Todo
Improve autoapi module
circadapt.components.patch
Patch objects.
Module Contents
Classes
The Patch describes the relationship between |
|
Patch2022 is based on Patch in Walmsley 2015. |
Objects
- class circadapt.components.patch.Patch(model, objects=None, wall_locs=None)
Bases:
circadapt.components.ComponentThe Patch describes the relationship between \({\sigma}_f = {\varepsilon}_f\).
Parameters
- Am_ref [\(m^2\)]: float
Reference wall area at \(l_{s} = l_{s,ref}\).
- V_wall [\(m^3\)]: float
Wall volume
- v_max [\(\mu m/s\)]: float
Maximum shortening velocity
- l_se0 [\(\mu m\)]: float
lgth of the series elastic element, i.e. \(l_{s} -l_{si}\) for which stress is zero.
- l_s0 [\(\mu m\)]: float
Reference sarcomere lgth for which at \(A_m (l_{s,ref}) = A_{m,ref}\).
- dl_s_pas [\(\mu m\)]: float
Nonlinear exponent of Titin stress
- Sf_pas [Pa]: float
Linear ECM stress coefficient
- fac_Sf_tit [-]: float
Contribution factor of titen stress multiplied with Sf_act
- k1 [-]: float
Nonlinear exponent ECM stress component
- tr [s]: float
Contraction time constant
- td [s]: float
Relaxation time constant
- time_act [-]: float
Relative contraction duration
- Sf_act [Pa]: float
Linear active stress component
- dt [s]: float
Activation delay relative to intrinsic activation
- C_rest [-]: float
Rest contractility
- l_si0 [\(\mu m\)]: float
Reference lgth for zero-active-stress
- LDAD [s]: float
strain dependend activation duration
- ADO [s]: float
activation duration offset
- LDCC [-]: float
stretch dependend contractility coefficient
- Sf_pasMaxT: float
Maximum ecm stress (adaptation sens variable)
- Sf_pasActT: float
Active weighted passive stress (adaptation sens variable)
- FacSf_actT: float
Active stress (adaptation sens variable)
- LsPasActT: float
Weighted sarcomere lgth average (adaptation sens variable)
- adapt_gamma: bool
Adaptation constant
Signals
Signals are arrays. Each point in the array represents a point in time with step-size controlled by the solver.
- l_s [\(\mu m\)]: array
Sarcomere lgth
- l_si [\(\mu m\)]: array
State variable: Intrinsic sarcomere lgth
- LsiDot [\(\mu m/s\)]: array
State variable: Intrinsic sarcomere lgth time-derivative
- C [-]: array
State variable: contraction curve
- C_dot [1/s]: array
State variable: contraction time-derivative
- Am [m:sup:2]: array
Patch mid-wall area
- Am0 [m:sup:2]: array
Patch mid-wall zero-stress area
- Ef [-]: array
Natural strain
- dA_dT [m / N]: array
Area-tension derivative
- Sf [Pa]: array
Total fibre stress at mid-wall
- Sf_pasT [Pa]: array
Total passive stress at mid-wall
- SfEcm [Pa]: array
Total ECM stress at mid-wall
- dSf_dEf [Pa]: array
Total stiffness coefficient
- dSf_pas_dEf [Pa]: array
Total passive stiffness coefficient
- SfEcmMax: array
Adaptation: Maximum ECM stress
- Sf_actMax: array
Adaptation: maximum active stress
- Sf_pasAct: array
Adaptation: active-weighted passive stress
- LsPasAct: array
Adaptation: active-weigthed sarcomere lgth
- parameters = "['Am_ref', 'V_wall', 'v_max', 'l_se0', 'l_s0', 'l_s_ref', 'dl_s_pas', 'Sf_pas', 'ft1_const',..."
- signals = "['l_s', 'l_si', 'l_si_dot', 'C', 'C_dot', 'Cm', 'Am', 'Am0', 'Ef', 'dA_dT', 'Sf',..."
- parameter_on_set
- build()
(re)build patch locations based on wall locations.
There is no compatibility with different types of patches used in the model. If you use different type of patches, please use the direct way of interacting with the c++ object, i.e. set() and get().
- get_all_patches()
Get all patches of the walls included in this pointer object.
- add_object(o)
- __repr__()
Object representation in string format.
- __getitem__(arg: any) any
Get data.
This function is called when self[arg].
Parameters
- arg: slice or string
If slice, return a components object with locs obtained from slice. If str, return the parameter or signal for all locs
- __setitem__(arg: str, val: any) any
Set data.
Set data of the parameter given in arg. Only parameter names can be used.
Parameters
- arg: str
Parameter name
- val: float/int/bool
Value will automatically be translated to type to
- __iter__()
Iterate over object, used for dict(self).
- add(name)
- class circadapt.components.patch.Patch2022(model, objects=None, wall_locs=None)
Bases:
circadapt.components.ComponentPatch2022 is based on Patch in Walmsley 2015.
Parameters
- Am_ref [\(m^2\)]: float
Reference wall area at \(l_{s} = l_{s,ref}\).
- V_wall [\(m^3\)]: float
Wall volume
- v_max [\(\mu m/s\)]: float
Maximum shortening velocity
- l_se0 [\(\mu m\)]: float
lgth of the series elastic element, i.e. \(l_{s} -l_{si}\) for which stress is zero.
- l_s0 [\(\mu m\)]: float
Reference sarcomere lgth for which at \(A_m (l_{s,ref}) = A_{m,ref}\).
- dl_s_pas [\(\mu m\)]: float
Nonlinear exponent of Titin stress
- Sf_pas [Pa]: float
Linear ECM stress coefficient
- fac_Sf_tit [-]: float
Contribution factor of titen stress multiplied with Sf_act
- k1 [-]: float
Nonlinear exponent ECM stress component
- tr [s]: float
Contraction time constant
- td [s]: float
Relaxation time constant
- time_act [-]: float
Relative contraction duration
- Sf_act [Pa]: float
Linear active stress component
- dt [s]: float
Activation delay relative to intrinsic activation
- C_rest [-]: float
Rest contractility
- l_si0 [\(\mu m\)]: float
Reference lgth for zero-active-stress
- LDAD [s]: float
strain dependend activation duration
- ADO [s]: float
activation duration offset
- LDCC [-]: float
stretch dependend contractility coefficient
- Sf_pasMaxT: float
Maximum ecm stress (adaptation sens variable)
- Sf_pasActT: float
Active weighted passive stress (adaptation sens variable)
- FacSf_actT: float
Active stress (adaptation sens variable)
- LsPasActT: float
Weighted sarcomere lgth average (adaptation sens variable)
- adapt_gamma: bool
Adaptation constant
Signals
Signals are arrays. Each point in the array represents a point in time with step-size controlled by the solver.
- l_s [\(\mu m\)]: array
Sarcomere lgth
- l_si [\(\mu m\)]: array
State variable: Intrinsic sarcomere lgth
- LsiDot [\(\mu m/s\)]: array
State variable: Intrinsic sarcomere lgth time-derivative
- C [-]: array
State variable: contraction curve
- C_dot [1/s]: array
State variable: contraction time-derivative
- Am [m:sup:2]: array
Patch mid-wall area
- Am0 [m:sup:2]: array
Patch mid-wall zero-stress area
- Ef [-]: array
Natural strain
- T [Nm]: array
Mid-wall tension
- dA_dT [m / N]: array
Area-tension derivative
- Sf [Pa]: array
Total fibre stress at mid-wall
- Sf_pasT [Pa]: array
Total passive stress at mid-wall
- SfEcm [Pa]: array
Total ECM stress at mid-wall
- dSf_dEf [Pa]: array
Total stiffness coefficient
- dSf_pas_dEf [Pa]: array
Total passive stiffness coefficient
- SfEcmMax: array
Adaptation: Maximum ECM stress
- Sf_actMax: array
Adaptation: maximum active stress
- Sf_pasAct: array
Adaptation: active-weighted passive stress
- LsPasAct: array
Adaptation: active-weigthed sarcomere lgth
- parameters = "['Am_ref', 'V_wall', 'v_max', 'l_se0', 'l_s0', 'l_s_ref', 'dl_s_pas', 'Sf_pas', 'tr', 'td',..."
- signals = "['l_s', 'l_si', 'l_si_dot', 'C', 'C_dot', 'Cm', 'Am', 'Am0', 'Ef', 'T', 'dA_dT', 'Sf',..."
- parameter_on_set
- build()
(re)build patch locations based on wall locations.
There is no compatibility with different types of patches used in the model. If you use different type of patches, please use the direct way of interacting with the c++ object, i.e. set() and get().
- get_all_patches()
Get all patches of the walls included in this pointer object.
- add_object(o)
- __repr__()
Object representation in string format.
- __getitem__(arg: any) any
Get data.
This function is called when self[arg].
Parameters
- arg: slice or string
If slice, return a components object with locs obtained from slice. If str, return the parameter or signal for all locs
- __setitem__(arg: str, val: any) any
Set data.
Set data of the parameter given in arg. Only parameter names can be used.
Parameters
- arg: str
Parameter name
- val: float/int/bool
Value will automatically be translated to type to
- __iter__()
Iterate over object, used for dict(self).
- add(name)