Bibliography
- Bernetti2020
- Mattia Bernetti and Giovanni BussiPressure control using stochastic cell rescalingJ. Chem. Phys. 153, 114107 (2020)DOI: 10.1063/5.0020514
- Berendsen1984
- H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, A. DiNola, and J. R. HaakMolecular dynamics with coupling to an external bathJ. Chem. Phys. 81, 3684 (1984)DOI: 10.1063/1.448118
- Bitzek2006
- Erik Bitzek, Pekka Koskinen, Franz Gähler, Michael Moseler, and Peter GumbschStructural Relaxation Made SimplePhys. Rev. Lett. 97, 170201 (2006)
- Brorsson2021
- Joakim Brorsson, Arsalan Hashemi, Zheyong Fan, Erik Fransson, Fredrik Eriksson, Tapio Ala-Nissila, Arkady V. Krasheninnikov, Hannu-Pekka Komsa, and Paul ErhartEfficient calculation of the lattice thermal conductivity by atomistic simulations with ab-initio accuracyAdvanced Theory and Simulations 4, 2100217 (2021)
- Bussi2007a
- Giovanni Bussi and Michele ParrinelloAccurate sampling using Langevin dynamicsPhys. Rev. E 75, 056707 (2007)
- Bussi2007b
- Giovanni Bussi, Davide Donadio, and Michele ParrinelloCanonical sampling through velocity rescalingJ. Chem. Phys. 126, 014101 (2007)DOI: 10.1063/1.2408420
- Ceriotti2010
- Michele Ceriotti, Michele Parrinello, Thomas E. Markland, and David E. ManolopoulosEfficient stochastic thermostatting of path integral molecular dynamicsJ. Chem. Phys. 133, 124104 (2010)DOI: 10.1063/1.3489925
- Craig2004
- Ian R. Craig and David E. ManolopoulosQuantum statistics and classical mechanics: Real time correlation functions from ring polymer molecular dynamicsJ. Chem. Phys. 121, 3368 (2004)DOI: 10.1063/1.1777575
- Dai2006
- X. D. Dai, Y. Kong, J. H. Li, and B. X. LiuExtended Finnis–Sinclair potential for bcc and fcc metals and alloysJ. Phys.: Condens. Matter 18, 4527 (2006)
- Drautz2019
- Ralf DrautzAtomic cluster expansion for accurate and transferable interatomic potentialsPhys. Rev. B 99, 014104 (2019)
- Eriksson2019
- Fredrik Eriksson, Erik Fransson, and Paul ErhartThe Hiphive Package for the Extraction of High-Order Force Constants by Machine LearningAdvanced Theory and Simulations, 2, 1800184 (2019)
- Fan2015
- Zheyong Fan, Luiz Felipe C. Pereira, Hui-Qiong Wang, Jin-Cheng Zheng, Davide Donadio, and Ari HarjuForce and heat current formulas for many-body potentials in molecular dynamics simulations with applications to thermal conductivity calculationsPhys. Rev. B 92, 094301 (2015)
- Fan2017
- Zheyong Fan, Luiz Felipe C. Pereira, Petri Hirvonen, Mikko M. Ervasti, Ken R. Elder, Davide Donadio, Tapio Ala-Nissila, and Ari HarjuThermal conductivity decomposition in two-dimensional materials: Application to graphenePhys. Rev. B 95, 144309 (2017)
- Fan2019
- Zheyong Fan, Haikuan Dong, Ari Harju, and Tapio Ala-NissilaHomogeneous nonequilibrium molecular dynamics method for heat transport and spectral decomposition with many-body potentialsPhys. Rev. B 99, 064308 (2019)
- Fan2020
- Zheyong Fan, Yanzhou Wang, Xiaokun Gu, Ping Qian, Yanjing Su, and Tapio Ala-NissilaA minimal Tersoff potential for diamond silicon with improved descriptions of elastic and phonon transport propertiesJ. Phys.: Condens. Matter 32, 135901 (2020)
- Fan2021
- Zheyong Fan, Zezhu Zeng, Cunzhi Zhang, Yanzhou Wang, Keke Song, Haikuan Dong, Yue Chen, and Tapio Ala-NissilaNeuroevolution machine learning potentials: Combining high accuracy and low cost in atomistic simulations and application to heat transportPhys. Rev. B. 104, 104309 (2021)
- Fan2021b
- Zheyong Fan, Jose Hugo Garcia, Aron W Cummings, Jose Eduardo Barrios-Vargas, Michel Panhans, Ari Harju, Frank Ortmann, and Stephan RocheLinear scaling quantum transport methodologiesPhysics Reports 903, 1 (2021)
- Fan2022a
- Zheyong FanImproving the accuracy of the neuroevolution machine learning potentials for multi-component systemsJournal of Physics: Condensed Matter 34, 125902 (2022)
- Fan2022b
- Zheyong Fan, Yanzhou Wang, Penghua Ying, Keke Song, Junjie Wang, Yong Wang, Zezhu Zeng, Ke Xu, Eric Lindgren, J. Magnus Rahm, Alexander J. Gabourie, Jiahui Liu, Haikuan Dong, Jianyang Wu, Yue Chen, Zheng Zhong, Jian Sun, Paul Erhart, Yanjing Su, and Tapio Ala-NissilaGPUMD: A package for constructing accurate machine-learned potentials and performing highly efficient atomistic simulationsJournal of Chemical Physics 157, 114801 (2022)DOI: 10.1063/5.0106617
- Freitas2016
- Rodrigo Freitas, Mark Asta, Maurice de KoningNonequilibrium free-energy calculation of solids using LAMMPSComputational Materials Science, 112, 333 (2016)
- Gabourie2021
- Alexander J. Gabourie, Zheyong Fan, Tapio Ala-Nissila, and Eric PopSpectral Decomposition of Thermal Conductivity: Comparing Velocity Decomposition Methods in Homogeneous Molecular Dynamics SimulationsPhys. Rev. B 103, 205421 (2021)
- Grimme2010
- Stefan Grimme, Jens Antony, Stephan Ehrlich, and Helge KriegA consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-PuJ. Chem. Phys. 132, 154104 (2010)DOI: 10.1063/1.3382344
- Grimme2011
- Stefan Grimme, Stephan Ehrlich, and Lars GoerigkEffect of the damping function in dispersion corrected density functional theoryJournal of Computational Chemistry 32, 1456 (2011)DOI: 10.1002/jcc.21759
- Guénolé2020
- Julien Guénolé, Wolfram G. Nöhring, Aviral Vaid, Frédéric Houllé, Zhuocheng Xie, Aruna Prakash, and Erik BitzekAssessment and optimization of the fast inertial relaxation engine (fire) for energy minimization in atomistic simulations and its implementation in lammpsComputational Materials Science 175, 109584 (2020)
- Hoover1996
- William G. Hoover and Brad Lee HolianKinetic moments method for the canonical ensemble distributionPhysics Letters A, 211, 253-257 (1996)DOI: 10.1016/0375-9601(95)00973-6 <https://doi.org/10.1016/0375-9601(95)00973-6>
- Leimkuhler2013
- Benedict Leimkuhler and Charles MatthewsRational construction of stochastic numerical methods for molecular samplingApplied Mathematics Research eXpress 2013, 34 (2013)DOI: 10.1093/amrx/abs010
- Li2019
- Zhen Li, Shiyun Xiong, Charles Sievers, Yue Hu, Zheyong Fan, Ning Wei, Hua Bao, Shunda Chen, Davide Donadio, and Tapio Ala-NissilaInfluence of Thermostatting on Nonequilibrium Molecular Dynamics Simulations of Heat Conduction in SolidsJ. Chem. Phys. 151, 234105 (2019)DOI: 10.1063/1.5132543
- Lv2016
- Wei Lv and Asegun HenryDirect calculation of modal contributions to thermal conductivity via Green-Kubo modal analysisNew J. Phys. 18, 013028 (2016)
- Martyna1994
- Glenn J. Martyna, Douglas J. Tobias, and Michael L. KleinConstant pressure molecular dynamics algorithmsThe Journal of Chemical Physics, 101, 4177-4189 (1994)DOI: 10.1063/1.467468 <https://doi.org/10.1063/1.467468>
- Parrinello1981
- M. Parrinello and A. RahmanPolymorphic transitions in single crystals: A new molecular dynamics methodJournal of Applied Physics, 52, 7182-7190 (1981)DOI: 10.1063/1.328693 <https://doi.org/10.1063/1.328693>
- Rahm2021
- J. Magnus Rahm, Joakim Löfgren, Erik Fransson, and Paul ErhartA tale of two phase diagrams: Interplay of ordering and hydrogen uptake in Pd–Au–HActa Materialia, 211, 116893 (2021)DOI: 10.1016/j.actamat.2021.116893 <https://doi.org/10.1016/j.actamat.2021.116893>
- Ravelo2004
- Ravelo, R. and Holian, B. L. and Germann, T. C. and Lomdahl, P. S.Constant-stress Hugoniostat method for following the dynamical evolution of shocked matterPhys. Rev. B. 70, 014103 (2004)
- Reed2003
- Evan J. Reed, Laurence E. Fried, and J. D. JoannopoulosA Method for Tractable Dynamical Studies of Single and Double Shock CompressionPhys. Rev. Lett. 90, 235503 (2003)
- Rossi2014
- Mariana Rossi, Michele Ceriotti, and David E. ManolopoulosHow to remove the spurious resonances from ring polymer molecular dynamicsJ. Chem. Phys. 140, 234116 (2014)DOI: 10.1063/1.4883861
- Sadigh2012a
- Babak Sadigh, Paul Erhart, Alexander Stukowski, Alfredo Caro, Enrique Martinez, and Luis Zepeda-RuizScalable parallel Monte Carlo algorithm for atomistic simulations of precipitation in alloysPhys. Rev. B 85, 184203 (2012)
- Sadigh2012b
- Babak Sadigh and Paul ErhartCalculation of excess free energies of precipitates via direct thermodynamic integration across phase boundariesPhys. Rev. B 86, 134204 (2012)
- Schaul2011
- T. Schaul, T. Glasmachers, and J. SchmidhuberHigh dimensions and heavy tails for natural evolution strategiesIn: Proceedings of the 13th Annual Conference on Genetic and Evolutionary ComputationGECCO ‘11 (Association for Computing Machinery), New York, USA (2011), pp. 845–852
- Tersoff1988
- Jerry TersoffNew empirical approach for the structure and energy of covalent systemsPhys. Rev. B 37, 6991 (1988)
- Tersoff1989
- Jerry TersoffModeling solid-state chemistry: Interatomic potentials for multicomponent systemsPhys. Rev. B 39, 5566(R) (1989)
- Tuckerman2010
- Mark E. TuckermanStatistical Mechanics: Theory and Molecular Simulation (Oxford Graduate Texts)1st Edition, Oxford University Press (2010)
- Zhou2004
- X. W. Zhou, R. A. Johnson, and H. N. G. WadleyMisfit-energy-increasing dislocations in vapor-deposited CoFe/NiFe multilayersPhys. Rev. B 69, 144113 (2004)
- Ziegler1985
- J. F. Ziegler, J. P. Biersack, and U. LittmarkIn The Stopping and Range of Ions in Matter, volume 1New York, 1985. Pergamon. ISBN 0-08-022053-3
- Koning2001
- Maurice de Koning, Alex Antonelli, and Sidney YipSingle-simulation determination of phase boundaries: A dynamic Clausius–Clapeyron integration methodJ. Chem. Phys. 115, 11025–11035 (2001)DOI: 10.1063/1.1420486
- Cajahuaringa2022
- Samuel Cajahuaringa and Alex AntonelliNon-equilibrium free-energy calculation of phase-boundaries using LAMMPSComputational Materials Science 207, 111275 (2022)