7
I recently made charge densities available for the MOFs and coordination polymers of the Quantum MOF (QMOF) Database. Please read the GitHub page for details on how to access the charge densities. That being said, given the large size of the files, I wish you luck downloading it in bulk.
7
I'm not sure precisely what you mean, but if you want to convert a Cube file to an ($N\times4$) matrix where $N$ is the number of points and the 4 columns are (x,y,z,value), you can try the following code snippet taken from my GitHub repository here, which I reproduce below:
cube_filepath = '/path/to/mycube.cube' # Path to Cube File
def cube_to_xyzval(...
6
You generally cannot calculate a 2D system per se with a plane-wave program, but rather you should do a vacuum slab calculation. As for graphene, you would essentially do a calculation on graphite, but with the interlayer distance set at a large value, say 20 Angstrom (and the lattice constant c enlarged accordingly), so that the different layers of graphene ...
6
Judging by your initial energies, it looks like you're starting a calculation from scratch. I've had good luck so far converging spin-polarized calculations by first doing a non-spin-polarized calculation, writing the CHG, CHGCAR, and WAVECAR files, and using those to start a spin-polarized calculation. This is the recommended method if such calculations ...
6
From the Vaspwiki, the CHGCAR file writes out the density using this Fortran snippet:
WRITE(IU,FORM) (((C(NX,NY,NZ),NX=1,NGXF),NY=1,NGYF),NZ=1,NGZF)
Basically, this will iterate through the coordinates in the order X, then Y, then Z. For your case, this would look something like with $(N_x,N_y,N_z)$: $(1,1,1),(2,1,1),...,(64,1,1),(1,2,1),(2,2,1),...$
The ...
4
The VASP package solving the KS-equation with periodic boundary conditions (PBC). For two-dimensional materials such as graphene, you only have two periodic directions along $\vec{a}$ and $\vec{b}$ but the VASP assumes you still have three directions. To avoid this, you need to add enough vacuum (in general large than 15 angstroms) along the $\vec{c}$ ...
4
The perfect resource for this is John Kitchin's "Modeling Materials Using Density Functional Theory" ebook. There are numerous real examples using VASP (and the Atomic Simulation Environment) that you can use to confirm you are setting up your workflow correctly.
3
I've never done this before but here is my guess of how you can do it.
If the numbers you posted are the unit cell axes vectors with a vector for each column then their direct matrices are.
$$\tag{1}\mathbf{A} = \begin{bmatrix}3.31 & 0.00 & 0.00 \\
0.00 & 10.47 & 0.00 \\
0.00 & 0.00 & 4.37\end{bmatrix}...
3
While a CIF is not a suitable file format for handling volumetric charge density data, you may find Henkelman's chg2cube.pl script to achieve what you're looking for. It will convert a VASP CHGCAR file into a Cube format, the latter of which many programs can also read and is fairly easy to understand.
3
While its technically more of a direct programming question at this point (since you don't necessarily need to know the source of this data to parse the format), this can be done fairly easily with numpy and pandas.
As a test case, I used a toy version of your data in a file called data.txt:
11 2 3
0.27296628474E+03 0.27129538645E+03 0.26632236747E+...
1
VESAT can understand the data format of CHGCAR outputted by VASP. You just need to move CHGCAR to CHGCAR.vasp and then open with VESTA.
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