PAN Blend Project
Summary
modelling
photons-and-neutrons modelling

This metapackage will install all modelling software for X-ray photons-and-neutrons PAN

Description

For a better overview of the project's availability as a Debian package, each head row has a color code according to this scheme:

If you discover a project which looks like a good candidate for PAN Blend to you, or if you have prepared an unofficial Debian package, please do not hesitate to send a description of that project to the PAN Blend mailing list

Links to other tasks

PAN Blend modelling packages

Official Debian packages with high relevance

debichem-analytical-biochemistry
DebiChem Analytical BioChemistry
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This metapackage will install packages which enable you to:

  • load and convert mass spectrometric data files;
  • edit biopolymer sequences;
  • elaborate complex mass spectrometry workflows;
  • perform protein database searches using tandem-ms data;
  • visualize and explore mass spectrometric data;
  • simulate isotopic clusters;
  • implement proteomics workflows.
debichem-cheminformatics
DebiChem Cheminformatics
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This metapackage will install cheminformatics packages useful for chemists.

debichem-development
DebiChem C/C++/Fortran Development
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This metapackage will install development packages useful for chemists.

debichem-input-generation-output-processing
DebiChem input preparation and output processing
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This metapackage will install graphical frontends and input generators/output processors for computational chemistry packages which might be useful for chemists.

debichem-molecular-abinitio
DebiChem Molecular Ab Initio Calculations
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This metapackage will install packages doing molecular ab initio calculations which might be useful for chemists.

debichem-molecular-dynamics
DebiChem Molecular Dynamics
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This metapackage will install Molecular Dynamics packages which might be useful for chemists.

debichem-molecular-modelling
DebiChem 3D Molecular Modelling and Visualization
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This metapackage will install 3D Molecular Modelling and Visualization which might be useful for chemists.

debichem-periodic-abinitio
DebiChem Periodic Ab Initio Calculations
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This metapackage will install packages doing periodic ab initio calculations which might be useful for chemists.

debichem-semiempirical
DebiChem Semi Empirical
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This metapackage will install Semi Empirical which might be useful for chemists.

debichem-visualisation
DebiChem 3D Viewers
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This metapackage will install 3D Viewers which might be useful for chemists.

libmcpl-dev
Monte Carlo Particle Lists - development files
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This package includes the shared library for reading and writing *.mcpl files, a binary format with lists of particle state information, for interchanging and reshooting events between various Monte Carlo simulation applications.

libncrystal-bin
Monte Carlo simulations of neutrons in crystals (utilities)
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This is a source distribution of NCrystal, a library and associated tools which enables calculations for Monte Carlo simulations of thermal neutrons in crystals.

This package contains the command-line utilities.

libxrl-dev
library for interactions of X-rays with matter (headers)
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Quantitative estimate of elemental composition by spectroscopic and imaging techniques using X-ray fluorescence requires the availability of accurate data of X-ray interaction with matter. Although a wide number of computer codes and data sets are reported in literature, none of them is presented in the form of freely available library functions which can be easily included in software applications for X-ray fluorescence. This work presents a compilation of data sets from different published works and an xraylib interface in the form of callable functions. Although the target applications are on X-ray fluorescence, cross sections of interactions like photoionization, coherent scattering and Compton scattering, as well as form factors and anomalous scattering functions, are also available.

xraylib provides access to some of the most respected databases of physical data in the field of X-rays. The core of xraylib is a library, written in ANSI C, containing over 40 functions to be used to retrieve data from these databases. This C library can be directly linked with any program written in C, C++ or Objective-C.

This package contains the header files.

mcpl
Monte Carlo Particle Lists - libraries and tools
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This package includes the core utilities for reading and writing *.mcpl files, a binary format with lists of particle state information, for interchanging and reshooting events between various Monte Carlo simulation applications. The core utilities include both command line tools and programming interfaces for C/C++ and python.

mcstas
Neutron ray-trace simulation
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McStas is a tool for carrying out Monte Carlo ray-tracing simulations of neutron scattering instruments with high complexity and precision. The simulations can compute all aspects of the performance of instruments and can thus be used to optimize the use of existing equipment, design new instrumentation, and carry out virtual experiments for e.g. training, experimental planning or data analysis.

McStas is based on a unique design where an automatic compilation process translates high-level textual instrument descriptions into efficient ISO-C code.

This package contains the McStas engine itself.

mcstas-comps
Neutron ray-trace simulation - components
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McStas is a tool for carrying out Monte Carlo ray-tracing simulations of neutron scattering instruments with high complexity and precision. The simulations can compute all aspects of the performance of instruments and can thus be used to optimize the use of existing equipment, design new instrumentation, and carry out virtual experiments for e.g. training, experimental planning or data analysis.

McStas is based on a unique design where an automatic compilation process translates high-level textual instrument descriptions into efficient ISO-C code.

This package contains the McStas components (i.e. models for simulated instruments and objects).

mcstas-suite-python
Neutron ray-trace simulation - full simulation suite
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McStas is a tool for carrying out Monte Carlo ray-tracing simulations of neutron scattering instruments with high complexity and precision. The simulations can compute all aspects of the performance of instruments and can thus be used to optimize the use of existing equipment, design new instrumentation, and carry out virtual experiments for e.g. training, experimental planning or data analysis.

McStas is based on a unique design where an automatic compilation process translates high-level textual instrument descriptions into efficient ISO-C code.

This metapackage contains the full python suite of tools.

mcxtrace
X-ray ray-trace simulation
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McXtrace is a tool for carrying out highly complex Monte Carlo ray-tracing simulations of X-ray beamlines to high precision. The simulations can compute all aspects of the performance of beamlines and can thus be used to optimize the use of existing equipment, design new instrumentation, and carry out virtual experiments for e.g. training, experimental planning or data analysis.

McXtrace is based on a unique design, inhereted from its sister McStas, where an automatic compilation process translates high-level textual instrument descriptions into efficient ANSI-C code. This design makes it simple to set up typical simulations and also gives essentially unlimited freedom to handle more unusual cases.

This package contains the McXtrace engine itself.

mcxtrace-comps
X-ray ray-trace simulation - components
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McXtrace is a tool for carrying out highly complex Monte Carlo ray-tracing simulations of X-ray beamlines to high precision. The simulations can compute all aspects of the performance of beamlines and can thus be used to optimize the use of existing equipment, design new instrumentation, and carry out virtual experiments for e.g. training, experimental planning or data analysis.

McXtrace is based on a unique design, inhereted from its sister McStas, where an automatic compilation process translates high-level textual instrument descriptions into efficient ANSI-C code. This design makes it simple to set up typical simulations and also gives essentially unlimited freedom to handle more unusual cases.

This package contains the McXtrace components (i.e. models for simulated beamlines and objects).

mcxtrace-suite-python
X-ray ray-trace simulation - full simulation suite
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McXtrace is a tool for carrying out highly complex Monte Carlo ray-tracing simulations of X-ray beamlines to high precision. The simulations can compute all aspects of the performance of beamlines and can thus be used to optimize the use of existing equipment, design new instrumentation, and carry out virtual experiments for e.g. training, experimental planning or data analysis.

McXtrace is based on a unique design, inhereted from its sister McStas, where an automatic compilation process translates high-level textual instrument descriptions into efficient ANSI-C code. This design makes it simple to set up typical simulations and also gives essentially unlimited freedom to handle more unusual cases.

This metapackage contains the full Python suite of tools.

python3-phonopy
phonon calculations at harmonic and quasi-harmonic levels (Python 3)
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Phonopy is an open source package for phonon calculations at harmonic and quasi-harmonic levels.

This package contains Python 3 module.

python3-pymatgen
Python Materials Genomics for materials analysis
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Pymatgen (Python Materials Genomics) is a robust, open-source Python library for materials analysis. These are some of the main features:

1.Highly flexible classes for the representation of Element, Site, Molecule, Structure objects.

  1. Extensive input/output support, including support for VASP (http://cms.mpi.univie.ac.at/vasp/), ABINIT (http://www.abinit.org/), CIF, Gaussian, XYZ, and many other file formats.

  2. Powerful analysis tools, including generation of phase diagrams, Pourbaix diagrams, diffusion analyses, reactions, etc.

  3. Electronic structure analyses, such as density of states and band structure.

  4. Integration with the Materials Project REST API, Crystallography Open Database.

This package provides the pymtgen module for Python 3.

python3-xrt
XRay Tracer and wave propagation (Python 3)
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XRayTracer is a python software library for ray tracing and wave propagation in x-ray regime. It is primarily meant for modeling synchrotron sources, beamlines and beamline elements. Includes a GUI for creating a beamline and interactively viewing it in 3D.

This package installs the library for Python 3.

quantum-espresso-data-sssp
Standard solid-state pseudopotentials (SSSP) library
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The convergence pattern of each element includes for each of the considered family:

  • the total number of electrons in the valence, Z;
  • delta value (the error in the equation of state compared with all-electron WIEN2k results, developed by Cottenier group), at full converged cutoff;
  • the largest phonon frequency, ωmax, at the zone boundary (as a number), at full cutoff;
  • and then as a function of wave function cutoff:
  • the discrepancy of all phonon frequencies, δω̄, at the zone boundary, with respect to the converged value;
  • the convergence of the pressure, δVpress, with respect to the converged value;
  • the convergence of the cohesive energy, δEcoh, with respect to the converged value;
  • the convergence of the bands structure, η10 and max η10 with respect to the converged value.

Debian packages in contrib or non-free

mumax3
GPU-accelerated micromagnetic simulator
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mumax3 is a GPU-accelerated micromagnetic simulation program developed at the DyNaMat group of Prof. Van Waeyenberge at Ghent University.

A speed-up of the order of 100x compared to CPU-based simulations can easily be reached, even with relatively inexpensive gaming GPUs. Additionally, the software is optimized for low memory use and can handle about 16 million FD cells with 2GB of GPU RAM.

Features:

  • Landau-Lifshitz micromagnetic formalism
  • Magnetostatic field
  • Heisenberg exchange
  • Arbitrary inter-region exchange like RKKY coupling
  • Dzyaloshinskii-Moriya interaction
  • Spin-transfer torque (Zhang-Li and Slonczewski)
  • Uniaxial and cubic magnetocrystalline anisotropy
  • Thermal fluctuations (Brown)
  • Voronoi tessellation
  • Time- and space dependent material parameters
  • Arbitrary complex excitation (field, current)
  • Simulation window can automatically follow a moving domain wall
  • Edge charges can be removed to simulate an infinitely long geometry
  • Optional 1D, 2D or 3D periodic boundary conditions
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