schrodinger.application.jaguar.input module¶
Functions and classes for reading and creating Jaguar input files.
It allows setting and querying of keyword values in Jaguar input &gen sections and also provides an interface to some of the mmjag library.
The JaguarInput class also provides for the running of jobs.
- class schrodinger.application.jaguar.input.OrbSpec(is_alpha: bool, is_homo: Optional[bool], index: int)¶
Bases:
NamedTuple
Stores orbital specification data, used by
_parse_orb_pairs
- is_alpha: bool¶
Alias for field number 0
- is_homo: Optional[bool]¶
Alias for field number 1
- index: int¶
Alias for field number 2
- class schrodinger.application.jaguar.input.GuessOrbital(energy: float, occupation: float, symm: Optional[str])¶
Bases:
NamedTuple
Stores information about guess orbitals, namely energy, occupation, and symmetry
- energy: float¶
Alias for field number 0
- occupation: float¶
Alias for field number 1
- symm: Optional[str]¶
Alias for field number 2
- class schrodinger.application.jaguar.input.MixedPairs(alpha_mix: List[Tuple[int, int, float]], beta_mix: Optional[List[Tuple[int, int, float]]], alpha_beta_mix: Optional[List[Tuple[int, int, float]]])¶
Bases:
NamedTuple
Store orbital pairs and their mixing angles for the &orbman section
alpha_mix
is passed to hfiglcmoa (or hfiglcmo if restricted)beta_mix
is passed to hfiglcmob (or not included if restricted)alpha_beta_mix
is passed hfiglcmoab (or not included if restricted)
- exception schrodinger.application.jaguar.input.ConstraintError¶
Bases:
Exception
Exception to be raised when Constraint is invalid, e.g. no atoms specified.
- exception schrodinger.application.jaguar.input.InputVerificationError¶
Bases:
Exception
Exception for non-matching JaguarInput instances. Generated by isEquivalentInput.
- schrodinger.application.jaguar.input.launch_file(input: str, wait: bool = False, save: bool = False, disp: Optional[str] = None, **kwargs) schrodinger.job.jobcontrol.Job ¶
Launch a Jaguar job from the Jaguar input file ‘input’. Returns a jobcontrol.Job object.
- Parameters
input – Name of input file
wait – Do not return until the job is complete.
save – Set to True to save the scratch directory.
disp – Set to a valid jobcontrol disposition.
- Returns
Job instance
- schrodinger.application.jaguar.input.apply_jaguar_atom_naming(struc: schrodinger.structure._structure.Structure)¶
Apply jaguar unique atom naming to all atoms in the specified structure
- Parameters
struc – The structure to apply atom naming to
- schrodinger.application.jaguar.input.read(filename: str, index: int = 1, **kwargs)¶
Create and return a JaguarInput object from a Jaguar .in file or a maestro .mae file. Additional keyword args are passed on to the JaguarInput constructor.
- Parameters
filename – Can be a Jaguar input .in file, Maestro structure .mae file, or the basename of a file of one of these types.
index – The index of the structure to use for an .mae input file.
- kwargs (additional keyword arguments)
All keyword arguments are passed on to the JaguarInput constructor.
- schrodinger.application.jaguar.input.get_name_file(name: str) Tuple[str, str] ¶
Get the input filename and jobname, given either the input filename or the jobname.
Return a tuple of (jobname, filename).
- schrodinger.application.jaguar.input.split_structure_files(files: List[str])¶
Given a list of structure (.in or .mae) files, split all .mae files into individual structures and write them back to disk with new names.
Return the list of structure files, each of which contains a single structure. Any split mae files are named with either the entry ID (if available) or the source file basename with an index suffix.
- class schrodinger.application.jaguar.input.JaguarInput(input: Optional[str] = None, name: Optional[str] = None, handle: Optional[int] = None, structure: Optional[schrodinger.structure._structure.Structure] = None, genkeys: Optional[dict] = None, reload: Optional[bool] = None, run_kwargs: Optional[dict] = None, text: Optional[str] = None, qsite_ok: bool = False, rename_directives: bool = False, compute_connectivity: bool = True)¶
Bases:
object
A class for specifying Jaguar input.
This is a thin wrapper to the mmjag library and carries very little internal information.
- __init__(input: Optional[str] = None, name: Optional[str] = None, handle: Optional[int] = None, structure: Optional[schrodinger.structure._structure.Structure] = None, genkeys: Optional[dict] = None, reload: Optional[bool] = None, run_kwargs: Optional[dict] = None, text: Optional[str] = None, qsite_ok: bool = False, rename_directives: bool = False, compute_connectivity: bool = True)¶
There are three main ways to create a JaguarInput instance: from a Jaguar input file ‘input’, an mmjag handle ‘handle’, or a Structure instance ‘structure’.
The ‘input’ parameter will provide for initialization and job name from an existing Jaguar input file. (If no new name is provided, calling the save() method will overwrite the original file.)
Note that the structure and name parameters will modify the object status after loading from a file or initialization from a handle has completed. This can be utilized to get the settings from a Jaguar input file but replace the geometry for a new calculation.
- Parameters
input – A jaguar input file; a default name will be derived from the input value.
name – A jaguar job name that will override the name derived from ‘input’.
handle – An mmjag handle, pointing to an existing mmjag instance in memory.
structure – A structure that will populate a new mmjag instance. If specified with ‘input’ or ‘handle’ it will replace any structure provided by them.
genkeys – A dictionary of keyword/value pairs to set in the input &gen section. If keywords are specified in this mapping and the file, the genkeys value will be used.
reload – Specifies whether to reload the job from an output file in the run() method. Default value is False, but can be modified by setting JaguarInput.reload to a different value.
run_kwargs – The run_kwargs dictionary provides default keyword settings for the run function that is called from the launch and run methods. Default is to set no defaults, but this can be modified by setting JaguarInput.run_kwargs to a different value.
text – The complete text of a Jaguar input file.
qsite_ok – Allows this class to be initialized from a QSite input file
rename_directives – When copying directives from an existing input file with relative paths, rename them to match the new input file name.
compute_connectivity – Whether to compute connectivity for the structure of the read in input. This can be slow for large systems and isn’t needed for most calculations. Default is True. Note QSite inputs will always take their connectivity from the mae file, regardless of this keyword.
- reload = False¶
- run_kwargs = {}¶
- launch(*args, **kwargs)¶
Save the file and launch a job. Returns a jobcontrol.Job object.
Uses the class run_kwargs value as base for keyword arguments to the run function.
- run(**kwargs)¶
Save the file and launch a job with the wait option. Returns a JaguarOutput object. Raises an exception if the job failed.
Set the class (or instance) attribute reload to True to load existing output files of the same name.
- save(follow_links: int = 0, validate: Optional[bool] = None)¶
Write an input file to name.in.
- Parameters
follow_links –
Flag specifying whether to follow links in the structure to a Jaguar restart file, if present, to append additional sections. Options are:
mm.MMJAG_APPEND_OFF: don’t follow links to append additional sections (default)
mm.MMJAG_APPEND_OVERWRITE: append sections from link, overwriting any that overlap
mm.MMJAG_APPEND_NO_OVERWRITE: append sections from link, not overwriting any that overlap
mm.MMJAG_APPEND_X_OVERWRITE: exclusively append sections from link, deleting any already present
mm.MMJAG_APPEND_X_NO_OVERWRITE: append sections from link only if no such sections already present
validate – If True, sections dependent upon geometry, molecular state, basis set are removed if invalid. If not entered (None), default is to validate if “following links”.
- saveAs(file: str, follow_links: int = 0, validate: Optional[bool] = None)¶
Write an input file to name.in and set the object’s name attribute.
- Parameters
file – Filename to use for save file
follow_links –
Flag telling whether to follow links in the structure to a Jaguar restart file, if present, to append additional sections. Options are:
mm.MMJAG_APPEND_OFF: don’t follow links to append additional sections (default)
mm.MMJAG_APPEND_OVERWRITE: append sections from link, overwriting any that overlap
mm.MMJAG_APPEND_NO_OVERWRITE: append sections from link, not overwriting any that overlap
mm.MMJAG_APPEND_X_OVERWRITE: exclusively append sections from link, deleting any already present
mm.MMJAG_APPEND_X_NO_OVERWRITE: append sections from link only if no such sections already present
validate – If True, sections dependent upon geometry, molecular state, basis set are removed if invalid. If not entered (None), default is to validate if “following links”.
- getSectionText(section: str) Optional[str] ¶
Return text of section as a string.
Note this does not use mm.mmjag_get_sect_text, which has a small, fixed buffer size of 1024 that can be exceeded by even fairly small sections.
- Parameters
section – Name of section to return
- Returns
Text of section, or None if section not present
- createModifiedGuess(orbital_pairs: List[Tuple[Union[int, str], Union[int, str]]], mixing_angles: Union[List[float], float], restricted: bool = False, delta_scf: int = 0, charge: Optional[int] = None, multiplicity: Optional[int] = None, write: bool = False, suffix: str = '_copy') schrodinger.application.jaguar.input.JaguarInput ¶
Write a copy of current input file with a modified guess.
This function should be used in scripts to modify the guess of an existing Jaguar input file. To modify a guess from the commandline, use the
modify_scf_guess
utility script.- Parameters
orbital_pairs – List of orbital pairs to mix. Optionally specify the spin (a=alpha, b=beta), followed by their absolute index or their index relative to the HOMO (H) or LUMO (L). If spin is not given, it will be assumed to be alpha. For example
orbital_pairs = [('aH1','bL2'), (17,18)]
would mix the alpha HOMO-1 orbital with the beta LUMO+2 and alpha orbital 17 with alpha orbital 18. Note, HOMO/LUMO refer to the orbitals of the new guess (i.e. with the specified charge/multiplicity)mixing_angles – Angle to mix orbitals, in degrees. 90 will simply swap orbitals, while 45 will create an even mixture. Can select a single angle for all pairs or an angle for each pair.
restricted – Make the new input a restricted spin calculation. An unrestricted calculation is needed for single spin orbital mixing, while a restricted calculation will mix both spin orbitals for each index specified.
delta_scf – Set the Delta SCF algorithm to use. 0 = Don’t use Delta SCF 1 = Initial Maximum Overlap Method (IMOM) 2 = Maximum Overlap Method (MOM)
charge – Set the charge for the new input file
multiplicity – Set the multiplicity for the new input file
write – Write the new input file.
suffix – Suffix to append to original filename.
- Returns
New JaguarInput object with modified guess.
- Raises
WorkflowValidationError – If charge/multiplicity are inconsistent with the number of electrons.
JaguarRuntimeError – If the input file doesn’t have a guess or if the number of orbital pairs doesn’t match the number of mixing angles.
- getInputText() str ¶
Return the text of the input file. Note that the input file will not be saved to self._file.
- Returns
The text of the input file
- getZmatText(zmat: int = 0) str ¶
Return the input file text corresponding to the specified Z matrix.
- Parameters
zmat – The z matrix to return the text for. Must be one of mm.MMJAG_ZMAT1, mm.MMJAG_ZMAT2, or mm.MMJAG_ZMAT3.
- Returns
The text for the specified Z matrix
- property name: str¶
Set the jobname; also updates the filename based on the jobname.
- property filename: str¶
Return the filename of the JaguarInput object.
On Windows, with paths over the Windows max path length, we must prepend an extended path tag.
- getAtomCount(zmat: int = 0) int ¶
Return the number of atoms for the specified zmat.
- getValue(key)¶
Return the &gen section value for keyword ‘key’.
The return type is as defined by mmjag_key_type().
- getDefault(key)¶
Return the default value for &gen section keyword ‘key’.
- setValue(key, value)¶
Set the &gen section keyword ‘key’ to the value provided.
If value is None, the keyword will be unset.
- setValues(dict_)¶
Set multiple &gen section keywords from the provided dictionary
Note that one easy way to specify the
dict_
argument is via the"dict(basis='6-31g**', igeopt=1)"
syntax for constructing a dictionary.
- deleteKey(key)¶
Remove a key from the &gen section.
- deleteKeys(keys)¶
Remove a list of keys from the &gen section.
- getNonDefault()¶
Return a dictionary of all non-default keys except ‘multip’ and ‘molchg’, which must be retrieved explicitly since they are connected to the geometry.
- isNonDefault(key: str) bool ¶
Has the specified key been set to a non-default value?
- Parameters
key – The key to check
- Returns
True if the specified key is set to a non-default value. False otherwise.
- setDirective(name: str, value)¶
Set a file specification directive.
- getDirective(name: str)¶
Get a file specification directive.
- getDirectives()¶
Get all file specification directives, except for MAEFILE, which is weeded out by the mmjag function itself.
- writeMaefile(filename: Optional[str] = None, structs: Optional[List[schrodinger.structure._structure.Structure]] = None)¶
Write an associated .mae file and set the MAEFILE directive. If no name is provided, use jobname.mae. If no structs are provided, use self.getStructure().
If an absolute filename is not provided but the input file is known, write the mae file relative to the input file.
If no filename is given and no jobname is set, a random filename will be generated in the current directory.
- Parameters
filename – Name to give the mae file
structs – A list of structures
- getMaefilename(dont_create: bool = False) Optional[str] ¶
Get the filename of the Maestro file containing the input structure. If no such file exists, it will be created unless c{dont_create} is True.
- Parameters
dont_create – If False, a Maestro file will be created if one does not yet exist. If True, None will be returned if no file exists.
- Returns
The requested filename as an absolute path. If no file exists and
dont_create
is True, None will be returned.- Raises
RuntimeError – If no structure is present.
- property restart: str¶
Get the restart name associated with the input file.
- getStructure(zmat: int = 0) schrodinger.structure._structure.Structure ¶
Return a Structure representation of the specified zmat section.
Note that if the JaguarInput instance was created from a Jaguar input file that has no associated Maestro file (MAEFILE), the Lewis structure is determined automatically based on atom distances.
- Parameters
zmat – The zmat to return (MMJAG_ZMAT1, MMJAG_ZMAT2, or MMJAG_ZMAT3).
- getStructures() List[schrodinger.structure._structure.Structure] ¶
Return a list of all available structure representations for zmat sections
The first call to getStructure is required because getStructure is guaranteed to return a structure, which might have been set in a different way
- setStructure(struct: schrodinger.structure._structure.Structure, zmat: int = 0, set_molchg_multip: bool = True)¶
Set one of the zmat sections from the provided Structure (or MMCT handle).
If set_molchg_multip is True, calling this method will update the values of molchg and multip. molchg will be consistent with the sum of formal charges in the provided CT, while multip will be set according to the CT-level i_m_Spin_multiplicity property.
Note one may call self.clearAllConstraints() to remove any unwanted constraints or scan-coordinates after updating the Structure. By default, such info will be preserved if the new Structure has the same atoms and connectivity as the original Structure; only XYZs (and charges/multiplicity) will be updated.
- Parameters
struct – The structure to use for setting.
zmat – The zmat to set (MMJAG_ZMAT1, MMJAG_ZMAT2, or MMJAG_ZMAT3).
set_molchg_multip – Whether to update molecular charge and multiplicity (default is yes)
- hasStructure(zmat: int = 0) bool ¶
Does this handle have a structure for the specified zmat section?
- Parameters
zmat – The zmat to check (MMJAG_ZMAT1, MMJAG_ZMAT2, or MMJAG_ZMAT3)
- Returns
True if the specified structure is present. False otherwise.
- resetStructure(struct: schrodinger.structure._structure.Structure, molchg: int, multip: int, zmat: int = 0)¶
Redefine the connectivity and formal charges for the input CT, and store the new structure in the current mmjag object, in the &zmat section indicated by the zmat argument.
This function is used when the molecular geometry has changed such that it may not be consistent with its original CT description in terms of bond orders and formal charges, and we want to force the creation of a new Lewis structure.
- Parameters
struct – The structure to use for setting.
molchg – The value to use for the net molecular charge.
multip – The value to use for the net molecular spin.
zmat – The zmat to set (MMJAG_ZMAT1, MMJAG_ZMAT2, or MMJAG_ZMAT3).
- deleteStructure(zmat: int = 0)¶
Delete the specified structure
- Parameters
zmat – The z matrix to delete. Must be one of mm.MMJAG_ZMAT1, mm.MMJAG_ZMAT2, or mm.MMJAG_ZMAT3.
- preflight() str ¶
Run a preflight check and return any warnings.
- Returns
A string containing any warnings raised by the preflight check. If there were no warnings, an empty string is returned.
- makeInternalCoords(zmat: int = 0)¶
Convert the specified Z-matrix to internal coordinates
- Parameters
zmat – The Z-matrix to modify. Must be one of mm.MMJAG_ZMAT1, mm.MMJAG_ZMAT2, or mm.MMJAG_ZMAT3.
- makeCartesianCoords(zmat: int = 0)¶
Convert the specified Z-matrix to Cartesian coordinates
- Parameters
zmat – The Z-matrix to modify. Must be one of mm.MMJAG_ZMAT1, mm.MMJAG_ZMAT2, or mm.MMJAG_ZMAT3.
- getUnknownKeywords() dict ¶
Return a dictionary of all unknown keywords and their values
- Returns
A dictionary of all unknown keywords and their values
- sectionDefined(sect: str) bool ¶
Determine if the specified section is defined
- Parameters
sect – The section to check for
- Returns
True if the specified section is defined. False otherwise.
- createSection(sect: str)¶
Create the specified section
- Parameters
sect – The section to create
- deleteSection(sect: str)¶
Delete the specified section if it exists
- Parameters
sect – the section to delete
- clearAllConstraints()¶
Delete all constraints and their associated coord entries. (Note that mm.mmjag_constraint_delete_all() does not delete the associated coord entries.)
- scanCount() int ¶
This function returns the total number of scan coordinates.
- Returns
scan count
- getScanCoordinate(i: int) schrodinger.application.jaguar.utils.ScanCoord ¶
This function returns i-th scan coordinate.
- Returns
namedtuple (ScanCoord) that contains coordinate type, list of atoms, initial and final coordinate values, number of steps, step, and constraint type.
- setScanCoordinate(coord_type: int, atoms: List[int], initial_value: float, final_value: float, num_steps: int, step: float, const_type: int = 4)¶
This function defines scan coordinate. If atoms list size is less than 4, we add zeros to the list.
- Parameters
coord_type – coordinate type
atoms – list of atom indices
initial_value – coordinate initial value
final_value – coordinate final value
num_steps – number of steps
step – step value
const_type – constraint type of the scan coordinate
- constrainAtomXYZ(index: int)¶
Constrain the XYZ coordinates of an atom.
- Parameters
index – The index of the atom to constrain
- constrainInternal(atom1: int, atom2: int, atom3: int = 0, atom4: int = 0)¶
Constrain an internal coordinate (bond, angle or torsion)
- Parameters
atom1 – The index of the first atom in the internal coordinate definition
atom2 – The index of the second atom in the internal coordinate definition
atom3 – The index of the third atom in the internal coordinate definition (0 if this coordinate is a bond)
atom4 – The index of the fourth atom in the internal coordinate definition (0 if this coordinate is a bond or angle)
- constraintCount() int ¶
This function returns the total number of constraints.
- Returns
constraint count
- constraints() Iterator[Optional[Tuple[int, List[int], Optional[float]]]] ¶
Generator function that yields constraints instead of returning a list.
- getConstraint(i)¶
This function returns i-th constraint.
- Returns
tuple that contains coordinate type, list of atoms and target value (may be None if constraint is not dynamic). If constraint type is MMJAG_SCAN_CONSTRAINT return None, so that we scan coordinates don’t appear as constraints.
- Raises
if constraint index is out of range, a MmException is raised if the atom list is empty, a ConstraintError is raised
- setConstraint(coordinate_type: int, atoms: List[int], value: Optional[float] = None)¶
This function defines static, dynamic, and natural torsion constraints. If atoms list size is less than 4, we add zeros to the list. If the coordinate_type is a natural torsion, a ConstraintError is raised if the number of atoms supplied is not 2. Otherwise, if value is not None, we set this constraint as ‘dynamic’.
- Parameters
coordinate_type – coordinate type
atoms – list of atom indices
value – target value (for dynamic constraints only)
- setMonomialConstraint(coordinate_type: int, atoms: List[int], fc: float, width: float, center: Optional[float] = None)¶
Defines a monomial (e.g. harmonic) constraint. If atoms list size is less than 4, we add zeros to the list.
- Parameters
coordinate_type – coordinate type
atoms – list of atom indices
fc – force constant for potential
width – half-width for flat bottom of potential
center – center for internal coordinate constraints. If None, Jaguar will not use the center
- setActiveCoord(coordinate_type: int, atoms: List[int])¶
This function defines an active coordinate. If atoms list size is less than 4, we add zeros to the list.
- Parameters
coordinate_type – coordinate type
atoms – list of atom indices
- anyConstraintsActive() bool ¶
Check if any coordinate constraints are active
- Returns
Are any coordinate constraints active
- allConstraintsActive() bool ¶
Check if all coordinate constraints are active
- Returns
True if all coordinate constraints are active otherwise returns False. Will return False if there are no constraints set.
- getConstraintIndicesByType(reference_type: int) List[int] ¶
Returns a list of constraint indices (1 based indexing) that are of the given constraint type
- Parameters
reference_type – Check for constraints with this type (mm.MMJag_constraint_type)
- Returns
A list of indices with the given type, 1 indexed
- setNotes(text: str)¶
Set comments/notes in input file
- Raises
ValueError – Note contains “&”
RuntimeError – Any other mmexception from mmjag_note_set
- getNotes() str ¶
Get comments/notes from input file. Removes any whitespace/newline at end of comment string.
- setAtomicBasis(atom_num: int, basis: str)¶
Set a per-atom basis set
- Parameters
atom_num – The atom number to set the basis set for
basis – The basis set
- Raises
ValueError – Invalid atomic number
MmException – General failure from
mmjag_atomic_char_set
- getAtomicBasis(atom_num: int) Optional[str] ¶
Get the per-atom basis set for the specified atom
- Parameters
atom_num – The atom index to get the basis set for
- Returns
The basis set, or None if no basis set has been set for this atom
- Raises
ValueError – Invalid atomic number
MmException – General failure from
mmjag_atomic_char_get
- getAllAtomicBases() Dict[int, str] ¶
Get all per-atom basis sets
- Returns
A dictionary of {atom index: basis set}. Atoms which do not have a per-atom basis set are not included in this dictionary.
- clearAtomicBases()¶
Clear all per-atom basis sets
- setAtomicCharge(atom_index: int, charge: int)¶
Set atomic charge of
atom_index
tocharge
- Raises
ValueError – Invalid atomic number
MmException – General failure from
mmjag_atomic_int_set
- getAtomicCharge(atom_index: int) int ¶
Get atomic charge of
atom_index
- Raises
ValueError – Invalid atomic number
MmException – General failure from
mmjag_atomic_int_get
- setAtomicMultiplicity(atom_index: int, multip: int)¶
Set atomic multiplicity of
atom_index
tomultip
- Raises
ValueError – Invalid atomic number
MmException – General failure from
mmjag_atomic_int_set
- getAtomicMultiplicity(atom_index: int) int ¶
Get atomic multiplicity of
atom_index
- Raises
ValueError – Invalid atomic number
MmException – General failure from
mmjag_atomic_int_get
- getChargeConstraints() List[Tuple[float, Dict[int, float]]] ¶
Parse CDFT input file section to get charge constraints. Assume &cdft section takes the form:
&cdft net-charge weight1 first-atom1 last-atom1 weight2 first-atom2 last-atom2 net-charge weight3 first-atom3 last-atom3 weight4 first-atom4 last-atom4 &
- Return constraints
- list of CDFT constraints in the form
[ (charge1, weights1), (charge2, weights2), …]
- where:
charge: The target charge value for the specified atoms weights: A dictionary of {atom index: weight}
Return empty list if keyword icdft!=1 (i.e. not CDFT done)
- :raise InvalidCDFTError if &cdft section invalid or not found
when icdft keyword is 1
- appendChargeConstraints(charge: float, weights: Dict[int, float])¶
Set charge constraints for CDFT. Append to existing constraints if previously set.
- Parameters
charge – The target charge value for the specified atoms
weights – A dictionary of {atom index: weight}
- setChargeConstraints(constraints: List[Tuple[int, Dict[int, float]]])¶
Set charge constraints for CDFT. Overwrite existing constraints if previously set.
- Parameters
constraints (list) – List of CDFT constraints. Each item of the list should be a (charge, weights) tuple, where weights is a dictionary with atom index as key and weight as value.
- clearChargeConstraints()¶
Clear all CDFT charge constraints
- isEquivalentInput(other, thresh: float = 0.1) bool ¶
Checks whether two JaguarInput instances are describing essentially the same job.
The comparison checks: 1) that the non-default Jaguar keywords are the same 2) that the number of atoms are the same 3) that the structures can be superposed on each other to within a given threshold 4) that all atoms identities (elements and isotopes) are the same.
NB: this means that renumberings of the same structure will be parsed as non-matching. If any of the tests fail, an InputVerificationError is raised (with a message indicating the failed test), otherwise True is returned.
- getHessian() numpy.ndarray[Any, numpy.dtype[numpy.float64]] | None ¶
Get the Hessian matrix from the input file, if present
- Returns
The Hessian matrix as a numpy array, if present. None otherwise.
- setHessian(hess: numpy.ndarray[Any, numpy.dtype[numpy.float64]])¶
Set the Hessian matrix in the input file.
- Parameters
hess – The Hessian matrix to set
- schrodinger.application.jaguar.input.create_guesses(inputs: List[Union[schrodinger.application.jaguar.input.JaguarInput, str, pathlib.Path]], guesses: List[List[Tuple[Union[int, str], Union[int, str]]]], mixing_angles: Optional[List[List[float]]] = None, mix: bool = False, restricted: bool = False, delta_scf: int = 0, charge: Optional[int] = None, multiplicity: Optional[int] = None, write: bool = False) List[List[schrodinger.application.jaguar.input.JaguarInput]] ¶
Write new Jaguar input files with modified guess sections.
mix
will evenly mix each orbital pair (45 degree mixing angle).mixing_angles
will overridemix
if provided. If neithermix
normixing_angles
are provided, each orbital pair will be swapped (90 degree mixing angle).- Parameters
inputs – List of Jaguar input files to modify
guesses – List of lists of orbital pairs to mix/swap
mixing_angles – List of lists of mixing angles for Delta SCF
mix – Evenly mix selected orbital pairs
restricted – Use restricted spin SCF
delta_scf – Delta SCF method to use. 0=None, 1=IMOM, 2=MOM
charge – Charge of the molecule
multiplicity – Multiplicity of the molecule
write – Write new Jaguar input files
- Returns
List of new Jaguar input files
- Raises
JaguarRuntimeError – If the number of mixing angles lists are inconsistent with the number of orbital pair lists. If the number of mixing angles of any list are inconsistent with the number of orbital pairs in the corresponding list.
- schrodinger.application.jaguar.input.hess_section_from_array(hess: numpy.ndarray[Any, numpy.dtype[numpy.float64]]) str ¶
Convert a Hessian matrix to a &hess section string. The &hess section is written out in lower triangular blocks, writing up to 5 columns of data per row at a time.
- Parameters
hess – The Hessian matrix to convert
- Returns
The &hess section string
- schrodinger.application.jaguar.input.hess_array_from_section(hess_str: str) numpy.ndarray[Any, numpy.dtype[numpy.float64]] ¶
Convert a &hess section string to a Hessian matrix. The &hess section is assumed to be written out in lower triangular blocks, with up to 5 columns of data per row at a time.
- Parameters
hess_str – The &hess section string to convert. Can include
&hess &
wrapping, but this is not required.- Returns
The Hessian matrix
- exception schrodinger.application.jaguar.input.InvalidCDFTError¶
Bases:
Exception