DebiChem Project
Summary
Molecular ab initio calculations
DebiChem Molecular Ab Initio Calculations

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

Description

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If you discover a project which looks like a good candidate for DebiChem to you, or if you have prepared an unofficial Debian package, please do not hesitate to send a description of that project to the DebiChem mailing list

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DebiChem Molecular ab initio calculations packages

Official Debian packages with high relevance

Aces3
Advanced Concepts in Electronic Structure III
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ACESIII is an electronic structure calculation program with a focus on correlated methods. It is the parallel successor to ACESII, employing the Super Instruction Assembly Language (SIAL) as parallelization framework. Features include:

Energies, analytic gradients and analytic hessians for the following methods:

  • Restricted/unrestricted spin or restricted open-shell Hartree-Fock (HF)
  • Second-order Moeller-Plesset pertubation theory (MP2)

Energies and analytic gradients for the following methods:

  • Coupled cluster singles and doubles (CCSD)

Additionally, it can compute energies for the following methods:

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

Excited states can be calculated by the following methods:

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

It also includes an internal coordinate geometry optimizer. If analytic gradients are not available, numerical gradients via finite differences are used.

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
Computational Chemistry Package
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BAGEL (Brilliantly Advanced General Electronic-structure Library) is a computational chemistry package aimed at large-scale parallel computations. It specializes on highgly accurate methods and includes density-fitting and relativistic effects for most of the methods it implements.

It can compute energies and gradients for the following methods:

  • 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)

Additionally, it can compute energies for the following methods:

  • 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 dimers and for multiple sites via density matrix renormalization group (ASD-DMRG)

BAGEL is able to optimize stationary geometries and conical intersections and to compute vibrational frequencies.

BAGEL does not include a disk interface, so computations need to fit in memory.

Please cite: T. Shiozaki: BAGEL, Brilliantly Advanced General Electronic-structure Library. WIREs Comput. Mol. Sci. :e1331 (2017)
Chemps2
Executable to call libchemps2-3 from the command line
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chemps2 is a scientific library which contains a spin-adapted implementation of the density matrix renormalization group (DMRG) for ab initio quantum chemistry. This wavefunction method allows one to obtain numerical accuracy in active spaces beyond the capabilities of full configuration interaction (FCI), and allows one to extract the 2-, 3-, and 4-particle reduced density matrices (2-, 3- and 4-RDM) of the active space.

For general active spaces up to 40 electrons in 40 orbitals can be handled with DMRG, and for one-dimensional active spaces up to 100 electrons in 100 orbitals. The 2-RDM of these active spaces can also be easily extracted, while the 3- and 4-RDM are limited to about 28 orbitals.

When the active space size becomes prohibitively expensive for FCI, DMRG can be used to replace the FCI solver in the complete active space self consistent field (CASSCF) method and the corresponding complete active space second order perturbation theory (CASPT2). The corresponding methods are called DMRG-SCF and DMRG-CASPT2, respectively. For DMRG-SCF the active space 2-RDM is required, and for DMRG-CASPT2 the active space 4-RDM.

This package installs the executable which parses Hamiltonians in fcidump format, performs DMRG-SCF and DMRG-CASPT2 calculations as specified by the user.

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)

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
All-Electron Density-Functional Electronic Structure Code
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Elk is an all-electron full-potential linearised augmented-plane wave (FP-LAPW) code. By not including pseudo-potentials, Elk can provide very reliable high-precision results and works for every chemical element. Features include:

  • FP-LAPW basis with local-orbitals
  • APW radial derivative matching to arbitrary orders at muffin-tin surface (super-LAPW, etc.)
  • Arbitrary number of local-orbitals allowed (all core states can be made valence for example)
  • Total energies resolved into components
  • Forces - including incomplete basis set (IBS) and core corrections work with spin-orbit coupling, non-collinear magnetism and LDA+U
  • LSDA, GGA and (potential-only) meta-GGA functionals available
  • LDA+U: fully localised limit (FLL), around mean field (AFM) and interpolation between the two; works with SOC, NCM and spin-spirals
  • Isolated molecules or periodic systems
  • Core states treated with the radial Dirac equation
  • Spin-orbit coupling (SOC) included in second-variational scheme
  • Non-collinear magnetism (NCM) with arbitrary on-site magnetic fields
  • Fixed spin-moment calculations (with SOC and NCM)
  • Time-dependent density functional theory (TDDFT) for linear optical response calculations
  • First-order optical response
  • Non-linear optical (NLO) second harmonic generation

Elk is parallelized via hybrid OpenMP/OpenMPI.

Ergo
Quantum chemistry program for large-scale calculations
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ErgoSCF is a quantum chemistry program for large-scale self-consistent field calculations. It employs modern linear scaling techniques like fast multipole methods, hierarchic sparse matrix algebra, density matrix purification, and efficient integral screening. Linear scaling is achieved not only in terms of CPU usage but also memory utilization. It uses Gaussian basis sets.

It can compute single-point energies for the following methods:

  • Restricted and unrestricted Hartree-Fock (HF) theory
  • Restricted and unrestricted Kohn-Sham density functional theory (DFT)
  • Full Configuration-Interaction (FCI)

The following Exchange-Correlational (XC) density functionals are included:

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

Further features include:

  • Linear response calculations (polarizabilities and excitation energies) for restricted reference densities
  • External electric fields
  • Electron dynamics via Time-Dependent 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 is an ab-inito quantum chemistry program. It is especially designed to compute molecules in a highly parallelized fashion.

It can compute energies and gradients for the following methods:

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

Additionally, it can compute energies for the following methods:

  • 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)

It also includes an internal coordinate geometry optimizer.

MPQC is built upon the Scientific Computing Toolkit (SC).

Mpqc3
Massively Parallel Quantum Chemistry Program
Maintainer: Debichem Team (Adrian Bunk)
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MPQC3 is an ab-inito quantum chemistry program. It is especially designed to compute molecules in an explicitly-correlated fashion.

It can compute energies and gradients for the following methods:

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

Additionally, it can compute energies for the following methods:

  • 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 with 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)

It also includes an internal coordinate geometry optimizer.

Nwchem
High-performance computational chemistry software
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NWChem is a computational chemistry program package. It provides methods which are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters.

NWChem can handle:

  • Molecular electronic structure methods using gaussian basis functions for high-accuracy calculations of molecules
  • Pseudopotentials plane-wave electronic structure methods for calculating molecules, liquids, crystals, surfaces, semi-conductors or metals
  • Ab-initio and classical molecular dynamics simulations
  • Mixed quantum-classical simulations
  • Parallel scaling to thousands of processors

Features include:

  • 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
Quantum Chemical Program Suite
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PSI3 is an ab-initio quantum chemistry program. It is especially designed to accurately compute properties of small to medium molecules using highly correlated techniques.

It can compute energies and gradients for the following methods:

  • Closed shell and general restricted open shell Hartree-Fock (RHF/ROHF) (including analytical hessians 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)) (only for unrestricted (UHF) reference wavefunctions)

Additionally, it can compute energies for the following methods:

  • 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)

Further features include:

  • Flexible, modular and customizable input format
  • Excited state calculations with the CC2/CC3, EOM-CCSD, CASSCF, MRCI and MRCCSD methods
  • Internal coordinate geometry optimizer
  • Harmonic frequencies calculations
  • One-electron properties like dipole/quadrupole moments, natural orbitals, electrostatic potential, hyperfine coupling constants or spin density
  • Utilization of molecular point-group symmetry to increase efficiency
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Psi4
Quantum Chemical Program Suite
Versions of package psi4
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stretch1.0-1amd64,arm64,armhf,i386,mips64el,ppc64el,s390x
buster1.2.1-2amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
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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, gradients and hessians for the following methods:

  • Restricted Hartree-Fock (RHF)

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)
  • Density-fitted Moeller-Plesset perturbation theory (DF-MP2)
  • Density-fitted Orbital-Optimized MP2 theory (DF-OMP2)
  • (Orbital-Optimized) MP3 theory (OMP3/MP3)
  • Coupled-cluster singles doubles (CCSD)
  • Density-fitted coupled-cluster singles doubles (DF-CCSD) and with perturbative triples (DF-CCSD(T))
  • Second-order approximate coupled-cluster singles doubles (CC2)
  • Equation-of-motion coupled-cluster singles doubles (EOM-CCSD)

Additionally, it can compute energies for the following methods:

  • Spin-component scaled MP2 theory (SCS-MP2)
  • Fourth order Moeller-Plesset perturbation theory (MP4)
  • Density-fitted symmetry-adapted perturbation theory (DF-SAPT)
  • Density-fitted complete active space SCF (DF-CASSCF)
  • Configuration-interaction singles doubles (CISD)
  • Full configuration-interaction (FCI)
  • 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))
  • Density Matrix Renormalization Group SCF (DMRG-SCF), CASPT2 (DMRG-CASPT2) and CI (DMRG-CI)

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
  • Scalar-relativistic corrections via two-component approach (X2C)
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 202569