27 votes
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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 ...
Geoff Hutchison's user avatar
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 ...
Cody Aldaz's user avatar
  • 8,017
19 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 ...
S R Maiti's user avatar
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19 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 ...
wzkchem5's user avatar
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18 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 ...
wzkchem5's user avatar
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17 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-...
I have no free time anymore's user avatar
15 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. ...
Xiaoming Wang's user avatar
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 ...
ProfM's user avatar
  • 11k
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 ...
Tristan Maxson's user avatar
14 votes
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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 ...
Tyberius's user avatar
  • 15.5k
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 ...
Kristof Bal's user avatar
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14 votes
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How can I specify different theory levels for different atoms in Gaussian?

While ONIOM QM/QM is possible, I don't think that is what you want to be doing. From your example input, it looks like you are just trying to use a different basis function on specific atoms, but the ...
Tyberius's user avatar
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13 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 ...
Peter Nagy's user avatar
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 ...
I have no free time anymore's user avatar
13 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: ...
Jack's user avatar
  • 15.1k
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 ...
Y. Zhai's user avatar
  • 1,124
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)....
Wychh's user avatar
  • 2,157
11 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 ...
S R Maiti's user avatar
  • 6,841
10 votes
Accepted

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 ...
ProfM's user avatar
  • 11k
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 ...
Hans Wurst's user avatar
10 votes
Accepted

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 <...
Tyberius's user avatar
  • 15.5k
10 votes
Accepted

Do the U values affect structure optimization with the DFT+U simulation to optimize crystal structure?

This isn't possible to answer with any certainty without trying it. Strictly speaking, if you need a Hubbard U to correct for the spurious self-interaction, then you need it to model the material ...
Phil Hasnip's user avatar
  • 7,262
10 votes

Which output file from CASTEP after geometry optimization is like with the CONTCAR from VASP?

The main structural output of a geometry optimization in Castep is in the file with the ".geom" extension. That file contains blocks with lattice parameters and atomic positions at each step ...
ProfM's user avatar
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9 votes
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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 ...
Brandon Bocklund's user avatar
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 ...
Tyler Sterling's user avatar
9 votes
Accepted

How to eliminate imaginary frequencies during a Gaussian geometry optimization?

Use tighter convergence criteria. If the geometry is already converged with default convergence criteria, then just using tighter convergence thresholds should work. Look at the tight option in the ...
jheindel's user avatar
  • 3,534
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 ...
I have no free time anymore's user avatar
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'...
Geoff Hutchison's user avatar
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 ...
Abd-Elazeem Mohamed's user avatar
9 votes
Accepted

Symmetry group of p-benzoquinone

tldr: For a UV/Vis spectra, it shouldn't matter much. I've found that Gaussian's AM1 / PM3 implementation often breaks symmetry during optimization. So I'm not surprised at your finding. Moreover, in ...
Geoff Hutchison's user avatar

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