ChemToolsMeet March 08
From BlueObelisk
This page is a first attempt to summarise some of the outcomes from the Molecular Modelling: Tools, GUIs and Visualisation that took place at the Runcorn Holiday Inn and Daresbury Laboratory on the 11th-13th March 2008.
A list of the talks and links to the slides and audio of the presentations is below.
The meeting was very successful at bringing together a number of projects that work in closely related areas, but often have little direct contact between the users and developers. As such a number of areas of common interest and problems that were experienced by all the projects came up repeatedly in discussions.
There was general agreement that the various projects should try to collaborate together on looking at these areas and use the Blue Obelisk site as a focus for their activities.
A list of the main areas, with links to pages where they can be explored in greater depth, follows below.
A list of the specific outcomes of the meeting, and the list of the initial tasks that we have agreed to work on, can be found at the bottom of this page.
This is a collaborative effort and we are very keen for other people with an interest in this area to get involved, so if you do have anything to add, please get involved by editing the wiki or sending an email to the Blue Obelisk Mailing List.
From Left to Right: David Zorilla : Angel Herráez : Hannes Löffler : Peter Knowles : Johannes Kaestner : Jens Thomas : Chris Morley : Huub Van Dam : Tris Youngs : Mario Valle : Jan Jensen : Michael Zeidan : Marcus Hanwell : Tom Hawkins : Noel O'Boyle : Michael Dension : Toon Verstraelen
(Missing from the photo are: Philip Couch, Donald E. Curtis and Paul Sherwood)
For a linked image see here.
Builders, visualisers and general tools for working with molecules
There are a large number of GUIs, tools and visualisers for working with molecules available today. However, many in the community are not aware of the tools or what their capabilities are (this is despite some useful sites like Mario Valle's list of Free Chemistry Visualisation Tools and the list at Linux4Chemistry).
One of the things we would therefore like to do is create a list of various tools, grouped according to functionality and with brief summaries of their strengths and weakness. This will help users decide on the tool best suited to the job in hand.
Tools that were of interest included:
- Molecular Builders and Visualisers
- Data Parsers (OpenBabel, cclib, AgentX)
- Plotting MOs, densities etc. from basis/orbital information
- Optimisers
- Force Field builders
Data formats in Quantum Chemistry
There are a large number of Quantum Chemistry codes in the community, each with different strengths, capabilities, but in particular different output formats. This makes it difficult to share data between codes and compare the results of complex calculations between them. There are various efforts to try and standardise on particular formats (such as XML/CML), but currently very few codes make use of this.
The aim of this section is to provide a focus for discussion about standard formats and also to provide a place to describe the existing formats for users interested in parsing the outputs of the programs.
The list of formats is currently being maintained here.
Tutorials/How Tos for computational chemistry
This section aims to provide a place for people to provide links to tutorials and How-Tos on how to do common or particularly difficult tasks in computational chemistry.
The links can be found at TutorialsAndHowTos
Building and testing codes
Testing is one of the most important steps in developing a code. However developers often find it difficult to access all of the architectures/OS/compiler combinations that they would like to test their code on and may not have much experience of building on these different platforms. Regularly testing a code on a number of different platforms also implies some sort of automatic testing framework.
The BuildAndTest section of the site is therefore intended to explore these issues and provide a place for developers to document their experiences.
Code projects
There is always a need to for new functionality in existing projects, or areas where there is no existing code/script to perform a required function. As there are a large number of talented developers in the community and also new students who are interested in becoming involved in projects and learning how to program, this section is intended to provide:
- A list of missing/required functionality for programmers looking to start work on something new.
- A list of simple code projects for novice programmers.
Presentations: Slides and Audio
The first two talks were not focussed on any particular code and were concerned with general issues around visualisation and GUIs in general.
Standard and Unusual Visualisation at CSCS - Mario Valle
GUIs: What's in it for me? - Jan Jensen
The following three talks were given by developers of Electronic Structure codes and were intended to provide an overview of their functionality and what they require in the area of visualisation GUIs and associated tools.
Molpro - functionality and interfaces - Peter Knowles
- Slides as PDF
- Audio as mp3 NB: unfortunately the first few seconds of Peter's talk is missing.
GAMESS-US - Jan Jensen
Scientific Data Visualisation: The GAMESS-UK Perspective - Huub van Dam
Discussion of the requirements for GUIs & tools suggested by the preceding presentations - chaired by Paul Sherwood
The remaining talks were given by developers of various chemistry GUIs and tools.
The CCP1GUI - Jens Thomas
OpenBabel - Chris Morley
Avogadro - Marcus D. Hanwell and Donald E. Curtis
Chemistry visualization research themes at CSCS (Molekel) - Mario Valle
Molpro- a tightly-coupled GUI - Peter Knowles
Jmol - Angel Herráez
Zeobuilder (& Tracks) - Toon Verstraelen
Aten - Tris Youngs
cclib, Pybel, GaussSum and CCDC - Noel O'Boyle
AgentX and data exchange - Phil Couch
- Phil - we need your slides as a PDF!
- Audio as mp3
Final discussion and wrap up
Specific Outcomes
This section lists the specific outcomes and tasks that arose from the meeting:
- Collaborate on a wiki (hosted on the Blue Obelisk site) to provide a focus for the activities and give any developments a presence on the web.
- Create a list of chemistry tools, grouped according to functionality and with brief summaries of their strengths and weaknesses.
- Create a list of the human and machine-readable files generated by different QM codes.
- Work out a strategy for developing a build/testing farm for use by the developers of the different codes.
- AgentX and OpenBabel developers to collaborate to see if their data models can be made to work together.
- Clean up the CCP1GUI jobmanager functionality so that it can be used by other codes (Avogadro as first test-case).
- Developers of Zeobuilder and Avogadro to collaborate to see if building/minimisation functionality can be shared between the two codes.
- GAMESS-UK developers to write parsers for their input/output files for OpenBabel.
- Computational Chemistry group at Daresbury Laboratory to help the developers of cclib with parsing data generated by different QM codes.
- Developers of Avogadro and the CCP1GUI to see if the existing python code to create inputs and run QM calculations from the CCP1GUI can be incorporated into Avogadro.
