Fixed issue with pushing arrays with addValue.

parser/parser-cp2k/cp2kparser/generic/inputparsing.py

@@ -164,21 +164,6 @@ class InputObject(object):
         self.data_dimension = None
         self.default_value = None
 
-
-#===============================================================================
-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_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.
@@ -214,6 +199,21 @@ class Keyword(InputObject):
 
         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):
         """If the units of this value can be changed, return a value and the
         unit separately.
@@ -252,7 +252,7 @@ class Keyword(InputObject):
 
 
 #===============================================================================
-class Section(InputObject):
+class Section(object):
     """An input section in a CP2K calculation.
     """
     __slots__ = ['accessed', 'name', 'keywords', 'default_keyword_names', 'default_keyword', 'section_parameter', 'sections', 'description']
@@ -305,8 +305,9 @@ class SectionParameters(InputObject):
 class DefaultKeyword(InputObject):
     """Default keyword in the CP2K input.
     """
+    __slots__ = ['lone_value']
+
     def __init__(self):
         super(DefaultKeyword, self).__init__("DEFAULT_KEYWORD")
-        self.default_value = None
         self.lone_value = None
         self.value = ""

parser/parser-cp2k/cp2kparser/tools/xmlpreparser.py

@@ -227,8 +227,8 @@ def generate_input_object_metainfo_json(child, parent, name_stack):
 
     # Description
     description = child.description
-    if description is None:
-        description = ""
+    if description is None or description.isspace():
+        description = "Settings for {}".format(child.name)
     json_obj["description"] = description
 
     # Shape
@@ -264,8 +264,8 @@ def generate_section_metainfo_json(child, parent, name_stack):
     json_obj["superNames"] = ["x_cp2k_{}".format(path)]
 
     description = child.description
-    if description is None:
-        description = ""
+    if description is None or description.isspace():
+        description = "Settings for {}".format(child.name)
     json_obj["description"] = description
     return json_obj
 

parser/parser-cp2k/cp2kparser/versions/cp2k262/inputparser.py

@@ -278,17 +278,24 @@ class CP2KInputParser(BasicParser):
             keywords = section.keywords.get(default_name)
             for keyword in keywords:
                 if keyword.value is not None:
+                    name = "{}.{}".format(path, keyword.default_name)
                     formatted_value = keyword.get_formatted_value()
-                    if formatted_value is not None:
-                        self.backend.addValue("{}.{}".format(path, keyword.default_name), formatted_value)
+                    self.add_formatted_value_to_backend(name, formatted_value)
 
         # Section parameter
-        if section.section_parameter is not None:
-            self.backend.addValue("{}.SECTION_PARAMETERS".format(path), section.section_parameter.value)
+        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)
 
         # Default keyword
-        if section.default_keyword is not None:
-            self.backend.addValue("{}.DEFAULT_KEYWORD".format(path), section.default_keyword.value)
+        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)
 
         # Subsections
         for name, subsections in section.sections.iteritems():
@@ -299,6 +306,13 @@ 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
         cp2k_input.xml is version specific. By calling this function before

test/unittests/cp2k_2.6.2/run_tests.py

@@ -270,7 +270,7 @@ class TestEnergyForce(unittest.TestCase):
     @classmethod
     def setUpClass(cls):
         cls.results = get_results("energy_force", "section_run")
-        # cls.results.print_summary()
+        cls.results.print_summary()
 
     def test_energy_total_scf_iteration(self):
         energy_total = self.results["energy_total_scf_iteration"]
@@ -450,14 +450,14 @@ 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(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(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))
     alltests = unittest.TestSuite(suites)
     unittest.TextTestRunner(verbosity=0).run(alltests)