Change log

Changes in progress

version 0.8.0

• A directory to put common MD data analysis tools has been added
• Changed strategy for handling multiple T1 transitions per cell / vertex
• Numerous small changes

version 0.7.1

• Support for non-square boxes... DelaunayCGAL calls currently implemented, but not DelaunayLoc
• Nose-Hoover thermostat-chain NVT simulations
• Starting transition away from Simple2DActiveCell class by using velocity GPUArrays in SPP updater

version 0.7

• Cell death added. This removes a cell in Voronoi model, or does a T2 transition in vertex model
• BoxPtrs implemented...will eventually make different box shapes easier
• rationalize naming scheme of vertex and voronoi models
  • There are now vertexModelBase and voronoiModelBase classes
  • Derived classes of these largely just need to implement force laws
• include tree cleaning

version 0.6.2

• Implement cell division in both vertex and Voronoi models
• Major bug fix in "quadratic" vertex model force computations

version 0.6.1

• system-wide refactoring into simulation components: updaters, configurations, pieces, and a Simulation to tie them together
• added simple Brownian dynamics equation of motion
• added a (somewhat specialized) calculation of the quadratic voronoi model dynamical matrix

version 0.6

• started refactoring class structures... beginning with equations of motion

version 0.5.1

• added FIRE minimization algorithm
• Simplified interface to SPV2D and AVM2D; have all models implement virtual functions to provide a common interface for MD

version 0.5

• First major restructuring of class structure...

cellGPU version 0.4

• The AVM2D class implements a simple active vertex model
• numerous bug fixes
• GPU optimizations

version 0.3

• SPV2D class inherits from DelaunayMD; implements the 2D self-propelled voronoi model
• references to Triangle are removed; CGAL becomes the default triangulation library

DelGPU version 0.2

• "DelGPU" implements the DelaunayCheck class to assess the validity of a proposed triangulation on either the CPU or GPU; DelaunayMD provides a simple interface to an MD-like protocol

VoroGuppy version 0.1

• "VoroGuppy" has a CPU implementation of Chen and Gotsman's localized Delaunay triangulation, comparisons with Shewchuck's Triangle program and a Bowyer-Watson implementation.