Kindly let me know how to assign nonstandard ions/atoms (i.e., not in the periodic table) in the cell file of Castep Academic (for Linux) DFT code. According to the Cell keyword guide, one has to define the pseudopotential for the nonstandard atom. However, this does not work. I simply need to give Fe atom names such as Fe1, Fe2, ... so that the PDOS orbitals correspond to these Fe1, Fe2, ... at different Wyckoff positions.
Can you specify what such a nonstandard atom would look like?
Normally, DFT codes only apply the nuclear charge (=number of electrons) and nuclear mass (relevant for vibrational frequencies) and then you pick a basis set for the atom.
Which aspect should be nonstandard?
I would like to express my gratitude to Dr.@ Jürgen Weippert for his valuable comments. I am currently exploring the possibility of obtaining the projected density of states (PDOS) for individual iron atoms within my Cell file. While Castep provides the PDOS for all atoms collectively, I have observed that Quantum Espresso offers the PDOS for each atom's orbitals in files distinguished by their ordinal positions. I would appreciate any guidance on how to extract the PDOS specifically for each iron atom in my Castep Cell file. Thank you for your assistance.
Ah, so the calculation is still normal, but you want to evaluate the results in a special way.
A partial density of states sounds like what you're looking for, is the second paragraph here helpful?
https://www.tcm.phy.cam.ac.uk/castep/documentation/WebHelp/content/modules/castep/tskcastepdispdos.htm
@ Dr Jürgen Weippert, thank you so much for this information. Regards
If you just want to label atoms, you use the "LABEL" attribute on the atomic positions line in the cell file. For example,
%block positions_frac
Si 0.0 0.0 0.0
Si 0.5 0.5 0.0 label=my_atom
%endblock positions_frac
The two atoms are treated identically in CASTEP, including in the symmetry-finder, but will be tagged in any output, e.g. this is the population analysis output from a bulk (8-atom) silicon calculation with the 2nd atom labelled as above:
Species Ion s p d f Total Charge (e)
==========================================================================
Si 1 1.363 2.637 0.000 0.000 4.000 0.000
Si[my_atom] 2 1.363 2.637 0.000 0.000 4.000 0.000
If you want the atoms to be treated differently, for example to apply a different Hubbard U or a different pseudopotential, then you use a colon in the name, ":", followed by an identifier. For example,
%block positions_frac
Si 0.0 0.0 0.0
Si:my_atom 0.5 0.5 0.0
%endblock positions_frac
Note that CASTEP will now consider these atoms to be completely different, for example they are not considered to be symmetry-equivalent. One of the common use-cases is in EELS calculations where one of the atoms has an "excited-core" pseudopotential.
As a final note, if all you want to do is to look at them separately in PDOS then many analysis tools let you specify a subset of atoms already. For example, Optados (www.optados.org) lets you plot PDOS from CASTEP output with user-defined collections of atoms summed.
Dear Dr. @Philip James Hansip, Thank you so much for this detailed answer. Yes, currently, I use optados for this purpose. May I add another query? I noticed that SCF convergence with PBE is quite lengthy compared to LSDA. Should it be the opposite, as GGA is more accurate than LDA? I guess.
No, why would it be the opposite?
GGA requires more calculation of integrals, so it scales worse with respect to the number of basis functions. If you go for hybrids or meta-GGA that will be even more accurate, but more computation demanding.
- Badges
- Science topic
- Similar topics
- Physical Sciences
- Materials Science
- Materials
- Inorganic Materials
- Metals
- Alloys
- Steel