Tool for converting LAMMPS trajectories into compiled graphics objects for visualization in PyMol. The \fIflavor_file\fR is an input file that describes the color, transparency, and size/shape of each atom type. The \fIflavor_file\fR consists of two possible line formats. For spherical particles, the format is:
.PD 0
.PP
.PD 1
.PD 0
.PP
.PD 1
\fIatom_type color alpha diameter\fR
.PD 0
.PP
.PD 1
.PD 0
.PP
.PD 1
where alpha is used to adjust the transparency of the particle. For ellipsoidal particles, the format is:
.PD 0
.PP
.PD 1
.PD 0
.PP
.PD 1
\fIatom_type color alpha diameter_x diameter_y diameter_z\fR
.PD 0
.PP
.PD 1
.PD 0
.PP
.PD 1
Ellipsoidal and spherical line formats can be mixed in the same \fIflavor_file\fR For any atom type not listed in the \fIflavor_file\fR a blue sphere of size 1 is assumed.
.PD 0
.PP
.PD 1
.PD 0
.PP
.PD 1
The \fIdump_file\fR is a LAMMPS trajectory. For atom types specified as spherical in the \fIflavor_file\fR, the \fIdump_file\fR must contain \fItag type x y z\fR as the first columns. For atom types specified as ellipsoidal in the \fIflavor_file\fR, the columns are \fItag type x y z quatw quati quatj quatk\fR.The latter can be gerenated, for example, with the LAMMPS dump_style custom command with the following arguments in order:
The output file is a python file for input to Pymol. This can be viewed from the command line using \fIpymol output.py\fR or by using the \fIrun\fR command from within Pymol.
Render the specified frame interval inclusive between \fIstart_frame\fR and \fIend_frame\fR. \fIskip\fR gives the number of frames to \fIskip\fR between each rendered frame. A value of 0 outputs every frame between \fIstart_frame\fR and \fIend_frame\fR. The first frame in the dump file is frame 0.
.TP
\fB-n\fR \fInotice_level\fR
.PD 0
.TP
.PP
.PD 1
Set the degree of program output. Use:
.PD 0
.PP
.PD 1
.PD 0
.PP
.PD 1
\fB-n\fR 0 No output
.PD 0
.PP
.PD 1
\fB-n\fR 10 Normal program output
.PD 0
.PP
.PD 1
\fB-n\fR 20 Parameters useful for reproducing the results