And I asked it to Gemini, Google’s AI.
Here is her response 😲
=========================
Yes, it's possible to include the zero-point energy (ZPE) correction for both a
2D surface and a 2D surface with adsorbed atoms using Quantum ESPRESSO. This
correction is crucial for accurately calculating energies, such as adsorption
energies, as it accounts for the vibrational energy of the atoms even at
absolute zero temperature (0 K).
To calculate the ZPE correction, you must perform phonon calculations for your
systems. Quantum ESPRESSO's phonon code, ph.x, is the primary tool for this.
The ZPE is half the sum of all vibrational frequencies, represented by the
following formula:
ZPE=21i∑ℏωi
Where:
• ℏ is the reduced Planck constant.
• ωi are the vibrational frequencies (eigenfrequencies) of the system's
normal modes.
1. Zero-Point Energy Correction for a 2D Surface
To calculate the ZPE for a 2D surface, you'll follow these general steps:
• Optimize the geometry of your 2D surface slab to find the lowest-energy
configuration.
• Run a self-consistent field (SCF) calculation on the optimized structure.
This calculation is a prerequisite for the phonon calculation.
• Perform a phonon calculation using ph.x. This involves calculating the
vibrational modes across a q-point grid in the Brillouin zone. The output will
be the phonon frequencies.
• Process the phonon output to get the total ZPE. This often involves using
a post-processing tool like matdyn.x to diagonalize the dynamical matrices and
sum up the positive frequencies. The ZPE is then calculated from this sum.
For a 2D surface, it's important to use a supercell that is large enough to
minimize the interactions between periodic images and to ensure a sufficient
vacuum layer in the z-direction.
2. ZPE Correction for an Adsorbed System
For a system with an adsorbed molecule on a 2D surface, the process is similar
but with an important distinction: you need to calculate the ZPE correction for
three separate systems to determine the corrected adsorption energy.
The ZPE-corrected adsorption energy (ΔEadsZPE) is calculated as follows:
ΔEadsZPE=(Eslab+adsorbateDFT+ZPEslab+adsorbate)−(EslabDFT+ZPEslab)−(EadsorbateDFT+ZPEadsorbate)
Where:
• EDFT is the ground-state electronic energy from a standard DFT
calculation (e.g., using pw.x).
• ZPE is the zero-point energy of each system.
To get the ZPEs, you'll perform a phonon calculation for each of the three
components:
• Adsorbed System (Slab + Adsorbate):
• Optimize the geometry of the combined system.
• Run an SCF calculation.
• Run a phonon calculation using ph.x. To save computational time, you
can often freeze the atoms of the bulk surface layers and only allow the
adsorbate atoms and the top surface layer atoms to move. This is a common
approximation.
• Calculate the ZPE from the phonon frequencies.
• Isolated Surface (Slab):
• Optimize the geometry of the clean surface slab.
• Run an SCF calculation.
• Run a phonon calculation. Again, you can freeze the bottom layers to
reduce the computational cost.
• Calculate the ZPE.
• Isolated Adsorbate (Molecule):
• Optimize the geometry of the isolated molecule in a large vacuum cell.
• Run an SCF calculation.
• Run a phonon calculation. For a molecule, all atoms are allowed to
move.
• Calculate the ZPE from the frequencies.
After obtaining the ZPE values for all three systems, you can substitute them
into the equation to get the final ZPE-corrected adsorption energy.
> 2025/08/12 17:28、Chiara Cignarella via users
> <users@lists.quantum-espresso.org>のメール:
>
> Dear Ashley,
>
> You can use the frequencies obtained by phonon calculations to compute the
> zero-point energy using the formula (you can find that in textbooks on the
> quantum harmonic oscillator part - for example Ashcroft pag. 451- ), i.e.
> doing the sum \sum_i 1/2 * \omega_i * hbar (divided by appropriate
> normalization factor for your sum)
>
> Note that the computed phonons do not contain themselves the ZPM
> contributions!
>
>
> Hope this is useful.
>
>
> Best regards,
>
> Chiara Cignarella
> -------------------------------------
> Post-doc researcher
> University of Bremen
>
>> On 12 Aug 2025, at 09:51, Barsha Pal <barsha....@aus.ac.in> wrote:
>>
>> Hello,
>> I have a small doubt regarding whether or not zero-point energy calculation
>> is possible in Quantum Espresso, I want to perform that for a 2D material
>> and adsorption cases. The property that I aim, includes the zero-point
>> energy correction for the 2D surface and the 2D surface with adsorbed atoms.
>> AI tells me that it is possible to do by phonon calculation. If indeed this
>> is possible, can you guide me towards a short example?
>>
>> Thank you.
>> Ashley Cooper
>> Phd
>> _______________________________________________________________________________
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>
> _______________________________________________________________________________
> The Quantum ESPRESSO Foundation stands in solidarity with all civilians
> worldwide who are victims of terrorism, military aggression, and
> indiscriminate warfare.
> --------------------------------------------------------------------------------
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> users mailing list users@lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users
西館数芽
Kazume NISHIDATE Ph.D
Department of Systems Innovation Engineering,
Graduate School of Science and Engineering, Iwate University
4-3-5 Ueda, Morioka, Iwate, 020-8551 JAPAN
Phone:+81-19-621-6391
kazume.nishid...@gmail.com, nisid...@iwate-u.ac.jp
https://sites.google.com/site/nisidatelab/
_______________________________________________________________________________
The Quantum ESPRESSO Foundation stands in solidarity with all civilians
worldwide who are victims of terrorism, military aggression, and indiscriminate
warfare.
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