Unsupervised landmark analysis for jump detection in molecular dynamics simulations


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{
  "updated": "2019-02-12T00:00:00+00:00", 
  "id": "102", 
  "revision": 1, 
  "created": "2020-05-12T13:52:34.751049+00:00", 
  "metadata": {
    "description": "Molecular dynamics is a versatile and powerful method to study diffusion in solid-state ionic conductors, requiring minimal prior knowledge of equilibrium or transition states of the system's free energy surface. However, the analysis of trajectories for relevant but rare events, such as a jump of the diffusing mobile ion, is still rather cumbersome, requiring prior knowledge of the diffusive process in order to get meaningful results. In this work we present a novel approach to detect the relevant events in a diffusive system without assuming prior information regarding the underlying process. We start from a projection of the atomic coordinates into a landmark basis to identify the dominant features in a mobile ion's environment. Subsequent clustering in landmark space enables a discretization of any trajectory into a sequence of distinct states. As a final step, the use of the Smooth Overlap of Atomic Positions descriptor allows distinguishing between different environments in a straightforward way. We apply this algorithm to ten Li-ionic systems and conduct in-depth analyses of cubic Li7La3Zr2O12, tetragonal Li10GeP2S12, and the \u03b2-eucryptite LiAlSiO4. We compare our results to existing methods, underscoring strong points, weaknesses, and insights into the diffusive behavior of the ionic conduction in the materials investigated. ", 
    "status": "published", 
    "title": "Unsupervised landmark analysis for jump detection in molecular dynamics simulations", 
    "is_last": true, 
    "license": "Creative Commons Attribution 4.0 International", 
    "publication_date": "Feb 12, 2019, 00:00:00", 
    "id": "102", 
    "_oai": {
      "id": "oai:materialscloud.org:102"
    }, 
    "version": 1, 
    "keywords": [
      "molecular dynamics", 
      "site analysis", 
      "tracer diffusion"
    ], 
    "conceptrecid": "101", 
    "edited_by": 98, 
    "_files": [
      {
        "description": "The README contains information on the notebooks and some guidance on installing the necessary packages.", 
        "checksum": "md5:e9514c5cfe2cc1fc63631e401e86eb24", 
        "key": "README.txt", 
        "size": 936
      }, 
      {
        "description": "The compressed file contains two jupyter notebooks, and a subfolder with the necessary data, namely two molecular dynamics trajectories. The trajectories are saved in a custom format, but the raw data is also available in xyz-format.", 
        "checksum": "md5:1bd90db05d70cf4a88752f82deb07b91", 
        "key": "unsupervised.tar.gz", 
        "size": 1313575191
      }
    ], 
    "mcid": "2019.0008/v1", 
    "doi": "10.24435/materialscloud:2019.0008/v1", 
    "contributors": [
      {
        "affiliations": [
          "Theory and Simulation of Materials (THEOS) and National Centre for Computational Design and Discovery of Novel Materials (MARVEL), \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne, Lausanne, Switzerland"
        ], 
        "givennames": "Leonid", 
        "familyname": "Kahle", 
        "email": "leonid.kahle@epfl.ch"
      }, 
      {
        "affiliations": [
          "Theory and Simulation of Materials (THEOS) and National Centre for Computational Design and Discovery of Novel Materials (MARVEL), \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne, Lausanne, Switzerland"
        ], 
        "givennames": "Albert", 
        "familyname": "Musaelian"
      }, 
      {
        "affiliations": [
          "Theory and Simulation of Materials (THEOS) and National Centre for Computational Design and Discovery of Novel Materials (MARVEL), \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne, Lausanne, Switzerland"
        ], 
        "givennames": "Nicola", 
        "familyname": "Marzari"
      }, 
      {
        "affiliations": [
          "John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA"
        ], 
        "givennames": "Boris", 
        "familyname": "Kozinsky"
      }
    ], 
    "license_addendum": "", 
    "references": [
      {
        "comment": "Preprint discussing data and results of the same analysis for the two materials", 
        "doi": "", 
        "type": "Preprint", 
        "citation": "L. Kahle, A. Musaelian, N. Marzari, and B. Kozinsky, arXiv:1902.02107 [cond-mat], February 2019", 
        "url": "https://arxiv.org/abs/1902.02107"
      }
    ], 
    "owner": 2
  }
}