This keyword defines the pathname of a disk file that contains the crystal data needed to define the atomic positions in the crystal.
Data input follows the rules specified in Chapter “Data Input”. In particular, any line beginning with either ! or # is a comment line, and data are provided in the form of a keyword followed by arguments. The following data types are usually required:
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.
The following two inputs define the crystal by specifying the lattice type and the symmetry operations. They differ from each other only in the syntax used to insert the symmetry operations.
!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
!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
Both produce the same print output:
”.
In particular, any line beginning with either ! or # is a comment line, and
data are provided in the form of a keyword followed by
arguments. The following data types are usually required:
*******************************************************************************
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
The following two inputs define the crystal by specifying the space group. In the first input the space group is indicated by its number and in the second input it is specified by its symbol.
!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
!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
Both produce the same print output:
*******************************************************************************
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