Index A | B | C | D | E | F | G | H | I | L | M | N | O | P | R | S | T | U | V | W A add_contribution() (directupsampling.fesurface.FreeEnergySurface method) allgather() (directupsampling.parallel.BaseMPI method) (directupsampling.parallel.DummyMPI method) (directupsampling.parallel.MPI4Py method) (directupsampling.sampling.sampling.GridSeeder method) asarray() (directupsampling.eos.EOS method) ase2mlip_stress() (in module directupsampling.utils) attach (directupsampling.sampling.settings.SamplingSetting attribute) attach() (directupsampling.sampling.md.MDHandler method) (directupsampling.sampling.sampling.GridSampler method) B BaseMPI (class in directupsampling.parallel) BasePhonons (class in directupsampling.effqh.phonons) best_fit (directupsampling.tifit.ThermoIntFit property) bounds (directupsampling.fecontrib.FreeEnergyContrib property) (directupsampling.fesurface.FreeEnergySurface property) broadcast() (directupsampling.parallel.BaseMPI method) (directupsampling.parallel.DummyMPI method) (directupsampling.parallel.MPI4Py method) (in module directupsampling.parallel) buffer_for_writing (directupsampling.sampling.settings.SamplingSetting attribute) build_function() (directupsampling.fecontrib.VTBasis method) C calc (directupsampling.effqh.effqh.EffQH property) calculate() (directupsampling.calculators.effqh.EffQHCalculator method) calculate_debye_temperature() (directupsampling.debye.Debye method) calculate_fep() (in module directupsampling.upsampling) calculate_properties() (directupsampling.thermo.Thermo method) calculate_snapshots() (directupsampling.upsampling.Upsampling method) calculate_with() (directupsampling.sampling.sampling.GridSampler method) call_observers() (directupsampling.sampling.sampling.GridSampler method) change_reference() (directupsampling.effqh.effqh.EffQH method) change_size() (directupsampling.effqh.effqh.EffQH method) check_if_empty() (in module directupsampling.ti) check_pressure_unit() (in module directupsampling.eos) check_raw_data() (directupsampling.tifit.ThermoIntFit method) chunks() (in module directupsampling.utils) class_type (directupsampling.sampling.settings.ThermostatSetting attribute) coefficients (directupsampling.effqh.fcfit.ForceConstantFit property) coerce() (directupsampling.snapshots.index.IndexView method) comm (directupsampling.sampling.settings.MDLogSetting attribute) create_ndarray() (in module directupsampling.io.jsonio) D data (directupsampling.snapshots.container.SnapshotContainer property) Debye (class in directupsampling.debye) debye_function() (in module directupsampling.debye) default() (directupsampling.io.jsonio.MyEncoder method) (in module directupsampling.io.jsonio) default_grid_names() (directupsampling.snapshots.index.IndexView method) directupsampling.calculators.effqh module directupsampling.calculators.emt module directupsampling.data module directupsampling.debye module directupsampling.effqh.effqh module directupsampling.effqh.fcfit module directupsampling.effqh.phonons module directupsampling.effqh.utils module directupsampling.eos module directupsampling.fecontrib module directupsampling.fesurface module directupsampling.folders.read module directupsampling.folders.write module directupsampling.grid module directupsampling.io.jsonio module directupsampling.parallel module directupsampling.plot_tools module directupsampling.sampling.md module directupsampling.sampling.sampling module directupsampling.sampling.settings module directupsampling.snapshots.container module directupsampling.snapshots.index module directupsampling.thermo module directupsampling.ti module directupsampling.tifit module directupsampling.upsampling module directupsampling.utils module directupsampling_objtype (directupsampling.effqh.fcfit.ForceConstantFit attribute) (directupsampling.effqh.phonons.ExactPhonons attribute) (directupsampling.effqh.phonons.MeshPhonons attribute) (directupsampling.eos.Vinet attribute) (directupsampling.fecontrib.FreeEnergyContrib attribute) (directupsampling.fecontrib.FreeEnergyFit attribute) (directupsampling.fecontrib.OldFormatFreeEnergy attribute) (directupsampling.fecontrib.VTBasis attribute) (directupsampling.fesurface.FreeEnergySurface attribute) discard_indices() (directupsampling.snapshots.container.SnapshotContainer method) DummyMDSampler (class in directupsampling.sampling.md) DummyMPI (class in directupsampling.parallel) E EffQH (class in directupsampling.effqh.effqh) EffQHCalculator (class in directupsampling.calculators.effqh) energy (directupsampling.eos.RawData attribute) (directupsampling.tifit.RawData attribute) energy_differences (directupsampling.upsampling.Upsampling property) EOS (class in directupsampling.eos) EOSPlot (class in directupsampling.plot_tools) error (directupsampling.fecontrib.RawData attribute) (directupsampling.tifit.RawData attribute) evib_classical() (in module directupsampling.effqh.phonons) evib_qm() (in module directupsampling.effqh.phonons) exact_free_energy_surface (directupsampling.effqh.effqh.EffQH property) exact_phonons (directupsampling.effqh.effqh.EffQH property) ExactPhonons (class in directupsampling.effqh.phonons) ExactPhononsPlot (class in directupsampling.plot_tools) extend() (directupsampling.snapshots.container.SnapshotContainer method) extend_from_db() (directupsampling.snapshots.container.SnapshotContainer method) extract_fc_potentials() (directupsampling.effqh.effqh.EffQH method) extract_free_energy_difference() (directupsampling.ti.ThermoInt method) F fdebye() (in module directupsampling.debye) FEContribPlot (class in directupsampling.plot_tools) fermi_dirac_distribution() (in module directupsampling.folders.read) file (directupsampling.sampling.settings.SamplingSetting attribute) filter() (directupsampling.snapshots.container.SnapshotContainer method) (directupsampling.snapshots.index.IndexView method) fit() (directupsampling.eos.EOS class method) (directupsampling.fecontrib.FreeEnergyFit method) (directupsampling.tifit.ThermoIntFit method) fit_data() (directupsampling.fecontrib.FreeEnergyContrib method) fit_force_constants() (directupsampling.effqh.fcfit.ForceConstantFit method) fit_from_hiphive() (directupsampling.effqh.fcfit.ForceConstantFit class method) fit_snapshots() (directupsampling.effqh.effqh.EffQH method) fit_types (directupsampling.tifit.ThermoIntFit attribute) fix_int_keys_in_dicts() (in module directupsampling.io.jsonio) fixcm (directupsampling.sampling.settings.ThermostatSetting attribute) force_constants_to_frequencies() (directupsampling.effqh.phonons.BasePhonons method) (directupsampling.effqh.phonons.ExactPhonons method) (directupsampling.effqh.phonons.MeshPhonons method) ForceConstantFit (class in directupsampling.effqh.fcfit) free_energy (directupsampling.fecontrib.RawData attribute) free_energy_differences (directupsampling.ti.ThermoInt property) (directupsampling.upsampling.Upsampling property) free_energy_surface (directupsampling.debye.Debye property) FreeEnergyContrib (class in directupsampling.fecontrib) FreeEnergyFit (class in directupsampling.fecontrib) FreeEnergySurface (class in directupsampling.fesurface) FreeEnergySurfacePlot (class in directupsampling.plot_tools) FREQ_WARN_TOL (directupsampling.effqh.phonons.BasePhonons attribute) friction (directupsampling.sampling.settings.ThermostatSetting attribute) from_any() (directupsampling.grid.Grid class method) (directupsampling.sampling.settings.SamplingSetting class method) from_fcfit() (directupsampling.effqh.phonons.BasePhonons class method) from_list() (directupsampling.snapshots.container.SnapshotContainer class method) fromdict() (directupsampling.effqh.fcfit.ForceConstantFit class method) (directupsampling.eos.EOS class method) (directupsampling.fecontrib.FreeEnergyContrib class method) (directupsampling.fecontrib.FreeEnergyFit class method) fvib_classical() (in module directupsampling.effqh.phonons) fvib_qm() (in module directupsampling.effqh.phonons) G gather() (directupsampling.parallel.BaseMPI method) (directupsampling.parallel.DummyMPI method) (directupsampling.parallel.MPI4Py method) gather_chunks() (in module directupsampling.utils) gather_container() (directupsampling.snapshots.container.SnapshotContainer method) get() (directupsampling.snapshots.container.SnapshotContainer method) get_avg_and_err() (directupsampling.ti.ThermoInt static method) get_bounds_from_contributions() (directupsampling.fesurface.FreeEnergySurface method) get_bulk_modulus() (directupsampling.eos.EOS method) (directupsampling.eos.Vinet method) get_calcs_names() (in module directupsampling.utils) get_energy() (directupsampling.effqh.phonons.BasePhonons method) (directupsampling.eos.EOS method) (directupsampling.eos.Vinet method) get_eos() (directupsampling.fesurface.FreeEnergySurface method) get_eos_from_folders() (in module directupsampling.eos) get_fah_fit_func() (in module directupsampling.fecontrib) get_fel_fit_func() (in module directupsampling.fecontrib) get_fit_func() (in module directupsampling.fecontrib) get_fixdos_fel() (in module directupsampling.folders.read) get_force_constants() (directupsampling.effqh.fcfit.ForceConstantFit method) get_free_energy() (directupsampling.debye.Debye method) (directupsampling.effqh.phonons.BasePhonons method) (directupsampling.fecontrib.FreeEnergyContrib method) (directupsampling.fecontrib.FreeEnergyFit method) (directupsampling.fecontrib.OldFormatFreeEnergy method) (directupsampling.fesurface.FreeEnergySurface method) get_frequencies() (directupsampling.effqh.phonons.BasePhonons method) (directupsampling.effqh.phonons.PhonopyHandler method) get_fvib_fit_func() (in module directupsampling.fecontrib) get_gibbs_energy() (directupsampling.fesurface.FreeEnergySurface method) get_grid() (directupsampling.snapshots.index.IndexView method) get_kwargs() (directupsampling.sampling.settings.ThermostatSetting method) get_poly_fit_func() (in module directupsampling.fecontrib) get_pressure() (directupsampling.eos.EOS method) (directupsampling.eos.Vinet method) (directupsampling.fesurface.FreeEnergySurface method) get_ref_atoms() (in module directupsampling.effqh.utils) get_volume() (directupsampling.eos.EOS method) (directupsampling.fesurface.FreeEnergySurface method) get_weights() (directupsampling.effqh.phonons.PhonopyHandler method) glogit() (in module directupsampling.tifit) Grid (class in directupsampling.grid) GridPoint (class in directupsampling.grid) GridSampler (class in directupsampling.sampling.sampling) GridSeeder (class in directupsampling.sampling.sampling) H header (directupsampling.sampling.settings.MDLogSetting attribute) I implemented_properties (directupsampling.calculators.effqh.EffQHCalculator attribute) IndexPoint (class in directupsampling.snapshots.index) IndexView (class in directupsampling.snapshots.index) initialize() (directupsampling.sampling.md.MDHandler method) insert() (directupsampling.snapshots.container.SnapshotContainer method) insert_contribution() (directupsampling.fesurface.FreeEnergySurface method) interval (directupsampling.sampling.settings.MDLogSetting attribute) intkey() (in module directupsampling.io.jsonio) irun() (directupsampling.sampling.md.MDHandler method) is_sampling_time() (directupsampling.sampling.md.MDSampler method) iscatter() (directupsampling.grid.Grid method) L lambda_ (directupsampling.grid.GridPoint attribute) (directupsampling.tifit.RawData attribute) log_md (directupsampling.sampling.settings.SamplingSetting attribute) logfile (directupsampling.sampling.settings.MDLogSetting attribute) logit() (in module directupsampling.tifit) M make_grid_seeds() (directupsampling.sampling.sampling.GridSeeder method) make_phonons() (directupsampling.effqh.phonons.PhonopyHandler method) make_seed() (directupsampling.sampling.sampling.GridSeeder method) (directupsampling.sampling.sampling.Seeder method) make_single_point_calculator() (in module directupsampling.utils) MDHandler (class in directupsampling.sampling.md) mdlogger_setting (directupsampling.sampling.settings.SamplingSetting attribute) MDLogSetting (class in directupsampling.sampling.settings) MDSampler (class in directupsampling.sampling.md) mesh_free_energy_surface (directupsampling.effqh.effqh.EffQH property) mesh_phonons (directupsampling.effqh.effqh.EffQH property) MeshPhonons (class in directupsampling.effqh.phonons) MeshPhononsPlot (class in directupsampling.plot_tools) mlip2ase_stress() (in module directupsampling.utils) mode (directupsampling.sampling.settings.MDLogSetting attribute) module directupsampling.calculators.effqh directupsampling.calculators.emt directupsampling.data directupsampling.debye directupsampling.effqh.effqh directupsampling.effqh.fcfit directupsampling.effqh.phonons directupsampling.effqh.utils directupsampling.eos directupsampling.fecontrib directupsampling.fesurface directupsampling.folders.read directupsampling.folders.write directupsampling.grid directupsampling.io.jsonio directupsampling.parallel directupsampling.plot_tools directupsampling.sampling.md directupsampling.sampling.sampling directupsampling.sampling.settings directupsampling.snapshots.container directupsampling.snapshots.index directupsampling.thermo directupsampling.ti directupsampling.tifit directupsampling.upsampling directupsampling.utils MPI (class in directupsampling.parallel) MPI4Py (class in directupsampling.parallel) MyEncoder (class in directupsampling.io.jsonio) N nsteps (directupsampling.sampling.md.MDHandler property) O object_hook() (in module directupsampling.io.jsonio) OldFormatFreeEnergy (class in directupsampling.fecontrib) optimize_global() (in module directupsampling.fesurface) P parcall() (in module directupsampling.parallel) parlog() (in module directupsampling.parallel) paropen() (in module directupsampling.parallel) parprint() (in module directupsampling.parallel) parse_expression() (directupsampling.fecontrib.VTBasis method) peratom (directupsampling.sampling.settings.MDLogSetting attribute) perturbation_average() (in module directupsampling.upsampling) phonons (directupsampling.effqh.phonons.PhonopyHandler property) PhononsPlot (class in directupsampling.plot_tools) PhonopyHandler (class in directupsampling.effqh.phonons) plot() (directupsampling.plot_tools.EOSPlot method) (directupsampling.plot_tools.FEContribPlot method) (directupsampling.plot_tools.ThermoIntFitPlot method) (directupsampling.plot_tools.ThermoIntPlot method) (directupsampling.plot_tools.ThermoPlot method) (in module directupsampling.plot_tools) plot_all() (directupsampling.plot_tools.ThermoIntFitPlot method) plot_frequencies() (directupsampling.plot_tools.ExactPhononsPlot method) (directupsampling.plot_tools.MeshPhononsPlot method) (directupsampling.plot_tools.PhononsPlot method) plot_phonon_dispersion() (directupsampling.effqh.phonons.PhonopyHandler method) (directupsampling.plot_tools.ExactPhononsPlot method) (directupsampling.plot_tools.MeshPhononsPlot method) (directupsampling.plot_tools.PhononsPlot method) plot_pressure() (directupsampling.plot_tools.EOSPlot method) plot_raw_data() (directupsampling.plot_tools.ThermoIntFitPlot method) plot_raw_data_vs_temperature() (directupsampling.plot_tools.FEContribPlot method) plot_raw_data_vs_volume() (directupsampling.plot_tools.FEContribPlot method) plot_vs_temperature() (directupsampling.plot_tools.FEContribPlot method) plot_vs_volume() (directupsampling.plot_tools.FEContribPlot method) (directupsampling.plot_tools.FreeEnergySurfacePlot method) pressure (directupsampling.grid.GridPoint attribute) properties (directupsampling.thermo.Thermo property) R rank (directupsampling.parallel.DummyMPI attribute) RawData (class in directupsampling.eos) (class in directupsampling.fecontrib) (class in directupsampling.tifit) read() (directupsampling.effqh.fcfit.ForceConstantFit class method) (directupsampling.eos.EOS class method) (directupsampling.fesurface.FreeEnergySurface class method) (directupsampling.snapshots.container.SnapshotContainer class method) (directupsampling.ti.ThermoInt class method) read_contrib_file() (in module directupsampling.fesurface) read_eos() (in module directupsampling.eos) read_fc_fit() (directupsampling.effqh.effqh.EffQH class method) read_fcp() (directupsampling.effqh.effqh.EffQH class method) read_folders() (directupsampling.sampling.sampling.GridSampler class method) (directupsampling.upsampling.Upsampling class method) read_folders_to_sampler() (in module directupsampling.folders.read) read_grid_from_folders() (in module directupsampling.folders.read) read_json() (in module directupsampling.io.jsonio) read_old_format() (directupsampling.fecontrib.FreeEnergyContrib method) (directupsampling.fesurface.FreeEnergySurface class method) reduce_fix_values() (directupsampling.plot_tools.FEContribPlot method) reference_snapshot_container (directupsampling.upsampling.Upsampling property) replace() (directupsampling.sampling.settings.Setting method) rescale() (directupsampling.fecontrib.VTBasis method) rescale_to_different_supercell() (in module directupsampling.upsampling) reshape_phonopy_to_sphinx() (in module directupsampling.effqh.utils) reshape_sphinx_to_phonopy() (in module directupsampling.effqh.utils) rng (directupsampling.sampling.settings.SamplingSetting attribute) run() (directupsampling.sampling.md.DummyMDSampler method) (directupsampling.sampling.md.MDHandler method) (directupsampling.sampling.md.MDSampler method) run_sampling() (directupsampling.ti.ThermoInt method) S sample() (directupsampling.sampling.md.MDSampler method) sample_atoms (directupsampling.sampling.settings.SamplingSetting attribute) sample_snapshots() (directupsampling.sampling.sampling.GridSampler method) sampling_interval (directupsampling.sampling.settings.SamplingSetting attribute) sampling_offset (directupsampling.sampling.settings.SamplingSetting attribute) SamplingSetting (class in directupsampling.sampling.settings) scatter() (directupsampling.parallel.BaseMPI method) (directupsampling.parallel.DummyMPI method) (directupsampling.parallel.MPI4Py method) scatter_grid_seeds() (directupsampling.sampling.sampling.GridSeeder method) seed (directupsampling.sampling.settings.SamplingSetting attribute) (directupsampling.snapshots.index.IndexPoint attribute) Seeder (class in directupsampling.sampling.sampling) set_bounds_from_raw_data() (directupsampling.eos.EOS method) set_common() (directupsampling.plot_tools.FEContribPlot method) set_index_defaults() (directupsampling.snapshots.container.SnapshotContainer method) set_logger() (directupsampling.sampling.md.MDHandler method) set_thermostat() (directupsampling.sampling.md.MDHandler method) set_volume() (in module directupsampling.utils) Setting (class in directupsampling.sampling.settings) size (directupsampling.parallel.DummyMPI attribute) snapshot_container (directupsampling.upsampling.Upsampling property) SnapshotContainer (class in directupsampling.snapshots.container) step (directupsampling.snapshots.index.IndexPoint attribute) stress (directupsampling.sampling.settings.MDLogSetting attribute) sum_over_frequencies() (directupsampling.effqh.phonons.BasePhonons method) T tan() (in module directupsampling.tifit) tan2() (in module directupsampling.tifit) temperature (directupsampling.fecontrib.RawData attribute) (directupsampling.grid.GridPoint attribute) Thermo (class in directupsampling.thermo) ThermoInt (class in directupsampling.ti) ThermoIntFit (class in directupsampling.tifit) ThermoIntFitPlot (class in directupsampling.plot_tools) ThermoIntPlot (class in directupsampling.plot_tools) ThermoPlot (class in directupsampling.plot_tools) thermostat_setting (directupsampling.sampling.settings.SamplingSetting attribute) ThermostatSetting (class in directupsampling.sampling.settings) timestep (directupsampling.sampling.settings.ThermostatSetting attribute) to_pandas() (directupsampling.snapshots.container.SnapshotContainer method) todict() (directupsampling.effqh.fcfit.ForceConstantFit method) (directupsampling.effqh.phonons.BasePhonons method) (directupsampling.eos.EOS method) (directupsampling.fecontrib.FreeEnergyContrib method) (directupsampling.fecontrib.FreeEnergyFit method) (directupsampling.fecontrib.OldFormatFreeEnergy method) (directupsampling.fecontrib.VTBasis method) (directupsampling.fesurface.FreeEnergySurface method) (directupsampling.grid.GridPoint method) (directupsampling.sampling.settings.Setting method) U Upsampling (class in directupsampling.upsampling) V Vinet (class in directupsampling.eos) volume (directupsampling.eos.RawData attribute) (directupsampling.fecontrib.RawData attribute) (directupsampling.grid.GridPoint attribute) VTBasis (class in directupsampling.fecontrib) W write() (directupsampling.effqh.fcfit.ForceConstantFit method) (directupsampling.eos.EOS method) (directupsampling.fesurface.FreeEnergySurface method) (directupsampling.snapshots.container.SnapshotContainer method) write_buffer_to_database() (directupsampling.sampling.md.DummyMDSampler method) (directupsampling.sampling.md.MDSampler method) write_fc_fit() (directupsampling.effqh.effqh.EffQH method) write_folders() (directupsampling.sampling.sampling.GridSampler method) (directupsampling.ti.ThermoInt method) (directupsampling.upsampling.Upsampling method) write_folders_from_sampler() (in module directupsampling.folders.write) write_hessian() (directupsampling.effqh.effqh.EffQH method) write_joblist() (in module directupsampling.folders.write) write_json() (in module directupsampling.io.jsonio) write_snapshots() (in module directupsampling.folders.write)