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PLMD::generic::WholeMolecules Member List

This is the complete list of members for PLMD::generic::WholeMolecules, including all inherited members.

Action(const ActionOptions &)PLMD::Actionexplicit
ActionAtomistic(const ActionOptions &ao)PLMD::ActionAtomisticexplicit
actionHasForces() overridePLMD::generic::WholeMoleculesinlinevirtual
actionMoldatPLMD::ActionAtomisticprivate
actionPbcPLMD::ActionAtomisticprivate
ActionPilot(const ActionOptions &)PLMD::ActionPilotexplicit
actionPositionsPLMD::ActionAtomisticprivate
actionStridePLMD::ActionPilotprivate
activate()PLMD::Actionvirtual
addDependency(Action *)PLMD::Action
addForce(const std::pair< std::size_t, std::size_t > &a, const Vector &f)PLMD::ActionAtomisticinline
addrefPLMD::generic::WholeMoleculesprivate
apply() overridePLMD::generic::WholeMoleculesinlinevirtual
atom_value_indPLMD::ActionAtomisticprivate
atom_value_ind_groupedPLMD::ActionAtomisticprivate
beforeUpdate()PLMD::Actioninlinevirtual
boxValuePLMD::ActionAtomisticprivate
calculate() overridePLMD::generic::WholeMoleculesvirtual
calculateAtomicNumericalDerivatives(ActionWithValue *a, const unsigned &startnum)PLMD::ActionAtomistic
calculateFromPDB(const PDB &)PLMD::Action
calculateNumericalDerivatives(ActionWithValue *a=NULL) overridePLMD::ActionAtomisticvirtual
castToActionAtomistic() noexcept finalPLMD::ActionAtomisticinlinevirtual
castToActionForInterface() noexceptPLMD::Actioninlinevirtual
castToActionShortcut() noexceptPLMD::Actioninlinevirtual
castToActionToGetData() noexceptPLMD::Actioninlinevirtual
castToActionToPutData() noexceptPLMD::Actioninlinevirtual
castToActionWithArguments() noexceptPLMD::Actioninlinevirtual
castToActionWithValue() noexceptPLMD::Actioninlinevirtual
castToActionWithVirtualAtom() noexceptPLMD::Actioninlinevirtual
castToDomainDecomposition() noexceptPLMD::Actioninlinevirtual
castToPbcAction() noexceptPLMD::Actioninlinevirtual
changeBox(const Tensor &newbox)PLMD::ActionAtomistic
chargesPLMD::ActionAtomisticprivate
chargesWereSetPLMD::ActionAtomisticprotected
chargevPLMD::ActionAtomisticprivate
checkForDependency(Action *)PLMD::Action
checkNeedsGradients() constPLMD::Actioninlinevirtual
checkNumericalDerivatives() constPLMD::Actioninlinevirtual
checkRead()PLMD::Action
checkUpdate() constPLMD::Action
cite(const std::string &s)PLMD::Action
clearDependencies()PLMD::Action
clearOptions()PLMD::Actionvirtual
commPLMD::Action
deactivate()PLMD::Actioninlinevirtual
Dependencies typedefPLMD::Action
doemstPLMD::generic::WholeMoleculesprivate
doNotForce()PLMD::ActionAtomisticinline
donotforcePLMD::ActionAtomisticprivate
doNotRetrieve()PLMD::ActionAtomisticinline
donotretrievePLMD::ActionAtomisticprivate
energyPLMD::ActionAtomisticprivate
error(const std::string &msg) constPLMD::Action
exit(int c=0)PLMD::Action
fclose(FILE *fp)PLMD::Action
fflush()PLMD::Action
filesPLMD::Action
fopen(const char *path, const char *mode)PLMD::Action
forceOnEnergyPLMD::ActionAtomisticprivate
forceOnExtraCVPLMD::ActionAtomisticprivate
forcesPLMD::ActionAtomisticprivate
getAbsoluteIndex(int i) constPLMD::ActionAtomisticinline
getAbsoluteIndexes() constPLMD::ActionAtomisticinlinevirtual
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::ActionAtomisticstatic
getBox() constPLMD::ActionAtomisticinline
getCharge(int i) constPLMD::ActionAtomisticinline
getCharges(const bool allowempty=false) constPLMD::ActionAtomisticinline
getCPT() constPLMD::Action
getDefaultString() constPLMD::Actioninline
getDependencies() constPLMD::Actioninline
getEnergy() constPLMD::ActionAtomisticinline
getExchangeStep() constPLMD::Action
getForce(const std::pair< std::size_t, std::size_t > &a) constPLMD::ActionAtomisticinline
getGlobalPosition(const std::pair< std::size_t, std::size_t > &) constPLMD::ActionAtomisticinline
getGradient(const unsigned &ind, Vector &deriv, std::map< AtomNumber, Vector > &gradients) constPLMD::ActionAtomistic
getKBoltzmann() constPLMD::Actionprotected
getkBT()PLMD::Action
getKeyword(const std::string &key)PLMD::Action
getLabel() constPLMD::Actioninline
getMass(int i) constPLMD::ActionAtomisticinline
getMasses() constPLMD::ActionAtomisticinline
getName() constPLMD::Actioninline
getNumberOfAtoms() constPLMD::ActionAtomisticinline
getPbc() constPLMD::ActionAtomisticinline
getPosition(int) constPLMD::ActionAtomisticinline
getPositions() constPLMD::ActionAtomisticinline
getRestart() constPLMD::Actioninline
getStep() constPLMD::Action
getStride() constPLMD::ActionPilot
getTime() constPLMD::Action
getTimeStep() constPLMD::Action
getTotAtoms() constPLMD::ActionAtomistic
getUnique() constPLMD::ActionAtomisticinline
getUniqueLocal() constPLMD::ActionAtomisticinline
getUnits() constPLMD::Actionprotected
getValueIndices(const AtomNumber &i) constPLMD::ActionAtomisticprotected
getVirial() constPLMD::ActionAtomistic
indexesPLMD::ActionAtomisticprivate
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::ActionAtomisticstatic
isActive() constPLMD::Actioninline
isOptionOn(const std::string &s) constPLMD::Actioninline
keywordsPLMD::Action
lockRequestAtomsPLMD::ActionAtomisticprivate
lockRequests() overridePLMD::ActionAtomisticinlinevirtual
logPLMD::Action
makeWhole()PLMD::ActionAtomistic
massesPLMD::ActionAtomisticprivate
massesWereSetPLMD::ActionAtomisticprotected
masvPLMD::ActionAtomisticprivate
modifyForceOnEnergy()PLMD::ActionAtomisticinline
multi_sim_commPLMD::Action
onStep() constPLMD::ActionPilotvirtual
p_groupsPLMD::generic::WholeMoleculesprivate
p_rootsPLMD::generic::WholeMoleculesprivate
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_fwdPLMD::ActionAtomisticprivate
pbcApply(std::vector< Vector > &dlist, unsigned max_index=0) constPLMD::ActionAtomistic
pbcDistance(const Vector &, const Vector &) constPLMD::ActionAtomisticinline
plumedPLMD::Action
prepare()PLMD::Actionvirtual
readAtomsFromPDB(const PDB &pdb) overridePLMD::ActionAtomisticvirtual
refsPLMD::generic::WholeMoleculesprivate
registerKeywords(Keywords &keys)PLMD::generic::WholeMoleculesstatic
requestAtoms(const std::vector< AtomNumber > &a, const bool clearDep=true)PLMD::ActionAtomistic
resetStoredTimestep()PLMD::Action
retrieveAtoms(const bool &force=false)PLMD::ActionAtomisticvirtual
runFinalJobs()PLMD::Actioninlinevirtual
setExtraCV(const std::string &name)PLMD::ActionAtomisticprotected
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::ActionAtomisticinline
setOption(const std::string &s)PLMD::Actionvirtual
setStride(unsigned n)PLMD::ActionPilot
setupConstantValues(const bool &have_atoms)PLMD::Action
treePLMD::ActionAtomisticprivate
uniquePLMD::ActionAtomisticprivate
unique_localPLMD::ActionAtomisticprivate
unique_local_needs_updatePLMD::ActionAtomisticprivate
unlockRequests() overridePLMD::ActionAtomisticinlinevirtual
update()PLMD::Actioninlinevirtual
updateUniqueLocal(const bool &useunique, const std::vector< int > &g2l)PLMD::ActionAtomisticprivate
usingNaturalUnits() constPLMD::Actionprotected
value_dependsPLMD::ActionAtomisticprivate
warning(const std::string &msg)PLMD::Action
WholeMolecules(const ActionOptions &ao)PLMD::generic::WholeMoleculesexplicit
writeInGraph() constPLMD::Actionvirtual
xposPLMD::ActionAtomisticprivate
yposPLMD::ActionAtomisticprivate
zposPLMD::ActionAtomisticprivate
~Action()PLMD::Actionvirtual
~ActionAtomistic()PLMD::ActionAtomistic
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