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.

We extend to quenched disordered systems the variational scheme for real space renormalization group calculations that we recently introduced for homogeneous spin Hamiltonians. When disorder is present our approach gives access to the flow of the renormalized Hamiltonian distribution, from which one can compute the critical exponents if the correlations of the renormalized couplings retain finite range. Key to the variational approach is the bias potential found by minimizing a convex functional in statistical mechanics. This potential reduces dramatically the Monte Carlo relaxation time in large disordered systems. We demonstrate the method with applications to the two-dimensional dilute Ising model, the random transverse field quantum Ising chain, and the random field Ising in two and three dimensional lattices.

Monte Carlo Renormalization Group for Systems with Quenched Disorder

How to partition a chemical system into its constituent parts is a classic problem of theoretical chemistry. A formally exact solution has recently been developed, partition theory (PT), based on density functional theory [Cohen, M. H.; Wasserman, A. J. Phys. Chem. A 2007, 111, 2229]. PT presents a constrained optimization problem to which the Car-Parrinello (CP) method of electronic structure theory is well suited. We propose here a generalization of the CP method suitable for PT and thereby make way for its practical numerical implementation. We demonstrate that this CP implementation of PT need not increase the complexity of the computation of the system's electronic structure. The scheme provides an exact DFT formulation of, e.g., atoms in molecules theory that is amenable to numerical implementation.

Dynamical optimization for partition theory.

We investigate static and dynamic properties of hydrogen in crystalline and amorphous silicon by means of ab initio molecular dynamics simulations. In the crystalline case we focus mainly on the diffusion process of an isolated positively charged hydrogen impurity at high temperature. In the amorphous case we analyze the local order and the dynamical properties corresponding to an atomic hydrogen concentration of ~ 11%, typical of a device quality material. In both crystalline and amorphous cases, our results are in good agreement with available experimental data and give unique insight into the microscopic details of hydrogen incorporation in silicon.

https://www.cambridge.org/core/services/aop-cambridge-core/content/view/S1946427400465632

Hydrogen in Crystalline and Amorphous Silicon

We model, via large-scale molecular dynamics simulations, the isothermal compression of low-density amorphous ice (LDA) to generate high-density amorphous ice (HDA) and the corresponding decompression extending to negative pressures to recover the low-density amorphous phase (LDAHDA). Both LDA and HDA are nearly hyperuniform and are characterized by a dynamical HBN, showing that amorphous ices are nonstatic materials and implying that nearly hyperuniformity can be accommodated in dynamical networks. In correspondence with both the LDA-to-HDA and the HDA-to-LDAHDA phase transitions, the (partial) activation of rotational degrees of freedom activates a cascade effect that induces a drastic change in the connectivity and a pervasive reorganization of the HBN topology which, ultimately, break the samples' hyperuniform character. Key to this effect is the rapid rate at which changes occur, and not their magnitude. The inspection of structural properties from the short- to the long-range shows that signatures of metastability are present at all length-scales, hence providing further solid evidence in support of the liquid-liquid critical point scenario. LDA and LDAHDA differ in terms of HBN and structural properties, implying that they are distinct low-density glasses. Our work unveils the role of molecular rotations in the phase transitions between amorphous ices and shows how the unfreezing of rotational degrees of freedom generates a cascade effect that propagates over multiple length-scales. Our findings greatly improve our basic understanding of water and amorphous ices and can potentially impact the field of molecular network-forming materials at large.

Molecular Rotations, Multiscale Order, Hyperuniformity, and Signatures of Metastability during the Compression/Decompression Cycles of Amorphous Ices.

PbTiO3 is a prototypical ferroelectric material that exhibits a single structural phase transition (cubic to tetragonal): it is a soft mode driven, predominantly displacive, transition. In this paper, we study the behavior of PbTiO3 at finite temperature by ab‐initio molecular dynamics simulations. In this approach classical mechanics is used to describe nuclear dynamics, while the interatomic potential is generated on the fly from the ground state of the electrons within density functional theory. Fluctuations of volume and shape of the simulation cell are included by means of Parrinello‐Rahman constant pressure scheme. Extensive convergence studies based on static calculations indicate that a 3×3×3 supercell containing 135 atoms, with a single k‐point sampling, is sufficient to represent accurately the T = 0 energetics of this material. Although computationally demanding, ab‐initio molecular dynamics simulations for PbTiO3 using a 3×3×3 cell are feasible with current computational methodologies. Here we report preliminary results of simulations that are both below and above the phase‐transition temperature. We discuss, in particular, how phonon softening occurs with temperature and how thermal expansion affects the results.

Roberto Car

Papers

Monte Carlo Renormalization Group for Systems with Quenched Disorder

Dynamical optimization for partition theory.

Hydrogen in Crystalline and Amorphous Silicon

Molecular Rotations, Multiscale Order, Hyperuniformity, and Signatures of Metastability during the Compression/Decompression Cycles of Amorphous Ices.

PbTiO3 at Finite Temperature: An Ab‐initio Molecular Dynamics Study