PLMD::matrixtools::DiagonalizeMatrix Member List

This is the complete list of members for PLMD::matrixtools::DiagonalizeMatrix, including all inherited members.

Action(const ActionOptions &)PLMD::Actionexplicit
Action(const Action &a)=deletePLMD::Actionprivate
PLMD::ActionWithArguments(const ActionOptions &)PLMD::ActionWithArgumentsexplicit
ActionWithValue(const ActionOptions &ao)PLMD::ActionWithValueexplicit
activate()PLMD::Actionvirtual
activePLMD::Actionprivate
addComponent(const std::string &name, const std::vector< unsigned > &shape=std::vector< unsigned >())PLMD::ActionWithValue
addComponentWithDerivatives(const std::string &name, const std::vector< unsigned > &shape=std::vector< unsigned >())PLMD::ActionWithValuevirtual
addDependency(Action *)PLMD::Action
addForcesOnArguments(const unsigned &argstart, const std::vector< double > &forces, unsigned &ind, const std::string &c)PLMD::ActionWithArguments
addValue(const std::vector< unsigned > &shape=std::vector< unsigned >())PLMD::ActionWithValue
addValueWithDerivatives(const std::vector< unsigned > &shape=std::vector< unsigned >())PLMD::ActionWithValuevirtual
afterPLMD::Actionprivate
apply() overridePLMD::matrixtools::MatrixOperationBasevirtual
argumentsPLMD::ActionWithArgumentsprivate
beforeUpdate()PLMD::Actioninlinevirtual
bringBackInPbc(int i, double d1) constPLMD::ActionWithArgumentsinline
calculate() overridePLMD::matrixtools::DiagonalizeMatrixvirtual
calculateConstantValues(const bool &have_atoms)PLMD::ActionWithArgumentsvirtual
calculateFromPDB(const PDB &)PLMD::Action
calculateNumericalDerivatives(ActionWithValue *a=NULL) overridePLMD::ActionWithArgumentsvirtual
calculateOnUpdate()PLMD::ActionWithValuevirtual
castToActionAtomistic() noexceptPLMD::Actioninlinevirtual
castToActionForInterface() noexceptPLMD::Actioninlinevirtual
castToActionShortcut() noexceptPLMD::Actioninlinevirtual
castToActionToGetData() noexceptPLMD::Actioninlinevirtual
castToActionToPutData() noexceptPLMD::Actioninlinevirtual
castToActionWithArguments() noexcept finalPLMD::ActionWithArgumentsinlinevirtual
PLMD::castToActionWithValue() noexceptPLMD::Actioninlinevirtual
PLMD::ActionWithValue::castToActionWithValue() noexcept finalPLMD::ActionWithValueinlinevirtual
castToActionWithVirtualAtom() noexceptPLMD::Actioninlinevirtual
castToDomainDecomposition() noexceptPLMD::Actioninlinevirtual
castToPbcAction() noexceptPLMD::Actioninlinevirtual
checkFieldsAllowed()PLMD::ActionWithValueinlinevirtual
checkForDependency(Action *)PLMD::Action
checkForForces()PLMD::ActionWithValueprotected
checkNeedsGradients() constPLMD::Actioninlinevirtual
PLMD::checkNumericalDerivatives() constPLMD::Actioninlinevirtual
PLMD::ActionWithValue::checkNumericalDerivatives() const overridePLMD::ActionWithValueinlinevirtual
checkRead()PLMD::Action
checkUpdate() constPLMD::Action
cite(const std::string &s)PLMD::Action
clearDependencies()PLMD::Action
clearDerivatives(const bool &force=false)PLMD::ActionWithValuevirtual
clearInputForces(const bool &force=false)PLMD::ActionWithValuevirtual
clearOptions()PLMD::Actionvirtual
commPLMD::Action
componentIsNotPeriodic(const std::string &name)PLMD::ActionWithValue
componentIsPeriodic(const std::string &name, const std::string &min, const std::string &max)PLMD::ActionWithValue
copyOutput(const std::string &name) constPLMD::ActionWithValue
copyOutput(const unsigned &n) constPLMD::ActionWithValue
deactivate()PLMD::Actioninlinevirtual
defaultsPLMD::Actionprivate
Dependencies typedefPLMD::Action
desired_vectorsPLMD::matrixtools::DiagonalizeMatrixprivate
DiagonalizeMatrix(const ActionOptions &)PLMD::matrixtools::DiagonalizeMatrixexplicit
difference(int, double, double) constPLMD::ActionWithArgumentsinline
doCheckPointPLMD::Actionprivate
doNotCalculateDerivatives() constPLMD::ActionWithValueinlinevirtual
eigvalsPLMD::matrixtools::DiagonalizeMatrixprivate
eigvecsPLMD::matrixtools::DiagonalizeMatrixprivate
error(const std::string &msg) constPLMD::Action
exists(const std::string &name) constPLMD::ActionWithValue
exit(int c=0)PLMD::Action
expandArgKeywordInPDB(const PDB &pdb)PLMD::ActionWithArgumentsprotected
fclose(FILE *fp)PLMD::Action
fflush()PLMD::Action
filesPLMD::Action
firststepPLMD::ActionWithValueprivate
fopen(const char *path, const char *mode)PLMD::Action
forcesForApplyPLMD::ActionWithValueprivate
getArgument(const unsigned n) constPLMD::ActionWithArgumentsinline
getArguments() constPLMD::ActionWithArgumentsinlinevirtual
getComponent(const std::string &name) constPLMD::ActionWithValueprivate
getComponentsList() constPLMD::ActionWithValue
getComponentsVector() constPLMD::ActionWithValue
getConstPntrToComponent(int i) constPLMD::ActionWithValueprotected
getCPT() constPLMD::Action
getDefaultString() constPLMD::Actioninline
getDependencies() constPLMD::Actioninline
getExchangeStep() constPLMD::Action
getForceOnMatrixElement(const unsigned &jrow, const unsigned &krow) const overridePLMD::matrixtools::DiagonalizeMatrixvirtual
getForcesToApply() constPLMD::ActionWithValueinlineprotected
getKBoltzmann() constPLMD::Actionprotected
getkBT()PLMD::Action
getKeyword(const std::string &key)PLMD::Action
getLabel() constPLMD::Actioninline
getMatrixColumnTitles(std::vector< std::string > &argnames) constPLMD::ActionWithValuevirtual
getName() constPLMD::Actioninline
getNumberOfArguments() constPLMD::ActionWithArgumentsinlinevirtual
getNumberOfComponents() constPLMD::ActionWithValueinline
getNumberOfDerivatives() overridePLMD::matrixtools::DiagonalizeMatrixinlinevirtual
getOutputComponentDescription(const std::string &cname, const Keywords &keys) constPLMD::ActionWithValuevirtual
getOutputQuantity(const unsigned j) constPLMD::ActionWithValueinline
getOutputQuantity(const std::string &name) constPLMD::ActionWithValueinline
getPntrToArgument(const unsigned n) constPLMD::ActionWithArgumentsinline
getPntrToComponent(int i)PLMD::ActionWithValueprotected
getPntrToComponent(const std::string &name)PLMD::ActionWithValueprotected
getPntrToValue()PLMD::ActionWithValueinlineprotected
getProjection(unsigned i, unsigned j) constPLMD::ActionWithArguments
getRestart() constPLMD::Actioninline
getStep() constPLMD::Action
getTime() constPLMD::Action
getTimeStep() constPLMD::Action
getUnits() constPLMD::Actionprotected
interpretArgumentList(const std::vector< std::string > &c, const ActionSet &as, Action *action, std::vector< Value * > &arg)PLMD::ActionWithArgumentsstatic
isActive() constPLMD::Actioninline
isOptionOn(const std::string &s) constPLMD::Actioninline
keywordsPLMD::Action
labelPLMD::Actionprivate
linePLMD::Actionprivate
lockRequestArgumentsPLMD::ActionWithArgumentsprivate
lockRequests() overridePLMD::ActionWithArgumentsinlinevirtual
logPLMD::Action
MatrixOperationBase(const ActionOptions &)PLMD::matrixtools::MatrixOperationBaseexplicit
multi_sim_commPLMD::Action
mymatrixPLMD::matrixtools::DiagonalizeMatrixprivate
namePLMD::Actionprivate
never_activatePLMD::Actionprivate
noAnalyticalDerivatives(Keywords &keys)PLMD::ActionWithValuestatic
noderivPLMD::ActionWithValueprivate
numericalDerivativesPLMD::ActionWithValueprivate
operator=(const Action &a)=deletePLMD::Actionprivate
optionsPLMD::Actionprivate
pairsPLMD::matrixtools::MatrixOperationBaseprivate
parse(const std::string &key, T &t)PLMD::Action
parseArgumentList(const std::string &key, std::vector< Value * > &args)PLMD::ActionWithArguments
parseArgumentList(const std::string &key, int i, std::vector< Value * > &args)PLMD::ActionWithArguments
parseFlag(const std::string &key, bool &t)PLMD::Action
parseNumbered(const std::string &key, const int no, T &t)PLMD::Action
parseNumberedVector(const std::string &key, const int no, std::vector< T > &t)PLMD::Action
parseVector(const std::string &key, std::vector< T > &t)PLMD::Action
plumedPLMD::Action
prepare() overridePLMD::matrixtools::DiagonalizeMatrixvirtual
readAtomsFromPDB(const PDB &)PLMD::Actioninlinevirtual
registerKeywords(Keywords &keys)PLMD::matrixtools::DiagonalizeMatrixstatic
replica_indexPLMD::Actionprivate
requestArguments(const std::vector< Value * > &arg)PLMD::ActionWithArguments
requestExtraDependencies(const std::vector< Value * > &extra)PLMD::ActionWithArguments
resetStoredTimestep()PLMD::Action
restartPLMD::Actionprivate
retrieveFullMatrix(Matrix< double > &mymatrix)PLMD::matrixtools::MatrixOperationBaseprotected
runFinalJobs()PLMD::Actioninlinevirtual
setGradients(Value *myval, unsigned &start) constPLMD::ActionWithArguments
setGradientsIfNeeded()PLMD::ActionWithValuevirtual
setNotPeriodic()PLMD::ActionWithValue
setOption(const std::string &s)PLMD::Actionvirtual
setPeriodic(const std::string &min, const std::string &max)PLMD::ActionWithValue
setupConstantValues(const bool &have_atoms)PLMD::Action
setValue(const double &d)PLMD::ActionWithValueinlineprotected
setValue(Value *, double)PLMD::ActionWithValue
timestepPLMD::Actionprivate
turnOnDerivatives()PLMD::ActionWithValuevirtual
unlockRequests() overridePLMD::ActionWithArgumentsinlinevirtual
update()PLMD::Actioninlinevirtual
update_fromPLMD::Actionprivate
update_untilPLMD::Actionprivate
useCustomisableComponents(Keywords &keys)PLMD::ActionWithValuestatic
useNumericalDerivatives()PLMD::ActionWithValueinline
usingNaturalUnits() constPLMD::Actionprotected
valsPLMD::matrixtools::MatrixOperationBaseprivate
valsToForcePLMD::ActionWithValueprivate
valuesPLMD::ActionWithValueprivate
warning(const std::string &msg)PLMD::Action
writeInGraph() constPLMD::Actionvirtual
~Action()PLMD::Actionvirtual
~ActionWithArguments()PLMD::ActionWithArgumentsinlinevirtual
~ActionWithValue()PLMD::ActionWithValue
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