24 votes
Accepted

Is it right to neglect very small imaginary frequencies?

tldr: This is something of an eternal debate. IMHO very small imaginary frequencies can be okay, but it depends on your system and needs. As you might see from the various comments above, there are ...
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19 votes

Geometry optimization: what happens in the algorithm?

First, realize that optimization is a general thing that can be done for all types of problems. In the geometry optimization of atoms and molecules, what we want to find is the configuration of the ...
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  • 7,744
18 votes

Geometry optimization: what happens in the algorithm?

To add to the other answer, the energy of a molecule (or any chemical species) can be expressed as a function of the coordinates of the atoms. Most softwares convert the 3N cartesian coordinates into ...
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  • 5,499
16 votes
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Geometry optimization: what happens in the algorithm?

GDIIS (Geometry Direct Inversion in Iterative Subspace) This is a very popular method, implemented in almost all the major quantum chemistry software packages, which is quite different from the quasi-...
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  • 27.8k
15 votes

Is it right to neglect very small imaginary frequencies?

Just want to add a small comment upon Geoff's excellent answer. One may be tempted to think that a $<\pu{10 cm-1}$ imaginary frequency introduces a negligible error to the energy or the property of ...
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  • 6,408
14 votes

Logic of published geometry optimization results without checking phonons

In general it is not justified to published the geometry of a system without performing a phonon calculation. This is where you may end up in the potential energy surface depending on which type of ...
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  • 10k
14 votes

Logic of published geometry optimization results without checking phonons

Phonon calculations tend to be very expensive to run. That being said, for gas phase molecules it is very common and expected that frequency calculations are run to ensure the molecule is not on a ...
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14 votes

Are dispersion correction methods for DFT (such as D3) useful for geometry optimization?

Yes, vdW interaction affects energies but, also, geometries. This effect is the most pronounced if a DFT method predicts an interaction in a dimer to be repulsive: a geometry optimization will then ...
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13 votes

Can I use two different codes?

Absolutely. I do this all the time, and often use several codes, since each code has its own strengths and weaknesses. I used 7 different codes in this paper where all I was doing was the ionization ...
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13 votes
Accepted

Why is CPHF/CPKS necessary for calculating second derivatives?

It comes down to the fact that HF and KS both are variational methods. This short article by Julien Toulouse gives a great description of ways to compute static/dynamic response properties. I'll just ...
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13 votes

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

'vc-relax' and 'relax' are two quite different functionalities of the PW module. 'vc' stands for 'variable cell', so the cell shape (angles and length) as well as the atomic coordinates are optimized. ...
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13 votes

Are dispersion correction methods for DFT (such as D3) useful for geometry optimization?

Dispersion correction DOES affect the final geometry. The dispersion interaction is a function of geometry. A crude approximation is to write the dispersion interaction between two neutral molecules ...
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13 votes
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Choice of coordinate system for geometry optimization

You may want to have a look at this paper: "Geometry optimization made simple with translation and rotation coordinates" https://aip.scitation.org/doi/10.1063/1.4952956 This is not a ...
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12 votes
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Analytic gradient for DLPNO-CCSD

Note that the DLPNO method is only implemented in ORCA. There are indeed analogous and similarly efficient and accurate methods, the PNO-LCCSD method in Molpro [doi.org/10.1021/acs.jctc.7b00799] and ...
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12 votes

Geometry optimization for n-layers in VASP

I highly recommend reading: Efficient creation and convergence of surface slabs The following answer will assume a reasonable level of VASP knowledge (where keywords can be looked up at the VASP wiki)....
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11 votes
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Geometry optimization for n-layers in VASP

What is the best way to optimize monolayer geometry in VASP? For the geometric optimization of the monolayer in VASP, you should use the following key tags: ...
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10 votes

Are dispersion correction methods for DFT (such as D3) useful for geometry optimization?

Optimization routines typically use the negative gradient of the energy in some form to determine the displacement during an optimization step and the dispersion correction changes the energy, which ...
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10 votes

What's the best quantum chemistry output parser for the command line?

CCLIB Cclib is an open source python library that can parse and interpret output files of common computational chemistry programs. As of now, it supports Psi4 version 1.0 and 1.2.1. It can be called ...
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  • 5,499
9 votes

Can I use two different codes?

Depending on what properties you care about.. maybe. I don't suggest this in general. I work on phonon calculations where forces must relaxed to a pretty strict tolerance. It has been my experience ...
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9 votes
Accepted

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

By making a supercell and modifying it in some way, you are creating an entirely new structure which you hope can give you some insight by being compared to the original structure. Any of the ...
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9 votes
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SCAN-RVV10 geometry optimization

Imagine you have a (hypothetical) method that can exactly capture the van der Waals interaction. Then when you do a geometry optimization, you are neglecting the quantum and thermal fluctuations of ...
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  • 10k
9 votes
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Why does Gaussian ignore the opt=maxcycles keyword for optimizations?

This requires an additional IOP to do. It seems that Gaussian sets a separate lower and upper bound on the number of optimization steps that will be performed based on the number of coordinates and <...
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9 votes

Geometry optimization with Moller-Plesset MP4

Gaussian can do all the way up to MP5 for single-point energies, but analytic gradients are only available for MP2, MP3, MP4(DQ) and MP4(SDQ), the latter including only single, double and quadruple ...
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9 votes

Which is the recommended way to optimize "big" systems?

Suggestions for Molecular-Like Systems (not periodic unit cells) I'll make some general suggestions for molecular / isolated systems, not crystals. (In the case of periodic systems, some methods aren'...
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9 votes

Is it reasonable to calculate TDDFT excitation energies at a geometry optimized with a different method?

From my point of view, it will not affect so much on the excitation energy, but it is preferred to use the same level of functional and basis set unless you will increase the level of theory to get ...
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8 votes
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Is there a possibility to change the initial crystal system during full geometric relaxation?

In general this depends on the potential energy surface. If symmetry is turned off and the cell is allowed to change shape and size, then no promises are made either way on what will be found. ...
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8 votes

Candidate structures for global minimum determination

Confab OpenBabel source documentation: https://open-babel.readthedocs.io/en/latest/3DStructureGen/multipleconformers.html Example: ...
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  • 7,744
8 votes

Can I use two different codes?

This has been done previously. In my experience the geometry is found with one code, and solvent corrections are performed with another. I have personally done this[1], and have had the results ...
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  • 1,486
8 votes

How to define a nonconventional geometry to obtain exchange spring hysteresis loop structure using MuMax3?

I'll try to give you an answer and a way to proceed However, our experimental system is quite different from the conventional soft-hard structure. This system will also be a bilayer system like the ...
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  • 4,268
8 votes

Analytic gradient for DLPNO-CCSD

As far as I know, analytic gradients for DLPNO-CCSD are not available in ORCA. Analytic first derivatives are available for both closed-shell and high-spin open-shell cases, which could be used for ...
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