12
votes
Accepted
How can I scan the whole PES of a bulk structure?
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,...
- 11k
11
votes
What is the procedure for constructing an ab initio potential energy surface for CH3Cl + Ar?
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 ...
- 1,653
11
votes
Accepted
How to create a Potential Energy Surface in Chemcraft?
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 ...
- 406
9
votes
Accepted
What are some available software packages for automated finding of local and absolute minima on PES?
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 ...
- 7,361
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 ...
- 1,494
8
votes
What is the procedure for constructing an ab initio potential energy surface for CH3Cl + Ar?
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 ...
- 1,124
8
votes
What is the procedure for constructing an ab initio potential energy surface for CH3Cl + Ar?
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 ...
8
votes
Accepted
Software for generating ensembles of dimer pairs of organic molecules
Generating all possible structures systematically might be difficult. When it comes to the generation and refinement of chemically useful structure guesses, I'd recommend looking into CREST by Stefan ...
- 546
8
votes
Candidate structures for global minimum determination
Confab OpenBabel
source documentation: https://open-babel.readthedocs.io/en/latest/3DStructureGen/multipleconformers.html
Example:
...
- 8,017
8
votes
Which SCF energy to use to plot PES after calculations with SMD?
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) ...
- 1,546
7
votes
Parameterising a Lennard-Jones interaction: Which atoms should I scan to build potential energy surface?
I searched a lot, they always said you should do scan between two atoms and then fit with Lennard-Jones Equation, but they don't explain which atom should I select or depend on what should I select ...
- 23.3k
7
votes
Accepted
Restart potential energy scan in Gaussian with additional scan points
If I'm understanding correctly, something like this should work.
...
- 15.5k
7
votes
Accepted
Is it reasonable to calculate TDDFT excitation energies at a geometry optimized with a different method?
The question, in some sense, is "how accurate is the geometry?"
Yes, in principal, you should do TD-DFT on a true minimum geometry. However, the diagram also indicates that if you displace ...
- 9,265
7
votes
Is it possible to do a Gaussian redundant scan with some fixed bonds?
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 ...
- 2,373
7
votes
Accepted
PES of Tetramethylthiuramdisulfid / Problem with Disulfidbridge
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 ...
- 6,841
7
votes
Candidate structures for global minimum determination
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.
- 19.1k
6
votes
3D Poisson equation solver for arbitrary charge distribution?
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 ...
- 19.1k
6
votes
Accepted
Permissible amount of forces on ions in a relaxed structure
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, ...
- 7,361
6
votes
Candidate structures for global minimum determination
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) ...
- 11k
6
votes
A good 2D function for plotting and visual demonstration of transition state, reaction coordinate etc
I would suggest using the egg holder function which is defined by the following formula
$
f(x) = -(x_2+47)sin\left(\sqrt{\left| x_2+\frac{x_1}{2} + 47 \right|}\right) - x_1sin\left(\sqrt{\left| x_1-(...
- 3,912
6
votes
A good 2D function for plotting and visual demonstration of transition state, reaction coordinate etc
EDIT:
Turns out it can be extremely simple to do. Here are the ingredients:
Component
Expression
Curved minimum energy path (path follows $y = 0.4 (x^2 - 4x)$)
$[y - 0.4(x^2-4x)]^2$
Ridge (runs ...
- 2,943
5
votes
Permissible amount of forces on ions in a relaxed structure
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 ...
- 1,118
5
votes
Accepted
What is the equilibrium bond length for a Lennard-Jones potential?
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 ...
5
votes
Accepted
Is it possible to do a Gaussian redundant scan with some fixed bonds?
I think @romaichenko's answer covers everything. But for a full answer I believe a sample input file is necessary.
...
- 6,841
5
votes
Parameterising a Lennard-Jones interaction: Which atoms should I scan to build potential energy surface?
You linked to my answer about parameterizing force fields. For reference, this isn't my area of expertise, although a colleague's group does this frequently.
My understanding of your question is that ...
- 9,265
5
votes
Accepted
Slope of the potential when both molecules "touch"?
If you have two atoms colliding, we rarely talk about them "touching" because the potential energy between them will tend to infinity as the internuclear distance tends to zero. For example, ...
5
votes
Do conformations arise from vibrations?
Yes, you can think of conformations as arising from vibrational modes, typically low-energy ones. In fact, some conformational search methods use low-energy dynamics or projection to find new ...
- 9,265
5
votes
Accepted
Gaussian 16: Relaxed scan using Jacobi coordinates expressed using generalized internal coordinates
Based on the GIC page in Gaussian website and your picture, the definition of the coordinates would be:
...
- 6,841
4
votes
Script to draw one-dimensional PES comparing harmonic and anharmonic vibrational modes
A script that works for arbitrary potentials
My script has produced the following figures for this paper.
Simple single-well potential:
Double-minimum potential with a small barrier and a "shelf&...
4
votes
Accepted
Are there any available tools to implement Jellium models?
The GPAW density functional theory code has a jellium mode (tutorials here). There is, e.g., a JelliumSlab class, where the charge neutralizing jellium background does not extend over all space, but ...
- 356
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