ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@643 f3b2605a-c512-4ea7-a41b-209d697bcdaa

Browse Source
This commit is contained in:
sjplimp
2007-06-22 17:00:20 +00:00
parent cea0208207
commit f93cd8f7ad
5 changed files with 53 additions and 32 deletions
Download Patch File Download Diff File Expand all files Collapse all files

14
tools/pymol_asphere/doc/asphere_vis.manpage
View File

@ -1,6 +1,6 @@
.TH asphere_vis 1 "June 11, 2007" "asphere_vis (Graphics Utilities) 0.1" "Graphics Utilities"
.TH asphere_vis 1 "June 22, 2007" "asphere_vis (Graphics Utilities) 0.1" "Graphics Utilities"
.SH NAME
\fBasphere_vis\fR - Tools for LAMMPS ellipsoid trajectory visualization in PyMol.
\fBasphere_vis\fR - Tools for ellipsoid visualization in PyMol of a LAMMPS trajectory.
.PD 2
.SH VERSION
.PD 1
@ -9,12 +9,12 @@ Version 0.1
.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]
\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]
.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:
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:
.PD 0
.PP
.PD 1
@ -40,10 +40,10 @@ When used with \fB-s\fR, the option will number the filenames based on the frame
.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.
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.
.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.
Use a LAMMPS input script rather than a data file for extracting atom shape information. The input script is specified as \fIinput_file\fR.
.TP
\fB-f\fR \fImax_frame\fR
.PD 0
@ -94,7 +94,7 @@ Set the degree of program output. Use:
.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.
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.