def highlightPatch(mesh, patch_id, tri_proxy):
"""
Highlight the STEPS compartment.
Parameters:
* mesh Associated Tetmesh object created in STEPS
* patch_id Name of the patch
* tri_proxy Triangle element proxy generated by STEPS mesh importing function
Return:
None
"""
patch = sgeom.castToTmPatch(mesh.getPatch(patch_id))
data = patch.getAllTriIndices()
highlightSTEPSTris(data, tri_proxy)
def init_sim(model, mesh, seed, param):
# previous setup
# rng = srng.create('r123', 512)
# rng.initialize(seed)
# sim = ssolver.Tetexact(model, mesh, rng, True)
# Create the solver objects
if param['SSA_solver'] == 'TetODE':
sim = ssolver.TetODE(model,
mesh,
calcMembPot=sim_parameters['EF_solver'])
sim.setTolerances(1.0e-6, 1e-6)
elif param['SSA_solver'] == 'Tetexact':
rng = srng.create('mt19937', 512)
rng.initialize(seed)
sim = ssolver.Tetexact(model,
mesh,
rng,
calcMembPot=sim_parameters['EF_solver'])
sim.reset()
sim.setEfieldDT(param['EF_dt'])
else:
raise ValueError('SSA solver ' + param['SSA_solver'] + 'not available')
print('Running Rallpack1 test with ' + param['SSA_solver'])
# Correction factor for deviation between mesh and model cylinder:
area_cylinder = np.pi * param['diameter'] * param['length']
area_mesh_factor = sim.getPatchArea('memb') / area_cylinder
# Set initial conditions
memb = sgeom.castToTmPatch(mesh.getPatch('memb'))
for t in memb.tris:
sim.setTriCount(t, 'Leak', 1)
sim.setMembPotential('membrane', param['E_M'])
sim.setMembVolRes('membrane', param['R_A'])
sim.setMembCapac('membrane', param['C_M'] / area_mesh_factor)
v_zmin = mesh.getROIData('v_zmin')
I = param['Iinj'] / len(v_zmin)
for v in v_zmin:
sim.setVertIClamp(v, I)
return sim
def build_model(mesh, param):
mdl = smodel.Model()
memb = sgeom.castToTmPatch(mesh.getPatch('memb'))
ssys = smodel.Surfsys('ssys', mdl)
memb.addSurfsys('ssys')
L = smodel.Chan('L', mdl)
Leak = smodel.ChanState('Leak', mdl, L)
# membrane conductance
area_cylinder = np.pi * param['diameter'] * param['length']
L_G_tot = area_cylinder / param['R_M']
g_leak_sc = L_G_tot / len(memb.tris)
OC_L = smodel.OhmicCurr('OC_L', ssys, chanstate = Leak, erev = param['E_M'], g = g_leak_sc)
return mdl
def init_sim(model, mesh, seed, param):
rng = srng.create('r123', 512)
# previous setup
# rng.initialize(seed)
rng.initialize(steps.mpi.rank + 1000)
memb = sgeom.castToTmPatch(mesh.getPatch('memb'))
# partition geometry across hosts
(tet_hosts, tri_hosts) = host_assignment_by_axis(mesh, memb.tris)
# sim = ssolver.TetOpSplit(model, mesh, rng, True, tet_hosts, tri_hosts)
sim = ssolver.TetOpSplit(model, mesh, rng, param['EF_solver'], tet_hosts,
tri_hosts)
# Correction factor for deviation between mesh and model cylinder:
area_cylinder = np.pi * param['diameter'] * param['length']
area_mesh_factor = sim.getPatchArea('memb') / area_cylinder
# Set initial conditions
sim.reset()
for t in memb.tris:
sim.setTriCount(t, 'Leak', 1)
sim.setEfieldDT(param['EF_dt'])
sim.setMembPotential('membrane', param['E_M'])
sim.setMembVolRes('membrane', param['R_A'])
sim.setMembCapac('membrane', param['C_M'] / area_mesh_factor)
v_zmin = mesh.getROIData('v_zmin')
I = param['Iinj'] / len(v_zmin)
for v in v_zmin:
sim.setVertIClamp(v, I)
return sim