Transport modules#
Velocity#
Description#
Analyse mean velocity..
Reads in coordinates and velocities from a trajectory and calculates a velocity profile along a given axis. The obtained profile is averaged over the 4 symmetric slab halfs.Error bars are estimated via block averaging as described in [1].
- [1] Hess, B. Determining the shear viscosity of model liquids from molecular
dynamics simulations. The Journal of Chemical Physics 116, 209-217 (2002).
Parameters#
- atomgroupAtomGroup
Atomgroup on which the analysis is executed
- dimint
Dimension for position binning (x=0, y=1, z=2)
- vdimint
Dimension for velocity binning (x=0, y=1, z=2)
- n_binsint
Number of bins. For making use of symmetry must be a multiple of 4.
- n_blockint
Maximum number of blocks for block averaging error estimate; 1 results in standard error
- make_wholebool
Make molecules whole; If the input already contains whole molecules this can be disabled to gain speedup
- output_suffixstr
Suffix for output filenames
- concfreqint
Default number of frames after which results are calculated and files refreshed. If 0 results are only calculated at the end of the analysis and not saved by default.
- verbosebool
Turn on more logging and debugging
Attributes#
- results.znp.ndarray
bins [nm]
- results.vnp.ndarray
velocity profile [m/s]
- results.eesnp.ndarray
velocity error estimate [m/s]
- results.symznp.ndarray
symmetrized bins [nm]
- results.symvelnp.ndarray
symmetrized velocity profile [m/s]
- results.symeesnp.ndarray
symmetrized velocity error estimate [m/s]