Zeo++ - High throughput analysis of crystalline porous mateirals

Structure files

The structure of a to-be-analyzed material has to be provided in one of Zeo++ compatible file format: CSSR, CUC, V1, CIF, CAR, DLP and PDB. Additional requirement for the formats is that the structure file contains the complete unit cell (P1 symmetry). Therefore, any structure represented by an assymetric unit and symmetry information has to be extended to P1 symmetry (i.e. the unit cell needs to be constructed) before it can be processed with Zeo++. CIF files can contain either the entire unit cell with all atoms or an asymmetric unit with symmetric information. In the current version the latter has to be specified in terms of a list of symmetry operations in order to have Zeo++ build the full unit cell.
Moreover Zeo++ can also read structures from MOPAC's .arc output files.

Discussed file formats: CSSR | CUC | V1 | CIF | ARC and others.

CSSR file format

CSSR format is a file format used by many molecular simulation packages and therefore it was adopted in Zeo++. A CSSR file contains unit cell definition and a list of atoms with their fractional coordinates.

First line contains unit cell dimentions, lengths of a, b and c
Second line contains unit cell angels and symmetry information (currently ignored)
Third line contains number of atoms followed by "0"
Fourth line starts with 0 followed by structure name
Fifth and the following lines contain ID, atom type, three fractional coordinates 
        and other 9 numbers (currently ignored)

An example of CSSR file for IZA's EDI zeolite is provided below:

                                  6.926  6.926  6.41
                   90   90   90   SPGR =  1 P 1         OPT = 1
15   0
0 EDI       : EDI
  1 O  0.189800  0.000000  0.355000  0  0  0  0  0  0  0  0  0.00
  2 O  0.000000  0.810200  0.645000  0  0  0  0  0  0  0  0  0.00
  3 O  0.000000  0.189800  0.645000  0  0  0  0  0  0  0  0  0.00
  4 O  0.810200  0.000000  0.355000  0  0  0  0  0  0  0  0  0.00
  5 O  0.189700  0.189700  0.000000  0  0  0  0  0  0  0  0  0.00
  6 O  0.189700  0.810300  0.000000  0  0  0  0  0  0  0  0  0.00
  7 O  0.810300  0.189700  0.000000  0  0  0  0  0  0  0  0  0.00
  8 O  0.810300  0.810300  0.000000  0  0  0  0  0  0  0  0  0.00
  9 O  0.500000  0.000000  0.118300  0  0  0  0  0  0  0  0  0.00
  10 O  0.000000  0.500000  0.881700  0  0  0  0  0  0  0  0  0.00
  11 Si  0.267900  0.000000  0.118400  0  0  0  0  0  0  0  0  0.00
  12 Si  0.000000  0.732100  0.881600  0  0  0  0  0  0  0  0  0.00
  13 Si  0.000000  0.267900  0.881600  0  0  0  0  0  0  0  0  0.00
  14 Si  0.732100  0.000000  0.118400  0  0  0  0  0  0  0  0  0.00
  15 Si  0.000000  0.000000  0.500000  0  0  0  0  0  0  0  0  0.00

We also noticed that CSSR files generated by Open Babel have slightly different format. In order to read those into Zeo++, please change their names to .obcssr before running Zeo++.

CUC file format (subject to change)

CUC is a custom format introduced on the course of development of Zeo++. It contains the same information as the CSSR format but it has a simpler format. The first line is a comment/title line. The second line contains periodic unit cell information: lengths of a, b and c vectors and three unit cell angels. The third and following lines specify atoms and their fractional coordinates.

An example of CUC file for IZA's EDI zeolite is provided below:

Processing: EDI.cm
Unit_cell:   6.926   6.926   6.41   90   90   90
O   0.1898   0.0   0.35499999999999998
O   0.0   0.81020000000000003   0.64500000000000002
O   0.0   0.1898   0.64500000000000002
O   0.81020000000000003   0.0   0.35499999999999998
O   0.18970000000000001   0.18970000000000001   0.0
O   0.18970000000000001   0.81030000000000002   0.0
O   0.81030000000000002   0.18970000000000001   0.0
O   0.81030000000000002   0.81030000000000002   0.0
O   0.5   0.0   0.1183
O   0.0   0.5   0.88170000000000004
Si   0.26790000000000003   0.0   0.11840000000000001
Si   0.0   0.73209999999999997   0.88159999999999994
Si   0.0   0.26790000000000003   0.88159999999999994
Si   0.73209999999999997   0.0   0.11840000000000001
Si   0.0   0.0   0.5

V1 file format

V1 is a custom format introducted on the course of development of Zeo++. It contains periodic unit cell definition and a list of atoms. The unit cell is defined using three vectors. It is required that y and z coordinates of the first vectors as well as z coordinate of the third vector are set to zero (vectors alligned with axis of the coordinate system). The unit cell definition is followed by an integer - a number of atoms, and then a list of atoms with their Cartesian coordinates.

An example of v1 file for IZA's EDI zeolite is provided below:

Unit cell vectors:
va= 6.926 0 0
vb= 0 6.926 0
vc= 0 0 6.41
15
O 1.3145548 0 2.27555
O 0 5.6114452 4.13445
O 0 1.3145548 4.13445
O 5.6114452 0 2.27555
O 1.3138622 1.3138622 0
O 1.3138622 5.6121378 0
O 5.6121378 1.3138622 0
O 5.6121378 5.6121378 0
O 3.463 0 0.758303
O 0 3.463 5.651697
Si 1.8554754 0 0.758944
Si 0 5.0705246 5.651056
Si 0 1.8554754 5.651056
Si 5.0705246 0 0.758944
Si 0 0 3.205

CIF file format

CIF file format is a common format for storing crystal structure information (esp. experimental data). The CIF file reader in Zeo++ is under development: it can handle most of the files but occassionally fails on misformetted CIFs. Please contact us if it happens. Alternatively, other codes (e.g. CCTBX) can be used for converting your files into CSSR or other formats handled by Zeo++.

An example of cif file for IZA's EDI zeolite.

ARC and others

The recent versions of semiempirical electronic structure code, MOPAC, can handle periodic systems. It makes it suitable to investigate porous polymers, structure of which can be also analyzed using Zeo++.

Other files formats such as .dlp, .car, .pdb can be also read by Zeo++. However, we noticed some variations in these and sometime the source code needs to be altered a bit to process a particular file.