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It has been fitted with QUIP/GAP [1,2] by generating a new database of atomic structures containing:\r\n\r\ndimers;fcc, bcc, hcp and simple-cubic supercells, including strained, distorted and high-temperature configurations;surface slabs;clusters (nanoparticles).\r\n\r\nVersion 2 of this potential included more clusters in the training set than version 1.\r\n\r\nThe calculations were carried out at the PBE level of theory [3] using the VASP code [4,5]. This potential uses 2-body (distance_2b) and SOAP-type descriptors (soap_turbo) [6,7]. The files can be used both with QUIP/GAP (compiled with the soap_turbo libraries) and TurboGAP [8]. A reference publication will be added when available.\r\n\r\nReferences\r\n\r\nA.P. Bartók, M.C. Payne, R. Kondor, and G. Csányi. Phys. Rev. Lett. 104, 136403 (2010).LibAtoms: https://libatoms.github.ioJ.P. Perdew, K. Burke and M. Ernzerhof. Phys. Rev. Lett. 77, 3865 (1996).VASP: http://vasp.atG. Kresse and J. Furthmüller. Phys. Rev. B 54, 11169 (1996).A.P. Bartók, R. Kondor, and G. Csányi. Phys. Rev. B 87, 184115 (2013).M.A. Caro. Phys. Rev. B 100, 024112 (2019).TurboGAP: http://turbogap.fi"},"field_of_science":[{"id":"fd80ad86-b461-4ffb-abbd-888bc2ffd653","url":"http://www.yso.fi/onto/okm-tieteenala/ta213","in_scheme":"http://www.yso.fi/onto/okm-tieteenala/conceptscheme","pref_label":{"en":"Electronic, automation and communications engineering, electronics","fi":"Sähkö-, automaatio- ja tietoliikennetekniikka, elektroniikka","sv":"El-, automations- och telekommunikationsteknik, elektronik"}}],"infrastructure":[],"issued":"2022-12-08","keyword":[],"language":[],"metadata_owner":{"id":"829302c3-f5d4-4d20-9ec3-5148bcf385cc","organization":"aalto.fi","admin_organization":"aalto.fi"},"other_identifiers":[],"persistent_identifier":"doi:10.5281/zenodo.7415216","pid_generated_by_fairdata":false,"projects":[],"provenance":[],"relation":[],"remote_resources":[],"spatial":[],"state":"published","temporal":[],"theme":[],"title":{"en":"General-purpose GAP potential for platinum"},"created":"2025-12-04T08:02:17Z","modified":"2026-03-26T06:45:30Z","dataset_versions":[{"id":"bfdbff12-7e1c-4611-ad6c-74d2dd648993","title":{"en":"General-purpose GAP potential for platinum"},"persistent_identifier":"doi:10.5281/zenodo.7415216","state":"published","created":"2025-12-04T08:02:17Z","version":1}],"published_revision":2,"version":1,"api_version":3,"metadata_repository":"Fairdata"},{"id":"bd479484-c684-4cf8-83a9-b358bf8edb66","access_rights":{"id":"05f08728-c18c-4ece-b352-806d0da15432","license":[{"id":"add72c17-4fca-4d00-a2c7-b849c424c42f","url":"http://uri.suomi.fi/codelist/fairdata/license/code/CC-BY-4.0","in_scheme":"http://uri.suomi.fi/codelist/fairdata/license","pref_label":{"en":"Creative Commons Attribution 4.0 International (CC BY 4.0)","fi":"Creative Commons Nimeä 4.0 Kansainvälinen (CC BY 4.0)"}}],"access_type":{"id":"b41462f7-00bf-4e50-935b-2bf1184453a7","url":"http://uri.suomi.fi/codelist/fairdata/access_type/code/open","in_scheme":"http://uri.suomi.fi/codelist/fairdata/access_type","pref_label":{"en":"Open","fi":"Avoin"}},"restriction_grounds":[]},"actors":[{"id":"0a72f761-4256-47aa-8106-398e672245b3","roles":["creator"],"person":{"id":"a868f479-8cec-485e-9262-fd921b423f58","name":"Miguel A. 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One can observe how the formation of the stable bulk fcc motifs is nucleated inward from the surface. A paper reference will be added when available.\r\n\r\nReferences\r\n\r\nJ. Kloppenburg and M.A. Caro. General-purpose GAP potential for platinum. DOI: 10.5281/zenodo.7415219."},"field_of_science":[{"id":"fd80ad86-b461-4ffb-abbd-888bc2ffd653","url":"http://www.yso.fi/onto/okm-tieteenala/ta213","in_scheme":"http://www.yso.fi/onto/okm-tieteenala/conceptscheme","pref_label":{"en":"Electronic, automation and communications engineering, electronics","fi":"Sähkö-, automaatio- ja tietoliikennetekniikka, elektroniikka","sv":"El-, automations- och telekommunikationsteknik, elektronik"}}],"infrastructure":[],"issued":"2022-12-08","keyword":[],"language":[],"metadata_owner":{"id":"829302c3-f5d4-4d20-9ec3-5148bcf385cc","organization":"aalto.fi","admin_organization":"aalto.fi"},"other_identifiers":[],"persistent_identifier":"doi:10.5281/zenodo.7415630","pid_generated_by_fairdata":false,"projects":[],"provenance":[],"relation":[],"remote_resources":[{"title":{"en":"Data in remote location","fi":"Aineisto ulkoisessa palvelussa","sv":"Material i en extern tjänst","und":"Data in remote location"},"use_category":{"id":"1ad1b146-d147-45db-a2fd-1096abc94984","url":"http://uri.suomi.fi/codelist/fairdata/use_category/code/source","in_scheme":"http://uri.suomi.fi/codelist/fairdata/use_category","pref_label":{"en":"Source material","fi":"Lähdeaineisto"}},"download_url":"https://zenodo.org/record/7415631"}],"spatial":[],"state":"published","temporal":[],"theme":[],"title":{"en":"Spontaneous crystallization of a large Pt nanoparticle"},"created":"2025-12-04T08:02:14Z","modified":"2026-03-26T06:45:27Z","dataset_versions":[{"id":"bd479484-c684-4cf8-83a9-b358bf8edb66","title":{"en":"Spontaneous crystallization of a large Pt nanoparticle"},"persistent_identifier":"doi:10.5281/zenodo.7415630","state":"published","created":"2025-12-04T08:02:14Z","version":1}],"published_revision":2,"version":1,"api_version":3,"metadata_repository":"Fairdata"},{"id":"1ef39e74-3c0b-469b-95fb-08494c2d8601","access_rights":{"id":"0743cd7a-6874-4028-9fe1-0a280cdb28f5","license":[{"id":"add72c17-4fca-4d00-a2c7-b849c424c42f","url":"http://uri.suomi.fi/codelist/fairdata/license/code/CC-BY-4.0","in_scheme":"http://uri.suomi.fi/codelist/fairdata/license","pref_label":{"en":"Creative Commons Attribution 4.0 International (CC BY 4.0)","fi":"Creative Commons Nimeä 4.0 Kansainvälinen (CC BY 4.0)"}}],"access_type":{"id":"b41462f7-00bf-4e50-935b-2bf1184453a7","url":"http://uri.suomi.fi/codelist/fairdata/access_type/code/open","in_scheme":"http://uri.suomi.fi/codelist/fairdata/access_type","pref_label":{"en":"Open","fi":"Avoin"}},"restriction_grounds":[]},"actors":[{"id":"d501da20-0890-4f4a-be71-e9ae465f6216","roles":["creator"],"person":{"id":"1f59cbf4-c1e0-4b4e-a434-8eb9da1b7395","name":"Jan Kloppenburg","external_identifier":"https://orcid.org/0000-0002-7236-9400"},"organization":{"id":"ba189058-f2f0-4f47-88f3-50c70776f197","pref_label":{"en":"Department of Electrical Engineering and Automation","fi":"Department of Electrical Engineering and Automation","sv":"Department of Electrical Engineering and Automation","und":"Department of Electrical Engineering and Automation"},"url":"http://uri.suomi.fi/codelist/fairdata/organization/code/10076-T410","in_scheme":"http://uri.suomi.fi/codelist/fairdata/organization","parent":{"id":"2f9f9011-4061-4a93-96af-768471abada7","pref_label":{"en":"Aalto University","fi":"Aalto-yliopisto","sv":"Aalto-universitetet","und":"Aalto-yliopisto"},"url":"http://uri.suomi.fi/codelist/fairdata/organization/code/10076","in_scheme":"http://uri.suomi.fi/codelist/fairdata/organization"}}},{"id":"530ad9f0-e9c6-4e3b-ac18-954c70ad2f57","roles":["creator"],"person":{"id":"a763f2c1-a9dd-4ab5-b8b1-90e0e7ab0232","name":"Miguel A. 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The files are provided in ASE's extended XYZ format. The database contains the following entries:\r\n\r\nNP-DB01.yxz: 8000 Pt nanoparticles with sizes between 10 and 349 atoms, generated with a \"cooking\" protocol.NP-DB02.yxz: 3400 Pt nanoparticles with sizes between 10 and 349 atoms, generated with a \"crystallization\" protocol.\r\n\r\nA paper reference will be added when available.\r\n\r\nProtocols\r\n\r\n\"Cooking\": annealing at 1500 K for 20 ps from fcc + quenching down to 100 K over 20 ps + geometry relaxation to local minimum.\"Crystallization\": annealing at 1150 K for 20 ps from a random spherical distribution + quenching down to 100 K over 20 ps + geometry relaxation to local minimum.\r\n\r\nReferences\r\n\r\nJ. Kloppenburg and M.A. Caro. General-purpose GAP potential for platinum. DOI: 10.5281/zenodo.7415219."},"field_of_science":[{"id":"fd80ad86-b461-4ffb-abbd-888bc2ffd653","url":"http://www.yso.fi/onto/okm-tieteenala/ta213","in_scheme":"http://www.yso.fi/onto/okm-tieteenala/conceptscheme","pref_label":{"en":"Electronic, automation and communications engineering, electronics","fi":"Sähkö-, automaatio- ja tietoliikennetekniikka, elektroniikka","sv":"El-, automations- och telekommunikationsteknik, elektronik"}}],"infrastructure":[],"issued":"2022-12-08","keyword":[],"language":[],"metadata_owner":{"id":"829302c3-f5d4-4d20-9ec3-5148bcf385cc","organization":"aalto.fi","admin_organization":"aalto.fi"},"other_identifiers":[],"persistent_identifier":"doi:10.5281/zenodo.7415541","pid_generated_by_fairdata":false,"projects":[],"provenance":[],"relation":[],"remote_resources":[{"title":{"en":"Data in remote location","fi":"Aineisto ulkoisessa palvelussa","sv":"Material i en extern tjänst","und":"Data in remote location"},"use_category":{"id":"1ad1b146-d147-45db-a2fd-1096abc94984","url":"http://uri.suomi.fi/codelist/fairdata/use_category/code/source","in_scheme":"http://uri.suomi.fi/codelist/fairdata/use_category","pref_label":{"en":"Source material","fi":"Lähdeaineisto"}},"download_url":"https://zenodo.org/record/7415542"}],"spatial":[],"state":"published","temporal":[],"theme":[],"title":{"en":"Platinum nanoparticle database"},"created":"2025-12-04T08:02:12Z","modified":"2026-03-26T06:45:24Z","dataset_versions":[{"id":"1ef39e74-3c0b-469b-95fb-08494c2d8601","title":{"en":"Platinum nanoparticle database"},"persistent_identifier":"doi:10.5281/zenodo.7415541","state":"published","created":"2025-12-04T08:02:12Z","version":1}],"published_revision":2,"version":1,"api_version":3,"metadata_repository":"Fairdata"},{"id":"85e164be-363c-4643-bccd-d9c797466abe","access_rights":{"id":"c3bce564-f22b-432c-b6ce-3b77645a00f9","license":[{"id":"add72c17-4fca-4d00-a2c7-b849c424c42f","url":"http://uri.suomi.fi/codelist/fairdata/license/code/CC-BY-4.0","in_scheme":"http://uri.suomi.fi/codelist/fairdata/license","pref_label":{"en":"Creative Commons Attribution 4.0 International (CC BY 4.0)","fi":"Creative Commons Nimeä 4.0 Kansainvälinen (CC BY 4.0)"}}],"access_type":{"id":"b41462f7-00bf-4e50-935b-2bf1184453a7","url":"http://uri.suomi.fi/codelist/fairdata/access_type/code/open","in_scheme":"http://uri.suomi.fi/codelist/fairdata/access_type","pref_label":{"en":"Open","fi":"Avoin"}},"restriction_grounds":[]},"actors":[{"id":"0ee9d671-cc80-4a99-81b3-ffdd87c7f8a7","roles":["creator"],"person":{"id":"580da353-d517-43a1-ad31-94c7786dce18","name":"Ville Kukkonen","external_identifier":"https://orcid.org/0000-0002-4482-5309"},"organization":{"id":"ba189058-f2f0-4f47-88f3-50c70776f197","pref_label":{"en":"Department of Electrical Engineering and Automation","fi":"Department of Electrical Engineering and Automation","sv":"Department of Electrical Engineering and Automation","und":"Department of Electrical Engineering and Automation"},"url":"http://uri.suomi.fi/codelist/fairdata/organization/code/10076-T410","in_scheme":"http://uri.suomi.fi/codelist/fairdata/organization","parent":{"id":"2f9f9011-4061-4a93-96af-768471abada7","pref_label":{"en":"Aalto University","fi":"Aalto-yliopisto","sv":"Aalto-universitetet","und":"Aalto-yliopisto"},"url":"http://uri.suomi.fi/codelist/fairdata/organization/code/10076","in_scheme":"http://uri.suomi.fi/codelist/fairdata/organization"}}},{"id":"7ed93b7b-cfb6-4b80-8b23-b3e30371ee71","roles":["publisher"],"organization":{"id":"199ca259-da5e-4895-a252-422e316192a7","pref_label":{"en":"Zenodo","fi":"Zenodo","sv":"Zenodo"}}}],"cumulative_state":0,"data_catalog":"urn:nbn:fi:att:data-catalog-acris","description":{"en":"This directory contains the following:\r\n\r\n- Two sets of RDF triples using different ontologies, modeling the same \"MZVAV-2\" air handling unit from the data inventory by Granderson et al. 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Parameters used in the simulation, if not otherwise stated: channel height H 500 nm, temperature 250°C, 250 cycles, inert carrier gas partial pressure 500 Pa, Reactant A molar mass 100 g/mol, inert carrier gas molar mass 28 g/mol, Reactant A diameter 0.600 nm, inert gas diameter 0.374 nm, adsorption capacity 4 metal atoms per nm2, density of the material grown 3.5 g/cm3, pulse time 0.1 s, Reactant A partial pressure 100 Pa, sticking coefficient 0.01. \r\n\r\nAbbreviations: ALD = atomic layer deposition, LHAR = lateral high aspect ratio"},"field_of_science":[{"id":"b6d4a4d0-aeab-46fc-bc18-9e4121cb189e","url":"http://www.yso.fi/onto/okm-tieteenala/ta116","in_scheme":"http://www.yso.fi/onto/okm-tieteenala/conceptscheme","pref_label":{"en":"Chemical 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(2022). Understanding Electron Transfer Reactions using Constrained Density Functional Theory: Complications due to Surface Interactions\", this database provides the input files and CDFT-AIMD trajectory information. Please refer to the publication if you wish to use these data.\r\n\r\n---------------------------------------**************************************************************************-------------------------------------------------\r\n\r\n<em>This study was financed by the Horizon 2020 Framework Programme CompBat with project number 875565. We also thank CSC-IT Center for Science Ltd. and Aalto Science-IT project for generous grants of computer time.</em>\r\n-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------\r\n\r\nThe content of a directory is shown in a tree-like format:\r\n├── 1DMDQ\r\n│   ├── 1_md\r\n│   │   ├── dft-common-params.inc\r\n│   │   ├── dmdq-md-pos-1.xyz\r\n│   │   ├── md.inp\r\n│   │   ├── pos.xyz\r\n│   │   ├── submit.sh\r\n│   │   └── subsys.inc\r\n│   ├── 2_cdftaimd\r\n│   │   ├── state_a\r\n│   │   │   ├── becke_twoconstraints.inc\r\n│   │   │   ├── cdft_md.bash\r\n│   │   │   ├── cdft_md.inp\r\n│   │   │   ├── dft-common-params.inc\r\n│   │   │   ├── frame-cdft-pos-total.xyz.tar.gz\r\n│   │   │   ├── frame.xyz\r\n│   │   │   └── subsys.inc\r\n│   │   ├── state_b\r\n│   │   │   ├── becke_twoconstraints.inc\r\n│   │   │   ├── cdft_md.bash\r\n│   │   │   ├── cdft_md.inp\r\n│   │   │   ├── dft-common-params.inc\r\n│   │   │   ├── frame-cdft-pos-total.xyz.tar.gz\r\n│   │   │   └── subsys.inc\r\n│   │   └── state_c\r\n│   │       ├── becke_twoconstraints.inc\r\n│   │       ├── cdft_md.bash\r\n│   │       ├── cdft_md.inp\r\n│   │       ├── dft-common-params.inc\r\n│   │       ├── frame-cdft-pos-total.xyz.tar.gz\r\n│   │       └── subsys.inc\r\n│   └── 3_cdft_wH2O_sccs\r\n│       ├── state_a\r\n│       │   ├── framePrint.py\r\n│       │   ├── input_files\r\n│       │   │   ├── 1_energy_cdft_STATE1.bash\r\n│       │   │   ├── 2_energy_cdft_STATE2.bash\r\n│       │   │   ├── 3_energy_cdft_mixed.bash\r\n│       │   │   ├── becke_twoconstraints.inc\r\n│       │   │   ├── dft-common-params.inc\r\n│       │   │   ├── energy_cdft.inp\r\n│       │   │   ├── energy_mixed_cdft.inp\r\n│       │   │   └── subsys.inc\r\n│       │   └── README\r\n│       ├── state_b\r\n│       │   ├── b_to_a.tar.gz\r\n│       │   └── b_to_c.tar.gz\r\n│       └── state_c\r\n│           ├── framePrint.py\r\n│           ├── input_files\r\n│           │   ├── 1_energy_cdft_STATE1.bash\r\n│           │   ├── 2_energy_cdft_STATE2.bash\r\n│           │   ├── 3_energy_cdft_mixed.bash\r\n│           │   ├── becke_twoconstraints.inc\r\n│           │   ├── dft-common-params.inc\r\n│           │   ├── energy_cdft.inp\r\n│           │   ├── energy_mixed_cdft.inp\r\n│           │   └── subsys.inc\r\n│           └── README\r\n├── 2MeVi\r\n│   ├── 1_md\r\n│   │   ├── dft-common-params.inc\r\n│   │   ├── md.inp\r\n│   │   ├── mevi-md-pos-1.xyz\r\n│   │   ├── pos.xyz\r\n│   │   ├── submit.sh\r\n│   │   └── subsys.inc\r\n│   ├── 2_cdftaimd\r\n│   │   ├── state_a\r\n│   │   │   ├── becke_twoconstraints.inc\r\n│   │   │   ├── cdft_md.bash\r\n│   │   │   ├── cdft_md.inp\r\n│   │   │   ├── dft-common-params.inc\r\n│   │   │   ├── frame-cdft-pos-total.xyz.tar.gz\r\n│   │   │   └── subsys.inc\r\n│   │   ├── state_b\r\n│   │   │   ├── becke_twoconstraints.inc\r\n│   │   │   ├── cdft_md.bash\r\n│   │   │   ├── cdft_md.inp\r\n│   │   │   ├── dft-common-params.inc\r\n│   │   │   ├── frame-cdft-pos-total.xyz.tar.gz\r\n│   │   │   ├── frame.xyz\r\n│   │   │   └── subsys.inc\r\n│   │   └── state_c\r\n│   │       ├── becke_twoconstraints.inc\r\n│   │       ├── cdft_md.bash\r\n│   │       ├── cdft_md.inp\r\n│   │       ├── dft-common-params.inc\r\n│   │       ├── frame-cdft-pos-total.xyz.tar.gz\r\n│   │       ├── frame.xyz\r\n│   │       └── subsys.inc\r\n│   └── 3_cdft_wH2O_sccs\r\n│       ├── state_a\r\n│       │   ├── framePrint.py\r\n│       │   ├── input_files\r\n│       │   │   ├── 1_energy_cdft_STATE1.bash\r\n│       │   │   ├── 2_energy_cdft_STATE2.bash\r\n│       │   │   ├── 3_energy_cdft_mixed.bash\r\n│       │   │   ├── becke_twoconstraints.inc\r\n│       │   │   ├── dft-common-params.inc\r\n│       │   │   ├── energy_cdft.inp\r\n│       │   │   ├── energy_mixed_cdft.inp\r\n│       │   │   └── subsys.inc\r\n│       │   └── README\r\n│       ├── state_b\r\n│       │   ├── b_to_a\r\n│       │   │   ├── framePrint.py\r\n│       │   │   ├── input_files\r\n│       │   │   │   ├── 1_energy_cdft_STATE1.bash\r\n│       │   │   │   ├── 2_energy_cdft_STATE2.bash\r\n│       │   │   │   ├── 3_energy_cdft_mixed.bash\r\n│       │   │   │   ├── becke_twoconstraints.inc\r\n│       │   │   │   ├── dft-common-params.inc\r\n│       │   │   │   ├── energy_cdft.inp\r\n│       │   │   │   ├── energy_mixed_cdft.inp\r\n│       │   │   │   └── subsys.inc\r\n│       │   │   └── README\r\n│       │   └── b_to_c\r\n│       │       ├── framePrint.py\r\n│       │       ├── input_files\r\n│       │       │   ├── 1_energy_cdft_STATE1.bash\r\n│       │       │   ├── 2_energy_cdft_STATE2.bash\r\n│       │       │   ├── 3_energy_cdft_mixed.bash\r\n│       │       │   ├── becke_twoconstraints.inc\r\n│       │       │   ├── dft-common-params.inc\r\n│       │       │   ├── energy_cdft.inp\r\n│       │       │   ├── energy_mixed_cdft.inp\r\n│       │       │   └── subsys.inc\r\n│       │       └── README\r\n│       └── state_c\r\n│           ├── framePrint.py\r\n│           ├── input_files\r\n│           │   ├── 1_energy_cdft_STATE1.bash\r\n│           │   ├── 2_energy_cdft_STATE2.bash\r\n│           │   ├── 3_energy_cdft_mixed.bash\r\n│           │   ├── becke_twoconstraints.inc\r\n│           │   ├── dft-common-params.inc\r\n│           │   ├── energy_cdft.inp\r\n│           │   ├── energy_mixed_cdft.inp\r\n│           │   └── subsys.inc\r\n│           └── README\r\n├── 3OHVi\r\n│   ├── 1_md\r\n│   │   ├── dft-common-params.inc\r\n│   │   ├── md.inp\r\n│   │   ├── ohvi-md-pos-1.xyz\r\n│   │   ├── pos.xyz\r\n│   │   ├── submit.sh\r\n│   │   └── subsys.inc\r\n│   ├── 2_cdftaimd\r\n│   │   ├── state_a\r\n│   │   │   ├── becke_twoconstraints.inc\r\n│   │   │   ├── cdft_md.bash\r\n│   │   │   ├── cdft_md.inp\r\n│   │   │   ├── dft-common-params.inc\r\n│   │   │   ├── frame-cdft-pos-total.xyz.tar.gz\r\n│   │   │   ├── frame.xyz\r\n│   │   │   └── subsys.inc\r\n│   │   ├── state_b\r\n│   │   │   ├── becke_twoconstraints.inc\r\n│   │   │   ├── cdft_md.bash\r\n│   │   │   ├── cdft_md.inp\r\n│   │   │   ├── dft-common-params.inc\r\n│   │   │   ├── frame-cdft-pos-total.xyz.tar.gz\r\n│   │   │   ├── frame.xyz\r\n│   │   │   └── subsys.inc\r\n│   │   └── state_c\r\n│   │       ├── becke_twoconstraints.inc\r\n│   │       ├── cdft_md.bash\r\n│   │       ├── cdft_md.inp\r\n│   │       ├── dft-common-params.inc\r\n│   │       ├── frame-cdft-pos-total.xyz.tar.gz\r\n│   │       ├── frame.xyz\r\n│   │       └── subsys.inc\r\n│   └── 3_cdft_wH2O_sccs\r\n│       ├── state_a\r\n│       │   ├── framePrint.py\r\n│       │   ├── input_files\r\n│       │   │   ├── 1_energy_cdft_STATE1.bash\r\n│       │   │   ├── 2_energy_cdft_STATE2.bash\r\n│       │   │   ├── 3_energy_cdft_mixed.bash\r\n│       │   │   ├── becke_twoconstraints.inc\r\n│       │   │   ├── dft-common-params.inc\r\n│       │   │   ├── energy_cdft.inp\r\n│       │   │   ├── energy_mixed_cdft.inp\r\n│       │   │   └── subsys.inc\r\n│       │   └── README\r\n│       ├── state_b\r\n│       │   ├── b_to_a\r\n│       │   │   ├── framePrint.py\r\n│       │   │   ├── input_files\r\n│       │   │   │   ├── 1_energy_cdft_STATE1.bash\r\n│       │   │   │   ├── 2_energy_cdft_STATE2.bash\r\n│       │   │   │   ├── 3_energy_cdft_mixed.bash\r\n│       │   │   │   ├── becke_twoconstraints.inc\r\n│       │   │   │   ├── dft-common-params.inc\r\n│       │   │   │   ├── energy_cdft.inp\r\n│       │   │   │   ├── energy_mixed_cdft.inp\r\n│       │   │   │   └── subsys.inc\r\n│       │   │   └── README\r\n│       │   ├── b_to_a.tar.gz\r\n│       │   ├── b_to_c\r\n│       │   │   ├── framePrint.py\r\n│       │   │   ├── input_files\r\n│       │   │   │   ├── 1_energy_cdft_STATE1.bash\r\n│       │   │   │   ├── 2_energy_cdft_STATE2.bash\r\n│       │   │   │   ├── 3_energy_cdft_mixed.bash\r\n│       │   │   │   ├── becke_twoconstraints.inc\r\n│       │   │   │   ├── dft-common-params.inc\r\n│       │   │   │   ├── energy_cdft.inp\r\n│       │   │   │   ├── energy_mixed_cdft.inp\r\n│       │   │   │   └── subsys.inc\r\n│       │   │   └── README\r\n│       │   └── b_to_c.tar.gz\r\n│       └── state_c\r\n│           ├── framePrint.py\r\n│           ├── input_files\r\n│           │   ├── 1_energy_cdft_STATE1.bash\r\n│           │   ├── 2_energy_cdft_STATE2.bash\r\n│           │   ├── 3_energy_cdft_mixed.bash\r\n│           │   ├── becke_twoconstraints.inc\r\n│           │   ├── dft-common-params.inc\r\n│           │   ├── energy_cdft.inp\r\n│           │   ├── energy_mixed_cdft.inp\r\n│           │   └── subsys.inc\r\n│           └── README\r\n├── 4dBR5\r\n│   ├── 1_md\r\n│   │   ├── dft-common-params.inc\r\n│   │   ├── dmdq-md-pos-1.xyz\r\n│   │   ├── md.inp\r\n│   │   ├── pos.xyz\r\n│   │   ├── submit.sh\r\n│   │   └── subsys.inc\r\n│   ├── 2_cdftaimd\r\n│   │   ├── state_a\r\n│   │   │   ├── becke_twoconstraints.inc\r\n│   │   │   ├── cdft_md.bash\r\n│   │   │   ├── cdft_md.inp\r\n│   │   │   ├── dft-common-params.inc\r\n│   │   │   ├── frame-cdft-pos-total.xyz.tar.gz\r\n│   │   │   ├── frame.xyz\r\n│   │   │   └── subsys.inc\r\n│   │   ├── state_b\r\n│   │   │   ├── becke_twoconstraints.inc\r\n│   │   │   ├── cdft_md.bash\r\n│   │   │   ├── cdft_md.inp\r\n│   │   │   ├── dft-common-params.inc\r\n│   │   │   ├── frame-cdft-pos-total.xyz.tar.gz\r\n│   │   │   ├── frame.xyz\r\n│   │   │   └── subsys.inc\r\n│   │   └── state_c\r\n│   │       ├── becke_twoconstraints.inc\r\n│   │       ├── cdft_md.bash\r\n│   │       ├── cdft_md.inp\r\n│   │       ├── dft-common-params.inc\r\n│   │       ├── frame-cdft-pos-total.xyz.tar.gz\r\n│   │       ├── frame.xyz\r\n│   │       └── subsys.inc\r\n│   └── 3_cdft_wH2O_sccs\r\n│       ├── state_a\r\n│       │   ├── framePrint.py\r\n│       │   ├── input_files\r\n│       │   │   ├── 1_energy_cdft_STATE1.bash\r\n│       │   │   ├── 2_energy_cdft_STATE2.bash\r\n│       │   │   ├── 3_energy_cdft_mixed.bash\r\n│       │   │   ├── becke_twoconstraints.inc\r\n│       │   │   ├── dft-common-params.inc\r\n│       │   │   ├── energy_cdft.inp\r\n│       │   │   ├── energy_mixed_cdft.inp\r\n│       │   │   └── subsys.inc\r\n│       │   └── README\r\n│       ├── state_b\r\n│       │   ├── b_to_a.tar.gz\r\n│       │   └── b_to_c.tar.gz\r\n│       └── state_c\r\n│           ├── framePrint.py\r\n│           ├── input_files\r\n│           │   ├── 1_energy_cdft_STATE1.bash\r\n│           │   ├── 2_energy_cdft_STATE2.bash\r\n│           │   ├── 3_energy_cdft_mixed.bash\r\n│           │   ├── becke_twoconstraints.inc\r\n│           │   ├── dft-common-params.inc\r\n│           │   ├── energy_cdft.inp\r\n│           │   ├── energy_mixed_cdft.inp\r\n│           │   └── subsys.inc\r\n│           └── README\r\n├── 52HNQ\r\n│   ├── 1_md\r\n│   │   ├── dft-common-params.inc\r\n│   │   ├── hnq-md-pos-1.xyz\r\n│   │   ├── md.inp\r\n│   │   ├── pos.xyz\r\n│   │   ├── submit.sh\r\n│   │   └── subsys.inc\r\n│   ├── 2_cdftaimd\r\n│   │   ├── state_a\r\n│   │   │   ├── becke_twoconstraints.inc\r\n│   │   │   ├── cdft_md.bash\r\n│   │   │   ├── cdft_md.inp\r\n│   │   │   ├── dft-common-params.inc\r\n│   │   │   ├── frame-cdft-pos-total.xyz.tar.gz\r\n│   │   │   ├── frame.xyz\r\n│   │   │   └── subsys.inc\r\n│   │   ├── state_b\r\n│   │   │   ├── becke_twoconstraints.inc\r\n│   │   │   ├── cdft_md.bash\r\n│   │   │   ├── cdft_md.inp\r\n│   │   │   ├── dft-common-params.inc\r\n│   │   │   ├── frame-cdft-pos-total.xyz.tar.gz\r\n│   │   │   ├── frame.xyz\r\n│   │   │   └── subsys.inc\r\n│   │   └── state_c\r\n│   │       ├── becke_twoconstraints.inc\r\n│   │       ├── cdft_md.bash\r\n│   │       ├── cdft_md.inp\r\n│   │       ├── dft-common-params.inc\r\n│   │       ├── frame-cdft-pos-total.xyz.tar.gz\r\n│   │       ├── frame.xyz\r\n│   │       └── subsys.inc\r\n│   └── 3_cdft_wH2O_sccs\r\n│       ├── state_a\r\n│       │   ├── framePrint.py\r\n│       │   ├── input_files\r\n│       │   │   ├── 1_energy_cdft_STATE1.bash\r\n│       │   │   ├── 2_energy_cdft_STATE2.bash\r\n│       │   │   ├── 3_energy_cdft_mixed.bash\r\n│       │   │   ├── becke_twoconstraints.inc\r\n│       │   │   ├── dft-common-params.inc\r\n│       │   │   ├── energy_cdft.inp\r\n│       │   │   ├── energy_mixed_cdft.inp\r\n│       │   │   └── subsys.inc\r\n│       │   └── README\r\n│       ├── state_b\r\n│       │   ├── b_to_a.tar.gz\r\n│       │   └── b_to_c.tar.gz\r\n│       └── state_c\r\n│           ├── framePrint.py\r\n│           ├── input_files\r\n│           │   ├── 1_energy_cdft_STATE1.bash\r\n│           │   ├── 2_energy_cdft_STATE2.bash\r\n│           │   ├── 3_energy_cdft_mixed.bash\r\n│           │   ├── becke_twoconstraints.inc\r\n│           │   ├── dft-common-params.inc\r\n│           │   ├── energy_cdft.inp\r\n│           │   ├── energy_mixed_cdft.inp\r\n│           │   └── subsys.inc\r\n│           └── README\r\n└── 6_n_H2O_effect_mevi\r\n    ├── 08h2o\r\n    │   ├── framePrint.py\r\n    │   ├── README\r\n    │   ├── state_a.tar.gz\r\n    │   └── state_b.tar.gz\r\n    ├── 10h2o\r\n    │   ├── framePrint.py\r\n    │   ├── README\r\n    │   ├── state_a.tar.gz\r\n    │   └── state_b.tar.gz\r\n    ├── 20h2o\r\n    │   ├── framePrint.py\r\n    │   ├── README\r\n    │   ├── state_a.tar.gz\r\n    │   └── state_b.tar.gz\r\n    ├── 40h2o\r\n    │   ├── framePrint.py\r\n    │   ├── README\r\n    │   ├── state_a.tar.gz\r\n    │   └── state_b.tar.gz\r\n    ├── 97h2o\r\n    │   ├── framePrint.py\r\n    │   ├── README\r\n    │   ├── state_a.tar.gz\r\n    │   └── state_b.tar.gz\r\n    └── fig3.png\r\n\r\n74 directories, 301 files\r\n-------------------------------------------------------\r\nThere are 6 directories: 1DMDQ, 2MeVi, 3OHVi,   4dBR5,  52HNQ,  6_n_H2O_effect_mevi. Except for \"6_n_H2O_effect_mevi\", we see 3 subdirectories named 1_md, 2_cdftaimd, and 3_cdft_wH2O_sccs. The input files and AIMD trajectories can be found in 1_md. While 2_cdftaimd contains the CDFT-AIMD input files and trajectories. To reproduce snapshots and input files of 3_cdft_wH2O_sccs, follow the README files in the subdirectories.\r\n\r\nThe directory \"6_n_H2O_effect_mevi\" contains the number of water effects (Figure 3 of the publication). 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It has been fitted with QUIP/GAP [1,2] by recomputing the Si database of Bartók et al. [3] at the PW91 level of theory [4] using the VASP code [5,6,7]. This potential uses 2-body (distance_2b) and 3-body (angle_3b) descriptors [5] plus SOAP-type descriptors (soap_turbo) [9,10], as implemented in the TurboGAP code [11]. The files can be used both with QUIP/GAP (compiled with the soap_turbo libraries) and TurboGAP. More details will follow in a scientific\r\npublication in due course (bibligraphical data will be added as it becomes available).\r\n\r\nReferences\r\n\r\nA.P. Bartók, M.C. Payne, R. Kondor, and G. Csányi. Phys. Rev. Lett. 104, 136403 (2010).LibAtoms: https://libatoms.github.ioA.P. Bartók, J. Kermode, N. Bernstein, and G. Csányi. Phys. Rev. X 8, 041048 (2018).J.P. Perdew and Y. Wang. Phys. Rev. B 45, 13244 (1992).V.L. Deringer and G. Csányi. Phys. Rev. B 95, 094203 (2017).VASP: http://vasp.atG. Kresse and J. Furthmüller. Phys. Rev. B 54, 11169 (1996).T. Bucko, S. Lebègue, T. Gould, and J.G. Ángyán, J. Phys.: Condens. Matter 28, 045201 (2016).A.P. Bartók, R. Kondor, and G. Csányi. Phys. Rev. B 87, 184115 (2013).M.A. Caro. Phys. Rev. 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Foster, and Takeshi Fukuma.\r\n\r\nIt contains:\r\n\r\n- The system's starting geometry (water-chitin.pdb)\r\n\r\n- The production trajectory, in .dcd format (nvt_prod_chitin.tar.xz, uncompressed size 1.9 GB)\r\n\r\n- The resulting water density, in .cube format, computed on each of the chitin surfaces (chitin_cube_densities_vmd.tar.xz, uncompressed size 3.1 GB)"},"field_of_science":[{"id":"f8d5f9ab-1c7d-4c5c-8ed5-e9ce964d798d","url":"http://www.yso.fi/onto/okm-tieteenala/ta114","in_scheme":"http://www.yso.fi/onto/okm-tieteenala/conceptscheme","pref_label":{"en":"Physical sciences","fi":"Fysiikka","sv":"Fysik"}}],"infrastructure":[],"issued":"1970-01-01","keyword":[],"language":[],"metadata_owner":{"id":"829302c3-f5d4-4d20-9ec3-5148bcf385cc","organization":"aalto.fi","admin_organization":"aalto.fi"},"other_identifiers":[],"persistent_identifier":"doi:10.5281/zenodo.5578599","pid_generated_by_fairdata":false,"projects":[],"provenance":[],"relation":[],"remote_resources":[{"title":{"en":"Data in remote location","fi":"Aineisto ulkoisessa palvelussa","sv":"Material i en extern tjänst","und":"Data in remote location"},"use_category":{"id":"1ad1b146-d147-45db-a2fd-1096abc94984","url":"http://uri.suomi.fi/codelist/fairdata/use_category/code/source","in_scheme":"http://uri.suomi.fi/codelist/fairdata/use_category","pref_label":{"en":"Source material","fi":"Lähdeaineisto"}},"download_url":"https://zenodo.org/record/5578600"}],"spatial":[],"state":"published","temporal":[],"theme":[],"title":{"en":"Molecular dynamics simulation of chitin nanocrystal-water interfaces"},"created":"2025-12-04T08:01:35Z","modified":"2026-03-26T06:44:40Z","dataset_versions":[{"id":"9f067562-c5ed-455d-8ebd-985d1456af08","title":{"en":"Molecular dynamics simulation of chitin nanocrystal-water interfaces"},"persistent_identifier":"doi:10.5281/zenodo.5578599","state":"published","created":"2025-12-04T08:01:35Z","version":1}],"published_revision":2,"version":1,"api_version":3,"metadata_repository":"Fairdata"}]}