Action(const ActionOptions &) | PLMD::Action | explicit |
Action(const Action &a)=delete | PLMD::Action | private |
ActionAtomistic(const ActionOptions &ao) | PLMD::ActionAtomistic | explicit |
ActionWithValue(const ActionOptions &ao) | PLMD::ActionWithValue | explicit |
activate() | PLMD::Action | virtual |
active | PLMD::Action | private |
addComponent(const std::string &name) | PLMD::ActionWithValue | |
addComponentWithDerivatives(const std::string &name) | PLMD::ActionWithValue | |
addDependency(Action *) | PLMD::Action | |
addValue() | PLMD::ActionWithValue | |
addValueWithDerivatives() | PLMD::ActionWithValue | |
after | PLMD::Action | private |
allowToAccessGlobalForces() | PLMD::ActionAtomistic | inline |
apply() override | PLMD::Colvar | protectedvirtual |
applyForces() | PLMD::ActionAtomistic | |
atoms | PLMD::ActionAtomistic | protected |
beforeUpdate() | PLMD::Action | inlinevirtual |
calculate() override | PLMD::colvar::RMSD | virtual |
calculateAtomicNumericalDerivatives(ActionWithValue *a, const unsigned &startnum) | PLMD::ActionAtomistic | |
calculateFromPDB(const PDB &) | PLMD::Action | |
calculateNumericalDerivatives(ActionWithValue *a=NULL) override | PLMD::ActionAtomistic | virtual |
changeBox(const Tensor &newbox) | PLMD::ActionAtomistic | |
charges | PLMD::ActionAtomistic | private |
chargesWereSet | PLMD::ActionAtomistic | private |
checkFieldsAllowed() | PLMD::ActionWithValue | inlinevirtual |
checkIsEnergy() | PLMD::Colvar | inline |
checkNeedsGradients() const | PLMD::Action | inlinevirtual |
PLMD::checkNumericalDerivatives() const | PLMD::Action | inlinevirtual |
PLMD::ActionWithValue::checkNumericalDerivatives() const override | 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 |
clearOutputForces() | PLMD::ActionAtomistic | |
Colvar(const ActionOptions &) | PLMD::Colvar | explicit |
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 | |
doCheckPoint | PLMD::Action | private |
doNotCalculateDerivatives() const | PLMD::ActionWithValue | inlinevirtual |
doNotForce() | PLMD::ActionAtomistic | inline |
donotforce | PLMD::ActionAtomistic | private |
doNotRetrieve() | PLMD::ActionAtomistic | inline |
donotretrieve | PLMD::ActionAtomistic | private |
energy | PLMD::ActionAtomistic | private |
error(const std::string &msg) const | PLMD::Action | |
exists(const std::string &name) const | PLMD::ActionWithValue | |
exit(int c=0) | PLMD::Action | |
extraCV | PLMD::ActionAtomistic | private |
fclose(FILE *fp) | PLMD::Action | |
fflush() | PLMD::Action | |
files | PLMD::Action | |
fopen(const char *path, const char *mode) | PLMD::Action | |
forceOnEnergy | PLMD::ActionAtomistic | private |
forceOnExtraCV | PLMD::ActionAtomistic | private |
forces | PLMD::ActionAtomistic | private |
getAbsoluteIndex(int i) const | PLMD::ActionAtomistic | inline |
getAbsoluteIndexes() const | PLMD::ActionAtomistic | inlinevirtual |
getBox() const | PLMD::ActionAtomistic | inline |
getBoxDerivatives() const | PLMD::Colvar | protected |
getCharge(int i) const | PLMD::ActionAtomistic | inline |
getComponent(const std::string &name) const | PLMD::ActionWithValue | private |
getComponentsList() const | PLMD::ActionWithValue | |
getComponentsVector() const | PLMD::ActionWithValue | |
getCPT() const | PLMD::Action | |
getDependencies() const | PLMD::Action | inline |
getDocumentation() const | PLMD::Action | virtual |
getEnergy() const | PLMD::ActionAtomistic | inline |
getExchangeStep() const | PLMD::Action | |
getForce() const | PLMD::Colvar | protected |
getGlobalPosition(AtomNumber) const | PLMD::ActionAtomistic | inline |
getKeyword(const std::string &key) | PLMD::Action | |
getLabel() const | PLMD::Action | inline |
getMass(int i) const | PLMD::ActionAtomistic | inline |
getName() const | PLMD::Action | inline |
getNumberOfAtoms() const | PLMD::ActionAtomistic | inline |
getNumberOfComponents() const | PLMD::ActionWithValue | inline |
getNumberOfDerivatives() override | PLMD::Colvar | inlinevirtual |
getOutputQuantity(const unsigned j) const | PLMD::ActionWithValue | inline |
getOutputQuantity(const std::string &name) const | PLMD::ActionWithValue | inline |
getPbc() const | PLMD::ActionAtomistic | inline |
getPntrToComponent(int i) | PLMD::ActionWithValue | protected |
getPntrToComponent(const std::string &name) | PLMD::ActionWithValue | protected |
getPntrToValue() | PLMD::ActionWithValue | protected |
getPosition(int) const | PLMD::ActionAtomistic | inline |
getPositions() const | PLMD::ActionAtomistic | inline |
getRestart() const | PLMD::Action | inline |
getStep() const | PLMD::Action | |
getTime() const | PLMD::Action | |
getTimeStep() const | PLMD::Action | |
getTotAtoms() const | PLMD::ActionAtomistic | inline |
getUnique() const | PLMD::ActionAtomistic | inline |
getUniqueLocal() const | PLMD::ActionAtomistic | inline |
indexes | PLMD::ActionAtomistic | private |
interpretAtomList(std::vector< std::string > &strings, std::vector< AtomNumber > &t) | PLMD::ActionAtomistic | |
isActive() const | PLMD::Action | inline |
isEnergy | PLMD::Colvar | protected |
isExtraCV | PLMD::Colvar | protected |
isOptionOn(const std::string &s) const | PLMD::Action | inline |
keywords | PLMD::Action | |
label | PLMD::Action | private |
line | PLMD::Action | private |
lockRequestAtoms | PLMD::ActionAtomistic | private |
lockRequests() override | PLMD::ActionAtomistic | inlinevirtual |
log | PLMD::Action | |
makeWhole() | PLMD::ActionAtomistic | |
masses | PLMD::ActionAtomistic | private |
modifyForceOnEnergy() | PLMD::ActionAtomistic | inline |
modifyForceOnExtraCV() | PLMD::ActionAtomistic | inline |
modifyForces() | PLMD::ActionAtomistic | inline |
modifyGlobalForce(AtomNumber) | PLMD::ActionAtomistic | inline |
modifyGlobalPbc() | PLMD::ActionAtomistic | inline |
modifyGlobalPosition(AtomNumber) | PLMD::ActionAtomistic | inline |
modifyGlobalVirial() | PLMD::ActionAtomistic | inline |
modifyVirial() | PLMD::ActionAtomistic | inline |
multi_sim_comm | PLMD::Action | |
mypack | PLMD::colvar::RMSD | private |
myvals | PLMD::colvar::RMSD | private |
name | PLMD::Action | private |
noAnalyticalDerivatives(Keywords &keys) | PLMD::ActionWithValue | static |
noderiv | PLMD::ActionWithValue | private |
nopbc | PLMD::colvar::RMSD | 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 | |
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 | |
pbc | PLMD::ActionAtomistic | private |
pbc_fwd | PLMD::ActionAtomistic | private |
pbcApply(std::vector< Vector > &dlist, unsigned max_index=0) const | PLMD::ActionAtomistic | |
pbcDistance(const Vector &, const Vector &) const | PLMD::ActionAtomistic | |
plumed | PLMD::Action | |
positions | PLMD::ActionAtomistic | private |
prepare() | PLMD::Action | virtual |
readAtomsFromPDB(const PDB &pdb) override | PLMD::ActionAtomistic | virtual |
registerKeywords(Keywords &keys) | PLMD::colvar::RMSD | static |
replica_index | PLMD::Action | private |
requestAtoms(const std::vector< AtomNumber > &a) | PLMD::Colvar | protected |
PLMD::ActionAtomistic::requestAtoms(const std::vector< AtomNumber > &a, const bool clearDep=true) | PLMD::ActionAtomistic | |
restart | PLMD::Action | private |
retrieveAtoms() | PLMD::ActionAtomistic | virtual |
rmsd | PLMD::colvar::RMSD | private |
RMSD(const ActionOptions &) | PLMD::colvar::RMSD | explicit |
runFinalJobs() | PLMD::Action | inlinevirtual |
setAtomsDerivatives(int, const Vector &) | PLMD::Colvar | inlineprotected |
setAtomsDerivatives(Value *, int, const Vector &) | PLMD::Colvar | inlineprotected |
setBoxDerivatives(const Tensor &) | PLMD::Colvar | inlineprotected |
setBoxDerivatives(Value *, const Tensor &) | PLMD::Colvar | inlineprotected |
setBoxDerivativesNoPbc() | PLMD::Colvar | inlineprotected |
setBoxDerivativesNoPbc(Value *) | PLMD::Colvar | protected |
setExtraCV(const std::string &name) | PLMD::ActionAtomistic | inlineprotected |
setForcesOnAtoms(const std::vector< double > &forcesToApply, unsigned ind=0) | PLMD::ActionAtomistic | |
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 | |
squared | PLMD::colvar::RMSD | private |
turnOnDerivatives() | PLMD::ActionWithValue | virtual |
unique | PLMD::ActionAtomistic | private |
unique_local | PLMD::ActionAtomistic | private |
unlockRequests() override | PLMD::ActionAtomistic | inlinevirtual |
update() | PLMD::Action | inlinevirtual |
update_from | PLMD::Action | private |
update_until | PLMD::Action | private |
updateUniqueLocal() | PLMD::ActionAtomistic | |
useCustomisableComponents(Keywords &keys) | PLMD::ActionWithValue | static |
useNumericalDerivatives() | PLMD::ActionWithValue | inline |
values | PLMD::ActionWithValue | private |
virial | PLMD::ActionAtomistic | private |
warning(const std::string &msg) | PLMD::Action | |
~Action() | PLMD::Action | virtual |
~ActionAtomistic() | PLMD::ActionAtomistic | |
~ActionWithValue() | PLMD::ActionWithValue | |
~Colvar() | PLMD::Colvar | inline |