PLMD::generic::DumpAtoms Member List

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

Action(const ActionOptions &)PLMD::Actionexplicit
Action(const Action &a)=deletePLMD::Actionprivate
ActionAtomistic(const ActionOptions &ao)PLMD::ActionAtomisticexplicit
actionHasForces() overridePLMD::generic::DumpAtomsinlinevirtual
ActionPilot(const ActionOptions &)PLMD::ActionPilotexplicit
ActionWithArguments(const ActionOptions &)PLMD::ActionWithArgumentsexplicit
activate()PLMD::Actionvirtual
activePLMD::Actionprivate
addDependency(Action *)PLMD::Action
addForce(const std::pair< std::size_t, std::size_t > &a, const Vector &f)PLMD::ActionAtomisticinline
addForcesOnArguments(const unsigned &argstart, const std::vector< double > &forces, unsigned &ind, const std::string &c)PLMD::ActionWithArguments
afterPLMD::Actionprivate
apply() overridePLMD::generic::DumpAtomsinlinevirtual
argumentsPLMD::ActionWithArgumentsprivate
atom_value_indPLMD::ActionAtomisticprivate
atom_value_ind_groupedPLMD::ActionAtomisticprivate
beforeUpdate()PLMD::Actioninlinevirtual
boundsPLMD::generic::DumpAtomsprivate
boxValuePLMD::ActionAtomisticprivate
bringBackInPbc(int i, double d1) constPLMD::ActionWithArgumentsinline
calculate() overridePLMD::generic::DumpAtomsinlinevirtual
calculateAtomicNumericalDerivatives(ActionWithValue *a, const unsigned &startnum)PLMD::ActionAtomistic
calculateConstantValues(const bool &have_atoms)PLMD::ActionWithArgumentsvirtual
calculateFromPDB(const PDB &)PLMD::Action
calculateNumericalDerivatives(ActionWithValue *a=NULL) overridePLMD::generic::DumpAtomsvirtual
castToActionAtomistic() noexcept finalPLMD::ActionAtomisticinlinevirtual
castToActionForInterface() noexceptPLMD::Actioninlinevirtual
castToActionShortcut() noexceptPLMD::Actioninlinevirtual
castToActionToGetData() noexceptPLMD::Actioninlinevirtual
castToActionToPutData() noexceptPLMD::Actioninlinevirtual
PLMD::castToActionWithArguments() noexceptPLMD::Actioninlinevirtual
PLMD::ActionWithArguments::castToActionWithArguments() noexcept finalPLMD::ActionWithArgumentsinlinevirtual
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
defaultsPLMD::Actionprivate
Dependencies typedefPLMD::Action
difference(int, double, double) constPLMD::ActionWithArgumentsinline
doCheckPointPLMD::Actionprivate
doNotForce()PLMD::ActionAtomisticinline
donotforcePLMD::ActionAtomisticprivate
doNotRetrieve()PLMD::ActionAtomisticinline
donotretrievePLMD::ActionAtomisticprivate
DumpAtoms(const ActionOptions &)PLMD::generic::DumpAtomsexplicit
energyPLMD::ActionAtomisticprivate
error(const std::string &msg) constPLMD::Action
exit(int c=0)PLMD::Action
expandArgKeywordInPDB(const PDB &pdb)PLMD::ActionWithArgumentsprotected
fclose(FILE *fp)PLMD::Action
fflush()PLMD::Action
filesPLMD::Action
fmt_gro_boxPLMD::generic::DumpAtomsprivate
fmt_gro_posPLMD::generic::DumpAtomsprivate
fmt_xyzPLMD::generic::DumpAtomsprivate
fopen(const char *path, const char *mode)PLMD::Action
forceOnEnergyPLMD::ActionAtomisticprivate
forceOnExtraCVPLMD::ActionAtomisticprivate
forcesPLMD::ActionAtomisticprivate
getAbsoluteIndex(int i) constPLMD::ActionAtomisticinline
getAbsoluteIndexes() constPLMD::ActionAtomisticinlinevirtual
getArgument(const unsigned n) constPLMD::ActionWithArgumentsinline
getArguments() constPLMD::ActionWithArgumentsinlinevirtual
getBox() constPLMD::ActionAtomisticinline
getCharge(int i) 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
getName() constPLMD::Actioninline
getNumberOfArguments() constPLMD::ActionWithArgumentsinlinevirtual
getNumberOfAtoms() constPLMD::ActionAtomisticinline
getPbc() constPLMD::ActionAtomisticinline
getPntrToArgument(const unsigned n) constPLMD::ActionWithArgumentsinline
getPosition(int) constPLMD::ActionAtomisticinline
getPositions() constPLMD::ActionAtomisticinline
getProjection(unsigned i, unsigned j) constPLMD::ActionWithArguments
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
interpretArgumentList(const std::vector< std::string > &c, const ActionSet &as, Action *action, std::vector< Value * > &arg)PLMD::ActionWithArgumentsstatic
interpretAtomList(std::vector< std::string > &strings, std::vector< AtomNumber > &t)PLMD::ActionAtomistic
iprecisionPLMD::generic::DumpAtomsprivate
isActive() constPLMD::Actioninline
isOptionOn(const std::string &s) constPLMD::Actioninline
keywordsPLMD::Action
labelPLMD::Actionprivate
lenunitPLMD::generic::DumpAtomsprivate
linePLMD::Actionprivate
lockRequestArgumentsPLMD::ActionWithArgumentsprivate
lockRequestAtomsPLMD::ActionAtomisticprivate
lockRequests() overridePLMD::generic::DumpAtomsvirtual
logPLMD::Action
makeWhole()PLMD::ActionAtomistic
massesPLMD::ActionAtomisticprivate
masvPLMD::ActionAtomisticprivate
modifyForceOnEnergy()PLMD::ActionAtomisticinline
multi_sim_commPLMD::Action
namePLMD::Actionprivate
namesPLMD::generic::DumpAtomsprivate
never_activatePLMD::Actionprivate
ofPLMD::generic::DumpAtomsprivate
onStep() constPLMD::ActionPilotvirtual
operator=(const Action &a)=deletePLMD::Actionprivate
optionsPLMD::Actionprivate
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
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
pbcPLMD::ActionAtomisticprivate
pbc_fwdPLMD::ActionAtomisticprivate
pbcApply(std::vector< Vector > &dlist, unsigned max_index=0) constPLMD::ActionAtomistic
pbcDistance(const Vector &, const Vector &) constPLMD::ActionAtomisticinline
plumedPLMD::Action
positionsPLMD::ActionAtomisticprivate
prepare()PLMD::Actionvirtual
readAtomsFromPDB(const PDB &pdb) overridePLMD::ActionAtomisticvirtual
registerKeywords(Keywords &keys)PLMD::generic::DumpAtomsstatic
replica_indexPLMD::Actionprivate
requestArguments(const std::vector< Value * > &arg)PLMD::ActionWithArguments
requestAtoms(const std::vector< AtomNumber > &a, const bool clearDep=true)PLMD::ActionAtomistic
requestExtraDependencies(const std::vector< Value * > &extra)PLMD::ActionWithArguments
residueNamesPLMD::generic::DumpAtomsprivate
residueNumbersPLMD::generic::DumpAtomsprivate
restartPLMD::Actionprivate
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
setGradients(Value *myval, unsigned &start) constPLMD::ActionWithArguments
setOption(const std::string &s)PLMD::Actionvirtual
setStride(const int &n)PLMD::ActionPilot
setupConstantValues(const bool &have_atoms)PLMD::Action
stridePLMD::ActionPilotprivate
timestepPLMD::Actionprivate
typePLMD::generic::DumpAtomsprivate
uniquePLMD::ActionAtomisticprivate
unique_localPLMD::ActionAtomisticprivate
unique_local_needs_updatePLMD::ActionAtomisticprivate
unlockRequests() overridePLMD::generic::DumpAtomsvirtual
update() overridePLMD::generic::DumpAtomsvirtual
update_fromPLMD::Actionprivate
update_untilPLMD::Actionprivate
updateUniqueLocal(const bool &useunique, const std::vector< int > &g2l)PLMD::ActionAtomisticprivate
usingNaturalUnits() constPLMD::Actionprotected
value_dependsPLMD::ActionAtomisticprivate
warning(const std::string &msg)PLMD::Action
writeInGraph() constPLMD::Actionvirtual
xdPLMD::generic::DumpAtomsprivate
xposPLMD::ActionAtomisticprivate
yposPLMD::ActionAtomisticprivate
zposPLMD::ActionAtomisticprivate
~Action()PLMD::Actionvirtual
~ActionAtomistic()PLMD::ActionAtomistic
~ActionWithArguments()PLMD::ActionWithArgumentsinlinevirtual
~DumpAtoms()PLMD::generic::DumpAtoms
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