Action(const ActionOptions &) | PLMD::Action | explicit |
Action(const Action &a)=delete | PLMD::Action | private |
ActionPilot(const ActionOptions &) | PLMD::ActionPilot | explicit |
ActionWithArguments(const ActionOptions &) | PLMD::ActionWithArguments | explicit |
ActionWithValue(const ActionOptions &ao) | PLMD::ActionWithValue | explicit |
activate() | PLMD::Action | virtual |
active | PLMD::Action | private |
addComponent(const std::string &name) | PLMD::ActionWithValue | |
addComponentWithDerivatives(const std::string &name) | PLMD::ActionWithValue | |
addDependency(Action *) | PLMD::Action | |
addForcesOnArguments(const std::vector< double > &forces) | PLMD::ActionWithArguments | |
addValue() | PLMD::ActionWithValue | |
addValueWithDerivatives() | PLMD::ActionWithValue | |
after | PLMD::Action | private |
apply() override | PLMD::bias::Bias | virtual |
apply_bias() | PLMD::fisst::FISST | private |
arguments | PLMD::ActionWithArguments | private |
b_adaptive_ | PLMD::fisst::FISST | private |
b_first_restart_sample_ | PLMD::fisst::FISST | private |
b_freeze_ | PLMD::fisst::FISST | private |
b_restart_ | PLMD::fisst::FISST | private |
b_write_observable_ | PLMD::fisst::FISST | private |
b_write_restart_ | PLMD::fisst::FISST | private |
beforeUpdate() | PLMD::Action | inlinevirtual |
beta_ | PLMD::fisst::FISST | private |
Bias(const ActionOptions &ao) | PLMD::bias::Bias | explicit |
bringBackInPbc(int i, double d1) const | PLMD::ActionWithArguments | inline |
calculate() | PLMD::fisst::FISST | virtual |
calculateFromPDB(const PDB &) | PLMD::Action | |
PLMD::calculateNumericalDerivatives(ActionWithValue *a=NULL) | PLMD::Action | virtual |
PLMD::ActionWithArguments::calculateNumericalDerivatives(ActionWithValue *a=NULL) override | PLMD::ActionWithArguments | virtual |
center_ | PLMD::fisst::FISST | private |
checkFieldsAllowed() | PLMD::ActionWithValue | inlinevirtual |
checkNeedsGradients() const | PLMD::Action | inlinevirtual |
PLMD::checkNumericalDerivatives() const | PLMD::Action | inlinevirtual |
PLMD::ActionWithValue::checkNumericalDerivatives() const override | PLMD::ActionWithValue | inlinevirtual |
checkRead() | PLMD::Action | |
checkUpdate() const | PLMD::Action | |
cite(const std::string &s) | PLMD::Action | |
clearDependencies() | PLMD::Action | |
clearDerivatives() | PLMD::ActionWithValue | virtual |
clearInputForces() | PLMD::ActionWithValue | |
clearOptions() | PLMD::Action | virtual |
comm | PLMD::Action | |
componentIsNotPeriodic(const std::string &name) | PLMD::ActionWithValue | |
componentIsPeriodic(const std::string &name, const std::string &min, const std::string &max) | PLMD::ActionWithValue | |
componentsAreNotOptional(Keywords &keys) | PLMD::ActionWithValue | static |
compute_observable_weight() | PLMD::fisst::FISST | private |
copyOutput(const std::string &name) const | PLMD::ActionWithValue | |
copyOutput(const unsigned &n) const | PLMD::ActionWithValue | |
current_avg_force_ | PLMD::fisst::FISST | private |
deactivate() | PLMD::Action | inlinevirtual |
Dependencies typedef | PLMD::Action | |
difference(int, double, double) const | PLMD::ActionWithArguments | inline |
doCheckPoint | PLMD::Action | private |
doNotCalculateDerivatives() const | PLMD::ActionWithValue | inlinevirtual |
error(const std::string &msg) const | PLMD::Action | |
exists(const std::string &name) const | PLMD::ActionWithValue | |
exit(int c=0) | PLMD::Action | |
expandArgKeywordInPDB(const PDB &pdb) | PLMD::ActionWithArguments | protected |
fclose(FILE *fp) | PLMD::Action | |
fflush() | PLMD::Action | |
files | PLMD::Action | |
FISST(const ActionOptions &) | PLMD::fisst::FISST | explicit |
fmt_ | PLMD::fisst::FISST | private |
fopen(const char *path, const char *mode) | PLMD::Action | |
force_weight_ | PLMD::fisst::FISST | private |
forces_ | PLMD::fisst::FISST | private |
gauss_weight_ | PLMD::fisst::FISST | private |
getArgument(const unsigned n) const | PLMD::ActionWithArguments | inline |
getArguments() const | PLMD::ActionWithArguments | inlinevirtual |
getComponent(const std::string &name) const | PLMD::ActionWithValue | private |
getComponentsList() const | PLMD::ActionWithValue | |
getComponentsVector() const | PLMD::ActionWithValue | |
getCPT() const | PLMD::Action | |
getDependencies() const | PLMD::Action | inline |
getDocumentation() const | PLMD::Action | virtual |
getExchangeStep() const | PLMD::Action | |
getKeyword(const std::string &key) | PLMD::Action | |
getLabel() const | PLMD::Action | inline |
getName() const | PLMD::Action | inline |
getNumberOfArguments() const | PLMD::ActionWithArguments | inlinevirtual |
getNumberOfComponents() const | PLMD::ActionWithValue | inline |
getNumberOfDerivatives() override | PLMD::bias::Bias | inlinevirtual |
getOutputQuantity(const unsigned j) const | PLMD::ActionWithValue | inline |
getOutputQuantity(const std::string &name) const | PLMD::ActionWithValue | inline |
getPntrToArgument(const unsigned n) | PLMD::ActionWithArguments | inline |
getPntrToComponent(int i) | PLMD::ActionWithValue | protected |
getPntrToComponent(const std::string &name) | PLMD::ActionWithValue | protected |
getPntrToValue() | PLMD::ActionWithValue | protected |
getProjection(unsigned i, unsigned j) const | PLMD::ActionWithArguments | |
getRestart() const | PLMD::Action | inline |
getStep() const | PLMD::Action | |
getStride() const | PLMD::ActionPilot | |
getTime() const | PLMD::Action | |
getTimeStep() const | PLMD::Action | |
in_restart_ | PLMD::fisst::FISST | private |
in_restart_name_ | PLMD::fisst::FISST | private |
initial_weight_dist_ | PLMD::fisst::FISST | private |
initial_weight_rate_ | PLMD::fisst::FISST | 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 |
kbt_ | PLMD::fisst::FISST | private |
keywords | PLMD::Action | |
label | PLMD::Action | private |
line | PLMD::Action | private |
lockRequestArguments | PLMD::ActionWithArguments | private |
PLMD::lockRequests() | PLMD::Action | inlinevirtual |
PLMD::ActionWithArguments::lockRequests() override | PLMD::ActionWithArguments | inlinevirtual |
log | PLMD::Action | |
max_force_ | PLMD::fisst::FISST | private |
min_force_ | PLMD::fisst::FISST | private |
multi_sim_comm | PLMD::Action | |
n_interpolation_ | PLMD::fisst::FISST | private |
n_samples_ | PLMD::fisst::FISST | private |
name | PLMD::Action | private |
ncvs_ | PLMD::fisst::FISST | private |
noAnalyticalDerivatives(Keywords &keys) | PLMD::ActionWithValue | static |
noderiv | PLMD::ActionWithValue | private |
NormalizeForceWeights() | PLMD::fisst::FISST | private |
numericalDerivatives | PLMD::ActionWithValue | private |
observable_freq_ | PLMD::fisst::FISST | private |
observable_weight_ | PLMD::fisst::FISST | private |
onStep() const | PLMD::ActionPilot | virtual |
operator=(const Action &a)=delete | PLMD::Action | private |
options | PLMD::Action | private |
out_observable_ | PLMD::fisst::FISST | private |
out_observable_name_ | PLMD::fisst::FISST | private |
out_restart_ | PLMD::fisst::FISST | private |
out_restart_name_ | PLMD::fisst::FISST | private |
outputForces | PLMD::bias::Bias | private |
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 | |
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 | |
partition_estimate_ | PLMD::fisst::FISST | private |
period_ | PLMD::fisst::FISST | private |
plumed | PLMD::Action | |
prepare() | PLMD::Action | virtual |
rand_ | PLMD::fisst::FISST | private |
readAtomsFromPDB(const PDB &) | PLMD::Action | inlinevirtual |
readInRestart() | PLMD::fisst::FISST | private |
registerKeywords(Keywords &keys) | PLMD::fisst::FISST | static |
replica_index | PLMD::Action | private |
requestArguments(const std::vector< Value * > &arg) | PLMD::ActionWithArguments | |
requestExtraDependencies(const std::vector< Value * > &extra) | PLMD::ActionWithArguments | |
reset_period_ | PLMD::fisst::FISST | private |
restart | PLMD::Action | private |
runFinalJobs() | PLMD::Action | inlinevirtual |
setBias(double bias) | PLMD::bias::Bias | inlineprotected |
setGradientsIfNeeded() | PLMD::ActionWithValue | |
setNotPeriodic() | PLMD::ActionWithValue | |
setOption(const std::string &s) | PLMD::Action | virtual |
setOutputForce(int i, double f) | PLMD::bias::Bias | inlineprotected |
setPeriodic(const std::string &min, const std::string &max) | PLMD::ActionWithValue | |
setStride(const int &n) | PLMD::ActionPilot | |
setupOutObservable() | PLMD::fisst::FISST | private |
setupOutRestart() | PLMD::fisst::FISST | private |
setValue(const double &d) | PLMD::ActionWithValue | inlineprotected |
setValue(Value *, double) | PLMD::ActionWithValue | |
stride | PLMD::ActionPilot | private |
threshold_ | PLMD::fisst::FISST | private |
turnOnDerivatives() | PLMD::fisst::FISST | virtual |
PLMD::unlockRequests() | PLMD::Action | inlinevirtual |
PLMD::ActionWithArguments::unlockRequests() override | PLMD::ActionWithArguments | inlinevirtual |
update() | PLMD::fisst::FISST | virtual |
update_bias() | PLMD::fisst::FISST | private |
update_from | PLMD::Action | private |
update_statistics() | PLMD::fisst::FISST | private |
update_until | PLMD::Action | private |
useCustomisableComponents(Keywords &keys) | PLMD::ActionWithValue | static |
useNumericalDerivatives() | PLMD::ActionWithValue | inline |
value_force2_ | PLMD::fisst::FISST | private |
valueBias | PLMD::bias::Bias | private |
values | PLMD::ActionWithValue | private |
warning(const std::string &msg) | PLMD::Action | |
writeOutObservable() | PLMD::fisst::FISST | private |
writeOutRestart() | PLMD::fisst::FISST | private |
~Action() | PLMD::Action | virtual |
~ActionWithArguments() | PLMD::ActionWithArguments | inlinevirtual |
~ActionWithValue() | PLMD::ActionWithValue | |
~FISST() | PLMD::fisst::FISST | |