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Yaff Documentation — Yaff 1.4.2 documentation
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Yaff Documentation¶
Yaff stands for “Yet another force field”. It is a pythonic force-field (FF) code used at the Center for Molecular Modeling (CMM) to test-drive new FF models. The original motivation to develop Yaff was to provide a good reference implementation of the force fields developed at the CMM. In its current version, Yaff is general and flexible enough to handle a large variety of force field models.
User Guide¶
This guide is a gentle introduction to Yaff with many examples.
Tutorials¶
Reference Guide¶
This guide is mostly generated automatically based on the doc strings in the source code.
- 1.
yaff– YAFF - Yet another force field - 2.
yaff.pes– Force-field potential energy surfaces (PESs)- 2.1.
yaff.pes.dlist– Short-range neighbor lists for covalent energy terms - 2.2.
yaff.pes.ff– Force field models - 2.3.
yaff.pes.generator– Automatically generate force field models - 2.4.
yaff.pes.iclist– Internal-coordinate lists for covalent energy terms - 2.5.
yaff.pes.nlist– Neighbor lists for pairwise (non-bonding) interactions - 2.6.
yaff.pes.parameters– Object-oriented representation of parameter files - 2.7.
yaff.pes.scaling– Short-range scaling of pairwise interactions - 2.8.
yaff.pes.vlist– Module for the complete list of covalent energy terms.
- 2.1.
- 3.
yaff.sampling– Phase-space sampling- 3.1.
yaff.sampling.dof– Abstraction layer for degrees of freedom - 3.2.
yaff.sampling.harmonic– Harmonic models - 3.3.
yaff.sampling.io– Trajectory writers - 3.4.
yaff.sampling.iterative– Base class for iterative algorithms - 3.5.
yaff.sampling.npt– Barostats - 3.6.
yaff.sampling.nvt– Thermostats - 3.7.
yaff.sampling.opt– Geometry/Cell optimization - 3.8.
yaff.sampling.trajectory– Computations on a reference trajectory - 3.9.
yaff.sampling.utils– Auxiliary routines for initial velocities - 3.10.
yaff.sampling.verlet– Generic Verlet integrator
- 3.1.
- 4.
yaff.analysis– Trajectory analysis- 4.1.
yaff.analysis.basic– Basic trajectory analysis routines - 4.2.
yaff.analysis.blav– The block-average method - 4.3.
yaff.analysis.diffusion– Diffusion constants - 4.4.
yaff.analysis.hook– Abstract hook implementation for trajectory analysis - 4.5.
yaff.analysis.pca– Toolkit for Principal Component Analysis (PCA) - 4.6.
yaff.analysis.rdf– Radial distribution functions - 4.7.
yaff.analysis.spectrum– Spectral analysis and autocorrelation functions - 4.8.
yaff.analysis.utils– Auxiliary analysis routines
- 4.1.
- 5.
yaff.conversion– Conversion of external trajectory data - 6.
yaff.tune– Tools to calibrated FF parameters
Indices and tables¶
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© Copyright 2011, Toon Verstraelen, Louis Vanduyfhuys.
Created using Sphinx 1.6.3.