cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/t2mbshyptz.1
title: CMBE v05—Implementation of a toy-model for chaos analysis of relativistic nuclear collisions at the present BNL energies

description: Abstract In this paper we present a new version of Chaos Many-Body Engine (CMBE) Grossu et al. (2014) [1]. Inspired by the Mean Free Path concept, we implemented a new parameter, namely the “Mean Free Time”, which is defined as the mean time between one particle’s creation and its stimulated decay. This new parameter should be understood as an effect of the nuclear environment and, as opposed to the particle lifetime, it has the advantage of not being affected by the relativistic dilation. In [2] we p... Title of program: Chaos Many-Body Engine v05 Catalogue Id: AEGH_v5_0 Nature of problem Toy-model for relativistic nuclear collisions at present BNL energies. Versions of this program held in the CPC repository in Mendeley Data AEGH_v1_0; Chaos Many-Body Engine v01; 10.1016/j.cpc.2010.04.015 AEGH_v2_0; Chaos Many-Body Engine v02; 10.1016/j.cpc.2012.01.009 AEGH_v3_0; Chaos Many-Body Engine v03; 10.1016/j.cpc.2012.12.012 AEGH_v4_0; Chaos Many-Body Engine v04.1; 10.1016/j.cpc.2013.12.024 AEGH_v5_0; Chaos Many-Body Engine v05; 10.1016/j.cpc.2014.06.014 AEGH_v6_0; Chaos Many-Body Engine v06; 10.1016/j.cpc.2015.04.027 This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018)
DOI: 10.17632/3wmvbfwm4f.1
title: Langmuir probe RF plasma compensation using a simulation method

description: Abstract The problem of Langmuir probe data deformation due to RF pickup by the probe is treated through a computer simulation method. It is pointed out that proper RF compensations can be obtained by treatment of the Langmuir probe raw data through the use of computer software. It is demonstrated that correct, RF unaffected probe I – V characteristics can be accurately reproduced from the RF contaminated data. This eliminates the need for the use of any filters or other hardware procedures. User frie... Title of program: RF Compensation Catalogue Id: AEQR_v1_0 Nature of problem In RF plasma Langmuir probe diagnostics, the probe I-V characteristics obtained experimentally does nor represent the true I-V. This is because the probe picks up some RF plasma voltage which modulates the applied bias voltage and causes a current flow that corresponds the RF affected bias rather that the actual DC bias. This if untreated, can lead false results for the values of plasma parameters derived from the obtained I-V. Several hardware based methods are used to perform such correction ( ... Versions of this program held in the CPC repository in Mendeley Data AEQR_v1_0; RF Compensation; 10.1016/j.cpc.2013.09.003 This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018)
DOI: 10.17632/78mrzcmz8v.1
title: Using Python for scientific computing: Efficient and flexible evaluation of the statistical characteristics of functions with multivariate random inputs

description: Abstract This paper examines the feasibility of high-level Python based utilities for numerically intensive applications via an example of a multidimensional integration for the evaluation of the statistical characteristics of a random variable. We discuss the approaches to the implementation of mathematically formulated incremental expressions using high-level scripting code and low-level compiled code. Due to the dynamic typing of the Python language, components of the algorithm can be easily coded ... Title of program: spirrid Catalogue Id: AENL_v1_0 Nature of problem Evaluation of the statistical moments of a function of random variables. Versions of this program held in the CPC repository in Mendeley Data AENL_v1_0; spirrid; 10.1016/j.cpc.2012.08.021 This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018)
DOI: 10.17632/k7zdngs2r3.1
title: Fission Reaction Event Yield Algorithm, FREYA — For event-by-event simulation of fission

description: Abstract From nuclear materials accountability to detection of special nuclear material, SNM, the need for better modeling of fission has grown over the past decades. Current radiation transport codes compute average quantities with great accuracy and performance, but performance and averaging come at the price of limited interaction-by-interaction modeling. For fission applications, these codes often lack the capability of modeling interactions exactly: energy is not conserved, energies of emitted pa... Title of program: FREYA 1.0 Catalogue Id: AEVS_v1_0 Nature of problem Modeling of fission events. Versions of this program held in the CPC repository in Mendeley Data AEVS_v1_0; FREYA 1.0; 10.1016/j.cpc.2015.02.002 This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018)
DOI: 10.17632/tnvbfzgy65.1
title: ALOHA: Automatic libraries of helicity amplitudes for Feynman diagram computations

description: Abstract We present an application that automatically writes the Helas (HELicity Amplitude Subroutines) library corresponding to the Feynman rules of any quantum field theory Lagrangian. The code is written in Python and takes the Universal FeynRules Output (Ufo) as an input. From this input it produces the complete set of routines, wave-functions and amplitudes, that are needed for the computation of Feynman diagrams at leading as well as at higher orders. The representation is language independent a... Title of program: ALOHA Catalogue Id: AEMS_v1_0 Nature of problem An effcient numerical evaluation of a squared matrix element can be done with the help of the helicity routines implemented in the HELAS library [1]. This static library contains a limited number of helicity functions and is therefore not always able to provide the needed routine in the presence of an arbitrary interaction. This program provides a way to automatically create the corresponding routines for any given model. Versions of this program held in the CPC repository in Mendeley Data AEMS_v1_0; ALOHA; 10.1016/j.cpc.2012.05.004 This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018)
DOI: 10.17632/2jngk5tzm4.1
title: The VENUS/NWChem software package. Tight coupling between chemical dynamics simulations and electronic structure theory

description: Abstract The interface for VENUS and NWChem, and the resulting software package for direct dynamics simulations are described. The coupling of the two codes is considered to be a tight coupling since the two codes are compiled and linked together and act as one executable with data being passed between the two codes through routine calls. The advantages of this type of coupling are discussed. The interface has been designed to have as little interference as possible with the core codes of both VENUS a... Title of program: VENUS/NWChem Catalogue Id: AERS_v1_0 Nature of problem Direct dynamics simulations play an important role in investigating and understanding atomic-level chemical dynamics information such as atomistic reaction mechanisms, unimolecular and bimolecular rate constants, intramolecular vibrational energy redistribution rates, etc. The ability to couple direct dynamics with electronic structure methods brings a level of fidelity to the simulations that is important for complex systems. However, a tight coupling between two codes that have their own devel ... Versions of this program held in the CPC repository in Mendeley Data AERS_v1_0; VENUS/NWChem; 10.1016/j.cpc.2013.11.011 This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018)
DOI: 10.17632/9cbzhp98mc.1
title: PDB4DNA: Implementation of DNA geometry from the Protein Data Bank (PDB) description for Geant4-DNA Monte-Carlo simulations

description: Abstract This paper describes PDB4DNA, a new Geant4 user application, based on an independent, cross-platform, free and open source C++ library, so-called PDBlib, which enables use of atomic level description of DNA molecule in Geant4 Monte Carlo particle transport simulations. For the evaluation of direct damage induced on the DNA molecule by ionizing particles, the application makes use of an algorithm able to determine the closest atom in the DNA molecule to energy depositions. Both the PDB4DNA app... Title of program: PDB4DNA Catalogue Id: AEWB_v1_0 Nature of problem To evaluate strand breaks induced on the DNA molecule by ionizing particles using Monte Carlo method. It requires the implementation of DNA geometry, physical processes adapted to nanodosimetry simulations and an algorithm to determine the closest atom in the DNA molecule to energy depositions. Versions of this program held in the CPC repository in Mendeley Data AEWB_v1_0; PDB4DNA; 10.1016/j.cpc.2015.02.026 This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018)
DOI: 10.17632/kp87hnf2ky.1
title: PLUMED-GUI: An environment for the interactive development of molecular dynamics analysis and biasing scripts

description: Abstract PLUMED-GUI is an interactive environment to develop and test complex PLUMED scripts within the Visual Molecular Dynamics (VMD) environment. Computational biophysicists can take advantage of both PLUMED’s rich syntax to define collective variables (CVs) and VMD’s chemically-aware atom selection language, while working within a natural point-and-click interface. Pre-defined templates and syntax mnemonics facilitate the definition of well-known reaction coordinates. Complex CVs, e.g. involving r... Title of program: PLUMED-GUI (Collective variable analysis plugin) Catalogue Id: AERU_v1_0 Nature of problem Compute and visualize values of collective variables on molecular dynamics trajectories from within VMD, and interactively develop biasing scripts for the estimation of free-energy surfaces in PLUMED. Versions of this program held in the CPC repository in Mendeley Data AERU_v1_0; PLUMED-GUI (Collective variable analysis plugin); 10.1016/j.cpc.2013.11.019 This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018)
DOI: 10.17632/nj3fhsppg8.1
title: Polycrystalline neutron scattering for Geant4: NXSG4

description: Abstract An extension to Geant4 based on the nxs library is presented. It has been implemented in order to include effects of low-energy neutron scattering in polycrystalline materials, and is made available to the scientific community. Title of program: NXSG4 Catalogue Id: AEUZ_v1_0 Nature of problem Simulation of neutron scattering in polycrystalline materials Versions of this program held in the CPC repository in Mendeley Data AEUZ_v1_0; NXSG4; 10.1016/j.cpc.2014.11.009 This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018)
DOI: 10.15468/qmi7am
title: Camellia debaoensis (Theaceae), a new species of yellow camellia from limestone karsts in southwestern China

description: This dataset contains the digitized treatments in Plazi based on the original journal article Hu, Renchuan, Wei, Sujuan, Liufu, Yongqing, Nong, Yunkai, Fang, Wei (2019): Camellia debaoensis (Theaceae), a new species of yellow camellia from limestone karsts in southwestern China. PhytoKeys 135: 49-58, DOI: http://dx.doi.org/10.3897/phytokeys.135.38756, URL: http://dx.doi.org/10.3897/phytokeys.135.38756
DOI: 10.17632/3bff4w4ywx.1
title: Data for: An iterative linear procedure using frequency-dependent soil parameters for site response analyses

description: The data files contain the numerical code implemented to generate the strain amplitude spectrum required in the proposed frequency-dependent equivalent linear method.
DOI: 10.17632/5n9vprvyhz.1
title: Reaction Mechanism Generator: Automatic construction of chemical kinetic mechanisms

description: Abstract Reaction Mechanism Generator (RMG) constructs kinetic models composed of elementary chemical reaction steps using a general understanding of how molecules react. Species thermochemistry is estimated through Benson group additivity and reaction rate coefficients are estimated using a database of known rate rules and reaction templates. At its core, RMG relies on two fundamental data structures: graphs and trees. Graphs are used to represent chemical structures, and trees are used to represent ... Title of program: RMG Catalogue Id: AEZW_v1_0 Nature of problem Automatic generation of chemical kinetic mechanisms for molecules containing C, H, O, S, and N. Versions of this program held in the CPC repository in Mendeley Data AEZW_v1_0; RMG; 10.1016/j.cpc.2016.02.013 This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018)
DOI: 10.17632/9z3hm8jwgn.1
title: Data for: 4D history of the Nimbus VHMS ore deposit in the Yilgarn Craton, Western Australia

description: Supplementary data a. 40Ar/39Ar results for the sericitized plagioclase from the dacites at the nimbus deposit.
DOI: 10.17632/d5z89nnyv6.1
title: MEAMfit: A reference-free modified embedded atom method (RF-MEAM) energy and force-fitting code

description: Abstract MEAMfit v1.02. Changes: various bug fixes; speed of single-shot energy and force calculations (not optimization) increased by × 10 ; elements up to Cn ( Z = 112 ) now correctly read from vasprun.xml files; EAM fits now produce Camelion output files; changed max number of vasprun.xml files to 10,000 (an unnecessary lower limit of 10 was allowed in the previous version). Title of program: MEAMfit Catalogue Id: AEWY_v1_1 Nature of problem Fitting embedded atom method (EAM) and reference-free modified embedded atom method (RF-MEAM) potentials [2-3] to energies and forces produced by VASP [4-7]. Versions of this program held in the CPC repository in Mendeley Data AEWY_v1_0; MEAMfit; 10.1016/j.cpc.2015.05.016 AEWY_v1_1; MEAMfit; 10.1016/j.cpc.2016.02.015 This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018)
DOI: 10.17632/wgj3sc4dhz.1
title: Details of tetrahedral anisotropic mesh adaptation

description: Abstract We have implemented tetrahedral anisotropic mesh adaptation using the local operations of coarsening, swapping, refinement and smoothing in MATLAB without the use of any for- N loops, i.e. the script is fully vectorised. In the process of doing so, we have made three observations related to details of the implementation: 1. restricting refinement to a single edge split per element not only simplifies the code, it also improves mesh quality, 2. face to edge swapping is unnecessary, and 3. opti... Title of program: trullekrul v0.1.0 Catalogue Id: AEZC_v1_0 Nature of problem Adaptation of tetrahedral meshes to metric fields. Versions of this program held in the CPC repository in Mendeley Data AEZC_v1_0; trullekrul v0.1.0; 10.1016/j.cpc.2015.12.002 This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018)
DOI: 10.17632/xzjzw6scdx.1
title: Nexus: A modular workflow management system for quantum simulation codes

description: Abstract The management of simulation workflows represents a significant task for the individual computational researcher. Automation of the required tasks involved in simulation work can decrease the overall time to solution and reduce sources of human error. A new simulation workflow management system, Nexus, is presented to address these issues. Nexus is capable of automated job management on workstations and resources at several major supercomputing centers. Its modular design allows many quantum ... Title of program: Nexus Catalogue Id: AEXN_v1_0 Nature of problem Quantum simulation workflows with multiple dependencies between various electronic structure codes. Job management of simulations on arbitrary workstation and supercomputing environments. Aggregation and analysis of output data. Versions of this program held in the CPC repository in Mendeley Data AEXN_v1_0; Nexus; 10.1016/j.cpc.2015.08.012 This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018)
DOI: 10.17632/ms96jvbgdt.1
title: FESTR: Finite-Element Spectral Transfer of Radiation spectroscopic modeling and analysis code

description: Abstract We report on the development of a new spectral postprocessor of hydrodynamic simulations of hot, dense plasmas. Based on given time histories of one-, two-, and three-dimensional spatial distributions of materials, and their local temperature and density conditions, spectroscopically-resolved signals are computed. The effects of radiation emission and absorption by the plasma on the emergent spectra are simultaneously taken into account. This program can also be used independently of hydrodyn... Title of program: FESTR Catalogue Id: AFAR_v1_0 Nature of problem Calculation of spectral signals by postprocessing hydrodynamics simulations. Analysis of experimental spectroscopic data to infer plasma temperature and density conditions, and its chemical composition. Simultaneous treatment of spatial non-uniformity (on 3D unstructured meshes) along with spectroscopic-quality radiation transport. Versions of this program held in the CPC repository in Mendeley Data AFAR_v1_0; FESTR; 10.1016/j.cpc.2016.05.027 This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018)
DOI: 10.17632/mt46trxrsk.1
title: JETSPIN: A specific-purpose open-source software for simulations of nanofiber electrospinning

description: Abstract We present the open-source computer program JETSPIN, specifically designed to simulate the electrospinning process of nanofibers. Its capabilities are shown with proper reference to the underlying model, as well as a description of the relevant input variables and associated test-case simulations. The various interactions included in the electrospinning model implemented in JETSPIN are discussed in detail. The code is designed to exploit different computational architectures, from single to p... Title of program: JETSPIN Catalogue Id: AEXQ_v1_0 Nature of problem Dynamics of the electrospinning process to produce nanofibers Versions of this program held in the CPC repository in Mendeley Data AEXQ_v1_0; JETSPIN; 10.1016/j.cpc.2015.08.013 This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018)
DOI: 10.17632/rpm3xv2myn.1
title: MPBEC, a Matlab Program for Biomolecular Electrostatic Calculations

description: Abstract One of the most used and efficient approaches to compute electrostatic properties of biological systems is to numerically solve the Poisson–Boltzmann (PB) equation. There are several software packages available that solve the PB equation for molecules in aqueous electrolyte solutions. Most of these software packages are useful for scientists with specialized training and expertise in computational biophysics. However, the user is usually required to manually take several important choices, de... Title of program: MPBEC Catalogue Id: AEXW_v1_0 Nature of problem Numerical solution of the linearized PB equation. Versions of this program held in the CPC repository in Mendeley Data AEXW_v1_0; MPBEC; 10.1016/j.cpc.2015.08.029 This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018)
DOI: 10.7910/dvn/euics1/ohiala
title: Use-of-Psychometric-Tests-in-the-Process-of-Recruitment-in-Human-Resource-Management-Docx.pdf

description: :unav
DOI: 10.17632/76gp8sd2z3.1
title: Optimized higher-order automatic differentiation for the Faddeeva function

description: Abstract Considerable research efforts have been directed at implementing the Faddeeva function w ( z ) and its derivatives with respect to z , but these did not consider the key computing issue of a possible dependence of z on some variable t . The general case is to differentiate the compound function w ( z ( t ) ) = w ∘ z ( t ) with respect to t by applying the chain rule for a first order derivative, or Faà di Bruno’s formula for higher-order ones. Higher-order automatic differentiation (HOAD) is ... Title of program: HOAD_MathFun Catalogue Id: AFAG_v1_0 Nature of problem General optimized higher-order automatic differentiation of mathematical functions. Complex refractive index as a case study. Versions of this program held in the CPC repository in Mendeley Data AFAG_v1_0; HOAD_MathFun; 10.1016/j.cpc.2016.04.009 This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018)
DOI: 10.17632/86njc664zj.1
title: MaMiCo: Software design for parallel molecular-continuum flow simulations

description: Abstract The macro–micro-coupling tool (MaMiCo) was developed to ease the development of and modularize molecular-continuum simulations, retaining sequential and parallel performance. We demonstrate the functionality and performance of MaMiCo by coupling the spatially adaptive Lattice Boltzmann framework waLBerla with four molecular dynamics (MD) codes: the light-weight Lennard-Jones-based implementation SimpleMD, the node-level optimized software ls1 mardyn, and the community codes ESPResSo and LAMMP... Title of program: MaMiCo Catalogue Id: AEYW_v1_0 Nature of problem Coupled molecular-continuum simulation for multi-resolution fluid dynamics: parts of the domain are resolved by molecular dynamics whereas large parts are covered by a CFD solver, e.g. a lattice Boltzmann automaton Versions of this program held in the CPC repository in Mendeley Data AEYW_v1_0; MaMiCo; 10.1016/j.cpc.2015.10.029 This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018)
DOI: 10.17632/n6m3gtsh3w.1
title: PCTDSE: A parallel Cartesian-grid-based TDSE solver for modeling laser–atom interactions

description: Abstract We present a parallel Cartesian-grid-based time-dependent Schrödinger equation (TDSE) solver for modeling laser–atom interactions. It can simulate the single-electron dynamics of atoms in arbitrary time-dependent vector potentials. We use a split-operator method combined with fast Fourier transforms (FFT), on a three-dimensional (3D) Cartesian grid. Parallelization is realized using a 2D decomposition strategy based on the Message Passing Interface (MPI) library, which results in a good... Title of program: PCTDSE Catalogue Id: AFBM_v1_0 Nature of problem Simulate the single-electron dynamics of atoms under the strong fields of modern lasers according to the time-dependent Schrödinger equation. Versions of this program held in the CPC repository in Mendeley Data AFBM_v1_0; PCTDSE; 10.1016/j.cpc.2016.09.016 This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018)
DOI: 10.17632/p528xpts54.1
title: FabSim: Facilitating computational research through automation on large-scale and distributed e-infrastructures

description: Abstract We present FabSim, a toolkit developed to simplify a range of computational tasks for researchers in diverse disciplines. FabSim is flexible, adaptable, and allows users to perform a wide range of tasks with ease. It also provides a systematic way to automate the use of resources, including HPC and distributed machines, and to make tasks easier to repeat by recording contextual information. To demonstrate this, we present three use cases where FabSim has enhanced our research productivity. Th... Title of program: FabSim Catalogue Id: AFAO_v1_0 Nature of problem Running advanced computations using remote resources is an activity that requires considerable time and human attention. These activities, such as organizing data, configuring software and setting up individual runs often vary slightly each time they are performed. To lighten this burden, we required an approach that introduced little burden of its own to set up and adapt, beyond which very substantial productivity ensues. Versions of this program held in the CPC repository in Mendeley Data AFAO_v1_0; FabSim; 10.1016/j.cpc.2016.05.020 This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018)