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Re: proposal for valence items

  • To: Multiple recipients of list <coredmg@iucr.org>
  • Subject: Re: proposal for valence items
  • From: Gotzon Madariaga <wmpmameg@lg.ehu.es>
  • Date: Wed, 29 Nov 2000 17:55:18 GMT
Given that I promoted the inclusion of twin data items in the Core here is a
proposal of what I consider the essential definitions. The approach is very 
practical and probably it will start a new dicussion. I would not want to 
interfere with the approval of other more mature items like those concerning 
bond valence. I have followed the treatment given to the twinning problem by two
 programs Shelx (Sheldrick, 19xx) and Jana (Petricek,19xx-2000). Since I
am more familiar with the effects twinning causes in reciprocal space my
proposal includes twin matrices operating on Miller indices and I have not
considered antiphase domains. Criticisms are welcome. 

The proposed definitions are:

===============================================================================
data_diffrn_reflns_twin_id
    _name                   '_diffrn_reflns_twin_id'
    _category                diffrn_reflns
    _type                    char
    _list                    yes
    _list_link_child         '_refine_ls_twin_id'
    _definition
;              A unique identifier for each domain detected in the sample.
;

data_diffrn_reflns_twin_matrix_
    loop_ _name              '_diffrn_reflns_twin_matrix_11'
                             '_diffrn_reflns_twin_matrix_12'
                             '_diffrn_reflns_twin_matrix_13'
                             '_diffrn_reflns_twin_matrix_21'
                             '_diffrn_reflns_twin_matrix_22'
                             '_diffrn_reflns_twin_matrix_23'
                             '_diffrn_reflns_twin_matrix_31'
                             '_diffrn_reflns_twin_matrix_32'
                             '_diffrn_reflns_twin_matrix_33'
    _category                diffrn_reflns
    _type                    numb
    _list                    yes
    _list_reference          '_diffrn_reflns_twin_id'
    _definition
;              The matrices that generate the Miller indices of each domain from
the Miller indices of the first one:

                (h~i~)   (m~11~ m~12~ m~13~) (h~1~)
                (k~i~) = (m~21~ m~22~ m~23~) (h~2~)
                (l~i~)   (m~31~ m~32~ m~33~) (h~3~)

The twin matrices are referred to the basis reciprocal to that given by 
_cell_length_ and _cell_angle_. All the twin matrices including the identity 
should be entered. 
;

data_refine_ls_twin_id
    _name                   '_refine_ls_twin_id'
    _category                refine
    _type                    char
    _list                    yes
    _list_link_parent        '_diffrn_reflns_twin_id'
    _definition
;              An identifier for the refined twin fractions. It must match a
corresponding _diffrn_reflns_twin_id.
;

data_refine_ls_twin_fraction
    _category                refine
    _type                    numb
    _type_conditions         esd
    _list                    yes
    _list_reference          'refine_ls_twin_id'
    _definition
;              The refined values of the twin fractions. Twin fractions, k(i),
are defined through the following expression:

               F^2^~c~=s^2^ Sumi k(i)F^2^~c,i~    (i=1,n)

where F~c~ is the calculated structure factor, F~c,i~ the calculated structure 
factor of domain i, s the overall scale factor and n the number of domains. The 
sum of twin fractions must be unity and therefore only k(2)...k(n) are refined.
However all the twin fractions including k(1) should be entered.
;

###very long name...

data_refine_diff_twin_F_obs_deconvolution_description   
    _name               '_refine_diff_twin_F_obs_deconvolution_description'
    _category                refine
    _type                    char
    _definition
;              A description of the method used to calculate the "observed"
structure factor of the first domain used to evaluate the difference Fourier 
map.
;

===============================================================================

Best regards

Gotzon


-----------------------------------------------------------------------------
Gotzon Madariaga                          |   E-mail: wmpmameg@lg.ehu.es
Dpto. Fisica de la Materia Condensada     |
Facultad de Ciencias                      |   Phone: 34 946012467 
Universidad del Pais Vasco                |   FAX  : 34 944648500
Apdo. 644                                 |
48080 Bilbao (SPAIN)                      |
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