Debian Science Nanoscale Physics packages

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.

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.

Avogadro는 분자 및 생체분자를 대상으로 하는 분자 그래픽 및 모델링 시스템입 니다. 분자 궤도 및 정전기 전위와 같은 특성을 시각화할 수 있으며 직관적인 분 자 빌더를 특징으로 합니다.

특징은 아래와 같습니다:

• 자동 force-field 기반에 지오메트리 최적화 기능을 갖춘 분자 모델러
• 제약 조건 및 이형태체 검색을 포함하는 분자 역학
• 분자 궤도 및 일반 등밀도면 시각화
• 진동의 시각화 및 진동 스펙트럼 플로팅
• 결정학상의 단위 세포 지원
• Gaussian, GAMESS 및 MOLPRO 양자 화학 패키지를 위한 입력 생성
• 유연한 플러그인 아키텍쳐 및 파이썬 스크립팅

Avogadro가 읽을 수 있는 파일 형식은 PDB, XYZ, CML, CIF, Molden 및 Gaussian, GAMESS, MOLPRO 출력입니다.

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.

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).

DRAWxtl은 단위 셀 파라미터, 공간 그룹, 원자 좌표, 온도 매개 변수 또는 푸리 에 맵을 포함하는 크리스탈 구조의 기본적인 설명을 읽고, 다면체, 평면, 고립 전자쌍 콘, 구 또는 타원체, 결합, iso-surface 푸리에 윤곽, 및 단위 셀 경계를 포함하는 기하학적 객체를 출력합니다.

네개의 그래픽 형식을 만듭니다:

• 바로 볼 수 있는 OpenGL 윈도우
• 출판물 품질의 그림을 위한 비전 레이 추적기의 지속성 (Persistence of Vision Ray Tracer/POV-RAY) 장면 언어
• 인터넷을 통해 제공되는 가상 현실 모델링 언어 (Virtual Reality Modeling Language/VRML)
• 고품질 출력을 원하지만 POV-RAY는 설치되지 않은 사람들을 위한 OpenGL 윈도우의 포스트스크립트 랜더링.

파일 형식 DRAWxtl은 CIF, FDAT, FullProf (pcr), GSAS, SCHAKAL, SHELX, DISCUS, WIEN2k들을 읽을 수 있습니다.

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.

FeynMF는 전문가급의 파인먼 다이어그램과 원자 입자의 근본적 상호작용을 묘사하는 그림을 쉽게 그릴수 있도록 하는 LaTeX 패키지입니다. 다이어그램은 메타폰트 또는 메타포스트 프로그램중 어느 것을 사용해도 만들 수 있습니다. FeynMF은 수동 개입할 필요없이 그래프의 구조에서 만족스런 대부분의 다이어그램을 배치합니다. 그럼에도 불구하고 메타글꼴 또는 메타포스트의 기능 모두는 더 애매한 경우에 사용할 수 있습니다.

FeynMF의 메타포스트 기반의 버젼을 사용하기 위해서는 texlive-metapos 패키지가 필요할 것임을 기억하십시요.

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.

분리된 분자, 주기 시스템 및 결정 습관을 표시하고 조작하기 위한 GTK+ 기반 프로그램. 개발 중이지만 그럼에도 상당한 기능을 가지고 있습니다. 아래와 같은 기능을 포함합니다:

• 여러 파일 형식 지원 (CIF, BIOSYM, XYZ, XTL, MARVIN, GULP)
• 간단한 분자 생성 및 조작 도구
• 분자 역학 시뮬레이션을 위해 시작 구성을 생성하는 대화 상자
• 시각화를 위한 다양한 도구 (기하학적 정보, 영역 강조 표시등)
• BIOSYM 파일 애니메이션 (렌더링된 애니메이션도 있음, 아래 참조)

GDIS를 사용하면 다른 패키지들을 통해 다음 기능을 수행할 수 있습니다:

• 모델 렌더링 (POVRay 제공)
• 에너지 최소화 (GULP 제공)
• 형태 계산 (cdd 제공)
• 공간 그룹 처리 (SgInfo 제공)
• 주기율표 보기 (GPeriodic 제공)
• PDB와 같은, 추가 파일 시스템 로드 (Babel 제공)

GGobi는 고차원 데이타 탐색을 위한 오픈소스 시각화 프로그램입니다. 산포도, 막대그래프, 평행좌표 그림과 같은 익숙한 그래픽뿐만 아니라 투어같은 매우 동 적이며 인터렉티브한 그래픽을 제공합니다. 그림은 인터렉티브하며 브러싱 및 증 명서와 연결됩니다.

자세한 정보는 아래 주소에서 확인할 수 있습니다. http://www.ggobi.org

Ghemical은 C++로 작성된 계산 화학 소프트웨어 패키지입니다. Ghemical은 그래 피컬 사용자 인터페이스를 가지고 있으며, 양자 역학 (반경험적) 모델과 분자 역 학 모델 양쪽을 모두 지원합니다. 구조 최적화, 분자 동력학 그리고 OpenGL을 사 용하는 여러가지 시각화 도구등이 현재 사용할 수 있습니다.

Ghemical은 양자 역학 계산을 제공하는 외부 코드에 의존합니다. 반경험적 방법 MNDO, MINDO/3, AM1 그리고 PM3은 MoPAC7 (퍼블릭 도메인)패키지에서 가져왔으 며, 이 패키지에 포함되어 있습니다. MPQC 패키지는 순이론 방법을 제공하기 위 해서 사용되고 있습니다: Hartree-Fock 이론에 근거한 이 방법은 현재 STO-3G 에 서 6-31G** 까지 범위를 기본 세트로 함께 지원됩니다.

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.

GPeriodic은 화학 원소의 주기율표를 통해 검색하고, 각 요소의 자세한 정보를 볼 수 있도록 하는 작은 X/GTK+ 기반 프로그램입니다. 118 요소는 현재 리스트되어 있습니다.

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.

Graph drawing addresses the problem of visualizing structural information by constructing geometric representations of abstract graphs and networks. Automatic generation of graph drawings has important applications in key technologies such as database design, software engineering, VLSI and network design and visual interfaces in other domains. Situations where these tools might be particularly useful include:

• you would like to restructure a program and first need to understand the relationships between its types, procedures, and source files
• you need to find the bottlenecks in an Internet backbone - not only individual links, but their relationships
• you're debugging a protocol or microarchitecture represented as a finite state machine and need to figure out how a certain error state arises
• you would like to browse a database schema, knowledge base, or distributed program represented graphically
• you would like to see an overview of a collection of linked documents
• you would like to discover patterns and communities of interest in a database of telephone calls or e-mail messages

This package contains the command-line tools.

The GNU Scientific Library (GSL) is a collection of routines for numerical analysis. The routines are written from scratch by the GSL team in C, and present a modern API for C programmers, while allowing wrappers to be written for very high level languages.

This package provides several example binaries.

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 (기본 선형 대수 서브루틴)은 대부분의 기본적인 벡터와 매트릭스 작업을 위한 효율적인 루틴의 집합입니다. 이 루틴들은 lapack 과 linpack 같은 다른 고 품질 선형 대수 소프트웨어를 위한 기초로 널리 사용됩니다. 이 구현은 netlib에 서 발견된 포트란 77 참조 구현입니다.

이 패키지는 라이브러리의 공유 버전을 포함합니다.

The GNU Scientific Library (GSL) is a collection of routines for numerical analysis. The routines are written from scratch by the GSL team in C, and present a modern API for C programmers, while allowing wrappers to be written for very high level languages.

GSL includes data types and routines for complex numbers, vectors, matrices, basic linear algebra subroutines (BLAS), eigensystems, simulated annealing, minimization, root finding, pseudo-random numbers, least-squares fitting, fast Fourier transforms (FFT), differential equations, quadrature, Monte Carlo integration, special functions, physical constants, and much more.

This package provides the shared libraries required to run programs compiled with GNU GSL. To compile your own programs you also need to install libgsl0-dev.

LAPACK 벼전 3.x는 매트릭스 반전, 방정식의 선형 세트에 대한 최소 제곱 솔루 션, 고유 벡터 분석, 특이 값 분해등을 포함하는, 선형 대수 연산을 수행하는 포 괄적인 포트란 라이브러리 입니다. 이 라이브러리는 과학계에서 광범위한 사용을 찾을 수 있는 매우 포괄적이고 신뢰할 수 있는 패키지입니다.

이 패키지는 라이브러리의 공유 버전을 포함합니다.

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.

MPICH is a high-performance and widely portable implementation of the MPI-3.1 standard from the Argonne National Laboratory. It efficiently supports different computation and communication platforms including commodity clusters, SMPs, massively parallel systems, and high-speed networks. This release has all MPI 3.1 functions and features required by the standard with the exception of support for the "external32" portable I/O format and user-defined data representations for I/O.

This package includes the program binaries necessary to run MPICH programs.

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.

Contains the programs ncdump and ncgen which convert NetCDF files to ASCII and back, respectively. 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.

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.

PSI3은 제1원리 계산 프로그램입니다. 이 프로그램은 특히 고도로 연관된 기술을 사용하여 중간 분자에 대한 작은 성질을 정밀하게 계산하도록 설계되었습니다.

이 프로그램은 다음과 같은 방법을 위해 에너지와 변화도를 계산할 수 있습니다:

• 닫힌 쉘과 일반적으로 제한된 열린 쉘 하트리-폭 (RHF/ROHF) (RHF에 대한 분석 헤센 포함)
• 폐각 Moeller-Plesset pertubation 이론 (MP2)
• 완전한 활동 공간 SCF (CASSCF)
• Coupled-cluster singles doubles (CCSD)
• Coupled-cluster singles doubles with pertubative triples (CCSD(T)) (오직 제한되지 않는 (UHF) 참조 파동 함수를 위해)

추가로, 이 프로그램은 다음과 같은 방법을 위해 에너지를 계산할 수 있습니다:

• 무제한 열린 쉘 하트리-폭 (UHF)
• 닫힌/열린 쉘 Moeller-Plesset의 pertubation 이론 (MP2)
• 폐각 명시적 상관 관계 MP2 이론 (MP2-R12) 및 스핀 구성 요소 확장 MP2 이론 (SCS-MP2)
• 다중 참조 구성 상호 작용 (MRCI)
• Coupled-cluster singles doubles with pertubative triples (CCSD(T))
• 2/3차 근사 coupled-cluster singles doubles (CC2/CC3)
• 다중 참조 coupled-cluster singles doubles (MRCCSD)
• 닫힌 쉘과 일반적으로 제한된 열린 쉘 운동 방정식 coupled-cluster singles doubles (EOM-CCSD)

추가적인 기능으로 다음을 포함합니다:

• 유연하고, 모듈형이며 그리고 사용자 정의가 가능한 입력 형식
• CC2/CC3, EOM-CCSD, CASSCF and MRCI 및 MRCCSD 방법을 통한 흥분 상태 계산
• 내부 좌표 기하학 최적화
• 고주파 주파수 계산
• 쌍극자 / 사극자 능률, 자연 궤도, 정전기 전위, 미세 커플링 상수 또는 스핀 밀도와 같은 1 전자 특성
• 효율성을 높이기 위한 분자 포인트 그룹 대칭의 활용

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 (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

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.

이 메타패키지는 수치 계산에 유용한 Debian Science 패키지를 설치할 것입니다. 패키지는 과학 계산 및 데이타 분석을 위한 배열 지향 계산 및 시각화 시스템을 제공합니다. 이 패키지들은 Matlab 및 IDL같은 상용 시스템과 매우 유사합니다.

Scilab은 매트릭스 기반의 과학 소프트웨어 패키지입니다. Scilab은 수백의 내장 수학 함수, 다양한 데이타 구조(다항식, 유리수, 선형 시스템, 배열, 등등...)를 포함하며 그리고 제어, 신호 처리, 등등을 위한 다수의 특정 툴박스가 부속합니다.

이 패키지는 또한 하이브리드 동적 시스템 모델을 설계할 수 있는 그래픽 편집기 인, Xcos를 제공합니다. 모델을 설계, 로드, 저장, 컴파일 및 시뮬레이트 할 수 있습니다. 기업과 학교의 요구에 대한 안정적이고 효과적인 솔루션, Xcos는 기계 시스템(자동차, 항공기..), 유압 회로(댐, 파이프 모델링...), 제어 시스템등의 모델링 기능을 제공합니다.

Scilab의 최소 사양을 원한다면, "scilab-cli" 패키지를 설치하십시요.

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_Sim은 결정, 입자 경계, 분자등과 같은 원자 구조를 시각화합니다 (이진 형식 또는 일반 텍스트 형식).

렌더링은 구 (원자) 또는 화살표 (회전)를 사용하여 의사 3D로 수행됩니다. 사용자는 보기 선택, 바인딩 설정, 절단면 그리기, 스칼라 필드에서 표면 계산, 노드 복제, 형상 측정과 같은 여러 기능을 통해 상호작용 할 수 있습니다. 또한 V_Sim은 뷰를 PNG, JPG, PDF (bitmap), SVG (스키마) 및 기타형식의 이미지로 내보낼 수 있습니다. 몇몇 도구들은 데이타 값에서 원자를 색상화 하거나 또는 화면상에 많은 위치 파일을 애니메이션화하는데 사용할 수 도 있습니다.

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 is useful for research and development of mathematical algorithms. It defines a strongly typed, mathematically correct type hierarchy. It has a programming language and a built-in compiler.

Axiom has been in development since 1973 and was sold as a commercial product. It has been released as free software.

Efforts are underway to extend this software to (a) develop a better user interface (b) make it useful as a teaching tool (c) develop an algebra server protocol (d) integrate additional mathematics (e) rebuild the algebra in a literate programming style (f) integrate logic programming (g) develop an Axiom Journal with refereed submissions.

This package contains the main program binary and all precompiled algebra and autoloadable modules.

데이터 익스플로러는 데이터를 시각화하는 도구이자 사용자 인터페이스 시스템입니다. 일반적으로 데이터 시각화는 3단계 과정으로 생각할 수 있습니다.

   1. 데이터를 기설하고 들여오기
   2. 시각화 프로그램을 통해 데이터 처리하기
   3. 결과 이미지를 보여주기
이것은 주 패키지입니다.

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.

이 패키지는 OpenDX Data Explorer를 위한 스크립트와 네트워크의 예제가 들어 있습니다. 그것은 OpenDX 지침서에서 참조되어집니다, 그러나 검색과 조사를 위해 독립적으로 사용할 수도 있습니다.

Provides some applications codes(source and executables) such as laplacian with cG and dG methods, stokes, heat transfer, solid mechanics(static and dynamic).

Feel++ is a versatile finite element library to solve partial differential equations

Support 1D, 2D, 3D

Support the following basic entities: simplices (segment, triangle, tetrahedron) and product of simplices (quadrangle, hexahedron)

Support various point sets on these basic entities: equispaced points, quadrature points, interpolation points (Gauss-Lobatto, Fekete, WarpBlend?)

Support continuous and discontinuous Galerkin methods

Support various polynomial sets:

• Lagrange(continuous,discontinuous,all dimensions,all interpolation point sets)

• Dubiner(discontinuous), boundary adapted(continuous)

• Legendre(discontinuous), boundary adapted(continuous)

Provide mathematical concept for higher order abstraction (Function spaces and associated elements, forms and operators)

Provide a language embedded in C++ for variational formulations, projection and numerical integration

Gpiv is a Graphic User Interface program using the GTK/GNOME libraries for Particle Image Velocimetry (PIV). The program gives a quick overview of the parameter settings of the processes and allows to change them easy, running the processes, individually or in a chain, visualizes and displays the results. The processes that may be invoked by Gpiv are:

Image processing: typical image manipulations that might be needed for PIV interrogation.

Image interrogation, resulting into estimators of particle image displacements.

Data validation to test on outliers, peak-locking effect and velocity gradients over the interrogation area's.

Data post-processing: data manipulation, spatial and time scaling to obtain a velocity field from the PIV data, calculation of spatial averages, vorticity and strain.

A collection of programs for images that are generated during a Particle Image Velocimetry (PIV) experiment. This is a technique to obtain the velocity field of a fluid flow quantitatively and is performed by tracking tracer particles that have been seeded to a fluid. The technique is also applied for observing deformations at surfaces of (solid) bodies. The package contains:

• an image processing program for typical filtering and manipulation routines that may be convenient for PIV.
• an image interrogation program resulting into estimators of particle image displacements.
• validation programs to test on outliers, peak-locking effect and velocity gradients.
• post-processing programs for data manipulation (flipping, rotation etc), spatial and time scaling, calculation of spatial averages and derivative quantities from the PIV data, like vorticity and strain.
• miscellaneous programs and scripts to perform image format conversion, batch-processing, pipeline processing (image evaluation, validation and post-processing at once), calculation of time averages from a series of PIV data sets, data-visualization and data-manipulation.

All programs start with gpiv_.

This package contains all files used by gpivtools and gpivtools-mpi, like the man pages.

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/).

Maxima는 완전한 심볼 계산 프로그램입니다. 다항식, 행렬, 유리 함수, 적분, 유 한 그룹 분석을 위한 Todd-coxeter 방법, 그래프, 다중 정밀도 부동 소수점 계산 에 대한 완전한 심볼 처리 기능을 제공합니다. maxima 코드를 위한 심볼 소스 레 벨 디버거가 있습니다. Maxima는 1970년대 MIT에서 개발된 Macsyma를 기반으로 합니다. 높은 신뢰성이 있으며, 성능 좋은 가비지 컬렉션을 가지고 있고, 그리고 메모리 누수도 없습니다. 수백가지의 자체 테스트들이 제공됩니다.

이 패키지는 주요 실행 파일과 기본 시스템 파일을 포함합니다.

MPICH is a high-performance and widely portable implementation of the MPI-3.1 standard from the Argonne National Laboratory. It efficiently supports different computation and communication platforms including commodity clusters, SMPs, massively parallel systems, and high-speed networks. This release has all MPI 3.1 functions and features required by the standard with the exception of support for the "external32" portable I/O format and user-defined data representations for I/O.

This package includes the MPICH documentation.

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.

Qtiplot는 OriginLab Origin 소프트웨어와 유사한 완벽한 플로팅 소프트웨어입니 다 (Origin에 대한 자세한 내용은 http://www.originlab.com 을 참조하십시요).

데이타 세트와 함수 양쪽 모두에 있어서 출판 품질의 2,3차원 플롯을 만들 수 있 습니다. 비선형 피팅 및 다중 피크 피팅을 할 수 있습니다.

일부 기능들:

• 크로스 플랫폼: Windows, Mac OS X, 리눅스/유닉스 시스템을 기본적으로 지원합니다.
• Python 스크립트 완벽 지원
• OpenGL 기반 3D 플로팅
• 출판 품질 플롯 및 다양한 이미지 형식으로 쉬운 내보내기 (EMF, EPS, PS, PDF, SVG, BMP, JPG, PNG, TIFF 등등..)
• LaTeX 조판 시스템과의 쉬운 통합
• 열 논리 계산 및 다중 파일의 쉬운 import/export 기능을 갖는 강력하고 다재다능한 스프레드쉬트
• 광범위한 내장 데이타 분석 루틴을 위한 원클릭 엑세스
• 고급 통계 분석: 학생들의 t-Test, ANOVA, 분산에 대한 카이 제곱 테스트, 정규성 테스트 (Shapiro-Wilk)
• 가중치를 갖는 선형 및 비선형 커브 피팅 그리고 적합 매개변수의 통계 오차 추정
• 다중 피크 피팅
• 이미지 분석 도구
• 템플릿 지원: 플롯, 테이블, 메트릭스에 대한 모든 설정은 빠른 편집 프로세스를 위해 저장되고 추후에 복구될 수 있습니다.
• 폴더에 기반한 프로젝트 파일, 드래그 앤 드롭 및 검색 기능을 내장한 강력한 프로젝트 탐색기
• 엑셀 워크북과 Open Document Format 스프레드쉬트, dBase, SQLite 그리고 마이크로소프트 엑세스 데이타베이스 전체 가져오기

SciDAVis is a free interactive application aimed at data analysis and publication-quality plotting. It combines a shallow learning curve and an intuitive, easy-to-use graphical user interface with powerful features such as scriptability and extensibility.

SciDAVis is similar in its field of application to proprietary Windows applications like Origin and SigmaPlot as well as free applications like QtiPlot, Labplot and Gnuplot.

What sets SciDAVis apart from the above is its emphasis on providing a friendly and open environment for new and experienced users alike.

이 메타패키지는 수학과 관련된 데비안 과학 패키지를 설치할 것 입니다. 또한 field::mathematics debtag 및 사용자 관심에 따라 education-mathematics 메타패키지에도 관심을 가질 수 있습니다.