def test_empty_file(self):
"""
make sure an empty file does not throw an error when reverse_readline
is called this was a problem with an earlier implementation
"""
with open(os.path.join(test_dir, "empty_file.txt")) as f:
for idx, line in enumerate(reverse_readline(f)):
raise ValueError("an empty file is being read!")
def test_empty_file(self):
"""
make sure an empty file does not throw an error when reverse_readline
is called this was a problem with an earlier implementation
"""
with open(os.path.join(test_dir, "empty_file.txt")) as f:
for idx, line in enumerate(reverse_readline(f)):
raise ValueError("an empty file is being read!")
def test_reverse_readline_fake_big(self):
"""
Make sure that large textfiles are read properly
"""
with open(os.path.join(test_dir, "3000_lines.txt"), "rt") as f:
for idx, line in enumerate(reverse_readline(f, max_mem=0)):
self.assertEqual(
int(line), self.NUMLINES - idx,
"read_backwards read {} whereas it should "
"have read {}".format(int(line), self.NUMLINES - idx))
def test_reverse_readline_fake_big(self):
"""
Make sure that large textfiles are read properly
"""
with open(os.path.join(test_dir, "3000_lines.txt")) as f:
for idx, line in enumerate(reverse_readline(f, max_mem=0)):
self.assertEqual(int(line), self.NUMLINES - idx,
"read_backwards read {} whereas it should "
"have read {}".format(
int(line), self.NUMLINES - idx))
def test_reverse_readline_bz2(self):
"""
We are making sure a file containing line numbers is read in reverse
order, i.e. the first line that is read corresponds to the last line.
number
"""
lines = []
with zopen(os.path.join(test_dir, "myfile_bz2.bz2"), "rb") as f:
for line in reverse_readline(f):
lines.append(line.strip())
self.assertEqual("HelloWorld.", lines[-1].strip())
def test_reverse_readline_bz2(self):
"""
We are making sure a file containing line numbers is read in reverse
order, i.e. the first line that is read corresponds to the last line.
number
"""
lines = []
with zopen(os.path.join(test_dir, "myfile_bz2.bz2"), "rb") as f:
for line in reverse_readline(f):
lines.append(line.strip())
self.assertEqual("HelloWorld.", lines[-1].strip())
def test_reverse_readfile_gz(self):
"""
We are making sure a file containing line numbers is read in reverse
order, i.e. the first line that is read corresponds to the last line.
number
"""
with open(os.path.join(test_dir, "three_thousand_lines.txt")) as f:
for idx, line in enumerate(reverse_readline(f)):
self.assertEqual(
int(line), self.NUMLINES - idx,
"read_backwards read {} whereas it should "
"have read {}".format(int(line), self.NUMLINES - idx))
def test_reverse_readline(self):
"""
We are making sure a file containing line numbers is read in reverse
order, i.e. the first line that is read corresponds to the last line.
number
"""
with open(os.path.join(test_dir, "3000_lines.txt")) as f:
for idx, line in enumerate(reverse_readline(f)):
self.assertEqual(int(line), self.NUMLINES - idx,
"read_backwards read {} whereas it should "
"have read {}".format(
int(line), self.NUMLINES - idx))
def track_file(self, launch_dir=None):
"""
Reads the monitored file and returns back the last N lines
:param launch_dir: directory where job was launched in case of relative filename
:return:
"""
m_file = self.filename
if launch_dir and not os.path.isabs(self.filename):
m_file = os.path.join(launch_dir, m_file)
lines = []
if os.path.exists(m_file):
with zopen(zpath(m_file)) as f:
for l in reverse_readline(f):
lines.append(l)
if len(lines) == self.nlines:
break
self.content = '\n'.join(reversed(lines))
return self.content
def track_file(self, launch_dir=None):
"""
Reads the monitored file and returns back the last N lines
:param launch_dir: directory where job was launched in case of relative filename
:return:
"""
m_file = self.filename
if launch_dir and not os.path.isabs(self.filename):
m_file = os.path.join(launch_dir, m_file)
lines = []
if os.path.exists(m_file):
with zopen(zpath(m_file)) as f:
for l in reverse_readline(f):
lines.append(l)
if len(lines) == self.nlines:
break
self.content = '\n'.join(reversed(lines))
return self.content
def track_file(self, launch_dir=None):
"""
Reads the monitored file and returns back the last N lines
Args:
launch_dir (str): directory where job was launched in case of relative filename
Returns:
str: the content(last N lines)
"""
m_file = self.filename
if launch_dir and not os.path.isabs(self.filename):
m_file = os.path.join(launch_dir, m_file)
lines = []
if self.allow_zipped:
m_file = zpath(m_file)
if os.path.exists(m_file):
with zopen(m_file, "rt") as f:
for l in reverse_readline(f):
lines.append(l)
if len(lines) == self.nlines:
break
self.content = '\n'.join(reversed(lines))
return self.content
def track_file(self, launch_dir=None):
"""
Reads the monitored file and returns back the last N lines
Args:
launch_dir (str): directory where job was launched in case of relative filename
Returns:
str: the content(last N lines)
"""
m_file = self.filename
if launch_dir and not os.path.isabs(self.filename):
m_file = os.path.join(launch_dir, m_file)
lines = []
if self.allow_zipped:
m_file = zpath(m_file)
if os.path.exists(m_file):
with zopen(m_file, "rt") as f:
for l in reverse_readline(f):
lines.append(l)
if len(lines) == self.nlines:
break
self.content = '\n'.join(reversed(lines))
return self.content
def _parse_logfile(self, logfile):
"""
Parse the formatted logfile.
"""
cycle_patt = re.compile(r"Coordinates\sin\sGeometry\sCycle\s(\d+)")
coord_patt = re.compile(r"\s+([0-9]+)\.([A-Za-z]+)" +
3 * r"\s+([-\.0-9]+)")
energy_patt = re.compile(
r"<.*>\s<.*>\s+current\senergy\s+([-\.0-9]+)\sHartree")
final_energy_patt = re.compile(
r"<.*>\s<.*>\s+Bond\sEnergy\s+([-\.0-9]+)\sa\.u\.")
error_patt = re.compile(r"<.*>\s<.*>\s+ERROR\sDETECTED:\s(.*)")
runtype_patt = re.compile(r"<.*>\s<.*>\s+RunType\s+:\s(.*)")
end_patt = re.compile(r"<.*>\s<.*>\s+END")
parse_cycle = False
sites = []
last_cycle = -1
parse_final = False
# Stop parsing the logfile is this job is not terminated successfully.
# The last non-empty line of the logfile must match the end pattern.
# Otherwise the job has some internal failure. The TAPE13 part of the
# ADF manual has a detailed explanantion.
with open(logfile) as f:
for line in reverse_readline(f):
if line == "":
continue
if end_patt.search(line) is None:
self.is_internal_crash = True
self.error = "Internal crash. TAPE13 is generated!"
self.is_failed = True
return
break
with open(logfile) as f:
for line in f:
m = error_patt.search(line)
if m:
self.is_failed = True
self.error = m.group(1)
break
if self.run_type is None:
m = runtype_patt.search(line)
if m:
if m.group(1) == "FREQUENCIES":
self.freq_type = "Numerical"
self.run_type = "NumericalFreq"
elif m.group(1) == "GEOMETRY OPTIMIZATION":
self.run_type = "GeometryOptimization"
elif m.group(1) == "CREATE":
self.run_type = None
elif m.group(1) == "SINGLE POINT":
self.run_type = "SinglePoint"
else:
raise AdfOutputError("Undefined Runtype!")
elif self.run_type == "SinglePoint":
m = coord_patt.search(line)
if m:
sites.append(
[m.groups()[0],
list(map(float,
m.groups()[2:]))])
else:
m = final_energy_patt.search(line)
if m:
self.final_energy = float(m.group(1))
self.final_structure = self._sites_to_mol(sites)
elif self.run_type == "GeometryOptimization":
m = cycle_patt.search(line)
if m:
cycle = int(m.group(1))
if cycle <= 0:
raise AdfOutputError(f"Wrong cycle {cycle}")
if cycle > last_cycle:
parse_cycle = True
last_cycle = cycle
else:
parse_final = True
elif parse_cycle:
m = coord_patt.search(line)
if m:
sites.append([
m.groups()[1],
list(map(float,
m.groups()[2:]))
])
else:
m = energy_patt.search(line)
if m:
self.energies.append(float(m.group(1)))
mol = self._sites_to_mol(sites)
self.structures.append(mol)
parse_cycle = False
sites = []
elif parse_final:
m = final_energy_patt.search(line)
if m:
self.final_energy = float(m.group(1))
elif self.run_type == "NumericalFreq":
break
if not self.is_failed:
if self.run_type == "GeometryOptimization":
if len(self.structures) > 0:
self.final_structure = self.structures[-1]
if self.final_energy is None:
raise AdfOutputError("The final energy can not be read!")
elif self.run_type == "SinglePoint":
if self.final_structure is None:
raise AdfOutputError("The final structure is missing!")
if self.final_energy is None:
raise AdfOutputError("The final energy can not be read!")
def _parse_logfile(self, logfile):
"""
Parse the formatted logfile.
"""
cycle_patt = re.compile(r"Coordinates\sin\sGeometry\sCycle\s(\d+)")
coord_patt = re.compile(r"\s+([0-9]+)\.([A-Za-z]+)"+3*r"\s+([-\.0-9]+)")
energy_patt = re.compile(r"<.*>\s<.*>\s+current\senergy\s+([-\.0-9]+)\s"
"Hartree")
final_energy_patt = re.compile(
r"<.*>\s<.*>\s+Bond\sEnergy\s+([-\.0-9]+)\sa\.u\.")
error_patt = re.compile(r"<.*>\s<.*>\s+ERROR\sDETECTED:\s(.*)")
runtype_patt = re.compile(r"<.*>\s<.*>\s+RunType\s+:\s(.*)")
end_patt = re.compile(r"<.*>\s<.*>\s+END")
parse_cycle = False
sites = []
last_cycle = -1
parse_final = False
# Stop parsing the logfile is this job is not terminated successfully.
# The last non-empty line of the logfile must match the end pattern.
# Otherwise the job has some internal failure. The TAPE13 part of the
# ADF manual has a detailed explanantion.
with open(logfile, "r") as f:
for line in reverse_readline(f):
if line == "":
continue
if end_patt.search(line) is None:
self.is_internal_crash = True
self.error = "Internal crash. TAPE13 is generated!"
self.is_failed = True
return
else:
break
with open(logfile, "r") as f:
for line in f:
m = error_patt.search(line)
if m:
self.is_failed = True
self.error = m.group(1)
break
if self.run_type is None:
m = runtype_patt.search(line)
if m:
if m.group(1) == 'FREQUENCIES':
self.freq_type = "Numerical"
self.run_type = "NumericalFreq"
elif m.group(1) == 'GEOMETRY OPTIMIZATION':
self.run_type = "GeometryOptimization"
elif m.group(1) == 'CREATE':
self.run_type = None
elif m.group(1) == 'SINGLE POINT':
self.run_type = 'SinglePoint'
else:
raise AdfOutputError("Undefined Runtype!")
elif self.run_type == 'SinglePoint':
m = coord_patt.search(line)
if m:
sites.append([m.groups()[0],
list(map(float, m.groups()[2:]))])
else:
m = final_energy_patt.search(line)
if m:
self.final_energy = float(m.group(1))
self.final_structure = self._sites_to_mol(sites)
elif self.run_type == 'GeometryOptimization':
m = cycle_patt.search(line)
if m:
cycle = int(m.group(1))
if cycle <= 0:
raise AdfOutputError("Wrong cycle {}".format(cycle))
if cycle > last_cycle:
parse_cycle = True
last_cycle = cycle
else:
parse_final = True
elif parse_cycle:
m = coord_patt.search(line)
if m:
sites.append([m.groups()[1],
list(map(float, m.groups()[2:]))])
else:
m = energy_patt.search(line)
if m:
self.energies.append(float(m.group(1)))
mol = self._sites_to_mol(sites)
self.structures.append(mol)
parse_cycle = False
sites = []
elif parse_final:
m = final_energy_patt.search(line)
if m:
self.final_energy = float(m.group(1))
elif self.run_type == "NumericalFreq":
break
if not self.is_failed:
if self.run_type == "GeometryOptimization":
if len(self.structures) > 0:
self.final_structure = self.structures[-1]
if self.final_energy is None:
raise AdfOutputError("The final energy can not be read!")
elif self.run_type == "SinglePoint":
if self.final_structure is None:
raise AdfOutputError("The final structure is missing!")
if self.final_energy is None:
raise AdfOutputError("The final energy can not be read!")
