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.

The structural and dynamical properties of cubic ${\mathrm{H}}_{2}$O and ${\mathrm{D}}_{2}$O ice phases are studied using ab initio molecular dynamics combined with ultrasoft pseudopotentials. Phonon frequencies are extracted from the velocity autocorrelation functions; contributions from different normal modes in the phonon spectra are separated and easily identified. For the low-pressure phases, the agreement with the experimental data is reasonable and the isotope effects are well reproduced. High-pressure phases are also studied. The equations of state for cubic ice (ice ${\mathrm{I}}_{\mathit{c}}$), and for the ice VII-VIII-X family, are calculated. It is found that the local-density approximation must be augmented with gradient corrections in order to obtain a proper description of the hydrogen bond. Finally, the hydrogen-bond symmetrization, which is responsible for the transition from ice VII-VIII to ice X, is studied and is predicted to occur at 49 GPa. The nature of the phase transition is found to be that of a mode-softening transition. The corresponding symmetrization is also studied in ice ${\mathrm{I}}_{\mathit{c}}$, but it is found to occur at a pressure of 7 GPa at which ice ${\mathrm{I}}_{\mathit{c}}$ is unstable with respect to denser phases.

Ab initio studies on the structural and dynamical properties of ice.

Exact (Hartree-Fock) exchange is needed to overcome some of the limitations of local and semilocal approximations of density-functional theory. So far, however, computational cost has limited the use of exact exchange in plane-wave calculations for extended systems. We show that this difficulty can be overcome by performing a unitary transformation from Bloch to maximally localized Wannier functions in combination with an efficient technique to compute real-space Coulomb integrals. The resulting scheme scales linearly with system size. We validate the scheme with representative applications.

Order-N implementation of exact exchange in extended insulating systems

We calculate the near-edge x-ray-absorption fine structure of H(2)O in the gas, hexagonal ice, and liquid phases using heuristic density-functional based methods. We present a detailed comparison of our results with experiment. The differences between the ice and water spectra can be rationalized in terms of the breaking of hydrogen bonds around the absorbing molecule. In particular the increase in the pre-edge absorption feature from ice to water is shown to be due to the breaking of a donor hydrogen bond. We also find that in water approximately 19% of hydrogen bonds are broken.

Calculation of near-edge x-ray-absorption fine structure at finite temperatures: Spectral signatures of hydrogen bond breaking in liquid water

The electronic states and dynamical properties of dilute liquid K-KCl solutions are studied by simultaneous integration of the coupled time-dependent Schr\"odinger equation for the excess electrons and classical equations of motion for the ions. Excess electrons are found to spend most of their time in localized F-center states, whose size and shape can fluctuate significantly. Transport is mostly due to jumps between localized states, with a jumping rate \ensuremath{\simeq}3\ifmmode\times\else\texttimes\fi{}${10}^{12}$ ${\mathrm{s}}^{\mathrm{\ensuremath{-}}1}$. The optical excitation spectrum and the electron diffusion coefficient are calculated and found to be in agreement with the experimental data.

Localization, hopping, and diffusion of electrons in molten salts.

Water is of the utmost importance for life and technology. However, a genuinely predictive ab initio model of water has eluded scientists. We demonstrate that a fully ab initio approach, relying on the strongly constrained and appropriately normed (SCAN) density functional, provides such a description of water. SCAN accurately describes the balance among covalent bonds, hydrogen bonds, and van der Waals interactions that dictates the structure and dynamics of liquid water. Notably, SCAN captures the density difference between water and ice Ih at ambient conditions, as well as many important structural, electronic, and dynamic properties of liquid water. These successful predictions of the versatile SCAN functional open the gates to study complex processes in aqueous phase chemistry and the interactions of water with other materials in an efficient, accurate, and predictive, ab initio manner.

Roberto Car

Papers

Ab initio studies on the structural and dynamical properties of ice.

Order-N implementation of exact exchange in extended insulating systems

Calculation of near-edge x-ray-absorption fine structure at finite temperatures: Spectral signatures of hydrogen bond breaking in liquid water

Localization, hopping, and diffusion of electrons in molten salts.

Ab initio theory and modeling of water