DebiChem Project
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.


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DebiChem Periodic Ab Initio Calculations packages

Official Debian packages with high relevance

package for electronic structure calculations
Versions of package abinit
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fieldchemistry, physics
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ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave basis.

ABINIT also includes options to optimize the geometry according to the DFT forces and stresses, or to perform molecular dynamics simulations using these forces, or to generate dynamical matrices, Born effective charges, and dielectric tensors. Excited states can be computed within the Time-Dependent Density Functional Theory (for molecules), or within Many-Body Perturbation Theory (the GW approximation). In addition to the main ABINIT code, different utility programs are provided.

This package contains the executables needed to perform calculations (however, pseudopotentials are not supplied). For a set of pseudopotentials, install the abinit-data package.

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)
Ab Initio Molecular Dynamics
Versions of package cp2k
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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).

DFT and beyond within the projector-augmented wave method
Versions of package gpaw
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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)
High-performance computational chemistry software (default MPI)
Versions of package nwchem
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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.

This package provides example input scripts and depends on nwchem built for the default MPI implementation for the architecture.

The default MPI is openmpi for most debian systems. OpenMPI has known problems running nwchem over multiple nodes. If you need to compute large molecules using cluster computation, you may want to use the MPICH build provided by nwchem-mpich instead.

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)
Screenshots of package nwchem
package for nano-scale material simulations
Versions of package openmx
Debtags of package openmx:
fieldchemistry, physics
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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.

Screenshots of package openmx
Electronic-Structure and Ab-Initio Molecular Dynamics Suite
Versions of package quantum-espresso
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Quantum ESPRESSO (formerly known as PWscf) is an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving, ultrasoft, and PAW).

Features include:

  • Ground-state single-point and band structure calculations using plane-wave self-consistent total energies, forces and stresses
  • Separable norm-conserving and ultrasoft (Vanderbilt) pseudo-potentials, PAW (Projector Augmented Waves)
  • Various exchange-correlation functionals, from LDA to generalized-gradient corrections (PW91, PBE, B88-P86, BLYP) to meta-GGA, exact exchange (HF) and hybrid functionals (PBE0, B3LYP, HSE)
  • Car-Parrinello and Born-Oppenheimer Molecular Dynamics
  • Structural Optimization including transition states and minimum energy paths
  • Spin-orbit coupling and noncollinear magnetism
  • Response properties including phonon frequencies and eigenvectors, effective charges and dielectric tensors, Infrared and Raman cross-sections, EPR and NMR chemical shifts
  • Spectroscopic properties like K- and L1-edge X-ray Absorption Spectra (XAS) and electronic excitations
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)
Maximally Localized Wannier Functions - executables
Versions of package wannier90
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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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