Mold: a LAMMPS package to compute interfacial free energies and nucleation rates

dc.contributor.authorTejedor Reyes, Andrés
dc.contributor.authorSánchez Burgos, Ignacio
dc.contributor.authorSanz, Eduardo
dc.contributor.authorVega, C.
dc.contributor.authorJiménez Blas, Felipe
dc.contributor.authorDavidchack, Ruslan L.
dc.contributor.authorDi Pasquale, Nicodemo
dc.contributor.authorRamírez García, Jorge
dc.contributor.authorReñe Espinosa, Jorge
dc.date.accessioned2025-06-13T06:27:22Z
dc.date.available2025-06-13T06:27:22Z
dc.date.issued2024-03
dc.description.abstractThe determination of the free energy cost of forming an interface between two phases, i.e. the interfacial free energy, is critical for characterizing a phase transition. In the particular case of liquid-to-solid transitions, it is not straightforward to obtain this quantity through experiment or computation. Here, we present the computational package Mold, which is integrated in the Molecular Dynamics open-source software LAMMPS (Thompson et al., 2022). Mold enables direct calculation of the interfacial free energy between arbitrarily complex crystal structures and liquids/solutions at coexistence conditions through the Mold Integration method (Espinosa et al., 2014). Furthermore, the extension of this method for determining crystal nucleation rates—the probablity of a critical nucleus to emerge per unit of volume and time within a metastable phase—is also incorporated in the package, termed Lattice Mold method (Espinosa, Sampedro, et al., 2016). Altogether, we detail here the required codes, scripts, and instructions for evaluating the two most challenging quantities determining the feasibility of a liquid-to-solid transition, implemented to work alongside the MD package LAMMPS.es_ES
dc.description.departmentCiencias Integradases_ES
dc.description.sponsorshipThis project was funded by projects PID2022-136919NA-C33, PID2022-136919NB-C31, and PID2022-136919NB-C32 and PID2022-136919NB-C33 of the MICINN, and the Oppenheimer Research Fellowship of the University of Cambridge. I.S.-B. acknowledges funding from the Oppenheimer Fellowship, Derek Brewer scholarship of Emmanuel College and EPSRC Doctoral Training Programme studentship, number EP/T517847/1. N. D. P. acknowledges support from the CECAM and CCP5 through the CECAM/CCP5 sandpit grant (2022) and the EP/V028537/1 grant. J. R. acknowledges funding from the Spanish Ministry of Economy and Competitivity (PID2019-105898GA-C22) and the Madrid Government (Comunidad de Madrid-Spain) under the Multiannual Agreement with Universidad Politécnica de Madrid in the line Excellence Programme for University Professors, in the context of the V PRICIT (Regional Programme of Research and Technological Innovation). J.R.E. also acknowledges funding from the Ramon y Cajal fellowship (RYC2021-030937-I). A.R.T. acknowledges funding from the European Research Council (ERC) under the European Union Horizon 2020 research and innovation programme (grant agreement 803326), and from the Ramon y Cajal fellowship. This work has been performed using resources provided by the Cambridge Tier-2 system operated by the University of Cambridge Research Computing Service (http://www.hpc.cam.ac.uk) funded by EPSRC Tier-2 capital grant EP/P020259/1 and by the Sulis High-Performance Computational Center under the grant EP/T022108/1.This project made use of time on HPC granted via the UK High–End Computing Consortium for Biomolecular Simulation, HECBioSim (http://hecbiosim.ac.uk), supported by EPSRC (grant no. EP/X035603/1). F. J. B. also acknowledges Ministerio de Ciencia e Innovación (Grant No. PID2021-125081NB-I00), Junta de Andalucía (P20-00363), and Universidad de Huelva (P.O. FEDER UHU-1255522 and FEDER-UHU-202034), all four cofinanced by EU FEDER funds.es_ES
dc.identifier.citationTejedor, A. R., Sanchez-Burgos, I., Sanz, E., Vega, C., Blas, F. J., Davidchack, R. L., Pasquale, N. D., Ramirez, J., & Espinosa, J. R. (2024). Mold: a LAMMPS package to compute interfacial free energies and nucleation rates. Journal of Open Source Software, 9(95), 6083. https://doi.org/10.21105/joss.06083es_ES
dc.identifier.doi10.21105/joss.06083
dc.identifier.issn2475-9066 (electrónico)
dc.identifier.urihttps://hdl.handle.net/10272/25684
dc.language.isoenges_ES
dc.publisherOpen Journalses_ES
dc.rightsAtribución-NoComercial-SinDerivadas 3.0 España*
dc.rights.accessRightsopen accesses_ES
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/3.0/es/*
dc.subject.otherLAMMPSes_ES
dc.subject.otherMolecular simulationses_ES
dc.subject.otherPhase Transitionses_ES
dc.subject.otherNucleation theoryes_ES
dc.subject.unesco22 Físicaes_ES
dc.titleMold: a LAMMPS package to compute interfacial free energies and nucleation rateses_ES
dc.typejournal articlees_ES
dc.type.hasVersionVoRes_ES
dspace.entity.typePublication
relation.isAuthorOfPublication5fbe9948-210f-4a30-a57a-3638ef025f06
relation.isAuthorOfPublication.latestForDiscovery5fbe9948-210f-4a30-a57a-3638ef025f06

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