LEV00 & TETR:
user-friendly packages for DFT codes
VASP / SIESTA / QUICKSTEP / CRYSTAL / Quantum Espresso

L. N. Kantorovich

This is a documentation for a package of utilities which have been written (initially at Keele and then continued in London at UCL and KCL) as pre- and post-processing tools for DFT codes working with periodic boundary conditions. At the beginning, DFT codes CASTEP and CETEP were supported. At a later stage a complete support for the VASP code has also been added. Then, the whole structure of the two codes has been reshuffled in order to allow for a more flexible support for other codes and input/output formats. An almost complete support for the SIESTA code has also been added. Recently, as of version 4.1, some basic support for QUICKSTEP has also been added! From version 4.70 partial support for Quantum Espresso was also added in TETR. No manual has been updated yet, I'll do it some time. Hopefully, this is self-explanatory and there is no hurry!

The applications (i.e. offered functionality) include:

• various modifications of the system geometry (e.g. changing lattice vectors, breeding the system (supercells), merging geometries from several files of different formats (e.g. adding a molecule from another file to the surface), constructing a surface cell from a bulk one, terminating it with H atoms, etc.);
• construction of molecular clusters with specific boundary conditions out of a bulk unit cell;
• a powerful engine for phonons calculations (molecules and crystals), IR intensity via Born charges;
• calculations of the electronic Density of States (DOS),
• plotting of charge and spin total and partial densities, calculating atomic charges, saving the cube format file for gOpenMol contour plotting, etc.
• an intelligent search for surface states, exploration of the (partial) electronic (spin) density
• and a lot more!
• all these options can be run inside a shellscript, listing all the commands in a file, e.g., 'inp' and then e.g. running

  tetr < inp > out

  lev00 < inp > out

  This way all the instructions given in the file 'inp' will be executed (e.g. a moleule or AFM tip moved by some distance along a particular direction), a new input file for a DFT calculation saved, so that this DFT calculation can be run for a new geometry. Very useful when many similar task are to be performed automatically, e.g. in a loop.

Please, send me a short note about your current interest in the codes. I would also much appreciate it if you can give me any feedback on the codes: were they useful to you, and if not, why. If you did find the codes useful, do not forget to cite them as it is suggested in the manual as:

L. N. Kantorovich, User-friendly visualisation program for ab initio DFT codes VASP, SIESTA, QE and QUICKSTEP, 1996-2012, unpublished.

Many thanks!
The codes can be downloaded below (the latest versions, updated 12.12.2023):
For all NEW features see the README file in the distribution.

TETR

tetr version 6.33 (for all NEW features see the README file in the distribution as well as the manual file below). This is a fully functioning F90 version of the code! Several bugs were found and the code was cleaned up and streamlined whenever possible. Huge preallocated arrays have been removed as well, so the excutable should not be as large as in the previous F77 version. No common blocks either. Also an automatic test system has been created. Finally, the code now writes (in tetr.log) the log of all commands entered while running it. This can be useful when using TETR as a UNIX script routine.
NEW: Tetr is now working seemlessly with CHIMERA. See detailed instructions here. IMPORTANT: after installing the plugin, please replace the file gui.py with the one from here.
We would like to thank EPSRC for funding, grant EP/K038583/1.
The plugin was written by Gordon Gibb, Jeremy Nowell and Iain Bethune from EPCC (Edinburgh, U.K.).

When a change is made in TETR (e.g. in menu M), the system is automatically updated on the CHIMERA screen.

It is possible to highlight atoms on the CHIMERA screen (e.g. using Ctrl + left mouse button) and then get the atomic numbers in the TETR window, e.g. for option T, by hitting Get Selection button in the TETR window.
===> For instance, normally, to choose certain atoms in the M menu, you can use T and then type the required atomic numbers. Now you can, instead of typing atomic numbers directly, simply select atoms in the CHIMERA window and then hit Get Selection in the TETR window, and all their numbers will appear in the Command line of the TETR window; hit ENTER and the atoms will be tagged.

TUTORIALS for TETR

Getting started . You need a graphene SIESTA file which is here.

Graphene nanoribbon 6-ZGNR . You need a graphene SIESTA file which is here.

Graphene nanoribbon 11-AGNR . You need a graphene SIESTA file which is here.

Vibrations of the H2O molecule . You need a H2O molecule VASP input file which is here.

Vibrations of the MgO crystal. You need a VASP input file which is here.

BSSE correction for the adsorption energy of a cytosine molecule on the gold surface. You need a SIESTA input file which is here.

Construction of a c(4x2) Si(001) surface. You need a SIESTA input file for the Si bulk which is here.

Construction of the calcite bulk primitive cell and a supercell using information from the International Tables for Crystallography (created by Chiara Paris).

Construction of the calcite (104) surface using Miller indices (created by Chiara Paris).

Construction of the NiAl3 bulk unit cell (created by Chiara Paris).

Construction of a cluster from the bulk (e.g. an AFM tip) terminated with H atoms (planned)

Construction of a bulk cell from its space group symbol (planned)

Forcing symmetry for a SIESTA calculation (constr.f file) (planned)

LEV00

lev00 version 4.81 - please, UPDATE (last updated 09.23.2023) Note that since version 3.12 there was a bug affecting atomic positions read in from SIESTA input files.

Since version 3.0 this is a F90 version delivering a lot of convenience as it only needs to be compiled once! AT LAST!!!

From v. 3.30 lev00 acquired a nice STM plotter, pease try!

One can also use gOpenmol option for the constant LDOS image in which case atoms can be viewed underneath the LDOS surface as well, which is cool!

From version 3.21, lev00 is supposed to work with the new version of vasp v.5.2 . However, as this version is fairly new, there could be still some problems. If you experience anything unusual or the code crashes, please send me: lev00 output, POSCAR, INCAR, OUTCAR, CHGCAR, KPOINTS. tar and gzip these files into a single tar-ball and email to me. If you tried to run a DOS or PDOS calculation, then send brill.dat (generated with tetr), band.out and any other files needed as described in the manual. Your help will be greatly appreciated! By the way, to get directly the output from lev00 you may run it like this:

lev00 | tee output

NEW: lev00 is now working seemlessly with CHIMERA. See detailed instructions here.
We would like to thank EPSRC for funding, grant EP/K038583/1.
The plugin was written by Gordon Gibb, Jeremy Nowell and Iain Bethune from EPCC (Edinburgh, U.K.).

When lev00 starts, it shows atomic geometry automatically on the CHIMERA screen. The system can be extended using the familiar Bb option od TETR.

When reading electron density, in option gO one can preview it in CHIMERA window

WARNING: currently, only electron density is implemented; wait for an update which will show complete functionality.

MANUAL for TETR and LEV00

You can get it here for both codes. The last update: 07.07.11. The menus changed in some parts, so the manual is not exactly up-to-date, but it should give you an idea of what you should do and how. There are specific sections (which were updated) on SIESTA and VASP. QUICKSTEP and QE sections are not yet written, although many features of TETR work.
The online manual below is NOT updated, however, it may give you some idea of what this is all about. Please, use the pdf file above for the complete (and up-to-date) description of all features.

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