Creating a Structure File¶

Before running a workflow, we need a crystal structure. There are numerous ways to obtain a crystal structure, such as downloading one online or creating one from scratch. In this guide, we will create a structure file from scratch so that we understand the information it contains.

Understanding File Extensions¶

Most computer files you will interact with are text files, but have text organized with a specific pattern/format. This is where file extensions come in (.txt, .cif, .csv, .pdf, ...).

These extensions indicate the format we are using. For example, files named example.cif inform programs that we have a text file written in the CIF structure format. The .cif extension can tell us stuff like "the first line of the file represents the chemical formula" and so forth.

One popular format in material's science is made by VASP. VASP is unique because it uses the name POSCAR (without any file extension) to indicate its format. This isn't best practice, but it is import to keep in mind when reading files.

Fun-fact

A Microsoft Word document is essentially a folder of text files. The .docx file extension 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 to explore. Most programs operate in a similar manner!

Creating a POSCAR File¶

create a new text file named POSCAR.txt. You can use any text editor of your choice (Notepad, Sublime, etc.). Alternatively, you can create the file using the command line:
```
nano POSCAR.txt
```
Ensure that the .txt extension is visible by enabling "show file name extensions" in your File window.
Example

To do this on Windows 10:
1. Open File Explorer
2. Click the View tab in File Explorer
3. Click the box next to File name extensions to see file extensions
copy and paste the following text into the file:
```
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 represents a structure, which consists of a lattice and a list of atomic sites. The lattice is defined by a 3x3 matrix (lines 3-5), and the sites are a list of xyz coordinates with an element (lines 8-9 show fractional coordinates).
Renaming Your File from POSCAR.txt file to POSCAR. If you're using the command-line to create/edit this file, you can use the copy (cp) command to rename it:
```
cp POSCAR.txt POSCAR
```
Note

On Windows, you may receive a warning about changing the file extension. You can safely ignore this warning and change the extension.
Your structure file is now ready to use!

Exploring a Different Format (cif)¶

There are various ways to write structure information. The example above uses the VASP's "POSCAR" format. Another common format is CIF (Crystallographic Information File). Although it's not as neat as a POSCAR, it contains similar information. You can use CIFs, POSCAR, and many other formats when using Simmate.

For example, this would be a file named NaCl.cif:

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