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10 results for “Modular design”
Supplementary codes and datasets for "Modular-topology optimization of structures and mechanisms with free material design and clustering"
<p>This repository supports Tyburec, M., Doškář, M., Zeman, J., & Kružík, M. (2022). Modular-topology optimization of structures and mechanisms with free material design and clustering. <em>Computer Methods in Applied Mechanics and Engineering</em>, <em>395</em>, 114977. <a href="https://doi.org/10.1016/j.cma.2022.114977">https://doi.org/10.1016/j.cma.2022.114977</a> (first published as preprint <a href="http://arxiv.org/abs/2111.10439">2111.10439</a> at arXiv.org).</p> <p>This repository contains:</p> <ol> <li>MATLAB source codes for <em>(modular) free material optimisation</em> and <em>hierarchical stiffness clustering</em> (folder <code>./mFMO/</code>)</li> <li>C++ source codes for <em>modular topology optimization</em> (folder <code>./MTO/</code>)</li> <li>Input/output data of the test suite (folder <code>./data/</code>)</li> </ol> <p><strong>1. Data flow</strong></p> <p>The test suite considered in the manuscript covers 4 problems:</p> <ol> <li>Messerschmitt-Bölkow-Blohm beam (labelled as <code>mbb</code>)</li> <li>Inverter compliant mechanism (labelled as <code>inv</code>)</li> <li>Gripper compliant mechanism (labelled as <code>grip</code>)</li> <li>Reusable design of both compliant mechanisms (labelled as <code>invgrip</code>)</li> </ol> <p>Each problem in the dataset is stored within a separate subfolder named according to the labels mentioned above. The final level of subdirectories <code>{X}color</code> comprises of the results for problems with <code>X</code> denoting the number of edge codes considered for each edge direction during the clustering (<code>0color</code> stands for a non-modular design and <code>1color</code> represents the design based on Periodic Unit Cell).</p> <p>Each of the folders contains outputs of the modular free material optimisation in the following form:</p> <ul> <li><code>{label}{X}.mat</code></li> <li><code>{label}{X}.til</code></li> <li><code>{label}{X}.tset</code></li> <li><code>{label}{X}guess.mat</code></li> </ul> <p>Files <code>*.til</code>, <code>*.tset</code>, and <code>*guess.mat</code> are then converted into a JSON input file for the modular topology optimization code with generator scripts which can be found in <code>./MTO/scripts</code> folder. Note that each of the problems in the test suite has its own generator script <code>generate_modular_problem_{MBB,inverter,gripper,inverterAndGripper}.mat</code>. The generator scripts make a directory named according to the key <code>MTO_{n}_kernelSensitivity</code>, where <code>n</code> denotes the resolution of each module (i.e. the number of nodes along one direction). The directory also contains the outputs of the modular topology optimisation in the form of the initial and the final state of the optimization in <code>VTK</code> files and visualisation of the final state in <code>SVG</code> files. The log file <code>log.txt</code> stores the optimized objective and progress of the value along with stopping criteria quantities during iterations.</p> <p><strong>2. Running codes</strong></p> <p><strong>2.1 Modular free material optimisation</strong></p> <p>MATLAB scripts and functions for (modular) Free Material Optimization (FMO) are contained in the <code>mFMO</code> data folder. The codes have been tested with MATLAB R2019b. To run the codes the user is required to install the <a href="http://www.penopt.com">PENNON optimizer</a>. A free academic license is provided by its authors on request.</p> <p>Input files for individual problems are defined in the <code>mFMO/problems</code> folder and are launched with the <code>runproblem(problemName, numClusters)</code>, where <code>problemName</code> refers to the file in the <code>mFMO/problems</code> folder without the file extension and <code>numClusters</code> denotes the maximum number of color codes in Wang tiling formalism.</p> <p>If successful, the optimization produces output files in <code>mFMO/fmo_fig/{label}/{X}colors/{T}/</code>:</p> <ul> <li><code>{label}{X}.mat</code> (contains clustering and tiling information)</li> <li><code>{label}{X}_tmp.mat</code> (contains results of non-modular FMO)</li> <li><code>{label}{X}.til</code> (the assembly plan)</li> <li><code>{label}{X}.tset</code> (Wang tile set)</li> <li><code>{label}{X}guess.mat</code> (guess for TO)</li> </ul> <p>where <code>T</code> is the optimization time stamp.</p> <p><strong>2.2 Modular topology optimisation</strong></p> <p>All results were obtained with version <code>v1.1.2</code>, which is also provided in the folder <code>MTO</code>, and linked Intel® oneAPI Math Kernel Library and the incorporated PARDISO sparse solver. For the recent development of the code see the open git repository at <a href="https://gitlab.com/MartinDoskar/modular-topology-optimization">https://gitlab.com/MartinDoskar/modular-topology-optimization</a>. The repository also contains a detailed description of input parameters and code design.</p> <p>Modular topology optimisation code uses CMake for the cross-platform build automation. For instance, under Linux, the whole code can be compiled in the standard five steps:</p> <pre><code>cd ./MTO mkdir build cd ./build cmake -DCMAKE_BUILD_TYPE=Release .. make </code></pre> <p>All executables are automatically stored in <code>./MTO/bin/</code> folder. Individual problems can be optimized by parsing the JSON files obtained from the generator scripts as an argument to the MTO.Application binary, e.g.,</p> <pre><code>./MTO/bin/MTO.Application.exe path_to_data/mbb/2color/MTO_100_kernelSensitivity/input_modular_mbb_2colours_100.json </code></pre> <p><strong>Acknowledgement</strong></p> <p>The related research and code development was supported by the <a href="https://gacr.cz/en/">Czech Science Foundation</a>, project No. 19-26143X.</p>
Supplementary codes and datasets for "Wang tiles enable combinatorial design and robot-assisted manufacturing of modular mechanical metamaterials"
<p>This repository provides data and codes for manuscript “Wang tiles enable combinatorial design and robot-assisted manufacturing of modular mechanical metamaterials” by M. Doškář, M. Somr, R. Hlůžek, J. Havelka, J. Novák, and J. Zeman, published first as a preprint <a href="https://arxiv.org/abs/2305.09280">arXiv:2305.09280</a> at arXiv.org; see the actual description of the Zenodo entry for the latest reference.</p> <p>This repository contains:</p> <ol> <li>MATLAB and C++ source codes for combinatorial design and numerical analyses (folder <code>./numerics/</code>),</li> <li>experimental data (folder <code>./experiments/</code>),</li> <li>3D models of parts used in robotic-assembly (folder <code>./models/</code>),</li> <li>a control script for robotic assembly (folder <code>./robotics/</code>).</li> </ol> <p><strong>Numerics</strong></p> <p>All simulations were performed with an in-house MATLAB code, which extends the finite element toolbox for finite strain calculations accompanying the work of <a href="https://doi.org/10.1016/j.cma.2020.113333">van Bree, S. E. H. M., Rokoš, O., Peerlings, R. H. J., Doškář, M., & Geers, M. G. D. (2020). A Newton solver for micromorphic computational homogenization enabling multiscale buckling analysis of pattern-transforming metamaterials. Computer Methods in Applied Mechanics and Engineering, 372, 113333</a>. In particular, this snapshot corresponds to a cleaned-up version (excluding files unrelated to the publications) of commit <code>21cfc2e9</code>.</p> <p>The MATLAB codebase contains MEX files written in C++ to accelerate selected procedures. In order to run any code, these MEX files must be compiled first. We use CMake build automation, with the main <code>CMakeLists.txt</code> located in <code>./numerics/mex</code>.</p> <p>Combinatorial search was performed by the <code>RUN_modular_exploration.m</code> script; see definition of problems with the script. The results of the enumerations, stored in <code>./dat/exploration</code>, were analysed with <code>POST_modular_S_v3.m</code>, identifying layouts leading to the extreme (min/max) tilt angles.</p> <p>Comparison against experimental measurements was facilitated by a series of scripts <code>POST_DIC_{...}.m</code>. First, run <code>POST_DIC_step1_extract_points_in_mesh.m</code> to identify locations.mat. Next, post-process extensometer data with <code>POST_DIC_step2_merge_extensometer_data.m</code>, and use <code>POST_DIC_step3_impose_extracted_BC.m</code> to parse DIC results in a format suitable for imposing BC later in this script. Finally, comparison between experimental and computed displacements is provided by <code>POST_DIC_step4_modular_comparison_experiments.m</code>. (Note that the particular files need to be manually provided in the “Compute deformation process” part of <code>POST_DIC_step4_modular_comparison_experiments.m</code>.)</p> <p><strong>Experimental data</strong></p> <p>This folder contains data from (i) an unixaial tension test of a dogbone specimen (both from a MTS loading machine and DIC data) and (ii) two measurement sessions extracting the L-shape domain responses using DIC (<code>20_11_30 - Hluzek_Elka_newassemblyplan</code> and <code>21_04_12 - Hluzek_ Elka_quarters</code> with lower loading threshold). For post-processing, see the above-mentioned <code>POST_DIC_{...}.m</code> scripts. <code>*.mat</code> files present directly in <code>./experiments/</code> folder were obtained and are need by those scripts.</p> <p><strong>3D models</strong></p> <p>The folder contains geometrical models for individual parts needed for robot-assisted assembly of module molds for casting. This includes:</p> <ol> <li>a silo extension to store more tiles (file <code>silo_extension.stl</code>),</li> <li>formwork modules around the main structure for the purpose of casting silicone (file <code>tile_formwork.stl</code>),</li> <li>all types of tiles for the inside structure (file <code>tile_inside_types.stl</code>),</li> <li>a spacer shaped for YuMi base to ensure correct distance of the silo and build plate (file <code>yumi_base_1.stl</code>),</li> <li>a spacer shaped for YuMi base to ensure correct distance of the silo and build plate (file <code>yumi_base_2.stl</code>),</li> <li>a spacer shaped for YuMi base to ensure correct distance of the silo and build plate (file <code>yumi_base_3.stl</code>),</li> <li>connection for spacers (file <code>yumi_base_4.stl</code>),</li> <li>spacer holding a silo and the build plate (file <code>yumi_base_5.stl</code>),</li> <li>YuMi grippers with extensions to hold the tiles (file <code>grippers_extend.st</code>).</li> </ol> <p><strong>Robotics</strong></p> <p>The folder contains a single file with a script created in RobotStudio (RobotWare Version: 6.08.01.00, SmartGripper Version: 3.55.0000.00) to assemble the plan with YuMi IRB 14000-0.5/0.5 left hand.</p> <p><strong>Acknowledgement</strong></p> <p>The related research, experiments, and code development were supported by the <a href="https://gacr.cz/en/">Czech Science Foundation</a>, project No. 19-26143X.</p>
Benne: A Modular Data Stream Clustering Algorithm with Flexible Design Choices
<p>All of the source dataset with preprocessed format [id features class] that have been used for evaluation in the paper.</p>
Modular nanomagnet design for spin qubits confined in a linear chain
<p>supporting data</p>
Design of Modular Autoproteolytic Gene Switches Responsive to Anti-Coronavirus Drug Candidates
<p>Data underlying the figures in the publication “Design of modular autoproteolytic gene switches responsive to anti-coronavirus drug candidates”, published in <em>Nat. Commun.</em>, <strong>2021</strong>, 12, 6786.</p> <p><a href="https://doi.org/10.1038/s41467-021-27072-3">https://doi.org/10.1038/s41467-021-27072-3</a></p> <p> </p> <p>Table of contents:</p> <p><strong>1. Supplementary Information.pdf</strong>: Document containing the Supplementary Tables 1-7 and the Supplementary Figures 1-10.</p> <p><strong>2. Dataset 1</strong>: Raw data points used to create the main and supplementary figures of the paper arranged in worksheets panel by panel.</p> <p> </p> <p>Data availability</p> <p>Sequence data of plasmids encoding PLpro-TAGS and Mpro-TAGS have been deposited in GenBank under accession codes OK425851, OK425852, and OK425853. Original plasmids are available upon request. All vector information is provided in Supplementary Table 4. Detailed statistical analysis is provided in Supplementary Table 7. Source data is provided in the Source data file. Source data are provided with this paper.</p>
Extension of Towards Large Scale Automated Algorithm Design by Integrating Modular Benchmarking Frameworks
<p>This provides the dataset and the corresponding parsing scripts that extend the "Towards Large Scale Automated Algorithm Design by Integrating Modular Benchmarking Frameworks" study.</p>
Dataset: On the Stability of a Modular 1000 kV HVDC divider design
<p>In order to calibrate high voltage dividers in testing laboratories and HVDC converter substations, a new measurement infrastructure for on-site calibration up to 1000 kV was established in 2013. A 1000 kV wide-band modular HVDC divider was built divided into stackable 200 kV HV modules for agile on-site assessment, with protection against damage from transients, and for measuring of ripple voltage. Nine 200 kV modules were built by the five NMIs and stacked to one 1000 kV divider and one 800 kV voltage divider. The scale factors of the two dividers were determined in a comparison campaign in June 2013, resulting in a combined expanded uncertainty better than 20 μV/V at 1000 kV, and better than 15 μV/V for 200 kV. Traceability of five modular systems have since been<br> maintained using three methods; where the first method is calibration of the HV resistance of each module and LV arm, calculating the scale factors. The second method uses the Hamon transfer method, applied by RISE with five 200 kV modules. The third method is by comparison of the scale factor which includes the LV arm against a lower voltage reference divider. This paper presents the stability and robustness of all divider systems from June 2013 to spring 2022. The long-term stability is presented for the resistance of both the high voltage and the low voltage arm as well as the scale factor. The result shows an unprecedented stability of a HV divider system.</p>
Femoral Remodeling Following Total Hip Arthroplasty With OMNI Apex Modular™ and OMNI Apex ARC™ Stem Compared to Competitive Designs
ClinicalTrials.gov study NCT01359540. IPD Sharing: Not stated. Countries: 1. Publications: 0.
A supernumerary designer chromosome for modular in vivo pathway assembly in Saccharomyces cerevisiae
GEO Series GSE159524. Saccharomyces cerevisiae. 6 samples. Type: Expression profiling by high throughput sequencing.
Modular Design of T Cell Nanoengagers for Tumor Immunotherapy via Genetically Engineered Lipid-Tagged Antibody Fragments
GEO Series GSE293206. Mus musculus. 9 samples. Type: Expression profiling by high throughput sequencing.
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