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BioDynaMo 1.02
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@LukasBreitwieser LukasBreitwieser released this 29 Nov 12:25
· 200 commits to master since this release
v1.02
22bf7ea
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Learn about vigilant mode.

The following people have contributed to this version
(ordered by the number of contributions):

  • Lukas Breitwieser
  • Tobias Duswald
  • Fons Rademakers
  • Ahmad Hesam
  • Will Hemsley

New Features

  • Enabled one-line install script to install arbitrary BioDynaMo versions #231
  • Add Scheduler function to print operation information
  • Added parallelized optimization manager #205
  • Added googletest support for simulations #187
  • Improved biodynamo cli #215
  • Added experimental version of the automated benchmarking suite #202
  • Added CopyExecutionContext
  • Added support for different execution orders
  • Introduced execution context interface #189
  • Reduced memory consumption of the BDM memory manager #186
  • Added SphericalAgent
  • Added toroidal space boundary condition
  • Added RandomizedRm to randomize the iteration over all agents
  • Added support for hierarchical agent-based models
  • Added analysis classes to simplify data collection and plotting #177
  • Improved random number generation
  • Added Scheduler::SimulateUntil(exit_condition)
  • Added class LambdaFunctor and function L2F to simplify functor creation #175
  • Added octree and kd-tree as alternative environments #169

Bug Fixes

  • Fixed environment inconsistencies #226
  • Added simulation dependent diffusion time step #198
  • Fixed bug in diffusion grid initialization #199
  • Fixed MathArray::Norm and Normalize for zero vector #194
  • Do not call Rm::EndOfIteration in ExecCtxt::SetupIterationAll
  • Fixed errors in the static agent detection mechanism #191
  • Fixed race condition in DiffusionGrid::ChangeConcentrationBy
  • Changed BioDynaMo version from vXX.YY-ZZ-gSHA to vXX.YY.ZZ-SHA #216

Examples

New Demos

  • Binding cells
  • Pyramidal cell growth

New Notebooks

  • ST01-model-initializer.ipynb
  • ST02-user-defined-random-number-distribution.ipynb
  • ST03-agent-reproduction-mortality.ipynb
  • ST04-agent-reproduction-with-behaviors.ipynb
  • ST05-agent-reproduction-advanced.ipynb
  • ST06-environment-search.ipynb
  • ST07-multi-scale-simulation.ipynb
  • ST08-histograms.ipynb
  • ST09-timeseries-plotting-basic.ipynb
  • ST10-timeseries-plotting-and-analysis.ipynb
  • ST11-multiple-experiments-statistical-analysis.ipynb
  • ST12-hierarchical-model.ipynb
  • ST13-dynamic-scheduling.ipynb
  • ST14-randomize-iteration-order.ipynb
  • ST15-replace-interaction-force.ipynb

Supported Platforms

  • Ubuntu 18.04, 20.04
  • CentOS 7
  • macOS 10.15, >=11.6 and >=12.0
Assets 2
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