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tools/pymol_asphere/README

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asphere_vis: Tool for triangulating aspherical particles

	     to convert LAMMPS output to PyMol input



Building the tool:



cd src

make       # may need to edit Makefile for your system



This will place the asphere_vis executable in the bin directory.



Documentation is in the doc directory.  Note that the doc file says

the ellipsoid axes are specified by an "Ellipsoid" section in the data

file.  In the current version of LAMPS, this is now a "Shapes"

section.



See instructions on how to run an example ellipsoid viz in the

examples dir.



Mike Brown, Sandia National Labs

wmbrown at sandia.gov

June 2007

tools/pymol_asphere/doc/asphere_vis.1

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.if !'\*(.T'ps' .if !'\*(.T'html' .tm warning: eqn should have been given a `-T\*(.T' option

.if '\*(.T'html' .if !'ps'ps' .tm warning: eqn should have been given a `-Tps' option

.if '\*(.T'html' .if !'ps'ps' .tm warning: (it is advisable to invoke groff via: groff -Thtml -e)

.lf 1 /usr/share/groff/1.18.1.1/tmac/eqnrc

.\" Startup file for eqn.

.EQ

.nr 0C \n(.C

.cp 0

.ds 10

.cp \n(0C

.lf 63

.EN

.lf 1 asphere_vis.manpage

.TH asphere_vis 1 "June 11, 2007" "asphere_vis (Graphics Utilities) 0.1" "Graphics Utilities"

.SH NAME

\fBasphere_vis\fR - Tools for LAMMPS ellipsoid trajectory visualization in PyMol.

.PD 2

.SH VERSION

.PD 1

Version 0.1

.PD 2

.SH SYNOPSIS

.PD 1

.TP

\fBasphere_vis\fR input_data_file input_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]

.br

.PD 2

.SH DESCRIPTION

.PD 1

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:

.PD 0

.PP

.PD 1



.PD 0

.TP

.PP

.PD 1

\fItag type x y z quatw quati quatj quatk\fR

.PD 0

.PP

.PD 1



.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-c\fR \fIcolor_file\fR

.PD 0

.TP

.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.

.TP

\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.

.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-r\fR \fIellip_res\fR

.PD 0

.TP

.PP

.PD 1

Resolution of ellipsoids in trajectory. 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

.PD 1

	marine

.PD 0

.PP

.PD 1

	orange

.PD 0

.PP

.PD 1

	purple

.PD 0

.PP

.PD 1

	red

.PD 0

.PP

.PD 1

	slate

.PD 0

.PP

.PD 1

	teal

.PD 0

.PP

.PD 1

	wheat

.PD 0

.PP

.PD 1

	white

.PD 0

.PP

.PD 1

	yellow

.PD 0

.PP

.PD 1



.PD 2

.SH KNOWN BUGS

.PD 1

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.

.PD 2

.SH AUTHORS

.PD 1

W. Michael Brown

tools/pymol_asphere/doc/asphere_vis.manpage

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Original line number Diff line number Diff line 
.TH asphere_vis 1 "June 11, 2007" "asphere_vis (Graphics Utilities) 0.1" "Graphics Utilities"

.SH NAME

\fBasphere_vis\fR - Tools for LAMMPS ellipsoid trajectory visualization in PyMol.

.PD 2

.SH VERSION

.PD 1

Version 0.1

.PD 2

.SH SYNOPSIS

.PD 1

.TP

\fBasphere_vis\fR input_data_file input_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]

.br

.PD 2

.SH DESCRIPTION

.PD 1

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:

.PD 0

.PP

.PD 1



.PD 0

.TP

.PP

.PD 1

\fItag type x y z quatw quati quatj quatk\fR

.PD 0

.PP

.PD 1



.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-c\fR \fIcolor_file\fR

.PD 0

.TP

.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.

.TP

\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.

.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-r\fR \fIellip_res\fR

.PD 0

.TP

.PP

.PD 1

Resolution of ellipsoids in trajectory. 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

.PD 1

	marine

.PD 0

.PP

.PD 1

	orange

.PD 0

.PP

.PD 1

	purple

.PD 0

.PP

.PD 1

	red

.PD 0

.PP

.PD 1

	slate

.PD 0

.PP

.PD 1

	teal

.PD 0

.PP

.PD 1

	wheat

.PD 0

.PP

.PD 1

	white

.PD 0

.PP

.PD 1

	yellow

.PD 0

.PP

.PD 1



.PD 2

.SH KNOWN BUGS

.PD 1

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.

.PD 2

.SH AUTHORS

.PD 1

W. Michael Brown

tools/pymol_asphere/doc/asphere_vis.pdf

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tools/pymol_asphere/examples/README

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The asphere_vis tool needs an input script and a dump file

from a LAMMPS run.



In examples/ellipse, you can run LAMMPS with in.ellipse

to generate dump.ellipse



Copy in.ellipse and dump.ellipse to this dir.



Run the tool to create a PyMol input file called ellipse.py by typing:



../bin/asphere_vis in.ellipse dump.ellipse ellipse.py -c colors.ellipse -d



Launch PyMol on this input and you should see a nice viz of

4 ellipsoids in a box of LJ particles:



pymol ellipse.py

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