Bibliography

Bernetti2020

Mattia Bernetti and Giovanni Bussi

Pressure control using stochastic cell rescaling

J. 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. Haak

Molecular dynamics with coupling to an external bath

J. Chem. Phys. 81, 3684 (1984)

DOI: 10.1063/1.448118

Bitzek2006

Erik Bitzek, Pekka Koskinen, Franz Gähler, Michael Moseler, and Peter Gumbsch

Structural Relaxation Made Simple

Phys. Rev. Lett. 97, 170201 (2006)

DOI: 10.1103/PhysRevLett.97.170201

Brorsson2021

Joakim Brorsson, Arsalan Hashemi, Zheyong Fan, Erik Fransson, Fredrik Eriksson, Tapio Ala-Nissila, Arkady V. Krasheninnikov, Hannu-Pekka Komsa, and Paul Erhart

Efficient calculation of the lattice thermal conductivity by atomistic simulations with ab-initio accuracy

Advanced Theory and Simulations 4, 2100217 (2021)

DOI: 10.1002/adts.202100217

Bussi2007a

Giovanni Bussi and Michele Parrinello

Accurate sampling using Langevin dynamics

Phys. Rev. E 75, 056707 (2007)

DOI: 10.1103/PhysRevE.75.056707

Bussi2007b

Giovanni Bussi, Davide Donadio, and Michele Parrinello

Canonical sampling through velocity rescaling

J. Chem. Phys. 126, 014101 (2007)

DOI: 10.1063/1.2408420

Ceriotti2010

Michele Ceriotti, Michele Parrinello, Thomas E. Markland, and David E. Manolopoulos

Efficient stochastic thermostatting of path integral molecular dynamics

J. Chem. Phys. 133, 124104 (2010)

DOI: 10.1063/1.3489925

Craig2004

Ian R. Craig and David E. Manolopoulos

Quantum statistics and classical mechanics: Real time correlation functions from ring polymer molecular dynamics

J. Chem. Phys. 121, 3368 (2004)

DOI: 10.1063/1.1777575

Dai2006

X. D. Dai, Y. Kong, J. H. Li, and B. X. Liu

Extended Finnis–Sinclair potential for bcc and fcc metals and alloys

J. Phys.: Condens. Matter 18, 4527 (2006)

DOI: 10.1088/0953-8984/18/19/008

Drautz2019

Ralf Drautz

Atomic cluster expansion for accurate and transferable interatomic potentials

Phys. Rev. B 99, 014104 (2019)

DOI: 10.1103/PhysRevB.99.014104

Eriksson2019

Fredrik Eriksson, Erik Fransson, and Paul Erhart

The Hiphive Package for the Extraction of High-Order Force Constants by Machine Learning

Advanced Theory and Simulations, 2, 1800184 (2019)

DOI: 10.1002/adts.201800184

Fan2015

Zheyong Fan, Luiz Felipe C. Pereira, Hui-Qiong Wang, Jin-Cheng Zheng, Davide Donadio, and Ari Harju

Force and heat current formulas for many-body potentials in molecular dynamics simulations with applications to thermal conductivity calculations

Phys. Rev. B 92, 094301 (2015)

DOI: 10.1103/PhysRevB.92.094301

Fan2017

Zheyong Fan, Luiz Felipe C. Pereira, Petri Hirvonen, Mikko M. Ervasti, Ken R. Elder, Davide Donadio, Tapio Ala-Nissila, and Ari Harju

Thermal conductivity decomposition in two-dimensional materials: Application to graphene

Phys. Rev. B 95, 144309 (2017)

DOI: 10.1103/PhysRevB.95.144309

Fan2019

Zheyong Fan, Haikuan Dong, Ari Harju, and Tapio Ala-Nissila

Homogeneous nonequilibrium molecular dynamics method for heat transport and spectral decomposition with many-body potentials

Phys. Rev. B 99, 064308 (2019)

DOI: 10.1103/PhysRevB.99.064308

Fan2020

Zheyong Fan, Yanzhou Wang, Xiaokun Gu, Ping Qian, Yanjing Su, and Tapio Ala-Nissila

A minimal Tersoff potential for diamond silicon with improved descriptions of elastic and phonon transport properties

J. Phys.: Condens. Matter 32, 135901 (2020)

DOI: 10.1088/1361-648X/ab5c5f

Fan2021

Zheyong Fan, Zezhu Zeng, Cunzhi Zhang, Yanzhou Wang, Keke Song, Haikuan Dong, Yue Chen, and Tapio Ala-Nissila

Neuroevolution machine learning potentials: Combining high accuracy and low cost in atomistic simulations and application to heat transport

Phys. Rev. B. 104, 104309 (2021)

DOI: 10.1103/PhysRevB.104.104309

Fan2021b

Zheyong Fan, Jose Hugo Garcia, Aron W Cummings, Jose Eduardo Barrios-Vargas, Michel Panhans, Ari Harju, Frank Ortmann, and Stephan Roche

Linear scaling quantum transport methodologies

Physics Reports 903, 1 (2021)

DOI: 10.1016/j.physrep.2020.12.001

Fan2022a

Zheyong Fan

Improving the accuracy of the neuroevolution machine learning potentials for multi-component systems

Journal of Physics: Condensed Matter 34, 125902 (2022)

DOI: 10.1088/1361-648X/ac462b

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-Nissila

GPUMD: A package for constructing accurate machine-learned potentials and performing highly efficient atomistic simulations

Journal of Chemical Physics 157, 114801 (2022)

DOI: 10.1063/5.0106617

Freitas2016

Rodrigo Freitas, Mark Asta, Maurice de Koning

Nonequilibrium free-energy calculation of solids using LAMMPS

Computational Materials Science, 112, 333 (2016)

DOI: 10.1016/j.commatsci.2015.10.050

Gabourie2021

Alexander J. Gabourie, Zheyong Fan, Tapio Ala-Nissila, and Eric Pop

Spectral Decomposition of Thermal Conductivity: Comparing Velocity Decomposition Methods in Homogeneous Molecular Dynamics Simulations

Phys. Rev. B 103, 205421 (2021)

DOI: 10.1103/PhysRevB.103.205421

Grimme2010

Stefan Grimme, Jens Antony, Stephan Ehrlich, and Helge Krieg

A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu

J. Chem. Phys. 132, 154104 (2010)

DOI: 10.1063/1.3382344

Grimme2011

Stefan Grimme, Stephan Ehrlich, and Lars Goerigk

Effect of the damping function in dispersion corrected density functional theory

Journal 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 Bitzek

Assessment and optimization of the fast inertial relaxation engine (fire) for energy minimization in atomistic simulations and its implementation in lammps

Computational Materials Science 175, 109584 (2020)

DOI: 10.1016/j.commatsci.2020.109584

Hoover1996

William G. Hoover and Brad Lee Holian

Kinetic moments method for the canonical ensemble distribution

Physics 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 Matthews

Rational construction of stochastic numerical methods for molecular sampling

Applied 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-Nissila

Influence of Thermostatting on Nonequilibrium Molecular Dynamics Simulations of Heat Conduction in Solids

J. Chem. Phys. 151, 234105 (2019)

DOI: 10.1063/1.5132543

Lv2016

Wei Lv and Asegun Henry

Direct calculation of modal contributions to thermal conductivity via Green-Kubo modal analysis

New J. Phys. 18, 013028 (2016)

DOI: 10.1088/1367-2630/18/1/013028

Martyna1994

Glenn J. Martyna, Douglas J. Tobias, and Michael L. Klein

Constant pressure molecular dynamics algorithms

The 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. Rahman

Polymorphic transitions in single crystals: A new molecular dynamics method

Journal 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 Erhart

A tale of two phase diagrams: Interplay of ordering and hydrogen uptake in Pd–Au–H

Acta 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 matter

Phys. Rev. B. 70, 014103 (2004)

DOI: 10.1103/PhysRevB.70.014103

Reed2003

Evan J. Reed, Laurence E. Fried, and J. D. Joannopoulos

A Method for Tractable Dynamical Studies of Single and Double Shock Compression

Phys. Rev. Lett. 90, 235503 (2003)

DOI: 10.1103/PhysRevLett.90.235503

Rossi2014

Mariana Rossi, Michele Ceriotti, and David E. Manolopoulos

How to remove the spurious resonances from ring polymer molecular dynamics

J. Chem. Phys. 140, 234116 (2014)

DOI: 10.1063/1.4883861

Sadigh2012a

Babak Sadigh, Paul Erhart, Alexander Stukowski, Alfredo Caro, Enrique Martinez, and Luis Zepeda-Ruiz

Scalable parallel Monte Carlo algorithm for atomistic simulations of precipitation in alloys

Phys. Rev. B 85, 184203 (2012)

DOI: 10.1103/PhysRevB.85.184203

Sadigh2012b

Babak Sadigh and Paul Erhart

Calculation of excess free energies of precipitates via direct thermodynamic integration across phase boundaries

Phys. Rev. B 86, 134204 (2012)

DOI: 10.1103/PhysRevB.86.134204

Schaul2011

T. Schaul, T. Glasmachers, and J. Schmidhuber

High dimensions and heavy tails for natural evolution strategies

In: Proceedings of the 13th Annual Conference on Genetic and Evolutionary Computation

GECCO ‘11 (Association for Computing Machinery), New York, USA (2011), pp. 845–852

DOI: 10.1145/2001576.2001692

Tersoff1988

Jerry Tersoff

New empirical approach for the structure and energy of covalent systems

Phys. Rev. B 37, 6991 (1988)

DOI: 10.1103/PhysRevB.37.6991

Tersoff1989

Jerry Tersoff

Modeling solid-state chemistry: Interatomic potentials for multicomponent systems

Phys. Rev. B 39, 5566(R) (1989)

DOI: 10.1103/PhysRevB.39.5566

Tuckerman2010

Mark E. Tuckerman

Statistical 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. Wadley

Misfit-energy-increasing dislocations in vapor-deposited CoFe/NiFe multilayers

Phys. Rev. B 69, 144113 (2004)

DOI: 10.1103/PhysRevB.69.144113

Ziegler1985

J. F. Ziegler, J. P. Biersack, and U. Littmark

In The Stopping and Range of Ions in Matter, volume 1

New York, 1985. Pergamon. ISBN 0-08-022053-3

Koning2001

Maurice de Koning, Alex Antonelli, and Sidney Yip

Single-simulation determination of phase boundaries: A dynamic Clausius–Clapeyron integration method

J. Chem. Phys. 115, 11025–11035 (2001)

DOI: 10.1063/1.1420486

Cajahuaringa2022

Samuel Cajahuaringa and Alex Antonelli

Non-equilibrium free-energy calculation of phase-boundaries using LAMMPS

Computational Materials Science 207, 111275 (2022)

DOI: 10.1016/j.commatsci.2022.111275