Wolfram Language Paclet Repository
Community-contributed installable additions to the Wolfram Language
Importing crystal data
In order to make use of the basic functions in this package, some basic input is required, such as lattice parameters, space group and atom positions. In this tutorial, we will learn how to import the relevant crystallographic information to Mathematica automatically from cif files.
The package must be loaded:
In[1]:=
Needs["StianRamsnes`MaXrd`"]
contains all crystal data entries | |
deletes data – currently only to a DISCUS format | |
imports data form cif files into Mathematica |
Functions related to crystal/compound data.
Storing crystal data
In this package, crystal data is by default stored in the file:
MaXrd ▶ Kernel ▶ Data ▶ UserData ▶ CrystalData.m
Under each data entry, or crystal, we find the following relevant information:
◼
Chemical formula
◼
Space group
◼
Lattice parameters
◼
Wavelength (may be omitted)
◼
Atom data (element, occupation factor, fractional coordinates, displacement parameters)
All this information is stored as an in the Wolfram Language. See The association structure of crystallographic data tutorial if you are unfamiliar with this construct.
When the MaXrd package is loaded, the mentioned file is loaded and the symbol is assigned for the association within.
In[2]:=
?
 | $CrystalData |
Out[2]=
Some example crystal data is included in the package, i.e. the file CrystalData.m contains some entries already.
In[3]:=
data=
["GalliumArsenide"]
 | $CrystalData |
Out[3]=
ChemicalFormulaGaAs,FormulaUnits4,SpaceGroupF3m,LatticeParametersa,b,c,α,β,γ,AtomDataElementGa,OccupationFactor1.,FractionalCoordinates{0,0,0},DisplacementParameters0.631,TypeBiso,ElementAs,OccupationFactor1.,FractionalCoordinates,,,DisplacementParameters0.679,TypeBiso,NotesInformation{West}
4
5.6534
Å
5.6534
Å
5.6534
Å
90
°
90
°
90
°
1
4
1
4
1
4
In[4]:=
Dataset@data
Out[4]=
An overview of all entries:
In[5]:=
MulticolumnKeys@
,3
 | $CrystalData |
Out[5]=
Aluminium | Germanium | Polonium |
Austenite | Glycyl-L-alanine | PrussianBlue |
CalciumFluoride | Ice | Quartz |
Cobalt(II)Fluoride | LanthanumHexaboride | Silicon |
Copper | LithiumCobaltate | Silver |
CopperTungstenOxide | LithiumManganesePhosphate | Sodalite |
Corundum | ManganeseSilicon | SodiumChloride |
Diamond | Nickel | Sphalerite |
Ferrite | OxalicAcid | Tungsten |
GalliumArsenide | Perovskite | Zinc |
To see how we may put this data into use, see Performing calculations on crystal data. Alternatively, continue to the next section to learn how to import crystal data to Mathematica.
Importing data manually
There are two ways to enter the data manually:
◼
Arrange all information in a list/pattern specified by the signature of the function
◼
In essence, the second method and automatic method that will be elaborated in the next section, just organise the same information and feeds it into the “main” function.
The labels and expected values should be evident. A worked example using this method is available on the the function's documentation page; no more details will be given here.
Importing data from CIF files
Although «manual» input is an option, the function is built for automatic import in mind.
The can be used to find cif files for testing purposes. We will be using a random cif file from that site in this demonstration; the actual file is found in:
MaXrd ▶ Kernel ▶ Data ▶ ExampleFiles ▶ CIF ▶ COD_2203515.cif
First we need the file path. You can also use the menu in Mathematica: Insert ▶ File Path…
In[1]:=
filepath=FileNameJoin
,"Resources","ExampleFiles","CIF","COD_2203515.cif";
 | $MaXrdPath |
In[2]:=
?
| ImportCrystalData |
Out[2]=
In[3]:=
| ImportCrystalData |
Out[3]=
ChemicalFormulaCCaFK,FormulaUnits1,SpaceGroupPm2,LatticeParametersa,b,c,α,β,γ,AtomData{5}
O
3
6
5.10093
Å
5.10093
Å
4.4551
Å
90
°
90
°
120
°
Data on the crystal is now stored under in , since we did not specify a . If we wanted another name, for instance , we would write:
"TutorialData"
label
"My test crystal"
In[4]:=
| ImportCrystalData |
Out[4]=
ChemicalFormulaCCaFK,FormulaUnits1,SpaceGroupPm2,LatticeParametersa,b,c,α,β,γ,AtomData{5}
O
3
6
5.10093
Å
5.10093
Å
4.4551
Å
90
°
90
°
120
°
Look up the newly added crystal:
In[5]:=
| $CrystalData |
Out[5]=
ChemicalFormulaCCaFK,FormulaUnits1,SpaceGroupPm2,LatticeParametersa,b,c,α,β,γ,AtomData{ElementK,FractionalCoordinates{0,0,0},DisplacementParameters0.0126,TypeUiso,ElementC,FractionalCoordinates{0.66667,0.33333,0.5},DisplacementParameters0.018,TypeUiso,ElementCa,FractionalCoordinates{0.33333,0.66667,0.5},DisplacementParameters0.01,TypeUiso,ElementO,FractionalCoordinates{0.812,0.188,0.5},DisplacementParameters0.0129,TypeUiso,ElementF,FractionalCoordinates{0.33333,0.66667,0},DisplacementParameters0.0196,TypeUiso}
O
3
6
5.10093
Å
5.10093
Å
4.4551
Å
90
°
90
°
120
°
In[6]:=
| $CrystalData |
Out[6]=
Applications of this kind of data is covered in other tutorials. The imported data is stored in the CrystalData.m file and thus kept even after Mathematica shuts down or the kernel is quit. The user may also specify a custom file to store the data in, but more about this can be read in the documentation on .
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