def readVFE(filename):
with open(filename, 'r') as f:
cleanStr = f.read()
# Define Grammars
header = pp.OneOrMore(pp.pythonStyleComment).setParseAction(
pp.replaceWith(''))
divider = (pp.Literal('---') + pp.restOfLine).setParseAction(
pp.replaceWith(''))
flt = pp.Word(pp.nums + '.+-')
colHeader = pp.Suppress(pp.Literal('Temp (K) vfe (J/mol-c)'))
tempTable = pp.Group(pp.OneOrMore(pp.Group(flt * 2)))
datum = pp.Group(colHeader + tempTable)
data = pp.OneOrMore(datum)
# Parse String
try:
for grammar in [header, divider]:
cleanStr = grammar.transformString(cleanStr)
ppresults = data.parseString(cleanStr).asList()
except pp.ParseException as pe:
print(('Parsing Error using pyparsing: invalid input:', pe))
sys.exit()
# Format Results
results = {}
for ppr in ppresults:
temps = list(map(float, list(zip(*ppr[0]))[0]))
vfes = list(map(float, list(zip(*ppr[0]))[1]))
key = 'Temp (K)'
if key not in results:
results[key] = temps
key = 'VFE (J/mol-c)'
if key not in results:
results[key] = vfes
else:
results[key] = [sum(x) for x in zip(results[key], vfes)]
return results
def read_s2(filename, tempgrid):
with open(filename, 'r') as f:
cleanStr = f.read()
# Define Grammars
header = pp.OneOrMore(pp.pythonStyleComment).setParseAction(
pp.replaceWith(''))
divider = (pp.Literal('---') + pp.restOfLine).setParseAction(
pp.replaceWith(''))
index = pp.Word(pp.nums)
path = pp.Literal('Path Indices:').suppress() + pp.Group(
pp.OneOrMore(index))
colon = pp.Literal(':')
flt = pp.Word(pp.nums + '.+-')
pathlength = pp.Suppress(
pp.Literal('Path Len') + pp.SkipTo(colon) + colon) + flt
# Debug: FDV
# print tempgrid
# sys.exit()
# ntemp = int(tempgrid.split()[0])
ntemp = int(tempgrid[0])
if ntemp is 1:
datum = pp.Group(path + pathlength + flt)
else:
colHeader = pp.Suppress(pp.Literal('Temp (K) s^2 (1e-3 Ang^2)'))
tempTable = pp.Group(pp.OneOrMore(pp.Group(flt * 2)))
datum = pp.Group(path + pathlength + colHeader + tempTable)
data = pp.OneOrMore(datum)
# Parse String
try:
for grammar in [header, divider]:
cleanStr = grammar.transformString(cleanStr)
ppresults = data.parseString(cleanStr).asList()
except pp.ParseException as pe:
print(('Parsing Error using pyparsing: invalid input:', pe))
sys.exit()
# Format Results
results = {}
for ppr in ppresults:
key = ','.join(ppr[0])
if ntemp is 1:
temps = float(tempgrid.split()[1])
dwfs = float(ppr[2])
else:
temps = list(map(float, list(zip(*ppr[2]))[0]))
dwfs = list(map(float, list(zip(*ppr[2]))[1]))
results[key] = {
'Pathlength (Ang)': float(ppr[1]),
'Temp (K)': temps,
's^2': dwfs
}
return results
def getU(file, addDS=''):
token = pp.Literal('etotal' + addDS)
value = pp.Word(pp.nums + ".+-E")
end = pp.Literal('END DATASET(S)')
etotal = (pp.SkipTo(end) + pp.SkipTo(token) + token).suppress() + value
f = open(file, 'r')
try:
u = etotal.parseString(f.read()).asList()[0]
except pp.ParseException as pe:
print(('Parsing Error using pyparsing: invalid input:', pe))
sys.exit()
f.close()
return float(u)
def getacell(file):
token = pp.Keyword('acell')
vector = pp.Group(pp.Word(pp.nums + ".+-E")*3)
end = pp.Literal('END DATASET(S)')
acell = (pp.SkipTo(end) + pp.SkipTo(token) + token).suppress() + vector
f = open(file, 'r')
try:
a = acell.parseString(f.read()).asList()[0]
except pp.ParseException as pe:
print(('Parsing Error using pyparsing: invalid input:', pe))
sys.exit()
f.close()
return ' '.join(a)
def expandedList(string, length=3):
assert isinstance(string, str)
value = pp.Word(pp.nums + ".+-E")
prefix = pp.Combine(pp.Optional(pp.Word(pp.nums)) + pp.Literal('*'))
numList = pp.OneOrMore(pp.Optional(prefix) + value)
expanded = []
num = 1
for x in numList.parseString(string).asList():
if num != 1:
expanded.extend([x]*num)
num = 1
elif '*' in x:
if x[:-1] == '':
num = length
else:
num = int(x[:-1])
else:
expanded.append(x)
return expanded
def read_u2(filename, tempgrid):
with open(filename, 'r') as f:
cleanStr = f.read()
# Define Grammars
header = pp.OneOrMore(pp.pythonStyleComment).setParseAction(
pp.replaceWith(''))
divider = (pp.Literal('===') + pp.restOfLine).setParseAction(
pp.replaceWith(''))
index = pp.Word(pp.nums)
at_index = pp.Literal('Atom Index:').suppress() + pp.Group(
pp.OneOrMore(index))
dir = pp.Word(pp.alphas, max=1)
coord_dir = pp.Group(pp.OneOrMore('-')).suppress() + pp.Literal(
'Direction').suppress() + dir + pp.Group(pp.OneOrMore('-')).suppress()
colon = pp.Literal(':')
flt = pp.Word(pp.nums + '.+-')
# Modified by FDV
# ntemp = int(tempgrid.split()[0])
ntemp = int(tempgrid[0])
if ntemp is 1:
colHeader = pp.Suppress(pp.Literal('u^2 (1e-3 Ang^2):'))
datum = pp.Group(at_index + coord_dir + colHeader + flt)
else:
colHeader = pp.Suppress(pp.Literal('Temp (K) u^2 (1e-3 Ang^2)'))
tempTable = pp.Group(pp.OneOrMore(pp.Group(flt * 2)))
datum = pp.Group(at_index + coord_dir + colHeader + tempTable)
data = pp.OneOrMore(datum)
# Parse String
try:
for grammar in [header, divider]:
cleanStr = grammar.transformString(cleanStr)
ppresults = data.parseString(cleanStr).asList()
except pp.ParseException as pe:
print(('Parsing Error using pyparsing: invalid input:', pe))
sys.exit()
# Format Results
results = {}
for ppr in ppresults:
key = ','.join([ppr[0][0], ppr[1]])
if ntemp is 1:
temps = float(tempgrid.split()[1])
dwfs = float(ppr[2])
else:
temps = list(map(float, list(zip(*ppr[2]))[0]))
dwfs = list(map(float, list(zip(*ppr[2]))[1]))
results[key] = {'Temp (K)': temps, 'u^2': dwfs}
return results