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Merge pull request #12 from ComputationalPhysiology/ruff
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@finsberg
finsberg authored Jan 17, 2025
2 parents df02436 + 3b057b1 commit 4d17ccc
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Showing 22 changed files with 665 additions and 1,054 deletions.
85 changes: 40 additions & 45 deletions ...cy_checks_across_split_schemes/CaTrpn_split/land_CaTrpnsplit_consistent_with_zetasplit.py
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Original file line number Diff line number Diff line change
Expand Up @@ -26,55 +26,52 @@ def _Zeta(Zeta_prev, A, c, dLambda, dt, scheme: Scheme):
# Forward euler
return Zeta_prev + dZetas_dt * dt


# For CaTrpn split
def _XS(XS_prev, XW, gammasu, ksu, kws, dt):
dXS_dt_linearized = -gammasu - ksu
dXS_dt = -XS_prev * gammasu - XS_prev * ksu + XW * kws
return XS_prev + np.where(
(np.abs(dXS_dt_linearized)> 1e-8),
dXS_dt * (np.exp(dXS_dt_linearized*dt) - 1) / dXS_dt_linearized,
dXS_dt * dt
)
(np.abs(dXS_dt_linearized) > 1e-8),
dXS_dt * (np.exp(dXS_dt_linearized * dt) - 1) / dXS_dt_linearized,
dXS_dt * dt,
)


def _XW(XW_prev, XU, gammawu, kws, kuw, kwu, dt):
dXW_dt_linearized = -gammawu - kws - kwu
dXW_dt = -XW_prev * gammawu - XW_prev * kws + XU * kuw - XW_prev * kwu
return XW_prev + np.where(
(np.abs(dXW_dt_linearized)> 1e-8),
dXW_dt * (np.exp(dXW_dt_linearized*dt) - 1) / dXW_dt_linearized,
dXW_dt * dt
)
(np.abs(dXW_dt_linearized) > 1e-8),
dXW_dt * (np.exp(dXW_dt_linearized * dt) - 1) / dXW_dt_linearized,
dXW_dt * dt,
)


def _TmB(TmB_prev, CaTrpn, XU, ntm, kb, ku, dt):
dTmB_dt_linearized = -(CaTrpn ** (ntm / 2)) * ku
dTmB_dt = -TmB_prev * CaTrpn ** (ntm / 2) * ku + XU * (
kb * np.where(
(CaTrpn ** (-1 / 2 * ntm)<100),
CaTrpn ** (-1 / 2 * ntm),
100
)
)
kb * np.where((CaTrpn ** (-1 / 2 * ntm) < 100), CaTrpn ** (-1 / 2 * ntm), 100)
)

return TmB_prev + np.where(
(np.abs(dTmB_dt_linearized)> 1e-8),
(np.abs(dTmB_dt_linearized) > 1e-8),
dTmB_dt * (np.exp(dTmB_dt_linearized * dt) - 1) / dTmB_dt_linearized,
dTmB_dt * dt
)
dTmB_dt * dt,
)


def _XU(XW, XS, TmB):
return -XW -XS + 1 - TmB
return -XW - XS + 1 - TmB


def _gammawu(Zetaw, gammaw):
return gammaw * np.abs(Zetaw)


def _gammasu(Zetas, gammas):
return gammas * np.where(
(Zetas > 0),
Zetas,
np.where((Zetas < -1),
-Zetas - 1, 0)
)
return gammas * np.where((Zetas > 0), Zetas, np.where((Zetas < -1), -Zetas - 1, 0))


_parameters = {
"Beta0": 2.3,
Expand All @@ -87,9 +84,9 @@ def _gammasu(Zetas, gammas):
"rw": 0.5,
"gammas": 0.0085, # New parameters CaTrpn split
"gammaw": 0.615, # New parameters CaTrpn split
"Trpn50": 0.35, # New parameters CaTrpn split
"ntm": 2.4, # New parameters CaTrpn split.
"ku": 0.04, # New parameters CaTrpn split.
"Trpn50": 0.35, # New parameters CaTrpn split
"ntm": 2.4, # New parameters CaTrpn split.
"ku": 0.04, # New parameters CaTrpn split.
}


Expand All @@ -101,7 +98,7 @@ def __init__(
n0,
CaTrpn, # New variables CaTrpn split (missing)
mesh,
TmB=None, # New variables CaTrpn split
TmB=None, # New variables CaTrpn split
XS=None,
XW=None,
parameters=None,
Expand Down Expand Up @@ -140,7 +137,7 @@ def __init__(
self.TmB_prev = dolfin.Function(self.function_space)
if TmB is not None:
self.TmB_prev.assign(TmB)
else: # Set initial TmB value
else: # Set initial TmB value
self._TmB.interpolate(dolfin.Constant(1))
self.TmB_prev.interpolate(dolfin.Constant(1))
""" """
Expand Down Expand Up @@ -173,21 +170,21 @@ def __init__(
self._dLambda_tol = dLambda_tol
self._t_prev = 0.0


""" For CaTrpn split"""

@property
def ksu(self):
kws = self._parameters["kws"]
rw = self._parameters["rw"]
rs = self._parameters["rs"]
return ((kws * rw) * (-1 + 1 / rs))
return (kws * rw) * (-1 + 1 / rs)

@property
def kwu(self):
kuw = self._parameters["kuw"]
rw = self._parameters["rw"]
kws = self._parameters["kws"]
return (kuw * (-1 + 1 / rw) - kws)
return kuw * (-1 + 1 / rw) - kws

@property
def kb(self):
Expand All @@ -196,7 +193,7 @@ def kb(self):
ku = self._parameters["ku"]
rs = self._parameters["rs"]
rw = self._parameters["rw"]
return ((Trpn50**ntm * ku) / (-rw * (1 - rs) + 1 - rs))
return (Trpn50**ntm * ku) / (-rw * (1 - rs) + 1 - rs)

@property
def XS(self):
Expand Down Expand Up @@ -231,8 +228,8 @@ def update_TmB(self):
self._parameters["ntm"],
self.kb,
self._parameters["ku"],
self.dt
)
self.dt,
)

def update_XS(self):
logger.debug("update XS")
Expand All @@ -242,8 +239,8 @@ def update_XS(self):
self.gammasu.vector().get_local(),
self.ksu,
self._parameters["kws"],
self.dt
)
self.dt,
)

def update_XW(self):
logger.debug("update XW")
Expand All @@ -254,8 +251,8 @@ def update_XW(self):
self._parameters["kws"],
self._parameters["kuw"],
self.kwu,
self.dt
)
self.dt,
)

# Calculate monitors
def calculate_XU(self):
Expand All @@ -264,28 +261,28 @@ def calculate_XU(self):
self.XW_prev.vector().get_local(),
self.XS_prev.vector().get_local(),
self.TmB_prev.vector().get_local(),
)
)

def calculate_gammasu(self):
logger.debug("update gammasu")
self._gammasu.vector()[:] = _gammasu(
self.Zetas_prev.vector().get_local(),
self._parameters["gammas"],
)
)

def calculate_gammawu(self):
logger.debug("update gammawu")
self._gammawu.vector()[:] = _gammawu(
self.Zetaw_prev.vector().get_local(),
self._parameters["gammaw"],
)
)

def dLambda(self, lmbda):
logger.debug("Evaluate dLambda")
if self.dt == 0:
return self._dLambda
else:
return (lmbda - self.lmbda_prev)/self.dt
return (lmbda - self.lmbda_prev) / self.dt

@property
def Aw(self):
Expand Down Expand Up @@ -334,7 +331,6 @@ def cs(self):
/ (rs * scale_popu_rs)
)


def update_Zetas(self, lmbda):
logger.debug("update Zetas")
self._projector(
Expand Down Expand Up @@ -387,7 +383,6 @@ def Zetaw(self, lmbda):
def dt(self) -> float:
return self.t - self._t_prev


def update_prev(self):
logger.debug("update previous")
self.Zetas_prev.vector()[:] = self._Zetas.vector()
Expand Down
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