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This document is a user manual for SES_IO, a low-level library for reading and writing sesame files. The purpose of the SES_IO library is to provide a simple user interface for accessing and creating sesame files that does not change across sesame format type (such as binary, ascii, and xml).
The ASCII MCNP output file is converted to an interactive PDF using legacy printer control characters.
A message passing interface (MPI)-based implementation (Autodock4.lga.MPI) of the grid-based docking program Autodock4 has been developed to allow simultaneous and independent docking of multiple compounds on up to thousands of central processing units (CPUs) using the Lamarkian genetic algorithm. The MPI version reads a single binary file containing precalculated grids that represent the protein-ligand interactions, i.e., van der Waals, electrostatic, and desolvation potentials, and needs only two input parameter files for the entire docking run. In comparison, the serial version of Autodock4 reads ASCII grid files and requires one parameter file per compound. The modifications performed result in significantly reduced input/output activity compared with the serial version. Autodock4.lga.MPI scales up to 8192 CPUs with a maximal overhead of 16.3%, of which two thirds is due to input/output operations and one third originates from MPI operations. The optimal docking strategy, which minimizes docking CPU time without lowering the quality of the database enrichments, comprises the docking of ligands preordered from the most to the least flexible and the assignment of the number of energy evaluations as a function of the number of rotatable bounds. In 24 h, on 8192 high-performance computing CPUs, the present MPI version would allow docking to a rigid protein of about 300K small flexible compounds or 11 million rigid compounds.
he accurate description of nuclear β − -decay has far-reaching consequences for applications spanning nuclear reactors to the creation of heavy elements in astrophysical environments. We present the nuclear particle spectra associated with the β -decay of neutron-rich nuclei calculated with the well benchmarked coupled Quasi-particle Random Phase Approximation and Hauser–Feshbach (QRPA+HF) model. This approach begins with the population of the daughter nucleus via semi-microscopic Gamow-Teller or First-Forbidden strength distributions (QRPA) and follows the statistical de-excitation (HF) until the initial available excitation energy is exhausted. At each stage of de-excitation the emission by neutrons and $γ$-rays is considered obeying quantum mechanical selection rules. For completeness we also provide parsed Auger and Internal Conversion (IC) electron spectra from Evaluated Nuclear Data Files (ENDF). Our results are tabulated and provided in parsable ASCII formatted tables that are suitable for inclusion in various applications.
© 2016 Elsevier B.V. Ultra-peripheral collisions (UPCs) have been a significant source of study at RHIC and the LHC. In these collisions, the two colliding nuclei interact electromagnetically, via two-photon or photonuclear interactions, but not hadronically; they effectively miss each other. Photonuclear interactions produce vector meson states or more general photonuclear final states, while two-photon interactions can produce lepton or meson pairs, or single mesons. In these interactions, the collision geometry plays a major role. We present a program, STARlight, that calculates the cross-sections for a variety of UPC final states and also creates, via Monte Carlo simulation, events for use in determining detector efficiency. Program summary Program Title: STARlight (v2.2) Program Files doi: http://dx.doi.org/10.17632/xjpf4rxtbj.1 Licensing provisions: GNU GPLv3 Programming Language: C++ External Routines: PYTHIA 8.2 and DPMJET 3.0 are needed for some final states. Nature of problem: The cross-section for ultra-peripheral collisions is obtained by integrating the photon fluxes in transverse impact parameter space, subject to the requirement (which is also impact parameter dependent) that the colliding nuclei do not interact hadronically. The program is a two step process. First, it calculates the cross-sections for the reaction of interest, as a function of W (photon–Pomeron or two-photon center of mass energy), Y (final state rapidity) and pT (final state transverse momentum). Second, STARlight generates Monte Carlo events which can be used to determine cross-sections within specific kinematic constraints or for studies of detector efficiencies. The second step includes the decay of any unstable particles produced in the reaction, with appropriate consideration of particle spins and parity. It outputs these events in ASCII format. Solution method: The program generates a two dimensional look-up table of the production cross-section as a function of final state rapidity and mass. The dimensions of the table are selectable, allowing the user to choose the desired accuracy. For certain final states, a second two-dimensional look-up table, giving the transverse momentum distribution, as a function of rapidity, is also used. With these look-up tables, the program generates final states. Particle decays and the final angular distributions are calculated for each event. Restrictions: The program is focused on ultra-relativistic collisions at Brookhaven's RHIC (Relativistic Heavy Ion Collider) and CERN's LHC (Large Hadron Collider), with final states that are visible in a central detector. At lower energies (i.e., at the CERN SPS), caution should be exercised because STARlight does not account for the longitudinal momentum transfer to the nucleus; this is larger at low beam energies. References: http://starlight.hepforge.org and references in this article.
The PEST protocol has been implemented into the iTOUGH2 code, allowing the user to link any simulation program (with ASCII-based inputs and outputs) to iTOUGH2's sensitivity analysis, inverse modeling, and uncertainty quantification capabilities. These application models can be pre- or post-processors of the TOUGH2 non-isothermal multiphase flow and transport simulator, or programs that are unrelated to the TOUGH suite of codes. PEST-style template and instruction files are used, respectively, to pass input parameters updated by the iTOUGH2 optimization routines to the model, and to retrieve the model-calculated values that correspond to observable variables. We summarize the iTOUGH2 capabilities and demonstrate the flexibility added by the PEST protocol for the solution of a variety of simulation-optimization problems. In particular, the combination of loosely coupled and tightly integrated simulation and optimization routines provides both the flexibility and control needed to solve challenging inversion problems for the analysis of multiphase subsurface flow and transport systems.
Here, a line list for the N second positive system, $B^3Π_g—C^3Π_u$, has been compiled using the PGOPHER spectral simulation software. The line list extends the number of vibrational states of the $B^3Π_g$ up to v=29 and a maximum rotational state of J=150 for simulation temperatures up to 7000 K. New electronic–vibrational transition moments were calculated using refined potential energy curves and a transition dipole moment with the DUO software. Comparisons to experimental data and the SPECAIR software have been used to validate the new line list. The results are available in ASCII ExoMol .state and .trans files and as a PGOPHER input file for use in spectral analysis.
A relational database has been developed based on the original (n,n'γ) work carried out by A. M. Demidov et al., at the Nuclear Research Institute in Baghdad, Iraq (Demidov et al., 1978) for 105 independent measurements comprising 76 elemental samples of natural composition and 29 isotopically-enriched samples. The information from this Atlas includes: γ-ray energies and relative intensities; nuclide and level data corresponding to the residual nucleus and meta data associated with the target sample that allows for the extraction of the flux-weighted (n,n'γ) cross sections for a given transition relative to a defined value. The optimized angular-distribution-corrected fast-neutron flux-weighted partial γ-ray cross section for the production of the 846.8-keV 21+→0gs+γ-ray transition in 56Fe, determined to be $\langle$σγ$\rangle$=143(29) mb, is used for this purpose. However, different values for the adopted cross section can be readily implemented to accommodate user preference based on revised determinations of this quantity. The Atlas (n,n'γ) data has been compiled into a series of CSV-style ASCII data sets and a suite of Python scripts have been developed to build and install the database locally. The database can then be accessed directly through the SQLite engine, or using alternative methods such as the Jupyter Notebook Python-browser interface. Several examples exploiting different interaction methodologies are distributed with the complete software package.
Most of the development of the MCNPX/6 burnup capability focused on features that were applied to the Boltzman transport or used to prepare coefficients for use in CINDER90, with little change to CINDER90 or the CINDER90 data. Though a scheme exists for best solving the coupled Boltzman and Bateman equations, the most significant approximation is that the employed nuclear data are correct and complete. Thus, the CINDER90 library file contains 60 different actinide fission yields encompassing 36 fissionable actinides (thermal, fast, high energy and spontaneous fission). Fission reaction data exists for more than 60 actinides and as a result, fission yield data must be approximated for actinides that do not possess fission yield information. Several types of approximations are used for estimating fission yields for actinides which do not possess explicit fission yield data. The objective of this study is to test whether or not certain approximations of fission yield selection have any impact on predictability of major actinides and fission products. Further we assess which other fission products, available in MCNP6 Tier 3, result in the largest difference in production. Because the CINDER90 library file is in ASCII format and therefore easily amendable, we assess reasons for choosing, as well as compare actinide and major fission product prediction for the H. B. Robinson benchmark for, three separate fission yield selection methods: (1) the current CINDER90 library file method (Base); (2) the element method (Element); and (3) the isobar method (Isobar). Results show that the three methods tested result in similar prediction of major actinides, Tc-99 and Cs-137; however, certain fission products resulted in significantly different production depending on the method of choice.
SGRAPH program is considered one of the seismological programs that maintain seismic data. SGRAPH is considered unique for being able to read a wide range of data formats and manipulate complementary tools in different seismological subjects in a stand-alone Windows-based application. SGRAPH efficiently performs the basic waveform analysis and solves advanced seismological problems. The graphical user interface (GUI) utilities and the Windows facilities such as, dialog boxes, menus, and toolbars simplified the user interaction with data. SGRAPH supported the common data formats like, SAC, SEED, GSE, ASCII, and Nanometrics Y-format, and others. It provides the facilities to solve many seismological problems with the built-in inversion and modeling tools. In this paper, I discuss some of the inversion tools built-in SGRAPH related to source parameters and hypocentral location estimation. Firstly, a description of the SGRAPH program is given discussing some of its features. Secondly, the inversion tools are applied to some selected events of the Dahshour earthquakes as an example of estimating the spectral and source parameters of local earthquakes. In addition, the hypocentral location of these events are estimated using the Hypoinverse 2000 program operated by SGRAPH.
We report on the experimental realization of the analogy of quantum dense coding in classical optical communication using classical optical correlations. Compared to quantum dense coding that uses pairs of photons entangled in polarization, we find that the proposed design exhibits many advantages. Considering that it is convenient to realize in optical communication, the attainable channel capacity in the experiment for dense coding can reach 2 bits, which is higher than that of the usual quantum coding capacity (1.585 bits). This increased channel capacity has been proven experimentally by transmitting ASCII characters in 12 quaternary digitals instead of the usual 24 bits.
The Chandra Transmission Grating Data Archive and Catalog (TGCat) provides easy access to analysis-ready products, specifically, high-resolution X-ray count spectra and their corresponding calibrations. The web interface makes it easy to find observations of a particular object, type of object, or type of observation; to quickly assess the quality and potential usefulness of the spectra from pre-computed summary plots; or to customize a view with an interactive plotter, optionally combining spectra over multiple orders or observations. Data and responses can be downloaded as a package or as individual files, and the query results themselves can be retrieved as ASCII or Virtual Observatory tables. Portable reprocessing scripts used to create the archive and which use the Chandra X-ray Center's (CXC's) software and other publicly available software are also available, facilitating standard or customized reprocessing from Level 1 CXC archival data to spectra and responses with minimal user interaction.
Understanding the diversity in spectra is the key to determining the physical parameters of galaxies. The optical spectra of galaxies are highly convoluted with continuum and lines that are potentially sensitive to different physical parameters. Defining the wavelength regions of interest is therefore an important question. In this work, we identify informative wavelength regions in a single-burst stellar population model using the CUR Matrix Decomposition. Simulating the Lick/IDS spectrograph configuration, we recover the widely used D {sub n}(4000), Hβ, and Hδ {sub A} to be most informative. Simulating the Sloan Digital Sky Survey spectrograph configuration with a wavelength range 3450-8350 Å and a model-limited spectral resolution of 3 Å, the most informative regions are: first region—the 4000 Å break and the Hδ line; second region—the Fe-like indices; third region—the Hβ line; and fourth region—the G band and the Hγ line. A principal component analysis on the first region shows that the first eigenspectrum tells primarily the stellar age, the second eigenspectrum is related to the age-metallicity degeneracy, and the third eigenspectrum shows an anti-correlation between the strengths of the Balmer and the Ca K and H absorptions. The regions can be used to determine the stellar age and metallicity in early-type galaxies that have solar abundance ratios, no dust, and a single-burst star formation history. The region identification method can be applied to any set of spectra of the user's interest, so that we eliminate the need for a common, fixed-resolution index system. We discuss future directions in extending the current analysis to late-type galaxies. ASCII formatted tables of the regional eigenspectra are available.
We present an online catalog containing spectra and supporting information for cataclysmic variables that have been observed with the Far-Ultraviolet Spectroscopic Explorer (FUSE). For each object in the catalog we list some of the basic system parameters such as (R.A., decl.), period, inclination, and white dwarf mass, as well as information on the available FUSE spectra: data ID, observation date and time, and exposure time. In addition, we provide parameters needed for the analysis of the FUSE spectra such as the reddening E(B - V), distance, and state (high, low, intermediate) of the system at the time it was observed. For some of these spectra we have carried out model fits to the continuum with synthetic stellar and/or disk spectra using the codes TLUSTY and SYNSPEC. We provide the parameters obtained from these model fits; this includes the white dwarf temperature, gravity, projected rotational velocity, and elemental abundances of C, Si, S, and N, together with the disk mass accretion rate, the resulting inclination, and model-derived distance (when unknown). For each object one or more figures are provided (as gif files) with line identification and model fit(s) when available. The FUSE spectra and the synthetic spectra are directly available for download as ASCII tables. References are provided for each object, as well as for the model fits. In this article we present 36 objects, and additional ones will be added to the online catalog in the future. In addition to cataclysmic variables, we also include a few related objects, such as a wind-accreting white dwarf, a pre-cataclysmic variable, and some symbiotics.
For a few years now, the artdaq data acquisition software toolkit has provided numerous experiments with ready-to-use components which allow for rapid development and deployment of DAQ systems. Developed within the Fermilab Scientific Computing Division, artdaq provides data transfer, event building, run control, and event analysis functionality. This latter feature includes built-in support for the art event analysis framework, allowing experiments to run art modules for real-time filtering, compression, disk writing and online monitoring; as art, also developed at Fermilab, is also used for online analysis, a major advantage of artdaq is that it allows developers to easily switch between developing online and online software. artdaq continues to be improved. Support for an alternate mode of running whereby data from some subdetector components are only streamed if requested has been added; this option will reduce unnecessary DAQ throughput. Real-time reporting of DAQ metrics has been implemented, along with the flexibility to choose the format through which experiments receive the reports; these formats include the Ganglia, Graphite and syslog software packages, along with at ASCII files. Additionally, work has been performed investigating more flexible modes of online monitoring, including the capability of being able to run multiple online monitoring processes on different hosts, each running its own set of art modules. Finally, a web-based GUI interface through which users can configure details of their DAQ system has been implemented, increasing the ease of use of the system. Already successfully deployed on the LArIAT, DarkSide-50, DUNE 35ton and Mu2e experiments, artdaq will be employed for SBND and is a strong candidate for use on ICARUS and protoDUNE. With each experiment comes new ideas for how artdaq can be made more flexible and powerful; the above improvements will be described, along with potential ideas for the future.
In this work, we have calculated a complete set of primary fission fragment mass yields, Y(A), for heavy nuclei across the chart of nuclides, including those of particular relevance to the rapid neutron capture process (r process) of nucleosynthesis. We assume that the nuclear shape dynamics are strongly damped, which allows for a description of the fission process via Brownian shape motion across nuclear potential-energy surfaces. The macroscopic energy of the potential was obtained with the Finite-Range Liquid-Drop Model (FRLDM), while the microscopic terms were extracted from the single-particle level spectra in the fissioning system by the Strutinsky procedure for the shell energies and the BCS treatment for the pairing energies. For each nucleus considered, the fission fragment mass yield, Y(A), is obtained from 50 000 to 500 000 random walks on the appropriate potential-energy surface. The full mass and charge yield, Y(Z,A), is then calculated by invoking the Wahl systematics. With this method, we have calculated a comprehensive set of fission-fragment yields from over 3800 nuclides bounded by 80 ≤ Z ≤ 130 and A ≤ 330; these yields are provided as an ASCII formatted database in the Supplemental Material. We compare our yields to known data and discuss general trends that emerge in low-energy fission yields across the chart of nuclides.
Beta-delayed neutron emission and β-delayed fission (βdf) probabilities were calculated for heavy, neutronrich nuclei using the Los Alamos coupled quasiparticle random-phase approximation plus Hauser-Feshbach (QRPA + HF) approach. In this model, the compound nucleus is initially populated by β decay and is followed through subsequent statistical decays taking into account competition among neutrons, γ rays, and fission. The primary output of these calculations includes branching ratios along with neutron and γ -ray spectra. Here, we find a relatively large region of heavy nuclides where the probability of βdf is near 100%. For a subset of nuclei near the neutron drip line, delayed neutron emission and the probability of fission are both large, which leads to the possibility of multichance βdf (mc-βdf). We comment on prospective neutron-rich nuclei that could be probed by future experimental campaigns and provide a full table of branching ratios in ASCII format in the Supplemental Material for use in various applications.
In this work we calculate the corrections to the amputated Green's functions of four-fermion operators, in 1-loop lattice perturbation theory. One of the novel aspects of our calculations is that they are carried out to second order in the lattice spacing, O(a{sup 2}). We employ the Wilson/clover action for massless fermions (also applicable for the twisted mass action in the chiral limit) and a family of Symanzik improved actions for gluons. Our calculations have been carried out in a general covariant gauge. Results have been obtained for several popular choices of values for the Symanzik coefficients (Plaquette, Tree-level Symanzik, Iwasaki, TILW and DBW2 action). While our Green's function calculations regard any pointlike four-fermion operators which do not mix with lower dimension ones, we pay particular attention to {Delta}F=2 operators, both parity conserving and parity violating (F stands for flavor: S, C, B). By appropriately projecting those bare Green's functions we compute the perturbative renormalization constants for a complete basis of four-fermion operators and we study their mixing pattern. For some of the actions considered here, even O(a{sup 0}) results did not exist in the literature to date. The correction terms which we calculate (along with our previous O(a{sup 2}) calculation of Z{sub {Psi}}[M. Constantinou, V. Lubicz, H. Panagopoulos, and F. Stylianou, J. High Energy Phys. 10 (2009) 064.][M. Constantinou, P. Dimopoulos, R. Frezzotti, G. Herdoiza, K. Jansen, V. Lubicz, H. Panagopoulos, G. C. Rossi, S. Simula, F. Stylianou, and A. Vladikas, J. High Energy Phys. 08 (2010) 068.][C. Alexandrou, M. Constantinou, T. Korzec, H. Panagopoulos, and F. Stylianou (unpublished).]) are essential ingredients for minimizing the lattice artifacts which are present in nonperturbative evaluations of renormalization constants with the RI{sup '}-MOM method. Our perturbative results, for the matrix elements of {Delta}F=2 operators and for the corresponding renormalization matrices, depend on a large number of parameters: coupling constant, number of colors, lattice spacing, external momentum, clover parameter, Symanzik coefficients, gauge parameter. To make these results most easily accessible to the reader, we have included them in the distribution package of this paper, as an ASCII file named: 4-fermi.m; the file is best perused as Mathematica input. The main results of this work have been applied to improve nonperturbative estimates of the B{sub K}-parameter in N{sub F}=2 twisted mass lattice QCD [M. Constantinou, P. Dimopoulos, R. Frezzotti, K. Jansen, V. Gimenez, V. Lubicz, F. Mescia, H. Panagopoulos, M. Papinutto, G. C. Rossi, S. Simula, A. Skouroupathis, F. Stylianou, and A. Vladikas, arXiv:1009.5606.].