Community Codes, Computational Engines, and Frameworks
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Join Policy: Restricted
Created: 06 Sep 2019
Engines and Community Codes
Engines and Community Codes Installed in nanoHUB
These tool engines and community codes are available for nanoHUB Tool Developers. They are all installed in nanoHUB, but some may have restricted use due to licensing requirements. Links to the community websites are also provided. If you would like to build a tool with an open source code or library that is not yet installed in nanoHUB, you can request that it be installed using the tool ticket system.
You can additionally generate a list of the environments available using the use command in a terminal or in the nanoHUB Workspace. See this FAQ for details and a saved list of nanoHUB environments.
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Abinit
- 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 basis.
- https://www.abinit.org/
- ARPACK
- ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.
- https://www.caam.rice.edu/software/ARPACK/
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ASTER
- Analysis of Structures and Thermodynamics for Studies & Research
- https://www.code-aster.org/spip.php?rubrique2
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ATAT
- The Alloy-Theoretic Automated Toolkit
- https://www.brown.edu/Departments/Engineering/Labs/avdw/atat/
- Avogadro
- Avogadro is an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible high quality rendering and a powerful plugin architecture.
- https://avogadro.cc/
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Berkeley GW
- Quasiparticle and Optical Excitations
- https://berkeleygw.org/
- binvox
- binvox is a straight-forward program that reads a 3D model file, rasterizes it into a binary 3D voxel grid, and writes the resulting voxel file. binvox is not supported by nanoHUB, contact the authors directly with any questions or problems
- https://www.patrickmin.com/binvox/
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Biopython
- Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics. The source code is made available under the Biopython License, which is extremely liberal and compatible with almost every license in the world. We work along with the Open Bioinformatics Foundation, who generously host our website, bug tracker, and mailing lists.
- https://biopython.org/
- Bison
- Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables. As an experimental feature, Bison can also generate IELR(1) or canonical LR(1) parser tables. Once you are proficient with Bison, you can use it to develop a wide range of language parsers, from those used in simple desk calculators to complex programming languages.
- https://www.gnu.org/software/bison/
- Blender
- Blender is a free and open source 3D animation suite. It supports the entirety of the 3D pipeline--modeling, rigging, animation, simulation, rendering, compositing and motion tracking, even video editing and game creation.
- https://www.blender.org/
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cadnano
- cadnano simplifies and enhances the process of designing three-dimensional DNA origami nanostructures.
- http://cadnano.org/
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calculix
- Three-Dimensional Structural Finite Element Program
- http://www.calculix.de/
- cgal
- The Computational Geometry Algorithms Library (CGAL), offers data structures and algorithms like triangulations (2D constrained triangulations, and Delaunay triangulations and periodic triangulations in 2D and 3D), Voronoi diagrams (for 2D and 3D points, 2D additively weighted Voronoi diagrams, and segment Voronoi diagrams), polygons (Boolean operations, offsets, straight skeleton), polyhedra (Boolean operations), arrangements of curves and their applications (2D and 3D envelopes, Minkowski sums), mesh generation (2D Delaunay mesh generation and 3D surface and volume mesh generation, skin surfaces), geometry processing (surface mesh simplification, subdivision and parameterization, as well as estimation of local differential properties, and approximation of ridges and umbilics), alpha shapes, convex hull algorithms (in 2D, 3D and dD), search structures (kd trees for nearest neighbor search, and range and segment trees), interpolation (natural neighbor interpolation and placement of streamlines), shape analysis, fitting, and distances (smallest enclosing sphere of points or spheres, smallest enclosing ellipsoid of points, principal component analysis), and kinetic data structures.
- https://www.cgal.org/
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CompuCell3D
- CompuCell3D is a flexible scriptable modeling environment, which allows the rapid construction of sharable Virtual Tissue in silico simulations of a wide variety of multi-scale, multi-cellular problems including angiogenesis, bacterial colonies, cancer, developmental biology, evolution, the immune system, tissue engineering, toxicology and even non-cellular soft materials.
- http://compucell3d.org/
- DDSCAT
- Discrete Dipole Approximation Scattering (DDSCAT) code
- http://ddscat.wikidot.com/
- FEAP
- Finite Element Analysis Program
- http://projects.ce.berkeley.edu/feap/
- FFTW
- FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST).
- http://www.fftw.org/
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FiPy
- FiPy - A Finite Volume PDE Solver
- https://www.ctcms.nist.gov/fipy/
- FFTK
- FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL and its built-in GLUT emulation
- https://www.fltk.org/
- FVM
- The finite-volume method (FVM) is a method for representing and evaluating partial differential equations in the form of algebraic equations
- http://openfvm.sourceforge.net/
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GAMESS
- The General Atomic and Molecular Electronic Structure System (GAMESS) is a general ab initio quantum chemistry package. GAMESS is maintained by the members of the Gordon research group at Iowa State University.
- https://www.msg.chem.iastate.edu/gamess/
- Geomview
- Geomview is an interactive 3D viewing program for Unix. Geomview lets you view and manipulate three-dimensional objects
- http://www.geomview.org/
- GibbsPy
- GibbsPy - A Gibbs Solver
- GMP
- GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating-point numbers. There is no practical limit to the precision except the ones implied by the available memory in the machine GMP runs on. GMP has a rich set of functions, and the functions have a regular interface.
- https://gmplib.org/
- Gmsh
- Gmsh is a 3D finite element grid generator with a build-in CAD engine and post-processor. Its design goal is to provide a fast, light and user-friendly meshing tool with parametric input and advanced visualization capabilities. Gmsh is built around four modules
- https://gmsh.info/
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gpy
- Gaussian Process Toolbox
- https://sheffieldml.github.io/GPy/
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GROMACS
- The GROningen MAchine for Chemical Simulations
- http://www.gromacs.org/
- Gnuplot
- Gnuplot is a portable command-line driven graphing utility for Linux, OS/2, MS Windows, OSX, VMS, and many other platforms. The source code is copyrighted but freely distributed (i.e., you don't have to pay for it). It was originally created to allow scientists and students to visualize mathematical functions and data interactively, but has grown to support many non-interactive uses such as web scripting. It is also used as a plotting engine by third-party applications like Octave. Gnuplot has been supported and under active development since 1986.
- http://www.gnuplot.info/
- GOAP
- GOAP is a generalized orientation-dependent, all-atom statistical potential for protein structure prediction. It was benchmarked against other state-the-art similar potentials and was shown to be significantly better for discriminating native structures from decoys.
- https://omictools.com/goap-tool
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HyperSpy
- HyperSpy
- https://hyperspy.org/
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ImageMagick
- ImageMagick® is a software suite to create, edit, and compose bitmap images.
- https://imagemagick.org/index.php
- IMOD
- IMOD is a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections. The package contains tools for assembling and aligning data within multiple types and sizes of image stacks, viewing 3-D data from any orientation, and modeling and display of the image files. IMOD was developed primarily by David Mastronarde, Rick Gaudette, Sue Held, Jim Kremer, and Quanren Xiong at the Boulder Laboratory for 3-D Electron Microscopy of Cells.
- https://bio3d.colorado.edu/imod/
- Jmol
- JOOMMF
- OOMMF for Jupyter notebooks
- https://joommf.github.io/
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LAMMPS
- Large-scale Atomic/Molecular Massively Parallel Simulator
- https://lammps.sandia.gov/
- LIBEFP
- LIBEFP is a full implementation of the Effective Fragment Potential (EFP) method. LIBEFP facilitates extension of unique electronic structure methodologies designed for accurate simulations in the gas phase to condensed phases via QM/EFP.
- Libxc
- Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals that can be used by all the ETSF codes and also other codes.
- https://www.tddft.org/programs/libxc/
- LLVM
- The LLVM Project is a collection of modular and reusable compiler and toolchain technologies. Despite its name, LLVM has little to do with traditional virtual machines.
- https://llvm.org/
- mac-4z
- Micromechanics Analysis Code Generalized Method of Cells
- https://ntrs.nasa.gov/archive/nasa/casi.ntrs.nasa.gov/19990032036.pdf
- Matlab
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MEEP
- Meep - MIT Electromagnetic Equation Propagation
- https://meep.readthedocs.io/en/latest/
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minimol
- A Minimal Molecular Dynamics/Statics Program
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MIT Photonic Bands (MPB)
- MIT Photonic Bands (MPB) electromagnetic eigenmode solver
- https://mpb.readthedocs.io/en/latest/
- MOLDEN
- MOLDEN is a pre- and post processing program of molecular and electronic structure
- http://cheminf.cmbi.ru.nl/molden/
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Moose
- Multiphysics Object-Oriented Simsulation Environment. An Open-source, Parallet finite element framework.
- https://www.mooseframework.org
- MSIM
- This is an industry-proven SPICE simulator with optimzied algorithms to deliver unparalleled accuracy, performance and value. TSMC has certified MSIM for accuracy and performance on advanced nanometer circuit designs.
- http://www.ednc.com/wp/wp-content/uploads/2012/09/MSIM_rev12.12.pdf
- NAMD
- NAMD - Scalable Molecular Dynamics
- https://www.ks.uiuc.edu/Research/namd/
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NEMO 5
- NanoElectronics MOdeling Tool for atomic-resolution calculation of nanostructure properties
- https://nanohub.org/groups/nemo5distribution
- NESSUS
- NESSUS is a modular computer software program for performing probabilistic analysis of structural/mechanical components and systems.
- https://www.swri.org/nessus
- NETGEN
- NETGEN is an automatic 3d tetrahedral mesh generator. It accepts input from constructive solid geometry (CSG) or boundary representation (BRep) from STL file format. The connection to a geometry kernel allows the handling of IGES and STEP files. NETGEN contains modules for mesh optimization and hierarchical mesh refinement. Netgen is open source based on the LGPL license.
- https://ngsolve.org/
- ngspice
- Ngspice project aims to improve the spice3f5 circuit simulator.
- http://ngspice.sourceforge.net/
- numexpr
- The numexpr package evaluates multiple-operator array expressions many times faster than NumPy can. It accepts the expression as a string, analyzes it, rewrites it more efficiently, and compiles it on the fly into code for its internal virtual machine (VM).
- https://pypi.org/project/numexpr/
- NumPy
- Numpy contains a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran code, and useful linear algebra, Fourier transform, and random number capabilities.
- https://numpy.org/
- Octave
- OCTAVE is a numerical computing environment and programming language. It allows for easy matrix manipulation. It is an alternative to Matlab
- https://www.gnu.org/software/octave/
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Octopus
- Octopus is a scientific program aimed at the ab initio virtual experimentation on a hopefully ever increasing range of systems types. Electrons are described quantum-mechanically within the Density-Functional Theory (DFT), in its time-dependent form (TDDFT) when doing simulations in time. Nuclei are described classically as point particles. Electron-nucleus interaction is described within the Pseudopotential approximation.
- https://octopus-code.org/wiki/Main_Page
- Oncvpsp
- Open-source pseudopotential code
- http://www.quantum-simulation.org/potentials/sg15_oncv/
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OOF2
- OOF2 Finite Element Analysis of microstructures
- https://www.ctcms.nist.gov/oof/oof2/
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OOF3D
- OOF3D is just like OOF2 but in three dimensions. It calculates the physical properties of three dimensional microstructures, basing the calculations on three dimensional micrographs.
- https://www.ctcms.nist.gov/oof/oof3d/
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OOMMF
- The Object Oriented MicroMagnetic Framework
- https://math.nist.gov/oommf/
- Open Babel
- The Open Source Chemistry Toolbox - Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.
- http://openbabel.org/wiki/Main_Page
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OpenCalphad
- OpenCalphad is an informal international collaboration of scientists and researchers interested in the development of high quality software and databases for thermodynamic calculations for all kinds of applications.
- http://www.opencalphad.com/
- Open CASCADE
- Welcome to Open CASCADE Technology (OCCT), a software development platform providing services for 3D surface and solid modeling, CAD data exchange, and visualization.
- https://www.opencascade.com/
- Open KIM
- An online resource for standardized testing and long-term warehousing of interatomic models and data. This includes the development of application programming interface (API) standards for coupling atomistic simulation codes and interatomic potential subroutines.
- https://openkim.org/
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ORCA
- The program ORCA is a modern electronic structure program package written by F. Neese, with contributions from many current and former coworkers and several collaborating groups. The binaries of ORCA are available free of charge for academic users for a variety of platforms. 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. Due to the user-friendly style, ORCA is considered to be a helpful tool not only for computational chemists, but also for chemists, physicists and biologists that are interested in developing the full information content of their experimental data with help of calculations.
- https://www.its.hku.hk/services/research/hpc/software/orca
- Oregano
- Application for schematic capture and printing of electronic circuits.
- https://linux.softpedia.com/get/Science-and-Engineering/Electronic-Design-Automation-EDA-/Oregano-1924.shtml
- osMESA
- Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics.
- https://www.mesa3d.org/osmesa.html
- Ovito
- OVITO is a scientific visualization and analysis software for atomistic simulation data developed by Alexander Stukowski at Darmstadt University of Technology, Germany.
- https://www.ovito.org/
- p4est
- The p4est software library enables the dynamic management of a collection of adaptive octrees, conveniently called a forest of octrees.
- http://www.p4est.org/
- packmol
- Initial configurations for Molecular Dynamics Simulations by packing optimization.
- http://m3g.iqm.unicamp.br/packmol/home.shtml
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PADRE
- Agere PADRE device simulator
- http://gloworm.stanford.edu/local/DOC/PADRE/intro.html
- Paraview
- An open-source, multi-platform application designed to visualize data sets of size varying from small to very large.
- https://www.paraview.org/
- Pegasus
- Pegasus Workflow Management System
- https://pegasus.isi.edu/
- phasefield
- PIMC
- PIMC - Path integral Monte Carlo powered by pi
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Poreblazer
- Poreblazer is a set of tools for structural characterization of porous materials. The calculated properties include accessible surface area, porosity, pore size distribution, maximum pore size and pore limiting diameter.
- http://www.homepages.ed.ac.uk/lsarkiso/Research.html
- POVRAY
- Persistence of Vision Raytracer
- http://www.povray.org/
- PRISMS-Phase Field (PF)
- PROPHET
- PROPHET is a computer program for solution of sets of partial differential equations in one, two, or three spatial dimensions. All model coefficients and material parameters are contained in a database library which can be modified or added to by the user. Even the equations to be solved can be specified by the end user. PROPHET was originally developed for semiconductor process simulation. Device simulation capabilities are currently under development.
- PUQ
- PUQ Uncertainty Quantification Tool
- https://pypi.org/project/puq/
- pydesign
- Design points for random experiments
- https://pypi.org/project/py-design/
- pymatgen
- Pymatgen (Python Materials Genomics) is a robust, open-source Python library for materials analysis.
- https://pymatgen.org/
- pymol
- A comprehensive software package for rendering and animating 3D structures
- https://pymol.org/2/
- pyqtgraph
- Scientific Graphics and GUI Library for Python
- http://www.pyqtgraph.org/
- pysparse
- Pysparse is a fast sparse matrix library for Python. It provides several sparse matrix storage formats and conversion methods. It also implements a number of iterative solvers, preconditioners, and interfaces to efficient factorization packages.
- http://pysparse.sourceforge.net/introduction.html
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QSTEM
- QSTEM TEM and STEM visualization
- https://www.physics.hu-berlin.de/en/sem/software/software_qstem
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Quantum ESPRESSO
- 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).
- https://www.quantum-espresso.org/
- QuocMesh
- QuocMesh is a libary for finite elements on cartesian grids that is developed in the group of Prof. Rumpf at the Institute for Numerical Simulation together with external collaborators. You may use it according to the rules of the Common Development and Distribution License.
- https://archive.ins.uni-bonn.de/numod.ins.uni-bonn.de/software/quocmesh/index9aff.html
- R
- R is a system for statistical computation and graphics. It consists of a language plus a run-time environment with graphics, a debugger, access to certain system functions, and the ability to run programs stored in script files.
- https://www.r-project.org/
- Rappture
- The Rappture tool environment (released version).
- RasMol
- RasMol is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. The program is aimed at display, teaching and generation of publication quality images. The program has been developed at the University of Edinburgh's Biocomputing Research Unit and the Biomolecular Structures Group at Glaxo Research and Development, Greenford, UK.
- http://www.openrasmol.org/
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Raspa
- This software is a general purpose classical simulation package. It has been developed at Northwestern University (Evanston, USA) during 2006-2011 in active collaboration with University Pablo de Olavide (Seville, Spain), and the Technical University of Delft. It can be used for the simulation of molecules in gases, fluids, zeolites, aluminosilicates, metal-organic frameworks, carbon nanotubes and external fields.
- https://pypi.org/project/RASPA2/
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RoadRunner
- RoadRunner is a high performance and portable simulation engine for systems and synthetic biology.
- https://zenodo.org/record/3256691#.XpS5cZp7n6g
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S4
- S4 is a frequency domain code to solve layered periodic structures. Internally, it uses Rigorous Coupled Wave Analysis (RCWA; also called the Fourier Modal Method (FMM)) and the S-matrix algorithm. S4 was developed by Victor Liu of the Fan Group in the Stanford Electrical Engineering Department.
- https://web.stanford.edu/group/fan/S4/
- SALOME
- SALOME is an open-source software that provides a generic Pre- and Post-Processing platform for numerical simulation. It is based on an open and flexible architecture made of reusable components.
- https://www.salome-platform.org/
- SciPy
- SciPy is open-source software for mathematics, science, and engineering. It is also the name of a very popular conference on scientific programming with Python. The SciPy library depends on NumPy, which provides convenient and fast N-dimensional array manipulation. The SciPy library is built to work with NumPy arrays, and provides many user-friendly and efficient numerical routines such as routines for numerical integration and optimization.
- https://www.scipy.org/
- SCWRL
- SCWRL program for prediction of protein side-chain conformations. SCWRL4.0 is based on an algorithm based on graph theory that solves the combinatorial problem in side-chain prediction more rapidly than many other available program.
- http://dunbrack.fccc.edu/SCWRL3.php/
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SeqQuest
- SeqQuest is a general-purpose electronic structure code to compute energies and forces for periodic surfaces (slabs) or solids, or finite molecules. SeqQuest uses density functional theory (DFT), and is capable of calculations using either LDA or GGA, with or without spin-polarization. It will do energy minimization of atomic positions through force elimination, cell shape optimization by stress-elimination, and molecular dynamics. SeqQuest rigorously and automatically corrects for supercell effects using the Local Moment Counter Charge method. SeqQuest uses norm-conserving pseudopotentials and high-quality contracted-Gaussian basis sets in a "Linear Combination of Atomic Orbitals" (LCAO) approach in its description of the electronic structure, and is a very efficient, compact code that enables very large-scale calculations (100's, even 1000+ atoms on large memory workstations) using rather modest computational resources (single-processor work stations, or small clusters). Key to this performance is the implementation of algorithms for the generation of the Hamiltonian matrix that scale linearly with problem size.
- https://dft.sandia.gov/Quest/
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SIESTA
- SIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids. SIESTA's efficiency stems from the use of strictly localized basis sets and from the implementation of linear-scaling algorithms which can be applied to suitable systems. A very important feature of the code is that its accuracy and cost can be tuned in a wide range, from quick exploratory calculations to highly accurate simulations matching the quality of other approaches, such as plane-wave and all-electron methods.
- https://departments.icmab.es/leem/siesta/
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SPARTA
- Stochastic PArallel Rarefied-gas Time-accurate Analyzer
- https://sparta.sandia.gov/
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SPICE
- General-purpose circuit simulation program for nonlinear dc, nonlinear transient, and linear ac analysis
- http://bwrcs.eecs.berkeley.edu/Classes/IcBook/SPICE/
- SUNDIALS
- SUite of Nonlinear and DIfferential/ALgebraic equation Solvers
- https://computing.llnl.gov/projects/sundials
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TINKER
- The TINKER molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers. TINKER has the ability to use any of several common parameter sets, such as Amber (ff94, ff96, ff98, ff99, ff99SB), CHARMM (19, 22, 22CMAP), Allinger MM (MM2-1991 and MM3-2000), OPLS (OPLS-UA, OPLS-AA), Merck Molecular Force Field (MMFF), Liam Dang's polarizable potentials, and our own AMOEBA polarizable atomic multipole force field. Parameter sets for other standard force fields such as GROMOS, UFF, ENCAD and MM4 are under consideration for future releases.
- https://dasher.wustl.edu/tinker/
- TRAVIS
- TRajectory Analyzer and VISualizer
- http://www.travis-analyzer.de/
- Triangle
- Triangle - A Two-Dimensional Quality Mesh Generator and Delaunay Triangulator
- https://www.cs.cmu.edu/~quake/triangle.html
- Trilinos
- The Trilinos Project is an effort to develop and implement robust algorithms and enabling technologies using modern object-oriented software design, while still leveraging the value of established libraries such as PETSc, Metis/ParMetis, SuperLU, Aztec, the BLAS and LAPACK. It emphasizes abstract interfaces for maximum flexibility of component interchanging, and provides a full-featured set of concrete classes that implement all abstract interfaces.
- https://trilinos.github.io/
- TVMET
- Tiny Vector Matrix library using Expression Templates
- http://tvmet.sourceforge.net/
- UQTk
- UQTk is a collection of libraries and tools for the quantification of uncertainty in numerical model predictions.
- Vis5D
- Vis5D is a software system for visualizing data made by numerical weather models and similar sources.
- https://www.ssec.wisc.edu/~billh/vis5d.html
- Visit
- VisIt is an interactive parallel visualization and graphical analysis tool for viewing scientific data on Unix and PC platforms.
- https://wci.llnl.gov/simulation/computer-codes/visit/
- VMD
- Visual Molecular Dynamics
- https://www.ks.uiuc.edu/Research/vmd/
- vtk
- The Visualization Toolkit
- https://vtk.org/
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Wannier90
- Wannier90
- http://www.wannier.org/
- Wulffman
- Wulffman is a program for interactively examining the Wulff shapes of crystals with specified symmetries. The Wulff shape is the shape that possesses the lowest surface energy for a fixed volume, and hence represents the ideal shape that the crystal would take in the absence of other constraints.
- https://www.ctcms.nist.gov/wulffman/overview_1.2.html
- wxmacmolplt
- A modern graphics program for plotting 3-D molecular structures and normal modes (vibrations).
- https://brettbode.github.io/wxmacmolplt/
- XCrySDen
- XCrySDen is a crystalline and molecular structure visualisation program aiming at display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated.
- http://www.xcrysden.org/
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Xyce
- Xyce is an open source, SPICE-compatible, high-performance analog circuit simulator, capable of solving extremely large circuit problems by supporting large-scale parallel computing platforms. It also supports serial execution on all common desktop platforms, and small-scale parallel runs on Unix-like systems. In addition to analog electronic simulation, Xyce has also been used to investigate more general network systems, such as neural networks and power grids.
- https://xyce.sandia.gov/