DebiChem Project
Summary
Periodic Ab Initio Calculations
DebiChem Periodic Ab Initio Calculations

This metapackage will install packages doing periodic ab initio calculations which might be useful for chemists.

Description

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DebiChem Periodic Ab Initio Calculations packages

Official Debian packages with high relevance

abinit
paquet pour les calculs de structure électronique
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ABINIT est un paquet dont le programme principal permet de trouver l'énergie totale, la densité de charge et la structure électronique de systèmes composés d'électrons et de noyaux (molécules et solides périodiques) dans le cadre de la théorie fonctionnelle de la densité (DFT, « Density Functional Theory ») en utilisant des pseudo-potentiels et une base d'onde plane.

ABINIT inclut également des options pour optimiser la géométrie suivant les forces et stress de la DFT, pour faire des simulations de dynamique moléculaire en utilisant ces forces ou pour créer des matrices dynamiques, des charges effectives de Born et des tenseurs diélectriques. Les états excités peuvent être calculés suivant la DFT dépendante du temps (pour les molécules) ou suivant la théorie des perturbations multicorps (l'approximation GW). En plus du code principal d'ABINIT, différents utilitaires sont fournis.

Ce paquet fournit les exécutables nécessaires aux calculs (mais les pseudo-potentiels ne sont pas fournis). Le paquet abinit-data fournit un ensemble de pseudo-potentiels.

Please cite: X. Gonze, B. Amadon, P.-M. Anglade, J.-M. Beuken, F. Bottin, P. Boulanger, F. Bruneval, D. Caliste, R. Caracas, M. Côté, T. Deutsch, L. Genovese, Ph. Ghosez, M. Giantomassi, S. Goedecker, D.R. Hamann, P. Hermet, F. Jollet, G. Jomard, S. Leroux, M. Mancini, S. Mazevet, M. J. T. Oliveira, G. Onida, Y. Pouillon, T. Rangel, G.-M. Rignanese, D. Sangalli, R. Shaltaf, M. Torrent, M. J. Verstraete, G. Zerah and J. W. Zwanziger: ABINIT: First-principles approach to material and nanosystem properties. (eprint) Comput. Phys. Commun. 180(12):2582-2615 (2009)
cp2k
Ab Initio Molecular Dynamics
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CP2K is a program to perform simulations of solid state, liquid, molecular and biological systems. It is especially aimed at massively parallel and linear scaling electronic structure methods and state-of-the-art ab-initio molecular dynamics (AIMD) simulations.

CP2K is optimized for the mixed Gaussian and Plane-Waves (GPW) method based on pseudopotentials, but is able to run all-electron or pure plane-wave/Gaussian calculations as well. Features include:

Ab-initio Electronic Structure Theory Methods using the QUICKSTEP module:

  • Density-Functional Theory (DFT) energies and forces
  • Hartree-Fock (HF) energies and forces
  • Moeller-Plesset 2nd order perturbation theory (MP2) energies and forces
  • Random Phase Approximation (RPA) energies
  • Gas phase or Periodic boundary conditions (PBC)
  • Basis sets include various standard Gaussian-Type Orbitals (GTOs), Pseudo- potential plane-waves (PW), and a mixed Gaussian and (augmented) plane wave approach (GPW/GAPW)
  • Norm-conserving, seperable Goedecker-Teter-Hutter (GTH) and non-linear core corrected (NLCC) pseudopotentials, or all-electron calculations
  • Local Density Approximation (LDA) XC functionals including SVWN3, SVWN5, PW92 and PADE
  • Gradient-corrected (GGA) XC functionals including BLYP, BP86, PW91, PBE and HCTH120 as well as the meta-GGA XC functional TPSS
  • Hybrid XC functionals with exact Hartree-Fock Exchange (HFX) including B3LYP, PBE0 and MCY3
  • Double-hybrid XC functionals including B2PLYP and B2GPPLYP
  • Additional XC functionals via LibXC
  • Dispersion corrections via DFT-D2 and DFT-D3 pair-potential models
  • Non-local van der Waals corrections for XC functionals including B88-vdW, PBE-vdW and B97X-D
  • DFT+U (Hubbard) correction
  • Density-Fitting for DFT via Bloechl or Density Derived Atomic Point Charges (DDAPC) charges, for HFX via Auxiliary Density Matrix Methods (ADMM) and for MP2/RPA via Resolution-of-identity (RI)
  • Sparse matrix and prescreening techniques for linear-scaling Kohn-Sham (KS) matrix computation
  • Orbital Transformation (OT) or Direct Inversion of the iterative subspace (DIIS) self-consistent field (SCF) minimizer
  • Local Resolution-of-Identity Projector Augmented Wave method (LRIGPW)
  • Absolutely Localized Molecular Orbitals SCF (ALMO-SCF) energies for linear scaling of molecular systems
  • Excited states via time-dependent density-functional perturbation theory (TDDFPT)

Ab-initio Molecular Dynamics:

  • Born-Oppenheimer Molecular Dynamics (BOMD)
  • Ehrenfest Molecular Dynamics (EMD)
  • PS extrapolation of initial wavefunction
  • Time-reversible Always Stable Predictor-Corrector (ASPC) integrator
  • Approximate Car-Parrinello like Langevin Born-Oppenheimer Molecular Dynamics (Second-Generation Car-Parrinello Molecular Dynamics (SGCP))

Mixed quantum-classical (QM/MM) simulations:

  • Real-space multigrid approach for the evaluation of the Coulomb interactions between the QM and the MM part
  • Linear-scaling electrostatic coupling treating of periodic boundary conditions
  • Adaptive QM/MM

Further Features include:

  • Single-point energies, geometry optimizations and frequency calculations
  • Several nudged-elastic band (NEB) algorithms (B-NEB, IT-NEB, CI-NEB, D-NEB) for minimum energy path (MEP) calculations
  • Global optimization of geometries
  • Solvation via the Self-Consistent Continuum Solvation (SCCS) model
  • Semi-Empirical calculations including the AM1, RM1, PM3, MNDO, MNDO-d, PNNL and PM6 parametrizations, density-functional tight-binding (DFTB) and self-consistent-polarization tight-binding (SCP-TB), with or without periodic boundary conditions
  • Classical Molecular Dynamics (MD) simulations in microcanonical ensemble (NVE) or canonical ensmble (NVT) with Nose-Hover and canonical sampling through velocity rescaling (CSVR) thermostats
  • Metadynamics including well-tempered Metadynamics for Free Energy calculations
  • Classical Force-Field (MM) simulations
  • Monte-Carlo (MC) KS-DFT simulations
  • Static (e.g. spectra) and dynamical (e.g. diffusion) properties
  • ATOM code for pseudopotential generation
  • Integrated molecular basis set optimization

CP2K does not implement conventional Car-Parrinello Molecular Dynamics (CPMD).

gpaw
DFT and beyond within the projector-augmented wave method
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A density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) method and the atomic simulation environment (ASE). It uses real-space uniform grids and multigrid methods, atom-centered basis-functions or plane-waves.

Please cite: J. J. Mortensen, L. B. Hansen and K. W. Jacobsen: Real-space grid implementation of the projector augmented wave method. (eprint) Physical Review B 71(3) (2005)
nwchem
??? missing short description for package nwchem :-(
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Please cite: M. Valiev, E.J. Bylaska, N. Govind, K. Kowalski, T.P. Straatsma, H.J.J. van Dam, D. Wang, J. Nieplocha, E. Apra, T.L. Windus and W.A. de Jong: NWChem: a comprehensive and scalable open-source solution for large scale molecular simulations. Comput. Phys. Commun. 181(9):1477-1489 (2010)
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openmx
paquet de simulations nanométriques
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OpenMX (Open source package for Material eXplorer) est un paquet de programmes pour des simulations de matériaux nanométriques basées sur la théorie de la fonctionnelle de la densité, le pseudopotentiel à norme conservée et des fonctions de base localisées au pseudo-atome. Puisque le code est conçu pour la réalisation de calculs ab initio à très grande échelle sur des ordinateurs parallélisés, il est prévu qu’OpenMX puisse être un outil utile et puissant pour les sciences des matériaux nanométriques pour une large diversité de systèmes tels que les biomatériaux, les nanotubes de carbone, les matériaux magnétiques et les conducteurs nanométriques.

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quantum-espresso
suite Electronic-Structure et Ab-Initio Molecular Dynamics
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ESPRESSO Quantum (anciennement connu sous le nom PWscf) est une suite intégrée de codes informatiques pour les calculs de structure électronique et de modélisation de matériaux à l'échelle nanométrique. Elle est basée sur la théorie de la densité fonctionnelle, les ondes planes et les pseudopotentiels (tous conservant les normes, ultrasoft et PAW).

Please cite: P. Giannozzi, S. Baroni, N. Bonini, M. Calandra, R. Car, C. Cavazzoni, D. Ceresoli, G. L. Chiarotti, M. Cococcioni, I. Dabo, A. Dal Corso, S. Fabris, G. Fratesi, S. de Gironcoli, R. Gebauer, U. Gerstmann, C. Gougoussis, A. Kokalj, M. Lazzeri, L. Martin-Samos, N. Marzari, F. Mauri, R. Mazzarello, S. Paolini, A. Pasquarello, L. Paulatto, C. Sbraccia, S. Scandolo, G. Sclauzero, A. P. Seitsonen, A. Smogunov, P. Umari and R. M. Wentzcovitch: QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials. J. Phys. Condens. Matter 21:395502 (2009)
wannier90
Maximally Localized Wannier Functions - executables
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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.

This package provides Wannier90 executables.

Please cite: Giovanni Pizzi, Valerio Vitale, Ryotaro Arita, Stefan Blügel, Frank Freimuth, Guillaume G{\'{e}}ranton, Marco Gibertini, Dominik Gresch, Charles Johnson, Takashi Koretsune, Julen Iba{\~{n}}ez-Azpiroz, Hyungjun Lee, Jae-Mo Lihm, Daniel Marchand, Antimo Marrazzo, Yuriy Mokrousov, Jamal I Mustafa, Yoshiro Nohara, Yusuke Nomura, Lorenzo Paulatto, Samuel Ponc{\'{e}}, Thomas Ponweiser, Junfeng Qiao, Florian Thöle, Stepan S Tsirkin, Ma{\l}gorzata Wierzbowska, Nicola Marzari, David Vanderbilt, Ivo Souza, Arash A Mostofi and Jonathan R Yates: Wannier90 as a community code: new features and applications. Journal of Physics: Condensed Matter 32(16):165902 (2020)
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