Action(const ActionOptions &) | PLMD::Action | explicit |
Action(const Action &a)=delete | PLMD::Action | private |
ActionAtomistic(const ActionOptions &ao) | PLMD::ActionAtomistic | 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 |
allowToAccessGlobalForces() | PLMD::ActionAtomistic | inline |
apply() override | PLMD::isdb::MetainferenceBase | inlinevirtual |
applyForces() | PLMD::ActionAtomistic | |
arguments | PLMD::ActionWithArguments | private |
atoms | PLMD::ActionAtomistic | protected |
average_weights_ | PLMD::isdb::MetainferenceBase | private |
beforeUpdate() | PLMD::Action | inlinevirtual |
bringBackInPbc(int i, double d1) const | PLMD::ActionWithArguments | inline |
calc_data_ | PLMD::isdb::MetainferenceBase | private |
calculate() override | PLMD::isdb::RDC | virtual |
calculateAtomicNumericalDerivatives(ActionWithValue *a, const unsigned &startnum) | PLMD::ActionAtomistic | |
calculateFromPDB(const PDB &) | PLMD::Action | |
calculateNumericalDerivatives(ActionWithValue *a) override | PLMD::isdb::MetainferenceBase | inlinevirtual |
changeBox(const Tensor &newbox) | PLMD::ActionAtomistic | |
charges | PLMD::ActionAtomistic | private |
chargesWereSet | PLMD::ActionAtomistic | 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 |
clearOutputForces() | PLMD::ActionAtomistic | |
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 |
Const | PLMD::isdb::RDC | private |
copyOutput(const std::string &name) const | PLMD::ActionWithValue | |
copyOutput(const unsigned &n) const | PLMD::ActionWithValue | |
coupl | PLMD::isdb::RDC | private |
deactivate() | PLMD::Action | inlinevirtual |
decay_w_ | PLMD::isdb::MetainferenceBase | private |
Dependencies typedef | PLMD::Action | |
Dftilde_ | PLMD::isdb::MetainferenceBase | private |
difference(int, double, double) const | PLMD::ActionWithArguments | inline |
do_optsigmamean_ | PLMD::isdb::MetainferenceBase | private |
do_regression_zero(const std::vector< double > &mean) | PLMD::isdb::MetainferenceBase | private |
do_reweight_ | PLMD::isdb::MetainferenceBase | private |
do_svd() | PLMD::isdb::RDC | private |
doCheckPoint | PLMD::Action | private |
Doffset_ | PLMD::isdb::MetainferenceBase | private |
doMonteCarlo(const std::vector< double > &mean) | PLMD::isdb::MetainferenceBase | private |
doNotCalculateDerivatives() const | PLMD::ActionWithValue | inlinevirtual |
donotforce | PLMD::ActionAtomistic | private |
doNotForce() | PLMD::ActionAtomistic | inline |
donotretrieve | PLMD::ActionAtomistic | private |
doNotRetrieve() | PLMD::ActionAtomistic | inline |
dooffset_ | PLMD::isdb::MetainferenceBase | private |
doregres_zero_ | PLMD::isdb::MetainferenceBase | private |
doscale_ | PLMD::isdb::MetainferenceBase | private |
doscore_ | PLMD::isdb::MetainferenceBase | private |
Dscale_ | PLMD::isdb::MetainferenceBase | private |
Dsigma_ | PLMD::isdb::MetainferenceBase | private |
energy | PLMD::ActionAtomistic | private |
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 |
extraCV | PLMD::ActionAtomistic | private |
fclose(FILE *fp) | PLMD::Action | |
fflush() | PLMD::Action | |
files | PLMD::Action | |
firstTime | PLMD::isdb::MetainferenceBase | private |
firstTimeW | PLMD::isdb::MetainferenceBase | private |
fopen(const char *path, const char *mode) | PLMD::Action | |
forceOnEnergy | PLMD::ActionAtomistic | private |
forceOnExtraCV | PLMD::ActionAtomistic | private |
forces | PLMD::isdb::MetainferenceBase | private |
forcesToApply | PLMD::isdb::MetainferenceBase | private |
ftilde_ | PLMD::isdb::MetainferenceBase | private |
GAUSS enum value | PLMD::isdb::MetainferenceBase | private |
gen_likelihood_ | PLMD::isdb::MetainferenceBase | private |
GENERIC enum value | PLMD::isdb::MetainferenceBase | private |
get_sigma_mean(const double weight, const double norm, const double neff, const std::vector< double > &mean) | PLMD::isdb::MetainferenceBase | private |
get_weights(double &weight, double &norm, double &neff) | PLMD::isdb::MetainferenceBase | private |
getAbsoluteIndex(int i) const | PLMD::ActionAtomistic | inline |
getAbsoluteIndexes() const | PLMD::ActionAtomistic | inlinevirtual |
getArgument(const unsigned n) const | PLMD::ActionWithArguments | inline |
getArguments() const | PLMD::ActionWithArguments | inlinevirtual |
getBox() const | PLMD::ActionAtomistic | inline |
getCalcData(const unsigned index) | PLMD::isdb::MetainferenceBase | inlineprivate |
getCharge(int i) const | PLMD::ActionAtomistic | inline |
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 |
getDoScore() | PLMD::isdb::MetainferenceBase | inline |
getEnergy() const | PLMD::ActionAtomistic | inline |
getEnergyForceGJ(const std::vector< double > &mean, const std::vector< double > &dmean_x, const std::vector< double > &dmean_b) | PLMD::isdb::MetainferenceBase | private |
getEnergyForceGJE(const std::vector< double > &mean, const std::vector< double > &dmean_x, const std::vector< double > &dmean_b) | PLMD::isdb::MetainferenceBase | private |
getEnergyForceMIGEN(const std::vector< double > &mean, const std::vector< double > &dmean_x, const std::vector< double > &dmean_b) | PLMD::isdb::MetainferenceBase | private |
getEnergyForceSP(const std::vector< double > &mean, const std::vector< double > &dmean_x, const std::vector< double > &dmean_b) | PLMD::isdb::MetainferenceBase | private |
getEnergyForceSPE(const std::vector< double > &mean, const std::vector< double > &dmean_x, const std::vector< double > &dmean_b) | PLMD::isdb::MetainferenceBase | private |
getEnergyGJ(const std::vector< double > &mean, const std::vector< double > &sigma, const double scale, const double offset) | PLMD::isdb::MetainferenceBase | private |
getEnergyGJE(const std::vector< double > &mean, const std::vector< double > &sigma, const double scale, const double offset) | PLMD::isdb::MetainferenceBase | private |
getEnergyMIGEN(const std::vector< double > &mean, const std::vector< double > &ftilde, const std::vector< double > &sigma, const double scale, const double offset) | PLMD::isdb::MetainferenceBase | private |
getEnergySP(const std::vector< double > &mean, const std::vector< double > &sigma, const double scale, const double offset) | PLMD::isdb::MetainferenceBase | private |
getEnergySPE(const std::vector< double > &mean, const std::vector< double > &sigma, const double scale, const double offset) | PLMD::isdb::MetainferenceBase | private |
getExchangeStep() const | PLMD::Action | |
getGlobalPosition(AtomNumber) const | PLMD::ActionAtomistic | inline |
getKeyword(const std::string &key) | PLMD::Action | |
getLabel() const | PLMD::Action | inline |
getMass(int i) const | PLMD::ActionAtomistic | inline |
getMetaDer(const unsigned index) | PLMD::isdb::MetainferenceBase | inline |
getName() const | PLMD::Action | inline |
getNarg() | PLMD::isdb::MetainferenceBase | inline |
getNumberOfArguments() const | PLMD::ActionWithArguments | inlinevirtual |
getNumberOfAtoms() const | PLMD::ActionAtomistic | inline |
getNumberOfComponents() const | PLMD::ActionWithValue | inline |
getNumberOfDerivatives() override | PLMD::isdb::MetainferenceBase | inlinevirtual |
getOutputQuantity(const unsigned j) const | PLMD::ActionWithValue | inline |
getOutputQuantity(const std::string &name) const | PLMD::ActionWithValue | inline |
getPbc() const | PLMD::ActionAtomistic | 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 |
getPosition(int) const | PLMD::ActionAtomistic | inline |
getPositions() const | PLMD::ActionAtomistic | inline |
getProjection(unsigned i, unsigned j) const | PLMD::ActionWithArguments | |
getRestart() const | PLMD::Action | inline |
getScore() | PLMD::isdb::MetainferenceBase | |
getStep() const | PLMD::Action | |
getTime() const | PLMD::Action | |
getTimeStep() const | PLMD::Action | |
getTotAtoms() const | PLMD::ActionAtomistic | inline |
getUnique() const | PLMD::ActionAtomistic | inline |
getUniqueLocal() const | PLMD::ActionAtomistic | inline |
getWstride() | PLMD::isdb::MetainferenceBase | inline |
indexes | PLMD::ActionAtomistic | private |
Initialise(const unsigned input) | PLMD::isdb::MetainferenceBase | |
interpretArgumentList(const std::vector< std::string > &c, std::vector< Value * > &arg) | PLMD::ActionWithArguments | |
interpretAtomList(std::vector< std::string > &strings, std::vector< AtomNumber > &t) | PLMD::ActionAtomistic | |
isActive() const | PLMD::Action | inline |
iselect | PLMD::isdb::MetainferenceBase | private |
isOptionOn(const std::string &s) const | PLMD::Action | inline |
kbt_ | PLMD::isdb::MetainferenceBase | private |
keywords | PLMD::Action | |
label | PLMD::Action | private |
LIKE_GAUSS enum value | PLMD::isdb::MetainferenceBase | private |
LIKE_LOGN enum value | PLMD::isdb::MetainferenceBase | private |
line | PLMD::Action | private |
lockRequestArguments | PLMD::ActionWithArguments | private |
lockRequestAtoms | PLMD::ActionAtomistic | private |
lockRequests() override | PLMD::isdb::MetainferenceBase | inlinevirtual |
log | PLMD::Action | |
makeWhole() | PLMD::ActionAtomistic | |
masses | PLMD::ActionAtomistic | private |
master | PLMD::isdb::MetainferenceBase | private |
MCaccept_ | PLMD::isdb::MetainferenceBase | private |
MCacceptFT_ | PLMD::isdb::MetainferenceBase | private |
MCacceptScale_ | PLMD::isdb::MetainferenceBase | private |
MCchunksize_ | PLMD::isdb::MetainferenceBase | private |
MCsteps_ | PLMD::isdb::MetainferenceBase | private |
MCtrial_ | PLMD::isdb::MetainferenceBase | private |
metader_ | PLMD::isdb::MetainferenceBase | private |
MetainferenceBase(const ActionOptions &) | PLMD::isdb::MetainferenceBase | explicit |
MGAUSS enum value | PLMD::isdb::MetainferenceBase | private |
modifyForceOnEnergy() | PLMD::ActionAtomistic | inline |
modifyForceOnExtraCV() | PLMD::ActionAtomistic | inline |
modifyForces() | PLMD::ActionAtomistic | inline |
modifyGlobalForce(AtomNumber) | PLMD::ActionAtomistic | inline |
modifyGlobalPbc() | PLMD::ActionAtomistic | inline |
modifyGlobalPosition(AtomNumber) | PLMD::ActionAtomistic | inline |
modifyGlobalVirial() | PLMD::ActionAtomistic | inline |
modifyVirial() | PLMD::ActionAtomistic | inline |
MOUTLIERS enum value | PLMD::isdb::MetainferenceBase | private |
moveScaleOffset(const std::vector< double > &mean_, double &old_energy) | PLMD::isdb::MetainferenceBase | private |
moveSigmas(const std::vector< double > &mean_, double &old_energy, const unsigned i, const std::vector< unsigned > &indices, bool &breaknow) | PLMD::isdb::MetainferenceBase | private |
moveTilde(const std::vector< double > &mean_, double &old_energy) | PLMD::isdb::MetainferenceBase | private |
mu_s | PLMD::isdb::RDC | private |
multi_sim_comm | PLMD::Action | |
N_optimized_step_ | PLMD::isdb::MetainferenceBase | private |
name | PLMD::Action | private |
narg | PLMD::isdb::MetainferenceBase | private |
noAnalyticalDerivatives(Keywords &keys) | PLMD::ActionWithValue | static |
noderiv | PLMD::ActionWithValue | private |
noise_type_ | PLMD::isdb::MetainferenceBase | private |
nregres_zero_ | PLMD::isdb::MetainferenceBase | private |
nrep_ | PLMD::isdb::MetainferenceBase | private |
nsel_ | PLMD::isdb::MetainferenceBase | private |
numericalDerivatives | PLMD::ActionWithValue | private |
offset_ | PLMD::isdb::MetainferenceBase | private |
offset_max_ | PLMD::isdb::MetainferenceBase | private |
offset_min_ | PLMD::isdb::MetainferenceBase | private |
offset_mu_ | PLMD::isdb::MetainferenceBase | private |
offset_prior_ | PLMD::isdb::MetainferenceBase | private |
operator=(const Action &a)=delete | PLMD::Action | private |
optimized_step_ | PLMD::isdb::MetainferenceBase | private |
options | PLMD::Action | private |
optsigmamean_stride_ | PLMD::isdb::MetainferenceBase | private |
OUTLIERS enum value | PLMD::isdb::MetainferenceBase | private |
parameters | PLMD::isdb::MetainferenceBase | 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 | |
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 | |
parseVector(const std::string &key, std::vector< T > &t) | PLMD::Action | |
pbc | PLMD::isdb::RDC | private |
pbc_fwd | PLMD::ActionAtomistic | private |
pbcApply(std::vector< Vector > &dlist, unsigned max_index=0) const | PLMD::ActionAtomistic | |
pbcDistance(const Vector &, const Vector &) const | PLMD::ActionAtomistic | |
plumed | PLMD::Action | |
positions | PLMD::ActionAtomistic | private |
prepare() | PLMD::Action | virtual |
random | PLMD::isdb::MetainferenceBase | private |
RDC(const ActionOptions &) | PLMD::isdb::RDC | explicit |
readAtomsFromPDB(const PDB &pdb) override | PLMD::ActionAtomistic | virtual |
registerKeywords(Keywords &keys) | PLMD::isdb::RDC | static |
replica_ | PLMD::isdb::MetainferenceBase | private |
replica_averaging(const double weight, const double norm, std::vector< double > &mean, std::vector< double > &dmean_b) | PLMD::isdb::MetainferenceBase | private |
replica_index | PLMD::Action | private |
requestArguments(const std::vector< Value * > &arg) | PLMD::ActionWithArguments | |
requestAtoms(const std::vector< AtomNumber > &a, const bool clearDep=true) | PLMD::ActionAtomistic | |
requestExtraDependencies(const std::vector< Value * > &extra) | PLMD::ActionWithArguments | |
restart | PLMD::Action | private |
retrieveAtoms() | PLMD::ActionAtomistic | virtual |
runFinalJobs() | PLMD::Action | inlinevirtual |
SC_FLAT enum value | PLMD::isdb::MetainferenceBase | private |
SC_GAUSS enum value | PLMD::isdb::MetainferenceBase | private |
scale | PLMD::isdb::RDC | private |
scale_ | PLMD::isdb::MetainferenceBase | private |
scale_max_ | PLMD::isdb::MetainferenceBase | private |
scale_min_ | PLMD::isdb::MetainferenceBase | private |
scale_mu_ | PLMD::isdb::MetainferenceBase | private |
scale_prior_ | PLMD::isdb::MetainferenceBase | private |
Selector() | PLMD::isdb::MetainferenceBase | |
selector_ | PLMD::isdb::MetainferenceBase | private |
setArgDerivatives(Value *v, const double &d) | PLMD::isdb::MetainferenceBase | inline |
setAtomsDerivatives(Value *v, const unsigned i, const Vector &d) | PLMD::isdb::MetainferenceBase | inline |
setBoxDerivatives(Value *v, const Tensor &d) | PLMD::isdb::MetainferenceBase | inline |
setCalcData(const unsigned index, const double datum) | PLMD::isdb::MetainferenceBase | inline |
setCalcData(const std::vector< double > &data) | PLMD::isdb::MetainferenceBase | inline |
setDerivatives() | PLMD::isdb::MetainferenceBase | inline |
setExtraCV(const std::string &name) | PLMD::ActionAtomistic | inlineprotected |
setForcesOnAtoms(const std::vector< double > &forcesToApply, unsigned ind=0) | PLMD::ActionAtomistic | |
setGradientsIfNeeded() | PLMD::ActionWithValue | |
setMetaDer(const unsigned index, const double der) | PLMD::isdb::MetainferenceBase | inlineprivate |
setNarg(const unsigned input) | PLMD::isdb::MetainferenceBase | inline |
setNotPeriodic() | PLMD::ActionWithValue | |
setOption(const std::string &s) | PLMD::Action | virtual |
setParameter(const double input) | PLMD::isdb::MetainferenceBase | inline |
setParameters(const std::vector< double > &input) | PLMD::isdb::MetainferenceBase | inline |
setPeriodic(const std::string &min, const std::string &max) | PLMD::ActionWithValue | |
setScore(const double score) | PLMD::isdb::MetainferenceBase | inline |
setValue(const double &d) | PLMD::ActionWithValue | inlineprotected |
setValue(Value *, double) | PLMD::ActionWithValue | |
sfile_ | PLMD::isdb::MetainferenceBase | private |
sigma_ | PLMD::isdb::MetainferenceBase | private |
sigma_max_ | PLMD::isdb::MetainferenceBase | private |
sigma_max_est_ | PLMD::isdb::MetainferenceBase | private |
sigma_mean2_ | PLMD::isdb::MetainferenceBase | private |
sigma_mean2_last_ | PLMD::isdb::MetainferenceBase | private |
sigma_min_ | PLMD::isdb::MetainferenceBase | private |
sigmamax_opt_done_ | PLMD::isdb::MetainferenceBase | private |
status_file_name_ | PLMD::isdb::MetainferenceBase | private |
svd | PLMD::isdb::RDC | private |
turnOnDerivatives() override | PLMD::isdb::MetainferenceBase | inlinevirtual |
unique | PLMD::ActionAtomistic | private |
unique_local | PLMD::ActionAtomistic | private |
unlockRequests() override | PLMD::isdb::MetainferenceBase | inlinevirtual |
update() override | PLMD::isdb::RDC | virtual |
update_from | PLMD::Action | private |
update_until | PLMD::Action | private |
updateUniqueLocal() | PLMD::ActionAtomistic | |
useCustomisableComponents(Keywords &keys) | PLMD::ActionWithValue | static |
useNumericalDerivatives() | PLMD::ActionWithValue | inline |
valueAccept | PLMD::isdb::MetainferenceBase | private |
valueAcceptFT | PLMD::isdb::MetainferenceBase | private |
valueAcceptScale | PLMD::isdb::MetainferenceBase | private |
valueFtilde | PLMD::isdb::MetainferenceBase | private |
valueOffset | PLMD::isdb::MetainferenceBase | private |
values | PLMD::ActionWithValue | private |
valueScale | PLMD::isdb::MetainferenceBase | private |
valueScore | PLMD::isdb::MetainferenceBase | private |
valueSigma | PLMD::isdb::MetainferenceBase | private |
valueSigmaMean | PLMD::isdb::MetainferenceBase | private |
virial | PLMD::ActionAtomistic | private |
warning(const std::string &msg) | PLMD::Action | |
write_stride_ | PLMD::isdb::MetainferenceBase | private |
writeStatus() | PLMD::isdb::MetainferenceBase | |
~Action() | PLMD::Action | virtual |
~ActionAtomistic() | PLMD::ActionAtomistic | |
~ActionWithArguments() | PLMD::ActionWithArguments | inlinevirtual |
~ActionWithValue() | PLMD::ActionWithValue | |
~MetainferenceBase() | PLMD::isdb::MetainferenceBase | |