General Information

ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis. ABINIT also includes options to optimize the geometry according to the DFT forces and stresses, or to perform molecular dynamics simulations using these forces, or to generate dynamical matrices, Born effective charges, and dielectric tensors, based on Density-Functional Perturbation Theory, and many more properties. Excited states can be computed within the Many-Body Perturbation Theory (the GW approximation and the Bethe-Salpeter equation), and Time-Dependent Density Functional Theory (for molecules). In addition to the main ABINIT code, different utility programs are provided.  netcdf, bigdft, wannier90, etsf_io, libxc, etc. plugins are included. 7.0.4 version is installed.

How to send Abinit

The programs are in /software/bin/abinit. For instance, to execute abinit in the queue system scripts use

/software/bin/abinit/abinit < input.files > out.log

Depending on the number of cores asked to the queue system it will execute in parallel. The jobs can be also submitted with the [intlink id=”233″ type=”post”]interactive qsub[/intlink] command.

There are other utilities like aim, anaddb, band2eps, conducti, cut3d, lwf, macroave, mrgddb, mrggkk, newsp, optic, etc.

Benchmark

We have made a small benchmark with the 6.12.3 version.

We observe that Abinit works fine in itanium and xeon nodes while in opteron nodes is slower.

More information

Abinit web page.

Online manuals.

General information

Amsterdam Density Functional (2016.01)

The ADF package is software for first-principles electronic structure calculations. ADF is used by academic and industrial researchers in such diverse fields as pharmacochemistry and materials science. It is particularly popular in the research areas of homogeneous and heterogeneous catalysis, inorganic chemistry, heavy element chemistry, various types of spectroscopy, and biochemistry. Key Benefits of ADF

• Spectroscopic properties and environments for any type of molecule
• Excels in transition and heavy metal compounds
• Accurate, robust, and fast
• Expert staff and active community
• Uses Slater functions, beats Gaussians!

ADF can be used for finite systems (molecules) and periodic systems by using ADFBAND. ADF includes graphical interfaces and analysis tools available from Katramila server.

The Service has license for 4 cores.

How to use

To execute the graphical interfaces for input and result visualization use in Katramila:

adfview

To submit an ADF input name input.run created with adfinput program we recommend to use the send_adf

command:

<code>send_adf JOBNAME NODES PROCS[property] TIME MEM [``Otherqueue options'' ]

• JOBNAME: Input name without the extension
• NODES: Number of nodes
• PROCS: Number of processors.
• TIME: Requested time in hh:mm:ss format.
• MEM: Memory in GB.
• [“Otras opciones de Torque”] Other queue oprions.

Example

To submit the au_min2.run input file to 4 processors, with a 20 hours walltime and 4 GB of RAM use

send_adf au_min2.run 1 4 20:00:00 4

More information

ADF web page.

ADF documentation.

General information

TeraChem 1.45 is general purpose quantum chemistry software designed to run on NVIDIA GPU architectures under a 64-bit Linux operating system. Some of TeraChem features include:

• Full support for both NVIDIA Tesla and Fermi GPUs
• Restricted Hartree-Fock and Kohn-Sham single point energy and gradient calculations
• Various DFT functionals (BLYP, B3LYP, PBE, etc) and DFT grids (800-80,000 grid points per atom)
• Empirical dispersion corrections (DFT-D)
• Geometry optimization and transition state search (including constraints)
• Ab initio molecular dynamics (NVE and NVT ensembles)
• Support of multiple-GPU systems
• Up to 1000 times faster than conventional CPU-based codes
• Designed for large molecules – reads/writes PDB files directly
• Optimization including geometric constraints
• Improved mixed-precision for increased accuracy

How to send Terachem

[intlink id=”3851″ type=”post”]send_terachem[/intlink] command exist to facilitate the job submision to the cluster.

More information

Terachem web page.

User guide.