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Cantera CTML writer
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| units(length = "cm", time = "s", quantity = "mol", act_energy = "cal/mol") | |
| RedlichKwongMFTP(name = "carbondioxide", | |
| elements = " C O H ", | |
| species = """ CO2 H2O """, | |
| activity_coefficients = (pureFluidParameters(species="CO2", a_coeff = [7.54e12, -4.13e9], b_coeff = 27.80), | |
| pureFluidParameters(species="H2O", a_coeff = [1.7458E13, -8.0E9], b_coeff = 18.18), | |
| crossFluidParameters(species="CO2 H2O", a_coeff = [7.897e12, 0]) ), | |
| initial_state = state(temperature = 300.0, | |
| pressure = OneAtm, | |
| mole_fractions = 'CO2:0.9999, H2O:0.0001') ) | |
| #------------------------------------------------------------------------------- | |
| # Species data | |
| #------------------------------------------------------------------------------- | |
| species(name = "CO2", | |
| atoms = " C:1 O:2 ", | |
| thermo = ( | |
| NASA( [ 200.00, 1000.00], [ 2.356773520E+00, 8.984596770E-03, | |
| -7.123562690E-06, 2.459190220E-09, -1.436995480E-13, | |
| -4.837196970E+04, 9.901052220E+00] ), | |
| NASA( [ 1000.00, 3500.00], [ 3.857460290E+00, 4.414370260E-03, | |
| -2.214814040E-06, 5.234901880E-10, -4.720841640E-14, | |
| -4.875916600E+04, 2.271638060E+00] ) | |
| ), | |
| ) | |
| species(name = "H2O", | |
| atoms = " H:2 O:1 ", | |
| thermo = ( | |
| NASA( [ 273.00, 1000.00], [ 4.198640560E+00, -2.036434100E-03, | |
| 6.520402110E-06, -5.487970620E-09, 1.771978170E-12, | |
| -3.029372670E+04, -8.490322080E-01] ), | |
| NASA( [ 1000.00, 1600.00], [ 3.033992490E+00, 2.176918040E-03, | |
| -1.640725180E-07, -9.704198700E-11, 1.682009920E-14, | |
| -3.000429710E+04, 4.966770100E+00] ) | |
| ), | |
| ) |
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| #!/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.""" | |
| 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.""" | |
| f = open(filename, 'w') | |
| f.write('<?xml version="1.0"?>\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+'<!--') | |
| if len(self._value) > 0: | |
| if self._value[0] != ' ': | |
| self._value = ' '+self._value | |
| if self._value[-1] != ' ': | |
| self._value = self._value+' ' | |
| f.write(self._value+'-->') | |
| 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 = self._value.lstrip() | |
| ieol = vv.find('\n') | |
| if ieol >= 0: | |
| while 1 > 0: | |
| ieol = vv.find('\n') | |
| if ieol >= 0: | |
| f.write('\n '+indnt+vv[:ieol]) | |
| vv = vv[ieol+1:].lstrip() | |
| 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('</'+self._name+'>') | |
| #-------------------------------------------------- | |
| # 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 <element>:<atoms> 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: | |
| if self._num < 10: | |
| nstr = '000'+str(self._num) | |
| elif self._num < 100: | |
| nstr = '00'+str(self._num) | |
| elif self._num < 1000: | |
| nstr = '0'+str(self._num) | |
| else: | |
| nstr = str(self._num) | |
| id = nstr | |
| self.mdim = 0 | |
| self.ldim = 0 | |
| rstr = '' | |
| rxnph = [] | |
| for s in self._r.keys(): | |
| ns = self._rxnorder[s] | |
| nm = -999 | |
| nl = -999 | |
| rstr += s+':'+str(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") | |
| 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' | |
| 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': | |
| 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' | |
| rstr = rstr[:-1] | |
| r.addChild('reactants',rstr) | |
| pstr = '' | |
| for s in self._p.keys(): | |
| ns = self._p[s] | |
| pstr += s+':'+repr(ns)+' ' | |
| pstr = pstr[:-1] | |
| 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 falloff_reaction(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 | |
| # 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)'] | |
| 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 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 additiona 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 fluid with a complete liqui/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 = '', | |
| initial_state = None, | |
| activity_coefficients = None, | |
| options = []): | |
| phase.__init__(self,name, 3, elements, species, 'none', | |
| initial_state,options) | |
| self._pure = 0 | |
| 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) | |
| 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) 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).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).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:]) |
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Starting from version from Cantera trunk as of Subversion revision 2391