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upi commit dec 2019 (#380)
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* Fixed Ca channel proto, thanks to Harshavardan

* Fix to vclamp in rdesigneur. Fix to ConcChan handling involving many files

* Fix to HSolve so that assignment of passive properties Em, Cm and Rm reflects in the solver calculations without having to rebuild the entire solver.

* Fix conversion for ConcChan in ReadKkit, corresponding fix to calculations in Dsolve

* Fixed test_Xchan1.py to work with fixed ConcChan permeability units
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@upibhalla @hrani
upibhalla authored and hrani committed Jan 6, 2020
1 parent 3d2d554 commit 8d68b6d
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Showing 14 changed files with 169 additions and 59 deletions.
34 changes: 19 additions & 15 deletions diffusion/ConcChanInfo.h
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Original file line number Diff line number Diff line change
Expand Up @@ -14,22 +14,26 @@
*/
class ConcChanInfo
{
public:
ConcChanInfo();
ConcChanInfo( unsigned int my, unsigned int other,
unsigned int chan, double perm, bool isSwapped )
: myPool( my ), otherPool( other ), chanPool( chan ),
swapped( isSwapped ),
permeability( perm )
{;}
public:
ConcChanInfo();
ConcChanInfo( unsigned int my, unsigned int other,
unsigned int chan, double perm, bool isSwapped, bool _isLocal )
: myPool( my ), otherPool( other ), chanPool( chan ),
swapped( isSwapped ),
isLocal( _isLocal ),
permeability( perm )
{;}

unsigned int myPool;
unsigned int otherPool;
unsigned int chanPool;
bool swapped; // Flag records whether myPool/otherPool are
// swapped wrt inPool/outPool. System expects
// that inPool should be in same compt as chanPool.
double permeability;
unsigned int myPool; /// This is not Id, it is internal PoolIndex
/// Obtained using convertIdToPoolIndex.
unsigned int otherPool; /// Internal PoolIndex
unsigned int chanPool; /// Internal PoolIndex
bool swapped; // Flag records whether myPool/otherPool are
// swapped wrt inPool/outPool. System expects
// that inPool should be in same compt as chanPool.
bool isLocal; // Flag, records odd cases where the channel is
// entirely local to one compartment.
double permeability;
};

#endif // _CONC_CHAN_INFO_H
147 changes: 111 additions & 36 deletions diffusion/Dsolve.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -412,6 +412,8 @@ void Dsolve::calcJnChan( const DiffJunction& jn, Dsolve* other, double dt )

for ( unsigned int i = 0; i < jn.myChannels.size(); ++i )
{
if ( channels_[ jn.myChannels[i] ].isLocal )
continue;
ConcChanInfo& myChan = channels_[ jn.myChannels[i] ];
DiffPoolVec& myDv = pools_[ myChan.myPool ];
DiffPoolVec& otherDv = other->pools_[ myChan.otherPool ];
Expand All @@ -426,7 +428,7 @@ void Dsolve::calcJnChan( const DiffJunction& jn, Dsolve* other, double dt )
double chanN = chanDv.getN( j->first );
// Stick in a conversion factor for the myN and otherN into
// concentrations. Note that SI is millimolar.
double perm = myChan.permeability * chanN * 1000.0 / NA;
double perm = myChan.permeability * chanN / NA;
myN = integ( myN, perm * myN/j->firstVol,
perm * otherN/j->secondVol, dt );
otherN += lastN - myN; // Mass consv
Expand All @@ -446,6 +448,8 @@ void Dsolve::calcOtherJnChan( const DiffJunction& jn, Dsolve* other, double dt )
{
for ( unsigned int i = 0; i < jn.otherChannels.size(); ++i )
{
if ( other->channels_[ jn.otherChannels[i] ].isLocal )
continue;
ConcChanInfo& otherChan = other->channels_[ jn.otherChannels[i] ];
// This is the DiffPoolVec for the pools on the other Dsolve,
// the one with the channel.
Expand All @@ -465,7 +469,7 @@ void Dsolve::calcOtherJnChan( const DiffJunction& jn, Dsolve* other, double dt )
double chanN = chanDv.getN( j->second );
// Stick in a conversion factor for the myN and otherN into
// concentrations. Note that SI is millimolar.
double perm = otherChan.permeability * chanN * 1000.0 / NA;
double perm = otherChan.permeability * chanN / NA;
myN = integ( myN, perm * myN/j->firstVol,
perm * otherN/j->secondVol, dt );
otherN += lastN - myN; // Mass consv
Expand All @@ -480,6 +484,46 @@ void Dsolve::calcOtherJnChan( const DiffJunction& jn, Dsolve* other, double dt )
}
}

void Dsolve::calcLocalChan( double dt )
{
// There may be some chans which connect within the compartment.
// This is odd biologically, but happens for modelling convenience.
// The channels have a flag indicating if this is so. It is a simple
// calculation, but lacks numerical accuracy as it is outside the
// solver framework.

ChemCompt* cc = reinterpret_cast< ChemCompt* >( compartment_.eref().data() );
const vector< double >& vols = cc->vGetVoxelVolume();
for (auto ch = channels_.begin(); ch != channels_.end(); ++ch ) {
if ( ch->isLocal ) {
DiffPoolVec& myDv = pools_[ ch->myPool ];
DiffPoolVec& otherDv = pools_[ ch->otherPool ];
DiffPoolVec& chanDv = pools_[ ch->chanPool ];
assert( myDv.getNumVoxels() == numVoxels_ );
for (unsigned int i = 0; i < numVoxels_; ++i ) {
double myN = myDv.getN( i );
double lastN = myN;
double otherN = otherDv.getN( i );
double chanN = chanDv.getN( i );
double vol = vols[i];
// Stick in a conversion factor for the myN and otherN into
// concentrations. Note that SI is millimolar.
double perm = ch->permeability * chanN / NA;
myN = integ( myN, perm * myN/vol, perm * otherN/vol, dt );
otherN += lastN - myN; // Mass consv
if ( otherN < 0.0 ) // Avoid negatives
{
myN += otherN;
otherN = 0.0;
}
myDv.setN( i, myN );
otherDv.setN( i, otherN );
}
}
}
}


/**
* Computes flux through a junction between diffusion solvers.
* Most used at junctions on spines and PSDs, but can also be used
Expand Down Expand Up @@ -525,6 +569,7 @@ void Dsolve::reinit( const Eref& e, ProcPtr p )

void Dsolve::updateJunctions( double dt )
{
calcLocalChan( dt );
for (auto i = junctions_.begin(); i != junctions_.end(); ++i )
calcJunction( *i, dt );
}
Expand Down Expand Up @@ -614,7 +659,8 @@ void Dsolve::fillConcChans( const vector< ObjId >& chans )
ret.clear();
unsigned int outPoolValue = outPool.id.value();
bool swapped = false;
if ( !( inPool.bad() or chanPool.bad() ) )
bool isLocal = false;
if ( !( inPool.bad() || chanPool.bad() ) )
{
unsigned int inPoolIndex = convertIdToPoolIndex( inPool.id );
unsigned int chanPoolIndex = convertIdToPoolIndex(chanPool.id);
Expand All @@ -623,14 +669,22 @@ void Dsolve::fillConcChans( const vector< ObjId >& chans )
inPoolIndex = convertIdToPoolIndex( outPool.id );
outPoolValue = inPool.id.value();
swapped = true;
}
} else {
unsigned int outPoolIndex = convertIdToPoolIndex( outPool.id );
// edge case where both in and out are on same compartment.
// Not much sense in bio, but a common convenience hack.
if ( outPoolIndex != ~0U ) {
outPoolValue = outPoolIndex;
isLocal = true;
}

}
if ( ( inPoolIndex != ~0U) && (chanPoolIndex != ~0U ) )
{
ConcChanInfo cci(
inPoolIndex, outPoolValue, chanPoolIndex,
Field< double >::get( *i, "permeability" ),
////// Fix it below ////////
swapped
swapped, isLocal
);
channels_.push_back( cci );
}
Expand Down Expand Up @@ -972,27 +1026,29 @@ void Dsolve::mapChansBetweenDsolves( DiffJunction& jn, Id self, Id other)
unsigned int outIndex;
for ( unsigned int i = 0; i < ch.size(); ++i )
{
unsigned int chanIndex = ch[i].chanPool;
outIndex = otherSolve->convertIdToPoolIndex( ch[i].otherPool );
if ( (outIndex != ~0U) && (chanIndex != ~0U ) )
{
if ( ch[i].isLocal ) {
jn.myChannels.push_back(i);
ch[i].otherPool = outIndex; // replace the Id with the index.
ch[i].chanPool = chanIndex; //chanIndex may be on either Dsolve
} else {
outIndex = otherSolve->convertIdToPoolIndex( ch[i].otherPool );
if (outIndex != ~0U) {
ch[i].otherPool = outIndex; // replace Id with the index.
jn.myChannels.push_back(i);
}
}
}
// Now set up the other Dsolve.
vector< ConcChanInfo >& ch2 = otherSolve->channels_;
for ( unsigned int i = 0; i < ch2.size(); ++i )
{
unsigned int chanIndex = ch2[i].chanPool;
outIndex = selfSolve->convertIdToPoolIndex( ch2[i].otherPool );
if ( (outIndex != ~0U) && (chanIndex != ~0U) )
{
if ( ch2[i].isLocal ) {
jn.otherChannels.push_back(i);
ch2[i].otherPool = outIndex; // replace the Id with the index
ch2[i].chanPool = chanIndex; //chanIndex may be on either Dsolve
}
} else {
outIndex = selfSolve->convertIdToPoolIndex( ch2[i].otherPool );
if ( outIndex != ~0U ) {
ch2[i].otherPool = outIndex; // replace Id with the index
jn.otherChannels.push_back(i);
}
}
}
}

Expand Down Expand Up @@ -1063,15 +1119,18 @@ void Dsolve::setNumAllVoxels( unsigned int num )

unsigned int Dsolve::convertIdToPoolIndex( const Id id ) const
{
bool verbose = false;
unsigned int i = id.value() - poolMapStart_;
if ( i < poolMap_.size() )
{
return poolMap_[i];
}
cout << "Warning: Dsolve::convertIdToPoollndex: Id out of range, (" <<
if ( verbose ) {
cout << "Warning: Dsolve::convertIdToPoollndex: Id out of range, (" <<
poolMapStart_ << ", " << id << ", " << id.path() << ", " <<
poolMap_.size() + poolMapStart_ << "\n";
return 0;
}
return ~0U;
}

unsigned int Dsolve::convertIdToPoolIndex( const Eref& e ) const
Expand All @@ -1083,7 +1142,7 @@ void Dsolve::setN( const Eref& e, double v )
{
unsigned int pid = convertIdToPoolIndex( e );
// Ignore silently, as this may be a valid pid for the ksolve to use.
if ( pid >= pools_.size() )
if ( pid == ~0U || pid >= pools_.size() )
return;
unsigned int vox = e.dataIndex();
if ( vox < numVoxels_ )
Expand All @@ -1098,7 +1157,7 @@ void Dsolve::setN( const Eref& e, double v )
double Dsolve::getN( const Eref& e ) const
{
unsigned int pid = convertIdToPoolIndex( e );
if ( pid >= pools_.size() ) return 0.0; // ignore silently
if ( pid == ~0U || pid >= pools_.size() ) return 0.0; //ignore silently
unsigned int vox = e.dataIndex();
if ( vox < numVoxels_ )
{
Expand All @@ -1112,7 +1171,7 @@ double Dsolve::getN( const Eref& e ) const
void Dsolve::setNinit( const Eref& e, double v )
{
unsigned int pid = convertIdToPoolIndex( e );
if ( pid >= pools_.size() ) // Ignore silently
if ( pid == ~0U || pid >= pools_.size() ) // Ignore silently
return;
unsigned int vox = e.dataIndex();
if ( vox < numVoxels_ )
Expand All @@ -1127,7 +1186,7 @@ void Dsolve::setNinit( const Eref& e, double v )
double Dsolve::getNinit( const Eref& e ) const
{
unsigned int pid = convertIdToPoolIndex( e );
if ( pid >= pools_.size() ) return 0.0; // ignore silently
if ( pid == ~0U || pid >= pools_.size() ) return 0.0; //ignore silently
unsigned int vox = e.dataIndex();
if ( vox < numVoxels_ )
{
Expand All @@ -1141,36 +1200,52 @@ double Dsolve::getNinit( const Eref& e ) const
void Dsolve::setDiffConst( const Eref& e, double v )
{
unsigned int pid = convertIdToPoolIndex( e );
if ( pid >= pools_.size() ) // Ignore silently, out of range.
if ( pid == ~0U || pid >= pools_.size() ) // Ignore silently, out of range.
return;
pools_[ convertIdToPoolIndex( e ) ].setDiffConst( v );
pools_[ pid ].setDiffConst( v );
}

double Dsolve::getDiffConst( const Eref& e ) const
{
unsigned int pid = convertIdToPoolIndex( e );
if ( pid >= pools_.size() ) // Ignore silently, out of range.
if ( pid == ~0U || pid >= pools_.size() ) // Ignore silently, out of range.
return 0.0;
return pools_[ convertIdToPoolIndex( e ) ].getDiffConst();
return pools_[ pid ].getDiffConst();
}

void Dsolve::setMotorConst( const Eref& e, double v )
{
unsigned int pid = convertIdToPoolIndex( e );
if ( pid >= pools_.size() ) // Ignore silently, out of range.
if ( pid == ~0U || pid >= pools_.size() ) // Ignore silently, out of range.
return;
pools_[ convertIdToPoolIndex( e ) ].setMotorConst( v );
pools_[ pid ].setMotorConst( v );
}

void Dsolve::setNumPools( unsigned int numPoolSpecies )
void Dsolve::setNumVarTotPools( unsigned int var, unsigned int tot )
{
// Decompose numPoolSpecies here, assigning some to each node.
numTotPools_ = numPoolSpecies;
numLocalPools_ = numPoolSpecies;
numTotPools_ = tot;
numLocalPools_ = var;
poolStartIndex_ = 0;

pools_.resize( numLocalPools_ );
for ( unsigned int i = 0 ; i < numLocalPools_; ++i )
pools_.resize( numTotPools_ );
for ( unsigned int i = 0 ; i < numTotPools_; ++i )
{
pools_[i].setNumVoxels( numVoxels_ );
// pools_[i].setId( reversePoolMap_[i] );
// pools_[i].setParent( me );
}
}

void Dsolve::setNumPools( unsigned int numVarPoolSpecies )
{
// Decompose numPoolSpecies here, assigning some to each node.
numTotPools_ = numVarPoolSpecies;
numLocalPools_ = numVarPoolSpecies;
poolStartIndex_ = 0;

pools_.resize( numTotPools_ );
for ( unsigned int i = 0 ; i < numTotPools_; ++i )
{
pools_[i].setNumVoxels( numVoxels_ );
// pools_[i].setId( reversePoolMap_[i] );
Expand Down
3 changes: 3 additions & 0 deletions diffusion/Dsolve.h
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Original file line number Diff line number Diff line change
Expand Up @@ -136,6 +136,8 @@ class Dsolve: public ZombiePoolInterface

void setNumPools( unsigned int num );
unsigned int getNumPools() const;
void setNumVarTotPools( unsigned int var, unsigned int tot );

unsigned int getNumLocalVoxels() const;
VoxelPoolsBase* pools( unsigned int i );
double volume( unsigned int i ) const;
Expand Down Expand Up @@ -185,6 +187,7 @@ class Dsolve: public ZombiePoolInterface
void calcJnChan( const DiffJunction& jn, Dsolve* other, double dt );
void calcOtherJnChan( const DiffJunction& jn, Dsolve* other,
double dt );
void calcLocalChan( double dt );
void fillConcChans( const vector< ObjId >& chans );

/**
Expand Down
12 changes: 9 additions & 3 deletions hsolve/HSolveInterface.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -89,8 +89,10 @@ void HSolve::setCm( Id id, double value )
{
unsigned int index = localIndex( id );
assert( index < tree_.size() );
// Also update data structures used for calculations.
tree_[ index ].Cm = value;
// Also update data structures used for calculations.
assert( tree_.size() == compartment_.size() );
compartment_[index].CmByDt = 2.0 * value / dt_;
}

double HSolve::getEm( Id id ) const
Expand All @@ -104,8 +106,10 @@ void HSolve::setEm( Id id, double value )
{
unsigned int index = localIndex( id );
assert( index < tree_.size() );
// Also update data structures used for calculations.
tree_[ index ].Em = value;
// Also update data structures used for calculations.
assert( tree_.size() == compartment_.size() );
compartment_[index].EmByRm = value / tree_[index].Rm;
}

double HSolve::getRm( Id id ) const
Expand All @@ -119,8 +123,10 @@ void HSolve::setRm( Id id, double value )
{
unsigned int index = localIndex( id );
assert( index < tree_.size() );
// Also update data structures used for calculations.
tree_[ index ].Rm = value;
// Also update data structures used for calculations.
assert( tree_.size() == compartment_.size() );
compartment_[index].EmByRm = tree_[index].Em / value;
}

double HSolve::getRa( Id id ) const
Expand Down
3 changes: 2 additions & 1 deletion kinetics/ReadKkit.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1192,7 +1192,8 @@ Id ReadKkit::buildChan( const vector< string >& args )
//
double permeability = atof( args[ chanMap_["perm"] ].c_str() );
Id chan = shell_->doCreate( "ConcChan", pa, tail, 1 );
Field< double >::set( chan, "permeability", permeability );
// Convert from perm in uM in GENESIS, to mM for MOOSE.
Field< double >::set( chan, "permeability", permeability *1000.0 );
assert( chan != Id() );
string chanPath = clean.substr( 10 );
chanIds_[ chanPath ] = chan;
Expand Down
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