From e5152fe3be6d734ad17c80e02afa39eda05ed9ef Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Asia=20J=C4=99drzejewska-Szmek?= <asia@in.waw.pl>
Date: Fri, 20 Jan 2017 15:49:30 -0500
Subject: [PATCH] Add MMPump to DifShell
---
moose-core/biophysics/DifShell.cpp | 4 ++--
moose-core/biophysics/DifShellBase.cpp | 27 ++++++++++++--------------
2 files changed, 14 insertions(+), 17 deletions(-)
diff --git a/moose-core/biophysics/DifShell.cpp b/moose-core/biophysics/DifShell.cpp
index a9f9ee77..7a8cf71c 100644
--- a/moose-core/biophysics/DifShell.cpp
+++ b/moose-core/biophysics/DifShell.cpp
@@ -23,7 +23,7 @@ const Cinfo* DifShell::initCinfo()
static string doc[] =
{
"Name", "DifShell",
- "Author", "Niraj Dudani. Ported to async13 by Subhasis Ray.",
+ "Author", "Niraj Dudani. Ported to async13 by Subhasis Ray. Rewritten by Asia Jedrzejewska-Szmek",
"Description", "DifShell object: Models diffusion of an ion (typically calcium) within an "
"electric compartment. A DifShell is an iso-concentration region with respect to "
"the ion. Adjoining DifShells exchange flux of this ion, and also keep track of "
@@ -431,7 +431,7 @@ void DifShell::vEqTauPump(const Eref& e, double kP )
void DifShell::vMMPump(const Eref& e, double vMax, double Kd )
{
- Cmultiplier_ += -( vMax / volume_ ) / ( C_ + Kd ) ;
+ Cmultiplier_ += ( vMax / volume_ ) / ( C_ + Kd ) ;
}
void DifShell::vHillPump(const Eref& e, double vMax, double Kd, unsigned int hill )
diff --git a/moose-core/biophysics/DifShellBase.cpp b/moose-core/biophysics/DifShellBase.cpp
index 2400e392..e6d1e533 100644
--- a/moose-core/biophysics/DifShellBase.cpp
+++ b/moose-core/biophysics/DifShellBase.cpp
@@ -50,6 +50,9 @@ const Cinfo* DifShellBase::initCinfo()
"Shared message to receive Process message from scheduler",
processShared, sizeof( processShared ) / sizeof( Finfo* ));
+
+
+
static DestFinfo reaction( "reaction",
"Here the DifShell receives reaction rates (forward and backward), and concentrations for the "
"free-buffer and bound-buffer molecules.",
@@ -58,21 +61,16 @@ const Cinfo* DifShellBase::initCinfo()
static Finfo* bufferShared[] = {
DifShellBase::concentrationOut(), &reaction
};
+
static SharedFinfo buffer( "buffer",
- "This is a shared message from a DifShell to a Buffer (FixBuffer or DifBuffer). "
- "During stage 0:\n "
- " - DifShell sends ion concentration\n"
- " - Buffer updates buffer concentration and sends it back immediately using a call-back.\n"
- " - DifShell updates the time-derivative ( dC / dt ) \n"
- "\n"
- "During stage 1: \n"
- " - DifShell advances concentration C \n\n"
- "This scheme means that the Buffer does not need to be scheduled, and it does its computations when "
- "it receives a cue from the DifShell. May not be the best idea, but it saves us from doing the above "
- "computations in 3 stages instead of 2." ,
+ "This is a shared message from a DifShell to a Buffer (FixBuffer or DifBuffer). " ,
bufferShared,
sizeof( bufferShared ) / sizeof( Finfo* ));
-
+ /////
+
+
+
+
static DestFinfo fluxFromOut( "fluxFromOut",
"Destination message",
new EpFunc2< DifShellBase, double, double > ( &DifShellBase::fluxFromOut ));
@@ -137,7 +135,8 @@ const Cinfo* DifShellBase::initCinfo()
&DifShellBase::setInnerArea,
&DifShellBase::getInnerArea );
-
+ static DestFinfo mmPump( "mmPump", "Here DifShell receives pump outflux",
+ new EpFunc2< DifShellBase, double, double >( &DifShellBase::mmPump ) );
static DestFinfo influx( "influx", "",
new EpFunc1< DifShellBase, double > (&DifShellBase::influx ));
static DestFinfo outflux( "outflux", "",
@@ -154,8 +153,6 @@ const Cinfo* DifShellBase::initCinfo()
new EpFunc2< DifShellBase, double, double >( &DifShellBase::tauPump ) );
static DestFinfo eqTauPump( "eqTauPump", "",
new EpFunc1< DifShellBase, double >( &DifShellBase::eqTauPump ) );
- static DestFinfo mmPump( "mmPump", "",
- new EpFunc2< DifShellBase, double, double >( &DifShellBase::mmPump ) );
static DestFinfo hillPump( "hillPump", "",
new EpFunc3< DifShellBase, double, double, unsigned int >( &DifShellBase::hillPump ) );
static Finfo* difShellBaseFinfos[] = {
--
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