Questions tagged [orbitals]
For questions about properties and types of orbitals
51
questions
3
votes
1
answer
118
views
Verifying periodicity of crystalline orbital modulus in PySCF
I'm trying to verify that the modulus of the crystalline atomic/molecular orbitals computed by PySCF satisfy the correct periodicity condition for the supercell. I'm considering a hydrogen chain ...
- 61
1
vote
0
answers
19
views
Change bonding thresholds in NBO Calculations?
I'm looking at a system with really long bond lengths, and I'm trying to determine if there's any interaction at all between orbitals on two particular atoms.
I'm using NBO7 with the GENNBO interface, ...
- 11
2
votes
1
answer
32
views
Does the relaxed density (and therefore the relaxed orbitals) depend on the final energy in OO-DHDF+D calculations?
During an OO-RI-ωB97X-2-D2 calculation on ORCA, the non-dispersion-corrected OO-DHDF part of the calculation is performed, the D2 dispersion correction energy added to the resulting OO-DHDF energy, ...
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3
votes
1
answer
48
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How is the LUMO lower energy than the HOMO for triplet state restricted-open shell DFT calculation?
I recently ran a calculation using the ROB3LYP/LANL2DZ level of theory for a triplet spin molecule. While analyzing the results, the HOMO is doubly degenerate and the LUMO is singly degenerate. I ...
- 145
2
votes
1
answer
37
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Is it possible to plot the pDOS or visualize the molecular orbitals from GAMESS outputs?
I'm using the GAMESS software and want to try to plot the pDOS for my systems and visualize the molecular orbitals. I was thinking I could get the data from one of the ...
- 53
3
votes
1
answer
105
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How to get the crystal/ligand field splitting of d orbital of Fe complex using Quantum Espresso
So I am working with Quantum Espresso (6.5) and we have built a few square planar Fe complexes (to be specific $\ce{Fe(NH_2)_2(OH)_2}$ cis and trans), and we ran scf (self consistent calculation) and ...
5
votes
1
answer
219
views
How to plot HOMO-LUMO diagram using python?
I'm trying to create a HOMO-LUMO diagram for a presentation, similar to the below figure from ResearchGate. I would like to learn how to do this with Python if possible, since I know this language (...
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6
votes
2
answers
94
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NBO analysis of potentially hypervalent compounds
I know that one can determine which type of bond is present between different atoms in a molecule by analyzing the output of an NBO analysis. Furthermore the second order perturbation theory analysis ...
- 523
7
votes
1
answer
179
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Spin-Orbit coupling effects in topological insulator Bi2Se3
I'm currently trying to understand this paper explaining the origin of band inversion in the topological insulator Bi2Se3. In Fig. 2 (see below) they explain by means of 4 steps how certain atomic (...
- 141
7
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1
answer
317
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How is the zero energy defined for molecular orbitals?
In DFT and Hartree-Fock bonding orbitals have negative energies while antibonding orbitals have positive energies. Why is this the case? It seems this is due to the zero-point energy being defined for ...
- 321
1
vote
0
answers
53
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Question on possible cancellations in the computation of Dyson orbitals from FCC/FCI wavefunctions [closed]
Dyson orbitals are mathematically meaningful, in the sense that they, unlike the DFT orbitals for instance, are actual observables of the wavefunction, instead of being "the other way around"...
- 870
4
votes
1
answer
222
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How many electrons and orbitals should I include in a CASSCF calculation?
I'm interested in running CASSCF calculations to get a dissociation curve for a number of systems of the form: atom-atom, atom-diatomic or diatomic-diatomic (e.g. Li+ ... O-, K+ ... O2, or N(3-) ... ...
- 801
6
votes
1
answer
126
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Importance of orbitals other than HOMO and LUMO
I know that the HOMO, LUMO, and its gap are useful in understanding the physical properties and chemical reactions of molecules.
Here, are there any phenomena in physics or chemistry that other ...
- 1,779
6
votes
0
answers
102
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Basic but fundamental question on the extended Koopman theorem using Dyson orbitals
Let there be some ground-state N-electron species named A. A Dyson orbital for Q is defined as the overlap between Q and (Q with one electron removed). The extended Koopmans theorem now states that ...
- 870
4
votes
0
answers
71
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Do the orbital energies of ground-state Dyson orbitals exactly capture arbitrary excitation energies and/or ionisation potentials/electron affinities?
According to an answer to my question on whether the Kohn-Sham orbital energies theoretically exactly capture arbitrary ionisation potentials and/or excitation energies, the answer is no for both ...
- 870
6
votes
2
answers
208
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Closed-form expression for excitation energies, given the exact XC functional
In an answer to my question regarding the theoretical rigour in computing excitation energies using only the Kohn-Sham orbital energies, the rigour turned out to be nonexistent.
After looking this ...
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3
votes
1
answer
164
views
How to determine the concrete value for the wavenumber in tight-binding approximation
As a simple problem setting,
consider a one-dimensional linear crystal of NaCl with only 1s orbitals,
where the atomic distance between Na and Cl is also assumed to be 0.5 Å
for simplicity (Fig. 1).
...
- 1,779
4
votes
1
answer
412
views
Molecular orbital values on grid points in PySCF?
I am looking for a way to easily evaluate individual molecular orbitals on a grid(assuming a single determinant method for now) in PySCF.
I am aware on how to generate efficient grids for real-space ...
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4
votes
1
answer
144
views
What is the difference between NBO program and NBO that we find in Gaussian?
I'm a little bit lost with NBO (natural bond orbital) analysis in Gaussian. I was told that pop=NBO in Gaussian gives me the charges of atoms, but that the NBO ...
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5
votes
1
answer
200
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How can I distinguish between n, pi, pi* orbitals when looking for excited states?
I recently asked about how to distinguish between transition types. I got an answer there about determining the character or type of the orbitals.
My problem now is that I'm not sure how to determine ...
- 795
7
votes
1
answer
533
views
How to select the projections and inner/outer window for Wannier90 calculations?
I am new to Wannier90 calculations. I am trying to obtain the Wannier functions and Wannier interpolated band structure.
But I am having a problem in setting the parameters like ...
- 2,521
10
votes
1
answer
447
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How to calculate molecular orbitals of octaoxygen under high pressure?
This question about octaoxygen:
Why is octaoxygen diamagnetic?,
was asked in chemistry, but I really don't have an answer in terms of molecular orbitals. I think it could be a mixing of the O$_2$'s $\...
- 593
9
votes
1
answer
95
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Too large value of s-orbital in near nucleus
After my previous question (here), I'm now studying the orbitals actually used in Gaussian through calculating them myself using Basis Set Exchange data. However, I found that some orbital exponents ...
- 1,779
9
votes
3
answers
342
views
The number of orbitals in Gaussian/GAMESS log file
After calculating the energy of a $\ce{CH4}$ molecule with a 6-31G(d,p) basis set, I obtained the Gaussian/GAMESS log file and describe a part of the log file as follows.
...
- 1,779
17
votes
1
answer
1k
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Do we know for sure that all atomic and molecular wavefunctions decay exponentially as r goes to infinity?
Slater type orbitals (STO) are considered to be more accurate than gaussian type orbitals (GTO) for atomic and molecular QM calculations because - among other reasons - they decay with $e^{-\alpha r}$ ...
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10
votes
0
answers
866
views
How to visualize natural atomic orbitals from PySCF [closed]
I'm trying to visualize the different methods of getting localized orbital (LO) given in the User Guide. I went through the example, saved the orbitals as cube files, then opened the files in ...
- 303
8
votes
1
answer
60
views
Does the INIWAV tag in VASP assume that the wavefunctions are plane waves?
I am trying to figure out how to set the initial wavefunction in VASP, on the VASP wiki page of INIWAV, it is said that VASP would fill wavefunction arrays with random numbers.
...
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7
votes
0
answers
87
views
Is the formula of a Dyson orbital independent of whether there is degeneracy or not in the HOMO of the neutral?
A Dyson orbital is defined as:
$$
\textrm{Dy}(x) = \int dx_1 \ldots dx_{N-1} \, (\Psi^+(x_1,\ldots,x_{N-1}))^* \, \Psi^0(x_1,\ldots,x_{N-1}, x),\tag{1}
$$
where $\Psi^0$ and $\Psi^+$ are the total ...
- 595
5
votes
1
answer
566
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Modify ORCA orbitals for CASSCF
I have run a HF calculation on naphthalene and I have checked the MOs that have been obtained. Now, I have to select my active and inactive orbitals for CASCF(10,10). As there are 34 occupied orbitals,...
- 967
6
votes
0
answers
58
views
Confused by NBO output, due to missing bonds [closed]
I'm about to do an NBO analysis to evaluate bond characteristics in a novel transition-metal complex.
As I have never done anything like that, I tried to understand the basic output for an octahedral ...
- 171
10
votes
1
answer
167
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Orthonormality of Kohn-Sham orbitals
I was wondering if Kohn-Sham orbitals corresponding to a different Bloch wavevector should be orthogonal? I know that we should have $$\int d \boldsymbol{r}\phi_i(\boldsymbol{r}) \phi_j^*(\boldsymbol{...
- 103
6
votes
0
answers
63
views
Orbital space clustering [closed]
I am interested in how the orbital space of a system can be partitioned into clusters.
I read reading 'Cluster many-body expansion: A many-body expansion of the electron correlation energy about a ...
- 2,003
10
votes
1
answer
663
views
Molecular orbitals and active space
During the same minute as asking this question, I also asked this at Quantum Computing SE.
In Qiskit, each qubit corresponds to one spin orbital. For example, the $\ce{N2}$ molecule would have 10 ...
- 435
5
votes
0
answers
149
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Predict the density of states (DOS) diagram for rhenium oxide (ReO3) from the molecular orbital diagram [closed]
Yesterday I made this query on Chemistry Stack Exchange, and a user has felt that perhaps here I will get a quicker answer.
The structure of rhenium(VI) oxide, $\ce{ReO3}$, is similar to that of ...
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8
votes
2
answers
1k
views
Is the number of basis functions same in the different atoms in the 6-31G basis set?
I'm now studying the quantum chemistry calculation and Gaussian basis set.
For example, when using the 6-31G basis set,
the C atom has 6 basis functions in 1s orbital:
3+1=4 in $2s$,
3+1=4 in $2p_x$,
...
- 1,779
11
votes
2
answers
957
views
Critical difference and roles of Slater- and Gaussian-type orbitals
I was very interested in the following question and answer about the Slater- and Gaussian-type orbitals (STO and GTO) used in quantum chemistry and a practical calculation.
Gaussian-type orbitals vs ...
- 1,779
12
votes
1
answer
525
views
How to calculate and plot localised orbitals with xTB?
The question is similar to How to calculate/plot molecular orbitals with XTB? Hence we can produce molden files from xTB calculations, which include the molecular orbitals. How do I proceed to get ...
- 1,561
7
votes
0
answers
89
views
Is there a software package to analyse interactions in crystals? [closed]
I have been using Quantum ESPRESSO, specifically the pp.x module to
study interactions via charge density plots. The process is slow as
for crystals containing ...
- 159
5
votes
0
answers
43
views
Kinetic energy cut-off for Gaussian-type orbitals when applying periodic boundary conditions [duplicate]
I have a solid with PBC (periodic boundary conditions) and I want to perform a DFT simulation. I use GTO as the basis. In a paper I read, I can transform the GTO to a Bloch function (crystalline ...
- 261
9
votes
1
answer
417
views
How can I implement the Cartesian harmonics?
I'm studying the quantum chemistry calculation and now trying to implement the basic methods.
For example, given a water molecule,
$M = {(\ce{O}, R_\ce{O}), (\ce{H}, R_\ce{H}), (\ce{H}, R_\ce{H})}$,
...
- 93
16
votes
1
answer
2k
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Gaussian-type orbitals vs Slater-type orbitals in terms of computational efficiency
When creating molecular orbitals via the linear combination of atomic orbitals method I am told that Slater orbitals provide a more accurate representation whilst Gaussian orbitals are computationally ...
- 841
5
votes
0
answers
452
views
How can I calculate and plot the molecular orbitals (MO's) from the Gaussian wavefunction file? [closed]
This a follow-up question to my previous question. And as per the answer one could create M.O orbitals from the primitives.
As a new user of Gaussian, is there any method (or algorithm) to followed so ...
- 957
8
votes
2
answers
467
views
How do I interpret the Gaussian16 wavefunction file?
I'm new to gaussian16. The wave function file that I obtain as a result of the "Energy" calculation. It consists of five distinct parts :
PART 1 :
...
- 957
8
votes
1
answer
1k
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How to get the .47 file from ORCA for natural bonding orbital analysis
I am trying to perform NBO analysis with relaxed density matrix with the open-source program JANPA. I am following the guide here. The first step is to get the NBO input .47 file from Orca v4.2.1. The ...
- 6,436
9
votes
1
answer
278
views
How are molecular orbitals constructed from the coefficients and basis set?
When an SCF calculation is done in a QM program, the MO coefficients of the solution are printed into the output. Now, graphical softwares can plot 3D molecular orbitals from these coefficients, ...
- 6,436
10
votes
1
answer
297
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How to calculate/plot molecular orbitals with XTB?
I started playing with the XTB program (XTB is developed by Prof. Grimme group's, is based on tight binding and uses the GFN force field).
Question: How can I calculate/plot the molecular orbitals?
I ...
- 22k
12
votes
2
answers
499
views
Is there any relation between static correlation and finite-temperature smearing?
I am new to this field, so there is a chance that I am mixing two entirely different concepts together, but it seems to be that static correlation and finite-temperature smearing in DFT are somehow ...
- 6,436
6
votes
0
answers
185
views
Unresolvable inconsistency between charge and multiplicity and orbital occupancies. Error while Distance Scan [closed]
I get the message mentioned in the title after a distance scan with a Gaussian calculation. I have bound a gold atom to a carbon in the pyridine ring and now pull this further and further out with a ...
- 816
15
votes
2
answers
375
views
What is the difference between orbital localisation and NBO?
I am new to computational chemistry, I have used mainly GAMESS and Orca. In GAMESS, there are orbital localisation schemes like Pipek-Mezey, Ruedenberg-Edminston, etc. which generate orbitals that ...
- 6,436
10
votes
1
answer
331
views
How to interpret molden AO/MO coefficients?
A simple calculation with Molpro 2012 on H2 molecule in cc-pvtz basis produces a molden file with 28 molecular orbitals. Each MO is defined with 30 AO/MO coefficient, but the number of symmetric AOs ...
- 103