Subsections


align_tensor.init

Image align_tensor Image align_tensor

Synopsis

Initialise an alignment tensor.

Defaults

align_tensor.init(tensor=None, align_id=None, domain=None, params=None, scale=1.0, angle_units=`deg', param_types=2, errors=False)

Keyword arguments

tensor: The optional alignment tensor ID string, required if multiple tensors exist per alignment.

align_id: The alignment ID string that the tensor corresponds to.

domain: The optional domain ID string that the tensor corresponds to.

params: The alignment tensor data.

scale: The alignment tensor eigenvalue scaling value.

angle_units: The units for the angle parameters.

param_types: A flag to select different parameter combinations.

errors: A flag which determines if the alignment tensor data or its errors are being input.

Description

The tensor ID is only required if there are multiple unique tensors per alignment. An example is if internal domain motions cause multiple parts of the molecule to align differently. The tensor ID is optional and in the case of only a single tensor per alignment, the tensor can be identified using the alignment ID instead.

The alignment tensor parameters should be a tuple of floating point numbers (a list surrounded by round brakets). These correspond to the parameters of the tensor which can be specified by the parameter types whereby the values correspond to:

0 -
{Sxx, Syy, Sxy, Sxz, Syz} (unitless),
1 -
{Szz, Sxx-yy, Sxy, Sxz, Syz} (Pales default format),
2 -
{Axx, Ayy, Axy, Axz, Ayz} (unitless),
3 -
{Azz, Axx-yy, Axy, Axz, Ayz} (unitless),
4 -
{Axx, Ayy, Axy, Axz, Ayz} (units of Hertz),
5 -
{Azz, Axx-yy, Axy, Axz, Ayz} (units of Hertz),
6 -
{Pxx, Pyy, Pxy, Pxz, Pyz} (unitless),
7 -
{Pzz, Pxx-yy, Pxy, Pxz, Pyz} (unitless).

Other formats may be added later. The relationship between the Saupe order matrix S and the alignment tensor A is

S = 3/2 A.

The probability matrix P is related to the alignment tensor A by

A = P - 1/3 I,

where I is the identity matrix. For the alignment tensor to be supplied in Hertz, the bond vectors must all be of equal length.

Prompt examples

To set a rhombic tensor for the domain labelled `domain 1' with the alignment named `super media', type one of:

[numbers=none]
relax> align_tensor.init('domain 1', 'super media', (-8.6322e-05, -5.5786e-04, -3.1732e-05, 2.2927e-05, 2.8599e-04), param_types=1)

[numbers=none]
relax> align_tensor.init(tensor='domain 1', align_id='super media', params=(-8.6322e-05, -5.5786e-04, -3.1732e-05, 2.2927e-05, 2.8599e-04), param_types=1)


The relax user manual (PDF), created 2016-10-28.