Making a structure file¶

Before we run a workflow, we need a crystal structure to run it on. There are many ways to get a crystal structure -- such as downloading one online or using a program to create one from scratch. Here, in order to learn about structure files, we are going to make one from scratch without any program.

Making a text (txt) file¶

First, make a new text file on your Desktop named POSCAR.txt. You can use which text editor you prefer (Notepad, Sublime, etc.). You can also create the file using the command like with:

nano POSCAR.txt

Note, we can see the .txt ending because we enabled "show file name extensions" above.

Once you have this file, copy/paste this text into it:

Na1 Cl1
1.0
3.485437 0.000000 2.012318
1.161812 3.286101 2.012318
0.000000 0.000000 4.024635
Na Cl
1 1
direct
0.000000 0.000000 0.000000 Na
0.500000 0.500000 0.500000 Cl

This text is everything we need to represent a structure, which is just a lattice and a list of atomic sites. The lattice is defined by a 3x3 matrix (lines 3-5) and the sites are just a list of xyz coordinates with an element (lines 8-9 show fractional coordinates).

Trying a different format (cif)¶

There are many different ways to write structure information; above we are using the VASP's "POSCAR" format. Another popular format is CIF. It's not as clean and tidy as a POSCAR, but it holds similar information:

data_NaCl
_symmetry_space_group_name_H-M   'P 1'
_cell_length_a   4.02463542
_cell_length_b   4.02463542
_cell_length_c   4.02463542
_cell_angle_alpha   60.00000000
_cell_angle_beta   60.00000000
_cell_angle_gamma   60.00000000
_symmetry_Int_Tables_number   1
_chemical_formula_structural   NaCl
_chemical_formula_sum   'Na1 Cl1'
_cell_volume   46.09614833
_cell_formula_units_Z   1
loop_
 _symmetry_equiv_pos_site_id
 _symmetry_equiv_pos_as_xyz
  1  'x, y, z'
loop_
 _atom_site_type_symbol
 _atom_site_label
 _atom_site_symmetry_multiplicity
 _atom_site_fract_x
 _atom_site_fract_y
 _atom_site_fract_z
 _atom_site_occupancy
  Na  Na0  1  0.00000000  0.00000000  0.00000000  1
  Cl  Cl1  1  0.50000000  0.50000000  0.50000000  1

You can use either CIFs or POSCAR formats when using Simmate. It's up to you.

Understanding file extensions¶

Nearly all files that you will interact with are text files -- just in different formats. That's where file extensions come in (.txt, .cif, .csv, ...).

These ending indicate what format we are using. Files named something.cif just tell programs we have a text file written in the CIF structure format.

VASP uses the name POSCAR (without any file extension) to show its format. If we renamed our file from POSCAR.txt to POSCAR, and now all programs (VESTA, OVITO, and others) will know what to do with your structure.

Note

In Windows, you will often receive a warning about changing the file extension. Ignore the warning and change the extension.

Fun-fact

a Microsoft Word document is just a folder of text files. The .docx file ending tells Word that we have the folder in their desired format. Try renaming a word file from my_file.docx to my_file.zip and open it up to explore. Nearly all programs do something like this!

Rename your file in the command-line¶

If you're using the command-line to create/edit this file, you can use the copy (cp) command to move your POSCAR.txt file into a file named POSCAR:

cp POSCAR.txt POSCAR

We now have our structure ready to go!