maml.apps package

Subpackages

• maml.apps.bowsr package

  • Subpackages

    • maml.apps.bowsr.model package

      • EnergyModel

        • EnergyModel.predict_energy()

      • maml.apps.bowsr.model.base module

        • EnergyModel

          • EnergyModel.predict_energy()

      • maml.apps.bowsr.model.cgcnn module

      • maml.apps.bowsr.model.dft module

        • DFT

          • DFT.predict_energy()

      • maml.apps.bowsr.model.megnet module

  • maml.apps.bowsr.acquisition module

    • AcquisitionFunction

      • AcquisitionFunction._ei()

      • AcquisitionFunction._gpucb()

      • AcquisitionFunction._poi()

      • AcquisitionFunction._ucb()

      • AcquisitionFunction.calculate()

    • _trunc()

    • ensure_rng()

    • lhs_sample()

    • predict_mean_std()

    • propose_query_point()

  • maml.apps.bowsr.optimizer module

    • BayesianOptimizer

      • BayesianOptimizer.add_query()

      • BayesianOptimizer.as_dict()

      • BayesianOptimizer.from_dict()

      • BayesianOptimizer.get_derived_structure()

      • BayesianOptimizer.get_formation_energy()

      • BayesianOptimizer.get_optimized_structure_and_energy()

      • BayesianOptimizer.gpr

      • BayesianOptimizer.optimize()

      • BayesianOptimizer.propose()

      • BayesianOptimizer.set_bounds()

      • BayesianOptimizer.set_gpr_params()

      • BayesianOptimizer.set_space_empty()

      • BayesianOptimizer.space

    • atoms_crowded()

    • struct2perturbation()

  • maml.apps.bowsr.perturbation module

    • LatticePerturbation

      • LatticePerturbation.abc

      • LatticePerturbation.fit_lattice

      • LatticePerturbation.lattice

      • LatticePerturbation.sanity_check()

    • WyckoffPerturbation

      • WyckoffPerturbation.fit_site

      • WyckoffPerturbation.get_orbit()

      • WyckoffPerturbation.sanity_check()

      • WyckoffPerturbation.site

      • WyckoffPerturbation.standardize()

    • crystal_system()

    • get_standardized_structure()

    • perturbation_mapping()

  • maml.apps.bowsr.preprocessing module

    • DummyScaler

      • DummyScaler.as_dict()

      • DummyScaler.fit()

      • DummyScaler.from_dict()

      • DummyScaler.inverse_transform()

      • DummyScaler.transform()

    • StandardScaler

      • StandardScaler.as_dict()

      • StandardScaler.fit()

      • StandardScaler.from_dict()

      • StandardScaler.inverse_transform()

      • StandardScaler.transform()

  • maml.apps.bowsr.target_space module

    • TargetSpace

      • TargetSpace.bounds

      • TargetSpace.lhs_sample()

      • TargetSpace.params

      • TargetSpace.probe()

      • TargetSpace.register()

      • TargetSpace.set_bounds()

      • TargetSpace.set_empty()

      • TargetSpace.target

      • TargetSpace.uniform_sample()

    • _hashable()

• maml.apps.gbe package

  • maml.apps.gbe.describer module

    • GBBond

      • GBBond.NNDict

      • GBBond._get_bond_mat()

      • GBBond.as_dict()

      • GBBond.bond_matrix

      • GBBond.from_dict()

      • GBBond.get_breakbond_ratio()

      • GBBond.get_mean_bl_chg()

      • GBBond.max_bl

      • GBBond.min_bl

    • GBDescriber

      • GBDescriber._abc_impl

      • GBDescriber._sklearn_auto_wrap_output_keys

      • GBDescriber.generate_bulk_ref()

      • GBDescriber.transform_one()

    • convert_hcp_direction()

    • convert_hcp_plane()

    • get_elemental_feature()

    • get_structural_feature()

  • maml.apps.gbe.presetfeatures module

    • my_quant

      • my_quant.latex

      • my_quant.name

      • my_quant.unit

  • maml.apps.gbe.utils module

    • load_b0_dict()

    • load_data()

    • load_mean_delta_bl_dict()

    • update_b0_dict()

• maml.apps.pes package

  • DefectFormation

    • DefectFormation._parse()

    • DefectFormation._sanity_check()

    • DefectFormation._setup()

    • DefectFormation.calculate()

    • DefectFormation.get_unit_cell()

  • ElasticConstant

    • ElasticConstant._RESTART_CONFIG

    • ElasticConstant._parse()

    • ElasticConstant._sanity_check()

    • ElasticConstant._setup()

  • EnergyForceStress

    • EnergyForceStress._parse()

    • EnergyForceStress._rotate_force_stress()

    • EnergyForceStress._sanity_check()

    • EnergyForceStress._setup()

    • EnergyForceStress.calculate()

  • GAPotential

    • GAPotential._abc_impl

    • GAPotential._line_up()

    • GAPotential.evaluate()

    • GAPotential.from_config()

    • GAPotential.pair_coeff

    • GAPotential.pair_style

    • GAPotential.read_cfgs()

    • GAPotential.save()

    • GAPotential.train()

    • GAPotential.write_cfgs()

    • GAPotential.write_param()

  • LMPStaticCalculator

    • LMPStaticCalculator._COMMON_CMDS

    • LMPStaticCalculator._parse()

    • LMPStaticCalculator._sanity_check()

    • LMPStaticCalculator._setup()

    • LMPStaticCalculator.allowed_kwargs

    • LMPStaticCalculator.calculate()

    • LMPStaticCalculator.set_lmp_exe()

  • LatticeConstant

    • LatticeConstant.calculate()

  • MTPotential

    • MTPotential._abc_impl

    • MTPotential._line_up()

    • MTPotential.evaluate()

    • MTPotential.from_config()

    • MTPotential.pair_coeff

    • MTPotential.pair_style

    • MTPotential.read_cfgs()

    • MTPotential.train()

    • MTPotential.write_cfg()

    • MTPotential.write_ini()

    • MTPotential.write_param()

  • NNPotential

    • NNPotential._abc_impl

    • NNPotential._line_up()

    • NNPotential.bohr_to_angstrom

    • NNPotential.eV_to_Ha

    • NNPotential.evaluate()

    • NNPotential.from_config()

    • NNPotential.load_input()

    • NNPotential.load_scaler()

    • NNPotential.load_weights()

    • NNPotential.pair_coeff

    • NNPotential.pair_style

    • NNPotential.read_cfgs()

    • NNPotential.train()

    • NNPotential.write_cfgs()

    • NNPotential.write_input()

    • NNPotential.write_param()

  • NudgedElasticBand

    • NudgedElasticBand._parse()

    • NudgedElasticBand._sanity_check()

    • NudgedElasticBand._setup()

    • NudgedElasticBand.calculate()

    • NudgedElasticBand.get_unit_cell()

  • Potential

  • SNAPotential

    • SNAPotential._abc_impl

    • SNAPotential.evaluate()

    • SNAPotential.from_config()

    • SNAPotential.pair_coeff

    • SNAPotential.pair_style

    • SNAPotential.train()

    • SNAPotential.write_param()

  • SpectralNeighborAnalysis

    • SpectralNeighborAnalysis._CMDS

    • SpectralNeighborAnalysis._parse()

    • SpectralNeighborAnalysis._sanity_check()

    • SpectralNeighborAnalysis._setup()

    • SpectralNeighborAnalysis.get_bs_subscripts()

    • SpectralNeighborAnalysis.n_bs

  • get_default_lmp_exe()

  • maml.apps.pes._base module

    • Potential

    • PotentialMixin

      • PotentialMixin.evaluate()

      • PotentialMixin.from_config()

      • PotentialMixin.predict_efs()

      • PotentialMixin.train()

      • PotentialMixin.write_param()

  • maml.apps.pes._gap module

    • GAPotential

      • GAPotential._abc_impl

      • GAPotential._line_up()

      • GAPotential.evaluate()

      • GAPotential.from_config()

      • GAPotential.pair_coeff

      • GAPotential.pair_style

      • GAPotential.read_cfgs()

      • GAPotential.save()

      • GAPotential.train()

      • GAPotential.write_cfgs()

      • GAPotential.write_param()

  • maml.apps.pes._lammps module

    • DefectFormation

      • DefectFormation._parse()

      • DefectFormation._sanity_check()

      • DefectFormation._setup()

      • DefectFormation.calculate()

      • DefectFormation.get_unit_cell()

    • ElasticConstant

      • ElasticConstant._RESTART_CONFIG

      • ElasticConstant._parse()

      • ElasticConstant._sanity_check()

      • ElasticConstant._setup()

    • EnergyForceStress

      • EnergyForceStress._parse()

      • EnergyForceStress._rotate_force_stress()

      • EnergyForceStress._sanity_check()

      • EnergyForceStress._setup()

      • EnergyForceStress.calculate()

    • LMPRelaxationCalculator

      • LMPRelaxationCalculator._parse()

      • LMPRelaxationCalculator._sanity_check()

      • LMPRelaxationCalculator._setup()

    • LMPStaticCalculator

      • LMPStaticCalculator._COMMON_CMDS

      • LMPStaticCalculator._parse()

      • LMPStaticCalculator._sanity_check()

      • LMPStaticCalculator._setup()

      • LMPStaticCalculator.allowed_kwargs

      • LMPStaticCalculator.calculate()

      • LMPStaticCalculator.set_lmp_exe()

    • LammpsPotential

      • LammpsPotential._abc_impl

      • LammpsPotential.predict_efs()

    • LatticeConstant

      • LatticeConstant.calculate()

    • NudgedElasticBand

      • NudgedElasticBand._parse()

      • NudgedElasticBand._sanity_check()

      • NudgedElasticBand._setup()

      • NudgedElasticBand.calculate()

      • NudgedElasticBand.get_unit_cell()

    • SpectralNeighborAnalysis

      • SpectralNeighborAnalysis._CMDS

      • SpectralNeighborAnalysis._parse()

      • SpectralNeighborAnalysis._sanity_check()

      • SpectralNeighborAnalysis._setup()

      • SpectralNeighborAnalysis.get_bs_subscripts()

      • SpectralNeighborAnalysis.n_bs

    • SurfaceEnergy

      • SurfaceEnergy.calculate()

    • _pretty_input()

    • _read_dump()

    • get_default_lmp_exe()

  • maml.apps.pes._mtp module

    • MTPotential

      • MTPotential._abc_impl

      • MTPotential._line_up()

      • MTPotential.evaluate()

      • MTPotential.from_config()

      • MTPotential.pair_coeff

      • MTPotential.pair_style

      • MTPotential.read_cfgs()

      • MTPotential.train()

      • MTPotential.write_cfg()

      • MTPotential.write_ini()

      • MTPotential.write_param()

    • feed()

  • maml.apps.pes._nnp module

    • NNPotential

      • NNPotential._abc_impl

      • NNPotential._line_up()

      • NNPotential.bohr_to_angstrom

      • NNPotential.eV_to_Ha

      • NNPotential.evaluate()

      • NNPotential.from_config()

      • NNPotential.load_input()

      • NNPotential.load_scaler()

      • NNPotential.load_weights()

      • NNPotential.pair_coeff

      • NNPotential.pair_style

      • NNPotential.read_cfgs()

      • NNPotential.train()

      • NNPotential.write_cfgs()

      • NNPotential.write_input()

      • NNPotential.write_param()

  • maml.apps.pes._snap module

    • SNAPotential

      • SNAPotential._abc_impl

      • SNAPotential.evaluate()

      • SNAPotential.from_config()

      • SNAPotential.pair_coeff

      • SNAPotential.pair_style

      • SNAPotential.train()

      • SNAPotential.write_param()

• maml.apps.symbolic package

  • AdaptiveLasso

    • AdaptiveLasso._penalty_jac()

    • AdaptiveLasso.get_w()

    • AdaptiveLasso.penalty()

    • AdaptiveLasso.select()

  • DantzigSelector

    • DantzigSelector.construct_constraints()

    • DantzigSelector.construct_jac()

    • DantzigSelector.construct_loss()

  • FeatureGenerator

    • FeatureGenerator.augment()

  • ISIS

    • ISIS.evaluate()

    • ISIS.run()

  • L0BrutalForce

    • L0BrutalForce.select()

  • Lasso

    • Lasso._penalty_jac()

    • Lasso.penalty()

  • Operator

    • Operator.compute()

    • Operator.from_str()

    • Operator.gen_name()

    • Operator.is_binary

    • Operator.is_commutative

    • Operator.is_unary

    • Operator.support_op_rep

  • SCAD

    • SCAD._penalty_jac()

    • SCAD.penalty()

  • SIS

    • SIS.compute_residual()

    • SIS.run()

    • SIS.screen()

    • SIS.select()

    • SIS.set_gamma()

    • SIS.set_selector()

    • SIS.update_gamma()

  • maml.apps.symbolic._feature_generator module

    • FeatureGenerator

      • FeatureGenerator.augment()

    • Operator

      • Operator.compute()

      • Operator.from_str()

      • Operator.gen_name()

      • Operator.is_binary

      • Operator.is_commutative

      • Operator.is_unary

      • Operator.support_op_rep

    • _my_abs_diff()

    • _my_abs_log10()

    • _my_abs_sqrt()

    • _my_abs_sum()

    • _my_diff()

    • _my_div()

    • _my_exp()

    • _my_exp_power_2()

    • _my_exp_power_3()

    • _my_mul()

    • _my_power()

    • _my_sum()

    • _my_sum_exp()

    • _my_sum_power_2()

    • _my_sum_power_3()

    • _update_df()

    • generate_feature()

  • maml.apps.symbolic._selectors module

    • AdaptiveLasso

      • AdaptiveLasso._penalty_jac()

      • AdaptiveLasso.get_w()

      • AdaptiveLasso.penalty()

      • AdaptiveLasso.select()

    • BaseSelector

      • BaseSelector._get_param_names()

      • BaseSelector.compute_residual()

      • BaseSelector.construct_constraints()

      • BaseSelector.construct_jac()

      • BaseSelector.construct_loss()

      • BaseSelector.evaluate()

      • BaseSelector.get_coef()

      • BaseSelector.get_feature_indices()

      • BaseSelector.get_params()

      • BaseSelector.predict()

      • BaseSelector.select()

      • BaseSelector.set_params()

    • DantzigSelector

      • DantzigSelector.construct_constraints()

      • DantzigSelector.construct_jac()

      • DantzigSelector.construct_loss()

    • L0BrutalForce

      • L0BrutalForce.select()

    • Lasso

      • Lasso._penalty_jac()

      • Lasso.penalty()

    • PenalizedLeastSquares

      • PenalizedLeastSquares._penalty_jac()

      • PenalizedLeastSquares._sse_jac()

      • PenalizedLeastSquares.construct_constraints()

      • PenalizedLeastSquares.construct_jac()

      • PenalizedLeastSquares.construct_loss()

      • PenalizedLeastSquares.penalty()

    • SCAD

      • SCAD._penalty_jac()

      • SCAD.penalty()

  • maml.apps.symbolic._selectors_cvxpy module

    • AdaptiveLassoCP

      • AdaptiveLassoCP.get_w()

      • AdaptiveLassoCP.penalty()

      • AdaptiveLassoCP.select()

    • BaseSelectorCP

      • BaseSelectorCP.construct_constraints()

      • BaseSelectorCP.construct_loss()

      • BaseSelectorCP.select()

    • DantzigSelectorCP

      • DantzigSelectorCP.construct_constraints()

      • DantzigSelectorCP.construct_loss()

    • LassoCP

      • LassoCP.penalty()

    • PenalizedLeastSquaresCP

      • PenalizedLeastSquaresCP.construct_loss()

      • PenalizedLeastSquaresCP.penalty()

  • maml.apps.symbolic._sis module

    • ISIS

      • ISIS.evaluate()

      • ISIS.run()

    • SIS

      • SIS.compute_residual()

      • SIS.run()

      • SIS.screen()

      • SIS.select()

      • SIS.set_gamma()

      • SIS.set_selector()

      • SIS.update_gamma()

    • _best_combination()

    • _eval()

    • _get_coeff()