K-Q
LAMMPS
LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for
solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to
model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. LAMMPS runs on single processors or in
parallel using message-passing techniques and a spatial-decomposition of the simulation domain. The code is designed to be easy to modify or extend with
new functionality.
More information
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- Homepage: https://www.lammps.org
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LLVM
The LLVM Core libraries provide a modern source- and target-independent optimizer, along with code generation support for many popular CPUs (as well as
some less common ones!) These libraries are built around a well specified code representation known as the LLVM intermediate representation ("LLVM IR").
The LLVM Core libraries are well documented, and it is particularly easy to invent your own language (or port an existing compiler) to use LLVM as an
optimizer and code generator.
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Lua
Lua is a powerful, fast, lightweight, embeddable scripting language. Lua combines simple procedural syntax with powerful data description constructs
based on associative arrays and extensible semantics. Lua is dynamically typed, runs by interpreting bytecode for a register-based virtual machine, and
has automatic memory management with incremental garbage collection, making it ideal for configuration, scripting, and rapid prototyping.
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Mathematica
Mathematica is a computational software program used in many scientific, engineering, mathematical and computing fields.
More information
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- Homepage: https://www.wolfram.com/mathematica
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Mesa
Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics.
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Meson
Meson is a cross-platform build system designed to be both as fast and as user friendly as possible.
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MuJoCo
MuJoCo stands for Multi-Joint dynamics with Contact. It is a general purpose physics engine that aims to facilitate research and development in
robotics, biomechanics, graphics and animation, machine learning, and other areas which demand fast and accurate simulation of articulated structures
interacting with their environment.
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NCCL
The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective communication primitives that are performance
optimized for NVIDIA GPUs.
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NEURON
Empirically-based simulations of neurons and networks of neurons.
More information
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- Homepage: https://www.neuron.yale.edu/neuron
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NVHPC
C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI)
More information
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- Homepage: https://developer.nvidia.com/hpc-sdk/
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Ninja
Ninja is a small build system with a focus on speed.
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ORCA
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.
More information
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- Homepage: https://orcaforum.kofo.mpg.de
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OpenFOAM
OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving
chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics.
More information
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- Homepage: https://www.openfoam.com/
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OpenMPI
The Open MPI Project is an open source MPI-4/3 implementation.
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OpenSlide
OpenSlide is a C library that provides a simple interface to read whole-slide images (also known as virtual slides).
More information
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- Homepage: https://openslide.org/
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PLINK
Whole-genome association analysis toolset
More information
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- Homepage: https://www.cog-genomics.org/plink/2.0/
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PLUMED
PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics
engines. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of
the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced
with both fortran and C/C++ codes.
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ParaView
ParaView is a scientific parallel visualizer.
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Perl
Larry Wall's Practical Extraction and Report Language
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PostgreSQL
PostgreSQL is a powerful, open source object-relational database system. It is fully ACID compliant, has full support for foreign keys, joins, views,
triggers, and stored procedures (in multiple languages). It includes most SQL:2008 data types, including INTEGER, NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE,
INTERVAL, and TIMESTAMP. It also supports storage of binary large objects, including pictures, sounds, or video. It has native programming interfaces
for C/C++, Java, .Net, Perl, Python, Ruby, Tcl, ODBC, among others, and exceptional documentation.
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PyCharm
PyCharm Community Edition: Python IDE for Professional Developers
More information
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- Homepage: https://www.jetbrains.com/pycharm/
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PyTorch-Geometric
PyTorch Geometric (PyG) is a geometric deep learning extension library for PyTorch.
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PyTorch
Tensors and Dynamic neural networks in Python with strong GPU acceleration. PyTorch is a deep learning framework that puts Python first.
Other possible modules matches:
PyTorch-Geometric
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Python
Python is a programming language that lets you work more quickly and integrate your systems more effectively.
Other possible modules matches:
Biopython IPython flatbuffers-python protobuf-python spglib-python
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QUAST
QUAST evaluates genome assemblies by computing various metrics. It works both with and without reference genomes. The tool accepts multiple assemblies,
thus is suitable for comparison.
More information
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- Homepage: https://github.com/ablab/quast
Included extensions
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QUAST-5.0.2, simplejson-3.17.2
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Qhull
Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furthest-site Delaunay triangulation, and
furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and higher dimensions. Qhull implements the Quickhull algorithm for computing the
convex hull.
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QuantumESPRESSO
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).
More information
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- Homepage: https://www.quantum-espresso.org