Questions tagged [geometry-optimization]
Questions about finding the molecular or material geometry that has the lowest energy.
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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
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 ...
iwab
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How to handle explicit solvent molecules when calculating energies of reactant molecules in isolation
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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Lennard Jones Clusters in Python
I would like to explore the global optimisation of Lennard-Jones clusters in Python. I do not come from a physical chemistry background. I would like to be able to calculate the cluster energy ...
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CP2K geometry optimization SCF takes 3000s for a step [closed]
I am new to CP2K and doing a geometry optimization for a cluster. At the beginning everything looks good, each SCF step takes about 13 seconds, the energy drops quickly and the convergence looks like ...
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A different way to optimize triplets?
I am studying a system with TD-DFT method implemented in Gaussian. I am not sure whether this two inputs are adequate by the mean of output - optimization of T1?
...
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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 ...
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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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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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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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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 [closed]
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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Force convergence in Wannier orbitals based DFT code [closed]
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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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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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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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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