#!/usr/local/bin/python """ Cantera .cti input file processor The functions and classes in this module process Cantera .cti input files and produce CTML files. It can be imported as a module, or used as a script. script usage: python ctml_writer.py infile.cti This will produce CTML file 'infile.xml' """ import string class CTI_Error: """Exception raised if an error is encountered while parsing the input file.""" def __init__(self, msg): print '\n\n***** Error parsing input file *****\n\n' print msg print indent = ['', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' '] #----------------------------------------------------- class XMLnode: """This is a minimal class to allow easy creation of an XML tree from Python. It can write XML, but cannot read it.""" def __init__(self, name="--", value = ""): """Create a new node. Usually this only needs to be explicitly called to create the root element. Method addChild calls this constructor to create the new child node.""" self._name = name # convert 'value' to a string if it is not already, and # strip leading whitespace if type(value) <> types.StringType: self._value = string.lstrip(`value`) else: self._value = string.lstrip(value) self._attribs = {} # dictionary of attributes self._children = [] # list of child nodes self._childmap = {} # dictionary of child nodes def name(self): """The tag name of the node.""" return self._name def nChildren(self): """Number of child elements.""" return len(self._children) def addChild(self, name, value=""): """Add a child with tag 'name', and set its value if the value parameter is supplied.""" # create a new node for the child c = XMLnode(name = name, value = value) # add it to the list of children, and to the dictionary # of children self._children.append(c) self._childmap[name] = c return c def addComment(self, comment): """Add a comment.""" self.addChild(name = '_comment_', value = comment) def value(self): """A string containing the element value.""" return self._value def child(self, name=""): """The child node with specified name.""" return self._childmap[name] def __getitem__(self, key): """Get an attribute using the syntax node[key]""" return self._attribs[key] def __setitem__(self, key, value): """Set a new attribute using the syntax node[key] = value.""" self._attribs[key] = value def __call__(self): """Allows getting the value using the syntax 'node()'""" return self._value def write(self, file): """Write out the XML tree to a file.""" f = open(file,'w') f.write('\n') self._write(f, 0) f.write('\n') def _write(self, f, level = 0): """Internal method used to write the XML representation of each node.""" if self._name == "": return indnt = indent[level] # handle comments if self._name == '_comment_': f.write('\n'+indnt+'') return # write the opening tag and attributes f.write(indnt + '<' + self._name) for a in self._attribs.keys(): f.write(' '+a+'="'+self._attribs[a]+'"') if (self._value == "" and self.nChildren() == 0): f.write('/>') else: f.write('>') if self._value <> "": vv = string.lstrip(self._value) ieol = vv.find('\n') if ieol >= 0: while 1 > 0: ieol = vv.find('\n') if ieol >= 0: f.write('\n '+indnt+vv[:ieol]) vv = string.lstrip(vv[ieol+1:]) else: f.write('\n '+indnt+vv) break else: f.write(self._value) for c in self._children: f.write('\n') c._write(f, level + 2) if (self.nChildren() > 0): f.write('\n'+indnt) f.write('') #-------------------------------------------------- # constants that can be used in .cti files OneAtm = 1.01325e5 OneBar = 1.0e5 import types, math, copy # default units _ulen = 'm' _umol = 'kmol' _umass = 'kg' _utime = 's' _ue = 'J/kmol' _uenergy = 'J' _upres = 'Pa' # used to convert reaction pre-exponentials _length = {'cm':0.01, 'm':1.0, 'mm':0.001} _moles = {'kmol':1.0, 'mol':0.001, 'molec':1.0/6.023e26} _time = {'s':1.0, 'min':60.0, 'hr':3600.0} # default std state pressure _pref = 1.0e5 # 1 bar _name = 'noname' # these lists store top-level entries _elements = [] _species = [] _speciesnames = [] _phases = [] _reactions = [] _atw = {} _enames = {} _valsp = '' _valrxn = '' _valexport = '' _valfmt = '' def export_species(file, fmt = 'CSV'): global _valexport global _valfmt _valexport = file _valfmt = fmt def validate(species = 'yes', reactions = 'yes'): global _valsp global _valrxn _valsp = species _valrxn = reactions def isnum(a): """True if a is an integer or floating-point number.""" if type(a) == types.IntType or type(a) == types.FloatType: return 1 else: return 0 def is_local_species(name): """true if the species named 'name' is defined in this file""" if name in _speciesnames: return 1 return 0 def dataset(nm): "Set the dataset name. Invoke this to change the name of the xml file." global _name _name = nm def standard_pressure(p0): """Set the default standard-state pressure.""" global _pref _pref = p0 def units(length = '', quantity = '', mass = '', time = '', act_energy = '', energy = '', pressure = ''): """set the default units.""" global _ulen, _umol, _ue, _utime, _umass, _uenergy, _upres if length: _ulen = length if quantity: _umol = quantity if act_energy: _ue = act_energy if time: _utime = time if mass: _umass = mass if energy: _uenergy = energy if pressure: _upres = pressure def ufmt(base, n): """return a string representing a unit to a power n.""" if n == 0: return '' if n == 1: return '-'+base if n == -1: return '/'+base if n > 0: return '-'+base+`n` if n < 0: return '/'+base+`-n` def write(): """write the CTML file.""" x = XMLnode("ctml") v = x.addChild("validate") v["species"] = _valsp v["reactions"] = _valrxn if _elements: ed = x.addChild("elementData") for e in _elements: e.build(ed) for ph in _phases: ph.build(x) s = species_set(name = _name, species = _species) s.build(x) r = x.addChild('reactionData') r['id'] = 'reaction_data' for rx in _reactions: rx.build(r) if _name <> 'noname': x.write(_name+'.xml') else: print x if _valexport: f = open(_valexport,'w') for s in _species: s.export(f, _valfmt) f.close() def addFloat(x, nm, val, fmt='', defunits=''): """ Add a child element to XML element x representing a floating-point number. """ u = '' s = '' if isnum(val): fval = float(val) if fmt: s = fmt % fval else: s = `fval` xc = x.addChild(nm, s) if defunits: xc['units'] = defunits else: v = val[0] u = val[1] if fmt: s = fmt % v else: s = `v` xc = x.addChild(nm, s) xc['units'] = u def getAtomicComp(atoms): if type(atoms) == types.DictType: return atoms a = atoms.replace(',',' ') toks = a.split() d = {} for t in toks: b = t.split(':') d[b[0]] = int(b[1]) return d def getReactionSpecies(s): """Take a reaction string and return a dictionary mapping species names to stoichiometric coefficients. If any species appears more than once, the returned stoichiometric coefficient is the sum. >>> s = 'CH3 + 3 H + 5.2 O2 + 0.7 H' >>> getReactionSpecies(s) >>> {'CH3':1, 'H':3.7, 'O2':5.2} """ # get rid of the '+' signs separating species. Only plus signs # surrounded by spaces are replaced, so that plus signs may be # used in species names (e.g. 'Ar3+') toks = s.replace(' + ',' ').split() d = {} n = 1.0 for t in toks: # try to convert the token to a number. try: n = float(t) if n < 0.0: raise CTI_Error("negative stoichiometric coefficient:" +s) #if t > '0' and t < '9': # n = int(t) #else: # token isn't a number, so it must be a species name except: if d.has_key(t): # already seen this token d[t] += n # so increment its value by the last # value of n else: d[t] = n # first time this token has been seen, # so set its value to n n = 1 # reset n to 1.0 for species that do not # specify a stoichiometric coefficient return d class element: def __init__(self, symbol = '', atomic_mass = 0.01, atomic_number = 0): self._sym = symbol self._atw = atomic_mass self._num = atomic_number global _elements _elements.append(self) def build(self, db): e = db.addChild("element") e["name"] = self._sym e["atomicWt"] = `self._atw` e["atomicNumber"] = `self._num` class species_set: def __init__(self, name = '', species = []): self._s = species self._name = name #self.type = SPECIES_SET def build(self, p): p.addComment(' species definitions ') sd = p.addChild("speciesData") sd["id"] = "species_data" for s in self._s: #if s.type == SPECIES: s.build(sd) #else: # raise 'wrong object type in species_set: '+s.__class__ class species: """A species.""" def __init__(self, name = 'missing name!', atoms = '', note = '', thermo = None, transport = None, charge = -999, size = 1.0): self._name = name self._atoms = getAtomicComp(atoms) self._comment = note if thermo: self._thermo = thermo else: self._thermo = const_cp() self._transport = transport chrg = 0 self._charge = charge if self._atoms.has_key('E'): chrg = -self._atoms['E'] if self._charge <> -999: if self._charge <> chrg: raise CTI_Error('specified charge inconsistent with number of electrons') else: self._charge = chrg self._size = size global _species global _enames _species.append(self) global _speciesnames if name in _speciesnames: raise CTI_Error('species '+name+' multiply defined.') _speciesnames.append(name) for e in self._atoms.keys(): _enames[e] = 1 def export(self, f, fmt = 'CSV'): global _enames if fmt == 'CSV': str = self._name+',' for e in _enames: if self._atoms.has_key(e): str += `self._atoms[e]`+',' else: str += '0,' f.write(str) if type(self._thermo) == types.InstanceType: self._thermo.export(f, fmt) else: nt = len(self._thermo) for n in range(nt): self._thermo[n].export(f, fmt) f.write('\n') def build(self, p): hdr = ' species '+self._name+' ' p.addComment(hdr) s = p.addChild("species") s["name"] = self._name a = '' for e in self._atoms.keys(): a += e+':'+`self._atoms[e]`+' ' s.addChild("atomArray",a) if self._comment: s.addChild("note",self._comment) if self._charge <> -999: s.addChild("charge",self._charge) if self._size <> 1.0: s.addChild("size",self._size) if self._thermo: t = s.addChild("thermo") if type(self._thermo) == types.InstanceType: self._thermo.build(t) else: nt = len(self._thermo) for n in range(nt): self._thermo[n].build(t) if self._transport: t = s.addChild("transport") if type(self._transport) == types.InstanceType: self._transport.build(t) else: nt = len(self._transport) for n in range(nt): self._transport[n].build(t) class thermo: """Base class for species standard-state thermodynamic properties.""" def _build(self, p): return p.addChild("thermo") def export(self, f, fmt = 'CSV'): pass class NASA(thermo): """NASA polynomial parameterization.""" def __init__(self, range = (0.0, 0.0), coeffs = [], p0 = -1.0): self._t = range self._pref = p0 if len(coeffs) <> 7: raise CTI_Error('NASA coefficient list must have length = 7') self._coeffs = coeffs def export(self, f, fmt='CSV'): if fmt == 'CSV': str = 'NASA,'+`self._t[0]`+','+`self._t[1]`+',' for i in range(7): str += '%17.9E, ' % self._coeffs[i] f.write(str) def build(self, t): n = t.addChild("NASA") n['Tmin'] = `self._t[0]` #n['Tmid'] = `self._t[1]` n['Tmax'] = `self._t[1]` if self._pref <= 0.0: n['P0'] = `_pref` else: n['P0'] = `self._pref` str = '' for i in range(4): str += '%17.9E, ' % self._coeffs[i] str += '\n' str += '%17.9E, %17.9E, %17.9E' % (self._coeffs[4], self._coeffs[5], self._coeffs[6]) #if i > 0 and 3*((i+1)/3) == i: str += '\n' #str = str[:-2] u = n.addChild("floatArray", str) u["size"] = "7" u["name"] = "coeffs" class Shomate(thermo): """Shomate polynomial parameterization.""" def __init__(self, range = (0.0, 0.0), coeffs = [], p0 = -1.0): self._t = range self._pref = p0 if len(coeffs) <> 7: raise CTI_Error('Shomate coefficient list must have length = 7') self._coeffs = coeffs def build(self, t): n = t.addChild("Shomate") n['Tmin'] = `self._t[0]` n['Tmax'] = `self._t[1]` if self._pref <= 0.0: n['P0'] = `_pref` else: n['P0'] = `self._pref` str = '' for i in range(4): str += '%17.9E, ' % self._coeffs[i] str += '\n' str += '%17.9E, %17.9E, %17.9E' % (self._coeffs[4], self._coeffs[5], self._coeffs[6]) u = n.addChild("floatArray", str) u["size"] = "7" u["name"] = "coeffs" class const_cp(thermo): """Constant specific heat.""" def __init__(self, t0 = 298.15, cp0 = 0.0, h0 = 0.0, s0 = 0.0, tmax = 5000.0, tmin = 100.0): self._t = [tmin, tmax] self._c = [t0, h0, s0, cp0] def build(self, t): #t = self._build(p) c = t.addChild('const_cp') if self._t[0] >= 0.0: c['Tmin'] = `self._t[0]` if self._t[1] >= 0.0: c['Tmax'] = `self._t[1]` energy_units = _uenergy+'/'+_umol addFloat(c,'t0',self._c[0], defunits = 'K') addFloat(c,'h0',self._c[1], defunits = energy_units) addFloat(c,'s0',self._c[2], defunits = energy_units+'/K') addFloat(c,'cp0',self._c[3], defunits = energy_units+'/K') class gas_transport: """Transport coefficients for ideal gas transport model.""" def __init__(self, geom = 'nonlin', diam = 0.0, well_depth = 0.0, dipole = 0.0, polar = 0.0, rot_relax = 0.0): self._geom = geom self._diam = diam self._well_depth = well_depth self._dipole = dipole self._polar = polar self._rot_relax = rot_relax def build(self, t): #t = s.addChild("transport") t['model'] = 'gas_transport' # t.addChild("geometry", self._geom) tg = t.addChild('string',self._geom) tg['title'] = 'geometry' addFloat(t, "LJ_welldepth", (self._well_depth, 'K'), '%8.3f') addFloat(t, "LJ_diameter", (self._diam, 'A'),'%8.3f') addFloat(t, "dipoleMoment", (self._dipole, 'Debye'),'%8.3f') addFloat(t, "polarizability", (self._polar, 'A3'),'%8.3f') addFloat(t, "rotRelax", self._rot_relax,'%8.3f') class Arrhenius: def __init__(self, A = 0.0, n = 0.0, E = 0.0, coverage = [], rate_type = ''): self._c = [A, n, E] self._type = rate_type if coverage: if type(coverage[0]) == types.StringType: self._cov = [coverage] else: self._cov = coverage else: self._cov = None def build(self, p, units_factor = 1.0, gas_species = [], name = '', rxn_phase = None): a = p.addChild('Arrhenius') if name: a['name'] = name # check for sticking probability if self._type: a['type'] = self._type if self._type == 'stick': ngas = len(gas_species) if ngas <> 1: raise CTI_Error(""" Sticking probabilities can only be used for reactions with one gas-phase reactant, but this reaction has """+`ngas`+': '+`gas_species`) else: a['species'] = gas_species[0] units_factor = 1.0 # if a pure number is entered for A, multiply by the conversion # factor to SI and write it to CTML as a pure number. Otherwise, # pass it as-is through to CTML with the unit string. if isnum(self._c[0]): addFloat(a,'A',self._c[0]*units_factor, fmt = '%14.6E') elif len(self._c[0]) == 2 and self._c[0][1] == '/site': addFloat(a,'A',self._c[0][0]/rxn_phase._sitedens, fmt = '%14.6E') else: addFloat(a,'A',self._c[0], fmt = '%14.6E') # The b coefficient should be dimensionless, so there is no # need to use 'addFloat' a.addChild('b',`self._c[1]`) # If a pure number is entered for the activation energy, # add the default units, otherwise use the supplied units. addFloat(a,'E', self._c[2], fmt = '%f', defunits = _ue) # for surface reactions, a coverage dependence may be specified. if self._cov: for cov in self._cov: c = a.addChild('coverage') c['species'] = cov[0] addFloat(c, 'a', cov[1], fmt = '%f') c.addChild('m', `cov[2]`) addFloat(c, 'e', cov[3], fmt = '%f', defunits = _ue) def stick(A = 0.0, n = 0.0, E = 0.0, coverage = []): return Arrhenius(A = A, n = n, E = E, coverage = coverage, rate_type = 'stick') def getPairs(s): toks = s.split() m = {} for t in toks: key, val = t.split(':') m[key] = float(val) return m class reaction: def __init__(self, equation = '', kf = None, id = '', order = '', options = [] ): self._id = id self._e = equation self._order = order if type(options) == types.StringType: self._options = [options] else: self._options = options global _reactions self._num = len(_reactions)+1 r = '' p = '' for e in ['<=>', '=>', '=']: if self._e.find(e) >= 0: r, p = self._e.split(e) if e in ['<=>','=']: self.rev = 1 else: self.rev = 0 break self._r = getReactionSpecies(r) self._p = getReactionSpecies(p) self._rxnorder = copy.copy(self._r) if self._order: ord = getPairs(self._order) for o in ord.keys(): if self._rxnorder.has_key(o): self._rxnorder[o] = ord[o] else: raise CTI_Error("order specified for non-reactant: "+o) self._kf = kf self._igspecies = [] self._dims = [0]*4 self._rxnphase = None self._type = '' _reactions.append(self) def build(self, p): if self._id: id = self._id else: if self._num < 10: nstr = '000'+`self._num` elif self._num < 100: nstr = '00'+`self._num` elif self._num < 1000: nstr = '0'+`self._num` else: nstr = `self._num` id = nstr mdim = 0 ldim = 0 str = '' rxnph = [] for s in self._r.keys(): ns = self._rxnorder[s] nm = -999 nl = -999 str += s+':'+`self._r[s]`+' ' mindim = 4 for ph in _phases: if ph.has_species(s): nm, nl = ph.conc_dim() if ph.is_ideal_gas(): self._igspecies.append(s) if not ph in rxnph: rxnph.append(ph) self._dims[ph._dim] += 1 if ph._dim < mindim: self._rxnphase = ph mindim = ph._dim break if nm == -999: raise CTI_Error("species "+s+" not found") mdim += nm*ns ldim += nl*ns p.addComment(" reaction "+id+" ") r = p.addChild('reaction') r['id'] = id if self.rev: r['reversible'] = 'yes' else: r['reversible'] = 'no' noptions = len(self._options) for nss in range(noptions): s = self._options[nss] if s == 'duplicate': r['duplicate'] = 'yes' elif s == 'negative_A': r['negative_A'] = 'yes' ee = self._e.replace('<','[') ee = ee.replace('>',']') r.addChild('equation',ee) if self._order: for osp in self._rxnorder.keys(): o = r.addChild('order',self._rxnorder[osp]) o['species'] = osp # adjust the moles and length powers based on the dimensions of # the rate of progress (moles/length^2 or moles/length^3) if self._type == 'surface': mdim += -1 ldim += 2 p = self._dims[:3] if p[0] <> 0 or p[1] <> 0 or p[2] > 1: raise CTI_Error(self._e +'\nA surface reaction may contain at most '+ 'one surface phase.') elif self._type == 'edge': mdim += -1 ldim += 1 p = self._dims[:2] if p[0] <> 0 or p[1] > 1: raise CTI_Error(self._e+'\nAn edge reaction may contain at most '+ 'one edge phase.') else: mdim += -1 ldim += 3 # add the reaction type as an attribute if it has been specified. if self._type: r['type'] = self._type # The default rate coefficient type is Arrhenius. If the rate # coefficient has been specified as a sequence of three # numbers, then create a new Arrhenius instance for it; # otherwise, just use the supplied instance. nm = '' kfnode = r.addChild('rateCoeff') if self._type == '': self._kf = [self._kf] elif self._type == 'surface': self._kf = [self._kf] elif self._type == 'edge': self._kf = [self._kf] elif self._type == 'threeBody': self._kf = [self._kf] mdim += 1 ldim -= 3 if self._type == 'edge': if self._beta > 0: electro = kfnode.addChild('electrochem') electro['beta'] = `self._beta` for kf in self._kf: unit_fctr = (math.pow(_length[_ulen], -ldim) * math.pow(_moles[_umol], -mdim) / _time[_utime]) if type(kf) == types.InstanceType: k = kf else: k = Arrhenius(A = kf[0], n = kf[1], E = kf[2]) k.build(kfnode, unit_fctr, gas_species = self._igspecies, name = nm, rxn_phase = self._rxnphase) # set values for low-pressure rate coeff if falloff rxn mdim += 1 ldim -= 3 nm = 'k0' str = str[:-1] r.addChild('reactants',str) str = '' for s in self._p.keys(): ns = self._p[s] str += s+':'+`ns`+' ' str = str[:-1] r.addChild('products',str) return r #------------------- class three_body_reaction(reaction): def __init__(self, equation = '', kf = None, efficiencies = '', id = '', options = [] ): reaction.__init__(self, equation, kf, id, '', options) self._type = 'threeBody' self._effm = 1.0 self._eff = efficiencies # clean up reactant and product lists for r in self._r.keys(): if r == 'M' or r == 'm': del self._r[r] for p in self._p.keys(): if p == 'M' or p == 'm': del self._p[p] def build(self, p): r = reaction.build(self, p) if r == 0: return kfnode = r.child('rateCoeff') if self._eff: eff = kfnode.addChild('efficiencies',self._eff) eff['default'] = `self._effm` #--------------- class falloff_reaction(reaction): def __init__(self, equation = '', kf0 = None, kf = None, efficiencies = '', falloff = None, id = '', options = [] ): kf2 = (kf, kf0) reaction.__init__(self, equation, kf2, id, '', options) self._type = 'falloff' # use a Lindemann falloff function by default self._falloff = falloff if self._falloff == None: self._falloff = Lindemann() self._effm = 1.0 self._eff = efficiencies # clean up reactant and product lists del self._r['(+'] del self._p['(+'] if self._r.has_key('M)'): del self._r['M)'] del self._p['M)'] if self._r.has_key('m)'): del self._r['m)'] del self._p['m)'] else: for r in self._r.keys(): if r[-1] == ')' and r.find('(') < 0: if self._eff: raise CTI_Error('(+ '+mspecies+') and '+self._eff+' cannot both be specified') self._eff = r[-1]+':1.0' self._effm = 0.0 del self._r[r] del self._p[r] def build(self, p): r = reaction.build(self, p) if r == 0: return kfnode = r.child('rateCoeff') if self._eff and self._effm >= 0.0: eff = kfnode.addChild('efficiencies',self._eff) eff['default'] = `self._effm` if self._falloff: self._falloff.build(kfnode) class surface_reaction(reaction): def __init__(self, equation = '', kf = None, id = '', order = '', options = []): reaction.__init__(self, equation, kf, id, order, options) self._type = 'surface' class edge_reaction(reaction): def __init__(self, equation = '', kf = None, id = '', order = '', beta = 0.0, options = []): reaction.__init__(self, equation, kf, id, order, options) self._type = 'edge' self._beta = beta #-------------- class state: def __init__(self, temperature = None, pressure = None, mole_fractions = None, mass_fractions = None, density = None, coverages = None): self._t = temperature self._p = pressure self._rho = density self._x = mole_fractions self._y = mass_fractions self._c = coverages def build(self, ph): st = ph.addChild('state') if self._t: addFloat(st, 'temperature', self._t, defunits = 'K') if self._p: addFloat(st, 'pressure', self._p, defunits = _upres) if self._rho: addFloat(st, 'density', self._rho, defunits = _umass+'/'+_ulen+'3') if self._x: st.addChild('moleFractions', self._x) if self._y: st.addChild('massFractions', self._y) if self._c: st.addChild('coverages', self._c) class phase: """Base class for phases of matter.""" def __init__(self, name = '', dim = 3, elements = '', species = '', reactions = 'none', initial_state = None, options = []): self._name = name self._dim = dim self._el = elements self._sp = [] self._rx = [] if type(options) == types.StringType: self._options = [options] else: self._options = options self.debug = 0 if 'debug' in options: self.debug = 1 #-------------------------------- # process species #-------------------------------- # if a single string is entered, make it a list if type(species) == types.StringType: self._species = [species] else: self._species = species self._skip = 0 # dictionary of species names self._spmap = {} # for each species string, check whether or not the species # are imported or defined locally. If imported, the string # contains a colon (:) for sp in self._species: icolon = sp.find(':') if icolon > 0: #datasrc, spnames = sp.split(':') datasrc = sp[:icolon].strip() spnames = sp[icolon+1:] self._sp.append((datasrc+'.xml', spnames)) else: spnames = sp self._sp.append(('', spnames)) # strip the commas, and make the list of species names # 10/31/03: commented out the next line, so that species names may contain commas #sptoks = spnames.replace(',',' ').split() sptoks = spnames.split() for s in sptoks: # check for stray commas if s <> ',': if s[0] == ',': s = s[1:] if s[-1] == ',': s = s[:-1] if s <> 'all' and self._spmap.has_key(s): raise CTI_Error('Multiply-declared species '+s+' in phase '+self._name) self._spmap[s] = self._dim self._rxns = reactions # check that species have been declared if len(self._spmap) == 0: raise CTI_Error('No species declared for phase '+self._name) # and that only one species is declared if it is a pure phase if self.is_pure() and len(self._spmap) > 1: raise CTI_Error('Stoichiometric phases must declare exactly one species, \n'+ 'but phase '+self._name+' declares '+`len(self._spmap)`+'.') self._initial = initial_state # add this phase to the global phase list global _phases _phases.append(self) def is_ideal_gas(self): """True if the entry represents an ideal gas.""" return 0 def is_pure(self): return 0 def has_species(self, s): """Return 1 is a species with name 's' belongs to the phase, or 0 otherwise.""" if self._spmap.has_key(s): return 1 return 0 def conc_dim(self): """Concentration dimensions. Used in computing the units for reaction rate coefficients.""" return (1, -self._dim) def buildrxns(self, p): if type(self._rxns) == types.StringType: self._rxns = [self._rxns] # for each reaction string, check whether or not the reactions # are imported or defined locally. If imported, the string # contains a colon (:) for r in self._rxns: icolon = r.find(':') if icolon > 0: #datasrc, rnum = r.split(':') datasrc = r[:icolon].strip() rnum = r[icolon+1:] self._rx.append((datasrc+'.xml', rnum)) else: rnum = r self._rx.append(('', rnum)) for r in self._rx: datasrc = r[0] ra = p.addChild('reactionArray') ra['datasrc'] = datasrc+'#reaction_data' if 'skip_undeclared_species' in self._options: rk = ra.addChild('skip') rk['species'] = 'undeclared' rtoks = r[1].split() if rtoks[0] <> 'all': i = ra.addChild('include') #i['prefix'] = 'reaction_' i['min'] = rtoks[0] if len(rtoks) > 2 and (rtoks[1] == 'to' or rtoks[1] == '-'): i['max'] = rtoks[2] else: i['max'] = rtoks[0] def build(self, p): p.addComment(' phase '+self._name+' ') ph = p.addChild('phase') ph['id'] = self._name ph['dim'] = `self._dim` # ------- error tests ------- #err = ph.addChild('validation') #err.addChild('duplicateReactions','halt') #err.addChild('thermo','warn') e = ph.addChild('elementArray',self._el) e['datasrc'] = 'elements.xml' for s in self._sp: datasrc, names = s sa = ph.addChild('speciesArray',names) sa['datasrc'] = datasrc+'#species_data' if 'skip_undeclared_elements' in self._options: sk = sa.addChild('skip') sk['element'] = 'undeclared' if self._rxns <> 'none': self.buildrxns(ph) #self._eos.build(ph) if self._initial: self._initial.build(ph) return ph class ideal_gas(phase): """An ideal gas mixture.""" def __init__(self, name = '', elements = '', species = '', reactions = 'none', kinetics = 'GasKinetics', transport = 'None', initial_state = None, options = []): phase.__init__(self, name, 3, elements, species, reactions, initial_state, options) self._pure = 0 self._kin = kinetics self._tr = transport if self.debug: print 'Read ideal_gas entry '+self._name try: print 'in file '+__name__ except: pass def build(self, p): ph = phase.build(self, p) e = ph.addChild("thermo") e['model'] = 'IdealGas' k = ph.addChild("kinetics") k['model'] = self._kin t = ph.addChild('transport') t['model'] = self._tr def is_ideal_gas(self): return 1 class stoichiometric_solid(phase): """A solid compound or pure element.Stoichiometric solid phases contain exactly one species, which always has unit activity. The solid is assumed to have constant density. Therefore the rates of reactions involving these phases do not contain any concentration terms for the (one) species in the phase, since the concentration is always the same. """ def __init__(self, name = '', elements = '', species = '', density = -1.0, transport = 'None', initial_state = None, options = []): phase.__init__(self, name, 3, elements, species, 'none', initial_state, options) self._dens = density self._pure = 1 if self._dens < 0.0: raise CTI_Error('density must be specified.') self._tr = transport def conc_dim(self): """A stoichiometric solid always has unit activity, so the generalized concentration is 1 (dimensionless).""" return (0,0) def build(self, p): ph = phase.build(self, p) e = ph.addChild("thermo") e['model'] = 'StoichSubstance' addFloat(e, 'density', self._dens, defunits = _umass+'/'+_ulen+'3') if self._tr: t = ph.addChild('transport') t['model'] = self._tr k = ph.addChild("kinetics") k['model'] = 'none' class stoichiometric_liquid(stoichiometric_solid): """A stoichiometric liquid. Currently, there is no distinction between stoichiometric liquids and solids.""" def __init__(self, name = '', elements = '', species = '', density = -1.0, transport = 'None', initial_state = None, options = []): stoichiometric_solid.__init__(self, name, elements, species, density, transport, initial_state, options) ## class pure_solid(stoichiometric_solid): ## """Deprecated. Use stoichiometric_solid""" ## def __init__(self, ## name = '', ## elements = '', ## species = '', ## density = -1.0, ## transport = 'None', ## initial_state = None, ## options = []): ## stoichiometric_solid.__init__(self, name, 3, elements, ## species, 'none', ## initial_state, options) ## self._dens = density ## self._pure = 1 ## if self._dens < 0.0: ## raise CTI_Error('density must be specified.') ## self._tr = transport ## print 'WARNING: entry type pure_solid is deprecated.' ## print 'Use stoichiometric_solid instead.' class metal(phase): """A metal.""" def __init__(self, name = '', elements = '', species = '', density = -1.0, transport = 'None', initial_state = None, options = []): phase.__init__(self, name, 3, elements, species, 'none', initial_state, options) self._dens = density self._pure = 0 self._tr = transport def conc_dim(self): return (0,0) def build(self, p): ph = phase.build(self, p) e = ph.addChild("thermo") e['model'] = 'Metal' addFloat(e, 'density', self._dens, defunits = _umass+'/'+_ulen+'3') if self._tr: t = ph.addChild('transport') t['model'] = self._tr k = ph.addChild("kinetics") k['model'] = 'none' class incompressible_solid(phase): """An incompressible solid.""" def __init__(self, name = '', elements = '', species = '', density = -1.0, transport = 'None', initial_state = None, options = []): phase.__init__(self, name, 3, elements, species, 'none', initial_state, options) self._dens = density self._pure = 0 if self._dens < 0.0: raise CTI_Error('density must be specified.') self._tr = transport def conc_dim(self): return (1,-3) def build(self, p): ph = phase.build(self, p) e = ph.addChild("thermo") e['model'] = 'Incompressible' addFloat(e, 'density', self._dens, defunits = _umass+'/'+_ulen+'3') if self._tr: t = ph.addChild('transport') t['model'] = self._tr k = ph.addChild("kinetics") k['model'] = 'none' class lattice: def __init__(self, name = '', site_density = -1.0, vacancy_species = ''): self._name = name self._n = site_density self._vac = vacancy_species if name == '': raise CTI_Error('sublattice name must be specified') if site_density < 0.0: raise CTI_Error('sublattice '+name +' site density must be specified') def build(self,p): lat = p.addChild('Lattice') lat['name'] = self._name addFloat(lat, 'site_density', self._n, defunits = _umol+'/'+_ulen+'3') if self._vac: lat.addChild('vacancy_species',self._vac) class lattice_solid(phase): """A solid crystal consisting of one or more sublattices.""" def __init__(self, name = '', elements = '', species = '', lattices = [], transport = 'None', initial_state = None, options = []): phase.__init__(self, name, 3, elements, species, 'none', initial_state, options) self._lattices = lattices if lattices == []: raise CTI_Error('One or more sublattices must be specified.') self._pure = 0 self._tr = transport def conc_dim(self): return (0,0) def build(self, p): ph = phase.build(self, p) e = ph.addChild("thermo") e['model'] = 'LatticeSolid' if self._lattices: lat = e.addChild('LatticeArray') for n in self._lattices: n.build(lat) if self._tr: t = ph.addChild('transport') t['model'] = self._tr k = ph.addChild("kinetics") k['model'] = 'none' class liquid_vapor(phase): """A fluid with a complete liquid/vapor equation of state. This entry type selects one of a set of predefined fluids with built-in liquid/vapor equations of state. The substance_flag parameter selects the fluid. See purefluids.py for the usage of this entry type.""" def __init__(self, name = '', elements = '', species = '', substance_flag = 0, initial_state = None, options = []): phase.__init__(self, name, 3, elements, species, 'none', initial_state, options) self._subflag = substance_flag self._pure = 1 def conc_dim(self): return (0,0) def build(self, p): ph = phase.build(self, p) e = ph.addChild("thermo") e['model'] = 'PureFluid' e['fluid_type'] = `self._subflag` k = ph.addChild("kinetics") k['model'] = 'none' class ideal_interface(phase): """An ideal interface.""" def __init__(self, name = '', elements = '', species = '', reactions = 'none', site_density = 0.0, phases = [], kinetics = 'Interface', transport = 'None', initial_state = None, options = []): self._type = 'surface' phase.__init__(self, name, 2, elements, species, reactions, initial_state, options) self._pure = 0 self._kin = kinetics self._tr = transport self._phases = phases self._sitedens = site_density def build(self, p): ph = phase.build(self, p) e = ph.addChild("thermo") e['model'] = 'Surface' addFloat(e, 'site_density', self._sitedens, defunits = _umol+'/'+_ulen+'2') k = ph.addChild("kinetics") k['model'] = self._kin t = ph.addChild('transport') t['model'] = self._tr p = ph.addChild('phaseArray',self._phases) def conc_dim(self): return (1, -2) class edge(phase): """A 1D boundary between two surface phases.""" def __init__(self, name = '', elements = '', species = '', reactions = 'none', site_density = 0.0, phases = [], kinetics = 'Edge', transport = 'None', initial_state = None, options = []): self._type = 'edge' phase.__init__(self, name, 1, elements, species, reactions, initial_state, options) self._pure = 0 self._kin = kinetics self._tr = transport self._phases = phases self._sitedens = site_density def build(self, p): ph = phase.build(self, p) e = ph.addChild("thermo") e['model'] = 'Edge' addFloat(e, 'site_density', self._sitedens, defunits = _umol+'/'+_ulen) k = ph.addChild("kinetics") k['model'] = self._kin t = ph.addChild('transport') t['model'] = self._tr p = ph.addChild('phaseArray',self._phases) def conc_dim(self): return (1, -1) #------------------------------------------------------------------- # falloff parameterizations class Troe: def __init__(self, A = 0.0, T3 = 0.0, T1 = 0.0, T2 = -999.9): if T2 <> -999.9: self._c = (A, T3, T1, T2) else: self._c = (A, T3, T1) def build(self, p): s = '' for num in self._c: s += '%g ' % num f = p.addChild('falloff', s) f['type'] = 'Troe' class SRI: def __init__(self, A = 0.0, B = 0.0, C = 0.0, D = -999.9, E=-999.9): if D <> -999.9 and E <> -999.9: self._c = (A, B, C, D, E) else: self._c = (A, B, C) def build(self, p): s = '' for num in self._c: s += '%g ' % num f = p.addChild('falloff', s) f['type'] = 'SRI' class Lindemann: def __init__(self): pass def build(self, p): f = p.addChild('falloff') f['type'] = 'Lindemann' #get_atomic_wts() validate() if __name__ == "__main__": import sys, os file = sys.argv[1] base = os.path.basename(file) root, ext = os.path.splitext(base) dataset(root) execfile(file) write()