OPS Piggybacker (legacy file converter)¶
Authors: David W.H. Swenson
This module provides a library for converting path sampling simulations from legacy codes into a format that can be analyzed by OpenPathSampling. The implementation in this module works with flexible-length transition path sampling (TPS) with one-way shooting and uniform shooting point selection.
OpenPathSampling contains excellent tools for analyzing simulations, as well as excellent tools for sampling. However, since OpenPathSampling is a new software package, users may already have simulations that they have run with other packages. The purpose of this module is to provide tools that allow the user to easily convert legacy script output into a format that can be analyzed by OpenPathSampling. It is a library of tools that can be used with data from any existing path sampling simulation output, and specifically includes tools to simplify the use of flexible-length TPS with one-way shooting and uniform shooting point selection. Extending to the library to work with other simulation types will be part of future work.
The OPSPiggybacker essentially fakes a simulation, based on data from
another source. In this module, it has the ability to read in data from
one-way TPS. The user must create the appropriate OPS
object (including defining the correct collective variables and state
volumes). Then the code creates a
MoveScheme, but instead of actually
running the simulation, it reads in the results of an existing simulation
and provides the same output that the
MoveScheme would have provided.
We call this a “pseudo-simulation.”
Classes implemented in this module include:
ShootingPseudoSimulator, subclass of
openpathsampling.PathSimulator. This acts like the OPS simulator, and runs the pseudo-simulation. Instead of taking an integer saying how many steps to run, it takes a list of data that describes each shooting move.
ShootingStub, subclass of
openpathsampling.pathmovers.PathMover. This acts like the
openpathsampling.OneWayShootingMover. It reads in the data and creates the appropriate output that can be analyzed by OPS.
OneWayTPSConverter, subclass of
ShootingPseudoSimulator. This pseudo-simulator is designed to read a specific type of input file, which can be prepared based on the output from legacy simulation tools. Depending on the nature of the input trajectory files, several options can be set to ensure that the resulting OPS trajectories are correct. This is an abstract superclass, subclasses must define how to read trajectory files of the appropriate format.
GromacsOneWayTPSConverter, subclass of
OneWayTPSConverter. Specialized for reading in GROMACS files (using MDTraj).
This module builds on OpenPathSampling, a Python package for path sampling simulations. To learn more about OpenPathSampling, you might be interested in reading:
- OPS documentation: http://openpathsampling.org
- OPS source code: http://github.com/openpathsampling/openpathsampling
Tests use the nose package.
To test this module, first install its requirements (namely
OpenPathSampling). Next, download OPSPiggybacker code, either by git or by
.zip of this release and decompressing it.
Change into the root directory of the OPSPiggybacker, and run
ops_piggybacker/tests/common_test_data.py to prepare some test data. After
that, use the
nosetests command to run the actual tests (this can be
done from the same directory).
Installation of this package can be performed with
install. Installation can be done before or after testing.
Several examples are in the examples/ directory of the code:
The module is for the 0.1 release of the OPSPiggybacker project. This includes all the work on that project through pull request #15 (merged on 28 December, 2016).
The source code for this module can be found in: https://github.com/dwhswenson/OPSPiggybacker/releases/tag/v0.1.0