def test_roundtrip_canonical():
cp2k_parser = CP2KInputParser(DEFAULT_CP2K_INPUT_XML)
with open(TEST_DIR.joinpath("inputs/test01.inp"), "r") as fhandle:
ref_tree = cp2k_parser.parse(fhandle)
cp2k_generator = CP2KInputGenerator(DEFAULT_CP2K_INPUT_XML)
fhandle = io.StringIO("\n".join(cp2k_generator.line_iter(ref_tree)))
# reinitialize parser and generators to clear any internal state they might have
cp2k_parser = CP2KInputParser(DEFAULT_CP2K_INPUT_XML)
fhandle.name = "StringIO" # add a filename (required by parser for context)
assert cp2k_parser.parse(fhandle) == ref_tree
def test_missing_section_end():
cp2k_parser = CP2KInputParser(DEFAULT_CP2K_INPUT_XML)
fhandle = io.StringIO("""
&GLOBAL
! &END GLOBAL
&FORCE_EVAL
&END FORCE_EVAL
""")
with pytest.raises(InvalidSectionError) as excinfo:
cp2k_parser.parse(fhandle)
assert "invalid section" in excinfo.value.args[0]
fhandle = io.StringIO("""
&GLOBAL
&END GLOBAL
&FORCE_EVAL
""")
with pytest.raises(SectionMismatchError) as excinfo:
cp2k_parser.parse(fhandle)
assert "not closed" in excinfo.value.args[0]
def test_inline_comment():
cp2k_parser = CP2KInputParser(DEFAULT_CP2K_INPUT_XML)
with open(TEST_DIR.joinpath("inputs/inline_comment.inp"), "r") as fhandle:
tree = cp2k_parser.parse(fhandle)
assert tree
def test_repeated_kinds_canonical():
cp2k_parser = CP2KInputParser(DEFAULT_CP2K_INPUT_XML)
with open(TEST_DIR.joinpath("inputs/test04.inp"), "r") as fhandle:
tree = cp2k_parser.parse(fhandle)
assert tree["+force_eval"][0]["+subsys"]["+kind"] == [
{
"_": "O",
"element": "O",
"potential": "GTH-PBE-q6",
"basis_set": [("ORB", "TZVP-MOLOPT-SR-GTH")]
},
{
"_": "C",
"element": "C",
"potential": "GTH-PBE-q4",
"basis_set": [("ORB", "TZVP-MOLOPT-SR-GTH")]
},
{
"_": "Ti",
"element": "Ti",
"potential": "GTH-PBE-q12",
"basis_set": [("ORB", "TZVP-MOLOPT-SR-GTH")]
},
]
def cp2kget(fhandle, paths, base_dir, var_values, canonical):
"""Get values by path from a CP2K input file
Examples for paths:
force_eval/dft/mgrid/cutoff
"""
if canonical:
cp2k_parser = CP2KInputParser(base_dir=base_dir, key_trafo=str.lower)
else:
cp2k_parser = CP2KInputParserSimplified(base_dir=base_dir,
key_trafo=str.lower)
tree = cp2k_parser.parse(fhandle, dict(var_values))
def _(val):
if isinstance(val, list):
return ", ".join(str(v) for v in val)
return val
for path in paths:
sections = path.split("/")
ref = tree
for section in sections:
if isinstance(ref, (list, tuple)):
section = int(
section
) # if we encounter a list, convert the respective path element
ref = ref[
section] # exploit Python using references into dicts/lists
print(f"{path}: {_(ref)}")
def test_start_empty_lines():
cp2k_parser = CP2KInputParser(DEFAULT_CP2K_INPUT_XML)
with open(TEST_DIR.joinpath("inputs/empty_lines.inp"), "r") as fhandle:
tree = cp2k_parser.parse(fhandle)
assert tree
def test_simple_canonical():
cp2k_parser = CP2KInputParser(DEFAULT_CP2K_INPUT_XML)
with open(TEST_DIR.joinpath("inputs/test01.inp"), "r") as fhandle:
tree = cp2k_parser.parse(fhandle)
assert isinstance(tree, dict)
assert "+global" in tree
def test_unterminated_string():
cp2k_parser = CP2KInputParser(DEFAULT_CP2K_INPUT_XML)
with open(TEST_DIR.joinpath("inputs/unterminated_string.inp"),
"r") as fhandle:
with pytest.raises(UnterminatedStringError) as excinfo:
cp2k_parser.parse(fhandle)
assert excinfo.value.args[1]["linenr"] == 14
def test_roundtrip2_canonical():
cp2k_parser = CP2KInputParser(DEFAULT_CP2K_INPUT_XML)
with open(TEST_DIR.joinpath("inputs/test04.inp"), "r") as fhandle:
ref_tree = cp2k_parser.parse(fhandle)
ref_tree["+force_eval"][0]["+subsys"]["+kind"].sort(
key=lambda d: d["_"])
cp2k_generator = CP2KInputGenerator(DEFAULT_CP2K_INPUT_XML)
fhandle = io.StringIO("\n".join(cp2k_generator.line_iter(ref_tree)))
# reinitialize parser and generators to clear any internal state they might have
cp2k_parser = CP2KInputParser(DEFAULT_CP2K_INPUT_XML)
fhandle.name = "StringIO" # add a filename (required by parser for context)
tree = cp2k_parser.parse(fhandle)
tree["+force_eval"][0]["+subsys"]["+kind"].sort(key=lambda d: d["_"])
assert tree == ref_tree
def test_endif_garbage():
cp2k_parser = CP2KInputParser(DEFAULT_CP2K_INPUT_XML)
fhandle = io.StringIO("""@IF 1\n@ENDIF foo""")
with pytest.raises(PreprocessorError) as excinfo:
cp2k_parser.parse(fhandle)
assert "garbage found after @ENDIF" in excinfo.value.args[0]
def test_unknown_preprocessor():
cp2k_parser = CP2KInputParser(DEFAULT_CP2K_INPUT_XML)
fhandle = io.StringIO("""@FOOBAR foo""")
with pytest.raises(PreprocessorError) as excinfo:
cp2k_parser.parse(fhandle)
assert "unknown preprocessor directive found" in excinfo.value.args[0]
def test_endif_without_if():
cp2k_parser = CP2KInputParser(DEFAULT_CP2K_INPUT_XML)
fhandle = io.StringIO("""@ENDIF""")
with pytest.raises(PreprocessorError) as excinfo:
cp2k_parser.parse(fhandle)
assert "found @ENDIF without a previous @IF" in excinfo.value.args[0]
def test_nested_if():
cp2k_parser = CP2KInputParser(DEFAULT_CP2K_INPUT_XML)
fhandle = io.StringIO("""@IF 1\n@IF 0\n@ENDIF\n@ENDIF""")
with pytest.raises(PreprocessorError) as excinfo:
cp2k_parser.parse(fhandle)
assert "nested @IF are not allowed" in excinfo.value.args[0]
def test_undefined_var():
cp2k_parser = CP2KInputParser(DEFAULT_CP2K_INPUT_XML)
fhandle = io.StringIO("""${undef}""")
with pytest.raises(PreprocessorError) as excinfo:
cp2k_parser.parse(fhandle)
assert "undefined variable 'undef'" in excinfo.value.args[0]
def test_include_multiple():
cp2k_parser = CP2KInputParser(DEFAULT_CP2K_INPUT_XML)
fhandle = io.StringIO("@INCLUDE 'foo' 'bar'")
with pytest.raises(PreprocessorError) as excinfo:
cp2k_parser.parse(fhandle)
assert "@INCLUDE requires exactly one argument" in excinfo.value.args[0]
def test_xctype():
cp2k_parser = CP2KInputParser(DEFAULT_CP2K_INPUT_XML,
base_dir=[TEST_DIR.joinpath("inputs/")])
with open(TEST_DIR.joinpath("inputs/He_PBE.inp"), "r") as fhandle:
tree = cp2k_parser.parse(fhandle)
assert tree
assert tree["+force_eval"][0]["+dft"]["+xc"]["+xc_functional"][
"_"] == "PBE"
def test_if_without_endif():
cp2k_parser = CP2KInputParser(DEFAULT_CP2K_INPUT_XML)
fhandle = io.StringIO("""@IF 1\n""")
with pytest.raises(PreprocessorError) as excinfo:
cp2k_parser.parse(fhandle)
assert "conditional block not closed at end of file" in excinfo.value.args[
0]
def test_undefined_preprocessor_var():
cp2k_parser = CP2KInputParser(DEFAULT_CP2K_INPUT_XML)
with open(TEST_DIR.joinpath("inputs/preprocesser_undefined_var.inp"),
"r") as fhandle:
with pytest.raises(PreprocessorError) as excinfo:
cp2k_parser.parse(fhandle)
assert "undefined variable 'HP'" in excinfo.value.args[0]
assert excinfo.value.args[1]["linenr"] == 30
def test_fractional_values():
cp2k_parser = CP2KInputParser(DEFAULT_CP2K_INPUT_XML)
with open(TEST_DIR.joinpath("inputs/fractional_values.inp"),
"r") as fhandle:
tree = cp2k_parser.parse(fhandle)
assert tree
assert tree["+force_eval"][0]["+subsys"]["+cell"]["a"][
0] == 4.0 # specified as 8/2
def test_var_default_val():
cp2k_parser = CP2KInputParser(DEFAULT_CP2K_INPUT_XML)
with open(TEST_DIR.joinpath("inputs/default_var_val.inp"), "r") as fhandle:
tree_with = cp2k_parser.parse(fhandle)
fhandle.seek(0)
tree_without = cp2k_parser.parse(fhandle,
initial_variable_values={"HP": 0})
assert "+kpoints" in tree_with["+force_eval"][0]["+dft"]
assert "+kpoints" not in tree_without["+force_eval"][0]["+dft"]
def test_simple_canonical_inclusion():
cp2k_parser = CP2KInputParser(DEFAULT_CP2K_INPUT_XML,
base_dir=TEST_DIR.joinpath("inputs/"))
with open(TEST_DIR.joinpath("inputs/test02.inp"), "r") as fhandle:
tree = cp2k_parser.parse(fhandle)
assert isinstance(tree, dict)
assert "+global" in tree
assert "+force_eval" in tree
assert isinstance(tree["+force_eval"], list)
assert isinstance(tree["+force_eval"][0], dict)
def test_error_invalid_number_of_parameters():
cp2k_parser = CP2KInputParser(DEFAULT_CP2K_INPUT_XML)
with open(TEST_DIR.joinpath("inputs/error_nvar.inp"), "r") as fhandle:
with pytest.raises(InvalidParameterError) as excinfo:
cp2k_parser.parse(fhandle)
assert "invalid values for keyword: A" in excinfo.value.args[0]
assert excinfo.value.args[1]["linenr"] == 41
assert isinstance(excinfo.value.__cause__, InvalidParameterError)
assert "keyword expects exactly 3 values, 2 were given" in excinfo.value.__cause__.args[
0]
def __init__(self, cp2k_inputs_file: str, logger: logging.Logger = None):
if logger is None:
self.logger = logging.getLogger(__name__)
else:
self.logger = logger
with open(cp2k_inputs_file) as f:
parser = CP2KInputParser()
self.cp2k_dict = parser.parse(f)
self._atoms = None
self._init_free_energy_section()
self._init_print_section()
def test_section_parameter_error():
cp2k_parser = CP2KInputParser(DEFAULT_CP2K_INPUT_XML)
fhandle = io.StringIO("""
&GLOBAL invalidparam
&END GLOBAL
""")
with pytest.raises(InvalidParameterError) as excinfo:
cp2k_parser.parse(fhandle)
assert "section parameters given for non-parametrized section" in excinfo.value.args[
0]
def test_section_end_mismatch():
cp2k_parser = CP2KInputParser(DEFAULT_CP2K_INPUT_XML)
fhandle = io.StringIO("""
&GLOBAL
&END GLOBI
&FORCE_EVAL
&END FORCE_EVAL
""")
with pytest.raises(SectionMismatchError) as excinfo:
cp2k_parser.parse(fhandle)
assert "could not match open section" in excinfo.value.args[0]
def cp2klint(fhandle, var_values, base_dir):
"""Check the passed CP2K file for syntax errors"""
cp2k_parser = CP2KInputParser(base_dir=base_dir)
try:
cp2k_parser.parse(fhandle, dict(var_values))
except (TokenizerError, ParserError) as exc:
ctx = exc.args[1]
line = ctx.line.rstrip()
print(f"Syntax error: {exc.args[0]}, in {ctx.filename}:")
if exc.__cause__:
print(f" {exc.__cause__}")
print(f"line {ctx.linenr:>4}: {line}")
if ctx.colnr is not None:
count = 0 # number of underline chars after (positiv) or before (negative) the marker if ref_colnr given
nchars = ctx.colnr # relevant line length
if ctx.ref_colnr is not None:
count = ctx.ref_colnr - ctx.colnr
nchars = min(ctx.ref_colnr,
ctx.colnr) # correct if ref comes before
if ctx.colnrs:
# shift by the number of left-stripped ws
# ctx.colnrs contains the left shift for each possibly continued line
nchars += ctx.colnrs[0] # assume no line-continuation for now
# replace all non-ws chars with spaces:
# - assuming a monospace font
# - preserving other whitespace we don't know the width
underline = re.sub(r"\S", " ", ctx.line[:nchars])
if count >= 0:
print(f"{str():>9} {underline}^{str():~>{count}}")
else:
print(f"{str():>9} {underline}{str():~>{-count}}^")
if ctx.ref_line is not None:
print("previous definition:")
print(f"line {str():>4}: {ctx.ref_line.rstrip()}")
sys.exit(1)
print("All done! Happy calculating!")
def test_line_continuation():
cp2k_parser = CP2KInputParser(DEFAULT_CP2K_INPUT_XML)
with open(TEST_DIR.joinpath("inputs/line_continuation.inp"),
"r") as fhandle:
tree = cp2k_parser.parse(fhandle)
assert isinstance(tree, dict)
assert tree == {
"+global": {
"print_level": "medium",
"project_name": "fatman.calc",
"run_type": "energy"
}
}
def test_multiple_defined_non_repeating_section():
cp2k_parser = CP2KInputParser(DEFAULT_CP2K_INPUT_XML)
fhandle = io.StringIO("""
&GLOBAL
&END GLOBAL
&GLOBAL
&END GLOBAL
""")
with pytest.raises(InvalidNameError) as excinfo:
cp2k_parser.parse(fhandle)
assert "the section 'GLOBAL' can not be defined multiple times" in excinfo.value.args[
0]
def test_invalid_keyword():
cp2k_parser = CP2KInputParser(DEFAULT_CP2K_INPUT_XML)
fhandle = io.StringIO("""
&FORCE_EVAL
&SUBSYS
BASIS_SET TZVPd-MOLOPT-SR-GTH
&END SUBSYS
&END FORCE_EVAL
""")
with pytest.raises(InvalidNameError) as excinfo:
cp2k_parser.parse(fhandle)
assert "invalid keyword" in excinfo.value.args[0]
def validate_inputs(self, inputs: dict) -> (bool, str):
if "cp2k_inputs" not in inputs:
return False, "cp2k_inputs required for cp2k"
# Validate the CP2K input file. Parser will throw exceptions if invalid
# TODO: More specific error handling for .inp file
try:
with open(inputs["cp2k_inputs"]) as f:
parser = CP2KInputParser()
parser.parse(f)
except Exception as e:
return False, f"cp2k_inputs: {str(e)}"
# Otherwise let the base class validate
return super().validate_inputs(inputs)
