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Commit ad2dbd63 authored by Lauri Himanen's avatar Lauri Himanen
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Simplified parsing structure.

parent 7936bfae
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parser/parser-cp2k/cp2kparser/parsing/outputparsing.py
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......@@ -3,18 +3,6 @@ from nomadcore.caching_backend import CachingLevel
import numpy as np
#===============================================================================
class MetaInfo(object):
def __init__(self, name, description="", dtypeStr="c", shape=[], dependencies=[]):
self.name = name
self.description = description
self.dtypeStr = dtypeStr
self.shape = shape
if not isinstance(dependencies, list):
dependencies = [dependencies]
self.dependencies = dependencies
#===============================================================================
class CP2KOutputParser262(object):
"""The object that goes through the CP2K output file and parses everything
......@@ -33,124 +21,111 @@ class CP2KOutputParser262(object):
# Define the output parsing tree for this version
self.outputstructure = SM(
startReStr="",
sections=['section_run'],
subMatchers=[
# SM(
# sections=['cp2k_section_dbcsr'],
# startReStr=r" DBCSR\| Multiplication driver",
# ),
# SM(
# sections=['cp2k_section_startinformation'],
# startReStr=r"[\*\s]+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})",
# forwardMatch=True,
# subMatchers=[
# SM(
# startReStr=r"[\*\s]+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})",
# ),
# SM(
# startReStr=r" CP2K\| version string:\s+(?P<program_version>[\w\d\W\s]+)",
# sections=['program_info'],
# ),
# SM(
# startReStr=r" CP2K\| source code revision number:\s+svn:(?P<cp2k_svn_revision>\d+)",
# )
# ]
# ),
SM(
startReStr=r" DBCSR\| Multiplication driver",
endReStr="[.\*]+PROGRAM STOPPED IN",
required=True,
sections=['section_run'],
sections=["cp2k_section_cell"],
startReStr=" CELL\|",
forwardMatch=True,
subMatchers=[
SM(
startReStr=r"[\*\s]+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})",
startReStr=" CELL\| Vector a \[angstrom\]:\s+(?P<cp2k_cell_vector_a>[\d\.]+\s+[\d\.]+\s+[\d\.]+)+"
),
SM(
startReStr=r" CP2K\| version string:\s+(?P<program_version>[\w\d\W\s]+)",
startReStr=" CELL\| Vector b \[angstrom\]:\s+(?P<cp2k_cell_vector_b>[\d\.]+\s+[\d\.]+\s+[\d\.]+)+"
),
SM(
startReStr=r" CP2K\| source code revision number:\s+svn:(?P<cp2k_svn_revision>\d+)",
startReStr=" CELL\| Vector c \[angstrom\]:\s+(?P<cp2k_cell_vector_c>[\d\.]+\s+[\d\.]+\s+[\d\.]+)+"
),
]
),
SM(
sections=["cp2k_section_functional"],
startReStr=" FUNCTIONAL\|",
forwardMatch=True,
otherMetaInfo=["XC_functional"],
subMatchers=[
SM(
repeats=True,
startReStr=" FUNCTIONAL\| (?P<cp2k_functional_name>[\w\d\W]+):"
)
]
),
SM(
sections=["cp2k_section_total_numbers"],
startReStr=" TOTAL NUMBERS AND MAXIMUM NUMBERS",
subMatchers=[
SM(
startReStr="\s+- Atoms:\s+(?P<number_of_atoms>\d+)",
sections=["section_system_description"]
),
# System Description
SM(
startReStr="",
sections=["cp2k_system_description"],
otherMetaInfo=["number_of_atoms"],
dependencies={"atom_number": ["cp2k_atom_number"]},
startReStr="\s+- Shell sets:\s+(?P<cp2k_shell_sets>\d+)"
)
]
),
SM(
sections=["cp2k_section_md"],
startReStr=" MD| Molecular Dynamics Protocol",
forwardMatch=True,
subMatchers=[
SM(
repeats=True,
startReStr=" ENERGY\| Total FORCE_EVAL",
sections=["cp2k_section_md_step"],
subMatchers=[
SM(
startReStr=" CELL\|",
forwardMatch=True,
sections=["cp2k_section_cell"],
subMatchers=[
SM(
startReStr=" CELL\| Vector a \[angstrom\]:\s+(?P<cp2k_cell_vector_a>[\d\.]+\s+[\d\.]+\s+[\d\.]+)+"
),
SM(
startReStr=" CELL\| Vector b \[angstrom\]:\s+(?P<cp2k_cell_vector_b>[\d\.]+\s+[\d\.]+\s+[\d\.]+)+"
),
SM(
startReStr=" CELL\| Vector c \[angstrom\]:\s+(?P<cp2k_cell_vector_c>[\d\.]+\s+[\d\.]+\s+[\d\.]+)+"
),
]
),
SM(
startReStr=" FUNCTIONAL\|",
forwardMatch=True,
sections=["section_method", "cp2k_section_functionals"],
otherMetaInfo=["XC_functional"],
startReStr=" ATOMIC FORCES in \[a\.u\.\]",
sections=["cp2k_section_md_forces"],
subMatchers=[
SM(
startReStr="\s+\d+\s+\d+\s+[\w\W\d]+\s+(?P<cp2k_md_force_atom_string>{0}\s+{0}\s+{0})".format(self.f_regex),
sections=["cp2k_section_md_force_atom"],
repeats=True,
startReStr=" FUNCTIONAL\| (?P<cp2k_functional_name>[\w\d\W]+):"
)
]
),
# SM(
# startReStr=" MODULE QUICKSTEP: ATOMIC COORDINATES IN angstrom",
# subMatchers=[
# SM(
# repeats=True,
# startReStr="\s+\d+\s+\d+\s+(?P<cp2k_atom_label>\w+)\s+\d+\s+{}\s+{}\s+{}".format(self.f_regex)
# )
# ]
# )
SM(
startReStr=" TOTAL NUMBERS AND MAXIMUM NUMBERS",
sections=["cp2k_section_numbers"],
subMatchers=[
SM(
startReStr="\s+- Atoms:\s+(?P<cp2k_atom_number>\d+)"
),
SM(
startReStr="\s+- Shell sets:\s+(?P<cp2k_shell_sets>\d+)"
)
]
)
]
),
# Molecular Dynamics
SM(
startReStr=" MD| Molecular Dynamics Protocol",
forwardMatch=True,
sections=["cp2k_section_md"],
subMatchers=[
startReStr=" STEP NUMBER\s+=\s+(?P<cp2k_md_step_number>\d+)"
),
SM(
startReStr=" TIME \[fs\]\s+=\s+(?P<cp2k_md_step_time>\d+\.\d+)"
),
SM(
startReStr=" TEMPERATURE \[K\]\s+=\s+(?P<cp2k_md_temperature_instantaneous>{0})\s+(?P<cp2k_md_temperature_average>{0})".format(self.f_regex)
),
SM(
repeats=True,
startReStr=" ENERGY\| Total FORCE_EVAL",
sections=["cp2k_section_md_step"],
startReStr=" i =",
sections=["cp2k_section_md_coordinates"],
otherMetaInfo=["cp2k_md_coordinates"],
dependencies={"cp2k_md_coordinates": ["cp2k_md_coordinate_atom_string"]},
subMatchers=[
SM(
startReStr=" ATOMIC FORCES in \[a\.u\.\]",
sections=["cp2k_section_md_forces"],
subMatchers=[
SM(
startReStr="\s+\d+\s+\d+\s+[\w\W\d]+\s+(?P<cp2k_md_force_atom_string>{0}\s+{0}\s+{0})".format(self.f_regex),
sections=["cp2k_section_md_force_atom"],
repeats=True,
)
]
),
SM(
startReStr=" STEP NUMBER\s+=\s+(?P<cp2k_md_step_number>\d+)"
),
SM(
startReStr=" TIME \[fs\]\s+=\s+(?P<cp2k_md_step_time>\d+\.\d+)"
),
SM(
startReStr=" TEMPERATURE \[K\]\s+=\s+(?P<cp2k_md_temperature_instantaneous>{0})\s+(?P<cp2k_md_temperature_average>{0})".format(self.f_regex)
),
SM(
startReStr=" i =",
sections=["cp2k_section_md_coordinates"],
otherMetaInfo=["cp2k_md_coordinates"],
dependencies={"cp2k_md_coordinates": ["cp2k_md_coordinate_atom_string"]},
subMatchers=[
SM(
startReStr=" \w+\s+(?P<cp2k_md_coordinate_atom_string>{0}\s+{0}\s+{0})".format(self.f_regex),
endReStr="\n",
sections=["cp2k_section_md_coordinate_atom"],
repeats=True,
)
]
startReStr=" \w+\s+(?P<cp2k_md_coordinate_atom_string>{0}\s+{0}\s+{0})".format(self.f_regex),
endReStr="\n",
sections=["cp2k_section_md_coordinate_atom"],
repeats=True,
)
]
)
......@@ -160,14 +135,13 @@ class CP2KOutputParser262(object):
)
]
)
#=======================================================================
# The cache settings
self.cachingLevelForMetaName = {
'cp2k_cell_vector_a': CachingLevel.Cache,
'cp2k_cell_vector_b': CachingLevel.Cache,
'cp2k_cell_vector_c': CachingLevel.Cache,
'cp2k_section_cell': CachingLevel.Cache,
'cp2k_system_description': CachingLevel.Cache,
'cp2k_section_atom_position': CachingLevel.Cache,
'cp2k_functional_name': CachingLevel.Cache,
'cp2k_section_functionals': CachingLevel.Cache,
'cp2k_section_numbers': CachingLevel.Cache,
......@@ -185,49 +159,36 @@ class CP2KOutputParser262(object):
'cp2k_md_force_atom_float': CachingLevel.Cache,
}
# The trigger functions
def onClose_cp2k_system_description(self, backend, gIndex, section):
#===========================================================================
# The functions that trigger when sections are closed
def onClose_cp2k_section_cell(self, backend, gIndex, section):
"""When the cell definition finishes, gather the results to a 3x3
matrix. Or if not present, ask the cp2kparser for help.
"""
# Open the common system description section
backend.openSection("section_system_description")
# Get the cell information
cell = section["cp2k_section_cell"]
if cell:
cell = cell[0]
gIndex = backend.openSection("section_system_description")
# Get the cell vector strings
a = cell["cp2k_cell_vector_a"][0]
b = cell["cp2k_cell_vector_b"][0]
c = cell["cp2k_cell_vector_c"][0]
# Get the cell vector strings
a = section["cp2k_cell_vector_a"][0]
b = section["cp2k_cell_vector_b"][0]
c = section["cp2k_cell_vector_c"][0]
# Extract the components and put into numpy array
a_comp = a.split()
b_comp = b.split()
c_comp = c.split()
# Extract the components and put into numpy array
a_comp = a.split()
b_comp = b.split()
c_comp = c.split()
cell = np.zeros((3, 3))
cell[0, :] = a_comp
cell[1, :] = b_comp
cell[2, :] = c_comp
cell = np.zeros((3, 3))
cell[0, :] = a_comp
cell[1, :] = b_comp
cell[2, :] = c_comp
backend.addArrayValues("simulation_cell", cell, unit="angstrom")
# Get the number of atoms
numbers = section["cp2k_section_numbers"]
if numbers:
numbers = numbers[0]
n_atoms = numbers["cp2k_atom_number"]
if n_atoms:
n_atoms = n_atoms[0]
backend.addValue("number_of_atoms", n_atoms)
backend.addArrayValues("simulation_cell", cell, unit="angstrom")
# Close the common system description section
backend.closeSection("section_system_description", 0)
backend.closeSection("section_system_description", gIndex)
def onClose_cp2k_section_functionals(self, backend, gIndex, section):
def onClose_cp2k_section_functional(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.
......@@ -253,12 +214,14 @@ class CP2KOutputParser262(object):
functionals = "_".join(sorted(functionals))
# Push the functional string into the backend
gIndex = backend.openSection("section_method")
backend.addValue('XC_functional', functionals)
backend.closeSection("section_method", gIndex)
def onClose_cp2k_section_atom_position(self, backend, gIndex, section):
"""Get the initial atomic positions from cp2kparser.
"""
pass
# def onClose_cp2k_section_atom_position(self, backend, gIndex, section):
# """Get the initial atomic positions from cp2kparser.
# """
# pass
# positions, unit = self.cp2kparser.get_initial_atom_positions_and_unit()
# backend.addArrayValues("atom_position", positions)
......@@ -295,3 +258,6 @@ class CP2KOutputParser262(object):
forces = section["cp2k_md_force_atom_float"]
forces = np.array(forces)
backend.addArrayValues("cp2k_md_forces", forces, unit="force_au")
#===========================================================================
# adHoc functions that are used to do custom parsing.
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