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axon_rotsym_withER.lua
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axon_rotsym_withER.lua
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--------------------------------------------------------------------------------
-- 3D cable equation on axon with Ranvier nodes. --
-- Inside the axon, a concentric cylinder of about 1/10 the neuron's volume --
-- is inserted as a kind of obstacle or additional condenser). --
-- The implementation relies on perfect rotational symmetry to reduce the --
-- discretization to a 2d problem. --
-- --
-- Author: Markus Breit --
-- Date: 2019-01-04 --
--------------------------------------------------------------------------------
ug_load_script("ug_util.lua")
ug_load_script("util/load_balancing_util.lua")
AssertPluginsLoaded({"neuro_collection", "Parmetis"})
-- choose algebra
InitUG(2, AlgebraType("CPU", 1))
------------------------------------
-- process command line arguments --
------------------------------------
-- grid
grid = util.GetParam("-grid", "grids/axon5_2d_er.ugx")
nRanvier = util.GetParam("-nRanv", 5)
-- time stepping
numTimeSteps = util.GetParamNumber("-nSteps", 2000, "number of timesteps")
dt = util.GetParamNumber("-dt", 0.005, "time step in milliseconds")
-- spatial discretization
numRefs = util.GetParamNumber("-numRefs", 1, "number of refinements")
numAnisoRefs = util.GetParamNumber("-numAnisoRefs", 0, "number of anisotropic refinements")
-- choose outfile directory
outDir = util.GetParam("-outName", "test/neuron")
outDir = outDir.."/"
-- generate vtk output? (every modulo-th step)
generateVTKoutput = util.HasParamOption("-vtk")
modulo = util.GetParamNumber("-modulo", 1)
-- choose whether the ER is to be treated as pure obstacle or as capacitor
erAsPureObstacle = util.HasParamOption("-erAsPureObstacle")
---------------------------------------
-- problem constants and stimulation --
---------------------------------------
-- conductivities
sigma_in = 2.4556479647688e3 -- deduced from PNP model, in fC / (ms mV um)
sigma_out = 1.8866027810257e3 -- deduced from PNP model, in fC / (ms mV um)
-- ER handling
sigma_er = sigma_in
-- membrane specific capacitance
ranvier_cap = 3.6120456108572e-3 -- 3.54167512e-03 -- in C / (V m^2)
myelin_cap = 2.4101772506797e-4 -- 0.05*ranvier_cap -- 10 layers with 2 membranes each
-- channel conductances
g_Na = 1.2e-00 -- in fC / (mV ms um^2)
g_K = 3.6e-01 -- in fC / (mV ms um^2)
g_L = 3.0e-03 -- in fC / (mV ms um^2)
-- equilibrium potentials
phi_eq_in = -70.0 -- in mV
phi_eq_out = 0.0 -- in mV
E_Na = 64.0 -- in mV
E_K = -94.0 -- in mV
leak_K = 0.03092
leak_Na = -0.00293
E_L = (phi_eq_in-phi_eq_out) + (leak_K+leak_Na)/g_L
-- injection current density
injCurrentDensity = 3.0 -- in fC / (ms um^2)
injectionStart = 0 -- in ms
injectionEnd = 1000 -- in ms
function electrodeCurrent(z, r, t, si)
if t >= injectionStart and t <= injectionEnd then
return 2.0*math.pi*r * injCurrentDensity
end
return 0.0
end
-------------------------------
-- approximation space setup --
-------------------------------
neededSubsets = {"in", "out", "er", "myelin", "ermem", "bnd", "ranvier1"}
for i = 2,nRanvier do
neededSubsets[4+i] = "ranvier" .. i
end
dom = util.CreateDomain(grid, 0, neededSubsets)
balancer.partitioner = "parmetis"
balancer.staticProcHierarchy = true
balancer.firstDistLvl = 0
balancer.redistSteps = 4
balancer.firstDistProcs = 40
balancer.redistProcs = 64
balancer.parallelElementThreshold = 24
balancer.ParseParameters()
loadBalancer = balancer.CreateLoadBalancer(dom)
if loadBalancer ~= nil then
if balancer.partitioner == "parmetis" then
mu = ManifoldUnificator(dom)
mu:add_protectable_subsets("myelin")
for i = 1,nRanvier do
mu:add_protectable_subsets("ranvier"..i)
end
mu:add_protectable_subsets("ermem")
cdgm = ClusteredDualGraphManager()
cdgm:add_unificator(SiblingUnificator())
cdgm:add_unificator(mu)
balancer.defaultPartitioner:set_dual_graph_manager(cdgm)
end
balancer.Rebalance(dom, loadBalancer)
loadBalancer:estimate_distribution_quality()
loadBalancer:print_quality_records()
end
-- name some useful subset collections
ranvier = "ranvier1"
for i = 2,nRanvier do
ranvier = ranvier .. ", ranvier" .. i
end
memAll = "myelin, " .. ranvier
volOut = "out, bnd, " .. memAll
volIn = "in, " .. memAll .. ", ermem"
volER = "er, ermem"
injection = "ranvier1"
-- create approximation space
approxSpace = ApproximationSpace(dom)
approxSpace:add_fct("phiOut", "Lagrange", 1, volOut)
approxSpace:add_fct("phiIn", "Lagrange", 1, volIn)
approxSpace:add_fct("phiER", "Lagrange", 1, volER)
approxSpace:add_fct("n", "Lagrange", 1, ranvier)
approxSpace:add_fct("m", "Lagrange", 1, ranvier)
approxSpace:add_fct("h", "Lagrange", 1, ranvier)
approxSpace:init_top_surface()
approxSpace:init_levels()
-- anisotropic refinements
refiner = HangingNodeDomainRefiner(dom)
AddShadowCopyAdjuster(refiner)
for i = 1, numAnisoRefs do
MarkAnisotropicX(refiner, dom, 0.707)
unmark_ranvier_areas(refiner, approxSpace, ranvier, i <= 3)
refiner:refine()
refiner:clear_marks()
balancer.qualityRecordName = "anisoRef " .. i
balancer.Rebalance(dom, loadBalancer)
if loadBalancer ~= nil then
loadBalancer:estimate_distribution_quality()
end
end
-- isotropic refinements
for i = 1, numRefs do
MarkGlobal(refiner, dom)
refiner:refine()
balancer.qualityRecordName = " globRef " .. i
balancer.Rebalance(dom, loadBalancer)
if loadBalancer ~= nil then
loadBalancer:estimate_distribution_quality()
end
end
delete(refiner)
if loadBalancer ~= nil then
loadBalancer:print_quality_records()
end
print()
print(dom:domain_info():to_string())
--SaveGridHierarchyTransformed(dom:grid(), dom:subset_handler(), outDir.."grid/refined_grid_hierarchy" .."_p" .. ProcRank() .. ".ugx", 2.0)
--SaveParallelGridLayout(dom:grid(), fileName.."grid/parallel_grid_layout_lv".. i .."_p"..ProcRank()..".ugx", offsetForGridHierarchy)
--------------------------
-- discretization setup --
--------------------------
-- scaled coefficient functions
function scaled_conductivity_out(z,r,t)
local s = 2*math.pi*r * sigma_out
return s, 0,
0, s
end
function scaled_conductivity_in(z,r,t)
local s = 2*math.pi*r * sigma_in
return s, 0,
0, s
end
function scaled_conductivity_er(z,r,t)
local s = 2*math.pi*r * sigma_er
return s, 0,
0, s
end
function myelin_capacitance(z,r,t)
return 2*math.pi*r * myelin_cap
end
function myelin_capacitance_neg(z,r,t)
return - 2*math.pi*r * myelin_cap
end
function ranvier_capacitance(z,r,t)
return 2*math.pi*r * ranvier_cap
end
function ranvier_capacitance_neg(z,r,t)
return - 2*math.pi*r * ranvier_cap
end
function rotSym_scale(z,r,t)
return 2*math.pi*r
end
-- outer potential
elemDiscPhiOut = ConvectionDiffusion("phiOut", "out", "fv1")
elemDiscPhiOut:set_diffusion("scaled_conductivity_out")
elemDiscPhiOut:set_mass_scale(0.0)
-- inner potential
elemDiscPhiIn = ConvectionDiffusion("phiIn", "in", "fv1")
elemDiscPhiIn:set_diffusion("scaled_conductivity_in")
elemDiscPhiIn:set_mass_scale(0.0)
-- ER potential
elemDiscPhiER = ConvectionDiffusion("phiER", "er", "fv1")
elemDiscPhiER:set_diffusion("scaled_conductivity_er")
elemDiscPhiER:set_mass_scale(0.0)
-- gatings --
function zeroDeriv()
return 0.0
end
-- n particle
elemDiscN = ConvectionDiffusion("n", ranvier, "fv1")
function rhsN(n, phiOut, phiIn)
-- bit tricky: the result is computed in such a way
-- that using it as (explicit) rhs in 'dn/dt = f' will make the solution
-- of that ODE with the expl. Euler method
-- the analytical solution for one time step (with constant Vm)
local vm = phiIn - phiOut
local term = (n_inf(vm) - n)/dt
return -term*(1.0-math.exp(-dt/tau_n(vm)))
end
rhsNData = LuaUserFunctionNumber("rhsN", 3)
rhsNData:set_input(0, elemDiscN:value())
rhsNData:set_input(1, elemDiscPhiOut:value())
rhsNData:set_input(2, elemDiscPhiIn:value())
rhsNData:set_deriv(0, "zeroDeriv")
rhsNData:set_deriv(1, "zeroDeriv")
rhsNData:set_deriv(2, "zeroDeriv")
elemDiscN:set_reaction(rhsNData)
-- m particle
elemDiscM = ConvectionDiffusion("m", ranvier, "fv1")
function rhsM(m, phiOut, phiIn)
local vm = phiIn - phiOut
local term = (m_inf(vm) - m)/dt
return -term*(1.0 - math.exp(-dt/tau_m(vm)))
end
rhsMData = LuaUserFunctionNumber("rhsM", 3)
rhsMData:set_input(0, elemDiscM:value())
rhsMData:set_input(1, elemDiscPhiOut:value())
rhsMData:set_input(2, elemDiscPhiIn:value())
rhsMData:set_deriv(0, "zeroDeriv")
rhsMData:set_deriv(1, "zeroDeriv")
rhsMData:set_deriv(2, "zeroDeriv")
elemDiscM:set_reaction(rhsMData)
-- h particle
elemDiscH = ConvectionDiffusion("h", ranvier, "fv1")
function rhsH(h, phiOut, phiIn)
local vm = phiIn - phiOut
local term = (h_inf(vm) - h)/dt
return -term*(1.0-math.exp(-dt/tau_h(vm)))
end
rhsHData = LuaUserFunctionNumber("rhsH", 3)
rhsHData:set_input(0, elemDiscH:value())
rhsHData:set_input(1, elemDiscPhiOut:value())
rhsHData:set_input(2, elemDiscPhiIn:value())
rhsHData:set_deriv(0, "zeroDeriv")
rhsHData:set_deriv(1, "zeroDeriv")
rhsHData:set_deriv(2, "zeroDeriv")
elemDiscH:set_reaction(rhsHData)
-- Hodgkin-Huxley current
function hhCurrent(phiOut, phiIn, n, m, h, z, r, t, si)
local potassiumFlux = g_K * n*n*n*n * (phiIn - phiOut - E_K)
local sodiumFlux = g_Na * m*m*m*h * (phiIn - phiOut - E_Na)
local leakageFlux = g_L * (phiIn - phiOut - E_L)
return 2*math.pi*r * (potassiumFlux + sodiumFlux + leakageFlux)
end
hhCurrentFunction = LuaUserFunctionNumber("hhCurrent", 5, true)
hhCurrentFunction:set_input(0, elemDiscPhiOut:value())
hhCurrentFunction:set_input(1, elemDiscPhiIn:value())
hhCurrentFunction:set_input(2, elemDiscN:value())
hhCurrentFunction:set_input(3, elemDiscM:value())
hhCurrentFunction:set_input(4, elemDiscH:value())
hhCurrentFunction:set_deriv(0, "zeroDeriv")
hhCurrentFunction:set_deriv(1, "zeroDeriv")
hhCurrentFunction:set_deriv(2, "zeroDeriv")
hhCurrentFunction:set_deriv(3, "zeroDeriv")
hhCurrentFunction:set_deriv(4, "zeroDeriv")
linkerOut = ScaleAddLinkerNumber()
linkerOut:add(-1.0, hhCurrentFunction)
elemDiscHHOut = ConvectionDiffusionFV1("phiOut", ranvier)
elemDiscHHOut:set_mass_scale(0.0)
elemDiscHHOut:set_reaction(linkerOut)
linkerIn = ScaleAddLinkerNumber()
linkerIn:add(1.0, hhCurrentFunction)
elemDiscHHIn = ConvectionDiffusionFV1("phiIn", ranvier)
elemDiscHHIn:set_mass_scale(0.0)
elemDiscHHIn:set_reaction(linkerIn)
-- capacitive current
myelinCapData = LuaUserNumber("myelin_capacitance")
myelinCapDataNeg = LuaUserNumber("myelin_capacitance_neg")
ranvierCapData = LuaUserNumber("ranvier_capacitance")
ranvierCapDataNeg = LuaUserNumber("ranvier_capacitance_neg")
elemDiscCapMyelinOut = ConvectionDiffusion("phiOut", "myelin", "fv1")
elemDiscCapMyelinOut:set_mass_scale(myelinCapData)
linkerCapOutMyelin = ScaleAddLinkerNumber()
linkerCapOutMyelin:add(myelinCapDataNeg, elemDiscPhiIn:value())
elemDiscCapMyelinOut:set_mass(linkerCapOutMyelin)
elemDiscCapRanvierOut = ConvectionDiffusion("phiOut", ranvier, "fv1")
elemDiscCapRanvierOut:set_mass_scale(ranvierCapData)
linkerCapOutRanvier = ScaleAddLinkerNumber()
linkerCapOutRanvier:add(ranvierCapDataNeg, elemDiscPhiIn:value())
elemDiscCapRanvierOut:set_mass(linkerCapOutRanvier)
elemDiscCapMyelinIn = ConvectionDiffusion("phiIn", "myelin", "fv1")
elemDiscCapMyelinIn:set_mass_scale(myelinCapData)
linkerCapInMyelin = ScaleAddLinkerNumber()
linkerCapInMyelin:add(myelinCapDataNeg, elemDiscPhiOut:value())
elemDiscCapMyelinIn:set_mass(linkerCapInMyelin)
elemDiscCapRanvierIn = ConvectionDiffusion("phiIn", ranvier, "fv1")
elemDiscCapRanvierIn:set_mass_scale(ranvierCapData)
linkerCapInRanvier = ScaleAddLinkerNumber()
linkerCapInRanvier:add(ranvierCapDataNeg, elemDiscPhiOut:value())
elemDiscCapRanvierIn:set_mass(linkerCapInRanvier)
elemDiscCapERMOut = ConvectionDiffusion("phiIn", "ermem", "fv1")
elemDiscCapERMOut:set_mass_scale(ranvierCapData)
linkerCapERMOut = ScaleAddLinkerNumber()
linkerCapERMOut:add(ranvierCapDataNeg, elemDiscPhiER:value())
elemDiscCapERMOut:set_mass(linkerCapERMOut)
elemDiscCapERMIn = ConvectionDiffusion("phiER", "ermem", "fv1")
elemDiscCapERMIn:set_mass_scale(ranvierCapData)
linkerCapERMIn = ScaleAddLinkerNumber()
linkerCapERMIn:add(ranvierCapDataNeg, elemDiscPhiIn:value())
elemDiscCapERMIn:set_mass(linkerCapERMIn)
-- injection current
elemDiscInjection = UserFluxBoundaryFV1("phiIn, phiOut", injection) -- function order: to, from
elemDiscInjection:set_flux_function("electrodeCurrent")
-- Dirichlet-0 boundary for outer potential
dirichletBndPhiOut = DirichletBoundary(true)
dirichletBndPhiOut:add(0.0, "phiOut", "bnd")
if erAsPureObstacle then
dirichletBndPhiOut:add(0.0, "phiER", "er")
dirichletBndPhiOut:add(0.0, "phiER", "ermem")
end
-- domain discretization
domainDiscImpl = DomainDiscretization(approxSpace)
domainDiscImpl:add(elemDiscPhiOut)
domainDiscImpl:add(elemDiscPhiIn)
domainDiscImpl:add(elemDiscCapMyelinOut)
domainDiscImpl:add(elemDiscCapRanvierOut)
domainDiscImpl:add(elemDiscCapMyelinIn)
domainDiscImpl:add(elemDiscCapRanvierIn)
domainDiscImpl:add(dirichletBndPhiOut)
if not erAsPureObstacle then
domainDiscImpl:add(elemDiscPhiER)
domainDiscImpl:add(elemDiscCapERMOut)
domainDiscImpl:add(elemDiscCapERMIn)
end
domainDiscExpl = DomainDiscretization(approxSpace)
domainDiscExpl:add(elemDiscN)
domainDiscExpl:add(elemDiscM)
domainDiscExpl:add(elemDiscH)
domainDiscExpl:add(elemDiscHHOut)
domainDiscExpl:add(elemDiscHHIn)
domainDiscExpl:add(elemDiscInjection) -- needs to be explicit, otherwise not assembled
-- time discretization
timeDiscImpl = ThetaTimeStep(domainDiscImpl)
timeDiscImpl:set_theta(1.0)
timeDiscExpl = ThetaTimeStep(domainDiscExpl)
timeDiscExpl:set_theta(0.0)
timeDisc = CompositeTimeDiscretization()
timeDisc:add_time_disc(timeDiscImpl)
timeDisc:add_time_disc(timeDiscExpl)
-- create linear operator
opLinear = AssembledLinearOperator(timeDisc)
-------------------
-- algebra setup --
-------------------
-- linear operator
op = AssembledLinearOperator(timeDisc)
-- debug writer
dbgWriter = GridFunctionDebugWriter(approxSpace)
dbgWriter:set_vtk_output(false)
dbgWriter:set_base_dir(outDir)
convCheck = ConvCheck()
convCheck:set_maximum_steps(100)
convCheck:set_minimum_defect(1e-30)
convCheck:set_reduction(1e-08)
convCheck:set_verbose(true)
--[[
convCheck = CompositeConvCheck(approxSpace, 100, 1e-30, 1e-08)
convCheck:set_group_check("phiOut, phiIn", 1e-30, 1e-08)
convCheck:set_group_check("n, m, h", 1e-30, 1e-08)
convCheck:set_verbose(true)
convCheck:set_time_measurement(true)
--]]
-- solver setup --
solver = CG()--LinearSolver()
gmg = GeometricMultiGrid(approxSpace)
gmg:set_discretization(timeDisc)
gmg:set_base_level(0)
gmg:set_gathered_base_solver_if_ambiguous(true)
--gmg:set_debug(dbgWriter)
base = SuperLU()
gmg:set_base_solver(base)
smoother = ILU()--SymmetricGaussSeidel()
smoother:enable_consistent_interfaces(true)
smoother:set_sort(true) -- important since natural UG sorting is somewhat awkward
gmg:set_smoother(smoother)
gmg:set_smooth_on_surface_rim(true)
gmg:set_cycle_type(1)
gmg:set_num_presmooth(3)
gmg:set_num_postsmooth(3)
gmg:set_rap(true)
solver:set_preconditioner(gmg)
solver:set_convergence_check(convCheck)
--solver:set_debug(dbgWriter)
-------------------
-- Time stepping --
-------------------
-- initial values
time = 0
step = 0
u = GridFunction(approxSpace)
u:set(0.0)
InterpolateInner(phi_eq_out, u,"phiOut", volOut, time)
InterpolateInner(phi_eq_in, u, "phiIn", volIn, time)
InterpolateInner(phi_eq_in, u, "phiER", volER, time)
n_eq = n_inf(phi_eq_in-phi_eq_out)
m_eq = m_inf(phi_eq_in-phi_eq_out)
h_eq = h_inf(phi_eq_in-phi_eq_out)
InterpolateInner(n_eq, u, "n", ranvier, time)
InterpolateInner(m_eq, u, "m", ranvier, time)
InterpolateInner(h_eq, u, "h", ranvier, time)
-- write start solutions
if generateVTKoutput then
out = VTKOutput()
out:print(outDir.."vtk/solution", u, step, time)
end
-- measure initial potential
take_measurement(u, time, ranvier, "phiIn, phiOut", outDir.."meas/meas")
-- create new grid functions for old value and rhs
uOld = u:clone()
b = GridFunction(approxSpace)
-- store grid function in vector of old solutions
solTimeSeries = SolutionTimeSeries()
solTimeSeries:push(uOld, time)
-- start the time stepping
for step = 1, numTimeSteps do
print("++++++ TIMESTEP " .. step .. " BEGIN ++++++")
-- prepare step
timeDisc:prepare_step(solTimeSeries, dt)
if step == 1 then
-- assemble inner Vm problem (matrix and rhs)
timeDisc:assemble_linear(op, b)
-- init solver (invert matrix - the actual solving)
solver:init(op)
else
-- assemble inner Vm problem (only rhs, matrix is const)
timeDisc:assemble_rhs(b)
end
if not solver:apply(u, b) then
print("Error: Solver for membrane potential problem did not converge.")
out:write_time_pvd(outDir.."vtk/solution", u)
exit()
end
-- update to new time
time = time + dt
-- plot solution
if generateVTKoutput and step % modulo == 0 then
out:print(outDir.."vtk/solution", u, step/modulo, time)
end
-- measure potential
take_measurement(u, time, ranvier, "phiIn, phiOut", outDir.."meas/meas")
-- update time series
oldSol = solTimeSeries:oldest()
VecScaleAssign(oldSol, 1.0, u)
solTimeSeries:push_discard_oldest(oldSol, time)
print("++++++ TIMESTEP " .. step .. " END ++++++++")
end
-- end timeseries, produce gathering file
if generateVTKoutput then
out:write_time_pvd(outDir.."vtk/solution", u)
end