CRY |
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Synopsis
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[-]cry filename
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Description
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This keyword allows entering the pathname of the disk file that contains crystal data needed to define the atomic positions in the crystal, i.e.:
- cell constants
- either lattice and symmetry specification or space group number (1-230) or symbol
- fractional coordinates of atoms in the asymmetric unit
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Aim
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The "cry" file provides PAMoC with data needed to build up a crystal, i.e. to define the positions of atoms in the crystal. Afterwards, PAMoC will be able to estimate the interaction energy of molecular dimers in the crystal as well as the cohesive energy of the crystal. These data must be provided, for instance, when the interface data file (IDF) is an AIMPAC wavefunction file.
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Syntax rules for keywords and options specification
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Any line beginning with either ! or # is a comment line.
Data are provided in the form of a keyword followed by arguments, as shown in the following Table:
| keyword | arguments | remarks |
| cell | a b c alpha beta gamma | Cell parameters, with lengths in angstrom or 1/angstrom and angles in degrees or cosines of angles. |
| latt | x y | Here, x is either A or C, for Acentric or Centrosymmetric crystal respectively, and y specifies the lattice type as P,I,R,F,A,B,C.
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| sym|symm|symtry |
symmetry operation elements |
The symmetry operation elements are given exactly as in the International Tables, the three general position coordinates being separated either by commas or spaces. More than one position may be given within one sym entry, if desired, by placing a semicolon between each of them.
Alternatively, the symmetry operation is written in a purely numerical way by giving a translation vector and a 3 by 3 rotation matrix, i.e.: tx r11 r12 r13 ty r21 r22 r23 tz r31 r32 r33. |
| spac[e group] | number | symbol |
A space group can be specified either by its International Tables number (1 through 230) or by its symbol. Explicit definition of the space group is an alternative to specify the lattice type (latt) and symmetry operations (sym) separately.
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| coord | [type] [number-of-atoms] |
Here, type specifies the units of the atomic coordinates that will be entered, i.e. fract[ional] (the default), angstrom, bohr, au. Atom coordinates must follow this line, on separate lines, one for each atom. If the number-of-atoms is omitted, coordinate lines will be read until either the end-of-file or an end line is encountered.
Any coordinate line must have either 4 fields, i.e.
IAn X Y Z
Symb X Y Z
or 5 fields, i.e.
Symb IAn X Y Z
IAn Symb X Y Z
Usually, the coordinate section is optional. However it should be present to specify the atoms belonging to the asymmetric unit, when the number of atoms in the asymmetric unit is not equal to the number of atoms in the molecule. |
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Example 1
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The input files:
!urea crystal
CELL 5.5840 5.5840 4.6890 90.0000 90.0000 90.0000
LATT A P
SYM X,Y,Z
SYM -X,-Y,Z
SYM 1/2+X,1/2-Y,-Z
SYM 1/2-X,1/2+Y,-Z
SYM 1/2+Y,1/2+X,Z
SYM 1/2-Y,1/2-X,Z
SYM Y,-X,-Z
SYM -Y,X,-Z
COORD
6 .0000 .5000 .3280
8 .0000 .5000 .5962
7 .1447 .6447 .1785
1 .2557 .7557 .2841
1 .1431 .6431 -.0348
END
and:
!urea crystal
CELL 5.5840 5.5840 4.6890 90.0000 90.0000 90.0000
LATT A P
SYM -X,-Y,Z; 1/2+X,1/2-Y,-Z; 1/2-X,1/2+Y,-Z; 1/2+Y,1/2+X,Z; 1/2-Y,1/2-X,Z; Y,-X,-Z; -Y,X,-Z
COORD
6 .0000 .5000 .3280
8 .0000 .5000 .5962
7 .1447 .6447 .1785
1 .2557 .7557 .2841
1 .1431 .6431 -.0348
END
produce the following image on the output file:
*******************************************************************************
PAMOC Version 30.01.2008 PAMOC
Properties of Atoms and Molecules (in Molecular Crystals)
M.Barzaghi@istm.cnr.it www.istm.cnr.it/~barz/pamoc
*******************************************************************************
Direct Cell Parameters
a b c alpha beta gamma
5.5840 5.5840 4.6890 90.000 90.000 90.000
cosin 0.000000 0.000000 0.000000
Volume = 146.2080
Reciprocal Cell Parameters
a* b* c* alpha* beta* gamma*
0.179083 0.179083 0.213265 90.000 90.000 90.000
cosin 0.000000 0.000000 0.000000
Volume = 0.006840
Symmetry information: the crystal is non-centrosymmetric, lattice type P ( 1)
Symmetry:
SYMTRY X, Y, Z
SYMTRY -X, -Y, Z
SYMTRY 1/2+X, 1/2-Y, -Z
SYMTRY 1/2-X, 1/2+Y, -Z
SYMTRY 1/2+Y, 1/2+X, Z
SYMTRY 1/2-Y, 1/2-X, Z
SYMTRY Y, -X, -Z
SYMTRY -Y, X, -Z
FRACTIONAL COORDINATES OF ATOMS
1) C 6 0.0000 0.5000 0.3280
2) O 8 0.0000 0.5000 0.5962
3) N 7 0.1447 0.6447 0.1785
4) H 1 0.2557 0.7557 0.2841
5) H 1 0.1431 0.6431 -0.0348
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Example 2
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The input files:
!urea crystal
CELL 5.5840 5.5840 4.6890 90.0000 90.0000 90.0000
SPAC 113
COORD
6 .0000 .5000 .3280
8 .0000 .5000 .5962
7 .1447 .6447 .1785
1 .2557 .7557 .2841
1 .1431 .6431 -.0348
END
and:
!urea crystal
CELL 5.5840 5.5840 4.6890 90.0000 90.0000 90.0000
SPACE GROUP P -4 21 M
COORD
6 .0000 .5000 .3280
8 .0000 .5000 .5962
7 .1447 .6447 .1785
1 .2557 .7557 .2841
1 .1431 .6431 -.0348
END
have the following image on the output file:
*******************************************************************************
PAMOC Version 30.01.2008 PAMOC
Properties of Atoms and Molecules (in Molecular Crystals)
M.Barzaghi@istm.cnr.it www.istm.cnr.it/~barz/pamoc
*******************************************************************************
Direct Cell Parameters
a b c alpha beta gamma
5.5840 5.5840 4.6890 90.000 90.000 90.000
cosin 0.000000 0.000000 0.000000
Volume = 146.2080
Reciprocal Cell Parameters
a* b* c* alpha* beta* gamma*
0.179083 0.179083 0.213265 90.000 90.000 90.000
cosin 0.000000 0.000000 0.000000
Volume = 0.006840
International Tables number 113 - Space Group P -4 21 M TETRAGONAL
Noncentrosymmetric
---------------------------------------------------------------
Fractional Rotation matrices Translation vectors
---------------------------------------------------------------
1 1.000 0.000 0.000 0.000
0.000 1.000 0.000 0.000
0.000 0.000 1.000 0.000
2 -1.000 0.000 0.000 0.000
0.000 -1.000 0.000 0.000
0.000 0.000 1.000 0.000
3 1.000 0.000 0.000 0.500
0.000 -1.000 0.000 0.500
0.000 0.000 -1.000 0.000
4 -1.000 0.000 0.000 0.500
0.000 1.000 0.000 0.500
0.000 0.000 -1.000 0.000
5 0.000 1.000 0.000 0.500
1.000 0.000 0.000 0.500
0.000 0.000 1.000 0.000
6 0.000 -1.000 0.000 0.500
-1.000 0.000 0.000 0.500
0.000 0.000 1.000 0.000
7 0.000 -1.000 0.000 0.000
1.000 0.000 0.000 0.000
0.000 0.000 -1.000 0.000
8 0.000 1.000 0.000 0.000
-1.000 0.000 0.000 0.000
0.000 0.000 -1.000 0.000
FRACTIONAL COORDINATES OF ATOMS
1) C 6 0.0000 0.5000 0.3280
2) O 8 0.0000 0.5000 0.5962
3) N 7 0.1447 0.6447 0.1785
4) H 1 0.2557 0.7557 0.2841
5) H 1 0.1431 0.6431 -0.0348
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