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 computer codes for electronic-structure calculations and materials modeling, based on density-functional theory, plane waves, and pseudopotentials (norm-conserving, ultrasoft, and projector-augmented wave). The acronym ESPRESSO stands for opEn Source Package for Research in Electronic Structure, Simulation, and Optimization. It is freely available to researchers around the world under the terms of the GNU General Public License. QUANTUM ESPRESSO builds upon newly-restructured electronic-structure codes that have been developed and tested by some of the original authors of novel electronic-structure algorithms and applied in the last twenty years by some of the leading materials modeling groups worldwide. Innovation and efficiency are still its main focus, with special attention paid to massively parallel architectures, and a great effort being devoted to user friendliness. QUANTUM ESPRESSO is evolving towards a distribution of independent and interoperable codes in the spirit of an open-source project, where researchers active in the field of electronic-structure calculations are encouraged to participate in the project by contributing their own codes or by implementing their own ideas into existing codes.

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QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials

First-principles simulation, meaning density-functional theory calculations with plane waves and pseudopotentials, has become a prized technique in condensed-matter theory. Here I look at the basics of the suject, give a brief review of the theory, examining the strengths and weaknesses of its implementation, and illustrating some of the ways simulators approach problems through a small case study. I also discuss why and how modern software design methods have been used in writing a completely new modular version of the CASTEP code.

https://iopscience.iop.org/article/10.1088/0953-8984/14/11/301/pdf

First-principles simulation: ideas, illustrations and the CASTEP code

This article reviews the current status of lattice-dynamical calculations in crystals, using density-functional perturbation theory, with emphasis on the plane-wave pseudopotential method. Several specialized topics are treated, including the implementation for metals, the calculation of the response to macroscopic electric fields and their relevance to long-wavelength vibrations in polar materials, the response to strain deformations, and higher-order responses. The success of this methodology is demonstrated with a number of applications existing in the literature.

/pdf/phonons-and-related-crystal-properties-from-density-3mdybdn8w1.pdf

Phonons and related crystal properties from density-functional perturbation theory

https://repository.kulib.kyoto-u.ac.jp/dspace/bitstream/2433/202086/1/j.scriptamat.2015.07.021.pdf

First principles phonon calculations in materials science

In this article, the relative stability of different high-pressure phases of various cesium halides is studied from first principles and analyzed using the Landau theory of phase transitions.

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High-pressure low-symmetry phases of cesium halides.

We describe the porting of PWscf (Plane-Wave Self Consistent Field), a key component of the Quantum ESPRESSO open-source suite of codes for materials modeling, to GPU systems using CUDA Fortran. Kernel loop directives (CUF kernels) have been extensively used in order to have a single source code for both CPU and GPU implementations. The results of the GPU version have been carefully validated and the performance of the code on several GPU systems (both x86 and POWER8 based) has been compared with traditional Intel multi-core (CPU only) systems. This current GPU version can reduce the time-to-solution by an average factor of 2–3 running two different input cases widely used as benchmarks on small and large high performance computing systems.

A Performance Study of Quantum ESPRESSO’s PWscf Code on Multi-core and GPU Systems

Ab initio or first-principles methods have emerged in the last two decades as a powerful tool to probe the properties of matter at the microscopic scale. These approaches are used to derive macroscopic observables under the controlled condition of a “computational experiment,” and with a predictive power rooted in the quantum-mechanical description of interacting atoms and electrons. Density-functional theory (DFT) has become de facto the method of choice for most applications, due to its combination of reasonable scaling with system size and good accuracy in reproducing most ground state properties. Such an electronic-structure approach can then be combined with classical molecular dynamics to provide an accurate description of thermodynamic properties and phase stability, atomic dynamics, and chemical reactions, or as a tool to sample the features of a potential energy surface.

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First-Principles Molecular Dynamics

The relative stability of various high-pressure phases of CsI is studied from first principles and analyzed using the Landau theory of phase transitions. We demonstrate that the cubic-to-orthorhombic transition recently observed to occur slightly below 20 GPa is driven by the softening of an acoustic phonon at the M point of the Brillouin zone. The coupling between this mode and anisotropic strain makes the transition slightly first order (with a volume variation of the order of 0.1%), and stabilizes the experimentally observed orthorhombic phase with respect to other competing symmetry-allowed structures

/pdf/phonon-softening-and-high-pressure-low-symmetry-phases-of-1rmwk0k28l.pdf

Phonon Softening and High-Pressure Low-Symmetry Phases of Cesium Iodide

The relative stability of different high-pressure phases of various Cesium Halides is studied from first principles and analyzed using the Landau theory of phase transitions We present results for CsI, CsBr, and CsCl up to pressures of about 100 GPa A cubic-to-orthorhombic transition, driven by the softening of an acoustic phonon at the M point of the Brillouin zone, is competing with the cubic-to-tetragonal martensitic transition typical of these compounds The phonon softening takes place only in CsI and CsBr at a residual volume of 064, 052 respectively A cubic-to-tetragonal instability is found instead to occur at 054 for all the compounds considered here The orthorhombic phase is stable only in CsI, whereas it is taken over by the tetragonal one in the case of CsBr Our analysis reveals the essential role played by the phonon-strain coupling in stabilizing the orthorhombic phase and in making the corresponding transition first-order

Paolo Giannozzi

Papers

High-pressure low-symmetry phases of cesium halides.

A Performance Study of Quantum ESPRESSO’s PWscf Code on Multi-core and GPU Systems

First-Principles Molecular Dynamics

Phonon Softening and High-Pressure Low-Symmetry Phases of Cesium Iodide

High-Pressure Low-Symmetry Phases of Cesium Halides from First Principle Techniques