DebiChem Ab initio calculations packages

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.

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.

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)

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 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 matching 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
• LSDA- og GGA-funktionaler er tilgængelige
• Isolerede molekyler eller periodiske systemer
• Grundlæggende tilstande behandlet med radial Dirac-ligningen

Elk parallelliseres via OpenMP.

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)

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 pertubation 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).

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
• Complete active space SCF (CASSCF)
• Time-Dependent Density Functional Theory (TDDFT)
• Molecular electronic structure methods, single-point energies:
• MP2 with resolution of the identity integral approximation (RI-MP2) or spin-component scaled approach (SCS-MP2), using RHF and UHF reference
• 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.

OpenMX (Open source package for Material eXplorer) is a program package for nano-scale material simulations based on density functional theories (DFT), norm-conserving pseudopotentials and pseudo-atomic localized basis functions. Since the code is designed for the realization of large-scale ab initio calculations on parallel computers, it is anticipated that OpenMX can be a useful and powerful tool for nano-scale material sciences in a wide variety of systems such as biomaterials, carbon nanotubes, magnetic materials, and nanoscale conductors.

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

PSI4 is an ab-initio quantum chemistry program. It is especially designed to accurately compute properties of small to medium molecules using highly correlated techniques. PSI4 is the parallelized successor of PSI3 and includes many state-of-the-art theoretical methods.

It can compute energies and gradients for the following methods:

• Restricted, unrestricted and general restricted open shell Hartree-Fock (RHF/ROHF)
• Restricted, unrestricted and general restricted open shell Densitry-Functional Theory, including density-fitting (DF-DFT)
• Density Cumulant Functional Theory (DCFT)
• Closed-shell Density-fitted Moeller-Plesset perturbation theory (DF-MP2)
• Unrestricted Moeller-Plesset perturbation theory (MP2)
• Orbital-Optimized MP2 theory (OMP2)
• Third order Moeller-Plesset perturbation theory (MP3)
• Orbital-Optimized MP3 theory (OMP3)
• Coupled-cluster singles doubles (CCSD)
• Coupled-cluster singles doubles with perturbative triples (CCSD(T)) (only for unrestricted (UHF) reference wavefunctions)
• Equation-of-motion coupled-cluster singles doubles (EOM-CCSD)

Additionally, it can compute energies for the following methods:

• Closed/open shell Moeller-Plesset perturbation theory (MP2)
• Spin-component scaled MP2 theory (SCS-MP2)
• Fourth order Moeller-Plesset perturbation theory (MP4)
• Density-fitted symmetry-adapted perturbation theory (DF-SAPT)
• Multireference configuration-interaction (MRCI)
• Closed-shell Density-fitted coupled-cluster singles doubles (DF-CCSD)
• Closed-shell Density-fitted Coupled-cluster singles doubles with perturbative triples (DF-CCSD(T))
• Second/third-order approximate coupled-cluster singles doubles (CC2/CC3)
• Mukherjee Multireference coupled-cluster singles doubles theory (mk-MRCCSD)
• Mukherjee Multireference coupled-cluster singles doubles with perturbative triples theory (mk-MRCCSD(T))
• Second order algebraic-diagrammatic construction theory (ADC(2))
• Quadratic configuration interaction singles doubles (QCISD)
• Quadratic configuration interaction singles doubles with perturbative triples (QCISD(T))

Further features include:

• Flexible, modular and customizable input format via python
• Excited state calculations with the EOM-CC2/CC3, EOM-CCSD, ADC(2), MRCI and mk-MRCC methods
• Utilization of molecular point-group symmetry to increase efficiency
• Internal coordinate geometry optimizer
• Harmonic frequencies calculations (via finite differences)
• Potential surface scans
• Counterpoise correction
• One-electron properties like dipole/quadrupole moments, transition dipole moments, natural orbitals occupations or electrostatic potential
• Composite methods like complete basis set extrapolation or G2/G3

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