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Dear cp2k-input-tools developper(s),

I have been trying to use your library to create a python dict from an existing CP2K input, to then use this dict to run new calculations in the aiida-cp2k framework. However I face the following issue.

When I use the CP2KInputParserSimplified parser, the KIND section is in the form :

'KIND': {'Te': {'BASIS_SET': 'TZVP-MOLOPT-SR-GTH', 'POTENTIAL': 'GTH-BLYP-q6'}, 'O': {'BASIS_SET': 'TZVP-GTH-q6', 'POTENTIAL': 'GTH-BLYP-q6'}}

My problem is that this tree-structure is not understood by AiiDA, which requires a format that seems to correspond to what you call "canonical form", generated by the CP2KInputParser :

'+KIND': [{'BASIS_SET': ['TZVP-MOLOPT-SR-GTH'], 'POTENTIAL': 'GTH-BLYP-q6', '': 'Te'}, {'BASIS_SET': ['TZVP-GTH-q6'], 'POTENTIAL': 'GTH-BLYP-q6', '': 'O'}]

except that in this case the '+' signs that are added to most dict key names for a reason that I do not quite understand are problematic. I do not yet know whether aiida-cp2k is able to recognize the key names despite the presence of these + signs, but it will create section duplicates if I try to modify the inoput parameters afterwards within aiida-cp2k.

In summary, is there a way to obtain the tree structure of the 'canonical form' (in particular for the 'KIND' section) without the '+' signs ?

Thanks for your help.
Best regards.

Sylvian

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ok, we probably need a parsing/abstract syntax tree for this, then it could work like:

1. parse until cursor line
2. if the syntax is correct until here we should get the AST/parsing tree (if we are driving the parsing directly we can simply stop, if not by catching an exception)
3. from the parsing we should get the current section in the schema
4. lookup other keys/values

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We currently have a copy of the v8.1 schema, but it keeps evolving and we might want to test against multiple schemas·

I am not sure how often this is used for other places in the input file, but e.g. the LIST keyword of ISOLATED_ATOMS.
takes a range of the form start..end with integers start and end.
However, right now this is coded as integer in https://github.com/cp2k/cp2k-input-tools/blob/develop/cp2k_input_tools/cp2k_input.xml
(line 429209). This errors out when parsing.

A temporary fix is to change it to string, though this does not give us structured data to work with.

Newer XML schemas can mark keywords as deprecated, we should probably emit a warning if we detect such a case.

When I run:

$ fromcp2k  -f yaml aiida.inp --base-dir files/

I get the following error:

Traceback (most recent call last):
  File "/home/aiida/.local/bin/fromcp2k", line 8, in <module>
    sys.exit(fromcp2k())
  File "/opt/conda/lib/python3.7/site-packages/click/core.py", line 829, in __call__
    return self.main(*args, **kwargs)
  File "/opt/conda/lib/python3.7/site-packages/click/core.py", line 782, in main
    rv = self.invoke(ctx)
  File "/opt/conda/lib/python3.7/site-packages/click/core.py", line 1066, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/opt/conda/lib/python3.7/site-packages/click/core.py", line 610, in invoke
    return callback(*args, **kwargs)
  File "/home/aiida/.local/lib/python3.7/site-packages/cp2k_input_tools/cli/fromcp2k.py", line 64, in fromcp2k
    tree = cp2k_parser.parse(fhandle, dict(var_values))
  File "/home/aiida/.local/lib/python3.7/site-packages/cp2k_input_tools/parser.py", line 205, in parse
    preprocessor = CP2KPreprocessor(fhandle, self._base_inc_dir, initial_variable_values)
  File "/home/aiida/.local/lib/python3.7/site-packages/cp2k_input_tools/preprocessor.py", line 38, in __init__
    self._inc_dirs = [Path(b) for b in base_dir]
  File "/home/aiida/.local/lib/python3.7/site-packages/cp2k_input_tools/preprocessor.py", line 38, in <listcomp>
    self._inc_dirs = [Path(b) for b in base_dir]
  File "/opt/conda/lib/python3.7/pathlib.py", line 1027, in __new__
    self = cls._from_parts(args, init=False)
  File "/opt/conda/lib/python3.7/pathlib.py", line 674, in _from_parts
    drv, root, parts = self._parse_args(args)
  File "/opt/conda/lib/python3.7/pathlib.py", line 658, in _parse_args
    a = os.fspath(a)
TypeError: expected str, bytes or os.PathLike object, not int

It looks like the bytes object is recognised as Sequence here:

Currently we're always converting keyword values to their default unit.
This is not needed for linting, only when converting to JSON or YAML and may even lead to problems when the XML schema lists internal_cp2k as the default unit, see #54.

It might be a good idea to delay the actual conversion to a time when it is actually needed and/or avoid it completely by changing the JSON/YAML format to yield a string containing the original unit.

The parser tries to normalize values here:

The reason for this is that for serialization formats like json and yaml we yield values in the CP2K default unit since we do not export any unit specification.

It's a bit unfortunate that CP2K defines the internal units as abstract internal_cp2k rather than effective unit, especially for things where there would be a physical unit behind it (other than relative tolerances where this seems to be used otherwise).
This makes external linting of input files impossible since we could only validate such values by hardcoding the effective internal unit of those parameters within cp2k-input-tools.

I guess the proper way forward is to:

1. store an explicitly given unit for a quantity with a default unit of internal_cp2k and only validate it, do not attempt to convert the value from or to internal_cp2k.
2. when converting to a format (json or yaml) where the unit would be lost, either yield an error if the unit was explicitly given (since we can't convert it and the recipient of the json/yaml wouldn't know which unit it is), or yield the value as a string with the unit either suffixed (1.23 angstrom) or prefixed as in the CP2K input [angstrom] 1.23.

This would also delay unit conversion to the point when it becomes necessary (for linting it is not), rather than just attempting it all the time.

The intermediate solution: if the default unit is internal_cp2k, store as is, if there is an explicit unit given, raise an error since we can't convert to internal_cp2k.

Originally posted by @dev-zero in #54 (comment)

I came across a problem when using CP2KInputParserSimplified with multiple basis sets for an atomic kind (say, an ADMM calculation) and wanted to check if it is something that should be fixed, or if I need to use the full parser. Specifically, given the input snippet

&FORCE_EVAL
  &SUBSYS
    &KIND H
      POTENTIAL GTH-PBE-q1
      BASIS_SET TZV2P-MOLOPT-GTH
      BASIS_SET AUX_FIT pFIT3
    &END KIND
  &END SUBSYS
&END FORCE_EVAL

and the code

from cp2k_input_tools.parser import CP2KInputParserSimplified
tree = CP2KInputParserSimplified().parse(open('test-basis.inp'))
print(tree['force_eval']['subsys']['kind']['H'])

I get

{'potential': 'GTH-PBE-q1', 'basis_set': [['AUX_FIT', 'pFIT3'], ['AUX_FIT', 'pFIT3']]}

which is incorrect and also ends up with an incorrect input file when written using CP2KInputGenerator.

Adding an explicit ORB to the primary basis does not help, as it results in:

{'potential': 'GTH-PBE-q1', 'basis_set': ['ORB', 'TZV2P-MOLOPT-GTH', ['AUX_FIT', 'pFIT3']]}

Switching the order of the two lines changes the output to the still incorrect

{'potential': 'GTH-PBE-q1', 'basis_set': ['AUX_FIT', 'pFIT3', 'TZV2P-MOLOPT-GTH']}

On the other hand, CP2KInputParser processes it fine. Is this a bug or expected behavior for the simplified parser? If so, should it perhaps raise an exception instead? Thank you for looking at this.

see also #42 and #34

I've tried to use cp2k-input-tools with a fairly standard MM Force-eval, but unfortunately there are problems with the K keywords in the BEND and BOND sections.

It seems that the parser tries to determine the standard unit for these variables, which are extracted from the cp2k_input.xml file. However, there are multiple definitions of K in there and it looks like the parser takes a definition with default unit 'internal_cp2k', which eventually triggers the following error:

in read_input_cp2k
    tree = parser.parse(f_in)
  File "/home/ucapcsc/software/miniconda3/lib/python3.7/site-packages/cp2k_input_tools/parser.py", line 216, in parse
    self._parse_as_keyword(line)
  File "/home/ucapcsc/software/miniconda3/lib/python3.7/site-packages/cp2k_input_tools/parser.py", line 149, in _parse_as_keyword
    kw = Keyword.from_string(kw_node, kw_value, self._key_trafo)  # the key_trafo is needed to mangle keywords
  File "/home/ucapcsc/software/miniconda3/lib/python3.7/site-packages/cp2k_input_tools/keyword_helpers.py", line 127, in from_string
    default_unit = UREG.parse_expression(default_unit)
  File "/home/ucapcsc/software/miniconda3/lib/python3.7/site-packages/pint/registry.py", line 1264, in parse_expression
    lambda x: self._eval_token(x, case_sensitive=case_sensitive, **values)
  File "/home/ucapcsc/software/miniconda3/lib/python3.7/site-packages/pint/pint_eval.py", line 102, in evaluate
    return define_op(self.left)
  File "/home/ucapcsc/software/miniconda3/lib/python3.7/site-packages/pint/registry.py", line 1264, in <lambda>
    lambda x: self._eval_token(x, case_sensitive=case_sensitive, **values)
  File "/home/ucapcsc/software/miniconda3/lib/python3.7/site-packages/pint/registry.py", line 1159, in _eval_token
    {self.get_name(token_text, case_sensitive=case_sensitive): 1}
  File "/home/ucapcsc/software/miniconda3/lib/python3.7/site-packages/pint/registry.py", line 643, in get_name
    raise UndefinedUnitError(name_or_alias)
pint.errors.UndefinedUnitError: 'internal_cp2k' is not defined in the unit registry

I have circumvented this problem by changing all 'internal_cp2k' occasions in cp2k_input.xml to 'hartree', but this is a rather ugly fix...

Hey and first of all, thanks for this great tool!
We use it to make CP2k compatible with https://dvc.org/ for our research data management and parameter tracking.

We include cp2k-input-tools as a dependency in our package https://github.com/zincware/IPSuite which allows us to build the workflows and much more.

I've seen that you migrated to pydantic v2 in 3706fae .
We have also updated some of our tools to use the new pydantic release.

I was wondering what criteria you have on your side until you release the next version of cp2k-input-tools?
This would allow us, to also release a new version of our tool including cp2k-input-tools` on PyPi, because the package can't depend on the src.

More and more packages require a bump of the Pydantic dependency. I was happy to see it has already happened for this library's 0.9.0 version.

However, for some reason, it didn't make it to PyPI. @dev-zero, do you know if it was intentional?

Hi,

It seems that the cp2k-input-tools parser does not properly deals with the situation where multiple basis set file names are needed (different files for different elements in th system) :

&DFT
BASIS_SET_FILE_NAME /gpfs/home/scadars/CP2K/CP2K6.1/data/GTH_BASIS_SETS
BASIS_SET_FILE_NAME /gpfs/home/scadars/CP2K/CP2K6.1/data/BASIS_MOLOPT_UCL
POTENTIAL_FILE_NAME /gpfs/home/scadars/CP2K/CP2K6.1/data/GTH_POTENTIALS

In this case the parse() method of the CP2KInputParserSimplified class with the following options :

parser = CP2KInputParserSimplified(key_trafo=str.upper,
multi_value_unpack=False,
repeated_section_unpack=False,
level_reduction_blacklist=["KIND"])

returns a nested dict which contains among other key/value pairs of the dict value associated with the 'DFT' key :

'BASIS_SET_FILE_NAME': ['/gpfs/home/scadars/CP2K/CP2K6.1/data/BASIS_MOLOPT_UCL', '/gpfs/home/scadars/CP2K/CP2K6.1/data/BASIS_MOLOPT_UCL'],
'POTENTIAL_FILE_NAME': '/gpfs/home/scadars/CP2K/CP2K6.1/data/GTH_POTENTIALS'

It appears that the parser correctly interprets the fact that there are 2 values associated with 'BASIS_SET_FILE_NAME' but only the first value is used, and repeated, instead of using the second.

Another related issue is from the aiida-cp2k side, where the builder associated with cp2k code does not seem to accept lists of files as values for the 'basis' key in the builder.file (see aiida-cp2k issue 139 here : [(https://github.com/aiidateam/aiida-cp2k/issues/139)]).

Please note that, being unfamiliar with the CP2K code I don't know how common this situation, but I got sample my input files from a definitely experienced user, and the code itself is able to deal with such a situation.

Thank you very much for your help.
Best regards.

Sylvian

Recently, I came across an unexpected error when using the cp2klint command line tool which clashes with a recently (from version 9.1 onwards) added CP2K keyword PRINT_ATOM_KIND under CP2K_INPUT/MOTION/PRINT/FORCES. Specifically, trying to lint the following MWE input

&MOTION
  &PRINT  
    &FORCES  
      PRINT_ATOM_KIND TRUE  
    &END FORCES  
  &END PRINT  
&END MOTION

raises an invalid keyword error, which ideally should not be the case. Commenting out the problematic keyword in the input removes the error.

Hi,

I tried to use the simplified parser to read a structure (as well as other parameters) from a CP2K input file containing the following COORD section :

&COORD
  UNIT angstrom
  Kr  0 0 0
  Kr  4 0 0
&END COORD

with the following paser options :

parser = CP2KInputParserSimplified(key_trafo=str.upper,
multi_value_unpack=False,
repeated_section_unpack=False,
level_reduction_blacklist=["KIND"])

The parser.parse(fhandle) method returns a dict that contains the following erroneous 'COORD' value :

'COORD': {'UNIT': 'angstrom', '*': ['Kr 4 0 0', 'Kr 4 0 0']}}

Two problems here. The '*' may cause problems in CP2K (see below). Maybe more importantly the coordinates of both atoms are idendical and correpond to the second atom in the original input file.

When I tried to submit this calculation with a script generated with :

fromcp2k -f aiida-cp2k-calc CP1K_INPUT_FILE

with the follwing 2 lines commented to use the structure provided in the input file :

structure = StructureData(...)

builder.structure = structure # read from original CP2K input file

The calculations is succesfully submitted by aiida to the (remote) computer, but the COORD section in the aiida.inp file looks as follows (again same coordinates for both atoms) :

  &COORD
     * Kr  4 0 0
     * Kr  4 0 0
     UNIT angstrom
  &END COORD

And the aiida.out file reads :

• ___ *
• / \ *
• [ABORT] Incorrectly formatted input line for atom 1 found in COORD section. *
• ___/ A floating point type object was expected, found Input line: *
• | <* Kr 4 0 0> *
• O/| *
• /| | *
• / \ atoms_input.F:209 *

Note that in the aiida-cp2k example wherein structure is read from the cp2k input file (here) the COORD value of the dict reads as follows :

                'COORD': {
                    ' ': ['H    2.0   2.0   2.737166', 'H    2.0   2.0   2.000000']
                },

No '*' sign here, but a blank key instead...

Thank you for your help.
Best wishes.

Sylvian.

Hi, thanks on a nice project, I just discovered it while preparing something "simple" for myself :)
There's a failure when you have got comments on the same line as keyword, such as:

&POISSON  #your comment goes here

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  - dataclasses requires Python >=3.6, <3.7

Because dataclasses (0.7) requires Python >=3.6, <3.7
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I have found an error message when building supercells with atomic displacements using a combination of phonopy (2.23.1, 2.24.1, 2.24.2), cp2k_input_tools (0.9.1, 0.8.2, 0.7.2, 0.6.0, etc) and transitions (0.8.11, 0.7.2, 0.7.0, etc), also python versions 3.8 and 3.12. I do not understand the error message below, so I will appreciate any suggestions. Thanks.

pereira@debye:~/WORK/CP2K/Force% phonopy --cp2k -c aGST_ENERGY_FORCE.inp -d --dim 1 1 1
_
_ __ | |__ ___ _ __ ___ _ __ _ _
| '_ | '_ \ / _ | '_ \ / _ \ | '_ | | | |
| |) | | | | () | | | | () || |) | || |
| .__/|| ||___/|| ||___() ./ _, |
|| || |/
2.23.1

Compiled with OpenMP support (max 8 threads).
Python version 3.12.3
Spglib version 2.3.1

Traceback (most recent call last):
File "/opt/homebrew/Caskroom/miniforge/base/envs/phonopy/bin/phonopy", line 45, in
main(**argparse_control)
File "/opt/homebrew/Caskroom/miniforge/base/envs/phonopy/lib/python3.12/site-packages/phonopy/cui/phonopy_script.py", line 1853, in main
cell_info = get_cell_info(settings, cell_filename, log_level)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/homebrew/Caskroom/miniforge/base/envs/phonopy/lib/python3.12/site-packages/phonopy/cui/phonopy_script.py", line 1641, in get_cell_info
cell_info = collect_cell_info(
^^^^^^^^^^^^^^^^^^
File "/opt/homebrew/Caskroom/miniforge/base/envs/phonopy/lib/python3.12/site-packages/phonopy/cui/collect_cell_info.py", line 142, in collect_cell_info
unitcell, optional_structure_info = read_crystal_structure(
^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/homebrew/Caskroom/miniforge/base/envs/phonopy/lib/python3.12/site-packages/phonopy/interface/calculator.py", line 472, in read_crystal_structure
unitcell, config_tree = read_cp2k(cell_filename)
^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/homebrew/Caskroom/miniforge/base/envs/phonopy/lib/python3.12/site-packages/phonopy/interface/cp2k.py", line 78, in read_cp2k
tree = parser.parse(fhandle)
^^^^^^^^^^^^^^^^^^^^^
File "/opt/homebrew/Caskroom/miniforge/base/envs/phonopy/lib/python3.12/site-packages/cp2k_input_tools/parser.py", line 215, in parse
self._parse_as_keyword(line)
File "/opt/homebrew/Caskroom/miniforge/base/envs/phonopy/lib/python3.12/site-packages/cp2k_input_tools/parser.py", line 149, in _parse_as_keyword
kw = Keyword.from_string(kw_node, kw_value, self._key_trafo) # the key_trafo is needed to mangle keywords
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/homebrew/Caskroom/miniforge/base/envs/phonopy/lib/python3.12/site-packages/cp2k_input_tools/keyword_helpers.py", line 106, in from_string
tokens = tokenize(vstring)
^^^^^^^^^^^^^^^^^
File "/opt/homebrew/Caskroom/miniforge/base/envs/phonopy/lib/python3.12/site-packages/cp2k_input_tools/tokenizer.py", line 129, in tokenize
char_map.get(char, tokenizer.token_char)(string, colnr)
File "/opt/homebrew/Caskroom/miniforge/base/envs/phonopy/lib/python3.12/site-packages/transitions/core.py", line 405, in trigger
return self.machine._process(func)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/homebrew/Caskroom/miniforge/base/envs/phonopy/lib/python3.12/site-packages/transitions/core.py", line 1079, in _process
return trigger()
^^^^^^^^^
File "/opt/homebrew/Caskroom/miniforge/base/envs/phonopy/lib/python3.12/site-packages/transitions/core.py", line 421, in _trigger
raise MachineError(msg)
transitions.core.MachineError: "Can't trigger event quote_char from state comment!"

Dependabot can't resolve your Python dependency files.

As a result, Dependabot couldn't update your dependencies.

The error Dependabot encountered was:

Creating virtualenv cp2k-input-tools-2RVZUAfo-py3.9 in /home/dependabot/.cache/pypoetry/virtualenvs
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  Package pygls (0.8.1) not found.

  at /usr/local/.pyenv/versions/3.9.0/lib/python3.9/site-packages/poetry/repositories/pool.py:144 in package
      140│                     self._packages.append(package)
      141│ 
      142│                     return package
      143│ 
    → 144│         raise PackageNotFound("Package {} ({}) not found.".format(name, version))
      145│ 
      146│     def find_packages(
      147│         self, dependency,
      148│     ):

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Hi

I'm trying to parse an input file using the new libxc subsections of &XC_FUNCTIONAL. But these sections are not recognized and I get the following error:

cp2k_input_tools.parser_errors.InvalidSectionError: ("invalid section 'MGGA_C_R2SCAN'", defaultdict(<function Context.. at 0x2b26fa545790>, {'filename': 'phonon.inp', 'linenr': 358, 'colnrs': [8], 'line': '&R2MGGA_C_SCAN', 'section': Section(name='XC_FUNCTIONAL', node=<Element 'SECTION' at 0x2b26f7505bd0>, subsections=[], keywords=[], param=None, repeats=False)}))

Can I somehow add these sections?

Thanks in advance,
Fabian