Summary
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.
Description
For a better overview of the project's availability as a Debian package, each head row has a color code according to this scheme:
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
Links to other tasks
|
DebiChem Periodic Ab Initio Calculations packages
Official Debian packages with high relevance
abinit
pacote para cálculos estruturados eletrônicos
|
Versions of package abinit |
Release | Version | Architectures |
stretch | 8.0.8-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 9.10.4-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 9.10.4-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,s390x |
bookworm | 9.6.2-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 9.2.2-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 8.8.4-2 | amd64,arm64,armhf,i386 |
jessie | 7.8.2-2 | amd64,armel,armhf,i386 |
upstream | 10.0.3 |
Debtags of package abinit: |
field | chemistry, physics |
role | program |
|
License: DFSG free
|
ABINIT é um pacote cujo programa principal permite encontrar a energia
total, densidade de carga e estrutura eletrônica de sistemas feitos de
elétrons e núcleos (moléculas e periódicos sólidos) dentro da Teoria
Funcional da Densidade (DFT - Density Functional Theory), usando
pseudopotenciais e uma base de curva plana.
ABINIT também inclui opções para otimizar a geometria de acordo com
forças e estresses DFT, ou realizar simulações de dinâmica molecular
usando essas forças, ou gerar matrizes dinâmicas, cargas efetivas Born
e tensores dielétricos. Estados de excitação podem ser computados dentro
da Teoria Funcional da Densidade Dependente do Tempo (para moléculas), ou
dentro da Teoria da Perturbação de Vários Corpos (a aproximação GW).
Adicionalmente ao código ABINIT, diferentes programas utilitários são
fornecidos.
Este pacote contém os executáveis necessários para realizar cálculos (no entanto,
pseudopotenciais não são fornecidos). Para um conjunto de pseudopotenciais, instale
* pacote 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
|
Versions of package cp2k |
Release | Version | Architectures |
buster | 6.1-2 | amd64,arm64,armhf,i386 |
jessie | 2.5.1-3 | amd64,armel,armhf,i386 |
sid | 2023.2-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,s390x |
bookworm | 2023.1-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 4.1-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bullseye | 8.1-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
upstream | 2024.1 |
|
License: DFSG free
|
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 and beyond within the projector-augmented wave method
|
Versions of package gpaw |
Release | Version | Architectures |
stretch | 1.1.0-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.5.1-1 | amd64,arm64,armhf,i386 |
bullseye | 21.1.0-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 22.8.0-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 23.9.1-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,s390x |
sid | 24.1.0-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
|
License: DFSG free
|
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.
|
|
nwchem
High-performance computational chemistry software (default MPI)
|
Versions of package nwchem |
Release | Version | Architectures |
sid | 7.2.2-2 | all |
buster | 6.8.1-5 | amd64,arm64,armhf,i386 |
bullseye | 7.0.2-1 | amd64,arm64,armhf,i386,mips64el,ppc64el,s390x |
jessie | 6.5+r26243-4 | amd64,armel,armhf,i386 |
bookworm | 7.0.2-4 | all |
trixie | 7.2.2-1 | all |
Debtags of package nwchem: |
field | chemistry |
role | program |
|
License: DFSG free
|
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.
|
|
openmx
pacote para simulação de materiais em escala nanométrica
|
Versions of package openmx |
Release | Version | Architectures |
sid | 3.8.5+dfsg1-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,s390x |
stretch | 3.7.6-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 3.7.6-1 | amd64,armel,armhf,i386 |
buster | 3.8.5+dfsg1-1 | amd64,arm64,armhf,i386 |
upstream | 3.9.9 |
Debtags of package openmx: |
field | chemistry, physics |
|
License: DFSG free
|
OpenMX (Open source package for Material eXplorer) é um pacote de programa para simulações de materiais em escala nanométrica baseadas em teorias de
densidade funcional (DFT - Density Functional Theory), pseudopotenciais de
norma conservada e funções de base localizadas pseudoatômicas. Como o código
foi projetado para a realização de cálculos em larga escala em computadores
paralelos, é esperado que o OpenMX seja uma poderosa ferramenta para as
ciências dos materiais em escala nanométrica em uma grande variedade de
sistemas como biomateriais, nanotubos de carbono, materiais magnéticos e
condutores nanométricos.
|
|
quantum-espresso
Electronic-Structure and Ab-Initio Molecular Dynamics Suite
|
Versions of package quantum-espresso |
Release | Version | Architectures |
bookworm | 6.7-2 | amd64,arm64,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 6.7-2 | amd64,arm64,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 6.0-3 | amd64,arm64,armhf,i386,mips,mipsel,ppc64el,s390x |
jessie | 5.1+dfsg-3 | amd64,armel,armhf,i386 |
buster | 6.3-4 | amd64,arm64,armhf,i386 |
bullseye | 6.7-2 | amd64,arm64,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 6.7-2 | amd64,arm64,armhf,i386,mips64el,ppc64el,s390x |
Debtags of package quantum-espresso: |
role | program |
|
License: DFSG free
|
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)
|
|
wannier90
Maximally Localized Wannier Functions - executables
|
Versions of package wannier90 |
Release | Version | Architectures |
sid | 3.1.0+ds-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 3.1.0+ds-7 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,s390x |
bookworm | 3.1.0+ds-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 3.1.0+ds-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
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)
|
|
|