Questions tagged [geometry-optimization]
Questions about finding the molecular or material geometry that has the lowest energy.
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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
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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How to solve "step out of bounds" error in Gaussian?
I am trying to optimize a molecular geometry with Gaussian 16 and this is the line of instructions:
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CP2K geometry optimization SCF takes 3000s for a step
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
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
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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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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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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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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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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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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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 ...
user115080
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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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