void testHSolvePassive()
{
// TEST_BEGIN;
Shell* shell = reinterpret_cast< Shell* >( Id().eref().data() );
vector< int* > childArray;
vector< unsigned int > childArraySize;
/**
* We test passive-cable solver for the following cell:
*
* Soma---> 15 - 14 - 13 - 12
* | |
* | L 11 - 10
* |
* L 16 - 17 - 18 - 19
* |
* L 9 - 8 - 7 - 6 - 5
* | |
* | L 4 - 3
* |
* L 2 - 1 - 0
*
* The numbers are the hines indices of compartments. Compartment X is the
* child of compartment Y if X is one level further away from the soma (#15)
* than Y. So #17 is the parent of #'s 2, 9 and 18.
*/
int childArray_1[ ] =
{
/* c0 */ -1,
/* c1 */ -1, 0,
/* c2 */ -1, 1,
/* c3 */ -1,
/* c4 */ -1, 3,
/* c5 */ -1,
/* c6 */ -1, 5,
/* c7 */ -1, 4, 6,
/* c8 */ -1, 7,
/* c9 */ -1, 8,
/* c10 */ -1,
/* c11 */ -1, 10,
/* c12 */ -1,
/* c13 */ -1, 12,
/* c14 */ -1, 11, 13,
/* c15 */ -1, 14, 16,
/* c16 */ -1, 17,
/* c17 */ -1, 2, 9, 18,
/* c18 */ -1, 19,
/* c19 */ -1,
};
childArray.push_back( childArray_1 );
childArraySize.push_back( sizeof( childArray_1 ) / sizeof( int ) );
/**
* Cell 2:
*
* 3
* |
* Soma---> 2
* / \
* / \
* 1 0
*
*/
int childArray_2[ ] =
{
/* c0 */ -1,
/* c1 */ -1,
/* c2 */ -1, 0, 1, 3,
/* c3 */ -1,
};
childArray.push_back( childArray_2 );
childArraySize.push_back( sizeof( childArray_2 ) / sizeof( int ) );
/**
* Cell 3:
*
* 3
* |
* 2
* / \
* / \
* 1 0 <--- Soma
*
*/
int childArray_3[ ] =
{
/* c0 */ -1, 2,
/* c1 */ -1,
/* c2 */ -1, 1, 3,
/* c3 */ -1,
};
childArray.push_back( childArray_3 );
childArraySize.push_back( sizeof( childArray_3 ) / sizeof( int ) );
/**
* Cell 4:
*
* 3 <--- Soma
* |
* 2
* / \
* / \
* 1 0
*
*/
int childArray_4[ ] =
{
/* c0 */ -1,
/* c1 */ -1,
/* c2 */ -1, 0, 1,
/* c3 */ -1, 2,
};
childArray.push_back( childArray_4 );
childArraySize.push_back( sizeof( childArray_4 ) / sizeof( int ) );
/**
* Cell 5:
*
* 1 <--- Soma
* |
* 2
* / \
* 4 0
* / \
* 3 5
*
*/
int childArray_5[ ] =
{
/* c0 */ -1,
/* c1 */ -1, 2,
/* c2 */ -1, 0, 4,
/* c3 */ -1,
/* c4 */ -1, 3, 5,
/* c5 */ -1,
};
childArray.push_back( childArray_5 );
childArraySize.push_back( sizeof( childArray_5 ) / sizeof( int ) );
/**
* Cell 6:
*
* 3 <--- Soma
* L 4
* L 6
* L 5
* L 2
* L 1
* L 0
*
*/
int childArray_6[ ] =
{
/* c0 */ -1,
/* c1 */ -1,
/* c2 */ -1,
/* c3 */ -1, 4,
/* c4 */ -1, 0, 1, 2, 5, 6,
/* c5 */ -1,
/* c6 */ -1,
};
childArray.push_back( childArray_6 );
childArraySize.push_back( sizeof( childArray_6 ) / sizeof( int ) );
/**
* Cell 7: Single compartment
*/
int childArray_7[ ] =
{
/* c0 */ -1,
};
childArray.push_back( childArray_7 );
childArraySize.push_back( sizeof( childArray_7 ) / sizeof( int ) );
/**
* Cell 8: 3 compartments; soma is in the middle.
*/
int childArray_8[ ] =
{
/* c0 */ -1,
/* c1 */ -1, 0, 2,
/* c2 */ -1,
};
childArray.push_back( childArray_8 );
childArraySize.push_back( sizeof( childArray_8 ) / sizeof( int ) );
/**
* Cell 9: 3 compartments; first compartment is soma.
*/
int childArray_9[ ] =
{
/* c0 */ -1, 1,
/* c1 */ -1, 2,
/* c2 */ -1,
};
childArray.push_back( childArray_9 );
childArraySize.push_back( sizeof( childArray_9 ) / sizeof( int ) );
////////////////////////////////////////////////////////////////////////////
// Run tests
////////////////////////////////////////////////////////////////////////////
/*
* Solver instance.
*/
HSolvePassive HP;
/*
* This is the full reference matrix which will be compared to its sparse
* implementation.
*/
vector< vector< double > > matrix;
/*
* Model details.
*/
double dt = 1.0;
vector< TreeNodeStruct > tree;
vector< double > Em;
vector< double > B;
vector< double > V;
vector< double > VMid;
/*
* Loop over cells.
*/
int i;
int j;
//~ bool success;
int nCompt;
int* array;
unsigned int arraySize;
for ( unsigned int cell = 0; cell < childArray.size(); cell++ )
{
array = childArray[ cell ];
arraySize = childArraySize[ cell ];
nCompt = count( array, array + arraySize, -1 );
//////////////////////////////////////////
// Prepare local information on cell
//////////////////////////////////////////
tree.clear();
tree.resize( nCompt );
Em.clear();
V.clear();
for ( i = 0; i < nCompt; i++ )
{
tree[ i ].Ra = 15.0 + 3.0 * i;
tree[ i ].Rm = 45.0 + 15.0 * i;
tree[ i ].Cm = 500.0 + 200.0 * i * i;
Em.push_back( -0.06 );
V.push_back( -0.06 + 0.01 * i );
}
int count = -1;
for ( unsigned int a = 0; a < arraySize; a++ )
if ( array[ a ] == -1 )
count++;
else
tree[ count ].children.push_back( array[ a ] );
//////////////////////////////////////////
// Create cell inside moose; setup solver.
//////////////////////////////////////////
Id n = shell->doCreate( "Neutral", Id(), "n", 1 );
vector< Id > c( nCompt );
for ( i = 0; i < nCompt; i++ )
{
ostringstream name;
name << "c" << i;
c[ i ] = shell->doCreate( "Compartment", n, name.str() , 1);
Field< double >::set( c[ i ], "Ra", tree[ i ].Ra );
Field< double >::set( c[ i ], "Rm", tree[ i ].Rm );
Field< double >::set( c[ i ], "Cm", tree[ i ].Cm );
Field< double >::set( c[ i ], "Em", Em[ i ] );
Field< double >::set( c[ i ], "initVm", V[ i ] );
Field< double >::set( c[ i ], "Vm", V[ i ] );
}
for ( i = 0; i < nCompt; i++ )
{
vector< unsigned int >& child = tree[ i ].children;
for ( j = 0; j < ( int )( child.size() ); j++ )
{
ObjId mid = shell->doAddMsg(
"Single", c[ i ], "axial", c[ child[ j ] ], "raxial" );
ASSERT( ! mid.bad(), "Creating test model" );
}
}
HP.setup( c[ 0 ], dt );
/*
* Here we check if the cell was read in correctly by the solver.
* This test only checks if all the created compartments were read in.
* It doesn't check if they have been assigned hines' indices correctly.
*/
vector< Id >& hc = HP.compartmentId_;
ASSERT( ( int )( hc.size() ) == nCompt, "Tree traversal" );
for ( i = 0; i < nCompt; i++ )
ASSERT(
find( hc.begin(), hc.end(), c[ i ] ) != hc.end(), "Tree traversal"
);
//////////////////////////////////////////
// Setup local matrix
//////////////////////////////////////////
/*
* First we need to ensure that the hines' indices for the local model
* and those inside the solver match. If the numbering is different,
* then the matrices will not agree.
*
* In the following, we find out the indices assigned by the solver,
* and impose them on the local data structures.
*/
// Figure out new indices
vector< unsigned int > permutation( nCompt );
for ( i = 0; i < nCompt; i++ )
{
unsigned int newIndex =
find( hc.begin(), hc.end(), c[ i ] ) - hc.begin();
permutation[ i ] = newIndex;
}
// Shuffle compartment properties according to new order
permute< TreeNodeStruct >( tree, permutation );
permute< double >( Em, permutation );
permute< double >( V, permutation );
// Update indices of children
for ( i = 0; i < nCompt; i++ )
{
vector< unsigned int >& child = tree[ i ].children;
for ( j = 0; j < ( int )( child.size() ); j++ )
child[ j ] = permutation[ child[ j ] ];
}
// Create local reference matrix
makeFullMatrix( tree, dt, matrix );
VMid.resize( nCompt );
B.resize( nCompt );
vector< vector< double > > matrixCopy;
matrixCopy.assign( matrix.begin(), matrix.end() );
//////////////////////////////////////////
// Run comparisons
//////////////////////////////////////////
double tolerance;
/*
* Compare initial matrices
*/
tolerance = 2.0;
for ( i = 0; i < nCompt; ++i )
for ( j = 0; j < nCompt; ++j )
{
ostringstream error;
error << "Testing matrix construction:"
<< " Cell# " << cell + 1
<< " A(" << i << ", " << j << ")";
ASSERT (
isClose< double >( HP.getA( i, j ), matrix[ i ][ j ], tolerance ),
error.str()
);
}
/*
*
* Gaussian elimination
*
*/
tolerance = 4.0; // ratio to machine epsilon
for ( int pass = 0; pass < 2; pass++ )
{
/*
* First update terms in the equation. This involves setting up the B
* in Ax = B, using the latest voltage values. Also, the coefficients
* stored in A have to be restored to their original values, since
* the matrix is modified at the end of every pass of gaussian
* elimination.
*/
// Do so in the solver..
HP.updateMatrix();
// ..locally..
matrix.assign( matrixCopy.begin(), matrixCopy.end() );
for ( i = 0; i < nCompt; i++ )
B[ i ] =
V[ i ] * tree[ i ].Cm / ( dt / 2.0 ) +
Em[ i ] / tree[ i ].Rm;
// ..and compare B.
for ( i = 0; i < nCompt; ++i )
{
ostringstream error;
error << "Updating right-hand side values:"
<< " Pass " << pass
<< " Cell# " << cell + 1
<< " B(" << i << ")";
ASSERT (
isClose< double >( HP.getB( i ), B[ i ], tolerance ),
error.str()
);
}
/*
* Forward elimination..
*/
// ..in solver..
HP.forwardEliminate();
// ..and locally..
int k;
for ( i = 0; i < nCompt - 1; i++ )
for ( j = i + 1; j < nCompt; j++ )
{
double div = matrix[ j ][ i ] / matrix[ i ][ i ];
for ( k = 0; k < nCompt; k++ )
matrix[ j ][ k ] -= div * matrix[ i ][ k ];
B[ j ] -= div * B[ i ];
}
// ..then compare A..
for ( i = 0; i < nCompt; ++i )
for ( j = 0; j < nCompt; ++j )
{
ostringstream error;
error << "Forward elimination:"
<< " Pass " << pass
<< " Cell# " << cell + 1
<< " A(" << i << ", " << j << ")";
ASSERT (
isClose< double >( HP.getA( i, j ), matrix[ i ][ j ], tolerance ),
error.str()
);
}
// ..and also B.
for ( i = 0; i < nCompt; ++i )
{
ostringstream error;
error << "Forward elimination:"
<< " Pass " << pass
<< " Cell# " << cell + 1
<< " B(" << i << ")";
ASSERT (
isClose< double >( HP.getB( i ), B[ i ], tolerance ),
error.str()
);
}
/*
* Backward substitution..
*/
// ..in solver..
HP.backwardSubstitute();
// ..and full back-sub on local matrix equation..
for ( i = nCompt - 1; i >= 0; i-- )
{
VMid[ i ] = B[ i ];
for ( j = nCompt - 1; j > i; j-- )
VMid[ i ] -= VMid[ j ] * matrix[ i ][ j ];
VMid[ i ] /= matrix[ i ][ i ];
V[ i ] = 2 * VMid[ i ] - V[ i ];
}
// ..and then compare VMid.
for ( i = nCompt - 1; i >= 0; i-- )
{
ostringstream error;
error << "Back substitution:"
<< " Pass " << pass
<< " Cell# " << cell + 1
<< " VMid(" << i << ")";
ASSERT (
isClose< double >( HP.getVMid( i ), VMid[ i ], tolerance ),
error.str()
);
}
for ( i = nCompt - 1; i >= 0; i-- )
{
ostringstream error;
error << "Back substitution:"
<< " Pass " << pass
<< " Cell# " << cell + 1
<< " V(" << i << ")";
ASSERT (
isClose< double >( HP.getV( i ), V[ i ], tolerance ),
error.str()
);
}
}
// cleanup
shell->doDelete( n );
}
// TEST_END;
}
void testHinesMatrix()
{
return;
//~ cout << "\nTesting HinesMatrix" << flush;
vector< int* > childArray;
vector< unsigned int > childArraySize;
/**
* We test if the Hines' matrix is correctly setup for the following cell:
*
* Soma---> 15 - 14 - 13 - 12
* | |
* | L 11 - 10
* |
* L 16 - 17 - 18 - 19
* |
* L 9 - 8 - 7 - 6 - 5
* | |
* | L 4 - 3
* |
* L 2 - 1 - 0
*
* The numbers are the hines indices of compartments. Compartment X is the
* child of compartment Y if X is one level further away from the soma (#15)
* than Y. So #17 is the parent of #'s 2, 9 and 18.
*/
int childArray_1[ ] =
{
/* c0 */ -1,
/* c1 */ -1, 0,
/* c2 */ -1, 1,
/* c3 */ -1,
/* c4 */ -1, 3,
/* c5 */ -1,
/* c6 */ -1, 5,
/* c7 */ -1, 4, 6,
/* c8 */ -1, 7,
/* c9 */ -1, 8,
/* c10 */ -1,
/* c11 */ -1, 10,
/* c12 */ -1,
/* c13 */ -1, 12,
/* c14 */ -1, 11, 13,
/* c15 */ -1, 14, 16,
/* c16 */ -1, 17,
/* c17 */ -1, 2, 9, 18,
/* c18 */ -1, 19,
/* c19 */ -1,
};
childArray.push_back( childArray_1 );
childArraySize.push_back( sizeof( childArray_1 ) / sizeof( int ) );
/**
* Cell 2:
*
* 3
* |
* Soma---> 2
* / \
* / \
* 1 0
*
*/
int childArray_2[ ] =
{
/* c0 */ -1,
/* c1 */ -1,
/* c2 */ -1, 0, 1, 3,
/* c3 */ -1,
};
childArray.push_back( childArray_2 );
childArraySize.push_back( sizeof( childArray_2 ) / sizeof( int ) );
/**
* Cell 3:
*
* 3
* |
* 2
* / \
* / \
* 1 0 <--- Soma
*
*/
int childArray_3[ ] =
{
/* c0 */ -1, 2,
/* c1 */ -1,
/* c2 */ -1, 1, 3,
/* c3 */ -1,
};
childArray.push_back( childArray_3 );
childArraySize.push_back( sizeof( childArray_3 ) / sizeof( int ) );
/**
* Cell 4:
*
* 3 <--- Soma
* |
* 2
* / \
* / \
* 1 0
*
*/
int childArray_4[ ] =
{
/* c0 */ -1,
/* c1 */ -1,
/* c2 */ -1, 0, 1,
/* c3 */ -1, 2,
};
childArray.push_back( childArray_4 );
childArraySize.push_back( sizeof( childArray_4 ) / sizeof( int ) );
/**
* Cell 5:
*
* 1 <--- Soma
* |
* 2
* / \
* 4 0
* / \
* 3 5
*
*/
int childArray_5[ ] =
{
/* c0 */ -1,
/* c1 */ -1, 2,
/* c2 */ -1, 0, 4,
/* c3 */ -1,
/* c4 */ -1, 3, 5,
/* c5 */ -1,
};
childArray.push_back( childArray_5 );
childArraySize.push_back( sizeof( childArray_5 ) / sizeof( int ) );
/**
* Cell 6:
*
* 3 <--- Soma
* L 4
* L 6
* L 5
* L 2
* L 1
* L 0
*
*/
int childArray_6[ ] =
{
/* c0 */ -1,
/* c1 */ -1,
/* c2 */ -1,
/* c3 */ -1, 4,
/* c4 */ -1, 0, 1, 2, 5, 6,
/* c5 */ -1,
/* c6 */ -1,
};
childArray.push_back( childArray_6 );
childArraySize.push_back( sizeof( childArray_6 ) / sizeof( int ) );
/**
* Cell 7: Single compartment
*/
int childArray_7[ ] =
{
/* c0 */ -1,
};
childArray.push_back( childArray_7 );
childArraySize.push_back( sizeof( childArray_7 ) / sizeof( int ) );
/**
* Cell 8: 3 compartments; soma is in the middle.
*/
int childArray_8[ ] =
{
/* c0 */ -1,
/* c1 */ -1, 0, 2,
/* c2 */ -1,
};
childArray.push_back( childArray_8 );
childArraySize.push_back( sizeof( childArray_8 ) / sizeof( int ) );
/**
* Cell 9: 3 compartments; first compartment is soma.
*/
int childArray_9[ ] =
{
/* c0 */ -1, 1,
/* c1 */ -1, 2,
/* c2 */ -1,
};
childArray.push_back( childArray_9 );
childArraySize.push_back( sizeof( childArray_9 ) / sizeof( int ) );
////////////////////////////////////////////////////////////////////////////
// Run tests
////////////////////////////////////////////////////////////////////////////
HinesMatrix H;
vector< TreeNodeStruct > tree;
double dt = 1.0;
/*
* This is the full reference matrix which will be compared to its sparse
* implementation.
*/
vector< vector< double > > matrix;
double epsilon = 1e-17;
unsigned int i;
unsigned int j;
unsigned int nCompt;
int* array;
unsigned int arraySize;
for ( unsigned int cell = 0; cell < childArray.size(); cell++ ) {
array = childArray[ cell ];
arraySize = childArraySize[ cell ];
nCompt = count( array, array + arraySize, -1 );
// Prepare cell
tree.clear();
tree.resize( nCompt );
for ( i = 0; i < nCompt; ++i ) {
tree[ i ].Ra = 15.0 + 3.0 * i;
tree[ i ].Rm = 45.0 + 15.0 * i;
tree[ i ].Cm = 500.0 + 200.0 * i * i;
}
int count = -1;
for ( unsigned int a = 0; a < arraySize; a++ )
if ( array[ a ] == -1 )
count++;
else
tree[ count ].children.push_back( array[ a ] );
// Prepare local matrix
makeFullMatrix( tree, dt, matrix );
// Prepare sparse matrix
H.setup( tree, dt );
// Compare matrices
cout << "Testing Hines Matrix" << endl;
cout << "Cell number " << cell << endl;
for ( i = 0; i < nCompt; ++i ) {
for ( j = 0; j < nCompt; ++j ) {
ostringstream error;
error << "Testing Hines' Matrix: Cell# "
<< cell + 1 << ", entry (" << i << ", " << j << ")";
ASSERT(
fabs( matrix[ i ][ j ] - H.getA( i, j ) ) < epsilon,
error.str()
);
cout << matrix[i][j] << " ";
}
cout << endl;
}
}
cout << ".";
}
