Action(const ActionOptions &) | PLMD::Action | explicit |
Action(const Action &a)=delete | PLMD::Action | private |
ActionAtomistic(const ActionOptions &ao) | PLMD::ActionAtomistic | explicit |
ActionPilot(const ActionOptions &) | PLMD::ActionPilot | explicit |
ActionWithInputVessel(const ActionOptions &) | PLMD::vesselbase::ActionWithInputVessel | explicit |
activate() | PLMD::Action | virtual |
active | PLMD::Action | private |
addBridgeForces(const std::vector< double > &bb) | PLMD::vesselbase::ActionWithInputVessel | inlinevirtual |
addDependency(Action *) | PLMD::Action | |
addForcesOnArguments(const std::vector< double > &forces) | PLMD::vesselbase::ActionWithInputVessel | protected |
after | PLMD::Action | private |
allowToAccessGlobalForces() | PLMD::ActionAtomistic | inline |
apply() override | PLMD::multicolvar::DumpMultiColvar | inlinevirtual |
applyBridgeForces(const std::vector< double > &bb) | PLMD::vesselbase::ActionWithInputVessel | |
applyForces() | PLMD::ActionAtomistic | |
arguments | PLMD::vesselbase::ActionWithInputVessel | private |
atoms | PLMD::ActionAtomistic | protected |
beforeUpdate() | PLMD::Action | inlinevirtual |
calculate() override | PLMD::multicolvar::DumpMultiColvar | inlinevirtual |
calculateAtomicNumericalDerivatives(ActionWithValue *a, const unsigned &startnum) | PLMD::ActionAtomistic | |
calculateFromPDB(const PDB &) | PLMD::Action | |
calculateNumericalDerivatives(ActionWithValue *vv) override | PLMD::multicolvar::DumpMultiColvar | inlinevirtual |
changeBox(const Tensor &newbox) | PLMD::ActionAtomistic | |
charges | PLMD::ActionAtomistic | private |
chargesWereSet | PLMD::ActionAtomistic | private |
checkNeedsGradients() const | PLMD::Action | inlinevirtual |
checkNumericalDerivatives() const | PLMD::Action | inlinevirtual |
checkRead() | PLMD::Action | |
checkUpdate() const | PLMD::Action | |
cite(const std::string &s) | PLMD::Action | |
clearDependencies() | PLMD::Action | |
clearOptions() | PLMD::Action | virtual |
clearOutputForces() | PLMD::ActionAtomistic | |
comm | PLMD::Action | |
deactivate() | PLMD::Action | inlinevirtual |
Dependencies typedef | PLMD::Action | |
doCheckPoint | PLMD::Action | private |
doNotForce() | PLMD::ActionAtomistic | inline |
donotforce | PLMD::ActionAtomistic | private |
doNotRetrieve() | PLMD::ActionAtomistic | inline |
donotretrieve | PLMD::ActionAtomistic | private |
DumpMultiColvar(const ActionOptions &) | PLMD::multicolvar::DumpMultiColvar | explicit |
energy | PLMD::ActionAtomistic | private |
error(const std::string &msg) const | PLMD::Action | |
exit(int c=0) | PLMD::Action | |
extraCV | PLMD::ActionAtomistic | private |
fclose(FILE *fp) | PLMD::Action | |
fflush() | PLMD::Action | |
files | PLMD::Action | |
fmt_xyz | PLMD::multicolvar::DumpMultiColvar | private |
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 |
getCharge(int i) const | PLMD::ActionAtomistic | inline |
getCPT() const | PLMD::Action | |
getDependencies() const | PLMD::Action | inline |
getDocumentation() const | PLMD::Action | virtual |
getEnergy() const | PLMD::ActionAtomistic | inline |
getExchangeStep() const | PLMD::Action | |
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 |
getPbc() const | PLMD::ActionAtomistic | inline |
getPntrToArgument() | PLMD::vesselbase::ActionWithInputVessel | inlineprotected |
getPosition(int) const | PLMD::ActionAtomistic | inline |
getPositions() const | PLMD::ActionAtomistic | inline |
getRestart() const | PLMD::Action | inline |
getStep() const | PLMD::Action | |
getStride() const | PLMD::ActionPilot | |
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 |
isOptionOn(const std::string &s) const | PLMD::Action | inline |
keywords | PLMD::Action | |
label | PLMD::Action | private |
lenunit | PLMD::multicolvar::DumpMultiColvar | private |
line | PLMD::Action | private |
lockRequestAtoms | PLMD::ActionAtomistic | private |
PLMD::lockRequests() | PLMD::Action | inlinevirtual |
PLMD::ActionAtomistic::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 | |
myBridgeVessel | PLMD::vesselbase::ActionWithInputVessel | private |
mycolv | PLMD::multicolvar::DumpMultiColvar | private |
name | PLMD::Action | private |
of | PLMD::multicolvar::DumpMultiColvar | private |
onStep() const | PLMD::ActionPilot | virtual |
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 |
readArgument(const std::string &type) | PLMD::vesselbase::ActionWithInputVessel | protected |
PLMD::readAtomsFromPDB(const PDB &) | PLMD::Action | inlinevirtual |
PLMD::ActionAtomistic::readAtomsFromPDB(const PDB &pdb) override | PLMD::ActionAtomistic | virtual |
registerKeywords(Keywords &keys) | PLMD::multicolvar::DumpMultiColvar | static |
replica_index | PLMD::Action | private |
requestAtoms(const std::vector< AtomNumber > &a, const bool clearDep=true) | PLMD::ActionAtomistic | |
restart | PLMD::Action | private |
retrieveAtoms() | PLMD::ActionAtomistic | virtual |
runFinalJobs() | PLMD::Action | inlinevirtual |
setExtraCV(const std::string &name) | PLMD::ActionAtomistic | inlineprotected |
setForcesOnAtoms(const std::vector< double > &forcesToApply, unsigned ind=0) | PLMD::ActionAtomistic | |
setOption(const std::string &s) | PLMD::Action | virtual |
setStride(const int &n) | PLMD::ActionPilot | |
stride | PLMD::ActionPilot | private |
unique | PLMD::ActionAtomistic | private |
unique_local | PLMD::ActionAtomistic | private |
PLMD::unlockRequests() | PLMD::Action | inlinevirtual |
PLMD::ActionAtomistic::unlockRequests() override | PLMD::ActionAtomistic | inlinevirtual |
update() override | PLMD::multicolvar::DumpMultiColvar | virtual |
update_from | PLMD::Action | private |
update_until | PLMD::Action | private |
updateUniqueLocal() | PLMD::ActionAtomistic | |
virial | PLMD::ActionAtomistic | private |
warning(const std::string &msg) | PLMD::Action | |
~Action() | PLMD::Action | virtual |
~ActionAtomistic() | PLMD::ActionAtomistic | |
~ActionWithInputVessel() | PLMD::vesselbase::ActionWithInputVessel | inlinevirtual |
~DumpMultiColvar() | PLMD::multicolvar::DumpMultiColvar | |