Questions tagged [ab-initio-calculations]
For questions about ab-initio (first principle) calculations.
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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 solve this problem.
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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 ...
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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 ...
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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, ...
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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 ...
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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!
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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," &...
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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{\...
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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. ...
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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 "...
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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 :
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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 ...
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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 ...
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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'...
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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 ...
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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 ...
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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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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.
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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 ...
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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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