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Questions tagged [phonopy]

Tag this when using the phonopy package for phonon calculations at harmonic and quasi-harmonic levels.

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29 votes
3 answers
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How big should a supercell be in phonon calculations?

Is 2x2x2 enough, or is larger needed? I know that a convergence test must be carried out, but increasing supercell size enormously increases computational time, and I am using the Python program ...
Alfred's user avatar
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21 votes
1 answer
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Are there differences in accuracy and reliability between the frozen phonon method and Density Functional Perturbation Theory?

When proposing or predicting new materials, whether in the bulk or in two dimensions, it is important to discuss the stability of the system. This is usually done through thermodynamics and(or) ...
epalos's user avatar
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20 votes
1 answer
4k views

What do negative phonon frequencies signify?

Negative frequencies "in general" mean the direction of displacement is reverse to that in positive frequencies. Does it mean two frequencies with opposite signs but the same magnitude give ...
Hitanshu Sachania's user avatar
20 votes
1 answer
661 views

What do phonon dispersion (or lattice dynamics) studies include?

I use the codes phonopy and phonopy-qha for phonon dispersion studies. phonopy-qha gives ...
Hitanshu Sachania's user avatar
14 votes
1 answer
2k views

How to determine LA/TA, ZA/ZO and LO/TO by PHONOPY

I would like to ask how to use PHONOPY to define which band is LO, TO or LA, TA, or ZO or ZA. I attach a picture from https://iopscience.iop.org/article/10.1088/0953-8984/28/10/103005
Binh Thien's user avatar
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13 votes
2 answers
377 views

Can we do anything to reduce the number of displacements in a frozen phonon lattice dynamics study?

I realize that the more ordered the supercell is, the lower the number of displacements. Perhaps, we could say the same with respect to symmetry. Is there anything that can be done to reduce the ...
Hitanshu Sachania's user avatar
13 votes
1 answer
190 views

Phonon density of states in statistical thermodynamics

Phonon density of states (DoS), $g_{(\omega_i)}$, help understand the distribution of states across frequencies of vibration. $\int g_{(\omega_i)}d\omega_i =$ the number of states between $\omega_i$ ...
Hitanshu Sachania's user avatar
12 votes
1 answer
199 views

Reliability about the predicted two-dimensional crystal structures based on DFT high-throughput calculation?

Computational 2D Materials Database (C2DB), 2D structures and layered materials, and 2D Materials Encyclopedia are three major databases for two-dimensional materials based on DFT calculation. However,...
Jack's user avatar
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11 votes
1 answer
2k views

Why do we need to build a supercell to use the DFPT in Phonopy interfaced with VASP?

The following passage about the merits of density-functional perturbation theory (DFPT) is extracted from this seminal paper: Phonons and related crystal properties from density-functional ...
Jack's user avatar
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10 votes
2 answers
565 views

Temperature effect on elastic constant using VASP

I want to incorporate the temperature effect on elastic constant (EC) of a system using VASP. From literature, there are two ways which can be used to get the temperature effect on EC i) ab initio ...
Niraja moharana's user avatar
10 votes
1 answer
2k views

Tools to Visualize Phonons

Software such as ChemCraft or GaussView is easy to find for vibrational calculations in gas phase, but I am finding it much more difficult to find good visualization software for phonons. I have ...
Tristan Maxson's user avatar
10 votes
0 answers
255 views

Phonon density of states as a function of frequency vs energy [closed]

Lattice dynamics codes like Phonopy output density of states, $g_{(\omega)}$, as a function of frequency. Since $\int g_{(\omega)}d\omega$ is the number of states ...
Hitanshu Sachania's user avatar
9 votes
2 answers
617 views

"Input forces are not enough to calculate force constants" Phonopy error?

I am doing a phonon calculation for a phase using a 2x2x1 supercell (after geometry optimization of the structure). I am getting an error when computing the DOS and band structure after computing the ...
Niraja moharana's user avatar
9 votes
2 answers
1k views

Calculating lattice thermal conductivity using Quantum ESPRESSO and phonopy

How should I calculate lattice thermal conductivity in Quantum ESPRESSO? I have installed phonopy. My Linux distribution is Ubuntu.
epsilon02fft's user avatar
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8 votes
1 answer
655 views

Calculation of linear coefficient of thermal expansion using VASP-Phonopy for Hexagonal material

We use quasi-harmonic approximation using VASP-Phonopy. In whole calculation we only assume Free energy as function of volume but in case of HCP material which have ...
Pranav kumar's user avatar
  • 4,268
8 votes
1 answer
589 views

Should all q-points in the first Brillouin zone be sampled in phonon density of states calculations?

For electronic density of states (DoS) calculations with VASP, it is recommended that VASP's internal symmetry routine is turned ...
Hitanshu Sachania's user avatar
8 votes
1 answer
233 views

Phonon frequencies and free energy with respect to polymorphs

I have a material that can crystallize in either a cubic or tetragonal polymorph depending on the synthesis. I used DFPT in VASP and calculated the phonon band structures. I see that the cubic has all ...
DoubleKx's user avatar
  • 1,070
7 votes
1 answer
1k views

How to solve this Phonopy-related problem?

I have used the finite displacements method for phonon spectrum calculation, and when I typed the command to create force sets: ...
Chi Kou's user avatar
  • 5,843
7 votes
1 answer
570 views

Which IBRION tag should be used for finite displacement method in calculating Phonons spectrum?

I am planning to use the finite displacement method for calculating phonon spectrum, and I have prepared the INCAR file below to try it on a transition metal trihalide monolayer (e.g., VI$_3$). I ...
Chi Kou's user avatar
  • 5,843
7 votes
1 answer
148 views

Can we translate vibrational frequencies at q-points to vibrational frequencies of atoms?

Lattice dynamics codes like phonopy output vibrational frequencies at q-points. Can we get data of vibrational frequencies for each of the atoms in the supercell? (...
Hitanshu Sachania's user avatar
6 votes
1 answer
1k views

Best practice(s) for q-points convergence in phonon density of states calculations

The answer can be a complete description of all the things we must be attentive to while converging q-points. A peculiar thing that I feel contradicted about: Generally, we don't take an equal # of k-...
Hitanshu Sachania's user avatar
6 votes
1 answer
120 views

Do the bottom layers of the slab need to be fixed when we use DFPT or finite displacement methods to compute the phonon spectrum of a surface?

When using DFPT or the finite displacement (also known as the frozen phonon) method to compute surface phonon spectra, it is generally necessary to perform high-precision optimization on the slab ...
James's user avatar
  • 55
6 votes
1 answer
293 views

Lattice Thermal conductivity calculation error

I have been trying to calculate Lattice Thermal Conductivity on my system using QuantumEspresso. I used phonopy and phono3py. I was successful to run these codes on Si system for practice. Now when I ...
epsilon02fft's user avatar
  • 1,522
6 votes
1 answer
288 views

Getting the Phonon Dispersion Using fix phonon in LAMMPS

I am using fix phonon in LAMMPS to get the phonon dispersion relation, but this requires a post-processing code that takes the generated binary file and produces ...
Mohamed's user avatar
  • 695
6 votes
0 answers
78 views

How can we calculate transverse and longitudinal optical phonon frequencies

Could you please help me to calculate the "transverse and longitudinal optical phonon frequencies" from phonopy+vasp output files? These parameters will help me to calculate the high-...
rekha's user avatar
  • 61
6 votes
0 answers
187 views

What is the minimum supercell size for phonon spectrum calculation for this monolayer system? [closed]

Following the previous threads on this topic, I would like to know the minimum supercell size suitable for Phonon spectrum calculation using Phonopy (DFPT) for CrI$_3$ monolayer system given by this ...
Chi Kou's user avatar
  • 5,843
6 votes
0 answers
151 views

How can I find primitive axis for any bulk or 2D (monolayer) material [closed]

I am doing DFPT calculations using VASP+Phonopy. To plot phonon band structure, I need a band.conf file in which we need to ...
astha's user avatar
  • 1,673
5 votes
1 answer
348 views

Phonon calculations using DFPT

I'm currently working on phonon calculations using Phonopy and VASP DFPT approach with a 2x2x1 supercell. I'm seeking guidance on: K-Points Selection: How should I determine the appropriate k-points ...
Farah Shehzadi's user avatar
5 votes
1 answer
260 views

k-path for phonon band structure

I have observed in research papers that the k-path chosen for electronic band structure and for phonon band structure to be different. I am currently using VASPKIT in order to obtain the path for ...
Parmeet Singh EP 066's user avatar
5 votes
1 answer
99 views

Phonon branch-resolved harmonic sampling

I would like to do a phonon band-resolved harmonic sampling, following the recipes from the paper by West and Estreicher (harmonic sampling). In fact, the method presented in the paper is already ...
Nikita Rybin's user avatar
4 votes
1 answer
75 views

Causes of Straight Bands in Phonon Dispersion Calculations

In my phonon calculation utilizing DFPT in VASP for a monolayer material with space group 187, I've noticed that while most of the phonon bands are positive, two of them appear to be straight. What ...
Farah Shehzadi's user avatar
4 votes
1 answer
52 views

Exploring Phonon Dispersion in Two-Dimensional Materials: Analytical Techniques and Mode Identification

How can one analyze the phonon dispersion of 2D materials like graphene to discern specific curves corresponding to particular phonon modes, such as acoustic or optical, as well as longitudinal and ...
Farah Shehzadi's user avatar
4 votes
1 answer
97 views

Why dipole correction does not work in VASP DFPT + phonopy calculation for a stable 2D material

Seems that DFPT method in VASP has many defects. It can't include vdw interaction. Now I found it also can't include dipole correction, which leads to a large negative frequency at $\Gamma$ point. I ...
mollen's user avatar
  • 101
4 votes
1 answer
62 views

Inconsistencies in Phonon Dispersion Results Using Phonopy DFPT with Different Supercell Sizes

I am observing discrepancies in the phonon dispersion results obtained using the Density Functional Perturbation Theory (DFPT) method implemented in Phonopy. Specifically, when I use the same INCAR ...
Farah Shehzadi's user avatar
4 votes
1 answer
232 views

How to calculate the lattice parameter of a supercell using Phonopy? (For Quantum ESPRESSO)

I found in the internet a method to generate a supercell from the input file using Phonopy code. And I have a question if someone can clarify my doubts please. The method is as following: We make an ...
Camilla's user avatar
  • 2,169
4 votes
0 answers
50 views

Comparison of Brillouin Zone Sampling Methods: K-points vs. Q-points

When conducting phonon calculations in VASP using DFPT (Density Functional Perturbation Theory), how do the results obtained using KPOINTS and QPOINTS files compare?
Farah Shehzadi's user avatar
4 votes
0 answers
111 views

An issue of running Phonopy for graphene using Siesta [closed]

I have used Siesta in the example attached with phonopy to run phonon for graphene, and when I typed the command to create force ...
Omar Alrawi's user avatar
4 votes
0 answers
205 views

How to correct units in the band.yaml file of QE, to band.yaml of VASP [closed]

I see from the phonopy web page 1 that the physical unit systems used for the calculators are different for different codes 1. On the same page, it is mentioned that "For these sets of physical ...
kcb's user avatar
  • 153
3 votes
1 answer
186 views

Thermal Properties Calculated with Phonopy

In Phonopy the thermal properties, free energy, heat capacity, and entropy, are calculated from their statistical thermodynamic expressions using phonon frequencies on a sampling mesh in the ...
Jaafar Mehrez's user avatar
3 votes
0 answers
36 views

How to extract the displacement eigenvectors from a phonon calculation?

I'm an undergraduate student using GPAW/ASE for research, and am currently working with the phonon module. I can extract the modes, but aside from using phonopy I can't seem to find a way to get the ...
cinder_shot's user avatar
3 votes
0 answers
103 views

Interpreting Phonon calculations for 2D materials [closed]

What is the meaning of phonon calculation in 2D materials? And is it enough to predict the stability of materials based on positive phonon only?
Maulesh VALA's user avatar
2 votes
0 answers
210 views

How to create a band.conf File for Phonon Calculations of Graphene with DFPT Method?

How can one generate a band.conf file for performing phonon calculations of graphene with a dim 1x1x1 using the (DFPT) method?
Farah Shehzadi's user avatar
2 votes
0 answers
31 views

Dynamical Matrix for the Thermal Transmission Coefficient Calculation

The dynamical matrix for the thermal transmission coefficient calculation is written as follows: $$D_{I\alpha,J\beta}(\overrightarrow{q})=\frac{1}{\sqrt{M_{I}M_{J}}}\sum_{b}K_{I\alpha,J\beta}(a,b)e^{i\...
Kieran's user avatar
  • 753
2 votes
0 answers
104 views

Phonon calculations using Phonopy

Hello everyone: I am doing phonon calculations to plot Helmholtz free energy against temperature. I am using Phonopy with DFPT method. Now I am done but appears if I want to use Phonopy-qha I need the ...
Nana Kofi Boakye's user avatar
2 votes
0 answers
77 views

Comparing phonon dispersions generated with phonopy to those generated with Quantum Espresso

I've generated a phonon dispersion for BCC lithium using the python api for phonopy. I specified the following q-point path ...
A quarky name's user avatar
2 votes
0 answers
48 views

Phonon Angular Momentum

Can anyone help me understand what is Phonon Angular Momentum? How does it affect thermal properties? Any relevant books and papers are welcome, if you have suggestions.
epsilon02fft's user avatar
  • 1,522
2 votes
0 answers
105 views

How to determine the TA/LA by phonopy [closed]

I would like to ask how to use PHONOPY to define which band is LO, TO or ...
Hu Chenhui's user avatar
1 vote
0 answers
273 views

can anyone please explain what is meaning of band.conf , mesh.conf and pdos.conf in phonon calculation? [closed]

Can anyone please explain, what is the physical meaning of band.conf, mesh.conf and pdos.conf in phonon calculation? if it is possible please explain about tags used in it.
Maulesh VALA's user avatar