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replace tabs and remove trailing whitespace in lib folder with updated script

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This commit is contained in:
Axel Kohlmeyer
2021-08-22 20:45:24 -04:00
parent 30821b37e5
commit 92b5b159e5
311 changed files with 9176 additions and 9176 deletions
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84
lib/atc/TransferLibrary.cpp
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@ -37,7 +37,7 @@ namespace ATC {
shapeFunction_(shapeFunction),
lammpsInterface_(atc->lammps_interface()),
feEngine_(atc->fe_engine()),
tol_(1.e-10)
tol_(1.e-10)
{
shapeFunction_->register_dependence(this);
}
@ -65,7 +65,7 @@ namespace ATC {
_scale_.resize(nNodes);
for (int i = 0; i < nNodes; i++) {
if ((abs(lhs(i,i)) > 0.))
if ((abs(lhs(i,i)) > 0.))
_scale_(i) = 1.;
else
_scale_(i) = 0.;
@ -78,7 +78,7 @@ namespace ATC {
}
}
lhs.compress();
// solve equation
LinearSolver solver(lhs, ATC::LinearSolver::ITERATIVE_SOLVE_SYMMETRIC, true);
solver.set_max_iterations(lhs.nRows());
@ -146,7 +146,7 @@ namespace ATC {
shapeFunction_(shapeFunction),
atomElement_(atomElement),
feEngine_(atc->fe_engine()),
tol_(1.e-10)
tol_(1.e-10)
{
shapeFunction_->register_dependence(this);
if (!atomElement_) {
@ -162,7 +162,7 @@ namespace ATC {
void NodalAtomVolumeElement::reset_quantity() const
{
// Using analyses by G. Wagner and J. Templeton, weights ~ phi*M^{-1}*V
// where phi are the dimensionless shape/weighting functions,
// where phi are the dimensionless shape/weighting functions,
// M is the "mass" matrix M_IJ,
// V is the vector of nodal and element volumes
//
@ -185,11 +185,11 @@ namespace ATC {
int thisCol = nNodes+atomElement(a,0);
nodEltShpFcnMatrix.set(a,thisCol,1);
}
SPAR_MAT neMassMatrix(neSize,neSize);
atc_->compute_consistent_md_mass_matrix(nodEltShpFcnMatrix,neMassMatrix);
// form vector of nodal and elemental volumes
// form vector of nodal and elemental volumes
_nodeVolumesMatrix_.resize(nNodes,nNodes);
feEngine_->compute_lumped_mass_matrix(_nodeVolumesMatrix_);
_nodeVolumes_.resize(nNodes);
@ -217,13 +217,13 @@ namespace ATC {
averageEltVolume += (maxx-minx)*(maxy-miny)*(maxz-minz);
}
averageEltVolume /= nElts;
// correct entries of mass matrix if no atoms in shape function support
double totalNodalVolume = _nodeVolumes_.sum();
double averageNodalVolume = totalNodalVolume/nNodes;
_scale_.resize(neSize);
for (int i = 0; i < neSize; i++) {
if ((abs(neMassMatrix(i,i)) > 0.)) {
if ((abs(neMassMatrix(i,i)) > 0.)) {
_scale_(i) = 1.;
} else {
printf("No atoms are in support of node/element %i\n",i);
@ -234,7 +234,7 @@ namespace ATC {
for (int i = 0; i < neSize; i++) {
if (_scale_(i) < 0.5) {
neMassMatrix.set(i,i,1.);
if (i < nNodes) {
if (i < nNodes) {
_nodeElementVolumes_(i) = averageNodalVolume;
} else {
_nodeElementVolumes_(i) = averageEltVolume;
@ -242,11 +242,11 @@ namespace ATC {
}
}
neMassMatrix.compress();
// solve equation
LinearSolver solver(neMassMatrix, ATC::LinearSolver::ITERATIVE_SOLVE_SYMMETRIC, true);
solver.set_max_iterations(neMassMatrix.nRows());
double myTol = 1.e-10;
double myTol = 1.e-10;
solver.set_tolerance(myTol);
quantity_.resize(neSize,0);
CLON_VEC tempQuantity(quantity_,CLONE_COL,0);
@ -329,7 +329,7 @@ namespace ATC {
if (!hasGhost_) {
hasGhost_ = (atc->interscale_manager()).dense_matrix_int("ElementHasGhost");
}
hasInternal_->register_dependence(this);
if (hasGhost_) hasGhost_->register_dependence(this);
}
@ -354,7 +354,7 @@ namespace ATC {
quantity_(i,0) = !hasInternal(i,0);
}
}
const set<int> & nullElements = feEngine_->null_elements();
set<int>::const_iterator iset;
for (iset = nullElements.begin(); iset != nullElements.end(); iset++) {
@ -421,7 +421,7 @@ namespace ATC {
SetDependencyManager<int> * nodeSet) :
nodeSet_(nodeSet),
feMesh_((atc->fe_engine())->fe_mesh())
{
{
nodeSet_->register_dependence(this);
}
@ -483,15 +483,15 @@ namespace ATC {
_nodesGhost_.reset(nNodes_);
_nodesGhost_ = 0;
Array<int> nodes;
vector<int> myElems = feEngine_->fe_mesh()->owned_elts();
if (hasGhost_) {
const INT_ARRAY & hasGhost(hasGhost_->quantity()) ;
// iterate through all elements owned by this processor
for (vector<int>::iterator elemsIter = myElems.begin();
elemsIter != myElems.end();
++elemsIter)
@ -510,7 +510,7 @@ namespace ATC {
}
}
// sum up partial result arrays
lammpsInterface_->logical_or(MPI_IN_PLACE, _nodesInternal_.ptr(), _nodesInternal_.size());
lammpsInterface_->logical_or(MPI_IN_PLACE, _nodesGhost_.ptr(), _nodesGhost_.size());
}
@ -582,9 +582,9 @@ namespace ATC {
_nodesGhost_.reset(nNodes_);
_nodesGhost_ = 0;
Array<int> nodes;
vector<int> myElems = feEngine_->fe_mesh()->owned_elts();
// iterate through all elements owned by this processor
for (vector<int>::iterator elemsIter = myElems.begin();
@ -605,7 +605,7 @@ namespace ATC {
}
}
}
// sum up partial result arrays
lammpsInterface_->logical_or(MPI_IN_PLACE, _nodesInternal_.ptr(), _nodesInternal_.size());
lammpsInterface_->logical_or(MPI_IN_PLACE, _nodesGhost_.ptr(), _nodesGhost_.size());
@ -882,7 +882,7 @@ namespace ATC {
}
}
}
//--------------------------------------------------------
//--------------------------------------------------------
// Class MappedQuantity
@ -967,7 +967,7 @@ namespace ATC {
{
const INT_ARRAY & nodeType(nodalGeometryType_->quantity());
quantity_.clear();
for (int i = 0; i < nodeType.size(); ++i) {
if (nodeType(i,0) != FE_ONLY) {
quantity_.insert(i);
@ -981,7 +981,7 @@ namespace ATC {
void RegulatedNodes::insert_boundary_nodes() const
{
const INT_ARRAY & nodeType(nodalGeometryType_->quantity());
for (int i = 0; i < nodeType.size(); ++i) {
if (nodeType(i,0) == BOUNDARY) {
quantity_.insert(i);
@ -1012,7 +1012,7 @@ namespace ATC {
//--------------------------------------------------------
void RegulatedNodes::insert_fixed_nodes() const
{
const INT_ARRAY & nodeType(nodalGeometryType_->quantity());
map<FieldName,int>::const_iterator fs_iter;
@ -1038,7 +1038,7 @@ namespace ATC {
const INT_ARRAY & nodeType(nodalGeometryType_->quantity());
set<int>::const_iterator inode;
map<FieldName,int>::const_iterator fs_iter;
for (fs_iter = fieldSizes_.begin(); fs_iter != fieldSizes_.end(); fs_iter++) {
for (int j = 0; j < fs_iter->second; j++) {
set<int> faceFluxNodes = prescribedDataManager_->flux_face_nodes(fs_iter->first,j);
@ -1104,7 +1104,7 @@ namespace ATC {
void FluxNodes::reset_quantity() const
{
quantity_.clear();
// a) they have a fixed face flux
RegulatedNodes::insert_face_fluxes();
@ -1161,7 +1161,7 @@ namespace ATC {
void FixedNodes::reset_quantity() const
{
quantity_.clear();
// a) they are a fixed node
RegulatedNodes::insert_fixed_nodes();
}
@ -1533,7 +1533,7 @@ namespace ATC {
DENS_MAN* atomCoarseGrainingPositions):
atc_(atc),
source_(source),
kernelFunction_(kernelFunction),
kernelFunction_(kernelFunction),
atomCoarseGrainingPositions_(atomCoarseGrainingPositions),
feMesh_((atc_->fe_engine())->fe_mesh())
{
@ -1551,7 +1551,7 @@ namespace ATC {
int nNodes = feMesh_->num_nodes_unique();
quantity_.resize(nNodes,source.nCols());
_quantityLocal_.reset(nNodes,source.nCols());
if (source.nRows()>0) {
DENS_VEC xI(positions.nCols()),xa(positions.nCols()),xaI(positions.nCols());
double val;
@ -1696,7 +1696,7 @@ namespace ATC {
_localWeights_ = (accumulant_->quantity()).col_sum();
}
lammpsInterface_->allsum(_localWeights_.ptr(),_weights_.ptr(),nNodes);
// assign weights
quantity_.resize(nNodes,nNodes);
for (int i = 0; i < nNodes; i++) {
@ -1732,7 +1732,7 @@ namespace ATC {
{
const DENS_MAT & weights(weights_->quantity());
int nNodes = weights.nRows();
// assign weights
quantity_.resize(nNodes,nNodes);
for (int i = 0; i < nNodes; i++) {
@ -1756,7 +1756,7 @@ namespace ATC {
//--------------------------------------------------------
KernelInverseVolumes::KernelInverseVolumes(ATC_Method * atc,
KernelFunction* kernelFunction):
kernelFunction_(kernelFunction),
kernelFunction_(kernelFunction),
feMesh_((atc->fe_engine())->fe_mesh())
{
// do nothing
@ -1807,7 +1807,7 @@ namespace ATC {
quantity_.resize(nNodes,source.nCols());
_quantityLocal_.reset(nNodes,source.nCols());
DENS_VEC xj(atc_->nsd());
if (source.nRows()>0) {
for (int j = 0; j < source.nRows(); j++) {
for (int k = 0; k < atc_->nsd(); k++) {
@ -1820,7 +1820,7 @@ namespace ATC {
//quantity_(inode,k) += shp(I)*source(j,k);
_quantityLocal_(inode,k) += shp(I)*source(j,k);
}
}
}
}
}
// accumulate across processors
@ -1946,7 +1946,7 @@ namespace ATC {
//--------------------------------------------------------
void NativeShapeFunctionGradient::reset_quantity() const
{
feEngine_->compute_gradient_matrix(quantity_);
feEngine_->compute_gradient_matrix(quantity_);
}
//--------------------------------------------------------
@ -1971,7 +1971,7 @@ namespace ATC {
//--------------------------------------------------------
// destructor
//--------------------------------------------------------
OnTheFlyShapeFunctionProlongation::~OnTheFlyShapeFunctionProlongation()
OnTheFlyShapeFunctionProlongation::~OnTheFlyShapeFunctionProlongation()
{
atomCoarseGrainingPositions_->remove_dependence(this);
};