Center for Molecular Modeling - A. Yakovlev https://molmod.ugent.be/publication-authors/yakovlev en ReaxFF Parameter Optimization with Monte-Carlo and Evolutionary Algorithms: Guidelines and Insights https://molmod.ugent.be/publications/reaxff-parameter-optimization-monte-carlo-and-evolutionary-algorithms-guidelines-and <div class="field field-name-field-a1-authors field-type-taxonomy-term-reference field-label-hidden"> <span class="field-items"> G. Shchygol, A. Yakovlev, T. Trnka, A.C.T. van Duin, T. Verstraelen </span> </div> <div class="field field-name-field-journal-title field-type-taxonomy-term-reference field-label-hidden"> <span class="field-items"> Journal of Chemical Theory and Computation </span> </div> <div class="field field-name-field-vol-iss field-type-text field-label-hidden"> <div class="field-items"> <div class="field-item even">15, 12, 6799-6812</div> </div> </div> <div class="field field-name-field-a1year field-type-datestamp field-label-hidden"> <div class="field-items"> <div class="field-item even"><span class="date-display-single" property="dc:date" datatype="xsd:dateTime" content="2019-01-01T00:00:00+01:00">2019</span></div> </div> </div> <div class="field field-name-field-a1-type field-type-list-text field-label-hidden"> <div class="field-items"> <div class="field-item even">A1</div> </div> </div> <div class="field field-name-field-not-a-cmm-publication field-type-list-boolean field-label-hidden"> <div class="field-items"> <div class="field-item even"></div> </div> </div> <div class="field field-name-body field-type-text-with-summary field-label-above"> <h3><div class="field-label">Abstract&nbsp;</div></h3> <div class="field-items"> <div class="field-item even" property="content:encoded"><div class="tex2jax"><p>ReaxFF is a computationally efficient force field to simulate complex reactive dynamics in extended molecular models with diverse chemistries, if reliable force-field parameters are available for the chemistry of interest. If not, they must be optimized by minimizing the error ReaxFF makes on a relevant training set. Because this optimization is far from trivial, many methods, in particular, genetic algorithms (GAs), have been developed to search for the global optimum in parameter space. Recently, two alternative parameter calibration techniques were proposed, that is, Monte-Carlo force field optimizer (MCFF) and covariance matrix adaptation evolutionary strategy (CMA-ES). In this work, CMA-ES, MCFF, and a GA method (OGOLEM) are systematically compared using three training sets from the literature. By repeating optimizations with different random seeds and initial parameter guesses, it is shown that a single optimization run with any of these methods should not be trusted blindly: nonreproducible, poor or premature convergence is a common deficiency. GA shows the smallest risk of getting trapped into a local minimum, whereas CMA-ES is capable of reaching the lowest errors for two-third of the cases, although not systematically. For each method, we provide reasonable default settings, and our analysis offers useful guidelines for their usage in future work. An important side effect impairing parameter optimization is numerical noise. A detailed analysis reveals that it can be reduced, for example, by using exclusively unambiguous geometry optimization in the training set. Even without this noise, many distinct near-optimal parameter vectors can be found, which opens new avenues for improving the training set and detecting overfitting artifacts.</p> </div></div> </div> </div> <div class="field field-name-field-open-access field-type-list-boolean field-label-hidden"> <div class="field-items"> <div class="field-item even"></div> </div> </div> <div class="field field-name-field-doi field-type-text field-label-above"> <h3><div class="field-label">DOI&nbsp;</div></h3> <div class="field-items"> <div class="field-item even"><p>10.1021/acs.jctc.9b00769</p> </div> </div> </div> Thu, 28 Nov 2019 11:31:09 +0000 toon 5475 at https://molmod.ugent.be https://molmod.ugent.be/publications/reaxff-parameter-optimization-monte-carlo-and-evolutionary-algorithms-guidelines-and#comments ReaxFF parameter optimization: recent advances and insights https://molmod.ugent.be/c1_c3_publications/reaxff-parameter-optimization-recent-advances-and-insights <div class="field field-name-field-a1-authors field-type-taxonomy-term-reference field-label-hidden"> <span class="field-items"> <a href="/publication-authors/shchygol" typeof="skos:Concept" property="rdfs:label skos:prefLabel" datatype="">A. Shchygol</a>, <a href="/publication-authors/yakovlev" typeof="skos:Concept" property="rdfs:label skos:prefLabel" datatype="">A. Yakovlev</a>, <a href="/publication-authors/t-trnka" typeof="skos:Concept" property="rdfs:label skos:prefLabel" datatype="">T. Trnka</a>, <a href="/publication-authors/t-verstraelen" typeof="skos:Concept" property="rdfs:label skos:prefLabel" datatype="">T. Verstraelen</a> </span> </div> <div class="field field-name-field-isbn-issn field-type-text field-label-hidden"> <div class="field-items"> <div class="field-item even">ISBN/ISSN:</div> </div> </div> <div class="field field-name-field-poster-or-talk field-type-list-text field-label-hidden"> <div class="field-items"> <div class="field-item even">Talk</div> </div> </div> <div class="field field-name-field-conference-name field-type-text field-label-above"> <h3><div class="field-label">Conference / event / venue&nbsp;</div></h3> <div class="field-items"> <div class="field-item even">ADF Developer Meeting</div> </div> </div> <div class="field field-name-field-conference-location field-type-text field-label-hidden"> <div class="field-items"> <div class="field-item even">Amsterdam, The Netherlands</div> </div> </div> <div class="field field-name-field-conference-dates field-type-date field-label-hidden"> <div class="field-items"> <div class="field-item even"><span class="date-display-range"><span class="date-display-start" property="dc:date" datatype="xsd:dateTime" content="2018-03-26T00:00:00+02:00">Monday, 26 March, 2018</span> to <span class="date-display-end" property="dc:date" datatype="xsd:dateTime" content="2018-03-30T00:00:00+02:00">Friday, 30 March, 2018</span></span></div> </div> </div> Mon, 26 Nov 2018 13:05:51 +0000 toon 5245 at https://molmod.ugent.be https://molmod.ugent.be/c1_c3_publications/reaxff-parameter-optimization-recent-advances-and-insights#comments The curse (or joy) of dimensionality https://molmod.ugent.be/c1_c3_publications/curse-or-joy-dimensionality <div class="field field-name-field-a1-authors field-type-taxonomy-term-reference field-label-hidden"> <span class="field-items"> <a href="/publication-authors/shchygol" typeof="skos:Concept" property="rdfs:label skos:prefLabel" datatype="">A. Shchygol</a>, <a href="/publication-authors/yakovlev" typeof="skos:Concept" property="rdfs:label skos:prefLabel" datatype="">A. Yakovlev</a>, <a href="/publication-authors/t-verstraelen" typeof="skos:Concept" property="rdfs:label skos:prefLabel" datatype="">T. Verstraelen</a> </span> </div> <div class="field field-name-field-isbn-issn field-type-text field-label-hidden"> <div class="field-items"> <div class="field-item even">ISBN/ISSN:</div> </div> </div> <div class="field field-name-field-poster-or-talk field-type-list-text field-label-hidden"> <div class="field-items"> <div class="field-item even">Talk</div> </div> </div> <div class="field field-name-field-conference-name field-type-text field-label-above"> <h3><div class="field-label">Conference / event / venue&nbsp;</div></h3> <div class="field-items"> <div class="field-item even">Visit Software for Chemistry and Materials</div> </div> </div> <div class="field field-name-field-conference-location field-type-text field-label-hidden"> <div class="field-items"> <div class="field-item even">Amsterdam, The Netherlands</div> </div> </div> <div class="field field-name-field-conference-dates field-type-date field-label-hidden"> <div class="field-items"> <div class="field-item even"><span class="date-display-range"><span class="date-display-start" property="dc:date" datatype="xsd:dateTime" content="2017-11-21T00:00:00+01:00">Tuesday, 21 November, 2017</span> to <span class="date-display-end" property="dc:date" datatype="xsd:dateTime" content="2017-11-23T00:00:00+01:00">Thursday, 23 November, 2017</span></span></div> </div> </div> Mon, 26 Nov 2018 12:44:35 +0000 toon 5241 at https://molmod.ugent.be https://molmod.ugent.be/c1_c3_publications/curse-or-joy-dimensionality#comments