Terms used in Diamond User Manual

This page offers explanations for frequently used terms in the Diamond user manual.

Table of contents

Structure data
Atoms, atom codes, atom groups, bonds, bond groups etc.
Structure representation
User interface

Structure data

Relative Entry Number

Indicates the serial number of a crystal structure description within a file, beginning with 1. Since the structure list may be sorted, the rank order in the list does not necessarily agree with the order in the file.

Authors

The authors’ names are given in Diamond: surname <blank> capital(s) of the prename(s). Names of multiple authors’ are separated by commas.

Title

Represents usually the title of the publication of the structure. But beyond that any title can be assigned by the user.

Citation

Represents the ASTM Journal Coden of the periodical as well as volume number, first and last page and the year.

ASTM Journal Coden

Five character code for a journal’s title. This can be succeeded by a sixth character (proof character), e.g. ANCEA.

Trivial name

Represents the usual (trivial) name of the compound, i.e. a name that need not agree with IUPAC nomenclature.

Systematic name

Represents the complete name according to IUPAC or Chemical Abstracts nomenclature, e.g. lithium[4,6,7,11-tetramethyl-3,5,8,10-octakis-(methylamino)-spiro[5,5]tetrasila-2,9-dioxa-4,6,7,11-tetraaza-1-aluminate].

Structure type

Represents the name of the structure type. Usually a structure type is applied to minerals and inorganic compounds only, e.g. perovskite, sphalerite, C3

Mineral name

Represents a mineral name defined by the International Mineralogical Association, e.g. chalcopyrite.

Source of compound or mineral

Describes the place where a mineral was found or the origin of a natural product, e.g. from Kaiserstuhl, Germany.

Formula sum

Represents the stoichiometric composition which has been calculated from the parameter list. Therefore site occupation factors and multiplicities of the atomic parameters are used as well as the number of formula units in the unit cell.

Structural formula

Element symbol and stoichiometric indices are arranged to express components (e.g. molecule ions). This formula need not agree with the formula sum generated from the parameter list.

Analytical formula

Represents elements and stoichiometric indices resulting from a separate analytical determination and often contains trace elements which do not appear explicitely in the parameter list. Thus the formula need not agree with the formula generated from the parameter list.

Formula type

Represents the stoichiometry of the compound. Elements with positive oxidation numbers are indicated with the first letters of the alphabet (A-M), elements with negative oxidation numbers with the last letters (X-Z, W, V, U, T, S), and elements with oxidation number 0 with the letters N-R. Hydrogen and its isotopes are not considered unless they have the oxidation number -1. If an element occurs in different oxidation numbers in the same compound, different letters must be used. Letters are sorted for ascending indices within one and the same group of letters.
For a defect structure incomplete site occupation is not taken into consideration. But atoms on the same site (i.e. mixed sites) are considered as equal and indicated with the letter of the most common element.
Examples:

Ca₂SiO₄                                   AB2X4

CaSO₄ (H₂O)₂                           ABX6           (sulphate's O and water's O are summarized)

(Na_0.2K_0.8)(AlSi₃)O₈                    AB4X8         (mixed site of Na and K)

NaTl                                         NO              (intermetallic compound, oxidation numbers 0)

H₂O                                         X                 (positive hydrogen is not considered)

CaH₂                                        AX2             (hydrid anions)

Na₂S₂O₃                                   AB2XY3           (S in two different oxidation numbers)

Wyckoff sequence

Determines what sites are occupied by how many atoms. The sequence consists of letters and integer numbers. The letters represent the Wyckoff symbols of the sites, the indices the number of asymmetric atoms on each site. The letters are noted in reverse alphabetic order.

Examples: a⁷ means that only the a site is occupied (by seven asymmetric atoms); f b² a represents one asymmetric atoms on sites f and a each and additionally two atoms on site b.

Pearson symbol (Pearson code)

Defines centering, crystal system, and the sum of the multiplicities of all sites in the atomic parameter list. The first character is a lower case letter defining the crystal system (with a for anorthic = triclinic; trigonal is given as hexagonal). The second character is an upper case letter defining the centering. The multiplicity is given immediately after these two letters.

Formula weight

Diamond distinguishes between two kinds of formula weights:

(1) The formula mass in daltons measured by a non-diffraction experiment. This corresponds to the CIF data name _chemical_formula_weight_meas.

(2) The formula mass calculated by Diamond from the atomic parameter list. This is the sum of the atomic masses of the chemical elements defined in the atomic parameter list regarding multiplicities and site occupation factors, and then divided by the number of formula units (Z). This corresponds to the CIF data name _chemical_formula_weight.

Number of formula units in the unit cell (Z value)

An integer value used to calculate the formula sum from the elements in the atomic parameter list.

Example:

The unit cell of sodium chloride (standard modification) contains 4 Na and 4 Cl atoms. The Z value of 4 is used to get the stoichometric indices of 1 in NaCl (Na4 Cl4 / 4 = NaCl).

Density

Diamond distinguishes between two kinds of densities. Both densities are given in grams per cubic centimeter.

(1) The measured density using standard chemical and physical methods. This value corresponds to the CIF data name _exptl_crystal_density_meas.

(2) The density calculated from the calculated formula weight, the number of formula units (Z) and the cell volume (cvol):

density_calc = fweight_calc * Z / cvol * 1.0 / 0.60225

Residual factor ("R value")

Diamond stores the residual factor for all reflection data as well as the factor for those reflection data classified as "observed". These factors correspond to the CIF data names _refine_ls_R_factor_all and _refine_ls_R_factor_obs rsp. R = S½½Fm½ - ½Fc½½ / S½Fm½, where Fm and Fc are measured and calculated structure factors. This is the conventional R factor.

Comment

Enables the definition of a (maximum 32k long) multiline comment. If the compound has been imported from a crystallographic database, this field may contain data that do not fit the standard data fields of DIAMOND, e.g. PRE 5 GPa; TWI (from ICSD: measured at 5 GPa; twinned crystal).

Atoms, atom codes, atom groups, bonds, bond groups etc.

Atom code

Defines how to create an atom from a specific atom of the parameter list by applying specific symmetry operators, Bravais translations and integer cell translations. The code has the general form AXYZSSB and is similar to the code used in the program ORTEP. A is the number of the atom in the parameter list (the first atom has number 1). SS is the number of the symmetry operation and B the number of the Bravais translation. Both SS and B depend on the space group and can have a maximum of 48 and 4 rsp. X, Y, and Z determine what integer values (minus 5) must be added to the x-, y- and z-coordinates (crystal coordinates). That means no integer cell translations will be applied if XYZ is "555". For "364" e.g. -2 is added to the x-, +1 to the y- and -1 to the z-value.

CIF symmetry code

A code consisting of a single number or of the type "S_XYZ". The single number or the number "S" is the sequence number of the symmetry elements as listed in the _symmetry_equiv_pos_as_xyz loop. "XYZ" are connected integer cell translations along the a, b, and c axes with respect to the base number "555".
Examples:

".": no symmetry operations or translations;

"4": 4^th symmetry operation to be applied;

"7_645": 7^th symmetry operation, +1 in a-, -1 in b-direction, no translation in c-direction.

Dummy atom

A dummy atom is an atom in the parameter list or its symmetry equivalent created atom, which has coordinates but no chemical meaning. It is normally used as a geometric auxiliary point, for example in the center of a cyclopentadienyl ring or the center of a polyhedron.

Connectivity

Describes a list of all N(N+1)/2 combinations of N atom types of a structure. For each atom type pair a bonding sphere is defined and a flag if this bonding sphere is active or not, i.e. whether bonds are allowed for that atom type pair or not.

Structure representation

Standard uncertainties (Standard deviations)

Standard uncertainties may be given in Diamond optionally for cell parameters (lattice constants) and atomic parameters in brackets directly attached (without blanks) to the numerous value, e.g. 0.4386(22) means a value of 0.4386 with a standard uncertainty of 0.0022.

Coordinate systems

DIAMOND distinguishs between three coordinate system:

The crystal coordinate system describes a coordinate system defined by the three basic vectors of the unit cell a, b and c. Thus crystal coordinates (x/a, y/b and z/c) have no dimensions. The corner opposite of the origin (0,0,0) has the coordinates (1,1,1) in any case.

The reference coordinate system describes a rectangular (right-handed) coordinate system with unit length 1 Angstroem. Thus coordinates x, y and z are given in Angstroem in any case. The x-axis runs parallel with the a-axis of the crystal coordinate system, y lies in the ab-plane (and is parallel with b if the angle g has 90°), and z points to the viewer.

The view coordinate system is rectangular and right-handed like the reference coordinate system. But the axes x, y and z are fixed independent of the current orientation of the structure. Thus the x-axis points to the right, the y-axis to top and the z-axis to the viewer.

Auto color

This color is white in normal mode (where the background color is usually rather dark). In black-on-white mode it is black, instead.

Black-on-white mode

In black-on-white mode, the background is painted or remains white. The background color will be ignored. The color "Automatic" is black.

Model

Usually a crystal structure will be represented in the ball-and-stick model with atoms as spheres and bonds as thin lines or tubes.

The ellipsoid model is a variant of the ball-and-stick model where the atoms are not drawn as spheres but as ellipsoids - provided that anisotropic displacement parameters are given for the corresponding atom sites. The bonds are drawn like in ball-and-stick-model.

The wire model displays only the bonds as thin lines with the colors of the bonded atoms in parts. Non-bonded atoms are displayed as dots.

The space-filling model displays only atoms (and cell edges) but no bonds. The radii of the spheres representing atoms are taken from the van der Waals radii.

User interface

Session

A Diamond session begins with the start of the program and ends with the closing of the application.

Panes

The Diamond document window consists of different parts, called "panes", the main pane, which displays the structure picture (or an overview of thumbnail pictures), and a secondary pane on the right that displays textual information such as the data sheet, the list of distances and angles, or several lists (tables) for objects (atoms, bonds, etc.). The main pane is often called "graphics pane", the secondary pane often "data pane". The data pane usually has an additional "Properties view" below the actual data sheet or list showing details of the object (atom. bond, etc.) that is marked in the table above or that is marked in the structure picture.

List with extended selection

Enables the independent selection of multiple entries of a list. You may mark successive entries by moving the mouse cursor with left mouse button down vertically through the list. Or use the keys Cursor up or Cursor down with the Shift key pressed down. If you press the Ctrl key and click an entry with the mouse, this entry will be marked on or off independent of the other entries.

Color select box

A special kind of combobox where you can select from pre-defined colors, including the Auto color, store user-defined colors as well can request a new color. To define a new color, scroll down to the bottom of the color select box, which will automatically open the MS Windows standard dialog to define a new color or select a color from existing colors.