Changes between Version 3 and Version 4 of PaperTutorials/Frontiers2014


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Timestamp:
Dec 15, 2014, 3:48:46 PM (6 years ago)
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tutorial
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Auto tutorial submission based on revision r23235

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  • PaperTutorials/Frontiers2014

    v3 v4  
    99Welcome to the Chaste wiki.
    1010
    11 This section contains pages generated automatically from the source code accompanying "Cellular cardiac electrophysiology modelling with Chaste and CellML", our paper in Frontiers in Physiology.
     11This section contains pages generated automatically from the source code accompanying "[http://dx.doi.org/10.3389/fphys.2014.00511 Cellular cardiac electrophysiology modelling with Chaste and CellML]", our paper in [http://journal.frontiersin.org/ResearchTopic/2502 Frontiers in Physiology].
    1212
    1313Before running these examples you will need to [wiki:InstallGuides/InstallGuide install Chaste's dependencies] and the [http://www.cs.ox.ac.uk/chaste/download.html source code for version 3.3].
     
    3030== Tissue electrophysiology benchmarks ==
    3131
    32 The steps required to reproduce the study are:
    33  1. Study the convergence of reference monodomain tissue simulation solutions ([wiki:./MonodomainConvergence Monodomain Convergence])
     32The [wiki:./MonodomainConvergence preliminary study examining convergence properties in space and time for the different models] was run separately.
     33We then hardcoded suitable space and time steps for the PDE in the following steps, which can be followed to reproduce the study:
    3434 1. Calculate the required ODE solver timesteps to meet target PDE accuracy ([wiki:./MonodomainCalculateRequiredTimesteps Monodomain Calculate Required Timesteps])
    3535 1. Benchmark monodomain tissue simulation solving times with different numerical methods ([wiki:./MonodomainSolvingTimes Monodomain Solving Times])
     
    3939== Sample commands to install and run everything ==
    4040
    41 If you wish to install Chaste and this project direct from our repository, you may do so from the command line as follows:
     41If you wish to install the latest versions Chaste and this project direct from our repository, you may do so from the command line as follows:
    4242{{{
    4343#!sh
     
    4747}}}
    4848
    49 To run all the steps listed above, exploiting multiple cores on your machine, use:
     49To run all the steps listed above, exploiting multiple cores on your machine where appropriate, use:
    5050{{{
    5151#!sh
     
    5757
    5858# Note the change in build= option: these simulations cannot run in parallel
    59 scons chaste_libs=1 brief=1 build=GccOptNative -j8 projects/Frontiers2014/test/TestMonodomainConvergenceLiteratePaper.hpp
    6059scons chaste_libs=1 brief=1 build=GccOptNative -j8 projects/Frontiers2014/test/TestMonodomainCalculateRequiredTimestepsLiteratePaper.hpp
    6160scons chaste_libs=1 brief=1 build=GccOptNative -j8 projects/Frontiers2014/test/TestMonodomainSolvingTimesLiteratePaper.hpp
     61
     62# To run the preliminary study on PDE convergence, use
     63scons chaste_libs=1 brief=1 build=GccOptNative -j8 projects/Frontiers2014/test/TestMonodomainConvergenceLiteratePaper.hpp run_time_flags="--timestep 0.001 --spacestep 0.001 --reset"
     64# Other values for timestep & spacestep can be given, as desired.
     65# The --reset flag says to reset CVODE fully at each PDE time step.
    6266}}}
    6367