*.xtal File Description (version 2)
•Contents of File
This is a description of a *.xtal file that describes a crystal lattice and the included atoms.
These files are standard xml files, and follow all of the rules for xml.
ALL of the information is contained in the <cif version="2" dim="3"> ... </cif> section.
Note, the dim="3" is for 3D structures. For 2D strcutures, use dim="2".
To determine the symmetry, the best thing is to use the <id> tag (there are 530 of them).
If you just use <IT_number>, then you leave an ambiguity (e.g. space group 15 has 18 different settings).
The <H-M> or <Hall> are also good, since they uniquely identify the space group setting, but are sometimes ambiguous.
Or, you could just list all of the symmetry operations in the <symops> block.
The <cif version="2" dim="3"> ... </cif> section contains the following tags:.
<space_group> ... </space_group>
This contains all of the symmetry information needed to identify the structure, it includes some of the following:
<id> the Space Group id, something like "167:H"<IT_number> the Space Group number, something like "167" in range [1-230] (for 2D [1-17])<H-M> the H-M symbol, e.g. R -3 c:H<Hall> the Hall symbol e.g. -R 3 2''c<symops>...<symops> the list of all symmetry operations.
This will contain a list of tags such as: <op>"-x+1/4" "-y+1/4" "-z+1/4"<op>,
one for each symmetry operation.
Enough of these tags must be included in <space_group> to identify the symmetry of the crystal.
<cell> ... </cell>
This contains the information needed to define the unit cell, and optionally the measurment conditions.
Required tags are the unit cell parameters:
<a>, <b>, <c>
These are all of the form: <a unit="nm">0.4759092</a>
where the unit is any length unit: nm, pm, Å, m, inch, parsec, and with prefixes, e.g. cm, or ypc, ...
If the unit is not specified, it defaults to Å.
<alpha>, <beta>, <gamma>
These are all of the form: <alpha unit="°">90</alpha>
where the unit is one of [deg, °, rad, circle, arcmin, arcsec, grad, cos], again SI prefixes are allowed.
If the unit is not specified, it defaults to degree.
For 2D structures, only at most <a>, <b>, and <alpha> are needed.
Optional tags are:
<temperature> Temperature where measurement was made.
Again the temperature can have units, known units are: [C, K, F, R, Planck], default is K, and SI prefixes are allowed<alphaT> Coefficient of expansion, used to get lattice constant at different temperatures. Units are 1/C.<pressure> Pressure where measurement was made.
An example is:
<pressure unit="GPa">100</pressure>
<atom_site> ... </atom_site>
There should be one for each type of atom.
Required tags are:
<label>
These are all of the form: <label>Al01</label> or <label>Al</label>
The value is a string that is unique for each atom site, numbers are usually used when the same element has multiple sites.
<fract>0 0 0.352</fract>
The three number represent the fractional coordinates of the atom.
Note, for 2D structures, there will only be 2 fractional coordinates, e.g. <fract>1/3 2/3</fract>
(note that fractions may be used for fractional coordinates).
Optional tags are:
<symbol>Al</symbol>
Not needed if the element can be determined from the label.
e.g. "Al01" → Al, and "Ge" → Ge, but "atom1" → ???
<valence>3</valence>
An integer describing the oxidation state. If not given, assume 0.
<occupancy>0.3</occupancy>
The occupancy of the site, a number. If not given, assume 1. Should be in range (0,1].
<WyckoffSymbol>c</WyckoffSymbol>
A letter that is the Wyckoff symbol. If not given, it will be determined from symmetry info.
In this example it is "c"
<U_iso unit="Å^2">0.0049</U_iso>
The isotropic U, in this example the units are Ų, any length² unit is allowed, default is Ų.
<B_iso unit="Å^2">1.1</B_iso>
The isotropic B, in this example the units are Ų, any length² unit is allowed, default is Ų.
<aniso_U_11 unit="Å^2">0.01807</aniso_U_11>
The anisotropic U values, in this example the units are Ų, any length² unit is allowed, default is Ų.
You will probably also want to use: <aniso_U_22>, <aniso_U_33>, <aniso_U_12>, <aniso_U_13>, <aniso_U_23>
Any unspecified values will be set to 0, and so have no effect.
<DebyeTemperature unit="K">670</DebyeTemperature>
The Debye Temperature. This will allow a temperature dependent strength of reflections.
The default unit is K, and all temperatuere units are allowed.
<citation> ... </citation> Optional
Holds the citation of the article where these values came from.
The opener can specify an "id" or a "doi" as in:
<citation id="2" doi="10.1107/S0365110X63002012">
The id is needed when multiple <citation> blocks are present, id="primary" is the main one, id="2" is secondary, ...
The contents of the <citation> block can be just plain text, or you can strcuture it using the following optional tags:
<title>The crystal structure of something</title>, the title of the article.<author>W.H. Zachariasen</author>, there can be multiple author tags in a citation.<journal>Acta Cryst.</journal>, name of the journal.<year>1963</year>, year the journal was published.<volume>1963</volume>, the volume of the journal<pages>777 783</pages>, the page range of the article, a single number is also allowed.
<database_code db="COD">9008678</database_code> Optional
Holds the value for a particular data base, again where these values came from.
COD refers to the "Crystallography Open Database"
Other examples are:
<database_code db="ICSD">18189</database_code>, "Inorganic Crystal Structue Database"."
<database_code db="AMCSD">0012345</database_code>, "American Minerologist Crystal Structue Database"."
<chemical_name_common>Gallium Arsenide</chemical_name_common> Optional
Common name of the material. Something that makes a nice title.
<chemical_formula>GaAs</chemical_formula> Optional
Chemical Formula, again something that look nice in a title.
<chemical_formula_structural>GaAs</chemical_formula_structural> Optional
A longer more interesting looking formula, may be useful for complicated organic materials.
<bond_chemical unit="nm" n0="Na1" n1="Cl001">0.2418</bond_chemical> Optional
Defines a bond. n0 and n1 refer to the label of two atom types (n0 and n1 can be the same),
and the value is the bond length using the given units.
There can be multiple bonds, use one line for each type.
•Exmaple File, Copper
<?xml version="1.0" encoding="UTF-8" ?>
<cif version="2" dim="3">
<chemical_name_common>Copper</chemical_name_common>
<space_group>
<IT_number>225</IT_number>
<H-M>Fm-3m</H-M>
</space_group>
<cell>
<a unit="nm">0.361496</a>
<b unit="nm">0.361496</b>
<c unit="nm">0.361496</c>
<alpha>90</alpha>
<beta>90</beta>
<gamma>90</gamma>
<temperature unit="C">22.5</temperature>
<alphaT>17e-6</alphaT> <!-- a = ao*(1+alphaT*(TempC-22.5)) -->
</cell>
<atom_site>
<label>Cu</label>
<symbol>Cu</symbol>
<fract>0 0 0</fract>
<DebyeTemperature unit="K">343.5</DebyeTemperature>
</atom_site>
<bond_chemical unit="nm" n0="Cu" n1="Cu">0.255616</bond_chemical>
<citation>
<author>Wyckoff, R W G</author>
<journal>Crystal Structures</journal>
<volume>1</volume>
<year>1963</year>
<pages>7 83</pages>
Second edition. Interscience Publishers, New York, New York
</citation>
</cif>