Questions tagged [geometry-optimization]
Questions about finding the molecular or material geometry that has the lowest energy.
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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 ...
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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 ...
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LBFGS -- Incomplete Convergence due to BadIntpln
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?
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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. ...
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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 ...
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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(...
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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?
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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 ...
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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 ...
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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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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 ...
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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. ...
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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 ...
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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 ...
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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) ...
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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 ...
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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 ...
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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
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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 ...
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How can I predict the time of a simulation using Quantum ESPRESSO?
I performed a vc-relax calculation with hybrid functional on a 2 atoms material using the command ...
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Why is line search not popular in quasi-Newton geometry optimisers?
One of the most important quasi-Newton optimisation methods is the BFGS (which uses an iterated Hessian update scheme to avoid recalculation of the actual Hessian). Most numerical optimisation ...
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Constrained optimisation on a hypersphere
I am currently trying to implement a GS2 (Gonzalez-Schlegel second order) IRC algorithm in a python code. I am following the original paper ref(1).
The main problem is in the constrained optimisation ...
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How to calculate the lattice parameter of a supercell using Phonopy? (For Quantum ESPRESSO)
I found in the internet a method to generate a supercell from the input file using Phonopy code. And I have a question if someone can clarify my doubts please. The method is as following:
We make an ...
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What's the appropriate method to create a supercell for Quantum ESPRESSO?
I created a CIF file using the experimental parameters of my material, then I used it to create my input file for the unit cell using Cif2Cell. After that, I ...
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Hessian used for calculating GDIIS error vectors
GDIIS (Geometry optimisation with Direct Inversion of Iterative Subspace) is a well known method used by many QM codes for geometry optimisation. It is inspired from the almost universal DIIS method ...
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How do you project the Hessian along a certain vector?
I have been trying to understand the Gaussian optimiser (Berny optimiser algorithm) from what has been written in their manual. So far, I have understood most of it, but one part has been giving me ...
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What is the bond length of O2--?
I need the bond length in Å for $\ce{O_2^{--}}$ from this geometry database page (type "O2--" for the input).
I get a bunch of possible values. I don't know much about those yet but after ...
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How to handle explicit solvent molecules when calculating energies of reactant molecules in isolation [closed]
When determining the energy barrier, it is recommended to compute the energies of reactant molecules in isolation to account for the entropy change of forming the reactant complex (hence factoring ...
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ORCA: Getting the error "mpirun noticed that process rank 0 with PID 383161 on node exited on signal 11 (Segmentation fault)."
I am getting a segmentation fault error when running the following input file below. The calculation runs fine in gas phase and CPCM modes, but fails with SMD. What could be the issue? Some are saying ...
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Is it ok to start from an identity matrix Hessian guess for optimisation?
I am attempting to implement an algorithm for transition state finding (in Python, but that's not important). The algorithm is called BITSS (Binary Image-pair Transition State Search). It defines a ...
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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 ...
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Perovskite Optimization does not converge using gaussian [closed]
I am trying to optimize the geometry of (C5H14N2)[CuCl4] using g09. However, the calculation is not converging at any level of theory in 250 cycles. I am new to this field and I think I have made a ...
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Crash of DF-CCSD or DF-CCSD(T) geometry optimization (MRCC package)
I am interested in geometry optimization at the CCSD(T) or DF-CCSD(T) level, with MRCC.
The calculation, however, crashes when executing prop:
...
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Optimizing geometry of materials under pressure using VASP [closed]
I am currently trying to reproduce the results of [1], wherein they have pressurized $\ce{Cs_2SnI_6}$ from $0$ to $20$ GPa.
I ran calculations with PBEsol and used the PSTRESS tag in order to optimize ...
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Predicting parameters by taking a weighted average of multiple possible structures with energy rather than the structure with least energy
I am currently looking to predict the structure of a material who we know exists under the conditions I am intrusted in(pressure), but the cif file does not exist. Now I have to first make the cif ...
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How does ORCA treat intermediates in Nudged Elastic Band (NEB) calculations
I'm trying to run a quite complicated NEB optimization with (hopefully) one intermediate structure.
But before losing time, I was wondering:
how does ORCA treat that intermediate?
does ORCA optimize ...
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maxstep Gaussian keywords
I'm running a Berny optimization and I need to include the keyword maxstep=1.
Observing the output, in the convergence summary table I can see that the ...
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Change in space group upon application of stress during geometry relaxation in VASP
I am trying to duplicate the results of this study using VASP. Where they have observed that the structure of $\ce{Cs_2SnI_6}$ switches from Fm-3m to I2/m upon application of pressure more than 3.3 ...
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Failure to converge geometry of ringed structure
Hi I'm trying to optimise a molecule by using the b3lyp/6-31G(d) method , the calculus took more than 2 days and the energy never converged .
Here is my input code
...
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Restart geometry optimization in Gaussian after hangup error [closed]
I am trying to optimize the geometry of a paraquat molecule interacting with a gold bulk. The optimization is stopping after a few steps. The error shown in the .log...
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How to restart an interrupted TS optimization job in Gaussian16 without the CalcFC option from the chk file?
I have to do the TS optimization of a very large structure.
Initially, I used the typical opt(ts,calcfc,noeigentest) at the route section, but during the ...
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