[ck2cti] Minor spacing updates to improve legibility
This commit is contained in:
Bryan W. Weber
Ray Speth
parent
bed546ad92
commit
990f995796
1 changed files with 39 additions and 40 deletions
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@ -269,7 +269,7 @@ class Reaction(object):
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def _coeff_string(self, coeffs):
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L = []
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for stoichiometry,species in coeffs:
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for stoichiometry, species in coeffs:
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if stoichiometry != 1:
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L.append('{0} {1}'.format(stoichiometry, species))
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else:
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@ -369,7 +369,7 @@ class KineticsModel(object):
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def efficiencyString(self):
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return ' '.join('{0}:{1}'.format(mol, eff)
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for mol,eff in self.efficiencies.items())
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for mol, eff in self.efficiencies.items())
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class KineticsData(KineticsModel):
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@ -489,7 +489,6 @@ class SurfaceArrhenius(Arrhenius):
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return s.rstrip()[:-1] + '])'
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def to_cti(self, reactantstr, arrow, productstr, indent=0):
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rxnstring = reactantstr + arrow + productstr
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return 'surface_reaction({0!r},{1})'.format(rxnstring, self.rateStr())
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@ -533,7 +532,7 @@ class PDepArrhenius(KineticsModel):
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lines = ['pdep_arrhenius({0!r},'.format(rxnstring)]
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prefix = ' '*(indent+15)
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template = '[({0}, {1!r}), {2.A[0]:e}, {2.b}, {2.Ea[0]}],'
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for pressure,arrhenius in zip(self.pressures[0], self.arrhenius):
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for pressure, arrhenius in zip(self.pressures[0], self.arrhenius):
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lines.append(prefix + template.format(pressure,
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self.pressures[1],
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arrhenius))
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@ -901,11 +900,12 @@ def get_index(seq, value):
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if isinstance(seq, string_types):
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seq = seq.split()
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value = value.lower().strip()
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for i,item in enumerate(seq):
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for i, item in enumerate(seq):
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if item.lower() == value:
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return i
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return None
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def contains(seq, value):
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if isinstance(seq, string_types):
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return value.lower() in seq.lower()
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@ -924,17 +924,17 @@ class Surface(object):
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class Parser(object):
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def __init__(self):
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self.processed_units = False
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self.energy_units = 'cal/mol' # for the current REACTIONS section
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self.output_energy_units = 'cal/mol' # for the output file
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self.quantity_units = 'mol' # for the current REACTIONS section
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self.output_quantity_units = 'mol' # for the output file
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self.energy_units = 'cal/mol' # for the current REACTIONS section
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self.output_energy_units = 'cal/mol' # for the output file
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self.quantity_units = 'mol' # for the current REACTIONS section
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self.output_quantity_units = 'mol' # for the output file
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self.motz_wise = None
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self.warning_as_error = True
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self.elements = []
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self.element_weights = {} # for custom elements only
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self.speciesList = [] # bulk species only
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self.speciesDict = {} # bulk and surface species
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self.element_weights = {} # for custom elements only
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self.speciesList = [] # bulk species only
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self.speciesDict = {} # bulk and surface species
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self.surfaces = []
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self.reactions = []
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self.finalReactionComment = ''
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@ -1041,7 +1041,6 @@ class Parser(object):
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raise InputParseError("Error parsing elemental composition for "
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"species '{0}'".format(species))
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# Extract the NASA polynomial coefficients
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# Remember that the high-T polynomial comes first!
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Tmin = fortFloat(lines[0][45:55])
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@ -1064,8 +1063,6 @@ class Parser(object):
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elif all(c == 0 for c in coeffs_high) and Tmax == Tint:
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coeffs_high = coeffs_low
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# Construct and return the thermodynamics model
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thermo = MultiNASA(
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polynomials=[
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@ -1130,7 +1127,7 @@ class Parser(object):
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# reaction string. Checking this character is necessary to correctly
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# identify species with names ending in '+' or '='.
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self.species_tokens = set()
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for next_char in ('<','=','(','+','\n'):
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for next_char in ('<', '=', '(', '+', '\n'):
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self.species_tokens.update(k + next_char for k in self.speciesDict)
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self.other_tokens = {'M': 'third-body', 'm': 'third-body',
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'(+M)': 'falloff3b', '(+m)': 'falloff3b',
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@ -1217,17 +1214,17 @@ class Parser(object):
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products = []
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stoichiometry = 1
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lhs = True
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for token,kind in [v for k,v in sorted(locs.items())]:
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for token, kind in [v for k,v in sorted(locs.items())]:
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if kind == 'equal':
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reversible = token in ('<=>', '=')
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lhs = False
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elif kind == 'coeff':
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stoichiometry = token
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elif lhs:
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reactants.append((stoichiometry,token,kind))
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reactants.append((stoichiometry, token, kind))
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stoichiometry = 1
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else:
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products.append((stoichiometry,token,kind))
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products.append((stoichiometry, token, kind))
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stoichiometry = 1
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if lhs is True:
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@ -1240,7 +1237,7 @@ class Parser(object):
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falloff3b = None
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thirdBody = False # simple third body reaction (non-falloff)
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photon = False
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for stoichiometry,species,kind in expression:
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for stoichiometry, species, kind in expression:
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if kind == 'third-body':
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thirdBody = True
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elif kind == 'falloff3b':
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@ -1289,7 +1286,7 @@ class Parser(object):
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# The rest of the first line contains Arrhenius parameters
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reaction_type = SurfaceArrhenius if surface else Arrhenius
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arrhenius = reaction_type(
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A=(A,kunits),
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A=(A, kunits),
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b=b,
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Ea=(Ea, energy_units),
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T0=(1,"K"),
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@ -1326,9 +1323,9 @@ class Parser(object):
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# Low-pressure-limit Arrhenius parameters for "falloff" reaction
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tokens = tokens[1].split()
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arrheniusLow = Arrhenius(
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A=(float(tokens[0].strip()),klow_units),
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A=(float(tokens[0].strip()), klow_units),
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b=float(tokens[1].strip()),
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Ea=(float(tokens[2].strip()),energy_units),
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Ea=(float(tokens[2].strip()), energy_units),
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T0=(1,"K"),
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parser=self
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)
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@ -1338,9 +1335,9 @@ class Parser(object):
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# activated" reaction
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tokens = tokens[1].split()
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arrheniusHigh = Arrhenius(
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A=(float(tokens[0].strip()),kunits),
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A=(float(tokens[0].strip()), kunits),
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b=float(tokens[1].strip()),
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Ea=(float(tokens[2].strip()),energy_units),
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Ea=(float(tokens[2].strip()), energy_units),
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T0=(1,"K"),
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parser=self
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)
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@ -1357,9 +1354,9 @@ class Parser(object):
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reversible=False)
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tokens = tokens[1].split()
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revReaction.kinetics = Arrhenius(
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A=(float(tokens[0].strip()),klow_units),
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A=(float(tokens[0].strip()), klow_units),
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b=float(tokens[1].strip()),
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Ea=(float(tokens[2].strip()),energy_units),
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Ea=(float(tokens[2].strip()), energy_units),
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T0=(1,"K"),
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parser=self
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)
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@ -1433,7 +1430,7 @@ class Parser(object):
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tokens2 = tokens[1].split()
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chebyshev.degreeT = int(float(tokens2[0].strip()))
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chebyshev.degreeP = int(float(tokens2[1].strip()))
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chebyshev.coeffs = np.zeros((chebyshev.degreeT,chebyshev.degreeP), np.float64)
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chebyshev.coeffs = np.zeros((chebyshev.degreeT, chebyshev.degreeP), np.float64)
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chebyshevCoeffs.extend([float(t.strip()) for t in tokens2[2:]])
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else:
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tokens2 = tokens[1].split()
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@ -1445,9 +1442,9 @@ class Parser(object):
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pdepArrhenius = []
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tokens = tokens[1].split()
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pdepArrhenius.append([float(tokens[0].strip()), Arrhenius(
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A=(float(tokens[1].strip()),kunits),
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A=(float(tokens[1].strip()), kunits),
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b=float(tokens[2].strip()),
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Ea=(float(tokens[3].strip()),energy_units),
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Ea=(float(tokens[3].strip()), energy_units),
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T0=(1,"K"),
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parser=self
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)])
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@ -1471,7 +1468,7 @@ class Parser(object):
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reaction.kinetics = chebyshev
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elif pdepArrhenius is not None:
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reaction.kinetics = PDepArrhenius(
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pressures=([P for P, arrh in pdepArrhenius],"atm"),
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pressures=([P for P, arrh in pdepArrhenius], "atm"),
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arrhenius=[arrh for P, arrh in pdepArrhenius],
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parser=self
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)
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@ -1568,7 +1565,7 @@ class Parser(object):
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# Fix the case where there THERMO ALL or REAC UNITS
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# ends the species section
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if (tokens[-1].upper().startswith('THER') or
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tokens[-1].upper().startswith('REAC')):
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tokens[-1].upper().startswith('REAC')):
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tokens.pop()
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break
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@ -1616,7 +1613,7 @@ class Parser(object):
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# Fix the case where there THERMO ALL or REAC UNITS
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# ends the species section
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if (tokens[-1].upper().startswith('THER') or
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tokens[-1].upper().startswith('REAC')):
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tokens[-1].upper().startswith('REAC')):
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tokens.pop()
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break
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@ -1770,7 +1767,7 @@ class Parser(object):
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for token in tokens[1:]:
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token = token.upper()
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if token in ENERGY_UNITS:
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self.energy_units =ENERGY_UNITS[token]
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self.energy_units = ENERGY_UNITS[token]
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if not self.processed_units:
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self.output_energy_units = ENERGY_UNITS[token]
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elif token in QUANTITY_UNITS:
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@ -1840,7 +1837,7 @@ class Parser(object):
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self.setupKinetics()
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for kinetics, comment, line_number in zip(kineticsList, commentsList, startLines):
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try:
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reaction,revReaction = self.readKineticsEntry(kinetics, surface)
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reaction, revReaction = self.readKineticsEntry(kinetics, surface)
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except Exception as e:
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logging.error('Error reading reaction entry starting on line {0}:'.format(line_number))
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raise
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@ -1904,15 +1901,15 @@ class Parser(object):
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for reactions in possible_duplicates.values():
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for r1,r2 in itertools.combinations(reactions, 2):
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if r1.duplicate and r2.duplicate:
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pass # marked duplicate reaction
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pass # marked duplicate reaction
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elif (r1.thirdBody and r1.thirdBody.upper() == 'M' and
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r1.kinetics.efficiencies.get(r2.thirdBody) == 0):
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pass # explicit zero efficiency
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pass # explicit zero efficiency
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elif (r2.thirdBody and r2.thirdBody.upper() == 'M' and
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r2.kinetics.efficiencies.get(r1.thirdBody) == 0):
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pass # explicit zero efficiency
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pass # explicit zero efficiency
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elif r1.thirdBody != r2.thirdBody:
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pass # distinct third bodies
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pass # distinct third bodies
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else:
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raise InputParseError(message.format(r1, r1.line_number, r2.line_number))
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@ -2052,7 +2049,7 @@ class Parser(object):
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lines.append('# Element data')
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lines.append(delimiterLine)
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lines.append('')
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for name,weight in self.element_weights.items():
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for name, weight in self.element_weights.items():
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lines.append('element(symbol={0!r}, atomic_mass={1})'.format(name, weight))
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# Write the individual species data
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@ -2211,6 +2208,7 @@ duplicate transport data) to be ignored.
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print('Mechanism contains {0} species and {1} reactions.'.format(len(self.speciesList), len(self.reactions)))
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return surface_names
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def main(argv):
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longOptions = ['input=', 'thermo=', 'transport=', 'surface=', 'id=',
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@ -2286,6 +2284,7 @@ def main(argv):
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print(e)
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sys.exit(1)
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def script_entry_point():
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main(sys.argv[1:])
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