Index

_

_extract_transitions() (pyssian.linkjobparsers.Link914 method) _guess_type() (pyssian.linkjobparsers.Link1 method) _locate_CCSDT() (pyssian.linkjobparsers.Link913 method) _locate_charge_spin() (pyssian.linkjobparsers.Link101 method) _locate_commandline() (pyssian.linkjobparsers.Link1 method) _locate_convergence() (pyssian.linkjobparsers.Link103 method) _locate_dipole() (pyssian.linkjobparsers.Link716 method) _locate_DistanceMatrix() (pyssian.linkjobparsers.Link202 method) _locate_energy() (pyssian.linkjobparsers.Link502 method) _locate_ExcitedStates() (pyssian.linkjobparsers.Link914 method) _locate_frequencies() (pyssian.linkjobparsers.Link716 method) _locate_internaljob() (pyssian.linkjobparsers.Link1 method)

_locate_IOps() (pyssian.linkjobparsers.Link1 method) _locate_irc_step() (pyssian.linkjobparsers.Link123 method) _locate_IRSpectrum() (pyssian.linkjobparsers.Link716 method) _locate_link0() (pyssian.linkjobparsers.Link1 method) _locate_mode() (pyssian.linkjobparsers.Link103 method) _locate_MP2() (pyssian.linkjobparsers.Link804 method) _locate_MP4() (pyssian.linkjobparsers.Link913 method) _locate_numbers() (pyssian.linkjobparsers.Link103 method) _locate_orientation() (pyssian.linkjobparsers.Link123 method) (pyssian.linkjobparsers.Link202 method) _locate_parameters() (pyssian.linkjobparsers.Link103 method) _locate_SpinComponents() (pyssian.linkjobparsers.Link804 method) _locate_thermochemistry() (pyssian.linkjobparsers.Link716 method)

A

add_chk() (pyssian.GaussianInFile method)

atoms (pyssian.classutils.Cube attribute)

B

basis (pyssian.classutils.Cube attribute) (pyssian.GaussianInFile attribute)

C

CCSDT (pyssian.linkjobparsers.Link913 attribute) change_basis() (pyssian.GaussianInFile method) change_method() (pyssian.GaussianInFile method) charge (pyssian.GaussianInFile attribute) (pyssian.linkjobparsers.Link101 attribute) ChemistryUtilsTest (class in pyssian.tests.test_chemistryutils)

clean() (pyssian.GaussianOutFile method) (pyssian.InternalJob method) close() (pyssian.GaussianInFile method) commandline (pyssian.GaussianInFile attribute) (pyssian.linkjobparsers.Link1 attribute) conversion (pyssian.linkjobparsers.Link103 attribute) Cube (class in pyssian.classutils)

D

derivatives (pyssian.linkjobparsers.Link103 attribute) dipole (pyssian.linkjobparsers.Link716 attribute)

direction (pyssian.linkjobparsers.Link123 attribute) DirectoryTree (class in pyssian.classutils) DistanceMatrix (pyssian.linkjobparsers.Link202 attribute)

E

EContribs (pyssian.linkjobparsers.Link716 attribute) energy (pyssian.linkjobparsers.Link502 attribute) (pyssian.linkjobparsers.Link508 attribute)

enthalpy (pyssian.linkjobparsers.Link716 attribute) excitedstates (pyssian.linkjobparsers.Link914 attribute)

F

from_file() (pyssian.classutils.Cube class method) from_Input() (pyssian.classutils.Geometry class method)

from_L202() (pyssian.classutils.Geometry class method) from_xyz() (pyssian.classutils.Geometry class method)

G

GaussianInFile (class in pyssian) GaussianOutFile (class in pyssian) GeneralLinkJob (class in pyssian.linkjobparsers) Geometry (class in pyssian.classutils) geometry (pyssian.GaussianInFile attribute)

get_atom_mapping() (pyssian.linkjobparsers.Link202 method) get_links() (pyssian.GaussianOutFile method) (pyssian.InternalJob method) get_SCScorr() (pyssian.linkjobparsers.Link804 method) gibbs (pyssian.linkjobparsers.Link716 attribute) guess_info() (pyssian.InternalJob method)

I

info (pyssian.linkjobparsers.Link1 attribute) InternalJob (class in pyssian) InternalJobs (pyssian.GaussianOutFile attribute) IOps (pyssian.linkjobparsers.Link1 attribute)

IRSpectrum (pyssian.linkjobparsers.Link716 attribute) is_basis() (in module pyssian.chemistryutils) is_method() (in module pyssian.chemistryutils) isUnrestricted (pyssian.classutils.Cube attribute)

L

link0 (pyssian.linkjobparsers.Link1 attribute) Link1 (class in pyssian.linkjobparsers) Link101 (class in pyssian.linkjobparsers) Link103 (class in pyssian.linkjobparsers) Link123 (class in pyssian.linkjobparsers) Link202 (class in pyssian.linkjobparsers) Link502 (class in pyssian.linkjobparsers)

Link508 (class in pyssian.linkjobparsers) Link601 (class in pyssian.linkjobparsers) Link716 (class in pyssian.linkjobparsers) Link804 (class in pyssian.linkjobparsers) Link913 (class in pyssian.linkjobparsers) Link914 (class in pyssian.linkjobparsers) LinkJob (class in pyssian.linkjobparsers) Links (pyssian.InternalJob attribute)

M

matrix (pyssian.classutils.Cube attribute) mem (pyssian.GaussianInFile attribute) (pyssian.linkjobparsers.Link1 attribute) method (pyssian.GaussianInFile attribute) MO_Ids (pyssian.classutils.Cube attribute) mode (pyssian.linkjobparsers.Link103 attribute) (pyssian.linkjobparsers.Link716 attribute) module pyssian pyssian.chemistryutils pyssian.classutils pyssian.gaussianclasses pyssian.linkjobparsers pyssian.tests.test_chemistryutils pyssian.tests.test_linkjobparsers

MP2 (pyssian.linkjobparsers.Link804 attribute) MP4 (pyssian.linkjobparsers.Link913 attribute) mulliken (pyssian.linkjobparsers.Link601 attribute) mulliken_heavy (pyssian.linkjobparsers.Link601 attribute)

N

natoms (pyssian.classutils.Cube attribute) newpath() (pyssian.classutils.DirectoryTree method) nMO (pyssian.classutils.Cube attribute) nprocs (pyssian.GaussianInFile attribute) (pyssian.linkjobparsers.Link1 attribute) number (pyssian.InternalJob attribute) (pyssian.linkjobparsers.GeneralLinkJob attribute) (pyssian.linkjobparsers.Link1 attribute) (pyssian.linkjobparsers.Link103 attribute) (pyssian.linkjobparsers.Link123 attribute) (pyssian.linkjobparsers.Link202 attribute) (pyssian.linkjobparsers.LinkJob attribute)

O

orientation (pyssian.linkjobparsers.Link123 attribute) (pyssian.linkjobparsers.Link202 attribute)

origin (pyssian.classutils.Cube attribute)

P

parameters (pyssian.linkjobparsers.Link103 attribute) parse_commandline() (pyssian.GaussianInFile method) parse_geometry() (pyssian.GaussianInFile method) parse_preprocessing() (pyssian.GaussianInFile method) parse_tail() (pyssian.GaussianInFile method) pop_chk() (pyssian.GaussianInFile method) preprocessing (pyssian.GaussianInFile attribute) print_convergence() (pyssian.linkjobparsers.Link103 method) print_excitedstates() (pyssian.linkjobparsers.Link914 method) print_file_structure() (pyssian.GaussianOutFile method) print_orientation() (pyssian.linkjobparsers.Link123 method) (pyssian.linkjobparsers.Link202 method) pyssian module

pyssian.chemistryutils module pyssian.classutils module pyssian.gaussianclasses module pyssian.linkjobparsers module pyssian.tests.test_chemistryutils module pyssian.tests.test_linkjobparsers module

R

reactioncoord (pyssian.linkjobparsers.Link123 attribute) read() (pyssian.GaussianInFile method) (pyssian.GaussianOutFile method)

RecursiveFileSystemGenerator() (pyssian.classutils.DirectoryTree static method) Register (pyssian.linkjobparsers.LinkJob attribute) RegisterLinkJob() (in module pyssian.linkjobparsers)

S

scanpoint (pyssian.linkjobparsers.Link103 attribute) setUp() (pyssian.tests.test_chemistryutils.ChemistryUtilsTest method) setUpClass() (pyssian.tests.test_linkjobparsers.TestGeneralLinkJob class method) (pyssian.tests.test_linkjobparsers.TestLink1 class method) (pyssian.tests.test_linkjobparsers.TestLink101 class method) (pyssian.tests.test_linkjobparsers.TestLink103 class method) (pyssian.tests.test_linkjobparsers.TestLink123 class method) (pyssian.tests.test_linkjobparsers.TestLink202 class method) (pyssian.tests.test_linkjobparsers.TestLink502 class method) (pyssian.tests.test_linkjobparsers.TestLink601 class method) (pyssian.tests.test_linkjobparsers.TestLink716 class method) (pyssian.tests.test_linkjobparsers.TestLink804 class method) (pyssian.tests.test_linkjobparsers.TestLink913 class method) (pyssian.tests.test_linkjobparsers.TestLink914 class method)

shape (pyssian.classutils.Cube attribute) spin (pyssian.GaussianInFile attribute) (pyssian.linkjobparsers.Link101 attribute) SpinComponents (pyssian.linkjobparsers.Link804 attribute) state (pyssian.linkjobparsers.Link103 attribute) step (pyssian.linkjobparsers.Link123 attribute) stepnumber (pyssian.linkjobparsers.Link103 attribute) structure (pyssian.GaussianInFile attribute)

T

tail (pyssian.GaussianInFile attribute) test_AtNum2Sym() (pyssian.tests.test_linkjobparsers.TestLink202 method) test_AtNum2Sym_error() (pyssian.tests.test_linkjobparsers.TestLink202 method) test_CCSDT() (pyssian.tests.test_linkjobparsers.TestLink913 method) test_charge_spin() (pyssian.tests.test_linkjobparsers.TestLink101 method) test_commandline() (pyssian.tests.test_linkjobparsers.TestLink1 method) test_DistanceMatrix() (pyssian.tests.test_linkjobparsers.TestLink202 method) test_energy() (pyssian.tests.test_linkjobparsers.TestLink502 method) test_extract_transitions() (pyssian.tests.test_linkjobparsers.TestLink914 method) test_fake_isbasis() (pyssian.tests.test_chemistryutils.ChemistryUtilsTest method) test_fake_ismethod() (pyssian.tests.test_chemistryutils.ChemistryUtilsTest method) test_guess_type() (pyssian.tests.test_linkjobparsers.TestLink1 method) test_info() (pyssian.tests.test_linkjobparsers.TestLink1 method) test_init() (pyssian.tests.test_linkjobparsers.TestGeneralLinkJob method) (pyssian.tests.test_linkjobparsers.TestLink1 method) (pyssian.tests.test_linkjobparsers.TestLink101 method) (pyssian.tests.test_linkjobparsers.TestLink103 method) (pyssian.tests.test_linkjobparsers.TestLink123 method) (pyssian.tests.test_linkjobparsers.TestLink202 method) (pyssian.tests.test_linkjobparsers.TestLink502 method) (pyssian.tests.test_linkjobparsers.TestLink601 method) (pyssian.tests.test_linkjobparsers.TestLink716 method) (pyssian.tests.test_linkjobparsers.TestLink804 method) (pyssian.tests.test_linkjobparsers.TestLink913 method) (pyssian.tests.test_linkjobparsers.TestLink914 method) test_init_empty() (pyssian.tests.test_linkjobparsers.TestGeneralLinkJob method) (pyssian.tests.test_linkjobparsers.TestLink1 method) (pyssian.tests.test_linkjobparsers.TestLink101 method) (pyssian.tests.test_linkjobparsers.TestLink103 method) (pyssian.tests.test_linkjobparsers.TestLink123 method) (pyssian.tests.test_linkjobparsers.TestLink202 method) (pyssian.tests.test_linkjobparsers.TestLink502 method) (pyssian.tests.test_linkjobparsers.TestLink601 method) (pyssian.tests.test_linkjobparsers.TestLink716 method) (pyssian.tests.test_linkjobparsers.TestLink804 method) (pyssian.tests.test_linkjobparsers.TestLink913 method) (pyssian.tests.test_linkjobparsers.TestLink914 method) test_locate_ExcitedStates() (pyssian.tests.test_linkjobparsers.TestLink914 method) test_locate_irc_step() (pyssian.tests.test_linkjobparsers.TestLink123 method) test_locate_mode() (pyssian.tests.test_linkjobparsers.TestLink103 method) test_locate_numbers() (pyssian.tests.test_linkjobparsers.TestLink103 method) test_MP2() (pyssian.tests.test_linkjobparsers.TestLink804 method) test_MP4() (pyssian.tests.test_linkjobparsers.TestLink913 method) test_orientation() (pyssian.tests.test_linkjobparsers.TestLink202 method) test_regex() (pyssian.tests.test_linkjobparsers.TestGeneralLinkJob method) (pyssian.tests.test_linkjobparsers.TestLink202 method) test_regex_ccsdt() (pyssian.tests.test_linkjobparsers.TestLink913 method) test_regex_charge() (pyssian.tests.test_linkjobparsers.TestLink101 method)

test_regex_commandline() (pyssian.tests.test_linkjobparsers.TestLink1 method) test_regex_convergence() (pyssian.tests.test_linkjobparsers.TestLink103 method) test_regex_derivatives() (pyssian.tests.test_linkjobparsers.TestLink103 method) test_regex_dipole() (pyssian.tests.test_linkjobparsers.TestLink716 method) test_regex_EContrib() (pyssian.tests.test_linkjobparsers.TestLink716 method) test_regex_energy() (pyssian.tests.test_linkjobparsers.TestLink502 method) test_regex_ExcitedState() (pyssian.tests.test_linkjobparsers.TestLink914 method) test_regex_Frequencies() (pyssian.tests.test_linkjobparsers.TestLink716 method) test_regex_internaljob() (pyssian.tests.test_linkjobparsers.TestLink1 method) test_regex_IOps() (pyssian.tests.test_linkjobparsers.TestLink1 method) test_regex_IRSpectrum() (pyssian.tests.test_linkjobparsers.TestLink716 method) test_regex_link0() (pyssian.tests.test_linkjobparsers.TestLink1 method) test_regex_MP2() (pyssian.tests.test_linkjobparsers.TestLink804 method) test_regex_MP4() (pyssian.tests.test_linkjobparsers.TestLink913 method) test_regex_MullikenAtoms() (pyssian.tests.test_linkjobparsers.TestLink601 method) test_regex_MullikenHeavy() (pyssian.tests.test_linkjobparsers.TestLink601 method) test_regex_orientation() (pyssian.tests.test_linkjobparsers.TestLink123 method) test_regex_parameters() (pyssian.tests.test_linkjobparsers.TestLink103 method) test_regex_spin() (pyssian.tests.test_linkjobparsers.TestLink101 method) test_regex_Thermo() (pyssian.tests.test_linkjobparsers.TestLink716 method) test_regex_transition() (pyssian.tests.test_linkjobparsers.TestLink914 method) test_SCSCorr() (pyssian.tests.test_linkjobparsers.TestLink804 method) test_SpinComponents() (pyssian.tests.test_linkjobparsers.TestLink804 method) test_usual_keywords() (pyssian.tests.test_chemistryutils.ChemistryUtilsTest method) test_valid_isbasis() (pyssian.tests.test_chemistryutils.ChemistryUtilsTest method) test_valid_ismethod() (pyssian.tests.test_chemistryutils.ChemistryUtilsTest method) TestGeneralLinkJob (class in pyssian.tests.test_linkjobparsers) TestLink1 (class in pyssian.tests.test_linkjobparsers) TestLink101 (class in pyssian.tests.test_linkjobparsers) TestLink103 (class in pyssian.tests.test_linkjobparsers) TestLink123 (class in pyssian.tests.test_linkjobparsers) TestLink202 (class in pyssian.tests.test_linkjobparsers) TestLink502 (class in pyssian.tests.test_linkjobparsers) TestLink601 (class in pyssian.tests.test_linkjobparsers) TestLink716 (class in pyssian.tests.test_linkjobparsers) TestLink804 (class in pyssian.tests.test_linkjobparsers) TestLink913 (class in pyssian.tests.test_linkjobparsers) TestLink914 (class in pyssian.tests.test_linkjobparsers) text (pyssian.linkjobparsers.GeneralLinkJob attribute) (pyssian.linkjobparsers.Link1 attribute) (pyssian.linkjobparsers.Link103 attribute) (pyssian.linkjobparsers.Link123 attribute) (pyssian.linkjobparsers.Link202 attribute) (pyssian.linkjobparsers.LinkJob attribute) thermal_energy (pyssian.linkjobparsers.Link716 attribute) title (pyssian.GaussianInFile attribute) type (pyssian.classutils.Cube attribute) (pyssian.InternalJob attribute)

U

units (pyssian.linkjobparsers.Link716 attribute)

update() (pyssian.GaussianOutFile method) update_atoms() (pyssian.classutils.Geometry method)

W

write() (pyssian.classutils.Cube method) (pyssian.classutils.Geometry method) (pyssian.GaussianInFile method)

write_values() (pyssian.classutils.Cube method)

Z

zeropoint (pyssian.linkjobparsers.Link716 attribute)