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MathCancer committed Nov 3, 2017
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4 changes: 2 additions & 2 deletions BioFVM/BioFVM.h
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# If you use BioFVM in your project, please cite BioFVM and the version #
# number, such as below: #
# #
# We solved the diffusion equations using BioFVM (Version 1.1.4) [1] #
# We solved the diffusion equations using BioFVM (Version 1.1.5) [1] #
# #
# [1] A. Ghaffarizaeh, S.H. Friedman, and P. Macklin, BioFVM: an efficient #
# [1] A. Ghaffarizadeh, S.H. Friedman, and P. Macklin, BioFVM: an efficient #
# parallelized diffusive transport solver for 3-D biological simulations,#
# Bioinformatics 32(8): 1256-8, 2016. DOI: 10.1093/bioinformatics/btv730 #
# #
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4 changes: 2 additions & 2 deletions BioFVM/BioFVM_MultiCellDS.cpp
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# If you use BioFVM in your project, please cite BioFVM and the version #
# number, such as below: #
# #
# We solved the diffusion equations using BioFVM (Version 1.1.4) [1] #
# We solved the diffusion equations using BioFVM (Version 1.1.5) [1] #
# #
# [1] A. Ghaffarizaeh, S.H. Friedman, and P. Macklin, BioFVM: an efficient #
# [1] A. Ghaffarizadeh, S.H. Friedman, and P. Macklin, BioFVM: an efficient #
# parallelized diffusive transport solver for 3-D biological simulations,#
# Bioinformatics 32(8): 1256-8, 2016. DOI: 10.1093/bioinformatics/btv730 #
# #
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4 changes: 2 additions & 2 deletions BioFVM/BioFVM_MultiCellDS.h
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# If you use BioFVM in your project, please cite BioFVM and the version #
# number, such as below: #
# #
# We solved the diffusion equations using BioFVM (Version 1.1.4) [1] #
# We solved the diffusion equations using BioFVM (Version 1.1.5) [1] #
# #
# [1] A. Ghaffarizaeh, S.H. Friedman, and P. Macklin, BioFVM: an efficient #
# [1] A. Ghaffarizadeh, S.H. Friedman, and P. Macklin, BioFVM: an efficient #
# parallelized diffusive transport solver for 3-D biological simulations,#
# Bioinformatics 32(8): 1256-8, 2016. DOI: 10.1093/bioinformatics/btv730 #
# #
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4 changes: 2 additions & 2 deletions BioFVM/BioFVM_agent_container.cpp
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# If you use BioFVM in your project, please cite BioFVM and the version #
# number, such as below: #
# #
# We solved the diffusion equations using BioFVM (Version 1.1.4) [1] #
# We solved the diffusion equations using BioFVM (Version 1.1.5) [1] #
# #
# [1] A. Ghaffarizaeh, S.H. Friedman, and P. Macklin, BioFVM: an efficient #
# [1] A. Ghaffarizadeh, S.H. Friedman, and P. Macklin, BioFVM: an efficient #
# parallelized diffusive transport solver for 3-D biological simulations,#
# Bioinformatics 32(8): 1256-8, 2016. DOI: 10.1093/bioinformatics/btv730 #
# #
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4 changes: 2 additions & 2 deletions BioFVM/BioFVM_agent_container.h
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# If you use BioFVM in your project, please cite BioFVM and the version #
# number, such as below: #
# #
# We solved the diffusion equations using BioFVM (Version 1.1.4) [1] #
# We solved the diffusion equations using BioFVM (Version 1.1.5) [1] #
# #
# [1] A. Ghaffarizaeh, S.H. Friedman, and P. Macklin, BioFVM: an efficient #
# [1] A. Ghaffarizadeh, S.H. Friedman, and P. Macklin, BioFVM: an efficient #
# parallelized diffusive transport solver for 3-D biological simulations,#
# Bioinformatics 32(8): 1256-8, 2016. DOI: 10.1093/bioinformatics/btv730 #
# #
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6 changes: 3 additions & 3 deletions BioFVM/BioFVM_basic_agent.cpp
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# If you use BioFVM in your project, please cite BioFVM and the version #
# number, such as below: #
# #
# We solved the diffusion equations using BioFVM (Version 1.1.4) [1] #
# We solved the diffusion equations using BioFVM (Version 1.1.5) [1] #
# #
# [1] A. Ghaffarizaeh, S.H. Friedman, and P. Macklin, BioFVM: an efficient #
# [1] A. Ghaffarizadeh, S.H. Friedman, and P. Macklin, BioFVM: an efficient #
# parallelized diffusive transport solver for 3-D biological simulations,#
# Bioinformatics 32(8): 1256-8, 2016. DOI: 10.1093/bioinformatics/btv730 #
# #
Expand Down Expand Up @@ -202,7 +202,7 @@ void delete_basic_agent( Basic_Agent* pDelete )
return;
}

int Basic_Agent::get_nearest_voxel_index( void )
int Basic_Agent::get_current_voxel_index( void )
{
return current_voxel_index;
}
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8 changes: 3 additions & 5 deletions BioFVM/BioFVM_basic_agent.h
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# If you use BioFVM in your project, please cite BioFVM and the version #
# number, such as below: #
# #
# We solved the diffusion equations using BioFVM (Version 1.1.4) [1] #
# We solved the diffusion equations using BioFVM (Version 1.1.5) [1] #
# #
# [1] A. Ghaffarizaeh, S.H. Friedman, and P. Macklin, BioFVM: an efficient #
# [1] A. Ghaffarizadeh, S.H. Friedman, and P. Macklin, BioFVM: an efficient #
# parallelized diffusive transport solver for 3-D biological simulations,#
# Bioinformatics 32(8): 1256-8, 2016. DOI: 10.1093/bioinformatics/btv730 #
# #
Expand Down Expand Up @@ -104,9 +104,7 @@ class Basic_Agent
// if no microenvironment indicated, use the currently selected microenvironment.
void simulate_secretion_and_uptake( Microenvironment* M, double dt );

// get the index of current voxel for the indicated microenvironment
int get_nearest_voxel_index( int microenvironment_index );
int get_nearest_voxel_index( void );
int get_current_voxel_index( void );
// directly access the substrate vector at the nearest voxel at the indicated microenvironment
std::vector<double>& nearest_density_vector( int microenvironment_index );
std::vector<double>& nearest_density_vector( void );
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4 changes: 2 additions & 2 deletions BioFVM/BioFVM_matlab.cpp
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# If you use BioFVM in your project, please cite BioFVM and the version #
# number, such as below: #
# #
# We solved the diffusion equations using BioFVM (Version 1.1.4) [1] #
# We solved the diffusion equations using BioFVM (Version 1.1.5) [1] #
# #
# [1] A. Ghaffarizaeh, S.H. Friedman, and P. Macklin, BioFVM: an efficient #
# [1] A. Ghaffarizadeh, S.H. Friedman, and P. Macklin, BioFVM: an efficient #
# parallelized diffusive transport solver for 3-D biological simulations,#
# Bioinformatics 32(8): 1256-8, 2016. DOI: 10.1093/bioinformatics/btv730 #
# #
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4 changes: 2 additions & 2 deletions BioFVM/BioFVM_matlab.h
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# If you use BioFVM in your project, please cite BioFVM and the version #
# number, such as below: #
# #
# We solved the diffusion equations using BioFVM (Version 1.1.4) [1] #
# We solved the diffusion equations using BioFVM (Version 1.1.5) [1] #
# #
# [1] A. Ghaffarizaeh, S.H. Friedman, and P. Macklin, BioFVM: an efficient #
# [1] A. Ghaffarizadeh, S.H. Friedman, and P. Macklin, BioFVM: an efficient #
# parallelized diffusive transport solver for 3-D biological simulations,#
# Bioinformatics 32(8): 1256-8, 2016. DOI: 10.1093/bioinformatics/btv730 #
# #
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4 changes: 2 additions & 2 deletions BioFVM/BioFVM_mesh.cpp
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# If you use BioFVM in your project, please cite BioFVM and the version #
# number, such as below: #
# #
# We solved the diffusion equations using BioFVM (Version 1.1.4) [1] #
# We solved the diffusion equations using BioFVM (Version 1.1.5) [1] #
# #
# [1] A. Ghaffarizaeh, S.H. Friedman, and P. Macklin, BioFVM: an efficient #
# [1] A. Ghaffarizadeh, S.H. Friedman, and P. Macklin, BioFVM: an efficient #
# parallelized diffusive transport solver for 3-D biological simulations,#
# Bioinformatics 32(8): 1256-8, 2016. DOI: 10.1093/bioinformatics/btv730 #
# #
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4 changes: 2 additions & 2 deletions BioFVM/BioFVM_mesh.h
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# If you use BioFVM in your project, please cite BioFVM and the version #
# number, such as below: #
# #
# We solved the diffusion equations using BioFVM (Version 1.1.4) [1] #
# We solved the diffusion equations using BioFVM (Version 1.1.5) [1] #
# #
# [1] A. Ghaffarizaeh, S.H. Friedman, and P. Macklin, BioFVM: an efficient #
# [1] A. Ghaffarizadeh, S.H. Friedman, and P. Macklin, BioFVM: an efficient #
# parallelized diffusive transport solver for 3-D biological simulations,#
# Bioinformatics 32(8): 1256-8, 2016. DOI: 10.1093/bioinformatics/btv730 #
# #
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4 changes: 2 additions & 2 deletions BioFVM/BioFVM_microenvironment.cpp
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# If you use BioFVM in your project, please cite BioFVM and the version #
# number, such as below: #
# #
# We solved the diffusion equations using BioFVM (Version 1.1.4) [1] #
# We solved the diffusion equations using BioFVM (Version 1.1.5) [1] #
# #
# [1] A. Ghaffarizaeh, S.H. Friedman, and P. Macklin, BioFVM: an efficient #
# [1] A. Ghaffarizadeh, S.H. Friedman, and P. Macklin, BioFVM: an efficient #
# parallelized diffusive transport solver for 3-D biological simulations,#
# Bioinformatics 32(8): 1256-8, 2016. DOI: 10.1093/bioinformatics/btv730 #
# #
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4 changes: 2 additions & 2 deletions BioFVM/BioFVM_microenvironment.h
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# If you use BioFVM in your project, please cite BioFVM and the version #
# number, such as below: #
# #
# We solved the diffusion equations using BioFVM (Version 1.1.4) [1] #
# We solved the diffusion equations using BioFVM (Version 1.1.5) [1] #
# #
# [1] A. Ghaffarizaeh, S.H. Friedman, and P. Macklin, BioFVM: an efficient #
# [1] A. Ghaffarizadeh, S.H. Friedman, and P. Macklin, BioFVM: an efficient #
# parallelized diffusive transport solver for 3-D biological simulations,#
# Bioinformatics 32(8): 1256-8, 2016. DOI: 10.1093/bioinformatics/btv730 #
# #
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4 changes: 2 additions & 2 deletions BioFVM/BioFVM_solvers.cpp
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# If you use BioFVM in your project, please cite BioFVM and the version #
# number, such as below: #
# #
# We solved the diffusion equations using BioFVM (Version 1.1.4) [1] #
# We solved the diffusion equations using BioFVM (Version 1.1.5) [1] #
# #
# [1] A. Ghaffarizaeh, S.H. Friedman, and P. Macklin, BioFVM: an efficient #
# [1] A. Ghaffarizadeh, S.H. Friedman, and P. Macklin, BioFVM: an efficient #
# parallelized diffusive transport solver for 3-D biological simulations,#
# Bioinformatics 32(8): 1256-8, 2016. DOI: 10.1093/bioinformatics/btv730 #
# #
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4 changes: 2 additions & 2 deletions BioFVM/BioFVM_solvers.h
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# If you use BioFVM in your project, please cite BioFVM and the version #
# number, such as below: #
# #
# We solved the diffusion equations using BioFVM (Version 1.1.4) [1] #
# We solved the diffusion equations using BioFVM (Version 1.1.5) [1] #
# #
# [1] A. Ghaffarizaeh, S.H. Friedman, and P. Macklin, BioFVM: an efficient #
# [1] A. Ghaffarizadeh, S.H. Friedman, and P. Macklin, BioFVM: an efficient #
# parallelized diffusive transport solver for 3-D biological simulations,#
# Bioinformatics 32(8): 1256-8, 2016. DOI: 10.1093/bioinformatics/btv730 #
# #
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4 changes: 2 additions & 2 deletions BioFVM/BioFVM_utilities.cpp
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# If you use BioFVM in your project, please cite BioFVM and the version #
# number, such as below: #
# #
# We solved the diffusion equations using BioFVM (Version 1.1.4) [1] #
# We solved the diffusion equations using BioFVM (Version 1.1.5) [1] #
# #
# [1] A. Ghaffarizaeh, S.H. Friedman, and P. Macklin, BioFVM: an efficient #
# [1] A. Ghaffarizadeh, S.H. Friedman, and P. Macklin, BioFVM: an efficient #
# parallelized diffusive transport solver for 3-D biological simulations,#
# Bioinformatics 32(8): 1256-8, 2016. DOI: 10.1093/bioinformatics/btv730 #
# #
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4 changes: 2 additions & 2 deletions BioFVM/BioFVM_utilities.h
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Original file line number Diff line number Diff line change
Expand Up @@ -3,9 +3,9 @@
# If you use BioFVM in your project, please cite BioFVM and the version #
# number, such as below: #
# #
# We solved the diffusion equations using BioFVM (Version 1.1.4) [1] #
# We solved the diffusion equations using BioFVM (Version 1.1.5) [1] #
# #
# [1] A. Ghaffarizaeh, S.H. Friedman, and P. Macklin, BioFVM: an efficient #
# [1] A. Ghaffarizadeh, S.H. Friedman, and P. Macklin, BioFVM: an efficient #
# parallelized diffusive transport solver for 3-D biological simulations,#
# Bioinformatics 32(8): 1256-8, 2016. DOI: 10.1093/bioinformatics/btv730 #
# #
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4 changes: 2 additions & 2 deletions BioFVM/BioFVM_vector.cpp
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# If you use BioFVM in your project, please cite BioFVM and the version #
# number, such as below: #
# #
# We solved the diffusion equations using BioFVM (Version 1.1.4) [1] #
# We solved the diffusion equations using BioFVM (Version 1.1.5) [1] #
# #
# [1] A. Ghaffarizaeh, S.H. Friedman, and P. Macklin, BioFVM: an efficient #
# [1] A. Ghaffarizadeh, S.H. Friedman, and P. Macklin, BioFVM: an efficient #
# parallelized diffusive transport solver for 3-D biological simulations,#
# Bioinformatics 32(8): 1256-8, 2016. DOI: 10.1093/bioinformatics/btv730 #
# #
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4 changes: 2 additions & 2 deletions BioFVM/BioFVM_vector.h
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Original file line number Diff line number Diff line change
Expand Up @@ -3,9 +3,9 @@
# If you use BioFVM in your project, please cite BioFVM and the version #
# number, such as below: #
# #
# We solved the diffusion equations using BioFVM (Version 1.1.4) [1] #
# We solved the diffusion equations using BioFVM (Version 1.1.5) [1] #
# #
# [1] A. Ghaffarizaeh, S.H. Friedman, and P. Macklin, BioFVM: an efficient #
# [1] A. Ghaffarizadeh, S.H. Friedman, and P. Macklin, BioFVM: an efficient #
# parallelized diffusive transport solver for 3-D biological simulations,#
# Bioinformatics 32(8): 1256-8, 2016. DOI: 10.1093/bioinformatics/btv730 #
# #
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