LAMMPS VMD plugin

VMD molfile plugin

On the attachment links below, you'll find updated VMD molfile plugins with enhancements that may not be available in the latest VMD release.

Documentation

This plugin reads text mode LAMMPS trajectory files (aka dumps) in atom style or custom style. Not all fields of the custom style output are supported in the molfile API and thus cannot be communicated directly to VMD. Also the file format itself allows for a variable number of atoms which VMD currently cannot handle. 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. Please see below for using the environment variable LAMMPSMAXATOMS for a crude workaround.

A brief summary of the "atom" LAMMPS trajectory dump format for orthorhombic boxes is below. 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. Upon writing VMD will currently only write "atom" style dump files.

The characters following the BOX BOUNDS keyword indicate the boundary conditions for each side in x-, y-, and z-direction respectively. 'p' stands for periodic boundaries, but also 'f' (=fixed), 's' (=shrinkwrap), and 'm' (=shrinkwrap with minimum) are possible or combinations thereof. 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.

Coordinates can be given in different variants: regular or as fractional coordinates (indicated by the postfix 's'). Similarly can they be output as wrapped back into the principal unitcell or unwrapped (indicated by the postfix 'u'). 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. In "atom" style dumps, the dump_modify command in LAMMPS can be used to change the output format. Multiple coordinate representations can be present in "custom" style dumps. The lammpsplugin will make the best effort to reconstruct unscaled (=regular) and unwrapped coordinates from the available information and the simulation cell dimension information.

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 plugin assumes a format for a frame similar to what is shown here:

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) ...

Notes

Triclinic Cells

Support for automatic unscaling and unwrapping of coordinates from simulations using triclinic cells is currently not supported.

Unused Data

This plugin only reads properties from the available data that is compatible with the molfile plugin API. 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. Any additional data recorded for an atom is ignored, unless the environment variable LAMMPSREMAPFIELDS is used to replace a supported property with an unsupported one. For details see below.

Legacy LAMMPS Dump Files

The LAMMPS dump file format described above corresponds to recent versions of LAMMPS. It has been incrementally improved over the years. Older versions may not provide all the detail. The plugin will make a best effort to guess missing information, but that may not always produce the desired result.

Environment Variables

Some aspects of the behavior of the plugin can be controlled through environment variables, that can be set either externally before launching VMD or from the VMD console via manipulation of the env array (use "global env;" to access it in a subroutine).

LAMMPSDIPOLE2ATOMS

With this environment variable set to a number > 0.0 any point dipolar particle will be converted into two particles a certain distance away from the center and thus signifying the direction of the dipole. The numerical value of the LAMMPSDIPOLE2ATOMS environment variable is interpreted as a scaling factor for this conversion with respect to the magnitude of the dipole moment.

LAMMPSREMAPFIELDS

This environment variable allows to map certain columns in a LAMMPS trajectory file to others and thus allows to read in properies, which VMD is normally not able to read. The content of the variable is the list of mappings in the format old=new and separated by commas. For example to read in forces into the velocities fields, the following mapping is required: vx=fx,vy=fy,vz=fz. This approach can be applied to any data in the dump file, even the output from variables, fixes, or computes.

Only the fields for coordinates and velocities will be read and stored in every time step and thus a suitable to transferring per timestep data into VMD through this mechanism. In addition VMD will read in the fields name, type, mass, radius/diameter, and charge and thus those can also be remapped, but those will only be read in on the first timestep.

LAMMPSMAXATOMS

This environment variable instructs the plugin to reserve space for more atoms than actually present in the first frame of the trajectory. The VMD molfile API assumes that there is a fixed number of atoms in a trajectory and that those atom's identity and properties (outside of position and velocity vectors) will not change. By setting this environment variable to a suitable number the lammps plugin can handle trajectories where atoms are added. Those "dummy" atoms will be assigned coordinates over the course of the trajectory as they appear. This still will not assign them suitable structure information, that would have to be added through different means (e.g. loading a suitably sized .psf file). All dummy atoms will be initialized to the following properties: name = @, type = X, resname = @@@, segid = @@@, chain = @, mass =0, charge=0, radius=0, element=X. For coordinates of inactive atoms, please see the next paragraph.

LAMMPSDUMMYPOS

This environment variable allows to set the position of inactive atoms when reading a native LAMMPS trajectory dump with a varying number of atoms. By default, those atoms will be assigned the position (0.0,0.0,0.0). However this environment variable allows to change this default, e.g.: set env(LAMMPSDUMMYPOS) {0.0 0.0 -10.0} will move the inactive atom position to a z-value of -10.