Questions tagged [orbitals]

For questions about properties and types of orbitals

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Orthonormality of AOs and MOs in PySCF

I have a basic question about how to calculate molecular-orbitals from atomic-orbitals in PySCF using the self-consistent field approach. My understanding mathematically is as follows: we start with a ...
Solarflare0's user avatar
3 votes
1 answer
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How to get the HOMO/LUMO from spin up/down eigenvalues?

I'm working with OpenMX and see that I have eigenvalues in the output in two columns: one for spin up and one for spin down. How would I know what the total eigenvalue is? Would I just add them ...
lzzard's user avatar
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How to orthonormalize a set of Molecular orbitals?

I am using PySCF, and checked that the molecular orbitals(MO) from the HF calculation are orthonormal. If S is the Overlap matrix, and V is the matrix of the MO coefficients, It can be seen from the ...
Pro's user avatar
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2 votes
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How do I determine the charge and spin multiplicity of a system?

I have a compound (5c from here) as below which I wish to optimize in ORCA. However, I am not sure what is its charge and multiplicity. This is an Ir(III) complex. Iridium has a valence configuration ...
farmaceut's user avatar
7 votes
1 answer
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Numerical atomic orbitals vs Gaussian-type orbitals for molecular calculations

Gaussian-type-orbitals (GTOs) are the work horse of modern molecular quantum chemistry calculations. They are computationally efficient and allow for analytic evaluation of integrals. However, there's ...
Fracton's user avatar
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Finding HOMO/LUMO from SCF calculation: VASP

I'm running some SCF calculations in VASP, and when looking at the OUTCAR, I see that for each KPOINT there is a slightly different value for the HOMO/LUMO (looking at Band No. and Occupation values, ...
lzzard's user avatar
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How to evaluate excited state MO coefficients using Dalton Pacakge?

I need the excited state (T1) wavefunction associated with my benzene molecule, but even after trying multiple times using multiple input formats, I am not able to find the correct input to evaluate ...
compcal's user avatar
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Is there a way to add 4f-oribital information in Pseudopotential?

Now, I'm calculating with a Quantum Espresso program I want to need Eu pseudopotential file with 4f orbital information. But I couldn't find that file, no matter how much I search on the internet. ...
Y. S. Lym's user avatar
4 votes
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195 views

How may I calculate atomic orbital energies using VASP?

I am trying to calculate the d orbital energy of the Cu single atom, like in this page, I have tried to use the Eigenband energies minus the vacuum energy level(about 0.007eV). ...
Jack's user avatar
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3 votes
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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 ...
phonon's user avatar
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Change bonding thresholds in NBO Calculations? [closed]

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, ...
NicoleJ's user avatar
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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, ...
Kanghun Kim's user avatar
3 votes
1 answer
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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 ...
Kevin Freddo's user avatar
2 votes
1 answer
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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 ...
lzzard's user avatar
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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 ...
Harshdeep Chhabra's user avatar
5 votes
1 answer
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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 (...
diamond999's user avatar
6 votes
2 answers
112 views

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 ...
C_Swann22's user avatar
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7 votes
1 answer
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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 (...
Mika R.'s user avatar
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1 answer
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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 ...
lex2763's user avatar
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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"...
Kanghun Kim's user avatar
4 votes
1 answer
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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-) ... ...
Alex I's user avatar
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6 votes
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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 ...
neco's user avatar
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Basic but fundamental question on the extended Koopman theorem using Dyson orbitals [closed]

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 ...
Kanghun Kim's user avatar
4 votes
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Do the orbital energies of ground-state Dyson orbitals exactly capture arbitrary excitation energies and/or ionisation potentials/electron affinities? [closed]

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 ...
Kanghun Kim's user avatar
6 votes
2 answers
213 views

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 ...
Kanghun Kim's user avatar
3 votes
1 answer
168 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). ...
neco's user avatar
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4 votes
1 answer
549 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 ...
Szgoger's user avatar
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1 answer
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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 ...
diamond999's user avatar
5 votes
1 answer
287 views

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 ...
diamond999's user avatar
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1 answer
1k 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 ...
UJM's user avatar
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10 votes
1 answer
455 views

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 $\...
Arc's user avatar
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9 votes
1 answer
101 views

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 ...
neco's user avatar
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9 votes
3 answers
396 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. ...
neco's user avatar
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18 votes
1 answer
1k views

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 $e^{-\alpha r}$ ...
Arc's user avatar
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10 votes
0 answers
1k 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 ...
Steve Cox's user avatar
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8 votes
1 answer
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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. ...
Jack's user avatar
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7 votes
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96 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 ...
nougako's user avatar
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5 votes
1 answer
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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,...
Paul Logan's user avatar
6 votes
0 answers
71 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 ...
O2_AC's user avatar
  • 171
10 votes
1 answer
183 views

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{...
A quarky name's user avatar
6 votes
0 answers
64 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 ...
Wychh's user avatar
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10 votes
1 answer
754 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 ...
ironmanaudi's user avatar
5 votes
0 answers
172 views

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 ...
Carlos's user avatar
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8 votes
2 answers
2k 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 $2p_x$, ...
neco's user avatar
  • 1,779
11 votes
2 answers
1k 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 ...
neco's user avatar
  • 1,779
12 votes
1 answer
665 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 ...
Martin - マーチン's user avatar
7 votes
0 answers
90 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 ...
Hydrogen's user avatar
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5 votes
0 answers
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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 ...
Suslik's user avatar
  • 261
9 votes
1 answer
463 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, $M = {(\ce{O}, R_\ce{O}), (\ce{H}, R_\ce{H}), (\ce{H}, R_\ce{H})}$, ...
Lin Lin's user avatar
  • 93
17 votes
1 answer
2k views

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 ...
DJA's user avatar
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