Questions tagged [ab-initio-calculations]
For questions about ab-initio (first principle) calculations.
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Atomic species flag for deuterium is replaced by Phonopy in Quantum ESPRESSO inputs
I am running some Phonopy calculations with a deuterated material. I already know that Quantum ESPRESSO does not understand D at atomic species, but instead we need ...
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Why do photochemical simulations use linear interpolation in internal coordinates?
Is anyone here familiar with theoretical photochemistry? If the linear interpolation (LIIC) does not represent the true minimum-energy pathway (MEP), why do I see a lot of papers using it to simulate ...
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How long must a sample last in a molecular dynamics run for it to be considered non-labile?
So I have a few unusual molecules and I wanted to know whether or not they are kinetically stable (non-labile) across a certain range of temperatures. The methods for synthesizing these molecules isn'...
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Choosing Between a Small Cluster and a Workstation for MD Simulations and Quantum Chemistry Calculations
I am part of a research group and we are in the process of deciding on a computing resource for our simulation and data analysis needs.
Our primary tasks include:molecular Dynamics (MD) simulations (...
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Workflow for modelling the final prodcut of a chemical reaction
I have done some DFT simulations before in cp2k and siesta but the kind of systems I am about to study is new to me so I would appreciate it if I got helpful suggestions from the experts.
The system ...
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Nudged Elastic Band vs Linear Synchronous Transit/Quadratic Synchronous Transit Method
I have noticed that both the CI-NEB and LST/QST methods have been used in the literature for calculating the transition state energies and migration barriers. Since the CI-NEB method calculates the ...
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Why does Car-Parrinello molecular dynamics not need an SCF procedure at every time-step?
Reading the various terms of the Lagrangian in CPMD I'm trying to understand why there is not an SCF procedure hidden there.
In fact, it seems to me like the second term of the Euler-Lagrange equation ...
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Physical Properties from Variable Cell Relax Calculations in Quantum ESPRESSO
I want to know what physical quantities can I calculate using the output file of variables cell relax calculations (vc-relax) in Quantum ESPRESSO or using its post processing tools.
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How to determine if hybridization takes place between orbitals in an ab initio calculation using Quantum ESPRESSO?
I'm using Quantum ESPRESSO to determine the electronic properties of systems. Now I want to confirm if hybridization takes place between orbitals. I have generated density of states and projected ...
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Calculation of spin-seebeck coefficient
I have been working with the calculation of transport properties of ferromagnets using the BoltzTraP2 package. I have managed to compute Seebeck coefficient, electrical conductivity, and power factor ...
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Berry curvature with wien2k+wannier90
I searched the tutorial of wannier90, and found the example18 iron which could be calculated Berry curvature by w90. However, this way used QE, I'd like to know how can I use wien2k + wannier90 ...
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How to find lattice constant (Si/GaAs/any material) at finite temperature using Car-Parrinello Molecular Dynamics (CPMD)?
Would anyone please guide me stepwise how can I find lattice parameters of a material, for example: Si, GaAs, at a finite temperature using Car-Parrinello Molecular Dynamics (CPMD)?
Thank you
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CASTEP: specification of uniform pressure in a non-orthogonal unit cell?
I want to get confirmation as to the correct way to specify a uniform isotropic EXTERNAL_PRESSURE for geometry optimization in a non-orthogonal unit cell using the ...
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Consequences of starting a new relaxation calculation from the final coordinates of an interrupted run
In order to address oscillating total force during an ongoing relaxation calculation in Quantum ESPRESSO, I've found it effective to interrupt the current run and commence a new relaxation calculation ...
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Does the size of atoms influence the speed of DFT calculations when comparing systems with almost the same number of atoms
How does the size of atoms within a structure influence the speed of DFT (Density Functional Theory) calculations?
considering that the calculation speed is known to scale cubically with the number of ...
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Explain ab initio molecular dynamics like I'm five
In Kashiwaya, S., Shi, Y., Lu, J. et al. Synthesis of goldene comprising single-atom layer gold. Nat. Synth (2024) monolayers of hexagonal Au(111) planes are produced and released into solution where ...
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Different results from MP2 calculations on same geometry in ORCA
I am trying to do a segmented potential energy scan around a dihedral for a molecule. I have optimized the geometry to a minima, and the scan runs from [-180, 180] in steps of two points at a time.
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Stopping an ongoing relax calculation with provision to continuing the calculation later on from that checkpoint
How can I interrupt an ongoing relaxation calculation in Quantum ESPRESSO on my system, while ensuring that I can resume it later from the same point?
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Comparing results of various DFT calculations in Quantum ESPRESSO
To verify the reliability of calculation scheme, I want to compare lattice constants, bond length and band gap calculated by the different functionals with the experimental results.
So in order to do ...
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How to determine energy convergence threshold and force convergence threshold in Quantum Espresso [closed]
In the computational investigation of $MoS_2$ monolayer for its catalytic activity in the hydrogen evolution reaction, how are parameters such as forc_conv_thr and <...
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Understanding algorithm of Quantum ESPRESSO from scratch
As someone new to this field, what are some effective strategies or resources I can utilize to study and understand the Quantum ESPRESSO algorithm from scratch?
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What is the correct way to set up occupation for single atom in CFOUR software?
I am doing some calculations on single oxygen atom (O) using CFOUR. According to a previous answer to this question and according to how CFOUR treats non-Abelian groups, I am considering the (O) atom ...
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When orbitals are labeled based on their irreps in D2h, how are the orbitals ordered for an N atom?
I am performing calculations on a Nitrogen atom using CFOUR. A nitrogen atom has a point group of Dinfh, but CFOUR uses a lower symmetry of D2h instead. So, looking at the available Irreducible ...
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Why is my hydrogen energy not equal to -0.5 hartrees?
I'm trying to calculate the HOMO of various molecules in water solution. I first tried to see how PySCF calculates the HOMO of hydrogen. I ran the following code:
...
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Query regarding individual polarization calculation using CP2K
I am seeking assistance in calculating the individual polarization matrix from CP2K. While utilizing the Polar input under FORCE_EVAL -> PROPERTIES -> LINRES -> POLAR, I observed that the ...
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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 ...
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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 ...
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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,
...
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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 ...
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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 &...
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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 ...
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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 ...
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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 ...
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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 ...
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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-...
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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 ...
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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.
...
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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 ...
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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 ...
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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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