In short:
XCrySDen is a
crystalline and molecular structure render program,
with additional capabilities of rendering contours,
isosurfaces, Wigner-Seitz cells (also Brillouin zone),
Fermi surfaces and so on. Some of its features are the
following:
- widget with periodic table of elements:
- displaying molecular and crystalline structure in
several different display modes:
- displaying crystal and Wigner-Seitz cells:
- displaying smaller or bigger portion of crystal
(multiplying the unit cells)
- visualizing the forces as vectors:
- animations
- displaying contours and colorplanes
- displaying isosurfaces:
- reciprocal-space analysis:
+ selecting a k-path inside the
Brillouin-zone
+ visualizing Fermi surfaces
- and more ...
This is the
XCrySDen main window:
So what do we see:
-
Top:
-
A menu widget is at the top of the main
window. Please notice the Palette menu
(small palette-like icon) at the left of
File menu. A background of the render
window can be set here to an arbitrary color.
-
Middle:
-
A big display area, where a portion of the GaAs
surface with adsorbed hydrogen is displayed, is a
render window. Its background color can be
set via Palette menu (small palette-like
icon) at the left of File menu.
-
Left:
-
A toolbox panel is on the left side of the
main window. Please note a slider at its left. With
it we can drag the panel up and down, in order to
reach all tools-widgets on the panel.
-
Bottom:
-
A measure buttons (AtomInfo, Distance,
Angle, Dihedral) are at the bottom of the main
window. Here you can
found how to measure distances, angles and
dihedrals. At a very right is the Exit
button.
Here you can found detailed
description of the
XCrySDen main window. It
was written for an old
XCrySDen's version 0.3.
The main window of the current version differs a bit,
but nevertheless the document is still useful.
-
Rotation: press-and-hold left
mouse button and move the pointer
-
Translation: press-and-hold
middle mouse button (or both buttons for
two-button mouse) and move the pointer
-
Zoom (+): press-and-hold Shift +
Left mouse button and move the pointer up
-
Zoom (-): press-and-hold Shift +
Left mouse button and move the pointer down
-
Fullscreen mode: double-click the
left mouse button. To exit from the fullscreen mode
perform another double click with the left mouse
button.
-
Pop-up menu: press-and-hold the
right mouse button
XCrySDen has two levels
of display modes, these are so-called:
-
Lighting-On mode yields fancy
graphics with shades. Example:
-
Lighting-Off mode is very simple
and fast, but without shades. Example:
WARNING:
Lighting-Off mode
can display only structure, crystal cages
and nothing else !!!
NOTE:
I got several dozens Emails
per year claiming: not able to render
isosurface. And the reason is always the
Lighting-Off mode.
When rendering an isosurface or some other complex
object (i.e. isosurface) switch to
Lighting-On
mode, otherwise it will not appear !!!
If your graphics card isn't fast, then the
rotation will be quite slow when rendering in
Lighting-On mode a very complex object
(hundreds of atoms, isosurfaces, etc.). In such a case,
simply switch to
Lighting-Off mode (this will
turn off the complexity) and rotate, translate, zoom
and so on until you are satisfied with the setting.
Then switch back to
Lighting-On mode (this
will turn on the isosurface) and you will have the
desired picture !!!
After the installation of the
XCrySDen program (the
Installation instructions can be found
here) we are ready to run
XCrySDen for
the first time. The name of
XCrySDen executable is
xcrysden. I suggest that you start
exploring the program capabilities by running the
provided examples as explained below.
XCrySDen distribution
provides several example files. They can be loaded via
File-->XCrySDen Examples ...
cascade menu. There one can choose among different
provided files in several supported formats. After
loading the structure, start to explore the
functionality of the toolbox panel buttons. The panel
is located on the left side of the main window. Try
also to measure some distances or angles by clicking
the corresponding measure buttons located at the bottom
of the main window (the
HOWTO Measure
instructions can be found
here).
There are two ways to load the structure into
XCrySDen:
(i) trough
File-->Open * menus
(where "*" is a wildcard standing for any text), or
(ii) via command line options. Execute:
xcrysden
--help to display all supported options.
XCrySDen
supports well-known
XYZ and
PDB file
formats. In the latter case only a subset of the file
is read, namely the ATOMS section, while all others are
ignored. But these file formats do not have support for
crystal structures. Therefore
XCrySDen has its own
file format, which is called
XCrySDen
Structure
File (XSF) format. Many other
formats (like WIEN2k struct file or PWscf input file)
are supported through conversion to the XSF format.
Here you can find the
XSF
format specification.
The following file formats are supported in
XCrySDen:
-
Molecular structure formats:
-
- XYZ
- PDB
- GAUSSIAN Z-Matrix file (requires BABEL
program)
- GAUSSIAN output file
-
Crystal structure formats:
-
-
XSF
(XCrySDen Structure File)
- CRYSTAL files:
+ input file
+ unit 9 (i.e. properties file)
- WIEN2k struct file
- PWscf files:
+ input file
+ output file (structural
optimization run only)
- FHI98MD files:
+ inp.ini file
+ coord.out file
In addition, Jens Kunstmann has written an
XSF-converting tool
xsfConvert. Currently it can convert the data from
the
TB-LMTO-ASA
and
VASP programs
to the XSF format.
The measurement of angles, distances and dihedrals
can be easily achieved by pressing corresponding
measure button. These
buttons are located at the bottom of
XCrySDen main window.
After pressing one of these buttons, the
measure toplevel window will pop up. Please
note that while in
measure mode most of the
functionality of
XCrySDen is frozen (for
example: the display-mode
cannot be changed).
But we
can rotate the displayed structure, and
this feature is quite useful for complex structures. If
we want to measure the distance between two atoms, then
after pressing the
Distance button, simply
click on two atoms. If some atom is selected then it is
changed to light green color and its coordinates appear
in the
measure window. Below we can see a
snapshot of the measurement of the angle:
There are three buttons at the bottom of
the
measure window. The functionality of these
buttons is:
-
Done:
-
calculates/determines the measured property
-
Next:
-
de-selects all selected atoms, and begins new
selection
-
Close:
-
destroys the measure window and exits from
selection mode
XCrySDen menu widget is
located at the top of main window. There are the
following menu-buttons:
Palette, File, Display,
Modify, AdvGeom, Properties, and
Tools.
They are shortly explained below, but the detailed
description can be found
here.
I suggest you start by exploring various entries in the
Display and
Modify menus.
-
(Palette):
-
a background of the render window can be set here
-
File:
-
this menu is intended for Open, Save, Print,
Exit operations
-
Display:
-
this menu is intended for various "display"
possibilities. It consists of check- and
radio-buttons.
- By clicking appropriate checkbuttons inside
Display menu one can render:
Coordinates system (XYZ base vectors are
displayed at the bottom-left of the render
window), Atomic symbols, Crystal cells,
Forces, Wigner-Seitz cells, Molecular
surface.
- By clicking the appropriate radiobutton one
can choose among:
- primitive or conventional setting of the
unit cell
(Primitive cell Mode/Conventional Cell
Mode radiobuttons)
- criteria of rendering the ball and
spacefill sizes, either based on
covalent or van der Waals
radii
(radiobuttons in "Balls As ..."
and "SpaceFill As ..." cascade
menus)
- display style of crystal cells, either as
lines or rods
(radiobuttons in "Crystal Cells As
..." cascade menu)
- crystal unit type ("Unit of
Repetition ..." cascade menu). One can
choose among Unit Cell and
Translational asymmetric unit. What
do we mean by this? Simply rendering just
atoms belonging to the zero reference unit
cell would not appear very nice. Why? Let us
take for example an fcc unit cell.
The atoms belonging to this cell have the
following crystal (i.e. fractional)
coordinates: (0,0,0); (1/2,1/2,0);
(1/2,0,1/2); (0,1/2,1/2). If solely this
atoms are rendered they appear as shown on
the left of the below figure. Instead, what
one really wants is the shown on the right of
the figure:
The content displayed on the
left of the figure is called
Translational asymmetric unit,
while the one on the right is called
"nicely cut unit cell" or shortly
Unit Cell.
-
Modify:
-
this menu is dedicated to: (i) modifying
miscellaneous items, like various colors
(for example: atom and cell colors), atomic
radii, widths of bonds and cells, ball-factor,
tessellation-factor, ...; (ii) setting the
display of forces, Wigner-Seitz cells, molecular
surfaces, animation. Read more ...
-
AdvGeom:
-
this menu is mented solely for CRYSTAL GUI. Here
one can manipulate an existing structure by various
procedures. Among supported options are: (i)
cutting a slab out of a crystal, (ii) generating a
supercell, (iii) adding, removing and substituting
atoms, ...
-
Properties:
-
this menu is mented solely for CRYSTAL GUI. Here
one can perform some property analysis. Among
supported options are the plotting of (i) band
widths, (ii) density-of-states, (iii) band
structure (one can select th k-path inside
Brillouin zone graphically), (iv) electronic
densities and electrostatic potentials as 2D
contours or 3D isosurfaces.
-
Tools: (in old versions this menu was called
Analysis)
-
A few useful tools can be found here. This
includes: Color Scheme, Data-Grid, k-path Selection and
Periodic Table of Elements.
![[Figure]](img/xcrysden-picture-small-new.jpg)
