Questions tagged [geometry-optimization]

Questions about finding the molecular or material geometry that has the lowest energy.

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Converging geometry of iron slab

I am a sort-of-beginner in Quantum Espresso. I do understand certain terminology in the INPUT file but I am faced with a dilemma. I have been trying to optimize $\ce{Fe}(110)$ system of 100 atoms ...
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7 votes
1 answer
166 views

Molecular geometry optimization for cyclooctatetraene with pyscf

I am trying to reproduce the cyclooctatetraene isometrization process pulished here. In figure 3 of the paper, it shows the potential energy surface as a variable of the polar angle using the CAS(8,8) ...
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4 votes
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Decide the position of oxygen vacancy via the configuration with the lowest energy?

I am trying to determine the position of oxygen vacancy in $\ce{TiO2}$, is it reasonable to decide it by choosing the configuration with the lowest energy? It doesn't feel quite right to always choose ...
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2 votes
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Reciprocal lattice and k-lattice belong to different groups in VASP

I am trying to do geometry optimization of TiO2 with VASP. Here is the POSCAR file, which I get from the Materials Project. ...
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Error: hangup in Gaussian 09

I have the following problem to run a calculation using Gaussian 9. The calculation starts running and after a few hours stop. The nohup file has the following ...
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1 vote
0 answers
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Force convergence in Wannier orbitals based DFT code

I am working on Pt(111) / nanoparticles with various ligands, I am mainly using two softwares: A well known general purpose plane-wave code (Quantum Espresso). A less known software that is also ...
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4 votes
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Variable cell relaxation method is not converging in Quantum ESPRESSO

I am trying to optimize the lattice constants 'a' and 'c' for a hexagonal lattice. I am using the PAW pseudopotential here. I have run the SCF calculation with ...
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7 votes
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What are the output files generated by an NEB calculation?

I just used Orca for the first time. Can someone address me a valid guide to understand all the files in the directory? I'd like to perform a Nudged Elastic Band (NEB) calculation, but I'm stuck ...
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5 votes
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Do the U values affect structure optimization with the DFT+U simulation to optimize crystal structure?

I am trying to do structure optimization of TiO2, since titanium is a transition metal, I need to use DFT+U to simulate the right band structure, but the electronic band structure would also affect ...
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Quantum Espresso error: "SCF correction compared to forces is large: reduce conv_thr to get better values". How to solve? [closed]

I'm getting an error when trying to perform a relax calculation for $\ce{H2}$ on $221$ $\ce{MoS2}$. I have tried changing conv_thr and ...
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7 votes
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Symmetry group of p-benzoquinone

I am trying to calculate the UV-visible spectrum of p-benzoquinone. In the literature, the point group of p-benzoquinone is $D_{2h}$, but when I optimize this molecule in the ground state with ...
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Is it reasonable to calculate TDDFT excitation energies at a geometry optimized with a different method?

I am working on a project where I have to calculate the TDDFT excitation energies of organic molecules (to compare to the experimental UV/visible i.e. optical absorption spectrum). Now, if I ...
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Which is the recommended way to optimize "big" systems?

Let suppose the we have a "big" system. By "big" I mean a system that have a certain number of atoms that the software is not capable to treat with the default initial parameters. ...
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6 votes
1 answer
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How does electronic iteration work in a VASP relaxation calculation?

I am a beginner using VASP to do material modeling, and I'm confused about the following questions: How does the electronic iteration work in VASP relaxation calculation? Is the electronic iteration ...
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Software for generating ensembles of dimer pairs of organic molecules

For two organic molecules of essentially unlimited size (up to and including, and sometimes exceeding MW = 1000 g/mol), I would like to generate all possible dimer pairs in vacuum. The pairs may be ...
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Geometry optimization using DFT

I have been attempting to optimize the structure of a Si nanowire using SIESTA. The original structure fed into the optimization is as follows. Once it is optimized, the structure would change to ...
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2 answers
343 views

Geometry optimization with Moller-Plesset MP4

Can we optimize a molecular structure using Moller-Plesset MP4 method on GAUSSIAN software? If yes what keyword do we have to add?
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How to eliminate imaginary frequencies during a Gaussian geometry optimization?

When conducting a minimization on Gaussian software, What are the procedures used to eliminate imaginary frequencies if we have already found a stationary point? Are there any keywords that would help ...
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3 votes
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Simple Pt111 slab not converging using Quantum Espresso [closed]

I would like to perform a "vc-relax" calculation on a simple 3x4x5 $\ce{Pt}111$ slab, this calculation is running well but as soon as I add the ESM ...
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Variable Cell Optimization of Halfnium Crystal

Reference: Density Functional Theory: A Practical Introduction, David Sholl, Janice A. Steckel, Chapter 2, Page No. 46 Hf is experimentally observed to be an hcp metal with c/a 1.58. Perform ...
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11 votes
1 answer
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How would one find a material's equilibrium structure at any specific temperature?

Let's take an example of a simple FCC material, a binary alloy. Above absolute zero K, the alloy will start to disorder and become an FCC solid solution. The alloy would develop defects as it ...
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6 votes
2 answers
191 views

SCF not converging during RHF/STO-3G geometry optimisation

I'm new in the field of QM methods and I've run into a problem for which I can't find a solution online. I have tried with different basis sets, I've raised the maximum number of iterations and number ...
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4 votes
1 answer
87 views

How to do a proper relaxation of the multicomponent structure?

I have a beta Ti (Space Group 229) structure with 16 atoms, I prepared 15 disordered TiNb structures with 5 atoms of Nb. I did it using VASPKIT. However, before the ...
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2 votes
1 answer
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Determining the geometry of UOx and WOx for (x=1-3)

Is there a way to work out the geometries for the $\ce{UO_x}$ and $\ce{WO_x}$ species for ($x=1-3$). I know that deducing the multiplicity (the number of unpaired electrons) in d and f block ...
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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 ...
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  • 343
15 votes
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What's the best quantum chemistry output parser for the command line?

This question is about tools like Open Babel. Are there any good command-line parsers for quantum chemistry program outputs? A good Python library could come in as a close second. I am interested e.g. ...
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5 votes
1 answer
86 views

Define a geometry region using 'for' loop in MuMax3

I was trying to define regions using a 'for' loop. Please find the regions: ...
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6 votes
2 answers
470 views

Analytic Hessian at the level of full CI?

This is a follow-up question to my previous question: Computing analytic derivatives of molecular Hamiltonians obtained from solving Hartree-Fock equations. After looking at various quantum chemistry ...
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9 votes
2 answers
242 views

Is it possible to do a Gaussian redundant scan with some fixed bonds?

I'm trying to do a redundant PES scan of a hydrogen abstraction in a Gaussian job while maintaining the rest of the system fixed. I need to scan the coordinate where H5 approaches to H6, maintaining ...
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5 votes
2 answers
93 views

How to use fractional numbers as arguments for keywords in Gaussian input?

I have used both Gaussian09 and Gaussian16 and one thing that seemed unusual to me is that I was unable to enter any fractional number as one of the arguments for a keyword in the Gaussian input file. ...
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12 votes
1 answer
612 views

Why does Gaussian ignore the opt=maxcycles keyword for optimizations?

I have been using both Gaussian09 and Gaussian16 recently to optimize some metal complexes. The Gaussian manual (for both versions) indicates that the maximum number of steps in a geometry ...
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6 votes
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How to optimize the geometry of beta PHB in VASP? [closed]

I would like to calculate the elastic constants of beta PHB. From this paper. I know that it has P3221 space group. The beta PHB has upward and downward chains, which exist at one lattice site with 50%...
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11 votes
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Choice of coordinate system for geometry optimization

For geometry optimization, most QM codes tend to use internal coordinates. Most codes also support Cartesian coordinates. I have always heard the usual "use Cartesian as a last resort, always use ...
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14 votes
5 answers
910 views

Are dispersion correction methods for DFT (such as D3) useful for geometry optimization?

For what I know the DFT-D3 method or similar corrections that take into account dispersion effect, add this type of contribution through calculation of atom pairwise interactions at the end of an ...
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6 votes
1 answer
223 views

Gaussian: Transition state convergence question

I am running a TS computation in Gaussian 16. It performs several steps. At the end of each there is a summary on whether Maximum Force, ...
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  • 135
23 votes
3 answers
2k views

Geometry optimization: what happens in the algorithm?

Geometry optimization using density functional theory (DFT) is done by moving the atoms of a molecule to get the most stable structure with the lowest possible ground state energy. My question is what ...
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  • 1,515
9 votes
1 answer
174 views

SCAN-RVV10 geometry optimization

I'm using SCAN-RVV10 to optimize the hexagonal-BN but the optimized geometry doesn't look true as the calculated interlayer distance is far smaller than the experimental value(exp=3.35 Aangstrom, calc=...
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  • 1,011
11 votes
1 answer
170 views

Using "soft" constraints / bias in geometry optimization?

I study molecules weakly bound to nanoclusters and surfaces. During geometry optimization, I often run into problems like for example a small metal cluster behave nicely and has a given, stable ...
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8 votes
1 answer
286 views

What are the input parameters of VASP for 2D material geometry optimization?

Apparently, my input parameters are not good for geometry relaxation of 2D materials using VASP. ...
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  • 1,011
6 votes
2 answers
136 views

Symmetry-preserving low-level structural relaxation

I would like some suggestions on how to do structural relaxation (while I'm at it, let me list some synonyms for search exposure - geometry optimization, structural refinement, energy minimization etc)...
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  • 271
13 votes
1 answer
108 views

Excited state energy gradient during geometry optimization of a target excited state

During the geometry optimization of the ground state of a molecule, we try to optimize the energy gradient with respect to the nuclear positions such that the system remains in its lowest energy state....
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10 votes
1 answer
222 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 ...
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5 votes
1 answer
123 views

Dispersion correction and band structure

Let's say I optimized geometry with PBE+D3. I want to carry out band structure calculation with HSE06, should I add the dispersion correction to the band structure calculation or not? I tried both and ...
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6 votes
1 answer
108 views

Understanding QuantumEspresso Toolbox through Maestro

Anyone here uses Quantum Espresso through Maestro can tell me a bit more about the calculation panel setting: I understand that -npools option must be divisible by ...
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  • 317
24 votes
2 answers
591 views

Is it right to neglect very small imaginary frequencies?

I'm running a DFT optimization (B3LYP/def2-TZVP) and frequencies in ORCA for a molecule. And I get one or two very small (1-6 cm^-1) imaginary frequencies which corresponds to a slight bend of the ...
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  • 2,293
7 votes
1 answer
60 views

Relax vs VC-Relax for interstitial incorporation energy

In order to model an interstitial trapped in a metal lattice, and the associated incorporation energy, which should be used - "relax" or "vc-relax"? I want to understand the ...
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  • 457
16 votes
1 answer
468 views

Why is CPHF/CPKS necessary for calculating second derivatives?

This question is coming from an answer to one of my previous questions. During optimizations, QM programs usually compute the gradient(first derivative) analytically, and take a guess of the hessian (...
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12 votes
1 answer
283 views

Geometric optimization taking a long time. Are my convergence criteria too tight in CP2K?

I have been having trouble with the VIBRATIONAL_ANALYSIS routine. Namely, the routine keeps timing out. I am trying to find the vibrational modes of Pyridine in a non periodic system, as well as $\ce{...
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10 votes
1 answer
92 views

How to define a nonconventional geometry to obtain exchange spring hysteresis loop structure using MuMax3?

I have tried to simulate the hysteresis loop for the exchange spring structure using Mumax3. I have already simulated the hysteresis loop for the conventional bilayer soft-hard structure. Please find ...
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12 votes
2 answers
330 views

Comparing calculations in plane wave and atomic orbital bases for the same functional

Let's say I have two codes. One is plane wave, and the other is using atomic orbitals as basis sets. How can I compare these two codes with the same functional? And let's say I want to optimise the ...
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