PLMD::generic::FitToTemplate Member List

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

Action(const ActionOptions &)PLMD::Actionexplicit
ActionAtomistic(const ActionOptions &ao)PLMD::ActionAtomisticexplicit
ActionPilot(const ActionOptions &)PLMD::ActionPilotexplicit
ActionWithValue(const ActionOptions &ao)PLMD::ActionWithValueexplicit
activate()PLMD::Actionvirtual
addComponent(const std::string &name)PLMD::ActionWithValue
addComponentWithDerivatives(const std::string &name)PLMD::ActionWithValue
addDependency(Action *)PLMD::Action
addValue()PLMD::ActionWithValue
addValueWithDerivatives()PLMD::ActionWithValue
alignedPLMD::generic::FitToTemplateprivate
allowToAccessGlobalForces()PLMD::ActionAtomisticinline
apply()PLMD::generic::FitToTemplatevirtual
applyForces()PLMD::ActionAtomistic
atomsPLMD::ActionAtomisticprotected
beforeUpdate()PLMD::Actioninlinevirtual
calculate()PLMD::generic::FitToTemplatevirtual
calculateAtomicNumericalDerivatives(ActionWithValue *a, const unsigned &startnum)PLMD::ActionAtomistic
calculateFromPDB(const PDB &)PLMD::Action
PLMD::calculateNumericalDerivatives(ActionWithValue *a=NULL)PLMD::Actionvirtual
PLMD::ActionAtomistic::calculateNumericalDerivatives(ActionWithValue *a=NULL)PLMD::ActionAtomisticvirtual
centerPLMD::generic::FitToTemplateprivate
center_positionsPLMD::generic::FitToTemplateprivate
centeredpositionsPLMD::generic::FitToTemplateprivate
changeBox(const Tensor &newbox)PLMD::ActionAtomistic
checkFieldsAllowed()PLMD::ActionWithValueinlinevirtual
checkNeedsGradients() constPLMD::Actioninlinevirtual
PLMD::checkNumericalDerivatives() constPLMD::Actioninlinevirtual
PLMD::ActionWithValue::checkNumericalDerivatives() constPLMD::ActionWithValueinlinevirtual
checkRead()PLMD::Action
checkUpdate() constPLMD::Action
cite(const std::string &s)PLMD::Action
clearDependencies()PLMD::Action
clearDerivatives()PLMD::ActionWithValuevirtual
clearInputForces()PLMD::ActionWithValue
clearOptions()PLMD::Actionvirtual
clearOutputForces()PLMD::ActionAtomistic
commPLMD::Action
componentIsNotPeriodic(const std::string &name)PLMD::ActionWithValue
componentIsPeriodic(const std::string &name, const std::string &min, const std::string &max)PLMD::ActionWithValue
componentsAreNotOptional(Keywords &keys)PLMD::ActionWithValuestatic
copyOutput(const std::string &name) constPLMD::ActionWithValue
copyOutput(const unsigned &n) constPLMD::ActionWithValue
ddistdposPLMD::generic::FitToTemplateprivate
DDistDRefPLMD::generic::FitToTemplateprivate
deactivate()PLMD::Actioninlinevirtual
Dependencies typedefPLMD::Action
doNotCalculateDerivatives() constPLMD::ActionWithValueinlinevirtual
doNotForce()PLMD::ActionAtomisticinline
doNotRetrieve()PLMD::ActionAtomisticinline
drotdposPLMD::generic::FitToTemplateprivate
error(const std::string &msg) constPLMD::Action
exists(const std::string &name) constPLMD::ActionWithValue
exit(int c=0)PLMD::Action
fclose(FILE *fp)PLMD::Action
fflush()PLMD::Action
filesPLMD::Action
files_iterator typedefPLMD::Action
FitToTemplate(const ActionOptions &ao)PLMD::generic::FitToTemplateexplicit
fopen(const char *path, const char *mode)PLMD::Action
getAbsoluteIndex(int i) constPLMD::ActionAtomisticinline
getAbsoluteIndexes() constPLMD::ActionAtomisticinlinevirtual
getBox() constPLMD::ActionAtomisticinline
getCharge(int i) constPLMD::ActionAtomisticinline
getComponentsList() constPLMD::ActionWithValue
getComponentsVector() constPLMD::ActionWithValue
getCPT() constPLMD::Action
getDependencies() constPLMD::Actioninline
getDocumentation() constPLMD::Actionvirtual
getEnergy() constPLMD::ActionAtomisticinline
getExchangeStep() constPLMD::Action
getKeyword(const std::string &key)PLMD::Action
getLabel() constPLMD::Actioninline
getMass(int i) constPLMD::ActionAtomisticinline
getName() constPLMD::Actioninline
getNumberOfAtoms() constPLMD::ActionAtomisticinline
getNumberOfComponents() constPLMD::ActionWithValueinline
getNumberOfDerivatives()PLMD::generic::FitToTemplateinlinevirtual
getOutputQuantity(const unsigned j) constPLMD::ActionWithValueinline
getOutputQuantity(const std::string &name) constPLMD::ActionWithValueinline
getPbc() constPLMD::ActionAtomisticinline
getPntrToComponent(int i)PLMD::ActionWithValueprotected
getPntrToComponent(const std::string &name)PLMD::ActionWithValueprotected
getPntrToValue()PLMD::ActionWithValueprotected
getPosition(int) constPLMD::ActionAtomisticinline
getPosition(AtomNumber) constPLMD::ActionAtomisticinline
getPositions() constPLMD::ActionAtomisticinline
getRestart() constPLMD::Actioninline
getStep() constPLMD::Action
getStride() constPLMD::ActionPilot
getTime() constPLMD::Action
getTimeStep() constPLMD::Action
getTotAtoms() constPLMD::ActionAtomisticinline
getUnique() constPLMD::ActionAtomisticinline
interpretAtomList(std::vector< std::string > &strings, std::vector< AtomNumber > &t)PLMD::ActionAtomistic
isActive() constPLMD::Actioninline
isOptionOn(const std::string &s) constPLMD::Actioninline
keywordsPLMD::Action
PLMD::lockRequests()PLMD::Actioninlinevirtual
PLMD::ActionAtomistic::lockRequests()PLMD::ActionAtomisticinlinevirtual
logPLMD::Action
makeWhole()PLMD::ActionAtomistic
modifyForceOnEnergy()PLMD::ActionAtomisticinline
modifyForces()PLMD::ActionAtomisticinline
modifyGlobalForce(AtomNumber)PLMD::ActionAtomisticinline
modifyGlobalPbc()PLMD::ActionAtomisticinline
modifyGlobalVirial()PLMD::ActionAtomisticinline
modifyPosition(AtomNumber)PLMD::ActionAtomisticinline
modifyVirial()PLMD::ActionAtomisticinline
multi_sim_commPLMD::Action
noAnalyticalDerivatives(Keywords &keys)PLMD::ActionWithValuestatic
onStep() constPLMD::ActionPilotvirtual
parse(const std::string &key, T &t)PLMD::Action
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
pbcApply(std::vector< Vector > &dlist, unsigned max_index=0) constPLMD::ActionAtomistic
pbcDistance(const Vector &, const Vector &) constPLMD::ActionAtomistic
plumedPLMD::Action
positionsPLMD::generic::FitToTemplateprivate
prepare()PLMD::Actionvirtual
PLMD::readAtomsFromPDB(const PDB &)PLMD::Actioninlinevirtual
PLMD::ActionAtomistic::readAtomsFromPDB(const PDB &pdb)PLMD::ActionAtomisticvirtual
registerKeywords(Keywords &keys)PLMD::generic::FitToTemplatestatic
requestAtoms(const std::vector< AtomNumber > &a)PLMD::ActionAtomistic
retrieveAtoms()PLMD::ActionAtomisticvirtual
rmsdPLMD::generic::FitToTemplateprivate
rotationPLMD::generic::FitToTemplateprivate
runFinalJobs()PLMD::Actioninlinevirtual
setForcesOnAtoms(const std::vector< double > &forcesToApply, unsigned ind=0)PLMD::ActionAtomistic
setGradientsIfNeeded()PLMD::ActionWithValue
setNotPeriodic()PLMD::ActionWithValue
setOption(const std::string &s)PLMD::Actionvirtual
setPeriodic(const std::string &min, const std::string &max)PLMD::ActionWithValue
setValue(const double &d)PLMD::ActionWithValueinlineprotected
setValue(Value *, double)PLMD::ActionWithValue
shiftPLMD::generic::FitToTemplateprivate
turnOnDerivatives()PLMD::ActionWithValuevirtual
typePLMD::generic::FitToTemplateprivate
PLMD::unlockRequests()PLMD::Actioninlinevirtual
PLMD::ActionAtomistic::unlockRequests()PLMD::ActionAtomisticinlinevirtual
update()PLMD::Actioninlinevirtual
useCustomisableComponents(Keywords &keys)PLMD::ActionWithValuestatic
useNumericalDerivatives()PLMD::ActionWithValueinline
warning(const std::string &msg)PLMD::Action
weightsPLMD::generic::FitToTemplateprivate
~Action()PLMD::Actionvirtual
~ActionAtomistic()PLMD::ActionAtomistic
~ActionWithValue()PLMD::ActionWithValue
~FitToTemplate()PLMD::generic::FitToTemplate
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