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An Abaqus plug-in to simulate fatigue crack growth

ENGINEERING WITH COMPUTERS 2022年第4期38卷 2991-3005页

作者： Malekan, Mohammad Khosravi, Ali St-Pierre, Luc Aarhus Univ Dept Mech & Prod Engn DK-8000 Aarhus C Denmark Aalto Univ Dept Mech Engn Espoo Finland

Fatigue crack propagation is an important consideration in evaluating the design life of engineering components, especially in the energy and transport industries. Despite its importance, fatigue analyses are not usually supported by commercial Finite Element (FE) codes;in fact, most FE codes require the addition of costly plug-ins to perform fatigue crack growth simulations. Therefore, this paper introduces a new, freely distributed plug-in to simulate fatigue crack growth with the commercial FE code Abaqus. The plug-in includes five different fatigue crack growth models and relies on the extended FE method to simulate crack propagation. The plug-in is limited to 2D analyses, but covers all necessary steps for fatigue crack growth simulations, from creating the geometry to job submission and post-processing. The implementation of the plug-in is validated by comparing its predictions to analytical and experimental results. Finally, we hope that the simplicity of the plug-in and the fact that it is distributed freely will make it a useful simulation tool for industrial, research and educational purposes.

关键词： Fatigue crack growth Abaqus plug-in python scripting Finite element method Life estimation

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Direct Visualization of the Earliest Stages of Crystallization

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MICROSCOPY AND MICROANALYSIS 2021年第4期27卷 659-665页

作者： Singh, Manish Kumar Ghosh, Chanchal Miller, Benjamin Carter, C. Barry Univ Connecticut Dept Mat Sci & Engn Storrs CT 06269 USA Gatan Inc 5794 W Las Positas Blvd Pleasanton CA 94588 USA Univ Connecticut Dept Chem & Biomol Engn Storrs CT 06269 USA Sandia Natl Labs Ctr Integrated Nanotechnol POB 5800 Albuquerque NM 87185 USA

Investigating the earliest stages of crystallization requires the transmission electron microscope (TEM) and is particularly challenging for materials which can be affected by the electron beam. Typically, when imaging at magnifications high enough to observe local crystallinity, the electron beam's current density must be high to produce adequate image contrast. Yet, minimizing the electron dose is necessary to reduce the changes caused by the beam. With the advent of a sensitive, high-speed, direct-detection camera for a TEM that is corrected for spherical aberration, it is possible to probe the early stages of crystallization at the atomic scale. High-quality images with low contrast can now be analyzed using new computing methods. In the present paper, this approach is illustrated for crystallization in a Ge2Sb2Te5 (GST-225) phase-change material which can undergo particularly rapid phase transformations and is sensitive to the electron beam. A thin (20 nm) film of GST-225 has been directly imaged in the TEM and the low-dose images processed using python scripting to extract details of the nanoscale nuclei. Quantitative analysis of the processed images in a video sequence also allows the growth of such nuclei to be followed.

关键词： beam-sensitive crystallization Ge2Sb2Te5 low-dose python scripting

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Design approach against failure of the earth support using the finite element method

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BAUTECHNIK 2023年第9期100卷 526-534页

作者： Jurgens, Hauke Henke, Sascha Univ Bundeswehr Hamburg Helmut Schmidt Univ Geotechn Holstenhofweg 85 D-22043 Hamburg Germany

The application of the finite element method (FEM) in geotechnical engineering has been established in the last decades for the prediction of deformations in the serviceability limit state (SLS). In practice, stability analyses in the ultimate limit state (ULS) are only partially performed using the FEM and are currently still state of the art. The next generation of Eurocode 7 is intended to regulate numerical methods with regard to their application in the ULS. However, the handling of the additionally required analysis of the German National Annex and DIN 1054 is still unsolved. In this paper, an approach for the numerical analysis of the earth support is presented. Following the wellestablished strength reduction method, the weight of the soil. and the cohesion c0 on the earth resistance side are reduced until failure occurs. On the basis of this, the analysis in ULS is carried out by defining a safety factor for the existing embedment depth of the retaining wall. This is followed by a comparison with the analytical free earth support method, identifying system reserves using the FEM.

关键词： FEM soil-structure-interaction excavation pits ULS verification earth support python scripting

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NMRbot: python scripts enable high-throughput data collection on current Bruker BioSpin NMR spectrometers

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METABOLOMICS 2013年第3期9卷 558-563页

作者： Clos, Lawrence J., II Jofre, M. Fransisca Ellinger, James J. Westler, William M. Markley, John L. Univ Wisconsin Natl Magnet Resonance Facil Madison Dept Biochem Madison WI 53706 USA

To facilitate the high-throughput acquisition of nuclear magnetic resonance (NMR) experimental data on large sets of samples, we have developed a simple and straightforward automated methodology that capitalizes on recent advances in Bruker BioSpin NMR spectrometer hardware and software. Given the daunting challenge for non-NMR experts to collect quality spectra, our goal was to increase user accessibility, provide customized functionality, and improve the consistency and reliability of resultant data. This methodology, NMRbot, is encoded in a set of scripts written in the python programming language accessible within the Bruker BioSpin TopSpin (TM) software. NMRbot improves automated data acquisition and offers novel tools for use in optimizing experimental parameters on the fly. This automated procedure has been successfully implemented for investigations in metabolomics, small-molecule library profiling, and protein-ligand titrations on four Bruker BioSpin NMR spectrometers at the National Magnetic Resonance Facility at Madison. The investigators reported benefits from ease of setup, improved spectral quality, convenient customizations, and overall time savings.

关键词： NMR spectroscopy Metabolomics Compound screening Automation Data collection python scripting

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Simplifying and enhancing the use of PyMOL with horizontal scripts

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PROTEIN SCIENCE 2016年第10期25卷 1873-1882页

作者： Mooers, Blaine H. M. Univ Oklahoma Hlth Sci Ctr Dept Biochem & Mol Biol Oklahoma City OK 73190 USA Univ Oklahoma Hlth Sci Ctr Stephenson Canc Ctr Oklahoma City OK USA

Scripts are used in PyMOL to exert precise control over the appearance of the output and to ease remaking similar images at a later time. We developed horizontal scripts to ease script development. A horizontal script makes a complete scene in PyMOL like a traditional vertical script. The commands in a horizontal script are separated by semicolons. These scripts are edited interactively on the command line with no need for an external text editor. This simpler workflow accelerates script development. In using PyMOL, the illustration of a molecular scene requires an 18-element matrix of view port settings. The default format spans several lines and is laborious to manually reformat for one line. This default format prevents the fast assembly of horizontal scripts that can reproduce a molecular scene. We solved this problem by writing a function that displays the settings on one line in a compact format suitable for horizontal scripts. We also demonstrate the mapping of aliases to horizontal scripts. Many aliases can be defined in a single script file, which can be useful for applying costume molecular representations to any structure. We also redefined horizontal scripts as python functions to enable the use of the help function to print documentation about an alias to the command history window. We discuss how these methods of using horizontal scripts both simplify and enhance the use of PyMOL in research and education.

关键词： molecular graphics molecular visualization molecular artwork scientific illustration scientific communication python scripting molecular literacy molecular orientation reproducible research

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Shortcuts for faster image creation in PyMOL

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PROTEIN SCIENCE 2020年第1期29卷 268-276页

作者： Mooers, Blaine H. M. Univ Oklahoma Hlth Sci Ctr Dept Biochem & Mol Biol Oklahoma City OK 73190 USA Univ Oklahoma Hlth Sci Ctr Stephenson Canc Ctr Oklahoma City OK USA

PyMOL is often used to generate images of biomolecular structures. Hundreds of parameters in PyMOL provide precise control over the appearance of structures. We developed 241 python functions-called "shortcuts"-that extend and ease the use of PyMOL. A user runs a shortcut by entering its name at the PyMOL prompt. We clustered the shortcuts by functionality into 25 groups for faster look-up. One set of shortcuts generates new styles of molecular representation. Another group saves files with time stamps in the file names;the unique filenames avoid overwriting files that have already been developed. A third group submits search terms in the user's web browser. The help function prints the function's documentation to the command history window. This documentation includes the PyMOL commands that the user can reuse by copying and pasting onto the command line or into a script file. The shortcuts should save the average PyMOL user many hours per year searching for code fragments in their computer or on-line. Statement for Lay Public Computer-generated images of protein structures are vital to the interpretation of and communication about the molecular structure of proteins. PyMOL is a popular computer program for generating such images. We made a large collection of macros or shortcuts that save time by executing complex operations with a few keystrokes.

关键词： macros molecular artwork molecular graphics molecular illustration molecular visualization PyMOL scripting language python scripting scientific illustration shortcuts visual narratives

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Development of methodology for assessment of long-term morphodynamic impact on flood hazard

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JOURNAL OF FLOOD RISK MANAGEMENT 2020年第4期13卷

作者： Dysarz, Tomasz Poznan Univ Life Sci Dept Hydraul & Sanit Engn Ul Wojska Polskiego 28 PL-60637 Poznan Poland

A methodology for quantification of the impact of sediment transport on flood hazard is proposed. The applied algorithm consists of several python scripts for automation of sediment routing, hydrodynamic simulations, and geoprocessing of results. Flood hazard maps are uniquely linked with particular simulations of morphological changes in a river. Finally, the maps are stochastically processed. The proposed procedure was applied for a selected reach of the Warta river, located in Poland. Simulations were run for 6- and 12-year flow series composed randomly on the basis of historical data. The 30 flow series for each period and four functions describing the transport of sediment were treated as uncertain variables. It was assumed that the features characterising the mean sample may properly represent the sediment content in the river reach studied. The final results are presented as maps showing the probabilities of inundation. The comparison of results with literature data confirmed the significance of the impact related to sediment transport processes on the quantification of flood hazard uncertainty. The main advantages of the presented algorithm are effective management of simulations and processing of results obtained in 240 runs of the sediment routing model.

关键词： flood hazard assessment flood mapping modelling of sediment transport python scripting

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TopoStats - A program for automated tracing of biomolecules from AFM images

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METHODS 2021年 193卷 68-79页

作者： Beton, Joseph G. Moorehead, Robert Helfmann, Luzie Gray, Robert Hoogenboom, Bart W. Joseph, Agnel Praveen Topf, Maya Pyne, Alice L. B. Birkbeck Univ London Inst Struct & Mol Biol London WC1E 7HX England Leibniz Inst Expt Virol Heinrich Pette Inst Ctr Struct Syst Biol Hamburg Germany Univ Klinikum Hamburg Eppendorf Hamburg Germany Univ Sheffield Henry Royce Inst Sir Robert Hadfield Bldg Sheffield S1 3JD S Yorkshire England Univ Sheffield Dept Mat Sci & Engn Sir Robert Hadfield Bldg Sheffield S1 3JD S Yorkshire England UCL London Ctr Nanotechnol London WC1H 0AH England

We present TopoStats, a python toolkit for automated editing and analysis of Atomic Force Microscopy images. The program automates identification and tracing of individual molecules in circular and linear conformations without user input. TopoStats was able to identify and trace a range of molecules within AFM images, finding, on average, similar to 90% of all individual molecules and molecular assemblies within a wide field of view, and without the need for prior processing. DNA minicircles of varying size, DNA origami rings and pore forming proteins were identified and accurately traced with contour lengths of traces typically within 10 nm of the predicted contour length. TopoStats was also able to reliably identify and trace linear and enclosed circular molecules within a mixed population. The program is freely available via GitHub (https://***/afm-spm/topostates) and is intended to be modified and adapted for use if required.

关键词： Atomic Force Microscopy (AFM) Single-molecule imaging Image analysis python scripting Biomolecular structure DNA

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Development of a relative coastal vulnerability index in a macro-tidal environment for climate change adaptation

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JOURNAL OF COASTAL CONSERVATION 2013年第4期17卷 775-797页

作者： Tibbetts, Jeremy R. van Proosdij, Danika St Marys Univ Dept Geog Halifax NS B3H 3C3 Canada

Coastal vulnerability assessments to climate change impacts have been conducted in the past. However, few if any account for the highly variable risk associated with tidal stage in macro-tidal environments. The purpose of this research was to develop a geomatics tool which interactively determines the biophysical vulnerability of a macro-tidal estuary in the Bay of Fundy to varying levels of storm surge and tide state. A conceptual framework was designed to illustrate the relative interrelationships between exposure conditions (surge height, tidal stage), biophysical state (freeboard, exposure, width of foreshore, intertidal slope, observed erodibility, shore protection) and morphological resilience condition. This conceptual framework was then used to develop a dynamic, custom python programming script within ArcGIS 9.3 to calculate coastal vulnerability for user determined combinations of surge height and tide state. The analysis was conducted for four coastlines, backshore, upper foreshore, middle foreshore and lower foreshore, to reflect varying biophysical states with varying tide levels. The results of the tool were compared with known areas of concern (high erosion, dyke overtopping), as determined by historical records, local expert knowledge and GIS analysis of aerial photography. The number of known locations of concern is lower than that of the results produced by the tool. This is most likely due to the results being analyzed at extreme water levels, greater than higher high water large tide. However, this estimation of vulnerability may limit negative impacts of climate change by highlighting vulnerable areas prior to an event, allowing coastal managers and planners to install measures to reduce the vulnerability and enhance the adaptive capacity of local communities.

关键词： Coastal vulnerability assessment Geographic information system python scripting Storm surge Shoreline

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Performance Analysis on Network Automation Interaction with Network Devices Using python 11

Performance Analysis on Network Automation Interaction with ...

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11th IEEE Symposium on Computer Applications and Industrial Electronics (ISCAIE)

作者： Mazin, Aladhami Mahmood Ab Rahman, Ruhani Kassim, Murizah Mahmud, Abd Razak Univ Teknol MARA Fac Elect Engn Uitm Shah Alam 40450 Selangor Malaysia

ISBN: (纸本)9781665403382

Recent research has shown that 95% of network tasks are monitored manually. This has consumed a lot of money and time. Many workers need to be employed for the same tasks in network deployment. This analysis aims to identify the best method that can improve the efficiency of scripting in configuring network devices and to find the differences in performance in the time needed to configure network devices between manual method and automation. Network topology was designed that contains 36 Cisco devices with different IOS versions. The topology was designed precisely to implement automation in a practical way that can reduce the time needed for configuration with no errors. Based on data analysis from the emulator that mimics a realistic network environment, it is identified that automation is a superior method in configuring Cisco devices because automation can save up to 99% of the time needed. The performance presents the automation method required only 120 seconds to configure all Cisco devices compared to the manual method that required 5797 seconds. Besides, zero errors were reported in automation, while 2 errors were identified in the manual method. This research is significant and practical in helping the network administrators to handle network configurations and automation in deployments of the network systems in an organization.

关键词： Performance analysis network automation python scripting Software-defined network Cisco DevNet

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