BioFVM Files

BioFVM: Finite Volume Solver for Biological Problems. 

Version:      1.0.2
Release date: 4 December 2015

Homepage:     http://BioFVM.MathCancer.org
Downloads:    http://BioFVM.sf.net

Summary: 
This contains performance improvements for BioFVM, particularly in 
the cell-based secretion/uptake functions. 

In our testing, this improves the performance of diffusion-decay 
equations with cell-centered secretion/uptake by a factor of ~2.
That is, example performance_test_numcells now requires ~3 seconds 
to simulate 2 minutes of transport (dt = 0.01 min) with 1 substrate 
on 125,000 voxels, with secretion/uptake by ~1 million cells. This 
example previously required approximately 6 seconds. Similarly, 
the computational time for dt = 0.01 min with 4 million cells on 
125,000 voxels decreases from approximately 18 seconds to 
approximately 9 seconds. 

These accelerations will be particularly useful when incorporating 
BioFVM into large agent-based simulations (e.g., in PhysiCell). 


New features:
+ Added protected int current_voxel_index to each Basic_Agent 
  to reduce expensive calls to nearest_voxel_index() and related 
  functions.

+ Updated assign_position function to automatically update 
  current_voxel_index

+ Updated the cell source/sink functions 

Bugfixes: 
+ none