This project is an example of how to write a plugin for OpenMM. It includes nearly everything you would want in a real plugin, including implementations for the Reference, OpenCL, and CUDA platforms, serialization support, test cases, and a Python API. It is useful as a starting point for anyone who wants to write a plugin.
This plugin defines a single Force subclass called ExampleForce, which implements an anharmonic bond force of the form E(r)=k*r4. Of course, you don't actually need a plugin to implement a force of that form: you could do it trivially with CustomBondForce. But since it is so simple, it makes a very good example.
I assume you are already familiar with the OpenMM API, and that you have already read the OpenMM Developer Guide. If not, go read it now. I will not repeat anything that is covered there, and only focus on what is unique to this plugin.
This project uses CMake for its build system. To build it, follow these steps:
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Create a directory in which to build the plugin.
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Run the CMake GUI or ccmake, specifying your new directory as the build directory and the top level directory of this project as the source directory.
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Press "Configure".
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Set OPENMM_DIR to point to the directory where OpenMM is installed. This is needed to locate the OpenMM header files and libraries.
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Set CMAKE_INSTALL_PREFIX to the directory where the plugin should be installed. Usually, this will be the same as OPENMM_DIR, so the plugin will be added to your OpenMM installation.
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If you plan to build the OpenCL platform, make sure that OPENCL_INCLUDE_DIR and OPENCL_LIBRARY are set correctly, and that EXAMPLE_BUILD_OPENCL_LIB is selected.
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If you plan to build the CUDA platform, make sure that CUDA_TOOLKIT_ROOT_DIR is set correctly and that EXAMPLE_BUILD_CUDA_LIB is selected.
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Press "Configure" again if necessary, then press "Generate".
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Use the build system you selected to build and install the plugin. For example, if you selected Unix Makefiles, type
make install.
To run all the test cases build the "test" target, for example by typing make test.
This project contains several different directories for test cases: one for each platform, and
another for serialization related code. Each of these directories contains a CMakeLists.txt file
that automatically creates a test from every file whose name starts with "Test" and ends with
".cpp". To create new tests, just add a new file to any of these directories. The file should
contain a main() function that executes any tests in the file and returns 0 if all tests were
successful or 1 if any of them failed.
Usually plugins are loaded dynamically at runtime, but that doesn't work well for test cases:
you want to be able to run the tests before the plugin has yet been installed into the plugins
directory. Instead, the test cases directly link against the relevant plugin libraries. But
that creates another problem: when a plugin is dynamically loaded at runtime, its platforms and
kernels are registered automatically, but that doesn't happen for code that statically links
against it. Therefore, the very first line of each main() function typically invokes a method
to do the registration that would have been done if the plugin were loaded automatically:
registerExampleOpenCLKernelFactories();
The OpenCL and CUDA test directories create three tests from each source file: the program is
invoked three times while passing the strings "single", "mixed", and "double" as a command line
argument. The main() function should take this value and set it as the default precision for
the platform:
if (argc > 1)
Platform::getPlatformByName("OpenCL").setPropertyDefaultValue("OpenCLPrecision", string(argv[1]));
This causes the plugin to be tested in all three of the supported precision modes every time you run the test suite.
The OpenCL and CUDA platforms compile all of their kernels from source at runtime. This requires you to store all your kernel source in a way that makes it accessible at runtime. That turns out to be harder than you might think: simply storing source files on disk is brittle, since it requires some way of locating the files, and ordinary library files cannot contain arbitrary data along with the compiled code. Another option is to store the kernel source as strings in the code, but that is very inconvenient to edit and maintain, especially since C++ doesn't have a clean syntax for multi-line strings.
This project (like OpenMM itself) uses a hybrid mechanism that provides the best of both
approaches. The source code for the OpenCL and CUDA implementations each include a "kernels"
directory. At build time, a CMake script loads every .cl (for OpenCL) or .cu (for CUDA) file
contained in the directory and generates a class with all the file contents as strings. For
example, the OpenCL kernels directory contains a single file called exampleForce.cl. You can
put anything you want into this file, and then C++ code can access the content of that file
as OpenCLExampleKernelSources::exampleForce. If you add more .cl files to this directory,
correspondingly named variables will automatically be added to OpenCLExampleKernelSources.
OpenMM uses SWIG to generate its Python API. SWIG takes an "interface file", which is essentially a C++ header file with some extra annotations added, as its input. It then generates a Python extension module exposing the C++ API in Python.
When building OpenMM's Python API, the interface file is generated automatically from the C++ API. That guarantees the C++ and Python APIs are always synchronized with each other and avoids the potential bugs that would come from have duplicate definitions. It takes a lot of complex processing to do that, though, and for a single plugin it's far simpler to just write the interface file by hand. You will find it in the "python" directory.
To build and install the Python API, build the "PythonInstall" target, for example by typing "make PythonInstall". (If you are installing into the system Python, you may need to use sudo.) This runs SWIG to generate the C++ and Python files for the extension module (ExamplePluginWrapper.cpp and exampleplugin.py), then runs a setup.py script to build and install the module. Once you do that, you can use the plugin from your Python scripts:
from simtk.openmm import System
from exampleplugin import ExampleForce
system = System()
force = ExampleForce()
system.addForce(force)
This is part of the OpenMM molecular simulation toolkit originating from Simbios, the NIH National Center for Physics-Based Simulation of Biological Structures at Stanford, funded under the NIH Roadmap for Medical Research, grant U54 GM072970. See https://simtk.org.
Portions copyright (c) 2014 Stanford University and the Authors.
Authors: Peter Eastman
Contributors:
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.