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#!/usr/bin/python3
"""
Feff85L monolithic main program.
This runs all (or selected) modules of Feff85L in order:
feff8l_rdinp
feff8l_pot
feff8l_xsph
feff8l_pathfinder
feff8l_genfmt
feff8l_ff2x
"""
from __future__ import print_function
import os
import sys
import glob
import tempfile
from datetime import datetime
from subprocess import Popen, PIPE
from optparse import OptionParser
import pkg_resources
bytes2str = str
if sys.version[0] == '3':
def bytes2str(s):
if isinstance(s, str):
return s
elif isinstance(s, bytes):
return s.decode(sys.stdout.encoding)
return str(s, sys.stdout.encoding)
usage = """usage: %prog [options] folder(s)
run feff8l (or selected modules) on one
or more folders containing feff.inp files.
Example:
feff8l --no-ff2chi Structure1 Structure2
"""
parser = OptionParser(usage=usage, prog="feff8l",
version="Feff85L for EXAFS version 8.5L, build 001")
parser.add_option("-q", "--quiet", dest="quiet", action="store_true",
default=False, help="set quiet mode, default=False")
parser.add_option("--no-pot", dest="no_pot", action="store_true",
default=False, help="do not run POT module")
parser.add_option("--no-phases", dest="no_phases", action="store_true",
default=False, help="do not run XSPH module")
parser.add_option("--no-paths", dest="no_paths", action="store_true",
default=False, help="do not run PATHFINDER module")
parser.add_option("--no-genfmt", dest="no_genfmt", action="store_true",
default=False, help="do not run GENFMT module")
parser.add_option("--no-ff2chi", dest="no_ff2chi", action="store_true",
default=False, help="do not run FF2CHI module")
ERR_FEFFDIR = "Could not find folder '{:s}'"
ERR_FEFFINP = "Could not find feff.inp file in folder '{:s}'"
TOP_DIR, _ = os.path.split(os.path.abspath(__file__))
FEFFINP = 'feff.inp'
def isotime():
return datetime.now().strftime('%Y-%m-%d %H:%M:%S')
class Feff8LRunner(object):
modules = ('rdinp', 'pot', 'xsph', 'pathfinder', 'genfmt', 'ff2x')
def __init__(self, run=True):
try:
self.logfile = open('feff8l.log', 'w+')
except:
self.logfile = tempfile.NamedTemporaryFile(prefix='feff8l')
self.verbose = True
if run:
self.run()
def write(self, msg, verbose=True):
msg = bytes2str(msg)
if verbose:
sys.stdout.write(msg)
self.logfile.write(msg)
def run(self, rdinp=True, pot=True, xsph=True, pathfinder=True,
genfmt=True, ff2x=True, verbose=True):
"""
run all or selected modules of Feff85L
Arguments
---------
rdinp (bool) : run read-input module [True]
pot (bool) : run potentials module[True]
xsph (bool) : run xsph / phases module [True]
pathfinder (bool) : run path finder module [True]
genfmt (bool) : run genfmt / feff module [True]
ff2x (bool) : run ff2chi module [True]
verbose (bool) : write normal output to screen as well as log file [True]
"""
dorun = dict(rdinp=rdinp, pot=pot, xsph=xsph, pathfinder=pathfinder,
genfmt=genfmt, ff2x=ff2x)
self.write("#= Feff85l {:s}\n".format(isotime()), verbose=True)
for module in self.modules:
if not dorun[module]:
continue
self.write(("#= Feff85l {:s} module\n".format(module)), verbose=True)
cmd = [os.path.join(TOP_DIR, "feff8l_{:s}".format(module))]
proc = Popen(cmd, stdout=PIPE, stderr=PIPE)
while True:
msg = bytes2str(proc.stdout.read())
if msg == '':
break
self.write(msg, verbose=verbose)
while True:
msg = bytes2str(proc.stdout.read())
if msg == '':
break
self.write("#ERROR %s" % msg, verbose=True)
self.logfile.flush()
for fname in glob.glob('log*.dat'):
try:
os.unlink(fname)
except IOError:
pass
self.write("#= Feff85l done {:s}\n".format(isotime()), verbose=True)
if __name__ == '__main__':
(options, args) = parser.parse_args()
runopts = dict(rdinp=True,
pot=not options.no_pot,
xsph=not options.no_phases,
pathfinder=not options.no_paths,
genfmt=not options.no_genfmt,
ff2x=not options.no_ff2chi,
verbose=not options.quiet)
if len(args) == 0:
args = ['.']
for dirname in args:
if os.path.exists(dirname) and os.path.isdir(dirname):
thisdir = os.path.abspath(os.curdir)
os.chdir(dirname)
if os.path.exists(FEFFINP) and os.path.isfile(FEFFINP):
f8 = Feff8LRunner(run=False)
f8.run(**runopts)
else:
print(ERR_FEFFINP.format(os.path.abspath(os.curdir)))
os.chdir(thisdir)
else:
print(ERR_FEFFDIR.format(dirname))
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