Mathematical model of tumor angiogenesis Quite a few libraries will be required to utilize the code "ABM_unbreakable" Petsc, Libmesh (and other various valgrind gnu mpich gsl boost)
The smaller tools generally come with Xcode on Mac or are built in on other platforms.
Download Petsc source files cd /source/petsc-3.8.2/
% Configure petsc ./configure --prefix=/PETSc382/ --download-cmake --with-mpi-dir=$MPI_DIR --with-debugging=false --COPTFLAGS='-O3' --CXXOPTFLAGS='-O3' --FOPTFLAGS='-O3' --download-fblaslapack=1 --with-mumps=1 --download-mumps=1 --with-metis=1 --download-metis=1 --with-parmetis=1 --download-parmetis=1 --with-scalapack=1 --download-scalapack=1 --with-superlu=1 --download-superlu=1 --with-valgrind-dir=/opt/ohpc/pub/valgrind/3.11.0/ make PETSC_DIR=/data/source/petsc-3.8.2 PETSC_ARCH=arch-linux2-c-opt all make PETSC_DIR=/data/source/petsc-3.8.2 PETSC_ARCH=arch-linux2-c-opt install
Download Libmesh source files cd /source/libmesh-1.2.1
% Configre Libmesh export PETSC_DIR=/PETSc382/ ./configure --prefix=/libMesh121/ --with-metis=PETSc make make install
%% Running the Code! full_abm.c - this allows you to change some of the parameters we studied in a sensitivity analysis main_abm_oxy.c - the main function that execudes the code cell_abm.c - houses both update_states and compute_forces, the crux of the simulations update_state - where phenotypic transitions take place compute_forces - where the forces are computed and the cells move accordingly generate_figures - generates the ABM figures options.in - simulation settings (how many timesteps, where to restart, print solution, etc.)
To do the sensitivity analysis, run 'generate_random.C' to generate the matrix for the variance-based method. This will save everything in the 'files-A.txt','files-B.txt','files-C.txt'. Each line is a set of parameters that must be ran using the ABM model above. 'analyze.C' will do the analysis on the solutions output from the ABM model. Then 'run_res.sh' will create the figures of results of the sensitivities.