Action(const ActionOptions &) | PLMD::Action | explicit |
action_pntr_ | PLMD::ves::TargetDistribution | private |
activate() | PLMD::Action | virtual |
addDependency(Action *) | PLMD::Action | |
allow_bias_cutoff_ | PLMD::ves::TargetDistribution | private |
allowBiasCutoff() | PLMD::ves::TargetDistribution | inline |
apply() override | PLMD::ves::TargetDistribution | inlinevirtual |
applyTargetDistModiferToGrid(TargetDistModifer *modifer_pntr) | PLMD::ves::TargetDistribution | protected |
beforeUpdate() | PLMD::Action | inlinevirtual |
bias_cutoff_active_ | PLMD::ves::TargetDistribution | private |
bias_grid_pntr_ | PLMD::ves::TargetDistribution | private |
bias_withoutcutoff_grid_pntr_ | PLMD::ves::TargetDistribution | private |
biasCutoffActive() const | PLMD::ves::TargetDistribution | inline |
biasGridNeeded() const | PLMD::ves::TargetDistribution | inline |
biasWithoutCutoffGridNeeded() const | PLMD::ves::TargetDistribution | inline |
calculate() override | PLMD::ves::TargetDistribution | inlinevirtual |
calculateFromPDB(const PDB &) | PLMD::Action | |
calculateNumericalDerivatives(ActionWithValue *a=NULL) | PLMD::Action | virtual |
calculateStaticDistributionGrid() | PLMD::ves::TargetDistribution | private |
check_nan_inf_ | PLMD::ves::TargetDistribution | private |
check_nonnegative_ | PLMD::ves::TargetDistribution | private |
check_normalization_ | PLMD::ves::TargetDistribution | private |
checkNanAndInf() | PLMD::ves::TargetDistribution | private |
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 | |
clearLogTargetDistGrid() | PLMD::ves::TargetDistribution | |
clearOptions() | PLMD::Action | virtual |
comm | PLMD::Action | |
deactivate() | PLMD::Action | inlinevirtual |
Dependencies typedef | PLMD::Action | |
dimension_ | PLMD::ves::TargetDistribution | private |
doNotAllowBiasCutoff() | PLMD::ves::TargetDistribution | inline |
dynamic_targetdist enum value | PLMD::ves::TargetDistribution | private |
error(const std::string &msg) const | PLMD::Action | |
exit(int c=0) | PLMD::Action | |
fclose(FILE *fp) | PLMD::Action | |
fes_grid_pntr_ | PLMD::ves::TargetDistribution | private |
fesGridNeeded() const | PLMD::ves::TargetDistribution | inline |
fflush() | PLMD::Action | |
files | PLMD::Action | |
fopen(const char *path, const char *mode) | PLMD::Action | |
force_normalization_ | PLMD::ves::TargetDistribution | private |
forcedNormalization() const | PLMD::ves::TargetDistribution | inline |
getBeta() const | PLMD::ves::TargetDistribution | protected |
getBiasGridPntr() const | PLMD::ves::TargetDistribution | inlineprotected |
getBiasWithoutCutoffGridPntr() const | PLMD::ves::TargetDistribution | inlineprotected |
getCPT() const | PLMD::Action | |
getDependencies() const | PLMD::Action | inline |
getDimension() const | PLMD::ves::TargetDistribution | inline |
getDocumentation() const | PLMD::Action | virtual |
getExchangeStep() const | PLMD::Action | |
getFesGridPntr() const | PLMD::ves::TargetDistribution | inlineprotected |
getKeyword(const std::string &key) | PLMD::Action | |
getLabel() const | PLMD::Action | inline |
getLogTargetDistGridPntr() const | PLMD::ves::TargetDistribution | inline |
getMarginal(const std::vector< std::string > &) | PLMD::ves::TargetDistribution | |
getMarginalDistributionGrid(Grid *, const std::vector< std::string > &) | PLMD::ves::TargetDistribution | static |
getName() const | PLMD::Action | inline |
getPntrToAction() const | PLMD::ves::TargetDistribution | inlineprotected |
getPntrToVesBias() const | PLMD::ves::TargetDistribution | inlineprotected |
getRestart() const | PLMD::Action | inline |
getStep() const | PLMD::Action | |
getTargetDistGridPntr() const | PLMD::ves::TargetDistribution | inline |
getTime() const | PLMD::Action | |
getTimeStep() const | PLMD::Action | |
getValue(const std::vector< double > &) const =0 | PLMD::ves::TargetDistribution | pure virtual |
grid_args_ | PLMD::ves::TargetDistribution | private |
integrateGrid(const Grid *) | PLMD::ves::TargetDistribution | static |
isActive() const | PLMD::Action | inline |
isBiasCutoffAllowed() const | PLMD::ves::TargetDistribution | inline |
isDynamic() const | PLMD::ves::TargetDistribution | inline |
isOptionOn(const std::string &s) const | PLMD::Action | inline |
isStatic() const | PLMD::ves::TargetDistribution | inline |
isTargetDistGridShiftedToZero() const | PLMD::ves::TargetDistribution | inline |
keywords | PLMD::Action | |
linkAction(Action *) | PLMD::ves::TargetDistribution | virtual |
linkBiasGrid(Grid *) | PLMD::ves::TargetDistribution | virtual |
linkBiasWithoutCutoffGrid(Grid *) | PLMD::ves::TargetDistribution | virtual |
linkFesGrid(Grid *) | PLMD::ves::TargetDistribution | virtual |
linkVesBias(VesBias *) | PLMD::ves::TargetDistribution | virtual |
lockRequests() | PLMD::Action | inlinevirtual |
log | PLMD::Action | |
log_targetdist_grid_pntr_ | PLMD::ves::TargetDistribution | private |
logTargetDistGrid() const | PLMD::ves::TargetDistribution | inlineprotected |
multi_sim_comm | PLMD::Action | |
needs_bias_grid_ | PLMD::ves::TargetDistribution | private |
needs_bias_withoutcutoff_grid_ | PLMD::ves::TargetDistribution | private |
needs_fes_grid_ | PLMD::ves::TargetDistribution | private |
normalizeGrid(Grid *) | PLMD::ves::TargetDistribution | static |
normalizeTargetDistGrid() | PLMD::ves::TargetDistribution | inlineprotected |
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 | |
plumed | PLMD::Action | |
prepare() | PLMD::Action | virtual |
readAtomsFromPDB(const PDB &) | PLMD::Action | inlinevirtual |
readInRestartTargetDistGrid(const std::string &) | PLMD::ves::TargetDistribution | |
registerKeywords(Keywords &) | PLMD::ves::TargetDistribution | static |
runFinalJobs() | PLMD::Action | inlinevirtual |
setBiasGridNeeded() | PLMD::ves::TargetDistribution | inlineprotected |
setBiasWithoutCutoffGridNeeded() | PLMD::ves::TargetDistribution | inlineprotected |
setDimension(const unsigned int dimension) | PLMD::ves::TargetDistribution | |
setDynamic() | PLMD::ves::TargetDistribution | inlineprotected |
setFesGridNeeded() | PLMD::ves::TargetDistribution | inlineprotected |
setForcedNormalization() | PLMD::ves::TargetDistribution | inlineprotected |
setMinimumOfTargetDistGridToZero() | PLMD::ves::TargetDistribution | protected |
setOption(const std::string &s) | PLMD::Action | virtual |
setStatic() | PLMD::ves::TargetDistribution | inlineprotected |
setupAdditionalGrids(const std::vector< Value *> &, const std::vector< std::string > &, const std::vector< std::string > &, const std::vector< unsigned int > &) | PLMD::ves::TargetDistribution | inlineprotectedvirtual |
setupBiasCutoff() | PLMD::ves::TargetDistribution | |
setupGrids(const std::vector< Value *> &, const std::vector< std::string > &, const std::vector< std::string > &, const std::vector< unsigned int > &) | PLMD::ves::TargetDistribution | |
shift_targetdist_to_zero_ | PLMD::ves::TargetDistribution | private |
static_grid_calculated | PLMD::ves::TargetDistribution | private |
static_targetdist enum value | PLMD::ves::TargetDistribution | private |
targetdist_grid_pntr_ | PLMD::ves::TargetDistribution | private |
targetdist_modifer_pntrs_ | PLMD::ves::TargetDistribution | private |
targetDistGrid() const | PLMD::ves::TargetDistribution | inlineprotected |
TargetDistribution(const ActionOptions &) | PLMD::ves::TargetDistribution | explicit |
TargetDistType enum name | PLMD::ves::TargetDistribution | private |
type_ | PLMD::ves::TargetDistribution | private |
unlockRequests() | PLMD::Action | inlinevirtual |
unsetForcedNormalization() | PLMD::ves::TargetDistribution | inlineprotected |
update() override | PLMD::ves::TargetDistribution | inlinevirtual |
updateBiasCutoffForTargetDistGrid() | PLMD::ves::TargetDistribution | private |
updateGrid() | PLMD::ves::TargetDistribution | inlineprotectedvirtual |
updateLogTargetDistGrid() | PLMD::ves::TargetDistribution | protected |
updateTargetDist() | PLMD::ves::TargetDistribution | |
vesbias_pntr_ | PLMD::ves::TargetDistribution | private |
warning(const std::string &msg) | PLMD::Action | |
~Action() | PLMD::Action | virtual |
~TargetDistribution() | PLMD::ves::TargetDistribution | |