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 report an ab initio multi-scale study of lead titanate using the Deep Potential (DP) models, a family of machine learning-based atomistic models, trained on ﬁrst-principles density functional theory data, to represent potential and polarization surfaces. Our approach includes anharmonic eﬀects beyond the limitations of reduced models and of the linear approximation for the polarization. The calculated enthalpy, spontaneous polarization, speciﬁc heat and dielectric susceptibility agree well with experiments on single crystals. In addition, we study how the free energy depends on the polarization with enhanced sampling methods, further supporting the ﬁrst-order and order-disorder character of the transition. The latter is evidenced by persistence of local dipoles above the transition temperature. The simulated free energy surface as a function of the global polarization leads to a Landau-Devonshire theory of the single domain crystal.

Ab initio multi-scale modeling of ferroelectrics: The case of PbTiO3

We report detailed and extensive first-principles molecular-dynamics (MD) simulations of the structure and electronic properties of amorphous InP produced by rapid quenching from the liquid. The structure of the material is found to be strongly ordered chemically, even though there is a significant number of coordination defects and despite the presence of odd-membered rings. We find, as a consequence, that there exists ``wrong bonds'' in the system, in an amount of about 8%; these result from the presence of coordination defects, not of local composition fluctuations, as has been conjectured. The system, in fact, is found to be over-coordinated, which might be the reason for the observed higher density of a-InP compared to c-InP. We have also investigated the possibility of pressure-amorphizing InP. Our calculations indicate that the cost of a transformation of the compressed zinc-blende crystal into an amorphous phase is so large that it is very unlikely that it would take place.

Amorphous indium phosphide from first principles

Following manuscript publication, P. Vajda has brought to our attention the existence of experimental references on the threshold displacement energy in vanadium, 29,31–35 which were inadvertently missed in our literature review. Additionally, P. Vajda also brought to our attention our erroneous description of literature data as being experimentally obtained, when in fact they were produced by computer simulation. Thus, we present: (i) a modified version of Fig. 2 that includes the measured TDE values in vanadium along the low index k100l, k110l, andk111l directions due to Kenik and Mitchell; 29

Erratum: Molecular dynamics study of the threshold displacement energy in vanadium [Phys. Rev. B 67, 134114 (2003)]

We investigate the quantum-mechanical localization of protonated and deterated isotopes in the symmetric low-barrier hydrogen-bonds of potassium dihydrogen phosphate (KDP) crystals in the paraelectric phase. The spatial density distributions of these hydrogen atoms are suspected to be responsible for the surprisingly large isotope effect observed for the ferroelectric phase transition in KDP. We employ ab initio path integral molecular dynamics simulations to obtain the nuclear real-space and momentum-space densities n(R) and n(k) of protons and deuterons, which are compared to experimental Neutron Compton Scattering data. Our results suggest a qualitative difference in the nature of the paraelectic phase in KDP between the two isotopes. We are able to discriminate between real quantum delocalization and vibration-assisted hopping and thus provide evidence for two distinct mechanisms of the ferroelectric phase transition in this class of materials.

The isotope-effect in the phase transition of KDP: New insights from ab initio path-integral simulations

The study of the structural and electronic properties of microclusters is a field of growing interest. Ab-initio molecular dynamics has provided a new and important tool for the theoretical approach to these questions. Here we present some very recent results on small semiconductor aggregates with special reference to calculations of equilibrium shapes and temperature effects. Results of simulations on alkali-metal microclusters are briefly mentioned.

Roberto Car

Papers

Ab initio multi-scale modeling of ferroelectrics: The case of PbTiO3

Amorphous indium phosphide from first principles

Erratum: Molecular dynamics study of the threshold displacement energy in vanadium [Phys. Rev. B 67, 134114 (2003)]

The isotope-effect in the phase transition of KDP: New insights from ab initio path-integral simulations

Ab-initio molecular dynamics studies of microclljsters