[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]
Reply to: [list | sender only]
Final draft of Phase-ID report
- To: Phase-ID Group <phase-identifiers@iucr.org>
- Subject: Final draft of Phase-ID report
- From: David Brown <idbrown@mcmaster.ca>
- Date: Tue, 29 Jun 2004 11:49:31 -0400
?Dear Colleagues Please find attached the final draft of the report of the Working Group on Crystallographic Phase Identifiers. It differs from the previous draft (#2) only in a few minor editorial aspects. The next stage is to submit this report to the IUCr Commission of Crystallographic Nomenclature who may refer some parts back for further consideration or may approve the report as it is. When approved by the Commission, it will be posted on the web and published in Acta Cryst. over the names of the members of the Working Group, namely: 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) I need therefore to hear from every one of you who has an asterisk (*) by his or her name above that you approve the report. Please reply to this email or send your reply to phase- identifiers@iucr.org. When you send in your approval (or your reservations) please keep in mind that you were selected for this Working Group because of your membership in the organizations listed after your name. Your approval will indicate that, as far as you can tell, your organization would be able to implement the phase identifier if it wished. I cannot submit the report until I have heard from every one of you and until I get your approval I will continue to send reminders. YOUR NAME WILL APPEAR ON THE FINAL REPORT. DRAFT #3 The only comments I received on draft #2 of the report of the Working Group on Crystallographic Phase Identifiers was from Sidney Abrahams who suggested several corrections and improvements to the wording to improve the accuracy and clarity of the report. Those suggestions that do not change the meaning have been made in the text, but Sidney also made three other comments that have I have not included for the reasons given below. Sidney: In 6.3 Layer 7. Wyckoff Sequence It would be more appropriate here to use the same Wyckoff site order as used in ITA, i.e. number, followed by letter. It would also be helpful if the example contained at least two sites with multiplicity other than 1, so that it becomes, for example, 1a 2c 3f 6g or a2c3f6g, to avoid possible confusion with the dropped 1 (which I agree should be dropped). Response: This is a misunderstanding of what the numbers in the Wyckoff sequence mean. They are not the multiplicities given in International Tables but the number of crystallographically independent atoms that occupy these sites. The key sentence has been clarified (by ADDING 'lower-case' and replacing 'accompanied' with 'followed') to read: "Each lower-case letter is followed 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 expression 'symmetry- independent' is the key to the meaning of these numbers. Sidney: In 7.2.1 Composition, it is appropriate to provide a clear definition of tolerance factor if it is to be required. Response: The tolerance factor is not part of the identifier. It is a number chosen by the person using the identifier in a search. Depending on the value of the tolerance factor selected, the search can be made broader or more focused. The smaller the tolerance factor, the fewer structures will be retrieved, but the greater the chance of excluding a valid hit. Sidney: Sidney proposed adding the following wording in Section 8.1 "The combined IChI and CCN Phase Transition Nomenclature identifier symbol provides, in principle, all the information necessary to access the appropriate database entries available on a given material." Response: The IChI is sufficient by itself to access all the database entries available on a given material. Combining IChI with the CCN Phase Transition Nomenclature will, unless very carefully handled, actually reduce the chance of retrieving a relevant entry if the search is performed by computer because of the difficulty a computer has in handling the CCN Nomenclature which allows for free text and non-ASCII characters whose representation is not uniquely defined. The inability of the CCN Nomeclature to be uniquely expressed in digital form was the principal reason why the Phase Indentifier Working Group was established. Please check the attached report and send your approval to phase-identifiers@iucr.org as soon as possible if you don't wish to receive reminders. David -- Dr. I.D.Brown, Professor Emeritus, Department of Physics and Astronomy McMaster University, Hamilton Ontario, Canada
************************************************************** ************************************************************** $ Lines beginning with $ are not part of the draft report. $ They will be deleted before the report is submitted. $ $ DRAFT #3 2004-7-1 $ $ 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) ********************************************* REPORT OF THE WORKING GROUP ON CRYSTAL PHASE IDENTIFIERS 2004-07-1 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 on phase transition nomenclature (Tol‚dano et al., 1998, 2001) 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 as by the chemical community. 2. TERMS OF REFERENCE OF THE WORKING GROUP ------------------------------------------ The Working Group was charged with recommending 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. 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 not 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. 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 defined as a phase for which, in principle, it is possible to assign one of the 230 space groups listed in International Tables for Crystallography Vol. A, even if that space group is only a subgroup of the full space group (as in the case of aperiodic 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). 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 except for aperiodic crystals, cf. Jansen et al.(2002). 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 in 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 conventional 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 lower-case letter is followed 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. 6.4 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 letters */ /* 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 lower-case 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, see Parth‚ & Gelato (1984, 1985), Gelato & Parth‚ (1987). 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)3NCH2COOúCaCl2ú2H2O 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 (Tol‚dano et al. (1998, 2001)*. ---------------- Footnote -------------------- * Available on the IUCr web page: http://www.iucr.org - under Commissions/Commission on Crystallographic Nomenclature/CNOM on-lineinformation/Structural Phase Transition Nomenclature. -------------End of Footnote -------------------- 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 identification information density for the phase, whereas the philosophy of IChI is to include only the minimum information needed for phase identification. Both include the space group but otherwise there is little overlap between them. The two symbols are complementary and serve different purposes. The IChI could be added to the CCN Phase Transition Nomenclature but it is not clear where this would offer any advantage. A method for combining the two, should this be desired, 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 untwinned alpha (ferromagnetic) iron cannot be isotropic Im-3m (229) but the deviation from higher symmetry is very small and the correct space group is not yet determined. 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 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. REFERENCES Abrahams, S. C., Ihringer, J., Marsh, P. & Nassau, K. (1984). J. Chem. Phys. 81, 2082-2087. Donohue, J. (1974). The Structure of the Elements. New York: John Wiley & Sons. Gelato, L.M., Parth‚, E. (1987). J. Appl. Cryst. 20, 139-143. Ihringer, J. & Abrahams, S. C. (1984) Phys. Rev. B30, 6540-6548 (1984). Janssen, T. , Birman, J. L., D‚noyer, F., Koptsik, V. A., Verger- Gaugry, J. L., Weigel, D., Yamamoto, A., Abrahams, S. C. & Kopsky, V.(2002). Acta Cryst., A58, 605-621. Parth‚, E., Gelato, L.M. (1984). Acta Cryst. A40, 169-183, Parth‚, E., Gelato, L.M. (1985). Acta Cryst. A41, 142-151. Tol‚dano, J.-C., Glazer, A. M., Hahn, Th., Parthe, E., Roth, R. S. Berry, R. S., Metselaar, R. & Abrahams, S. C. (1998). Acta Cryst. (1998). A54, 1028-1033. Tol‚dano, J.-C., Berry, R. S., Brown, P. J., Glazer, A. M., Metselaar, R., Pandey, D., Perez-Mato, J. M., Roth, R. S. & Abrahams, S. C. (2001). Acta Cryst. (2001). A57, 614-626. END OF THE REPORT OF THE WORKING GROUP ---------------------------------------
_______________________________________________ phase-identifiers mailing list phase-identifiers@iucr.org http://scripts.iucr.org/mailman/listinfo/phase-identifiers
Reply to: [list | sender only]
- Follow-Ups:
- RE: Final draft of Phase-ID report (S. C. Abrahams)
- Re: Final draft of Phase-ID report (Sam Motherwell)
- Re: Final draft of Phase-ID report (Brian McMahon)
- Prev by Date: RE: Phase ID draft report
- Next by Date: Re: Final draft of Phase-ID report
- Prev by thread: The IUPAC-NIST Chemical Identifier
- Next by thread: Re: Final draft of Phase-ID report
- Index(es):