IMDgroup-pymatgen

User Guide

  • Key Features & Optimizations
    • Optimized for High-Throughput (Caching)
    • Automated Health Checks & Warnings
    • Extensions to pymatgen
  • Getting Help
    • Command Line
    • Python Code
  • Installation
  • Command Line Interface
    • imdg status
    • imdg analyze
    • imdg create
    • imdg derive
      • General usage
      • Subcommands
      • NEB and Diffusion
    • imdg diff
    • imdg visualize
      • neb
      • atat
      • hull
      • voltage
    • pmg-insert-molecule
  • Python API
    • Opening ATAT structure files (str.out, lat.in)
    • VASP Directory Handling
    • Transformations
      • Inserting Molecules
      • Symmetry Cloning
    • Diffusion Analysis
  • Acknowledgements

API Reference

  • API Reference
    • Core
      • groupby_cmp()
      • IMDStructure
        • IMDStructure.from_file()
        • IMDStructure.from_structure()
        • IMDStructure.to()
        • IMDStructure.to_file()
      • StructureDuplicateWarning
      • get_matched_structure()
      • get_supercell_size()
      • merge_structures()
      • reduce_supercell()
      • structure_diff()
      • structure_distance()
      • structure_interpolate2()
      • structure_is_valid2()
      • structure_matches()
      • structure_perturb()
      • structure_remove_duplicates()
      • structure_strain()
    • I/O
      • IMDGVaspDir
        • IMDGVaspDir.CACHE_VERSION
        • IMDGVaspDir.EXCLUDE_PATTERNS
        • IMDGVaspDir.FILE_MAPPINGS
        • IMDGVaspDir.TIMEOUT
        • IMDGVaspDir.__init__()
        • IMDGVaspDir.check_displacements()
        • IMDGVaspDir.check_framework_symmetry()
        • IMDGVaspDir.converged
        • IMDGVaspDir.converged_electronic
        • IMDGVaspDir.converged_ionic
        • IMDGVaspDir.converged_manual
        • IMDGVaspDir.converged_sequence
        • IMDGVaspDir.final_energy
        • IMDGVaspDir.final_energy_reliable
        • IMDGVaspDir.flush_cache()
        • IMDGVaspDir.initial_structure
        • IMDGVaspDir.logs()
        • IMDGVaspDir.max_force()
        • IMDGVaspDir.mtime()
        • IMDGVaspDir.neb_dirs()
        • IMDGVaspDir.nebp
        • IMDGVaspDir.prev_dirs()
        • IMDGVaspDir.read_vaspdirs()
        • IMDGVaspDir.refresh()
        • IMDGVaspDir.reset()
        • IMDGVaspDir.structure
        • IMDGVaspDir.total_magnetization
        • IMDGVaspDir.warnings
      • TimeoutException
      • timeout_handler()
      • Incar
        • Incar.IBRION_IONIC_RELAX_CGA
        • Incar.IBRION_IONIC_RELAX_DAMPED_MD
        • Incar.IBRION_IONIC_RELAX_FORCE_FAST
        • Incar.IBRION_IONIC_RELAX_values
        • Incar.IBRION_MD
        • Incar.IBRION_NONE
        • Incar.IFIX_FIX_POS_VOL
        • Incar.ISIF_FIX_NONE
        • Incar.ISIF_FIX_POS
        • Incar.ISIF_FIX_POS_SHAPE
        • Incar.ISIF_FIX_SHAPE
        • Incar.ISIF_FIX_SHAPE_VOL
        • Incar.ISIF_FIX_SHAPE_VOL_FAST
        • Incar.ISIF_FIX_SHAPE_VOL_TRACE
        • Incar.ISIF_FIX_VOL
        • Incar.ISIF_RELAX_POS
        • Incar.ISIF_RELAX_POS_FAST
        • Incar.ISIF_RELAX_POS_SHAPE
        • Incar.ISIF_RELAX_POS_SHAPE_VOL
        • Incar.ISIF_RELAX_POS_TRACE
        • Incar.ISIF_RELAX_POS_VOL
        • Incar.ISIF_RELAX_SHAPE
        • Incar.ISIF_RELAX_SHAPE_VOL
        • Incar.ISIF_RELAX_VOL
        • Incar.get_recipe()
        • Incar.group_incars()
        • Incar.image_dir_names()
      • Outcar
        • Outcar.as_dict()
        • Outcar.file
        • Outcar.final_forces
      • Vasplog
        • Vasplog.__init__()
      • VasplogMixin
        • VasplogMixin.MAX_SIZE
        • VasplogMixin.VASP_LOG_FILES
        • VasplogMixin.VASP_PROGRESS
        • VasplogMixin.VASP_WARNINGS
        • VasplogMixin.from_dir()
        • VasplogMixin.parse()
        • VasplogMixin.progress
        • VasplogMixin.vasp_log_files()
        • VasplogMixin.warnings
      • Vasprun
        • Vasprun.PRESSURE_CONVERGENCE_THRESHOLD
        • Vasprun.check_forces()
        • Vasprun.check_stress()
        • Vasprun.converged_ionic
        • Vasprun.final_energy
        • Vasprun.warnings
      • IMDDerivedInputSet
        • IMDDerivedInputSet.directory
        • IMDDerivedInputSet.force_prev_incar_file
        • IMDDerivedInputSet.force_prev_kpoints_file
        • IMDDerivedInputSet.images
        • IMDDerivedInputSet.incar
        • IMDDerivedInputSet.inherit_prev_incarpy
        • IMDDerivedInputSet.kpoints
        • IMDDerivedInputSet.kpoints_updates
      • IMDGraphite
        • IMDGraphite.CONFIG
        • IMDGraphite.force_gamma
      • IMDNEBVaspInputSet
        • IMDNEBVaspInputSet.CONFIG
        • IMDNEBVaspInputSet.fix_cutoff
        • IMDNEBVaspInputSet.frac_tol
        • IMDNEBVaspInputSet.incar
        • IMDNEBVaspInputSet.method
        • IMDNEBVaspInputSet.target_directory
        • IMDNEBVaspInputSet.update_images()
        • IMDNEBVaspInputSet.write_input()
      • IMDNEBVaspInputSetWarning
      • IMDRelaxCellulose
        • IMDRelaxCellulose.CONFIG
        • IMDRelaxCellulose.force_gamma
      • IMDStandardVaspInputSet
        • IMDStandardVaspInputSet.CONFIG
      • IMDStandardVaspInputSet_relax
        • IMDStandardVaspInputSet_relax.CONFIG
      • IMDStandardVaspInputSet_scf
        • IMDStandardVaspInputSet_scf.CONFIG
      • IMDVaspInputSet
        • IMDVaspInputSet.CONFIG
        • IMDVaspInputSet.functional
        • IMDVaspInputSet.images
        • IMDVaspInputSet.incar
        • IMDVaspInputSet.incar_updates
        • IMDVaspInputSet.kpoints
        • IMDVaspInputSet.name
        • IMDVaspInputSet.no_incar
        • IMDVaspInputSet.no_kpoints
        • IMDVaspInputSet.no_poscar
        • IMDVaspInputSet.no_potcar
        • IMDVaspInputSet.poscar
        • IMDVaspInputSet.potcar
        • IMDVaspInputSet.potcar_symbols
        • IMDVaspInputSet.write_input()
      • write_selective_dynamics_summary_maybe()
      • check_sublattice_flip()
      • check_volume_distortion()
      • fit_sublattice_to_structure()
    • Diffusion
      • NEB_Graph
        • NEB_Graph.structures
        • NEB_Graph.multithread
        • NEB_Graph.jimage_idxs
        • NEB_Graph.__init__()
        • NEB_Graph.all_diffusion_paths_infinite()
        • NEB_Graph.connected()
        • NEB_Graph.diffusion_path_infinite()
        • NEB_Graph.get_min_cutoff()
      • get_neb_pairs()
      • get_neb_pairs_warning
    • Transformations
      • InsertMoleculeTransformation
        • InsertMoleculeTransformation.molecule
        • InsertMoleculeTransformation.step
        • InsertMoleculeTransformation.step_noise
        • InsertMoleculeTransformation.anglestep
        • InsertMoleculeTransformation.proximity_threshold
        • InsertMoleculeTransformation.label
        • InsertMoleculeTransformation.selective_dynamics
        • InsertMoleculeTransformation.reduce_supercell
        • InsertMoleculeTransformation.matcher
        • InsertMoleculeTransformation.multithread
        • InsertMoleculeTransformation.__init__()
        • InsertMoleculeTransformation.all_inserts()
        • InsertMoleculeTransformation.apply_transformation()
        • InsertMoleculeTransformation.is_one_to_many
        • InsertMoleculeTransformation.rotate_molecule_euler()
      • get_all_molecule_inserts()
      • SymmetryCloneTransformation
        • SymmetryCloneTransformation.sym_operations
        • SymmetryCloneTransformation.tol
        • SymmetryCloneTransformation.filter_cls
        • SymmetryCloneTransformation.__init__()
        • SymmetryCloneTransformation.apply_transformation()
        • SymmetryCloneTransformation.get_all_clones()
        • SymmetryCloneTransformation.is_one_to_many
      • SymmetryFillTransformation
        • SymmetryFillTransformation.__init__()
        • SymmetryFillTransformation.apply_transformation()
      • apply_operation_keep_lattice()
    • Command-line interface
      • main()
      • setup_logger()
      • add_args()
      • analyze()
      • read_field()
      • add_args()
      • create()
      • create_from_atom_name()
      • create_from_file()
      • create_from_mpid()
      • add_args()
      • atat()
      • atat_add_args()
      • delete()
      • delete_add_args()
      • derive()
      • fill()
      • fill_add_args()
      • fix()
      • fix_add_args()
      • functional()
      • functional_add_args()
      • incar()
      • incar_add_args()
      • insert()
      • insert_add_args()
      • kpoints()
      • kpoints_add_args()
      • neb()
      • neb_add_args()
      • neb_diffusion()
      • neb_diffusion_add_args()
      • perturb()
      • perturb_add_args()
      • relax()
      • relax_add_args()
      • scf()
      • scf_add_args()
      • strain()
      • strain_add_args()
      • supercell()
      • supercell_add_args()
      • add_args()
      • diff()
      • diff_incar()
      • diff_structures()
      • incar_add_args()
      • structure_add_args()
      • add_args()
      • custom_showwarning()
      • print_seconds()
      • slurm_runningp()
      • status()
      • vasp_output_time()
      • add_args()
      • atat()
      • atat_add_args()
      • hull()
      • hull_add_args()
      • neb()
      • neb_add_args()
      • selective_dynamics()
      • selective_dynamics_add_args()
      • visualize()
      • voltage()
      • voltage_add_args()
    • Utilities
      • mpl_defaults()
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