BioFVM Files

BioFVM: Finite Volume Solver for Biological Problems. 

Version:      1.1.5
Release date: 19 July 2017

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

Summary:  
This update includes small bug fixes and enhancements for 
compatibiltiy with PhysiCell. 

New features:
+ Added Microenvironment::find_substrate_index( std::string ) to make it 
  easier to find . 
  
+ Added Basic_Agent::nearest_gradient( int substrate_index ) to directly 
  access the gradient of the indicated substrate at the agent's  
  current_voxel_index. 
  
+ Added Basic_Agent::nearest_gradient_vector( void ) to directly 
  access a vector of gradients (one for each substrate in the 
  microenvironment) at the agent's current_voxel_index. 
 
+ Added Microenvironment::is_dirichlet_node( int voxel_index ) to 
  easily check if the voxel is a Dirichlet node. 
  
+ Added new class Microenvironment_Options, with a default 
  default_microenvironment_options, to simplify Microenvironment
  setup. The defaults are dx = dy = dz = 20 microns, on 1 cubic mm. 
  
+ Added function initialize_microenvironment() to set up the 
  microenvironment using the options in 
  default_microenvironment_options. The code sets oxygen as the 
  default field, with D = 1e5 micron^2/min, and decay rate = 0.1 1/min
  (a 1 mm diffusion length scale). If 
  default_microenvironment_options.outer_Dirichlet_conditions = true, 
  then we set a 38 mmHg condition on the outer edges, corresponding to
  5% oxygenation (physioxic conditions). 

+ Updated the makefile to default to MARCH := native, which allows
  automated performance tuning without user editing of the Makefile.

Bugfixes: 
+ correct typos in citation information in all source files 

+ updated citation information 

+ added void set_default_microenvironment( Microenvironment* M ) declaration to 
  BioFVM_Microenvironment.h
 
+ set volume_is_changed = false in Basic_Agent::set_internal_uptake_constants(); 

+ Set the MultiCellDS options Booleans to extern bool in BioFVM_MultiCellDS.h 
  so that PhysiCell can read these options. 

+ Updated the simlified_data field in MultiCellDS XML output to include a 
  new "source" attribute with value "BioFVM".

+ Updated Microenvironment::update_dirichlet_node() and 
  Microenvironment::remove_dirichlet_node() to check against 
  mesh.voxels[].is_Dirichlet to provide a cheap and early exit 
  if the node isn't Dirichlet in the first place. 
  
+ Changed to a thread-safe data structure for Dirichlet nodes 
  (e.g., if a custom cell function in an OMP loop adds or removes 
  Dirichlet nodes). 
  
+ Fixed convergence_test3.cpp, convergence_test4_1.cpp, 
  convergence_test4_2.cpp, convergence_test5.cpp, 
  performance_test_numcells.cpp, tutorial1_BioFVM.cpp, 
  and main_experiment.cpp to use Basic_Agent::set_total_volume(). 

+ Fixed tutorial3_BioFVM.cpp to use dirichlet_one instead of 
  dirichlet_zero.