From 4e3b1201032f9fdb946a32fd3344b27004a0fb9e Mon Sep 17 00:00:00 2001
From: "Himanen, Lauri (himanel1)" <lauri.himanen@aalto.fi>
Date: Mon, 25 Apr 2016 11:58:03 +0300
Subject: [PATCH] Added parsing of input file if found, added support for more
functionals, corrected the formatting of functionals, restructured the
package a bit.
---
README.md | 18 +-
parser/parser-cp2k/cp2kparser/__init__.py | 3 +-
.../cp2kparser/parsing/__init__.py | 0
.../parser-cp2k/cp2kparser/parsing/parser.py | 45 -
.../cp2kparser/parsing/versions/__init__.py | 0
.../parsing/versions/cp2k262/__init__.py | 0
.../parsing/versions/cp2k262/mainparser.py | 347 ----
.../parsing/versions/versionsetup.py | 21 -
.../parser-cp2k/cp2kparser/utils/__init__.py | 0
.../cp2kparser/utils/baseclasses.py | 511 ------
.../parser-cp2k/cp2kparser/utils/logconfig.py | 99 --
.../parser-cp2k/cp2kparser/utils/testing.py | 66 -
.../eu/nomad_lab/parsers/Cp2kParser.scala | 23 +-
.../XC_functional/becke88/unittest.out | 1434 -----------------
.../XC_functional/blyp/unittest.out | 82 +-
.../cp2k_2.6.2/energy_force/unittest.out | 539 ++++++-
test/unittests/cp2k_2.6.2/run_tests.py | 45 +-
17 files changed, 592 insertions(+), 2641 deletions(-)
delete mode 100644 parser/parser-cp2k/cp2kparser/parsing/__init__.py
delete mode 100644 parser/parser-cp2k/cp2kparser/parsing/parser.py
delete mode 100644 parser/parser-cp2k/cp2kparser/parsing/versions/__init__.py
delete mode 100644 parser/parser-cp2k/cp2kparser/parsing/versions/cp2k262/__init__.py
delete mode 100644 parser/parser-cp2k/cp2kparser/parsing/versions/cp2k262/mainparser.py
delete mode 100644 parser/parser-cp2k/cp2kparser/parsing/versions/versionsetup.py
delete mode 100644 parser/parser-cp2k/cp2kparser/utils/__init__.py
delete mode 100644 parser/parser-cp2k/cp2kparser/utils/baseclasses.py
delete mode 100644 parser/parser-cp2k/cp2kparser/utils/logconfig.py
delete mode 100644 parser/parser-cp2k/cp2kparser/utils/testing.py
delete mode 100644 test/unittests/cp2k_2.6.2/XC_functional/becke88/unittest.out
diff --git a/README.md b/README.md
index 9673843..ffa5513 100644
--- a/README.md
+++ b/README.md
@@ -70,12 +70,18 @@ easily readable formatting is also provided for the log messages.
## Testing
The parsers can become quite complicated and maintaining them without
-systematic testing can become troublesome. Unit tests provide one way to
-test each parseable quantity and python has a very good [library for
-unit testing](https://docs.python.org/2/library/unittest.html). When the parser
-supports a new quantity it is quite fast to create unit tests for it. These
-tests will validate the parsing, and also easily detect bugs that may rise when
-the code is modified in the future.
+systematic testing is impossible. There are general tests that are
+performed automatically in the scala layer for all parsers. This is essential,
+but can only test that the data is outputted in the correct format and
+according to some general rules. These tests cannot verify that the contents
+are correct.
+
+In order to truly test the parser output, unit testing is needed. Unit tests
+provide one way to test each parseable quantity and python has a very good
+[library for unit testing](https://docs.python.org/2/library/unittest.html).
+When the parser supports a new quantity it is quite fast to create unit tests
+for it. These tests will validate the parsing, and also easily detect bugs that
+may rise when the code is modified in the future.
## Unit conversion
You can find unit conversion tools from the python-common repository and its
diff --git a/parser/parser-cp2k/cp2kparser/__init__.py b/parser/parser-cp2k/cp2kparser/__init__.py
index 0a1233a..382f845 100644
--- a/parser/parser-cp2k/cp2kparser/__init__.py
+++ b/parser/parser-cp2k/cp2kparser/__init__.py
@@ -1,2 +1 @@
-import cp2kparser.utils.logconfig
-from cp2kparser.parsing.parser import CP2KParser
+from cp2kparser.parser import CP2KParser
diff --git a/parser/parser-cp2k/cp2kparser/parsing/__init__.py b/parser/parser-cp2k/cp2kparser/parsing/__init__.py
deleted file mode 100644
index e69de29..0000000
diff --git a/parser/parser-cp2k/cp2kparser/parsing/parser.py b/parser/parser-cp2k/cp2kparser/parsing/parser.py
deleted file mode 100644
index d78d8db..0000000
--- a/parser/parser-cp2k/cp2kparser/parsing/parser.py
+++ /dev/null
@@ -1,45 +0,0 @@
-import re
-import logging
-from cp2kparser.utils.baseclasses import ParserInterface
-from cp2kparser.parsing.versions.versionsetup import get_main_parser
-logger = logging.getLogger(__name__)
-
-
-#===============================================================================
-class CP2KParser(ParserInterface):
- """This class handles the initial setup before any parsing can happen. It
- determines which version of CP2K was used to generate the output and then
- sets up a correct implementation.
-
- 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):
- super(CP2KParser, self).__init__(main_file, metainfo_to_keep, backend, default_units, metainfo_units)
-
- def setup_version(self):
- """Setups the version by looking at the output file and the version
- specified in it.
- """
- # Search for the version specification and initialize a correct
- # implementation for this version
- regex = re.compile(r" CP2K\| version string:\s+CP2K version ([\d\.]+)")
- n_lines = 30
- with open(self.parser_context.main_file, 'r') as outputfile:
- for i_line in xrange(n_lines):
- line = next(outputfile)
- result = regex.match(line)
- if result:
- version_id = result.group(1).replace('.', '')
- break
- if not result:
- logger.error("Could not find a version specification from the given main file.")
-
- self.parser_context.file_storage.setup_file_id(self.parser_context.main_file, "output")
- self.main_parser = get_main_parser(version_id)(self.parser_context.main_file, self.parser_context)
-
- def get_metainfo_filename(self):
- return "cp2k.nomadmetainfo.json"
-
- def get_parser_info(self):
- return {'name': 'cp2k-parser', 'version': '1.0'}
diff --git a/parser/parser-cp2k/cp2kparser/parsing/versions/__init__.py b/parser/parser-cp2k/cp2kparser/parsing/versions/__init__.py
deleted file mode 100644
index e69de29..0000000
diff --git a/parser/parser-cp2k/cp2kparser/parsing/versions/cp2k262/__init__.py b/parser/parser-cp2k/cp2kparser/parsing/versions/cp2k262/__init__.py
deleted file mode 100644
index e69de29..0000000
diff --git a/parser/parser-cp2k/cp2kparser/parsing/versions/cp2k262/mainparser.py b/parser/parser-cp2k/cp2kparser/parsing/versions/cp2k262/mainparser.py
deleted file mode 100644
index 8b2ebe8..0000000
--- a/parser/parser-cp2k/cp2kparser/parsing/versions/cp2k262/mainparser.py
+++ /dev/null
@@ -1,347 +0,0 @@
-import re
-from nomadcore.simple_parser import SimpleMatcher as SM
-from nomadcore.caching_backend import CachingLevel
-from cp2kparser.utils.baseclasses import MainParser
-import numpy as np
-import logging
-logger = logging.getLogger("nomad.CP2KParser")
-
-
-#===============================================================================
-class CP2KMainParser(MainParser):
- """The main parser class.
- """
- def __init__(self, file_path, parser_context):
- """Initialize an output parser.
- """
- super(CP2KMainParser, self).__init__(file_path, parser_context)
- self.regex_f = "-?\d+\.\d+(?:E(?:\+|-)\d+)?" # Regex for a floating point value
- self.regex_i = "-?\d+" # Regex for an integer
-
- # Define the output parsing tree for this version
- self.root_matcher = SM("",
- forwardMatch=True,
- sections=['section_run', "section_system_description"],
- subMatchers=[
- SM( r" DBCSR\| Multiplication driver",
- sections=['cp2k_section_dbcsr'],
- ),
- SM( r" \*\*\*\* \*\*\*\* \*\*\*\*\*\* \*\* PROGRAM STARTED AT\s+(?P<cp2k_run_start_date>\d{4}-\d{2}-\d{2}) (?P<cp2k_run_start_time>\d{2}:\d{2}:\d{2}.\d{3})",
- sections=['cp2k_section_startinformation'],
- ),
- SM( r" CP2K\|",
- sections=['cp2k_section_programinformation'],
- forwardMatch=True,
- subMatchers=[
- SM( r" CP2K\| version string:\s+(?P<program_version>[\w\d\W\s]+)"),
- SM( r" CP2K\| source code revision number:\s+svn:(?P<cp2k_svn_revision>\d+)"),
- ]
- ),
- SM( r" CP2K\| Input file name\s+(?P<cp2k_input_filename>.+$)",
- sections=['cp2k_section_filenames'],
- subMatchers=[
- SM( r" GLOBAL\| Basis set file name\s+(?P<cp2k_basis_set_filename>.+$)"),
- SM( r" GLOBAL\| Geminal file name\s+(?P<cp2k_geminal_filename>.+$)"),
- SM( r" GLOBAL\| Potential file name\s+(?P<cp2k_potential_filename>.+$)"),
- SM( r" GLOBAL\| MM Potential file name\s+(?P<cp2k_mm_potential_filename>.+$)"),
- SM( r" GLOBAL\| Coordinate file name\s+(?P<cp2k_coordinate_filename>.+$)"),
- ]
- ),
- SM( " CELL\|",
- adHoc=self.adHoc_cp2k_section_cell(),
- otherMetaInfo=["simulation_cell"]
- ),
- SM( " DFT\|",
- sections=["section_method"],
- otherMetaInfo=["XC_functional", "self_interaction_correction_method"],
- forwardMatch=True,
- subMatchers=[
- SM( " DFT\| Multiplicity\s+(?P<target_multiplicity>{})".format(self.regex_i)),
- SM( " DFT\| Charge\s+(?P<total_charge>{})".format(self.regex_i)),
- SM( " DFT\| Self-interaction correction \(SIC\)\s+(?P<self_interaction_correction_method>[^\n]+)"),
- SM( " FUNCTIONAL\| ([\w\d\W\s]+):",
- forwardMatch=True,
- repeats=True,
- sections=["section_XC_functionals"],
- adHoc=self.adHoc_section_XC_functionals()
- )
- ]
- ),
- SM( " TOTAL NUMBERS AND MAXIMUM NUMBERS",
- sections=["cp2k_section_total_numbers"],
- subMatchers=[
- SM( "\s+- Atoms:\s+(?P<number_of_atoms>\d+)"),
- SM( "\s+- Shell sets:\s+(?P<cp2k_shell_sets>\d+)")
- ]
- ),
- SM( " MODULE QUICKSTEP: ATOMIC COORDINATES IN angstrom",
- adHoc=self.adHoc_cp2k_section_quickstep_atom_information(),
- otherMetaInfo=["atom_label", "atom_position"]
- ),
- SM( " SCF WAVEFUNCTION OPTIMIZATION",
- sections=["section_single_configuration_calculation"],
- subMatchers=[
- SM( r"\s+\d+\s+\S+\s+{0}\s+{0}\s+{0}\s+(?P<energy_total_scf_iteration__hartree>{0})\s+{0}".format(self.regex_f),
- sections=["section_scf_iteration"],
- repeats=True,
- ),
- SM( r" ENERGY\| Total FORCE_EVAL \( \w+ \) energy \(a\.u\.\):\s+(?P<energy_total__hartree>{0})".format(self.regex_f)),
- SM( r" ATOMIC FORCES in \[a\.u\.\]"),
- SM( r" # Atom Kind Element X Y Z",
- adHoc=self.adHoc_atom_forces()
- ),
- ]
- ),
- SM( " MD| Molecular Dynamics Protocol",
- sections=["cp2k_section_md"],
- forwardMatch=True,
- subMatchers=[
- SM( " ENERGY\| Total FORCE_EVAL",
- repeats=True,
- sections=["cp2k_section_md_step"],
- subMatchers=[
- SM( " ATOMIC FORCES in \[a\.u\.\]",
- sections=["cp2k_section_md_forces"],
- subMatchers=[
- SM( "\s+\d+\s+\d+\s+[\w\W\d]+\s+(?P<cp2k_md_force_atom_string>{0}\s+{0}\s+{0})".format(self.regex_f),
- sections=["cp2k_section_md_force_atom"],
- repeats=True,
- )
- ]
- ),
- SM( " STEP NUMBER\s+=\s+(?P<cp2k_md_step_number>\d+)"),
- SM( " TIME \[fs\]\s+=\s+(?P<cp2k_md_step_time>\d+\.\d+)"),
- SM( " TEMPERATURE \[K\]\s+=\s+(?P<cp2k_md_temperature_instantaneous>{0})\s+(?P<cp2k_md_temperature_average>{0})".format(self.regex_f)),
- SM( " i =",
- sections=["cp2k_section_md_coordinates"],
- otherMetaInfo=["cp2k_md_coordinates"],
- dependencies={"cp2k_md_coordinates": ["cp2k_md_coordinate_atom_string"]},
- subMatchers=[
- SM( " \w+\s+(?P<cp2k_md_coordinate_atom_string>{0}\s+{0}\s+{0})".format(self.regex_f),
- endReStr="\n",
- sections=["cp2k_section_md_coordinate_atom"],
- repeats=True,
- )
- ]
- )
- ]
- )
- ]
- )
- ]
- )
- #=======================================================================
- # The cache settings
- self.caching_level_for_metaname = {
- 'section_XC_functionals': CachingLevel.ForwardAndCache,
- 'self_interaction_correction_method': CachingLevel.Cache,
- 'cp2k_section_md_coordinates': CachingLevel.Cache,
- 'cp2k_section_md_coordinate_atom': CachingLevel.Cache,
- 'cp2k_md_coordinate_atom_string': CachingLevel.Cache,
- 'cp2k_md_coordinate_atom_float': CachingLevel.Cache,
-
- 'cp2k_section_md_forces': CachingLevel.Cache,
- 'cp2k_section_md_force_atom': CachingLevel.Cache,
- 'cp2k_md_force_atom_string': CachingLevel.Cache,
- 'cp2k_md_force_atom_float': CachingLevel.Cache,
- }
-
- #===========================================================================
- # The functions that trigger when sections are closed
- def onClose_section_method(self, backend, gIndex, section):
- """When all the functional definitions have been gathered, matches them
- with the nomad correspondents and combines into one single string which
- is put into the backend.
- """
- # Combine the functional names into a one big string that is placed
- # into XC_functional
- functional_names = []
- section_XC_functionals = section["section_XC_functionals"]
-
- for functional in section_XC_functionals:
- functional_name = functional["XC_functional_name"][0]
- functional_names.append(functional_name)
-
- functionals = "_".join(sorted(functional_names))
- backend.addValue('XC_functional', functionals)
-
- # Transform the CP2K self-interaction correction string to the NOMAD
- # correspondent, and push directly to the superBackend to avoid caching
- sic_cp2k = section["self_interaction_correction_method"][0]
- sic_map = {
- "NO": "",
- "AD SIC": "SIC_AD",
- "Explicit Orbital SIC": "SIC_EXPLICIT_ORBITALS",
- "SPZ/MAURI SIC": "SIC_MAURI_SPZ",
- "US/MAURI SIC": "SIC_MAURI_US",
- }
- sic_nomad = sic_map.get(sic_cp2k)
- if sic_nomad is not None:
- backend.superBackend.addValue('self_interaction_correction_method', sic_nomad)
- else:
- logger.warning("Unknown self-interaction correction method used.")
-
- def onClose_cp2k_section_md_coordinate_atom(self, backend, gIndex, section):
- """Given the string with the coordinate components for one atom, make it
- into a numpy array of coordinate components and store for later
- concatenation.
- """
- force_string = section["cp2k_md_coordinate_atom_string"][0]
- components = np.array([float(x) for x in force_string.split()])
- backend.addArrayValues("cp2k_md_coordinate_atom_float", components)
-
- def onClose_cp2k_section_md_coordinates(self, backend, gIndex, section):
- """When all the coordinates for individual atoms have been gathered,
- concatenate them into one big array and forward to the backend.
- """
- forces = section["cp2k_md_coordinate_atom_float"]
- forces = np.array(forces)
- backend.addArrayValues("cp2k_md_coordinates", forces)
-
- def onClose_cp2k_section_md_force_atom(self, backend, gIndex, section):
- """Given the string with the force components for one atom, make it
- into a numpy array of force components and store for later
- concatenation.
- """
- force_string = section["cp2k_md_force_atom_string"][0]
- components = np.array([float(x) for x in force_string.split()])
- backend.addArrayValues("cp2k_md_force_atom_float", components)
-
- def onClose_cp2k_section_md_forces(self, backend, gIndex, section):
- """When all the forces for individual atoms have been gathered,
- concatenate them into one big array and forward to the backend.
- """
- forces = section["cp2k_md_force_atom_float"]
- forces = np.array(forces)
- backend.addArrayValues("cp2k_md_forces", forces, unit="forceAu")
-
- #===========================================================================
- # adHoc functions that are used to do custom parsing. Primarily these
- # functions are used for data that is formatted as a table or a list.
- def adHoc_section_XC_functionals(self):
- """Used to extract the functional information.
- """
- def wrapper(parser):
-
- # Define the regex that extracts the information
- regex_string = " FUNCTIONAL\| ([\w\d\W\s]+):"
- regex_compiled = re.compile(regex_string)
-
- # Parse out the functional name
- functional_name = None
- line = parser.fIn.readline()
- result = regex_compiled.match(line)
-
- if result:
- functional_name = result.groups()[0]
-
- # Define a mapping for the functionals
- functional_map = {
- "LYP": "GGA_C_LYP",
- "BECKE88": "GGA_X_B88",
- "PADE": "LDA_XC_TETER93",
- "LDA": "LDA_XC_TETER93",
- "BLYP": "HYB_GGA_XC_B3LYP",
- }
-
- # If match found, add the functional definition to the backend
- nomad_name = functional_map.get(functional_name)
- if nomad_name is not None:
- parser.backend.addValue('XC_functional_name', nomad_name)
-
- return wrapper
-
- def adHoc_cp2k_section_cell(self):
- """Used to extract the cell information.
- """
- def wrapper(parser):
- # Read the lines containing the cell vectors
- a_line = parser.fIn.readline()
- b_line = parser.fIn.readline()
- c_line = parser.fIn.readline()
-
- # Define the regex that extracts the components and apply it to the lines
- regex_string = r" CELL\| Vector \w \[angstrom\]:\s+({0})\s+({0})\s+({0})".format(self.regex_f)
- regex_compiled = re.compile(regex_string)
- a_result = regex_compiled.match(a_line)
- b_result = regex_compiled.match(b_line)
- c_result = regex_compiled.match(c_line)
-
- # Convert the string results into a 3x3 numpy array
- cell = np.zeros((3, 3))
- cell[0, :] = [float(x) for x in a_result.groups()]
- cell[1, :] = [float(x) for x in b_result.groups()]
- cell[2, :] = [float(x) for x in c_result.groups()]
-
- # Push the results to the correct section
- parser.backend.addArrayValues("simulation_cell", cell, unit="angstrom")
-
- return wrapper
-
- def adHoc_cp2k_section_quickstep_atom_information(self):
- """Used to extract the initial atomic coordinates and names in the
- Quickstep module.
- """
- 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.regex_f)
- regex_compiled = re.compile(regex_string)
-
- match = True
- coordinates = []
- labels = []
-
- # Currently these three lines are not processed
- parser.fIn.readline()
- parser.fIn.readline()
- parser.fIn.readline()
-
- while match:
- line = parser.fIn.readline()
- result = regex_compiled.match(line)
-
- if result:
- match = True
- label = result.groups()[0]
- labels.append(label)
- coordinate = [float(x) for x in result.groups()[1:]]
- coordinates.append(coordinate)
- else:
- match = False
- coordinates = np.array(coordinates)
- labels = np.array(labels)
-
- # If anything found, push the results to the correct section
- if len(coordinates) != 0:
- parser.backend.addArrayValues("atom_position", coordinates, unit="angstrom")
- parser.backend.addArrayValues("atom_label", labels)
-
- return wrapper
-
- def adHoc_atom_forces(self):
- """Used to extract the final atomic forces printed at the end of an
- ENERGY_FORCE calculation is the PRINT setting is on.
- """
- def wrapper(parser):
-
- end_str = " SUM OF ATOMIC FORCES"
- end = False
- force_array = []
-
- # Loop through coordinates until the sum of forces is read
- while not end:
- line = parser.fIn.readline()
- if line.startswith(end_str):
- end = True
- else:
- forces = line.split()[-3:]
- forces = [float(x) for x in forces]
- force_array.append(forces)
- force_array = np.array(force_array)
-
- # If anything found, push the results to the correct section
- if len(force_array) != 0:
- parser.backend.addArrayValues("atom_forces", force_array, unit="forceAu")
-
- return wrapper
diff --git a/parser/parser-cp2k/cp2kparser/parsing/versions/versionsetup.py b/parser/parser-cp2k/cp2kparser/parsing/versions/versionsetup.py
deleted file mode 100644
index 8b8fd01..0000000
--- a/parser/parser-cp2k/cp2kparser/parsing/versions/versionsetup.py
+++ /dev/null
@@ -1,21 +0,0 @@
-
-"""Returns the implementation classes based on the given version identifier.
-The different version are grouped into subpackages.
-"""
-import importlib
-import logging
-logger = logging.getLogger(__name__)
-
-
-def get_main_parser(version_id):
-
- # Currently the version id is a pure integer, so it can directly be mapped
- # into a package name.
- base = "cp2kparser.parsing.versions.cp2k{}.".format(version_id)
- try:
- main_parser = importlib.import_module(base + "mainparser").CP2KMainParser
- except ImportError:
- logger.debug("A parser with the version id '{}' could not be found. Defaulting to the base implementation based on CP2K 2.6.2.".format(version_id))
- base = "cp2kparser.parsing.versions.cp2k262."
- main_parser = importlib.import_module(base + "mainparser").CP2KMainParser
- return main_parser
diff --git a/parser/parser-cp2k/cp2kparser/utils/__init__.py b/parser/parser-cp2k/cp2kparser/utils/__init__.py
deleted file mode 100644
index e69de29..0000000
diff --git a/parser/parser-cp2k/cp2kparser/utils/baseclasses.py b/parser/parser-cp2k/cp2kparser/utils/baseclasses.py
deleted file mode 100644
index 3cee84d..0000000
--- a/parser/parser-cp2k/cp2kparser/utils/baseclasses.py
+++ /dev/null
@@ -1,511 +0,0 @@
-"""
-This module contains the base classes that help in building parsers for the
-NoMaD project.
-"""
-
-import os
-import logging
-from abc import ABCMeta, abstractmethod
-from nomadcore.unit_conversion import unit_conversion
-from nomadcore.simple_parser import AncillaryParser, mainFunction
-from nomadcore.local_backend import LocalBackend
-from nomadcore.local_meta_info import load_metainfo
-from nomadcore.caching_backend import CachingLevel
-logger = logging.getLogger(__name__)
-
-
-#===============================================================================
-class ParserInterface(object):
- """This class provides the interface parsing. The end-user will typically
- only interact with this class. All the input is given to this class (or
- typically a subclass) and the parsing is done by calling the parse()
- method. The parsing output is determined by the backend object that is
- given in the constructor as a dependency.
-
- Attributes:
- main_parser: Object that actually does the parsing and is
- setup by this class based on the given contents.
- parser_context: A wrapper class for all the parser related information.
- This is contructed here and then passed onto the different
- subparsers.
- """
- __metaclass__ = ABCMeta
-
- def __init__(self, main_file, metainfo_to_keep=None, backend=None, default_units=None, metainfo_units=None):
- """
- Args:
- main_file: A special file that can be considered the main file of the
- calculation.
- metainfo_to_keep: A list of metainfo names. This list is used to
- optimize the parsing process as optimally only the information
- relevant to these metainfos will be parsed.
- backend: An object to which the parser will give all the parsed data.
- The backend will then determine where and when to output that data.
- """
- self.initialize(main_file, metainfo_to_keep, backend, default_units, metainfo_units)
-
- def initialize(self, main_file, metainfo_to_keep, backend, default_units, metainfo_units):
- """Initialize the parser with the given environment.
- """
- self.parser_context = ParserContext()
- self.parser_context.metainfo_to_keep = metainfo_to_keep
- self.parser_context.main_file = main_file
- self.parser_context.file_storage = FileStorage()
- self.parser_context.parser_info = self.get_parser_info()
- self.main_parser = None
-
- # Check that the main file exists
- if not os.path.isfile(main_file):
- logger.error("Couldn't find the main file {}. Check that the path is valid and the file exists on this path.".format(main_file))
-
- # Load metainfo environment
- metainfo_env, warn = load_metainfo(self.get_metainfo_filename())
- self.parser_context.metainfo_env = metainfo_env
-
- # Initialize the backend. Use local backend if none given
- if backend is not None:
- self.parser_context.backend = backend(metainfo_env)
- else:
- self.parser_context.backend = LocalBackend(metainfo_env)
-
- # Check the list of default units
- default_unit_map = {}
- if default_units is not None:
- for unit in default_units:
- dimension = unit_conversion.ureg(unit).dimensionality
- old_value = default_unit_map.get(str(dimension))
- if old_value is not None:
- raise LookupError("You can only specify one default value per dimension in the 'default_units' list. There are two different units given for the dimension '{}'".format(dimension))
- default_unit_map[str(dimension)] = unit
-
- # Check the list of metainfo units
- if metainfo_units is not None:
- for metaname, unit in metainfo_units.iteritems():
-
- # Check that the unit is OK
- unit_conversion.ureg(unit)
-
- # Check that the metaname is OK
- meta = metainfo_env.infoKinds.get(metaname)
- if meta is None:
- raise KeyError("The metainfo name '{}' could not be found. Check for typos or try updating the metainfo repository.".format(metaname))
-
- # Save the default units
- self.parser_context.default_units = default_unit_map
- self.parser_context.metainfo_units = metainfo_units
-
- @abstractmethod
- def setup_version(self):
- """Deduce the version of the software that was used and setup a correct
- main parser. The main parser should subclass MainParser and be stored
- to the 'main_parser' attribute of this class. You can give the
- 'parser_context' wrapper object in the main parser constructor to pass
- all the relevant data for it.
- """
- pass
-
- @abstractmethod
- def get_metainfo_filename(self):
- """This function should return the name of the metainfo file that is
- specific for this parser. When the parser is started, the metainfo
- environment is loaded from this file that is located within a separate
- repository (nomad-meta-info).
-
- Returns:
- A string containing the metainfo filename for this parser.
- """
- return None
-
- @abstractmethod
- def get_parser_info(self):
- """This function should return a dictionary containing the parser info.
- This info is printed to the JSON backend. it should be of the form:
-
- {'name': 'softwarename-parser', 'version': '1.0'}
-
- Returns:
- A dictionary containing information about this parser.
- """
- return None
-
- def parse(self):
- """Starts the actual parsing process, and outputs the results to the
- backend specified in the constructor.
- """
- self.setup_version()
- if not self.main_parser:
- logger.error("The main parser has not been set up.")
-
- self.main_parser.parse()
-
- # If using a local backend, the results will have been saved to a
- # separate results dictionary which should be returned.
- try:
- return self.parser_context.backend.results
- except AttributeError:
- return None
-
-
-#===============================================================================
-class FileStorage(object):
- """Used to map file paths to certain ID's. This helps in setting up the
- Secondary parsers as you can associate file paths to simpler ID's that are
- easier to use.
-
- Attributes:
- _file_handles: A "private" dictionary containing the cached file handles
- _file_contents: A "private" dictionary containing the cached file contents
- _file_sizes: A "private" dictionary containing the cached file sizes
- file_ids: A dictionary containing the mapping between file ids and filepaths
- """
- def __init__(self):
- self._file_handles = {}
- self._file_contents = {}
- self._file_sizes = {}
- self.file_ids = {}
-
- def setup_file_id(self, path, file_id):
- """Used to map a simple identifier string to a file path. When a file
- id has been setup, you can easily access the file by using the
- functions get_file_handle() or get_file_contents()
- """
- old = self.file_ids.get(file_id)
- if old is not None:
- raise LookupError("The path '{}' is already associated with id '{}'".format(old, file_id))
- self.file_ids[file_id] = path
-
- def add_file_id(self, path, file_id):
- value = self.file_ids.get(file_id)
- if value:
- if isinstance(value, list):
- value.append(path)
- else:
- raise LookupError("You have already setup an unique file_path '{}' to this id.".format(value))
- else:
- pathlist = []
- pathlist.append(path)
- self.file_ids[file_id] = pathlist
-
- def get_filepath_by_id(self, file_id, show_warning=True):
- """Get the file paths that were registered with the given id.
- """
- value = self.file_ids.get(file_id)
- if value:
- if isinstance(value, list):
- n = len(value)
- if n == 0:
- if show_warning:
- logger.warning("No files set with id '{}'".format(file_id))
- return None
- else:
- if show_warning:
- logger.debug("Multiple files set with id '{}'".format(file_id))
- return value
- else:
- return value
- else:
- if show_warning:
- logger.warning("No files set with id '{}'".format(file_id))
-
- def get_file_handle(self, file_id, show_warning=True):
- """Get the handle for a single file with the given id. Uses cached result
- if available. Always seeks to beginning of file before returning it.
- """
- # Get the filepath(s)
- path = self.get_filepath_by_id(file_id, show_warning)
- if not path:
- if show_warning:
- logger.warning("No filepaths registered to id '{}'. Register id's with setup_file_id().".format(file_id))
- return
-
- if isinstance(path, list):
- if len(path) == 0:
- return
- elif len(path) != 1:
- logger.error("Multiple filepaths found with id '{}'. Use get_file_handles() instead if you expect to have multiple files.".format(file_id))
- return
- else:
- path = path[0]
-
- # Search for filehandles, if not present create one
- handle = self._file_handles.get(path)
- if not handle:
- try:
- handle = open(path, "r")
- except (OSError, IOError):
- logger.error("Could not open file: '{}'".format(path))
- else:
- self._file_handles[file_id] = handle
- handle.seek(0, os.SEEK_SET)
- return handle
-
- def get_file_handles(self, file_id, show_warning=True):
- """Get the handles for multiple files with the given id. Uses cached result
- if available. Always seeks to beginning of files before returning them.
- """
- # Get the filepath(s)
- paths = self.get_filepath_by_id(file_id, show_warning)
- if not paths:
- return
- if not isinstance(paths, list):
- paths = [paths]
-
- # Search for filehandles, if not present create one
- handles = []
- for path in paths:
- handle = self._file_handles.get(path)
- if not handle:
- try:
- handle = open(path, "r")
- except (OSError, IOError):
- logger.error("Could not open file: '{}'".format(path))
- else:
- self._file_handles[file_id] = handle
- handle.seek(0, os.SEEK_SET)
- handles.append(handle)
-
- # Return handles
- if len(handles) == 0:
- return None
- else:
- return handles
-
- def get_file_contents(self, file_id):
- """Get the contents for the file with the given id. Uses cached result
- if available. Does not cache files that are bigger than a certain
- limit.
- """
- cache_limit = 10000
- contents = self._file_contents.get(file_id)
- if not contents:
- fh = self.get_file_handle(file_id)
- fh.seek(0)
- contents = fh.read()
- if self.get_file_size(file_id) <= cache_limit:
- self._file_contents[file_id] = contents
- return contents
-
- def get_file_size(self, file_id):
- """Get the size of a file with the given id. Uses cached result
- if available.
- """
- size = self._file_sizes.get(file_id)
- if not size:
- fh = self.get_file_handle(file_id)
- fh.seek(0, os.SEEK_END)
- size = fh.tell()
- self._file_sizes[file_id] = size
- return size
-
-
-#===============================================================================
-class HierarchicalParser(object):
- """A base class for all parsers that do parsing based on the SimpleMatcher
- hierarchy.
-
- Attributes:
- root_matcher: The root of this parsers SimpleMatcher tree.
- """
- def __init__(self, file_path):
- self.file_path = file_path
- self.root_matcher = None
- self.caching_level_for_metaname = {}
- self.default_data_caching_level = CachingLevel.ForwardAndCache
- self.default_section_caching_level = CachingLevel.Forward
- self.onClose = {}
- self.simple_parser = None
-
-
-#===============================================================================
-class SecondaryParser(HierarchicalParser):
- """A base class for ancillary file parsers. Instantiated and run by a
- MainParser.
-
- Attributes:
- ancillary_parser: An nomadcore.simple_parser.AncillaParser object
- """
- def __init__(self, file_path, simple_parser):
- """
- Args:
- file_path: The path of the file to parse. Can be absolute or relative path.
- simple_parser: The SimpleParser object that is does the actual
- parsing. Shared with ther SecondaryParsers and the MainParser.
- """
- super(SecondaryParser, self).__init__(file_path)
- self.simple_parser = simple_parser
- self.ancillary_parser = None
-
- def parse(self):
- """Parser the given ancillary file in place.
- """
- self.ancillary_parser = AncillaryParser(self.root_matcher, self.simple_parser, self.caching_levels, self)
-
- # Try opening the given file
- try:
- with open(self.file_path) as fIn:
- self.ancillary_parser.parseFile(fIn)
- except IOError:
- dir_name, file_name = os.path.split(os.path.abspath(self.file_path))
- logger.warning("Could not find file '{}' in directory '{}'. No data will be parsed from this file".format(dir_name, file_name))
-
-
-#===============================================================================
-class MainParser(HierarchicalParser):
- """Base class for main parsers. Will call AncillaryParsers to parse additional
- files. Typically this main parser is also tied to a file ("main file").
-
- A subclass of ParserImplementation will initialize only one MainParser.
-
- Attributes:
- file_path: Path to the main file.
- """
-
- def __init__(self, file_path, parser_context):
- """
- Args:
- files: A list of filenames that are parsed and analyzed by this
- object.
- parser_context: The parsing context that contains e.g. the backend.
- """
- super(MainParser, self).__init__(file_path)
- if parser_context:
- self.parser_context = parser_context
- self.backend = parser_context.backend
- self.metainfo_to_keep = parser_context.metainfo_to_keep
- self.version_id = parser_context.version_id
- self.caching_backend = None
-
- def parse(self):
- """Starts the parsing. By default uses the SimpleParser scheme, if you
- want to use something else or customize the process just override this
- method.
- """
- mainFunction(
- mainFileDescription=self.root_matcher,
- metaInfoEnv=self.parser_context.metainfo_env,
- parserInfo=self.parser_context.parser_info,
- outF=self.parser_context.backend.fileOut,
- cachingLevelForMetaName=self.caching_level_for_metaname,
- superContext=self,
- onClose={},
- default_units=self.parser_context.default_units,
- metainfo_units=self.parser_context.metainfo_units,
- superBackend=self.parser_context.backend,
- mainFile=self.parser_context.main_file)
-
- def get_metainfos(self):
- """Get a list of all the metainfo names that are parsed by this
- FileParser. This information is used by the ParserImplementation to
- optimize the parsing process according to the given 'metainfo_to_keep'
- list.
- """
- return self.root_matcher.allMetaNames()
-
- def startedParsing(self, fInName, parser):
- """Function is called when the parsing starts.
-
- Get compiled parser.
- Later one can compile a parser for parsing an external file.
- """
- self.simple_parser = parser
-
-
-#===============================================================================
-class ParserContext(object):
- """A container class for storing and moving information about the parsing
- environment. A single ParserContext object is initialized by the Parser
- class, or it's subclass.
- """
- def __init__(self, main_file=None, metainfo_to_keep=None, backend=None, version_id=None, default_units=None, metainfo_units=None, file_storage=None, metainfo_env=None, parser_info=None):
- self.main_file = main_file
- self.version_id = version_id
- self.metainfo_to_keep = metainfo_to_keep
- self.backend = backend
- self.default_units = default_units
- self.metainfo_units = metainfo_units
- self.file_storage = file_storage
- self.metainfo_env = metainfo_env
- self.parser_info = parser_info
-
-
-#===============================================================================
-# class ParserImplementation(object):
- # """The base class for a version specific parser implementation in. Provides
- # some useful tools for setting up file access.
-
- # Attributes:
- # parser_context: ParserContext object
- # file_storage: FileStorage object
- # main_parser: MainParser object
- # """
- # def __init__(self, parser_context):
-
- # self.parser_context = parser_context
- # self.file_storage = FileStorage()
- # self.main_parser = None
-
- # # Copy all the attributes from the ParserContext object for quick access
- # attributes = dir(parser_context)
- # for attribute in attributes:
- # if not attribute.startswith("__"):
- # setattr(self, attribute, getattr(parser_context, attribute))
-
- # # self.file_parsers = []
-
- # # def setup_given_file_ids(self):
- # # """Saves the file id's that were given in the JSON input.
- # # """
- # # for path, file_id in self.files.iteritems():
- # # if file_id:
- # # self.file_storage.setup_file_id(path, file_id)
-
- # def parse(self):
- # """Start the parsing. Will try to parse everything unless given special
- # rules (metaInfoToKeep)."""
- # self.main_parser.parse()
- # for file_parser in self.file_parsers:
- # file_parser.parse()
-
-
-
- # Initialize the parser builder
- # default_units = self.parser_context.default_units
- # metainfo_units = self.parser_context.metainfo_units
- # parserBuilder = SimpleParserBuilder(self.root_matcher, self.backend.metaInfoEnv(), self.metainfo_to_keep, default_units=default_units, metainfo_units=metainfo_units)
-
- # # Verify the metainfo
- # if not parserBuilder.verifyMetaInfo(sys.stderr):
- # sys.exit(1)
-
- # # Gather onClose functions from supercontext
- # onClose = dict(self.onClose)
- # for attr, callback in extractOnCloseTriggers(self).items():
- # oldCallbacks = onClose.get(attr, None)
- # if oldCallbacks:
- # oldCallbacks.append(callback)
- # else:
- # onClose[attr] = [callback]
-
- # # Setup the backend that caches ond handles triggers
- # self.caching_backend = ActiveBackend.activeBackend(
- # metaInfoEnv=self.backend.metaInfoEnv(),
- # cachingLevelForMetaName=self.caching_level_for_metaname,
- # defaultDataCachingLevel=self.default_data_caching_level,
- # defaultSectionCachingLevel=self.default_section_caching_level,
- # onClose=onClose,
- # superBackend=self.backend,
- # default_units=default_units,
- # metainfo_units=metainfo_units)
-
- # # Compile the SimpleMatcher tree
- # parserBuilder.compile()
-
- # self.backend.fileOut.write("[")
- # uri = "file://" + self.file_path
- # parserInfo = {'name': 'cp2k-parser', 'version': '1.0'}
- # self.caching_backend.startedParsingSession(uri, parserInfo)
- # with open(self.file_path, "r") as fIn:
- # parser = parserBuilder.buildParser(PushbackLineFile(fIn), self.caching_backend, superContext=self)
- # parser.parse()
- # self.caching_backend.finishedParsingSession("ParseSuccess", None)
- # self.backend.fileOut.write("]\n")
diff --git a/parser/parser-cp2k/cp2kparser/utils/logconfig.py b/parser/parser-cp2k/cp2kparser/utils/logconfig.py
deleted file mode 100644
index efa805e..0000000
--- a/parser/parser-cp2k/cp2kparser/utils/logconfig.py
+++ /dev/null
@@ -1,99 +0,0 @@
-"""
-This module is used to control the logging of the parser.
-
-Each module in the package can have it's own logger, so that you can control
-the logging on a modular level easily.
-
-If you want to use a logger on a module simply add the following in the module
-preamble:
- import logging
- logger = logging.getLogger(__name__)
-
-This creates a logger with a hierarchical name. The hierarchical name allows
-the logger to inherit logger properties from a parent logger, but also allows
-module level control for logging.
-
-A custom formatting is also used for the log messages. The formatting is done
-by the LogFormatter class and is different for different levels.
-"""
-import logging
-import textwrap
-
-
-#===============================================================================
-class LogFormatter(logging.Formatter):
-
- def format(self, record):
- level = record.levelname
- module = record.module
- message = record.msg
-
- if level == "INFO" or level == "DEBUG":
- return make_titled_message("{}:{}".format(level, module), message)
- else:
- return "\n " + make_title(level, width=64) + "\n" + make_message(message, width=64, spaces=8) + "\n"
-
-
-#===============================================================================
-def make_titled_message(title, message, width=80):
- """Styles a message to be printed into console.
- """
- wrapper = textwrap.TextWrapper(width=width-5)
- lines = wrapper.wrap(message)
- styled_message = ""
- first = True
- for line in lines:
- if first:
- new_line = " >> {}: ".format(title) + line
- styled_message += new_line
- first = False
- else:
- new_line = 5*" " + line
- styled_message += "\n" + new_line
-
- return styled_message
-
-
-#===============================================================================
-def make_message(message, width=80, spaces=0):
- """Styles a message to be printed into console.
- """
- wrapper = textwrap.TextWrapper(width=width-6)
- lines = wrapper.wrap(message)
- styled_message = ""
- first = True
- for line in lines:
- new_line = spaces*" " + "| " + line + (width-6-len(line))*" " + " |"
- if first:
- styled_message += new_line
- first = False
- else:
- styled_message += "\n" + new_line
- styled_message += "\n" + spaces*" " + "|" + (width-2)*"-" + "|"
- return styled_message
-
-
-#===============================================================================
-def make_title(title, width=80):
- """Styles a title to be printed into console.
- """
- space = width-len(title)-4
- pre_space = space/2-1
- post_space = space-pre_space
- line = "|" + str((pre_space)*"=") + " "
- line += title
- line += " " + str((post_space)*"=") + "|"
- return line
-
-
-#===============================================================================
-# The highest level logger setup
-root_logger = logging.getLogger("cp2kparser")
-root_logger.setLevel(logging.INFO)
-
-# Create console handler and set level to debug
-root_console_handler = logging.StreamHandler()
-root_console_handler.setLevel(logging.DEBUG)
-root_console_formatter = LogFormatter()
-root_console_handler.setFormatter(root_console_formatter)
-root_logger.addHandler(root_console_handler)
diff --git a/parser/parser-cp2k/cp2kparser/utils/testing.py b/parser/parser-cp2k/cp2kparser/utils/testing.py
deleted file mode 100644
index cd35e8a..0000000
--- a/parser/parser-cp2k/cp2kparser/utils/testing.py
+++ /dev/null
@@ -1,66 +0,0 @@
-"""
-Tools for testing a nomad parser.
-"""
-
-import os
-import sys
-import json
-import numpy as np
-
-
-#===============================================================================
-def get_parser(path, metainfopath, parserbuilderclass, metainfo_to_keep=[], metainfo_to_skip=[], stream=sys.stdout):
- """Initialize a parser that is able to parse the contents in the given path.
-
- Args:
- path: String pointing to a path where all the calculation files are
- stream: The stream where the results are dumped.
- metainfopath: The metainfo filepath as a Get string
- parserbuilder: An object that inherits the ParserBuilder class and can
- create optimized parsers.
- """
- # Scan the given path for all files
- files = {}
- for filename in os.listdir(path):
- files[os.path.join(path, filename)] = ""
-
- json_input = {
- "version": "nomadparsein.json 1.0",
- "metaInfoFile": metainfopath,
- "metainfoToKeep": metainfo_to_keep,
- "metainfoToSkip": metainfo_to_skip,
- "files": files
- }
- parser = parserbuilderclass(json.dumps(json_input), stream=stream).build_parser()
- return parser
-
-
-#===============================================================================
-def get_metainfo(metaname, json_list):
- """After the parsing has been done by a parser, you can pass the resulting
- json list along with a metaname and the result will be returned to you.
-
- Args:
- metaname: String identifying a metainfo
- json_list: A json list object (see the python json package)
- """
-
- # Search for the metainfo
- # print json.dumps(json_list, sort_keys=True, indent=4, separators=(',', ': '))
- event_list = json_list[0]["events"]
- for event in event_list:
- name = event.get("metaName")
- if name and name == metaname:
-
- # Return value if present
- values = event.get("value")
- if values:
- yield values
-
- # Return reshaped flatvalues if present
- flat_values = event.get("flatValues")
- shape = event.get("valuesShape")
-
- if flat_values and shape:
- shaped_values = np.reshape(flat_values, shape)
- yield shaped_values
diff --git a/src/main/scala/eu/nomad_lab/parsers/Cp2kParser.scala b/src/main/scala/eu/nomad_lab/parsers/Cp2kParser.scala
index 49086b4..87a6235 100644
--- a/src/main/scala/eu/nomad_lab/parsers/Cp2kParser.scala
+++ b/src/main/scala/eu/nomad_lab/parsers/Cp2kParser.scala
@@ -33,19 +33,18 @@ object Cp2kParser extends SimpleExternalParserGenerator(
"${mainFilePath}"),
cmdCwd = "${mainFilePath}/..",
resList = Seq(
- "parser-cp2k/setup.py",
- "parser-cp2k/cp2kparser/setup_paths.py",
"parser-cp2k/cp2kparser/__init__.py",
- "parser-cp2k/cp2kparser/utils/__init__.py",
- "parser-cp2k/cp2kparser/utils/logconfig.py",
- "parser-cp2k/cp2kparser/utils/testing.py",
- "parser-cp2k/cp2kparser/utils/baseclasses.py",
- "parser-cp2k/cp2kparser/parsing/__init__.py",
- "parser-cp2k/cp2kparser/parsing/versions/cp2k262/__init__.py",
- "parser-cp2k/cp2kparser/parsing/versions/cp2k262/mainparser.py",
- "parser-cp2k/cp2kparser/parsing/versions/__init__.py",
- "parser-cp2k/cp2kparser/parsing/versions/versionsetup.py",
- "parser-cp2k/cp2kparser/parsing/parser.py",
+ "parser-cp2k/cp2kparser/setup_paths.py",
+ "parser-cp2k/cp2kparser/parser.py",
+ "parser-cp2k/cp2kparser/generic/__init__.py",
+ "parser-cp2k/cp2kparser/generic/baseclasses.py",
+ "parser-cp2k/cp2kparser/generic/inputparsing.py",
+ "parser-cp2k/cp2kparser/versions/__init__.py",
+ "parser-cp2k/cp2kparser/versions/versionsetup.py",
+ "parser-cp2k/cp2kparser/versions/cp2k262/__init__.py",
+ "parser-cp2k/cp2kparser/versions/cp2k262/mainparser.py",
+ "parser-cp2k/cp2kparser/versions/cp2k262/inputparser.py",
+ "parser-cp2k/cp2kparser/versions/cp2k262/input_data/cp2k_input_tree.pickle",
"parser-cp2k/cp2kparser/scalainterface.py",
"nomad_meta_info/public.nomadmetainfo.json",
"nomad_meta_info/common.nomadmetainfo.json",
diff --git a/test/unittests/cp2k_2.6.2/XC_functional/becke88/unittest.out b/test/unittests/cp2k_2.6.2/XC_functional/becke88/unittest.out
deleted file mode 100644
index 5dcf8e7..0000000
--- a/test/unittests/cp2k_2.6.2/XC_functional/becke88/unittest.out
+++ /dev/null
@@ -1,1434 +0,0 @@
- 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 2016-04-19 13:05:36.986
- ***** ** *** *** ** PROGRAM STARTED ON lauri-Lenovo-Z50-70
- ** **** ****** PROGRAM STARTED BY lauri
- ***** ** ** ** ** PROGRAM PROCESS ID 10424
- **** ** ******* ** PROGRAM STARTED IN /home/lauri/Dropbox/nomad-dev/nomad-l
- ab-base/parsers/cp2k/test/unittests/c
- p2k_2.6.2/XC_functional/becke88
-
- 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 ke 4.11.2015 08.48.42 +0200
- CP2K| Program compiled on lauri-Lenovo-Z50-70
- CP2K| Program compiled for Linux-x86-64-gfortran_basic
- CP2K| Input file name becke88.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_bulk
- 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 MEDIUM
- 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 8070380 8070380 8070380 8070380
- MEMORY| MemFree 3137636 3137636 3137636 3137636
- MEMORY| Buffers 879396 879396 879396 879396
- MEMORY| Cached 1938604 1938604 1938604 1938604
- MEMORY| Slab 465048 465048 465048 465048
- MEMORY| SReclaimable 424656 424656 424656 424656
- MEMORY| MemLikelyFree 6380292 6380292 6380292 6380292
-
-
- *** 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
-
- 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) **
- ** **
- *******************************************************************************
-
- 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| BECKE88:
- FUNCTIONAL| A. Becke, Phys. Rev. A 38, 3098 (1988) {LDA version}
-
- QS| Method: GPW
- QS| Density plane wave grid type NON-SPHERICAL FULLSPACE
- QS| Number of grid levels: 2
- QS| Density cutoff [a.u.]: 25.0
- QS| Multi grid cutoff [a.u.]: 1) grid level 25.0
- QS| 2) grid level 8.3
- QS| Grid level progression factor: 3.0
- QS| Relative density cutoff [a.u.]: 12.5
- QS| Consistent realspace mapping and integration
- QS| Interaction thresholds: eps_pgf_orb: 3.2E-02
- QS| eps_filter_matrix: 0.0E+00
- QS| eps_core_charge: 1.0E-05
- QS| eps_rho_gspace: 1.0E-03
- QS| eps_rho_rspace: 1.0E-03
- QS| eps_gvg_rspace: 3.2E-02
- QS| eps_ppl: 1.0E-02
- QS| eps_ppnl: 3.2E-04
-
-
- ATOMIC KIND INFORMATION
-
- 1. Atomic kind: Si Number of atoms: 1
-
- 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
-
-
- MOLECULE KIND INFORMATION
-
-
- All atoms are their own molecule, skipping detailed information
-
-
- TOTAL NUMBERS AND MAXIMUM NUMBERS
-
- Total number of - Atomic kinds: 1
- - Atoms: 1
- - Shell sets: 2
- - Shells: 5
- - Primitive Cartesian functions: 5
- - Cartesian basis functions: 14
- - Spherical basis functions: 13
-
- 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
-
-
-
-
- SCF PARAMETERS Density guess: ATOMIC
- --------------------------------------------------------
- max_scf: 100
- max_scf_history: 0
- max_diis: 4
- --------------------------------------------------------
- eps_scf: 1.00E-03
- eps_scf_history: 0.00E+00
- eps_diis: 1.00E-01
- eps_eigval: 1.00E-05
- --------------------------------------------------------
- level_shift [a.u.]: 0.00
- --------------------------------------------------------
- Mixing method: DIRECT_P_MIXING
- --------------------------------------------------------
- No outer SCF
-
- PW_GRID| Information for grid number 1
- PW_GRID| Cutoff [a.u.] 25.0
- PW_GRID| spherical cutoff: NO
- PW_GRID| Bounds 1 -12 11 Points: 24
- PW_GRID| Bounds 2 -12 11 Points: 24
- PW_GRID| Bounds 3 -12 11 Points: 24
- PW_GRID| Volume element (a.u.^3) 0.7819E-01 Volume (a.u.^3) 1080.8451
- PW_GRID| Grid span FULLSPACE
-
- PW_GRID| Information for grid number 2
- PW_GRID| Cutoff [a.u.] 8.3
- PW_GRID| spherical cutoff: NO
- PW_GRID| Bounds 1 -7 7 Points: 15
- PW_GRID| Bounds 2 -7 7 Points: 15
- PW_GRID| Bounds 3 -7 7 Points: 15
- PW_GRID| Volume element (a.u.^3) 0.3203 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 -12 11 Points: 24
- RS_GRID| Bounds 2 -12 11 Points: 24
- RS_GRID| Bounds 3 -12 11 Points: 24
-
- RS_GRID| Information for grid number 2
- RS_GRID| Bounds 1 -7 7 Points: 15
- RS_GRID| Bounds 2 -7 7 Points: 15
- RS_GRID| Bounds 3 -7 7 Points: 15
-
- DISTRIBUTION OF THE PARTICLES (ROWS)
- Process row Number of particles Number of matrix rows
- 0 1 -1
- Sum 1 -1
-
- DISTRIBUTION OF THE PARTICLES (COLUMNS)
- Process col Number of particles Number of matrix columns
- 0 1 -1
- Sum 1 -1
-
- DISTRIBUTION OF THE NEIGHBOR LISTS
- Total number of particle pairs: 7
- Total number of matrix elements: 1183
- Average number of particle pairs: 7
- Maximum number of particle pairs: 7
- Average number of matrix element: 1183
- Maximum number of matrix elements: 1183
-
-
- DISTRIBUTION OF THE OVERLAP MATRIX
- Number of non-zero blocks: 1
- Percentage non-zero blocks: 100.00
- Average number of blocks per CPU: 1
- Maximum number of blocks per CPU: 1
- Average number of matrix elements per CPU: 179
- Maximum number of matrix elements per CPU: 179
-
- Number of electrons: 4
- Number of occupied orbitals: 2
- Number of molecular orbitals: 2
-
- Number of orbital functions: 13
- Number of independent orbital functions: 13
-
- 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: Si
-
- 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
-
- Re-scaling the density matrix to get the right number of electrons
- # Electrons Trace(P) Scaling factor
- 4 3.957 1.011
-
-
- SCF WAVEFUNCTION OPTIMIZATION
-
- Step Update method Time Convergence Total energy Change
- ------------------------------------------------------------------------------
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998453719 0.0001546281
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036805695
- Total charge density g-space grids: -0.0036805695
-
- 1 P_Mix/Diag. 0.40E+00 0.0 0.58834082 -3.6916243010 -3.69E+00
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998057271 0.0001942729
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036409247
- Total charge density g-space grids: -0.0036409247
-
- 2 P_Mix/Diag. 0.40E+00 0.0 1.03136858 -3.6876787572 3.95E-03
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998152806 0.0001847194
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036504782
- Total charge density g-space grids: -0.0036504782
-
- 3 P_Mix/Diag. 0.40E+00 0.0 1.05100784 -3.6865162206 1.16E-03
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998211915 0.0001788085
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036563891
- Total charge density g-space grids: -0.0036563891
-
- 4 P_Mix/Diag. 0.40E+00 0.0 0.93987743 -3.6861588603 3.57E-04
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9997995686 0.0002004314
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036347662
- Total charge density g-space grids: -0.0036347662
-
- 5 P_Mix/Diag. 0.40E+00 0.0 1.00715451 -3.6853760165 7.83E-04
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998117103 0.0001882897
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036469080
- Total charge density g-space grids: -0.0036469080
-
- 6 P_Mix/Diag. 0.40E+00 0.0 0.96664076 -3.6850397852 3.36E-04
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998166311 0.0001833689
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036518287
- Total charge density g-space grids: -0.0036518287
-
- 7 P_Mix/Diag. 0.40E+00 0.0 1.00486142 -3.6848332031 2.07E-04
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998017011 0.0001982989
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036368987
- Total charge density g-space grids: -0.0036368987
-
- 8 P_Mix/Diag. 0.40E+00 0.0 0.81603691 -3.6847328319 1.00E-04
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998074250 0.0001925750
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036426227
- Total charge density g-space grids: -0.0036426227
-
- 9 P_Mix/Diag. 0.40E+00 0.0 1.00248934 -3.6847258825 6.95E-06
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998136161 0.0001863839
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036488137
- Total charge density g-space grids: -0.0036488137
-
- 10 P_Mix/Diag. 0.40E+00 0.0 1.06622177 -3.6845850442 1.41E-04
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998064017 0.0001935983
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036415993
- Total charge density g-space grids: -0.0036415993
-
- 11 P_Mix/Diag. 0.40E+00 0.0 0.96757587 -3.6844817657 1.03E-04
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998040238 0.0001959762
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036392215
- Total charge density g-space grids: -0.0036392215
-
- 12 P_Mix/Diag. 0.40E+00 0.0 0.98133571 -3.6846258848 -1.44E-04
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998109096 0.0001890904
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036461072
- Total charge density g-space grids: -0.0036461072
-
- 13 P_Mix/Diag. 0.40E+00 0.0 1.20075357 -3.6844966608 1.29E-04
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998089433 0.0001910567
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036441409
- Total charge density g-space grids: -0.0036441409
-
- 14 P_Mix/Diag. 0.40E+00 0.0 1.08759312 -3.6843758464 1.21E-04
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998048164 0.0001951836
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036400140
- Total charge density g-space grids: -0.0036400140
-
- 15 P_Mix/Diag. 0.40E+00 0.0 1.21688007 -3.6844493741 -7.35E-05
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998088816 0.0001911184
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036440793
- Total charge density g-space grids: -0.0036440793
-
- 16 P_Mix/Diag. 0.40E+00 0.0 1.45889012 -3.6842909933 1.58E-04
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998087142 0.0001912858
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036439118
- Total charge density g-space grids: -0.0036439118
-
- 17 P_Mix/Diag. 0.40E+00 0.0 1.47944942 -3.6842560988 3.49E-05
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998072269 0.0001927731
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036424245
- Total charge density g-space grids: -0.0036424245
-
- 18 P_Mix/Diag. 0.40E+00 0.0 1.50458255 -3.6842646411 -8.54E-06
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998080422 0.0001919578
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036432398
- Total charge density g-space grids: -0.0036432398
-
- 19 P_Mix/Diag. 0.40E+00 0.0 1.51880247 -3.6842483460 1.63E-05
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998080413 0.0001919587
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036432389
- Total charge density g-space grids: -0.0036432389
-
- 20 P_Mix/Diag. 0.40E+00 0.0 1.52044775 -3.6842473408 1.01E-06
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998078150 0.0001921850
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036430126
- Total charge density g-space grids: -0.0036430126
-
- 21 P_Mix/Diag. 0.40E+00 0.0 1.52052905 -3.6842506244 -3.28E-06
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079257 0.0001920743
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431233
- Total charge density g-space grids: -0.0036431233
-
- 22 P_Mix/Diag. 0.40E+00 0.0 1.52113420 -3.6842483764 2.25E-06
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079296 0.0001920704
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431272
- Total charge density g-space grids: -0.0036431272
-
- 23 P_Mix/Diag. 0.40E+00 0.0 1.52131369 -3.6842483435 3.29E-08
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079007 0.0001920993
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036430983
- Total charge density g-space grids: -0.0036430983
-
- 24 P_Mix/Diag. 0.40E+00 0.0 1.52119562 -3.6842489887 -6.45E-07
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079169 0.0001920831
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431146
- Total charge density g-space grids: -0.0036431146
-
- 25 P_Mix/Diag. 0.40E+00 0.0 1.52127113 -3.6842485693 4.19E-07
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079184 0.0001920816
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431160
- Total charge density g-space grids: -0.0036431160
-
- 26 P_Mix/Diag. 0.40E+00 0.0 1.52130006 -3.6842485721 -2.86E-09
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079147 0.0001920853
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431123
- Total charge density g-space grids: -0.0036431123
-
- 27 P_Mix/Diag. 0.40E+00 0.0 1.52127198 -3.6842486891 -1.17E-07
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079173 0.0001920827
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431150
- Total charge density g-space grids: -0.0036431150
-
- 28 P_Mix/Diag. 0.40E+00 0.0 1.52128683 -3.6842486095 7.96E-08
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079178 0.0001920822
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431154
- Total charge density g-space grids: -0.0036431154
-
- 29 P_Mix/Diag. 0.40E+00 0.0 1.52129185 -3.6842486118 -2.30E-09
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079173 0.0001920827
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431149
- Total charge density g-space grids: -0.0036431149
-
- 30 P_Mix/Diag. 0.40E+00 0.0 1.52128603 -3.6842486320 -2.02E-08
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079178 0.0001920822
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431154
- Total charge density g-space grids: -0.0036431154
-
- 31 P_Mix/Diag. 0.40E+00 0.0 1.52128920 -3.6842486172 1.48E-08
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079179 0.0001920821
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431156
- Total charge density g-space grids: -0.0036431156
-
- 32 P_Mix/Diag. 0.40E+00 0.0 1.52129005 -3.6842486181 -8.62E-10
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079179 0.0001920821
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431155
- Total charge density g-space grids: -0.0036431155
-
- 33 P_Mix/Diag. 0.40E+00 0.0 1.52128889 -3.6842486213 -3.26E-09
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079180 0.0001920820
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431156
- Total charge density g-space grids: -0.0036431156
-
- 34 P_Mix/Diag. 0.40E+00 0.0 1.52128958 -3.6842486187 2.67E-09
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079180 0.0001920820
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 35 P_Mix/Diag. 0.40E+00 0.0 1.52128971 -3.6842486189 -2.67E-10
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079180 0.0001920820
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 36 P_Mix/Diag. 0.40E+00 0.0 1.52128949 -3.6842486194 -4.60E-10
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 37 P_Mix/Diag. 0.40E+00 0.0 1.52128964 -3.6842486189 4.58E-10
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 38 P_Mix/Diag. 0.40E+00 0.0 1.52128966 -3.6842486190 -7.52E-11
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 39 P_Mix/Diag. 0.40E+00 0.0 1.52128962 -3.6842486191 -4.50E-11
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 40 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 7.25E-11
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 41 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 -2.01E-11
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 42 P_Mix/Diag. 0.40E+00 0.0 1.52128964 -3.6842486190 2.37E-12
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 43 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 9.68E-12
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 44 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 -5.15E-12
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 45 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 3.22E-12
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 46 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 7.24E-13
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 47 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 -1.28E-12
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 48 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 1.31E-12
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 49 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 -1.65E-13
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 50 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 -3.11E-13
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 51 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 4.24E-13
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 52 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 -1.15E-13
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 53 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 -7.33E-14
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 54 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 1.23E-13
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 55 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 -4.40E-14
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 56 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 -1.55E-14
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 57 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 3.24E-14
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 58 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 -1.33E-14
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 59 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 -4.44E-15
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 60 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 9.33E-15
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 61 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 -4.00E-15
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 62 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 4.44E-16
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 63 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 1.33E-15
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 64 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 -1.33E-15
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 65 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 -8.88E-16
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 66 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 1.33E-15
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 67 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 -4.44E-16
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 68 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 -8.88E-16
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 69 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 0.00E+00
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 70 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 8.88E-16
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 71 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 -8.88E-16
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 72 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 4.44E-16
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 73 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 4.44E-16
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 74 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 -8.88E-16
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 75 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 8.88E-16
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 76 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 -8.88E-16
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 77 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 8.88E-16
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 78 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 -1.33E-15
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 79 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 1.78E-15
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 80 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 -4.44E-16
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 81 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 -8.88E-16
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 82 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 4.44E-16
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 83 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 -4.44E-16
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 84 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 8.88E-16
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 85 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 0.00E+00
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 86 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 -4.44E-16
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 87 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 4.44E-16
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 88 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 -4.44E-16
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 89 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 -4.44E-16
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 90 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 0.00E+00
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 91 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 4.44E-16
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 92 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 -8.88E-16
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 93 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 -4.44E-16
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 94 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 1.33E-15
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 95 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 -1.33E-15
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 96 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 8.88E-16
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 97 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 0.00E+00
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 98 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 0.00E+00
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 99 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 0.00E+00
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- 100 P_Mix/Diag. 0.40E+00 0.0 1.52128965 -3.6842486190 0.00E+00
-
- *** SCF run NOT converged ***
-
-
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
- Overlap energy of the core charge distribution: 0.00000000000000
- Self energy of the core charge distribution: -10.25799242814102
- Core Hamiltonian energy: 1.95097899111943
- Hartree energy: 5.52868797609633
- Exchange-correlation energy: -0.90592315808038
-
- Total energy: -3.68424861900565
-
-
- MULLIKEN POPULATION ANALYSIS
-
- # Atom Element Kind Atomic population Net charge
- 1 Si 1 4.000000 -0.000000
- # Total charge 4.000000 -0.000000
-
-
- !-----------------------------------------------------------------------------!
- Hirschfeld Charges
-
- #Atom Element Kind Ref Charge Population Net charge
- 1 Si 1 4.000 3.450 0.550
-
- Total Charge 0.550
- !-----------------------------------------------------------------------------!
-
- Trace(PS): 4.0000000000
- Electronic density on regular grids: -3.9998079181 0.0001920819
- Core density on regular grids: 3.9961648024 -0.0038351976
- Total charge density on r-space grids: -0.0036431157
- Total charge density g-space grids: -0.0036431157
-
-
- ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.): -3.669248396643794
-
-
- -------------------------------------------------------------------------------
- - -
- - DBCSR STATISTICS -
- - -
- -------------------------------------------------------------------------------
- COUNTER CPU ACC ACC%
- number of processed stacks 101 0 0.0
- matmuls inhomo. stacks 0 0 0.0
- matmuls total 101 0 0.0
- flops 13 x 13 x 2 68276 0 0.0
- flops total 68276 0 0.0
- marketing flops 68276
- -------------------------------------------------------------------------------
-
- -------------------------------------------------------------------------------
- ---- MULTIGRID INFO ----
- -------------------------------------------------------------------------------
- count for grid 1: 311 cutoff [a.u.] 25.00
- count for grid 2: 332 cutoff [a.u.] 8.33
- total gridlevel count : 643
-
- -------------------------------------------------------------------------------
- - -
- - MESSAGE PASSING PERFORMANCE -
- - -
- -------------------------------------------------------------------------------
-
- ROUTINE CALLS TOT TIME [s] AVE VOLUME [Bytes] PERFORMANCE [MB/s]
- MP_Group 3 0.000
- MP_Bcast 102 0.000 4. 1.73
- MP_Allreduce 1170 0.001 8. 16.75
- MP_Sync 2 0.000
- MP_Alltoall 2316 0.001 522. 858.42
- MP_Wait 2424 0.001
- MP_ISend 808 0.001 228. 131.80
- MP_IRecv 808 0.000 228. 421.71
- MP_Memory 2424 0.001
- -------------------------------------------------------------------------------
-
-
- -------------------------------------------------------------------------------
- - -
- - 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
-
-
- BECKE, AD. PHYSICAL REVIEW A, 38 (6), 3098-3100 (1988).
- DENSITY-FUNCTIONAL EXCHANGE-ENERGY APPROXIMATION WITH CORRECT
- ASYMPTOTIC-BEHAVIOR.
- http://dx.doi.org/10.1103/PhysRevA.38.3098
-
-
- -------------------------------------------------------------------------------
- - -
- - T I M I N G -
- - -
- -------------------------------------------------------------------------------
- SUBROUTINE CALLS ASD SELF TIME TOTAL TIME
- MAXIMUM AVERAGE MAXIMUM AVERAGE MAXIMUM
- CP2K 1 1.0 0.002 0.002 1.000 1.000
- qs_forces 1 2.0 0.000 0.000 0.975 0.975
- qs_energies_scf 1 3.0 0.000 0.000 0.967 0.967
- scf_env_do_scf 1 4.0 0.000 0.000 0.952 0.952
- scf_env_do_scf_inner_loop 100 5.0 0.007 0.007 0.951 0.951
- rebuild_ks_matrix 101 7.0 0.000 0.000 0.701 0.701
- qs_ks_build_kohn_sham_matrix 101 8.0 0.008 0.008 0.701 0.701
- qs_ks_update_qs_env 100 6.0 0.000 0.000 0.696 0.696
- qs_vxc_create 101 9.0 0.001 0.001 0.496 0.496
- xc_vxc_pw_create 101 10.0 0.022 0.022 0.495 0.495
- fft_wrap_pw1pw2 1314 10.7 0.004 0.004 0.407 0.407
- fft_wrap_pw1pw2_30 1112 11.8 0.022 0.022 0.391 0.391
- xc_rho_set_and_dset_create 101 11.0 0.052 0.052 0.305 0.305
- fft3d_s 1315 12.7 0.265 0.265 0.275 0.275
- qs_rho_update_rho 101 6.0 0.000 0.000 0.146 0.146
- calculate_rho_elec 101 7.0 0.057 0.057 0.145 0.145
- sum_up_and_integrate 101 9.0 0.003 0.003 0.132 0.132
- integrate_v_rspace 101 10.0 0.076 0.076 0.129 0.129
- xc_functional_eval 101 12.0 0.000 0.000 0.125 0.125
- xb88_lda_eval 101 13.0 0.125 0.125 0.125 0.125
- density_rs2pw 101 8.0 0.001 0.001 0.088 0.088
- pw_scatter_s 707 13.0 0.056 0.056 0.056 0.056
- calculate_dm_sparse 100 6.0 0.000 0.000 0.056 0.056
- cp_dbcsr_plus_fm_fm_t_native 101 7.0 0.001 0.001 0.055 0.055
- pw_gather_s 607 12.5 0.049 0.049 0.049 0.049
- potential_pw2rs 101 11.0 0.001 0.001 0.048 0.048
- dbcsr_mm_cannon_multiply 101 8.0 0.004 0.004 0.041 0.041
- pw_derive 606 11.5 0.035 0.035 0.035 0.035
- quickstep_create_force_env 1 2.0 0.000 0.000 0.023 0.023
- dbcsr_complete_redistribute 302 9.0 0.010 0.010 0.022 0.022
- copy_dbcsr_to_fm 400 7.0 0.003 0.003 0.022 0.022
- pw_poisson_solve 101 9.0 0.016 0.016 0.021 0.021
- pw_copy 909 11.2 0.020 0.020 0.020 0.020
- -------------------------------------------------------------------------------
-
- **** **** ****** ** PROGRAM ENDED AT 2016-04-19 13:05:38.048
- ***** ** *** *** ** PROGRAM RAN ON lauri-Lenovo-Z50-70
- ** **** ****** PROGRAM RAN BY lauri
- ***** ** ** ** ** PROGRAM PROCESS ID 10424
- **** ** ******* ** PROGRAM STOPPED IN /home/lauri/Dropbox/nomad-dev/nomad-l
- ab-base/parsers/cp2k/test/unittests/c
- p2k_2.6.2/XC_functional/becke88
diff --git a/test/unittests/cp2k_2.6.2/XC_functional/blyp/unittest.out b/test/unittests/cp2k_2.6.2/XC_functional/blyp/unittest.out
index 7865d70..c4816be 100644
--- a/test/unittests/cp2k_2.6.2/XC_functional/blyp/unittest.out
+++ b/test/unittests/cp2k_2.6.2/XC_functional/blyp/unittest.out
@@ -9,10 +9,10 @@
DBCSR| Communication thread load 87
- **** **** ****** ** PROGRAM STARTED AT 2016-04-19 13:06:03.013
+ **** **** ****** ** PROGRAM STARTED AT 2016-04-25 10:00:50.624
***** ** *** *** ** PROGRAM STARTED ON lauri-Lenovo-Z50-70
** **** ****** PROGRAM STARTED BY lauri
- ***** ** ** ** ** PROGRAM PROCESS ID 10563
+ ***** ** ** ** ** PROGRAM PROCESS ID 11701
**** ** ******* ** PROGRAM STARTED IN /home/lauri/Dropbox/nomad-dev/nomad-l
ab-base/parsers/cp2k/test/unittests/c
p2k_2.6.2/XC_functional/blyp
@@ -46,12 +46,12 @@
MEMORY| system memory details [Kb]
MEMORY| rank 0 min max average
MEMORY| MemTotal 8070380 8070380 8070380 8070380
- MEMORY| MemFree 3092784 3092784 3092784 3092784
- MEMORY| Buffers 879616 879616 879616 879616
- MEMORY| Cached 1936196 1936196 1936196 1936196
- MEMORY| Slab 465272 465272 465272 465272
- MEMORY| SReclaimable 424832 424832 424832 424832
- MEMORY| MemLikelyFree 6333428 6333428 6333428 6333428
+ MEMORY| MemFree 3001100 3001100 3001100 3001100
+ MEMORY| Buffers 843640 843640 843640 843640
+ MEMORY| Cached 2004444 2004444 2004444 2004444
+ MEMORY| Slab 484152 484152 484152 484152
+ MEMORY| SReclaimable 444984 444984 444984 444984
+ MEMORY| MemLikelyFree 6294168 6294168 6294168 6294168
*** Fundamental physical constants (SI units) ***
@@ -1309,13 +1309,13 @@
ROUTINE CALLS TOT TIME [s] AVE VOLUME [Bytes] PERFORMANCE [MB/s]
MP_Group 3 0.000
- MP_Bcast 102 0.000 4. 1.46
- MP_Allreduce 1170 0.001 8. 15.79
+ MP_Bcast 102 0.000 4. 1.70
+ MP_Allreduce 1170 0.001 8. 17.33
MP_Sync 2 0.000
- MP_Alltoall 2316 0.002 522. 804.03
+ MP_Alltoall 2316 0.001 522. 848.94
MP_Wait 2424 0.001
- MP_ISend 808 0.001 228. 131.68
- MP_IRecv 808 0.000 228. 395.24
+ MP_ISend 808 0.001 228. 133.66
+ MP_IRecv 808 0.000 228. 429.62
MP_Memory 2424 0.001
-------------------------------------------------------------------------------
@@ -1400,43 +1400,43 @@
-------------------------------------------------------------------------------
SUBROUTINE CALLS ASD SELF TIME TOTAL TIME
MAXIMUM AVERAGE MAXIMUM AVERAGE MAXIMUM
- CP2K 1 1.0 0.002 0.002 1.129 1.129
- qs_forces 1 2.0 0.000 0.000 1.090 1.090
- qs_energies_scf 1 3.0 0.000 0.000 1.079 1.079
- scf_env_do_scf 1 4.0 0.000 0.000 1.062 1.062
- scf_env_do_scf_inner_loop 100 5.0 0.007 0.007 1.062 1.062
- rebuild_ks_matrix 101 7.0 0.000 0.000 0.808 0.808
- qs_ks_build_kohn_sham_matrix 101 8.0 0.009 0.009 0.807 0.807
- qs_ks_update_qs_env 100 6.0 0.001 0.001 0.800 0.800
- qs_vxc_create 101 9.0 0.001 0.001 0.600 0.600
- xc_vxc_pw_create 101 10.0 0.022 0.022 0.599 0.599
- fft_wrap_pw1pw2 1314 10.7 0.005 0.005 0.412 0.412
- xc_rho_set_and_dset_create 101 11.0 0.053 0.053 0.408 0.408
- fft_wrap_pw1pw2_30 1112 11.8 0.023 0.023 0.395 0.395
- fft3d_s 1315 12.7 0.266 0.266 0.277 0.277
- xc_functional_eval 202 12.0 0.001 0.001 0.227 0.227
- qs_rho_update_rho 101 6.0 0.000 0.000 0.151 0.151
- calculate_rho_elec 101 7.0 0.059 0.059 0.151 0.151
+ CP2K 1 1.0 0.002 0.002 1.108 1.108
+ qs_forces 1 2.0 0.000 0.000 1.082 1.082
+ qs_energies_scf 1 3.0 0.000 0.000 1.074 1.074
+ scf_env_do_scf 1 4.0 0.000 0.000 1.059 1.059
+ scf_env_do_scf_inner_loop 100 5.0 0.007 0.007 1.059 1.059
+ rebuild_ks_matrix 101 7.0 0.000 0.000 0.809 0.809
+ qs_ks_build_kohn_sham_matrix 101 8.0 0.009 0.009 0.809 0.809
+ qs_ks_update_qs_env 100 6.0 0.000 0.000 0.802 0.802
+ qs_vxc_create 101 9.0 0.001 0.001 0.602 0.602
+ xc_vxc_pw_create 101 10.0 0.022 0.022 0.602 0.602
+ fft_wrap_pw1pw2 1314 10.7 0.004 0.004 0.411 0.411
+ xc_rho_set_and_dset_create 101 11.0 0.053 0.053 0.409 0.409
+ fft_wrap_pw1pw2_30 1112 11.8 0.022 0.022 0.395 0.395
+ fft3d_s 1315 12.7 0.268 0.268 0.279 0.279
+ xc_functional_eval 202 12.0 0.001 0.001 0.228 0.228
+ qs_rho_update_rho 101 6.0 0.000 0.000 0.147 0.147
+ calculate_rho_elec 101 7.0 0.058 0.058 0.147 0.147
sum_up_and_integrate 101 9.0 0.003 0.003 0.133 0.133
integrate_v_rspace 101 10.0 0.076 0.076 0.130 0.130
- xb88_lda_eval 101 13.0 0.125 0.125 0.125 0.125
- lyp_lda_eval 101 13.0 0.101 0.101 0.101 0.101
- density_rs2pw 101 8.0 0.001 0.001 0.091 0.091
- pw_scatter_s 707 13.0 0.057 0.057 0.057 0.057
- cp_dbcsr_plus_fm_fm_t_native 101 7.0 0.001 0.001 0.056 0.056
- calculate_dm_sparse 100 6.0 0.000 0.000 0.056 0.056
- pw_gather_s 607 12.5 0.049 0.049 0.049 0.049
+ xb88_lda_eval 101 13.0 0.126 0.126 0.126 0.126
+ lyp_lda_eval 101 13.0 0.102 0.102 0.102 0.102
+ density_rs2pw 101 8.0 0.001 0.001 0.088 0.088
+ pw_scatter_s 707 13.0 0.056 0.056 0.056 0.056
+ calculate_dm_sparse 100 6.0 0.000 0.000 0.055 0.055
+ cp_dbcsr_plus_fm_fm_t_native 101 7.0 0.001 0.001 0.055 0.055
potential_pw2rs 101 11.0 0.001 0.001 0.049 0.049
- dbcsr_mm_cannon_multiply 101 8.0 0.004 0.004 0.042 0.042
- quickstep_create_force_env 1 2.0 0.000 0.000 0.036 0.036
+ pw_gather_s 607 12.5 0.049 0.049 0.049 0.049
+ dbcsr_mm_cannon_multiply 101 8.0 0.004 0.004 0.041 0.041
pw_derive 606 11.5 0.035 0.035 0.035 0.035
+ quickstep_create_force_env 1 2.0 0.000 0.000 0.023 0.023
dbcsr_complete_redistribute 302 9.0 0.010 0.010 0.023 0.023
-------------------------------------------------------------------------------
- **** **** ****** ** PROGRAM ENDED AT 2016-04-19 13:06:04.193
+ **** **** ****** ** PROGRAM ENDED AT 2016-04-25 10:00:51.812
***** ** *** *** ** PROGRAM RAN ON lauri-Lenovo-Z50-70
** **** ****** PROGRAM RAN BY lauri
- ***** ** ** ** ** PROGRAM PROCESS ID 10563
+ ***** ** ** ** ** PROGRAM PROCESS ID 11701
**** ** ******* ** PROGRAM STOPPED IN /home/lauri/Dropbox/nomad-dev/nomad-l
ab-base/parsers/cp2k/test/unittests/c
p2k_2.6.2/XC_functional/blyp
diff --git a/test/unittests/cp2k_2.6.2/energy_force/unittest.out b/test/unittests/cp2k_2.6.2/energy_force/unittest.out
index 0a03d03..9cbb501 100644
--- a/test/unittests/cp2k_2.6.2/energy_force/unittest.out
+++ b/test/unittests/cp2k_2.6.2/energy_force/unittest.out
@@ -9,10 +9,10 @@
DBCSR| Communication thread load 87
- **** **** ****** ** PROGRAM STARTED AT 2016-04-19 13:04:19.054
+ **** **** ****** ** PROGRAM STARTED AT 2016-04-21 11:16:59.995
***** ** *** *** ** PROGRAM STARTED ON lauri-Lenovo-Z50-70
** **** ****** PROGRAM STARTED BY lauri
- ***** ** ** ** ** PROGRAM PROCESS ID 10277
+ ***** ** ** ** ** PROGRAM PROCESS ID 9923
**** ** ******* ** PROGRAM STARTED IN /home/lauri/Dropbox/nomad-dev/nomad-l
ab-base/parsers/cp2k/test/unittests/c
p2k_2.6.2/energy_force
@@ -38,7 +38,7 @@
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 MEDIUM
+ 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
@@ -46,12 +46,12 @@
MEMORY| system memory details [Kb]
MEMORY| rank 0 min max average
MEMORY| MemTotal 8070380 8070380 8070380 8070380
- MEMORY| MemFree 3211476 3211476 3211476 3211476
- MEMORY| Buffers 878968 878968 878968 878968
- MEMORY| Cached 1918964 1918964 1918964 1918964
- MEMORY| Slab 464628 464628 464628 464628
- MEMORY| SReclaimable 424272 424272 424272 424272
- MEMORY| MemLikelyFree 6433680 6433680 6433680 6433680
+ MEMORY| MemFree 2667660 2667660 2667660 2667660
+ MEMORY| Buffers 889632 889632 889632 889632
+ MEMORY| Cached 1940508 1940508 1940508 1940508
+ MEMORY| Slab 513132 513132 513132 513132
+ MEMORY| SReclaimable 470984 470984 470984 470984
+ MEMORY| MemLikelyFree 5968784 5968784 5968784 5968784
*** Fundamental physical constants (SI units) ***
@@ -107,6 +107,13 @@
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.
@@ -147,6 +154,79 @@
** **
*******************************************************************************
+ RADII: ORBITAL BASIS in angstrom Kind Label Radius OCE Radius
+ 1 Si 7.289139 7.289139
+
+ RADII: SHELL SETS OF ORBITAL BASIS in angstrom Kind Label Set Radius
+ 1 Si 1 7.289139
+ 2 3.018919
+
+ RADII: PRIMITIVE GAUSSIANS OF ORBITAL BASIS in anKindomLabel Set Radius
+ 1 Si 1 1.540830
+ 2.581331
+ 4.306488
+ 7.289139
+ 1 Si 2 3.018919
+
+ RADII: GEMINAL BASIS in angstrom Kind Label Radius
+ 1 Si no basis
+
+ RADII: SHELL SETS OF GEMINAL BASIS in angstrom Kind Label Set Radius
+ 1 Si no basis
+
+ RADII: PRIMITIVE GEMINALS OF GEMINAL BASIS in angKindm Label Set Radius
+ 1 Si no basis
+
+ RADII: AUXILLIARY BASIS in angstrom Kind Label Radius OCE Radius
+ 1 Si no basis
+
+ RADII: SHELL SETS OF AUXILLIARY BASIS in angstromKind Label Set Radius
+ 1 Si no basis
+
+ RADII: PRIMITIVE GAUSSIANS OF AUXILLIARY BASIS inKindstLabel Set Radius
+ 1 Si no basis
+
+ RADII: LOCAL RI BASIS in angstrom Kind Label Radius OCE Radius
+ 1 Si no basis
+
+ RADII: SHELL SETS OF LOCAL RI BASIS in angstrom Kind Label Set Radius
+ 1 Si no basis
+
+ RADII: PRIMITIVE GAUSSIANS OF LOCAL RI BASIS in aKindroLabel Set Radius
+ 1 Si no basis
+
+ RADII: CORE CHARGE DISTRIBUTIONS in angstrom Kind Label Radius
+ 1 Si 1.764766
+
+ RADII: LOCAL PART OF GTH/ELP PP in angstrom Kind Label Radius
+ 1 Si 0.845813
+
+ RADII: NON-LOCAL PART OF GTH PP in angstrom Kind Label Radius
+ 1 Si 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 5 6 7 8
+
DFT| Spin restricted Kohn-Sham (RKS) calculation RKS
DFT| Multiplicity 1
DFT| Number of spin states 1
@@ -303,6 +383,8 @@
+ REQUESTED STRUCTURE DATA
+
SCF PARAMETERS Density guess: ATOMIC
--------------------------------------------------------
@@ -391,6 +473,29 @@
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= ( 8,),
+ local_rows=(
+( 1, 2, 3, 4, 5,
+ 6, 7, 8 )
+ ),
+ n_local_cols= ( 8,),
+ 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: 2952
Total number of matrix elements: 498888
@@ -408,6 +513,8 @@
Average number of matrix elements per CPU: 6094
Maximum number of matrix elements per CPU: 6094
+ Initializing the DDAPC Environment
+
Number of electrons: 32
Number of occupied orbitals: 16
Number of molecular orbitals: 16
@@ -478,6 +585,13 @@
Total charge density on r-space grids: -0.0000000043
Total charge density g-space grids: -0.0000000043
+
+ Core Hamiltonian energy: 17.2606520455
+ Hartree energy: 42.0267986132
+ Exchange-correlation energy: -9.4555961214
+ Coulomb (electron-electron) energy: 1.8994070931
+ 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 0.9 0.75558724 -32.2320848878 -3.22E+01
Trace(PS): 32.0000000000
@@ -486,6 +600,13 @@
Total charge density on r-space grids: -0.0000000017
Total charge density g-space grids: -0.0000000017
+
+ Core Hamiltonian energy: 18.3474682194
+ Hartree energy: 42.1175796106
+ Exchange-correlation energy: -9.5429219531
+ Coulomb (electron-electron) energy: 2.1318687193
+ Maximum deviation from MO S-orthonormality 0.1998E-14
+ Minimum/Maximum MO magnitude 0.6228E+00 0.1890E+01
2 Broy./Diag. 0.40E+00 1.4 0.05667976 -31.1418135481 1.09E+00
Trace(PS): 32.0000000000
@@ -494,6 +615,13 @@
Total charge density on r-space grids: 0.0000000033
Total charge density g-space grids: 0.0000000033
+
+ Core Hamiltonian energy: 18.2312708091
+ Hartree energy: 42.3503780825
+ Exchange-correlation energy: -9.7151098081
+ Coulomb (electron-electron) energy: 2.5340985498
+ Maximum deviation from MO S-orthonormality 0.2220E-14
+ Minimum/Maximum MO magnitude 0.5994E+00 0.2050E+01
3 Broy./Diag. 0.40E+00 1.4 0.09691469 -31.1974003416 -5.56E-02
Trace(PS): 32.0000000000
@@ -502,6 +630,13 @@
Total charge density on r-space grids: 0.0000000042
Total charge density g-space grids: 0.0000000042
+
+ Core Hamiltonian energy: 18.0592667329
+ Hartree energy: 42.3803701993
+ Exchange-correlation energy: -9.7135449111
+ Coulomb (electron-electron) energy: 2.5282191572
+ Maximum deviation from MO S-orthonormality 0.2220E-14
+ Minimum/Maximum MO magnitude 0.5666E+00 0.2348E+01
4 Broy./Diag. 0.40E+00 1.4 0.00245608 -31.3378474040 -1.40E-01
Trace(PS): 32.0000000000
@@ -510,6 +645,13 @@
Total charge density on r-space grids: 0.0000000051
Total charge density g-space grids: 0.0000000051
+
+ Core Hamiltonian energy: 18.0647145020
+ Hartree energy: 42.4121545902
+ Exchange-correlation energy: -9.7138951069
+ Coulomb (electron-electron) energy: 2.5264107289
+ Maximum deviation from MO S-orthonormality 0.2442E-14
+ Minimum/Maximum MO magnitude 0.5678E+00 0.2340E+01
5 Broy./Diag. 0.40E+00 1.4 0.00235460 -31.3009654398 3.69E-02
Trace(PS): 32.0000000000
@@ -518,6 +660,13 @@
Total charge density on r-space grids: 0.0000000051
Total charge density g-space grids: 0.0000000051
+
+ Core Hamiltonian energy: 18.0687450544
+ Hartree energy: 42.4120460503
+ Exchange-correlation energy: -9.7140675731
+ Coulomb (electron-electron) energy: 2.5267629790
+ Maximum deviation from MO S-orthonormality 0.2220E-14
+ Minimum/Maximum MO magnitude 0.5688E+00 0.2335E+01
6 Broy./Diag. 0.40E+00 1.4 0.00007565 -31.2972158934 3.75E-03
Trace(PS): 32.0000000000
@@ -526,6 +675,13 @@
Total charge density on r-space grids: 0.0000000050
Total charge density g-space grids: 0.0000000050
+
+ Core Hamiltonian energy: 18.0686754393
+ Hartree energy: 42.4117950535
+ Exchange-correlation energy: -9.7142604426
+ Coulomb (electron-electron) energy: 2.5271673228
+ Maximum deviation from MO S-orthonormality 0.1998E-14
+ Minimum/Maximum MO magnitude 0.5688E+00 0.2336E+01
7 Broy./Diag. 0.40E+00 1.4 0.00009004 -31.2977293749 -5.13E-04
Trace(PS): 32.0000000000
@@ -534,6 +690,13 @@
Total charge density on r-space grids: 0.0000000051
Total charge density g-space grids: 0.0000000051
+
+ Core Hamiltonian energy: 18.0685872217
+ Hartree energy: 42.4117665962
+ Exchange-correlation energy: -9.7142598092
+ Coulomb (electron-electron) energy: 2.5271694810
+ Maximum deviation from MO S-orthonormality 0.1554E-14
+ Minimum/Maximum MO magnitude 0.5688E+00 0.2336E+01
8 Broy./Diag. 0.40E+00 1.4 0.00000186 -31.2978454163 -1.16E-04
Trace(PS): 32.0000000000
@@ -542,6 +705,13 @@
Total charge density on r-space grids: 0.0000000051
Total charge density g-space grids: 0.0000000051
+
+ Core Hamiltonian energy: 18.0685858541
+ Hartree energy: 42.4117283490
+ Exchange-correlation energy: -9.7142583272
+ Coulomb (electron-electron) energy: 2.5271711411
+ Maximum deviation from MO S-orthonormality 0.1998E-14
+ Minimum/Maximum MO magnitude 0.5688E+00 0.2336E+01
9 Broy./Diag. 0.40E+00 1.4 0.00000252 -31.2978835492 -3.81E-05
Trace(PS): 32.0000000000
@@ -550,6 +720,13 @@
Total charge density on r-space grids: 0.0000000051
Total charge density g-space grids: 0.0000000051
+
+ Core Hamiltonian energy: 18.0685842971
+ Hartree energy: 42.4117282458
+ Exchange-correlation energy: -9.7142583232
+ Coulomb (electron-electron) energy: 2.5271711399
+ Maximum deviation from MO S-orthonormality 0.1776E-14
+ Minimum/Maximum MO magnitude 0.5688E+00 0.2336E+01
10 Broy./Diag. 0.40E+00 1.4 5.6405E-09 -31.2978852054 -1.66E-06
*** SCF run converged in 10 steps ***
@@ -565,9 +742,15 @@
Core Hamiltonian energy: 18.06858429706012
Hartree energy: 42.41172824581675
Exchange-correlation energy: -9.71425832315954
+ Coulomb Electron-Electron Interaction Energy
+ - Already included in the total Hartree term 2.52717113991578
Total energy: -31.29788520535767
+ The electron density is written in cube file format to the file:
+
+ Si_bulk8-ELECTRON_DENSITY-1_0.cube
+
MULLIKEN POPULATION ANALYSIS
@@ -598,6 +781,64 @@
Total Charge -0.000
!-----------------------------------------------------------------------------!
+ Electronic kinetic energy: 13.31525592466418
+
+
+ LOWDIN POPULATION ANALYSIS
+
+ *** 11:17:16 WARNING in population_analyses:lowdin_population_analysis :: ***
+ *** Overlap matrix exhibits linear dependencies. At least some ***
+ *** eigenvalues have been quenched. ***
+
+
+ # Atom Element Kind Atomic population Net charge
+ 1 Si 1 4.000000 -0.000000
+ 2 Si 1 4.000000 0.000000
+ 3 Si 1 4.000000 0.000000
+ 4 Si 1 4.000000 0.000000
+ 5 Si 1 4.000000 -0.000000
+ 6 Si 1 4.000000 0.000000
+ 7 Si 1 4.000000 -0.000000
+ 8 Si 1 4.000000 -0.000000
+ # Total charge 32.000000 0.000000
+
+ DDAP FULL DENSITY charges:
+ Atom | Charge
+
+ 1 Si -0.000000
+ 2 Si 0.000000
+ 3 Si 0.000000
+ 4 Si 0.000000
+ 5 Si 0.000000
+ 6 Si 0.000000
+ 7 Si 0.000000
+ 8 Si 0.000000
+ 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= -0.00000003 Y= -0.00000003 Z= -0.00000002 Total= 0.00000004
+
+ Eigenvalues of the occupied subspace spin 1
+ ---------------------------------------------
+ -0.24280735 -0.09103786 -0.09103786 -0.09103786
+ -0.09103785 -0.09103785 -0.09103785 0.09085421
+ 0.09085421 0.09085421 0.09085422 0.09085422
+ 0.09085422 0.20028206 0.20028206 0.20028207
+ Fermi Energy [eV] : 5.449952
+
+ Lowest eigenvalues of the unoccupied subspace spin 1
+ ---------------------------------------------
+
Trace(PS): 32.0000000000
Electronic density on regular grids: -31.9999999889 0.0000000111
@@ -606,6 +847,194 @@
Total charge density g-space grids: 0.0000000051
+ Core Hamiltonian energy: 18.0685842936
+ Hartree energy: 42.4117280752
+ Exchange-correlation energy: -9.7142583166
+ Coulomb (electron-electron) energy: 2.5271711387
+
+
+ FORCES [a.u.]
+
+ Atom Kind Component X Y Z
+
+ 1 1 overlap -0.000000 -0.000000 -0.000000
+ 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 -0.000000
+ 1 1 gth_nlcc 0.000000 0.000000 0.000000
+ 1 1 gth_ppnl 0.000000 0.000000 0.000000
+ 1 1 core_overlap -0.000000 -0.000000 -0.000000
+ 1 1 rho_core -0.000000 -0.000000 -0.000000
+ 1 1 rho_elec -0.000000 -0.000000 -0.000000
+ 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 -0.000000
+ 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 0.000000
+ 2 1 gth_nlcc 0.000000 0.000000 0.000000
+ 2 1 gth_ppnl -0.000000 -0.000000 -0.000000
+ 2 1 core_overlap 0.000000 -0.000000 -0.000000
+ 2 1 rho_core -0.000000 0.000000 0.000000
+ 2 1 rho_elec 0.000000 0.000000 0.000000
+ 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 0.000000
+ 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 0.000000
+ 3 1 gth_nlcc 0.000000 0.000000 0.000000
+ 3 1 gth_ppnl -0.000000 -0.000000 -0.000000
+ 3 1 core_overlap -0.000000 -0.000000 0.000000
+ 3 1 rho_core 0.000000 0.000000 -0.000000
+ 3 1 rho_elec 0.000000 -0.000000 0.000000
+ 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 -0.000000
+ 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 0.000000
+ 4 1 gth_nlcc 0.000000 0.000000 0.000000
+ 4 1 gth_ppnl -0.000000 -0.000000 -0.000000
+ 4 1 core_overlap -0.000000 0.000000 -0.000000
+ 4 1 rho_core 0.000000 -0.000000 0.000000
+ 4 1 rho_elec 0.000000 0.000000 0.000000
+ 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 1 overlap 0.000000 -0.000000 0.000000
+ 5 1 overlap_admm 0.000000 0.000000 0.000000
+ 5 1 kinetic -0.000000 0.000000 -0.000000
+ 5 1 gth_ppl -0.000000 -0.000000 0.000000
+ 5 1 gth_nlcc 0.000000 0.000000 0.000000
+ 5 1 gth_ppnl 0.000000 0.000000 -0.000000
+ 5 1 core_overlap 0.000000 0.000000 0.000000
+ 5 1 rho_core 0.000000 -0.000000 0.000000
+ 5 1 rho_elec 0.000000 -0.000000 0.000000
+ 5 1 rho_lri_el 0.000000 0.000000 0.000000
+ 5 1 ch_pulay 0.000000 0.000000 0.000000
+ 5 1 dispersion 0.000000 0.000000 0.000000
+ 5 1 other 0.000000 0.000000 0.000000
+ 5 1 fock_4c 0.000000 0.000000 0.000000
+ 5 1 hfx_ri 0.000000 0.000000 0.000000
+ 5 1 ehrenfest 0.000000 0.000000 0.000000
+ 5 1 efield 0.000000 0.000000 0.000000
+ 5 1 eev 0.000000 0.000000 0.000000
+ 5 1 mp2_non_sep 0.000000 0.000000 0.000000
+ 5 1 mp2_sep 0.000000 0.000000 0.000000
+ 5 1 total 0.000000 0.000000 0.000000
+
+ 6 1 overlap -0.000000 -0.000000 -0.000000
+ 6 1 overlap_admm 0.000000 0.000000 0.000000
+ 6 1 kinetic 0.000000 0.000000 0.000000
+ 6 1 gth_ppl -0.000000 -0.000000 -0.000000
+ 6 1 gth_nlcc 0.000000 0.000000 0.000000
+ 6 1 gth_ppnl 0.000000 0.000000 0.000000
+ 6 1 core_overlap 0.000000 0.000000 0.000000
+ 6 1 rho_core -0.000000 -0.000000 -0.000000
+ 6 1 rho_elec -0.000000 -0.000000 -0.000000
+ 6 1 rho_lri_el 0.000000 0.000000 0.000000
+ 6 1 ch_pulay 0.000000 0.000000 0.000000
+ 6 1 dispersion 0.000000 0.000000 0.000000
+ 6 1 other 0.000000 0.000000 0.000000
+ 6 1 fock_4c 0.000000 0.000000 0.000000
+ 6 1 hfx_ri 0.000000 0.000000 0.000000
+ 6 1 ehrenfest 0.000000 0.000000 0.000000
+ 6 1 efield 0.000000 0.000000 0.000000
+ 6 1 eev 0.000000 0.000000 0.000000
+ 6 1 mp2_non_sep 0.000000 0.000000 0.000000
+ 6 1 mp2_sep 0.000000 0.000000 0.000000
+ 6 1 total 0.000000 0.000000 0.000000
+
+ 7 1 overlap 0.000000 0.000000 0.000000
+ 7 1 overlap_admm 0.000000 0.000000 0.000000
+ 7 1 kinetic 0.000000 -0.000000 -0.000000
+ 7 1 gth_ppl -0.000000 0.000000 -0.000000
+ 7 1 gth_nlcc 0.000000 0.000000 0.000000
+ 7 1 gth_ppnl 0.000000 -0.000000 0.000000
+ 7 1 core_overlap 0.000000 0.000000 0.000000
+ 7 1 rho_core -0.000000 0.000000 0.000000
+ 7 1 rho_elec -0.000000 0.000000 0.000000
+ 7 1 rho_lri_el 0.000000 0.000000 0.000000
+ 7 1 ch_pulay 0.000000 0.000000 0.000000
+ 7 1 dispersion 0.000000 0.000000 0.000000
+ 7 1 other 0.000000 0.000000 0.000000
+ 7 1 fock_4c 0.000000 0.000000 0.000000
+ 7 1 hfx_ri 0.000000 0.000000 0.000000
+ 7 1 ehrenfest 0.000000 0.000000 0.000000
+ 7 1 efield 0.000000 0.000000 0.000000
+ 7 1 eev 0.000000 0.000000 0.000000
+ 7 1 mp2_non_sep 0.000000 0.000000 0.000000
+ 7 1 mp2_sep 0.000000 0.000000 0.000000
+ 7 1 total 0.000000 0.000000 0.000000
+
+ 8 1 overlap 0.000000 0.000000 -0.000000
+ 8 1 overlap_admm 0.000000 0.000000 0.000000
+ 8 1 kinetic -0.000000 -0.000000 0.000000
+ 8 1 gth_ppl -0.000000 0.000000 -0.000000
+ 8 1 gth_nlcc 0.000000 0.000000 0.000000
+ 8 1 gth_ppnl 0.000000 -0.000000 0.000000
+ 8 1 core_overlap 0.000000 0.000000 0.000000
+ 8 1 rho_core 0.000000 0.000000 -0.000000
+ 8 1 rho_elec 0.000000 0.000000 0.000000
+ 8 1 rho_lri_el 0.000000 0.000000 0.000000
+ 8 1 ch_pulay 0.000000 0.000000 0.000000
+ 8 1 dispersion 0.000000 0.000000 0.000000
+ 8 1 other 0.000000 0.000000 0.000000
+ 8 1 fock_4c 0.000000 0.000000 0.000000
+ 8 1 hfx_ri 0.000000 0.000000 0.000000
+ 8 1 ehrenfest 0.000000 0.000000 0.000000
+ 8 1 efield 0.000000 0.000000 0.000000
+ 8 1 eev 0.000000 0.000000 0.000000
+ 8 1 mp2_non_sep 0.000000 0.000000 0.000000
+ 8 1 mp2_sep 0.000000 0.000000 0.000000
+ 8 1 total 0.000000 0.000000 0.000000
+
+ Sum of total 0.000000 0.000000 0.000000
+
ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.): -31.297885372811063
@@ -622,28 +1051,39 @@
8 1 Si -0.00000001 -0.00000001 -0.00000001
SUM OF ATOMIC FORCES -0.00000000 -0.00000000 -0.00000000 0.00000000
+
+ *************************************************************************
+ *** WARNING in force_env_calc_energy_force (MODULE force_env_methods) ***
+ *************************************************************************
+
+ *** To print the stress tensor switch on the virial evaluation with the ***
+ *** keyword: STRESS_TENSOR ***
+
-------------------------------------------------------------------------------
- -
- DBCSR STATISTICS -
- -
-------------------------------------------------------------------------------
COUNTER CPU ACC ACC%
- number of processed stacks 11 0 0.0
+ number of processed stacks 29 0 0.0
matmuls inhomo. stacks 0 0 0.0
- matmuls total 396 0 0.0
+ matmuls total 1676 0 0.0
+ flops 13 x 8 x 13 173056 0 0.0
+ flops 13 x 32 x 13 2076672 0 0.0
flops 13 x 13 x 16 2141568 0 0.0
- flops total 2141568 0 0.0
- marketing flops 3807232
+ flops 13 x 16 x 13 5537792 0 0.0
+ flops total 9929088 0 0.0
+ marketing flops 11594752
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
---- MULTIGRID INFO ----
-------------------------------------------------------------------------------
count for grid 1: 360 cutoff [a.u.] 150.00
- count for grid 2: 4516 cutoff [a.u.] 50.00
- count for grid 3: 7804 cutoff [a.u.] 16.67
- count for grid 4: 3048 cutoff [a.u.] 5.56
- total gridlevel count : 15728
+ count for grid 2: 4524 cutoff [a.u.] 50.00
+ count for grid 3: 7820 cutoff [a.u.] 16.67
+ count for grid 4: 3064 cutoff [a.u.] 5.56
+ total gridlevel count : 15768
-------------------------------------------------------------------------------
- -
@@ -653,14 +1093,14 @@
ROUTINE CALLS TOT TIME [s] AVE VOLUME [Bytes] PERFORMANCE [MB/s]
MP_Group 5 0.000
- MP_Bcast 12 0.016 5. 0.00
- MP_Allreduce 171 0.000 42. 30.47
- MP_Sync 4 0.000
- MP_Alltoall 183 0.000 15743. 6691.06
- MP_Wait 264 0.000
- MP_ISend 88 0.001 13472. 872.54
- MP_IRecv 88 0.000 13472. 11472.52
- MP_Memory 264 0.000
+ MP_Bcast 15 0.010 7. 0.01
+ MP_Allreduce 256 0.000 52. 45.82
+ MP_Sync 6308 0.000
+ MP_Alltoall 462 0.000 11970. 11741.11
+ MP_Wait 672 0.000
+ MP_ISend 224 0.001 37354. 6126.00
+ MP_IRecv 224 0.000 37354. 17942.46
+ MP_Memory 604 0.000
-------------------------------------------------------------------------------
@@ -731,35 +1171,34 @@
-------------------------------------------------------------------------------
SUBROUTINE CALLS ASD SELF TIME TOTAL TIME
MAXIMUM AVERAGE MAXIMUM AVERAGE MAXIMUM
- CP2K 1 1.0 0.057 0.057 17.482 17.482
- qs_forces 1 2.0 0.001 0.001 16.988 16.988
- qs_energies_scf 1 3.0 0.018 0.018 15.160 15.160
- scf_env_do_scf 1 4.0 0.000 0.000 13.773 13.773
- scf_env_do_scf_inner_loop 10 5.0 0.003 0.003 13.773 13.773
- rebuild_ks_matrix 11 6.7 0.000 0.000 9.107 9.107
- qs_ks_build_kohn_sham_matrix 11 7.7 0.002 0.002 9.107 9.107
- sum_up_and_integrate 11 8.7 0.004 0.004 8.808 8.808
- integrate_v_rspace 11 9.7 8.673 8.673 8.805 8.805
- qs_ks_update_qs_env 10 6.0 0.000 0.000 7.978 7.978
- qs_rho_update_rho 11 6.0 0.000 0.000 6.020 6.020
- calculate_rho_elec 11 7.0 5.765 5.765 6.020 6.020
- qs_ks_update_qs_env_forces 1 3.0 0.000 0.000 1.129 1.129
- init_scf_run 1 4.0 0.009 0.009 0.782 0.782
- scf_env_initial_rho_setup 1 5.0 0.017 0.017 0.700 0.700
- build_core_hamiltonian_matrix_ 1 3.0 0.000 0.000 0.698 0.698
- fft_wrap_pw1pw2 120 9.8 0.001 0.001 0.557 0.557
- qs_energies_init_hamiltonians 1 4.0 0.001 0.001 0.539 0.539
- fft_wrap_pw1pw2_150 54 10.1 0.027 0.027 0.510 0.510
- build_core_hamiltonian_matrix 1 5.0 0.041 0.041 0.455 0.455
- fft3d_s 121 11.7 0.339 0.339 0.407 0.407
- build_core_ppnl_forces 1 4.0 0.400 0.400 0.400 0.400
- quickstep_create_force_env 1 2.0 0.043 0.043 0.375 0.375
+ CP2K 1 1.0 0.048 0.048 17.498 17.498
+ qs_forces 1 2.0 0.002 0.002 17.036 17.036
+ qs_energies_scf 1 3.0 0.016 0.016 15.328 15.328
+ scf_env_do_scf 1 4.0 0.000 0.000 13.772 13.772
+ scf_env_do_scf_inner_loop 10 5.0 0.013 0.013 13.772 13.772
+ rebuild_ks_matrix 11 6.7 0.000 0.000 9.067 9.067
+ qs_ks_build_kohn_sham_matrix 11 7.7 0.003 0.003 9.067 9.067
+ sum_up_and_integrate 11 8.7 0.003 0.003 8.708 8.708
+ integrate_v_rspace 11 9.7 8.581 8.581 8.705 8.705
+ qs_ks_update_qs_env 10 6.0 0.000 0.000 8.001 8.001
+ qs_rho_update_rho 11 6.0 0.000 0.000 5.950 5.950
+ calculate_rho_elec 11 7.0 5.713 5.713 5.950 5.950
+ qs_ks_update_qs_env_forces 1 3.0 0.000 0.000 1.067 1.067
+ init_scf_run 1 4.0 0.001 0.001 0.740 0.740
+ scf_env_initial_rho_setup 1 5.0 0.001 0.001 0.681 0.681
+ build_core_hamiltonian_matrix_ 1 3.0 0.000 0.000 0.640 0.640
+ fft_wrap_pw1pw2 132 9.6 0.001 0.001 0.605 0.605
+ fft_wrap_pw1pw2_150 63 9.8 0.033 0.033 0.558 0.558
+ fft3d_s 133 11.5 0.383 0.383 0.450 0.450
+ scf_post_calculation_gpw 1 4.0 0.000 0.000 0.447 0.447
+ quickstep_create_force_env 1 2.0 0.069 0.069 0.353 0.353
+ qs_energies_init_hamiltonians 1 4.0 0.000 0.000 0.351 0.351
-------------------------------------------------------------------------------
- **** **** ****** ** PROGRAM ENDED AT 2016-04-19 13:04:37.223
+ **** **** ****** ** PROGRAM ENDED AT 2016-04-21 11:17:18.146
***** ** *** *** ** PROGRAM RAN ON lauri-Lenovo-Z50-70
** **** ****** PROGRAM RAN BY lauri
- ***** ** ** ** ** PROGRAM PROCESS ID 10277
+ ***** ** ** ** ** PROGRAM PROCESS ID 9923
**** ** ******* ** PROGRAM STOPPED IN /home/lauri/Dropbox/nomad-dev/nomad-l
ab-base/parsers/cp2k/test/unittests/c
p2k_2.6.2/energy_force
diff --git a/test/unittests/cp2k_2.6.2/run_tests.py b/test/unittests/cp2k_2.6.2/run_tests.py
index a27dfe7..dd17a51 100644
--- a/test/unittests/cp2k_2.6.2/run_tests.py
+++ b/test/unittests/cp2k_2.6.2/run_tests.py
@@ -50,19 +50,35 @@ class TestXCFunctional(unittest.TestCase):
def test_pade(self):
xc = get_result("XC_functional/pade", "XC_functional")
- self.assertEqual(xc, "LDA_XC_TETER93")
+ self.assertEqual(xc, "1*LDA_XC_TETER93")
def test_lda(self):
xc = get_result("XC_functional/lda", "XC_functional")
- self.assertEqual(xc, "LDA_XC_TETER93")
-
- def test_becke88(self):
- xc = get_result("XC_functional/becke88", "XC_functional")
- self.assertEqual(xc, "GGA_X_B88")
+ self.assertEqual(xc, "1*LDA_XC_TETER93")
def test_blyp(self):
xc = get_result("XC_functional/blyp", "XC_functional")
- self.assertEqual(xc, "GGA_C_LYP_GGA_X_B88")
+ self.assertEqual(xc, "1*GGA_C_LYP+1*GGA_X_B88")
+
+ def test_b3lyp(self):
+ xc = get_result("XC_functional/b3lyp", "XC_functional")
+ self.assertEqual(xc, "1*HYB_GGA_XC_B3LYP")
+
+ def test_olyp(self):
+ xc = get_result("XC_functional/olyp", "XC_functional")
+ self.assertEqual(xc, "1*GGA_C_LYP+1*GGA_X_OPTX")
+
+ def test_hcth120(self):
+ xc = get_result("XC_functional/hcth120", "XC_functional")
+ self.assertEqual(xc, "1*GGA_XC_HCTH_120")
+
+ def test_pbe0(self):
+ xc = get_result("XC_functional/pbe0", "XC_functional")
+ self.assertEqual(xc, "1*HYB_GGA_XC_PBEH")
+
+ def test_pbe(self):
+ xc = get_result("XC_functional/pbe", "XC_functional")
+ self.assertEqual(xc, "1*GGA_C_PBE+1*GGA_X_PBE")
#===============================================================================
@@ -104,11 +120,26 @@ class TestEnergyForce(unittest.TestCase):
expected_result = convert_unit(np.array(-32.2320848878), "hartree")
self.assertTrue(np.array_equal(energy_total[0], expected_result))
+ def test_energy_change_scf_iteration(self):
+ energy_change = self.results["energy_change_scf_iteration"]
+ expected_result = convert_unit(np.array(-3.22E+01), "hartree")
+ self.assertTrue(np.array_equal(energy_change[0], expected_result))
+
+ def test_energy_XC_scf_iteration(self):
+ result = self.results["energy_XC_scf_iteration"]
+ expected_result = convert_unit(np.array(-9.4555961214), "hartree")
+ self.assertTrue(np.array_equal(result[0], expected_result))
+
def test_energy_total(self):
energy_total = self.results["energy_total"]
expected_result = convert_unit(np.array(-31.297885372811063), "hartree")
self.assertTrue(np.array_equal(energy_total, expected_result))
+ def test_electronic_kinetic_energy(self):
+ result = self.results["electronic_kinetic_energy"]
+ expected_result = convert_unit(np.array(13.31525592466418), "hartree")
+ self.assertTrue(np.array_equal(result, expected_result))
+
def test_atom_forces(self):
atomic_forces = self.results["atom_forces"]
expected_result = convert_unit(
--
GitLab