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revise/refacor Type Label section parsing and Atoms section parsing

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- do not ignore numeric type in Type Label sections
- refuse invalid numeric types that will overflow arrays
- check for duplicate numeric type entries or non-unique labels
- better error messages
- use Tokenizer class instead of sscanf()
This commit is contained in:
Axel Kohlmeyer
2022-09-04 01:01:36 -04:00
parent 389c87ab7e
commit ad8a931fe4
5 changed files with 77 additions and 73 deletions
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36
doc/src/labelmap.rst
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@ -24,8 +24,8 @@ Examples
.. code-block:: LAMMPS
labelmap atom 3 carbon
labelmap bond 1 carbonyl 2 nitrile
labelmap atom 3 carbon 4 'c3"' 5 "c1'" 6 "c#"
labelmap bond 1 carbonyl 2 nitrile 3 """ c1'-c2" """
labelmap atom $(label(carbon)) C # change type label from 'carbon' to 'C'
labelmap clear
labelmap write mymap.include
@ -46,29 +46,33 @@ Bond Type Labels, etc. See the :doc:`Howto type labels
labels can be used.
Valid type labels may contain any alphanumeric character, but must not
start with a number. They can also contain other standard ASCII
characters such as angular or square brackets '<' and '>' or '[' and
']', parenthesis '(' and ')', dash '-', underscore '_', plus '+' and
equals '=' signs and more. Note that type labels must be put in
quotation marks if they contain the '#' character when used in a context
where the '#' character would be interpreted as starting a comment like
in the LAMMPS input file.
start with a number, a '#', or a '*' character. They may contain other
standard ASCII characters such as angular or square brackets '<' and '>'
or '[' and ']', parenthesis '(' and ')', dash '-', underscore '_', plus
'+' and equals '=' signs and more. The must not contain blanks or any
other whitespace. Note that type labels must be put in single or double
quotation marks if they contain the '#' character, or a double (") or
single quotation mark ("). If the label contains both, single and double
quotes, triple quotation (""") must be used. When using quotation
marks, the LAMMPS input parser may require adding leading or trailing
blanks so it can identify the quotation marks. Those blanks will be
removed when defining the label.
A *labelmap* command can only modify the label map for one type-kind
(atom types, bond types, etc). Any number of numeric-type/type-label
pairs may follow. If a type label already exists for a given numeric
type, it will be overwritten. Type labels must be unique; assigning
the same type label to multiple numeric types is not allowed. In some
cases, such as when reading and writing data files, it is required
that when type labels are used, that there is a label defined for
*every* numeric type.
pairs may follow. If a type label already exists for the same numeric
type, it will be overwritten. Type labels must be unique; assigning the
same type label to multiple numeric types is not allowed. In some
cases, such as when reading and writing data files, it is required that
when type labels are used, that there is a label defined for *every*
numeric type.
The *clear* option resets the labelmap and thus discards all previous
settings.
The *write* option takes a filename as argument and writes the current
label mappings to a file as labelmap commands, so the file can be copied
into a different LAMMPS input file or read using the :doc:`include
into a new LAMMPS input file or read in using the :doc:`include
<include>` command.
----------