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Pushing the frontiers of polymer simulation with texture memory

Airidas Korolkovas

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  "publisher": "Zenodo", 
  "DOI": "10.5281/zenodo.1305227", 
  "container_title": "Advanced Theory and Simulations", 
  "language": "eng", 
  "title": "Pushing the frontiers of polymer simulation with texture memory", 
  "issued": {
    "date-parts": [
  "abstract": "<p>Pushing the frontiers of polymer simulation with texture memory<br>\n---------------------------------------------------------------</p>\n\n<p><br>\nWelcome to the Source Code for simulating entangled star polymers.<br>\nThis custom software was used to generate data for the article &ldquo;Five dimensional entanglement in star polymer dynamics&quot;<br>\npublished in Advanced Theory and Simulations (Wiley)<br>\nA preprint is available here:</p>\n\n<p>The demo provided here simulates Brownian dynamics of NS=104 stars with 3 arms, of length N=356 beads per arm.<br>\nIt requires a CUDA-enabled GPU card, which is managed from a Matlab environment using the launchstars.m script.<br>\nThe .cu source files are included and have been pre-compiled for several star sizes using this command:<br>\n&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; mexcuda</p>\n\n<p>Now simply run:<br>\n&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; launchstars.m</p>\n\n<p>The default settings create the initial polymer configuration in Matlab, which is then transferred to GPU and processed by CUDA for 1000 steps.<br>\nThe resulting configuration is returned to Matlab, and selected data is stored for later analysis.<br>\nThis cycle is repeated 200 times, and the real-space configuration is optionally plotted in 3D (see a snapshot in the Figures folder).<br>\nOnce the demo is complete, you may verify the speed of the computation using this command (it runs an extra numIterations=1000 steps):</p>\n\n<p>&nbsp;&nbsp; &nbsp;tic; [R, randvector, ~] = fh(single(gpuArray(R)), randvector, b, vstrong, rstrong, cosbeta, numIterations, timeStep); toc;<br>\n&nbsp;&nbsp; &nbsp;Elapsed time is 0.398752 seconds.</p>\n\n<p>The above figure is for a box of 104*3*356=111072 beads, 1000 iterations, using a Titan XP card donated by the NVIDIA Corporation.<br>\nThe whole demo lasts about 1 minute 30 seconds.<br>\nThe branch point trajectory may be analysed by running the script autodiff.m provided in the Data Analysis Tools folder.<br>\nA typical result is shown in the MSD.pdf figure. Sub-reptative behaviour (negative slope) is apparent within one minute of simulation.</p>\n\n<p><br>\nAuthor:<br>\nAiridas Korolkovas, PhD<br>\nInstitut Laue-Langevin<br>\nUppsala University<br>\<br>\</p>\n\n<p>July 04, 2018</p>", 
  "author": [
      "family": "Airidas Korolkovas"
  "type": "article", 
  "id": "1305227"
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