XSF Plugin, Version 0.7

This plugin reads the regular and the animated form of XCrySDen structure files (.xsf and .axsf) as they are read and written by the XCrySDen visualization program and created by the Quantum Espresso (also known as PWScf) package of plane wave DFT based electronic structure and MD programs. The format allows storing of atomic data with or without periodicity in 1, 2, or 3 dimensions, variable cell size trajectories and multiple 2d, and 3d grid data set. See the extensive format description on the XCrySDen home page for more details.

Notes:

Trajectories
This plugin supports animation XSF files (axsf) even in combination with grid data sets. All timesteps, however have to have the same number of atoms (VMD does not support this currently anyways). Also the elements have to always be in the same order, only the first timestep will be used to read the element names. From all successive timesteps only the coordinates will be read.

Coordinate Rotation / Periodic Display
VMD currently can only display periodic images of the unit cell correctly, if the first cell vector is collinear with the x-axis and the second cell vector in the xy-plane. Upon loading of the xsf file, the coordinates and the grid vectors are rotated accordingly. Unfortunately, that may make the atomic positions incompatible to some other coordinate files containing matching coordinates, but no unit cell information.

Atom Masses
The plugin assigns masses to the atoms according to the natural isotope distribution of the elements (see e.g. http://www.webelements.com/). If an element could not been recognized, a mass of 0 is assigned. To set the mass for those elements or assign a different mass for the other atoms, you have to use to create a selection with atomselect and then use the selection subcommands to set the mass.

Conventional Cell Coordinates
This plugin currently only reads the primitive unit cell vectors and coordinates. Data for the conventional cell will be ignored.

2D Data Grids
VMD does not currently provide visualizations for two-dimensional data grids or means to store them, so this plugin ignores those data sets.

Incompatibilities
The plugin follows the description of the format on the XCrySDen homepage, but due to the differences between the parsers, files that may be readable without a problem in XCrySDen, will not read completely or correctly by this plugin. A few examples were already spotted 'in the wild' and the required amendmends to the plugins were made.