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Core CIF: Fourth round of proposed changes
- To: Multiple recipients of list <coredmg@iucr.org>
- Subject: Core CIF: Fourth round of proposed changes
- From: "I. David Brown" <idbrown@mcmail.cis.mcmaster.ca>
- Date: Mon, 11 Nov 2002 17:01:20 GMT
Dear Colleagues,
Having had no response by the Nov 11 deadline to the last set of
proposed changes to the CIF core dictionary, I assume that everyone is in
favour and these items have now been marked as approved.
I enclose below the final set of trivial (or almost trivial) changes.
Once these are approved we can start on the more contentious changes.
However, the changes below are not entirely trivial and I need some guidance
on the _refine_ls_extinction items in answer to a number of queries following
each of the definitions. PLEASE can I have some feed back. If there are
potential problems you will be the people who have to live with them if you do
not respond.
The deadline for reply is 16 December, though this can be extended if a
longer period of discussion is needed.
I look forward to hearing from you all.
David
*****************************************************
Dr.I.David Brown, Professor Emeritus
Brockhouse Institute for Materials Research,
McMaster University, Hamilton, Ontario, Canada
Tel: 1-(905)-525-9140 ext 24710
Fax: 1-(905)-521-2773
idbrown@mcmaster.ca
*****************************************************
ROUND 4 OF THE CORE REVISION PROPOSALS.
# Items included in this round
#
# EXPTL_CRYSTAL
# _exptl_crystal_colour (modification)
# _exptl_crystal_density_meas_gt
# _exptl_crystal_density_meas_lt
# _exptl_crystal_density_meas_temp_gt
# _exptl_crystal_density_meas_temp_lt
# _exptl_crystal_recrystallization
# PUBL
# _publ_contact_author_id_iucr
# PUBL_AUTHOR
# _publ_author_id_iucr
# REFINE
# _refine_ls_extinction_coef (replace?)
# _refine_ls_extinction_coef_Zach
# _refine_ls_extinction_coef_Becker-Coppens_1
# _refine_ls_extinction_coef_Becker-Coppens_2
# _refine_ls_extinction_BC_type
# _refine_ls_extinction_expression (replace?)
# _refine_ls_extinction_method (replace?)
# _refine_ls_shift/su_max_lt
# _refine_ls_shift/su_mean_lt
#
# Detailed description of proposed changes
#
#################################################
#
# EXPTL_CRYSTAL
#
#################################################
data_exptl_crystal_colour
_name '_exptl_crystal_colour'
_category exptl_crystal
_type char
_list both
_list_reference '_exptl_crystal_id'
loop_ _example
dark_green
reddish_orange_metallic
_definition
; The colour of the crystal used in the experiment. The
following list of standardized names developed for the
International Center for Diffraction Data should be used.
Combinations of descriptors should be linked by an underscore.
The allowed colours are: colourless, white, black, gray, brown,
red, pink, orange, yellow, green, blue, violet.
Colours may be modified by using one of the prefixes: light,
dark, whitish, blackish, grayish, brownish,reddish, pinkish,
orangish, yellowish, greenish, bluish.
Intermediate hues may be indicated by linking two colours,
e.g. blue_green or bluish_green
Metallic colours are indicated by adding 'metallic' as a suffix,
e.g. reddish_orange_metallic for copper.
;
# COMMENT: This scheme is based on a scheme developed by the ICDD and
# recommended for use in the powder CIF. It is already being checked
# in submissions to Acta Cryst. It would be helpful to have it as part of the
# dictionary description, though it is difficult to define an enumeration list
# for the colours.
# STATUS: Open for discussion
data_exptl_crystal_density_meas_*
loop_ _name
'_exptl_crystal_density_meas_gt'
'_exptl_crystal_density_meas_lt'
_category exptl_crystal
_type numb
_type_conditions esd
_list both
_list_reference '_exptl_crystal_id'
_enumeration_range 0.0:
_units Mg^-3^
_units_detail 'megagrams per cubic metre'
_definition
; The lower (_*_gt) or upper limit (_*_lt) on the value of the
density measured using standard chemical and physical
methods. The units are megagrams per cubic metre (grams per
cubic centimetre).
;
data_exptl_crystal_density_meas_temp_*
loop_
_name '_exptl_crystal_density_meas_temp_gt'
'_exptl_crystal_density_meas_temp_lt'
_category exptl_crystal
_type numb
_type_conditions esd
_list both
_list_reference '_exptl_crystal_id'
_enumeration_range 0.0:
_units K
_units_detail 'Kelvins'
_definition
; Temperature in kelvins above which (_*_gt) or below which
(_*_lt)_exptl_crystal_density_meas was determined.
;
# COMMENT: The above two items suggested by CCDC.
# STATUS: Open for discussion
data_exptl_crystal_recrystallization
_name '_exptl_crystal_recrystallization'
_category exptl_crystal
_type char
_example ?
_definition
; Describes the method used to recrystallize the sample
;
# COMMENT: Suggested by CCDC.
# STATUS: Open for discussion
##########################################################
#
# PUBL category
#
##########################################################
data_publ_contact_author_id_iucr
_name '_publ_contact_author_id_iucr'
_category publ
_type char
_list yes
_example 2985
_definition
; Identifier in the IUCr contact database of the author
submitting the manuscript and datablock. This identifier may
be available from the World Directory of Crystallographers
(http://wdc.iucr.org).
;
# COMMENT: Submitted by Brian McMahon This identifier will allow linking to
# other publications or files by the contact author.
# (Linking based on name alone is inefficient because
# individuals change their names or spelling of the names. A complementary
# data name is proposed for the authors in the PUBL_AUTHOR category.
# STATUS: Open for discussion
#########################################################
#
# PUBL_AUTHOR category
#
#########################################################
data_publ_author_id_iucr
_name '_publ_author_id_iucr'
_category publ_author
_type char
_list yes
_example 2985
_definition
; Identifier in the IUCr contact database of a publication
author. This identifier may be available from the World
Directory of Crystallographers (http://wdc.iucr.org).
;
# COMMENT: Submitted by Brian McMahon. See _publ_contact_author_id_iucr for
# further details.
# STATUS: Open for discussion
#########################################
#
# REFINE category
#
#########################################
# The next five items relate to extinction and are an attempt to tighten up
# our definitions. The first item is the current definition which we may
# wish to replace or restrict.
data_refine_ls_extinction_coef
_name '_refine_ls_extinction_coef'
_category refine
_type numb
_type_conditions esd
_example 3472(52)
_example_detail 'Zachariasen coefficient r* = 0.347(5) E04'
_definition
; The extinction coefficient used to calculate the correction
factor applied to the structure-factor data. The nature of the
extinction coefficient is given in the definitions of
_refine_ls_extinction_expression and
_refine_ls_extinction_method.
For the 'Zachariasen' method it is the r* value; for the
'Becker-Coppens type 1 isotropic' method it is the 'g' value,
and for 'Becker-Coppens type 2 isotropic' corrections it is
the 'rho' value. Note that the magnitude of these values is
usually of the order of 10000.
Ref: Becker, P. J. & Coppens, P. (1974). Acta Cryst. A30,
129-153.
Zachariasen, W. H. (1967). Acta Cryst. 23, 558-564.
Larson, A. C. (1967). Acta Cryst. 23, 664-665.
;
# COMMENT: This item is context sensitive in that it is necessary to know the
# _*_detail in order to interpret the coefficient. Since there is no
# enumeration list for _*_detail, machine interpretation is impossible. This
# item should be replaced for standard extinction methods by the following
# list of proposed items. Can we retain the above definition to cover cases
# where a non-standard extinction correction was performed, or should we
# retire this name and devise a new one? In any case we require a new
# definition.
# STATUS: open for comment
data_refine_ls_extinction_coef_*
loop_ _name '_refine_ls_extinction_coef_Zach'
'_refine_ls_extinction_coef_Becker-Coppens_1'
'_refine_ls_extinction_coef_Becker-Coppens_2'
_category refine
_type numb
_type_conditions esd
_example 3472(52)
_example_detail 'Zachariasen coefficient r* = 0.347(5) E04'
_definition
; The extinction coefficient used to calculate the correction
factor applied to the observed structure-factors.
For _refine_ls_extinction_coef_Zach (the Zachariasen, also known as
the Larson, method) the value given is the r* value,
For _refine_ls_extinction_coef_Becker-Coppens_1 (the Becker-Coppens
type 1 isotropic method) it is the 'g' value,
For _refine_ls_extinction_coef_Becker-Coppens_2 (Becker-Coppens type
2 isotropic method) it is the 'rho' value.
Note that the magnitude of these values is usually of the order of
10000.
The Becker-Coppens procedure is referred to as 'type 1' when
correcting secondary extinction dominated by the mosaic spread;
as 'type 2' when secondary extinction is dominated by particle
size and includes a primary extinction component; It is also
possible to use a mixture of types 1 and 2.
For the Becker-Coppens method it is necessary to set the
mosaic distribution as either 'Gaussian' or 'Lorentzian' in
_refine_ls_extinction_B-C_type. If an anisotropic extinction
correction has been made the multiple coefficients cannot be
contained in *_extinction_coef_Becker-Coppens_* and they must be
listed in _refine_special_details.
Ref: Becker, P. J. & Coppens, P. (1974). Acta Cryst. A30,
129-153.
Zachariasen, W. H. (1967). Acta Cryst. 23, 558-564.
Larson, A. C. (1967). Acta Cryst. 23, 664-665.
;
# COMMENT: This is a new item which allows the specific extinction parameter
# to be given for each of the standard extinction corrections. Whichever item
# is given will identify the method used to determine the extinction so
# _*_expression and _*_method would not be needed.
# STATUS: Open for discussion.
data_refine_ls_extinction_BC_type
_name '_refine_ls_extinction_BC_type'
_category refine_ls
_type char
loop_ _related_item
'_refine_ls_extinction_coef_Becker-Coppens_1'
'_refine_ls_extinction_coef_Becker-Coppens_2'
_related_function ?
loop_ _enumeration Gaussian
Lorentzian
_definition
; For the Becker-Coppens extinction correction, a statement is
needed of the function used to describe the mosaic spread.
Ref: Becker, P. J. & Coppens, P. (1974). Acta Cryst. A30,
129-153.
;
# COMMENT: This is a new item is needed to complement the Becker-Coppens
# coefficients
# STATUS: Open for discussion
data_refine_ls_extinction_expression
_name '_refine_ls_extinction_expression'
_category refine
_type char
# _example
#; Larson, A. C. (1970). "Crystallographic Computing",
# edited by F. R. Ahmed. Eq. (22) p. 292.
# Copenhagen: Munksgaard.
#;
# A new example will be needed if the revised definition is adopted.
_definition
; A description or reference for the extinction correction equation
used to apply the data item _refine_ls_extinction_coef when this
is not one of the standard types defined under
_refine_ls_extinction_coef_*.
This information must be sufficient to reproduce the extinction
correction factors applied to the structure factors.
;
# COMMENT: This is an existing data item but its name suggests an algebraic
# expression while the example suggests that a reference is intended. I have
# changed the definition so maybe a different dataname is needed. It is not
# clear to me what the difference between _*_expression and _*_method was
# intended to be.
# STATUS: open for discussion.
data_refine_ls_extinction_method
_name '_refine_ls_extinction_method'
_category refine
_type char
# _enumeration_default 'Zachariasen'
# loop_ _example 'B-C type 2 Gaussian isotropic'
# 'none'
_definition
; A description of the extinction correction method applied with
the data item _refine_ls_extinction_coef when one of the standard
methods is not used.
# (The rest of this text should be deleted or transferred. The text above has
# been modified. The enumeration default should in any case be deleted. and
# a different example given.)
#
# This description should
# include information about the correction method, either
# 'Becker-Coppens' or 'Zachariasen'. The latter is sometimes
# referred to as the 'Larson' method even though it employs
# Zachariasen's formula.
#
# The Becker-Coppens procedure is referred to as 'type 1' when
# correcting secondary extinction dominated by the mosaic spread;
# as 'type 2' when secondary extinction is dominated by particle
# size and includes a primary extinction component; and as 'mixed'
# when there is a mixture of types 1 and 2.
#
# For the Becker-Coppens method it is also necessary to set the
# mosaic distribution as either 'Gaussian' or 'Lorentzian'; and
# the nature of the extinction as 'isotropic' or 'anisotropic'.
# Note that if either the 'mixed' or 'anisotropic' corrections
# are applied the multiple coefficients cannot be contained in
# *_extinction_coef and must be listed in _refine_special_details.
#
# Ref: Becker, P. J. & Coppens, P. (1974). Acta Cryst. A30,
# 129-153.
# Zachariasen, W. H. (1967). Acta Cryst. 23, 558-564.
# Larson, A. C. (1967). Acta Cryst. 23, 664-665.
;
# COMMENT: The default should be deleted since there should be no presumption
# about the method used. This proposal changes the meaning of this item in a
# significant way and perhaps a different dataname should be used.
# STATUS: Open for comment
data_refine_ls_shift/su_max_lt
_name '_refine_ls_shift/su_max_lt'
_category refine
_type numb
_related_item '_refine_ls_shift/su_max'
_related_function ?
_enumeration_range 0.0:
_definition
; An upper limit for the largest ratio of the final
least-squares parameter shift divided by the final
standard uncertainty. This
item is used when the largest value of the shift
divided by the final standard uncertainty is too
small to measure.
;
# STATUS: Open for discussion
data_refine_ls_shift/su_mean_lt
_name '_refine_ls_shift/su_mean_lt'
_category refine
_type numb
_related_item '_refine_ls_shift/su_mean'
_related_function ?
_enumeration_range 0.0:
_definition
; An upper limit for the average ratio of the final
least-squares parameter shift divided by the
final standard uncertainty. This
item is used when the average value of the shift divided by
the final standard uncertainty is too small to measure.
;
# STATUS: Open for discussion
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