`JobType` classes#

various job types for Theory() instances

AaronTools.theory.job_types.job_from_string(name, **kwargs)#

get a job name given a simple name

Parameters:

name (str) –

“opt” or “conf” with “.ts”, “.transition_state”, “.change”, and “.con” extensions
- .ts and .transition_state indicate a transition state optimization
- .con indicates a constrained optimization - “constraints” should be in kwargs and the value should be a dictionary conformable with the keyword of OptimizationJob
”freq” with “.num” extensions
- .num indicates a numerical frequnecy, as does kwargs[“numerical”] = True kwargs can also have a “temperature” key
”sp” or “energy” or “single-point”
”force” or “gradient” with a “.num” extension
- .num indicates a numerical frequnecy, as does kwargs[“numerical”] = True

Returns:

job types for the given string

class AaronTools.theory.job_types.JobType#

parent class of all job types initialization keywords should be the same as attribute names

__init__()#

get_gaussian()#: overwrite to return dict with GAUSSIAN_* keys

get_orca()#: overwrite to return dict with ORCA_* keys

get_psi4()#: overwrite to return dict with PSI4_* keys

get_sqm()#: overwrite to return a dict with SQM_* keys

get_qchem()#: overwrite to return a dict with QCHEM_* keys

get_xtb()#: overwrite to return a dict with XTB_* keys

static resolve_error(error, theory, exec_type, geometry=None)#

returns a copy of theory or modifies theory to attempt to resolve an error

theory will be modified if it is not possible for the current theory to work for any job

if the error is specific to the molecule and settings, theory will be copied, modified, and returned raises NotImplementedError if this job type has no fix for the error code

Parameters:

error (str) – error code (e.g. SCF_CONV; see fileIO ERROR)
theory (Theory) – Theory instance used when the error happened
exec_type (str) – software program (i.e. gaussian, orca, etc.)
geometry (Geometry) – (optional) structure might be adjusted slightly if there are close contacts

class AaronTools.theory.job_types.OptimizationJob(transition_state=False, constraints=None, geometry=None)#

optimization job

__init__(transition_state=False, constraints=None, geometry=None)#

Parameters:

transition_state (bool) – request a transition state optimization
constraints (dict) –
keys are

available for ORCA, Gaussian, and Psi4
- ’atoms’ - atom identifiers/finders - atoms to constrain
- ’bonds’ - list(atom idenifiers/finders) - distances to constrain each atom identifier in the list should result in exactly 2 atoms
- ’angles’ - list(atom idenifiers/finders) - 1-3 angles to constrain each atom identifier should result in exactly 3 atoms
- ’torsions’ - list(atom identifiers/finders) - constrained dihedral angles each atom identifier should result in exactly 4 atoms
available for Gaussian and Psi4
- ’x’ - list(atom identifiers/finders) - constrain the x coordinate of these atoms. Similarly, ‘y’ and ‘z’ are also accepted.
- ’xgroup’ - list(tuple(list(atom idenifiers), x_val, hold)) - constrain the x coordinate of these atoms to be the same
  - x_val - set x-coordinate to this value
  - hold - hold this value constant during the optimization if ‘hold’ is omitted, the value will not be held constant during the optimization
    
    e.g. ‘xgroup’:[(“1-6”, 0, False), (“13-24”, 3.25, False)]
    
    this will keep atoms 1-6 and 13-24 in parallel planes, while also allowing those planes to move
- ’ygroup’ and ‘zgroup’ are also available, with analagous options
NOTE

for Gaussian, ‘bonds’, ‘angles’, and ‘torsions’ constraints cannot be mixed with ‘x’, ‘y’, ‘z’, ‘xgroup’, ‘ygroup’, or ‘zgroup’ constraints
geometry (Geometry) – will be set when using an AaronTools FileWriter

get_gaussian()#: returns a dict with keys: GAUSSIAN_ROUTE, GAUSSIAN_CONSTRAINTS

get_orca()#: returns a dict with keys: ORCA_ROUTE, ORCA_BLOCKS

get_psi4()#: returns a dict with keys: PSI4_JOB, PSI4_OPTKING, PSI4_BEFORE_GEOM

get_xtb()#

Generates xcontrol file constraints

Returns: dict(fix, constrain, metadyn, cli)

get_sqm()#: returns a dict(), warnings for optimization jobs

get_qchem()#: overwrite to return a dict with QCHEM_* keys

static resolve_error(error, theory, exec_type, geometry=None)#: resolves optimization-specific errors errors resolved by JobType take priority

class AaronTools.theory.job_types.FrequencyJob(numerical=False, temperature=None)#

frequnecy job

__init__(numerical=False, temperature=None)#: temperature in K for thermochem info, defaults to 298.15 K

get_gaussian()#: returns a dict with keys: GAUSSIAN_ROUTE

get_orca()#: returns a dict with keys: ORCA_ROUTE

get_psi4()#: returns a dict with keys: PSI4_JOB

get_sqm()#: overwrite to return a dict with SQM_* keys

get_qchem()#: overwrite to return a dict with QCHEM_* keys

get_xtb()#: overwrite to return a dict with XTB_* keys

static resolve_error(error, theory, exec_type, geometry=None)#: resolves frequnecy-specific errors errors resolved by JobType take priority

class AaronTools.theory.job_types.SinglePointJob#

single point energy

get_gaussian()#: returns a dict with keys: GAUSSIAN_ROUTE

get_orca()#: returns a dict with keys: ORCA_ROUTE

get_psi4()#: returns a dict with keys: PSI4_JOB

get_sqm()#: returns a dict with keys: SQM_QMMM

get_qchem()#: overwrite to return a dict with QCHEM_* keys

class AaronTools.theory.job_types.ForceJob(numerical=False)#

force/gradient job

__init__(numerical=False)#

get_gaussian()#: returns a dict with keys: GAUSSIAN_ROUTE

get_orca()#: returns a dict with keys: ORCA_ROUTE

get_psi4()#: returns a dict with keys: PSI4_JOB

get_qchem()#: overwrite to return a dict with QCHEM_* keys

get_xtb()#: overwrite to return a dict with XTB_* keys

class AaronTools.theory.job_types.ConformerSearchJob(constraints=None, geometry=None)#

conformer search (basically only for crest)

__init__(constraints=None, geometry=None)#

Parameters:

constraints (dict) –
valid keys are:
- ’atoms’ - atom identifiers/finders - atoms to constrain
- ’bonds’ - list(atom idenifiers/finders) - distances to constrain each atom identifier in the list should result in exactly 2 atoms
- ’angles’ - list(atom idenifiers/finders) - 1-3 angles to constrain each atom identifier should result in exactly 3 atoms
- ’torsions’ - list(atom identifiers/finders) - constrained dihedral angles
  each atom identifier should result in exactly 4 atoms
geometry (Geometry) – will be set when using an AaronTools FileWriter

class AaronTools.theory.job_types.TDDFTJob(roots, root_of_interest=0, compute_nacmes=False)#

TD-DFT job

__init__(roots, root_of_interest=0, compute_nacmes=False)#

Parameters:

roots (int) – number of roots
root_of_interest (int) – root for further computations (e.g. forces)
compute_nacmes (bool) – request nonadiabatic coupling matrix elements

get_gaussian()#: overwrite to return dict with GAUSSIAN_* keys

get_orca()#: overwrite to return dict with ORCA_* keys

get_psi4()#: overwrite to return dict with PSI4_* keys

get_qchem()#: overwrite to return a dict with QCHEM_* keys

JobType classes#

`JobType` classes#