__init__(self,
model=None,
init_params=None,
full_tensors=None,
full_in_ref_frame=None,
rdcs=None,
rdc_errors=None,
rdc_weights=None,
rdc_vect=None,
dip_const=None,
pcs=None,
pcs_errors=None,
pcs_weights=None,
atomic_pos=None,
temp=None,
frq=None,
paramag_centre=array([ 0., 0., 0.]),
scaling_matrix=None,
sobol_max_points=200,
sobol_oversample=100,
com=None,
ave_pos_pivot=array([ 0., 0., 0.]),
pivot=None,
pivot_opt=False,
quad_int=False)
(Constructor)
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Set up the target functions for the Frame Order theories.
- Parameters:
model (str) - The name of the Frame Order model.init_params (numpy float64 array) - The initial parameter values.full_tensors (numpy nx5D, rank-1 float64 array) - An array of the {Axx, Ayy, Axy, Axz, Ayz} values for all full
alignment tensors. The format is [Axx1, Ayy1, Axy1, Axz1, Ayz1,
Axx2, Ayy2, Axy2, Axz2, Ayz2, ..., Axxn, Ayyn, Axyn, Axzn, Ayzn].full_in_ref_frame (numpy rank-1 array) - An array of flags specifying if the tensor in the reference frame
is the full or reduced tensor.rdcs (numpy rank-2 array) - The RDC lists. The first index must correspond to the different
alignment media i and the second index to the spin systems j.rdc_errors (numpy rank-2 array) - The RDC error lists. The dimensions of this argument are the
same as for 'rdcs'.rdc_weights (numpy rank-2 array) - The RDC weight lists. The dimensions of this argument are the
same as for 'rdcs'.rdc_vect (numpy rank-2 array) - The unit XH vector lists corresponding to the RDC values. The
first index must correspond to the spin systems and the second
index to the x, y, z elements.dip_const (numpy rank-1 array) - The dipolar constants for each RDC. The indices correspond to
the spin systems j.pcs (numpy rank-2 array) - The PCS lists. The first index must correspond to the different
alignment media i and the second index to the spin systems j.pcs_errors (numpy rank-2 array) - The PCS error lists. The dimensions of this argument are the
same as for 'pcs'.pcs_weights (numpy rank-2 array) - The PCS weight lists. The dimensions of this argument are the
same as for 'pcs'.atomic_pos (numpy rank-3 array) - The atomic positions of all spins for the PCS and PRE data. The
first index is the spin systems j and the second is the structure
or state c.temp (numpy rank-1 array) - The temperature of each PCS data set.frq (numpy rank-1 array) - The frequency of each PCS data set.paramag_centre (numpy rank-1, 3D array or rank-2, Nx3 array) - The paramagnetic centre position (or positions).scaling_matrix (numpy rank-2 array) - The square and diagonal scaling matrix.sobol_max_points (int) - The maximum number of Sobol' points to use for the numerical PCS
integration technique.sobol_oversample (int) - The oversampling factor Ov used for the total number of points N
* Ov * 10**M, where N is the maximum number of Sobol' points and
M is the number of dimensions or torsion-tilt angles for the
system.com (numpy 3D rank-1 array) - The centre of mass of the system. This is used for defining the
rotor model systems.ave_pos_pivot (numpy 3D rank-1 array) - The pivot point to rotate all atoms about to the average domain
position. In most cases this will be the centre of mass of the
moving domain. This pivot is shifted by the translation vector.pivot (numpy rank-1, 3D array or None) - The pivot point for the ball-and-socket joint motion. This is
needed if PCS or PRE values are used.pivot_opt (bool) - A flag which if True will allow the pivot point of the motion to
be optimised.quad_int (bool) - A flag which if True will perform high precision numerical
integration via the scipy.integrate quad(), dblquad() and
tplquad() integration methods rather than the rough quasi-random
numerical integration.
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