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Phoebus documentation master file, created by + sphinx-quickstart on Thu Sep 26 15:18:20 2024. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +Phoebus: Performance portable GRRMHD for supernovae, mergers, and more +====================================================================== + +`Phoebus`_ is a performance portable general relativistic neutrino radiation magnetohydrodynamics code built upon the `Parthenon`_ adaptive mesh refinement framework. + +.. _Parthenon: https://github.com/parthenon-hpc-lab/parthenon +.. _Phoebus: https://github.com/lanl/phoebus + +Key Features +^^^^^^^^^^^^^ + +* Finite volume GRMHD +* Neutrino transport with Monte Carlo and moment methods +* Analytic and tabulated spacetimes +* Monopolar general relativistic gravity for core-collapse supernovae +* Lagrangian tracer particles +* Support for arbitrary equations of state + +.. note:: + + These docs are under active development. + +.. toctree:: + :maxdepth: 1 + :caption: Contents: + :glob: + + src/* + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`search` diff --git a/blb/frontier/_sources/src/building.rst.txt b/blb/frontier/_sources/src/building.rst.txt new file mode 100644 index 00000000..2533a8ff --- /dev/null +++ b/blb/frontier/_sources/src/building.rst.txt @@ -0,0 +1,190 @@ +Building +======== + +Obtaining the Source Code +------------------------- + +``phoebus`` uses submodules extensively. To make sure you get them all, +clone it as + +.. code:: bash + + git clone --recursive git@github.com:lanl/phoebus.git + +or as + +.. code:: bash + + git clone git@github.com:lanl/phoebus.git + cd phoebus + git submodule update --init --recursive + + +Prerequisites +------------- + +To build ``phoebus``, you need to create a build directly, as in-source builds are not supported. +After cloning the repository, + +.. code:: bash + + cd phoebus + mkdir bin + cd bin + +Example builds +-------------- + +Below are some example build commands + +MPI-parallel only +~~~~~~~~~~~~~~~~~ + +The following will build ``phoebus`` with MPI parallelism but no shared +memory parallelism + +.. code:: bash + + cmake .. + make -j + +OpenMP-parallel +~~~~~~~~~~~~~~~ + +The following will build ``phoebus`` with OpenMP parallelism only + +.. code:: bash + + cmake -DPHOEBUS_ENABLE_MPI=Off -DPHOEBUS_ENABLE_OPENMP=ON .. + make -j + +Cuda +~~~~ + +The following will build ``phoebus`` with no MPI or OpenMP parallelism. + +.. code:: bash + + cmake -DPHOEBUS_ENABLE_CUDA=On -DCMAKE_CXX_COMPILER=${HOME}/phoebus/external/singularity-eos/utils/kokkos/bin/nvcc_wrapper -DKokkos_ARCH_HSW=ON -DKokkos_ARCH_VOLTA70=ON -DPHOEBUS_ENABLE_MPI=OFF .. + +A few notes for this one: - Note here the ``-DCMAKE_CXX_COMPILER`` flag. +This is necessary. You *must* set the compiler to ``nvcc_wrapper`` +provided by Kokkos. - Note the ``-DKokkos_ARCH_*`` flags. Those set the +host and device microarchitectures and are required. The choice here is +on an ``x86_64`` machine with a ``volta`` GPU. + +Build Options +------------- + +The build options explicitly provided by ``phoebus`` are: + ++-----------------------+----------+-----------------------------------------------+ +| Option | Default | Comment | ++=======================+==========+===============================================+ +| PHOEBUS_ENABLE_CUDA | OFF | Cuda | ++-----------------------+----------+-----------------------------------------------+ +| PHOEBUS_ENABLE_HDF5 | ON | HDF5. Required for output and restarts. | ++-----------------------+----------+-----------------------------------------------+ +| PHOEBUS_ENABLE_MPI | ON | MPI. Required for distributed memory | +| | | parallelism. | ++-----------------------+----------+-----------------------------------------------+ +| PHOEBUS_ENABLE_OPENMP | OFF | OpenMP. Required for shared memory | +| | | parallelism. | ++-----------------------+----------+-----------------------------------------------+ +| MACHINE_CFG | None | Machine-specific config file, optional. | ++-----------------------+----------+-----------------------------------------------+ + +Some relevant settings from Parthenon and Kokkos you may need to play +with are: + ++---------------------+----------+---------------------------------------------+ +| Option | Default | Comment | ++=====================+==========+=============================================+ +| CMAKE_CXX_COMPILER | None | Must be set to ``nvcc_wrapper`` with cuda | +| | | backend | ++---------------------+----------+---------------------------------------------+ +| Kokkos_ARCH_XXXX | OFF | You must set the GPU architecture when | +| | | compiling for Cuda | ++---------------------+----------+---------------------------------------------+ + +You can see all the Parthenon build options +`here `__ +and all the Kokkos build options +`here `__ + +Cmake machine configs +--------------------- + +If you are proficient with ``cmake`` You can optionally write a +``cmake`` file that sets the configure parameters that you like on a +given machine. Both ``phoebus`` and ``parthenon`` can make use of it. +You can point to the file with + +:: + + -DMACHINE_CFG=path/to/machine/file + +at config time or by setting the environment variable ``MACHINE_CFG`` to +point at it, e.g., + +.. code:: bash + + export MACHINE_CFG=path/to/machine/file + +An example machine file might look like + +:: + + # Machine file for x86_64-volta on Darwin + message(STATUS "Loading machine configuration for Darwin x86-volta node") + message(STATUS "Assumes: module load module load gcc/7.4.0 cuda/10.2 openmpi/4.0.3-gcc_7.4.0 anaconda/Anaconda3.2019.10 cmake && spack load hdf5") + message(STATUS "Also assumes you have a valid spack installation loaded.") + + set(PHOEBUS_ENABLE_CUDA ON CACHE BOOL "Cuda backend") + set(PHOEBUS_ENABLE_MPI OFF CACHE BOOL "No MPI") + set(Kokkos_ARCH_HSW ON CACHE BOOL "Haswell target") + set(Kokkos_ARCH_VOLTA70 ON CACHE BOOL "volta target") + set(CMAKE_CXX_COMPILER /home/jonahm/phoebus/external/parthenon/external/Kokkos/bin/nvcc_wrapper CACHE STRING "nvcc wrapper") + +you could then configure and compile as + +.. code:: bash + + cmake -DMACHINE_CFG=path/to/machine/file .. + make -j + +Running +------- + +Run phoebus from the ``build`` directory as + +.. code:: bash + + ./src/phoebus -i path/to/input/file.pin + +The input files are in ``phoebus/inputs/*``. There’s typically one input +file per problem setup file. + +Submodules +---------- + +- ``parthenon`` asynchronous tasking and block-AMR infrastructure +- ``singularity-eos`` provides performance-portable equations of state + and PTE solvers +- ``singularity-opac`` provides performance-portable opacities and + emissivities +- ``Kokkos`` provides performance portable shared-memory parallelism. + It allows our loops to be CUDA, OpenMP, or something else. By default + we use the ``Kokkos`` shipped with ``parthenon``. + +External (Required) +------------------- + +- ``cmake`` for building + +Optional +-------- + +- ``hdf5`` for output (must be parallel if MPI is enabled) +- ``MPI`` for distributed memory parallelism +- ``python3`` for visualization diff --git a/blb/frontier/_sources/src/code_of_conduct.rst.txt b/blb/frontier/_sources/src/code_of_conduct.rst.txt new file mode 100644 index 00000000..6edc7037 --- /dev/null +++ b/blb/frontier/_sources/src/code_of_conduct.rst.txt @@ -0,0 +1,28 @@ +.. _lanlcode: https://lanl.github.io/singularity-eos + +Code of Conduct +===================================== + +We as users, members, contributors, and leaders agree to make participation in our +community a harassment-free experience for everyone. +We will interact in ways that contribute to an open, welcoming, +diverse, inclusive, and healthy community. + +We agree to uphold the `LANL Code of Conduct `_ in all spaces relevant. +Of note: + +:: + + - Foster a mutually respectful working environment that is free from + discrimination, intimidation, and harassment (including sexual + harassment). + - Do not discriminate against others on the basis of any + characteristic protected by law or LANL policy. + - Do not engage in behaviors that create an offensive, hostile, or + intimidating work environment, including shouting, abusive + language, threats of violence, the use of obscenities or other + non-verbal expressions of aggression, horseplay such as kicking + co-workers’ chairs or using personal insults, or the use of + offensive nicknames or other derogatory remarks. + - Avoid behavior that a reasonable person would find to be demeaning + or humiliating. diff --git a/blb/frontier/_sources/src/contributing.rst.txt b/blb/frontier/_sources/src/contributing.rst.txt new file mode 100644 index 00000000..8acd9250 --- /dev/null +++ b/blb/frontier/_sources/src/contributing.rst.txt @@ -0,0 +1,269 @@ +.. _singularity-eos: https://lanl.github.io/singularity-eos +.. _Catch2: https://github.com/catchorg/Catch2 + +Contributing +============================= + +To contribute to ``Phoebus``, feel free to submit a pull +request or open an issue. + +1. Create a new fork of ``main`` where your changes can be made. +2. After completing, create a pull request, describe the final approach + and ensure the branch has no conflicts with current Regression Tests + and Formatting Checks. +3. Assign external reviewers (a minimum of 1, one of which should be a + Maintainer, and which cannot be the contributor). Provide concise + description of changes. +4. Once comments/feedback is addressed, the PR will be merged into the + main branch and changes will be added to list of changes in the next + release. +5. At present, Releases (with a git version tag) for the ``main`` branch + of ``Phoebus`` will occur at a 6 to 12 month cadence or following + implementation of a major enhancement or capability to the code base. + +*Maintainers* of ``Phoebus`` will follow the same process for +contributions as above except for the following differences: they may +create branches directly within ``Phoebus``, they will hold repository +admin privileges, and actively participate in the technical review of +contributions to ``Phoebus``. + + +Pull request protocol +---------------------- + +When submitting a pull request, there is a default template that is automatically +populated. The pull request should sufficiently summarize all changes. +As necessary, tests should be added for new features of bugs fixed. + +Before a pull request will be merged, the code should be formatted. We +use clang-format for this, pinned to version 12. +The script ``scripts/bash/format.sh`` will apply ``clang-format`` +to C++ source files in the repository as well as ``black`` to python files, if available. +The script takes two CLI arguments +that may be useful, ``CFM``, which can be set to the path for your +clang-format binary, and ``VERBOSE``, which if set to ``1`` adds +useful output. For example: + +.. code-block:: bash + + CFM=clang-format-12 VERBOSE=1 ./scripts/bash/format.sh + +In order for a pull request to merge, we require: + +- Provide a thorough summary of changes, especially if they are breaking changes +- Obey style guidleines (format with ``clang-format`` and pass the necessary test) +- Pass the existing test suite +- Have at least one approval from a Maintainer +- If applicable: + + - Write new tests for new features or bugs + - Include or update documentation in ``doc/`` + +Test Suite +---------- + +Several sets of tests are triggered on a pull request: a static format +check, a docs buld, and a suite of unit and regression tests. +These are run through github's CPU infrastructure. These tests +help ensure that modifications to the code do not break existing capabilities +and ensure a consistent code style. + +Adding Tests +```````````` + +There are two primary categories of tests written in ``Phoebus``: +unit tests and regression tests. + +Unit +^^^^ + +Unit tests live in ``tst/unit/``. They are implemented using the +`Catch2`_ unit testing framework. They are integrated with ``cmake`` +and can be run, when enabled, with ``ctest``. There are a few necessary ``cmake`` +configurations to beuild tests: + +========================== ========= ======================================= + Option Default Description +========================== ========= ======================================= +PHOEBUS_ENABLE_UNIT_TESTS OFF Enables Catch2 unit tests +PHOEBUS_ENABLE_DOWNLOADS OFF Enables unit tests using tabulated EOS +========================== ========= ======================================= + +Regression +^^^^^^^^^^ +Regression tests run existing simulations and test against saved output +in order to verify sustained capabilities. +They are implemented in Python in +``test/regression/``. To run the tests you will need a Python environment with +at least ``numpy`` and ``h5py``. Tests can be ran manually as, e.g., + +.. code-block:: bash + + python linear_modes.py + +This will build Phoebus locally in ``phoebus/tst/regression/build`` and run it in +``phoebus/tst/regression/run``. Ensure that these directories do not already exist. +Each script ``test.py`` has a correspodning "gold file" ``test.gold``. +The gold files contain the gold standard data that the output of the regression test +is compared against. To generate new gold data, for example if a change is implemented +that changes the behavior of a test (not erroneously) or a new test is created, run the test +script with the ``--upgold`` option. This will create or update the corresponding ``.gold`` file. +To add a new test: + +1. Create a new test script. + + - Update the ``modified_inputs`` struct to change any input deck options + - Set the ``variables`` list to contain the quantities to test against +2. Run the script with the ``--upgold`` option +3. Commit the test script and gold file +4. Update the CI to include the new test (``phoebus/.github/workflows/tests.yml``) + + +Expectations for code review +----------------------------- + +Much of what follows is adapted from `singularity-eos`_. + +From the perspective of the contributor +```````````````````````````````````````` + +Code review is an integral part of the development process +for ``Phoebus``. You can expect at least one, perhaps many, +core developers to read your code and offer suggestions. +You should treat this much like scientific or academic peer review. +You should listen to suggestions but also feel entitled to push back +if you believe the suggestions or comments are incorrect or +are requesting too much effort. + +Reviewers may offer conflicting advice, if this is the case, it's an +opportunity to open a discussion and communally arrive at a good +approach. You should feel empowered to argue for which of the +conflicting solutions you prefer or to suggest a compromise. If you +don't feel strongly, that's fine too, but it's best to say so to keep +the lines of communication open. + +Big contributions may be difficult to review in one piece and you may +be requested to split your pull request into two or more separate +contributions. You may also receive many "nitpicky" comments about +code style or structure. These comments help keep a broad codebase, +with many contributors uniform in style and maintainable with +consistent expectations accross the code base. While there is no +formal style guide for now, the regular contributors have a sense for +the broad style of the project. You should take these stylistic and +"nitpicky" suggestions seriously, but you should also feel free to +push back. + +As with any creative endeavor, we put a lot of ourselves into our +code. It can be painful to receive criticism on your contribution and +easy to take it personally. While you should resist the urge to take +offense, it is also partly code reviewer's responsiblity to create a +constructive environment, as discussed below. + +Expectations of code reviewers +```````````````````````````````` + +A good code review builds a contribution up, rather than tearing it +down. Here are a few rules to keep code reviews constructive and +congenial: + +* You should take the time needed to review a contribution and offer + meaningful advice. Unless a contribution is very small, limit + the times you simply click "approve" with a "looks good to me." + +* You should keep your comments constructive. For example, rather than + saying "this pattern is bad," try saying "at this point, you may + want to try this other pattern." + +* Avoid language that can be misconstrued, even if it's common + notation in the commnunity. For example, avoid phrases like "code + smell." + +* Explain why you make a suggestion. In addition to saying "try X + instead of Y" explain why you like pattern X more than pattern Y. + +* A contributor may push back on your suggestion. Be open to the + possibility that you're either asking too much or are incorrect in + this instance. Code review is an opportunity for everyone to learn. + +* Don't just highlight what you don't like. Also highlight the parts + of the pull request you do like and thank the contributor for their + effort. + +General principle for everyone +``````````````````````````````` + +It's hard to convey tone in text correspondance. Try to read what +others write favorably and try to write in such a way that your tone +can't be mis-interpreted as malicious. + +A Large Ecosystem +------------------------ + +``Phoebus`` depends on several other open-source, Los Alamos +maintained, projects. In particular, ``Parthenon``, ``singularity-eos``, +``singularity-opac``, and ``spiner``. +If you have issues with these projects, ideally +submit issues on the relevant github pages. However, if you can't +figure out where an issue belongs, no big deal. Submit where you can +and we'll engage with you to figure out how to proceed. + +Becoming a Contributor +---------------------- + +For the purpose of our development model, we label *Contributors* or +*Maintainers* of ``Phoebus``. Below we describe these labels and the +process for contributing to ``Phoebus``. + +We welcome contributions from scientists from a large variety of +relativistic astrophysics. New users are welcome to contributions to +``Phoebus`` via the *Contributors* process. Contributors with 6 merged +pull requests into the main branch (over a minimum of 6 months) will +be eligible to join as a *Maintainer* of ``Phoebus`` with additional +repository access and roles. However, final approval of *Maintainer* +status will require a approval by vote by existing +*Maintainers*, a necessary step to ensure the safety and integrity of +the code base for all users of ``Phoebus``. + +The *Maintainers* of ``Phoebus`` consist of the original developers of +the code and those that have a demonstrated history in the development +of ``Phoebus`` prior to the implementation of the *Development Model* +described here. Maintainers hold admin access, serve as +reviewers for pull requests, and are in charge of the maintaining, +deployment, and improvement of efforts towards: regression testing, +documentation, science test cases (gold standards), and continuous +integration. + +Maintainers are excepted to make a good faith effort to adhere to +:ref:`these suggestions ` in order to maintain a supportive and +productive environment. + +List of Current Maintainers of Phoebus +------------------------------------------ + ++-------------------+--------------------------------+-----------------------+ +| Name | Handle | Team | ++===================+================================+=======================+ +| Brandon Barker | | Los Alamos National | +| | `@AstroBarker `__ | | ++-------------------+--------------------------------+-----------------------+ +| Josh Dolence | `@jdolence `__ | Lab | ++-------------------+--------------------------------+-----------------------+ +| Carl Fields | | University of Arizona | +| | `@carlnotsagan `__ | | ++-------------------+--------------------------------+-----------------------+ +| Mariam | `@mari2895 `__ | | ++-------------------+--------------------------------+-----------------------+ +| Jonah Miller | `@Yurlungur `__ | Lab | ++-------------------+--------------------------------+-----------------------+ +| Jeremiah Murphy | | Florida State | +| | `@curiousmiah `__ | | ++-------------------+--------------------------------+-----------------------+ +| Ben Ryan | `@brryan `__ | Lab | ++-------------------+--------------------------------+-----------------------+ diff --git a/blb/frontier/_sources/src/governance.rst.txt b/blb/frontier/_sources/src/governance.rst.txt new file mode 100644 index 00000000..78a4c1fe --- /dev/null +++ b/blb/frontier/_sources/src/governance.rst.txt @@ -0,0 +1,140 @@ +Organizational Structure +========================== + +| ``Phoebus`` uses a *hybrid flat-and-hierarchical* organizational + structure. +| The flat structure fosters power sharing among senior and junior + members and avoids the many pitfalls of power-over dynamics. For + example, in power-over structures, someone with explicit power can + inadvertently, or on rare occasions intentionally, silence critical + voices. +| This dynamic can quickly lead to an organization overlooking inherent + problems that could lead to ineffectiveness or even catastrophic + failure of the team. + +| In contrast, our aim is to illuminate potential problems early and + quickly find solutions. +| This strategy also efficiently taps into the diverse wealth of + knowledge of the team. +| At the same time, the PI and Co-PI have financial and reporting + responsibilities to their respective universities and funding + agencies. +| The general procedure for the hybrid structure is as follows. +| The flat structure will make major decisions in direction and + resources, and the PI and Co-PI will assume the responsibility for + executing those decisions. +| The following gives details on this hybrid structure. + +Team +---- + +The founding team consists of the following: original core developers +and Maintainers at Los Alamos National Lab, Jeremiah Murphy at Florida +State University, and Carl Fields at University of Arizona. + +Since, an objective of Phoebus is to grow the developer and user base, +the Phoebus Project will have an explicit mechanism for adding new +members. There are three categories for ``Phoebus`` members: +maintainers, contributors, and users. + +**User**: As open-source software, anyone may download, compile, and +execute ``Phoebus``. New users will encouraged to join communication +channels for connection with the larger ``Phoebus`` community. + +**Contributor**: Users who wish to contribute to ``Phoebus`` may do so +following our Development Model for new users. These changes will be +integrated into the main branch of the code upon approval. Consistent +contributions also provides the opportunity for Contributors to be +eligible to join as a *Maintainer*, the final approval of which will +require a vote. + +**Maintainer**: These are the core team who have “merge” permissions on +the repo and are working to keep the code sustainable long term. + +To maintain their relevant active status, all members must +make a food faith effort to maintain a supportive, productive environment. + + +.. _mou: + +Memorandum of Understanding +--------------------------- + +In addition to our Community Code of Conduct, we ask that maintainers +especially keep the following suggestions in mind to help +facilitate an efficient and welcoming collaboration: + +- Maintainers should uphold and exemplify the *Development Model* + outlined as part of the ``phoebus`` Community described + :doc:`here `. +- Within reason, maintainers will make a good-faith effort to attend team + meetings. In an effort to accommodate the dynamic schedules and + availability of many of the core team of *Maintainers*, + coordination efforts will be made to ensure that *at least* + 1 *Maintainer* is present for all meetings. +- Maintainers will make a good-faith effort to monitor the fraction of + the meeting time that they speak. The meeting time is limited, and + several people may have something interesting to say, report on their + updates, or contribute constructive arguments. One should be + self-aware and notice if one is dominating conversations, and attempt + to make a conscious effort to include other voices and perspectives + in the discussion. +- Maintainers consider it their responsibility to voice their questions + and/or concerns as early as possible. This will ensure that the + organization addresses concerns rapidly and effectively. +- Maintainers consider it their responsibility to listen and understand + questions or concerns raised by other partners or through concerns + communicated through email to individual *Maintainers*. + +Approval by Vote: +----------------- + +| Many of the decisions in the organization will be enacted after an + approval by majority vote of active Maintainers. The process of listening + and adjusting strategies to meet everyone’s needs is vital for + power-sharing organizations. +| Importantly, spending a little time up front to listen and resolve + concerns reduces the pain and time spent later in intense conflict + resolution. + +Communication and Connection: +----------------------------- + +| To facilitate open and effective communication, the ``Phoebus`` will + offer multiple levels of communication. + Developers will communicate via email, GitHub, and a ``Phoebus`` Slack + channel. + +| To respond to user inquiries, the Phoebus Project will host a mailing + list via Google or similar. +| To maintain a standing record of user inquiries and responses, we will + post the inquiries and responses on a public-facing site. +| All Maintainers will have the option to respond to the inquires; to + ensure that someone is responsive to the user inquiries, the team will + triage tickets/questions in developer meetings. + +| Subject to availability, monthly Maintainer meetings will also + be an important part of ensuring productivity and timeliness. +| Each meeting will last up to 60 minutes. We will assess and discuss + the goals from the previous meeting. +| In particular, we will take note which goals were completed and which + were not. If there are uncompleted goals, we will assess why they were + not completed. Next, we will discuss the goals for the upcoming month, + quarter, and year. +| We will decide which goals to prioritize. +| All of this will be recorded on an online document which will be + available to all Maintainers. + +| Each meeting of the core Maintainers will be managed by a meeting + manager. +| The primary job of the meeting manager is to: 1) gather a list of + agenda items for the next meeting, 2) ensure that the meeting runs on + schedule, and 3) ensure equitable participation by all participants. +| Again, in keeping with power-sharing, the meeting manager position + will rotate among the core Maintainers, even junior members. + +.. note:: + We maintain some flexibility in the cadence and structure of meetings, in + particular, in periods of low activity, meetings may be skipped or + held in a less formal manner. We recognize that the availability + of maintainers is contingent upon many factors. diff --git a/blb/frontier/_sources/src/sphinx-doc.rst.txt b/blb/frontier/_sources/src/sphinx-doc.rst.txt new file mode 100644 index 00000000..c85d9e4b --- /dev/null +++ b/blb/frontier/_sources/src/sphinx-doc.rst.txt @@ -0,0 +1,134 @@ +.. _sphinx-doc: + +.. _Sphinx CheatSheet: https://thomas-cokelaer.info/tutorials/sphinx/rest_syntax.html + +How to Use Sphinx for Writing Docs +=================================== + +How to convert a Markdown file to rst +------------------------------------------ + +We are using the `reStructuredText`_ (rst) format for our documentation. +If you have a markdown file you would like to convert to rst, +as a first pass, you can have `Pandoc`_ convert your file. For example: + +.. code-block:: bash + + pandoc Metadata.md --from markdown --to rst -s -o metadata.rst + +Pandoc can be installed easily through a Linux package manager. For example on Ubuntu, + +.. code-block:: bash + + apt install pandoc + +will get you the tool. + +.. _reStructuredText: https://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html + +.. _Pandoc: https://pandoc.org/ + +How to have github build your documentation for you +---------------------------------------------------- + +Github can automatically build your documentation for you through the continuous integration pipeline. +After you submit a pull request with your .rst changes for documentation on `github-pages`_, +the documentation will automatically get built. You will see a "build and deploy documentation" job +at the bottom of the pull request page. If this passes, your documentation will have been generated. + +On the bottom left of the documentation page on `github-pages`_, you can select the branch/build +of the documentation, one of which should be the branch you wrote your changes on. + +.. _github-pages: https://lanl.github.io/phoebus + + +Building documentation locally +------------------------------ + +While you can rely on the CI to build the documentation associated with your +branch, you can also very easily build sphinx documentation locally through +python. These instructions also *do not* require admin access and are usable +with shared machines or python distributions. + +First, ensure that you are running a modern version of python (i.e. python 3 of +some flavor) + +.. code-block:: bash + + $ python --version + Python 3.9.7 + +Then, use pip to install :code:`spinx` and the RTD theme + +.. code-block:: bash + + pip install --user sphinx sphinx-rtd-theme + +Now, navigate to the :code:`../doc/sphinx` directory where a :code:`make help` +shows all of the available ways to build the documentation + +.. code-block:: + + $ make help + Sphinx v4.2.0 + Please use `make target' where target is one of + html to make standalone HTML files + dirhtml to make HTML files named index.html in directories + singlehtml to make a single large HTML file + pickle to make pickle files + json to make JSON files + htmlhelp to make HTML files and an HTML help project + qthelp to make HTML files and a qthelp project + devhelp to make HTML files and a Devhelp project + epub to make an epub + latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter + latexpdf to make LaTeX and PDF files (default pdflatex) + latexpdfja to make LaTeX files and run them through platex/dvipdfmx + text to make text files + man to make manual pages + texinfo to make Texinfo files + info to make Texinfo files and run them through makeinfo + gettext to make PO message catalogs + changes to make an overview of all changed/added/deprecated items + xml to make Docutils-native XML files + pseudoxml to make pseudoxml-XML files for display purposes + linkcheck to check all external links for integrity + doctest to run all doctests embedded in the documentation (if enabled) + coverage to run coverage check of the documentation (if enabled) + clean to remove everything in the build directory + +Making the documentation will create a new directory, :code:`_build` in the +:code:`sphinx` directory along with whichever type of documentation you wanted +to build. + +For example, building the HTML documentation with :code:`make html` produces the +:code:`../doc/sphinx/_build/html` directory with an :code:`index.html` file that +you can point a browser to in order to view the documenation. + + +How to Get the Dependencies +--------------------------- + +Using Docker +^^^^^^^^^^^^ + +If you are using `Docker`_, then simply pull the docker image specified below: + +.. _Docker: https://www.docker.com + +.. code-block:: + + image: sphinxdoc/sphinx-latexpdf + +Then, after running :code:`docker run -it /bin/bash`, install the theme we are using with :code:`pip install sphinx_rtd_theme` + +More Info. +---------- + +* `Sphinx Installation`_ + +.. _Sphinx Installation: https://www.sphinx-doc.org/en/master/usage/installation.html + +* `Sphinx reStructuredText Documentation`_ + +.. _Sphinx reStructuredText Documentation: https://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html diff --git a/blb/frontier/_sources/src/tracers.rst.txt b/blb/frontier/_sources/src/tracers.rst.txt new file mode 100644 index 00000000..58cee20f --- /dev/null +++ b/blb/frontier/_sources/src/tracers.rst.txt @@ -0,0 +1,97 @@ +.. _parthenon-swarms: https://parthenon-hpc-lab.github.io/parthenon/develop/src/particles.html + +Tracer Particles +================ + +``Phoebus`` includes Lagrangian tracer particles. +These are primarily for the purpose of post-processing simulation data for, e.g., nucleosynthesis. +They are operator spit from the hydrodynamics and advected with a standard second order Runge-Kutta +integrator. As ``Phoebus`` is a general relativistic code, we evolve tracer positions using a +relativistic advection equation: + +.. math:: + + \frac{dx^i}{dt} = \frac{u^i}{u^0} = \alpha v^i - \beta^i + +Tracers may be enabled by in the ``Phoebus`` input deck as follow: + +.. code-block:: + + + tracers = true + + + num_tracers = 1024 + +Similarly, tracers may be output by modifying an existing Parthenon output block, or creating a new one: + +.. code-block:: + + + // ... + swarms = tracers + tracers_variables = rho, temperature, ye + + file_type = hdf5 + dt = // output cadence + +Note that the position variables x, y, z are output for all swarms by default. +See the `Parthenon docs `_ for more information. + +Tracers must, however, be configured in the problem generator. +In the generator, the tracers should be distributed through the domain, assigned positions +and unique ids. An example from the advection pgen is shown below. + +.. code-block:: c++ + + pmb->par_for( + "ProblemGenerator::Advection::DistributeTracers", 0, max_active_index, + KOKKOS_LAMBDA(const int n) { + if (swarm_d.IsActive(n)) { + auto rng_gen = rng_pool.get_state(); + + // sample in ball + Real r2 = 1.0 + rin * rin; // init > rin^2 + while (r2 > rin * rin) { + x(n) = x_min + rng_gen.drand() * (x_max - x_min); + y(n) = y_min + rng_gen.drand() * (y_max - y_min); + z(n) = z_min + rng_gen.drand() * (z_max - z_min); + r2 = x(n) * x(n) + y(n) * y(n) + z(n) * z(n); + } + id(n) = num_tracers_total * gid + n; + + bool on_current_mesh_block = true; + swarm_d.GetNeighborBlockIndex(n, x(n), y(n), z(n), on_current_mesh_block); + rng_pool.free_state(rng_gen); + } + }); + +In addition to position, tracers track a number of potentially useful quantities. +These quantities include (bold quantities are 3-vectors with components _x, _y, _z) + +=================== ================ =================== + Quantity SwarmVar Name Description +=================== ================ =================== +Density rho Primitive density +Temperature temperature Temperature +Ye ye Electron fraction (0 if ye is disabled) +Internal energy energy Primitive internal energy +Entropy entropy Entropy +**Velocity** vel_x, ... Three velocity +Lorentz factor lorentz Relativistic Lorentz factor +Lapse lapse Relativistic lapse +Metric determinant detgamma Spatial metric determinant +**Shift** shift_x, ... Relativistic shift +Mass mass Tracer mass +Total energy bernoulli Total energy Bernoulli quantity +**Magnetic field** B_x, ... Primitive 3-magnetic field components (if mhd enabled) +=================== ================ =================== + +To minimize unnecessary work, these quantities are only populated before output using ``phoebus::UserWorkBeforeOutput``. + +.. cpp:function:: void UserWorkBeforeOutput(MeshBlock *pmb, ParameterInput *pin) + :no-contents-entry: + + Describes work to be done prior to HDF5 output, such as populating tracer variables. + This is connected to the appropriate Parthenon function. + diff --git a/blb/frontier/_static/_sphinx_javascript_frameworks_compat.js b/blb/frontier/_static/_sphinx_javascript_frameworks_compat.js new file mode 100644 index 00000000..81415803 --- /dev/null +++ b/blb/frontier/_static/_sphinx_javascript_frameworks_compat.js @@ -0,0 +1,123 @@ +/* Compatability shim for jQuery and underscores.js. + * + * Copyright Sphinx contributors + * Released under the two clause BSD licence + */ + +/** + * small helper function to urldecode strings + * + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL + */ +jQuery.urldecode = function(x) { + if (!x) { + return x + } + return decodeURIComponent(x.replace(/\+/g, ' ')); +}; + +/** + * small helper function to urlencode strings + */ +jQuery.urlencode = encodeURIComponent; + +/** + * This function returns the parsed url parameters of the + * current request. 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+ }); + } + } + var addItems = []; + var result = this.each(function() { + highlight(this, addItems); + }); + for (var i = 0; i < addItems.length; ++i) { + jQuery(addItems[i].parent).before(addItems[i].target); + } + return result; +}; + +/* + * backward compatibility for jQuery.browser + * This will be supported until firefox bug is fixed. + */ +if (!jQuery.browser) { + jQuery.uaMatch = function(ua) { + ua = ua.toLowerCase(); + + var match = /(chrome)[ \/]([\w.]+)/.exec(ua) || + /(webkit)[ \/]([\w.]+)/.exec(ua) || + /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) || + /(msie) ([\w.]+)/.exec(ua) || + ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) || + []; + + return { + browser: match[ 1 ] || "", + version: match[ 2 ] || "0" + }; + }; + jQuery.browser = {}; + jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true; +} diff --git a/blb/frontier/_static/basic.css b/blb/frontier/_static/basic.css new file mode 100644 index 00000000..7ebbd6d0 --- /dev/null +++ b/blb/frontier/_static/basic.css @@ -0,0 +1,914 @@ +/* + * Sphinx stylesheet -- basic theme. + */ + +/* -- main layout ----------------------------------------------------------- */ + +div.clearer { + clear: both; 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+ padding-right: 5px; +} + +dl.field-list > dd { + padding-left: 0.5em; + margin-top: 0em; + margin-left: 0em; + margin-bottom: 0em; +} + +dl { + margin-bottom: 15px; +} + +dd > :first-child { + margin-top: 0px; +} + +dd ul, dd table { + margin-bottom: 10px; +} + +dd { + margin-top: 3px; + margin-bottom: 10px; + margin-left: 30px; +} + +.sig dd { + margin-top: 0px; + margin-bottom: 0px; +} + +.sig dl { + margin-top: 0px; + margin-bottom: 0px; +} + +dl > dd:last-child, +dl > dd:last-child > :last-child { + margin-bottom: 0; +} + +dt:target, span.highlighted { + background-color: #fbe54e; +} + +rect.highlighted { + fill: #fbe54e; +} + +dl.glossary dt { + font-weight: bold; + font-size: 1.1em; +} + +.versionmodified { + font-style: italic; +} + +.system-message { + background-color: #fda; + padding: 5px; + border: 3px solid red; +} + +.footnote:target { + background-color: #ffa; +} + +.line-block { + display: block; + margin-top: 1em; + margin-bottom: 1em; +} + +.line-block .line-block { + margin-top: 0; + margin-bottom: 0; + margin-left: 1.5em; +} + +.guilabel, .menuselection { + font-family: sans-serif; +} + +.accelerator { + text-decoration: underline; +} + +.classifier { + font-style: oblique; +} + +.classifier:before { + font-style: normal; + margin: 0 0.5em; + content: ":"; + display: inline-block; +} + +abbr, acronym { + border-bottom: dotted 1px; + cursor: help; +} + +.translated { + background-color: rgba(207, 255, 207, 0.2) +} + +.untranslated { + background-color: rgba(255, 207, 207, 0.2) +} + +/* -- code displays --------------------------------------------------------- */ + +pre { + overflow: auto; + overflow-y: hidden; /* fixes display issues on Chrome browsers */ +} + +pre, div[class*="highlight-"] { + clear: both; +} + +span.pre { + -moz-hyphens: none; + -ms-hyphens: none; + -webkit-hyphens: none; + hyphens: none; + white-space: nowrap; +} + +div[class*="highlight-"] { + margin: 1em 0; +} + +td.linenos pre { + border: 0; + background-color: transparent; + color: #aaa; +} + +table.highlighttable { + display: block; +} + +table.highlighttable tbody { + display: block; +} + +table.highlighttable tr { + display: flex; +} + +table.highlighttable td { + margin: 0; + padding: 0; +} + +table.highlighttable td.linenos { + padding-right: 0.5em; +} + +table.highlighttable td.code { + flex: 1; + overflow: hidden; +} + +.highlight .hll { + display: block; +} + +div.highlight pre, +table.highlighttable pre { + margin: 0; +} + +div.code-block-caption + div { + margin-top: 0; +} + +div.code-block-caption { + margin-top: 1em; + padding: 2px 5px; + font-size: small; +} + +div.code-block-caption code { + background-color: transparent; +} + +table.highlighttable td.linenos, +span.linenos, +div.highlight span.gp { /* gp: Generic.Prompt */ + user-select: none; + -webkit-user-select: text; /* Safari fallback only */ + -webkit-user-select: none; /* Chrome/Safari */ + -moz-user-select: none; /* Firefox */ + -ms-user-select: none; /* IE10+ */ +} + +div.code-block-caption span.caption-number { + padding: 0.1em 0.3em; + font-style: italic; +} + +div.code-block-caption span.caption-text { +} + +div.literal-block-wrapper { + margin: 1em 0; +} + +code.xref, a code { + background-color: transparent; + font-weight: bold; +} + +h1 code, h2 code, h3 code, h4 code, h5 code, h6 code { + background-color: transparent; +} + +.viewcode-link { + float: right; +} + +.viewcode-back { + float: right; + font-family: sans-serif; +} + +div.viewcode-block:target { + margin: -1px -10px; + padding: 0 10px; +} + +/* -- math display ---------------------------------------------------------- */ + +img.math { + vertical-align: middle; +} + +div.body div.math p { + text-align: center; +} + +span.eqno { + float: right; +} + +span.eqno a.headerlink { + position: absolute; + z-index: 1; +} + +div.math:hover a.headerlink { + visibility: visible; +} + +/* -- printout stylesheet --------------------------------------------------- */ + +@media print { + div.document, + div.documentwrapper, + div.bodywrapper { + margin: 0 !important; + width: 100%; + } + + div.sphinxsidebar, + div.related, + div.footer, + #top-link { + display: none; + } +} \ No newline at end of file diff --git a/blb/frontier/_static/check-solid.svg b/blb/frontier/_static/check-solid.svg new file mode 100644 index 00000000..92fad4b5 --- /dev/null +++ b/blb/frontier/_static/check-solid.svg @@ -0,0 +1,4 @@ + + + + diff --git a/blb/frontier/_static/clipboard.min.js b/blb/frontier/_static/clipboard.min.js new file mode 100644 index 00000000..54b3c463 --- /dev/null +++ b/blb/frontier/_static/clipboard.min.js @@ -0,0 +1,7 @@ +/*! + * clipboard.js v2.0.8 + * https://clipboardjs.com/ + * + * Licensed MIT © Zeno Rocha + */ +!function(t,e){"object"==typeof exports&&"object"==typeof module?module.exports=e():"function"==typeof define&&define.amd?define([],e):"object"==typeof exports?exports.ClipboardJS=e():t.ClipboardJS=e()}(this,function(){return n={686:function(t,e,n){"use strict";n.d(e,{default:function(){return o}});var e=n(279),i=n.n(e),e=n(370),u=n.n(e),e=n(817),c=n.n(e);function a(t){try{return document.execCommand(t)}catch(t){return}}var f=function(t){t=c()(t);return a("cut"),t};var l=function(t){var e,n,o,r=1 + + + + diff --git a/blb/frontier/_static/copybutton.css b/blb/frontier/_static/copybutton.css new file mode 100644 index 00000000..f1916ec7 --- /dev/null +++ b/blb/frontier/_static/copybutton.css @@ -0,0 +1,94 @@ +/* Copy buttons */ +button.copybtn { + position: absolute; + display: flex; + top: .3em; + right: .3em; + width: 1.7em; + height: 1.7em; + opacity: 0; + transition: opacity 0.3s, border .3s, background-color .3s; + user-select: none; + padding: 0; + border: none; + outline: none; + border-radius: 0.4em; + /* The colors that GitHub uses */ + border: #1b1f2426 1px solid; + background-color: #f6f8fa; + color: #57606a; +} + +button.copybtn.success { + border-color: #22863a; + color: #22863a; +} + +button.copybtn svg { + stroke: currentColor; + width: 1.5em; + height: 1.5em; + padding: 0.1em; +} + +div.highlight { + position: relative; +} + +/* Show the copybutton */ +.highlight:hover button.copybtn, button.copybtn.success { + opacity: 1; +} + +.highlight button.copybtn:hover { + background-color: rgb(235, 235, 235); +} + +.highlight button.copybtn:active { + background-color: rgb(187, 187, 187); +} + +/** + * A minimal CSS-only tooltip copied from: + * https://codepen.io/mildrenben/pen/rVBrpK + * + * To use, write HTML like the following: + * + *

Short

+ */ + .o-tooltip--left { + position: relative; + } + + .o-tooltip--left:after { + opacity: 0; + visibility: hidden; + position: absolute; + content: attr(data-tooltip); + padding: .2em; + font-size: .8em; + left: -.2em; + background: grey; + color: white; + white-space: nowrap; + z-index: 2; + border-radius: 2px; + transform: translateX(-102%) translateY(0); + transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); +} + +.o-tooltip--left:hover:after { + display: block; + opacity: 1; + visibility: visible; + transform: translateX(-100%) translateY(0); + transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); + transition-delay: .5s; +} + +/* By default the copy button shouldn't show up when printing a page */ +@media print { + button.copybtn { + display: none; + } +} diff --git a/blb/frontier/_static/copybutton.js b/blb/frontier/_static/copybutton.js new file mode 100644 index 00000000..2ea7ff3e --- /dev/null +++ b/blb/frontier/_static/copybutton.js @@ -0,0 +1,248 @@ +// Localization support +const messages = { + 'en': { + 'copy': 'Copy', + 'copy_to_clipboard': 'Copy to clipboard', + 'copy_success': 'Copied!', + 'copy_failure': 'Failed to copy', + }, + 'es' : { + 'copy': 'Copiar', + 'copy_to_clipboard': 'Copiar al portapapeles', + 'copy_success': '¡Copiado!', + 'copy_failure': 'Error al copiar', + }, + 'de' : { + 'copy': 'Kopieren', + 'copy_to_clipboard': 'In die Zwischenablage kopieren', + 'copy_success': 'Kopiert!', + 'copy_failure': 'Fehler beim Kopieren', + }, + 'fr' : { + 'copy': 'Copier', + 'copy_to_clipboard': 'Copier dans le presse-papier', + 'copy_success': 'Copié !', + 'copy_failure': 'Échec de la copie', + }, + 'ru': { + 'copy': 'Скопировать', + 'copy_to_clipboard': 'Скопировать в буфер', + 'copy_success': 'Скопировано!', + 'copy_failure': 'Не удалось скопировать', + }, + 'zh-CN': { + 'copy': '复制', + 'copy_to_clipboard': '复制到剪贴板', + 'copy_success': '复制成功!', + 'copy_failure': '复制失败', + }, + 'it' : { + 'copy': 'Copiare', + 'copy_to_clipboard': 'Copiato negli appunti', + 'copy_success': 'Copiato!', + 'copy_failure': 'Errore durante la copia', + } +} + +let locale = 'en' +if( document.documentElement.lang !== undefined + && messages[document.documentElement.lang] !== undefined ) { + locale = document.documentElement.lang +} + +let doc_url_root = DOCUMENTATION_OPTIONS.URL_ROOT; +if (doc_url_root == '#') { + doc_url_root = ''; +} + +/** + * SVG files for our copy buttons + */ +let iconCheck = ` + ${messages[locale]['copy_success']} + + +` + +// If the user specified their own SVG use that, otherwise use the default +let iconCopy = ``; +if (!iconCopy) { + iconCopy = ` + ${messages[locale]['copy_to_clipboard']} + + + +` +} + +/** + * Set up copy/paste for code blocks + */ + +const runWhenDOMLoaded = cb => { + if (document.readyState != 'loading') { + cb() + } else if (document.addEventListener) { + document.addEventListener('DOMContentLoaded', cb) + } else { + document.attachEvent('onreadystatechange', function() { + if (document.readyState == 'complete') cb() + }) + } +} + +const codeCellId = index => `codecell${index}` + +// Clears selected text since ClipboardJS will select the text when copying +const clearSelection = () => { + if (window.getSelection) { + window.getSelection().removeAllRanges() + } else if (document.selection) { + document.selection.empty() + } +} + +// Changes tooltip text for a moment, then changes it back +// We want the timeout of our `success` class to be a bit shorter than the +// tooltip and icon change, so that we can hide the icon before changing back. +var timeoutIcon = 2000; +var timeoutSuccessClass = 1500; + +const temporarilyChangeTooltip = (el, oldText, newText) => { + el.setAttribute('data-tooltip', newText) + el.classList.add('success') + // Remove success a little bit sooner than we change the tooltip + // So that we can use CSS to hide the copybutton first + setTimeout(() => el.classList.remove('success'), timeoutSuccessClass) + setTimeout(() => el.setAttribute('data-tooltip', oldText), timeoutIcon) +} + +// Changes the copy button icon for two seconds, then changes it back +const temporarilyChangeIcon = (el) => { + el.innerHTML = iconCheck; + setTimeout(() => {el.innerHTML = iconCopy}, timeoutIcon) +} + +const addCopyButtonToCodeCells = () => { + // If ClipboardJS hasn't loaded, wait a bit and try again. This + // happens because we load ClipboardJS asynchronously. + if (window.ClipboardJS === undefined) { + setTimeout(addCopyButtonToCodeCells, 250) + return + } + + // Add copybuttons to all of our code cells + const COPYBUTTON_SELECTOR = 'div.highlight pre'; + const codeCells = document.querySelectorAll(COPYBUTTON_SELECTOR) + codeCells.forEach((codeCell, index) => { + const id = codeCellId(index) + codeCell.setAttribute('id', id) + + const clipboardButton = id => + `` + codeCell.insertAdjacentHTML('afterend', clipboardButton(id)) + }) + +function escapeRegExp(string) { + return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string +} + +/** + * Removes excluded text from a Node. + * + * @param {Node} target Node to filter. + * @param {string} exclude CSS selector of nodes to exclude. + * @returns {DOMString} Text from `target` with text removed. + */ +function filterText(target, exclude) { + const clone = target.cloneNode(true); // clone as to not modify the live DOM + if (exclude) { + // remove excluded nodes + clone.querySelectorAll(exclude).forEach(node => node.remove()); + } + return clone.innerText; +} + +// Callback when a copy button is clicked. Will be passed the node that was clicked +// should then grab the text and replace pieces of text that shouldn't be used in output +function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; + var match; + + // Do we check for line continuation characters and "HERE-documents"? + var useLineCont = !!lineContinuationChar + var useHereDoc = !!hereDocDelim + + // create regexp to capture prompt and remaining line + if (isRegexp) { + regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') + } else { + regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') + } + + const outputLines = []; + var promptFound = false; + var gotLineCont = false; + var gotHereDoc = false; + const lineGotPrompt = []; + for (const line of textContent.split('\n')) { + match = line.match(regexp) + if (match || gotLineCont || gotHereDoc) { + promptFound = regexp.test(line) + lineGotPrompt.push(promptFound) + if (removePrompts && promptFound) { + outputLines.push(match[2]) + } else { + outputLines.push(line) + } + gotLineCont = line.endsWith(lineContinuationChar) & useLineCont + if (line.includes(hereDocDelim) & useHereDoc) + gotHereDoc = !gotHereDoc + } else if (!onlyCopyPromptLines) { + outputLines.push(line) + } else if (copyEmptyLines && line.trim() === '') { + outputLines.push(line) + } + } + + // If no lines with the prompt were found then just use original lines + if (lineGotPrompt.some(v => v === true)) { + textContent = outputLines.join('\n'); + } + + // Remove a trailing newline to avoid auto-running when pasting + if (textContent.endsWith("\n")) { + textContent = textContent.slice(0, -1) + } + return textContent +} + + +var copyTargetText = (trigger) => { + var target = document.querySelector(trigger.attributes['data-clipboard-target'].value); + + // get filtered text + let exclude = '.linenos'; + + let text = filterText(target, exclude); + return formatCopyText(text, '', false, true, true, true, '', '') +} + + // Initialize with a callback so we can modify the text before copy + const clipboard = new ClipboardJS('.copybtn', {text: copyTargetText}) + + // Update UI with error/success messages + clipboard.on('success', event => { + clearSelection() + temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_success']) + temporarilyChangeIcon(event.trigger) + }) + + clipboard.on('error', event => { + temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_failure']) + }) +} + +runWhenDOMLoaded(addCopyButtonToCodeCells) \ No newline at end of file diff --git a/blb/frontier/_static/copybutton_funcs.js b/blb/frontier/_static/copybutton_funcs.js new file mode 100644 index 00000000..dbe1aaad --- /dev/null +++ b/blb/frontier/_static/copybutton_funcs.js @@ -0,0 +1,73 @@ +function escapeRegExp(string) { + return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string +} + +/** + * Removes excluded text from a Node. + * + * @param {Node} target Node to filter. + * @param {string} exclude CSS selector of nodes to exclude. + * @returns {DOMString} Text from `target` with text removed. + */ +export function filterText(target, exclude) { + const clone = target.cloneNode(true); // clone as to not modify the live DOM + if (exclude) { + // remove excluded nodes + clone.querySelectorAll(exclude).forEach(node => node.remove()); + } + return clone.innerText; +} + +// Callback when a copy button is clicked. Will be passed the node that was clicked +// should then grab the text and replace pieces of text that shouldn't be used in output +export function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; + var match; + + // Do we check for line continuation characters and "HERE-documents"? + var useLineCont = !!lineContinuationChar + var useHereDoc = !!hereDocDelim + + // create regexp to capture prompt and remaining line + if (isRegexp) { + regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') + } else { + regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') + } + + const outputLines = []; + var promptFound = false; + var gotLineCont = false; + var gotHereDoc = false; + const lineGotPrompt = []; + for (const line of textContent.split('\n')) { + match = line.match(regexp) + if (match || gotLineCont || gotHereDoc) { + promptFound = regexp.test(line) + lineGotPrompt.push(promptFound) + if (removePrompts && promptFound) { + outputLines.push(match[2]) + } else { + outputLines.push(line) + } + gotLineCont = line.endsWith(lineContinuationChar) & useLineCont + if (line.includes(hereDocDelim) & useHereDoc) + gotHereDoc = !gotHereDoc + } else if (!onlyCopyPromptLines) { + outputLines.push(line) + } else if (copyEmptyLines && line.trim() === '') { + outputLines.push(line) + } + } + + // If no lines with the prompt were found then just use original lines + if (lineGotPrompt.some(v => v === true)) { + textContent = outputLines.join('\n'); + } + + // Remove a trailing newline to avoid auto-running when pasting + if (textContent.endsWith("\n")) { + textContent = textContent.slice(0, -1) + } + return textContent +} diff --git a/blb/frontier/_static/css/badge_only.css b/blb/frontier/_static/css/badge_only.css new file mode 100644 index 00000000..88ba55b9 --- /dev/null +++ b/blb/frontier/_static/css/badge_only.css 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+ document.dispatchEvent(event); + }); +}); \ No newline at end of file diff --git a/blb/frontier/_static/language_data.js b/blb/frontier/_static/language_data.js new file mode 100644 index 00000000..c7fe6c6f --- /dev/null +++ b/blb/frontier/_static/language_data.js @@ -0,0 +1,192 @@ +/* + * This script contains the language-specific data used by searchtools.js, + * namely the list of stopwords, stemmer, scorer and splitter. + */ + +var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"]; + + +/* Non-minified version is copied as a separate JS file, if available */ + +/** + * Porter Stemmer + */ +var Stemmer = function() { + + var step2list = { + ational: 'ate', + tional: 'tion', + enci: 'ence', + anci: 'ance', + izer: 'ize', + bli: 'ble', + alli: 'al', + entli: 'ent', + eli: 'e', + ousli: 'ous', + ization: 'ize', + ation: 'ate', + ator: 'ate', + alism: 'al', + iveness: 'ive', + fulness: 'ful', + ousness: 'ous', + aliti: 'al', + iviti: 'ive', + biliti: 'ble', + logi: 'log' + }; 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+ re2 = /^(.+?)(ed|ing)$/; + if (re.test(w)) { + var fp = re.exec(w); + re = new RegExp(mgr0); + if (re.test(fp[1])) { + re = /.$/; + w = w.replace(re,""); + } + } + else if (re2.test(w)) { + var fp = re2.exec(w); + stem = fp[1]; + re2 = new RegExp(s_v); + if (re2.test(stem)) { + w = stem; + re2 = /(at|bl|iz)$/; + re3 = new RegExp("([^aeiouylsz])\\1$"); + re4 = new RegExp("^" + C + v + "[^aeiouwxy]$"); + if (re2.test(w)) + w = w + "e"; + else if (re3.test(w)) { + re = /.$/; + w = w.replace(re,""); + } + else if (re4.test(w)) + w = w + "e"; + } + } + + // Step 1c + re = /^(.+?)y$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(s_v); + if (re.test(stem)) + w = stem + "i"; + } + + // Step 2 + re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = new RegExp(mgr0); + if (re.test(stem)) + w = stem + step2list[suffix]; 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+ +/** + * Simple result scoring code. + */ +if (typeof Scorer === "undefined") { + var Scorer = { + // Implement the following function to further tweak the score for each result + // The function takes a result array [docname, title, anchor, descr, score, filename] + // and returns the new score. + /* + score: result => { + const [docname, title, anchor, descr, score, filename, kind] = result + return score + }, + */ + + // query matches the full name of an object + objNameMatch: 11, + // or matches in the last dotted part of the object name + objPartialMatch: 6, + // Additive scores depending on the priority of the object + objPrio: { + 0: 15, // used to be importantResults + 1: 5, // used to be objectResults + 2: -5, // used to be unimportantResults + }, + // Used when the priority is not in the mapping. + objPrioDefault: 0, + + // query found in title + title: 15, + partialTitle: 7, + // query found in terms + term: 5, + partialTerm: 2, + }; +} + +// Global search result kind enum, used by themes to style search results. +class SearchResultKind { + static get index() { return "index"; } + static get object() { return "object"; } + static get text() { return "text"; } + static get title() { return "title"; } +} + +const _removeChildren = (element) => { + while (element && element.lastChild) element.removeChild(element.lastChild); +}; + +/** + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping + */ +const _escapeRegExp = (string) => + string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string + +const _displayItem = (item, searchTerms, highlightTerms) => { + const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; + const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; + const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; + const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; + const contentRoot = document.documentElement.dataset.content_root; + + const [docName, title, anchor, descr, score, _filename, kind] = item; + + let listItem = document.createElement("li"); + // Add a class representing the item's type: + // can be used by a theme's CSS selector for styling + // See SearchResultKind for the class names. + listItem.classList.add(`kind-${kind}`); + let requestUrl; + let linkUrl; + if (docBuilder === "dirhtml") { + // dirhtml builder + let dirname = docName + "/"; + if (dirname.match(/\/index\/$/)) + dirname = dirname.substring(0, dirname.length - 6); + else if (dirname === "index/") dirname = ""; + requestUrl = contentRoot + dirname; + linkUrl = requestUrl; + } else { + // normal html builders + requestUrl = contentRoot + docName + docFileSuffix; + linkUrl = docName + docLinkSuffix; + } + let linkEl = listItem.appendChild(document.createElement("a")); + linkEl.href = linkUrl + anchor; + linkEl.dataset.score = score; + linkEl.innerHTML = title; + if (descr) { + listItem.appendChild(document.createElement("span")).innerHTML = + " (" + descr + ")"; + // highlight search terms in the description + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + } + else if (showSearchSummary) + fetch(requestUrl) + .then((responseData) => responseData.text()) + .then((data) => { + if (data) + listItem.appendChild( + Search.makeSearchSummary(data, searchTerms, anchor) + ); + // highlight search terms in the summary + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + }); + Search.output.appendChild(listItem); +}; +const _finishSearch = (resultCount) => { + Search.stopPulse(); + Search.title.innerText = _("Search Results"); + if (!resultCount) + Search.status.innerText = Documentation.gettext( + "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." + ); + else + Search.status.innerText = Documentation.ngettext( + "Search finished, found one page matching the search query.", + "Search finished, found ${resultCount} pages matching the search query.", + resultCount, + ).replace('${resultCount}', resultCount); +}; +const _displayNextItem = ( + results, + resultCount, + searchTerms, + highlightTerms, +) => { + // results left, load the summary and display it + // this is intended to be dynamic (don't sub resultsCount) + if (results.length) { + _displayItem(results.pop(), searchTerms, highlightTerms); + setTimeout( + () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), + 5 + ); + } + // search finished, update title and status message + else _finishSearch(resultCount); +}; +// Helper function used by query() to order search results. +// Each input is an array of [docname, title, anchor, descr, score, filename, kind]. +// Order the results by score (in opposite order of appearance, since the +// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. +const _orderResultsByScoreThenName = (a, b) => { + const leftScore = a[4]; + const rightScore = b[4]; + if (leftScore === rightScore) { + // same score: sort alphabetically + const leftTitle = a[1].toLowerCase(); + const rightTitle = b[1].toLowerCase(); + if (leftTitle === rightTitle) return 0; + return leftTitle > rightTitle ? -1 : 1; // inverted is intentional + } + return leftScore > rightScore ? 1 : -1; +}; + +/** + * Default splitQuery function. Can be overridden in ``sphinx.search`` with a + * custom function per language. + * + * The regular expression works by splitting the string on consecutive characters + * that are not Unicode letters, numbers, underscores, or emoji characters. + * This is the same as ``\W+`` in Python, preserving the surrogate pair area. + */ +if (typeof splitQuery === "undefined") { + var splitQuery = (query) => query + .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) + .filter(term => term) // remove remaining empty strings +} + +/** + * Search Module + */ +const Search = { + _index: null, + _queued_query: null, + _pulse_status: -1, + + htmlToText: (htmlString, anchor) => { + const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); + for (const removalQuery of [".headerlink", "script", "style"]) { + htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); + } + if (anchor) { + const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); + if (anchorContent) return anchorContent.textContent; + + console.warn( + `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` + ); + } + + // if anchor not specified or not found, fall back to main content + const docContent = htmlElement.querySelector('[role="main"]'); + if (docContent) return docContent.textContent; + + console.warn( + "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." + ); + return ""; + }, + + init: () => { + const query = new URLSearchParams(window.location.search).get("q"); + document + .querySelectorAll('input[name="q"]') + .forEach((el) => (el.value = query)); + if (query) Search.performSearch(query); + }, + + loadIndex: (url) => + (document.body.appendChild(document.createElement("script")).src = url), + + setIndex: (index) => { + Search._index = index; + if (Search._queued_query !== null) { + const query = Search._queued_query; + Search._queued_query = null; + Search.query(query); + } + }, + + hasIndex: () => Search._index !== null, + + deferQuery: (query) => (Search._queued_query = query), + + stopPulse: () => (Search._pulse_status = -1), + + startPulse: () => { + if (Search._pulse_status >= 0) return; + + const pulse = () => { + Search._pulse_status = (Search._pulse_status + 1) % 4; + Search.dots.innerText = ".".repeat(Search._pulse_status); + if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); + }; + pulse(); + }, + + /** + * perform a search for something (or wait until index is loaded) + */ + performSearch: (query) => { + // create the required interface elements + const searchText = document.createElement("h2"); + searchText.textContent = _("Searching"); + const searchSummary = document.createElement("p"); + searchSummary.classList.add("search-summary"); + searchSummary.innerText = ""; + const searchList = document.createElement("ul"); + searchList.setAttribute("role", "list"); + searchList.classList.add("search"); + + const out = document.getElementById("search-results"); + Search.title = out.appendChild(searchText); + Search.dots = Search.title.appendChild(document.createElement("span")); + Search.status = out.appendChild(searchSummary); + Search.output = out.appendChild(searchList); + + const searchProgress = document.getElementById("search-progress"); + // Some themes don't use the search progress node + if (searchProgress) { + searchProgress.innerText = _("Preparing search..."); + } + Search.startPulse(); + + // index already loaded, the browser was quick! + if (Search.hasIndex()) Search.query(query); + else Search.deferQuery(query); + }, + + _parseQuery: (query) => { + // stem the search terms and add them to the correct list + const stemmer = new Stemmer(); + const searchTerms = new Set(); + const excludedTerms = new Set(); + const highlightTerms = new Set(); + const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); + splitQuery(query.trim()).forEach((queryTerm) => { + const queryTermLower = queryTerm.toLowerCase(); + + // maybe skip this "word" + // stopwords array is from language_data.js + if ( + stopwords.indexOf(queryTermLower) !== -1 || + queryTerm.match(/^\d+$/) + ) + return; + + // stem the word + let word = stemmer.stemWord(queryTermLower); + // select the correct list + if (word[0] === "-") excludedTerms.add(word.substr(1)); + else { + searchTerms.add(word); + highlightTerms.add(queryTermLower); + } + }); + + if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js + localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) + } + + // console.debug("SEARCH: searching for:"); + // console.info("required: ", [...searchTerms]); + // console.info("excluded: ", [...excludedTerms]); + + return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; + }, + + /** + * execute search (requires search index to be loaded) + */ + _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + const allTitles = Search._index.alltitles; + const indexEntries = Search._index.indexentries; + + // Collect multiple result groups to be sorted separately and then ordered. + // Each is an array of [docname, title, anchor, descr, score, filename, kind]. + const normalResults = []; + const nonMainIndexResults = []; + + _removeChildren(document.getElementById("search-progress")); + + const queryLower = query.toLowerCase().trim(); + for (const [title, foundTitles] of Object.entries(allTitles)) { + if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { + for (const [file, id] of foundTitles) { + const score = Math.round(Scorer.title * queryLower.length / title.length); + const boost = titles[file] === title ? 1 : 0; // add a boost for document titles + normalResults.push([ + docNames[file], + titles[file] !== title ? `${titles[file]} > ${title}` : title, + id !== null ? "#" + id : "", + null, + score + boost, + filenames[file], + SearchResultKind.title, + ]); + } + } + } + + // search for explicit entries in index directives + for (const [entry, foundEntries] of Object.entries(indexEntries)) { + if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { + for (const [file, id, isMain] of foundEntries) { + const score = Math.round(100 * queryLower.length / entry.length); + const result = [ + docNames[file], + titles[file], + id ? "#" + id : "", + null, + score, + filenames[file], + SearchResultKind.index, + ]; + if (isMain) { + normalResults.push(result); + } else { + nonMainIndexResults.push(result); + } + } + } + } + + // lookup as object + objectTerms.forEach((term) => + normalResults.push(...Search.performObjectSearch(term, objectTerms)) + ); + + // lookup as search terms in fulltext + normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + + // let the scorer override scores with a custom scoring function + if (Scorer.score) { + normalResults.forEach((item) => (item[4] = Scorer.score(item))); + nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); + } + + // Sort each group of results by score and then alphabetically by name. + normalResults.sort(_orderResultsByScoreThenName); + nonMainIndexResults.sort(_orderResultsByScoreThenName); + + // Combine the result groups in (reverse) order. + // Non-main index entries are typically arbitrary cross-references, + // so display them after other results. + let results = [...nonMainIndexResults, ...normalResults]; + + // remove duplicate search results + // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept + let seen = new Set(); + results = results.reverse().reduce((acc, result) => { + let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); + if (!seen.has(resultStr)) { + acc.push(result); + seen.add(resultStr); + } + return acc; + }, []); + + return results.reverse(); + }, + + query: (query) => { + const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); + const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); + + // for debugging + //Search.lastresults = results.slice(); // a copy + // console.info("search results:", Search.lastresults); + + // print the results + _displayNextItem(results, results.length, searchTerms, highlightTerms); + }, + + /** + * search for object names + */ + performObjectSearch: (object, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const objects = Search._index.objects; + const objNames = Search._index.objnames; + const titles = Search._index.titles; + + const results = []; + + const objectSearchCallback = (prefix, match) => { + const name = match[4] + const fullname = (prefix ? prefix + "." : "") + name; + const fullnameLower = fullname.toLowerCase(); + if (fullnameLower.indexOf(object) < 0) return; + + let score = 0; + const parts = fullnameLower.split("."); + + // check for different match types: exact matches of full name or + // "last name" (i.e. last dotted part) + if (fullnameLower === object || parts.slice(-1)[0] === object) + score += Scorer.objNameMatch; + else if (parts.slice(-1)[0].indexOf(object) > -1) + score += Scorer.objPartialMatch; // matches in last name + + const objName = objNames[match[1]][2]; + const title = titles[match[0]]; + + // If more than one term searched for, we require other words to be + // found in the name/title/description + const otherTerms = new Set(objectTerms); + otherTerms.delete(object); + if (otherTerms.size > 0) { + const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); + if ( + [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) + ) + return; + } + + let anchor = match[3]; + if (anchor === "") anchor = fullname; + else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; + + const descr = objName + _(", in ") + title; + + // add custom score for some objects according to scorer + if (Scorer.objPrio.hasOwnProperty(match[2])) + score += Scorer.objPrio[match[2]]; + else score += Scorer.objPrioDefault; + + results.push([ + docNames[match[0]], + fullname, + "#" + anchor, + descr, + score, + filenames[match[0]], + SearchResultKind.object, + ]); + }; + Object.keys(objects).forEach((prefix) => + objects[prefix].forEach((array) => + objectSearchCallback(prefix, array) + ) + ); + return results; + }, + + /** + * search for full-text terms in the index + */ + performTermsSearch: (searchTerms, excludedTerms) => { + // prepare search + const terms = Search._index.terms; + const titleTerms = Search._index.titleterms; + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + + const scoreMap = new Map(); + const fileMap = new Map(); + + // perform the search on the required terms + searchTerms.forEach((word) => { + const files = []; + const arr = [ + { files: terms[word], score: Scorer.term }, + { files: titleTerms[word], score: Scorer.title }, + ]; + // add support for partial matches + if (word.length > 2) { + const escapedWord = _escapeRegExp(word); + if (!terms.hasOwnProperty(word)) { + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + } + if (!titleTerms.hasOwnProperty(word)) { + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); + }); + } + } + + // no match but word was a required one + if (arr.every((record) => record.files === undefined)) return; + + // found search word in contents + arr.forEach((record) => { + if (record.files === undefined) return; + + let recordFiles = record.files; + if (recordFiles.length === undefined) recordFiles = [recordFiles]; + files.push(...recordFiles); + + // set score for the word in each file + recordFiles.forEach((file) => { + if (!scoreMap.has(file)) scoreMap.set(file, {}); + scoreMap.get(file)[word] = record.score; + }); + }); + + // create the mapping + files.forEach((file) => { + if (!fileMap.has(file)) fileMap.set(file, [word]); + else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); + }); + }); + + // now check if the files don't contain excluded terms + const results = []; + for (const [file, wordList] of fileMap) { + // check if all requirements are matched + + // as search terms with length < 3 are discarded + const filteredTermCount = [...searchTerms].filter( + (term) => term.length > 2 + ).length; + if ( + wordList.length !== searchTerms.size && + wordList.length !== filteredTermCount + ) + continue; + + // ensure that none of the excluded terms is in the search result + if ( + [...excludedTerms].some( + (term) => + terms[term] === file || + titleTerms[term] === file || + (terms[term] || []).includes(file) || + (titleTerms[term] || []).includes(file) + ) + ) + break; + + // select one (max) score for the file. + const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); + // add result to the result list + results.push([ + docNames[file], + titles[file], + "", + null, + score, + filenames[file], + SearchResultKind.text, + ]); + } + return results; + }, + + /** + * helper function to return a node containing the + * search summary for a given text. keywords is a list + * of stemmed words. + */ + makeSearchSummary: (htmlText, keywords, anchor) => { + const text = Search.htmlToText(htmlText, anchor); + if (text === "") return null; + + const textLower = text.toLowerCase(); + const actualStartPosition = [...keywords] + .map((k) => textLower.indexOf(k.toLowerCase())) + .filter((i) => i > -1) + .slice(-1)[0]; + const startWithContext = Math.max(actualStartPosition - 120, 0); + + const top = startWithContext === 0 ? "" : "..."; + const tail = startWithContext + 240 < text.length ? "..." : ""; + + let summary = document.createElement("p"); + summary.classList.add("context"); + summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; + + return summary; + }, +}; + +_ready(Search.init); diff --git a/blb/frontier/_static/sphinx_highlight.js b/blb/frontier/_static/sphinx_highlight.js new file mode 100644 index 00000000..8a96c69a --- /dev/null +++ b/blb/frontier/_static/sphinx_highlight.js @@ -0,0 +1,154 @@ +/* Highlighting utilities for Sphinx HTML documentation. */ +"use strict"; + +const SPHINX_HIGHLIGHT_ENABLED = true + +/** + * highlight a given string on a node by wrapping it in + * span elements with the given class name. + */ +const _highlight = (node, addItems, text, className) => { + if (node.nodeType === Node.TEXT_NODE) { + const val = node.nodeValue; + const parent = node.parentNode; + const pos = val.toLowerCase().indexOf(text); + if ( + pos >= 0 && + !parent.classList.contains(className) && + !parent.classList.contains("nohighlight") + ) { + let span; + + const closestNode = parent.closest("body, svg, foreignObject"); + const isInSVG = closestNode && closestNode.matches("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.classList.add(className); + } + + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + const rest = document.createTextNode(val.substr(pos + text.length)); + parent.insertBefore( + span, + parent.insertBefore( + rest, + node.nextSibling + ) + ); + node.nodeValue = val.substr(0, pos); + /* There may be more occurrences of search term in this node. So call this + * function recursively on the remaining fragment. + */ + _highlight(rest, addItems, text, className); + + if (isInSVG) { + const rect = document.createElementNS( + "http://www.w3.org/2000/svg", + "rect" + ); + const bbox = parent.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute("class", className); + addItems.push({ parent: parent, target: rect }); + } + } + } else if (node.matches && !node.matches("button, select, textarea")) { + node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); + } +}; +const _highlightText = (thisNode, text, className) => { + let addItems = []; + _highlight(thisNode, addItems, text, className); + addItems.forEach((obj) => + obj.parent.insertAdjacentElement("beforebegin", obj.target) + ); +}; + +/** + * Small JavaScript module for the documentation. + */ +const SphinxHighlight = { + + /** + * highlight the search words provided in localstorage in the text + */ + highlightSearchWords: () => { + if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight + + // get and clear terms from localstorage + const url = new URL(window.location); + const highlight = + localStorage.getItem("sphinx_highlight_terms") + || url.searchParams.get("highlight") + || ""; + localStorage.removeItem("sphinx_highlight_terms") + url.searchParams.delete("highlight"); + window.history.replaceState({}, "", url); + + // get individual terms from highlight string + const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); + if (terms.length === 0) return; // nothing to do + + // There should never be more than one element matching "div.body" + const divBody = document.querySelectorAll("div.body"); + const body = divBody.length ? divBody[0] : document.querySelector("body"); + window.setTimeout(() => { + terms.forEach((term) => _highlightText(body, term, "highlighted")); + }, 10); + + const searchBox = document.getElementById("searchbox"); + if (searchBox === null) return; + searchBox.appendChild( + document + .createRange() + .createContextualFragment( + '

' + + '' + + _("Hide Search Matches") + + "

" + ) + ); + }, + + /** + * helper function to hide the search marks again + */ + hideSearchWords: () => { + document + .querySelectorAll("#searchbox .highlight-link") + .forEach((el) => el.remove()); + document + .querySelectorAll("span.highlighted") + .forEach((el) => el.classList.remove("highlighted")); + localStorage.removeItem("sphinx_highlight_terms") + }, + + initEscapeListener: () => { + // only install a listener if it is really needed + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; + if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { + SphinxHighlight.hideSearchWords(); + event.preventDefault(); + } + }); + }, +}; + +_ready(() => { + /* Do not call highlightSearchWords() when we are on the search page. + * It will highlight words from the *previous* search query. + */ + if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); + SphinxHighlight.initEscapeListener(); +}); diff --git a/blb/frontier/genindex.html b/blb/frontier/genindex.html new file mode 100644 index 00000000..9a5d3c3f --- /dev/null +++ b/blb/frontier/genindex.html @@ -0,0 +1,137 @@ + + + + + + + + Index — Phoebus 1.0.0 documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Index
    • +
  • +
    • +
+
+
+
+
+ + +

Index

+ +
+ U + +
+

U

+ + +
+ + + +
+
+
+ +
+ +
+

© Copyright 2024, Triad National Security.

+
+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
+
+
+
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+ +
+ + Other Versions + v: blb/frontier + + +
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+
Branches
+
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+
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+
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+
+ + + \ No newline at end of file diff --git a/blb/frontier/index.html b/blb/frontier/index.html new file mode 100644 index 00000000..828c6f1b --- /dev/null +++ b/blb/frontier/index.html @@ -0,0 +1,165 @@ + + + + + + + + + Phoebus: Performance portable GRRMHD for supernovae, mergers, and more — Phoebus 1.0.0 documentation + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
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  • Phoebus: Performance portable GRRMHD for supernovae, mergers, and more
    • +
  • + View page source +
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+ +
+

Phoebus: Performance portable GRRMHD for supernovae, mergers, and more

+

Phoebus is a performance portable general relativistic neutrino radiation magnetohydrodynamics code built upon the Parthenon adaptive mesh refinement framework.

+
+

Key Features

+
    +

  • Finite volume GRMHD

    • +

  • Neutrino transport with Monte Carlo and moment methods

    • +

  • Analytic and tabulated spacetimes

    • +

  • Monopolar general relativistic gravity for core-collapse supernovae

    • +

  • Lagrangian tracer particles

    • +

  • Support for arbitrary equations of state

    • +
+
+

Note

+

These docs are under active development.

+
+
+

Contents:

+ +
+
+
+
+

Indices and tables

+ +
+ + +
+
+ +
+
+
+
+ +
+ + Other Versions + v: blb/frontier + + +
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+
main
+
blb/frontier
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+ + + \ No newline at end of file diff --git a/blb/frontier/objects.inv b/blb/frontier/objects.inv new file mode 100644 index 00000000..24933d14 --- /dev/null +++ b/blb/frontier/objects.inv @@ -0,0 +1,7 @@ +# Sphinx inventory version 2 +# Project: Phoebus +# Version: +# The remainder of this file is compressed using zlib. +xڽSKO0Wǖ+.cpjqEvkTMJvox_ߖ'M}& p~x +ݴtW `k]vNH=M,{mDQ6?Wnj[;8_فgqjIQh JQHzb/b\-$ 7qH[ C3XjkCͶ Q& 5F( Xۦ |,>|̀CɪxrB6X$oU]rϨW4@ոNQ@)rRLrzUǵ#)Sou +6H?eZW9ZVyOhNL@ij4+a{R)Ŀ^]^ \ No newline at end of file diff --git a/blb/frontier/search.html b/blb/frontier/search.html new file mode 100644 index 00000000..6c4d85d4 --- /dev/null +++ b/blb/frontier/search.html @@ -0,0 +1,143 @@ + + + + + + + + Search — Phoebus 1.0.0 documentation + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + \ No newline at end of file diff --git a/blb/frontier/searchindex.js b/blb/frontier/searchindex.js new file mode 100644 index 00000000..61d09607 --- /dev/null +++ b/blb/frontier/searchindex.js @@ -0,0 +1 @@ +Search.setIndex({"alltitles": {"A Large Ecosystem": [[3, "a-large-ecosystem"]], "Adding Tests": [[3, "adding-tests"]], "Approval by Vote:": [[4, "approval-by-vote"]], "Becoming a Contributor": [[3, "becoming-a-contributor"]], "Build Options": [[1, "build-options"]], "Building": [[1, null]], "Building documentation locally": [[5, "building-documentation-locally"]], "Cmake machine configs": [[1, "cmake-machine-configs"]], "Code of Conduct": [[2, null]], "Communication and Connection:": [[4, "communication-and-connection"]], "Contents:": [[0, null]], "Contributing": [[3, null]], "Cuda": [[1, "cuda"]], "Example builds": [[1, "example-builds"]], "Expectations for code review": [[3, "expectations-for-code-review"]], "Expectations of code reviewers": [[3, 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"stylist": 3, "subject": 4, "submit": [3, 5], "suffici": 3, "suggest": [3, 4], "summar": 3, "summari": 3, "support": [0, 1, 3, 4], "sure": 1, "sustain": [3, 4], "swarm": 6, "swarm_d": 6, "swarmvar": 6, "t": 3, "tabul": [0, 3], "tag": 3, "take": [3, 4], "tap": 4, "target": [1, 5], "task": 1, "team": 3, "tear": 3, "technic": 3, "temperatur": 6, "templat": 3, "term": 4, "texinfo": 5, "text": [3, 5], "than": 3, "thank": 3, "thei": [3, 4, 6], "them": [1, 5], "theme": 5, "thi": [1, 3, 4, 5, 6], "thorough": 3, "those": [1, 3, 4], "threat": 2, "three": [4, 6], "through": [3, 4, 5, 6], "ticket": 4, "time": [1, 3, 4], "timeli": 4, "tone": 3, "too": 3, "tool": 5, "total": 6, "toward": 3, "tracer": 0, "tracers_vari": 6, "track": 6, "transport": 0, "treat": 3, "triag": 4, "trigger": 3, "true": 6, "try": 3, "tst": 3, "two": 3, "type": 5, "typic": 1, "u": 6, "ubuntu": 5, "uncomplet": 4, "under": 0, "uniform": 3, "uniqu": 6, "univers": [3, 4], "unless": 3, "unnecessari": 6, "up": [3, 4], "upcom": 4, 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3, "you": [1, 3], "your": 3, "yurlungur": 3, "z": 6, "z_max": 6, "z_min": 6}, "titles": ["Phoebus: Performance portable GRRMHD for supernovae, mergers, and more", "Building", "Code of Conduct", "Contributing", "Organizational Structure", "How to Use Sphinx for Writing Docs", "Tracer Particles"], "titleterms": {"A": 3, "ad": 3, "approv": 4, "becom": 3, "build": [1, 5], "cmake": 1, "code": [1, 2, 3], "commun": 4, "conduct": 2, "config": 1, "connect": 4, "content": 0, "contribut": 3, "contributor": 3, "convert": 5, "cuda": 1, "current": 3, "depend": 5, "doc": 5, "docker": 5, "document": 5, "ecosystem": 3, "everyon": 3, "exampl": 1, "expect": 3, "extern": 1, "featur": 0, "file": 5, "from": 3, "gener": 3, "get": 5, "github": 5, "grrmhd": 0, "have": 5, "how": 5, "indic": 0, "info": 5, "kei": 0, "larg": 3, "list": 3, "local": 5, "machin": 1, "maintain": 3, "markdown": 5, "memorandum": 4, "merger": 0, "more": [0, 5], "mpi": 1, "obtain": 1, "onli": 1, "openmp": 1, "option": 1, "organiz": 4, "parallel": 1, "particl": 6, "perform": 0, "perspect": 3, "phoebu": [0, 3], "portabl": 0, "prerequisit": 1, "principl": 3, "protocol": 3, "pull": 3, "regress": 3, "request": 3, "requir": 1, "review": 3, "rst": 5, "run": 1, "sourc": 1, "sphinx": 5, "structur": 4, "submodul": 1, "suit": 3, "supernova": 0, "tabl": 0, "team": 4, "test": 3, "tracer": 6, "understand": 4, "unit": 3, "us": 5, "vote": 4, "write": 5, "you": 5, "your": 5}}) \ No newline at end of file diff --git a/blb/frontier/sitemap.xml b/blb/frontier/sitemap.xml new file mode 100644 index 00000000..7c1cea97 --- /dev/null +++ b/blb/frontier/sitemap.xml @@ -0,0 +1,2 @@ + +https://lanl.github.io/phoebusen/index.htmlhttps://lanl.github.io/phoebusen/src/building.htmlhttps://lanl.github.io/phoebusen/src/code_of_conduct.htmlhttps://lanl.github.io/phoebusen/src/contributing.htmlhttps://lanl.github.io/phoebusen/src/governance.htmlhttps://lanl.github.io/phoebusen/src/sphinx-doc.htmlhttps://lanl.github.io/phoebusen/src/tracers.htmlhttps://lanl.github.io/phoebusen/genindex.htmlhttps://lanl.github.io/phoebusen/search.html \ No newline at end of file diff --git a/blb/frontier/src/building.html b/blb/frontier/src/building.html new file mode 100644 index 00000000..c20f7183 --- /dev/null +++ b/blb/frontier/src/building.html @@ -0,0 +1,336 @@ + + + + + + + + + Building — Phoebus 1.0.0 documentation + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Building

+
+

Obtaining the Source Code

+

phoebus uses submodules extensively. To make sure you get them all, +clone it as

+
git clone --recursive git@github.com:lanl/phoebus.git
+
+
+

or as

+
git clone git@github.com:lanl/phoebus.git
+cd phoebus
+git submodule update --init --recursive
+
+
+
+
+

Prerequisites

+

To build phoebus, you need to create a build directly, as in-source builds are not supported. +After cloning the repository,

+
cd phoebus
+mkdir bin
+cd bin
+
+
+
+
+

Example builds

+

Below are some example build commands

+
+

MPI-parallel only

+

The following will build phoebus with MPI parallelism but no shared +memory parallelism

+
cmake ..
+make -j
+
+
+
+
+

OpenMP-parallel

+

The following will build phoebus with OpenMP parallelism only

+
cmake -DPHOEBUS_ENABLE_MPI=Off -DPHOEBUS_ENABLE_OPENMP=ON ..
+make -j
+
+
+
+
+

Cuda

+

The following will build phoebus with no MPI or OpenMP parallelism.

+
cmake -DPHOEBUS_ENABLE_CUDA=On -DCMAKE_CXX_COMPILER=${HOME}/phoebus/external/singularity-eos/utils/kokkos/bin/nvcc_wrapper -DKokkos_ARCH_HSW=ON -DKokkos_ARCH_VOLTA70=ON -DPHOEBUS_ENABLE_MPI=OFF ..
+
+
+

A few notes for this one: - Note here the -DCMAKE_CXX_COMPILER flag. +This is necessary. You must set the compiler to nvcc_wrapper +provided by Kokkos. - Note the -DKokkos_ARCH_* flags. Those set the +host and device microarchitectures and are required. The choice here is +on an x86_64 machine with a volta GPU.

+
+
+
+

Build Options

+

The build options explicitly provided by phoebus are:

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Option

Default

Comment

PHOEBUS_ENABLE_CUDA

OFF

Cuda

PHOEBUS_ENABLE_HDF5

ON

HDF5. Required for output and restarts.

PHOEBUS_ENABLE_MPI

ON

MPI. Required for distributed memory +parallelism.

PHOEBUS_ENABLE_OPENMP

OFF

OpenMP. Required for shared memory +parallelism.

MACHINE_CFG

None

Machine-specific config file, optional.

+

Some relevant settings from Parthenon and Kokkos you may need to play +with are:

+ + + + + + + + + + + + + + + + + +

Option

Default

Comment

CMAKE_CXX_COMPILER

None

Must be set to nvcc_wrapper with cuda +backend

Kokkos_ARCH_XXXX

OFF

You must set the GPU architecture when +compiling for Cuda

+

You can see all the Parthenon build options +here +and all the Kokkos build options +here

+
+
+

Cmake machine configs

+

If you are proficient with cmake You can optionally write a +cmake file that sets the configure parameters that you like on a +given machine. Both phoebus and parthenon can make use of it. +You can point to the file with

+
-DMACHINE_CFG=path/to/machine/file
+
+
+

at config time or by setting the environment variable MACHINE_CFG to +point at it, e.g.,

+
export MACHINE_CFG=path/to/machine/file
+
+
+

An example machine file might look like

+
# Machine file for x86_64-volta on Darwin
+message(STATUS "Loading machine configuration for Darwin x86-volta node")
+message(STATUS "Assumes: module load module load gcc/7.4.0 cuda/10.2 openmpi/4.0.3-gcc_7.4.0 anaconda/Anaconda3.2019.10 cmake && spack load hdf5")
+message(STATUS "Also assumes you have a valid spack installation loaded.")
+
+set(PHOEBUS_ENABLE_CUDA ON CACHE BOOL "Cuda backend")
+set(PHOEBUS_ENABLE_MPI OFF CACHE BOOL "No MPI")
+set(Kokkos_ARCH_HSW ON CACHE BOOL "Haswell target")
+set(Kokkos_ARCH_VOLTA70 ON CACHE BOOL "volta target")
+set(CMAKE_CXX_COMPILER /home/jonahm/phoebus/external/parthenon/external/Kokkos/bin/nvcc_wrapper CACHE STRING "nvcc wrapper")
+
+
+

you could then configure and compile as

+
cmake -DMACHINE_CFG=path/to/machine/file ..
+make -j
+
+
+
+
+

Running

+

Run phoebus from the build directory as

+
./src/phoebus -i path/to/input/file.pin
+
+
+

The input files are in phoebus/inputs/*. There’s typically one input +file per problem setup file.

+
+
+

Submodules

+
    +

  • parthenon asynchronous tasking and block-AMR infrastructure

    • +

  • singularity-eos provides performance-portable equations of state +and PTE solvers

    • +

  • singularity-opac provides performance-portable opacities and +emissivities

    • +

  • Kokkos provides performance portable shared-memory parallelism. +It allows our loops to be CUDA, OpenMP, or something else. By default +we use the Kokkos shipped with parthenon.

    • +
+
+
+

External (Required)

+
    +

  • cmake for building

    • +
+
+
+

Optional

+
    +

  • hdf5 for output (must be parallel if MPI is enabled)

    • +

  • MPI for distributed memory parallelism

    • +

  • python3 for visualization

    • +
+
+
+ + +
+
+ +
+
+
+
+ +
+ + Other Versions + v: blb/frontier + + +
+
+
Branches
+
main
+
blb/frontier
+
+
+
+ + + \ No newline at end of file diff --git a/blb/frontier/src/code_of_conduct.html b/blb/frontier/src/code_of_conduct.html new file mode 100644 index 00000000..6f30c461 --- /dev/null +++ b/blb/frontier/src/code_of_conduct.html @@ -0,0 +1,153 @@ + + + + + + + + + Code of Conduct — Phoebus 1.0.0 documentation + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Code of Conduct

+

We as users, members, contributors, and leaders agree to make participation in our +community a harassment-free experience for everyone. +We will interact in ways that contribute to an open, welcoming, +diverse, inclusive, and healthy community.

+

We agree to uphold the LANL Code of Conduct in all spaces relevant. +Of note:

+
-  Foster a mutually respectful working environment that is free from
+   discrimination, intimidation, and harassment (including sexual
+   harassment).
+-  Do not discriminate against others on the basis of any
+   characteristic protected by law or LANL policy.
+-  Do not engage in behaviors that create an offensive, hostile, or
+   intimidating work environment, including shouting, abusive
+   language, threats of violence, the use of obscenities or other
+   non-verbal expressions of aggression, horseplay such as kicking
+   co-workers’ chairs or using personal insults, or the use of
+   offensive nicknames or other derogatory remarks.
+-  Avoid behavior that a reasonable person would find to be demeaning
+   or humiliating.
+
+
+
+ + +
+
+ +
+
+
+
+ +
+ + Other Versions + v: blb/frontier + + +
+
+
Branches
+
main
+
blb/frontier
+
+
+
+ + + \ No newline at end of file diff --git a/blb/frontier/src/contributing.html b/blb/frontier/src/contributing.html new file mode 100644 index 00000000..147b1629 --- /dev/null +++ b/blb/frontier/src/contributing.html @@ -0,0 +1,421 @@ + + + + + + + + + Contributing — Phoebus 1.0.0 documentation + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Contributing

+

To contribute to Phoebus, feel free to submit a pull +request or open an issue.

+
    +

  1. Create a new fork of main where your changes can be made.

    2. +

  2. After completing, create a pull request, describe the final approach +and ensure the branch has no conflicts with current Regression Tests +and Formatting Checks.

    3. +

  3. Assign external reviewers (a minimum of 1, one of which should be a +Maintainer, and which cannot be the contributor). Provide concise +description of changes.

    4. +

  4. Once comments/feedback is addressed, the PR will be merged into the +main branch and changes will be added to list of changes in the next +release.

    5. +

  5. At present, Releases (with a git version tag) for the main branch +of Phoebus will occur at a 6 to 12 month cadence or following +implementation of a major enhancement or capability to the code base.

    6. +
+

Maintainers of Phoebus will follow the same process for +contributions as above except for the following differences: they may +create branches directly within Phoebus, they will hold repository +admin privileges, and actively participate in the technical review of +contributions to Phoebus.

+
+

Pull request protocol

+

When submitting a pull request, there is a default template that is automatically +populated. The pull request should sufficiently summarize all changes. +As necessary, tests should be added for new features of bugs fixed.

+

Before a pull request will be merged, the code should be formatted. We +use clang-format for this, pinned to version 12. +The script scripts/bash/format.sh will apply clang-format +to C++ source files in the repository as well as black to python files, if available. +The script takes two CLI arguments +that may be useful, CFM, which can be set to the path for your +clang-format binary, and VERBOSE, which if set to 1 adds +useful output. For example:

+
CFM=clang-format-12 VERBOSE=1 ./scripts/bash/format.sh
+
+
+

In order for a pull request to merge, we require:

+
    +

  • Provide a thorough summary of changes, especially if they are breaking changes

    • +

  • Obey style guidleines (format with clang-format and pass the necessary test)

    • +

  • Pass the existing test suite

    • +

  • Have at least one approval from a Maintainer

    • +

  • If applicable:

    +
      +

    • Write new tests for new features or bugs

      • +

    • Include or update documentation in doc/

      • +
    +
    • +
+
+
+

Test Suite

+

Several sets of tests are triggered on a pull request: a static format +check, a docs buld, and a suite of unit and regression tests. +These are run through github’s CPU infrastructure. These tests +help ensure that modifications to the code do not break existing capabilities +and ensure a consistent code style.

+
+

Adding Tests

+

There are two primary categories of tests written in Phoebus: +unit tests and regression tests.

+
+

Unit

+

Unit tests live in tst/unit/. They are implemented using the +Catch2 unit testing framework. They are integrated with cmake +and can be run, when enabled, with ctest. There are a few necessary cmake +configurations to beuild tests:

+ + + + + + + + + + + + + + + + + +

Option

Default

Description

PHOEBUS_ENABLE_UNIT_TESTS

OFF

Enables Catch2 unit tests

PHOEBUS_ENABLE_DOWNLOADS

OFF

Enables unit tests using tabulated EOS

+
+
+

Regression

+

Regression tests run existing simulations and test against saved output +in order to verify sustained capabilities. +They are implemented in Python in +test/regression/. To run the tests you will need a Python environment with +at least numpy and h5py. Tests can be ran manually as, e.g.,

+
python linear_modes.py
+
+
+

This will build Phoebus locally in phoebus/tst/regression/build and run it in +phoebus/tst/regression/run. Ensure that these directories do not already exist. +Each script test.py has a correspodning “gold file” test.gold. +The gold files contain the gold standard data that the output of the regression test +is compared against. To generate new gold data, for example if a change is implemented +that changes the behavior of a test (not erroneously) or a new test is created, run the test +script with the --upgold option. This will create or update the corresponding .gold file. +To add a new test:

+
    +

  1. Create a new test script.

    +
      +

    • Update the modified_inputs struct to change any input deck options

      • +

    • Set the variables list to contain the quantities to test against

      • +
    +
    2. +

  2. Run the script with the --upgold option

    3. +

  3. Commit the test script and gold file

    4. +

  4. Update the CI to include the new test (phoebus/.github/workflows/tests.yml)

    5. +
+
+
+
+
+

Expectations for code review

+

Much of what follows is adapted from singularity-eos.

+
+

From the perspective of the contributor

+

Code review is an integral part of the development process +for Phoebus. You can expect at least one, perhaps many, +core developers to read your code and offer suggestions. +You should treat this much like scientific or academic peer review. +You should listen to suggestions but also feel entitled to push back +if you believe the suggestions or comments are incorrect or +are requesting too much effort.

+

Reviewers may offer conflicting advice, if this is the case, it’s an +opportunity to open a discussion and communally arrive at a good +approach. You should feel empowered to argue for which of the +conflicting solutions you prefer or to suggest a compromise. If you +don’t feel strongly, that’s fine too, but it’s best to say so to keep +the lines of communication open.

+

Big contributions may be difficult to review in one piece and you may +be requested to split your pull request into two or more separate +contributions. You may also receive many “nitpicky” comments about +code style or structure. These comments help keep a broad codebase, +with many contributors uniform in style and maintainable with +consistent expectations accross the code base. While there is no +formal style guide for now, the regular contributors have a sense for +the broad style of the project. You should take these stylistic and +“nitpicky” suggestions seriously, but you should also feel free to +push back.

+

As with any creative endeavor, we put a lot of ourselves into our +code. It can be painful to receive criticism on your contribution and +easy to take it personally. While you should resist the urge to take +offense, it is also partly code reviewer’s responsiblity to create a +constructive environment, as discussed below.

+
+
+

Expectations of code reviewers

+

A good code review builds a contribution up, rather than tearing it +down. Here are a few rules to keep code reviews constructive and +congenial:

+
    +

  • You should take the time needed to review a contribution and offer +meaningful advice. Unless a contribution is very small, limit +the times you simply click “approve” with a “looks good to me.”

    • +

  • You should keep your comments constructive. For example, rather than +saying “this pattern is bad,” try saying “at this point, you may +want to try this other pattern.”

    • +

  • Avoid language that can be misconstrued, even if it’s common +notation in the commnunity. For example, avoid phrases like “code +smell.”

    • +

  • Explain why you make a suggestion. In addition to saying “try X +instead of Y” explain why you like pattern X more than pattern Y.

    • +

  • A contributor may push back on your suggestion. Be open to the +possibility that you’re either asking too much or are incorrect in +this instance. Code review is an opportunity for everyone to learn.

    • +

  • Don’t just highlight what you don’t like. Also highlight the parts +of the pull request you do like and thank the contributor for their +effort.

    • +
+
+
+

General principle for everyone

+

It’s hard to convey tone in text correspondance. Try to read what +others write favorably and try to write in such a way that your tone +can’t be mis-interpreted as malicious.

+
+
+
+

A Large Ecosystem

+

Phoebus depends on several other open-source, Los Alamos +maintained, projects. In particular, Parthenon, singularity-eos, +singularity-opac, and spiner. +If you have issues with these projects, ideally +submit issues on the relevant github pages. However, if you can’t +figure out where an issue belongs, no big deal. Submit where you can +and we’ll engage with you to figure out how to proceed.

+
+
+

Becoming a Contributor

+

For the purpose of our development model, we label Contributors or +Maintainers of Phoebus. Below we describe these labels and the +process for contributing to Phoebus.

+

We welcome contributions from scientists from a large variety of +relativistic astrophysics. New users are welcome to contributions to +Phoebus via the Contributors process. Contributors with 6 merged +pull requests into the main branch (over a minimum of 6 months) will +be eligible to join as a Maintainer of Phoebus with additional +repository access and roles. However, final approval of Maintainer +status will require a approval by vote by existing +Maintainers, a necessary step to ensure the safety and integrity of +the code base for all users of Phoebus.

+

The Maintainers of Phoebus consist of the original developers of +the code and those that have a demonstrated history in the development +of Phoebus prior to the implementation of the Development Model +described here. Maintainers hold admin access, serve as +reviewers for pull requests, and are in charge of the maintaining, +deployment, and improvement of efforts towards: regression testing, +documentation, science test cases (gold standards), and continuous +integration.

+

Maintainers are excepted to make a good faith effort to adhere to +these suggestions in order to maintain a supportive and +productive environment.

+
+
+

List of Current Maintainers of Phoebus

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Name

Handle

Team

Brandon Barker

@AstroBarker

Los Alamos National +Lab

Josh Dolence

@jdolence

Los Alamos National +Lab

Carl Fields

@carlnotsagan

University of Arizona

Mariam +Gogilashvili

@mari2895

Niels Bohr Institute

Jonah Miller

@Yurlungur

Los Alamos National +Lab

Jeremiah Murphy

@curiousmiah

Florida State +University

Ben Ryan

@brryan

Los Alamos National +Lab

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+ + Other Versions + v: blb/frontier + + +
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Branches
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main
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blb/frontier
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+ + + \ No newline at end of file diff --git a/blb/frontier/src/governance.html b/blb/frontier/src/governance.html new file mode 100644 index 00000000..6f8b2fdb --- /dev/null +++ b/blb/frontier/src/governance.html @@ -0,0 +1,275 @@ + + + + + + + + + Organizational Structure — Phoebus 1.0.0 documentation + + + + + + + + + + + + + + + + + + + + + +
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Organizational Structure

+
+
Phoebus uses a hybrid flat-and-hierarchical organizational +structure.
+
The flat structure fosters power sharing among senior and junior +members and avoids the many pitfalls of power-over dynamics. For +example, in power-over structures, someone with explicit power can +inadvertently, or on rare occasions intentionally, silence critical +voices.
+
This dynamic can quickly lead to an organization overlooking inherent +problems that could lead to ineffectiveness or even catastrophic +failure of the team.
+
+
+
In contrast, our aim is to illuminate potential problems early and +quickly find solutions.
+
This strategy also efficiently taps into the diverse wealth of +knowledge of the team.
+
At the same time, the PI and Co-PI have financial and reporting +responsibilities to their respective universities and funding +agencies.
+
The general procedure for the hybrid structure is as follows.
+
The flat structure will make major decisions in direction and +resources, and the PI and Co-PI will assume the responsibility for +executing those decisions.
+
The following gives details on this hybrid structure.
+
+
+

Team

+

The founding team consists of the following: original core developers +and Maintainers at Los Alamos National Lab, Jeremiah Murphy at Florida +State University, and Carl Fields at University of Arizona.

+

Since, an objective of Phoebus is to grow the developer and user base, +the Phoebus Project will have an explicit mechanism for adding new +members. There are three categories for Phoebus members: +maintainers, contributors, and users.

+

User: As open-source software, anyone may download, compile, and +execute Phoebus. New users will encouraged to join communication +channels for connection with the larger Phoebus community.

+

Contributor: Users who wish to contribute to Phoebus may do so +following our Development Model for new users. These changes will be +integrated into the main branch of the code upon approval. Consistent +contributions also provides the opportunity for Contributors to be +eligible to join as a Maintainer, the final approval of which will +require a vote.

+

Maintainer: These are the core team who have “merge” permissions on +the repo and are working to keep the code sustainable long term.

+

To maintain their relevant active status, all members must +make a food faith effort to maintain a supportive, productive environment.

+
+
+

Memorandum of Understanding

+

In addition to our Community Code of Conduct, we ask that maintainers +especially keep the following suggestions in mind to help +facilitate an efficient and welcoming collaboration:

+
    +

  • Maintainers should uphold and exemplify the Development Model +outlined as part of the phoebus Community described +here.

    • +

  • Within reason, maintainers will make a good-faith effort to attend team +meetings. In an effort to accommodate the dynamic schedules and +availability of many of the core team of Maintainers, +coordination efforts will be made to ensure that at least +1 Maintainer is present for all meetings.

    • +

  • Maintainers will make a good-faith effort to monitor the fraction of +the meeting time that they speak. The meeting time is limited, and +several people may have something interesting to say, report on their +updates, or contribute constructive arguments. One should be +self-aware and notice if one is dominating conversations, and attempt +to make a conscious effort to include other voices and perspectives +in the discussion.

    • +

  • Maintainers consider it their responsibility to voice their questions +and/or concerns as early as possible. This will ensure that the +organization addresses concerns rapidly and effectively.

    • +

  • Maintainers consider it their responsibility to listen and understand +questions or concerns raised by other partners or through concerns +communicated through email to individual Maintainers.

    • +
+
+
+

Approval by Vote:

+
+
Many of the decisions in the organization will be enacted after an +approval by majority vote of active Maintainers. The process of listening +and adjusting strategies to meet everyone’s needs is vital for +power-sharing organizations.
+
Importantly, spending a little time up front to listen and resolve +concerns reduces the pain and time spent later in intense conflict +resolution.
+
+
+
+

Communication and Connection:

+
+
To facilitate open and effective communication, the Phoebus will +offer multiple levels of communication. +Developers will communicate via email, GitHub, and a Phoebus Slack +channel.
+
+
+
To respond to user inquiries, the Phoebus Project will host a mailing +list via Google or similar.
+
To maintain a standing record of user inquiries and responses, we will +post the inquiries and responses on a public-facing site.
+
All Maintainers will have the option to respond to the inquires; to +ensure that someone is responsive to the user inquiries, the team will +triage tickets/questions in developer meetings.
+
+
+
Subject to availability, monthly Maintainer meetings will also +be an important part of ensuring productivity and timeliness.
+
Each meeting will last up to 60 minutes. We will assess and discuss +the goals from the previous meeting.
+
In particular, we will take note which goals were completed and which +were not. If there are uncompleted goals, we will assess why they were +not completed. Next, we will discuss the goals for the upcoming month, +quarter, and year.
+
We will decide which goals to prioritize.
+
All of this will be recorded on an online document which will be +available to all Maintainers.
+
+
+
Each meeting of the core Maintainers will be managed by a meeting +manager.
+
The primary job of the meeting manager is to: 1) gather a list of +agenda items for the next meeting, 2) ensure that the meeting runs on +schedule, and 3) ensure equitable participation by all participants.
+
Again, in keeping with power-sharing, the meeting manager position +will rotate among the core Maintainers, even junior members.
+
+
+

Note

+

We maintain some flexibility in the cadence and structure of meetings, in +particular, in periods of low activity, meetings may be skipped or +held in a less formal manner. We recognize that the availability +of maintainers is contingent upon many factors.

+
+
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+ + +
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+ + Other Versions + v: blb/frontier + + +
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Branches
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main
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blb/frontier
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+ + + \ No newline at end of file diff --git a/blb/frontier/src/sphinx-doc.html b/blb/frontier/src/sphinx-doc.html new file mode 100644 index 00000000..8ba677c9 --- /dev/null +++ b/blb/frontier/src/sphinx-doc.html @@ -0,0 +1,239 @@ + + + + + + + + + How to Use Sphinx for Writing Docs — Phoebus 1.0.0 documentation + + + + + + + + + + + + + + + + + + + + + +
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How to Use Sphinx for Writing Docs

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How to convert a Markdown file to rst

+

We are using the reStructuredText (rst) format for our documentation. +If you have a markdown file you would like to convert to rst, +as a first pass, you can have Pandoc convert your file. For example:

+
pandoc Metadata.md --from markdown --to rst -s -o metadata.rst
+
+
+

Pandoc can be installed easily through a Linux package manager. For example on Ubuntu,

+
apt install pandoc
+
+
+

will get you the tool.

+
+
+

How to have github build your documentation for you

+

Github can automatically build your documentation for you through the continuous integration pipeline. +After you submit a pull request with your .rst changes for documentation on github-pages, +the documentation will automatically get built. You will see a “build and deploy documentation” job +at the bottom of the pull request page. If this passes, your documentation will have been generated.

+

On the bottom left of the documentation page on github-pages, you can select the branch/build +of the documentation, one of which should be the branch you wrote your changes on.

+
+
+

Building documentation locally

+

While you can rely on the CI to build the documentation associated with your +branch, you can also very easily build sphinx documentation locally through +python. These instructions also do not require admin access and are usable +with shared machines or python distributions.

+

First, ensure that you are running a modern version of python (i.e. python 3 of +some flavor)

+
$ python --version
+Python 3.9.7
+
+
+

Then, use pip to install spinx and the RTD theme

+
pip install --user sphinx sphinx-rtd-theme
+
+
+

Now, navigate to the ../doc/sphinx directory where a make help +shows all of the available ways to build the documentation

+
$ make help
+Sphinx v4.2.0
+Please use `make target' where target is one of
+  html        to make standalone HTML files
+  dirhtml     to make HTML files named index.html in directories
+  singlehtml  to make a single large HTML file
+  pickle      to make pickle files
+  json        to make JSON files
+  htmlhelp    to make HTML files and an HTML help project
+  qthelp      to make HTML files and a qthelp project
+  devhelp     to make HTML files and a Devhelp project
+  epub        to make an epub
+  latex       to make LaTeX files, you can set PAPER=a4 or PAPER=letter
+  latexpdf    to make LaTeX and PDF files (default pdflatex)
+  latexpdfja  to make LaTeX files and run them through platex/dvipdfmx
+  text        to make text files
+  man         to make manual pages
+  texinfo     to make Texinfo files
+  info        to make Texinfo files and run them through makeinfo
+  gettext     to make PO message catalogs
+  changes     to make an overview of all changed/added/deprecated items
+  xml         to make Docutils-native XML files
+  pseudoxml   to make pseudoxml-XML files for display purposes
+  linkcheck   to check all external links for integrity
+  doctest     to run all doctests embedded in the documentation (if enabled)
+  coverage    to run coverage check of the documentation (if enabled)
+  clean       to remove everything in the build directory
+
+
+

Making the documentation will create a new directory, _build in the +sphinx directory along with whichever type of documentation you wanted +to build.

+

For example, building the HTML documentation with make html produces the +../doc/sphinx/_build/html directory with an index.html file that +you can point a browser to in order to view the documenation.

+
+
+

How to Get the Dependencies

+
+

Using Docker

+

If you are using Docker, then simply pull the docker image specified below:

+
image: sphinxdoc/sphinx-latexpdf
+
+
+

Then, after running docker run -it <docker-image-name> /bin/bash, install the theme we are using with pip install sphinx_rtd_theme

+
+
+
+

More Info.

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+ + Other Versions + v: blb/frontier + + +
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Branches
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blb/frontier
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+ + + \ No newline at end of file diff --git a/blb/frontier/src/tracers.html b/blb/frontier/src/tracers.html new file mode 100644 index 00000000..325fee13 --- /dev/null +++ b/blb/frontier/src/tracers.html @@ -0,0 +1,256 @@ + + + + + + + + + Tracer Particles — Phoebus 1.0.0 documentation + + + + + + + + + + + + + + + + + + + + + +
+ + +
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+ +
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+ +
+

Tracer Particles

+

Phoebus includes Lagrangian tracer particles. +These are primarily for the purpose of post-processing simulation data for, e.g., nucleosynthesis. +They are operator spit from the hydrodynamics and advected with a standard second order Runge-Kutta +integrator. As Phoebus is a general relativistic code, we evolve tracer positions using a +relativistic advection equation:

+
+\[\frac{dx^i}{dt} = \frac{u^i}{u^0} = \alpha v^i - \beta^i\]
+

Tracers may be enabled by in the Phoebus input deck as follow:

+
<physics>
+tracers = true
+
+<tracers>
+num_tracers = 1024
+
+
+

Similarly, tracers may be output by modifying an existing Parthenon output block, or creating a new one:

+
<parthenon/output1>
+// ...
+swarms = tracers
+tracers_variables = rho, temperature, ye
+
+file_type = hdf5
+dt = // output cadence
+
+
+

Note that the position variables x, y, z are output for all swarms by default. +See the Parthenon docs for more information.

+

Tracers must, however, be configured in the problem generator. +In the generator, the tracers should be distributed through the domain, assigned positions +and unique ids. An example from the advection pgen is shown below.

+
pmb->par_for(
+    "ProblemGenerator::Advection::DistributeTracers", 0, max_active_index,
+    KOKKOS_LAMBDA(const int n) {
+      if (swarm_d.IsActive(n)) {
+        auto rng_gen = rng_pool.get_state();
+
+        // sample in ball
+        Real r2 = 1.0 + rin * rin; // init > rin^2
+        while (r2 > rin * rin) {
+          x(n) = x_min + rng_gen.drand() * (x_max - x_min);
+          y(n) = y_min + rng_gen.drand() * (y_max - y_min);
+          z(n) = z_min + rng_gen.drand() * (z_max - z_min);
+          r2 = x(n) * x(n) + y(n) * y(n) + z(n) * z(n);
+        }
+        id(n) = num_tracers_total * gid + n;
+
+        bool on_current_mesh_block = true;
+        swarm_d.GetNeighborBlockIndex(n, x(n), y(n), z(n), on_current_mesh_block);
+        rng_pool.free_state(rng_gen);
+      }
+    });
+
+
+

In addition to position, tracers track a number of potentially useful quantities. +These quantities include (bold quantities are 3-vectors with components _x, _y, _z)

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Quantity

SwarmVar Name

Description

Density

rho

Primitive density

Temperature

temperature

Temperature

Ye

ye

Electron fraction (0 if ye is disabled)

Internal energy

energy

Primitive internal energy

Entropy

entropy

Entropy

Velocity

vel_x, …

Three velocity

Lorentz factor

lorentz

Relativistic Lorentz factor

Lapse

lapse

Relativistic lapse

Metric determinant

detgamma

Spatial metric determinant

Shift

shift_x, …

Relativistic shift

Mass

mass

Tracer mass

Total energy

bernoulli

Total energy Bernoulli quantity

Magnetic field

B_x, …

Primitive 3-magnetic field components (if mhd enabled)

+

To minimize unnecessary work, these quantities are only populated before output using phoebus::UserWorkBeforeOutput.

+
+
+void UserWorkBeforeOutput(MeshBlock *pmb, ParameterInput *pin)
+

Describes work to be done prior to HDF5 output, such as populating tracer variables. +This is connected to the appropriate Parthenon function.

+
+ +
+ + +
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+ + Other Versions + v: blb/frontier + + +
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+ + + \ No newline at end of file diff --git a/index.html b/index.html new file mode 100644 index 00000000..e98ca1e3 --- /dev/null +++ b/index.html @@ -0,0 +1,10 @@ + + + + + Redirecting to main branch + + + + + diff --git a/main/.buildinfo b/main/.buildinfo new file mode 100644 index 00000000..30896ef3 --- /dev/null +++ b/main/.buildinfo @@ -0,0 +1,4 @@ +# Sphinx build info version 1 +# This file records the configuration used when building these files. When it is not found, a full rebuild will be done. +config: 77aa85a4592f59a5b0073869434b2d07 +tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/main/.doctrees/environment.pickle b/main/.doctrees/environment.pickle new file mode 100644 index 00000000..d4d70569 Binary files /dev/null and b/main/.doctrees/environment.pickle differ diff --git a/main/.doctrees/index.doctree b/main/.doctrees/index.doctree new file mode 100644 index 00000000..298ccae4 Binary files /dev/null and b/main/.doctrees/index.doctree differ diff --git a/main/.doctrees/src/building.doctree b/main/.doctrees/src/building.doctree new file mode 100644 index 00000000..3941ddf9 Binary files /dev/null and b/main/.doctrees/src/building.doctree differ diff --git a/main/.doctrees/src/code_of_conduct.doctree b/main/.doctrees/src/code_of_conduct.doctree new file mode 100644 index 00000000..be9a8cb3 Binary files /dev/null and b/main/.doctrees/src/code_of_conduct.doctree differ diff --git a/main/.doctrees/src/contributing.doctree b/main/.doctrees/src/contributing.doctree new file mode 100644 index 00000000..b919a573 Binary files /dev/null and b/main/.doctrees/src/contributing.doctree differ diff --git a/main/.doctrees/src/governance.doctree b/main/.doctrees/src/governance.doctree new file mode 100644 index 00000000..561bda4f Binary files /dev/null and b/main/.doctrees/src/governance.doctree differ diff --git a/main/.doctrees/src/sphinx-doc.doctree b/main/.doctrees/src/sphinx-doc.doctree new file mode 100644 index 00000000..0b8c909f Binary files /dev/null and b/main/.doctrees/src/sphinx-doc.doctree differ diff --git a/main/.doctrees/src/tracers.doctree b/main/.doctrees/src/tracers.doctree new file mode 100644 index 00000000..3aeae502 Binary files /dev/null and b/main/.doctrees/src/tracers.doctree differ diff --git a/main/_sources/index.rst.txt b/main/_sources/index.rst.txt new file mode 100644 index 00000000..7cd7b372 --- /dev/null +++ b/main/_sources/index.rst.txt @@ -0,0 +1,39 @@ +.. Phoebus documentation master file, created by + sphinx-quickstart on Thu Sep 26 15:18:20 2024. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +Phoebus: Performance portable GRRMHD for supernovae, mergers, and more +====================================================================== + +`Phoebus`_ is a performance portable general relativistic neutrino radiation magnetohydrodynamics code built upon the `Parthenon`_ adaptive mesh refinement framework. + +.. _Parthenon: https://github.com/parthenon-hpc-lab/parthenon +.. _Phoebus: https://github.com/lanl/phoebus + +Key Features +^^^^^^^^^^^^^ + +* Finite volume GRMHD +* Neutrino transport with Monte Carlo and moment methods +* Analytic and tabulated spacetimes +* Monopolar general relativistic gravity for core-collapse supernovae +* Lagrangian tracer particles +* Support for arbitrary equations of state + +.. note:: + + These docs are under active development. + +.. toctree:: + :maxdepth: 1 + :caption: Contents: + :glob: + + src/* + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`search` diff --git a/main/_sources/src/building.rst.txt b/main/_sources/src/building.rst.txt new file mode 100644 index 00000000..2533a8ff --- /dev/null +++ b/main/_sources/src/building.rst.txt @@ -0,0 +1,190 @@ +Building +======== + +Obtaining the Source Code +------------------------- + +``phoebus`` uses submodules extensively. To make sure you get them all, +clone it as + +.. code:: bash + + git clone --recursive git@github.com:lanl/phoebus.git + +or as + +.. code:: bash + + git clone git@github.com:lanl/phoebus.git + cd phoebus + git submodule update --init --recursive + + +Prerequisites +------------- + +To build ``phoebus``, you need to create a build directly, as in-source builds are not supported. +After cloning the repository, + +.. code:: bash + + cd phoebus + mkdir bin + cd bin + +Example builds +-------------- + +Below are some example build commands + +MPI-parallel only +~~~~~~~~~~~~~~~~~ + +The following will build ``phoebus`` with MPI parallelism but no shared +memory parallelism + +.. code:: bash + + cmake .. + make -j + +OpenMP-parallel +~~~~~~~~~~~~~~~ + +The following will build ``phoebus`` with OpenMP parallelism only + +.. code:: bash + + cmake -DPHOEBUS_ENABLE_MPI=Off -DPHOEBUS_ENABLE_OPENMP=ON .. + make -j + +Cuda +~~~~ + +The following will build ``phoebus`` with no MPI or OpenMP parallelism. + +.. code:: bash + + cmake -DPHOEBUS_ENABLE_CUDA=On -DCMAKE_CXX_COMPILER=${HOME}/phoebus/external/singularity-eos/utils/kokkos/bin/nvcc_wrapper -DKokkos_ARCH_HSW=ON -DKokkos_ARCH_VOLTA70=ON -DPHOEBUS_ENABLE_MPI=OFF .. + +A few notes for this one: - Note here the ``-DCMAKE_CXX_COMPILER`` flag. +This is necessary. You *must* set the compiler to ``nvcc_wrapper`` +provided by Kokkos. - Note the ``-DKokkos_ARCH_*`` flags. Those set the +host and device microarchitectures and are required. The choice here is +on an ``x86_64`` machine with a ``volta`` GPU. + +Build Options +------------- + +The build options explicitly provided by ``phoebus`` are: + ++-----------------------+----------+-----------------------------------------------+ +| Option | Default | Comment | ++=======================+==========+===============================================+ +| PHOEBUS_ENABLE_CUDA | OFF | Cuda | ++-----------------------+----------+-----------------------------------------------+ +| PHOEBUS_ENABLE_HDF5 | ON | HDF5. Required for output and restarts. | ++-----------------------+----------+-----------------------------------------------+ +| PHOEBUS_ENABLE_MPI | ON | MPI. Required for distributed memory | +| | | parallelism. | ++-----------------------+----------+-----------------------------------------------+ +| PHOEBUS_ENABLE_OPENMP | OFF | OpenMP. Required for shared memory | +| | | parallelism. | ++-----------------------+----------+-----------------------------------------------+ +| MACHINE_CFG | None | Machine-specific config file, optional. | ++-----------------------+----------+-----------------------------------------------+ + +Some relevant settings from Parthenon and Kokkos you may need to play +with are: + ++---------------------+----------+---------------------------------------------+ +| Option | Default | Comment | ++=====================+==========+=============================================+ +| CMAKE_CXX_COMPILER | None | Must be set to ``nvcc_wrapper`` with cuda | +| | | backend | ++---------------------+----------+---------------------------------------------+ +| Kokkos_ARCH_XXXX | OFF | You must set the GPU architecture when | +| | | compiling for Cuda | ++---------------------+----------+---------------------------------------------+ + +You can see all the Parthenon build options +`here `__ +and all the Kokkos build options +`here `__ + +Cmake machine configs +--------------------- + +If you are proficient with ``cmake`` You can optionally write a +``cmake`` file that sets the configure parameters that you like on a +given machine. Both ``phoebus`` and ``parthenon`` can make use of it. +You can point to the file with + +:: + + -DMACHINE_CFG=path/to/machine/file + +at config time or by setting the environment variable ``MACHINE_CFG`` to +point at it, e.g., + +.. code:: bash + + export MACHINE_CFG=path/to/machine/file + +An example machine file might look like + +:: + + # Machine file for x86_64-volta on Darwin + message(STATUS "Loading machine configuration for Darwin x86-volta node") + message(STATUS "Assumes: module load module load gcc/7.4.0 cuda/10.2 openmpi/4.0.3-gcc_7.4.0 anaconda/Anaconda3.2019.10 cmake && spack load hdf5") + message(STATUS "Also assumes you have a valid spack installation loaded.") + + set(PHOEBUS_ENABLE_CUDA ON CACHE BOOL "Cuda backend") + set(PHOEBUS_ENABLE_MPI OFF CACHE BOOL "No MPI") + set(Kokkos_ARCH_HSW ON CACHE BOOL "Haswell target") + set(Kokkos_ARCH_VOLTA70 ON CACHE BOOL "volta target") + set(CMAKE_CXX_COMPILER /home/jonahm/phoebus/external/parthenon/external/Kokkos/bin/nvcc_wrapper CACHE STRING "nvcc wrapper") + +you could then configure and compile as + +.. code:: bash + + cmake -DMACHINE_CFG=path/to/machine/file .. + make -j + +Running +------- + +Run phoebus from the ``build`` directory as + +.. code:: bash + + ./src/phoebus -i path/to/input/file.pin + +The input files are in ``phoebus/inputs/*``. There’s typically one input +file per problem setup file. + +Submodules +---------- + +- ``parthenon`` asynchronous tasking and block-AMR infrastructure +- ``singularity-eos`` provides performance-portable equations of state + and PTE solvers +- ``singularity-opac`` provides performance-portable opacities and + emissivities +- ``Kokkos`` provides performance portable shared-memory parallelism. + It allows our loops to be CUDA, OpenMP, or something else. By default + we use the ``Kokkos`` shipped with ``parthenon``. + +External (Required) +------------------- + +- ``cmake`` for building + +Optional +-------- + +- ``hdf5`` for output (must be parallel if MPI is enabled) +- ``MPI`` for distributed memory parallelism +- ``python3`` for visualization diff --git a/main/_sources/src/code_of_conduct.rst.txt b/main/_sources/src/code_of_conduct.rst.txt new file mode 100644 index 00000000..6edc7037 --- /dev/null +++ b/main/_sources/src/code_of_conduct.rst.txt @@ -0,0 +1,28 @@ +.. _lanlcode: https://lanl.github.io/singularity-eos + +Code of Conduct +===================================== + +We as users, members, contributors, and leaders agree to make participation in our +community a harassment-free experience for everyone. +We will interact in ways that contribute to an open, welcoming, +diverse, inclusive, and healthy community. + +We agree to uphold the `LANL Code of Conduct `_ in all spaces relevant. +Of note: + +:: + + - Foster a mutually respectful working environment that is free from + discrimination, intimidation, and harassment (including sexual + harassment). + - Do not discriminate against others on the basis of any + characteristic protected by law or LANL policy. + - Do not engage in behaviors that create an offensive, hostile, or + intimidating work environment, including shouting, abusive + language, threats of violence, the use of obscenities or other + non-verbal expressions of aggression, horseplay such as kicking + co-workers’ chairs or using personal insults, or the use of + offensive nicknames or other derogatory remarks. + - Avoid behavior that a reasonable person would find to be demeaning + or humiliating. diff --git a/main/_sources/src/contributing.rst.txt b/main/_sources/src/contributing.rst.txt new file mode 100644 index 00000000..8acd9250 --- /dev/null +++ b/main/_sources/src/contributing.rst.txt @@ -0,0 +1,269 @@ +.. _singularity-eos: https://lanl.github.io/singularity-eos +.. _Catch2: https://github.com/catchorg/Catch2 + +Contributing +============================= + +To contribute to ``Phoebus``, feel free to submit a pull +request or open an issue. + +1. Create a new fork of ``main`` where your changes can be made. +2. After completing, create a pull request, describe the final approach + and ensure the branch has no conflicts with current Regression Tests + and Formatting Checks. +3. Assign external reviewers (a minimum of 1, one of which should be a + Maintainer, and which cannot be the contributor). Provide concise + description of changes. +4. Once comments/feedback is addressed, the PR will be merged into the + main branch and changes will be added to list of changes in the next + release. +5. At present, Releases (with a git version tag) for the ``main`` branch + of ``Phoebus`` will occur at a 6 to 12 month cadence or following + implementation of a major enhancement or capability to the code base. + +*Maintainers* of ``Phoebus`` will follow the same process for +contributions as above except for the following differences: they may +create branches directly within ``Phoebus``, they will hold repository +admin privileges, and actively participate in the technical review of +contributions to ``Phoebus``. + + +Pull request protocol +---------------------- + +When submitting a pull request, there is a default template that is automatically +populated. The pull request should sufficiently summarize all changes. +As necessary, tests should be added for new features of bugs fixed. + +Before a pull request will be merged, the code should be formatted. We +use clang-format for this, pinned to version 12. +The script ``scripts/bash/format.sh`` will apply ``clang-format`` +to C++ source files in the repository as well as ``black`` to python files, if available. +The script takes two CLI arguments +that may be useful, ``CFM``, which can be set to the path for your +clang-format binary, and ``VERBOSE``, which if set to ``1`` adds +useful output. For example: + +.. code-block:: bash + + CFM=clang-format-12 VERBOSE=1 ./scripts/bash/format.sh + +In order for a pull request to merge, we require: + +- Provide a thorough summary of changes, especially if they are breaking changes +- Obey style guidleines (format with ``clang-format`` and pass the necessary test) +- Pass the existing test suite +- Have at least one approval from a Maintainer +- If applicable: + + - Write new tests for new features or bugs + - Include or update documentation in ``doc/`` + +Test Suite +---------- + +Several sets of tests are triggered on a pull request: a static format +check, a docs buld, and a suite of unit and regression tests. +These are run through github's CPU infrastructure. These tests +help ensure that modifications to the code do not break existing capabilities +and ensure a consistent code style. + +Adding Tests +```````````` + +There are two primary categories of tests written in ``Phoebus``: +unit tests and regression tests. + +Unit +^^^^ + +Unit tests live in ``tst/unit/``. They are implemented using the +`Catch2`_ unit testing framework. They are integrated with ``cmake`` +and can be run, when enabled, with ``ctest``. There are a few necessary ``cmake`` +configurations to beuild tests: + +========================== ========= ======================================= + Option Default Description +========================== ========= ======================================= +PHOEBUS_ENABLE_UNIT_TESTS OFF Enables Catch2 unit tests +PHOEBUS_ENABLE_DOWNLOADS OFF Enables unit tests using tabulated EOS +========================== ========= ======================================= + +Regression +^^^^^^^^^^ +Regression tests run existing simulations and test against saved output +in order to verify sustained capabilities. +They are implemented in Python in +``test/regression/``. To run the tests you will need a Python environment with +at least ``numpy`` and ``h5py``. Tests can be ran manually as, e.g., + +.. code-block:: bash + + python linear_modes.py + +This will build Phoebus locally in ``phoebus/tst/regression/build`` and run it in +``phoebus/tst/regression/run``. Ensure that these directories do not already exist. +Each script ``test.py`` has a correspodning "gold file" ``test.gold``. +The gold files contain the gold standard data that the output of the regression test +is compared against. To generate new gold data, for example if a change is implemented +that changes the behavior of a test (not erroneously) or a new test is created, run the test +script with the ``--upgold`` option. This will create or update the corresponding ``.gold`` file. +To add a new test: + +1. Create a new test script. + + - Update the ``modified_inputs`` struct to change any input deck options + - Set the ``variables`` list to contain the quantities to test against +2. Run the script with the ``--upgold`` option +3. Commit the test script and gold file +4. Update the CI to include the new test (``phoebus/.github/workflows/tests.yml``) + + +Expectations for code review +----------------------------- + +Much of what follows is adapted from `singularity-eos`_. + +From the perspective of the contributor +```````````````````````````````````````` + +Code review is an integral part of the development process +for ``Phoebus``. You can expect at least one, perhaps many, +core developers to read your code and offer suggestions. +You should treat this much like scientific or academic peer review. +You should listen to suggestions but also feel entitled to push back +if you believe the suggestions or comments are incorrect or +are requesting too much effort. + +Reviewers may offer conflicting advice, if this is the case, it's an +opportunity to open a discussion and communally arrive at a good +approach. You should feel empowered to argue for which of the +conflicting solutions you prefer or to suggest a compromise. If you +don't feel strongly, that's fine too, but it's best to say so to keep +the lines of communication open. + +Big contributions may be difficult to review in one piece and you may +be requested to split your pull request into two or more separate +contributions. You may also receive many "nitpicky" comments about +code style or structure. These comments help keep a broad codebase, +with many contributors uniform in style and maintainable with +consistent expectations accross the code base. While there is no +formal style guide for now, the regular contributors have a sense for +the broad style of the project. You should take these stylistic and +"nitpicky" suggestions seriously, but you should also feel free to +push back. + +As with any creative endeavor, we put a lot of ourselves into our +code. It can be painful to receive criticism on your contribution and +easy to take it personally. While you should resist the urge to take +offense, it is also partly code reviewer's responsiblity to create a +constructive environment, as discussed below. + +Expectations of code reviewers +```````````````````````````````` + +A good code review builds a contribution up, rather than tearing it +down. Here are a few rules to keep code reviews constructive and +congenial: + +* You should take the time needed to review a contribution and offer + meaningful advice. Unless a contribution is very small, limit + the times you simply click "approve" with a "looks good to me." + +* You should keep your comments constructive. For example, rather than + saying "this pattern is bad," try saying "at this point, you may + want to try this other pattern." + +* Avoid language that can be misconstrued, even if it's common + notation in the commnunity. For example, avoid phrases like "code + smell." + +* Explain why you make a suggestion. In addition to saying "try X + instead of Y" explain why you like pattern X more than pattern Y. + +* A contributor may push back on your suggestion. Be open to the + possibility that you're either asking too much or are incorrect in + this instance. Code review is an opportunity for everyone to learn. + +* Don't just highlight what you don't like. Also highlight the parts + of the pull request you do like and thank the contributor for their + effort. + +General principle for everyone +``````````````````````````````` + +It's hard to convey tone in text correspondance. Try to read what +others write favorably and try to write in such a way that your tone +can't be mis-interpreted as malicious. + +A Large Ecosystem +------------------------ + +``Phoebus`` depends on several other open-source, Los Alamos +maintained, projects. In particular, ``Parthenon``, ``singularity-eos``, +``singularity-opac``, and ``spiner``. +If you have issues with these projects, ideally +submit issues on the relevant github pages. However, if you can't +figure out where an issue belongs, no big deal. Submit where you can +and we'll engage with you to figure out how to proceed. + +Becoming a Contributor +---------------------- + +For the purpose of our development model, we label *Contributors* or +*Maintainers* of ``Phoebus``. Below we describe these labels and the +process for contributing to ``Phoebus``. + +We welcome contributions from scientists from a large variety of +relativistic astrophysics. New users are welcome to contributions to +``Phoebus`` via the *Contributors* process. Contributors with 6 merged +pull requests into the main branch (over a minimum of 6 months) will +be eligible to join as a *Maintainer* of ``Phoebus`` with additional +repository access and roles. However, final approval of *Maintainer* +status will require a approval by vote by existing +*Maintainers*, a necessary step to ensure the safety and integrity of +the code base for all users of ``Phoebus``. + +The *Maintainers* of ``Phoebus`` consist of the original developers of +the code and those that have a demonstrated history in the development +of ``Phoebus`` prior to the implementation of the *Development Model* +described here. Maintainers hold admin access, serve as +reviewers for pull requests, and are in charge of the maintaining, +deployment, and improvement of efforts towards: regression testing, +documentation, science test cases (gold standards), and continuous +integration. + +Maintainers are excepted to make a good faith effort to adhere to +:ref:`these suggestions ` in order to maintain a supportive and +productive environment. + +List of Current Maintainers of Phoebus +------------------------------------------ + ++-------------------+--------------------------------+-----------------------+ +| Name | Handle | Team | ++===================+================================+=======================+ +| Brandon Barker | | Los Alamos National | +| | `@AstroBarker `__ | | ++-------------------+--------------------------------+-----------------------+ +| Josh Dolence | `@jdolence `__ | Lab | ++-------------------+--------------------------------+-----------------------+ +| Carl Fields | | University of Arizona | +| | `@carlnotsagan `__ | | ++-------------------+--------------------------------+-----------------------+ +| Mariam | `@mari2895 `__ | | ++-------------------+--------------------------------+-----------------------+ +| Jonah Miller | `@Yurlungur `__ | Lab | ++-------------------+--------------------------------+-----------------------+ +| Jeremiah Murphy | | Florida State | +| | `@curiousmiah `__ | | ++-------------------+--------------------------------+-----------------------+ +| Ben Ryan | `@brryan `__ | Lab | ++-------------------+--------------------------------+-----------------------+ diff --git a/main/_sources/src/governance.rst.txt b/main/_sources/src/governance.rst.txt new file mode 100644 index 00000000..78a4c1fe --- /dev/null +++ b/main/_sources/src/governance.rst.txt @@ -0,0 +1,140 @@ +Organizational Structure +========================== + +| ``Phoebus`` uses a *hybrid flat-and-hierarchical* organizational + structure. +| The flat structure fosters power sharing among senior and junior + members and avoids the many pitfalls of power-over dynamics. For + example, in power-over structures, someone with explicit power can + inadvertently, or on rare occasions intentionally, silence critical + voices. +| This dynamic can quickly lead to an organization overlooking inherent + problems that could lead to ineffectiveness or even catastrophic + failure of the team. + +| In contrast, our aim is to illuminate potential problems early and + quickly find solutions. +| This strategy also efficiently taps into the diverse wealth of + knowledge of the team. +| At the same time, the PI and Co-PI have financial and reporting + responsibilities to their respective universities and funding + agencies. +| The general procedure for the hybrid structure is as follows. +| The flat structure will make major decisions in direction and + resources, and the PI and Co-PI will assume the responsibility for + executing those decisions. +| The following gives details on this hybrid structure. + +Team +---- + +The founding team consists of the following: original core developers +and Maintainers at Los Alamos National Lab, Jeremiah Murphy at Florida +State University, and Carl Fields at University of Arizona. + +Since, an objective of Phoebus is to grow the developer and user base, +the Phoebus Project will have an explicit mechanism for adding new +members. There are three categories for ``Phoebus`` members: +maintainers, contributors, and users. + +**User**: As open-source software, anyone may download, compile, and +execute ``Phoebus``. New users will encouraged to join communication +channels for connection with the larger ``Phoebus`` community. + +**Contributor**: Users who wish to contribute to ``Phoebus`` may do so +following our Development Model for new users. These changes will be +integrated into the main branch of the code upon approval. Consistent +contributions also provides the opportunity for Contributors to be +eligible to join as a *Maintainer*, the final approval of which will +require a vote. + +**Maintainer**: These are the core team who have “merge” permissions on +the repo and are working to keep the code sustainable long term. + +To maintain their relevant active status, all members must +make a food faith effort to maintain a supportive, productive environment. + + +.. _mou: + +Memorandum of Understanding +--------------------------- + +In addition to our Community Code of Conduct, we ask that maintainers +especially keep the following suggestions in mind to help +facilitate an efficient and welcoming collaboration: + +- Maintainers should uphold and exemplify the *Development Model* + outlined as part of the ``phoebus`` Community described + :doc:`here `. +- Within reason, maintainers will make a good-faith effort to attend team + meetings. In an effort to accommodate the dynamic schedules and + availability of many of the core team of *Maintainers*, + coordination efforts will be made to ensure that *at least* + 1 *Maintainer* is present for all meetings. +- Maintainers will make a good-faith effort to monitor the fraction of + the meeting time that they speak. The meeting time is limited, and + several people may have something interesting to say, report on their + updates, or contribute constructive arguments. One should be + self-aware and notice if one is dominating conversations, and attempt + to make a conscious effort to include other voices and perspectives + in the discussion. +- Maintainers consider it their responsibility to voice their questions + and/or concerns as early as possible. This will ensure that the + organization addresses concerns rapidly and effectively. +- Maintainers consider it their responsibility to listen and understand + questions or concerns raised by other partners or through concerns + communicated through email to individual *Maintainers*. + +Approval by Vote: +----------------- + +| Many of the decisions in the organization will be enacted after an + approval by majority vote of active Maintainers. The process of listening + and adjusting strategies to meet everyone’s needs is vital for + power-sharing organizations. +| Importantly, spending a little time up front to listen and resolve + concerns reduces the pain and time spent later in intense conflict + resolution. + +Communication and Connection: +----------------------------- + +| To facilitate open and effective communication, the ``Phoebus`` will + offer multiple levels of communication. + Developers will communicate via email, GitHub, and a ``Phoebus`` Slack + channel. + +| To respond to user inquiries, the Phoebus Project will host a mailing + list via Google or similar. +| To maintain a standing record of user inquiries and responses, we will + post the inquiries and responses on a public-facing site. +| All Maintainers will have the option to respond to the inquires; to + ensure that someone is responsive to the user inquiries, the team will + triage tickets/questions in developer meetings. + +| Subject to availability, monthly Maintainer meetings will also + be an important part of ensuring productivity and timeliness. +| Each meeting will last up to 60 minutes. We will assess and discuss + the goals from the previous meeting. +| In particular, we will take note which goals were completed and which + were not. If there are uncompleted goals, we will assess why they were + not completed. Next, we will discuss the goals for the upcoming month, + quarter, and year. +| We will decide which goals to prioritize. +| All of this will be recorded on an online document which will be + available to all Maintainers. + +| Each meeting of the core Maintainers will be managed by a meeting + manager. +| The primary job of the meeting manager is to: 1) gather a list of + agenda items for the next meeting, 2) ensure that the meeting runs on + schedule, and 3) ensure equitable participation by all participants. +| Again, in keeping with power-sharing, the meeting manager position + will rotate among the core Maintainers, even junior members. + +.. note:: + We maintain some flexibility in the cadence and structure of meetings, in + particular, in periods of low activity, meetings may be skipped or + held in a less formal manner. We recognize that the availability + of maintainers is contingent upon many factors. diff --git a/main/_sources/src/sphinx-doc.rst.txt b/main/_sources/src/sphinx-doc.rst.txt new file mode 100644 index 00000000..c85d9e4b --- /dev/null +++ b/main/_sources/src/sphinx-doc.rst.txt @@ -0,0 +1,134 @@ +.. _sphinx-doc: + +.. _Sphinx CheatSheet: https://thomas-cokelaer.info/tutorials/sphinx/rest_syntax.html + +How to Use Sphinx for Writing Docs +=================================== + +How to convert a Markdown file to rst +------------------------------------------ + +We are using the `reStructuredText`_ (rst) format for our documentation. +If you have a markdown file you would like to convert to rst, +as a first pass, you can have `Pandoc`_ convert your file. For example: + +.. code-block:: bash + + pandoc Metadata.md --from markdown --to rst -s -o metadata.rst + +Pandoc can be installed easily through a Linux package manager. For example on Ubuntu, + +.. code-block:: bash + + apt install pandoc + +will get you the tool. + +.. _reStructuredText: https://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html + +.. _Pandoc: https://pandoc.org/ + +How to have github build your documentation for you +---------------------------------------------------- + +Github can automatically build your documentation for you through the continuous integration pipeline. +After you submit a pull request with your .rst changes for documentation on `github-pages`_, +the documentation will automatically get built. You will see a "build and deploy documentation" job +at the bottom of the pull request page. If this passes, your documentation will have been generated. + +On the bottom left of the documentation page on `github-pages`_, you can select the branch/build +of the documentation, one of which should be the branch you wrote your changes on. + +.. _github-pages: https://lanl.github.io/phoebus + + +Building documentation locally +------------------------------ + +While you can rely on the CI to build the documentation associated with your +branch, you can also very easily build sphinx documentation locally through +python. These instructions also *do not* require admin access and are usable +with shared machines or python distributions. + +First, ensure that you are running a modern version of python (i.e. python 3 of +some flavor) + +.. code-block:: bash + + $ python --version + Python 3.9.7 + +Then, use pip to install :code:`spinx` and the RTD theme + +.. code-block:: bash + + pip install --user sphinx sphinx-rtd-theme + +Now, navigate to the :code:`../doc/sphinx` directory where a :code:`make help` +shows all of the available ways to build the documentation + +.. code-block:: + + $ make help + Sphinx v4.2.0 + Please use `make target' where target is one of + html to make standalone HTML files + dirhtml to make HTML files named index.html in directories + singlehtml to make a single large HTML file + pickle to make pickle files + json to make JSON files + htmlhelp to make HTML files and an HTML help project + qthelp to make HTML files and a qthelp project + devhelp to make HTML files and a Devhelp project + epub to make an epub + latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter + latexpdf to make LaTeX and PDF files (default pdflatex) + latexpdfja to make LaTeX files and run them through platex/dvipdfmx + text to make text files + man to make manual pages + texinfo to make Texinfo files + info to make Texinfo files and run them through makeinfo + gettext to make PO message catalogs + changes to make an overview of all changed/added/deprecated items + xml to make Docutils-native XML files + pseudoxml to make pseudoxml-XML files for display purposes + linkcheck to check all external links for integrity + doctest to run all doctests embedded in the documentation (if enabled) + coverage to run coverage check of the documentation (if enabled) + clean to remove everything in the build directory + +Making the documentation will create a new directory, :code:`_build` in the +:code:`sphinx` directory along with whichever type of documentation you wanted +to build. + +For example, building the HTML documentation with :code:`make html` produces the +:code:`../doc/sphinx/_build/html` directory with an :code:`index.html` file that +you can point a browser to in order to view the documenation. + + +How to Get the Dependencies +--------------------------- + +Using Docker +^^^^^^^^^^^^ + +If you are using `Docker`_, then simply pull the docker image specified below: + +.. _Docker: https://www.docker.com + +.. code-block:: + + image: sphinxdoc/sphinx-latexpdf + +Then, after running :code:`docker run -it /bin/bash`, install the theme we are using with :code:`pip install sphinx_rtd_theme` + +More Info. +---------- + +* `Sphinx Installation`_ + +.. _Sphinx Installation: https://www.sphinx-doc.org/en/master/usage/installation.html + +* `Sphinx reStructuredText Documentation`_ + +.. _Sphinx reStructuredText Documentation: https://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html diff --git a/main/_sources/src/tracers.rst.txt b/main/_sources/src/tracers.rst.txt new file mode 100644 index 00000000..58cee20f --- /dev/null +++ b/main/_sources/src/tracers.rst.txt @@ -0,0 +1,97 @@ +.. _parthenon-swarms: https://parthenon-hpc-lab.github.io/parthenon/develop/src/particles.html + +Tracer Particles +================ + +``Phoebus`` includes Lagrangian tracer particles. +These are primarily for the purpose of post-processing simulation data for, e.g., nucleosynthesis. +They are operator spit from the hydrodynamics and advected with a standard second order Runge-Kutta +integrator. As ``Phoebus`` is a general relativistic code, we evolve tracer positions using a +relativistic advection equation: + +.. math:: + + \frac{dx^i}{dt} = \frac{u^i}{u^0} = \alpha v^i - \beta^i + +Tracers may be enabled by in the ``Phoebus`` input deck as follow: + +.. code-block:: + + + tracers = true + + + num_tracers = 1024 + +Similarly, tracers may be output by modifying an existing Parthenon output block, or creating a new one: + +.. code-block:: + + + // ... + swarms = tracers + tracers_variables = rho, temperature, ye + + file_type = hdf5 + dt = // output cadence + +Note that the position variables x, y, z are output for all swarms by default. +See the `Parthenon docs `_ for more information. + +Tracers must, however, be configured in the problem generator. +In the generator, the tracers should be distributed through the domain, assigned positions +and unique ids. An example from the advection pgen is shown below. + +.. code-block:: c++ + + pmb->par_for( + "ProblemGenerator::Advection::DistributeTracers", 0, max_active_index, + KOKKOS_LAMBDA(const int n) { + if (swarm_d.IsActive(n)) { + auto rng_gen = rng_pool.get_state(); + + // sample in ball + Real r2 = 1.0 + rin * rin; // init > rin^2 + while (r2 > rin * rin) { + x(n) = x_min + rng_gen.drand() * (x_max - x_min); + y(n) = y_min + rng_gen.drand() * (y_max - y_min); + z(n) = z_min + rng_gen.drand() * (z_max - z_min); + r2 = x(n) * x(n) + y(n) * y(n) + z(n) * z(n); + } + id(n) = num_tracers_total * gid + n; + + bool on_current_mesh_block = true; + swarm_d.GetNeighborBlockIndex(n, x(n), y(n), z(n), on_current_mesh_block); + rng_pool.free_state(rng_gen); + } + }); + +In addition to position, tracers track a number of potentially useful quantities. +These quantities include (bold quantities are 3-vectors with components _x, _y, _z) + +=================== ================ =================== + Quantity SwarmVar Name Description +=================== ================ =================== +Density rho Primitive density +Temperature temperature Temperature +Ye ye Electron fraction (0 if ye is disabled) +Internal energy energy Primitive internal energy +Entropy entropy Entropy +**Velocity** vel_x, ... Three velocity +Lorentz factor lorentz Relativistic Lorentz factor +Lapse lapse Relativistic lapse +Metric determinant detgamma Spatial metric determinant +**Shift** shift_x, ... Relativistic shift +Mass mass Tracer mass +Total energy bernoulli Total energy Bernoulli quantity +**Magnetic field** B_x, ... Primitive 3-magnetic field components (if mhd enabled) +=================== ================ =================== + +To minimize unnecessary work, these quantities are only populated before output using ``phoebus::UserWorkBeforeOutput``. + +.. cpp:function:: void UserWorkBeforeOutput(MeshBlock *pmb, ParameterInput *pin) + :no-contents-entry: + + Describes work to be done prior to HDF5 output, such as populating tracer variables. + This is connected to the appropriate Parthenon function. + diff --git a/main/_static/_sphinx_javascript_frameworks_compat.js b/main/_static/_sphinx_javascript_frameworks_compat.js new file mode 100644 index 00000000..81415803 --- /dev/null +++ b/main/_static/_sphinx_javascript_frameworks_compat.js @@ -0,0 +1,123 @@ +/* Compatability shim for jQuery and underscores.js. + * + * Copyright Sphinx contributors + * Released under the two clause BSD licence + */ + +/** + * small helper function to urldecode strings + * + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL + */ +jQuery.urldecode = function(x) { + if (!x) { + return x + } + return decodeURIComponent(x.replace(/\+/g, ' ')); +}; + +/** + * small helper function to urlencode strings + */ +jQuery.urlencode = encodeURIComponent; + +/** + * This function returns the parsed url parameters of the + * current request. Multiple values per key are supported, + * it will always return arrays of strings for the value parts. + */ +jQuery.getQueryParameters = function(s) { + if (typeof s === 'undefined') + s = document.location.search; + var parts = s.substr(s.indexOf('?') + 1).split('&'); + var result = {}; + for (var i = 0; i < parts.length; i++) { + var tmp = parts[i].split('=', 2); + var key = jQuery.urldecode(tmp[0]); + var value = jQuery.urldecode(tmp[1]); + if (key in result) + result[key].push(value); + else + result[key] = [value]; + } + return result; +}; + +/** + * highlight a given string on a jquery object by wrapping it in + * span elements with the given class name. + */ +jQuery.fn.highlightText = function(text, className) { + function highlight(node, addItems) { + if (node.nodeType === 3) { + var val = node.nodeValue; + var pos = val.toLowerCase().indexOf(text); + if (pos >= 0 && + !jQuery(node.parentNode).hasClass(className) && + !jQuery(node.parentNode).hasClass("nohighlight")) { + var span; + var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.className = className; + } + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + node.parentNode.insertBefore(span, node.parentNode.insertBefore( + document.createTextNode(val.substr(pos + text.length)), + node.nextSibling)); + node.nodeValue = val.substr(0, pos); + if (isInSVG) { + var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect"); + var bbox = node.parentElement.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute('class', className); + addItems.push({ + "parent": node.parentNode, + "target": rect}); + } + } + } + else if (!jQuery(node).is("button, select, textarea")) { + jQuery.each(node.childNodes, function() { + highlight(this, addItems); + }); + } + } + var addItems = []; + var result = this.each(function() { + highlight(this, addItems); + }); + for (var i = 0; i < addItems.length; ++i) { + jQuery(addItems[i].parent).before(addItems[i].target); + } + return result; +}; + +/* + * backward compatibility for jQuery.browser + * This will be supported until firefox bug is fixed. + */ +if (!jQuery.browser) { + jQuery.uaMatch = function(ua) { + ua = ua.toLowerCase(); + + var match = /(chrome)[ \/]([\w.]+)/.exec(ua) || + /(webkit)[ \/]([\w.]+)/.exec(ua) || + /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) || + /(msie) ([\w.]+)/.exec(ua) || + ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) || + []; + + return { + browser: match[ 1 ] || "", + version: match[ 2 ] || "0" + }; + }; + jQuery.browser = {}; + jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true; +} diff --git a/main/_static/basic.css b/main/_static/basic.css new file mode 100644 index 00000000..7ebbd6d0 --- /dev/null +++ b/main/_static/basic.css @@ -0,0 +1,914 @@ +/* + * Sphinx stylesheet -- basic theme. + */ + +/* -- main layout ----------------------------------------------------------- */ + +div.clearer { + clear: both; +} + +div.section::after { + display: block; + content: ''; + clear: left; +} + +/* -- relbar ---------------------------------------------------------------- */ + +div.related { + width: 100%; + font-size: 90%; +} + +div.related h3 { + display: none; +} + +div.related ul { + margin: 0; + padding: 0 0 0 10px; + list-style: none; +} + +div.related li { + display: inline; +} + +div.related li.right { + float: right; + margin-right: 5px; +} + +/* -- sidebar --------------------------------------------------------------- */ + +div.sphinxsidebarwrapper { + padding: 10px 5px 0 10px; +} + +div.sphinxsidebar { + float: left; + width: 230px; + margin-left: -100%; + font-size: 90%; + word-wrap: break-word; + overflow-wrap : break-word; +} + +div.sphinxsidebar ul { + list-style: none; +} + +div.sphinxsidebar ul ul, +div.sphinxsidebar ul.want-points { + margin-left: 20px; + list-style: square; +} + +div.sphinxsidebar ul ul { + margin-top: 0; + margin-bottom: 0; +} + +div.sphinxsidebar form { + margin-top: 10px; +} + +div.sphinxsidebar input { + border: 1px solid #98dbcc; + font-family: sans-serif; + font-size: 1em; +} + +div.sphinxsidebar #searchbox form.search { + overflow: hidden; +} + +div.sphinxsidebar #searchbox input[type="text"] { + float: left; + width: 80%; + padding: 0.25em; + box-sizing: border-box; +} + +div.sphinxsidebar #searchbox input[type="submit"] { + float: left; + width: 20%; + border-left: none; + padding: 0.25em; + box-sizing: border-box; +} + + +img { + border: 0; + max-width: 100%; +} + +/* -- search page ----------------------------------------------------------- */ + +ul.search { + margin-top: 10px; +} + +ul.search li { + padding: 5px 0; +} + +ul.search li a { + font-weight: bold; +} + +ul.search li p.context { + color: #888; + margin: 2px 0 0 30px; + text-align: left; +} + +ul.keywordmatches li.goodmatch a { + font-weight: bold; +} + +/* -- index page ------------------------------------------------------------ */ + +table.contentstable { + width: 90%; + margin-left: auto; + margin-right: auto; +} + +table.contentstable p.biglink { + line-height: 150%; +} + +a.biglink { + font-size: 1.3em; +} + +span.linkdescr { + font-style: italic; + padding-top: 5px; + font-size: 90%; +} + +/* -- general index --------------------------------------------------------- */ + +table.indextable { + width: 100%; +} + +table.indextable td { + text-align: left; + vertical-align: top; +} + +table.indextable ul { + margin-top: 0; + margin-bottom: 0; + list-style-type: none; +} + +table.indextable > tbody > tr > td > ul { + padding-left: 0em; +} + +table.indextable tr.pcap { + height: 10px; +} + +table.indextable tr.cap { + margin-top: 10px; + background-color: #f2f2f2; +} + +img.toggler { + margin-right: 3px; + margin-top: 3px; + cursor: pointer; +} + +div.modindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +div.genindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +/* -- domain module index --------------------------------------------------- */ + +table.modindextable td { + padding: 2px; + border-collapse: collapse; +} + +/* -- general body styles --------------------------------------------------- */ + +div.body { + min-width: 360px; + max-width: 800px; +} + +div.body p, div.body dd, div.body li, div.body blockquote { + -moz-hyphens: auto; + -ms-hyphens: auto; + -webkit-hyphens: auto; + hyphens: auto; +} + +a.headerlink { + visibility: hidden; +} + +a:visited { + color: #551A8B; +} + +h1:hover > a.headerlink, +h2:hover > a.headerlink, +h3:hover > a.headerlink, +h4:hover > a.headerlink, +h5:hover > a.headerlink, +h6:hover > a.headerlink, +dt:hover > a.headerlink, +caption:hover > a.headerlink, +p.caption:hover > a.headerlink, +div.code-block-caption:hover > a.headerlink { + visibility: visible; +} + +div.body p.caption { + text-align: inherit; +} + +div.body td { + text-align: left; +} + +.first { + margin-top: 0 !important; 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+ float: right; + clear: right; + overflow-x: auto; +} + +p.sidebar-title { + font-weight: bold; +} + +nav.contents, +aside.topic, +div.admonition, div.topic, blockquote { + clear: left; +} + +/* -- topics ---------------------------------------------------------------- */ + +nav.contents, +aside.topic, +div.topic { + border: 1px solid #ccc; + padding: 7px; + margin: 10px 0 10px 0; +} + +p.topic-title { + font-size: 1.1em; + font-weight: bold; + margin-top: 10px; +} + +/* -- admonitions ----------------------------------------------------------- */ + +div.admonition { + margin-top: 10px; + margin-bottom: 10px; + padding: 7px; +} + +div.admonition dt { + font-weight: bold; +} + +p.admonition-title { + margin: 0px 10px 5px 0px; + font-weight: bold; +} + +div.body p.centered { + text-align: center; + margin-top: 25px; +} + +/* -- content of sidebars/topics/admonitions -------------------------------- */ + +div.sidebar > :last-child, +aside.sidebar > :last-child, +nav.contents > :last-child, +aside.topic > :last-child, +div.topic > :last-child, +div.admonition > :last-child { + margin-bottom: 0; +} + +div.sidebar::after, +aside.sidebar::after, +nav.contents::after, +aside.topic::after, +div.topic::after, +div.admonition::after, +blockquote::after { + display: block; + content: ''; + clear: both; +} + +/* -- tables ---------------------------------------------------------------- */ + +table.docutils { + margin-top: 10px; + margin-bottom: 10px; + border: 0; + border-collapse: collapse; +} + +table.align-center { + margin-left: auto; + margin-right: auto; +} + +table.align-default { + margin-left: auto; + margin-right: auto; +} + +table caption span.caption-number { + font-style: italic; +} + +table caption span.caption-text { +} + +table.docutils td, table.docutils th { + padding: 1px 8px 1px 5px; + border-top: 0; + border-left: 0; + border-right: 0; + border-bottom: 1px solid #aaa; +} + +th { + text-align: left; + padding-right: 5px; +} + +table.citation { + border-left: solid 1px gray; + margin-left: 1px; +} + +table.citation td { + border-bottom: none; +} + +th > :first-child, +td > :first-child { + margin-top: 0px; +} + +th > :last-child, +td > :last-child { + margin-bottom: 0px; +} + +/* -- figures --------------------------------------------------------------- */ + +div.figure, figure { + margin: 0.5em; + padding: 0.5em; +} + +div.figure p.caption, figcaption { + padding: 0.3em; +} + +div.figure p.caption span.caption-number, +figcaption span.caption-number { + font-style: italic; +} + +div.figure p.caption span.caption-text, +figcaption span.caption-text { +} + +/* -- field list styles ----------------------------------------------------- */ + +table.field-list td, table.field-list th { + border: 0 !important; +} + +.field-list ul { + margin: 0; + padding-left: 1em; +} + +.field-list p { + margin: 0; +} + +.field-name { + -moz-hyphens: manual; + -ms-hyphens: manual; + -webkit-hyphens: manual; + hyphens: manual; +} + +/* -- hlist styles ---------------------------------------------------------- */ + +table.hlist { + margin: 1em 0; +} + +table.hlist td { + vertical-align: top; +} + +/* -- object description styles --------------------------------------------- */ + +.sig { + font-family: 'Consolas', 'Menlo', 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', monospace; +} + +.sig-name, code.descname { + background-color: transparent; + font-weight: bold; +} + +.sig-name { + font-size: 1.1em; +} + +code.descname { + font-size: 1.2em; +} + +.sig-prename, code.descclassname { + background-color: transparent; +} + +.optional { + font-size: 1.3em; +} + +.sig-paren { + font-size: larger; +} + +.sig-param.n { + font-style: italic; +} + +/* C++ specific styling */ + +.sig-inline.c-texpr, +.sig-inline.cpp-texpr { + font-family: unset; +} + +.sig.c .k, .sig.c .kt, +.sig.cpp .k, .sig.cpp .kt { + color: #0033B3; +} + +.sig.c .m, +.sig.cpp .m { + color: #1750EB; +} + +.sig.c .s, .sig.c .sc, +.sig.cpp .s, .sig.cpp .sc { + color: #067D17; +} + + +/* -- other body styles ----------------------------------------------------- */ + +ol.arabic { + list-style: decimal; +} + +ol.loweralpha { + list-style: lower-alpha; +} + +ol.upperalpha { + list-style: upper-alpha; +} + +ol.lowerroman { + list-style: lower-roman; +} + +ol.upperroman { + list-style: upper-roman; +} + +:not(li) > ol > li:first-child > :first-child, +:not(li) > ul > li:first-child > :first-child { + margin-top: 0px; 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+ display: flex; + top: .3em; + right: .3em; + width: 1.7em; + height: 1.7em; + opacity: 0; + transition: opacity 0.3s, border .3s, background-color .3s; + user-select: none; + padding: 0; + border: none; + outline: none; + border-radius: 0.4em; + /* The colors that GitHub uses */ + border: #1b1f2426 1px solid; + background-color: #f6f8fa; + color: #57606a; +} + +button.copybtn.success { + border-color: #22863a; + color: #22863a; +} + +button.copybtn svg { + stroke: currentColor; + width: 1.5em; + height: 1.5em; + padding: 0.1em; +} + +div.highlight { + position: relative; +} + +/* Show the copybutton */ +.highlight:hover button.copybtn, button.copybtn.success { + opacity: 1; +} + +.highlight button.copybtn:hover { + background-color: rgb(235, 235, 235); +} + +.highlight button.copybtn:active { + background-color: rgb(187, 187, 187); +} + +/** + * A minimal CSS-only tooltip copied from: + * https://codepen.io/mildrenben/pen/rVBrpK + * + * To use, write HTML like the following: + * + *

Short

+ */ + .o-tooltip--left { + position: relative; + } + + .o-tooltip--left:after { + opacity: 0; + visibility: hidden; + position: absolute; + content: attr(data-tooltip); + padding: .2em; + font-size: .8em; + left: -.2em; + background: grey; + color: white; + white-space: nowrap; + z-index: 2; + border-radius: 2px; + transform: translateX(-102%) translateY(0); + transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); +} + +.o-tooltip--left:hover:after { + display: block; + opacity: 1; + visibility: visible; + transform: translateX(-100%) translateY(0); + transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); + transition-delay: .5s; +} + +/* By default the copy button shouldn't show up when printing a page */ +@media print { + button.copybtn { + display: none; + } +} diff --git a/main/_static/copybutton.js b/main/_static/copybutton.js new file mode 100644 index 00000000..2ea7ff3e --- /dev/null +++ b/main/_static/copybutton.js @@ -0,0 +1,248 @@ +// Localization support +const messages = { + 'en': { + 'copy': 'Copy', + 'copy_to_clipboard': 'Copy to clipboard', + 'copy_success': 'Copied!', + 'copy_failure': 'Failed to copy', + }, + 'es' : { + 'copy': 'Copiar', + 'copy_to_clipboard': 'Copiar al portapapeles', + 'copy_success': '¡Copiado!', + 'copy_failure': 'Error al copiar', + }, + 'de' : { + 'copy': 'Kopieren', + 'copy_to_clipboard': 'In die Zwischenablage kopieren', + 'copy_success': 'Kopiert!', + 'copy_failure': 'Fehler beim Kopieren', + }, + 'fr' : { + 'copy': 'Copier', + 'copy_to_clipboard': 'Copier dans le presse-papier', + 'copy_success': 'Copié !', + 'copy_failure': 'Échec de la copie', + }, + 'ru': { + 'copy': 'Скопировать', + 'copy_to_clipboard': 'Скопировать в буфер', + 'copy_success': 'Скопировано!', + 'copy_failure': 'Не удалось скопировать', + }, + 'zh-CN': { + 'copy': '复制', + 'copy_to_clipboard': '复制到剪贴板', + 'copy_success': '复制成功!', + 'copy_failure': '复制失败', + }, + 'it' : { + 'copy': 'Copiare', + 'copy_to_clipboard': 'Copiato negli appunti', + 'copy_success': 'Copiato!', + 'copy_failure': 'Errore durante la copia', + } +} + +let locale = 'en' +if( document.documentElement.lang !== undefined + && messages[document.documentElement.lang] !== undefined ) { + locale = document.documentElement.lang +} + +let doc_url_root = DOCUMENTATION_OPTIONS.URL_ROOT; +if (doc_url_root == '#') { + doc_url_root = ''; +} + +/** + * SVG files for our copy buttons + */ +let iconCheck = ` + ${messages[locale]['copy_success']} + + +` + +// If the user specified their own SVG use that, otherwise use the default +let iconCopy = ``; +if (!iconCopy) { + iconCopy = ` + ${messages[locale]['copy_to_clipboard']} + + + +` +} + +/** + * Set up copy/paste for code blocks + */ + +const runWhenDOMLoaded = cb => { + if (document.readyState != 'loading') { + cb() + } else if (document.addEventListener) { + document.addEventListener('DOMContentLoaded', cb) + } else { + document.attachEvent('onreadystatechange', function() { + if (document.readyState == 'complete') cb() + }) + } +} + +const codeCellId = index => `codecell${index}` + +// Clears selected text since ClipboardJS will select the text when copying +const clearSelection = () => { + if (window.getSelection) { + window.getSelection().removeAllRanges() + } else if (document.selection) { + document.selection.empty() + } +} + +// Changes tooltip text for a moment, then changes it back +// We want the timeout of our `success` class to be a bit shorter than the +// tooltip and icon change, so that we can hide the icon before changing back. +var timeoutIcon = 2000; +var timeoutSuccessClass = 1500; + +const temporarilyChangeTooltip = (el, oldText, newText) => { + el.setAttribute('data-tooltip', newText) + el.classList.add('success') + // Remove success a little bit sooner than we change the tooltip + // So that we can use CSS to hide the copybutton first + setTimeout(() => el.classList.remove('success'), timeoutSuccessClass) + setTimeout(() => el.setAttribute('data-tooltip', oldText), timeoutIcon) +} + +// Changes the copy button icon for two seconds, then changes it back +const temporarilyChangeIcon = (el) => { + el.innerHTML = iconCheck; + setTimeout(() => {el.innerHTML = iconCopy}, timeoutIcon) +} + +const addCopyButtonToCodeCells = () => { + // If ClipboardJS hasn't loaded, wait a bit and try again. This + // happens because we load ClipboardJS asynchronously. + if (window.ClipboardJS === undefined) { + setTimeout(addCopyButtonToCodeCells, 250) + return + } + + // Add copybuttons to all of our code cells + const COPYBUTTON_SELECTOR = 'div.highlight pre'; + const codeCells = document.querySelectorAll(COPYBUTTON_SELECTOR) + codeCells.forEach((codeCell, index) => { + const id = codeCellId(index) + codeCell.setAttribute('id', id) + + const clipboardButton = id => + `` + codeCell.insertAdjacentHTML('afterend', clipboardButton(id)) + }) + +function escapeRegExp(string) { + return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string +} + +/** + * Removes excluded text from a Node. + * + * @param {Node} target Node to filter. + * @param {string} exclude CSS selector of nodes to exclude. + * @returns {DOMString} Text from `target` with text removed. + */ +function filterText(target, exclude) { + const clone = target.cloneNode(true); // clone as to not modify the live DOM + if (exclude) { + // remove excluded nodes + clone.querySelectorAll(exclude).forEach(node => node.remove()); + } + return clone.innerText; +} + +// Callback when a copy button is clicked. Will be passed the node that was clicked +// should then grab the text and replace pieces of text that shouldn't be used in output +function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; + var match; + + // Do we check for line continuation characters and "HERE-documents"? + var useLineCont = !!lineContinuationChar + var useHereDoc = !!hereDocDelim + + // create regexp to capture prompt and remaining line + if (isRegexp) { + regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') + } else { + regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') + } + + const outputLines = []; + var promptFound = false; + var gotLineCont = false; + var gotHereDoc = false; + const lineGotPrompt = []; + for (const line of textContent.split('\n')) { + match = line.match(regexp) + if (match || gotLineCont || gotHereDoc) { + promptFound = regexp.test(line) + lineGotPrompt.push(promptFound) + if (removePrompts && promptFound) { + outputLines.push(match[2]) + } else { + outputLines.push(line) + } + gotLineCont = line.endsWith(lineContinuationChar) & useLineCont + if (line.includes(hereDocDelim) & useHereDoc) + gotHereDoc = !gotHereDoc + } else if (!onlyCopyPromptLines) { + outputLines.push(line) + } else if (copyEmptyLines && line.trim() === '') { + outputLines.push(line) + } + } + + // If no lines with the prompt were found then just use original lines + if (lineGotPrompt.some(v => v === true)) { + textContent = outputLines.join('\n'); + } + + // Remove a trailing newline to avoid auto-running when pasting + if (textContent.endsWith("\n")) { + textContent = textContent.slice(0, -1) + } + return textContent +} + + +var copyTargetText = (trigger) => { + var target = document.querySelector(trigger.attributes['data-clipboard-target'].value); + + // get filtered text + let exclude = '.linenos'; + + let text = filterText(target, exclude); + return formatCopyText(text, '', false, true, true, true, '', '') +} + + // Initialize with a callback so we can modify the text before copy + const clipboard = new ClipboardJS('.copybtn', {text: copyTargetText}) + + // Update UI with error/success messages + clipboard.on('success', event => { + clearSelection() + temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_success']) + temporarilyChangeIcon(event.trigger) + }) + + clipboard.on('error', event => { + temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_failure']) + }) +} + +runWhenDOMLoaded(addCopyButtonToCodeCells) \ No newline at end of file diff --git a/main/_static/copybutton_funcs.js b/main/_static/copybutton_funcs.js new file mode 100644 index 00000000..dbe1aaad --- /dev/null +++ b/main/_static/copybutton_funcs.js @@ -0,0 +1,73 @@ +function escapeRegExp(string) { + return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string +} + +/** + * Removes excluded text from a Node. + * + * @param {Node} target Node to filter. + * @param {string} exclude CSS selector of nodes to exclude. + * @returns {DOMString} Text from `target` with text removed. + */ +export function filterText(target, exclude) { + const clone = target.cloneNode(true); // clone as to not modify the live DOM + if (exclude) { + // remove excluded nodes + clone.querySelectorAll(exclude).forEach(node => node.remove()); + } + return clone.innerText; +} + +// Callback when a copy button is clicked. Will be passed the node that was clicked +// should then grab the text and replace pieces of text that shouldn't be used in output +export function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; + var match; + + // Do we check for line continuation characters and "HERE-documents"? + var useLineCont = !!lineContinuationChar + var useHereDoc = !!hereDocDelim + + // create regexp to capture prompt and remaining line + if (isRegexp) { + regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') + } else { + regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') + } + + const outputLines = []; + var promptFound = false; + var gotLineCont = false; + var gotHereDoc = false; + const lineGotPrompt = []; + for (const line of textContent.split('\n')) { + match = line.match(regexp) + if (match || gotLineCont || gotHereDoc) { + promptFound = regexp.test(line) + lineGotPrompt.push(promptFound) + if (removePrompts && promptFound) { + outputLines.push(match[2]) + } else { + outputLines.push(line) + } + gotLineCont = line.endsWith(lineContinuationChar) & useLineCont + if (line.includes(hereDocDelim) & useHereDoc) + gotHereDoc = !gotHereDoc + } else if (!onlyCopyPromptLines) { + outputLines.push(line) + } else if (copyEmptyLines && line.trim() === '') { + outputLines.push(line) + } + } + + // If no lines with the prompt were found then just use original lines + if (lineGotPrompt.some(v => v === true)) { + textContent = outputLines.join('\n'); + } + + // Remove a trailing newline to avoid auto-running when pasting + if (textContent.endsWith("\n")) { + textContent = textContent.slice(0, -1) + } + return textContent +} diff --git a/main/_static/css/badge_only.css b/main/_static/css/badge_only.css new file mode 100644 index 00000000..88ba55b9 --- /dev/null +++ b/main/_static/css/badge_only.css @@ -0,0 +1 @@ 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Languages
+ ${config.projects.translations + .map( + (translation) => ` +
+ ${translation.language.code} +
+ `, + ) + .join("\n")} + + `; + return languagesHTML; + } + + function renderVersions(config) { + if (!config.versions.active.length) { + return ""; + } + const versionsHTML = ` +
+
Versions
+ ${config.versions.active + .map( + (version) => ` +
+ ${version.slug} +
+ `, + ) + .join("\n")} +
+ `; + return versionsHTML; + } + + function renderDownloads(config) { + if (!Object.keys(config.versions.current.downloads).length) { + return ""; + } + const downloadsNameDisplay = { + pdf: "PDF", + epub: "Epub", + htmlzip: "HTML", + }; + + const downloadsHTML = ` +
+
Downloads
+ ${Object.entries(config.versions.current.downloads) + .map( + ([name, url]) => ` +
+ ${downloadsNameDisplay[name]} +
+ `, + ) + .join("\n")} +
+ `; + return downloadsHTML; + } + + document.addEventListener("readthedocs-addons-data-ready", function (event) { + const config = event.detail.data(); + + const flyout = ` +
+ + Read the Docs + v: ${config.versions.current.slug} + + +
+
+ ${renderLanguages(config)} + ${renderVersions(config)} + ${renderDownloads(config)} +
+
On Read the Docs
+
+ Project Home +
+
+ Builds +
+
+ Downloads +
+
+
+
Search
+
+
+ +
+
+
+
+ + Hosted by Read the Docs + +
+
+ `; + + // Inject the generated flyout into the body HTML element. + document.body.insertAdjacentHTML("beforeend", flyout); + + // Trigger the Read the Docs Addons Search modal when clicking on the "Search docs" input from inside the flyout. + document + .querySelector("#flyout-search-form") + .addEventListener("focusin", () => { + const event = new CustomEvent("readthedocs-search-show"); + document.dispatchEvent(event); + }); + }) +} + +if (themeLanguageSelector || themeVersionSelector) { + function onSelectorSwitch(event) { + const option = event.target.selectedIndex; + const item = event.target.options[option]; + window.location.href = item.dataset.url; + } + + document.addEventListener("readthedocs-addons-data-ready", function (event) { + const config = event.detail.data(); + + const versionSwitch = document.querySelector( + "div.switch-menus > div.version-switch", + ); + if (themeVersionSelector) { + let versions = config.versions.active; + if (config.versions.current.hidden || config.versions.current.type === "external") { + versions.unshift(config.versions.current); + } + const versionSelect = ` + + `; + + versionSwitch.innerHTML = versionSelect; + versionSwitch.firstElementChild.addEventListener("change", onSelectorSwitch); + } + + const languageSwitch = document.querySelector( + "div.switch-menus > div.language-switch", + ); + + if (themeLanguageSelector) { + if (config.projects.translations.length) { + // Add the current language to the options on the selector + let languages = config.projects.translations.concat( + config.projects.current, + ); + languages = languages.sort((a, b) => + a.language.name.localeCompare(b.language.name), + ); + + const languageSelect = ` + + `; + + languageSwitch.innerHTML = languageSelect; + languageSwitch.firstElementChild.addEventListener("change", onSelectorSwitch); + } + else { + languageSwitch.remove(); + } + } + }); +} + +document.addEventListener("readthedocs-addons-data-ready", function (event) { + // Trigger the Read the Docs Addons Search modal when clicking on "Search docs" input from the topnav. + document + .querySelector("[role='search'] input") + .addEventListener("focusin", () => { + const event = new CustomEvent("readthedocs-search-show"); + document.dispatchEvent(event); + }); +}); \ No newline at end of file diff --git a/main/_static/language_data.js b/main/_static/language_data.js new file mode 100644 index 00000000..c7fe6c6f --- /dev/null +++ b/main/_static/language_data.js @@ -0,0 +1,192 @@ +/* + * This script contains the language-specific data used by searchtools.js, + * namely the list of stopwords, stemmer, scorer and splitter. + */ + +var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"]; + + +/* Non-minified version is copied as a separate JS file, if available */ + +/** + * Porter Stemmer + */ +var Stemmer = function() { + + var step2list = { + ational: 'ate', + tional: 'tion', + enci: 'ence', + anci: 'ance', + izer: 'ize', + bli: 'ble', + alli: 'al', + entli: 'ent', + eli: 'e', + ousli: 'ous', + ization: 'ize', + ation: 'ate', + ator: 'ate', + alism: 'al', + iveness: 'ive', + fulness: 'ful', + ousness: 'ous', + aliti: 'al', + iviti: 'ive', + biliti: 'ble', + logi: 'log' + }; + + var step3list = { + icate: 'ic', + ative: '', + alize: 'al', + iciti: 'ic', + ical: 'ic', + ful: '', + ness: '' + }; + + var c = "[^aeiou]"; // consonant + var v = "[aeiouy]"; // vowel + var C = c + "[^aeiouy]*"; // consonant sequence + var V = v + "[aeiou]*"; // vowel sequence + + var mgr0 = "^(" + C + ")?" + V + C; // [C]VC... is m>0 + var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$"; // [C]VC[V] is m=1 + var mgr1 = "^(" + C + ")?" + V + C + V + C; // [C]VCVC... is m>1 + var s_v = "^(" + C + ")?" + v; // vowel in stem + + this.stemWord = function (w) { + var stem; + var suffix; + var firstch; + var origword = w; + + if (w.length < 3) + return w; + + var re; + var re2; + var re3; + var re4; + + firstch = w.substr(0,1); + if (firstch == "y") + w = firstch.toUpperCase() + w.substr(1); + + // Step 1a + re = /^(.+?)(ss|i)es$/; + re2 = /^(.+?)([^s])s$/; + + if (re.test(w)) + w = w.replace(re,"$1$2"); + else if (re2.test(w)) + w = w.replace(re2,"$1$2"); + + // Step 1b + re = /^(.+?)eed$/; + re2 = /^(.+?)(ed|ing)$/; + if (re.test(w)) { + var fp = re.exec(w); + re = new RegExp(mgr0); + if (re.test(fp[1])) { + re = /.$/; + w = w.replace(re,""); + } + } + else if (re2.test(w)) { + var fp = re2.exec(w); + stem = fp[1]; + re2 = new RegExp(s_v); + if (re2.test(stem)) { + w = stem; + re2 = /(at|bl|iz)$/; + re3 = new RegExp("([^aeiouylsz])\\1$"); + re4 = new RegExp("^" + C + v + "[^aeiouwxy]$"); + if (re2.test(w)) + w = w + "e"; + else if (re3.test(w)) { + re = /.$/; + w = w.replace(re,""); + } + else if (re4.test(w)) + w = w + "e"; + } + } + + // Step 1c + re = /^(.+?)y$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(s_v); + if (re.test(stem)) + w = stem + "i"; + } + + // Step 2 + re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = new RegExp(mgr0); + if (re.test(stem)) + w = stem + step2list[suffix]; + } + + // Step 3 + re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = new RegExp(mgr0); + if (re.test(stem)) + w = stem + step3list[suffix]; + } + + // Step 4 + re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/; + re2 = /^(.+?)(s|t)(ion)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(mgr1); + if (re.test(stem)) + w = stem; + } + else if (re2.test(w)) { + var fp = re2.exec(w); + stem = fp[1] + fp[2]; + re2 = new RegExp(mgr1); + if (re2.test(stem)) + w = stem; + } + + // Step 5 + re = /^(.+?)e$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(mgr1); + re2 = new RegExp(meq1); + re3 = new RegExp("^" + C + v + "[^aeiouwxy]$"); + if (re.test(stem) || (re2.test(stem) && !(re3.test(stem)))) + w = stem; + } + re = /ll$/; + re2 = new RegExp(mgr1); + if (re.test(w) && re2.test(w)) { + re = /.$/; + w = w.replace(re,""); + } + + // and turn initial Y back to y + if (firstch == "y") + w = firstch.toLowerCase() + w.substr(1); + return w; + } +} + diff --git a/main/_static/minus.png b/main/_static/minus.png new file mode 100644 index 00000000..d96755fd Binary files /dev/null and b/main/_static/minus.png differ diff --git a/main/_static/placeholder b/main/_static/placeholder new file mode 100644 index 00000000..0173ef8b --- /dev/null +++ b/main/_static/placeholder @@ -0,0 +1 @@ +PLACE_HOLDER diff --git a/main/_static/plus.png b/main/_static/plus.png new file mode 100644 index 00000000..7107cec9 Binary files /dev/null and b/main/_static/plus.png differ diff --git a/main/_static/pygments.css b/main/_static/pygments.css new file mode 100644 index 00000000..84ab3030 --- /dev/null +++ b/main/_static/pygments.css @@ -0,0 +1,75 @@ +pre { line-height: 125%; } +td.linenos .normal { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; } +span.linenos { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; } +td.linenos .special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; } +span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; } +.highlight .hll { background-color: #ffffcc } +.highlight { background: #f8f8f8; } +.highlight .c { color: #3D7B7B; font-style: italic } /* Comment */ +.highlight .err { border: 1px solid #FF0000 } /* Error */ +.highlight .k { color: #008000; font-weight: bold } /* Keyword */ +.highlight .o { color: #666666 } /* Operator */ +.highlight .ch { color: #3D7B7B; font-style: italic } /* Comment.Hashbang */ +.highlight .cm { color: #3D7B7B; font-style: italic } /* Comment.Multiline */ +.highlight .cp { color: #9C6500 } /* Comment.Preproc */ +.highlight .cpf { color: #3D7B7B; font-style: italic } /* Comment.PreprocFile */ +.highlight .c1 { color: #3D7B7B; font-style: italic } /* Comment.Single */ +.highlight .cs { color: #3D7B7B; font-style: italic } /* Comment.Special */ +.highlight .gd { color: #A00000 } /* Generic.Deleted */ +.highlight .ge { font-style: italic } /* Generic.Emph */ +.highlight .ges { font-weight: bold; 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font-style: italic } /* Literal.String.Doc */ +.highlight .s2 { color: #BA2121 } /* Literal.String.Double */ +.highlight .se { color: #AA5D1F; font-weight: bold } /* Literal.String.Escape */ +.highlight .sh { color: #BA2121 } /* Literal.String.Heredoc */ +.highlight .si { color: #A45A77; font-weight: bold } /* Literal.String.Interpol */ +.highlight .sx { color: #008000 } /* Literal.String.Other */ +.highlight .sr { color: #A45A77 } /* Literal.String.Regex */ +.highlight .s1 { color: #BA2121 } /* Literal.String.Single */ +.highlight .ss { color: #19177C } /* Literal.String.Symbol */ +.highlight .bp { color: #008000 } /* Name.Builtin.Pseudo */ +.highlight .fm { color: #0000FF } /* Name.Function.Magic */ +.highlight .vc { color: #19177C } /* Name.Variable.Class */ +.highlight .vg { color: #19177C } /* Name.Variable.Global */ +.highlight .vi { color: #19177C } /* Name.Variable.Instance */ +.highlight .vm { color: #19177C } /* Name.Variable.Magic */ +.highlight .il { color: #666666 } /* Literal.Number.Integer.Long */ \ No newline at end of file diff --git a/main/_static/searchtools.js b/main/_static/searchtools.js new file mode 100644 index 00000000..2c774d17 --- /dev/null +++ b/main/_static/searchtools.js @@ -0,0 +1,632 @@ +/* + * Sphinx JavaScript utilities for the full-text search. + */ +"use strict"; + +/** + * Simple result scoring code. + */ +if (typeof Scorer === "undefined") { + var Scorer = { + // Implement the following function to further tweak the score for each result + // The function takes a result array [docname, title, anchor, descr, score, filename] + // and returns the new score. + /* + score: result => { + const [docname, title, anchor, descr, score, filename, kind] = result + return score + }, + */ + + // query matches the full name of an object + objNameMatch: 11, + // or matches in the last dotted part of the object name + objPartialMatch: 6, + // Additive scores depending on the priority of the object + objPrio: { + 0: 15, // used to be importantResults + 1: 5, // used to be objectResults + 2: -5, // used to be unimportantResults + }, + // Used when the priority is not in the mapping. + objPrioDefault: 0, + + // query found in title + title: 15, + partialTitle: 7, + // query found in terms + term: 5, + partialTerm: 2, + }; +} + +// Global search result kind enum, used by themes to style search results. +class SearchResultKind { + static get index() { return "index"; } + static get object() { return "object"; } + static get text() { return "text"; } + static get title() { return "title"; } +} + +const _removeChildren = (element) => { + while (element && element.lastChild) element.removeChild(element.lastChild); +}; + +/** + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping + */ +const _escapeRegExp = (string) => + string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string + +const _displayItem = (item, searchTerms, highlightTerms) => { + const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; + const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; + const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; + const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; + const contentRoot = document.documentElement.dataset.content_root; + + const [docName, title, anchor, descr, score, _filename, kind] = item; + + let listItem = document.createElement("li"); + // Add a class representing the item's type: + // can be used by a theme's CSS selector for styling + // See SearchResultKind for the class names. + listItem.classList.add(`kind-${kind}`); + let requestUrl; + let linkUrl; + if (docBuilder === "dirhtml") { + // dirhtml builder + let dirname = docName + "/"; + if (dirname.match(/\/index\/$/)) + dirname = dirname.substring(0, dirname.length - 6); + else if (dirname === "index/") dirname = ""; + requestUrl = contentRoot + dirname; + linkUrl = requestUrl; + } else { + // normal html builders + requestUrl = contentRoot + docName + docFileSuffix; + linkUrl = docName + docLinkSuffix; + } + let linkEl = listItem.appendChild(document.createElement("a")); + linkEl.href = linkUrl + anchor; + linkEl.dataset.score = score; + linkEl.innerHTML = title; + if (descr) { + listItem.appendChild(document.createElement("span")).innerHTML = + " (" + descr + ")"; + // highlight search terms in the description + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + } + else if (showSearchSummary) + fetch(requestUrl) + .then((responseData) => responseData.text()) + .then((data) => { + if (data) + listItem.appendChild( + Search.makeSearchSummary(data, searchTerms, anchor) + ); + // highlight search terms in the summary + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + }); + Search.output.appendChild(listItem); +}; +const _finishSearch = (resultCount) => { + Search.stopPulse(); + Search.title.innerText = _("Search Results"); + if (!resultCount) + Search.status.innerText = Documentation.gettext( + "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." + ); + else + Search.status.innerText = Documentation.ngettext( + "Search finished, found one page matching the search query.", + "Search finished, found ${resultCount} pages matching the search query.", + resultCount, + ).replace('${resultCount}', resultCount); +}; +const _displayNextItem = ( + results, + resultCount, + searchTerms, + highlightTerms, +) => { + // results left, load the summary and display it + // this is intended to be dynamic (don't sub resultsCount) + if (results.length) { + _displayItem(results.pop(), searchTerms, highlightTerms); + setTimeout( + () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), + 5 + ); + } + // search finished, update title and status message + else _finishSearch(resultCount); +}; +// Helper function used by query() to order search results. +// Each input is an array of [docname, title, anchor, descr, score, filename, kind]. +// Order the results by score (in opposite order of appearance, since the +// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. +const _orderResultsByScoreThenName = (a, b) => { + const leftScore = a[4]; + const rightScore = b[4]; + if (leftScore === rightScore) { + // same score: sort alphabetically + const leftTitle = a[1].toLowerCase(); + const rightTitle = b[1].toLowerCase(); + if (leftTitle === rightTitle) return 0; + return leftTitle > rightTitle ? -1 : 1; // inverted is intentional + } + return leftScore > rightScore ? 1 : -1; +}; + +/** + * Default splitQuery function. Can be overridden in ``sphinx.search`` with a + * custom function per language. + * + * The regular expression works by splitting the string on consecutive characters + * that are not Unicode letters, numbers, underscores, or emoji characters. + * This is the same as ``\W+`` in Python, preserving the surrogate pair area. + */ +if (typeof splitQuery === "undefined") { + var splitQuery = (query) => query + .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) + .filter(term => term) // remove remaining empty strings +} + +/** + * Search Module + */ +const Search = { + _index: null, + _queued_query: null, + _pulse_status: -1, + + htmlToText: (htmlString, anchor) => { + const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); + for (const removalQuery of [".headerlink", "script", "style"]) { + htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); + } + if (anchor) { + const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); + if (anchorContent) return anchorContent.textContent; + + console.warn( + `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` + ); + } + + // if anchor not specified or not found, fall back to main content + const docContent = htmlElement.querySelector('[role="main"]'); + if (docContent) return docContent.textContent; + + console.warn( + "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." + ); + return ""; + }, + + init: () => { + const query = new URLSearchParams(window.location.search).get("q"); + document + .querySelectorAll('input[name="q"]') + .forEach((el) => (el.value = query)); + if (query) Search.performSearch(query); + }, + + loadIndex: (url) => + (document.body.appendChild(document.createElement("script")).src = url), + + setIndex: (index) => { + Search._index = index; + if (Search._queued_query !== null) { + const query = Search._queued_query; + Search._queued_query = null; + Search.query(query); + } + }, + + hasIndex: () => Search._index !== null, + + deferQuery: (query) => (Search._queued_query = query), + + stopPulse: () => (Search._pulse_status = -1), + + startPulse: () => { + if (Search._pulse_status >= 0) return; + + const pulse = () => { + Search._pulse_status = (Search._pulse_status + 1) % 4; + Search.dots.innerText = ".".repeat(Search._pulse_status); + if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); + }; + pulse(); + }, + + /** + * perform a search for something (or wait until index is loaded) + */ + performSearch: (query) => { + // create the required interface elements + const searchText = document.createElement("h2"); + searchText.textContent = _("Searching"); + const searchSummary = document.createElement("p"); + searchSummary.classList.add("search-summary"); + searchSummary.innerText = ""; + const searchList = document.createElement("ul"); + searchList.setAttribute("role", "list"); + searchList.classList.add("search"); + + const out = document.getElementById("search-results"); + Search.title = out.appendChild(searchText); + Search.dots = Search.title.appendChild(document.createElement("span")); + Search.status = out.appendChild(searchSummary); + Search.output = out.appendChild(searchList); + + const searchProgress = document.getElementById("search-progress"); + // Some themes don't use the search progress node + if (searchProgress) { + searchProgress.innerText = _("Preparing search..."); + } + Search.startPulse(); + + // index already loaded, the browser was quick! + if (Search.hasIndex()) Search.query(query); + else Search.deferQuery(query); + }, + + _parseQuery: (query) => { + // stem the search terms and add them to the correct list + const stemmer = new Stemmer(); + const searchTerms = new Set(); + const excludedTerms = new Set(); + const highlightTerms = new Set(); + const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); + splitQuery(query.trim()).forEach((queryTerm) => { + const queryTermLower = queryTerm.toLowerCase(); + + // maybe skip this "word" + // stopwords array is from language_data.js + if ( + stopwords.indexOf(queryTermLower) !== -1 || + queryTerm.match(/^\d+$/) + ) + return; + + // stem the word + let word = stemmer.stemWord(queryTermLower); + // select the correct list + if (word[0] === "-") excludedTerms.add(word.substr(1)); + else { + searchTerms.add(word); + highlightTerms.add(queryTermLower); + } + }); + + if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js + localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) + } + + // console.debug("SEARCH: searching for:"); + // console.info("required: ", [...searchTerms]); + // console.info("excluded: ", [...excludedTerms]); + + return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; + }, + + /** + * execute search (requires search index to be loaded) + */ + _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + const allTitles = Search._index.alltitles; + const indexEntries = Search._index.indexentries; + + // Collect multiple result groups to be sorted separately and then ordered. + // Each is an array of [docname, title, anchor, descr, score, filename, kind]. + const normalResults = []; + const nonMainIndexResults = []; + + _removeChildren(document.getElementById("search-progress")); + + const queryLower = query.toLowerCase().trim(); + for (const [title, foundTitles] of Object.entries(allTitles)) { + if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { + for (const [file, id] of foundTitles) { + const score = Math.round(Scorer.title * queryLower.length / title.length); + const boost = titles[file] === title ? 1 : 0; // add a boost for document titles + normalResults.push([ + docNames[file], + titles[file] !== title ? `${titles[file]} > ${title}` : title, + id !== null ? "#" + id : "", + null, + score + boost, + filenames[file], + SearchResultKind.title, + ]); + } + } + } + + // search for explicit entries in index directives + for (const [entry, foundEntries] of Object.entries(indexEntries)) { + if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { + for (const [file, id, isMain] of foundEntries) { + const score = Math.round(100 * queryLower.length / entry.length); + const result = [ + docNames[file], + titles[file], + id ? "#" + id : "", + null, + score, + filenames[file], + SearchResultKind.index, + ]; + if (isMain) { + normalResults.push(result); + } else { + nonMainIndexResults.push(result); + } + } + } + } + + // lookup as object + objectTerms.forEach((term) => + normalResults.push(...Search.performObjectSearch(term, objectTerms)) + ); + + // lookup as search terms in fulltext + normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + + // let the scorer override scores with a custom scoring function + if (Scorer.score) { + normalResults.forEach((item) => (item[4] = Scorer.score(item))); + nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); + } + + // Sort each group of results by score and then alphabetically by name. + normalResults.sort(_orderResultsByScoreThenName); + nonMainIndexResults.sort(_orderResultsByScoreThenName); + + // Combine the result groups in (reverse) order. + // Non-main index entries are typically arbitrary cross-references, + // so display them after other results. + let results = [...nonMainIndexResults, ...normalResults]; + + // remove duplicate search results + // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept + let seen = new Set(); + results = results.reverse().reduce((acc, result) => { + let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); + if (!seen.has(resultStr)) { + acc.push(result); + seen.add(resultStr); + } + return acc; + }, []); + + return results.reverse(); + }, + + query: (query) => { + const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); + const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); + + // for debugging + //Search.lastresults = results.slice(); // a copy + // console.info("search results:", Search.lastresults); + + // print the results + _displayNextItem(results, results.length, searchTerms, highlightTerms); + }, + + /** + * search for object names + */ + performObjectSearch: (object, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const objects = Search._index.objects; + const objNames = Search._index.objnames; + const titles = Search._index.titles; + + const results = []; + + const objectSearchCallback = (prefix, match) => { + const name = match[4] + const fullname = (prefix ? prefix + "." : "") + name; + const fullnameLower = fullname.toLowerCase(); + if (fullnameLower.indexOf(object) < 0) return; + + let score = 0; + const parts = fullnameLower.split("."); + + // check for different match types: exact matches of full name or + // "last name" (i.e. last dotted part) + if (fullnameLower === object || parts.slice(-1)[0] === object) + score += Scorer.objNameMatch; + else if (parts.slice(-1)[0].indexOf(object) > -1) + score += Scorer.objPartialMatch; // matches in last name + + const objName = objNames[match[1]][2]; + const title = titles[match[0]]; + + // If more than one term searched for, we require other words to be + // found in the name/title/description + const otherTerms = new Set(objectTerms); + otherTerms.delete(object); + if (otherTerms.size > 0) { + const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); + if ( + [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) + ) + return; + } + + let anchor = match[3]; + if (anchor === "") anchor = fullname; + else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; + + const descr = objName + _(", in ") + title; + + // add custom score for some objects according to scorer + if (Scorer.objPrio.hasOwnProperty(match[2])) + score += Scorer.objPrio[match[2]]; + else score += Scorer.objPrioDefault; + + results.push([ + docNames[match[0]], + fullname, + "#" + anchor, + descr, + score, + filenames[match[0]], + SearchResultKind.object, + ]); + }; + Object.keys(objects).forEach((prefix) => + objects[prefix].forEach((array) => + objectSearchCallback(prefix, array) + ) + ); + return results; + }, + + /** + * search for full-text terms in the index + */ + performTermsSearch: (searchTerms, excludedTerms) => { + // prepare search + const terms = Search._index.terms; + const titleTerms = Search._index.titleterms; + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + + const scoreMap = new Map(); + const fileMap = new Map(); + + // perform the search on the required terms + searchTerms.forEach((word) => { + const files = []; + const arr = [ + { files: terms[word], score: Scorer.term }, + { files: titleTerms[word], score: Scorer.title }, + ]; + // add support for partial matches + if (word.length > 2) { + const escapedWord = _escapeRegExp(word); + if (!terms.hasOwnProperty(word)) { + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + } + if (!titleTerms.hasOwnProperty(word)) { + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); + }); + } + } + + // no match but word was a required one + if (arr.every((record) => record.files === undefined)) return; + + // found search word in contents + arr.forEach((record) => { + if (record.files === undefined) return; + + let recordFiles = record.files; + if (recordFiles.length === undefined) recordFiles = [recordFiles]; + files.push(...recordFiles); + + // set score for the word in each file + recordFiles.forEach((file) => { + if (!scoreMap.has(file)) scoreMap.set(file, {}); + scoreMap.get(file)[word] = record.score; + }); + }); + + // create the mapping + files.forEach((file) => { + if (!fileMap.has(file)) fileMap.set(file, [word]); + else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); + }); + }); + + // now check if the files don't contain excluded terms + const results = []; + for (const [file, wordList] of fileMap) { + // check if all requirements are matched + + // as search terms with length < 3 are discarded + const filteredTermCount = [...searchTerms].filter( + (term) => term.length > 2 + ).length; + if ( + wordList.length !== searchTerms.size && + wordList.length !== filteredTermCount + ) + continue; + + // ensure that none of the excluded terms is in the search result + if ( + [...excludedTerms].some( + (term) => + terms[term] === file || + titleTerms[term] === file || + (terms[term] || []).includes(file) || + (titleTerms[term] || []).includes(file) + ) + ) + break; + + // select one (max) score for the file. + const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); + // add result to the result list + results.push([ + docNames[file], + titles[file], + "", + null, + score, + filenames[file], + SearchResultKind.text, + ]); + } + return results; + }, + + /** + * helper function to return a node containing the + * search summary for a given text. keywords is a list + * of stemmed words. + */ + makeSearchSummary: (htmlText, keywords, anchor) => { + const text = Search.htmlToText(htmlText, anchor); + if (text === "") return null; + + const textLower = text.toLowerCase(); + const actualStartPosition = [...keywords] + .map((k) => textLower.indexOf(k.toLowerCase())) + .filter((i) => i > -1) + .slice(-1)[0]; + const startWithContext = Math.max(actualStartPosition - 120, 0); + + const top = startWithContext === 0 ? "" : "..."; + const tail = startWithContext + 240 < text.length ? "..." : ""; + + let summary = document.createElement("p"); + summary.classList.add("context"); + summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; + + return summary; + }, +}; + +_ready(Search.init); diff --git a/main/_static/sphinx_highlight.js b/main/_static/sphinx_highlight.js new file mode 100644 index 00000000..8a96c69a --- /dev/null +++ b/main/_static/sphinx_highlight.js @@ -0,0 +1,154 @@ +/* Highlighting utilities for Sphinx HTML documentation. */ +"use strict"; + +const SPHINX_HIGHLIGHT_ENABLED = true + +/** + * highlight a given string on a node by wrapping it in + * span elements with the given class name. + */ +const _highlight = (node, addItems, text, className) => { + if (node.nodeType === Node.TEXT_NODE) { + const val = node.nodeValue; + const parent = node.parentNode; + const pos = val.toLowerCase().indexOf(text); + if ( + pos >= 0 && + !parent.classList.contains(className) && + !parent.classList.contains("nohighlight") + ) { + let span; + + const closestNode = parent.closest("body, svg, foreignObject"); + const isInSVG = closestNode && closestNode.matches("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.classList.add(className); + } + + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + const rest = document.createTextNode(val.substr(pos + text.length)); + parent.insertBefore( + span, + parent.insertBefore( + rest, + node.nextSibling + ) + ); + node.nodeValue = val.substr(0, pos); + /* There may be more occurrences of search term in this node. So call this + * function recursively on the remaining fragment. + */ + _highlight(rest, addItems, text, className); + + if (isInSVG) { + const rect = document.createElementNS( + "http://www.w3.org/2000/svg", + "rect" + ); + const bbox = parent.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute("class", className); + addItems.push({ parent: parent, target: rect }); + } + } + } else if (node.matches && !node.matches("button, select, textarea")) { + node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); + } +}; +const _highlightText = (thisNode, text, className) => { + let addItems = []; + _highlight(thisNode, addItems, text, className); + addItems.forEach((obj) => + obj.parent.insertAdjacentElement("beforebegin", obj.target) + ); +}; + +/** + * Small JavaScript module for the documentation. + */ +const SphinxHighlight = { + + /** + * highlight the search words provided in localstorage in the text + */ + highlightSearchWords: () => { + if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight + + // get and clear terms from localstorage + const url = new URL(window.location); + const highlight = + localStorage.getItem("sphinx_highlight_terms") + || url.searchParams.get("highlight") + || ""; + localStorage.removeItem("sphinx_highlight_terms") + url.searchParams.delete("highlight"); + window.history.replaceState({}, "", url); + + // get individual terms from highlight string + const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); + if (terms.length === 0) return; // nothing to do + + // There should never be more than one element matching "div.body" + const divBody = document.querySelectorAll("div.body"); + const body = divBody.length ? divBody[0] : document.querySelector("body"); + window.setTimeout(() => { + terms.forEach((term) => _highlightText(body, term, "highlighted")); + }, 10); + + const searchBox = document.getElementById("searchbox"); + if (searchBox === null) return; + searchBox.appendChild( + document + .createRange() + .createContextualFragment( + '

' + + '' + + _("Hide Search Matches") + + "

" + ) + ); + }, + + /** + * helper function to hide the search marks again + */ + hideSearchWords: () => { + document + .querySelectorAll("#searchbox .highlight-link") + .forEach((el) => el.remove()); + document + .querySelectorAll("span.highlighted") + .forEach((el) => el.classList.remove("highlighted")); + localStorage.removeItem("sphinx_highlight_terms") + }, + + initEscapeListener: () => { + // only install a listener if it is really needed + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; + if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { + SphinxHighlight.hideSearchWords(); + event.preventDefault(); + } + }); + }, +}; + +_ready(() => { + /* Do not call highlightSearchWords() when we are on the search page. + * It will highlight words from the *previous* search query. + */ + if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); + SphinxHighlight.initEscapeListener(); +}); diff --git a/main/genindex.html b/main/genindex.html new file mode 100644 index 00000000..e3dc714f --- /dev/null +++ b/main/genindex.html @@ -0,0 +1,137 @@ + + + + + + + + Index — Phoebus 1.0.0 documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Index
    • +
  • +
    • +
+
+
+
+
+ + +

Index

+ +
+ U + +
+

U

+ + +
+ + + +
+
+
+ +
+ +
+

© Copyright 2024, Triad National Security.

+
+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
+
+
+
+
+ +
+ + Other Versions + v: main + + +
+
+
Branches
+
main
+
blb/frontier
+
+
+
+ + + \ No newline at end of file diff --git a/main/index.html b/main/index.html new file mode 100644 index 00000000..5e25feda --- /dev/null +++ b/main/index.html @@ -0,0 +1,165 @@ + + + + + + + + + Phoebus: Performance portable GRRMHD for supernovae, mergers, and more — Phoebus 1.0.0 documentation + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Phoebus: Performance portable GRRMHD for supernovae, mergers, and more
    • +
  • + View page source +
    • +
+
+
+
+
+ +
+

Phoebus: Performance portable GRRMHD for supernovae, mergers, and more

+

Phoebus is a performance portable general relativistic neutrino radiation magnetohydrodynamics code built upon the Parthenon adaptive mesh refinement framework.

+
+

Key Features

+
    +

  • Finite volume GRMHD

    • +

  • Neutrino transport with Monte Carlo and moment methods

    • +

  • Analytic and tabulated spacetimes

    • +

  • Monopolar general relativistic gravity for core-collapse supernovae

    • +

  • Lagrangian tracer particles

    • +

  • Support for arbitrary equations of state

    • +
+
+

Note

+

These docs are under active development.

+
+
+

Contents:

+ +
+
+
+
+

Indices and tables

+ +
+ + +
+
+ +
+
+
+
+ +
+ + Other Versions + v: main + + +
+
+
Branches
+
main
+
blb/frontier
+
+
+
+ + + \ No newline at end of file diff --git a/main/objects.inv b/main/objects.inv new file mode 100644 index 00000000..24933d14 --- /dev/null +++ b/main/objects.inv @@ -0,0 +1,7 @@ +# Sphinx inventory version 2 +# Project: Phoebus +# Version: +# The remainder of this file is compressed using zlib. +xڽSKO0Wǖ+.cpjqEvkTMJvox_ߖ'M}& p~x +ݴtW `k]vNH=M,{mDQ6?Wnj[;8_فgqjIQh JQHzb/b\-$ 7qH[ C3XjkCͶ Q& 5F( Xۦ |,>|̀CɪxrB6X$oU]rϨW4@ոNQ@)rRLrzUǵ#)Sou +6H?eZW9ZVyOhNL@ij4+a{R)Ŀ^]^ \ No newline at end of file diff --git a/main/search.html b/main/search.html new file mode 100644 index 00000000..09f7635e --- /dev/null +++ b/main/search.html @@ -0,0 +1,143 @@ + + + + + + + + Search — Phoebus 1.0.0 documentation + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
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  • Search
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+
+
+
+
+ + + + +
+ +
+ +
+
+
+ +
+ +
+

© Copyright 2024, Triad National Security.

+
+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
+
+
+
+
+ +
+ + Other Versions + v: main + + +
+
+
Branches
+
main
+
blb/frontier
+
+
+
+ + + + + + + + \ No newline at end of file diff --git a/main/searchindex.js b/main/searchindex.js new file mode 100644 index 00000000..61d09607 --- /dev/null +++ b/main/searchindex.js @@ -0,0 +1 @@ +Search.setIndex({"alltitles": {"A Large Ecosystem": [[3, "a-large-ecosystem"]], "Adding Tests": [[3, "adding-tests"]], "Approval by Vote:": [[4, "approval-by-vote"]], "Becoming a Contributor": [[3, "becoming-a-contributor"]], "Build Options": [[1, "build-options"]], "Building": [[1, null]], "Building documentation locally": [[5, "building-documentation-locally"]], "Cmake machine configs": [[1, "cmake-machine-configs"]], "Code of Conduct": [[2, null]], "Communication and Connection:": [[4, "communication-and-connection"]], "Contents:": [[0, null]], "Contributing": [[3, null]], "Cuda": [[1, "cuda"]], "Example builds": [[1, "example-builds"]], "Expectations for code review": [[3, "expectations-for-code-review"]], "Expectations of code reviewers": [[3, "expectations-of-code-reviewers"]], 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3, "you": [1, 3], "your": 3, "yurlungur": 3, "z": 6, "z_max": 6, "z_min": 6}, "titles": ["Phoebus: Performance portable GRRMHD for supernovae, mergers, and more", "Building", "Code of Conduct", "Contributing", "Organizational Structure", "How to Use Sphinx for Writing Docs", "Tracer Particles"], "titleterms": {"A": 3, "ad": 3, "approv": 4, "becom": 3, "build": [1, 5], "cmake": 1, "code": [1, 2, 3], "commun": 4, "conduct": 2, "config": 1, "connect": 4, "content": 0, "contribut": 3, "contributor": 3, "convert": 5, "cuda": 1, "current": 3, "depend": 5, "doc": 5, "docker": 5, "document": 5, "ecosystem": 3, "everyon": 3, "exampl": 1, "expect": 3, "extern": 1, "featur": 0, "file": 5, "from": 3, "gener": 3, "get": 5, "github": 5, "grrmhd": 0, "have": 5, "how": 5, "indic": 0, "info": 5, "kei": 0, "larg": 3, "list": 3, "local": 5, "machin": 1, "maintain": 3, "markdown": 5, "memorandum": 4, "merger": 0, "more": [0, 5], "mpi": 1, "obtain": 1, "onli": 1, "openmp": 1, "option": 1, "organiz": 4, "parallel": 1, "particl": 6, "perform": 0, "perspect": 3, "phoebu": [0, 3], "portabl": 0, "prerequisit": 1, "principl": 3, "protocol": 3, "pull": 3, "regress": 3, "request": 3, "requir": 1, "review": 3, "rst": 5, "run": 1, "sourc": 1, "sphinx": 5, "structur": 4, "submodul": 1, "suit": 3, "supernova": 0, "tabl": 0, "team": 4, "test": 3, "tracer": 6, "understand": 4, "unit": 3, "us": 5, "vote": 4, "write": 5, "you": 5, "your": 5}}) \ No newline at end of file diff --git a/main/sitemap.xml b/main/sitemap.xml new file mode 100644 index 00000000..7c1cea97 --- /dev/null +++ b/main/sitemap.xml @@ -0,0 +1,2 @@ + +https://lanl.github.io/phoebusen/index.htmlhttps://lanl.github.io/phoebusen/src/building.htmlhttps://lanl.github.io/phoebusen/src/code_of_conduct.htmlhttps://lanl.github.io/phoebusen/src/contributing.htmlhttps://lanl.github.io/phoebusen/src/governance.htmlhttps://lanl.github.io/phoebusen/src/sphinx-doc.htmlhttps://lanl.github.io/phoebusen/src/tracers.htmlhttps://lanl.github.io/phoebusen/genindex.htmlhttps://lanl.github.io/phoebusen/search.html \ No newline at end of file diff --git a/main/src/building.html b/main/src/building.html new file mode 100644 index 00000000..5ae14341 --- /dev/null +++ b/main/src/building.html @@ -0,0 +1,336 @@ + + + + + + + + + Building — Phoebus 1.0.0 documentation + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Building

+
+

Obtaining the Source Code

+

phoebus uses submodules extensively. To make sure you get them all, +clone it as

+
git clone --recursive git@github.com:lanl/phoebus.git
+
+
+

or as

+
git clone git@github.com:lanl/phoebus.git
+cd phoebus
+git submodule update --init --recursive
+
+
+
+
+

Prerequisites

+

To build phoebus, you need to create a build directly, as in-source builds are not supported. +After cloning the repository,

+
cd phoebus
+mkdir bin
+cd bin
+
+
+
+
+

Example builds

+

Below are some example build commands

+
+

MPI-parallel only

+

The following will build phoebus with MPI parallelism but no shared +memory parallelism

+
cmake ..
+make -j
+
+
+
+
+

OpenMP-parallel

+

The following will build phoebus with OpenMP parallelism only

+
cmake -DPHOEBUS_ENABLE_MPI=Off -DPHOEBUS_ENABLE_OPENMP=ON ..
+make -j
+
+
+
+
+

Cuda

+

The following will build phoebus with no MPI or OpenMP parallelism.

+
cmake -DPHOEBUS_ENABLE_CUDA=On -DCMAKE_CXX_COMPILER=${HOME}/phoebus/external/singularity-eos/utils/kokkos/bin/nvcc_wrapper -DKokkos_ARCH_HSW=ON -DKokkos_ARCH_VOLTA70=ON -DPHOEBUS_ENABLE_MPI=OFF ..
+
+
+

A few notes for this one: - Note here the -DCMAKE_CXX_COMPILER flag. +This is necessary. You must set the compiler to nvcc_wrapper +provided by Kokkos. - Note the -DKokkos_ARCH_* flags. Those set the +host and device microarchitectures and are required. The choice here is +on an x86_64 machine with a volta GPU.

+
+
+
+

Build Options

+

The build options explicitly provided by phoebus are:

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Option

Default

Comment

PHOEBUS_ENABLE_CUDA

OFF

Cuda

PHOEBUS_ENABLE_HDF5

ON

HDF5. Required for output and restarts.

PHOEBUS_ENABLE_MPI

ON

MPI. Required for distributed memory +parallelism.

PHOEBUS_ENABLE_OPENMP

OFF

OpenMP. Required for shared memory +parallelism.

MACHINE_CFG

None

Machine-specific config file, optional.

+

Some relevant settings from Parthenon and Kokkos you may need to play +with are:

+ + + + + + + + + + + + + + + + + +

Option

Default

Comment

CMAKE_CXX_COMPILER

None

Must be set to nvcc_wrapper with cuda +backend

Kokkos_ARCH_XXXX

OFF

You must set the GPU architecture when +compiling for Cuda

+

You can see all the Parthenon build options +here +and all the Kokkos build options +here

+
+
+

Cmake machine configs

+

If you are proficient with cmake You can optionally write a +cmake file that sets the configure parameters that you like on a +given machine. Both phoebus and parthenon can make use of it. +You can point to the file with

+
-DMACHINE_CFG=path/to/machine/file
+
+
+

at config time or by setting the environment variable MACHINE_CFG to +point at it, e.g.,

+
export MACHINE_CFG=path/to/machine/file
+
+
+

An example machine file might look like

+
# Machine file for x86_64-volta on Darwin
+message(STATUS "Loading machine configuration for Darwin x86-volta node")
+message(STATUS "Assumes: module load module load gcc/7.4.0 cuda/10.2 openmpi/4.0.3-gcc_7.4.0 anaconda/Anaconda3.2019.10 cmake && spack load hdf5")
+message(STATUS "Also assumes you have a valid spack installation loaded.")
+
+set(PHOEBUS_ENABLE_CUDA ON CACHE BOOL "Cuda backend")
+set(PHOEBUS_ENABLE_MPI OFF CACHE BOOL "No MPI")
+set(Kokkos_ARCH_HSW ON CACHE BOOL "Haswell target")
+set(Kokkos_ARCH_VOLTA70 ON CACHE BOOL "volta target")
+set(CMAKE_CXX_COMPILER /home/jonahm/phoebus/external/parthenon/external/Kokkos/bin/nvcc_wrapper CACHE STRING "nvcc wrapper")
+
+
+

you could then configure and compile as

+
cmake -DMACHINE_CFG=path/to/machine/file ..
+make -j
+
+
+
+
+

Running

+

Run phoebus from the build directory as

+
./src/phoebus -i path/to/input/file.pin
+
+
+

The input files are in phoebus/inputs/*. There’s typically one input +file per problem setup file.

+
+
+

Submodules

+
    +

  • parthenon asynchronous tasking and block-AMR infrastructure

    • +

  • singularity-eos provides performance-portable equations of state +and PTE solvers

    • +

  • singularity-opac provides performance-portable opacities and +emissivities

    • +

  • Kokkos provides performance portable shared-memory parallelism. +It allows our loops to be CUDA, OpenMP, or something else. By default +we use the Kokkos shipped with parthenon.

    • +
+
+
+

External (Required)

+
    +

  • cmake for building

    • +
+
+
+

Optional

+
    +

  • hdf5 for output (must be parallel if MPI is enabled)

    • +

  • MPI for distributed memory parallelism

    • +

  • python3 for visualization

    • +
+
+
+ + +
+
+ +
+
+
+
+ +
+ + Other Versions + v: main + + +
+
+
Branches
+
main
+
blb/frontier
+
+
+
+ + + \ No newline at end of file diff --git a/main/src/code_of_conduct.html b/main/src/code_of_conduct.html new file mode 100644 index 00000000..52cef1e5 --- /dev/null +++ b/main/src/code_of_conduct.html @@ -0,0 +1,153 @@ + + + + + + + + + Code of Conduct — Phoebus 1.0.0 documentation + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Code of Conduct

+

We as users, members, contributors, and leaders agree to make participation in our +community a harassment-free experience for everyone. +We will interact in ways that contribute to an open, welcoming, +diverse, inclusive, and healthy community.

+

We agree to uphold the LANL Code of Conduct in all spaces relevant. +Of note:

+
-  Foster a mutually respectful working environment that is free from
+   discrimination, intimidation, and harassment (including sexual
+   harassment).
+-  Do not discriminate against others on the basis of any
+   characteristic protected by law or LANL policy.
+-  Do not engage in behaviors that create an offensive, hostile, or
+   intimidating work environment, including shouting, abusive
+   language, threats of violence, the use of obscenities or other
+   non-verbal expressions of aggression, horseplay such as kicking
+   co-workers’ chairs or using personal insults, or the use of
+   offensive nicknames or other derogatory remarks.
+-  Avoid behavior that a reasonable person would find to be demeaning
+   or humiliating.
+
+
+
+ + +
+
+ +
+
+
+
+ +
+ + Other Versions + v: main + + +
+
+
Branches
+
main
+
blb/frontier
+
+
+
+ + + \ No newline at end of file diff --git a/main/src/contributing.html b/main/src/contributing.html new file mode 100644 index 00000000..2ec01256 --- /dev/null +++ b/main/src/contributing.html @@ -0,0 +1,421 @@ + + + + + + + + + Contributing — Phoebus 1.0.0 documentation + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Contributing

+

To contribute to Phoebus, feel free to submit a pull +request or open an issue.

+
    +

  1. Create a new fork of main where your changes can be made.

    2. +

  2. After completing, create a pull request, describe the final approach +and ensure the branch has no conflicts with current Regression Tests +and Formatting Checks.

    3. +

  3. Assign external reviewers (a minimum of 1, one of which should be a +Maintainer, and which cannot be the contributor). Provide concise +description of changes.

    4. +

  4. Once comments/feedback is addressed, the PR will be merged into the +main branch and changes will be added to list of changes in the next +release.

    5. +

  5. At present, Releases (with a git version tag) for the main branch +of Phoebus will occur at a 6 to 12 month cadence or following +implementation of a major enhancement or capability to the code base.

    6. +
+

Maintainers of Phoebus will follow the same process for +contributions as above except for the following differences: they may +create branches directly within Phoebus, they will hold repository +admin privileges, and actively participate in the technical review of +contributions to Phoebus.

+
+

Pull request protocol

+

When submitting a pull request, there is a default template that is automatically +populated. The pull request should sufficiently summarize all changes. +As necessary, tests should be added for new features of bugs fixed.

+

Before a pull request will be merged, the code should be formatted. We +use clang-format for this, pinned to version 12. +The script scripts/bash/format.sh will apply clang-format +to C++ source files in the repository as well as black to python files, if available. +The script takes two CLI arguments +that may be useful, CFM, which can be set to the path for your +clang-format binary, and VERBOSE, which if set to 1 adds +useful output. For example:

+
CFM=clang-format-12 VERBOSE=1 ./scripts/bash/format.sh
+
+
+

In order for a pull request to merge, we require:

+
    +

  • Provide a thorough summary of changes, especially if they are breaking changes

    • +

  • Obey style guidleines (format with clang-format and pass the necessary test)

    • +

  • Pass the existing test suite

    • +

  • Have at least one approval from a Maintainer

    • +

  • If applicable:

    +
      +

    • Write new tests for new features or bugs

      • +

    • Include or update documentation in doc/

      • +
    +
    • +
+
+
+

Test Suite

+

Several sets of tests are triggered on a pull request: a static format +check, a docs buld, and a suite of unit and regression tests. +These are run through github’s CPU infrastructure. These tests +help ensure that modifications to the code do not break existing capabilities +and ensure a consistent code style.

+
+

Adding Tests

+

There are two primary categories of tests written in Phoebus: +unit tests and regression tests.

+
+

Unit

+

Unit tests live in tst/unit/. They are implemented using the +Catch2 unit testing framework. They are integrated with cmake +and can be run, when enabled, with ctest. There are a few necessary cmake +configurations to beuild tests:

+ + + + + + + + + + + + + + + + + +

Option

Default

Description

PHOEBUS_ENABLE_UNIT_TESTS

OFF

Enables Catch2 unit tests

PHOEBUS_ENABLE_DOWNLOADS

OFF

Enables unit tests using tabulated EOS

+
+
+

Regression

+

Regression tests run existing simulations and test against saved output +in order to verify sustained capabilities. +They are implemented in Python in +test/regression/. To run the tests you will need a Python environment with +at least numpy and h5py. Tests can be ran manually as, e.g.,

+
python linear_modes.py
+
+
+

This will build Phoebus locally in phoebus/tst/regression/build and run it in +phoebus/tst/regression/run. Ensure that these directories do not already exist. +Each script test.py has a correspodning “gold file” test.gold. +The gold files contain the gold standard data that the output of the regression test +is compared against. To generate new gold data, for example if a change is implemented +that changes the behavior of a test (not erroneously) or a new test is created, run the test +script with the --upgold option. This will create or update the corresponding .gold file. +To add a new test:

+
    +

  1. Create a new test script.

    +
      +

    • Update the modified_inputs struct to change any input deck options

      • +

    • Set the variables list to contain the quantities to test against

      • +
    +
    2. +

  2. Run the script with the --upgold option

    3. +

  3. Commit the test script and gold file

    4. +

  4. Update the CI to include the new test (phoebus/.github/workflows/tests.yml)

    5. +
+
+
+
+
+

Expectations for code review

+

Much of what follows is adapted from singularity-eos.

+
+

From the perspective of the contributor

+

Code review is an integral part of the development process +for Phoebus. You can expect at least one, perhaps many, +core developers to read your code and offer suggestions. +You should treat this much like scientific or academic peer review. +You should listen to suggestions but also feel entitled to push back +if you believe the suggestions or comments are incorrect or +are requesting too much effort.

+

Reviewers may offer conflicting advice, if this is the case, it’s an +opportunity to open a discussion and communally arrive at a good +approach. You should feel empowered to argue for which of the +conflicting solutions you prefer or to suggest a compromise. If you +don’t feel strongly, that’s fine too, but it’s best to say so to keep +the lines of communication open.

+

Big contributions may be difficult to review in one piece and you may +be requested to split your pull request into two or more separate +contributions. You may also receive many “nitpicky” comments about +code style or structure. These comments help keep a broad codebase, +with many contributors uniform in style and maintainable with +consistent expectations accross the code base. While there is no +formal style guide for now, the regular contributors have a sense for +the broad style of the project. You should take these stylistic and +“nitpicky” suggestions seriously, but you should also feel free to +push back.

+

As with any creative endeavor, we put a lot of ourselves into our +code. It can be painful to receive criticism on your contribution and +easy to take it personally. While you should resist the urge to take +offense, it is also partly code reviewer’s responsiblity to create a +constructive environment, as discussed below.

+
+
+

Expectations of code reviewers

+

A good code review builds a contribution up, rather than tearing it +down. Here are a few rules to keep code reviews constructive and +congenial:

+
    +

  • You should take the time needed to review a contribution and offer +meaningful advice. Unless a contribution is very small, limit +the times you simply click “approve” with a “looks good to me.”

    • +

  • You should keep your comments constructive. For example, rather than +saying “this pattern is bad,” try saying “at this point, you may +want to try this other pattern.”

    • +

  • Avoid language that can be misconstrued, even if it’s common +notation in the commnunity. For example, avoid phrases like “code +smell.”

    • +

  • Explain why you make a suggestion. In addition to saying “try X +instead of Y” explain why you like pattern X more than pattern Y.

    • +

  • A contributor may push back on your suggestion. Be open to the +possibility that you’re either asking too much or are incorrect in +this instance. Code review is an opportunity for everyone to learn.

    • +

  • Don’t just highlight what you don’t like. Also highlight the parts +of the pull request you do like and thank the contributor for their +effort.

    • +
+
+
+

General principle for everyone

+

It’s hard to convey tone in text correspondance. Try to read what +others write favorably and try to write in such a way that your tone +can’t be mis-interpreted as malicious.

+
+
+
+

A Large Ecosystem

+

Phoebus depends on several other open-source, Los Alamos +maintained, projects. In particular, Parthenon, singularity-eos, +singularity-opac, and spiner. +If you have issues with these projects, ideally +submit issues on the relevant github pages. However, if you can’t +figure out where an issue belongs, no big deal. Submit where you can +and we’ll engage with you to figure out how to proceed.

+
+
+

Becoming a Contributor

+

For the purpose of our development model, we label Contributors or +Maintainers of Phoebus. Below we describe these labels and the +process for contributing to Phoebus.

+

We welcome contributions from scientists from a large variety of +relativistic astrophysics. New users are welcome to contributions to +Phoebus via the Contributors process. Contributors with 6 merged +pull requests into the main branch (over a minimum of 6 months) will +be eligible to join as a Maintainer of Phoebus with additional +repository access and roles. However, final approval of Maintainer +status will require a approval by vote by existing +Maintainers, a necessary step to ensure the safety and integrity of +the code base for all users of Phoebus.

+

The Maintainers of Phoebus consist of the original developers of +the code and those that have a demonstrated history in the development +of Phoebus prior to the implementation of the Development Model +described here. Maintainers hold admin access, serve as +reviewers for pull requests, and are in charge of the maintaining, +deployment, and improvement of efforts towards: regression testing, +documentation, science test cases (gold standards), and continuous +integration.

+

Maintainers are excepted to make a good faith effort to adhere to +these suggestions in order to maintain a supportive and +productive environment.

+
+
+

List of Current Maintainers of Phoebus

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Name

Handle

Team

Brandon Barker

@AstroBarker

Los Alamos National +Lab

Josh Dolence

@jdolence

Los Alamos National +Lab

Carl Fields

@carlnotsagan

University of Arizona

Mariam +Gogilashvili

@mari2895

Niels Bohr Institute

Jonah Miller

@Yurlungur

Los Alamos National +Lab

Jeremiah Murphy

@curiousmiah

Florida State +University

Ben Ryan

@brryan

Los Alamos National +Lab

+
+
+ + +
+
+ +
+
+
+
+ +
+ + Other Versions + v: main + + +
+
+
Branches
+
main
+
blb/frontier
+
+
+
+ + + \ No newline at end of file diff --git a/main/src/governance.html b/main/src/governance.html new file mode 100644 index 00000000..0976bf70 --- /dev/null +++ b/main/src/governance.html @@ -0,0 +1,275 @@ + + + + + + + + + Organizational Structure — Phoebus 1.0.0 documentation + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Organizational Structure

+
+
Phoebus uses a hybrid flat-and-hierarchical organizational +structure.
+
The flat structure fosters power sharing among senior and junior +members and avoids the many pitfalls of power-over dynamics. For +example, in power-over structures, someone with explicit power can +inadvertently, or on rare occasions intentionally, silence critical +voices.
+
This dynamic can quickly lead to an organization overlooking inherent +problems that could lead to ineffectiveness or even catastrophic +failure of the team.
+
+
+
In contrast, our aim is to illuminate potential problems early and +quickly find solutions.
+
This strategy also efficiently taps into the diverse wealth of +knowledge of the team.
+
At the same time, the PI and Co-PI have financial and reporting +responsibilities to their respective universities and funding +agencies.
+
The general procedure for the hybrid structure is as follows.
+
The flat structure will make major decisions in direction and +resources, and the PI and Co-PI will assume the responsibility for +executing those decisions.
+
The following gives details on this hybrid structure.
+
+
+

Team

+

The founding team consists of the following: original core developers +and Maintainers at Los Alamos National Lab, Jeremiah Murphy at Florida +State University, and Carl Fields at University of Arizona.

+

Since, an objective of Phoebus is to grow the developer and user base, +the Phoebus Project will have an explicit mechanism for adding new +members. There are three categories for Phoebus members: +maintainers, contributors, and users.

+

User: As open-source software, anyone may download, compile, and +execute Phoebus. New users will encouraged to join communication +channels for connection with the larger Phoebus community.

+

Contributor: Users who wish to contribute to Phoebus may do so +following our Development Model for new users. These changes will be +integrated into the main branch of the code upon approval. Consistent +contributions also provides the opportunity for Contributors to be +eligible to join as a Maintainer, the final approval of which will +require a vote.

+

Maintainer: These are the core team who have “merge” permissions on +the repo and are working to keep the code sustainable long term.

+

To maintain their relevant active status, all members must +make a food faith effort to maintain a supportive, productive environment.

+
+
+

Memorandum of Understanding

+

In addition to our Community Code of Conduct, we ask that maintainers +especially keep the following suggestions in mind to help +facilitate an efficient and welcoming collaboration:

+
    +

  • Maintainers should uphold and exemplify the Development Model +outlined as part of the phoebus Community described +here.

    • +

  • Within reason, maintainers will make a good-faith effort to attend team +meetings. In an effort to accommodate the dynamic schedules and +availability of many of the core team of Maintainers, +coordination efforts will be made to ensure that at least +1 Maintainer is present for all meetings.

    • +

  • Maintainers will make a good-faith effort to monitor the fraction of +the meeting time that they speak. The meeting time is limited, and +several people may have something interesting to say, report on their +updates, or contribute constructive arguments. One should be +self-aware and notice if one is dominating conversations, and attempt +to make a conscious effort to include other voices and perspectives +in the discussion.

    • +

  • Maintainers consider it their responsibility to voice their questions +and/or concerns as early as possible. This will ensure that the +organization addresses concerns rapidly and effectively.

    • +

  • Maintainers consider it their responsibility to listen and understand +questions or concerns raised by other partners or through concerns +communicated through email to individual Maintainers.

    • +
+
+
+

Approval by Vote:

+
+
Many of the decisions in the organization will be enacted after an +approval by majority vote of active Maintainers. The process of listening +and adjusting strategies to meet everyone’s needs is vital for +power-sharing organizations.
+
Importantly, spending a little time up front to listen and resolve +concerns reduces the pain and time spent later in intense conflict +resolution.
+
+
+
+

Communication and Connection:

+
+
To facilitate open and effective communication, the Phoebus will +offer multiple levels of communication. +Developers will communicate via email, GitHub, and a Phoebus Slack +channel.
+
+
+
To respond to user inquiries, the Phoebus Project will host a mailing +list via Google or similar.
+
To maintain a standing record of user inquiries and responses, we will +post the inquiries and responses on a public-facing site.
+
All Maintainers will have the option to respond to the inquires; to +ensure that someone is responsive to the user inquiries, the team will +triage tickets/questions in developer meetings.
+
+
+
Subject to availability, monthly Maintainer meetings will also +be an important part of ensuring productivity and timeliness.
+
Each meeting will last up to 60 minutes. We will assess and discuss +the goals from the previous meeting.
+
In particular, we will take note which goals were completed and which +were not. If there are uncompleted goals, we will assess why they were +not completed. Next, we will discuss the goals for the upcoming month, +quarter, and year.
+
We will decide which goals to prioritize.
+
All of this will be recorded on an online document which will be +available to all Maintainers.
+
+
+
Each meeting of the core Maintainers will be managed by a meeting +manager.
+
The primary job of the meeting manager is to: 1) gather a list of +agenda items for the next meeting, 2) ensure that the meeting runs on +schedule, and 3) ensure equitable participation by all participants.
+
Again, in keeping with power-sharing, the meeting manager position +will rotate among the core Maintainers, even junior members.
+
+
+

Note

+

We maintain some flexibility in the cadence and structure of meetings, in +particular, in periods of low activity, meetings may be skipped or +held in a less formal manner. We recognize that the availability +of maintainers is contingent upon many factors.

+
+
+
+ + +
+
+ +
+
+
+
+ +
+ + Other Versions + v: main + + +
+
+
Branches
+
main
+
blb/frontier
+
+
+
+ + + \ No newline at end of file diff --git a/main/src/sphinx-doc.html b/main/src/sphinx-doc.html new file mode 100644 index 00000000..21c4e502 --- /dev/null +++ b/main/src/sphinx-doc.html @@ -0,0 +1,239 @@ + + + + + + + + + How to Use Sphinx for Writing Docs — Phoebus 1.0.0 documentation + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
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+ +
+
+
+
+ +
+

How to Use Sphinx for Writing Docs

+
+

How to convert a Markdown file to rst

+

We are using the reStructuredText (rst) format for our documentation. +If you have a markdown file you would like to convert to rst, +as a first pass, you can have Pandoc convert your file. For example:

+
pandoc Metadata.md --from markdown --to rst -s -o metadata.rst
+
+
+

Pandoc can be installed easily through a Linux package manager. For example on Ubuntu,

+
apt install pandoc
+
+
+

will get you the tool.

+
+
+

How to have github build your documentation for you

+

Github can automatically build your documentation for you through the continuous integration pipeline. +After you submit a pull request with your .rst changes for documentation on github-pages, +the documentation will automatically get built. You will see a “build and deploy documentation” job +at the bottom of the pull request page. If this passes, your documentation will have been generated.

+

On the bottom left of the documentation page on github-pages, you can select the branch/build +of the documentation, one of which should be the branch you wrote your changes on.

+
+
+

Building documentation locally

+

While you can rely on the CI to build the documentation associated with your +branch, you can also very easily build sphinx documentation locally through +python. These instructions also do not require admin access and are usable +with shared machines or python distributions.

+

First, ensure that you are running a modern version of python (i.e. python 3 of +some flavor)

+
$ python --version
+Python 3.9.7
+
+
+

Then, use pip to install spinx and the RTD theme

+
pip install --user sphinx sphinx-rtd-theme
+
+
+

Now, navigate to the ../doc/sphinx directory where a make help +shows all of the available ways to build the documentation

+
$ make help
+Sphinx v4.2.0
+Please use `make target' where target is one of
+  html        to make standalone HTML files
+  dirhtml     to make HTML files named index.html in directories
+  singlehtml  to make a single large HTML file
+  pickle      to make pickle files
+  json        to make JSON files
+  htmlhelp    to make HTML files and an HTML help project
+  qthelp      to make HTML files and a qthelp project
+  devhelp     to make HTML files and a Devhelp project
+  epub        to make an epub
+  latex       to make LaTeX files, you can set PAPER=a4 or PAPER=letter
+  latexpdf    to make LaTeX and PDF files (default pdflatex)
+  latexpdfja  to make LaTeX files and run them through platex/dvipdfmx
+  text        to make text files
+  man         to make manual pages
+  texinfo     to make Texinfo files
+  info        to make Texinfo files and run them through makeinfo
+  gettext     to make PO message catalogs
+  changes     to make an overview of all changed/added/deprecated items
+  xml         to make Docutils-native XML files
+  pseudoxml   to make pseudoxml-XML files for display purposes
+  linkcheck   to check all external links for integrity
+  doctest     to run all doctests embedded in the documentation (if enabled)
+  coverage    to run coverage check of the documentation (if enabled)
+  clean       to remove everything in the build directory
+
+
+

Making the documentation will create a new directory, _build in the +sphinx directory along with whichever type of documentation you wanted +to build.

+

For example, building the HTML documentation with make html produces the +../doc/sphinx/_build/html directory with an index.html file that +you can point a browser to in order to view the documenation.

+
+
+

How to Get the Dependencies

+
+

Using Docker

+

If you are using Docker, then simply pull the docker image specified below:

+
image: sphinxdoc/sphinx-latexpdf
+
+
+

Then, after running docker run -it <docker-image-name> /bin/bash, install the theme we are using with pip install sphinx_rtd_theme

+
+
+
+

More Info.

+ + +
+
+ + +
+
+ +
+
+
+
+ +
+ + Other Versions + v: main + + +
+
+
Branches
+
main
+
blb/frontier
+
+
+
+ + + \ No newline at end of file diff --git a/main/src/tracers.html b/main/src/tracers.html new file mode 100644 index 00000000..3d257378 --- /dev/null +++ b/main/src/tracers.html @@ -0,0 +1,256 @@ + + + + + + + + + Tracer Particles — Phoebus 1.0.0 documentation + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
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+ +
+
+
+
+ +
+

Tracer Particles

+

Phoebus includes Lagrangian tracer particles. +These are primarily for the purpose of post-processing simulation data for, e.g., nucleosynthesis. +They are operator spit from the hydrodynamics and advected with a standard second order Runge-Kutta +integrator. As Phoebus is a general relativistic code, we evolve tracer positions using a +relativistic advection equation:

+
+\[\frac{dx^i}{dt} = \frac{u^i}{u^0} = \alpha v^i - \beta^i\]
+

Tracers may be enabled by in the Phoebus input deck as follow:

+
<physics>
+tracers = true
+
+<tracers>
+num_tracers = 1024
+
+
+

Similarly, tracers may be output by modifying an existing Parthenon output block, or creating a new one:

+
<parthenon/output1>
+// ...
+swarms = tracers
+tracers_variables = rho, temperature, ye
+
+file_type = hdf5
+dt = // output cadence
+
+
+

Note that the position variables x, y, z are output for all swarms by default. +See the Parthenon docs for more information.

+

Tracers must, however, be configured in the problem generator. +In the generator, the tracers should be distributed through the domain, assigned positions +and unique ids. An example from the advection pgen is shown below.

+
pmb->par_for(
+    "ProblemGenerator::Advection::DistributeTracers", 0, max_active_index,
+    KOKKOS_LAMBDA(const int n) {
+      if (swarm_d.IsActive(n)) {
+        auto rng_gen = rng_pool.get_state();
+
+        // sample in ball
+        Real r2 = 1.0 + rin * rin; // init > rin^2
+        while (r2 > rin * rin) {
+          x(n) = x_min + rng_gen.drand() * (x_max - x_min);
+          y(n) = y_min + rng_gen.drand() * (y_max - y_min);
+          z(n) = z_min + rng_gen.drand() * (z_max - z_min);
+          r2 = x(n) * x(n) + y(n) * y(n) + z(n) * z(n);
+        }
+        id(n) = num_tracers_total * gid + n;
+
+        bool on_current_mesh_block = true;
+        swarm_d.GetNeighborBlockIndex(n, x(n), y(n), z(n), on_current_mesh_block);
+        rng_pool.free_state(rng_gen);
+      }
+    });
+
+
+

In addition to position, tracers track a number of potentially useful quantities. +These quantities include (bold quantities are 3-vectors with components _x, _y, _z)

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Quantity

SwarmVar Name

Description

Density

rho

Primitive density

Temperature

temperature

Temperature

Ye

ye

Electron fraction (0 if ye is disabled)

Internal energy

energy

Primitive internal energy

Entropy

entropy

Entropy

Velocity

vel_x, …

Three velocity

Lorentz factor

lorentz

Relativistic Lorentz factor

Lapse

lapse

Relativistic lapse

Metric determinant

detgamma

Spatial metric determinant

Shift

shift_x, …

Relativistic shift

Mass

mass

Tracer mass

Total energy

bernoulli

Total energy Bernoulli quantity

Magnetic field

B_x, …

Primitive 3-magnetic field components (if mhd enabled)

+

To minimize unnecessary work, these quantities are only populated before output using phoebus::UserWorkBeforeOutput.

+
+
+void UserWorkBeforeOutput(MeshBlock *pmb, ParameterInput *pin)
+

Describes work to be done prior to HDF5 output, such as populating tracer variables. +This is connected to the appropriate Parthenon function.

+
+ +
+ + +
+
+ +
+
+
+
+ +
+ + Other Versions + v: main + + +
+
+
Branches
+
main
+
blb/frontier
+
+
+
+ + + \ No newline at end of file