def clean(self, prefix='test', queue_num=None):
"""Method which cleans up after a calculation.
The default files generated OpenMX will be deleted IF this
method is called.
"""
self.prind("Cleaning Data")
fileName = get_file_name('', self.label)
pbs_Name = get_file_name('', self.label)
files = [
# prefix+'.out',#prefix+'.dat',#prefix+'.BAND*',
fileName + '.cif', fileName + '.dden.cube', fileName + \
'.ene', fileName + '.md', fileName + '.md2',
fileName + '.tden.cube', fileName + '.sden.cube', fileName + \
'.v0.cube', fileName + '.v1.cube',
fileName + '.vhart.cube', fileName + '.den0.cube', fileName + \
'.bulk.xyz', fileName + '.den1.cube',
fileName + '.xyz', pbs_Name + '.o' + \
str(queue_num), pbs_Name + '.e' + str(queue_num)
]
for f in files:
try:
self.prind("Removing" + f)
os.remove(f)
except OSError:
self.prind("There is no such file named " + f)
def write_openmx(label=None, atoms=None, parameters=None, properties=None,
system_changes=None):
"""
From atom image, 'images', write '.dat' file.
First, set
Write input (dat)-file.
See calculator.py for further details.
Parameters:
- atoms : The Atoms object to write.
- properties : The properties which should be calculated.
- system_changes : List of properties changed since last run.
"""
from ase.calculators.openmx import parameters as param
filtered_keywords = parameters_to_keywords(label=label, atoms=atoms,
parameters=parameters,
properties=properties,
system_changes=system_changes)
keys = ['string', 'bool', 'integer', 'float',
'tuple_integer', 'tuple_float', 'tuple_bool',
'matrix', 'list_int', 'list_bool', 'list_float']
# Start writing the file
filename = get_file_name('.dat', label)
with open(filename, 'w') as f:
# Write 1-line keywords
for fltrd_keyword in filtered_keywords.keys():
for key in keys:
openmx_keywords = getattr(param, key+'_keys')
write = globals()['write_'+key]
for omx_keyword in openmx_keywords:
if fltrd_keyword == get_standard_key(omx_keyword):
write(f, omx_keyword, filtered_keywords[fltrd_keyword])
def read_version(self, label=None):
version = None
if label is None:
label = self.label
for line in open(get_file_name('.out', label)):
if line.find('Ver.') != -1:
version = line.split()[-1]
break
return version
def run_openmx(self):
def isRunning(process=None):
''' Check mpi is running'''
return process.poll() is None
runfile = get_file_name('.dat', self.label, absolute_directory=False)
outfile = get_file_name('.log', self.label)
olddir = os.getcwd()
abs_dir = os.path.join(olddir, self.directory)
try:
os.chdir(abs_dir)
if self.command is None:
self.command = 'openmx'
command = self.command + ' %s > %s'
command = command % (runfile, outfile)
self.prind(command)
p = subprocess.Popen(command, shell=True, universal_newlines=True)
self.print_file(file=outfile, running=isRunning, process=p)
finally:
os.chdir(olddir)
self.prind("Calculation Finished")
def run_mpi(self):
"""
Run openmx using MPI method. If keyword `mpi` is declared, it will
run.
"""
def isRunning(process=None):
''' Check mpi is running'''
return process.poll() is None
processes = self.processes
threads = self.threads
runfile = get_file_name('.dat', self.label, absolute_directory=False)
outfile = get_file_name('.log', self.label)
olddir = os.getcwd()
abs_dir = os.path.join(olddir, self.directory)
try:
os.chdir(abs_dir)
command = self.get_command(processes, threads, runfile, outfile)
self.prind(command)
p = subprocess.Popen(command, shell=True, universal_newlines=True)
self.print_file(file=outfile, running=isRunning, process=p)
finally:
os.chdir(olddir)
self.prind("Calculation Finished")
def calculate(self,
atoms=None,
properties=None,
system_changes=all_changes):
"""
Capture the RuntimeError from FileIOCalculator.calculate
and add a little debug information from the OpenMX output.
See base FileIOCalculator for documentation.
"""
if self.parameters.data_path is None:
if not 'OPENMX_DFT_DATA_PATH' in os.environ:
warnings.warn('Please either set OPENMX_DFT_DATA_PATH as an'
'enviroment variable or specify dft_data_path as'
'a keyword argument')
self.prind("Start Calculation")
if properties is None:
properties = self.implemented_properties
try:
Calculator.calculate(self, atoms, properties, system_changes)
self.write_input(atoms=self.atoms,
parameters=self.parameters,
properties=properties,
system_changes=system_changes)
self.print_input(debug=self.debug, nohup=self.nohup)
self.run()
# self.read_results()
self.version = self.read_version()
output_atoms = read_openmx(filename=self.label, debug=self.debug)
self.output_atoms = output_atoms
# XXX The parameters are supposedly inputs, so it is dangerous
# to update them from the outputs. --askhl
self.parameters.update(output_atoms.calc.parameters)
self.results = output_atoms.calc.results
# self.clean()
except RuntimeError as e:
try:
with open(get_file_name('.log'), 'r') as f:
lines = f.readlines()
debug_lines = 10
print('##### %d last lines of the OpenMX output' % debug_lines)
for line in lines[-20:]:
print(line.strip())
print('##### end of openMX output')
raise e
except RuntimeError as e:
raise e
def print_input(self, debug=None, nohup=None):
"""
For a debugging purpose, print the .dat file
"""
if debug is None:
debug = self.debug
if nohup is None:
nohup = self.nohup
self.prind('Reading input file' + self.label)
filename = get_file_name('.dat', self.label)
if not nohup:
with open(filename, 'r') as f:
while True:
line = f.readline()
print(line.strip())
if not line:
break
