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Nektar
Nektar
Commits
5176fd17
Commit
5176fd17
authored
Jun 26, 2014
by
Chris Cantwell
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Plain Diff
Removed old ten tusscher models, tidied new code.
parent
9a471326
Changes
10
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10 changed files
with
50 additions
and
1896 deletions
+50
-1896
solvers/CardiacEPSolver/CMakeLists.txt
solvers/CardiacEPSolver/CMakeLists.txt
+0
-3
solvers/CardiacEPSolver/CellModels/TenTusscher06.cpp
solvers/CardiacEPSolver/CellModels/TenTusscher06.cpp
+45
-36
solvers/CardiacEPSolver/CellModels/TenTusscher06.h
solvers/CardiacEPSolver/CellModels/TenTusscher06.h
+5
-1
solvers/CardiacEPSolver/CellModels/TenTusscher06Endo.cpp
solvers/CardiacEPSolver/CellModels/TenTusscher06Endo.cpp
+0
-536
solvers/CardiacEPSolver/CellModels/TenTusscher06Endo.h
solvers/CardiacEPSolver/CellModels/TenTusscher06Endo.h
+0
-80
solvers/CardiacEPSolver/CellModels/TenTusscher06Epi.cpp
solvers/CardiacEPSolver/CellModels/TenTusscher06Epi.cpp
+0
-538
solvers/CardiacEPSolver/CellModels/TenTusscher06Epi.h
solvers/CardiacEPSolver/CellModels/TenTusscher06Epi.h
+0
-77
solvers/CardiacEPSolver/CellModels/TenTusscher06M.cpp
solvers/CardiacEPSolver/CellModels/TenTusscher06M.cpp
+0
-539
solvers/CardiacEPSolver/CellModels/TenTusscher06M.h
solvers/CardiacEPSolver/CellModels/TenTusscher06M.h
+0
-83
solvers/CardiacEPSolver/Utilities/PrePacing/CMakeLists.txt
solvers/CardiacEPSolver/Utilities/PrePacing/CMakeLists.txt
+0
-3
No files found.
solvers/CardiacEPSolver/CMakeLists.txt
View file @
5176fd17
...
...
@@ -15,9 +15,6 @@ IF( NEKTAR_SOLVER_CARDIAC_EP )
./CellModels/LuoRudy91.cpp
./CellModels/Fox02.cpp
./CellModels/Winslow99.cpp
./CellModels/TenTusscher06Epi.cpp
./CellModels/TenTusscher06M.cpp
./CellModels/TenTusscher06Endo.cpp
./CellModels/TenTusscher06.cpp
./Filters/FilterCheckpointCellModel.cpp
./Filters/FilterElectrogram.cpp
...
...
solvers/CardiacEPSolver/CellModels/TenTusscher06.cpp
View file @
5176fd17
...
...
@@ -73,30 +73,50 @@ namespace Nektar
TenTusscher06
::
Variants
>
(
"CellModelVariant"
);
switch
(
model_variant
)
{
case
eEpicardium
:
g_to
=
0.294
;
g_Ks
=
0.392
;
s_inf_factor
=
20.0
;
k_0
=
5.4
;
break
;
case
eEndocardium
:
g_to
=
0.073
;
g_Ks
=
0.392
;
s_inf_factor
=
28.0
;
k_0
=
5.4
;
break
;
case
eMid
:
g_to
=
0.294
;
g_Ks
=
0.098
;
s_inf_factor
=
20.0
;
k_0
=
5.4
;
break
;
case
eIschemia
:
g_to
=
0.294
;
g_Ks
=
0.392
;
s_inf_factor
=
20.0
;
k_0
=
9.0
;
break
;
case
eEpicardium
:
g_to
=
0.294
;
g_Ks
=
0.392
;
s_inf_factor
=
20.0
;
s_tau_f1
=
85.0
;
s_tau_f2
=
45.0
;
s_tau_f3
=
320.0
;
s_tau_f4
=
0.0
;
s_tau_f5
=
1.0
;
k_0
=
5.4
;
break
;
case
eEndocardium
:
g_to
=
0.073
;
g_Ks
=
0.392
;
s_inf_factor
=
28.0
;
s_tau_f1
=
1000.0
;
s_tau_f2
=
67.0
;
s_tau_f3
=
1000.0
;
s_tau_f4
=
8.0
;
s_tau_f5
=
0.0
;
k_0
=
5.4
;
break
;
case
eMid
:
g_to
=
0.294
;
g_Ks
=
0.098
;
s_inf_factor
=
20.0
;
s_tau_f1
=
85.0
;
s_tau_f2
=
45.0
;
s_tau_f3
=
320.0
;
s_tau_f4
=
0.0
;
s_tau_f5
=
1.0
;
k_0
=
5.4
;
break
;
case
eIschemia
:
g_to
=
0.294
;
g_Ks
=
0.392
;
s_inf_factor
=
20.0
;
s_tau_f1
=
85.0
;
s_tau_f2
=
45.0
;
s_tau_f3
=
320.0
;
s_tau_f4
=
0.0
;
s_tau_f5
=
1.0
;
k_0
=
9.0
;
break
;
}
m_nvar
=
19
;
...
...
@@ -361,18 +381,7 @@ namespace Nektar
// const NekDouble var_L_type_Ca_current__L_type_Ca_current_fCass_gate__d_fCass_d_environment__time = var_L_type_Ca_current_fCass_gate__d_fCass_d_environment__time; // per_millisecond
const
NekDouble
var_transient_outward_current_s_gate__V
=
var_transient_outward_current__V
;
// millivolt
const
NekDouble
var_transient_outward_current_s_gate__s_inf
=
1.0
/
(
1.0
+
exp
((
var_transient_outward_current_s_gate__V
+
s_inf_factor
)
/
5.0
));
// dimensionless
NekDouble
var_transient_outward_current_s_gate__tau_s
;
switch
(
model_variant
)
{
case
eEpicardium
:
case
eMid
:
case
eIschemia
:
var_transient_outward_current_s_gate__tau_s
=
(
85.0
*
exp
((
-
pow
(
var_transient_outward_current_s_gate__V
+
45.0
,
2.0
))
/
320.0
))
+
(
5.0
/
(
1.0
+
exp
((
var_transient_outward_current_s_gate__V
-
20.0
)
/
5.0
)))
+
3.0
;
// millisecond
break
;
case
eEndocardium
:
var_transient_outward_current_s_gate__tau_s
=
(
1000.0
*
exp
((
-
pow
(
var_transient_outward_current_s_gate__V
+
67.0
,
2.0
))
/
1000.0
))
+
8.0
;
// millisecond
break
;
}
const
NekDouble
var_transient_outward_current_s_gate__tau_s
=
(
s_tau_f1
*
exp
((
-
pow
(
var_transient_outward_current_s_gate__V
+
s_tau_f2
,
2.0
))
/
s_tau_f3
))
+
s_tau_f4
+
s_tau_f5
*
((
5.0
/
(
1.0
+
exp
((
var_transient_outward_current_s_gate__V
-
20.0
)
/
5.0
)))
+
3.0
);
// millisecond
// const NekDouble var_transient_outward_current_s_gate__s = var_transient_outward_current__s; // dimensionless
// const NekDouble var_transient_outward_current_s_gate__d_s_d_environment__time = (var_transient_outward_current_s_gate__s_inf - var_transient_outward_current_s_gate__s) / var_transient_outward_current_s_gate__tau_s; // per_millisecond
// const NekDouble var_transient_outward_current__transient_outward_current_s_gate__d_s_d_environment__time = var_transient_outward_current_s_gate__d_s_d_environment__time; // per_millisecond
...
...
solvers/CardiacEPSolver/CellModels/TenTusscher06.h
View file @
5176fd17
...
...
@@ -75,7 +75,11 @@ namespace Nektar
NekDouble
g_to
;
NekDouble
g_Ks
;
NekDouble
s_inf_factor
;
NekDouble
s_tau_factor
;
NekDouble
s_tau_f1
;
NekDouble
s_tau_f2
;
NekDouble
s_tau_f3
;
NekDouble
s_tau_f4
;
NekDouble
s_tau_f5
;
NekDouble
k_0
;
enum
Variants
{
...
...
solvers/CardiacEPSolver/CellModels/TenTusscher06Endo.cpp
deleted
100644 → 0
View file @
9a471326
This diff is collapsed.
Click to expand it.
solvers/CardiacEPSolver/CellModels/TenTusscher06Endo.h
deleted
100644 → 0
View file @
9a471326
///////////////////////////////////////////////////////////////////////////////
//
// File TenTusscher06Endo.h
//
// For more information, please see: http://www.nektar.info
//
// The MIT License
//
// Copyright (c) 2006 Division of Applied Mathematics, Brown University (USA),
// Department of Aeronautics, Imperial College London (UK), and Scientific
// Computing and Imaging Institute, University of Utah (USA).
//
// License for the specific language governing rights and limitations under
// Permission is hereby granted, free of charge, to any person obtaining a
// copy of this software and associated documentation files (the "Software"),
// to deal in the Software without restriction, including without limitation
// the rights to use, copy, modify, merge, publish, distribute, sublicense,
// and/or sell copies of the Software, and to permit persons to whom the
// Software is furnished to do so, subject to the following conditions:
//
// The above copyright notice and this permission notice shall be included
// in all copies or substantial portions of the Software.
//
// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
// OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
// THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
// FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
// DEALINGS IN THE SOFTWARE.
//
// Description: ten Tusscher 2006 Endocardium cell model
//
///////////////////////////////////////////////////////////////////////////////
#ifndef NEKTAR_SOLVERS_ADRSOLVER_EQUATIONSYSTEMS_TENTUSSCHER_PANFILOV_2006_ENDO_CELL_H
#define NEKTAR_SOLVERS_ADRSOLVER_EQUATIONSYSTEMS_TENTUSSCHER_PANFILOV_2006_ENDO_CELL_H
#include <CardiacEPSolver/CellModels/CellModel.h>
namespace
Nektar
{
class
TenTusscher06Endo
:
public
CellModel
{
public:
/// Creates an instance of this class
static
CellModelSharedPtr
create
(
const
LibUtilities
::
SessionReaderSharedPtr
&
pSession
,
const
MultiRegions
::
ExpListSharedPtr
&
pField
)
{
return
MemoryManager
<
TenTusscher06Endo
>::
AllocateSharedPtr
(
pSession
,
pField
);
}
/// Name of class
static
std
::
string
className
;
/// Constructor
TenTusscher06Endo
(
const
LibUtilities
::
SessionReaderSharedPtr
&
pSession
,
const
MultiRegions
::
ExpListSharedPtr
&
pField
);
/// Desctructor
virtual
~
TenTusscher06Endo
()
{}
protected:
/// Computes the reaction terms $f(u,v)$ and $g(u,v)$.
virtual
void
v_Update
(
const
Array
<
OneD
,
const
Array
<
OneD
,
NekDouble
>
>&
inarray
,
Array
<
OneD
,
Array
<
OneD
,
NekDouble
>
>&
outarray
,
const
NekDouble
time
);
/// Prints a summary of the model parameters.
virtual
void
v_GenerateSummary
(
SummaryList
&
s
);
virtual
void
v_SetInitialConditions
();
};
}
#endif
solvers/CardiacEPSolver/CellModels/TenTusscher06Epi.cpp
deleted
100644 → 0
View file @
9a471326
This diff is collapsed.
Click to expand it.
solvers/CardiacEPSolver/CellModels/TenTusscher06Epi.h
deleted
100644 → 0
View file @
9a471326
///////////////////////////////////////////////////////////////////////////////
//
// File TenTusscher06Epi.h
//
// For more information, please see: http://www.nektar.info
//
// The MIT License
//
// Copyright (c) 2006 Division of Applied Mathematics, Brown University (USA),
// Department of Aeronautics, Imperial College London (UK), and Scientific
// Computing and Imaging Institute, University of Utah (USA).
//
// License for the specific language governing rights and limitations under
// Permission is hereby granted, free of charge, to any person obtaining a
// copy of this software and associated documentation files (the "Software"),
// to deal in the Software without restriction, including without limitation
// the rights to use, copy, modify, merge, publish, distribute, sublicense,
// and/or sell copies of the Software, and to permit persons to whom the
// Software is furnished to do so, subject to the following conditions:
//
// The above copyright notice and this permission notice shall be included
// in all copies or substantial portions of the Software.
//
// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
// OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
// THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
// FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
// DEALINGS IN THE SOFTWARE.
//
// Description: ten Tusscher 2006 Epicardium cell model
//
///////////////////////////////////////////////////////////////////////////////
#ifndef NEKTAR_SOLVERS_ADRSOLVER_EQUATIONSYSTEMS_TENTUSSCHER_PANFILOV_2006_EPI_CELL_H
#define NEKTAR_SOLVERS_ADRSOLVER_EQUATIONSYSTEMS_TENTUSSCHER_PANFILOV_2006_EPI_CELL_H
#include <CardiacEPSolver/CellModels/CellModel.h>
namespace
Nektar
{
class
TenTusscher06Epi
:
public
CellModel
{
public:
/// Creates an instance of this class
static
CellModelSharedPtr
create
(
const
LibUtilities
::
SessionReaderSharedPtr
&
pSession
,
const
MultiRegions
::
ExpListSharedPtr
&
pField
)
{
return
MemoryManager
<
TenTusscher06Epi
>::
AllocateSharedPtr
(
pSession
,
pField
);
}
/// Name of class
static
std
::
string
className
;
/// Constructor
TenTusscher06Epi
(
const
LibUtilities
::
SessionReaderSharedPtr
&
pSession
,
const
MultiRegions
::
ExpListSharedPtr
&
pField
);
/// Desctructor
virtual
~
TenTusscher06Epi
()
{}
protected:
virtual
void
v_Update
(
const
Array
<
OneD
,
const
Array
<
OneD
,
NekDouble
>
>&
inarray
,
Array
<
OneD
,
Array
<
OneD
,
NekDouble
>
>&
outarray
,
const
NekDouble
time
);
/// Prints a summary of the model parameters.
virtual
void
v_GenerateSummary
(
SummaryList
&
s
);
virtual
void
v_SetInitialConditions
();
};
}
#endif
solvers/CardiacEPSolver/CellModels/TenTusscher06M.cpp
deleted
100644 → 0
View file @
9a471326
This diff is collapsed.
Click to expand it.
solvers/CardiacEPSolver/CellModels/TenTusscher06M.h
deleted
100644 → 0
View file @
9a471326
///////////////////////////////////////////////////////////////////////////////
//
// File TenTusscher06M.h
//
// For more information, please see: http://www.nektar.info
//
// The MIT License
//
// Copyright (c) 2006 Division of Applied Mathematics, Brown University (USA),
// Department of Aeronautics, Imperial College London (UK), and Scientific
// Computing and Imaging Institute, University of Utah (USA).
//
// License for the specific language governing rights and limitations under
// Permission is hereby granted, free of charge, to any person obtaining a
// copy of this software and associated documentation files (the "Software"),
// to deal in the Software without restriction, including without limitation
// the rights to use, copy, modify, merge, publish, distribute, sublicense,
// and/or sell copies of the Software, and to permit persons to whom the
// Software is furnished to do so, subject to the following conditions:
//
// The above copyright notice and this permission notice shall be included
// in all copies or substantial portions of the Software.
//
// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
// OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
// THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
// FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
// DEALINGS IN THE SOFTWARE.
//
// Description: ten Tusscher 2006 Mid-myocardium cell model
//
///////////////////////////////////////////////////////////////////////////////
#ifndef NEKTAR_SOLVERS_ADRSOLVER_EQUATIONSYSTEMS_TENTUSSCHER_PANFILOV_2006_M_CELL_H
#define NEKTAR_SOLVERS_ADRSOLVER_EQUATIONSYSTEMS_TENTUSSCHER_PANFILOV_2006_M_CELL_H
#include <CardiacEPSolver/CellModels/CellModel.h>
namespace
Nektar
{
class
TenTusscher06M
:
public
CellModel
{
public:
/// Creates an instance of this class
static
CellModelSharedPtr
create
(
const
LibUtilities
::
SessionReaderSharedPtr
&
pSession
,
const
MultiRegions
::
ExpListSharedPtr
&
pField
)
{
return
MemoryManager
<
TenTusscher06M
>::
AllocateSharedPtr
(
pSession
,
pField
);
}
/// Name of class
static
std
::
string
className
;
/// Constructor
TenTusscher06M
(
const
LibUtilities
::
SessionReaderSharedPtr
&
pSession
,
const
MultiRegions
::
ExpListSharedPtr
&
pField
);
/// Destructor
virtual
~
TenTusscher06M
()
{}
protected:
/// Computes the reaction terms $f(u,v)$ and $g(u,v)$.
virtual
void
v_Update
(
const
Array
<
OneD
,
const
Array
<
OneD
,
NekDouble
>
>&
inarray
,
Array
<
OneD
,
Array
<
OneD
,
NekDouble
>
>&
outarray
,
const
NekDouble
time
);
/// Prints a summary of the model parameters.
virtual
void
v_GenerateSummary
(
SummaryList
&
s
);
virtual
void
v_SetInitialConditions
();
private:
};
}
#endif
solvers/CardiacEPSolver/Utilities/PrePacing/CMakeLists.txt
View file @
5176fd17
...
...
@@ -14,9 +14,6 @@ SET(PP_SOURCES ./Prepacing.cpp
../../CellModels/CellModel.cpp
../../CellModels/CourtemancheRamirezNattel98.cpp
../../CellModels/FentonKarma.cpp
../../CellModels/TenTusscher06Endo.cpp
../../CellModels/TenTusscher06Epi.cpp
../../CellModels/TenTusscher06M.cpp
../../CellModels/TenTusscher06.cpp
../../Stimuli/Stimulus.cpp
../../Stimuli/StimulusPoint.cpp
...
...
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