Open Knowledgebase of Interatomic Models - OpenKIM

DL_POLY_4 force-field allows for model interactions specification by using an OpenKIM model - https://openkim.org/. A KIM model contains all necessary (non-bonded) interactions and their parameters for a specific model within a designated container. Thus a KIM model can be used as a force-field container when made available to DL_POLY_4 at run time (see the description of the FIELD file in Section The FIELD File) upon a specification within FIELD together with a matching molecular description for the model system, also specified in FIELD. Due to the history of the OpenKIM initiative and the constraints of the logic of the DL_POLY_4 FIELD file the designated place for a KIM model specification is in the non-bonded interactions section Non-bonded Interactions.

Employing OpenKIM interatomic models (IMs) provides DL_POLY_4 users with multiple benefits, including:

Reliability

  • All content archived in OpenKIM is reviewed by the KIM Editor for quality.

  • IMs in OpenKIM are archived with full provenance control. Each is associated with a maintainer responsible for the integrity of the content. All changes are tracked and recorded.

  • IMs in OpenKIM are exhaustively tested using KIM Tests that compute a host of material properties, and KIM Verification Checks that provide the user with information on various aspects of the IM behavior and coding correctness. This information is displayed on the IM’s page accessible through the OpenKIM browse interface.

Reproducibility

  • Each IM in OpenKIM is issued a unique identifier (KIM ID), which includes a version number (last three digits). Any changes that can result in different numerical values lead to a version increment in the KIM ID. This makes it possible to reproduce simulations since the specific version of a specific IM used can be retrieved using its KIM ID.

  • OpenKIM is a member organization of DataCite and issues digital object identifiers (DOIs) to all IMs archived in OpenKIM. This makes it possible to cite the IM code used in a simulation in a publications to give credit to the developers and further facilitate reproducibility.

Currently, DL_POLY_4 supports one type of IM archived in OpenKIM, which is called a KIM Portable Model (PM). A KIM PM is an independent computer implementation of an IM written in one of the languages supported by KIM (C, C++, Fortran) that conforms to the KIM Application Programming Interface (KIM API) Portable Model Interface (PMI) standard. A KIM PM will work seamlessly with any simulation code that supports the KIM API/PMI standard (including ; see complete list of supported codes).

OpenKIM IMs are uniquely identified by a KIM ID. The extended KIM ID consists of a human-readable prefix identifying the type of IM, authors, publication year, and supported species, separated by two underscores from the KIM ID itself, which begins with an IM code (MO for a KIM Portable Model) followed by a unique 12-digit code and a 3-digit version identifier (e.g. SNAP_ChenDengTran_2017_Mo__MO_698578166685_000).

Each OpenKIM IM has a dedicated “Model Page” on OpenKIM providing all the information on the IM including a title, description, authorship and citation information, test and verification check results, visualizations of results, a wiki with documentation and user comments, and access to raw files, and other information. The URL for the Model Page is constructed from the extended KIM ID of the IM as https://openkim.org/id/extended_KIM_ID.

For example, for the spectral neighbor analysis potential (SNAP) listed above the Model Page is located at: https://openkim.org/id/SNAP_ChenDengTran_2017_Mo__MO_698578166685_000.

See the current list of KIM PMs archived in OpenKIM. This list is sorted by species and can be filtered to display only IMs for certain species combinations. You can also see Obtaining KIM Models to learn how to install a pre-build binary of the OpenKIM repository of models.

Note

It is also possible to locally install IMs not archived in OpenKIM, in which case their names do not have to conform to the KIM ID format.

To download, build, and install the KIM library on your system, see the detailed instructions .

Note

To use OpenKIM functionality within DL_POLY_4 one must further ensure that DL_POLY_4 is compiled with OpenKIM support (see building.md).

Citation of OpenKIM IMs

When publishing results obtained using OpenKIM IMs researchers are requested to cite the OpenKIM project (Tadmor), KIM API (Elliott), and the specific IM codes used in the simulations, in addition to the relevant scientific references for the IM. The citation format for an IM is displayed on its page on OpenKIM along with the corresponding BibTex file, and is automatically added to the DL_POLY_4    log.cite file.

Citing the IM software (KIM infrastructure and specific PM or SM codes) used in the simulation gives credit to the researchers who developed them and enables open source efforts like OpenKIM to function.