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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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Spin-orbit coupling(SOC) in geometry optimisation

When I tried including SOC during the optimization of InBi lattice constants, the lattice constant increased from 4.6 Å (without SOC) to more than 6 Å (with SOC), which seems like an 'incorrect' ...
James's user avatar
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4 votes
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27 views

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
6 votes
1 answer
64 views

Geometry optimisation with low frequency modes

I am currently running a transition state (TS) optimisation in ORCA. One of the issues that I am seeing is that whenever the Hessian (updated or calculated) has an eigenvalue with small magnitude (i.e....
S R Maiti's user avatar
  • 7,001
7 votes
0 answers
73 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
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How can i do a variable cell relaxation under the influence of constant field in GPAW?

As a continuation of my previous question, I would like to do variable cell relaxation of BaTiO3 under the influence of a constant electric field. The script I've used is given below: ...
Atom's user avatar
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6 votes
1 answer
121 views

Convergence Issues in VASP Relaxation Calculations

I'm encountering convergence issues in my VASP relaxation calculations, specifically related to the message 'BRIONS problems: POTIM should be increased.' I've tried adjusting POTIM, but I'm still ...
Farah Shehzadi's user avatar
1 vote
0 answers
21 views

Optimization error in quantum dot graphene doping with antimony atoms

...
fatemeh's user avatar
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3 votes
1 answer
51 views

ASE GPAW variable cell relaxation

Ive been trying to do a vc relax using GPAW and ASE on the BaTiO3 unitcell. The input file is as below: ...
Atom's user avatar
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4 votes
1 answer
123 views

Is it possible to do a vc-relax calculation using GPAW?

I wanted to do a variable-cell relaxation calculation using GPAW (similar to the one present in quantum ESPRESSO). It would be nice if I could get pointers on how to approach this. ...
Atom's user avatar
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5 votes
0 answers
209 views

Help regarding Geometry Optimization of a bimetallic surface

I am trying to perform a geometry optimization (GEO_OPT) of a FCC 111 Pt$_{0.5}$Au$_{0.5}$ bimetallic surface (10x10x3) generated from ASE, with a lattice parameter of 3.9 $\overset{\circ}{\mathrm{A}}$...
ARKA PRAVA SARKAR's user avatar
6 votes
1 answer
149 views

MOPAC: Is there a simple way to display geometry trajectories

I would like to display MOPAC geometry trajectories for structure minimization and transition state searching. Is there a simple way to achieve that ? Avogadro can display only final geometry from ...
Miro Iliaš's user avatar
2 votes
0 answers
66 views

Different QM and MM gradients in geometry optimization

I calculated the single point energy of some small molecule using the PM7 method (with COSMO solvation model) in MOPAC and calculated the gradients. Then I calculated MM potential energy with ...
klani's user avatar
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2 votes
1 answer
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Si Thin film phonon dispersion with negative frequency

I have a Si slab of thickness 0.5nm for which I want to calculate the phonon dispersion. The unitcell has 5 atomic layers and 10 Si atoms with vacuum of 10A in z-direction (a 2x2 supercell is shown ...
Mohamed Saleh's user avatar
2 votes
0 answers
87 views

Prerelaxation before AIMD with VASP

I am investigating a bulk structure by ab initio molecular dynamics (AIMD) implemented in VASP. I was wondering, how to choose the initial geometry (= POSCAR file) to run the AIMD simulation. In the ...
Lukas's user avatar
  • 303
3 votes
1 answer
100 views

Making Deuterium POTCAR file for optimization in VASP software

How to make Deuterium POTCAR file? i have Hydrogen POTCAR file.
Rubi Agrawal's user avatar
1 vote
1 answer
95 views

Why is this geometry optimization in Gaussian not working for a system containing an amino acid, a water molecule and a metal (Pb) ion?

I started optimising a system containing amino acid residue, water molecule and a toxic metal ion, in proving a supposed reaction steps that might take place in inhibiting enzyme activity. The ...
PriZarah's user avatar
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1 vote
1 answer
77 views

What is the best way to optimize molecules with 8000 atoms. This includes C,H,O,N,Si

My molecule includes C,H,O,N,Si
AKM's user avatar
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4 votes
1 answer
81 views

How do I do a PES (potential energy surface) scan for the excited electronic state?

I know how to do a PES scan for a ground electronic state. But for the nth-excited state, is it the same (i.e. an excited state optimization and just rotating the dihedral to simulate the ...
WALOWLA's user avatar
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1 vote
0 answers
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Disappearing vacuum layer when relaxing bilayered hBN with VASP

I'm doing geometry optimization of bilayer h-BN, a 72-atom supercell (6x6x1) with vacuum thickness of 20 Å, and I set the parameters in INCAR as below: ...
Meifeng WANG's user avatar
3 votes
0 answers
32 views

Which is the best way to plot E_tot vs Lattice graph for structures with two lattice parameters?

I made the graph using the ratio between the parameters x E_tot (trigonal structure), but I would like to know if there is a better way to do this.
Gabriel Elyas's user avatar
3 votes
1 answer
237 views

Singlet excited state optimization gaussian issue

I hope someone here can help me with some TD-DFT calculations. I am trying to calculate the excited state optimised structures and energies of some Germanium compounds. Firstly, I run a TD calculation ...
F Leon's user avatar
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4 votes
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Incorporating Phonon Calculations as a Criterion for Geometrical Relaxation

In the context of first-principles calculations, such as DFT, lattice vibrations are often determined through phonon calculations, providing valuable insights into the stability and dynamics of ...
Jaafar Mehrez's user avatar
5 votes
1 answer
84 views

Large energy differences across successive geometry optimization steps in SIESTA

I am trying to calculate adsorption energies of acetophenone on a 6x6x3 nickel surface with about 12 Angstrom of vacuum above it using SIESTA 5. I have arranged the molecule so that the ring plane is ...
user1420303's user avatar
2 votes
0 answers
74 views

Wrong lattice parameter of CeO2 after structure relaxation with VASP

I am calculating the lattice parameter of CeO2 with VASP, but the optimized lattice parameter is wrong according to many references (Physical Review B 75, 035109 (2007); The Journal of Chemical ...
FaDA's user avatar
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1 vote
0 answers
40 views

LBFGS -- Incomplete Convergence due to BadIntpln [closed]

I am doing energy minimization of a molecular system in TINKER. While doing so, I am getting the error in the title of this question. What might be my problem?
Himanshu's user avatar
4 votes
1 answer
158 views

Computing proton-proton potentials for infinite periodic materials

For electronic structure calculation, when optimizing the wavefunction for an infinite periodic material, the proton-proton energy is needed to monitor the convergence of the SCF loop. How is the ...
mle's user avatar
  • 1,031
3 votes
0 answers
30 views

Constrained geometry optmization: Molecule interacts with its surroundings

I have a water cluster(suppose) generated from MD run. Now, I want to optimize the geometry of only one water molecule of interest using QC methods (e.g. B3LYP/6-31+G(d,p)). I intend that the water ...
Pro's user avatar
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3 votes
0 answers
68 views

Discrepancy between Force Convergence in Geometrical Optimization and SCF Calculation in VASP: Reasons and Troubleshooting Suggestions

During a geometrical optimization of ions and lattice parameters in VASP, the forces acting on atoms were minimized to less than 0.01 eV/Å. However, when performing the subsequent self-consistent ...
Jaafar Mehrez's user avatar
1 vote
0 answers
102 views

Structural phase transition under uniaxial strain

I am trying calculate a strain-induced phase transition in some weakly correlated crystalline material using Quantum ESPRESSO (QE). The compound has two (experimentally observed) phases, one of which ...
manju9's user avatar
  • 248
2 votes
1 answer
231 views

Optimal choice between ISIF = 3 and ISIF = 4 for lattice parameter and atomic position relaxation in VASP calculations

In my VASP calculations, I am interested in simultaneously optimizing both the lattice parameters and atomic positions of my system. I understand that using ISIF = 3 allows for relaxation of both ...
Jaafar Mehrez's user avatar
4 votes
1 answer
333 views

How to pre-optimize metal-organic complexes in RDKit using UFF?

I have run into a particular problem while trying to automate my input file generation for ORCA calculations. Apparently, I either do not fully understand how SMILES strings work, or I am demanding ...
J.Doe's user avatar
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3 votes
0 answers
136 views

Quantum Espresso optimization calculation not converging

I have been trying to optimize the geometry of a copper based metal halide perovskite. I opened the CIF file using BURAI GUI and generated the VC-RELAX input file. I have increased the steps to be 200 ...
Kamal Nassar's user avatar
9 votes
0 answers
114 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
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7 votes
1 answer
123 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
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3 votes
1 answer
187 views

UseSym Keyword in ORCA fails to find appropriate number of SALCs

I am trying to run some geometry optimizations in ORCA 5.0.4 and I am using the UseSym keyword to ensure that my molecules retain Cs Symmetry during optimization. ...
J.Doe's user avatar
  • 493
5 votes
1 answer
323 views

ORCA crashes because of RI approximation?

I am doing a geometry optimization for a cationic imidazolate-zinc complex. I'm trying to run an optimization using this input file. It uses the RI approximation. ORCA seems to be running fine until ...
J.Doe's user avatar
  • 493
5 votes
1 answer
177 views

Is it okay to use semi-empirical methods to optimize structures if I perform high-level energy calculations?

For non-covalent systems comprised of small-molecule monomers, folks are usually interested in understanding the interaction and binding energies of small (gas-phase) clusters ... things like $\ce{X(...
epalos's user avatar
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2 votes
2 answers
157 views

How to select charge and multiplicity for macro-molecules?

In optimising proteins with DFT/B3LYP, how can we detect the charge and multiplicity of the protein?
PriZarah's user avatar
  • 409
4 votes
2 answers
104 views

Cannot optimize hexa aqua Cu(II) and Fe(III)

I try to optimize very simple systems - hexa aqua Cu(II) and hexa aqua Fe(III) - in Gaussian 16. The inputs are provided in the end of the post. Unfortunately, the geometry optimization never finishes ...
farmaceut's user avatar
  • 566
6 votes
1 answer
132 views

Use of genetic algorithm based methods for geometry optimization

What are the benefits or pitfalls in using a GA based optimizer for geometry optimization instead of a more traditional Hessian based algorithm? It can be argued that performing single point energy ...
Hemanth Haridas's user avatar
6 votes
2 answers
259 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
5 votes
1 answer
398 views

Convergence problem in geometry optimization in Gaussian16

I have a quite big set of molecules to optimize and study and, after some research in the literature, I selected B3LYP/6-311G* level of theory. These molecules are quite big and wobbly, so I expected ...
Laura's user avatar
  • 1,267
10 votes
1 answer
572 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
4 votes
0 answers
50 views

How to compute only part of molecular Hessian accurately (hybrid Hessian or partial Hessian calculation)?

Hessian is required for minimisation and transition state (TS) optimisation algorithms. While the full Hessian at a certain level of theory is calculated usually for TS optimisation, usually ...
S R Maiti's user avatar
  • 7,001
3 votes
1 answer
579 views

Why the relaxation of my material in Quantum ESPRESSO wasn't achieved?

I did a vc-relax calculation using HSE by Quantum ESPRESSO and after 22h time WALL the job was complete and JOB DONE was mentionned in the end of the output file ...
Camilla's user avatar
  • 2,169
5 votes
1 answer
170 views

DFT calculation for conjugated polymers

I am new to DFT calculation. I want to know the structure of conjugated polymers (plane angle, etc.) and their electronic and optical properties (such as HOMO-LUMO, IR, etc.). I am using 6-311+G(d) ...
Duy-Minh Hoang's user avatar
7 votes
1 answer
202 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
5 votes
1 answer
160 views

Is the Broyden's algorithm sufficient to obtain the crystal structure of a hypothetical alloy, or should something else be used?

The Broyden (Broyden—Fletcher—Goldfarb—Shanno or BFGS) algorithm can be known in the matter modeling to optimize a crystal lattice geometry — to clarify positions of nodes of a crystal lattice in ...
SFriendly's user avatar
  • 927
4 votes
0 answers
437 views

VASP geometry optimization not converging [closed]

I have tried everything I could find online but I am not able to relax this structure in VASP. I started out with the basic INCAR ...
Chan's user avatar
  • 649
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