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()
