DebiChem Project
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

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DebiChem Periodic Ab Initio Calculations packages

Official Debian packages with high relevance

abinit
전자 구조 계산을 위한 패키지
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ABINIT는 메인 프로그램이 퍼텐션의 슈우도 및 평면파 기저를 사용해서 밀도 함 수 이론 (Density Functional Theory (DFT))내에서 전자와 핵 (분자 및 주기적 고체)으로 구성된 시스템의 전체 에너지, 전하 밀도, 전자 구조를 찾을 수 있게 해주는 패키지입니다.

ABINIT는 또한 DFT 힘과 압력에 따라 지오메트리를 최적화하거나, 또는 이러한 힘들을 사용하여 분자동역학적 모의실험을 수행하거나, 또는 동적 매트릭스, Born 유효 전하, 및 유전체 텐서를 생성하는 옵션을 포함합니다. 여기 상태는 시간 종 속 밀도 함수 이론 (또는 분자) 또는 다체 섭동론 (GW 근사법)내에서 계산될 수 있습니다. 주요 ABINIT 코드외에도 여러 유틸리티 프로그램이 제공됩니다.

이 패키지는 계산 수행에 필요한 실행 파일들을 포함합니다 (단, 퍼텐션의 슈우 도는 제공되지 않습니다). 퍼텐션의 슈우도 세트를 위해 abinit-data 패키지를 설치하십시오.

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
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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).

gpaw
DFT and beyond within the projector-augmented wave method
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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)
nwchem
??? missing short description for package nwchem :-(
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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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openmx
package for nano-scale material simulations
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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.

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quantum-espresso
전자 구조 및 Ab-Initio Molecular Dynamics Suite
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Quantum ESPRESSO (이전에는 PWscf로 알려져 있음)은 나노스케일에서 전자 구조 계산 및 재료 모델링을 위한 통합 컴퓨터 코드 모음입니다. 밀도 함수 이론, 평면파, 의사 전위 (표준 보존, 울트라소프트, PAW 모두)를 기반으로 합니다

기능은 아래와 같습니다:

  • 평면파 자체 일관된 총 에너지, 힘 및 응력을 사용해서 지상 상태 단일 지점 및 대역 구조 계산
  • 분리가능한 표준 보존 및 울트라소프트 (밴더빌드) 의사 전위, PAW (Projector Augmented Waves)
  • LDA 부터 일반화 기울기 보정 (PW91, PBE, B88-P86, BLYP), meta-GGA, 정확한 교환 (HF) 및 하이브리드 기능 (PBE0, B3LYP, HSE)
  • Car-Parrinello 및 Born-Oppenheimer 분자 역학
  • 전환 상태 및 최소 에너지 경로를 포함한 구조 최적화
  • 스핀 궤도 결합 및 비공선 자기
  • 포논 주파수 및 고유 벡터, 유효 전하 및 유전체 텐서, 적외선 및 라만 단면, EPR 및 NMR 화학적 이동을 포함한 응답 특성
  • K- 및 L1-에지 X-ray 흡수 스펙트럼 (XAS) 및 전자 여기와 같은 분광 특성
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
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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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