High Level functions and Classes

The following documentation pertains to the classes and functions that would most likely be useful for running optimizations directly through optkings python API and functions that would be helpful for driver level operations.

optking.opt_helper Module

Helpers to provide high-level interfaces for optking. The Helpers allow individual steps to be taken easily. EngineHelper runs calculations through QCEngine. CustomHelper adds the abilility to directly input gradients.

Classes

ABC()	Helper class that provides a standard way to create an ABC using inheritance.
AlgError([mesg, newLinearBends])
CustomHelper(mol_src[, params])	Class allows for easy setup of optking. Accepts custom forces, energies,
EngineHelper(optimization_input, **kwargs)	Perform an optimization using qcengine to compute properties. Use OptimizationInput to setup
Helper([params])	Base class for CustomHelper (accepts user provided gradients) and EngineHelper (uses MolSSI's QCEngine for gradients)
IntrinsicReactionCoordinate(molsys, history, ...)
OptError([mesg, err_type])
OptimizationManager(molsys, history_object, ...)	Recommended use of Optking's Optimization Algorithms is to create this class and then loop over take_step.

Class Inheritance Diagram

optking.optimize Module

Provides some of the high level functions and classes to run optimizations. This is a good starting place for anyone looking to add features to the code to familarize themselves with the overall workings of optking. Functions may be useful to users seeking greater control over the inner workings of optking than provided by the OptHelpers. For instance if manually creating a molecular system or manually controlling / switching algorithms on the fly.

See also OptimizationAlgorithm <stepalgorithms.OptimizationAlgorithm> and `OptimizationInterface <stepalgorithms.OptimizationInterface>`for core functionality common to all the optimization algorithms like backtransformation and displacement.

Functions

get_hess_grad(computer, o_molsys)	Compute hessian and fetch gradient from output if possible.
get_pes_info(H, computer, o_molsys, ...[, ...])	Calculate, update, or guess hessian as appropriate.
make_internal_coords(o_molsys[, params])	Add optimization coordinates to molecule system.
optimization_factory(method, molsys, ...[, ...])	create optimization algorithms. method may be redundant however params is allowed
optimize(o_molsys, computer)	Driver for OptKing's optimization procedure.
prepare_opt_output(o_molsys, computer[, ...])
print_array_string(M[, Ncol, title, form])	Formats Arrays for Logging or Printing
print_geom_grad(geom, grad)
print_mat_string(M[, Ncol, title])	Formats a Matrix for Logging or Printing

Classes

AlgError([mesg, newLinearBends])
ComputeWrapper(molecule, model, keywords, ...)	An implementation of MolSSI's qc schema
Molsys(fragments[, dimer_intcos])
OptError([mesg, err_type])
OptimizationManager(molsys, history_object, ...)	Recommended use of Optking's Optimization Algorithms is to create this class and then loop over take_step.

Class Inheritance Diagram