In the second article of the series, we present the Gibbs2 code, a Fortran90 reimplementation of the original Gibbs program Comput. Phys. Commun. 158 (2004) 57 for the calculation of ...pressure–temperature dependent thermodynamic properties of solids under the quasiharmonic approximation. We have taken advantage of the detailed analysis carried out in the first paper to implement robust fitting techniques. In addition, new models to introduce temperature effects have been incorporated, from the simple Debye model contained in the original article to a full quasiharmonic model that requires the phonon density of states at each calculated volume. Other interesting novel features include the empirical energy corrections, that rectify systematic errors in the calculation of equilibrium volumes caused by the choice of the exchange-correlation functional, the electronic contributions to the free energy and the automatic computation of phase diagrams. Full documentation in the form of a userʼs guide and a complete set of tests and sample data are provided along with the source code.
Program title:Gibbs2
Catalogue identifier: AEJI_v1_0
Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEJI_v1_0.html
Program obtainable from: CPC Program Library, Queenʼs University, Belfast, N. Ireland
Licensing provisions: GNU General Public License, v3
No. of lines in distributed program, including test data, etc.: 936 087
No. of bytes in distributed program, including test data, etc.: 8 596 671
Distribution format: tar.gz
Programming language: Fortran90
Computer: Any running Unix/Linux
Operating system: Unix, GNU/Linux
Classification: 7.8
External routines: Part of the minpack, pppack and slatec libraries (downloaded from www.netlib.org) are distributed along with the program.
Nature of problem: Given the static E(V) curve, and possibly vibrational information such as the phonon density of states, calculate the equilibrium volume and thermodynamic properties of a solid at arbitrary temperatures and pressures in the framework of the quasiharmonic approximation.
Additional comments: A detailed analysis concerning the fitting of equations of state has been carried out in the first part of this article, and implemented in the code presented here.
Running time: The tests provided only take a few seconds to run.
► Calculation of thermodynamic properties from first principles data. ► Robust fitting of energy versus volume curves using averages of strain polynomials. ► Models for introducing ab initio temperature effects under the quasiharmonic approximation. ► A Fortran90 program implementing the techniques: Gibbs2.
Lumped hydrological models are catchment-scale representations of the transformation of precipitation into discharge. They are widely-used tools for real-time flow forecasting, flood design and ...climate change impact assessment, and they are often used for training and educational purposes. This article presents an R-package, airGR, to facilitate the implementation of the GR lumped hydrological models (including GR4J) and a snow-accumulation and melt model. The package allows users to calibrate and run hourly to annual models on catchment sets and to analyse their outputs. While the core of the models is implemented in Fortran, the user can manage the input/output data within R. A number of options and plotting functions are proposed to ease automate tests and analyses of the results. The codes are flexible enough to include external models, other calibration routines or efficiency criteria. To illustrate the features of airGR, we present one application example for a French mountainous catchment.
EPW (
Electron–
Phonon coupling using
Wannier functions) is a program written in
Fortran90 for calculating the electron–phonon coupling in periodic systems using density-functional perturbation ...theory and maximally localized Wannier functions.
EPW can calculate electron–phonon interaction self-energies, electron–phonon spectral functions, and total as well as mode-resolved electron–phonon coupling strengths. The calculation of the electron–phonon coupling requires a very accurate sampling of electron–phonon scattering processes throughout the Brillouin zone, hence reliable calculations can be prohibitively time-consuming.
EPW combines the Kohn–Sham electronic eigenstates and the vibrational eigenmodes provided by the
Quantum ESPRESSO package (see Giannozzi et al., 2009
1) with the maximally localized Wannier functions provided by the
wannier90 package (see Mostofi et al., 2008
2) in order to generate electron–phonon matrix elements on arbitrarily dense Brillouin zone grids using a generalized Fourier interpolation. This feature of
EPW leads to fast and accurate calculations of the electron–phonon coupling, and enables the study of the electron–phonon coupling in large and complex systems.
Program title: EPW
Catalogue identifier: AEHA_v1_0
Program summary URL:
http://cpc.cs.qub.ac.uk/summaries/AEHA_v1_0.html
Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland
Licensing provisions: GNU Public License
No. of lines in distributed program, including test data, etc.: 304 443
No. of bytes in distributed program, including test data, etc.: 1 487 466
Distribution format: tar.gz
Programming language: Fortran 90
Computer: Any architecture with a Fortran 90 compiler
Operating system: Any environment with a Fortran 90 compiler
Has the code been vectorized or parallelized?: Yes, optimized for 1 to 64 processors
RAM: Heavily system dependent, as small as a few MB
Supplementary material: A copy of the “EPW/examples” directory containing the phonon binary files can be downloaded
Classification: 7
External routines: MPI, Quantum-ESPRESSO package 1, BLAS, LAPACK, FFTW. (The necessary Blas, Lapack and FFTW routines are included in the Quantum-ESPRESSO package 1.)
Nature of problem: The calculation of the electron–phonon coupling from first-principles requires a very accurate sampling of electron–phonon scattering processes throughout the Brillouin zone; hence reliable calculations can be prohibitively timeconsuming.
Solution method: EPW makes use of a real-space formulation and combines the Kohn–Sham electronic eigenstates and the vibrational eigenmodes provided by the Quantum-ESPRESSO package with the maximally localized Wannier functions provided by the wannier90 package in order to generate electron–phonon matrix elements on arbitrarily dense Brillouin zone grids using a generalized Fourier interpolation.
Running time: Single processor examples typically take 5–10 minutes.
References:
1
P. Giannozzi, et al., J. Phys. Condens. Matter 21 (2009), 395502,
http://www.quantum-espresso.org/.
This paper provides FORTRAN subroutines for the calculation of the partially-Correlated quadratic-Speed-Dependent Hard-Collision (pCqSDHC) profile and of its two limits: the quadratic-Speed-Dependent ...Voigt (qSDV) and the quadratic-Speed-Dependent Hard-Collision (qSDHC) profiles. Numerical tests successfully confirm the analytically derived fact that all these profiles can be expressed as combinations of complex Voigt probability functions. Based on a slightly improved version of the CPF subroutine Humlicek. J Quant Spectrosc Radiat Transfer 1979;21:309 for the calculation of the complex probability function, we show that the pCqSDHC, qSDHC and qSDV profiles can be quickly calculated with an accuracy better than 10−4.
•FORTRAN subroutines of some speed-dependent profiles are provided.•These profiles can be expressed as combinations of the complex probability function.•They can be accurately calculated with reasonable computer cost.
The knowledge of the local electronic structure of heterogeneous solid materials is crucial for understanding their electronic, magnetic, transport, optical, and other properties. VASP, one of the ...mostly used packages for density-functional calculations, provides local electronic structure either by projecting the electronic wave functions on atomic spheres, or as a band-decomposed partial charge density. Here, we present a simple tool which takes the partial charge density and the energy eigenvalues calculated by VASP as input and constructs local charge and spin densities. The new data provides a much better spatial understanding than the projection on the atomic spheres. It can be visualized directly in the real space e.g. with Vesta, or averaged along planes spanned by two of the lattice vectors of the periodic unit cell. The plane-averaged local (spin) density of states can be easily plotted e.g. as color-coded data using almost any plotting program. DensityTool can be applied to visualize and understand the local electronic structure of any system calculated with VASP. We expect it to be useful especially for researchers concerned with inhomogeneous systems, such as interfaces, defects, surfaces, adsorbed molecules, or hybrid inorganic-organic composites.
Program Title: DensityTool
CPC Library link to program files:https://doi.org/10.17632/26mcg4jwvd.1
Developer's repository link:https://github.com/llodeiro/DensityTool
Licensing provisions: MIT
Programming language: FORTRAN
Supplementary material: A complementary User Manual and examples can be found in the developer's repository link.
Nature of problem: Total and local density of states (LDOS) are widely-used quantities for understanding the electronic structure of condensed matter. In VASP, one of the mostly used packages for numerically solving the Kohn-Sham equations of density-functional theory, one does not directly obtain the LDOS. Usually, one works with partial density of states (PDOS), where the wave function is projected onto atomic orbitals. Alternatively, it is possible to calculate the band- and wavevector-dependent charge densities. Together with the band structure, LDOS can be obtained using post-processing tools.
Solution method: DensityTool combines the band structure with band- and wavevector-dependent charge densities calculated by VASP to construct LDOS. In addition, spin-resolved LDOS (LSDOS) can be calculated for magnetic systems. Thus obtained LDOS and LSDOS can be further processed with DensityTool. In particular, it can be averaged along chosen spatial directions, which is convenient for example to demonstrate the spatially-resolved electronic structure of inhomogeneous systems.
DensityTool can handle all three types of approaches implemented in VASP (non-magnetic, collinear magnetic, non-collinear magnetic including spin-orbit coupling), as well as all types of self-consistent band calculations as DFT (e.g., LDA, GGA, mGGA, BJ, and hybrid exchange-correlation functionals) and HF.
For convenience, the output of DensityTool follows the format of VASP (the CHGCAR file), which can be easily used in other programs for visualization. We provide a sample python script to plot averaged L(S)DOS from the calculated data.
After its introduction by Koenker and Basset (1978), quantile regression has become an important and popular tool to investigate the conditional response distribution in regression. The R package ...bayesQR contains a number of routines to estimate quantile regression parameters using a Bayesian approach based on the asymmetric Laplace distribution. The package contains functions for the typical quantile regression with continuous dependent variable, but also supports quantile regression for binary dependent variables. For both types of dependent variables, an approach to variable selection using the adaptive lasso approach is provided. For the binary quantile regression model, the package also contains a routine that calculates the fitted probabilities for each vector of predictors. In addition, functions for summarizing the results, creating traceplots, posterior histograms and drawing quantile plots are included. This paper starts with a brief overview of the theoretical background of the models used in the bayesQR package. The main part of this paper discusses the computational problems that arise in the implementation of the procedure and illustrates the usefulness of the package through selected examples.
An educational computational application for analyzing plane stress problems oriented to engineering students called EsfPlano2D is presented to motivate students to study the subject and strengthen ...didactic strategies in the classroom. The application assists the step-by-step calculation of plane stress problems, which is a fundamental topic in teaching the subject of Mechanics of Materials in engineering careers. The application is a computer program developed in Fortran, linked to the free Computer Algebra System MAXIMA to plot Mohr’s circle of stresses. The developed tool is user-friendly and completely solves the plane stress problem, the associated deformations, and the strain energy by drawing Mohr’s circle of plane stresses. A validation case is presented with a typical example of the mechanics of materials. The results show the feasibility of using custom-designed tools to strengthen classroom learning and autonomous work.
The Sunway TaihuLight supercomputer is the world＇s first system with a peak performance greater than 100 PFlops. In this paper, we provide a detailed introduction to the TaihuLight system. In ...contrast with other existing heterogeneous supercomputers, which include both CPU processors and PCIe-connected many-core accelerators （NVIDIA GPU or Intel Xeon Phi）, the computing power of TaihuLight is provided by a homegrown many-core SW26010 CPU that includes both the management processing elements （MPEs） and computing processing elements （CPEs） in one chip. With 260 processing elements in one CPU, a single SW26010 provides a peak performance of over three TFlops. To alleviate the memory bandwidth bottleneck in most applications, each CPE comes with a scratch pad memory, which serves as a user-controlled cache. To support the parallelization of programs on the new many-core architecture, in addition to the basic C/C＋＋ and Fortran compilers, the system provides a customized Sunway OpenACC tool that supports the OpenACC 2.0 syntax. This paper also reports our preliminary efforts on developing and optimizing applications on the TaihuLight system, focusing on key application domains, such as earth system modeling, ocean surface wave modeling, atomistic simulation, and phase-field simulation.
We present an open-source software framework called PERMIX for multiscale modeling and simulation of fracture in solids. The framework is an object oriented open-source effort written primarily in ...Fortran 2003 standard with Fortran/C++ interfaces to a number of other libraries such as LAMMPS, ABAQUS, LS-DYNA and GMSH. Fracture on the continuum level is modeled by the extended finite element method (XFEM). Using several novel or state of the art methods, the piece software handles semi-concurrent multiscale methods as well as concurrent multiscale methods for fracture, coupling two continuum domains or atomistic domains to continuum domains, respectively. The efficiency of our open-source software is shown through several simulations including a 3D crack modeling in clay nanocomposites, a semi-concurrent FE-FE coupling, a 3D Arlequin multiscale example and an MD-XFEM coupling for dynamic crack propagation.
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