210 lines
3.9 KiB
Groff
Executable File
210 lines
3.9 KiB
Groff
Executable File
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.\" Startup file for eqn.
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.EQ
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.nr 0C \n(.C
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.EN
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.lf 1 asphere_vis.manpage
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.TH asphere_vis 1 "June 22, 2007" "asphere_vis (Graphics Utilities) 0.1" "Graphics Utilities"
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.SH NAME
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\fBasphere_vis\fR - Tools for ellipsoid visualization in PyMol of a LAMMPS trajectory.
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.PD 2
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.SH VERSION
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.PD 1
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Version 0.1
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.PD 2
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.SH SYNOPSIS
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.PD 1
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.TP
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\fBasphere_vis\fR input_file dump_file output_py_file [\fB-b\fR] [\fB-c\fR \fIcolor_file\fR] [\fB-d\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-r\fR \fIellip_res\fR] [\fB-s\fR]
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.br
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.PD 2
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.SH DESCRIPTION
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.PD 1
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Tool for ellipsoid visualization in PyMol of a LAMMPS trajectory. The \fIinput_file\fR is a LAMMPS data file with a 'Shapes' section or a LAMMPS input script file with ellipsoid diameters specified using the 'shape' command. The trajectory is input from \fIdump_file\fR that must be generated using a LAMMPS dump_style custom command with the following arguments in order:
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.PD 0
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.PP
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.PD 1
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.PD 0
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.TP
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.PP
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.PD 1
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\fItag type x y z quatw quati quatj quatk\fR
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.PD 0
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.PP
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.PD 1
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.PD 2
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.SH PARAMETERS
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.PD 1
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.TP
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\fB-b\fR
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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.
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.TP
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\fB-c\fR \fIcolor_file\fR
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.PD 0
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.TP
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.PP
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.PD 1
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Color the atom_types and set transparency based on the color file. The color file contains a space delimited set sequence of the color for an atom followed by the alpha. The color should be the string name and the alpha should be between 0 and 1.
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.TP
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\fB-d\fR
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Use a LAMMPS input script rather than a data file for extracting atom shape information. The input script is specified as \fIinput_file\fR.
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.TP
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\fB-f\fR \fImax_frame\fR
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.PD 0
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.TP
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.PP
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.PD 1
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Do not write more than \fImax_frame\fR frames to the output file.
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.TP
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\fB-h\fR
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Print out the man page for help
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.TP
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\fB-i\fR \fIstart_frame\fR \fIskip\fR \fIend_frame\fR
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.PD 0
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.TP
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.PP
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.PD 1
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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.
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.TP
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\fB-n\fR \fInotice_level\fR
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.PD 0
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.TP
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.PP
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.PD 1
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Set the degree of program output. Use:
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.PD 0
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.PP
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.PD 1
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.PD 0
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.PP
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.PD 1
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\fB-n\fR 0 No output
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.PD 0
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.PP
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.PD 1
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\fB-n\fR 10 Normal program output
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.PD 0
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.PP
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.PD 1
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\fB-n\fR 20 Parameters useful for reproducing the results
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.PD 0
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.PP
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.PD 1
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\fB-n\fR 30 All output
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.TP
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\fB-r\fR \fIellip_res\fR
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.PD 0
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.TP
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.PP
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.PD 1
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Resolution of ellipsoids in PyMol. The number of triangles per ellipsoid is equal to 2*(\fIellip_res\fR^2). Default is 10.
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.TP
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\fB-s\fR
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Output the results into separate .py files. The filename and extension for the output files is taken from \fIoutput_py_file\fR.
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.PD 2
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.SH AVAILABLE COLORS
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blue
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brown
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green
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grey
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.PD 0
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hotpink
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.PD 0
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magenta
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.PD 0
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marine
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.PD 0
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.PP
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orange
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.PD 0
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purple
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.PP
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red
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.PD 0
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.PP
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slate
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yellow
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.PD 2
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.SH KNOWN BUGS
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.PD 1
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Comments are not allowed at any point between a section header and the end of the contents for a section in either the data file or the input file.
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.PD 2
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.SH AUTHORS
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.PD 1
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W. Michael Brown
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