6. yaff.tune – Tools to calibrated FF parameters

6.1. yaff.tune.cost – Cost functions for the calibration of FF parameters

Cost functions for the calibration of FF parameters

class yaff.tune.cost.CostFunction(parameter_transform, test_groups)

Bases: object

__call__(x)
class yaff.tune.cost.Simulation(name, system, **kwargs)

Bases: object

__call__(parameters)
run(ff)
class yaff.tune.cost.GeoOptSimulation(name, system, **kwargs)

Bases: yaff.tune.cost.Simulation

run(ff)
class yaff.tune.cost.GeoOptHessianSimulation(name, system, **kwargs)

Bases: yaff.tune.cost.GeoOptSimulation

run(ff)
class yaff.tune.cost.ICGroup(system, rules=None, cases=None)

Bases: object

natom = None
compute_ic(pos, indexes)
compute_tangent(pos, indexes, tangent)
class yaff.tune.cost.BondGroup(system, rules=None, cases=None)

Bases: yaff.tune.cost.ICGroup

natom = 2
class yaff.tune.cost.BendGroup(system, rules=None, cases=None)

Bases: yaff.tune.cost.ICGroup

natom = 3
class yaff.tune.cost.Test(tolerance, simulations)

Bases: object

__call__(results)
filter_results(results)
compute_error(results)
class yaff.tune.cost.ICTest(tolerance, refpos, simulation, icgroup)

Bases: yaff.tune.cost.Test

compute_error(results)
class yaff.tune.cost.FCTest(tolerance, refpos, refhessian, simulation, icgroup)

Bases: yaff.tune.cost.Test

A test for force constants

This is special in the sense that the force constants derived from the hessian are not sensitive to either orientation of the molecule or the choice of other internal coordinates. This is realized by comparing the second order derivatives along PES scanes of selected internal coordinates.

compute_error(results)
compute_fc(pos, hessian, indexes)

6.2. yaff.tune.transform – Specification of variables in a parameters file

Specification of variables in a parameters file

class yaff.tune.transform.ParameterTransform(parameters0, mods)

Bases: object

get_init()
__call__(x)
class yaff.tune.transform.ParameterModifier(rules)

Bases: object

get_init()
__call__(x, parameters)
class yaff.tune.transform.ModifierRule(prefix, suffix, regex, index)

Bases: object

__call__(x, parameters)
modify_value(x, value)
get_init()
class yaff.tune.transform.ScaleRule(prefix, suffix, regex, index)

Bases: yaff.tune.transform.ModifierRule

modify_value(x, value)
get_init()
class yaff.tune.transform.IncrementRule(prefix, suffix, regex, index)

Bases: yaff.tune.transform.ModifierRule

modify_value(x, value)
get_init()