Questions tagged [ab-initio-calculations]

For questions about ab-initio (first principle) calculations.

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6 votes
0 answers
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What are the parameters in PySCF's Selected Configuration Interaction code

Dear StackExchange Members, I'm using the native PySCF implementation of selected configuration interaction (SCI). However, I can't seem to find any documentation detailing the algorithm or various ...
7 votes
1 answer
337 views

Have quantum computers been proven to speed up any matter modeling algorithm?

Personally, I think quantum chemistry is one of the most promising applications for quantum computers because the problem itself is fundamentally quantum, so there is an obvious argument why we should ...
4 votes
0 answers
53 views

CCSD calculation between two orbitals

I am trying to calculate the CCSD energies between two orbitals. Suppose I have a system, ...
2 votes
0 answers
35 views

Clarification Needed about Topological Invariants

I am seeking clarification on whether choosing the appropriate topological invariants has any relation to the dimensionality of the system. I understand that in three-dimensional (3D) materials, the ...
4 votes
0 answers
61 views

What do Negative Atomic Orbital Contributions in a Mulliken Population Analysis mean?

I am performing a Mulliken population analysis (MPA) for a molecular system of interest (calculated with B3LYP/Def2-TZVP). I am analyzing the LCAO-MO coefficients/contributions associated with each &...
4 votes
3 answers
120 views

Terminology: "Calculated" vs "Computed" for Properties Studied with First-Principles

When discussing properties studied using first-principles methods like density functional theory (DFT), I often come across the terms "calculated" and "computed" to describe the ...
1 vote
0 answers
39 views

Error in VASP calculation

I have been trying to do Piezoelectric and Elastic calculations for my system in VASP, and i ended up with this error. Spin polarized Harris functional is a good joke What am I doing wrong? Here is ...
3 votes
1 answer
75 views

vdW Corrections for Comparing the Effects on Small Molecule Adsorption

Is it necessary to perform a new geometric relaxation with vdW corrections enabled for each implementation (DFT-D2, DFT-D3, etc.) when comparing their effects on the adsorption of small molecules on a ...
9 votes
2 answers
376 views

Quantifying relativistic effects in DFT calculations

I am wondering what is the best approach to quantify the contribution of relativistic corrections to a result of an electronic structure calculation. As far as I understand, from a user perspective ...
3 votes
0 answers
34 views

What is a relaxed reduced density matrix?

I am trying to understand how to calculate electronic properties using reduced density matrices from electronic structure calculation. So far, I understand (I think) that for the expectation value of ...
4 votes
0 answers
41 views

Photorealistic Rendering: How To?

i have started computationally modelling materials from first principles recently, my code of choice being VASP [6.1.0]. Recently i have come across this paper in Nature: DOI:10.1038/s41567-023-01960-...
5 votes
2 answers
72 views

ASE: How to plot the irreducible Brillouin zone and this bandpath from a bandpath object

I am using ASE (Atomic Simulation Environment) for theoretical chemistry and I see an option to plot the irreducible Brillouin zone and this bandpath but I can't figure out how. I'm not a programmer. ...
4 votes
1 answer
53 views

Finding optical properties (epsilon) by Quantum ESPRESSO

I am calculating the dielectric (Epsilon) for ZnO by quantum espresso, when I run the eps.in file, I always get this error. Reading namelist energy_grid' How do I ...
4 votes
0 answers
41 views

Carbon Capture Research - Force Constants & Basis Sets

Greetings Matter Modeling, I'm researching carbon capture dynamics in the context of sorbent regeneration. The UN IPCC Net-Zero goal requires 75 Mt-CO₂/year captured by 2030. According to the IEA, we ...
4 votes
1 answer
90 views

Unrestricted Hartree-Fock : Density matrices initialization

I have some results about the energy of H2 as a function of the bond length using Restricted HF (RHF) and Unrestricted HF (UHF) methods. With a zero-initialization of the density matrix I have the ...
6 votes
1 answer
127 views

Has non-orthogonal CI (NOCI) been implemented in PySCF?

I'm kinda new to Pyscf and was wondering if there is a way to do non-orthogonal CI calculations with it. I would appreciate any help.
2 votes
1 answer
91 views

Relationship between grand potential and free energy?

What is the fundamental relationship between grand potential and free energy? In other words, what assumptions need to be made in order to obtain the free energy equation rather than the grand ...
8 votes
3 answers
752 views

How to calculate formation energy using DFT+U?

I noticed that a lot of articles use DFT+U methods to calculate different formation energies when using regular DFT and DFT+U methods. For example, in the attached paper[1] on $\ce{In2O3}$, the ...
6 votes
1 answer
144 views

How are 2-electron integrals usually computed?

I want to compute 2-electron coulomb integrals. When the Primitive Gaussian is not centered at 0, my quadrature scheme fails unless I increase the number of quadrature points. I am currently using a ...
6 votes
1 answer
93 views

How can I calculate the elastic properties of a unit cell and a supercell?

Can someone please share with me a method to compute the elastic constants of the unit cell and doped supercell of a material? In my calculation I use Quantum ESPRESSO. And I already tried Thermo_pw, ...
2 votes
1 answer
183 views

Energy of formation Vs Formation Energy Vs Heat of Formation Vs Energy Above Hull differences

I work in the field of materials science. While exploring the concepts related to material stability, I have come across terms such as "Energy of Formation," "Formation Energy," &...
3 votes
1 answer
65 views

What is the gold standard ab initio pair-potential between two water molecules?

There are a myriad of pair potentials available for simulating the interactions between water molecules, ranging from simpler models like the SPC/E to more sophisticated ones based on high-level ...
4 votes
2 answers
91 views

How to get DOS for each iteration?

Do any DFT codes (for example, QE ABINIT, Fleur, ....) provide the availability of getting the DOS that produced by each iteration? If no, so, how can I get them? Thanks in advance!
5 votes
0 answers
147 views

Actual calculation of Coulomb energy in DFT softwares

I have a question about the actual calculation of classical Coulomb interaction term in density functional theory (DFT) softwares. Of course I understand the form Coulomb energy as: $\int\int \frac{\...
4 votes
1 answer
134 views

Which lattice parameter should be used, the one obtained by vc-relax or the optimized value acquired through the Birch-Murnaghen equation?

To determine the lattice parameter of a material, I did a VC-RELAX calculation using Quantum ESPRESSO, and I also applied the Birch-Murnaghen equation to obtain the optimized lattice parameter. ...
2 votes
0 answers
78 views

BURAI eliminates atoms when I try to modify the input file

I'd like to get the monolayer input file for MoS2 using BURAI 1.3. I downloaded the .cif file from Materials Project and with the Modeler function I created a Monolayer MoS2 but when I clicked "...
6 votes
2 answers
228 views

Number of k-points for unit and super cell

I am just new with solid state calculation and would like to know one thing. Why is plane wave basis set is good for 1s and 2s orbitals, but for higher convergence is poor? Why is it better to use ...
1 vote
1 answer
115 views

Vc-Relax never stops

I'm a newbye in DFT calculations and it's my first time I use vc-relax. I have to find optimal cell parameters for mono-layer $MoS_2$ and that's my code : ...
4 votes
0 answers
64 views

What kinds of calculations have to execute for obtaining the velocity of the chemical precipitation of some salt on a thread from a water-salt mix?

Some salt ($\ce{NaCl}$ or another one) of $m$ grams is dissolved in some water of $V$ liters. After mixing up, the substance looks transparent or to put it more exact as a chemical solution. Then a ...
7 votes
1 answer
2k views

Raman Spectra in Quantum Espresso

Does anyone have any experience simulating Raman spectra in Quantum ESPRESSO? Following the example 15 that comes with QE, I have attempted to simulate the Raman spectrum of MgO. I know the lraman ...
5 votes
1 answer
114 views

How the adsorption energies calculated at DFT level, is valid at finite temperatures?

The adsorption energies of atoms or molecules on any surface in a standalone DFT are inherently devoid of any temperature influence. so, let's say an atom/molecule has very weak binding, in ...
2 votes
1 answer
190 views

What files are important while taking backup of a VASP calculation?

I have more than 10000 files related to calculations done using Vienna Ab-initio Simulation Package. These files are stored in my University's server. I want to take these files in my personal drive ...
3 votes
1 answer
116 views

How to maintain constant liquid density during AIMD with NPT ensembe?

I have constructed a solid-liquid interface model with water as the liquid phase. During the AIMD simulation, I used the NPT ensemble. However, I noticed that under the NPT ensemble, the entire model'...
3 votes
2 answers
67 views

How to remove f functions from a cc-pVQZ basis set in CFOUR format?

I need to perform a calculation on a BN system with using cc-pVQZ stripped of the f functions. However, I don't really know how to do this and I have not been able to find a revised one already. I ...
4 votes
1 answer
172 views

Computing the kinetic energy of a molecular orbital

I want to compute the kinetic energy of the molecular orbitals computed by Gaussian 09, the variable U in this paper. Can it be computed from the orbital energy using a formula or does it need to be ...
7 votes
2 answers
231 views

How to get the directives of a slurm for my Quantum ESPRESSO calculations?

Context I saw some examples of SLURM scripts on the internet like the one below: ...
5 votes
1 answer
123 views

A terminology for QM calculation methods

I wonder if there is any terminology (or name of classification) that refers to ab-initio QM methods based on the Schrodinger equation and basis functions, such as HF and post-HF methods, but not DFT ...
14 votes
2 answers
383 views

Translating fractional coordinates resulting from conventional cell and primitive cell

I have calculated the band structure of some material where the unit cell was the conventional one (i.e. the lattice vectors are orthogonal). I'm trying now to calculate the same band structure only ...
5 votes
3 answers
491 views

Energy of each fragment in ORCA?

After the definition of the fragments in the geometry section of the calculation, is there a method to call, or a keyword to turn on, in order to obtain the energy of the fragments themselves? ...
5 votes
0 answers
113 views

How to scan Improper Dihedral in Orca? [closed]

I am using Orca 4.2.1 for the ab initio calculation. Scanning the redundant coordinates I am trying to scan potential surface for different type of bonds, angles and dihedrals. How can I do so for ...
4 votes
0 answers
67 views

How to locate HOMO-LUMO molecular orbitals in Transmisson and PDOS graphs? [closed]

I have done TBtrans calculations using SIESTA (v4.0.2) and plotted transmission, as well as PDOS Vs Energy graphs. I want to know how to locate HOMO-LUMO MOs in those graphs (or) how can I say which ...
7 votes
1 answer
113 views

Is there a system of multiple interacting quantum particles for which the density can be obtained analytically?

I know that it is impossible for real electrons and nuclei. In the Kohn and Sham approach, a system of interacting electrons is approximated by a system of non-interacting Kohn-Sham particles in an ...
3 votes
1 answer
127 views

Can the electrical conductivity tensor of a crystal be obtained from a Hartree-Fock calculation?

Let’s assume that a crystal has been calculated by Hartree–Fock (HF) method (or DFT one), i.d., so to speak, the "first characteristics", which are eigenvalues and eigenvectors, as well as ...
7 votes
1 answer
277 views

What are Crystal Electric Field Parameters?

What does the following notation mean? $$A_{20}\left<r^2\right> = -100 \mathrm{K}$$ Where $A_{20}$ is termed a Crystal Electric Field Parameter. I often see this notation when reading papers on ...
4 votes
0 answers
99 views

Setting a frozen core in Molpro

I am carrying out a project which involves obtaining the RHF result and the integrals for the chromium dimer (Cr2) under Ahlrichs' SV basis. In the literature against which we attempt to benchmark, ...
6 votes
1 answer
209 views

Transport calculations using Transiesta

I have recently started calculating transport properties using Transiesta and TBTrans. However, I have noticed that: the TS.Contours.Eq.Pole value recommended is the default. In the last version of ...
2 votes
0 answers
53 views

Excited state frequency for periodic systems [closed]

Is there any way to calculate the excited state frequencies of a period system using DFT?
15 votes
1 answer
288 views

What are the ways to add dynamic correlation to an MCSCF wavefunction?

We recently learned about the many types of MCSCF, which treat "static" electron correlation. There are then many ways to treat further "dynamic" electron correlation to try and ...
7 votes
1 answer
260 views

Ab-initio molecular dynamics of liquid systems: best tools and resources

I have been studying liquid systems (particularly deep eutectic solvents) using classical molecular dynamics (MD) simulations. The main drawback of classical MD is the arbitrariness of the potential ...
8 votes
1 answer
423 views

How to run 2nd generation CPMD in CP2K?

I believe CP2K by default implements Born–Oppenheimer MD. I have seen many recent papers that use 2nd generation Car–Parrinello MD using CP2K. But I couldn't find any direct way of switching to 2nd-...