Layla Martin-Samos

QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials

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.

Ab initio complex band structure of conjugated polymers: Effects of hydrid density functional theory and GW schemes

The non-resonant tunneling regime for charge transfer across nanojunctions is critically dependent on the so-called \beta{} parameter, governing the exponential decay of the current as the length of the junction increases. For periodic materials, this parameter can be theoretically evaluated by computing the complex band structure (CBS) -- or evanescent states -- of the material forming the tunneling junction. In this work we present the calculation of the CBS for organic polymers using a variety of computational schemes, including standard local, semilocal, and hybrid-exchange density functionals, and many-body perturbation theory within the GW approximation. We compare the description of localization and \beta{} parameters among the adopted methods and with experimental data. We show that local and semilocal density functionals systematically underestimate the \beta{} parameter, while hybrid-exchange schemes partially correct for this discrepancy, resulting in a much better agreement with GW calculations and experiments. Self-consistency effects and self-energy representation issues of the GW corrections are discussed together with the use of Wannier functions to interpolate the electronic band-structure.

SaX: An open source package for electronic-structure and optical-properties calculations in the GW approximation ☆

Abstract We present here SaX (Self-energies and eXcitations), a plane-waves package aimed at electronic-structure and optical-properties calculations in the GW framework, namely using the GW approximation for quasi-particle properties and the Bethe–Salpeter equation for the excitonic effects. The code is mostly written in FORTRAN90 in a modern style, with extensive use of data abstraction (i.e. objects). SaX employs state of the art techniques and can treat large systems. The package is released with an open source license and can be also download from http://www.sax-project.org/ . Program summary Program title: SaX (Self-energies and eXcitations) Catalogue identifier: AEDF_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEDF_v1_0.html Program obtainable from: CPC Program Library, Queens University, Belfast, N. Ireland Licensing provisions: GNU General Public License No. of lines in distributed program, including test data, etc.: 779 771 No. of bytes in distributed program, including test data, etc.: 4 894 755 Distribution format: tar.gz Programming language: FORTRAN, plus some C utilities Computer: Linux PC, Linux clusters, IBM-SP5 Operating system: Linux, Aix Has the code been vectorised or parallelized?: Yes RAM: depending on the system complexity Classification: 7.3 External routines: Message-Passing Interface (MPI) to perform parallel computations. ESPRESSO ( http://www.quantum-espresso.org ) Nature of problem: SaX is designed to calculate the electronic band-structure of semiconductors, including quasi-particle effects and optical properties including excitonic effects. Solution method: The electronic band-structure is calculated using the GW approximation for the self-energy operator. The optical properties are calculated solving the Bethe–Salpeter equation in the GW approximation. The wavefunctions are expanded on a plane-waves basis set, using norm-conserving pseudopotentials. Restrictions: Many objects are non-local matrix represented in plane wave basis sets. The memory required by the program in the allocation of such objects increases with the increase of the simulation cell volume. Other quantities are built calculating electronic transitions, so that the computational time increase with their number, and scales as N v × N c × N k 2 , where N v and N c are the number of valence and conduction bands implied in the transition and N k is the number of special k vectors. Symmetries are not exploited yet. Finally, metallic systems cannot be studied yet. Unusual features: SaX is written using FORTRAN90 in an object-oriented way. Thus, it is easy to add new features and to reuse the code. Running time: The 3 examples, contained in the distribution file, each take only a few seconds to run. For systems of interest, the run may take a number of days with a typical memory allocation of 1600 Mb per processor.

Ge(2), Ge(1) and Ge-E′ centers in irradiated Ge-doped silica: a first-principles EPR study

We present a first-principles investigation of Ge paramagnetic centers in Ge-doped vitreous silica (v-SiO2) based on calculations of the electron paramagnetic resonance (EPR) parameters. We infer, by analyzing g-values differences with respect to our Ge-E′ configurations, that the EPR signal of the Ge(2) center may arise from Ge forward-oriented (Ge-FO) configurations, where the unpaired spin is localized at a three-fold Ge atom featuring a weak bond with a three-fold O atom, ∼ 1.9 A long. Moreover we show that two-fold Ge atoms, i.e. the germanium lone pair centers (GLPC), under irradiation can easily convert into Ge-FO configurations consistently with experimental observations.

Irradiation Temperature Influence on the In Situ Measured Radiation Induced Attenuation of Ge-Doped Fibers

We report an experimental investigation on the radiation-induced attenuation (RIA) in the ultraviolet-visible domain for Ge-doped optical fibers, during X-ray (10 keV) exposure at different temperatures. The objective is to characterize the impact of the irradiation temperature on the RIA levels and kinetics. Our data highlight that for dose exceeding 1 kGy(SiO2) the RIA spectrum changes with the irradiation temperature. In particular, for wavelengths below 470 nm the RIA depends both on the dose and on the irradiation temperature, whereas at higher wavelengths the RIA depends only on the dose. From the microscopic point of view the origin of this behavior is explained by a larger impact of the irradiation temperature on the Ge(1) defects generation mechanism with respect to the one of GeX defects, which appears as poorly temperature sensitive in the tested range. This finding prevents us from easily establishing a conclusive relation between the generation mechanisms of these two types of defects. The lower content of radiation induced Ge(1), in fiber irradiated at higher temperature, is supported by the electron paramagnetic resonance (EPR) results acquired after the irradiation. In situ RIA and postmortem EPR data show a significant correspondence of the Ge(1) growth as a function of the dose. Confocal microscopy luminescence experiments indicate that the non-bridging oxygen hole center concentration is higher at 473 K in comparison with those observed at 300 and 373 K.

Optical absorption spectra of P defects in vitreous silica

We present an investigation of the optical properties of diamagnetic P centers in P-doped silica by means of first-principles calculations, including many-body perturbation theory (GW and Bethe-Salpeter Equation) techniques. The calculated absorption spectra indicate that the 6.9 eV band is originated from the presence of a large number of [(O–)3P(=O)]0 tetrahedra, while only a negligible number of [(O–)2P(=O)2]− tetrahedra could occur. Furthermore we show that positively charged substitutional P atoms can affect the silica absorption spectrum only above ∼8 eV, while three-fold P defects are not likely to occur as they should give rise to strong features, not observed, below ∼6.5 eV.

Effect of irradiation temperature on the radiation induced attenuation of Ge-doped fibers

The UV-visible radiation induced attenuation (RIA) was studied in Ge-doped optical fibers, during X-ray (10 keV) irradiations at different temperatures. By comparing the spectra recorded in dissimilarly irradiated samples we evidenced the impact of the irradiation temperature. In details, we highlighted that, from a certain dose, increasing the temperature the RIA decreases for wavelengths lower than 470 nm, whereas at higher wavelengths the RIA depends only on the dose. Such findings suggest that it is possible to distinguish the irradiation temperature by comparing the signal at two different wavelengths. From the microscopic point of view, it appears that the RIA behavior is mainly related to a dissimilar content of induced Ge(1) defects, whereas the so called GeX defects features only small variations. The impact of the irradiation temperature on the Ge(1) induced concentration, as a function of the irradiation temperature, is confirmed by the post-irradiation electron paramagnetic resonance measurements that we acquired for samples that were irradiated at room temperature and at 200 °C.

QMMMW: A wrapper for QM/MM simulations with QUANTUM ESPRESSO and LAMMPS

We present QMMMW, a new program aimed at performing Quantum Mechanics/Molecular Mechanics (QM/MM) molecular dynamics. The package operates as a wrapper that patches PWscf code included in the QUANTUM ESPRESSO distribution and LAMMPS Molecular Dynamics Simulator. It is designed with a paradigm based on three guidelines: (i) minimal amount of modifications on the parent codes, (ii) flexibility and computational efficiency of the communication layer and (iii) accuracy of the Hamiltonian describing the interaction between the QM and MM subsystems. These three features are seldom present simultaneously in other implementations of QMMM. The QMMMW project is hosted by qe-forge at (http://qe-forge.org/gf/project/qmmmw/). Program summary Program title: QMMMW Catalogue identifier: AEWS_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEWS_v1_0.html Program obtainable from: CPC Program Library, Queens University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 7544822 No. of bytes in distributed program, including test data, etc.: 121657035 Distribution format: tar.gz Programming language: Python, C and Fortran95. Computer: All Linux based workstations and parallel supercomputers. Operating system: GNU/Linux. Classification: 3, 7.7, 16.1, 23. Nature of problem: Calculation of the hybrid quantum mechanics/molecular mechanics of molecular systems. Solution method: With the current patches QMMMW allows the performance of QM/MM simulations with mechanical coupling (i.e. classical point charge based, QM and the MM system interacts electrostatically only at the classical level.) and electrostatic coupling according to the scheme proposed by Laio, VandeVondele and Rothlisberger, J. Chem Phys. 116, 6941 (2002). Restrictions: Only coded for orthorhombic cell. The interactions coupling QM and MM degrees of freedom cannot be bonded. The QM region can only be modeled with PWscf. Unusual features: Minimal amount of modifications to the parent codes. Flexibility and computational efficiency of the communication layer. Accuracy of the Hamiltonian describing the interaction between the QM and MM subsystems. Additional comments: Relevant versions of QUANTUM ESPRESSO and LAMMPS are included in the distribution file and in the number of lines and number of bytes shown. 11111 The distribution file for this program is over 121 Mbytes and therefore is not delivered directly when download or Email is requested. Instead a html file giving details of how the program can be obtained is sent. 11111 Running time: From a few minutes for small molecules on serial machines up to many hours on multiple processors for complex nanosystems with hundreds of atoms

Simulation of Single-Particle Displacement Damage in Silicon—Part III: First Principle Characterization of Defect Properties

A first principle study of the defects generated by displacement cascades in silicon is performed. This paper is particularly focused on two defect configurations; the divacancy and the tri-interstitial, both identified in previous molecular dynamics and kinetic activation relaxation technique simulations. By combining structural, energy and migration properties evaluated within the framework of the standard density functional theory and electronic properties calculated within the

Photoactivated processes in optical fibers: generation and conversion mechanisms of twofold coordinated Si and Ge atoms

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