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An atomic basis of a crystal is the motif of chemical species $s_j$ and relative positions $r_j$ attached identically to every lattice point $R$ of a Bravais lattice $\Lambda$. The ideal periodic structure is the labeled setThe primitive lattice translation vectors generate $R$ by integer combinations; the atomic basis lists what is repeated at $R$. These are different meanings of the word basis. In particular, the offsets $r_j$ need not be linearly independent vectors, and one of them may be zero. A primitive unit cell represents $N$ motif sites, even though it represents only one lattice point.

Changing the origin, choosing another primitive unit cell, or moving a motif site by a Bravais lattice translation changes the coordinates used to describe the same infinite crystal structure. The grouping into a motif does not, by itself, identify bonded molecules. In solid sodium chloride, grouping one sodium cation and one chlorine anion into an atomic basis does not create a collection of discrete NaCl molecules; the ionic crystal has an extended network of equivalent neighboring ions.

Crystallography studies crystal structures and their symmetries. A structure determination connects measurements such as crystal scattering patterns to a model of the unit cell and its atomic basis of a crystal.

X-ray crystallographic structure inference makes that connection explicit: compare proposed crystal structures through the positions and wave intensities of their predicted reflections. The main difficulty is that a diffraction pattern encodes wave interference, so it must be interpreted through a model rather than read as a direct picture of the chemical atoms.

A crystal structure specifies the chemical species and spatial arrangement of the chemical atoms or ions in a crystal. For an ideal periodic structure, separate two ingredients: a Bravais lattice specifies the translations that repeat the arrangement, and an atomic basis of a crystal specifies the chemical motif repeated at every lattice point. The outward shape, or crystal habit, is a different description: the internal arrangement is what this article describes.

For a concrete two-dimensional model, choose primitive lattice translation vectors $a_1=(2,0)$ and $a_2=(0,1.5)$ in arbitrary length units. At every lattice point $R=m{a}_1+n{a}_2$, with integers $m,n$, place species A at $R$ and a different species B at $R+(0.65,0.55)$. Translating by $a_1$ or $a_2$ preserves both the positions and their chemical labels. Translating by $(0.65,0.55)$ sends one A position to a B position, so it is not a translation symmetry of the labeled structure. A picture of dots with the labels erased can therefore conceal essential chemical information.

A primitive unit cell contains one lattice point, but may contain several chemical atoms. A conventional unit cell can contain several lattice points to display the symmetry more clearly. Thus the conventional cube of a face-centered cubic lattice contains four lattice points, whereas a body-centered cubic lattice has two. Neither lattice name alone specifies which chemical species occupies the repeated motif. The NaCl conventional cell and coordination example makes the distinction explicit.

This separation is useful experimentally: interplanar spacings constrain the repeating geometry, while relative wave intensities also depend on the atomic basis of a crystal through the crystal basis structure factor. The Bragg crystal reflection experiment of 1913 describes the X-ray spectrometer, angular scans and detector checks in detail. Its conversion from angle to length is developed under Bragg's law; a geometrically possible reflection can still have zero wave intensity.

William Lawrence Bragg's 1913 structure determination supplied a complementary test. He directed X-rays through sodium chloride sections cut parallel to a cube face and recorded spots on photographic plates. Comparing section thicknesses tested how transmission altered the pattern: the relative spot strengths changed. Comparing related salts led him to two interpenetrating face-centered cubic lattices, one for each kind of constituent. He explicitly distinguished evidence for that arrangement from the still-needed identification of a single chemical atom with each scattering center. The photographs were evidence for a structural model, not direct pictures of labeled ions.^[ref]

Consider a chosen primitive cubic lattice $a{\mathbb{Z}}^3$ with $a=0.400\mathrm{nm}$ and one identical point scatterer per primitive unit cell. Retain the incident wavelength $\lambda =0.154\mathrm{nm}$. This is an ideal point model. Its reciprocal lattice vectors are $q=(2\pi /a)(h,k,l)$ for integer triples other than $(0,0,0)$. Write $S=h^2+k^2+l^2$. The associated interplanar spacing and first-order Bragg angle satisfyThe reflection labels $(hkl)$ use the Miller index convention, keeping unreduced triples to encode diffraction order. With that convention, set $n=1$ in Bragg's law for each label. The $(200)$ reflection is equivalently the second diffraction order of $(100)$: $d_{200}=a/2$ does not imply extra scatterers halfway between the occupied $(100)$ planes. Counting both descriptions as distinct reflections would count the same direction twice.

For $(100)$, $(110)$, $(111)$ and $(200)$, respectively, $S=1,2,3,4$ and the calculated interplanar spacings are $0.400000$, $0.282843$, $0.230940$ and $0.200000\mathrm{nm}$. Their calculated deflections $2\theta$ are $22.197435^{\circ }$, $31.594744^{\circ }$, $38.952948^{\circ }$ and $45.287481^{\circ }$. Equal steps in $S$ give equal steps in ${\sin }^2\theta$, not equal steps in $2\theta$. This regularity makes an angular pattern a test of a proposed crystal structure.

A real crystal structure has a Bravais lattice together with an atomic basis of a crystal. The crystal lattice structure factor selects the periodic directions; the crystal basis structure factor combines the scattering amplitudes of atoms within a unit cell and can cancel a reflection. Consequently Bragg's law alone predicts neither allowed reflections nor their wave intensities. ^[ref] Systematic absences further restrict observed families; for example, face-centered cubic lattice centering permits only indices all even or all odd in conventional cubic indexing. The four strips above apply to the stated primitive cubic lattice, not to sodium chloride or a face-centered cubic lattice. ^[ref]

A member of a set of linearly independent vectors whose integer combinations generate every lattice point of a Bravais lattice. Such basis vectors specify translations; an atomic basis of a crystal specifies the chemical motif repeated under them.

X-ray crystallographic structure inference is an inverse problem: infer a crystal structure from measured X-ray diffraction. A proposed unit cell and atomic basis of a crystal predict a pattern; structure determination asks which proposals survive comparison with that pattern. The useful separation is between directions and strengths. Peak positions constrain the reciprocal lattice and hence interplanar spacings; relative wave intensities constrain the motif through the crystal basis structure factor. Knowing a repeat distance does not locate all the chemical atoms within that repeat.

The lattice constant from two indexed reflections example isolates the geometric inference. Basis intensities and phase ambiguity then holds the translations fixed while changing the motif. Even complete, noiseless wave intensity data need not determine all wave phases: this is the phase problem. Chemical composition, symmetry, and additional measurements can supply constraints beyond the original pattern.^[ref]

X-ray crystallography infers a crystal structure from measured X-ray diffraction. Peak positions constrain the lattice geometry, while intensities constrain the atomic basis of a crystal; the inference also needs an experimental model and does not directly observe every atomic position.