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A
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B
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C
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D
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E
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F
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G
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H
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I
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K
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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U
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V
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W
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Z
A
add_file() (in module flare.output)
add_one_env() (flare.gp.GaussianProcess method)
add_stream() (in module flare.output)
adjust_cutoffs() (flare.gp.GaussianProcess method)
all_separate_groups() (flare.utils.parameter_helper.ParameterHelper method)
append_atom_lists() (in module flare.otf_parser)
as_dict() (flare.env.AtomicEnvironment method)
(flare.gp.GaussianProcess method)
(flare.mgp.mgp.MappedGaussianProcess method)
(flare.struc.Structure method)
(flare.utils.parameter_helper.ParameterHelper method)
as_str() (flare.env.AtomicEnvironment method)
(flare.struc.Structure method)
ASE_OTF (class in flare.ase.otf)
AtomicEnvironment (class in flare.env)
B
backward_arguments() (flare.gp.GaussianProcess static method)
backward_attributes() (flare.gp.GaussianProcess static method)
C
calculate() (flare.ase.calculator.FLARE_Calculator method)
check_instantiation() (flare.gp.GaussianProcess method)
check_L_alpha() (flare.gp.GaussianProcess method)
check_vasprun() (in module flare.dft_interface.vasp_util)
compute_matrices() (flare.gp.GaussianProcess method)
compute_properties() (flare.ase.otf.ASE_OTF method)
(flare.otf.OTF method)
conclude_run() (flare.output.Output method)
coordination_number() (in module flare.kernels.kernels)
cosine_cutoff() (in module flare.kernels.cutoffs)
cubic_cutoff() (in module flare.kernels.cutoffs)
CubicSpline (class in flare.mgp.splines_methods)
D
define_group() (flare.utils.parameter_helper.ParameterHelper method)
dft_input_to_structure() (in module flare.dft_interface.cp2k_util)
(in module flare.dft_interface.qe_util)
(in module flare.dft_interface.vasp_util)
E
edit_dft_input_positions() (in module flare.dft_interface.cp2k_util)
(in module flare.dft_interface.qe_util)
(in module flare.dft_interface.vasp_util)
efs_energy_vector() (in module flare.gp_algebra)
efs_force_vector() (in module flare.gp_algebra)
element_to_Z() (in module flare.utils.element_coder)
energy_energy_vector() (in module flare.gp_algebra)
energy_energy_vector_unit() (in module flare.gp_algebra)
energy_force_vector() (in module flare.gp_algebra)
energy_force_vector_unit() (in module flare.gp_algebra)
extract_gp_info() (in module flare.otf_parser)
F
fill_in_parameters() (flare.utils.parameter_helper.ParameterHelper method)
find_group() (flare.utils.parameter_helper.ParameterHelper method)
flare.ase.calculator (module)
flare.ase.nosehoover (module)
flare.ase.otf (module)
flare.dft_interface (module)
flare.dft_interface.cp2k_util (module)
flare.dft_interface.qe_util (module)
flare.dft_interface.vasp_util (module)
flare.env (module)
flare.gp (module)
flare.gp_algebra (module)
flare.gp_from_aimd (module)
flare.kernels.cutoffs (module)
flare.kernels.kernels (module)
flare.kernels.mc_3b_sepcut (module)
flare.kernels.mc_mb_sepcut (module)
flare.kernels.mc_sephyps (module)
flare.kernels.mc_simple (module)
flare.kernels.sc (module)
flare.mgp.mgp (module)
flare.mgp.splines_methods (module)
flare.otf (module)
flare.otf_parser (module)
flare.output (module)
flare.predict (module)
flare.struc (module)
flare.utils.element_coder (module)
flare.utils.env_getarray (module)
flare.utils.flare_io (module)
flare.utils.learner (module)
flare.utils.md_helper (module)
flare.utils.parameter_helper (module)
FLARE_Calculator (class in flare.ase.calculator)
force_energy_vector() (in module flare.gp_algebra)
force_energy_vector_unit() (in module flare.gp_algebra)
force_force_vector() (in module flare.gp_algebra)
force_force_vector_unit() (in module flare.gp_algebra)
force_helper() (in module flare.kernels.kernels)
from_ase_atoms() (flare.struc.Structure static method)
from_dict() (flare.env.AtomicEnvironment static method)
(flare.gp.GaussianProcess static method)
(flare.mgp.mgp.MappedGaussianProcess static method)
(flare.struc.Structure static method)
(flare.utils.parameter_helper.ParameterHelper static method)
from_file() (flare.env.AtomicEnvironment static method)
(flare.gp.GaussianProcess static method)
(flare.struc.Structure static method)
from_pmg_structure() (flare.struc.Structure static method)
G
GaussianProcess (class in flare.gp)
get_2_body_arrays() (in module flare.utils.env_getarray)
get_3_body_arrays() (in module flare.utils.env_getarray)
get_cell_dot() (flare.struc.Structure static method)
get_distance_mat_pack() (in module flare.gp_algebra)
get_force_block() (in module flare.gp_algebra)
get_force_block_pack() (in module flare.gp_algebra)
get_ky_and_hyp() (in module flare.gp_algebra)
get_ky_and_hyp_pack() (in module flare.gp_algebra)
get_like_from_mats() (in module flare.gp_algebra)
get_like_grad_from_mats() (in module flare.gp_algebra)
get_m2_body_arrays() (in module flare.utils.env_getarray)
get_m3_body_arrays() (in module flare.utils.env_getarray)
get_max_cutoff() (in module flare.utils.learner)
get_neg_like() (in module flare.gp_algebra)
get_neg_like_grad() (in module flare.gp_algebra)
get_random_velocities() (in module flare.utils.md_helper)
get_supercell_positions() (in module flare.utils.md_helper)
get_unique_species() (in module flare.struc)
grid (flare.mgp.splines_methods.CubicSpline attribute)
H
hard_cutoff() (in module flare.kernels.cutoffs)
I
indices_of_specie() (flare.struc.Structure method)
inject_user_definition() (in module flare.utils.element_coder)
interpolate() (flare.mgp.splines_methods.CubicSpline method)
is_force_in_bound_per_species() (in module flare.utils.learner)
is_std_in_bound() (in module flare.utils.learner)
is_std_in_bound_per_species() (in module flare.utils.learner)
is_valid() (flare.struc.Structure method)
K
k_sq_exp_dev() (in module flare.kernels.kernels)
k_sq_exp_double_dev() (in module flare.kernels.kernels)
kernel_distance_mat() (in module flare.gp_algebra)
L
list_groups() (flare.utils.parameter_helper.ParameterHelper method)
list_parameters() (flare.utils.parameter_helper.ParameterHelper method)
M
make_gp() (flare.otf_parser.OtfAnalysis method)
many_body() (in module flare.kernels.sc)
many_body_en() (in module flare.kernels.sc)
many_body_en_jit() (in module flare.kernels.sc)
many_body_force_en() (in module flare.kernels.sc)
many_body_force_en_jit() (in module flare.kernels.sc)
many_body_grad() (in module flare.kernels.sc)
many_body_grad_jit() (in module flare.kernels.sc)
many_body_jit() (in module flare.kernels.sc)
many_body_mc() (in module flare.kernels.mc_sephyps)
(in module flare.kernels.mc_simple)
many_body_mc_en() (in module flare.kernels.mc_sephyps)
(in module flare.kernels.mc_simple)
many_body_mc_en_jit() (in module flare.kernels.mc_simple)
many_body_mc_en_sepcut_jit() (in module flare.kernels.mc_mb_sepcut)
many_body_mc_force_en() (in module flare.kernels.mc_sephyps)
(in module flare.kernels.mc_simple)
many_body_mc_force_en_jit() (in module flare.kernels.mc_simple)
many_body_mc_force_en_sepcut_jit() (in module flare.kernels.mc_mb_sepcut)
many_body_mc_grad() (in module flare.kernels.mc_sephyps)
(in module flare.kernels.mc_simple)
many_body_mc_grad_jit() (in module flare.kernels.mc_simple)
many_body_mc_grad_sepcut_jit() (in module flare.kernels.mc_mb_sepcut)
many_body_mc_jit() (in module flare.kernels.mc_simple)
many_body_mc_sepcut_jit() (in module flare.kernels.mc_mb_sepcut)
MappedGaussianProcess (class in flare.mgp.mgp)
mb_grad_helper_ls() (in module flare.kernels.kernels)
mb_grad_helper_ls_() (in module flare.kernels.kernels)
md_step() (flare.ase.otf.ASE_OTF method)
(flare.otf.OTF method)
md_trajectory_from_file() (in module flare.utils.flare_io)
md_trajectory_from_vasprun() (in module flare.dft_interface.vasp_util)
md_trajectory_to_file() (in module flare.utils.flare_io)
multicomponent_velocities() (in module flare.utils.md_helper)
N
NoseHoover (class in flare.ase.nosehoover)
NumpyEncoder (class in flare.utils.element_coder)
O
obtain_noise_len() (in module flare.gp_algebra)
open_new_log() (flare.output.Output method)
OTF (class in flare.otf)
OtfAnalysis (class in flare.otf_parser)
Output (class in flare.output)
output_md_structures() (flare.otf_parser.OtfAnalysis method)
P
par (flare.gp.GaussianProcess attribute)
ParameterHelper (class in flare.utils.parameter_helper)
parse_dft_forces() (in module flare.dft_interface.cp2k_util)
(in module flare.dft_interface.qe_util)
(in module flare.dft_interface.vasp_util)
parse_dft_forces_and_energy() (in module flare.dft_interface.cp2k_util)
(in module flare.dft_interface.qe_util)
(in module flare.dft_interface.vasp_util)
parse_dft_input() (in module flare.dft_interface.cp2k_util)
(in module flare.dft_interface.qe_util)
(in module flare.dft_interface.vasp_util)
parse_frame_line() (in module flare.otf_parser)
parse_header_information() (in module flare.otf_parser)
parse_pos_otf() (flare.otf_parser.OtfAnalysis method)
parse_snapshot() (in module flare.otf_parser)
parse_trajectory_trainer_output() (in module flare.gp_from_aimd)
partition_force_energy_block() (in module flare.gp_algebra)
partition_matrix() (in module flare.gp_algebra)
partition_matrix_custom() (in module flare.gp_algebra)
partition_vector() (in module flare.gp_algebra)
PCASplines (class in flare.mgp.splines_methods)
predict() (flare.gp.GaussianProcess method)
(flare.mgp.mgp.MappedGaussianProcess method)
predict_efs() (flare.gp.GaussianProcess method)
predict_force_xyz() (flare.gp.GaussianProcess method)
predict_local_energy() (flare.gp.GaussianProcess method)
predict_local_energy_and_var() (flare.gp.GaussianProcess method)
predict_on_atom() (in module flare.predict)
predict_on_atom_efs() (in module flare.predict)
predict_on_atom_en() (in module flare.predict)
predict_on_atom_en_std() (in module flare.predict)
predict_on_structure() (in module flare.predict)
predict_on_structure_en() (in module flare.predict)
predict_on_structure_mgp() (in module flare.predict)
predict_on_structure_par() (in module flare.predict)
predict_on_structure_par_en() (in module flare.predict)
Q
q3_value_mc() (in module flare.utils.env_getarray)
q_value() (in module flare.kernels.kernels)
q_value_mc() (in module flare.kernels.kernels)
quadratic_cutoff() (in module flare.kernels.cutoffs)
quadratic_cutoff_bound() (in module flare.kernels.cutoffs)
queue_wrapper() (in module flare.gp_algebra)
R
raw_to_relative() (flare.struc.Structure static method)
relative_to_raw() (flare.struc.Structure static method)
remove_force_data() (flare.gp.GaussianProcess method)
rescale_temperature() (flare.ase.otf.ASE_OTF method)
(flare.otf.OTF method)
run() (flare.otf.OTF method)
run_dft() (flare.otf.OTF method)
(in module flare.dft_interface.vasp_util)
run_dft_en_par() (in module flare.dft_interface.cp2k_util)
(in module flare.dft_interface.qe_util)
run_dft_par() (in module flare.dft_interface.cp2k_util)
(in module flare.dft_interface.qe_util)
S
set_constraints() (flare.utils.parameter_helper.ParameterHelper method)
set_L_alpha() (flare.gp.GaussianProcess method)
set_logger() (in module flare.output)
set_parameters() (flare.utils.parameter_helper.ParameterHelper method)
set_values() (flare.mgp.splines_methods.CubicSpline method)
step() (flare.ase.nosehoover.NoseHoover method)
strip_and_split() (in module flare.otf_parser)
Structure (class in flare.struc)
structures_from_gpfa_output() (in module flare.gp_from_aimd)
subset_of_frame_by_element() (in module flare.utils.learner)
summarize_group() (flare.utils.parameter_helper.ParameterHelper method)
supercell_custom() (in module flare.utils.md_helper)
T
three_body() (in module flare.kernels.sc)
three_body_en() (in module flare.kernels.sc)
three_body_en_jit() (in module flare.kernels.sc)
three_body_force_en() (in module flare.kernels.sc)
three_body_force_en_jit() (in module flare.kernels.sc)
three_body_grad() (in module flare.kernels.sc)
three_body_grad_jit() (in module flare.kernels.sc)
three_body_jit() (in module flare.kernels.sc)
three_body_mc() (in module flare.kernels.mc_sephyps)
(in module flare.kernels.mc_simple)
three_body_mc_en() (in module flare.kernels.mc_sephyps)
(in module flare.kernels.mc_simple)
three_body_mc_en_jit() (in module flare.kernels.mc_simple)
three_body_mc_force_en() (in module flare.kernels.mc_sephyps)
(in module flare.kernels.mc_simple)
three_body_mc_force_en_jit() (in module flare.kernels.mc_sephyps)
(in module flare.kernels.mc_simple)
three_body_mc_force_en_sepcut_jit() (in module flare.kernels.mc_3b_sepcut)
three_body_mc_grad() (in module flare.kernels.mc_sephyps)
(in module flare.kernels.mc_simple)
three_body_mc_grad_jit() (in module flare.kernels.mc_sephyps)
(in module flare.kernels.mc_simple)
three_body_mc_grad_sepcut_jit() (in module flare.kernels.mc_3b_sepcut)
three_body_mc_jit() (in module flare.kernels.mc_simple)
three_body_se_jit() (in module flare.kernels.mc_simple)
three_body_sf_jit() (in module flare.kernels.mc_simple)
three_body_ss_jit() (in module flare.kernels.mc_simple)
to_pmg_structure() (flare.struc.Structure method)
to_xyz() (flare.otf_parser.OtfAnalysis method)
(flare.struc.Structure method)
train() (flare.gp.GaussianProcess method)
train_gp() (flare.otf.OTF method)
training_statistics (flare.gp.GaussianProcess attribute)
two_body() (in module flare.kernels.sc)
two_body_en() (in module flare.kernels.sc)
two_body_en_jit() (in module flare.kernels.sc)
two_body_force_en() (in module flare.kernels.sc)
two_body_force_en_jit() (in module flare.kernels.sc)
two_body_grad() (in module flare.kernels.sc)
two_body_grad_jit() (in module flare.kernels.sc)
two_body_jit() (in module flare.kernels.sc)
two_body_mc() (in module flare.kernels.mc_sephyps)
(in module flare.kernels.mc_simple)
two_body_mc_en() (in module flare.kernels.mc_sephyps)
(in module flare.kernels.mc_simple)
two_body_mc_en_jit() (in module flare.kernels.mc_sephyps)
(in module flare.kernels.mc_simple)
two_body_mc_force_en() (in module flare.kernels.mc_sephyps)
(in module flare.kernels.mc_simple)
two_body_mc_force_en_jit() (in module flare.kernels.mc_sephyps)
(in module flare.kernels.mc_simple)
two_body_mc_grad() (in module flare.kernels.mc_sephyps)
(in module flare.kernels.mc_simple)
two_body_mc_grad_jit() (in module flare.kernels.mc_sephyps)
(in module flare.kernels.mc_simple)
two_body_mc_jit() (in module flare.kernels.mc_sephyps)
(in module flare.kernels.mc_simple)
two_body_mc_stress_en_jit() (in module flare.kernels.mc_simple)
two_body_mc_stress_force_jit() (in module flare.kernels.mc_simple)
two_body_mc_stress_stress_jit() (in module flare.kernels.mc_simple)
two_plus_many_body() (in module flare.kernels.sc)
two_plus_many_body_en() (in module flare.kernels.sc)
two_plus_many_body_force_en() (in module flare.kernels.sc)
two_plus_many_body_grad() (in module flare.kernels.sc)
two_plus_many_body_mc() (in module flare.kernels.mc_simple)
two_plus_many_body_mc_en() (in module flare.kernels.mc_simple)
two_plus_many_body_mc_force_en() (in module flare.kernels.mc_simple)
two_plus_many_body_mc_grad() (in module flare.kernels.mc_simple)
two_plus_three_body() (in module flare.kernels.sc)
two_plus_three_body_grad() (in module flare.kernels.sc)
two_plus_three_body_mc() (in module flare.kernels.mc_sephyps)
(in module flare.kernels.mc_simple)
two_plus_three_body_mc_grad() (in module flare.kernels.mc_sephyps)
(in module flare.kernels.mc_simple)
two_plus_three_en() (in module flare.kernels.sc)
two_plus_three_force_en() (in module flare.kernels.sc)
two_plus_three_mc_en() (in module flare.kernels.mc_sephyps)
(in module flare.kernels.mc_simple)
two_plus_three_mc_force_en() (in module flare.kernels.mc_sephyps)
(in module flare.kernels.mc_simple)
two_plus_three_plus_many_body() (in module flare.kernels.sc)
two_plus_three_plus_many_body_en() (in module flare.kernels.sc)
two_plus_three_plus_many_body_force_en() (in module flare.kernels.sc)
two_plus_three_plus_many_body_grad() (in module flare.kernels.sc)
two_plus_three_plus_many_body_mc() (in module flare.kernels.mc_simple)
two_plus_three_plus_many_body_mc_en() (in module flare.kernels.mc_simple)
two_plus_three_plus_many_body_mc_force_en() (in module flare.kernels.mc_simple)
two_plus_three_plus_many_body_mc_grad() (in module flare.kernels.mc_simple)
two_three_many_body_mc() (in module flare.kernels.mc_sephyps)
two_three_many_body_mc_grad() (in module flare.kernels.mc_sephyps)
two_three_many_mc_en() (in module flare.kernels.mc_sephyps)
two_three_many_mc_force_en() (in module flare.kernels.mc_sephyps)
U
update_db() (flare.gp.GaussianProcess method)
update_gp() (flare.ase.otf.ASE_OTF method)
(flare.otf.OTF method)
update_L_alpha() (flare.gp.GaussianProcess method)
update_temperature() (flare.ase.otf.ASE_OTF method)
(flare.otf.OTF method)
V
vec_eval_cubic_spline() (in module flare.mgp.splines_methods)
W
wrap_positions() (flare.struc.Structure method)
write_gp_dft_comparison() (flare.output.Output method)
write_header() (flare.output.Output method)
write_hyps() (flare.output.Output method)
write_lmp_file() (flare.mgp.mgp.MappedGaussianProcess method)
write_md_config() (flare.output.Output method)
write_model() (flare.gp.GaussianProcess method)
(flare.mgp.mgp.MappedGaussianProcess method)
write_to_log() (flare.output.Output method)
write_xyz_config() (flare.output.Output method)
Z
Z_to_element() (in module flare.utils.element_coder)
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