Most improvements have been described already in the previous Newsletter. Here we will focus only on a very recent advance. An extensive list of changes is presented in the Changes document on the documentation part of the SCM website. Further details are available in the updated User's Guide.
Our new colleague, Dr. Alexei Yakovlev, has been working, among other things, on improvements for the Windows version
of ADF. The functionality of this version is identical to that for Unix
and Linux platforms.
The improvements can be summarized as follows:
Windows installation of ADF2004 proceeds in the same easy way as for any normal Windows program.
Because ADF uses a numerical integration scheme, the gradients needed to perform geometry optimizations and frequency calculations are subject to small fluctuations with changing geometry. These fluctuations arise due to changes in the number and placement of the integration points, and can undermine the effectiveness of optimization algorithms for certain types of challenging problems. The fluctuations also lead to less accurate second derivative evaluations in frequency calculations using finite difference, which made it necessary to use a much larger than default integration grid for ADF frequency runs.
ADF2004 introduces new functionality that can help alleviate these problems. A gradient smoothing option has been added, which, when activated, endeavors to conserve the number of integration points from one geometry to the next. With smoothly varying integration points, the errors in the gradients also vary in a smooth fashion, rather than exhibiting random jumps. The second derivative matrix (Hessian) calculated from these gradients should be much more stable, aiding geometry optimization schemes, and improving the accuracy of finite difference frequency calculations at lower computational cost. In some test calculations the integration accuracy could be reduced from 6 to 4 while retaining the same accuracy for frequencies. This implies a speed-up of about a factor of four. Several challenging geometry optimizations that did not converge previously did converge when applying the gradient smoothing option in combination with another change in the input that determines how the grid is built up.
To make use of the new smoothing options, you simply need to add a subkey to the 'geometry' block of the ADF2004 input file. There are different levels of smoothing, which impact the integration point generation to varying degrees. Please refer to the ADF2004 User's Guide to learn more about the gradient smoothing options. It should be noted that this very recent new functionality has undergone only limited testing, so we consider it to be in a beta state at the moment.
As the figure below shows in the top left panel, new modules (ADFspectra, ADFmovie, ADFtail, BOB) have been added to the existing GUI modules (ADFinput, ADFview). Furthermore, these modules have been more tightly integrated from the user point of view. Now one can start up another GUI module from within any GUI module that is already active. If applicable, the new GUI module will then automatically show relevant data for the same calculation. If that is not possible, the appropriate file can be selected from within the module. In this way, the GUI modules work together seamlessly and more intuitively than before, especially for Windows and Macintosh users. The panel selected on the right shows the new option to calculate hybrid xc energy functionals after the SCF.
Platforms available for ADF2004 at this moment:
| HP/Compaq (AlphaServerSC) OSF1 (True64 5.1) | Quadrics MPI |
| HP/Compaq (Alpha) OSF1 (True64 4.0) | PVM (PVM_ARCH=ALPHA) |
| HP Itanium2 with Linu | PVM (PVM_ARCH=LINUX64), MPI (MPICH ch_p4) |
| HP Itanium2 with HPUX | Serial, MPI (HP MPI) |
| HP RISC with HP-UX | MPI |
| IBM (AIX5, Power4&Power3) | PVM (PVM_ARCH=AIX46K), MPI (poe) |
| PC Linux (RedHat 9 or later) | PVM (PVM_ARCH=LINUX), MPI (MPICH ch_p4) |
| PC Linux (RedHat 7 or RedHat 8) | PVM (PVM_ARCH=LINUX), MPI (MPICH ch_p4) |
| Macintosh OS X (disk image) | Serial, PVM (PVM_ARCH=MACOSX) |
| SGI IRIX 6.5 | PVM (PVM_ARCH=SGI6), MPI |
| SGI Itanium2 Linux (Altix) | MPI |
SCM is working on the following platforms:
If you would like to see ADF working on other platforms as well, feel free to contact us with your request.
The minor bugs that were fixed in the weeks after the first tar-files were put on the website:
These bugs have all been fixed in the files that are now available for download on our website. Should you encounter any of these issues, we recommend to download the new tar-file. If you do not encounter any problems on your system, there is no reason to install ADF2004 again.
The PC Linux versions of ADF also work correctly and efficiently on Athlon64 and Opteron machines. They also work on non-RedHat Linux distributions and on more recent Linux variants, such as the RedHat Enterprise editions.
SCM is proud to introduce new partners in different regions of the world, who will form local contact points in these regions for new ADF users.
SCM has recently signed a reseller contract with ADDITIVE GmbH, a scientific software reseller in the German speaking countries in Europe, the so-called DACh region.
"ADDITIVE GmbH is a modern system vendor offering products and services for technical and scientific applications. The Engineering + Science (ES) department core strengths are in the fields of software for mathematics and statistics, software for statistical quality management and software for Chemistry and Life Science. The ADDITIVE IT-branch offers a variety of hardware platforms for High Performance Computing preinstalled with the ADF package."
More info on ADF in German: http://www.additive-net.de/software/adf/index.shtml
Hongcam Hongcam is a value-added scientific software reseller serving the Chinese market, with its head office in Beijing. Hongcam is offering several chemistry software packages, now including ADF. Hongcam also offers an abstract book on ADF-related papers (description of methods as well as applications) in the scientific literature.
A Chinese version of the ADF brochure is also freely available from Hongcam, as well as Chinese language support during installation and usage of ADF. Hongcam has collaborations with hardware vendors and can offer also combined software + hardware solutions that are price effective for ADF.
More info on ADF in Chinese: http://hongcam.com.cn/product/product-detail.asp?id=169
Seascapelearning has offices in India and California. Seascapelearning started in the drug discovery area as a business partner for Tripos in India. Currently activities are being started up in California as well and its activities are now broadened to include material science, nanotechnology as well as research consulting and software services.
It is almost becoming a tradition that SCM visits Japan regularly, accompanied by one or two academic ADF researchers who have contributed to the ADF program in the past. This year a visit is tentatively scheduled for the week of 4-8 October 2004.
As on previous occasions, seminars on recent developments in ADF will be presented in different places in Japan, including the Tokyo and Osaka area. If you are interested in receiving an invitation for one of these seminars, feel free to contact Ryoka (adf@cubs.bio.rsi.co.jp). You will then receive more detailed information once the final schedule is known.
This time, the tentative speakers are:
Topics will include molecular property calculations (magnetic, chiral, electric), relativistic effects, exact exchange / hybrid functionals, general overview of recent and ongoing developments in ADF, and more.
Any questions or comments regarding the above, or other questions related to ADF, are very 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.
