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.lf 1 asphere_vis.manpage
.TH asphere_vis 1 "October 22, 2007" "asphere_vis (Graphics Utilities) 0.2" "Graphics Utilities"
.SH NAME
\fBasphere_vis\fR - Tools for ellipsoid visualization in PyMol of a LAMMPS trajectory.
.PD 2
.SH VERSION
.PD 1
Version 0.2
.PD 2
.SH SYNOPSIS
.PD 1
.TP
\fBasphere_vis\fR flavor_file dump_file output_py_file [\fB-b\fR] [\fB-f\fR \fImax_frame\fR] [\fB-h\fR] [\fB-i\fR \fIstart_frame\fR \fIskip\fR \fIend_frame\fR] [\fB-n\fR \fInotice_level\fR] [\fB-o\fR] [\fB-r\fR \fIellip_res\fR] [\fB-s\fR]
.br
.PD 2
.SH DESCRIPTION
.PD 1
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.
.TP
\fB-h\fR
Print out the man page for help
.TP
\fB-i\fR \fIstart_frame\fR \fIskip\fR \fIend_frame\fR
.PD 0
.TP
.PP
.PD 1
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.
.PD 2
.SH AVAILABLE COLORS
.PD 1
.PD 0
.PP
.PD 1
black
.PD 0
.PP
.PD 1
blue
.PD 0
.PP
.PD 1
brown
.PD 0
.PP
.PD 1
cmyk_blue
.PD 0
.PP
.PD 1
cmyk_marine
.PD 0
.PP
.PD 1
deep
.PD 0
.PP
.PD 1
forest
.PD 0
.PP
.PD 1
green
.PD 0
.PP
.PD 1
grey
.PD 0
.PP
.PD 1
hotpink
.PD 0
.PP
.PD 1
magenta
.PD 0
.PP
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marine
.PD 0
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orange
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.PD 1
purple
.PD 0
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.PD 1
red
.PD 0
.PP
.PD 1
slate
.PD 0
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teal
.PD 0
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wheat
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white
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yellow
.PD 0
.PP
.PD 1
.PD 2
.SH AUTHORS
.PD 1
W. Michael Brown
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