Commit 67cd5560 authored by Daniel Sussman's avatar Daniel Sussman
Browse files

grouping into version 0.8

parent 040d03aa
......@@ -2,7 +2,11 @@
### 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
......
......@@ -37,6 +37,8 @@ range of parameters.
# Mac OS X Instructions
IMPORTANT NOTE: Current versions of Mac OsX do not support CUDA installation... it may be possible to hack some solution together, but for the moment it looks like Mac will not be supported. As such, these mac install instructions are for historical reference for systems running OsX 12 and earlier.
The following instructions for compiling cellGPU on Mac OSX were contributed by Gonca Erdemci-Tandogan (https://goncaerdemci.wordpress.com/).
It does not include how to get Eigen (for the dynamical matrix diagonalization), but that is a header-only library.
......
......@@ -2,7 +2,7 @@
CellGPU is released under the MIT license
Copyright (c) 2016 - 2018 Daniel M. Sussman
Copyright (c) 2016 - 2019 Daniel M. Sussman
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated
documentation files (the "Software"), to deal in the Software without restriction, including without limitation
......
......@@ -32,7 +32,7 @@ int main(int argc, char*argv[])
Dscalar dt = 0.01; //the time step size
Dscalar p0 = 4.0; //the preferred perimeter
Dscalar a0 = 1.0; // the preferred area
Dscalar v0 = 0.1; // the self-propulsion
Dscalar v0 = 0.05; // the self-propulsion
Dscalar Dr = 1.0; //the rotational diffusion constant of the cell directors
int program_switch = 0; //various settings control output
......@@ -76,7 +76,7 @@ int main(int argc, char*argv[])
//possibly save output in netCDF format
char dataname[256];
sprintf(dataname,"../test.nc");
sprintf(dataname,"./data/test_p%.3f.nc",p0);
int Nvert = 2*numpts;
AVMDatabaseNetCDF ncdat(Nvert,dataname,NcFile::Replace);
......@@ -95,7 +95,7 @@ int main(int argc, char*argv[])
//set the cell activity to have D_r = 1. and a given v_0
avm->setv0Dr(v0,1.0);
//when an edge gets less than this long, perform a simple T1 transition
avm->setT1Threshold(0.04);
avm->setT1Threshold(0.1);
vector<int> vi(3*Nvert);
vector<int> vf(3*Nvert);
......
......@@ -38,7 +38,7 @@ PROJECT_NAME = "CellGPU"
# could be handy for archiving the generated documentation or if some version
# control system is used.
PROJECT_NUMBER = "0.7.1"
PROJECT_NUMBER = "0.8.0"
# Using the PROJECT_BRIEF tag one can provide an optional one line description
# for a project that appears at the top of each page and should give viewer a
......
......@@ -10,10 +10,10 @@ NVCC := nvcc
INCLUDES = -I. -I./src/ -I./ext_src/ -I./inc/ -I$(CUDA_INC) -I/home/user/CGAL/CGAL-4.9/include -I/opt/local/include
INCLUDES += -I/usr/local/Cellar/cgal/4.9/include -I/usr/local/Cellar/boost/1.62.0/include -I/usr/local/Cellar/gmp/6.1.2/include -I/usr/local/Cellar/mpfr/3.1.5/include -I/usr/local/Cellar/netcdf/4.4.1.1_4/include -I/home/dmsussma/eigen-eigen-8d1ccfd9c5a0 -I/usr/local/include/eigen3
LIB_CUDA = -L. -L/home/gerdemci/cudalibs -L$(CUDA_LIB) -L$(CUDA_LIB2) -lcuda -lcudart
LIB_CUDA = -L. -L$(CUDA_LIB) -L$(CUDA_LIB2) -lcuda -lcudart
LIB_CGAL += -L/usr/local/Cellar/cgal/4.9/lib -L/usr/local/Cellar/gmp/6.1.2/lib -L/usr/local/Cellar/mpfr/3.1.5/lib
LIB_CGAL += -L/home/user/CGAL/CGAL-4.9/lib -lCGAL -lCGAL_Core -lgmp -lmpfr
LIB_NETCDF = -lnetcdf -lnetcdf_c++ -L/opt/local/lib -L/usr/local/Cellar/netcdf/4.4.1.1_4/lib
LIB_NETCDF = -lnetcdf -lnetcdf_c++ -L/opt/local/lib
#common flags
COMMONFLAGS += $(INCLUDES) -std=c++11 -DCGAL_DISABLE_ROUNDING_MATH_CHECK -O3
......
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