12

The potential energy surface (PES) is a 3N-dimensional function for a bulk system containing N atoms (in reality 3N-3 to account for the trivial translational degrees of freedom). For a bulk structure, N typically represents the number of atoms in a simualtion cell with periodic boundary conditions, which is of the order of $10^2$-$10^3$, so the function is ...


11

We attempted to solve a similar problem when studying the (also highly symmetrical) $\ce{CH4}$ and $\ce{CF4}$ homo- and hetero-dimers. I found it easiest to use internal coordinates and fixed molecular geometries to generate the hypersurface, but we also had large computational resources at our disposal and we might have benefitted from using even more, ...


9

The Atomic Simulation Environment has two nice implementations of global optimization algorithms. The first is a basin hopping algorithm from a 1997 paper by Wales and Doye in J. Phys. Chem. A. The second is a minima hopping algorithm from a 2004 paper by Goedecker in J. Chem. Phys. There are several nice example use-cases here. If you're looking at ...


9

I am the author of Chemcraft. Your job contains a 2-dimensional PES scan, and currently Chemcraft can visualize only 1-dimensional scans. I plan to implement support of 2d scans in future. It is unclear for me (please give me some advice), in what form should these scans be visualized: colored map, or 3-d surface which can be rotated, or simply the ...


8

On the fitting, I would recommend Dr. Nike Dattani's answer. You can also try some other methods such as those using neural networks. I read your discussion and find that may be you have also some issues with the scanning using ab initio methods. The intermolecular interaction is often read $$\Delta V_{\rm int}=\Delta V_{\rm int}(R, \theta, \phi),$$ where $...


8

For 1D analytic potentials, I highly recommend to use my potential energy form or a slight simplification of it, which I can help you with. This is known as the Morse/Long-Range (MLR) potential and is now the "industry standard" in high-accuracy spectroscopy and some other areas. For analytic multi-dimensional potential energy surfaces, there's a ...


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 ...


7

Generally you want to use the same settings when trying to combine results from different jobs. However, below is the general procedure that I have seen performed for a basic, publishable PES. 1) Perform geometry optimization 2) Perform solvent/frequency calculations 3) Combine solvent energy and enthalpy (from frequency calculation "Total Enthalp...") 4)...


6

It can be done using ModRedundant option in Gaussian (more on that here). You just freeze everything in space except for the 5th and 6th hydrogen. However, in my opinion it would be better to perform a so called relaxed scan (a series of optimizations with the scanned coordinate fixed to certain values) as it yields better geometries for system states during ...


6

Without seeing the result of the scan, my guess would be that it is a visualization problem with gaussview, and it has nothing to do with the calculation. Gaussview detects bonds by the distance between two atoms, and sometimes it does not show up, even though the distance is right. You can try two things—first, in the frames where you can't see the bonds, ...


6

This completely depends on what you're looking to model and the type of material you're modeling. A standard rule-of-thumb is generally no greater than 0.05 eV/Å for the maximum net force on any atom, but even this can often be too large, particularly (but not exclusively) in the case of highly flexible materials or molecular crystals. Personally, I like 0....


6

CCDC The Cambridge Crystallographic Data Centre organizes a regular organic crystal structure prediction blind test as detailed in their website. These started in 1999 and the latest (the sixth one) was held in 2015. Participants, which include leading research groups in structure prediction, are asked to predict the structure of a range of molecules, the ...


6

xtb The Grimme group's freely available xtb tight binding program based on the GFN force field can be used to rank candidate structures in energy with the CREST tool.


5

As others have mentioned, there is no 'rule of thumb', but I do phonon calculations (PHONOPY and DFPT) and did some checking a long time ago to converge the phonon energies. I found ~ 0.001 eV/A to be more than low enough for all cases that I checked. Note that, while relaxation to high precision is expensive, once it gets close to the minimum, the positions ...


5

It would help to know what you need the potentials for, since this will affect the techniques that are necessary to evaluate the potential. Point charges are trivial, as the potential generated by each charge is just -Z/r; the trick is mostly how to make the evaluation efficient, this is achieved with methods like fast multipoles or particle mesh Ewald. (...


5

I searched for the word "minimum" on the Wikipedia page for Lennard-Jones potential, and the 2nd paragraph says: "The potential minimum is at $r=r_m = 2^{1/6}\sigma$." You can obtain this by calculating the derivative of the Lennard-Jones potential with respect to $r$ and finding which $r$ value makes that derivative equal to 0.


4

I think @romaichenko's answer covers everything. But for a full answer I believe a sample input file is necessary. # B3LYP/6-31G(d) Opt=ModRedundant methane with H 0 2 C -1.41531 0.37839 0.00000 H -0.34531 0.37839 0.00000 H -1.77197 0.64640 -0.97255 H -1.77198 1.08664 0....


4

Bayesian Optimization There are some nice options for exploring potential energy surfaces using Bayesian optimization. This has the advantage of using Gaussian Process regression to build a surrogate to the potential energy surface Bayesian optimization works extremely well for "expensive" functions (e.g., minutes to hours per point) in which the ...


2

I really don't know the output structure of Q-Chem, but in SIESTA, we have the following information: siesta: Final energy (eV): siesta: Band Struct. = -6333.862502 siesta: Kinetic = 15927.632813 siesta: Hartree = 72644.682988 siesta: Eldau = 0.000000 siesta: Eso = 0.000000 siesta: Ext. field = 0....


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