19
votes
Accepted
Why is my hydrogen energy not equal to -0.5 hartrees?
Yes, the exact orbital energy of the hydrogen atom is $-1/2\ E_h$. The problems in the calculation are as follows.
First, you are running ROKS. ROKS has many definitions in the literature; PySCF ...
- 19.1k
12
votes
Why is my hydrogen energy not equal to -0.5 hartrees?
The exact non-relativistic ground state electronic energy of a hydrogen-like atom, assuming that the nucleus is "clamped", point-sized, and with an infinitely large mass compared to the mass ...
5
votes
Finding HOMO/LUMO from SCF calculation: VASP
No, the HOMO is the highest energy eigenvalue for the corresponding band, across the Brillouin zone. It isn't technically a HOMO because it isn't a molecular orbital ("MO") it's a band, so ...
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5
votes
Accepted
What is the correct way to set up occupation for single atom in CFOUR software?
Your setting is incorrect for the dominant Slater determinant when calculating the electronic ground state of an O atom:
OCCUPATION=2-1-1-1-0-0-0-0/2-1-0-0-0-0-0-0
...
5
votes
Is the electron-electron interaction to blame, for the added complexity of using "orbitals" for an N-electron system?
Interpreting the question
For a 1-electron system, wavefunctions and orbitals are the same thing. For a 2-electron system, or any N-electron system with N>1, we can use "orbitals" to ...
4
votes
Accepted
Orthonormality of AOs and MOs in PySCF
Solving the Hartree-Fock equations is equivalent to unitary rotations of the orbitals, but you are missing the key piece: before Hartree-Fock, the basis set is orthonormalized to produce an ...
- 19.1k
3
votes
Accepted
How to plot HOMO-LUMO diagram using python?
The e_Lumo and e_Homo can be calculated using pyscf and scipy.
I will demonstrate using a simple molecule such as ethanol:
Code:
Helper functions and init:
...
- 3,043
3
votes
How to select the projections and inner/outer window for Wannier90 calculations?
Notes on my answer: I'll mainly link to arXiv versions of papers, but will also link the peer-reviewed version if the arXiv page doesn't do that itself. DFA means "density functional ...
- 916
3
votes
Accepted
Verifying periodicity of crystalline orbital modulus in PySCF
Setting the unit='Bohr' flag in gto.M (as originally suggested in the comments) resolved the issue in the latest version of the ...
- 61
3
votes
Accepted
Does the relaxed density (and therefore the relaxed orbitals) depend on the final energy in OO-DHDF+D calculations?
The DFT-D family of corrections, including DFT-D2, DFT-D3 and DFT-D4, are energy corrections that depend on the atomic coordinates but not the wavefunction. (The DFT-D4 energy does depend on atomic ...
- 9,621
3
votes
Accepted
How is the LUMO lower energy than the HOMO for triplet state restricted-open shell DFT calculation?
It would be better to use the word SOMO (Singly Occupied Molecular Orbital), not HOMO. Now assume that you have two SOMOs (or SOMO and SOMO-1 if you prefer). Here are my suggestions:
The first thing ...
- 806
3
votes
Accepted
When orbitals are labeled based on their irreps in D2h, how are the orbitals ordered for an N atom?
"Nitrogen atom has a point group of Dinfh, but CFOUR uses a lower symmetry of D2h instead"
The point group of the N atom (or any atom) is $K_h$, not $D_{\infty_h}$, the latter would be ...
2
votes
In which irreducible representations shall I put the electrons in an F atom in PySCF?
If for oxygen you have:
{'A1g': (2,2), 'E1ux': (1,0), 'E1uy': (1,0),'A1u': (1,1)}
Then for fluorine I would simply put one more electron in either of ...
2
votes
How to get the HOMO/LUMO from spin up/down eigenvalues?
If you want to have eigenvalues for each spin, you need to run a spin polarized calculations. This will set the program to treat both spins differently. After that, you could obtain different values ...
- 23.3k
2
votes
Accepted
How to orthonormalize a set of Molecular orbitals?
Since S is created from orthonormal orbitals, it has 1.00 as diagonal elements.
If ${\bf S}$ is created from orthonormal orbitals, the overlap matrix is simply the unit matrix, ${\bf S}={\bf 1}$. ...
- 19.1k
2
votes
How do I determine the charge and spin multiplicity of a system?
My answer to "How to select charge and multiplicity for macro-molecules?" explains how to find the charge and multiplicity of a system. The reason why you cannot just figure it out based on ...
2
votes
Numerical atomic orbitals vs Gaussian-type orbitals for molecular calculations
In some cases at least, NAO give smaller BSSE (basis set superposition error).
Here is the figure from the FHI-aims paper:
The BSSE here is the difference between red and black lines. It is small, ...
- 710
2
votes
Is it possible to plot the pDOS or visualize the molecular orbitals from GAMESS outputs?
Yes, you can get what you want. If you have a Gaussian .fch file, you can visualize MOs using GaussView/Multiwfn/... any GUI you like. And you can plot PDOS by loading the .fch file in Multiwfn(http://...
- 806
1
vote
Is there a way to add 4f-oribital information in Pseudopotential?
You can try the PP: Eu.pbe-spdfn-kjpaw_psl.1.0.0.UPF. I have used this one for Hubbard correction of Eu-4f orbitals a while back. I have uploaded it here: https://drive.google.com/file/d/...
- 51
1
vote
How may I calculate atomic orbital energies using VASP?
I will suppose that you have done the following as your approach looks correct, you shoud have performed an (SCF) calculation and include a sufficient number of bands to accurately capture the d ...
- 3,273
1
vote
How do I interpret the Gaussian16 wavefunction file?
https://aim.tkgristmill.com/wfxformat.html
WFX format specification. WFX is an AIM file.
Yes, Cartesian.
https://wordpress.nmsu.edu/tmanz/files/2020/06/WFX_file_programmers_guide_06_14_2020.pdf
WFX ...
- 11
1
vote
How to get the crystal/ligand field splitting of d orbital of Fe complex using Quantum Espresso
You should take into account that for this type of square planar complex the set of 5 "d" orbilals of the iron atom are the ones that must be considered for the calculation. Usually, ...
- 11
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