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Of course, in no case an isolated molecule would have access to neighboring functions. But in the crystal it does. If its own basis is not complete, a molecule in the crystal can get extra-stabilized by the neighboring functions not because of a "physical" or "chemical" interaction with neighboring molecules but because of an artifact due to the incompleteness of its basis. So if you were to compute the cohesive energy just as energy of the crystal - energy of the bare molecule, you would get an extra unphysical interaction. To make sure you get the right cohesive energy you could do one of two things: i) remove the extra interaction from the calculation on the crystal; ii) add it also to the molecular calculation so that it cancels when taking the difference (this is the MOLEBSSE strategy, also known as Boys-Bernardi counterpoise correction).

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Hi Jonas,

As you correctly point out, in this case the molecular calculations are not affected by BSSE as you are extracting a single molecule (i.e. with no neighbors).

The calculation that is affected by BSSE is the one on the crystal, where each molecule within the molecular crystal could potentially "benefit" from the basis functions of the neighboring molecules if its own basis is not complete. So we use MOLEBSSE for this, to make sure we compare apples with apples (i.e. the energy of a molecule in the crystal that has access to the basis functions from neighboring molecules, with the energy of an isolated molecule that also has access to the same neighboring basis functions).

Hope this helps clarifying things a little,

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Dear Prof. Piquini,
I am sorry but I never received your files. Could you please try again?

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Hi,

In the context of TOPOND, PS does indeed label an atom for which a PSeudopotential is used. At some point of the output the coordinates of the PS atomic center are printed, which should allow for its identification.

Hope this helps,

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Dear Piquini,
thank you for your email. Is there any possibility to have a look at your input-output files? If you prefer you can send them to [email protected].

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Excellent, thank you for the quick feedback.

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Hi,

We have checked the implementation. The values printed in the output of the BETAVIB calculation for SHG and Pockels are expressed in atomic units and correspond to \( \frac{1}{2}{\boldsymbol{ \beta}} \). That is, the factor of \( \frac{2\pi}{V} \) seems to be missing to make them the d tensor. In other words, by multiplying the values in the output by \( \frac{2\pi}{V} \) you should get d.

Please, let me know if you think this makes sense based on the values you get for your system.

Sorry for the confusion.
Hope this helps,

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Dear leszec_malec,

You can bypass the error by using a functional parameterized for DFT-D3 (BJ), for example PBE, and then manually defining the dispersion parameters.

Please see the DFTD3 block below:

DFTD3
VERSION
4
FUNC
PBE
S6
1.0000
S8
1.6112
A1
0.0000
A2
7.3539
END

Best regards,

Lorenzo

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Formally, if finite temperature effects are to be included, the internal static energy E needs to be substituted with the free energy F in the definition of the Hessian. This is easier said than done. However, for the elastic tensor, we do have an implementation to compute free energy derivatives with respect to lattice strain (i.e. thermo-elasticity). See also:

https://www.mdpi.com/2075-163X/9/1/16

The elastic tensor is not defined for 0D systems, where you could just explore the "dynamical stability" in terms of the vibration frequencies.

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Hi,

Stability is a broad concept that can be interpreted and analyzed in many ways. One way to look at it is the following: checking whether or not the Hessian of second energy derivatives is positive-definite (all eigenvalues are positive) or not, i.e. if the structure is a local minimum of the potential energy surface (PES). Indeed if small structural perturbations produce an energy decrease rather than increase (that is if some of the eigenvalues are negative) the structure can not be considered "stable".

Two types of Hessian matrix can be considered, which correspond to two types of stability:

Hessian with respect to atomic displacements within a fixed cell for dynamical (phonon) stability. This corresponds to checking if all harmonic frequencies are positive.
Hessian with respect to lattice distortions for mechanical stability (so-called Born stability conditions). This corresponds to checking if all the eigenvalues of the elastic tensor are positive.

Hope this helps,

Developer

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