XtalOpt: An open-source evolutionary algorithm for crystal structure prediction

Lonie, David; Zurek, Eva

doi:10.1016/j.cpc.2010.07.048

Cited by 317 publications

(277 citation statements)

References 51 publications

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“…Crystal structure predictions were then run at 20, 50, and 100 GPa, with two and four formula units per unit cell, and using approaches based on evolutionary algorithms and the particle swarm optimization method as implemented in the XtalOpt and CALYPSO packages (57,58). Around 600 structures were optimized in each search run.…”

Section: Methodsmentioning

confidence: 99%

High-pressure phase of brucite stable at Earth’s mantle transition zone and lower mantle conditions

Hermann

Mookherjee

2016

Proc. Natl. Acad. Sci. U.S.A.

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We investigate the high-pressure phase diagram of the hydrous mineral brucite, Mg(OH) 2 , using structure search algorithms and ab initio simulations. We predict a high-pressure phase stable at pressure and temperature conditions found in cold subducting slabs in Earth's mantle transition zone and lower mantle. This prediction implies that brucite can play a much more important role in water transport and storage in Earth's interior than hitherto thought. The predicted high-pressure phase, stable in calculations between 20 and 35 GPa and up to 800 K, features MgO 6 octahedral units arranged in the anatase-TiO 2 structure. Our findings suggest that brucite will transform from a layered to a compact 3D network structure before eventual decomposition into periclase and ice. We show that the high-pressure phase has unique spectroscopic fingerprints that should allow for straightforward detection in experiments. The phase also has distinct elastic properties that might make its direct detection in the deep Earth possible with geophysical methods.brucite | pressure | phase transition | electronic structure calculations W ater plays an important role in sustaining geological activity. For instance, water helps in lowering the mantle's melting temperature, enhancing diffusion and creep thus affecting rheology of rocks, and also influences mineral phase boundaries. Current estimates suggest that the Earth's mantle is likely to contain a mass of water equivalent to the mass of the world's oceans (1, 2). The exchange of water between the surface and deep mantle reservoirs is vital for the sustenance of surface water over geological time scales (3). Hydrous minerals stable in the hydrated oceanic crust and mantle play an important role in transporting water into the Earth's interior. Hydrated peridotite, the major mantle rock type, can be understood by considering mineral phases stable in the ternary system of MgO-SiO 2 -H 2 O (MSH). Brucite, Mg(OH) 2 , is arguably the simplest hydrous mineral in the MSH system. Brucite is also the most important MgO-H 2 O binary and the most water-rich phase within the MSH ternary system.The crystal structure of brucite consists of Mg 2+ cations and OH − anions arranged in layers, in an overall trigonal structure (space group symmetry P 3m1); Fig. 1. The common ionic compound CdI 2 is the archetype crystal structure for brucite as well as for portlandite [Ca(OH) 2 )] and several other transition metal hydroxides M(OH) 2 where M = Mn, Ni, Co, Fe, Cd,. In brucite, the crystal structure comprises layers of edge-sharing MgO 6 polyhedra. The interaction between the layers is weak at ambient conditions, where each upward-pointing OH group is surrounded by three downward-pointing OH groups in the adjacent layer and vice versa. Under compression the H-H repulsive interactions lead to positional disordering of the protons, which are displaced from the 2d Wyckoff site into one of three equivalent 6i sites as documented from neutron diffraction studies (11,12). Vibrational spectroscopic studies incl...

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Section: Methodsmentioning

confidence: 99%

High-pressure phase of brucite stable at Earth’s mantle transition zone and lower mantle conditions

Hermann

Mookherjee

2016

Proc. Natl. Acad. Sci. U.S.A.

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“…Genetic or evolutionary algorithms rely on concepts borrowed from biological evolution to locate the global minimum on the potential energy surface. Here, we use the open source program XtalOpt (20) to perform an evolutionary algorithm based structure search. For a proposed structure the enthalpies are computed by density functional theory (DFT) with the VASP software package (21), making use of the Perdew-Burke-Ernzerhof parametrization of the exchangecorrelation energy density (22), and the Projector Augmented Wave (PAW) method to describe the electron-ion interaction (23,24).…”

Section: Searching Methodologymentioning

confidence: 99%

High pressure ices

Hermann

Ashcroft

Hoffmann

2011

Proc. Natl. Acad. Sci. U.S.A.

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H 2 O will be more resistant to metallization than previously thought. From computational evolutionary structure searches, we find a sequence of new stable and meta-stable structures for the ground state of ice in the 1-5 TPa (10 to 50 Mbar) regime, in the static approximation. The previously proposed Pbcm structure is superseded by a Pmc2 1 phase at p ¼ 930 GPa, followed by a predicted transition to a P2 1 crystal structure at p ¼ 1.3 TPa. This phase, featuring higher coordination at O and H, is stable over a wide pressure range, reaching 4.8 TPa. We analyze carefully the geometrical changes in the calculated structures, especially the buckling at the H in O-H-O motifs. All structures are insulatingchemistry burns a deep and (with pressure increase) lasting hole in the density of states near the highest occupied electronic levels of what might be component metallic lattices. Metallization of ice in our calculations occurs only near 4.8 TPa, where the metallic C2∕m phase becomes most stable. In this regime, zero-point energies much larger than typical enthalpy differences suggest possible melting of the H sublattice, or even the entire crystal.hydrogen bonds | compressed water

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“…A typical computational strategy is to investigate the relative stability of a series of candidate high pressure phases, although increasingly methods including random structure search and evolutionary algorithms are being applied to predict the structures of new high pressure phases [104][105][106]. In general, DFT calculations yield a quite accurate assessment of the relative enthalpies of different phases.…”

Section: Theoretical Predictionsmentioning

confidence: 99%

Nitrogen-rich transition metal nitrides

Salamat

Hector

Kroll

et al. 2013

Coordination Chemistry Reviews

130

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The solid state chemistry leading to the synthesis and characterization of metal nitrides with N:M ratios > 1 is summarized. Studies of these compounds represent an emerging area of research. Most transition metal nitrides have much lower nitrogen contents, and they often form with nonor sub-stoichiometric compositions. These materials are typically metallic with often superconducting properties, and they provide highly refractory, high hardness materials with many technological applications. The higher metal nitrides should achieve formal oxidation states (OS) attaining those found among corresponding oxides, and they are expected to have useful semiconducting properties. Only a very few examples of such high OS nitrogen-rich compounds are known at present. The main group elements typically form covalently bonded nitride ceramics such as Si 3 N 4 , Ge 3 N 4 and Sn 3 N 4 , and the early transition metals Zr and Hf produce Zr 3 N 4 and Hf 3 N 4 . However, the only main example of a highly nitrided transition metal compound known to date is Ta 3 N 5 , that has a formal oxidation state +5 and is a semiconductor with visible light absorption leading to applications as a pigment and in photocatalysis. New synthesis routes are being explored to study the possible formation of other N-rich materials that are predicted to exist by ab initio calculations. There is a useful interplay between theoretical predictions and experimental synthesis studies at ambient and high pressure conditions, as we explore and establish the existence and structure-property relations of these new nitride compounds and polymorphs. Here we review the state of current investigations and indicate possible new directions for further work.[a] European Synchrotron Radiation Facility,

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XtalOpt: An open-source evolutionary algorithm for crystal structure prediction

Cited by 317 publications

References 51 publications

High-pressure phase of brucite stable at Earth’s mantle transition zone and lower mantle conditions

High-pressure phase of brucite stable at Earth’s mantle transition zone and lower mantle conditions

High pressure ices

Nitrogen-rich transition metal nitrides

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