Index _ | A | B | C | D | E | F | G | I | K | L | M | N | O | P | R | S | T | U | V | W _ __init__() (gnrs.cluster.ap.APCluster method) (gnrs.cluster.cluster_task.ClusterSelectionTask method) (gnrs.cluster.kmeans.KMEANSCluster method) (gnrs.core.cluster.ClusterABC method) (gnrs.core.descriptor.DescriptorABC method) (gnrs.core.energy.EnergyCalculatorABC method) (gnrs.core.gpu.GPUDeviceManager method) (gnrs.core.logging.GenarrisLogger method) (gnrs.core.molecule.Molecule method) (gnrs.core.optimizer.GeometryOptimizerABC method) (gnrs.core.selection.SelectionABC method) (gnrs.core.structure.Structure method) (gnrs.core.task.TaskABC method) (gnrs.deduplication.deduplication_task.DuplicateRemovalTask method) (gnrs.descriptor.acsf.ACSFDescriptor method) (gnrs.descriptor.descriptor_task.DescriptorEvaluationTask method) (gnrs.energy.aimnet.AIMNETEnergy method) (gnrs.energy.aims.AIMSEnergy method) (gnrs.energy.dftbp.DFTBPEnergy method) (gnrs.energy.energy_task.EnergyCalculationTask method) (gnrs.energy.maceoff.MACEOFFEnergy method) (gnrs.energy.uma.UMAEnergy method) (gnrs.energy.vasp.VASP method) (gnrs.generation.generation_task.StructureGenerationTask method) (gnrs.gnrsutil.molecule_bonding.BondNeighborhood method) (gnrs.gnrsutil.molecule_bonding.MoleculeBonding method) (gnrs.gnrsutil.volume_estimation.MoleculeVolumeEstimator method) (gnrs.optimize.bfgs.BFGSOptimizer method) (gnrs.optimize.lbfgs.LBFGSOptimizer method) (gnrs.optimize.optimization_task.GeometryOptimizationTask method) (gnrs.optimize.rigid_press.RIGID_PRESSOptimizer method) (gnrs.optimize.symm_rigid_press.SYMM_RIGID_PRESSOptimizer method) (gnrs.parallel.structs.DistributedStructs method) (gnrs.workflow.Genarris method) A ACSFDescriptor (class in gnrs.descriptor.acsf) adapt_array() (in module gnrs.core.structure) add_lattice_vector() (gnrs.core.structure.Structure method) AIMNETEnergy (class in gnrs.energy.aimnet) AIMSEnergy (class in gnrs.energy.aims) analyze() (gnrs.cluster.cluster_task.ClusterSelectionTask method) (gnrs.core.task.TaskABC method) (gnrs.deduplication.deduplication_task.DuplicateRemovalTask method) (gnrs.descriptor.descriptor_task.DescriptorEvaluationTask method) (gnrs.energy.energy_task.EnergyCalculationTask method) (gnrs.generation.generation_task.StructureGenerationTask method) (gnrs.optimize.optimization_task.GeometryOptimizationTask method) angle() (gnrs.core.structure.Structure method) APCluster (class in gnrs.cluster.ap) append() (gnrs.core.structure.Structure method) assigned_worker() (gnrs.core.gpu.GPUDeviceManager method) attempt_restart() (gnrs.workflow.Genarris method) B BFGSOptimizer (class in gnrs.optimize.bfgs) bond_neighberhood_model() (gnrs.gnrsutil.volume_estimation.MoleculeVolumeEstimator method) BondNeighborhood (class in gnrs.gnrsutil.molecule_bonding) build_geo_by_atom() (gnrs.core.structure.Structure method) build_geo_by_atom_array() (gnrs.core.structure.Structure method) build_geo_by_whole_atom() (gnrs.core.structure.Structure method) build_geo_from_atom_file() (gnrs.core.structure.Structure method) build_geo_whole() (gnrs.core.structure.Structure method) build_geo_whole_atom_format() (gnrs.core.structure.Structure method) build_struct_from_json_path() (gnrs.core.structure.Structure method) C calc() (gnrs.gnrsutil.molecule_bonding.BondNeighborhood method) (gnrs.gnrsutil.volume_estimation.MoleculeVolumeEstimator method) calc_stoic() (in module gnrs.core.structure) cell_opt (gnrs.optimize.bfgs.BFGSOptimizer attribute) (gnrs.optimize.lbfgs.LBFGSOptimizer attribute) CENTERSelection (class in gnrs.cluster.selection.center) check_convergence() (gnrs.cluster.ap.APCluster method) check_if_exp_found() (in module gnrs.gnrsutil.core) checkpoint_load() (gnrs.parallel.structs.DistributedStructs method) checkpoint_save() (gnrs.parallel.structs.DistributedStructs method) cleanup() (gnrs.core.cluster.ClusterABC method) ClusterABC (class in gnrs.core.cluster) ClusterSelectionTask (class in gnrs.cluster.cluster_task) collect_property() (gnrs.parallel.structs.DistributedStructs method) collect_results() (gnrs.cluster.cluster_task.ClusterSelectionTask method) (gnrs.core.task.TaskABC method) (gnrs.deduplication.deduplication_task.DuplicateRemovalTask method) (gnrs.descriptor.descriptor_task.DescriptorEvaluationTask method) (gnrs.energy.energy_task.EnergyCalculationTask method) (gnrs.generation.generation_task.StructureGenerationTask method) (gnrs.optimize.optimization_task.GeometryOptimizationTask method) compute() (gnrs.core.descriptor.DescriptorABC method) (gnrs.core.energy.EnergyCalculatorABC method) (gnrs.descriptor.acsf.ACSFDescriptor method) (gnrs.energy.aimnet.AIMNETEnergy method) (gnrs.energy.aims.AIMSEnergy method) (gnrs.energy.dftbp.DFTBPEnergy method) (gnrs.energy.maceoff.MACEOFFEnergy method) (gnrs.energy.uma.UMAEnergy method) (gnrs.energy.vasp.VASP method) construct_intermolecular_dist_dict() (in module gnrs.gnrsutil.molecule_bonding) construct_pair_keys() (in module gnrs.gnrsutil.molecule_bonding) converged (gnrs.optimize.bfgs.BFGSOptimizer attribute) (gnrs.optimize.lbfgs.LBFGSOptimizer attribute) convert_array() (in module gnrs.core.structure) copy_molecule() (in module gnrs.core.folders) create_folders() (gnrs.cluster.cluster_task.ClusterSelectionTask method) (gnrs.core.task.TaskABC method) (gnrs.deduplication.deduplication_task.DuplicateRemovalTask method) (gnrs.descriptor.descriptor_task.DescriptorEvaluationTask method) (gnrs.energy.energy_task.EnergyCalculationTask method) (gnrs.generation.generation_task.StructureGenerationTask method) (gnrs.optimize.optimization_task.GeometryOptimizationTask method) D debug_flag (gnrs.optimize.symm_rigid_press.SYMM_RIGID_PRESSOptimizer attribute) dedup_group() (in module gnrs.deduplication.dedup) delete_property() (gnrs.core.structure.Structure method) DescriptorABC (class in gnrs.core.descriptor) DescriptorEvaluationTask (class in gnrs.descriptor.descriptor_task) device (gnrs.core.energy.EnergyCalculatorABC property) (gnrs.core.gpu.GPUDeviceManager property) DFTBPEnergy (class in gnrs.energy.dftbp) DistributedStructs (class in gnrs.parallel.structs) document() (gnrs.core.structure.Structure method) dumps() (gnrs.core.structure.Structure method) DuplicateRemovalTask (class in gnrs.deduplication.deduplication_task) E EnergyCalculationTask (class in gnrs.energy.energy_task) EnergyCalculatorABC (class in gnrs.core.energy) eV2kJ() (in module gnrs.gnrsutil.core) F feeder_ranks (gnrs.core.gpu.GPUDeviceManager property) finalize() (gnrs.cluster.ap.APCluster method) (gnrs.cluster.cluster_task.ClusterSelectionTask method) (gnrs.cluster.kmeans.KMEANSCluster method) (gnrs.cluster.selection.center.CENTERSelection method) (gnrs.cluster.selection.window.WINDOWSelection method) (gnrs.core.cluster.ClusterABC method) (gnrs.core.descriptor.DescriptorABC method) (gnrs.core.energy.EnergyCalculatorABC method) (gnrs.core.optimizer.GeometryOptimizerABC method) (gnrs.core.selection.SelectionABC method) (gnrs.core.task.TaskABC method) (gnrs.deduplication.deduplication_task.DuplicateRemovalTask method) (gnrs.descriptor.acsf.ACSFDescriptor method) (gnrs.descriptor.descriptor_task.DescriptorEvaluationTask method) (gnrs.energy.aimnet.AIMNETEnergy method) (gnrs.energy.aims.AIMSEnergy method) (gnrs.energy.dftbp.DFTBPEnergy method) (gnrs.energy.energy_task.EnergyCalculationTask method) (gnrs.energy.maceoff.MACEOFFEnergy method) (gnrs.energy.uma.UMAEnergy method) (gnrs.energy.vasp.VASP method) (gnrs.generation.generation_task.StructureGenerationTask method) (gnrs.optimize.optimization_task.GeometryOptimizationTask method) find_matches() (gnrs.parallel.structs.DistributedStructs method) find_spg() (gnrs.parallel.structs.DistributedStructs method) fit() (gnrs.cluster.ap.APCluster method) (gnrs.cluster.kmeans.KMEANSCluster method) (gnrs.core.cluster.ClusterABC method) fix_sym (gnrs.optimize.bfgs.BFGSOptimizer attribute) (gnrs.optimize.lbfgs.LBFGSOptimizer attribute) fmax (gnrs.optimize.bfgs.BFGSOptimizer attribute) (gnrs.optimize.lbfgs.LBFGSOptimizer attribute) from_ase() (gnrs.core.structure.Structure method) from_dict() (gnrs.core.structure.Structure method) from_geo_array() (gnrs.core.structure.Structure method) from_pymatgen() (gnrs.core.structure.Structure method) G Genarris (class in gnrs.workflow) GenarrisLogger (class in gnrs.core.logging) GeometryOptimizationTask (class in gnrs.optimize.optimization_task) GeometryOptimizerABC (class in gnrs.core.optimizer) get_aims() (gnrs.core.structure.Structure method) get_ase_atoms() (gnrs.core.structure.Structure method) get_atom_distance() (gnrs.core.structure.Structure method) get_atom_types() (gnrs.core.structure.Structure method) get_calculator() (gnrs.core.energy.EnergyCalculatorABC method) get_crystal_cutoff_matrix() (gnrs.gnrsutil.molecule_bonding.MoleculeBonding method) get_cutoff_matrix() (gnrs.gnrsutil.molecule_bonding.MoleculeBonding method) get_cutoff_matrix_vdw() (gnrs.gnrsutil.molecule_bonding.MoleculeBonding method) get_energy() (gnrs.cluster.selection.window.WINDOWSelection method) get_frac_data() (gnrs.core.structure.Structure method) get_geo_array() (gnrs.core.structure.Structure method) get_geo_from_file() (in module gnrs.core.structure) get_geometry() (gnrs.core.structure.Structure method) get_geometry_atom_format() (gnrs.core.structure.Structure method) get_input_ref() (gnrs.core.structure.Structure method) get_lattice_angles() (gnrs.core.structure.Structure method) get_lattice_magnitudes() (gnrs.core.structure.Structure method) get_lattice_vectors() (gnrs.core.structure.Structure method) get_lattice_vectors_better() (gnrs.core.structure.Structure method) get_n_atoms() (gnrs.core.structure.Structure method) get_n_atoms_per_mol() (gnrs.core.structure.Structure method) get_num_structs() (gnrs.parallel.structs.DistributedStructs method) get_path() (gnrs.core.structure.Structure method) get_property() (gnrs.core.structure.Structure method) get_pymatgen_structure() (gnrs.core.structure.Structure method) get_statistics() (gnrs.parallel.structs.DistributedStructs method) get_stoic() (gnrs.core.structure.Structure method) get_stoic_str() (gnrs.core.structure.Structure method) get_string() (gnrs.core.structure.StoicDict method) get_struct_id() (gnrs.core.structure.Structure method) get_unit_cell_volume() (gnrs.core.structure.Structure method) get_vdw_distance_cutoff_matrix() (in module gnrs.gnrsutil.molecule_bonding) get_window_across_ranks() (gnrs.cluster.selection.window.WINDOWSelection method) gnrs.cluster module gnrs.cluster.ap module gnrs.cluster.cluster_task module gnrs.cluster.kmeans module gnrs.cluster.selection.center module gnrs.cluster.selection.window module gnrs.core module gnrs.core.cluster module gnrs.core.descriptor module gnrs.core.energy module gnrs.core.folders module gnrs.core.gpu module gnrs.core.logging module gnrs.core.molecule module gnrs.core.optimizer module gnrs.core.registry module gnrs.core.selection module gnrs.core.structure module gnrs.core.task module gnrs.deduplication module gnrs.deduplication.dedup module gnrs.deduplication.deduplication_task module gnrs.descriptor module gnrs.descriptor.acsf module gnrs.descriptor.descriptor_task module gnrs.energy module gnrs.energy.aimnet module gnrs.energy.aims module gnrs.energy.dftbp module gnrs.energy.energy_task module gnrs.energy.maceoff module gnrs.energy.uma module gnrs.energy.vasp module gnrs.generation module gnrs.generation.generation_task module gnrs.gnrsutil module gnrs.gnrsutil.core module gnrs.gnrsutil.molecule_bonding module gnrs.gnrsutil.volume_estimation module gnrs.optimize module gnrs.optimize.bfgs module gnrs.optimize.lbfgs module gnrs.optimize.optimization_task module gnrs.optimize.rigid_press module gnrs.optimize.symm_rigid_press module gnrs.parallel module gnrs.parallel.io module gnrs.parallel.structs module gnrs.workflow module GPUDeviceManager (class in gnrs.core.gpu) group_by_spg() (in module gnrs.deduplication.dedup) I init_folders() (in module gnrs.core.folders) init_parallel() (in module gnrs.parallel) initialize() (gnrs.cluster.ap.APCluster method) (gnrs.cluster.cluster_task.ClusterSelectionTask method) (gnrs.cluster.kmeans.KMEANSCluster method) (gnrs.cluster.selection.center.CENTERSelection method) (gnrs.cluster.selection.window.WINDOWSelection method) (gnrs.core.cluster.ClusterABC method) (gnrs.core.descriptor.DescriptorABC method) (gnrs.core.energy.EnergyCalculatorABC method) (gnrs.core.optimizer.GeometryOptimizerABC method) (gnrs.core.selection.SelectionABC method) (gnrs.core.task.TaskABC method) (gnrs.deduplication.deduplication_task.DuplicateRemovalTask method) (gnrs.descriptor.acsf.ACSFDescriptor method) (gnrs.descriptor.descriptor_task.DescriptorEvaluationTask method) (gnrs.energy.aimnet.AIMNETEnergy method) (gnrs.energy.aims.AIMSEnergy method) (gnrs.energy.dftbp.DFTBPEnergy method) (gnrs.energy.energy_task.EnergyCalculationTask method) (gnrs.energy.maceoff.MACEOFFEnergy method) (gnrs.energy.uma.UMAEnergy method) (gnrs.energy.vasp.VASP method) (gnrs.generation.generation_task.StructureGenerationTask method) (gnrs.optimize.optimization_task.GeometryOptimizationTask method) (gnrs.optimize.rigid_press.RIGID_PRESSOptimizer method) (gnrs.optimize.symm_rigid_press.SYMM_RIGID_PRESSOptimizer method) int_scale (gnrs.optimize.symm_rigid_press.SYMM_RIGID_PRESSOptimizer attribute) is_feeder (gnrs.core.gpu.GPUDeviceManager property) is_worker (gnrs.core.gpu.GPUDeviceManager property) K KMEANSCluster (class in gnrs.cluster.kmeans) L LBFGSOptimizer (class in gnrs.optimize.lbfgs) loads() (gnrs.core.structure.Structure method) M MACEOFFEnergy (class in gnrs.energy.maceoff) maxiter (gnrs.optimize.symm_rigid_press.SYMM_RIGID_PRESSOptimizer attribute) MC() (gnrs.gnrsutil.volume_estimation.MoleculeVolumeEstimator method) method (gnrs.optimize.symm_rigid_press.SYMM_RIGID_PRESSOptimizer attribute) mkdir() (in module gnrs.core.folders) module gnrs.cluster gnrs.cluster.ap gnrs.cluster.cluster_task gnrs.cluster.kmeans gnrs.cluster.selection.center gnrs.cluster.selection.window gnrs.core gnrs.core.cluster gnrs.core.descriptor gnrs.core.energy gnrs.core.folders gnrs.core.gpu gnrs.core.logging gnrs.core.molecule gnrs.core.optimizer gnrs.core.registry gnrs.core.selection gnrs.core.structure gnrs.core.task gnrs.deduplication gnrs.deduplication.dedup gnrs.deduplication.deduplication_task gnrs.descriptor gnrs.descriptor.acsf gnrs.descriptor.descriptor_task gnrs.energy gnrs.energy.aimnet gnrs.energy.aims gnrs.energy.dftbp gnrs.energy.energy_task gnrs.energy.maceoff gnrs.energy.uma gnrs.energy.vasp gnrs.generation gnrs.generation.generation_task gnrs.gnrsutil gnrs.gnrsutil.core gnrs.gnrsutil.molecule_bonding gnrs.gnrsutil.volume_estimation gnrs.optimize gnrs.optimize.bfgs gnrs.optimize.lbfgs gnrs.optimize.optimization_task gnrs.optimize.rigid_press gnrs.optimize.symm_rigid_press gnrs.parallel gnrs.parallel.io gnrs.parallel.structs gnrs.workflow Molecule (class in gnrs.core.molecule) MoleculeBonding (class in gnrs.gnrsutil.molecule_bonding) MoleculeVolumeEstimator (class in gnrs.gnrsutil.volume_estimation) N num_feeders (gnrs.core.gpu.GPUDeviceManager property) num_workers (gnrs.core.gpu.GPUDeviceManager property) O opt_name (gnrs.optimize.bfgs.BFGSOptimizer attribute) (gnrs.optimize.lbfgs.LBFGSOptimizer attribute) (gnrs.optimize.symm_rigid_press.SYMM_RIGID_PRESSOptimizer attribute) optimize() (gnrs.core.optimizer.GeometryOptimizerABC method) (gnrs.optimize.bfgs.BFGSOptimizer method) (gnrs.optimize.lbfgs.LBFGSOptimizer method) (gnrs.optimize.rigid_press.RIGID_PRESSOptimizer method) (gnrs.optimize.symm_rigid_press.SYMM_RIGID_PRESSOptimizer method) P pack_geometry() (gnrs.core.structure.Structure method) pack_settings() (gnrs.cluster.cluster_task.ClusterSelectionTask method) (gnrs.core.task.TaskABC method) (gnrs.deduplication.deduplication_task.DuplicateRemovalTask method) (gnrs.descriptor.descriptor_task.DescriptorEvaluationTask method) (gnrs.energy.energy_task.EnergyCalculationTask method) (gnrs.generation.generation_task.StructureGenerationTask method) (gnrs.optimize.optimization_task.GeometryOptimizationTask method) perform_task() (gnrs.cluster.cluster_task.ClusterSelectionTask method) (gnrs.core.task.TaskABC method) (gnrs.deduplication.deduplication_task.DuplicateRemovalTask method) (gnrs.descriptor.descriptor_task.DescriptorEvaluationTask method) (gnrs.energy.energy_task.EnergyCalculationTask method) (gnrs.generation.generation_task.StructureGenerationTask method) (gnrs.optimize.optimization_task.GeometryOptimizationTask method) predict() (gnrs.cluster.ap.APCluster method) (gnrs.cluster.kmeans.KMEANSCluster method) (gnrs.core.cluster.ClusterABC method) predict_cell_volume() (in module gnrs.gnrsutil.volume_estimation) print_settings() (gnrs.cluster.cluster_task.ClusterSelectionTask method) (gnrs.core.task.TaskABC method) (gnrs.deduplication.deduplication_task.DuplicateRemovalTask method) (gnrs.descriptor.descriptor_task.DescriptorEvaluationTask method) (gnrs.energy.energy_task.EnergyCalculationTask method) (gnrs.generation.generation_task.StructureGenerationTask method) (gnrs.optimize.optimization_task.GeometryOptimizationTask method) R read() (gnrs.core.molecule.Molecule class method) read_data() (in module gnrs.core.structure) read_geometry_out() (in module gnrs.parallel.io) read_parallel() (in module gnrs.parallel.io) redistribute() (gnrs.parallel.structs.DistributedStructs method) requires_gpu (gnrs.core.energy.EnergyCalculatorABC attribute) (gnrs.energy.aimnet.AIMNETEnergy attribute) (gnrs.energy.maceoff.MACEOFFEnergy attribute) (gnrs.energy.uma.UMAEnergy attribute) reset_lattice_vectors() (gnrs.core.structure.Structure method) reset_loglevel() (gnrs.core.logging.GenarrisLogger method) resolve_task() (in module gnrs.core.registry) RIGID_PRESSOptimizer (class in gnrs.optimize.rigid_press) rmdir() (in module gnrs.core.folders) run() (gnrs.core.cluster.ClusterABC method) (gnrs.core.descriptor.DescriptorABC method) (gnrs.core.energy.EnergyCalculatorABC method) (gnrs.core.optimizer.GeometryOptimizerABC method) (gnrs.core.selection.SelectionABC method) (gnrs.core.task.TaskABC method) (gnrs.workflow.Genarris method) run_batch() (gnrs.core.energy.EnergyCalculatorABC method) S select() (gnrs.cluster.selection.center.CENTERSelection method) (gnrs.cluster.selection.window.WINDOWSelection method) (gnrs.core.selection.SelectionABC method) SelectionABC (class in gnrs.core.selection) set_input_ref() (gnrs.core.structure.Structure method) set_lattice_angles() (gnrs.core.structure.Structure method) set_lattice_vectors() (gnrs.core.structure.Structure method) set_property() (gnrs.core.structure.Structure method) setup_main_folders() (in module gnrs.core.folders) standardize_orientation() (gnrs.core.molecule.Molecule method) steps (gnrs.optimize.bfgs.BFGSOptimizer attribute) (gnrs.optimize.lbfgs.LBFGSOptimizer attribute) StoicDict (class in gnrs.core.structure) str2atoms() (in module gnrs.parallel.io) Structure (class in gnrs.core.structure) StructureGenerationTask (class in gnrs.generation.generation_task) SYMM_RIGID_PRESSOptimizer (class in gnrs.optimize.symm_rigid_press) T TASK_NAME (gnrs.deduplication.deduplication_task.DuplicateRemovalTask attribute) TaskABC (class in gnrs.core.task) tol (gnrs.optimize.symm_rigid_press.SYMM_RIGID_PRESSOptimizer attribute) U UMAEnergy (class in gnrs.energy.uma) unpack_geometry() (gnrs.core.structure.Structure method) update() (gnrs.core.optimizer.GeometryOptimizerABC method) (gnrs.optimize.bfgs.BFGSOptimizer method) (gnrs.optimize.lbfgs.LBFGSOptimizer method) (gnrs.optimize.rigid_press.RIGID_PRESSOptimizer method) (gnrs.optimize.symm_rigid_press.SYMM_RIGID_PRESSOptimizer method) V VASP (class in gnrs.energy.vasp) vol_tol (gnrs.optimize.symm_rigid_press.SYMM_RIGID_PRESSOptimizer attribute) W WINDOWSelection (class in gnrs.cluster.selection.window) worker_ranks (gnrs.core.gpu.GPUDeviceManager property) write_parallel() (in module gnrs.parallel.io)