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Merge pull request #15 from TLDSZ/swl
add the rest of channels and fix bugs
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -792,10 +792,10 @@ class ICav12_Ma2020(CalciumChannel): | |
| def __init__( | ||
| self, | ||
| size: bst.typing.Size, | ||
| g_max: Union[bst.typing.ArrayLike, Callable] = 0 * (bu.cm / bu.second), | ||
| g_max: Union[bst.typing.ArrayLike, Callable] = 0 * (bu.mS / bu.cm**2), | ||
| V_sh: Union[bst.typing.ArrayLike, Callable] = 0 * bu.mV, | ||
| T_base: bst.typing.ArrayLike = 3 , | ||
| T: bst.typing.ArrayLike = 32., | ||
| T: bst.typing.ArrayLike = 22., | ||
| name: Optional[str] = None, | ||
| mode: Optional[bst.mixin.Mode] = None, | ||
| ): | ||
|
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@@ -823,8 +823,8 @@ def init_state(self, V, Ca: IonInfo, batch_size: int = None): | |
| self.n = State4Integral(bst.init.param(bu.math.zeros, self.varshape, batch_size)) | ||
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||
| def reset_state(self, V, Ca, batch_size=None): | ||
| self.m.value = self.f_m_inf(V,Ca) | ||
| self.h.value = self.f_h_inf(V,Ca) | ||
| self.m.value = self.f_m_inf(V) | ||
| self.h.value = self.f_h_inf(V) | ||
| self.n.value = self.f_n_inf(V,Ca) | ||
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||
| def compute_derivative(self, V, Ca): | ||
|
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@@ -837,11 +837,11 @@ def f_m_inf(self, V): | |
| return 1/(1 + bu.math.exp((V + 8.9)/(-6.7))) | ||
| def f_h_inf(self, V): | ||
| V = V / bu.mV | ||
| return self.VDI/(1 + exp((V +55)/8)) + (1-self.VDI) | ||
| return self.VDI/(1 + bu.math.exp((V +55)/8)) + (1-self.VDI) | ||
|
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||
| def f_n_inf(self, V, Ca): | ||
| V = V / bu.mV | ||
| return self.kf/(self.kf + Ca.C/bu.mM) | ||
| return bu.math.ones_like(V)*self.kf/(self.kf + Ca.C/bu.mM) | ||
|
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||
| def f_m_tau(self, V): | ||
| V = V / bu.mV | ||
|
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@@ -902,8 +902,8 @@ def init_state(self, V, Ca: IonInfo, batch_size: int = None): | |
| self.n = State4Integral(bst.init.param(bu.math.zeros, self.varshape, batch_size)) | ||
|
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||
| def reset_state(self, V, Ca, batch_size=None): | ||
| self.m.value = self.f_m_inf(V,Ca) | ||
| self.h.value = self.f_h_inf(V,Ca) | ||
| self.m.value = self.f_m_inf(V) | ||
| self.h.value = self.f_h_inf(V) | ||
| self.n.value = self.f_n_inf(V,Ca) | ||
|
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||
| def compute_derivative(self, V, Ca): | ||
|
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@@ -922,7 +922,7 @@ def f_h_inf(self, V): | |
|
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||
| def f_n_inf(self, V, Ca): | ||
| V = V / bu.mV | ||
| return self.kf/(self.kf + Ca.C/bu.mM) | ||
| return bu.math.ones_like(V)*self.kf/(self.kf + Ca.C/bu.mM) | ||
|
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||
| def f_m_tau(self, V): | ||
| V = V / bu.mV | ||
|
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@@ -988,8 +988,8 @@ def init_state(self, V, Ca: IonInfo, batch_size: int = None): | |
|
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|
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||
| def reset_state(self, V, Ca, batch_size=None): | ||
| self.m.value = self.f_m_inf(V,Ca) | ||
| self.h.value = self.f_h_inf(V,Ca) | ||
| self.m.value = self.f_m_inf(V) | ||
| self.h.value = self.f_h_inf(V) | ||
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|
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| def compute_derivative(self, V, Ca): | ||
|
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@@ -1033,7 +1033,6 @@ class ICav31_Ma2020(CalciumChannel): | |
| Contact: Haroon Anwar ([email protected]) | ||
| ''' | ||
|
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||
| __module__ = 'dendritex.channels' | ||
|
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||
| root_type = Calcium | ||
|
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@@ -1043,7 +1042,7 @@ def __init__( | |
| size: bst.typing.Size, | ||
| g_max: Union[bst.typing.ArrayLike, Callable] = 2.5e-4 * (bu.cm / bu.second), | ||
| V_sh: Union[bst.typing.ArrayLike, Callable] = 0 * bu.mV, | ||
| T_base: bst.typing.ArrayLike = 3 , | ||
| T_base: bst.typing.ArrayLike = 3 , | ||
| T: bst.typing.ArrayLike = 22., | ||
| name: Optional[str] = None, | ||
| mode: Optional[bst.mixin.Mode] = None, | ||
|
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@@ -1061,8 +1060,23 @@ def __init__( | |
| self.V_sh = bst.init.param(V_sh, self.varshape, allow_none=False) | ||
| self.phi = bst.init.param(T_base ** ((T - 37) / 10), self.varshape, allow_none=False) | ||
|
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||
| self.ci = 1e-4 | ||
| self.co = 2 | ||
| self.v0_m_inf = -52 | ||
| self.v0_h_inf = -72 | ||
| self.k_m_inf = -5 | ||
| self.k_h_inf = 7 | ||
|
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||
| self.C_tau_m = 1 | ||
| self.A_tau_m = 1.0 | ||
| self.v0_tau_m1 = -40 | ||
| self.v0_tau_m2 = -102 | ||
| self.k_tau_m1 = 9 | ||
| self.k_tau_m2 = -18 | ||
|
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||
| self.C_tau_h = 15 | ||
| self.A_tau_h = 1.0 | ||
| self.v0_tau_h1 = -32 | ||
| self.k_tau_h1 = 7 | ||
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| def init_state(self, V, Ca: IonInfo, batch_size: int = None): | ||
|
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@@ -1079,33 +1093,34 @@ def compute_derivative(self, V, Ca): | |
|
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||
| def f_p_inf(self, V): | ||
| V = V / bu.mV | ||
| return 1.0 / ( 1 + bu.math.exp((V - (-42.206)-self.V_sh)/-4.7056) )^(1/3) | ||
| return 1.0 / ( 1 + bu.math.exp((V - self.v0_m_inf)/self.k_m_inf) ) | ||
|
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||
| def f_q_inf(self, V): | ||
| V = V / bu.mV | ||
| return 1.0 / ( 1 + bu.math.exp((V - (-75.118)-self.V_sh)/6.4635 ) ) | ||
| return 1.0 / ( 1 + bu.math.exp((V - self.v0_h_inf)/self.k_h_inf) ) | ||
|
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||
| def f_p_tau(self, V): | ||
| V = V / bu.mV | ||
| return 1/( 1.2757 -2.3199 / (1. + bu.math.exp((-48.048 -V- self.V_sh)/ 30.655))+2.5712/ (1. + bu.math.exp((-28.386-V-self.V_sh)/ 9.6306))) | ||
| return bu.math.where(V<=-90, 1, (self.C_tau_m + self.A_tau_m / (bu.math.exp((V - self.v0_tau_m1)/ self.k_tau_m1) + bu.math.exp((V - self.v0_tau_m2)/self.k_tau_m2))) ) | ||
| def f_p_tau(self, V): | ||
| V = V / bu.mV | ||
| return 1/( 0.0076 + 0.17746 / (1. + bu.math.exp((-58.535-V-self.V_sh)/ 6.2692))+ 0.13402/ (1. + bu.math.exp((-101.436-V-self.V_sh)/-5.5845))) | ||
| return ( self.C_tau_h + self.A_tau_h / bu.math.exp((V - self.v0_tau_h1)/self.k_tau_h1) ) | ||
|
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||
| def ghk(self, V, Ca: IonInfo): | ||
| E = (1e-3) * V/bu.mV | ||
| zeta = (2*bu.faraday_constant * E )/( bu.gas_constant * (273.15 + self.T) * bu.kelvin ) | ||
| ci = self.ci | ||
| co = self.co | ||
|
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||
| if bu.math.maximum((1-bu.math.exp(-zeta)),0) <= 1e-6: | ||
| g = (1e-6) * bu.faraday_constant * (ci - co *bu.math.exp(-zeta)) * (1 + zeta/2) | ||
| else: | ||
| g = (1e-6) * (zeta*bu.faraday_constant) * (ci - co*bu.math.exp(-zeta)) / (1-bu.math.exp(-zeta)) | ||
| return g | ||
| def ghk(self, V, Ca: IonInfo): | ||
| E = (1e-3) * V | ||
| zeta = (2 * bu.faraday_constant * E )/( bu.gas_constant * (273.15 + self.T) * bu.kelvin) | ||
| zeta = zeta.to_decimal() | ||
| ci = Ca.C | ||
| co = 2 * bu.mM #co = Ca.C0 for Calciumdetailed | ||
| g_1 = (1e-6) * bu.faraday_constant * (ci - co * bu.math.exp(-zeta)) * (1 + zeta/2) | ||
| print(g_1) | ||
| g_2= (1e-6) * (zeta*bu.faraday_constant) * (ci - co*bu.math.exp(-zeta)) / (1-bu.math.exp(-zeta)) | ||
| return bu.math.where(bu.math.abs((1-bu.math.exp(-zeta))) <= 1e-6,g_1,g_2) | ||
|
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||
| def current(self, V, Ca: IonInfo): | ||
| return (1e3)*self.g_max * self.p.value ** 3 * self.q.value * self.ghk(V,Ca) | ||
| i = (1e3)*self.g_max * self.p.value ** 2 * self.q.value * self.ghk(V,Ca) | ||
| print(self.ghk(V,Ca)) | ||
| return (1e3)*self.g_max * self.p.value ** 2 * self.q.value * self.ghk(V,Ca) | ||
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@@ -1145,7 +1160,7 @@ def __init__( | |
| self.T = bst.init.param(T, self.varshape, allow_none=False) | ||
| self.T_base = bst.init.param(T_base, self.varshape, allow_none=False) | ||
| self.V_sh = bst.init.param(V_sh, self.varshape, allow_none=False) | ||
| self.phi = bst.init.param( T_base ** ((T - 37) / 10), self.varshape, allow_none=False) | ||
| self.phi = bst.init.param( T_base ** ((T - 20) / 10), self.varshape, allow_none=False) | ||
|
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| self.eca = 129.33 * bu.mV | ||
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@@ -1173,8 +1188,8 @@ def init_state(self, V, Ca: IonInfo, batch_size: int = None): | |
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| def reset_state(self, V, Ca, batch_size=None): | ||
| self.m.value = self.f_m_inf(V,Ca) | ||
| self.h.value = self.f_h_inf(V,Ca) | ||
| self.m.value = self.f_m_inf(V) | ||
| self.h.value = self.f_h_inf(V) | ||
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| def compute_derivative(self, V, Ca): | ||
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