Index

_

__all__ (dragonfruit.vasp.workflows attribute)

A

accept_run() (dragonfruit.ErrorHandler class method) (dragonfruit.vasp.ErrorHandler class method) (dragonfruit.vasp.vasp_errors.ErrorHandler class method) AdfOptimisation (class in dragonfruit.ionic_liquids) (class in dragonfruit.ionic_liquids.adf_scripts) AdfTask (class in dragonfruit.ionic_liquids) (class in dragonfruit.ionic_liquids.adf_scripts) ADJUSTMENT (dragonfruit.Fexcp attribute) (dragonfruit.Invgrp attribute) (dragonfruit.NotHermitian attribute) (dragonfruit.Posmap attribute) (dragonfruit.Pssyevx attribute) (dragonfruit.PssyevxParallelization attribute) (dragonfruit.Pzstein attribute) (dragonfruit.Rhosyg attribute) (dragonfruit.Sgrcon attribute) (dragonfruit.SimpleAdjustment attribute) (dragonfruit.vasp.Fexcp attribute) (dragonfruit.vasp.Invgrp attribute) (dragonfruit.vasp.NotHermitian attribute) (dragonfruit.vasp.Posmap attribute) (dragonfruit.vasp.Pssyevx attribute) (dragonfruit.vasp.PssyevxParallelization attribute) (dragonfruit.vasp.Pzstein attribute) (dragonfruit.vasp.Rhosyg attribute) (dragonfruit.vasp.Sgrcon attribute) (dragonfruit.vasp.SimpleAdjustment attribute) (dragonfruit.vasp.vasp_default_errors.Fexcp attribute) (dragonfruit.vasp.vasp_default_errors.Invgrp attribute) (dragonfruit.vasp.vasp_default_errors.NotHermitian attribute) (dragonfruit.vasp.vasp_default_errors.Posmap attribute) (dragonfruit.vasp.vasp_default_errors.Pssyevx attribute) (dragonfruit.vasp.vasp_default_errors.PssyevxParallelization attribute) (dragonfruit.vasp.vasp_default_errors.Pzstein attribute) (dragonfruit.vasp.vasp_default_errors.Rhosyg attribute) (dragonfruit.vasp.vasp_default_errors.Sgrcon attribute) (dragonfruit.vasp.vasp_default_errors.SimpleAdjustment attribute) (dragonfruit.vasp.vasp_default_errors.WavecarUnusable attribute) (dragonfruit.vasp.vasp_default_errors.Zbrent attribute) (dragonfruit.vasp.WavecarUnusable attribute) (dragonfruit.vasp.Zbrent attribute) (dragonfruit.WavecarUnusable attribute) (dragonfruit.Zbrent attribute) append_run() (dragonfruit.vasp.base.VaspTask method) (dragonfruit.vasp.VaspTask method) (dragonfruit.VaspTask method) AseVisualizable (class in dragonfruit) (class in dragonfruit.ase_utils) atoms (dragonfruit.ionic_liquids.adf_scripts.AdfTask property) (dragonfruit.ionic_liquids.AdfTask property) (dragonfruit.vasp.base.VaspRun property) (dragonfruit.vasp.base.VaspTask property) (dragonfruit.vasp.VaspRun property) (dragonfruit.vasp.VaspTask property) (dragonfruit.vasp.workflows.ConvergenceWorkflow property) (dragonfruit.vasp.workflows.ConvergenceWorkflowChain property) (dragonfruit.vasp.workflows.SingleTaskWorkflow property) (dragonfruit.vasp.workflows.VolumeMetaConvergence property) (dragonfruit.vasp.workflows.workflows.ConvergenceWorkflow property) (dragonfruit.vasp.workflows.workflows.ConvergenceWorkflowChain property) (dragonfruit.vasp.workflows.workflows.SingleTaskWorkflow property) (dragonfruit.vasp.workflows.workflows.VolumeMetaConvergence property) (dragonfruit.VaspRun property) (dragonfruit.VaspTask property)

atoms_history (dragonfruit.ionic_liquids.adf_scripts.AdfTask property) (dragonfruit.ionic_liquids.AdfTask property) (dragonfruit.vasp.base.VaspRun property) (dragonfruit.vasp.base.VaspTask property) (dragonfruit.vasp.VaspRun property) (dragonfruit.vasp.VaspTask property) (dragonfruit.vasp.workflows.VolumeMetaConvergence property) (dragonfruit.vasp.workflows.workflows.VolumeMetaConvergence property) (dragonfruit.VaspRun property) (dragonfruit.VaspTask property) atoms_to_spglib_cell() (in module dragonfruit.tools) ATTRS (dragonfruit.clease.scripts.RunWorkflow attribute) (dragonfruit.clease.scripts.simple_vasp.RunWorkflow attribute) (dragonfruit.environments.SchedulerEnvironment attribute) (dragonfruit.MaxRestarts attribute) (dragonfruit.mince.Process attribute) (dragonfruit.mince.process.Process attribute) (dragonfruit.RunRestarter attribute) (dragonfruit.SchedulerEnvironment attribute) (dragonfruit.vasp.base.VaspRun attribute) (dragonfruit.vasp.base.VaspTask attribute) (dragonfruit.vasp.MaxRestarts attribute) (dragonfruit.vasp.project.VaspProject attribute) (dragonfruit.vasp.RunRestarter attribute) (dragonfruit.vasp.vasp_default_errors.MaxRestarts attribute) (dragonfruit.vasp.vasp_default_errors.ZbrentAlternative attribute) (dragonfruit.vasp.vasp_errors.RunRestarter attribute) (dragonfruit.vasp.VaspProject attribute) (dragonfruit.vasp.VaspRun attribute) (dragonfruit.vasp.VaspTask attribute) (dragonfruit.vasp.workflows.ConvergenceWorkflowChain attribute) (dragonfruit.vasp.workflows.legacy.LegacyVolumeMetaConvergence attribute) (dragonfruit.vasp.workflows.legacy.LegacyWorkflow attribute) (dragonfruit.vasp.workflows.SingleTaskWorkflow attribute) (dragonfruit.vasp.workflows.VolumeMetaConvergence attribute) (dragonfruit.vasp.workflows.workflows.ConvergenceWorkflowChain attribute) (dragonfruit.vasp.workflows.workflows.SingleTaskWorkflow attribute) (dragonfruit.vasp.workflows.workflows.VolumeMetaConvergence attribute) (dragonfruit.vasp.ZbrentAlternative attribute) (dragonfruit.VaspProject attribute) (dragonfruit.VaspRun attribute) (dragonfruit.VaspTask attribute) (dragonfruit.ZbrentAlternative attribute)

B

base_settings (dragonfruit.vasp.workflows.ConvergenceWorkflowChain property) (dragonfruit.vasp.workflows.workflows.ConvergenceWorkflowChain property)

C

clean_large_vasp_files() (in module dragonfruit) (in module dragonfruit.vasp) (in module dragonfruit.vasp.vasp_utils) CLEASE_FINAL (dragonfruit.clease.Meta attribute) (dragonfruit.clease.pyos.Meta attribute) CLEASE_GROUP (dragonfruit.clease.Meta attribute) (dragonfruit.clease.pyos.Meta attribute) CLEASE_INITIAL (dragonfruit.clease.Meta attribute) (dragonfruit.clease.pyos.Meta attribute) clease_temporary_database() (in module dragonfruit.clease.utils) converged (dragonfruit.vasp.base.VaspRun property) (dragonfruit.vasp.base.VaspTask property) (dragonfruit.vasp.VaspRun property) (dragonfruit.vasp.VaspTask property) (dragonfruit.vasp.workflows.ConvergenceWorkflow property) (dragonfruit.vasp.workflows.ConvergenceWorkflowChain property) (dragonfruit.vasp.workflows.legacy.LegacyVolumeMetaConvergence property) (dragonfruit.vasp.workflows.SingleTaskWorkflow property) (dragonfruit.vasp.workflows.VolumeMetaConvergence property) (dragonfruit.vasp.workflows.workflows.ConvergenceWorkflow property) (dragonfruit.vasp.workflows.workflows.ConvergenceWorkflowChain property) (dragonfruit.vasp.workflows.workflows.SingleTaskWorkflow property) (dragonfruit.vasp.workflows.workflows.VolumeMetaConvergence property) (dragonfruit.VaspRun property) (dragonfruit.VaspTask property) ConvergenceWorkflow (class in dragonfruit.vasp.workflows) (class in dragonfruit.vasp.workflows.workflows) ConvergenceWorkflowChain (class in dragonfruit.vasp.workflows) (class in dragonfruit.vasp.workflows.workflows) copy_many() (in module dragonfruit.utils) copy_one() (in module dragonfruit.utils) count (dragonfruit.vasp.vasp_default_errors.ZbrentAlternative attribute) (dragonfruit.vasp.ZbrentAlternative attribute) (dragonfruit.ZbrentAlternative attribute)

crashed (dragonfruit.vasp.base.VaspRun property) (dragonfruit.vasp.base.VaspTask property) (dragonfruit.vasp.VaspRun property) (dragonfruit.vasp.VaspTask property) (dragonfruit.VaspRun property) (dragonfruit.VaspTask property) create_command() (in module dragonfruit.slurm) (in module dragonfruit.slurm.sbatch) create_copy() (dragonfruit.vasp.workflows.ConvergenceWorkflow method) (dragonfruit.vasp.workflows.SingleTaskWorkflow method) (dragonfruit.vasp.workflows.VolumeMetaConvergence method) (dragonfruit.vasp.workflows.workflows.ConvergenceWorkflow method) (dragonfruit.vasp.workflows.workflows.SingleTaskWorkflow method) (dragonfruit.vasp.workflows.workflows.VolumeMetaConvergence method) create_next_run() (in module dragonfruit.vasp.workflows) (in module dragonfruit.vasp.workflows.utils) create_restart() (dragonfruit.RunRestarter method) (dragonfruit.SimpleVaspWorkflow method) (dragonfruit.vasp.base.VaspRun method) (dragonfruit.vasp.RunRestarter method) (dragonfruit.vasp.simple_workflows.SimpleVaspWorkflow method) (dragonfruit.vasp.SimpleVaspWorkflow method) (dragonfruit.vasp.vasp_errors.RunRestarter method) (dragonfruit.vasp.VaspRun method) (dragonfruit.VaspRun method) (in module dragonfruit.vasp.workflows) (in module dragonfruit.vasp.workflows.utils) create_settings() (in module dragonfruit.clease) (in module dragonfruit.clease.pyos) current_workflow (dragonfruit.vasp.workflows.ConvergenceWorkflowChain property) (dragonfruit.vasp.workflows.workflows.ConvergenceWorkflowChain property)

D

default_profile (dragonfruit.Settings property) (dragonfruit.settings.Settings property) dependency() (in module dragonfruit.slurm) (in module dragonfruit.slurm.sbatch) deregister() (dragonfruit.RunRestarter method) (dragonfruit.vasp.RunRestarter method) (dragonfruit.vasp.vasp_errors.RunRestarter method) do_run() (dragonfruit.SimpleVaspWorkflow method) (dragonfruit.vasp.simple_workflows.SimpleVaspWorkflow method) (dragonfruit.vasp.SimpleVaspWorkflow method) done (dragonfruit.mince.Process property) (dragonfruit.mince.process.Process property) dragonfruit module dragonfruit.alloys module dragonfruit.alloys.vegard module dragonfruit.ase_utils module dragonfruit.clease module dragonfruit.clease.paths module dragonfruit.clease.pyos module dragonfruit.clease.scripts module dragonfruit.clease.scripts.simple_vasp module dragonfruit.clease.utils module dragonfruit.cli module dragonfruit.cli.db module dragonfruit.cli.main module dragonfruit.cli.profile_config module dragonfruit.cli.sbatch module dragonfruit.defaults module dragonfruit.environments module dragonfruit.ionic_liquids module dragonfruit.ionic_liquids.adf_scripts module dragonfruit.ionic_liquids.adf_task_scripts module dragonfruit.ionic_liquids.constants module

dragonfruit.ionic_liquids.plams_scripts module dragonfruit.mince module dragonfruit.mince.gui module dragonfruit.mince.process module dragonfruit.mince.utils module dragonfruit.mincepy module dragonfruit.pyos_utils module dragonfruit.settings module dragonfruit.slurm module dragonfruit.slurm.sbatch module dragonfruit.slurm.utils module dragonfruit.tools module dragonfruit.utils module dragonfruit.vasp module dragonfruit.vasp.base module dragonfruit.vasp.project module dragonfruit.vasp.simple_workflows module dragonfruit.vasp.vasp_default_errors module dragonfruit.vasp.vasp_errors module dragonfruit.vasp.vasp_parsers module dragonfruit.vasp.vasp_utils module dragonfruit.vasp.workflows module dragonfruit.vasp.workflows.legacy module dragonfruit.vasp.workflows.utils module dragonfruit.vasp.workflows.workflows module dragonfruit.version module

E

ERROR_STRING (dragonfruit.Fexcp attribute) (dragonfruit.Invgrp attribute) (dragonfruit.NotHermitian attribute) (dragonfruit.Posmap attribute) (dragonfruit.Pssyevx attribute) (dragonfruit.PssyevxParallelization attribute) (dragonfruit.Pzstein attribute) (dragonfruit.Rhosyg attribute) (dragonfruit.Sgrcon attribute) (dragonfruit.SimpleAdjustment attribute) (dragonfruit.vasp.Fexcp attribute) (dragonfruit.vasp.Invgrp attribute) (dragonfruit.vasp.NotHermitian attribute) (dragonfruit.vasp.Posmap attribute) (dragonfruit.vasp.Pssyevx attribute) (dragonfruit.vasp.PssyevxParallelization attribute) (dragonfruit.vasp.Pzstein attribute) (dragonfruit.vasp.Rhosyg attribute) (dragonfruit.vasp.Sgrcon attribute) (dragonfruit.vasp.SimpleAdjustment attribute) (dragonfruit.vasp.vasp_default_errors.Fexcp attribute) (dragonfruit.vasp.vasp_default_errors.Invgrp attribute) (dragonfruit.vasp.vasp_default_errors.NotHermitian attribute) (dragonfruit.vasp.vasp_default_errors.Posmap attribute) (dragonfruit.vasp.vasp_default_errors.Pssyevx attribute) (dragonfruit.vasp.vasp_default_errors.PssyevxParallelization attribute) (dragonfruit.vasp.vasp_default_errors.Pzstein attribute) (dragonfruit.vasp.vasp_default_errors.Rhosyg attribute) (dragonfruit.vasp.vasp_default_errors.Sgrcon attribute) (dragonfruit.vasp.vasp_default_errors.SimpleAdjustment attribute) (dragonfruit.vasp.vasp_default_errors.WavecarUnusable attribute) (dragonfruit.vasp.vasp_default_errors.Zbrent attribute) (dragonfruit.vasp.vasp_default_errors.ZbrentAlternative attribute) (dragonfruit.vasp.WavecarUnusable attribute) (dragonfruit.vasp.Zbrent attribute) (dragonfruit.vasp.ZbrentAlternative attribute) (dragonfruit.WavecarUnusable attribute) (dragonfruit.Zbrent attribute) (dragonfruit.ZbrentAlternative attribute)

ErrorHandler (class in dragonfruit) (class in dragonfruit.vasp) (class in dragonfruit.vasp.vasp_errors) execute_run() (dragonfruit.vasp.base.VaspTask method) (dragonfruit.vasp.VaspTask method) (dragonfruit.VaspTask method) extra (dragonfruit.environments.SchedulerEnvironment property) (dragonfruit.SchedulerEnvironment property)

F

fake_run() (dragonfruit.vasp.base.VaspRun method) (dragonfruit.vasp.VaspRun method) (dragonfruit.VaspRun method) Fexcp (class in dragonfruit) (class in dragonfruit.vasp) (class in dragonfruit.vasp.vasp_default_errors)

final_atoms (dragonfruit.ionic_liquids.adf_scripts.AdfTask property) (dragonfruit.ionic_liquids.AdfTask property) from_vasp_run() (dragonfruit.vasp.base.VaspRun class method) (dragonfruit.vasp.VaspRun class method) (dragonfruit.VaspRun class method)

G

generate_atoms_meta() (in module dragonfruit.tools) generate_symmetry_info() (in module dragonfruit.tools) get_atoms() (in module dragonfruit.clease) (in module dragonfruit.clease.pyos) get_atoms_sort_map() (in module dragonfruit.utils) get_concentrations() (in module dragonfruit.alloys.vegard) get_default_handlers() (in module dragonfruit) (in module dragonfruit.vasp) (in module dragonfruit.vasp.vasp_default_errors) get_elemental_cells() (in module dragonfruit.alloys.vegard) get_file() (in module dragonfruit) (in module dragonfruit.vasp) (in module dragonfruit.vasp.vasp_parsers) get_file_contents() (dragonfruit.vasp.base.VaspRun method) (dragonfruit.vasp.VaspRun method) (dragonfruit.VaspRun method) get_historian() (in module dragonfruit) (in module dragonfruit.mince) (in module dragonfruit.mince.utils) get_last_run() (dragonfruit.vasp.base.VaspTask method) (dragonfruit.vasp.VaspTask method) (dragonfruit.VaspTask method) get_ok_output_files() (in module dragonfruit) (in module dragonfruit.vasp) (in module dragonfruit.vasp.vasp_parsers) get_or_create() (dragonfruit.vasp.project.VaspProject class method) (dragonfruit.vasp.VaspProject class method) (dragonfruit.VaspProject class method) get_pair_name() (in module dragonfruit.ionic_liquids.adf_task_scripts) get_profile() (dragonfruit.Settings method) (dragonfruit.settings.Settings method) get_restarter() (dragonfruit.vasp.base.VaspTask method) (dragonfruit.vasp.VaspTask method) (dragonfruit.VaspTask method)

get_scheduler_environment() (in module dragonfruit) (in module dragonfruit.environments) get_settings() (in module dragonfruit) (in module dragonfruit.clease) (in module dragonfruit.clease.pyos) (in module dragonfruit.settings) get_structure_settings() (in module dragonfruit.clease) (in module dragonfruit.clease.pyos) get_types() (in module dragonfruit.mincepy) get_vasp_task() (dragonfruit.vasp.workflows.ConvergenceWorkflow method) (dragonfruit.vasp.workflows.ConvergenceWorkflowChain method) (dragonfruit.vasp.workflows.SingleTaskWorkflow method) (dragonfruit.vasp.workflows.VolumeMetaConvergence method) (dragonfruit.vasp.workflows.workflows.ConvergenceWorkflow method) (dragonfruit.vasp.workflows.workflows.ConvergenceWorkflowChain method) (dragonfruit.vasp.workflows.workflows.SingleTaskWorkflow method) (dragonfruit.vasp.workflows.workflows.VolumeMetaConvergence method) get_visualizable() (dragonfruit.ase_utils.AseVisualizable method) (dragonfruit.AseVisualizable method) (dragonfruit.ionic_liquids.adf_scripts.AdfTask method) (dragonfruit.ionic_liquids.AdfTask method) (dragonfruit.vasp.base.VaspRun method) (dragonfruit.vasp.base.VaspTask method) (dragonfruit.vasp.VaspRun method) (dragonfruit.vasp.VaspTask method) (dragonfruit.vasp.workflows.ConvergenceWorkflowChain method) (dragonfruit.vasp.workflows.SingleTaskWorkflow method) (dragonfruit.vasp.workflows.VolumeMetaConvergence method) (dragonfruit.vasp.workflows.workflows.ConvergenceWorkflowChain method) (dragonfruit.vasp.workflows.workflows.SingleTaskWorkflow method) (dragonfruit.vasp.workflows.workflows.VolumeMetaConvergence method) (dragonfruit.VaspRun method) (dragonfruit.VaspTask method) (in module dragonfruit) (in module dragonfruit.ase_utils)

I

import_ase_db() (in module dragonfruit.clease) (in module dragonfruit.clease.pyos) init() (in module dragonfruit.clease) (in module dragonfruit.clease.pyos) init_bulk() (in module dragonfruit.clease) (in module dragonfruit.clease.pyos) initial_atoms (dragonfruit.ionic_liquids.adf_scripts.AdfTask property) (dragonfruit.ionic_liquids.AdfTask property) (dragonfruit.vasp.base.VaspTask property) (dragonfruit.vasp.VaspTask property) (dragonfruit.vasp.workflows.ConvergenceWorkflow property) (dragonfruit.vasp.workflows.ConvergenceWorkflowChain property) (dragonfruit.vasp.workflows.SingleTaskWorkflow property) (dragonfruit.vasp.workflows.VolumeMetaConvergence property) (dragonfruit.vasp.workflows.workflows.ConvergenceWorkflow property) (dragonfruit.vasp.workflows.workflows.ConvergenceWorkflowChain property) (dragonfruit.vasp.workflows.workflows.SingleTaskWorkflow property) (dragonfruit.vasp.workflows.workflows.VolumeMetaConvergence property) (dragonfruit.VaspTask property) initial_settings (dragonfruit.vasp.base.VaspTask property) (dragonfruit.vasp.VaspTask property) (dragonfruit.vasp.workflows.ConvergenceWorkflow property) (dragonfruit.vasp.workflows.SingleTaskWorkflow property) (dragonfruit.vasp.workflows.VolumeMetaConvergence property) (dragonfruit.vasp.workflows.workflows.ConvergenceWorkflow property) (dragonfruit.vasp.workflows.workflows.SingleTaskWorkflow property) (dragonfruit.vasp.workflows.workflows.VolumeMetaConvergence property) (dragonfruit.VaspTask property)

internal_path() (in module dragonfruit.clease) (in module dragonfruit.clease.pyos) InvalidStateException, [1] Invgrp (class in dragonfruit) (class in dragonfruit.vasp) (class in dragonfruit.vasp.vasp_default_errors) is_converged() (in module dragonfruit) (in module dragonfruit.vasp) (in module dragonfruit.vasp.vasp_utils) is_outcar_corrupt() (in module dragonfruit) (in module dragonfruit.vasp) (in module dragonfruit.vasp.vasp_parsers) is_output_corrupt() (in module dragonfruit) (in module dragonfruit.vasp) (in module dragonfruit.vasp.vasp_parsers) is_relaxation() (in module dragonfruit) (in module dragonfruit.vasp) (in module dragonfruit.vasp.vasp_utils) is_slurm() (in module dragonfruit.slurm) (in module dragonfruit.slurm.utils) is_stress_converged() (in module dragonfruit) (in module dragonfruit.vasp) (in module dragonfruit.vasp.vasp_utils) is_string_in_file() (in module dragonfruit.utils) is_xml_corrupt() (in module dragonfruit) (in module dragonfruit.vasp) (in module dragonfruit.vasp.vasp_parsers)

K

keep_files (dragonfruit.ionic_liquids.adf_scripts.AdfOptimisation property) (dragonfruit.ionic_liquids.AdfOptimisation property)

L

label (dragonfruit.ionic_liquids.adf_scripts.AdfTask property) (dragonfruit.ionic_liquids.AdfTask property) LegacyVolumeMetaConvergence (class in dragonfruit.vasp.workflows.legacy) LegacyWorkflow (class in dragonfruit.vasp.workflows.legacy) list_all_profiles() (in module dragonfruit.cli.profile_config) list_single_profile() (in module dragonfruit.cli.profile_config) load() (in module dragonfruit) (in module dragonfruit.mince) (in module dragonfruit.mince.utils) load_instance_state() (dragonfruit.ionic_liquids.adf_scripts.AdfTask method) (dragonfruit.ionic_liquids.AdfTask method) (dragonfruit.SimpleVaspWorkflow method) (dragonfruit.vasp.base.VaspRun method) (dragonfruit.vasp.simple_workflows.SimpleVaspWorkflow method) (dragonfruit.vasp.SimpleVaspWorkflow method) (dragonfruit.vasp.VaspRun method) (dragonfruit.VaspRun method)

load_module() (in module dragonfruit.utils) load_object() (in module dragonfruit.utils) log_to_stdout() (in module dragonfruit.utils)

M

make_new_settings() (dragonfruit.vasp.workflows.ConvergenceWorkflowChain method) (dragonfruit.vasp.workflows.workflows.ConvergenceWorkflowChain method) make_new_workflow() (dragonfruit.vasp.workflows.ConvergenceWorkflowChain method) (dragonfruit.vasp.workflows.workflows.ConvergenceWorkflowChain method) make_vegard_atoms() (in module dragonfruit.alloys.vegard) max_count (dragonfruit.vasp.vasp_default_errors.ZbrentAlternative attribute) (dragonfruit.vasp.ZbrentAlternative attribute) (dragonfruit.ZbrentAlternative attribute) MaxRestarts (class in dragonfruit) (class in dragonfruit.vasp) (class in dragonfruit.vasp.vasp_default_errors) Meta (class in dragonfruit.clease) (class in dragonfruit.clease.pyos) module dragonfruit dragonfruit.alloys dragonfruit.alloys.vegard dragonfruit.ase_utils dragonfruit.clease dragonfruit.clease.paths dragonfruit.clease.pyos dragonfruit.clease.scripts dragonfruit.clease.scripts.simple_vasp dragonfruit.clease.utils dragonfruit.cli dragonfruit.cli.db dragonfruit.cli.main dragonfruit.cli.profile_config dragonfruit.cli.sbatch dragonfruit.defaults dragonfruit.environments dragonfruit.ionic_liquids dragonfruit.ionic_liquids.adf_scripts dragonfruit.ionic_liquids.adf_task_scripts dragonfruit.ionic_liquids.constants dragonfruit.ionic_liquids.plams_scripts dragonfruit.mince dragonfruit.mince.gui dragonfruit.mince.process dragonfruit.mince.utils dragonfruit.mincepy dragonfruit.pyos_utils dragonfruit.settings dragonfruit.slurm dragonfruit.slurm.sbatch dragonfruit.slurm.utils dragonfruit.tools dragonfruit.utils dragonfruit.vasp dragonfruit.vasp.base dragonfruit.vasp.project dragonfruit.vasp.simple_workflows dragonfruit.vasp.vasp_default_errors dragonfruit.vasp.vasp_errors dragonfruit.vasp.vasp_parsers dragonfruit.vasp.vasp_utils dragonfruit.vasp.workflows dragonfruit.vasp.workflows.legacy dragonfruit.vasp.workflows.utils dragonfruit.vasp.workflows.workflows dragonfruit.version

N

NAME (dragonfruit.ErrorHandler attribute) (dragonfruit.Fexcp attribute) (dragonfruit.Invgrp attribute) (dragonfruit.MaxRestarts attribute) (dragonfruit.NotHermitian attribute) (dragonfruit.Posmap attribute) (dragonfruit.Pssyevx attribute) (dragonfruit.PssyevxParallelization attribute) (dragonfruit.Pzstein attribute) (dragonfruit.Rhosyg attribute) (dragonfruit.Sgrcon attribute) (dragonfruit.SimpleAdjustment attribute) (dragonfruit.SlurmTimedOut attribute) (dragonfruit.vasp.ErrorHandler attribute) (dragonfruit.vasp.Fexcp attribute) (dragonfruit.vasp.Invgrp attribute) (dragonfruit.vasp.MaxRestarts attribute) (dragonfruit.vasp.NotHermitian attribute) (dragonfruit.vasp.Posmap attribute) (dragonfruit.vasp.Pssyevx attribute) (dragonfruit.vasp.PssyevxParallelization attribute) (dragonfruit.vasp.Pzstein attribute) (dragonfruit.vasp.Rhosyg attribute) (dragonfruit.vasp.Sgrcon attribute) (dragonfruit.vasp.SimpleAdjustment attribute) (dragonfruit.vasp.SlurmTimedOut attribute) (dragonfruit.vasp.vasp_default_errors.Fexcp attribute) (dragonfruit.vasp.vasp_default_errors.Invgrp attribute) (dragonfruit.vasp.vasp_default_errors.MaxRestarts attribute) (dragonfruit.vasp.vasp_default_errors.NotHermitian attribute) (dragonfruit.vasp.vasp_default_errors.Posmap attribute) (dragonfruit.vasp.vasp_default_errors.Pssyevx attribute) (dragonfruit.vasp.vasp_default_errors.PssyevxParallelization attribute) (dragonfruit.vasp.vasp_default_errors.Pzstein attribute) (dragonfruit.vasp.vasp_default_errors.Rhosyg attribute) (dragonfruit.vasp.vasp_default_errors.Sgrcon attribute) (dragonfruit.vasp.vasp_default_errors.SimpleAdjustment attribute) (dragonfruit.vasp.vasp_default_errors.SlurmTimedOut attribute) (dragonfruit.vasp.vasp_default_errors.WavecarUnusable attribute) (dragonfruit.vasp.vasp_default_errors.Zbrent attribute) (dragonfruit.vasp.vasp_default_errors.ZbrentAlternative attribute) (dragonfruit.vasp.vasp_errors.ErrorHandler attribute) (dragonfruit.vasp.WavecarUnusable attribute) (dragonfruit.vasp.Zbrent attribute) (dragonfruit.vasp.ZbrentAlternative attribute) (dragonfruit.WavecarUnusable attribute) (dragonfruit.Zbrent attribute) (dragonfruit.ZbrentAlternative attribute)

new_endpoints() (in module dragonfruit.clease) (in module dragonfruit.clease.pyos) new_random_structures() (in module dragonfruit.clease) (in module dragonfruit.clease.pyos) new_run() (dragonfruit.vasp.base.VaspTask method) (dragonfruit.vasp.VaspTask method) (dragonfruit.VaspTask method) NotASlurmEnvironment, [1] NotHermitian (class in dragonfruit) (class in dragonfruit.vasp) (class in dragonfruit.vasp.vasp_default_errors) null_context() (in module dragonfruit.utils) num_settings (dragonfruit.vasp.workflows.ConvergenceWorkflowChain property) (dragonfruit.vasp.workflows.workflows.ConvergenceWorkflowChain property) num_workflows (dragonfruit.vasp.workflows.ConvergenceWorkflowChain property) (dragonfruit.vasp.workflows.workflows.ConvergenceWorkflowChain property)

O

optimise_pair_task() (in module dragonfruit.ionic_liquids.adf_task_scripts)

optimise_task() (in module dragonfruit.ionic_liquids.adf_task_scripts)

P

parse_scf() (in module dragonfruit) (in module dragonfruit.vasp) (in module dragonfruit.vasp.vasp_parsers) PermanentFailure, [1], [2] PlamsTask (class in dragonfruit.ionic_liquids) (class in dragonfruit.ionic_liquids.plams_scripts) populate_atoms_meta() (in module dragonfruit.tools) populate_database() (in module dragonfruit.clease) (in module dragonfruit.clease.pyos) Posmap (class in dragonfruit) (class in dragonfruit.vasp) (class in dragonfruit.vasp.vasp_default_errors) print_file_contents() (dragonfruit.vasp.base.VaspRun method) (dragonfruit.vasp.VaspRun method) (dragonfruit.VaspRun method)

Process (class in dragonfruit.mince) (class in dragonfruit.mince.process) profiles (dragonfruit.Settings property) (dragonfruit.settings.Settings property) Pssyevx (class in dragonfruit) (class in dragonfruit.vasp) (class in dragonfruit.vasp.vasp_default_errors) PssyevxParallelization (class in dragonfruit) (class in dragonfruit.vasp) (class in dragonfruit.vasp.vasp_default_errors) py_to_sh() (in module dragonfruit.slurm) (in module dragonfruit.slurm.sbatch) Pzstein (class in dragonfruit) (class in dragonfruit.vasp) (class in dragonfruit.vasp.vasp_default_errors)

R

raises (dragonfruit.MaxRestarts attribute) (dragonfruit.vasp.MaxRestarts attribute) (dragonfruit.vasp.vasp_default_errors.MaxRestarts attribute) read_is_converged() (in module dragonfruit) (in module dragonfruit.vasp) (in module dragonfruit.vasp.vasp_parsers) read_is_crashed() (in module dragonfruit) (in module dragonfruit.vasp) (in module dragonfruit.vasp.vasp_parsers) read_settings() (dragonfruit.Settings method) (dragonfruit.settings.Settings method) register() (dragonfruit.RunRestarter method) (dragonfruit.vasp.RunRestarter method) (dragonfruit.vasp.vasp_errors.RunRestarter method) register_many() (dragonfruit.RunRestarter method) (dragonfruit.vasp.RunRestarter method) (dragonfruit.vasp.vasp_errors.RunRestarter method) reset_state() (dragonfruit.mince.Process method) (dragonfruit.mince.process.Process method) resort (dragonfruit.vasp.base.VaspRun property) (dragonfruit.vasp.VaspRun property) (dragonfruit.VaspRun property) resort_atoms_and_results() (in module dragonfruit.utils) result() (dragonfruit.mince.Process method) (dragonfruit.mince.process.Process method) results (dragonfruit.vasp.base.VaspRun property) (dragonfruit.vasp.base.VaspTask property) (dragonfruit.vasp.VaspRun property) (dragonfruit.vasp.VaspTask property) (dragonfruit.VaspRun property) (dragonfruit.VaspTask property) results_history (dragonfruit.ionic_liquids.adf_scripts.AdfOptimisation property) (dragonfruit.ionic_liquids.AdfOptimisation property) (dragonfruit.vasp.base.VaspRun property) (dragonfruit.vasp.base.VaspTask property) (dragonfruit.vasp.VaspRun property) (dragonfruit.vasp.VaspTask property) (dragonfruit.VaspRun property) (dragonfruit.VaspTask property) Rhosyg (class in dragonfruit) (class in dragonfruit.vasp) (class in dragonfruit.vasp.vasp_default_errors) root() (in module dragonfruit.clease) (in module dragonfruit.clease.pyos)

run() (dragonfruit.clease.scripts.RunWorkflow method) (dragonfruit.clease.scripts.simple_vasp.RunWorkflow method) (dragonfruit.ionic_liquids.adf_scripts.AdfOptimisation method) (dragonfruit.ionic_liquids.AdfOptimisation method) (dragonfruit.ionic_liquids.plams_scripts.PlamsTask method) (dragonfruit.ionic_liquids.PlamsTask method) (dragonfruit.SimpleVaspWorkflow method) (dragonfruit.vasp.base.VaspRun method) (dragonfruit.vasp.simple_workflows.SimpleVaspWorkflow method) (dragonfruit.vasp.SimpleVaspWorkflow method) (dragonfruit.vasp.VaspRun method) (dragonfruit.vasp.workflows.ConvergenceWorkflow method) (dragonfruit.vasp.workflows.ConvergenceWorkflowChain method) (dragonfruit.vasp.workflows.legacy.LegacyVolumeMetaConvergence method) (dragonfruit.vasp.workflows.legacy.LegacyWorkflow method) (dragonfruit.vasp.workflows.SingleTaskWorkflow method) (dragonfruit.vasp.workflows.VolumeMetaConvergence method) (dragonfruit.vasp.workflows.workflows.ConvergenceWorkflow method) (dragonfruit.vasp.workflows.workflows.ConvergenceWorkflowChain method) (dragonfruit.vasp.workflows.workflows.SingleTaskWorkflow method) (dragonfruit.vasp.workflows.workflows.VolumeMetaConvergence method) (dragonfruit.VaspRun method) run_clease_pyos() (in module dragonfruit.clease.scripts) (in module dragonfruit.clease.scripts.simple_vasp) run_clease_pyos_workflow() (in module dragonfruit.clease.scripts) (in module dragonfruit.clease.scripts.simple_vasp) run_path (dragonfruit.vasp.base.VaspRun property) (dragonfruit.vasp.VaspRun property) (dragonfruit.VaspRun property) run_settings (dragonfruit.vasp.base.VaspRun property) (dragonfruit.vasp.VaspRun property) (dragonfruit.VaspRun property) run_with_restart() (in module dragonfruit.vasp.workflows) (in module dragonfruit.vasp.workflows.utils) RunRestarter (class in dragonfruit) (class in dragonfruit.vasp) (class in dragonfruit.vasp.vasp_errors) runs (dragonfruit.vasp.base.VaspTask property) (dragonfruit.vasp.VaspTask property) (dragonfruit.VaspTask property) RunWorkflow (class in dragonfruit.clease.scripts) (class in dragonfruit.clease.scripts.simple_vasp)

S

sanitize_meta() (in module dragonfruit) (in module dragonfruit.pyos_utils) save() (in module dragonfruit) (in module dragonfruit.mince) (in module dragonfruit.mince.utils) save_instance_state() (dragonfruit.vasp.base.VaspRun method) (dragonfruit.vasp.base.VaspTask method) (dragonfruit.vasp.VaspRun method) (dragonfruit.vasp.VaspTask method) (dragonfruit.vasp.workflows.SingleTaskWorkflow method) (dragonfruit.vasp.workflows.VolumeMetaConvergence method) (dragonfruit.vasp.workflows.workflows.SingleTaskWorkflow method) (dragonfruit.vasp.workflows.workflows.VolumeMetaConvergence method) (dragonfruit.VaspRun method) (dragonfruit.VaspTask method) save_settings() (in module dragonfruit.clease) (in module dragonfruit.clease.pyos) scheduler (dragonfruit.environments.SchedulerEnvironment property) (dragonfruit.SchedulerEnvironment property) scheduler_env (dragonfruit.vasp.base.VaspRun property) (dragonfruit.vasp.VaspRun property) (dragonfruit.VaspRun property) SchedulerEnvironment (class in dragonfruit) (class in dragonfruit.environments) self_dependency() (in module dragonfruit.slurm) (in module dragonfruit.slurm.sbatch) set_final() (in module dragonfruit.clease) (in module dragonfruit.clease.pyos) set_initial() (in module dragonfruit.clease) (in module dragonfruit.clease.pyos) set_result() (dragonfruit.mince.Process method) (dragonfruit.mince.process.Process method) Settings (class in dragonfruit) (class in dragonfruit.settings) settings (dragonfruit.ionic_liquids.adf_scripts.AdfTask property) (dragonfruit.ionic_liquids.AdfTask property) (dragonfruit.vasp.base.VaspRun property) (dragonfruit.vasp.base.VaspTask property) (dragonfruit.vasp.VaspRun property) (dragonfruit.vasp.VaspTask property) (dragonfruit.VaspRun property) (dragonfruit.VaspTask property)

settings_changes (dragonfruit.vasp.workflows.ConvergenceWorkflowChain property) (dragonfruit.vasp.workflows.workflows.ConvergenceWorkflowChain property) settings_overwrites (dragonfruit.vasp.base.VaspRun property) (dragonfruit.vasp.VaspRun property) (dragonfruit.VaspRun property) Sgrcon (class in dragonfruit) (class in dragonfruit.vasp) (class in dragonfruit.vasp.vasp_default_errors) SimpleAdjustment (class in dragonfruit) (class in dragonfruit.vasp) (class in dragonfruit.vasp.vasp_default_errors) SimpleVaspWorkflow (class in dragonfruit) (class in dragonfruit.vasp) (class in dragonfruit.vasp.simple_workflows) SingleTaskWorkflow (class in dragonfruit.vasp.workflows) (class in dragonfruit.vasp.workflows.workflows) SKIP (dragonfruit.ErrorHandler attribute) (dragonfruit.vasp.ErrorHandler attribute) (dragonfruit.vasp.vasp_errors.ErrorHandler attribute) SlurmTimedOut (class in dragonfruit) (class in dragonfruit.vasp) (class in dragonfruit.vasp.vasp_default_errors) sort (dragonfruit.vasp.base.VaspRun property) (dragonfruit.vasp.VaspRun property) (dragonfruit.VaspRun property) stderr (dragonfruit.environments.SchedulerEnvironment property) (dragonfruit.SchedulerEnvironment property) stdout (dragonfruit.environments.SchedulerEnvironment property) (dragonfruit.SchedulerEnvironment property) stored_files (dragonfruit.ionic_liquids.adf_scripts.AdfOptimisation property) (dragonfruit.ionic_liquids.AdfOptimisation property) (dragonfruit.ionic_liquids.plams_scripts.PlamsTask property) (dragonfruit.ionic_liquids.PlamsTask property) (dragonfruit.vasp.base.VaspRun property) (dragonfruit.vasp.VaspRun property) (dragonfruit.VaspRun property) submit_script() (in module dragonfruit.slurm) (in module dragonfruit.slurm.sbatch) submit_structures() (in module dragonfruit.clease) (in module dragonfruit.clease.pyos) submit_workflow() (in module dragonfruit.clease) (in module dragonfruit.clease.pyos)

T

take_charge_from (dragonfruit.ionic_liquids.adf_scripts.AdfTask property) (dragonfruit.ionic_liquids.AdfTask property) task_list (dragonfruit.vasp.workflows.VolumeMetaConvergence property) (dragonfruit.vasp.workflows.workflows.VolumeMetaConvergence property) TEMPORARY (dragonfruit.SimpleAdjustment attribute) (dragonfruit.vasp.SimpleAdjustment attribute) (dragonfruit.vasp.vasp_default_errors.SimpleAdjustment attribute) (dragonfruit.vasp.vasp_default_errors.WavecarUnusable attribute) (dragonfruit.vasp.WavecarUnusable attribute) (dragonfruit.WavecarUnusable attribute) TYPE_ID (dragonfruit.clease.scripts.RunWorkflow attribute) (dragonfruit.clease.scripts.simple_vasp.RunWorkflow attribute) (dragonfruit.environments.SchedulerEnvironment attribute) (dragonfruit.Fexcp attribute) (dragonfruit.Invgrp attribute) (dragonfruit.ionic_liquids.adf_scripts.AdfOptimisation attribute) (dragonfruit.ionic_liquids.adf_scripts.AdfTask attribute) (dragonfruit.ionic_liquids.AdfOptimisation attribute) (dragonfruit.ionic_liquids.AdfTask attribute) (dragonfruit.ionic_liquids.plams_scripts.PlamsTask attribute) (dragonfruit.ionic_liquids.PlamsTask attribute) (dragonfruit.MaxRestarts attribute) (dragonfruit.NotHermitian attribute) (dragonfruit.Posmap attribute) (dragonfruit.Pssyevx attribute) (dragonfruit.PssyevxParallelization attribute) (dragonfruit.Pzstein attribute) (dragonfruit.Rhosyg attribute) (dragonfruit.RunRestarter attribute) (dragonfruit.SchedulerEnvironment attribute) (dragonfruit.Sgrcon attribute) (dragonfruit.SimpleVaspWorkflow attribute) (dragonfruit.SlurmTimedOut attribute) (dragonfruit.vasp.base.VaspRun attribute) (dragonfruit.vasp.base.VaspTask attribute) (dragonfruit.vasp.Fexcp attribute) (dragonfruit.vasp.Invgrp attribute) (dragonfruit.vasp.MaxRestarts attribute) (dragonfruit.vasp.NotHermitian attribute) (dragonfruit.vasp.Posmap attribute) (dragonfruit.vasp.project.VaspProject attribute) (dragonfruit.vasp.Pssyevx attribute) (dragonfruit.vasp.PssyevxParallelization attribute) (dragonfruit.vasp.Pzstein attribute) (dragonfruit.vasp.Rhosyg attribute) (dragonfruit.vasp.RunRestarter attribute) (dragonfruit.vasp.Sgrcon attribute) (dragonfruit.vasp.simple_workflows.SimpleVaspWorkflow attribute) (dragonfruit.vasp.SimpleVaspWorkflow attribute) (dragonfruit.vasp.SlurmTimedOut attribute) (dragonfruit.vasp.vasp_default_errors.Fexcp attribute) (dragonfruit.vasp.vasp_default_errors.Invgrp attribute) (dragonfruit.vasp.vasp_default_errors.MaxRestarts attribute) (dragonfruit.vasp.vasp_default_errors.NotHermitian attribute) (dragonfruit.vasp.vasp_default_errors.Posmap attribute) (dragonfruit.vasp.vasp_default_errors.Pssyevx attribute) (dragonfruit.vasp.vasp_default_errors.PssyevxParallelization attribute) (dragonfruit.vasp.vasp_default_errors.Pzstein attribute) (dragonfruit.vasp.vasp_default_errors.Rhosyg attribute) (dragonfruit.vasp.vasp_default_errors.Sgrcon attribute) (dragonfruit.vasp.vasp_default_errors.SlurmTimedOut attribute) (dragonfruit.vasp.vasp_default_errors.WavecarUnusable attribute) (dragonfruit.vasp.vasp_default_errors.Zbrent attribute) (dragonfruit.vasp.vasp_default_errors.ZbrentAlternative attribute) (dragonfruit.vasp.vasp_errors.RunRestarter attribute) (dragonfruit.vasp.VaspProject attribute) (dragonfruit.vasp.VaspRun attribute) (dragonfruit.vasp.VaspTask attribute) (dragonfruit.vasp.WavecarUnusable attribute) (dragonfruit.vasp.workflows.ConvergenceWorkflowChain attribute) (dragonfruit.vasp.workflows.legacy.LegacyVolumeMetaConvergence attribute) (dragonfruit.vasp.workflows.legacy.LegacyWorkflow attribute) (dragonfruit.vasp.workflows.SingleTaskWorkflow attribute) (dragonfruit.vasp.workflows.VolumeMetaConvergence attribute) (dragonfruit.vasp.workflows.workflows.ConvergenceWorkflowChain attribute) (dragonfruit.vasp.workflows.workflows.SingleTaskWorkflow attribute) (dragonfruit.vasp.workflows.workflows.VolumeMetaConvergence attribute) (dragonfruit.vasp.Zbrent attribute) (dragonfruit.vasp.ZbrentAlternative attribute) (dragonfruit.VaspProject attribute) (dragonfruit.VaspRun attribute) (dragonfruit.VaspTask attribute) (dragonfruit.WavecarUnusable attribute) (dragonfruit.Zbrent attribute) (dragonfruit.ZbrentAlternative attribute)

U

update_and_set_results() (dragonfruit.vasp.base.VaspRun method) (dragonfruit.vasp.VaspRun method) (dragonfruit.VaspRun method)

update_results() (dragonfruit.vasp.base.VaspRun method) (dragonfruit.vasp.VaspRun method) (dragonfruit.VaspRun method)

V

vasp_stdout (dragonfruit.vasp.base.VaspRun property) (dragonfruit.vasp.VaspRun property) (dragonfruit.VaspRun property) vasp_task (dragonfruit.vasp.workflows.legacy.LegacyWorkflow property) (dragonfruit.vasp.workflows.SingleTaskWorkflow property) (dragonfruit.vasp.workflows.workflows.SingleTaskWorkflow property) VaspProject (class in dragonfruit) (class in dragonfruit.vasp) (class in dragonfruit.vasp.project)

VaspRun (class in dragonfruit) (class in dragonfruit.vasp) (class in dragonfruit.vasp.base) VaspTask (class in dragonfruit) (class in dragonfruit.vasp) (class in dragonfruit.vasp.base) VolumeMetaConvergence (class in dragonfruit.vasp.workflows) (class in dragonfruit.vasp.workflows.workflows)

W

WavecarUnusable (class in dragonfruit) (class in dragonfruit.vasp) (class in dragonfruit.vasp.vasp_default_errors) workflows (dragonfruit.vasp.workflows.ConvergenceWorkflowChain property) (dragonfruit.vasp.workflows.workflows.ConvergenceWorkflowChain property)

working_directory() (in module dragonfruit.utils) write_settings() (dragonfruit.Settings method) (dragonfruit.settings.Settings method)

Z

Zbrent (class in dragonfruit) (class in dragonfruit.vasp) (class in dragonfruit.vasp.vasp_default_errors)

ZbrentAlternative (class in dragonfruit) (class in dragonfruit.vasp) (class in dragonfruit.vasp.vasp_default_errors)