MedeA 2.3 - Release notes

MedeA 2.3 adds a number of improvements and new features to existing modules while building on the tradition of adding new functionality to the MedeA core with each release. This article provides a short summary of the main changes, for more details please refer to the release notes on the customer club page or in the updated MedeA documentation!

Release 2.3 overview

Bringing the binary edition of the Pauling file into the platform has enlarged the spectrum of structural data covered by MedeA-InfomaticA. Also, by adding the Pauling file we have opened the way for the integration of experimental thermodynamical data (interactive phase diagrams) into the software later this year.

A Gibbs ensemble Monte Carlo code, MedeA-Gibbs, was added to the suite of MedeA codes. Based on state of the art force-fields, MedeA-Gibbs allows to calculate phase equilibria between solids, liquids and gases and a range of single/multi phase properties.

A new module, the molecular builder was added to the MedeA core. The molecular builder allows all MedeA users to edit periodic structures as molecules/clusters, to build complex molecules and to add these systems to solids, surfaces or interfaces.

The latest version of PHONON was added to the release 2.3. The new PHONON code has a significantly improved performance, thus allowing for dispersion calculation for systems containing a much larger number of atoms.

The VASP code was recompiled on both 32/64 bit Linux/Windows platforms resulting in improved performance and stability.

The interface search module received a work over: New functionality was made available like e.g. the individual control of interface gaps for non-identical interface slab models or the capability of splitting an interface into two independent surfaces.

A new bond algorithm was implemented resulting in much faster display of structures containing a large number of atoms and consequently bonds.

The MedeA documentation (user guide and reference guide) received a new improved layout. Application notes on building adsorbate-adsorbent systems and on calculating adsorption energies where added.

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MedeA 2.2 - Release notes

The MedeA 2.2 release puts an emphasis on stability and efficiency of large-scale calculations and sites with many machines and large numbers of jobs. We, and many of our customers, are routinely running thousands of calculations -- many of which are large MT or PHONON calculations, and which may involve hundreds of tasks.

Changes and new features 

64/32-bit support under Windows

There are new Windows VASP executables for 32 architectures. These are probably faster in most, if not all, cases. In addition, there are now 64-bit executables that allow essentially unlimited memory on the AMD64 - EM64T platforms.

Parallel VASP – An integrated MPI-2 standard

MedeA 2.2 used the MPI-2 standard as implemented in MPICH-2. MedeA 2.2 fully supports all types of Windows machines, including the recent dual-core processors.

Job Control – Improved support for large-scale installations

Improved performance when retrieving results such as structures, phonon dispersions, etc., from the job server in cases where the server has more than a few thousand jobs. The performance lack was due in part to fundamental problems with the disk structure under the Windows operating system. Part of the workaround for the Windows issue is to split the jobs directory into smaller subdirectories: You will now see subdirectories dir0, dir500, dir1000, etc., with 500 jobs per directory. The job server automatically reorganizes existing jobs into this format.

Improved jobserver-taskserver communication

The MedeA2.2 jobserver monitors all taskservers registered and handles cases where a taskserver goes down or looses its network connection. A monitoring interval of 5 minutes and a detection time-out of 30 seconds were implemented.  In addition, a manual check is now possible on the Administration / Task Servers page of the jobserver. 

Job database (MDJobsn.ldf/mdf) backup

Version 2.2 of the job server writes a file 'db.backup' in each job directory with a backup of that jobs database entries, so backing up the Jobs/ directory is now complete and sufficient. The need to back up the SQL database files has become OBSOLETE. In the Maintenance program under the "Manage Jobserver", an option to import and reconnect jobs can be found (Manage jobserver). This implies, you can copy a job directory and import it into another job server. Imported jobs can then be accessed like any “local” job, and can be rerun if desired.

Test job suite

MedeA 2.2 comes with a suite of 16 test jobs (as zipped directories) in the MD/TestJobs directory.  Run these test jobs to exercise various parts of MedeA.  To run, unzip a job directory, import and change the queue to one of your active queues (select job in Jobs page and click "Change Queue" at the bottom of the page). You can then "Restart Over" the calculations to check that the installation works, learn about the calculations, and so on.

New Job Control features

The many improvements in the user interface for the job server include:

	Ability to hold running jobs. This does not affect running tasks, but does stop new tasks from starting.
	Changing queues and priorities of jobs. This works for running jobs, too. Tasks that are already running will continue properly, but new tasks will go to the new queue using the new priority.
	In each detailed job page there’s now a "Restart..." button that allows you to restart the job with control over rerunning tasks, etc. This is a essentially a GUI for editing the restart.dat file and is particularly useful for large phonon calculations for which a network problem or machine crash causes problems.
	Phonon and MT calculations now bring back all the tasks and check for errors, rather than stopping at the first error. This makes handling problems in these large calculations much easier.

Band structure/Phonon/DOS plot export

Export functionality of the electronic and phonon dispersion and DOS to Excel was implemented. If you export more than one at a time, the upper and lower bounds of the graphs are automatically set to the same scale, or you can manually set the scale if needed.

Improved naming of structure windows and jobs

The structures are now always prefixed with the formula and space group, which is automatically updated as you edit
and transform the system.

For VASP, phonon and other jobs, the title carries a reasonable history.  Also, additional information is automatically put in the comments section and if you add comments at the end, the first portion will automatically update as you submit more calculations leaving your comments intact. This is useful for submitting a series of related calculations

Bug fixes

Many bug fixes were made. Details can be found below or in the MedeA help (MedeA user interface > Help > User Guide > Reference guide > Release Notes) or directly in the MedeA installer when running the update.

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