Software Open Access
{ "inLanguage": { "alternateName": "eng", "@type": "Language", "name": "English" }, "@type": "SoftwareSourceCode", "@id": "https://doi.org/10.14278/rodare.3034", "keywords": [ "Micro-origami simulation", "Drop encapsulation", "Self-folding", "Fluid-structure interaction" ], "datePublished": "2024-07-01", "url": "https://rodare.hzdr.de/record/3034", "version": "1.1", "license": "https://creativecommons.org/licenses/by/4.0/legalcode", "creator": [ { "@type": "Person", "affiliation": "Helmholtz-Zentrum Dresden-Rossendorf", "@id": "https://orcid.org/0000-0003-0540-3426", "name": "Lecrivain, Gregory" } ], "sameAs": [ "https://www.hzdr.de/publications/Publ-37084" ], "identifier": "https://doi.org/10.14278/rodare.3034", "@context": "https://schema.org/", "description": "<p>Source files and selected raw data related to the manuscript "Self-folding of two-dimensional thin templates into pyramidal micro-structures by a liquid drop - a numerical model" by Gregory Lecrivain, Helmholtz-Zentrum Dresden-Rossendorf, Germany, 2024.</p>\n\n<p>1) folder "manuscript",<br>\nThis folder contains all text documents related to manuscript. Text and final figures are found in the directory.</p>\n\n<p>2) folder "scripts"<br>\nThis folder contains python and bash scripts used to post-process the raw data and prepare the figures. You will need to install some python3 libraries. Use the following command: pip install pyquaternion matplotlib scipy intersect.</p>\n\n<p>3) folder "figures"<br>\nThis folder contain information on how to run the simulations related to the figure. More information can be found in the README text file located in each figure/figX subfolder, where X the figure number in the manuscript.</p>\n\n<p>4) folder "src"<br>\nThis folder contains the all c++ files related to the source code.</p>\n\n<p>4.1)<br>\nPrior to compiling, you should have gcc(7.3.0), openmpi(2.1.2), make(4.3), cmake(3.20.2), python(3.8.0), blas(3.8.0), lapack(3.8.0), boost(1.78.0), and git(2.30.1) available on your machine. The version number in the parenthesis corresponds to the one I used on the local HPC available at my institution. In my case, I type "module load gcc/7.3.0 openmpi/2.1.2 make/4.3 cmake/3.20.2 python/3.8.0 blas/3.8.0 lapack/3.8.0 boost/1.78.0 git/2.30.1".</p>\n\n<p>4.2)<br>\nTo compile the libraries, open a terminal, cd to the src directory and type "make libs". All outputs will placed in the folder $HOME/local. The libraries' tarballs needed to compile the code are placed in the Libs directory.</p>\n\n<p>4.3)<br>\nI have manually installed paraview 5.9.1. pvpython is used to export txt data (hinge, drop and three-phase contact line) to vtk format.</p>\n\n<p>4.4)<br>\nOpen your ~/.bashrc file and add the following lines.<br>\nexport IGL_NUM_THREADS=1<br>\nexport LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/local/libconfig-1.7.3/lib<br>\nexport LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/local/gmp-6.2.1/lib<br>\nexport LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/local/mpfr-4.1.0/lib<br>\nexport PATH=$PATH:$HOME/microorigami/src #(or whereever, your chosen parent directory is)<br>\nexport PATH=$PATH:$HOME/microorigami/scripts #(or whereever, your chosen parent directory is)<br>\nexport PATH=$PATH:$HOME/microorigami/paraview/bin #(or whatever path you used)</p>\n\n<p>4.5)<br>\nopen a new terminal, cd to the src directory and type "make check_library_path". The terminal should return<br>\n"library path to libconfig is correct"<br>\n"library path to gmp is correct"<br>\n"library path to mpfr is correct"<br>\nIf that is the case, i.e. the paths are correctly set. To compile, type "make main post". Alternatively, one can speed up the installation by typing "make -j 4 main post", where 4 is the number of cpus I use.</p>\n\n<p>4.6)<br>\nHelp is available in each header file (.h) in the form of doxygen comments. Type "make doxy". The folder html will appear under src.</p>\n\n<p>4.7)<br>\nType "make clean" to clean the src folder</p>\n\n<p>5) folders "caX_sideY_ecZ.zip"<br>\nThe zip files contains the raw data related to Figure 10. Here, X = 70 is the contact angle, Y = 5 the number of side panels and Z = 0.8, 1.6 and 2.4 the elasto-capillary number. After data extraction, three folders will be created, namely wd/ca70/side5/ec0.8, wd/ca70/side5/ec1.6 and wd/ca70/side5/ec2.4, where wd is your working directory. To convert the data into human-readable format (txt, vtk, stl,...) type "source Utils.sh; ExportScript --verbose --submit" in the working directory wd on the hpc. The bash function ExportScript is located in "scripts/Utils.sh". All other raw data can be obtained by following the commands in the README text file located in each figX folder, with X=1,2,...,13. With Paraview, one is able to visualize the self-folding by loading the stl files.</p>", "contributor": [ { "@type": "Person", "affiliation": "Helmholtz-Zentrum Dresden-Rossendorf", "name": "Lecrivain, Gregory" } ], "name": "Self-folding of two-dimensional thin templates into pyramidal micro-structures by a liquid drop - a numerical model" }
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