add readme.rst

Classical-MD-Modules/modules/OpenPathSampling/ops_rpe/readme.rst

+.. _ost_example:
+
+#################
+OPS-based modules
+#################
+
+.. sidebar:: Software Technical Information
+
+  The information in this section describes OpenPathSampling as a whole.
+  Information specific to the additions in this module are in subsequent
+  sections.
+
+  Language
+    Python (2.7)
+
+  Documentation Tool
+    Sphinx, numpydoc format (ReST)
+
+  Application Documentation
+    http://openpathsampling.org
+
+  Relevant Training Material
+    http://openpathsampling.org/latest/examples/
+
+  Licence
+    LGPL, v. 2.1 or later
+
+.. contents:: :local:
+
+Authors: Alan O'Cais 
+
+This is the template for an E-CAM *module* based on OpenPathSampling (OPS). Several
+sections are already pre-filled with the details of OPS. Please fill out the
+rest in order to make your module. Feel free to add additional information as
+well. This section should provide a very brief description of your module.
+
+To add your module, please follow the instructions in ":ref:`contributing`" but create your module 
+in a subdirectory of ``modules/OpenPathSampling`` and use a copy of 
+:download:`this file <./ops_module_template.rst>` as a starting point.
+Push your changes
+back to GitLab and immediately open a merge request from your feature branch
+against our repository. We can discuss your module in the merge request and
+help you get it accepted.
+
+For more details and the syntax for further functionality, see the generic example module in the
+``modules/example_module/`` directory (:ref:`example`).
+
+Purpose of Module
+_________________
+
+.. Give a brief overview of why the module is/was being created.
+Interface optimization is an important issue in TIS simulations. In general TIS procedure developed to perform TPS calculations on a separate ensembles, each is represented by its interface. With TIS algorithm it is possible obtain larger crossing probabilities and then collect the results. For more accurate results it is better to use a lot of interface, but for better performance the interfaces has to be optimized.
+
+
+Background Information
+______________________
+
+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
+
+
+Testing
+_______
+
+Tests in OpenPathSampling use the `nose`_ package.
+
+.. IF YOUR MODULE IS IN OPS CORE:
+
+.. This module has been included in the OpenPathSampling core. Its tests can
+.. be run by setting up a developer install of OpenPathSampling and running
+.. the command ``nosetests`` from the root directory of the repository.
+
+.. IF YOUR MODULE IS IN A SEPARATE REPOSITORY
+
+.. The tests for this module can be run by downloading its source code, 
+.. installing its requirements, and running the command ``nosetests`` from the
+.. root directory of the repository.
+
+Examples
+________
+
+Link to examples, if you have one. May be a file within your source code.
+
+Source Code
+___________
+
+.. link the source code
+
+.. IF YOUR MODULE IS IN OPS CORE
+
+.. This module has been merged into OpenPathSampling. It is composed of the
+.. following pull requests:
+
+.. * link PRs
+
+.. IF YOUR MODULE IS A SEPARATE REPOSITORY
+
+.. The source code for this module can be found in: URL.
+
+.. CLOSING MATERIAL -------------------------------------------------------
+
+.. Here are the URL references used
+
+.. _nose: http://nose.readthedocs.io/en/latest/
+