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Phase ID draft report
- To: A Working Group of the IUCr Commission on Crystallographic Nomenclature <phase-identifiers@iucr.org>
- Subject: Phase ID draft report
- From: David Brown <idbrown@mcmaster.ca>
- Date: Fri, 16 Apr 2004 11:42:19 -0400
Dear colleagues,
I enclose below the complete draft of the report of the
Crystalline Phase Identifier Working Group. It is open for your
approval or comment. I have included in the draft the comments
that I have received since the last draft was circulated, but
these comments (on lines beginning with $) are not part of the
report and will be removed before it is submitted. This document
prints out on about 19 pages.
This draft could serve as the final report if everyone is in
agreement, so this is your last chance to comment. If I receive
no comments that suggest we need to make changes, I will be
looking for your explicit approval since your name appears on the
letter of submission. Please check this document carefully -
this is your last chance.
Can those of you who represent a database please discuss the
report with your colleagues and let the rest of the Working Group
know if your database would have any difficulties in implementing
the recommended identifier?
Please circulate your approval or comments to the whole
group at phase-identifiers@iucr.org, if possible before May 31,
2004. If you need more time, let me know, and I will adjust the
deadline. If I receive no comment by the end of May I will be
looking for your final approval.
Best wishes
David Brown
***************************************
I.David Brown, Professor Emeritus of Physics
Brockhouse Institute for Materials Research
McMaster University, Hamilton, Ontario
Canada L8S 4M1
Tel: +905 525 9140 ext 24710
Fax: +905 521 2773
email: idbrown@mcmaster.ca
***************************************
**************************************************************
**************************************************************
$ Lines beginning with $ are comments provided by members of the
$ working group and are not part of the draft report. They will
$ be deleted before the report is submitted.
LETTER OF SUBMISSION
Andre Authier
Chair
IUCr Commission on Crystallographic Nomenclature
The undersigned are pleased to submit herewith the final report
of the Working Group on a Crystallographic Phase Identifier to
the Commission on Crystallographic Nomenclature.
Signed:
David Brown (chair)
*Sidney Abrahams (chair of CCN ex officio at time the
working group was established)
+Michael Berndt (Crystal Impact)
*John Faber (International Center for Diffraction Data)
*Vicky Karen (National Institute for Science and Technology
and the Inorganic Crystal Structure Database)
*Sam Motherwell (Cambridge Crystallographic Data Centre)
*Jean-Claude Toledano (Chair, CCN working group on Phase
Transition Nomenclature)
*Pierre Villars (Pauling File)
*John Westbrook (Protein Databank)
*Brian McMahon (IUCr, consultant)
+ Deceased
* Approval not yet received
$ (The asterisks will be removed as individual approvals are
$ received)
*********************************************
DRAFT REPORT OF THE WORKING GROUP ON CRYSTAL PHASE IDENTIFIERS
2004-04-14
SUMMARY
-------
The proposed crystallographic phase identifier consists of a
number of components (layers) describing enough properties of the
phase to allow a unique identification. These layers consist of
the chemical formula, a flag indicating the state of matter, the
space group number and the Wyckoff sequence. They are defined in
such a way that they can be incorporated into to the IUPAC
Chemical Identifier proposed by the International Union of Pure
and Applied Chemistry (IUPAC).
1. INTRODUCTION
---------------
The International Union of Pure and Applied Chemistry (IUPAC) has
been examining standards for the electronic representation of
chemical information, and as part of this effort it has
established a working group to propose an IUPAC Chemical
Identifier (IChI) which would uniquely identify any chemical
compound appearing in an electronic database. The IChI working
group approached the Commission on Crystallographic Nomenclature
(CCN) of the International Union of Crystallography (IUCr) to
enquire if any conventions existed for a crystallographic phase
identifier that might be incorporated into IChI. As the only
such convention already approved by the CCN (the Phase Transition
Nomenclature) is not readily adaptable for electronic use, the
CCN established the Working Group on Crystalline Phase
Identifiers to make recommendations that could be of use to the
IChI working group. This document is the report of this Group.
The Working Group carried out all its discussions by email,
initially independently of the IChI project, but the resulting
recommendations of the two groups developed structures for the
identifiers that are so similar that incorporating the
crystallographic phase information into IChI should be trivial.
Our recommendations are therefore cast in the form of additions
to IChI, in the knowledge that the resulting identifier can be as
readily used by the crystallographic community as by the
chemical.
2. TERMS OF REFERENCE OF THE WORKING GROUP
------------------------------------------
The group will recommend to the IUCr Commission on
Crystallographic Nomenclature:
1. The best method of defining a crystalline phase identifier
that uniquely and unambiguously identifies each crystalline phase
in a way that would allow it to be used to link the same material
appearing in different electronic databases.
2. To recommend the best way in which this identifier can be
implemented, including its incorporation in the CCN recommended
phase transition nomenclature.
Keeping in mind that the primary purpose of the crystal phase
identifier is to allow the properties of a given material to be
located in different databases, the working group should consult
with appropriate crystallographic databases to ensure that the
proposed identifier will be acceptable.
3. MEMBERSHIP
-------------
The following were appointed members of the Working Group:
David Brown (chair)
Sidney Abrahams (chair of CCN ex officio at time the
working group was established)
Michael Berndt (Crystal Impact) [deceased]
John Faber (International Center for Diffraction Data, ICDD)
Vicky Karen (National Institute for Science and Technology,
NIST and the Inorganic Crystal Structure
Database, ICSD)
Sam Motherwell (Cambridge Crystallographic Data Centre,
CCDC)
Jean-Claude Toledano (Chair, CCN working group on Phase
Transition Nomenclature)
Pierre Villars (Pauling File)
John Westbrook (Protein Databank)
Brian McMahon (IUCr, consultant)
4. GENERAL CONSIDERATIONS
-------------------------
Early discussions revealed that many phases have not been
sufficiently well characterized to allow an unambiguous
assignment of an identifier, and in some cases phases have been
incorrectly characterized. In these situations no identifier can
be expected to meet the requirements of the terms of reference
but an identifier may be able to retrieve a number of possible
matches from which the user could make a final choice.
For well-characterized materials the working group examined two
models. In the first an arbitrary character string is assigned
to each crystallographic phase by a competent authority (similar
to the Chemical Abstracts Registry Number) In the second a
character string is generated from the known properties of the
compound according to a defined set of rules.
The first choice was rejected on the grounds that we would be
unlikely to find a competent authority willing to take on the
project. Such an authority would require external funding, since
it would have to assign identifiers on request in a timely manner
and would have to maintain a public list of the identifiers
already assigned.
The second choice has the advantage that the identifier can be
constructed by anyone with access to the information needed to
characterize the material. The identifier can be kept to a
manageable size because it only needs to include sufficient
information to distinguish between known phases. Even if more
information about the phase is available, it is not included in
the identifier if it not needed for characterization. For
example, OsI3, which is known in only one crystalline form, is
fully characterized by its chemical formula alone and no further
information, chemical or crystallographic, need be included.
The first component of any phase identifier must be the
composition and, where necessary, the isomer. Only then does it
make sense to identify the crystalline form. Since IChI is
designed to identify the composition and bond topology of the
compound, the Working Group's job was to suggest an identifier
that would distinguish between the different crystalline forms of
a given chemical compound.
5. THE IChI IDENTIFIER
----------------------
Before presenting the recommendations of the Working Group, we
give a brief description of the proposed IChI identifier which
has, however, not yet been officially adopted by IUPAC.
The IChI working group is recommending an identifier made up of
several components or layers:
The first (top) layer, which is always present, gives the
chemical composition. The lower layers, which constitute the
identifier proper, are included only if they are necessary to
distinguish between two compounds with the same composition.
The second layer distinguishes between different isomers by
describing the bond topology. It contains several sublayers or
levels, the first giving the bonding topology ignoring all the
bonds to metals, cations and hydrogen atoms. The second level
adds the bonding to fixed hydrogen atoms, the third adds the
bonding to variable hydrogen atoms (to distinguish between
tautomers if this is needed) and the fourth level adds bonds to
metal atoms and cations and is used in the rare cases when a
compound forms different coordination isomers.
The third layer contains information on chiral centers and is
included only when it is necessary to distinguish between
stereoisomers.
The fourth layer is used to identify isotopically enriched
compounds. Further layers can be added as needed. For many
compounds only the first layer is needed and for most of the
others it is only necessary to add the top levels of the second
layer.
5.1 Construction of the IUPAC chemical identifier
-------------------------------------------------
At the time of writing the final form of IChI has not been fixed,
but sufficient details have been developed to allow the
definition of a crystalline phase identifier. IChI can be
formatted in different ways, in particular as an ASCII string or
an XML file. As the ASCII string is more compact and easier to
follow, IChI is described below in this format. In the following
example a slash, /, is used to separate the layers.
1.00Beta/C6H9N3O3/CT:7-4(10)1-2(5(8)11)3(1)6(9)12/H:1-
3H,(H2,7,10)(H2,8,11)(H2,9,12)/SC:1-,2-,3-
/I:(1D)/SC:m/is:0/ST:abs
The following is an explanation of the above IChI. The important
items are the first three or four - the remainder in this example
deal with a description of the stereochemistry and will not
frequently be used.
1.00Beta/ # Version of IChI
C6H9N3O3/ # Sum formula
# The identifier proper begins here
CT:7-4(10)1-2(5(8)11)3(1)6(9)12/ # Basic connectivity
H:1-3H,(H2,7,10)(H2,8,11)(H2,9,12)/ # Hydrogen connectivity
SC:1-,2-,3-/ # Stereocenters, sp3
I:(1D)/ # Isotopes (H1 is deuterium)
SC:m/ # Same as in main
is:0/ # Inverted stereo (absolute
stereo only)
ST:abs # Abs (absolute), rel
(relative) or rac (racemic)
# End of identifier
The identifier may be followed by auxiliary information such as
atomic coordinates. These are not part of the identifier proper
and are shown here. They are not further discussed in this
report.
All but the first two items (which are required and are not part
of the identifier proper) are introduced by one of the following
tags:
"CT:"; /* connectivity */
"H:"; /* H-atoms */
"C:"; /* charge */
"DB:"; /* double bond stereo */
"SC:"; /* stereo centers sp3 */
"is:"; /* mark sp3 inverted stereo */
"SR:"; /* mark sp3 racemic stereo */
"ST:"; /* abs, rel, rac */
"I:"; /* isotopic atoms */
"fH:"; /* fixed H -- first item in non-taut */
"N:"; /* orig. at numbers in canonical order */
"NT:"; /* non-tautomeric orig. at numbers */
/* in canonical order -- first item */
/* in non-tautomeric aux info */
"E:"; /* atoms equivalence */
"tE:"; /* tautomeric groups equivalence */
"iC:"; /* inverted (stereo) Centers */
"iN:"; /* inverted sp3 stereo orig. atom */
/* numbers in canonical order */
"NI:"; /* isotopic orig. at numbers in */
/* canonical order */
/* first item in isotopic aux info */
"TR:"; /* transposition of components in */
/* non-tautomeric representation */
"CRV:"; /* charges, radical, valence*/
"XYZ:"; /* xyz-coordinates */
The development of IChI has so far focused on organic molecules
and resolving isomers, tautomers and enantiomers. Version 1.0
will therefore be restricted to describing the topology of finite
molecules and is not being designed to describe the connectivity
of infinite structures. This should not present a problem for
devising an IChI for crystalline phase identification, because if
the composition and space group of an infinitely connected
inorganic compound are given (the two essential layers for any
phase identification), the connectivity is rarely needed.
6. RECOMMENDATIONS
------------------
We RECOMMEND that the phase identifier be included as part of the
proposed IChI symbol and that the crystallographic
characterization appear in IChI in three additional layers, which
are numbered 5, 6 and 7 in the recommendations below.
Note that it is only necessary to define the format of the value
of each layer. The layers can be assembled in various ways as
they are in the IChI standard, e.g., as an ASCII string labelled
with tags (used in this document) or as an XML file. There is no
canonical form for the whole identifier, only for the individual
layers which may be used with or without their associated tag.
$ Comments from members of the working group
$-------------------------------------------
$ Abrahams
$ --------
$ However, a number of questions are likely to arise in
$ reading our Report and I suggest it would be of value to our
$ readers if it contained a section that addressed these and
$ related issues so that our recommendations are set in their
$ fullest context. These issues include the following:
$ 1. Once a unique identifier system has been agreed, must it
$ be reduced to a single algorithm to avoid the introduction of
$ variant identifiers?
$ 2. If the latter is the case, then would it be advantageous
$ to state or merely refer to the algorithm?
$ 3. Must each database adapt the algorithm to match its
$ specific contents or is that the responsibility of the user?
$ To the extent possible, the new section should respond to these
$ and similar questions.
$
$ IDB response:
$ -------------
$ These questions are now addressed, mostly in the previous
$ paragraph.
$
6.1 Layer 5: State of Matter
----------------------------
This layer gives the state of matter: gas, liquid, crystal etc.
according to the following enumeration list:
gas gas phase
liq liquid phase
sol solid phase of unknown form
xtl crystalline solid
qxl quasi-crystal
ams amorphous solid
lxl liquid crystal or other anomalous
quasi-liquid phase
Only if this flag is set to xtl would layers 6 and 7 be needed.
A crystal is define as a phase for which, in principle, it is
possible to assign a space group, even if that space group is
only an approximation (as in incommensurate structures). The
presence therefore of a space group field implies that the state
of matter is xtl. In the case where the space group is given the
state of matter field is redundant and may be omitted (though it
is included in some of the examples below by way of
illustration).
$ More comments from the members of the working group
$ ---------------------------------------------------
$ Sidney Abrahams
$ ---------------
$ I suggest that we add each of the crystalline
$ states for which a specific nomenclature is given in the second
$ CCN Phase Transition Nomenclature Report, namely magnetic,
$ incommensurate, composition-changed morphotropic, polytype and
$ transient-structural in addition to quasicrystalline phases.
$ Incidentally, the abbreviation 'amp' for amorphous is not very
$ intuitive; perhaps a five-letter symbol would be clearer, e.g.
$
$ liqud liquid
$ amphs amorphous
$ solid solid of unknown form
$ cryst crystal
$ liqcr liquid crystal
$ magcr magnetic crystal
$ inccr incommensurate crystal
$ comcr composition-changed morphotropic crystal
$ polcr polytype crystal
$ trncr transient-structural crystal
$ quasi quasicrystal
$
$ Comment by IDB
$ --------------
$ I have changed 'amp' to 'ams' in the draft report but I am not
$ convinced of the need to use five letter codes.
$
$ The xtl classification would be used for any
$ material for which it is possible in principle to assign one
$ of the regular 230 space groups. Magnetic, morphotropic,
$ polytypic and transitional crystals would then all be
$ classified as xtl. To show that these classes should
$ not be differentiated in the state of matter field consider,
$ for example, how one would decide whether to use magcr or xtl.
$ All compounds are either ferro-, ferri-, para- or
$ diamagnetic and therefore all are magnetic crystals and should
$ be classified as magcr as well as xtl. If it became
$ necessary to distinguish between a paramagnetic and
$ ferromagnetic phase with the same space group and Wyckoff
$ sequence, a magnetic layer could be added to the identifier.
$ Using a magnetic layer would also allow the magnetic
$ properties of amorphous materials and liquids to be
$ specified. The morphotropic category refers to
$ compositionally dependent phase transitions
$ and these phases are, by definition, distinguished by their
$ composition field. Polytypes are distinguished by their space
$ groups and Wyckoff sequence, and transitional crystals are the
$ same as regular crystals except that they are unstable.
$
$ It is less clear how to handle incommensurate crystals
$ because many incommensurations in crystals are not reported
$ (and in many cases probably not noticed). To maximize the
$ chance of scoring a correct hit during a search, incommensurate
$ crystals should be included under xtl and listed under their
$ parent space group (which might, however, not be unique).
$ Again a further layer giving the incommensurate space group
$ could be added if needed. See Section 6.5 below.
$
$ I recommend that we defer defining magnetic and
$ incommensurate layers until it is clear that they are needed.
$ They can then be included in a later version of IChI which is
$ in any case seen as an evolving standard.
$
6.2 Layer 6: Space Group
------------------------
This layer contains the space group number as given in
International Tables for Crystallography Vol. A. It consists of
a number between 1 and 230 that uniquely identifies the space
group type. The only ambiguity occurs for space groups such as
P41 (76) and P43 (78) that are identical except for their
chirality which is more appropriately identified in the IChI
stereochemistry layer. Chirality is an important molecular
property but the chirality of a crystal, which is often not
determined, is usually only of interest if the crystal contains a
chiral molecule. Chiral space groups should therefore be treated
as equivalent. We recommend that only the lowest number of each
chiral pair of space groups be given, but search algorithms
should equivalence these pairs in case the higher space group
number is inadvertently used. The equivalent space groups are
listed below.
Problems in assigning the space group can arise in several
situations. Many inorganic compounds have polymorphs with
similar structures that crystallize with different, but related,
space groups. In these cases it is easy to assign the wrong
space group, if only a subcell of the true crystallographic unit
cell is reported. Incommensurately modulated structures, which
are frequently associated with polymorphism, have additional
symmetries that do not appear in the standard table of space
groups. Usually an average space group can be assigned, but
this is not always unique. Quasicrystals cannot be assigned a
space group and are best treated as a different state of matter
(see Section 6.1 above).
6.3 Layer 7. Wyckoff Sequence
-----------------------------
In the rare event that two phases of the same compound have the
same space group, the Wyckoff sequence can be given. This is a
list containing the Wyckoff letters associated with the occupied
special positions (sites of high symmetry). Details of the
special positions and their Wyckoff letters for all 230 space
groups are given in International Tables for Crystallography Vol.
A. Each letter is accompanied by a number indicating the number
of symmetry-independent atoms occupying sites of that kind (the
default number is 1), e.g, 'a1 d1 i6' which is written as 'adi6'.
The enumeration list contains all the letters of the alphabet
plus & for 'alpha' and the letters are listed in alphabetic
order. Before determining the Wyckoff sequence it is essential
that the structure be standardized using the program STRUCTURE
TIDY or other program using the same algorithm. Details are given
in Section 7.2.4.
6.5 Possible further layers.
----------------------------
There are a few cases where the layers proposed above do not
fully differentiate between distinct phases of the same compound.
For example metallic iron (see Section 8.2 below) has two body
centered cubic phases separated by a face centered cubic phase.
These two phases have exactly the same identifier using the
layers defined above. However, they could be differentiated
using their reduced cells. With experience in using the layers
defined above the need for further layers may become apparent.
At that time it would be appropriate to consider what further
layers should be added. Possibilities include the reduced cell,
an incommensuration flag or an indicator of magnetic or electric
properties.
7. PROPOSED ADDITIONS TO IChI FOR PHASE IDENTIFICATION
------------------------------------------------------
This section provides the text that should be inserted into any
IChI definition that incorporates the proposals of this document.
7.1 New tags
------------
The following is a list of additional tags required for phase
identification expressed in the form of an IChI. These would be
used in conjunction with existing IChI tags:
"PH:" /* phase or state of matter. Allowed values are: */
/* gas, liq, ams, sol, xtl, lxl, qxl */
"SG:" /* Space group number, integers between 1 and 230 */
"WS:" /* Wyckoff sequence, any lower case letter */
/* or & (for alpha), possibly separated by numbers */
7.2 Formal definitions
----------------------
7.2.1 Composition
---------------
The composition layer in IChI for a crystalline phase must give
the contents of the formula unit of the crystal. This is a unit
in general no smaller than the crystallographic asymmetric unit
and no larger than the primitive unit cell. It is NOT the same
as the formula of the molecule of interest unless the molecule is
the only component of the crystal. All components, including
solvents of crystallization, MUST BE EXPLICITLY INCLUDED.
Wherever possible the formula unit is chosen so that the
multipliers of the elements are integers with no common divisor.
In cases where it is not possible to choose a formula unit
smaller than the primitive unit cell without using non-integral
multipliers, e.g., FeS1.83 = Fe1.09S2, La1.95NiO4.31 and many
minerals, the size of the formula unit is indeterminate and only
the relative multipliers are meaningful. Testing should be
carried out in this case by normalizing the multipliers. Any
normalization can be used but an obvious one would be to reduce
the largest multiplier to 1.00 and the others in proportion.
When non-integral multipliers are encountered, searches should
include a tolerance factor to allow for experimental
uncertainties or to retrieve related compounds of the same phase
having a similar but not identical composition. The tolerance
should be large enough to recognize that phase identifiers that
include trace elements are equivalent to identifiers in which the
trace elements have been omitted either because they were not
determined or because they were not considered to be important.
The size of the tolerance factor is not defined in this standard
and its choice will be determined by the nature of the required
search. For example, a search on FeS2 might include a tolerance
factor of 0.2 to be sure of locating all examples of the phase.
7.2.2 PH: The state of matter
------------------------------
Seven flags are defined for a number of different states.
gas
liq liquid
ams amorphous
sol solid of unknown form
xtl crystal (capable of being assigned a space group)
lxl liquid crystal
qxl quasi-crystal
Only if the value of PH is 'xtl' will the following two layers be
meaningful. Therefore if the SG: field is given, the PH: field
may be omitted.
7.2.3 SG: Space group
--------------------
This is a number between 1 and 230 inclusive, being the number of
the space group of the crystal as given in International Tables
for Crystallography Vol A. The following space group pairs are
identical except for their chirality: 76=78, 91=95, 92=96,
144=145, 152=153, 169=170, 171=172, 178=179, 180=181, 212=213.
Only the lower space group number of each pair should be used.
The chirality is often not determined and is only significant if
the crystal contains a molecule whose chirality is described
elsewhere in IChI. However, one of the forbidden space group
numbers may be inadvertently used and software should be prepared
to convert it to its legal equivalent. There are many cases
where the true space group is not known. Different approximate
space groups might be assigned by different workers in which case
a valid match would be missed, but there is little that can be
done to overcome this problem. Incommensurate phases should be
assigned the space group of their parent structure (the first
portion of the incommensurate space group symbol).
7.2.4 WS: The Wyckoff sequence
-----------------------------
This is an alphabetic list of the Wyckoff symbols (letters) of
the occupied special positions. International Tables for
Crystallography Vol. A lists the Wyckoff letters for all
special position, that is, all sites having a
crystallographically distinct site symmetry. Each letter is
followed by a number indicating the number of
symmetry-independent atoms occupying sites of that kind (the
number 1 is omitted), e.g, 'a1 d1 i6' which is written as 'adi6'.
The enumeration list contains all the letters of the alphabet
plus '&' for 'alpha' found in space group 47. The letters are
listed in alphabetic order but before determining
the Wyckoff sequence, the structure must be normalized according
to the algorithm used in the program STRUCTURE TIDY, details of
which are given in:
Parthe, E., Gelato, L.M. (1984). Acta Crystallogr. A40, 169-183,
Parthe, E., Gelato, L.M. (1985). Acta Crystallogr. A41, 142-151.
and Gelato, L.M., Parthe, E. (1987). J. Appl. Crystallogr. 20,
139-143.
7.3 Examples
------------
In both the following examples of IChIs that define crystalline
phases, the PH: field is not needed and the WS: field is also
probably not necessary, but they are included for the purposes of
illustration.
Further examples are given in Section 8.2
Rutile 1.02/TiO2/PH:xtl/SG:136/WS:af2
(CH3)3NCH2COOśCaCl2ś2H2O
1.02/C4H15CaCl2NO4/PH:xtl/SG:33/WS:ae28
8. INCORPORATION OF THE PHASE IDENTIFIER INTO THE IUCr-CCN PHASE
TRANSITION SYMBOL
------------------------------------------------------------
8.1 Description of the IUCr-CCN phase transition symbol.
--------------------------------------------------------
Recently the Commission on Crystallographic Nomenclature of the
International Union of Crystallography adopted a Phase Transition
Nomenclature (Acta Cryst. (2001). A57, 614-626; Acta Cryst.
(1998). A54, 1028-1033) described on the IUCr web page:
http://www.iucr.org - look for Commissions/Commission on
Crystallographic Nomenclature/CNOM on-lineinformation/Structural
Phase Transition Nomenclature. The phase transitions are
identified by the two phases that bracket the transition, so the
nomenclature is more properly a nomenclature of the phases
themselves. The IUCr-CCN Phase Transition Symbol is composed of
six fields defined as follows:
1. The common symbol used to identify the phase (e.g., alpha, II,
etc.).
2. The temperature range (pressure range or other external
condition) in which the phase is stable.
3. The Hermann-Mauguin symbol and number of the space group.
More than one space group may be given, or the Bravais symbol may
be given if the space group is not known.
4. Z, the number of formula units in the conventional unit cell
(though the formula unit is not defined within the symbol).
5. The ferroic properties.
6. The structure type.
Any field may be omitted if inapplicable or if the value is not
known. As the symbol was not designed for computer use, the
formats are not tightly structured and may contain non-ASCII
characters. The intent of this symbol is to include the maximum
amount of information about the phase,
whereas the philosophy of IChI is to include only the minimum
needed for phase identification. The two symbols therefore are
complementary and serve different purposes. Both include the
space group, but otherwise there is little overlap between them.
The IChI could be added to the CCN Phase Transition Nomenclature,
but it is not clear where this would be an advantage. A method
for doing this is described in Section 8.3.
8.2 Examples of the CCN Nomenclature and the IChI Phase
Identifier
-------------------------------------------------------
In each of the following examples the phase transition
nomenclature is given first followed on the next line by the
proposed IChI symbol.
8.2.1 Three phases of potassium tellurium bromide (K2TeBr6)
Abrahams et al., 1984; Ihringer & Abrahams, 1984).
----------------------------------------------------------
I|>434K|Fm(-3)m (225)|Z = 4|non-ferroic|Type = K2PtCl6.
1.02/Br6K2Te/SG:225
II|434-400K|P4/mnc (128)|Z = 2|ferroelastic|3 variants.
1.02/Br2K2Te/SG:128
III|< 400K|P21/n (14)|Z = 2|ferroelastic|12 variants.
1.02/Br6K2Te/SG:14
8.2.2 Iron (Fe) (Donohue, 1974)
-------------------------------
delta|1663K|Im(-3)m (229)|Z=2|non-ferroic|Type = W.Melting at
1808 K.
1.02/Fe/SG:229
gamma|1663-1183K|Fm(-3)m (225)|Z = 4|non-ferroic|Type = Cu.
1.02/Fe/SG:225
beta|1183-1043K|Im(-3)m (229)|Z = 2|paramagnetic|Type = W.
1.02/Fe/SG:229
alpha|<1043K|Im(-3)m (229)*|Z = 2|ferromagnetic|Type = W.
*Magnetic structure is pseudocubic.
1.02/Fe/SG:229
epsilon|13GPa|P63/mmc (194)|Z = 2|-|Type = Mg.
1.02/Fe/SG:194
Note that the delta and beta phases both have the body centred
cubic structure and therefore have identical IChIs, but they are
distinct phases with different cell dimensions. The Wyckoff
sequence /WS:a/ is omitted because it is the same for both phases
and does not further distinguish between them. The correct space
group of alpha iron is presumably not 229, being lowered by
magnetostriction, but the deviation from the higher symmetry is
very small and the correct space group is not known. This
illustrates one of the problems that will be encountered in the
use of this identifier. At worst, searching on Fe/SG:229 will
bring up a number of false matches.
8.3 Examples of how the IChI might be incorporated into the CCN
phase nomenclature
---------------------------------------------------------------
The IChI can be included in the CCN Phase Nomenclature in several
different ways. We recommend that the IChI be placed in front of
the phase nomenclature using vertical line separators rather than
slashes. A double vertical line separates the two identifiers.
If desired a program could easily split off the IChI for further
analysis. The first example is the same compound as shown in
Section 8.2.1, the second example is the same compound as shown
in Section 7.3.
1.02|Br6K2Te|SG:14||III|<400K|P21/n(14)|Z=2|Ferroelastic|12
variants
1.02|C4H15CaCl2NO4|SG:33|WS:ae28||XVI|<50K, 4GPa,<180K|
Pn21a(33)|Z=4|Ferroelectric|Nonmodulated ferroelectric
polarization along b
$ Comments by members of the working group
$ ----------------------------------------
$ Sidney Abrahams
$ ---------------
$ Addition of the comprehensive IChI identifier in a new field,
$ probably the leading field, in the CCN phase nomenclature [see
$ Acta Cryst. (2001). A57, 614-626 and Acta Cryst. (1998). A54,
$ 1028-1033)] would be appropriate in database compilations. It
$ would probably be inappropriate elsewhere.
$ Responding to your invitation that we suggest 'the best' way
$ in which the IChI phase identifier could be incorporated into
$ the IUCr phase transition nomenclature, I would argue that a
$ union of the two symbolic systems has greater value than the
$ sum of the two used separately, at least when first
$ introduced. As suggested by the examples [above], the united
$ symbol indicates to the potential user a means of searching the
$ literature for a given inorganic or organic crystalline phase
$ for all cases in which that phase can be appropriately
$ identified.
$
$ IDB
$ ---
$ In a database the CCN Phase Nomenclature and the IChI would
$ likely be stored in separate fields where they would be easier
$ to access. Indeed the values of the different IChI layers
$ would likely be stored in their own fields and the full symbol
$ only reconstructed as needed (See Section 9 below).
$
$ Abrahams
$ --------
$ You also ask for some additional examples. Combining the two
$ requests, an example taken from each of the two IUCr Phase
$ Nomenclature Reports is presented as follows:
$
$ K2TeBr6|PH:xtl|SG:14:ae4||III|<400K|P21/n(14)|Z=2|Ferroelastic|
$ 12 variants
$
$ (CH3)3NCH2COOśCaCl2ś2H2O|PH:xtl(inccr)|SG:33:a28||XVI|<50K,
$ 4GPa,<180K|Pn21a(33|Z=4|Ferroelectric|Nonmodulated
$ ferroelectric polarization along b
$
$ IDB
$ ---
$ These examples given by Sidney have been incorporated in
$ Section 8.3 after editing. There are several problems with
$ Sidney's examples as given, particularly relating to the
$ content and formatting of the layers. I show them here because
$ they illustrate some of the philosophical differences between
$ the two nomenclatures. Firstly, the examples as sent to me in
$ a WORD file were formatted using subscripts, bold and italic
$ script, all of which were lost when they were transcribed to
$ ASCII. This loss is only cosmetic as the formatting symbols
$ are not semantically important. Sidney has incorporated the
$ IChI as a prefix to the CCN nomenclature, separating the two
$ with a double vertical line. This is a useful convention which
$ I have incorporated in Section 8.3.
$ However the IChIs are not correctly constructed (c.f. my edited
$ versions in Section 8.3 above). The composition field must be
$ given as a sum formula with the elements listed in alphabetic
$ order (except that if C is present, C appears first followed by
$ H). In the second example '(inccr)' has been added to the PH:
$ field even though this is not one of the allowed flags. In
$ both cases the Wyckoff sequence has been given, but it is given
$ in the SG: layer rather than in its own WS: layer. In the
$ first case the Wyckoff sequence is not needed. It may not be
$ needed in the second case either but I have retained it in the
$ report to illustrate how it would be used. Since searching
$ requires the comparison of the IChI symbol layer by layer, the
$ rules for constructing each layer must be exactly observed.
$
$ Villars:
$ -------
$ If the structure type assignment is properly done (after
$ standardization with STIDY and COMPARE), and each prototype is
$ defined by a unique combination of Space Group Number/Wyckoff
$ Sequence/AET's all is included in item 6) the structure type.
$
$ IDB response:
$ -------------
$ Pierre is referring to the formal structure type as defined in
$ the Pauling file. The structure type defined as item 6 in the
$ CCN nomenclature can be any descriptor chosen by the user and
$ is therefore not suitable for machine searching and should not
$ be restricted by the tight rules used in the Pauling file.
9. THE USE OF PHASE IDENTIFIER IN DATABASES
--------------------------------------------
Since the IChI Phase Identifier is parsable, each of the layers
can be formatted and stored in any way that suits the needs of a
particular database. Most crystallographic databases will
already have fields containing the sum formula and the space
group number, and can readily add a field for the Wyckoff
sequence if this is needed. The 'state of matter' field, PH:,
would require a further field in the database but could be
omitted if the database contains only crystal structures. The
canonical form of the IChI could be recreated at any time if
required or it could be parsed into its respective layers. It is
not appropriate to carry out a search using the canonical form of
IChI. Searches must be carried out layer by layer since two
different identifiers may not contain the same number of layers,
or the search may not be carried out to its full depth if, for
example, chirality or isotopic content were not important.
All the proposed layers can be searched by looking for identical
bit sequences, though the SG: field should be initially screened
for illegal numbers, and the composition field should be
normalized if non-integral multipliers are present.
$ Previously IDB posed the question:
$ Would IChI, extended to cover crystalline phases as described
$ above, be an acceptable identifier for inclusion in all the
$ crystallographic databases?
$
$ Only one response was received and I therefore assume that the
$ ICSD, CSD, PDB and PDF have no objection and can work with the
$ identifier as described above.
$
$ Villars:
$ -------
$ Yes, it [the phase identifier as proposed in the first
$ draft] is acceptable. The Pauling File has already included
$ this information.
END OF DRAFT REPORT OF THE WORKING GROUP
---------------------------------------
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