diff --git a/parser/parser-cp2k/cp2kparser/parser.py b/parser/parser-cp2k/cp2kparser/parser.py
index 0bca72450628fb0d02b32963d083caadd66d6bcc..c1dabfc9e9b6e3469762a24b525328a18dd24101 100644
--- a/parser/parser-cp2k/cp2kparser/parser.py
+++ b/parser/parser-cp2k/cp2kparser/parser.py
@@ -3,8 +3,8 @@ from builtins import range
import os
import re
import logging
+import importlib
from nomadcore.baseclasses import ParserInterface
-from cp2kparser.versions.versionsetup import get_main_parser
logger = logging.getLogger("nomad")
@@ -58,10 +58,69 @@ class CP2KParser(ParserInterface):
# Setup the correct main parser based on the version id. If no match
# for the version is found, use the main parser for CP2K 2.6.2
- self.main_parser = get_main_parser(version_id, run_type)(self.parser_context.main_file, self.parser_context)
+ self.setup_main_parser({"version_id": version_id, "run_type": run_type})
def get_metainfo_filename(self):
return "cp2k.nomadmetainfo.json"
def get_parser_info(self):
return {'name': 'cp2k-parser', 'version': '1.0'}
+
+ def setup_main_parser(self, version_dictionary):
+ """
+ Setups a main parser class for this calculation. The main class can be
+ different for each version and run type.
+
+ Args:
+ version_id: An integer representing the CP2K version. The version
+ number is originally a string the form '2.6.2', but here the numbers
+ are just concatenated into a single integer number 262.
+ run_type: A string that identifies the RUN_TYPE for the calculation.
+ All the possible run types can be found in the CP2K reference manual.
+
+ Returns:
+ A python class that should be instantiated later with the correct
+ parameters.
+ """
+ run_type = version_dictionary["run_type"]
+ version_id = version_dictionary["version_id"]
+
+ # Search for a RUN_TYPE specific parser
+ parser_map = {
+ "ENERGY": "SinglePointParser",
+ "ENERGY_FORCE": "SinglePointParser",
+ "WAVEFUNCTION_OPTIMIZATION": "SinglePointParser",
+ "WFN_OPT": "SinglePointParser",
+ "GEO_OPT": "GeoOptParser",
+ "GEOMETRY_OPTIMIZATION": "GeoOptParser",
+ "MD": "MDParser",
+ "MOLECULAR_DYNAMICS": "MDParser",
+ }
+ try:
+ parser = parser_map[run_type]
+ except KeyError:
+ logger.exception("A parser corresponding to the run_type '{}' could not be found.".format(run_type))
+ raise
+
+ # Currently the version id is a pure integer, so it can directly be mapped
+ # into a package name.
+ base = "cp2kparser.versions.cp2k{}.{}".format(version_id, parser.lower())
+ parser_module = None
+ parser_class = None
+ try:
+ parser_module = importlib.import_module(base)
+ except ImportError:
+ logger.warning("Could not find a parser for version '{}' and run type '{}'. Trying to default to the base implementation for CP2K 2.6.2".format(version_id, run_type))
+ base = "cp2kparser.versions.cp2k262.{}".format(parser.lower())
+ try:
+ parser_module = importlib.import_module(base)
+ except ImportError:
+ logger.exception("Tried to default to the CP2K 2.6.2 implementation but could not find the correct modules for run_type '{}'.".format(run_type))
+ raise
+ try:
+ parser_class = getattr(parser_module, "CP2K{}".format(parser))
+ except AttributeError:
+ logger.exception("A parser class '{}' could not be found in the module '[]'.".format(parser_class, parser_module))
+ raise
+
+ self.main_parser = parser_class(self.parser_context.main_file, self.parser_context)
diff --git a/parser/parser-cp2k/cp2kparser/versions/cp2k262/commonmatcher.py b/parser/parser-cp2k/cp2kparser/versions/cp2k262/commonmatcher.py
index 52bc4311bd1abf47545a3029d335ccf6412252eb..b6a4140ec3c3052bed13aef12d004887dc61a8a3 100644
--- a/parser/parser-cp2k/cp2kparser/versions/cp2k262/commonmatcher.py
+++ b/parser/parser-cp2k/cp2kparser/versions/cp2k262/commonmatcher.py
@@ -1,36 +1,25 @@
from __future__ import absolute_import
from builtins import str
-from builtins import object
import re
import numpy as np
import logging
from nomadcore.simple_parser import SimpleMatcher as SM
-from nomadcore.simple_parser import extractOnCloseTriggers
from nomadcore.caching_backend import CachingLevel
from nomadcore.unit_conversion.unit_conversion import convert_unit
+from nomadcore.baseclasses import CommonMatcher
from .inputparser import CP2KInputParser
logger = logging.getLogger("nomad")
#===============================================================================
-class CommonMatcher(object):
+class CP2KCommonMatcher(CommonMatcher):
"""
This class is used to store and instantiate common parts of the
hierarchical SimpleMatcher structure used in the parsing of a CP2K
output file.
"""
def __init__(self, parser_context):
-
- # Repeating regex definitions
- self.parser_context = parser_context
- self.backend = parser_context.caching_backend
- self.file_service = parser_context.file_service
- self.cache_service = parser_context.cache_service
- self.regex_f = "-?\d+\.\d+(?:E(?:\+|-)\d+)?" # Regex for a floating point value
- self.regex_i = "-?\d+" # Regex for an integer
- self.regex_word = "[\S]+" # Regex for a single word. Can contain anything else but whitespace
- self.regex_letter = "[^\W\d_]" # Regex for a single alphabetical letter
- self.regex_eol = "[^\n]+" # Regex for a single alphabetical letter
+ super(CP2KCommonMatcher, self).__init__(parser_context)
self.section_method_index = None
self.section_system_index = None
self.test_electronic_structure_method = "DFT"
@@ -68,25 +57,25 @@ class CommonMatcher(object):
forwardMatch=True,
sections=['x_cp2k_section_dbcsr'],
subMatchers=[
- SM( " DBCSR\| Multiplication driver\s+(?P<x_cp2k_dbcsr_multiplication_driver>{})".format(self.regex_word)),
- SM( " DBCSR\| Multrec recursion limit\s+(?P<x_cp2k_dbcsr_multrec_recursion_limit>{})".format(self.regex_i)),
- SM( " DBCSR\| Multiplication stack size\s+(?P<x_cp2k_dbcsr_multiplication_stack_size>{})".format(self.regex_i)),
- SM( " DBCSR\| Multiplication size stacks\s+(?P<x_cp2k_dbcsr_multiplication_size_stacks>{})".format(self.regex_i)),
- SM( " DBCSR\| Use subcommunicators\s+(?P<x_cp2k_dbcsr_use_subcommunicators>{})".format(self.regex_letter)),
- SM( " DBCSR\| Use MPI combined types\s+(?P<x_cp2k_dbcsr_use_mpi_combined_types>{})".format(self.regex_letter)),
- SM( " DBCSR\| Use MPI memory allocation\s+(?P<x_cp2k_dbcsr_use_mpi_memory_allocation>{})".format(self.regex_letter)),
- SM( " DBCSR\| Use Communication thread\s+(?P<x_cp2k_dbcsr_use_communication_thread>{})".format(self.regex_letter)),
- SM( " DBCSR\| Communication thread load\s+(?P<x_cp2k_dbcsr_communication_thread_load>{})".format(self.regex_i)),
+ SM( " DBCSR\| Multiplication driver\s+(?P<x_cp2k_dbcsr_multiplication_driver>{})".format(self.regexs.regex_word)),
+ SM( " DBCSR\| Multrec recursion limit\s+(?P<x_cp2k_dbcsr_multrec_recursion_limit>{})".format(self.regexs.regex_i)),
+ SM( " DBCSR\| Multiplication stack size\s+(?P<x_cp2k_dbcsr_multiplication_stack_size>{})".format(self.regexs.regex_i)),
+ SM( " DBCSR\| Multiplication size stacks\s+(?P<x_cp2k_dbcsr_multiplication_size_stacks>{})".format(self.regexs.regex_i)),
+ SM( " DBCSR\| Use subcommunicators\s+(?P<x_cp2k_dbcsr_use_subcommunicators>{})".format(self.regexs.regex_letter)),
+ SM( " DBCSR\| Use MPI combined types\s+(?P<x_cp2k_dbcsr_use_mpi_combined_types>{})".format(self.regexs.regex_letter)),
+ SM( " DBCSR\| Use MPI memory allocation\s+(?P<x_cp2k_dbcsr_use_mpi_memory_allocation>{})".format(self.regexs.regex_letter)),
+ SM( " DBCSR\| Use Communication thread\s+(?P<x_cp2k_dbcsr_use_communication_thread>{})".format(self.regexs.regex_letter)),
+ SM( " DBCSR\| Communication thread load\s+(?P<x_cp2k_dbcsr_communication_thread_load>{})".format(self.regexs.regex_i)),
]
),
SM( " **** **** ****** ** PROGRAM STARTED AT".replace("*", "\*"),
forwardMatch=True,
sections=['x_cp2k_section_startinformation'],
subMatchers=[
- SM( " **** **** ****** ** PROGRAM STARTED AT\s+(?P<x_cp2k_start_time>{})".replace("*", "\*").format(self.regex_eol)),
- SM( " ***** ** *** *** ** PROGRAM STARTED ON\s+(?P<x_cp2k_start_host>{})".replace("*", "\*").format(self.regex_word)),
- SM( " ** **** ****** PROGRAM STARTED BY\s+(?P<x_cp2k_start_user>{})".replace("*", "\*").format(self.regex_word)),
- SM( " ***** ** ** ** ** PROGRAM PROCESS ID\s+(?P<x_cp2k_start_id>{})".replace("*", "\*").format(self.regex_i)),
+ SM( " **** **** ****** ** PROGRAM STARTED AT\s+(?P<x_cp2k_start_time>{})".replace("*", "\*").format(self.regexs.regex_eol)),
+ SM( " ***** ** *** *** ** PROGRAM STARTED ON\s+(?P<x_cp2k_start_host>{})".replace("*", "\*").format(self.regexs.regex_word)),
+ SM( " ** **** ****** PROGRAM STARTED BY\s+(?P<x_cp2k_start_user>{})".replace("*", "\*").format(self.regexs.regex_word)),
+ SM( " ***** ** ** ** ** PROGRAM PROCESS ID\s+(?P<x_cp2k_start_id>{})".replace("*", "\*").format(self.regexs.regex_i)),
SM( " **** ** ******* ** PROGRAM STARTED IN".replace("*", "\*"),
forwardMatch=True,
adHoc=self.adHoc_run_dir(),
@@ -97,29 +86,29 @@ class CommonMatcher(object):
sections=['x_cp2k_section_program_information'],
forwardMatch=True,
subMatchers=[
- SM( " CP2K\| version string:\s+(?P<program_version>{})".format(self.regex_eol)),
+ SM( " CP2K\| version string:\s+(?P<program_version>{})".format(self.regexs.regex_eol)),
SM( " CP2K\| source code revision number:\s+svn:(?P<x_cp2k_svn_revision>\d+)"),
- SM( " CP2K\| is freely available from{}".format(self.regex_eol)),
- SM( " CP2K\| Program compiled at\s+(?P<x_cp2k_program_compilation_datetime>{})".format(self.regex_eol)),
- SM( " CP2K\| Program compiled on\s+(?P<program_compilation_host>{})".format(self.regex_eol)),
- SM( " CP2K\| Program compiled for{}".format(self.regex_eol)),
- SM( " CP2K\| Input file name\s+(?P<x_cp2k_input_filename>{})".format(self.regex_eol)),
+ SM( " CP2K\| is freely available from{}".format(self.regexs.regex_eol)),
+ SM( " CP2K\| Program compiled at\s+(?P<x_cp2k_program_compilation_datetime>{})".format(self.regexs.regex_eol)),
+ SM( " CP2K\| Program compiled on\s+(?P<program_compilation_host>{})".format(self.regexs.regex_eol)),
+ SM( " CP2K\| Program compiled for{}".format(self.regexs.regex_eol)),
+ SM( " CP2K\| Input file name\s+(?P<x_cp2k_input_filename>{})".format(self.regexs.regex_eol)),
]
),
SM( " GLOBAL\|",
sections=['x_cp2k_section_global_settings'],
subMatchers=[
SM( " GLOBAL\| Force Environment number"),
- SM( " GLOBAL\| Basis set file name\s+(?P<x_cp2k_basis_set_filename>{})".format(self.regex_eol)),
- SM( " GLOBAL\| Geminal file name\s+(?P<x_cp2k_geminal_filename>{})".format(self.regex_eol)),
- SM( " GLOBAL\| Potential file name\s+(?P<x_cp2k_potential_filename>{})".format(self.regex_eol)),
- SM( " GLOBAL\| MM Potential file name\s+(?P<x_cp2k_mm_potential_filename>{})".format(self.regex_eol)),
- SM( " GLOBAL\| Coordinate file name\s+(?P<x_cp2k_coordinate_filename>{})".format(self.regex_eol)),
- SM( " GLOBAL\| Method name\s+(?P<x_cp2k_method_name>{})".format(self.regex_eol)),
+ SM( " GLOBAL\| Basis set file name\s+(?P<x_cp2k_basis_set_filename>{})".format(self.regexs.regex_eol)),
+ SM( " GLOBAL\| Geminal file name\s+(?P<x_cp2k_geminal_filename>{})".format(self.regexs.regex_eol)),
+ SM( " GLOBAL\| Potential file name\s+(?P<x_cp2k_potential_filename>{})".format(self.regexs.regex_eol)),
+ SM( " GLOBAL\| MM Potential file name\s+(?P<x_cp2k_mm_potential_filename>{})".format(self.regexs.regex_eol)),
+ SM( " GLOBAL\| Coordinate file name\s+(?P<x_cp2k_coordinate_filename>{})".format(self.regexs.regex_eol)),
+ SM( " GLOBAL\| Method name\s+(?P<x_cp2k_method_name>{})".format(self.regexs.regex_eol)),
SM( " GLOBAL\| Project name"),
- SM( " GLOBAL\| Preferred FFT library\s+(?P<x_cp2k_preferred_fft_library>{})".format(self.regex_eol)),
- SM( " GLOBAL\| Preferred diagonalization lib.\s+(?P<x_cp2k_preferred_diagonalization_library>{})".format(self.regex_eol)),
- SM( " GLOBAL\| Run type\s+(?P<x_cp2k_run_type>{})".format(self.regex_eol)),
+ SM( " GLOBAL\| Preferred FFT library\s+(?P<x_cp2k_preferred_fft_library>{})".format(self.regexs.regex_eol)),
+ SM( " GLOBAL\| Preferred diagonalization lib.\s+(?P<x_cp2k_preferred_diagonalization_library>{})".format(self.regexs.regex_eol)),
+ SM( " GLOBAL\| Run type\s+(?P<x_cp2k_run_type>{})".format(self.regexs.regex_eol)),
SM( " GLOBAL\| All-to-all communication in single precision"),
SM( " GLOBAL\| FFTs using library dependent lengths"),
SM( " GLOBAL\| Global print level"),
@@ -153,8 +142,8 @@ class CommonMatcher(object):
sections=["x_cp2k_section_scf_iteration"],
repeats=True,
subMatchers=[
- SM( r" Exchange-correlation energy:\s+(?P<x_cp2k_energy_XC_scf_iteration__hartree>{})".format(self.regex_f)),
- SM( r"\s+\d+\s+\S+\s+{0}\s+{0}\s+{0}\s+(?P<x_cp2k_energy_total_scf_iteration__hartree>{0})\s+(?P<x_cp2k_energy_change_scf_iteration__hartree>{0})".format(self.regex_f)),
+ SM( r" Exchange-correlation energy:\s+(?P<x_cp2k_energy_XC_scf_iteration__hartree>{})".format(self.regexs.regex_f)),
+ SM( r"\s+\d+\s+\S+\s+{0}\s+{0}\s+{0}\s+(?P<x_cp2k_energy_total_scf_iteration__hartree>{0})\s+(?P<x_cp2k_energy_change_scf_iteration__hartree>{0})".format(self.regexs.regex_f)),
]
),
SM( r" \*\*\* SCF run converged in\s+(\d+) steps \*\*\*",
@@ -165,12 +154,12 @@ class CommonMatcher(object):
otherMetaInfo=["single_configuration_calculation_converged"],
adHoc=self.adHoc_single_point_not_converged()
),
- SM( r" Electronic kinetic energy:\s+(?P<x_cp2k_electronic_kinetic_energy__hartree>{})".format(self.regex_f)),
+ SM( r" Electronic kinetic energy:\s+(?P<x_cp2k_electronic_kinetic_energy__hartree>{})".format(self.regexs.regex_f)),
SM( r" **************************** NUMERICAL STRESS ********************************".replace("*", "\*"),
# endReStr=" **************************** NUMERICAL STRESS END *****************************".replace("*", "\*"),
adHoc=self.adHoc_stress_calculation(),
),
- SM( r" ENERGY\| Total FORCE_EVAL \( \w+ \) energy \(a\.u\.\):\s+(?P<x_cp2k_energy_total__hartree>{0})".format(self.regex_f),
+ SM( r" ENERGY\| Total FORCE_EVAL \( \w+ \) energy \(a\.u\.\):\s+(?P<x_cp2k_energy_total__hartree>{0})".format(self.regexs.regex_f),
otherMetaInfo=["energy_total"],
),
SM( r" ATOMIC FORCES in \[a\.u\.\]"),
@@ -185,8 +174,8 @@ class CommonMatcher(object):
adHoc=self.adHoc_stress_tensor(),
otherMetaInfo=["stress_tensor", "section_stress_tensor"],
),
- SM( " 1/3 Trace\(stress tensor\):\s+(?P<x_cp2k_stress_tensor_one_third_of_trace__GPa>{})".format(self.regex_f)),
- SM( " Det\(stress tensor\)\s+:\s+(?P<x_cp2k_stress_tensor_determinant__GPa3>{})".format(self.regex_f)),
+ SM( " 1/3 Trace\(stress tensor\):\s+(?P<x_cp2k_stress_tensor_one_third_of_trace__GPa>{})".format(self.regexs.regex_f)),
+ SM( " Det\(stress tensor\)\s+:\s+(?P<x_cp2k_stress_tensor_determinant__GPa3>{})".format(self.regexs.regex_f)),
SM( " EIGENVECTORS AND EIGENVALUES OF THE STRESS TENSOR",
adHoc=self.adHoc_stress_tensor_eigenpairs()),
]
@@ -203,10 +192,10 @@ class CommonMatcher(object):
SM( " DFT\|",
forwardMatch=True,
subMatchers=[
- SM( " DFT\| Spin restricted Kohn-Sham (RKS) calculation\s+(?P<x_cp2k_spin_restriction>{})".format(self.regex_word)),
- SM( " DFT\| Multiplicity\s+(?P<spin_target_multiplicity>{})".format(self.regex_i)),
- SM( " DFT\| Number of spin states\s+(?P<number_of_spin_channels>{})".format(self.regex_i)),
- SM( " DFT\| Charge\s+(?P<total_charge>{})".format(self.regex_i)),
+ SM( " DFT\| Spin restricted Kohn-Sham (RKS) calculation\s+(?P<x_cp2k_spin_restriction>{})".format(self.regexs.regex_word)),
+ SM( " DFT\| Multiplicity\s+(?P<spin_target_multiplicity>{})".format(self.regexs.regex_i)),
+ SM( " DFT\| Number of spin states\s+(?P<number_of_spin_channels>{})".format(self.regexs.regex_i)),
+ SM( " DFT\| Charge\s+(?P<total_charge>{})".format(self.regexs.regex_i)),
SM( " DFT\| Self-interaction correction \(SIC\)\s+(?P<self_interaction_correction_method>[^\n]+)"),
],
otherMetaInfo=["self_interaction_correction_method"],
@@ -217,41 +206,41 @@ class CommonMatcher(object):
SM( " QS\|",
forwardMatch=True,
subMatchers=[
- SM( " QS\| Method:\s+(?P<x_cp2k_quickstep_method>{})".format(self.regex_word)),
- SM( " QS\| Density plane wave grid type\s+{}".format(self.regex_eol)),
- SM( " QS\| Number of grid levels:\s+{}".format(self.regex_i)),
- SM( " QS\| Density cutoff \[a\.u\.\]:\s+(?P<x_cp2k_planewave_cutoff>{})".format(self.regex_f)),
- SM( " QS\| Multi grid cutoff \[a\.u\.\]: 1\) grid level\s+{}".format(self.regex_f)),
- SM( " QS\| 2\) grid level\s+{}".format(self.regex_f)),
- SM( " QS\| 3\) grid level\s+{}".format(self.regex_f)),
- SM( " QS\| 4\) grid level\s+{}".format(self.regex_f)),
- SM( " QS\| Grid level progression factor:\s+{}".format(self.regex_f)),
- SM( " QS\| Relative density cutoff \[a\.u\.\]:".format(self.regex_f)),
+ SM( " QS\| Method:\s+(?P<x_cp2k_quickstep_method>{})".format(self.regexs.regex_word)),
+ SM( " QS\| Density plane wave grid type\s+{}".format(self.regexs.regex_eol)),
+ SM( " QS\| Number of grid levels:\s+{}".format(self.regexs.regex_i)),
+ SM( " QS\| Density cutoff \[a\.u\.\]:\s+(?P<x_cp2k_planewave_cutoff>{})".format(self.regexs.regex_f)),
+ SM( " QS\| Multi grid cutoff \[a\.u\.\]: 1\) grid level\s+{}".format(self.regexs.regex_f)),
+ SM( " QS\| 2\) grid level\s+{}".format(self.regexs.regex_f)),
+ SM( " QS\| 3\) grid level\s+{}".format(self.regexs.regex_f)),
+ SM( " QS\| 4\) grid level\s+{}".format(self.regexs.regex_f)),
+ SM( " QS\| Grid level progression factor:\s+{}".format(self.regexs.regex_f)),
+ SM( " QS\| Relative density cutoff \[a\.u\.\]:".format(self.regexs.regex_f)),
SM( " QS\| Consistent realspace mapping and integration"),
- SM( " QS\| Interaction thresholds: eps_pgf_orb:\s+{}".format(self.regex_f)),
- SM( " QS\| eps_filter_matrix:\s+{}".format(self.regex_f)),
- SM( " QS\| eps_core_charge:\s+{}".format(self.regex_f)),
- SM( " QS\| eps_rho_gspace:\s+{}".format(self.regex_f)),
- SM( " QS\| eps_rho_rspace:\s+{}".format(self.regex_f)),
- SM( " QS\| eps_gvg_rspace:\s+{}".format(self.regex_f)),
- SM( " QS\| eps_ppl:\s+{}".format(self.regex_f)),
- SM( " QS\| eps_ppnl:\s+{}".format(self.regex_f)),
+ SM( " QS\| Interaction thresholds: eps_pgf_orb:\s+{}".format(self.regexs.regex_f)),
+ SM( " QS\| eps_filter_matrix:\s+{}".format(self.regexs.regex_f)),
+ SM( " QS\| eps_core_charge:\s+{}".format(self.regexs.regex_f)),
+ SM( " QS\| eps_rho_gspace:\s+{}".format(self.regexs.regex_f)),
+ SM( " QS\| eps_rho_rspace:\s+{}".format(self.regexs.regex_f)),
+ SM( " QS\| eps_gvg_rspace:\s+{}".format(self.regexs.regex_f)),
+ SM( " QS\| eps_ppl:\s+{}".format(self.regexs.regex_f)),
+ SM( " QS\| eps_ppnl:\s+{}".format(self.regexs.regex_f)),
],
),
SM( " ATOMIC KIND INFORMATION",
sections=["x_cp2k_section_atomic_kinds", "section_method_basis_set"],
subMatchers=[
- SM( "\s+(?P<x_cp2k_kind_number>{0})\. Atomic kind: (?P<x_cp2k_kind_element_symbol>{1})\s+Number of atoms:\s+(?P<x_cp2k_kind_number_of_atoms>{1})".format(self.regex_i, self.regex_word),
+ SM( "\s+(?P<x_cp2k_kind_number>{0})\. Atomic kind: (?P<x_cp2k_kind_element_symbol>{1})\s+Number of atoms:\s+(?P<x_cp2k_kind_number_of_atoms>{1})".format(self.regexs.regex_i, self.regexs.regex_word),
repeats=True,
sections=["x_cp2k_section_atomic_kind", "x_cp2k_section_kind_basis_set"],
subMatchers=[
- SM( " Orbital Basis Set\s+(?P<x_cp2k_kind_basis_set_name>{})".format(self.regex_word)),
- SM( " Number of orbital shell sets:\s+(?P<x_cp2k_basis_set_number_of_orbital_shell_sets>{})".format(self.regex_i)),
- SM( " Number of orbital shells:\s+(?P<x_cp2k_basis_set_number_of_orbital_shells>{})".format(self.regex_i)),
- SM( " Number of primitive Cartesian functions:\s+(?P<x_cp2k_basis_set_number_of_primitive_cartesian_functions>{})".format(self.regex_i)),
- SM( " Number of Cartesian basis functions:\s+(?P<x_cp2k_basis_set_number_of_cartesian_basis_functions>{})".format(self.regex_i)),
- SM( " Number of spherical basis functions:\s+(?P<x_cp2k_basis_set_number_of_spherical_basis_functions>{})".format(self.regex_i)),
- SM( " Norm type:\s+(?P<x_cp2k_basis_set_norm_type>{})".format(self.regex_i)),
+ SM( " Orbital Basis Set\s+(?P<x_cp2k_kind_basis_set_name>{})".format(self.regexs.regex_word)),
+ SM( " Number of orbital shell sets:\s+(?P<x_cp2k_basis_set_number_of_orbital_shell_sets>{})".format(self.regexs.regex_i)),
+ SM( " Number of orbital shells:\s+(?P<x_cp2k_basis_set_number_of_orbital_shells>{})".format(self.regexs.regex_i)),
+ SM( " Number of primitive Cartesian functions:\s+(?P<x_cp2k_basis_set_number_of_primitive_cartesian_functions>{})".format(self.regexs.regex_i)),
+ SM( " Number of Cartesian basis functions:\s+(?P<x_cp2k_basis_set_number_of_cartesian_basis_functions>{})".format(self.regexs.regex_i)),
+ SM( " Number of spherical basis functions:\s+(?P<x_cp2k_basis_set_number_of_spherical_basis_functions>{})".format(self.regexs.regex_i)),
+ SM( " Norm type:\s+(?P<x_cp2k_basis_set_norm_type>{})".format(self.regexs.regex_i)),
]
)
]
@@ -292,11 +281,11 @@ class CommonMatcher(object):
SM( " SCF PARAMETERS",
forwardMatch=True,
subMatchers=[
- SM( " SCF PARAMETERS Density guess:\s+{}".format(self.regex_eol)),
- SM( " max_scf:\s+(?P<scf_max_iteration>{})".format(self.regex_i)),
- SM( " max_scf_history:\s+{}".format(self.regex_i)),
- SM( " max_diis:\s+{}".format(self.regex_i)),
- SM( " eps_scf:\s+(?P<scf_threshold_energy_change>{})".format(self.regex_f)),
+ SM( " SCF PARAMETERS Density guess:\s+{}".format(self.regexs.regex_eol)),
+ SM( " max_scf:\s+(?P<scf_max_iteration>{})".format(self.regexs.regex_i)),
+ SM( " max_scf_history:\s+{}".format(self.regexs.regex_i)),
+ SM( " max_diis:\s+{}".format(self.regexs.regex_i)),
+ SM( " eps_scf:\s+(?P<scf_threshold_energy_change>{})".format(self.regexs.regex_f)),
]
),
SM( " MP2\|",
@@ -428,7 +417,7 @@ class CommonMatcher(object):
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_string = r" CELL\| Vector \w \[angstrom\]:\s+({0})\s+({0})\s+({0})".format(self.regexs.regex_f)
regex_compiled = re.compile(regex_string)
a_result = regex_compiled.match(a_line)
b_result = regex_compiled.match(b_line)
@@ -533,7 +522,7 @@ class CommonMatcher(object):
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_string = r"\s+\d+\s+(\d+)\s+(\w+)\s+\d+\s+({0})\s+({0})\s+({0})".format(self.regexs.regex_f)
regex_compiled = re.compile(regex_string)
match = True
@@ -610,17 +599,6 @@ class CommonMatcher(object):
#===========================================================================
# MISC functions
- def getOnCloseTriggers(self):
- """
- Returns:
- A dictionary containing a section name as a key, and a list of
- trigger functions associated with closing that section.
- """
- onClose = {}
- for attr, callback in extractOnCloseTriggers(self).items():
- onClose[attr] = [callback]
- return onClose
-
def get_atomic_number(self, symbol):
""" Returns the atomic number when given the atomic symbol.
diff --git a/parser/parser-cp2k/cp2kparser/versions/cp2k262/geooptparser.py b/parser/parser-cp2k/cp2kparser/versions/cp2k262/geooptparser.py
index 3f667438b6e0f593ef35d9461c09825b22c09bfa..e586df18bb42f59e33a90999ccbe4f6c009278c7 100644
--- a/parser/parser-cp2k/cp2kparser/versions/cp2k262/geooptparser.py
+++ b/parser/parser-cp2k/cp2kparser/versions/cp2k262/geooptparser.py
@@ -4,7 +4,7 @@ from builtins import next
from builtins import range
from nomadcore.simple_parser import SimpleMatcher as SM
from nomadcore.baseclasses import MainHierarchicalParser
-from .commonmatcher import CommonMatcher
+from .commonmatcher import CP2KCommonMatcher
import cp2kparser.generic.configurationreading
import cp2kparser.generic.csvparsing
from nomadcore.caching_backend import CachingLevel
@@ -21,7 +21,7 @@ class CP2KGeoOptParser(MainHierarchicalParser):
"""
"""
super(CP2KGeoOptParser, self).__init__(file_path, parser_context)
- self.setup_common_matcher(CommonMatcher(parser_context))
+ self.setup_common_matcher(CP2KCommonMatcher(parser_context))
self.traj_iterator = None
self.energy_reeval_quickstep = None
@@ -34,7 +34,7 @@ class CP2KGeoOptParser(MainHierarchicalParser):
#=======================================================================
# Cache levels
- self.caching_level_for_metaname.update({
+ self.caching_levels.update({
'x_cp2k_section_geometry_optimization_step': CachingLevel.ForwardAndCache,
'x_cp2k_section_quickstep_calculation': CachingLevel.ForwardAndCache,
'x_cp2k_section_geometry_optimization': CachingLevel.ForwardAndCache,
@@ -65,8 +65,8 @@ class CP2KGeoOptParser(MainHierarchicalParser):
# subMatchers=[
# self.cm.quickstep_calculation(),
# SM( " -------- Informations at step"),
- # SM( " Optimization Method =\s+(?P<x_cp2k_optimization_method>{})".format(self.cm.regex_word)),
- # SM( " Total Energy =\s+(?P<x_cp2k_optimization_energy__hartree>{})".format(self.cm.regex_f),
+ # SM( " Optimization Method =\s+(?P<x_cp2k_optimization_method>{})".format(self.regexs.regex_word)),
+ # SM( " Total Energy =\s+(?P<x_cp2k_optimization_energy__hartree>{})".format(self.regexs.regex_f),
# otherMetaInfo=["frame_sequence_potential_energy"]
# ),
# ],
@@ -87,7 +87,7 @@ class CP2KGeoOptParser(MainHierarchicalParser):
subMatchers=[
# SM( "",
# forwardMatch=True,
- # endReStr=" *** MNBRACK - NUMBER OF ENERGY EVALUATIONS :\s+{}\s+***".replace("*", "\*").format(self.cm.regex_i),
+ # endReStr=" *** MNBRACK - NUMBER OF ENERGY EVALUATIONS :\s+{}\s+***".replace("*", "\*").format(self.regexs.regex_i),
# subMatchers=[
# SM(" SCF WAVEFUNCTION OPTIMIZATION",
# forwardMatch=True,
@@ -100,7 +100,7 @@ class CP2KGeoOptParser(MainHierarchicalParser):
# ),
# SM( "",
# forwardMatch=True,
- # endReStr=" *** BRENT - NUMBER OF ENERGY EVALUATIONS :\s+{}\s+***".replace("*", "\*").format(self.cm.regex_i),
+ # endReStr=" *** BRENT - NUMBER OF ENERGY EVALUATIONS :\s+{}\s+***".replace("*", "\*").format(self.regexs.regex_i),
# subMatchers=[
# SM(" SCF WAVEFUNCTION OPTIMIZATION",
# forwardMatch=True,
@@ -112,27 +112,27 @@ class CP2KGeoOptParser(MainHierarchicalParser):
# ]
# ),
SM( " -------- Informations at step"),
- SM( " Optimization Method =\s+(?P<x_cp2k_optimization_method>{})".format(self.cm.regex_word)),
- SM( " Total Energy =\s+(?P<x_cp2k_optimization_energy__hartree>{})".format(self.cm.regex_f),
+ SM( " Optimization Method =\s+(?P<x_cp2k_optimization_method>{})".format(self.regexs.regex_word)),
+ SM( " Total Energy =\s+(?P<x_cp2k_optimization_energy__hartree>{})".format(self.regexs.regex_f),
otherMetaInfo=["frame_sequence_potential_energy"]
),
- SM( " Real energy change =\s+(?P<x_cp2k_optimization_energy_change__hartree>{})".format(self.cm.regex_f)),
- SM( " Decrease in energy =\s+(?P<x_cp2k_optimization_energy_decrease>{})".format(self.cm.regex_word)),
- SM( " Used time =\s+(?P<x_cp2k_optimization_used_time>{})".format(self.cm.regex_f)),
- SM( " Max. step size =\s+(?P<x_cp2k_optimization_max_step_size__bohr>{})".format(self.cm.regex_f)),
- SM( " Conv. limit for step size =\s+(?P<x_cp2k_optimization_step_size_convergence_limit__bohr>{})".format(self.cm.regex_f),
+ SM( " Real energy change =\s+(?P<x_cp2k_optimization_energy_change__hartree>{})".format(self.regexs.regex_f)),
+ SM( " Decrease in energy =\s+(?P<x_cp2k_optimization_energy_decrease>{})".format(self.regexs.regex_word)),
+ SM( " Used time =\s+(?P<x_cp2k_optimization_used_time>{})".format(self.regexs.regex_f)),
+ SM( " Max. step size =\s+(?P<x_cp2k_optimization_max_step_size__bohr>{})".format(self.regexs.regex_f)),
+ SM( " Conv. limit for step size =\s+(?P<x_cp2k_optimization_step_size_convergence_limit__bohr>{})".format(self.regexs.regex_f),
otherMetaInfo=["geometry_optimization_geometry_change"]
),
- SM( " Convergence in step size =\s+(?P<x_cp2k_optimization_step_size_convergence>{})".format(self.cm.regex_word)),
- SM( " RMS step size =\s+(?P<x_cp2k_optimization_rms_step_size__bohr>{})".format(self.cm.regex_f)),
- SM( " Convergence in RMS step =\s+(?P<x_cp2k_optimization_rms_step_size_convergence>{})".format(self.cm.regex_word)),
- SM( " Max. gradient =\s+(?P<x_cp2k_optimization_max_gradient__bohr_1hartree>{})".format(self.cm.regex_f)),
- SM( " Conv. limit for gradients =\s+(?P<x_cp2k_optimization_gradient_convergence_limit__bohr_1hartree>{})".format(self.cm.regex_f),
+ SM( " Convergence in step size =\s+(?P<x_cp2k_optimization_step_size_convergence>{})".format(self.regexs.regex_word)),
+ SM( " RMS step size =\s+(?P<x_cp2k_optimization_rms_step_size__bohr>{})".format(self.regexs.regex_f)),
+ SM( " Convergence in RMS step =\s+(?P<x_cp2k_optimization_rms_step_size_convergence>{})".format(self.regexs.regex_word)),
+ SM( " Max. gradient =\s+(?P<x_cp2k_optimization_max_gradient__bohr_1hartree>{})".format(self.regexs.regex_f)),
+ SM( " Conv. limit for gradients =\s+(?P<x_cp2k_optimization_gradient_convergence_limit__bohr_1hartree>{})".format(self.regexs.regex_f),
otherMetaInfo=["geometry_optimization_threshold_force"]
),
- SM( " Conv. for gradients =\s+(?P<x_cp2k_optimization_max_gradient_convergence>{})".format(self.cm.regex_word)),
- SM( " RMS gradient =\s+(?P<x_cp2k_optimization_rms_gradient__bohr_1hartree>{})".format(self.cm.regex_f)),
- SM( " Conv. in RMS gradients =\s+(?P<x_cp2k_optimization_rms_gradient_convergence>{})".format(self.cm.regex_word)),
+ SM( " Conv. for gradients =\s+(?P<x_cp2k_optimization_max_gradient_convergence>{})".format(self.regexs.regex_word)),
+ SM( " RMS gradient =\s+(?P<x_cp2k_optimization_rms_gradient__bohr_1hartree>{})".format(self.regexs.regex_f)),
+ SM( " Conv. in RMS gradients =\s+(?P<x_cp2k_optimization_rms_gradient_convergence>{})".format(self.regexs.regex_word)),
],
# adHoc=self.adHoc_step()
),
diff --git a/parser/parser-cp2k/cp2kparser/versions/cp2k262/mdparser.py b/parser/parser-cp2k/cp2kparser/versions/cp2k262/mdparser.py
index 15e9cd8f268697647335a3507f066b594f79f117..054725e8fd7db003e2c2b699fd793b690de6bb96 100644
--- a/parser/parser-cp2k/cp2kparser/versions/cp2k262/mdparser.py
+++ b/parser/parser-cp2k/cp2kparser/versions/cp2k262/mdparser.py
@@ -4,7 +4,7 @@ from builtins import range
import numpy as np
from nomadcore.simple_parser import SimpleMatcher as SM
from nomadcore.baseclasses import MainHierarchicalParser
-from .commonmatcher import CommonMatcher
+from .commonmatcher import CP2KCommonMatcher
import cp2kparser.generic.configurationreading
import cp2kparser.generic.csvparsing
from nomadcore.caching_backend import CachingLevel
@@ -23,7 +23,7 @@ class CP2KMDParser(MainHierarchicalParser):
"""
"""
super(CP2KMDParser, self).__init__(file_path, parser_context)
- self.setup_common_matcher(CommonMatcher(parser_context))
+ self.setup_common_matcher(CP2KCommonMatcher(parser_context))
self.traj_iterator = None
self.vel_iterator = None
self.energy_iterator = None
@@ -42,7 +42,7 @@ class CP2KMDParser(MainHierarchicalParser):
#=======================================================================
# Cache levels
- self.caching_level_for_metaname.update({
+ self.caching_levels.update({
'x_cp2k_section_md_settings': CachingLevel.ForwardAndCache,
'x_cp2k_section_md_step': CachingLevel.ForwardAndCache,
'x_cp2k_section_quickstep_calculation': CachingLevel.ForwardAndCache,
@@ -61,20 +61,20 @@ class CP2KMDParser(MainHierarchicalParser):
forwardMatch=True,
sections=["section_sampling_method", "x_cp2k_section_md_settings"],
subMatchers=[
- SM( " MD\| Ensemble Type\s+(?P<x_cp2k_md_ensemble_type>{})".format(self.cm.regex_word)),
- SM( " MD\| Number of Time Steps\s+(?P<x_cp2k_md_number_of_time_steps>{})".format(self.cm.regex_i)),
- SM( " MD\| Time Step \[fs\]\s+(?P<x_cp2k_md_time_step__fs>{})".format(self.cm.regex_f)),
- SM( " MD\| Temperature \[K\]\s+(?P<x_cp2k_md_target_temperature>{})".format(self.cm.regex_f)),
- SM( " MD\| Temperature tolerance \[K\]\s+(?P<x_cp2k_md_target_temperature_tolerance>{})".format(self.cm.regex_f)),
- SM( " MD\| Pressure \[Bar\]\s+(?P<x_cp2k_md_target_pressure>{})".format(self.cm.regex_f)),
- SM( " MD\| Barostat time constant \[ fs\]\s+(?P<x_cp2k_md_barostat_time_constant>{})".format(self.cm.regex_f)),
- SM( " MD\| Print MD information every\s+(?P<x_cp2k_md_print_frequency>{}) step\(s\)".format(self.cm.regex_i)),
+ SM( " MD\| Ensemble Type\s+(?P<x_cp2k_md_ensemble_type>{})".format(self.regexs.regex_word)),
+ SM( " MD\| Number of Time Steps\s+(?P<x_cp2k_md_number_of_time_steps>{})".format(self.regexs.regex_i)),
+ SM( " MD\| Time Step \[fs\]\s+(?P<x_cp2k_md_time_step__fs>{})".format(self.regexs.regex_f)),
+ SM( " MD\| Temperature \[K\]\s+(?P<x_cp2k_md_target_temperature>{})".format(self.regexs.regex_f)),
+ SM( " MD\| Temperature tolerance \[K\]\s+(?P<x_cp2k_md_target_temperature_tolerance>{})".format(self.regexs.regex_f)),
+ SM( " MD\| Pressure \[Bar\]\s+(?P<x_cp2k_md_target_pressure>{})".format(self.regexs.regex_f)),
+ SM( " MD\| Barostat time constant \[ fs\]\s+(?P<x_cp2k_md_barostat_time_constant>{})".format(self.regexs.regex_f)),
+ SM( " MD\| Print MD information every\s+(?P<x_cp2k_md_print_frequency>{}) step\(s\)".format(self.regexs.regex_i)),
SM( " MD\| File type Print frequency\[steps\] File names"),
- SM( " MD\| Coordinates\s+(?P<x_cp2k_md_coordinates_print_frequency>{})\s+(?P<x_cp2k_md_coordinates_filename>{})".format(self.cm.regex_i, self.cm.regex_word)),
- SM( " MD\| Simulation Cel\s+(?P<x_cp2k_md_simulation_cell_print_frequency>{})\s+(?P<x_cp2k_md_simulation_cell_filename>{})".format(self.cm.regex_i, self.cm.regex_word)),
- SM( " MD\| Velocities\s+(?P<x_cp2k_md_velocities_print_frequency>{})\s+(?P<x_cp2k_md_velocities_filename>{})".format(self.cm.regex_i, self.cm.regex_word)),
- SM( " MD\| Energies\s+(?P<x_cp2k_md_energies_print_frequency>{})\s+(?P<x_cp2k_md_energies_filename>{})".format(self.cm.regex_i, self.cm.regex_word)),
- SM( " MD\| Dump\s+(?P<x_cp2k_md_dump_print_frequency>{})\s+(?P<x_cp2k_md_dump_filename>{})".format(self.cm.regex_i, self.cm.regex_word)),
+ SM( " MD\| Coordinates\s+(?P<x_cp2k_md_coordinates_print_frequency>{})\s+(?P<x_cp2k_md_coordinates_filename>{})".format(self.regexs.regex_i, self.regexs.regex_word)),
+ SM( " MD\| Simulation Cel\s+(?P<x_cp2k_md_simulation_cell_print_frequency>{})\s+(?P<x_cp2k_md_simulation_cell_filename>{})".format(self.regexs.regex_i, self.regexs.regex_word)),
+ SM( " MD\| Velocities\s+(?P<x_cp2k_md_velocities_print_frequency>{})\s+(?P<x_cp2k_md_velocities_filename>{})".format(self.regexs.regex_i, self.regexs.regex_word)),
+ SM( " MD\| Energies\s+(?P<x_cp2k_md_energies_print_frequency>{})\s+(?P<x_cp2k_md_energies_filename>{})".format(self.regexs.regex_i, self.regexs.regex_word)),
+ SM( " MD\| Dump\s+(?P<x_cp2k_md_dump_print_frequency>{})\s+(?P<x_cp2k_md_dump_filename>{})".format(self.regexs.regex_i, self.regexs.regex_word)),
]
),
SM( " ************************** Velocities initialization **************************".replace("*", "\*"),
@@ -84,14 +84,14 @@ class CP2KMDParser(MainHierarchicalParser):
subMatchers=[
self.cm.quickstep_calculation(),
SM( " ******************************** GO CP2K GO! **********************************".replace("*", "\*")),
- SM( " INITIAL POTENTIAL ENERGY\[hartree\] =\s+(?P<x_cp2k_md_potential_energy_instantaneous__hartree>{})".format(self.cm.regex_f)),
- SM( " INITIAL KINETIC ENERGY\[hartree\] =\s+(?P<x_cp2k_md_kinetic_energy_instantaneous__hartree>{})".format(self.cm.regex_f)),
- SM( " INITIAL TEMPERATURE\[K\] =\s+(?P<x_cp2k_md_temperature_instantaneous>{})".format(self.cm.regex_f)),
- SM( " INITIAL BAROSTAT TEMP\[K\] =\s+(?P<x_cp2k_md_barostat_temperature_instantaneous>{})".format(self.cm.regex_f)),
- SM( " INITIAL PRESSURE\[bar\] =\s+(?P<x_cp2k_md_pressure_instantaneous__bar>{})".format(self.cm.regex_f)),
- SM( " INITIAL VOLUME\[bohr\^3\] =\s+(?P<x_cp2k_md_volume_instantaneous__bohr3>{})".format(self.cm.regex_f)),
- SM( " INITIAL CELL LNTHS\[bohr\] =\s+(?P<x_cp2k_md_cell_length_a_instantaneous__bohr>{0})\s+(?P<x_cp2k_md_cell_length_b_instantaneous__bohr>{0})\s+(?P<x_cp2k_md_cell_length_c_instantaneous__bohr>{0})".format(self.cm.regex_f)),
- SM( " INITIAL CELL ANGLS\[deg\] =\s+(?P<x_cp2k_md_cell_angle_a_instantaneous__deg>{0})\s+(?P<x_cp2k_md_cell_angle_b_instantaneous__deg>{0})\s+(?P<x_cp2k_md_cell_angle_c_instantaneous__deg>{0})".format(self.cm.regex_f)),
+ SM( " INITIAL POTENTIAL ENERGY\[hartree\] =\s+(?P<x_cp2k_md_potential_energy_instantaneous__hartree>{})".format(self.regexs.regex_f)),
+ SM( " INITIAL KINETIC ENERGY\[hartree\] =\s+(?P<x_cp2k_md_kinetic_energy_instantaneous__hartree>{})".format(self.regexs.regex_f)),
+ SM( " INITIAL TEMPERATURE\[K\] =\s+(?P<x_cp2k_md_temperature_instantaneous>{})".format(self.regexs.regex_f)),
+ SM( " INITIAL BAROSTAT TEMP\[K\] =\s+(?P<x_cp2k_md_barostat_temperature_instantaneous>{})".format(self.regexs.regex_f)),
+ SM( " INITIAL PRESSURE\[bar\] =\s+(?P<x_cp2k_md_pressure_instantaneous__bar>{})".format(self.regexs.regex_f)),
+ SM( " INITIAL VOLUME\[bohr\^3\] =\s+(?P<x_cp2k_md_volume_instantaneous__bohr3>{})".format(self.regexs.regex_f)),
+ SM( " INITIAL CELL LNTHS\[bohr\] =\s+(?P<x_cp2k_md_cell_length_a_instantaneous__bohr>{0})\s+(?P<x_cp2k_md_cell_length_b_instantaneous__bohr>{0})\s+(?P<x_cp2k_md_cell_length_c_instantaneous__bohr>{0})".format(self.regexs.regex_f)),
+ SM( " INITIAL CELL ANGLS\[deg\] =\s+(?P<x_cp2k_md_cell_angle_a_instantaneous__deg>{0})\s+(?P<x_cp2k_md_cell_angle_b_instantaneous__deg>{0})\s+(?P<x_cp2k_md_cell_angle_c_instantaneous__deg>{0})".format(self.regexs.regex_f)),
],
adHoc=self.adHoc_save_md_quickstep()
),
@@ -105,20 +105,20 @@ class CP2KMDParser(MainHierarchicalParser):
self.cm.quickstep_calculation(),
SM( " ENSEMBLE TYPE ="),
SM( " STEP NUMBER ="),
- SM( " TIME \[fs\] =\s+(?P<x_cp2k_md_time__fs>{})".format(self.cm.regex_f)),
- SM( " CONSERVED QUANTITY \[hartree\] =\s+(?P<x_cp2k_md_conserved_quantity__hartree>{})".format(self.cm.regex_f)),
- SM( " CPU TIME \[s\] =\s+(?P<x_cp2k_md_cpu_time_instantaneous>{})\s+(?P<x_cp2k_md_cpu_time_average>{})".format(self.cm.regex_f, self.cm.regex_f)),
- SM( " ENERGY DRIFT PER ATOM \[K\] =\s+(?P<x_cp2k_md_energy_drift_instantaneous>{})\s+(?P<x_cp2k_md_energy_drift_average>{})".format(self.cm.regex_f, self.cm.regex_f)),
- SM( " POTENTIAL ENERGY\[hartree\] =\s+(?P<x_cp2k_md_potential_energy_instantaneous__hartree>{})\s+(?P<x_cp2k_md_potential_energy_average__hartree>{})".format(self.cm.regex_f, self.cm.regex_f)),
- SM( " KINETIC ENERGY \[hartree\] =\s+(?P<x_cp2k_md_kinetic_energy_instantaneous__hartree>{})\s+(?P<x_cp2k_md_kinetic_energy_average__hartree>{})".format(self.cm.regex_f, self.cm.regex_f)),
- SM( " TEMPERATURE \[K\] =\s+(?P<x_cp2k_md_temperature_instantaneous>{})\s+(?P<x_cp2k_md_temperature_average>{})".format(self.cm.regex_f, self.cm.regex_f)),
- SM( " PRESSURE \[bar\] =\s+(?P<x_cp2k_md_pressure_instantaneous__bar>{0})\s+(?P<x_cp2k_md_pressure_average__bar>{0})".format(self.cm.regex_f)),
- SM( " BAROSTAT TEMP\[K\] =\s+(?P<x_cp2k_md_barostat_temperature_instantaneous>{0})\s+(?P<x_cp2k_md_barostat_temperature_average>{0})".format(self.cm.regex_f)),
- SM( " VOLUME\[bohr\^3\] =\s+(?P<x_cp2k_md_volume_instantaneous__bohr3>{0})\s+(?P<x_cp2k_md_volume_average__bohr3>{0})".format(self.cm.regex_f)),
- SM( " CELL LNTHS\[bohr\] =\s+(?P<x_cp2k_md_cell_length_a_instantaneous__bohr>{0})\s+(?P<x_cp2k_md_cell_length_b_instantaneous__bohr>{0})\s+(?P<x_cp2k_md_cell_length_c_instantaneous__bohr>{0})".format(self.cm.regex_f)),
- SM( " AVE. CELL LNTHS\[bohr\] =\s+(?P<x_cp2k_md_cell_length_a_average__bohr>{0})\s+(?P<x_cp2k_md_cell_length_b_average__bohr>{0})\s+(?P<x_cp2k_md_cell_length_c_average__bohr>{0})".format(self.cm.regex_f)),
- SM( " CELL ANGLS\[deg\] =\s+(?P<x_cp2k_md_cell_angle_a_instantaneous__deg>{0})\s+(?P<x_cp2k_md_cell_angle_b_instantaneous__deg>{0})\s+(?P<x_cp2k_md_cell_angle_c_instantaneous__deg>{0})".format(self.cm.regex_f)),
- SM( " AVE. CELL ANGLS\[deg\] =\s+(?P<x_cp2k_md_cell_angle_a_average__deg>{0})\s+(?P<x_cp2k_md_cell_angle_b_average__deg>{0})\s+(?P<x_cp2k_md_cell_angle_c_average__deg>{0})".format(self.cm.regex_f)),
+ SM( " TIME \[fs\] =\s+(?P<x_cp2k_md_time__fs>{})".format(self.regexs.regex_f)),
+ SM( " CONSERVED QUANTITY \[hartree\] =\s+(?P<x_cp2k_md_conserved_quantity__hartree>{})".format(self.regexs.regex_f)),
+ SM( " CPU TIME \[s\] =\s+(?P<x_cp2k_md_cpu_time_instantaneous>{})\s+(?P<x_cp2k_md_cpu_time_average>{})".format(self.regexs.regex_f, self.regexs.regex_f)),
+ SM( " ENERGY DRIFT PER ATOM \[K\] =\s+(?P<x_cp2k_md_energy_drift_instantaneous>{})\s+(?P<x_cp2k_md_energy_drift_average>{})".format(self.regexs.regex_f, self.regexs.regex_f)),
+ SM( " POTENTIAL ENERGY\[hartree\] =\s+(?P<x_cp2k_md_potential_energy_instantaneous__hartree>{})\s+(?P<x_cp2k_md_potential_energy_average__hartree>{})".format(self.regexs.regex_f, self.regexs.regex_f)),
+ SM( " KINETIC ENERGY \[hartree\] =\s+(?P<x_cp2k_md_kinetic_energy_instantaneous__hartree>{})\s+(?P<x_cp2k_md_kinetic_energy_average__hartree>{})".format(self.regexs.regex_f, self.regexs.regex_f)),
+ SM( " TEMPERATURE \[K\] =\s+(?P<x_cp2k_md_temperature_instantaneous>{})\s+(?P<x_cp2k_md_temperature_average>{})".format(self.regexs.regex_f, self.regexs.regex_f)),
+ SM( " PRESSURE \[bar\] =\s+(?P<x_cp2k_md_pressure_instantaneous__bar>{0})\s+(?P<x_cp2k_md_pressure_average__bar>{0})".format(self.regexs.regex_f)),
+ SM( " BAROSTAT TEMP\[K\] =\s+(?P<x_cp2k_md_barostat_temperature_instantaneous>{0})\s+(?P<x_cp2k_md_barostat_temperature_average>{0})".format(self.regexs.regex_f)),
+ SM( " VOLUME\[bohr\^3\] =\s+(?P<x_cp2k_md_volume_instantaneous__bohr3>{0})\s+(?P<x_cp2k_md_volume_average__bohr3>{0})".format(self.regexs.regex_f)),
+ SM( " CELL LNTHS\[bohr\] =\s+(?P<x_cp2k_md_cell_length_a_instantaneous__bohr>{0})\s+(?P<x_cp2k_md_cell_length_b_instantaneous__bohr>{0})\s+(?P<x_cp2k_md_cell_length_c_instantaneous__bohr>{0})".format(self.regexs.regex_f)),
+ SM( " AVE. CELL LNTHS\[bohr\] =\s+(?P<x_cp2k_md_cell_length_a_average__bohr>{0})\s+(?P<x_cp2k_md_cell_length_b_average__bohr>{0})\s+(?P<x_cp2k_md_cell_length_c_average__bohr>{0})".format(self.regexs.regex_f)),
+ SM( " CELL ANGLS\[deg\] =\s+(?P<x_cp2k_md_cell_angle_a_instantaneous__deg>{0})\s+(?P<x_cp2k_md_cell_angle_b_instantaneous__deg>{0})\s+(?P<x_cp2k_md_cell_angle_c_instantaneous__deg>{0})".format(self.regexs.regex_f)),
+ SM( " AVE. CELL ANGLS\[deg\] =\s+(?P<x_cp2k_md_cell_angle_a_average__deg>{0})\s+(?P<x_cp2k_md_cell_angle_b_average__deg>{0})\s+(?P<x_cp2k_md_cell_angle_c_average__deg>{0})".format(self.regexs.regex_f)),
],
adHoc=self.adHoc_save_md_quickstep()
),
diff --git a/parser/parser-cp2k/cp2kparser/versions/cp2k262/singlepointparser.py b/parser/parser-cp2k/cp2kparser/versions/cp2k262/singlepointparser.py
index 2a0bc1b8a5341c317db5aa3b2a82ac97dc2be3f7..29a3913dfa90f3b76227ac57cf65ef0528919a28 100644
--- a/parser/parser-cp2k/cp2kparser/versions/cp2k262/singlepointparser.py
+++ b/parser/parser-cp2k/cp2kparser/versions/cp2k262/singlepointparser.py
@@ -3,7 +3,7 @@ from nomadcore.simple_parser import SimpleMatcher as SM
from nomadcore.baseclasses import MainHierarchicalParser
from .singlepointforceparser import CP2KSinglePointForceParser
from nomadcore.caching_backend import CachingLevel
-from .commonmatcher import CommonMatcher
+from .commonmatcher import CP2KCommonMatcher
import logging
logger = logging.getLogger("nomad")
@@ -18,11 +18,11 @@ class CP2KSinglePointParser(MainHierarchicalParser):
"""
"""
super(CP2KSinglePointParser, self).__init__(file_path, parser_context)
- self.setup_common_matcher(CommonMatcher(parser_context))
+ self.setup_common_matcher(CP2KCommonMatcher(parser_context))
#=======================================================================
# Cache levels
- self.caching_level_for_metaname.update({
+ self.caching_levels.update({
'x_cp2k_energy_total_scf_iteration': CachingLevel.ForwardAndCache,
'x_cp2k_energy_XC_scf_iteration': CachingLevel.ForwardAndCache,
'x_cp2k_energy_change_scf_iteration': CachingLevel.ForwardAndCache,
diff --git a/parser/parser-cp2k/cp2kparser/versions/versionsetup.py b/parser/parser-cp2k/cp2kparser/versions/versionsetup.py
deleted file mode 100644
index 6bbd36446678b2e1f49b59fbeea2c89f32578be9..0000000000000000000000000000000000000000
--- a/parser/parser-cp2k/cp2kparser/versions/versionsetup.py
+++ /dev/null
@@ -1,62 +0,0 @@
-import importlib
-import logging
-logger = logging.getLogger("nomad")
-
-
-#===============================================================================
-def get_main_parser(version_id, run_type):
- """
- Setups a main parser class for this calculation. The main class can be
- different for each version and run type.
-
- Args:
- version_id: An integer representing the CP2K version. The version
- number is originally a string the form '2.6.2', but here the numbers
- are just concatenated into a single integer number 262.
- run_type: A string that identifies the RUN_TYPE for the calculation.
- All the possible run types can be found in the CP2K reference manual.
-
- Returns:
- A python class that should be instantiated later with the correct
- parameters.
- """
-
- # Search for a RUN_TYPE specific parser
- parser_map = {
- "ENERGY": "SinglePointParser",
- "ENERGY_FORCE": "SinglePointParser",
- "WAVEFUNCTION_OPTIMIZATION": "SinglePointParser",
- "WFN_OPT": "SinglePointParser",
- "GEO_OPT": "GeoOptParser",
- "GEOMETRY_OPTIMIZATION": "GeoOptParser",
- "MD": "MDParser",
- "MOLECULAR_DYNAMICS": "MDParser",
- }
- try:
- parser = parser_map[run_type]
- except KeyError:
- logger.exception("A parser corresponding to the run_type '{}' could not be found.".format(run_type))
- raise
-
- # Currently the version id is a pure integer, so it can directly be mapped
- # into a package name.
- base = "cp2kparser.versions.cp2k{}.{}".format(version_id, parser.lower())
- parser_module = None
- parser_class = None
- try:
- parser_module = importlib.import_module(base)
- except ImportError:
- logger.warning("Could not find a parser for version '{}' and run type '{}'. Trying to default to the base implementation for CP2K 2.6.2".format(version_id, run_type))
- base = "cp2kparser.versions.cp2k262.{}".format(parser.lower())
- try:
- parser_module = importlib.import_module(base)
- except ImportError:
- logger.exception("Tried to default to the CP2K 2.6.2 implementation but could not find the correct modules for run_type '{}'.".format(run_type))
- raise
- try:
- parser_class = getattr(parser_module, "CP2K{}".format(parser))
- except AttributeError:
- logger.exception("A parser class '{}' could not be found in the module '[]'.".format(parser_class, parser_module))
- raise
-
- return parser_class
diff --git a/test/unittests/cp2k_2.6.2/run_tests.py b/test/unittests/cp2k_2.6.2/run_tests.py
index 5c1c3d69e32f07fffff75ae946d292cacd022864..2cb0d12529c062c8cefdaa01d45b723f067c6a7c 100644
--- a/test/unittests/cp2k_2.6.2/run_tests.py
+++ b/test/unittests/cp2k_2.6.2/run_tests.py
@@ -1030,21 +1030,21 @@ if __name__ == '__main__':
logger.setLevel(logging.ERROR)
suites = []
- # suites.append(unittest.TestLoader().loadTestsFromTestCase(TestErrors))
- # suites.append(unittest.TestLoader().loadTestsFromTestCase(TestXCFunctional))
+ suites.append(unittest.TestLoader().loadTestsFromTestCase(TestErrors))
+ suites.append(unittest.TestLoader().loadTestsFromTestCase(TestXCFunctional))
suites.append(unittest.TestLoader().loadTestsFromTestCase(TestEnergyForce))
- # suites.append(unittest.TestLoader().loadTestsFromTestCase(TestStressTensorMethods))
- # suites.append(unittest.TestLoader().loadTestsFromTestCase(TestSelfInteractionCorrectionMethod))
- # suites.append(unittest.TestLoader().loadTestsFromTestCase(TestConfigurationPeriodicDimensions))
- # suites.append(unittest.TestLoader().loadTestsFromTestCase(TestSCFConvergence))
- # suites.append(unittest.TestLoader().loadTestsFromTestCase(TestForceFiles))
- # suites.append(unittest.TestLoader().loadTestsFromTestCase(TestPreprocessor))
- # suites.append(unittest.TestLoader().loadTestsFromTestCase(TestGeoOpt))
- # suites.append(unittest.TestLoader().loadTestsFromTestCase(TestGeoOptTrajFormats))
- # suites.append(unittest.TestLoader().loadTestsFromTestCase(TestGeoOptOptimizers))
- # suites.append(unittest.TestLoader().loadTestsFromTestCase(TestGeoOptTrajectory))
- # suites.append(unittest.TestLoader().loadTestsFromTestCase(TestMD))
- # suites.append(unittest.TestLoader().loadTestsFromTestCase(TestMDEnsembles))
- # suites.append(unittest.TestLoader().loadTestsFromTestCase(TestElectronicStructureMethod))
+ suites.append(unittest.TestLoader().loadTestsFromTestCase(TestStressTensorMethods))
+ suites.append(unittest.TestLoader().loadTestsFromTestCase(TestSelfInteractionCorrectionMethod))
+ suites.append(unittest.TestLoader().loadTestsFromTestCase(TestConfigurationPeriodicDimensions))
+ suites.append(unittest.TestLoader().loadTestsFromTestCase(TestSCFConvergence))
+ suites.append(unittest.TestLoader().loadTestsFromTestCase(TestForceFiles))
+ suites.append(unittest.TestLoader().loadTestsFromTestCase(TestPreprocessor))
+ suites.append(unittest.TestLoader().loadTestsFromTestCase(TestGeoOpt))
+ suites.append(unittest.TestLoader().loadTestsFromTestCase(TestGeoOptTrajFormats))
+ suites.append(unittest.TestLoader().loadTestsFromTestCase(TestGeoOptOptimizers))
+ suites.append(unittest.TestLoader().loadTestsFromTestCase(TestGeoOptTrajectory))
+ suites.append(unittest.TestLoader().loadTestsFromTestCase(TestMD))
+ suites.append(unittest.TestLoader().loadTestsFromTestCase(TestMDEnsembles))
+ suites.append(unittest.TestLoader().loadTestsFromTestCase(TestElectronicStructureMethod))
alltests = unittest.TestSuite(suites)
unittest.TextTestRunner(verbosity=0).run(alltests)