@misc{MAST-development-team2014,
author = {MAST-development-team},
title = {{MAterials Simulation Toolkit (MAST)}},
url = {http://pypi.python.org/pypi/MAST http://pythonhosted.org/MAST},
year = {2014}
}
@article{Angsten2014,
author = {Angsten, Thomas and Mayeshiba, Tam and Wu, Henry and Morgan, Dane},
doi = {10.1088/1367-2630/16/1/015018},
issn = {1367-2630},
journal = {New Journal of Physics},
month = jan,
number = {1},
pages = {015018},
title = {{Elemental vacancy diffusion database from high-throughput first-principles calculations for fcc and hcp structures}},
url = {http://stacks.iop.org/1367-2630/16/i=1/a=015018?key=crossref.c128bdcaae349e3f04ed771d816dd245},
volume = {16},
year = {2014}
}
@article{Ong2013,
author = {Ong, Shyue Ping and Richards, William Davidson and Jain, Anubhav and Hautier, Geoffroy and Kocher, Michael and Cholia, Shreyas and Gunter, Dan and Chevrier, Vincent L. and Persson, Kristin a. and Ceder, Gerbrand},
doi = {10.1016/j.commatsci.2012.10.028},
issn = {09270256},
journal = {Computational Materials Science},
month = feb,
pages = {314--319},
publisher = {Elsevier B.V.},
title = {{Python Materials Genomics (pymatgen): A robust, open-source python library for materials analysis}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0927025612006295},
volume = {68},
year = {2013}
}
@article{Togo2009,
author = {Togo, Atsushi},
title = {{Spglib}},
url = {http://spglib.sourceforge.net/},
year = {2009}
}
@article{Kresse1996,
author = {Kresse, G and Furthm\"{u}ller, J.},
doi = {10.1016/0927-0256(96)00008-0},
issn = {09270256},
journal = {Computational Materials Science},
month = jul,
number = {1},
pages = {15--50},
title = {{Efficiency of ab-initio total energy calculations for metals and semiconductors using a plane-wave basis set}},
url = {http://linkinghub.elsevier.com/retrieve/pii/0927025696000080},
volume = {6},
year = {1996}
}
@article{Kresse1993,
author = {Kresse, G. and Hafner, J.},
doi = {10.1103/PhysRevB.47.558},
issn = {0163-1829},
journal = {Physical Review B},
month = jan,
number = {1},
pages = {558--561},
title = {{Ab initio molecular dynamics for liquid metals}},
url = {http://link.aps.org/doi/10.1103/PhysRevB.47.558},
volume = {47},
year = {1993}
}
@article{Kresse1994,
author = {Kresse, G. and Hafner, J.},
doi = {10.1103/PhysRevB.49.14251},
issn = {0163-1829},
journal = {Physical Review B},
month = may,
number = {20},
pages = {14251--14269},
title = {{Ab initio molecular-dynamics simulation of the liquid-metal–amorphous-semiconductor transition in germanium}},
url = {http://link.aps.org/doi/10.1103/PhysRevB.49.14251},
volume = {49},
year = {1994}
}
@article{Kresse1996,
author = {Kresse, G and Furthm\"{u}ller, J.},
doi = {10.1103/PhysRevB.54.11169},
issn = {0163-1829},
journal = {Physical Review B},
month = oct,
number = {16},
pages = {11169--11186},
title = {{Efficient iterative schemes for ab initio total-energy calculations using a plane-wave basis set}},
url = {http://link.aps.org/doi/10.1103/PhysRevB.54.11169},
volume = {54},
year = {1996}
}
@article{Kresse1994,
author = {Kresse, G and Hafner, J},
doi = {10.1088/0953-8984/6/40/015},
issn = {0953-8984},
journal = {Journal of Physics: Condensed Matter},
month = oct,
number = {40},
pages = {8245--8257},
title = {{Norm-conserving and ultrasoft pseudopotentials for first-row and transition elements}},
url = {http://stacks.iop.org/0953-8984/6/i=40/a=015?key=crossref.c873d42d314a5d78c0adf9bdfc34516c},
volume = {6},
year = {1994}
}
@article{Kresse1999,
author = {Kresse, G and Joubert, D},
doi = {10.1103/PhysRevB.59.1758},
issn = {1098-0121},
journal = {Physical Review B},
month = jan,
number = {3},
pages = {1758--1775},
title = {{From ultrasoft pseudopotentials to the projector augmented-wave method}},
url = {http://link.aps.org/doi/10.1103/PhysRevB.59.1758},
volume = {59},
year = {1999}
}
@incollection{Jonsson1998,
author = {J\'{o}nsson, Hannes and Mills, Greg and Jacobsen, Karsten W.},
booktitle = {Classical and Quantum Dynamics in Condensed Phase Simulations},
editor = {Berne, B. J. and Ciccotti, G. and Coker, D. F.},
pages = {385},
publisher = {World Scientific},
title = {{Nudged Elastic Band Method for Finding Minimum Energy Paths of Transitions}},
year = {1998}
}
@article{Henkelman2000a,
author = {Henkelman, Graeme and J\'{o}nsson, Hannes},
doi = {10.1063/1.1323224},
issn = {00219606},
journal = {The Journal of Chemical Physics},
number = {22},
pages = {9978},
title = {{Improved tangent estimate in the nudged elastic band method for finding minimum energy paths and saddle points}},
volume = {113},
year = {2000}
}
@article{Henkelman2000,
author = {Henkelman, Graeme and Uberuaga, Blas P. and J\'{o}nsson, Hannes},
doi = {10.1063/1.1329672},
issn = {00219606},
journal = {The Journal of Chemical Physics},
number = {22},
pages = {9901},
title = {{A climbing image nudged elastic band method for finding saddle points and minimum energy paths}},
volume = {113},
year = {2000}
}
@article{Sheppard2008,
abstract = {A comparison of chain-of-states based methods for finding minimum energy pathways (MEPs) is presented. In each method, a set of images along an initial pathway between two local minima is relaxed to find a MEP. We compare the nudged elastic band (NEB), doubly nudged elastic band, string, and simplified string methods, each with a set of commonly used optimizers. Our results show that the NEB and string methods are essentially equivalent and the most efficient methods for finding MEPs when coupled with a suitable optimizer. The most efficient optimizer was found to be a form of the limited-memory Broyden-Fletcher-Goldfarb-Shanno method in which the approximate inverse Hessian is constructed globally for all images along the path. The use of a climbing-image allows for finding the saddle point while representing the MEP with as few images as possible. If a highly accurate MEP is desired, it is found to be more efficient to descend from the saddle to the minima than to use a chain-of-states method with many images. Our results are based on a pairwise Morse potential to model rearrangements of a heptamer island on Pt(111), and plane-wave based density functional theory to model a rollover diffusion mechanism of a Pd tetramer on MgO(100) and dissociative adsorption and diffusion of oxygen on Au(111).},
annote = {United States},
author = {Sheppard, Daniel and Terrell, Rye and Henkelman, Graeme},
doi = {10.1063/1.2841941},
isbn = {0021-9606},
issn = {0021-9606},
journal = {The Journal of chemical physics},
language = {English},
month = apr,
number = {13},
pages = {134106},
pmid = {18397052},
title = {{Optimization methods for finding minimum energy paths.}},
volume = {128},
year = {2008}
}
@article{Sheppard2012,
abstract = {A generalized solid-state nudged elastic band (G-SSNEB) method is presented for determining reaction pathways of solid-solid transformations involving both atomic and unit-cell degrees of freedom. We combine atomic and cell degrees of freedom into a unified description of the crystal structure so that calculated reaction paths are insensitive to the choice of periodic cell. For the rock-salt to wurtzite transition in CdSe, we demonstrate that the method is robust for mechanisms dominated either by atomic motion or by unit-cell deformation; notably, the lowest-energy transition mechanism found by our G-SSNEB changes with cell size from a concerted transformation of the cell coordinates in small cells to a nucleation event in large cells. The method is efficient and can be applied to systems in which the force and stress tensor are calculated using density functional theory.},
author = {Sheppard, Daniel and Xiao, Penghao and Chemelewski, William and Johnson, Duane D and Henkelman, Graeme},
doi = {10.1063/1.3684549},
issn = {1089-7690},
journal = {The Journal of chemical physics},
month = feb,
number = {7},
pages = {074103},
pmid = {22360232},
title = {{A generalized solid-state nudged elastic band method.}},
volume = {136},
year = {2012}
}

@article{Sheppard2011,
abstract = {A recent letter to the editor (Quapp and Bofill, J Comput Chem 2010, 31, 2526) claims that the nudged elastic band (NEB) method can converge toward gradient extremal paths and not to steepest descent paths, as has been assumed. Here, we show that the NEB does in fact converge to steepest descent paths and that the observed tendency for the NEB to approach gradient extremal paths was a consequence of implementation errors. We also note that while the NEB finds steepest descent paths, these are not necessarily minimum energy paths in the sense of being a set of points which are minima in the potential energy surface perpendicular to the path. An example is given where segments of steepest descent paths follow potential energy ridges.},
author = {Sheppard, Daniel and Henkelman, Graeme},
doi = {10.1002/jcc.21748},
issn = {1096-987X},
journal = {Journal of computational chemistry},
month = jun,
number = {8},
pages = {1769--71; author reply 1772--3},
pmid = {21328409},
title = {{Paths to which the nudged elastic band converges.}},
volume = {32},
year = {2011}
}
