def run_feff8l(modules):
""" run selected modules of Feff85L """
try:
logfile = open('feff8l.log', 'w+')
except:
logfile = tempfile.NamedTemporaryFile(prefix='feff8l')
def write(msg):
msg = bytes2str(msg)
sys.stdout.write(msg)
logfile.write(msg)
write("#= Feff85l %s\n" % isotime())
for mod in modules:
write("#= Feff85l %s module\n" % mod)
exe = find_exe('feff8l_%s' % mod)
proc = Popen(exe, stdout=PIPE, stderr=PIPE)
while True:
msg = bytes2str(proc.stdout.read())
if msg == '':
break
write(msg)
while True:
msg = bytes2str(proc.stderr.read())
if msg == '':
break
write("#ERROR %s" % msg)
logfile.flush()
for fname in glob.glob('log*.dat'):
try:
os.unlink(fname)
except IOError:
pass
write("#= Feff85l done %s\n" % isotime())
def run_feff8l(modules):
""" run selected modules of Feff85L """
try:
logfile = open('feff8l.log', 'w+')
except:
logfile = tempfile.NamedTemporaryFile(prefix='feff8l')
def write(msg):
msg = bytes2str(msg)
sys.stdout.write(msg)
logfile.write(msg)
write("#= Feff85l %s\n" % isotime())
for mod in modules:
write("#= Feff85l %s module\n" % mod)
exe = find_exe('feff8l_%s' % mod)
proc = Popen(exe, stdout=PIPE, stderr=PIPE)
while True:
msg = bytes2str(proc.stdout.read())
if msg == '':
break
write(msg)
while True:
msg = bytes2str(proc.stderr.read())
if msg == '':
break
write("#ERROR %s" % msg)
logfile.flush()
for fname in glob.glob('log*.dat'):
try:
os.unlink(fname)
except IOError:
pass
write("#= Feff85l done %s\n" % isotime())
def write(msg):
msg = bytes2str(msg)
msg = " : {:s}\n".format(msg.strip().rstrip())
if self._larch is not None:
self._larch.writer.write(msg)
else:
sys.stdout.write(msg)
def write(msg):
msg = bytes2str(msg)
msg = " : {:s}\n".format(msg.strip().rstrip())
if self._larch is not None:
self._larch.writer.write(msg)
else:
sys.stdout.write(msg)
def run(self, feffinp=None, folder=None, exe='feff8l'):
"""
Make system call to run one or more of the stand-alone executables,
writing a log file to the folder containing the input file.
"""
if folder is not None:
self.folder = folder
if feffinp is not None:
self.feffinp = feffinp
if self.feffinp is None:
raise Exception("no feff.inp file was specified")
savefile = '.save_.inp'
here = abspath(os.getcwd())
os.chdir(abspath(self.folder))
feffinp_dir, feffinp_file = os.path.split(self.feffinp)
feffinp_dir = dirname(self.feffinp)
if len(feffinp_dir) > 0:
os.chdir(feffinp_dir)
if not isfile(feffinp_file):
raise Exception("feff.inp file '%s' could not be found" % feffinp_file)
if exe is None:
for module in self.Feff8l_modules:
os.chdir(here)
self.run(exe=module)
return
#
# exe is set, find the corresponding executable file
## find program to run:
program = None
if exe in self.Feff8l_modules:
exe = "feff8l_%s" % exe
resolved_exe = find_exe(exe)
if resolved_exe is not None:
program = resolved_exe
else:
try:
program = self._larch.symtable.get_symbol('_xafs._feff_executable')
except (NameError, AttributeError) as exc:
program = None
if program is not None:
if not os.access(program, os.X_OK):
program = None
if program is None: # Give up!
os.chdir(here)
raise Exception("'%s' executable cannot be found" % exe)
## preserve an existing feff.inp file if this is not called feff.inp
if feffinp_file != 'feff.inp':
if isfile('feff.inp'):
copy('feff.inp', savefile)
copy(feffinp_file, 'feff.inp')
_, logname = os.path.split(program)
if logname.endswith('.exe'):
logname = logname[:4]
log = 'feffrun_%s.log' % logname
if isfile(log):
os.unlink(log)
f = open(log, 'a')
header = "\n======== running Feff module %s ========\n" % exe
def write(msg):
msg = bytes2str(msg)
msg = " : {:s}\n".format(msg.strip().rstrip())
if self._larch is not None:
self._larch.writer.write(msg)
else:
sys.stdout.write(msg)
if self.verbose:
write(header)
f.write(header)
process=subprocess.Popen(program, shell=False,
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT)
flag = False
thislist = []
while True:
if process.returncode is None:
process.poll()
time.sleep(0.01)
line = bytes2str(process.stdout.readline())
if not line:
break
if self.verbose:
write(line)
## snarf threshold energy
pattern = re.compile('mu_(new|old)=\s+(-?\d\.\d+)')
match = pattern.search(line)
if match is not None:
self.threshold.append(match.group(2))
## snarf charge transfer
if line.strip().startswith('Charge transfer'):
thislist = []
flag = True
elif line.strip().startswith('SCF ITERATION'):
self.chargetransfer.append(list(thislist))
flag = False
elif line.strip().startswith('Done with module 1'):
self.chargetransfer.append(list(thislist))
flag = False
elif flag:
this = line.split()
thislist.append(this[1])
f.write(line)
f.close
if isfile(savefile):
move(savefile, 'feff.inp')
os.chdir(here)
return None
def write(msg):
msg = bytes2str(msg)
sys.stdout.write(msg)
logfile.write(msg)
def write(msg):
msg = bytes2str(msg)
sys.stdout.write(msg)
logfile.write(msg)
def run(self, feffinp=None, folder=None, exe='feff8l'):
"""
Make system call to run one or more of the stand-alone executables,
writing a log file to the folder containing the input file.
"""
if folder is not None:
self.folder = folder
if feffinp is not None:
self.feffinp = feffinp
if self.feffinp is None:
raise Exception("no feff.inp file was specified")
savefile = '.save_.inp'
here = abspath(os.getcwd())
os.chdir(abspath(self.folder))
feffinp_dir, feffinp_file = os.path.split(self.feffinp)
feffinp_dir = dirname(self.feffinp)
if len(feffinp_dir) > 0:
os.chdir(feffinp_dir)
if not isfile(feffinp_file):
raise Exception("feff.inp file '%s' could not be found" %
feffinp_file)
if exe is None:
for module in self.Feff8l_modules:
os.chdir(here)
self.run(exe=module)
return
#
# exe is set, find the corresponding executable file
## find program to run:
program = None
if exe in self.Feff8l_modules:
exe = "feff8l_%s" % exe
resolved_exe = find_exe(exe)
if resolved_exe is not None:
program = resolved_exe
else:
try:
program = self._larch.symtable.get_symbol(
'_xafs._feff_executable')
except (NameError, AttributeError) as exc:
program = None
if program is not None:
if not os.access(program, os.X_OK):
program = None
if program is None: # Give up!
os.chdir(here)
raise Exception("'%s' executable cannot be found" % exe)
## preserve an existing feff.inp file if this is not called feff.inp
if feffinp_file != 'feff.inp':
if isfile('feff.inp'):
copy('feff.inp', savefile)
copy(feffinp_file, 'feff.inp')
_, logname = os.path.split(program)
if logname.endswith('.exe'):
logname = logname[:4]
log = 'feffrun_%s.log' % logname
if isfile(log):
os.unlink(log)
f = open(log, 'a')
header = "\n======== running Feff module %s ========\n" % exe
def write(msg):
msg = bytes2str(msg)
msg = " : {:s}\n".format(msg.strip().rstrip())
if self._larch is not None:
self._larch.writer.write(msg)
else:
sys.stdout.write(msg)
if self.verbose:
write(header)
f.write(header)
process = subprocess.Popen(program,
shell=False,
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT)
flag = False
thislist = []
while True:
if process.returncode is None:
process.poll()
time.sleep(0.01)
line = bytes2str(process.stdout.readline())
if not line:
break
if self.verbose:
write(line)
## snarf threshold energy
pattern = re.compile('mu_(new|old)=\s+(-?\d\.\d+)')
match = pattern.search(line)
if match is not None:
self.threshold.append(match.group(2))
## snarf charge transfer
if line.strip().startswith('Charge transfer'):
thislist = []
flag = True
elif line.strip().startswith('SCF ITERATION'):
self.chargetransfer.append(list(thislist))
flag = False
elif line.strip().startswith('Done with module 1'):
self.chargetransfer.append(list(thislist))
flag = False
elif flag:
this = line.split()
thislist.append(this[1])
f.write(line)
f.close
if isfile(savefile):
move(savefile, 'feff.inp')
os.chdir(here)
return None