Index

_

_adaptive_A variable _adaptive_floor variable _dist_metric variable

_threshold variable _use_adaptive_threshold variable

A

accept_tau variable accept_tau_relative variable accumulateBlockContribution function acquisition variable AcquisitionType enum actdist_fro variable, [1] activateFrozenAtoms function alpha_cache variable alpha_samples variable AlphaCacheFn typedef, [1] analyticalPrefactor function applyCorrection function applyCrossBlockGeometryToVector function applyTheta function approximateKernel function ase_potential() (in module gpr_optim) assembleDirectionalCovarianceDerivatives function assembleExactHessian function assembleMatrixOfRepetitiveCoordinates function assembleVectorFromEnergyAndGradient function assertMsg function assignBlockToMatrix function

assignFromField function atmd namespace atmd::AtomicDimer class atmd::AtomicDimer::early_stopping_t struct atmd::AtomicDimer::VarianceGateConfig struct atom_types variable atomic_nrs variable AtomicDimer function atomicNrs variable atoms_config variable atoms_config_from_ase() (in module gpr_optim) atoms_froz_active variable atoms_froz_inactive variable atoms_mov variable aux namespace aux::AtomSignature struct aux::AuxiliaryFunctionality class aux::Distance class aux::Gradient class aux::InverseDistanceCache struct aux::ProblemSetUp class

B

back_solve function back_solve_mat function bond_length_angstrom function bondLength function

build function buildCrossBlockGeometry function buildGrid function buildRFFModel function

C

cacheDistances function cacheInverseDistances function calculate() (gpr_optim.GPRCalculator method) calculateCovarianceMatrix function, [1] calculateDerivativesDiffDim function calculateDerivativesSameDim function calculateDirectionalCovarianceMatrix function calculateDirectionalCovarianceMatrixWithDerivatives function calculateDirectionalCovarianceMatrixWithDerivatives2 function calculateDirectionalLogPriorCurvature function calculateGeneralPotential function calculateGradOfCovMatrix function, [1] calculateGradOfCovMatrixWithDerivatives function, [1] calculateGradOfCovMatrixWithDerivatives2 function, [1] calculateLogPrior function, [1] calculateLogPriorGradient function, [1] calculatePotential function, [1] calculatePotentialBMA function calculatePotentialDispatched function calculatePotentialLaplace function calculatePotentialLaplaceSlice function calculatePotentialSVGD function calculateTrainingCovarianceMatrix function calculateVariance function, [1], [2] calculateVarianceDispatched function calculateVarianceLaplace function calculateVarianceLaplaceSlice function callGeneralPotentialFromEON function ceres namespace cholesky function cholesky_inverse function ci_activation_tol variable class atmd::AtomicDimer aux::AuxiliaryFunctionality aux::Distance aux::Gradient aux::ProblemSetUp dimer::Dimer funcmin::ADAM funcmin::Ceres funcmin::GprCostFunction funcmin::SCG gpr::ARDGridSearch gpr::BayesianModelAveraging gpr::ConstantCF gpr::FactorizedLikelihood gpr::GaussianProcessRegression gpr::InverseDistanceDescriptor gpr::io::ErrorManager gpr::io::FileManager gpr::io::LogManager gpr::laplace::PsisLaplace gpr::laplace::ScopedKernelState gpr::laplace::SliceSampler gpr::laplace::SteinVariational gpr::laplace::TCovSecondOrder gpr::LaplaceINLA gpr::LikGaussian gpr::linalg::DenseLLTInverse gpr::linalg::detail::CublasLib gpr::linalg::detail::CusolverLib gpr::linalg::KernelInverse gpr::linalg::ProbeExecutor gpr::linalg::ScalapackState gpr::neb::NEBPath gpr::NoiseGridSearch gpr::ObservationLikelihood gpr::optim::LBFGS gpr::PriorBase gpr::PriorGaussian gpr::PriorLogNormal gpr::PriorLogUnif gpr::priors::CovalentBondPrior gpr::PriorSqrtt gpr::PriorT gpr::PriorUnif gpr::RandomFourierFeatures gpr::RFFModel gpr::SexpatCF gpr::StudentTProcessRegression gpr::TrustRadius math::DistributionFunctions math::MatrixProperties pot::PotentialWrapper

clearDistanceCache function climbing_image variable clipToTrust function collectiveIdppInterpolation function combineParameters function, [1], [2] compute function, [1] computeNEBForces function computeWithJacobian function const_sigma2 variable conv_norm variable conv_tol variable, [1], [2] convergence_force_norm variable ConvergenceNormType enum cordero_radius_angstrom function CovalentBondPrior function cutOffEnergy function

D

DebugLevels enum default_gpr_parameters() (in module gpr_optim) default_parameters() (in module gpr_optim) deltaF variable deltaOrient variable deterministic_axial_grid variable Dimer function dimer namespace dimer::Dimer class dimer_sep variable, [1] DimerAlgorithm enum Directions enum

disp_max variable, [1] dist_at function dist_at_cached function dist_at_cached_sq function dist_at_vec function dist_emd function dist_max1Dlog function dist_rmsd function DistanceMetricType enum distanceToTraining function divisor_T_dimer_gp variable, [1]

E

E_all_init variable E_init variable enableClimbingImage function enum AcquisitionType ConvergenceNormType DebugLevels DimerAlgorithm Directions DistanceMetricType FrozenAndMovingAtoms gpr_acquisition_t gpr_conv_norm_t gpr_model_type_t gpr_neb_mode_t gpr_optim_alg_t gpr_uncertainty_mode_t HyperparameterOptimizationMode Kind Likelihood NEBMode OptimizationAlgorithms OptionsForGradCalculation Potentials ScgCurvatureMode UncertaintyMode enumvalue GAUSSIAN_CLOSED_FORM GPR_MODEL_GP GPR_MODEL_TP GPR_NEB_AIE GPR_NEB_OIE GPR_NEB_STANDARD GPR_NORM_L2 GPR_NORM_LINF GPR_NORM_MAX_ATOM GPR_OPT_FACTORIZED GPR_OPT_SCG NON_GAUSSIAN T_CLOSED_FORM

erfinv function estimateParetoKHat function estimateRotationalAngle function eval_image1 variable, [1] evals_per_iter variable evaluateCovarianceMatrix function evaluateCrossBlockGeometry function evaluateDirectionalCurvature function evaluateEnergyAndGradient function evaluateEnergyAndGradientLocal function evaluateGP function evaluateLogPrior function evaluateLogPriorGradient function evaluateTP function evaluateTrainingCovarianceMatrix function, [1] execute function, [1] expandToTriplet function extractCoordinatesByIndex function extractUniqueIndices function

F

F_old variable factorise function featureDimension function featurePairtypes function findFMode function fit function, [1], [2], [3], [4] flatDot function fmin namespace force function forward_solve function forward_solve_mat function forward_solve_mat_colwise_squared_norm function fps_history variable from_rgpot function FrozenAndMovingAtoms enum funcmin namespace funcmin::ADAM class funcmin::Ceres class funcmin::GprCostFunction class funcmin::SCG class function accumulateBlockContribution activateFrozenAtoms analyticalPrefactor applyCorrection applyCrossBlockGeometryToVector applyTheta approximateKernel assembleDirectionalCovarianceDerivatives assembleExactHessian assembleMatrixOfRepetitiveCoordinates assembleVectorFromEnergyAndGradient assertMsg assignBlockToMatrix assignFromField AtomicDimer back_solve back_solve_mat bond_length_angstrom bondLength build buildCrossBlockGeometry buildGrid buildRFFModel cacheDistances cacheInverseDistances calculateCovarianceMatrix, [1] calculateDerivativesDiffDim calculateDerivativesSameDim calculateDirectionalCovarianceMatrix calculateDirectionalCovarianceMatrixWithDerivatives calculateDirectionalCovarianceMatrixWithDerivatives2 calculateDirectionalLogPriorCurvature calculateGeneralPotential calculateGradOfCovMatrix, [1] calculateGradOfCovMatrixWithDerivatives, [1] calculateGradOfCovMatrixWithDerivatives2, [1] calculateLogPrior, [1] calculateLogPriorGradient, [1] calculatePotential, [1] calculatePotentialBMA calculatePotentialDispatched calculatePotentialLaplace calculatePotentialLaplaceSlice calculatePotentialSVGD calculateTrainingCovarianceMatrix calculateVariance, [1], [2] calculateVarianceDispatched calculateVarianceLaplace calculateVarianceLaplaceSlice callGeneralPotentialFromEON cholesky cholesky_inverse clearDistanceCache clipToTrust collectiveIdppInterpolation combineParameters, [1], [2] compute, [1] computeNEBForces computeWithJacobian cordero_radius_angstrom CovalentBondPrior cutOffEnergy Dimer dist_at dist_at_cached dist_at_cached_sq dist_at_vec dist_emd dist_max1Dlog dist_rmsd distanceToTraining enableClimbingImage erfinv estimateParetoKHat estimateRotationalAngle evaluateCovarianceMatrix evaluateCrossBlockGeometry evaluateDirectionalCurvature evaluateEnergyAndGradient evaluateEnergyAndGradientLocal evaluateGP evaluateLogPrior evaluateLogPriorGradient evaluateTP evaluateTrainingCovarianceMatrix, [1] execute, [1] expandToTriplet extractCoordinatesByIndex extractUniqueIndices factorise featureDimension featurePairtypes findFMode fit, [1], [2], [3], [4] flatDot force forward_solve forward_solve_mat forward_solve_mat_colwise_squared_norm from_rgpot getEnergyForAllObservationPointsRef getFinalCoordOfMidPoint getFinalCurvature getFinalEnergy getFinalForceAtMidPoint getFinalOrientation getGPRModel getGradientForAllObservationPointsRef getIterations getL getMidPointCoordForAllObservationPointsRef getNumberOfRepetitiveIndices getSigma2 getTotalForceCalls getTotalGPRForceCalls getTPPrefactor getWeights ginput2, [1] ginput3, [1] ginput4, [1] gp_minimize gpNEB gpr_atoms_config_defaults, [1] gpr_atoms_create, [1] gpr_atoms_create_simple, [1] gpr_atoms_destroy, [1] gpr_atoms_n_moving, [1] gpr_atoms_n_pairtypes, [1] gpr_atoms_simple, [1] gpr_backend_name, [1] gpr_backend_requires_mpi, [1] gpr_dimer_search, [1] gpr_last_error, [1] gpr_minimize, [1] gpr_model_create, [1] gpr_model_destroy, [1] gpr_model_get_alpha, [1] gpr_model_get_jitter, [1] gpr_model_get_lengthscales, [1] gpr_model_get_magn_sigma2, [1] gpr_model_get_sigma2, [1] gpr_model_init, [1] gpr_model_n_lengthscales, [1] gpr_model_n_observations, [1] gpr_model_predict, [1] gpr_model_predict_batch, [1] gpr_model_predict_full, [1] gpr_model_predict_variance, [1] gpr_model_set_lengthscales, [1] gpr_model_set_magn_sigma2, [1] gpr_model_set_sigma2, [1] gpr_model_tp_prefactor, [1] gpr_model_train, [1] gpr_model_type, [1] gpr_model_update, [1] gpr_mpi_initialized, [1] gpr_mpi_world_rank, [1] gpr_mpi_world_size, [1] gpr_neb_result_all_energies, [1] gpr_neb_result_barrier, [1] gpr_neb_result_converged, [1] gpr_neb_result_destroy, [1] gpr_neb_result_image_energy, [1] gpr_neb_result_image_positions, [1] gpr_neb_result_max_energy_image, [1] gpr_neb_result_n_images, [1] gpr_neb_result_oracle_calls, [1] gpr_neb_result_outer_iterations, [1] gpr_neb_search, [1] gpr_omp_max_threads, [1] gpr_oracle_leps, [1] gpr_oracle_lj, [1] gpr_oracle_muller_brown, [1] gpr_potential_leps, [1] gpr_potential_lj, [1] gpr_potential_muller_brown, [1] gpr_version, [1] gpr_version_components, [1] gradLogProb gridPoints hasBeenOptimized hessianInverse highestEnergyImageIndex hilbert_3d hilbert_permutation idppEnergy idppGradient idppInterpolation image initFromCCD initialize, [1] initializeEnergyAndGradient initializeIDPP intermediatePositions invalidate is_distributed isDD isFinalConvergenceReached isPD isPSD isRotationalConvergenceReached isWithinTrust kind, [1] laplaceMarginalLogLik lengthScalePerPairtype leps_energy_gradient lj_energy_gradient loadParametersFromCapnp local log_det, [1] log_det_cholesky logGaussianDensity logProb lScale mindist_interatomic morton_3d morton_to_hilbert_3d muller_brown_energy_gradient nebForce NEBPath negHessDiag nLs NoiseGridSearch normalCDF normalCDFInverse operator<<, [1] optimize, [1], [2] optimizeFactorized pairwiseDistances particles perpendicularSigma precisionMatrix predict, [1] project_out_rot_trans_with_feedback RandomFourierFeatures readDataFile readFromPlainFile readInputFile refreshVariancePrefactor removeColumn removeDuplicatedAtoms repmatConst restore rotate rotateDimer rotateForce run sample ScopedKernelState searchGP, [1] searchTP selectNextImage selfNormalisedWeights setAlgorithmSettings, [1] setAtomsConfiguration setConstSigma2 setEigendecomposition setFromObservation setGrid setHessian setHyperparameters setHyperpriorParameters setJitterSigma2 setLengthscale setObservationLikelihood setPairtypeForMovingAtoms setParameters, [1], [2] setRFFFeaturesRequested setSigma2 setSVGDConfig setTheta0 setTPHyperprior setTrainingData setUncertaintyMode setUpDefault setUseDeltaMethod setUsePsisDeterministicGrid setUsePsisLaplace setVarianceAcceptTau setVarianceAcceptTauRelative solve, [1] solve_assignment_problem solve_mat, [1] theta0 tpPrefactor trace_inv_times, [1] trace_product transform transformBatch translate translateDimer translateForce uniformWeights updateActiveFrozenAtoms updateConf updateConfiguration updateModelWithFullData valid

G

G_all_init variable G_init variable GAUSSIAN_CLOSED_FORM enumvalue getEnergyForAllObservationPointsRef function getFinalCoordOfMidPoint function getFinalCurvature function getFinalEnergy function getFinalForceAtMidPoint function getFinalOrientation function getGPRModel function getGradientForAllObservationPointsRef function getIterations function getL function getMidPointCoordForAllObservationPointsRef function getNumberOfRepetitiveIndices function getSigma2 function getTotalForceCalls function getTotalGPRForceCalls function getTPPrefactor function getWeights function ginput2 function, [1] ginput3 function, [1] ginput4 function, [1] global namespace gp_jitter variable gp_max_iter variable gp_minimize function gp_sigma2 variable gp_train_iter variable gpNEB function gpr namespace, [1], [2], [3], [4] gpr::AdamOptimizationSettings struct gpr::ARDGridSearch class gpr::ARDSearchResult struct gpr::AtomsConfiguration struct gpr::AtomsPositionAndType struct gpr::BayesianModelAveraging class gpr::BMAPrediction struct gpr::CeresOptimizationSettings struct gpr::ConstantCF class gpr::coord namespace gpr::Derivatives struct gpr::EnergyAndGradient struct gpr::EnergySurfaceOutputInfo struct gpr::FactorizedLikelihood class gpr::field namespace gpr::GaussianProcessRegression class gpr::GaussianProcessRegression::farthest_point_sampling_t struct gpr::GaussianProcessRegression::LaplacePosteriorFactor struct gpr::GaussianProcessRegression::LaplacePosteriorSignature struct gpr::GaussianProcessRegression::LaplacePosteriorStamp struct gpr::GaussianProcessRegression::LaplacePosteriorState struct gpr::GaussianProcessRegression::LaplaceTrainingCovarianceGeometry struct gpr::GaussianProcessRegression::LaplaceTrainingCovarianceGeometry::Block struct gpr::GaussianProcessRegression::SliceLaplaceState struct gpr::GPRSetup struct gpr::Indices2D struct gpr::INLAPrediction struct gpr::InputParameters struct gpr::InverseDistanceDescriptor class gpr::io namespace gpr::io::ErrorManager class gpr::io::FileManager class gpr::io::LogManager class gpr::IterationsLimits struct gpr::KeyValuePair struct gpr::laplace namespace gpr::laplace::PsisLaplace class gpr::laplace::PsisLaplaceOptions struct gpr::laplace::PsisLaplaceState struct gpr::laplace::ScopedKernelState class gpr::laplace::SliceSampler class gpr::laplace::SliceSamplerOptions struct gpr::laplace::SliceSamplerState struct gpr::laplace::SteinVariational class gpr::laplace::SteinVariationalConfig struct gpr::laplace::TCovSecondOrder class gpr::LaplaceINLA class gpr::LBFGSInfo struct gpr::LikGaussian class gpr::linalg namespace gpr::linalg::DenseLLTInverse class gpr::linalg::detail namespace gpr::linalg::detail::CublasLib class gpr::linalg::detail::CusolverLib class gpr::linalg::detail::DevBuf struct gpr::linalg::detail::DeviceState struct gpr::linalg::detail::DevInt struct gpr::linalg::KernelInverse class gpr::linalg::MpiContext struct gpr::linalg::ProbeExecutor class gpr::linalg::ScalapackState class gpr::linalg::ScalapackState::DescCacheEntry struct gpr::neb namespace gpr::neb::GPNEBConfig struct gpr::neb::GPNEBResult struct gpr::neb::Image struct gpr::neb::NEBPath class gpr::NoiseGridSearch class gpr::NoiseSearchResult struct gpr::Observation struct gpr::ObservationLikelihood class gpr::optim namespace gpr::optim::LBFGS class gpr::optim::MinimizationConfig struct gpr::optim::MinimizationResult struct gpr::OptimizerCommonSettings struct gpr::Pair struct gpr::potentials namespace gpr::PriorBase class

gpr::PriorGaussian class gpr::PriorLogNormal class gpr::PriorLogUnif class gpr::priors namespace gpr::priors::CovalentBondPrior class gpr::PriorSqrtt class gpr::PriorT class gpr::PriorUnif class gpr::RandomFourierFeatures class gpr::RFFModel class gpr::ScgOptimizationSettings struct gpr::SexpatCF class gpr::SexpatCF::CrossBlockGeometry struct gpr::SexpatLocalOracleScope struct gpr::sfc namespace gpr::StopCriteriaForDimer struct gpr::StructuredPermutation struct gpr::StudentTProcessRegression class gpr::tests namespace gpr::TransitionParameters struct gpr::Triplet struct gpr::TrustRadius class gpr_acquisition_t enum gpr_atoms_config_defaults function, [1] gpr_atoms_config_t struct gpr_atoms_create function, [1] gpr_atoms_create_simple function, [1] gpr_atoms_destroy function, [1] gpr_atoms_n_moving function, [1] gpr_atoms_n_pairtypes function, [1] gpr_atoms_s struct gpr_atoms_simple function, [1] gpr_backend_name function, [1] gpr_backend_requires_mpi function, [1] gpr_conv_norm_t enum gpr_dimer_config_t struct gpr_dimer_search function, [1] gpr_force_fn typedef gpr_last_error function, [1] gpr_lj_params_t struct gpr_minimize function, [1] gpr_minimize_config_t struct gpr_model_config_t struct gpr_model_create function, [1] gpr_model_destroy function, [1] gpr_model_get_alpha function, [1] gpr_model_get_jitter function, [1] gpr_model_get_lengthscales function, [1] gpr_model_get_magn_sigma2 function, [1] gpr_model_get_sigma2 function, [1] GPR_MODEL_GP enumvalue gpr_model_init function, [1] gpr_model_n_lengthscales function, [1] gpr_model_n_observations function, [1] gpr_model_predict function, [1] gpr_model_predict_batch function, [1] gpr_model_predict_full function, [1] gpr_model_predict_variance function, [1] gpr_model_s struct gpr_model_set_lengthscales function, [1] gpr_model_set_magn_sigma2 function, [1] gpr_model_set_sigma2 function, [1] gpr_model_t typedef GPR_MODEL_TP enumvalue gpr_model_tp_prefactor function, [1] gpr_model_train function, [1] gpr_model_type function, [1] gpr_model_type_t enum gpr_model_update function, [1] gpr_mpi_initialized function, [1] gpr_mpi_world_rank function, [1] gpr_mpi_world_size function, [1] GPR_NEB_AIE enumvalue gpr_neb_config_t struct gpr_neb_mode_t enum GPR_NEB_OIE enumvalue gpr_neb_result_all_energies function, [1] gpr_neb_result_barrier function, [1] gpr_neb_result_converged function, [1] gpr_neb_result_destroy function, [1] gpr_neb_result_image_energy function, [1] gpr_neb_result_image_positions function, [1] gpr_neb_result_max_energy_image function, [1] gpr_neb_result_n_images function, [1] gpr_neb_result_oracle_calls function, [1] gpr_neb_result_outer_iterations function, [1] gpr_neb_s struct gpr_neb_search function, [1] GPR_NEB_STANDARD enumvalue GPR_NORM_L2 enumvalue GPR_NORM_LINF enumvalue GPR_NORM_MAX_ATOM enumvalue gpr_omp_max_threads function, [1] GPR_OPT_FACTORIZED enumvalue GPR_OPT_SCG enumvalue gpr_optim module gpr_optim_alg_t enum gpr_oracle_fn typedef gpr_oracle_leps function, [1] gpr_oracle_lj function, [1] gpr_oracle_muller_brown function, [1] gpr_potential_leps function, [1] gpr_potential_lj function, [1] gpr_potential_muller_brown function, [1] gpr_uncertainty_mode_t enum gpr_version function, [1] gpr_version_components function, [1] GPRCalculator (class in gpr_optim) gradLogProb function GradOracle typedef gridPoints function

H

hasBeenOptimized function hessian_jitter_max variable hessianInverse function highestEnergyImageIndex function

hilbert_3d function hilbert_permutation function HyperparameterOptimizationMode enum

I

id variable idppEnergy function idppGradient function idppInterpolation function image function init_f0 variable initFromCCD function initial_width variable initialize function, [1] initializeEnergyAndGradient function initializeIDPP function initrot_nogp variable, [1]

inner_step_size variable intermediatePositions function invalidate function is_distributed function is_frozen variable, [1] isDD function isFinalConvergenceReached function islarge_num_iter variable, [1] isPD function isPSD function isRotationalConvergenceReached function isWithinTrust function

J

jitter_sigma2 variable, [1]

K

k_hat variable k_hat_threshold variable kCorderoRadiusPm variable KernelBuilder typedef, [1]

KernelMatrixBuilder typedef Kind enum kind function, [1] kTrustTau variable

L

laplace namespace laplaceMarginalLogLik function lengthScalePerPairtype function leps_energy_gradient function Likelihood enum linalg namespace lj_energy_gradient function load_file variable loadParametersFromCapnp function

local function log_det function, [1] log_det_cholesky function log_weights_raw variable logGaussianDensity function LogPrior typedef logProb function LogTarget typedef, [1] lScale function

M

magn_sigma2 variable math namespace math::DistributionFunctions class math::MatrixProperties class max_doublings variable max_inner_iter variable max_iter variable, [1] max_move variable max_oracle_calls variable max_outer_iter variable max_shrinks variable max_step_length variable

max_training_points variable mean variable method_rot variable method_trans variable mindist_interatomic function mode variable module gpr_optim morton_3d function morton_to_hilbert_3d function MORTON_TO_HILBERT_LUT variable muller_brown_energy_gradient function

N

n_accepted variable n_atoms variable n_atoms_total variable n_burnin variable n_grid_points variable n_initial_perturb variable n_iterations variable n_pt variable n_samples variable, [1] n_steps variable n_stuck variable n_target_evals variable, [1] namespace atmd aux ceres dimer fmin funcmin global gpr, [1], [2], [3], [4] gpr::coord gpr::field gpr::io gpr::laplace gpr::linalg gpr::linalg::detail gpr::neb gpr::optim gpr::potentials gpr::priors gpr::sfc gpr::tests laplace linalg math pot std

nebForce function NEBMode enum NEBOracle typedef NEBPath function negHessDiag function nLs function NoiseGridSearch function NON_GAUSSIAN enumvalue normalCDF function normalCDFInverse function nprune_vals variable, [1] num_bigiter variable, [1] num_bigiter_initloc variable, [1] num_bigiter_initparam variable, [1] num_cg_iter variable num_iter variable, [1] num_iter_initrot variable, [1] num_iter_rot_gp variable, [1] num_lbfgs_iter variable

O

observation_from_ase() (in module gpr_optim) operator<< function, [1] optim_alg variable OptimizationAlgorithms enum optimize function, [1], [2]

optimizeFactorized function OptionsForGradCalculation enum OracleFn typedef orient_init variable

P

pairtype variable pairwiseDistances function param_trans variable particles function perpendicularSigma function perturb_scale variable positions variable, [1] pot namespace pot::PotentialWrapper class

Potentials enum precisionMatrix function predict function, [1] preset_parameters() (in module gpr_optim) prior_mu variable prior_nu variable prior_s2 variable project_out_rot_trans_with_feedback function prune_threshold variable, [1]

R

R_all_init variable R_init variable RandomFourierFeatures function ratio_at_limit variable, [1] readDataFile function readFromPlainFile function readInputFile function refreshVariancePrefactor function reliable variable

removeColumn function removeDuplicatedAtoms function repmatConst function report_level variable, [1] restore function rotate function rotateDimer function rotateForce function run function run_dimer() (in module gpr_optim)

S

sample function save_file variable ScgCurvatureMode enum ScopedKernelState function searchGP function, [1] searchTP function seed variable, [1], [2], [3] selectNextImage function selfNormalisedWeights function setAlgorithmSettings function, [1] setAtomsConfiguration function setConstSigma2 function setEigendecomposition function setFromObservation function setGrid function setHessian function setHyperparameters function setHyperpriorParameters function setJitterSigma2 function setLengthscale function setObservationLikelihood function setPairtypeForMovingAtoms function setParameters function, [1], [2] setRFFFeaturesRequested function setSigma2 function setSVGDConfig function setTheta0 function setTPHyperprior function setTrainingData function setUncertaintyMode function setUpDefault function setUseDeltaMethod function setUsePsisDeterministicGrid function setUsePsisLaplace function setVarianceAcceptTau function setVarianceAcceptTauRelative function sexpat_local_oracle_active variable sigma2 variable solve function, [1]

solve_assignment_problem function solve_mat function, [1] spring_constant variable start_prune_at variable, [1] std namespace step_length variable step_size variable struct atmd::AtomicDimer::early_stopping_t atmd::AtomicDimer::VarianceGateConfig aux::AtomSignature aux::InverseDistanceCache gpr::AdamOptimizationSettings gpr::ARDSearchResult gpr::AtomsConfiguration gpr::AtomsPositionAndType gpr::BMAPrediction gpr::CeresOptimizationSettings gpr::Derivatives gpr::EnergyAndGradient gpr::EnergySurfaceOutputInfo gpr::GaussianProcessRegression::farthest_point_sampling_t gpr::GaussianProcessRegression::LaplacePosteriorFactor gpr::GaussianProcessRegression::LaplacePosteriorSignature gpr::GaussianProcessRegression::LaplacePosteriorStamp gpr::GaussianProcessRegression::LaplacePosteriorState gpr::GaussianProcessRegression::LaplaceTrainingCovarianceGeometry gpr::GaussianProcessRegression::LaplaceTrainingCovarianceGeometry::Block gpr::GaussianProcessRegression::SliceLaplaceState gpr::GPRSetup gpr::Indices2D gpr::INLAPrediction gpr::InputParameters gpr::IterationsLimits gpr::KeyValuePair gpr::laplace::PsisLaplaceOptions gpr::laplace::PsisLaplaceState gpr::laplace::SliceSamplerOptions gpr::laplace::SliceSamplerState gpr::laplace::SteinVariationalConfig gpr::LBFGSInfo gpr::linalg::detail::DevBuf gpr::linalg::detail::DeviceState gpr::linalg::detail::DevInt gpr::linalg::MpiContext gpr::linalg::ScalapackState::DescCacheEntry gpr::neb::GPNEBConfig gpr::neb::GPNEBResult gpr::neb::Image gpr::NoiseSearchResult gpr::Observation gpr::optim::MinimizationConfig gpr::optim::MinimizationResult gpr::OptimizerCommonSettings gpr::Pair gpr::ScgOptimizationSettings gpr::SexpatCF::CrossBlockGeometry gpr::SexpatLocalOracleScope gpr::StopCriteriaForDimer gpr::StructuredPermutation gpr::TransitionParameters gpr::Triplet gpr_atoms_config_t gpr_atoms_s gpr_dimer_config_t gpr_lj_params_t gpr_minimize_config_t gpr_model_config_t gpr_model_s gpr_neb_config_t gpr_neb_s

T

T_anglerot_gp variable, [1] T_anglerot_init variable, [1] T_CLOSED_FORM enumvalue T_dimer variable, [1] theta0 function theta_map variable theta_samples variable, [1] tol_func variable tol_sol variable total_gpr_calls (gpr_optim.GPRCalculator property) total_inner_calls (gpr_optim.GPRCalculator property) tp_hyperprior_a variable tp_hyperprior_b variable tpPrefactor function trace_inv_times function, [1]

trace_product function transform function transformBatch function translate function translateDimer function translateForce function trust_radius variable type variable typedef AlphaCacheFn, [1] gpr_force_fn gpr_model_t gpr_oracle_fn GradOracle KernelBuilder, [1] KernelMatrixBuilder LogPrior LogTarget, [1] NEBOracle OracleFn VarianceEstimator

U

ucb_kappa variable uncertainty_mode variable UncertaintyMode enum uniformWeights function updateActiveFrozenAtoms function updateConf function updateConfiguration function

updateModelWithFullData function use_delta_method variable use_idpp variable use_prune variable use_psis_deterministic variable use_psis_laplace variable use_triplet variable

V

valid function variable, [1] variable _adaptive_A _adaptive_floor _dist_metric _threshold _use_adaptive_threshold accept_tau accept_tau_relative acquisition actdist_fro, [1] alpha_cache alpha_samples atom_types atomic_nrs atomicNrs atoms_config atoms_froz_active atoms_froz_inactive atoms_mov ci_activation_tol climbing_image const_sigma2 conv_norm conv_tol, [1], [2] convergence_force_norm deltaF deltaOrient deterministic_axial_grid dimer_sep, [1] disp_max, [1] divisor_T_dimer_gp, [1] E_all_init E_init eval_image1, [1] evals_per_iter F_old fps_history G_all_init G_init gp_jitter gp_max_iter gp_sigma2 gp_train_iter hessian_jitter_max id init_f0 initial_width initrot_nogp, [1] inner_step_size is_frozen, [1] islarge_num_iter, [1] jitter_sigma2, [1] k_hat k_hat_threshold kCorderoRadiusPm kTrustTau load_file log_weights_raw magn_sigma2 max_doublings max_inner_iter max_iter, [1] max_move max_oracle_calls max_outer_iter max_shrinks max_step_length max_training_points mean method_rot method_trans mode MORTON_TO_HILBERT_LUT n_accepted n_atoms n_atoms_total n_burnin n_grid_points n_initial_perturb n_iterations n_pt n_samples, [1] n_steps n_stuck n_target_evals, [1] nprune_vals, [1] num_bigiter, [1] num_bigiter_initloc, [1] num_bigiter_initparam, [1] num_cg_iter num_iter, [1] num_iter_initrot, [1] num_iter_rot_gp, [1] num_lbfgs_iter optim_alg orient_init pairtype param_trans perturb_scale positions, [1] prior_mu prior_nu prior_s2 prune_threshold, [1] R_all_init R_init ratio_at_limit, [1] reliable report_level, [1] save_file seed, [1], [2], [3] sexpat_local_oracle_active sigma2 spring_constant start_prune_at, [1] step_length step_size T_anglerot_gp, [1] T_anglerot_init, [1] T_dimer, [1] theta_map theta_samples, [1] tol_func tol_sol tp_hyperprior_a tp_hyperprior_b trust_radius type ucb_kappa uncertainty_mode use_delta_method use_idpp use_prune use_psis_deterministic use_psis_laplace use_triplet valid, [1] variance variance_accept_tau variance_accept_tau_relative variance_estimator verbose, [1] weights

variance variable variance_accept_tau variable variance_accept_tau_relative variable variance_estimator variable VarianceEstimator typedef verbose variable, [1]

W

weights variable