#include <VClamp.h>

Collaboration diagram for moose::VClamp:

Public Member Functions
double	getCommand () const

double	getCurrent () const

double	getGain () const

unsigned int	getMode () const

double	getTau () const

double	getTd () const

double	getTi () const

double	getVin () const

void	process (const Eref &e, ProcPtr p)

void	reinit (const Eref &e, ProcPtr p)

void	setCommand (double v)

void	setGain (double value)

void	setMode (unsigned int mode)

void	setTau (double value)

void	setTd (double value)

void	setTi (double value)

void	setVin (double v)

	VClamp ()

	~VClamp ()

Static Public Member Functions
static SrcFinfo1< double > *	currentOut ()

static const Cinfo *	initCinfo ()

Protected Attributes
double	cmdIn_

double	command_

double	current_

double	dtByTi_

double	e1_

double	e2_

double	e_

double	expt_

double	Kp_

unsigned int	mode_

double	oldCmdIn_

double	tau_

double	tauByDt_

double	td_

double	tdByDt_

double	ti_

double	v1_

double	vIn_

Static Private Attributes
static const unsigned	DERIVATIVE_ON_PV = 1

static const unsigned	PROPORTIONAL_ON_PV = 2

Detailed Description

Definition at line 51 of file VClamp.h.

Constructor & Destructor Documentation

VClamp::VClamp ( )

Definition at line 196 of file VClamp.cpp.

               : vIn_(0.0), command_(0.0), current_(0.0), mode_(0), ti_(0.0), td_(-1.0),
                   Kp_(0.0),
                   tau_(0.0),
                   tdByDt_(1.0),
                   dtByTi_(1.0),
                   e_(0.0),
                   e1_(0.0),
                   e2_(0.0)
 {
 }

VClamp::~VClamp ( )

Definition at line 207 of file VClamp.cpp.

 {
     ;
 }

Member Function Documentation

SrcFinfo1< double > * VClamp::currentOut ( )

static

Definition at line 58 of file VClamp.cpp.

Referenced by initCinfo(), process(), and reinit().

 {
     static SrcFinfo1< double > currentOut("currentOut",
                                           "Sends out current output of the clamping circuit. This should be"
                                           " connected to the `injectMsg` field of a compartment to voltage clamp"
                                           " it.");
     return &currentOut;
 }

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double VClamp::getCommand ( ) const

Definition at line 217 of file VClamp.cpp.

References cmdIn_.

Referenced by initCinfo().

 {
     return cmdIn_;
 }

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double VClamp::getCurrent ( ) const

Definition at line 261 of file VClamp.cpp.

References current_.

Referenced by initCinfo().

 {
     return current_;
 }

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double VClamp::getGain ( ) const

Definition at line 256 of file VClamp.cpp.

References Kp_.

Referenced by initCinfo().

 {
     return Kp_;
 }

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unsigned int VClamp::getMode ( ) const

Definition at line 282 of file VClamp.cpp.

References mode_.

Referenced by initCinfo().

 {
     return mode_;
 }

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double VClamp::getTau ( ) const

Definition at line 246 of file VClamp.cpp.

References tau_.

Referenced by initCinfo().

 {
     return tau_;
 }

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double VClamp::getTd ( ) const

Definition at line 236 of file VClamp.cpp.

References td_.

Referenced by initCinfo().

 {
     return td_;
 }

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double VClamp::getTi ( ) const

Definition at line 227 of file VClamp.cpp.

References ti_.

Referenced by initCinfo().

 {
     return ti_;
 }

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double VClamp::getVin ( ) const

Definition at line 271 of file VClamp.cpp.

References vIn_.

Referenced by initCinfo().

 {
     return vIn_;
 }

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const Cinfo * VClamp::initCinfo ( )

static

Definition at line 68 of file VClamp.cpp.

References currentOut(), getCommand(), getCurrent(), getGain(), getMode(), getTau(), getTd(), getTi(), getVin(), Neutral::initCinfo(), process(), reinit(), setCommand(), setGain(), setMode(), setTau(), setTd(), setTi(), setVin(), and vclampCinfo.

 {
     static DestFinfo process("process",
                              "Handles 'process' call on each time step.",
                              new ProcOpFunc< VClamp >( &VClamp::process));
     static DestFinfo reinit("reinit",
                             "Handles 'reinit' call",
                             new ProcOpFunc< VClamp >( &VClamp::reinit));
     static Finfo * processShared[] = {
         &process,
         &reinit
     };
 
     static SharedFinfo proc("proc",
                             "Shared message to receive Process messages from the scheduler",
                             processShared, sizeof(processShared) / sizeof(Finfo*));
 
     static ValueFinfo< VClamp, double> command("command",
                                                "Command input received by the clamp circuit.",
                                                &VClamp::setCommand,
                                                &VClamp::getCommand);
     static ValueFinfo< VClamp, unsigned int> mode("mode",
                                                   "Working mode of the PID controller.\n"
                                                   "\n"
                                                   "   mode = 0, standard PID with proportional, integral and derivative"
                                                   " all acting on the error.\n"
                                                   "\n"
                                                   "   mode = 1, derivative action based on command input\n"
                                                   "\n"
                                                   "   mode = 2, proportional action and derivative action are based on"
                                                   " command input.",
                                                   &VClamp::setMode,
                                                   &VClamp::getMode);
     static ValueFinfo< VClamp, double> ti("ti",
                                           "Integration time of the PID controller. Defaults to 1e9, i.e. integral"
                                           " action is negligibly small.",
                                           &VClamp::setTi,
                                           &VClamp::getTi);
 
     static ValueFinfo< VClamp, double> td("td",
                                           "Derivative time of the PID controller. This defaults to 0,"
                                           "i.e. derivative action is unused.",
                                           &VClamp::setTd,
                                           &VClamp::getTd);
     static ValueFinfo< VClamp, double> tau("tau",
                                           "Time constant of the lowpass filter at input of the PID"
                                            " controller. This smooths out abrupt changes in the input. Set it to "
                                            " 5 * dt or more to avoid overshoots.",
                                           &VClamp::setTau,
                                           &VClamp::getTau);
     static ValueFinfo< VClamp, double> gain("gain",
                                           "Proportional gain of the PID controller.",
                                           &VClamp::setGain,
                                           &VClamp::getGain);
     static ReadOnlyValueFinfo< VClamp, double> current("current",
                                             "The amount of current injected by the clamp into the membrane.",
                                             &VClamp::getCurrent);
 
 
     static ReadOnlyValueFinfo<VClamp, double> sensed("sensed",
                                                      "Membrane potential read from compartment.",
                                                      &VClamp::getVin);
     static DestFinfo sensedIn("sensedIn",
                               "The `VmOut` message of the Compartment object should be connected"
                               " here.",
                               new OpFunc1<VClamp, double>( &VClamp::setVin));
 
     static DestFinfo commandIn("commandIn",
                               "  The command voltage source should be connected to this.",
                               new OpFunc1<VClamp, double>( &VClamp::setCommand));
 
     static Finfo* vclampFinfos[] = {
         currentOut(),
         &command,
         &current,
         &sensed,
         &mode,
         &ti,
         &td,
         &tau,
         &gain,
         &sensedIn,
         &commandIn,
         &proc
     };
 
     static string doc[] = {
         "Name", "VClamp",
         "Author", "Subhasis Ray",
         "Description", "Voltage clamp object for holding neuronal compartments at a specific"
         " voltage.\n"
         "\n"
         "This implementation uses a builtin RC circuit to filter the "
         " command input and then use a PID to bring the sensed voltage (Vm from"
         " compartment) to the filtered command potential.\n"
         "\n"
         "Usage: Connect the `currentOut` source of VClamp to `injectMsg`"
         " dest of Compartment. Connect the `VmOut` source of Compartment to"
         " `set_sensed` dest of VClamp. Either set `command` field to a"
         " fixed value, or connect an appropriate source of command potential"
         " (like the `outputOut` message of an appropriately configured"
         " PulseGen) to `set_command` dest.\n"
         "The default settings for the RC filter and PID controller should be"
         " fine. For step change in command voltage, good defaults with"
         "integration time step dt are as follows:\n"
         "    time constant of RC filter, tau = 5 * dt\n"
         "    proportional gain of PID, gain = Cm/dt where Cm is the membrane"
         "    capacitance of the compartment\n"
         "    integration time of PID, ti = dt\n"
         "    derivative time  of PID, td = 0\n"
         "\n",
     };
 
     static Dinfo< VClamp > dinfo;
     static Cinfo vclampCinfo(
         "VClamp",
         Neutral::initCinfo(),
         vclampFinfos,
         sizeof(vclampFinfos) / sizeof(Finfo*),
         &dinfo,
         doc,
         sizeof(doc)/sizeof(string));
 
     return &vclampCinfo;
 }

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void VClamp::process	(	const Eref &	e,
		ProcPtr	p
	)

Definition at line 287 of file VClamp.cpp.

References cmdIn_, command_, current_, currentOut(), DERIVATIVE_ON_PV, dtByTi_, e1_, e2_, e_, expt_, Kp_, mode_, oldCmdIn_, PROPORTIONAL_ON_PV, tau_, tauByDt_, td_, tdByDt_, ti_, v1_, and vIn_.

Referenced by initCinfo().

 {
     assert(ti_ > 0);
     assert(td_ >= 0);
     assert(tau_ > 0);
     double dCmd = cmdIn_ - oldCmdIn_;
     command_ = cmdIn_ + dCmd * ( 1 - tauByDt_) + (command_ - cmdIn_ + dCmd * tauByDt_) * expt_;
     oldCmdIn_ = cmdIn_;
     e_ = command_ - vIn_;
     if (mode_ == 0){
         current_ +=  Kp_ * ((1 + dtByTi_ + tdByDt_) * e_ - ( 1 + 2 * tdByDt_) * e1_ + tdByDt_ * e2_);
         e2_ = e1_;
         e1_ = e_;
     } else if (mode_ == DERIVATIVE_ON_PV){ // Here the derivative error term is replaced by process variable
         current_ +=  Kp_ * ((1 + dtByTi_) * e_ - e1_ + tdByDt_ * ( vIn_ - 2 * v1_ + e2_));
         e2_ = v1_;
         v1_ = vIn_;
         e1_ = e_;
     } else if (mode_ == PROPORTIONAL_ON_PV){ // Here the proportional as well as the derivative error term is replaced by process variable
         current_ +=  Kp_ * (vIn_ - v1_ + dtByTi_ * e_ + tdByDt_ * ( vIn_ - 2 * v1_ + e2_));
         e2_ = v1_;
         v1_ = vIn_;
     }
     currentOut()->send(e, current_);
 }

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void VClamp::reinit	(	const Eref &	e,
		ProcPtr	p
	)

Definition at line 313 of file VClamp.cpp.

References cmdIn_, command_, currentOut(), ProcInfo::dt, dtByTi_, e1_, e2_, e_, Eref::element(), expt_, Field< A >::get(), Element::getNeighbors(), Kp_, oldCmdIn_, tau_, tauByDt_, td_, tdByDt_, ti_, v1_, and vIn_.

Referenced by initCinfo().

 {
 
     vIn_ = 0.0;
     v1_ = 0;
     command_ = cmdIn_ = oldCmdIn_ = e_ = e1_ = e2_ = 0;
     if (ti_ == 0){
         ti_ = p->dt;
     }
     if (td_ < 0){
         td_ = 0.0;
     }
     if (tau_ == 0.0){
         tau_ = 5 * p->dt;
     }
     if (p->dt / tau_ > 1e-15){
         expt_ = exp(-p->dt/tau_);
     } else {
         expt_ = 1 - p->dt/tau_;
     }
     tauByDt_ = tau_ / p->dt;
     dtByTi_ = p->dt/ti_;
     tdByDt_ = td_ / p->dt;
 
     vector<Id> compartments;
     unsigned int numComp = e.element()->getNeighbors(compartments, currentOut());
     if (numComp > 0){
         double Cm = Field<double>::get(compartments[0], "Cm");
         if (Kp_ == 0){
             Kp_ = Cm / p->dt;
         }
         command_ = cmdIn_ = oldCmdIn_ = 
             Field<double>::get(compartments[0], "initVm");
     }
 }

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void VClamp::setCommand ( double v )

Definition at line 212 of file VClamp.cpp.

References cmdIn_, and value.

Referenced by initCinfo().

 {
     cmdIn_ = value;
 }

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void VClamp::setGain ( double value )

Definition at line 251 of file VClamp.cpp.

References Kp_, and value.

Referenced by initCinfo().

 {
     Kp_ = value;
 }

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void VClamp::setMode ( unsigned int mode )

Definition at line 277 of file VClamp.cpp.

References mode_.

Referenced by initCinfo().

 {
     mode_ = mode;
 }

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void VClamp::setTau ( double value )

Definition at line 241 of file VClamp.cpp.

References tau_, and value.

Referenced by initCinfo().

 {
     tau_ = value;
 }

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void VClamp::setTd ( double value )

Definition at line 231 of file VClamp.cpp.

References td_, and value.

Referenced by initCinfo().

 {
     td_ = value;
 }

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void VClamp::setTi ( double value )

Definition at line 222 of file VClamp.cpp.

References ti_, and value.

Referenced by initCinfo().

 {
     ti_ = value;
 }

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void VClamp::setVin ( double v )

Definition at line 266 of file VClamp.cpp.

References value, and vIn_.

Referenced by initCinfo().

 {
     vIn_ = value;
 }

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Member Data Documentation

double moose::VClamp::cmdIn_

protected

Definition at line 99 of file VClamp.h.

Referenced by getCommand(), process(), reinit(), and setCommand().

double moose::VClamp::command_

protected

Definition at line 83 of file VClamp.h.

Referenced by process(), and reinit().

double moose::VClamp::current_

protected

Definition at line 84 of file VClamp.h.

Referenced by getCurrent(), and process().

const unsigned int VClamp::DERIVATIVE_ON_PV = 1

staticprivate

Definition at line 53 of file VClamp.h.

Referenced by process().

double moose::VClamp::dtByTi_

protected

Definition at line 93 of file VClamp.h.

Referenced by process(), and reinit().

double moose::VClamp::e1_

protected

Definition at line 96 of file VClamp.h.

Referenced by process(), and reinit().

double moose::VClamp::e2_

protected

Definition at line 97 of file VClamp.h.

Referenced by process(), and reinit().

double moose::VClamp::e_

protected

Definition at line 95 of file VClamp.h.

Referenced by process(), and reinit().

double moose::VClamp::expt_

protected

Definition at line 101 of file VClamp.h.

Referenced by process(), and reinit().

double moose::VClamp::Kp_

protected

Definition at line 90 of file VClamp.h.

Referenced by getGain(), process(), reinit(), and setGain().

unsigned int moose::VClamp::mode_

protected

Definition at line 85 of file VClamp.h.

Referenced by getMode(), process(), and setMode().

double moose::VClamp::oldCmdIn_

protected

Definition at line 100 of file VClamp.h.

Referenced by process(), and reinit().

const unsigned int VClamp::PROPORTIONAL_ON_PV = 2

staticprivate

Definition at line 54 of file VClamp.h.

Referenced by process().

double moose::VClamp::tau_

protected

Definition at line 91 of file VClamp.h.

Referenced by getTau(), process(), reinit(), and setTau().

double moose::VClamp::tauByDt_

protected

Definition at line 94 of file VClamp.h.

Referenced by process(), and reinit().

double moose::VClamp::td_

protected

Definition at line 89 of file VClamp.h.

Referenced by getTd(), process(), reinit(), and setTd().

double moose::VClamp::tdByDt_

protected

Definition at line 92 of file VClamp.h.

Referenced by process(), and reinit().

double moose::VClamp::ti_

protected

Definition at line 88 of file VClamp.h.

Referenced by getTi(), process(), reinit(), and setTi().

double moose::VClamp::v1_

protected

Definition at line 98 of file VClamp.h.

Referenced by process(), and reinit().

double moose::VClamp::vIn_

protected

Definition at line 82 of file VClamp.h.

Referenced by getVin(), process(), reinit(), and setVin().

The documentation for this class was generated from the following files:

moose-core/biophysics/VClamp.h
moose-core/biophysics/VClamp.cpp

Public Member Functions

Static Public Member Functions

Protected Attributes

Static Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation