From d2ec7d43141f028be89799733d7e2c6e634083e8 Mon Sep 17 00:00:00 2001
From: Aliaksei Mazheika <mazh@labdev-nomad.esc.rzg.mpg.de>
Date: Tue, 27 Sep 2016 18:19:28 +0200
Subject: [PATCH] Eigenvalues, occupations, irrep's were fixed
---
parser/parser-turbomole/TurbomoleParser.py | 87 ++++++++++++++--------
1 file changed, 56 insertions(+), 31 deletions(-)
diff --git a/parser/parser-turbomole/TurbomoleParser.py b/parser/parser-turbomole/TurbomoleParser.py
index 1f99699..e3543c2 100644
--- a/parser/parser-turbomole/TurbomoleParser.py
+++ b/parser/parser-turbomole/TurbomoleParser.py
@@ -9,6 +9,9 @@ from nomadcore.simple_parser import AncillaryParser, mainFunction
from nomadcore.simple_parser import SimpleMatcher as SM
from TurbomoleCommon import get_metaInfo
import logging, os, re, sys
+from nomadcore.unit_conversion.unit_conversion import convert_unit_function
+
+eV2J = convert_unit_function("eV","J")
############################################################
# This is the parser for the main file of turbomole.
@@ -32,6 +35,21 @@ class TurbomoleParserContext(object):
self.lastCalculationGIndex = None
self.singleConfCalcs = []
self.geoConvergence = None
+ self.eigenvalues = []
+ self.occupation = []
+ self.evSymm = []
+ self.alphaEv = None
+
+ def switchEVSpins(self):
+ """stores alpha spin and prepares for beta spin"""
+ self.alphaEv = {
+ 'eigenvalues': self.eigenvalues,
+ 'occupation': self.occupation,
+ 'evSymm': self.evSymm
+ }
+ self.eigenvalues = []
+ self.occupation = []
+ self.evSymm = []
def startedParsing(self, fInName, parser):
"""Function is called when the parsing starts.
@@ -49,6 +67,10 @@ class TurbomoleParserContext(object):
# allows to reset values if the same superContext is used to parse different files
self.initialize_values()
+ def onClose_section_eigenvalues(self, backend, gIndex, section):
+ """write eigenvalues to the backend and then cleans local storage"""
+ pass
+
def onClose_section_run(self, backend, gIndex, section):
if self.geoConvergence is not None:
@@ -154,30 +176,23 @@ class TurbomoleParserContext(object):
atom_labels[i] = atom_labels[i].capitalize()
backend.addArrayValues('atom_labels', np.asarray(atom_labels))
- def onClose_x_turbomole_section_irrep_list(self, backend, gIndex, section):
-
+ def onClose_x_turbomole_section_eigenvalues_list(self, backend, gIndex, section):
irrep_name = section['x_turbomole_irreducible_representation_state_str']
for item in range(len(irrep_name)):
Irrepresent = irrep_name[item].split()
- for i in range(len(Irrepresent)):
- backend.addValue('x_turbomole_irreducible_representation_state', Irrepresent[i])
-
- def onClose_x_turbomole_section_eigenvalues_list(self, backend, gIndex, section):
+ self.evSymm += Irrepresent
- s = backend.openSection("section_eigenvalues")
eigenvalues_name = section['x_turbomole_eigenvalue_eigenvalue_str']
for mem in range(len(eigenvalues_name)):
Eigenval = eigenvalues_name[mem].split()
- for t in range(len(Eigenval)):
- backend.addValue('eigenvalues_values', float(Eigenval[t])*1.602176565e-19)
+ self.eigenvalues += map(lambda x: eV2J(float(x)), Eigenval)
occupation_name = section['x_turbomole_eigenvalue_occupation_str']
if not occupation_name == None:
for ele in range(len(occupation_name)):
Occupat = occupation_name[ele].split()
- for e in range(len(Occupat)):
- backend.addValue('eigenvalues_occupation', float(Occupat[e]))
- backend.closeSection("section_eigenvalues", s)
+ self.occupation += map(float, Occupat)
+ self.occupation += [0.0 for i in range(len(self.evSymm)-len(self.occupation))]
def onOpen_section_single_configuration_calculation(self, backend, gIndex, section):
self.singleConfCalcs.append(gIndex)
@@ -295,22 +310,33 @@ def build_TurbomoleMainFileSimpleMatcher():
"(?P<x_turbomole_geometry_atom_labels>[a-zA-Z]+)\s+(?P<x_turbomole_geometry_atom_charge>[0-9.]+)", repeats = True)
])
])
- IrRepresentationSubMatcher = SM(name = 'IrRep',
- repeats =True,
- startReStr = r"\s*(?: alpha|beta)\:\s*",
- sections = ['x_turbomole_section_irrep_list'],
- subMatchers = [
- SM (r"\s*(?: irrep)\s*(?P<x_turbomole_irreducible_representation_state_str>[0-9a-z\s]+)", repeats = True)
- ])
EigenvaluesSubMatcher = SM(name = 'Eigenvalues',
- repeats =True,
- #startReStr = r"\s*(?: alpha|beta)\:\s*",
- startReStr = r"\s*eigenvalues H",
- endReStr = r"\s*irrep",
- sections = ['x_turbomole_section_eigenvalues_list'],
+ repeats = False,
+ sections = ["section_eigenvalues"],
+ startReStr = r"\s*(?:alpha:|(?: irrep)\s*(?P<x_turbomole_irreducible_representation_state_str>[0-9a-z\s]+))\s*",
+ forwardMatch = True,
subMatchers = [
- SM (r"\s*(?: eV)\s*(?P<x_turbomole_eigenvalue_eigenvalue_str>[-+0-9a-z.eEdD\s]+)", repeats = True),
- SM (r"\s*(?: occupation)\s*(?P<x_turbomole_eigenvalue_occupation_str>[0-9.\s]+)", repeats = True)
+ SM(r"\s*(?:alpha:)\s*"),
+ SM(r"\s*(?: irrep)\s*(?P<x_turbomole_irreducible_representation_state_str>[0-9a-z\s]+)",
+ repeats = True,
+ sections = ['x_turbomole_section_eigenvalues_list'],
+ subMatchers = [
+ SM(r"\s*eigenvalues H"),
+ SM (r"\s*(?: eV)\s*(?P<x_turbomole_eigenvalue_eigenvalue_str>[-+0-9a-z.eEdD\s]+)", repeats = True),
+ SM (r"\s*(?: occupation)\s*(?P<x_turbomole_eigenvalue_occupation_str>[0-9.\s]+)", repeats = True)
+ ]),
+ SM(r"\s*(?:beta:)\s*",
+ adHoc = lambda parser: parser.superContext.switchEVSpins(),
+ subMatchers = [
+ SM(r"\s*(?: irrep)\s*(?P<x_turbomole_irreducible_representation_state_str>[0-9a-z\s]+)",
+ repeats = True,
+ sections = ['x_turbomole_section_eigenvalues_list'],
+ subMatchers = [
+ SM(r"\s*eigenvalues H"),
+ SM (r"\s*(?: eV)\s*(?P<x_turbomole_eigenvalue_eigenvalue_str>[-+0-9a-z.eEdD\s]+)", repeats = True),
+ SM (r"\s*(?: occupation)\s*(?P<x_turbomole_eigenvalue_occupation_str>[0-9.\s]+)", repeats = True)
+ ])
+ ])
])
########################################
# submatcher for atomic forces
@@ -419,7 +445,7 @@ def build_TurbomoleMainFileSimpleMatcher():
RelaxationSubMatcher = SM (name = "relaxation",
#sections = ["section_single_configuration_calculation"],
- sections = ["section_single_configuration_calculation","section_run"],
+ sections = ["section_single_configuration_calculation"],
startReStr = r"\s*CONVERGENCY CRITERIA (?P<x_turbomole_geometry_optimization_converged>FULFILLED) IN CYCLE",
subMatchers = [])
########################################
@@ -531,7 +557,6 @@ def build_TurbomoleMainFileSimpleMatcher():
SM (name = 'PeriodicEmbeddingSettings',
startReStr = r"\s*\|\s*EMBEDDING IN PERIODIC POINT CHARGES\s*\|",
#sections = ['section_method'],
- sections = ['section_run'],
subMatchers = [
#SmearingOccupation,
EmbeddingSubMatcher
@@ -545,10 +570,10 @@ def build_TurbomoleMainFileSimpleMatcher():
#SmearingOccupation,
TotalEnergyScfSubMatcher,
TotalEnergySubMatcher#,
- ])#, # END ScfInitialization
+ ]), # END ScfInitialization
+ EigenvaluesSubMatcher,
+ ForcesMatcher,
]), # END SingleConfigurationCalculation
- EigenvaluesSubMatcher,
- ForcesMatcher,
SM (name = 'PostHFTotalEnergies',
startReStr = r"\s*Energy of reference wave function is",
sections = ['section_single_configuration_calculation','section_scf_iteration'],
--
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