#!/usr/bin/env python ## # @file ctml_writer.py # # Cantera .cti input file processor # @defgroup pygroup Cantera Python Interface # # 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' from __future__ import print_function class CTI_Error(Exception): """Exception raised if an error is encountered while parsing the input file. @ingroup pygroup""" def __init__(self, msg): print('\n\n***** Error parsing input file *****\n\n') print(msg) print() indent = ['', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' '] #----------------------------------------------------- class XMLnode(object): """This is a minimal class to allow easy creation of an XML tree from Python. It can write XML, but cannot read it.""" __slots__ = ('_name', '_value', '_attribs', '_children', '_childmap') 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 not isinstance(value, str): self._value = repr(value).lstrip() else: self._value = value.lstrip() 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 children(self): """ An iterator over the child nodes """ for c in self._children: yield c 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, filename): """Write out the XML tree to a file.""" s = ['\n'] self._write(s, 0) s.append('\n') with open(filename, 'w') as f: f.write(''.join(s)) def write_comment(self, s, level): s.append('\n'+indent[level]+'') def write_attribs(self, s): for a in self._attribs: s.append(' '+a+'="'+self._attribs[a]+'"') def write_value(self, s, level): indnt = indent[level] vv = self._value.lstrip() ieol = vv.find('\n') if ieol >= 0: while True: ieol = vv.find('\n') if ieol >= 0: s.extend(('\n ', indnt, vv[:ieol])) vv = vv[ieol+1:].lstrip() else: s.extend(('\n ',indnt,vv)) break else: s.append(self._value) def _write(self, s, level = 0): """Internal method used to write the XML representation of each node.""" if not self.name: return # handle comments if self._name == '_comment_': self.write_comment(s, level) return indnt = indent[level] # write the opening tag and attributes s.extend((indnt, '<', self._name)) self.write_attribs(s) if not self._value and not self._children: s.append('/>') else: s.append('>') if self._value: self.write_value(s, level) for c in self._children: s.append('\n') c._write(s, level + 2) if self._children: s.extend(('\n', indnt)) s.extend(('')) #-------------------------------------------------- # constants that can be used in .cti files OneAtm = 1.01325e5 OneBar = 1.0e5 # Conversion from eV to J/kmol (electronCharge * Navrog) eV = 9.64853364595687e7 # Electron Mass in kg ElectronMass = 9.10938291e-31 import 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':1.0/6.02214129e26} _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(filename, fmt = 'CSV'): global _valexport global _valfmt _valexport = filename _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 isinstance(a, (int, float)): 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. :param length: The default units for length. Default: ``'m'`` :param mass: The default units for mass. Default: ``'kg'`` :param quantity: The default units to specify number of molecules. Default: ``'kmol'`` :param time: The default units for time. Default: ``'s'`` :param energy: The default units for energies. Default: ``'J'`` :param act_energy: The default units for activation energies. Default: ``'K'`` :param pressure: The default units for pressure. Default: ``'Pa'`` """ 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+str(n) if n < 0: return '/'+base+str(-n) def write(outName=None): """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 outName is not None: x.write(outName) elif _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 = repr(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 = repr(v) xc = x.addChild(nm, s) xc['units'] = u def getAtomicComp(atoms): if isinstance(atoms, dict): 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: # already seen this token so increment its value by the last # value of n if t in d: d[t] += n else: # first time this token has been seen, so set its value to n d[t] = n # reset n to 1.0 for species that do not specify a stoichiometric # coefficient n = 1 return d class element(object): """ An atomic element or isotope. """ def __init__(self, symbol = '', atomic_mass = 0.01, atomic_number = 0): """ :param symbol: The symbol for the element or isotope. :param atomic_mass: The atomic mass in amu. """ 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"] = repr(self._atw) e["atomicNumber"] = repr(self._num) class species_set(object): 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(object): """A constituent of a phase or interface.""" def __init__(self, name = 'missing name!', atoms = '', note = '', thermo = None, transport = None, charge = -999, size = 1.0): """ :param name: The species name (or formula). The name may be arbitrarily long, although usually a relatively short, abbreviated name is most convenient. Required parameter. :param atoms: The atomic composition, specified by a string containing space-delimited : pairs. The number of atoms may be either an integer or a floating-point number. :param thermo: The parameterization to use to compute the reference-state thermodynamic properties. This must be one of the entry types described in :ref:`sec-thermo-models`. To specify multiple parameterizations, each for a different temperature range, group them in parentheses. :param transport: An entry specifying parameters to compute this species' contribution to the transport properties. This must be one of the entry types described in :ref:`sec-species-transport-models`, and must be consistent with the transport model of the phase into which the species is imported. To specify parameters for multiple transport models, group the entries in parentheses. :param size: The species "size". Currently used only for surface species, where it represents the number of sites occupied. :param charge: The charge, in multiples of :math:`|e|`. If not specified, the charge will be calculated from the number of "atoms" of element ``E``, which represents an electron. """ 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 'E' in self._atoms: 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': s = self._name+',' for e in _enames: if e in self._atoms: s += repr(self._atoms[e])+',' else: s += '0,' f.write(s) if isinstance(self._thermo, thermo): 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+':'+str(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 isinstance(self._thermo, thermo): 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 isinstance(self._transport, transport): self._transport.build(t) else: nt = len(self._transport) for n in range(nt): self._transport[n].build(t) class thermo(object): """Base class for species standard-state thermodynamic properties.""" def _build(self, p): return p.addChild("thermo") def export(self, f, fmt = 'CSV'): pass class Mu0_table(thermo): """Properties are computed by specifying a table of standard chemical potentials vs. T.""" def __init__(self, Trange = (0.0, 0.0), h298 = 0.0, mu0 = None, p0 = -1.0): self._t = Trange self._h298 = h298 self._mu0 = mu0 self._pref = p0 def build(self, t): n = t.addChild("Mu0") n['Tmin'] = repr(self._t[0]) n['Tmax'] = repr(self._t[1]) if self._pref <= 0.0: n['P0'] = repr(_pref) else: n['P0'] = repr(self._pref) energy_units = _uenergy+'/'+_umol addFloat(n,"H298", self._h298, defunits = energy_units) n.addChild("numPoints", len(self._mu0)) mustr = '' tstr = '' col = 0 for v in self._mu0: mu0 = v[1] t = v[0] tstr += '%17.9E, ' % t mustr += '%17.9E, ' % mu0 col += 1 if col == 3: tstr = tstr[:-2]+'\n' mustr = mustr[:-2]+'\n' col = 0 u = n.addChild("floatArray", mustr) u["size"] = "numPoints" u["name"] = "Mu0Values" u = n.addChild("floatArray", tstr) u["size"] = "numPoints" u["name"] = "Mu0Temperatures" class NASA(thermo): """The 7-coefficient NASA polynomial parameterization.""" def __init__(self, Trange = (0.0, 0.0), coeffs = [], p0 = -1.0): r""" :param Trange: The temperature range over which the parameterization is valid. This must be entered as a sequence of two temperature values. Required. :param coeffs: Array of seven coefficients :math:`(a_0, \ldots , a_6)` :param p0: The reference-state pressure, usually 1 atm or 1 bar. If omitted, the default value is used, which is set by the ``standard_pressure`` directive. """ self._t = Trange 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': s = 'NASA,'+str(self._t[0])+','+str(self._t[1])+',' for i in range(7): s += '%17.9E, ' % self._coeffs[i] f.write(s) def build(self, t): n = t.addChild("NASA") n['Tmin'] = repr(self._t[0]) #n['Tmid'] = repr(self._t[1]) n['Tmax'] = repr(self._t[1]) if self._pref <= 0.0: n['P0'] = repr(_pref) else: n['P0'] = repr(self._pref) s = '' for i in range(4): s += '%17.9E, ' % self._coeffs[i] s += '\n' s += '%17.9E, %17.9E, %17.9E' % (self._coeffs[4], self._coeffs[5], self._coeffs[6]) #if i > 0 and 3*((i+1)/3) == i: s += '\n' #s = s[:-2] u = n.addChild("floatArray", s) u["size"] = "7" u["name"] = "coeffs" class NASA9(thermo): """NASA9 polynomial parameterization for a single temperature region.""" def __init__(self, Trange = (0.0, 0.0), coeffs = [], p0 = -1.0): self._t = Trange # Range of the polynomial representation self._pref = p0 # Reference pressure if len(coeffs) != 9: raise CTI_Error('NASA9 coefficient list must have length = 9') self._coeffs = coeffs def export(self, f, fmt='CSV'): if fmt == 'CSV': s = 'NASA9,'+str(self._t[0])+','+str(self._t[1])+',' for i in range(9): s += '%17.9E, ' % self._coeffs[i] f.write(s) def build(self, t): n = t.addChild("NASA9") n['Tmin'] = repr(self._t[0]) n['Tmax'] = repr(self._t[1]) if self._pref <= 0.0: n['P0'] = repr(_pref) else: n['P0'] = repr(self._pref) s = '' for i in range(4): s += '%17.9E, ' % self._coeffs[i] s += '\n' s += '%17.9E, %17.9E, %17.9E, %17.9E,' % (self._coeffs[4], self._coeffs[5], self._coeffs[6], self._coeffs[7]) s += '\n' s += '%17.9E' % (self._coeffs[8]) u = n.addChild("floatArray", s) u["size"] = "9" u["name"] = "coeffs" class activityCoefficients(object): pass class pureFluidParameters(activityCoefficients): """ """ def __init__(self, species = None, a_coeff = [], b_coeff = 0): """ """ self._species = species self._acoeff = a_coeff self._bcoeff = b_coeff def build(self,a): f= a.addChild("pureFluidParameters") f['species'] = self._species s = '%10.4E, %10.4E \n' % (self._acoeff[0], self._acoeff[1]) ac = f.addChild("a_coeff",s) ac["units"] = _upres+'-'+_ulen+'6/'+_umol+'2' ac["model"] = "linear_a" s = '%0.2f \n' % self._bcoeff bc = f.addChild("b_coeff",s) bc["units"] = _ulen+'3/'+_umol class crossFluidParameters(activityCoefficients): def __init__(self, species = None, a_coeff = [], b_coeff = []): self._species1, self._species2 = species.split(' ') self._acoeff = a_coeff self._bcoeff = b_coeff def build(self,a): f= a.addChild("crossFluidParameters") f["species2"] = self._species2 f["species1"] = self._species1 s = '%10.4E, %10.4E \n' % (self._acoeff[0], self._acoeff[1]) ac = f.addChild("a_coeff",s) ac["units"] = _upres+'-'+_ulen+'6/'+_umol+'2' ac["model"] = "linear_a" if self._bcoeff: s = '%0.2f \n' % self._bcoeff bc = f.addChild("b_coeff",s) bc["units"] = _ulen+'3/'+_umol class Shomate(thermo): """Shomate polynomial parameterization.""" def __init__(self, Trange = (0.0, 0.0), coeffs = [], p0 = -1.0): r""" :param Trange: The temperature range over which the parameterization is valid. This must be entered as a sequence of two temperature values. Required input. :param coeffs: Sequence of seven coefficients :math:`(A, \ldots ,G)` :param p0: The reference-state pressure, usually 1 atm or 1 bar. If omitted, the default value set by the ``standard_pressure`` directive is used. """ self._t = Trange 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'] = repr(self._t[0]) n['Tmax'] = repr(self._t[1]) if self._pref <= 0.0: n['P0'] = repr(_pref) else: n['P0'] = repr(self._pref) s = '' for i in range(4): s += '%17.9E, ' % self._coeffs[i] s += '\n' s += '%17.9E, %17.9E, %17.9E' % (self._coeffs[4], self._coeffs[5], self._coeffs[6]) u = n.addChild("floatArray", s) u["size"] = "7" u["name"] = "coeffs" class Adsorbate(thermo): """Adsorbed species characterized by a binding energy and a set of vibrational frequencies.""" def __init__(self, Trange = (0.0, 0.0), binding_energy = 0.0, frequencies = [], p0 = -1.0): self._t = Trange self._pref = p0 self._freqs = frequencies self._be = binding_energy def build(self, t): n = t.addChild("adsorbate") n['Tmin'] = repr(self._t[0]) n['Tmax'] = repr(self._t[1]) if self._pref <= 0.0: n['P0'] = repr(_pref) else: n['P0'] = repr(self._pref) energy_units = _uenergy+'/'+_umol addFloat(n,'binding_energy',self._be, defunits = energy_units) s = "" nfreq = len(self._freqs) for i in range(nfreq): s += '%17.9E, ' % self._freqs[i] s += '\n' u = n.addChild("floatArray", s) u["size"] = repr(nfreq) u["name"] = "freqs" 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): """ :param t0: Temperature parameter T0. Default: 298.15 K. :param cp0: Reference-state molar heat capacity (constant). Default: 0.0. :param h0: Reference-state molar enthalpy at temperature T0. Default: 0.0. :param s0: Reference-state molar entropy at temperature T0. Default: 0.0. """ 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'] = repr(self._t[0]) if self._t[1] >= 0.0: c['Tmax'] = repr(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 transport(object): pass class gas_transport(transport): """ Species-specific Transport coefficients for ideal gas transport models. """ def __init__(self, geom = 'nonlin', diam = 0.0, well_depth = 0.0, dipole = 0.0, polar = 0.0, rot_relax = 0.0): """ :param geom: A string specifying the molecular geometry. One of ``atom``, ``linear``, or ``nonlin``. Required. :param diam: The Lennard-Jones collision diameter in Angstroms. Required. :param well_depth: The Lennard-Jones well depth in Kelvin. Required. :param dipole: The permanent dipole moment in Debye. Default: 0.0 :param polar: The polarizability in A^3. Default: 0.0 :param rot_relax: The rotational relaxation collision number at 298 K. Dimensionless. Default: 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 rate_expression(object): pass class Arrhenius(rate_expression): def __init__(self, A = 0.0, n = 0.0, E = 0.0, coverage = [], rate_type = ''): """ :param A: The pre-exponential coefficient. Required input. If entered without units, the units will be computed considering all factors that affect the units. The resulting units string is written to the CTML file individually for each reaction pre-exponential coefficient. :param n: The temperature exponent. Dimensionless. Default: 0.0. :param E: Activation energy. Default: 0.0. """ self._c = [A, n, E] self._type = rate_type if coverage: if isinstance(coverage[0], str): 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 """+str(ngas)+': '+str(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', repr(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', repr(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(object): """ A homogeneous chemical reaction with pressure-independent rate coefficient and mass-action kinetics. """ def __init__(self, equation = '', kf = None, id = '', order = '', options = []): """ :param equation: A string specifying the chemical equation. :param rate_coeff: The rate coefficient for the forward direction. If a sequence of three numbers is given, these will be interpreted as [A, n,E] in the modified Arrhenius function :math:`A T^n exp(-E/\hat{R}T)`. :param id: An optional identification string. If omitted, it defaults to a four-digit numeric string beginning with 0001 for the first reaction in the file. :param options: Processing options, as described in :ref:`sec-phase-options`. """ self._id = id self._e = equation self._order = order if isinstance(options, str): 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: order = getPairs(self._order) for o in order.keys(): if o in self._rxnorder: self._rxnorder[o] = order[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 unit_factor(self): """ Conversion factor from given rate constant units to the MKS (+kmol) used internally by Cantera, taking into account the reaction order. """ return (math.pow(_length[_ulen], -self.ldim) * math.pow(_moles[_umol], -self.mdim) / _time[_utime]) def build(self, p): if self._id: id = self._id else: id = '%04i' % self._num self.mdim = 0 self.ldim = 0 rxnph = [] for s in self._r: ns = self._rxnorder[s] nm = -999 nl = -999 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") self.mdim += nm*ns self.ldim += nl*ns p.addComment(" reaction "+id+" ") r = p.addChild('reaction') r['id'] = id if self.rev: r['reversible'] = 'yes' else: r['reversible'] = 'no' for s in self._options: if s == 'duplicate': r['duplicate'] = 'yes' elif s == 'negative_A': r['negative_A'] = 'yes' ee = self._e.replace('<','[').replace('>',']') r.addChild('equation',ee) if self._order: for osp in self._rxnorder: 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': self.mdim += -1 self.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': self.mdim += -1 self.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: self.mdim += -1 self.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] self.mdim += 1 self.ldim -= 3 elif self._type == 'chebyshev': self._kf = [] if self._type == 'edge': if self._beta > 0: electro = kfnode.addChild('electrochem') electro['beta'] = repr(self._beta) for kf in self._kf: if isinstance(kf, rate_expression): k = kf else: k = Arrhenius(A = kf[0], n = kf[1], E = kf[2]) k.build(kfnode, self.unit_factor(), gas_species = self._igspecies, name = nm, rxn_phase = self._rxnphase) if self._type == 'falloff': # set values for low-pressure rate coeff if falloff rxn self.mdim += 1 self.ldim -= 3 nm = 'k0' elif self._type == 'chemAct': # set values for high-pressure rate coeff if this is a # chemically activated reaction self.mdim -= 1 self.ldim += 3 nm = 'kHigh' rstr = ' '.join('%s:%s' % item for item in self._r.items()) pstr = ' '.join('%s:%s' % item for item in self._p.items()) r.addChild('reactants',rstr) r.addChild('products', pstr) return r #------------------- class three_body_reaction(reaction): """ A three-body reaction. """ def __init__(self, equation = '', kf = None, efficiencies = '', id = '', options = [] ): """ :param equation: A string specifying the chemical equation. The reaction can be written in either the association or dissociation directions, and may be reversible or irreversible. :param rate_coeff: The rate coefficient for the forward direction. If a sequence of three numbers is given, these will be interpreted as [A,n,E] in the modified Arrhenius function. :param efficiencies: A string specifying the third-body collision efficiencies. The efficiencies for unspecified species are set to 1.0. :param id: An optional identification string. If omitted, it defaults to a four-digit numeric string beginning with 0001 for the first reaction in the file. :param options: Processing options, as described in :ref:`sec-phase-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 list(self._r.keys()): if r == 'M' or r == 'm': del self._r[r] for p in list(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'] = repr(self._effm) class pdep_reaction(reaction): """ Base class for falloff_reaction and chemically_activated_reaction """ def clean_up_reactants_products(self): del self._r['(+'] del self._p['(+'] if 'M)' in self._r: del self._r['M)'] del self._p['M)'] elif 'm)' in self._r: del self._r['m)'] del self._p['m)'] else: for r in list(self._r.keys()): if r[-1] == ')' and r.find('(') < 0: species = r[:-1] if self._eff: raise CTI_Error('(+ '+species+') and '+self._eff+' cannot both be specified') self._eff = species+':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'] = repr(self._effm) if self._falloff: self._falloff.build(kfnode) class falloff_reaction(pdep_reaction): """ A gas-phase falloff reaction. """ def __init__(self, equation, kf0, kf, efficiencies='', falloff=None, id='', options=[]): """ :param equation: A string specifying the chemical equation. :param rate_coeff_inf: The rate coefficient for the forward direction in the high-pressure limit. If a sequence of three numbers is given, these will be interpreted as [A, n,E] in the modified Arrhenius function. :param rate_coeff_0: The rate coefficient for the forward direction in the low-pressure limit. If a sequence of three numbers is given, these will be interpreted as [A, n,E] in the modified Arrhenius function. :param efficiencies: A string specifying the third-body collision efficiencies. The efficiency for unspecified species is set to 1.0. :param falloff: An embedded entry specifying a falloff function. If omitted, a unity falloff function (Lindemann form) will be used. :param id: An optional identification string. If omitted, it defaults to a four-digit numeric string beginning with 0001 for the first reaction in the file. :param options: Processing options, as described in :ref:`sec-phase-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 self.clean_up_reactants_products() class chemically_activated_reaction(pdep_reaction): """ A gas-phase, chemically activated reaction. """ def __init__(self, equation, kLow, kHigh, efficiencies='', falloff=None, id='', options=[]): """ :param equation: A string specifying the chemical equation. :param kLow: The rate coefficient for the forward direction in the low-pressure limit. If a sequence of three numbers is given, these will be interpreted as [A, n,E] in the modified Arrhenius function. :param kHigh: The rate coefficient for the forward direction in the high-pressure limit. If a sequence of three numbers is given, these will be interpreted as [A, n,E] in the modified Arrhenius function. :param efficiencies: A string specifying the third-body collision efficiencies. The efficiency for unspecified species is set to 1.0. :param falloff: An embedded entry specifying a falloff function. If omitted, a unity falloff function (Lindemann form) will be used. :param id: An optional identification string. If omitted, it defaults to a four-digit numeric string beginning with 0001 for the first reaction in the file. :param options: Processing options, as described in :ref:`sec-phase-options`. """ reaction.__init__(self, equation, (kLow, kHigh), id, '', options) self._type = 'chemAct' # use a Lindemann falloff function by default self._falloff = falloff if self._falloff == None: self._falloff = Lindemann() self._effm = 1.0 self._eff = efficiencies self.clean_up_reactants_products() class pdep_arrhenius(reaction): """ Pressure-dependent rate calculated by interpolating between Arrhenius expressions at different pressures. :param equation: A string specifying the chemical equation. :param args: Each additional argument is a sequence of four elements specifying the pressure and the Arrhenius parameters at that pressure. """ def __init__(self, equation='', *args, **kwargs): self.pressures = [] self.arrhenius = [] for p, A, n, Ea in args: self.pressures.append(p) self.arrhenius.append((A, n, Ea)) reaction.__init__(self, equation, self.arrhenius, **kwargs) self._type = 'plog' def build(self, p): r = reaction.build(self, p) kfnode = r.child('rateCoeff') for i,c in enumerate(kfnode.children()): assert c.name() == 'Arrhenius' addFloat(c, 'P', self.pressures[i]) class chebyshev_reaction(reaction): """ Pressure-dependent rate calculated in terms of a bivariate Chebyshev polynomial. :param equation: A string specifying the chemical equation. :param Tmin: The minimum temperature at which the rate expression is defined :param Tmax: the maximum temperature at which the rate expression is defined :param Pmin: The minimum pressure at which the rate expression is defined :param Pmax: The maximum pressure at which the rate expression is defined :param coeffs: A 2D array of the coefficients defining the rate expression. For a polynomial with M points in temperature and N points in pressure, this should be a list of M lists each with N elements. """ def __init__(self, equation='', Tmin=300.0, Tmax=2500.0, Pmin=(0.001, 'atm'), Pmax=(100.0, 'atm'), coeffs=[[]], **kwargs): reaction.__init__(self, equation, **kwargs) self._type = 'chebyshev' self.Pmin = Pmin self.Pmax = Pmax self.Tmin = Tmin self.Tmax = Tmax self.coeffs = coeffs # clean up reactant and product lists del self._r['(+'] del self._p['(+'] if 'M)' in self._r: del self._r['M)'] del self._p['M)'] if 'm)' in self._r: del self._r['m)'] del self._p['m)'] def build(self, p): r = reaction.build(self, p) kfnode = r.child('rateCoeff') addFloat(kfnode, 'Tmin', self.Tmin) addFloat(kfnode, 'Tmax', self.Tmax) addFloat(kfnode, 'Pmin', self.Pmin) addFloat(kfnode, 'Pmax', self.Pmax) self.coeffs[0][0] += math.log10(self.unit_factor()); lines = [] for line in self.coeffs: lines.append(', '.join('{0:12.5e}'.format(val) for val in line)) coeffNode = kfnode.addChild('floatArray', ',\n'.join(lines)) coeffNode['name'] = 'coeffs' coeffNode['degreeT'] = str(len(self.coeffs)) coeffNode['degreeP'] = str(len(self.coeffs[0])) class surface_reaction(reaction): """ A heterogeneous chemical reaction with pressure-independent rate coefficient and mass-action kinetics. """ def __init__(self, equation='', kf=None, id='', order='', options=[]): """ :param equation: A string specifying the chemical equation. :param rate_coeff: The rate coefficient for the forward direction. If a sequence of three numbers is given, these will be interpreted as [A, n,E] in the modified Arrhenius function. :param sticking_prob: The reactive sticking probability for the forward direction. This can only be specified if there is only one bulk-phase reactant and it belongs to an ideal gas phase. If a sequence of three numbers is given, these will be interpreted as [A, n,E] in the modified Arrhenius function. :param id: An optional identification string. If omitted, it defaults to a four-digit numeric string beginning with 0001 for the first reaction in the file. :param options: Processing options, as described in :ref:`sec-phase-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(object): """ An embedded entry that specifies the thermodynamic state of a phase or interface. """ def __init__(self, temperature = None, pressure = None, mole_fractions = None, mass_fractions = None, density = None, coverages = None, solute_molalities = None): """ :param temperature: The temperature. :param pressure: The pressure. :param density: The density. Cannot be specified if the phase is incompressible. :param mole_fractions: A string specifying the species mole fractions. Unspecified species are set to zero. :param mass_fractions: A string specifying the species mass fractions. Unspecified species are set to zero. :param coverages: A string specifying the species coverages. Unspecified species are set to zero. Can only be specified for interfaces. """ self._t = temperature self._p = pressure self._rho = density self._x = mole_fractions self._y = mass_fractions self._c = coverages self._m = solute_molalities 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) if self._m: st.addChild('soluteMolalities', self._m) class phase(object): """Base class for phases of matter.""" def __init__(self, name = '', dim = 3, elements = '', species = '', reactions = 'none', initial_state = None, options = []): """ :param name: A string to identify the phase. Must be unique among the phase names within the file. :param elements: The elements. A string of element symbols. :param species: The species. A string or sequence of strings in the format described in :ref:`sec-defining-species`. :param reactions: The homogeneous reactions. If omitted, no reactions will be included. A string or sequence of strings in the format described in :ref:`sec-declaring-reactions`. This field is not allowed for stoichiometric_solid and stoichiometric_liquid entries. :param kinetics: The kinetics model. Optional; if omitted, the default model for the phase type will be used. :param transport: The transport property model. Optional. If omitted, transport property calculation will be disabled. :param initial_state: Initial thermodynamic state, specified with an embedded state entry. :param options: Special processing options. Optional. """ self._name = name self._dim = dim self._el = elements self._sp = [] self._rx = [] if isinstance(options, str): 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 isinstance(species, str): 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 s in self._spmap: 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 '+str(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 s in self._spmap: 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 isinstance(self._rxns, str): 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' rk = None if 'skip_undeclared_species' in self._options: rk = ra.addChild('skip') rk['species'] = 'undeclared' if 'skip_undeclared_third_bodies' in self._options: if not rk: rk = ra.addChild('skip') rk['third_bodies'] = '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'] = repr(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 = []): """ The parameters correspond to those of :class:`.phase`, with the following modifications: :param kinetics: The kinetics model. Usually this field is omitted, in which case kinetics model GasKinetics, appropriate for reactions in ideal gas mixtures, is used. :param transport: The transport property model. One of the strings ``'none'``, ``'multi'``, or ``'mix'``. Default: ``'none'``. """ 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 = None, transport = 'None', initial_state = None, options = []): """ See :class:`.phase` for descriptions of the parameters. """ phase.__init__(self, name, 3, elements, species, 'none', initial_state, options) self._dens = density self._pure = 1 if self._dens is None: 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): """ An incompressible 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 = []): """ See :class:`.phase` for descriptions of the parameters. """ stoichiometric_solid.__init__(self, name, elements, species, density, transport, initial_state, options) 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 semiconductor(phase): """A semiconductor.""" def __init__(self, name = '', elements = '', species = '', density = -1.0, bandgap = 1.0 * eV, effectiveMass_e = 1.0 * ElectronMass, effectiveMass_h = 1.0 * ElectronMass, 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 self._emass = effectiveMass_e self._hmass = effectiveMass_h self._bandgap = bandgap def conc_dim(self): return (1,-3) def build(self, p): ph = phase.build(self, p) e = ph.addChild("thermo") e['model'] = 'Semiconductor' addFloat(e, 'density', self._dens, defunits = _umass+'/'+_ulen+'3') addFloat(e, 'effectiveMass_e', self._emass, defunits = _umass) addFloat(e, 'effectiveMass_h', self._hmass, defunits = _umass) addFloat(e, 'bandgap', self._bandgap, defunits = 'eV') 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(phase): def __init__(self, name = '', elements = '', species = '', reactions = 'none', transport = 'None', initial_state = None, options = [], site_density = -1.0, vacancy_species = ''): phase.__init__(self, name, 3, elements, species, 'none', initial_state, options) self._tr = transport self._n = site_density self._vac = vacancy_species self._species = species if name == '': raise CTI_Error('sublattice name must be specified') if species == '': raise CTI_Error('sublattice species must be specified') if site_density < 0.0: raise CTI_Error('sublattice '+name +' site density must be specified') def build(self,p, visible = 0): #if visible == 0: # return ph = phase.build(self, p) e = ph.addChild('thermo') e['model'] = 'Lattice' addFloat(e, 'site_density', self._n, defunits = _umol+'/'+_ulen+'3') if self._vac: e.addChild('vacancy_species',self._vac) if self._tr: t = ph.addChild('transport') t['model'] = self._tr k = ph.addChild("kinetics") k['model'] = 'none' 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 = []): # find elements elist = [] for lat in lattices: e = lat._el.split() for el in e: if not el in elist: elist.append(el) elements = ' '.join(elist) # find species slist = [] for lat in lattices: _sp = "" for spp in lat._species: _sp = _sp + spp s = _sp.split() for sp in s: if not sp in slist: slist.append(sp) species = ' '.join(slist) 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, visible = 1) 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'] = repr(self._subflag) k = ph.addChild("kinetics") k['model'] = 'none' class RedlichKwongMFTP(phase): """A multi-component fluid model for non-ideal gas fluids. """ def __init__(self, name = '', elements = '', species = '', initial_state = None, activity_coefficients = None, transport = 'None', options = []): phase.__init__(self,name, 3, elements, species, 'none', initial_state,options) self._pure = 0 self._tr = transport self._activityCoefficients = activity_coefficients def conc_dim(self): return (0,0) def build(self, p): ph = phase.build(self,p) e = ph.addChild("thermo") e['model'] = 'RedlichKwongMFTP' if self._activityCoefficients: a = e.addChild("activityCoefficients") if isinstance(self._activityCoefficients, activityCoefficients): self._activityCoefficients.build(a) else: na = len(self._activityCoefficients) for n in range(na): self._activityCoefficients[n].build(a) if self._tr: t = ph.addChild('transport') t['model'] = self._tr k = ph.addChild("kinetics") k['model'] = 'none' class redlich_kwong(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 = 7, initial_state = None, Tcrit = 1.0, Pcrit = 1.0, options = []): phase.__init__(self, name, 3, elements, species, 'none', initial_state, options) self._subflag = 7 self._pure = 1 self._tc = 1 self._pc = 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'] = repr(self._subflag) addFloat(e, 'Tc', self._tc, defunits = "K") addFloat(e, 'Pc', self._pc, defunits = "Pa") addFloat(e, 'MolWt', self._mw, defunits = _umass+"/"+_umol) ph.addChild("kinetics") k['model'] = 'none' class ideal_interface(phase): """A chemically-reacting ideal surface solution of multiple species.""" def __init__(self, name = '', elements = '', species = '', reactions = 'none', site_density = 0.0, phases = [], kinetics = 'Interface', transport = 'None', initial_state = None, options = []): """ The parameters correspond to those of :class:`.phase`, with the following modifications: :param reactions: The heterogeneous reactions at this interface. If omitted, no reactions will be included. A string or sequence of strings in the format described in :ref:`sec-declaring-reactions`. :param site_density: The number of adsorption sites per unit area. :param phases: A string listing the bulk phases that participate in reactions at this interface. """ 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) ## class binary_salt_parameters: ## def __init__(self, ## cation = "", ## anion = "", ## beta0 = None, ## beta1 = None, ## beta2 = None, ## Cphi = None, ## Alpha1 = -1.0): ## self._cation = cation ## self._anion = anion ## self._beta0 = beta0 ## self._beta1 = beta1 ## self._Cphi = Cphi ## self._Alpha1 = Alpha1 ## def build(self, a): ## s = a.addChild("binarySaltParameters") ## s["cation"] = self._cation ## s["anion"] = self._anion ## s.addChild("beta0", self._beta0) ## s.addChild("beta1", self._beta1) ## s.addChild("beta2", self._beta2) ## s.addChild("Cphi", self._Cphi) ## s.addChild("Alpha1", self._Alpha1) ## class theta_anion: ## def __init__(self, ## anions = None, ## theta = 0.0): ## self._anions = anions ## self._theta = theta ## def build(self, a): ## s = a.addChild("thetaAnion") ## s["anion1"] = self._anions[0] ## s["anion2"] = self._anions[1] ## s.addChild("Theta", self._theta) ## class psi_common_cation: ## def __init__(self, ## anions = None, ## cation = '', ## theta = 0.0, ## psi = 0.0): ## self._anions = anions ## self._cation = cation ## self._theta = theta ## self._psi = psi ## def build(self, a): ## s = a.addChild("psiCommonCation") ## s["anion1"] = self._anions[0] ## s["anion2"] = self._anions[1] ## s["cation"] = self._cation ## s.addChild("Theta", self._theta) ## s.addChild("Psi", self._psi) ## class psi_common_anion: ## def __init__(self, ## anion = '', ## cations = None, ## theta = 0.0, ## psi = 0.0): ## self._anion = anion ## self._cations = cations ## self._theta = theta ## self._psi = psi ## def build(self, a): ## s = a.addChild("psiCommonAnion") ## s["anion1"] = self._cations[0] ## s["anion2"] = self._cations[1] ## s["cation"] = self._anion ## s.addChild("Theta", self._theta) ## s.addChild("Psi", self._psi) ## class theta_cation: ## def __init__(self, ## cations = None, ## theta = 0.0): ## self._cations = cations ## self._theta = theta ## def build(self, a): ## s = a.addChild("thetaCation") ## s["cation1"] = self._anions[0] ## s["cation2"] = self._anions[1] ## s.addChild("Theta", self._theta) ## class pitzer: ## def __init__(self, ## temp_model = "", ## A_Debye = "", ## default_ionic_radius = -1.0, ## class electrolyte(phase): ## """An electrolye solution obeying the HMW model.""" ## def __init__(self, ## name = '', ## elements = '', ## species = '', ## transport = 'None', ## initial_state = None, ## solvent = '', ## standard_concentration = '', ## activity_coefficients = None, ## options = []): ## phase.__init__(self, name, 3, elements, species, 'none', ## initial_state, options) ## self._pure = 0 ## self._solvent = solvent ## self._stdconc = standard_concentration ## def conc_dim(self): ## return (1,-3) ## def build(self, p): ## ph = phase.build(self, p) ## e = ph.addChild("thermo") ## sc = e.addChild("standardConc") ## sc['model'] = self._stdconc ## e['model'] = 'HMW' ## e.addChild("activity_coefficients") ## 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' #------------------------------------------------------------------- # falloff parameterizations class Troe(object): """The Troe falloff function.""" def __init__(self, A = 0.0, T3 = 0.0, T1 = 0.0, T2 = -999.9): """ Parameters: *A*, *T3*, *T1*, *T2*. These must be entered as pure numbers with no attached dimensions. """ 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(object): """ The SRI falloff function.""" def __init__(self, A = 0.0, B = 0.0, C = 0.0, D = -999.9, E=-999.9): """ Parameters: *A*, *B*, *C*, *D*, *E*. These must be entered as pure numbers without attached dimensions. """ 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(object): """The Lindemann falloff function.""" def __init__(self): """ This falloff function takes no parameters.""" pass def build(self, p): f = p.addChild('falloff') f['type'] = 'Lindemann' #get_atomic_wts() validate() def convert(filename, outName=None): import os, sys base = os.path.basename(filename) root, _ = os.path.splitext(base) dataset(root) try: with open(filename, 'rU') as f: code = compile(f.read(), filename, 'exec') exec(code) except SyntaxError as err: # Show more context than the default SyntaxError message # to help see problems in multi-line statements text = open(filename, 'rU').readlines() print('%s in "%s" on line %i:\n' % (err.__class__.__name__, err.filename, err.lineno)) print('| Line |') for i in range(max(err.lineno-6, 0), min(err.lineno+3, len(text))): print('| % 5i |' % (i+1), text[i].rstrip()) if i == err.lineno-1: print(' '* (err.offset+9) + '^') print() sys.exit(3) except TypeError as err: import traceback text = open(filename, 'rU').readlines() tb = traceback.extract_tb(sys.exc_info()[2]) lineno = tb[-1][1] print('%s on line %i of %s:' % (err.__class__.__name__, lineno, filename)) print(err) print('\n| Line |') for i in range(max(lineno-6, 0), min(lineno+3, len(text))): if i == lineno-1: print('> % 4i >' % (i+1), text[i].rstrip()) else: print('| % 4i |' % (i+1), text[i].rstrip()) sys.exit(4) write(outName) if __name__ == "__main__": import sys if len(sys.argv) not in (2,3): raise ValueError('Incorrect number of command line arguments.') convert(*sys.argv[1:])