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Questions tagged [geometry-optimization]

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

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27 votes
2 answers
3k 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 ...
Roman's user avatar
  • 2,373
25 votes
3 answers
5k 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 ...
Shalini's user avatar
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21 votes
2 answers
871 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 (...
S R Maiti's user avatar
  • 7,011
18 votes
2 answers
994 views

Logic of published geometry optimization results without checking phonons

I see that in many papers where optimization results presented, they do not mention phonons and their force convergence criterion is 0.01 eV/A. Can you publish a result like that? And is not this ...
Bereau's user avatar
  • 861
16 votes
3 answers
4k views

Geometry optimization for n-layers in VASP

What is the best way to optimize monolayer geometry in VASP? Should the same method be used for an n-layer (n=2,3,4,5)?
M_Fisher's user avatar
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16 votes
2 answers
939 views

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 ...
S R Maiti's user avatar
  • 7,011
16 votes
2 answers
971 views

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. ...
Susi Lehtola's user avatar
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15 votes
3 answers
202 views

Candidate structures for global minimum determination

What are the best packages that can generate candidate structures for quantum chemical optimization (DFT or CCSD) to find the global minimum? I am working on the gas-phase small inorganic clusters (...
Somnath Bhowmick's user avatar
15 votes
1 answer
3k 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 ...
S R Maiti's user avatar
  • 7,011
14 votes
5 answers
2k 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 ...
NickZ's user avatar
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14 votes
5 answers
2k views

Can I use two different codes?

Can I use one code for geometry optimization and another code for a single point calculation on that optimized geometry? Can one publish results like that?
Bereau's user avatar
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14 votes
1 answer
299 views

Is there a software that has implemented forces of TDDFT calculations for solids?

I'd like to investigate the structural relaxations of the excited state for periodic systems. BSE and TDDFT are two promising methods for this purpose. While there is a discussion on forces with BSE ...
Xiaoming Wang's user avatar
13 votes
1 answer
7k views

When should "vc-relax" be performed over "relax" calculations in Quantum ESPRESSO?

I'm new to Quantum ESPRESSO and I have read that there are several scenarios when relax calculations are preferred over vc-relax calculations, for example in maintaining vacuum while modelling surface....
Anoop A Nair's user avatar
  • 4,506
13 votes
1 answer
379 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....
Bikash Patra's user avatar
12 votes
2 answers
302 views

Permissible amount of forces on ions in a relaxed structure

An equilibrium structure would be at a local minimum but that doesn't happen with all relaxation calculations. Relaxed structures tend to have some resultant forces on ions. What amount of these ...
Hitanshu Sachania's user avatar
12 votes
2 answers
812 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 ...
user avatar
12 votes
1 answer
417 views

How do I predict the structure of a nanoparticle with Calypso and Quantum ESPRESSO?

I want to create a nanoparticle of CuO and predict it's structure. I've done unit cell relaxation with Quantum ESPRESSO. One tool to predict nanocluster structure is Calypso which is PSO-based. I'm ...
Shafayet Rahat's user avatar
12 votes
1 answer
634 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{...
Jason M Gray's user avatar
11 votes
2 answers
1k views

Analytic gradient for DLPNO-CCSD

Is there a formula for analytical gradients (for geometry optimization) for the DLPNO-CCSD method? I ask because I know that it is not implemented in ORCA. Maybe PNO-CCSD is implemented in MRCC or ...
Paulie Bao's user avatar
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11 votes
1 answer
258 views

How would you report the lattice parameters of an alloy, modelled using a supercell

There is a whole lot of literature behind ab initio modelling of alloys with statistical site occupancies. These include VCA, SQS, CPA, supercell approach, etc. This question does not aim to compare ...
Achintha Ihalage's user avatar
11 votes
1 answer
272 views

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 ...
Hitanshu Sachania's user avatar
11 votes
1 answer
251 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 ...
Greg's user avatar
  • 1,807
10 votes
1 answer
585 views

How can I specify different theory levels for different atoms in Gaussian?

I have a bunch of geometry optimisations I want to run for a cation Metal-organic complex. This is going to be a repeat of calculations that were done in "Turbomole" previously and my Prof. ...
J.Doe's user avatar
  • 493
10 votes
2 answers
2k 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 ...
christian's user avatar
  • 103
10 votes
2 answers
982 views

Should I do vc-relax with nspin=2 in Quantum Espresso for magnetic samples?

I'm a beginner when it comes to DFT and Quantum Espresso. Consider I have a lattice which has associated magnetic properties. So for geometric optimization should I take into account the magnetic ...
Anoop A Nair's user avatar
  • 4,506
10 votes
1 answer
322 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=...
Savir's user avatar
  • 1,051
10 votes
1 answer
1k views

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 ...
sarra6's user avatar
  • 579
10 votes
1 answer
195 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 ...
Arindam Samanta's user avatar
10 votes
1 answer
979 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 ...
ABDELHAMID AIT MHID's user avatar
9 votes
3 answers
714 views

Which output file from CASTEP after geometry optimization is like with the CONTCAR from VASP?

I am trying to use the atomic positions in geometry optimized crystal structure to get the radial distribution function. I know that some codes can read the positions of the atoms from the CONTCAR ...
Yongyun Zhang's user avatar
9 votes
2 answers
747 views

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 ...
S R Maiti's user avatar
  • 7,011
9 votes
2 answers
315 views

Is there a possibility to change the initial crystal system during full geometric relaxation?

One of the challenges of modelling completely new material using DFT is the selection of initial geometry. Usually, an experimental structure (cif) which appears to be similar to the new material in ...
Achintha Ihalage's user avatar
9 votes
1 answer
288 views

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 ...
PBH's user avatar
  • 2,653
9 votes
0 answers
115 views

How does the line search in geometry optimisations work?

I am trying to write a Newton-Raphson geometry optimisation script in python (Current version of my code) using the energy, gradient and Hessian from Gaussian 16. In order to reach a minimum, I would ...
evd's user avatar
  • 91
8 votes
1 answer
619 views

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 ...
Jack's user avatar
  • 2,057
8 votes
1 answer
219 views

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 ...
sarra6's user avatar
  • 579
8 votes
1 answer
416 views

Do I have to use the same functional for dielectric function calculations, as the one used for relaxing the structure?

This is a general question regarding the practices of doing optical calculations and the role of the ionic contribution to the dielectric function (with heavy reference to VASP). Based on VASP's ...
CW Tan's user avatar
  • 1,316
8 votes
1 answer
1k 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. ...
Savir's user avatar
  • 1,051
8 votes
0 answers
271 views

ASE's fmax and FHI-AIMS's relax_geometry bfgs "tolerance". Are they same? [closed]

They look like the same thing, but their definitions are confusing. Additionally, while it's possible to use 'tolerance'< 0.05 in AIMS easily, in ASE, some structures never optimize if you choose ...
Alfred's user avatar
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7 votes
3 answers
201 views

What would be the preferred format for a geometry database?

Introduction (analogy to basis set database files) Many programs have a database of basis sets stored in a file such as the following (so that users can just specify in their input file something like ...
Nike Dattani - No Free Time's user avatar
7 votes
1 answer
320 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) ...
ironmanaudi's user avatar
7 votes
1 answer
896 views

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 ...
Andrea Pellegrini's user avatar
7 votes
1 answer
127 views

How many non-redundant internal coordinates are needed for optimisation of linear molecule?

I have been working to implement optimisation in internal coordinates (for a transition state search software I am working on). However, the implementation details are almost always glossed over in ...
S R Maiti's user avatar
  • 7,011
7 votes
1 answer
204 views

Geometry optimization: nuclear coordinates vs lattice parameters

I would like to know whether, at least in principle, minimization of energy with respect to nuclear coordinates leads to the same result as minimization of cell energy with respect to lattice ...
chemdamned's user avatar
7 votes
1 answer
87 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 ...
Dr.Viper's user avatar
  • 457
7 votes
1 answer
684 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, ...
Bpi's user avatar
  • 145
7 votes
0 answers
83 views

Correct method for structure optimization using DFT tools

Lets's say I want to start off DFT calculations for a material whose experimental cell constants are known. So I have two ways to get the correct structure to later on calculate, say, band structure ...
AbPhys's user avatar
  • 811
6 votes
2 answers
746 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?
sarra6's user avatar
  • 579
6 votes
2 answers
585 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 ...
Jack Ceroni's user avatar
6 votes
2 answers
331 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)...
David CY's user avatar
  • 271