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MaXrd

Guides

  • MaXrd – Mathematica X-ray diffraction package

Tech Notes

  • Applying crystal data
  • Basic computations
  • Computations on reflections
  • Formulas in crystallography
  • Importing crystal data
  • Quick guide to conditions
  • References
  • Symmetry calculations
  • The association structure of crystallographic data
  • Using the rotation options

Symbols

  • AttenuationCoefficient
  • BraggAngle
  • ConstructDomains
  • CrystalDensity
  • CrystalFormulaUnits
  • CrystalPlot
  • DarwinWidth
  • DistortStructure
  • DomainPlot
  • EmbedStructure
  • ExpandCrystal
  • ExportCrystalData
  • ExtinctionLength
  • FindPixelClusters
  • GetAtomCoordinates
  • GetAtomicScatteringFactors
  • GetCrystalMetric
  • GetElements
  • GetLatticeParameters
  • GetLaueClass
  • GetScatteringCrossSections
  • GetSymmetryData
  • GetSymmetryOperations
  • ImportCrystalData
  • InputCheck
  • InterplanarSpacing
  • MergeDomains
  • MergeSymmetryEquivalentReflections
  • MillerNotationToList
  • MillerNotationToString
  • ReciprocalImageCheck
  • ReciprocalSpaceSimulation
  • ReflectionList
  • RelatedFunctionsGraph
  • ResetCrystalData
  • ResizeStructure
  • SimulateDiffractionPattern
  • StructureFactor
  • StructureFactorTable
  • SymmetryEquivalentPositions
  • SymmetryEquivalentReflections
  • SymmetryEquivalentReflectionsQ
  • SynthesiseStructure
  • SystematicAbsentQ
  • ToStandardSetting
  • TransformAtomicDisplacementParameters
  • UnitCellTransformation
  • $CrystalData
  • $GroupSymbolRedirect
  • $LaueClasses
  • $MaXrdPath
  • $MaXrdVersion
  • $PeriodicTable
  • $PointGroups
  • $SpaceGroups
  • $TransformationMatrices
Formulas in crystallography
Metric
Reciprocal space
Transformations
Unit conversions
Interplanar spacing
Scattering
The formulas are gathered from [
Julian, 2015
], [
Giacovazzo,
1992] and [
Wikipedia
].
Metric
Basis vectors
a,b,c
Basis vectors in reciprocal space
*
a
,
*
b
,
*
c
Metric matrix
G=
a
b
c
(
a
b
c
)=
a·a
a·b
a·c
a·b
b·b
b·c
a·c
b·c
c·c
=
2
a
abcosγ
accosβ
abcosγ
2
b
bccosα
accosβ
bccosα
2
c
Metric matrix of reciprocal space (sometimes denoted by
H
)
*
G
=
-1
G
Volume
V=
detG
Fractional coordinates (unitless)
x,y,z
Miller (or Laue) indices
h,k,l
Coordinate vector (in direct space)
r=r(x,y,z)
=
xa+yb+zc
Reciprocal lattice vector (
Q
,
OH
,
G
or
*
r
hkl
is sometimes used instead of
H
)
H=
H
hkl
=H(h,k,l)=h
*
a
+k
*
b
+l
*
c
H=
H
hkl
≠H
Node in reciprocal space/lattice
H=(
h
k
l
)
Coordinate matrix (unitless)
X=
x
y
z
Magnitude of coordinate vector
r
r=
T
X
GX
Interatomic bond length
r
12
=
T
X
12
G
X
12
;
X
12
=
x
2
-
x
1
y
2
-
y
1
z
2
-
z
1
Interatomic bond angle (vertex at atom
1
)
cosθ=
T
X
12
G
X
13
r
12
r
13
=
T
X
12
G
X
13
T
X
12
G
X
12
T
X
13
G
X
13
Density
ρ=
ZM
V
N
A
;
Z=formulaunitsperunitcell
M=atomicmassofoneunit
V=unitcellvolume
N
A
=Avogadro'snumber
Transformations
Transformation matrix
P
Transforming basis vectors
(
a
2
b
2
c
2
)=(
a
1
b
1
c
1
)P
Transforming coordinates
X
2
=
-1
P
X
1
(
X
1
=P
X
2
)
Transforming metric matrices
G
2
=
T
P
G
1
P
Volume relation
detP=
V
2
V
1
Conversion from crystal coordinates to Cartesian coordinates (note: this is stored as
$TransformationMatrices["CrystallographicToCartesian"]
)
P
C
=
a
bcosγ
ccosβ
0
bsinγ
c(cosα-cosγcosβ)
sinγ
0
0
c
1-
2
cos
β-
2
(cosα-cosγcosβ)
2
sin
γ
​​=
a
bcosγ
ccosβ
0
bsinγ
c
C
1
0
0
c
C
2
,
C
1
=
cosα-cosγcosβ
sinγ
,
C
2
=
1-
2
cos
β-
2
C
1
Interplanar spacing
From correspondence between crystallographic planes and reciprocal lattice points:
d
hkl
=
1
H
=
1
H
*
G
T
H
Cubic
1
2
d
hkl
=
2
h
+
2
k
+
2
l
2
a
Tetragonal
1
2
d
hkl
=
2
h
+
2
k
2
a
+
2
l
2
c
Orthorhombic
1
2
d
hkl
=
2
h
2
a
+
2
k
2
b
+
2
l
2
c
Hexagonal and trigonal (
P
centring)
1
2
d
hkl
=
4
3
2
a
(
2
h
+
2
k
+hk)+
2
l
2
c
Rhombohedral (trigonal
R
centring)
1
2
d
hkl
=
1
2
a
(
2
h
+
2
k
+
2
l
)
2
sin
α+2(hk+hl+kl)(
2
cos
α-cosα)
1+2
3
cos
α-3
2
cos
α
Monoclinic
1
2
d
hkl
=
2
h
2
a
2
sin
β
+
2
k
2
b
+
2
l
2
c
2
sin
β
-
2hlcosβ
ac
2
sin
β
=
2
h
2
a
+
2
k
2
sin
β
2
b
+
2
l
2
c
-
2hlcosβ
ac
2
csc
β
Triclinic
Reciprocal space
Definition of the reciprocal lattice
Accordingly relations
Angles in reciprocal space
Volume relations
Unit conversions
Scattering
Common absorption edges

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