DebiChem Project
Summary
Molecular ab initio calculations
DebiChem - molekylære Ab Initio-beregninger

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

Description

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Links to other tasks

DebiChem Molecular ab initio calculations packages

Official Debian packages with high relevance

Aces3
Avancerede koncepter i Electronic Structure III
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ACESIII er et program for elektronisk stukturberegning med fokus på korrelaterede metoder. Det er den parallelle efterfølger til ACESII, der indarbejder Super Instruction Assembly Language (SIAL) som paralleliseringsrammeværktøj. Inkluderede funktioner:

Energier, analytiske gradienter og analytiske hessematricer for de følgende metoder:

  • Begrænset/ubegrænset spin eller begrænset open-shell Hartree-Fock (HF)
  • Andenrangs Moeller-Plesset perbutationsteori (MP2)

Energier og analytiske gradienter for de følgende metoder:

  • Coupled cluster singles and doubles (CCSD)

Derudover kan programmet beregne de følgende metoder:

  • Coupled cluster singles and doubles with pertubative triples (CCSD(T))
  • Quadratic configuration-interaction singles and doubles (QCISD)

Forhøjede tilstande kan beregnes med de følgende metoder:

  • Qadratic configuration interaction singles and doubles
  • Coupled cluster equation-of-motion (EOM-CC)

Programmet inkluderer også et internt optimeringsprogram for koordinatgeometri. Hvis analytiske gradienter ikke er tilgængelige, så bruges numeriske gradienter via finitte forskelle.

Please register by following this link if you are using aces3.
Please cite: V. Lotrich, N. Flocke, M. Ponton, A. Yau, A. Perera, E. Deumens and R. J. Bartlett: Parallel Implementation of Electronic Structure Energy, Gradient and Hessian Calculations. J. Chem. Phys. 128:194104 (2008)
Bagel
Beregningskemipakke
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BAGEL (Brilliantly Advanced General Electronic-structure Library) er en beregningskemipakke rettet mod parallelle beregninger i stor skala. Pakken specialiserer sig i meget præcise metoder og inkluderer tæthedstilpasning og relativistiske effekter for de fleste af metoderne den implementerer.

Pakken kan beregne energier og overgange for de følgende metoder:

  • Hartree-Fock (HF)
  • Density-Functional Theory (DFT)
  • Second-order Moeller-Plesset perturbation theory (MP2)
  • Complete active space SCF (CASSCF)
  • Complete active space second order perturbation theory (CASPT2)
  • Extended multistate CASPT2 (XMS-CASPT2)

Derudover kan der beregnes energier for de følgende metoder:

  • Configuration-interaction singles (CIS)
  • Full configuration-interaction (FCI)
  • Multi-state internally contracted multireference configuration- interaction (ic-MRCI)
  • N-electron valence-state second order perturbation theory (NEVPT2)
  • Active-space decomposition (ASD) for dimere og for flere sider via density matrix renormalization group (ASD-DMRG)

BAGEL kan optimere stationære geometrier og koniske kryds og beregne vibrationsfrekvenser.

BAGEL inkluderer ikke en diskgrænseflade, så beregninger skal passe ind i hukommelsen.

Please cite: T. Shiozaki: BAGEL, Brilliantly Advanced General Electronic-structure Library. WIREs Comput. Mol. Sci. :e1331 (2017)
Chemps2
Kørbar fil til at kalde libchemps2-3 fra kommandolinjen
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Chemps2 er et videnskabeligt bibliotek, som indeholder en spin-tilpasset implementering af »density matrix renormalization group« (DMRG) for ab initio-kvantumkemi. Denne metode giver mulighed for at opnå numerisk præcision i aktive rum udover funktionaliteten for »full configuration interaction« (FCI) og tillader udtrækning af 2-, 3- og 4-partikel reducerede tæthedsmatricer (2-, 3-, og 4-RDM) for det aktive rum.

For generelle aktive rum kan op til 40 elektroner i 40 baner håndteres med DRMG og for en-dimensional aktive rum op til 100 elektroner i 100 baner. 2-RDM'en for disse aktive rum kan også nemt udtrækkes, mens 3- og 4-RDM er begrænsede til omkring 28 baner.

Når den aktive rumstørrelse bliver uoverkommeligt dyr for FCI, kan DMRG bruges til at erstatte FCI-løseren i metoden »complete active space self consistent field« (CASSCF) og den tilsvarende »complete active space second order perturbation theory« (CASPT2). De tilsvarende metoder kaldes DMRG-SCF og DMRG-CASPT2, respektiv. For DMRG-SCF er det aktive rum 2-RDM krævet og for DMRG-CASPT2 det aktive rum 4-RDM.

Denne pakke installerer den kørbare fil, som fortolker hamiltonianere i fcidump-format, udfører DMRG-SCF- og DMRG-CASTP-beregninger som angivet af brugeren.

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).

Elk-lapw
Kun-elektron tæthed-funktionel elektronisk strukturkode
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ELK er en all-electron full-potential linearised augmented-plane wave-kode (FP-LAPW). Ved ikke at inkludere pseudopotentialer kan Elk tilbyde meget troværdige resultater med høj præcision og det fungerer for alle kemiske elementer. Inkluderede funktioner:

  • FP-LAPW-basis med »local-orbitals«
  • APW radial afledt matchning til vilkårlige rækkefølger på muffin-tin- overflade (super-LAPW osv.)
  • Vilkårligt antal af lokal-orbitale er tilladt (alle kernetilstande kan gøres valens for eksempel
  • Alle energier opløst i komponenter
  • Forces - inklusive ufuldstændige basissæt (IBS) og kernekorrektioner fungerer med spin-orbit kobling, ikke-collinear magnetisme og LDA+U
  • LSDA-, GGA- og (kun-potentielt) meta-GGA-funktionaler er tilgængelige
  • LDA+U: fuldt lokaliseret begræsning (FLL), omkring middelfelt (AFM) og interpolation mellem de to; fungerer med SOC, NCM og spin-spirals
  • Isolerede molekyler eller periodiske systemer
  • Grundlæggende tilstande behandlet med radial Dirac-ligningen
  • Spin-orbit coupling (SOC) inkluderet i »second-variational« skema
  • Non-collinear magnetism (NCM) med arbitrær on-site magnetiske felter
  • Fast spin-moment-kalkulationer (med SOC og NCM)
  • Time-dependent density functional theory (TDDFT) for lineær optisk svarkalkulationer
  • Første-orden optisk svar
  • Non-linear optical (NLO) anden harmonisk oprettelse

Elk parallelliseres via hybrid OpenMP/OpenMPI.

Ergo
Kvante-kemiprogram for beregninger i stor skala
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ErgoSCF er et kvantekemisk program for storstilet selvkonsistent feltberegninger. Den anvender moderne lineære skaleringsteknikker såsom hurtig multipole-metoder, hierarkisk sparsom matrix-algebra, tæthedsmatrix rensning, og effektiv integreret screening. Lineær skalering opnås ikke kun i form af CPU-forbrug, men også hukommelsesudnyttelse. Der bruges gaussiske basissæt.

Programmet kan beregne enkeltpunkt-energier for de følgende metoder:

  • Begrænset og ubegrænset Hartree-Fock-teori (HF)
  • Begrænset og ubegrænset Kohn-Sham-tæthedsfunktionelteori (DFT)
  • Fuld konfiguration-interaktion (FCI)

De følgende Exchange-Correlational (XC) tæthedsfunktionaler er inkluderet:

  • Local Density Approximation (LDA)
  • Gradient-corrected (GGA) XC-funktionaler BLYP, BP86, PW91 og PBE
  • Hybrid XC-functionaler B3LYP, BHandHLYP, PBE0 og CAMB3LYP

Yderligere funktioner inkluderer:

  • Lineære responsberegninger (polarizabilities- og excitation-energier) for begrænsede referencetæthed
  • Eksterne elektriske felter
  • Elektron dynamik via tidsafhængig Hartree-Fock (TDHF)
Please cite: Elias Rudberg, Emanuel H. Rubensson and Pawel Salek: Kohn-Sham density functional theory electronic structure calculations with linearly scaling computational time and memory usage. J. Chem. Theory Comput. 7(2):340-350 (2011)
Mpqc
Massively Parallel Quantum Chemistry Program
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MPQC er et ab-inito kvantum kemiprogram. Det er specielt designet til at beregne molekyler på en meget paralleliseret måde.

Programmet kan beregne energier og gradienter for de følgende metoder:

  • Closed shell and general restricted open shell Hartree-Fock (HF)
  • Density Functional Theory (DFT)
  • Closed shell second-order Moeller-Plesset perturbation theory (MP2)

Derudover kan programmet beregne energier for de følgende metoder:

  • Open shell MP2 and closed shell explicitly correlated MP2 theory (MP2-R12)
  • Second order open shell pertubation theory (OPT2[2])
  • Z-averaged pertubation theory (ZAPT2)

Programmet inkluderer også et internt optimiseringsprogram for koordinatgeometri.

MPQC er bygget oven på Scientific Computing Toolkit (SC).

Mpqc3
Massively Parallel Quantum Chemistry Program
Maintainer: Debichem Team (Adrian Bunk)
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MPQC3 er et ab-inito kvantekemi program. Det er specielt designet til at beregne molekyler på en eksplicit korreleret måde.

Det kan beregne energier og gradienter for de følgende metoder:

  • Hartree-Fock (HF)
  • Density Functional Theory (DFT)
  • Second-order Moeller-Plesset pertubation theory (MP2)

Derudover kan det beregne energier for de følgende metoder:

  • Local MP2 (LMP2)
  • Explicitly-correlated density-fitted MP2 (DF-MP2-F12)
  • Explicitly-correlated density-fitted coupled-cluster singles doubles (DF-CCSD-F12)
  • Explicitly-correlated density-fitted coupled-cluster singles doubles med perturbative triples (DF-CCSD(T)-F12)
  • Explicitly-correlated density-fitted complete active space SCF (DF-CASSCF-F12)
  • Explicitly-correlated density-fitted multi-reference configuration interaction (DF-MRCI-F12)

Programmet inkluderer også et internt optimiseringsprogram for koordinatgeometri.

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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Psi3
Kvantum kemisk programpakke
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stretch3.4.0-6amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bullseye3.4.0-6amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid3.4.0-6amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
squeeze3.4.0-2amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
wheezy3.4.0-4amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
jessie3.4.0-5amd64,armel,armhf,i386
buster3.4.0-6amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
Debtags of package psi3:
fieldchemistry, physics
interfacecommandline
roleprogram
sciencecalculation
scopesuite
usecalculating
Popcon: 13 users (4 upd.)*
Versions and Archs
License: DFSG free
Svn

PSI3 er et ab-initio quantum chemistry program. Det er specielt designet til præcist at beregne egenskaber for små til mellemstørrelse molekyler, med brug af højt korrelerede teknikker.

Programmet kan beregne energier og overgange for de følgende metoder:

  • Closed shell and general restricted open shell Hartree-Fock (RHF/ROHF) (inklusive analytiske hessianer for RHF)
  • Closed shell Moeller-Plesset pertubation theory (MP2)
  • Complete active space SCF (CASSCF)
  • Coupled-cluster singles doubles (CCSD)
  • Coupled-cluster singles doubles with pertubative triples (CCSD(T)) (kun for ubegrænsede (UHF) reference-wavefunktioner)

Derudover kan programmet beregne energier for de følgende metoder:

  • Unrestricted open shell Hartree-Fock (UHF)
  • Closed/open shell Moeller-Plesset pertubation theory (MP2)
  • Closed shell explicitly correlated MP2 theory (MP2-R12) and spin- component scaled MP2 theory (SCS-MP2)
  • Multireference configuration-interaction (MRCI)
  • Coupled-cluster singles doubles with pertubative triples (CCSD(T))
  • Second/third-order approximate coupled-cluster singles doubles (CC2/CC3)
  • Multireference coupled-cluster singles doubles (MRCCSD)
  • Closed shell and general restricted open shell equation-of-motion coupled-cluster singles doubles (EOM-CCSD)

Yderligere funktioner inkluderer:

  • Fleksibelt, modulært og tilpasningsparat inddataformat
  • Spændte tilstandsberegninger med CC2/CC3-, EOM-CCSD-, CASSCF-, MRCI- og MRCCSD-metoderne
  • Internal coordinate geometry optimizer
  • Harmonic frequencies calculations
  • One-electron properties like dipole/quadrupole moments, natural orbitals, electrostatic potential, hyperfine coupling constants or spin density
  • Udnyttelse af molekylær point-group-symmetri for at øge effektivitet
Screenshots of package psi3
Psi4
Kvantum kemisk programpakke
Versions of package psi4
ReleaseVersionArchitectures
bullseye1.3.2-3amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
buster1.2.1-2amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
stretch1.0-1amd64,arm64,armhf,i386,mips64el,ppc64el,s390x
jessie4.0~beta5+dfsg-2amd64,armel,armhf,i386
sid1.3.2-3amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
Popcon: 7 users (1 upd.)*
Versions and Archs
License: DFSG free
Git

PSI4 er et ab-initio kvantekemiprogram. Det er specielt designet til nøjagtigt at beregne egenskaber for små til mellemstore molekyler ved hjælp af højt korrelerede teknikker. PSI4 er den parallelle efterfølger til PSI3 og indeholder mange moderne teoretiske metoder.

Please cite: Robert M. Parrish, Lori A. Burns, Daniel G. A. Smith, Andrew C. Simmonett, A. Eugene DePrince, Edward G. Hohenstein, Uğur Bozkaya, Alexander Yu. Sokolov, Roberto Di Remigio, Ryan M. Richard, Jérôme F. Gonthier, Andrew M. James, Harley R. McAlexander, Ashutosh Kumar, Masaaki Saitow, Xiao Wang, Benjamin P. Pritchard, Prakash Verma, Henry F. Schaefer, Konrad Patkowski, Rollin A. King, Edward F. Valeev, Francesco A. Evangelista, Justin M. Turney, T. Daniel Crawford and C. David Sherrill: Psi4 1.1: An Open-Source Electronic Structure Program Emphasizing Automation, Advanced Libraries, and Interoperability. (eprint) J. Chem. Theory Comput. 13(7):3185-3197 (2017)
*Popularitycontest results: number of people who use this package regularly (number of people who upgraded this package recently) out of 199698