Also in keeping with the plugin API only coordinates and velocities are read in for every frame all other properties are taken from the very first frame. This plugin only reads properties from the available data that is compatible with the molfile plugin API. Support for automatic unscaling and unwrapping of coordinates from simulations using triclinic cells is currently not supported. ITEM: TIMESTEP %d (timestep number) ITEM: NUMBER OF ATOMS %d (number of atoms) ITEM: BOX BOUNDS pp pp pp %f %f (xlo, xhi) %f %f (ylo, yhi) %f %f (zlo, zhi) ITEM: ATOMS id type xs ys zs %d %d %f %f %f (atomid, type, x-, y-, z, coordinates). The plugin assumes a format for a frame similar to what is shown here:
If the BOX BOUNDS line also optionally contains the 'xy yz yz' flags, then the box is no longer orthorhombic and the corresponding 'tilt factors' are written out in a 3rd column of numbers in the following three lines with the box boundaries. The lammpsplugin will make the best effort to reconstruct unscaled (=regular) and unwrapped coordinates from the available information and the simulation cell dimension information. Multiple coordinate representations can be present in "custom" style dumps. In "atom" style dumps, the dump_modify command in LAMMPS can be used to change the output format. In addition to wrapped coordinates, also the image flags ('ix', 'iy', 'iz') that are counters for how many times an atom has passed through the cell in the respective direction. Similarly can they be output as wrapped back into the principal unitcell or unwrapped (indicated by the postfix 'u'). When writing LAMMPS dumps, periodic boundaries are assumed if non-zero box dimensions are given if not, then shrinkwrap is assumed and the corresponding lo-/hi-values are determined by the plugin.Ĭoordinates can be given in different variants: regular or as fractional coordinates (indicated by the postfix 's'). 'p' stands for periodic boundaries, but also 'f' (=fixed), 's' (=shrinkwrap), and 'm' (=shrinkwrap with minimum) are possible or combinations thereof. The characters following the BOX BOUNDS keyword indicate the boundary conditions for each side in x-, y-, and z-direction respectively. Upon writing VMD will currently only write "atom" style dump files.
LAMMPS also supports a "custom" dump style that is very similar to the "atom" style, but it allows to output a custom selection of a large variety of per-atom properties, including data created by "fix"es or "compute"s. Please see below for using the environment variable LAMMPSMAXATOMS for a crude workaround.Ī brief summary of the "atom" LAMMPS trajectory dump format for orthorhombic boxes is below. Therefore the plugin will stop reading any trajectory file with an error message at the first frame that has a different number of atoms compared the previous ones. Also the file format itself allows for a variable number of atoms which VMD currently cannot handle. Not all fields of the custom style output are supported in the molfile API and thus cannot be communicated directly to VMD. This plugin reads text mode LAMMPS trajectory files (aka dumps) in atom style or custom style.
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