Merge branch 'main' into jet_deflect

* main: (449 commits)
  Minor
  Minor
  Add comments
  Add execute premission check
  Bugfix string length
  Apply suggestions from code review
  [Workflow] Update all parameters wiki page
  Update output format
  Update description
  Load Opt__Output_Text_Length_Int when restert
  Rename DUMP_DIR to OUTPUT_DIR
  [Workflow] Update all parameters wiki page
  Let OUTPUT_DIR shorter
  Add file premission check
  Fix file path
  Remove useless variable
  Fix Input__Note output
  Update missed filename
  Rename DUMP_DIR to OUTPUT_DIR
  Apply suggestions from code review
  ...

.github/workflows/update_all_parameter_page.yml

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+name: Update all parameters wiki page
+
+on:
+  workflow_dispatch:
+  push:
+    paths:
+      - 'example/test_problem/Template/Input__Parameter'
+      - 'tool/wiki/sync_runtime_parameter.py'
+      - 'src/Init/Init_Load_Parameter.cpp'
+
+env:
+  GIT_AUTHOR_NAME: ${{ github.actor }}
+  GIT_AUTHOR_EMAIL: ${{ secrets.MY_EMAIL }}
+
+jobs:
+  Update-all-parameters-page:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout Repo
+        uses: actions/checkout@v4
+        with:
+          token: ${{ secrets.TOKEN_FOR_WIKI }}
+      - name: run script
+        run: |
+          cd tool/wiki
+          python --version
+          python sync_runtime_parameter.py
+      - name: move markdown
+        run: |
+          mv tool/wiki/Runtime-Parameters:-All.md doc/wiki/Runtime-Parameters-related
+      - name: set git config
+        run: |
+          git config --global user.email "${{env.GIT_AUTHOR_EMAIL}}"
+          git config --global user.name "${{env.GIT_AUTHOR_NAME}}"
+      - name: make a commit and push if the file changed
+        run: |
+          git diff --exit-code doc/wiki/Runtime-Parameters-related/Runtime-Parameters:-All.md || \
+          ( git add doc/wiki/Runtime-Parameters-related/Runtime-Parameters:-All.md && \
+          git commit -m "[Workflow] Update all parameters wiki page" && \
+          git push )

configs/forerunnerI_gnu.config

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+# forerunnerI
+### Caution!! Load modules under module_CALAB on TwnIII first before compiling, such that FFTW3_PATH, MPI_PATH, HDF5_PATH and GSL_PATH can be found:
+###     module use  /home/d07222009/module_CALAB
+###     module load gnu_13.2.0/gcc/13.2.0 gnu_13.2.0/fftw/3.3.10 gnu_13.2.0/gsl/2.8.0 gnu_13.2.0/hdf5/1.14.4 gnu_13.2.0/openmpi/5.0.0  gnu_13.2.0/openucx/1.18.0
+###
+CUDA_PATH
+FFTW2_PATH
+FFTW3_PATH      $(FFTW3_PATH)
+MPI_PATH        $(MPI_PATH)
+HDF5_PATH       $(HDF5_PATH)
+GRACKLE_PATH
+GSL_PATH        $(GSL_PATH)
+LIBYT_PATH
+CUFFTDX_PATH
+
+# compilers
+CXX     g++-13.2.0
+CXX_MPI mpicxx
+
+# flags
+CXXFLAG -g
+CXXFLAG -O3
+#CXXFLAG -std=c++11
+#CXXFLAG -Ofast
+CXXFLAG -Wall
+CXXFLAG -Wextra
+CXXFLAG -Wno-unused-variable
+CXXFLAG -Wno-unused-parameter
+CXXFLAG -Wno-maybe-uninitialized
+CXXFLAG -Wno-unused-but-set-variable
+CXXFLAG -Wno-unused-function
+CXXFLAG -Wno-unused-result
+CXXFLAG -Wno-implicit-fallthrough
+CXXFLAG -Wno-parentheses
+CXXFLAG -Wno-unknown-pragmas
+
+OPENMPFLAG -fopenmp
+
+LIBFLAG
+
+NVCCFLAG_COM -O3
+#NVCCFLAG_COM -use_fast_math
+NVCCFLAG_FLU -Xptxas -dlcm=ca -prec-div=false -ftz=true
+NVCCFLAG_POT -Xptxas -dlcm=ca
+
+# for debugging
+#CXXFLAG -fstack-protector-all
+#CXXFLAG -fstack-protector-strong
+#CXXFLAG -fsanitize=undefined -fsanitize=address
+#LIBFLAG -fsanitize=undefined -fsanitize=address

configs/forerunnerI_intel.config

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+# forerunnerI
+### Caution!! Load modules under module_CALAB on TwnIII first before compiling, such that FFTW3_PATH, MPI_PATH, HDF5_PATH and GSL_PATH can be found:
+###     module use  /home/d07222009/module_CALAB
+###     module load intel/2024_01_46 oneapi_2024/fftw/3.3.10 oneapi_2024/gsl/2.8.0 oneapi_2024/hdf5/1.14.4 oneapi_2024/openmpi/5.0.0 oneapi_2024/openucx/1.18.0
+###
+CUDA_PATH
+FFTW2_PATH
+FFTW3_PATH      $(FFTW3_PATH)
+MPI_PATH        $(MPI_PATH)
+HDF5_PATH       $(HDF5_PATH)
+GRACKLE_PATH
+GSL_PATH        $(GSL_PATH)
+LIBYT_PATH
+CUFFTDX_PATH
+
+# compilers
+CXX     icpx
+CXX_MPI mpicxx
+
+# flags
+# for warning flags fro oneapi, see: https://www.intel.com/content/dam/develop/external/us/en/documents/oneapi_dpcpp_cpp_compiler.pdf
+CXXFLAG -g
+CXXFLAG -O3
+CXXFLAG -fp-model precise -fstack-protector-all
+#CXXFLAG -std=c++11
+#CXXFLAG -gxx-name=YOUR_G++
+CXXFLAG -Werror -Wfatal-errors -Woverflow
+CXXFLAG -Wno-uninitialized -Wno-absolute-value -Wno-unknown-pragmas -diag-disable 3180 -diag-disable 10441
+
+OPENMPFLAG -qopenmp
+
+LIBFLAG -limf
+
+NVCCFLAG_COM -O3
+#NVCCFLAG_COM -use_fast_math
+NVCCFLAG_FLU -Xptxas -dlcm=ca -prec-div=false -ftz=true
+NVCCFLAG_POT -Xptxas -dlcm=ca
+
+# for debugging
+#CXXFLAG -fstack-protector-all
+#CXXFLAG -fstack-protector-strong  # somehow it can capture issues not detected by -fstack-protector-all
+#LIBFLAG -lssp

configs/taiwania3_gnu.config

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+# TaiwaniaIII
+### Caution!! Load modules under module_CALAB on TwnIII first before compiling, such that FFTW3_PATH, MPI_PATH, HDF5_PATH and GSL_PATH can be found:
+###     module use  /home/d07222009/module_CALAB
+###     module load gcc/13.2.0 gnu_13.2.0/fftw/3.3.10 gnu_13.2.0/gsl/2.8.0 gnu_13.2.0/hdf5/1.14.4 gnu_13.2.0/openmpi/5.0.5  gnu_13.2.0/openucx/1.18.0
+###
+CUDA_PATH
+FFTW2_PATH
+FFTW3_PATH      $(FFTW3_PATH)
+MPI_PATH        $(MPI_PATH)
+HDF5_PATH       $(HDF5_PATH)
+GRACKLE_PATH
+GSL_PATH        $(GSL_PATH)
+LIBYT_PATH
+CUFFTDX_PATH
+
+# compilers
+CXX     g++
+CXX_MPI mpicxx
+
+# flags
+CXXFLAG -g
+CXXFLAG -O3
+CXXFLAG -std=c++11
+#CXXFLAG -Ofast
+CXXFLAG -Wall
+CXXFLAG -Wextra
+CXXFLAG -Wno-unused-variable
+CXXFLAG -Wno-unused-parameter
+CXXFLAG -Wno-maybe-uninitialized
+CXXFLAG -Wno-unused-but-set-variable
+CXXFLAG -Wno-unused-function
+CXXFLAG -Wno-unused-result
+CXXFLAG -Wno-implicit-fallthrough
+CXXFLAG -Wno-parentheses
+CXXFLAG -Wno-unknown-pragmas
+CXXFLAG -Wno-cast-function-type
+
+OPENMPFLAG -fopenmp
+
+LIBFLAG
+
+NVCCFLAG_COM -O3
+#NVCCFLAG_COM -use_fast_math
+NVCCFLAG_FLU -Xptxas -dlcm=ca -prec-div=false -ftz=true
+NVCCFLAG_POT -Xptxas -dlcm=ca
+
+# for debugging
+#CXXFLAG -fstack-protector-all
+#CXXFLAG -fstack-protector-strong
+#CXXFLAG -fsanitize=undefined -fsanitize=address
+#LIBFLAG -fsanitize=undefined -fsanitize=address

configs/taiwania3_intel.config

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+# TaiwaniaIII
+### Caution!! Load modules under module_CALAB on TwnIII first before compiling, such that FFTW3_PATH, MPI_PATH, HDF5_PATH and GSL_PATH can be found:
+###     module use  /home/d07222009/module_CALAB
+###     module load intel/2024 intel_2024/fftw/3.3.10 intel_2024/gsl/2.8.0 intel_2024/hdf5/1.14.4 intel_2024/openmpi/5.0.5 intel_2024/openucx/1.18.0
+###
+CUDA_PATH
+FFTW2_PATH
+FFTW3_PATH      $(FFTW3_PATH)
+MPI_PATH        $(MPI_PATH)
+HDF5_PATH       $(HDF5_PATH)
+GRACKLE_PATH
+GSL_PATH        $(GSL_PATH)
+LIBYT_PATH
+CUFFTDX_PATH
+
+# compilers
+CXX     icpx
+CXX_MPI mpicxx
+
+# flags
+CXXFLAG -g
+CXXFLAG -O3
+CXXFLAG -fp-model precise -fstack-protector-all
+#CXXFLAG -std=c++11
+#CXXFLAG -gxx-name=YOUR_G++
+CXXFLAG -Werror -Wfatal-errors -Woverflow
+CXXFLAG -Wno-uninitialized -Wno-absolute-value -Wno-unknown-pragmas -diag-disable 3180 -diag-disable 10441
+
+OPENMPFLAG -qopenmp
+
+LIBFLAG -limf
+
+NVCCFLAG_COM -O3
+#NVCCFLAG_COM -use_fast_math
+NVCCFLAG_FLU -Xptxas -dlcm=ca -prec-div=false -ftz=true
+NVCCFLAG_POT -Xptxas -dlcm=ca
+
+# for debugging
+#CXXFLAG -fstack-protector-all
+#CXXFLAG -fstack-protector-strong  # somehow it can capture issues not detected by -fstack-protector-all
+#LIBFLAG -lssp