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Questions tagged [ab-initio-calculations]

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

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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 ...
Joyal sunny's user avatar
7 votes
1 answer
90 views

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 ...
Joyal sunny's user avatar
6 votes
1 answer
111 views

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 ...
uhoh's user avatar
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8 votes
3 answers
206 views

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. ...
Hemanth Haridas's user avatar
7 votes
1 answer
113 views

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?
Joyal sunny's user avatar
9 votes
1 answer
286 views

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 ...
Joyal sunny's user avatar
5 votes
1 answer
83 views

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 <...
Joyal sunny's user avatar
6 votes
1 answer
537 views

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?
Joyal sunny's user avatar
6 votes
1 answer
200 views

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 ...
Jaafar Mehrez's user avatar
4 votes
1 answer
92 views

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 ...
Hemanth Haridas's user avatar
15 votes
2 answers
2k views

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: ...
nkam's user avatar
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4 votes
0 answers
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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 ...
Simantini Paul's user avatar
6 votes
0 answers
66 views

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
353 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
0 answers
61 views

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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3 votes
0 answers
38 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
5 votes
0 answers
70 views

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
2 votes
0 answers
74 views

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
77 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
  • 31
9 votes
2 answers
401 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
  • 624
3 votes
0 answers
52 views

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
  • 624
4 votes
0 answers
45 views

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
123 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
128 views

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
  • 61
4 votes
0 answers
42 views

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
92 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
102 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
  • 1,031
6 votes
1 answer
156 views

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
  • 1,031
6 votes
1 answer
118 views

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
  • 2,169
3 votes
1 answer
65 views

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
93 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
  • 245
2 votes
1 answer
511 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
  • 21
5 votes
0 answers
149 views

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
  • 1,789
4 votes
1 answer
152 views

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
  • 2,169
2 votes
0 answers
96 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
161 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
260 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
68 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
  • 927
3 votes
1 answer
125 views

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
5 votes
2 answers
75 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
  • 566
7 votes
2 answers
281 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
  • 693
4 votes
1 answer
223 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
8 votes
2 answers
255 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
  • 2,169
5 votes
1 answer
126 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
  • 53
6 votes
1 answer
136 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
  • 343
6 votes
1 answer
138 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
74 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
578 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
8 votes
1 answer
337 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
  • 343