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Mapped Gaussian Process
Construct Atomic Environment
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diff --git a/searchindex.js b/searchindex.js
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@@ -1 +1 @@
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(flare.bffs.gp.gp.gaussianprocess method)": [[7, "flare.bffs.gp.gp.GaussianProcess.predict"]], "predict_efs() (flare.bffs.gp.gp.gaussianprocess method)": [[7, "flare.bffs.gp.gp.GaussianProcess.predict_efs"]], "predict_force_xyz() (flare.bffs.gp.gp.gaussianprocess method)": [[7, "flare.bffs.gp.gp.GaussianProcess.predict_force_xyz"]], "predict_local_energy() (flare.bffs.gp.gp.gaussianprocess method)": [[7, "flare.bffs.gp.gp.GaussianProcess.predict_local_energy"]], "predict_local_energy_and_var() (flare.bffs.gp.gp.gaussianprocess method)": [[7, "flare.bffs.gp.gp.GaussianProcess.predict_local_energy_and_var"]], "random() (in module flare.bffs.gp.gp)": [[7, "flare.bffs.gp.gp.random"]], "remove_force_data() (flare.bffs.gp.gp.gaussianprocess method)": [[7, "flare.bffs.gp.gp.GaussianProcess.remove_force_data"]], "set_l_alpha() (flare.bffs.gp.gp.gaussianprocess method)": [[7, "flare.bffs.gp.gp.GaussianProcess.set_L_alpha"]], "train() (flare.bffs.gp.gp.gaussianprocess method)": [[7, 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"energy_force_vector() (in module flare.bffs.gp.gp_algebra)": [[8, "flare.bffs.gp.gp_algebra.energy_force_vector"]], "energy_force_vector_unit() (in module flare.bffs.gp.gp_algebra)": [[8, "flare.bffs.gp.gp_algebra.energy_force_vector_unit"]], "flare.bffs.gp.gp_algebra": [[8, "module-flare.bffs.gp.gp_algebra"]], "force_energy_vector() (in module flare.bffs.gp.gp_algebra)": [[8, "flare.bffs.gp.gp_algebra.force_energy_vector"]], "force_energy_vector_unit() (in module flare.bffs.gp.gp_algebra)": [[8, "flare.bffs.gp.gp_algebra.force_energy_vector_unit"]], "force_force_vector() (in module flare.bffs.gp.gp_algebra)": [[8, "flare.bffs.gp.gp_algebra.force_force_vector"]], "force_force_vector_unit() (in module flare.bffs.gp.gp_algebra)": [[8, "flare.bffs.gp.gp_algebra.force_force_vector_unit"]], "get_distance_mat_pack() (in module flare.bffs.gp.gp_algebra)": [[8, "flare.bffs.gp.gp_algebra.get_distance_mat_pack"]], "get_force_block() (in module flare.bffs.gp.gp_algebra)": [[8, "flare.bffs.gp.gp_algebra.get_force_block"]], "get_force_block_pack() (in module flare.bffs.gp.gp_algebra)": [[8, "flare.bffs.gp.gp_algebra.get_force_block_pack"]], "get_ky_and_hyp() (in module flare.bffs.gp.gp_algebra)": [[8, "flare.bffs.gp.gp_algebra.get_ky_and_hyp"]], "get_ky_and_hyp_pack() (in module flare.bffs.gp.gp_algebra)": [[8, "flare.bffs.gp.gp_algebra.get_ky_and_hyp_pack"]], "get_like_from_mats() (in module flare.bffs.gp.gp_algebra)": [[8, "flare.bffs.gp.gp_algebra.get_like_from_mats"]], "get_like_grad_from_mats() (in module flare.bffs.gp.gp_algebra)": [[8, "flare.bffs.gp.gp_algebra.get_like_grad_from_mats"]], "get_neg_like() (in module flare.bffs.gp.gp_algebra)": [[8, "flare.bffs.gp.gp_algebra.get_neg_like"]], "get_neg_like_grad() (in module flare.bffs.gp.gp_algebra)": [[8, "flare.bffs.gp.gp_algebra.get_neg_like_grad"]], "kernel_distance_mat() (in module flare.bffs.gp.gp_algebra)": [[8, "flare.bffs.gp.gp_algebra.kernel_distance_mat"]], "obtain_noise_len() (in module flare.bffs.gp.gp_algebra)": [[8, "flare.bffs.gp.gp_algebra.obtain_noise_len"]], "partition_force_energy_block() (in module flare.bffs.gp.gp_algebra)": [[8, "flare.bffs.gp.gp_algebra.partition_force_energy_block"]], "partition_matrix() (in module flare.bffs.gp.gp_algebra)": [[8, "flare.bffs.gp.gp_algebra.partition_matrix"]], "partition_matrix_custom() (in module flare.bffs.gp.gp_algebra)": [[8, "flare.bffs.gp.gp_algebra.partition_matrix_custom"]], "partition_vector() (in module flare.bffs.gp.gp_algebra)": [[8, "flare.bffs.gp.gp_algebra.partition_vector"]], "queue_wrapper() (in module flare.bffs.gp.gp_algebra)": [[8, "flare.bffs.gp.gp_algebra.queue_wrapper"]], "flare.bffs.gp.predict": [[9, "module-flare.bffs.gp.predict"]], "predict_on_atom() (in module flare.bffs.gp.predict)": [[9, "flare.bffs.gp.predict.predict_on_atom"]], "predict_on_atom_efs() (in module flare.bffs.gp.predict)": [[9, "flare.bffs.gp.predict.predict_on_atom_efs"]], "predict_on_atom_en() (in module flare.bffs.gp.predict)": [[9, "flare.bffs.gp.predict.predict_on_atom_en"]], "predict_on_atom_en_std() (in module flare.bffs.gp.predict)": [[9, "flare.bffs.gp.predict.predict_on_atom_en_std"]], "predict_on_structure() (in module flare.bffs.gp.predict)": [[9, "flare.bffs.gp.predict.predict_on_structure"]], "predict_on_structure_en() (in module flare.bffs.gp.predict)": [[9, "flare.bffs.gp.predict.predict_on_structure_en"]], "predict_on_structure_mgp() (in module flare.bffs.gp.predict)": [[9, "flare.bffs.gp.predict.predict_on_structure_mgp"]], "predict_on_structure_par() (in module flare.bffs.gp.predict)": [[9, "flare.bffs.gp.predict.predict_on_structure_par"]], "predict_on_structure_par_en() (in module flare.bffs.gp.predict)": [[9, "flare.bffs.gp.predict.predict_on_structure_par_en"]], "mappedgaussianprocess (class in flare.bffs.mgp.mgp)": [[11, "flare.bffs.mgp.mgp.MappedGaussianProcess"]], "as_dict() (flare.bffs.mgp.mgp.mappedgaussianprocess method)": [[11, "flare.bffs.mgp.mgp.MappedGaussianProcess.as_dict"]], "flare.bffs.mgp.mgp": [[11, "module-flare.bffs.mgp.mgp"]], "from_dict() (flare.bffs.mgp.mgp.mappedgaussianprocess static method)": [[11, "flare.bffs.mgp.mgp.MappedGaussianProcess.from_dict"]], "predict() (flare.bffs.mgp.mgp.mappedgaussianprocess method)": [[11, "flare.bffs.mgp.mgp.MappedGaussianProcess.predict"]], "write_lmp_file() (flare.bffs.mgp.mgp.mappedgaussianprocess method)": [[11, "flare.bffs.mgp.mgp.MappedGaussianProcess.write_lmp_file"]], "write_model() (flare.bffs.mgp.mgp.mappedgaussianprocess method)": [[11, "flare.bffs.mgp.mgp.MappedGaussianProcess.write_model"]], "cubicspline (class in flare.bffs.mgp.splines_methods)": [[12, "flare.bffs.mgp.splines_methods.CubicSpline"]], "pcasplines (class in flare.bffs.mgp.splines_methods)": [[12, "flare.bffs.mgp.splines_methods.PCASplines"]], "flare.bffs.mgp.splines_methods": [[12, "module-flare.bffs.mgp.splines_methods"]], "grid (flare.bffs.mgp.splines_methods.cubicspline property)": [[12, "flare.bffs.mgp.splines_methods.CubicSpline.grid"]], "interpolate() (flare.bffs.mgp.splines_methods.cubicspline method)": [[12, "flare.bffs.mgp.splines_methods.CubicSpline.interpolate"]], "set_values() (flare.bffs.mgp.splines_methods.cubicspline method)": [[12, "flare.bffs.mgp.splines_methods.CubicSpline.set_values"]], "vec_eval_cubic_spline() (in module flare.bffs.mgp.splines_methods)": [[12, "flare.bffs.mgp.splines_methods.vec_eval_cubic_spline"]], "sgp_calculator (class in flare.bffs.sgp.calculator)": [[13, "flare.bffs.sgp.calculator.SGP_Calculator"]], "calculate() (flare.bffs.sgp.calculator.sgp_calculator method)": [[13, "flare.bffs.sgp.calculator.SGP_Calculator.calculate"]], "flare.bffs.sgp.calculator": [[13, "module-flare.bffs.sgp.calculator"]], "implemented_properties (flare.bffs.sgp.calculator.sgp_calculator attribute)": [[13, "flare.bffs.sgp.calculator.SGP_Calculator.implemented_properties"]], "sgp_wrapper (class in flare.bffs.sgp.sparse_gp)": [[14, "flare.bffs.sgp.sparse_gp.SGP_Wrapper"]], "compute_negative_likelihood() (in module flare.bffs.sgp.sparse_gp)": [[14, "flare.bffs.sgp.sparse_gp.compute_negative_likelihood"]], "compute_negative_likelihood_grad() (in module flare.bffs.sgp.sparse_gp)": [[14, "flare.bffs.sgp.sparse_gp.compute_negative_likelihood_grad"]], "compute_negative_likelihood_grad_stable() (in module flare.bffs.sgp.sparse_gp)": [[14, "flare.bffs.sgp.sparse_gp.compute_negative_likelihood_grad_stable"]], "flare.bffs.sgp.sparse_gp": [[14, "module-flare.bffs.sgp.sparse_gp"]], "from_dict() (flare.bffs.sgp.sparse_gp.sgp_wrapper static method)": [[14, "flare.bffs.sgp.sparse_gp.SGP_Wrapper.from_dict"]], "optimize_hyperparameters() (in module flare.bffs.sgp.sparse_gp)": [[14, "flare.bffs.sgp.sparse_gp.optimize_hyperparameters"]], "write_model() (flare.bffs.sgp.sparse_gp.sgp_wrapper method)": [[14, "flare.bffs.sgp.sparse_gp.SGP_Wrapper.write_model"]], "atomicenvironment (class in flare.descriptors.env)": [[16, "flare.descriptors.env.AtomicEnvironment"]], "as_dict() (flare.descriptors.env.atomicenvironment method)": [[16, "flare.descriptors.env.AtomicEnvironment.as_dict"]], "as_str() (flare.descriptors.env.atomicenvironment method)": [[16, "flare.descriptors.env.AtomicEnvironment.as_str"]], "flare.descriptors.env": [[16, "module-flare.descriptors.env"]], "from_dict() (flare.descriptors.env.atomicenvironment static method)": [[16, "flare.descriptors.env.AtomicEnvironment.from_dict"]], "from_file() (flare.descriptors.env.atomicenvironment static method)": [[16, "flare.descriptors.env.AtomicEnvironment.from_file"]], "otfanalysis (class in flare.io.otf_parser)": [[19, "flare.io.otf_parser.OtfAnalysis"]], "append_atom_lists() (in module flare.io.otf_parser)": [[19, "flare.io.otf_parser.append_atom_lists"]], "extract_gp_info() (in module flare.io.otf_parser)": [[19, "flare.io.otf_parser.extract_gp_info"]], "flare.io.otf_parser": [[19, "module-flare.io.otf_parser"]], "make_gp() (flare.io.otf_parser.otfanalysis method)": [[19, "flare.io.otf_parser.OtfAnalysis.make_gp"]], "output_md_structures() (flare.io.otf_parser.otfanalysis method)": [[19, "flare.io.otf_parser.OtfAnalysis.output_md_structures"]], "parse_frame_line() (in module flare.io.otf_parser)": [[19, "flare.io.otf_parser.parse_frame_line"]], "parse_header_information() (in module flare.io.otf_parser)": [[19, "flare.io.otf_parser.parse_header_information"]], "parse_pos_otf() (flare.io.otf_parser.otfanalysis method)": [[19, "flare.io.otf_parser.OtfAnalysis.parse_pos_otf"]], "parse_snapshot() (in module flare.io.otf_parser)": [[19, "flare.io.otf_parser.parse_snapshot"]], "strip_and_split() (in module flare.io.otf_parser)": [[19, "flare.io.otf_parser.strip_and_split"]], "to_xyz() (flare.io.otf_parser.otfanalysis method)": [[19, "flare.io.otf_parser.OtfAnalysis.to_xyz"]], "output (class in flare.io.output)": [[20, "flare.io.output.Output"]], "add_file() (in module flare.io.output)": [[20, "flare.io.output.add_file"]], "add_stream() (in module flare.io.output)": [[20, "flare.io.output.add_stream"]], "conclude_run() (flare.io.output.output method)": [[20, "flare.io.output.Output.conclude_run"]], "flare.io.output": [[20, "module-flare.io.output"]], "open_new_log() (flare.io.output.output method)": [[20, "flare.io.output.Output.open_new_log"]], "set_logger() (in module flare.io.output)": [[20, "flare.io.output.set_logger"]], "write_gp_dft_comparison() (flare.io.output.output method)": [[20, "flare.io.output.Output.write_gp_dft_comparison"]], "write_header() (flare.io.output.output method)": [[20, "flare.io.output.Output.write_header"]], "write_hyps() (flare.io.output.output method)": [[20, "flare.io.output.Output.write_hyps"]], "write_md_config() (flare.io.output.output method)": [[20, "flare.io.output.Output.write_md_config"]], "write_to_log() (flare.io.output.output method)": [[20, "flare.io.output.Output.write_to_log"]], "write_xyz_config() (flare.io.output.output method)": [[20, "flare.io.output.Output.write_xyz_config"]], "cosine_cutoff() (in module flare.kernels.cutoffs)": [[21, "flare.kernels.cutoffs.cosine_cutoff"]], "cubic_cutoff() (in module flare.kernels.cutoffs)": [[21, "flare.kernels.cutoffs.cubic_cutoff"]], "flare.kernels.cutoffs": [[21, "module-flare.kernels.cutoffs"]], "hard_cutoff() (in module flare.kernels.cutoffs)": [[21, "flare.kernels.cutoffs.hard_cutoff"]], "quadratic_cutoff() (in module flare.kernels.cutoffs)": [[21, "flare.kernels.cutoffs.quadratic_cutoff"]], "quadratic_cutoff_bound() (in module flare.kernels.cutoffs)": [[21, "flare.kernels.cutoffs.quadratic_cutoff_bound"]], "coordination_number() (in module flare.kernels.kernels)": [[22, "flare.kernels.kernels.coordination_number"]], "flare.kernels.kernels": [[22, "module-flare.kernels.kernels"]], "force_helper() (in module flare.kernels.kernels)": [[22, "flare.kernels.kernels.force_helper"]], "k_sq_exp_dev() (in module flare.kernels.kernels)": [[22, "flare.kernels.kernels.k_sq_exp_dev"]], "k_sq_exp_double_dev() (in module flare.kernels.kernels)": [[22, "flare.kernels.kernels.k_sq_exp_double_dev"]], "mb_grad_helper_ls() (in module flare.kernels.kernels)": [[22, "flare.kernels.kernels.mb_grad_helper_ls"]], "mb_grad_helper_ls_() (in module flare.kernels.kernels)": [[22, "flare.kernels.kernels.mb_grad_helper_ls_"]], "q_value() (in module flare.kernels.kernels)": [[22, "flare.kernels.kernels.q_value"]], "q_value_mc() (in module flare.kernels.kernels)": [[22, "flare.kernels.kernels.q_value_mc"]], "flare.kernels.mc_3b_sepcut": [[24, "module-flare.kernels.mc_3b_sepcut"]], "flare.kernels.mc_mb_sepcut": [[24, "module-flare.kernels.mc_mb_sepcut"]], "flare.kernels.mc_sephyps": [[24, "module-flare.kernels.mc_sephyps"]], "many_body_mc() (in module flare.kernels.mc_sephyps)": [[24, "flare.kernels.mc_sephyps.many_body_mc"]], "many_body_mc_en() (in module flare.kernels.mc_sephyps)": [[24, "flare.kernels.mc_sephyps.many_body_mc_en"]], "many_body_mc_en_sepcut_jit() (in module flare.kernels.mc_mb_sepcut)": [[24, "flare.kernels.mc_mb_sepcut.many_body_mc_en_sepcut_jit"]], "many_body_mc_force_en() (in module flare.kernels.mc_sephyps)": [[24, "flare.kernels.mc_sephyps.many_body_mc_force_en"]], "many_body_mc_force_en_sepcut_jit() (in module flare.kernels.mc_mb_sepcut)": [[24, "flare.kernels.mc_mb_sepcut.many_body_mc_force_en_sepcut_jit"]], "many_body_mc_grad() (in module flare.kernels.mc_sephyps)": [[24, "flare.kernels.mc_sephyps.many_body_mc_grad"]], "many_body_mc_grad_sepcut_jit() (in module flare.kernels.mc_mb_sepcut)": [[24, "flare.kernels.mc_mb_sepcut.many_body_mc_grad_sepcut_jit"]], "many_body_mc_sepcut_jit() (in module flare.kernels.mc_mb_sepcut)": [[24, "flare.kernels.mc_mb_sepcut.many_body_mc_sepcut_jit"]], "three_body_mc() (in module flare.kernels.mc_sephyps)": [[24, "flare.kernels.mc_sephyps.three_body_mc"]], "three_body_mc_en() (in module flare.kernels.mc_sephyps)": [[24, "flare.kernels.mc_sephyps.three_body_mc_en"]], "three_body_mc_force_en() (in module flare.kernels.mc_sephyps)": [[24, "flare.kernels.mc_sephyps.three_body_mc_force_en"]], "three_body_mc_force_en_jit() (in module flare.kernels.mc_sephyps)": [[24, "flare.kernels.mc_sephyps.three_body_mc_force_en_jit"]], "three_body_mc_force_en_sepcut_jit() (in module flare.kernels.mc_3b_sepcut)": [[24, "flare.kernels.mc_3b_sepcut.three_body_mc_force_en_sepcut_jit"]], "three_body_mc_grad() (in module flare.kernels.mc_sephyps)": [[24, "flare.kernels.mc_sephyps.three_body_mc_grad"]], "three_body_mc_grad_jit() (in module flare.kernels.mc_sephyps)": [[24, "flare.kernels.mc_sephyps.three_body_mc_grad_jit"]], "three_body_mc_grad_sepcut_jit() (in module flare.kernels.mc_3b_sepcut)": [[24, "flare.kernels.mc_3b_sepcut.three_body_mc_grad_sepcut_jit"]], "two_body_mc() (in module flare.kernels.mc_sephyps)": [[24, "flare.kernels.mc_sephyps.two_body_mc"]], "two_body_mc_en() (in module flare.kernels.mc_sephyps)": [[24, "flare.kernels.mc_sephyps.two_body_mc_en"]], "two_body_mc_en_jit() (in module flare.kernels.mc_sephyps)": [[24, "flare.kernels.mc_sephyps.two_body_mc_en_jit"]], "two_body_mc_force_en() (in module flare.kernels.mc_sephyps)": [[24, "flare.kernels.mc_sephyps.two_body_mc_force_en"]], "two_body_mc_force_en_jit() (in module flare.kernels.mc_sephyps)": [[24, "flare.kernels.mc_sephyps.two_body_mc_force_en_jit"]], "two_body_mc_grad() (in module flare.kernels.mc_sephyps)": [[24, "flare.kernels.mc_sephyps.two_body_mc_grad"]], "two_body_mc_grad_jit() (in module flare.kernels.mc_sephyps)": [[24, "flare.kernels.mc_sephyps.two_body_mc_grad_jit"]], "two_body_mc_jit() (in module flare.kernels.mc_sephyps)": [[24, "flare.kernels.mc_sephyps.two_body_mc_jit"]], "two_plus_three_body_mc() (in module flare.kernels.mc_sephyps)": [[24, "flare.kernels.mc_sephyps.two_plus_three_body_mc"]], "two_plus_three_body_mc_grad() (in module flare.kernels.mc_sephyps)": [[24, "flare.kernels.mc_sephyps.two_plus_three_body_mc_grad"]], "two_plus_three_mc_en() (in module flare.kernels.mc_sephyps)": [[24, "flare.kernels.mc_sephyps.two_plus_three_mc_en"]], "two_plus_three_mc_force_en() (in module flare.kernels.mc_sephyps)": [[24, "flare.kernels.mc_sephyps.two_plus_three_mc_force_en"]], "two_three_many_body_mc() (in module flare.kernels.mc_sephyps)": [[24, "flare.kernels.mc_sephyps.two_three_many_body_mc"]], "two_three_many_body_mc_grad() (in module flare.kernels.mc_sephyps)": [[24, "flare.kernels.mc_sephyps.two_three_many_body_mc_grad"]], "two_three_many_mc_en() (in module flare.kernels.mc_sephyps)": [[24, "flare.kernels.mc_sephyps.two_three_many_mc_en"]], "two_three_many_mc_force_en() (in module flare.kernels.mc_sephyps)": [[24, "flare.kernels.mc_sephyps.two_three_many_mc_force_en"]], "flare.kernels.mc_simple": [[25, "module-flare.kernels.mc_simple"]], "many_body_mc() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.many_body_mc"]], "many_body_mc_en() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.many_body_mc_en"]], "many_body_mc_en_jit() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.many_body_mc_en_jit"]], "many_body_mc_force_en() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.many_body_mc_force_en"]], "many_body_mc_force_en_jit() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.many_body_mc_force_en_jit"]], "many_body_mc_grad() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.many_body_mc_grad"]], "many_body_mc_grad_jit() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.many_body_mc_grad_jit"]], "many_body_mc_jit() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.many_body_mc_jit"]], "three_body_mc() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.three_body_mc"]], "three_body_mc_en() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.three_body_mc_en"]], "three_body_mc_en_jit() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.three_body_mc_en_jit"]], "three_body_mc_force_en() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.three_body_mc_force_en"]], "three_body_mc_force_en_jit() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.three_body_mc_force_en_jit"]], "three_body_mc_grad() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.three_body_mc_grad"]], "three_body_mc_grad_jit() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.three_body_mc_grad_jit"]], "three_body_mc_jit() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.three_body_mc_jit"]], "three_body_se_jit() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.three_body_se_jit"]], "three_body_sf_jit() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.three_body_sf_jit"]], "three_body_ss_jit() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.three_body_ss_jit"]], "two_body_mc() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.two_body_mc"]], "two_body_mc_en() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.two_body_mc_en"]], "two_body_mc_en_jit() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.two_body_mc_en_jit"]], "two_body_mc_force_en() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.two_body_mc_force_en"]], "two_body_mc_force_en_jit() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.two_body_mc_force_en_jit"]], "two_body_mc_grad() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.two_body_mc_grad"]], "two_body_mc_grad_jit() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.two_body_mc_grad_jit"]], "two_body_mc_jit() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.two_body_mc_jit"]], "two_body_mc_stress_en_jit() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.two_body_mc_stress_en_jit"]], "two_body_mc_stress_force_jit() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.two_body_mc_stress_force_jit"]], "two_body_mc_stress_stress_jit() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.two_body_mc_stress_stress_jit"]], "two_plus_many_body_mc() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.two_plus_many_body_mc"]], "two_plus_many_body_mc_en() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.two_plus_many_body_mc_en"]], "two_plus_many_body_mc_force_en() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.two_plus_many_body_mc_force_en"]], "two_plus_many_body_mc_grad() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.two_plus_many_body_mc_grad"]], "two_plus_three_body_mc() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.two_plus_three_body_mc"]], "two_plus_three_body_mc_grad() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.two_plus_three_body_mc_grad"]], "two_plus_three_mc_en() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.two_plus_three_mc_en"]], "two_plus_three_mc_force_en() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.two_plus_three_mc_force_en"]], "two_plus_three_plus_many_body_mc() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.two_plus_three_plus_many_body_mc"]], "two_plus_three_plus_many_body_mc_en() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.two_plus_three_plus_many_body_mc_en"]], "two_plus_three_plus_many_body_mc_force_en() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.two_plus_three_plus_many_body_mc_force_en"]], "two_plus_three_plus_many_body_mc_grad() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.two_plus_three_plus_many_body_mc_grad"]], "flare.kernels.sc": [[26, "module-flare.kernels.sc"]], "many_body() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.many_body"]], "many_body_en() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.many_body_en"]], "many_body_en_jit() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.many_body_en_jit"]], "many_body_force_en() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.many_body_force_en"]], "many_body_force_en_jit() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.many_body_force_en_jit"]], "many_body_grad() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.many_body_grad"]], "many_body_grad_jit() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.many_body_grad_jit"]], "many_body_jit() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.many_body_jit"]], "three_body() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.three_body"]], "three_body_en() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.three_body_en"]], "three_body_en_jit() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.three_body_en_jit"]], "three_body_force_en() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.three_body_force_en"]], "three_body_force_en_jit() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.three_body_force_en_jit"]], "three_body_grad() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.three_body_grad"]], "three_body_grad_jit() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.three_body_grad_jit"]], "three_body_jit() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.three_body_jit"]], "two_body() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.two_body"]], "two_body_en() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.two_body_en"]], "two_body_en_jit() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.two_body_en_jit"]], "two_body_force_en() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.two_body_force_en"]], "two_body_force_en_jit() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.two_body_force_en_jit"]], "two_body_grad() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.two_body_grad"]], "two_body_grad_jit() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.two_body_grad_jit"]], "two_body_jit() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.two_body_jit"]], "two_plus_many_body() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.two_plus_many_body"]], "two_plus_many_body_en() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.two_plus_many_body_en"]], "two_plus_many_body_force_en() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.two_plus_many_body_force_en"]], "two_plus_many_body_grad() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.two_plus_many_body_grad"]], "two_plus_three_body() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.two_plus_three_body"]], "two_plus_three_body_grad() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.two_plus_three_body_grad"]], "two_plus_three_en() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.two_plus_three_en"]], "two_plus_three_force_en() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.two_plus_three_force_en"]], "two_plus_three_plus_many_body() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.two_plus_three_plus_many_body"]], "two_plus_three_plus_many_body_en() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.two_plus_three_plus_many_body_en"]], "two_plus_three_plus_many_body_force_en() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.two_plus_three_plus_many_body_force_en"]], "two_plus_three_plus_many_body_grad() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.two_plus_three_plus_many_body_grad"]], "flare.learners.gp_from_aimd": [[27, "module-flare.learners.gp_from_aimd"]], "parse_trajectory_trainer_output() (in module flare.learners.gp_from_aimd)": [[27, "flare.learners.gp_from_aimd.parse_trajectory_trainer_output"]], "structures_from_gpfa_output() (in module flare.learners.gp_from_aimd)": [[27, "flare.learners.gp_from_aimd.structures_from_gpfa_output"]], "lmpotf (class in flare.learners.lmpotf)": [[29, "flare.learners.lmpotf.LMPOTF"]], "flare.learners.lmpotf": [[29, "module-flare.learners.lmpotf"]], "step() (flare.learners.lmpotf.lmpotf method)": [[29, "flare.learners.lmpotf.LMPOTF.step"]], "otf (class in flare.learners.otf)": [[30, "flare.learners.otf.OTF"]], "compute_properties() (flare.learners.otf.otf method)": [[30, "flare.learners.otf.OTF.compute_properties"]], "flare.learners.otf": [[30, "module-flare.learners.otf"]], "md_step() (flare.learners.otf.otf method)": [[30, "flare.learners.otf.OTF.md_step"]], "rescale_temperature() (flare.learners.otf.otf method)": [[30, "flare.learners.otf.OTF.rescale_temperature"]], "run() (flare.learners.otf.otf method)": [[30, "flare.learners.otf.OTF.run"]], "run_dft() (flare.learners.otf.otf method)": [[30, "flare.learners.otf.OTF.run_dft"]], "train_gp() (flare.learners.otf.otf method)": [[30, "flare.learners.otf.OTF.train_gp"]], "update_gp() (flare.learners.otf.otf method)": [[30, "flare.learners.otf.OTF.update_gp"]], "update_temperature() (flare.learners.otf.otf method)": [[30, "flare.learners.otf.OTF.update_temperature"]], "flare.learners.utils": [[31, "module-flare.learners.utils"]], "get_max_cutoff() (in module flare.learners.utils)": [[31, "flare.learners.utils.get_max_cutoff"]], "is_force_in_bound_per_species() (in module flare.learners.utils)": [[31, "flare.learners.utils.is_force_in_bound_per_species"]], "is_std_in_bound() (in module flare.learners.utils)": [[31, "flare.learners.utils.is_std_in_bound"]], "is_std_in_bound_per_species() (in module flare.learners.utils)": [[31, "flare.learners.utils.is_std_in_bound_per_species"]], "subset_of_frame_by_element() (in module flare.learners.utils)": [[31, "flare.learners.utils.subset_of_frame_by_element"]], "fakedft (class in flare.md.fake)": [[32, "flare.md.fake.FakeDFT"]], "fakemd (class in flare.md.fake)": [[32, "flare.md.fake.FakeMD"]], "calculate() (flare.md.fake.fakedft method)": [[32, "flare.md.fake.FakeDFT.calculate"]], "flare.md.fake": [[32, "module-flare.md.fake"]], "implemented_properties (flare.md.fake.fakedft attribute)": [[32, "flare.md.fake.FakeDFT.implemented_properties"]], "lammps_md (class in flare.md.lammps)": [[33, "flare.md.lammps.LAMMPS_MD"]], "lammps_mod (class in flare.md.lammps)": [[33, "flare.md.lammps.LAMMPS_MOD"]], "backup() (flare.md.lammps.lammps_md method)": [[33, "flare.md.lammps.LAMMPS_MD.backup"]], "calculate() (flare.md.lammps.lammps_mod method)": [[33, "flare.md.lammps.LAMMPS_MOD.calculate"]], "check_sgp_match() (in module flare.md.lammps)": [[33, "flare.md.lammps.check_sgp_match"]], "flare.md.lammps": [[33, "module-flare.md.lammps"]], "get_kinetic_stress() (in module flare.md.lammps)": [[33, "flare.md.lammps.get_kinetic_stress"]], "step() (flare.md.lammps.lammps_md method)": [[33, "flare.md.lammps.LAMMPS_MD.step"]], "nosehoover (class in flare.md.nosehoover)": [[35, "flare.md.nosehoover.NoseHoover"]], "flare.md.nosehoover": [[35, "module-flare.md.nosehoover"]], "step() (flare.md.nosehoover.nosehoover method)": [[35, "flare.md.nosehoover.NoseHoover.step"]], "flare.utils.env_getarray": [[36, "module-flare.utils.env_getarray"]], "get_2_body_arrays() (in module flare.utils.env_getarray)": [[36, "flare.utils.env_getarray.get_2_body_arrays"]], "get_3_body_arrays() (in module flare.utils.env_getarray)": [[36, "flare.utils.env_getarray.get_3_body_arrays"]], "get_m2_body_arrays() (in module flare.utils.env_getarray)": [[36, "flare.utils.env_getarray.get_m2_body_arrays"]], "get_m3_body_arrays() (in module flare.utils.env_getarray)": [[36, "flare.utils.env_getarray.get_m3_body_arrays"]], "q3_value_mc() (in module flare.utils.env_getarray)": [[36, "flare.utils.env_getarray.q3_value_mc"]], "parameterhelper (class in flare.utils.parameter_helper)": [[37, "flare.utils.parameter_helper.ParameterHelper"]], "all_separate_groups() (flare.utils.parameter_helper.parameterhelper method)": [[37, "flare.utils.parameter_helper.ParameterHelper.all_separate_groups"]], "as_dict() (flare.utils.parameter_helper.parameterhelper method)": [[37, "flare.utils.parameter_helper.ParameterHelper.as_dict"]], "define_group() (flare.utils.parameter_helper.parameterhelper method)": [[37, "flare.utils.parameter_helper.ParameterHelper.define_group"]], "fill_in_parameters() (flare.utils.parameter_helper.parameterhelper method)": [[37, "flare.utils.parameter_helper.ParameterHelper.fill_in_parameters"]], "find_group() (flare.utils.parameter_helper.parameterhelper method)": [[37, "flare.utils.parameter_helper.ParameterHelper.find_group"]], "flare.utils.parameter_helper": [[37, "module-flare.utils.parameter_helper"]], "flare.utils.parameters": [[37, "module-flare.utils.parameters"]], "from_dict() (flare.utils.parameter_helper.parameterhelper static method)": [[37, "flare.utils.parameter_helper.ParameterHelper.from_dict"]], "list_groups() (flare.utils.parameter_helper.parameterhelper method)": [[37, "flare.utils.parameter_helper.ParameterHelper.list_groups"]], "list_parameters() (flare.utils.parameter_helper.parameterhelper method)": [[37, "flare.utils.parameter_helper.ParameterHelper.list_parameters"]], "nprandom() (in module flare.utils.parameter_helper)": [[37, "flare.utils.parameter_helper.nprandom"]], "random() (in module flare.utils.parameters)": [[37, "flare.utils.parameters.random"]], "set_constraints() (flare.utils.parameter_helper.parameterhelper method)": [[37, "flare.utils.parameter_helper.ParameterHelper.set_constraints"]], "set_parameters() (flare.utils.parameter_helper.parameterhelper method)": [[37, "flare.utils.parameter_helper.ParameterHelper.set_parameters"]], "summarize_group() (flare.utils.parameter_helper.parameterhelper method)": [[37, "flare.utils.parameter_helper.ParameterHelper.summarize_group"]], "numpyencoder (class in flare.utils)": [[38, "flare.utils.NumpyEncoder"]], "flare.utils": [[38, "module-flare.utils"]], "sparsegp (c++ class)": [[39, "_CPPv48SparseGP"]], "sparsegp::knk_e (c++ member)": [[39, "_CPPv4N8SparseGP5KnK_eE"]], "sparsegp::knk_f (c++ member)": [[39, "_CPPv4N8SparseGP5KnK_fE"]], "sparsegp::knk_s (c++ member)": [[39, "_CPPv4N8SparseGP5KnK_sE"]], "sparsegp::kuf (c++ member)": [[39, "_CPPv4N8SparseGP3KufE"]], "sparsegp::kuf_e_noise_kfu (c++ member)": [[39, "_CPPv4N8SparseGP15Kuf_e_noise_KfuE"]], "sparsegp::kuf_f_noise_kfu (c++ member)": [[39, "_CPPv4N8SparseGP15Kuf_f_noise_KfuE"]], "sparsegp::kuf_kernels (c++ member)": [[39, "_CPPv4N8SparseGP11Kuf_kernelsE"]], "sparsegp::kuf_s_noise_kfu (c++ member)": [[39, "_CPPv4N8SparseGP15Kuf_s_noise_KfuE"]], "sparsegp::kuu (c++ member)": [[39, "_CPPv4N8SparseGP3KuuE"]], "sparsegp::kuu_inverse (c++ member)": [[39, "_CPPv4N8SparseGP11Kuu_inverseE"]], "sparsegp::kuu_jitter (c++ member)": [[39, "_CPPv4N8SparseGP10Kuu_jitterE"]], "sparsegp::kuu_kernels (c++ member)": [[39, "_CPPv4N8SparseGP11Kuu_kernelsE"]], "sparsegp::l_diag (c++ member)": [[39, "_CPPv4N8SparseGP6L_diagE"]], "sparsegp::l_inv (c++ member)": [[39, "_CPPv4N8SparseGP5L_invE"]], "sparsegp::r_inv (c++ member)": [[39, "_CPPv4N8SparseGP5R_invE"]], "sparsegp::r_inv_diag (c++ member)": [[39, "_CPPv4N8SparseGP10R_inv_diagE"]], "sparsegp::sigma (c++ member)": [[39, "_CPPv4N8SparseGP5SigmaE"]], "sparsegp::sparsegp (c++ function)": [[39, "_CPPv4N8SparseGP8SparseGPENSt6vectorIP6KernelEEddd"], [39, "_CPPv4N8SparseGP8SparseGPEv"]], "sparsegp::add_all_environments (c++ function)": [[39, "_CPPv4N8SparseGP20add_all_environmentsERK9Structure"]], "sparsegp::add_random_environments (c++ function)": [[39, "_CPPv4N8SparseGP23add_random_environmentsERK9StructureRKNSt6vectorIiEE"]], "sparsegp::add_specific_environments (c++ function)": [[39, "_CPPv4N8SparseGP25add_specific_environmentsERK9StructureKNSt6vectorIiEE"]], "sparsegp::add_training_structure (c++ function)": [[39, "_CPPv4N8SparseGP22add_training_structureERK9StructureKNSt6vectorIiEEddd"]], "sparsegp::add_uncertain_environments (c++ function)": [[39, "_CPPv4N8SparseGP26add_uncertain_environmentsERK9StructureRKNSt6vectorIiEE"]], "sparsegp::alpha (c++ member)": [[39, "_CPPv4N8SparseGP5alphaE"]], "sparsegp::complexity_penalty (c++ member)": [[39, "_CPPv4N8SparseGP18complexity_penaltyE"]], "sparsegp::compute_knk (c++ function)": [[39, "_CPPv4N8SparseGP11compute_KnKEb"]], "sparsegp::compute_cluster_uncertainties (c++ function)": [[39, "_CPPv4N8SparseGP29compute_cluster_uncertaintiesERK9Structure"]], "sparsegp::compute_dknk (c++ function)": [[39, "_CPPv4N8SparseGP12compute_dKnKEi"]], "sparsegp::compute_likelihood (c++ function)": [[39, "_CPPv4N8SparseGP18compute_likelihoodEv"]], "sparsegp::compute_likelihood_gradient (c++ function)": [[39, 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"energy_force_vector_unit() (in module flare.bffs.gp.gp_algebra)": [[8, "flare.bffs.gp.gp_algebra.energy_force_vector_unit"]], "flare.bffs.gp.gp_algebra": [[8, "module-flare.bffs.gp.gp_algebra"]], "force_energy_vector() (in module flare.bffs.gp.gp_algebra)": [[8, "flare.bffs.gp.gp_algebra.force_energy_vector"]], "force_energy_vector_unit() (in module flare.bffs.gp.gp_algebra)": [[8, "flare.bffs.gp.gp_algebra.force_energy_vector_unit"]], "force_force_vector() (in module flare.bffs.gp.gp_algebra)": [[8, "flare.bffs.gp.gp_algebra.force_force_vector"]], "force_force_vector_unit() (in module flare.bffs.gp.gp_algebra)": [[8, "flare.bffs.gp.gp_algebra.force_force_vector_unit"]], "get_distance_mat_pack() (in module flare.bffs.gp.gp_algebra)": [[8, "flare.bffs.gp.gp_algebra.get_distance_mat_pack"]], "get_force_block() (in module flare.bffs.gp.gp_algebra)": [[8, "flare.bffs.gp.gp_algebra.get_force_block"]], "get_force_block_pack() (in module flare.bffs.gp.gp_algebra)": [[8, "flare.bffs.gp.gp_algebra.get_force_block_pack"]], "get_ky_and_hyp() (in module flare.bffs.gp.gp_algebra)": [[8, "flare.bffs.gp.gp_algebra.get_ky_and_hyp"]], "get_ky_and_hyp_pack() (in module flare.bffs.gp.gp_algebra)": [[8, "flare.bffs.gp.gp_algebra.get_ky_and_hyp_pack"]], "get_like_from_mats() (in module flare.bffs.gp.gp_algebra)": [[8, "flare.bffs.gp.gp_algebra.get_like_from_mats"]], "get_like_grad_from_mats() (in module flare.bffs.gp.gp_algebra)": [[8, "flare.bffs.gp.gp_algebra.get_like_grad_from_mats"]], "get_neg_like() (in module flare.bffs.gp.gp_algebra)": [[8, "flare.bffs.gp.gp_algebra.get_neg_like"]], "get_neg_like_grad() (in module flare.bffs.gp.gp_algebra)": [[8, "flare.bffs.gp.gp_algebra.get_neg_like_grad"]], "kernel_distance_mat() (in module flare.bffs.gp.gp_algebra)": [[8, "flare.bffs.gp.gp_algebra.kernel_distance_mat"]], "obtain_noise_len() (in module flare.bffs.gp.gp_algebra)": [[8, "flare.bffs.gp.gp_algebra.obtain_noise_len"]], "partition_force_energy_block() (in module flare.bffs.gp.gp_algebra)": [[8, "flare.bffs.gp.gp_algebra.partition_force_energy_block"]], "partition_matrix() (in module flare.bffs.gp.gp_algebra)": [[8, "flare.bffs.gp.gp_algebra.partition_matrix"]], "partition_matrix_custom() (in module flare.bffs.gp.gp_algebra)": [[8, "flare.bffs.gp.gp_algebra.partition_matrix_custom"]], "partition_vector() (in module flare.bffs.gp.gp_algebra)": [[8, "flare.bffs.gp.gp_algebra.partition_vector"]], "queue_wrapper() (in module flare.bffs.gp.gp_algebra)": [[8, "flare.bffs.gp.gp_algebra.queue_wrapper"]], "flare.bffs.gp.predict": [[9, "module-flare.bffs.gp.predict"]], "predict_on_atom() (in module flare.bffs.gp.predict)": [[9, "flare.bffs.gp.predict.predict_on_atom"]], "predict_on_atom_efs() (in module flare.bffs.gp.predict)": [[9, "flare.bffs.gp.predict.predict_on_atom_efs"]], "predict_on_atom_en() (in module flare.bffs.gp.predict)": [[9, "flare.bffs.gp.predict.predict_on_atom_en"]], "predict_on_atom_en_std() (in module flare.bffs.gp.predict)": [[9, "flare.bffs.gp.predict.predict_on_atom_en_std"]], "predict_on_structure() (in module flare.bffs.gp.predict)": [[9, "flare.bffs.gp.predict.predict_on_structure"]], "predict_on_structure_en() (in module flare.bffs.gp.predict)": [[9, "flare.bffs.gp.predict.predict_on_structure_en"]], "predict_on_structure_mgp() (in module flare.bffs.gp.predict)": [[9, "flare.bffs.gp.predict.predict_on_structure_mgp"]], "predict_on_structure_par() (in module flare.bffs.gp.predict)": [[9, "flare.bffs.gp.predict.predict_on_structure_par"]], "predict_on_structure_par_en() (in module flare.bffs.gp.predict)": [[9, "flare.bffs.gp.predict.predict_on_structure_par_en"]], "mappedgaussianprocess (class in flare.bffs.mgp.mgp)": [[11, "flare.bffs.mgp.mgp.MappedGaussianProcess"]], "as_dict() (flare.bffs.mgp.mgp.mappedgaussianprocess method)": [[11, "flare.bffs.mgp.mgp.MappedGaussianProcess.as_dict"]], "flare.bffs.mgp.mgp": [[11, "module-flare.bffs.mgp.mgp"]], "from_dict() (flare.bffs.mgp.mgp.mappedgaussianprocess static method)": [[11, "flare.bffs.mgp.mgp.MappedGaussianProcess.from_dict"]], "predict() (flare.bffs.mgp.mgp.mappedgaussianprocess method)": [[11, "flare.bffs.mgp.mgp.MappedGaussianProcess.predict"]], "write_lmp_file() (flare.bffs.mgp.mgp.mappedgaussianprocess method)": [[11, "flare.bffs.mgp.mgp.MappedGaussianProcess.write_lmp_file"]], "write_model() (flare.bffs.mgp.mgp.mappedgaussianprocess method)": [[11, "flare.bffs.mgp.mgp.MappedGaussianProcess.write_model"]], "cubicspline (class in flare.bffs.mgp.splines_methods)": [[12, "flare.bffs.mgp.splines_methods.CubicSpline"]], "pcasplines (class in flare.bffs.mgp.splines_methods)": [[12, "flare.bffs.mgp.splines_methods.PCASplines"]], "flare.bffs.mgp.splines_methods": [[12, "module-flare.bffs.mgp.splines_methods"]], "grid (flare.bffs.mgp.splines_methods.cubicspline property)": [[12, "flare.bffs.mgp.splines_methods.CubicSpline.grid"]], "interpolate() (flare.bffs.mgp.splines_methods.cubicspline method)": [[12, "flare.bffs.mgp.splines_methods.CubicSpline.interpolate"]], "set_values() (flare.bffs.mgp.splines_methods.cubicspline method)": [[12, "flare.bffs.mgp.splines_methods.CubicSpline.set_values"]], "vec_eval_cubic_spline() (in module flare.bffs.mgp.splines_methods)": [[12, "flare.bffs.mgp.splines_methods.vec_eval_cubic_spline"]], "sgp_calculator (class in flare.bffs.sgp.calculator)": [[13, "flare.bffs.sgp.calculator.SGP_Calculator"]], "calculate() (flare.bffs.sgp.calculator.sgp_calculator method)": [[13, "flare.bffs.sgp.calculator.SGP_Calculator.calculate"]], "flare.bffs.sgp.calculator": [[13, "module-flare.bffs.sgp.calculator"]], "implemented_properties (flare.bffs.sgp.calculator.sgp_calculator attribute)": [[13, "flare.bffs.sgp.calculator.SGP_Calculator.implemented_properties"]], "sgp_wrapper (class in flare.bffs.sgp.sparse_gp)": [[14, "flare.bffs.sgp.sparse_gp.SGP_Wrapper"]], "compute_negative_likelihood() (in module flare.bffs.sgp.sparse_gp)": [[14, "flare.bffs.sgp.sparse_gp.compute_negative_likelihood"]], "compute_negative_likelihood_grad() (in module flare.bffs.sgp.sparse_gp)": [[14, "flare.bffs.sgp.sparse_gp.compute_negative_likelihood_grad"]], "compute_negative_likelihood_grad_stable() (in module flare.bffs.sgp.sparse_gp)": [[14, "flare.bffs.sgp.sparse_gp.compute_negative_likelihood_grad_stable"]], "flare.bffs.sgp.sparse_gp": [[14, "module-flare.bffs.sgp.sparse_gp"]], "from_dict() (flare.bffs.sgp.sparse_gp.sgp_wrapper static method)": [[14, "flare.bffs.sgp.sparse_gp.SGP_Wrapper.from_dict"]], "optimize_hyperparameters() (in module flare.bffs.sgp.sparse_gp)": [[14, "flare.bffs.sgp.sparse_gp.optimize_hyperparameters"]], "write_model() (flare.bffs.sgp.sparse_gp.sgp_wrapper method)": [[14, "flare.bffs.sgp.sparse_gp.SGP_Wrapper.write_model"]], "atomicenvironment (class in flare.descriptors.env)": [[16, "flare.descriptors.env.AtomicEnvironment"]], "as_dict() (flare.descriptors.env.atomicenvironment method)": [[16, "flare.descriptors.env.AtomicEnvironment.as_dict"]], "as_str() (flare.descriptors.env.atomicenvironment method)": [[16, "flare.descriptors.env.AtomicEnvironment.as_str"]], "flare.descriptors.env": [[16, "module-flare.descriptors.env"]], "from_dict() (flare.descriptors.env.atomicenvironment static method)": [[16, "flare.descriptors.env.AtomicEnvironment.from_dict"]], "from_file() (flare.descriptors.env.atomicenvironment static method)": [[16, "flare.descriptors.env.AtomicEnvironment.from_file"]], "otfanalysis (class in flare.io.otf_parser)": [[19, "flare.io.otf_parser.OtfAnalysis"]], "append_atom_lists() (in module flare.io.otf_parser)": [[19, "flare.io.otf_parser.append_atom_lists"]], "extract_gp_info() (in module flare.io.otf_parser)": [[19, "flare.io.otf_parser.extract_gp_info"]], "flare.io.otf_parser": [[19, "module-flare.io.otf_parser"]], "make_gp() (flare.io.otf_parser.otfanalysis method)": [[19, "flare.io.otf_parser.OtfAnalysis.make_gp"]], "output_md_structures() (flare.io.otf_parser.otfanalysis method)": [[19, "flare.io.otf_parser.OtfAnalysis.output_md_structures"]], "parse_frame_line() (in module flare.io.otf_parser)": [[19, "flare.io.otf_parser.parse_frame_line"]], "parse_header_information() (in module flare.io.otf_parser)": [[19, "flare.io.otf_parser.parse_header_information"]], "parse_pos_otf() (flare.io.otf_parser.otfanalysis method)": [[19, "flare.io.otf_parser.OtfAnalysis.parse_pos_otf"]], "parse_snapshot() (in module flare.io.otf_parser)": [[19, "flare.io.otf_parser.parse_snapshot"]], "strip_and_split() (in module flare.io.otf_parser)": [[19, "flare.io.otf_parser.strip_and_split"]], "to_xyz() (flare.io.otf_parser.otfanalysis method)": [[19, "flare.io.otf_parser.OtfAnalysis.to_xyz"]], "output (class in flare.io.output)": [[20, "flare.io.output.Output"]], "add_file() (in module flare.io.output)": [[20, "flare.io.output.add_file"]], "add_stream() (in module flare.io.output)": [[20, "flare.io.output.add_stream"]], "conclude_run() (flare.io.output.output method)": [[20, "flare.io.output.Output.conclude_run"]], "flare.io.output": [[20, "module-flare.io.output"]], "open_new_log() (flare.io.output.output method)": [[20, "flare.io.output.Output.open_new_log"]], "set_logger() (in module flare.io.output)": [[20, "flare.io.output.set_logger"]], "write_gp_dft_comparison() (flare.io.output.output method)": [[20, "flare.io.output.Output.write_gp_dft_comparison"]], "write_header() (flare.io.output.output method)": [[20, "flare.io.output.Output.write_header"]], "write_hyps() (flare.io.output.output method)": [[20, "flare.io.output.Output.write_hyps"]], "write_md_config() (flare.io.output.output method)": [[20, "flare.io.output.Output.write_md_config"]], "write_to_log() (flare.io.output.output method)": [[20, "flare.io.output.Output.write_to_log"]], "write_xyz_config() (flare.io.output.output method)": [[20, "flare.io.output.Output.write_xyz_config"]], "cosine_cutoff() (in module flare.kernels.cutoffs)": [[21, "flare.kernels.cutoffs.cosine_cutoff"]], "cubic_cutoff() (in module flare.kernels.cutoffs)": [[21, "flare.kernels.cutoffs.cubic_cutoff"]], "flare.kernels.cutoffs": [[21, "module-flare.kernels.cutoffs"]], "hard_cutoff() (in module flare.kernels.cutoffs)": [[21, "flare.kernels.cutoffs.hard_cutoff"]], "quadratic_cutoff() (in module flare.kernels.cutoffs)": [[21, "flare.kernels.cutoffs.quadratic_cutoff"]], "quadratic_cutoff_bound() (in module flare.kernels.cutoffs)": [[21, "flare.kernels.cutoffs.quadratic_cutoff_bound"]], "coordination_number() (in module flare.kernels.kernels)": [[22, "flare.kernels.kernels.coordination_number"]], "flare.kernels.kernels": [[22, "module-flare.kernels.kernels"]], "force_helper() (in module flare.kernels.kernels)": [[22, "flare.kernels.kernels.force_helper"]], "k_sq_exp_dev() (in module flare.kernels.kernels)": [[22, "flare.kernels.kernels.k_sq_exp_dev"]], "k_sq_exp_double_dev() (in module flare.kernels.kernels)": [[22, "flare.kernels.kernels.k_sq_exp_double_dev"]], "mb_grad_helper_ls() (in module flare.kernels.kernels)": [[22, "flare.kernels.kernels.mb_grad_helper_ls"]], "mb_grad_helper_ls_() (in module flare.kernels.kernels)": [[22, "flare.kernels.kernels.mb_grad_helper_ls_"]], "q_value() (in module flare.kernels.kernels)": [[22, "flare.kernels.kernels.q_value"]], "q_value_mc() (in module flare.kernels.kernels)": [[22, "flare.kernels.kernels.q_value_mc"]], "flare.kernels.mc_3b_sepcut": [[24, "module-flare.kernels.mc_3b_sepcut"]], "flare.kernels.mc_mb_sepcut": [[24, "module-flare.kernels.mc_mb_sepcut"]], "flare.kernels.mc_sephyps": [[24, "module-flare.kernels.mc_sephyps"]], "many_body_mc() (in module flare.kernels.mc_sephyps)": [[24, "flare.kernels.mc_sephyps.many_body_mc"]], "many_body_mc_en() (in module flare.kernels.mc_sephyps)": [[24, "flare.kernels.mc_sephyps.many_body_mc_en"]], "many_body_mc_en_sepcut_jit() (in module flare.kernels.mc_mb_sepcut)": [[24, "flare.kernels.mc_mb_sepcut.many_body_mc_en_sepcut_jit"]], "many_body_mc_force_en() (in module flare.kernels.mc_sephyps)": [[24, "flare.kernels.mc_sephyps.many_body_mc_force_en"]], "many_body_mc_force_en_sepcut_jit() (in module flare.kernels.mc_mb_sepcut)": [[24, "flare.kernels.mc_mb_sepcut.many_body_mc_force_en_sepcut_jit"]], "many_body_mc_grad() (in module flare.kernels.mc_sephyps)": [[24, "flare.kernels.mc_sephyps.many_body_mc_grad"]], "many_body_mc_grad_sepcut_jit() (in module flare.kernels.mc_mb_sepcut)": [[24, "flare.kernels.mc_mb_sepcut.many_body_mc_grad_sepcut_jit"]], "many_body_mc_sepcut_jit() (in module flare.kernels.mc_mb_sepcut)": [[24, "flare.kernels.mc_mb_sepcut.many_body_mc_sepcut_jit"]], "three_body_mc() (in module flare.kernels.mc_sephyps)": [[24, "flare.kernels.mc_sephyps.three_body_mc"]], "three_body_mc_en() (in module flare.kernels.mc_sephyps)": [[24, "flare.kernels.mc_sephyps.three_body_mc_en"]], "three_body_mc_force_en() (in module flare.kernels.mc_sephyps)": [[24, "flare.kernels.mc_sephyps.three_body_mc_force_en"]], "three_body_mc_force_en_jit() (in module flare.kernels.mc_sephyps)": [[24, "flare.kernels.mc_sephyps.three_body_mc_force_en_jit"]], "three_body_mc_force_en_sepcut_jit() (in module flare.kernels.mc_3b_sepcut)": [[24, "flare.kernels.mc_3b_sepcut.three_body_mc_force_en_sepcut_jit"]], "three_body_mc_grad() (in module flare.kernels.mc_sephyps)": [[24, "flare.kernels.mc_sephyps.three_body_mc_grad"]], "three_body_mc_grad_jit() (in module flare.kernels.mc_sephyps)": [[24, "flare.kernels.mc_sephyps.three_body_mc_grad_jit"]], "three_body_mc_grad_sepcut_jit() (in module flare.kernels.mc_3b_sepcut)": [[24, "flare.kernels.mc_3b_sepcut.three_body_mc_grad_sepcut_jit"]], "two_body_mc() (in module flare.kernels.mc_sephyps)": [[24, "flare.kernels.mc_sephyps.two_body_mc"]], "two_body_mc_en() (in module flare.kernels.mc_sephyps)": [[24, "flare.kernels.mc_sephyps.two_body_mc_en"]], "two_body_mc_en_jit() (in module flare.kernels.mc_sephyps)": [[24, "flare.kernels.mc_sephyps.two_body_mc_en_jit"]], "two_body_mc_force_en() (in module flare.kernels.mc_sephyps)": [[24, "flare.kernels.mc_sephyps.two_body_mc_force_en"]], "two_body_mc_force_en_jit() (in module flare.kernels.mc_sephyps)": [[24, "flare.kernels.mc_sephyps.two_body_mc_force_en_jit"]], "two_body_mc_grad() (in module flare.kernels.mc_sephyps)": [[24, "flare.kernels.mc_sephyps.two_body_mc_grad"]], "two_body_mc_grad_jit() (in module flare.kernels.mc_sephyps)": [[24, "flare.kernels.mc_sephyps.two_body_mc_grad_jit"]], "two_body_mc_jit() (in module flare.kernels.mc_sephyps)": [[24, "flare.kernels.mc_sephyps.two_body_mc_jit"]], "two_plus_three_body_mc() (in module flare.kernels.mc_sephyps)": [[24, "flare.kernels.mc_sephyps.two_plus_three_body_mc"]], "two_plus_three_body_mc_grad() (in module flare.kernels.mc_sephyps)": [[24, "flare.kernels.mc_sephyps.two_plus_three_body_mc_grad"]], "two_plus_three_mc_en() (in module flare.kernels.mc_sephyps)": [[24, "flare.kernels.mc_sephyps.two_plus_three_mc_en"]], "two_plus_three_mc_force_en() (in module flare.kernels.mc_sephyps)": [[24, "flare.kernels.mc_sephyps.two_plus_three_mc_force_en"]], "two_three_many_body_mc() (in module flare.kernels.mc_sephyps)": [[24, "flare.kernels.mc_sephyps.two_three_many_body_mc"]], "two_three_many_body_mc_grad() (in module flare.kernels.mc_sephyps)": [[24, "flare.kernels.mc_sephyps.two_three_many_body_mc_grad"]], "two_three_many_mc_en() (in module flare.kernels.mc_sephyps)": [[24, "flare.kernels.mc_sephyps.two_three_many_mc_en"]], "two_three_many_mc_force_en() (in module flare.kernels.mc_sephyps)": [[24, "flare.kernels.mc_sephyps.two_three_many_mc_force_en"]], "flare.kernels.mc_simple": [[25, "module-flare.kernels.mc_simple"]], "many_body_mc() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.many_body_mc"]], "many_body_mc_en() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.many_body_mc_en"]], "many_body_mc_en_jit() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.many_body_mc_en_jit"]], "many_body_mc_force_en() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.many_body_mc_force_en"]], "many_body_mc_force_en_jit() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.many_body_mc_force_en_jit"]], "many_body_mc_grad() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.many_body_mc_grad"]], "many_body_mc_grad_jit() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.many_body_mc_grad_jit"]], "many_body_mc_jit() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.many_body_mc_jit"]], "three_body_mc() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.three_body_mc"]], "three_body_mc_en() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.three_body_mc_en"]], "three_body_mc_en_jit() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.three_body_mc_en_jit"]], "three_body_mc_force_en() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.three_body_mc_force_en"]], "three_body_mc_force_en_jit() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.three_body_mc_force_en_jit"]], "three_body_mc_grad() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.three_body_mc_grad"]], "three_body_mc_grad_jit() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.three_body_mc_grad_jit"]], "three_body_mc_jit() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.three_body_mc_jit"]], "three_body_se_jit() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.three_body_se_jit"]], "three_body_sf_jit() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.three_body_sf_jit"]], "three_body_ss_jit() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.three_body_ss_jit"]], "two_body_mc() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.two_body_mc"]], "two_body_mc_en() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.two_body_mc_en"]], "two_body_mc_en_jit() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.two_body_mc_en_jit"]], "two_body_mc_force_en() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.two_body_mc_force_en"]], "two_body_mc_force_en_jit() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.two_body_mc_force_en_jit"]], "two_body_mc_grad() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.two_body_mc_grad"]], "two_body_mc_grad_jit() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.two_body_mc_grad_jit"]], "two_body_mc_jit() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.two_body_mc_jit"]], "two_body_mc_stress_en_jit() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.two_body_mc_stress_en_jit"]], "two_body_mc_stress_force_jit() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.two_body_mc_stress_force_jit"]], "two_body_mc_stress_stress_jit() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.two_body_mc_stress_stress_jit"]], "two_plus_many_body_mc() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.two_plus_many_body_mc"]], "two_plus_many_body_mc_en() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.two_plus_many_body_mc_en"]], "two_plus_many_body_mc_force_en() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.two_plus_many_body_mc_force_en"]], "two_plus_many_body_mc_grad() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.two_plus_many_body_mc_grad"]], "two_plus_three_body_mc() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.two_plus_three_body_mc"]], "two_plus_three_body_mc_grad() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.two_plus_three_body_mc_grad"]], "two_plus_three_mc_en() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.two_plus_three_mc_en"]], "two_plus_three_mc_force_en() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.two_plus_three_mc_force_en"]], "two_plus_three_plus_many_body_mc() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.two_plus_three_plus_many_body_mc"]], "two_plus_three_plus_many_body_mc_en() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.two_plus_three_plus_many_body_mc_en"]], "two_plus_three_plus_many_body_mc_force_en() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.two_plus_three_plus_many_body_mc_force_en"]], "two_plus_three_plus_many_body_mc_grad() (in module flare.kernels.mc_simple)": [[25, "flare.kernels.mc_simple.two_plus_three_plus_many_body_mc_grad"]], "flare.kernels.sc": [[26, "module-flare.kernels.sc"]], "many_body() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.many_body"]], "many_body_en() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.many_body_en"]], "many_body_en_jit() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.many_body_en_jit"]], "many_body_force_en() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.many_body_force_en"]], "many_body_force_en_jit() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.many_body_force_en_jit"]], "many_body_grad() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.many_body_grad"]], "many_body_grad_jit() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.many_body_grad_jit"]], "many_body_jit() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.many_body_jit"]], "three_body() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.three_body"]], "three_body_en() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.three_body_en"]], "three_body_en_jit() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.three_body_en_jit"]], "three_body_force_en() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.three_body_force_en"]], "three_body_force_en_jit() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.three_body_force_en_jit"]], "three_body_grad() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.three_body_grad"]], "three_body_grad_jit() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.three_body_grad_jit"]], "three_body_jit() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.three_body_jit"]], "two_body() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.two_body"]], "two_body_en() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.two_body_en"]], "two_body_en_jit() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.two_body_en_jit"]], "two_body_force_en() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.two_body_force_en"]], "two_body_force_en_jit() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.two_body_force_en_jit"]], "two_body_grad() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.two_body_grad"]], "two_body_grad_jit() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.two_body_grad_jit"]], "two_body_jit() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.two_body_jit"]], "two_plus_many_body() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.two_plus_many_body"]], "two_plus_many_body_en() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.two_plus_many_body_en"]], "two_plus_many_body_force_en() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.two_plus_many_body_force_en"]], "two_plus_many_body_grad() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.two_plus_many_body_grad"]], "two_plus_three_body() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.two_plus_three_body"]], "two_plus_three_body_grad() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.two_plus_three_body_grad"]], "two_plus_three_en() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.two_plus_three_en"]], "two_plus_three_force_en() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.two_plus_three_force_en"]], "two_plus_three_plus_many_body() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.two_plus_three_plus_many_body"]], "two_plus_three_plus_many_body_en() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.two_plus_three_plus_many_body_en"]], "two_plus_three_plus_many_body_force_en() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.two_plus_three_plus_many_body_force_en"]], "two_plus_three_plus_many_body_grad() (in module flare.kernels.sc)": [[26, "flare.kernels.sc.two_plus_three_plus_many_body_grad"]], "flare.learners.gp_from_aimd": [[27, "module-flare.learners.gp_from_aimd"]], "parse_trajectory_trainer_output() (in module flare.learners.gp_from_aimd)": [[27, "flare.learners.gp_from_aimd.parse_trajectory_trainer_output"]], "structures_from_gpfa_output() (in module flare.learners.gp_from_aimd)": [[27, "flare.learners.gp_from_aimd.structures_from_gpfa_output"]], "lmpotf (class in flare.learners.lmpotf)": [[29, "flare.learners.lmpotf.LMPOTF"]], "flare.learners.lmpotf": [[29, "module-flare.learners.lmpotf"]], "step() (flare.learners.lmpotf.lmpotf method)": [[29, "flare.learners.lmpotf.LMPOTF.step"]], "otf (class in flare.learners.otf)": [[30, "flare.learners.otf.OTF"]], "compute_properties() (flare.learners.otf.otf method)": [[30, "flare.learners.otf.OTF.compute_properties"]], "flare.learners.otf": [[30, "module-flare.learners.otf"]], "md_step() (flare.learners.otf.otf method)": [[30, "flare.learners.otf.OTF.md_step"]], "rescale_temperature() (flare.learners.otf.otf method)": [[30, "flare.learners.otf.OTF.rescale_temperature"]], "run() (flare.learners.otf.otf method)": [[30, "flare.learners.otf.OTF.run"]], "run_dft() (flare.learners.otf.otf method)": [[30, "flare.learners.otf.OTF.run_dft"]], "train_gp() (flare.learners.otf.otf method)": [[30, "flare.learners.otf.OTF.train_gp"]], "update_gp() (flare.learners.otf.otf method)": [[30, "flare.learners.otf.OTF.update_gp"]], "update_temperature() (flare.learners.otf.otf method)": [[30, "flare.learners.otf.OTF.update_temperature"]], "flare.learners.utils": [[31, "module-flare.learners.utils"]], "get_max_cutoff() (in module flare.learners.utils)": [[31, "flare.learners.utils.get_max_cutoff"]], "is_force_in_bound_per_species() (in module flare.learners.utils)": [[31, "flare.learners.utils.is_force_in_bound_per_species"]], "is_std_in_bound() (in module flare.learners.utils)": [[31, "flare.learners.utils.is_std_in_bound"]], "is_std_in_bound_per_species() (in module flare.learners.utils)": [[31, "flare.learners.utils.is_std_in_bound_per_species"]], "subset_of_frame_by_element() (in module flare.learners.utils)": [[31, "flare.learners.utils.subset_of_frame_by_element"]], "fakedft (class in flare.md.fake)": [[32, "flare.md.fake.FakeDFT"]], "fakemd (class in flare.md.fake)": [[32, "flare.md.fake.FakeMD"]], "calculate() (flare.md.fake.fakedft method)": [[32, "flare.md.fake.FakeDFT.calculate"]], "flare.md.fake": [[32, "module-flare.md.fake"]], "implemented_properties (flare.md.fake.fakedft attribute)": [[32, "flare.md.fake.FakeDFT.implemented_properties"]], "lammps_md (class in flare.md.lammps)": [[33, "flare.md.lammps.LAMMPS_MD"]], "lammps_mod (class in flare.md.lammps)": [[33, "flare.md.lammps.LAMMPS_MOD"]], "backup() (flare.md.lammps.lammps_md method)": [[33, "flare.md.lammps.LAMMPS_MD.backup"]], "calculate() (flare.md.lammps.lammps_mod method)": [[33, "flare.md.lammps.LAMMPS_MOD.calculate"]], "check_sgp_match() (in module flare.md.lammps)": [[33, "flare.md.lammps.check_sgp_match"]], "flare.md.lammps": [[33, "module-flare.md.lammps"]], "get_kinetic_stress() (in module flare.md.lammps)": [[33, "flare.md.lammps.get_kinetic_stress"]], "step() (flare.md.lammps.lammps_md method)": [[33, "flare.md.lammps.LAMMPS_MD.step"]], "nosehoover (class in flare.md.nosehoover)": [[35, "flare.md.nosehoover.NoseHoover"]], "flare.md.nosehoover": [[35, "module-flare.md.nosehoover"]], "step() (flare.md.nosehoover.nosehoover method)": [[35, "flare.md.nosehoover.NoseHoover.step"]], "flare.utils.env_getarray": [[36, "module-flare.utils.env_getarray"]], "get_2_body_arrays() (in module flare.utils.env_getarray)": [[36, "flare.utils.env_getarray.get_2_body_arrays"]], "get_3_body_arrays() (in module flare.utils.env_getarray)": [[36, "flare.utils.env_getarray.get_3_body_arrays"]], "get_m2_body_arrays() (in module flare.utils.env_getarray)": [[36, "flare.utils.env_getarray.get_m2_body_arrays"]], "get_m3_body_arrays() (in module flare.utils.env_getarray)": [[36, "flare.utils.env_getarray.get_m3_body_arrays"]], "q3_value_mc() (in module flare.utils.env_getarray)": [[36, "flare.utils.env_getarray.q3_value_mc"]], "parameterhelper (class in flare.utils.parameter_helper)": [[37, "flare.utils.parameter_helper.ParameterHelper"]], "all_separate_groups() (flare.utils.parameter_helper.parameterhelper method)": [[37, "flare.utils.parameter_helper.ParameterHelper.all_separate_groups"]], "as_dict() (flare.utils.parameter_helper.parameterhelper method)": [[37, "flare.utils.parameter_helper.ParameterHelper.as_dict"]], "define_group() (flare.utils.parameter_helper.parameterhelper method)": [[37, "flare.utils.parameter_helper.ParameterHelper.define_group"]], "fill_in_parameters() (flare.utils.parameter_helper.parameterhelper method)": [[37, "flare.utils.parameter_helper.ParameterHelper.fill_in_parameters"]], "find_group() (flare.utils.parameter_helper.parameterhelper method)": [[37, "flare.utils.parameter_helper.ParameterHelper.find_group"]], "flare.utils.parameter_helper": [[37, "module-flare.utils.parameter_helper"]], "flare.utils.parameters": [[37, "module-flare.utils.parameters"]], "from_dict() (flare.utils.parameter_helper.parameterhelper static method)": [[37, "flare.utils.parameter_helper.ParameterHelper.from_dict"]], "list_groups() (flare.utils.parameter_helper.parameterhelper method)": [[37, "flare.utils.parameter_helper.ParameterHelper.list_groups"]], "list_parameters() (flare.utils.parameter_helper.parameterhelper method)": [[37, "flare.utils.parameter_helper.ParameterHelper.list_parameters"]], "nprandom() (in module flare.utils.parameter_helper)": [[37, "flare.utils.parameter_helper.nprandom"]], "set_constraints() (flare.utils.parameter_helper.parameterhelper method)": [[37, "flare.utils.parameter_helper.ParameterHelper.set_constraints"]], "set_parameters() (flare.utils.parameter_helper.parameterhelper method)": [[37, "flare.utils.parameter_helper.ParameterHelper.set_parameters"]], "summarize_group() (flare.utils.parameter_helper.parameterhelper method)": [[37, "flare.utils.parameter_helper.ParameterHelper.summarize_group"]], "numpyencoder (class in flare.utils)": [[38, "flare.utils.NumpyEncoder"]], "flare.utils": [[38, "module-flare.utils"]], "sparsegp (c++ class)": [[39, "_CPPv48SparseGP"]], "sparsegp::knk_e (c++ member)": [[39, "_CPPv4N8SparseGP5KnK_eE"]], "sparsegp::knk_f (c++ member)": [[39, "_CPPv4N8SparseGP5KnK_fE"]], "sparsegp::knk_s (c++ member)": [[39, "_CPPv4N8SparseGP5KnK_sE"]], "sparsegp::kuf (c++ member)": [[39, "_CPPv4N8SparseGP3KufE"]], "sparsegp::kuf_e_noise_kfu (c++ member)": [[39, "_CPPv4N8SparseGP15Kuf_e_noise_KfuE"]], "sparsegp::kuf_f_noise_kfu (c++ member)": [[39, "_CPPv4N8SparseGP15Kuf_f_noise_KfuE"]], "sparsegp::kuf_kernels (c++ member)": [[39, "_CPPv4N8SparseGP11Kuf_kernelsE"]], "sparsegp::kuf_s_noise_kfu (c++ member)": [[39, "_CPPv4N8SparseGP15Kuf_s_noise_KfuE"]], "sparsegp::kuu (c++ member)": [[39, "_CPPv4N8SparseGP3KuuE"]], "sparsegp::kuu_inverse (c++ member)": [[39, "_CPPv4N8SparseGP11Kuu_inverseE"]], "sparsegp::kuu_jitter (c++ member)": [[39, "_CPPv4N8SparseGP10Kuu_jitterE"]], "sparsegp::kuu_kernels (c++ member)": [[39, "_CPPv4N8SparseGP11Kuu_kernelsE"]], "sparsegp::l_diag (c++ member)": [[39, "_CPPv4N8SparseGP6L_diagE"]], "sparsegp::l_inv (c++ member)": [[39, "_CPPv4N8SparseGP5L_invE"]], "sparsegp::r_inv (c++ member)": [[39, "_CPPv4N8SparseGP5R_invE"]], "sparsegp::r_inv_diag (c++ member)": [[39, "_CPPv4N8SparseGP10R_inv_diagE"]], "sparsegp::sigma (c++ member)": [[39, "_CPPv4N8SparseGP5SigmaE"]], "sparsegp::sparsegp (c++ function)": [[39, "_CPPv4N8SparseGP8SparseGPENSt6vectorIP6KernelEEddd"], [39, "_CPPv4N8SparseGP8SparseGPEv"]], "sparsegp::add_all_environments (c++ function)": [[39, "_CPPv4N8SparseGP20add_all_environmentsERK9Structure"]], "sparsegp::add_random_environments (c++ function)": [[39, "_CPPv4N8SparseGP23add_random_environmentsERK9StructureRKNSt6vectorIiEE"]], "sparsegp::add_specific_environments (c++ function)": [[39, "_CPPv4N8SparseGP25add_specific_environmentsERK9StructureKNSt6vectorIiEE"]], "sparsegp::add_training_structure (c++ function)": [[39, "_CPPv4N8SparseGP22add_training_structureERK9StructureKNSt6vectorIiEEddd"]], "sparsegp::add_uncertain_environments (c++ function)": [[39, "_CPPv4N8SparseGP26add_uncertain_environmentsERK9StructureRKNSt6vectorIiEE"]], "sparsegp::alpha (c++ member)": [[39, "_CPPv4N8SparseGP5alphaE"]], "sparsegp::complexity_penalty (c++ member)": [[39, "_CPPv4N8SparseGP18complexity_penaltyE"]], "sparsegp::compute_knk (c++ function)": [[39, "_CPPv4N8SparseGP11compute_KnKEb"]], "sparsegp::compute_cluster_uncertainties (c++ function)": [[39, "_CPPv4N8SparseGP29compute_cluster_uncertaintiesERK9Structure"]], "sparsegp::compute_dknk (c++ function)": [[39, "_CPPv4N8SparseGP12compute_dKnKEi"]], "sparsegp::compute_likelihood (c++ function)": [[39, "_CPPv4N8SparseGP18compute_likelihoodEv"]], "sparsegp::compute_likelihood_gradient (c++ function)": [[39, "_CPPv4N8SparseGP27compute_likelihood_gradientERKN5Eigen8VectorXdE"]], "sparsegp::compute_likelihood_gradient_stable (c++ function)": [[39, "_CPPv4N8SparseGP34compute_likelihood_gradient_stableEb"]], "sparsegp::compute_likelihood_stable (c++ function)": [[39, "_CPPv4N8SparseGP25compute_likelihood_stableEv"]], "sparsegp::constant_term (c++ member)": [[39, "_CPPv4N8SparseGP13constant_termE"]], "sparsegp::data_fit (c++ member)": [[39, "_CPPv4N8SparseGP8data_fitE"]], "sparsegp::e_noise_one (c++ member)": [[39, "_CPPv4N8SparseGP11e_noise_oneE"]], "sparsegp::energy_noise (c++ member)": [[39, "_CPPv4N8SparseGP12energy_noiseE"]], "sparsegp::f_noise_one (c++ member)": [[39, "_CPPv4N8SparseGP11f_noise_oneE"]], "sparsegp::force_noise (c++ member)": [[39, "_CPPv4N8SparseGP11force_noiseE"]], "sparsegp::hyperparameters (c++ member)": [[39, "_CPPv4N8SparseGP15hyperparametersE"]], "sparsegp::initialize_sparse_descriptors (c++ function)": [[39, "_CPPv4N8SparseGP29initialize_sparse_descriptorsERK9Structure"]], "sparsegp::inv_e_noise_one (c++ member)": [[39, "_CPPv4N8SparseGP15inv_e_noise_oneE"]], "sparsegp::inv_f_noise_one (c++ member)": [[39, "_CPPv4N8SparseGP15inv_f_noise_oneE"]], "sparsegp::inv_s_noise_one (c++ member)": [[39, 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