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:
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 (
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, and now all programs (VESTA, OVITO, and others) will know what to do with your structure.
In Windows, you will often receive a warning about changing the file extension. Ignore the warning and change the extension.
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.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
cp POSCAR.txt POSCAR
We now have our structure ready to go!