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Commit 13a258c5 authored by Lauri Himanen's avatar Lauri Himanen
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Made the input file parsing more straightworward.

parent 30ab469a
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Showing with 69 additions and 66 deletions
parser/parser-cp2k/cp2kparser/generic/inputparsing.py
View file @ 13a258c5
......@@ -164,30 +164,54 @@ class InputObject(object):
self.data_dimension = None
self.default_value = None
def get_formatted_value(self):
""" Used to set the value of the keyword. The data will be transformed
into the correct data type and dimension from a simple string.
#===============================================================================
class Keyword(InputObject):
"""Information about a keyword in a CP2K calculation.
"""
__slots__ = ['unit', 'value_no_unit', 'default_unit', 'default_name']
def __init__(self, name, default_value, default_unit, default_name):
super(Keyword, self).__init__(name)
self.unit = None
self.value_no_unit = None
self.default_unit = default_unit
self.default_value = default_value
self.default_name = default_name
def get_value(self):
"""Returns the value stored in this keyword by removing the possible
unit definition and formatting the string into the correct data type.
"""
# Decode the unit and the value if not done before
if self.default_unit:
if not self.value_no_unit:
self.decode_cp2k_unit_and_value()
if self.value_no_unit is not None:
proper_value = self.value_no_unit
else:
proper_value = self.value
returned = None
dim = int(self.data_dimension)
splitted = self.value.split()
splitted = proper_value.split()
if len(splitted) != dim:
logger.error("The dimensions of the CP2K input parameter {} do not match the specification in the XML file.".format(self.name))
if dim == 1:
try:
if self.data_type == "integer":
returned = int(self.value)
returned = int(proper_value)
elif self.data_type == "real":
returned = float(self.value)
returned = float(proper_value)
elif self.data_type == "word":
returned = str(self.value)
returned = str(proper_value)
elif self.data_type == "keyword":
returned = str(self.value)
returned = str(proper_value)
elif self.data_type == "string":
returned = str(self.value)
returned = str(proper_value)
elif self.data_type == "logical":
returned = str(self.value)
returned = str(proper_value)
else:
logger.error("Unknown data type '{}'".format(self.data_type))
return
......@@ -217,22 +241,7 @@ class InputObject(object):
return returned
#===============================================================================
class Keyword(InputObject):
"""Information about a keyword in a CP2K calculation.
"""
__slots__ = ['unit', 'value_no_unit', 'default_unit', 'default_name']
def __init__(self, name, default_value, default_unit, default_name):
super(Keyword, self).__init__(name)
self.unit = None
self.value_no_unit = None
self.default_unit = default_unit
self.default_value = default_value
self.default_name = default_name
def get_value(self):
def determine_value_and_unit(self):
"""If the units of this value can be changed, return a value and the
unit separately.
"""
......@@ -244,12 +253,15 @@ class Keyword(InputObject):
return self.value
def get_unit(self):
# Decode the unit and the value if not done before
if self.default_unit:
if not self.unit:
self.decode_cp2k_unit_and_value()
return self.unit
else:
logger.error("The keyword '{}' does not have a unit.".format(self.default_name))
return None
def decode_cp2k_unit_and_value(self):
"""Given a CP2K unit name, decode it as Pint unit definition.
......
parser/parser-cp2k/cp2kparser/tools/xmlpreparser.py
View file @ 13a258c5
......@@ -222,8 +222,8 @@ def generate_metainfo_recursively(obj, parent, container, name_stack):
def generate_input_object_metainfo_json(child, parent, name_stack):
path = ".".join(name_stack)
json_obj = {}
json_obj["name"] = "cp2k_{}.{}".format(path, child.name)
json_obj["superNames"] = ["cp2k_{}".format(path)]
json_obj["name"] = "x_cp2k_{}.{}".format(path, child.name)
json_obj["superNames"] = ["x_cp2k_{}".format(path)]
# Description
description = child.description
......@@ -232,22 +232,23 @@ def generate_input_object_metainfo_json(child, parent, name_stack):
json_obj["description"] = description
# Shape
data_dim = int(child.data_dimension)
if data_dim == -1:
data_dim = "n"
if data_dim == 1:
json_obj["shape"] = []
else:
json_obj["shape"] = [data_dim]
# data_dim = int(child.data_dimension)
# if data_dim == -1:
# data_dim = "n"
# if data_dim == 1:
# json_obj["shape"] = []
# else:
# json_obj["shape"] = [data_dim]
json_obj["shape"] = []
# Determine data type according to xml info
mapping = {
"keyword": "C",
"logical": "C",
"string": "C",
"integer": "i",
"integer": "C",
"word": "C",
"real": "f",
"real": "C",
}
json_obj["dtypeStr"] = mapping[child.data_type]
return json_obj
......@@ -259,9 +260,9 @@ def generate_section_metainfo_json(child, parent, name_stack):
path = ".".join(name_stack[:-1])
json_obj = {}
json_obj["name"] = "cp2k_{}".format(name)
json_obj["name"] = "x_cp2k_{}".format(name)
json_obj["kindStr"] = "type_section"
json_obj["superNames"] = ["cp2k_{}".format(path)]
json_obj["superNames"] = ["x_cp2k_{}".format(path)]
description = child.description
if description is None or description.isspace():
......
parser/parser-cp2k/cp2kparser/versions/cp2k262/inputparser.py
View file @ 13a258c5
......@@ -330,23 +330,20 @@ class CP2KInputParser(BasicParser):
for keyword in keywords:
if keyword.value is not None:
name = "{}.{}".format(path, keyword.default_name)
formatted_value = keyword.get_formatted_value()
self.add_formatted_value_to_backend(name, formatted_value)
self.backend.addValue(name, keyword.value)
# Section parameter
section_parameter = section.section_parameter
if section_parameter is not None:
name = "{}.SECTION_PARAMETERS".format(path)
formatted_value = section_parameter.get_formatted_value()
self.add_formatted_value_to_backend(name, formatted_value)
self.backend.addValue(name, section_parameter.value)
# Default keyword
default_keyword = section.default_keyword
if default_keyword is not None:
name = "{}.DEFAULT_KEYWORD".format(path)
formatted_value = default_keyword.get_formatted_value()
self.add_formatted_value_to_backend(name, formatted_value)
self.backend.addValue(name, default_keyword.value)
# Subsections
for name, subsections in section.sections.iteritems():
......@@ -357,13 +354,6 @@ class CP2KInputParser(BasicParser):
name_stack.pop()
def add_formatted_value_to_backend(self, name, formatted_value):
if formatted_value is not None:
if isinstance(formatted_value, np.ndarray):
self.backend.addArrayValues(name, formatted_value)
else:
self.backend.addValue(name, formatted_value)
def setup_version(self, version_number):
""" The pickle file which contains preparsed data from the
x_cp2k_input.xml is version specific. By calling this function before
......
test/unittests/cp2k_2.6.2/run_tests.py
View file @ 13a258c5
......@@ -444,15 +444,15 @@ class TestPreprocessor(unittest.TestCase):
def test_variable_multiple(self):
result = get_result("input_preprocessing/variable_multiple", "x_cp2k_CP2K_INPUT.FORCE_EVAL.DFT.MGRID.CUTOFF", optimize=False)
self.assertEqual(result, 50)
self.assertEqual(result, "50")
def test_comments(self):
result = get_result("input_preprocessing/comments", "x_cp2k_CP2K_INPUT.FORCE_EVAL.DFT.MGRID.CUTOFF", optimize=False)
self.assertEqual(result, 120)
self.assertEqual(result, "120")
def test_tabseparator(self):
result = get_result("input_preprocessing/tabseparator", "x_cp2k_CP2K_INPUT.FORCE_EVAL.DFT.MGRID.CUTOFF", optimize=False)
self.assertEqual(result, 120)
self.assertEqual(result, "120")
#===============================================================================
......@@ -617,17 +617,17 @@ if __name__ == '__main__':
logger.setLevel(logging.ERROR)
suites = []
# suites.append(unittest.TestLoader().loadTestsFromTestCase(TestErrors))
# suites.append(unittest.TestLoader().loadTestsFromTestCase(TestXCFunctional))
# suites.append(unittest.TestLoader().loadTestsFromTestCase(TestEnergyForce))
# suites.append(unittest.TestLoader().loadTestsFromTestCase(TestStressTensorMethods))
# suites.append(unittest.TestLoader().loadTestsFromTestCase(TestSelfInteractionCorrectionMethod))
# suites.append(unittest.TestLoader().loadTestsFromTestCase(TestConfigurationPeriodicDimensions))
# suites.append(unittest.TestLoader().loadTestsFromTestCase(TestSCFConvergence))
# suites.append(unittest.TestLoader().loadTestsFromTestCase(TestForceFiles))
suites.append(unittest.TestLoader().loadTestsFromTestCase(TestErrors))
suites.append(unittest.TestLoader().loadTestsFromTestCase(TestXCFunctional))
suites.append(unittest.TestLoader().loadTestsFromTestCase(TestEnergyForce))
suites.append(unittest.TestLoader().loadTestsFromTestCase(TestStressTensorMethods))
suites.append(unittest.TestLoader().loadTestsFromTestCase(TestSelfInteractionCorrectionMethod))
suites.append(unittest.TestLoader().loadTestsFromTestCase(TestConfigurationPeriodicDimensions))
suites.append(unittest.TestLoader().loadTestsFromTestCase(TestSCFConvergence))
suites.append(unittest.TestLoader().loadTestsFromTestCase(TestForceFiles))
suites.append(unittest.TestLoader().loadTestsFromTestCase(TestPreprocessor))
# suites.append(unittest.TestLoader().loadTestsFromTestCase(TestGeoOpt))
# suites.append(unittest.TestLoader().loadTestsFromTestCase(TestGeoOptTrajFormats))
# suites.append(unittest.TestLoader().loadTestsFromTestCase(TestGeoOptOptimizers))
suites.append(unittest.TestLoader().loadTestsFromTestCase(TestGeoOpt))
suites.append(unittest.TestLoader().loadTestsFromTestCase(TestGeoOptTrajFormats))
suites.append(unittest.TestLoader().loadTestsFromTestCase(TestGeoOptOptimizers))
alltests = unittest.TestSuite(suites)
unittest.TextTestRunner(verbosity=0).run(alltests)
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