def yaml_read_irred_perts(filename, doc_tag="!IrredPerts"):
"""Read the lisr of irreducible perturbations from file."""
with YamlTokenizer(filename) as r:
doc = r.next_doc_with_tag(doc_tag)
d = myaml.load(doc.text_notag)
return d["irred_perts"]
def yaml_read_kpoints(filename, doc_tag="!Kpoints"):
"""Read the K-points from file."""
with YamlTokenizer(filename) as r:
doc = r.next_doc_with_tag(doc_tag)
d = myaml.load(doc.text_notag)
return np.array(d["reduced_coordinates_of_qpoints"])
def yaml_read_irred_perts(filename, doc_tag="!IrredPerts"):
"""Read the lisr of irreducible perturbations from file."""
with YamlTokenizer(filename) as r:
doc = r.next_doc_with_tag(doc_tag)
d = myaml.load(doc.text_notag)
return d["irred_perts"]
def yaml_read_kpoints(filename, doc_tag="!Kpoints"):
"""Read the K-points from file."""
with YamlTokenizer(filename) as r:
doc = r.next_doc_with_tag(doc_tag)
d = myaml.load(doc.text_notag)
return np.array(d["reduced_coordinates_of_qpoints"])
def parse(filename):
"""
This is the new parser, it will be used when we implement
the new format in abinit.
"""
run_completed = False
filename = os.path.abspath(filename)
report = EventReport(filename)
# TODO Use CamelCase for the Fortran messages.
w = WildCard("*Error|*Warning|*Comment|*ERROR|*WARNING|*COMMENT")
with YamlTokenizer(filename) as tokens:
for doc in tokens:
#print(80*"*")
#print("doc.tag", doc.tag)
#print("doc",doc)
#print(80*"*")
if w.match(doc.tag):
#print("got doc.tag", doc.tag,"--")
try:
event = myaml.load(doc.text)
except:
# Wrong YAML doc. Check tha doc tag and instantiate the proper event.
message = "Malformatted YAML document at line: %d\n" % doc.lineno
message += doc.text
# This call is very expensive when we have many exceptions due to malformatted YAML docs.
#message += "Traceback:\n %s" % straceback()
if "error" in doc.tag.lower():
print("It seems an error", doc.tag)
event = AbinitYamlError(message=message,
src_file=__file__,
src_line=0)
else:
event = AbinitYamlWarning(message=message,
src_file=__file__,
src_line=0)
event.lineno = doc.lineno
report.append(event)
# Check whether the calculation completed.
if doc.tag == "!FinalSummary":
run_completed = True
# TODO: Add YAML doc with FinalSummary.
#MAGIC = "Calculation completed."
#with open(filename) as fh:
# for line in fh:
# if MAGIC in line:
# run_completed = True
# break
report.set_run_completed(run_completed)
return report
def parse(filename):
"""
This is the new parser, it will be used when we implement
the new format in abinit.
"""
run_completed = False
filename = os.path.abspath(filename)
report = EventReport(filename)
# TODO Use CamelCase for the Fortran messages.
w = WildCard("*Error|*Warning|*Comment|*ERROR|*WARNING|*COMMENT")
with YamlTokenizer(filename) as tokens:
for doc in tokens:
#print(80*"*")
#print("doc.tag", doc.tag)
#print("doc",doc)
#print(80*"*")
if w.match(doc.tag):
#print("got doc.tag", doc.tag,"--")
try:
event = myaml.load(doc.text)
except:
# Wrong YAML doc. Check tha doc tag and instantiate the proper event.
message = "Malformatted YAML document at line: %d\n" % doc.lineno
message += doc.text
# This call is very expensive when we have many exceptions due to malformatted YAML docs.
#message += "Traceback:\n %s" % straceback()
if "error" in doc.tag.lower():
print("It seems an error",doc.tag)
event = AbinitYamlError(message=message, src_file=__file__, src_line=0)
else:
event = AbinitYamlWarning(message=message, src_file=__file__, src_line=0)
event.lineno = doc.lineno
report.append(event)
# Check whether the calculation completed.
if doc.tag == "!FinalSummary":
run_completed = True
# TODO: Add YAML doc with FinalSummary.
#MAGIC = "Calculation completed."
#with open(filename) as fh:
# for line in fh:
# if MAGIC in line:
# run_completed = True
# break
report.set_run_completed(run_completed)
return report
def from_file(cls, filepath):
"""Read the configuration parameters from a Yaml file."""
with open(filepath, "r") as fh:
d = myaml.load(fh)
return cls(**d)
def from_file(cls, filepath):
"""Read the configuration parameters from a Yaml file."""
with open(filepath, "r") as fh:
d = myaml.load(fh)
return cls(**d)
