FORKPOINT=$(git show -s --pretty=format:"%h" `git merge-base gerrit_master HEAD`)
REF=`git show -s --pretty=format:"%h"`
+## Sample MD extension code
+
+`sample_restraint` is a subtree containing a complete CMake project for building
+pluggable GROMACS MD extensions for execution through gmxapi. Up to and
+including version 0.0.7.3 of the sample code, the sub-project lived at
+https://github.com/kassonlab/sample_restraint/ and was supported by GROMACS 2019.
+
+The GROMACS repository becomes the upstream source for the sample code for
+GROMACS releases 2020 and higher.
+
## External project code
Refer to `./src/external/README.md` for current details on the copied external
ADD --chown=testing:testing scripts /home/testing/scripts
ADD --chown=testing:testing test /home/testing/test
+ADD --chown=testing:testing sample_restraint /home/testing/sample_restraint
+
+RUN . $HOME/testing/bin/activate && \
+ . /usr/local/gromacs/bin/GMXRC && \
+ (cd $HOME/sample_restraint && \
+ mkdir build && \
+ cd build && \
+ cmake .. && \
+ make -j4 install \
+ )
+
# TODO: this can be in the root user section above once it is stable
COPY docker/entrypoint.sh /
--- /dev/null
+# Files in this directory are sample code distributed without GROMACS copyright.
+* !filter
--- /dev/null
+*build*
+.cache
+.idea
+*.pyc
--- /dev/null
+# Recipe for build and integration testing on Travis-CI
+
+# Try beta version of new travis-yml checker
+version: "= 0"
+# For extra debugging of failed jobs, see
+# https://docs.travis-ci.com/user/common-build-problems/#Troubleshooting-Locally-in-a-Docker-Image
+
+os: linux
+dist: xenial
+language: cpp
+
+# If we set 'ccache: true', Travis installs replacement ccache wrappers of system compilers, which we don't want,
+# so we'll do our own ccache management.
+# Note the heuristics for whether cache is shared or distinct:
+# https://docs.travis-ci.com/user/caching/#Caches-and-build-matrices
+cache:
+ pip: true
+ directories:
+ # Note: if a cache store forks due to a stage with parallel jobs that Travis identifies as part of the same flow,
+ # we must make sure that the parallel jobs do not write to any of the same caches. Also note that all stages use the
+ # same cache, so early stage jobs may see caches from later stages from previous builds in the same branch.
+ - $HOME/.ccache_gromacs
+ - $HOME/.ccache_py
+# Allows us to build and install GROMACS in one CI stage, then use the installation in a subsequent stage
+# - $HOME/install
+
+compiler: gcc
+
+env:
+# Python 2.7 and 3.6 are the only generations provided by pyenv on Travis-CI out-of-the-box
+ - PY=2.7
+ - PY=3.6
+
+addons:
+ apt:
+ sources:
+ - sourceline: 'ppa:ubuntu-toolchain-r/test'
+ packages:
+ - cmake
+ - cmake-data
+ - doxygen
+ - libblas-dev
+ - libcr-dev
+ - libfftw3-dev
+ - liblapack-dev
+ - libmpich-dev
+ - libxml2-dev
+ - mpich
+
+# Set up for all jobs
+before_install:
+ - pyenv versions
+ # get exactly one Python version: the last listed patch version for the selected minor version
+ - pyenv whence python${PY} && export PY_VER=`pyenv whence python${PY} | tail -1`
+ - pyenv shell $PY_VER && pyenv shell
+# - python-config --includes
+ - pyenv prefix ${PY_VER} && export PYTHON_PREFIX=`pyenv prefix ${PY_VER}`
+ - pyenv which python && export PYTHON=`pyenv which python`
+ - source ./ci_scripts/set_compilers
+
+install:
+ - export CCACHE_DIR=$HOME/.ccache_gromacs
+ - ccache -s
+ - ./ci_scripts/install_gromacs_2019.sh
+# Need to update infrastructure for new CMake version requirements to build against devel.
+# - if [ "${TRAVIS_BRANCH}" != "master" ] ; then ./ci_scripts/install_gromacs_devel.sh ; fi
+
+before_script:
+ - export CCACHE_DIR=$HOME/.ccache_py
+ - ccache -s
+ - pip install --upgrade pip setuptools
+ - pip install --upgrade packaging scikit-build
+ - pip install --no-cache-dir --upgrade --no-binary ":all:" --force-reinstall networkx mpi4py MarkupSafe
+ - pip install pytest numpy networkx sphinx sphinx_rtd_theme
+
+script:
+ - source $HOME/install/gromacs_2019/bin/GMXRC && ./ci_scripts/pygmx_0_0_7.sh
+ - ./ci_scripts/sample_restraint.sh
+# Need to update infrastructure for new CMake version requirements to build against devel.
+# - |
+# if [ "${TRAVIS_BRANCH}" != master ] ; then
+# source $HOME/install/gromacs_devel/bin/GMXRC
+# ./ci_scripts/pygmx_devel.sh
+# ./ci_scripts/sample_restraint.sh
+# fi
--- /dev/null
+cmake_minimum_required(VERSION 3.4.3)
+# If you are using this repository as a template, you should probably change the
+# project name and adopt your own versioning scheme.
+project(sample_restraint VERSION 0.0.7)
+
+# This project requires a GROMACS supporting gmxapi 0.0.7 or higher. It should
+# be sufficient to source the GMXRC, but you can also set the GROMACS_DIR or
+# gmxapi_DIR environment variable to help CMake find the GROMACS installation.
+
+# Note that the code will need to be built separately for different versions of Python and for substantially different
+# versions of GROMACS. If building from the command line, you can specify a Python executable with the PYTHON_EXECUTABLE
+# variable. For instance, to make sure you are building for your default Python, cmake -DPYTHON_EXECUTABLE=`which python`.
+
+set(CMAKE_CXX_STANDARD 14)
+set(CMAKE_CXX_VISIBILITY_PRESET hidden)
+
+# CMake modules are in a subdirectory to keep this file cleaner
+list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake)
+
+# Assuming GROMACS is in our path or that we have set either the gmxapi_DIR or GROMACS_DIR environment variables,
+# this will find the CMake configuration for the GROMACS libraries we need and define the CMake library objects
+# Gromacs::gmxapi
+find_package(gmxapi
+ 0.0.7 REQUIRED CONFIG
+ PATHS "$ENV{GROMACS_DIR}"
+ )
+
+if(gmxapi_FOUND)
+ message("gmxapi found")
+endif()
+message("Found gmxapi version ${gmxapi_VERSION_MAJOR}.${gmxapi_VERSION_MINOR}.${gmxapi_VERSION_PATCH}")
+
+
+######################################################
+# The following is boiler-plate recommended by GROMACS
+######################################################
+# In principle, this could be deduced from GROMACS_IS_DOUBLE returned by
+# find_package(GROMACS) based on the suffix alone, but it is clearer that the
+# user explicitly sets what they want to get, and then need to provide a suffix
+# to match.
+option(GMX_DOUBLE "Use double precision" OFF)
+set(GMX_SUFFIX "" CACHE STRING "Suffix for the GROMACS installation to use (empty for default)")
+
+# This does not allow for a non-suffixed double-precision libgromacs, but
+# that should be rare enough for demonstration purposes.
+if (GMX_DOUBLE AND NOT GMX_SUFFIX)
+ set(GROMACS_SUFFIX "_d")
+else()
+ set(GROMACS_SUFFIX ${GMX_SUFFIX})
+endif()
+
+find_package(GROMACS REQUIRED)
+gromacs_check_double(GMX_DOUBLE)
+gromacs_check_compiler(CXX)
+include_directories(${GROMACS_INCLUDE_DIRS})
+add_definitions(${GROMACS_DEFINITIONS})
+
+# Use static linking on MSVC
+if (CMAKE_GENERATOR MATCHES "Visual Studio")
+ string(REPLACE /MD /MT CMAKE_C_FLAGS_RELEASE ${CMAKE_C_FLAGS_RELEASE})
+ set(CMAKE_C_FLAGS_RELEASE ${CMAKE_C_FLAGS_RELEASE} CACHE STRING "" FORCE)
+ string(REPLACE /MD /MT CMAKE_C_FLAGS_DEBUG ${CMAKE_C_FLAGS_DEBUG})
+ set(CMAKE_C_FLAGS_DEBUG ${CMAKE_C_FLAGS_DEBUG} CACHE STRING "" FORCE)
+endif()
+########################################################
+
+# Stuff for our plugin:
+#
+# If the user is not in a virtual environment and is not a privileged user and has not specified an install location
+# for the Python module (GMXPLUGIN_INSTALL_PATH), this option causes the automatic install location to query the user
+# site-packages directory instead of using the default site-packages directory for the interpreter.
+option(GMXPLUGIN_USER_INSTALL
+ "Override the default site-packages directory with the user-specific Python packages directory. \
+ (Do not use with virtual environments.) \
+ Has no effect if GMXPLUGIN_INSTALL_PATH is defined or cached. \
+ Use -UGMXPLUGIN_INSTALL_PATH to force recalculation."
+ OFF)
+
+# Since a user may have multiple virtual environments with different Python interpreters, it is generally confusing to
+# have a package for a virtual environment installed in the user's default user site-packages directory. If virtual
+# environments are in use at all, we recommend you do _not_ perform a "user" install in or out of a virtual env. If you do
+# not use any Python virtual environments, we recommend you _do_ perform "user" installs exclusively. Overall, we
+# we recommend you use Python virtual environments and activate one before performing a regular (non-"user") install.
+
+unset(PYTHONINTERP_FOUND)
+unset(PYTHONLIBS_FOUND)
+find_package(PythonInterp)
+if (PYTHONINTERP_FOUND)
+ message(STATUS "Found Python interpreter: ${PYTHON_EXECUTABLE}")
+ add_subdirectory(src/external/pybind11)
+ if (PYTHON_LIBRARIES)
+ if (GMXPLUGIN_USER_INSTALL)
+ execute_process(COMMAND ${PYTHON_EXECUTABLE} "-m" "site" "--user-site"
+ OUTPUT_VARIABLE GMXPLUGIN_DEFAULT_SITE_PACKAGES
+ OUTPUT_STRIP_TRAILING_WHITESPACE)
+ message(STATUS "Python user site-packages directory is ${GMXPLUGIN_DEFAULT_SITE_PACKAGES}")
+ else()
+ execute_process(COMMAND ${PYTHON_EXECUTABLE} -c
+ "import sys; import os; \
+ print(os.path.abspath(os.path.join(sys.prefix, \
+ 'lib', \
+ 'python${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}', \
+ 'site-packages')))"
+ OUTPUT_VARIABLE GMXPLUGIN_DEFAULT_SITE_PACKAGES
+ OUTPUT_STRIP_TRAILING_WHITESPACE)
+ message(STATUS "Python site-packages directory is ${GMXPLUGIN_DEFAULT_SITE_PACKAGES}")
+ endif()
+ else()
+ message(FATAL_ERROR
+ "Found Python interpreter ${PYTHON_EXECUTABLE} but this Python installation does not have developer tools."
+ "Set PYTHON_EXECUTABLE to the Python interpreter that was installed with a working Python.h header file.")
+ endif()
+else()
+ message(FATAL "Could not find Python interpreter. Set CMake flag -DPYTHON_EXECUTABLE=/path/to/python to hint.")
+endif()
+
+# At some point this may be part of a CMake package with several components for which a single CMAKE_INSTALL_PREFIX does
+# not make sense, so let's manage the install path separately.
+set(GMXPLUGIN_INSTALL_PATH ${GMXPLUGIN_DEFAULT_SITE_PACKAGES} CACHE PATH
+ "Path to Python module install location (site-packages). For an automatically determined install location based on \
+ the Python installation, leave undefined or explicitly undefined with -UGMXPLUGIN_INSTALL_PATH and, optionally, set \
+ GMXPLUGIN_USER_INSTALL on or off to specify the installation's site-packages directory or the 'user' site-packages \
+ directory.")
+
+message(STATUS "Python module will be installed to GMXPLUGIN_INSTALL_PATH cache value ${GMXPLUGIN_INSTALL_PATH}")
+
+
+# Set up testing options.
+include(CTest)
+
+# Either use the git subtree in tests/googletest or download a fresh copy of
+# googletest master branch.
+option(DOWNLOAD_GOOGLETEST OFF "Download the latest master branch of googletest.")
+mark_as_advanced(DOWNLOAD_GOOGLETEST)
+
+# Prevent overriding the parent project's compiler/linker
+# settings on Windows
+set(gtest_force_shared_crt ON CACHE BOOL "" FORCE)
+
+
+# Now move on to building the custom code.
+add_subdirectory(src)
+
+# Set up documentation build targets (work in progress).
+add_subdirectory(docs)
+
+
+# Process CMake configuration for Python and C++ tests.
+if(BUILD_TESTING)
+ add_subdirectory(tests)
+endif()
--- /dev/null
+# Build docker image with sample plugin `myplugin`.
+
+# From the root directory of the repository (where this Dockerfile is), build an image named "restraint_test" with
+# docker build -t sample_restraint .
+# Note that public images for dockerhub are build with `docker build -t gmxapi/sample_restraint:tag .`
+#
+# Launch an ephemeral container with
+# docker run --rm -ti -p 8888:8888 sample_restraint
+# for the Jupyter notebook server, or, for just a shell
+# docker run --rm -ti sample_restraint bash
+# The container will be removed when the process (notebook server or shell) exits.
+# To create and run a named container, do something like the following.
+# docker run -ti --name restraint_test sample_restraint
+#
+# Test with
+# docker run --cpus 2 --rm -ti sample_restraint bash -c \
+# "cd /home/jovyan/sample_restraint/tests && mpiexec -n 2 python -m mpi4py -m pytest"
+# or replace `gmxapi/sample_restraint:devel` with your local image name
+
+
+# The base image is available on DockerHub, but you can also build your own from the gmxapi repository.
+FROM gmxapi/gmxapi:0.0.7
+
+# Hot fix: clean out accidental cruft from an upstream base image.
+RUN rm -rf /home/jovyan/sample_restraint /home/jovyan/plugin-build
+
+# Grab some additional useful biomolecular simulation analysis tools.
+RUN conda config --add channels conda-forge
+RUN conda install mdanalysis
+
+# This is a bit risky and troublesome, but I want to test the current repo state without committing.
+# Another problem is that changes to directories do not trigger build cache invalidation!
+COPY --chown=1000 CMakeLists.txt README.md /home/jovyan/sample_restraint/
+COPY --chown=1000 cmake/ /home/jovyan/sample_restraint/cmake/
+COPY --chown=1000 docs/ /home/jovyan/sample_restraint/docs/
+COPY --chown=1000 src/ /home/jovyan/sample_restraint/src/
+COPY --chown=1000 tests/ /home/jovyan/sample_restraint/tests/
+COPY --chown=1000 examples/example.ipynb /home/jovyan/sample_restraint/examples/
+COPY --chown=1000 examples/job.sh /home/jovyan/sample_restraint/examples/
+COPY --chown=1000 examples/restrained-ensemble.py /home/jovyan/sample_restraint/examples/
+COPY --chown=1000 examples/strip_notebook.py /home/jovyan/sample_restraint/examples/
+
+# Prune the directory after removed or find will try to descend into a nonexistant directory
+RUN find /home/jovyan -name __pycache__ -exec rm -rf \{\} \; -prune
+
+# Build and install the plugin in the Conda virtual environment from the scipy-jupyter base image.
+RUN mkdir /home/jovyan/plugin-build && \
+ (cd /home/jovyan/plugin-build && \
+ GROMACS_DIR=/home/jovyan/install/gromacs gmxapi_DIR=/home/jovyan/install/gromacs \
+ cmake ../sample_restraint -DPYTHON_EXECUTABLE=/opt/conda/bin/python && \
+ LD_LIBRARY_PATH=/opt/conda/lib make && \
+ make test && \
+ make install) && \
+ PYTHONPATH=plugin-build/src/pythonmodule CONDA_DIR=/opt/conda \
+ /opt/conda/bin/python -m pytest sample_restraint/tests --verbose
+
+# The jupyter notebook server might not pick this up, but we can make it a little easier to find the
+# `gmx` binary from the default user shell.
+RUN echo "source install/gromacs/bin/GMXRC.bash" >> /home/jovyan/.profile
--- /dev/null
+Sample MD restraint plugin
+==========================
+
+[](https://travis-ci.org/kassonlab/sample_restraint)
+
+This [repository](https://github.com/kassonlab/sample_restraint)
+provides a complete and working implementation of a few GROMACS
+restraint potentials. It is intended as both a tutorial and as a
+template for implementing new custom restraint potentials.
+
+Restraint potentials are implemented as \"plugins\" to GROMACS. The
+required GROMACS modifications are available at this [GitHub
+repository](https://github.com/kassonlab/gromacs-gmxapi)
+
+The plugin potentials are loaded and configured via Python and are
+compatible with the [gmxapi](https://github.com/kassonlab/gmxapi) Python
+package for MD simulation workflows.
+
+For a quick start, consider pulling a recent Docker image that has
+already been configured for gmxapi and this plug-in.
+
+Reference:
+
+Irrgang, M. E., Hays, J. M., & Kasson, P. M. gmxapi: a high-level
+interface for advanced control and extension of molecular dynamics
+simulations. *Bioinformatics* 2018. DOI:
+[10.1093/bioinformatics/bty484](https://doi.org/10.1093/bioinformatics/bty484)
+
+Repository Contents
+-------------------
+
+This repository uses CMake to build and install a Python C++ extension
+package.
+
+- `CMakeLists.txt`, `cmake/FindGROMACS.cmake`, and
+ `src/CMakeLists.txt` provide necessary CMake infrastructure. You
+ should not need to edit these.
+- `src/cpp` contains a header and `cpp` file for each restraint
+ potential built with this module. When adding new potentials, you
+ will update `CMakeLists.txt` to create build targets. Use the
+ existing potentials as examples.
+- `src/pythonmodule/` contains `CMakeLists.txt`, `export_plugin.h`,
+ and `export_plugin.cpp`. When you have written a new potential, you
+ can add it to `CMakeLists.txt` and `export_plugin.cpp`. This is the
+ code that produces the C++ extension for Python. `HarmonicRestraint`
+ is a simple example that applies a Hooke\'s Law spring between two
+ atoms. `EnsembleHarmonic` applies a more complicated potential and
+ uses additional facilities provided by gmxapi.
+- `src/pybind11` is just a copy of the Python bindings framework from
+ the Pybind project (ref <https://github.com/pybind/pybind11> ). It
+ is used to wrap the C++ restraint code and give it a Python
+ interface.
+- `tests/` contains C++ and Python tests for the provided code. Update
+ `CMakeLists.txt` to add your own, based on these examples. C++ unit
+ tests use [googletest](https://github.com/google/googletest). Python
+ tests use the [pytest](https://docs.pytest.org/en/latest/). Refer to
+ those respective projects for more about how they make test-writing
+ easier.
+- `examples` contains a sample SLURM job script and
+ `restrained-ensemble.py` gmxapi script that have been used to do
+ restrained ensemble simulations. `example.py` and `example.ipynb`
+ explore a toy alanine dipeptide system. `strip_notebook.py` is a
+ helper script to remove extra output and state data from an iPython
+ notebook before checking updates back into the repository.
+- `Dockerfile` is a recipe to build a Docker image from the root of
+ the repository.
+
+Docker quick-start
+------------------
+
+Pull the docker image and launch a container with port 8888 on the host
+mapped to port 8888 in the container. :
+
+ docker run --rm -ti -p 8888:8888 gmxapi/sample_restraint:devel
+
+Note that the `--rm` option tells docker not to save any changes you
+make after launching the container. You can, however, download any
+changes you make to the notebook through the web interface. Refer to the
+[Docker documentation](https://docs.docker.com) for more options on
+managing containers.
+
+You should then see something like the following, but with a different
+`token` for the URL. Open the URL in a browser on the same (host)
+machine to access the notebook server. Browse to `sample_restraint` and
+`examples` and then launch the `example` notebook for an interactive
+walk-through. Example output:
+
+ Execute the command: jupyter notebook
+ [I 15:26:07.683 NotebookApp] Writing notebook server cookie secret to /home/jovyan/.local/share/jupyter/runtime/notebook_cookie_secret
+ [W 15:26:08.184 NotebookApp] WARNING: The notebook server is listening on all IP addresses and not using encryption. This is not recommended.
+ [I 15:26:08.223 NotebookApp] JupyterLab alpha preview extension loaded from /opt/conda/lib/python3.6/site-packages/jupyterlab
+ [I 15:26:08.230 NotebookApp] Serving notebooks from local directory: /home/jovyan
+ [I 15:26:08.230 NotebookApp] 0 active kernels
+ [I 15:26:08.230 NotebookApp] The Jupyter Notebook is running at:
+ [I 15:26:08.230 NotebookApp] http://[all ip addresses on your system]:8888/?token=948d611453ea3f03ad406dc375bfc186c4315fa68c50e23d
+ [I 15:26:08.230 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
+ [C 15:26:08.231 NotebookApp]
+
+ Copy/paste this URL into your browser when you connect for the first time,
+ to login with a token:
+ http://localhost:8888/?token=948d611453ea3f03ad406dc375bfc186c4315fa68c50e23d
+
+The basics
+----------
+
+This repository provides a potentially useful plugin, but also serves as
+documentation by example and as a template for developing GROMACS
+extension code in the gmxapi framework.
+
+### Build and install
+
+To download, build, and install, you may need to first install `wget`,
+`git`, and/or `cmake`.
+
+The plugin requires libgmxapi to build. See
+[gromacs-gmxapi](https://github.com/kassonlab/gromacs-gmxapi) :
+
+ # install GROMACS. Instead of `master`, you can choose a specific release or the `devel` branch.
+ wget https://github.com/kassonlab/gromacs-gmxapi/archive/master.zip
+ unzip master.zip
+ cd gromacs-gmxapi-master
+ mkdir build
+ cd mkdir build
+ cmake .. -DCMAKE_INSTALL_PREFIX=$HOME/gromacs -DGMX_THREAD_MPI=ON
+ make install # use -j10 to build in parallel with 10 cores (or however many you have)
+ cd ../..
+
+We use CMake to configure and build a C++ library and a Python module
+for interacting with it. After installing the modified GROMACS (see
+above), either source the GMXRC file provided with the GROMACS
+installation or provide the install location to CMake with the
+`gmxapi_DIR` environment variable.
+
+As with [gmxapi](https://github.com/kassonlab/gromacs-gmxapi), we
+recommend installing and using this code in a Python virtual
+environment. (See the documentation for your `gmxapi` distribution or
+<http://gmxapi.readthedocs.io/en/latest/install.html> ) Accordingly, if
+you choose to install the plugin rather than just to use it out of
+its build directory, consider whether you want to have to set your
+`PYTHONPATH` environment variable or where you can install it that
+Python will find it. You can explicitly set the installation location by
+setting `-DGMXPLUGIN_INSTALL_PATH=/path/to/install/directory` or you can
+let CMake determine an appropriate location automatically for your
+Python interpreter. If you have administrative privileges (such as when
+running on a desktop computer) or if you are using a Python virtual
+environment (recommended), you don\'t need to specify anything
+additional. If you are an unprivileged user (such as on a shared
+machine) and are not in a Python virtual environment, set
+-DGMXPLUGIN\_USER\_INSTALL=ON to install into the \"user\" Python
+packages directory in your home directory. (Equivalent to the `--user`
+option to `pip`)
+
+If you have multiple Python installations or just want to be
+unambiguous, provide CMake with the Python interpreter you wish to use
+(the same as you are using for `gmxapi`) with
+`-DPYTHON_EXECUTABLE=/path/to/python`. For instance, if you have both
+Python 3.x and Python 2.7, but you plan to use Python 2.7, use
+`` -DPYTHON_EXECUTABLE=`which python2` `` or
+`` -DPYTHON_EXECUTABLE=`which python` `` (if `python` points to the
+Python 2 interpreter). :
+
+ # build sample restraint
+ git clone https://github.com/kassonlab/sample_restraint.git
+ # optionally, check out the development branch
+ # pushd sample_restraint ; git checkout devel ; popd
+ # perform an out-of-source build
+ mkdir build
+ cd build
+ # Get the GROMACS environment settings
+ source $HOME/gromacs/bin/GMXRC
+ # Configure the build environment with CMake
+ cmake ../sample_restraint
+ # or
+ # cmake ../sample_restraint -DGMXPLUGIN_INSTALL_PATH=/path/to/install/directory
+ # or
+ # cmake ../sample_restraint -DGMXPLUGIN_USER_INSTALL=ON -DPYTHON_EXECUTABLE=`which python`
+ make
+ # run C++ tests
+ make test
+ # optionally, install
+ make install
+
+If you choose not to install the plugin module, you can tell Python
+where to find it by setting your PYTHONPATH environment variable. For
+instance, while still in the build directory:
+
+ export PYTHONPATH=`pwd`/src/pythonmodule
+
+The Python module `gmx` is required for testing. See
+[gmxapi](https://github.com/kassonlab/gmxapi)
+
+### Running
+
+The `examples` directory contains some sample scripts for running
+`gmxapi` workflows using the restraint potential samples in this
+repository. You may also find `tests/test_binding.py` informative.
+
+For a basic walk-through with a toy system, launch a Jupyter notebook
+server and navigate to `examples/example.py`
+
+### What\'s going on
+
+This sample project builds several C++ libraries with names such as
+`harmonicpotential`. The actual filename will be something like
+`libharmonicpotential.so` or `harmonicpotential.dll` or something
+depending on your operating system. These libraries are used to build a
+Python module named `myplugin`.
+
+When setting up a workflow, a Python script provides gmxapi with
+parameters and a factory function for a plugin restraint potential. This
+Python interface is defined in `src/pythonmodule/export_plugin.cpp`.
+When a Session is launched, an C++ object that performs restraint force
+calculations is created and given to the GROMACS library. During each MD
+step, part of the MD force evaluation includes a call to the
+calculations performed by the restraint. For the pair restraints
+demonstrated here, GROMACS provides relative coordinates of two atomic
+sites to the calculation code in the plugin. If multiple restrained
+pairs are needed, multiple restraints are attached to the simulation.
+Coordination across an ensemble of simulations is possible using
+resources provided by the Session.
+
+Fundamentally, a new restraint potential is implemented by creating a
+class that provides a `calculate()` method and using wrappers to give it
+interfaces to GROMACS and to Python. C++ wrappers allow the basic class
+implementing the potential to be presented to the GROMACS library in a
+way that can be used to evaluate forces during a simulation. Other C++
+template code wraps the potential in a portable way so that it can be
+passed to GROMACS through a Python interface and to receive parameters
+from the Python interpreter. Pybind11 syntax in `export_plugin.cpp`
+provides the code to actually expose the plugin as a class in a Python
+module that is compatible with the `gmx` package provided in the
+`gmxapi` project.
+
+By version 0.1.0, additional wrappers and boilerplate code will be
+migrated out of the files that define the `calculate()` methods. Until
+then, some amount of copy-and-paste or editing is necessary to implement
+a new potential. Refer to `src/cpp/harmonicpotential.h` and to
+`src/cpp/harmonicpotential.cpp` for a documented example of a simple
+pair restraint. A more complex example is found in the
+`ensemblepotential` files. The code in `src/cpp` is sufficient to
+produce testable object code, but the Python module is exported in
+`src/pythonmodule/export_plugin.cpp`. If you add additional source files
+for a new potential, you will need to update `src/cpp/CMakeLists.txt` as
+well.
+
+Python tests
+------------
+
+For the Python-level testing, you will need `pytest` and `gmxapi`. We
+recommend setting up a Python virtual environment as described at
+[<https://github.com/kassonlab/gmxapi>](https://github.com/kassonlab/gmxapi)
+
+You will also need a functioning MPI installation and the `mpi4py`
+package.
+
+Python tests can be run from the root directory of the repository after
+building. Assuming you built in a subdirecory of the repository named
+`build` (as above):
+
+ PYTHONPATH=build/src/pythonmodule/ python -m pytest tests
+
+This command causes the directory named `tests` to be explored for
+Python files with names like `test_*.py` or `*_test.py`. Matching files
+will be imported and any functions with similarly obvious names will be
+run and errors reported. In particular, `assert` statements will be
+evaluated to perform individual tests. See also
+<https://docs.pytest.org/en/latest/goodpractices.html#test-discovery>
+
+The tests assume that the package is already installed or is available
+on the default Python path (such as by setting the `PYTHONPATH`
+environment variable). If you just run `pytest` with no arguments, it
+will discover and try to run tests from elsewhere in the repository that
+were not intended, and they will fail.
+
+To run the full set of tests for the ensemble workflow features, first
+make sure that you have an MPI-capable environment and `mpi4py`
+installed. Refer to <http://mpi4py.readthedocs.io/en/stable/> and
+<https://github.com/kassonlab/gmxapi> for more information.
+
+The ensemble tests assume that 2 ranks are available. After installing
+the plugin, run (for example):
+
+ mpiexec -n 2 python -m mpi4py -m pytest
+
+If you do not have MPI set up for your system, you could build a docker
+image using the Dockerfile in this repository.
+
+ docker build -t samplerestraint . Dockerfile
+ docker run --cpus 2 --rm -ti samplerestraint bash -c \
+ "cd /home/jovyan/sample_restraint/tests &&
+ mpiexec -n 2 python -m mpi4py -m pytest"
+
+To test with a pre-built image from our docker hub repository, do
+
+ docker run --cpus 2 --rm -ti gmxapi/sample_restraint bash -c \
+ "cd /home/jovyan/sample_restraint/tests &&
+ mpiexec -n 2 python -m mpi4py -m pytest"
--- /dev/null
+#!/bin/bash
+set -ev
+
+export GMX_DOUBLE=OFF
+export GMX_MPI=OFF
+export GMX_THREAD_MPI=ON
+
+export GMX_SRC_DIR=gromacs-2019
+
+export CCACHE_DIR=$HOME/.ccache_gmxapi
+ccache -s
+
+pushd $HOME
+ [ -d gromacs-gmxapi ] || \
+ git clone \
+ --depth=1 \
+ --no-single-branch \
+ https://github.com/gromacs/gromacs.git \
+ ${GMX_SRC_DIR}
+ pushd ${GMX_SRC_DIR}
+ git branch -a
+ git checkout release-2019
+ pwd
+ rm -rf build
+ mkdir build
+ pushd build
+ cmake -DCMAKE_CXX_COMPILER=$CXX \
+ -DGMX_ENABLE_CCACHE=ON \
+ -DCMAKE_C_COMPILER=$CC \
+ -DGMX_DOUBLE=$GMX_DOUBLE \
+ -DGMX_MPI=$GMX_MPI \
+ -DGMX_THREAD_MPI=$GMX_THREAD_MPI \
+ -DGMXAPI=ON \
+ -DCMAKE_INSTALL_PREFIX=$HOME/install/gromacs_2019 \
+ ..
+ make -j2 install
+ popd
+ popd
+popd
+ccache -s
--- /dev/null
+#!/bin/bash
+set -ev
+
+export GMX_DOUBLE=OFF
+export GMX_MPI=OFF
+export GMX_THREAD_MPI=ON
+
+export GMX_SRC_DIR=gromacs-kassonlab
+
+export CCACHE_DIR=$HOME/.ccache_gmxapi
+ccache -s
+
+pushd $HOME
+ [ -d "${GMX_SRC_DIR}" ] || \
+ git clone \
+ --depth=1 \
+ --no-single-branch \
+ https://github.com/kassonlab/gromacs-gmxapi.git \
+ ${GMX_SRC_DIR}
+ pushd ${GMX_SRC_DIR}
+ git branch -a
+ git checkout devel
+ pwd
+ rm -rf build
+ mkdir build
+ pushd build
+ cmake -DGMX_BUILD_HELP=OFF \
+ -DGMX_ENABLE_CCACHE=ON \
+ -DCMAKE_CXX_COMPILER=$CXX \
+ -DCMAKE_C_COMPILER=$CC \
+ -DGMX_DOUBLE=$GMX_DOUBLE \
+ -DGMX_MPI=$GMX_MPI \
+ -DGMX_THREAD_MPI=$GMX_THREAD_MPI \
+ -DCMAKE_INSTALL_PREFIX=$HOME/install/gromacs_devel \
+ ..
+ make -j2 install
+ popd
+ popd
+popd
+ccache -s
--- /dev/null
+#!/bin/bash
+set -ev
+
+pushd $HOME
+ [ -d gmxapi ] || git clone --depth=1 --no-single-branch https://github.com/kassonlab/gmxapi.git
+ pushd gmxapi
+ git checkout release-0_0_7
+ rm -rf build
+ mkdir -p build
+ pushd build
+ cmake .. -DCMAKE_CXX_COMPILER=$CXX -DCMAKE_C_COMPILER=$CC -DPYTHON_EXECUTABLE=$PYTHON
+ make -j2 install
+ popd
+ popd
+ mpiexec -n 2 $PYTHON -m mpi4py -m pytest --log-cli-level=WARN --pyargs gmx -s
+# mpiexec -n 2 $PYTHON -m mpi4py -m pytest --log-cli-level=DEBUG --pyargs gmx -s --verbose
+ ccache -s
+popd
--- /dev/null
+#!/bin/bash
+set -ev
+
+pushd $HOME
+ [ -d gmxapi ] || git clone --depth=1 --no-single-branch https://github.com/kassonlab/gmxapi.git
+ pushd gmxapi
+ git checkout devel
+ rm -rf build
+ mkdir -p build
+ pushd build
+ cmake .. -DCMAKE_CXX_COMPILER=$CXX -DCMAKE_C_COMPILER=$CC -DPYTHON_EXECUTABLE=$PYTHON
+ make -j2 install
+ make -j2 docs
+ popd
+ popd
+# mpiexec -n 2 $PYTHON -m mpi4py -m pytest --log-cli-level=DEBUG --pyargs gmx -s --verbose
+ mpiexec -n 2 $PYTHON -m mpi4py -m pytest --pyargs gmx -s --verbose
+ ccache -s
+popd
--- /dev/null
+#!/bin/bash
+set -ev
+
+rm -rf build
+mkdir build
+pushd build
+ cmake .. -DPYTHON_EXECUTABLE=$PYTHON
+ make -j2 install
+ make -j2 test
+ $PYTHON -c "import myplugin"
+popd
+pushd tests
+ $PYTHON -m pytest
+ mpiexec -n 2 $PYTHON -m mpi4py -m pytest --log-cli-level=DEBUG -s --verbose
+popd
--- /dev/null
+export CC=`which mpicc`
+export CXX=`which mpicxx`
+export CCACHE_COMPILERCHECK=content
+${CC} --version
+${CXX} --version
--- /dev/null
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2014, by the GROMACS development team, led by
+# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+# and including many others, as listed in the AUTHORS file in the
+# top-level source directory and at http://www.gromacs.org.
+#
+# GROMACS is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public License
+# as published by the Free Software Foundation; either version 2.1
+# of the License, or (at your option) any later version.
+#
+# GROMACS is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# If you want to redistribute modifications to GROMACS, please
+# consider that scientific software is very special. Version
+# control is crucial - bugs must be traceable. We will be happy to
+# consider code for inclusion in the official distribution, but
+# derived work must not be called official GROMACS. Details are found
+# in the README & COPYING files - if they are missing, get the
+# official version at http://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+
+# This file should remain version-agnostic, with all things specific to a
+# particular GROMACS version remaining in the package configuration files.
+# This find module only provides some convenience functionality to manage the
+# suffixes etc.
+# That should allow using the same FindGROMACS.cmake file with multiple
+# different GROMACS installations on the same machine.
+
+# Propagate all flags passed to parent find_package() to the config call below.
+set(_gmx_find_args "")
+if (GROMACS_FIND_VERSION)
+ if (GROMACS_FIND_VERSION VERSION_LESS "5.1")
+ message(FATAL_ERROR
+ "This version of FindGROMACS.cmake requires GROMACS-provided "
+ "package configuration files, and only works to find "
+ "GROMACS 5.1 or later.")
+ endif()
+ list(APPEND _gmx_find_args ${GROMACS_FIND_VERSION})
+ if (GROMACS_FIND_VERSION_EXACT)
+ list(APPEND _gmx_find_args EXACT)
+ endif()
+endif()
+if (GROMACS_FIND_REQUIRED)
+ list(APPEND _gmx_find_args REQUIRED)
+endif()
+if (GROMACS_FIND_QUIETLY)
+ list(APPEND _gmx_find_args QUIET)
+endif()
+
+# Determine the actual name of the package configuration files.
+set(_gmx_pkg_name gromacs)
+if (DEFINED GROMACS_SUFFIX)
+ set(_gmx_pkg_name gromacs${GROMACS_SUFFIX})
+endif()
+# Delegate all the actual work to the package configuration files.
+# The CONFIGS option is not really necessary, but provides a bit better error
+# messages, since we actually know what the config file should be called.
+find_package(GROMACS ${_gmx_find_args} CONFIG
+ NAMES ${_gmx_pkg_name}
+ CONFIGS ${_gmx_pkg_name}-config.cmake)
+unset(_gmx_find_args)
+unset(_gmx_pkg_name)
--- /dev/null
+configure_file(Doxyfile.in Doxyfile)
+
+find_package(Doxygen)
+if (DOXYGEN_FOUND)
+ add_custom_target(docs
+ COMMAND ${DOXYGEN_EXECUTABLE} Doxyfile
+ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+ COMMENT "Generating developer documentation"
+ VERBATIM )
+else (DOXYGEN_FOUND)
+ message("Doxygen need to be installed to generate the C++ documentation")
+endif (DOXYGEN_FOUND)
--- /dev/null
+# Doxyfile 1.8.14
+
+# This file describes the settings to be used by the documentation system
+# doxygen (www.doxygen.org) for a project.
+#
+# All text after a double hash (##) is considered a comment and is placed in
+# front of the TAG it is preceding.
+#
+# All text after a single hash (#) is considered a comment and will be ignored.
+# The format is:
+# TAG = value [value, ...]
+# For lists, items can also be appended using:
+# TAG += value [value, ...]
+# Values that contain spaces should be placed between quotes (\" \").
+
+#---------------------------------------------------------------------------
+# Project related configuration options
+#---------------------------------------------------------------------------
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+# built into libc) for the transcoding. See
+# https://www.gnu.org/software/libiconv/ for the list of possible encodings.
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+
+DOXYFILE_ENCODING = UTF-8
+
+# The PROJECT_NAME tag is a single word (or a sequence of words surrounded by
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+# project for which the documentation is generated. This name is used in the
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+# The default value is: My Project.
+
+PROJECT_NAME = "gmxapi sample MD extension"
+
+# The PROJECT_NUMBER tag can be used to enter a project or revision number. This
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+PROJECT_NUMBER =
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+# The default value is: NO.
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+CREATE_SUBDIRS = NO
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+INLINE_INHERITED_MEMB = NO
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+# The default value is: YES.
+
+MARKDOWN_SUPPORT = YES
+
+# When the TOC_INCLUDE_HEADINGS tag is set to a non-zero value, all headings up
+# to that level are automatically included in the table of contents, even if
+# they do not have an id attribute.
+# Note: This feature currently applies only to Markdown headings.
+# Minimum value: 0, maximum value: 99, default value: 0.
+# This tag requires that the tag MARKDOWN_SUPPORT is set to YES.
+
+TOC_INCLUDE_HEADINGS = 0
+
+# When enabled doxygen tries to link words that correspond to documented
+# classes, or namespaces to their corresponding documentation. Such a link can
+# be prevented in individual cases by putting a % sign in front of the word or
+# globally by setting AUTOLINK_SUPPORT to NO.
+# The default value is: YES.
+
+AUTOLINK_SUPPORT = YES
+
+# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want
+# to include (a tag file for) the STL sources as input, then you should set this
+# tag to YES in order to let doxygen match functions declarations and
+# definitions whose arguments contain STL classes (e.g. func(std::string);
+# versus func(std::string) {}). This also make the inheritance and collaboration
+# diagrams that involve STL classes more complete and accurate.
+# The default value is: NO.
+
+BUILTIN_STL_SUPPORT = NO
+
+# If you use Microsoft's C++/CLI language, you should set this option to YES to
+# enable parsing support.
+# The default value is: NO.
+
+CPP_CLI_SUPPORT = NO
+
+# Set the SIP_SUPPORT tag to YES if your project consists of sip (see:
+# https://www.riverbankcomputing.com/software/sip/intro) sources only. Doxygen
+# will parse them like normal C++ but will assume all classes use public instead
+# of private inheritance when no explicit protection keyword is present.
+# The default value is: NO.
+
+SIP_SUPPORT = NO
+
+# For Microsoft's IDL there are propget and propput attributes to indicate
+# getter and setter methods for a property. Setting this option to YES will make
+# doxygen to replace the get and set methods by a property in the documentation.
+# This will only work if the methods are indeed getting or setting a simple
+# type. If this is not the case, or you want to show the methods anyway, you
+# should set this option to NO.
+# The default value is: YES.
+
+IDL_PROPERTY_SUPPORT = YES
+
+# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC
+# tag is set to YES then doxygen will reuse the documentation of the first
+# member in the group (if any) for the other members of the group. By default
+# all members of a group must be documented explicitly.
+# The default value is: NO.
+
+DISTRIBUTE_GROUP_DOC = NO
+
+# If one adds a struct or class to a group and this option is enabled, then also
+# any nested class or struct is added to the same group. By default this option
+# is disabled and one has to add nested compounds explicitly via \ingroup.
+# The default value is: NO.
+
+GROUP_NESTED_COMPOUNDS = NO
+
+# Set the SUBGROUPING tag to YES to allow class member groups of the same type
+# (for instance a group of public functions) to be put as a subgroup of that
+# type (e.g. under the Public Functions section). Set it to NO to prevent
+# subgrouping. Alternatively, this can be done per class using the
+# \nosubgrouping command.
+# The default value is: YES.
+
+SUBGROUPING = YES
+
+# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and unions
+# are shown inside the group in which they are included (e.g. using \ingroup)
+# instead of on a separate page (for HTML and Man pages) or section (for LaTeX
+# and RTF).
+#
+# Note that this feature does not work in combination with
+# SEPARATE_MEMBER_PAGES.
+# The default value is: NO.
+
+INLINE_GROUPED_CLASSES = NO
+
+# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and unions
+# with only public data fields or simple typedef fields will be shown inline in
+# the documentation of the scope in which they are defined (i.e. file,
+# namespace, or group documentation), provided this scope is documented. If set
+# to NO, structs, classes, and unions are shown on a separate page (for HTML and
+# Man pages) or section (for LaTeX and RTF).
+# The default value is: NO.
+
+INLINE_SIMPLE_STRUCTS = NO
+
+# When TYPEDEF_HIDES_STRUCT tag is enabled, a typedef of a struct, union, or
+# enum is documented as struct, union, or enum with the name of the typedef. So
+# typedef struct TypeS {} TypeT, will appear in the documentation as a struct
+# with name TypeT. When disabled the typedef will appear as a member of a file,
+# namespace, or class. And the struct will be named TypeS. This can typically be
+# useful for C code in case the coding convention dictates that all compound
+# types are typedef'ed and only the typedef is referenced, never the tag name.
+# The default value is: NO.
+
+TYPEDEF_HIDES_STRUCT = NO
+
+# The size of the symbol lookup cache can be set using LOOKUP_CACHE_SIZE. This
+# cache is used to resolve symbols given their name and scope. Since this can be
+# an expensive process and often the same symbol appears multiple times in the
+# code, doxygen keeps a cache of pre-resolved symbols. If the cache is too small
+# doxygen will become slower. If the cache is too large, memory is wasted. The
+# cache size is given by this formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range
+# is 0..9, the default is 0, corresponding to a cache size of 2^16=65536
+# symbols. At the end of a run doxygen will report the cache usage and suggest
+# the optimal cache size from a speed point of view.
+# Minimum value: 0, maximum value: 9, default value: 0.
+
+LOOKUP_CACHE_SIZE = 0
+
+#---------------------------------------------------------------------------
+# Build related configuration options
+#---------------------------------------------------------------------------
+
+# If the EXTRACT_ALL tag is set to YES, doxygen will assume all entities in
+# documentation are documented, even if no documentation was available. Private
+# class members and static file members will be hidden unless the
+# EXTRACT_PRIVATE respectively EXTRACT_STATIC tags are set to YES.
+# Note: This will also disable the warnings about undocumented members that are
+# normally produced when WARNINGS is set to YES.
+# The default value is: NO.
+
+EXTRACT_ALL = NO
+
+# If the EXTRACT_PRIVATE tag is set to YES, all private members of a class will
+# be included in the documentation.
+# The default value is: NO.
+
+EXTRACT_PRIVATE = NO
+
+# If the EXTRACT_PACKAGE tag is set to YES, all members with package or internal
+# scope will be included in the documentation.
+# The default value is: NO.
+
+EXTRACT_PACKAGE = NO
+
+# If the EXTRACT_STATIC tag is set to YES, all static members of a file will be
+# included in the documentation.
+# The default value is: NO.
+
+EXTRACT_STATIC = NO
+
+# If the EXTRACT_LOCAL_CLASSES tag is set to YES, classes (and structs) defined
+# locally in source files will be included in the documentation. If set to NO,
+# only classes defined in header files are included. Does not have any effect
+# for Java sources.
+# The default value is: YES.
+
+EXTRACT_LOCAL_CLASSES = YES
+
+# This flag is only useful for Objective-C code. If set to YES, local methods,
+# which are defined in the implementation section but not in the interface are
+# included in the documentation. If set to NO, only methods in the interface are
+# included.
+# The default value is: NO.
+
+EXTRACT_LOCAL_METHODS = NO
+
+# If this flag is set to YES, the members of anonymous namespaces will be
+# extracted and appear in the documentation as a namespace called
+# 'anonymous_namespace{file}', where file will be replaced with the base name of
+# the file that contains the anonymous namespace. By default anonymous namespace
+# are hidden.
+# The default value is: NO.
+
+EXTRACT_ANON_NSPACES = NO
+
+# If the HIDE_UNDOC_MEMBERS tag is set to YES, doxygen will hide all
+# undocumented members inside documented classes or files. If set to NO these
+# members will be included in the various overviews, but no documentation
+# section is generated. This option has no effect if EXTRACT_ALL is enabled.
+# The default value is: NO.
+
+HIDE_UNDOC_MEMBERS = NO
+
+# If the HIDE_UNDOC_CLASSES tag is set to YES, doxygen will hide all
+# undocumented classes that are normally visible in the class hierarchy. If set
+# to NO, these classes will be included in the various overviews. This option
+# has no effect if EXTRACT_ALL is enabled.
+# The default value is: NO.
+
+HIDE_UNDOC_CLASSES = NO
+
+# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, doxygen will hide all friend
+# (class|struct|union) declarations. If set to NO, these declarations will be
+# included in the documentation.
+# The default value is: NO.
+
+HIDE_FRIEND_COMPOUNDS = NO
+
+# If the HIDE_IN_BODY_DOCS tag is set to YES, doxygen will hide any
+# documentation blocks found inside the body of a function. If set to NO, these
+# blocks will be appended to the function's detailed documentation block.
+# The default value is: NO.
+
+HIDE_IN_BODY_DOCS = NO
+
+# The INTERNAL_DOCS tag determines if documentation that is typed after a
+# \internal command is included. If the tag is set to NO then the documentation
+# will be excluded. Set it to YES to include the internal documentation.
+# The default value is: NO.
+
+INTERNAL_DOCS = NO
+
+# If the CASE_SENSE_NAMES tag is set to NO then doxygen will only generate file
+# names in lower-case letters. If set to YES, upper-case letters are also
+# allowed. This is useful if you have classes or files whose names only differ
+# in case and if your file system supports case sensitive file names. Windows
+# and Mac users are advised to set this option to NO.
+# The default value is: system dependent.
+
+CASE_SENSE_NAMES = NO
+
+# If the HIDE_SCOPE_NAMES tag is set to NO then doxygen will show members with
+# their full class and namespace scopes in the documentation. If set to YES, the
+# scope will be hidden.
+# The default value is: NO.
+
+HIDE_SCOPE_NAMES = NO
+
+# If the HIDE_COMPOUND_REFERENCE tag is set to NO (default) then doxygen will
+# append additional text to a page's title, such as Class Reference. If set to
+# YES the compound reference will be hidden.
+# The default value is: NO.
+
+HIDE_COMPOUND_REFERENCE= NO
+
+# If the SHOW_INCLUDE_FILES tag is set to YES then doxygen will put a list of
+# the files that are included by a file in the documentation of that file.
+# The default value is: YES.
+
+SHOW_INCLUDE_FILES = YES
+
+# If the SHOW_GROUPED_MEMB_INC tag is set to YES then Doxygen will add for each
+# grouped member an include statement to the documentation, telling the reader
+# which file to include in order to use the member.
+# The default value is: NO.
+
+SHOW_GROUPED_MEMB_INC = NO
+
+# If the FORCE_LOCAL_INCLUDES tag is set to YES then doxygen will list include
+# files with double quotes in the documentation rather than with sharp brackets.
+# The default value is: NO.
+
+FORCE_LOCAL_INCLUDES = NO
+
+# If the INLINE_INFO tag is set to YES then a tag [inline] is inserted in the
+# documentation for inline members.
+# The default value is: YES.
+
+INLINE_INFO = YES
+
+# If the SORT_MEMBER_DOCS tag is set to YES then doxygen will sort the
+# (detailed) documentation of file and class members alphabetically by member
+# name. If set to NO, the members will appear in declaration order.
+# The default value is: YES.
+
+SORT_MEMBER_DOCS = YES
+
+# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the brief
+# descriptions of file, namespace and class members alphabetically by member
+# name. If set to NO, the members will appear in declaration order. Note that
+# this will also influence the order of the classes in the class list.
+# The default value is: NO.
+
+SORT_BRIEF_DOCS = NO
+
+# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen will sort the
+# (brief and detailed) documentation of class members so that constructors and
+# destructors are listed first. If set to NO the constructors will appear in the
+# respective orders defined by SORT_BRIEF_DOCS and SORT_MEMBER_DOCS.
+# Note: If SORT_BRIEF_DOCS is set to NO this option is ignored for sorting brief
+# member documentation.
+# Note: If SORT_MEMBER_DOCS is set to NO this option is ignored for sorting
+# detailed member documentation.
+# The default value is: NO.
+
+SORT_MEMBERS_CTORS_1ST = NO
+
+# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the hierarchy
+# of group names into alphabetical order. If set to NO the group names will
+# appear in their defined order.
+# The default value is: NO.
+
+SORT_GROUP_NAMES = NO
+
+# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be sorted by
+# fully-qualified names, including namespaces. If set to NO, the class list will
+# be sorted only by class name, not including the namespace part.
+# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES.
+# Note: This option applies only to the class list, not to the alphabetical
+# list.
+# The default value is: NO.
+
+SORT_BY_SCOPE_NAME = NO
+
+# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to do proper
+# type resolution of all parameters of a function it will reject a match between
+# the prototype and the implementation of a member function even if there is
+# only one candidate or it is obvious which candidate to choose by doing a
+# simple string match. By disabling STRICT_PROTO_MATCHING doxygen will still
+# accept a match between prototype and implementation in such cases.
+# The default value is: NO.
+
+STRICT_PROTO_MATCHING = NO
+
+# The GENERATE_TODOLIST tag can be used to enable (YES) or disable (NO) the todo
+# list. This list is created by putting \todo commands in the documentation.
+# The default value is: YES.
+
+GENERATE_TODOLIST = YES
+
+# The GENERATE_TESTLIST tag can be used to enable (YES) or disable (NO) the test
+# list. This list is created by putting \test commands in the documentation.
+# The default value is: YES.
+
+GENERATE_TESTLIST = YES
+
+# The GENERATE_BUGLIST tag can be used to enable (YES) or disable (NO) the bug
+# list. This list is created by putting \bug commands in the documentation.
+# The default value is: YES.
+
+GENERATE_BUGLIST = YES
+
+# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or disable (NO)
+# the deprecated list. This list is created by putting \deprecated commands in
+# the documentation.
+# The default value is: YES.
+
+GENERATE_DEPRECATEDLIST= YES
+
+# The ENABLED_SECTIONS tag can be used to enable conditional documentation
+# sections, marked by \if <section_label> ... \endif and \cond <section_label>
+# ... \endcond blocks.
+
+ENABLED_SECTIONS =
+
+# The MAX_INITIALIZER_LINES tag determines the maximum number of lines that the
+# initial value of a variable or macro / define can have for it to appear in the
+# documentation. If the initializer consists of more lines than specified here
+# it will be hidden. Use a value of 0 to hide initializers completely. The
+# appearance of the value of individual variables and macros / defines can be
+# controlled using \showinitializer or \hideinitializer command in the
+# documentation regardless of this setting.
+# Minimum value: 0, maximum value: 10000, default value: 30.
+
+MAX_INITIALIZER_LINES = 30
+
+# Set the SHOW_USED_FILES tag to NO to disable the list of files generated at
+# the bottom of the documentation of classes and structs. If set to YES, the
+# list will mention the files that were used to generate the documentation.
+# The default value is: YES.
+
+SHOW_USED_FILES = YES
+
+# Set the SHOW_FILES tag to NO to disable the generation of the Files page. This
+# will remove the Files entry from the Quick Index and from the Folder Tree View
+# (if specified).
+# The default value is: YES.
+
+SHOW_FILES = YES
+
+# Set the SHOW_NAMESPACES tag to NO to disable the generation of the Namespaces
+# page. This will remove the Namespaces entry from the Quick Index and from the
+# Folder Tree View (if specified).
+# The default value is: YES.
+
+SHOW_NAMESPACES = YES
+
+# The FILE_VERSION_FILTER tag can be used to specify a program or script that
+# doxygen should invoke to get the current version for each file (typically from
+# the version control system). Doxygen will invoke the program by executing (via
+# popen()) the command command input-file, where command is the value of the
+# FILE_VERSION_FILTER tag, and input-file is the name of an input file provided
+# by doxygen. Whatever the program writes to standard output is used as the file
+# version. For an example see the documentation.
+
+FILE_VERSION_FILTER =
+
+# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed
+# by doxygen. The layout file controls the global structure of the generated
+# output files in an output format independent way. To create the layout file
+# that represents doxygen's defaults, run doxygen with the -l option. You can
+# optionally specify a file name after the option, if omitted DoxygenLayout.xml
+# will be used as the name of the layout file.
+#
+# Note that if you run doxygen from a directory containing a file called
+# DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE
+# tag is left empty.
+
+LAYOUT_FILE =
+
+# The CITE_BIB_FILES tag can be used to specify one or more bib files containing
+# the reference definitions. This must be a list of .bib files. The .bib
+# extension is automatically appended if omitted. This requires the bibtex tool
+# to be installed. See also https://en.wikipedia.org/wiki/BibTeX for more info.
+# For LaTeX the style of the bibliography can be controlled using
+# LATEX_BIB_STYLE. To use this feature you need bibtex and perl available in the
+# search path. See also \cite for info how to create references.
+
+CITE_BIB_FILES =
+
+#---------------------------------------------------------------------------
+# Configuration options related to warning and progress messages
+#---------------------------------------------------------------------------
+
+# The QUIET tag can be used to turn on/off the messages that are generated to
+# standard output by doxygen. If QUIET is set to YES this implies that the
+# messages are off.
+# The default value is: NO.
+
+QUIET = NO
+
+# The WARNINGS tag can be used to turn on/off the warning messages that are
+# generated to standard error (stderr) by doxygen. If WARNINGS is set to YES
+# this implies that the warnings are on.
+#
+# Tip: Turn warnings on while writing the documentation.
+# The default value is: YES.
+
+WARNINGS = YES
+
+# If the WARN_IF_UNDOCUMENTED tag is set to YES then doxygen will generate
+# warnings for undocumented members. If EXTRACT_ALL is set to YES then this flag
+# will automatically be disabled.
+# The default value is: YES.
+
+WARN_IF_UNDOCUMENTED = YES
+
+# If the WARN_IF_DOC_ERROR tag is set to YES, doxygen will generate warnings for
+# potential errors in the documentation, such as not documenting some parameters
+# in a documented function, or documenting parameters that don't exist or using
+# markup commands wrongly.
+# The default value is: YES.
+
+WARN_IF_DOC_ERROR = YES
+
+# This WARN_NO_PARAMDOC option can be enabled to get warnings for functions that
+# are documented, but have no documentation for their parameters or return
+# value. If set to NO, doxygen will only warn about wrong or incomplete
+# parameter documentation, but not about the absence of documentation.
+# The default value is: NO.
+
+WARN_NO_PARAMDOC = NO
+
+# If the WARN_AS_ERROR tag is set to YES then doxygen will immediately stop when
+# a warning is encountered.
+# The default value is: NO.
+
+WARN_AS_ERROR = NO
+
+# The WARN_FORMAT tag determines the format of the warning messages that doxygen
+# can produce. The string should contain the $file, $line, and $text tags, which
+# will be replaced by the file and line number from which the warning originated
+# and the warning text. Optionally the format may contain $version, which will
+# be replaced by the version of the file (if it could be obtained via
+# FILE_VERSION_FILTER)
+# The default value is: $file:$line: $text.
+
+WARN_FORMAT = "$file:$line: $text"
+
+# The WARN_LOGFILE tag can be used to specify a file to which warning and error
+# messages should be written. If left blank the output is written to standard
+# error (stderr).
+
+WARN_LOGFILE =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the input files
+#---------------------------------------------------------------------------
+
+# The INPUT tag is used to specify the files and/or directories that contain
+# documented source files. You may enter file names like myfile.cpp or
+# directories like /usr/src/myproject. Separate the files or directories with
+# spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
+# Note: If this tag is empty the current directory is searched.
+
+INPUT = ${CMAKE_CURRENT_SOURCE_DIR}/../README.md ${CMAKE_CURRENT_SOURCE_DIR}/../src/cpp
+${CMAKE_CURRENT_SOURCE_DIR}/../src/pythonmodule
+
+# This tag can be used to specify the character encoding of the source files
+# that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
+# libiconv (or the iconv built into libc) for the transcoding. See the libiconv
+# documentation (see: https://www.gnu.org/software/libiconv/) for the list of
+# possible encodings.
+# The default value is: UTF-8.
+
+INPUT_ENCODING = UTF-8
+
+# If the value of the INPUT tag contains directories, you can use the
+# FILE_PATTERNS tag to specify one or more wildcard patterns (like *.cpp and
+# *.h) to filter out the source-files in the directories.
+#
+# Note that for custom extensions or not directly supported extensions you also
+# need to set EXTENSION_MAPPING for the extension otherwise the files are not
+# read by doxygen.
+#
+# If left blank the following patterns are tested:*.c, *.cc, *.cxx, *.cpp,
+# *.c++, *.java, *.ii, *.ixx, *.ipp, *.i++, *.inl, *.idl, *.ddl, *.odl, *.h,
+# *.hh, *.hxx, *.hpp, *.h++, *.cs, *.d, *.php, *.php4, *.php5, *.phtml, *.inc,
+# *.m, *.markdown, *.md, *.mm, *.dox, *.py, *.pyw, *.f90, *.f95, *.f03, *.f08,
+# *.f, *.for, *.tcl, *.vhd, *.vhdl, *.ucf and *.qsf.
+
+FILE_PATTERNS = *.c \
+ *.cc \
+ *.cxx \
+ *.cpp \
+ *.c++ \
+ *.java \
+ *.ii \
+ *.ixx \
+ *.ipp \
+ *.i++ \
+ *.inl \
+ *.idl \
+ *.ddl \
+ *.odl \
+ *.h \
+ *.hh \
+ *.hxx \
+ *.hpp \
+ *.h++ \
+ *.cs \
+ *.d \
+ *.php \
+ *.php4 \
+ *.php5 \
+ *.phtml \
+ *.inc \
+ *.m \
+ *.markdown \
+ *.md \
+ *.mm \
+ *.dox \
+ *.py \
+ *.pyw \
+ *.f90 \
+ *.f95 \
+ *.f03 \
+ *.f08 \
+ *.f \
+ *.for \
+ *.tcl \
+ *.vhd \
+ *.vhdl \
+ *.ucf \
+ *.qsf
+
+# The RECURSIVE tag can be used to specify whether or not subdirectories should
+# be searched for input files as well.
+# The default value is: NO.
+
+RECURSIVE = NO
+
+# The EXCLUDE tag can be used to specify files and/or directories that should be
+# excluded from the INPUT source files. This way you can easily exclude a
+# subdirectory from a directory tree whose root is specified with the INPUT tag.
+#
+# Note that relative paths are relative to the directory from which doxygen is
+# run.
+
+EXCLUDE =
+
+# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
+# directories that are symbolic links (a Unix file system feature) are excluded
+# from the input.
+# The default value is: NO.
+
+EXCLUDE_SYMLINKS = NO
+
+# If the value of the INPUT tag contains directories, you can use the
+# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude
+# certain files from those directories.
+#
+# Note that the wildcards are matched against the file with absolute path, so to
+# exclude all test directories for example use the pattern */test/*
+
+EXCLUDE_PATTERNS =
+
+# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
+# (namespaces, classes, functions, etc.) that should be excluded from the
+# output. The symbol name can be a fully qualified name, a word, or if the
+# wildcard * is used, a substring. Examples: ANamespace, AClass,
+# AClass::ANamespace, ANamespace::*Test
+#
+# Note that the wildcards are matched against the file with absolute path, so to
+# exclude all test directories use the pattern */test/*
+
+EXCLUDE_SYMBOLS =
+
+# The EXAMPLE_PATH tag can be used to specify one or more files or directories
+# that contain example code fragments that are included (see the \include
+# command).
+
+EXAMPLE_PATH =
+
+# If the value of the EXAMPLE_PATH tag contains directories, you can use the
+# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and
+# *.h) to filter out the source-files in the directories. If left blank all
+# files are included.
+
+EXAMPLE_PATTERNS = *
+
+# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
+# searched for input files to be used with the \include or \dontinclude commands
+# irrespective of the value of the RECURSIVE tag.
+# The default value is: NO.
+
+EXAMPLE_RECURSIVE = NO
+
+# The IMAGE_PATH tag can be used to specify one or more files or directories
+# that contain images that are to be included in the documentation (see the
+# \image command).
+
+IMAGE_PATH =
+
+# The INPUT_FILTER tag can be used to specify a program that doxygen should
+# invoke to filter for each input file. Doxygen will invoke the filter program
+# by executing (via popen()) the command:
+#
+# <filter> <input-file>
+#
+# where <filter> is the value of the INPUT_FILTER tag, and <input-file> is the
+# name of an input file. Doxygen will then use the output that the filter
+# program writes to standard output. If FILTER_PATTERNS is specified, this tag
+# will be ignored.
+#
+# Note that the filter must not add or remove lines; it is applied before the
+# code is scanned, but not when the output code is generated. If lines are added
+# or removed, the anchors will not be placed correctly.
+#
+# Note that for custom extensions or not directly supported extensions you also
+# need to set EXTENSION_MAPPING for the extension otherwise the files are not
+# properly processed by doxygen.
+
+INPUT_FILTER =
+
+# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern
+# basis. Doxygen will compare the file name with each pattern and apply the
+# filter if there is a match. The filters are a list of the form: pattern=filter
+# (like *.cpp=my_cpp_filter). See INPUT_FILTER for further information on how
+# filters are used. If the FILTER_PATTERNS tag is empty or if none of the
+# patterns match the file name, INPUT_FILTER is applied.
+#
+# Note that for custom extensions or not directly supported extensions you also
+# need to set EXTENSION_MAPPING for the extension otherwise the files are not
+# properly processed by doxygen.
+
+FILTER_PATTERNS =
+
+# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using
+# INPUT_FILTER) will also be used to filter the input files that are used for
+# producing the source files to browse (i.e. when SOURCE_BROWSER is set to YES).
+# The default value is: NO.
+
+FILTER_SOURCE_FILES = NO
+
+# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file
+# pattern. A pattern will override the setting for FILTER_PATTERN (if any) and
+# it is also possible to disable source filtering for a specific pattern using
+# *.ext= (so without naming a filter).
+# This tag requires that the tag FILTER_SOURCE_FILES is set to YES.
+
+FILTER_SOURCE_PATTERNS =
+
+# If the USE_MDFILE_AS_MAINPAGE tag refers to the name of a markdown file that
+# is part of the input, its contents will be placed on the main page
+# (index.html). This can be useful if you have a project on for instance GitHub
+# and want to reuse the introduction page also for the doxygen output.
+
+USE_MDFILE_AS_MAINPAGE = ${CMAKE_CURRENT_SOURCE_DIR}/../README.md
+
+#---------------------------------------------------------------------------
+# Configuration options related to source browsing
+#---------------------------------------------------------------------------
+
+# If the SOURCE_BROWSER tag is set to YES then a list of source files will be
+# generated. Documented entities will be cross-referenced with these sources.
+#
+# Note: To get rid of all source code in the generated output, make sure that
+# also VERBATIM_HEADERS is set to NO.
+# The default value is: NO.
+
+SOURCE_BROWSER = NO
+
+# Setting the INLINE_SOURCES tag to YES will include the body of functions,
+# classes and enums directly into the documentation.
+# The default value is: NO.
+
+INLINE_SOURCES = NO
+
+# Setting the STRIP_CODE_COMMENTS tag to YES will instruct doxygen to hide any
+# special comment blocks from generated source code fragments. Normal C, C++ and
+# Fortran comments will always remain visible.
+# The default value is: YES.
+
+STRIP_CODE_COMMENTS = YES
+
+# If the REFERENCED_BY_RELATION tag is set to YES then for each documented
+# function all documented functions referencing it will be listed.
+# The default value is: NO.
+
+REFERENCED_BY_RELATION = NO
+
+# If the REFERENCES_RELATION tag is set to YES then for each documented function
+# all documented entities called/used by that function will be listed.
+# The default value is: NO.
+
+REFERENCES_RELATION = NO
+
+# If the REFERENCES_LINK_SOURCE tag is set to YES and SOURCE_BROWSER tag is set
+# to YES then the hyperlinks from functions in REFERENCES_RELATION and
+# REFERENCED_BY_RELATION lists will link to the source code. Otherwise they will
+# link to the documentation.
+# The default value is: YES.
+
+REFERENCES_LINK_SOURCE = YES
+
+# If SOURCE_TOOLTIPS is enabled (the default) then hovering a hyperlink in the
+# source code will show a tooltip with additional information such as prototype,
+# brief description and links to the definition and documentation. Since this
+# will make the HTML file larger and loading of large files a bit slower, you
+# can opt to disable this feature.
+# The default value is: YES.
+# This tag requires that the tag SOURCE_BROWSER is set to YES.
+
+SOURCE_TOOLTIPS = YES
+
+# If the USE_HTAGS tag is set to YES then the references to source code will
+# point to the HTML generated by the htags(1) tool instead of doxygen built-in
+# source browser. The htags tool is part of GNU's global source tagging system
+# (see https://www.gnu.org/software/global/global.html). You will need version
+# 4.8.6 or higher.
+#
+# To use it do the following:
+# - Install the latest version of global
+# - Enable SOURCE_BROWSER and USE_HTAGS in the config file
+# - Make sure the INPUT points to the root of the source tree
+# - Run doxygen as normal
+#
+# Doxygen will invoke htags (and that will in turn invoke gtags), so these
+# tools must be available from the command line (i.e. in the search path).
+#
+# The result: instead of the source browser generated by doxygen, the links to
+# source code will now point to the output of htags.
+# The default value is: NO.
+# This tag requires that the tag SOURCE_BROWSER is set to YES.
+
+USE_HTAGS = NO
+
+# If the VERBATIM_HEADERS tag is set the YES then doxygen will generate a
+# verbatim copy of the header file for each class for which an include is
+# specified. Set to NO to disable this.
+# See also: Section \class.
+# The default value is: YES.
+
+VERBATIM_HEADERS = YES
+
+#---------------------------------------------------------------------------
+# Configuration options related to the alphabetical class index
+#---------------------------------------------------------------------------
+
+# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index of all
+# compounds will be generated. Enable this if the project contains a lot of
+# classes, structs, unions or interfaces.
+# The default value is: YES.
+
+ALPHABETICAL_INDEX = YES
+
+# The COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns in
+# which the alphabetical index list will be split.
+# Minimum value: 1, maximum value: 20, default value: 5.
+# This tag requires that the tag ALPHABETICAL_INDEX is set to YES.
+
+COLS_IN_ALPHA_INDEX = 5
+
+# In case all classes in a project start with a common prefix, all classes will
+# be put under the same header in the alphabetical index. The IGNORE_PREFIX tag
+# can be used to specify a prefix (or a list of prefixes) that should be ignored
+# while generating the index headers.
+# This tag requires that the tag ALPHABETICAL_INDEX is set to YES.
+
+IGNORE_PREFIX =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the HTML output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_HTML tag is set to YES, doxygen will generate HTML output
+# The default value is: YES.
+
+GENERATE_HTML = YES
+
+# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: html.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_OUTPUT = html
+
+# The HTML_FILE_EXTENSION tag can be used to specify the file extension for each
+# generated HTML page (for example: .htm, .php, .asp).
+# The default value is: .html.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_FILE_EXTENSION = .html
+
+# The HTML_HEADER tag can be used to specify a user-defined HTML header file for
+# each generated HTML page. If the tag is left blank doxygen will generate a
+# standard header.
+#
+# To get valid HTML the header file that includes any scripts and style sheets
+# that doxygen needs, which is dependent on the configuration options used (e.g.
+# the setting GENERATE_TREEVIEW). It is highly recommended to start with a
+# default header using
+# doxygen -w html new_header.html new_footer.html new_stylesheet.css
+# YourConfigFile
+# and then modify the file new_header.html. See also section "Doxygen usage"
+# for information on how to generate the default header that doxygen normally
+# uses.
+# Note: The header is subject to change so you typically have to regenerate the
+# default header when upgrading to a newer version of doxygen. For a description
+# of the possible markers and block names see the documentation.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_HEADER =
+
+# The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each
+# generated HTML page. If the tag is left blank doxygen will generate a standard
+# footer. See HTML_HEADER for more information on how to generate a default
+# footer and what special commands can be used inside the footer. See also
+# section "Doxygen usage" for information on how to generate the default footer
+# that doxygen normally uses.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_FOOTER =
+
+# The HTML_STYLESHEET tag can be used to specify a user-defined cascading style
+# sheet that is used by each HTML page. It can be used to fine-tune the look of
+# the HTML output. If left blank doxygen will generate a default style sheet.
+# See also section "Doxygen usage" for information on how to generate the style
+# sheet that doxygen normally uses.
+# Note: It is recommended to use HTML_EXTRA_STYLESHEET instead of this tag, as
+# it is more robust and this tag (HTML_STYLESHEET) will in the future become
+# obsolete.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_STYLESHEET =
+
+# The HTML_EXTRA_STYLESHEET tag can be used to specify additional user-defined
+# cascading style sheets that are included after the standard style sheets
+# created by doxygen. Using this option one can overrule certain style aspects.
+# This is preferred over using HTML_STYLESHEET since it does not replace the
+# standard style sheet and is therefore more robust against future updates.
+# Doxygen will copy the style sheet files to the output directory.
+# Note: The order of the extra style sheet files is of importance (e.g. the last
+# style sheet in the list overrules the setting of the previous ones in the
+# list). For an example see the documentation.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_EXTRA_STYLESHEET =
+
+# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or
+# other source files which should be copied to the HTML output directory. Note
+# that these files will be copied to the base HTML output directory. Use the
+# $relpath^ marker in the HTML_HEADER and/or HTML_FOOTER files to load these
+# files. In the HTML_STYLESHEET file, use the file name only. Also note that the
+# files will be copied as-is; there are no commands or markers available.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_EXTRA_FILES =
+
+# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen
+# will adjust the colors in the style sheet and background images according to
+# this color. Hue is specified as an angle on a colorwheel, see
+# https://en.wikipedia.org/wiki/Hue for more information. For instance the value
+# 0 represents red, 60 is yellow, 120 is green, 180 is cyan, 240 is blue, 300
+# purple, and 360 is red again.
+# Minimum value: 0, maximum value: 359, default value: 220.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_COLORSTYLE_HUE = 220
+
+# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of the colors
+# in the HTML output. For a value of 0 the output will use grayscales only. A
+# value of 255 will produce the most vivid colors.
+# Minimum value: 0, maximum value: 255, default value: 100.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_COLORSTYLE_SAT = 100
+
+# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to the
+# luminance component of the colors in the HTML output. Values below 100
+# gradually make the output lighter, whereas values above 100 make the output
+# darker. The value divided by 100 is the actual gamma applied, so 80 represents
+# a gamma of 0.8, The value 220 represents a gamma of 2.2, and 100 does not
+# change the gamma.
+# Minimum value: 40, maximum value: 240, default value: 80.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_COLORSTYLE_GAMMA = 80
+
+# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML
+# page will contain the date and time when the page was generated. Setting this
+# to YES can help to show when doxygen was last run and thus if the
+# documentation is up to date.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_TIMESTAMP = NO
+
+# If the HTML_DYNAMIC_MENUS tag is set to YES then the generated HTML
+# documentation will contain a main index with vertical navigation menus that
+# are dynamically created via Javascript. If disabled, the navigation index will
+# consists of multiple levels of tabs that are statically embedded in every HTML
+# page. Disable this option to support browsers that do not have Javascript,
+# like the Qt help browser.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_DYNAMIC_MENUS = YES
+
+# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
+# documentation will contain sections that can be hidden and shown after the
+# page has loaded.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_DYNAMIC_SECTIONS = NO
+
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of entries
+# shown in the various tree structured indices initially; the user can expand
+# and collapse entries dynamically later on. Doxygen will expand the tree to
+# such a level that at most the specified number of entries are visible (unless
+# a fully collapsed tree already exceeds this amount). So setting the number of
+# entries 1 will produce a full collapsed tree by default. 0 is a special value
+# representing an infinite number of entries and will result in a full expanded
+# tree by default.
+# Minimum value: 0, maximum value: 9999, default value: 100.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
+# If the GENERATE_DOCSET tag is set to YES, additional index files will be
+# generated that can be used as input for Apple's Xcode 3 integrated development
+# environment (see: https://developer.apple.com/tools/xcode/), introduced with
+# OSX 10.5 (Leopard). To create a documentation set, doxygen will generate a
+# Makefile in the HTML output directory. Running make will produce the docset in
+# that directory and running make install will install the docset in
+# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find it at
+# startup. See https://developer.apple.com/tools/creatingdocsetswithdoxygen.html
+# for more information.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_DOCSET = NO
+
+# This tag determines the name of the docset feed. A documentation feed provides
+# an umbrella under which multiple documentation sets from a single provider
+# (such as a company or product suite) can be grouped.
+# The default value is: Doxygen generated docs.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
+
+DOCSET_FEEDNAME = "Doxygen generated docs"
+
+# This tag specifies a string that should uniquely identify the documentation
+# set bundle. This should be a reverse domain-name style string, e.g.
+# com.mycompany.MyDocSet. Doxygen will append .docset to the name.
+# The default value is: org.doxygen.Project.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
+
+DOCSET_BUNDLE_ID = org.doxygen.Project
+
+# The DOCSET_PUBLISHER_ID tag specifies a string that should uniquely identify
+# the documentation publisher. This should be a reverse domain-name style
+# string, e.g. com.mycompany.MyDocSet.documentation.
+# The default value is: org.doxygen.Publisher.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
+
+DOCSET_PUBLISHER_ID = org.doxygen.Publisher
+
+# The DOCSET_PUBLISHER_NAME tag identifies the documentation publisher.
+# The default value is: Publisher.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
+
+DOCSET_PUBLISHER_NAME = Publisher
+
+# If the GENERATE_HTMLHELP tag is set to YES then doxygen generates three
+# additional HTML index files: index.hhp, index.hhc, and index.hhk. The
+# index.hhp is a project file that can be read by Microsoft's HTML Help Workshop
+# (see: http://www.microsoft.com/en-us/download/details.aspx?id=21138) on
+# Windows.
+#
+# The HTML Help Workshop contains a compiler that can convert all HTML output
+# generated by doxygen into a single compiled HTML file (.chm). Compiled HTML
+# files are now used as the Windows 98 help format, and will replace the old
+# Windows help format (.hlp) on all Windows platforms in the future. Compressed
+# HTML files also contain an index, a table of contents, and you can search for
+# words in the documentation. The HTML workshop also contains a viewer for
+# compressed HTML files.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_HTMLHELP = NO
+
+# The CHM_FILE tag can be used to specify the file name of the resulting .chm
+# file. You can add a path in front of the file if the result should not be
+# written to the html output directory.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+CHM_FILE =
+
+# The HHC_LOCATION tag can be used to specify the location (absolute path
+# including file name) of the HTML help compiler (hhc.exe). If non-empty,
+# doxygen will try to run the HTML help compiler on the generated index.hhp.
+# The file has to be specified with full path.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+HHC_LOCATION =
+
+# The GENERATE_CHI flag controls if a separate .chi index file is generated
+# (YES) or that it should be included in the master .chm file (NO).
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+GENERATE_CHI = NO
+
+# The CHM_INDEX_ENCODING is used to encode HtmlHelp index (hhk), content (hhc)
+# and project file content.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+CHM_INDEX_ENCODING =
+
+# The BINARY_TOC flag controls whether a binary table of contents is generated
+# (YES) or a normal table of contents (NO) in the .chm file. Furthermore it
+# enables the Previous and Next buttons.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+BINARY_TOC = NO
+
+# The TOC_EXPAND flag can be set to YES to add extra items for group members to
+# the table of contents of the HTML help documentation and to the tree view.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+TOC_EXPAND = NO
+
+# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and
+# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated that
+# can be used as input for Qt's qhelpgenerator to generate a Qt Compressed Help
+# (.qch) of the generated HTML documentation.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_QHP = NO
+
+# If the QHG_LOCATION tag is specified, the QCH_FILE tag can be used to specify
+# the file name of the resulting .qch file. The path specified is relative to
+# the HTML output folder.
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QCH_FILE =
+
+# The QHP_NAMESPACE tag specifies the namespace to use when generating Qt Help
+# Project output. For more information please see Qt Help Project / Namespace
+# (see: http://doc.qt.io/qt-4.8/qthelpproject.html#namespace).
+# The default value is: org.doxygen.Project.
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_NAMESPACE = org.doxygen.Project
+
+# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating Qt
+# Help Project output. For more information please see Qt Help Project / Virtual
+# Folders (see: http://doc.qt.io/qt-4.8/qthelpproject.html#virtual-folders).
+# The default value is: doc.
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_VIRTUAL_FOLDER = doc
+
+# If the QHP_CUST_FILTER_NAME tag is set, it specifies the name of a custom
+# filter to add. For more information please see Qt Help Project / Custom
+# Filters (see: http://doc.qt.io/qt-4.8/qthelpproject.html#custom-filters).
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_CUST_FILTER_NAME =
+
+# The QHP_CUST_FILTER_ATTRS tag specifies the list of the attributes of the
+# custom filter to add. For more information please see Qt Help Project / Custom
+# Filters (see: http://doc.qt.io/qt-4.8/qthelpproject.html#custom-filters).
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_CUST_FILTER_ATTRS =
+
+# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this
+# project's filter section matches. Qt Help Project / Filter Attributes (see:
+# http://doc.qt.io/qt-4.8/qthelpproject.html#filter-attributes).
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_SECT_FILTER_ATTRS =
+
+# The QHG_LOCATION tag can be used to specify the location of Qt's
+# qhelpgenerator. If non-empty doxygen will try to run qhelpgenerator on the
+# generated .qhp file.
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHG_LOCATION =
+
+# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files will be
+# generated, together with the HTML files, they form an Eclipse help plugin. To
+# install this plugin and make it available under the help contents menu in
+# Eclipse, the contents of the directory containing the HTML and XML files needs
+# to be copied into the plugins directory of eclipse. The name of the directory
+# within the plugins directory should be the same as the ECLIPSE_DOC_ID value.
+# After copying Eclipse needs to be restarted before the help appears.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_ECLIPSEHELP = NO
+
+# A unique identifier for the Eclipse help plugin. When installing the plugin
+# the directory name containing the HTML and XML files should also have this
+# name. Each documentation set should have its own identifier.
+# The default value is: org.doxygen.Project.
+# This tag requires that the tag GENERATE_ECLIPSEHELP is set to YES.
+
+ECLIPSE_DOC_ID = org.doxygen.Project
+
+# If you want full control over the layout of the generated HTML pages it might
+# be necessary to disable the index and replace it with your own. The
+# DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs) at top
+# of each HTML page. A value of NO enables the index and the value YES disables
+# it. Since the tabs in the index contain the same information as the navigation
+# tree, you can set this option to YES if you also set GENERATE_TREEVIEW to YES.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+DISABLE_INDEX = NO
+
+# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
+# structure should be generated to display hierarchical information. If the tag
+# value is set to YES, a side panel will be generated containing a tree-like
+# index structure (just like the one that is generated for HTML Help). For this
+# to work a browser that supports JavaScript, DHTML, CSS and frames is required
+# (i.e. any modern browser). Windows users are probably better off using the
+# HTML help feature. Via custom style sheets (see HTML_EXTRA_STYLESHEET) one can
+# further fine-tune the look of the index. As an example, the default style
+# sheet generated by doxygen has an example that shows how to put an image at
+# the root of the tree instead of the PROJECT_NAME. Since the tree basically has
+# the same information as the tab index, you could consider setting
+# DISABLE_INDEX to YES when enabling this option.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_TREEVIEW = NO
+
+# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that
+# doxygen will group on one line in the generated HTML documentation.
+#
+# Note that a value of 0 will completely suppress the enum values from appearing
+# in the overview section.
+# Minimum value: 0, maximum value: 20, default value: 4.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+ENUM_VALUES_PER_LINE = 4
+
+# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be used
+# to set the initial width (in pixels) of the frame in which the tree is shown.
+# Minimum value: 0, maximum value: 1500, default value: 250.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+TREEVIEW_WIDTH = 250
+
+# If the EXT_LINKS_IN_WINDOW option is set to YES, doxygen will open links to
+# external symbols imported via tag files in a separate window.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+EXT_LINKS_IN_WINDOW = NO
+
+# Use this tag to change the font size of LaTeX formulas included as images in
+# the HTML documentation. When you change the font size after a successful
+# doxygen run you need to manually remove any form_*.png images from the HTML
+# output directory to force them to be regenerated.
+# Minimum value: 8, maximum value: 50, default value: 10.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+FORMULA_FONTSIZE = 10
+
+# Use the FORMULA_TRANSPARENT tag to determine whether or not the images
+# generated for formulas are transparent PNGs. Transparent PNGs are not
+# supported properly for IE 6.0, but are supported on all modern browsers.
+#
+# Note that when changing this option you need to delete any form_*.png files in
+# the HTML output directory before the changes have effect.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+FORMULA_TRANSPARENT = YES
+
+# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax (see
+# https://www.mathjax.org) which uses client side Javascript for the rendering
+# instead of using pre-rendered bitmaps. Use this if you do not have LaTeX
+# installed or if you want to formulas look prettier in the HTML output. When
+# enabled you may also need to install MathJax separately and configure the path
+# to it using the MATHJAX_RELPATH option.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+USE_MATHJAX = NO
+
+# When MathJax is enabled you can set the default output format to be used for
+# the MathJax output. See the MathJax site (see:
+# http://docs.mathjax.org/en/latest/output.html) for more details.
+# Possible values are: HTML-CSS (which is slower, but has the best
+# compatibility), NativeMML (i.e. MathML) and SVG.
+# The default value is: HTML-CSS.
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_FORMAT = HTML-CSS
+
+# When MathJax is enabled you need to specify the location relative to the HTML
+# output directory using the MATHJAX_RELPATH option. The destination directory
+# should contain the MathJax.js script. For instance, if the mathjax directory
+# is located at the same level as the HTML output directory, then
+# MATHJAX_RELPATH should be ../mathjax. The default value points to the MathJax
+# Content Delivery Network so you can quickly see the result without installing
+# MathJax. However, it is strongly recommended to install a local copy of
+# MathJax from https://www.mathjax.org before deployment.
+# The default value is: https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.2/.
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_RELPATH = https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.2/
+
+# The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax
+# extension names that should be enabled during MathJax rendering. For example
+# MATHJAX_EXTENSIONS = TeX/AMSmath TeX/AMSsymbols
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_EXTENSIONS =
+
+# The MATHJAX_CODEFILE tag can be used to specify a file with javascript pieces
+# of code that will be used on startup of the MathJax code. See the MathJax site
+# (see: http://docs.mathjax.org/en/latest/output.html) for more details. For an
+# example see the documentation.
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_CODEFILE =
+
+# When the SEARCHENGINE tag is enabled doxygen will generate a search box for
+# the HTML output. The underlying search engine uses javascript and DHTML and
+# should work on any modern browser. Note that when using HTML help
+# (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets (GENERATE_DOCSET)
+# there is already a search function so this one should typically be disabled.
+# For large projects the javascript based search engine can be slow, then
+# enabling SERVER_BASED_SEARCH may provide a better solution. It is possible to
+# search using the keyboard; to jump to the search box use <access key> + S
+# (what the <access key> is depends on the OS and browser, but it is typically
+# <CTRL>, <ALT>/<option>, or both). Inside the search box use the <cursor down
+# key> to jump into the search results window, the results can be navigated
+# using the <cursor keys>. Press <Enter> to select an item or <escape> to cancel
+# the search. The filter options can be selected when the cursor is inside the
+# search box by pressing <Shift>+<cursor down>. Also here use the <cursor keys>
+# to select a filter and <Enter> or <escape> to activate or cancel the filter
+# option.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+SEARCHENGINE = YES
+
+# When the SERVER_BASED_SEARCH tag is enabled the search engine will be
+# implemented using a web server instead of a web client using Javascript. There
+# are two flavors of web server based searching depending on the EXTERNAL_SEARCH
+# setting. When disabled, doxygen will generate a PHP script for searching and
+# an index file used by the script. When EXTERNAL_SEARCH is enabled the indexing
+# and searching needs to be provided by external tools. See the section
+# "External Indexing and Searching" for details.
+# The default value is: NO.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+SERVER_BASED_SEARCH = NO
+
+# When EXTERNAL_SEARCH tag is enabled doxygen will no longer generate the PHP
+# script for searching. Instead the search results are written to an XML file
+# which needs to be processed by an external indexer. Doxygen will invoke an
+# external search engine pointed to by the SEARCHENGINE_URL option to obtain the
+# search results.
+#
+# Doxygen ships with an example indexer (doxyindexer) and search engine
+# (doxysearch.cgi) which are based on the open source search engine library
+# Xapian (see: https://xapian.org/).
+#
+# See the section "External Indexing and Searching" for details.
+# The default value is: NO.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+EXTERNAL_SEARCH = NO
+
+# The SEARCHENGINE_URL should point to a search engine hosted by a web server
+# which will return the search results when EXTERNAL_SEARCH is enabled.
+#
+# Doxygen ships with an example indexer (doxyindexer) and search engine
+# (doxysearch.cgi) which are based on the open source search engine library
+# Xapian (see: https://xapian.org/). See the section "External Indexing and
+# Searching" for details.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+SEARCHENGINE_URL =
+
+# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the unindexed
+# search data is written to a file for indexing by an external tool. With the
+# SEARCHDATA_FILE tag the name of this file can be specified.
+# The default file is: searchdata.xml.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+SEARCHDATA_FILE = searchdata.xml
+
+# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the
+# EXTERNAL_SEARCH_ID tag can be used as an identifier for the project. This is
+# useful in combination with EXTRA_SEARCH_MAPPINGS to search through multiple
+# projects and redirect the results back to the right project.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+EXTERNAL_SEARCH_ID =
+
+# The EXTRA_SEARCH_MAPPINGS tag can be used to enable searching through doxygen
+# projects other than the one defined by this configuration file, but that are
+# all added to the same external search index. Each project needs to have a
+# unique id set via EXTERNAL_SEARCH_ID. The search mapping then maps the id of
+# to a relative location where the documentation can be found. The format is:
+# EXTRA_SEARCH_MAPPINGS = tagname1=loc1 tagname2=loc2 ...
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+EXTRA_SEARCH_MAPPINGS =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the LaTeX output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_LATEX tag is set to YES, doxygen will generate LaTeX output.
+# The default value is: YES.
+
+GENERATE_LATEX = YES
+
+# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: latex.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_OUTPUT = latex
+
+# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be
+# invoked.
+#
+# Note that when enabling USE_PDFLATEX this option is only used for generating
+# bitmaps for formulas in the HTML output, but not in the Makefile that is
+# written to the output directory.
+# The default file is: latex.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_CMD_NAME = latex
+
+# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to generate
+# index for LaTeX.
+# The default file is: makeindex.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+MAKEINDEX_CMD_NAME = makeindex
+
+# If the COMPACT_LATEX tag is set to YES, doxygen generates more compact LaTeX
+# documents. This may be useful for small projects and may help to save some
+# trees in general.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+COMPACT_LATEX = NO
+
+# The PAPER_TYPE tag can be used to set the paper type that is used by the
+# printer.
+# Possible values are: a4 (210 x 297 mm), letter (8.5 x 11 inches), legal (8.5 x
+# 14 inches) and executive (7.25 x 10.5 inches).
+# The default value is: a4.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+PAPER_TYPE = a4
+
+# The EXTRA_PACKAGES tag can be used to specify one or more LaTeX package names
+# that should be included in the LaTeX output. The package can be specified just
+# by its name or with the correct syntax as to be used with the LaTeX
+# \usepackage command. To get the times font for instance you can specify :
+# EXTRA_PACKAGES=times or EXTRA_PACKAGES={times}
+# To use the option intlimits with the amsmath package you can specify:
+# EXTRA_PACKAGES=[intlimits]{amsmath}
+# If left blank no extra packages will be included.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+EXTRA_PACKAGES =
+
+# The LATEX_HEADER tag can be used to specify a personal LaTeX header for the
+# generated LaTeX document. The header should contain everything until the first
+# chapter. If it is left blank doxygen will generate a standard header. See
+# section "Doxygen usage" for information on how to let doxygen write the
+# default header to a separate file.
+#
+# Note: Only use a user-defined header if you know what you are doing! The
+# following commands have a special meaning inside the header: $title,
+# $datetime, $date, $doxygenversion, $projectname, $projectnumber,
+# $projectbrief, $projectlogo. Doxygen will replace $title with the empty
+# string, for the replacement values of the other commands the user is referred
+# to HTML_HEADER.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_HEADER =
+
+# The LATEX_FOOTER tag can be used to specify a personal LaTeX footer for the
+# generated LaTeX document. The footer should contain everything after the last
+# chapter. If it is left blank doxygen will generate a standard footer. See
+# LATEX_HEADER for more information on how to generate a default footer and what
+# special commands can be used inside the footer.
+#
+# Note: Only use a user-defined footer if you know what you are doing!
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_FOOTER =
+
+# The LATEX_EXTRA_STYLESHEET tag can be used to specify additional user-defined
+# LaTeX style sheets that are included after the standard style sheets created
+# by doxygen. Using this option one can overrule certain style aspects. Doxygen
+# will copy the style sheet files to the output directory.
+# Note: The order of the extra style sheet files is of importance (e.g. the last
+# style sheet in the list overrules the setting of the previous ones in the
+# list).
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_EXTRA_STYLESHEET =
+
+# The LATEX_EXTRA_FILES tag can be used to specify one or more extra images or
+# other source files which should be copied to the LATEX_OUTPUT output
+# directory. Note that the files will be copied as-is; there are no commands or
+# markers available.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_EXTRA_FILES =
+
+# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated is
+# prepared for conversion to PDF (using ps2pdf or pdflatex). The PDF file will
+# contain links (just like the HTML output) instead of page references. This
+# makes the output suitable for online browsing using a PDF viewer.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+PDF_HYPERLINKS = YES
+
+# If the USE_PDFLATEX tag is set to YES, doxygen will use pdflatex to generate
+# the PDF file directly from the LaTeX files. Set this option to YES, to get a
+# higher quality PDF documentation.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+USE_PDFLATEX = YES
+
+# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \batchmode
+# command to the generated LaTeX files. This will instruct LaTeX to keep running
+# if errors occur, instead of asking the user for help. This option is also used
+# when generating formulas in HTML.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_BATCHMODE = NO
+
+# If the LATEX_HIDE_INDICES tag is set to YES then doxygen will not include the
+# index chapters (such as File Index, Compound Index, etc.) in the output.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_HIDE_INDICES = NO
+
+# If the LATEX_SOURCE_CODE tag is set to YES then doxygen will include source
+# code with syntax highlighting in the LaTeX output.
+#
+# Note that which sources are shown also depends on other settings such as
+# SOURCE_BROWSER.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_SOURCE_CODE = NO
+
+# The LATEX_BIB_STYLE tag can be used to specify the style to use for the
+# bibliography, e.g. plainnat, or ieeetr. See
+# https://en.wikipedia.org/wiki/BibTeX and \cite for more info.
+# The default value is: plain.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_BIB_STYLE = plain
+
+# If the LATEX_TIMESTAMP tag is set to YES then the footer of each generated
+# page will contain the date and time when the page was generated. Setting this
+# to NO can help when comparing the output of multiple runs.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_TIMESTAMP = NO
+
+#---------------------------------------------------------------------------
+# Configuration options related to the RTF output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_RTF tag is set to YES, doxygen will generate RTF output. The
+# RTF output is optimized for Word 97 and may not look too pretty with other RTF
+# readers/editors.
+# The default value is: NO.
+
+GENERATE_RTF = NO
+
+# The RTF_OUTPUT tag is used to specify where the RTF docs will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: rtf.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+RTF_OUTPUT = rtf
+
+# If the COMPACT_RTF tag is set to YES, doxygen generates more compact RTF
+# documents. This may be useful for small projects and may help to save some
+# trees in general.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+COMPACT_RTF = NO
+
+# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated will
+# contain hyperlink fields. The RTF file will contain links (just like the HTML
+# output) instead of page references. This makes the output suitable for online
+# browsing using Word or some other Word compatible readers that support those
+# fields.
+#
+# Note: WordPad (write) and others do not support links.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+RTF_HYPERLINKS = NO
+
+# Load stylesheet definitions from file. Syntax is similar to doxygen's config
+# file, i.e. a series of assignments. You only have to provide replacements,
+# missing definitions are set to their default value.
+#
+# See also section "Doxygen usage" for information on how to generate the
+# default style sheet that doxygen normally uses.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+RTF_STYLESHEET_FILE =
+
+# Set optional variables used in the generation of an RTF document. Syntax is
+# similar to doxygen's config file. A template extensions file can be generated
+# using doxygen -e rtf extensionFile.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+RTF_EXTENSIONS_FILE =
+
+# If the RTF_SOURCE_CODE tag is set to YES then doxygen will include source code
+# with syntax highlighting in the RTF output.
+#
+# Note that which sources are shown also depends on other settings such as
+# SOURCE_BROWSER.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+RTF_SOURCE_CODE = NO
+
+#---------------------------------------------------------------------------
+# Configuration options related to the man page output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_MAN tag is set to YES, doxygen will generate man pages for
+# classes and files.
+# The default value is: NO.
+
+GENERATE_MAN = NO
+
+# The MAN_OUTPUT tag is used to specify where the man pages will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it. A directory man3 will be created inside the directory specified by
+# MAN_OUTPUT.
+# The default directory is: man.
+# This tag requires that the tag GENERATE_MAN is set to YES.
+
+MAN_OUTPUT = man
+
+# The MAN_EXTENSION tag determines the extension that is added to the generated
+# man pages. In case the manual section does not start with a number, the number
+# 3 is prepended. The dot (.) at the beginning of the MAN_EXTENSION tag is
+# optional.
+# The default value is: .3.
+# This tag requires that the tag GENERATE_MAN is set to YES.
+
+MAN_EXTENSION = .3
+
+# The MAN_SUBDIR tag determines the name of the directory created within
+# MAN_OUTPUT in which the man pages are placed. If defaults to man followed by
+# MAN_EXTENSION with the initial . removed.
+# This tag requires that the tag GENERATE_MAN is set to YES.
+
+MAN_SUBDIR =
+
+# If the MAN_LINKS tag is set to YES and doxygen generates man output, then it
+# will generate one additional man file for each entity documented in the real
+# man page(s). These additional files only source the real man page, but without
+# them the man command would be unable to find the correct page.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_MAN is set to YES.
+
+MAN_LINKS = NO
+
+#---------------------------------------------------------------------------
+# Configuration options related to the XML output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_XML tag is set to YES, doxygen will generate an XML file that
+# captures the structure of the code including all documentation.
+# The default value is: NO.
+
+GENERATE_XML = NO
+
+# The XML_OUTPUT tag is used to specify where the XML pages will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: xml.
+# This tag requires that the tag GENERATE_XML is set to YES.
+
+XML_OUTPUT = xml
+
+# If the XML_PROGRAMLISTING tag is set to YES, doxygen will dump the program
+# listings (including syntax highlighting and cross-referencing information) to
+# the XML output. Note that enabling this will significantly increase the size
+# of the XML output.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_XML is set to YES.
+
+XML_PROGRAMLISTING = YES
+
+#---------------------------------------------------------------------------
+# Configuration options related to the DOCBOOK output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_DOCBOOK tag is set to YES, doxygen will generate Docbook files
+# that can be used to generate PDF.
+# The default value is: NO.
+
+GENERATE_DOCBOOK = NO
+
+# The DOCBOOK_OUTPUT tag is used to specify where the Docbook pages will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be put in
+# front of it.
+# The default directory is: docbook.
+# This tag requires that the tag GENERATE_DOCBOOK is set to YES.
+
+DOCBOOK_OUTPUT = docbook
+
+# If the DOCBOOK_PROGRAMLISTING tag is set to YES, doxygen will include the
+# program listings (including syntax highlighting and cross-referencing
+# information) to the DOCBOOK output. Note that enabling this will significantly
+# increase the size of the DOCBOOK output.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_DOCBOOK is set to YES.
+
+DOCBOOK_PROGRAMLISTING = NO
+
+#---------------------------------------------------------------------------
+# Configuration options for the AutoGen Definitions output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_AUTOGEN_DEF tag is set to YES, doxygen will generate an
+# AutoGen Definitions (see http://autogen.sourceforge.net/) file that captures
+# the structure of the code including all documentation. Note that this feature
+# is still experimental and incomplete at the moment.
+# The default value is: NO.
+
+GENERATE_AUTOGEN_DEF = NO
+
+#---------------------------------------------------------------------------
+# Configuration options related to the Perl module output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_PERLMOD tag is set to YES, doxygen will generate a Perl module
+# file that captures the structure of the code including all documentation.
+#
+# Note that this feature is still experimental and incomplete at the moment.
+# The default value is: NO.
+
+GENERATE_PERLMOD = NO
+
+# If the PERLMOD_LATEX tag is set to YES, doxygen will generate the necessary
+# Makefile rules, Perl scripts and LaTeX code to be able to generate PDF and DVI
+# output from the Perl module output.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_PERLMOD is set to YES.
+
+PERLMOD_LATEX = NO
+
+# If the PERLMOD_PRETTY tag is set to YES, the Perl module output will be nicely
+# formatted so it can be parsed by a human reader. This is useful if you want to
+# understand what is going on. On the other hand, if this tag is set to NO, the
+# size of the Perl module output will be much smaller and Perl will parse it
+# just the same.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_PERLMOD is set to YES.
+
+PERLMOD_PRETTY = YES
+
+# The names of the make variables in the generated doxyrules.make file are
+# prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. This is useful
+# so different doxyrules.make files included by the same Makefile don't
+# overwrite each other's variables.
+# This tag requires that the tag GENERATE_PERLMOD is set to YES.
+
+PERLMOD_MAKEVAR_PREFIX =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the preprocessor
+#---------------------------------------------------------------------------
+
+# If the ENABLE_PREPROCESSING tag is set to YES, doxygen will evaluate all
+# C-preprocessor directives found in the sources and include files.
+# The default value is: YES.
+
+ENABLE_PREPROCESSING = YES
+
+# If the MACRO_EXPANSION tag is set to YES, doxygen will expand all macro names
+# in the source code. If set to NO, only conditional compilation will be
+# performed. Macro expansion can be done in a controlled way by setting
+# EXPAND_ONLY_PREDEF to YES.
+# The default value is: NO.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+MACRO_EXPANSION = NO
+
+# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES then
+# the macro expansion is limited to the macros specified with the PREDEFINED and
+# EXPAND_AS_DEFINED tags.
+# The default value is: NO.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+EXPAND_ONLY_PREDEF = NO
+
+# If the SEARCH_INCLUDES tag is set to YES, the include files in the
+# INCLUDE_PATH will be searched if a #include is found.
+# The default value is: YES.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+SEARCH_INCLUDES = YES
+
+# The INCLUDE_PATH tag can be used to specify one or more directories that
+# contain include files that are not input files but should be processed by the
+# preprocessor.
+# This tag requires that the tag SEARCH_INCLUDES is set to YES.
+
+INCLUDE_PATH =
+
+# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
+# patterns (like *.h and *.hpp) to filter out the header-files in the
+# directories. If left blank, the patterns specified with FILE_PATTERNS will be
+# used.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+INCLUDE_FILE_PATTERNS =
+
+# The PREDEFINED tag can be used to specify one or more macro names that are
+# defined before the preprocessor is started (similar to the -D option of e.g.
+# gcc). The argument of the tag is a list of macros of the form: name or
+# name=definition (no spaces). If the definition and the "=" are omitted, "=1"
+# is assumed. To prevent a macro definition from being undefined via #undef or
+# recursively expanded use the := operator instead of the = operator.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+PREDEFINED =
+
+# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then this
+# tag can be used to specify a list of macro names that should be expanded. The
+# macro definition that is found in the sources will be used. Use the PREDEFINED
+# tag if you want to use a different macro definition that overrules the
+# definition found in the source code.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+EXPAND_AS_DEFINED =
+
+# If the SKIP_FUNCTION_MACROS tag is set to YES then doxygen's preprocessor will
+# remove all references to function-like macros that are alone on a line, have
+# an all uppercase name, and do not end with a semicolon. Such function macros
+# are typically used for boiler-plate code, and will confuse the parser if not
+# removed.
+# The default value is: YES.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+SKIP_FUNCTION_MACROS = YES
+
+#---------------------------------------------------------------------------
+# Configuration options related to external references
+#---------------------------------------------------------------------------
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+DOT_CLEANUP = YES
--- /dev/null
+{
+ "cells": [
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "# gmxapi Python module demonstration\n",
+ "This notebook illustrates the Python interface for gmxapi with current and planned functionality and syntax.\n",
+ "Additional design aspects are illustrated where possible."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# module built and installed with https://github.com/kassonlab/gmxapi\n",
+ "import gmx\n",
+ "# module built and installed with https://github.com/kassonlab/sample_restraint\n",
+ "import myplugin"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# Inline Python documentation extracted from the source code.\n",
+ "help(gmx)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# C++ extension has automatically generated contents and signatures, plus whatever is explicitly added as doc strings.\n",
+ "help(myplugin)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# Some test files are bundled with the package\n",
+ "from gmx.data import tpr_filename"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# submodules provide helper functions to create API objects while procedural interface evolves\n",
+ "simulation = gmx.workflow.from_tpr(tpr_filename)\n",
+ "print(simulation)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "The object returned is an element of a complete specification of runnable work.\n",
+ "\n",
+ "(version 0.1.0) WorkElement is a view into a WorkSpec object\n",
+ "\n",
+ "(version 0.0.5) WorkElement has a reference to the WorkSpec it is associated with.\n",
+ "\n",
+ "Though the helper function generates more than one WorkElement, the element associated with the MD simulation is the only meaningful thing to return a handle to. With a convention that all elements have an attribute for the associated workspec, functions requiring workspec inputs can be much more flexible and intuitive to users.\n",
+ "\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "simulation.workspec"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# WorkElement is individually serializeable as JSON\n",
+ "simulation.serialize()"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# Referenced WorkSpec is serializeable for persistence and portability.\n",
+ "simulation.workspec.serialize()"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "print(simulation.workspec)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "The first version of the schema to represent user-requested work has a data structure that is easily serialized with simple grammar. Dependencies of one element on another determines order of processing and allows binding between API objects to be managed at launch. \"gmxapi\" and \"gromacs\" namespaces are reserved for operations provided by the libraries. Other namespaces are assumed to be accessible Python modules.\n",
+ "\n",
+ "Schema version 0.2 should probably specify a character encoding, but will not have major syntactical differences. Its primary purpose will be to establish tighter constraints on content and more elaborate semantics.\n",
+ "\n",
+ "The workflow (and subsets thereof) must be uniquely identifiable to support artifact management and optimal restartability."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "simulation.workspec.uid()"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "MD extension code binds itself to the MD runner at run time with a library API. The user interface just expresses the work components and dependencies in launching the workflow. The WorkSpec is buit up with additional elements that assert a loadable module (_namespace_), a Director functor for building up the execution graph (_operation_), parameters to the operation (_params_), and launch sequence (_depends_). The user should not be required to view or understand these details, but automated generation of appropriate helper functions has not yet been added to gmxapi or the sample plugin template code."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# Parameters for Hooke's law pair restraint\n",
+ "params = {'sites': [1,4], # indices of participating sites\n",
+ " 'R0': 2.0, # equilibrium separation\n",
+ " 'k': 100.0 # spring constant\n",
+ " }"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "if gmx.version.api_is_at_least(0, 1, 0):\n",
+ " # Near-term planned feature is automatic helper functions for plugins\n",
+ " potential = myplugin.harmonic_restraint(**params)\n",
+ " \n",
+ "else:\n",
+ " # This API should not really be visible to users...\n",
+ " potential = gmx.workflow.WorkElement(namespace='myplugin',\n",
+ " operation='create_restraint',\n",
+ " params=params)\n",
+ " potential.name = 'harmonicRestraint'\n",
+ "\n",
+ "print(gmx.__version__) "
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# Procedural interface hides several abstraction layers\n",
+ "simulation.add_dependency(potential)\n",
+ "status = gmx.run(simulation)\n",
+ "\n",
+ "# gmx.Status interface needs some work\n",
+ "bool(status)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "`gmx.run()` provides the \"big green go button\" that users expect, but the hidden layers of abstraction are also accessible to users. gmxapi 0.1 specificies that gmx.run() will use or configure an appropriate execution context for the specified work, launch a session, and run until data flow for results is resolved. It is assumed to be essentially an alias for the following."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "with gmx.get_context(simulation.workspec) as session:\n",
+ " session.run()"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "The Context abstraction exists to allow modular handling of computing resources and environments. The user could specify non-default Context implementations or load Contexts from other Python modules.\n",
+ "\n",
+ "```\n",
+ "context = gmx.context.ParallelArrayContext(simulation)\n",
+ "with context as session:\n",
+ " session.run()\n",
+ "```\n",
+ "\n",
+ "Near term plans for Context extensions include\n",
+ "\n",
+ "* support for tMPI or MPI GROMACS builds,\n",
+ "* serial execution fallback for workflows when MPI is not available\n",
+ "* remote SLURM execution\n",
+ "* container management"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Operations in work specifications are essentially assumed to be \"vectorized\" for parallel pipelines. The degree of required synchrony depends on whether and how often \"ensemble\" operations occur that block across multiple pipelines.\n",
+ "\n",
+ "The API to express synchrony is not yet specified. For the short term, parallel pipelines must be executed synchronously to allow operations to communicate using Session-provided ensemble resources.\n",
+ "\n",
+ "Through 0.0.5, gmxapi uses mpi4py to execute arrays of work synchronously. \"Width\" of the workflow can be asserted by work elements according to input parameters, such as the length of a list of input filenames."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "simulation = gmx.workflow.from_tpr([tpr_filename, tpr_filename])\n",
+ "print(simulation.workspec)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "`simulation` now represents an array of MD simulation jobs. The singular restraint potential is \"broadcast\" across the trajectory ensemble. Each simulation is bound to separate instances of the restraint potential, each initialized with the same parameters.\n",
+ "\n",
+ "At launch, the restraint code is provided with ensemble resources by the Session with which to perform operations such as an ensemble-wide reduction of array data.\n",
+ "\n",
+ "Individual restraint objects don't know or care whether or how many other members are in the ensemble.\n",
+ "\n",
+ "The Context proxies access to the various filesystem-backed results and to the parallel (MPI) execution context."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "if gmx.version.api_is_at_least(0, 1, 0):\n",
+ " potential = myplugin.harmonic_restraint(**params)\n",
+ "else:\n",
+ " potential = gmx.workflow.WorkElement(namespace='myplugin',\n",
+ " operation='create_restraint',\n",
+ " params=params)\n",
+ " potential.name = 'harmonicRestraint'\n",
+ "\n",
+ "simulation.add_dependency(potential)\n",
+ "\n",
+ "print(simulation.workspec)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "`sample_restraint/examples/restrained-ensemble.py` is the (updated) script used for the restrained ensemble proof-of-concept workflow implemented with gmxapi 0.0.4. [DOI: 10.1093/bioinformatics/bty484](https://doi.org/10.1093/bioinformatics/bty484)\n",
+ "\n",
+ "As formulated below, an ensemble of 20 trajectories was coupled by a restrained ensemble plugin potential that periodically combined statistical information from across the ensemble to refine a restraint potential."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# Restrained-ensemble formalism is a variant of that defined by Roux et al., 2013\n",
+ "\n",
+ "import os\n",
+ "import sys\n",
+ "import gmx\n",
+ "\n",
+ "import logging\n",
+ "logging.getLogger().setLevel(logging.DEBUG)\n",
+ "# create console handler\n",
+ "ch = logging.StreamHandler()\n",
+ "ch.setLevel(logging.DEBUG)\n",
+ "# create formatter and add it to the handler\n",
+ "formatter = logging.Formatter('%(asctime)s:%(name)s:%(levelname)s: %(message)s')\n",
+ "ch.setFormatter(formatter)\n",
+ "# add the handlers to the logger\n",
+ "logging.getLogger().addHandler(ch)\n",
+ "logger = logging.getLogger()\n",
+ "\n",
+ "import myplugin\n",
+ "\n",
+ "logger.info(\"myplugin is {}\".format(myplugin.__file__))\n",
+ "\n",
+ "if len(sys.argv) > 1:\n",
+ " size = int(sys.argv[1])\n",
+ "else:\n",
+ " size = 20\n",
+ "input_dir_list = ['aa_{:02d}'.format(i) for i in range(size)]\n",
+ "print(\"Input directory list: {}\".format(input_dir_list))\n",
+ "\n",
+ "tpr_list = [os.path.abspath(os.path.join(directory, 'mRMR.tpr')) for directory in input_dir_list]\n",
+ "\n",
+ "# dt = 0.002\n",
+ "# First restraint applied between atoms 387 and 2569\n",
+ "# Second restraint applied between atom 1330 and 2520\n",
+ "# Restraint site coordinates relative to atom 1735\n",
+ "# Gathers 50 distance samples over 10ps, then averages the histogram across the ensemble to\n",
+ "# get a smooth histogram for the sample window. At each update (10 ps), updates the bias\n",
+ "# potential with the average statistics from the last 20 windows.\n",
+ "params = {\n",
+ " 'sites': [387, 1735, 2569],\n",
+ " 'k': 100.,\n",
+ " 'sigma': 0.2,\n",
+ " 'nbins': 70,\n",
+ " 'binWidth': 0.1,\n",
+ " 'max_dist': 6.0,\n",
+ " 'min_dist': 1.9,\n",
+ " 'experimental': [1.799741371805743e-21, 1.394386099050501e-19, 8.502972718446353e-18, 4.085581973134053e-16, 1.548764419813057e-14, 4.638792711370235e-13, 1.0996581066864261e-11, 2.0673577567003664e-10, 3.0896196375481035e-09, 3.680765701683053e-08, 3.5071251461730994e-07, 2.683161946307409e-06, 1.6559233749685584e-05, 8.289071953350906e-05, 0.00033870482482321125, 0.0011381605345541928, 0.0031720369601255603, 0.007403098031042665, 0.014627984136430199, 0.024781412546281113, 0.036538520471987135, 0.04776926450937005, 0.056703917249967935, 0.06290983130284482, 0.06723680313442071, 0.07080726976949929, 0.07402160052652465, 0.0765402296381977, 0.07828089499810763, 0.08047585508402359, 0.08570745927698609, 0.09674399700081715, 0.11510583738691207, 0.14051216332953817, 0.17140325711911122, 0.20554101371952832, 0.23970384865306096, 0.2690817283268939, 0.2883208679737597, 0.2947929622276882, 0.2912919631495654, 0.28445334990710786, 0.27916526960634136, 0.2740440567694397, 0.2627885645671059, 0.24084583312911054, 0.2119920710658402, 0.18961266641719554, 0.19160148241368294, 0.23183520488057596, 0.31258390292452404, 0.4212625964074282, 0.5329315503397933, 0.6177862653849041, 0.6510130306580447, 0.621354685844679, 0.5350130330039692, 0.4131558700737114, 0.28383821525616004, 0.17174126508493523, 0.0904869618596048, 0.04102083542122555, 0.0158113507543527, 0.00512381828028717, 0.0013817258262933331, 0.00030725601604590235, 5.5898129564429734e-05, 8.270145724798172e-06, 1.066958972950409e-06, 8.525674649177577e-07],\n",
+ " 'nsamples': 5, # window size: 100 ps\n",
+ " 'sample_period': 10000*0.002, # 20 ps\n",
+ " 'nwindows': 100, # averaging period: 10 ns\n",
+ " }\n",
+ "\n",
+ "potential1 = gmx.workflow.WorkElement(\n",
+ " namespace=\"myplugin\",\n",
+ " operation=\"ensemble_restraint\",\n",
+ " depends=[],\n",
+ " params=params\n",
+ " )\n",
+ "potential1.name = \"ensemble_restraint_1\"\n",
+ "\n",
+ "params['sites'] = [1330, 1735, 2520]\n",
+ "params['experimental'] = [8.750538172089207e-20, 4.963054541010076e-18, 2.2585602895138136e-16, 8.296295971141421e-15, 2.4727072025999945e-13, 6.001704592322284e-12, 1.188164346191529e-10, 1.917922517069427e-09, 2.52033705254017e-08, 2.691327568605142e-07, 2.3326113123212396e-06, 1.641120092881496e-05, 9.38976910432654e-05, 0.0004385427322814972, 0.0016815454179692623, 0.005334700709331302, 0.014137960662648396, 0.03164990069467528, 0.06058416858044986, 0.10044829089636065, 0.1462620702334438, 0.19008247987025195, 0.22511473247247643, 0.2496090827957139, 0.2672559820151655, 0.28375718473756745, 0.3027960501795795, 0.3245600144118122, 0.346907132615181, 0.3674499825469857, 0.3851742255922683, 0.40052661472987944, 0.4135408960076755, 0.4218337765359014, 0.42147736029942173, 0.4107213639593705, 0.39238589395514606, 0.37160127657310765, 0.3512844290946452, 0.3307655537130543, 0.30883452118638083, 0.2868146457416455, 0.2677676912313197, 0.2532530719313838, 0.2417481938021803, 0.23018156335307405, 0.21644933221299598, 0.20050997978961216, 0.18377185607646654, 0.16786393271557773, 0.15362016010974153, 0.1405238761751657, 0.12680145743115132, 0.11034786248372368, 0.09017088591908493, 0.06741463593670398, 0.045069844741355614, 0.026422842565654883, 0.013359579997979203, 0.005742341678209477, 0.0020723966306519146, 0.0006212767709345187, 0.00015329363473072974, 3.088693304526221e-05, 5.048219168357052e-06, 6.655228160961857e-07, 7.04490968489331e-08, 6.246463184699169e-09, 4.5050655561489735e-09, 4.676670950356501e-08]\n",
+ "\n",
+ "potential2 = gmx.workflow.WorkElement(\n",
+ " namespace=\"myplugin\",\n",
+ " operation=\"ensemble_restraint\",\n",
+ " depends=[],\n",
+ " params=params\n",
+ ")\n",
+ "potential2.name = \"ensemble_restraint_2\"\n",
+ "\n",
+ "\n",
+ "# Settings for a 20 core HPC node. Use 18 threads for domain decomposition for pair potentials\n",
+ "# and the remaining 2 threads for PME electrostatics.\n",
+ "md = gmx.workflow.from_tpr(tpr_list, tmpi=20, grid=[3, 3, 2], ntomp_pme=1, npme=2, ntomp=1)\n",
+ "md.add_dependency(potential1)\n",
+ "md.add_dependency(potential2)\n",
+ "\n",
+ "context = gmx.context.ParallelArrayContext(md)\n",
+ "\n",
+ "with context as session:\n",
+ " session.run()"
+ ]
+ }
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": "Python 3",
+ "language": "python",
+ "name": "python3"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 3
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython3",
+ "version": "3.6.3"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}
--- /dev/null
+#!/bin/bash
+#SBATCH -N 12
+#SBATCH --ntasks-per-node=1
+#SBATCH --cpus-per-task=20
+#SBATCH -t 00:60:00
+#SBATCH -p parallel
+#SBATCH -A kas_dev
+
+# Run parallel program over Infiniband using OpenMPI
+module load gcc
+module load openmpi
+
+srun python -m mpi4py restrained-ensemble.py 12
--- /dev/null
+#!/usr/bin/env python
+"""Run restrained-ensemble sampling and biasing workflow.
+
+Irrgang, M. E., Hays, J. M., & Kasson, P. M.
+gmxapi: a high-level interface for advanced control and extension of molecular dynamics simulations.
+*Bioinformatics* 2018.
+DOI: `10.1093/bioinformatics/bty484 <https://doi.org/10.1093/bioinformatics/bty484>`_
+"""
+
+# Restrained-ensemble formalism is a variant of that defined by Roux et al., 2013
+
+import os
+import sys
+# Of course, the location of the Python plugin module is user-specific and could be
+# passed by PYTHONPATH instead of programatically here.
+sys.path.append('/home/mei2n/sample_restraint/build/src/pythonmodule')
+
+import gmx
+
+import logging
+logging.getLogger().setLevel(logging.DEBUG)
+# create console handler
+ch = logging.StreamHandler()
+ch.setLevel(logging.DEBUG)
+# create formatter and add it to the handler
+formatter = logging.Formatter('%(asctime)s:%(name)s:%(levelname)s: %(message)s')
+ch.setFormatter(formatter)
+# add the handlers to the logger
+logging.getLogger().addHandler(ch)
+logger = logging.getLogger()
+
+import myplugin
+
+logger.info("myplugin is {}".format(myplugin.__file__))
+
+if len(sys.argv) > 1:
+ size = int(sys.argv[1])
+else:
+ size = 20
+input_dir_list = ['aa_{:02d}'.format(i) for i in range(size)]
+print("Input directory list: {}".format(input_dir_list))
+
+tpr_list = [os.path.abspath(os.path.join(directory, 'mRMR.tpr')) for directory in input_dir_list]
+
+# dt = 0.002
+# First restraint applied between atoms 387 and 2569
+# Second restraint applied between atom 1330 and 2520
+# Restraint site coordinates relative to atom 1735
+# Gathers 50 distance samples over 10ps, then averages the histogram across the ensemble to
+# get a smooth histogram for the sample window. At each update (10 ps), updates the bias
+# potential with the average statistics from the last 20 windows.
+params = {
+ 'sites': [387, 1735, 2569],
+ 'k': 100.,
+ 'sigma': 0.2,
+ 'nbins': 70,
+ 'binWidth': 0.1,
+ 'max_dist': 6.0,
+ 'min_dist': 1.9,
+ 'experimental': [1.799741371805743e-21, 1.394386099050501e-19, 8.502972718446353e-18, 4.085581973134053e-16, 1.548764419813057e-14, 4.638792711370235e-13, 1.0996581066864261e-11, 2.0673577567003664e-10, 3.0896196375481035e-09, 3.680765701683053e-08, 3.5071251461730994e-07, 2.683161946307409e-06, 1.6559233749685584e-05, 8.289071953350906e-05, 0.00033870482482321125, 0.0011381605345541928, 0.0031720369601255603, 0.007403098031042665, 0.014627984136430199, 0.024781412546281113, 0.036538520471987135, 0.04776926450937005, 0.056703917249967935, 0.06290983130284482, 0.06723680313442071, 0.07080726976949929, 0.07402160052652465, 0.0765402296381977, 0.07828089499810763, 0.08047585508402359, 0.08570745927698609, 0.09674399700081715, 0.11510583738691207, 0.14051216332953817, 0.17140325711911122, 0.20554101371952832, 0.23970384865306096, 0.2690817283268939, 0.2883208679737597, 0.2947929622276882, 0.2912919631495654, 0.28445334990710786, 0.27916526960634136, 0.2740440567694397, 0.2627885645671059, 0.24084583312911054, 0.2119920710658402, 0.18961266641719554, 0.19160148241368294, 0.23183520488057596, 0.31258390292452404, 0.4212625964074282, 0.5329315503397933, 0.6177862653849041, 0.6510130306580447, 0.621354685844679, 0.5350130330039692, 0.4131558700737114, 0.28383821525616004, 0.17174126508493523, 0.0904869618596048, 0.04102083542122555, 0.0158113507543527, 0.00512381828028717, 0.0013817258262933331, 0.00030725601604590235, 5.5898129564429734e-05, 8.270145724798172e-06, 1.066958972950409e-06, 8.525674649177577e-07],
+ 'nsamples': 5, # window size: 100 ps
+ 'sample_period': 10000*0.002, # 20 ps
+ 'nwindows': 100, # averaging period: 10 ns
+ }
+
+potential1 = gmx.workflow.WorkElement(
+ namespace="myplugin",
+ operation="ensemble_restraint",
+ depends=[],
+ params=params
+ )
+potential1.name = "ensemble_restraint_1"
+
+params['sites'] = [1330, 1735, 2520]
+params['experimental'] = [8.750538172089207e-20, 4.963054541010076e-18, 2.2585602895138136e-16, 8.296295971141421e-15, 2.4727072025999945e-13, 6.001704592322284e-12, 1.188164346191529e-10, 1.917922517069427e-09, 2.52033705254017e-08, 2.691327568605142e-07, 2.3326113123212396e-06, 1.641120092881496e-05, 9.38976910432654e-05, 0.0004385427322814972, 0.0016815454179692623, 0.005334700709331302, 0.014137960662648396, 0.03164990069467528, 0.06058416858044986, 0.10044829089636065, 0.1462620702334438, 0.19008247987025195, 0.22511473247247643, 0.2496090827957139, 0.2672559820151655, 0.28375718473756745, 0.3027960501795795, 0.3245600144118122, 0.346907132615181, 0.3674499825469857, 0.3851742255922683, 0.40052661472987944, 0.4135408960076755, 0.4218337765359014, 0.42147736029942173, 0.4107213639593705, 0.39238589395514606, 0.37160127657310765, 0.3512844290946452, 0.3307655537130543, 0.30883452118638083, 0.2868146457416455, 0.2677676912313197, 0.2532530719313838, 0.2417481938021803, 0.23018156335307405, 0.21644933221299598, 0.20050997978961216, 0.18377185607646654, 0.16786393271557773, 0.15362016010974153, 0.1405238761751657, 0.12680145743115132, 0.11034786248372368, 0.09017088591908493, 0.06741463593670398, 0.045069844741355614, 0.026422842565654883, 0.013359579997979203, 0.005742341678209477, 0.0020723966306519146, 0.0006212767709345187, 0.00015329363473072974, 3.088693304526221e-05, 5.048219168357052e-06, 6.655228160961857e-07, 7.04490968489331e-08, 6.246463184699169e-09, 4.5050655561489735e-09, 4.676670950356501e-08]
+
+potential2 = gmx.workflow.WorkElement(
+ namespace="myplugin",
+ operation="ensemble_restraint",
+ depends=[],
+ params=params
+)
+potential2.name = "ensemble_restraint_2"
+
+
+# Settings for a 20 core HPC node. Use 18 threads for domain decomposition for pair potentials
+# and the remaining 2 threads for PME electrostatics.
+md = gmx.workflow.from_tpr(tpr_list, tmpi=20, grid=[3, 3, 2], ntomp_pme=1, npme=2, ntomp=1)
+md.add_dependency(potential1)
+md.add_dependency(potential2)
+
+context = gmx.context.ParallelArrayContext(md)
+
+with context as session:
+ session.run()
--- /dev/null
+#!/usr/bin/env python
+# This script takes an ipython notebook as an argument and rewrites the file
+# with metadata stripped to make change tracking with git easier.
+import sys
+import json
+import os
+import shutil
+
+infile = sys.argv[1]
+if not os.path.exists(infile):
+ sys.exit('command line argument must be an existing filename')
+tempfile = infile+'.tmp'
+
+with open(infile, 'r') as fh:
+ json_in = json.load(fh)
+
+nb_metadata = json_in["metadata"]
+def strip_output_from_cell(cell):
+ if "outputs" in cell:
+ cell["outputs"] = []
+ if "execution_count" in cell:
+ cell["execution_count"] = None
+
+for cell in json_in["cells"]:
+ strip_output_from_cell(cell)
+
+with open(tempfile, 'w') as fh:
+ json.dump(json_in, fh, sort_keys=True, indent=1, separators=(",",": "))
+shutil.move(tempfile, infile)
--- /dev/null
+# Build a C++ library using libgmxapi to extend GROMACS.
+# We process this subdirectory first to reaffirm that this code does not depend
+# on other substantial infrastructure, such as a particular Python bindings
+# framework or the Googletest framework.
+add_subdirectory(cpp)
+
+
+# Import the Googletest targets, unless the user has requested that the repository
+# be downloaded instead (see tests/CMakeLists.txt)
+if(NOT ${DOWNLOAD_GOOGLETEST})
+ if(${BUILD_TESTING})
+ add_subdirectory(external/googletest EXCLUDE_FROM_ALL)
+ endif()
+endif()
+
+
+# Build a Python extension package from our new library.
+add_subdirectory(pythonmodule)
--- /dev/null
+# Defines targets for the C++ restraints implemented here. These CMake targets are used by the
+# unit tests and by the Python module target defined in ../pythonmodule/CMakeLists.txt
+
+# Create a shared object library for a simple restraint.
+add_library(harmonicpotential STATIC
+ harmonicpotential.h
+ harmonicpotential.cpp
+ sessionresources.cpp)
+set_target_properties(harmonicpotential PROPERTIES POSITION_INDEPENDENT_CODE ON)
+
+target_include_directories(harmonicpotential PUBLIC
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>
+ $<INSTALL_INTERFACE:include>
+ )
+# RPATH management
+# don't skip the full RPATH for the build tree
+set_target_properties(harmonicpotential PROPERTIES SKIP_BUILD_RPATH FALSE)
+
+# (but later on when installing)
+# If building with setuptools, CMake will not be performing the install
+set_target_properties(harmonicpotential PROPERTIES BUILD_WITH_INSTALL_RPATH TRUE)
+
+target_link_libraries(harmonicpotential PRIVATE Gromacs::gmxapi)
+
+
+# Create a shared object library for our restrained ensemble plugin.
+add_library(ensemblepotential STATIC
+ ensemblepotential.h
+ ensemblepotential.cpp
+ sessionresources.cpp)
+set_target_properties(ensemblepotential PROPERTIES POSITION_INDEPENDENT_CODE ON)
+
+target_include_directories(ensemblepotential PUBLIC
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>
+ $<INSTALL_INTERFACE:include>
+ )
+# RPATH management
+# don't skip the full RPATH for the build tree
+set_target_properties(ensemblepotential PROPERTIES SKIP_BUILD_RPATH FALSE)
+
+# (but later on when installing)
+# If building with setuptools, CMake will not be performing the install
+set_target_properties(ensemblepotential PROPERTIES BUILD_WITH_INSTALL_RPATH TRUE)
+
+target_link_libraries(ensemblepotential PRIVATE Gromacs::gmxapi)
--- /dev/null
+//
+// Created by Eric Irrgang on 2/26/18.
+//
+
+/*! \file
+ * \brief Code to implement the potential declared in ensemblepotential.h
+ *
+ * This file currently contains boilerplate that will not be necessary in future gmxapi releases, as
+ * well as additional code used in implementing the restrained ensemble example workflow.
+ *
+ * A simpler restraint potential would only update the calculate() function. If a callback function is
+ * not needed or desired, remove the callback() code from this file and from ensemblepotential.h
+ */
+
+#include "ensemblepotential.h"
+
+#include <cassert>
+#include <cmath>
+
+#include <memory>
+#include <vector>
+
+#include "gmxapi/context.h"
+#include "gmxapi/session.h"
+#include "gmxapi/md/mdsignals.h"
+
+#include "sessionresources.h"
+
+namespace plugin
+{
+
+/*!
+ * \brief Apply a Gaussian blur when building a density grid for a list of values.
+ *
+ * Normalize such that the area under each sample is 1.0/num_samples.
+ */
+class BlurToGrid
+{
+ public:
+ /*!
+ * \brief Contsruct the blurring functor.
+ *
+ * \param low The coordinate value of the first grid point.
+ * \param gridSpacing Distance between grid points.
+ * \param sigma Gaussian parameter for blurring inputs onto the grid.
+ */
+ BlurToGrid(double low,
+ double gridSpacing,
+ double sigma) :
+ low_{low},
+ binWidth_{gridSpacing},
+ sigma_{sigma}
+ {
+ };
+
+ /*!
+ * \brief Callable for the functor.
+ *
+ * \param samples A list of values to be blurred onto the grid.
+ * \param grid Pointer to the container into which to accumulate a blurred histogram of samples.
+ *
+ * Example:
+ *
+ * # Acquire 3 samples to be discretized with blurring.
+ * std::vector<double> someData = {3.7, 8.1, 4.2};
+ *
+ * # Create an empty grid to store magnitudes for points 0.5, 1.0, ..., 10.0.
+ * std::vector<double> histogram(20, 0.);
+ *
+ * # Specify the above grid and a Gaussian parameter of 0.8.
+ * auto blur = BlurToGrid(0.5, 0.5, 0.8);
+ *
+ * # Collect the density grid for the samples.
+ * blur(someData, &histogram);
+ *
+ */
+ void operator()(const std::vector<double>& samples,
+ std::vector<double>* grid)
+ {
+ const auto nbins = grid->size();
+ const double& dx{binWidth_};
+ const auto num_samples = samples.size();
+
+ const double denominator = 1.0 / (2 * sigma_ * sigma_);
+ const double normalization = 1.0 / (num_samples * sqrt(2.0 * M_PI * sigma_ * sigma_));
+ // We aren't doing any filtering of values too far away to contribute meaningfully, which
+ // is admittedly wasteful for large sigma...
+ for (size_t i = 0;i < nbins;++i)
+ {
+ double bin_value{0};
+ const double bin_x{low_ + i * dx};
+ for (const auto distance : samples)
+ {
+ const double relative_distance{bin_x - distance};
+ const auto numerator = -relative_distance * relative_distance;
+ bin_value += normalization * exp(numerator * denominator);
+ }
+ grid->at(i) = bin_value;
+ }
+ };
+
+ private:
+ /// Minimum value of bin zero
+ const double low_;
+
+ /// Size of each bin
+ const double binWidth_;
+
+ /// Smoothing factor
+ const double sigma_;
+};
+
+EnsembleHarmonic::EnsembleHarmonic(size_t nbins,
+ double binWidth,
+ double minDist,
+ double maxDist,
+ PairHist experimental,
+ unsigned int nSamples,
+ double samplePeriod,
+ unsigned int nWindows,
+ double k,
+ double sigma) :
+ nBins_{nbins},
+ binWidth_{binWidth},
+ minDist_{minDist},
+ maxDist_{maxDist},
+ histogram_(nbins,
+ 0),
+ experimental_{std::move(experimental)},
+ nSamples_{nSamples},
+ currentSample_{0},
+ samplePeriod_{samplePeriod},
+ // In actuality, we have nsamples at (samplePeriod - dt), but we don't have access to dt.
+ nextSampleTime_{samplePeriod},
+ distanceSamples_(nSamples),
+ nWindows_{nWindows},
+ currentWindow_{0},
+ windowStartTime_{0},
+ nextWindowUpdateTime_{nSamples * samplePeriod},
+ windows_{},
+ k_{k},
+ sigma_{sigma}
+{}
+
+EnsembleHarmonic::EnsembleHarmonic(const input_param_type& params) :
+ EnsembleHarmonic(params.nBins,
+ params.binWidth,
+ params.minDist,
+ params.maxDist,
+ params.experimental,
+ params.nSamples,
+ params.samplePeriod,
+ params.nWindows,
+ params.k,
+ params.sigma)
+{
+}
+
+//
+//
+// HERE is the (optional) function that updates the state of the restraint periodically.
+// It is called before calculate() once per timestep per simulation (on the master rank of
+// a parallelized simulation).
+//
+//
+void EnsembleHarmonic::callback(gmx::Vector v,
+ gmx::Vector v0,
+ double t,
+ const EnsembleResources& resources)
+{
+ const auto rdiff = v - v0;
+ const auto Rsquared = dot(rdiff,
+ rdiff);
+ const auto R = sqrt(Rsquared);
+
+ // Store historical data every sample_period steps
+ if (t >= nextSampleTime_)
+ {
+ distanceSamples_[currentSample_++] = R;
+ nextSampleTime_ = (currentSample_ + 1) * samplePeriod_ + windowStartTime_;
+ };
+
+ // Every nsteps:
+ // 0. Drop oldest window
+ // 1. Reduce historical data for this restraint in this simulation.
+ // 2. Call out to the global reduction for this window.
+ // 3. On update, checkpoint the historical data source.
+ // 4. Update historic windows.
+ // 5. Use handles retained from previous windows to reconstruct the smoothed working histogram
+ if (t >= nextWindowUpdateTime_)
+ {
+ // Get next histogram array, recycling old one if available.
+ std::unique_ptr<Matrix<double>> new_window = std::make_unique<Matrix<double>>(1,
+ nBins_);
+ std::unique_ptr<Matrix<double>> temp_window;
+ if (windows_.size() == nWindows_)
+ {
+ // Recycle the oldest window.
+ // \todo wrap this in a helper class that manages a buffer we can shuffle through.
+ windows_[0].swap(temp_window);
+ windows_.erase(windows_.begin());
+ }
+ else
+ {
+ auto new_temp_window = std::make_unique<Matrix<double>>(1,
+ nBins_);
+ assert(new_temp_window);
+ temp_window.swap(new_temp_window);
+ }
+
+ // Reduce sampled data for this restraint in this simulation, applying a Gaussian blur to fill a grid.
+ auto blur = BlurToGrid(0.0,
+ binWidth_,
+ sigma_);
+ assert(new_window != nullptr);
+ assert(distanceSamples_.size() == nSamples_);
+ assert(currentSample_ == nSamples_);
+ blur(distanceSamples_,
+ new_window->vector());
+ // We can just do the blur locally since there aren't many bins. Bundling these operations for
+ // all restraints could give us a chance at some parallelism. We should at least use some
+ // threading if we can.
+
+ // We request a handle each time before using resources to make error handling easier if there is a failure in
+ // one of the ensemble member processes and to give more freedom to how resources are managed from step to step.
+ auto ensemble = resources.getHandle();
+ // Get global reduction (sum) and checkpoint.
+ assert(temp_window != nullptr);
+ // Todo: in reduce function, give us a mean instead of a sum.
+ ensemble.reduce(*new_window,
+ temp_window.get());
+
+ // Update window list with smoothed data.
+ windows_.emplace_back(std::move(new_window));
+
+ // Get new histogram difference. Subtract the experimental distribution to get the values to use in our potential.
+ for (auto& bin : histogram_)
+ {
+ bin = 0;
+ }
+ for (const auto& window : windows_)
+ {
+ for (size_t i = 0;i < window->cols();++i)
+ {
+ histogram_.at(i) += (window->vector()->at(i) - experimental_.at(i)) / windows_.size();
+ }
+ }
+
+
+ // Note we do not have the integer timestep available here. Therefore, we can't guarantee that updates occur
+ // with the same number of MD steps in each interval, and the interval will effectively lose digits as the
+ // simulation progresses, so _update_period should be cleanly representable in binary. When we extract this
+ // to a facility, we can look for a part of the code with access to the current timestep.
+ windowStartTime_ = t;
+ nextWindowUpdateTime_ = nSamples_ * samplePeriod_ + windowStartTime_;
+ ++currentWindow_; // This is currently never used. I'm not sure it will be, either...
+
+ // Reset sample bufering.
+ currentSample_ = 0;
+ // Reset sample times.
+ nextSampleTime_ = t + samplePeriod_;
+ };
+
+}
+
+
+//
+//
+// HERE is the function that does the calculation of the restraint force.
+//
+//
+gmx::PotentialPointData EnsembleHarmonic::calculate(gmx::Vector v,
+ gmx::Vector v0,
+ double t)
+{
+ // This is not the vector from v to v0. It is the position of a site
+ // at v, relative to the origin v0. This is a potentially confusing convention...
+ const auto rdiff = v - v0;
+ const auto Rsquared = dot(rdiff,
+ rdiff);
+ const auto R = sqrt(Rsquared);
+
+
+ // Compute output
+ gmx::PotentialPointData output;
+ // Energy not needed right now.
+// output.energy = 0;
+
+ if (R != 0) // Direction of force is ill-defined when v == v0
+ {
+
+ double f{0};
+
+ if (R > maxDist_)
+ {
+ // apply a force to reduce R
+ f = k_ * (maxDist_ - R);
+ }
+ else if (R < minDist_)
+ {
+ // apply a force to increase R
+ f = k_ * (minDist_ - R);
+ }
+ else
+ {
+ double f_scal{0};
+
+ const size_t numBins = histogram_.size();
+ double normConst = sqrt(2 * M_PI) * sigma_ * sigma_ * sigma_;
+
+ for (size_t n = 0;n < numBins;n++)
+ {
+ const double x{n * binWidth_ - R};
+ const double argExp{-0.5 * x * x / (sigma_ * sigma_)};
+ f_scal += histogram_.at(n) * exp(argExp) * x / normConst;
+ }
+ f = -k_ * f_scal;
+ }
+
+ const auto magnitude = f / norm(rdiff);
+ output.force = rdiff * static_cast<decltype(rdiff[0])>(magnitude);
+ }
+ return output;
+}
+
+std::unique_ptr<ensemble_input_param_type>
+makeEnsembleParams(size_t nbins,
+ double binWidth,
+ double minDist,
+ double maxDist,
+ const std::vector<double>& experimental,
+ unsigned int nSamples,
+ double samplePeriod,
+ unsigned int nWindows,
+ double k,
+ double sigma)
+{
+ using std::make_unique;
+ auto params = make_unique<ensemble_input_param_type>();
+ params->nBins = nbins;
+ params->binWidth = binWidth;
+ params->minDist = minDist;
+ params->maxDist = maxDist;
+ params->experimental = experimental;
+ params->nSamples = nSamples;
+ params->samplePeriod = samplePeriod;
+ params->nWindows = nWindows;
+ params->k = k;
+ params->sigma = sigma;
+
+ return params;
+};
+
+// Important: Explicitly instantiate a definition for the templated class declared in ensemblepotential.h.
+// Failing to do this will cause a linker error.
+template
+class ::plugin::RestraintModule<EnsembleRestraint>;
+
+} // end namespace plugin
--- /dev/null
+//
+// Created by Eric Irrgang on 2/26/18.
+//
+
+#ifndef HARMONICRESTRAINT_ENSEMBLEPOTENTIAL_H
+#define HARMONICRESTRAINT_ENSEMBLEPOTENTIAL_H
+
+/*! \file
+ * \brief Provide restrained ensemble MD potential for GROMACS plugin.
+ *
+ * The restraint implemented here uses a facility provided by gmxapi to perform averaging of some
+ * array data across an ensemble of simulations. Simpler pair restraints can use less of this
+ * example code.
+ *
+ * Contains a lot of boiler plate that is being generalized and migrate out of this file, but other
+ * pair restraints can be implemented by following the example in this and ``ensemblepotential.cpp``.
+ * The ``CMakeLists.txt`` file will need to be updated if you add additional source files, and
+ * ``src/pythonmodule/export_plugin.cpp`` will need to be updated if you add or change the name of
+ * potentials.
+ */
+
+#include <vector>
+#include <array>
+#include <mutex>
+
+#include "gmxapi/gromacsfwd.h"
+#include "gmxapi/session.h"
+#include "gmxapi/md/mdmodule.h"
+
+#include "gromacs/restraint/restraintpotential.h"
+#include "gromacs/utility/real.h"
+
+#include "sessionresources.h"
+
+namespace plugin
+{
+
+// Histogram for a single restrained pair.
+using PairHist = std::vector<double>;
+
+struct ensemble_input_param_type
+{
+ /// distance histogram parameters
+ size_t nBins{0};
+ double binWidth{0.};
+
+ /// Flat-bottom potential boundaries.
+ double minDist{0};
+ double maxDist{0};
+
+ /// Experimental reference distribution.
+ PairHist experimental{};
+
+ /// Number of samples to store during each window.
+ unsigned int nSamples{0};
+ double samplePeriod{0};
+
+ /// Number of windows to use for smoothing histogram updates.
+ unsigned int nWindows{0};
+
+ /// Harmonic force coefficient
+ double k{0};
+ /// Smoothing factor: width of Gaussian interpolation for histogram
+ double sigma{0};
+
+};
+
+// \todo We should be able to automate a lot of the parameter setting stuff
+// by having the developer specify a map of parameter names and the corresponding type, but that could get tricky.
+// The statically compiled fast parameter structure would be generated with a recursive variadic template
+// the way a tuple is. ref https://eli.thegreenplace.net/2014/variadic-templates-in-c/
+
+std::unique_ptr<ensemble_input_param_type>
+makeEnsembleParams(size_t nbins,
+ double binWidth,
+ double minDist,
+ double maxDist,
+ const std::vector<double>& experimental,
+ unsigned int nSamples,
+ double samplePeriod,
+ unsigned int nWindows,
+ double k,
+ double sigma);
+
+/*!
+ * \brief a residue-pair bias calculator for use in restrained-ensemble simulations.
+ *
+ * Applies a force between two sites according to the difference between an experimentally observed
+ * site pair distance distribution and the distance distribution observed earlier in the simulation
+ * trajectory. The sampled distribution is averaged from the previous `nwindows` histograms from all
+ * ensemble members. Each window contains a histogram populated with `nsamples` distances recorded at
+ * `sample_period` step intervals.
+ *
+ * \internal
+ * During a the window_update_period steps of a window, the potential applied is a harmonic function of
+ * the difference between the sampled and experimental histograms. At the beginning of the window, this
+ * difference is found and a Gaussian blur is applied.
+ */
+class EnsembleHarmonic
+{
+ public:
+ using input_param_type = ensemble_input_param_type;
+
+ /* No default constructor. Parameters must be provided. */
+// EnsembleHarmonic();
+
+ /*!
+ * \brief Constructor called by the wrapper code to produce a new instance.
+ *
+ * This constructor is called once per simulation per GROMACS process. Note that until
+ * gmxapi 0.0.8 there is only one instance per simulation in a thread-MPI simulation.
+ *
+ * \param params
+ */
+ explicit EnsembleHarmonic(const input_param_type& params);
+
+ /*!
+ * \brief Deprecated constructor taking a parameter list.
+ *
+ * \param nbins
+ * \param binWidth
+ * \param minDist
+ * \param maxDist
+ * \param experimental
+ * \param nSamples
+ * \param samplePeriod
+ * \param nWindows
+ * \param k
+ * \param sigma
+ */
+ EnsembleHarmonic(size_t nbins,
+ double binWidth,
+ double minDist,
+ double maxDist,
+ PairHist experimental,
+ unsigned int nSamples,
+ double samplePeriod,
+ unsigned int nWindows,
+ double k,
+ double sigma);
+
+ /*!
+ * \brief Evaluates the pair restraint potential.
+ *
+ * In parallel simulations, the gmxapi framework does not make guarantees about where or
+ * how many times this function is called. It should be simple and stateless; it should not
+ * update class member data (see ``ensemblepotential.cpp``. For a more controlled API hook
+ * and to manage state in the object, use ``callback()``.
+ *
+ * \param v position of the site for which force is being calculated.
+ * \param v0 reference site (other member of the pair).
+ * \param t current simulation time (ps).
+ * \return container for force and potential energy data.
+ */
+ // Implementation note for the future: If dispatching this virtual function is not fast
+ // enough, the compiler may be able to better optimize a free
+ // function that receives the current restraint as an argument.
+ gmx::PotentialPointData calculate(gmx::Vector v,
+ gmx::Vector v0,
+ gmx_unused double t);
+
+ /*!
+ * \brief An update function to be called on the simulation master rank/thread periodically by the Restraint framework.
+ *
+ * Defining this function in a plugin potential is optional. If the function is defined,
+ * the restraint framework calls this function (on the first rank only in a parallel simulation) before calling calculate().
+ *
+ * The callback may use resources provided by the Session in the callback to perform updates
+ * to the local or global state of an ensemble of simulations. Future gmxapi releases will
+ * include additional optimizations, allowing call-back frequency to be expressed, and more
+ * general Session resources, as well as more flexible call signatures.
+ */
+ void callback(gmx::Vector v,
+ gmx::Vector v0,
+ double t,
+ const EnsembleResources& resources);
+
+ private:
+ /// Width of bins (distance) in histogram
+ size_t nBins_;
+ double binWidth_;
+
+ /// Flat-bottom potential boundaries.
+ double minDist_;
+ double maxDist_;
+ /// Smoothed historic distribution for this restraint. An element of the array of restraints in this simulation.
+ // Was `hij` in earlier code.
+ PairHist histogram_;
+ PairHist experimental_;
+
+ /// Number of samples to store during each window.
+ unsigned int nSamples_;
+ unsigned int currentSample_;
+ double samplePeriod_;
+ double nextSampleTime_;
+ /// Accumulated list of samples during a new window.
+ std::vector<double> distanceSamples_;
+
+ /// Number of windows to use for smoothing histogram updates.
+ size_t nWindows_;
+ size_t currentWindow_;
+ double windowStartTime_;
+ double nextWindowUpdateTime_;
+ /// The history of nwindows histograms for this restraint.
+ std::vector<std::unique_ptr<plugin::Matrix<double>>> windows_;
+
+ /// Harmonic force coefficient
+ double k_;
+ /// Smoothing factor: width of Gaussian interpolation for histogram
+ double sigma_;
+};
+
+/*!
+ * \brief Use EnsembleHarmonic to implement a RestraintPotential
+ *
+ * This is boiler plate that will be templated and moved.
+ */
+class EnsembleRestraint : public ::gmx::IRestraintPotential, private EnsembleHarmonic
+{
+ public:
+ using EnsembleHarmonic::input_param_type;
+
+ EnsembleRestraint(std::vector<int> sites,
+ const input_param_type& params,
+ std::shared_ptr<EnsembleResources> resources
+ ) :
+ EnsembleHarmonic(params),
+ sites_{std::move(sites)},
+ resources_{std::move(resources)}
+ {}
+
+ ~EnsembleRestraint() override = default;
+
+ /*!
+ * \brief Implement required interface of gmx::IRestraintPotential
+ *
+ * \return list of configured site indices.
+ *
+ * \todo remove to template header
+ * \todo abstraction of site references
+ */
+ std::vector<int> sites() const override
+ {
+ return sites_;
+ }
+
+ /*!
+ * \brief Implement the interface gmx::IRestraintPotential
+ *
+ * Dispatch to calculate() method.
+ *
+ * \param r1 coordinate of first site
+ * \param r2 reference coordinate (second site)
+ * \param t simulation time
+ * \return calculated force and energy
+ *
+ * \todo remove to template header.
+ */
+ gmx::PotentialPointData evaluate(gmx::Vector r1,
+ gmx::Vector r2,
+ double t) override
+ {
+ return calculate(r1,
+ r2,
+ t);
+ };
+
+ /*!
+ * \brief An update function to be called on the simulation master rank/thread periodically by the Restraint framework.
+ *
+ * Implements optional override of gmx::IRestraintPotential::update
+ *
+ * This boilerplate will disappear into the Restraint template in an upcoming gmxapi release.
+ */
+ void update(gmx::Vector v,
+ gmx::Vector v0,
+ double t) override
+ {
+ // Todo: use a callback period to mostly bypass this and avoid excessive mutex locking.
+ callback(v,
+ v0,
+ t,
+ *resources_);
+ };
+
+ /*!
+ * \brief Implement the binding protocol that allows access to Session resources.
+ *
+ * The client receives a non-owning pointer to the session and cannot extent the life of the session. In
+ * the future we can use a more formal handle mechanism.
+ *
+ * \param session pointer to the current session
+ */
+ void bindSession(gmxapi::SessionResources* session) override
+ {
+ resources_->setSession(session);
+ }
+
+ void setResources(std::unique_ptr<EnsembleResources>&& resources)
+ {
+ resources_ = std::move(resources);
+ }
+
+ private:
+ std::vector<int> sites_;
+// double callbackPeriod_;
+// double nextCallback_;
+ std::shared_ptr<EnsembleResources> resources_;
+};
+
+
+// Important: Just declare the template instantiation here for client code.
+// We will explicitly instantiate a definition in the .cpp file where the input_param_type is defined.
+extern template
+class RestraintModule<EnsembleRestraint>;
+
+} // end namespace plugin
+
+#endif //HARMONICRESTRAINT_ENSEMBLEPOTENTIAL_H
--- /dev/null
+//
+// Created by Eric Irrgang on 10/13/17.
+//
+
+#include "harmonicpotential.h"
+#include <cmath>
+
+#include <array>
+
+namespace plugin
+{
+
+gmx::PotentialPointData Harmonic::calculate(gmx::Vector v,
+ gmx::Vector v0,
+ gmx_unused double t)
+{
+ // Our convention is to think of the second coordinate as a reference location
+ // such that we consider the relative location of the site at v
+ // and find the force that should be applied. For example, think
+ // of a single particle harmonically bound to a site at the origin
+ // and let v0 == {0,0,0}. In the convention of the PairRestraint,
+ // though, we assume the reference coordinate is also a site to which
+ // we will apply and equal and opposite force. In the long run,
+ // considering domain decomposition, it might make more sense to
+ // explicitly evaluate each site in a pair with the other as a reference.
+ const auto rdiff = v - v0;
+ const auto Rsquared = dot(rdiff,
+ rdiff);
+ const auto R = sqrt(Rsquared);
+
+ // Potential energy is 0.5 * k * (norm(r1) - R0)**2
+ // Force in direction of r1 is -k * (norm(r1) - R0) * r1/norm(r1)
+ gmx::PotentialPointData output;
+ // output.energy = real(0.5) * k * (norm(r1) - R0) * (norm(r1) - R0);
+ output.energy = real(0.5) * k_ * (Rsquared + (-2 * R * R0_) + R0_ * R0_);
+ // Direction of force is ill-defined when v == v0
+ if (R != 0)
+ {
+ // F = -k * (1.0 - R0/norm(r1)) * r1
+ const auto magnitude = k_ * (double(R0_) / R - 1.0);
+ output.force = rdiff * static_cast<decltype(rdiff[0])>(magnitude);
+ }
+
+ return output;
+}
+
+gmx::PotentialPointData HarmonicRestraint::evaluate(gmx::Vector r1,
+ gmx::Vector r2,
+ double t)
+{
+ // Use calculate() method inherited from HarmonicPotential
+ return calculate(r1,
+ r2,
+ t);
+}
+
+std::vector<int> HarmonicRestraint::sites() const
+{
+ return {site1_, site2_};
+}
+
+} // end namespace plugin
--- /dev/null
+//
+// Created by Eric Irrgang on 10/13/17.
+//
+
+#ifndef GROMACS_HARMONICPOTENTIAL_H
+#define GROMACS_HARMONICPOTENTIAL_H
+
+#include <iostream>
+
+#include "gmxapi/gromacsfwd.h"
+#include "gmxapi/md/mdmodule.h"
+
+#include "gromacs/restraint/restraintpotential.h"
+#include "gromacs/utility/real.h"
+
+/*! \file
+ * \brief Implement a harmonic pair force.
+ *
+ * Calculations and additional behavior is defined in harmonicpotential.cpp
+ *
+ * \todo This code has not been updated in a while...
+ * This needs to be updated and tested more rigorously.
+ *
+ * Ref. https://github.com/kassonlab/gmxapi/issues/55
+ * https://github.com/kassonlab/gmxapi/issues/77
+ * https://github.com/kassonlab/gmxapi/issues/78
+ */
+
+namespace plugin
+{
+
+class Harmonic
+{
+ public:
+ Harmonic(real equilibrium,
+ real springconstant) :
+ R0_{equilibrium},
+ k_{springconstant}
+ {};
+
+ Harmonic() :
+ Harmonic{0.0, 0.0}
+ {};
+
+ // Allow easier automatic generation of bindings.
+ struct input_param_type
+ {
+// not yet used
+ };
+
+ /*!
+ * \brief Calculate harmonic force on particle at position v in reference to position v0.
+ *
+ * \param v position at which to evaluate force
+ * \param v0 position of harmonic bond reference
+ * \return F = -k ((v - v0)/|v - v0| - R0);
+ *
+ * R0 == 1.0 is the equilibrium distance in the harmonic potential.
+ * k == 1.0 is the spring constant.
+ *
+ * In the case of a pair of harmonically bonded particles, the force on particle i is evaluated with particle j as
+ * the reference point with
+ * \code
+ * auto force = calculateForce(r_i, r_j);
+ * \endcode
+ *
+ * The force on particle j is the opposite as the force vector for particle i. E.g.
+ * \code
+ * assert(-1 * force, calculateForce(r_j, r_i));
+ * \endcode
+ */
+ gmx::PotentialPointData calculate(gmx::Vector v,
+ gmx::Vector v0,
+ gmx_unused double t);
+
+ // The class will either be inherited as a mix-in or inherit a CRTP base class. Either way, it probably needs
+ // proper virtual destructor management.
+ virtual ~Harmonic()
+ {
+ }
+
+ private:
+ // set equilibrium separation distance in GROMACS units.
+ // TODO: be clearer about units
+ real R0_;
+ // set spring constant in native GROMACS units.
+ // TODO: be clearer about units
+ real k_;
+};
+
+// implement IRestraintPotential in terms of Harmonic
+// To be templated and moved.
+class HarmonicRestraint : public ::gmx::IRestraintPotential, private Harmonic
+{
+ public:
+ /*!
+ * \brief Create an instance of the restraint (used in libgromacs)
+ *
+ * Each pair restraint instance operates on one pair of atomic sites.
+ *
+ * \param site1 first atomic site in the pair.
+ * \param site2 second atomic site in the pair.
+ * \param R0 targeted equilibrium pair separation.
+ * \param k spring constant.
+ */
+ HarmonicRestraint(int site1,
+ int site2,
+ real R0,
+ real k) :
+ Harmonic{R0, k},
+ site1_{site1},
+ site2_{site2}
+ {};
+
+ ~HarmonicRestraint() override = default;
+
+ /*!
+ * \brief Implement required interface of gmx::IRestraintPotential
+ *
+ * \return list of configured site indices.
+ *
+ * \todo remove to template header
+ * \todo abstraction of site references
+ */
+ std::vector<int> sites() const override;
+
+ /*!
+ * \brief Implement the interface gmx::IRestraintPotential
+ *
+ * Dispatch to calculate() method.
+ *
+ * \param r1 coordinate of first site
+ * \param r2 reference coordinate (second site)
+ * \param t simulation time
+ * \return calculated force and energy
+ *
+ * \todo remove to template header.
+ */
+ gmx::PotentialPointData evaluate(gmx::Vector r1,
+ gmx::Vector r2,
+ double t) override;
+
+ private:
+ int site1_{0};
+ int site2_{0};
+};
+
+/*!
+ * \brief Wraps HarmonicPotential with a gmxapi compatible "module".
+ *
+ * Objects of this type allow the potential class to be instantiated as the simulation is launched.
+ */
+class HarmonicModule : public gmxapi::MDModule
+{
+ public:
+ using param_t = Harmonic::input_param_type;
+
+ HarmonicModule(int site1,
+ int site2,
+ real R0,
+ real k)
+ {
+ site1_ = site1;
+ site2_ = site2;
+ R0_ = R0;
+ k_ = k;
+ }
+
+
+ const char* name() const override
+ {
+ return "HarmonicModule";
+ }
+
+ /*!
+ * \brief implement gmxapi::MDModule::getRestraint()
+ *
+ * \return Handle to configured library object.
+ */
+ std::shared_ptr<gmx::IRestraintPotential> getRestraint() override
+ {
+ auto restraint = std::make_shared<HarmonicRestraint>(site1_,
+ site2_,
+ R0_,
+ k_);
+ return restraint;
+ }
+
+ /*!
+ * \brief Set restraint parameters.
+ *
+ * \todo generalize this
+ * \param site1
+ * \param site2
+ * \param k
+ * \param R0
+ */
+ void setParams(int site1,
+ int site2,
+ real R0,
+ real k)
+ {
+ site1_ = site1;
+ site2_ = site2;
+ R0_ = R0;
+ k_ = k;
+ }
+
+ private:
+ int site1_;
+ int site2_;
+ real R0_;
+ real k_;
+};
+
+} // end namespace plugin
+
+#endif //GROMACS_HARMONICPOTENTIAL_H
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#ifndef GMX_COMPAT_MAKE_UNIQUE_H
+#define GMX_COMPAT_MAKE_UNIQUE_H
+/*! \libinternal
+ * \file
+ * \brief Provides template gmx::compat::make_unique
+ *
+ * The implementation of gmx::compat::make_unique is copied with little
+ * modification from C++ standardization doc N3656
+ * at http://www.open-std.org/jtc1/sc22/wg21/docs/papers/2013/n3656.htm
+ * though additional wrapping has been added for use in \Gromacs.
+ *
+ * \author M. Eric Irrgang <ericirrgang@gmail.com>
+ * \ingroup group_compatibility
+ */
+/*! \addtogroup group_compatibility
+ * ### gmx::compat::make_unique
+ *
+ * Provide a trivially adapted implementation of the C++ standard library `make_unique` function template.
+ * When All supported \Gromacs build platforms provide `std::make_unique`, this should be removed.
+ *
+ */
+#include <cstddef>
+
+#include <memory>
+#include <type_traits>
+#include <utility>
+
+namespace gmx
+{
+namespace compat
+{
+
+///\cond
+
+// All gmx::compat code should use std::unique_ptr
+using ::std::unique_ptr;
+
+template<class T> struct Unique_if {
+ typedef unique_ptr<T> Single_object;
+};
+
+template<class T> struct Unique_if<T[]> {
+ typedef unique_ptr<T[]> Unknown_bound;
+};
+
+template<class T, size_t N> struct Unique_if<T[N]> {
+ typedef void Known_bound;
+};
+
+template<class T, class ... Args>
+typename Unique_if<T>::Single_object
+make_unique(Args && ... args)
+{
+ return unique_ptr<T>(new T(::std::forward<Args>(args) ...));
+}
+
+template<class T>
+typename Unique_if<T>::Unknown_bound
+make_unique(size_t n)
+{
+ typedef typename ::std::remove_extent<T>::type U;
+ return unique_ptr<T>(new U[n]());
+}
+
+template<class T, class ... Args>
+typename Unique_if<T>::Known_bound
+make_unique(Args && ...) = delete;
+
+///\endcond
+
+} // namespace gmx::compat
+} // namespace gmx
+
+#endif // header guard
--- /dev/null
+//
+// Created by Eric Irrgang on 6/11/18.
+//
+
+#include "sessionresources.h"
+
+#include <cassert>
+
+#include <memory>
+
+#include "gmxapi/exceptions.h"
+#include "gmxapi/md/mdsignals.h"
+
+namespace plugin
+{
+
+// Explicit instantiation.
+template
+class ::plugin::Matrix<double>;
+
+void EnsembleResourceHandle::reduce(const Matrix<double>& send,
+ Matrix<double>* receive) const
+{
+ assert(reduce_);
+ if (*reduce_)
+ {
+ (*reduce_)(send,
+ receive);
+ }
+ else
+ {
+ throw gmxapi::ProtocolError("'reduce' functor was not initialized before use.");
+ }
+}
+
+void EnsembleResourceHandle::stop()
+{
+ assert(session_);
+ auto signaller = gmxapi::getMdrunnerSignal(session_,
+ gmxapi::md::signals::STOP);
+
+ // Should probably check that the function object has been initialized...
+ signaller();
+}
+//
+//gmxapi::session::OutputStream* EnsembleResourceHandle::ostream()
+//{
+// return ostream_.get();
+//}
+
+EnsembleResourceHandle EnsembleResources::getHandle() const
+{
+ auto handle = EnsembleResourceHandle();
+
+ if (!bool(reduce_))
+ {
+ throw gmxapi::ProtocolError("reduce operation functor is not set, which should not happen...");
+ }
+ handle.reduce_ = &reduce_;
+
+ if (!session_)
+ {
+ throw gmxapi::ProtocolError("EnsembleResources::getHandle() must not be called before setSession() has been called.");
+ }
+ handle.session_ = session_;
+
+ return handle;
+}
+
+void EnsembleResources::setSession(gmxapi::SessionResources* session)
+{
+ if (!session)
+ {
+ throw gmxapi::ProtocolError("EnsembleResources::setSession received a null SessionResources pointer.");
+ }
+ session_ = session;
+}
+//
+//void EnsembleResources::setOutputStream(std::unique_ptr<gmxapi::session::OutputStream> ostream)
+//{
+// ostream_ = std::move(ostream);
+//}
+
+} // end namespace myplugin
+
--- /dev/null
+//
+// Created by Eric Irrgang on 6/11/18.
+//
+
+#ifndef RESTRAINT_SESSIONRESOURCES_H
+#define RESTRAINT_SESSIONRESOURCES_H
+
+#include <functional>
+#include <memory>
+#include <mutex>
+#include <vector>
+
+#include "gmxapi/gromacsfwd.h"
+#include "gmxapi/session.h"
+#include "gmxapi/session/resources.h"
+#include "gmxapi/md/mdmodule.h"
+
+#include "gromacs/restraint/restraintpotential.h"
+#include "gromacs/utility/real.h"
+
+namespace plugin
+{
+
+// Stop-gap for cross-language data exchange pending SharedData implementation and inclusion of Eigen.
+// Adapted from pybind docs.
+template<class T>
+class Matrix
+{
+ public:
+ Matrix(size_t rows,
+ size_t cols) :
+ rows_(rows),
+ cols_(cols),
+ data_(rows_ * cols_,
+ 0)
+ {
+ }
+
+ explicit Matrix(std::vector<T>&& captured_data) :
+ rows_{1},
+ cols_{captured_data.size()},
+ data_{std::move(captured_data)}
+ {
+ }
+
+ std::vector<T>* vector()
+ { return &data_; }
+
+ T* data()
+ { return data_.data(); };
+
+ size_t rows() const
+ { return rows_; }
+
+ size_t cols() const
+ { return cols_; }
+
+ private:
+ size_t rows_;
+ size_t cols_;
+ std::vector<T> data_;
+};
+
+// Defer implicit instantiation to ensemblepotential.cpp
+extern template
+class Matrix<double>;
+
+/*!
+ * \brief An active handle to ensemble resources provided by the Context.
+ *
+ * The semantics of holding this handle aren't determined yet, but it should be held as briefly as possible since it
+ * may involve locking global resources or preventing the simulation from advancing. Basically, though, it allows the
+ * Context implementation flexibility in how or where it provides services.
+ *
+ * Resources may be incoming input data or functors to trigger output data events.
+ *
+ * \internal
+ * It is not yet clear whether we want to assume that default behavior is for an operation to be called for each edge
+ * on every iterative graph execution, leaving less frequent calls as an optimization, or to fully support occasional
+ * data events issued by nodes during their execution.
+ *
+ * In this example, assume the plugin has specified that it provides a `.ostream.stop` port that provides asynchronous
+ * boolean events. We can provide a template member function that will handle either execution mode.
+ *
+ * ResourceHandle::ostream() will return access to a gmxapi::session::OutputStream object, which will provide
+ * set("stop", true), to give access to a function pointer from a member vector of function pointers.
+ *
+ * In the case that we are triggering asynchronous data events, the function will make the appropriate call. In the case
+ * that we have output at regular intervals, the function will update internal state for the next time the edge is
+ * evaluated.
+ *
+ * In an alternative implementation, we could maintain a data object that could be queried by subscribers, but a publish
+ * and subscribe model seems much more useful, optimizeable, and robust. We can issue the calls to the subscribers and
+ * then be done with it.
+ *
+ * If we need to optimize for reuse of memory locations, we can do one of two things: require that
+ * the subscribing object not return until it has done what it needed with the data (including deep copy) or use
+ * managed handles for the data, possibly with a custom allocator, that prevents rewriting while there are read handles
+ * still open. One way that came up in conversation with Mark to allow some optimization is to allow the recipient of
+ * the handle to make either an `open` that gets a potentially blocking read-lock or an `open` that requests ownership.
+ * If no other consumers of the data request ownership, the ownership can be transferred without a copy. Otherwise, a
+ * copy is made.
+ */
+class EnsembleResourceHandle
+{
+ public:
+ /*!
+ * \brief Ensemble reduce.
+ *
+ * \param send Matrices to be summed across the ensemble using Context resources.
+ * \param receive destination of reduced data instead of updating internal Matrix.
+ */
+ void reduce(const Matrix<double>& send,
+ Matrix<double>* receive) const;
+
+ /*!
+ * \brief Issue a stop condition event.
+ *
+ * Can be called on any or all ranks. Sets a condition that will cause the current simulation to shut down
+ * after the current step.
+ */
+ void stop();
+
+ // to be abstracted and hidden...
+ const std::function<void(const Matrix<double>&,
+ Matrix<double>*)>* reduce_;
+
+ gmxapi::SessionResources* session_;
+};
+
+/*!
+ * \brief Reference to workflow-level resources managed by the Context.
+ *
+ * Provides a connection to the higher-level workflow management with which to access resources and operations. The
+ * reference provides no resources directly and we may find that it should not extend the life of a Session or Context.
+ * Resources are accessed through Handle objects returned by member functions.
+ *
+ * gmxapi version 0.1.0 will provide this functionality through SessionResources.
+ */
+class EnsembleResources
+{
+ public:
+ /*!
+ * \brief Create a new resources object.
+ *
+ * This constructor is called by the framework during Session launch to provide the plugin
+ * potential with external resources.
+ *
+ * \note If getHandle() is going to be used, setSession() must be called first.
+ *
+ * \param reduce ownership of a function object providing ensemble averaging of a 2D matrix.
+ */
+ explicit EnsembleResources(std::function<void(const Matrix<double>&,
+ Matrix<double>*)>&& reduce) :
+ reduce_(reduce),
+ session_(nullptr)
+ {};
+
+ /*!
+ * \brief Grant the caller an active handle for the currently executing block of code.
+ *
+ * Objects should not keep resource handles open for longer than a single block of code.
+ * calculate() and callback() functions get a handle to the resources for the current time step
+ * by calling getHandle().
+ *
+ * \note setSession() must be called before this function can be used.
+ * This clumsy protocol requires other infrastructure before it can be
+ * cleaned up for gmxapi 0.1
+ *
+ * \return resource handle
+ *
+ * In this release, the only facility provided by the resources is a function object for
+ * the ensemble averaging function provided by the Context.
+ */
+ EnsembleResourceHandle getHandle() const;
+
+ /*!
+ * \brief Acquires a pointer to a Session managing these resources.
+ *
+ * \param session non-owning pointer to Session resources.
+ */
+ void setSession(gmxapi::SessionResources* session);
+
+ private:
+ //! bound function object to provide ensemble reduce facility.
+ std::function<void(const Matrix<double>&,
+ Matrix<double>*)> reduce_;
+
+ // Raw pointer to the session in which these resources live.
+ gmxapi::SessionResources* session_;
+};
+
+/*!
+ * \brief Template for MDModules from restraints.
+ *
+ * Allows a GROMACS module to be produced easily from the provided class. Refer to
+ * src/pythonmodule/export_plugin.cpp for how this template is used.
+ *
+ * \tparam R a class implementing the gmx::IRestraintPotential interface.
+ *
+ * The template type parameter should define a ``input_param_type`` member type.
+ *
+ * \todo move this to a template header in gmxapi */
+template<class R>
+class RestraintModule : public gmxapi::MDModule // consider names
+{
+ public:
+ using param_t = typename R::input_param_type;
+
+ /*!
+ * \brief Construct a named restraint module.
+ *
+ * Objects of this type are created during Session launch, so this code really doesn't belong
+ * here. The Director / Builder for the restraint uses a generic interface to pass standard
+ * parameters for pair restraints: a list of sites, a (custom) parameters structure, and
+ * resources provided by the Session.
+ *
+ * \param name
+ * \param sites
+ * \param params
+ * \param resources
+ */
+ RestraintModule(std::string name,
+ std::vector<int> sites,
+ const typename R::input_param_type& params,
+ std::shared_ptr<EnsembleResources> resources) :
+ sites_{std::move(sites)},
+ params_{params},
+ resources_{std::move(resources)},
+ name_{std::move(name)}
+ {
+
+ };
+
+ ~RestraintModule() override = default;
+
+ /*!
+ * \brief Implement gmxapi::MDModule interface to get module name.
+ *
+ * name is provided during the building stage.
+ * \return
+ */
+ // \todo make member function const
+ const char* name() const override
+ {
+ return name_.c_str();
+ }
+
+ /*!
+ * \brief Implement gmxapi::MDModule interface to create a restraint for libgromacs.
+ *
+ * \return (Possibly shared) Ownership of a restraint instance
+ *
+ * Creates the restraint instance if it does not already exist. Only creates one restraint
+ * instance in the lifetime of the RestraintModule.
+ *
+ * Note this interface is not stable but requires other GROMACS and gmxapi infrastructure
+ * to mature before it is clear whether we will be creating a new instance or sharing ownership
+ * of the object. A future version may use a std::unique_ptr.
+ */
+ std::shared_ptr<gmx::IRestraintPotential> getRestraint() override
+ {
+ std::lock_guard<std::mutex> lock(restraintInstantiation_);
+ if (!restraint_)
+ {
+ restraint_ = std::make_shared<R>(sites_,
+ params_,
+ resources_);
+ }
+ return restraint_;
+ }
+
+ private:
+ std::vector<int> sites_;
+ param_t params_;
+
+ // Need to figure out if this is copyable or who owns it.
+ std::shared_ptr<EnsembleResources> resources_;
+
+ const std::string name_;
+ std::shared_ptr<R> restraint_{nullptr};
+ std::mutex restraintInstantiation_;
+};
+
+/*!
+ * \brief Filehandle management helper class.
+ *
+ * Use the RAII pattern to make sure that a (newly) constructed object has an open filehandle and that
+ * a the filehandle for a destructed object is closed. Closing a file is not guaranteed to be error-free,
+ * so the programmer should explicitly call close() and check for errors (see the C library docs
+ * for fclose()).
+ *
+ * RAIIFile makes sure that fclose() is called exactly once, whether client code issues close()
+ * or not.
+ */
+class RAIIFile
+{
+ public:
+
+ /*!
+ * \brief Open a file in the chosen access mode.
+ *
+ * \param filename Name of file to be opened.
+ * \param mode access mode as described for the fopen C library call.
+ */
+ RAIIFile(const char* filename,
+ const char* mode) :
+ fh_{fopen(filename,
+ mode)}
+ {}
+
+ /*!
+ * \brief Open a file for writing.
+ *
+ * \param filename Name of file to be opened.
+ *
+ * File is opened in mode "w", which truncates data if the file already exists.
+ * For other file access modes, use RAIIFile(const char* filename, const char* mode)
+ */
+ explicit RAIIFile(const char* filename) :
+ RAIIFile(filename,
+ "w")
+ {}
+
+ /*!
+ * \brief Explicitly close the associated filehandle.
+ *
+ * It is good practice to explicitly close the file at a known point in the client code, though
+ * it is not strictly necessary. If the filehandle is still open when the RAIIFile object is
+ * destroyed, the fclose will be called then.
+ *
+ * Calling close() additional times on the same RAIIFile object is fine and has no effect in
+ * single-threaded code. However, the destructor and close() routines are not thread-safe, so
+ * the client code should make sure that close() is not called at the same time by multiple threads.
+ * Standard reference-counting constructs, like std::shared_ptr, can be used to make sure the
+ * object destructor is called exactly once if it needs to be shared.
+ *
+ * Refer to documentation on fclose() on checking for and interpreting `errno`.
+ */
+ void close()
+ {
+ if (fh_ != nullptr)
+ {
+ fclose(fh_);
+ }
+ fh_ = nullptr;
+ }
+
+ /*!
+ * \brief RAII destructor.
+ *
+ * Make sure the filehandle gets closed exactly once.
+ */
+ ~RAIIFile()
+ {
+ if (fh_ != nullptr)
+ {
+ fclose(fh_);
+ }
+ }
+
+ RAIIFile(const RAIIFile&) = delete;
+
+ RAIIFile& operator=(const RAIIFile&) = delete;
+
+ RAIIFile(RAIIFile&&) = default;
+
+ RAIIFile& operator=(RAIIFile&&) = default;
+
+ /*!
+ * \brief Get the managed filehandle.
+ *
+ * \return raw pointer to the underlying filehandle.
+ */
+ FILE* fh() const noexcept
+ {
+ return fh_;
+ }
+
+ private:
+ /// file handle
+ FILE* fh_{nullptr};
+};
+
+} // end namespace plugin
+
+#endif //RESTRAINT_SESSIONRESOURCES_H
--- /dev/null
+# The first argument sets the name of the target for CMake bookkeeping purposes. It is the default name of the
+# shared object library that is produced, but we can override that. There is no particular reason to
+# change "sampleplugin" here unless you need different CMake target names to build several modules in
+# a single project.
+pybind11_add_module(sampleplugin MODULE export_plugin.cpp)
+
+# Set the name of the shared object library (and the name of the Python module) to "myplugin".
+# If you change "myplugin" you must also change the argument to the macro ``PYBIND11_MODULE(myplugin, m)`` in
+# export_plugin.cpp
+set_target_properties(sampleplugin PROPERTIES OUTPUT_NAME myplugin)
+
+# We can't easily/reliably let a debug build of a Python module have a "d" suffix and still be importable with the same
+# name.
+set_target_properties(sampleplugin PROPERTIES DEBUG_POSTFIX "")
+
+# We expect to be building against an installed GROMACS that we will continue to dynamically link against at runtime.
+set_target_properties(sampleplugin PROPERTIES BUILD_WITH_INSTALL_RPATH TRUE)
+set_target_properties(sampleplugin PROPERTIES INSTALL_RPATH_USE_LINK_PATH TRUE)
+
+# The Python module requires the new library we wrote as well as the gmxapi that we found in the top-level
+# CMakeLists.txt
+target_link_libraries(sampleplugin PRIVATE Gromacs::gmxapi harmonicpotential ensemblepotential)
+
+install(TARGETS sampleplugin
+ LIBRARY DESTINATION ${GMXPLUGIN_INSTALL_PATH}
+ ARCHIVE DESTINATION ${GMXPLUGIN_INSTALL_PATH}
+ RUNTIME DESTINATION ${GMXPLUGIN_INSTALL_PATH}
+ )
--- /dev/null
+/*! \file
+ * \brief Provide Python bindings and helper functions for setting up restraint potentials.
+ *
+ * There is currently a lot of boilerplate here that will be generalized and removed in a future version.
+ * In the mean time, follow the example for EnsembleRestraint to create the proper helper functions
+ * and instantiate the necessary templates.
+ *
+ * \author M. Eric Irrgang <ericirrgang@gmail.com>
+ */
+
+#include "export_plugin.h"
+
+#include <cassert>
+
+#include <memory>
+
+#include "gmxapi/exceptions.h"
+#include "gmxapi/md.h"
+#include "gmxapi/md/mdmodule.h"
+#include "gmxapi/gmxapi.h"
+
+#include "harmonicpotential.h"
+#include "ensemblepotential.h"
+
+// Make a convenient alias to save some typing...
+namespace py = pybind11;
+
+////////////////////////////////
+// Begin PyRestraint static code
+/*!
+ * \brief Templated wrapper to use in Python bindings.
+ *
+ * Boilerplate
+ *
+ * Mix-in from below. Adds a bind behavior, a getModule() method to get a gmxapi::MDModule adapter,
+ * and a create() method that assures a single shared_ptr record for an object that may sometimes
+ * be referred to by a raw pointer and/or have shared_from_this called.
+ * \tparam T class implementing gmx::IRestraintPotential
+ *
+ */
+template<class T>
+class PyRestraint : public T, public std::enable_shared_from_this<PyRestraint<T>>
+{
+ public:
+ void bind(py::object object);
+
+ using T::name;
+
+ /*!
+ * \brief
+ *
+ * T must either derive from gmxapi::MDModule or provide a template specialization for
+ * PyRestraint<T>::getModule(). If T derives from gmxapi::MDModule, we can keep a weak pointer
+ * to ourself and generate a shared_ptr on request, but std::enable_shared_from_this already
+ * does that, so we use it when we can.
+ * \return
+ */
+ std::shared_ptr<gmxapi::MDModule> getModule();
+
+ /*!
+ * \brief Factory function to get a managed pointer to a new restraint.
+ *
+ * \tparam ArgsT
+ * \param args
+ * \return
+ */
+ template<typename ... ArgsT>
+ static std::shared_ptr<PyRestraint<T>> create(ArgsT... args)
+ {
+ auto newRestraint = std::make_shared<PyRestraint<T>>(args...);
+ return newRestraint;
+ }
+
+ template<typename ... ArgsT>
+ explicit PyRestraint(ArgsT... args) :
+ T{args...}
+ {}
+
+};
+
+/*!
+ * \brief Implement the gmxapi binding protocol for restraints.
+ *
+ * All restraints will use this same code automatically.
+ *
+ * \tparam T restraint class exported below.
+ * \param object Python Capsule object to allow binding with a simple C API.
+ */
+template<class T>
+void PyRestraint<T>::bind(py::object object)
+{
+ PyObject * capsule = object.ptr();
+ if (PyCapsule_IsValid(capsule,
+ gmxapi::MDHolder::api_name))
+ {
+ auto holder = static_cast<gmxapi::MDHolder*>(PyCapsule_GetPointer(capsule,
+ gmxapi::MDHolder::api_name));
+ auto workSpec = holder->getSpec();
+ std::cout << this->name() << " received " << holder->name();
+ std::cout << " containing spec of size ";
+ std::cout << workSpec->getModules().size();
+ std::cout << std::endl;
+
+ auto module = getModule();
+ workSpec->addModule(module);
+ }
+ else
+ {
+ throw gmxapi::ProtocolError("bind method requires a python capsule as input");
+ }
+}
+// end PyRestraint static code
+//////////////////////////////
+
+
+/*!
+ * \brief Interact with the restraint framework and gmxapi when launching a simulation.
+ *
+ * This should be generalized and removed from here. Unfortunately, some things need to be
+ * standardized first. If a potential follows the example of EnsembleRestraint or HarmonicRestraint,
+ * the template specializations below can be mimicked to give GROMACS access to the potential.
+ *
+ * \tparam T class implementing the gmxapi::MDModule interface.
+ * \return shared ownership of a T object via the gmxapi::MDModule interface.
+ */
+// If T is derived from gmxapi::MDModule, create a default-constructed std::shared_ptr<T>
+// \todo Need a better default that can call a shared_from_this()
+template<class T>
+std::shared_ptr<gmxapi::MDModule> PyRestraint<T>::getModule()
+{
+ auto module = std::make_shared<typename std::enable_if<std::is_base_of<gmxapi::MDModule, T>::value, T>::type>();
+ return module;
+}
+
+template<>
+std::shared_ptr<gmxapi::MDModule> PyRestraint<plugin::HarmonicModule>::getModule()
+{
+ return shared_from_this();
+}
+
+template<>
+std::shared_ptr<gmxapi::MDModule> PyRestraint<plugin::RestraintModule<plugin::EnsembleRestraint>>::getModule()
+{
+ return shared_from_this();
+}
+//////////////////////////////////////////////////////////////////////////////////////////
+// New restraints mimicking EnsembleRestraint should specialize getModule() here as above.
+//////////////////////////////////////////////////////////////////////////////////////////
+
+
+
+////////////////////
+// Begin MyRestraint
+/*!
+ * \brief No-op restraint class for testing and demonstration.
+ */
+class MyRestraint
+{
+ public:
+ static const char* docstring;
+
+ static std::string name()
+ { return "MyRestraint"; };
+};
+
+template<>
+std::shared_ptr<gmxapi::MDModule> PyRestraint<MyRestraint>::getModule()
+{
+ auto module = std::make_shared<gmxapi::MDModule>();
+ return module;
+}
+
+
+// Raw string will have line breaks and indentation as written between the delimiters.
+const char* MyRestraint::docstring =
+ R"rawdelimiter(Some sort of custom potential.
+)rawdelimiter";
+// end MyRestraint
+//////////////////
+
+/*!
+ * \brief Graph updater for Restraint element.
+ *
+ * Returned by create_builder(), translates the workflow operation into API operations.
+ */
+class HarmonicRestraintBuilder
+{
+ public:
+ /*!
+ * \brief Create directly from workflow element.
+ *
+ * \param element a Python object implementing the gmx.workflow.WorkElement interface.
+ *
+ * It doesn't make sense to take a py::object here. We could take a serialized version of the element
+ * iff we also got a reference to the current context, but right now we use the gmx.workflow.WorkElement's
+ * reference to the WorkSpec, which has a reference to the Context, to get, say, the communicator.
+ * Arguably, a builder provided by the restraint shouldn't do such a thing.
+ *
+ * Either the builder / translator / DAG updater should be Context agnostic or should actually be
+ * implemented in the Context, in which case we need some better convention about what that translation
+ * should look like and what resources need to be provided by the module to do it.
+ */
+ explicit HarmonicRestraintBuilder(py::object element)
+ {
+ // Params attribute should be a Python list
+ auto parameter_dict = py::cast<py::dict>(element.attr("params"));
+ // Get positional parameters: two ints and two doubles.
+ assert(parameter_dict.contains("sites"));
+ assert(parameter_dict.contains("R0"));
+ assert(parameter_dict.contains("k"));
+ py::list sites = parameter_dict["sites"];
+ site1Index_ = py::cast<int>(sites[0]);
+ site2Index_ = py::cast<int>(sites[1]);
+ equilibriumPosition_ = py::cast<real>(parameter_dict["R0"]);
+ springConstant_ = py::cast<real>(parameter_dict["k"]);
+ };
+
+ /*!
+ * \brief Add node(s) to graph for the work element.
+ *
+ * \param graph networkx.DiGraph object still evolving in gmx.context.
+ *
+ * \todo This does not follow the latest graph building protocol as described.
+ */
+ void build(py::object graph)
+ {
+ if (!subscriber_)
+ {
+ return;
+ }
+ else
+ {
+ if (!py::hasattr(subscriber_, "potential")) throw gmxapi::ProtocolError("Invalid subscriber");
+ }
+ auto potential = PyRestraint<plugin::HarmonicModule>::create(site1Index_,
+ site2Index_,
+ equilibriumPosition_,
+ springConstant_);
+
+ auto subscriber = subscriber_;
+ py::list potential_list = subscriber.attr("potential");
+ potential_list.append(potential);
+
+ // does note add a launcher to the graph.
+ //std::unique_ptr<RestraintLauncher>();
+ };
+
+ /*!
+ * \brief Accept subscription of an MD task.
+ *
+ * \param subscriber Python object with a 'potential' attribute that is a Python list.
+ *
+ * During build, an object is added to the subscriber's self.potential, which is then bound with
+ * system.add_potential(potential) during the subscriber's launch()
+ */
+ void add_subscriber(py::object subscriber)
+ {
+ assert(py::hasattr(subscriber,
+ "potential"));
+ subscriber_ = subscriber;
+ };
+
+ py::object subscriber_;
+ int site1Index_;
+ int site2Index_;
+ real equilibriumPosition_;
+ real springConstant_;
+};
+
+
+class EnsembleRestraintBuilder
+{
+ public:
+ explicit EnsembleRestraintBuilder(py::object element)
+ {
+ name_ = py::cast<std::string>(element.attr("name"));
+ assert(!name_.empty());
+
+ // It looks like we need some boilerplate exceptions for plugins so we have something to
+ // raise if the element is invalid.
+ assert(py::hasattr(element,
+ "params"));
+
+ // Params attribute should be a Python list
+ py::dict parameter_dict = element.attr("params");
+ // \todo Check for the presence of these dictionary keys to avoid hard-to-diagnose error.
+
+ // Get positional parameters.
+ py::list sites = parameter_dict["sites"];
+ for (auto&& site : sites)
+ {
+ siteIndices_.emplace_back(py::cast<int>(site));
+ }
+
+ auto nbins = py::cast<size_t>(parameter_dict["nbins"]);
+ auto binWidth = py::cast<double>(parameter_dict["binWidth"]);
+ auto minDist = py::cast<double>(parameter_dict["min_dist"]);
+ auto maxDist = pybind11::cast<double>(parameter_dict["max_dist"]);
+ auto experimental = pybind11::cast<std::vector<double>>(parameter_dict["experimental"]);
+ auto nSamples = pybind11::cast<unsigned int>(parameter_dict["nsamples"]);
+ auto samplePeriod = pybind11::cast<double>(parameter_dict["sample_period"]);
+ auto nWindows = pybind11::cast<unsigned int>(parameter_dict["nwindows"]);
+ auto k = pybind11::cast<double>(parameter_dict["k"]);
+ auto sigma = pybind11::cast<double>(parameter_dict["sigma"]);
+
+ auto params = plugin::makeEnsembleParams(nbins,
+ binWidth,
+ minDist,
+ maxDist,
+ experimental,
+ nSamples,
+ samplePeriod,
+ nWindows,
+ k,
+ sigma);
+ params_ = std::move(*params);
+
+ // Note that if we want to grab a reference to the Context or its communicator, we can get it
+ // here through element.workspec._context. We need a more general API solution, but this code is
+ // in the Python bindings code, so we know we are in a Python Context.
+ assert(py::hasattr(element,
+ "workspec"));
+ auto workspec = element.attr("workspec");
+ assert(py::hasattr(workspec,
+ "_context"));
+ context_ = workspec.attr("_context");
+ }
+
+ /*!
+ * \brief Add node(s) to graph for the work element.
+ *
+ * \param graph networkx.DiGraph object still evolving in gmx.context.
+ *
+ * \todo This may not follow the latest graph building protocol as described.
+ */
+ void build(py::object graph)
+ {
+ if (!subscriber_)
+ {
+ return;
+ }
+ else
+ {
+ if (!py::hasattr(subscriber_, "potential")) throw gmxapi::ProtocolError("Invalid subscriber");
+ }
+
+ // Temporarily subvert things to get quick-and-dirty solution for testing.
+ // Need to capture Python communicator and pybind syntax in closure so EnsembleResources
+ // can just call with matrix arguments.
+
+ // This can be replaced with a subscription and delayed until launch, if necessary.
+ if (!py::hasattr(context_, "ensemble_update"))
+ {
+ throw gmxapi::ProtocolError("context does not have 'ensemble_update'.");
+ }
+ // make a local copy of the Python object so we can capture it in the lambda
+ auto update = context_.attr("ensemble_update");
+ // Make a callable with standardizeable signature.
+ const std::string name{name_};
+ auto functor = [update, name](const plugin::Matrix<double>& send,
+ plugin::Matrix<double>* receive) {
+ update(send,
+ receive,
+ py::str(name));
+ };
+
+ // To use a reduce function on the Python side, we need to provide it with a Python buffer-like object,
+ // so we will create one here. Note: it looks like the SharedData element will be useful after all.
+ auto resources = std::make_shared<plugin::EnsembleResources>(std::move(functor));
+
+ auto potential = PyRestraint<plugin::RestraintModule<plugin::EnsembleRestraint>>::create(name_,
+ siteIndices_,
+ params_,
+ resources);
+
+ auto subscriber = subscriber_;
+ py::list potentialList = subscriber.attr("potential");
+ potentialList.append(potential);
+
+ };
+
+ /*!
+ * \brief Accept subscription of an MD task.
+ *
+ * \param subscriber Python object with a 'potential' attribute that is a Python list.
+ *
+ * During build, an object is added to the subscriber's self.potential, which is then bound with
+ * system.add_potential(potential) during the subscriber's launch()
+ */
+ void addSubscriber(py::object subscriber)
+ {
+ assert(py::hasattr(subscriber,
+ "potential"));
+ subscriber_ = subscriber;
+ };
+
+ py::object subscriber_;
+ py::object context_;
+ std::vector<int> siteIndices_;
+
+ plugin::ensemble_input_param_type params_;
+
+ std::string name_;
+};
+
+/*!
+ * \brief Factory function to create a new builder for use during Session launch.
+ *
+ * \param element WorkElement provided through Context
+ * \return ownership of new builder object
+ */
+std::unique_ptr<HarmonicRestraintBuilder> createHarmonicBuilder(const py::object& element)
+{
+ std::unique_ptr<HarmonicRestraintBuilder> builder{new HarmonicRestraintBuilder(element)};
+ return builder;
+}
+
+/*!
+ * \brief Factory function to create a new builder for use during Session launch.
+ *
+ * \param element WorkElement provided through Context
+ * \return ownership of new builder object
+ */
+std::unique_ptr<EnsembleRestraintBuilder> createEnsembleBuilder(const py::object& element)
+{
+ using std::make_unique;
+ auto builder = make_unique<EnsembleRestraintBuilder>(element);
+ return builder;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////////////////
+// New potentials modeled after EnsembleRestraint should define a Builder class and define a
+// factory function here, following the previous two examples. The factory function should be
+// exposed to Python following the examples near the end of the PYBIND11_MODULE block.
+////////////////////////////////////////////////////////////////////////////////////////////
+
+
+//////////////////////////////////////////////////////////////////////////////////////////////////
+// The PYBIND11_MODULE block uses the pybind11 framework (ref https://github.com/pybind/pybind11 )
+// to generate Python bindings to the C++ code elsewhere in this repository. A copy of the pybind11
+// source code is included with this repository. Use syntax from the examples below when exposing
+// a new potential, along with its builder and parameters structure. In future releases, there will
+// be less code to include elsewhere, but more syntax in the block below to define and export the
+// interface to a plugin. pybind11 is not required to write a GROMACS extension module or for
+// compatibility with the ``gmx`` module provided with gmxapi. It is sufficient to implement the
+// various protocols, C API and Python function names, but we do not provide example code
+// for other Python bindings frameworks.
+//////////////////////////////////////////////////////////////////////////////////////////////////
+
+// The first argument is the name of the module when importing to Python. This should be the same as the name specified
+// as the OUTPUT_NAME for the shared object library in the CMakeLists.txt file. The second argument, 'm', can be anything
+// but it might as well be short since we use it to refer to aspects of the module we are defining.
+PYBIND11_MODULE(myplugin, m) {
+ m.doc() = "sample plugin"; // This will be the text of the module's docstring.
+
+ // Matrix utility class (temporary). Borrowed from http://pybind11.readthedocs.io/en/master/advanced/pycpp/numpy.html#arrays
+ py::class_<plugin::Matrix<double>, std::shared_ptr<plugin::Matrix<double>>>(m,
+ "Matrix",
+ py::buffer_protocol())
+ .def_buffer([](plugin::Matrix<double>& matrix) -> py::buffer_info {
+ return py::buffer_info(
+ matrix.data(), /* Pointer to buffer */
+ sizeof(double), /* Size of one scalar */
+ py::format_descriptor<double>::format(), /* Python struct-style format descriptor */
+ 2, /* Number of dimensions */
+ {matrix.rows(), matrix.cols()}, /* Buffer dimensions */
+ {sizeof(double) * matrix.cols(), /* Strides (in bytes) for each index */
+ sizeof(double)}
+ );
+ });
+
+
+ // New plan: Instead of inheriting from gmx.core.MDModule, we can use a local import of
+ // gmxapi::MDModule in both gmxpy and in extension modules. When md.add_potential() is
+ // called, instead of relying on a binary interface to the MDModule, it will pass itself
+ // as an argument to that module's bind() method. Then, all MDModules are dependent only
+ // on libgmxapi as long as they provide the required function name. This is in line with
+ // the Pythonic idiom of designing interfaces around functions instead of classes.
+ //
+ // Example: calling md.add_potential(mypotential) in Python causes to be called mypotential.bind(api_object), where
+ // api_object is a member of `md` that is a type exposed directly from gmxapi with
+ // module_local bindings. To interact properly, then, mypotential just has to be something with a
+ // bind() method that takes the same sort of gmxapi object, such as is defined locally. For simplicity
+ // and safety, this gmxapi object will be something like
+ // class MdContainer { public: shared_ptr<Md> md; };
+ // and the bind method will grab and operate on the member pointer. It is possible to work
+ // with the reference counting and such in Python, but it is easier and more compatible with
+ // other Python extensions if we just keep the bindings as simple as possible and manage
+ // object lifetime and ownership entirely in C++.
+ //
+ // We can provide a header or document in gmxapi or gmxpy specifically with the the set of containers
+ // necessary to interact with gmxpy in a bindings-agnostic way, and in gmxpy and/or this repo, we can provide an export
+ // function that provides pybind11 bindings.
+
+ // Make a null restraint for testing.
+ py::class_<PyRestraint<MyRestraint>, std::shared_ptr<PyRestraint<MyRestraint>>> md_module(m,
+ "MyRestraint");
+ md_module.def(
+ py::init<>(
+ []() { return PyRestraint<MyRestraint>::create(); }
+ ),
+ "Create default MyRestraint"
+ );
+ md_module.def("bind",
+ &PyRestraint<MyRestraint>::bind);
+ // This bindings specification could actually be done in a templated function to automatically
+ // generate parameter setters/getters
+
+
+ /////////////////////////////////////////////////////
+ // Begin HarmonicRestraint
+ //
+ // Builder to be returned from create_restraint,
+ py::class_<HarmonicRestraintBuilder> harmonicBuilder(m,
+ "HarmonicBuilder");
+ harmonicBuilder.def("add_subscriber",
+ &HarmonicRestraintBuilder::add_subscriber);
+ harmonicBuilder.def("build",
+ &HarmonicRestraintBuilder::build);
+
+ // API object to build.
+ // We use a shared_ptr handle because both the Python interpreter and libgromacs may need to extend
+ // the lifetime of the object.
+ py::class_<PyRestraint<plugin::HarmonicModule>, std::shared_ptr<PyRestraint<plugin::HarmonicModule>>>
+ harmonic(m, "HarmonicRestraint");
+
+ // Deprecated constructor directly taking restraint paramaters.
+ harmonic.def(
+ py::init(
+ [](int site1,
+ int site2,
+ real R0,
+ real k) {
+ return PyRestraint<plugin::HarmonicModule>::create(site1,
+ site2,
+ R0,
+ k);
+ }
+ ),
+ "Construct HarmonicRestraint"
+ );
+ harmonic.def("bind",
+ &PyRestraint<plugin::HarmonicModule>::bind);
+ /*
+ * To implement gmxapi_workspec_1_0, the module needs a function that a Context can import that
+ * produces a builder that translates workspec elements for session launching. The object returned
+ * by our function needs to have an add_subscriber(other_builder) method and a build(graph) method.
+ * The build() method returns None or a launcher. A launcher has a signature like launch(rank) and
+ * returns None or a runner.
+ */
+ m.def("create_restraint",
+ [](const py::object element) { return createHarmonicBuilder(element); });
+ //
+ // End HarmonicRestraint
+ ///////////////////////////////////////////////////////
+
+
+ //////////////////////////////////////////////////////////////////////////
+ // Begin EnsembleRestraint
+ //
+ // Define Builder to be returned from ensemble_restraint Python function defined further down.
+ pybind11::class_<EnsembleRestraintBuilder> ensembleBuilder(m,
+ "EnsembleBuilder");
+ ensembleBuilder.def("add_subscriber",
+ &EnsembleRestraintBuilder::addSubscriber);
+ ensembleBuilder.def("build",
+ &EnsembleRestraintBuilder::build);
+
+ // Get more concise name for the template instantiation...
+ using PyEnsemble = PyRestraint<plugin::RestraintModule<plugin::EnsembleRestraint>>;
+
+ // Export a Python class for our parameters struct
+ py::class_<plugin::EnsembleRestraint::input_param_type> ensembleParams(m, "EnsembleRestraintParams");
+ m.def("make_ensemble_params",
+ &plugin::makeEnsembleParams);
+
+ // API object to build.
+ py::class_<PyEnsemble, std::shared_ptr<PyEnsemble>> ensemble(m, "EnsembleRestraint");
+ // EnsembleRestraint can only be created via builder for now.
+ ensemble.def("bind",
+ &PyEnsemble::bind,
+ "Implement binding protocol");
+ /*
+ * To implement gmxapi_workspec_1_0, the module needs a function that a Context can import that
+ * produces a builder that translates workspec elements for session launching. The object returned
+ * by our function needs to have an add_subscriber(other_builder) method and a build(graph) method.
+ * The build() method returns None or a launcher. A launcher has a signature like launch(rank) and
+ * returns None or a runner.
+ */
+
+ // Generate the name operation that will be used to specify elements of Work in gmxapi workflows.
+ // WorkElements will then have namespace: "myplugin" and operation: "ensemble_restraint"
+ m.def("ensemble_restraint",
+ [](const py::object element) { return createEnsembleBuilder(element); });
+ //
+ // End EnsembleRestraint
+ ///////////////////////////////////////////////////////////////////////////
+
+
+
+
+}
--- /dev/null
+#ifndef GMXAPI_SAMPLE_RESTRAINT_EXPORT_PLUGIN_H
+#define GMXAPI_SAMPLE_RESTRAINT_EXPORT_PLUGIN_H
+
+#include "pybind11/pybind11.h"
+#include "pybind11/stl.h"
+
+#endif //GMXAPI_SAMPLE_RESTRAINT_EXPORT_PLUGIN_H
--- /dev/null
+cmake_minimum_required(VERSION 3.4.3)
+project(googletest-download NONE)
+
+include(ExternalProject)
+ExternalProject_Add(googletest
+ GIT_REPOSITORY https://github.com/google/googletest.git
+ GIT_TAG master
+ SOURCE_DIR "${CMAKE_CURRENT_BINARY_DIR}/googletest-src"
+ BINARY_DIR "${CMAKE_CURRENT_BINARY_DIR}/googletest-build"
+ CONFIGURE_COMMAND ""
+ BUILD_COMMAND ""
+ INSTALL_COMMAND ""
+ TEST_COMMAND ""
+ )
--- /dev/null
+# Activate the CTest module for this directory.
+enable_testing()
+
+
+if(DOWNLOAD_GOOGLETEST)
+ # Download and unpack googletest at configure time
+ configure_file(CMakeLists.gtest.in googletest-download/CMakeLists.txt)
+ execute_process(COMMAND ${CMAKE_COMMAND} -G "${CMAKE_GENERATOR}" .
+ RESULT_VARIABLE result
+ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/googletest-download)
+ if(result)
+ message(WARNING "CMake step for googletest failed: ${result}")
+ # message(FATAL_ERROR "CMake step for googletest failed: ${result}")
+ endif()
+ execute_process(COMMAND ${CMAKE_COMMAND} --build .
+ RESULT_VARIABLE result
+ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/googletest-download)
+ if(result)
+ message(WARNING "Build step for googletest failed: ${result}")
+ # message(FATAL_ERROR "Build step for googletest failed: ${result}")
+ endif()
+
+ # Add googletest directly to our build. This defines
+ # the gtest and gtest_main targets.
+ add_subdirectory(${CMAKE_CURRENT_BINARY_DIR}/googletest-src
+ ${CMAKE_CURRENT_BINARY_DIR}/googletest-build
+ EXCLUDE_FROM_ALL)
+
+else()
+ # use googletest git subtree from the current repository
+ # subdirectory already included in src/external/CMakeLists.txt
+endif() # DOWNLOAD_GOOGLETEST
+
+#
+# Set up our tests
+#
+
+
+# Copy test files to test directory
+configure_file(data/topol.tpr topol.tpr COPYONLY)
+configure_file(data/water.gro water.gro COPYONLY)
+
+configure_file(testingconfiguration.in.h testingconfiguration.h)
+
+# Test that the library can access its dependencies and build.
+add_executable(library-test test_binding.cpp)
+add_test(BasicPlugin library-test)
+
+target_include_directories(library-test PRIVATE ${CMAKE_CURRENT_BINARY_DIR})
+target_link_libraries(library-test Gromacs::gmxapi gtest_main)
+
+set_tests_properties(BasicPlugin PROPERTIES
+ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+ COMPILE_DEFINITIONS "${GMOCK_COMPILE_DEFINITIONS}"
+ COMPILE_FLAGS "${GMOCK_COMPILE_FLAGS}")
+
+
+# Test the C++ code implementing the basic harmonic potential.
+add_executable(harmonic-test test_harmonic.cpp)
+add_test(HarmonicPotentialPlugin harmonic-test)
+
+target_include_directories(harmonic-test PRIVATE ${CMAKE_CURRENT_BINARY_DIR})
+
+set_target_properties(harmonic-test PROPERTIES SKIP_BUILD_RPATH FALSE)
+target_link_libraries(harmonic-test harmonicpotential Gromacs::gmxapi
+ gtest_main)
+
+set_tests_properties(HarmonicPotentialPlugin PROPERTIES
+ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+ COMPILE_DEFINITIONS "${GMOCK_COMPILE_DEFINITIONS}"
+ COMPILE_FLAGS "${GMOCK_COMPILE_FLAGS}")
+
+# Test the C++ force evaluation for the restrained-ensemble biasing potential.
+add_executable(histogram-test test_histogram.cpp)
+add_test(EnsembleHistogramPotentialPlugin histogram-test)
+
+target_include_directories(histogram-test PRIVATE ${CMAKE_CURRENT_BINARY_DIR})
+
+set_target_properties(histogram-test PROPERTIES SKIP_BUILD_RPATH FALSE)
+target_link_libraries(histogram-test ensemblepotential Gromacs::gmxapi
+ gtest_main)
+
+set_tests_properties(EnsembleHistogramPotentialPlugin PROPERTIES
+ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+ COMPILE_DEFINITIONS "${GMOCK_COMPILE_DEFINITIONS}"
+ COMPILE_FLAGS "${GMOCK_COMPILE_FLAGS}")
+
+# Test the flat-bottom bounding potential built in to the ensemble restraint.
+add_executable(bounding-test test_bounding_restraint.cpp)
+add_test(EnsembleBoundingPotentialPlugin bounding-test)
+
+target_include_directories(bounding-test PRIVATE ${CMAKE_CURRENT_BINARY_DIR})
+
+set_target_properties(bounding-test PROPERTIES SKIP_BUILD_RPATH FALSE)
+target_link_libraries(bounding-test ensemblepotential Gromacs::gmxapi
+ gtest_main)
+
+set_tests_properties(EnsembleBoundingPotentialPlugin PROPERTIES
+ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+ COMPILE_DEFINITIONS "${GMOCK_COMPILE_DEFINITIONS}"
+ COMPILE_FLAGS "${GMOCK_COMPILE_FLAGS}")
--- /dev/null
+"""Configuration and fixtures for pytest."""
+
+import pytest
+import tempfile
+import os
+
+@pytest.fixture()
+def cleandir():
+ """Provide a clean working directory for tests.
+
+ Example usage:
+
+ import os
+ import pytest
+
+ @pytest.mark.usefixtures("cleandir")
+ class TestDirectoryInit(object):
+ def test_cwd_starts_empty(self):
+ assert os.listdir(os.getcwd()) == []
+ with open("myfile", "w") as f:
+ f.write("hello")
+
+ def test_cwd_again_starts_empty(self):
+ assert os.listdir(os.getcwd()) == []
+
+ Ref: https://docs.pytest.org/en/latest/fixture.html#using-fixtures-from-classes-modules-or-projects
+ """
+ newpath = tempfile.mkdtemp()
+ os.chdir(newpath)
+
+
+try:
+ from mpi4py import MPI
+ withmpi_only = pytest.mark.skipif(not MPI.Is_initialized() or MPI.COMM_WORLD.Get_size() < 2,
+ reason="Test requires at least 2 MPI ranks, but MPI is not initialized or too small.")
+except ImportError:
+ withmpi_only = pytest.mark.skip(reason="Test requires at least 2 MPI ranks, but mpi4py is not available.")
+
+@pytest.fixture()
+def tpr_filename():
+ """Provide a sample TPR file by filename."""
+ current_dir = os.path.dirname(__file__)
+ file_path = os.path.join(current_dir, 'data', 'topol.tpr')
+ return os.path.abspath(file_path)
--- /dev/null
+# The existence of this file should suppress the default pytest behavior that looks at higher level for rootdir.
+# We don't want to recurse into the google test directories when running the tests in this directory.
--- /dev/null
+//
+// Created by Eric Irrgang on 11/9/17.
+//
+
+#include "testingconfiguration.h"
+
+#include <memory>
+#include <vector>
+
+#include "gmxapi/context.h"
+#include "gmxapi/md/mdmodule.h"
+#include "gmxapi/md.h"
+#include "gmxapi/session.h"
+#include "gmxapi/status.h"
+#include "gmxapi/system.h"
+
+#include "gromacs/math/vectypes.h"
+#include "gromacs/restraint/restraintpotential.h"
+#include "gromacs/utility/classhelpers.h"
+#include "gromacs/utility/arrayref.h"
+
+#include <gtest/gtest.h>
+
+namespace
+{
+
+const auto filename = plugin::testing::sample_tprfilename;
+
+class NullRestraint : public gmx::IRestraintPotential
+{
+ public:
+ gmx::PotentialPointData evaluate(gmx::Vector r1,
+ gmx::Vector r2,
+ double t) override
+ {
+ return {};
+ }
+
+ std::vector<int> sites() const override
+ {
+ return {0,0};
+ }
+};
+
+class SimpleApiModule : public gmxapi::MDModule
+{
+ public:
+ const char *name() const override
+ {
+ return "NullApiModule";
+ }
+
+ std::shared_ptr<gmx::IRestraintPotential> getRestraint() override
+ {
+ auto restraint = std::make_shared<NullRestraint>();
+ return restraint;
+ }
+};
+
+// This should be in a validation test suite, not a unit test...
+//TEST(ApiRestraint, MdAndPlugin)
+//{
+//
+// {
+// // Run a lot of steps of a large system.
+// std::string waterfile = "water.tpr";
+// auto system = gmxapi::fromTprFile(waterfile);
+// std::shared_ptr<gmxapi::Context> context = gmxapi::defaultContext();
+//
+// auto module = std::make_shared<SimpleApiModule>();
+// system->setRestraint(module);
+//
+// auto session = system->launch(context);
+//
+// gmxapi::Status status;
+// ASSERT_NO_THROW(status = session->run());
+//// ASSERT_TRUE(module->force_called() > 0);
+//// ASSERT_NO_THROW(session->run(1000));
+// ASSERT_TRUE(status.success());
+// }
+//
+//}
+
+} // end anonymous namespace
--- /dev/null
+# The myplugin module must be locatable by Python.
+# If you configured CMake in the build directory ``/path/to/repo/build`` then,
+# assuming you are in ``/path/to/repo``, run the tests with something like
+# PYTHONPATH=./cmake-build-debug/src/pythonmodule mpiexec -n 2 python -m mpi4py -m pytest tests/
+
+# This test is not currently run automatically in any way. Build the module, point your PYTHONPATH at it,
+# and run pytest in the tests directory.
+
+import logging
+import os
+
+import gmx
+import pytest
+from tests.conftest import withmpi_only
+
+logging.getLogger().setLevel(logging.DEBUG)
+# create console handler
+ch = logging.StreamHandler()
+ch.setLevel(logging.DEBUG)
+# create formatter and add it to the handler
+formatter = logging.Formatter('%(asctime)s:%(name)s:%(levelname)s: %(message)s')
+ch.setFormatter(formatter)
+# add the handlers to the logger
+logging.getLogger().addHandler(ch)
+
+logger = logging.getLogger()
+
+
+def test_import():
+ import myplugin
+ assert myplugin
+
+
+@pytest.mark.usefixtures("cleandir")
+def test_harmonic_potential(tpr_filename):
+ print("Testing plugin potential with input file {}".format(os.path.abspath(tpr_filename)))
+
+ md = gmx.workflow.from_tpr(tpr_filename, append_output=False)
+
+ # Create a WorkElement for the potential
+ #potential = gmx.core.TestModule()
+ params = {'sites': [1, 4],
+ 'R0': 2.0,
+ 'k': 10000.0}
+ potential_element = gmx.workflow.WorkElement(namespace="myplugin",
+ operation="create_restraint",
+ params=params)
+ # Note that we could flexibly capture accessor methods as workflow elements, too. Maybe we can
+ # hide the extra Python bindings by letting myplugin.HarmonicRestraint automatically convert
+ # to a WorkElement when add_dependency is called on it.
+ potential_element.name = "harmonic_restraint"
+ before = md.workspec.elements[md.name]
+ md.add_dependency(potential_element)
+ assert potential_element.name in md.workspec.elements
+ assert potential_element.workspec is md.workspec
+ after = md.workspec.elements[md.name]
+ assert before is not after
+
+ # Context will need to do these in __enter__
+ # potential = myplugin.HarmonicRestraint()
+ # potential.set_params(1, 4, 2.0, 10000.0)
+
+ with gmx.get_context(md) as session:
+ session.run()
+
+
+@pytest.mark.usefixtures("cleandir")
+def test_ensemble_potential_nompi(tpr_filename):
+ """Test ensemble potential without an ensemble.
+ """
+
+ print("Testing plugin potential with input file {}".format(os.path.abspath(tpr_filename)))
+
+ assert gmx.version.api_is_at_least(0,0,5)
+ assert not gmx.version.api_is_at_least(0,0,8)
+ md = gmx.workflow.from_tpr([tpr_filename], append_output=False)
+
+ # Create a WorkElement for the potential
+ #potential = gmx.core.TestModule()
+ params = {'sites': [1, 4],
+ 'nbins': 10,
+ 'binWidth': 0.1,
+ 'min_dist': 0.,
+ 'max_dist': 10.,
+ 'experimental': [1.]*10,
+ 'nsamples': 1,
+ 'sample_period': 0.001,
+ 'nwindows': 4,
+ 'k': 10000.,
+ 'sigma': 1.}
+ potential = gmx.workflow.WorkElement(namespace="myplugin",
+ operation="ensemble_restraint",
+ params=params)
+ # Note that we could flexibly capture accessor methods as workflow elements, too. Maybe we can
+ # hide the extra Python bindings by letting myplugin.HarmonicRestraint automatically convert
+ # to a WorkElement when add_dependency is called on it.
+ potential.name = "ensemble_restraint"
+ md.add_dependency(potential)
+
+ with gmx.get_context(md) as session:
+ session.run()
+
+
+@withmpi_only
+@pytest.mark.usefixtures("cleandir")
+def test_ensemble_potential_withmpi(tpr_filename):
+ import os
+
+ from mpi4py import MPI
+ rank = MPI.COMM_WORLD.Get_rank()
+
+ rank_dir = os.path.join(os.getcwd(), str(rank))
+ os.mkdir(rank_dir)
+
+ logger.info("Testing plugin potential with input file {}".format(os.path.abspath(tpr_filename)))
+
+ assert gmx.version.api_is_at_least(0,0,5)
+ assert not gmx.version.api_is_at_least(0,0,8)
+ md = gmx.workflow.from_tpr([tpr_filename, tpr_filename], append_output=False)
+
+ # Create a WorkElement for the potential
+ #potential = gmx.core.TestModule()
+ params = {'sites': [1, 4],
+ 'nbins': 10,
+ 'binWidth': 0.1,
+ 'min_dist': 0.,
+ 'max_dist': 10.,
+ 'experimental': [0.5]*10,
+ 'nsamples': 1,
+ 'sample_period': 0.001,
+ 'nwindows': 4,
+ 'k': 10000.,
+ 'sigma': 1.}
+
+ potential = gmx.workflow.WorkElement(namespace="myplugin",
+ operation="ensemble_restraint",
+ params=params)
+ # Note that we could flexibly capture accessor methods as workflow elements, too. Maybe we can
+ # hide the extra Python bindings by letting myplugin.HarmonicRestraint automatically convert
+ # to a WorkElement when add_dependency is called on it.
+ potential.name = "ensemble_restraint"
+ md.add_dependency(potential)
+
+ with gmx.get_context(md) as session:
+ session.run()
--- /dev/null
+//
+// Created by Eric Irrgang on 3/24/18.
+//
+
+#include "testingconfiguration.h"
+
+#include <iostream>
+#include <vector>
+
+#include "ensemblepotential.h"
+
+#include "gromacs/utility/classhelpers.h"
+#include "gromacs/utility/arrayref.h"
+
+#include <gtest/gtest.h>
+
+namespace {
+
+using ::gmx::Vector;
+
+std::ostream& operator<<(std::ostream& stream, const gmx::Vector& vec)
+{
+ stream << "(" << vec[0] << "," << vec[1] << "," << vec[2] << ")";
+ return stream;
+}
+
+const auto filename = plugin::testing::sample_tprfilename;
+
+TEST(EnsembleBoundingPotentialPlugin, ForceCalc)
+{
+ const Vector zerovec {0, 0, 0};
+ // define some unit vectors
+ const Vector e1{real(1), real(0), real(0)};
+ const Vector e2{real(0), real(1), real(0)};
+ const Vector e3{real(0), real(0), real(1)};
+
+ const real R0{1.0};
+ const real k{1.0};
+
+ // store temporary values long enough for inspection
+ Vector force{};
+
+ // Get a dummy EnsembleResources. We aren't testing that here.
+ auto dummyFunc = [](const plugin::Matrix<double>&, plugin::Matrix<double>*){
+ return;};
+ auto resource = std::make_shared<plugin::EnsembleResources>(dummyFunc);
+
+ // Define a reference distribution with a triangular peak at the 1.0 bin.
+ const std::vector<double>
+ experimental{{0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1}};
+
+
+ plugin::EnsembleHarmonic restraint{10, // nbins
+ 1.0, // binWidth
+ 5.0, // minDist
+ 5.0, // maxDist
+ experimental, // experimental reference histogram
+ 1, // nSamples
+ 0.001, // samplePeriod
+ 1, // nWindows
+ 100., // k
+ 1.0 // sigma
+ };
+
+ auto calculateForce =
+ [&restraint](const Vector& a, const Vector& b, double t)
+ {
+ return restraint.calculate(a,b,t).force;
+ };
+
+ // Atoms should be driven towards each other when above maxDist and and away under minDist.
+ force = calculateForce(e1,
+ static_cast<real>(3)*e1,
+ 0.001);
+ ASSERT_LT(force[0], 0.) << " where force is (" << force[0] << ", " << force[1] << ", " << force[2] << ")\n";
+ force = calculateForce(e1,
+ static_cast<real>(7)*e1,
+ 0.001);
+ ASSERT_GT(force[0], 0.) << " where force is (" << force[0] << ", " << force[1] << ", " << force[2] << ")\n";
+}
+
+} // end anonymous namespace
+
+int main(int argc, char* argv[])
+{
+ ::testing::InitGoogleTest(&argc, argv);
+ return RUN_ALL_TESTS();
+}
--- /dev/null
+//
+// Created by Eric Irrgang on 10/13/17.
+//
+
+#include "testingconfiguration.h"
+
+#include <iostream>
+#include <memory>
+
+#include "harmonicpotential.h"
+
+#include "gmxapi/context.h"
+#include "gmxapi/md.h"
+#include "gmxapi/session.h"
+#include "gmxapi/status.h"
+#include "gmxapi/system.h"
+
+#include "gromacs/utility/classhelpers.h"
+#include "gromacs/utility/arrayref.h"
+
+#include <gtest/gtest.h>
+
+namespace {
+
+std::ostream& operator<<(std::ostream& stream, const ::gmx::Vector& vec)
+{
+ stream << "(" << vec[0] << "," << vec[1] << "," << vec[2] << ")";
+ return stream;
+}
+
+const auto filename = plugin::testing::sample_tprfilename;
+
+TEST(HarmonicPotentialPlugin, Build)
+{
+ ASSERT_TRUE(true);
+ ASSERT_FALSE(false);
+
+ plugin::Harmonic puller;
+}
+
+TEST(HarmonicPotentialPlugin, ForceCalc)
+{
+ const ::gmx::Vector zerovec = {0, 0, 0};
+ // define some unit vectors
+ const ::gmx::Vector e1{real(1), real(0), real(0)};
+ const ::gmx::Vector e2{real(0), real(1), real(0)};
+ const ::gmx::Vector e3{real(0), real(0), real(1)};
+
+ const real R0{1.0};
+ const real k{1.0};
+
+ // store temporary values long enough for inspection
+ ::gmx::Vector force{};
+
+ plugin::Harmonic puller{R0, k};
+
+ // When input vectors are equal, output vector is meaningless and magnitude is set to zero.
+ auto calculateForce = [&puller](const ::gmx::Vector& a, const ::gmx::Vector& b) { return puller.calculate(a,b,0).force; };
+ EXPECT_FLOAT_EQ(0., norm(calculateForce(e1, e1)));
+
+ // Default equilibrium distance is 1.0, so force should be zero when norm(r12) == 1.0.
+ force = calculateForce(zerovec, e1);
+ EXPECT_FLOAT_EQ(0., norm(zerovec - force)) << " where force is (" << force[0] << ", " << force[1] << ", " <<
+ force[2] <<
+ ")\n";
+
+ force = calculateForce(e1, zerovec);
+ EXPECT_FLOAT_EQ(0., norm(zerovec - force)) << " where force is (" << force[0] << ", " << force[1] << ", " <<
+ force[2] << ")"
+ "\n";
+
+ force = calculateForce(e1,
+ static_cast<real>(2)*e1);
+ EXPECT_FLOAT_EQ(0., norm(zerovec - force)) << " where force is (" << force[0] << ", " << force[1] << ", " <<
+ force[2] << ")\n";
+
+ // -kx should give vector (1, 0, 0) when vector r1 == r2 - (2, 0, 0)
+ force = calculateForce(static_cast<real>(-2)*e1, zerovec);
+ EXPECT_FLOAT_EQ(1., force[0]);
+ force = calculateForce(static_cast<real>(-2)*e1, zerovec);
+ EXPECT_FLOAT_EQ(0., norm(e1 - force)) << " where force is (" << force[0] << ", " << force[1] << ", " << force[2] <<
+ ")\n";
+
+ // -kx should give vector (-2, 0, 0) when vector r1 == r2 + (2, 0, 0)
+ force = calculateForce(static_cast<real>(2)*e1,
+ static_cast<real>(-1)*e1);
+ EXPECT_FLOAT_EQ(0., norm(static_cast<real>(-2)*e1 - force)) << " where force is (" << force[0] << ", " << force[1]
+ <<
+ ", " <<
+ force[2] << ")\n";
+}
+
+TEST(HarmonicPotentialPlugin, EnergyCalc)
+{
+ const ::gmx::Vector zerovec = {0, 0, 0};
+ // define some unit vectors
+ const ::gmx::Vector e1{real(1), real(0), real(0)};
+ const ::gmx::Vector e2{real(0), real(1), real(0)};
+ const ::gmx::Vector e3{real(0), real(0), real(1)};
+
+ const real R0{1.0};
+ const real k{1.0};
+
+ // store temporary values long enough for inspection
+ real energy{0};
+
+ plugin::Harmonic puller{R0, k};
+
+ // When input vectors are equal, potential energy is still calculable.
+ auto calculateEnergy = [&puller](const ::gmx::Vector& a, const ::gmx::Vector& b) { return puller.calculate(a,b,0).energy; };
+ EXPECT_FLOAT_EQ(real(0.5*k*R0*R0), calculateEnergy(e1, e1));
+
+ // Default equilibrium distance is 1.0, so energy should be zero when norm(r12) == 1.0.
+ energy = calculateEnergy(zerovec, e1);
+ EXPECT_FLOAT_EQ(0, energy) << " where energy is " << energy << "\n";
+
+ energy = calculateEnergy(e1, zerovec);
+ EXPECT_FLOAT_EQ(0, energy) << " where energy is " << energy << "\n";
+
+ energy = calculateEnergy(e1,
+ static_cast<real>(2)*e1);
+ EXPECT_FLOAT_EQ(0, energy) << " where energy is " << energy << "\n";
+
+ // -kx should give vector (1, 0, 0) when vector r1 == r2 - (2, 0, 0)
+ energy = calculateEnergy(static_cast<real>(-2)*e1, zerovec);
+ EXPECT_FLOAT_EQ(real(0.5*k*R0*R0), energy) << " where energy is " << energy << "\n";
+
+ // -kx should give vector (-2, 0, 0) when vector r1 == r2 + (2, 0, 0)
+ energy = calculateEnergy(static_cast<real>(2)*e1,
+ static_cast<real>(-1)*e1);
+ EXPECT_FLOAT_EQ(real(0.5*k*4*R0*R0), energy) << " where energy is " << energy << "\n";
+}
+
+// This should be part of a validation test, not a unit test.
+//TEST(HarmonicPotentialPlugin, Bind)
+//{
+//
+// {
+// std::string waterfile = "water.tpr";
+// auto system = gmxapi::fromTprFile(waterfile);
+// std::shared_ptr<gmxapi::Context> context = gmxapi::defaultContext();
+//
+// auto module = std::make_shared<plugin::HarmonicModule>();
+// module->setParams(1, 4, 2.0, 100.0);
+// system->setRestraint(module);
+//
+// auto session = system->launch(context);
+//
+// gmxapi::Status status;
+// ASSERT_NO_THROW(status = session->run());
+//// ASSERT_TRUE(module->force_called() > 0);
+//// ASSERT_NO_THROW(session->run(1000));
+// ASSERT_TRUE(status.success());
+// }
+//
+//}
+
+} // end anonymous namespace
+
+int main(int argc, char* argv[])
+{
+ ::testing::InitGoogleTest(&argc, argv);
+ return RUN_ALL_TESTS();
+}
--- /dev/null
+//
+// Created by Eric Irrgang on 3/24/18.
+//
+
+#include "testingconfiguration.h"
+
+#include <iostream>
+#include <vector>
+
+#include "gromacs/utility/classhelpers.h"
+#include "gromacs/utility/arrayref.h"
+
+#include "ensemblepotential.h"
+#include "sessionresources.h"
+
+#include <gtest/gtest.h>
+
+using ::gmx::Vector;
+
+namespace {
+
+std::ostream& operator<<(std::ostream& stream, const Vector& vec)
+{
+ stream << "(" << vec[0] << "," << vec[1] << "," << vec[2] << ")";
+ return stream;
+}
+
+TEST(EnsembleHistogramPotentialPlugin, ForceCalc)
+{
+ const Vector zerovec = {0, 0, 0};
+ // define some unit vectors
+ const Vector e1{real(1), real(0), real(0)};
+ const Vector e2{real(0), real(1), real(0)};
+ const Vector e3{real(0), real(0), real(1)};
+
+ const real R0{1.0};
+ const real k{1.0};
+
+ // store temporary values long enough for inspection
+ Vector force{};
+
+ /*! We need to be able to mock up a Session or otherwise get a dummy SessionResources.
+ // Get a dummy EnsembleResources. We aren't testing that here.
+ auto dummyFunc = [](const plugin::Matrix<double>&, plugin::Matrix<double>*){
+ return;};
+ auto resource = std::make_shared<plugin::EnsembleResources>(dummyFunc);
+ */
+
+ // Define a reference distribution with a triangular peak at the 1.0 bin.
+ const std::vector<double>
+ experimental{{0, 1, 0, 0, 0, 0, 0, 0, 0, 0}};
+
+
+ plugin::EnsembleHarmonic restraint{10, // nbins
+ 1.0, // binWidth
+ 0.0, // minDist
+ 10.0, // maxDist
+ experimental, // experimental reference histogram
+ 1, // nSamples
+ 0.001, // samplePeriod
+ 1, // nWindows
+ 100., // k
+ 1.0 // sigma
+ };
+
+ auto calculateForce =
+ [&restraint](const Vector& a, const Vector& b, double t)
+ {
+ return restraint.calculate(a,b,t).force;
+ };
+
+ // With the initial histogram (all zeros) the force should be zero no matter where the particles are.
+ ASSERT_EQ(static_cast<real>(0.0), norm(calculateForce(e1, e1, 0.)));
+ ASSERT_EQ(static_cast<real>(0.0), norm(calculateForce(e1, e2, 0.)));
+ ASSERT_EQ(static_cast<real>(0.0), norm(calculateForce(e1, static_cast<real>(-1)*e1, 0.)));
+
+ /* In 0.0.7, we cannot have a SessionResource without a Session. We can't
+ * really do this mock-up test in the 0.0.7 infrastructure without some
+ * colossal kludges, so we'll remove this until the new SessionResources
+ * protocol is further along.
+ * See https://github.com/kassonlab/gmxapi/issues/77
+ * See https://github.com/kassonlab/gmxapi/issues/186
+
+ // Establish a history of the atoms being 2.0 apart.
+ restraint.callback(e1, static_cast<real>(3)*e1, 0.001, *resource);
+
+ // Atoms should now be driven towards each other where the difference in experimental and historic distributions is greater.
+ force = calculateForce(e1, static_cast<real>(3)*e1, 0.001);
+ ASSERT_GT(force[0], 0.) << " where force is (" << force[0] << ", " << force[1] << ", " << force[2] << ")\n";
+ force = calculateForce(static_cast<real>(3)*e1, e1, 0.001);
+ ASSERT_LT(force[0], 0.) << " where force is (" << force[0] << ", " << force[1] << ", " << force[2] << ")\n";
+
+ // When input vectors are equal, output vector is meaningless and magnitude is set to zero.
+ ASSERT_EQ(static_cast<real>(0.0), norm(calculateForce(e1, e1, 0.001)));
+ */
+}
+
+// This should be part of a validation test, not a unit test.
+//TEST(HarmonicPotentialPlugin, Bind)
+//{
+//
+// {
+// std::string waterfile = "water.tpr";
+// auto system = gmxapi::fromTprFile(waterfile);
+// std::shared_ptr<gmxapi::Context> context = gmxapi::defaultContext();
+//
+// auto module = std::make_shared<plugin::HarmonicModule>();
+// module->setParams(1, 4, 2.0, 100.0);
+// system->setRestraint(module);
+//
+// auto session = system->launch(context);
+//
+// gmxapi::Status status;
+// ASSERT_NO_THROW(status = session->run());
+//// ASSERT_TRUE(module->force_called() > 0);
+//// ASSERT_NO_THROW(session->run(1000));
+// ASSERT_TRUE(status.success());
+// }
+//
+//}
+
+} // end anonymous namespace
+
+int main(int argc, char* argv[])
+{
+ ::testing::InitGoogleTest(&argc, argv);
+ return RUN_ALL_TESTS();
+}
--- /dev/null
+//
+// Created by Eric Irrgang on 11/9/17.
+//
+
+#ifndef HARMONICRESTRAINT_TESTINGCONFIGURATION_IN_H
+#define HARMONICRESTRAINT_TESTINGCONFIGURATION_IN_H
+
+
+#include <string>
+
+namespace plugin
+{
+
+namespace testing
+{
+
+// Todo: Need to set up a test fixture...
+static const std::string sample_tprfilename = "${CMAKE_CURRENT_BINARY_DIR}/topol.tpr";
+
+} // end namespace plugin::testing
+
+} // end namespace plugin
+
+
+#endif //HARMONICRESTRAINT_TESTINGCONFIGURATION_IN_H
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff