Questions tagged [ab-initio-calculations]

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

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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 ...
AWPrentice's user avatar
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 ...
taciteloquence's user avatar
4 votes
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CCSD calculation between two orbitals

I am trying to calculate the CCSD energies between two orbitals. Suppose I have a system, ...
Pro's user avatar
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2 votes
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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 ...
Jaafar Mehrez's user avatar
4 votes
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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 &...
Kevin Freddo's user avatar
1 vote
0 answers
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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 ...
Vivek karunakaran's user avatar
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 ...
Phill's user avatar
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9 votes
2 answers
377 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 ...
Szgoger's user avatar
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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 ...
Szgoger's user avatar
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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-...
F.N.'s user avatar
  • 41
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 ...
Jaafar Mehrez's user avatar
5 votes
2 answers
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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. ...
Samaray's user avatar
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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 ...
Phill McGee's user avatar
4 votes
1 answer
54 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 ...
user307903's user avatar
4 votes
1 answer
93 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 ...
mle's user avatar
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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 ...
mle's user avatar
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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, ...
Camilla's user avatar
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3 votes
1 answer
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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 ...
Lodin Ellingsen's user avatar
4 votes
2 answers
92 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!
Bekaso's user avatar
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2 votes
1 answer
192 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," &...
hamza's user avatar
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5 votes
0 answers
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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{\...
neco's user avatar
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4 votes
1 answer
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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. ...
Camilla's user avatar
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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 "...
CoolerThanACooler's user avatar
1 vote
1 answer
116 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 : ...
CoolerThanACooler's user avatar
6 votes
2 answers
229 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 ...
Alexander Teryahskin's user avatar
4 votes
0 answers
65 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 ...
SFriendly's user avatar
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3 votes
1 answer
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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'...
Tieyuan Bian's user avatar
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 ...
farmaceut's user avatar
  • 536
2 votes
1 answer
191 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 ...
Sufyan's user avatar
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4 votes
1 answer
173 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 ...
Gotaquestion's user avatar
7 votes
2 answers
232 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: ...
Camilla's user avatar
  • 2,049
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 ...
nonon's user avatar
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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 ...
Alukaar's user avatar
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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.
master_disaster's user avatar
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 ...
Shanmuka Rao's user avatar
5 votes
3 answers
497 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? ...
Andrea Pellegrini's user avatar
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?
sthomas's user avatar
  • 21
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 ...
user35952's user avatar
  • 331
4 votes
1 answer
119 views

Crash of DF-CCSD or DF-CCSD(T) geometry optimization (MRCC package)

I am interested in geometry optimization at the CCSD(T) or DF-CCSD(T) level, with MRCC. The calculation, however, crashes when executing prop: ...
EvGeniy's user avatar
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6 votes
1 answer
211 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 ...
Laura's user avatar
  • 1,187
4 votes
1 answer
200 views

The relation between applied voltage and band gap in Transport calculation (DFT+NEGF)

Hello Dear StackExchange Comunity, Based on some interesting papers related to quantum transport calculation (Transiesta published paper...), the voltage applied in the device shifts the Fermi level ...
Hananab's user avatar
  • 359
4 votes
3 answers
537 views

Does the RI method actually accelerate basis convergence of MP2, "by one more zeta"?

It is often said that the resolution of the identity (RI) method accelerates the basis set convergence rate of MP2 "by one more zeta", e.g. that RI-MP2/cc-pVTZ/cc-pVTZ results are close to ...
Kanghun Kim's user avatar
2 votes
0 answers
53 views

How to calculate the forces of attraction between a surface and molecules of a substance at a corrosion affection? [closed]

Previously, a question was asked about an equation that is able to calculate the forces of attraction between a surface and molecules (of another substance). During the discussion of the question a ...
SFriendly's user avatar
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8 votes
1 answer
808 views

How to detect an "open shell" molecule?

I feel like this is a really stupid question, and I've been ashamed to ask for a while... When I'm about to run some electronic structure calculation on a molecule, how do I know if I need to use an ...
Zane Beckwith's user avatar
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 ...
Manasi Vyas's user avatar
3 votes
1 answer
230 views

Grand potential vs. Gibbs free energy of adsorption for ab initio thermodynamics

I have seen descriptions of ab initio thermodynamics where the phase energy diagram for the oxidation of metal surfaces can be constructed in terms of minimizing the grand potential or the Gibbs free ...
Manasi Vyas's user avatar
5 votes
0 answers
114 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 ...
Md. Rifat Hossain Kawshik's user avatar
6 votes
1 answer
229 views

Which functionals should I include for a simple hydrogen atom system?

I am writing my own (orbital-free, for now) 3D density functional theory code from scratch. It currently works correctly for the simple harmonic oscillator potential $V_\text{ext}(\mathbf r) = \frac12\...
dftsolo's user avatar
  • 61
7 votes
2 answers
456 views

Do bonds between the atoms influence ab-initio energies?

As you know, oxygen has two available states. However, the picture above illustrates oxygen (red) has a just one bonding with one carbon. I am kind of afraid it makes differences compared that an ...
Seung Hwan Kim's user avatar
7 votes
2 answers
532 views

What are the limitations of FCI?

I am aware of the fact that Full Configuration Interaction scales poorly. Taking into account that the number of $n$-times excited Slater determinants of an $N$-particle System with $M$ basis ...
Jannis Erhard's user avatar