Index

Symbols

--acs tcmu-cite command line option --charge tcmu-optimize command line option --exit tcmu-workflow-status command line option --folder tcmu-resize command line option --hash tcmu-workflow-clear command line option tcmu-workflow-status command line option --keep tcmu-optimize command line option --level tcmu-optimize command line option --list_citations tcmu-cite command line option --log_level tcmu-concat-irc command line option --output tcmu-cite command line option tcmu-concat-irc command line option tcmu-optimize command line option --padding tcmu-resize command line option --properties tcmu-read command line option --pyramidal tcmu-geo command line option --reverse tcmu-concat-irc command line option --rsc tcmu-cite command line option --soa tcmu-geo command line option --spinpol tcmu-optimize command line option

--status tcmu-read command line option --wiley tcmu-cite command line option -a tcmu-cite command line option -c tcmu-optimize command line option -f tcmu-resize command line option -h tcmu-workflow-clear command line option tcmu-workflow-status command line option -k tcmu-optimize command line option -l tcmu-cite command line option tcmu-concat-irc command line option tcmu-optimize command line option -o tcmu-cite command line option tcmu-concat-irc command line option tcmu-optimize command line option -p tcmu-geo command line option tcmu-read command line option tcmu-resize command line option -r tcmu-cite command line option tcmu-concat-irc command line option -s tcmu-geo command line option tcmu-optimize command line option tcmu-read command line option -w tcmu-cite command line option -x tcmu-workflow-status command line option

A

Ada (class in tcmu.connect) add_column() (DocxTable method) add_column_group() (DocxTable method) add_empty_row() (DocxTable method) add_figure() (SI method) add_footnote() (DocxTable method) add_fragment() (ADFFragmentJob method), [1] add_header_row() (DocxTable method) add_heading() (SI method) add_image() (DocxFigure method) add_nics_point() (NMRJob method), [1] add_page_break() (SI method) add_row() (DocxTable method) add_table() (SI method) add_title() (in module tcmu.report.formatters.xyz) add_toc() (SI method) add_xyz() (SI method) ADFFragmentJob (class in tcmu) (class in tcmu.job.adf) ADFJob (class in tcmu) (class in tcmu.job.adf)

align_to_plane() (MolTransform method), [1] align_to_vector() (MolTransform method), [1] alpb() (QCGJob method), [1] AMSJob (class in tcmu) (class in tcmu.job.ams) ANGLE (GeometricParameter attribute) angstrom (Emojis attribute) apply() (Transform method), [1] apply_rotmat() (in module tcmu) (in module tcmu.geometry) as_dict() (Result method), [1] as_plams_settings() (Result method), [1] atom_index (VDDCharge attribute), [1] ATOM_INDICES tcmu-geo command line option atom_number() (in module tcmu.data.atom) atom_symbol (VDDCharge attribute), [1] atom_to_index() (MolTransform method), [1] avg_relative_bond_length_delta() (in module tcmu) (in module tcmu.analysis.vibration.ts_vibration)

B

basis_set() (ADFJob method), [1] (ORCAJob method), [1] best_conformer_path (CRESTJob property), [1] (GOATJob property), [1] (TDJob property)

best_ensemble_path (QCGJob property), [1] boxed() (in module tcmu.log)

C

cache() (in module tcmu) (in module tcmu.cache) cache_file() (in module tcmu) (in module tcmu.cache) caller_name() (in module tcmu.log) can_skip() (DensfJob method) cancel (Emojis attribute) cd() (Connection method), [1] center() (MolTransform method), [1] change_unit() (VDDCharge method), [1] (VDDChargeManager method) charge (VDDCharge attribute), [1] charge() (AMSJob method), [1] (CRESTJob method), [1] (ORCAJob method), [1] (TDJob method) (XTBJob method), [1] charge_is_conserved() (VDDChargeManager method) check() (in module tcmu.spell_check) check_if_job_is_suitable_for_xyz_format() (in module tcmu.report.formatters.xyz) chmod() (Connection method), [1] (Local method), [1]

cite() (in module tcmu) (in module tcmu.cite) clear_lines() (in module tcmu.cli_scripts.workflow) close() (Connection method), [1] color() (in module tcmu.data.atom) combine_transforms() (Transform method), [1] concatenate_irc_trajectories() (in module tcmu) (in module tcmu.analysis.task_specific.irc) conformer_directory (CRESTJob property), [1] (TDJob property) Connection (class in tcmu) (class in tcmu.connect) constraint() (AMSJob method), [1] coord() (PyFragResult method), [1] COORDINATE (GeometricParameter attribute) copy() (Result method), [1] create_result_objects() (in module tcmu.analysis.task_specific.irc) create_vdd_charge_manager() (in module tcmu.analysis.vdd.manager) crest_path (CRESTJob property), [1] CRESTJob (class in tcmu) (class in tcmu.job.crest) critical() (in module tcmu.log)

D

debug() (in module tcmu.log) delete() (in module tcmu.job.workflow_db) DensfJob (class in tcmu) density() (DensfJob method) determine_ts_reactioncoordinate() (in module tcmu) (in module tcmu.analysis.vibration.ts_vibration) DFTBJob (class in tcmu) (class in tcmu.job.dftb)

DIHEDRAL (GeometricParameter attribute) DISTANCE (GeometricParameter attribute) do_crossing() (CRESTJob method), [1] Docx (class in tcmu.cli_scripts.cite) DocxFigure (class in tcmu.report.report) DocxTable (class in tcmu.report.report) download() (Connection method), [1] (Local method), [1]

E

E (XYZData attribute) electric_field() (AMSJob method), [1] element() (in module tcmu.data.atom) Emojis (class in tcmu.log) empty (Emojis attribute) ensemble_directory (QCGJob property), [1] ensemble_mode() (QCGJob method), [1] ensure_2d() (in module tcmu.typing_utilities)

ensure_list() (in module tcmu.typing_utilities) error() (in module tcmu.log) excitations() (ADFJob method), [1] execute() (Connection method), [1] (Local method), [1] (WorkFlow method), [1] extract_func_code() (in module tcmu.job.workflow) (in module tcmu.job.workflow3) extras_install (TCMUMissingOptionalPackageError attribute)

F

fail (Emojis attribute) finish (Emojis attribute) flow() (in module tcmu.log) format() (StandardXYZFormatter method) (WordFormatter method) format_paragraph() (in module tcmu.cli_scripts.cite) format_xyz() (in module tcmu.report.formatters.xyz) frag_index (VDDCharge attribute), [1]

frag_occupations() (ADFFragmentJob method), [1] fragments (PyFragResult property), [1] from_string() (in module tcmu) (in module tcmu.molecule) full_path() (Connection method), [1] functional() (ADFJob method), [1] functional_name_from_path_safe_name() (in module tcmu) (in module tcmu.data.functionals)

G

G (XYZData attribute) generate_vtk() (DensfJob method) GeometricParameter (class in tcmu.cli_scripts.geo) geometry_convergence() (AMSJob method), [1] get() (in module tcmu.data.molecules) (in module tcmu.results.cache) get_ams_info() (in module tcmu.results.ams) get_ams_version() (in module tcmu.results.ams) get_available_functionals() (in module tcmu) (in module tcmu.data.functionals) get_calc_files() (in module tcmu.results.ams) (in module tcmu.results.crest) (in module tcmu.results.orca) (in module tcmu.results.xtb) get_calc_settings() (in module tcmu.results.adf) (in module tcmu.results.dftb) (in module tcmu.results.orca) get_calculation_status() (in module tcmu.results.ams) (in module tcmu.results.crest) (in module tcmu.results.orca) (in module tcmu.results.xtb) get_closest() (in module tcmu.spell_check) get_conformer_xyz() (CRESTJob method), [1] (TDJob method) get_current_server() (in module tcmu.connect) get_data_for_xyz_format() (in module tcmu.report.formatters.xyz) get_ensemble_xyz() (QCGJob method), [1] get_functional() (in module tcmu) (in module tcmu.data.functionals) get_geometry() (PyFragResult method), [1] get_history() (in module tcmu.results.ams) get_info() (in module tcmu) (in module tcmu.results.crest) (in module tcmu.results.orca) (in module tcmu.results.read) (in module tcmu.results.xtb) get_input() (in module tcmu.results.crest) (in module tcmu.results.orca) (in module tcmu.results.xtb) (ORCAJob method), [1] get_input_blocks() (in module tcmu.results.ams) get_level_of_theory() (in module tcmu.results.adf) (in module tcmu.results.orca) get_memory_usage() (ORCAJob method), [1] get_molecules() (in module tcmu.data.molecules) (in module tcmu.results.ams) (in module tcmu.results.crest) (in module tcmu.results.orca) (in module tcmu.results.xtb) (PyFragResult method), [1]

get_multi_key() (Result method), [1] get_parent_tree() (Result method), [1] get_pixel_width() (in module tcmu.report.character) get_properties() (in module tcmu.results.adf) (in module tcmu.results.dftb) (in module tcmu.results.orca) (in module tcmu.results.xtb) get_property() (PyFragResult method), [1] get_pyfrag_results() (in module tcmu) (in module tcmu.analysis.pyfrag) get_rotamer_xyz() (CRESTJob method), [1] (TDJob method) get_rotmat() (in module tcmu) (in module tcmu.geometry) (Transform method), [1] get_sbatch() (WorkFlow method) get_status() (in module tcmu.job.workflow_db) get_subdirectories() (in module tcmu.pathfunc) get_subdirs() (in module tcmu.report.report) get_summed_vdd_charges() (VDDChargeManager method) get_summed_vdd_charges_dataframe() (VDDChargeManager method) get_summed_vdd_charges_table() (VDDChargeManager method) get_translation() (Transform method), [1] get_vdd_charges() (VDDChargeManager method) get_vdd_charges_dataframe() (VDDChargeManager method) get_vdd_charges_table() (VDDChargeManager method) get_version() (in module tcmu.results.crest) (in module tcmu.results.orca) (in module tcmu.results.xtb) get_vibrations() (in module tcmu.results.orca) get_workflow_name() (in module tcmu.job.workflow_db) getsizeof() (Result method), [1] ghost_atoms() (ORCAJob method), [1] GOATJob (class in tcmu) (class in tcmu.job.orca) good (Emojis attribute) grid() (DensfJob method) grid_around_mol() (DensfJob method) gridsize() (DensfJob method) guess_fragments() (ADFFragmentJob method), [1] (in module tcmu) (in module tcmu.molecule)

H

H (XYZData attribute) handle_return_statements() (in module tcmu.job.workflow) (in module tcmu.job.workflow3)

hash() (in module tcmu.job.workflow) (in module tcmu.job.workflow3) home (Local attribute), [1]

I

imag_freqs (XYZData attribute) info (Emojis attribute) info() (in module tcmu.log) interaction_energy() (PyFragResult method), [1]

ionic_radius() (in module tcmu.data.atom) IRC() (AMSJob method), [1] irrep_occupations() (ADFJob method), [1] is_available (WorkFlowOutput property), [1] items() (Result method), [1]

J

JOBS tcmu-concat-irc command line option

K

KabschTransform (class in tcmu) (class in tcmu.geometry) KEYS tcmu-read command line option

keys() (Result method), [1] kspace() (DFTBJob method), [1]

L

larrow (Emojis attribute) LINUX (OSName attribute) load() (in module tcmu) (in module tcmu.molecule) loadbar() (in module tcmu.log)

Local (class in tcmu) (class in tcmu.connect) log() (in module tcmu.log) lrarrow (Emojis attribute) ls() (Connection method), [1] (Local method), [1]

M

MACOS (OSName attribute) main() (in module tcmu.report.report) (ORCAJob method), [1] make_suggestion() (in module tcmu.spell_check) match() (in module tcmu.pathfunc) md_length() (CRESTJob method), [1] (TDJob method) md_temperature() (CRESTJob method), [1] (TDJob method) merge_cells() (DocxTable method) method() (ORCAJob method), [1] mkdir() (Connection method), [1] (Local method), [1] model() (DFTBJob method), [1] (XTBJob method), [1] module tcmu tcmu.analysis tcmu.analysis.pyfrag tcmu.analysis.task_specific tcmu.analysis.task_specific.irc tcmu.analysis.vdd tcmu.analysis.vdd.charge tcmu.analysis.vdd.manager tcmu.analysis.vibration tcmu.analysis.vibration.ts_vibration tcmu.cache tcmu.cite tcmu.cli_scripts tcmu.cli_scripts.cite tcmu.cli_scripts.concatenate_irc tcmu.cli_scripts.geo tcmu.cli_scripts.job_script tcmu.cli_scripts.read tcmu.cli_scripts.resize_figures tcmu.cli_scripts.tcparser tcmu.cli_scripts.workflow tcmu.connect tcmu.constants tcmu.data tcmu.data.atom tcmu.data.basis_sets tcmu.data.cosmo tcmu.data.functionals tcmu.data.molecules tcmu.environment tcmu.errors tcmu.formula tcmu.geometry tcmu.job tcmu.job.adf tcmu.job.ams tcmu.job.crest tcmu.job.dftb tcmu.job.generic tcmu.job.models tcmu.job.nmr tcmu.job.orca tcmu.job.postscripts tcmu.job.postscripts.clean_workdir tcmu.job.postscripts.split_crest_xyz tcmu.job.postscripts.write_converged_geoms tcmu.job.workflow tcmu.job.workflow3 tcmu.job.workflow_db tcmu.job.workflow_status tcmu.job.xtb tcmu.log tcmu.molecule tcmu.pathfunc tcmu.report tcmu.report.character tcmu.report.figure_resizer tcmu.report.formatters tcmu.report.formatters.generic tcmu.report.formatters.xyz tcmu.report.report tcmu.results tcmu.results.adf tcmu.results.ams tcmu.results.cache tcmu.results.crest tcmu.results.dftb tcmu.results.orca tcmu.results.read tcmu.results.result tcmu.results.xtb tcmu.slurm tcmu.spell_check tcmu.timer tcmu.typing_utilities

molecule (XYZData attribute) molecule() (in module tcmu.formula) (ORCAJob method), [1] MolTransform (class in tcmu) (class in tcmu.geometry) multi_keys() (Result method), [1] multiplicity() (ADFJob method), [1] (CRESTJob method), [1] (ORCAJob method), [1] (TDJob method) (XTBJob method), [1]

N

naive_recursive() (in module tcmu.spell_check) NAME tcmu-workflow-clear command line option tcmu-workflow-status command line option name (XYZData attribute) NCI() (DensfJob method) NMRJob (class in tcmu) (class in tcmu.job.nmr)

nofix() (QCGJob method), [1] NoPrint (class in tcmu.log) nsolv() (QCGJob method), [1] num_imag_modes (XYZData attribute) number_of_electrons() (in module tcmu) (in module tcmu.molecule) number_of_orbitals() (in module tcmu.data.basis_sets) number_of_virtuals() (in module tcmu.data.basis_sets)

O

OBJECTS tcmu-cite command line option occupations() (ADFJob method), [1] open() (Connection method), [1] (Docx method) open_file() (Connection method), [1] (Local method), [1] optimization() (AMSJob method), [1] (ORCAJob method), [1] (XTBJob method), [1]

orbital() (DensfJob method) orbital_energy_gap() (PyFragResult method), [1] orbs() (PyFragResult method), [1] ORCAJob (class in tcmu) (class in tcmu.job.orca) OSName (class in tcmu.connect) output_cub_paths (DensfJob property) output_mol_path (AMSJob property), [1] (ORCAJob property), [1] (XTBJob property), [1] overlap() (PyFragResult method), [1]

P

parse_element() (in module tcmu.data.atom) parse_line() (in module tcmu.job.workflow_db) parse_molecule() (in module tcmu.formula) PATH tcmu-geo command line option path_depth() (in module tcmu.pathfunc) path_exists() (Connection method), [1] (Local method), [1] PESScan() (AMSJob method), [1] (XTBJob method), [1] plot_vdd_charges_per_atom() (VDDChargeManager method) postamble_defaults (Ada attribute) (Local attribute), [1] (Server attribute), [1]

preamble_defaults (Ada attribute) (Local attribute), [1] (Server attribute), [1] print_timings() (in module tcmu.timer) program_modules (Ada attribute) (Local attribute), [1] (Server attribute), [1] (Snellius attribute) prune() (Result method), [1] pwd() (Connection method), [1] (Local method), [1] PyFragResult (class in tcmu) (class in tcmu.analysis.pyfrag) PYRAMIDAL (GeometricParameter attribute)

Q

QCGJob (class in tcmu) (class in tcmu.job.crest) QRO() (ORCAJob method), [1]

quality() (ADFJob method), [1] question (Emojis attribute) quick_status() (in module tcmu) (in module tcmu.results.read)

R

radius() (in module tcmu.data.atom) rarrow (Emojis attribute) read() (in module tcmu) (in module tcmu.job.workflow_db) (in module tcmu.results.read) (TrackKFReader method) read_all() (in module tcmu.job.workflow_db) read_remote() (in module tcmu.job.workflow_db) receive (Emojis attribute) rectangle_list() (in module tcmu.log) reference() (ORCAJob method), [1] reflect() (Transform method), [1] relativity() (ADFJob method), [1] remove_main() (ORCAJob method), [1] remove_virtuals() (ADFFragmentJob method), [1] replace_files_rkf_to_ams_rkf() (in module tcmu.report.report) requires_optional_package() (in module tcmu) (in module tcmu.environment)

resize() (in module tcmu.report.figure_resizer) restart() (AMSJob method), [1] Result (class in tcmu) (class in tcmu.results.result) rlarrow (Emojis attribute) rm() (Connection method), [1] (Local method), [1] rmtree() (Connection method), [1] (Local method), [1] rotamer_directory (CRESTJob property), [1] (TDJob property) rotate() (in module tcmu) (in module tcmu.geometry) (Transform method), [1] rotmat_to_angles() (in module tcmu) (in module tcmu.geometry) ruff_check_script() (in module tcmu.job.workflow) (in module tcmu.job.workflow3) run() (ADFFragmentJob method), [1]

S

save() (in module tcmu) (in module tcmu.molecule) sbatch_defaults (Ada attribute) (Local attribute), [1] (Server attribute), [1] (Snellius attribute) scale() (Transform method), [1] SCF() (ADFJob method), [1] SCF_convergence() (ADFJob method), [1] send (Emojis attribute) server (Ada attribute) Server (class in tcmu) (class in tcmu.connect) server (Local attribute), [1] (Server attribute), [1] (Snellius attribute) ServerFile (class in tcmu) (class in tcmu.connect) set_coord() (PyFragResult method), [1] set_failed() (in module tcmu.job.workflow_db) set_finished() (in module tcmu.job.workflow_db) set_mask() (PyFragResult method), [1] set_property() (PyFragResult method), [1] set_running() (in module tcmu.job.workflow_db) set_status() (in module tcmu.job.workflow_db) sfo_coefficient() (PyFragResult method), [1]

shape (DocxTable property) SI (class in tcmu.report.report) single_point() (AMSJob method), [1] (ORCAJob method), [1] sleep (Emojis attribute) Snellius (class in tcmu.connect) solvent() (ADFJob method), [1] (CRESTJob method), [1] (DFTBJob method), [1] (QCGJob method), [1] (XTBJob method), [1] sort_by() (PyFragResult method), [1] spin_polarization() (ADFJob method), [1] (CRESTJob method), [1] (ORCAJob method), [1] (TDJob method) (XTBJob method), [1] split_all() (in module tcmu.pathfunc) squeeze_list() (in module tcmu.typing_utilities) stage() (in module tcmu.job.workflow_status) StandardXYZFormatter (class in tcmu.report.formatters.xyz) store() (in module tcmu.results.cache) strain_energy() (PyFragResult method), [1] SUMOFANGLES (GeometricParameter attribute) symbol() (in module tcmu.data.atom) symmetry() (ADFJob method), [1]

T

table() (in module tcmu.log) tcmu module tcmu-cite command line option --acs --list_citations --output --rsc --wiley -a -l -o -r -w OBJECTS tcmu-concat-irc command line option --log_level --output --reverse -l -o -r JOBS tcmu-geo command line option --pyramidal --soa -p -s ATOM_INDICES PATH tcmu-optimize command line option --charge --keep --level --output --spinpol -c -k -l -o -s XYZFILE tcmu-read command line option --properties --status -p -s KEYS WORKDIR tcmu-resize command line option --folder --padding -f -p tcmu-workflow-clear command line option --hash -h NAME tcmu-workflow-status command line option --exit --hash -h -x NAME tcmu.analysis module tcmu.analysis.pyfrag module tcmu.analysis.task_specific module tcmu.analysis.task_specific.irc module tcmu.analysis.vdd module tcmu.analysis.vdd.charge module tcmu.analysis.vdd.manager module tcmu.analysis.vibration module tcmu.analysis.vibration.ts_vibration module tcmu.cache module tcmu.cite module tcmu.cli_scripts module tcmu.cli_scripts.cite module tcmu.cli_scripts.concatenate_irc module tcmu.cli_scripts.geo module tcmu.cli_scripts.job_script module tcmu.cli_scripts.read module tcmu.cli_scripts.resize_figures module tcmu.cli_scripts.tcparser module tcmu.cli_scripts.workflow module tcmu.connect module tcmu.constants module tcmu.data module tcmu.data.atom module tcmu.data.basis_sets module tcmu.data.cosmo module tcmu.data.functionals module

tcmu.data.molecules module tcmu.environment module tcmu.errors module tcmu.formula module tcmu.geometry module tcmu.job module tcmu.job.adf module tcmu.job.ams module tcmu.job.crest module tcmu.job.dftb module tcmu.job.generic module tcmu.job.models module tcmu.job.nmr module tcmu.job.orca module tcmu.job.postscripts module tcmu.job.postscripts.clean_workdir module tcmu.job.postscripts.split_crest_xyz module tcmu.job.postscripts.write_converged_geoms module tcmu.job.workflow module tcmu.job.workflow3 module tcmu.job.workflow_db module tcmu.job.workflow_status module tcmu.job.xtb module tcmu.log module tcmu.molecule module tcmu.pathfunc module tcmu.report module tcmu.report.character module tcmu.report.figure_resizer module tcmu.report.formatters module tcmu.report.formatters.generic module tcmu.report.formatters.xyz module tcmu.report.report module tcmu.results module tcmu.results.adf module tcmu.results.ams module tcmu.results.cache module tcmu.results.crest module tcmu.results.dftb module tcmu.results.orca module tcmu.results.read module tcmu.results.result module tcmu.results.xtb module tcmu.slurm module tcmu.spell_check module tcmu.timer module tcmu.typing_utilities module TCMUCompDetailsError TCMUError TCMUJobError TCMUMissingOptionalPackageError TCMUMoleculeError TDJob (class in tcmu.job.models) text_width() (in module tcmu.report.character) time_stamp() (in module tcmu.log) timed_cache() (in module tcmu) (in module tcmu.cache) timer (class in tcmu) (class in tcmu.timer) to_vtkTransform() (Transform method), [1] total_energy() (PyFragResult method), [1] TrackKFReader (class in tcmu.results.cache) Transform (class in tcmu) (class in tcmu.geometry) transition_state() (AMSJob method), [1] (ORCAJob method), [1] translate() (Transform method), [1] try_to_get_property() (in module tcmu.report.formatters.xyz) ts_idx (PyFragResult property), [1]

U

unload() (in module tcmu.results.cache) unrestricted() (ADFJob method), [1] update() (in module tcmu.job.workflow_db)

upload() (Connection method), [1] (Local method), [1] use_version() (AMSJob method), [1]

V

validate_transitionstate() (in module tcmu) (in module tcmu.analysis.vibration.ts_vibration) value (WorkFlowOutput property), [1] VDDCharge (class in tcmu) (class in tcmu.analysis.vdd.charge)

VDDChargeManager (class in tcmu.analysis.vdd.manager) vector_align_rotmat() (in module tcmu) (in module tcmu.geometry) vibrations() (AMSJob method), [1] (ORCAJob method), [1] (XTBJob method), [1]

W

wagner_fischer() (in module tcmu.spell_check) wait (Emojis attribute) warn() (in module tcmu.log) warning (Emojis attribute) WINDOWS (OSName attribute) WordFormatter (class in tcmu.report.formatters.generic) WORKDIR tcmu-read command line option WorkFlow (class in tcmu.job.workflow) (class in tcmu.job.workflow3) WorkFlowOutput (class in tcmu.job.workflow) (class in tcmu.job.workflow3)

write() (DocxFigure method) (DocxTable method) (in module tcmu.job.workflow_db) write_cell() (DocxTable method) write_mol_to_amv_file() (in module tcmu) (in module tcmu.molecule) write_mol_to_xyz_file() (in module tcmu) (in module tcmu.molecule) write_paragraph() (Docx method) write_to_excel() (VDDChargeManager method) write_to_txt() (VDDChargeManager static method)

X

XTBJob (class in tcmu) (class in tcmu.job.xtb)

XYZData (class in tcmu.report.formatters.xyz) XYZFILE tcmu-optimize command line option