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zeoTsites version 1.2
Copyright (C) 2000-2001
by
German Sastre (1) and Julian D. Gale (2)
(1) Instituto de Tecnologia Quimica. gsastre@itq.upv.es
(2) Imperial College. j.gale@ic.ac.uk
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1. COPYRIGHT
zeoTsites is available free of charge to academic and research institutions
and non-commercial establishments only. Copies should be obtained from the
authors only and should not be distributed in any form by the user to a third
party without the express permission of the authors.
No claim is made that this program is free from errors and no liability will
be accepted for any loss or damage that may result. The users are responsible
for checking the validity of their results.
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2. WHAT IS zeoTsites FOR ?
zeoTsites is a program for calculating T-atom connectivity, vertex symbols,
and geometry analysis in zeolites, zeotypes, and other silicates
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3. UNIX INSTALLATION
(i) untar the original file zeots-1.2.tar by typing:
'tar xvf zeots-1.2.tar'
(ii) type: 'make'
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4. HOW TO USE THE PROGRAM ?
(i) execute by typing: './zeots'
(ii) you will then be prompted twice:
- "What is the zeotype ?"
you have to provide a name (no more than 20 characters) which will be
appended to the output files
- "Input file ?"
just give the complete name of the input file (.xtl format)
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5. INPUT AND OUTPUT FILES
zeoTsites is provided with some sample input files (in .xtl format),
and it produces 4 output files:
- "Connecty_of_filename"
this contains the coordination sequence of each T-atom in the unit
cell (up to the 13th shell), and it classifies each topologically
distinct atom with a number (in the column labelled "T-type")
then the vertex symbol of each T-atom is printed. For 4-connected
atoms, this consists of 6 symbols corresponding to the rings found
in the: O1-T-O2, O1-T-O3, O1-T-O4, O2-T-O3, O2-T-O4, O3-T-O4
directions. Each index indicates the number of T atoms in the ring,
and the sub-index indicates the number of them. The vertex symbols
are ordered (for 4-connected atoms) according to: ring size,
opposite angles, and ring multiplicity. Opposite angles are defined
(for 4-connected atoms) as: 1-4 and 2-3; 1-3 and 2-4; 1-2 and 3-4.
For connectivities other than 4, the opposite angle criterion is
not taken into account when ordering the vertex symbols.
then it prints the "Geometry analysis:" with the characteristics
of all the T-O-T units in the unit cell (T-type, atom numbers,
T-O-T angle, T-O and T-T distances, and atom labels). Atoms are
renumbered: first all T-atoms, and then all O-atoms. The same
numbering is followed in the "output_filename.xtl" file
then the "Average topological geometry analysis:" is printed which
consists on averages over T-T types and T-types. The number under
the column "Number" indicates the corresponding multiplicity
finally the "Average label geometry analysis:" is printed and these
averages are referred to the label of the T-atoms in the input
file. These averages can be particularly useful if the T and O atoms
are labelled according to their crystallographic positions. Averages
include T-O, T-T, T-O-T, and T averages
- "T1_sites_of_filename"
for each T-atom in the unit cell its T-first-neighbours are
output by indicating: atom number, atom label, cell code
atoms connected to a given atom can be in one of the adjacent
unit cells. the initial cell code is referred to as "0 0 0".
the other cells are indicated by numbers of relative shifts to
the central cell in the directions of the x,y,z axis respectively.
i.e. the contiguous cell at the right would be "1 0 0"
- "T2_sites_of_filename"
for each T-atom in the unit cell its T-second-neighbours are
output by indicating: atom number, atom label, cell code
T1_ and T2_ files can be useful for NMR applications. Complex unit
cells with a given distribution of Si,Al,P atoms can be used as
input files in order to find the neighbourhood of each T-atom
- "output_filename.xtl"
this is a .xtl file with the same input structure which contains
the topological T-type (divided by 1000) in the column corresponding
to the charges. This is useful for visual identification of the
T-types when using a visualisation software such as Cerius2
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6. CURRENT LIMITATIONS
(i) T-T connectivity is calculated through distance checks and confirmed
by label check. Non connected T-T atoms in the range indicated by the
parameters (adist1,adist2) will be identified as connected and the
program will fail
(ii) cations must be cleared from input file as they do not contribute to
the framework connectivity and they are not taken into account in
the geometry analysis. Otherwise some cations may be interpreted as
bonded to some of the framework atoms thus flawing the corresponding
connectivity and spoiling the geometry analysis
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7. REPORTING BUGS
There may be some glitches in this program. If you happen to find any,
please send an e-mail message to any of the authors describing the nature
of the problem. If possible please include the input file so that we can
use it to determine the cause of the problem
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8. HISTORY
These notes are for the benefit of present and future maintainers
Version 0.0:
G.S. Feb-98. finds the connectivity sequence of T sites in zeolites/zeotypes
G.S. Sep-98. finds TO,TT-distances and TOT-angles
Version 0.5:
G.S. Jun-99. average-geometry-analysis included
G.S. Jun-99. valid for .xtl files with H and Al
G.S. Jun-99. valid for .xtl files as they are output from GULP
Version 1.0:
G.S. Mar-00. labels of T1,O,T2 included in Connectivity output
J.G. Apr-00. name of output xtl file changed to end in .xtl
J.G. Apr-00. 8 extra cell images added for corner images
J.G. Apr-00. distance checks on square to avoid sqrt operation
J.G. Apr-00. reading of .xtl file made more robust
J.G. Apr-00. explicit declaration of variables added
J.G. Apr-00. bounds checking added
J.G. Apr-00. ordering of array subscripts altered for faster access
J.G. Apr-00. names of some variables clarified
J.G. Apr-00. extra check for periodic images added to T1-O-T2 search
G.S. May-00. averages for label (crystallographic) sites included
Version 1.1:
G.S. Jun-00. O-T-O geometry analysis and averages included
Version 1.2:
G.S. Sep-00. extended for T-coordination > 4
J.G. Sep-00. uses symmetry matrices to build full cell for non-P1 .xtl file
does not calculate vertex symbols
G.S. Oct-00. vertex symbols added
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9. CREDITS
xtl is a file format by Molecular Simulations Inc.
Cerius2 is a software licenced by Molecular Simulations Inc.
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10. CITATION
Title: ZeoTsites: a code for topological and crystallographic tetrahedral
sites analysis in zeolites and zeotypes
Authors: G. Sastre, J.D. Gale
Journal: Microporous and Mesoporous Materials
Year: 2001
Volume: 43
Issue: 1
Pages: 27-40
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