diff --git a/parser/parser-cp2k/cp2kparser/generic/inputparsing.py b/parser/parser-cp2k/cp2kparser/generic/inputparsing.py
index d8132de861b56f36d875b2e175f29d6fe5022552..4d918bbc0bcf5dd0e43e756a4b17c0ff34cfbd44 100644
--- a/parser/parser-cp2k/cp2kparser/generic/inputparsing.py
+++ b/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_"
#===============================================================================
diff --git a/parser/parser-cp2k/cp2kparser/parser.py b/parser/parser-cp2k/cp2kparser/parser.py
index c1dabfc9e9b6e3469762a24b525328a18dd24101..c827ce62166c25b71f5ac1f3e06c8169932e3710 100644
--- a/parser/parser-cp2k/cp2kparser/parser.py
+++ b/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
diff --git a/parser/parser-cp2k/cp2kparser/tools/xmlpreparser.py b/parser/parser-cp2k/cp2kparser/tools/xmlpreparser.py
index 24465b1a5b5a8e012033411fdcc0d5f18a572847..b260685518ea9d50de3ecf4817dcad99c23c1c3e 100644
--- a/parser/parser-cp2k/cp2kparser/tools/xmlpreparser.py
+++ b/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():
diff --git a/parser/parser-cp2k/cp2kparser/versions/cp2k262/commonparser.py b/parser/parser-cp2k/cp2kparser/versions/cp2k262/commonparser.py
index e0c81e8ffb8f1572a55b8eb73b7aa3aa0be62b17..d6783c4069ac53a14f2b27447eb6d225ac60566a 100644
--- a/parser/parser-cp2k/cp2kparser/versions/cp2k262/commonparser.py
+++ b/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
diff --git a/parser/parser-cp2k/cp2kparser/versions/cp2k262/geooptparser.py b/parser/parser-cp2k/cp2kparser/versions/cp2k262/geooptparser.py
index 5cd51d8906855b435ae0a852ee1986c4e91f0141..acfe003de8ae756ec058d9ce7c75ee4c584c585a 100644
--- a/parser/parser-cp2k/cp2kparser/versions/cp2k262/geooptparser.py
+++ b/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(),
]
)
diff --git a/parser/parser-cp2k/cp2kparser/versions/cp2k262/input_data/cp2k_input_tree.pickle b/parser/parser-cp2k/cp2kparser/versions/cp2k262/input_data/cp2k_input_tree.pickle
index 1bb32cd82a7065c7e1f1fc5ce116b4dc2bb3f3ad..9179b1cfff426da9b204ad22d0b88e462af24c60 100644
Binary files a/parser/parser-cp2k/cp2kparser/versions/cp2k262/input_data/cp2k_input_tree.pickle and b/parser/parser-cp2k/cp2kparser/versions/cp2k262/input_data/cp2k_input_tree.pickle differ
diff --git a/parser/parser-cp2k/cp2kparser/versions/cp2k262/inputparser.py b/parser/parser-cp2k/cp2kparser/versions/cp2k262/inputparser.py
index ef2a6ef38660c7f30e86d04d59892ecdec81e5f2..d282357755cc52a954bcfa8676c2de493f0b16b4 100644
--- a/parser/parser-cp2k/cp2kparser/versions/cp2k262/inputparser.py
+++ b/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)
diff --git a/parser/parser-cp2k/cp2kparser/versions/cp2k262/mdparser.py b/parser/parser-cp2k/cp2kparser/versions/cp2k262/mdparser.py
index 42eb8736adce5251105b255b70a53ac416efff44..ac948b76b0fd185c4b6e36c3a8af766ac4b6a74f 100644
--- a/parser/parser-cp2k/cp2kparser/versions/cp2k262/mdparser.py
+++ b/parser/parser-cp2k/cp2kparser/versions/cp2k262/mdparser.py
@@ -141,6 +141,7 @@ class CP2KMDParser(MainHierarchicalParser):
],
),
self.md,
+ self.cm.footer(),
]
)
diff --git a/parser/parser-cp2k/cp2kparser/versions/cp2k262/singlepointparser.py b/parser/parser-cp2k/cp2kparser/versions/cp2k262/singlepointparser.py
index 534a28d582e6dc0cb9b6c789750adc1baf146dea..ccf0cdb8ced29cfbd6c778a9b80844f03e2ba164 100644
--- a/parser/parser-cp2k/cp2kparser/versions/cp2k262/singlepointparser.py
+++ b/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(),
]
)
diff --git a/test/unittests/cp2k_2.6.2/kinds/Si_bulk8-nonbonded_nl_p0-1.out b/test/unittests/cp2k_2.6.2/kinds/Si_bulk8-nonbonded_nl_p0-1.out
new file mode 100644
index 0000000000000000000000000000000000000000..17f36a2fe1f9cbeff060b55bd75f237760dc125c
--- /dev/null
+++ b/test/unittests/cp2k_2.6.2/kinds/Si_bulk8-nonbonded_nl_p0-1.out
@@ -0,0 +1,22 @@
+
+
+ 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
diff --git a/test/unittests/cp2k_2.6.2/kinds/si_bulk8.inp b/test/unittests/cp2k_2.6.2/kinds/si_bulk8.inp
new file mode 100644
index 0000000000000000000000000000000000000000..898415717e708673d84307ebb649e25e49ff36ed
--- /dev/null
+++ b/test/unittests/cp2k_2.6.2/kinds/si_bulk8.inp
@@ -0,0 +1,69 @@
+&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
diff --git a/test/unittests/cp2k_2.6.2/kinds/unittest.out b/test/unittests/cp2k_2.6.2/kinds/unittest.out
new file mode 100644
index 0000000000000000000000000000000000000000..805f97ba6fa21e7f002cb1886c94c039f85afe53
--- /dev/null
+++ b/test/unittests/cp2k_2.6.2/kinds/unittest.out
@@ -0,0 +1,1363 @@
+ DBCSR| Multiplication driver SMM
+ DBCSR| Multrec recursion limit 512
+ DBCSR| Multiplication stack size 1000
+ DBCSR| Multiplication size stacks 3
+ DBCSR| Use subcommunicators T
+ DBCSR| Use MPI combined types F
+ DBCSR| Use MPI memory allocation T
+ DBCSR| Use Communication thread T
+ DBCSR| Communication thread load 87
+
+
+ **** **** ****** ** PROGRAM STARTED AT 2016-07-14 13:55:58.275
+ ***** ** *** *** ** PROGRAM STARTED ON lenovo700
+ ** **** ****** PROGRAM STARTED BY lauri
+ ***** ** ** ** ** PROGRAM PROCESS ID 10179
+ **** ** ******* ** PROGRAM STARTED IN /home/lauri/Dropbox/nomad-dev/nomad-l
+ ab-base/parsers/cp2k/test/unittests/c
+ p2k_2.6.2/kinds
+
+ CP2K| version string: CP2K version 2.6.2
+ CP2K| source code revision number: svn:15893
+ CP2K| is freely available from http://www.cp2k.org/
+ CP2K| Program compiled at ma 13.6.2016 11.25.35 +0300
+ CP2K| Program compiled on lenovo700
+ CP2K| Program compiled for Linux-x86-64-gfortran_basic
+ CP2K| Input file name si_bulk8.inp
+
+ GLOBAL| Force Environment number 1
+ GLOBAL| Basis set file name ../BASIS_SET
+ GLOBAL| Geminal file name BASIS_GEMINAL
+ GLOBAL| Potential file name ../GTH_POTENTIALS
+ GLOBAL| MM Potential file name MM_POTENTIAL
+ GLOBAL| Coordinate file name __STD_INPUT__
+ GLOBAL| Method name CP2K
+ GLOBAL| Project name Si_bulk8
+ GLOBAL| Preferred FFT library FFTW3
+ GLOBAL| Preferred diagonalization lib. SL
+ GLOBAL| Run type ENERGY_FORCE
+ GLOBAL| All-to-all communication in single precision F
+ GLOBAL| FFTs using library dependent lengths F
+ GLOBAL| Global print level HIGH
+ GLOBAL| Total number of message passing processes 1
+ GLOBAL| Number of threads for this process 1
+ GLOBAL| This output is from process 0
+
+ MEMORY| system memory details [Kb]
+ MEMORY| rank 0 min max average
+ MEMORY| MemTotal 7962000 7962000 7962000 7962000
+ MEMORY| MemFree 3247660 3247660 3247660 3247660
+ MEMORY| Buffers 121336 121336 121336 121336
+ MEMORY| Cached 1874160 1874160 1874160 1874160
+ MEMORY| Slab 169280 169280 169280 169280
+ MEMORY| SReclaimable 120292 120292 120292 120292
+ MEMORY| MemLikelyFree 5363448 5363448 5363448 5363448
+
+
+ *** Fundamental physical constants (SI units) ***
+
+ *** Literature: B. J. Mohr and B. N. Taylor,
+ *** CODATA recommended values of the fundamental physical
+ *** constants: 2006, Web Version 5.1
+ *** http://physics.nist.gov/constants
+
+ Speed of light in vacuum [m/s] 2.99792458000000E+08
+ Magnetic constant or permeability of vacuum [N/A**2] 1.25663706143592E-06
+ Electric constant or permittivity of vacuum [F/m] 8.85418781762039E-12
+ Planck constant (h) [J*s] 6.62606896000000E-34
+ Planck constant (h-bar) [J*s] 1.05457162825177E-34
+ Elementary charge [C] 1.60217648700000E-19
+ Electron mass [kg] 9.10938215000000E-31
+ Electron g factor [ ] -2.00231930436220E+00
+ Proton mass [kg] 1.67262163700000E-27
+ Fine-structure constant 7.29735253760000E-03
+ Rydberg constant [1/m] 1.09737315685270E+07
+ Avogadro constant [1/mol] 6.02214179000000E+23
+ Boltzmann constant [J/K] 1.38065040000000E-23
+ Atomic mass unit [kg] 1.66053878200000E-27
+ Bohr radius [m] 5.29177208590000E-11
+
+ *** Conversion factors ***
+
+ [u] -> [a.u.] 1.82288848426455E+03
+ [Angstrom] -> [Bohr] = [a.u.] 1.88972613288564E+00
+ [a.u.] = [Bohr] -> [Angstrom] 5.29177208590000E-01
+ [a.u.] -> [s] 2.41888432650478E-17
+ [a.u.] -> [fs] 2.41888432650478E-02
+ [a.u.] -> [J] 4.35974393937059E-18
+ [a.u.] -> [N] 8.23872205491840E-08
+ [a.u.] -> [K] 3.15774647902944E+05
+ [a.u.] -> [kJ/mol] 2.62549961709828E+03
+ [a.u.] -> [kcal/mol] 6.27509468713739E+02
+ [a.u.] -> [Pa] 2.94210107994716E+13
+ [a.u.] -> [bar] 2.94210107994716E+08
+ [a.u.] -> [atm] 2.90362800883016E+08
+ [a.u.] -> [eV] 2.72113838565563E+01
+ [a.u.] -> [Hz] 6.57968392072181E+15
+ [a.u.] -> [1/cm] (wave numbers) 2.19474631370540E+05
+ [a.u./Bohr**2] -> [1/cm] 5.14048714338585E+03
+
+
+ CELL_TOP| Volume [angstrom^3]: 160.165
+ CELL_TOP| Vector a [angstrom 5.431 0.000 0.000 |a| = 5.431
+ CELL_TOP| Vector b [angstrom 0.000 5.431 0.000 |b| = 5.431
+ CELL_TOP| Vector c [angstrom 0.000 0.000 5.431 |c| = 5.431
+ CELL_TOP| Angle (b,c), alpha [degree]: 90.000
+ CELL_TOP| Angle (a,c), beta [degree]: 90.000
+ CELL_TOP| Angle (a,b), gamma [degree]: 90.000
+ CELL_TOP| Numerically orthorhombic: YES
+
+
+ SUBCELL GRID INFO FOR THE NONBONDED NEIGHBOR LISTS
+
+ NUMBER OF SUBCELLS :: 2 2 2
+ NUMBER OF PERIODIC IMAGES :: 1 1 1
+ NUMBER OF INTERACTING SUBCELLS :: 2 2 2
+
+ GENERATE| Preliminary Number of Bonds generated: 0
+ GENERATE| Achieved consistency in connectivity generation.
+
+ CELL| Volume [angstrom^3]: 160.165
+ CELL| Vector a [angstrom]: 5.431 0.000 0.000 |a| = 5.431
+ CELL| Vector b [angstrom]: 0.000 5.431 0.000 |b| = 5.431
+ CELL| Vector c [angstrom]: 0.000 0.000 5.431 |c| = 5.431
+ CELL| Angle (b,c), alpha [degree]: 90.000
+ CELL| Angle (a,c), beta [degree]: 90.000
+ CELL| Angle (a,b), gamma [degree]: 90.000
+ CELL| Numerically orthorhombic: YES
+
+ CELL_REF| Volume [angstrom^3]: 160.165
+ CELL_REF| Vector a [angstrom 5.431 0.000 0.000 |a| = 5.431
+ CELL_REF| Vector b [angstrom 0.000 5.431 0.000 |b| = 5.431
+ CELL_REF| Vector c [angstrom 0.000 0.000 5.431 |c| = 5.431
+ CELL_REF| Angle (b,c), alpha [degree]: 90.000
+ CELL_REF| Angle (a,c), beta [degree]: 90.000
+ CELL_REF| Angle (a,b), gamma [degree]: 90.000
+ CELL_REF| Numerically orthorhombic: YES
+
+ *******************************************************************************
+ *******************************************************************************
+ ** **
+ ** ##### ## ## **
+ ** ## ## ## ## ## **
+ ** ## ## ## ###### **
+ ** ## ## ## ## ## ##### ## ## #### ## ##### ##### **
+ ** ## ## ## ## ## ## ## ## ## ## ## ## ## ## **
+ ** ## ## ## ## ## ## ## #### ### ## ###### ###### **
+ ** ## ### ## ## ## ## ## ## ## ## ## ## **
+ ** ####### ##### ## ##### ## ## #### ## ##### ## **
+ ** ## ## **
+ ** **
+ ** ... make the atoms dance **
+ ** **
+ ** Copyright (C) by CP2K Developers Group (2000 - 2014) **
+ ** **
+ *******************************************************************************
+
+ RADII: ORBITAL BASIS in angstrom Kind Label Radius OCE Radius
+ 1 SiA 7.289139 7.289139
+ 2 SiB 6.924148 6.924148
+
+ RADII: SHELL SETS OF ORBITAL BASIS in angstrom Kind Label Set Radius
+ 1 SiA 1 7.289139
+ 2 3.018919
+ 2 SiB 1 6.924148
+
+ RADII: PRIMITIVE GAUSSIANS OF ORBITAL BASIS in anKindomLabel Set Radius
+ 1 SiA 1 1.540830
+ 2.581331
+ 4.306488
+ 7.289139
+ 1 SiA 2 3.018919
+ 2 SiB 1 1.540830
+ 2.581331
+ 4.306488
+ 6.924148
+
+ RADII: GEMINAL BASIS in angstrom Kind Label Radius
+ 1 SiA no basis
+ 2 SiB no basis
+
+ RADII: SHELL SETS OF GEMINAL BASIS in angstrom Kind Label Set Radius
+ 1 SiA no basis
+ 2 SiB no basis
+
+ RADII: PRIMITIVE GEMINALS OF GEMINAL BASIS in angKindm Label Set Radius
+ 1 SiA no basis
+ 2 SiB no basis
+
+ RADII: AUXILLIARY BASIS in angstrom Kind Label Radius OCE Radius
+ 1 SiA no basis
+ 2 SiB no basis
+
+ RADII: SHELL SETS OF AUXILLIARY BASIS in angstromKind Label Set Radius
+ 1 SiA no basis
+ 2 SiB no basis
+
+ RADII: PRIMITIVE GAUSSIANS OF AUXILLIARY BASIS inKindstLabel Set Radius
+ 1 SiA no basis
+ 2 SiB no basis
+
+ RADII: LOCAL RI BASIS in angstrom Kind Label Radius OCE Radius
+ 1 SiA no basis
+ 2 SiB no basis
+
+ RADII: SHELL SETS OF LOCAL RI BASIS in angstrom Kind Label Set Radius
+ 1 SiA no basis
+ 2 SiB no basis
+
+ RADII: PRIMITIVE GAUSSIANS OF LOCAL RI BASIS in aKindroLabel Set Radius
+ 1 SiA no basis
+ 2 SiB no basis
+
+ RADII: CORE CHARGE DISTRIBUTIONS in angstrom Kind Label Radius
+ 1 SiA 1.764766
+ 2 SiB 1.764766
+
+ RADII: LOCAL PART OF GTH/ELP PP in angstrom Kind Label Radius
+ 1 SiA 0.845813
+ 2 SiB 0.845813
+
+ RADII: NON-LOCAL PART OF GTH PP in angstrom Kind Label Radius
+ 1 SiA 1.379482
+ 2 SiB 1.379482
+
+ RADII: ONE CENTER PROJECTORS in angstrom Kind Label Radius
+
+ DISTRIBUTION OF THE MOLECULES Process Number of molecules
+ 0 8
+ Sum 8
+
+ Process Kind Local molecules (global indices)
+ 0 1 1
+ 2 2
+ 3 3
+ 4 4
+ 5 5
+ 6 6
+ 7 7
+ 8 8
+
+ DISTRIBUTION OF THE PARTICLES Process Number of particles
+ 0 8
+ Sum 8
+
+ Process Kind Local particles (global indices)
+ 0 1 1 2 3 4
+ 2 5 6 7 8
+
+ DFT| Spin restricted Kohn-Sham (RKS) calculation RKS
+ DFT| Multiplicity 1
+ DFT| Number of spin states 1
+ DFT| Charge 0
+ DFT| Self-interaction correction (SIC) NO
+ DFT| Cutoffs: density 1.000000E-10
+ DFT| gradient 1.000000E-10
+ DFT| tau 1.000000E-10
+ DFT| cutoff_smoothing_range 0.000000E+00
+ DFT| XC density smoothing NONE
+ DFT| XC derivatives PW
+ FUNCTIONAL| ROUTINE=NEW
+ FUNCTIONAL| PADE:
+ FUNCTIONAL| S. Goedecker, M. Teter and J. Hutter, Phys. Rev. B 54, 1703 (1996)
+
+ QS| Method: GPW
+ QS| Density plane wave grid type NON-SPHERICAL FULLSPACE
+ QS| Number of grid levels: 4
+ QS| Density cutoff [a.u.]: 150.0
+ QS| Multi grid cutoff [a.u.]: 1) grid level 150.0
+ QS| 2) grid level 50.0
+ QS| 3) grid level 16.7
+ QS| 4) grid level 5.6
+ QS| Grid level progression factor: 3.0
+ QS| Relative density cutoff [a.u.]: 30.0
+ QS| Consistent realspace mapping and integration
+ QS| Interaction thresholds: eps_pgf_orb: 1.0E-05
+ QS| eps_filter_matrix: 0.0E+00
+ QS| eps_core_charge: 1.0E-12
+ QS| eps_rho_gspace: 1.0E-10
+ QS| eps_rho_rspace: 1.0E-10
+ QS| eps_gvg_rspace: 1.0E-05
+ QS| eps_ppl: 1.0E-02
+ QS| eps_ppnl: 1.0E-07
+
+
+ ATOMIC KIND INFORMATION
+
+ 1. Atomic kind: SiA Number of atoms: 4
+
+ Orbital Basis Set DZVP-GTH-PADE
+
+ Number of orbital shell sets: 2
+ Number of orbital shells: 5
+ Number of primitive Cartesian functions: 5
+ Number of Cartesian basis functions: 14
+ Number of spherical basis functions: 13
+ Norm type: 2
+
+ Normalised Cartesian orbitals:
+
+ Set Shell Orbital Exponent Coefficient
+
+ 1 1 3s 1.203242 0.269412
+ 0.468841 -0.102290
+ 0.167986 -0.147195
+ 0.057562 -0.015996
+
+ 1 2 4s 1.203242 0.000000
+ 0.468841 0.000000
+ 0.167986 0.000000
+ 0.057562 0.083755
+
+ 1 3 4px 1.203242 0.085242
+ 0.468841 -0.143473
+ 0.167986 -0.083408
+ 0.057562 -0.014565
+ 1 3 4py 1.203242 0.085242
+ 0.468841 -0.143473
+ 0.167986 -0.083408
+ 0.057562 -0.014565
+ 1 3 4pz 1.203242 0.085242
+ 0.468841 -0.143473
+ 0.167986 -0.083408
+ 0.057562 -0.014565
+
+ 1 4 5px 1.203242 0.000000
+ 0.468841 0.000000
+ 0.167986 0.000000
+ 0.057562 0.040189
+ 1 4 5py 1.203242 0.000000
+ 0.468841 0.000000
+ 0.167986 0.000000
+ 0.057562 0.040189
+ 1 4 5pz 1.203242 0.000000
+ 0.468841 0.000000
+ 0.167986 0.000000
+ 0.057562 0.040189
+
+ 2 1 3dx2 0.450000 0.406941
+ 2 1 3dxy 0.450000 0.704842
+ 2 1 3dxz 0.450000 0.704842
+ 2 1 3dy2 0.450000 0.406941
+ 2 1 3dyz 0.450000 0.704842
+ 2 1 3dz2 0.450000 0.406941
+
+ Potential information for GTH-PADE-q4
+
+ Description: Goedecker-Teter-Hutter pseudopotential
+ Goedecker et al., PRB 54, 1703 (1996)
+ Hartwigsen et al., PRB 58, 3641 (1998)
+ Krack, TCA 114, 145 (2005)
+
+ Gaussian exponent of the core charge distribution: 2.582645
+ Electronic configuration (s p d ...): 2 2
+
+ Parameters of the local part of the GTH pseudopotential:
+
+ rloc C1 C2 C3 C4
+ 0.440000 -7.336103
+
+ Parameters of the non-local part of the GTH pseudopotential:
+
+ l r(l) h(i,j,l)
+
+ 0 0.422738 5.906928 -1.261894
+ -1.261894 3.258196
+ 1 0.484278 2.727013
+
+ 2. Atomic kind: SiB Number of atoms: 4
+
+ Orbital Basis Set SZV-GTH-PADE
+
+ Number of orbital shell sets: 1
+ Number of orbital shells: 2
+ Number of primitive Cartesian functions: 4
+ Number of Cartesian basis functions: 4
+ Number of spherical basis functions: 4
+ Norm type: 2
+
+ Normalised Cartesian orbitals:
+
+ Set Shell Orbital Exponent Coefficient
+
+ 1 1 3s 1.203242 0.269412
+ 0.468841 -0.102290
+ 0.167986 -0.147195
+ 0.057562 -0.015996
+
+ 1 2 4px 1.203242 0.085242
+ 0.468841 -0.143473
+ 0.167986 -0.083408
+ 0.057562 -0.014565
+ 1 2 4py 1.203242 0.085242
+ 0.468841 -0.143473
+ 0.167986 -0.083408
+ 0.057562 -0.014565
+ 1 2 4pz 1.203242 0.085242
+ 0.468841 -0.143473
+ 0.167986 -0.083408
+ 0.057562 -0.014565
+
+ Potential information for GTH-PADE-q4
+
+ Description: Goedecker-Teter-Hutter pseudopotential
+ Goedecker et al., PRB 54, 1703 (1996)
+ Hartwigsen et al., PRB 58, 3641 (1998)
+ Krack, TCA 114, 145 (2005)
+
+ Gaussian exponent of the core charge distribution: 2.582645
+ Electronic configuration (s p d ...): 2 2
+
+ Parameters of the local part of the GTH pseudopotential:
+
+ rloc C1 C2 C3 C4
+ 0.440000 -7.336103
+
+ Parameters of the non-local part of the GTH pseudopotential:
+
+ l r(l) h(i,j,l)
+
+ 0 0.422738 5.906928 -1.261894
+ -1.261894 3.258196
+ 1 0.484278 2.727013
+
+
+ MOLECULE KIND INFORMATION
+
+
+ All atoms are their own molecule, skipping detailed information
+
+
+ TOTAL NUMBERS AND MAXIMUM NUMBERS
+
+ Total number of - Atomic kinds: 2
+ - Atoms: 8
+ - Shell sets: 12
+ - Shells: 28
+ - Primitive Cartesian functions: 36
+ - Cartesian basis functions: 72
+ - Spherical basis functions: 68
+
+ Maximum angular momentum of- Orbital basis functions: 2
+ - Local part of the GTH pseudopotential: 0
+ - Non-local part of the GTH pseudopotential: 2
+
+
+ MODULE QUICKSTEP: ATOMIC COORDINATES IN angstrom
+
+ Atom Kind Element X Y Z Z(eff) Mass
+
+ 1 1 Si 14 0.000000 0.000000 0.000000 4.00 28.0855
+ 2 1 Si 14 0.000000 2.715349 2.715349 4.00 28.0855
+ 3 1 Si 14 2.715349 2.715349 0.000000 4.00 28.0855
+ 4 1 Si 14 2.715349 0.000000 2.715349 4.00 28.0855
+ 5 2 Si 14 4.073023 1.357674 4.073023 4.00 28.0855
+ 6 2 Si 14 1.357674 1.357674 1.357674 4.00 28.0855
+ 7 2 Si 14 1.357674 4.073023 4.073023 4.00 28.0855
+ 8 2 Si 14 4.073023 4.073023 1.357674 4.00 28.0855
+
+
+
+ REQUESTED STRUCTURE DATA
+
+
+ SCF PARAMETERS Density guess: ATOMIC
+ --------------------------------------------------------
+ max_scf: 300
+ max_scf_history: 0
+ max_diis: 4
+ --------------------------------------------------------
+ eps_scf: 1.00E-07
+ eps_scf_history: 0.00E+00
+ eps_diis: 1.00E-01
+ eps_eigval: 1.00E-05
+ --------------------------------------------------------
+ level_shift [a.u.]: 0.00
+ --------------------------------------------------------
+ Mixing method: BROYDEN_MIXING
+ charge density mixing in g-space
+ --------------------------------------------------------
+ No outer SCF
+
+ PW_GRID| Information for grid number 1
+ PW_GRID| Cutoff [a.u.] 150.0
+ PW_GRID| spherical cutoff: NO
+ PW_GRID| Bounds 1 -30 29 Points: 60
+ PW_GRID| Bounds 2 -30 29 Points: 60
+ PW_GRID| Bounds 3 -30 29 Points: 60
+ PW_GRID| Volume element (a.u.^3) 0.5004E-02 Volume (a.u.^3) 1080.8451
+ PW_GRID| Grid span FULLSPACE
+
+ PW_GRID| Information for grid number 2
+ PW_GRID| Cutoff [a.u.] 50.0
+ PW_GRID| spherical cutoff: NO
+ PW_GRID| Bounds 1 -18 17 Points: 36
+ PW_GRID| Bounds 2 -18 17 Points: 36
+ PW_GRID| Bounds 3 -18 17 Points: 36
+ PW_GRID| Volume element (a.u.^3) 0.2317E-01 Volume (a.u.^3) 1080.8451
+ PW_GRID| Grid span FULLSPACE
+
+ PW_GRID| Information for grid number 3
+ PW_GRID| Cutoff [a.u.] 16.7
+ PW_GRID| spherical cutoff: NO
+ PW_GRID| Bounds 1 -10 9 Points: 20
+ PW_GRID| Bounds 2 -10 9 Points: 20
+ PW_GRID| Bounds 3 -10 9 Points: 20
+ PW_GRID| Volume element (a.u.^3) 0.1351 Volume (a.u.^3) 1080.8451
+ PW_GRID| Grid span FULLSPACE
+
+ PW_GRID| Information for grid number 4
+ PW_GRID| Cutoff [a.u.] 5.6
+ PW_GRID| spherical cutoff: NO
+ PW_GRID| Bounds 1 -6 5 Points: 12
+ PW_GRID| Bounds 2 -6 5 Points: 12
+ PW_GRID| Bounds 3 -6 5 Points: 12
+ PW_GRID| Volume element (a.u.^3) 0.6255 Volume (a.u.^3) 1080.8451
+ PW_GRID| Grid span FULLSPACE
+
+ POISSON| Solver PERIODIC
+ POISSON| Periodicity XYZ
+
+ RS_GRID| Information for grid number 1
+ RS_GRID| Bounds 1 -30 29 Points: 60
+ RS_GRID| Bounds 2 -30 29 Points: 60
+ RS_GRID| Bounds 3 -30 29 Points: 60
+
+ RS_GRID| Information for grid number 2
+ RS_GRID| Bounds 1 -18 17 Points: 36
+ RS_GRID| Bounds 2 -18 17 Points: 36
+ RS_GRID| Bounds 3 -18 17 Points: 36
+
+ RS_GRID| Information for grid number 3
+ RS_GRID| Bounds 1 -10 9 Points: 20
+ RS_GRID| Bounds 2 -10 9 Points: 20
+ RS_GRID| Bounds 3 -10 9 Points: 20
+
+ RS_GRID| Information for grid number 4
+ RS_GRID| Bounds 1 -6 5 Points: 12
+ RS_GRID| Bounds 2 -6 5 Points: 12
+ RS_GRID| Bounds 3 -6 5 Points: 12
+
+ DISTRIBUTION OF THE PARTICLES (ROWS)
+ Process row Number of particles Number of matrix rows
+ 0 8 -1
+ Sum 8 -1
+
+ DISTRIBUTION OF THE PARTICLES (COLUMNS)
+ Process col Number of particles Number of matrix columns
+ 0 8 -1
+ Sum 8 -1
+
+ <distribution_2d> { id_nr= 1 ref_count= 1,
+ n_row_distribution= 8,
+ row_distribution= ( 0, 0, 0, 0, 0, 0, 0, 0,),
+ n_col_distribution= 8,
+ col_distribution= ( 0, 0, 0, 0, 0, 0, 0, 0,),
+ n_local_rows= ( 4, 4,),
+ local_rows=(
+( 1, 2, 3, 4 )
+( 5, 6, 7, 8 )
+ ),
+ n_local_cols= ( 4, 4,),
+ local_cols=(
+( 1, 2, 3, 4 )
+( 5, 6, 7, 8 )
+ ),
+ blacs_env= group= 0, ref_count= 5,
+ mepos=( 0, 0),
+ num_pe=( 1, 1),
+ blacs2mpi= 0
+ para_env=<cp_para_env id= 0>,
+ my_pid= 0, n_pid= 1 }
+ }
+
+ DISTRIBUTION OF THE NEIGHBOR LISTS
+ Total number of particle pairs: 2856
+ Total number of matrix elements: 213636
+ Average number of particle pairs: 2856
+ Maximum number of particle pairs: 2856
+ Average number of matrix element: 213636
+ Maximum number of matrix elements: 213636
+
+
+ DISTRIBUTION OF THE OVERLAP MATRIX
+ Number of non-zero blocks: 36
+ Percentage non-zero blocks: 100.00
+ Average number of blocks per CPU: 36
+ Maximum number of blocks per CPU: 36
+ Average number of matrix elements per CPU: 2692
+ Maximum number of matrix elements per CPU: 2692
+
+ Initializing the DDAPC Environment
+
+ Number of electrons: 32
+ Number of occupied orbitals: 16
+ Number of molecular orbitals: 16
+
+ Number of orbital functions: 68
+ Number of independent orbital functions: 68
+
+ Extrapolation method: initial_guess
+
+ Atomic guess: The first density matrix is obtained in terms of atomic orbitals
+ and electronic configurations assigned to each atomic kind
+
+ Guess for atomic kind: SiA
+
+ Electronic structure
+ Total number of core electrons 10.00
+ Total number of valence electrons 4.00
+ Total number of electrons 14.00
+ Multiplicity not specified
+ S [ 2.00 2.00] 2.00
+ P [ 6.00] 2.00
+
+
+ *******************************************************************************
+ Iteration Convergence Energy [au]
+ *******************************************************************************
+ 1 0.191310 -3.618313869735
+ 2 0.731569E-01 -3.691159009622
+ 3 0.405574E-02 -3.699900512584
+ 4 0.328704E-02 -3.699908407293
+ 5 0.320845E-02 -3.699909118998
+ 6 0.316809E-02 -3.699909477757
+ 7 0.331859E-05 -3.699923449535
+ 8 0.110258E-06 -3.699923449550
+
+ Energy components [Hartree] Total Energy :: -3.699923449550
+ Band Energy :: -1.012729790251
+ Kinetic Energy :: 1.397012768229
+ Potential Energy :: -5.096936217779
+ Virial (-V/T) :: 3.648453567279
+ Core Energy :: -5.703543362687
+ XC Energy :: -0.980691562795
+ Coulomb Energy :: 2.984311475932
+ Total Pseudopotential Energy :: -7.145739758818
+ Local Pseudopotential Energy :: -7.987908627736
+ Nonlocal Pseudopotential Energy :: 0.842168868918
+ Confinement :: 0.451836279031
+
+ Orbital energies State L Occupation Energy[a.u.] Energy[eV]
+
+ 1 0 2.000 -0.378230 -10.292155
+
+ 1 1 2.000 -0.128135 -3.486734
+
+
+ Guess for atomic kind: SiB
+
+ Electronic structure
+ Total number of core electrons 10.00
+ Total number of valence electrons 4.00
+ Total number of electrons 14.00
+ Multiplicity not specified
+ S [ 2.00 2.00] 2.00
+ P [ 6.00] 2.00
+
+
+ *******************************************************************************
+ Iteration Convergence Energy [au]
+ *******************************************************************************
+ 1 0.00000 -3.698939295593
+
+ Energy components [Hartree] Total Energy :: -3.698939295593
+ Band Energy :: -2.912326140277
+ Kinetic Energy :: 1.350234186210
+ Potential Energy :: -5.049173481803
+ Virial (-V/T) :: 3.739479812739
+ Core Energy :: -5.669266714455
+ XC Energy :: -0.965154030174
+ Coulomb Energy :: 2.935481449036
+ Total Pseudopotential Energy :: -7.066612060196
+ Local Pseudopotential Energy :: -7.891728242282
+ Nonlocal Pseudopotential Energy :: 0.825116182086
+ Confinement :: 0.471111595310
+
+ Orbital energies State L Occupation Energy[a.u.] Energy[eV]
+
+ 1 0 2.000 -0.896599 -24.397695
+
+ 1 1 2.000 -0.559564 -15.226517
+
+ Re-scaling the density matrix to get the right number of electrons
+ # Electrons Trace(P) Scaling factor
+ 32 31.040 1.031
+
+
+ SCF WAVEFUNCTION OPTIMIZATION
+
+ Step Update method Time Convergence Total energy Change
+ ------------------------------------------------------------------------------
+
+ Trace(PS): 32.0000000000
+ Electronic density on regular grids: -31.9999999981 0.0000000019
+ Core density on regular grids: 31.9999999939 -0.0000000061
+ Total charge density on r-space grids: -0.0000000042
+ Total charge density g-space grids: -0.0000000042
+
+
+ Core Hamiltonian energy: 17.0950825679
+ Hartree energy: 42.1018496838
+ Exchange-correlation energy: -9.4386572684
+ Coulomb (electron-electron) energy: 1.8563293703
+ Maximum deviation from MO S-orthonormality 0.1000E+01
+ Minimum/Maximum MO magnitude 0.0000E+00 0.0000E+00
+ 1 NoMix/Diag. 0.40E+00 0.3 0.86151992 -32.3056644418 -3.23E+01
+
+ Trace(PS): 32.0000000000
+ Electronic density on regular grids: -31.9999999961 0.0000000039
+ Core density on regular grids: 31.9999999939 -0.0000000061
+ Total charge density on r-space grids: -0.0000000022
+ Total charge density g-space grids: -0.0000000022
+
+
+ Core Hamiltonian energy: 18.4387879920
+ Hartree energy: 42.1446281038
+ Exchange-correlation energy: -9.5212824108
+ Coulomb (electron-electron) energy: 2.0743832608
+ Maximum deviation from MO S-orthonormality 0.9385E-15
+ Minimum/Maximum MO magnitude 0.6404E+00 0.2276E+01
+ 2 Broy./Diag. 0.40E+00 1.0 0.09616185 -31.0018057400 1.30E+00
+
+ Trace(PS): 32.0000000000
+ Electronic density on regular grids: -31.9999999927 0.0000000073
+ Core density on regular grids: 31.9999999939 -0.0000000061
+ Total charge density on r-space grids: 0.0000000012
+ Total charge density g-space grids: 0.0000000012
+
+
+ Core Hamiltonian energy: 18.3482585800
+ Hartree energy: 42.2625027702
+ Exchange-correlation energy: -9.6657037092
+ Coulomb (electron-electron) energy: 2.4209219761
+ Maximum deviation from MO S-orthonormality 0.1776E-14
+ Minimum/Maximum MO magnitude 0.6167E+00 0.2373E+01
+ 3 Broy./Diag. 0.40E+00 0.7 0.13155525 -31.1188817840 -1.17E-01
+
+ Trace(PS): 32.0000000000
+ Electronic density on regular grids: -31.9999999919 0.0000000081
+ Core density on regular grids: 31.9999999939 -0.0000000061
+ Total charge density on r-space grids: 0.0000000020
+ Total charge density g-space grids: 0.0000000020
+
+
+ Core Hamiltonian energy: 18.2216789828
+ Hartree energy: 42.2932913599
+ Exchange-correlation energy: -9.6838616891
+ Coulomb (electron-electron) energy: 2.4614696327
+ Maximum deviation from MO S-orthonormality 0.1138E-14
+ Minimum/Maximum MO magnitude 0.5860E+00 0.2528E+01
+ 4 Broy./Diag. 0.40E+00 0.7 0.01093118 -31.2328307715 -1.14E-01
+
+ Trace(PS): 32.0000000000
+ Electronic density on regular grids: -31.9999999916 0.0000000084
+ Core density on regular grids: 31.9999999939 -0.0000000061
+ Total charge density on r-space grids: 0.0000000023
+ Total charge density g-space grids: 0.0000000023
+
+
+ Core Hamiltonian energy: 18.2091844936
+ Hartree energy: 42.3035816195
+ Exchange-correlation energy: -9.6846917135
+ Coulomb (electron-electron) energy: 2.4626797532
+ Maximum deviation from MO S-orthonormality 0.1998E-14
+ Minimum/Maximum MO magnitude 0.5834E+00 0.2542E+01
+ 5 Broy./Diag. 0.40E+00 0.7 0.00044468 -31.2358650254 -3.03E-03
+
+ Trace(PS): 32.0000000000
+ Electronic density on regular grids: -31.9999999915 0.0000000085
+ Core density on regular grids: 31.9999999939 -0.0000000061
+ Total charge density on r-space grids: 0.0000000024
+ Total charge density g-space grids: 0.0000000024
+
+
+ Core Hamiltonian energy: 18.2099237951
+ Hartree energy: 42.3095587046
+ Exchange-correlation energy: -9.6845933906
+ Coulomb (electron-electron) energy: 2.4619673269
+ Maximum deviation from MO S-orthonormality 0.1776E-14
+ Minimum/Maximum MO magnitude 0.5838E+00 0.2542E+01
+ 6 Broy./Diag. 0.40E+00 0.7 0.00060621 -31.2290503159 6.81E-03
+
+ Trace(PS): 32.0000000000
+ Electronic density on regular grids: -31.9999999915 0.0000000085
+ Core density on regular grids: 31.9999999939 -0.0000000061
+ Total charge density on r-space grids: 0.0000000024
+ Total charge density g-space grids: 0.0000000024
+
+
+ Core Hamiltonian energy: 18.2109477632
+ Hartree energy: 42.3094669559
+ Exchange-correlation energy: -9.6846640119
+ Coulomb (electron-electron) energy: 2.4621099178
+ Maximum deviation from MO S-orthonormality 0.1957E-14
+ Minimum/Maximum MO magnitude 0.5842E+00 0.2541E+01
+ 7 Broy./Diag. 0.40E+00 0.7 0.00005078 -31.2281887179 8.62E-04
+
+ Trace(PS): 32.0000000000
+ Electronic density on regular grids: -31.9999999915 0.0000000085
+ Core density on regular grids: 31.9999999939 -0.0000000061
+ Total charge density on r-space grids: 0.0000000024
+ Total charge density g-space grids: 0.0000000024
+
+
+ Core Hamiltonian energy: 18.2109183954
+ Hartree energy: 42.3093324372
+ Exchange-correlation energy: -9.6847326932
+ Coulomb (electron-electron) energy: 2.4622517209
+ Maximum deviation from MO S-orthonormality 0.1554E-14
+ Minimum/Maximum MO magnitude 0.5842E+00 0.2541E+01
+ 8 Broy./Diag. 0.40E+00 0.7 0.00005268 -31.2284212857 -2.33E-04
+
+ Trace(PS): 32.0000000000
+ Electronic density on regular grids: -31.9999999915 0.0000000085
+ Core density on regular grids: 31.9999999939 -0.0000000061
+ Total charge density on r-space grids: 0.0000000024
+ Total charge density g-space grids: 0.0000000024
+
+
+ Core Hamiltonian energy: 18.2108860662
+ Hartree energy: 42.3093209389
+ Exchange-correlation energy: -9.6847324879
+ Coulomb (electron-electron) energy: 2.4622526038
+ Maximum deviation from MO S-orthonormality 0.1384E-14
+ Minimum/Maximum MO magnitude 0.5842E+00 0.2541E+01
+ 9 Broy./Diag. 0.40E+00 0.7 0.00000064 -31.2284649079 -4.36E-05
+
+ Trace(PS): 32.0000000000
+ Electronic density on regular grids: -31.9999999915 0.0000000085
+ Core density on regular grids: 31.9999999939 -0.0000000061
+ Total charge density on r-space grids: 0.0000000024
+ Total charge density g-space grids: 0.0000000024
+
+
+ Core Hamiltonian energy: 18.2108854260
+ Hartree energy: 42.3093150539
+ Exchange-correlation energy: -9.6847323295
+ Coulomb (electron-electron) energy: 2.4622529681
+ Maximum deviation from MO S-orthonormality 0.1554E-14
+ Minimum/Maximum MO magnitude 0.5842E+00 0.2541E+01
+ 10 Broy./Diag. 0.40E+00 0.6 0.00000030 -31.2284712746 -6.37E-06
+
+ Trace(PS): 32.0000000000
+ Electronic density on regular grids: -31.9999999915 0.0000000085
+ Core density on regular grids: 31.9999999939 -0.0000000061
+ Total charge density on r-space grids: 0.0000000024
+ Total charge density g-space grids: 0.0000000024
+
+
+ Core Hamiltonian energy: 18.2108851038
+ Hartree energy: 42.3093056309
+ Exchange-correlation energy: -9.6847320483
+ Coulomb (electron-electron) energy: 2.4622534900
+ Maximum deviation from MO S-orthonormality 0.2220E-14
+ Minimum/Maximum MO magnitude 0.5842E+00 0.2541E+01
+ 11 Broy./Diag. 0.40E+00 0.6 0.00000046 -31.2284807386 -9.46E-06
+
+ Trace(PS): 32.0000000000
+ Electronic density on regular grids: -31.9999999915 0.0000000085
+ Core density on regular grids: 31.9999999939 -0.0000000061
+ Total charge density on r-space grids: 0.0000000024
+ Total charge density g-space grids: 0.0000000024
+
+
+ Core Hamiltonian energy: 18.2108846100
+ Hartree energy: 42.3093056071
+ Exchange-correlation energy: -9.6847320288
+ Coulomb (electron-electron) energy: 2.4622534494
+ Maximum deviation from MO S-orthonormality 0.1332E-14
+ Minimum/Maximum MO magnitude 0.5842E+00 0.2541E+01
+ 12 Broy./Diag. 0.40E+00 0.6 0.00000001 -31.2284812368 -4.98E-07
+
+ *** SCF run converged in 12 steps ***
+
+
+ Electronic density on regular grids: -31.9999999915 0.0000000085
+ Core density on regular grids: 31.9999999939 -0.0000000061
+ Total charge density on r-space grids: 0.0000000024
+ Total charge density g-space grids: 0.0000000024
+
+ Overlap energy of the core charge distribution: 0.00000000005320
+ Self energy of the core charge distribution: -82.06393942512820
+ Core Hamiltonian energy: 18.21088461003086
+ Hartree energy: 42.30930560708283
+ Exchange-correlation energy: -9.68473202880524
+ Coulomb Electron-Electron Interaction Energy
+ - Already included in the total Hartree term 2.46225344944663
+
+ Total energy: -31.22848123676655
+
+ The electron density is written in cube file format to the file:
+
+ Si_bulk8-ELECTRON_DENSITY-1_0.cube
+
+
+ MULLIKEN POPULATION ANALYSIS
+
+ # Atom Element Kind Atomic population Net charge
+ 1 Si 1 3.506163 0.493837
+ 2 Si 1 3.506162 0.493838
+ 3 Si 1 3.506162 0.493838
+ 4 Si 1 3.506162 0.493838
+ 5 Si 2 4.493838 -0.493838
+ 6 Si 2 4.493838 -0.493838
+ 7 Si 2 4.493838 -0.493838
+ 8 Si 2 4.493838 -0.493838
+ # Total charge 32.000000 -0.000000
+
+
+ !-----------------------------------------------------------------------------!
+ Hirschfeld Charges
+
+ #Atom Element Kind Ref Charge Population Net charge
+ 1 Si 1 4.000 3.982 0.018
+ 2 Si 1 4.000 3.982 0.018
+ 3 Si 1 4.000 3.982 0.018
+ 4 Si 1 4.000 3.982 0.018
+ 5 Si 2 4.000 4.018 -0.018
+ 6 Si 2 4.000 4.018 -0.018
+ 7 Si 2 4.000 4.018 -0.018
+ 8 Si 2 4.000 4.018 -0.018
+
+ Total Charge -0.000
+ !-----------------------------------------------------------------------------!
+ Electronic kinetic energy: 13.30052579210439
+
+
+ LOWDIN POPULATION ANALYSIS
+
+ # Atom Element Kind Atomic population Net charge
+ 1 Si 1 4.500279 -0.500279
+ 2 Si 1 4.500279 -0.500279
+ 3 Si 1 4.500279 -0.500279
+ 4 Si 1 4.500279 -0.500279
+ 5 Si 2 3.499721 0.500279
+ 6 Si 2 3.499721 0.500279
+ 7 Si 2 3.499721 0.500279
+ 8 Si 2 3.499721 0.500279
+ # Total charge 32.000000 -0.000000
+
+ DDAP FULL DENSITY charges:
+ Atom | Charge
+
+ 1 Si 0.133716
+ 2 Si 0.133717
+ 3 Si 0.133717
+ 4 Si 0.133717
+ 5 Si -0.133717
+ 6 Si -0.133716
+ 7 Si -0.133717
+ 8 Si -0.133717
+ Total 0.000000
+
+
+ ELECTRIC/MAGNETIC MOMENTS
+ Reference Point [Bohr] 0.00000000 0.00000000 0.00000000
+ Charges
+ Electronic= 32.00000000 Core= -32.00000000 Total= 0.00000000
+ Dipole vectors are based on the periodic (Berry phase) operator.
+ They are defined modulo integer multiples of the cell matrix [Debye].
+ [X] [ 26.08474943 0.00000000 0.00000000 ] [i]
+ [Y]=[ 0.00000000 26.08474943 0.00000000 ]*[j]
+ [Z] [ 0.00000000 0.00000000 26.08474943 ] [k]
+ Dipole moment [Debye]
+ X= -0.00000018 Y= -0.00000018 Z= -0.00004234 Total= 0.00004234
+
+ Eigenvalues of the occupied subspace spin 1
+ ---------------------------------------------
+ -0.24430835 -0.09140469 -0.09140469 -0.09140468
+ -0.09123064 -0.09123063 -0.09123063 0.08981556
+ 0.08981560 0.08981560 0.08981560 0.08981560
+ 0.08981564 0.20573402 0.20573403 0.20573404
+ Fermi Energy [eV] : 5.598308
+
+ Lowest eigenvalues of the unoccupied subspace spin 1
+ ---------------------------------------------
+
+
+ Trace(PS): 32.0000000000
+ Electronic density on regular grids: -31.9999999915 0.0000000085
+ Core density on regular grids: 31.9999999939 -0.0000000061
+ Total charge density on r-space grids: 0.0000000024
+ Total charge density g-space grids: 0.0000000024
+
+
+ Core Hamiltonian energy: 18.2108846238
+ Hartree energy: 42.3093056273
+ Exchange-correlation energy: -9.6847320024
+ Coulomb (electron-electron) energy: 2.4622533882
+
+
+ FORCES [a.u.]
+
+ Atom Kind Component X Y Z
+
+ 1 1 overlap -0.000000 -0.000000 -0.000001
+ 1 1 overlap_admm 0.000000 0.000000 0.000000
+ 1 1 kinetic 0.000000 0.000000 -0.000000
+ 1 1 gth_ppl 0.000000 0.000000 0.000001
+ 1 1 gth_nlcc 0.000000 0.000000 0.000000
+ 1 1 gth_ppnl -0.000000 -0.000000 -0.000002
+ 1 1 core_overlap -0.000000 -0.000000 -0.000000
+ 1 1 rho_core -0.000000 -0.000000 0.000001
+ 1 1 rho_elec 0.000000 0.000000 0.000001
+ 1 1 rho_lri_el 0.000000 0.000000 0.000000
+ 1 1 ch_pulay 0.000000 0.000000 0.000000
+ 1 1 dispersion 0.000000 0.000000 0.000000
+ 1 1 other 0.000000 0.000000 0.000000
+ 1 1 fock_4c 0.000000 0.000000 0.000000
+ 1 1 hfx_ri 0.000000 0.000000 0.000000
+ 1 1 ehrenfest 0.000000 0.000000 0.000000
+ 1 1 efield 0.000000 0.000000 0.000000
+ 1 1 eev 0.000000 0.000000 0.000000
+ 1 1 mp2_non_sep 0.000000 0.000000 0.000000
+ 1 1 mp2_sep 0.000000 0.000000 0.000000
+ 1 1 total -0.000000 -0.000000 0.000000
+
+ 2 1 overlap -0.000000 -0.000000 -0.000001
+ 2 1 overlap_admm 0.000000 0.000000 0.000000
+ 2 1 kinetic 0.000000 0.000000 -0.000000
+ 2 1 gth_ppl 0.000000 -0.000000 0.000001
+ 2 1 gth_nlcc 0.000000 0.000000 0.000000
+ 2 1 gth_ppnl -0.000000 0.000000 -0.000002
+ 2 1 core_overlap 0.000000 -0.000000 -0.000000
+ 2 1 rho_core -0.000000 0.000000 0.000001
+ 2 1 rho_elec 0.000000 -0.000000 0.000001
+ 2 1 rho_lri_el 0.000000 0.000000 0.000000
+ 2 1 ch_pulay 0.000000 0.000000 0.000000
+ 2 1 dispersion 0.000000 0.000000 0.000000
+ 2 1 other 0.000000 0.000000 0.000000
+ 2 1 fock_4c 0.000000 0.000000 0.000000
+ 2 1 hfx_ri 0.000000 0.000000 0.000000
+ 2 1 ehrenfest 0.000000 0.000000 0.000000
+ 2 1 efield 0.000000 0.000000 0.000000
+ 2 1 eev 0.000000 0.000000 0.000000
+ 2 1 mp2_non_sep 0.000000 0.000000 0.000000
+ 2 1 mp2_sep 0.000000 0.000000 0.000000
+ 2 1 total -0.000000 -0.000000 0.000000
+
+ 3 1 overlap -0.000000 -0.000000 -0.000001
+ 3 1 overlap_admm 0.000000 0.000000 0.000000
+ 3 1 kinetic 0.000000 0.000000 -0.000000
+ 3 1 gth_ppl -0.000000 -0.000000 0.000001
+ 3 1 gth_nlcc 0.000000 0.000000 0.000000
+ 3 1 gth_ppnl 0.000000 0.000000 -0.000002
+ 3 1 core_overlap -0.000000 -0.000000 0.000000
+ 3 1 rho_core 0.000000 0.000000 0.000001
+ 3 1 rho_elec -0.000000 -0.000000 0.000001
+ 3 1 rho_lri_el 0.000000 0.000000 0.000000
+ 3 1 ch_pulay 0.000000 0.000000 0.000000
+ 3 1 dispersion 0.000000 0.000000 0.000000
+ 3 1 other 0.000000 0.000000 0.000000
+ 3 1 fock_4c 0.000000 0.000000 0.000000
+ 3 1 hfx_ri 0.000000 0.000000 0.000000
+ 3 1 ehrenfest 0.000000 0.000000 0.000000
+ 3 1 efield 0.000000 0.000000 0.000000
+ 3 1 eev 0.000000 0.000000 0.000000
+ 3 1 mp2_non_sep 0.000000 0.000000 0.000000
+ 3 1 mp2_sep 0.000000 0.000000 0.000000
+ 3 1 total -0.000000 -0.000000 0.000000
+
+ 4 1 overlap -0.000000 -0.000000 -0.000001
+ 4 1 overlap_admm 0.000000 0.000000 0.000000
+ 4 1 kinetic 0.000000 0.000000 -0.000000
+ 4 1 gth_ppl -0.000000 0.000000 0.000001
+ 4 1 gth_nlcc 0.000000 0.000000 0.000000
+ 4 1 gth_ppnl 0.000000 -0.000000 -0.000002
+ 4 1 core_overlap -0.000000 0.000000 -0.000000
+ 4 1 rho_core 0.000000 -0.000000 0.000001
+ 4 1 rho_elec -0.000000 0.000000 0.000001
+ 4 1 rho_lri_el 0.000000 0.000000 0.000000
+ 4 1 ch_pulay 0.000000 0.000000 0.000000
+ 4 1 dispersion 0.000000 0.000000 0.000000
+ 4 1 other 0.000000 0.000000 0.000000
+ 4 1 fock_4c 0.000000 0.000000 0.000000
+ 4 1 hfx_ri 0.000000 0.000000 0.000000
+ 4 1 ehrenfest 0.000000 0.000000 0.000000
+ 4 1 efield 0.000000 0.000000 0.000000
+ 4 1 eev 0.000000 0.000000 0.000000
+ 4 1 mp2_non_sep 0.000000 0.000000 0.000000
+ 4 1 mp2_sep 0.000000 0.000000 0.000000
+ 4 1 total -0.000000 -0.000000 0.000000
+
+ 5 2 overlap 0.000000 0.000000 0.000001
+ 5 2 overlap_admm 0.000000 0.000000 0.000000
+ 5 2 kinetic -0.000000 -0.000000 0.000000
+ 5 2 gth_ppl 0.000000 -0.000000 -0.000001
+ 5 2 gth_nlcc 0.000000 0.000000 0.000000
+ 5 2 gth_ppnl -0.000000 0.000000 0.000002
+ 5 2 core_overlap 0.000000 0.000000 0.000000
+ 5 2 rho_core 0.000000 -0.000000 0.000002
+ 5 2 rho_elec -0.000000 0.000000 -0.000004
+ 5 2 rho_lri_el 0.000000 0.000000 0.000000
+ 5 2 ch_pulay 0.000000 0.000000 0.000000
+ 5 2 dispersion 0.000000 0.000000 0.000000
+ 5 2 other 0.000000 0.000000 0.000000
+ 5 2 fock_4c 0.000000 0.000000 0.000000
+ 5 2 hfx_ri 0.000000 0.000000 0.000000
+ 5 2 ehrenfest 0.000000 0.000000 0.000000
+ 5 2 efield 0.000000 0.000000 0.000000
+ 5 2 eev 0.000000 0.000000 0.000000
+ 5 2 mp2_non_sep 0.000000 0.000000 0.000000
+ 5 2 mp2_sep 0.000000 0.000000 0.000000
+ 5 2 total 0.000000 0.000000 -0.000000
+
+ 6 2 overlap 0.000000 0.000000 0.000001
+ 6 2 overlap_admm 0.000000 0.000000 0.000000
+ 6 2 kinetic -0.000000 -0.000000 0.000000
+ 6 2 gth_ppl -0.000000 -0.000000 -0.000001
+ 6 2 gth_nlcc 0.000000 0.000000 0.000000
+ 6 2 gth_ppnl 0.000000 0.000000 0.000002
+ 6 2 core_overlap 0.000000 0.000000 0.000000
+ 6 2 rho_core -0.000000 -0.000000 0.000002
+ 6 2 rho_elec 0.000000 0.000000 -0.000004
+ 6 2 rho_lri_el 0.000000 0.000000 0.000000
+ 6 2 ch_pulay 0.000000 0.000000 0.000000
+ 6 2 dispersion 0.000000 0.000000 0.000000
+ 6 2 other 0.000000 0.000000 0.000000
+ 6 2 fock_4c 0.000000 0.000000 0.000000
+ 6 2 hfx_ri 0.000000 0.000000 0.000000
+ 6 2 ehrenfest 0.000000 0.000000 0.000000
+ 6 2 efield 0.000000 0.000000 0.000000
+ 6 2 eev 0.000000 0.000000 0.000000
+ 6 2 mp2_non_sep 0.000000 0.000000 0.000000
+ 6 2 mp2_sep 0.000000 0.000000 0.000000
+ 6 2 total 0.000000 0.000000 -0.000000
+
+ 7 2 overlap 0.000000 0.000000 0.000001
+ 7 2 overlap_admm 0.000000 0.000000 0.000000
+ 7 2 kinetic -0.000000 -0.000000 0.000000
+ 7 2 gth_ppl -0.000000 0.000000 -0.000001
+ 7 2 gth_nlcc 0.000000 0.000000 0.000000
+ 7 2 gth_ppnl 0.000000 -0.000000 0.000002
+ 7 2 core_overlap 0.000000 0.000000 0.000000
+ 7 2 rho_core -0.000000 0.000000 0.000002
+ 7 2 rho_elec 0.000000 -0.000000 -0.000004
+ 7 2 rho_lri_el 0.000000 0.000000 0.000000
+ 7 2 ch_pulay 0.000000 0.000000 0.000000
+ 7 2 dispersion 0.000000 0.000000 0.000000
+ 7 2 other 0.000000 0.000000 0.000000
+ 7 2 fock_4c 0.000000 0.000000 0.000000
+ 7 2 hfx_ri 0.000000 0.000000 0.000000
+ 7 2 ehrenfest 0.000000 0.000000 0.000000
+ 7 2 efield 0.000000 0.000000 0.000000
+ 7 2 eev 0.000000 0.000000 0.000000
+ 7 2 mp2_non_sep 0.000000 0.000000 0.000000
+ 7 2 mp2_sep 0.000000 0.000000 0.000000
+ 7 2 total 0.000000 0.000000 -0.000000
+
+ 8 2 overlap 0.000000 0.000000 0.000001
+ 8 2 overlap_admm 0.000000 0.000000 0.000000
+ 8 2 kinetic -0.000000 -0.000000 0.000000
+ 8 2 gth_ppl 0.000000 0.000000 -0.000001
+ 8 2 gth_nlcc 0.000000 0.000000 0.000000
+ 8 2 gth_ppnl -0.000000 -0.000000 0.000002
+ 8 2 core_overlap 0.000000 0.000000 0.000000
+ 8 2 rho_core 0.000000 0.000000 0.000002
+ 8 2 rho_elec -0.000000 -0.000000 -0.000004
+ 8 2 rho_lri_el 0.000000 0.000000 0.000000
+ 8 2 ch_pulay 0.000000 0.000000 0.000000
+ 8 2 dispersion 0.000000 0.000000 0.000000
+ 8 2 other 0.000000 0.000000 0.000000
+ 8 2 fock_4c 0.000000 0.000000 0.000000
+ 8 2 hfx_ri 0.000000 0.000000 0.000000
+ 8 2 ehrenfest 0.000000 0.000000 0.000000
+ 8 2 efield 0.000000 0.000000 0.000000
+ 8 2 eev 0.000000 0.000000 0.000000
+ 8 2 mp2_non_sep 0.000000 0.000000 0.000000
+ 8 2 mp2_sep 0.000000 0.000000 0.000000
+ 8 2 total 0.000000 0.000000 -0.000000
+
+ Sum of total 0.000000 0.000000 0.000000
+
+ ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.): -31.228481176379148
+
+
+ ATOMIC FORCES in [a.u.]
+
+ # Atom Kind Element X Y Z
+ 1 1 Si 0.00000000 0.00000000 -0.00000041
+ 2 1 Si 0.00000000 0.00000002 -0.00000040
+ 3 1 Si 0.00000002 0.00000002 -0.00000041
+ 4 1 Si 0.00000002 0.00000000 -0.00000040
+ 5 2 Si -0.00000000 -0.00000002 0.00000041
+ 6 2 Si -0.00000002 -0.00000002 0.00000040
+ 7 2 Si -0.00000002 -0.00000000 0.00000041
+ 8 2 Si -0.00000000 -0.00000000 0.00000040
+ SUM OF ATOMIC FORCES -0.00000000 -0.00000000 -0.00000000 0.00000000
+
+ STRESS TENSOR [GPa]
+
+ X Y Z
+ X 9.29629231 -0.00062859 -0.00000110
+ Y -0.00062859 9.29629231 -0.00000110
+ Z -0.00000110 -0.00000110 9.29629231
+
+ 1/3 Trace(stress tensor): 9.29629231E+00
+
+ Det(stress tensor) : 8.03395346E+02
+
+
+ EIGENVECTORS AND EIGENVALUES OF THE STRESS TENSOR
+
+ 9.29566372 9.29629232 9.29692091
+
+ 0.70710465 -0.00174724 -0.70710676
+ 0.70710460 -0.00174633 0.70710681
+ 0.00247032 0.99999695 -0.00000064
+
+ -------------------------------------------------------------------------------
+ - -
+ - DBCSR STATISTICS -
+ - -
+ -------------------------------------------------------------------------------
+ COUNTER CPU ACC ACC%
+ number of processed stacks 132 0 0.0
+ matmuls inhomo. stacks 0 0 0.0
+ matmuls total 1812 0 0.0
+ flops 4 x 4 x 4 2048 0 0.0
+ flops 13 x 4 x 4 6656 0 0.0
+ flops 4 x 4 x 13 6656 0 0.0
+ flops 13 x 4 x 13 21632 0 0.0
+ flops 4 x 32 x 4 32768 0 0.0
+ flops 4 x 4 x 16 66560 0 0.0
+ flops 13 x 32 x 4 106496 0 0.0
+ flops 4 x 32 x 13 106496 0 0.0
+ flops 4 x 16 x 4 147456 0 0.0
+ flops 13 x 4 x 16 173056 0 0.0
+ flops 4 x 13 x 16 173056 0 0.0
+ flops 13 x 32 x 13 346112 0 0.0
+ flops 13 x 16 x 4 479232 0 0.0
+ flops 4 x 16 x 13 479232 0 0.0
+ flops 13 x 13 x 16 703040 0 0.0
+ flops 13 x 16 x 13 1557504 0 0.0
+ flops total 4408000 0 0.0
+ marketing flops 5215872
+ -------------------------------------------------------------------------------
+
+ -------------------------------------------------------------------------------
+ ---- MULTIGRID INFO ----
+ -------------------------------------------------------------------------------
+ count for grid 1: 600 cutoff [a.u.] 150.00
+ count for grid 2: 4240 cutoff [a.u.] 50.00
+ count for grid 3: 6964 cutoff [a.u.] 16.67
+ count for grid 4: 3112 cutoff [a.u.] 5.56
+ total gridlevel count : 14916
+
+ -------------------------------------------------------------------------------
+ - -
+ - MESSAGE PASSING PERFORMANCE -
+ - -
+ -------------------------------------------------------------------------------
+
+ ROUTINE CALLS TOT TIME [s] AVE VOLUME [Bytes] PERFORMANCE [MB/s]
+ MP_Group 5 0.000
+ MP_Bcast 29 0.000 9. 0.72
+ MP_Allreduce 331 0.000 40. 52.73
+ MP_Sync 6308 0.000
+ MP_Alltoall 526 0.000 6405. 9737.01
+ MP_Wait 768 0.000
+ MP_ISend 256 0.001 18042. 5695.74
+ MP_IRecv 256 0.000 18042. 28031.58
+ MP_Memory 692 0.000
+ -------------------------------------------------------------------------------
+
+
+ -------------------------------------------------------------------------------
+ - -
+ - R E F E R E N C E S -
+ - -
+ -------------------------------------------------------------------------------
+
+ CP2K version 2.6.2, the CP2K developers group (2015).
+ CP2K is freely available from http://www.cp2k.org/ .
+
+ Borstnik, U; VandeVondele, J; Weber, V; Hutter, J.
+ PARALLEL COMPUTING, 40 (5-6), 47-58 (2014).
+ Sparse matrix multiplication: The distributed block-compressed sparse
+ row library.
+ http://dx.doi.org/10.1016/j.parco.2014.03.012
+
+
+ Hutter, J; Iannuzzi, M; Schiffmann, F; VandeVondele, J.
+ WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE, 4 (1), 15-25 (2014).
+ CP2K: atomistic simulations of condensed matter systems.
+ http://dx.doi.org/10.1002/wcms.1159
+
+
+ Krack, M.
+ THEORETICAL CHEMISTRY ACCOUNTS, 114 (1-3), 145-152 (2005).
+ Pseudopotentials for H to Kr optimized for gradient-corrected
+ exchange-correlation functionals.
+ http://dx.doi.org/10.1007/s00214-005-0655-y
+
+
+ VandeVondele, J; Krack, M; Mohamed, F; Parrinello, M; Chassaing, T;
+ Hutter, J. COMPUTER PHYSICS COMMUNICATIONS, 167 (2), 103-128 (2005).
+ QUICKSTEP: Fast and accurate density functional calculations using a
+ mixed Gaussian and plane waves approach.
+ http://dx.doi.org/10.1016/j.cpc.2004.12.014
+
+
+ Frigo, M; Johnson, SG.
+ PROCEEDINGS OF THE IEEE, 93 (2), 216-231 (2005).
+ The design and implementation of FFTW3.
+ http://dx.doi.org/10.1109/JPROC.2004.840301
+
+
+ Hartwigsen, C; Goedecker, S; Hutter, J.
+ PHYSICAL REVIEW B, 58 (7), 3641-3662 (1998).
+ Relativistic separable dual-space Gaussian pseudopotentials from H to Rn.
+ http://dx.doi.org/10.1103/PhysRevB.58.3641
+
+
+ Lippert, G; Hutter, J; Parrinello, M.
+ MOLECULAR PHYSICS, 92 (3), 477-487 (1997).
+ A hybrid Gaussian and plane wave density functional scheme.
+ http://dx.doi.org/10.1080/002689797170220
+
+
+ Goedecker, S; Teter, M; Hutter, J.
+ PHYSICAL REVIEW B, 54 (3), 1703-1710 (1996).
+ Separable dual-space Gaussian pseudopotentials.
+ http://dx.doi.org/10.1103/PhysRevB.54.1703
+
+
+ -------------------------------------------------------------------------------
+ - -
+ - T I M I N G -
+ - -
+ -------------------------------------------------------------------------------
+ SUBROUTINE CALLS ASD SELF TIME TOTAL TIME
+ MAXIMUM AVERAGE MAXIMUM AVERAGE MAXIMUM
+ CP2K 1 1.0 0.003 0.003 10.708 10.708
+ qs_forces 1 2.0 0.001 0.001 10.581 10.581
+ qs_energies_scf 1 3.0 0.001 0.001 9.617 9.617
+ scf_env_do_scf 1 4.0 0.000 0.000 8.351 8.351
+ scf_env_do_scf_inner_loop 12 5.0 0.002 0.002 8.351 8.351
+ qs_rho_update_rho 13 6.0 0.000 0.000 4.776 4.776
+ calculate_rho_elec 13 7.0 4.583 4.583 4.776 4.776
+ rebuild_ks_matrix 13 6.8 0.000 0.000 4.648 4.648
+ qs_ks_build_kohn_sham_matrix 13 7.8 0.002 0.002 4.648 4.648
+ sum_up_and_integrate 13 8.8 0.003 0.003 4.260 4.260
+ integrate_v_rspace 13 9.8 4.160 4.160 4.256 4.256
+ qs_ks_update_qs_env 12 6.0 0.000 0.000 4.018 4.018
+ init_scf_run 1 4.0 0.000 0.000 0.772 0.772
+ scf_env_initial_rho_setup 1 5.0 0.000 0.000 0.766 0.766
+ qs_ks_update_qs_env_forces 1 3.0 0.000 0.000 0.631 0.631
+ fft_wrap_pw1pw2 154 9.6 0.001 0.001 0.475 0.475
+ fft_wrap_pw1pw2_150 73 9.9 0.033 0.033 0.436 0.436
+ build_core_hamiltonian_matrix_ 1 3.0 0.000 0.000 0.332 0.332
+ fft3d_s 155 11.5 0.315 0.315 0.322 0.322
+ scf_post_calculation_gpw 1 4.0 0.000 0.000 0.285 0.285
+ gspace_mixing 11 6.0 0.013 0.013 0.229 0.229
+ -------------------------------------------------------------------------------
+
+ **** **** ****** ** PROGRAM ENDED AT 2016-07-14 13:56:09.684
+ ***** ** *** *** ** PROGRAM RAN ON lenovo700
+ ** **** ****** PROGRAM RAN BY lauri
+ ***** ** ** ** ** PROGRAM PROCESS ID 10179
+ **** ** ******* ** PROGRAM STOPPED IN /home/lauri/Dropbox/nomad-dev/nomad-l
+ ab-base/parsers/cp2k/test/unittests/c
+ p2k_2.6.2/kinds
diff --git a/test/unittests/cp2k_2.6.2/run_tests.py b/test/unittests/cp2k_2.6.2/run_tests.py
index 9fac4cc10222e2134deb2a6c6478dbed194148b1..71366950be941855c1c60c5739e5d15bde0cd5a8 100644
--- a/test/unittests/cp2k_2.6.2/run_tests.py
+++ b/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
-# Setup the logger so that it doesn't spam messages during tests
-logging.basicConfig(
- level=logging.DEBUG,
- format=(
- '%(filename)s: '
- '%(levelname)s: '
- '%(funcName)s(): '
- '%(lineno)d:\t'
- '%(message)s'
- )
-)
-logger = logging.getLogger("nomad")
-logger.setLevel(logging.CRITICAL)
-logging.getLogger("nomadcore.caching_backend").setLevel(logging.CRITICAL)
-
#===============================================================================
def get_results(folder, metainfo_to_keep=None):
@@ -46,7 +31,7 @@ def get_results(folder, metainfo_to_keep=None):
"""
dirname = os.path.dirname(__file__)
filename = os.path.join(dirname, folder, "unittest.out")
- parser = CP2KParser(filename, None)
+ parser = CP2KParser(filename, None, debug=True, log_level=logging.CRITICAL)
results = parser.parse()
return results
@@ -293,6 +278,25 @@ class TestEnergyForce(unittest.TestCase):
result = self.results["scf_max_iteration"]
self.assertEqual(result, 300)
+ def test_basis_set(self):
+ section_basis_set = self.results["section_basis_set"][0]
+
+ # Basis name
+ name = section_basis_set["basis_set_name"][0]
+ self.assertEqual(name, "DZVP-GTH-PADE_PW_150.0")
+
+ # Basis kind
+ kind = section_basis_set["basis_set_kind"][0]
+ self.assertEqual(kind, "wavefunction")
+
+ # Cell dependent basis mapping
+ cell_basis_mapping = section_basis_set["mapping_section_basis_set_cell_dependent"][0]
+ self.assertEqual(cell_basis_mapping, 0)
+
+ # # Atom centered basis mapping
+ atom_basis_mapping = section_basis_set["mapping_section_basis_set_atom_centered"][0]
+ self.assertTrue(np.array_equal(atom_basis_mapping, np.array(8*[0])))
+
def test_scf_threshold_energy_change(self):
result = self.results["scf_threshold_energy_change"]
self.assertEqual(result, convert_unit(1.00E-07, "hartree"))
@@ -344,7 +348,7 @@ class TestEnergyForce(unittest.TestCase):
def test_atom_label(self):
atom_labels = self.results["atom_labels"]
- expected_labels = np.array(8*["Si1"])
+ expected_labels = np.array(8*["Si"])
self.assertTrue(np.array_equal(atom_labels, expected_labels))
def test_simulation_cell(self):
@@ -413,7 +417,7 @@ class TestEnergyForce(unittest.TestCase):
def test_section_method_atom_kind(self):
kind = self.results["section_method_atom_kind"][0]
self.assertEqual(kind["method_atom_kind_atom_number"][0], 14)
- self.assertEqual(kind["method_atom_kind_label"][0], "Si1")
+ self.assertEqual(kind["method_atom_kind_label"][0], "Si")
def test_section_method_basis_set(self):
kind = self.results["section_method_basis_set"][0]
@@ -482,23 +486,23 @@ class TestEnergyForce(unittest.TestCase):
class TestPreprocessor(unittest.TestCase):
def test_include(self):
- result = get_result("input_preprocessing/include", "x_cp2k_CP2K_INPUT.GLOBAL.PRINT_LEVEL", optimize=False)
+ result = get_result("input_preprocessing/include", "x_cp2k_input_GLOBAL.PRINT_LEVEL", optimize=False)
self.assertEqual(result, "LOW")
def test_variable(self):
- result = get_result("input_preprocessing/variable", "x_cp2k_CP2K_INPUT.GLOBAL.PROJECT_NAME", optimize=False)
+ result = get_result("input_preprocessing/variable", "x_cp2k_input_GLOBAL.PROJECT_NAME", optimize=False)
self.assertEqual(result, "variable_test")
def test_variable_multiple(self):
- result = get_result("input_preprocessing/variable_multiple", "x_cp2k_CP2K_INPUT.FORCE_EVAL.DFT.MGRID.CUTOFF", optimize=False)
+ result = get_result("input_preprocessing/variable_multiple", "x_cp2k_input_FORCE_EVAL.DFT.MGRID.CUTOFF", optimize=False)
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)
+ result = get_result("input_preprocessing/comments", "x_cp2k_input_FORCE_EVAL.DFT.MGRID.CUTOFF", optimize=False)
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)
+ result = get_result("input_preprocessing/tabseparator", "x_cp2k_input_FORCE_EVAL.DFT.MGRID.CUTOFF", optimize=False)
self.assertEqual(result, "120")