Prospective Packages

These are prospective packages for the Debichem project. Just because a project is listed here does not mean it needs to be packaged eventually, just that it was deemed interesting (i.e. is open-source and chemistry-related) at one point.

AmberTools

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://ambermd.org/#AmberTools
* License         : GPL-3
  Programming Lang: 
  Description     : 

AmberTools consists of several independently developed packages that work well by themselves, and with Amber itself. The suite can also be used to carry out complete (non-periodic) molecular dynamics simulations (using NAB), with generalized Born solvent models.

Aten

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://www.projectaten.net
* License         : GPL-3
  Programming Lang: 
  Description     : 

Aten is a tool to create, edit, and visualise coordinates. It was written primarily to be of use to people performing simulations of condensed matter, but it may very well be useful to others out there dealing with non-periodic systems.

Amongst other things, Aten can:

• Provide a GUI for editing atomic coordinates
• Create models, even periodic ones, from scratch
• Randomly add in molecules to periodic boxes, allowing disordered systems to be created
• Handle several crystal formats, and can replicate and scale unit cells
• Load and save model data in several model formats out of the box
• Cater for any model format you wish with its Filters system
• Render other primitive object types, as well as surface/gridded data
• Load in vibration/frequency data and animate it
• Be fully scripted / automated from the command line
• Load in and apply forcefield terms to a model with its easy-to-read typing language
• Energy minimise (periodic) models
• Run on Linux, Mac, and Windows

Atomsk

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://atomsk.univ-lille1.fr/
* License         : GPL
  Programming Lang: 
  Description     : 

Atomsk is a command-line program, developped under GNU/GPL licence, that aims at creating, manipulating, and converting atomic systems, for the purposes of ab initio calculations, classical potential simulations, or visualization. It supports the file formats used by many programs, including VASP, Quantum Espresso, LAMMPS, DL_POLY, IMD, Atomeye, or XCrySDen. Additionnaly Atomsk can also perform some simple transformations of atomic positions, like the creation of supercells, rotation, deformation, inserting dislocations

BerkeleyGW

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://www.berkeleygw.org/
* License         : BSD
  Programming Lang: 
  Description     : 

The BerkeleyGW package is a set of computer codes that calculates the quasiparticle properties and the optical responses of a large variety of materials from bulk periodic crystals to nanostructures such as slabs, wires and molecules. The package takes as input the mean-field results from various electronic structure codes such as the Kohn-Sham DFT eigenvalues and eigenvectors computed with PARATEC, Quantum ESPRESSO, SIESTA, Octopus, or TBPW (aka EPM).

The package consists of the three main component codes:

• Epsilon computes the irreducible polarizability in the Random Phase Approximation and uses it to generate the dielectric matrix and its inverse.
• Sigma computes the self-energy corrections to the DFT eigenenergies using the GW approximation of Hedin and Lundqvist, applying the first-principles methodology of Hybertsen and Louie within the generalized plasmon-pole model for the frequency-dependent dielectric matrix.
• BSE solves the Bethe-Salpeter equation for correlated electron-hole excitations.

BigDFT

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://bigdft.org/
* License         : GPL
  Programming Lang: 
  Description     : 

BigDFT is a DFT massively parallel electronic structure code using a wavelet basis set. Wavelets form a real space basis set distributed on an adaptive mesh (two levels of resolution in our implementation). GTH or HGH pseudopotentials are used to remove the core electrons. Thanks to our Poisson solver based on a Green function formalism, periodic systems, surfaces and isolated systems can be simulated with the proper boundary conditions.

BLOCK

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://chemists.princeton.edu/chan/software/block-code-for-dmrg/
* License         : GPL
  Programming Lang: 
  Description     : 

DMRG is a variational wavefunction method. Relative to other quantum chemical methods, its strength lies in its ability to efficiently describe strong or multi-reference correlation. It is especially suited to correlation that has a one-dimensional topology, i.e. where the orbitals are arranged with a chain-, strip-, or ring-like connectivity. If the correlation is dynamic in character, the DMRG may still be used, but other methods such as coupled cluster theory will usually be more computationally efficient. The recommended use of the DMRG is to treat correlation in active spaces too large for complete active space (CAS) techniques. Thus, if you are interested in (i) a CAS-like treatment of low-lying eigenstates in problems with 16-40 active orbitals, or (ii) one-dimensional orbital topologies with up to 100 active orbitals, and (iii) standard chemical accuracy (1 kcal/mol in energy differences), then DMRG may be the right method for you.

Features:

• DMRG sweep algorithm for quantum chemistry, Hubbard and Heisenberg hamiltonians
• Full spin-adaptation (SU(2) symmetry) and Abelian point-group symmetries
• State-averaged and state-specific excited states
• one-, two-, three- and four-particle density matrices
• one- and two-particle transition density matrices between two states
• perturbation methods including NEVPT2 and MPSPT
• DMRG-SCF or/and DMRG-NEVPT2 interfaces to the Molpro, ORCA, Q-Chem and Molcas program packages

c2x

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://www.check2xsf.org.uk/
* License         : GPL-3
  Programming Lang: 
  Description     : 

C2x provides a means of viewing isosurfaces from CASTEP, VASP and Onetep .check, .castep_bin, .chdiff, .cell and .pdb files and can write .cell, .cml, .pdb, .xyz, Gnuplot and .cube files. It can form supercells, generate k-point meshes, find primitive cells, and generate k-points. It can extract band energies and k-point positions from .check files. It can perform both Fourier and trilinear interpolation to plot densities on given lines through cells. It has some degree of support for writing .fdf, SHELX97 and .cif files, and reading .res files.

Cassandra

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : https://cassandra.nd.edu/
* License         : GPL-2
  Programming Lang: 
  Description     : 

Cassandra is an open source Monte Carlo package capable of simulating any number of molecules composed of rings, chains, or both. It can be used to simulate small organic molecules, oligomers, and ionic liquids. It handles a standard “Class I”-type force field having fixed bond lengths, harmonic bond angles and improper angles, a CHARMM or OPLS-style dihedral potential, a Lennard-Jones 12-6 potential or Mie potential and fixed partial charges. Cassandra can simulated the following ensembles: canonical (NVT), isothermal-isobaric (NPT), grand (muVT), osmotic (muPT), and Gibbs (NVT and NPT versions).

Cassandra uses OpenMP parallelization and comes with a number of scripts, utilities and examples to help with simulation setup. You can download it for free from this site. You will be asked for some minimal information before downloading the code so that we can let you know when new versions are released

CCP1GUI

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://www.stfc.ac.uk/CSE/randd/ccg/software/ccp1gui/25285.aspx
* License         : GPL
  Programming Lang: 
  Description     : 

The GUI has a highly-featured interface for the GAMESS-UK program, and there are working interfaces for Dalton, Molpro, ChemShell and MOPAC. It has arisen as a result of demand within the UK academic community (principally through CCP1) for a free, extensible Graphical User Interface (GUI) for community codes, particularly for teaching purposes. The GUI has been built around the Python open-source programming language and the VTK visualisation toolkit.

From its inception, the GUI was intended to work with a number of different codes, so a variety of file formats are supported both for reading in molecular structures and outputting data. As well as conventional formats such as Z-matrix and PDB, there are programme-specific formats for CHARMM, ChemShell, XMol and Gaussian, as well as support for XML. There is also an interface to the OpenBabel chemistry toolbox via its Python bindings.

CCP4-Suite (ITP,VCS)

* Package name    : libccp4
  Version         : 
  Upstream Author : 
* URL             : http://www.ccp4.ac.uk/html
* License         : 
  Programming Lang: 
  Description     : 

Collaborative Computational Project, Number 4. 1994. “The CCP4 Suite: Programs for Protein Crystallography”. Acta Cryst. D50, 760-763

ccwatcher

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://ccwatcher.sourceforge.net/
* License         : GPL
  Programming Lang: 
  Description     : 

ccwatcher monitors the progress of computational chemistry calculations during their runtime. It parses important output and plots SCF energies. ccwatcher is highly platform-independent thanks to Python and the Qt Toolkit.

It Supports most computational chemistry programs via cclib and includes a GUI and command-line interface.

CheSS

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : https://launchpad.net/chess
* License         : LGPL-3+
  Programming Lang: 
  Description     : 

CheSS (standing for Chebyshev Sparse Solvers) is a package providing various high level operations based on Chebyshev expansions for sparse matrices. Among other functionalities, it provides an implementation of the Fermi Operator Expansion (FOE) method to calculate the density matrix in an electronic structure calculation and an efficient way of calculating the power of a sparse matrix, i.e. A^x.

CMPTool

* Package name    : 
  Version         : 2.1.4
  Upstream Author : 
* URL             : https://cmsportal.caspur.it/index.php/CMPTool
* License         : unclear, likely FLOSS
  Programming Lang: 
  Description     : 

CMPTool performs classical molecular dynamics simulations using short range force models. With CMPTool you can run simulations in several ensembles using advanced continuous dynamics algorithms. CMPTool makes use of CMSapi. It can run in serial or parallel (MPI).

Features in Current Version:

• very fast simulations of huge systems (up to millions of atoms) both in serial and parallel (MPI)
• several short rate force models:
  • Stillinger-Weber
  • Tersoff
  • EDIP
• simulation of NVE, NVT (Nose-Hoover chains) ensemble, velocity-rescaling and damped dynamics (for geometry optimizations);
• an easy to extend molecular dynamics library CMSapi in C or Fortran;
• output trajectory and restart file written in machine independent format, using Hierarchy Data File format (HDF5);

NOTE: Roadmap says it is currently suspended, but there was a recent Arxiv paper (http://arxiv.org/abs/1206.5382) using it for advanced AIMD

CMSapi

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : https://cmsportal.caspur.it/index.php/CMSapi
* License         : unclear, likely FLOSS
  Programming Lang: 
  Description     : 

CMSapi is an Application Programming Interface (library of functions) for classical and tight binding molecular dynamics. The aim of CMSapi is to provide building blocks for quickly writing efficient codes for atomistic simulations. CMSapi provide most of the component required for writing a modern molecular dynamics program. Among the others, CMSapi provide sympletic integrator for several ensembles (NVE, NVT, NPH, NPT), several schemes for computing interaction lists, potentials (currently the list is restrictet to those of interest for materials science), and functions for calculating standard quantities such that kinetic energy, pressure and many more.

Features:

• sympletic integrator
• ensemble NVE, NVT (using Nose-Hoover chains), NPH and NPT (fully flexible cells)
• schemes for complete and incomplete simple interaction and combined Verlet+Linked Cells lists
• improved implementation scheme for MIC algorithm
• reordering algorithm scheme
• empirical potentials: Lenard-Jones, Stillinger-Weber, Tersoff, EDIP
• semi-empirical tight-binding with multicomponents parametrization
• routines to calculate properties (such as energetics, box geometry, fix momentum, etc.)
• specific mathematical library kernels for atomistic simulation not included in standard BLAS and LAPACK

NOTE: appears to be only available as part of CMPTool

CONQUEST

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://www.order-n.org/
* License         : GPL
  Programming Lang: 
  Description     : 

CONQUEST is a linear scaling DFT code which can be run at a number of different levels of accuracy (from non-self-consistent ab initio tight binding up to plane-wave accuracy full DFT). It features two different basis sets (numerical atomic orbitals and B-splines), compatibility with SIESTA pseudo-atomic orbitals and the FHI pseudopotentials provided by ABINIT and the ability to perform exact diagonalisation as well as linear scaling solution.

Coot (ITP,VCS)

* Package name    : coot
  Version         : 0.8.9.1
  Upstream Author : Paul Emsley <paul.emsley@bioch.ox.ac.uk>
* URL             : https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/
* License         : GPL-3+
  Programming Lang: C++
  Description     : model building program for macromolecular crystallography

Coot is a molecular-graphics application for model building and validation of biological macromolecules. The program displays electron-density maps and atomic models and allows model manipulations such as idealization, real-space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers and Ramachandran idealization. Furthermore, tools are provided for model validation as well as interfaces to external programs for refinement, validation and graphics.

Dalton LSDalton

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://daltonprogram.org
* License         : LGPL-2.1
  Programming Lang: 
  Description     : 

The Dalton suite consists of two separate executables, Dalton and LSDalton. The Dalton code is a powerful tool for a wide range of molecular properties at different levels of theory, whereas LSDalton is a linear-scaling HF and DFT code suitable for large molecular systems, now also with some CCSD capabilites.

For a full list of features, see http://daltonprogram.org/features/

DL_MG

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : https://ccpforge.cse.rl.ac.uk/gf/project/dl-mg/
* License         : BSD 3-Clause
  Programming Lang: 
  Description     : 

DL_MG is a parallel (MPI+OpenMP) 3D geometric high order finite difference multigrid solver for Poisson and Poisson-Boltzmann Equations.

DL_POLY Classic (ITP,VCS)

* Package name    : dl-poly-classic
  Version         : 4.09.1
  Upstream Author : 
* URL             : https://www.ccp5.ac.uk/DL_POLY_CLASSIC/
* License         : BSD
  Programming Lang: Fortran/Java
  Description     : general purpose molecular dynamics simulation package

DL_POLY Classic is a general purpose (parallel and serial) molecular dynamics simulation package.

It can be executed as a serial or parallel application. The code achieves parallelisation using the Replicated Data strategy, which is suitable for homogeneous, distributed-memory, parallel computers. The code is useful for simulations of up to 30,000 atoms with good parallel performance on up to 100 processors, though in some circumstances it can exceed or fail to reach these limits.

DMG-alpha

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://ww2.ii.uj.edu.pl/~szczelir/?category=dmga_test&lang=en
* License         : Modified BSD
  Programming Lang: 
  Description     : 

DMG-Alpha is capable of computing Power Diagrams in 3D for box geometries with arbitrary periodic information. All geometry constructs are easily accessible, and all kinds of attributes can be simply computed, e.g. areas of cell sides, volumes of cells, neighbouring information.

DockoMatic

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://sourceforge.net/projects/dockomatic/
* License         : LGPL-3+
  Programming Lang: 
  Description     : 

DockoMatic is a GUI application that is intended to ease and automate the creation and management of AutoDock jobs for high throughput screening of ligand/receptor interactions.

DP4

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : https://github.com/KristapsE/PyDP4
* License         : MIT
  Programming Lang: 
  Description     : 

The DP4 parameter, which provides a confidence level for NMR assignment, has been widely used to help assign the structures of many stereochemically-rich molecules.

TINKER molecular mechanics package and NWChem ab initio software have been integrated in a fully open-source DP4 workflow.

The new open-source workflow incorporates a method for the automatic generation of diastereomers using InChI strings and has been tested on a range of new structures. This improved workflow permits the rapid and convenient computational elucidation of structure and relative stereochemistry.

DynamO

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : https://www.marcusbannerman.co.uk/index.php/dynamo.html
* License         : GPL-3+
  Programming Lang: 
  Description     : 

DYNAMics of discrete Objects (DynamO) is a general, event driven simulation code capable of simulating millions of particles in short times on commodity computers.

Simple Systems:

• Smooth or rough hard spheres, square wells, soft cores and all the other simple EDMD potentials.
• Millions of particles for billions of events: Using 500 bytes per particle and running at around 75k events a second, even an old laptop can run huge simulations with accurate results.
• Non-Equilibrium Molecular Dynamics (NEMD): DynamO has Lees-Edwards boundary conditions for shearing systems, thermalised walls and Andersen or rescaling thermostats.
• Compression dynamics: Need high density systems? DynamO can compress any of its systems using isotropic compaction until the pressure diverges!
• Poly-dispersity: All interactions are generalised to fully poly-disperse particles.

Granular Systems/Complex Boundaries:

• Event driven dynamics with gravity: Almost all interactions work in the presence of gravity, allowing event driven simulations of macroscopic systems.
• Sleeping particles: In systems where particles come to a rest, the sleeping particles algorithm can remove the cost of simulating the particles completely.
• Triangle or sphere meshes: Arbitrary complex boundaries can be implemented using triangle meshes imported from CAD drawings.
• Stepped potentials: Arbitrary stepped potentials may be simulated to approximate any soft potential.

Polymeric Systems/Accelerated Dynamics:

• Parallel tempering/Replica exchange: Run multiple simulations in parallel and use this Monte Carlo technique to enhance the sampling of phase space.
• Histogram reweighting: Combine the results from replica exchange simulations and extrapolate to temperatures which were not simulated.
• Multicanonical simulations: Used in conjunction with replica exchange techniques, multicanonical simulations greatly enhance the sampling of phase space, helping find the true native state of the polymer.

ELSI

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : https://wordpress.elsi-interchange.org/
* License         : BSD
  Programming Lang: 
  Description     : 

ELSI provides and enhances scalable, open-source software library solutions for electronic structure calculations in materials science, condensed matter physics, chemistry, molecular biochemistry, and many other fields. ELSI focuses on methods that solve or circumvent the Kohn-Sham eigenvalue problem in density-functional theory. The ELSI infrastructure should also be useful for other challenging eigenvalue problems.

One of the key design pillars of ELSI is portability and support for various computing environments, from laptop-type computers all the way to the most efficient massively parallel supercomputers and new architectures (GPU and manycore processors).

The libraries supported and enhanced in ELSI are:

• ELPA (the Eigenvalue SoLvers for Petaflop-Applications)
• libOMM (the Orbital Minimization Method)
• PEXSI (the Pole EXpansion and Selected Inversion method)

Environ

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://www.quantum-environment.org
* License         : GPL
  Programming Lang: 
  Description     : 

A quantum ESPRESSO module to handle environment effects in first-principles quantum-mechanical simulations

Environ is a computational library aimed at introducing environment effects into atomistic first-principles simulations, in particular for applications in surface science and materials design. A hierarchical, multiscale, strategy is at the base of the different methods implemented: while the atomistic and electronic details of the system of interest are fully preserved, the degrees of freedom of the surrounding environment (being it a liquid solution of a more complex embedding) are treated using simplified approaches. By reducing the number of degrees of freedom and by exploiting intrinsic or faster statistical averaging, the implemented methods allow the systematic un-expensive study of large systems.

EPW

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://epw.org.uk/Main/About
* License         : GPL-2
  Programming Lang: 
  Description     : 

EPW is the short name for “Electron-phonon Wannier”. It calculates properties related to the electron-phonon interaction using Density-Functional Perturbation Theory and Maximally Localized Wannier Functions.

exciting is a full-potential all-electron density-functional-theory (DFT) package based on the linearized augmented plane-wave (LAPW) method. It can be applied to all kinds of materials, irrespective of the atomic species involved, and also allows for the investigation of the atomic-core region.

Its particular focus is on excited state properties, within the framework of time-dependent DFT (TDDFT) as well as within many-body perturbation theory (MBPT).

General features:

• High precision all-electron DFT code based on the FP-LAPW method including local-orbitals
• Various xc functionals available
• Calculation of forces and structural optimization
• Treatment of magnetism in the most general way, including spin-orbit coupling and non-collinear magnetism
• Plotting of band structure, Fermi surface, charge density, potential etc. (1D, 2D and 3D)
• Visualization with xmgrace and XCrySDen supported
• MPI k-point parallelization, as well as optimization for multithreaded numeric libraries (BLAS LAPACK)

Excited states features:

• Macroscopic dielectric function within time-dependent DFT and the Bethe-Salpeter equation
• Available exchange-correlation kernels: RPA, ALDA, long-range contribution model-kernels, BSE-derived kernel
• RPA and ALDA loss function for finite momentum transfer q-vectors

eQE (Embedded Quantum Espresso

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://eqe.rutgers.edu/
* License         : GPL2
  Programming Lang: 
  Description     : 

Subsystem DFT (embedded) flavor of Quantum ESPRESSO.

ERKALE

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : https://github.com/susilehtola/erkale
* License         : GPL-2
  Programming Lang: 
  Description     : 

ERKALE is a quantum chemistry program used to solve the electronic structure of atoms, molecules and molecular clusters. It is developed at the University of Helsinki. . The main use of ERKALE is the computation of x-ray properties, such as ground-state electron momentum densities and Compton profiles, and core (x-ray absorption and x-ray Raman scattering) and valence electron excitation spectra of atoms and molecules.

ESPResSo

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://espressomd.org
* License         : GPL-3
  Programming Lang: 
  Description     : 

ESPResSo is a highly versatile software package for performing and analyzing scientific Molecular Dynamics many-particle simulations of “coarse-grained” bead-spring models as they are used in soft matter research in physics, chemistry and molecular biology. It can be used to simulate systems such as polymers, liquid crystals, colloids, ferrofluids and biological systems

ESPResSo is capable of doing classical Molecular dynamics simulations of many types of systems in different statistical ensembles (NVE, NVT, NPT) and non-equilibrium situations, using standard potentials such as the Lennard-Jones or Morse potential. It contains many advanced simulation algorithms, which take into account hydrodynamic (lattice Boltzmann) and electrostatic interactions (P3M, ELC, MMMxD). Rigid bodies can be modelled by virtual site interactions, and it can integrate rotationally non-invariant particles.

Further features include:

• Statistical ensembles: NVE, NVT, NPT, μVT

• Nonbonded potentials: Lennard Jones, Buckingham, Morse, Generic tabulated potentials, etc.

• Bonded potentials: harmonic spring, FENE, generic tabulated bonded potentials, etc.
• Anisotropic interactions: e.g. Gay-Berne particles or other non-isotropic interactions
• Advanced methods for electro- and magnetostatics: e.g. P3M, MMM1D, MMM2D, ELC, dipolar P3M, DLC, MEMD, MMM2DIC, ELCIC, ICC, LB-EK
• Constraints: all or some of the coordinates of particles can be fixed, various spatial constraints (walls, spheres, pores, …) can interact with the particles
• Rigid bodies: arbitrary extended objects can be constructed from several particles
• Dynamic bonding: when particles collide, new bonds can be generated between them to study agglomeration
• Hydrodynamics: Lattice-Boltzmann fluid (optionally on a GPGPU), DPD (Dissipative Particle Dynamics)

ESPResSo++

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://www.espresso-pp.de
* License         : GPL-3
  Programming Lang: 
  Description     : 

ESPResSo++ is an extensible, flexible and parallel simulation software for the scientific simulation and analysis of coarse-grained atomistic or bead-spring models as they are used in soft matter research.

Features include:

• Molecular Dynamics:
• Langevin thermostat and barostat
• Berendsen thermostat and barostat
• Rattle and Settle algorithms
• Angular and dihedral interactions
• Bonded and non-bonded interactions (FENE, Lennard-Jones, etc.)
• Tabulated interactions
• Adaptive Resolution Simulations (AdResS)
• F-AdResS
• H-AdResS
• Lattice Boltzmann
• Coupling to MD via viscous drag
• Robust time-scale separation between MD and LB
• External forces

Exciting (ITP)

* Package name    : exciting
  Version         : 13 (nitrogen)
  Upstream Author : Claudia Ambrosch-Draxl <claudia.ambrosch-draxl@mu-leoben.at>
* URL             : http://exciting-code.org
* License         : GPL
  Programming Lang: Fortran 90
  Description     : All-electron full-potential electronic-structure code

exciting is a full-potential all-electron density-functional-theory (DFT) package based on the linearized augmented plane-wave (LAPW) method. It can be applied to all kinds of materials, irrespective of the atomic species involved, and also allows for the investigation of the atomic-core region.

Its particular focus is on excited state properties, within the framework of time-dependent DFT (TDDFT) as well as within many-body perturbation theory (MBPT).

General features:

• High precision all-electron DFT code based on the FP-LAPW method including local-orbitals
• Various xc functionals available
• Calculation of forces and structural optimization
• Treatment of magnetism in the most general way, including spin-orbit coupling and non-collinear magnetism
• Plotting of band structure, Fermi surface, charge density, potential etc. (1D, 2D and 3D)
• Visualization with xmgrace and XCrySDen supported
• MPI k-point parallelization, as well as optimization for multithreaded numeric libraries (BLAS LAPACK)

Excited states features:

• Macroscopic dielectric function within time-dependent DFT and the Bethe-Salpeter equation
• Available exchange-correlation kernels: RPA, ALDA, long-range contribution model-kernels, BSE-derived kernel
• RPA and ALDA loss function for finite momentum transfer q-vectors

This package will be part of the Debian Science nanoscale-physics metapackage.

ezDICOM

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://www.cabiatl.com/mricro/ezdicom/
* License         : BSD-2-clause
  Programming Lang: 
  Description     : 

This software is designed to display most medical images: MRI, CT, X-ray, and ultrasound. All versions of ezDICOM can automatically detect the format of a medical image and display it on the screen.

ezSpectrum

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : https://github.com/iopenshell/ezSpectrum
* License         : GPL
  Programming Lang: 
  Description     : 

ezSpectrum computes stick photoelectron/photodetachment spectra for polyatomic molecules within the double–harmonic approximation.

Franck-Condon factors (FCFs), the overlaps between the initial and target vibrational wavefunctions, can be calculated:

• in the parallel normal modes approximation as products of one-dimensional harmonic wave functions;
• including Duschinsky rotations of the normal modes as full-dimensional integrals in full dimensionality including Duschinsky rotations of the normal modes.

In both cases the overlap integrals are computed analytically.

The calculation requires equilibrium geometries, harmonic frequencies, and normal mode vectors for each electronic state, which can be computed by ab initio packages. The key feature of ezSpectrum is the program–independent xml input. It can be prepared either manually following the format description in the manual and the examples provided, or by running the python script that processes Q-Chem, ACESII, Molpro, GAMESS, and Gaussian outputs. The script can be easily modified to process outputs of other programs.

Forte

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : https://github.com/evangelistalab/forte
* License         : LGPL-3
  Programming Lang: 
  Description     : 

Forte is an open-source suite of state-of-the-art quantum chemistry methods applicable to chemical systems with strongly correlated electrons. The code is written as a plugin to Psi4 in C++ with C++11 functionality, and it takes advantage of shared memory parallelism throughout

Capabilities are composed of two types of methods:

• Active space methods
  • Full/complete active space configuration interaction (FCI)/(CASCI)
  • Adaptive configuration interaction (ACI)
  • Projector configuration interaction (PCI)
  • Complete active space self-consistent field (CASSCF)
  • Density Matrix Renormalization Group self-consistent field (DMRG-SCF)
• Methods for dynamical correlation
  • Driven similarity renormalization group (DSRG)
    • DSRG-MRPT2
    • DSRG-MRPT3
    • MR-LDSRG(2)
  • Uncontracted multireference configuraiton interaction (MRCI)

Note that the active space methods, notably FCI, ACI, and PCI, can operate within the full orbital basis defined by the user-selected basis set. In this case, these methods also recover dynamical correlation.

FreeOn

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : https://www.freeon.org/index.php/Main_Page
* License         : GPL-2+
  Programming Lang: 
  Description     : 

FreeON is an experimental, open source (GPL) suite of programs for linear scaling quantum chemistry. It is highly modular, and has been written from scratch for N-scaling SCF theory in Fortran95 and C. Platform independent I/O is supported with HDF5. FreeON performs Hartree-Fock, pure Density Functional, and hybrid HF/DFT calculations (e.g. B3LYP) in a Cartesian-Gaussian LCAO basis. All algorithms are O(N) or O(N log N) for non-metallic systems. Periodic boundary conditions in 1, 2 and 3 dimensions have been implemented through the Lorentz field (Gamma-point), and an internal coordinate geometry optimizer allows full (atom+cell) relaxation using analytic derivatives. Effective core potentials for energies and forces have been implemented. Advanced features include O(N) static and dynamic response, as well as time reversible Born Oppenheimer Molecular Dynamics (MD)

Frowns

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : 
* License         : BSDish
  Programming Lang: 
  Description     : 

Frowns is a chemoinformatics toolkit geared toward rapid development of chemistry related algorithms. It is written in almost 100% Python with a small portion written in C++.

Frowns is loosely based on the PyDaylight API that Andrew Dalke wrote to wrap the daylight C API. In some cases programs written using PyDaylight will also work under Frowns with a few minor changes. A good overview of PyDaylight is available at here.

A good place to look at what Smarts and Smiles are is at the daylight web site located at http://www.daylight.com/

Frowns Features:

• Smiles parser
• Smarts substructure searching
• SD file parser with SD field manipulations
• Depiction for SD files with coordinates
• Molecule Fingerprint generation
• Several forms of Ring Detection available
• Simple aromaticity perception
• Everything’s a graph (i.e. can form canonical strings from incomplete pieces of a molecule)
• Really bad depiction of arbitray molecules! (requires AT&T’s GraphViz)

gCP

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://www.thch.uni-bonn.de/tc/downloads/gcp/index.html
* License         : GPL-1+
  Programming Lang: 
  Description     : 

A computationally inexpensive approach to correcting for BSSE

A major discouragement for wider use of counterpoise correction is its computational cost. With the geometric counterpoise scheme (gCP), Kruse and Grimme offer a semi-empirical approach that is extremely cost effective and appears to strongly mimic the traditional counterpoise correction.

GENESIS

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://www.riken.jp/TMS2012/cbp/en/research/software/genesis/index.html
* License         : GPL-2
  Programming Lang: 
  Description     : 

GENeralized-Ensemble Simulation System(GENESIS) is molecular dynamics and modeling software for proteins or other biomolecular systems. It consists of two simulators, SPDYN and ATDYN. SPDYN shows high performance on massively parallel supercomputers like K computer in RIKEN AICS. ATDYN allows you to perform multi-scale simulations using coarse-grained models and all-atom models. Replica-exchange molecular dynamics methods or other generalized-ensemble algorithms are currently available only in ATDYN.

HANDE

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : https://github.com/hande-qmc/hande
* License         : LGPL-2.1
  Programming Lang: 
  Description     : 

HANDE is an efficient, highly parallel code for stochastic quantum chemistry. It can be used both as a standalone program or (optionally) as a library from an existing quantum chemistry code.

HANDE contains optimised, highly parallel implementations of the full configuration interaction quantum Monte Carlo (FCIQMC), coupled cluster Monte Carlo (CCMC) and Density Matrix Quantum Monte Carlo (DMQMC) algorithms for a variety of systems. Development work continues to add new features and investigate the algorithms and new applications.

HANDE can perform calculations on generic systems such as molecules via an externally generated integral file. The integral file is in the FCIDUMP format, which can be generated by several quantum chemistry codes such as MOLPRO, Q-Chem (with patches from Alex Thom) and PSI4 (with a plugin from James Spencer). HANDE can also perform calculations on model Hamiltonians, for which no additional integrals are required. The model Hamiltonians currently available are the Hubbard model, Heisenberg model and uniform electron gas.

Configuration interaction (CI) is also implemented using external libraries (lapack/scalapack and TRLan respectively) and can be performed in both serial and parallel. Lanczos diagonalisation can also be performed with or without precomputing the Hamiltonian matrix. Note that this is rather slow and intended for debugging purposes only. Most quantum chemistry codes (e.g. PSI4) contain a substantially more powerful and optimised CI implementation.

IboView

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://www.iboview.org/index.html
* License         : GPL-3
  Programming Lang: 
  Description     : 

IboView is a program for analyzing molecular electronic structure, based on Intrinsic Atomic Orbitals (IAOs). IboView’s main features include:

• Visualization of electronic structure from first-principles DFT, in terms of intuitive concepts (partial charges, bond orders, bond orbitals)—even in systems with complex or unusual bonding.
• Publication quality graphics, very fast visualizations, and a simple user interface
• Import of wave functions from Molpro, Orca, Molcas, and Turbomole. IboView can also compute simple Kohn-Sham wave functions by itself, using the embedded MicroScf program. Additionally, IboView can be used as a plain orbital viewer if advanced analysis features are not required.
• Visualization of electronic structure changes along reaction paths. Using the techniques described Electron flow in reaction mechanisms – revealed from first principles and implemented in IboView, curly arrow reaction mechanisms can be determined directly from first principles!

IMD

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://imd.itap.physik.uni-stuttgart.de/
* License         : GPL
  Programming Lang: 
  Description     : 

IMD is a software package for classical molecular dynamics simulations. Several types of interactions are supported, such as central pair potentials, EAM potentials for metals, Stillinger-Weber and Tersoff potentials for covalent systems, and Gay-Berne potentials for liquid crystals. A rich choice of simulation options is available: different integrators for the simulation of the various thermodynamic ensembles, options that allow to shear and deform the sample during the simulation, and many more. There is no restriction on the number of particle types.

InChI (ITP,VCS)

* Package name    : inchi
  Version         : 1.04
  Upstream Author : IUPAC and InChI Trust Limited
* URL             : https://www.inchi-trust.org
* License         : IUPAC-InChI Trust License 1.0 (more permissive then LGPL-2.1+)
  Programming Lang: C
  Description     : International Chemical Identifier generator

Library to generate Standard/non-Standard InChI/InChIKey.

Many chemistry related softwares (at least OpenBABEL which has been already packaged in debian) carry private copies of this library. This library should be packaged for better compliance to debian policy which discourages inclusions of 3rd party codes.

IQmol

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://iqmol.org/
* License         : GPL-3+
  Programming Lang: 
  Description     : 

IQmol is a free open-source molecular editor and visualization package. It offers a range of features including reading a variety of file formats, a molecular editor, surface generation (orbitals and densities) and animations (vibrational modes and reaction pathways).

It can read a variety of chemical file formats including xyz, cml, pdb, mol, fchk, cube data and Q-Chem input/output. It also includes a free-form molecular builder that allows arbitrary molecular structures to be created. These structures can be optimized using molecular mechanics force elds and symmetrized to ensure the structure has the correct point group symmetry. A library of molecules and functional groups also exists, and these can be used to facilitate building more complicated molecules

IQmol is capable of displaying a variety of molecular properties including atomic charges, dipole moments and normal modes. Several surface types can be displayed including molecular orbitals, (spin) densities and van der Waals surfaces. These surfaces can be colored according to an arbitrary scalar field, such as the electrostatic potential. Animations are also available for vibrational frequencies and reaction and optimization pathway

JADE

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://jade-package.github.io/JADE
* License         : GLP-3
  Programming Lang: 
  Description     : 

JADE is an on-the-fly surface hopping code for nonadiabatic molecular dynamics of poly-atomic systems.

Janus

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : https://github.com/CCQC/janus
* License         : BSD-3-Clause
  Programming Lang: 
  Description     : 

Janus is a open-source python library for the implementation and application of adaptive QM/MM methods.

The following adaptive methods are currently available in janus.

• Hot-Spot
• Oniom-XS
• Permuted Adaptive Partitioning
• Sorted Adaptive Partitioning
• Difference-based Adaptive Partitioning

Jumbo-Converters

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : https://bitbucket.org/wwmm/jumbo-converters
* License         : 
  Programming Lang: 
  Description     : 

A set of libraries (“converters”) which provide conversion to and from CML.

It contains converters for ChemDraw, ChemDrawXML, CIF, MolCAS, NWChem, Gaussian, GamessUS, Quantum ESPRESSO, Turbomole, GamessUK, DALTON, MOPAC, Jaguar, DLPoly, Amber, MDL Molfile, SDF, XYZ, PubchemSDF, PubchemXML, Bruker, JDX, OWL.

KryoMol

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://kde-apps.org/content/show.php/KryoMol?content=36260
* License         : GPL-2+
  Programming Lang: 
  Description     : 

KryoMol is a KParts based program for analysis and visualization of chemical data. Currently it can read many quantum chemical formats (Gaussian03/09, NwChem, CFOUR, CPMD…) and 3D structures (mol,xyz…). Experimentally it can display also 1D NMR and JCAMP-DX spectra.

LBNL-AMO-MCTDHF

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : https://commons.lbl.gov/display/csd/LBNL-AMO-MCTDHF
* License         : Apache License
  Programming Lang: 
  Description     : 

LBNL-AMO-MCTDHF is a suite of codes for Multiconfiguration Time-Dependent Hartree-Fock applied to ultrafast laser dynamics of atoms and molecules. It calculates nonadiabatic electronic and nuclear wave functions for the nonrelativistic Schrödinger equation. Currently it uses the dipole approximation in length and velocity gauge and has options for a variety of laser pulses. It contains analysis and output routines and auxiliary scripts for calculating absorption and stimulated emission, populations, total and partial photoionization, wave mixing, and other capabilities. It supports

• Electronic wave functions for atoms (chmctdhf_atom)
• Vibronic wave functions for diatoms using prolate spheroidal coordinates (chmctdhf_diatom)
• Electronic wave functions for polyatomics with fixed nuclei (chmctdhf_sinc)

libcint

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://wiki.sunqm.net/libcint
* License         : BSD
  Programming Lang: 
  Description     : 

libcint is an open source library for analytical Gaussian integrals. It provides C/Fortran API to evaluate one-electron / two-electron integrals for Cartesian / real-spheric / spinor Gaussian type functions.

LIBEFP

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : https://github.com/ilyak/libefp
* License         : BSD
  Programming Lang: 
  Description     : 

The Effective Fragment Potential (EFP) method allows one to describe large molecular systems by replacing chemically inert part of a system by a set of Effective Fragments while performing regular ab initio calculation on the chemically active part. The LIBEFP library is a full implementation of the EFP method. It allows users to easily incorporate EFP support into their favourite quantum chemistry package. LIBEFP is used by many major quantum chemistry packages, such as Q-Chem, PSI4, NWChem, GAMESS, Molcas, and others.

LiBELa

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : 
* License         : GPL
  Programming Lang: C++
  Description     : 

LiBELa is a C++ Object-Oriented framework for ligand binding energy evaluation. It allows the user to (i) dock a ligand into a macromolecular receptor; (ii) perform simulated annealing simulations of the ligand dynamics inside the receptor binding site and (iii) perform Monte Carlo (MC) dynamic of the ligand in the binding site.

The docking capabilities are probably the most important among the McLiBELa functions. It permits the user to provide any MOL2 file for a ligand (from ZINC website, for example) and search for the best poses of the provided ligand maximizing the overlay of the ligand with a reference ligand, provided to the program. LiBELa also performs a search for the conformers with lower energy prior to ligand docking.

The docking capability of LiBELa can be described in the following steps:

• Conformer generations. The user chooses one of the two conformer generators provided by openbabel API (weighted rotor search or genetic algorithm) and the number of conformers.
• Each conformer is superposed in the reference ligand looking for optimal overlay. Gaussian descriptors of molecular shape and charge are used to generate an optimal overlay.
• Each conformer docked in the active site is scored using one of the four scoring functions implemented in LiBELa (see below). The top n conformers ranked using binding energy as criteria are then used in a simplex minimization in Cartesian space (rigid ligand).
• The best conformer is written in a MOL2 file.

LiBELa uses NLOPT library for optimization. Among the optimizers provided by NLOPT, the user can choose among LBFGS, Simplex, Augmented Lagrangian, MMA, among other algorithms for overlay optimization and for energy minimization independently.

libOMM

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : https://esl.cecam.org/LibOMM
* License         : BSD
  Programming Lang: 
  Description     : 

libOMM solves the Kohn-Sham equation as a generalized eigenvalue problem for a fixed Hamiltonian. It implements the orbital minimization method (OMM), which works within a density matrix formalism. The basic strategy of the OMM is to find the set of Wannier functions (WFs) describing the occupied subspace by direct unconstrained minimization of an appropriately-constructed functional. The density matrix can then be calculated from the WFs. The solver is usually employed within an outer self-consistency (SCF) cycle. Therefore, the WFs resulting from one SCF iteration can be saved and then re-used as the initial guess for the next iteration.

Features:

• OMM functional of Mauri, Galli, and Car, and Ordejón et al.
• Real (Γ-point) and complex (arb. k point) Hamiltonians
• Efficient reuse of information within SCF loop and for multiple spins/k points
• Simple (orthogonal basis) and generalized (non-orthogonal basis) eigenvalue problems
• Cholesky factorization of generalized problem
• Preconditioner for localized orbital basis

libreta

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://www.zhjun-sci.com/software-libreta-download.php
* License         : BSD 3-Clause
  Programming Lang: C++
  Description     : 

Libreta is a C++ library for the evaluation of molecular integrals over both segmented and general contracted Gaussian type orbitals (GTOs). It is written in a black-box way that one can use it without knowing anything inside.

libtensor

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://iopenshell.usc.edu/downloads/tensor/
* License         : Boost License
  Programming Lang: 
  Description     : 

Tensor algebra library for computational chemistry.

The library is a set of performance linear tensor algebra routines for large tensors found in post-Hartree-Fock methods. The routines are able to dynamically balance the use of physical memory (RAM) and disk and perform computations on multiple CPUs or CPU cores in a shared-memory environment.

LICHEM

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : https://github.com/kratman/LICHEM_QMMM
* License         : GPL-3
  Programming Lang: 
  Description     : 

This package is designed to be an interface between QM and MM software so that QMMM calculations can be performed with polarizable and frozen electron density force fields. Functionality is also present for standard point-charge based force fields, pure MM, and pure QM calculations.

• Available calculations: single-point energies, geometry optimizations, classical Monte Carlo, path-integral Monte Carlo, and reaction pathways.

• Available QM wrappers: Gaussian, NWChem, PSI4

• Available MM wrappers: TINKER

• MM wrappers in development: AMBER, LAMMPS, OpenMM

LPMD

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://www.lpmd.cl
* License         : GPL
  Programming Lang: 
  Description     : 

Las Palmeras Molecular Dynamics (LPMD) is a Molecular Dynamics (MD) code written from scratch in C++, as user-friendly, modular and multiplatform as possible. Some of its features are that it is an Open Source code, it works using plugins, it reads simple and intuitive configuration files, and it also includes utility software to perform analysis, conversion, and visualization of MD simulations.

ls1 mardyn

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://www.ls1-mardyn.de/
* License         : BSD-2-clause
  Programming Lang: 
  Description     : 

The molecular dynamics (MD) simulation program ls1 mardyn was optimized for massively parallel execution on supercomputing architectures. The acronym stands for large systems 1: molecular dynamics. With an efficient MD simulation engine, explicit particle-based force-field models of the intermolecular interactions can be applied to length and time scales which were previously out of scope for molecular methods. Employing a dynamic load balancing scheme for an adaptable volume decomposition, ls1 mardyn delivers a high performance even for challenging heterogeneous configurations.

MATCH

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://brooks.chem.lsa.umich.edu/index.php?page=match&subdir=articles/resources/software
* License         : Perl
  Programming Lang: 
  Description     : 

A toolset of program libraries collectively titled multipurpose atom-typer for CHARMM (MATCH) for the automated assignment of atom types and force field parameters for molecular mechanics simulation of organic molecules. A general chemical pattern-matching engine achieves assignment of atom types, charges and force field parameters through comparison against a customizable list of chemical fragments.

(download behind dumb registration site)

MayaChemTools

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://www.mayachemtools.org
* License         : LGPL
  Programming Lang: 
  Description     : 

MayaChemTools is a growing collection of Perl scripts, modules and classes to support day-to-day computational discovery needs.

The current release of MayaChemTools provides command line scripts for the following tasks:

• Manipulation of SD, CSV/TSV, Sequence/Alignments and PDB files
• Analysis of data in SD, CSV/TSV and Sequence/Alignments files
• Information about data in SD, CSV/TSV, Sequence/Alignments, PDB and fingerprints files
• Exporting data from Oracle and MySQL tables into text files
• Properties of periodic table elements, amino acids and nucleic acids
• Elemental analysis
• Generation of fingerprints corresponding to atom neighborhoods, atom types, E-state indicies, extended connectivity, MACCS keys, path lengths, topological atom pairs, topological atom triplets, topological atom torsions, topological pharmacophore atom pairs and topological pharmacophore atom triplets
• Generation of fingerprints with atom types corresponding to atomic invariants, DREIDING, E-state, functional class, MMFF94, SLogP, SYBYL, TPSA and UFF
• Calculation of similarity matrices using a variety of similarity and distance coefficients
• Calculation of physicochemical properties including rotatable bonds, van der Waals molecular volume, hydrogen bond donors and acceptors, logP (SLogP), molar refractivity (SMR), topological polar surface area (TPSA), molecular complexity and so on
• Similarity searching using fingerprints

MCCI

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : https://github.com/MCCI/mcci
* License         : none
  Programming Lang: 
  Description     : 

Monte Carlo Configuration Interaction (MCCI) is a computer program that calculates electronic structure of molecular systems using a method based on Configuration Interaction (CI). In conventional CI, all configurations (usually spin-projected Slater Determinants, or Configuration State Functions (CSFs)) up to a given excitation level are included in the wave function. While this produces a highly accurate wave function, the number of CSFs to include (and thus also the dimensions of the matrix to be diagonalized) increases combinatorially with the truncation level. In addition, the fixed truncation level of conventional CI causes the method to be non-size-consistent.

MDAnalysis (VCS)

* Package name    : python-mdanalysis
  Version         : 
  Upstream Author : 
* URL             : http://www.mdanalysis.org
* License         : GPL-2, BSD
  Programming Lang: 
  Description     : 

MDAnalysis is an object-oriented python toolkit to analyze molecular dynamics trajectories generated in many popular formats including CHARMM, Gromacs, NAMD, LAMMPS and Amber.

It allows one to read molecular dynamics trajectories and access the atomic coordinates through numpy arrays. This provides a flexible and relatively fast framework for complex analysis tasks. In addition, CHARMM-style atom selection commands are implemented. Trajectories can also be manipulated (for instance, fit to a reference structure) and written out.

MDANSE

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : https://mdanse.org/
* License         : GPL-3
  Programming Lang: 
  Description     : 

MDANSE (Molecular Dynamics Analysis for Neutron Scattering Experiments) is a python application designed for computing properties that can be directly compared with neutron scattering experiments such as the coherent and incoherent intermediate scattering functions and their Fourier transforms, the elastic incoherent structure factor, the static coherent structure factor or the radial distribution function. Moreover, it can also compute quantities such as the mean-square displacement, the velocity autocorrelation function as well as its Fourier Transform (the so-called vibrational density of states) enlarging the scope of the program to a broader range of physico-chemical properties.

Most of MDANSE calculations can be applied to the whole system or to arbitrary subsets that can be defined in the graphical interface while less common selections can be specified via the command-line interface.

MESMER

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://www.chem.leeds.ac.uk/mesmer.html
* License         : LGPL-2
  Programming Lang: 
  Description     : 

MESMER (Master Equation Solver for Multi Energy-well Reactions) models the interaction between collisional energy transfer and chemical reaction for dissociation, isomerisation, association, and non-adiabatic hopping processes.

MOIL-opt

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : https://omictools.com/moil-tool
* License         : public-domain
  Programming Lang: 
  Description     : n/a

n/a

MOLDY

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://code.google.com/p/moldy/
* License         : GPL-2
  Programming Lang: 
  Description     : parallelised OpenMP short-ranged molecular dynamics program

MOLDY is a parallelised OpenMP short-ranged molecular dynamics program, first written at Harwell Laboratory in the 1980s. The program is written in a modular fashion to allow for easy user modification, in particular the implementation of new interatomic potentials. Using Link Cells and Neighbour Lists, the code fully exploits the short range of the potentials, and the slow diffusion expected for solid systems.

Molsketch

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://molsketch.sf.net
* License         : GPL-2+
  Programming Lang: 
  Description     : 

2D molecular editing tool with its goal to help draw molecules quick and easily. Creation can be exported afterwards in high quality in a number of vector and bitmap formats.

MoViPAC

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://www.reiher.ethz.ch/software/movipac
* License         : GPL-3, LGPL-3
  Programming Lang: 
  Description     : 

Vibrational Spectroscopy with a Robust Meta-Program for Massively Parallel Standard and Inverse Calculations

Key features:

• massively parallel calculation of full vibrational spectra (IR, Raman, ROA)
• calculation of full vibrational spectra from results obtained with smaller model systems using a Cartesian transfer approach
• inverse approaches to selectively calculate specific normal modes only (Mode- and Intensity-Tracking)
• Analysis of normal modes in terms of localized vibrations

NOTE: This one seems to be a biggie, by highly respected researchers, package

MRChem

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://mrchemdoc.readthedocs.io/en/latest/
* License         : LGPL-3
  Programming Lang: 
  Description     : 

MRChem is a numerical real-space code for molecular electronic structure calculations within the self-consistent field (SCF) approximations of quantum chemistry (Hartree-Fock and Density Functional Theory). The code is divided in two main parts: the MultiResolution Computation Program Package (MRCPP), which is a general purpose numerical mathematics library based on multiresolution analysis and the multiwavelet basis which provide low-scaling algorithms as well as rigorous error control in numerical computations, and the MultiResolution Chemistry (MRChem) program that uses the functionalities of MRCPP for computational chemistry applications.

Features as of July 2016:

• Spin restricted (closed-shell) Kohn-Sham DFT (LDA and GGA)
• Ground state energy and dipole moment
• Localized orbitals
• Shared memory parallelization (OpenMP)
• Size limitation: ~50 orbitals
• Accuracy limitation: ~nanoHartree

Upcoming features:

• Hartree-Fock exchange
• Spin unrestricted (open-shell) HF and DFT
• Linear response properties (electric, magnetic)
• Distributed memory parallelization (MPI + OpenMP)

MrPropa

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://ravel.pctc.uni-kiel.de/mrpropa/index.php/MrPropa
* License         : GPL-3+
  Programming Lang: 
  Description     : 

MrPropa is a general program to solve the time-dependent and time-independent Schrödinger equation for nearly arbitrary systems. The most important feature is that there is no principal restriction concerning the number and kind of DOFs which are treated explicitly and exactly. The exact treatment, however, implies that the numerical effort scales exponentially with the number of DOFs. Hence, in practical applications the number of DOFs which can be treated exactly is limited to 4-6. For larger systems three reduced dimensionality models of different accuracy can be applied. Another convenient feature of the MrPropa program is, that the geometry of a molecule can be described by means of a Z-matrix, as it is common in most quantum chemical programs.

NOTE: behind a user/password wall at http://ravel.pctc.uni-kiel.de/mrpropa/index.php/Download_MrPropa

MSL

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://msl-libraries.org/index.php/Main_Page
* License         : LGPL
  Programming Lang: 
  Description     : 

MSL is a library for analysis, manipulation, modeling and design of macromolecules.

Features include:

• Support for reading and writing PDB and CRD files.
• The ability of storing and switching between multiple atom coordinates, for conformational changes and rotameric representation of side chain conformational freedom.
• For protein design, the ability to build and store multiple residue identities (i.e. LEU, ILE, ALA) at a position and switch between them.
• Support for rotamer libraries.
• Transformations such as translations, rotations, and alignments.
• The CHARMM force field and other energy funtions.
• Support for CHARMM topology and parameter files.
• Structure building from scratch (using internal coordinates)
• Search algorithms such as Monte Carlo, Dead End Elimination, and Self Consistent Mean Field Monte Carlo.
• Local backbone sampling.
• Crystal lattice generation.
• A PyMOL Python Interface for calling MSL code from within PyMOL.
• A R Interface for calling arbitrary R algorithms or plotting routines from within MSL

MultiWell

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://aoss-research.engin.umich.edu/multiwell/
* License         : GPL-2
  Programming Lang: 
  Description     : 

Calculates time dependent concentrations, reaction yields, vibrational distributions, and rate constants as functions of temperature and pressure for multi-well, multi-channel unimolecular reactions systems that consist of stable species (wells) and multiple isomerization and/or dissociation reactions (channels). The stochastic method is used to solve the time-dependent Master Equation.

Mychem

* Package name    : mychem
  Version         : 
  Upstream Author : 
* URL             : http://mychem.sourceforge.net
* License         : GPL
  Programming Lang: 
  Description     : 

Mychem is a chemoinformatics extension for MySQL released under the GNU GPL license. This extension provides a set of functions that permits to handle chemical data within the MySQL database. These functions permit you to search, analyze and convert chemical data.

NECI

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : https://github.com/ghb24/NECI_STABLE
* License         : GPL-3
  Programming Lang: 
  Description     : 

The Full Configuration Interaction Quantum Monte Carlo (FCIQMC) technique is a stochastic method to compute the ground-state energy (and expectation values over two-particle operators of the ground state) of extremely large many-body Hamiltonians, usually in the context of ‘Full CI’ methods: that is to say electronic wavefunctions expanded in Slater determinant spaces comprising of all possible determinants constructable from a given spatial orbital basis.

nMOLDYN (ITP,VCS)

* Package name    : python-nmoldyn
  Version         : 3.0.11
  Upstream Author : 
* URL             : http://dirac.cnrs-orleans.fr/nMOLDYN.html
* License         : CeCILL Free Software License
  Programming Lang: 
  Description     : 

nMOLDYN is an interactive analysis program for Molecular Dynamics simulations. It is especially designed for the computation and decomposition of neutron scattering spectra, but also computes other quantities.

Quantities related to neutron scattering:

• coherent intermediate scattering function
• memory function for coherent scattering function
• dynamic structure factor
• incoherent intermediate scattering function
• elastic incoherent structure factor

Other quantities:

• mean-square displacement
• velocity autocorrelation function
• memory function for velocity autocorrelation function
• density of states
• angular velocity autocorrelation function (and its spectrum)
• reorientational correlation function

OpenMCTDHB

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://www.pci.uni-heidelberg.de/tc/usr/mctdhb/OpenMCTDHB.html
* License         : GPL-3
  Programming Lang: 
  Description     : 

OpenMCTDHB is an open-source package for the many-body dynamics of ultracold bosons. It is an implementation of the MCTDHB algorithm to solve the many-body Schrödinger equation for bosons.

OpenMCTDHB can solve the many-boson Schrödinger equation for 1D, 2D and 3D problems at variable degree of accuracy. The current version supports up to two orbitals and thereby allows to assess the validity of any Gross-Pitaevskii computation on the many-body level. The code is portable, serial and can be compiled using open-source software only. A number of scripts that come with the code allow to analyze the physics of a computation without the need to get deeply involved. The goal of OpenMCTDHB is to make many-boson dynamics accessible to everyone.

NOTE: likely not generally useful and too physics-oriented (only up to 3D/2 orbitals)

OpenMM (ITP,VCS)

* Package name    : openmm
  Version         : 7.3.1
  Upstream Author : Stanford University and the Authors
* URL             : http://openmm.org
* License         : MIT, LGPL, other
  Programming Lang: C
  Description     : high performance toolkit for molecular simulation

The OpenMM Software suite encompasses several essential software tools for molecular simulations:

• OpenMM: a library providing tools for modern molecular modeling simulation. It can be easily hooked into any code, and has a strong emphasis on hardware acceleration, thus providing not just a consistent API, but superior performance.
• PyOpenMM: a python API that wraps the OpenMM library, for those preferring to code in python.
• AMBER-compatible front end to OpenMM, designed for AMBER users that would like to enjoy the speed of OpenMM.
• MSMBuilder: analyze and combine data generated by molecular dynamics runs. MSM Builder provides a means to parallelize OpenMM runs across multiple GPUs
• OpenMM Zephyr: a user-friendly, easy to use, molecular simulation application, with OpenMM accelerated Gromacs inside, for studying molecular dynamics of proteins, RNA, and other molecules.

OpenMolcas (VCS)

* Package name    : openmolcas
  Version         : 
  Upstream Author : 
* URL             : https://gitlab.com/Molcas/OpenMolcas
* License         : LGPL
  Programming Lang: 
  Description     : 

(Open)Molcas is a Quantum Chemistry software package developed by scientists to be used by scientists.

The basic philosophy behind Molcas is to develop methods that allow accurate ab initio treatment of very general electronic structure problems for molecular systems in both ground and excited states which is not an easy task. Nowadays, knowledge about how to obtain accurate properties for single-reference dominated ground states is well developed, and Molcas contains a number of codes that can perform such calculations (MP2, CC, CPF, DFT etc). All these methods treat the electron correlation starting from a single determinant (closed or open shell) reference state. Such codes are today’s standard in most Quantum Chemistry program.

However, Molcas is to be able to treat, highly degenerate states, such as those oc- curring in excited states, transition states in chemical reactions, diradicaloid systems, heavy metal systems, as well as other chemically important problems, all at the same level of accuracy. This is a much more difficult problem, since a single-determinant approach does not work well in these cases. The key feature of Molcas is the mul- ticonfigurational approach. Molcas contains codes for general and effective multi- configurational SCF calculations at the Complete Active Space (CASSCF) level, but also employs more restricted MCSCF wave functions such as the Restricted Active Space, RASSCF, and the Generalized Active Space, GASSCF. It is also possible using either CASSCF or RASSCF to employ optimization techniques and obtain equilibrium geometries, transition-state structures, force fields, and vibrational energies using gra- dient techniques.

ORAC

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://www.chim.unifi.it/orac/
* License         : GPL-2
  Programming Lang: 
  Description     : 

ORAC is a suite to simulate at the atomistic level complex biosystems. It includes multiple time steps integration, Smooth Particle Mesh Ewald method, constant pressure and constant temperature simulations.

The present release has been supplemented with the most advanced techniques for enhanced sampling in atomistic systems including replica exchange with solute tempering, metadynamics on multidimensional reaction coordinates subspaces, and potential of mean force reconstruction along arbitrary reaction paths using non equilibrium molecular dynamics techniques. All these computational technologies have been implemented on parallel architectures using the standard MPI communication protocol.

ORBKIT

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : https://github.com/orbkit/orbkit/
* License         : LGPL-3
  Programming Lang: 
  Description     : 

ORBKIT is a toolbox for postprocessing electronic structure calculations based on a highly modular and portable Python architecture. The program allows computing a multitude of electronic properties of molecular systems on arbitrary spatial grids from the basis set representation of its electronic wavefunction, as well as several grid-independent properties. The required data can be extracted directly from the standard output of a large number of quantum chemistry programs. ORBKIT can be used as a standalone program to determine standard quantities, for example, the electron density, molecular orbitals, and derivatives thereof

The required data can be extracted from MOLPRO (Molden File Format), TURBOMOLE (AOMix file format), GAMESS-US, PROAIMS/AIMPAC (wfn/wfx file format), and Gaussian (.log File and Formatted Checkpoint File) output files. Futhermore, an interface to cclib, a parser for quantum chemical logfiles, is provided.

OSRA (ITP,VCS)

* Package name    : osra
  Version         : 2.0.0
  Upstream Author : Igor Filippov <igorf@helix.nih.gov>
* URL             : https://sourceforge.net/projects/osra/
* License         : GPL-2+
  Programming Lang: C++, Java
  Description     : optical structure recognition application

OSRA is a utility designed to convert graphical representations of chemical structures, as they appear in journal articles, patent documents, textbooks, trade magazines etc., into SMILES or SD files - a computer recognizable molecular structure format. OSRA can read a document in any of the over 90 graphical formats parseable by ImageMagick - including GIF, JPEG, PNG, TIFF, PDF, PS etc., and generate the SMILES or SDF representation of the molecular structure images encountered within that document.

PaDEL-Descriptor

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://padel.nus.edu.sg/software/padeldescriptor/
* License         : AGPLv3+, Apachev2, LGPLv2+, GPLv2/CDDL
  Programming Lang: 
  Description     : 

A software to calculate molecular descriptors and fingerprints. The software currently calculates 856 descriptors (722 1D, 2D descriptors and 134 3D descriptors) and 10 types of fingerprints. The descriptors and fingerprints are calculated using The Chemistry Development Kit (CDK) with some additional descriptors and fingerprints. These additions include atom type electrotopological state descriptors, extended topochemical atom (ETA) descriptors, McGowan volume, molecular linear free energy relation descriptors, ring counts, count of chemical substructures identified by Laggner, and binary fingerprints and count of chemical substructures identified by Klekota and Roth.

PCMSolver

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : https://github.com/PCMSolver/pcmsolver
* License         : LGPL-3
  Programming Lang: 
  Description     : 

PCMSolver is an API for the polarizable continuum model (PCM), a continuum solvation model. PCMSolver can be interfaced to a quantum chemistry host program to provide PCM functionality. In the current release the basic features of the PCM are made available:

• GePol cavity generator;
• IEFPCM and CPCM solvers for isotropic uniform dielectrics;
• flexible Green’s function definition for isotropic uniform dielectrics.

PDB Validation Suite

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://sw-tools.pdb.org/apps/VAL/index.html
* License         : UNKNOWN
  Programming Lang: 
  Description     : 

The PDB Validation Suite is a set of tools used by the PDB for processing and checking structure data.

PES-Learn

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : https://github.com/CCQC/PES-Learn
* License         : BSD-3-Clause
  Programming Lang: Python
  Description     : 

PES-Learn is a Python library designed to fit system-specific Born-Oppenheimer potential energy surfaces using modern machine learning models. PES-Learn assists in generating datasets, and features Gaussian process and neural network model optimization routines. The goal is to provide high-performance models for a given dataset without requiring user expertise in machine learning.

PES-Learn supports input file generation and output file parsing for arbitrary electronic structure theory packages such as Psi4, Molpro, Gaussian, NWChem, etc.

Data is generated with user-defined internal coordinate displacements with support for:

• Redundant geometry removal
• Configuration space filtering

PEXSI

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : https://math.berkeley.edu/~linlin/pexsi/
* License         : BSD
  Programming Lang: 
  Description     : 

The Pole EXpansion and Selected Inversion (PEXSI) method is a fast method for electronic structure calculation based on Kohn-Sham density functional theory. It efficiently evaluates certain selected elements of matrix functions, e.g., the Fermi-Dirac function of the KS Hamiltonian, which yields a density matrix. It can be used as an alternative to diagonalization methods for obtaining the density, energy and forces in electronic structure calculations. The PEXSI library is written in C++, and uses message passing interface (MPI) to parallelize the computation on distributed memory computing systems and achieve scalability on more than 10,000 processors.

From numerical linear algebra perspective, the PEXSI library can be used as a general tool for evaluating certain selected elements of a matrix function, and therefore has application beyond electronic structure calculation as well.

PHAISTOS

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://www.phaistos.org
* License         : GPL-3
  Programming Lang: 
  Description     : 

PHAISTOS is a Markov chain Monte Carlo framework for protein structure simulations. It contains a variety of both established and novel moves types, and provides support for several force-fields from the literature. In addition, an interface to the Muninn generalized ensemble package makes it possible to easily conduct multi-histogram based simulations, avoiding the convergence problems often associated with Metropolis-Hastings based sampling.

A unique feature of PHAISTOS is the use of probabilistic models to capture essential structural properties in proteins. These models are available both as proposal distributions (moves), and for likelihood evaluations (energies). This increases the flexibility when settings up a simulation, by allowing the user to choose how to incorporate the bias provided by these models in the simulation. For instance, similar to the use of fragment or rotamer libraries, using probabilistic models for sampling of backbone angles and sidechain angles corresponds to having an implicit energy term present in the simulation. Unlike fragment and rotamer libraries, however, when using probabilistic models, this term can be evaluated and compensated for if necessary. PHAISTOS currently incorporates models for the CA-only representation of protein backbones (FB5HMM), full-atom backbones (TORUSDBN), full-atom sidechains (BASILISK), and single-mass sidechains (COMPAS).

POLYANA

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://cag.dat.demokritos.gr/Software.mol.php
* License         : MIT
  Programming Lang: 
  Description     : 

A tool for the calculation of molecular radial distribution functions based on Molecular Dynamics trajectories (from DL_POLY)

Pteros

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://pteros.sourceforge.net/
* License         : Artistic
  Programming Lang: C++
  Description     : 

Pteros is a C++ library for molecular modeling. It is designed to simplify the development of custom programs for molecular modeling, analysis of molecular dynamics trajectories and implementing new simulation algorithms. Pteros provides facilities, which are routinely used in all such programs, namely input/output in popular file formats, powerful and flexible atom selections, geometry transformations, RMSD fitting and alignment, etc. Pteros also contains powerful facilities for parsing command-line arguments in custom programs and for running several analysis tasks in parallel, utilizing the power of modern multi-core processors.

Py-ChemShell

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : https://www.chemshell.org/
* License         : LGPL-3
  Programming Lang: 
  Description     : 

ChemShell is a scriptable computational chemistry environment with an emphasis on multiscale simulation of complex systems using combined quantum mechanical and molecular mechanical (QM/MM) methods. Motivated by a scientific need to efficiently and accurately model chemical reactions on surfaces and within microporous solids on massively parallel computing systems, Py-ChemShell provides a modern platform for advanced QM/MM embedding models. Py-ChemShell is capable of performing QM/MM calculations on systems of significantly increased size, which we illustrate with benchmarks on zirconium dioxide nanoparticles of over 160000 atoms.

pyEFP

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : https://github.com/ale-odinokov/pyEFP
* License         : LGPL-3
  Programming Lang: 
  Description     : 

pyEFP is a library and tools to represent large molecules as a union of small effective fragments.

pyMolDyn

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : https://pgi-jcns.fz-juelich.de/portal/pages/pymoldyn-main.html
* License         : MIT
  Programming Lang: 
  Description     : 

pyMolDyn is a viewer for atomic clusters, crystalline and amorphous materials in a unit cell corresponding to one of the seven 3D Bravais lattices. The program calculates cavities (vacancies, voids) according to three definitions.

Features include:

• Interactive viewer based on GR3
• Computation of cavities in all seven 3D Bravais lattice systems
• Creation of high resolution images appropriate for publications
• Video creation from a set of input frames to analyze cavity changes in materials over time
• Statistics including (i) Surfaces, volumes and surface/volume ratios of cavities and domains, (ii) Pair distribution functions (including cavities), bonds, bond (dihedral) angles and (iii) Gyration tensor, asphericity, acylindricity
• Filter for atoms and cavities
• Batch mode for simultaneous processing of multiple files

PyRETIS

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://www.pyretis.org/
* License         : LGPL-2.1+
  Programming Lang: 
  Description     : 

PyRETIS is a Python library for rare event molecular simulations with emphasis on methods based on transition interface sampling and replica exchange transition interface sampling. The PyRETIS library can be used to set up tailored simulations or one can use a Python flavored input file to run different kinds of path sampling simulations.

PyRETIS is open source, easy to use and can be interfaced with other simulation packages such as GROMACS or CP2K.

Pyrite

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : https://durrantlab.pitt.edu/pyrite/
* License         : GPL-3
  Programming Lang: 
  Description     : 

Pyrite is a Blender plugin that imports the atomic motions captured by molecular dynamics simulations. Using Pyrite, these motions can be rendered using Blender’s state-of-the-art computer-graphics algorithms. All 3D protein representations (e.g., surface, ribbon, VDW spheres) are supported.

PySCF

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://sunqm.net/pyscf/index.html
* License         : BSD 2-clause
  Programming Lang: 
  Description     : 

Pyscf is a quantum chemistry package written in python. The package aims to provide a simple, light-weight and efficient platform for quantum chemistry code developing and calculation.

Common quantum chemistry methods:

• Hartree-Fock
• DFT
• CASCI and CASSCF
• Full CI
• MP2
• SC-NEVPT2
• CCSD and CCSD(T)
• CCSD lambda
• EOM-CCSD
• Density fitting
• relativistic correction
• General integral transformation
• Gradients
• NMR
• TDDFT

PYXAID

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : https://www.acsu.buffalo.edu/~alexeyak/pyxaid/index.html
* License         : GPL-3
  Programming Lang: 
  Description     : 

The PYXAID program is developed for non-adiabatic molecular dynamics simulations in condensed matter systems. By applying the classical path approximation to the fewest switches surface hopping approach, it provides an efficient computational tool that can be applied to study photoinduced dynamics at the ab initio level in systems composed of hundreds of atoms and involving thousands of electronic states.

PYXAID can be interfaced with Quantum ESPRESSO.

Capabilities include:

• Basic non-adiabatic molecular dynamics: FSSH-CPA
• Decoherence correction via DISH
• Multi-electron basis functions
• Direct photoexcitation via light-matter interaction
• Advanced integration schemes for solving TD-SE
• Numerous pre- and post-processing utilities

Qbox

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://eslab.ucdavis.edu/software/qbox/index.htm
* License         : GPL
  Programming Lang: 
  Description     : 

Qbox is a C++/MPI scalable parallel implementation of first-principles molecular dynamics (FPMD) based on the plane-wave, pseudopotential formalism. Qbox is designed for operation on large parallel computers.

QMcBeaver

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://qmcbeaver.sourceforge.net/
* License         : GPL
  Programming Lang: 
  Description     : 

QMcBeaver is a finite, all electron variational and diffusion quantum Monte Carlo program.

Several features distinguish QMcBeaver from other QMC programs:

• The code runs on massively parallel architectures, and has a highly efficient decorrelation algorithm to properly decorrelate the data from different processors.
• The code uses a Manager-Worker based parallelization scheme which allows the efficient use of heterogeneous clusters.
• The code is written in modern object-oriented C++, and is clean, and easily understood and modified.

QMcBeaver can use trial wavefunctions from GAMESS and Jaguar.

QMCPACK

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://qmcpack.org/
* License         : BSD
  Programming Lang: 
  Description     : 

QMCPACK is a Quantum-Monte-Carlo code written in C++. It was developed at the University of Illinois and is designed for high-performance computers. It implements advanced QMC algorithms and is parallelized with both MPI and OpenMP. Generic programming enabled by templates in C++ is extensively utilized to achieve high efficiency on HPC systems.

QMMMW

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://qe-forge.org/gf/project/qmmmw/
* License         : GPL-3
  Programming Lang: 
  Description     : 

QMMM wrapper is based on the original idea and code MS2 of Riccardo Di Meo. QMMMW, works as an interface between the Born-Oppenheimer DFT engine of Quantum ESPRESSO and the classical Dynamics engine of LAMMPS.

Quantum Package

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : https://github.com/QuantumPackage/qp2
* License         : AGPL-3.0
  Programming Lang: 
  Description     : 

The Quantum Package is an open-source programming environment for quantum chemistry. It has been built from the developper point of view in order to help the design of new quantum chemistry methods, especially for wave function theory (WFT).

From the user point of view, the Quantum Package proposes a stand-alone path to use optimized selected configuration interaction sCI based on the CIPSI algorithm that can efficiently reach near-full configuration interaction FCI quality for relatively large systems.

The Quantum Package is not a general purpose quantum chemistry program. First of all, it is a library to develop new theories and algorithms in quantum chemistry. Therefore, beside the use of the programs of the core modules, the users of the Quantum Package should develop their own programs.

QUIP

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : https://github.com/libAtoms/QUIP
* License         : GPL-2
  Programming Lang: 
  Description     : 

The libAtoms package is a software library written in Fortran 95+ for the purposes of carrying out molecular dynamics simulations. The QUIP package, built on top of libAtoms, implements a wide variety of interatomic potentials and tight binding quantum mechanics, and is also able to call external packages. Various hybrid combinations are also supported in the style of QM/MM.

We try to strike a compromise between readability of code and efficiency, and think of QUIP/libAtoms as a “developer’s code”: nice when you want to try new ideas quickly, but not competitive in efficiency with other major md codes such as LAMMPS, Gromacs etc. We use several extensions to the Fortran 95 standard in order to make the coding style more object oriented. Several compilers support all the necessary extensions in their recent versions, e.g. GNU v4.4 and later. Support in the Intel compiler suite is there in principle, but not every recent version has correct implementation, although we have not encountered many problems past version 11. Get in touch for a list of versions known to compile correctly if you encounter difficulties.

The following interatomic potentials are presently coded or linked in QUIP:

• BKS (van Beest, Kremer and van Santen) (silica)
• EAM (fcc metals)
• Fanourgakis-Xantheas (water)
• Finnis-Sinclair (bcc metals)
• Flikkema-Bromley
• GAP (Gaussian Approximation Potentials: general many-body)
• Guggenheim-!McGlashan
• Brenner (carbon)
• OpenKIM (general interface)
• Lennard-Jones
• Morse
• Partridge-Schwenke (water monomer)
• Stillinger-Weber (carbon, silicon, germanium)
• SiMEAM (silicon)
• Sutton-Chen
• Tangney-Scandolo (silica, titania etc)
• Tersoff (silicon, carbon)

The following tight-binding functional forms and parametrisations are implemented:

• Bowler
• DFTB
• GSP
• NRL-TB

QWalk

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://www.qwalk.org/
* License         : GPL-2+
  Programming Lang: 
  Description     : 

QWalk is a program developed to perform high accuracy quantum Monte Carlo calculations of electronic structure in molecules and solids. It is specifically designed as a research vehicle for new algorithms and method developments, as well as being able to scale up to large system sizes.

RMG

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://rmg.mit.edu/
* License         : MIT
  Programming Lang: 
  Description     : 

Reaction Mechanism Generator (RMG) is an automatic chemical reaction mechanism generator that constructs kinetic models composed of elementary chemical reaction steps using a general understanding of how molecules react.

CanTherm (a part of RMG) is a tool for computing the thermodynamic properties of chemical species and high-pressure-limit rate coefficients for chemical reactions using the results of a quantum chemistry calculation. Thermodynamic properties are computed using the rigid rotor-harmonic oscillator approximation with optional corrections for hindered internal rotors. Kinetic parameters are computed using canonical transition state theory with optional tunneling correction.

CanTherm can also estimate pressure-dependent phenomenological rate coefficients k(T,P) for unimolecular reaction networks of arbitrary complexity. The approach is to first generate a detailed model of the reaction network using the one-dimensional master equation, then apply one of several available model reduction methods of varying accuracy, speed, and robustness to simplify the detailed model into a set of phenomenological rate coefficients. The result is a set of k(T,P) functions suitable for use in chemical reaction mechanisms.

RPMDrate

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://ysuleyma.scripts.mit.edu/index.html
* License         : MIT
  Programming Lang: 
  Description     : 

RPMDrate is an implementation of the ring polymer molecular dynamics (RPMD) method for calculating chemical reaction rates.

SCHAKAL

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://www.krist.uni-freiburg.de/de/content/download.html
* License         : public-domain
  Programming Lang: 
  Description     : 

FORTRAN program for the graphical representation of molecular and solid-state structure models.

Serenity

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : https://thclab.uni-muenster.de/serenity/serenity
* License         : LGPLv3
  Programming Lang: 
  Description     : 

Serenity implements a wide variety of functionalities with a focus on subsystem methodology. The modular code structure in combination with publicly available external tools and particular design concepts ensures extensibility and robustness with a focus on the needs of a subsystem program. Several important features of the program are exemplified with sample calculations with subsystem density-functional theory, potential reconstruction techniques, a projection-based embedding approach and combinations thereof with geometry optimization, semi-numerical frequency calculations and linear-response time-dependent density-functional theory.

SHARC

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : https://github.com/sharc-md/sharc
* License         : GPLv3
  Programming Lang: 
  Description     : 

The SHARC (Surface Hopping including ARbitrary Couplings) molecular dynamics (MD) program suite is an ab initio MD software package developed to study the excited-state dynamics of molecules.

SHARC

• can treat non-adiabatic couplings at conical intersections, intersystem crossing induced by spin-orbit coupling, and laser couplings on an equal footing.
• can treat any number of states of arbitrary multiplicities.
• has interfaces to MOLPRO, MOLCAS, COLUMBUS, ADF, TURBOMOLE (only ricc2), GAUSSIAN, analytical potentials, and linear-vibronic coupling potentials.
• comes with the WFoverlap program for efficient computation of nonadiabatic couplings and Dyson norms.
• can do on-the-fly wave function analysis through TheoDORE.
• includes auxiliary Python scripts for setup, maintenance and analysis of ensembles of trajectories.
• includes scripts to perform excited-state (crossing point) optimizations and single point calculations with all interfaced methods.
• has a comprehensive tutorial.

SIESTA

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : https://launchpad.net/siesta
* License         : GPL-3
  Programming Lang: 
  Description     : 

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. The possibility of treating large systems with some first-principles electronic-structure methods has opened up new opportunities in many disciplines.

Simint

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : https://www.bennyp.org/research/simint/
* License         : BSD
  Programming Lang: 
  Description     : 

Simint is a vectorized implementation of the Obara-Saika (OS) method of calculating electron repulsion integrals. Speedup is gained by vectorizing the primitive loop of the OS algorithm, with additional vectorization and optimizations left to the compiler.

Currently, Simint is limited to calculating ERI up to AM=7. It is not necessary to compile up to that high of angular momentum; a lower angular momentum can be selected at compile time with the SIMINT_MAXAM cmake option.

Simint is capable of calculating ERI with the angular momentum in any order. That is, it is possible to calculate (ds|ds) and (sd|ds) directly, without permutation of the resulting integrals.

Primitive screening is available.

SMASH

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://smash-qc.sourceforge.net/
* License         : Apache 2.0
  Programming Lang: 
  Description     : 

Scalable Molecular Analysis Solver for High-performance computing systems (SMASH) is open-source software for massively parallel quantum chemistry calculations written in the Fortran 90/95 language with MPI and OpenMP. Hartree-Fock (HF), Second-order Moller-Plesset perturbation theory (MP2) and Density Functional Theory (DFT) calculations can be performed.

Socorro

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://dft.sandia.gov/Socorro/about.html
* License         : GPL
  Programming Lang: 
  Description     : 

Socorro is a modular, object oriented code for performing self-consistent electronic-structure calculations utilizing the Kohn-Sham formulation of density-functional theory. Calculations are performed using a plane wave basis and either norm-conserving pseudopotentials or projector augmented wave functions. Several exchange-correlation functionals are available for use including the local-density approximation (Perdew-Zunger or Perdew-Wang parameterizations of the Ceperley-Alder QMC correlation results) and the generalized-gradient approximation (PW91, PBE, and BLYP). Both Fourier-space and real-space projectors have been implemented, and a variety of methods are available for relaxing atom positions, optimizing cell parameters, and performing molecular dynamics calculations.

Sparrow

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : https://scine.ethz.ch/download/sparrow
* License         : BSD-3-Clause
  Programming Lang: 
  Description     : 

SCINE Sparrow is a command-line tool that implements many popular semiempirical models. SCINE Sparrow contains methods which require a self-consistent solution of a Roothaan-Hall-type equation (semiempirical methods based on the neglect of diatomic differential overlap approximation and SCC-DFTB) and a non-self-consistent methods (non-SCC DFTB). The application of semiempirical models usually allows for rapid calculation of electronic energies and energy gradients for a small molecular structure with a given charge and spin state. The input is given in a user-friendly yaml format. Sparrow itself is able to calculate energies, gradients with respect to nuclear coordinates, and Hessian matrices (for vibrational frequencies and normal modes). More advanced calculations such as structure optimizations and transition state searches can be done through SCINE ReaDuct.

Current Features:

• MNDO-type models: MNDO(/d), AM1, AM1*, RM1, PM3, PM6
• DFTB models: non-SCC DFTB, SCC-DFTB, DFTB3

TAO

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://www.mcs.anl.gov/research/projects/tao/index.html
* License         : BSDish
  Programming Lang: 
  Description     : 

The TAO project focuses on the development of software for large-scale optimization problems. TAO uses an object-oriented design to create a flexible toolkit with strong emphasis on the reuse of external tools where appropriate. Our design enables bi-directional connection to lower level linear algebra support (for example, parallel sparse matrix data structures) as well as higher level application frameworks.

Towhee

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://towhee.sourceforge.net/
* License         : GPL-2
  Programming Lang: 
  Description     : 

Towhee is a Monte Carlo molecular simulation code originally designed for the prediction of fluid phase equilibria using atom-based force fields and the Gibbs ensemble with particular attention paid to algorithms addressing molecule conformation sampling. The code has subsequently been extended to several ensembles, many different force fields, and solid (or at least porous) phases.

v2rdm_casscf

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : https://github.com/edeprince3/v2rdm_casscf
* License         : GPL-2+
  Programming Lang: 
  Description     : 

A variational 2-RDM-driven CASSCF plugin to Psi4. This plugin to Psi4 performs variational two-electron reduced-density-matrix (2-RDM)-driven complete active space self consistent field (CASSCF) computations. In principle, because variational 2-RDM (v-2RDM) methods scale only polynomially with system size, v-2RDM-driven CASSCF computations can be performed using active spaces that are larger than can be used within conventional configuration-interaction-driven CASSCF methods.

Wannier90 (ITP,VCS)

* Package name    : wannier90
  Version         : 3.0.0
  Upstream Author : Arash Mostofi <a.mostofi@imperial.ac.uk>
* URL             : http://www.wannier.org/
* License         : GPL
  Programming Lang: Fortran 90
  Description     : Maximally Localized Wannier Functions

Wannier90 is an electronic-structure software computing maximally-localized Wannier functions (MLWF). It works on top of other electronic-structure software, such as Abinit, FLEUR, and PwSCF.

West

* Package name    : 
  Version         : 3.0.0
  Upstream Author : 
* URL             : http://www.west-code.org
* License         : GPL-2+
  Programming Lang: 
  Description     : 

XCFun

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://dftlibs.org/xcfun/
* License         : LGPL-3
  Programming Lang: 
  Description     : 

XCFun is a library of DFT exchange-correlation (XC) functionals. It is based on automatic differentiation and can therefore generate arbitrary order derivatives of these functionals.

XtalOpt (ITP)

* Package name    : xtalopt
  Version         : r12.0
  Upstream Author : David Lonie
* URL             : https://xtalopt.github.io
* License         : GPLv2, LGPLv2 and BSD
  Programming Lang: C, C++
  Description     : Evolutionary Crystal Structure Prediction

XtalOpt is a free and truly open source evolutionary algorithm designed to predict crystal structures. It is implemented as an extension to the Avogadro molecular editor. See the list of publications for some of the systems it has been used to explore.

XtalOpt runs on a workstation and supports using GULP, VASP, pwSCF (Quantum ESPRESSO), and CASTEP for geometry optimizations. The calculations can be performed remotely on a cluster running PBS or SGE, or on the workstation if a computing cluster is not available. There is no special set up needed server-side when running on remote queues, just install XtalOpt on the workstation and it’s ready to go!

Zeobuilder

* Package name    : 
  Version         : 
  Upstream Author : 
* URL             : http://molmod.ugent.be/code/wiki/Zeobuilder
* License         : GPL-3
  Programming Lang: 
  Description     : 

Zeobuilder is a user-friendly GUI toolkit for the construction of advanced molecular models. Zeobuilder’s main goal is to become the ultimate molecular editor, through an open and community-oriented development process.