seamm_geometric package#

Submodules#

seamm_geometric.seamm_geometric module#

class seamm_geometric.seamm_geometric.SEAMMEngine(step, molecule)[source]#

Bases: Engine

Helper class that is a geomeTRIC engine and connects to SEAMM.

calc_new(coords, dirname)[source]#

The method to calculate the new energy and forces.

Parameters:

  • coords (np.ndarray) – A 1-D Numpy array of the coordinates, in Bohr

  • dirname (The name of a directory (not used))

Returns:

data –

The result returned to geomeTRIC:

”energy” : The energy, in Hartree

”gradient” : The 1st derivative, or gradient, of the energy in Hartree/bohr as a 1-D Numpy array.

Return type:

{str : any}

copy_scratch(src, dest)[source]#
class seamm_geometric.seamm_geometric.geomeTRIC_mixin[source]#

Bases: object

A mixin class for running a geomeTRIC optimization.

describe_geomeTRIC_optimizer(P=None, short=False, natoms=None)[source]#

Describe the geomeTRIC optimizer.

Parameters:

  • P (dict) – An optional dictionary of the current values of the control parameters.

  • short (bool) – If True, return a short description of the step.

  • natoms (int) – The number of atoms in the structure.

Returns:

A description of the current step.

Return type:

str

geometric_calculate_gradients(coordinates)[source]#

Given the new coordinates, calculate the energy and gradients.

Parameters:

coordinates ([3, n_atoms] array of coordinates)

geometric_read_bibliography()[source]#

Read the bibliography from a file and add to the local bibliography

run_geomeTRIC_optimizer(P, PP)[source]#

Run an optimization using geomeTRIC.

Parameters:

  • P (dict) – The current values of the parameters

  • PP (dict) – The current values of the parameters, formatted for printing

Module contents#

Connector between SEAMM and ASE