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PLMD::analysis::Analysis Member List

This is the complete list of members for PLMD::analysis::Analysis, including all inherited members.

accumulate()PLMD::analysis::Analysis
Action(const ActionOptions &)PLMD::Action
ActionPilot(const ActionOptions &)PLMD::ActionPilot
ActionWithArguments(const ActionOptions &)PLMD::ActionWithArguments
activate()PLMD::Actionvirtual
addDependency(Action *)PLMD::Action
addForcesOnArguments(const std::vector< double > &forces)PLMD::ActionWithArguments
Analysis(const ActionOptions &)PLMD::analysis::Analysis
apply()PLMD::analysis::Analysisinlinevirtual
argsPLMD::analysis::Analysisprivate
biasesPLMD::analysis::Analysisprivate
bringBackInPbc(int i, double d1) const PLMD::ActionWithArgumentsinline
calculate()PLMD::analysis::Analysisvirtual
calculateFromPDB(const PDB &)PLMD::Action
PLMD::calculateNumericalDerivatives(ActionWithValue *a=NULL)PLMD::Actionvirtual
PLMD::ActionWithArguments::calculateNumericalDerivatives(ActionWithValue *a=NULL)PLMD::ActionWithArgumentsvirtual
checkNeedsGradients() const PLMD::Actioninlinevirtual
checkNumericalDerivatives() const PLMD::Actioninlinevirtual
checkRead()PLMD::Action
cite(const std::string &s)PLMD::Action
clearDependencies()PLMD::Action
clearOptions()PLMD::Actionvirtual
commPLMD::Action
dataPLMD::analysis::Analysisprivate
deactivate()PLMD::Actioninlinevirtual
Dependencies typedefPLMD::Action
difference(int, double, double) const PLMD::ActionWithArgumentsinline
error(const std::string &msg) const PLMD::Action
exit(int c=0)PLMD::Action
expandArgKeywordInPDB(PDB &pdb)PLMD::ActionWithArgumentsprotected
fclose(FILE *fp)PLMD::Action
fflush()PLMD::Action
filesPLMD::Action
files_iterator typedefPLMD::Action
finalizeWeights(const bool &ignore_weights)PLMD::analysis::Analysisprotected
firstAnalysisDonePLMD::analysis::Analysisprivate
fopen(const char *path, const char *mode)PLMD::Action
freqPLMD::analysis::Analysisprivate
getArgument(const unsigned n) const PLMD::ActionWithArgumentsinline
getArguments()PLMD::analysis::Analysisinlineprotected
getDataPoint(const unsigned &idata, std::vector< double > &point, double &weight) const PLMD::analysis::Analysisinlineprotected
getDependencies() const PLMD::Actioninline
getDocumentation() const PLMD::Actionvirtual
getExchangeStep() const PLMD::Action
getLabel() const PLMD::Actioninline
getName() const PLMD::Actioninline
getNormalization() const PLMD::analysis::Analysisprotected
getNumberOfArguments() const PLMD::analysis::Analysisinlineprotected
getNumberOfDataPoints() const PLMD::analysis::Analysisinlineprotected
getOutputFormat() const PLMD::analysis::Analysisinlineprotected
getPeriodicityInformation(const unsigned &i, std::string &dmin, std::string &dmax)PLMD::analysis::Analysisprotected
getPntrToArgument(const unsigned n)PLMD::ActionWithArgumentsinline
getProjection(unsigned i, unsigned j) const PLMD::ActionWithArguments
getStep() const PLMD::Action
getStride() const PLMD::ActionPilotprotected
getTime() const PLMD::Action
getTimeStep() const PLMD::Action
idataPLMD::analysis::Analysisprivate
ignore_reweightPLMD::analysis::Analysisprivate
interpretArgumentList(const std::vector< std::string > &c, std::vector< Value * > &arg)PLMD::ActionWithArguments
isActive() const PLMD::Actioninline
isOptionOn(const std::string &s) const PLMD::Actioninline
keywordsPLMD::Action
PLMD::lockRequests()PLMD::Actioninlinevirtual
PLMD::ActionWithArguments::lockRequests()PLMD::ActionWithArgumentsinlinevirtual
logPLMD::Action
logweightsPLMD::analysis::Analysisprivate
multi_sim_commPLMD::Action
mydatastashPLMD::analysis::Analysisprivate
ndataPLMD::analysis::Analysisprivate
needengPLMD::analysis::Analysisprivate
nomemoryPLMD::analysis::Analysisprivate
normPLMD::analysis::Analysisprivate
ofmtPLMD::analysis::Analysisprivate
old_normPLMD::analysis::Analysisprivate
onStep() const PLMD::ActionPilot
parse(const std::string &key, T &t)PLMD::Action
parseArgumentList(const std::string &key, std::vector< Value * > &args)PLMD::ActionWithArguments
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
parseOutputFile(const std::string &key, std::string &filename)PLMD::analysis::Analysisprotected
parseVector(const std::string &key, std::vector< T > &t)PLMD::Action
performAnalysis()=0PLMD::analysis::Analysispure virtual
plumedPLMD::Action
prepare()PLMD::analysis::Analysisvirtual
readAtomsFromPDB(const PDB &)PLMD::Actioninlinevirtual
readDataFromFile(const std::string &filename)PLMD::analysis::Analysisprivate
registerKeywords(Keywords &keys)PLMD::analysis::Analysisstatic
requestArguments(const std::vector< Value * > &arg)PLMD::ActionWithArguments
retrieveNorm() const PLMD::analysis::Analysisinlineprivate
reusing_dataPLMD::analysis::Analysisprivate
rfilePLMD::analysis::Analysisprivate
rtempPLMD::analysis::Analysisprivate
runAnalysis()PLMD::analysis::Analysis
runFinalJobs()PLMD::analysis::Analysisvirtual
setOption(const std::string &s)PLMD::Actionvirtual
simtempPLMD::analysis::Analysisprivate
single_runPLMD::analysis::Analysisprivate
PLMD::unlockRequests()PLMD::Actioninlinevirtual
PLMD::ActionWithArguments::unlockRequests()PLMD::ActionWithArgumentsinlinevirtual
update()PLMD::analysis::Analysisvirtual
usingMemory() const PLMD::analysis::Analysisinlineprotected
warning(const std::string &msg)PLMD::Action
weightsPLMD::analysis::Analysisprivate
write_chqPLMD::analysis::Analysisprivate
~Action()PLMD::Actionvirtual
~ActionWithArguments()PLMD::ActionWithArgumentsinlinevirtual
~Analysis()PLMD::analysis::Analysis
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