Index

A | B | C | D | E | F | G | H | I | L | M | N | O | P | Q | R | S | T | U | V | W

A

absolute_coordinates() (built-in function)

accepts_parameters() (pysic.interactions.bondorder.BondOrderParameters method)

accepts_target_list() (pysic.interactions.bondorder.BondOrderParameters method)

(pysic.interactions.local.Potential method)
(pysic.interactions.local.ProductPotential method)

access_dataset() (pysic.utility.archive.Archive method)

add_bond() (pysic.utility.outliers.Structure method)

add_bond_order_factor() (built-in function)

add_bond_order_parameters() (pysic.interactions.bondorder.Coordinator method)

add_calculator() (pysic.calculator.Pysic method)

add_dataset_metadata() (pysic.utility.archive.Archive method)

add_group_metadata() (pysic.utility.archive.Archive method)

add_hydrogen_links() (pysic.interaction.Interaction method)

add_indices() (pysic.interactions.local.Potential method)

(pysic.interactions.local.ProductPotential method)

add_interaction() (pysic.hybridcalculator.HybridCalculator method)

add_observer() (pysic.charges.relaxation.ChargeRelaxation method)

add_potential() (built-in function)

(pysic.calculator.Pysic method)
(pysic.interaction.Interaction method)
(pysic.interactions.local.ProductPotential method)

add_subsystem() (pysic.hybridcalculator.HybridCalculator method)

add_symbols() (pysic.interactions.bondorder.BondOrderParameters method)

(pysic.interactions.local.Potential method)
(pysic.interactions.local.ProductPotential method)

add_tags() (pysic.interactions.local.Potential method)

(pysic.interactions.local.ProductPotential method)

all_atoms (built-in variable)

all_loads (built-in variable)
allocate_bond_order_factors() (built-in function)
allocate_bond_order_storage() (built-in function)
allocate_ewald_arrays() (built-in function)
allocate_potentials() (built-in function)
Angle (class in pysic.utility.outliers)
angle() (in module pysic.utility.outliers)
append_file() (in module pysic.utility.mpi)
Archive (class in pysic.utility.archive)
assign_bond_order_factor_indices() (built-in function)
assign_max_bond_order_factor_cutoff() (built-in function)
assign_max_potential_cutoff() (built-in function)
assign_neighbor_list() (built-in function)
assign_potential_indices() (built-in function)
atom (built-in variable)
atom_buffer (built-in variable)
atoms (built-in variable)
atoms_created (built-in variable)
atoms_ready() (pysic.core.CoreMirror method)

B

balance_loads() (built-in function)
bo_factors (built-in variable)
bo_gradients (built-in variable)
bo_scaling (built-in variable)
bo_sums (built-in variable)
bo_temp (built-in variable)
bond_descriptors_created (built-in variable)
bond_factors (built-in variable)
bond_factors_allocated (built-in variable)

bond_order_descriptor (built-in variable)

bond_order_descriptors (built-in variable)

bond_order_factor_affects_atom() (built-in function)

bond_order_factor_is_in_group() (built-in function)

bond_order_parameters (built-in variable)

bond_storage_allocated (built-in variable)

BondOrderParameters (class in pysic.interactions.bondorder)

build() (pysic.calculator.FastNeighborList method)

(pysic.interactions.compound.CompoundPotential method)

C

c_scale_index (built-in variable)

calculate_bond_order_factors() (built-in function)

(pysic.interactions.bondorder.Coordinator method)

calculate_bond_order_gradients() (built-in function)

calculate_bond_order_gradients_of_factor() (built-in function)

calculate_derived_parameters_bond_bending() (built-in function)

calculate_derived_parameters_charge_exp() (built-in function)

calculate_derived_parameters_dihedral() (built-in function)

calculate_electronegativities() (built-in function)

(pysic.calculator.Pysic method)

calculate_energy() (built-in function)

(pysic.calculator.Pysic method)

calculate_ewald_electronegativities() (built-in function)

calculate_ewald_energy() (built-in function)

calculate_ewald_forces() (built-in function)

calculate_forces() (built-in function)

(pysic.calculator.Pysic method)
(pysic.hybridcalculator.HybridCalculator method)

calculate_link_atom_correction_energy() (pysic.interaction.InteractionInternal method)

calculate_link_atom_correction_forces() (pysic.interaction.InteractionInternal method)

calculate_potential_energy() (pysic.hybridcalculator.HybridCalculator method)

calculate_stress() (pysic.calculator.Pysic method)

calculate_subsystem_interaction_charges() (pysic.hybridcalculator.HybridCalculator method)

calculate_uncorrected_interaction_energy() (pysic.interaction.InteractionInternal method)

calculate_uncorrected_interaction_energy_pbc() (pysic.interaction.InteractionInternal method)

calculate_uncorrected_interaction_forces() (pysic.interaction.InteractionInternal method)

calculate_uncorrected_interaction_forces_pbc() (pysic.interaction.InteractionInternal method)

calculation_required() (pysic.calculator.Pysic method)

(pysic.hybridcalculator.HybridCalculator method)

call_observers() (pysic.charges.relaxation.ChargeRelaxation method)

cd() (in module pysic.utility.mpi)

cell (built-in variable)

Cell (class in pysic.utility.geometry)

cell_ready() (pysic.core.CoreMirror method)

char2int() (in module pysic.utility.f2py)

charge_relaxation() (pysic.charges.relaxation.ChargeRelaxation method)

ChargeRelaxation (class in pysic.charges.relaxation)

charges_ready() (pysic.core.CoreMirror method)

check_exclude() (pysic.interactions.comb.CombPotential method)

check_s_factor_array_allocation() (built-in function)

check_subsystem_indices() (pysic.hybridcalculator.HybridCalculator method)

check_subsystem_overlap() (pysic.hybridcalculator.HybridCalculator method)

clear_bond_order_factor_characterizers() (built-in function)

clear_observers() (pysic.charges.relaxation.ChargeRelaxation method)

clear_potential_characterizers() (built-in function)

clear_potential_multipliers() (built-in function)

clear_relaxation_pipe() (pysic.charges.relaxation.ChargeRelaxation method)

close_loadmonitor() (built-in function)

CombPotential (class in pysic.interactions.comb)

CompoundPotential (class in pysic.interactions.compound)

coordination_index (built-in variable)

Coordinator (class in pysic.interactions.bondorder)

core (pysic.calculator.Pysic attribute)

core_add_bond_order_factor() (built-in function)

core_add_bond_order_forces() (built-in function)

core_add_pair_bond_order_forces() (built-in function)

core_add_potential() (built-in function)

core_allocate_bond_order_factors() (built-in function)

core_allocate_bond_order_storage() (built-in function)

core_allocate_potentials() (built-in function)

core_assign_bond_order_factor_indices() (built-in function)

core_assign_potential_indices() (built-in function)

core_build_neighbor_lists() (built-in function)

core_calculate_bond_order_factors() (built-in function)

core_calculate_bond_order_gradients() (built-in function)

core_calculate_bond_order_gradients_of_factor() (built-in function)

core_calculate_electronegativities() (built-in function)

core_calculate_energy() (built-in function)

core_calculate_forces() (built-in function)

core_calculate_pair_bond_order_factor() (built-in function)

core_calculate_pair_bond_order_gradients() (built-in function)

core_clear_atoms() (built-in function)

core_clear_bond_order_factors() (built-in function)

core_clear_bond_order_storage() (built-in function)

core_clear_ewald_arrays() (built-in function)

core_clear_potential_multipliers() (built-in function)

core_clear_potentials() (built-in function)

core_create_cell() (built-in function)

core_create_neighbor_list() (built-in function)

core_create_space_partitioning() (built-in function)

core_debug_dump() (built-in function)

core_empty_bond_order_gradient_storage() (built-in function)

core_empty_bond_order_storage() (built-in function)

core_evaluate_local_doublet() (built-in function)

core_evaluate_local_doublet_electronegativities() (built-in function)

core_evaluate_local_doublet_electronegativities_B() (built-in function)

core_evaluate_local_doublet_energy() (built-in function)

core_evaluate_local_doublet_energy_B() (built-in function)

core_evaluate_local_doublet_forces() (built-in function)

core_evaluate_local_doublet_forces_B() (built-in function)

core_evaluate_local_quadruplet() (built-in function)

core_evaluate_local_quadruplet_B() (built-in function)

core_evaluate_local_singlet() (built-in function)

core_evaluate_local_triplet() (built-in function)

core_evaluate_local_triplet_B() (built-in function)

core_fill_bond_order_storage() (built-in function)

core_generate_atoms() (built-in function)

core_get_bond_order_factor_of_atom() (built-in function)

core_get_bond_order_factors() (built-in function)

core_get_bond_order_gradients() (built-in function)

core_get_bond_order_sums() (built-in function)

core_get_cell_vectors() (built-in function)

core_get_ewald_energy() (built-in function)

core_get_neighbor_list_of_atom() (built-in function)

core_get_number_of_atoms() (built-in function)

core_get_number_of_neighbors() (built-in function)

core_initialization_is_forced() (pysic.calculator.Pysic method)

core_loop_over_local_interactions() (built-in function)

core_post_process_bond_order_factors() (built-in function)

core_post_process_bond_order_gradients() (built-in function)

core_post_process_bond_order_gradients_of_factor() (built-in function)

core_post_process_pair_bond_order_factor() (built-in function)

core_post_process_pair_bond_order_gradients() (built-in function)

core_release_all_memory() (built-in function)

core_set_ewald_parameters() (built-in function)

core_update_atom_charges() (built-in function)

core_update_atom_coordinates() (built-in function)

CoreMirror (class in pysic.core)

coulomb_summation_ready() (pysic.core.CoreMirror method)

CoulombSummation (class in pysic.interactions.coulomb)

cpu_id (built-in variable)

cpu_id() (in module pysic.utility.mpi)

create_atoms() (built-in function)

create_bond_order_factor() (built-in function)

create_bond_order_factor_characterizer_coordination() (built-in function)

create_bond_order_factor_characterizer_power() (built-in function)

create_bond_order_factor_characterizer_scaler_1() (built-in function)

create_bond_order_factor_characterizer_scaler_sqrt() (built-in function)

create_bond_order_factor_characterizer_scaler_table() (built-in function)

create_bond_order_factor_characterizer_table() (built-in function)

create_bond_order_factor_characterizer_tersoff() (built-in function)

create_bond_order_factor_characterizer_triplet() (built-in function)

create_bond_order_factor_list() (built-in function)

create_cell() (built-in function)

create_dataset() (pysic.utility.archive.Archive method)

create_neighbor_list() (built-in function)

create_neighbor_lists() (pysic.calculator.Pysic method)

(pysic.utility.outliers.Structure method)

create_potential() (built-in function)

create_potential_characterizer_bond_bending() (built-in function)

create_potential_characterizer_buckingham() (built-in function)

create_potential_characterizer_charge_exp() (built-in function)

create_potential_characterizer_charge_pair() (built-in function)

create_potential_characterizer_charge_pair_abs() (built-in function)

create_potential_characterizer_charge_self() (built-in function)

create_potential_characterizer_constant_force() (built-in function)

create_potential_characterizer_constant_potential() (built-in function)

create_potential_characterizer_dihedral() (built-in function)

create_potential_characterizer_exp() (built-in function)

create_potential_characterizer_LJ() (built-in function)

create_potential_characterizer_power() (built-in function)

create_potential_characterizer_shift() (built-in function)

create_potential_characterizer_spring() (built-in function)

create_potential_characterizer_step() (built-in function)

create_potential_characterizer_table() (built-in function)

create_potential_list() (built-in function)

create_subgroup() (pysic.utility.archive.Archive method)

cross() (built-in function)

D

data() (pysic.utility.archive.Archive method)

deallocate_ewald_arrays() (built-in function)

define_elements() (pysic.interactions.comb.CombPotential method)

(pysic.interactions.compound.CompoundPotential method)
(pysic.interactions.suttonchen.SuttonChenPotential method)

delete_current_dataset() (pysic.utility.archive.Archive method)

delete_dataset() (pysic.utility.archive.Archive method)

delete_group() (pysic.utility.archive.Archive method)

delete_subgroup() (pysic.utility.archive.Archive method)

describe() (pysic.interactions.compound.CompoundPotential method)

(pysic.interactions.local.Potential method)
(pysic.interactions.suttonchen.SuttonChenPotential method)

description_of_bond_order_factor() (built-in function)

description_of_potential() (built-in function)

(in module pysic)

descriptions_of_parameters() (in module pysic)
descriptions_of_parameters_of_bond_order_factor() (built-in function)
descriptions_of_parameters_of_potential() (built-in function)
descriptors_created (built-in variable)
display() (pysic.utility.error.Warning method)
Distance (class in pysic.utility.outliers)
distribute_mpi() (built-in function)
divide_cell() (built-in function)
dot() (built-in function)

E

electronegativity_evaluation_index (built-in variable)
enable_cell_optimization() (pysic.subsystem.SubSystem method)
enable_charge_calculation() (pysic.subsystem.SubSystem method)
enable_comb_potential() (pysic.interaction.Interaction method)
enable_coulomb_potential() (pysic.interaction.Interaction method)
energy_evaluation_index (built-in variable)
error() (in module pysic.utility.error)
estimate_ewald_parameters() (in module pysic.interactions.coulomb)
evaluate_bond_order_factor() (built-in function)
evaluate_bond_order_factor_coordination() (built-in function)
evaluate_bond_order_factor_power() (built-in function)
evaluate_bond_order_factor_table() (built-in function)
evaluate_bond_order_factor_triplet() (built-in function)
evaluate_bond_order_gradient() (built-in function)
evaluate_bond_order_gradient_coordination() (built-in function)
evaluate_bond_order_gradient_power() (built-in function)
evaluate_bond_order_gradient_table() (built-in function)
evaluate_bond_order_gradient_triplet() (built-in function)
evaluate_electronegativity() (built-in function)
evaluate_electronegativity_charge_exp() (built-in function)
evaluate_electronegativity_charge_pair() (built-in function)
evaluate_electronegativity_charge_pair_abs() (built-in function)
evaluate_electronegativity_charge_self() (built-in function)
evaluate_electronegativity_component() (built-in function)
evaluate_energy() (built-in function)
evaluate_energy_bond_bending() (built-in function)
evaluate_energy_buckingham() (built-in function)
evaluate_energy_charge_exp() (built-in function)
evaluate_energy_charge_pair() (built-in function)
evaluate_energy_charge_pair_abs() (built-in function)
evaluate_energy_charge_self() (built-in function)
evaluate_energy_component() (built-in function)
evaluate_energy_constant_force() (built-in function)
evaluate_energy_constant_potential() (built-in function)
evaluate_energy_dihedral() (built-in function)
evaluate_energy_exp() (built-in function)
evaluate_energy_LJ() (built-in function)
evaluate_energy_power() (built-in function)
evaluate_energy_shift() (built-in function)
evaluate_energy_spring() (built-in function)
evaluate_energy_step() (built-in function)

evaluate_energy_table() (built-in function)
evaluate_ewald (built-in variable)
evaluate_force_bond_bending() (built-in function)
evaluate_force_buckingham() (built-in function)
evaluate_force_component() (built-in function)
evaluate_force_constant_force() (built-in function)
evaluate_force_constant_potential() (built-in function)
evaluate_force_dihedral() (built-in function)
evaluate_force_exp() (built-in function)
evaluate_force_LJ() (built-in function)
evaluate_force_power() (built-in function)
evaluate_force_shift() (built-in function)
evaluate_force_spring() (built-in function)
evaluate_force_step() (built-in function)
evaluate_force_table() (built-in function)
evaluate_forces() (built-in function)
evaluate_pair_bond_order_factor() (built-in function)
evaluate_pair_bond_order_factor_tersoff() (built-in function)
evaluate_pair_bond_order_gradient() (built-in function)
evaluate_pair_bond_order_gradient_tersoff() (built-in function)
ewald_allocated (built-in variable)
ewald_arrays_allocated (built-in variable)
ewald_cutoff (built-in variable)
ewald_epsilon (built-in variable)
ewald_forces (built-in variable)
ewald_k_cutoffs (built-in variable)
ewald_k_radius (built-in variable)
ewald_scaler (built-in variable)
ewald_sigma (built-in variable)
ewald_sum_forces (built-in variable)
ewald_tmp_enegs (built-in variable)
examine_atoms() (built-in function)
examine_bond_order_factors() (built-in function)
examine_cell() (built-in function)
examine_potentials() (built-in function)
exclude() (pysic.interactions.comb.CombPotential method)
exclude_all() (pysic.interactions.comb.CombPotential method)
expand_neighbor_storage() (built-in function)
expand_subcell_atom_capacity() (built-in function)
expand_symbols_string() (in module pysic.utility.convenience)
expand_symbols_table() (in module pysic.utility.convenience)

F

FastNeighborList (class in pysic.calculator)

find_subcell_for_atom() (built-in function)

finish_mpi() (built-in function)

(in module pysic)
(in module pysic.utility.mpi)

force_core_initialization() (pysic.calculator.Pysic method)
force_evaluation_index (built-in variable)
full_system_set() (pysic.hybridcalculator.HybridCalculator method)

G

generate_atoms() (built-in function)

generate_neighbor_lists() (built-in function)

generate_subsystem_indices() (pysic.hybridcalculator.HybridCalculator method)

generate_supercell() (built-in function)

genrand_init() (built-in function)

genrand_real1() (built-in function)

genrand_real2() (built-in function)

get_absolute_coordinates() (pysic.utility.geometry.Cell method)

get_all_angles() (pysic.utility.outliers.Structure method)

get_all_distances() (pysic.utility.outliers.Structure method)

get_atoms() (pysic.calculator.Pysic method)

(pysic.charges.relaxation.ChargeRelaxation method)
(pysic.core.CoreMirror method)
(pysic.hybridcalculator.HybridCalculator method)

get_bond_descriptor() (built-in function)

get_bond_length() (pysic.utility.outliers.Structure method)

get_bond_order_factors() (pysic.interactions.bondorder.Coordinator method)

get_bond_order_gradients() (pysic.interactions.bondorder.Coordinator method)

get_bond_order_gradients_of_factor() (pysic.interactions.bondorder.Coordinator method)

get_bond_order_parameters() (pysic.interactions.bondorder.Coordinator method)

get_bond_order_type() (pysic.interactions.bondorder.BondOrderParameters method)

get_calculator() (pysic.charges.relaxation.ChargeRelaxation method)

get_calculators() (pysic.calculator.Pysic method)

get_cell_vectors() (built-in function)

get_charge_relaxation() (pysic.calculator.Pysic method)

get_charges() (pysic.calculator.Pysic method)

get_colors() (pysic.hybridcalculator.HybridCalculator method)

get_contents() (pysic.utility.archive.Archive method)

get_coordinator() (pysic.interactions.local.Potential method)

(pysic.interactions.local.ProductPotential method)

get_coulomb_summation() (pysic.calculator.Pysic method)

get_cpu_id() (built-in function)

(in module pysic)
(in module pysic.utility.mpi)

get_cutoff() (pysic.interactions.bondorder.BondOrderParameters method)

(pysic.interactions.local.Potential method)
(pysic.interactions.local.ProductPotential method)

get_cutoff_margin() (pysic.interactions.bondorder.BondOrderParameters method)

(pysic.interactions.local.Potential method)
(pysic.interactions.local.ProductPotential method)

get_dataset() (pysic.utility.archive.Archive method)

get_dataset_metadata() (pysic.utility.archive.Archive method)

get_dataset_name() (pysic.utility.archive.Archive method)

get_description_of_bond_order_factor() (built-in function)

get_description_of_potential() (built-in function)

get_descriptions_of_parameters_of_bond_order_factor() (built-in function)

get_descriptions_of_parameters_of_potential() (built-in function)

get_descriptor() (built-in function)

get_different_indices() (pysic.interactions.local.Potential method)

(pysic.interactions.local.ProductPotential method)

get_different_symbols() (pysic.interactions.bondorder.BondOrderParameters method)

(pysic.interactions.local.Potential method)
(pysic.interactions.local.ProductPotential method)

get_different_tags() (pysic.interactions.local.Potential method)

(pysic.interactions.local.ProductPotential method)

get_distance() (pysic.utility.geometry.Cell method)

get_distances() (pysic.utility.outliers.Structure method)

get_distributions() (in module pysic.utility.outliers)

get_electronegativities() (pysic.calculator.Pysic method)

get_electronegativity_differences() (pysic.calculator.Pysic method)

get_elements() (pysic.interactions.compound.CompoundPotential method)

get_ewald_energy() (built-in function)

get_forces() (pysic.calculator.Pysic method)

(pysic.hybridcalculator.HybridCalculator method)
(pysic.subsystem.SubSystemInternal method)

get_group() (pysic.utility.archive.Archive method)

get_group_index() (pysic.interactions.bondorder.Coordinator method)

get_group_metadata() (pysic.utility.archive.Archive method)

get_group_name() (pysic.utility.archive.Archive method)

get_index_of_bond_order_factor() (built-in function)

get_index_of_parameter_of_bond_order_factor() (built-in function)

get_index_of_parameter_of_potential() (built-in function)

get_index_of_potential() (built-in function)

get_indices() (pysic.interactions.local.Potential method)

(pysic.interactions.local.ProductPotential method)

get_individual_cutoffs() (pysic.calculator.Pysic method)

get_interaction_energy() (pysic.interaction.InteractionInternal method)

get_interaction_forces() (pysic.interaction.InteractionInternal method)

get_level() (pysic.interactions.bondorder.BondOrderParameters method)

get_level_of_bond_order_factor() (built-in function)

get_level_of_bond_order_factor_index() (built-in function)

get_log_likelihoods() (in module pysic.utility.outliers)

get_mpi_list_of_atoms() (built-in function)

get_names_of_parameters_of_bond_order_factor() (built-in function)

get_names_of_parameters_of_potential() (built-in function)

get_neighbor_distances() (pysic.calculator.FastNeighborList method)

get_neighbor_list() (pysic.calculator.Pysic method)

get_neighbor_list_of_atom() (built-in function)

get_neighbor_lists() (pysic.calculator.Pysic method)

get_neighbor_separations() (pysic.calculator.FastNeighborList method)

get_neighbors() (pysic.calculator.FastNeighborList method)

(pysic.utility.outliers.Structure method)

get_number_of_atoms() (built-in function)

get_number_of_bond_order_factors() (built-in function)

get_number_of_cpus() (built-in function)

(in module pysic)
(in module pysic.utility.mpi)

get_number_of_neighbors_of_atom() (built-in function)

get_number_of_parameters() (pysic.interactions.bondorder.BondOrderParameters method)

(pysic.interactions.compound.CompoundPotential method)
(pysic.interactions.local.Potential method)

get_number_of_parameters_of_bond_order_factor() (built-in function)

get_number_of_parameters_of_potential() (built-in function)

get_number_of_potentials() (built-in function)

get_number_of_targets() (pysic.interactions.bondorder.BondOrderParameters method)

(pysic.interactions.local.Potential method)
(pysic.interactions.local.ProductPotential method)

get_number_of_targets_of_bond_order_factor() (built-in function)

get_number_of_targets_of_bond_order_factor_index() (built-in function)

get_number_of_targets_of_potential() (built-in function)

get_number_of_targets_of_potential_index() (built-in function)

get_numerical_bond_order_gradient() (pysic.calculator.Pysic method)

get_numerical_electronegativity() (pysic.calculator.Pysic method)

get_numerical_energy_gradient() (pysic.calculator.Pysic method)

get_optimal_splitting() (built-in function)

get_parameter_names() (pysic.interactions.bondorder.BondOrderParameters method)

(pysic.interactions.local.Potential method)

get_parameter_value() (pysic.interactions.bondorder.BondOrderParameters method)

(pysic.interactions.comb.CombPotential method)
(pysic.interactions.local.Potential method)

get_parameter_values() (pysic.interactions.bondorder.BondOrderParameters method)

(pysic.interactions.local.Potential method)

get_parameters() (pysic.charges.relaxation.ChargeRelaxation method)

(pysic.interactions.coulomb.CoulombSummation method)

get_parameters_as_list() (pysic.interactions.bondorder.BondOrderParameters method)

get_potential_energy() (pysic.calculator.Pysic method)

(pysic.hybridcalculator.HybridCalculator method)
(pysic.subsystem.SubSystemInternal method)

get_potential_type() (pysic.interactions.local.Potential method)

get_potentials() (pysic.calculator.Pysic method)

(pysic.interactions.local.Potential method)
(pysic.interactions.local.ProductPotential method)

get_pseudo_density() (pysic.subsystem.SubSystemInternal method)

get_realspace_cutoff() (pysic.interactions.coulomb.CoulombSummation method)

get_relative_coordinates() (pysic.utility.geometry.Cell method)

get_relaxation() (pysic.charges.relaxation.ChargeRelaxation method)

get_relaxation_pipe() (pysic.charges.relaxation.ChargeRelaxation method)

get_scaling_factors() (pysic.interactions.coulomb.CoulombSummation method)

get_separation() (pysic.utility.geometry.Cell method)

get_separations() (pysic.utility.outliers.Structure method)

get_soft_cutoff() (pysic.interactions.bondorder.BondOrderParameters method)

(pysic.interactions.local.Potential method)
(pysic.interactions.local.ProductPotential method)

get_stress() (pysic.calculator.Pysic method)

(pysic.hybridcalculator.HybridCalculator method)

get_subsystem() (pysic.hybridcalculator.HybridCalculator method)

get_subsystem_indices() (pysic.hybridcalculator.HybridCalculator method)

get_subsystem_pseudo_density() (pysic.hybridcalculator.HybridCalculator method)

get_summation() (pysic.interactions.coulomb.CoulombSummation method)

get_symbols() (pysic.interactions.bondorder.BondOrderParameters method)

(pysic.interactions.local.Potential method)
(pysic.interactions.local.ProductPotential method)

get_system() (pysic.utility.archive.Archive method)

get_tags() (pysic.interactions.local.Potential method)

(pysic.interactions.local.ProductPotential method)

get_unsubsystemized_atoms() (pysic.hybridcalculator.HybridCalculator method)

get_wrapped_coordinates() (pysic.utility.geometry.Cell method)

group() (pysic.utility.archive.Archive method)

group_index_save_slot (built-in variable)

H

HybridCalculator (class in pysic.hybridcalculator)

I

identical_atoms() (pysic.hybridcalculator.HybridCalculator method)

include() (pysic.interactions.comb.CombPotential method)

include_all() (pysic.interactions.comb.CombPotential method)

includes_scaling() (pysic.interactions.bondorder.BondOrderParameters method)

index_of_parameter() (in module pysic)

initialize_bond_order_factor_characterizers() (built-in function)

initialize_fortran_core() (pysic.calculator.Pysic method)

initialize_interaction() (pysic.hybridcalculator.HybridCalculator method)

initialize_load() (built-in function)

initialize_parameters() (pysic.charges.relaxation.ChargeRelaxation method)

(pysic.interactions.coulomb.CoulombSummation method)

initialize_potential_characterizers() (built-in function)

initialize_subsystem() (pysic.hybridcalculator.HybridCalculator method)

initialize_system() (pysic.hybridcalculator.HybridCalculator method)

int2char() (in module pysic.utility.f2py)

int2str() (built-in function)

Interaction (class in pysic.interaction)

InteractionInternal (class in pysic.interaction)

interactions (built-in variable)

ints2str() (in module pysic.utility.f2py)

InvalidCoordinatorError

InvalidParametersError

InvalidPotentialError

InvalidRelaxationError

InvalidSummationError

is_bond_order_factor() (built-in function)

(in module pysic)

is_charge_relaxation() (in module pysic)

is_excluded() (pysic.interactions.comb.CombPotential method)

is_included() (pysic.interactions.comb.CombPotential method)

is_master() (in module pysic.utility.mpi)

is_multiplier() (pysic.interactions.local.Potential method)

(pysic.interactions.local.ProductPotential method)

is_my_atom (built-in variable)

is_potential() (built-in function)

(in module pysic)

is_valid() (pysic.subsystem.SubSystem method)

is_valid_bond_order_factor() (built-in function)

(in module pysic)

is_valid_charge_relaxation() (in module pysic)

is_valid_potential() (built-in function)

(in module pysic)

L

label_length (built-in variable)

level_of_bond_order_factor() (built-in function)

list() (pysic.utility.archive.Archive method)

list_atoms() (built-in function)

list_bond_order_factors() (built-in function)

(in module pysic)

list_bonds() (built-in function)

list_cell() (built-in function)

list_excludes() (pysic.interactions.comb.CombPotential method)

list_interactions() (built-in function)

list_possible_excludes() (pysic.interactions.comb.CombPotential method)

list_potentials() (built-in function)

(in module pysic)

list_valid_bond_order_factors() (built-in function)

(in module pysic)

list_valid_potentials() (built-in function)

(in module pysic)

load_length (built-in variable)

loadout (built-in variable)

loads_mask (built-in variable)

LockedCoreError

M

MissingAtomsError
MissingNeighborsError
mkdir() (in module pysic.utility.mpi)
mono_const_index (built-in variable)
mono_none_index (built-in variable)
mono_qself_index (built-in variable)
move() (pysic.utility.archive.Archive method)
move_to_group() (pysic.utility.archive.Archive method)
move_to_parent_group() (pysic.utility.archive.Archive method)
move_to_root_group() (pysic.utility.archive.Archive method)
mpi_atoms_allocated (built-in variable)
mpi_barrier() (in module pysic.utility.mpi)
mpi_distribute() (built-in function)

mpi_finish() (built-in function)
mpi_initialize() (built-in function)
mpi_master_bcast_int() (built-in function)
mpi_stack() (built-in function)
mpi_sync() (built-in function)
mpi_wall_clock() (built-in function)
mpistat (built-in variable)
mpistatus (built-in variable)
mprint() (in module pysic.utility.mpi)
multipliers (built-in variable)
my_atoms (built-in variable)
my_load (built-in variable)

N

n_bond_factors (built-in variable)
n_bond_order_types (built-in variable)
n_cpus (built-in variable)
n_interactions (built-in variable)
n_max_params (built-in variable)
n_multi (built-in variable)
n_nbs (built-in variable)
n_potential_types (built-in variable)
n_saved_bond_order_factors (built-in variable)
names_of_parameters() (in module pysic)
names_of_parameters_of_bond_order_factor() (built-in function)
names_of_parameters_of_potential() (built-in function)
neighbor_list (built-in variable)
neighbor_lists_expanded() (pysic.calculator.Pysic method)

neighbor_lists_ready() (pysic.core.CoreMirror method)
neighbor_marginal (pysic.calculator.FastNeighborList attribute)
no_name (built-in variable)
norm_quaternion() (built-in function)
norm_tolerance (built-in variable)
number_of_atoms (built-in variable)
number_of_bond_order_factors() (built-in function)
number_of_parameters() (in module pysic)
number_of_parameters_of_bond_order_factor() (built-in function)
number_of_parameters_of_potential() (built-in function)
number_of_potentials() (built-in function)
number_of_targets() (in module pysic)
number_of_targets_of_bond_order_factor() (built-in function)
number_of_targets_of_potential() (built-in function)

O

open_loadmonitor() (built-in function)

optimize_cell() (pysic.subsystem.SubSystemInternal method)

P

pad_string() (built-in function)
pair_buck_index (built-in variable)
pair_exp_index (built-in variable)
pair_lj_index (built-in variable)
pair_power_index (built-in variable)
pair_qabs_index (built-in variable)
pair_qexp_index (built-in variable)
pair_qpair_index (built-in variable)
pair_shift_index (built-in variable)
pair_spring_index (built-in variable)
pair_step_index (built-in variable)
pair_table_index (built-in variable)
param_name_length (built-in variable)
param_note_length (built-in variable)
pi (built-in variable)
pick() (built-in function)
plot_abs_force_on_line() (in module pysic.utility.plot)
plot_abs_force_on_plane() (in module pysic.utility.plot)
plot_energy_on_line() (in module pysic.utility.plot)
plot_energy_on_plane() (in module pysic.utility.plot)
plot_force_component_on_plane() (in module pysic.utility.plot)
plot_tangent_force_on_line() (in module pysic.utility.plot)
plot_tangent_force_on_plane() (in module pysic.utility.plot)
post_process_bond_order_factor() (built-in function)
post_process_bond_order_factor_scaler_1() (built-in function)
post_process_bond_order_factor_scaler_sqrt() (built-in function)
post_process_bond_order_factor_scaler_table() (built-in function)
post_process_bond_order_factor_tersoff() (built-in function)
post_process_bond_order_gradient() (built-in function)
post_process_bond_order_gradient_scaler_1() (built-in function)
post_process_bond_order_gradient_scaler_sqrt() (built-in function)
post_process_bond_order_gradient_scaler_table() (built-in function)
post_process_bond_order_gradient_tersoff() (built-in function)
pot_name_length (built-in variable)
pot_note_length (built-in variable)

potential (built-in variable)
Potential (class in pysic.interactions.local)
potential_affects_atom() (built-in function)
potential_descriptor (built-in variable)
potential_descriptors (built-in variable)
potentials_allocated (built-in variable)
potentials_ready() (pysic.core.CoreMirror method)
power_index (built-in variable)
print_energy_summary() (pysic.hybridcalculator.HybridCalculator method)
print_force_summary() (pysic.hybridcalculator.HybridCalculator method)
print_interaction_charge_summary() (pysic.hybridcalculator.HybridCalculator method)
print_time_summary() (pysic.hybridcalculator.HybridCalculator method)
ProductPotential (class in pysic.interactions.local)
Pysic (class in pysic.calculator)
pysic (module)
pysic.calculator (module)
pysic.charges (module)
pysic.charges.relaxation (module)
pysic.core (module)
pysic.interactions (module)
pysic.interactions.bondorder (module)
pysic.interactions.coulomb (module)
pysic.interactions.local (module)
pysic.pysic_fortran (module)
pysic.pysic_fortran.pysic_interface (module)
pysic.utility (module)
pysic.utility.archive (module)
pysic.utility.convenience (module)
pysic.utility.debug (module)
pysic.utility.error (module)
pysic.utility.f2py (module)
pysic.utility.geometry (module)
pysic.utility.mpi (module)
pysic.utility.outliers (module)
pysic.utility.plot (module)

Q

q2angle() (built-in function)
q2axis() (built-in function)
q2matrix() (built-in function)
qconj() (built-in function)
qdiv() (built-in function)
qinv() (built-in function)
qminus() (built-in function)

qnorm() (built-in function)
qplus() (built-in function)
qprod() (built-in function)
qtimes() (built-in function)
qtimesB() (built-in function)
qtrn (built-in variable)
quad_dihedral_index (built-in variable)

R

read_table() (built-in function)
record_load() (built-in function)
relative_coordinates() (built-in function)
relaxation_modes (pysic.charges.relaxation.ChargeRelaxation attribute)
relaxation_parameter_descriptions (pysic.charges.relaxation.ChargeRelaxation attribute)
relaxation_parameters (pysic.charges.relaxation.ChargeRelaxation attribute)
release() (built-in function)
remove() (pysic.interactions.compound.CompoundPotential method)

remove_calculator() (pysic.calculator.Pysic method)
remove_dataset_metadata() (pysic.utility.archive.Archive method)
remove_group_metadata() (pysic.utility.archive.Archive method)
remove_potential() (pysic.calculator.Pysic method)
rot2q() (built-in function)
rotate_a() (built-in function)
rotate_au() (built-in function)
rotate_q() (built-in function)

S

s_factor (built-in variable)

s_factor_allocated (built-in variable)

saved_bond_order_factors (built-in variable)

saved_bond_order_gradients (built-in variable)

saved_bond_order_sums (built-in variable)

saved_bond_order_virials (built-in variable)

separation_vector() (built-in function)

set_atomic_momenta() (pysic.core.CoreMirror method)

set_atomic_positions() (pysic.core.CoreMirror method)

set_atoms() (pysic.calculator.Pysic method)

(pysic.charges.relaxation.ChargeRelaxation method)
(pysic.core.CoreMirror method)
(pysic.hybridcalculator.HybridCalculator method)
(pysic.subsystem.SubSystem method)

set_bond_order_parameters() (pysic.interactions.bondorder.Coordinator method)

set_calculator() (pysic.charges.relaxation.ChargeRelaxation method)

(pysic.interactions.comb.CombPotential method)
(pysic.subsystem.SubSystem method)

set_cell() (pysic.core.CoreMirror method)

set_charge_relaxation() (pysic.calculator.Pysic method)

set_charges() (pysic.core.CoreMirror method)

set_coordinator() (pysic.interactions.local.Potential method)

(pysic.interactions.local.ProductPotential method)

set_core() (pysic.calculator.Pysic method)

set_coulomb() (pysic.core.CoreMirror method)

set_coulomb_summation() (pysic.calculator.Pysic method)

set_cutoff() (pysic.interactions.bondorder.BondOrderParameters method)

(pysic.interactions.local.Potential method)
(pysic.interactions.local.ProductPotential method)

set_cutoff_margin() (pysic.interactions.bondorder.BondOrderParameters method)

(pysic.interactions.local.Potential method)
(pysic.interactions.local.ProductPotential method)

set_cutoffs() (pysic.calculator.Pysic method)

set_density_symbols() (pysic.interactions.suttonchen.SuttonChenPotential method)

set_ewald() (pysic.interactions.comb.CombPotential method)

set_ewald_parameters() (built-in function)

set_group_index() (pysic.interactions.bondorder.Coordinator method)

set_indices() (pysic.interactions.local.Potential method)

(pysic.interactions.local.ProductPotential method)

set_link_atom_correction() (pysic.interaction.Interaction method)

set_neighbor_lists() (pysic.core.CoreMirror method)

set_parameter_value() (pysic.charges.relaxation.ChargeRelaxation method)

(pysic.interactions.bondorder.BondOrderParameters method)
(pysic.interactions.comb.CombPotential method)
(pysic.interactions.coulomb.CoulombSummation method)
(pysic.interactions.local.Potential method)

set_parameter_values() (pysic.charges.relaxation.ChargeRelaxation method)

(pysic.interactions.bondorder.BondOrderParameters method)
(pysic.interactions.coulomb.CoulombSummation method)
(pysic.interactions.local.Potential method)

set_parameters() (pysic.charges.relaxation.ChargeRelaxation method)

(pysic.interactions.bondorder.BondOrderParameters method)
(pysic.interactions.coulomb.CoulombSummation method)
(pysic.interactions.local.Potential method)

set_potential_type() (pysic.interactions.compound.CompoundPotential method)

set_potentials() (pysic.calculator.Pysic method)

(pysic.core.CoreMirror method)
(pysic.interaction.Interaction method)
(pysic.interactions.local.ProductPotential method)

set_relaxation() (pysic.charges.relaxation.ChargeRelaxation method)

set_relaxation_pipe() (pysic.charges.relaxation.ChargeRelaxation method)

set_scaling_factors() (pysic.interactions.coulomb.CoulombSummation method)

set_soft_cutoff() (pysic.interactions.bondorder.BondOrderParameters method)

(pysic.interactions.local.Potential method)
(pysic.interactions.local.ProductPotential method)

set_summation() (pysic.interactions.coulomb.CoulombSummation method)

set_symbols() (pysic.interactions.bondorder.BondOrderParameters method)

(pysic.interactions.local.Potential method)
(pysic.interactions.local.ProductPotential method)

set_tags() (pysic.interactions.local.Potential method)

(pysic.interactions.local.ProductPotential method)

set_warning_level() (in module pysic.utility.error)

setup_comb_potential() (pysic.interaction.InteractionInternal method)

setup_coulomb_potential() (pysic.interaction.InteractionInternal method)

setup_hydrogen_links() (pysic.interaction.InteractionInternal method)

setup_potentials() (pysic.interaction.InteractionInternal method)

smoothening_derivative() (built-in function)

smoothening_factor() (built-in function)

smoothening_gradient() (built-in function)

sqrt_scale_index (built-in variable)

start_bond_order_factors() (built-in function)

start_mpi() (built-in function)

start_potentials() (built-in function)

start_rng() (built-in function)

start_timer() (built-in function)

state() (pysic.utility.archive.Archive method)

stopwatch (built-in variable)

store_system() (pysic.utility.archive.Archive method)

stored_factor_cutoffs (built-in variable)

str2int() (built-in function)

str2ints() (in module pysic.utility.f2py)

Structure (class in pysic.utility.outliers)

style_message() (in module pysic.utility.error)

subcell (built-in variable)

SubSystem (class in pysic.subsystem)

subsystem_defined() (pysic.hybridcalculator.HybridCalculator method)

SubSystemInternal (class in pysic.subsystem)

summation_modes (pysic.interactions.coulomb.CoulombSummation attribute)

summation_parameter_descriptions (pysic.interactions.coulomb.CoulombSummation attribute)

summation_parameters (pysic.interactions.coulomb.CoulombSummation attribute)

supercell (built-in variable)

SuttonChenPotential (class in pysic.interactions.suttonchen)

sync_mpi() (built-in function)

(in module pysic.utility.mpi)

T

table_bond_index (built-in variable)
table_prefix (built-in variable)
table_scale_index (built-in variable)
table_suffix (built-in variable)
temp_enegs (built-in variable)
temp_forces (built-in variable)
temp_gradient (built-in variable)
tersoff_index (built-in variable)

timer() (built-in function)
tmp_factor (built-in variable)
toggle_exclude() (pysic.interactions.comb.CombPotential method)
total_n_nbs (built-in variable)
track_loads (built-in variable)
tri_bend_index (built-in variable)
triplet_index (built-in variable)

U

update_atom_charges() (built-in function)
update_atom_coordinates() (built-in function)
update_atomic_charges() (built-in function)
update_atomic_positions() (built-in function)
update_charges() (pysic.subsystem.SubSystemInternal method)
update_charges_bader() (pysic.subsystem.SubSystemInternal method)
update_charges_van_der_waals() (pysic.subsystem.SubSystemInternal method)
update_core_charges() (pysic.calculator.Pysic method)
update_core_coordinates() (pysic.calculator.Pysic method)
update_core_coulomb() (pysic.calculator.Pysic method)

update_core_neighbor_lists() (pysic.calculator.Pysic method)
update_core_potential_lists() (pysic.calculator.Pysic method)
update_core_potentials() (pysic.calculator.Pysic method)
update_core_supercell() (pysic.calculator.Pysic method)
update_density_grid() (pysic.subsystem.SubSystemInternal method)
update_hydrogen_link_positions() (pysic.interaction.InteractionInternal method)
update_subsystem_charges() (pysic.interaction.InteractionInternal method)
update_system() (pysic.hybridcalculator.HybridCalculator method)
use_saved_bond_order_factors (built-in variable)
use_saved_bond_order_gradients (built-in variable)

V

vec2q() (built-in function)
vec_angle() (in module pysic.utility.outliers)
view_fortran() (pysic.core.CoreMirror method)

view_subsystems() (pysic.hybridcalculator.HybridCalculator method)
vnorm() (built-in function)

W

warn() (in module pysic.utility.error)
Warning (class in pysic.utility.error)
WarningInterruptException
wrapped_coordinates() (built-in function)

write_file() (in module pysic.utility.mpi)
write_loadmonitor() (built-in function)
write_to_file() (in module pysic.utility.outliers)

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