Tool for LAMMPS trajectory visualization in PyMol. The input is a LAMMPS 'data' file or a 'in' file with ellipsoid semi-axes specified using the ellipsoid command. The trajectory is input from a 'dump' file that must be generated using a custom style with the following arguments in order:
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\fItag type x y z quatw quati quatj quatk\fR
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.SH PARAMETERS
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.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.
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\fB-c\fR \fIcolor_file\fR
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.PP
.PD 1
Color the atom_types and set transparency based on the input file. The input 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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\fB-d\fR
Use a LAMMPS input file rather than a data file for extracting atom type information. The input filename is specified as \fIinput_data_file\fR.
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\fB-f\fR \fImax_frame\fR
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.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.
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\fB-n\fR \fInotice_level\fR
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Set the degree of program output. Use:
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\fB-n\fR 0 No output
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\fB-n\fR 10 Normal program output
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\fB-n\fR 20 Parameters useful for reproducing the results
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\fB-n\fR 30 All output
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\fB-r\fR \fIellip_res\fR
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Resolution of ellipsoids in trajectory. The number of triangles per ellipsoid is equal to 2*(\fIellip_res\fR^2). Default is 10.
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\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.
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.SH AVAILABLE COLORS
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black
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blue
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brown
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cmyk_blue
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cmyk_marine
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deep
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forest
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green
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grey
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hotpink
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magenta
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marine
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orange
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purple
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red
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slate
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teal
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wheat
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white
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yellow
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.SH KNOWN BUGS
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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.