Fixed bugs in the atomic kind labels, added some new basis set information.

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

@@ -3,7 +3,10 @@ from builtins import object
 import numpy as np
 import logging
 from collections import defaultdict
+
 logger = logging.getLogger("nomad")
+metainfo_section_prefix = "x_cp2k_section_input_"
+metainfo_data_prefix = "x_cp2k_input_"
 
 
 #===============================================================================

parser/parser-cp2k/cp2kparser/parser.py

@@ -17,8 +17,8 @@ class CP2KParser(ParserInterface):
     After the implementation has been setup, you can parse the files with
     parse().
     """
-    def __init__(self, main_file, metainfo_to_keep=None, backend=None, default_units=None, metainfo_units=None, debug=True, store=True):
-        super(CP2KParser, self).__init__(main_file, metainfo_to_keep, backend, default_units, metainfo_units, debug, store)
+    def __init__(self, main_file, metainfo_to_keep=None, backend=None, default_units=None, metainfo_units=None, debug=False, log_level=logging.ERROR, store=True):
+        super(CP2KParser, self).__init__(main_file, metainfo_to_keep, backend, default_units, metainfo_units, debug, log_level, store)
 
     def setup_version(self):
         """Setups the version by looking at the output file and the version

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

@@ -20,7 +20,7 @@ import xml.etree.cElementTree as ET
 import logging
 import json
 import pickle
-from cp2kparser.generic.inputparsing import *
+from cp2kparser.generic.inputparsing import Section, Keyword, DefaultKeyword, SectionParameters, CP2KInput, metainfo_data_prefix, metainfo_section_prefix
 logger = logging
 
 
@@ -201,15 +201,25 @@ def recursive_tree_generation(xml_element, for_metainfo=False, name_stack=[], ig
 
 #===============================================================================
 def generate_input_metainfos(object_tree):
+
+    json_root = {
+        "type": "nomad_meta_info_1_0",
+        "description": "Metainfo for the values parsed from a CP2K input file.",
+        "dependencies": [ {
+            "relativePath": "cp2k.general.nomadmetainfo.json"
+            }],
+    }
+
     parent = Section("dummy")
     root_section = object_tree.root_section
-    root_section.name = "CP2K_INPUT"
+    root_section.name = None
     root_section.description = "This section contains the explicitly stated keywords, default keywords, and section parameters in the CP2K input file. Only some of the sections that control printing (PRINT, EACH) are supported, because including all of them would double the size of this metadata without adding much useful information. The hidden input keywords starting with a double underscore are not included."
     container = []
     name_stack = []
     generate_metainfo_recursively(root_section, parent, container, name_stack)
+    json_root["metaInfos"] = container
     with open("input_metainfo.json", "w") as f:
-        f.write(json.dumps(container, indent=2, separators=(',', ': ')))
+        f.write(json.dumps(json_root, indent=2, separators=(',', ': ')))
 
 
 #===============================================================================
@@ -217,7 +227,8 @@ def generate_metainfo_recursively(obj, parent, container, name_stack):
 
     json = None
     if isinstance(obj, Section):
-        name_stack.append(obj.name)
+        if obj.name is not None:
+            name_stack.append(obj.name)
         json = generate_section_metainfo_json(obj, parent, name_stack)
         for child in obj.sections.values():
             generate_metainfo_recursively(child[0], obj, container, name_stack)
@@ -227,7 +238,8 @@ def generate_metainfo_recursively(obj, parent, container, name_stack):
             generate_metainfo_recursively(obj.section_parameter, obj, container, name_stack)
         if obj.default_keyword is not None:
             generate_metainfo_recursively(obj.default_keyword, obj, container, name_stack)
-        name_stack.pop()
+        if obj.name is not None:
+            name_stack.pop()
     else:
         json = generate_input_object_metainfo_json(obj, parent, name_stack)
     container.append(json)
@@ -236,9 +248,11 @@ def generate_metainfo_recursively(obj, parent, container, name_stack):
 #===============================================================================
 def generate_input_object_metainfo_json(child, parent, name_stack):
     path = ".".join(name_stack)
+    # if path.startswith("."):
+        # path = path[1:]
     json_obj = {}
-    json_obj["name"] = "x_cp2k_{}.{}".format(path, child.name)
-    json_obj["superNames"] = ["x_cp2k_section_{}".format(path)]
+    json_obj["name"] = metainfo_data_prefix + "{}.{}".format(path, child.name)
+    json_obj["superNames"] = [metainfo_section_prefix + "{}".format(path)]
 
     # Description
     description = child.description
@@ -271,13 +285,20 @@ def generate_input_object_metainfo_json(child, parent, name_stack):
 
 #===============================================================================
 def generate_section_metainfo_json(child, parent, name_stack):
-    name = ".".join(name_stack)
     path = ".".join(name_stack[:-1])
     json_obj = {}
+    if child.name is None:
+        json_obj["name"] = "x_cp2k_section_input"
+        json_obj["superNames"] = ["section_run"]
+    else:
+        name = ".".join(name_stack)
+        json_obj["name"] = metainfo_section_prefix + "{}".format(name)
+        if parent.name is not None:
+            json_obj["superNames"] = [metainfo_section_prefix + "{}".format(path)]
+        else:
+            json_obj["superNames"] = ["x_cp2k_section_input"]
 
-    json_obj["name"] = "x_cp2k_section_{}".format(name)
     json_obj["kindStr"] = "type_section"
-    json_obj["superNames"] = ["x_cp2k_section_{}".format(path)]
 
     description = child.description
     if description is None or description.isspace():

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

@@ -8,6 +8,7 @@ from nomadcore.caching_backend import CachingLevel
 from nomadcore.unit_conversion.unit_conversion import convert_unit
 from nomadcore.baseclasses import CommonParser
 from .inputparser import CP2KInputParser
+from collections import defaultdict
 logger = logging.getLogger("nomad")
 
 
@@ -24,6 +25,8 @@ class CP2KCommonParser(CommonParser):
         self.section_system_index = None
         self.test_electronic_structure_method = "DFT"
         self.basis_to_kind_mapping = []
+        self.atom_kind_info = defaultdict(dict)  # Map from kind number to kind information
+        self.basis_set_info = defaultdict(dict)  # Map from kind number to basis set information
 
         #=======================================================================
         # Cache levels
@@ -44,6 +47,13 @@ class CP2KCommonParser(CommonParser):
         self.cache_service.add("atom_positions", single=False, update=True)
         self.cache_service.add("atom_labels", single=False, update=False)
         self.cache_service.add("number_of_atoms", single=False, update=False)
+        self.cache_service.add("basis_set_kind", single=False, update=False)
+        self.cache_service.add("basis_set_name", single=False, update=False)
+        self.cache_service.add("basis_set_planewave_cutoff", update=False)
+        self.cache_service.add("mapping_section_basis_set_cell_dependent", single=False, update=False)
+        self.cache_service.add("map_kind_to_basis", single=False, update=False)
+        self.cache_service.add("map_index_to_kind", single=False, update=False)
+        self.cache_service.add("map_kind_number_to_basis_ref", single=False, update=False)
 
     #===========================================================================
     # SimpleMatchers
@@ -78,7 +88,7 @@ class CP2KCommonParser(CommonParser):
                         SM( " ***** **    ** ** **   PROGRAM PROCESS ID\s+(?P<x_cp2k_start_id>{})".replace("*", "\*").format(self.regexs.regex_i)),
                         SM( "  **** **  *******  **  PROGRAM STARTED IN".replace("*", "\*"),
                             forwardMatch=True,
-                            adHoc=self.adHoc_run_dir(),
+                            adHoc=self.adHoc_run_dir("x_cp2k_start_path"),
                         )
                     ]
                 ),
@@ -133,6 +143,28 @@ class CP2KCommonParser(CommonParser):
             ]
         )
 
+    # SimpleMatcher for the footer that is common to all run types
+    def footer(self):
+        return SM( " -                                DBCSR STATISTICS                             -",
+            forwardMatch=True,
+            subMatchers=[
+                SM( re.escape("  **** **** ******  **  PROGRAM ENDED AT"),
+                    forwardMatch=True,
+                    sections=['x_cp2k_section_end_information'],
+                    subMatchers=[
+                        SM( "  **** **** ******  **  PROGRAM ENDED AT\s+(?P<x_cp2k_end_time>{})".replace("*", "\*").format(self.regexs.regex_eol)),
+                        SM( " ***** ** ***  *** **   PROGRAM RAN ON\s+(?P<x_cp2k_end_host>{})".replace("*", "\*").format(self.regexs.regex_word)),
+                        SM( " **    ****   ******    PROGRAM RAN BY\s+(?P<x_cp2k_end_user>{})".replace("*", "\*").format(self.regexs.regex_word)),
+                        SM( " ***** **    ** ** **   PROGRAM PROCESS ID\s+(?P<x_cp2k_end_id>{})".replace("*", "\*").format(self.regexs.regex_i)),
+                        SM( "  **** **  *******  **  PROGRAM STOPPED IN".replace("*", "\*"),
+                            forwardMatch=True,
+                            adHoc=self.adHoc_run_dir("x_cp2k_end_path"),
+                        )
+                    ]
+                ),
+            ]
+        )
+
     # SimpleMatcher for an SCF wavefunction optimization
     def quickstep_calculation(self):
         return SM( " SCF WAVEFUNCTION OPTIMIZATION",
@@ -228,9 +260,9 @@ class CP2KCommonParser(CommonParser):
                     ],
                 ),
                 SM( " ATOMIC KIND INFORMATION",
-                    sections=["x_cp2k_section_atomic_kinds", "section_method_basis_set"],
+                    sections=["x_cp2k_section_atomic_kinds"],
                     subMatchers=[
-                        SM( "\s+(?P<x_cp2k_kind_number>{0})\. Atomic kind: (?P<x_cp2k_kind_element_symbol>{1})\s+Number of atoms:\s+(?P<x_cp2k_kind_number_of_atoms>{1})".format(self.regexs.regex_i, self.regexs.regex_word),
+                        SM( "\s+(?P<x_cp2k_kind_number>{0})\. Atomic kind: (?P<x_cp2k_kind_label>{1})\s+Number of atoms:\s+(?P<x_cp2k_kind_number_of_atoms>{1})".format(self.regexs.regex_i, self.regexs.regex_word),
                             repeats=True,
                             sections=["x_cp2k_section_atomic_kind", "x_cp2k_section_kind_basis_set"],
                             subMatchers=[
@@ -344,38 +376,86 @@ class CP2KCommonParser(CommonParser):
         backend.addValue("program_basis_set_type", "gaussian")
         backend.addValue("electronic_structure_method", self.test_electronic_structure_method)
 
-        # See if the cutoff is available
-        cutoff = section.get_latest_value("x_cp2k_planewave_cutoff")
-        if cutoff is not None:
+        # Collect the atomic kind information and push it to backend
+        kind_ids = {}
+        for kind_number, info in self.atom_kind_info.items():
+            kindID = backend.openSection("section_method_atom_kind")
+            kind_ids[kind_number] = kindID
+            label = info["label"]
+            atom_number = info.get("element_number")
+            if atom_number is not None:
+                backend.addValue("method_atom_kind_atom_number", atom_number)
+            backend.addValue("method_atom_kind_label", label)
+            backend.closeSection("section_method_atom_kind", kindID)
+
+        # Cell dependent basis information
+        ryd_cutoff = section.get_latest_value("x_cp2k_planewave_cutoff")
+        if ryd_cutoff is not None:
             gid = backend.openSection("section_basis_set_cell_dependent")
-            cutoff = convert_unit(2*cutoff, "hartree")
-            backend.addValue("basis_set_planewave_cutoff", cutoff)
+            self.cache_service["mapping_section_basis_set_cell_dependent"] = gid
+            ha_cutoff = convert_unit(2*ryd_cutoff, "hartree")
+            backend.addValue("basis_set_planewave_cutoff", ha_cutoff)
+            self.cache_service["basis_set_planewave_cutoff"] = ryd_cutoff
             backend.closeSection("section_basis_set_cell_dependent", gid)
 
-    def onClose_section_method_basis_set(self, backend, gIndex, section):
+        # Atom centered basis set information
+        basis_ids = {}
+        map_kind_number_to_basis_ref = {}
+        for kind_number, info in self.basis_set_info.items():
+            basis_section_id = backend.openSection("section_basis_set_atom_centered")
+            basis_ids[kind_number] = basis_section_id
+            map_kind_number_to_basis_ref[kind_number] = basis_section_id
+            name = info["name"]
+            atom_number = info.get("element_number")
+            if atom_number is not None:
+                backend.addValue("basis_set_atom_number", atom_number)
+            backend.addValue("basis_set_atom_centered_short_name", name)
+            backend.closeSection("section_basis_set_atom_centered", basis_section_id)
+        self.cache_service["map_kind_number_to_basis_ref"] = map_kind_number_to_basis_ref
+
+        # Add the basis infomation to section_method
+        mapping = []
+        dict_map = {}
+        for kind_number, basis_id in basis_ids.items():
+            kind_id = kind_ids[kind_number]
+            mapping.append((basis_id, kind_id))
+            dict_map[kind_id] = basis_id
+        method_basis_id = backend.openSection("section_method_basis_set")
+        if mapping:
+            mapping = np.array(mapping)
+            self.cache_service["map_kind_to_basis"] = dict_map
+            backend.addArrayValues("mapping_section_method_basis_set_atom_centered", np.array(mapping))
         backend.addValue("method_basis_set_kind", "wavefunction")
-        backend.addValue("number_of_basis_sets_atom_centered", len(self.basis_to_kind_mapping))
-        backend.addArrayValues("mapping_section_method_basis_set_atom_centered", np.array(self.basis_to_kind_mapping))
+        self.cache_service.push_value("mapping_section_method_basis_set_cell_associated")
+        backend.addValue("number_of_basis_sets_atom_centered", len(self.basis_set_info))
+        backend.closeSection("section_method_basis_set", method_basis_id)
 
     def onClose_x_cp2k_section_atomic_kind(self, backend, gIndex, section):
-        kindID = backend.openSection("section_method_atom_kind")
-        basisID = backend.openSection("section_basis_set_atom_centered")
+        # basisID = backend.openSection("section_basis_set_atom_centered")
 
-        element_symbol = section.get_latest_value("x_cp2k_kind_element_symbol")
-        kind_number = section.get_latest_value("x_cp2k_kind_number")
-        basis_set_name = section.get_latest_value(["x_cp2k_section_kind_basis_set", "x_cp2k_kind_basis_set_name"])
-        atom_number = self.get_atomic_number(element_symbol)
-        kind_label = element_symbol + str(kind_number)
-        backend.addValue("method_atom_kind_atom_number", atom_number)
-        backend.addValue("method_atom_kind_label", kind_label)
-        backend.addValue("basis_set_atom_number", atom_number)
-        backend.addValue("basis_set_atom_centered_short_name", basis_set_name)
+        # Save the kind labels. These wil be connected to atomic numbers later
+        # on when the atomic numbers are listed in the atomic positions.
+        kind_number = int(section.get_latest_value("x_cp2k_kind_number"))
+        kind_label = section.get_latest_value("x_cp2k_kind_label")
+        self.atom_kind_info[kind_number]["label"] = kind_label
 
-        # Add the reference based mapping between basis and atomic kind
-        self.basis_to_kind_mapping.append([basisID, kindID])
-
-        backend.closeSection("section_basis_set_atom_centered", basisID)
-        backend.closeSection("section_method_atom_kind", kindID)
+        # Save all the basis set information for later use. They will be pushed
+        # later when an atom number can be associated with the basis.
+        basis_set_name = section.get_latest_value(["x_cp2k_section_kind_basis_set", "x_cp2k_kind_basis_set_name"])
+        basis_info = self.basis_set_info[kind_number]
+        basis_info["name"] = basis_set_name
+
+    def onClose_x_cp2k_section_atomic_kinds(self, backend, gIndex, section):
+        # Store the name and kind of the basis set for later use (stored inside
+        # single_configuration_calculation).
+        atomic_kinds = section["x_cp2k_section_atomic_kind"]
+        long_basis_name = []
+        for kind in atomic_kinds:
+            kind_basis = kind["x_cp2k_section_kind_basis_set"][0]
+            basis_name = kind_basis["x_cp2k_kind_basis_set_name"][0]
+            long_basis_name.append(basis_name)
+        self.cache_service["basis_set_kind"] = "wavefunction"
+        self.cache_service["basis_set_name"] = "_".join(long_basis_name)
 
     def onClose_x_cp2k_section_program_information(self, backend, gIndex, section):
         input_file = section.get_latest_value("x_cp2k_input_filename")
@@ -405,6 +485,40 @@ class CP2KCommonParser(CommonParser):
         backend.addValue('single_configuration_to_calculation_method_ref', self.section_method_index)
         backend.addValue('single_configuration_calculation_to_system_ref', self.section_system_index)
 
+        scc_basis_id = backend.openSection("section_basis_set")
+
+        # Basis kind
+        self.cache_service.push_value("basis_set_kind")
+
+        # Basis name
+        basis_name = self.cache_service["basis_set_name"]
+        if basis_name is not None:
+            cutoff = self.cache_service["basis_set_planewave_cutoff"]
+            if cutoff is not None:
+                basis_name += "_PW_{}".format(cutoff)
+                backend.addValue("basis_set_name", basis_name)
+
+        # Gaussian mapping
+        map_index_to_basis = []
+        map_kind_number_to_basis_ref = self.cache_service["map_kind_number_to_basis_ref"]
+        map_index_to_kind = self.cache_service["map_index_to_kind"]
+        # print(map_kind_number_to_basis_ref)
+        # print(map_index_to_kind)
+
+        if map_index_to_kind is not None and map_kind_number_to_basis_ref is not None:
+            indices = map_index_to_kind.keys()
+            for index in sorted(indices):
+                kind = map_index_to_kind[index]
+                basis_ref = map_kind_number_to_basis_ref[kind]
+                map_index_to_basis.append(basis_ref)
+            map_index_to_basis = np.array(map_index_to_basis)
+            backend.addArrayValues("mapping_section_basis_set_atom_centered", map_index_to_basis)
+
+        # Cell dependent basis mapping
+        self.cache_service.push_value("mapping_section_basis_set_cell_dependent")
+
+        backend.closeSection("section_basis_set", scc_basis_id)
+
     #===========================================================================
     # adHoc functions
     def adHoc_x_cp2k_section_cell(self):
@@ -522,7 +636,7 @@ class CP2KCommonParser(CommonParser):
         def wrapper(parser):
 
             # Define the regex that extracts the information
-            regex_string = r"\s+\d+\s+(\d+)\s+(\w+)\s+\d+\s+({0})\s+({0})\s+({0})".format(self.regexs.regex_f)
+            regex_string = r"\s+(\d+)\s+(\d+)\s+(\w+)\s+(\d+)\s+({0})\s+({0})\s+({0})".format(self.regexs.regex_f)
             regex_compiled = re.compile(regex_string)
 
             match = True
@@ -533,6 +647,7 @@ class CP2KCommonParser(CommonParser):
             parser.fIn.readline()
             parser.fIn.readline()
             parser.fIn.readline()
+            map_index_to_kind = {}
 
             while match:
                 line = parser.fIn.readline()
@@ -540,14 +655,22 @@ class CP2KCommonParser(CommonParser):
 
                 if result:
                     match = True
-                    label = result.groups()[1] + result.groups()[0]
+                    kind_number = int(result.groups()[1])
+                    element_number = int(result.groups()[3])
+                    index = int(result.groups()[0])
+                    map_index_to_kind[index] = kind_number
+                    info = self.atom_kind_info[kind_number]
+                    label = info["label"]
+                    info["element_number"] = element_number
+                    self.basis_set_info[kind_number]["element_number"] = element_number
                     labels.append(label)
-                    coordinate = [float(x) for x in result.groups()[2:]]
+                    coordinate = [float(x) for x in result.groups()[4:]]
                     coordinates.append(coordinate)
                 else:
                     match = False
             coordinates = np.array(coordinates)
             labels = np.array(labels)
+            self.cache_service["map_index_to_kind"] = map_index_to_kind
 
             # If anything found, push the results to the correct section
             if len(coordinates) != 0:
@@ -556,16 +679,16 @@ class CP2KCommonParser(CommonParser):
 
         return wrapper
 
-    def adHoc_run_dir(self):
+    def adHoc_run_dir(self, metaname):
         def wrapper(parser):
             end_str = "\n"
             end = False
             path_array = []
 
-            # Loop through coordinates until the sum of forces is read
+            # Loop through lines until empty line is encountered
             while not end:
                 line = parser.fIn.readline()
-                if line.startswith(end_str):
+                if line == end_str or len(line) == 0:
                     end = True
                 else:
                     path_part = line.split()[-1]
@@ -573,7 +696,7 @@ class CP2KCommonParser(CommonParser):
 
             # Form the final path and push to backend
             path = "".join(path_array)
-            parser.backend.addValue("x_cp2k_start_path", path)
+            parser.backend.addValue(metaname, path)
 
         return wrapper
 

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

@@ -174,7 +174,8 @@ class CP2KGeoOptParser(MainHierarchicalParser):
                         self.cm.quickstep_header(),
                     ],
                 ),
-                self.geo_opt
+                self.geo_opt,
+                self.cm.footer(),
             ]
         )
 

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

@@ -7,7 +7,7 @@ import logging
 import pickle
 import numpy as np
 from nomadcore.baseclasses import BasicParser
-from cp2kparser.generic.inputparsing import *
+from cp2kparser.generic.inputparsing import metainfo_data_prefix, metainfo_section_prefix
 logger = logging.getLogger("nomad")
 
 
@@ -409,9 +409,13 @@ class CP2KInputParser(BasicParser):
         if not section.accessed:
             return
 
-        name_stack.append(section.name)
-        path = "x_cp2k_section_{}".format(".".join(name_stack))
-        not_section_path = "x_cp2k_{}".format(".".join(name_stack))
+        if section.name == "CP2K_INPUT":
+            path = "x_cp2k_section_input"
+        else:
+            name_stack.append(section.name)
+            path = metainfo_section_prefix + "{}".format(".".join(name_stack))
+
+        not_section_path = metainfo_data_prefix + "{}".format(".".join(name_stack))
 
         gid = self.backend.openSection(path)
 
@@ -444,14 +448,15 @@ class CP2KInputParser(BasicParser):
 
         self.backend.closeSection(path, gid)
 
-        name_stack.pop()
+        if section.name != "CP2K_INPUT":
+            name_stack.pop()
 
     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
         parsing the correct file can be found.
         """
-        pickle_path = os.path.dirname(__file__) + "/input_data/cp2k_input_tree.pickle".format(version_number)
+        pickle_path = os.path.dirname(__file__) + "/input_data/cp2k_input_tree.pickle"
         input_tree_pickle_file = open(pickle_path, 'rb')
         self.input_tree = pickle.load(input_tree_pickle_file)
 

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

@@ -141,6 +141,7 @@ class CP2KMDParser(MainHierarchicalParser):
                     ],
                 ),
                 self.md,
+                self.cm.footer(),
             ]
         )
 

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

@@ -40,6 +40,7 @@ class CP2KSinglePointParser(MainHierarchicalParser):
                 self.cm.header(),
                 self.cm.quickstep_header(),
                 self.cm.quickstep_calculation(),
+                self.cm.footer(),
             ]
         )
 

test/unittests/cp2k_2.6.2/kinds/Si_bulk8-nonbonded_nl_p0-1.out

+
+
+ NONBONDED NEIGHBOR LISTS IN angstrom (PROCESS 0)
+  Atom-A     X          Y          Z     Atom-B     X          Y          Z      Cell(i,j,k)          Distance ONFO VDW-scale EI-scale
+       7   1.357674  -1.357674  -1.357674     1   0.000000   0.000000   0.000000   0   0   0            2.3516
+       5  -1.357674   1.357674  -1.357674     1   0.000000   0.000000   0.000000   0   0   0            2.3516
+       8  -1.357674  -1.357674   1.357674     1   0.000000   0.000000   0.000000   0   0   0            2.3516
+       6   1.357674   1.357674   1.357674     1   0.000000   0.000000   0.000000   0   0   0            2.3516
+       6   1.357674   1.357674   1.357674     2   0.000000   2.715349   2.715349   0   0   0            2.3516
+       6   1.357674   1.357674   1.357674     3   2.715349   2.715349   0.000000   0   0   0            2.3516
+       6   1.357674   1.357674   1.357674     4   2.715349   0.000000   2.715349   0   0   0            2.3516
+       7   1.357674  -1.357674  -1.357674     3   2.715349   2.715349   0.000000   0  -1   0            2.3516
+       5  -1.357674   1.357674  -1.357674     3   2.715349   2.715349   0.000000  -1   0   0            2.3516
+       8  -1.357674  -1.357674   1.357674     4   2.715349   0.000000   2.715349  -1   0   0            2.3516
+       2   0.000000   2.715349   2.715349     8  -1.357674  -1.357674   1.357674   0   1   0            2.3516
+       3   2.715349   2.715349   0.000000     8  -1.357674  -1.357674   1.357674   1   1   0            2.3516
+       4   2.715349   0.000000   2.715349     7   1.357674  -1.357674  -1.357674   0   0   1            2.3516
+       2   0.000000   2.715349   2.715349     5  -1.357674   1.357674  -1.357674   0   0   1            2.3516
+       4   2.715349   0.000000   2.715349     5  -1.357674   1.357674  -1.357674   1   0   1            2.3516
+       2   0.000000   2.715349   2.715349     7   1.357674  -1.357674  -1.357674   0   1   1            2.3516
+
+ Total number of neighbor interactions for process 0: 16

test/unittests/cp2k_2.6.2/kinds/si_bulk8.inp

+&GLOBAL
+  PROJECT Si_bulk8
+  RUN_TYPE ENERGY_FORCE
+  PRINT_LEVEL HIGH
+&END GLOBAL
+&FORCE_EVAL
+  METHOD Quickstep
+  STRESS_TENSOR ANALYTICAL
+  &SUBSYS
+    &KIND SiA
+      ELEMENT   Si
+      BASIS_SET DZVP-GTH-PADE
+      POTENTIAL GTH-PADE-q4
+    &END KIND
+    &KIND SiB
+      ELEMENT   Si
+      BASIS_SET SZV-GTH-PADE
+      POTENTIAL GTH-PADE-q4
+    &END KIND
+    &CELL
+      A     5.430697500    0.000000000    0.000000000
+      B     0.000000000    5.430697500    0.000000000
+      C     0.000000000    0.000000000    5.430697500
+    &END CELL
+    &COORD
+      SiA    0.000000000    0.000000000    0.000000000
+      SiA    0.000000000    2.715348700    2.715348700
+      SiA    2.715348700    2.715348700    0.000000000
+      SiA    2.715348700    0.000000000    2.715348700
+      SiB    4.073023100    1.357674400    4.073023100
+      SiB    1.357674400    1.357674400    1.357674400
+      SiB    1.357674400    4.073023100    4.073023100
+      SiB    4.073023100    4.073023100    1.357674400
+    &END COORD
+  &END SUBSYS
+  &DFT
+    BASIS_SET_FILE_NAME  ../BASIS_SET
+    POTENTIAL_FILE_NAME  ../GTH_POTENTIALS
+    &QS
+      EPS_DEFAULT 1.0E-10
+    &END QS
+    &MGRID
+      NGRIDS 4
+      CUTOFF 300
+      REL_CUTOFF 60
+    &END MGRID
+    &XC
+      &XC_FUNCTIONAL PADE
+      &END XC_FUNCTIONAL
+    &END XC
+    &SCF
+      SCF_GUESS ATOMIC
+      EPS_SCF 1.0E-7
+      MAX_SCF 300
+      &DIAGONALIZATION  ON
+        ALGORITHM STANDARD
+      &END DIAGONALIZATION
+      &MIXING  T
+        METHOD BROYDEN_MIXING
+        ALPHA 0.4
+        NBROYDEN 8
+      &END MIXING
+    &END SCF
+  &END DFT
+  &PRINT
+    &FORCES ON
+    &END FORCES
+  &END PRINT
+&END FORCE_EVAL

test/unittests/cp2k_2.6.2/run_tests.py

@@ -17,21 +17,6 @@ import numpy as np
 from cp2kparser import CP2KParser
 from nomadcore.unit_conversion.unit_conversion import convert_unit