MINCRYST

Crystallographic and Crystallochemical Database for Mineral and their Structural Analogues

Mincryst as STAND-ALONE version is developed (since 1985) with the aim to create the original combination consisting of the Crystal Structure Database for Minerals, the automatically formed Calculated Powder X-ray Diffraction Standards (CPDS) SubBase and the Applied Program Package using saved information for Powder X-Ray Diffraction and Crystal Chemical Analysis.

Mincryst as WWW-version is developed on the basis of the stand-alone version  since 1997 (parallel) with the same purposes. Our strategic aim is to make WWW-MINCRYST by analogue of Stand-alone version on set of functions.

Stand-alone version is for the use at a separate PC or Organization network (PC Pentium, Microsoft Windows 9x/NT) and is developed under Database Management System on the basis of the Borland Delphi 2.0, DB-format - Paradox 5.0).

WWW-version is for working with MINCRYST in INTERNET. Any Internet User has an access to MINCRYST Database on the address: http://database.iem.ac.ru/mincryst.
            WWW-MINCRYST Database has been converted from the Paradox 5.0 format (Stand-alone version) into the SQL-format and is located on the Database Server of Institute of Experimental Mineralogy of Russian Academy of Sciences (http://database.iem.ac.ru/).

The WWW-interface provides the global access to MINCRYST Database with any graphical WWW-browser supporting Java 1.1.x..

Database Entries (Records) are kept in SQL-tables of mySQL Database Management System (DMS), placed on Database Server under the control of OC Digital Unix, Linux or Solaris. Server part of Mincryst is realized in different versions of OC Unix, Linux or Solaris with the of mySQL DMS and HTTP server Apache with the modules of Perl and PHP Script Languages integrated there, performing relationships between the Database Server and HTTP-Server and forming dynamic HTML-pages. Moreover, on the Server side, JavaScript and Java applets are developed and distributed to work with the graphic and multimedia Database Objects.

Client's inquiries are formed either through dynamically created HTML-pages with the standard mechanism of HTML forms or JavaScript Languages or in terms of Java-applets for the graphics.

            Mechanism of forming of inquiries transforms simple user's inquiries into complex structured SQL-inquiries to Database and provides view, search and selection of records on a set of parameters. A subsequent search with a chain of still more strict criteria is also to be realized.

A user gets the results of inquiries containing text-table information as dynamically created HTML-pages.

The objects, containing graphic information, are given to the user through the automatically loaded Java-applets. Java-applet offers not only to view graphic image, but also interactive work with the animated graphic image in On-line regime.

 Editing of records and import of records into Database as well as its administration is fulfilled in form of specialized WWW-interfaces.

            MINCRYST DATABASE  (Stand-alone and WWW-versions)

MINCRYST is Crystallographic Database for Minerals, which  nucleus makes Crystal Structure Database.

Information sources for Crystal Structure Database are original journal articles (hard copies) and Crystallographic Information Files (electronic form).

Crystal Structure Information is extracted and introduced into BDM-file (original format, ASCII-form) with keyboard. Saved information is examined with calculation of interatomic distances and other crystal structure characteristics with Program Package.

Mineral Crystal Structure Database includes more than 6000 entries (2500 unique mineral names). Each entry contains the crystal structure information extracted from the original publications: Mineral name, Specification, Crystal chemical formula, Space group, Unit cell parameters, Coordinates, Thermal factors and Occupancy of atomic positions as well as literature reference(s) on crystal structure determination.

Mineral CPDS SubBase includes 6000 entries, respectively. Each entry contains crystal structure information related to Powder X-Ray Diffraction Standards calculated on the basis of the Mineral Crystal Structure Database: Mineral name, Specification, Crystal chemical formula, Symmetry, Unit cell parameters, number of powder X-ray diffraction reflexes, as well as HKL-indexes, interplanar spacings and intensities of reflexes. This information is calculated by TRANS- and XRAYPOL-programs (see below) and is kept in BDP-files (origin format, ASCII-form).

Program Package (1985-1992 working out) for Stand-alone version

·        The TRANS interface program for full-automated preparation of the input file for the program XRAYPOL in the form of file TRANS.DAT using information stored in Mineral Crystal Structure Database. The TRANS-program performs calculations in the framework of 645 space groups (all non-standard set-ups are included) using the built-in MINCRYST Crystallographic Database.

·        The XRAYPOL program for calculation of Powder X-ray Diffraction Patterns, Standards for CPDS SubBase (BDP-file), Interatomic distances (to check the reliability of the input crystal structure data), Mineral Information Card (INF-file) as well as Input Files for the programs MIXIPOL and QUANTPOL (BDQ-file) and CRYSTPIC (BDI-file) in the full-automated mode using the TRANS.DAT-file.

·        The MIXIPOL program for calculation and displaying Full Powder X-ray Diffraction Profile of polycrystalline phases or their mixtures at set concentrations using the file FileName.BDQ. A profile of reflexes is described by the modified and asymmetric Lorentz function. DOS- and Windows (1997-adaptation)-versions of MIXIPOL is available.

·        The QUANTPOL program for a standartless X-ray quantitative phase analysis with refinement of all X-ray parameters of phases (except atomic positions parameters) using the file FileName.BDQ. A simplified Rietveld approach is realized in this algorithm (atomic coordinates and occupancies do not refine). The profile of reflexes is also described by a modified and asymmetrized Lorentz function. The simplex method is used for parameter's optimization.

·        The CRYSTPIC program for drawing crystal structure on the monitor screen as well as its HKL-fragments (automatically, with the orientation and thickness of the fragment depending on the value of HKL-indexes) using file FileName.BDI. Also the program performs calculations of bond lengths and angles. DOS- and Windows (1997-adaptation)-versions of CRYSTPIC is available.

·        The OPTIDENT program for identification the crystalline phase from its experimental X-ray diffraction patterns using the Mineral CPDS Subbase (RENTPOL-file). Special procedure is made to execute a choice of CPDS on the given set of chemical elements.

·        The MIXIDENT program for the Qualitative X-ray Diffraction Phase Analysis (preleminary version) also using the Mineral CPDS Subbase (RENTPOL-file). Chemical search is also included.

·        The REFLAT program performs the Unit Cell Parameters refinement of polycrystalline phase. Indicing of reflexes is performed on every step of the refinement procedure taking into account calculated intensities.

In 1992 the work under Package was interrupted due to Perestroika in Soviet Union.

It is assumed to complete development of the Program Package by the adapting DOS-Applied Program Package for work under Windows and also to improve Programs .

Work Scheme of Stand-alone version

BDM-files are imported with the origin Import Program into searchable Database.  Calculated BDP-files are imported simultaneously. If a single BDM-file is imported, then corresponding BDP-file is calculated with built-in TRANS+XRAYPOL-programs. Origin Editor-program for edition of entries within Database is worked out. Edition of BDM-part of entries within Database is accompanied with re-counted BDP-part of entries.

Search is realized with following parameters: mineral name, specification, formula (chemical element set and substring), space group, singony, references (author, year, journal), card number.

The built-in Management System Trans- and Xraypol-programs allow to calculate following files for selected mineral: BDP, BDI, BDQ, INF.

Those files can be used with Program Package for analytical purposes. Also the selected mineral entry can be exported from Database as BDM-file for use with Program Package in analytical purposes. All entries (or part) can be exported in form of RENTPOL-file for purposes of Qualitative X-ray Phase Analysis on the basis of CPDS SubBase.

Work Scheme of WWW-version

Ideology of the WWW-version is, in principle, analogous to those of the Stand-alone version. There are, however, marked differences. Primarily, in WWW-version a powerful search regime is available. In particular, a complex search for the chemical composition, reflected in the crystal chemical formula, and interplanar distances, contained in the CPDS SubBase, is, factually, adequate to the automatic Qualitative X-ray Phase Analysis. The Java-applets enable the transmission the Crystal Structure Model image and the X-ray Diffraction Powder Line-Diagram image from the Server to the Client PC at a rate of the text information translation.

The last WWW-version has new parts and, accordingly, new regimes: 'Structure' (on the basis of the BDI-file), 'X-ray Line Diagram' (on the basis of the INF-file), 'External Links'. User has the access to 'Full Information Card' (INF-file).

Import and Edition of Entries is realized with origin WWW-Editor program.

BDM-, BDP, BDI and INF-files are imported simultaneously. Last three types of files are calculated with Program Package (for Stand-alone version). It is possible to make import of entry group or single entry.

Full Information Card

The Mineral Information Card calculated with TRANS+XRAYPOL programs contains both crystal structure characteristics of mineral and its powder X-ray diffraction patterns. It reproduces the data from Crystal Structure Database and includes the following calculated data: full powder X-ray diffraction patterns (for each reflex: HKL-indices, angle position, S-parameter, LPG-factor, multiplicity factor, structure factor, integrated intensity); shortened powder X-ray diffraction pattern (for each reflex: HKL-indices, theta and 2-theta angle positions, d-spacing, integrated intensity normalized at 100 unit in maximum); co-ordinates of atomic positions in full unit cell; unit cell volume, molar volume and density; linear and mass absorption coefficients.

 

PRINCIPAL FEATURES OF MINCRYST

 

Three main features make Mincryst unique, having no analogues abroad or in Russia.

            First, MINCRYST is a universal system, containing information on chemical composition, crystal structures and X-ray diffraction properties of minerals and their structural analogues, characterizing a substance as a "monocrystal" on one side (fundamental characteristics - coordinates of atomic positions), and as a "poly-crystal" (fundamental characteristics - interplanar distances), on the other.

Second, MINCRYST - is a complex system, operating newly formed information resources (Crystal Structure Database); it increases a volume of information resources using with automatically formed CPDS SubBase and Calculated Information Cards; it contains Applied Program Package using the created resources as analytical purpose (Crystal chemical analysis and X-ray diffraction qualitative and quantitative phase analyses).

Third, MINCRYST solves one of the most important problems of polycrystal-standards for minerals through the development of  Calculated Powder X-ray Diffraction Standard SubBase, thus providing Calculated X-ray Diffraction Data to be used in Qualitative X-Ray Phase Analysis.

            In 1992 originator of MINCRYST said as follows: "The system of the calculated standards is the most real alternative to (JCPDS-ICDD)-system of the experimental standards. One can also hope that in many other cases it won't be as much as the alternative, but the effective addition to the (JCPDS-ICDD)-system ".

Chichagov A.V., Shilova Z.V., Lopatin A.L. "Qualitative X-Ray phase analysis on the basis of the calculated standards". - KRISTALLOGRAFIYA (1992), v.37, p.942 (in russian).

English translation: Sov. Phys. Crystallogr., 1992, 37(4) - American Institute Physics.

Meanwhile ICDD declared about the input into PDF2 of 40 thousand calculated standards only in 1998 (with the remark "first in the history of ICDD!").

Other distinctive features of MINCRYST are:

·        operation with crystal structure information and with the calculated powder X-ray diffraction information;

·        full-automated calculation and displaying of powder X-ray diffraction patterns on the basis of the reliable crystal structure data;

·        full-automated formation of CPDS Sub-base; the qualitative X-ray phase analysis on the basis of the calculated (non-experimental!) standards;

·        full-automated preparation of input files for the programs of the quantitative phase analysis and crystal chemical analysis.

MINCRYST as an information-calculating system presents a powerful tool for X-ray crystallographers. The Powder X-ray Diffraction Patterns is calculated and displayed in a few seconds. The drawing of a crystal structure requires from a few seconds to minutes depending on the type of the Computer (PC IBM/AT-compatible) and the complexity of the crystal structure. (The user does not need a special training.)

MINCRYST as an informative directory system may be useful for everyone concerned with the crystal structure characteristics of mineral.

Authors continue working at both filling up and edition of MINCRYST Information Fund and developing Program Package of both Stand-lone and Internet version.

* * * * *

At present MINCRYST Information Fund is specified according to low taxons of Mineral Classification (by A.A. Godovikov. Structural-chemical systematic of minerals, 1997).

Following legend is included in Specification of Information Card :

·        t-Structure Type (t-apatite for hexagonal BRITHOLITE);

·        td-Distorted Structure Type (td-apatite for monoclinic BRITHOLITE);

·        f-Family (f-pyroxene);

·        sf-SubFamily (sf-Ca-Na-pyroxene);

·        g-Group (g-calcite);

·        s-Series (s-garnet);

·        ss-SubSeries (ss-Tremolite).


Family. Minerals have similar or identical (for polymorphous types) composition, common genesis or paragenesis.
Subfamily. Minerals have similar composition and the same structure type.
  (For instance: Family of zeolites including SubFamilies: thomsonite, scolecite-natrolite, garronite, wairakite, gmelinite, stilbite, stellerite, mordenite).
Group. Minerals have the same composition type and the same structure type.
  (For instance: Dolomite group including dolomite, ankerite, benstonite, kutnohorite, eitelite, having one type structure, but not forming continuous solid solution with each other).
Series. Minerals form continuous solid solutions between two or more number of edge members.
  (For instance: Forsterite series and garnet series).
DF = defective structure. This is a Crystal Structure containing atomic positions with a low occupancies and a bad interatomic (interposition) distances (for instance, tobermorite [1]).
DN = This is a Crystal Structure containing atomic positions with a low occupancies and a good interatomic (interposition) distances (for instance, acmite [5]).

Useful properties:

ZL = zeolite,
LS = laser,
SC = superconductor,
CM = cement material,
MD = modulated structure,
MX = matrix for radioactive elements.

Analogue, Cr-analogue:

If synthetic inorganic phase is structure analogue of mineral, then it is written under name of this mineral.
For instance, NaGaSi3O8 - synthetic inorganic phase with structure of ALBITE is written as:
ALBITE [14], low, Ga-analogue

NOTES

Note: Asterisk at space group in Mineral Card means either different setting or different co-ordinate origin. For instance: R 3 - trigonal (hexagonal) setting; *R 3 - rhombohedral setting; F d3m - cubic, origin at 4(-)3m; *F d3m - cubic, origin at center 3(-)m.

Note: In connection with features of edition of WWW-MINCRYST the number of a mineral card is not saved to constants, but the name of a mineral + number of the specification is saved to constants, e.g., olivine [5]. Thus, the name of a mineral + number of the specification is the mineral identifier. Therefore the reference to our data on mineral can be done as follows, e.g.: WWW-MINCRYST, olivine [5]

N o t e: The Database contains minerals and inorganic phases - structural analogues of minerals. Also some selected inorganic compounds are included in a DataBase: the simple substances (Aluminium, Boron, Carbon, …), simple oxides (Ag2O, SeO2, …), silicates (SILICATE _ Ba _ Ca _ Cu, SILICATE _ Ag _ Sb, …), silicogermanates (SILICOGERMANATE _ Ca …), germanates (GERMANATE _ Na _ Sm, ...), phosphates (PHOSPHATE _ Ca _ U ...), silicophosphates (SILICOPHOSPHATE _ Ca _ Ce _ Mg, …) and some other inorganic compounds. You will easily find them by an part of the name or in the Letter Lists or the Full List). Also some inorganic compounds can be found in a DataBase by the name: NEWMINERAL, NEWPHASE, NEWPRODUCT.

All rights on MINCRYST are protected:

The priority of the ideas realized in MINCRYST is protected by its registration in the Russian State Register of Database (State Committee of Russian Federation on Communication and Informatization, Scientific Technical Center 'Informregister') numbered as 0229805169 (Registration Certificate No 4873 of 11.02.99) for WWW-version and as 0229805170 ((Registration Certificate No 4874 of 11.02.99) for Stand-alone version.

More detailed information about MINCRYST (contents, edition …) can be obtained at the address: Chichagov A.V., Institute of Experimental Mineralogy,142432 Chernogolovka, Moscow distr., Russia. E-mail: avch@iem.ac.ru.