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
package for electronic structure calculations
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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)
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
高性能計算化学ソフトウェア
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NWChem は計算化学プログラムパッケージです。大規模な計算化学の問題を 効率的に扱える点と、高性能並列スーパーコンピュータから従来型の ワークステーションクラスタまでの並列計算資源で利用可能であるという点に おいてスケーラブルな計算化学ツールとなることを目的としています。

NWChem ソフトウェアは次のような問題を解くことができます:

  • 分子についてのガウス基底を用いた高精度電子構造計算法
  • 分子、液体、結晶、表面、半導体、金属についての擬ポテンシャル平面基底 電子構造法
  • 第一原理および古典分子動力学シミュレーション
  • 量子・古典混合計算
  • 数千プロセッサまでスケールする並列計算

特徴一覧:

  • 分子電子構造法、解析的二次導関数
  • 制限・非制限ハートリーフォック法 (RHF/UHF)
  • 多数の局所・非局所 (勾配補正つき)・ハイブリッド (局所、非局所、HF) 交換相関ポテンシャルによる制限・非制限密度汎関数法 (DFT)
  • 分子電子構造法、解析的勾配
  • 制限開殻ハートリーフォック法 (ROHF)
  • 非制限密度汎関数法 (DFT)
  • 二次メラー・プレセット摂動法 (MP2)、RHF および UHF 参照波動関数
  • 恒等演算子分解近似 MP2 (MP2-RI)
  • 完全活性空間 SCF (CASSCF)
  • 時間依存密度汎関数法 (TDDFT)
  • 分子電子構造法、一点エネルギー計算
  • スピン成分スケール化 MP2 (SCS-MP2)
  • 結合クラスター一重・二重、三重および摂動展開三重励起 (CCSD, CCSDT, CCSD(T)) RHF および UHF参照波動関数
  • 配置間相互作用 (CISD, CISDT, CSISDTQ)
  • 二次近似結合クラスター一重・二重励起 (CC2)
  • 状態特異多参照結合クラスター法 (MRCC) (ブリュアン・ウィグナー法 (BW-MRCC) および Mukherjee法 (Mk-MRCC))
  • さらなる分子電子構造機能
  • 遷移状態探索、拘束付き最適化、最低エネルギー経路探索 (Nudged Elastic Band (NEB) 法もしくは零温度ストリング法による)を含む構造最適化
  • 振動周波数
  • RHF, ROHF, RDFT, UDFT を参照関数とする運動方程式 (EOM)-CCSD、 EOM-CCSDT、EOM-CCSD(T)、CC2、配置間相互作用一重励起 (CIS)、時間依存 HF (TDHF)による励起状態計算
  • 導体類似遮蔽モデル (COSMO) を用いた、RHF, ROHF, DFT による解析的勾配 を含む溶媒和計算
  • 二層・三層 ONIOM 法によるハイブリッド計算
  • スピンフリーおよびスピン軌道一電子 Douglas-Koll および零次正規近似 (ZORA) を通じた相対論効果補正と、スピン軌道ポテンシャルを使った DFT 向け一電子スピン軌道効果
  • 擬ポテンシャル平面波基底電子構造
  • 擬ポテンシャル平面波基底 (PSPW)、Projector Augmented Wave (PAW) 法 を用いた分子、液体、結晶、表面、半導体、金属に対するバンド構造法
  • 遷移状態探索を含む構造・単位胞最適化
  • 振動周波数
  • LDA, PBE96, PBE0 交換相関ポテンシャル (制限および非制限)
  • SIC、pert-OEP、ハートリーフォック、ハイブリッド汎関数 (制限および非制限)
  • Hamann, Troullier-Martis, Hartwigsen-Goedecker-Hutter 準内殻補正つき ノルム保存擬ポテンシャル
  • 波動関数、密度、静電、ワニエプロット
  • バンド構造と状態密度生成
  • カーパリネロ第一原理分子動力学法 (CPMD)
  • 定常エネルギーおよび定常温度動力学
  • ベルレ法による積分
  • デカルト座標系による構造拘束
  • 古典分子動力学法 (MD)
  • 単配置エネルギー評価
  • エネルギー最小化
  • 分子動力学シミュレーション
  • 自由エネルギーシミュレーション (多段熱力学的摂動法 (MSTP) もしくは 多配置熱力学的積分法 (MCTI)、単一および二重トポロジー、 二倍幅サンプリング、分離シフトスケーリングオプションつき)
  • 実行二体ポテンシャル、一次分極、自己無撞着分極、滑らかな粒子メッシュ エバルト法 (SPME)、周期的境界条件、SHAKE 拘束を提供する力場
  • 量子・古典混合
  • 量子・分子力学混合 (QM/MM) 最小化および分子動力学シミュレーション
  • 勾配を返せる全ての量子力学的手法を用いた量子分子動力学シミュレーション
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
電子構造および第一原理分子動力学スイート
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Quantum ESPRESSO(以前は PWscf という名前でした)は、電子構造計算および ナノスケールの材料モデリング用の一連のコンピュータコードです。密度汎関数法 および平面波基底、擬ポテンシャル(ノルム保存、ウルトラソフト、PAWの全て)に 基いています。

次のような機能があります。

  • 平面波基底を用いた基底状態一点計算によるバンド構造計算、自己無撞着 エネルギー計算、力および応力
  • 分離可能型ノルム保存擬ポテンシャルおよび(Vanderbiltの)ウルトラソフト 擬ポテンシャル、PAW (Projector Augmented Waves)
  • LDA から GGA (PW91, PBE, B88-P86, BLYP) やメタ GGA、厳密交換相互作用 (HF)、ハイブリッド汎関数 (PBE0, B3LYP, HSE) に至るまでの様々な交換相関 汎関数
  • カー・パリネロ分子動力学法およびボルン・オッペンハイマー分子動力学法
  • 遷移状態および最小エネルギーパスを含む構造最適化
  • スピン軌道相互作用および非共線的磁気構造
  • フォノン周波数および固有ベクトルや、有効電荷、誘電テンソル、赤外および ラマン散乱断面積、EPR および NMR 化学シフトなどの応答特性
  • X線吸光スペクトル (XAS) におけるK吸収端およびL1吸収端や電子励起などの スペクトル特性
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)
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