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()
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