Questions tagged [ab-initio-calculations]

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

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4
votes
2answers
30 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. ...
8
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2answers
639 views

Is there a benchmark paper that takes into account how often each molecule is studied?

There are many benchmark sets in different branches of computational chemistry and physics, that are frequently used to assess the "average error" of a method for a certain property, on a ...
9
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1answer
64 views

How to find the Cauchy stress tensor in solids using ab-initio methods?

I want to find the Cauchy stress tensor in certain materials with ab initio methods. I already have the analytical form of my own definition of "energy" and "forces" (not from DFT),...
6
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1answer
39 views

Transforming basis functions from Cartesian to speherical

I read the basis set from book A d-type GTO written in terms of the spherical functions has five components (Y2,2, Y2,1, Y2,0, Y2,1, Y2,2),but there appear to be six components in the Cartesian ...
5
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2answers
141 views

How can I get started on DFT?

This question is simply: How can we use DFT in the field of electrochemistry? What are the best resources (Books, reviews, papers, software ...) to learn about using DFT in electrochemistry? ...
6
votes
1answer
97 views

What are the electronic steps and ionic steps in VASP?

I am getting confused about what the electronic step and ionic step are in VASP. I used to think that finishing the following loop one time is called an electronic step. but I am not sure how to ...
6
votes
1answer
129 views

Why does it take 5-10 steps to obtain reasonable orbitals during initialization in VASP?

I am trying to figure out the initialization process of VASP, and I found an INCAR tag NELMDL, on the wiki page of NELMDL, it is said that VASP requires 5-10 steps to obtain the reasonable orbitals. ...
6
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0answers
68 views

How to interpret density of states and band structure of a material? [closed]

I am new on the VASP platform, and have learned how to calculate any material's DOS and Band structure. However, I don't know how to interpret these properties. Can you recommend resources that ...
13
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1answer
128 views

Physical interpretation of k-points

What is the Physical interpretation of the k-points used in ab initio calculations? Why must the number of k-points be optimized rather than just using some large fixed number of them?
6
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2answers
88 views

Relation between lattice parameter and energy for relaxations

We have been wanting to do relaxation of lattice parameters as a function of the energy. I want to know the mathematical expression for this, and also the theoretical background related to this method....
6
votes
1answer
102 views

Lattice Thermal conductivity calculation error

I have been trying to calculate Lattice Thermal Conductivity on my system using QuantumEspresso. I used phonopy and phono3py. I was successful to run these codes on Si system for practice. Now when I ...
6
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0answers
52 views

Comments on the electronic relaxation time variation between nanowire configurations

I am studying Si nanowires with different cross sections. In my work, I plan to evaluate the thermoelectric performance variation between different configurations. To achieve this, my current approach ...
10
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1answer
112 views

Can electron-phonon coupling be extracted from the dielectric function?

Computationally, there are various ways to calculate the electron-phonon coupling constants as a function of phonon index and momentum. My question is about the reverse process. Let us say that an ...
6
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0answers
42 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 ...
7
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1answer
47 views

Changing orientation of SQS structure generated from ATAT

I generated the following SQS cell using ATAT (the sructure is converted to POSCAR format) ...
7
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1answer
59 views

How Do you Produce your own MEAM Potentials?

I have come across the MEAM Parameter Calibration toolkit (link leads to Wiki, video tutorials, and download link for the package) for fitting your own MEAM potentials [1]. Is this the best software ...
5
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0answers
48 views

MedeA VASP: Determination of carrier concentration [duplicate]

My question is, how do I calculate the carrier concentration from a DFT study? I am using MedeA VASP for the DFT simulation.
5
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0answers
75 views

Methods to study reaction mechanisms in solid state reactions and identifying intermediates

An example of a solid state reaction: sintering of an initial powder of reactants leading to a product. Densification of the sintered powder giving a highly pure product powder. What methods (ab ...
11
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0answers
120 views

How may I calculate the "effective transfer integral" in free electronic-structure software?

I would like to calculate the following four quantities in a free electronic structure program: \begin{alignat}{2}\tag{1} e_1&=\langle\phi_1|H^{KS}|\phi_1\rangle,\\ e_2&=\langle\phi_2|H^{KS}|\...
12
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1answer
297 views

Comparing GAMESS, OpenMOLCAS and Psi4

Over the years many open-source ab initio packages have been developed and the diversity in subroutines, methods and portability (ability to interface with other software) is quite varied for ...
5
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2answers
86 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
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0answers
61 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 ...
6
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0answers
72 views

How to calculate energy gradient and Hessian with respect to only a few internal coordinates using Gaussian? [closed]

I would like to form the (numerical) gradient and the Hessian of the total electronic energy with respect only to a few internal coordinates (namely, the six intermolecular coordinates of a weakly ...
9
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0answers
61 views

Difference of high-frequency and static dielectric constants? [closed]

I found in an article [1] the following definition of FNV (Freysoldt, Neugebauer and Van de Walle) energy correction term for a charged defect in a cubic supercell: $$E_{\text{corr}}=\frac{\alpha_Mq^2}...
12
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2answers
345 views

For DFT and Hartree-Fock, how can we know that we have a true minimum? Is there an equivalent to the "frequency analysis" for geometry optimization?

In a geometry optimisation, one can check if they have reached a minimum by checking the phonons. And to a certain extent, the global minimum can be confirmed by relaxing from different starting ...
12
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2answers
227 views

What are the references in multi-reference methods?

After reading What exactly is meant by 'multi-configurational' and 'multireference'? I still don't understand what the multiple "references" are. I understand that you can for example use a ...
12
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2answers
88 views

What are properties of interest for energy storage materials?

In the field of simulation for energy storage materials, there is always a gap between theoretical calculations and demand for experimentalists. What could be directly calculated from ab initio ...
11
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1answer
103 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 ...
7
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2answers
102 views

What quantity to perform CBS extrapolation on for adsorption/binding energies?

When calculating complete basis set extrapolations for quantities, such as adsorption energies or binding energies, which depend on the difference between three quantities (i.e. $E_\textrm{prop} = E_\...
8
votes
1answer
210 views

Can I run an nscf calculation in Quantum ESPRESSO with disk_io='none'?

I had run an SCF calculation on a crystal system in Quantum ESPRESSO and had collected the converged charge density. However, during the NSCF calculation, there is the generation of ...
12
votes
6answers
1k views

How may I calculate the bond length between two atoms?

I have been looking into Lennard-Jones Potential and Morse potential. And what the formulas do is to calculate a potential and the 'well depth' and 'distance at which the intermolecular potential ...
16
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6answers
2k views

How do I simulate the interaction between two atoms?

I want to build a rough atom interaction simulator, where pushes two (or more) atoms toward each other and they should behave physically correctly: attract, bond or repel with some force. So that is ...
4
votes
1answer
62 views

Has there been any work done on fluid dynamic or acoustic modeling of the human oral (or nasal) cavity?

The purpose is for me to develop a deeper understanding of speech production and how distinct features that identify a phenome are produced. ab initio models based on classical & statistical ...
19
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3answers
3k views

Solving the Schrödinger equation as a service?

Does anyone know of a company with a cloud-based service which takes some representation of a molecule as an input, and then somehow solves the Schrödinger equation to some level of accuracy and ...
8
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2answers
724 views

Pressure applied DFT calculations in Quantum ESPRESSO

I am trying to perform the pressure-induced DFT calculations in Quantum ESPRESSO. For this, I have calculated the lattice constant of the cubic structure by vc-relax...
9
votes
1answer
101 views

What do the parameters at the top of an FCIDUMP file mean?

A while ago I wrote a simple program that takes in an FCIDUMP file (generated by MOLRPO) and can determine matrix elements (or ...
10
votes
3answers
317 views

Electronic structure calculations without SCF?

Is there an ab-initio calculation of electronic structure that does not involve self-consistent iteration? What I mean by self-consistent iteration is the iteration to solve the equation $$ \mathbf{y} ...
10
votes
1answer
236 views

How to calculate FCI matrix elements from an FCIDUMP file

I'm interested in writing a simple program (as an exercise) that takes an FCIDUMP file (e.g. from a Molpro calculation) and can determine FCI matrix elements (e.g. to construct the entire FCI matrix ...
8
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0answers
71 views

How to reproduce 2D small-angle X-ray scattering (SAXS) interferogram of water via ab-initio MD methods?

I am trying to reproduce the 2D SAXS interference pattern of bulk water via ab initio MD methods as shown in the figure below: The main aim is to recreate figure (a) via averaging MD configurations ...
13
votes
1answer
129 views

What is a good practical way to determine whether or not I need to use a multiconfigurational method?

I’m planning to run a calculation of single electron transfer where my system goes from singlet to triplet biradical (presumably). So I’m wondering how to decide if I need to use milticonfigurational ...
7
votes
1answer
602 views

Molecular Dynamics Simulations in VASP

I want to run molecular dynamics (MD) simulations with VASP for Mg2Si to investigate the simulation time vs ENCUT and KPOINTS, ...
7
votes
0answers
131 views

How to fix gauge in Quantum ESPRESSO?

I am trying to use Quantum ESPRESSO to manually calculate the Berry phase using the Berry connection, due to evolution along a closed loop in k-space. I want to do this manually instead of using ...
10
votes
1answer
134 views

Can I do a "constrained" geometry optimization in Quantum ESPRESSO, such that certain dopants appear in certain positions even after relaxation?

I am studying the magnetic properties of bulk ZnO, so I am doping it with transition metal elements in order to observe the magnetic spectrum. I replace a Zn atom with a transition metal element at ...
11
votes
1answer
544 views

How to understand the spin of exciton?

In very recent years, exciton physics has been intensively explored as the emergence of 2D materials. Exciton is a bound electron-hole pair and is bosonic, namely hosting an integer spin. My first ...
12
votes
1answer
605 views

When do we abandon ab initio methods?

This question is related to (and was originally asked in) another post about "quantum protectorates" I made here. Ab initio methods are nice because they directly solve a sort of "...
10
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1answer
240 views

"Quantum protectorates" and the limits of grand unified theories

I've recently made myself more familiar with Laughlin and Pines' "quantum protectorate" arguments (1, 2), which seems built on Anderson's famous More is Different article (3). This does seem ...
10
votes
1answer
352 views

How to understand the wavefunction outputed by QE with HDF5 format?

Following the answer to my question: What is the best program to manipulate numerical DFT wavefunctions to calculate custom matrix elements?, I compiled Quantum ESPRESSO with the hdf5 flag on, and now ...
10
votes
1answer
290 views

How to make sure that my SCF calculation is correct?

hope you are doing well. I am trying to study the electronic properties of ZnO doped with transition metals (Co, Ni, Fe) using DFT calculation, I am a beginner on DFT calculation using quantum ...
9
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0answers
84 views

Calculating single electron transfer

I'm thinking about doing some computational research about pyrazoline oxidation in chlorinated solvents under light. I've found plausible mechanism (article) that involves single electron transfer ...
13
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1answer
141 views

Are nuclear ab-initio methods related to materials ab-initio methods?

I just read this synopsis in Physics where scientists used first-principles nuclear physics calculations to predict the stability of 700 isotopes up to iron. I didn't know that this was possible, ...