Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

Quantum ESPRESSO is an integrated suite of open-source computer codes for quantum simulations of materials using state-of-the art electronic-structure techniques, based on density-functional theory, density-functional perturbation theory, and many-body perturbation theory, within the plane-wave pseudo-potential and projector-augmented-wave approaches. Quantum ESPRESSO owes its popularity to the wide variety of properties and processes it allows to simulate, to its performance on an increasingly broad array of hardware architectures, and to a community of researchers that rely on its capabilities as a core open-source development platform to implement theirs ideas. In this paper we describe recent extensions and improvements, covering new methodologies and property calculators, improved parallelization, code modularization, and extended interoperability both within the distribution and with external software.

/pdf/advanced-capabilities-for-materials-modelling-with-quantum-1mm65lmkt8.pdf

Advanced capabilities for materials modelling with Quantum ESPRESSO

Quantum ESPRESSO is an integrated suite of open-source computer codes for quantum simulations of materials using state-of-the-art electronic-structure techniques, based on density-functional theory, density-functional perturbation theory, and many-body perturbation theory, within the plane-wave pseudopotential and projector-augmented-wave approaches Quantum ESPRESSO owes its popularity to the wide variety of properties and processes it allows to simulate, to its performance on an increasingly broad array of hardware architectures, and to a community of researchers that rely on its capabilities as a core open-source development platform to implement their ideas In this paper we describe recent extensions and improvements, covering new methodologies and property calculators, improved parallelization, code modularization, and extended interoperability both within the distribution and with external software

/pdf/advanced-capabilities-for-materials-modelling-with-quantum-40poaosrve.pdf

Advanced capabilities for materials modelling with Quantum ESPRESSO.

Here we summarize recent progress in machine learning for the chemical sciences. We outline machine-learning techniques that are suitable for addressing research questions in this domain, as well as future directions for the field. We envisage a future in which the design, synthesis, characterization and application of molecules and materials is accelerated by artificial intelligence.

/pdf/machine-learning-for-molecular-and-materials-science-2c34wzvcqw.pdf

Machine learning for molecular and materials science.

Fully nonlocal two-projector norm-conserving pseudopotentials are shown to be compatible with a systematic approach to the optimization of convergence with the size of the plane-wave basis. A reformulation of the optimization is developed, including the ability to apply it to positive-energy atomic scattering states and to enforce greater continuity in the pseudopotential. The generalization of norm conservation to multiple projectors is reviewed and recast for the present purposes. Comparisons among the results of all-electron and one- and two-projector norm-conserving pseudopotential calculations of lattice constants and bulk moduli are made for a group of solids chosen to represent a variety of types of bonding and a sampling of the periodic table.

Optimized norm-conserving Vanderbilt pseudopotentials

We present the results of a high-throughput, first principles search for topological materials based on identifying materials with band inversion induced by spin-orbit coupling. Out of the currently available 30000 materials in our database, we investigate more than 4507 non-magnetic materials having heavy atoms and low bandgaps. We compute the spillage between the spin-orbit and non-spin-orbit wave functions, resulting in more than 1699 high-spillage candidate materials. We demonstrate that in addition to Z2 topological insulators, this screening method successfully identifies many semimetals and topological crystalline insulators. Our approach is applicable to the investigation of disordered or distorted materials, because it is not based on symmetry considerations, and it can be extended to magnetic materials. After our first screening step, we use Wannier-interpolation to calculate the topological invariants and to search for band crossings in our candidate materials. We discuss some individual example materials, as well as trends throughout our dataset, that is available at JARVIS-DFT website: this https URL.

High-throughput discovery of topological materials using spin-orbit spillage

Oxides have many potentially desirable characteristics for thermoelectric applications, including low cost and stability at high temperatures, but thus far there are few known high $zT$ $n$-type oxide thermoelectrics. In this work, we use high-throughput first principles calculations to screen transition metal oxides, nitrides, and sulfides for candidate materials with high power factors and low thermal conductivity. We find a variety of promising materials, and we investigate these materials in detail in order to understand the mechanisms that cause them to have high power factors. These materials all combine a high density of states near the Fermi level with dispersive bands, reducing the trade-off between the Seebeck coefficient and the electrical conductivity, but they do so for several different reasons. In addition, our calculations indicate that many of our candidate materials have low thermal conductivity.

First principles search for $n$-type oxide thermoelectrics

Finite-temperature disordered solid solutions and magnetic materials are difficult to study directly using first-principles calculations, due to the large unit cells and many independent samples that are required. In this work, we develop a combined cluster expansion and atomic displacement expansion, which we fit to first-principles energies, forces, and stresses. We then use the expansion to calculate thermodynamic quantities at nearly first-principles levels of accuracy. Our model naturally includes both configurational and vibrational entropy, including anharmonic contributions and structural phase transitions. In addition, we can treat coupling between atomic displacement and chemical or magnetic degrees of freedom. As examples, we use our expansion to calculate properties of ${\mathrm{Si}}_{1\ensuremath{-}x}{\mathrm{Ge}}_{x}$, magnetic MnO, Al with vacancies, and ${\mathrm{Ba}}_{x}{\mathrm{Sr}}_{1\ensuremath{-}x}{\mathrm{TiO}}_{3}$. Finally, we demonstrate that by treating all the relevant degrees of freedom explicitly, we can in some cases achieve improved convergence of fitting parameters versus distance as compared to a pure cluster expansion.

Combined cluster and atomic displacement expansion for solid solutions and magnetism

http://absimage.aps.org/image/MAR14/MWS_MAR14-2013-002043.pdf

Antiferroelectricity in ZrO$_2$ and related AXY compounds from first principles

Epitaxial oxide-Si heterostructures, which integrate the functionality of crystalline oxides with Si technology, are made possible by a submonolayer of Sr deposited on Si (001). We find by electron diffraction studies using single termination Si wafers that this Sr submonolayer replaces the top layer of Si when deposited at 650 degrees C. Supported by first-principles calculations, we propose a model for the reaction dynamics of Sr on the Si surface and its effect on oxide epitaxy. This model predicts, and we experimentally confirm, an unexplored 25 degrees C pathway to crystalline oxide epitaxy on Si.

http://absimage.aps.org/image/MAR09/MWS_MAR09-2008-005898.pdf

The role of strontium in oxide epitaxy on silicon (001).

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