PLMD::ActionWithMatrix Member List

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

Action(const ActionOptions &)PLMD::Actionexplicit
Action(const Action &a)=deletePLMD::Actionprivate
action_to_do_afterPLMD::ActionWithVectorprivate
action_to_do_beforePLMD::ActionWithVectorprivate
ActionAtomistic(const ActionOptions &ao)PLMD::ActionAtomisticexplicit
actionHasForces()PLMD::ActionAtomisticvirtual
actionInChain() constPLMD::ActionWithVectorinline
ActionWithArguments(const ActionOptions &)PLMD::ActionWithArgumentsexplicit
ActionWithMatrix(const ActionOptions &)PLMD::ActionWithMatrixexplicit
ActionWithValue(const ActionOptions &ao)PLMD::ActionWithValueexplicit
ActionWithVector(const ActionOptions &)PLMD::ActionWithVectorexplicit
activate()PLMD::Actionvirtual
activePLMD::Actionprivate
active_tasksPLMD::ActionWithVectorprivate
addActionToChain(const std::vector< std::string > &alabels, ActionWithVector *act)PLMD::ActionWithVectorprivate
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
addDerivativeOnMatrixArgument(const bool &inchain, const unsigned &ival, const unsigned &jarg, const unsigned &irow, const unsigned &jcol, const double &der, MultiValue &myvals) constPLMD::ActionWithMatrixinlineprotected
addDerivativeOnVectorArgument(const bool &inchain, const unsigned &ival, const unsigned &jarg, const unsigned &jelem, const double &der, MultiValue &myvals) constPLMD::ActionWithMatrixinlineprotected
addForce(const std::pair< std::size_t, std::size_t > &a, const Vector &f)PLMD::ActionAtomisticinline
addForcesOnArguments(const unsigned &argstart, const std::vector< double > &forces, unsigned &ind, const std::string &c)PLMD::ActionWithArguments
addForcesToInput(const std::vector< double > &forcesToApply, unsigned &ind)PLMD::ActionWithVectorprivate
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()PLMD::ActionWithVectorvirtual
areAllTasksRequired(std::vector< ActionWithVector * > &task_reducing_actions)PLMD::ActionWithVectorinlinevirtual
arg_deriv_startsPLMD::ActionWithVectorprotected
argumentDependsOn(const std::string &headstr, ActionWithVector *faction, Value *thearg)PLMD::ActionWithVectorprotected
argumentsPLMD::ActionWithArgumentsprivate
atom_value_indPLMD::ActionAtomisticprivate
atom_value_ind_groupedPLMD::ActionAtomisticprivate
atomsWereRetrievedPLMD::ActionWithVectorprivate
beforeUpdate()PLMD::Actioninlinevirtual
boxValuePLMD::ActionAtomisticprivate
bringBackInPbc(int i, double d1) constPLMD::ActionWithArgumentsinline
broadcastThatTasksAreReduced(ActionWithVector *aselect)PLMD::ActionWithVectorprivate
bufferPLMD::ActionWithVectorprivate
buildArgumentStore(const unsigned &argstart)PLMD::ActionWithVectorprotected
calculate() overridePLMD::ActionWithMatrixvirtual
calculateAtomicNumericalDerivatives(ActionWithValue *a, const unsigned &startnum)PLMD::ActionAtomistic
calculateConstantValues(const bool &have_atoms)PLMD::ActionWithArgumentsvirtual
calculateFromPDB(const PDB &)PLMD::Action
calculateNumericalDerivatives(ActionWithValue *av) overridePLMD::ActionWithVectorvirtual
calculateOnUpdate()PLMD::ActionWithValuevirtual
canBeAfterInChain(ActionWithVector *av)PLMD::ActionWithVectorinlinevirtual
canReduceTasks(std::vector< ActionWithVector * > &task_reducing_actions)PLMD::ActionWithVectorprivate
castToActionAtomistic() noexcept finalPLMD::ActionAtomisticinlinevirtual
castToActionForInterface() noexceptPLMD::Actioninlinevirtual
castToActionShortcut() noexceptPLMD::Actioninlinevirtual
castToActionToGetData() noexceptPLMD::Actioninlinevirtual
castToActionToPutData() noexceptPLMD::Actioninlinevirtual
PLMD::castToActionWithArguments() noexceptPLMD::Actioninlinevirtual
PLMD::ActionWithArguments::castToActionWithArguments() noexcept finalPLMD::ActionWithArgumentsinlinevirtual
PLMD::castToActionWithValue() noexceptPLMD::Actioninlinevirtual
PLMD::ActionWithValue::castToActionWithValue() noexcept finalPLMD::ActionWithValueinlinevirtual
castToActionWithVirtualAtom() noexceptPLMD::Actioninlinevirtual
castToDomainDecomposition() noexceptPLMD::Actioninlinevirtual
castToPbcAction() noexceptPLMD::Actioninlinevirtual
changeBox(const Tensor &newbox)PLMD::ActionAtomistic
chargesPLMD::ActionAtomisticprivate
chargesWereSetPLMD::ActionAtomisticprotected
chargevPLMD::ActionAtomisticprivate
checkChainForNonScalarForces() constPLMD::ActionWithVectorprivate
checkComponentsForForce() constPLMD::ActionWithVectorprivate
checkFieldsAllowed()PLMD::ActionWithValueinlinevirtual
checkForDependency(Action *)PLMD::Action
checkForForces()PLMD::ActionWithVectorprotected
checkForGrids(unsigned &nder) constPLMD::ActionWithVectorprivate
checkForTaskForce(const unsigned &itask, const Value *myval) const overridePLMD::ActionWithMatrixvirtual
checkNeedsGradients() constPLMD::Actioninlinevirtual
PLMD::checkNumericalDerivatives() constPLMD::Actioninlinevirtual
PLMD::ActionWithValue::checkNumericalDerivatives() const overridePLMD::ActionWithValueinlinevirtual
checkRead()PLMD::Action
checkTaskStatus(const unsigned &taskno, int &flag) constPLMD::ActionWithVectorinlinevirtual
checkUpdate() constPLMD::Action
cite(const std::string &s)PLMD::Action
clearDependencies()PLMD::Action
clearDerivatives(const bool &force=false) overridePLMD::ActionWithVectorvirtual
clearInputForces(const bool &force=false) overridePLMD::ActionWithVectorvirtual
clearMatrixElements(MultiValue &myvals) constPLMD::ActionWithMatrixprivate
clearOnEachCyclePLMD::ActionWithMatrixprotected
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
difference(int, double, double) constPLMD::ActionWithArgumentsinline
doCheckPointPLMD::Actionprivate
done_in_chainPLMD::ActionWithVectorprotected
doNotCalculateDerivatives() constPLMD::ActionWithValueinlinevirtual
doNotForce()PLMD::ActionAtomisticinline
donotforcePLMD::ActionAtomisticprivate
doNotRetrieve()PLMD::ActionAtomisticinline
donotretrievePLMD::ActionAtomisticprivate
energyPLMD::ActionAtomisticprivate
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
finishChainBuild(ActionWithVector *act)PLMD::ActionWithMatrixvirtual
finishComputations(const std::vector< double > &buf)PLMD::ActionWithVector
firststepPLMD::ActionWithValueprivate
fopen(const char *path, const char *mode)PLMD::Action
forceOnEnergyPLMD::ActionAtomisticprivate
forceOnExtraCVPLMD::ActionAtomisticprivate
forcesPLMD::ActionAtomisticprivate
forcesForApplyPLMD::ActionWithValueprivate
gatherAccumulators(const unsigned &taskCode, const MultiValue &myvals, std::vector< double > &buffer) constPLMD::ActionWithVectorprivate
gatherForces(const unsigned &i, const MultiValue &myvals, std::vector< double > &forces) constPLMD::ActionWithVectorprivate
gatherForcesOnStoredValue(const Value *myval, const unsigned &itask, const MultiValue &myvals, std::vector< double > &forces) const overridePLMD::ActionWithMatrixvirtual
gatherProcesses(std::vector< double > &buffer) overridePLMD::ActionWithMatrixvirtual
gatherStoredValue(const unsigned &valindex, const unsigned &code, const MultiValue &myvals, const unsigned &bufstart, std::vector< double > &buffer) const overridePLMD::ActionWithMatrixvirtual
gatherThreads(const unsigned &nt, const unsigned &bufsize, const std::vector< double > &omp_buffer, std::vector< double > &buffer, MultiValue &myvals) overridePLMD::ActionWithMatrixvirtual
getAbsoluteIndex(int i) constPLMD::ActionAtomisticinline
getAbsoluteIndexes() constPLMD::ActionAtomisticinlinevirtual
getActionWithDerivatives(ActionWithVector *depaction)PLMD::ActionWithVectorprivate
getAdditionalTasksRequired(ActionWithVector *action, std::vector< unsigned > &atasks)PLMD::ActionWithVectorvirtual
getAllActionLabelsInChain(std::vector< std::string > &mylabels) constPLMD::ActionWithVector
getAllActionLabelsInMatrixChain(std::vector< std::string > &mylabels) const overridePLMD::ActionWithMatrixvirtual
getArgument(const unsigned n) constPLMD::ActionWithArgumentsinline
getArgumentElement(const unsigned &ic, const unsigned &jelem, const MultiValue &myvals) constPLMD::ActionWithMatrixinlineprotected
getArguments() constPLMD::ActionWithArgumentsinlinevirtual
getAtomValuesFromPlumedObject(const PlumedMain &plumed, std::vector< Value * > &xpos, std::vector< Value * > &ypos, std::vector< Value * > &zpos, std::vector< Value * > &masv, std::vector< Value * > &chargev)PLMD::ActionAtomisticstatic
getBox() constPLMD::ActionAtomisticinline
getCharge(int i) constPLMD::ActionAtomisticinline
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
getElementOfMatrixArgument(const unsigned &imat, const unsigned &irow, const unsigned &jcol, const MultiValue &myvals) constPLMD::ActionWithMatrixinlineprotected
getEnergy() constPLMD::ActionAtomisticinline
getExchangeStep() constPLMD::Action
getFirstActionInChain() constPLMD::ActionWithVector
getFirstActionInChain()PLMD::ActionWithVector
getFirstMatrixInChain() constPLMD::ActionWithMatrix
getForce(const std::pair< std::size_t, std::size_t > &a) constPLMD::ActionAtomisticinline
getForcesToApply() constPLMD::ActionWithValueinlineprotected
getForceTasks(std::vector< unsigned > &force_tasks) constPLMD::ActionWithVectorprivate
getGlobalPosition(const std::pair< std::size_t, std::size_t > &) constPLMD::ActionAtomisticinline
getGradient(const unsigned &ind, Vector &deriv, std::map< AtomNumber, Vector > &gradients) constPLMD::ActionAtomistic
getKBoltzmann() constPLMD::Actionprotected
getkBT()PLMD::Action
getKeyword(const std::string &key)PLMD::Action
getLabel() constPLMD::Actioninline
getListOfActiveTasks(ActionWithVector *action)PLMD::ActionWithVectorprotected
getMass(int i) constPLMD::ActionAtomisticinline
getMatrixColumnTitles(std::vector< std::string > &argnames) constPLMD::ActionWithValuevirtual
getName() constPLMD::Actioninline
getNumberOfArguments() constPLMD::ActionWithArgumentsinlinevirtual
getNumberOfAtoms() constPLMD::ActionAtomisticinline
getNumberOfColumns() const =0PLMD::ActionWithMatrixpure virtual
getNumberOfComponents() constPLMD::ActionWithValueinline
getNumberOfDerivatives()=0PLMD::ActionWithValuepure virtual
getNumberOfStoredValues(Value *startat, unsigned &nvals, const unsigned &astart, const std::vector< Value * > &stopat)PLMD::ActionWithVectorprivate
getNumberOfStreamedDerivatives(unsigned &nderivatives, Value *stopat)PLMD::ActionWithVector
getNumberOfStreamedQuantities(const std::string &headstr, unsigned &nquants, unsigned &nmat, unsigned &maxcol, unsigned &nbookeeping)PLMD::ActionWithVectorprivate
getNumberOfTasks(unsigned &ntasks)PLMD::ActionWithVectorvirtual
getOutputComponentDescription(const std::string &cname, const Keywords &keys) constPLMD::ActionWithValuevirtual
getOutputQuantity(const unsigned j) constPLMD::ActionWithValueinline
getOutputQuantity(const std::string &name) constPLMD::ActionWithValueinline
getPbc() constPLMD::ActionAtomisticinline
getPntrToArgument(const unsigned n) constPLMD::ActionWithArgumentsinline
getPntrToComponent(int i)PLMD::ActionWithValueprotected
getPntrToComponent(const std::string &name)PLMD::ActionWithValueprotected
getPntrToValue()PLMD::ActionWithValueinlineprotected
getPosition(int) constPLMD::ActionAtomisticinline
getPositions() constPLMD::ActionAtomisticinline
getProjection(unsigned i, unsigned j) constPLMD::ActionWithArguments
getRestart() constPLMD::Actioninline
getSizeOfBuffer(const unsigned &nactive_tasks, unsigned &bufsize)PLMD::ActionWithVectorprivate
getStep() constPLMD::Action
getTime() constPLMD::Action
getTimeStep() constPLMD::Action
getTotalMatrixBookeeping(unsigned &stashsize)PLMD::ActionWithMatrixprivate
getTotAtoms() constPLMD::ActionAtomistic
getUnique() constPLMD::ActionAtomisticinline
getUniqueLocal() constPLMD::ActionAtomisticinline
getUnits() constPLMD::Actionprotected
getValueIndices(const AtomNumber &i) constPLMD::ActionAtomisticprotected
getVirial() constPLMD::ActionAtomistic
hasStoredArguments() constPLMD::ActionWithVector
indexesPLMD::ActionAtomisticprivate
interpretArgumentList(const std::vector< std::string > &c, const ActionSet &as, Action *action, std::vector< Value * > &arg)PLMD::ActionWithArgumentsstatic
interpretAtomList(std::vector< std::string > &strings, std::vector< AtomNumber > &t)PLMD::ActionAtomistic
interpretAtomList(std::vector< std::string > &strings, const std::vector< Value * > &xpos, Action *action, std::vector< AtomNumber > &t)PLMD::ActionAtomisticstatic
isActive() constPLMD::Actioninline
isAdjacencyMatrix() constPLMD::ActionWithMatrixinlinevirtual
isInSubChain(unsigned &nder)PLMD::ActionWithVectorinlinevirtual
isOptionOn(const std::string &s) constPLMD::Actioninline
keywordsPLMD::Action
labelPLMD::Actionprivate
linePLMD::Actionprivate
lockRequestArgumentsPLMD::ActionWithArgumentsprivate
lockRequestAtomsPLMD::ActionAtomisticprivate
lockRequests() overridePLMD::ActionWithVectorvirtual
logPLMD::Action
makeWhole()PLMD::ActionAtomistic
massesPLMD::ActionAtomisticprivate
massesWereSetPLMD::ActionAtomisticprotected
masvPLMD::ActionAtomisticprivate
matrix_bookeepingPLMD::ActionWithMatrixprivate
matrix_to_do_afterPLMD::ActionWithMatrixprivate
matrix_to_do_beforePLMD::ActionWithMatrixprivate
matrixChainContinues() constPLMD::ActionWithMatrixinlineprotected
modifyForceOnEnergy()PLMD::ActionAtomisticinline
multi_sim_commPLMD::Action
namePLMD::Actionprivate
never_activatePLMD::Actionprivate
never_reduce_tasksPLMD::ActionWithVectorprivate
next_action_in_chainPLMD::ActionWithMatrixprivate
noAnalyticalDerivatives(Keywords &keys)PLMD::ActionWithValuestatic
noderivPLMD::ActionWithValueprivate
numericalDerivativesPLMD::ActionWithValueprivate
operator=(const Action &a)=deletePLMD::Actionprivate
optionsPLMD::Actionprivate
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
parseAtomList(const std::string &key, std::vector< AtomNumber > &t)PLMD::ActionAtomistic
parseAtomList(const std::string &key, const int num, std::vector< AtomNumber > &t)PLMD::ActionAtomistic
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
pbcPLMD::ActionAtomisticprivate
pbc_fwdPLMD::ActionAtomisticprivate
pbcApply(std::vector< Vector > &dlist, unsigned max_index=0) constPLMD::ActionAtomistic
pbcDistance(const Vector &, const Vector &) constPLMD::ActionAtomisticinline
performTask(const unsigned &task_index, MultiValue &myvals) const overridePLMD::ActionWithMatrixvirtual
performTask(const std::string &controller, const unsigned &index1, const unsigned &index2, MultiValue &myvals) const =0PLMD::ActionWithMatrixpure virtual
plumedPLMD::Action
positionsPLMD::ActionAtomisticprivate
prepare() overridePLMD::ActionWithVectorvirtual
readAtomsFromPDB(const PDB &pdb) overridePLMD::ActionAtomisticvirtual
reallyBuildArgumentStore(const unsigned &argstart)PLMD::ActionWithVectorprivate
reduce_tasksPLMD::ActionWithVectorprivate
registerKeywords(Keywords &keys)PLMD::ActionWithMatrixstatic
replica_indexPLMD::Actionprivate
requestArguments(const std::vector< Value * > &arg)PLMD::ActionWithArguments
requestAtoms(const std::vector< AtomNumber > &a, const bool clearDep=true)PLMD::ActionAtomistic
requestExtraDependencies(const std::vector< Value * > &extra)PLMD::ActionWithArguments
resetStoredTimestep()PLMD::Action
restartPLMD::Actionprivate
retrieveAtoms(const bool &force=false) overridePLMD::ActionWithVectorvirtual
runAllTasks()PLMD::ActionWithVectorprotected
runEndOfRowJobs(const unsigned &ival, const std::vector< unsigned > &indices, MultiValue &myvals) const =0PLMD::ActionWithMatrixpure virtual
runFinalJobs()PLMD::Actioninlinevirtual
runInSerial() constPLMD::ActionWithVectorinlineprotected
runTask(const std::string &controller, const unsigned &current, const unsigned colno, MultiValue &myvals) constPLMD::ActionWithMatrixprivate
serialPLMD::ActionWithVectorprivate
setExtraCV(const std::string &name)PLMD::ActionAtomisticprotected
setForcesOnAtoms(const std::vector< double > &forcesToApply, unsigned &ind)PLMD::ActionAtomistic
setForcesOnCell(const std::vector< double > &forcesToApply, unsigned &ind)PLMD::ActionAtomistic
setForcesOnCell(const double *forcesToApply, std::size_t size, unsigned &ind)PLMD::ActionAtomistic
setGlobalPosition(const std::pair< std::size_t, std::size_t > &, const Vector &pos)PLMD::ActionAtomisticinline
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
setupForTask(const unsigned &task_index, std::vector< unsigned > &indices, MultiValue &myvals) const =0PLMD::ActionWithMatrixpure virtual
setupStreamedComponents(const std::string &headstr, unsigned &nquants, unsigned &nmat, unsigned &maxcol, unsigned &nbookeeping) overridePLMD::ActionWithMatrixvirtual
setValue(const double &d)PLMD::ActionWithValueinlineprotected
setValue(Value *, double)PLMD::ActionWithValue
switchTaskReduction(const bool &task_reduction, ActionWithVector *aselect)PLMD::ActionWithVectorinlinevirtual
task_control_listPLMD::ActionWithVectorprivate
taskIsActive(const unsigned &current, int &flag) constPLMD::ActionWithVectorprivate
timestepPLMD::Actionprivate
transferNonZeroMatrixElementsToValues(unsigned &nval, const std::vector< unsigned > &matbook)PLMD::ActionWithMatrixprivate
turnOnDerivatives()PLMD::ActionWithValuevirtual
uniquePLMD::ActionAtomisticprivate
unique_localPLMD::ActionAtomisticprivate
unique_local_needs_updatePLMD::ActionAtomisticprivate
unlockRequests() overridePLMD::ActionWithVectorvirtual
update()PLMD::Actioninlinevirtual
update_fromPLMD::Actionprivate
update_untilPLMD::Actionprivate
updateAdditionalIndices(const unsigned &ostrn, MultiValue &myvals) constPLMD::ActionWithVectorinlinevirtual
updateAllNeighbourLists()PLMD::ActionWithMatrixprivate
updateForceTasksFromValue(const Value *myval, std::vector< unsigned > &force_tasks) constPLMD::ActionWithVectorvirtual
updateNeighbourList()PLMD::ActionWithMatrixinlinevirtual
updateTaskListReductionStatus()PLMD::ActionWithVectorprotected
updateTaskReductionFlag(bool &head_reduce_tasks)PLMD::ActionWithVectorprivate
updateUniqueLocal(const bool &useunique, const std::vector< int > &g2l)PLMD::ActionAtomisticprivate
useCustomisableComponents(Keywords &keys)PLMD::ActionWithValuestatic
useNumericalDerivatives()PLMD::ActionWithValueinline
usingNaturalUnits() constPLMD::Actionprotected
valsToForcePLMD::ActionWithValueprivate
value_dependsPLMD::ActionAtomisticprivate
valuesPLMD::ActionWithValueprivate
warning(const std::string &msg)PLMD::Action
writeInGraph() constPLMD::Actionvirtual
xposPLMD::ActionAtomisticprivate
yposPLMD::ActionAtomisticprivate
zposPLMD::ActionAtomisticprivate
~Action()PLMD::Actionvirtual
~ActionAtomistic()PLMD::ActionAtomistic
~ActionWithArguments()PLMD::ActionWithArgumentsinlinevirtual
~ActionWithMatrix()PLMD::ActionWithMatrixvirtual
~ActionWithValue()PLMD::ActionWithValue
~ActionWithVector()PLMD::ActionWithVectorvirtual