| accumulate() | PLMD::analysis::Analysis | |
| Action(const ActionOptions &) | PLMD::Action | explicit |
| ActionAtomistic(const ActionOptions &ao) | PLMD::ActionAtomistic | explicit |
| ActionPilot(const ActionOptions &) | PLMD::ActionPilot | explicit |
| ActionWithArguments(const ActionOptions &) | PLMD::ActionWithArguments | explicit |
| ActionWithVessel(const ActionOptions &ao) | PLMD::vesselbase::ActionWithVessel | explicit |
| activate() | PLMD::Action | virtual |
| activateTheseTasks(std::vector< unsigned > &addtionalTasks) | PLMD::vesselbase::ActionWithVessel | |
| addBridgingVessel(ActionWithVessel *tome) | PLMD::vesselbase::ActionWithVessel | protected |
| addDependency(Action *) | PLMD::Action | |
| addForcesOnArguments(const std::vector< double > &forces) | PLMD::ActionWithArguments | |
| addTaskToList(const unsigned &taskCode) | PLMD::vesselbase::ActionWithVessel | protected |
| addVessel(const std::string &name, const std::string &input, const int numlab=0) | PLMD::vesselbase::ActionWithVessel | protected |
| addVessel(Vessel *vv) | PLMD::vesselbase::ActionWithVessel | protected |
| allowToAccessGlobalForces() | PLMD::ActionAtomistic | inline |
| Analysis(const ActionOptions &) | PLMD::analysis::Analysis | explicit |
| apply() | PLMD::analysis::Analysis | inlinevirtual |
| applyBridgeForces(const std::vector< double > &bb) | PLMD::vesselbase::ActionWithVessel | inlinevirtual |
| applyForces() | PLMD::ActionAtomistic | |
| argument_names | PLMD::analysis::Analysis | private |
| atoms | PLMD::ActionAtomistic | protected |
| biases | PLMD::analysis::Analysis | private |
| bridgeVariable | PLMD::vesselbase::ActionWithVessel | protected |
| bringBackInPbc(int i, double d1) const | PLMD::ActionWithArguments | inline |
| buildDataStashes(const bool &allow_wcutoff, const double &wtol) | PLMD::vesselbase::ActionWithVessel | |
| calculate() | PLMD::analysis::Analysis | virtual |
| calculateAllVessels(const unsigned &taskCode, MultiValue &myvals, MultiValue &bvals, std::vector< double > &buffer, std::vector< unsigned > &der_list) | PLMD::vesselbase::ActionWithVessel | protected |
| calculateAtomicNumericalDerivatives(ActionWithValue *a, const unsigned &startnum) | PLMD::ActionAtomistic | |
| calculateFromPDB(const PDB &) | PLMD::Action | |
| calculateNumericalDerivatives(ActionWithValue *a=NULL) | PLMD::analysis::Analysis | inlinevirtual |
| changeBox(const Tensor &newbox) | PLMD::ActionAtomistic | |
| 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 | |
| contributorsAreUnlocked | PLMD::vesselbase::ActionWithVessel | protected |
| current_args | PLMD::analysis::Analysis | private |
| data | PLMD::analysis::Analysis | protected |
| deactivate() | PLMD::Action | inlinevirtual |
| deactivate_task(const unsigned &task_index) | PLMD::vesselbase::ActionWithVessel | virtual |
| deactivateAllTasks() | PLMD::vesselbase::ActionWithVessel | protected |
| deactivateTasksInRange(const unsigned &lower, const unsigned &upper) | PLMD::vesselbase::ActionWithVessel | protected |
| Dependencies typedef | PLMD::Action | |
| derivativesAreRequired() const | PLMD::vesselbase::ActionWithVessel | inline |
| difference(int, double, double) const | PLMD::ActionWithArguments | inline |
| doJobsRequiredBeforeTaskList() | PLMD::vesselbase::ActionWithVessel | virtual |
| doNotForce() | PLMD::ActionAtomistic | inline |
| doNotRetrieve() | PLMD::ActionAtomistic | inline |
| error(const std::string &msg) const | PLMD::Action | |
| exit(int c=0) | PLMD::Action | |
| expandArgKeywordInPDB(PDB &pdb) | PLMD::ActionWithArguments | protected |
| fclose(FILE *fp) | PLMD::Action | |
| fflush() | PLMD::Action | |
| files | PLMD::Action | |
| files_iterator typedef | PLMD::Action | |
| finalizeWeights(const bool &ignore_weights) | PLMD::analysis::Analysis | protected |
| finishComputations(const std::vector< double > &buffer) | PLMD::vesselbase::ActionWithVessel | virtual |
| finishTaskListUpdate() | PLMD::vesselbase::ActionWithVessel | inlinevirtual |
| firstAnalysisDone | PLMD::analysis::Analysis | private |
| fopen(const char *path, const char *mode) | PLMD::Action | |
| freq | PLMD::analysis::Analysis | private |
| getAbsoluteIndex(int i) const | PLMD::ActionAtomistic | inline |
| getAbsoluteIndexes() const | PLMD::ActionAtomistic | inline |
| getActiveTask(const unsigned &ii) const | PLMD::vesselbase::ActionWithVessel | inlineprotected |
| getArgument(const unsigned n) const | PLMD::ActionWithArguments | inline |
| getArguments() | PLMD::analysis::Analysis | inlineprotected |
| PLMD::ActionWithArguments::getArguments() const | PLMD::ActionWithArguments | inline |
| getBox() const | PLMD::ActionAtomistic | inline |
| getCharge(int i) const | PLMD::ActionAtomistic | inline |
| getCurrentNumberOfActiveTasks() const | PLMD::vesselbase::ActionWithVessel | inlineprotected |
| getDataPoint(const unsigned &idata, std::vector< double > &point, double &weight) const | PLMD::analysis::Analysis | protected |
| getDependencies() const | PLMD::Action | inline |
| getDocumentation() const | PLMD::Action | virtual |
| getEnergy() const | PLMD::ActionAtomistic | inline |
| getExchangeStep() const | PLMD::Action | |
| getForcesFromVessels(std::vector< double > &forcesToApply) | PLMD::vesselbase::ActionWithVessel | protected |
| getFullNumberOfTasks() const | PLMD::vesselbase::ActionWithVessel | inline |
| getLabel() const | PLMD::Action | inline |
| getMass(int i) const | PLMD::ActionAtomistic | inline |
| getMetric() const | PLMD::analysis::Analysis | private |
| getMetricName() const | PLMD::analysis::Analysis | inlineprotected |
| getName() const | PLMD::Action | inline |
| getNLTolerance() const | PLMD::vesselbase::ActionWithVessel | inlineprotected |
| getNormalization() const | PLMD::analysis::Analysis | protected |
| getNumberOfArguments() const | PLMD::analysis::Analysis | inlineprotected |
| getNumberOfAtoms() const | PLMD::ActionAtomistic | inline |
| getNumberOfDataPoints() const | PLMD::analysis::Analysis | inlineprotected |
| getNumberOfDerivatives() | PLMD::analysis::Analysis | inlinevirtual |
| getNumberOfQuantities() | PLMD::vesselbase::ActionWithVessel | inlinevirtual |
| getNumberOfVessels() const | PLMD::vesselbase::ActionWithVessel | inlineprotected |
| getOutputFormat() const | PLMD::analysis::Analysis | inlineprotected |
| getPbc() const | PLMD::ActionAtomistic | inline |
| getPeriodicityInformation(const unsigned &i, std::string &dmin, std::string &dmax) | PLMD::analysis::Analysis | protected |
| getPntrToArgument(const unsigned n) | PLMD::ActionWithArguments | inline |
| getPntrToVessel(const unsigned &i) | PLMD::vesselbase::ActionWithVessel | inlineprotected |
| getPosition(int) const | PLMD::ActionAtomistic | inline |
| getPosition(AtomNumber) const | PLMD::ActionAtomistic | inline |
| getPositionInFullTaskList(const unsigned &ii) const | PLMD::vesselbase::ActionWithVessel | inline |
| getPositions() const | PLMD::ActionAtomistic | inline |
| getProjection(unsigned i, unsigned j) const | PLMD::ActionWithArguments | |
| getRestart() const | PLMD::Action | inline |
| getSizeOfBuffer(unsigned &bufsize) | PLMD::vesselbase::ActionWithVessel | protected |
| getStep() const | PLMD::Action | |
| getStride() const | PLMD::ActionPilot | protected |
| getTaskCode(const unsigned &ii) const | PLMD::vesselbase::ActionWithVessel | inline |
| getTemp() const | PLMD::analysis::Analysis | protected |
| getTime() const | PLMD::Action | |
| getTimeStep() const | PLMD::Action | |
| getTolerance() const | PLMD::vesselbase::ActionWithVessel | inlineprotected |
| getTotAtoms() const | PLMD::ActionAtomistic | inline |
| getUnique() const | PLMD::ActionAtomistic | inline |
| getVesselWithName(const std::string &mynam) | PLMD::vesselbase::ActionWithVessel | |
| getWeight(const unsigned &idata) const | PLMD::analysis::Analysis | protected |
| idata | PLMD::analysis::Analysis | private |
| ignore_reweight | PLMD::analysis::Analysis | private |
| interpretArgumentList(const std::vector< std::string > &c, std::vector< Value * > &arg) | PLMD::ActionWithArguments | |
| isActive() const | PLMD::Action | inline |
| isOptionOn(const std::string &s) const | PLMD::Action | inline |
| isPeriodic() | PLMD::analysis::Analysis | inlinevirtual |
| keywords | PLMD::Action | |
| lockContributors() | PLMD::vesselbase::ActionWithVessel | |
| lockRequests() | PLMD::analysis::Analysis | inlinevirtual |
| log | PLMD::Action | |
| logweights | PLMD::analysis::Analysis | private |
| makeWhole() | PLMD::ActionAtomistic | |
| metricname | PLMD::analysis::Analysis | private |
| modifyForceOnEnergy() | PLMD::ActionAtomistic | inline |
| modifyForces() | PLMD::ActionAtomistic | inline |
| modifyGlobalForce(AtomNumber) | PLMD::ActionAtomistic | inline |
| modifyGlobalVirial() | PLMD::ActionAtomistic | inline |
| modifyPosition(AtomNumber) | PLMD::ActionAtomistic | inline |
| modifyVirial() | PLMD::ActionAtomistic | inline |
| multi_sim_comm | PLMD::Action | |
| mydatastash | PLMD::analysis::Analysis | private |
| ndata | PLMD::analysis::Analysis | private |
| needeng | PLMD::analysis::Analysis | private |
| needsDerivatives() | PLMD::vesselbase::ActionWithVessel | protected |
| nomemory | PLMD::analysis::Analysis | private |
| norm | PLMD::analysis::Analysis | private |
| ofmt | PLMD::analysis::Analysis | private |
| old_norm | PLMD::analysis::Analysis | private |
| onStep() const | PLMD::ActionPilot | |
| parse(const std::string &key, T &t) | PLMD::Action | |
| parseArgumentList(const std::string &key, 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 | |
| parseOutputFile(const std::string &key, std::string &filename) | PLMD::analysis::Analysis | protected |
| parseVector(const std::string &key, std::vector< T > &t) | PLMD::Action | |
| pbcApply(std::vector< Vector > &dlist, unsigned max_index=0) const | PLMD::ActionAtomistic | |
| pbcDistance(const Vector &, const Vector &) const | PLMD::ActionAtomistic | |
| performAnalysis()=0 | PLMD::analysis::Analysis | pure virtual |
| performTask(const unsigned &, const unsigned &, MultiValue &) const =0 | PLMD::vesselbase::ActionWithVessel | pure virtual |
| plumed | PLMD::Action | |
| prepare() | PLMD::analysis::Analysis | virtual |
| PLMD::readAtomsFromPDB(const PDB &) | PLMD::Action | inlinevirtual |
| PLMD::ActionAtomistic::readAtomsFromPDB(const PDB &pdb) | PLMD::ActionAtomistic | virtual |
| readDataFromFile(const std::string &filename) | PLMD::analysis::Analysis | private |
| readVesselKeywords() | PLMD::vesselbase::ActionWithVessel | protected |
| registerKeywords(Keywords &keys) | PLMD::analysis::Analysis | static |
| requestArguments(const std::vector< Value * > &arg) | PLMD::ActionWithArguments | |
| requestAtoms(const std::vector< AtomNumber > &a) | PLMD::ActionAtomistic | |
| resizeFunctions() | PLMD::vesselbase::ActionWithVessel | protected |
| retrieveAtoms() | PLMD::ActionAtomistic | |
| retrieveDomain(std::string &min, std::string &max) | PLMD::vesselbase::ActionWithVessel | virtual |
| retrieveNorm() const | PLMD::analysis::Analysis | inlineprivate |
| reusing_data | PLMD::analysis::Analysis | private |
| rfile | PLMD::analysis::Analysis | private |
| rtemp | PLMD::analysis::Analysis | private |
| runAllTasks() | PLMD::vesselbase::ActionWithVessel | protected |
| runAnalysis() | PLMD::analysis::Analysis | |
| runFinalJobs() | PLMD::analysis::Analysis | virtual |
| serialCalculation() const | PLMD::vesselbase::ActionWithVessel | inlineprotected |
| setForcesOnAtoms(const std::vector< double > &forcesToApply, unsigned ind=0) | PLMD::ActionAtomistic | |
| setLowMemOption(const bool &) | PLMD::vesselbase::ActionWithVessel | inlineprotected |
| setOption(const std::string &s) | PLMD::Action | virtual |
| simtemp | PLMD::analysis::Analysis | private |
| single_run | PLMD::analysis::Analysis | private |
| transformBridgedDerivatives(const unsigned ¤t, MultiValue &invals, MultiValue &outvals) const | PLMD::vesselbase::ActionWithVessel | virtual |
| unlockContributors() | PLMD::vesselbase::ActionWithVessel | |
| unlockRequests() | PLMD::analysis::Analysis | inlinevirtual |
| update() | PLMD::analysis::Analysis | virtual |
| usingLowMem() const | PLMD::vesselbase::ActionWithVessel | inlineprotected |
| usingMemory() const | PLMD::analysis::Analysis | inlineprotected |
| warning(const std::string &msg) | PLMD::Action | |
| weightHasDerivatives | PLMD::vesselbase::ActionWithVessel | protected |
| weightWithDerivatives() const | PLMD::vesselbase::ActionWithVessel | inline |
| write_chq | PLMD::analysis::Analysis | private |
| ~Action() | PLMD::Action | virtual |
| ~ActionAtomistic() | PLMD::ActionAtomistic | |
| ~ActionWithArguments() | PLMD::ActionWithArguments | inlinevirtual |
| ~ActionWithVessel() | PLMD::vesselbase::ActionWithVessel | |
| ~Analysis() | PLMD::analysis::Analysis | |
1.8.10
