DOI: 10.5061/dryad.rr4xgxdj6
title: Data from: Anomalous thermal transport in Eshelby twisted van der Waals nanowires

description: Dislocations in van der Waals (vdW) layered nanomaterials induce strain
 and structural changes that substantially impact thermal transport.
 Understanding these effects could enable the manipulation of dislocations
 for improved thermoelectric and optoelectronic applications, but
 experimental insights remain limited. In this study, we use synthetic
 Eshelby twisted vdW GeS nanowires (NWs) with single screw dislocations as
 a model system to explore the interplay between dislocation-induced
 structural modifications and lattice thermal conductivity. Our
 measurements reveal a monoclinic structure stabilized by the dislocation,
 leading to a substantial drop in thermal conductivity for larger diameter
 NWs (70% at room temperature), supported by first-principles calculations.
 Interestingly, we also find an anomalous enhancement of thermal
 conductivity with decreasing diameter in twisted NWs, contrary to typical
 trends in non-twisted GeS NWs. This is attributed to increased
 conductivity near the NW cores due to compressive strain around the
 central dislocations and aligns with a density functional theory-informed
 core-shell model. Our results highlight the critical role of dislocations
 in thermal conduction, providing fundamental insights for defect and
 strain engineering in advanced thermal applications.
description: # Anomalous Thermal Transport in Eshelby Twisted Van der Waals Nanowires:
 Open Source Data The raw data used in lattice thermal conductivity
 calculations is made publicly available. The dataset includes crystal
 structure files (POSCAR), dielectric tensor and Born effective charges
 (BORN), second-order interatomic force constants (fc2.hdf5), and
 third-order interatomic force constants (fc3.hdf5) for GeS in both
 orthorhombic and monoclinic structures. The files are organized into the
 following directories: * **GeS_orthorhombic**: Contains the structure
 (POSCAR), Born effective charges (BORN), and second- and third-order
 interatomic force constants (fc2.hdf5 and fc3.hdf5) for GeS in the
 orthorhombic structure. * **GeS_monoclinic**: Contains the structure
 (POSCAR), Born effective charges (BORN), and second- and third-order
 interatomic force constants (fc2.hdf5 and fc3.hdf5) for GeS in the
 monoclinic structure. * **GeS_monoclinic_normal_compression**: Contains
 the structure (POSCAR), Born effective charges (BORN), and second- and
 third-order interatomic force constants (fc2.hdf5 and fc3.hdf5) for GeS in
 the monoclinic structure at 0%, 2%, 4%, and 6% normal compression. ##
 Descriptions ### POSCAR File Description The `POSCAR` file is a input for
 Vienna Ab initio Simulation Package (VASP), which is used for density
 functional theory (DFT) simulations. It defines the atomic structure of a
 material, including lattice parameters, atomic positions, and other
 essential data required for computational modeling. The POSCAR file is
 formatted in plain text. This file is used to parse the stucture
 information to the phonopy/phono3py code. **Structure and Content of the
 POSCAR File** The file is organized into specific sections: a descriptive
 comment line, a scaling factor, lattice vectors defining the unit cell,
 atomic species and their counts, and the atomic coordinates in either
 Cartesian or fractional form. For more information about the structure of
 POSCAR file please check:
 [https://phonopy.github.io/phonopy/input-files.html#vasp-poscar-like-format](https://phonopy.github.io/phonopy/input-files.html#vasp-poscar-like-format) ### BORN File Description The `BORN` file is used by Phonopy/Phono3py tools for phonon and lattice thermal conductivity calculations. This file provides the dielectric tensor and the Born effective charges, which are essential for incorporating non-analytical term corrections (NAC) in phonon dispersion calculations and lattice thermal conductivity. **Structure and Content of the BORN File** The `BORN` file is a plain text file with a specific format, organized as follows: * The first line contains a header with the atom indices for which the Born effective charges are provided. * In the second line, dielectric constant is specifed in Cartesian coordinates. The nine values correspond to the tensor elements of xx, xy, xz, yx, yy, yz, zx, zy, and zz. * From the third line, Born effective charges for the independent atoms in the primitive cell have to be written in Cartesian coordinates. The nine values correspond to the tensor elements of xx, xy, xz, yx, yy, yz, zx, zy, and zz. For the orthorhombic cell, there are two non-equivalent atomic sites (site 1 and site 5). For the monoclinic cell, there are four non-equivalent atomic sites (site 1, site 3, site 5, and site 7). Therefore, the BORN file for the orthorhombic cell contains 4 lines, and the BORN file for the monoclinic cell contains 6 lines. For more details about the structure of born file please check: [https://phonopy.github.io/phonopy/input-files.html#born-file](https://phonopy.github.io/phonopy/input-files.html#born-file) ### fc2.hdf5 File Description The `fc2.hdf5` file is used by **Phonopy/Phono3py** to store the second-order force constants in a structured format. These force constants describe the harmonic interactions between atoms in a crystal and are used for phonon calculations, such as phonon dispersion relations, density of states, and lattice thermal conductivity. **Structure and Content of fc2.hdf5**\ The `fc2.hdf5` file is written in the HDF5 (Hierarchical Data Format version 5), a versatile format for storing and organizing large amounts of numerical data. Second-order force constants are stored in units of eV/Å². The `fc2.hdf5` file contains three objects: `['force_constants', 'p2s_map', 'physical_unit']`. * The `force_constants` object is a NumPy array with dtype='double' and order='C', with the shape: (num_patom, num_satom, 3, 3). * `num_patom` refers to the number of atoms in the POSCAR file (here, `num_patom = 8`). * `num_satom` refers to the number of atoms in the 4x4x2 supercell of the POSCAR file, so the shape of the array is (8, 256, 3, 3). * Each atom pair has a 3x3 matrix of force constants corresponding to the Cartesian directions. * The `p2s_map` object provides the indices of atoms in the primitive cell relative to the supercell index system. * The `physical_unit` object specifies the physical unit of the interatomic force constants, which is eV/Å². For more details about the structure of `fc2.hdf5` file please check: [https://phonopy.github.io/phonopy/input-files.html#format-of-force-constants-hdf5](https://phonopy.github.io/phonopy/input-files.html#format-of-force-constants-hdf5) ### fc3.hdf5 File Description The `fc3.hdf5` file is used by Phono3py to store the third-order force constants in a structured format. These third-order force constants describe the anharmonic interactions between atoms in a crystal lattice, which are critical for understanding thermal transport and phonon lifetimes. **Structure and Content of fc3.hdf5** The `fc3.hdf5` file is written in the HDF5 format, with third-order force constants stored in units of eV/Å³. The `fc3.hdf5` file contains three objects: `['fc3', 'p2s_map', 'version']`. * The `fc3` object is a NumPy array with dtype='double' and order='C', with the shape: (num_satom, num_satom, num_satom, 3, 3, 3). * The first three `num_satom` values correspond to the atom indices in the 3x4x1 supercell based on the POSCAR file. * Therefore, the shape of the array is (96, 96, 96, 3, 3, 3). * For each atom triplet, there is a 3x3x3 matrix of force constants corresponding to the Cartesian directions. * The `p2s_map` object provides the indices of atoms in the primitive cell relative to the supercell index system. * The `version` object specifies the version of the Phono3py software used (2.6.0 in our case). For more details about the structure of `fc3.hdf5` file please check: [https://phonopy.github.io/phono3py/input-output-files.html#fc3-hdf5](https://phonopy.github.io/phono3py/input-output-files.html#fc3-hdf5) ### Key Information Sources ll datasets presented here were generated using a combination of Phonopy and Phono3py, alongside density functional theory (DFT) as implemented in the VASP code. Detailed information regarding the DFT calculations can be found in the manuscript. ## Code/Software To examine the HDF5 files, we recommend using the `h5py` package. The provided files require the use of the **Phonopy** and **Phono3py** packages. Both Phonopy ([https://phonopy.github.io/phonopy/](https://phonopy.github.io/phonopy/)) and Phono3py ([https://phonopy.github.io/phono3py/](https://phonopy.github.io/phono3py/)) are open-source Python tools developed by Dr. Atsushi Togo at Kyoto University, Japan. Installation instructions for these packages can be found on their respective websites. For further details on the methods implemented, please refer to the following pages: * [https://phonopy.github.io/phonopy/citation.html](https://phonopy.github.io/phonopy/citation.html) * [https://phonopy.github.io/phono3py/citation.html](https://phonopy.github.io/phono3py/citation.html)