26
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 ...
- 9,045
24
votes
Accepted
What do negative phonon frequencies signify?
Phonons are a measure of the curvature of the potential energy surface about a stationary point. In particular, the matrix of force constants is calculated as:
$$
D_{i\alpha,i^{\prime}\alpha^{\prime}}(...
- 10.9k
21
votes
Accepted
What's the point of doing high accuracy spectroscopy calculations?
The paper in your question currently has 159 citations and was published in one of the most prestigious journals (Physical Review Letters). It is about high-precision spectoscopy on $\ce{H2}$, which ...
- 33.5k
18
votes
Retrieving Translational and Rotational Modes
I've never done this myself, and there may be other approaches, but one possible detailed answer seems to be provided by the Gaussian webpage. For stability reasons, you can find this page via the ...
- 1,501
17
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 ...
- 9,076
14
votes
What does it mean if a strictly optimized experimental geometry presents imaginary frequencies?
Assuming that all calculation parameters associated with the electronic structure are properly converged, then obtaining imaginary frequencies can mean one of two things.
Physical imaginary ...
- 10.9k
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 ...
- 10.9k
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 ...
- 10.8k
11
votes
What's the point of doing high accuracy spectroscopy calculations?
One of the eternal questions in computational modeling is whether we truly understand all the relevant contributions.
I believe the combination of experiment and theory in the paper suggest that if ...
- 9,045
10
votes
Quantum harmonic oscillator, zero-point energy, and the quantum number n
The zero-point energy is of no importance here, since you can always choose your reference energy freely you can energy-shift your hamiltonian by $\frac{1}{2}\hbar\omega$
$$
H = \frac{p^2}{2m}+\frac{1}...
- 101
10
votes
Accepted
Morse potential for phonons in solids instead of the harmonic potential approximation?
Some people do:
In this paper there is a system coupled to a bath of Morse oscillators rather than a bath of harmonic oscillators, but it is not exactly solvable, they used a numerical approach called ...
- 33.5k
10
votes
Accepted
What are the methods that can be used to ensure that an optimized geometry is a local minimum?
This depends on what you are studying. For molecular systems without periodicity, the simplest approach is to carry out a vibrational frequency analysis and confirm that there are no imaginary modes. ...
- 7,281
9
votes
Accepted
Alternatives to VEDA 4 vibrational energy distribution analysis software?
LocVib (part of MoViPac)
I have never used VEDA before, but according to the paper, it decomposes the normal modes into vibrations of atomic groups, bond stretching, bending or something else. ...
- 1,124
9
votes
How to map molecular vibrations into lattice phonons?
If you index the molecule and the atoms in the crystallographic unit cell the same, you could extract the displacement from the phonon eigenvectors and the displacement from the normal modes. By ...
- 271
9
votes
Accepted
What is the largest system for which vibrationally resolved electronic spectra have been simulated using ML-MCTDH?
When you say MCTDH, I am assuming you mean the vanilla MCTDH without employing the multi-layer structure. In which case 24 modes seem to be the best known result (higher modes can be done, I have ...
- 701
9
votes
Accepted
Where did the "Computational Chemistry Comparison and Benchmark DataBase" find its scaling factors for vibrational specra?
I have a different page on the NIST website (https://cccbdb.nist.gov/vibscale.asp) that gives uncertainties in the scaling factors. I believe many of these were actually established by NIST themselves ...
- 9,045
8
votes
Accepted
Mismatched number of normal modes calculation in GAMESS
Firstly, a minor correction: a non-linear molecule has 3N-6 normal modes, not 3N-5 modes. Linear molecules have 3N-5 normal modes.
GAMESS automatically prints out some values in normal coordinate ...
- 6,516
8
votes
What is the largest system for which vibrationally resolved electronic spectra have been simulated using ML-MCTDH?
The developers of MCTDH from Heidelberg reported in the year 2000 [1]
The largest system treated with MCTDH to date is the pyrazine
molecule, where all 24 (!) vibrational modes were accounted for....
- 7,957
8
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 ...
- 3,524
8
votes
Accepted
Numerical Frequency Parallelization in ORCA
This is exactly what ORCA actually does. For example if you have 48 cores, then ORCA does 48 displacements at once, each using only a single core. This is trivial to implement and is one of the major ...
- 9,076
8
votes
What's the point of doing high accuracy spectroscopy calculations?
Your arguments can be said about numerous other articles (if not all but a very few ones).
What seems negligible in scientific impact at the publication time might be heavily influenced by other ...
- 3,084
7
votes
Transformation between two different sets of molecular vibrational normal coordinate systems
The paradox discovered by @HansWurst comes by the assumption that it is possible to treat both minima on the 1D PES separately and define a separate set of normal coordinates for them. 3N normal ...
- 896
7
votes
Accepted
Transformation between two different sets of molecular vibrational normal coordinate systems
I agree with Emil Zak's answer that normal mode coordinates from different minima should, in general, be put together with special care. However, relating the two different sets of normal mode origin ...
- 1,124
7
votes
Accepted
LDA vs GGA for vibrational properties?
This is a partial answer focusing on comparing phonons calculated with LDA or GGA in solids.
LDA tends to overbind solids, which means that LDA equilibrium volumes tend to be smaller than experimental ...
- 10.9k
7
votes
How many non-redundant internal coordinates are needed for optimisation of linear molecule?
Indeed, Baker's delocalized coordinates routines generate 3N-6 (or 3N-5 for linear molecules) coordinates automagically. Note our small contribution where we distinguish between strong and weak ...
- 1,034
6
votes
Morse potential for phonons in solids instead of the harmonic potential approximation?
Even in treating molecular vibrations, the Morse potential is not always the best, because:
There's cases where the potential is more "harmonic" than "Morse-like", for example in ...
- 1,124
6
votes
Phonon Calculations and Vibrational Modes
Let $u_{pi\alpha}$ be the displacement of atom $\alpha$ in the basis located in supercell with position $\mathbf{R}_p$ and in Cartesian direction $i$. With this "Cartesian" description of ...
- 10.9k
6
votes
What does it mean if a strictly optimized experimental geometry presents imaginary frequencies?
You mention phonons, so I assume you are doing periodic structures which I am not entirely familiar with since I study mostly single molecules. Although, when I get imaginary frequencies from ...
- 1,222
6
votes
Accepted
Optimization and vibrational analysis of excited state CO using GAMESS
I cannot see your output file, but I am pretty sure that the program is running into an error when starting the optimization i.e. when it is trying to generate the guess hessian.
You are using ...
- 6,516
6
votes
Quantum harmonic oscillator, zero-point energy, and the quantum number n
The quantum number n simply represents the different energy levels given by the harmonic oscillator.
$\mathbf{n=0}$ does not correspond to a given temperature, but its relative occupation to other ...
- 10.8k
Only top scored, non community-wiki answers of a minimum length are eligible