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()