cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/7drvvhbw92.1
title: Multi-photon Monte Carlo event generator KKMCee for lepton and quark pair production in lepton colliders

description: We present the KKMCee 5.00.2 Monte Carlo event generator for lepton and quark pair production for the high energy electron-positron annihilation process. It is still the most sophisticated event generator for such processes. Its entire source code is re-written in the modern C++ language. It reproduces all features of the older KKMC code in Fortran 77. However, a number of improvements in the Monte Carlo algorithm are also implemented. Most importantly, it is intended to be a starting point for the future improvements, which will be mandatory for the future high precision lepton collider projects. As in the older version, in addition to higher order QED corrections, it includes so-called O(α^1.5) genuine weak corrections using a version of the classic DIZET library and polarized τ decays using TAUOLA program. Both DIZET and TAUOLA external libraries are still in Fortran 77. In addition, a HEPMC3 interface to other MC programs, like parton showers and detector simulation, replaces the older HepEvt interface. The HEPMC3 interface is also exploited in the implementation of the additional photon final state emissions in τ decays using an external PHOTOS library rewritten in C.
DOI: 10.5519/qd.d3v1k5xv
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (8 records)
DOI: 10.17632/7zw25f428t.1
title: SBETHE: Stopping powers of materials for swift charged particles from the corrected Bethe formula

description: The Fortran program sbethe calculates the stopping power of materials for swift charged particles with small charges (electrons, muons, protons, their antiparticles, and alphas). The electronic stopping power is computed from the corrected Bethe formula, with the shell correction derived from numerical calculations with the plane-wave Born approximation (PWBA) for atoms, which were based on an independent-electron model with the Dirac–Hartree–Fock–Slater self-consistent potential for the ground-state configuration of the target atom. The density effect correction is evaluated from an empirical optical oscillator strength (OOS) model based on atomic subshell contributions obtained from PWBA calculations. For projectiles heavier than the electron, the Barkas correction is evaluated from the OOS model, and the Lindhard–Sørensen correction is estimated from an accurate parameterization of its numerical values. The calculated electronic stopping power is completely determined by a single empirical parameter, the mean excitation energy or I value of the material. The radiative stopping power for electrons, and positrons, is evaluated by means of Seltzer and Berger's cross section tables for bremsstrahlung emission. The program yields reliable stopping powers and particle ranges for arbitrary materials and projectiles with kinetic energy larger than a certain cutoff value E_cut, which is specific of each projectile kind. The program is accompanied by an extensive database that contains tables of relevant energy-dependent atomic quantities for all the elements from hydrogen to einsteinium. sbethe may be used to generate basic information for dosimetry calculations and Monte Carlo simulations of radiation transport, and as a pedagogical tool.
DOI: 10.17632/8j3ntp5c7k.1
title: Thermo4PFM: Facilitating Phase-field simulations of alloys with thermodynamic driving forces

description: Phase-field modeling is a popular front-tracking approach used to model solidification. Its time-evolution equations are often coupled to alloy composition and/or thermal diffusion in high-resolution multiphysics approaches. Materials thermodynamic properties tabulated in CALPHAD databases can be used for phase-field modeling to parameterize bulk energies of alloys. In addition, they can be naturally integrated into models such as the Kim-Kim-Suzuki (KKS) model where driving forces depend on the differences between chemical potentials of co-existing phases. In that case, a small system of coupled nonlinear equations needs to be solved at every point in space where the phase-field order parameter is to be updated and evolved in time. We present Thermo4PFM, a solver for the KKS equations for binary and ternary alloys, with two or three phases, and parameterized with CALPHAD models. Thermo4PFM is open source, written in C++, and can take advantage of Graphics Processing Units (GPU) accelerators. Using OpenMP offload capabilities for C++ classes, an excellent performance is demonstrated on GPU using the LLVM compiler. CALPHAD data is read from simple JSON files using an open source parser from the boost library.
DOI: 10.17632/8kzsyn79gh.1
title: MRADSIM-Converter: A new software for STEP to GDML conversion

description: Radiation effects analysis of instruments operative in harsh radiation environment is crucial for performance and functionality of electronic devices and components. Engineering design of instruments is usually carried out in Computer Aided Design (CAD) engineering software. Geant4-based Monte Carlo codes are extensively used for particle transport simulation and analysis. However, Geant4 is not prepared to accept CAD Standard for The Exchange of Product data (STEP) format. MRADSIM-Converter is a new software for STEP to Geometry Description Markup Language (GDML) format conversion, readable by Geant4-based Monte Carlo codes. Its validation with two different converters confirms its higher speed for importing CAD geometries with arbitrary size and complexity having a user-friendly interface for modifying volumes properties.
DOI: 10.17632/bd5m7tf5yr.1
title: GPU accelerated Monte Carlo simulation of high-intensity pulsed laser-electron interaction

description: We present a new Monte Carlo code for simulating strong field QED effects in high intensity Laser-Electron collisions, accelerated by massively parallel computations on GPUs. The numerical simulation tool is paired with a separate code which solves the Stratton-Chu vector diffraction integrals given the incoming beam on the focusing mirror, to more accurately describe the electromagnetic field at the focus of the mirror.
DOI: 10.17632/bhrtdbkxmy.1
title: Identification of vortices in quantum fluids: Finite element algorithms and programs

description: We present finite-element numerical algorithms for the identification of vortices in quantum fluids described by a macroscopic complex wave function. Their implementation using the free software FreeFem++ is distributed with this paper as a post-processing toolbox that can be used to analyse numerical or experimental data. Applications for Bose-Einstein condensates (BEC) and superfluid helium flows are presented. Programs are tested and validated using either numerical data obtained by solving the Gross-Pitaevskii equation or experimental images of rotating BEC. Vortex positions are computed as topological defects (zeros) of the wave function when numerical data are used. For experimental images, we compute vortex positions as local minima of the atomic density, extracted after a simple image processing. Once vortex centers are identified, we use a fit with a Gaussian to precisely estimate vortex radius. For vortex lattices, the lattice parameter (inter-vortex distance) is also computed. The post-processing toolbox offers a complete description of vortex configurations in superfluids. Tests for two-dimensional (giant vortex in rotating BEC, Abrikosov vortex lattice in experimental BEC) and three-dimensional (vortex rings, Kelvin waves and quantum turbulence fields in superfluid helium) configurations show the robustness of the software. The communication with programs providing the numerical or experimental wave function field is simple and intuitive. The post-processing toolbox can be also applied for the identification of vortices in superconductors.
DOI: 10.17632/bj27474v6f.1
title: VELAS: An open-source toolbox for visualization and analysis of elastic anisotropy

description: Although elastic properties and their anisotropy play a crucial role in materials science and technology, it is not straightforward to visualize how properties such as shear modulus vary with the direction of stress/strain. Here, written in GNU Octave, we have developed an easy-to-use, flexible, and user-friendly open-source toolbox with a graphical user interface, VELAS, which automatically visualizes and analyses the elastic anisotropy of arbitrary crystal systems using second-order elastic constants. Using Voigt-Reuss-Hill averaging scheme, VELAS allows the calculation of more than ten significant mechanical properties such as modulus, hardness, anisotropy index, ductility, and bond type. It also supports the determination of the mechanical stability of crystals at atmospheric and high pressures using the Born mechanical stability criterion. VELAS provides a new easy-to-use tool for detecting and identifying unusual mechanical properties such as negative Poisson's ratio, negative linear compressibility, and negative bulk modulus. VELAS offers several alternative visualization solutions for elastic properties, such as unit spherical projection, and map projection, and supports direct output of high-quality images. Furthermore, VELAS provides users an interface to read data from the Materials Project API in both online and offline modes. After introducing the basic theory, we detail the software framework, technical route, and installation specifications of VELAS. Moreover, the reliability and versatility of VELAS are confirmed by the analysis of the cases of negative linear compressibility, negative Poisson's ratio, hardness, and fracture toughness.
DOI: 10.17632/bx98gcrzbg.1
title: Molecular electrostatics and pKa shifts calculations with the Generalized Born model. A tutorial through examples with Bluues2

description: Biomolecular electrostatics is of key importance for biological function and recognition. The continuum electrostatic model based on the Poisson-Boltzmann (PB) equation has been widely used to study biomolecular electrostatics. The solution of the PB equation gives the electrostatic potential over the space enclosing the molecule(s) of interest, typically obtained at points of a suitable grid.

The Generalized Born (GB) model has been used to provide a useful approximation to the solution obtained by solving numerically the PB equation. The main advantage of the GB approach is to express the electrostatic energy of the system as the sum of pairwise interactions. The latter depend on geometric parameters (the GB radii) which depend on all atoms, and their radii, of the system. In this work we present a tutorial through examples for a more efficient and general version of the program Bluues which is able to compute:

1) the generalized Born radius of each atom;

2) the electrostatic potential at the surface of the molecule mapped to solvent accessible atoms;

3) the solvent accessible surface in a PDB formatted file;

4) the electrostatic potential in the volume surrounding the molecule;

5) the electrostatic free energy and different contributions to it;

6) the pH-dependent properties of proteins (total charge and pH-dependent free energy of folding) in the pH range −4 to 18;

7) the pKa shifts due to molecular structure of all ionizable groups.
DOI: 10.17632/by4ddckrpt.1
title: SLJCompact: A semiconductor-liquid junction solver for rapid band diagram insights into photoelectrochemical devices

description: SLJCompact is a Matlab based program that computes the band diagram and current-voltage characteristics of semiconductor photoanodes. To enable rapid insights, corresponding to various semiconductor-liquid junction (SLJ) properties and observable current-voltage characteristics, an abridged set of semi-analytical conservation equations are employed in the semiconductor region coupled with Gouy-Chapman screening within the liquid region. Electrostatic interactions between these regions across the junction are solved self-consistently through a variation on the Scharfetter-Gummel method. In this manner, the model is able to provide key band diagram insights regarding the correlated operation of photoanodes, both under illumination and in the dark, with respect to: current-voltage trends, quasi-Fermi level splitting, hole transfer rates, electron transfer rates, depletion region screening, hole inversion screening, and carrier recombination lifetimes. Motivated by Kroemer's lemma, SLJCompact is intended to further the adoption of band diagram methods within the photoelectrochemical device literature, by providing a computationally inexpensive approach residing between computationally intensive full continuity equation solvers and more approximate analytical expressions.
DOI: 10.17632/c5g2f92by3.2
title: Axially-deformed solution of the Skyrme-Hartree-Fock-Bogoliubov equations using the transformed harmonic oscillator basis (IV) HFBTHO (v4.0): A new version of the program

description: We describe the new version 4.0 of the code HFBTHO that solves the nuclear Hartree-Fock-Bogoliubov problem by using the deformed harmonic oscillator basis in cylindrical coordinates. In the new version, we have implemented the restoration of rotational, particle number, and reflection symmetry for even-even nuclei. The restoration of rotational symmetry does not require using bases closed under rotation. Furthermore, we added the SeaLL1 functional and improved the calculation of the Coulomb potential. Finally, we refactored the code to facilitate maintenance and future developments.
DOI: 10.17632/cvt9yz9gj8.2
title: Multiple elastic scattering of electrons in condensed matter (new version announcement)

description: The software MULTI_SCATT for calculations of parameters describing an electron transport in condensed matter in Jablonski (2017) [1] is replaced with a new program MULTI_SCATT_v2 which has the following improvements: (i) extension of electron energies to the range from 50 eV to 20 keV; (ii) detailed analysis of accuracy of elastic scattering cross sections from the implemented formalism; (iii) a new option for calculating the inelastic mean free path for compounds from elastic backscattering probabilities. The energy extension to 20 keV was stimulated by the current interest in applications of hard X-ray photoelectron spectroscopy (HAXPES).
DOI: 10.17632/dktybrydvf.1
title: VISROC 2.0: Updated Software for the Visualization of the significance of Receiver Operating Characteristics based on confidence ellipses

description: The Receiver Operating Characteristics (ROC) method is used to evaluate the diagnostic accuracy of binary quantitative tests in a broad spectrum of disciplines, including medicine, physics of complex systems, geophysics, meteorology, etc. The estimation of the significance of the examined prediction method is of high importance and it's usually approximated by Monte Carlo calculations. To simplify this problem, a FORTRAN code called VISROC was submitted to the CPC Program Library in 2014. VISROC evaluates the significance of binary diagnostic and prognostic tools for a family of k-ellipses which are based on confidence ellipses and cover the whole ROC space. Since that time, the code has been significantly improved and several new capabilities have been added. Most importantly, a Graphical User Interface (GUI) has been implemented, which can be invoked using either the R shiny web application or the Python application available for Windows, Mac, and Linux operating systems, both of which are described here.

The previous version of this program (AERY_v1_0) may be found here https://doi.org/10.1016/j.cpc.2013.12.009.
DOI: 10.17632/dmffpbjhsh.1
title: CNOK: A C++ Glauber model code for single-nucleon knockout reactions

description: A C++ program package was developed to calculate parallel momentum distributions (including the stripping mechanism and the diffractive dissociation mechanism) of the heavy residue (core) in single-nucleon knockout reactions induced by intermediate-energy (around and more than tens of MeV per nucleon) beams of stable and radioactive atomic nuclei. The program implements the Glauber reaction model that is based on the eikonal approximation and the sudden approximation when dealing with the scattering process, and uses a t-ρ-ρ method to build the projectile-target scattering optical potential, where the nucleonic densities of the core and the target are needed as input. The radial wavefunction of the valence nucleon is solved by a built-in bound-wave solver driven by a globally convergent search engine for optimized potential parameters of the valence nucleon to reproduce user-specified separation energies and root-mean-square (rms) radii of the valence nucleon. The YAML file format is adopted to facilitate user input. The program is expected to especially serve the interpretation of data analysis results of single-nucleon knockout from radioactive ion beams (RIBs), where the experimental practitioners may be more conversant with C++.
DOI: 10.17632/dp7gwrs94n.1
title: Contact-based molecular dynamics of structured and disordered proteins in a coarse-grained model: Fixed contacts, switchable contacts and those described by pseudo-improper-dihedral angles

description: We present a coarse-grained Cα-based protein model that can be used to simulate structured, intrinsically disordered and partially disordered proteins. We use a Go-like potential for the structured parts and two different variants of a transferable potential for the disordered parts. The first variant uses dynamic structure-based (DSB) contacts that form and disappear quasi-adiabatically during the simulation. By using specific structural criteria we distinguish sidechain-sidechain, sidechain-backbone and backbone-backbone contacts. The second variant is a non-radial multi-body pseudo-improper-dihedral (PID) potential that does not include time-dependent terms but requires more computational resources. Our model can simulate in reasonable time thousands of residues on millisecond time scales.
DOI: 10.3886/e190363
title: Data and Code for: Measuring Business Trends and Outlook through a New Survey

description: The Census Bureau’s new Business Trends and Outlook Survey (BTOS) provides timely information from businesses on their current trends and expectations over core concepts such as prices, employment, and revenue. BTOS collects qualitative information in order to produce extensive margins for core economic phenomena. BTOS results are representative of all single-location nonfarm businesses in the United States. We highlight sectoral differences in extensive margins of employment and prices using Finance and Insurance and Accommodation and Food Services as examples. We find businesses especially in Accommodation and Food Services anticipate future output price increases, possibly to accommodate rising current input prices.
description: The initial target population for BTOS is all nonfarm, single-location employer businesses with receipts of $1,000 or more that are in the United States, District of Columbia, and Puerto Rico. The following industries were designated as out of scope for the BTOS:Agriculture production (NAICS in [“110000,” “111,” “112”])Railroads (NAICS = "482")U.S. Postal Service (NAICS = "491")Monetary Authorities – Central Bank (NAICS = "521")Funds, Trusts, and other financial vehicles (NAICS = "525")Religious grant operations and religious organizations (NAICS = "813")Private households (NAICS = "814")Public administration (NAICS = "92")Unclassified with legal form of organization as tax-exempt or unknownBusinesses classified without a 2-digit NAICS (NAICS = "00") were not included.
DOI: 10.17632/dzb2z4tshd.1
title: QMeS-Derivation: Mathematica package for the symbolic derivation of functional equations

description: We present the Mathematica package QMeS-Derivation, available on GitHub. It derives symbolic functional equations from a given master equation. The latter include functional renormalisation group equations, Dyson-Schwinger equations, Slavnov-Taylor and Ward identities and their modifications in the presence of momentum cutoffs. The modules allow to derive the functional equations, take functional derivatives, trace over field space, apply a given truncation scheme, and do momentum routings while keeping track of prefactors and signs that arise from fermionic commutation relations. The package furthermore contains an installer as well as Mathematica notebooks with showcase examples.
DOI: 10.5517/ccdc.csd.cc2d5p1b
title: CCDC 2209991: Experimental Crystal Structure Determination

description: Related Article: Kyoung Chul Park, Preecha Kittikhunnatham, Jaewoong Lim, Grace C. Thaggard, Yuan Liu, Corey R. Martin, Gabrielle A. Leith, Donald J. Toler, An T. Ta, Nancy Birkner, Ingrid Lehman-Andino, Alejandra Hernandez-Jimenez, Gregory Morrison, Jake W. Amoroso, Hans-Conrad zur Loye, Dave P. DiPrete, Mark D. Smith, Kyle S. Brinkman, Simon R. Phillpot, Natalia B. Shustova|2023|Angew.Chem.,Int.Ed.|62|e202216349|doi:10.1002/anie.202216349
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.3886/e190363v1
title: Data and Code for: Measuring Business Trends and Outlook through a New Survey

description: The Census Bureau’s new Business Trends and Outlook Survey (BTOS) provides timely information from businesses on their current trends and expectations over core concepts such as prices, employment, and revenue. BTOS collects qualitative information in order to produce extensive margins for core economic phenomena. BTOS results are representative of all single-location nonfarm businesses in the United States. We highlight sectoral differences in extensive margins of employment and prices using Finance and Insurance and Accommodation and Food Services as examples. We find businesses especially in Accommodation and Food Services anticipate future output price increases, possibly to accommodate rising current input prices.
description: The initial target population for BTOS is all nonfarm, single-location employer businesses with receipts of $1,000 or more that are in the United States, District of Columbia, and Puerto Rico. The following industries were designated as out of scope for the BTOS:Agriculture production (NAICS in [“110000,” “111,” “112”])Railroads (NAICS = "482")U.S. Postal Service (NAICS = "491")Monetary Authorities – Central Bank (NAICS = "521")Funds, Trusts, and other financial vehicles (NAICS = "525")Religious grant operations and religious organizations (NAICS = "813")Private households (NAICS = "814")Public administration (NAICS = "92")Unclassified with legal form of organization as tax-exempt or unknownBusinesses classified without a 2-digit NAICS (NAICS = "00") were not included.