CRYSTAL geometry input

 


Overview and goals

Description of the geometry input section and the main optional keywords to edit the crystalline structure is presented. We primarily focus on systems with 3D periodicity: for 2D, 1D and 0D geometry refer to the CRYSTAL06 User's Manual. Note, however, that most of the 3D structures editing facilities can be applied to systems with lower periodicity.

Special attention will be given on how you can extract structural information from crystallographic databases and literature papers. Refer to CRYSTAL06 User's Manual for complete description of the geometry input section and related keywords. We will treat the simple case of MgO, introduces the main features of the geometry input for a very simple inorganic system. Standard input and geometry editing keywords will be discussed.

 

Geometry input is read and processed by the program crystal.

The keyword TESTGEOM stops the run after reading the geometry input block and processing the data. It is inserted in all geometry input examples. It is useful to check crystal structures.

A simple case: MgO

MgO crystallizes in a cubic cell with a rock-salt structure. The crystal structure can be described as a fcc lattice of Mg ions with O ions occupying all the octahedral holes or vice versa. The rock-salt structure is the most common for MX compounds. gO is an important oxidic system in minerals, in defective systems as well as in adsorption phenomena. Therefore, despite its simplicity, MgO has been the subject of many research studies. Thus, it represents a good example to show how geometry editing options can be used with CRYSTAL06.

Let us start from the crystallographic information you find on the ICSD database. Here is the output from an entry for MgO in the ICSD database.

COL ICSD Collection Code 9863
DATE Recorded Jan 1, 1980; updated Jan 19, 1999
NAME Magnesium oxide
MINR Periclase
FORM Mg O
= Mg O
TITL X-ray determination of electron-density distributions in oxides,
Mg O, Mn O, Co O, and Ni O, and atomic scattering factors of their
constituent atoms
REF Proceedings of the Japan Academy
PJACA 55 (1979) 43-48
AUT Sasaki S, FujinoK, TakeuchiY
SYM x, y, z y, z, x z, x, y
x, z, y y, x, z z, y, x
x, -y, -z y, -z, -x z, -x, -y
x, -z, -y y, -x, -z z, -y, -x
-x, y, -z -y, z, -x -z, x, -y
-x, z, -y -y, x, -z -z, y, -x
-x, -y, z -y, -z, x -z, -x, y
-x, -z, y -y, -x, z -z, -y, x
-x, -y, -z -y, -z, -x -z, -x, -y
-x, -z, -y -y, -x, -z -z, -y, -x
-x, y, z -y, z, x -z, x, y
-x, z, y -y, x, z -z, y, x
x, -y, z y, -z, x z, -x, y
x, -z, y y, -x, z z, -y, x
x, y, -z y, z, -x z, x, -y
x, z, -y y, x, -z z, y, -x
CELL a=4.217(1) b=4.217(1) c=4.217(1) alpha=90.0 beta=90.0 gamma=90.0
V=75.0 D=3.56 Z=4
SGR F m -3 m (225) - cubic
CLAS m-3m (Hermann-Mauguin) - Oh (Schoenflies)
PRS cF8
ANX AX
PARM Atom__No OxStat Wyck -----X----- -----Y----- -----Z----- -SOF-
Mg 1 2.000 4a 0. 0. 0.
O 1 -2.000 4b 0.5 0.5 0.5
WYCK b a
ITF Mg 1 B=0.312
ITF O 1 B=0.362
REM M PDF 43-1022
RVAL 0.013

The information you need to define the crystal structure is highlighted. Basically, the crystal structure is determined by the space group, by the shape and size of the unit cell and by the relative position of the atoms in the asymmetric unit.

MgO geometry input, derived from ICSD data, will be prepared and discussed, line by line.

1. Title section

MgO bulk: crystal structure from ICSD

The first line contains the title section. It can be useful to indicate the system in study and other relevant information about the job. The title section is printed in the output file, but it is not otherwise used by CRYSTAL.

2. Dimensionality of the system

CRYSTAL

The first record of the geometry definition must specify the dimensionality of the system. CRYSTAL adopts four keywords: CRYSTAL, SLAB, POLYMER and MOLECULE, for 3D, 2D, 1D and 0D systems, respectively. In this case the keyword to specify is CRYSTAL.

The keyword EXTERNAL allows geometry input from external file (see CRYSTAL User's Manual for further details).

3. Crystallographic information (for 3D systems only)

0 0 0

three integer numbers:
- convention for the space group identification: sequential number (0) or alphanumeric code (1).

- type of cell for rhombohedral groups: hexagonal (0) or rhombohedral (1).
- setting of the origin (see CRYSTAL User's Manual for further details).

4. Space group

225

It can be indicated either with its sequential number (0), as in this case, or by the Hermann-Mauguin alphanumeric code (1). In the ICSD file you can find both of them.

So, till now, the input file would look something like this:
MgO bulk: crystal structure from ICSD
CRYSTAL
0 0 0
225
MgO bulk: crystal structure from ICSD
CRYSTAL
1 0 0
F M 3 M

according to the sequential number (on the left) or the alphanumeric code (on the right).
Note: CRYSTAL adopts F M 3 M instead of F M -3 M for compatibility with a previous edition of the International Tables for Crystallography (see CRYSTAL User's Manual for further details).

5. Lattice parameters

4.21

The minimal set of crystallographic cell parameters is indicated (in Angstrom and degrees). For MgO, cubic system, the length of the edge of the cell fully defines shape and size of the conventional unit cell (note, however, that CRYSTAL works on the primitive cell).

6. Atomic position specification

2
12 0.0 0.0 0.0
8 0.5 0.5 0.5

The first line gives the number of atoms in the asymmetric unit. One line per atom in the asymmetric unit follows, to specify the conventional atomic number and the coordinates in fractional units of the crystallographic lattice vectors. These atoms are usually indicated as non-equivalent atoms, i.e. atoms not symmetry related. The whole structure of MgO is defined by 2 atoms.

7. Closing the geometry input section

END

This keyword ends the geometry input section. Before ending the section, you may specify optional keywords to modify the structure.

The completed input file looks like:
MgO bulk
CRYSTAL
0 0 0
225
4.21
2
12 0.0 0.0 0.0
8 0.5 0.5 0.5
1. Title of the job
2. Dimensionality of the system
3. Crystallographic information (3D only)
4. Space Group number
5. Lattice parameters
6. Number of atoms in asymmetric unit
Atomic position specification in fractionary coordinates
TESTGEOM Optional keyword to stop execution after geometry input
END 7. end of the geometry input section

Exercise:

Create a file mgo.d12 and type the geometry input above. Visualize the structure with XCrySDen

When running CRYSTAL with the previous input for MgO (crystal < mgo.d12) you will get the following output.


 *******************************************************************************
* *
* CRYSTAL06 *
* Release : 1.0 *
* cry06_060822 *
* *
* *
* *
* MAIN AUTHORS *
* *
* R. DOVESI(1), V.R. SAUNDERS(2), C. ROETTI(1), R. ORLANDO (1,3), *
* C.M. ZICOVICH-WILSON(1,4), F. PASCALE(5), B. CIVALLERI(1), K. DOLL(6), *
* N.M. HARRISON(2,7), I. J. BUSH(2), Ph. D'ARCO(8), M. LLUNELL(9) *
* *
* (1) THEORETICAL CHEMISTRY GROUP - UNIVERSITA' DI TORINO - TORINO (ITALY) *
* http://www.crystal.unito.it *
* (2) COMPUTATIONAL SCIENCE & ENGINEERING DEPARTMENT - CCLRC DARESBURY (UK) *
* http://www.cse.clrc.ac.uk/cmg/CRYSTAL/ *
* (3) UNIVERSITA' DEL PIEMONTE ORIENTALE - ALESSANDRIA (ITALY) *
* (4) UNIVERSIDAD AUTONOMA DEL ESTADO DE MORELOS - CUERNAVACA (MEXICO) *
* (5) UNIVERSITE' HENRI POINCARE' - NANCY (FRANCE) *
* (6) TU BRAUNSCHWEIG - BRAUNSCHWEIG (GERMANY) *
* (7) IMPERIAL COLLEGE - LONDON (UK) *
* (8) UNIVERSITE' PIERRE ET MARIE CURIE - PARIS (FRANCE) *
* (9) UNIVERSIDAD DE BARCELONA - BARCELONA (SPAIN) *
*******************************************************************************
EEEEEEEEEE STARTING DATE 26 08 2006 TIME 22:28:47.0
TEST11 - MGO BULK

The header of CRYSTAL reports the CRYSTAL version and the main authors of the code.
The title section from the input file follows.

CRYSTAL CALCULATION
(INPUT ACCORDING TO THE INTERNATIONAL TABLES FOR X-RAY CRYSTALLOGRAPHY)
CRYSTAL FAMILY : CUBIC
CRYSTAL CLASS (GROTH - 1921) : CUBIC HEXAKISOCTAHEDRAL

SPACE GROUP (CENTROSYMMETRIC) : F M 3 M

Summary of the crystallographic information. The periodicity of the system is indicated.
LATTICE PARAMETERS (ANGSTROMS AND DEGREES) - CONVENTIONAL CELL
A B C ALPHA BETA GAMMA
4.21000 4.21000 4.21000 90.00000 90.00000 90.00000

NUMBER OF IRREDUCIBLE ATOMS IN THE CONVENTIONAL CELL: 2

INPUT COORDINATES

ATOM AT. N. COORDINATES
1 12 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
2 8 5.000000000000E-01 5.000000000000E-01 5.000000000000E-01

The lattice parameters of the conventional cell and the atomic position of the atoms in the asymmetric unit, as given in input, are reported.
 *******************************************************************************

<< INFORMATION >>: FROM NOW ON, ALL COORDINATES REFER TO THE PRIMITIVE CELL

*******************************************************************************
 LATTICE PARAMETERS (ANGSTROMS AND DEGREES) - PRIMITIVE CELL
A B C ALPHA BETA GAMMA VOLUME
2.97692 2.97692 2.97692 60.0000 60.0000 60.0000 18.65462

COORDINATES OF THE EQUIVALENT ATOMS (FRACTIONARY UNITS)

N. ATOM EQUIV AT. N. X Y Z

1 1 1 12 MG 0.00000000000E+00 0.00000000000E+00 0.00000000000E+00

2 2 1 8 O -5.00000000000E-01 -5.00000000000E-01 -5.00000000000E-01

NUMBER OF SYMMETRY OPERATORS : 48

The crystallographic or conventional cell is used as standard option in input. It may be non-primitive, which means that it may not coincide with the cell of minimum volume (primitive cell) which contains just one lattice point. Note that, for maximum calculation efficiency, CRYSTAL works on the primitive cell. Hence, the conventional cell is transformed into the primitive cell (1/4 of the conventional cell), all the following structural information are referred to the primitive cell.

In the output file, the lattice parameters of the primitive cell and the corresponding atomic positions (in fractionary units) are reported. In this section, all the atoms in the primitive cell are displayed and indicated as equivalent atoms. For each non-equivalent atom the corresponding block of equivalent atoms is reported. For MgO two atoms only build up the primitive cell, as they are in special positions.

 

In figure, the conventional cell and the primitive cell, enclosed in the conventional cell, of MgO are shown:

CONVENTIONAL CELL PRIMITIVE CELL

With the following banner ends the standard CRYSTAL geometry output. After that, the output file continues with the geometry output section relative to the optional keywords.
*******************************************************************************
* GEOMETRY MANIPULATION - INPUT COORDINATES ARE GIVEN IN ANGSTROM
*******************************************************************************

Creating a super cell

The keyword SUPERCEL allows generation of a super cell by transformation of the lattice vectors of the primitive cell.

A super cell is obtained by defining the new unit cell vectors as linear combination of the primitive cell unit vectors. The new translation vectors b1', b2', b3' are defined in terms of the old vectors b1, b2, b3 and of the transformation matrix, E, read in input by rows, as follows:

b1' = e11 b1 + e12b2 + e13 b3
b2' = e21 b1 + e22b2 + e23 b3
b3' = e31 b1 + e32b2 + e33 b3

The symmetry is automatically reduced to the point symmetry operators without translational components and a further reduction of the symmetry is also possible. A shift of the origin to minimize the number of symmetry operators with translational component is automatically performed by crystal.

Note: super cells can be generated for 2D and 1D systems as well. In that case, the number of matrix elements decrease from 9 to 4 and to 1, respectively.

For instance, the MgO primitive cell can be transformed in the crystallographic one by the following matrix:
-1.000 1.000 1.000
1.000 -1.000 1.000
1.000 1.000 -1.000

This corresponds to defining a quadruple cell.

Here is reported the corresponding CRYSTAL geometry input:
MGO BULK super cell 8 atoms
CRYSTAL
0 0 0
225
4.21
2
12 0.0 0.0 0.0
8 0.5 0.5 0.5

Standard geometry input

SUPERCEL
-1.0 1.0 1.0
1.0 -1.0 1.0
1.0 1.0 -1.0
Keyword for generating the super cell

Input of the transformation matrix elements

TESTGEOM
END
Stop execution after geometry step
End of the geometry input section

Insert the highlighted lines in your MgO input file (mgo.d12), visualize the structure with XCrySDen and run CRYSTAL (crystal < mgo.d12).
Looking at the output file you will find the following section:
 *******************************************************************************
* SUPERCELL OPTION
*******************************************************************************


EXPANSION MATRIX OF PRIMITIVE CELL
E1 -1.000 1.000 1.000
E2 1.000 -1.000 1.000
E3 1.000 1.000 -1.000

NUMBER OF ATOMS PER SUPERCELL 8

DIRECT LATTICE VECTORS COMPONENTS (ANGSTROM)
B1 4.210 0.000 0.000
B2 0.000 4.210 0.000
B3 0.000 0.000 4.210

LATTICE PARAMETERS (ANGSTROM AND DEGREES)
A B C ALPHA BETA GAMMA VOLUME
4.21000 4.21000 4.21000 90.0000 90.0000 90.0000 74.61846


**** ATOMS BELONGING TO THE SUPERCELL
LABEL AT.NO. COORDINATES (ANGSTROM AND FRACTIONARY)
1 12 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
2 12 2.1050 2.1050 0.0000 0.5000 0.5000 0.0000
3 12 2.1050 0.0000 2.1050 0.5000 0.0000 0.5000
4 12 0.0000 2.1050 2.1050 0.0000 0.5000 0.5000
5 8 0.0000 0.0000 2.1050 0.0000 0.0000 0.5000
6 8 2.1050 2.1050 2.1050 0.5000 0.5000 0.5000
7 8 2.1050 0.0000 0.0000 0.5000 0.0000 0.0000
8 8 0.0000 2.1050 0.0000 0.0000 0.5000 0.0000

**************************** SUPERCELL GENERATED ****************************

The expansion matrix, given in input, the new lattice vectors components and lattice parameters, and the labels, atomic number, coordinates of the 8 atoms in the supercell are reported.

Atom label is the sequence number of the atom in the cell. In any geometry editing atoms are identified by their "label".

The new cell parameters correspond to the crystallographic lattice parameters. The new cell contains four MgO formula units.
 

Symmetry and geometry editing

When a geometry editing (removal, insertion, substitution, displacement of atoms) modifies a site of the structure, the program can maintain or modify (reduce) the number of symmetry operators. Two keywords control the symmetry:

KEEPSYMM: In any subsequent editing of the geometry, the program will endeavour to maintain the number of symmetry operators. The symmetry operators are applied to the "perturbation", and if the multiplicity of the site is greater than 1, the perturbation will be multiplied by application of the symmetry operators.

BREAKSYMM [default]: subsequent modification of the geometry are allowed to alter (reduce: the number of symmetry operators can not be reduced) the point group symmetry. The new group is a subgroup of the original group and it is automatically obtained by crystal

The keyword SYMMREMO removes all point symmetry operators.

See keyword MODISYMM (input block 2, "Basis set", CRYSTAL03 User's Manual) for removal of selected symmetry operators.

The keyword ATOMSYMM prints the point group associated with each atomic position and the set of symmetry related atoms.

The keyword SYMMDIR prints the symmetry allowed directions, corresponding to the internal degrees of freedom (to obtain printing full crystal input must be submitted, block 1 2 3 4, with keyword TESTPDIM in block 3 - See CRYSTAL03 User's Manual)

MgO primitive cell - 48 symmetry operators:

 ATOM 1 ATOMIC NUMBER 12 - NUMBER OF SYMMOPS WHICH DO NOT MOVE THE ATOM 48
NO EQUIVALENT ATOMS
ATOM 2 ATOMIC NUMBER 8 - NUMBER OF SYMMOPS WHICH DO NOT MOVE THE ATOM 48
NO EQUIVALENT ATOMS

THERE ARE NO SYMMETRY ALLOWED DIRECTIONS

MgO 16 atoms super cell
- 48 symmetry operators.
Translational symmetry is not recognized within the super cell.

 *******************************************************************************
ATOMS IN THE ASYMMETRIC UNIT 5 - ATOMS IN THE UNIT CELL: 16
ATOM X/A Y/B Z/C
*******************************************************************************
1 T 12 MG 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
2 T 12 MG -1.704907916233E-17 1.704907916233E-17 -5.000000000000E-01
3 F 12 MG -1.704907916233E-17 -5.000000000000E-01 1.704907916233E-17
4 F 12 MG 7.692414413785E-17 -5.000000000000E-01 -5.000000000000E-01
5 F 12 MG -5.000000000000E-01 -1.704907916233E-17 1.704907916233E-17
6 F 12 MG -5.000000000000E-01 7.272286071947E-17 -5.000000000000E-01
7 F 12 MG -5.000000000000E-01 -5.000000000000E-01 -1.085557425201E-17
8 T 12 MG 5.000000000000E-01 -5.000000000000E-01 -5.000000000000E-01
9 T 8 O -2.500000000000E-01 -2.500000000000E-01 2.500000000000E-01
10 T 8 O -2.500000000000E-01 -2.500000000000E-01 -2.500000000000E-01
11 F 8 O -2.500000000000E-01 2.500000000000E-01 2.500000000000E-01
12 F 8 O -2.500000000000E-01 2.500000000000E-01 -2.500000000000E-01
13 F 8 O 2.500000000000E-01 -2.500000000000E-01 2.500000000000E-01
14 F 8 O 2.500000000000E-01 -2.500000000000E-01 -2.500000000000E-01

15 F 8 O 2.500000000000E-01 2.500000000000E-01 2.500000000000E-01
16 F 8 O 2.500000000000E-01 2.500000000000E-01 -2.500000000000E-01

T = ATOM BELONGING TO THE ASYMMETRIC UNIT
 ATOM 1 ATOMIC NUMBER 12 - NUMBER OF SYMMOPS WHICH DO NOT MOVE THE ATOM 48
NO EQUIVALENT ATOMS

ATOM 2 ATOMIC NUMBER 12 - NUMBER OF SYMMOPS WHICH DO NOT MOVE THE ATOM 8
NUMBER OF ATOMS EQUIVALENT BY SYMMETRY 5
SEQUENCE NUMBERS OF THESE ATOMS 7 5 3 4 6

ATOM 3 ATOMIC NUMBER 12 - NUMBER OF SYMMOPS WHICH DO NOT MOVE THE ATOM 8
NUMBER OF ATOMS EQUIVALENT BY SYMMETRY 5
SEQUENCE NUMBERS OF THESE ATOMS 6 2 5 4 7

. . . . . . . . . . . . . .

ATOM 8 ATOMIC NUMBER 12 - NUMBER OF SYMMOPS WHICH DO NOT MOVE THE ATOM 48
NO EQUIVALENT ATOMS

ATOM 9 ATOMIC NUMBER 8 - NUMBER OF SYMMOPS WHICH DO NOT MOVE THE ATOM 8
NUMBER OF ATOMS EQUIVALENT BY SYMMETRY 5
SEQUENCE NUMBERS OF THESE ATOMS 16 14 12 11 13

ATOM 10 ATOMIC NUMBER 8 - NUMBER OF SYMMOPS WHICH DO NOT MOVE THE ATOM 24
NUMBER OF ATOMS EQUIVALENT BY SYMMETRY 1
SEQUENCE NUMBERS OF THESE ATOMS 15
. . . . . . . . . . . . .

SYMMETRY ALLOWED INTERNAL DEGREE(S) OF FREEDOM: 1

SYMMETRY ALLOWED DIRECTION 1 ATOM 9 (Z= 8)
0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
0.0000000 0.0000000 0.4082483 0.0000000 0.0000000 0.0000000
-0.4082483 0.0000000 0.0000000 0.0000000 0.4082483 0.0000000
0.0000000 -0.4082483 0.0000000 0.4082483 0.0000000 0.0000000
0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 -0.4082483

Substitution of atoms

A simple example of a defective systems are substitutional defects. For instance, CRYSTAL has been used to study the energy of formation of a Ca defect in MgO: C. Freyria-Fava, R. Dovesi, V.R. Saunders, M. Leslie and C. Roetti, ``Ca and Be substitution in bulk MgO: ab initio Hartree-Fock and ionic model supercell calculation'', J. Phys.: Cond. Matter 5, 4793-4804 (1993).

For this purpose a 16 atoms super cell of MgO was adopted. Here is reported the corresponding geometry input section:
SUPERCEL
2. 0. 0.
0. 2. 0.
0. 0. 2.
Keyword for generating the super cell

Input of the expansion matrix elements

ATOMSYMM
ATOMSUBS

1
1 20
Keyword for analyzing the site symmetry
Keyword for substituting atoms

Number of atoms to be substituted
Label of the atom to substitute, atomic number of the new atom
END End of the geometry input section

The keyword ATOMSUBS allows substitution of selected atoms in the cell, as defined when the keyword is entered. The total number of atoms to be substituted and, for each atom, the corresponding label and the new atomic number must be indicated.

Insert the lines shown above in your MgO input file and run CRYSTAL.
 *******************************************************************************
* SUBSTITUTION OF 1 ATOM(S)
*******************************************************************************
ATOM N. 1 MG (Z= 12) SUBSTITUTED WITH CA (Z= 20)

In the output file the section above is displayed. Note: ATOM N. stands for atom number.

So, the procedure to define a substitutional defect is:

 

Another example of defective systems are vacancies. One of them is the so-called trapped-electron-hole centre. In such centres there are very often charge compensating impurities, e.g. a H atom. In MgO, this kind of defects are denoted as MgO:[H]0. The H atom formally substitutes a Mg atom at its lattice position and migrates towards one of the neighbouring O atoms, forming a strong covalent bond with it. The hole localizes at the opposite O atom completely. This defective system has been the subject of a recent paper.

In order to create the final defective structure the initial MgO primitive cell have to be modified with a series of geometry keywords. The new part of the input file looks something like:
SUPERCELL
3. -1. -1.
-1. 3. -1.
-1. -1. 3.
Keyword for generating the super cell

Input of the expansion matrix elements

ATOMSUBS
1
1 1
Keyword for substituting atoms
Number of atoms to be substituted
Label of the atom to substitute, atomic number of the new atom
ATOMDISP
3
1 0. 0. 1.131
19 0. 0. -0.005
17 0. 0. -0.100
Keyword for displacing atoms - symmetry reduction allowed (default)
Number of atoms to be displaced
Label of the atoms to displace, displacements in cartesian coordinates (Angstrom)
KEEPSYMM Keyword for maintaining the symmetry in the following manipulations
ATOMDISP
1
21 0.11 0. 0.004

Atom 21
TESTGEOM
END
End of the geometry input section

Insert the new lines in the MgO bulk input, visualize the structure with XCrySDen and run CRYSTAL (crystal < mgo.d12).
 *******************************************************************************
* DISPLACEMENT OF 3 ATOMS
*******************************************************************************

ATOM N. 1 AT. N. 1 DISPLACED BY (A) 0.00000 0.00000 1.13100

ATOM N. 19 AT. N. 8 DISPLACED BY (A) 0.00000 0.00000 -0.00500

ATOM N. 17 AT. N. 8 DISPLACED BY (A) 0.00000 0.00000 -0.10000
THE NUMBER OF SYMMETRY OPERATORS HAS BEEN REDUCED FROM 48 TO 8
*******************************************************************************

Note that, in this example, the first atomic displacement has been done allowing a symmetry reduction. Indeed, the number of symmetry operators changes from 16 to 8 (see above). Whereas, after KEEPSYMM, in the second displacement, the current symmetry is maintained and all the atoms related by symmetry are moved (see below).
 *******************************************************************************
* DISPLACEMENT OF 1 ATOMS
*******************************************************************************

ATOM N. 21 AT. N. 8 DISPLACED BY (A) 0.11000 0.00000 0.00400

SYMMETRY MAINTAINED - 21 ATOM(S) SYMMETRY-RELATED : SEQUENCE NUMBER OF ATOM(S)
31 24 32
OLD COORDINATES (FRAC. UNITS) 0.00000 0.25000 0.25000
NEW COORDINATES (FRAC. UNITS) 0.00048 0.26354 0.26306

A 32 atoms super cell has been used as starting perfect cell and the defective center has been created substituting a Mg atom by a H atom. Atoms 17 and 19, Oxygens, are 2 of the six equivalent first neighbors of the atom at the origin. When H is at the origin, H moves towards Oxygen 19, to form an OH group.
ATOMDISP allows displacement of selected atoms in the cell as defined when the keyword is entered. The point symmetry of the system is reduced.

In summary, for this example, a 32 atoms super cell of MgO has been adopted. The Mg atom at the origin is substituted with a hydrogen atom. Some atomic positions are changed in two steps. First, the position of the three atoms involved in the defect center (O-H...O) are displaced, allowing a reduction of the symmetry, then, preserving the symmetry (keyword KEEPSYMM), the neighbor oxygen atoms are relaxed. ATOMDISP is used to relax the atoms of the defect zone, keeping the maximum symmetry compatible with the model of the defect.

Summary of the CRYSTAL geometry input keywords

Here is a summary of the CRYSTAL geometry input keywords. For each keyword a brief explanation is reported as well as whether the keyword requires a specific input.
Refer to CRYSTAL User's Manual for full documentation.
Symmetry information
SYMMOPS printing of point symmetry operators
ATOMSYMM printing of point symmetry at the atomic positions
Symmetry reduction
TRASREMO removal of symmetry operators with translational components
SYMMREMO removal of all symmetry operators
MODISYMM removal of selected symmetry operators
input
Modifications without reduction of symmetry
ATOMORDE reordering of atoms in molecular crystals
ORIGIN shift of the origin to minimize the number of symmetry operators with translational components
PRIMITIV crystallographic cell forced to be the primitive cell
REDEFINE define a new cell with xy parallel to a given plane
input
Symmetry control
BREAKSYM allow symmetry reduction following geometry modifications
KEEPSYMM maintain symmetry following geometry modifications
Atoms and cell manipulation (possible symmetry reduction)
ATOMSUBS substitution of atoms
input
ATOMREMO removal of atoms
input
ATOMINSE addition of atoms
input
ATOMDISP displacement of atoms
input
ATOMROT rotation of groups of atoms
input
SUPERCEL generation of super cell
input
ELASTIC distortion of the lattice
input
From crystals to slabs
SLABCUT generation of a slab parallel to a given plane
input
From periodic structure to clusters
CLUSTER cutting of a cluster from a periodic structure
input
Molecular crystals
MOLECULE extraction of a set of molecules from a molecular crystal
input
MOLSPLIT periodic structure of non interacting molecules
MOLEXP variation of lattice parameters at constant symmetry and molecular geometry
input
BSSE correction
MOLEBSSE counterpoise method for molecules (molecular crystals only)
input
ATOMBSSE counterpoise method for atoms
input
Auxiliary and control keywords
ANGSTROM Set input unit to Angstrom
BOHR Set input unit to bohr
FRACTION Set input unit to fractional
PARAMPRT output of parameters controlling code dimensions
NEIGHBOR number of neighbours in geometry analysis
input
ANGLES bond angles and dihedral angles analysis
input
PRINTOUT setting of printing options
input
RAYCOV modification of covalent radii
input
SETPRINT setting of printing options
input
TESTGEOM stop after checking the geometry input
STOP execution stops immediately
END terminate processing of geometry input
Output of data on external units
COORPRT output of the coordinates of all the atoms in the cell
EXTPRT generation of input file for visualization
MOLDRAW generation of input file for the program MOLDRAW
FINDSYM generation of input file for the program findsym

Note: the NEIGHBOR option requires the full CRYSTAL input.