RMCSANS
AtomEye3.1 configuration viewer
|
AtomEye is originally written
by J. Li and modified to create AtomEye3 by S.
Futoshi. It is a Linux –based software capable of visualizing atomistic
configurations.
In order to be able to use
AtomEye easily to display larger sphere with custom size, and to display a
sequence of configurations created by RMCSANS, and wait for the new
configurations if they are not yet available, AtomEye had to be modified.
The enhanced version is
called AtomEye3.1. Several changes and
few bug fixes were made, the most important are:
Ø New particle types (s1, s2, s3 and s4) were defined with initial radius 10.0, 12.0, 14.0,16.0 and 18.0 Angstrom and atomic number 1001, 1002, 1003, 1004 and 1005.
Ø The extended 'Ju Li' file format was slightly modified, if the line containing the mass contains two real number entry, the first treated as the mass, the second will be the custom radius in Angstrom fro this particle type.
Ø To automatically load the available sequential configurations a new command line argument -auto was created.
Ø If -auto is used, than the automatic script loading has to be initiated by the -af=scriptfilename command line option instead of the -f option!
Ø To
make the usage of the coordination number colouring easier, new command setting
directly the cutoff values were introduced. This can be used without going into
rcut_patch mode
set_rcut symbol1
symbol2 value
set_rcut_patch
value for the currently chose pair.
Ø The saving of the cutoff values if they were reset by the user was also introduced into the script file.
Ø Possibility of drawing transparent balls were introduced by giving 2 0 0 colour code during colour changing.
Ø In
case of cutting planes it is possible to toggle by pressing 'T' between the
original behaviour, where the filtered out balls were invisible, and a new
feature of transparent filtered out balls.
|
Downloads |
If you are new to AtomEye, read the original AtomEye manual and the short description of AtomEye3 first.
The manual for AtomEye3.1 can be downloaded from here.
There will be two executables compiled on different machines both using GNU gcc. You may need to install some libraries to be able to run them.
Download the source code of AtomEye3.1. Read the manual, and start compilation in the A3 directory by starting the new bat file.
Download the executable compiled under Debian or Uhu Linux.
Download a series of configuration created by RMCSANS with together with a script file, which can be viewed by AtomEye3.1. It can be started with executable -auto -af=slice_cmds t_s2_4_ae0000.cfg
and it will display a slice of the configuration box consecutively for the given 51 configuration. If you start it without -af=slcie_cmds, then all the atoms are displayed.
|
Some pictures created by AtomEye3.1 |
a-Si Coordination-number based colouring with transparent balls for
0-coordinated particles
Cutting planes with filtered out particles invisible or transparent
Stages of an aggregation process with coordination number-based colouring. The particles with higher coordination numbers are pink, red
Page created by Orsolya Gereben
Last modified 25/06/2010 by Orsolya Gereben