update readme, changes, and versions

Makefile

@@ -1,4 +1,4 @@
-VERSION := 1.3.1
+VERSION := 1.3.2
 PROGRAM_NAME := project
 
 CC := g++

README.txt

@@ -1,8 +1,8 @@
 PhysiCell: an Open Source Physics-Based Cell Simulator for 3-D 
 Multicellular Systems.
 
-Version:      1.3.1
-Release date: 31 July 2018 
+Version:      1.3.2
+Release date: 24 August 2018 
 
 Overview: 
 PhysiCell is a flexible open source framework for building 
@@ -61,168 +61,33 @@ See changes.txt for the full change log.
 
 Release summary: 
 
-This release introduces a new cycle model with an active cycling 
-state and a quiescent state. It also adds new functions to the 
-Mechanics class to make it easier to modify the cell-cell interaction 
-distance (while maintaining equilibrium cell-cell spacing), or 
-to modify the equilibrium cell-cell spacing. The release also 
-includes major reliability and performance improvements to 
-how gradients are calculated.
-
-As usual, the release also contains minor bugfixes and 
-improvements. 
+This release fixes a small gradient bug that I swear I had fixed before. 
 
 NOTE: OSX users must now define PHYSICELL_CPP system variable. 
       See the documentation.
 
 Major new features and changes:
 
-+ Implemented a new cell cycle model (cycling_quiescent), 
-  where quiescent cells can enter a cycling state. This 
-  model uses identical parameters to the Ki67-basic cycle 
-  model, but decouples the conceptual model from Ki67 
-  immunohistochemistry. 
-
-  Updated the documentation and coloring functions accordingly.
-
-  Updated update_cell_and_death_parameters_O2_based() to 
-  support the new cycling_quiescent cycle model.
-
-+ update_all_cells(t,dt,dt,dt) now checks to see if gradient 
-  calculations are enabled, and if so, computes it once per dt_mechanics.
-
-  This improves code performance by 2x to 3x in gradient-enabled codes, 
-  because we no longer need to calculate gradients once per dt_diffusion 
-  time step. (Gradients are only needed for cell velocity calculations, 
-  and occasionally for phenotype decisions.)
-
-  All sample projects have been updated to make use of this.    
-
-  Also, removed the explicit gradient calculations from the template 
-  and sample projects. 
-
-+ Added a new function to Mechanics class to simplify changes to cell 
-  interaction distances: 
-
-     void set_relative_maximum_adhesion_distance( double new_value ); 
-
-  Here, new_value is a multiple of the cell's (mean equivalent) radius. 
-  Our default is 1.25. This function preserves the cell's "repulsion" 
-  strength and adjusts the strength of cell-cell adhesion to maintain 
-  its prior equilibrium cell-cell spacing. 
-
-+ Added a new function to Mechanics class to simplify changes to cell 
-  equilibrium distances. 
-
-     void set_relative_equilibrium_distance( double new_value );   
-
-  Here, new_value is a multiple of the cell's (mean equivalent) radius. 
-  The default is around 1.9. This function preserves the cell's "repulsion" 
-  and the maximum interaction distance, and it adjusts the strength of 
-  cell-cell adhesion to match the new equilibrium cell-cell spacing. 
-
-  Note that this function performs a "sanity check" to ensure that you have 
-  not given a value greater than 2.0. 
-
-+ Added a new function to Mechanics class to simplify changes to cell 
-  equilibrium distances. 
-
-     void Mechanics::set_absolute_equilibrium_distance( Phenotype& phenotype, 
-     double new_value )
-
-  Here, new_value is the new equilibrium spacing (in units of microns). 
-  The function internally requires the cell's mean equivalent radius, 
-  and so you pass the cell's phenotype (by reference) as an additional 
-  argument. 
-
-  Note that this function performs a "sanity check" to ensure that you have 
-  not given a value greater than 2.0 * mean_cell_radius.  	
-
-  Also note that PhysiCell internally uses a relative spacing, so the 
-  absolute spacing will change from the value you set, over time.  
-
-+ Updated User_Guide to reflect new cell cycle model, 
-  including reference parameters chosen for consistency with 
-  the other cycle models. 
++ none
 
 Minor new features and changes: 
 
-+ Added the following constants to support the new cycle model
-
-     static const int cycling = 17; 
-     static const int quiescent = 18; 
-     static const int cycling_quiescent_model = 7; 
-
-+ Removed the (never-used) Mechanics.maximum_adhesion_distance. 
-
-+ Removed the legacy template_projects folder.
-
-
-Beta features (not fully supported):
-
-+ Added a function pointer to the Cell_Functions class for intended 
-  contact-based cell-cell interaction, like delta-Notch signaling. 
++ none
 
-     void (*contact_function)(Cell* pMyself, Phenotype& my_phenotype, 
-       Cell* pOther, Phenotype& other_phenotype, double dt ); 
-
-  It would be up to the user to define these functions and decide 
-  if the functions modify pMyself, pOther, or both. For now, 
-  the code will initialize the pointer to NULL and won't use it. 
+Beta features (not fully supported):
 
-+ Open to comments on handling cell-cell contact functions. Here's what 
-  I have in mind: 
-
-  notation: cell i interacts with cell j with function f(i,j). 
-
-  Each cell agent can hold one contact-based interaction function f, 
-  to be stored as a pointer in the cell's instance of the Cell_Functions 
-  class. 
-
-  We use the containers (and their interaction testing structures) to  
-  identify all interactions (i,j,f), and add it to a vector of interactions. 
-  The interaction (i,j,f) is added to the list so long as (j,i,f) is not 
-  already in the list, to avoid double-counting the interaction. 
-
-  The code will seek through the "container" interaction testing 
-  data structure, probably at the cell mechanics time scale, and update /
-  recreate the vector of contact-based interactions (i,j,f). 
-
-  The code would likely go through the vector of interactions and 
-  execute the codes once per dt_diffusion time step, since I would 
-  imagine molecular biology (with faster time scales) is intended here.
-
-  Since f(i,j) can potentially modify both cell i and cell j, it's probably 
-  not thread-safe. So we'll probably need that in a non-parallel loop. 
-
-  We will probably add a new time scale for interactions, dt_interactions, 
-  and update the interaction list on that time scale. 
-
-  For faster checking if (i,j,f) or (j,i,f) is already in the vector, 
-  we'll probably want some sort of hash map in addition to the vector 
-  of interactions. 
-
-  We'll probably implement this all in something like 
-  PhysiCell_contact_interctions.*, and add a global enable/disable option. 
-  I'd imagine we'd add code to the "update_all_cells" to keep this 
-  as simple to the users as possible. 
-
-  We should probably update each cell's "neighbors" data structure at 
-  when we're doing all this testing. 
-
-  In a longer-term update, we could leverage that for simpler interaction 
-  testing during velocity updates. 
++ none
 
 Bugfixes: 
 
-+ Added missing "omp_set_num_threads(PhysiCell_settings.omp_num_threads)" 
-  in the main-heterogeneity.cpp file for the heterogeneity sample project. 
-
 + In BioFVM, Microenvironment::compute_gradient_vector(int), removed "static"
   from "static std::vector<int> indices(3,0)" to prevent rare segfaults. 
 
-+ Changed <xml> root above the comment lines in output files for 
-  better Python parsing compatibility. Thanks, rheiland! 
++ In BioFVM, Microenvironment::compute_gradient_vector(int), replaced "static"
+  for "bool gradient_constants_defined = false". Yep, I removed static from 
+  the wrong line in 1.3.1 
+
++ Correct some errors in both the README.txt and changes.txt files. 
 
 Notices for intended changes that may affect backwards compatibility:
 

changes.txt

@@ -1,14 +1,74 @@
-changes in next version
+=======================================================================
 
+PhysiCell: an Open Source Physics-Based Cell Simulator for 3-D 
+Multicellular Systems.
+
+Version:      1.3.2
+Release date: 24 August 2018
 
-bugfixes: 
+Release summary: 
+
+This release fixes a small gradient bug that I swear I had fixed before. 
+
+NOTE: OSX users must now define PHYSICELL_CPP system variable. 
+      See the documentation.
+
+Major new features and changes:
+
++ none
+
+Minor new features and changes: 
+
++ none
+
+Beta features (not fully supported):
+
++ none
+
+Bugfixes: 
 
-MultiCellDS outputs used size 3 for all custom vector variables, instead 
-of actual size. Fixed to read the size from the vector. 
++ In BioFVM, Microenvironment::compute_gradient_vector(int), removed "static"
+  from "static std::vector<int> indices(3,0)" to prevent rare segfaults. 
+
++ In BioFVM, Microenvironment::compute_gradient_vector(int), replaced "static"
+  for "bool gradient_constants_defined = false". Yep, I removed static from 
+  the wrong line in 1.3.1 
 
-Fixed the ostream operator for Vector_Variable to correctly output all 
-the vector.value elements, rather than the original hard-coded output 
-of 3 elements regardless of size. 
++ Correct some errors in both the README.txt and changes.txt files. 
+
+Notices for intended changes that may affect backwards compatibility:
+
++ None.
+
+Planned future improvements: 
+
++ Further XML-based simulation setup. 
+
++ read saved simulation states (as MultiCellDS digital snapshots)
+
++ "mainline" prototype cell attach/detach mechanics as standard models 
+  (currently in the biorobots and immune examples)
+
++ integrate SBML-encoded systems of ODEs as custom data and functions 
+  for molecular-scale modeling 
+
++ integrate Boolean network support from PhysiBoSS into the mainline code 
+  (See https://doi.org/10.1101/267070.)
+
++ Develop contact-based cell-cell interactions. (Likely in next release.)
+
++ Add a new standard phenotype function that uses mechanobiology, 
+  where high pressure can arrest cycle progression. 
+  (See https://twitter.com/MathCancer/status/1022555441518338048.) 
+  (Likely in next release.) 
+
++ Add module for standardized pharmacodynamics, as prototyped in the 
+  nanobio project. (See https://nanohub.org/resources/pc4nanobio.) 
+
++ create an angiogenesis sample project 
+
++ create a small library of angiogenesis and vascularization codes as 
+  an optional standard module in ./modules (but not as a core component)
 
 =======================================================================
 
@@ -183,6 +243,13 @@ Bugfixes:
 
 + Changed <xml> root above the comment lines in output files for 
   better Python parsing compatibility. Thanks, rheiland! 
+
++ MultiCellDS outputs used size 3 for all custom vector variables, instead 
+  of actual size. Fixed to read the size from the vector. 
+
++ Fixed the ostream operator for Vector_Variable to correctly output all 
+  the vector.value elements, rather than the original hard-coded output 
+  of 3 elements regardless of size. 
 
 Notices for intended changes that may affect backwards compatibility:
 

config/PhysiCell_settings.xml

@@ -5,7 +5,7 @@
 # If you use PhysiCell in your project, please cite PhysiCell and the version #
 # number, such as below:                                                      #
 #                                                                             #
-# We implemented and solved the model using PhysiCell (Version 1.3.1) [1].    #
+# We implemented and solved the model using PhysiCell (Version 1.3.2) [1].    #
 #                                                                             #
 # [1] A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin, #
 #     PhysiCell: an Open Source Physics-Based Cell Simulator for Multicellu-  #
@@ -15,7 +15,7 @@
 # Because PhysiCell extensively uses BioFVM, we suggest you also cite BioFVM  #
 #     as below:                                                               #
 #                                                                             #
-# We implemented and solved the model using PhysiCell (Version 1.3.1) [1],    #
+# We implemented and solved the model using PhysiCell (Version 1.3.2) [1],    #
 # with BioFVM [2] to solve the transport equations.                           #
 #                                                                             #
 # [1] A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin, #

core/PhysiCell.h

@@ -3,7 +3,7 @@
 # If you use PhysiCell in your project, please cite PhysiCell and the version #
 # number, such as below:                                                      #
 #                                                                             #
-# We implemented and solved the model using PhysiCell (Version 1.3.1) [1].    #
+# We implemented and solved the model using PhysiCell (Version 1.3.2) [1].    #
 #                                                                             #
 # [1] A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin, #
 #     PhysiCell: an Open Source Physics-Based Cell Simulator for Multicellu-  #
@@ -13,7 +13,7 @@
 # Because PhysiCell extensively uses BioFVM, we suggest you also cite BioFVM  #
 #     as below:                                                               #
 #                                                                             #
-# We implemented and solved the model using PhysiCell (Version 1.3.1) [1],    #
+# We implemented and solved the model using PhysiCell (Version 1.3.2) [1],    #
 # with BioFVM [2] to solve the transport equations.                           #
 #                                                                             #
 # [1] A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin, #

core/PhysiCell_cell.cpp

@@ -3,7 +3,7 @@
 # If you use PhysiCell in your project, please cite PhysiCell and the version #
 # number, such as below:                                                      #
 #                                                                             #
-# We implemented and solved the model using PhysiCell (Version 1.3.1) [1].    #
+# We implemented and solved the model using PhysiCell (Version 1.3.2) [1].    #
 #                                                                             #
 # [1] A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin, #
 #     PhysiCell: an Open Source Physics-Based Cell Simulator for Multicellu-  #
@@ -13,7 +13,7 @@
 # Because PhysiCell extensively uses BioFVM, we suggest you also cite BioFVM  #
 #     as below:                                                               #
 #                                                                             #
-# We implemented and solved the model using PhysiCell (Version 1.3.1) [1],    #
+# We implemented and solved the model using PhysiCell (Version 1.3.2) [1],    #
 # with BioFVM [2] to solve the transport equations.                           #
 #                                                                             #
 # [1] A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin, #

core/PhysiCell_cell.h

@@ -3,7 +3,7 @@
 # If you use PhysiCell in your project, please cite PhysiCell and the version #
 # number, such as below:                                                      #
 #                                                                             #
-# We implemented and solved the model using PhysiCell (Version 1.3.1) [1].    #
+# We implemented and solved the model using PhysiCell (Version 1.3.2) [1].    #
 #                                                                             #
 # [1] A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin, #
 #     PhysiCell: an Open Source Physics-Based Cell Simulator for Multicellu-  #
@@ -13,7 +13,7 @@
 # Because PhysiCell extensively uses BioFVM, we suggest you also cite BioFVM  #
 #     as below:                                                               #
 #                                                                             #
-# We implemented and solved the model using PhysiCell (Version 1.3.1) [1],    #
+# We implemented and solved the model using PhysiCell (Version 1.3.2) [1],    #
 # with BioFVM [2] to solve the transport equations.                           #
 #                                                                             #
 # [1] A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin, #

core/PhysiCell_cell_container.cpp

@@ -3,7 +3,7 @@
 # If you use PhysiCell in your project, please cite PhysiCell and the version #
 # number, such as below:                                                      #
 #                                                                             #
-# We implemented and solved the model using PhysiCell (Version 1.3.1) [1].    #
+# We implemented and solved the model using PhysiCell (Version 1.3.2) [1].    #
 #                                                                             #
 # [1] A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin, #
 #     PhysiCell: an Open Source Physics-Based Cell Simulator for Multicellu-  #
@@ -13,7 +13,7 @@
 # Because PhysiCell extensively uses BioFVM, we suggest you also cite BioFVM  #
 #     as below:                                                               #
 #                                                                             #
-# We implemented and solved the model using PhysiCell (Version 1.3.1) [1],    #
+# We implemented and solved the model using PhysiCell (Version 1.3.2) [1],    #
 # with BioFVM [2] to solve the transport equations.                           #
 #                                                                             #
 # [1] A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin, #

core/PhysiCell_cell_container.h

@@ -3,7 +3,7 @@
 # If you use PhysiCell in your project, please cite PhysiCell and the version #
 # number, such as below:                                                      #
 #                                                                             #
-# We implemented and solved the model using PhysiCell (Version 1.3.1) [1].    #
+# We implemented and solved the model using PhysiCell (Version 1.3.2) [1].    #
 #                                                                             #
 # [1] A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin, #
 #     PhysiCell: an Open Source Physics-Based Cell Simulator for Multicellu-  #
@@ -13,7 +13,7 @@
 # Because PhysiCell extensively uses BioFVM, we suggest you also cite BioFVM  #
 #     as below:                                                               #
 #                                                                             #
-# We implemented and solved the model using PhysiCell (Version 1.3.1) [1],    #
+# We implemented and solved the model using PhysiCell (Version 1.3.2) [1],    #
 # with BioFVM [2] to solve the transport equations.                           #
 #                                                                             #
 # [1] A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin, #