# Tag Info

18

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 nuclei which is a minima on the potential energy surface. In other words, we want to find the positions, x which satisfy: $\min(E[x])$ Secondly, the quantum ...

17

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 internal coordinates (3N-6 for non-linear molecules, 3N-5 for linear), removing the rotational and translational degrees of freedom. Usually, the optimization ...

15

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-Newton and related approaches mentioned in Shoubhik's excellent answer. DIIS was originally published in 1982 by Peter Pulay for accelerating SCF convergence, ...

14

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 saddle point. In general, you can publish anything if it makes it past peer review. Phonon calculations are something you would do if you fear you are on the ...

14

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 simply dissociate the dimer. Normally, any vdW correction term does not only contribute energies, but als gradients, which in turn affect geometry optimizations (...

13

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 calculation you perform: Geometry optimization. With a geometry optimization, you may end up at a local minimum or at a saddle point of the potential energy ...

13

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 energy of one carbon atom (this means calculating the energy of a neutral carbon atom, and the energy of a singly ionized carbon cation and then reporting the ...

13

It comes down to the fact that HF/KS both are variational method. This short article by Julien Toulouse gives a great description of ways to compute static/dynamic response properties. Here, I'll just summarize the relevant portion. We can compute derivatives of the energy with respect to any variable $x$ as: $$\frac{dE}{dx}=\frac{\partial E}{\partial x}+\... 13 Dispersion correction DOES affect the final geometry. The dispersion interaction is a function of geometry. A crude approximation is to write the dispersion interaction between two neutral molecules as$$ \Delta E_{\rm disp}(R)=-\frac{C_6}{R^6},  where $R$ the distance between the two entities. In some special case, like the system in which two rare gas ...

13

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 comprehensive benchmark but it does contain a few examples ranging from water clusters of 12 water molecules to small proteins. According to this paper Cartesian ...

12

'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. Both the forces and stress tensor are calculated in 'vc-relax'. 'relax' only does the atomic coordinates optimization, i.e., only the forces are calculated. ...

11

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 the LNO-CCSD method in MRCC [doi.org/10.1021/acs.jctc.9b00511]. To my knowledge exact analytical gradients are not implemented for either of them. There is an ...

11

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). The best way to optimize a monolayer or surface in VASP follows: First, optimize your bulk structure. This will give you a reasonable estimation. From the ...

10

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: ISIF=4 % firstly using 4 then 2 IBRION=2 NSW=300 EDIFFG=-0.005 You can search the explanation for each tag in VASPWIKI. For completeness, I give an INCAR ...

10

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 changes the gradient, and thus the optimization. You may get the same result in some cases but those are special cases, in general dispersion correction does ...

9

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 conclusions you draw from your calculations will come from the modified supercell, rather than a version where you have converted it back into the primitive cell. Some ...

9

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 that the relaxed structure (using e.g. VASP) is not usually identical to what another code finds (e.g. ABINIT). Of course, the two structures are close and ...

9

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 often different opinions on whether very small imaginary frequencies matter. The truth is, that it depends a bit on the size of the molecule and what you plan to ...

9

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 the atoms, and you end up with what is called the static lattice approximation. As quantum and thermal fluctuations tend to expand the lattice, then you would ...

8

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 published. I performed a geometry optimization using QChem, and then solvent corrections using ORCA. Reference: [1] T. J. Doyon, J. C. Perkins, S. A. Baker Dockrey, E....

8

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. Shallow local minima may be skipped over due to the optimization process, which will likely send you to a higher symmetry if that is the most stable structure. This ...

8

Confab OpenBabel source documentation: https://open-babel.readthedocs.io/en/latest/3DStructureGen/multipleconformers.html Example: obabel <inputfile> -O <outputfile> --confab [confab options] Some of the options include ecutoff and rcutoff (which help eliminate duplicates) OpenBabel can be easily downloaded through Anaconda, the python package ...

8

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 conventional system. Additionally, we need to introduce the geometry as the following image (image-1.png) attached in the enclosure, where both the shaded black ...

8

Additive dispersion correction methods such as D3, D3(BJ), D3(BJ)+ATM, TS, MBD@rsSCS, etc. are good for geometry optimizations. These methods find the London dispersion interactions governed interlayer distance lower than the mean relative error of 2%. On the other hand, it's a good idea to avoid using these methods for energy calculations. For example, ...

8

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 opt(maxcycle=N) can only set the max value within this range, but not any higher. IOP(1/152=N) changes this internal max value, allowing maxcycle to be raised as ...

7

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 computing other first-order properties. As the first exercise to implement analytic gradients within the DLPNO setup, the DLPNO-MP2 method was considered and the ...

7

It is a bit difficult to answer this question, due to the information provided. If you are a beginner, using vc-relax will have its pros and cons. With regards to using nspin=2: Recall that when you use nspin=2, you are saying that you will define the initial magnetization for the involved species. So, just keep in mind that spin-polarized calculations will ...

7

Not necessarily. The LAPW method is often considered as the golden standard when it comes to correctness of DFT calculations. This happens because the atom-like orbitals within the muffin tin sphere closely resemble the physical condition hence you can have a greater accuracy when it comes to DFT predictions. But if you're refering to the case of using codes ...

7

ASE has a FixSymmetry constraint that preserves spacegroup symmetries. It works with a variety of structure optimization algorithms. You could use LAMMPS as the engine or one of the many other calculators, including some DFT options.

7

tldr; Use dispersion correction for optimization I asked a very similar question a few years ago. Many indications for dispersion corrections in density functional methods are for intermolecular interactions. Clearly these corrections are important in such intermolecular or long-range interactions (e.g., inter-layer spacing in a material.. far from the ...

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