ADF Newsletter, December 2010

Season's Greetings from the ADF team in Amsterdam!

Winterland in Amsterdam
Winterland in Rembrandtplein, Amsterdam

Contents summary

Christmas break

Because the Vrije Universiteit will close down for the period December 24, 2010 - January 2, 2011, the SCM staff will not be reachable during this period. We can also not prepare license files for you during this time. We are back in the office on January 3, 2011. If you urgently need a temporary license file for ADF, you can download it with your username and password. (Windows users should right click on the link then select "Save Link As..." to save this text file.) In case of emergencies, we might still be reachable now and then at "info at scm.com".

ADF2010.02 released: ReaxFF and MOPAC2009

The sub-release ADF2010.02 is now available for download from the SCM web site.

The release ADF2010.02 is now available for download for all currently supported operating systems.

The primary reason for the release is the introduction of two new computational methods in our suite:

Reactive Molecular Dynamics with ReaxFF

Over more than a year, SCM has collaborated with the group of Prof. Adri van Duin at Penn State to drastically improve their code in terms of:

Unlike other Molecular Dynamics codes, ReaxFF can deal with bond breaking and formation and is thereby capable of describing chemical reactions. ReaxFF beats DFT calculations on speed by several orders of magnitude. This makes it suitable for simulations of dynamic reactive systems with thousands of atoms, where neither traditional force fields, nor DFT codes would be of help. ReaxFF has been used over the past decade in various successful studies by Prof. van Duin, Prof. Goddard and coworkers on inhomogeneous reactive systems, including solvent environments, interfaces, and molecules on metal and metal oxide surfaces. See also the full list of publications by Dr. van Duin for specific examples. The current release comes with a number of parameter sets involving transition metals provided recently by Prof. van Duin's group.

All current users may request a free trial for ReaxFF that lasts until the end of February 2011.

MOPAC2009

SCM has recently signed an agreement with Stewart Computational Chemistry to become a value-added reseller for the standard binaries of MOPAC2009 on Windows, Mac OS X, and Linux. In ADF2010.02, these binaries are included in the ADF download files. After a standard installation of ADF, MOPAC2009 is ready for execution and can be run from the MOPAC section in ADFinput (part of ADF-GUI). MOPAC2009 is currently free of charge for academic ADF users, so if you have a valid license for ADF2010, contact us to activate MOPAC in your license file.

MOPAC can perform fast semi-empirical quantum chemistry calculations both on molecules and on periodic structures. It features the PM6 model that covers most elements in the periodic table. Energies, gradients, and Hessians calculated by MOPAC can be used in ONIOM-style calculations in the QUILD program, and can be used as initial guess for an ADF transition state search or geometry optimization.

The current visualization of MOPAC results is still very basic, and limited to bond orders, atomic charges, etc. SCM plans to support visualization of more results from MOPAC, reusing modules already available for ADF visualization.

Bug fixes BAND, minor bug fixes ADF, ADF-GUI, BAND-GUI

ADF2010.02 contains some noncritical bug fixes for ADF and the ADF-GUI. BAND users who run into technical problems are recommend to upgrade (too much memory was used in the gradient calculations, and a frozen-core check was disabled). Check the full list of changes for details. As always, any problems with this new release can be reported to support@scm.com.

Is a new license file needed for ADF2010.02?

If you already have a license file for ADF2010.01, you can continue to use it. Normally it will have version number 2010.99 which also covers 2010.02. You will need a new license file in case you wish to try ReaxFF or MOPAC. In that case, ADF users can contact SCM by E-mail or make use of the demo license file that works for all modules until the end of January.

New staff member, new QUASINANO project

In October of this year, Dr. Stefano Borini has joined us as a full-time developer. Stefano obtained his Ph.D. in quantum chemistry at Ferrara University, Italy and Université Sabatier, Toulouse, France. He possesses both academic and industrial experience in many different countries and laboratories, with focus on scientific software development for chemistry, nanotechnology and bioinformatics. Dr. Borini's expertise is in chemical data exchange and interoperability, code refactoring, databases, evaluation of optical properties in polymers and theoretical ab-initio techniques.

October 1, 2010 also marked the official beginning of the QUAntum-mechanical SImulations for the NANOscale (QUASINANO) project. This project is funded by the Research Executive Agency (REA) of the European Community REA-FP7-PEOPLE-2009-IAPP (Industry-Academia Partnerships and Pathways) program. The work will be a collaboration between researchers at Jacobs University in Bremen, Germany and Scientific Computing & Modelling in Amsterdam. Professor Thomas Heine and his group will be leading the development in Bremen, while various people in the SCM staff, including most notably Dr. Stefano Borini will lead the work being done here at SCM.

Cu-BTCMOF

Above: two views of a Cu3(BTC)2(H2O)3 Metal-Organic Framework (MOF) system. With approximate DFT methods, systems of this size can be routinely modeled.

The ambitious goal is to develop an approximate DFT (A-DFT) method which is applicable throughout large parts of the periodic table, including transition metals and is capable of dealing with systems of approximately 100,000 atoms. For highly accurate simulations and spectroscopy, a related hybrid method between DFT and A-DFT (AxDFT) is envisaged. Once this method will be incorporated into future ADF releases, it is expected that the methods can be applied to challenging applications in the fields of nanoelectromechanics, supramolecular / inorganic chemistry and nanoporous materials.

Meetings and workshops

In the later half of 2010 SCM conducted seminars and workshops in a few locations in Asia and Europe. First Dr. Matt Kundrat of SCM and Dr. Mike Seth of the University of Calgary represented ADF at the expo of the 240th ACS National Meeting & Exposition in Boston, MA, USA. Next Dr. Seth and Mr. Kento Mori of Ryoka Systems, Inc. teamed up with our own Dr. Stan van Gisbergen to hold an ADF seminar and demonstration in Tokyo, Japan. Then Stan joined the staff of Hongcam, Inc. for a talk and workshop in Beijing, China. Finally the remaining SCM development team in Amsterdam joined with the Dutch supercomputing center, SARA, for a workshop at SARA's computing center in Science Park, Amsterdam.

SCM will be present at one more meeting before the year's end, when Dr. Matt Kundrat represents SCM at the International Chemical Congress of Pacific Basin Societies (Pacifichem 2010) in Honolulu, Hawaii. The exposition will take place from 11:00 to 17:00 on Thursday Dec 16th and Friday Dec 17th, as well as from 11:00 to 14:00 on Saturday Dec 18th. SCM is in lucky booth number 113 in the Coral Lounge and Coral Ballroom of the Hilton Hawaiian Village hotel.

The Following spring we will be attending the 241st ACS National Meeting & Exposition. Look for us in Anaheim, CA at booth #1122 from March 28-30, 2011.

Suggestions, questions, comments, contributions

We always welcome suggestions for new ADF functionality that you would like to see included in a future release. Any questions or comments regarding this Newsletter, or other questions related to ADF, are also welcome and can be sent to info@scm.com. Feel free to contact us also in case you have some information that may be of interest to other ADF users, and that may be suitable material for a future Newsletter or news item on the SCM website.

More news...

These news items and more can be found in the news section of our website.

Subscribe or unsubscribe

You can (un)subscribe to this newsletter and view older newsletters on the Newsletters web page.
SCM Home Page
Quality Software. Quantum Science
*
*
85.10.201.17
Copyright Terms of UsePrivacy Policy