Action(const ActionOptions &) | PLMD::Action | explicit |
Action(const Action &a)=delete | PLMD::Action | private |
ActionWithArguments(const ActionOptions &) | PLMD::ActionWithArguments | explicit |
ActionWithValue(const ActionOptions &ao) | PLMD::ActionWithValue | explicit |
activate() | PLMD::Action | virtual |
active | PLMD::Action | private |
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::ActionWithValue | virtual |
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::ActionWithValue | virtual |
after | PLMD::Action | private |
apply() override | PLMD::bias::ReweightBase | inlinevirtual |
arguments | PLMD::ActionWithArguments | private |
beforeUpdate() | PLMD::Action | inlinevirtual |
bringBackInPbc(int i, double d1) const | PLMD::ActionWithArguments | inline |
buildsWeightStore() const | PLMD::bias::ReweightBase | inlinevirtual |
calculate() override | PLMD::bias::ReweightBase | virtual |
calculateConstantValues(const bool &have_atoms) | PLMD::ActionWithArguments | virtual |
calculateFromPDB(const PDB &) | PLMD::Action | |
PLMD::calculateNumericalDerivatives(ActionWithValue *a=NULL) | PLMD::Action | virtual |
PLMD::ActionWithArguments::calculateNumericalDerivatives(ActionWithValue *a=NULL) override | PLMD::ActionWithArguments | virtual |
calculateOnUpdate() | PLMD::ActionWithValue | virtual |
calculateWeights(const unsigned &nframes) | PLMD::bias::ReweightBase | inlinevirtual |
castToActionAtomistic() noexcept | PLMD::Action | inlinevirtual |
castToActionForInterface() noexcept | PLMD::Action | inlinevirtual |
castToActionShortcut() noexcept | PLMD::Action | inlinevirtual |
castToActionToGetData() noexcept | PLMD::Action | inlinevirtual |
castToActionToPutData() noexcept | PLMD::Action | inlinevirtual |
PLMD::castToActionWithArguments() noexcept | PLMD::Action | inlinevirtual |
PLMD::ActionWithArguments::castToActionWithArguments() noexcept final | PLMD::ActionWithArguments | inlinevirtual |
castToActionWithValue() noexcept final | PLMD::ActionWithValue | inlinevirtual |
castToActionWithVirtualAtom() noexcept | PLMD::Action | inlinevirtual |
castToDomainDecomposition() noexcept | PLMD::Action | inlinevirtual |
castToPbcAction() noexcept | PLMD::Action | inlinevirtual |
checkFieldsAllowed() | PLMD::ActionWithValue | inlinevirtual |
checkForDependency(Action *) | PLMD::Action | |
checkForForces() | PLMD::ActionWithValue | protected |
checkNeedsGradients() const | PLMD::Action | inlinevirtual |
checkNumericalDerivatives() const override | PLMD::ActionWithValue | inlinevirtual |
checkRead() | PLMD::Action | |
checkUpdate() const | PLMD::Action | |
cite(const std::string &s) | PLMD::Action | |
clearData() | PLMD::bias::ReweightBase | inlinevirtual |
clearDependencies() | PLMD::Action | |
clearDerivatives(const bool &force=false) | PLMD::ActionWithValue | virtual |
clearInputForces(const bool &force=false) | PLMD::ActionWithValue | virtual |
clearOptions() | PLMD::Action | virtual |
comm | PLMD::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) const | PLMD::ActionWithValue | |
copyOutput(const unsigned &n) const | PLMD::ActionWithValue | |
deactivate() | PLMD::Action | inlinevirtual |
defaults | PLMD::Action | private |
Dependencies typedef | PLMD::Action | |
difference(int, double, double) const | PLMD::ActionWithArguments | inline |
doCheckPoint | PLMD::Action | private |
doNotCalculateDerivatives() const | PLMD::ActionWithValue | inlinevirtual |
error(const std::string &msg) const | PLMD::Action | |
exists(const std::string &name) const | PLMD::ActionWithValue | |
exit(int c=0) | PLMD::Action | |
expandArgKeywordInPDB(const PDB &pdb) | PLMD::ActionWithArguments | protected |
fclose(FILE *fp) | PLMD::Action | |
fflush() | PLMD::Action | |
files | PLMD::Action | |
firststep | PLMD::ActionWithValue | private |
fopen(const char *path, const char *mode) | PLMD::Action | |
forcesForApply | PLMD::ActionWithValue | private |
getArgument(const unsigned n) const | PLMD::ActionWithArguments | inline |
getArguments() const | PLMD::ActionWithArguments | inlinevirtual |
getComponent(const std::string &name) const | PLMD::ActionWithValue | private |
getComponentsList() const | PLMD::ActionWithValue | |
getComponentsVector() const | PLMD::ActionWithValue | |
getConstPntrToComponent(int i) const | PLMD::ActionWithValue | protected |
getCPT() const | PLMD::Action | |
getDefaultString() const | PLMD::Action | inline |
getDependencies() const | PLMD::Action | inline |
getExchangeStep() const | PLMD::Action | |
getForcesToApply() const | PLMD::ActionWithValue | inlineprotected |
getKBoltzmann() const | PLMD::Action | protected |
getkBT() | PLMD::Action | |
getKeyword(const std::string &key) | PLMD::Action | |
getLabel() const | PLMD::Action | inline |
getLogWeight() override | PLMD::bias::ReweightMetad | virtual |
getMatrixColumnTitles(std::vector< std::string > &argnames) const | PLMD::ActionWithValue | virtual |
getName() const | PLMD::Action | inline |
getNumberOfArguments() const | PLMD::ActionWithArguments | inlinevirtual |
getNumberOfComponents() const | PLMD::ActionWithValue | inline |
getNumberOfDerivatives() override | PLMD::bias::ReweightBase | inlinevirtual |
getOutputComponentDescription(const std::string &cname, const Keywords &keys) const | PLMD::ActionWithValue | virtual |
getOutputQuantity(const unsigned j) const | PLMD::ActionWithValue | inline |
getOutputQuantity(const std::string &name) const | PLMD::ActionWithValue | inline |
getPntrToArgument(const unsigned n) const | PLMD::ActionWithArguments | inline |
getPntrToComponent(int i) | PLMD::ActionWithValue | protected |
getPntrToComponent(const std::string &name) | PLMD::ActionWithValue | protected |
getPntrToValue() | PLMD::ActionWithValue | inlineprotected |
getProjection(unsigned i, unsigned j) const | PLMD::ActionWithArguments | |
getRestart() const | PLMD::Action | inline |
getStep() const | PLMD::Action | |
getTime() const | PLMD::Action | |
getTimeStep() const | PLMD::Action | |
getUnits() const | PLMD::Action | protected |
getWeight(const unsigned &iweight) const | PLMD::bias::ReweightBase | inlinevirtual |
interpretArgumentList(const std::vector< std::string > &c, const ActionSet &as, Action *action, std::vector< Value * > &arg) | PLMD::ActionWithArguments | static |
isActive() const | PLMD::Action | inline |
isOptionOn(const std::string &s) const | PLMD::Action | inline |
keywords | PLMD::Action | |
label | PLMD::Action | private |
line | PLMD::Action | private |
lockRequestArguments | PLMD::ActionWithArguments | private |
PLMD::lockRequests() | PLMD::Action | inlinevirtual |
PLMD::ActionWithArguments::lockRequests() override | PLMD::ActionWithArguments | inlinevirtual |
log | PLMD::Action | |
multi_sim_comm | PLMD::Action | |
name | PLMD::Action | private |
never_activate | PLMD::Action | private |
noAnalyticalDerivatives(Keywords &keys) | PLMD::ActionWithValue | static |
noderiv | PLMD::ActionWithValue | private |
numericalDerivatives | PLMD::ActionWithValue | private |
operator=(const Action &a)=delete | PLMD::Action | private |
options | PLMD::Action | private |
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 | |
plumed | PLMD::Action | |
prepare() | PLMD::Action | virtual |
readAtomsFromPDB(const PDB &) | PLMD::Action | inlinevirtual |
registerKeywords(Keywords &) | PLMD::bias::ReweightMetad | static |
replica_index | PLMD::Action | private |
requestArguments(const std::vector< Value * > &arg) | PLMD::ActionWithArguments | |
requestExtraDependencies(const std::vector< Value * > &extra) | PLMD::ActionWithArguments | |
resetStoredTimestep() | PLMD::Action | |
restart | PLMD::Action | private |
ReweightBase(const ActionOptions &ao) | PLMD::bias::ReweightBase | explicit |
ReweightMetad(const ActionOptions &ao) | PLMD::bias::ReweightMetad | explicit |
runFinalJobs() | PLMD::Action | inlinevirtual |
setGradients(Value *myval, unsigned &start) const | PLMD::ActionWithArguments | |
setGradientsIfNeeded() | PLMD::ActionWithValue | virtual |
setNotPeriodic() | PLMD::ActionWithValue | |
setOption(const std::string &s) | PLMD::Action | virtual |
setPeriodic(const std::string &min, const std::string &max) | PLMD::ActionWithValue | |
setupConstantValues(const bool &have_atoms) | PLMD::Action | |
setValue(const double &d) | PLMD::ActionWithValue | inlineprotected |
setValue(Value *, double) | PLMD::ActionWithValue | |
simtemp | PLMD::bias::ReweightBase | protected |
timestep | PLMD::Action | private |
turnOnDerivatives() | PLMD::ActionWithValue | virtual |
PLMD::unlockRequests() | PLMD::Action | inlinevirtual |
PLMD::ActionWithArguments::unlockRequests() override | PLMD::ActionWithArguments | inlinevirtual |
update() | PLMD::Action | inlinevirtual |
update_from | PLMD::Action | private |
update_until | PLMD::Action | private |
useCustomisableComponents(Keywords &keys) | PLMD::ActionWithValue | static |
useNumericalDerivatives() | PLMD::ActionWithValue | inline |
usingNaturalUnits() const | PLMD::Action | protected |
valsToForce | PLMD::ActionWithValue | private |
values | PLMD::ActionWithValue | private |
warning(const std::string &msg) | PLMD::Action | |
writeInGraph() const | PLMD::Action | virtual |
~Action() | PLMD::Action | virtual |
~ActionWithArguments() | PLMD::ActionWithArguments | inlinevirtual |
~ActionWithValue() | PLMD::ActionWithValue | |