Search Results for "electron"
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Showing 31 open source projects for "electron"
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computem
Transmission Electron Microscope Image Simulation
These programs calculate high resolution conventional and scanning transmission electron microscope (CTEM, STEM) images of thin specimens from first principles using the multislice method for electrons in the energy range of approximately 60 keV to 1000 keV. The fundamental theory and usage are described in "Advanced Computing in Electron Microscopy" (Springer 2020) and Acta Cryst. A72 (2016) p. 1 by Earl J. Kirkland. -
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Hex
Hydrogen-Electron Collisions
A computer code for simulation of electron-hydrogen scattering. Contains three (more or less) finished sub-programs: (a) “hex-ecs” which solves the Schrödinger equation in the B-spline basis, (b) “hex-dwba” which computes scattering variables for high energies using the distorted wave Born approximation of the first order and finally (c) “hex-db” which is a user interface to a plain SQLite database, where the intermediate results are being stored, and which is used to extract derived quantities like a cross section from it. -
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Minsky
System dynamics program with additional features for economics
Minsky brings system dynamics and monetary modelling to economics. Models are defined using flowcharts on a drawing canvas (as are Matlab's Simulink, Vensim, Stella, etc). Minsky's unique feature is the "Godley Table", which uses double entry bookkeeping to generate stock-flow consistent models of financial flows. Minsky is good for demonstrating mathematics too, with the most "math-like" interface in system dynamics. Sign up to Minsky's Patreon page (for as little as $1 a month) at... -
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ShelXle
ShelXle is a Qt GUI for SHELXL
ShelXle combines an editor with syntax highlighting for the SHELXL-associated .ins (input) and .res (output) files with an interactive graphical display for visualization of a three-dimensional structure including the electron density (Fo) and difference density (Fo-Fc) maps. See J. Appl. Cryst. (2011). 44, 1281–1284. for details. -
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MCE - Marching Cube ELD
Crystallographic software for displaying voxel maps - electron density
MCE is an crystallographic experimental program for 3D and 2D electron density map visualization. The software is mainly focused on visualization of ELD calculated from X-ray diffraction data of small molecules, but it will work for small proteins as well. Download the installation file (default download) or find in "Files" the zip-file with instant copy of the program which does not require the installation. -
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ED Software project contains several programs used (mostly) for processing gas-phase electron diffraction (GED) experimental data.
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JDFTx
Joint Density Functional Theory
JDFTx is a plane-wave density functional theory code designed for electronic structure theory development. One prominent unique capability is the treatment of solvated electronic systems using joint density functional theory. Please see http://jdftx.org for download and compile instructions, tutorials, documentation and citation information. -
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ViennaSHE is a modern semiconductor device simulator for 1D, 2D and 3D device simulation. It relies on deterministic solutions of the Boltzmann Transport Equation using Spherical Harmonics Expansions.
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The Artificial SEM Image Generator (ARTIMAGEN) is a library that generates artificial scanning electron microscope (SEM) and helium-ion microscope images of various samples, including gold-on-carbon resolution sample, or some semiconductor features.
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Olex2 is visualisation software for small-molecule crystallography developed at Durham University/EPSRC. It provides comprehensive tools for crystallographic model manipulation for the end user and an extensible development framework for programmers. The project has been supported by Olexsys Ltd since 2010.
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Hammurabi Code
Astrophysical magnetic fields simulator
Hammurabi is a HEALPix-based tool for simulating observables such as polarized synchrotron and thermal dust emission from models of physical inputs such as magnetic fields, dust and electron distributions, etc. It is a modular C++ framework into which you can add your own models easily and then use it to perform the line-of-sight integration to compute the observables. See the wiki for installation and usage information. Please cite the original Waelkens et al. (2009) paper if you use hammurabi. This version of Hammurabi is deprecated and is no longer being supported. ... -
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PyTom
http://www.sciencedirect.com/science/article/pii/S1047847711003492
PyTom is a toolbox developed for interpreting cryo electron tomography data. All steps from reconstruction, localization, alignment and classification are covered with standard and improved methods. Please sign up to our mailing list to keep up with the most recent updates and versions. -
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RSchr-5
Solves one-electron Schrödinger equation, with SLEPc and PETSc
RSchr-5 calculates the smallest eigenvalues of the one-electron Schrödinger equation. The solved problem is defined on the finite domain, which is a box. The problem is solved with the zero Dirichlet boundary conditions. The implemented algorithm uses Finite Element Method with B-splines as basis functions. Disctretization leads to generalized eigenvalue problem. Program RSchr-5 solves the generalized eigenvalue problem by algorithms implemented in SLEPc amd PETSc libraries. ... -
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stellarics
Inverse Compton emission from heliospheres of sun and stars
...This program computes the spectrum and angular distribution of this emission. The software also includes general-purpose routines for inverse Compton scattering on a given electron spectrum, for example for interstellar or astrophysical source modelling. For further information see these publications: http://arxiv.org/abs/astro-ph/0607563, http://arxiv.org/abs/0801.2178, http://arxiv.org/abs/1104.2093, http://adsabs.harvard.edu/abs/2013NuPhS.239..266O and this conference presentation: https://confluence.slac.stanford.edu/download/attachments/130879399/poster_symposium_sun_2012.pdf and the corresponding conference paper http://arxiv.org/abs/1307.6798 2017 June 16: now available from gitlab https://gitlab.mpcdf.mpg.de/aws/stellarics which will be used for future develpments. -
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orbkit (Moved to Github)
A Modular Python Toolbox for Cross-Platform Post-Processing of Quantum
PLEASE NOTE ORBKIT HAS BEEN MOVED TO https://github.com/orbkit/orbkit orbkit is a parallel Python program package for post-processing wave function data extracted from output files of MOLPRO (Molden File Format), TURBOMOLE (AOMix file format), GAMESS-US, PROAIMS/AIMPAC (wfn/wfx file format), and Gaussian (Output File and Formatted Checkpoint File) output files. Futhermore, an interface to cclib, a parser for quantum chemical logfiles, is provided. If you use orbkit in your work,... -
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Tigris is an open source suite of classes and programs implemented in C++ for single particle electron microscopic image processing.
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XMIPP is an image processing suite for 3D-reconstruction of biological specimens from transmission electron microscopy data. NOTE that stable releases (including binaries) are longer stored at Sourceforge, but are available at http://xmipp.cnb.csic.es
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scipion-xmipp
Image processing framework to integrate EM software packages.
Scipion is an image processing framework to obtain 3D models of macromolecular complexes using Electron Microscopy (3DEM). It integrates several software packages and presents an unified interface for both biologists and developers. Scipion allows to execute workflows combining different software tools, while taking care of formats and conversions. Additionally, all steps are tracked and can be reproduced later on. Xmipp is a well-known package in the EM image processing. -
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xmipp
Image processing suite for Electron Microscopy
XMIPP is an image processing suite for 3D-reconstruction of biological specimens from transmission electron microscopy data. NOTE that stable releases (including binaries) are longer stored at Sourceforge, but are available at http://xmipp.cnb.csic.es -
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Acquisition software for electron microscopes. Runs on FEI Tecnai and Titan microscopes and is usable in material and life science applications
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Genesis 1.3
Time-dependent FEL Code
Three Dimensional, time-dependent Free-electron Laser Code Genesis -
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OpenRecon
OpenRecon is an open-source software library for image reconstruction.
Moved to https://bitbucket.org/bid/openrecon -
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aufbau
"aufbau" is a program that creates electron configuration of an atom.
This is version 1.2 of "aufbau". Its purpose is to create electron configuration of an atom, molecule or ion, following, of course, the "Aufbau" Principle. You can subscribe to the project's mailing lit here: https://lists.sourceforge.net/lists/listinfo/atomic-aufbau-news -
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Open-source Cube Files Manipulator Program (OpenCubMan)is a tool for computational chemists interested in performing operations on files with volumetric data representing wavefunctions or electron densities (often called cube files).
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