Action(const ActionOptions &) | PLMD::Action | explicit |
Action(const Action &a)=delete | PLMD::Action | private |
ActionAtomistic(const ActionOptions &ao) | PLMD::ActionAtomistic | explicit |
actionHasForces() | PLMD::ActionAtomistic | virtual |
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 | |
addForce(const std::pair< std::size_t, std::size_t > &a, const Vector &f) | PLMD::ActionAtomistic | inline |
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::Colvar | protectedvirtual |
atom_value_ind | PLMD::ActionAtomistic | private |
atom_value_ind_grouped | PLMD::ActionAtomistic | private |
beforeUpdate() | PLMD::Action | inlinevirtual |
boxValue | PLMD::ActionAtomistic | private |
calculate() override | PLMD::colvar::Volume | virtual |
calculateAtomicNumericalDerivatives(ActionWithValue *a, const unsigned &startnum) | PLMD::ActionAtomistic | |
calculateFromPDB(const PDB &) | PLMD::Action | |
calculateNumericalDerivatives(ActionWithValue *a=NULL) override | PLMD::ActionAtomistic | virtual |
calculateOnUpdate() | PLMD::ActionWithValue | virtual |
castToActionAtomistic() noexcept final | PLMD::ActionAtomistic | inlinevirtual |
castToActionForInterface() noexcept | PLMD::Action | inlinevirtual |
castToActionShortcut() noexcept | PLMD::Action | inlinevirtual |
castToActionToGetData() noexcept | PLMD::Action | inlinevirtual |
castToActionToPutData() noexcept | PLMD::Action | inlinevirtual |
castToActionWithArguments() noexcept | PLMD::Action | inlinevirtual |
PLMD::castToActionWithValue() noexcept | PLMD::Action | inlinevirtual |
PLMD::ActionWithValue::castToActionWithValue() noexcept final | PLMD::ActionWithValue | inlinevirtual |
castToActionWithVirtualAtom() noexcept | PLMD::Action | inlinevirtual |
castToDomainDecomposition() noexcept | PLMD::Action | inlinevirtual |
castToPbcAction() noexcept | PLMD::Action | inlinevirtual |
changeBox(const Tensor &newbox) | PLMD::ActionAtomistic | |
charges | PLMD::ActionAtomistic | private |
chargesWereSet | PLMD::ActionAtomistic | protected |
chargev | PLMD::ActionAtomistic | private |
checkFieldsAllowed() | PLMD::ActionWithValue | inlinevirtual |
checkForDependency(Action *) | PLMD::Action | |
checkForForces() | PLMD::ActionWithValue | protected |
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(const bool &force=false) | PLMD::ActionWithValue | virtual |
clearInputForces(const bool &force=false) | PLMD::ActionWithValue | virtual |
clearOptions() | PLMD::Action | virtual |
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 | |
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 | |
doCheckPoint | PLMD::Action | private |
doNotCalculateDerivatives() const | PLMD::ActionWithValue | inlinevirtual |
donotforce | PLMD::ActionAtomistic | private |
doNotForce() | PLMD::ActionAtomistic | inline |
donotretrieve | PLMD::ActionAtomistic | private |
doNotRetrieve() | PLMD::ActionAtomistic | inline |
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 | |
fclose(FILE *fp) | PLMD::Action | |
fflush() | PLMD::Action | |
files | PLMD::Action | |
firststep | PLMD::ActionWithValue | private |
fopen(const char *path, const char *mode) | PLMD::Action | |
forceOnEnergy | PLMD::ActionAtomistic | private |
forceOnExtraCV | PLMD::ActionAtomistic | private |
forces | PLMD::ActionAtomistic | private |
forcesForApply | PLMD::ActionWithValue | private |
getAbsoluteIndex(int i) const | PLMD::ActionAtomistic | inline |
getAbsoluteIndexes() const | PLMD::ActionAtomistic | inlinevirtual |
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::ActionAtomistic | static |
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 | |
getConstPntrToComponent(int i) const | PLMD::ActionWithValue | protected |
getCPT() const | PLMD::Action | |
getDefaultString() const | PLMD::Action | inline |
getDependencies() const | PLMD::Action | inline |
getEnergy() const | PLMD::ActionAtomistic | inline |
getExchangeStep() const | PLMD::Action | |
getForce() const | PLMD::Colvar | protected |
PLMD::ActionAtomistic::getForce(const std::pair< std::size_t, std::size_t > &a) const | PLMD::ActionAtomistic | inline |
getForcesToApply() const | PLMD::ActionWithValue | inlineprotected |
getGlobalPosition(const std::pair< std::size_t, std::size_t > &) const | PLMD::ActionAtomistic | inline |
getGradient(const unsigned &ind, Vector &deriv, std::map< AtomNumber, Vector > &gradients) const | PLMD::ActionAtomistic | |
getKBoltzmann() const | PLMD::Action | protected |
getkBT() | PLMD::Action | |
getKeyword(const std::string &key) | PLMD::Action | |
getLabel() const | PLMD::Action | inline |
getMass(int i) const | PLMD::ActionAtomistic | inline |
getMatrixColumnTitles(std::vector< std::string > &argnames) const | PLMD::ActionWithValue | virtual |
getName() const | PLMD::Action | inline |
getNumberOfAtoms() const | PLMD::ActionAtomistic | inline |
getNumberOfComponents() const | PLMD::ActionWithValue | inline |
getNumberOfDerivatives() override | PLMD::Colvar | 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 |
getPbc() const | PLMD::ActionAtomistic | inline |
getPntrToComponent(int i) | PLMD::ActionWithValue | protected |
getPntrToComponent(const std::string &name) | PLMD::ActionWithValue | protected |
getPntrToValue() | PLMD::ActionWithValue | inlineprotected |
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 | |
getUnique() const | PLMD::ActionAtomistic | inline |
getUniqueLocal() const | PLMD::ActionAtomistic | inline |
getUnits() const | PLMD::Action | protected |
getValueIndices(const AtomNumber &i) const | PLMD::ActionAtomistic | protected |
getVirial() const | PLMD::ActionAtomistic | |
indexes | PLMD::ActionAtomistic | private |
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::ActionAtomistic | 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 |
lockRequestAtoms | PLMD::ActionAtomistic | private |
lockRequests() override | PLMD::ActionAtomistic | inlinevirtual |
log | PLMD::Action | |
makeWhole() | PLMD::ActionAtomistic | |
masses | PLMD::ActionAtomistic | private |
massesWereSet | PLMD::ActionAtomistic | protected |
masv | PLMD::ActionAtomistic | private |
modifyForceOnEnergy() | PLMD::ActionAtomistic | inline |
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 | |
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 | inline |
plumed | PLMD::Action | |
positions | PLMD::ActionAtomistic | private |
prepare() | PLMD::Action | virtual |
readAtomsFromPDB(const PDB &pdb) override | PLMD::ActionAtomistic | virtual |
registerKeywords(Keywords &keys) | PLMD::colvar::Volume | 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 | |
resetStoredTimestep() | PLMD::Action | |
restart | PLMD::Action | private |
retrieveAtoms(const bool &force=false) | PLMD::ActionAtomistic | virtual |
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 |
setBoxDerivativesNoPbc(const std::vector< Vector > &pos, std::vector< std::vector< Vector > > &derivs, std::vector< Tensor > &virial) | PLMD::Colvar | static |
setExtraCV(const std::string &name) | PLMD::ActionAtomistic | protected |
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::ActionAtomistic | inline |
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 | |
timestep | PLMD::Action | private |
turnOnDerivatives() | PLMD::ActionWithValue | virtual |
unique | PLMD::ActionAtomistic | private |
unique_local | PLMD::ActionAtomistic | private |
unique_local_needs_update | PLMD::ActionAtomistic | private |
unlockRequests() override | PLMD::ActionAtomistic | inlinevirtual |
update() | PLMD::Action | inlinevirtual |
update_from | PLMD::Action | private |
update_until | PLMD::Action | private |
updateUniqueLocal(const bool &useunique, const std::vector< int > &g2l) | PLMD::ActionAtomistic | private |
useCustomisableComponents(Keywords &keys) | PLMD::ActionWithValue | static |
useNumericalDerivatives() | PLMD::ActionWithValue | inline |
usingNaturalUnits() const | PLMD::Action | protected |
valsToForce | PLMD::ActionWithValue | private |
value_depends | PLMD::ActionAtomistic | private |
values | PLMD::ActionWithValue | private |
Volume(const ActionOptions &) | PLMD::colvar::Volume | explicit |
warning(const std::string &msg) | PLMD::Action | |
writeInGraph() const | PLMD::Action | virtual |
xpos | PLMD::ActionAtomistic | private |
ypos | PLMD::ActionAtomistic | private |
zpos | PLMD::ActionAtomistic | private |
~Action() | PLMD::Action | virtual |
~ActionAtomistic() | PLMD::ActionAtomistic | |
~ActionWithValue() | PLMD::ActionWithValue | |
~Colvar() | PLMD::Colvar | inline |