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sorry, but I need this to read it
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@Iximiel
Iximiel committed Nov 26, 2024
1 parent 636898f commit aac6c47
Showing 1 changed file with 104 additions and 40 deletions.
144 changes: 104 additions & 40 deletions src/adjmat/AdjacencyMatrixBase.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -215,52 +215,81 @@ unsigned AdjacencyMatrixBase::retrieveNeighbours( const unsigned& current, std::

void AdjacencyMatrixBase::setupForTask( const unsigned& current, std::vector<unsigned> & indices, MultiValue& myvals ) const {
// Now retrieve bookeeping arrays
if( indices.size()!=(1+ablocks.size()+threeblocks.size()) ) indices.resize( 1+ablocks.size()+threeblocks.size() );
if( indices.size()!=(1+ablocks.size()+threeblocks.size()) ) {
indices.resize( 1+ablocks.size()+threeblocks.size() );
}

// Now get the positions
const Value* myval = getConstPntrToComponent(0);
unsigned natoms=retrieveNeighbours( current, indices ); myvals.setSplitIndex( natoms );
// const Value* myval = getConstPntrToComponent(0);
unsigned natoms=retrieveNeighbours( current, indices );
myvals.setSplitIndex( natoms );

//placing this on the stack
Vector currentAtom = ActionAtomistic::getPosition(current);
// Now retrieve everything for the third atoms
if( threeblocks.size()>0 ) {
unsigned ncells_required=0; std::vector<unsigned> cells_required( threecells.getNumberOfCells() );
threecells.addRequiredCells( threecells.findMyCell( ActionAtomistic::getPosition(current) ), ncells_required, cells_required );
unsigned ncells_required=0;
std::vector<unsigned> cells_required( threecells.getNumberOfCells() );
threecells.addRequiredCells( threecells.findMyCell( currentAtom ), ncells_required, cells_required );
threecells.retrieveAtomsInCells( ncells_required, cells_required, natoms, indices );
}
myvals.setNumberOfIndices( natoms );

// Apply periodic boundary conditions to atom positions
std::vector<std::vector<Vector> > & t_atoms( myvals.getFirstAtomDerivativeVector() ); if( t_atoms.size()!=1 ) t_atoms.resize(1);
if( t_atoms[0].size()<getNumberOfAtoms() ) t_atoms[0].resize( getNumberOfAtoms() );
for(unsigned i=0; i<natoms; ++i) t_atoms[0][i] = ActionAtomistic::getPosition(indices[i]) - ActionAtomistic::getPosition(current);
if( !nopbc ) pbcApply( t_atoms[0], natoms );
std::vector<std::vector<Vector> > & t_atoms( myvals.getFirstAtomDerivativeVector() );
//since I am usig this as a temp variable, just have to care if size is 0,
if( t_atoms.size()==0 )
t_atoms.resize(1);
if( t_atoms[0].size()<getNumberOfAtoms() )
t_atoms[0].resize( getNumberOfAtoms() );
for(unsigned i=0; i<natoms; ++i)
t_atoms[0][i] = ActionAtomistic::getPosition(indices[i]) - currentAtom;
if( !nopbc )
pbcApply( t_atoms[0], natoms );
// And collect atom position data
std::vector<Vector> & atoms( myvals.getAtomVector() );
if( atoms.size()<getNumberOfAtoms() ) atoms.resize( getNumberOfAtoms() );
for(unsigned i=0; i<natoms; ++i) atoms[ indices[i] ] = t_atoms[0][i];
if( atoms.size()<getNumberOfAtoms() )
atoms.resize( getNumberOfAtoms() );
for(unsigned i=0; i<natoms; ++i)
atoms[ indices[i] ] = t_atoms[0][i];
}

void AdjacencyMatrixBase::performTask( const std::string& controller, const unsigned& index1, const unsigned& index2, MultiValue& myvals ) const {
Vector zero; zero.zero(); plumed_dbg_assert( index2<myvals.getAtomVector().size() );
Vector zero; zero.zero();
plumed_dbg_assert( index2<myvals.getAtomVector().size() );
double weight = calculateWeight( zero, myvals.getAtomVector()[index2], myvals.getNumberOfIndices()-myvals.getSplitIndex(), myvals );
myvals.setValue( 0, weight );
if( fabs(weight)<epsilon ) { myvals.setValue( 0, 0 ); return; }
if( fabs(weight)<epsilon ) {
myvals.setValue( 0, 0 );
return;
}

if( !doNotCalculateDerivatives() ) {
// Update dynamic list indices for central atom
myvals.updateIndex( 0, 3*index1+0 ); myvals.updateIndex( 0, 3*index1+1 ); myvals.updateIndex( 0, 3*index1+2 );
myvals.updateIndex( 0, 3*index1+0 );
myvals.updateIndex( 0, 3*index1+1 );
myvals.updateIndex( 0, 3*index1+2 );
// Update dynamic list indices for atom forming this bond
myvals.updateIndex( 0, 3*index2+0 ); myvals.updateIndex( 0, 3*index2+1 ); myvals.updateIndex( 0, 3*index2+2 );
myvals.updateIndex( 0, 3*index2+0 );
myvals.updateIndex( 0, 3*index2+1 );
myvals.updateIndex( 0, 3*index2+2 );
// Now look after all the atoms in the third block
std::vector<unsigned> & indices( myvals.getIndices() );
for(unsigned i=myvals.getSplitIndex(); i<myvals.getNumberOfIndices(); ++i) {
myvals.updateIndex( 0, 3*indices[i]+0 ); myvals.updateIndex( 0, 3*indices[i]+1 ); myvals.updateIndex( 0, 3*indices[i]+2 );
myvals.updateIndex( 0, 3*indices[i]+0 );
myvals.updateIndex( 0, 3*indices[i]+1 );
myvals.updateIndex( 0, 3*indices[i]+2 );
}
// Update dynamic list indices for virial
unsigned base = 3*getNumberOfAtoms(); for(unsigned j=0; j<9; ++j) myvals.updateIndex( 0, base+j );
unsigned base = 3*getNumberOfAtoms();
for(unsigned j=0; j<9; ++j)
myvals.updateIndex( 0, base+j );
// And the indices for the derivatives of the row of the matrix
unsigned nmat_ind = myvals.getNumberOfMatrixRowDerivatives(); std::vector<unsigned>& matrix_indices( myvals.getMatrixRowDerivativeIndices() );
matrix_indices[nmat_ind+0]=3*index2+0; matrix_indices[nmat_ind+1]=3*index2+1; matrix_indices[nmat_ind+2]=3*index2+2;
unsigned nmat_ind = myvals.getNumberOfMatrixRowDerivatives();
std::vector<unsigned>& matrix_indices( myvals.getMatrixRowDerivativeIndices() );
matrix_indices[nmat_ind+0]=3*index2+0;
matrix_indices[nmat_ind+1]=3*index2+1;
matrix_indices[nmat_ind+2]=3*index2+2;
myvals.setNumberOfMatrixRowDerivatives( nmat_ind+3 );
}

Expand All @@ -269,36 +298,71 @@ void AdjacencyMatrixBase::performTask( const std::string& controller, const unsi
Vector atom = myvals.getAtomVector()[index2];
myvals.setValue( 1, atom[0] ); myvals.setValue( 2, atom[1] ); myvals.setValue( 3, atom[2] );
if( !doNotCalculateDerivatives() ) {
myvals.addDerivative( 1, 3*index1+0, -1 ); myvals.addDerivative( 1, 3*index2+0, +1 );
myvals.addDerivative( 1, 3*index1+1, 0 ); myvals.addDerivative( 1, 3*index2+1, 0 );
myvals.addDerivative( 1, 3*index1+2, 0 ); myvals.addDerivative( 1, 3*index2+2, 0 );
myvals.addDerivative( 2, 3*index1+0, 0 ); myvals.addDerivative( 2, 3*index2+0, 0 );
myvals.addDerivative( 2, 3*index1+1, -1 ); myvals.addDerivative( 2, 3*index2+1, +1 );
myvals.addDerivative( 2, 3*index1+2, 0 ); myvals.addDerivative( 2, 3*index2+2, 0 );
myvals.addDerivative( 3, 3*index1+0, 0 ); myvals.addDerivative( 3, 3*index2+0, 0 );
myvals.addDerivative( 3, 3*index1+1, 0 ); myvals.addDerivative( 3, 3*index2+1, 0 );
myvals.addDerivative( 3, 3*index1+2, -1 ); myvals.addDerivative( 3, 3*index2+2, +1 );
myvals.addDerivative( 1, 3*index1+0, -1 );
myvals.addDerivative( 1, 3*index2+0, +1 );
myvals.addDerivative( 1, 3*index1+1, 0 );
myvals.addDerivative( 1, 3*index2+1, 0 );
myvals.addDerivative( 1, 3*index1+2, 0 );
myvals.addDerivative( 1, 3*index2+2, 0 );
myvals.addDerivative( 2, 3*index1+0, 0 );
myvals.addDerivative( 2, 3*index2+0, 0 );
myvals.addDerivative( 2, 3*index1+1, -1 );
myvals.addDerivative( 2, 3*index2+1, +1 );
myvals.addDerivative( 2, 3*index1+2, 0 );
myvals.addDerivative( 2, 3*index2+2, 0 );
myvals.addDerivative( 3, 3*index1+0, 0 );
myvals.addDerivative( 3, 3*index2+0, 0 );
myvals.addDerivative( 3, 3*index1+1, 0 );
myvals.addDerivative( 3, 3*index2+1, 0 );
myvals.addDerivative( 3, 3*index1+2, -1 );
myvals.addDerivative( 3, 3*index2+2, +1 );
for(unsigned k=0; k<3; ++k) {
// Update dynamic lists for central atom
myvals.updateIndex( 1, 3*index1+k ); myvals.updateIndex( 2, 3*index1+k ); myvals.updateIndex( 3, 3*index1+k );
myvals.updateIndex( 1, 3*index1+k );
myvals.updateIndex( 2, 3*index1+k );
myvals.updateIndex( 3, 3*index1+k );
// Update dynamic lists for bonded atom
myvals.updateIndex( 1, 3*index2+k ); myvals.updateIndex( 2, 3*index2+k ); myvals.updateIndex( 3, 3*index2+k );
myvals.updateIndex( 1, 3*index2+k );
myvals.updateIndex( 2, 3*index2+k );
myvals.updateIndex( 3, 3*index2+k );
}
// Add derivatives of virial
unsigned base = 3*getNumberOfAtoms();
// Virial for x
myvals.addDerivative( 1, base+0, -atom[0] ); myvals.addDerivative( 1, base+3, -atom[1] ); myvals.addDerivative( 1, base+6, -atom[2] );
myvals.addDerivative( 1, base+1, 0 ); myvals.addDerivative( 1, base+4, 0 ); myvals.addDerivative( 1, base+7, 0 );
myvals.addDerivative( 1, base+2, 0 ); myvals.addDerivative( 1, base+5, 0 ); myvals.addDerivative( 1, base+8, 0 );
myvals.addDerivative( 1, base+0, -atom[0] );
myvals.addDerivative( 1, base+3, -atom[1] );
myvals.addDerivative( 1, base+6, -atom[2] );
myvals.addDerivative( 1, base+1, 0 );
myvals.addDerivative( 1, base+4, 0 );
myvals.addDerivative( 1, base+7, 0 );
myvals.addDerivative( 1, base+2, 0 );
myvals.addDerivative( 1, base+5, 0 );
myvals.addDerivative( 1, base+8, 0 );
// Virial for y
myvals.addDerivative( 2, base+0, 0 ); myvals.addDerivative( 2, base+3, 0 ); myvals.addDerivative( 2, base+6, 0 );
myvals.addDerivative( 2, base+1, -atom[0] ); myvals.addDerivative( 2, base+4, -atom[1] ); myvals.addDerivative( 2, base+7, -atom[2] );
myvals.addDerivative( 2, base+2, 0 ); myvals.addDerivative( 2, base+5, 0 ); myvals.addDerivative( 2, base+8, 0 );
myvals.addDerivative( 2, base+0, 0 );
myvals.addDerivative( 2, base+3, 0 );
myvals.addDerivative( 2, base+6, 0 );
myvals.addDerivative( 2, base+1, -atom[0] );
myvals.addDerivative( 2, base+4, -atom[1] );
myvals.addDerivative( 2, base+7, -atom[2] );
myvals.addDerivative( 2, base+2, 0 );
myvals.addDerivative( 2, base+5, 0 );
myvals.addDerivative( 2, base+8, 0 );
// Virial for z
myvals.addDerivative( 3, base+0, 0 ); myvals.addDerivative( 3, base+3, 0 ); myvals.addDerivative( 3, base+6, 0 );
myvals.addDerivative( 3, base+1, 0 ); myvals.addDerivative( 3, base+4, 0 ); myvals.addDerivative( 3, base+7, 0 );
myvals.addDerivative( 3, base+2, -atom[0] ); myvals.addDerivative( 3, base+5, -atom[1] ); myvals.addDerivative( 3, base+8, -atom[2] );
for(unsigned k=0; k<9; ++k) { myvals.updateIndex( 1, base+k ); myvals.updateIndex( 2, base+k ); myvals.updateIndex( 3, base+k ); }
myvals.addDerivative( 3, base+0, 0 );
myvals.addDerivative( 3, base+3, 0 );
myvals.addDerivative( 3, base+6, 0 );
myvals.addDerivative( 3, base+1, 0 );
myvals.addDerivative( 3, base+4, 0 );
myvals.addDerivative( 3, base+7, 0 );
myvals.addDerivative( 3, base+2, -atom[0] );
myvals.addDerivative( 3, base+5, -atom[1] );
myvals.addDerivative( 3, base+8, -atom[2] );
for(unsigned k=0; k<9; ++k) {
myvals.updateIndex( 1, base+k );
myvals.updateIndex( 2, base+k );
myvals.updateIndex( 3, base+k );
}
}
}
}
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