Exploring the free energy surface using ab initio molecular dynamics
Abstract
Efficient exploration of the configuration space and identification of metastable structures are challenging from both computational as well as algorithmic perspectives. Here, we extend the recently proposed orderparameter aided temperature accelerated sampling schemes to efficiently and systematically explore free energy surfaces, and search for metastable states and reaction pathways within the framework of density functional theory based molecular dynamics. The sampling method is applied to explore the relevant parts of the configuration space in prototypical materials SiO2 and Ti to identify the different metastable structures corresponding to different phases in these materials. In addition, we use the string method in collective variables to study the melting pathways in the high pressure cotunnite phase of SiO2 and the hcp to fcc phase transition in Ti.
- Authors:
-
- Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
- Publication Date:
- Research Org.:
- Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Basic Energy Sciences (BES)
- OSTI Identifier:
- 1262186
- Alternate Identifier(s):
- OSTI ID: 1249678
- Report Number(s):
- LLNL-JRNL-674389
Journal ID: ISSN 0021-9606; JCPSA6
- Grant/Contract Number:
- AC52-07NA27344
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Journal of Chemical Physics
- Additional Journal Information:
- Journal Volume: 144; Journal Issue: 16; Journal ID: ISSN 0021-9606
- Publisher:
- American Institute of Physics (AIP)
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SUPERFLUIDITY; Lagrangian mechanics; Free energy; Melting; Molecular dynamics
Citation Formats
Samanta, Amit, Morales, Miguel A., and Schwegler, Eric. Exploring the free energy surface using ab initio molecular dynamics. United States: N. p., 2016.
Web. doi:10.1063/1.4945653.
Samanta, Amit, Morales, Miguel A., & Schwegler, Eric. Exploring the free energy surface using ab initio molecular dynamics. United States. https://doi.org/10.1063/1.4945653
Samanta, Amit, Morales, Miguel A., and Schwegler, Eric. Fri .
"Exploring the free energy surface using ab initio molecular dynamics". United States. https://doi.org/10.1063/1.4945653. https://www.osti.gov/servlets/purl/1262186.
@article{osti_1262186,
title = {Exploring the free energy surface using ab initio molecular dynamics},
author = {Samanta, Amit and Morales, Miguel A. and Schwegler, Eric},
abstractNote = {Efficient exploration of the configuration space and identification of metastable structures are challenging from both computational as well as algorithmic perspectives. Here, we extend the recently proposed orderparameter aided temperature accelerated sampling schemes to efficiently and systematically explore free energy surfaces, and search for metastable states and reaction pathways within the framework of density functional theory based molecular dynamics. The sampling method is applied to explore the relevant parts of the configuration space in prototypical materials SiO2 and Ti to identify the different metastable structures corresponding to different phases in these materials. In addition, we use the string method in collective variables to study the melting pathways in the high pressure cotunnite phase of SiO2 and the hcp to fcc phase transition in Ti.},
doi = {10.1063/1.4945653},
journal = {Journal of Chemical Physics},
number = 16,
volume = 144,
place = {United States},
year = {Fri Apr 22 00:00:00 EDT 2016},
month = {Fri Apr 22 00:00:00 EDT 2016}
}
Web of Science
Works referenced in this record:
Accurate determination of crystal structures based on averaged local bond order parameters
journal, September 2008
- Lechner, Wolfgang; Dellago, Christoph
- The Journal of Chemical Physics, Vol. 129, Issue 11
Crystal structure prediction from first principles
journal, December 2008
- Woodley, Scott M.; Catlow, Richard
- Nature Materials, Vol. 7, Issue 12
On energy estimators in path integral Monte Carlo simulations: Dependence of accuracy on algorithm
journal, November 1989
- Cao, Jianshu; Berne, Bruce J.
- The Journal of Chemical Physics, Vol. 91, Issue 10
Second-order integrators for Langevin equations with holonomic constraints
journal, September 2006
- Vanden-Eijnden, Eric; Ciccotti, Giovanni
- Chemical Physics Letters, Vol. 429, Issue 1-3
Nonlinear Ill-Posed Problems
book, January 1998
- Tikhonov, A. N.; Leonov, A. S.; Yagola, A. G.
- Springer Dordrecht
On the use of the adiabatic molecular dynamics technique in the calculation of free energy profiles
journal, March 2002
- Rosso, Lula; Mináry, Peter; Zhu, Zhongwei
- The Journal of Chemical Physics, Vol. 116, Issue 11
A general strategy for designing seamless multiscale methods
journal, August 2009
- E., Weinan; Ren, Weiqing; Vanden-Eijnden, Eric
- Journal of Computational Physics, Vol. 228, Issue 15
Ab initio random structure searching
journal, January 2011
- Pickard, Chris J.; Needs, R. J.
- Journal of Physics: Condensed Matter, Vol. 23, Issue 5
From ultrasoft pseudopotentials to the projector augmented-wave method
journal, January 1999
- Kresse, G.; Joubert, D.
- Physical Review B, Vol. 59, Issue 3, p. 1758-1775
Thickness-dependent fcc–hcp phase transformation in polycrystalline titanium thin films
journal, April 2011
- Chakraborty, J.; Kumar, Kishor; Ranjan, Rajeev
- Acta Materialia, Vol. 59, Issue 7
Crystal structure prediction via particle-swarm optimization
journal, September 2010
- Wang, Yanchao; Lv, Jian; Zhu, Li
- Physical Review B, Vol. 82, Issue 9
A genetic algorithm for predicting the structures of interfaces in multicomponent systems
journal, February 2010
- Chua, Alvin L. -S.; Benedek, Nicole A.; Chen, Lin
- Nature Materials, Vol. 9, Issue 5
Temperature-Accelerated Method for Exploring Polymorphism in Molecular Crystals Based on Free Energy
journal, June 2011
- Yu, Tang-Qing; Tuckerman, Mark E.
- Physical Review Letters, Vol. 107, Issue 1
Global space-group optimization problem: Finding the stablest crystal structure without constraints
journal, March 2007
- Trimarchi, Giancarlo; Zunger, Alex
- Physical Review B, Vol. 75, Issue 10
A temperature accelerated method for sampling free energy and determining reaction pathways in rare events simulations
journal, July 2006
- Maragliano, Luca; Vanden-Eijnden, Eric
- Chemical Physics Letters, Vol. 426, Issue 1-3
Formation of face-centered-cubic titanium by mechanical attrition
journal, February 2003
- Manna, I.; Chattopadhyay, P. P.; Nandi, P.
- Journal of Applied Physics, Vol. 93, Issue 3
A theoretical study of the stability of anionic defects in cubic ZrO2 at extreme conditions
journal, February 2016
- Samanta, Amit
- Journal of Materials Science, Vol. 51, Issue 10
Locating landmarks on high-dimensional free energy surfaces
journal, March 2015
- Chen, Ming; Yu, Tang-Qing; Tuckerman, Mark E.
- Proceedings of the National Academy of Sciences, Vol. 112, Issue 11
Unified Approach for Molecular Dynamics and Density-Functional Theory
journal, November 1985
- Car, R.; Parrinello, M.
- Physical Review Letters, Vol. 55, Issue 22
Optimization-Based String Method for Finding Minimum Energy Path
journal, August 2013
- Samanta, Amit; E., Weinan
- Communications in Computational Physics, Vol. 14, Issue 2
Formation of a crystal nucleus from liquid
journal, July 2010
- Kawasaki, T.; Tanaka, H.
- Proceedings of the National Academy of Sciences, Vol. 107, Issue 32
Accurate sampling using Langevin dynamics
journal, May 2007
- Bussi, Giovanni; Parrinello, Michele
- Physical Review E, Vol. 75, Issue 5
Shock compression of stishovite and melting of silica at planetary interior conditions
journal, January 2015
- Millot, M.; Dubrovinskaia, N.; ernok, A.
- Science, Vol. 347, Issue 6220
Order-parameter-aided temperature-accelerated sampling for the exploration of crystal polymorphism and solid-liquid phase transitions
journal, June 2014
- Yu, Tang-Qing; Chen, Pei-Yang; Chen, Ming
- The Journal of Chemical Physics, Vol. 140, Issue 21
Generalized Gaussian moment thermostatting: A new continuous dynamical approach to the canonical ensemble
journal, January 2000
- Liu, Yi; Tuckerman, Mark E.
- The Journal of Chemical Physics, Vol. 112, Issue 4
Calculations of free energy barriers for local mechanisms of hydrogen diffusion in alanates
book, January 2008
- Monteferrante, Michele; Bonella, Sara; Meloni, Simone
- Lecture Notes in Computational Science and Engineering
Prediction of a hexagonal SiO2 phase affecting stabilities of MgSiO3 and CaSiO3 at multimegabar pressures
journal, January 2011
- Tsuchiya, T.; Tsuchiya, J.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 4
Self-Consistent Equations Including Exchange and Correlation Effects
journal, November 1965
- Kohn, W.; Sham, L. J.
- Physical Review, Vol. 140, Issue 4A, p. A1133-A1138
Fluid like behavior of oxygen in cubic zirconia under extreme conditions
journal, October 2012
- Samanta, Amit; Zhang, S. B.
- Applied Physics Letters, Vol. 101, Issue 18
Temperature-accelerated dynamics for simulation of infrequent events
journal, June 2000
- So/rensen, Mads R.; Voter, Arthur F.
- The Journal of Chemical Physics, Vol. 112, Issue 21
The quantum free energy barrier for hydrogen vacancy diffusion in Na3AlH6
journal, January 2012
- Poma, Adolfo; Monteferrante, Michele; Bonella, Sara
- Physical Chemistry Chemical Physics, Vol. 14, Issue 44
Nosé–Hoover chains: The canonical ensemble via continuous dynamics
journal, August 1992
- Martyna, Glenn J.; Klein, Michael L.; Tuckerman, Mark
- The Journal of Chemical Physics, Vol. 97, Issue 4
Single-sweep methods for free energy calculations
journal, May 2008
- Maragliano, Luca; Vanden-Eijnden, Eric
- The Journal of Chemical Physics, Vol. 128, Issue 18
Efficiency of ab-initio total energy calculations for metals and semiconductors using a plane-wave basis set
journal, July 1996
- Kresse, G.; Furthmüller, J.
- Computational Materials Science, Vol. 6, Issue 1, p. 15-50
Microscopic mechanisms of equilibrium melting of a solid
journal, November 2014
- Samanta, A.; Tuckerman, M. E.; Yu, T. -Q.
- Science, Vol. 346, Issue 6210
Bond-orientational order in liquids and glasses
journal, July 1983
- Steinhardt, Paul J.; Nelson, David R.; Ronchetti, Marco
- Physical Review B, Vol. 28, Issue 2
Replica Monte Carlo Simulation of Spin-Glasses
journal, November 1986
- Swendsen, Robert H.; Wang, Jian-Sheng
- Physical Review Letters, Vol. 57, Issue 21
Early Stage of the Dehydrogenation of NaAlH 4 by Ab Initio Rare Event Simulations
journal, September 2012
- Sterpone, Fabio; Bonella, Sara; Meloni, Simone
- The Journal of Physical Chemistry C, Vol. 116, Issue 37
Asymptotics for and against cross-validation
journal, January 1977
- Stone, M.
- Biometrika, Vol. 64, Issue 1
Efficient iterative schemes for ab initio total-energy calculations using a plane-wave basis set
journal, October 1996
- Kresse, G.; Furthmüller, J.
- Physical Review B, Vol. 54, Issue 16, p. 11169-11186
String method in collective variables: Minimum free energy paths and isocommittor surfaces
journal, July 2006
- Maragliano, Luca; Fischer, Alexander; Vanden-Eijnden, Eric
- The Journal of Chemical Physics, Vol. 125, Issue 2
Finite Temperature String Method for the Study of Rare Events †
journal, April 2005
- E., Weinan; Ren, Weiqing; Vanden-Eijnden, Eric
- The Journal of Physical Chemistry B, Vol. 109, Issue 14
Equilibrium and Rate Constants, and Reaction Mechanism of the HF Dissociation in the HF(H 2 O) 7 Cluster by ab Initio Rare Event Simulations
journal, December 2013
- Elena, Alin Marin; Meloni, Simone; Ciccotti, Giovanni
- The Journal of Physical Chemistry A, Vol. 117, Issue 49
Quantum dynamics via adiabatic ab initio centroid molecular dynamics
journal, May 1999
- Marx, Dominik; Tuckerman, Mark E.; Martyna, Glenn J.
- Computer Physics Communications, Vol. 118, Issue 2-3
Efficient and Direct Generation of Multidimensional Free Energy Surfaces via Adiabatic Dynamics without Coordinate Transformations
journal, December 2008
- Abrams, Jerry B.; Tuckerman, Mark E.
- The Journal of Physical Chemistry B, Vol. 112, Issue 49
Assessing the efficiency of free energy calculation methods
journal, February 2004
- Rodriguez-Gomez, David; Darve, Eric; Pohorille, Andrew
- The Journal of Chemical Physics, Vol. 120, Issue 8
Atomistic simulations of rare events using gentlest ascent dynamics
journal, March 2012
- Samanta, Amit; E., Weinan
- The Journal of Chemical Physics, Vol. 136, Issue 12
Thermal Properties of the Inhomogeneous Electron Gas
journal, March 1965
- Mermin, N. David
- Physical Review, Vol. 137, Issue 5A
Positron lifetime studies of the hcp to fcc transformation induced by mechanical attrition of elemental titanium
journal, July 2004
- Manna, I.; Chattopadhyay, P. P.; Nandi, P.
- Physics Letters A, Vol. 328, Issue 2-3
Constant pressure molecular dynamics algorithms
journal, September 1994
- Martyna, Glenn J.; Tobias, Douglas J.; Klein, Michael L.
- The Journal of Chemical Physics, Vol. 101, Issue 5
Design of quasisymplectic propagators for Langevin dynamics
journal, July 2007
- Melchionna, Simone
- The Journal of Chemical Physics, Vol. 127, Issue 4
Optimization by Simulated Annealing
journal, May 1983
- Kirkpatrick, S.; Gelatt, C. D.; Vecchi, M. P.
- Science, Vol. 220, Issue 4598
Crystal structure prediction using ab initio evolutionary techniques: Principles and applications
journal, June 2006
- Oganov, Artem R.; Glass, Colin W.
- The Journal of Chemical Physics, Vol. 124, Issue 24
Sampling saddle points on a free energy surface
journal, April 2014
- Samanta, Amit; Chen, Ming; Yu, Tang-Qing
- The Journal of Chemical Physics, Vol. 140, Issue 16
Works referencing / citing this record:
Predicting phase behavior of grain boundaries with evolutionary search and machine learning
text, January 2017
- Zhu, Qiang; Samanta, Amit; Li, Bingxi
- arXiv
Predicting phase behavior of grain boundaries with evolutionary search and machine learning
journal, February 2018
- Zhu, Qiang; Samanta, Amit; Li, Bingxi
- Nature Communications, Vol. 9, Issue 1
The thermodynamics of a liquid-solid interface at extreme conditions: A model close-packed system up to 100 GPa
journal, September 2018
- Samanta, Amit; Belof, Jonathan L.
- The Journal of Chemical Physics, Vol. 149, Issue 12
Predicting phase behavior of grain boundaries with evolutionary search and machine learning
journal, February 2018
- Zhu, Qiang; Samanta, Amit; Li, Bingxi
- Nature Communications, Vol. 9, Issue 1
Ab initio simulations of liquid electrolytes for energy conversion and storage
journal, October 2018
- Pham, Tuan Anh
- International Journal of Quantum Chemistry, Vol. 119, Issue 1