Download ACES II Release 2.5.0 User Manual

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File Formats
7.1
7.1.1
ZMAT
File anatomy
This specification pertains to a particular version of joda. Older versions might require
more rigid input formats, but the general structure of ZMAT should never change. Every line
in ZMAT can be at most 80 characters long. The parser does not check the length of each
line; therefore, there are no guarantees that the rules of ZMAT parsing will apply once the
line length has been exceeded.
1. Header
Three types of lines are allowed in the header:
• blank space (consisting of spaces and/or tabs)
• comments (first non-blank character is a hash mark, #)
• file directives (first non-blank character is a percent sign, %)
The header can have an arbitrary number of lines, but the first line that does not
qualify as one of these three will be read as the job title.
2. Job title
The first non-blank, non-comment, non-directive line is the job title. It may consist of
any character and may be at most 80 characters long.
3. Molecular system
The coordinate matrices must immediately follow the job title. Every line must describe
one atom (dummy or otherwise). The first blank or comment line terminates the
coordinate matrix. Atom descriptions may have hash-delimited comments and the
coordinate strings may be separated with spaces or tabs. There are two types of
coordinate matrices: internal (Z matrix) and Cartesian.
Internal coordinate matrices have two parts separated by a blank line: the Z matrix
and the parameter definitions.
Cartesian coordinate matrices are the standard X Y Z format with no blank lines.
For LST and QST geometry search algorithms, multiple XYZ and Z matrix parameter
matrices can be supplied in the following order: INITIAL-[TRANSITION]-FINAL.
The transition geometry is only used for QST. Supplying a transition geometry for
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