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 Classical Lattice Models with Quenched Disorder.

We propose an approach for learning accurately the dynamics of slow collective variables from atomistic data obtained from ab-initio quantum mechanical theory, using generalized Langevin equations (GLE). The force ﬁelds, memory kernel, and noise generator are constructed within the Mori-Zwanzig formalism under the constraint imposed by the ﬂuctuation-dissipation theorem. Com-bined with Deep Potential Molecular Dynamics (DeePMD) and density functional theory, this GLE approach opens the door to carry out ﬁrst-principles multi-scale modeling for a variety of systems. Here, we demonstrate this capability with a study of the dynamics of twin domain walls in ferroelectric lead titanate. The importance of memory eﬀects is illustrated by the fact that while ab-initio GLE agrees well with molecular dynamics at near-equilibrium conditions, Markovian Langevin dynamics underestimates the rate of rare events by several orders of magnitude.

Ab Initio Generalized Langevin Equations

We employ classical molecular dynamics simulations to investigate the molecular-level structure of water during the isothermal compression of hexagonal ice (I$h$) and low-density amorphous (LDA) ice at low temperatures. In both cases, the system transforms to high-density amorphous ice (HDA) via a first-order-like phase transition. We employ a sensitive local order metric (LOM) [Martelli et. al., Phys. Rev. B, 97, 064105 (2018)], that can discriminate among different crystalline and non crystalline ice structures and is based on the positions of the oxygen atoms in the first and/or second hydration shell. Our results confirm that LDA and HDA are indeed amorphous, i.e., they lack of polydispersed ice domains. Interestingly, HDA contains a small number of domains that are reminiscent of the unit cell of ice IV, although the hydrogen-bond network (HBN) of these domains differ from the HBN of ice IV. The presence of ice IV-like domains provides some support to the hypothesis that HDA could be the result of a detour on the HBN rearrangement along the I$h$-to-ice IV pressure induced transformation. Both nonequilibrium LDA-to-HDA and I$h$-to-HDA transformations are two-steps processes where a small distortion of the HBN first occurs at low pressures and then, a sudden, extensive re-arrangement of hydrogen bonds at the corresponding transformation pressure follows. Interestingly, the I$h$-to-HDA and LDA-to-HDA transformations occur when LDA and I$h$ have similar local order, as quantified by the site-averaged LOMs. Since I$h$ has a perfect tetrahedral HBN, while LDA does not, it follows that higher pressures are needed to transform I$h$ into HDA than that for the conversion of LDA to HDA. In correspondence with both first-order-like phase transitions, the samples are composed of a large HDA cluster that percolates within the I$h$/LDA samples.

Searching for crystal-ice domains in amorphous ices

The structural and electronic properties of liquid arsenic are calculated using density-functional quantum theory to calculate forces and trajectories of atoms. A semiconducting gap of 0.4 eV is found, and a coordination number of 2.8, close to the experimental values of 0.5 eV and 3. Our results support the existence of a Peierls-type distortion in liquid arsenic.

Properties of Liquid As: A First Principles Calculation

We propose a quantum Monte Carlo approach to solve the many-body Schrödinger equation for the electronic ground state. The method combines optimization from variational Monte Carlo and propagation from auxiliary field quantum Monte Carlo in a way that significantly alleviates the sign problem. In application to molecular systems, we obtain highly accurate results for configurations dominated by either dynamic or static electronic correlation.

Roberto Car

Papers

Monte Carlo Renormalization Group for Classical Lattice Models with Quenched Disorder.

Ab Initio Generalized Langevin Equations

Searching for crystal-ice domains in amorphous ices

Properties of Liquid As: A First Principles Calculation

Hybrid Auxiliary Field Quantum Monte Carlo for Molecular Systems.