OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. """ #ifndef #define TRIGGER_WIKI ## # Introduction ## In this tutorial we show how Chaste can be used to create, run and visualize mesh-based simulations. ## Full details of the mathematical model can be found in van Leeuwen et al. (2009) [doi:10.1111/j.1365-2184.2009.00627.x]. ## ## ## Imports and Setup import unittest # Python testing framework import matplotlib.pyplot as plt # Plotting import numpy as np # Matrix tools import chaste # The PyChaste module chaste.init() # Set up MPI import chaste.cell_based # Contains cell populations import chaste.mesh # Contains meshes import chaste.visualization # Visualization tools class TestRunningMeshBasedSimulationsTutorial( chaste.cell_based.AbstractCellBasedTestSuite): ## ## Test 1 - a basic mesh-based simulation ## In the first test, we run a simple mesh-based simulation, ## in which we create a monolayer of cells, using a mutable mesh. Each cell is assigned a stochastic cell-cycle model. def test_monolayer(self): # JUPYTER_SETUP
http://stackoverflow.com/questions/36932/how-can-i-represent-an-enum-in-python """ enums = dict(zip(sequential, range(len(sequential))), **named) return type('Enum', (), enums) # Define MPI message tags tags = enum('READY', 'DONE', 'EXIT', 'START') # Initializations and preliminaries comm = MPI.COMM_WORLD # get MPI communicator object size = comm.size # total number of processes rank = comm.rank # rank of this process status = MPI.Status() # get MPI status object local_comm = comm.Split(color=rank, key=rank) chaste.init(comm=local_comm) if rank == 0: # Master process executes code below work_dir = "Python/Cornea/Submission/Fixed_Case5" #work_dir = "Python/Cornea/Submission/Dynamic_Case1" tm = PostProcessingTaskManager(work_dir) #tm.setup_density_line_plots() #tm.setup_line_density_plot_merge() # serial only tm.setup_box_plots() # serial only #tm.setup_max_tip_density_plots() # serial only #tm.setup_max_conc_plots() # serial only #tm.setup_front_pos_plots() # serial only #tm.setup_pde_plots() # serial only, dynamic only
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. """ import unittest import chaste chaste.init() import chaste.mesh import chaste.cell_based import chaste.visualization class TestCell(chaste.cell_based.AbstractCellBasedTestSuite): def test_construct(self): file_handler = chaste.core.OutputFileHandler("Python/TestVertexBasedCellPopulation") # Set up the mesh mesh_generator = chaste.mesh.HoneycombVertexMeshGenerator(2, 2) mesh = mesh_generator.GetMesh()