DOI: 10.3217/0qwnq-sg154
title: Analyzing Heat Transport in Crystalline Polymers in Real and Reciprocal Space

description: General Remarks

The data given here corresponds to the data that is used in the paper "Analysing Heat Transport in Crystalline Polymers in Real and Reciprocal Space". A preprint of that paper can be found at https://arxiv.org/abs/2503.14289. In that paper, we explain how the simulations are performed, i.e., how the data are generated.

The data can be read with the programs, that it was created with, which are listed in the "Code availability"-section of our paper. In some instances, the data is in a plain text format and can be read, e.g., with a simple parser in Python.

The workflow for creating the moment tensor potentials (MTPs) is explained in "Analysing Heat Transport in Crystalline Polymers in Real and Reciprocal Space" and in more detail in our previous paper "Designing Accurate Moment Tensor Potentials for Phonon-Related Properties of Crystalline Polymers" (https://www.mdpi.com/1420-3049/29/16/3724).

The abbreviations used here are explained in the paper "Analysing Heat Transport in Crystalline Polymers in Real and Reciprocal Space" in great detail. Here, we only give a brief overview of the abbreviations:



MTP: moment tensor potential

MD: molecular dynamics

BTE: Boltzmann transport equation

MTP_MD: an MTP that was parametrised for the MD simulations

MTP_phonon: an MTP that was parametrised for the phonon and BTE simulations

PE: polyethylene

PT: polythiophene

ALD-BTE: BTE employing anharmonic lattice dynamics to obtain the phonon lifetimes

MD-BTE: BTE employing MD to obtain the phonon lifetimes

AEMD: approach-to-equilibrium molecular dynamics

NEMD: non-equilibrium molecular dynamics

RMSD_MD: root mean square deviation between the forces of an MTP and DFT. Forces come from an MD run.


 

Structure of the data



VASP training data generation. The training data for the MTPs is generated in these active learning runs.



PE



NPT ensemble, 15 - 500 K (split into segments 15 K – 30 K, 30 K - 150 K, 150 K - 300 K, 300 K - 400 K and 400 K - 500 K)

NVT ensemble (fixed at 300 K cell), 15 K - 100 K



PT



NPT ensemble, 15 - 500 K

NVT ensemble (fixed at 300 K cell), 15 K - 100 K





Moment Tensor Potential (MTP) training runs. Typically 5 training runs with different random initialisations are performed, which are labelled with a, b, c, d and e.



PE, MTP_MD



a, b, c, d ("best"), e



PE, MTP_phonon, NPT ensemble training data



a, b, c, d ("best"), e



PE, MTP_phonon, NVT ensemble training data



a, b, c ("best"), d, e



PT, MTP_MD



a, b, c ("best"), d, e



PT, MTP_phonon, NPT ensemble training data



a, b ("best"), c, d, e



PT, MTP_phonon, NVT ensemble training data



a, b, c, d, e








VASP validation runs. VASP active learning runs are performed at 300 K in an NPT ensemble to determine RMSD_MD



PE

PT








ALD-BTE calculations. collision matrices for each grid point are omitted due to their huge size.



PE (full BTE, 4×6×160 q-mesh)



DFT, 300 K cell

DFT, DFT-relaxed cell

MTP, 300 K cell

MTP, DFT-relaxed cell



PT (full BTE, 4×6×48 q-mesh)



MTP, 300 K unit cell

MTP, DFT unit cell







MD-BTE calculations. The file with the velocities (named velocities_dyn.dump) requires up to 300 GB; therefore it is omitted. The renormalized force constants require 5 GB of storage (for PT) and are thus also omitted. The calculation is performed in two steps, employing first LAMMPS, and then Dynaphopy.



PE (simulation time of 1 ns, resolution of power spectrum 0.004 THz)

PT (simulation time of 2 ns, resolution of power spectrum 0.002 THz)





AEMD simulations



PE



432, 720, 1080, 1440, and 2160 cell repetitions



PT



128, 192, 256, 384, and 512 cell repetitions







NEMD simulations



PE



216, 288, 432, 576, 720, 1080, and 1440 cell repetitions



PT



128, 256, 512, and 1024 cell repetitions






A Note on axis relabelling

In order to align the polymer chains along the z-direction, and to be consistent with our previous publication "Designing Accurate Moment Tensor Potentials for Phonon-Related Properties of Crystalline Polymers" (https://www.mdpi.com/1420-3049/29/16/3724), we relabeld the axis in the following way:

PE

x --> z

y --> y

z --> x

PT

x --> y

y --> x

z --> z

Example

The q-mesh for the phono3py calculation of PE is given as 160×15×10 in the job-submission-script where phono3py is called, but in the paper (and above) it is written as 10×15×160. All calculations (including POSCAR files etc.) are consistent with each other in terms of their axis labels. Just for the paper, the axis relabelling was performed.