/tag/chem
Spark on Rivanna
Description Spark is Hadoop MapReduce done in memory Software Category: devel
For detailed information, visit the Spark website.
Available Versions To find the available versions and learn how to load them, run:
module spider spark The output of the command shows the available Spark module versions.
For detailed information about a particular Spark module, including how to load the module, run the module spider command with the module’s full version label. For example:
module spider spark/3.1.2 ModuleVersion Module Load Command spark3.1.2 module load spark/3.1.2 Using Spark interactively Please request an ijob or a Desktop session.
AlphaFold on Rivanna
Description Open source code for AlphaFold
Software Category: URL: https://github.com/deepmind/alphafold For detailed information, visit the AlphaFold website.
Available Versions The current installation of AlphaFold incorporates the most popular packages. To find the available versions and learn how to load them, run:
module spider alphafold The output of the command shows the available AlphaFold module versions.
For detailed information about a particular AlphaFold module, including how to load the module, run the module spider command with the module’s full version label. For example:
module spider alphafold/2.1.2 ModuleVersion Module Load Command alphafold2.1.2 module load singularity/3.7.1 alphafold/2.1.2 alphafold2.2.0 module load singularity/3.
NAMD on Rivanna
Description NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Software Category: chem
For detailed information, visit the NAMD website.
Available Versions The current installation of NAMD incorporates the most popular packages. To find the available versions and learn how to load them, run:
module spider namd The output of the command shows the available NAMD module versions.
For detailed information about a particular NAMD module, including how to load the module, run the module spider command with the module’s full version label. For example:
module spider namd/2.14 ModuleVersion Module Load Command namd2.
ORCA on Rivanna
Description ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects. Software Category: chem
For detailed information, visit the ORCA website.
Available Versions The current installation of ORCA incorporates the most popular packages. To find the available versions and learn how to load them, run:
module spider orca The output of the command shows the available ORCA module versions.
Chemistry on Rivanna
Overview Many popular software packages for computational chemistry are available on Rivanna.
General considerations Most computational chemistry packages utilize MPI for parallel execution. Accordingly, the Slurm job scripts should contain the following two SBATCH directives:
#SBATCH -N <M> # request M nodes (replace with a number) #SBATCH –ntasks-per-node=<L> # request L MPI processes per node You should launch your program with srun as the MPI executor, for example for Quantum Espresso
srun pw.x -in mymol.in Please see the page of the particular package you wish to use for more details.
VASP Users The Vienna Ab-Initio Simulation Package, is licensed by individual groups and we do not have a common installation.
Gaussian on Rivanna
Description Gaussian is a suite of electronic-structure codes. Software Category: chem
For detailed information, visit the Gaussian website.
Available Versions The current installation of Gaussian incorporates the most popular packages. To find the available versions and learn how to load them, run:
module spider gaussian The output of the command shows the available Gaussian module versions.
For detailed information about a particular Gaussian module, including how to load the module, run the module spider command with the module’s full version label. For example:
module spider gaussian/g16 ModuleVersion Module Load Command gaussiang16 module load gaussian/g16 gaussiangrads16 module load gaussian/grads16 License and Permission We have a site license.
GROMACS on Rivanna
Description GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. Software Category: chem
For detailed information, visit the GROMACS website.
Available Versions To find the available versions and learn how to load them, run:
module spider gromacs The output of the command shows the available GROMACS module versions.
For detailed information about a particular GROMACS module, including how to load the module, run the module spider command with the module’s full version label. For example:
module spider gromacs/2021.2 ModuleVersion Module Load Command gromacs2021.
LAMMPS on Rivanna
Description LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a molecular-dynamics code. The code is designed to be easy to modify or extend with new functionality. LAMMPS can run on a single core but is designed to be highly efficient running on a large number of cores in parallel using message-passing techniques and a spatial decomposition of the simulation domain. It solves systems ranging from single atoms through polymers and proteins to rigid collections of particles. A variety of force fields is supported.
Local support is not available. LAMMPS has documentation and tutorials at its Website. It has a large and active community of users; to search or join the mailing list see the instructions here.
QuantumEspresso on Rivanna
Description Quantum ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft). Local support is not available. For detailed documentation and tutorials, visit the QuantumEspresso website. QuantumEspresso (QE) has a large and active community of users; to search or join the mailing list see the instructions here.
Software Category: chem
Available Versions We built versions of QE incorporating the most popular optional packages. To find the available versions and learn how to load them, run:
module spider quantumespresso The output of the command shows the available QuantumEspresso module versions.
TeX Live on Rivanna
Description TeX Live is TeX Live is intended to be a straightforward way to get up and running with the TeX document production system. It provides a comprehensive TeX system with binaries for most flavors of Unix, including GNU/Linux, macOS, and also Windows. It includes all the major TeX-related programs, macro packages, and fonts that are free software, including support for many languages around the world.
Software Category: tools
For detailed information, visit the TeX Live website.
Available Versions To find the available versions and learn how to load them, run:
module spider texlive The output of the command shows the available TeX Live module versions.
VASP on Rivanna
Description The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling. Local support is not available. The package is supported by its developers through their documentation site. VASP is licensed software and licenses are issued to individual research groups. Each group must build and maintain its own copy of the code.
Software Category: chem
For detailed information, visit the VASP website.
Available Versions To find the available versions and learn how to load them, run:
module spider vasp The output of the command shows the available VASP module versions.
For detailed information about a particular VASP module, including how to load the module, run the module spider command with the module’s full version label.
