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Overview

by Konrad Hinsen last modified 2007-03-22 12:54

ScientificPython functionality

ScientificPython is a collection of Python modules that are useful for scientific computing. In this collection you will find modules that cover basic geometry (vectors, tensors, transformations, vector and tensor fields), quaternions, automatic derivatives, (linear) interpolation, polynomials, elementary statistics, nonlinear least-squares fits, unit calculations, Fortran-compatible text formatting, 3D visualization via VRML, and two Tk widgets for simple line plots and 3D wireframe models. There are also interfaces to the netCDF library (portable structured binary files), to MPI (Message Passing Interface, message-based parallel programming), and to BSPlib (Bulk Synchronous Parallel programming). For details consult the manual.


Module overview

  • Scientific.IO: I/O-related modules.
    • Scientific.IO.TextFile: sequence-style access to text files (i.e. by looping over the lines) and transparent compression and decompression.
    • Scientific.IO.FortranFormat: input and output using Fortran-style format specifications, facilitates interfacing to Fortran programs.
    • Scientific.IO.ArrayIO: simple text I/O for one- and two-dimensional arrays.
    • Scientific.IO.NetCDF: array-level access to netCDF files.
    • Scientific.IO.PDB: object-oriented view of the contents of files that follow the Protein Data Bank format.
  • Scientific.Geometry: 3D vectors and tensors.
    • Scientific.Geometry.Transformation: linear transformations (translations and rotations) on vectors.
    • Scientific.Geometry.Quaternion: quaternions.
    • Scientific.Geometry.TensorAnalysis: scalar and tensor fields on a grid.
    • Scientific.Geometry.Objects3D: simple 3D objects and operations on them.
  • Scientific.Functions: modules related to mathematical functions.
    • Scientific.Functions.Derivatives: automatic derivatives.
    • Scientific.Functions.FirstDerivatives: automatic first-order derivatives (more efficient than the general module).
    • Scientific.Functions.Interpolation: function objects defined by values on a grid with linear interpolation.
    • Scientific.Functions.Polynomial: polynomials in several variables.
    • Scientific.Functions.LeastSquares: non-linear least-squares fits.
    • Scientific.Functions.FindRoot: finds roots of functions using a variant of the Newton-Raphson algorithm.
    • Scientific.Functions.Romberg: Romberg integration.
  • Scientific.Statistics: basic statistical operations.
    • Scientific.Statistics.Histogram: histogram generator.
  • Scientific.Clustering: identification of clusters in data sets with a similarity relation.
    • Scientific.Clustering.AffinityPropagation: the affinity propagation algorithm.
  • Scientific.Signals: signal processing
    • Scientific.Signals.Models: Autoregressive model.
  • Scientific.Physics: modules for physical applications.
    • Scientific.Physics.PhysicalQuantities: physical quantities with units, including unit conversion and arithmetic operations with unit checks.
    • Scientific.Physics.Potential: potential energy functions with automatic gradients.
  • Scientific.TkWidgets: useful widgets for scientific applications.
    • Scientific.TkWidgets.TkPlotCanvas: simple plotting canvas for Tk-based user interfaces.
    • Scientific.TkWidgets.TkVisualizationCanvas: slow-but-usable canvas for visualizing 3D wireframe models that can be manipulated interactively.
  • Scientific.Visualization: 3D visualization modules.
    • Scientific.Visualization.VRML: create VRML files containing simple geometrical objects.
    • Scientific.Visualization.VRML2: almost identical to VRML, but produces VRML2 syntax (aka VRML97)
    • Scientific.Visualization.VMD: provides data visualization via the molecular visualization program VMD.
    • Scientific.Visualization.VPython: provides data visualization via the VPython extension module.
  • Scientific.Threading: simple task scheduler for thread-based parallelization.
  • Scientific.MPI: Python interface to the MPI library (Message Passing Interface, used for parallel computers).
  • Scientific.BSP: High-level parallelization package.
  • Scientific.DistributedComputing: Support for simple parallelization of computations.
  • Scientific.indexing: construct tuples of slices in a nicer way.

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