# convert P type calcium current data to calcium influx profile
ca_curr_data = data_presets.readData(CA_P_CURR_DATA_FILE)
ca_influx_profile = data_presets.genCaInfluxProfile(
ca_curr_data, roi_areas, roi_vols, PRESET_DATA_START_TIME,
PRESET_DATA_START_TIME + SIM_TIME, INFLUX_UPDATE_INTERVAL)
# load preset background calcium concerntrations
ca_conc_preset_file = open(CA_CONC_PRESET, 'r')
ca_conc_preset = cPickle.load(ca_conc_preset_file)
ca_conc_preset_file.close()
########################### SIMULATION INITIALIZATION ###########################
r = srng.create_mt19937(512)
r.initialize(int(time.time()))
sim = ssolver.Tetexact(mdl, mesh, r)
sim.setCompConc('cyto', 'Mg', Mg_conc)
surfarea = sim.getPatchArea('memb')
pumpnbs = 6.022141e12 * surfarea
sim.setPatchCount('memb', 'Pump', round(pumpnbs))
sim.setPatchCount('memb', 'CaPump', 0)
sim.setCompConc('cyto', 'iCBsf', iCBsf_conc)
sim.setCompConc('cyto', 'iCBCaf', iCBCaf_conc)
sim.setCompConc('cyto', 'iCBsCa', iCBsCa_conc)
# Make the diff boundary tris with the intersection and convert to list
tris_DB = tris_compA.intersection(tris_compB)
tris_DB = list(tris_DB)
# Create the diffusion boundary between compA and compB
diffb = sgeom.DiffBoundary('diffb', mesh, tris_DB)
return mesh, tets_compA, tets_compB
########################################################################
mdl = gen_model()
mesh, tets_compA, tets_compB = gen_geom()
rng = srng.create_mt19937(256)
rng.initialize(432)
sim = solvmod.Tetexact(mdl, mesh, rng)
sim.reset()
tpnts = numpy.arange(0.0, 0.101, 0.001)
ntpnts = tpnts.shape[0]
# And fetch the total number of tets to make the data structures
ntets = mesh.countTets()
# Create the data structures: time points x tetrahedrons
resX = numpy.zeros((ntpnts, ntets))
resY = numpy.zeros((ntpnts, ntets))
# Make the diff boundary tris with the intersection and convert to list
tris_DB = tris_compA.intersection(tris_compB)
tris_DB = list(tris_DB)
# Create the diffusion boundary between compA and compB
diffb = sgeom.DiffBoundary('diffb', mesh, tris_DB)
return mesh, tets_compA, tets_compB
########################################################################
mdl = gen_model()
mesh, tets_compA, tets_compB = gen_geom()
rng = srng.create_mt19937(256)
rng.initialize(432)
sim = solvmod.Tetexact(mdl, mesh, rng)
sim.reset()
tpnts = numpy.arange(0.0, 0.101, 0.001)
ntpnts = tpnts.shape[0]
# And fetch the total number of tets to make the data structures
ntets = mesh.countTets()
# Create the data structures: time points x tetrahedrons
resX = numpy.zeros((ntpnts, ntets))
resY = numpy.zeros((ntpnts, ntets))
memb_stoch = sgeom.TmPatch('memb_stoch', mesh_stoch, memb_tris, cyto_stoch)
memb_stoch.addSurfsys('ssys_stoch')
# Determinsitic sim:
memb_det = sgeom.TmPatch('memb_det', mesh_det, memb_tris, cyto_det)
memb_det.addSurfsys('ssys_det')
# For EField calculation
print "Creating membrane.."
membrane = sgeom.Memb('membrane', mesh_stoch, [memb_stoch])
print "Membrane created."
# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # SIMULATION # # # # # # # # # # # # # # # # # # # # # #
r = srng.create_mt19937(512)
r.initialize(7)
r_dummy = srng.create_mt19937(512)
r_dummy.initialize(7)
print "Creating Tet exact solver"
#Creating two solvers
sim_stoch = ssolver.Tetexact(mdl_stoch, mesh_stoch, r, True)
print "Creating Tet ODE solver"
sim_det = ssolver.TetODE(mdl_det, mesh_det, r_dummy)
sim_det.setTolerances(1.0e-3, 1.0e-3)