More Than One Input File

MonoPhy: A simple R package to find and visualize monophyly issues

10.7287/peerj.preprints.1600v1 ◽

2015 ◽

Author(s):

Orlando Schwery ◽

Brian C O'Meara

Keyword(s):

Phylogenetic Tree ◽

R Package ◽

Input File ◽

Higher Taxa ◽

Additional Input

Background. The monophyly of taxa is an important attribute of a phylogenetic tree, as a lack of it may hint at shortcomings of either the tree or the current taxonomy and can misguide subsequent analyses. While monophyly is conceptually simple, it is manually tedious and time consuming to assess on modern phylogenies of hundreds to thousands of species. Results. The R package MonoPhy allows assessment and exploration of monophyly of taxa in a phylogeny. It can assess the monophyly of genera using the phylogeny only, and with an additional input file, any other desired higher taxa or unranked groups can be checked as well. Conclusion. Summary tables, easily subsettable results and several visualization options allow quick and convenient exploration of monophyly issues, thus making MonoPhy a valuable tool for any researcher working with phylogenies.

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Integrating layer by layer manufacturing for the realization of polymer complex geometries with scanning devices: re-building by digital data

10.25518/esaform21.459 ◽

2021 ◽

Author(s):

Carlo Bruni ◽

Luciano Greco ◽

Tommaso Mancia ◽

Massimiliano Pieralisi

Keyword(s):

Original Data ◽

Digital Data ◽

Complex Geometries ◽

Polymer Complex ◽

Layer By Layer ◽

Input File ◽

3D Scanner ◽

Photo Polymerization ◽

Layer Manufacturing ◽

Computer Aided

The additive manufacturing technique represents a way to realize components or prototypes without the use of conventional tools.The research presented aims at proposing a methodology based on the use of three different techniques that are the poly-jet 3D using UV photo-polymerization, the FDM of polyamide materials and the FDM of PLA materials. The original data were used at the beginning with the first technique in order to detect the shape and the geometry by a 3D SCANNER. The objective was the re-building of a model shape made using a procedure in which the input file characteristics were updated starting from those got by the scanning device in order to respect the original requirements defined in the computer aided environment. It was found that the physical re-building of an object is depending the characteristics of the input file that needs to be digitally processed in order to get the desired shape and geometry. In that way also FDM using PLA and polyamide materials can be utilized to get components or prototypes from scanned digital data. The results are reported in details.

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A Window Based Graphical User Interface for a Supersonic Combustion Fortran Code

ASME 1992 International Computers in Engineering Conference: Volume 1 — Artificial Intelligence; Expert Systems; CAD/CAM/CAE; Computers in Fluid Mechanics/Thermal Systems ◽

10.1115/cie1992-0064 ◽

1992 ◽

Author(s):

T. Gary Yip ◽

Ajay R. Patel

Keyword(s):

Real Time ◽

Input Sequence ◽

Supersonic Combustion ◽

Input File ◽

Input Interface ◽

Wide Acceptance ◽

Fortran Code ◽

Questions And Answers ◽

Application Programs ◽

Made In

Abstract Fortran has been used widely in number crunching applications. In recent years, as the size of application programs increases significantly, users begin to demand interactive capability so that they can interface with the applications in real time in a more flexible and convenient manner. In spite of the wide acceptance by engineers in various fields in the seventies and eighties, Fortran currently does not offer these features. INPUT/OUTPUT are structured rigidly by the order of the READ and WRITE statements in the application programs. The situation would get even worse when the program requires a large number of inputs from the user. A user can use a large input file in which the data must be in a fixed format and no comment statements are allowed. An alternative is to write a real time input interface with requests for inputs displayed on the screen. This leads to a long list of questions and answers scrolling up the screen. When a mistake is made in answering any one of the questions, the input sequence has to be restarted at the beginning of the program again.

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BaHaMAS A Bash Handler to Monitor and Administrate Simulations

EPJ Web of Conferences ◽

10.1051/epjconf/201817509003 ◽

2018 ◽

Vol 175 ◽

pp. 09003 ◽

Cited By ~ 2

Author(s):

Alessandro Sciarra

Keyword(s):

Physical Parameters ◽

Input File ◽

Script File

Numerical QCD is often extremely resource demanding and it is not rare to run hundreds of simulations at the same time. Each of these can last for days or even months and it typically requires a job-script file as well as an input file with the physical parameters for the application to be run. Moreover, some monitoring operations (i.e. copying, moving, deleting or modifying files, resume crashed jobs, etc.) are often required to guarantee that the final statistics is correctly accumulated. Proceeding manually in handling simulations is probably the most error-prone way and it is deadly uncomfortable and inefficient! BaHaMAS was developed and successfully used in the last years as a tool to automatically monitor and administrate simulations.

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Analysis Contour Plots in RELAP/SCDAPSIM/MOD 3.4 and MOD 4.1

Volume 4: Nuclear Safety, Security, and Cyber Security; Computer Code Verification and Validation ◽

10.1115/icone26-81991 ◽

2018 ◽

Author(s):

Heriberto Sánchez-Mora ◽

Carlos Chávez-Mercado ◽

Chris Allison ◽

Judith Hohorst

Keyword(s):

Nuclear Energy ◽

Nuclear Reactor ◽

Severe Accident ◽

Energy Industry ◽

Contour Plot ◽

Input File ◽

Systems Software ◽

Contour Plots ◽

Core Components ◽

Control Rods

RELAP/SCDAPSIM is a nuclear reactor simulator and accident analysis code that has been used in the nuclear energy industry for many years. Currently, Innovative Systems Software is developing a new tool that will show the behavior of the core components during a simulation of an accident. The addition of contour plots for the SCDAP components showing different properties: temperature, hydrogen production, etc. will allow a better understanding of core behavior during a severe accident in a nuclear reactor. The SCDAP components are fuel rods, electrically heated simulator rods, such as those used in the CORA experiments, control rods, a shroud and a BWR blade/box. This paper describes the progress in the development of the contour plot tool based on the OpenGL and FORTRAN90 libraries. The purpose of this tool is help to the user analyze the simulation of an accident and to debug an input file.

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job input file

Computer Science and Communications Dictionary ◽

10.1007/1-4020-0613-6_9683 ◽

2000 ◽

pp. 846-846

Author(s):

Martin H. Weik

Keyword(s):

Input File

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Coupling a Detonation Shock Dynamics Code to an Eulerian Hydrocode

Volume 4: Fluid-Structure Interaction ◽

10.1115/pvp2009-78100 ◽

2009 ◽

Author(s):

David L. Littlefield ◽

Young-Ho Kim ◽

David E. Lambert

Keyword(s):

Input File ◽

User Input ◽

Preliminary Work ◽

Shock Dynamics ◽

Boundary Information ◽

Detonation Shock ◽

Technical Effort

In this technical effort we have incorporated the Detonation Shock Dynamics (DSD) methodology into the Eulerian hydrocode CTH by coupling it to a DSD code called WAVETRACKER. Based on some preliminary work, we developed a strategy for coupling these two codes. Both CTH and WAVETRACKER are stand-alone codes. In the coupled code, CTH calls WAVETRACKER as a subroutine. Interface routines are developed to pass geometry, mesh and boundary information from CTH to WAVETRACKER. Additional parameters required by WAVETRACKER are read directly from a user input file. Results in the form of a burn table are interpolated and passed back from WAVETRACKER to CTH.

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