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:
.PD 0
.PP
.PD 1
.PD 0
.PP
.PD 1
\fItag type x y z quatw quati quatj quatk\fR
.PD 0
.PP
.PD 1
.PD 0
.PP
.PD 1
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.
.PD 2
.SH PARAMETERS
.PD 1
.TP
\fB-b\fR
When used with \fB-s\fR, the option will number the filenames based on the frame number. By default, they are numbered consequtively from zero.
.TP
\fB-f\fR \fImax_frame\fR
.PD 0
.TP
.PP
.PD 1
Do not write more than \fImax_frame\fR frames to the output file.
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
.PD 0
.PP
.PD 1
\fB-n\fR 30 All output
.TP
\fB-o\fR
Do not output the outline for the simulation box.
.TP
\fB-r\fR \fIellip_res\fR
.PD 0
.TP
.PP
.PD 1
Resolution of ellipsoids in PyMol. The number of triangles per ellipsoid is equal to 2*(\fIellip_res\fR^2). Default is 10.
.TP
\fB-s\fR
Output the results into separate .py files. The filename and extension for the output files is taken from \fIoutput_py_file\fR.