Debian Science Nanoscale Physics packages

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.

ASE is an Atomic Simulation Environment written in the Python programming language with the aim of setting up, stearing, and analyzing atomic simulations. ASE is part of CAMPOS, the CAMP Open Source project.

ASE contains Python interfaces to several different electronic structure codes including Abinit, Asap, Dacapo, Elk, GPAW and SIESTA.

This package provides the executable scripts.

Avogadro は、分子および生体分子をターゲットとする分子グラフィックスおよ び分子モデリングシステムです。分子軌道や静電ポテンシャルなどの分子の物 性を可視化でき、直感的な分子ビルダーを備えています。

次のような機能があります:

• 力場に基づいた配座の自動最適化機能を備える分子モデリングツール
• 拘束や配座異性体探索を含む分子力学法ツール
• 分子軌道その他のな同値面の可視化
• 振動の可視化、振動スペクトルのプロット
• 結晶単位格子の編集

• Gaussian, GAMESS および MOLPRO 量子化学パッケージ用の 入力データの生成

• 拡張可能なプラグインアーキテクチャ、Python でのスクリプティング

Avogadro は、PDB, XYZ, CML, CIF, Molden ファイルのほか、Gaussian, GAMESS, MOLPRO などの出力ファイルも読み込むことができます。

BINoculars is a tool for data reduction and analysis of large sets of surface diffraction data that have been acquired with a two-dimensional X-ray detector. The intensity of each pixel of a two-dimensional detector is projected onto a three-dimensional grid in reciprocal-lattice coordinates using a binning algorithm. This allows for fast acquisition and processing of high-resolution data sets and results in a significant reduction of the size of the data set. The subsequent analysis then proceeds in reciprocal space. It has evolved from the specific needs of the ID03 beamline at the ESRF, but it has a modular design and can be easily adjusted and extended to work with data from other beamlines or from other measurement techniques.

Cadabra は、特に場の理論に現われる問題を解くために設計された計算機代数 システムです。テンソル多項式の単純化用に広汎な機能があります。多項間 対称性、フェルミオンおよび反交換関係にある変数、クリフォード代数や フィルツ変換、暗黙の座標依存性、複数種類の添字など、他にも多くの機能が あります。入力フォーマットは TeX のサブセットです。

CBFlib is a library of ANSI-C functions providing a simple mechanism for accessing Crystallographic Binary Files (CBF files) and Image-supporting CIF (imgCIF) files.

This package contains various utility programs.

The CIF API provides a standard C interface for reading, writing, and manipulating Crystallographic Information Files (CIFs). It is targeted in particular at CIF 2.0, but it provides support for CIF 1.1 and earlier as well.

This package contains cif_linguist, an experimental program for converting data between various versions of the CIF format.

cod-tools is a set of Perl modules and command line tools for manipulating Crystallographic Information Format (CIF) v1.1 and v2.0 files.

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).

DRAWxtl reads a basic description of the crystal structure, which includes unit-cell parameters, space group, atomic coordinates, thermal parameters or a Fourier map, and outputs a geometry object that contains polyhedra, planes, lone-pair cones, spheres or ellipsoids, bonds, iso-surface Fourier contours and the unit-cell boundary.

Four forms of graphics are produced:

• an OpenGL window for immediate viewing
• the Persistence of Vision Ray Tracer (POV-RAY) scene language for publication-quality drawings
• the Virtual Reality Modeling Language (VRML) for dissemination across the Internet
• a Postscript rendering of the OpenGL window for those who want high-quality output but do not have POV-RAY installed.

File formats DRAWxtl can read include CIF, FDAT, FullProf (pcr), GSAS, SCHAKAL, SHELX, DISCUS and WIEN2k.

The European Theoretical Spectroscopy Facility (ETSF) is a European network dedicated to providing support and services for ongoing research in academic, government and industrial laboratories.

The ETSF is divided into 7 beamlines, each of which is concerned with a specific scientific topic:

• Optics ;
• Energy Loss Spectroscopy ;
• Quantum Transport ;
• Time-resolved Spectroscopy ;
• Photo-emission Spectroscopy ;
• Vibrational Spectroscopy ;
• X-Rays Spectroscopy.

To allow the adoption of its recommendations about standardization, the ETSF proposes different libraries and tools implementing or using these specifications, as well as widely usable pieces of software.

ETSF_IO is a library of F90 routines to read/write the ETSF file format. This package contains the user tools to:

• check file conformance to the specifications;
• extract data from files;
• merge multiple files from parallel runs, as specified in the specifications.

FeynMF is a LaTeX package for easy drawing of professional-quality Feynman diagrams, illustrations that depict the fundamental interactions of subatomic particles. The diagrams may be created using either the Metafont or MetaPost programs. FeynMF lays out most diagrams satisfactorily from the structure of the graph without any need for manual intervention. Nevertheless all the power of Metafont or MetaPost is available for more obscure cases.

Note that you will need the texlive-metapost package in order to use the MetaPost-based version of FeynMF.

Finalcif is a full-featured CIF file editor to make editing and validation of CIF files easy. It collects all the information from a work folder needed in order to finalize a CIF file for publication. In any case, one can also import a valid CIF file to complete the information. In ideal cases, it takes one click to have a publication-ready file.

Essentially, one should have the corresponding CIF file for FinalCif in its original 'work' folder, which contains all other files such as SAINT list files, SADABS list file, SHELX list files, etc. that led to this CIF file.

Checking the final CIF file with the IUCr CheckCIF server is a one-click problem in FinalCif. One gets a web and PDF report or just a local PLATON CIF check for computers without internet.

FinalCif generates beautiful CIF reports in seconds for publication as MS Word files (also compatible with Openoffice etc.). The report includes tables of structure properties like R-values or atom parameters and a report text about the experiment conditions.

The button "save cif file" saves the current file under 'name'-finalcif.cif. FinalCif will never make changes to the original CIF file.

Fityk is a flexible and portable program for nonlinear fitting of analytical functions (especially peak-shaped) to data (usually experimental data). In other words, for nonlinear peak separation and analysis.

It was developed for analyzing diffraction patterns, but can be also used in other fields, since concepts and operations specific for crystallography are separated from the rest of the program.

Fityk offers various nonlinear fitting methods, subtracting background, calibrating data, easy placement of peaks and changing peak parameters, automation of common tasks with scripts, and much more. The main advantage of the program is flexibility - parameters of peaks can be arbitrarily bound to each other, eg. the width of a peak can be an independent variable, can be the same as the width of another peak or can be given by a complicated - common to all peaks - formula.

libjs-sphinxdoc is necessary for the Javascript stuff in the documentation.

Garlic is written for the investigation of membrane proteins. It may be used to visualize other proteins, as well as some geometric objects. This version of garlic recognizes PDB format version 2.1. Garlic may also be used to analyze protein sequences.

It only depends on the X libraries, no other libraries are needed.

Features include:

• The slab position and thickness are visible in a small window.
• Atomic bonds as well as atoms are treated as independent drawable objects.
• The atomic and bond colors depend on position. Five mapping modes are available (as for slab).
• Capable to display stereo image.
• Capable to display other geometric objects, like membrane.
• Atomic information is available for atom covered by the mouse pointer. No click required, just move the mouse pointer over the structure!
• Capable to load more than one structure.
• Capable to draw Ramachandran plot, helical wheel, Venn diagram, averaged hydrophobicity and hydrophobic moment plot.
• The command prompt is available at the bottom of the main window. It is able to display one error message and one command string.

A GTK+ based program for the display and manipulation of isolated molecules, periodic systems and crystalline habits. It is in development, but is nonetheless fairly functional. It has the following features:

• Support for several file types (CIF, BIOSYM, XYZ, XTL, MARVIN, and GULP)
• A simple molecular creation and manipulation tool
• A dialogue for creating starting configurations for molecular dynamics simulations
• Assorted tools for visualization (geometry information, region highlighting, etc.)
• Animation of BIOSYM files (also rendered animations, see below)

GDIS also allows you to perform the following functions through other packages:

• Model rendering (courtesy of POVRay)
• Energy minimization (courtesy of GULP)
• Morphology calculation (courtesy of cdd)
• Space group processing (courtesy of SgInfo)
• View the Periodic Table (courtesy of GPeriodic)
• Load additional filetypes, such as PDB (courtesy of Babel)

GGobi は高次元のデータを探索するためのオープンソース版可視化プログラム です。ツアーのような非常に動的かつ対話的なグラフィックを提供するだけでなく、 散乱プロット、バーグラフや並列座標プロットのような見知ったグラフィックも 提供します。プロットは対話的であり、ブラシや識別にリンクされています。

詳細は http://www.ggobi.org をご覧ください。

Ghemical is a computational chemistry software package written in C++. It has a graphical user interface and it supports both quantum- mechanics (semi-empirical) models and molecular mechanics models. Geometry optimization, molecular dynamics and a large set of visualization tools using OpenGL are currently available.

Ghemical relies on external code to provide the quantum-mechanical calculations. Semi-empirical methods MNDO, MINDO/3, AM1 and PM3 come from the MOPAC7 package (Public Domain), and are included in the package. The MPQC package is used to provide ab initio methods: the methods based on Hartree-Fock theory are currently supported with basis sets ranging from STO-3G to 6-31G**.

Gnuplot is a portable command-line driven interactive data and function plotting utility that supports lots of output formats, including drivers for many printers, (La)TeX, (x)fig, Postscript, and so on. The X11-output is packaged in gnuplot-x11.

Data files and self-defined functions can be manipulated by the internal C-like language. Can perform smoothing, spline-fitting, or nonlinear fits, and can work with complex numbers.

This metapackage is to install a full-featured gnuplot (-qt, -x11 or -nox).

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.

GPeriodic は X/GTK+ ベースの小さなプログラムで、元素の周期表を閲覧した り、各元素の詳しいデータを見たりできるようになっています。現在 118 の 元素が表示されます。

Grace is a point-and-click tool that allows the user to draw X-Y plots. This is the program formerly known as Xmgr.

A few of its features are: User defined scaling, tick marks, labels, symbols, line styles, colors, polynomial regression, splines, running averages, DFT/FFT, cross/auto-correlation, batch mode for unattended plotting, and hardcopy support for PostScript, FrameMaker and several image formats.

グラフ描画は構造を持つ情報の視覚化の問題に対し、抽象的なグラフやネットワー クの幾何学的表現を作成することで対処します。グラフ描画の自動生成には、デー タベース設計や、ソフトウェアエンジニアリング、VLSI、ネットワーク設計、その 他の領域の視覚インタフェースなどのキーテクノロジにとって重要なアプリケー ションがあります。以下の状況では特に重要なツールとなる可能性があります。

• プログラムを再構成したいときに、プログラムの型、プロシージャ、ソース ファイルの関係性をまず理解する必要がある。
• インターネットバックボーンの個々の経路だけでなくその関係性におけるボト ルネックを見つける必要がある。
• 有限ステートマシンとして表わされるプロトコルやマイクロアーキテクチャを デバッグしているとき、エラー状態がどのように発生しているかを特定する必 要がある。
• データベーススキーマ、ナレッジベース、プログラムの配布を図式化して表現 したものを閲覧したい。
• リンクされたドキュメントの集まりの概観を見たい。
• 電話や電子メールのメッセージのデータベースからパターンや共通の関心を持 つコミュニティを発見したい。

このパッケージはコマンドラインツールを含みます。

GNU Scientific Library (GSL) は数値解析用ルーチン集です。 GSLに含まれるルーチンは C を使って GSL チームにより一から書かれており、 C プログラマに現代的な API を提供しています。 また、さらに高水準な言語用にはラッパーも提供されます。

本パッケージは複数のサンプルバイナリを提供します。

URL: http://www.gnu.org/software/gsl/

Gwyddion is a modular program for Scanning Probe Microscopy (SPM) data visualization and analysis. It is primarily intended for analysis of height field data obtained by microscopy techniques like

• Atomic Force Microscopy (AFM),
• Magnetic Force Microscopy (MFM),
• Scanning Tunneling Microscopy (STM),
• Near-field Scanning Optical Microscopy (SNOM or NSOM) and others. However, it can be used for arbitrary height field and image analysis.

This package contains the main application and its modules. It also contains a GNOME (and Xfce) thumbnailer which creates previews for all file types known to Gwyddion.

BLAS (Basic Linear Algebra Subroutines: 基本線形代数サブルーチン) は、ほと んどの基本的なベクトルおよび行列の演算の効率的なルーチン集です。これらは lapack や linpack など、他の高品質な線形代数ソフトウェアの基礎として広く使 われています。これは、netlib で公開されている Fortran 77 による実装です。

本パッケージには、共有バージョンのライブラリが含まれています。

LAPACK バージョン 3.X は線形代数演算を行う総合的な FORTRAN ライブラリで、 この演算には逆行列計算、線形方程式の集合に対する最小二乗解、固有ベクトルの 解析や特異値分解などが含まれます。これは非常に総合的で高い評価を受けている パッケージで、科学技術分野で広く利用されています。

本パッケージには、共有バージョンのライブラリが含まれています。

SSM is a macromolecular coordinate superposition library, written by Eugene Krissinel of the EBI.

The library implements the SSM algorithm of protein structure comparison in three dimensions, which includes an original procedure of matching graphs built on the protein's secondary-structure elements, followed by an iterative three-dimensional alignment of protein backbone Calpha atoms.

This package contains the binaries of the libraries

MayaVi2 is a cross-platform tool for 2-D and 3-D scientific data visualization. Its features include:

• Visualization of scalar, vector and tensor data in 2 and 3 dimensions
• Easy scriptability using Python
• Easy extendability via custom sources, modules, and data filters
• Reading several file formats: VTK (legacy and XML), PLOT3D, etc.
• Saving of visualizations
• Saving rendered visualization in a variety of image formats.

MayaVi2 has been designed with scriptability and extensibility in mind. While the mayavi2 application is usable by itself, it may be used as an Envisage plugin which allows it to be embedded in user applications natively. Alternatively, it may be used as a visualization engine for any application.

This package also provides TVTK, which wraps VTK objects to provide a convenient, Pythonic API, while supporting Traits attributes and NumPy/SciPy arrays. TVTK is implemented mostly in pure Python, except for a small extension module.

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).

NCO is a suite of programs known as operators. The operators are stand-alone, command-line programs executable in a POSIX shell. Operators take one or more netCDF files as input, perform operations (e.g., averaging, hyperslabbing), and produce a netCDF output file. NCO was originally designed to manipulate and analyze climate data, though it works on any netCDF format datasets.

You would use ncview to get a quick and easy, push-button look at your NetCDF files. You can view simple movies of the data, view along various dimensions, take a look at the actual data values, change color maps, invert the data and other simple visual operations.

NetCDF ファイルを ASCII ファイルへの変換、又はその逆変換を行う ncdump および ncgen プログラムが含まれます。NetCDF (network Common Data Form) は、科学データへのアクセス用インターフェイスおよびインターフェイスの 実装を供給するフリーで配布されているソフトウェアインターフェイスです。 netCDF ライブラリは、科学データを表現するためのマシンに依存しない フォーマットも定義します。 合わせて、インターフェイス、ライブラリ、そしてフォーマットは科学データの 作成、アクセス、そして共有機能をサポートします。

NeXus is a common data format for neutron, X-ray, and muon science. It is being developed as an international standard by scientists and programmers representing major scientific facilities in Europe, Asia, Australia, and North America in order to facilitate greater cooperation in the analysis and visualization of neutron, X-ray, and muon data.

This is the package containing some applications for reading and writing NeXus files.

Octave is a (mostly MATLAB® compatible) high-level language, primarily intended for numerical computations. It provides a convenient command-line interface for solving linear and nonlinear problems numerically.

Octave can be dynamically extended with user-supplied C++ files.

The KIM API is an Application Programming Interface for atomistic simulations. The API provides a standard for exchanging information between atomistic simulation codes (molecular dynamics, molecular statics, lattice dynamics, Monte Carlo, etc.) and interatomic models (potentials or force fields). It also includes a set of library routines for using the API with bindings for:

FORTRAN 77, Fortran 90/95, Fortran 2003 C, C++

Atomistic simulation codes that support the KIM API work seamlessly with the KIM-compliant interatomic models (KIM Models) distributed on this website. The interface is computationally efficient and often requires relatively minor changes to existing codes.

This package contains models and model-drivers for KIM-API

Open MPI is a project combining technologies and resources from several other projects (FT-MPI, LA-MPI, LAM/MPI, and PACX-MPI) in order to build the best MPI library available. A completely new MPI-3.1 compliant implementation, Open MPI offers advantages for system and software vendors, application developers and computer science researchers.

Features:

• Full MPI-3.1 standards conformance
• Thread safety and concurrency
• Dynamic process spawning
• High performance on all platforms
• Reliable and fast job management
• Network and process fault tolerance
• Support network heterogeneity
• Single library supports all networks
• Run-time instrumentation
• Many job schedulers supported
• Internationalized error messages
• Component-based design, documented APIs

This package contains the Open MPI utility programs.

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.

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

The lmfit Python package provides a simple, flexible interface to non-linear optimization or curve fitting problems. The package extends the optimization capabilities of scipy.optimize by replacing floating pointing values for the variables to be optimized with Parameter objects. These Parameters can be fixed or varied, have upper and/or lower bounds placed on its value, or written as an algebraic expression of other Parameters.

The principal advantage of using Parameters instead of simple variables is that the objective function does not have to be rewritten to reflect every change of what is varied in the fit, or what relationships or constraints are placed on the Parameters. This means a scientific programmer can write a general model that encapsulates the phenomenon to be optimized, and then allow user of that model to change what is varied and fixed, what range of values is acceptable for Parameters, and what constraints are placed on the model. The ease with which the model can be changed also allows one to easily test the significance of certain Parameters in a fitting model.

The lmfit package allows a choice of several optimization methods available from scipy.optimize. The default, and by far best tested optimization method used is the Levenberg-Marquardt algorithm from MINPACK-1 as implemented in scipy.optimize.leastsq. This method is by far the most tested and best support method in lmfit, and much of this document assumes this algorithm is used unless explicitly stated. An important point for many scientific analysis is that this is only method that automatically estimates uncertainties and correlations between fitted variables from the covariance matrix calculated during the fit.

A few other optimization routines are also supported, including Nelder-Mead simplex downhill, Powell's method, COBYLA, Sequential Least Squares methods as implemented in scipy.optimize.fmin, and several others from scipy.optimize. In their native form, some of these methods setting allow upper or lower bounds on parameter variables, or adding constraints on fitted variables. By using Parameter objects, lmfit allows bounds and constraints for all of these methods, and makes it easy to swap between methods without hanging the objective function or set of Parameters.

Finally, because the approach derived from MINPACK-1 usin the covariance matrix to determine uncertainties is sometimes questioned (and sometimes rightly so), lmfit supports methods to do a brute force search of the confidence intervals and correlations for sets of parameters.

This is the Python 3 version of the package.

SciPy supplements the popular NumPy module (python-numpy package), gathering a variety of high level science and engineering modules together as a single package.

SciPy is a set of Open Source scientific and numeric tools for Python. It currently supports special functions, integration, ordinary differential equation (ODE) solvers, gradient optimization, genetic algorithms, parallel programming tools, an expression-to-C++ compiler for fast execution, and others.

SymPy is a Python library for symbolic mathematics (manipulation). It aims to become a full-featured computer algebra system (CAS) while keeping the code as simple as possible in order to be comprehensible and easily extensible. SymPy is written entirely in Python and does not require any external libraries, except optionally for plotting support.

This package contains the Python 3 version of sympy.

Pyxplot is a multi-purpose graph plotting tool, scientific scripting language, vector graphics suite, and data processing package. Its interface is designed to make common tasks -- e.g., plotting labelled graphs of data -- accessible via short, simple, intuitive commands.

Pyxplot produces publication-quality figures. To this end, text is rendered with all of the beauty and flexibility of the LaTeX typesetting environment.

Extensive documentation and examples can be found in the pyxplot-doc package. A gallery of sample plots is available from the project's web site.

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

SasView is software for the analysis of Small-Angle Scattering (SAS) data.

It fits analytic functions describing different types of material microstructure to experimental data in order to determine the shape, size and degree of ordering.

SasView also includes tools for calculating scattering length densities, slit sizes, resolution, fringe thicknesses/d-spacings, the (Porod) invariant ('total scattering'), and distance distribution functions.

SasView is a Small Angle Scattering Analysis Software Package, originally developed as part of the NSF DANSE project under the name SansView, now managed by an international collaboration of facilities.

This package installs the sasview executable script.

This metapackage will install Debian Science packages useful for numerical computation. The packages provide an array oriented calculation and visualisation system for scientific computing and data analysis. These packages are similar to commercial systems such as Matlab and IDL.

Scilab は行列ベースの科学ソフトウェアパッケージです。 Scilab には何百もの組み込み数学関数、豊富なデータ構造 (多項式、有理数、線形 系、リストなど) が含まれ、制御、信号処理など向けに特有のツールボックスが付 属します。

本パッケージは、ハイブリッドダイナミカルシステムのモデルを設計するためのグ ラフィカルなエディタ Xcos も提供します。モデルの設計、読み込み、保存、コン パイル、シミュレーションができます。 産業および学術における安定で効率の良い解を求める需要に応えるため、Xcos は機 械システム (自動車、航空など)、流体回路 (ダム、パイプのモデリングなど)、制 御システムなどのモデリングのための機能を提供します。Modelica の機能も提供し ます。

最小版の scilab を入手するには、パッケージ "scilab-cli" をインストールして ください。

A free cross-platform library of fast C++ routines for plotting data in up to 3 dimensions. It can export plots to bitmaps and vector EPS, SVG, IDTF files. There are simple window interfaces based on GLUT, FLTK and/or Qt. MathGL can also be used in the console. There are interfaces to a set of languages, such as, C, Fortran, Pascal, Forth, Python, Octave.

This package contains the udav window environment based on mathgl.

V_Sim は結晶、結晶粒界、分子などの原子構造 (バイナリ形式もしくは プレインテキスト形式のもの) を可視化できます。

描画は擬似 3D で、球 (原子) や矢印 (スピン) で表されます。ユーザは、多くの 関数を使って対話することでビューの選択、バインディングの設定、断面の描画、 スカラー場からの表面の計算、ノードの複製、形状測定、などができます。さらに、 V_Sim ではビューを画像として PNG, JPG, PDF (ビットマップ), SVG (図) や 他の形式でエクスポートできます。原子をデータの値から色付けしたり、多くの 位置ファイルを画面上でアニメーション表示したりできるいくつかのツールも 利用できます。

The analysis of macromolecular structures often requires a comprehensive definition of atomic neighborhoods. Such a definition can be based on the Voronoi diagram of balls, where each ball represents an atom of some van der Waals radius. Voronota is a software tool for finding all the vertices of the Voronoi diagram of balls. Such vertices correspond to the centers of the empty tangent spheres defined by quadruples of balls. Voronota is especially suitable for processing three-dimensional structures of biological macromolecules such as proteins and RNA.

Since version 1.2 Voronota also uses the Voronoi vertices to construct inter-atom contact surfaces and solvent accessible surfaces. Voronota provides tools to query contacts, generate contacts graphics, compare contacts and evaluate quality of protein structural models using contacts.

axiom は数学アルゴリズムの研究や開発に便利です。強く型付され、数学的に 正確な型階層を定義します。プログラミング言語と内蔵コンパイラを備えてい ます。

axiom は 1973 年から開発が続けられ、商用製品として販売されていました。 そしてフリーソフトウェアとしてリリースされました。

以下の事項を目指すべく、本ソフトウエアを拡張するための努力が行なわれて います:

 (a) より優れたインターフェイスの開発
 (b) 教育用ツールとして便利なものにする
 (c) 代数サーバプロトコルの開発
 (d) 追加された数学分野の統合
 (e) 読み書き可能なプログラミングスタイルでの代数の再構築
 (f) 論理プログラミングの統合
 (g) 校閲者の提案による Axiom Journal の開発

本パッケージには、メインプログラムバイナリおよび全ての前もってコンパイル された代数モジュールと、自動ロード可能なモジュールが含まれます。

Data Explorer は、データを可視化するためのツールおよびユーザインターフェイスからなる システムです。一般的に言って、データの可視化は三段階の処理で構成されると考えられます:

   1. データの記述およびインポート
   2. 可視化プログラムを通じたデータの処理
   3. その結果得られた画像の表示。
これは、メインパッケージです。

Data Explorer is a system of tools and user interfaces for visualizing data. In general terms the visualization of data can be considered a 3-stage process:

   1. Describing and importing data
   2. Processing the data through a visualization program
   3. Presenting the resulting image.
This is the documentation package. It includes online help and html

documentation.

本パッケージには、OpenDX Data Explorer 用のスクリプトとネットワークの サンプルが含まれます。これらは、OpenDX チュートリアルで参照されますが、 閲覧と調査のために、スタンドアロンでも使用可能です。

Hierarchical Data Format 5 (HDF5) is a file format and library for storing scientific data. HDF5 was designed and implemented to address the deficiencies of HDF4.x. It has a more powerful and flexible data model, supports files larger than 2 GB, and supports parallel I/O.

This package contains helper tools for HDF5.

Hierarchical Data Format 5 (HDF5) is a file format and library for storing scientific data. HDF5 was designed and implemented to address the deficiencies of HDF4.x. It has a more powerful and flexible data model, supports files larger than 2 GB, and supports parallel I/O.

This package contains runtime tools for HDF5.

This module provides an interface to layout and image generation of directed and undirected graphs in a variety of formats (PostScript, PNG, etc.) using the "dot", "neato", "twopi", "circo" and "fdp" programs from the GraphViz project (http://www.graphviz.org/ or http://www.research.att.com/sw/tools/graphviz/).

Maxima は、完全に記号化された計算プログラムです。フル機能で、多項式、行列、 有理関数、積分、有限群分析用 Todd-coxeter 法、グラフ、多倍長精度浮動小数点 演算の記号的操作を行えます。maxima コード用の記号的なソースレベルのデバッガ を備えています。Maxima は 1970 年代に MIT で開発された元祖 Macsyma に基づい ています。非常に信頼性が高く、高性能なガベージコレクション機能を持ち、また メモリリークを起こしません。何百もの自己テストコードが付属します。

本パッケージには、主要実行ファイルと基礎的なシステムファイルが 含まれます。

NetCDF (network Common Data Form) is an interface for scientific data access and a freely-distributed software library that provides an implementation of the interface. The netCDF library also defines a machine-independent format for representing scientific data. Together, the interface, library, and format support the creation, access, and sharing of scientific data.

This package contains documentation for the NetCDF library in a variety of formats.

Open MPI is a project combining technologies and resources from several other projects (FT-MPI, LA-MPI, LAM/MPI, and PACX-MPI) in order to build the best MPI library available. A completely new MPI-3.1 compliant implementation, Open MPI offers advantages for system and software vendors, application developers and computer science researchers.

This package contains man pages describing the Message Passing Interface standard.

PyMca is set of applications and Python libraries for analysis of X-ray fluorescence spectra.

The applications included in this package are:

• edfviewer - Display and inspection of data files in ESRF Data Format
• elementsinfo - Displays element specific X-ray data
• mca2edf - Converts files from SPEC MCA format to EDF
• peakidentifier - Displays X-ray fluorescence peaks in a given energy range
• pymcabatch - Batch fitting of spectra
• pymcapostbatch - Post-processing of batch fitting results
• pymca - Interactive data-analysis
• pymcaroitool - Region-of-interest (ROI) imaging tool

The PyMca toolkit can read data files in SPEC, ESRF data file (EDF), OMNIC, HDF5, AIFIRA and SupaVisio formats.

This are the scripts of the package.

Pygraphviz is a Python interface to the Graphviz graph layout and visualization package.

With Pygraphviz you can create, edit, read, write, and draw graphs using Python to access the Graphviz graph data structure and layout algorithms.

This package contains the Python 3 version of python-pygraphviz.

Qtiplot is a fully fledged plotting software similar to the OriginLab Origin software (See http://www.originlab.com for more information about Origin).

It can make two and three dimensional plots of publication quality, both from datasets and functions. It can do non-linear fitting and multi-peak fitting.

Some Features:

• Cross platform: works natively on Windows, Mac OS X and Linux/Unix systems
• Fully Python scriptable
• OpenGL based 3D plotting
• Publication quality plots and easy export to various image formats (EMF, EPS, PS, PDF, SVG, BMP, JPG, PNG, TIFF, etc ...)
• Easy integration with LaTeX typesetting system
• Powerful and versatile spreadsheets with column-logic calculations and easy import/export of multiple files
• One-click access to extensive built-in data analysis routines
• Advanced statistical analysis: Student's t-Test, ANOVA, chi-square test for variance, normality test (Shapiro-Wilk)
• Linear and nonlinear curve fitting with weighting and estimation of statistical errors of the fit-parameters
• Multi-peak fitting
• Image analysis tools
• Templates support: all settings for plots, tables and matrices can be saved and restored later on for a fast editing process
• Project files based on folders, a powerful project explorer with built-in drag and drop and searching facilities
• Full import of Excel workbooks and Open Document Format spreadsheets, dBase, SQLite and Microsoft Access databases

このメタパッケージは、数学に関連する Debian Science パッケージ群をインス トールします。あなたの関心次第ですが、field::mathematics という debtag や、 メタパッケージ education-mathematics にも興味があるかもしれません。

このメタパッケージは Debian Pure Blend "Debian Science" の一部で、統計学に 関連したパッケージをインストールします。このタスクはどんな科学的研究にも使 える一般的なタスクです。たくさんの R パッケージに加え、統計処理を行うのに便 利な他のツールに依存します。さらに、オプションで数学関連の全ソフトウェアを インストールできる Science Mathematics タスクを提案します。