Editing Database bulk to surface builder

go back to [[Main Page]], [[Group Pages]], [[Núria López and Group]], [[Scripts_for_VASP]]


There are several pages where we can get the parameters that determine the structure according to their symmetry, such as:

http://cst-www.nrl.navy.mil/lattice/

You can also download the bulks of this website:

http://rruff.geo.arizona.edu/AMS/amcsd.php

in a CIF (Crystallographic Information File) file.

This file type has the minimum information positions, symmetry and even the source (author, book, ...) of the file has been generated. To convert this CIF file to [[VASP]] POSCAR file, it is necessary to make a previous step, as the CIF file does not contain all the necessary positions to make that transformation. To adapt the original CIF file to a convertible CIF file has to eliminate the symmetry of the file, ie converting to P1 symmetry. This process involves opening the file with the Materials Studio and apply the following procedure:

Download the CIF file desired.
Open the [[Materials Studio]] program in the [[Terminal Server]], import the CIF file (File → Import ...) and convert the file to P1 symmetry (Build → Symmetry → Make P1). Now save the result in CIF format (File → Export ...).

Now, you only need to convert the CIF file to POSCAR. There are two methods for carrying out this process.

1) Open the file (CIF or MSI) through [[MOLDEN]] and save it as VASP. This is done as follows:
Cub-shaped icon / Write / [[VASP]] This directly creates the POSCAR file in the selected directory.

2) Use the script cif2pos.pl [this script has an error that needs correction] this in a package of scripts (http://theory.cm.utexas.edu/vtsttools/downloads/vtstscripts_0.9.tar.gz) 
This script makes our CIF file in a POSCAR file.


Error of cif2pos.pl file:

The script must be changed cif2pos.pl Line 41:
                push(@coords,$F[3],$F[4],$F[5]);
for this other:
                push(@coords,$F[2],$F[3],$F[4]);


It is possible to convert the VASP files of coordinate (POSCAR and CONTCAR) in multi files to generate images (XYZ → JPG, POV, BMP ...) or manipulate other programs (e.g. Material Studio).

To manipulate these files by other programs such as [[Materials Studio]] without losing the information of the cell is necessary to convert the CONTCAR file to CIF or MSI format.
There are two methods to perform this operation.

1) With MOLDEN software and saving in one right format (CIF or MSI) (to open the CONTCAR or POSCAR file with MOLDEN, it must not contain the line Selective).

2) Another way is use the pos2cif.pl script, this script will generate a CIF file from a POSCAR or CONTCAR file.

With the Materials Studio program can manipulate CIF or MSI files for generating operations such as cuts and layers to calculate the surface from a bulk that we are optimized.
This will open the Material Studio program and perform the following operations:

1) Open the CIF file (File → Import ...) 

2) Generate the crystal (Build → Rebuild Crystal Crystal → ...), this open a window to introduce the symmetry.  If the CIF file was generated by one of the above methods then the symmetry is 1 P1. The other case, you must know the symmetry of the crystal. 

3) To make a cut to generate the surface (Build → Surfaces → Cleave Surface), this open a window where we select the plane to be cut (Cleave plane (hkl)) and the desired layers (Thickness). If the generated surface is not the desired (atoms on the surface undesired) can move the top to reduce or increase the atoms than appear or disappear on the surface (Top). The Surface Mesh tab can change the Mesh Origin to focus the generated surface from the bulk (I suggest use the 0.0, 0.0, 0.0 origin, before than move the Top). You can also select Options tab and select the option Reset orientation and origin after Cleave, to reorganize the generated surface in the correct order of XYZ. 

4) Now, you only need to generate the empty space needed for our calculations (Build → Build vacum → Crystal Slab). A window appears where you can enter the desired vacuum space or the total cell lenght  in the desired direction. Other options are the redefine the symmetry of the new cell (Build → Find → Symmetry Symmetry), this can find the symmetry and can  forcing to adopt the symmetry. And can generate a supercell from the unit cell (1x1) than already generated, this operation (Build → Symmetry → Supercell) will generate the supercell. 

5) Last step is to export the work to a CIF or MSI file, that can convert to POSCAR File. (File → Export ...) 

We can convert the CIF file with the cif2pos.pl script as described above. With this POSCAR can manipulate with [[p4vasp]] software, duplicate cells, freeze positions, etc ...