Package schrodinger :: Package application :: Package matsci :: Module mecp_mod :: Class MECPStep

Class MECPStep

object --+
         |
        MECPStep

Manage an MECP step, which can be an iteration or a line search iteration.

Instance Methods

[hide private]

__init__(self, iteration, call_number, x_initial, method, perp_factor, para_factor, verbose, logger, bfgs_obj)
Create an instance.

logInitialGeometry(self)
Log the initial geometry.

logHessianEigVals(self)
Log the Hessian eigenvalues.

logStepSize(self)
Log the step size.

handleFinalGeometry(self, x_final)
Handle the final geometry.

setInTemplates(self)
Set the Jaguar input templates.

numpy.array or None

getUnitNormalToDeltaForces(self, prev_mecp_step=None)
Get the unit vector that is normal to the delta forces vector.

setEnergiesAndForces(self, prev_mecp_step=None)
Set the energies and forces for the two states as well as well as the energy and forces to use for the MECP optimization.

setEnergiesAndForcesData(self, prev_mecp_step=None)
Set energies and forces data.

setJobData(self, jobs, prev_mecp_step=None)
Set job data.

logEnergyAndForces(self, header, energy, forces, max_force, rms_force, energy_header='Energy / Hartree', forces_header='Forces / Hartree/Ang.')
Log energy and forces.

str

getFormattedSummaryLine(self, entries)
Return a formatted summary line from the given data entries.

logSummaryHeader(self)
Log the summary header.

logSummary(self)
Log a summary.

logJobData(self)
Log job data.

terminate(self, convergence_dict)
Terminate the MECP optimization.

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, iteration, call_number, x_initial, method, perp_factor, para_factor, verbose, logger, bfgs_obj)
(Constructor)

Create an instance.

Parameters:

iteration (int) - the iteration
call_number (int) - the call number
x_initial (numpy.array) - the initial geometry vector (N X 1)
method (str) - the method to use to determine the MECP
perp_factor (float) - prefactor for the energy term whose gradient lies perpendicular to the crossing seam
para_factor (float) - prefactor for the energy term whose gradient lies parallel to the crossing seam
verbose (bool) - specifies verbose logging
logger (logging.Logger) - output logger
bfgs_obj (BFGS) - a BFGS object that manages the optimization

Overrides: object.__init__

handleFinalGeometry(self, x_final)

Handle the final geometry.

Parameters:

x_final (numpy.array) - the final geometry vector (N X 1)

getUnitNormalToDeltaForces(self, prev_mecp_step=None)

Get the unit vector that is normal to the delta forces vector.

Parameters:

prev_mecp_step (MECPStep or None) - MECPStep from the previous iteration or line search iteration or None if there isn't one

Returns: numpy.array or None

the unit vector perpendicular to the delta forces vector or None if there isn't one

setEnergiesAndForces(self, prev_mecp_step=None)

Set the energies and forces for the two states as well as well as the energy and forces to use for the MECP optimization.

Parameters:

prev_mecp_step (MECPStep or None) - MECPStep from the previous iteration or line search iteration or None if there isn't one

setEnergiesAndForcesData(self, prev_mecp_step=None)

Set energies and forces data.

Parameters:

prev_mecp_step (MECPStep or None) - MECPStep from the previous iteration or line search iteration or None if there isn't one

setJobData(self, jobs, prev_mecp_step=None)

Set job data.

Parameters:

jobs (list) - contains the JaguarJob instances for the two jobs
prev_mecp_step (MECPStep or None) - MECPStep from the previous iteration or line search iteration or None if there isn't one

logEnergyAndForces(self, header, energy, forces, max_force, rms_force, energy_header=`'Energy / Hartree'`, forces_header=`'Forces / Hartree/Ang.'`)

Log energy and forces.

Parameters:

header (str) - a header
energy (float or None) - the energy or None if there isn't one
forces (numpy.array) - the forces (natoms X 3)
max_force (float) - the magnitude of the largest forces element
rms_force (float) - the RMS of forces
energy_header (str) - an energy header
forces_header (str) - a forces header

getFormattedSummaryLine(self, entries)

Return a formatted summary line from the given data entries.

Parameters:

entries (list) - the data to format

Returns: str

a formatted summary line

terminate(self, convergence_dict)

Terminate the MECP optimization.

Parameters:

convergence_dict (dict) - contains various convergence thresholds

Class MECPStep

__init__(self, iteration, call_number, x_initial, method, perp_factor, para_factor, verbose, logger, bfgs_obj) (Constructor)

handleFinalGeometry(self, x_final)

getUnitNormalToDeltaForces(self, prev_mecp_step=None)

setEnergiesAndForces(self, prev_mecp_step=None)

setEnergiesAndForcesData(self, prev_mecp_step=None)

setJobData(self, jobs, prev_mecp_step=None)

logEnergyAndForces(self, header, energy, forces, max_force, rms_force, energy_header='Energy / Hartree', forces_header='Forces / Hartree/Ang.')

getFormattedSummaryLine(self, entries)

terminate(self, convergence_dict)

init(self, iteration, call_number, x_initial, method, perp_factor, para_factor, verbose, logger, bfgs_obj)
(Constructor)

logEnergyAndForces(self, header, energy, forces, max_force, rms_force, energy_header=`'Energy / Hartree'`, forces_header=`'Forces / Hartree/Ang.'`)