PLMD::maze::Memetic Member List

This is the complete list of members for PLMD::maze::Memetic, including all inherited members.

Action(const ActionOptions &)PLMD::Actionexplicit
Action(const Action &a)=deletePLMD::Actionprivate
ActionAtomistic(const ActionOptions &ao)PLMD::ActionAtomisticexplicit
ActionWithValue(const ActionOptions &ao)PLMD::ActionWithValueexplicit
activate()PLMD::Actionvirtual
activePLMD::Actionprivate
adaptation_PLMD::maze::Memeticprotected
adaptive_random_search(Member &m, const std::vector< double > &params={1.0, 1.e-5, 2.0, 2.0, 3.0, 3.0})PLMD::maze::Memeticprotected
addComponent(const std::string &name)PLMD::ActionWithValue
addComponentWithDerivatives(const std::string &name)PLMD::ActionWithValue
addDependency(Action *)PLMD::Action
addValue()PLMD::ActionWithValue
addValueWithDerivatives()PLMD::ActionWithValue
afterPLMD::Actionprivate
allowToAccessGlobalForces()PLMD::ActionAtomisticinline
annealing(Member &m, const std::vector< double > &params={300.0, 0.95})PLMD::maze::Memeticprotected
apply() overridePLMD::Colvarprotectedvirtual
applyForces()PLMD::ActionAtomistic
atomsPLMD::ActionAtomisticprotected
beforeUpdate()PLMD::Actioninlinevirtual
bound_PLMD::maze::Memeticprotected
calculate()PLMD::maze::Optimizervirtual
calculateAtomicNumericalDerivatives(ActionWithValue *a, const unsigned &startnum)PLMD::ActionAtomistic
calculateFromPDB(const PDB &)PLMD::Action
calculateNumericalDerivatives(ActionWithValue *a=NULL) overridePLMD::ActionAtomisticvirtual
capacity_PLMD::maze::Memeticprotected
cauchy_mean_alpha_PLMD::maze::Memeticprotected
cauchy_mean_beta_PLMD::maze::Memeticprotected
center_of_mass() constPLMD::maze::Optimizer
changeBox(const Tensor &newbox)PLMD::ActionAtomistic
chargesPLMD::ActionAtomisticprivate
chargesWereSetPLMD::ActionAtomisticprivate
checkFieldsAllowed()PLMD::ActionWithValueinlinevirtual
checkIsEnergy()PLMD::Colvarinline
checkNeedsGradients() constPLMD::Actioninlinevirtual
PLMD::checkNumericalDerivatives() constPLMD::Actioninlinevirtual
PLMD::ActionWithValue::checkNumericalDerivatives() const overridePLMD::ActionWithValueinlinevirtual
checkRead()PLMD::Action
checkUpdate() constPLMD::Action
cite(const std::string &s)PLMD::Action
clearDependencies()PLMD::Action
clearDerivatives()PLMD::ActionWithValuevirtual
clearInputForces()PLMD::ActionWithValue
clearOptions()PLMD::Actionvirtual
clearOutputForces()PLMD::ActionAtomistic
coding_len_PLMD::maze::Memeticprotected
Colvar(const ActionOptions &)PLMD::Colvarexplicit
commPLMD::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::ActionWithValuestatic
copyOutput(const std::string &name) constPLMD::ActionWithValue
copyOutput(const unsigned &n) constPLMD::ActionWithValue
create_coding()PLMD::maze::Memeticprivate
crossover(Member &m1, Member &m2)PLMD::maze::Memeticprivate
deactivate()PLMD::Actioninlinevirtual
Dependencies typedefPLMD::Action
doCheckPointPLMD::Actionprivate
doNotCalculateDerivatives() constPLMD::ActionWithValueinlinevirtual
donotforcePLMD::ActionAtomisticprivate
doNotForce()PLMD::ActionAtomisticinline
donotretrievePLMD::ActionAtomisticprivate
doNotRetrieve()PLMD::ActionAtomisticinline
energyPLMD::ActionAtomisticprivate
error(const std::string &msg) constPLMD::Action
exists(const std::string &name) constPLMD::ActionWithValue
exit(int c=0)PLMD::Action
extraCVPLMD::ActionAtomisticprivate
fclose(FILE *fp)PLMD::Action
fflush()PLMD::Action
filesPLMD::Action
first_step_PLMD::maze::Optimizerprotected
first_time_PLMD::maze::Optimizerprivate
fopen(const char *path, const char *mode)PLMD::Action
forceOnEnergyPLMD::ActionAtomisticprivate
forceOnExtraCVPLMD::ActionAtomisticprivate
forcesPLMD::ActionAtomisticprivate
get_capacity() constPLMD::maze::Memeticinline
get_cauchy_mean() constPLMD::maze::Memeticinline
get_cauchy_spread() constPLMD::maze::Memeticinline
get_coding_len() constPLMD::maze::Memeticinline
get_label() constPLMD::maze::Optimizerinline
get_local_search_rate() constPLMD::maze::Memeticinline
get_local_search_type() constPLMD::maze::Memeticinline
get_mating_rate() constPLMD::maze::Memeticinline
get_mutation_rate() constPLMD::maze::Memeticinline
get_n_global_iterations() constPLMD::maze::Memeticinline
get_n_iterations() constPLMD::maze::Optimizerinline
get_n_local_iterations() constPLMD::maze::Memeticinline
get_n_threads_openmp() constPLMD::maze::Optimizerinline
get_nl_cutofff() constPLMD::maze::Optimizerinline
get_nl_stride() constPLMD::maze::Optimizerinline
get_opt() constPLMD::maze::Optimizerinline
get_opt_value() constPLMD::maze::Optimizerinline
get_optimizer_stride() constPLMD::maze::Optimizerinline
get_rank_openmp() constPLMD::maze::Optimizerinline
get_sampling_radius() constPLMD::maze::Optimizerinline
get_stride_openmp() constPLMD::maze::Optimizerinline
getAbsoluteIndex(int i) constPLMD::ActionAtomisticinline
getAbsoluteIndexes() constPLMD::ActionAtomisticinlinevirtual
getBox() constPLMD::ActionAtomisticinline
getBoxDerivatives() constPLMD::Colvarprotected
getCharge(int i) constPLMD::ActionAtomisticinline
getComponent(const std::string &name) constPLMD::ActionWithValueprivate
getComponentsList() constPLMD::ActionWithValue
getComponentsVector() constPLMD::ActionWithValue
getCPT() constPLMD::Action
getDependencies() constPLMD::Actioninline
getDocumentation() constPLMD::Actionvirtual
getEnergy() constPLMD::ActionAtomisticinline
getExchangeStep() constPLMD::Action
getForce() constPLMD::Colvarprotected
getGlobalPosition(AtomNumber) constPLMD::ActionAtomisticinline
getKeyword(const std::string &key)PLMD::Action
getLabel() constPLMD::Actioninline
getMass(int i) constPLMD::ActionAtomisticinline
getName() constPLMD::Actioninline
getNumberOfAtoms() constPLMD::ActionAtomisticinline
getNumberOfComponents() constPLMD::ActionWithValueinline
getNumberOfDerivatives() overridePLMD::Colvarinlinevirtual
getOutputQuantity(const unsigned j) constPLMD::ActionWithValueinline
getOutputQuantity(const std::string &name) constPLMD::ActionWithValueinline
getPbc() constPLMD::ActionAtomisticinline
getPntrToComponent(int i)PLMD::ActionWithValueprotected
getPntrToComponent(const std::string &name)PLMD::ActionWithValueprotected
getPntrToValue()PLMD::ActionWithValueprotected
getPosition(int) constPLMD::ActionAtomisticinline
getPositions() constPLMD::ActionAtomisticinline
getRestart() constPLMD::Actioninline
getStep() constPLMD::Action
getTime() constPLMD::Action
getTimeStep() constPLMD::Action
getTotAtoms() constPLMD::ActionAtomisticinline
getUnique() constPLMD::ActionAtomisticinline
getUniqueLocal() constPLMD::ActionAtomisticinline
indexesPLMD::ActionAtomisticprivate
initialize_members()PLMD::maze::Memeticprivate
interpretAtomList(std::vector< std::string > &strings, std::vector< AtomNumber > &t)PLMD::ActionAtomistic
is_local_search_on() constPLMD::maze::Memeticinline
is_pbc_on() constPLMD::maze::Optimizerinline
isActive() constPLMD::Actioninline
isEnergyPLMD::Colvarprotected
isExtraCVPLMD::Colvarprotected
isOptionOn(const std::string &s) constPLMD::Actioninline
keywordsPLMD::Action
labelPLMD::Actionprivate
label_PLMD::maze::Optimizerprotected
linePLMD::Actionprivate
local_search(std::vector< Member > &members)PLMD::maze::Memeticprotected
local_search_off()PLMD::maze::Memeticinline
local_search_on()PLMD::maze::Memeticinline
local_search_on_PLMD::maze::Memeticprotected
local_search_rate_PLMD::maze::Memeticprotected
local_search_type_PLMD::maze::Memeticprotected
lockRequestAtomsPLMD::ActionAtomisticprivate
lockRequests() overridePLMD::ActionAtomisticinlinevirtual
logPLMD::Action
loss_PLMD::maze::Optimizerprivate
luus_jaakola(Member &m, const std::vector< double > &params)PLMD::maze::Memeticprotected
makeWhole()PLMD::ActionAtomistic
massesPLMD::ActionAtomisticprivate
mating(std::vector< Member > &members)PLMD::maze::Memeticprivate
mating_rate_PLMD::maze::Memeticprotected
member_best_PLMD::maze::Memeticprotected
members_PLMD::maze::Memeticprotected
Memetic(const ActionOptions &ao)PLMD::maze::Memeticexplicit
modifyForceOnEnergy()PLMD::ActionAtomisticinline
modifyForceOnExtraCV()PLMD::ActionAtomisticinline
modifyForces()PLMD::ActionAtomisticinline
modifyGlobalForce(AtomNumber)PLMD::ActionAtomisticinline
modifyGlobalPbc()PLMD::ActionAtomisticinline
modifyGlobalPosition(AtomNumber)PLMD::ActionAtomisticinline
modifyGlobalVirial()PLMD::ActionAtomisticinline
modifyVirial()PLMD::ActionAtomisticinline
multi_sim_commPLMD::Action
mutation(Member &m)PLMD::maze::Memeticprivate
mutation(std::vector< Member > &members)PLMD::maze::Memeticprivate
mutation_rate_PLMD::maze::Memeticprotected
n_global_iterations_PLMD::maze::Memeticprotected
n_iter_PLMD::maze::Optimizerprotected
n_local_iterations_PLMD::maze::Memeticprotected
n_threads_PLMD::maze::Optimizerprotected
namePLMD::Actionprivate
neighbor_list_PLMD::maze::Optimizerprotected
nl_cutoff_PLMD::maze::Optimizerprotected
nl_stride_PLMD::maze::Optimizerprotected
noAnalyticalDerivatives(Keywords &keys)PLMD::ActionWithValuestatic
noderivPLMD::ActionWithValueprivate
numericalDerivativesPLMD::ActionWithValueprivate
operator=(const Action &a)=deletePLMD::Actionprivate
opt_PLMD::maze::Optimizerprotected
opt_value_PLMD::maze::Optimizerprotected
optimize() overridePLMD::maze::Memeticvirtual
Optimizer(const ActionOptions &)PLMD::maze::Optimizerexplicit
optimizer_stride_PLMD::maze::Optimizerprotected
optionsPLMD::Actionprivate
out_of_bounds(double v)PLMD::maze::Memeticprivate
pairing(double distance) constPLMD::maze::Optimizervirtual
parse(const std::string &key, T &t)PLMD::Action
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
pbcPLMD::ActionAtomisticprivate
pbc_PLMD::maze::Optimizerprotected
pbc_fwdPLMD::ActionAtomisticprivate
pbc_off()PLMD::maze::Optimizerinline
pbc_on()PLMD::maze::Optimizerinline
pbcApply(std::vector< Vector > &dlist, unsigned max_index=0) constPLMD::ActionAtomistic
pbcDistance(const Vector &, const Vector &) constPLMD::ActionAtomistic
plumedPLMD::Action
positionsPLMD::ActionAtomisticprivate
prepare()PLMD::maze::Optimizervirtual
print_status() constPLMD::maze::Memeticprivate
random_restart_hill_climbing(Member &m, const std::vector< double > &params={10})PLMD::maze::Memeticprotected
rank_PLMD::maze::Optimizerprotected
readAtomsFromPDB(const PDB &pdb) overridePLMD::ActionAtomisticvirtual
registerKeywords(Keywords &keys)PLMD::maze::Memeticstatic
replica_indexPLMD::Actionprivate
requestAtoms(const std::vector< AtomNumber > &a)PLMD::Colvarprotected
PLMD::ActionAtomistic::requestAtoms(const std::vector< AtomNumber > &a, const bool clearDep=true)PLMD::ActionAtomistic
restartPLMD::Actionprivate
retrieveAtoms()PLMD::ActionAtomisticvirtual
runFinalJobs()PLMD::Actioninlinevirtual
sampling_r_PLMD::maze::Optimizerprotected
sampling_radius()PLMD::maze::Optimizer
score()PLMD::maze::Optimizer
score_best_PLMD::maze::Memeticprotected
score_mean()PLMD::maze::Memeticprivate
score_member(const Vector &v)PLMD::maze::Memeticprivate
score_members()PLMD::maze::Memeticprivate
score_worst_PLMD::maze::Memeticprotected
selection_roulette()PLMD::maze::Memeticprivate
serial_PLMD::maze::Optimizerprivate
set_capacity(unsigned int)PLMD::maze::Memeticinline
set_cauchy_mean(double)PLMD::maze::Memeticinline
set_cauchy_spread(double)PLMD::maze::Memeticinline
set_coding_len(unsigned int)PLMD::maze::Memeticinline
set_label(const std::string &)PLMD::maze::Optimizerinline
set_local_search_rate(double)PLMD::maze::Memeticinline
set_local_search_type(const std::string &)PLMD::maze::Memeticinline
set_mating_rate(double)PLMD::maze::Memeticinline
set_mutation_rate(double)PLMD::maze::Memeticinline
set_n_global_iterations(unsigned int)PLMD::maze::Memeticinline
set_n_iterations(unsigned int)PLMD::maze::Optimizerinline
set_n_local_iterations(unsigned int)PLMD::maze::Memeticinline
set_n_threads_openmp(unsigned int)PLMD::maze::Optimizerinline
set_nl_cutoff(double)PLMD::maze::Optimizerinline
set_nl_stride(unsigned int)PLMD::maze::Optimizerinline
set_opt(Vector)PLMD::maze::Optimizerinline
set_opt_value(double)PLMD::maze::Optimizerinline
set_optimizer_stride(unsigned int)PLMD::maze::Optimizerinline
set_rank_openmp(unsigned int)PLMD::maze::Optimizerinline
set_sampling_radius(double)PLMD::maze::Optimizerinline
set_stride_openmp(unsigned int)PLMD::maze::Optimizerinline
setAtomsDerivatives(int, const Vector &)PLMD::Colvarinlineprotected
setAtomsDerivatives(Value *, int, const Vector &)PLMD::Colvarinlineprotected
setBoxDerivatives(const Tensor &)PLMD::Colvarinlineprotected
setBoxDerivatives(Value *, const Tensor &)PLMD::Colvarinlineprotected
setBoxDerivativesNoPbc()PLMD::Colvarinlineprotected
setBoxDerivativesNoPbc(Value *)PLMD::Colvarprotected
setExtraCV(const std::string &name)PLMD::ActionAtomisticinlineprotected
setForcesOnAtoms(const std::vector< double > &forcesToApply, unsigned ind=0)PLMD::ActionAtomistic
setGradientsIfNeeded()PLMD::ActionWithValue
setNotPeriodic()PLMD::ActionWithValue
setOption(const std::string &s)PLMD::Actionvirtual
setPeriodic(const std::string &min, const std::string &max)PLMD::ActionWithValue
setValue(const double &d)PLMD::ActionWithValueinlineprotected
setValue(Value *, double)PLMD::ActionWithValue
solve()PLMD::maze::Memeticprotected
sort_members()PLMD::maze::Memeticprivate
start_step_0()PLMD::maze::Optimizerinline
start_step_stride()PLMD::maze::Optimizerinline
stochastic_hill_climbing(Member &m, const std::vector< double > &params={})PLMD::maze::Memeticprotected
stride_PLMD::maze::Optimizerprotected
turnOnDerivatives()PLMD::ActionWithValuevirtual
uniquePLMD::ActionAtomisticprivate
unique_localPLMD::ActionAtomisticprivate
unlockRequests() overridePLMD::ActionAtomisticinlinevirtual
update()PLMD::Actioninlinevirtual
update_fromPLMD::Actionprivate
update_nl()PLMD::maze::Optimizer
update_untilPLMD::Actionprivate
updateUniqueLocal()PLMD::ActionAtomistic
useCustomisableComponents(Keywords &keys)PLMD::ActionWithValuestatic
useNumericalDerivatives()PLMD::ActionWithValueinline
validate_list_PLMD::maze::Optimizerprivate
value_action_PLMD::maze::Optimizer
value_sampling_radius_PLMD::maze::Optimizer
value_x_PLMD::maze::Optimizer
value_y_PLMD::maze::Optimizer
value_z_PLMD::maze::Optimizer
valuesPLMD::ActionWithValueprivate
vec_loss_PLMD::maze::Optimizerprivate
virialPLMD::ActionAtomisticprivate
warning(const std::string &msg)PLMD::Action
~Action()PLMD::Actionvirtual
~ActionAtomistic()PLMD::ActionAtomistic
~ActionWithValue()PLMD::ActionWithValue
~Colvar()PLMD::Colvarinline
~Memetic()PLMD::maze::Memetic
~Optimizer()PLMD::maze::Optimizerinline
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