Efficiency of ab-initio total energy calculations for metals and semiconductors using a plane-wave basis set

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

抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

We present ab initio quantum-mechanical molecular-dynamics simulations of the liquid-metal--amorphous-semiconductor transition in Ge. Our simulations are based on (a) finite-temperature density-functional theory of the one-electron states, (b) exact energy minimization and hence calculation of the exact Hellmann-Feynman forces after each molecular-dynamics step using preconditioned conjugate-gradient techniques, (c) accurate nonlocal pseudopotentials, and (d) Nos\'e dynamics for generating a canonical ensemble. This method gives perfect control of the adiabaticity of the electron-ion ensemble and allows us to perform simulations over more than 30 ps. The computer-generated ensemble describes the structural, dynamic, and electronic properties of liquid and amorphous Ge in very good agreement with experiment. The simulation allows us to study in detail the changes in the structure-property relationship through the metal-semiconductor transition. We report a detailed analysis of the local structural properties and their changes induced by an annealing process. The geometrical, bonding, and spectral properties of defects in the disordered tetrahedral network are investigated and compared with experiment.

Ab initio molecular-dynamics simulation of the liquid-metal-amorphous-semiconductor transition in germanium.

Constant-pressure constant-temperature {\it ab initio} molecular dynamics simulations at high temperatures have been used to study MgSiO$_3$ liquid, the major constituent of the Earth's lower mantle to conditions of the Earth's core-mantle boundary (CMB). We have performed variable-cell {\it ab initio} molecular dynamic simulations at relevant thermodynamic conditions across one of the measured melting curves. The calculated equilibrium volumes and densities are compared with the simulations using an orthorhombic perovskite configuration under the same conditions. For molten MgSiO$_3$, we have determined the diffusion coefficients and shear viscosities at different thermodynamic conditions. Our results provide new constraints on the properties of molten MgSiO$_3$ at conditions near the core-mantle boundary. The volume change on fusion is positive throughout the pressure-temperature conditions examined and ranges from 5% at 88 GPa and 3500 K to 2.9% at 120 GPa and 5000 K. Nevertheless, neutral or negatively buoyant melts from (Mg,Fe)SiO$_3$ perovskite compositions at deep lower mantle conditions are consistent with existing experimental constraints on solid-liquid partition coefficients for Fe. Our simulations indicate that MgSiO$_3$ is liquid at 120 GPa and 4500 K, consistent with the lower range of experimental melting curves for this material. Linear extrapolation of our results indicates that the densities of liquid and solid perovskite MgSiO$_3$ will become equal near 180 GPa.

First principles study of density, viscosity, and diffusion coefficients of liquid MgSiO3 at conditions of the Earth's deep mantle

Density functional theory calculations can be carried out with different levels of accuracy, forming a hierarchy that is often represented by the rungs of a ladder. Now a new method has been developed that significantly improves the accuracy of the 'third rung' when calculating the properties of diversely bonded systems.

Density functional theory: Fixing Jacob's ladder.

The Fermi operator, i.e., the Fermi-Dirac function of the system Hamiltonian, is a fundamental quantity in the quantum mechanics of many-electron systems and is ubiquitous in condensed-matter physics. In the last decade the development of accurate and numerically efficient representations of the Fermi operator has attracted lot of attention in the quest for linear scaling electronic structure methods based on effective one-electron Hamiltonians. These approaches have numerical cost that scales linearly with N, the number of electrons, and thus hold the promise of making quantummechanical calculations of large systems feasible. Achieving linear scaling in realistic calculations is very challenging. Formulations based on the Fermi operator are appealing because this operator gives directly the single-particle density matrix without the need for Hamiltonian diagonalization. At finite temperature the density matrix can be expanded in terms of finite powers of the Hamiltonian, requiring computations that scale linearly with N owing to the sparse character of the Hamiltonian matrix. 1 These properties of the Fermi operator are valid not only for insulators but also for metals, making formulations based on the Fermi operator particularly attractive. Electronic structure algorithms using a Fermi operator expansion FOE were introduced by Baroni and Giannozzi 2 and Goedecker et al. 3,4 see also the review article 5 . These authors proposed polynomial and rational approximations of the Fermi operator. Major improvements were made recently in a series of publications by Parrinello and coauthors, 6‐11 in which a new form of Fermi operator expansion was introduced based on the grand canonical formalism.

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Multipole representation of the Fermi operator with application to the electronic structure analysis of metallic systems

[1] Constant-pressure constant-temperature ab initio molecular dynamics simulations at high temperatures have been used to study MgSiO3, the major constituent of the Earth's lower mantle to conditions of the Earth's core-mantle boundary. The calculated equilibrium volumes and densities are compared with simulations using an orthorhombic perovskite configuration under the same conditions. For molten MgSiO3, we have determined the diffusion coefficients and shear viscosities at different thermodynamic conditions. Our results provide new constraints on the properties of molten MgSiO3 at conditions near the core-mantle boundary. The volume of the liquid is greater than that of the solid throughout the pressure-temperature conditions examined, and the volume change on fusion ranges from 5% at 88 GPa and 3500 K to 2.9% at 120 GPa and 5000 K. Existing experimental constraints on solid-liquid partition coefficients for Fe suggest that Fe is preferentially partitioned into the liquid. Such enrichment of Fe increases the density of the liquid, thus allowing the possibility of negatively buoyant melts from (Mg,Fe)SiO3 perovskite compositions at deep lower mantle conditions for plausible values of solid-liquid partition coefficients for Fe. At 120 GPa and 4500–5000 K, the diffusion coefficient of liquid MgSiO3 is 2–3 × 10−5 cm 2/s and the diffusion rates of the different chemical species are similar. The shear viscosity is estimated using Zwanzig's formula to be 19–31 cP under these conditions. On the basis of our calculated diffusivities, MgSiO3 is above the glass transition temperature at 120 GPa and 4500 K.

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First‐principles study of density, viscosity, and diffusion coefficients of liquid MgSiO3 at conditions of the Earth's deep mantle

We introduce a general framework for constructing coarse-grained potential models without ad hoc approximations such as limiting the potential to two- and/or three-body contributions. The scheme, called Deep Coarse-Grained Potential (abbreviated DeePCG), exploits a carefully crafted neural network to construct a many-body coarse-grained potential. The network is trained with full atomistic data in a way that preserves the natural symmetries of the system. The resulting model is very accurate and can be used to sample the configurations of the coarse-grained variables in a much faster way than with the original atomistic model. As an application we consider liquid water and use the oxygen coordinates as the coarse-grained variables, starting from a full atomistic simulation of this system at the ab-initio molecular dynamics level. We found that the two-body, three-body and higher order oxygen correlation functions produced by the coarse-grained and full atomistic models agree very well with each other, illustrating the effectiveness of the DeePCG model on a rather challenging task.

Roberto Car

Papers

First principles study of density, viscosity, and diffusion coefficients of liquid MgSiO3 at conditions of the Earth's deep mantle

Density functional theory: Fixing Jacob's ladder.

Multipole representation of the Fermi operator with application to the electronic structure analysis of metallic systems

First‐principles study of density, viscosity, and diffusion coefficients of liquid MgSiO3 at conditions of the Earth's deep mantle

DeePCG: constructing coarse-grained models via deep neural networks