def Idiam(diam, **params):
dim = params["dim"]
x0 = params.pop("x0")
params.pop("diamPore")
Jon = []
Joff = []
# TODO bad hack
if dim==3:
params.update(h=1.5, Nmax=7e5)
if dim==2:
params.update(h=0.75, Nmax=1e5)
for d in diam:
# get diffusivity interpolation
cache_pugh_diffusivity(diamPore=d, **dparams[dim])
ddata = dict(dparams[dim], name="Dpugh", diamPore=d)
# current WITHOUT molecule
setup = pugh.Setup(x0=None, diamPore=d, diffusivity_data=ddata, **params)
pb, pnps = pugh.solve(setup, visualize=True)
Jon.append(pnps.evaluate(setup.phys.CurrentPNPS)["J"])
# current WITH molecule
setup = pugh.Setup(x0=x0, diamPore=d, diffusivity_data=ddata, **params)
pb, pnps = pugh.solve(setup, visualize=True)
Joff.append(pnps.evaluate(setup.phys.CurrentPNPS)["J"])
return dict(Jon=Jon, Joff=Joff)
def IVDetail(V, **params):
params["x0"] = None
for bV, result in collect_dict(V):
params["bV"] = bV
setup = pugh.Setup(**params)
pb, pnps = pugh.solve(setup)
result.new = pnps.evaluate(setup.phys.CurrentPNPSDetail)
return result
def IrhoDetail(Rho, **params):
params["x0"] = None
for rho, result in collect_dict(Rho):
params["dnaqsdamp"] = rho
setup = pugh.Setup(**params)
pb, pnps = pugh.solve(setup, visualize=True)
result.new = pnps.evaluate(setup.phys.CurrentPNPSDetail)
return result
def IV(V, **params):
params["x0"] = None
J = []
for bV in V:
params["bV"] = bV
setup = pugh.Setup(**params)
pb, pnps = pugh.solve(setup)
J.append(pnps.evaluate(setup.phys.CurrentPNPS)["J"])
return dict(J=J)
def Irho(Rho, **params):
params["x0"] = None
bV = params["bV"]
J = []
for rho in Rho:
params["dnaqsdamp"] = rho
setup = pugh.Setup(**params)
pb, pnps = pugh.solve(setup, visualize=True)
J.append(pnps.evaluate(setup.phys.CurrentPNPS)["J"])
cond = [abs(j / bV) for j in J]
return dict(J=J, cond=cond)
def Idiam(diam, **params):
dim = params["dim"]
x0 = params.pop("x0")
params.pop("diamPore")
Jon = []
Joff = []
for d in diam:
# get diffusivity interpolation
cache_pugh_diffusivity(geoname="pugh2", diamPore=d, **dparams[dim])
# current WITHOUT molecule
setup = pugh.Setup(x0=None, diamPore=d, **params)
pb, pnps = pugh.solve(setup, visualize=True)
Jon.append(pnps.evaluate(setup.phys.CurrentPNPS)["J"])
# current WITH molecule
setup = pugh.Setup(x0=x0, diamPore=d, **params)
pb, pnps = pugh.solve(setup, visualize=True)
Joff.append(pnps.evaluate(setup.phys.CurrentPNPS)["J"])
return dict(Jon=Jon, Joff=Joff)