New answers tagged density-functional-theory
2
The KPOINTS have an inverse relationship with the real space lattice vectors. In either way, you won't go wrong. I would prefer to test it using 1x1x2, 1x1x3, 1x1x4, etc. This is simply because your c axis is much smaller than the a and b axis. However, you might also want to explore the other alternatives such as 2x2x3, 2x2x4, etc. Since it is not ...
3
Please go through the userguide. At the bottom, it has some nice suggestions. Check this mail thread also.
Does the program stops because too many errors have not converged or,
the calculation keeps going on ?
If the calculation did not stop and keeps going on, then you can ignore these warnings. Please do some convergence tests before you proceed for vc-...
6
This page is a really good resource for doing linear response in VASP.
The general idea is you do a ground state calculation, apply linear response non-self-consistently, then apply it self-consistently. As far as I can tell, there is no good package that will do this for you and its a bit tricky to get working.
5
It's somewhat ambiguous to talk about approximating the XC energy as a Taylor expansion. A Taylor expansion is a series involving a fixed number of variables, and contains successively higher (non-negative integer) powers of the variables. But the hierarchy that you mentioned involves an increasing number of variables, where each variable is a successively ...
8
I agree with the comment by @jheindel. One issue is that the derivatives in GGA and meta-GGA functionals are not used like a Taylor series. The derivatives are used to obey more known constraints and to provide hooks to parameterize on.
I'll now try to address the spirit of your question, supposing that the derivatives were used to construct a Taylor series. ...
9
If a functional always gives the exact energy for arbitrary external potentials, then it is easy to see that the functional must always give the exact density. Consider two DFT calculations, one with an external potential $V(\mathbf{r})$, and another with the potential $V(\mathbf{r}) + \epsilon\delta(\mathbf{r}_0)$, where $\epsilon$ is infinitesimal. By ...
4
Atomic simulation environment can do this with the following line of logic.
Calculate the number of nearest neighbors for all atoms
Select the undercoordinated atoms
Calculate the direction away from the neighbors (sum vectors from
neighbor->atom and normalize)
Add your atom to cover the dangling bonds, such as H, in direction
of calculated vector
A ...
6
I'm posting this here as an answer so that if anyone else runs into the same problem, they can get it clarified.
After searching endlessly (because the SIESTA to BoltzTraP2 interface provided by the developers failed), I figured it out by myself. What happened was a problem of the k-point output file from SIESTA not being what BoltzTraP2 expects.
If you are ...
6
This error has been resolved now. Though I am not an expert but here are few thoughts. There may be several reasons for this error:
This error might appear due to numerical instability from overlapping atoms.
As mentioned by @Phil Hasnip, if the S-matrix eigenvalues are really small.
Some pseudopotential may not fit with calculation, USPP giving non-...
2
Perhaps not the most detailed answer, since I'm not hugely familiar with the precise functionality/details that would be involved, but GPAW does seem to have the functionality.
Caveat: The GPAW docs are currently undergoing a fairly complete overhaul, so the link may be dead in the medium/long-term future, but as of the writing of this answer, it works.
7
You mentioned DFT, which is typically used to calculate the electronic energy at zero temperature. You can adjust the geometry until this electronic energy is lowest, but then you might ask why for a given pressure, if you increase the temperature, a substance's geometry changes, perhaps from an ordered lattice, to a disordered liquid, to a bunch of ...
3
The effective mass is related to the second derivative of the E-k curve as
So an accurate value of effective mass requires an accurate dispersion curve at all k points. If enough k values are not taken to plot the curve, plotting tools will interpolate the values to have a smooth curve, and the values may vary significantly from the actual values. This may ...
7
The general answer to your question is that it depends on what scientific question you are wanting to answer. However, since you're interested in thermoelectric properties, the material you're studying is probably a semiconductor and has a band-gap. This means that the conductivity is essentially zero unless you dope it, so using the undoped Fermi energy ...
8
"But since the DFT works not so well when dealing with semiconductors and excited-state calculations, wouldn't NAMD be too erroneous considering the nuclei vibrations?"
First of all, DFT in this context might not be as bad as you think. For example, my answer to: What are some recent developments in density functional theory? shows that even 10 ...
5
You can use OpenBabel directly to obtain the Gaussian input from command line.
OpenBabel supports two types of Gaussian input generation:
Gaussian 98/03 Cartesian Input
Gaussian Z-matrix Input
To run OpenBabel:
obabel [-i<input-type>] <infilename> [-o<output-type>] -O<outfilename> [Options]
Take a look at this answer for ...
3
Just putting another software that can be used to develop all the input files such as INCAR, POSCAR, KPOINTS and POTCAR from a CIF file, is pymatgen. https://pymatgen.org/. It is a python based software toolkit that can help you not only with the input files but also analyzing the output files from vasp. This software is being used in the development of the ...
5
The siesta kgrid specification looks like this:
%block kgrid.MonkhorstPack
<int> <int> <int> <offset>
<int> <int> <int> <offset>
<int> <int> <int> <offset>
%endblock kgrid.MonkhorstPack
What $\Gamma$ centered means is that the offsets are all $0.$.
For some systems it may be ...
2
The energy should be variational with regard to encut, but this is not something to expect for kpoints. However, normally this results in the opposite of what you are observing with the kpoints showing some sort of oscillation.
The result you see is due to numerical noise in the encut convergence calculations. Try to tighten the electronic cutoff and you ...
6
To make Andrew Rosen's comment a full answer, you can use ASE to do this. ASE will still let you do some stupid things if you ask it to, but it can make selecting paw potentials easier (setup="materialsproject" for example will select potentials according to materials project, assuming you have the correct potentials available). It also helps ...
9
You don't give any real details on the system, but I can make a guess from your scaling that either the code doesn't properly support openmp (which is unlikely) or your system is way too small to see a benefit. I suspect if you use a bigger system (that can't finish in about 10 seconds on a single core) you will see an improvement.
Also keep in mind a ...
7
I think that there should be three considerations (and of course I could be wrong).
If you have not compiled the software to work in parallel, specifying multiple (N number of) threads sometimes is said to cause the same job to run in serial mode but N times.
Even though you have a multi-core calculation, the actual work being done may not really need more ...
4
The source of mistake is assuming one atom in the primitive cell of the hexagonal system. Actually there are two atoms, the atomic positions are
ATOMIC_POSITIONS {alat}
Hf 0.000000000 0.000000000 0.000000000
Hf 0.666666667 0.333333333 0.790000000
1
With the help of @Tyberius and @BrandonBocklund, I did the calculation of Cu in FCC lattice. Calculated lattice constant $a = 3.62613952 \, A^\circ$, where as experimental value is $a = 3.6149 \, A^\circ$. The major source of confusion is, I interpreted the question as FCC primitive cell has 4 Atoms.
&CONTROL
calculation = 'vc-relax' ,
...
4
ibrav = 2 in Quantum Espresso gives an fcc Bravis lattice, as mentioned in the answer by Tyberius, with the lattice vectors:
a(1) = ( -0.500000 0.000000 0.500000 )
a(2) = ( 0.000000 0.500000 0.500000 )
a(3) = ( -0.500000 0.500000 0.000000 )
Using an fcc Bravis lattice, which the primitive cell for fcc structures contains one atom. The cubic, ...
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