PackedColumn::PackedColumn(const std::string & name, InputParameters parameters) :
Material(name, parameters),
// Get the one parameter from the input file
_ball_radius(getParam<Real>("ball_radius")),
// Declare two material properties. This returns references that we
// hold onto as member variables
_permeability(declareProperty<Real>("permeability")),
_porosity(declareProperty<Real>("porosity")),
_viscosity(declareProperty<Real>("viscosity")),
_thermal_conductivity(declareProperty<Real>("thermal_conductivity")),
_heat_capacity(declareProperty<Real>("heat_capacity")),
_density(declareProperty<Real>("density"))
{
// Sigh: Still can't depend on C++11....
std::vector<Real> ball_sizes(2);
ball_sizes[0] = 1;
ball_sizes[1] = 3;
// From the paper: Table 1
std::vector<Real> permeability(2);
permeability[0] = 0.8451e-9;
permeability[1] = 8.968e-9;
// Set the x,y data on the LinearInterpolation object.
_permeability_interpolation.setData(ball_sizes, permeability);
}
const Cinfo* ChanBase::initCinfo()
{
/////////////////////////////////////////////////////////////////////
// Shared messages
/////////////////////////////////////////////////////////////////////
static DestFinfo process( "process",
"Handles process call",
new ProcOpFunc< ChanBase >( &ChanBase::process ) );
static DestFinfo reinit( "reinit",
"Handles reinit call",
new ProcOpFunc< ChanBase >( &ChanBase::reinit ) );
static Finfo* processShared[] =
{
&process, &reinit
};
static SharedFinfo proc( "proc",
"Shared message to receive Process message from scheduler",
processShared, sizeof( processShared ) / sizeof( Finfo* ) );
/////////////////////////////////////////////////////////////////////
/// ChannelOut SrcFinfo defined above.
static DestFinfo Vm( "Vm",
"Handles Vm message coming in from compartment",
new OpFunc1< ChanBase, double >( &ChanBase::handleVm ) );
static Finfo* channelShared[] =
{
channelOut(), &Vm
};
static SharedFinfo channel( "channel",
"This is a shared message to couple channel to compartment. "
"The first entry is a MsgSrc to send Gk and Ek to the compartment "
"The second entry is a MsgDest for Vm from the compartment.",
channelShared, sizeof( channelShared ) / sizeof( Finfo* )
);
///////////////////////////////////////////////////////
// Here we reuse the Vm DestFinfo declared above.
/// Permability SrcFinfo defined above.
static Finfo* ghkShared[] =
{
&Vm, permeability()
};
static SharedFinfo ghk( "ghk",
"Message to Goldman-Hodgkin-Katz object",
ghkShared, sizeof( ghkShared ) / sizeof( Finfo* ) );
///////////////////////////////////////////////////////
// Field definitions
///////////////////////////////////////////////////////
static ElementValueFinfo< ChanBase, double > Gbar( "Gbar",
"Maximal channel conductance",
&ChanBase::setGbar,
&ChanBase::getGbar
);
static ElementValueFinfo< ChanBase, double > modulation( "modulation",
"Modulation, i.e, scale factor for channel conductance."
"Note that this is a regular parameter, it is not "
"recomputed each timestep. Thus one can use a slow update, "
"say, from a molecule pool, to send a message to set "
"the modulation, and it will stay at the set value even if "
"the channel runs many timesteps before the next assignment. "
"This differs from the GENESIS semantics of a similar message,"
"which required update each timestep. ",
&ChanBase::setModulation,
&ChanBase::getModulation
);
static ElementValueFinfo< ChanBase, double > Ek( "Ek",
"Reversal potential of channel",
&ChanBase::setEk,
&ChanBase::getEk
);
static ElementValueFinfo< ChanBase, double > Gk( "Gk",
"Channel conductance variable",
&ChanBase::setGk,
&ChanBase::getGk
);
static ReadOnlyElementValueFinfo< ChanBase, double > Ik( "Ik",
"Channel current variable",
&ChanBase::getIk
);
///////////////////////////////////////////////////////
// MsgSrc definitions
///////////////////////////////////////////////////////
// IkOut SrcFinfo defined above.
///////////////////////////////////////////////////////
// MsgDest definitions
///////////////////////////////////////////////////////
///////////////////////////////////////////////////////
static Finfo* ChanBaseFinfos[] =
{
&channel, // Shared
&ghk, // Shared
&Gbar, // Value
&modulation, // Value
&Ek, // Value
&Gk, // Value
&Ik, // ReadOnlyValue
IkOut(), // Src
&proc, // Shared
};
static string doc[] =
{
"Name", "ChanBase",
"Author", "Upinder S. Bhalla, 2007-2014, NCBS",
"Description", "ChanBase: Base class for assorted ion channels."
"Presents a common interface for all of them. ",
};
static ZeroSizeDinfo< int > dinfo;
static Cinfo ChanBaseCinfo(
"ChanBase",
Neutral::initCinfo(),
ChanBaseFinfos,
sizeof( ChanBaseFinfos )/sizeof(Finfo *),
&dinfo,
doc,
sizeof(doc)/sizeof(string)
);
return &ChanBaseCinfo;
}
nec_float em::impedance() // was (ETA in old nec2)
{
nec_float ret = sqrt(permeability() / permittivity());
return ret; // 376.8
}
nec_float em::speed_of_light() // was (CVEL in old nec2) but we have changed it to be in meters per second
{
nec_float ret = 1.0 / sqrt(permeability() * permittivity());
return ret; // 299.8e6;
}
