Index _ | A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W _ __init__() (calphy.alchemy.Alchemy method) (calphy.composition_transformation.CompositionTransformation method) (calphy.liquid.Liquid method) (calphy.phase.Phase method) (calphy.phase_diagram.CScale method) (calphy.phase_diagram.PhaseDiagram method) (calphy.phase_diagram.SimpleCalculation method) (calphy.routines.MeltingTemp method) (calphy.scheduler.Local method) (calphy.scheduler.SGE method) (calphy.scheduler.SLURM method) (calphy.solid.Solid method) A addtest() (in module calphy) Alchemy (class in calphy.alchemy) alchemy_coupling (calphy.input.Calculation attribute) allow_all_swaps (calphy.input.MonteCarlo attribute) analyse_spring_constants() (calphy.solid.Solid method) api_key (calphy.input.MaterialsProject attribute) assign_spring_constants() (calphy.solid.Solid method) attempts (calphy.input.MeltingTemperature attribute) B barostat_damping (calphy.input.Berendsen attribute) (calphy.input.MD attribute) (calphy.input.NoseHoover attribute) (calphy.input.QuantumThermalBath attribute) berendsen (calphy.input.Calculation attribute) Berendsen (class in calphy.input) build_calphad_surface() (calphy.phase_diagram.PhaseDiagram method) C calculate() (calphy.phase_diagram.PhaseDiagram method) calculate_entropy_mix() (in module calphy.integrators) calculate_fe_impurity() (in module calphy.integrators) calculate_fe_mix() (in module calphy.integrators) calculate_tm() (calphy.routines.MeltingTemp method) Calculation (class in calphy.input) calphy module calphy.alchemy module calphy.clitools module calphy.composition_transformation module calphy.errors module calphy.helpers module calphy.input module calphy.integrators module calphy.kernel module calphy.liquid module calphy.phase module calphy.phase_diagram module calphy.postprocessing module calphy.queuekernel module calphy.routines module calphy.scheduler module calphy.solid module calphy.splines module check_dissipation() (calphy.phase.Phase method) check_if_any_is_none() (in module calphy.helpers) check_if_any_is_not_none() (in module calphy.helpers) check_if_melted() (calphy.phase.Phase method) check_if_solidfied() (calphy.phase.Phase method) clean_df() (in module calphy.postprocessing) clean_up() (calphy.phase.Phase method) cmdargs (calphy.input.MD attribute) commands (calphy.input.Queue attribute) composition_scaling (calphy.input.Calculation attribute) CompositionScaling (class in calphy.input) CompositionTransformation (class in calphy.composition_transformation) compute_msd() (in module calphy.helpers) compute_possible_mappings() (calphy.composition_transformation.CompositionTransformation method) conventional (calphy.input.MaterialsProject attribute) convert_to_pyscal() (calphy.composition_transformation.CompositionTransformation method) cores (calphy.input.Queue attribute) create_color_list() (in module calphy.phase_diagram) create_folders() (calphy.input.Calculation method) create_identifier() (calphy.input.Calculation method) create_object() (in module calphy.helpers) create_structure() (in module calphy.helpers) CROSSING_STENCIL (calphy.routines.MeltingTemp attribute) CScale (class in calphy.phase_diagram) CustomError D DETECTION_LIQUID_FRACTION (calphy.routines.MeltingTemp attribute) DETECTION_SOLID_FRACTION (calphy.routines.MeltingTemp attribute) dissipation (calphy.input.Tolerance attribute) dump_current_snapshot() (calphy.phase.Phase method) E ediss (calphy.phase.Phase attribute) ediss_high (calphy.phase.Phase attribute) element (calphy.input.Calculation attribute) emit_init_commands() (in module calphy.helpers) entropy_contribution (calphy.composition_transformation.CompositionTransformation property) equilibration_control (calphy.input.Calculation attribute) execution_mode (calphy.input.Calculation attribute) extrapolate_tm() (calphy.routines.MeltingTemp method) F f_max (calphy.input.QuantumThermalBath attribute) fe() (in module calphy.integrators) file_format (calphy.input.Calculation attribute) finalise_pressure() (calphy.phase.Phase method) find_fe() (in module calphy.integrators) find_solid_fraction() (in module calphy.helpers) find_tm() (calphy.routines.MeltingTemp method) find_transition_temperature() (in module calphy.postprocessing) find_w() (in module calphy.integrators) fix_berendsen() (calphy.phase.Phase method) fix_composition_scaling() (in module calphy.postprocessing) fix_data_file() (in module calphy.phase_diagram) fix_nose_hoover() (calphy.phase.Phase method) fix_paths() (calphy.input.Calculation method) fix_potential_path (calphy.input.Calculation attribute) fix_qtb() (calphy.phase.Phase method) folder_prefix (calphy.input.Calculation attribute) forward_swap_types (calphy.input.MonteCarlo attribute) from_df() (calphy.phase_diagram.PhaseDiagram class method) from_parquet() (calphy.phase_diagram.PhaseDiagram static method) from_pickle() (calphy.phase_diagram.PhaseDiagram static method) from_tdb() (calphy.phase_diagram.PhaseDiagram static method) G gather_results() (in module calphy.postprocessing) generate_metadata() (in module calphy.input) get_common_tangents() (in module calphy.phase_diagram) get_composition_transformation() (calphy.composition_transformation.CompositionTransformation method) get_einstein_crystal_fe() (in module calphy.integrators) get_folder_name() (calphy.input.Calculation method) get_free_energy_mixing() (in module calphy.phase_diagram) get_ideal_gas_fe() (in module calphy.integrators) get_mappings() (calphy.composition_transformation.CompositionTransformation method) get_phase_free_energy() (in module calphy.phase_diagram) get_random_index_of_species() (calphy.composition_transformation.CompositionTransformation method) get_structures() (calphy.phase.Phase method) (in module calphy.helpers) get_swap_types() (calphy.composition_transformation.CompositionTransformation method) get_tangent_type() (in module calphy.phase_diagram) get_trange() (calphy.routines.MeltingTemp method) get_uhlenbeck_ford_fe() (in module calphy.integrators) guess (calphy.input.MeltingTemperature attribute) H hybrid_pair_coeff_commands() (in module calphy.helpers) I init_commands (calphy.input.MD attribute) input_chemical_composition (calphy.phase_diagram.CScale property) inputfile (calphy.input.Calculation attribute) integrate_mass() (in module calphy.integrators) integrate_path() (in module calphy.integrators) integrate_pressure_scaling() (calphy.phase.Phase method) integrate_ps() (in module calphy.integrators) integrate_reversible_scaling() (calphy.phase.Phase method) integrate_rs() (in module calphy.integrators) is_overlay_potential() (in module calphy.helpers) iselement() (calphy.composition_transformation.CompositionTransformation method) J jobname (calphy.input.Queue attribute) K kernel (calphy.input.Calculation attribute) L lambda_schedule (calphy.input.Calculation attribute) lammps_close() (calphy.phase.Phase method) lammps_executable (calphy.input.Calculation attribute) LammpsExecutionError lattice (calphy.input.Calculation attribute) lattice_constant (calphy.input.Calculation attribute) (calphy.input.Tolerance attribute) Liquid (class in calphy.liquid) liquid_fraction (calphy.input.Tolerance attribute) Local (class in calphy.scheduler) M main() (in module calphy.kernel) (in module calphy.queuekernel) mark_atoms() (calphy.composition_transformation.CompositionTransformation method) mass (calphy.input.Calculation attribute) mass_integration() (calphy.alchemy.Alchemy method) materials_project (calphy.input.Calculation attribute) MaterialsProject (class in calphy.input) md (calphy.input.Calculation attribute) MD (class in calphy.input) melt_structure() (calphy.liquid.Liquid method) MeltedError melting_cycle (calphy.input.Calculation attribute) melting_temperature (calphy.input.Calculation attribute) MeltingTemp (class in calphy.routines) MeltingTemperature (class in calphy.input) memory (calphy.input.Queue attribute) mode (calphy.input.Calculation attribute) (calphy.input.PhaseTransitionDetection attribute) model_config (calphy.input.Berendsen attribute) (calphy.input.Calculation attribute) (calphy.input.CompositionScaling attribute) (calphy.input.MaterialsProject attribute) (calphy.input.MD attribute) (calphy.input.MeltingTemperature attribute) (calphy.input.MonteCarlo attribute) (calphy.input.NoseHoover attribute) (calphy.input.PhaseTransitionDetection attribute) (calphy.input.QuantumThermalBath attribute) (calphy.input.Queue attribute) (calphy.input.Tolerance attribute) (calphy.input.UFMP attribute) model_post_init() (calphy.input.Calculation method) (calphy.input.CompositionScaling method) module calphy calphy.alchemy calphy.clitools calphy.composition_transformation calphy.errors calphy.helpers calphy.input calphy.integrators calphy.kernel calphy.liquid calphy.phase calphy.phase_diagram calphy.postprocessing calphy.queuekernel calphy.routines calphy.scheduler calphy.solid calphy.splines monte_carlo (calphy.input.Calculation attribute) MonteCarlo (class in calphy.input) mpi_executable (calphy.input.Calculation attribute) N n_cycles (calphy.input.MD attribute) n_elements (calphy.input.Calculation attribute) n_equilibration_steps (calphy.input.Calculation attribute) n_every_steps (calphy.input.MD attribute) n_f (calphy.input.QuantumThermalBath attribute) n_iterations (calphy.input.Calculation attribute) n_print_steps (calphy.input.Calculation attribute) n_print_steps_equilibration (calphy.input.Calculation attribute) n_repeat_steps (calphy.input.MD attribute) n_small_steps (calphy.input.MD attribute) n_steps (calphy.input.MonteCarlo attribute) n_swaps (calphy.input.MonteCarlo attribute) n_switching_steps (calphy.input.Calculation attribute) nose_hoover (calphy.input.Calculation attribute) NoseHoover (class in calphy.input) npt (calphy.input.Calculation attribute) O onset_fraction (calphy.input.PhaseTransitionDetection attribute) options (calphy.input.Queue attribute) output_chemical_composition (calphy.input.CompositionScaling attribute) (calphy.phase_diagram.CScale property) P p (calphy.input.UFMP attribute) pair_coeff (calphy.input.Calculation attribute) pair_mode (calphy.input.Calculation attribute) pair_style (calphy.input.Calculation attribute) Phase (class in calphy.phase) phase_diagram() (in module calphy.clitools) phase_name (calphy.input.Calculation attribute) phase_transition_detection (calphy.input.Calculation attribute) PhaseDiagram (class in calphy.phase_diagram) PhaseTransitionDetection (class in calphy.input) PhaseTransitionError plot() (calphy.phase_diagram.PhaseDiagram method) plot_calphad_surface_fit() (calphy.phase_diagram.PhaseDiagram method) plot_convergence() (calphy.phase_diagram.PhaseDiagram method) plot_data_vs_fit() (calphy.phase_diagram.PhaseDiagram method) plot_free_energy() (calphy.phase_diagram.PhaseDiagram method) plot_free_energy_mixing() (calphy.phase_diagram.PhaseDiagram method) plot_pd() (in module calphy.phase_diagram) plot_phase_diagram() (in module calphy.phase_diagram) potential_file (calphy.input.Calculation attribute) prepare_calcs() (calphy.routines.MeltingTemp method) prepare_inputs_for_phase_diagram() (in module calphy.phase_diagram) prepare_log() (in module calphy.helpers) prepare_mappings() (calphy.composition_transformation.CompositionTransformation method) prepare_pair_lists() (calphy.composition_transformation.CompositionTransformation method) prescan_steps (calphy.input.PhaseTransitionDetection attribute) press() (in module calphy.integrators) pressure (calphy.input.Calculation attribute) (calphy.input.Tolerance attribute) pressure_coupling (calphy.input.Calculation attribute) pressure_scaling() (calphy.phase.Phase method) process_pressure() (calphy.phase.Phase method) Q qdiss (calphy.phase.Phase attribute) quantum_thermal_bath (calphy.input.Calculation attribute) QuantumThermalBath (class in calphy.input) queue (calphy.input.Calculation attribute) Queue (class in calphy.input) queuename (calphy.input.Queue attribute) R rattle_structure() (calphy.liquid.Liquid method) read_data() (in module calphy.helpers) read_inputfile() (in module calphy.input) read_report() (in module calphy.postprocessing) read_structure_composition() (in module calphy.phase_diagram) real_pair_compute_commands() (in module calphy.helpers) reference_composition (calphy.input.Calculation attribute) reference_phase (calphy.input.Calculation attribute) remap_box() (in module calphy.helpers) repeat (calphy.input.Calculation attribute) replace_nones() (in module calphy.helpers) resolve_api_key() (calphy.input.MaterialsProject class method) restrictions (calphy.input.CompositionScaling attribute) reverse_swap_types (calphy.input.MonteCarlo attribute) reversible_scaling() (calphy.phase.Phase method) routine_alchemy() (in module calphy.routines) routine_composition_scaling() (in module calphy.routines) routine_fe() (in module calphy.routines) routine_pscale() (in module calphy.routines) routine_ts() (in module calphy.routines) routine_tscale() (in module calphy.routines) run_averaging() (calphy.alchemy.Alchemy method) (calphy.liquid.Liquid method) (calphy.solid.Solid method) run_calculation() (in module calphy.queuekernel) run_constrained_pressure_convergence() (calphy.phase.Phase method) run_finite_pressure_equilibration() (calphy.phase.Phase method) run_integration() (calphy.alchemy.Alchemy method) (calphy.liquid.Liquid method) (calphy.solid.Solid method) run_jobs() (calphy.routines.MeltingTemp method) (in module calphy.kernel) run_pressure_convergence() (calphy.phase.Phase method) run_spring_constant_convergence() (calphy.solid.Solid method) run_zero_pressure_equilibration() (calphy.phase.Phase method) RunnerStateError S scaled_pair_style_command() (in module calphy.helpers) scan_temperature_range() (calphy.phase.Phase method) scheduler (calphy.input.Queue attribute) script_mode (calphy.input.Calculation attribute) seed (calphy.input.MD attribute) set_mass() (in module calphy.helpers) set_pair_coeff() (in module calphy.helpers) set_pair_style() (in module calphy.helpers) set_potential() (in module calphy.helpers) setup_calculation() (in module calphy.queuekernel) SGE (class in calphy.scheduler) sigma (calphy.input.UFMP attribute) SimpleCalculation (class in calphy.phase_diagram) single_p (calphy.input.UFMP attribute) single_sigma (calphy.input.UFMP attribute) SLURM (class in calphy.scheduler) Solid (class in calphy.solid) solid_fraction (calphy.input.Tolerance attribute) SolidifiedError spring_constant (calphy.input.Tolerance attribute) spring_constants (calphy.input.Calculation attribute) start_calculation() (calphy.routines.MeltingTemp method) start_equilibration_dump() (calphy.phase.Phase method) step (calphy.input.MeltingTemperature attribute) stop_equilibration_dump() (calphy.phase.Phase method) submit() (calphy.scheduler.Local method) (calphy.scheduler.SGE method) (calphy.scheduler.SLURM method) submit_report() (calphy.phase.Phase method) T target_natoms (calphy.input.MaterialsProject attribute) temperature (calphy.input.Calculation attribute) temperature_high (calphy.input.Calculation attribute) temperature_scaling() (calphy.phase.Phase method) thermodynamic_integration() (calphy.alchemy.Alchemy method) (calphy.liquid.Liquid method) (calphy.solid.Solid method) thermostat_damping (calphy.input.Berendsen attribute) (calphy.input.MD attribute) (calphy.input.NoseHoover attribute) (calphy.input.QuantumThermalBath attribute) timestep (calphy.input.MD attribute) to_df() (calphy.phase_diagram.PhaseDiagram method) to_list() (in module calphy.input) to_parquet() (calphy.phase_diagram.PhaseDiagram method) to_pickle() (calphy.phase_diagram.PhaseDiagram method) to_tdb() (calphy.phase_diagram.PhaseDiagram method) tolerance (calphy.input.Calculation attribute) Tolerance (class in calphy.input) U ufm_pair_coeff_commands() (calphy.phase.Phase method) UFMP (class in calphy.input) uhlenbeck_ford_model (calphy.input.Calculation attribute) unfix_berendsen() (calphy.phase.Phase method) unfix_nose_hoover() (calphy.phase.Phase method) unfix_qtb() (calphy.phase.Phase method) update_mappings() (calphy.composition_transformation.CompositionTransformation method) update_mark_atoms() (calphy.composition_transformation.CompositionTransformation method) update_pair_coeff() (calphy.composition_transformation.CompositionTransformation method) update_typedicts() (calphy.composition_transformation.CompositionTransformation method) update_types() (calphy.composition_transformation.CompositionTransformation method) use_custom_lammps (calphy.input.MonteCarlo attribute) V validate_spring_constants() (in module calphy.helpers) W walltime (calphy.input.Queue attribute) write_data() (in module calphy.helpers) write_script() (calphy.scheduler.Local method) (calphy.scheduler.SGE method) (calphy.scheduler.SLURM method) write_structure() (calphy.composition_transformation.CompositionTransformation method)