Commit 466b0c89 authored by Jony Castagna's avatar Jony Castagna

Merge branch 'master' into 'master'

Module: Direct Dynamics Database

See merge request !262
parents e698af87 b24ab39e
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......@@ -31,19 +31,24 @@ In the context of E-CAM, the definition of a software module is any piece of sof
community and that encapsulates some additional functionality, enhanced performance or improved usability for people
performing computational simulations in the domain areas of interest to the project.
This definition is deliberately broader than the traditional concept of a module as defined in the semantics of most
high-level programming languages and is intended to capture internal workflow scripts, analysis tools and test suites
as well as traditional subroutines and functions. Because such E-CAM modules will form a heterogeneous collection we
prefer to refer to this as an E-CAM software repository rather than a library (since the word library carries a
particular meaning in the programming world). The modules do however share with the traditional computer science
definition the concept of hiding the internal workings of a module behind simple and well-defined interfaces. It is
probable that in many cases the modules will result from the abstraction and refactoring of useful ideas from existing
codes rather than being written entirely de novo.
Perhaps more important than exactly what a module is, is how it is written and used. A final E-CAM module adheres to
current best-practice programming style conventions, is well documented and comes with either regression or unit tests
(and any necessary associated data). E-CAM modules should be written in such a way that they can potentially take
advantage of anticipated hardware developments in the near future (this is one of the training objectives of E-CAM).
This definition is deliberately broader than the traditional concept of a module as
defined in the semantics of most high-level programming languages and is intended
to capture internal workflow scripts, analysis tools and test suites
as well as traditional subroutines and functions. Because such E-CAM modules
will form a heterogeneous collection we prefer to refer to this as an E-CAM
software repository rather than a library (since the word library carries a
particular meaning in the programming world). The modules do however share with
the traditional computer science definition the concept of hiding the internal
workings of a module behind simple and well-defined interfaces.
It is probable that in many cases the modules will result from the abstraction
and refactoring of useful ideas from existing codes rather than being written entirely de novo.
Perhaps more important than exactly what a module is, is how it is written and used.
A final E-CAM module adheres to current best-practice programming style conventions,
is well documented and comes with either regression or unit tests
(and any necessary associated data). E-CAM modules should be written in such a way
that they can potentially take advantage of anticipated hardware developments in the
near future (this is one of the training objectives of E-CAM).
......@@ -479,6 +484,18 @@ as well as a set of examples that can also be used for testing.
The **Spin orbit coupling smoothing** module is to smooth spin orbit couplings along internuclear distance.
.. toctree::
:glob:
:maxdepth: 1
./modules/Direct_Dynamics_Database/readme
The **Direct Dynamics Database** The Direct Dynamics Database module is an improved,
more efficient version of the database used to provide the potential energy surfaces
in the Direct Dynamics variational multi-configuration Gaussian wavepacket (DD-vMCG)
method [Wor1]_ which is included in the powerful and flexible Quantics_ package
program [Wor2]_.
References
----------
......@@ -503,4 +520,7 @@ References
.. [Mey] H.-D. Meyer, G. A. Worth *Theor. Chem. Acc.* **109** (2003) 251 `DOI: 10.1007/s00214-003-0439-1 <https://doi.org/10.1007/s00214-003-0439-1>`_
.. [Ric] G. W. Richings, I. Polyak, K. E. Spinlove, G. A. Worth, I. Burghardt, B. Lasorne
*Int. Rev. Phys. Chem.* **34** (2015) 269 `DOI: 10.1080/0144235X.2015.1051354 <https://doi.org/10.1080/0144235X.2015.1051354>`_
.. [Wor1] G. A. Worth, M. A. Robb, B. L. Lasorne
*Mol. Phys.* **106** (2008) 2077–2091 `DOI: 10.1080/00268970802172503 <https://doi.org/10.1080/00268970802172503>`_
.. [Wor2] G. A. Worth, K. Giri, G. W. Richings, M. H. Beck, A. Jäckle, H.-D. Meyer
Quantics package, version 1.1, (2015)
..
.. _Direct_Dynamics_Database:
###########################################
Direct Dynamics Database improvements code
###########################################
.. sidebar:: Software Technical Information
Language
Fortran 2003
Licence
GNU General Lesser Public License
Documentation Tool
Documentation provided as in-line comments within the source code
Application Documentation
Useful documentation can be found `here <http://chemb125.chem.ucl.ac.uk/worthgrp/quantics/doc/>`_
Relevant Training Material
Training material is available through the test examples
Software Module Developed by
Quantics code: G. A. Worth, K. Giri, G. W. Richings, M. H. Beck, A. J ̈ackle, and H.-D. Meyer. Module: Georgia Christopoulou and Graham Worth.
.. contents:: :local:
Purpose of Module
_________________
The module focuses on improving the efficiency of Direct Dynamics variational
multi-configuration Gaussian wavepacket (DD-vMCG) method. During every
Direct Dynamics propagation step the calculated energies, gradients and
hessian matrix are stored in a database. One important challenge of this
method is the time needed to continually reread, sort and analyze this
database which makes the calculation of a large system very expensive.
Employing a dynamic and smaller version of the database with selected
points only relevant to each basis function, each time the program
needs to use stored data points, reduces massively the cost of the
calculation. Thus, treatment of larger systems is now possible.
The module has been added and tested within the Quantics quantum
dynamics package which is available on Gitlab and at the same
time the code benefits from parallel running.
Background Information
______________________
The latest version of quantics package and the code developed
related to this module within the Quantics
software package are merged and available through Quantics.gitlab_.
.. _Quantics.gitlab: https://gitlab.com/quantics
Application
______________________
This module will be extensively used in the near future to study the
photochemistry of large systems, whose size limited the application
of the previous version of the DD-vMCG code.
Testing
_______
After Quantics code has been successfully installed. The Quantics
README file will help you to install the Quantics code.
All the tests available for Direct Dynamics are suitable to test
this module and can be found at ``inputs/``. A good and quick
example is Butatriene. After you have copied the ``but_dd.inp``
file and the ``but_dddata`` directory, the test can be done
through the following command::
$ quantics but_dd.inp
Source Code
___________
The source code for this module can be found within the
Quantics software which can be downloaded via Quantics.gitlab_.
You firstly need to make an account (gitlab). The quantics
project has a private repository so you also need to ask
for access by emailing Graham Worth (g.a.worth@ucl.ac.uk).
In order to clone it into your computer, then type::
$ git clone https://gitlab.com/quantics/quantics.git
.. _Quantics.gitlab: https://gitlab.com/quantics
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