# First-principles lattice thermal conductivity calculation for Hg2GeO4 / Fddd (70) / materials id 13995 https://mdr.nims.go.jp/datasets/e1aac3ab-0292-4261-8c49-565f32af86d5 ## File - [FORCES_FC3.xz](https://mdr.nims.go.jp/filesets/11395a8f-6cfe-4eaa-bf89-28ed83a0c3b2/download) ([Detail](https://mdr.nims.go.jp/filesets/11395a8f-6cfe-4eaa-bf89-28ed83a0c3b2.md)) - [LTC-calc.log](https://mdr.nims.go.jp/filesets/8d58f906-d59b-49de-9a3f-84f86d0a5216/download) ([Detail](https://mdr.nims.go.jp/filesets/8d58f906-d59b-49de-9a3f-84f86d0a5216.md)) - [phono3py_mlp_eval_fc3_disp.yaml.xz](https://mdr.nims.go.jp/filesets/d74f5ecf-f232-45d0-9a5f-284d20cbe9a7/download) ([Detail](https://mdr.nims.go.jp/filesets/d74f5ecf-f232-45d0-9a5f-284d20cbe9a7.md)) - [phonopy_mlp_eval_fc2_dataset.yaml.xz](https://mdr.nims.go.jp/filesets/043c636c-a5ac-44b5-b671-23fc54db5a86/download) ([Detail](https://mdr.nims.go.jp/filesets/043c636c-a5ac-44b5-b671-23fc54db5a86.md)) - [phonopy_training_dataset.yaml.xz](https://mdr.nims.go.jp/filesets/78ce650a-4415-42e3-a6e9-9e23b520bf38/download) ([Detail](https://mdr.nims.go.jp/filesets/78ce650a-4415-42e3-a6e9-9e23b520bf38.md)) - [polymlp.yaml.xz](https://mdr.nims.go.jp/filesets/629614bb-fa97-4ede-91cf-f713e754ddea/download) ([Detail](https://mdr.nims.go.jp/filesets/629614bb-fa97-4ede-91cf-f713e754ddea.md)) - [vasp-settings.tar.xz](https://mdr.nims.go.jp/filesets/25256801-fd3a-427b-9b6a-6c81722b6911/download) ([Detail](https://mdr.nims.go.jp/filesets/25256801-fd3a-427b-9b6a-6c81722b6911.md)) - [band_pdos.png](https://mdr.nims.go.jp/filesets/4c0c8fa5-7414-4671-8cb7-d9ac6101b84c/download) ([Detail](https://mdr.nims.go.jp/filesets/4c0c8fa5-7414-4671-8cb7-d9ac6101b84c.md)) ## Id e1aac3ab-0292-4261-8c49-565f32af86d5 ## Local identifier identifier: MDR-LTC-2026Jan9/mp-13995 ## Visibility open_to_public ## State published ## Created at 2026-01-15T06:43:35.973317Z ## Updated at 2026-01-24T06:25:14.064552Z ## Published at 2026-01-24T01:53:13.449192Z ## Doi ## First published url ## Date published ## Recorded date published ## Resource type dataset ## Manuscript type na ## Collection - id: 0113dccc-ec45-42ed-86db-f455f9b63fb1 identifier: https://mdr.nims.go.jp/pid/0113dccc-ec45-42ed-86db-f455f9b63fb1 title: MDR lattice thermal conductivity calculation database ## Title - title: First-principles lattice thermal conductivity calculation for Hg2GeO4 / Fddd (70) / materials id 13995 title_type: original lang: en ## Description - description: | Input data used to calculate the lattice thermal conductivities of Hg2GeO4. description_type: abstract lang: en - description: | Initial geometry optimization of the conventional unit cell, standardized by the spglib code, was performed using the VASP code with the PBEsol exchange-correlation functional. Supercell forces and energies were calculated using the VASP code, and these data were used to develop polynomial machine learning potentials (MLPs) with the pypolymlp code. The generated MLPs are stored in polymlp.yaml.xz. Parameters required for the non-analytical term correction (Born effective charges and dielectric constants) were calculated using the VASP code with the primitive cell. These VASP results are provided in phonopy_training_dataset.yaml.xz, and the VASP input configurations can be found in vasp-settings.tar.xz. The primitive cell, unit cell, and supercell structures used for the VASP calculations are also provided in phonopy_training_dataset.yaml.xz. The internal atomic positions of the supercell were then optimized using the pypolymlp code under symmetry constraints; the relaxed structure can be found in phonopy_mlp_eval_fc2_dataset.yaml.xz (or phono3py_mlp_eval_fc3_disp.yaml.xz). Second-order force constants (fc2) can be calculated using the phonopy and symfc codes with the displacement–force dataset evaluated by the pypolymlp code, which is stored in phonopy_mlp_eval_fc2_dataset.yaml.xz. Third-order force constants (fc3) can be calculated using the built-in finite difference approach in the phono3py code with the displacement–force dataset stored in phono3py_mlp_eval_fc3_disp.yaml.xz (displacements) and FORCES_FC3.xz (forces). As an example, lattice thermal conductivities (LTCs) were calculated using the phono3py code with fc2 and fc3, and the calculation log is provided in LTC-calc.log. The harmonic phonon band structure and density of states are plotted in band_pdos.png. The band path was generated using the SeeK-path code. description_type: abstract lang: en ## Creator - name: Atsushi Togo role: author orcid: https://orcid.org/0000-0001-8393-9766 organization: National Institute for Materials Science department: Center for Basic Research on Materials ror: https://ror.org/026v1ze26 ## Contact agent - name: Atsushi Togo email: togo.atsushi@nims.go.jp organization: National Institute for Materials Science ror: https://ror.org/026v1ze26 ## Publisher organization: NIMS ror: https://ror.org/026v1ze26 ## Managing organization organization: National Institute for Materials Science department: CBRM ror: https://ror.org/026v1ze26 ## Keyword - subject: Lattice thermal conductivity schema: not_defined - subject: Hg2GeO4 schema: not_defined ## Rights - description: Creative Commons Attribution 4.0 International identifier: https://creativecommons.org/licenses/by/4.0/ ## Other identifier(s) ## Data origin - data_origin_type: simulation ## Embargo ## Journal ## Conference ## Related item ## Funding ## Instrument ## Instrument operator ## Instrument managing organization ## Measurement method ## Specimen - name: Hg2GeO4 description: Hg2GeO4 ## Chemical composition - identifier: Hg2GeO4 description: Hg2GeO4 ## Structure for specimen - description: Hg2GeO4 category_description: Hg2GeO4 ## Structural feature for specimen ## Specific property for specimen ## Process for specimen treatment ## Computational method ## Energy level/transition state ## Software - name: phono3py identifier: https://github.com/phonopy/phono3py - name: phonopy identifier: https://github.com/phonopy/phonopy - name: spglib identifier: https://github.com/spglib/spglib - name: symfc identifier: https://github.com/symfc/symfc - name: pypolymlp identifier: https://github.com/sekocha/pypolymlp - name: VASP identifier: https://www.vasp.at/ - name: Seek-path identifier: https://github.com/giovannipizzi/seekpath ## Custom property ## Fileset - id: 11395a8f-6cfe-4eaa-bf89-28ed83a0c3b2 filename: FORCES_FC3.xz content_type: application/x-xz size: 9304056 md5: c1adf867dcb9a6a15a2f281b4971b057 - id: 8d58f906-d59b-49de-9a3f-84f86d0a5216 filename: LTC-calc.log content_type: text/x-log size: 485944 md5: cd4d22e9872577611defe6c6f046a9e8 - id: d74f5ecf-f232-45d0-9a5f-284d20cbe9a7 filename: phono3py_mlp_eval_fc3_disp.yaml.xz content_type: application/x-xz size: 16688 md5: a737dc78f7884c58d5a271b1921dc4c9 - id: 043c636c-a5ac-44b5-b671-23fc54db5a86 filename: phonopy_mlp_eval_fc2_dataset.yaml.xz content_type: application/x-xz size: 934764 md5: ae1124dd2fba2afddca2544dcf82bb4a - id: 78ce650a-4415-42e3-a6e9-9e23b520bf38 filename: phonopy_training_dataset.yaml.xz content_type: application/x-xz size: 805448 md5: 8b5d024e8447eba3a420a5a8cc0778f6 - id: 629614bb-fa97-4ede-91cf-f713e754ddea filename: polymlp.yaml.xz content_type: application/x-xz size: 303568 md5: c877376fd4450c149b5d8d922ba4cf41 - id: 25256801-fd3a-427b-9b6a-6c81722b6911 filename: vasp-settings.tar.xz content_type: application/x-xz size: 584 md5: 11a3f11bac758154363c42e9004ce55e - id: 4c0c8fa5-7414-4671-8cb7-d9ac6101b84c filename: band_pdos.png content_type: image/png size: 69803 md5: 21f611f3996d2258cc23a0ba847e7488 ## Thumbnail fileset_id: 4c0c8fa5-7414-4671-8cb7-d9ac6101b84c filename: band_pdos.png