WIEN2k
Description
Program WIEN2k computes the electronic structure of solids. It is based on the Density Functional Theory (DFT) [W. Kohn and L. J. Sham: Phys. Rev. 140, A1133–A1138 (1965)]. It comprises full crystal potential and uses the Linearized Augmented Plane Wave method, LAPW [S. Cottenier: DFT and the Family of (L)APW-methods: a step-by-step introduction, University of Ghent, Belgium, 2004]).
License
Wien2k is a commercial product -- every user should have it's own (private) license (see license terms and conditions). Note: Including the version 14.1, the program directories are accessible only for the users which sent us a proof of holding the license...
Usage
Upcoming modulesystem change alert!
Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.
You can test the new version now by adding a line
source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules
to your script before loading a module. Then, you can list all versions of wien2k and load default version of wien2k as
module avail wien2k/ # list available modules module load wien2k # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail wien2k
and choose explicit version you want to use.
If you need to use k-point parallelization, you need to generate .machines file to working directory. For file generation you can use the script wien2k_machines, eg:
/software/wien2k-14.2/wien2k/wien2k_machines > .machines
Note: Since version wien2k-12.1 does not yet implement MPI parallelization. However, it uses the parallelization of Open MP. Your task will use so many processors how many you specify in the qsub command. For example, for two-processor task you submit:
$ qsub -l select=1:ncpus=2:mem=1gb ...
Do not use the -p switch when using run_lapw. Just
export SCRATCH=.
run_lapw -cc 0.0001 -i 90
echo y | clean_lapw -s
is enough for computing on more processors.
Documentation
FAQs
Q: There are processes left on machines after calculations.
A: Depends which mode of calculation you use.
- for interactive tjob you just simply look if there are some processes left on machines after finishing your task. These then can be canceled using:
$ ps -u YOURLOGIN
$ echo y | clean_lapw
$ echo y | cancel_lapw
- for batch job, you should add to your running script this line:
trap 'echo y | clean_lapw; echo y | cancel_lapw ' SIGTERM
Q: How to use WIEN2k only in text regime only (no graphics)?
A: It is possible. The problem is, that the w2web interface does not work on your local computer. In fact, you must launch a graphic browser iceweasel directly on the MetaCentrum machine. You may temporarily try to use non-graphic browser lynx or its later version links. This works.
$ lynx
After pressing the key g in lynx, you may specify the adress:
http://nympha.zcu.cz:7890
There, you can specify your struct file, run a calculation and so on. There is another way to specify your structure file, like this:
$ cp $WIENROOT/SRC_templates/case.struct ./myStructFile.struct
Some examples of structure files can be found in $WIENROOT/example_struct_files
Beware, the structure file is formatted.
After editing structure file you may initialize your structure in text regime using
$ init_lapw
Q: How to make calculations using WIEN2k if one has graphic support.
A: Log in for examle on nympha.zcu.cz.
$ ssh -X myUserName@nympha.zcu.cz
In your home directory, create the directory TiC and launch Wien2k. For example (change manik to your user name):
$ pwd
/storage/plzen1/home/manik
$ mkdir TiC
$ cd TiC
$ module add wien2k
$ w2web
Running first w2web: The computer asks you your user name and password. Choose non-trivial password (different from your MetaCentrum password). If there is an announcement:
w2web failed to bind port 7890 - port already in use!
You may want to try w2web -p portnumber
Then you should erase the w2web profile and try another port:
$ rm -r ~/.w2web
$ w2web -p 7891
If this happens, very probably some other user has forgotten to kill the process of his w2web. We kindly ask you not to forget to kill the process of w2web after finishing your work:
$ ps -u manik
PID TTY TIME CMD
19082 pts/0 00:00:00 bash
19141 ? 00:00:00 w2web
19142 pts/0 00:00:00 ps
$ kill 19141
Then launch the browser iceweasel on (for example) nympha.zcu.cz
$ iceweasel &
In the address field, type http://nympha.zcu.cz:7890 (eventually higher number of port 7891 or more, if 7890 is in use).
After typing your user name and password, you follow-up the
WIEN2k Usersguide.
In case of problems you can search WIEN2k WIEN2k FAQ or search the WIEN2k Mailing List. As a last resort, you can join the mailing list and pose your own question there. (http://www.wien2k.at/reg_user/index.html).
You can use the XCrysDen code to visualize your structure files and other task in WIEN2k.
$ cd TiC
$ module add xcrysden
$ xcrysden &
and choose File / Open WIEN2k / Open WIEN2k Struct File / TiC.struct. If you are using w2web, you may view the structure directly by clicking on view structure in Utils.
Q: sgroup crashes when initializing my structure
A: This was the problem in old version wien2k-05. Use higher version wien2k-12.1 or at least wien2k-08:
$ module rm wien2k-05
$ module add wien2k-12.1
Q: First iteration crashes (after lapw0) and there is error announcement in file case.dayfile: Segmentation fault
A: Before doing run_lapw or runsp_lapw type to command line (or add to your running script):
$ ulimit -s unlimited
This works for default bash shell. If using csh or tcsh, type
limit stacksize unlimited
(The following command tells your which shell you are using)
echo $SHELL
Q: I get the message: L2main - QTL-B Error
A: Have a look at WIEN2k FAQ page concerning this.
Q: How do I know which version of WIEN2k I am currently using:
A: By:
$ module list
or
$ which run_lapw
Safe mode to switch the WIEN2k versions is:
$ module rm wien2k-08
$ module add wien2k-12.1
Q: I want to make an immediate calculation now.
A: Firstly, it is forbidden to make calculation directly on frontends.
Simply use the interactive job.
$ qsub -q normal -l nodes=1:ppn=1:nfs4,mem=1gb -I
qsub: waiting for job 135447.arien.ics.muni.cz to start
wait a minute ...
qsub: job 135447.arien.ics.muni.cz ready
and you are on (for example) node skirit28.
$ hostname
skirit28.ics.muni.cz
$ pwd
/storage/brno1/home/manik/
$ cd /storage/plzen1/home/manik/TiC
$ module add wien2k-12.1
$ ulimit -s unlimited
$ export SCRATCH=.
$ run_lapw -cc 0.000001 -i 90
Wait till your calculation finishes and then tidy up your job:
$ clean_lapw
$ exit
qsub: job 135452.arien.ics.muni.cz completed
Q: Is there any default running script for WIEN2k?
A: Yes. When submitting this script, you must be in the case directory of your calculation.
#!/bin/bash
#PBS -j oe
module add wien2k-12.1
ulimit -s unlimited
hostname
echo "Your directory is $PBS_O_WORKDIR"
cd $PBS_O_WORKDIR
export SCRATCH=.
run_lapw -cc 0.0001 -i 90
echo y | clean_lapw > /dev/null
hostname