April 14, 2024 Software Open Access

Lecrivain, Gregory

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{
  "license": "https://creativecommons.org/licenses/by/4.0/legalcode", 
  "url": "https://rodare.hzdr.de/record/2803", 
  "contributor": [
    {
      "affiliation": "Helmholtz-Zentrum Dresden-Rossendorf", 
      "@type": "Person", 
      "name": "Lecrivain, Gregory"
    }
  ], 
  "datePublished": "2024-04-14", 
  "inLanguage": {
    "alternateName": "eng", 
    "@type": "Language", 
    "name": "English"
  }, 
  "@context": "https://schema.org/", 
  "name": "Self-folding of two-dimensional thin templates into pyramidal micro-structures by a liquid drop - a numerical model", 
  "creator": [
    {
      "affiliation": "Helmholtz-Zentrum Dresden-Rossendorf", 
      "@type": "Person", 
      "@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.2803", 
  "@type": "SoftwareSourceCode", 
  "@id": "https://doi.org/10.14278/rodare.2803", 
  "keywords": [
    "Micro-origami simulation", 
    "drop encapsulation", 
    "self-folding", 
    "fluid-structure interaction"
  ], 
  "version": "1.1", 
  "description": "<p>Source files and selected raw data related to the manuscript &quot;Self-folding of two-dimensional thin templates into pyramidal micro-structures by a liquid drop - a numerical model&quot; by Gregory Lecrivain, Helmholtz-Zentrum Dresden-Rossendorf, Germany, 2024.</p>\n\n<p>1) folder &quot;manuscript&quot;,<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 &quot;scripts&quot;<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<br>\npip install pyquaternion matplotlib scipy intersect</p>\n\n<p>3) folder &quot;figures&quot;<br>\nThis folder contain information on how to run the simulations related to the figure.<br>\nMore information in README file in each figure/figureX subfloder with X the figure number in the manuscript.</p>\n\n<p>4) folder &quot;src&quot;<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 &quot;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&quot;.</p>\n\n<p>4.2)<br>\nTo compile the libraries, open a terminal, cd to the src directory and type &quot;make libs&quot;. All outputs will placed in the folder $HOME/local. The libraries&#39; 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 in $HOME/Paraview/ParaView-5.9.1-MPI-Linux-Python3.8-64bit/. pvpython is used to export txt data (hinge, drop and three-phase contact line) to vtk format.</p>\n\n<p>4.4)<br>\nOpen your ~/.bashrc file and add the following lines.<br>\nexport IGL_NUM_THREADS=1<br>\nexport LD_LIBRARY_PATH=$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:$HOME/Documents/microorigami/src #(or whereever, your chosen parent directory is)<br>\nexport PATH=$PATH:$HOME/Documents/microorigami/scripts #(or whereever, your chosen parent directory is)<br>\nexport PATH=$PATH:$HOME/Documents/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 &quot;make check_library_path&quot;. The terminal should return<br>\n&quot;library path to libconfig is correct&quot;<br>\n&quot;library path to gmp is correct&quot;<br>\n&quot;library path to mpfr is correct&quot;<br>\nIf that is the case, i.e. the paths are correctly set. To compile, type &quot;make main post&quot;. Alternatively, one can speed up the installation by typing &quot;make -j 4 main post&quot;, 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 &quot;make doxy&quot;. The folder html will appear under src.</p>\n\n<p>4.7)<br>\nType &quot;make clean&quot; to clean the src folder</p>\n\n<p>5) folders &quot;caX_sideY_ecZ.zip&quot;<br>\nThe zip files contains, where where 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, are selected raw data related to Figure 10. All other raw data can be reproduced by following the commands in the README text file located in each figX folder, with X=1,2,...,13. After 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 &quot;source Utils.sh; ExportScript --verbose --submit&quot; in the working directory wd on the hpc. The bash function ExportScript is located in &quot;scripts/Utils.sh&quot;.</p>"
}