def calculate(self,
atoms=None,
properties=['energy'],
system_changes=all_changes):
"""Capture the RuntimeError from FileIOCalculator.calculate
and add a little debug information from the Siesta output.
See base FileIocalculator for documentation.
"""
try:
FileIOCalculator.calculate(
self,
atoms=atoms,
properties=properties,
system_changes=system_changes)
# Here a test to check if the potential are in the right place!!!
except RuntimeError as e:
try:
with open(self.label + '.out', 'r') as f:
lines = f.readlines()
debug_lines = 10
print('##### %d last lines of the Siesta output' % debug_lines)
for line in lines[-20:]:
print(line.strip())
print('##### end of siesta output')
raise e
except:
raise e
def calculate(self,
atoms=None,
properties=['energy'],
system_changes=all_changes):
"""Capture the RuntimeError from FileIOCalculator.calculate
and add a little debug information from the Siesta output.
See base FileIocalculator for documentation.
"""
try:
FileIOCalculator.calculate(self,
atoms=atoms,
properties=properties,
system_changes=system_changes)
# Here a test to check if the potential are in the right place!!!
except RuntimeError as e:
try:
with open(self.label + '.out', 'r') as f:
lines = f.readlines()
debug_lines = 10
print('##### %d last lines of the Siesta output' % debug_lines)
for line in lines[-20:]:
print(line.strip())
print('##### end of siesta output')
raise e
except:
raise e
def calculate(self, atoms=None, properties=['energy'],
system_changes=all_changes):
if 'forces' in properties:
self.parameters.task = 'gradient'
FileIOCalculator.calculate(self, atoms, properties, system_changes)
def calculate(self,
atoms=None,
properties=['energy'],
system_changes=all_changes):
if 'forces' in properties:
self.parameters.task = 'gradient'
FileIOCalculator.calculate(self, atoms, properties, system_changes)
def run_calculation(self, atoms, properties, system_changes):
'''
Hook for the more involved remote calculator to link into.
Actually invokes the parent calculation routine.
'''
# This is restarted calculation do not write anything.
# Nothing to do - just return.
if self.restart : return
FileIOCalculator.calculate(self, atoms, properties, system_changes)
def calculate(self, atoms=None, properties=['energy'], system_changes=all_changes):
# Remove, if any the previous calculation file
if os.path.exists("%s/%s.out" % (self.directory, self.label)):
os.remove("%s/%s.out" % (self.directory, self.label))
if os.path.exists("%s/TM-forces-1.xyz" % self.directory):
os.remove("%s/TM-forces-1.xyz" % self.directory)
if os.path.exists("%s/TM-stress-1.stress_tensor" % self.directory):
os.remove("%s/TM-stress-1.stress_tensor" % self.directory)
FileIOCalculator.calculate(self, atoms, properties, system_changes)
def calculate(self, atoms, properties=['energy'], system_changes=[]):
""" overrides parent calculate() method for testing reason
should not be in prod. version """
try:
FileIOCalculator.calculate(self, atoms, properties, system_changes)
#~ self.read_results() # to test
#~ self.results['energy'] = self.residual() # to test
except RuntimeError:
print('ERROR: RuntimeError')
self.results['energy'] = 999 # big value
def calculate(self, *args, **kwargs):
try:
FileIOCalculator.calculate(self, *args, **kwargs)
except:
print('molpro error')
i = 0
while Path('molerror' + str(i) + '.out').exists():
i += 1
copyfile(self.label + '.out', 'molerror' + str(i) + '.out')
os.remove(self.label + ".out")
os.remove(self.label + ".xml")
def calculate(self, *args, **kwargs):
gaussians = ('g16', 'g09', 'g03')
if 'GAUSSIAN' in self.command:
for gau in gaussians:
if which(gau):
self.command = self.command.replace('GAUSSIAN', gau)
break
else:
raise EnvironmentError(
'Missing Gaussian executable {}'.format(gaussians))
FileIOCalculator.calculate(self, *args, **kwargs)
def calculate(self, *args, **kwargs):
if self.userscr is None:
if 'rungms' in self.command:
self.userscr = get_userscr(self.prefix, self.command)
if self.userscr is None:
warnings.warn("Could not determine USERSCR! "
"GAMESS may refuse to run more than once for "
"this job. Please pass userscr to the GAMESSUS "
"Calculator if you run into problems!")
else:
clean_userscr(self.userscr, self.prefix)
FileIOCalculator.calculate(self, *args, **kwargs)
def calculate(self, *args, **kwargs):
gaussians = ('g16', 'g09', 'g03')
if 'GAUSSIAN' in self.command:
for gau in gaussians:
if which(gau):
self.command = self.command.replace('GAUSSIAN', gau)
break
else:
#raise EnvironmentError('Missing Gaussian executable {}'
#.format(gaussians))
pass
try:
FileIOCalculator.calculate(self, *args, **kwargs)
except:
print('Gaussian error')
i = 0
while Path('gauserror' + str(i) + '.log').exists():
i += 1
copyfile(self.label + '.log', 'gauserror' + str(i) + '.log')
def calculate(self,
atoms=None,
properties=['energy'],
system_changes=all_changes):
"""Capture the RuntimeError from FileIOCalculator.calculate
and add a little debug information from the Siesta output.
See base FileIocalculator for documentation.
"""
FileIOCalculator.calculate(self,
atoms=atoms,
properties=properties,
system_changes=system_changes)
# The below snippet would run if calculate() failed but I have
# disabled it for now since it looks to be just for debugging.
# --askhl
"""
def calculate(self, atoms=None, properties=['energy'],
system_changes=all_changes):
if os.path.isfile(self.label + '.dat') and self.delold:
os.remove('%s.dat' %self.label)
if os.path.isfile(self.label + '.trj') and self.delold:
os.remove('%s.trj' %self.label)
if os.path.isfile(self.label + '.rst') and self.delold:
os.remove('%s.rst' %self.label)
if os.path.isfile(self.label + '.efp') and self.delold:
os.remove('%s.efp' %self.label)
if 'forces' in properties:
self.parameters.task = 'gradient'
if 'polarizability' in properties:
self.parameters.task = 'ffield'
#FUDO| Do we want to set some default parameters like:, I'll just do it for my sake right now
self.parameters.raw += ' $scf conv=1.0d-7 fdiff=.false. $end\n $contrl icut=20 itol=30 $end\n'
FileIOCalculator.calculate(self, atoms, properties, system_changes)
def calculate(self,
atoms=None,
properties=['energy'],
system_changes=all_changes):
if os.path.isfile(self.label + '.dat') and self.delold:
os.remove('%s.dat' % self.label)
if os.path.isfile(self.label + '.trj') and self.delold:
os.remove('%s.trj' % self.label)
if os.path.isfile(self.label + '.rst') and self.delold:
os.remove('%s.rst' % self.label)
if os.path.isfile(self.label + '.efp') and self.delold:
os.remove('%s.efp' % self.label)
if 'forces' in properties:
self.parameters.task = 'gradient'
if 'polarizability' in properties:
self.parameters.task = 'ffield'
#FUDO| Do we want to set some default parameters like:, I'll just do it for my sake right now
self.parameters.raw += ' $scf conv=1.0d-7 fdiff=.false. $end\n $contrl icut=20 itol=30 $end\n'
FileIOCalculator.calculate(self, atoms, properties, system_changes)
