DebiChem Project
Summary
Periodic ab initio calculations
DebiChem - periodiske Ab Intio-beregninger

Denne metapakke vil installere pakker, der udfører periodisk ab initio-beregninger, som kan være nyttige for kemikere.

Description

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DebiChem Periodic ab initio calculations packages

Official Debian packages with high relevance

Abinit
Pakke for elektroniske strukturberegninger
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ABINIT er en pakke, hvis vigtigste program gør det muligt at finde den samlede energi, ladningstæthed og elektronisk struktur for systemer lavet af elektroner og kerner (molekyler og periodiske faste stoffer) inden for tæthedsfunktionalteori (DFT), via pseudopotentialer og planewave-basis.

ABINIT indeholder også muligheder for at optimere geometrien ifølge DFT-kræfter og -spændinger, eller til at udføre molekylære simuleringer ved hjælp af disse kræfter, eller til at generere dynamiske matricer, Born-effektive ladninger, og dielektriske tensorer. Opløftede tilstande kan beregnes inden den tidsafhængige tæthedsfunktionalteori (for molekyler), eller inden for Many-Body-perturbationsteorien (GW-tilnærmelsen). Ud over den vigtige ABINIT-kode, tilbydes forskellige redskabsprogrammer.

Denne pakke indeholder alle de programmer, der kræves for at udføre beregninger (pseudopotentialer er dog ikke indeholdt). For et sæt af pseudopotentialer installeres pakken abinit-data.

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 og derudover i den projektor-forstærket bølgemetode
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En tæthedsfunktionel teori (DFT) for Pythonkode baseret på projektor- forstærket bølgemetode (PAW) og atomare simuleringsmiljø (ASE). Den bruger real-space ensartede net- og flernetsmetoder, atom-centreret basis- funktioner eller plane-bølger.

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
Højtydende programmer til beregninger i kemi
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NWCHem er en programpakke til foretage beregninger i kemi. Den tilbyder metoder, der kan skalere i både evnen til effektiv håndtering af store problemer i videnskabelige beregninger inden for kemien, samt evnen til at gøre brug af parallelle beregningsressourcer fra højtydende parallel- supercomputere til konventionelle klynger af arbejdsstationer.

NWChem kan håndtere:

  • Molekylære, elektroniske strukturmetoder med brug af gaussisk basisfunktioner til molekylærberegninger med høj præcision
  • Elektronisk strukturmetoder til pseudopotentialer for planbølger til beregning af molekyler, væsker, krystaller, overflader, halvledere eller metaller
  • Ab-initio og klassisk simulering af molekylære dynamikker
  • Blandede, klassiske kvantum-simuleringer
  • Parallel skalering til tusinder af processorer

(Den efterfølgende beskrivelse af egenskaber bevares på engelsk).

  • Molecular electronic structure methods, analytic second derivatives:
  • Restricted/unrestricted Hartree-Fock (RHF, UHF)
  • Restricted Density Functional Theory (DFT) using many local, non-local (gradient-corrected) or hybrid (local, non-local, and HF) exchange-correlation potentials
  • Molecular electronic structure methods, analytic gradients:
  • Restricted open-shell Hartree-Fock (ROHF)
  • Unrestricted Density Functional Theory (DFT)
  • Second-order Moeller-Plesset perturbation theory (MP2), using RHF and UHF reference
  • MP2 with resolution of the identity approximation (RI-MP2)
  • Complete active space SCF (CASSCF)
  • Time-Dependent Density Functional Theory (TDDFT)
  • Molecular electronic structure methods, single-point energies:
  • MP2 spin-component scaled approach (SCS-MP2)
  • Coupled cluster singles and doubles, triples or pertubative triples (CCSD, CCSDT, CCSD(T)), with RHF and UHF reference
  • Configuration interaction (CISD, CISDT, and CISDTQ)
  • Second-order approximate coupled-cluster singles doubles (CC2)
  • State-specific multireference coupled cluster methods (MRCC) (Brillouin-Wigner (BW-MRCC) and Mukherjee (Mk-MRCC) approaches)
  • Further molecular electronic structure features:
  • Geometry optimization including transition state searches, constraints and minimum energy paths (via the Nudged Elastic Band (NEB) and Zero Temperature String methods)
  • Vibrational frequencies
  • Equation-of-motion (EOM)-CCSD, EOM-CCSDT, EOM-CCSD(T), CC2, Configuration-Interaction singles (CIS), time-dependent HF (TDHF) and TDDFT, for excited states with RHF, UHF, RDFT, or UDFT reference
  • Solvatisation using the Conductor-like screening model (COSMO) for RHF, ROHF and DFT, including analytical gradients
  • Hybrid calculations using the two- and three-layer ONIOM method
  • Relativistic effects via spin-free and spin-orbit one-electron Douglas-Kroll and zeroth-order regular approximations (ZORA) and one-electron spin-orbit effects for DFT via spin-orbit potentials
  • Pseudopotential plane-wave electronic structure:
  • Pseudopotential Plane-Wave (PSPW), Projector Augmented Wave (PAW) or band structure methods for calculating molecules, liquids, crystals, surfaces, semi-conductors or metals
  • Geometry/unit cell optimization including transition state searches
  • Vibrational frequencies
  • LDA, PBE96, and PBE0 exchange-correlation potentials (restricted and unrestricted)
  • SIC, pert-OEP, Hartree-Fock, and hybrid functionals (restricted and unrestricted)
  • Hamann, Troullier-Martins and Hartwigsen-Goedecker-Hutter norm- conserving pseudopotentials with semicore corrections
  • Wavefunction, density, electrostatic and Wannier plotting
  • Band structure and density of states generation
  • Car-Parrinello ab-initio molecular dynamics (CPMD):
  • Constant energy and constant temperature dynamics
  • Verlet algorithm for integration
  • Geometry constraints in cartesian coordinates
  • Classical molecular dynamics (MD):
  • Single configuration energy evaluation
  • Energy minimization
  • Molecular dynamics simulation
  • Free energy simulation (multistep thermodynamic perturbation (MSTP) or multiconfiguration thermodynamic integration (MCTI) methods with options of single and/or dual topologies, double wide sampling, and separation-shifted scaling)
  • Force fields providing effective pair potentials, first order polarization, self consistent polarization, smooth particle mesh Ewald (SPME), periodic boundary conditions and SHAKE constraints
  • Mixed quantum-classical:
  • Mixed quantum-mechanics and molecular-mechanics (QM/MM) minimizations and molecular dynamics simulations
  • Quantum molecular dynamics simulation by using any of the quantum mechanical methods capable of returning gradients.
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
Pakke for materialesimuleringer i nanoskala
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OpenMX (pakke udviklet i åben kildekode for Material eXplorer) er en programpakke for materialesimuleringer i nanoskala baseret på tæthedsfunktionelle teorier (DFT), norm-bevarende pseudopotentialer og pseudo-atomare oversatte basisfunktioner. Da koden er designet for realiseringen af ab initio-beregninger i stor skala på parallelle computere, så forventes det at OpenMX kan være et nyttigt og funktionsrigt værktøj for materialevidenskab i nanoskala indenfor en bred vifte af systemer såsom biomaterialer, kulstofnanorør, magnetiske materialer og konduktører i nanoskala.

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Quantum-espresso
Programpakke for elektronikstruktur og Ab-Initio molekylære dynamikker
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Quantum ESPRESSO (tidligere kendt som PWscf) er en integreret programpakke med computerkoder til elektronstrukturberegninger og materialemodellering på nanoskala. Den er baseret på tæthedsfunktionalteori med planbølger og pseudopotentialer (både normkonserverende, ultrasoft og PAW).

Funktionalitet:

  • Grundtilstands- og båndstrukturberegning ved hjælp af planbølger med selvkonsistent totalenergi, kræfter og mekanisk spænding
  • Separable normkonserverende samt Vanderbilt-pseudopotentialer (ultrasoft) og PAW-metoden (projector augmented wave method)
  • Diverse funktionaler for elektronkorrelation og -udveksling fra LDA til den generaliserede gradientapproksimation (PW91, PBE, B88-P86, BLYP), meta-GGA, eksakt udveksling (HF) og hybridfunktionaler (PBE0, B3LYP, HSE)
  • Car-Parrinello- og Born-Oppenheimer-molekylærdynamik
  • Strukturoptimering inklusive overgangstilstande og minimumsenergikurver
  • Spin-bane-kobling og ikke-kolineær magnetisme
  • Responsegenskaber inklusive fononfrekvenser og -egenvektorer, effektive ladninger og dielektriske tensorer, infrarøde og Raman- spredningstværsnit samt kemiske skift med EPR og NMR.
  • Spektroskopiske egenskaber såsom K- og L1-edge røntgenabsorptionsspektra (XAS) og elektronexcitationer
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)
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