Updates to Hsolve to be able to delete and recreate it. Still problematic for HHChannels. Also added Vclamp to the rdesigneurProtos.

Author: upibhalla

hsolve/HSolve.cpp

@@ -23,6 +23,7 @@
 #include "../biophysics/ChanBase.h"
 #include "../biophysics/ChanCommon.h"
 #include "../biophysics/HHChannel.h"
+#include "../biophysics/CaConc.h"
 #include "ZombieHHChannel.h"
 #include "../shell/Shell.h"
 
@@ -192,6 +193,11 @@ HSolve::HSolve()
     ;
 }
 
+HSolve::~HSolve()
+{
+    unzombify();
+}
+
 
 ///////////////////////////////////////////////////
 // Dest function definitions
@@ -215,23 +221,42 @@ void HSolve::zombify( Eref hsolve ) const
 
     for ( i = compartmentId_.begin(); i != compartmentId_.end(); ++i )
 		temp.push_back( ObjId( *i, 0 ) );
-    for ( i = compartmentId_.begin(); i != compartmentId_.end(); ++i )
+    for ( i = compartmentId_.begin(); i != compartmentId_.end(); ++i ) {
         CompartmentBase::zombify( i->eref().element(),
 					   ZombieCompartment::initCinfo(), hsolve.id() );
+	}
 
 	temp.clear();
     for ( i = caConcId_.begin(); i != caConcId_.end(); ++i )
 		temp.push_back( ObjId( *i, 0 ) );
 	// Shell::dropClockMsgs( temp, "process" );
-    for ( i = caConcId_.begin(); i != caConcId_.end(); ++i )
+    for ( i = caConcId_.begin(); i != caConcId_.end(); ++i ) {
         CaConcBase::zombify( i->eref().element(), ZombieCaConc::initCinfo(), hsolve.id() );
+	}
 
 	temp.clear();
     for ( i = channelId_.begin(); i != channelId_.end(); ++i )
 		temp.push_back( ObjId( *i, 0 ) );
-    for ( i = channelId_.begin(); i != channelId_.end(); ++i )
+    for ( i = channelId_.begin(); i != channelId_.end(); ++i ) {
         HHChannelBase::zombify( i->eref().element(),
 						ZombieHHChannel::initCinfo(), hsolve.id() );
+	}
+}
+
+void HSolve::unzombify() const
+{
+    vector< Id >::const_iterator i;
+
+    for ( i = compartmentId_.begin(); i != compartmentId_.end(); ++i )
+        CompartmentBase::zombify( i->eref().element(),
+					   Compartment::initCinfo(), Id() );
+
+    for ( i = caConcId_.begin(); i != caConcId_.end(); ++i )
+        CaConcBase::zombify( i->eref().element(), CaConc::initCinfo(), Id() );
+
+    for ( i = channelId_.begin(); i != channelId_.end(); ++i )
+        HHChannelBase::zombify( i->eref().element(),
+						HHChannel::initCinfo(), Id() );
 }
 
 void HSolve::setup( Eref hsolve )

hsolve/HSolve.h

@@ -17,6 +17,7 @@ class HSolve: public HSolveActive
 {
 public:
 	HSolve();
+	~HSolve();
 
 	void process( const Eref& hsolve, ProcPtr p );
 	void reinit( const Eref& hsolve, ProcPtr p );
@@ -157,6 +158,7 @@ class HSolve: public HSolveActive
 
 	void setup( Eref hsolve );
 	void zombify( Eref hsolve ) const;
+	void unzombify() const;
 
 	// Mapping global Id to local index. Defined in HSolveInterface.cpp.
 	void mapIds();

hsolve/HSolveActive.cpp

@@ -356,13 +356,13 @@ void HSolveActive::sendValues( ProcPtr info )
 {
     vector< unsigned int >::iterator i;
 
-    for ( i = outVm_.begin(); i != outVm_.end(); ++i )
+    for ( i = outVm_.begin(); i != outVm_.end(); ++i ) {
         Compartment::VmOut()->send(
             //~ ZombieCompartment::VmOut()->send(
             compartmentId_[ *i ].eref(),
             V_[ *i ]
         );
-
+	}
 
     for ( i = outIk_.begin(); i != outIk_.end(); ++i ){
 

hsolve/HSolveUtils.cpp

@@ -320,9 +320,9 @@ int HSolveUtils::targets(
 	e->getNeighbors( all, f );
 
 	vector< Id >::iterator ia;
-	if ( filter.empty() )
+	if ( filter.empty() ) {
 		target.insert( target.end(), all.begin(), all.end() );
-	else
+	} else {
 		for ( ia = all.begin(); ia != all.end(); ++ia ) {
 			string className = (*ia).element()->cinfo()->name();
 			bool hit =
@@ -335,6 +335,7 @@ int HSolveUtils::targets(
 			if ( ( hit && include ) || ( !hit && !include ) )
 				target.push_back( *ia );
 		}
+	}
 
 	return target.size() - oldSize;
 }

python/rdesigneur/rdesigneurProtos.py

@@ -325,6 +325,84 @@ def make_LCa( name = 'LCa', parent = '/library' ):
         ygate.tableA = yA
         ygate.tableB = yB
         return Ca
+######################################################################
+
+# Derived from : squid/electronics.py
+# Description: 
+# Author: Subhasis Ray
+# Maintainer: 
+# Created: Wed Feb 22 00:53:38 2012 (+0530)
+# Version: 
+# Last-Updated: Fri May 04 16:35:40 2018 (+0530)
+#           By: Upi
+#     Update #: 221
+
+# Change log:
+# 
+# 2012-02-22 23:22:30 (+0530) Subha - the circuitry put in a class.
+# 2018-05-04 23:22:30 (+0530) Upi - Adapted for Rdesigneur
+# 
+
+# Code:
+
+class ClampCircuit(moose.Neutral):
+    """Container for a Voltage-Clamp/Current clamp circuit."""
+    defaults = {
+        'level1': 25.0e-3,
+        'width1': 50.0e-3,
+        'delay1': 2.0e-3,
+        'delay2': 1e3,
+        'trigMode': 0,
+        'delay3': 1e6
+        }
+    def __init__(self, path ):
+        moose.Neutral.__init__(self, path)        
+        '''
+        self.pulsegen = moose.PulseGen(path+"/pulse") # holding voltage/current generator
+        self.pulsegen.count = 2
+        self.pulsegen.baseLevel = -65.0e-3
+        self.pulsegen.firstLevel = -40.0e-3
+        self.pulsegen.firstWidth = 50.0e-3
+        self.pulsegen.firstDelay = 2.0e-3
+        self.pulsegen.secondDelay = 0.0
+        self.pulsegen.trigMode = 2
+        self.gate = moose.PulseGen(path+"/gate") # holding voltage/current generator
+        self.gate.level[0] = 1.0
+        self.gate.delay[0] = 0.0
+        self.gate.width[0] = 1e3
+        moose.connect(self.gate, 'output', self.pulsegen, 'input')
+        '''
+        self.lowpass = moose.RC(path+"/lowpass") # lowpass filter
+        self.lowpass.R = 1.0
+        self.lowpass.C = 0.03
+        self.vclamp = moose.DiffAmp(path+"/vclamp")
+        self.vclamp.gain = 1.0
+        self.vclamp.saturation = 1e10
+        self.iclamp = moose.DiffAmp(path+"/iclamp")
+        self.iclamp.gain = 0.0
+        self.iclamp.saturation = 1e10
+        self.pid = moose.PIDController(path+"/pid")
+        self.pid.gain = 0.5
+        self.pid.tauI = 0.02e-3
+        self.pid.tauD = 0.005e-3
+        self.pid.saturation = 1e7
+        # Connect voltage clamp circuitry
+        #moose.connect(self.pulsegen, "output", self.lowpass, "injectIn")
+        moose.connect(self.lowpass, "output", self.vclamp, "plusIn")
+        moose.connect(self.vclamp, "output", self.pid, "commandIn")
+        #moose.connect(compartment, "VmOut", self.pid, "sensedIn")
+        #moose.connect(self.pid, "output", compartment, "injectMsg")
+        addmsg1 = moose.Mstring( path + '/addmsg1' )
+        addmsg1.value = './pid  output  ..  injectMsg'
+        addmsg2 = moose.Mstring( path + '/addmsg2' )
+        addmsg2.value = '.. VmOut ./pid  sensedIn'
+
+def make_vclamp( name = 'Vclamp', parent = '/library' ):
+    if moose.exists( '/library/' + name ):
+        return
+    vclamp = ClampCircuit( parent + '/' + name )
+
+######################################################################
 
     ################################################################
     # API function for building spine prototypes. Here we put in the