Index

A

add() (spycci.systems.Ensemble method) append() (spycci.core.geometry.MolecularGeometry method) atomcount (spycci.core.geometry.MolecularGeometry property) (spycci.systems.Ensemble property)

atomic_numbers (spycci.core.geometry.MolecularGeometry property) atoms (spycci.core.geometry.MolecularGeometry property) auto_calculate_pka() (in module spycci.functions)

B

boltzmann_average() (spycci.systems.Ensemble method)

buried_volume_fraction() (spycci.core.geometry.MolecularGeometry method)

C

calc_hess (spycci.engines.orca.OrcaJobInfo attribute) calculate_fukui() (in module spycci.functions) calculate_pka() (in module spycci.functions) calculate_reduction_potential() (in module spycci.functions) compress_dftb_trajectory() (in module spycci.tools) condensed_fukui_hirshfeld (spycci.core.properties.Properties property)

condensed_fukui_mulliken (spycci.core.properties.Properties property) conformer_search() (in module spycci.wrappers.crest) constraints (spycci.engines.orca.OrcaJobInfo attribute) coordinates (spycci.core.geometry.MolecularGeometry property) cpcm_block (spycci.engines.orca.OrcaJobInfo property) cube_dim (spycci.engines.orca.OrcaJobInfo attribute) cyclization_check() (in module spycci.tools)

D

deprotonate() (in module spycci.wrappers.crest) DFTBInput (class in spycci.engines.dftbplus)

dispersion (spycci.engines.dftbplus.DFTBInput attribute) dissociation_check() (in module spycci.tools)

E

electronic_energy (spycci.core.properties.Properties property) elprop_block (spycci.engines.orca.OrcaJobInfo property)

Engine (class in spycci.core.base) Ensemble (class in spycci.systems)

F

freq (spycci.engines.orca.OrcaJobInfo attribute) freq() (spycci.engines.orca.OrcaInput method) (spycci.engines.xtb.XtbInput method)

from_dict() (spycci.core.geometry.MolecularGeometry class method) (spycci.core.properties.Properties class method) from_xyz() (spycci.core.geometry.MolecularGeometry class method) fullscan (spycci.engines.orca.OrcaJobInfo attribute)

G

geom_block (spycci.engines.orca.OrcaJobInfo property)

gibbs_free_energy (spycci.core.properties.Properties property)

H

helmholtz_free_energy (spycci.core.properties.Properties property) hirshfeld (spycci.engines.orca.OrcaJobInfo attribute)

hirshfeld_charges (spycci.core.properties.Properties property) hirshfeld_spin_populations (spycci.core.properties.Properties property)

I

invert_constraints (spycci.engines.orca.OrcaJobInfo attribute)

is_periodic (spycci.systems.System property) is_singlet (spycci.engines.orca.OrcaJobInfo attribute)

L

level_of_theory_electronic (spycci.core.properties.Properties property) level_of_theory_geometry (spycci.core.geometry.MolecularGeometry attribute) level_of_theory_vibronic (spycci.core.properties.Properties property) load_xyz() (spycci.core.geometry.MolecularGeometry method) locate_crest() (in module spycci.core.dependency_finder)

locate_dftbparamdir() (in module spycci.core.dependency_finder) locate_dftbplus() (in module spycci.core.dependency_finder) locate_executable() (in module spycci.core.dependency_finder) locate_orca() (in module spycci.core.dependency_finder) locate_vmd() (in module spycci.core.dependency_finder) locate_xtb() (in module spycci.core.dependency_finder)

M

mass (spycci.core.geometry.MolecularGeometry property) maxcore (spycci.engines.orca.OrcaJobInfo property) maxdist() (in module spycci.tools) md_nvt() (spycci.engines.dftbplus.DFTBInput method) method (spycci.engines.dftbplus.DFTBInput attribute) module spycci.core.dependency_finder spycci.core.geometry spycci.tools.vmdtools

MolecularGeometry (class in spycci.core.geometry) mulliken_charges (spycci.core.properties.Properties property) mulliken_spin_populations (spycci.core.properties.Properties property)

N

name (spycci.systems.Ensemble attribute) ncores (spycci.engines.orca.OrcaJobInfo property) nearir (spycci.engines.orca.OrcaJobInfo attribute) neb_block (spycci.engines.orca.OrcaJobInfo property) neb_ci (spycci.engines.orca.OrcaJobInfo attribute) neb_ci() (spycci.engines.orca.OrcaInput method)

neb_images (spycci.engines.orca.OrcaJobInfo attribute) neb_preopt (spycci.engines.orca.OrcaJobInfo attribute) neb_product (spycci.engines.orca.OrcaJobInfo attribute) neb_ts() (spycci.engines.orca.OrcaInput method) neb_ts_guess (spycci.engines.orca.OrcaJobInfo attribute) nfreq (spycci.engines.orca.OrcaJobInfo attribute) nfreq() (spycci.engines.orca.OrcaInput method)

O

opt (spycci.engines.orca.OrcaJobInfo attribute) opt() (spycci.engines.dftbplus.DFTBInput method) (spycci.engines.orca.OrcaInput method) (spycci.engines.xtb.XtbInput method) opt_ts (spycci.engines.orca.OrcaJobInfo attribute) opt_ts() (spycci.engines.orca.OrcaInput method)

optimization_level (spycci.engines.orca.OrcaJobInfo property) OrcaInput (class in spycci.engines.orca) OrcaJobInfo (class in spycci.engines.orca) output_block (spycci.engines.orca.OrcaJobInfo property) output_suffix (spycci.engines.orca.OrcaInput property) (spycci.engines.xtb.XtbInput property)

P

packmol_cube() (in module spycci.wrappers.packmol) parallel (spycci.engines.dftbplus.DFTBInput attribute) parameters (spycci.engines.dftbplus.DFTBInput attribute) parse_output() (spycci.engines.dftbplus.DFTBInput method) (spycci.engines.orca.OrcaInput method) (spycci.engines.xtb.XtbInput method) parsed_blocks (spycci.engines.orca.OrcaJobInfo property)

pka (spycci.core.properties.Properties property) plots_block (spycci.engines.orca.OrcaJobInfo property) print_level (spycci.engines.orca.OrcaJobInfo property) process_output() (in module spycci.tools) Properties (class in spycci.core.properties) properties (spycci.systems.Ensemble attribute) protonate() (in module spycci.wrappers.crest)

Q

qcg_ensemble() (in module spycci.wrappers.crest)

qcg_grow() (in module spycci.wrappers.crest)

R

raman (spycci.engines.orca.OrcaJobInfo attribute) render_condensed_fukui() (in module spycci.tools.vmdtools)

render_fukui_cube() (in module spycci.tools.vmdtools) render_spin_density_cube() (in module spycci.tools.vmdtools) reorder_energies() (in module spycci.tools)

S

save_dftb_trajectory() (in module spycci.tools) save_json() (spycci.systems.System method) scan (spycci.engines.orca.OrcaJobInfo attribute) scan() (spycci.engines.orca.OrcaInput method) scan_ts (spycci.engines.orca.OrcaJobInfo attribute) scan_ts() (spycci.engines.orca.OrcaInput method) scf_convergence_level (spycci.engines.orca.OrcaJobInfo property) scf_convergence_strategy (spycci.engines.orca.OrcaJobInfo property) set_condensed_fukui_hirshfeld() (spycci.core.properties.Properties method) set_condensed_fukui_mulliken() (spycci.core.properties.Properties method) set_electronic_energy() (spycci.core.properties.Properties method) set_gibbs_free_energy() (spycci.core.properties.Properties method) set_helmholtz_free_energy() (spycci.core.properties.Properties method) set_hirshfeld_charges() (spycci.core.properties.Properties method) set_hirshfeld_spin_populations() (spycci.core.properties.Properties method) set_mulliken_charges() (spycci.core.properties.Properties method) set_mulliken_spin_populations() (spycci.core.properties.Properties method)

set_pka() (spycci.core.properties.Properties method) set_vibrational_data() (spycci.core.properties.Properties method) set_vibronic_energy() (spycci.core.properties.Properties method) simulated_annealing() (spycci.engines.dftbplus.DFTBInput method) solvent (spycci.engines.orca.OrcaJobInfo attribute) solver (spycci.engines.dftbplus.DFTBInput attribute) spe() (spycci.engines.dftbplus.DFTBInput method) (spycci.engines.orca.OrcaInput method) (spycci.engines.xtb.XtbInput method) split_multixyz() (in module spycci.tools) spycci.core.dependency_finder module spycci.core.geometry module spycci.tools.vmdtools module System (class in spycci.systems) systems (spycci.systems.Ensemble attribute)

T

tautomer_search() (in module spycci.wrappers.crest)

to_dict() (spycci.core.geometry.MolecularGeometry method) (spycci.core.properties.Properties method)

V

verbose (spycci.engines.dftbplus.DFTBInput attribute)

vibrational_data (spycci.core.properties.Properties property) vibronic_energy (spycci.core.properties.Properties property)

W

write_gen() (spycci.systems.System method)

write_input() (spycci.engines.orca.OrcaInput method) write_xyz() (spycci.core.geometry.MolecularGeometry method)

X

XtbInput (class in spycci.engines.xtb)