ActionWithInputMatrix class | PLMD::adjmat::AdjacencyMatrixVessel | friend |
activateIndices(ActionWithVessel *) | PLMD::vesselbase::StoreDataVessel | inlinevirtual |
addActionThatUses(ActionWithVessel *actionThatUses) | PLMD::vesselbase::StoreDataVessel | |
AdjacencyMatrixBase class | PLMD::adjmat::AdjacencyMatrixVessel | friend |
AdjacencyMatrixVessel(const vesselbase::VesselOptions &) | PLMD::adjmat::AdjacencyMatrixVessel | explicit |
applyForce(std::vector< double > &) | PLMD::vesselbase::StoreDataVessel | inlinevirtual |
bufstart | PLMD::vesselbase::Vessel | protected |
calculate(const unsigned ¤t, MultiValue &myvals, std::vector< double > &buffer, std::vector< unsigned > &der_index) const | PLMD::vesselbase::StoreDataVessel | virtual |
checkRead() | PLMD::vesselbase::Vessel | |
comm | PLMD::vesselbase::Vessel | protected |
completeSetup(const unsigned &, const unsigned &) | PLMD::vesselbase::StoreDataVessel | protected |
description() | PLMD::vesselbase::StoreDataVessel | inlinevirtual |
error(const std::string &errmsg) | PLMD::vesselbase::Vessel | protected |
finish(const std::vector< double > &buffer) | PLMD::vesselbase::StoreDataVessel | virtual |
function | PLMD::adjmat::AdjacencyMatrixVessel | private |
getAction() const | PLMD::vesselbase::Vessel | inlineprotected |
getAllInput() | PLMD::vesselbase::Vessel | protected |
getCutoffForConnection() const | PLMD::adjmat::AdjacencyMatrixVessel | |
getDataUser(const unsigned &) | PLMD::vesselbase::StoreDataVessel | inline |
getLabel() const | PLMD::vesselbase::Vessel | |
getLocalDerivative(const unsigned &ibuf) | PLMD::vesselbase::StoreDataVessel | protected |
getMatrixAction() | PLMD::adjmat::AdjacencyMatrixVessel | |
getMatrixIndices(const unsigned &code, unsigned &i, unsigned &j) const | PLMD::adjmat::AdjacencyMatrixVessel | |
getName() const | PLMD::vesselbase::Vessel | |
getNLTolerance() const | PLMD::vesselbase::Vessel | inlineprotected |
getNodePosition(const unsigned &taskIndex) const | PLMD::adjmat::AdjacencyMatrixVessel | |
getNumberOfColumns() const | PLMD::adjmat::AdjacencyMatrixVessel | |
getNumberOfComponents() const | PLMD::vesselbase::StoreDataVessel | inline |
getNumberOfDataUsers() const | PLMD::vesselbase::StoreDataVessel | inline |
getNumberOfDerivatives(const unsigned &) | PLMD::vesselbase::StoreDataVessel | |
getNumberOfDerivativeSpacesPerComponent() const | PLMD::vesselbase::StoreDataVessel | inlineprotected |
getNumberOfRows() const | PLMD::adjmat::AdjacencyMatrixVessel | |
getNumberOfStoredValues() const | PLMD::vesselbase::StoreDataVessel | inlinevirtual |
getNumericalLabel() const | PLMD::vesselbase::Vessel | inlineprotected |
getSizeOfBuffer() const | PLMD::vesselbase::Vessel | inlineprotected |
getSizeOfDerivativeList() const | PLMD::vesselbase::StoreDataVessel | inline |
getStoreIndex(const unsigned &) const | PLMD::vesselbase::StoreDataVessel | inline |
getStoreIndexFromMatrixIndices(const unsigned &ielem, const unsigned &jelem) const | PLMD::adjmat::AdjacencyMatrixVessel | |
getTemporyMultiValue(const unsigned &ind) | PLMD::vesselbase::StoreDataVessel | |
getTolerance() const | PLMD::vesselbase::Vessel | inlineprotected |
getTrueIndex(const unsigned &) const | PLMD::vesselbase::StoreDataVessel | inline |
hbonds | PLMD::adjmat::AdjacencyMatrixVessel | private |
isSymmetric() const | PLMD::adjmat::AdjacencyMatrixVessel | |
log | PLMD::vesselbase::Vessel | |
matrixElementIsActive(const unsigned &ielem, const unsigned &jelem) const | PLMD::adjmat::AdjacencyMatrixVessel | |
nodesAreConnected(const unsigned &iatom, const unsigned &jatom) const | PLMD::adjmat::AdjacencyMatrixVessel | |
parse(const std::string &key, T &t) | PLMD::vesselbase::Vessel | protected |
parseFlag(const std::string &key, bool &t) | PLMD::vesselbase::Vessel | protected |
parseVector(const std::string &key, std::vector< T > &t) | PLMD::vesselbase::Vessel | protected |
prepare() | PLMD::vesselbase::Vessel | inlinevirtual |
recalculateStoredQuantity(const unsigned &myelm, MultiValue &myvals) | PLMD::vesselbase::StoreDataVessel | inline |
registerKeywords(Keywords &keys) | PLMD::adjmat::AdjacencyMatrixVessel | static |
resize() | PLMD::vesselbase::StoreDataVessel | virtual |
resizeBuffer(const unsigned &n) | PLMD::vesselbase::Vessel | inlineprotected |
resizeTemporyMultiValues(const unsigned &nvals) | PLMD::vesselbase::StoreDataVessel | |
retrieveAdjacencyLists(std::vector< unsigned > &nneigh, Matrix< unsigned > &adj_list) | PLMD::adjmat::AdjacencyMatrixVessel | |
retrieveDerivatives(const unsigned &myelem, const bool &normed, MultiValue &myvals) | PLMD::vesselbase::StoreDataVessel | |
retrieveEdgeList(unsigned &nedge, std::vector< std::pair< unsigned, unsigned > > &edge_list) | PLMD::adjmat::AdjacencyMatrixVessel | |
retrieveMatrix(DynamicList< unsigned > &myactive_elements, Matrix< double > &mymatrix) | PLMD::adjmat::AdjacencyMatrixVessel | |
retrieveSequentialValue(const unsigned &myelem, const bool &normed, std::vector< double > &values) const | PLMD::vesselbase::StoreDataVessel | |
retrieveValueWithIndex(const unsigned &myelem, const bool &normed, std::vector< double > &values) const | PLMD::vesselbase::StoreDataVessel | |
retrieveWeightWithIndex(const unsigned &myelem) const | PLMD::vesselbase::StoreDataVessel | |
setActiveValsAndDerivatives(const std::vector< unsigned > &der_index) | PLMD::vesselbase::StoreDataVessel | |
setBufferStart(unsigned &start) | PLMD::vesselbase::Vessel | inlinevirtual |
setHardCutoffOnWeight(const double &mytol) | PLMD::vesselbase::StoreDataVessel | |
setLocalDerivative(const unsigned &ibuf, const double &val) | PLMD::vesselbase::StoreDataVessel | protected |
StoreDataVessel(const VesselOptions &) | PLMD::vesselbase::StoreDataVessel | explicit |
storeDerivatives(const unsigned &, MultiValue &myvals, std::vector< double > &, std::vector< unsigned > &) const | PLMD::vesselbase::StoreDataVessel | protected |
storedValueIsActive(const unsigned &iatom) const | PLMD::vesselbase::StoreDataVessel | inline |
storeValues(const unsigned &, MultiValue &, std::vector< double > &) const | PLMD::vesselbase::StoreDataVessel | protected |
symmetric | PLMD::adjmat::AdjacencyMatrixVessel | private |
transformDerivatives(const unsigned ¤t, MultiValue &myvals, MultiValue &bvals) | PLMD::vesselbase::Vessel | inlinevirtual |
transformName(const std::string &name) | PLMD::vesselbase::Vessel | static |
undirectedGraph() const | PLMD::adjmat::AdjacencyMatrixVessel | |
usingLowMem() | PLMD::vesselbase::StoreDataVessel | inlineprotected |
Vessel(const VesselOptions &da) | PLMD::vesselbase::Vessel | explicit |
weightHasDerivatives() | PLMD::vesselbase::StoreDataVessel | inlineprotected |
~Vessel() | PLMD::vesselbase::Vessel | inlinevirtual |