PAN Blend modelling packages

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.

Цей збірний пакунок встановить пакунки щодо хемоінформатики, корисні для хіміків.

This metapackage will install development packages useful for chemists.

This metapackage will install graphical frontends and input generators/output processors for computational chemistry packages which might be useful for chemists.

This metapackage will install packages doing molecular ab initio calculations which might be useful for chemists.

This metapackage will install Molecular Dynamics packages which might be useful for chemists.

This metapackage will install 3D Molecular Modelling and Visualization which might be useful for chemists.

This metapackage will install packages doing periodic ab initio calculations which might be useful for chemists.

This metapackage will install Semi Empirical which might be useful for chemists.

This metapackage will install 3D Viewers which might be useful for chemists.

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.

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 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 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).

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 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).

Phonopy is an open source package for phonon calculations at harmonic and quasi-harmonic levels.

This package contains Python 3 module.

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.

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.

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.

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