Commit 81e529a0 authored by srmnitc's avatar srmnitc

update pybop to reflect the new repo

parent 16d304a1
......@@ -148,14 +148,14 @@ to enumerate -- both academics and industry will benefit greatly from having
software for these methods.
The modules listed here deal with software to perform path sampling methods,
as well as other approaches to rare events.
as well as other approaches to rare events.
OpenPathSampling
================
Several modules were developed based on
`OpenPathSampling (OPS) <http://openpathsampling.org>`_. These include modules
that have been incorporated into the core of OPS, as well as some that remain
Several modules were developed based on
`OpenPathSampling (OPS) <http://openpathsampling.org>`_. These include modules
that have been incorporated into the core of OPS, as well as some that remain
separate projects. The modules that were incorporated into the core are:
.. toctree::
......@@ -182,7 +182,7 @@ The modules that are based on OPS, but remain separate, are:
.. toctree::
:glob:
:maxdepth: 1
./modules/annotated_trajectories/readme
./modules/ops_piggybacker/readme
./modules/contact_maps/readme
......@@ -190,9 +190,9 @@ The modules that are based on OPS, but remain separate, are:
./modules/dw_dimer_testsystem/readme
./modules/lammps_ops/readme
Nine of these modules were part of
Nine of these modules were part of
`E-CAM Deliverable 1.2 <https://www.e-cam2020.eu/deliverables/>`_. Those modules
provided improvements and new features in software for trajectory sampling and
provided improvements and new features in software for trajectory sampling and
for studying the thermodynamics and kinetics of rare events.
Pilot Projects
......@@ -221,8 +221,8 @@ The following modules were developed specifically for the Classical MD pilot pro
Extended Software Development Workshops (ESDWs)
===============================================
The first ESDW for the Classical MD workpackage was held in Traunkirchen,
Austria, in November 2016, with a follow-up to be held in Vienna in April 2017.
The first ESDW for the Classical MD workpackage was held in Traunkirchen,
Austria, in November 2016, with a follow-up to be held in Vienna in April 2017.
The following modules have been produced:
.. toctree::
......@@ -234,7 +234,7 @@ The following modules have been produced:
./modules/OpenPathSampling/ops_maxlikelihood/readme
./modules/OpenPathSampling/ops_interface_optimization/readme
The second ESDW for the Classical MD workpackage was held in Leiden, Holland, in
The second ESDW for the Classical MD workpackage was held in Leiden, Holland, in
August 2017. The following modules have been produced:
.. toctree::
......@@ -255,6 +255,6 @@ The third ESDW for the Classical MD workpackage was held in Turin, Italy in July
:maxdepth: 1
./modules/HTC/decorators/readme
./modules/pybop/readme
./modules/pyscal/readme
.. _E-CAM: https://www.e-cam2020.eu/
.. In ReStructured Text (ReST) indentation and spacing are very important (it is how ReST knows what to do with your
document). For ReST to understand what you intend and to render it correctly please to keep the structure of this
template. Make sure that any time you use ReST syntax (such as for ".. sidebar::" below), it needs to be preceded
and followed by white space (if you see warnings when this file is built they this is a common origin for problems).
.. We allow the template to be standalone, so that the library maintainers add it in the right place
.. Firstly, let's add technical info as a sidebar and allow text below to wrap around it. This list is a work in
progress, please help us improve it. We use *definition lists* of ReST_ to make this readable.
.. sidebar:: Software Technical Information
Name
pybop
Language
Python (2.7, 3.4, 3.5, 3.6)
Licence
`GNU General Public License v3.0 <https://www.gnu.org/licenses/gpl-3.0.en.html>`_
Documentation Tool
Sphinx/RST
Application Documentation
https://pybop.readthedocs.io/en/latest/
Relevant Training Material
https://mybinder.org/v2/gh/srmnitc/pybop/master?filepath=examples%2F
Software Module Developed by
Sarath Menon
.. In the next line you have the name of how this module will be referenced in the main documentation (which you can
reference, in this case, as ":ref:`example`"). You *MUST* change the reference below from "example" to something
unique otherwise you will cause cross-referencing errors. The reference must come right before the heading for the
reference to work (so don't insert a comment between).
#####
pybop
#####
.. Let's add a local table of contents to help people navigate the page
.. contents:: :local:
.. Add an abstract for a *general* audience here. Write a few lines that explains the "helicopter view" of why you are
creating this module. For example, you might say that "This module is a stepping stone to incorporating XXXX effects
into YYYY process, which in turn should allow ZZZZ to be simulated. If successful, this could make it possible to
produce compound AAAA while avoiding expensive process BBBB and CCCC."
``pybop`` is a python module for calculation of bond orientational order parameters [#]_. The core functionality of ``pybop`` is written in C++ with python wrappers using `pybind11 <https://pybind11.readthedocs.io/en/stable/intro.html>`_ . This allows for fast calculations with possibilities for seamless expansion in python.
Purpose of Module
_________________
.. Keep the helper text below around in your module by just adding ".. " in front of it, which turns it into a comment
Bond orientational order parameters have been widely used in distinction of crystal structures in computational studies [#]_. Additionally, these parameters have also been used to distinguish between solid and liquid particles in studies of crystallisation during solidification [#]_.
``pybop`` provides a flexible post-processing python environment for these calculations, at the same time ensuring speed and efficiency as the core code is written in C++ with `pybind11 bindings <https://pybind11.readthedocs.io/en/stable/intro.html>`_. ``pybop`` also links with `Voro++ <http://math.lbl.gov/voro++/>`_ code to carry out calculations of voronoi volumes, indices and face areas.
Some of the major uses of ``pybop`` are listed below-
- calculations including the bond order parameters :math:`q_{i}` where :math:`i = \{2,3 \to 12\}`.
- averaged versions which has been to improve the resolution in identification of crystal structures [#]_.
- weighted :math:`q_{i}` where the contributions are weighted by the voronoi face area shared with adjacent atoms [#]_.
- distinction of liquid and solid atoms based on :math:`q_{6}` parameter.
- calculation of the parameters in non-orthogonal simulation boxes.
- other quantities like radial distribution function, coordination number and voronoi volume of individual particles.
``pybop`` can read in output data from LAMMPS [#]_ `dump format <https://lammps.sandia.gov/doc/dump.html>`_ and POSCAR files from VASP. The module also provides an easy interface for extension of the available data formats or linking with other codes to read in input data.
.. I will add information about the paper and results using pybop.
Background Information
______________________
.. Keep the helper text below around in your module by just adding ".. " in front of it, which turns it into a comment
See the `application documentation <https://srmnitc.github.io/pybop/html/index.html>`_ for full details.
The utilisation of Dask within the project came about as a result of the `E-CAM High Throughput Computing ESDW <https://www.e-cam2020.eu/event/4424/?instance_id=71>`_ held in Turin in 2018 and 2019.
Building and Testing
____________________
.. Keep the helper text below around in your module by just adding ".. " in front of it, which turns it into a comment
**Installation**
First, clone the ``pybop`` repository by ``git clone https://github.com/srmnitc/pybop.git``.
After cloning the repository, ``pybop`` can be installed by running ``python setup.py install`` from main code directory. It can be uninstalled by ``pip uninstall pybop``. All the dependencies of ``pybop`` are installed automatically.
**Testing**
``pybop`` also contains automated tests which use the `pytest <https://docs.pytest.org/en/latest/>`_ python library, which can be installed by ``pip install pytest``. The tests can be run by executing the command ``pytest tests/`` from the main code directory.
**Examples**
Examples uses of ``pybop`` can be found `here <https://srmnitc.github.io/pybop/html/examples.html>`_. An `interactive notebook <https://mybinder.org/v2/gh/srmnitc/pybop/master?filepath=examples%2F>`_ using binder is also available.
Source Code
___________
.. Notice the syntax of a URL reference below `Text <URL>`_ the backticks matter!
The `source code <https://github.com/srmnitc/pybop>`_. of the module can be found on GitHub.
.. [#] Steinhardt, PJ, Nelson, DR, Ronchetti, M. Phys. Rev. B 28, 1983.
.. [#] Lechner, W, Dellago, C, Bolhuis, P.G. J. Chem. Phys. 125, 2011., Diaz Leines, G, Drautz, R, Rogal, J. J. Chem. Phys. 146, 2017.
.. [#] Diaz Leines, G, Drautz, R, Rogal, J. J. Chem. Phys. 146, 2017.
.. [#] Lechner, W, Dellago, C. J. Chem. Phys. 129, 2008.
.. [#] Mickel, W, Kapfer, S.C, Schroder-Turk, G.E, Mecke, K. J. Chem. Phys. 138, 2013.
.. [#] Plimpton, S. J Comp. Phys. 117, 1995.
.. sidebar:: Software Technical Information
Name
pyscal
Language
Python (2.7, 3.4, 3.5, 3.6)
Licence
`GNU General Public License v3.0 <https://www.gnu.org/licenses/gpl-3.0.en.html>`_
Documentation Tool
Sphinx/RST
Application Documentation
https://pyscal.readthedocs.io/en/latest/
Relevant Training Material
https://mybinder.org/v2/gh/srmnitc/pyscal/master?filepath=examples%2F
Software Module Developed by
Sarath Menon
Grisell Díaz Leines
Jutta Rogal
######
pyscal
######
.. contents:: :local:
**pyscal** is a python module for the calculation of local atomic structural environments including Steinhardt's bond orientational order parameters [1]_ during post-processing
of atomistic simulation data. The core functionality of pyscal is written in C++ with python wrappers using
`pybind11 <https://pybind11.readthedocs.io/en/stable/intro.html>`_ which allows for fast calculations and
easy extensions in python.
Purpose of Module
_________________
Steinhardt's order parameters are widely used for the identification of crystal structures [3]_. They are also used to distinguish
if an atom is in a solid or liquid environment [4]_. pyscal is inspired by the
`BondOrderAnalysis <https://homepage.univie.ac.at/wolfgang.lechner/bondorderparameter.html>`_ code,
but has since incorporated many additional features and modifications. The pyscal module includes the following functionalities:
* calculation of Steinhardt's order parameters and their averaged version [2]_.
* links with the `Voro++ <http://math.lbl.gov/voro++/>`_ code, for the calculation of Steinhardt parameters weighted using the face areas of Voronoi polyhedra [3]_.
* classification of atoms as solid or liquid [4]_.
* clustering of particles based on a user defined property.
* methods for calculating radial distribution functions, Voronoi volumes of particles, number of vertices and face area of Voronoi polyhedra, and coordination numbers.
Background Information
______________________
See the `application documentation <https://pyscal.readthedocs.io/en/latest/>`_ for full details.
The utilisation of Dask within the project came about as a result of the `E-CAM High Throughput Computing ESDW <https://www.e-cam2020.eu/event/4424/?instance_id=71>`_ held in Turin in 2018 and 2019.
Building and Testing
____________________
**Installation**
pyscal can be installed directly using `Conda <https://docs.conda.io/en/latest/>`_ by the following statement-
.. code:: console
conda install -c pyscal pyscal
pyscal can be built from the repository by-
.. code:: console
git clone https://github.com/srmnitc/pyscal.git
cd pyscal
python setup.py install --user
**Testing**
pyscal contains automated tests which
use the `pytest <https://docs.pytest.org/en/latest/>`_ python library, which can be installed by ``pip install pytest``.
The tests can be run by executing the command ``pytest tests/`` from the main code directory.
**Examples**
Examples using pyscal can be found `here <https://pyscal.readthedocs.io/en/latest/examples.html>`_.
An `interactive notebook <https://mybinder.org/v2/gh/srmnitc/pyscal/master?filepath=examples%2F>`_
using binder is also available.
Source Code
___________
The `source code <https://github.com/srmnitc/pyscal>`_. of the module can be found on GitHub.
.. [1] `Steinhardt, P. J., Nelson, D. R., & Ronchetti, M. (1983). Physical Review B, 28 <https://journals.aps.org/prb/abstract/10.1103/PhysRevB.28.784>`_.
.. [2] `Lechner, W., & Dellago, C. (2008). The Journal of Chemical Physics, 129 <https://aip.scitation.org/doi/full/10.1063/1.2977970>`_.
.. [3] `Mickel, W., Kapfer, S. C., Schröder-Turk, G. E., & Mecke, K. (2013). The Journal of Chemical Physics, 138 <https://aip.scitation.org/doi/full/10.1063/1.4774084>`_.
.. [4] `Auer, S., & Frenkel, D. (2005). Advances in Polymer Science, 173 <https://link.springer.com/chapter/10.1007/b99429>`_.
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