[xcrysden] XCrySDen Digest, Vol 45, Issue 5

[Sean Muir]

Hi Folks

Just in case it helps, here are some instructions I once wrote on how
to get XCrysden running on Windows for a solid state physics class I
was in.  I had no previous knowledge of UNIX commands at the time so
hopefully they are simple enough that a person entirely new to UNIX
and command line can follow.

Also they are written from the perspective of wanting to generate a
Fermi structure from Wien2K data or k path for use in Wien2K but have
general info on running xcrysden as well.

Cheers,

Sean Muir
Oregon State University


How to get XCrySDen running on a server with Windows (via Cygwin)

[SM 05-17-10] Cygwin is a UNIX emulation engine. Aside from the main
engine, additional ‘packages’ must be downloaded and installed. Each
package adds additional functionality to the emulation engine, all can
be viewed and marked for download via the main Cygwin setup program.

Go to http://cygwin.com/install.html and get the setup.exe file
(download link in the beginning text of the webpage).

Once you run the setup.exe file hit next> and then choose install from
internet, next>. Select install for all users and choose a root
directory for Cygwin (i.e. where you want it installed).

Next choose a download location for storing temporary files related to
the setup (just go with default folder if you have no other
preference). Select next>.

Choose Direct Connection next>.

Choose a website to download more needed files (specifically outlined
below) from. The ftp ones seemed to be quicker than the http. Select
next> and it should connect to the site and a select packages screen
will appear.

All the packages which may ever be needed are listed alphabetically
below. It is possible that the first package, cygwin, and the last
one, xinit, are the only two needed for opening an X Windows terminal
and running XCrySDen on the Jansen server, however the others are
needed when running XCrySDen on your own machine. Since the file size
of each package is pretty small it doesn't hurt to download them all
in case they may be called upon by the program in some way.

    cygwin
    bash
    bc
    coreutils
    gawk
    grep
    gzip
    ImageMagick
    less
    mesa
    more
    opengl
    openssh
    tcltk
    X-start-menu-icons
    xterm
    xinit

Use the search box in the corner to locate these. The easiest thing is
to have the select package screen in category view mode (button upper
right to change view). Type in the search word for each package in the
list above (e.g. cygwin). After the word All at the top of the file
structure tree click on the word Default so that it changes to
Install. This may download some unnecessary stuff but it is OK. For
the bc package using the search bar brings up a bunch of stuff since
those letters appear next to each other in a lot of the available
Cygwin packages. The only thing needed is bc: The GNU numeric…. under
the utils heading. Select next> and let it download and install any
dependent files if needed (it will warn you if so).

You should be able to grab all the packages in one go, but if not
continue to rerun the Cygwin setup.exe file with all the same initial
root directory and download folder options until each has been
installed.

After having completed the above steps, you should have two new
program folders available within the program start menu, these are
Cygwin and Cygwin-X. The first contains one program Cygwin Bash Shell.
This is a UNIX command line interface, which is needed if you want to
get XCrySDen running on your own PC (see below). The second, Cygwin-X,
contains a few programs, XWin Server and xterm.  These programs allow
XCrySDen located on a server somewhere to run on your PC.

XCrySDen on your own machine

You can download XCrySDen from http://www.xcrysden.org/. Some
configuration of the software will be necessary.
XCrySDen on a PC running Windows

[SM 05-17-10] First obtain all the necessary Cygwin packages as
outlined above for getting XCrysden on the Jansen server running on a
PC. Once done you are ready to get XCrySDen. Go to
http://www.xcrysden.org and download the
xc-1.5.18-cygwin-shared.tar.gz file. THESE INSTRUCTIONS WERE TESTED
USING THE XCrySDen CYGWIN BINARY PACKAGE 1.5.18. You will need a
program to unzip the .tar.gz file.
Recommended is 7-zip, http://www.7-zip.org/.

After unzipping the .tar.gz file and the .tar file that is inside,
rename the uncompressed folder (XCrySDen-1.5.18-bin-shared) to
something shorter (e.g. xcrysden) and copy. We will now place it in
the Cygwin root directory that you created on initial installation of
Cygwin. Specifically paste the uncompressed folder in the
Cygwin»home»username folder (i.e. the path including the pasted file
would be something like C:\Cygwin\home\yourusername\XCrySDen if your
Cygwin root directory was placed directly on the C drive).

Now we can go command-line-o. Open up Cygwin bash shell which should
be under your program menu. This is the UNIX emulator and a command
line interface. The user directory you are placed in when you open it
is the Cygwin»home»username folder (from above). We want to go into
the folder XCrySDen which we just moved. To do this we give a change
directory command followed by the name of the folder we want (i.e.
type cd XCrySDen). Some environmental settings need to be configured.
In the XCrySDen directory, enter ./XcConfigure.sh . Enter either 'no'
or the default setting should be fine for everything. The last setup
procedure is to run 'source ~/.bashrc' in the terminal. To go back to
the username folder (if needed) type cd with nothing after it. Now,
type the command ./xcrysden . This will launch the program XCrySDen
and you should see its interface open up. The configuration needs to
be done only once, but GOING INTO THE XCRYSDEN DIRECTORY IS NEEDED TO
LAUNCH THE PROGRAM EVERY TIME.

All that is left to do is place a Wien2K structure file into the
XCrySDen folder. To do this go onto your Wien2K via W2Web session and
go to files» struct file(s)» and download/copy the case.struct file to
XCrySDen (the folder from above).

Now from inside XCrySDen go File»Open Wien2K»Open Wien2K Struct file.
Choose the case.struct file you downloaded and open. You should see
the real space structure model.

Up at the top if you go to Tools»k-path selection the reciprocal
lattice view appears and it seems you should be able to generate the k
path file such as would be needed for Wien2K dispersion calculations.
However when the k-path file is generated having used OpenWien2K» Open
Wien2K Struct file the option to save as the appropriate .klist file
is not available (only .kpath and 2 other options are present). If we
were running XCrysden on a server with Wien2Kthe other option to go
File»OpenWien2K»select k-path would work but this does not appear to
function when running natively on a PC.

The solution and way to generate a .klist file involves going
command-line-o again. From the Cygwin bash shell type cd XCrySDen (if
not already there) next type ./xcrysden –wien_kpath case.struct Where
case.struct is of course the specific name of the wien structure file
you downloaded. The ./xcrysden command simply launches the program
just like before however the additional –wien_kpath command tells it
to launch directly into the reciprocal lattice view of your file. The
difference is that by doing it this way the option to save as a .klist
file will now be present . This file’s extension can then be modified
to .klist_band and it can then be uploaded back to your session folder
on the Jansen Wien2K server for use in the dispersion calculations. So
if all you want is to see is the reciprocal lattice and to generate a
.klist file you can skip the step where we launched entire program
(real space view) and jump right to this part.

The Fermi surface functionality does not work when running XCrySDen
locally, as it requires that the program communicate with Wien2K
subprograms on the Wien2K server. There may exist a way to tell it the
server's address and your W2Web password but thus far I have yet to
figure it out.




On Tue, Nov 1, 2011 at 12:35 AM, bahaareh tavakoli nejad
<bahaartv at gmail.com> wrote:
> hello.
> I have a 64 bit windows7. I download ''xc-1.5.18-cygwin-shared.tar'' and
> also i download ''Cygwin/X'' and   bash, gawk, grep, gzip, ImageMagic,less,
> more, opengle and tcltk.
> I Extract  the ''xc-1.5.18-cygwin-shared.tar'' in the folder that contain
> cygiwn. in the Xcrysden I built tho empty folder "XCRYSDEN_TOPDIR" and
> "XCRYSDEN_SCRATCH". Then i use the  ''$ ./xcConfigure'' command. but i get
> this error : bash: ./xcConfigure: No such file or directory.
> please explain me in detail what should i do.
>
> Thank you very much.
>
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