Molsys

class optking.molsys.Molsys(fragments, dimer_intcos=None)[source]

Bases: object

Attributes Summary

`Z`
`all_fragments`
`atom_symbols`
`dimer_intcos`
`dimer_psuedo_frags`
`frag_natoms`
`fragments`
`fragments_atom_list`
`frozen_intco_list`	Determine vector with 1 for any frozen internal coordinate
`geom`	cartesian geometry [a0]
`intco_lbls`
`intcos_present`
`masses`
`natom`
`nfragments`
`num_intcos`
`num_intrafrag_intcos`

Methods Summary

`Bmat`([massWeight])
`Gmat`([massWeight])	Calculates BuB^T (calculates B matrix)
`add_cartesian_intcos`()
`apply_external_forces`(fq, H, stepNumber)
`atom2frag_index`(atom_index)
`atom_list2unique_frag_list`(atomList)
`augment_connectivity_to_single_fragment`(C)
`clear`()
`closest_atoms_between_2_frags`(A, B)
`consolidate_fragments`()
`constraint_matrix`([fq])	Returns constraint matrix with 1 on diagonal for frozen coordinates
`dimerfrag_1st_intco`(iDI)
`dimerfrag_intco_range`(iDI)
`dimerfrag_intco_slice`(iDI)
`distance_matrix`()
`fix_bend_axes`()	See description in Fragment class.
`frag_1st_atom`(iF)
`frag_1st_intco`(iF)
`frag_atom_range`(iF)
`frag_atom_slice`(iF)
`frag_geom`(iF)	cartesian geometry for fragment i
`frag_intco_range`(iF)
`frag_intco_slice`(iF)
`from_dict`(d)
`from_psi4`(mol)	Creates a optking molecular system from psi4 mol.
`from_schema`(qc_molecule)	Creates optking molecular system from JSON input.
`gradient_to_cartesians`(g_q)	converts the gradient from internal into Cartesian coordinates
`gradient_to_internals`(g_x[, coeff, B, useMasses])	Transform cartesian gradient to internals :param g_x: (3nat, 1) cartesian gradient :type g_x: np.ndarray :param coeff: prefactor coefficient; -1 for forces :type coeff: float :param B: B matrix to use :type B: np.ndarray, optional :param useMasses: instead of identity, use u = 1/masses in transformation :type useMasses: boolean
`hessian_to_cartesians`(Hint[, g_q])
`hessian_to_internals`(H[, g_x, useMasses])	converts the hessian from cartesian coordinates into internal coordinates Hq = A^t (Hxy - Kxy) A, where K_xy = sum_q ( grad_q[I] d^2(q_I)/(dx dy) and A = (BuB^t)^-1 Bu
`interfrag_dq_discontinuity_correction`(dq)
`print_geom`()	Returns a string of the geometry for logging in [a0]
`print_intcos`()
`project_redundancies_and_constraints`(fq, H)	Project redundancies and constraints out of forces and Hessian
`purge_interfragment_connectivity`(C)
`q`()	Returns internal coordinate values in au as list.
`q_array`()	Returns internal coordinate values in au as array.
`q_show`()	returns internal coordinates values in Angstroms/degrees as list.
`q_show_array`()	returns internal coordinates values in Angstroms/degrees as array.
`q_show_forces`(forces)	Returns scaled forces as array.
`ranged_frozen_intco_list`(fq)	Determine vector with 1 for any ranged intco that is at its limit
`show_geom`()	Return a string of the geometry in [A]
`split_fragments_by_connectivity`()	Split any fragment not connected by bond connectivity.
`test_Bmat`()	Test the analytic B matrix (dq/dx) via finite differences.
`test_derivative_Bmat`()	Test the analytic derivative B matrix (d2q/dx2) via finite differences.
`to_dict`()
`unfix_bend_axes`()	See description in Fragment class.
`update_dihedral_orientations`()	See description in Fragment class.
`update_dimer_intco_reference_points`()

Attributes Documentation

Z

all_fragments

atom_symbols

dimer_intcos

dimer_psuedo_frags

frag_natoms

fragments

fragments_atom_list

frozen_intco_list: Determine vector with 1 for any frozen internal coordinate

geom: cartesian geometry [a0]

intco_lbls

intcos_present

masses

natom

nfragments

num_intcos

num_intrafrag_intcos

Methods Documentation

Bmat(massWeight=False)[source]

Gmat(massWeight=False)[source]

Calculates BuB^T (calculates B matrix)

Parameters: masses (List, optional) –

add_cartesian_intcos()[source]

apply_external_forces(fq, H, stepNumber)[source]

atom2frag_index(atom_index)[source]

atom_list2unique_frag_list(atomList)[source]

augment_connectivity_to_single_fragment(C)[source]

clear()[source]

closest_atoms_between_2_frags(A, B)[source]

consolidate_fragments()[source]

constraint_matrix(fq=None)[source]: Returns constraint matrix with 1 on diagonal for frozen coordinates

dimerfrag_1st_intco(iDI)[source]

dimerfrag_intco_range(iDI)[source]

dimerfrag_intco_slice(iDI)[source]

distance_matrix()[source]

fix_bend_axes()[source]: See description in Fragment class.

frag_1st_atom(iF)[source]

frag_1st_intco(iF)[source]

frag_atom_range(iF)[source]

frag_atom_slice(iF)[source]

frag_geom(iF)[source]: cartesian geometry for fragment i

frag_intco_range(iF)[source]

frag_intco_slice(iF)[source]

classmethod from_dict(d)[source]

static from_psi4(mol)[source]

Creates a optking molecular system from psi4 mol. Note that not all information is preserved. :param mol: psi4 mol :type mol: object

Returns: optking molecular system: list of fragments
Return type: cls

classmethod from_schema(qc_molecule)[source]

Creates optking molecular system from JSON input.

Parameters: qc_molecule (dict) – molecule key in MOLSSI QCSchema see http://molssi-qc-schema.readthedocs.io/en/latest/auto_topology.html
Returns: molsys cls consists of list of Frags
Return type: cls

gradient_to_cartesians(g_q)[source]

converts the gradient from internal into Cartesian coordinates

Parameters: g_q (ndarray) – internal coordinate gradient
Returns: g_x – Cartesian coordinate gradient
Return type: ndarray

gradient_to_internals(g_x, coeff=1.0, B=None, useMasses=False)[source]

Transform cartesian gradient to internals :param g_x: (3nat, 1) cartesian gradient :type g_x: np.ndarray :param coeff: prefactor coefficient; -1 for forces :type coeff: float :param B: B matrix to use :type B: np.ndarray, optional :param useMasses: instead of identity, use u = 1/masses in transformation :type useMasses: boolean

Returns: gradient in internal coordinates (coeff==1)
Return type: ndarray

Notes

g_q = (BuB^T)^(-1)*B*g_x

hessian_to_cartesians(Hint, g_q=None)[source]

hessian_to_internals(H, g_x=None, useMasses=False)[source]

converts the hessian from cartesian coordinates into internal coordinates Hq = A^t (Hxy - Kxy) A, where K_xy = sum_q ( grad_q[I] d^2(q_I)/(dx dy) and A = (BuB^t)^-1 Bu

Parameters

H (np.ndarray) – Hessian in cartesians
g_x (np.ndarray) – (nat, 3) gradient in cartesians (optional)
massWeight (boolean) – whether to keep arbitrary transformation matrix u=I or use 1/mass_i as in spectroscopy or cases where rotations/translations matter.

Returns

Hq – hessian in internal coordinates

Return type

np.ndarray

interfrag_dq_discontinuity_correction(dq)[source]

print_geom()[source]: Returns a string of the geometry for logging in [a0]

print_intcos()[source]

project_redundancies_and_constraints(fq, H)[source]: Project redundancies and constraints out of forces and Hessian

purge_interfragment_connectivity(C)[source]

q()[source]: Returns internal coordinate values in au as list.

q_array()[source]: Returns internal coordinate values in au as array.

q_show()[source]: returns internal coordinates values in Angstroms/degrees as list.

q_show_array()[source]: returns internal coordinates values in Angstroms/degrees as array.

q_show_forces(forces)[source]: Returns scaled forces as array.

ranged_frozen_intco_list(fq)[source]: Determine vector with 1 for any ranged intco that is at its limit

show_geom()[source]: Return a string of the geometry in [A]

split_fragments_by_connectivity()[source]: Split any fragment not connected by bond connectivity.

test_Bmat()[source]

Test the analytic B matrix (dq/dx) via finite differences. The 5-point formula should be good to DISP_SIZE^4 - a few unfortunates will be slightly worse.

Returns: passes – Returns True or False, doesn’t raise exceptions
Return type: boolean

test_derivative_Bmat()[source]

Test the analytic derivative B matrix (d2q/dx2) via finite differences. The 5-point formula should be good to DISP_SIZE^4 - a few unfortunates will be slightly worse.

Returns: passes – Returns True or False, doesn’t raise exceptions
Return type: boolean

to_dict()[source]

unfix_bend_axes()[source]: See description in Fragment class.

update_dihedral_orientations()[source]: See description in Fragment class.

update_dimer_intco_reference_points()[source]