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Merge pull request #22 from ukaea/dev-v1.2.1
v1.2.1 release
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‎CHANGELOG.md

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# CHANGELOG
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## v1.2.1, 2025-01-15
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- Added an option to remove the logLei discontinuity in NRL formulary fit
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- Added more output to BDE integrator
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- Added more unary transforms
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- Added key for controlling BDE integrator consolidation
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- Added 0-length timestep at the start of all simulations to fix extractor manipulator bug
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- Added option to ignore Jacobian in diffusion stencil
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### Breaking Changes
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- N/A
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### New Features
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- New standard textbook option to remoge logLei discontinuity in NRL formularly fit by moving branch cutoff to e^2 * Z^2 eV
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- BDE integrator now outputs the current number of substeps and progress through those
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- New "step" unary transform. 1 if the node evaluates > 0, 0 otherwise.
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- New "filterWithin" unary transform. 0 if the value of the node is not within the first two passed realParams, otherwise no effect.
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- New "BDEConsolidationInterval" key to set the number of timesteps for the integrator to attempt consolidation after. Defaults to 50 (old hardcoded value).
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- Some generators now explicitly output information about terms as they are generated
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- "ignoreJacobian" now valid option for diffusion stencil JSON interface
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### Bug Fixes
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- Fixed extractor manipulator bug with CRM models by performing a 0 length timestep at the start of all simulations before any output
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- Added a call to update all modelbound data before the 0-length timestep to avoid some edge-case model failure
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- Fixed bug where unsorted ingoing states in some transitions lead to the wrong required density variables being identified in some generators
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- Fixed bug with integrators that allow time evolution incrementing time twice when there is only one integration step
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- Fixed bug where composite integrator global timestep's requested size is overwritten if a timestep controller is used, leading to performance issues if output-driven timestepping is used.
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## v1.2.0, 2024-09-19
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- Added CVODE integrator as an option

‎docker/Dockerfile_mac.txt

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FROM --platform=linux/arm64 ubuntu:latest
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LABEL maintainer="[email protected]"
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LABEL version="1.2.1"
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LABEL description="Docker container for ReMKiT1D CI"
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# Disable Prompt During Packages Installation
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ARG DEBIAN_FRONTEND=noninteractive
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RUN apt update && apt install software-properties-common -y
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RUN add-apt-repository -y ppa:ubuntu-toolchain-r/test
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# Update and Installs Required Packages for ReMKiT1D and other Packages
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RUN apt update \
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&& apt install -y \
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gfortran-11 \
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g++-11 \
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python3 \
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python3-dev \
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pip \
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libblas-dev \
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libhdf5-dev \
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liblapack-dev \
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m4 \
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wget \
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git \
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gcovr \
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gcc-arm-linux-gnueabihf \
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build-essential \
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pkg-config
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# Packages need to be Compiled and Installed Using Fortran-11
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# CMake Commands State the Required Compilers to use
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ENV FC=gfortran-11
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ENV CC=gcc-11
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ENV CXX=g++-11
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WORKDIR /home
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# ReMKiT1D Requires CMake-3.18.0 and pFUnit-4.2.2 has some Incompatibilities with Newer Versions of CMake (v3.25.0-rc1)
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RUN wget https://github.com/Kitware/CMake/releases/download/v3.18.0/cmake-3.18.0.tar.gz
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RUN tar -zvxf cmake-3.18.0.tar.gz
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WORKDIR /home/cmake-3.18.0
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RUN ./bootstrap -- -DCMAKE_USE_OPENSSL=OFF
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RUN make
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RUN make install
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WORKDIR /home
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# ReMKiT1D Requires MPI and mpich-3.4.2 has been Tested and is used in the main.yml Workflow Script
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RUN wget -O mpich.tar.gz https://www.mpich.org/static/downloads/3.4.2/mpich-3.4.2.tar.gz
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RUN tar xfz mpich.tar.gz
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RUN mkdir mpich-install
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WORKDIR /home/mpich-3.4.2
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# ReMKiT1D Requires gfortran-11, gcc-11 and g++-11. CMake Installs the Package to the mpich-install Folder
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RUN ./configure CC=gcc-11 CXX=g++-11 FC=gfortran-11 --prefix=/home/mpich-install FFLAGS=-fallow-argument-mismatch --with-device=ch3
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RUN make
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RUN make install
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WORKDIR /home
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# Include the mpich-install PATH for Compilation of ReMKiT1D
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ENV PATH=/home/mpich-install/bin:$PATH
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# PETSc-3.17 is the Newest Release that has been Tested on ReMKiT1D (3.18 not Compatible)
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RUN git clone -b release-3.17 https://gitlab.com/petsc/petsc.git petsc
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WORKDIR petsc/
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#PETSc Requires MPI and PETSc is Told Where MPI (mpich-4.2.2) is Installed
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RUN ./configure --with-mpi-dir=/home/mpich-install --download-hypre=1 --download-fblaslapack=1 --with-debugging=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
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RUN make PETSC_DIR=/home/petsc PETSC_ARCH=arch-linux-c-opt all check
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WORKDIR /home
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# pFUnit-4.2.2 is Installed for the use of Unit Testing
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RUN git clone -b v4.2.2 https://github.com/Goddard-Fortran-Ecosystem/pFUnit.git
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WORKDIR pFUnit
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RUN mkdir build
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WORKDIR build
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# ReMKiT1D Requires gfortran-11, gcc-11 and g++-11. CMake Installs the Package to the 'installs' Folder
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RUN cmake .. -DSKIP_OPENMP=yes -DCMAKE_Fortran_COMPILER=gfortran-11 -DCMAKE_C_COMPILER=gcc-11 -DCMAKE_CXX_COMPILER=g++-11 -DCMAKE_INSTALL_PREFIX=/home/installs/pFUnit
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RUN make install
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WORKDIR /home
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# ReMKiT1D is Currently using json-fortran-8.2.5
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RUN git clone -b 8.2.5 https://github.com/jacobwilliams/json-fortran.git
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WORKDIR json-fortran
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RUN mkdir build
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WORKDIR build
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# ReMKiT1D Requires gfortran-11, gcc-11 and g++-11. CMake Installs the Package to the 'installs' Folder
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RUN cmake .. -DCMAKE_Fortran_COMPILER=gfortran-11 -DCMAKE_INSTALL_PREFIX=/home/installs/json-fortran -DSKIP_DOC_GEN=TRUE
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RUN make install
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WORKDIR /home
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# HDF5 is Required and HDF5-1.13.0 is used within the main.yml Workflow Script
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RUN git clone -b hdf5-1_13_0 https://github.com/HDFGroup/hdf5.git
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WORKDIR hdf5
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RUN mkdir build
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WORKDIR build
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# ReMKiT1D Requires gfortran-11, gcc-11 and g++-11. CMake Installs the Package to the 'installs' Folder
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RUN cmake .. -DCMAKE_Fortran_COMPILER=gfortran-11 -DCMAKE_C_COMPILER=gcc-11 -DCMAKE_CXX_COMPILER=g++-11 -DHDF5_BUILD_FORTRAN=ON -DCMAKE_INSTALL_PREFIX=/home/installs/hdf5
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RUN make install
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WORKDIR /home
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# ReMKiT1D v1.2.0+ requires sundials
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RUN git clone -b v7.2.1 https://github.com/LLNL/sundials.git
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WORKDIR sundials
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RUN mkdir build
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WORKDIR build
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RUN cmake .. -DENABLE_MPI=ON -DCMAKE_INSTALL_PREFIX=/home/installs/sundials -DENABLE_LAPACK=ON -DBUILD_FORTRAN_MODULE_INTERFACE=ON -DCMAKE_C_COMPILER=gcc-11
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RUN make
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RUN make install
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WORKDIR /home
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RUN echo LD_LIBRARY_PATH=/home/mpich-install/lib:$LD_LIBRARY_PATH
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# Add the PATH to assist CMake and Make Find the Required Compilation Files
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ENV PFUNIT_DIR=/home/installs/pFUnit
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ENV PETSC_DIR=/home/petsc
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ENV PETSC_ARCH=arch-linux-c-opt
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ENV PATH=$PATH:/home/installs/petsc
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ENV PATH=$PATH:/home/installs/hdf5
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ENV PATH=$PATH:/home/installs/json-fortran/jsonfortran-gnu-8.2.5
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ENV PATH=$PATH:/home/mpich-install/bin:$PATH
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ENV PATH=$PATH:/home/installs/sundials
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ENV LD_LIBRARY_PATH=/home/mpich-install/lib:$LD_LIBRARY_PATH
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ENV LD_LIBRARY_PATH=/home/sundials/lib:$LD_LIBRARY_PATH
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ENV SUNDIALS_DIR=/home/installs/sundials/lib/cmake/sundials

‎docs-pages/01-install.md

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Title: Building and Installing
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Author: Stefan Mijin
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Date: 19.09.2024.
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Date: 27.02.2025.
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## Prerequisites
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‎docs-pages/02-run.md

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Title: Running
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Author: Stefan Mijin
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Date: 19.09.2024.
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Date: 25.02.2025.
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If the build process is successful, the executable will be in build/src/executables/ReMKiT1D.
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ReMKiT1D requires a config.json file as input. Assuming a valid config file is available, the code can be run from the executable directory using, for example:

‎docs-pages/index.md

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Title: Documentation
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Author: Stefan Mijin
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Date: 19.09.2024.
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Date: 27.02.2025.
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# **Re**active **M**ultifluid and **Ki**netic **T**ransport in **1D**
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rEMKiT1D is a framework for building 1D multi-fluid models of the tokamak Scrape-Off Layer with support for kinetic electron effects and collisional-radiative modelling. The framework is controlled through a Python interface available [here](https://github.com/ukaea/ReMKiT1D-Python), where users can find high-level examples and documentation.
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ReMKiT1D is a framework for building 1D multi-fluid models of the tokamak Scrape-Off Layer with support for kinetic electron effects and collisional-radiative modelling. The framework is controlled through a Python interface available [here](https://github.com/ukaea/ReMKiT1D-Python), where users can find high-level examples and documentation.
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For an overview of both the Fortran framework and the Python interface see the [code paper](https://www.sciencedirect.com/science/article/pii/S0010465524001188).

‎src/modules/abstract_model_builder/term_generator_abstract.f90

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procedure ,public :: getNumImplicitTerms
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procedure ,public :: getNumGeneralTerms
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procedure ,public :: getGeneratorPrefix
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procedure ,public :: moveTerms
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integer(ik) :: numTerms
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end function getNumGeneralTerms
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!-----------------------------------------------------------------------------------------------------------------------------------
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pure module function getGeneratorPrefix(this) result(prefix)
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!! Get size of this%generalTerms
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class(TermGenerator) ,intent(in) :: this
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character(:) ,allocatable :: prefix
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end function getGeneratorPrefix
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!-----------------------------------------------------------------------------------------------------------------------------------
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module subroutine moveTerms(this,modelObj,impTermImpGroups,impTermGenGroups,genTermGroups)
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!! Move terms to modelObj
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!-----------------------------------------------------------------------------------------------------------------------------------
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end module term_generator_abstract_class
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!-----------------------------------------------------------------------------------------------------------------------------------
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‎src/modules/abstract_model_builder/term_generator_abstract_procedures.f90

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numTerms = size(this%generalTerms)
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end function getNumGeneralTerms
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!-----------------------------------------------------------------------------------------------------------------------------------
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pure module function getGeneratorPrefix(this) result(prefix)
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!! Get size of this%generalTerms
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class(TermGenerator) ,intent(in) :: this
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character(:) ,allocatable :: prefix
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prefix = this%generatorPrefix
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end function getGeneratorPrefix
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!-----------------------------------------------------------------------------------------------------------------------------------
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module subroutine moveTerms(this,modelObj,impTermImpGroups,impTermGenGroups,genTermGroups)
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!! Move terms to modelObj

‎src/modules/basic_integrators/implicit_PicardBDE_integrator.f90

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integer(ik) :: maxRestarts = 3 !! Maximum number of consecutive solver restart attempts before critical failure is announced
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integer(ik) :: consolidationInterval = 50 !! How many integration calls before currentNumSubsteps is again reduced to 1
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integer(ik) :: hardMaxRestarts = 10 !! Maximum number of consecutive solver restart attempts before critical failure is announced regardless of whether consolidation happened or not
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integer(ik) :: restartCount = 0 !! Counter for consecutive number of solver restars
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integer(ik) :: consolidationInterval = 50 !! How many integration calls before currentNumSubsteps is again reduced to 1
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integer(ik) :: stepsSinceLastConsolidation = 0 !! Counter for steps since last consolidation to 1 substep
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end type InternalControllerOptions

‎src/modules/basic_integrators/implicit_PicardBDE_integrator_procedures.f90

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end if
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varConverged(i) = relError < nonlinTol .or. absError < epsilon(absError)*absTol
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!if (.not. varConverged(i)) print*,i,varConverged(i),relError,absError
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if (.not. varConverged(i)) convergenceCounter(i) = convergenceCounter(i) + 1
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end do
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allocate(implicitVectorInit,source=this%implicitVectorOld)
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do i = 1, numSteps
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call printNamedValue(this%integratorName//": Current number of substeps",numSteps)
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call printNamedValue(this%integratorName//": Starting substep",i)
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if (inputVars%isVarNameRegistered("time")) &
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this%buffer%variables(timeVarIndex)%entry(1) = this%buffer%variables(timeVarIndex)%entry(1) + dt(i)
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‎src/modules/basic_support/physics_functions.f90

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end function logLee
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!-----------------------------------------------------------------------------------------------------------------------------------
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pure module function logLei(Te,ne,Z) result(res)
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pure module function logLei(Te,ne,Z,removeDisc) result(res)
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!! Calculate Coulomb logarithm for electron-ion collisions (NRL Formulary 2013 page 34 equation b). Assumes Te > Ti*Z*me/mi
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real(rk) ,intent(in) :: Te !! Electron temperature in eV
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real(rk) ,intent(in) :: ne !! Electron density in m^{-3}
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real(rk) ,intent(in) :: Z !! Ion charge
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real(rk) :: res
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real(rk) ,intent(in) :: Te !! Electron temperature in eV
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real(rk) ,intent(in) :: ne !! Electron density in m^{-3}
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real(rk) ,intent(in) :: Z !! Ion charge
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logical ,intent(in), optional :: removeDisc !! Remove the discontinuity at 10eV by moving the branch switch to Te = Z**2 * e**2 eV. Defaults to .false.
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real(rk) :: res
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end interface
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end module physics_functions
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!-----------------------------------------------------------------------------------------------------------------------------------
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!-----------------------------------------------------------------------------------------------------------------------------------

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