From 41dcc781aa4fe63380763e9acc100ed82b06a661 Mon Sep 17 00:00:00 2001
From: Lauri Himanen <lauri.himanen@aalto.fi>
Date: Tue, 27 Sep 2016 11:09:08 +0300
Subject: [PATCH] Added modules for vibration and properties calculation, fixed
issues with global cache having uninitialized values, fixedissues with empty
MD information.
---
parser/parser-cpmd/cpmdparser/parser.py | 12 +++++
.../versions/cpmd41/commonparser.py | 5 ++
.../cpmdparser/versions/cpmd41/inputparser.py | 4 --
.../cpmdparser/versions/cpmd41/mdparser.py | 35 +++++++------
.../versions/cpmd41/propertiesparser.py | 49 +++++++++++++++++++
.../versions/cpmd41/vibrationparser.py | 49 +++++++++++++++++++
6 files changed, 135 insertions(+), 19 deletions(-)
create mode 100644 parser/parser-cpmd/cpmdparser/versions/cpmd41/propertiesparser.py
create mode 100644 parser/parser-cpmd/cpmdparser/versions/cpmd41/vibrationparser.py
diff --git a/parser/parser-cpmd/cpmdparser/parser.py b/parser/parser-cpmd/cpmdparser/parser.py
index de76da8..476bedb 100644
--- a/parser/parser-cpmd/cpmdparser/parser.py
+++ b/parser/parser-cpmd/cpmdparser/parser.py
@@ -38,6 +38,8 @@ class CPMDParser(ParserInterface):
regex_single_point = re.compile(r" SINGLE POINT DENSITY OPTIMIZATION")
regex_geo_opt = re.compile(r" OPTIMIZATION OF IONIC POSITIONS")
regex_md = re.compile(r"( CAR-PARRINELLO MOLECULAR DYNAMICS)|( BORN-OPPENHEIMER MOLECULAR DYNAMICS)")
+ regex_vib = re.compile(r" PERFORM A VIBRATIONAL ANALYSIS BY FINITE DIFFERENCES")
+ regex_prop = re.compile(r" CALCULATE SOME PROPERTIES")
run_type = None
n_lines = 1000
version_id = None
@@ -68,6 +70,16 @@ class CPMDParser(ParserInterface):
if result_md:
run_type = CPMDRunType(module_name="mdparser", class_name="CPMDMDParser")
+ # Look for vibrational analysis
+ result_vib = regex_vib.match(line)
+ if result_vib:
+ run_type = CPMDRunType(module_name="vibrationparser", class_name="CPMDVibrationParser")
+
+ # Look for properties calculation
+ result_prop = regex_prop.match(line)
+ if result_prop:
+ run_type = CPMDRunType(module_name="propertiesparser", class_name="CPMDPropertiesParser")
+
if version_id is None:
msg = "Could not find a version specification from the given main file."
logger.exception(msg)
diff --git a/parser/parser-cpmd/cpmdparser/versions/cpmd41/commonparser.py b/parser/parser-cpmd/cpmdparser/versions/cpmd41/commonparser.py
index dfed5c7..718388d 100644
--- a/parser/parser-cpmd/cpmdparser/versions/cpmd41/commonparser.py
+++ b/parser/parser-cpmd/cpmdparser/versions/cpmd41/commonparser.py
@@ -30,6 +30,11 @@ class CPMDCommonParser(CommonParser):
self.cache_service.add("ensemble_type")
self.cache_service.add("time_step_ions")
+ self.cache_service.add("trajectory_range", False)
+ self.cache_service.add("trajectory_sample", False)
+ self.cache_service.add("print_freq", 1)
+ self.cache_service.add("configuration_periodic_dimensions", single=False, update=False)
+
#===========================================================================
# Common SimpleMatchers
def header(self):
diff --git a/parser/parser-cpmd/cpmdparser/versions/cpmd41/inputparser.py b/parser/parser-cpmd/cpmdparser/versions/cpmd41/inputparser.py
index 6c5f2ee..4535120 100644
--- a/parser/parser-cpmd/cpmdparser/versions/cpmd41/inputparser.py
+++ b/parser/parser-cpmd/cpmdparser/versions/cpmd41/inputparser.py
@@ -16,10 +16,6 @@ class CPMDInputParser(BasicParser):
"""
super(CPMDInputParser, self).__init__(file_path, parser_context)
self.input_tree = None
- self.cache_service.add("trajectory_range", False)
- self.cache_service.add("trajectory_sample", False)
- self.cache_service.add("print_freq", 1)
- self.cache_service.add("configuration_periodic_dimensions", single=False, update=False)
def parse(self):
self.setup_input_tree(self.parser_context.version_id)
diff --git a/parser/parser-cpmd/cpmdparser/versions/cpmd41/mdparser.py b/parser/parser-cpmd/cpmdparser/versions/cpmd41/mdparser.py
index e016d88..791a2b1 100644
--- a/parser/parser-cpmd/cpmdparser/versions/cpmd41/mdparser.py
+++ b/parser/parser-cpmd/cpmdparser/versions/cpmd41/mdparser.py
@@ -247,19 +247,24 @@ class CPMDMDParser(MainHierarchicalParser):
self.backend.closeSection("section_system", sys_id)
# Push the summaries
- potential_energies = np.array(potential_energies)
- self.backend.addArrayValues("frame_sequence_potential_energy", potential_energies, unit="hartree")
- kinetic_energies = np.array(kinetic_energies)
- self.backend.addArrayValues("frame_sequence_kinetic_energy", kinetic_energies, unit="hartree")
- conserved_quantities = np.array(conserved_quantities)
- self.backend.addArrayValues("frame_sequence_conserved_quantity", conserved_quantities, unit="hartree")
- temperatures = np.array(temperatures)
- self.backend.addArrayValues("frame_sequence_temperature", temperatures, unit="K")
+ if potential_energies:
+ potential_energies = np.array(potential_energies)
+ self.backend.addArrayValues("frame_sequence_potential_energy", potential_energies, unit="hartree")
+ if kinetic_energies:
+ kinetic_energies = np.array(kinetic_energies)
+ self.backend.addArrayValues("frame_sequence_kinetic_energy", kinetic_energies, unit="hartree")
- # Push the statistics. CPMD prints some statistics at the end, but the
- # mean and std of kinetic energy are missing
- kin_mean = kinetic_energies.mean()
- kin_temp = (kinetic_energies - kin_mean)
- kin_std = np.sqrt(np.dot(kin_temp, kin_temp)/kinetic_energies.size)
- kin_temp = None
- self.backend.addArrayValues("frame_sequence_kinetic_energy_stats", np.array([kin_mean, kin_std]), unit="hartree")
+ # Push the statistics. CPMD prints some statistics at the end, but the
+ # mean and std of kinetic energy are missing
+ kin_mean = kinetic_energies.mean()
+ kin_temp = (kinetic_energies - kin_mean)
+ kin_std = np.sqrt(np.dot(kin_temp, kin_temp)/kinetic_energies.size)
+ kin_temp = None
+ self.backend.addArrayValues("frame_sequence_kinetic_energy_stats", np.array([kin_mean, kin_std]), unit="hartree")
+
+ if conserved_quantities:
+ conserved_quantities = np.array(conserved_quantities)
+ self.backend.addArrayValues("frame_sequence_conserved_quantity", conserved_quantities, unit="hartree")
+ if temperatures:
+ temperatures = np.array(temperatures)
+ self.backend.addArrayValues("frame_sequence_temperature", temperatures, unit="K")
diff --git a/parser/parser-cpmd/cpmdparser/versions/cpmd41/propertiesparser.py b/parser/parser-cpmd/cpmdparser/versions/cpmd41/propertiesparser.py
new file mode 100644
index 0000000..61b5f10
--- /dev/null
+++ b/parser/parser-cpmd/cpmdparser/versions/cpmd41/propertiesparser.py
@@ -0,0 +1,49 @@
+from __future__ import absolute_import
+from nomadcore.simple_parser import SimpleMatcher as SM
+from nomadcore.baseclasses import MainHierarchicalParser
+import numpy as np
+from .commonparser import CPMDCommonParser
+import re
+import logging
+LOGGER = logging.getLogger("nomad")
+
+
+#===============================================================================
+class CPMDPropertiesParser(MainHierarchicalParser):
+ """The main parser class that is called for all run types. Parses the CPMD
+ output file.
+ """
+ def __init__(self, file_path, parser_context):
+ """
+ """
+ super(CPMDPropertiesParser, self).__init__(file_path, parser_context)
+ self.setup_common_matcher(CPMDCommonParser(parser_context))
+ self.n_frames = 0
+ self.sampling_method_gid = None
+ self.frame_refs = []
+ self.energies = []
+
+ #=======================================================================
+ # Main structure
+ self.root_matcher = SM("",
+ forwardMatch=True,
+ sections=['section_run', "section_method"],
+ subMatchers=[
+ self.cm.header(),
+ self.cm.method(),
+ self.cm.atoms(),
+ self.cm.cell(),
+ self.cm.initialization(),
+ self.cm.footer(),
+ ]
+ )
+
+ #=======================================================================
+ # onClose triggers
+ def onClose_section_system(self, backend, gIndex, section):
+ self.cache_service.addArrayValues("atom_labels")
+ self.cache_service.addArrayValues("simulation_cell", unit="bohr")
+ self.cache_service.addValue("number_of_atoms")
+
+ #=======================================================================
+ # adHoc
diff --git a/parser/parser-cpmd/cpmdparser/versions/cpmd41/vibrationparser.py b/parser/parser-cpmd/cpmdparser/versions/cpmd41/vibrationparser.py
new file mode 100644
index 0000000..93e825c
--- /dev/null
+++ b/parser/parser-cpmd/cpmdparser/versions/cpmd41/vibrationparser.py
@@ -0,0 +1,49 @@
+from __future__ import absolute_import
+from nomadcore.simple_parser import SimpleMatcher as SM
+from nomadcore.baseclasses import MainHierarchicalParser
+import numpy as np
+from .commonparser import CPMDCommonParser
+import re
+import logging
+LOGGER = logging.getLogger("nomad")
+
+
+#===============================================================================
+class CPMDVibrationParser(MainHierarchicalParser):
+ """The main parser class that is called for all run types. Parses the CPMD
+ output file.
+ """
+ def __init__(self, file_path, parser_context):
+ """
+ """
+ super(CPMDVibrationParser, self).__init__(file_path, parser_context)
+ self.setup_common_matcher(CPMDCommonParser(parser_context))
+ self.n_frames = 0
+ self.sampling_method_gid = None
+ self.frame_refs = []
+ self.energies = []
+
+ #=======================================================================
+ # Main structure
+ self.root_matcher = SM("",
+ forwardMatch=True,
+ sections=['section_run', "section_method"],
+ subMatchers=[
+ self.cm.header(),
+ self.cm.method(),
+ self.cm.atoms(),
+ self.cm.cell(),
+ self.cm.initialization(),
+ self.cm.footer(),
+ ]
+ )
+
+ #=======================================================================
+ # onClose triggers
+ def onClose_section_system(self, backend, gIndex, section):
+ self.cache_service.addArrayValues("atom_labels")
+ self.cache_service.addArrayValues("simulation_cell", unit="bohr")
+ self.cache_service.addValue("number_of_atoms")
+
+ #=======================================================================
+ # adHoc
--
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