Questions tagged [ab-initio-calculations]
For questions about ab-initio (first principle) calculations.
136
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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 ...
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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:
...
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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 ...
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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 ...
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How to locate HOMO-LUMO molecular orbitals in Transmisson and PDOS graphs?
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 ...
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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?
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Excited state frequency for periodic systems
Is there any way to calculate the excited state frequencies of a period system using DFT?
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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 ...
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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:
...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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\...
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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 ...
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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 ...
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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, ...
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What information does the 1RDM contain?
The one-electron reduced density matrix (1RDM) contains information useful for the prediction of molecular properties (for instance, dipole moments). As an example, the 1RDM can be easily obtained in ...
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Is it possible to obtain the current-voltage characteristic for a crystal using the Hartree–Fock (or DFT) calculation? [closed]
In continuation of the question of obtaining an electrical conductivity tensor (ECT) from the “first characteristics”, will my following suggestion be correct? Since a crystal with an applied-to-it ...
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How to define a chemical bond computationally? [closed]
I'm working with an amorphous system. With oxygen, my system has both covalent and ionic bond forming cations. I utilise the Wannier centre approach to define a covalent bond, and my theory is that if ...
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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 ...
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Slope of the potential when both molecules "touch"?
My aim is to model the potential energy surface for two colliding H2 molecules. More specifically, I needed the order of magnitude of the slope of the potential at the moment when two colliding H2 ...
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In which part of the Hartree–Fock algorithm (or DFT one) could a neural network be most effectively used?
I understand that the task of implementing machine learning in DFT and Hartree–Fock (HF) algorithm has already been solved, perhaps to some extent, but it is interesting to think about how to ...
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How to determine the TA/LA by phonopy [closed]
I would like to ask how to use PHONOPY to define which band is LO, TO or ...
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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 ...
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Which formalism is better suited to model a crystal with defects: Hartree–Fock, Kohn–Sham, or something else?
Let’s suppose that
(1) it’s required to calculate a crystal with certain parameters of a crystal lattice;
(2) this crystal has some defects (let it be Frenkel defects for simplicity);
(3) these ...
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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-...
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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 ...
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How are the exponents in a STO-nG basis set obtained?
STO-3G has exponent parameters which can be found in a reference book. Can these parameters be calculated using, for instance, a Hartree–Fock equation for one atom? Or using another way?
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Are there any open source codes that can generate LAMMPS potentials from DFT calculations? [duplicate]
Are there any opensource and freely distributed codes available which can be used to develop classical potentials for LAMMPS?
The MEAMfit code is free and opensource, but the input needs to be from ...
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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 $\...
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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.
...
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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 ...
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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),...
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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 ...
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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? ...
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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 ...
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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. ...
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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 ...
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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?
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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....
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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 ...
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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 ...
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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 ...
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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 ...
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