Action(const ActionOptions &) | PLMD::Action | explicit |
ActionWithArguments(const ActionOptions &) | PLMD::ActionWithArguments | explicit |
ActionWithValue(const ActionOptions &ao) | PLMD::ActionWithValue | explicit |
activate() | PLMD::Action | virtual |
addComponent(const std::string &name) | PLMD::ActionWithValue | |
addComponentWithDerivatives(const std::string &name) | PLMD::function::Function | protected |
addDependency(Action *) | PLMD::Action | |
addForcesOnArguments(const std::vector< double > &forces) | PLMD::ActionWithArguments | |
addValue() | PLMD::ActionWithValue | |
addValueWithDerivatives() | PLMD::function::Function | protected |
apply() | PLMD::function::Function | virtual |
beforeUpdate() | PLMD::Action | inlinevirtual |
bringBackInPbc(int i, double d1) const | PLMD::ActionWithArguments | inline |
calculate() | PLMD::function::Matheval | virtual |
calculateFromPDB(const PDB &) | PLMD::Action | |
PLMD::calculateNumericalDerivatives(ActionWithValue *a=NULL) | PLMD::Action | virtual |
PLMD::ActionWithArguments::calculateNumericalDerivatives(ActionWithValue *a=NULL) | PLMD::ActionWithArguments | virtual |
checkFieldsAllowed() | PLMD::ActionWithValue | inlinevirtual |
checkNeedsGradients() const | PLMD::Action | inlinevirtual |
checkNumericalDerivatives() const | PLMD::ActionWithValue | inlinevirtual |
checkRead() | PLMD::Action | |
checkUpdate() const | PLMD::Action | |
cite(const std::string &s) | PLMD::Action | |
clearDependencies() | PLMD::Action | |
clearDerivatives() | PLMD::ActionWithValue | virtual |
clearInputForces() | PLMD::ActionWithValue | |
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 | |
componentsAreNotOptional(Keywords &keys) | PLMD::ActionWithValue | static |
copyOutput(const std::string &name) const | PLMD::ActionWithValue | |
copyOutput(const unsigned &n) const | PLMD::ActionWithValue | |
deactivate() | PLMD::Action | inlinevirtual |
Dependencies typedef | PLMD::Action | |
difference(int, double, double) const | PLMD::ActionWithArguments | inline |
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(PDB &pdb) | PLMD::ActionWithArguments | protected |
fclose(FILE *fp) | PLMD::Action | |
fflush() | PLMD::Action | |
files | PLMD::Action | |
fopen(const char *path, const char *mode) | PLMD::Action | |
Function(const ActionOptions &) | PLMD::function::Function | explicit |
getArgument(const unsigned n) const | PLMD::ActionWithArguments | inline |
getArguments() const | PLMD::ActionWithArguments | inline |
getComponentsList() const | PLMD::ActionWithValue | |
getComponentsVector() const | PLMD::ActionWithValue | |
getCPT() const | PLMD::Action | |
getDependencies() const | PLMD::Action | inline |
getDocumentation() const | PLMD::Action | virtual |
getExchangeStep() const | PLMD::Action | |
getKeyword(const std::string &key) | PLMD::Action | |
getLabel() const | PLMD::Action | inline |
getName() const | PLMD::Action | inline |
getNumberOfArguments() const | PLMD::ActionWithArguments | inlinevirtual |
getNumberOfComponents() const | PLMD::ActionWithValue | inline |
getNumberOfDerivatives() | PLMD::function::Function | inlinevirtual |
getOutputQuantity(const unsigned j) const | PLMD::ActionWithValue | inline |
getOutputQuantity(const std::string &name) const | PLMD::ActionWithValue | inline |
getPntrToArgument(const unsigned n) | PLMD::ActionWithArguments | inline |
getPntrToComponent(int i) | PLMD::ActionWithValue | protected |
getPntrToComponent(const std::string &name) | PLMD::ActionWithValue | protected |
getPntrToValue() | PLMD::ActionWithValue | protected |
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 | |
interpretArgumentList(const std::vector< std::string > &c, std::vector< Value *> &arg) | PLMD::ActionWithArguments | |
isActive() const | PLMD::Action | inline |
isOptionOn(const std::string &s) const | PLMD::Action | inline |
keywords | PLMD::Action | |
PLMD::lockRequests() | PLMD::Action | inlinevirtual |
PLMD::ActionWithArguments::lockRequests() | PLMD::ActionWithArguments | inlinevirtual |
log | PLMD::Action | |
Matheval(const ActionOptions &) | PLMD::function::Matheval | explicit |
multi_sim_comm | PLMD::Action | |
noAnalyticalDerivatives(Keywords &keys) | PLMD::ActionWithValue | static |
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 &keys) | PLMD::function::Matheval | static |
requestArguments(const std::vector< Value *> &arg) | PLMD::ActionWithArguments | |
runFinalJobs() | PLMD::Action | inlinevirtual |
setDerivative(int, double) | PLMD::function::Function | inlineprotected |
setDerivative(Value *, int, double) | PLMD::function::Function | inlineprotected |
setGradientsIfNeeded() | PLMD::ActionWithValue | |
setNotPeriodic() | PLMD::ActionWithValue | |
setOption(const std::string &s) | PLMD::Action | virtual |
setPeriodic(const std::string &min, const std::string &max) | PLMD::ActionWithValue | |
setValue(const double &d) | PLMD::ActionWithValue | inlineprotected |
setValue(Value *, double) | PLMD::ActionWithValue | |
turnOnDerivatives() | PLMD::ActionWithValue | virtual |
PLMD::unlockRequests() | PLMD::Action | inlinevirtual |
PLMD::ActionWithArguments::unlockRequests() | PLMD::ActionWithArguments | inlinevirtual |
update() | PLMD::Action | inlinevirtual |
useCustomisableComponents(Keywords &keys) | PLMD::ActionWithValue | static |
useNumericalDerivatives() | PLMD::ActionWithValue | inline |
warning(const std::string &msg) | PLMD::Action | |
~Action() | PLMD::Action | virtual |
~ActionWithArguments() | PLMD::ActionWithArguments | inlinevirtual |
~ActionWithValue() | PLMD::ActionWithValue | |
~Function() | PLMD::function::Function | inlinevirtual |
~Matheval() | PLMD::function::Matheval | |