_nd_main.py ${{ matrix.dimension }}
+      - name: Modify Makefile
+        run: |
+          sed -i "s/DNDIMS=2/DNDIMS=${{ matrix.dimension }}/g" Makefile
+      - name: Compile
+        run: |
+          make all
+      - name: Commit and push change
+        run: |
+          set -x
+          set -e
+          git switch -c ${{ matrix.dimension }}d
+          git config --local user.email "36466440+NaokiHori@users.noreply.github.com"
+          git config --local user.name "NaokiHori"
+          # not include documentation in each branch
+          git rm -r docs
+          # let IC generator of the given dimension as main.py
+          cd initial_condition
+          find . -type f -not -name ${{ matrix.dimension }}d.py | xargs git rm
+          git mv ${{ matrix.dimension }}d.py main.py
+          cd ..
+          # declare to track others, just in case
+          git add exec.sh
+          git add include
+          git add LICENSE
+          git add Makefile
+          git add README.rst
+          git add src
+          # commit and push
+          git commit -m "Extract ${{ matrix.dimension }}d sources" -a || true
+          git push -f origin ${{ matrix.dimension }}d
+
+  build-and-run:
+    name: Build library and try to run test case
+    runs-on: ubuntu-latest
+    needs: [extract-nd]
+    strategy:
+      matrix:
+        dimension: [2, 3]
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@main
+        with:
+          repository: "NaokiHori/SpectralNSSolver1"
+          ref: ${{ matrix.dimension }}d
+          submodules: "recursive"
+      - name: Install dependencies
+        run: |
+          sudo apt-get -y update && \
+          sudo apt-get -y install make libopenmpi-dev libfftw3-dev
+      - name: Install python dependencies for pre-processing
+        run: |
+          python -m pip install --upgrade pip
+          pip install numpy
+      - name: Pre-process
+        run: |
+          set -x
+          set -e
+          cd initial_condition
+          python3 main.py 0
+          ls output
+          cd ..
+      - name: Build
+        run: |
+          set -x
+          set -e
+          make clean
+          make output
+          make all
+      - name: Run
+        run: |
+          export timemax=5.0e+0
+          export wtimemax=6.0e+2
+          export log_rate=5.0e-1
+          export save_rate=1.0e+0
+          export Re=1.0e+2
+          export Sc=1.0e-1
+          dirname_ic=initial_condition/output
+          mpirun -n 4 --oversubscribe ./a.out ${dirname_ic}
+

.github/workflows/documentation.yml

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+name: Documentation
+
+on:
+
+  push:
+    branches:
+      - main
+    paths:
+      - docs/**
+      - .github/workflows/documentation.yml
+
+jobs:
+
+  build-doc:
+    name: Build documentation
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@main
+        with:
+          repository: "NaokiHori/SpectralNSSolver1"
+          ref: ${{ github.ref_name }}
+      - name: Check dead links
+        run: |
+          docker run \
+            --rm \
+            --volume ${PWD}:/project \
+            --workdir /project \
+            sphinxdoc/sphinx:latest \
+            sphinx-build -M linkcheck "docs/source" "docs/build"
+          log=docs/build/linkcheck/output.txt
+          if [ -e ${log} ]; then
+            wc -l ${log}
+            cat ${log}
+          fi
+      - name: Build documentation using Sphinx
+        run: |
+          docker run \
+            --rm \
+            --volume ${PWD}:/project \
+            --workdir /project \
+            sphinxdoc/sphinx:latest \
+            sphinx-build -M html "docs/source" "docs/build"
+      - name: Upload HTML artifacts
+        uses: actions/upload-artifact@v3
+        with:
+          name: DocHTML
+          path: docs/build/html
+
+  deploy-doc:
+    name: Deploy documentation
+    permissions:
+      contents: read
+      pages: write
+      id-token: write
+    concurrency:
+      group: "pages"
+      cancel-in-progress: true
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    needs: [build-doc]
+    steps:
+      - name: Download HTML artifacts
+        uses: actions/download-artifact@v3
+        with:
+          name: DocHTML
+          path: docs/build/html
+      - name: Setup GitHub Pages
+        uses: actions/configure-pages@main
+      - name: Upload HTML
+        uses: actions/upload-pages-artifact@v1
+        with:
+          path: docs/build/html
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@main
+

.github/workflows/extract_nd_main.py

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+import os
+import sys
+import glob
+import enum
+
+def get_filenames(root):
+    results = glob.glob(f"{root}/**", recursive=True)
+    retvals = list()
+    for result in results:
+        if result.endswith(".c") or result.endswith(".h"):
+            retvals.append(result)
+    return retvals
+
+class NdimsType(enum.Enum):
+    OUT   = enum.auto()
+    IN_2D = enum.auto()
+    IN_3D = enum.auto()
+
+def extract(ndims, lines):
+    state = NdimsType.OUT
+    if_level = 0
+    if_level_ndims = 0
+    newlines = list()
+    for line in lines:
+        is_on_ndims_macro = False
+        if "#if" in line:
+            # found "if", increase nest counter
+            if_level += 1
+            if " NDIMS" in line:
+                if "NDIMS==2" in line.replace(" ", ""):
+                    is_on_ndims_macro = True
+                    # now in 2D condition
+                    state = NdimsType.IN_2D
+                    if_level_ndims = if_level
+                if "NDIMS==3" in line.replace(" ", ""):
+                    is_on_ndims_macro = True
+                    # now in 3D condition
+                    state = NdimsType.IN_3D
+                    if_level_ndims = if_level
+        elif "#else" in line:
+            # check this "else" is for ndims
+            if if_level == if_level_ndims:
+                is_on_ndims_macro = True
+                # if it is, swap state (3d if now 2d, vice versa)
+                if state == NdimsType.IN_2D:
+                    state = NdimsType.IN_3D
+                elif state == NdimsType.IN_3D:
+                    state = NdimsType.IN_2D
+                else:
+                    print("although we should be inside ndims condition, state is OUT")
+                    sys.exit()
+        elif "#endif" in line:
+            if if_level == if_level_ndims:
+                is_on_ndims_macro = True
+                state = NdimsType.OUT
+            # found "endif", reduce nest counter
+            if_level -= 1
+        if not is_on_ndims_macro:
+            # we do not include macro about ndims
+            if ndims == 2 and state != NdimsType.IN_3D:
+                newlines.append(line)
+            if ndims == 3 and state != NdimsType.IN_2D:
+                newlines.append(line)
+    return newlines
+
+def modify_comment(lines):
+    newlines = list()
+    for line in lines:
+        if "//" in line and "|" in line:
+            line = line.split("|")[0] + "\n"
+        newlines.append(line)
+    return newlines
+
+def main():
+    argv = sys.argv
+    # sanitise input
+    assert(len(argv) == 2)
+    ndims = int(argv[1])
+    # target scripts
+    fnames = \
+          get_filenames("src") \
+        + get_filenames("include") \
+        + get_filenames("initial_conditions/src") \
+        + get_filenames("initial_conditions/include")
+    for fname in fnames:
+        with open(fname, "r") as f:
+            lines = f.readlines()
+        lines = extract(ndims, lines)
+        lines = modify_comment(lines)
+        if 0 == len(lines):
+            os.system(f"rm {fname}")
+            continue
+        if "extern int dummy" in "".join(lines):
+            os.system(f"rm {fname}")
+            continue
+        with open(fname, "w") as f:
+            for line in lines:
+                f.write(line)
+
+if __name__ == "__main__":
+    main()
+

.gitmodules

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+[submodule "SimpleDecomp"]
+	path = SimpleDecomp
+	url = https://github.com/NaokiHori/SimpleDecomp
+	branch = submodule
+[submodule "SimpleNpyIO"]
+	path = SimpleNpyIO
+	url = https://github.com/NaokiHori/SimpleNpyIO
+	branch = submodule

LICENSE

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+MIT License
+
+Copyright (c) 2023 NaokiHori
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

Makefile

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+CC     := mpicc
+CFLAG  := -std=c99 -Wall -Wextra -O3 -DNDIMS=2
+INC    := -Iinclude -ISimpleDecomp/include -ISimpleNpyIO/include
+LIB    := -lfftw3 -lm
+SRCDIR := src SimpleDecomp/src SimpleNpyIO/src
+OBJDIR := obj
+SRCS   := $(shell find $(SRCDIR) -type f -name *.c)
+OBJS   := $(patsubst %.c,obj/%.o,$(SRCS))
+DEPS   := $(patsubst %.c,obj/%.d,$(SRCS))
+OUTDIR := output
+TARGET := a.out
+
+help:
+	@echo "all     : create \"$(TARGET)\""
+	@echo "clean   : remove \"$(TARGET)\" and object files under \"$(OBJDIR)\""
+	@echo "output  : create \"$(OUTDIR)\" to store output"
+	@echo "datadel : clean-up \"$(OUTDIR)\""
+	@echo "help    : show this message"
+
+all: $(TARGET)
+
+$(TARGET): $(OBJS)
+	$(CC) $(CFLAG) -o $@ $^ $(LIB)
+
+$(OBJDIR)/%.o: %.c
+	@if [ ! -e $(dir $@) ]; then \
+		mkdir -p $(dir $@); \
+	fi
+	$(CC) $(CFLAG) -MMD $(INC) -c $< -o $@
+
+clean:
+	$(RM) -r $(OBJDIR) $(TARGET)
+
+output:
+	@if [ ! -e $(OUTDIR)/save ]; then \
+	   mkdir -p $(OUTDIR)/save; \
+	fi
+	@if [ ! -e $(OUTDIR)/log ]; then \
+	   mkdir -p $(OUTDIR)/log; \
+	fi
+
+datadel:
+	$(RM) -r $(OUTDIR)/save/*
+	$(RM) -r $(OUTDIR)/log/*
+
+-include $(DEPS)
+
+.PHONY : all clean output datadel help
+