Action(const ActionOptions &) | PLMD::Action | explicit |
actionIsBridged | PLMD::vesselbase::ActionWithVessel | private |
ActionWithInputVessel class | PLMD::vesselbase::ActionWithVessel | friend |
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 | |
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 |
apply()=0 | PLMD::Action | pure virtual |
applyBridgeForces(const std::vector< double > &bb) | PLMD::vesselbase::ActionWithVessel | inlinevirtual |
bridgeVariable | PLMD::vesselbase::ActionWithVessel | protected |
BridgeVessel class | PLMD::vesselbase::ActionWithVessel | friend |
buffer | PLMD::vesselbase::ActionWithVessel | private |
buildDataStashes(const bool &allow_wcutoff, const double &wtol) | PLMD::vesselbase::ActionWithVessel | |
calculate()=0 | PLMD::Action | pure virtual |
calculateAllVessels(const unsigned &taskCode, MultiValue &myvals, MultiValue &bvals, std::vector< double > &buffer, std::vector< unsigned > &der_list) | PLMD::vesselbase::ActionWithVessel | protected |
calculateFromPDB(const PDB &) | PLMD::Action | |
calculateNumericalDerivatives(ActionWithValue *a=NULL) | PLMD::Action | virtual |
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 |
comm | PLMD::Action | |
contributorsAreUnlocked | PLMD::vesselbase::ActionWithVessel | 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 | |
der_list | PLMD::vesselbase::ActionWithVessel | private |
derivativesAreRequired() const | PLMD::vesselbase::ActionWithVessel | inline |
doJobsRequiredBeforeTaskList() | PLMD::vesselbase::ActionWithVessel | virtual |
error(const std::string &msg) const | PLMD::Action | |
exit(int c=0) | PLMD::Action | |
fclose(FILE *fp) | PLMD::Action | |
fflush() | PLMD::Action | |
files | PLMD::Action | |
files_iterator typedef | PLMD::Action | |
finishComputations(const std::vector< double > &buffer) | PLMD::vesselbase::ActionWithVessel | virtual |
finishTaskListUpdate() | PLMD::vesselbase::ActionWithVessel | inlinevirtual |
fopen(const char *path, const char *mode) | PLMD::Action | |
fullTaskList | PLMD::vesselbase::ActionWithVessel | private |
functions | PLMD::vesselbase::ActionWithVessel | private |
FunctionVessel class | PLMD::vesselbase::ActionWithVessel | friend |
getActiveTask(const unsigned &ii) const | PLMD::vesselbase::ActionWithVessel | inlineprotected |
getCurrentNumberOfActiveTasks() const | PLMD::vesselbase::ActionWithVessel | inlineprotected |
getDependencies() const | PLMD::Action | inline |
getDocumentation() const | PLMD::Action | virtual |
getExchangeStep() const | PLMD::Action | |
getForcesFromVessels(std::vector< double > &forcesToApply) | PLMD::vesselbase::ActionWithVessel | protected |
getFullNumberOfTasks() const | PLMD::vesselbase::ActionWithVessel | inline |
getLabel() const | PLMD::Action | inline |
getName() const | PLMD::Action | inline |
getNLTolerance() const | PLMD::vesselbase::ActionWithVessel | inlineprotected |
getNumberOfDerivatives()=0 | PLMD::vesselbase::ActionWithVessel | pure virtual |
getNumberOfQuantities() | PLMD::vesselbase::ActionWithVessel | inlinevirtual |
getNumberOfVessels() const | PLMD::vesselbase::ActionWithVessel | inlineprotected |
getPntrToVessel(const unsigned &i) | PLMD::vesselbase::ActionWithVessel | inlineprotected |
getPositionInFullTaskList(const unsigned &ii) const | PLMD::vesselbase::ActionWithVessel | inline |
getRestart() const | PLMD::Action | inline |
getSizeOfBuffer(unsigned &bufsize) | PLMD::vesselbase::ActionWithVessel | protected |
getStep() const | PLMD::Action | |
getTaskCode(const unsigned &ii) const | PLMD::vesselbase::ActionWithVessel | inline |
getTime() const | PLMD::Action | |
getTimeStep() const | PLMD::Action | |
getTolerance() const | PLMD::vesselbase::ActionWithVessel | inlineprotected |
getVesselWithName(const std::string &mynam) | PLMD::vesselbase::ActionWithVessel | |
indexOfTaskInFullList | PLMD::vesselbase::ActionWithVessel | private |
isActive() const | PLMD::Action | inline |
isOptionOn(const std::string &s) const | PLMD::Action | inline |
isPeriodic()=0 | PLMD::vesselbase::ActionWithVessel | pure virtual |
keywords | PLMD::Action | |
lockContributors() | PLMD::vesselbase::ActionWithVessel | |
lockRequests() | PLMD::Action | inlinevirtual |
log | PLMD::Action | |
lowmem | PLMD::vesselbase::ActionWithVessel | private |
maxderivatives | PLMD::vesselbase::ActionWithVessel | private |
multi_sim_comm | PLMD::Action | |
mydata | PLMD::vesselbase::ActionWithVessel | private |
nactive_tasks | PLMD::vesselbase::ActionWithVessel | private |
needsDerivatives() | PLMD::vesselbase::ActionWithVessel | protected |
nl_tolerance | PLMD::vesselbase::ActionWithVessel | private |
noderiv | PLMD::vesselbase::ActionWithVessel | private |
parse(const std::string &key, T &t) | PLMD::Action | |
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 | |
partialTaskList | PLMD::vesselbase::ActionWithVessel | private |
performTask(const unsigned &, const unsigned &, MultiValue &) const =0 | PLMD::vesselbase::ActionWithVessel | pure virtual |
plumed | PLMD::Action | |
prepare() | PLMD::Action | virtual |
readAtomsFromPDB(const PDB &) | PLMD::Action | inlinevirtual |
readVesselKeywords() | PLMD::vesselbase::ActionWithVessel | protected |
registerKeywords(Keywords &keys) | PLMD::vesselbase::ActionWithVessel | static |
resizeFunctions() | PLMD::vesselbase::ActionWithVessel | protected |
retrieveDomain(std::string &min, std::string &max) | PLMD::vesselbase::ActionWithVessel | virtual |
runAllTasks() | PLMD::vesselbase::ActionWithVessel | protected |
runFinalJobs() | PLMD::Action | inlinevirtual |
serial | PLMD::vesselbase::ActionWithVessel | private |
serialCalculation() const | PLMD::vesselbase::ActionWithVessel | inlineprotected |
setLowMemOption(const bool &) | PLMD::vesselbase::ActionWithVessel | inlineprotected |
setOption(const std::string &s) | PLMD::Action | virtual |
ShortcutVessel class | PLMD::vesselbase::ActionWithVessel | friend |
stopwatch | PLMD::vesselbase::ActionWithVessel | private |
StoreDataVessel class | PLMD::vesselbase::ActionWithVessel | friend |
taskFlags | PLMD::vesselbase::ActionWithVessel | private |
timers | PLMD::vesselbase::ActionWithVessel | private |
tmpforces | PLMD::vesselbase::ActionWithVessel | private |
tolerance | PLMD::vesselbase::ActionWithVessel | private |
transformBridgedDerivatives(const unsigned ¤t, MultiValue &invals, MultiValue &outvals) const | PLMD::vesselbase::ActionWithVessel | virtual |
unlockContributors() | PLMD::vesselbase::ActionWithVessel | |
unlockRequests() | PLMD::Action | inlinevirtual |
update() | PLMD::Action | inlinevirtual |
usingLowMem() const | PLMD::vesselbase::ActionWithVessel | inlineprotected |
Vessel class | PLMD::vesselbase::ActionWithVessel | friend |
warning(const std::string &msg) | PLMD::Action | |
weightHasDerivatives | PLMD::vesselbase::ActionWithVessel | protected |
weightWithDerivatives() const | PLMD::vesselbase::ActionWithVessel | inline |
~Action() | PLMD::Action | virtual |
~ActionWithVessel() | PLMD::vesselbase::ActionWithVessel | |