# in our 'lattice', all the cells are distance 1 apart
NCells = 60
cells = [Cell([x]) for x in np.linspace(1,NCells,NCells)]
# add these cells to the simulation
sim = Simulation()
for i in xrange(NCells):
sim.add_cell(cells[i])
im_id = sim.add_internal_model(IM)
# set all cells to have the same internal model
sim.set_internal_model(range(NCells),im_id)
# set boundary conditions before setting intercellular interactions
sim.set_boundary_conditions([0],'ref_on')
# cells adjacent to one another are connected
# for diffusion we include main diagonal
# equivalent to 3 wide diagonal
diff_connections = (np.eye(NCells,k=-1) + np.eye(NCells,k=0) + np.eye(NCells,k=1)) > 0
# add diffusion to h and u
sim.add_interaction('h','h','diffusion',diff_connections,params=[Dh/Th])
sim.add_interaction('u','u','diffusion',diff_connections,params=[Du/Tu])
# spi diffusion
sim.add_interaction('sp','sp','diffusion',diff_connections,params=[5.0/Tsp])
'''
# no just lateral connections
# place each cell at these vertices
cells = [Cell(c) for c in centers]
# add these cells to the simulation
sim = Simulation()
for i in xrange(NCells):
sim.add_cell(cells[i])
im_id = sim.add_internal_model(IM)
# set all cells to have the same internal model
sim.set_internal_model(range(NCells),im_id)
# set up reflecting boundary conditions at bottom edge
# sim.set_boundary_conditions(range(ncolumns),'ref_on')
sim.set_boundary_conditions(range((nrows-1)*ncolumns,nrows*ncolumns),'abs_on')
# need to figure out which cells are connect to which
connections = np.zeros((NCells,NCells)) > 0 # default boolean false array
tri = Delaunay(centers)
for k in xrange(NCells):
# if index is found in triangle, add indices of points
# in that triangle to connections
matches = [t for t in tri.vertices if k in t]
matches = reduce(lambda x,y: np.concatenate((x,y)),matches)
# need to filter out connections that are two rows away
# cells sticking out on the edge get triangulated with cells two rows away
matches = [m for m in matches if abs(m-k) < 2*ncolumns]
# duplicates don't really matter since we're just setting them all to True
connections[k,matches] = True
