Index

A

assemblies (mdse.rm.dbmanager.MongoDBEntry attribute)

B

build_website_locally() (in module mdse.cli)

C

calc_bulk_modulus() (mdse.md.resultMD.ResultMD method) calc_C11() (mdse.md.resultMD.ResultMD method) calc_C12() (mdse.md.resultMD.ResultMD method) calc_C44() (mdse.md.resultMD.ResultMD method) calc_chem_pot() (in module httk4mdse.httk_reader) calc_debye_temperature() (mdse.md.resultMD.ResultMD method) calc_density_of_states() (mdse.md.resultMD.ResultMD method) calc_formation_energy() (in module mdse.utils) calc_isobaric_enthalpy() (mdse.md.resultMD.ResultMD method) calc_isobaric_specific_heat() (in module mdse.cli) (mdse.md.resultMD.ResultMD method) calc_isochoric_heat_capacity_per_atom() (mdse.md.resultMD.ResultMD method) calc_lattice() (mdse.md.resultMD.ResultMD method) calc_lindemann() (in module mdse.cli) (mdse.md.resultMD.ResultMD method) calc_msd() (in module mdse.cli) (mdse.md.resultMD.ResultMD method)

calc_self_diff() (in module mdse.cli) (mdse.md.resultMD.ResultMD method) calc_shear_modulus() (mdse.md.resultMD.ResultMD method) calc_youngs_modulus() (mdse.md.resultMD.ResultMD method) calculate_defect_formation_energy() (in module mdse.cli) cartesian_site_positions (mdse.rm.dbmanager.MongoDBEntry attribute) check_equilibrium() (mdse.md.resultMD.ResultMD method) chemical_formula_anonymous (mdse.rm.dbmanager.MongoDBEntry attribute) chemical_formula_descriptive (mdse.rm.dbmanager.MongoDBEntry attribute) chemical_formula_hill (mdse.rm.dbmanager.MongoDBEntry attribute) chemical_formula_reduced (mdse.rm.dbmanager.MongoDBEntry attribute) ChemicalPotential (class in httk4mdse.classes) clear_collection() (mdse.rm.dbmanager.DBManager method) client (mdse.rm.dbmanager.DBManager attribute) convert_scalar() (in module mdse.cli) create_json_from_mongodbentries() (mdse.rm.dbmanager.DBManager static method) create_parser() (in module mdse.cli) crystal (mdse.md.simulationmanager.SimulationManager attribute)

D

DBManager (class in mdse.rm.dbmanager) defect_formation_energy() (in module mdse.utils) DefectCell (class in httk4mdse.classes) DefectHull (class in httk4mdse.classes)

DefectInfo (class in httk4mdse.classes) detect_outliers() (mdse.rm.dbmanager.DBManager method) dimension_types (mdse.rm.dbmanager.MongoDBEntry attribute) doping_plot() (in module mdse.visualizeDB.vis_plots)

E

elements (mdse.rm.dbmanager.MongoDBEntry attribute) elements_ratios (mdse.rm.dbmanager.MongoDBEntry attribute)

estimate_average_a() (mdse.md.resultMD.ResultMD method) estimate_nearest_neighbor_distance() (mdse.md.resultMD.ResultMD method) expand_parameter() (in module mdse.parser)

F

from_file() (mdse.md.resultMD.ResultMD class method)

G

get_all_values() (mdse.rm.dbmanager.DBManager method) get_chemical_potential() (in module httk4mdse.httk_reader) get_cohesive_energy() (mdse.md.resultMD.ResultMD method) get_def_size() (in module mdse.visualizeDB.read_dataDB) get_defect_cat() (in module mdse.visualizeDB.vis_plots) get_defect_formation_energy() (in module httk4mdse.httk_reader) get_defects() (in module httk4mdse.httk_reader) get_files() (in module mdse.parser) get_kin_energies() (mdse.md.resultMD.ResultMD method)

get_label_name() (in module mdse.visualizeDB.vis_plots) get_nelements() (in module mdse.utils) get_pot_energies() (mdse.md.resultMD.ResultMD method) get_pressure() (mdse.md.resultMD.ResultMD method) get_pressures() (mdse.md.resultMD.ResultMD method) get_temperatures() (mdse.md.resultMD.ResultMD method) get_time_axis() (mdse.md.resultMD.ResultMD method) get_tot_energies() (mdse.md.resultMD.ResultMD method) get_vacancy() (in module mdse.visualizeDB.read_dataDB)

H

heatmap_plot() (in module mdse.visualizeDB.vis_plots) HostSuperCell (class in httk4mdse.classes) HostSuperCellResult (class in httk4mdse.classes) HostUnitCellResult (class in httk4mdse.classes) httk4mdse module

httk4mdse.classes module httk4mdse.httk_reader module HullDistance (class in httk4mdse.classes)

I

id (mdse.rm.dbmanager.MongoDBEntry attribute)

insert_nested() (in module mdse.cli)

L

last_modified (mdse.rm.dbmanager.MongoDBEntry attribute)

lattice_vectors (mdse.rm.dbmanager.MongoDBEntry attribute)

M

main() (in module mdse.cli) main_read() (in module mdse.parser) make_plot() (in module mdse.visualizeDB.make_plot) md_simulations (mdse.rm.runmanager.RunManager attribute) mdse module mdse.cli module mdse.logging module mdse.md module mdse.md.resultMD module mdse.md.simulationmanager module mdse.md.visualize module mdse.parser module mdse.rm module mdse.rm.dbmanager module mdse.rm.runmanager module mdse.utils module mdse.visualizeDB module

mdse.visualizeDB.make_plot module mdse.visualizeDB.read_dataDB module mdse.visualizeDB.run_visDB module mdse.visualizeDB.vis_plots module mdse_fields (mdse.rm.dbmanager.MongoDBEntry attribute) module httk4mdse httk4mdse.classes httk4mdse.httk_reader mdse mdse.cli mdse.logging mdse.md mdse.md.resultMD mdse.md.simulationmanager mdse.md.visualize mdse.parser mdse.rm mdse.rm.dbmanager mdse.rm.runmanager mdse.utils mdse.visualizeDB mdse.visualizeDB.make_plot mdse.visualizeDB.read_dataDB mdse.visualizeDB.run_visDB mdse.visualizeDB.vis_plots MongoDBEntry (class in mdse.rm.dbmanager)

N

name() (httk4mdse.classes.HostSuperCell method) nelements (mdse.rm.dbmanager.MongoDBEntry attribute)

nest_lennard_jones() (in module mdse.parser) nperiodic_dimensions (mdse.rm.dbmanager.MongoDBEntry attribute) nsites (mdse.rm.dbmanager.MongoDBEntry attribute)

O

outlier_detection() (in module mdse.cli)

outputs (mdse.rm.runmanager.RunManager attribute)

P

parse_config() (in module mdse.cli) parse_value() (in module mdse.cli) path (mdse.rm.dbmanager.DBManager attribute) plot_avg() (in module mdse.visualizeDB.vis_plots) plot_density_of_states() (mdse.md.resultMD.ResultMD method)

plot_DOS() (mdse.md.visualize.VisualizeResult method) plot_energy() (mdse.md.visualize.VisualizeResult method) plot_histogram() (mdse.md.visualize.VisualizeResult method) plot_MSD() (mdse.md.visualize.VisualizeResult method) plot_scatter() (mdse.md.visualize.VisualizeResult method) print_energy() (mdse.md.simulationmanager.SimulationManager method)

R

read_data() (in module mdse.visualizeDB.read_dataDB) read_from_db() (mdse.rm.dbmanager.DBManager method) read_yaml_simulations() (in module mdse.parser) remove_all_traj() (in module mdse.cli)

ResultMD (class in mdse.md.resultMD) run_results() (mdse.rm.runmanager.RunManager method) run_simulations() (mdse.rm.runmanager.RunManager method) run_visualize_db() (in module mdse.visualizeDB.run_visDB) RunManager (class in mdse.rm.runmanager)

S

save_defects() (in module httk4mdse.httk_reader) save_to_cif() (in module httk4mdse.httk_reader) scatter_plot() (in module mdse.visualizeDB.vis_plots) ScreenCell (class in httk4mdse.classes) ScreenResult (class in httk4mdse.classes) setup_db() (in module httk4mdse.httk_reader) setup_logging() (in module mdse.logging) simulate() (in module mdse.cli) (mdse.md.simulationmanager.SimulationManager method) simulate_mpi() (in module mdse.cli) simulate_npt() (mdse.md.simulationmanager.SimulationManager method) simulate_nve() (mdse.md.simulationmanager.SimulationManager method) simulate_nvt() (mdse.md.simulationmanager.SimulationManager method)

SimulationManager (class in mdse.md.simulationmanager) single_atom_energy() (mdse.md.resultMD.ResultMD method) single_defect_plot() (in module mdse.visualizeDB.vis_plots) space_group_it_number (mdse.rm.dbmanager.MongoDBEntry attribute) space_group_symbol_hall (mdse.rm.dbmanager.MongoDBEntry attribute) space_group_symbol_hermann_mauguin (mdse.rm.dbmanager.MongoDBEntry attribute) space_group_symbol_hermann_mauguin_extended (mdse.rm.dbmanager.MongoDBEntry attribute) space_group_symmetry_operations_xyz (mdse.rm.dbmanager.MongoDBEntry attribute) species (mdse.rm.dbmanager.MongoDBEntry attribute) species_at_sites (mdse.rm.dbmanager.MongoDBEntry attribute) structure_features (mdse.rm.dbmanager.MongoDBEntry attribute) sub_sub_plot() (in module mdse.visualizeDB.vis_plots) symmetrize() (in module mdse.visualizeDB.vis_plots)

T

to_dict() (mdse.rm.dbmanager.MongoDBEntry method) to_file() (mdse.rm.dbmanager.MongoDBEntry method)

transfer_chemical_potential() (in module mdse.utils) transfer_defect_formation_energy() (in module mdse.utils) type (mdse.rm.dbmanager.MongoDBEntry attribute)

U

unnest_simulation_parameters() (in module mdse.parser)

V

valid_plot() (in module mdse.visualizeDB.make_plot) view_crystal() (in module mdse.cli) view_super_crystal() (mdse.md.simulationmanager.SimulationManager method)

view_website_browser() (in module mdse.cli) visualize_DB() (in module mdse.cli) visualize_msd() (mdse.md.resultMD.ResultMD method) VisualizeResult (class in mdse.md.visualize)

W

write_dict_to_db() (mdse.rm.dbmanager.DBManager method)

write_jsonfiles_to_db() (mdse.rm.dbmanager.DBManager method) write_to_database() (in module mdse.cli)