RT Journal Article
T1 Mold: a LAMMPS package to compute interfacial free energies and nucleation rates
A1 Tejedor Reyes, Andrés
A1 Sánchez Burgos, Ignacio
A1 Sanz, Eduardo
A1 Vega, C.
A1 Jiménez Blas, Felipe
A1 Davidchack, Ruslan L.
A1 Di Pasquale, Nicodemo
A1 Ramírez García, Jorge
A1 Reñe Espinosa, Jorge
AB The determination of the free energy cost of forming an interface between two phases, i.e. theinterfacial free energy, is critical for characterizing a phase transition. In the particular case ofliquid-to-solid transitions, it is not straightforward to obtain this quantity through experimentor computation. Here, we present the computational package Mold, which is integrated in theMolecular Dynamics open-source software LAMMPS (Thompson et al., 2022). Mold enablesdirect calculation of the interfacial free energy between arbitrarily complex crystal structuresand liquids/solutions at coexistence conditions through the Mold Integration method (Espinosaet al., 2014). Furthermore, the extension of this method for determining crystal nucleationrates—the probablity of a critical nucleus to emerge per unit of volume and time within ametastable 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 instructionsfor evaluating the two most challenging quantities determining the feasibility of a liquid-to-solidtransition, implemented to work alongside the MD package LAMMPS.
PB Open Journals
SN 2475-9066 (electrónico)
YR 2024
FD 2024-03
LK https://hdl.handle.net/10272/25684
UL https://hdl.handle.net/10272/25684
LA eng
NO Tejedor, 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.06083
NO This project was funded by projects PID2022-136919NA-C33,PID2022-136919NB-C31, and PID2022-136919NB-C32 and PID2022-136919NB-C33 of theMICINN, and the Oppenheimer Research Fellowship of the University of Cambridge. I.S.-B.acknowledges funding from the Oppenheimer Fellowship, Derek Brewer scholarship of EmmanuelCollege and EPSRC Doctoral Training Programme studentship, number EP/T517847/1. N. D.P. acknowledges support from the CECAM and CCP5 through the CECAM/CCP5 sandpitgrant (2022) and the EP/V028537/1 grant. J. R. acknowledges funding from the SpanishMinistry of Economy and Competitivity (PID2019-105898GA-C22) and the Madrid Government(Comunidad de Madrid-Spain) under the Multiannual Agreement with Universidad Politécnicade Madrid in the line Excellence Programme for University Professors, in the context ofthe 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 theRamon y Cajal fellowship. This work has been performed using resources provided by theCambridge 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 andby the Sulis High-Performance Computational Center under the grant EP/T022108/1.Thisproject made use of time on HPC granted via the UK High–End Computing Consortium forBiomolecular Simulation, HECBioSim (http://hecbiosim.ac.uk), supported by EPSRC (grantno. EP/X035603/1). F. J. B. also acknowledges Ministerio de Ciencia e Innovación (GrantNo. 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 FEDERfunds.
DS Repositorio Institucional de la Universidad de Huelva
RD 31 may 2026