The DOI matches its Crossref record; 19 of the 19 references it cites were found in a registry or an index.
Robust structural identification via polyhedral template matching
Open accessAbstract
Abstract Successful scientific applications of large-scale molecular dynamics often rely on automated methods for identifying the local crystalline structure of condensed phases. Many existing methods for structural identification, such as common neighbour analysis, rely on interatomic distances (or thresholds thereof) to classify atomic structure. As a consequence they are sensitive to strain and thermal displacements, and preprocessing such as quenching or temporal averaging of the atomic positions is necessary to provide reliable identifications. We propose a new method, polyhedral template matching (PTM), which classifies structures according to the topology of the local atomic environment, without any ambiguity in the classification, and with greater reliability than e.g. common neighbour analysis in the presence of thermal fluctuations. We demonstrate that the method can reliably be used to identify structures even in simulations near the melting point, and that it can identify the most common ordered alloy structures as well. In addition, the method makes it easy to identify the local lattice orientation in polycrystalline samples, and to calculate the local strain tensor. An implementation is made available under a Free and Open Source Software license.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Molecular dynamics with coupling to an external bath
Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., DiNola, A., & Haak, J. R. (1984) · The Journal of Chemical Physics · doi:10.1063/1.448118 · Cited by 30,700
The quickhull algorithm for convex hulls
Barber, C. B., Dobkin, D. P., & Huhdanpaa, H. (1996) · ACM Transactions on Mathematical Software · doi:10.1145/235815.235821 · Cited by 5,359
Closed-form solution of absolute orientation using unit quaternions
Horn, B. K. P. (1987) · Journal of the Optical Society of America A · doi:10.1364/josaa.4.000629 · Cited by 4,116
Molecular dynamics study of melting and freezing of small Lennard-Jones clusters
Honeycutt, J. D., & Andersen, H. C. (1987) · The Journal of Physical Chemistry · doi:10.1021/j100303a014 · Cited by 3,257
Dynamics of viscoplastic deformation in amorphous solids
Falk, M. L., & Langer, J. S. (1998) · Physical Review E · doi:10.1103/physreve.57.7192 · Cited by 2,221
Dislocation nucleation and defect structure during surface indentation
Kelchner, C. L., Plimpton, S. J., & Hamilton, J. C. (1998) · Physical Review B · doi:10.1103/physrevb.58.11085 · Cited by 2,154
Structural Relaxation Made Simple
Bitzek, E., Koskinen, P., Gähler, F., Moseler, M., & Gumbsch, P. (2006) · Physical Review Letters · doi:10.1103/physrevlett.97.170201 · Cited by 1,755
Computing the n-dimensional Delaunay tessellation with application to Voronoi polytopes
Watson, D. F. (1981) · The Computer Journal · doi:10.1093/comjnl/24.2.167 · Cited by 1,487
A Maximum in the Strength of Nanocrystalline Copper
Schiøtz, J., & Jacobsen, K. W. (2003) · Science · doi:10.1126/science.1086636 · Cited by 1,479
Self-citationSystematic analysis of local atomic structure combined with 3D computer graphics
Faken, D., & Jónsson, H. (1994) · Computational Materials Science · doi:10.1016/0927-0256(94)90109-0 · Cited by 1,447
Cited by
Thompson, A. P., Aktulga, H. M., Berger, R., Bolintineanu, D. S., Brown, W. M., Crozier, P. S., in 't Veld, P. J., Kohlmeyer, A., Moore, S. G., Nguyen, T. D., et al. (2022) · Computer Physics Communications · doi:10.1016/j.cpc.2021.108171 · Cited by 12,598
Locally ordered representation of 3D space in the entorhinal cortex
Ginosar, G., Aljadeff, J., Burak, Y., Sompolinsky, H., Las, L., & Ulanovsky, N. (2021) · Nature · doi:10.1038/s41586-021-03783-x · Cited by 111
Metadata
- Authors
- Larsen, P. M., Schmidt, S., & Schiøtz, J.
- Venue
- Modelling and Simulation in Materials Science and Engineering
- Publisher
- IOP Publishing
- Published
- 2016-05-13
- Volume
- 24
- Issue
- 5
- Pages
- 055007
- ISSN
- 0965-0393 (ISSN-L)
- 1361-651X
- OpenAlex
- W2297610696
- Cited by
- 1,121
- References
- 19
- FWCI
- 14.26
- Type
- journal article
- Language
- en
- Open access
- hybrid
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Robust structural identification via polyhedral template matching. https://app.cochat.ai/papers/10.1088/0965-0393/24/5/055007
- The paper
- Larsen, P. M., Schmidt, S., & Schiøtz, J. (2016). Robust structural identification via polyhedral template matching. Modelling and Simulation in Materials Science and Engineering. https://doi.org/10.1088/0965-0393/24/5/055007
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
