*** empty log message ***

Cantera/clib/src/ct.cpp

@@ -22,6 +22,7 @@
 #include "converters/ck2ctml.h"
 #include "Storage.h"
 #include "Cabinet.h"
+#include "InterfaceKinetics.h"
 
 #include "clib_defs.h"
 
@@ -475,10 +476,17 @@ extern "C" {
             return -10;
     }
 
+    int DLL_EXPORT th_setElectricPotential(int n, double v) {
+        th(n)->setElectricPotential(v);
+        return 0;
+    }
+
+
     //-------------- Kinetics ------------------//
 
     int DLL_EXPORT newKineticsFromXML(int mxml, int iphase, 
-        int neighbor1, int neighbor2) {
+        int neighbor1, int neighbor2, int neighbor3, 
+        int neighbor4) {
         try {
             XML_Node* x = _xml(mxml);
             vector<thermo_t*> phases;
@@ -487,6 +495,12 @@ extern "C" {
                 phases.push_back(th(neighbor1));
                 if (neighbor2 >= 0) {
                     phases.push_back(th(neighbor2));
+                    if (neighbor3 >= 0) {
+                        phases.push_back(th(neighbor3));
+                        if (neighbor4 >= 0) {
+                            phases.push_back(th(neighbor4));
+                        }
+                    }
                 }
             }
             Kinetics* kin = newKineticsMgr(*x, phases);
@@ -648,6 +662,10 @@ extern "C" {
         return kin(n)->multiplier(i);
     }
 
+    int DLL_EXPORT kin_phase(int n, int i) {
+        return thermo_index(kin(n)->thermo(i).id());
+    }
+
     int DLL_EXPORT kin_getEquilibriumConstants(int n, int len, double* kc) {
         try {
             Kinetics* k = kin(n);
@@ -684,6 +702,20 @@ extern "C" {
         catch (CanteraError) {return -1;}
     }
 
+    int DLL_EXPORT kin_advanceCoverages(int n, double tstep) {
+        try {
+            Kinetics* k = kin(n);
+            if (k->type() == cInterfaceKinetics) {
+                ((InterfaceKinetics*)k)->advanceCoverages(tstep);
+            }
+            else {
+                throw CanteraError("kin_advanceCoverages",
+                    "wrong kinetics manager type");
+            }
+            return 0;
+        }
+        catch (CanteraError) {return -1;}
+    }
 
     //------------------- Transport ---------------------------
 

Cantera/clib/src/ct.h

@@ -66,6 +66,7 @@ extern "C" {
     int DLL_IMPORT th_getEnthalpies_RT(int n, int lenm, double* h_rt);
     int DLL_IMPORT th_getEntropies_R(int n, int lenm, double* s_r);
     int DLL_IMPORT th_getCp_R(int n, int lenm, double* cp_r);
+    int DLL_IMPORT th_setElectricPotential(int n, double v);
     int DLL_IMPORT get_eos(char* fname, char* phase_id);
 
     int DLL_IMPORT th_set_HP(int n, double* vals);
@@ -75,7 +76,8 @@ extern "C" {
     int DLL_IMPORT th_equil(int n, int XY);
 
     int DLL_IMPORT newKineticsFromXML(int mxml, int iphase, 
-        int neighbor1=-1, int neighbor2=-1);
+        int neighbor1=-1, int neighbor2=-1, int neighbor3=-1,
+        int neighbor4=-1);
     int DLL_IMPORT installRxnArrays(int pxml, int ikin, 
         char* default_phase);
     int DLL_IMPORT kin_nSpecies(int n);
@@ -99,6 +101,8 @@ extern "C" {
     int DLL_IMPORT kin_type(int n);
     int DLL_IMPORT kin_start(int n, int p);
     int DLL_IMPORT kin_speciesIndex(int n, const char* nm, const char* ph);
+    int DLL_IMPORT kin_advanceCoverages(int n, double tstep);
+    int DLL_IMPORT kin_phase(int n, int i);
 
     int DLL_IMPORT newTransport(char* model,  
         int th, int loglevel);

Cantera/clib/src/ctsurf.cpp

@@ -2,6 +2,7 @@
 // Cantera includes
 #include "SurfPhase.h"
 #include "InterfaceKinetics.h"
+#include "ImplicitSurfChem.h"
 
 #include "Cabinet.h"
 #include "Storage.h"

Cantera/clib/src/ctxml.cpp

@@ -93,6 +93,16 @@ extern "C" {
         return 0;
     }
 
+    int DLL_EXPORT xml_addComment(int i, const char* comment) {
+        try {
+            string c = string(comment);
+            XML_Node& node = *_xml(i);
+            node.addComment(c);
+        }
+        catch (CanteraError) { return -1; }
+        return 0;
+    }
+
     int DLL_EXPORT xml_tag(int i, char* tag) {
         try {
             XML_Node& node = *_xml(i);

Cantera/clib/src/ctxml.h

@@ -12,6 +12,7 @@ extern "C" {
     int DLL_IMPORT xml_build(int i, const char* file);
     int DLL_IMPORT xml_attrib(int i, const char* key, char* value);
     int DLL_IMPORT xml_addAttrib(int i, const char* key, const char* value);
+    int DLL_IMPORT xml_addComment(int i, const char* comment);
     int DLL_IMPORT xml_value(int i, char* value);
     int DLL_IMPORT xml_tag(int i, char* tag);
     int DLL_IMPORT xml_child(int i, const char* loc);

Cantera/matlab/cantera/examples/prandtl2.m

@@ -13,10 +13,15 @@ else
 end
 
 pr = zeros(31,31);
+xh2 = zeros(31,31);
+visc = zeros(31,31);
+lambda = zeros(31,31);
 t = [];
 xo2 = [];
 io2 = speciesIndex(gas,'O2');
 ih2 = speciesIndex(gas,'H2');
+ih = speciesIndex(gas,'H');
+ih2o = speciesIndex(gas,'H2O');
 
 atm = oneatm;
 t0 = cputime;
@@ -29,9 +34,11 @@ for i = 1:31
       x(ih2) = 1.0 - xo2(j);
       set(gas,'T',t(i),'P',oneatm,'X',x);
       equilibrate(gas,'TP');
-      pr(i,j) = viscosity(gas)*cp_mass(gas)/ ...
-		thermalConductivity(gas);
-      
+      visc(i,j) = viscosity(gas);
+      lambda(i,j) = thermalConductivity(gas);  
+      pr(i,j) = visc(i,j)*cp_mass(gas)/lambda(i,j);
+      x = moleFractions(gas);
+      xh2(i,j) = x(ih2);      
    end
 end
 disp(['CPU time = ' num2str(cputime - t0)]);
@@ -39,8 +46,27 @@ disp(['CPU time = ' num2str(cputime - t0)]);
 % plot results
 
 figure(1);
+subplot(2,2,1);
 surf(xo2,t,pr);
 xlabel('Elemental O/(O+H)');
 ylabel('Temperature (K)');
 zlabel('Prandtl Number');
 
+subplot(2,2,2);
+surf(xo2,t,xh2);
+xlabel('Elemental O/(O+H)');
+ylabel('Temperature (K)');
+zlabel('H_2 Mole Fraction');
+
+subplot(2,2,3);
+surf(xo2,t,visc);
+xlabel('Elemental O/(O+H)');
+ylabel('Temperature (K)');
+zlabel('Viscosity');
+
+subplot(2,2,4);
+surf(xo2,t,lambda);
+xlabel('Elemental O/(O+H)');
+ylabel('Temperature (K)');
+zlabel('Thermal Conductivity');
+

Cantera/python/Cantera/Interface.py

@@ -22,17 +22,22 @@ class Interface(SurfacePhase, Kinetics):
 
         fn = string.split(src,'#')
         fn = fn[0]
+        id = ""
+        if len(fn) > 1: id = fn[1]        
         fname = os.path.basename(fn)
         ff = os.path.splitext(fname)
         
         # get the 'phase' element
-        s = XML.find_XML(src=src, root=root, name="phase")
+        if id:
+            s = XML.find_XML(src=src, root=root, id=id)
+        else:
+            s = XML.find_XML(src=src, root=root, name="phase")                
 
         # get the equation of state model
         SurfacePhase.__init__(self, xml_phase=s)
 
         # get the kinetics model
-        Kinetics.__init__(self, xml_phase=s, phases=[self]+phases)
+        Kinetics.__init__(self, xml_phase=s, phases=phases+[self])
 
 
     def __del__(self):

Cantera/python/Cantera/Kinetics.py

@@ -1,5 +1,5 @@
 
-from Cantera.exceptions import CanteraError
+from Cantera.exceptions import CanteraError, getCanteraError
 from Cantera.ThermoPhase import ThermoPhase
 from Cantera.XML import XML_Node
 import Numeric
@@ -47,23 +47,45 @@ class Kinetics:
                     the specification of the parameters.
         """
         np = len(phases)
+        self._np = np
         self._ph = {}
+        self._sp = []
+        for p in phases:
+            self._ph[p.thermophase()] = p
+        self._phnum = {}
+        
         self._end = [0]
         p0 = phases[0].thermophase()
-        self._ph[phases[0]] = 0
-        self._end.append(phases[0].nSpecies())
+        #self._ph[phases[0]] = phases
+        #self._end.append(phases[0].nSpecies())
         p1 = -1
         p2 = -1
+        p3 = -1
+        p4 = -1
         if np >= 2:
             p1 = phases[1].thermophase()
-            self._ph[phases[1]] = 1
-            self._end.append(self._end[-1] + phases[1].nSpecies())
         if np >= 3:
             p2 = phases[2].thermophase()
-            self._ph[phases[2]] = 2
-            self._end.append(self._end[-1] + phases[2].nSpecies())            
+        if np >= 4:
+            p3 = phases[3].thermophase()
+        if np >= 5:
+            p4 = phases[4].thermophase()
+        if np >= 6:
+            raise CanteraError("only 4 neighbor phases allowed")
+        #try:
         self.ckin = _cantera.KineticsFromXML(xml_phase,
-                                               p0, p1, p2)
+                                                 p0, p1, p2, p3, p4)
+        
+        for nn in range(self._np):
+                p = self.phase(nn)
+                self._phnum[p] = nn
+                self._end.append(self._end[-1]+p.nSpecies())
+                for k in range(p.nSpecies()):
+                    self._sp.append(p.speciesName(k))
+                
+        #except:
+        #    print getCanteraError()
+        #    self.ckin = 0
         self.phases = phases
         
 
@@ -85,6 +107,9 @@ class Kinetics:
 
     def kineticsStart(self, n):
         return _cantera.kin_start(self.ckin, n)
+
+    def phase(self, n):
+        return self._ph[_cantera.kin_phase(self.ckin, n)]
     
     def nReactions(self):
         """Number of reactions."""
@@ -101,18 +126,41 @@ class Kinetics:
         """Type of reaction 'i'"""
         return _cantera.kin_rxntype(self.ckin,i)
 
-    def reactionString(self,i):
-        return _cantera.kin_getstring(self.ckin,1,i)
+    #def reactionString(self,i):
+    #    return _cantera.kin_getstring(self.ckin,1,i)
 
     def reactionEqn(self,i):
         try:
             eqs = []
             for rxn in i:
-                eqs.append(_cantera.kin_getstring(self.ckin,1,rxn))
+                eqs.append(self.reactionString(rxn))
             return eqs
         except:
-            return _cantera.kin_getstring(self.ckin,1,i)
+            return self.reactionString(i)
 
+    def reactionString(self, i):
+        s = ''
+        nsp = _cantera.kin_nspecies(self.ckin)
+        for k in range(nsp):
+            nur = _cantera.kin_rstoichcoeff(self.ckin,k,i)
+            if nur <> 0.0:
+                if nur <> 1.0:
+                    s += `int(nur)`+' '
+                s += self._sp[k]+' + '
+        s = s[:-2]
+        if self.isReversible(i):
+            s += ' <=> '
+        else:
+            s += ' => '
+        for k in range(nsp):
+            nup = _cantera.kin_pstoichcoeff(self.ckin,k,i)
+            if nup <> 0.0:
+                if nup <> 1.0:
+                    s += `int(nup)`+' '
+                s += self._sp[k]+' + '
+        s = s[:-2]
+        return s
+    
     def reactantStoichCoeff(self,k,i):
         return _cantera.kin_rstoichcoeff(self.ckin,k,i)
     
@@ -152,22 +200,38 @@ class Kinetics:
     def creationRates(self, phase = None):
         c = _cantera.kin_getarray(self.ckin,50)
         if phase:
-            if self._ph.has_key(phase):
-                n = self._ph[phase]
+            if self._phnum.has_key(phase):
+                n = self._phnum[phase]
                 return c[self._end[n]:self._end[n+1]]
             else:
                 raise CanteraError('unknown phase')
         else:
-            return c
-                
+            return c                
                 
 
-    def destructionRates(self):
-        return _cantera.kin_getarray(self.ckin,60)
+    def destructionRates(self, phase = None):
+        d = _cantera.kin_getarray(self.ckin,60)
+        if phase:
+            if self._phnum.has_key(phase):
+                n = self._phnum[phase]
+                return d[self._end[n]:self._end[n+1]]
+            else:
+                raise CanteraError('unknown phase')
+        else:
+            return d
+
     
-    def netProductionRates(self):
-        return _cantera.kin_getarray(self.ckin,70)        
-
+    def netProductionRates(self, phase = None):
+        w = _cantera.kin_getarray(self.ckin,70)        
+        if phase:
+            if self._phnum.has_key(phase):
+                n = self._phnum[phase]
+                return w[self._end[n]:self._end[n+1]]
+            else:
+                raise CanteraError('unknown phase')
+        else:
+            return w
+        
     def sourceTerms(self):
         return _cantera.kin_getarray(self.ckin,80)        
 
@@ -177,7 +241,8 @@ class Kinetics:
     def setMultiplier(self,i,v):
         return _cantera.kin_setMultiplier(self.ckin,i,v)    
     
-
+    def advanceCoverages(self,dt):
+        return _cantera.kin_advanceCoverages(self.ckin,dt)    
 
 
 

Cantera/python/Cantera/ThermoPhase.py

@@ -237,6 +237,9 @@ class ThermoPhase(Phase):
         energy and the pressure."""        
         _cantera.thermo_setfp(self._phase_id, 5, s, p)        
 
+    def setElectricPotential(self, v):
+        _cantera.thermo_setfp(self._phase_id, 6, v, 0);
+        
     def equilibrate(self, XY):
         """Set to a state of chemical equilibrium holding property pair
         'XY' constant. The pair is specified by a two-letter string,

Cantera/python/Cantera/XML.py

@@ -82,6 +82,9 @@ class XML_Node:
 
     def addAttrib(self, key, value):
         _cantera.xml_addAttrib(self._xml_id, key, value)
+
+    def addComment(self, comment):
+        _cantera.xml_addComment(self._xml_id, comment)
         
     def value(self, loc=""):
         if loc:

Cantera/python/Cantera/__init__.py

@@ -7,6 +7,8 @@ from constants import *
 from gases import *
 from exceptions import *
 from set import set
+from importFromFile import *
+
 #from _version import __createdate__
 
 try:

Cantera/python/Cantera/ctml_writer.py

@@ -0,0 +1,941 @@
+#
+# Cantera input file processor
+#
+
+from Cantera import GasConstant
+from Cantera.XML import XML_Node
+import types, math
+
+SPECIES = 10
+SPECIES_SET = 20
+COLLECTION = 30
+THERMO = 40
+
+ALL = 10
+SKIP_UNDECLARED_ELEMENTS = 20
+SKIP_UNDECLARED_SPECIES = 30
+STOP = 0
+
+# default units
+_ulen = 'm' 
+_umol = 'kmol'
+_umass = 'kg'
+_utime = 's'
+_ue = 'J/kmol'
+
+# default std state pressure
+_pref = 1.0e5    # 1 bar
+
+_name = 'noname'
+
+_species = []
+_phases = []
+_reactions = []
+_atw = {}
+_mw = {}
+
+def isnum(a):
+    if type(a) == types.IntType or type(a) == types.FloatType:
+        return 1
+    else:
+        return 0
+    
+def dataset(nm):
+    global _name
+    _name = nm
+
+def standard_pressure(p0):
+    """Set the default standard-state pressure."""
+    global _pref
+    _pref = p0
+    
+def get_atomic_wts():
+    global _atw
+    edb = XML_Node('edb', src = 'elements.xml')
+    edata = edb.child('ctml/elementData')
+    e = edata.children()
+    for el in e:
+        _atw[el['name']] = el['atomicWt']
+    if el['atomicWt'] == '':
+        print 'no wt for ',el['name']
+    
+def units(length = '', quantity = '', mass = '', time = '', act_energy = ''):
+    global _ulen, _umol, _ue
+    if length: _ulen = length
+    if quantity: _umol = quantity
+    if act_energy: _ue = act_energy
+    if time: _utime = time
+    if mass: _umass = mass
+
+def ufmt(base, n):
+    if n == 0: return ''
+    if n == 1: return '-'+base
+    if n == -1: return '/'+base
+    if n > 0: return '-'+base+`n`
+    if n < 0: return '/'+base+`-n`    
+    
+def write():
+    x = XML_Node("ctml")
+    for ph in _phases:
+        ph.build(x)
+    s = species_set(name = _name, species = _species)
+    s.build(x)
+    
+    r = x.addChild('reactionData')
+    r['id'] = 'reaction_data'
+    for rx in _reactions:
+        rx.build(r)
+    
+    if _name <> 'noname':
+        x.write(_name+'.xml')
+    else:
+        print x
+            
+def addFloat(x, nm, val, fmt=''):
+    u = ''
+    s = ''
+    if isnum(val):
+        fval = float(val)
+        if fmt:
+            s = fmt % fval
+        else:
+            s = `fval`
+        x.addChild(nm, s)
+    else:
+        v = val[0]
+        u = val[1]
+        if fmt:
+            s = fmt % v
+        else:
+            s = `v`
+        xc = x.addChild(nm, s)
+        xc['units'] = u
+    
+def getAtomicComp(atoms):
+    if type(atoms) == types.DictType: return atoms
+    a = atoms.replace(',',' ')
+    toks = a.split()
+    d = {}
+    for t in toks:
+        b = t.split(':')
+        d[b[0]] = int(b[1])
+    return d
+
+def getEfficiencies(e):
+    if type(e) == types.DictType: return e
+    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):
+    toks = s.replace(' + ',' ').split()
+    d = {}
+    n = 1
+    for t in toks:
+        if t > '0' and t < '9':
+            n = int(t)
+        else:
+            if d.has_key(t):
+                d[t] += n
+            else:
+                d[t] = n
+            n = 1
+    return d
+
+class writer:
+    def write_ctml(self, file = ''):
+        x = XML_Node("ctml")
+        self.build(x)
+        if file:
+            x.write(file)
+        else:
+            print x
+    
+class collection(writer):
+    def __init__(self, s):
+        self._s = s
+        self.type = COLLECTION        
+    def build(self, p):
+        for s in self._s:
+            s.build(p)
+            
+class species_set(writer):
+    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.addAttrib("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(writer):
+    """A species."""
+    
+    def __init__(self,
+                 name = 'missing name!',
+                 atoms = 'missing atoms!',
+                 comment = '',
+                 thermo = None,
+                 transport = None,
+                 charge = -999):
+        self._name = name
+        self._atoms = getAtomicComp(atoms)
+        mw = 0.0
+        for a in self._atoms.keys():
+            mw += self._atoms[a]*float(_atw[a])
+        self._mw = mw
+        global _mw
+        _mw[name] = mw
+        self._comment = comment
+        self._thermo = thermo
+        self._transport = transport
+        chrg = 0
+        self._charge = charge
+        if self._atoms.has_key('E'):
+            chrg = -self._atoms['E']
+            if self._charge <> -999:
+                if self._charge <> chrg:
+                    raise 'specified charge inconsistent with number of electrons'
+            else:
+                self._charge = chrg
+        self.type = SPECIES
+        
+        global _species
+        _species.append(self)
+        
+
+    def build(self, p):
+        #phname = ''
+        #for ph in _phases:
+        #    if ph.has_species(self._name):
+        #        phname = ph._name
+        hdr = '    species '+self._name+'    '
+        p.addComment(hdr)        
+        s = p.addChild("species")
+        s.addAttrib("name",self._name)
+        a = ''
+        for e in self._atoms.keys():
+            a += e+':'+`self._atoms[e]`+' '
+        s.addChild("atomArray",a)
+        if self._comment:
+            s.addChild("note",self._comment)
+        if self._charge <> -999:
+            s.addChild("charge",self._charge)
+        if self._thermo:
+            t = s.addChild("thermo")
+            if type(self._thermo) == types.InstanceType:
+                self._thermo.build(t)
+            else:
+                nt = len(self._thermo)
+                for n in range(nt):
+                    self._thermo[n].build(t)
+        if self._transport:
+            t = s.addChild("transport")
+            if type(self._transport) == types.InstanceType:
+                self._transport.build(t)
+            else:
+                nt = len(self._transport)
+                for n in range(nt):
+                    self._transport[n].build(t)                    
+
+class thermo(writer):
+    """Base class for species standard-state thermodynamic properties."""
+    def _build(self, p):
+        return p.addChild("thermo")
+
+        
+class NASA(thermo):
+    """NASA polynomial parameterization."""
+    
+    def __init__(self, range = (0.0, 0.0), 
+                 coeffs = [], p0 = -1.0):
+        self._t = range
+        self._pref = p0
+        if len(coeffs) <> 7:
+            raise 'NASA coefficient list must have length = 7'
+        self._coeffs = coeffs
+
+        
+    def build(self, t):
+        n = t.addChild("NASA")
+        n['Tmin'] = `self._t[0]`
+        #n['Tmid'] = `self._t[1]`        
+        n['Tmax'] = `self._t[1]`
+        if self._pref <= 0.0:
+            n['P0'] = `_pref`
+        else:
+            n['P0'] = `self._pref`
+        str = ''
+        for i in  range(7):
+            str += '%17.9E, ' % self._coeffs[i]
+            if i > 0 and 3*((i+1)/3) == i: str += '\n'
+        str = str[:-2]
+        u = n.addChild("floatArray", str)
+        u["size"] = "7"
+        u["name"] = "coeffs"
+    
+                 
+class const_cp(thermo):
+    """Constant specific heat."""
+    
+    def __init__(self, tmax = -1.0, tmin = -1.0,
+                 t0 = 0.0, cp0 = 0.0, h0 = 0.0, s0 = 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'] = self._t[0]
+        if self._t[1] >= 0.0: c['Tmax'] = self._t[1]
+        addFloat(c,'t0',self._c[0])
+        addFloat(c,'h0',self._c[1])
+        addFloat(c,'s0',self._c[2])        
+        addFloat(c,'cp0',self._c[3])
+
+
+class gas_transport:
+    """Transport coefficients for ideal gas transport model."""
+
+    def __init__(self, geom = 'nonlin',
+                 diam = 0.0, well_depth = 0.0, dipole = 0.0,
+                 polar = 0.0, rot_relax = 0.0):
+        self._geom = geom
+        self._diam = diam
+        self._well_depth = well_depth
+        self._dipole = dipole
+        self._polar = polar
+        self._rot_relax = rot_relax
+
+    def build(self, t):
+        #t = s.addChild("transport")
+        t['model'] = 'gas_transport'
+        #        t.addChild("geometry", self._geom)
+        tg = t.addChild('string',self._geom)
+        tg['title'] = 'geometry'
+        addFloat(t, "LJ_welldepth", (self._well_depth, 'K'), '%8.3f')
+        addFloat(t, "LJ_diameter", (self._diam, 'A'),'%8.3f')
+        addFloat(t, "dipoleMoment", (self._dipole, 'Debye'),'%8.3f')        
+        addFloat(t, "polarizability", (self._polar, 'A3'),'%8.3f')
+        addFloat(t, "rotRelax", self._rot_relax,'%8.3f')        
+        
+class Arrhenius(writer):
+    def __init__(self,
+                 A = 0.0,
+                 n = 0.0,
+                 E = 0.0):
+        self._c = [A, n, E]
+        
+    def build(self, p, units = '', name = ''):
+        a = p.addChild('Arrhenius')
+        if name: a['name'] = name
+        if isnum(self._c[0]):
+            addFloat(a,'A', (self._c[0], units), fmt = '%14.6E')
+        else:
+            addFloat(a,'A',self._c[0], fmt = '%14.6E')
+        a.addChild('b',`self._c[1]`)
+        if isnum(self._c[2]):
+            addFloat(a,'E',(self._c[2],_ue), fmt = '%f')
+        else:
+            addFloat(a,'E',self._c[2], fmt = '%f')
+                     
+
+class sticking_prob(writer):
+    def __init__(self,
+                 A = 0.0,
+                 n = 0.0,
+                 E = 0.0,
+                 species = ''):
+        self._c = [A, n, E]
+        self._sp = species
+        
+    def build(self, p):
+        ig = ideal_gas()
+        for ph in _phases:
+            if ph.has_species(self._sp):
+                if ph._eos.__class__ == ig.__class__:
+                    pass
+                else:
+                    raise ('sticking probabilities only implemented for '
+                           +'species in ideal gas mixtures')
+                
+        a = p.addChild('Stick')
+        addFloat(a,'A',self._c[0],fmt = '%14.6E')
+        a.addChild('n',`self._c[1]`)
+        if type(self._c[2]) == types.FloatType:
+            addFloat(a,'E',(self._c[2],_ue))
+        else:
+            addFloat(a,'E',self._c[2])                
+
+        
+class reaction(writer):
+    def __init__(self,
+                 equation = '',
+                 rate_coeff = None,
+                 k_0 = None,
+                 k_inf = None, 
+                 efficiencies = '',
+                 falloff = None,
+                 id = ''
+                 ):
+
+        self._id = id
+        self._e = equation
+        self._falloff = falloff
+        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._kf = rate_coeff
+        self._kf0 = k_0
+        self._kfinf = k_inf
+        self._type = ''
+        self._effm = -1.0
+        self._eff = efficiencies
+        _reactions.append(self)
+
+        
+    def build(self, p):
+        if self._id:
+            id = self._id
+        else:
+            id = 'reaction_'+`self._num`
+        p.addComment("   reaction "+id+"    ")                
+        r = p.addChild('reaction')
+        r['id'] = id
+        if self.rev:
+            r['reversible'] = 'yes'
+        else:
+            r['reversible'] = 'no'
+
+        ee = self._e.replace('<','[')
+        ee = ee.replace('>',']')
+        r.addChild('equation',ee)
+        
+        mdim = 0
+        ldim = 0
+        str = ''
+
+        if self._r.has_key('(+'):
+            self._type = 'falloff'
+            if not self._falloff:
+                self._falloff = Lindemann()
+            if self._r.has_key('M)'):
+                self._effm = 1.0
+                del self._r['M)']
+                del self._p['M)']                
+            else:
+                for f in self._r.keys():
+                    if f[-1] == ')' and f.find('(') < 0:
+                        self._effm = 0.0
+                        self._eff = f[:-1]+':1.0'
+                        del self._r[f]
+                        del self._p[f]                        
+                        
+            del self._r['(+']
+            del self._p['(+']
+            
+        for s in self._r.keys():
+            ns = self._r[s]
+            nm = -999
+            nl = -999
+            if s == 'M' or s == 'm':
+                self._type = 'threeBody'
+                mdim += 1
+                ldim -= 3
+                self._effm = 1.0
+            else:
+                str += s+':'+`ns`+' '
+            
+                for ph in _phases:
+                    if ph.has_species(s):
+                        nm, nl = ph.conc_dim()
+                        break
+                if nm < 0:
+                    print self._r
+                    raise 'undeclared species '+s
+                else:
+                    mdim += nm*ns
+                    ldim += nl*ns
+
+        # adjust the moles and length powers based on the dimensions of
+        # the rate of progress (moles/length^2 or moles/length^3)
+        if self._type == 'surface':
+            mdim += -1
+            ldim += 2
+        else:
+            mdim += -1
+            ldim += 3
+
+        if self._type == 'falloff':
+            self._kf = (self._kfinf, self._kf0)
+        else:
+            self._kf = (self._kf,)
+            
+        # 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')
+        
+        for kf in self._kf:
+            
+            # compute the pre-exponential units string, and if it begins with a
+            # dash, remove it.
+            ku = ufmt(_ulen,-ldim) + ufmt(_umol,-mdim) + ufmt('s',-1)
+            if ku[0] == '-': ku = ku[1:]
+            mdim += 1
+            ldim -= 3
+            
+            if type(kf) == types.InstanceType:
+                k = kf
+            else:
+                k = Arrhenius(A = kf[0], n = kf[1], E = kf[2])
+            k.build(kfnode, units = ku, name = nm)
+            nm = 'k0'
+
+        if self._eff and self._effm >= 0.0:
+            eff = kfnode.addChild('efficiencies',self._eff)
+            eff['default'] = `self._effm`
+        
+        str = str[:-1]
+        r.addChild('reactants',str)
+        str = ''
+        for s in self._p.keys():
+            ns = self._p[s]
+            if s == 'M' or s == 'm':
+                pass
+            else:
+                str += s+':'+`ns`+' '
+        str = str[:-1]
+        r.addChild('products',str)
+
+        if self._falloff:
+            self._falloff.build(kfnode)
+
+
+
+#-------------------
+
+
+class falloff_reaction(writer):
+    def __init__(self,
+                 equation = '',
+                 k_0 = None,
+                 k_inf = None, 
+                 efficiencies = '',
+                 falloff = None,
+                 id = ''
+                 ):
+
+        if self._falloff:
+            self._falloff = falloff
+        else:
+            self._falloff = Lindemann()        
+        self._num = len(_reactions)+1
+        self._type = 'falloff'
+        self._effm = 1.0
+        self._eff = efficiencies
+        kf = (kfinf, kf0)        
+        reaction.__init__(self, equation, kf, id)
+
+
+        
+    def build(self, p):
+        r = reaction.build(self, p)
+        if self._r.has_key('M)'):
+            self._effm = 1.0
+            del self._r['M)']
+            del self._p['M)']                
+        else:
+            for f in self._r.keys():
+                if f[-1] == ')' and f.find('(') < 0:
+                    self._effm = 0.0
+                    self._eff = f[:-1]+':1.0'
+                    del self._r[f]
+                    del self._p[f]                        
+                        
+        del self._r['(+']
+        del self._p['(+']
+            
+            
+        r['type'] = 'falloff'
+
+        # 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._eff and self._effm >= 0.0:
+            eff = kfnode.addChild('efficiencies',self._eff)
+            eff['default'] = `self._effm`
+        
+        if self._falloff:
+            self._falloff.build(kfnode)
+
+
+#--------------            
+
+
+class state:
+    def __init__(self,
+                 temperature = None,
+                 pressure = None,
+                 moleFractions = None,
+                 massFractions = None,
+                 density = None,
+                 coverages = None):
+        self._t = temperature
+        self._p = pressure
+        self._rho = density
+        self._x = moleFractions
+        self._y = massFractions
+        self._c = coverages
+        
+    def build(self, ph):
+        st = ph.addChild('state')
+        if self._t: addFloat(st, 'temperature', self._t)
+        if self._p: addFloat(st, 'pressure', self._p)
+        if self._rho: addFloat(st, 'density', self._rho)
+        if self._x: st.addChild('moleFractions', self._x)
+        if self._y: st.addChild('massFractions', self._y)
+        if self._c: st.addChild('moleFractions', self._c)
+    
+
+class phase(writer):
+    """Base class for phases of matter."""
+    
+    def __init__(self,
+                 name = '',
+                 dim = 3,
+                 elements = '',
+                 species = '',
+                 reactions = 'none',
+                 initial_state = None):
+        
+        self._name = name
+        self._dim = dim
+        self._el = elements
+        self._sp = []
+        self._rx = []
+
+        #--------------------------------
+        #        process species
+        #--------------------------------
+        
+        # if a single string is entered, make it a list
+        if type(species) == types.StringType:
+            self._species = [species]
+        else:
+            self._species = species
+
+        self._skip = 0
+
+        # dictionary of species names 
+        self._spmap = {}
+
+        # for each species string, check whether or not the species
+        # are imported or defined locally. If imported, the string
+        # contains a colon (:) 
+        for sp in self._species:
+            if sp.find(':') > 0:
+                datasrc, spnames = sp.split(':')
+                self._sp.append((datasrc+'.xml', spnames))
+            else:
+                spnames = sp
+                self._sp.append(('', spnames))                
+
+            # strip the commas, and make the list of species names
+            sptoks = spnames.replace(',',' ').split()            
+            for s in sptoks:
+                if self._spmap.has_key(s):
+                    raise 'multiply-defined 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 '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 'Pure phases may only declare one species, but phase '+self._name+' declares '+`len(self._spmap)`+'.'
+
+        self._initial = initial_state
+
+        # add this phase to the global phase list
+        global _phases
+        _phases.append(self)
+
+
+    def is_pure(self):
+        return 0
+    
+    def has_species(self, s):
+        """Return 1 is a species with name 's' belongs to the phase,
+        or 0 otherwise."""
+        if self._spmap.has_key(s): return 1
+        return 0
+
+    def conc_dim(self):
+        """Concentration dimensions. Used in computing the units for reaction
+        rate coefficients."""
+        return (1, -self._dim) 
+
+    
+    def buildrxns(self, p):
+        
+        if type(self._rxns) == types.StringType:
+            self._rxns = [self._rxns]
+            
+        # for each reaction string, check whether or not the reactions
+        # are imported or defined locally. If imported, the string
+        # contains a colon (:) 
+        for r in self._rxns:
+            
+            if r.find(':') > 0:
+                datasrc, rnum = r.split(':')
+                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'
+            rtoks = r[1].split()
+            if rtoks[0] <> 'all':
+                i = ra.addChild('include')
+                i['prefix'] = 'reaction_'
+                i['min'] = rtoks[0]
+                if len(rtoks) > 2 and (rtoks[1] == 'to' or rtoks[1] == '-'):
+                    i['max'] = rtoks[2]
+                else:
+                    i['max'] = rtoks[0]                
+                    
+            
+    def build(self, p):
+        p.addComment('    phase '+self._name+'     ')
+        ph = p.addChild('phase')
+        ph['id'] = self._name
+        ph['dim'] = `self._dim`
+        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 self._skip:
+            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 = 'Mix',
+                 initial_state = None):
+        
+        phase.__init__(self, name, 3, elements, species, reactions,
+                       initial_state)
+        self._pure = 0
+        self._kin = kinetics
+        self._tr = transport
+
+        
+    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
+        
+        
+
+    
+#------------------ equations of state --------------------------
+
+class eos(writer):
+    def is_pure(self):
+        return self._pure
+    
+class incompressible_eos(eos):
+    def __init__(self, density = -1.0):
+        self._dens = density
+        self._pure = 0
+        if self._dens < 0.0:
+            raise 'density must be specified.'
+        
+    def build(self, p):
+        e = p.addChild("thermo")
+        e['model'] = 'Incompressible'
+        addFloat(e, 'density', self._dens)
+
+    def conc_dim(self):
+        return (1, -3)
+    
+class solid_compound_eos(eos):
+    def __init__(self, density = -1.0):
+        self._dens = density
+        self._pure = 1
+        if self._dens < 0.0:
+            raise 'density must be specified.'
+        
+    def build(self, p):
+        e = p.addChild("thermo")
+        e['model'] = 'SolidCompound'
+        addFloat(e, 'density', self._dens)
+        if len(self.parent._spmap) > 1:
+            raise 'A solid compound can only have one species.'
+        
+    def conc_dim(self):
+        return (0, 0)
+
+
+class ideal_gas_eos(eos):
+    def __init__(self, kinetics = 'GasKinetics',
+                 transport = 'none'):
+        self._pure = 0
+        self._kin = kinetics
+        self._tr = transport
+        global _idealgas_class
+        _idealgas_class = self.__class__
+        
+    def build(self, p):
+        e = p.addChild("thermo")
+        e['model'] = 'IdealGas'
+        k = p.addChild("kinetics")
+        k['model'] = self._kin
+        t = p.addChild('transport')
+        t['model'] = self._tr
+        
+    def conc_dim(self):
+        return (1, -3)
+
+
+class surface(eos):
+    def __init__(self, site_density = 0.0):
+        self._pure = 0
+        self._s0 = site_density
+    def build(self, p):
+        e = p.addChild("thermo")
+        e['model'] = 'Surface'
+        addFloat(e, 'site_density', self._s0, '%14.6E')
+        
+    def conc_dim(self):
+        return (1, -2)    
+        
+#-------------------------------------------------------------------
+
+# falloff parameterizations
+
+class Troe:
+    
+    def __init__(self, A = 0.0, T3 = 0.0, T1 = 0.0, T2 = -999.9):
+        if T2 <> -999.9:
+            self._c = (A, T3, T1, T2)
+        else:
+            self._c = (A, T3, T1)
+            
+    def build(self, p):
+        s = ''
+        for num in self._c:
+            s += '%g ' % num
+        f = p.addChild('falloff', s)
+        f['type'] = 'Troe'
+
+
+class SRI:
+    def __init__(self, A = 0.0, B = 0.0, C = 0.0, D = -999.9, E=-999.9):
+        if D <> -999.9 and E <> -999.9:
+            self._c = (A, B, C, D, E)
+        else:
+            self._c = (A, B, C)
+        
+    def build(self, p):
+        s = ''
+        for num in self._c:
+            s += '%g ' % num
+        f = p.addChild('falloff', s)
+        f['type'] = 'SRI'
+
+class Lindemann:
+    def __init__(self):
+        pass
+    def build(self, p):
+        f = p.addChild('falloff')
+        f['type'] = 'Lindemann'
+
+#--------------------------------------------------------------------
+
+## class gas_transport:
+##     def __init__(self, geom = 'nonlin',
+##                  welldepth = 0.0,
+##                  diam = 0.0,
+##                  dipole = 0.0,
+##                  polar = 0.0,
+##                  rot_relax = 0.0):
+##         self._sp = species
+##         self._geom = geom
+##         self._params = (welldepth, diam, dipole, polar, rotrelax)
+
+##         #global _trdata
+##         #_trdata[species] = self
+
+##     def build(self, s):
+##         tr = s.addChild('transport')
+##         g = tr.addChild('string','linear')
+##         g['title'] = 'geometry'
+##         tr.addChild('LJ_welldepth',`self._params[0]`)
+##         tr.addChild('LJ_diameter',`self._params[1]`)
+##         tr.addChild('dipoleMoment',`self._params[2]`)
+##         tr.addChild('polarizability',`self._params[3]`)
+##         tr.addChild('rotRelax',`self._params[4]`)        
+
+
+get_atomic_wts()

Cantera/python/Cantera/gases.py

@@ -34,13 +34,17 @@ def IdealGasMix(src="", root=None, transport='None',
     else:
         nm = ff
         ext = ''
-    if ext <> '.xml' and ext <> '.XML' and ext <> '.ctml' and ext <> '.CTML':
-        outfile = p+os.sep+nm+'.xml'
-        ck2ctml(infile = src, outfile = outfile, thermo = thermo,
-                transport = trandb, id = nm)
-        return Solution(src=outfile, root=None, transport=transport)
-    else:
-        return Solution(src=src, root=root, transport=transport)
+##     if ext <> '.xml' and ext <> '.XML' and ext <> '.ctml' and ext <> '.CTML':
+##         outfile = p+os.sep+nm+'.xml'
+##         if ext == '.py':
+##             from Cantera import pip
+##             pip.process(fname)
+##         else:
+##             ck2ctml(infile = src, outfile = outfile, thermo = thermo,
+##                     transport = trandb, id = nm)
+##         return Solution(src=outfile, root=None, transport=transport)
+##     else:
+    return Solution(src=src, root=root, transport=transport)
 
 def GRI30(transport='None'):
     """Return a Solution instance implementing reaction mechanism

Cantera/python/Cantera/importFromFile.py

@@ -1,8 +1,9 @@
+import solution
 
-import _cantera
-from Thermo import Thermo
-from Kinetics import Kinetics
-
-def importFromFile(t, k, params):
-    return _cantera.importFromFile(t.cthermo, k.ckin, params['import_file'],'',1)
+def importPhase(file = '', name = ''):
+    if name:
+        src = file+'#'+name
+    else:
+        src = file
+    return solution.Solution(src)
 

Cantera/python/Cantera/pip.py

@@ -0,0 +1,29 @@
+import sys, os
+from tempfile import mktemp
+
+def process(name):
+    parts = name.split('.')
+    base = parts[0]
+    if len(parts) == 2:
+        ext = parts[1]
+    fname = mktemp('.py')
+    fo = open(fname,'w')
+    txt = """from Cantera.ctml_writer import *
+import sys, os
+f = sys.argv[1]
+b = sys.argv[2]
+try:
+   os.remove(b+'.xml')
+except:
+   pass
+execfile(f)
+write()
+"""
+    fo.write(txt)
+    fo.close()
+    cmd = sys.executable+' '+fname+' '+name+' '+base
+    os.system(cmd)
+    os.remove(fname)
+
+
+

Cantera/python/Cantera/solution.py

@@ -1,7 +1,7 @@
 """
 """
 
-import string
+#import string
 import os
 
 from constants import *
@@ -29,30 +29,41 @@ class Solution(ThermoPhase, Kinetics, Transport):
     """
 
     def __init__(self, src="", root=None,
-                 transport = "None", thermo_db = "",
-                 transport_db = ""):
+                 transport = "", thermo_db = "",
+                 transport_db = "", phases=[]):
         
         self.ckin = 0
         self._owner = 0
         self.verbose = 1
-
-        fn = string.split(src,'#')
+        fn = src.split('#')
+        id = ""
+        if len(fn) > 1: id = fn[1]
         fn = fn[0]
+            
         fname = os.path.basename(fn)
         ff = os.path.splitext(fname)
         if ff[1] <> '.xml' and ff[1] <> '.ctml':
-            ctmodule.ck2ctml(src, thermo_db, transport_db, ff[0]+'.xml',
-                    ff[0])
+            #if ff[1] == '.py' or ff[1] == '.in':
+            from Cantera import pip
+            pip.process(fname)                
+            #else:
+            #    ctmodule.ck2ctml(src, thermo_db, transport_db, ff[0]+'.xml',
+            #                     ff[0])
             src = ff[0]+'.xml'
         
         # get the 'phase' element
-        s = XML.find_XML(src=src, root=root, name="phase")
+
+        if id:
+            s = XML.find_XML(src=src, root=root, id=id)
+        else:
+            s = XML.find_XML(src=src, root=root, name="phase")        
 
         # get the equation of state model
         ThermoPhase.__init__(self, xml_phase=s)
 
         # get the kinetics model
-        Kinetics.__init__(self, xml_phase=s, phases=[self])
+        ph = [self]+list(phases)
+        Kinetics.__init__(self, xml_phase=s, phases=ph)
 
         Transport.__init__(self, xml_phase=s, phase=self,
                            model = transport, loglevel=4)

Cantera/python/examples/flame2.py

@@ -7,7 +7,7 @@ from Cantera import units
 #from Cantera.gases import H_O_AR
 
 
-gas = GRI30(transport = 'Default')
+gas = GRI30(transport = 'Mix')
 
 flame = BurnerFlame(
     domain = (0, 0.01),

Cantera/python/src/ctbndry_methods.cpp

@@ -42,6 +42,19 @@ py_bndry_settemperature(PyObject *self, PyObject *args)
     return Py_BuildValue("i",0);
 }
 
+
+static PyObject*
+py_bndry_setspreadrate(PyObject *self, PyObject *args)
+{
+    int n;
+    double v;
+    if (!PyArg_ParseTuple(args, "id:bndry_setspreadrate", &n, &v))
+        return NULL;
+    int iok = bndry_setSpreadRate(n, v);
+    if (iok < 0) return reportError(iok);
+    return Py_BuildValue("i",0);
+}
+
 static PyObject*
 py_bndry_mdot(PyObject *self, PyObject *args)
 {

Cantera/python/src/ctkinetics_methods.cpp

@@ -1,11 +1,12 @@
 
 static PyObject*
 kin_newFromXML(PyObject *self, PyObject *args) {
-    int mxml, iphase, neighbor1, neighbor2;
-    if (!PyArg_ParseTuple(args, "iiii:newFromXML", &mxml, 
-            &iphase, &neighbor1, &neighbor2)) 
+    int mxml, iphase, neighbor1, neighbor2, neighbor3, neighbor4;
+    if (!PyArg_ParseTuple(args, "iiiiii:newFromXML", &mxml, 
+            &iphase, &neighbor1, &neighbor2, &neighbor3, &neighbor4)) 
         return NULL;
-    int n = newKineticsFromXML(mxml, iphase, neighbor1, neighbor2);
+    int n = newKineticsFromXML(mxml, iphase, neighbor1, neighbor2,
+        neighbor3, neighbor4);
     if (n < 0) return reportError(n);
     return Py_BuildValue("i",n);
 }
@@ -19,6 +20,13 @@ kin_delete(PyObject *self, PyObject *args)
     return Py_BuildValue("i",0);
 }
 
+static PyObject*
+kin_phase(PyObject *self, PyObject *args) {
+    int kin, n;
+    if (!PyArg_ParseTuple(args, "ii:kin_phase", &kin, &n)) return NULL;
+    return Py_BuildValue("i",kin_phase(kin, n));        
+}
+
 static PyObject*
 kin_nspecies(PyObject *self, PyObject *args) {
     int kin;
@@ -102,6 +110,17 @@ kin_speciesIndex(PyObject *self, PyObject *args) {
     return Py_BuildValue("i",kin_speciesIndex(kin,nm,ph));        
 }
 
+static PyObject*
+kin_advanceCoverages(PyObject *self, PyObject *args) {
+    int kin;
+    double dt;
+    if (!PyArg_ParseTuple(args, "id:kin_advanceCoverages", &kin, &dt)) 
+        return NULL;
+    int iok = kin_advanceCoverages(kin, dt);
+    if (iok < 0) return reportCanteraError();
+    return Py_BuildValue("i",0);        
+}
+
 static PyObject*
 kin_getarray(PyObject *self, PyObject *args)
 {

Cantera/python/src/ctthermo_methods.cpp

@@ -149,6 +149,8 @@ thermo_setfp(PyObject *self, PyObject *args)
         iok = th_set_SV(th, v); break;
     case 5:
         iok = th_set_SP(th, v); break;
+    case 6:
+        iok = th_setElectricPotential(th, v[0]); break;
     default:
         iok = -10; 
     }

Cantera/python/src/ctxml_methods.cpp

@@ -170,6 +170,18 @@ py_xml_addAttrib(PyObject *self, PyObject *args)
     return Py_BuildValue("i",m);
 }
 
+static PyObject*
+py_xml_addComment(PyObject *self, PyObject *args)
+{
+    int n;
+    char *comment;
+    if (!PyArg_ParseTuple(args, "is:xml_addComment", &n, &comment))
+        return NULL;
+    int m = xml_addComment(n, comment);
+    if (m < 0) return reportError(m);
+    return Py_BuildValue("i",m);
+}
+
 static PyObject*
 py_xml_removeChild(PyObject *self, PyObject *args)
 {

Cantera/python/src/methods.h

@@ -35,6 +35,7 @@ static PyMethodDef ct_methods[] = {
 
     {"xml_attrib", py_xml_attrib, METH_VARARGS},
     {"xml_addAttrib", py_xml_addAttrib, METH_VARARGS},
+    {"xml_addComment", py_xml_addComment, METH_VARARGS},
     {"xml_tag", py_xml_tag, METH_VARARGS},
     {"xml_value", py_xml_value, METH_VARARGS},
     {"xml_new", py_xml_new, METH_VARARGS},
@@ -66,6 +67,8 @@ static PyMethodDef ct_methods[] = {
     {"kin_speciesIndex", kin_speciesIndex,  METH_VARARGS},
     {"kin_getarray", kin_getarray,  METH_VARARGS},
     {"kin_getstring", kin_getstring,  METH_VARARGS},
+    {"kin_phase", kin_phase,  METH_VARARGS},
+    {"kin_advanceCoverages", kin_advanceCoverages,  METH_VARARGS},
 
     {"Transport", py_transport_new,  METH_VARARGS},
     {"tran_delete", py_transport_delete,  METH_VARARGS},
@@ -156,6 +159,7 @@ static PyMethodDef ct_methods[] = {
     {"bndry_setxin", py_bndry_setxin, METH_VARARGS},
     {"bndry_setxinbyname", py_bndry_setxinbyname, METH_VARARGS},
     {"bndry_settemperature", py_bndry_settemperature, METH_VARARGS},
+    {"bndry_setspreadrate", py_bndry_setspreadrate, METH_VARARGS},
     {"bndry_new", py_bndry_new, METH_VARARGS},
     {"bndry_del", py_bndry_del, METH_VARARGS},
     {"bndry_mdot", py_bndry_mdot, METH_VARARGS},

Cantera/src/ChemEquil.cpp

@@ -316,7 +316,6 @@ namespace Cantera {
         delete m_p2;
         bool tempFixed = true;
         initialize(s);
-
         switch (XY) {
         case TP: case PT:
             m_p1 = new TemperatureCalculator<thermo_t>;
@@ -346,7 +345,6 @@ namespace Cantera {
 
         xval = m_p1->value(s);
         yval = m_p2->value(s);
-
         int mm = m_mm;
         
         int m;
@@ -357,7 +355,6 @@ namespace Cantera {
     
         vector_fp res_trial(nvar);
         vector_fp elementMol(mm, 0.0);
-
         double perturb;
         for (m = 0; m < mm; m++) {
             perturb = Cutoff*(1.0 + rand());

Cantera/src/ConstDensityThermo.cpp

@@ -84,12 +84,12 @@ namespace Cantera {
             m_spthermo->update(tnow, m_cp0_R.begin(), m_h0_RT.begin(), 
                 m_s0_R.begin());
             m_tlast = tnow;
-            doublereal rrt = 1.0 / (GasConstant * tnow);
+            //            doublereal rrt = 1.0 / (GasConstant * tnow);
             int k;
-            doublereal deltaE;
+            //doublereal deltaE;
             for (k = 0; k < m_kk; k++) {
-                deltaE = rrt * m_pe[k];
-                m_h0_RT[k] += deltaE;
+                //deltaE = rrt * m_pe[k];
+                //m_h0_RT[k] += deltaE;
                 m_g0_RT[k] = m_h0_RT[k] - m_s0_R[k];
             }
             m_tlast = tnow;

Cantera/src/GRI_30_Kinetics.cpp

@@ -15,7 +15,7 @@
 #include "GRI_30_Kinetics.h"
 
 #include "ReactionData.h"
-#include "StoichManager.h"
+//#include "StoichManager.h"
 #include "Enhanced3BConc.h"
 #include "ThirdBodyMgr.h"
 #include "RateCoeffMgr.h"

Cantera/src/GasKinetics.cpp

@@ -17,7 +17,7 @@
 #include "GasKinetics.h"
 
 #include "ReactionData.h"
-#include "StoichManager.h"
+//#include "StoichManager.h"
 #include "Enhanced3BConc.h"
 #include "ThirdBodyMgr.h"
 #include "RateCoeffMgr.h"
@@ -52,6 +52,7 @@ namespace Cantera {
     {
         m_kdata = new GasKineticsData;
         m_kdata->m_temp = 0.0;
+        //        m_rxnstoich = new ReactionStoichMgr;
     }
 
     /**
@@ -128,8 +129,9 @@ namespace Cantera {
         fill(m_rkc.begin(), m_rkc.end(), 0.0);
 
         // compute Delta G^0 for all reversible reactions
-        m_reactantStoich.decrementReactions(m_grt.begin(), m_rkc.begin()); 
-        m_revProductStoich.incrementReactions(m_grt.begin(), m_rkc.begin());
+        m_rxnstoich.getRevReactionDelta(m_ii, m_grt.begin(), m_rkc.begin());
+            //m_reactantStoich.decrementReactions(m_grt.begin(), m_rkc.begin()); 
+            //m_revProductStoich.incrementReactions(m_grt.begin(), m_rkc.begin());
  
         doublereal logc0 = m_kdata->m_logc0;
         doublereal rrt = 1.0/(GasConstant * thermo().temperature());
@@ -157,11 +159,13 @@ namespace Cantera {
         fill(rkc.begin(), rkc.end(), 0.0);
         
         // compute Delta G^0 for all reactions
-        m_reactantStoich.decrementReactions(m_grt.begin(), rkc.begin()); 
-        m_revProductStoich.incrementReactions(m_grt.begin(), 
-            rkc.begin());
-        m_irrevProductStoich.incrementReactions(m_grt.begin(), 
-            rkc.begin());
+        m_rxnstoich.getReactionDelta(m_ii, m_grt.begin(), rkc.begin());
+
+            //        m_reactantStoich.decrementReactions(m_grt.begin(), rkc.begin()); 
+            //m_revProductStoich.incrementReactions(m_grt.begin(), 
+            //rkc.begin());
+            //m_irrevProductStoich.incrementReactions(m_grt.begin(), 
+            //rkc.begin());
  
         doublereal logc0 = m_kdata->m_logc0;
         doublereal rrt = 1.0/(GasConstant * thermo().temperature());
@@ -239,11 +243,13 @@ namespace Cantera {
         multiply_each(ropr.begin(), ropr.end(), m_rkc.begin());
 
         // multiply ropf by concentration products
-        m_reactantStoich.multiply(m_conc.begin(), ropf.begin()); 
+        m_rxnstoich.multiplyReactants(m_conc.begin(), ropf.begin()); 
+        //m_reactantStoich.multiply(m_conc.begin(), ropf.begin()); 
 
         // for reversible reactions, multiply ropr by concentration
         // products
-        m_revProductStoich.multiply(m_conc.begin(), ropr.begin());
+        m_rxnstoich.multiplyRevProducts(m_conc.begin(), ropr.begin()); 
+        //m_revProductStoich.multiply(m_conc.begin(), ropr.begin());
 
         for (int j = 0; j != m_ii; ++j) {
             ropnet[j] = ropf[j] - ropr[j];
@@ -390,26 +396,18 @@ namespace Cantera {
         m_kdata->m_rkcn.push_back(0.0);
         //        int nr = r.size();
         
-        //int i;
-        //for (i = 0; i < nr; i++) {
-        //     m_rrxn[r[i]][rnum] += 1.0;
-        //}
-        m_reactantStoich.add( reactionNumber(), rk);
-
-        //int np = p.size();
-        //
-        //for (i = 0; i < np; i++) {
-        //    m_prxn[p[i]][rnum] += 1.0;
-        // }
+        //m_reactantStoich.add( reactionNumber(), rk);
 
         if (r.reversible) {
-            m_revProductStoich.add(reactionNumber(), pk);
+            m_rxnstoich.add(reactionNumber(), rk, pk, true);
+            //m_revProductStoich.add(reactionNumber(), pk);
             m_dn.push_back(pk.size() - rk.size());
             m_revindex.push_back(reactionNumber());
             m_nrev++;
         }
         else {
-            m_irrevProductStoich.add(reactionNumber(), pk);
+            m_rxnstoich.add(reactionNumber(), rk, pk, false);
+            //m_irrevProductStoich.add(reactionNumber(), pk);
             m_dn.push_back(pk.size() - rk.size());            
             m_irrev.push_back( reactionNumber() );
             m_nirrev++;

Cantera/src/GasKinetics.h

@@ -21,7 +21,10 @@
 #include "Kinetics.h"
 
 #include "utilities.h"
-#include "StoichManager.h"
+
+//#include "StoichManager.h"
+
+#include "ReactionStoichMgr.h"
 #include "ThirdBodyMgr.h"
 #include "FalloffMgr.h"
 #include "RateCoeffMgr.h"
@@ -109,34 +112,39 @@ namespace Cantera {
 #ifdef HWMECH
             get_wdot(m_kdata->m_ropnet.begin(), net);
 #else
-            fill(net, net + m_kk, 0.0);
-            m_revProductStoich.incrementSpecies(
-                m_kdata->m_ropnet.begin(), net);
-            m_irrevProductStoich.incrementSpecies(
-                m_kdata->m_ropnet.begin(), net);
-            m_reactantStoich.decrementSpecies(
-                m_kdata->m_ropnet.begin(), net);
+            m_rxnstoich.getNetProductionRates(m_kk, m_kdata->m_ropnet.begin(), net); 
+            //fill(net, net + m_kk, 0.0);
+            //m_revProductStoich.incrementSpecies(
+            //    m_kdata->m_ropnet.begin(), net);
+            //m_irrevProductStoich.incrementSpecies(
+            //    m_kdata->m_ropnet.begin(), net);
+            //m_reactantStoich.decrementSpecies(
+            //    m_kdata->m_ropnet.begin(), net);
 #endif
         }
 
         virtual void getCreationRates(doublereal* cdot) {
             updateROP();
-            fill(cdot, cdot + m_kk, 0.0);
-            m_revProductStoich.incrementSpecies(
-                m_kdata->m_ropf.begin(), cdot);
-            m_irrevProductStoich.incrementSpecies(
-                m_kdata->m_ropf.begin(), cdot);
-            m_reactantStoich.incrementSpecies(
-                m_kdata->m_ropr.begin(), cdot);
+            m_rxnstoich.getCreationRates(m_kk, m_kdata->m_ropf.begin(), 
+                m_kdata->m_ropr.begin(), cdot); 
+            //fill(cdot, cdot + m_kk, 0.0);
+            //m_revProductStoich.incrementSpecies(
+            //    m_kdata->m_ropf.begin(), cdot);
+            //m_irrevProductStoich.incrementSpecies(
+            //    m_kdata->m_ropf.begin(), cdot);
+            //m_reactantStoich.incrementSpecies(
+            //    m_kdata->m_ropr.begin(), cdot);
         }
 
         virtual void getDestructionRates(doublereal* ddot) {
             updateROP();
-            fill(ddot, ddot + m_kk, 0.0);
-            m_revProductStoich.incrementSpecies(
-                m_kdata->m_ropr.begin(), ddot);
-            m_reactantStoich.incrementSpecies(
-                m_kdata->m_ropf.begin(), ddot);
+            m_rxnstoich.getDestructionRates(m_kk, m_kdata->m_ropf.begin(), 
+                m_kdata->m_ropr.begin(), ddot); 
+            //            fill(ddot, ddot + m_kk, 0.0);
+            //m_revProductStoich.incrementSpecies(
+            //    m_kdata->m_ropr.begin(), ddot);
+            //m_reactantStoich.incrementSpecies(
+            //    m_kdata->m_ropf.begin(), ddot);
         }
 
         virtual void getEquilibriumConstants(doublereal* kc);
@@ -204,9 +212,11 @@ namespace Cantera {
         
         vector<int> m_irrev;
 
-        StoichManagerN                      m_reactantStoich;
-        StoichManagerN                      m_revProductStoich;
-        StoichManagerN                      m_irrevProductStoich;
+        //StoichManagerN                      m_reactantStoich;
+        //StoichManagerN                      m_revProductStoich;
+        //StoichManagerN                      m_irrevProductStoich;
+
+        ReactionStoichMgr                   m_rxnstoich;
 
         vector<int>                         m_fwdOrder;
 

Cantera/src/IdealGasPhase.cpp

@@ -91,12 +91,12 @@ namespace Cantera {
             m_spthermo->update(tnow, m_cp0_R.begin(), m_h0_RT.begin(), 
                 m_s0_R.begin());
             m_tlast = tnow;
-            doublereal rrt = 1.0 / (GasConstant * tnow);
+            //            doublereal rrt = 1.0 / (GasConstant * tnow);
             int k;
-            doublereal deltaE;
+            //doublereal deltaE;
             for (k = 0; k < m_kk; k++) {
-                deltaE = rrt * m_pe[k];
-                m_h0_RT[k] += deltaE;
+                //deltaE = rrt * m_pe[k];
+                //m_h0_RT[k] += deltaE;
                 m_g0_RT[k] = m_h0_RT[k] - m_s0_R[k];
             }
             m_logc0 = log(m_p0/(GasConstant * tnow));

Cantera/src/ImplicitSurfChem.cpp

@@ -26,7 +26,8 @@ namespace Cantera {
           m_atol(1.e-14), m_rtol(1.e-7), m_maxstep(0.0)
     {
         m_integ = new CVodeInt;
-        m_surf = (SurfPhase*)&kin.thermo(kin.nPhases()-1);
+        m_surfindex = kin.surfacePhaseIndex();
+        m_surf = (SurfPhase*)&kin.thermo(m_surfindex);
 
         // use backward differencing, with a full Jacobian computed
         // numerically, and use a Newton linear iterator
@@ -38,6 +39,7 @@ namespace Cantera {
         m_work.resize(m_kin->nTotalSpecies());
     }
 
+
     // overloaded method of FuncEval. Called by the integrator to
     // get the initial conditions.
     void ImplicitSurfChem::getInitialConditions(double t0, size_t lenc, 
@@ -55,10 +57,12 @@ namespace Cantera {
         m_integ->initialize(t0, *this);
     }
 
+
     void ImplicitSurfChem::updateState(doublereal* c) {
         m_surf->setCoverages(c);
     }
 
+
     /**
      * Called by the integrator to evaluate ydot given y at time 'time'.
      */
@@ -69,10 +73,10 @@ namespace Cantera {
         doublereal rs0 = 1.0/m_surf->siteDensity();
         m_kin->getNetProductionRates(m_work.begin());
         int k;
-        int kbulk = m_kin->nTotalSpecies() - m_nsp;
+        int kstart = m_kin->start(m_surfindex);
         doublereal sum = 0.0;
         for (k = 1; k < m_nsp; k++) {
-            ydot[k] = m_work[kbulk + k] * rs0 * m_surf->size(k);
+            ydot[k] = m_work[kstart + k] * rs0 * m_surf->size(k);
             sum -= ydot[k];
         }
         //if (sum < 0.0) sum = 0.0;

Cantera/src/ImplicitSurfChem.h

@@ -93,7 +93,7 @@ namespace Cantera {
 
         SurfPhase* m_surf;
         InterfaceKinetics* m_kin;
-        int m_nsp;
+        int m_nsp, m_surfindex;
         Integrator* m_integ;         // pointer to integrator
         doublereal m_atol, m_rtol;   // tolerances
         doublereal m_maxstep;        // max step size

Cantera/src/InterfaceKinetics.cpp

@@ -19,6 +19,8 @@
 #include "StoichManager.h"
 #include "RateCoeffMgr.h"
 
+#include "ImplicitSurfChem.h"
+
 #include <iostream>
 using namespace std;
 
@@ -44,6 +46,9 @@ namespace Cantera {
         return mean_X(m_h0.begin());
     }
 
+    SurfPhase::
+    ~SurfPhase() { }
+
     /**
      * For a surface phase, the pressure is not a relevant
      * thermodynamic variable, and so the enthalpy is equal to the
@@ -101,20 +106,20 @@ namespace Cantera {
         _updateThermo(true);
     }
 
-
     void SurfPhase::
     setSiteDensity(doublereal n0) {
         doublereal x = n0;
         setParameters(1, &x);
     }
 
-    void SurfPhase::
-    setElectricPotential(doublereal V) {
-        for (int k = 0; k < m_kk; k++) {
-            m_pe[k] = charge(k)*Faraday*V;
-        }
-        _updateThermo(true);
-    }
+
+    //void SurfPhase::
+    //setElectricPotential(doublereal V) {
+    //    for (int k = 0; k < m_kk; k++) {
+    //        m_pe[k] = charge(k)*Faraday*V;
+    //    }
+    //    _updateThermo(true);
+    //}
 
     void SurfPhase::
     setCoverages(const doublereal* theta) {
@@ -141,12 +146,12 @@ namespace Cantera {
             m_tlast = tnow;
             doublereal rt = GasConstant * tnow;
             int k;
-            doublereal deltaE;
+            //doublereal deltaE;
             for (k = 0; k < m_kk; k++) {
                 m_h0[k] *= rt;
                 m_s0[k] *= GasConstant;
                 m_cp0[k] *= GasConstant;
-                deltaE = m_pe[k];
+                //deltaE = m_pe[k];
                 //m_h0[k] += deltaE;
                 m_mu0[k] = m_h0[k] - tnow*m_s0[k];
             }
@@ -169,29 +174,53 @@ namespace Cantera {
         m_redo_rates(false),
         m_nirrev(0), 
         m_nrev(0),
+        m_integrator(0),
         m_finalized(false)
     {
         m_kdata = new InterfaceKineticsData;
         m_kdata->m_temp = 0.0;
     }
 
+    InterfaceKinetics::
+    ~InterfaceKinetics(){
+        delete m_kdata;
+        delete m_integrator;
+    }
+
     void InterfaceKinetics::
     _update_rates_T() {
+        _update_rates_phi();
         doublereal T = thermo().temperature();
         if (T != m_kdata->m_temp || m_redo_rates) {
             doublereal logT = log(T);
             m_rates.update(T, logT, m_kdata->m_rfn.begin());
-            correctElectronTransferRates(m_kdata->m_rfn.begin());
+            applyButlerVolmerCorrection(m_kdata->m_rfn.begin());
             m_kdata->m_temp = T;
             updateKc();
             m_kdata->m_ROP_ok = false;
             m_redo_rates = false;
         }
-    };
+    }
+
+    void InterfaceKinetics::
+    _update_rates_phi() {
+        int np = nPhases();
+        for (int n = 0; n < np; n++) {
+            if (thermo(n).electricPotential() != m_phi[n]) {
+                m_phi[n] = thermo(n).electricPotential();
+                m_redo_rates = true;
+            }
+        }
+    }
+
 
 
     /**
-     * Update properties that depend on concentrations.
+     * Update properties that depend on concentrations. This method
+     * fills out the array of generalized concentrations by calling
+     * method getActivityConcentrations for each phase, which classes
+     * representing phases should overload to return the appropriate
+     * quantities.
      */         
     void InterfaceKinetics::
     _update_rates_C() {
@@ -203,8 +232,10 @@ namespace Cantera {
         m_kdata->m_ROP_ok = false;
     }
 
+
     /**
-     * Update the equilibrium constants in molar units.
+     * Update the equilibrium constants in molar units for all
+     * reversible reactions.
      */
     void InterfaceKinetics::updateKc() {
         int i, irxn;
@@ -215,14 +246,11 @@ namespace Cantera {
         doublereal rrt = 1.0/rt;
         int np = nPhases();
         for (n = 0; n < np; n++) {
-            //            cout << n << "start = " << m_start[n] << endl;
             thermo(n).getStandardChemPotentials(m_mu0.begin() + m_start[n]);
             nsp = thermo(n).nSpecies();
             for (k = 0; k < nsp; k++) {
-                //cout << ik << "mu0 = " << m_mu0[ik] << endl;
                 m_mu0[ik] -= rt*thermo(n).logStandardConc(k);
                 m_mu0[ik] += Faraday * m_phi[n] * thermo(n).charge(k);
-                //cout << ik << "mu0 = " << m_mu0[ik] << endl;
                 ik++;
             }
         }
@@ -235,9 +263,7 @@ namespace Cantera {
 
         for (i = 0; i < m_nrev; i++) {
             irxn = m_revindex[i];
-            //cout << "rev   " << irxn << "  " << m_rkc[irxn] << endl;
             m_rkc[irxn] = exp(m_rkc[irxn]*rrt);
-            //cout << "rev   " << irxn << "  " << m_rkc[irxn] << endl;
         }
 
         for(i = 0; i != m_nirrev; ++i) {
@@ -245,6 +271,7 @@ namespace Cantera {
         }
     }
 
+
     /**
      * Get the equilibrium constants of all reactions, whether
      * reversible or not.
@@ -260,14 +287,8 @@ namespace Cantera {
             thermo(n).getStandardChemPotentials(m_mu0.begin() + m_start[n]);
             nsp = thermo(n).nSpecies();
             for (k = 0; k < nsp; k++) {
-                //cout << thermo(n).id() << "  " << thermo(n).speciesName(k) 
-                //     << "   " << m_mu0[ik] << endl;
                 m_mu0[ik] -= rt*thermo(n).logStandardConc(k);
                 m_mu0[ik] += Faraday * m_phi[n] * thermo(n).charge(k);
-                //if (thermo(n).charge(k) != 0.0) {
-                //    cout << thermo(n).id() << "  " << thermo(n).speciesName(k) 
-                //         << "   " << m_phi[n] << "  " << thermo(n).charge(k) << endl;
-                //}
                 ik++;
             }
         }
@@ -285,16 +306,19 @@ namespace Cantera {
 
 
     /**
-     * Get the equilibrium constants of all reactions, whether
-     * reversible or not.
+     * For reactions that transfer charge across a potential difference,
+     * the activation energies are modified by the potential difference.
+     * (see, for example, ...). This method applies this correction.
      */
-    void InterfaceKinetics::correctElectronTransferRates(doublereal* kf) {
+    void InterfaceKinetics::applyButlerVolmerCorrection(doublereal* kf) {
         int i;
 
         int n, nsp, k, ik=0;
         doublereal rt = GasConstant*thermo(0).temperature();
         doublereal rrt = 1.0/rt;
         int np = nPhases();
+
+        // compute the electrical potential energy of each species
         for (n = 0; n < np; n++) {
             nsp = thermo(n).nSpecies();
             for (k = 0; k < nsp; k++) {
@@ -302,18 +326,25 @@ namespace Cantera {
                 ik++;
             }
         }
+
+        // compute the change in electrical potential energy for each
+        // reaction. This will only be non-zero if a potential
+        // difference is present.
         fill(m_rwork.begin(), m_rwork.begin() + m_ii, 0.0);
         m_reactantStoich.decrementReactions(m_pot.begin(), m_rwork.begin()); 
         m_revProductStoich.incrementReactions(m_pot.begin(), m_rwork.begin());
         m_irrevProductStoich.incrementReactions(m_pot.begin(), m_rwork.begin());
-        doublereal eamod, ea;
+        // modify the reaction rates. Only modify those with a
+        // non-zero activation energy, and do not decrease the
+        // activation energy below zero.
+        doublereal ea, eamod;
         for (i = 0; i < m_ii; i++) {
-            //loc = m_index[i].second;
-            //if (loc >= 0) {
-            //    const Arrhenius& r = m_rates.rateCoeff(m_index[i].second);
-            //  ea = GasConstant*r.activationEnergy_R();
             eamod = 0.5*m_rwork[i];
-            if (m_index[i].second >= 0) kf[i] *= exp(-eamod*rrt);
+            if (eamod != 0.0 && m_E[i] != 0.0) {
+                ea = GasConstant * m_E[i];
+                if (eamod + ea < 0.0) eamod = -ea;
+                kf[i] *= exp(-eamod*rrt);
+            }
         }
     }
 
@@ -386,6 +417,8 @@ namespace Cantera {
         iloc = m_rates.install( reactionNumber(),
             r.rateCoeffType, r.rateCoeffParameters.size(), 
             r.rateCoeffParameters.begin() );
+        // store activation energy
+        m_E.push_back(r.rateCoeffParameters[2]);
         // add constant term to rate coeff value vector
         m_kdata->m_rfn.push_back(r.rateCoeffParameters[0]);                
         registerReaction( reactionNumber(), ELEMENTARY_RXN, iloc);
@@ -500,6 +533,15 @@ namespace Cantera {
         return (m_finalized);
     }
 
+    void InterfaceKinetics::
+    advanceCoverages(doublereal tstep) {
+        if (m_integrator == 0) {
+            m_integrator = new ImplicitSurfChem(*this);
+            m_integrator->initialize();
+        }
+        m_integrator->integrate(0.0, tstep);
+    }
+
 }
 
 

Cantera/src/InterfaceKinetics.h

@@ -31,6 +31,7 @@ namespace Cantera {
     class ReactionData;
     class InterfaceKineticsData;
     class ThermoPhase;
+    class ImplicitSurfChem;
 
     /**
      * Holds mechanism-specific data.
@@ -62,12 +63,13 @@ namespace Cantera {
         InterfaceKinetics(thermo_t* thermo = 0);
 
         /// Destructor.
-        virtual ~InterfaceKinetics(){delete m_kdata;}
+        virtual ~InterfaceKinetics();
 
         virtual int ID() { return cInterfaceKinetics; }
+        virtual int type() { return cInterfaceKinetics; }
 
         void setElectricPotential(int n, doublereal V) {
-            m_phi[n] = V;
+            thermo(n).setElectricPotential(V);
             m_redo_rates = true;
         }
 
@@ -158,10 +160,12 @@ namespace Cantera {
                 < m_revindex.end()) return true;
             else return false;
         }
-        void correctElectronTransferRates(doublereal* kf);
         void _update_rates_T();
+        void _update_rates_phi();
         void _update_rates_C();
 
+        void advanceCoverages(doublereal tstep);
+
     protected:
 
         int                                 m_kk;
@@ -200,6 +204,9 @@ namespace Cantera {
         vector_fp m_phi;
         vector_fp m_pot;
         vector_fp m_rwork;
+        vector_fp m_E;
+
+        ImplicitSurfChem*                      m_integrator;
 
     private:
 
@@ -215,6 +222,7 @@ namespace Cantera {
         void registerReaction(int rxnNumber, int type, int loc) {
             m_index[rxnNumber] = pair<int, int>(type, loc);
         }
+        void applyButlerVolmerCorrection(doublereal* kf);
         bool m_finalized;
     };
 }

Cantera/src/Kinetics.h

@@ -16,7 +16,6 @@
 #define CT_KINETICS_H
 
 #include "ctexceptions.h"
-//#include "Phase.h"
 #include "ThermoPhase.h"
 
 namespace Cantera {
@@ -36,7 +35,7 @@ namespace Cantera {
         typedef ThermoPhase thermo_t;
 
         /// Constructors.
-        Kinetics() : m_ii(0), m_thermo(0), m_index(-1) {}
+        Kinetics() : m_ii(0), m_thermo(0), m_index(-1), m_surfphase(-1) {}
 
 	/**
 	 * This Constructor initializes with a starting phase.
@@ -44,7 +43,7 @@ namespace Cantera {
 	 * sets up are also done here.
 	 */
         Kinetics(thermo_t* thermo) 
-            : m_ii(0), m_index(-1) {
+            : m_ii(0), m_index(-1), m_surfphase(-1) {
             if (thermo) {
                 m_start.push_back(0);
                 m_thermo.push_back(thermo);
@@ -76,6 +75,8 @@ namespace Cantera {
             return n;
         }
 
+        int surfacePhaseIndex() { return m_surfphase; }
+
         /**
          * Stoichiometric coefficient of species k as a reactant in
          * reaction i.  
@@ -268,9 +269,20 @@ namespace Cantera {
 	 * @param k species index 
 	 * @param n phase index for the species
 	 */
-        int kineticsSpeciesIndex(int k, int n) {
+        int kineticsSpeciesIndex(int k, int n) const {
             return m_start[n] + k;
         }
+
+        string kineticsSpeciesName(int k) const {
+            int np = m_start.size();
+            for (int n = np-1; n >= 0; n--) {
+                if (k >= m_start[n]) {
+                    return thermo(n).speciesName(k - m_start[n]);
+                }
+            }
+            return "<unknown>";
+        }
+
 	/**
 	 * This routine will look up a species number based on
 	 * the input string nm. The lookup of species will
@@ -283,7 +295,7 @@ namespace Cantera {
 	 *   is returned. 
 	 *   If no match is found, the value -2 is returned.
 	 */
-        int kineticsSpeciesIndex(string nm, string ph = "<any>") {
+        int kineticsSpeciesIndex(string nm, string ph = "<any>") const {
 	  int np = m_thermo.size();
 	  int k;
 	  string id;
@@ -317,6 +329,17 @@ namespace Cantera {
             throw CanteraError("speciesPhase", "unknown species "+nm);
         }
 
+        thermo_t& speciesPhase(int k) {
+            int np = m_start.size();
+            for (int n = np-1; n >= 0; n--) {
+                if (k >= m_start[n]) {
+                    return thermo(n);
+                }
+            }
+            throw CanteraError("speciesPhase", 
+                "illegal species index: "+int2str(k));            
+        }
+
 
         /**
          * Prepare the class for the addition of reactions. This function
@@ -440,6 +463,8 @@ namespace Cantera {
         map<string, int> m_phaseindex;
         int m_index;
 
+        int m_surfphase;
+
     private:
 
         vector<grouplist_t> m_dummygroups;

Cantera/src/KineticsFactory.h

@@ -52,7 +52,7 @@ namespace Cantera {
 
 
     /**
-     *  Create a new thermo manager instance.
+     *  Create a new kinetics manager.
      */
     inline Kinetics* newKineticsMgr(XML_Node& phase,  
         vector<ThermoPhase*> th, KineticsFactory* f=0) {
@@ -64,7 +64,7 @@ namespace Cantera {
     }
 
     /**
-     *  Create a new thermo manager instance.
+     *  Create a new kinetics manager.
      */
     inline Kinetics* newKineticsMgr(string model, KineticsFactory* f=0) {
         if (f == 0) {

Cantera/src/Makefile.in

@@ -22,14 +22,15 @@ EXT        = ../../ext
 #----------------------
 
 # basic components always needed
-BASE       = Elements.o Constituents.o stringUtils.o misc.o importCTML.o plots.o \
+BASE       = State.o Elements.o Constituents.o stringUtils.o misc.o importCTML.o plots.o \
              xml.o Phase.o DenseMatrix.o ctml.o funcs.o ctvector.o phasereport.o
 
 # thermodynamic properties
 THERMO     = $(BASE) ThermoPhase.o IdealGasPhase.o ConstDensityThermo.o SolidCompound.o SpeciesThermoFactory.o ThermoFactory.o
 
 # homogeneous kinetics
-KINETICS   = GRI_30_Kinetics.o KineticsFactory.o GasKinetics.o FalloffFactory.o GasKineticsWriter.o $(THERMO)
+KINETICS   = GRI_30_Kinetics.o KineticsFactory.o GasKinetics.o FalloffFactory.o GasKineticsWriter.o \
+             ReactionStoichMgr.o $(THERMO)
 
 # heterogeneous kinetics
 HETEROKIN = InterfaceKinetics.o ImplicitSurfChem.o $(THERMO)

Cantera/src/Phase.cpp

@@ -207,13 +207,13 @@ namespace Cantera {
     }
 
 
-        void Phase::update_T(int n) const {
-            m_T_updater.update(n);
-        }
+//         void Phase::update_T(int n) const {
+//             m_T_updater.update(n);
+//         }
 
-        void Phase::update_C(int n) const {
-            m_C_updater.update(n);
-        }
+//         void Phase::update_C(int n) const {
+//             m_C_updater.update(n);
+//         }
 
         /** 
          *  Finished adding species, prepare to use them for calculation
@@ -238,11 +238,11 @@ namespace Cantera {
             return (m_kk > 0 && Constituents::ready() && State::ready());
         }
 
-        int Phase::installUpdater_T(Updater* u) {
-            return m_T_updater.install(u);
-        }
+//         int Phase::installUpdater_T(Updater* u) {
+//             return m_T_updater.install(u);
+//         }
 
-        int Phase::installUpdater_C(Updater* u) {
-            return m_C_updater.install(u);
-        }
+//         int Phase::installUpdater_C(Updater* u) {
+//             return m_C_updater.install(u);
+//         }
 }

Cantera/src/Phase.h

@@ -50,9 +50,9 @@ namespace Cantera {
         virtual ~Phase(){ delete m_xml; }
         
         XML_Node& xml() { return *m_xml; }
-        string id() { return m_id; }
+        string id() const { return m_id; }
         void setID(string id) {m_id = id;} 
-        int index() { return m_index; }
+        int index() const { return m_index; }
         void setIndex(int m) { m_index = m; }
 
         /** 
@@ -154,9 +154,9 @@ namespace Cantera {
          */
         doublereal chargeDensity() const;
 
-        void update_T(int n) const;
+        //void update_T(int n) const;
 
-        void update_C(int n) const;
+        //void update_C(int n) const;
 
         /// Number of spatial dimensions (1, 2, or 3)
         int nDim() {return m_ndim;}
@@ -170,9 +170,9 @@ namespace Cantera {
  
         virtual bool ready() const;
 
-        int installUpdater_T(Updater* u);
+//         int installUpdater_T(Updater* u);
 
-        int installUpdater_C(Updater* u);
+//         int installUpdater_C(Updater* u);
 
     protected:
 

Cantera/src/ReactionPath.cpp

@@ -37,7 +37,7 @@ namespace Cantera {
     }
         
     void SpeciesNode::printPaths() {
-        for (int i = 0; i < m_paths.size(); i++) {
+        for (int i = 0; i < int(m_paths.size()); i++) {
             cout << m_paths[i]->begin()->name << " -->  "
                  << m_paths[i]->end()->name << ":   "
                  << m_paths[i]->flow() << endl;
@@ -789,14 +789,13 @@ namespace Cantera {
 
     string reactionLabel(int i, int kr, int nr, const vector_int& slist, 
         const Kinetics& s) {
-
-        const Kinetics::thermo_t& ph = s.thermo();
-
+        
+        //int np = s.nPhases();
         string label = "";
         int l;
         for (l = 0; l < nr; l++) {
             if (l != kr) 
-                label += " + "+ ph.speciesName(slist[l]);
+                label += " + "+ s.kineticsSpeciesName(slist[l]);
         }
         if (s.reactionType(i) == THREE_BODY_RXN)
             label += " + M "; 
@@ -823,7 +822,7 @@ namespace Cantera {
         r.element = element;
         if (m < 0) return -1;
         
-        int k;
+        //int k;
         int kk = ph.nSpecies();
 
         s.getFwdRatesOfProgress(m_ropf.begin());
@@ -831,11 +830,11 @@ namespace Cantera {
 
         ph.getMoleFractions(m_x.begin());
 
-        doublereal sum = 0.0;
-        for (k = 0; k < kk; k++) {
-            sum += m_x[k] * ph.nAtoms(k,m);
-        }
-        sum *= ph.molarDensity();
+        //doublereal sum = 0.0;
+        //for (k = 0; k < kk; k++) {
+        //    sum += m_x[k] * ph.nAtoms(k,m);
+        //}
+        //sum *= ph.molarDensity();
 
         // species explicitly included or excluded
         vector<string>& in_nodes = r.included();
@@ -846,9 +845,9 @@ namespace Cantera {
         vector_int status;
 	status.resize(kk,0);
         for (int ni = 0; ni < nin; ni++) 
-            status[ph.speciesIndex(in_nodes[ni])] = 1;
+            status[s.kineticsSpeciesIndex(in_nodes[ni])] = 1;
         for (int ne = 0; ne < nout; ne++) 
-            status[ph.speciesIndex(out_nodes[ne])] = -1;
+            status[s.kineticsSpeciesIndex(out_nodes[ne])] = -1;
 
         for (i = 0; i < m_nr; i++) 
         {

Cantera/src/SolidCompound.h

@@ -40,8 +40,8 @@ namespace Cantera {
 	    m_kk(0),
 	    m_tmin(0.0),
 	    m_tmax(0.0),
-	    m_p0(OneAtm),
 	    m_press(OneAtm),
+	    m_p0(OneAtm),
 	    m_tlast(-1.0)  {}
 
         virtual ~SolidCompound() {}
@@ -71,8 +71,6 @@ namespace Cantera {
          */
         virtual doublereal intEnergy_mole() const {
             _updateThermo();
-            //            cout << "intEnergy: " << m_h0_RT[0] << "  " << m_p0/molarDensity()
-            //      << endl;
             return GasConstant * temperature() * m_h0_RT[0]
                 - m_p0 / molarDensity();
         }
@@ -82,7 +80,6 @@ namespace Cantera {
          */
         virtual doublereal entropy_mole() const {
             _updateThermo();
-            //cout << "s/r = " << m_s0_R[0] << endl;
             return GasConstant * m_s0_R[0];
         }
 
@@ -170,7 +167,7 @@ namespace Cantera {
     protected:
 
         int m_kk;
-        doublereal m_tmin, m_tmax, m_p0, m_press;
+        doublereal m_tmin, m_tmax, m_press, m_p0;
 
         mutable doublereal     m_tlast;
         mutable array_fp      m_h0_RT;

Cantera/src/SpeciesThermoFactory.cpp

@@ -32,33 +32,49 @@ namespace Cantera {
 
     SpeciesThermoFactory* SpeciesThermoFactory::__factory = 0;
 
+
+    static void getSpeciesThermoTypes(XML_Node* node, 
+        int& has_nasa, int& has_shomate, int& has_simple) {
+        XML_Node& sparray = *node;
+        vector<XML_Node*> sp;
+        sparray.getChildren("species",sp);
+        int ns = sp.size();
+        for (int n = 0; n < ns; n++) {
+            XML_Node& th = sp[n]->child("thermo");
+            if (th.hasChild("NASA")) has_nasa = 1;
+            if (th.hasChild("Shomate")) has_shomate = 1;
+            if (th.hasChild("const_cp")) has_simple = 1;
+            if (th.hasChild("poly")) {
+                if (th.child("poly")["order"] == "1") has_simple = 1;
+                else throw CanteraError("newSpeciesThermo",
+                    "poly with order > 1 not yet supported");
+            }
+        }
+    }
+
+
     /**
      * Return a species thermo manager to handle the parameterizations
      * specified in a CTML phase specification.
      */
     SpeciesThermo* SpeciesThermoFactory::newSpeciesThermo(XML_Node* node) {
-        XML_Node& sparray = *node; //node->child("speciesData");
-        vector<XML_Node*> sp;
-        sparray.getChildren("species",sp);
-        int ns = sp.size();
-        int inasa = 0;
-        int ishomate = 0;
-        int isimple = 0;
-        for (int n = 0; n < ns; n++) {
-            XML_Node& th = sp[n]->child("thermo");
-            if (th.hasChild("NASA")) inasa = 1;
-            if (th.hasChild("Shomate")) ishomate = 1;
-            if (th.hasChild("const_cp")) isimple = 1;
-            if (th.hasChild("poly")) {
-                if (th.child("poly")["order"] == "1") isimple = 1;
-                else throw CanteraError("newSpeciesThermo",
-                    "poly with order > 1 not yet supported");
-            }
-        }
-        return newSpeciesThermo(NASA*inasa 
+        int inasa = 0, ishomate = 0, isimple = 0;
+        getSpeciesThermoTypes(node, inasa, ishomate, isimple);
+        return newSpeciesThermo(NASA*inasa
             + SHOMATE*ishomate + SIMPLE*isimple);
     }
 
+    SpeciesThermo* SpeciesThermoFactory::newSpeciesThermo(vector<XML_Node*> nodes) {
+        int n = nodes.size();
+        int inasa = 0, ishomate = 0, isimple = 0;
+        for (int j = 0; j < n; j++) {
+            getSpeciesThermoTypes(nodes[j], inasa, ishomate, isimple);
+        }
+        return newSpeciesThermo(NASA*inasa
+            + SHOMATE*ishomate + SIMPLE*isimple);
+    }
+
+
     SpeciesThermo* SpeciesThermoFactory::newSpeciesThermo(int type) {
         
         switch (type) {

Cantera/src/SpeciesThermoFactory.h

@@ -45,6 +45,7 @@ namespace Cantera {
          */ 
         virtual SpeciesThermo* newSpeciesThermo(int type);
         virtual SpeciesThermo* newSpeciesThermo(XML_Node* node);
+        virtual SpeciesThermo* newSpeciesThermo(vector<XML_Node*> nodes);
 
     private:
         static SpeciesThermoFactory* __factory;
@@ -76,6 +77,15 @@ namespace Cantera {
         return sptherm;
     }
 
+    inline SpeciesThermo* newSpeciesThermoMgr(vector<XML_Node*> nodes, 
+        SpeciesThermoFactory* f=0) {
+        if (f == 0) {
+            f = SpeciesThermoFactory::factory();
+        }
+        SpeciesThermo* sptherm = f->newSpeciesThermo(nodes);
+        return sptherm;
+    }
+
 }
 
 #endif

Cantera/src/State.h

@@ -226,8 +226,6 @@ namespace Cantera {
 
     private:
 
-        doublereal m_temp, m_dens;
-
 	/**
 	 * Temperature. This is an independent variable 
 	 * units = Kelvin

Cantera/src/SurfPhase.h

@@ -36,7 +36,7 @@ namespace Cantera {
     public:
 
         SurfPhase(doublereal n0 = 0.0);
-        virtual ~SurfPhase() {}
+        virtual ~SurfPhase();
         virtual int eosType() const { return cSurf; }
         virtual doublereal enthalpy_mole() const;
         virtual doublereal intEnergy_mole() const;

Cantera/src/ThermoFactory.cpp

@@ -74,72 +74,72 @@ namespace Cantera {
         return th;
     }
 
-    /**
-     * Return a thermo manager to handle the parameterizations
-     * specified in a CTML phase specification.
-     */
-    ThermoPhase* ThermoFactory::newThermo(XML_Node& root, string id) {
+//     /**
+//      * Return a thermo manager to handle the parameterizations
+//      * specified in a CTML phase specification.
+//      */
+//     ThermoPhase* ThermoFactory::newThermo(XML_Node& root, string id) {
 
-        // Find the node with the specified id, check that it is
-        // a 'phase' node, and set the phase id to 'id'.
-        XML_Node* ph;
-        ph = root.findID(id);
-        if (ph == 0) return 0; // false;   // id not found
-        XML_Node& node = *ph;
+//         // Find the node with the specified id, check that it is
+//         // a 'phase' node, and set the phase id to 'id'.
+//         XML_Node* ph;
+//         ph = root.findID(id);
+//         if (ph == 0) return 0; // false;   // id not found
+//         XML_Node& node = *ph;
 
-        if (node.name() != "phase") 
-            throw CanteraError("newThermo","node with id = "+id
-                +" is not a phase object.");
+//         if (node.name() != "phase") 
+//             throw CanteraError("newThermo","node with id = "+id
+//                 +" is not a phase object.");
 
-        //Phase* p = new Phase;
-        //p->setID(id);                // set the phase id
+//         //Phase* p = new Phase;
+//         //p->setID(id);                // set the phase id
 
-        // get equaton of state type
-        XML_Node& eos = node.child("thermo");
-        string eostype = eos["model"];
-        int ieos=-1;
-        for (int n = 0; n < ntypes; n++) {
-            if (eostype == _types[n]) ieos = _itypes[n];
-        }
+//         // get equaton of state type
+//         XML_Node& eos = node.child("thermo");
+//         string eostype = eos["model"];
+//         int ieos=-1;
+//         for (int n = 0; n < ntypes; n++) {
+//             if (eostype == _types[n]) ieos = _itypes[n];
+//         }
 
-        // build species thermo manager
-        SpeciesThermo* spthermo = newSpeciesThermoMgr(&node);
+//         // build species thermo manager
+//         SpeciesThermo* spthermo = newSpeciesThermoMgr(&node);
 
-        ThermoPhase* th=0;
-        //        doublereal dens;
-        map<string, double> d;
-        switch (ieos) {
+//         ThermoPhase* th=0;
+//         //        doublereal dens;
+//         map<string, double> d;
+//         switch (ieos) {
 
-        case cIdealGas:
-            th = new IdealGasPhase;
-            break;
+//         case cIdealGas:
+//             th = new IdealGasPhase;
+//             break;
 
-        case cIncompressible:
-            th = new ConstDensityThermo;
-            break;
+//         case cIncompressible:
+//             th = new ConstDensityThermo;
+//             break;
 
-        case cSurf:
-            th = new SurfPhase;
-            break;
+//         case cSurf:
+//             th = new SurfPhase;
+//             break;
 
-        case cMetal:
-            th = new MetalPhase;
-            break;
+//         case cMetal:
+//             th = new MetalPhase;
+//             break;
 
-        case cSolidCompound:
-            th = new SolidCompound;
-            break;
+//         case cSolidCompound:
+//             th = new SolidCompound;
+//             break;
 
-        default:
-            throw CanteraError("newThermo",
-                "newThermo: unknown equation of state: "+eostype);
-        }
-        th->setSpeciesThermo(spthermo);
+//         default:
+//             throw CanteraError("newThermo",
+//                 "newThermo: unknown equation of state: "+eostype);
+//         }
+//         th->setSpeciesThermo(spthermo);
 
-        // import the phase specification
-        importPhase(node, th);
+//         // import the phase specification
+//         importPhase(node, th);
 
-        return th;
-    }
+//         return th;
+//     }
 
 }

Cantera/src/ThermoFactory.h

@@ -40,7 +40,7 @@ namespace Cantera {
          * Create a new thermodynamic property manager.
          * @param type the type to be created.
          */ 
-        virtual ThermoPhase* newThermo(XML_Node& node, string id);
+        //virtual ThermoPhase* newThermo(XML_Node& node, string id);
         virtual ThermoPhase* newThermoPhase(string model);
 
     private:
@@ -53,14 +53,14 @@ namespace Cantera {
     /**
      *  Create a new thermo manager instance.
      */
-    inline ThermoPhase* newThermoMgr(XML_Node& root, string id,  
-        ThermoFactory* f=0) {
-        if (f == 0) {
-            f = ThermoFactory::factory();
-        }
-        ThermoPhase* therm = f->newThermo(root, id);
-        return therm;
-    }
+//     inline ThermoPhase* newThermoMgr(XML_Node& root, string id,  
+//         ThermoFactory* f=0) {
+//         if (f == 0) {
+//             f = ThermoFactory::factory();
+//         }
+//         ThermoPhase* therm = f->newThermo(root, id);
+//         return therm;
+//     }
 
     /**
      *  Create a new thermo manager instance.

Cantera/src/ThermoPhase.h

@@ -199,6 +199,8 @@ namespace Cantera {
             err("setPressure");
         }
 
+        virtual void updateDensity() {}
+
         /**
          * @} 
          * @name Potential Energy
@@ -231,12 +233,16 @@ namespace Cantera {
         }
 
         void setElectricPotential(doublereal v) {
-            int nsp = nSpecies();
-            for (int k = 0; k < nsp; k++) {
-                setPotentialEnergy(k, v*charge(k)*Faraday);
-            }
+            //int nsp = nSpecies();
+            m_phi = v;
+            //for (int k = 0; k < nsp; k++) {
+            //    setPotentialEnergy(k, v*charge(k)*Faraday);
+            //}
         }
 
+        doublereal electricPotential() { return m_phi; }
+
+
         /**
          * @}
          * @name Chemical Potentials and Activities
@@ -594,6 +600,7 @@ namespace Cantera {
             m_spthermo = 0;
             m_index = -1;
             m_speciesData = 0;
+            m_phi = 0.0;
         }
 
     protected:
@@ -605,6 +612,7 @@ namespace Cantera {
 
         /// Index number
         int m_index;
+        doublereal m_phi;
 
     private:
 

Cantera/src/converters/Makefile.in

@@ -16,7 +16,7 @@ OBJDIR = .
 CXX_FLAGS = @CXXFLAGS@ $(CXX_OPT) 
 
 # Temporarily removed 'filter.o', since it was causing a compile error on Mac OS X.
-OBJS = ck2ctml.o atomicWeightDB.o CKParser.o CKReader.o Reaction.o ckr_utils.o thermoFunctions.o writelog.o
+OBJS = ck2ctml.o atomicWeightDB.o CKParser.o CKReader.o Reaction.o ckr_utils.o thermoFunctions.o writelog.o ck2ct.o
 
 CXX_INCLUDES = -I. -I..
 CONV_LIB = @buildlib@/libconverters.a

Cantera/src/converters/ck2ct.cpp

@@ -0,0 +1,462 @@
+/**
+ * @file ck2ctml.cpp
+ *
+ * Convert CK-format reaction mechanism files to CTML format.
+ *
+ */
+#ifdef WIN32
+#pragma warning(disable:4786)
+#pragma warning(disable:4503)
+#endif
+
+#include <iostream>
+#include <string>
+using namespace std;
+
+#include "CKReader.h"
+#include "Reaction.h"
+#include "writelog.h"
+
+#include "ck2ct.h"
+#include "../ct_defs.h"
+#include "ctml.h"
+using namespace Cantera;
+
+namespace pip {
+
+    struct trdata {
+        //trdata() {name = "-";}
+        //        string name;
+        int geom;
+        doublereal welldepth, diam, dipole, polar, rot;
+    };
+
+    static map<string, trdata> _trmap;
+    static bool _with_transport = false;
+
+    static void getTransportData(string trfile) {
+
+        _with_transport = true;
+        ifstream s(trfile.c_str());
+        if (!s) throw CanteraError("getTransportData",
+            "could not open transport database "+trfile);
+
+        /*
+         *  The first thing we will do is to read the entire transport
+         *  database and place its contents into a map structure,
+         *  indexed by the name of the species.
+         */
+	string rest;
+ 	while (! s.eof()) {
+#ifdef USE_STRINGSTREAM
+	  /*
+	   * Read a line from the file
+	   */
+	  getline(s, rest);
+	  /*
+	   * In the transport database, we allow comment lines that
+	   * consist of '#' and '!' as the first character in the
+	   * in the line. We also don't bother to parse short lines that
+	   * can't possibly have enough data in them to comprise a
+	   * properly formatted record.
+	   */
+	  if (rest[0] != '#' && rest[0] != '!' && rest.size() > 5) {
+	    /*
+	     * copy the string into a stringstream and parse the line
+	     * into the trdata object
+	     */
+	    std::istringstream ioline(rest);
+	    trdata t;
+            string nm;
+	    ioline >> nm >> t.geom >> t.welldepth >> t.diam 
+		   >> t.dipole >> t.polar >> t.rot;
+	    /*
+	     * Add the trdata object into the map database by making a
+	     * copy of it, and index it by the species name.
+	     */
+	    if (nm != "") { 
+                _trmap[nm] = t; // t.name] = t;
+	    }
+	  }
+#else
+            trdata t;
+            string nm;
+            s >> nm;
+            if (nm[0] != '!' && !s.eof()) {
+                s >> t.geom >> t.welldepth >> t.diam 
+                  >> t.dipole >> t.polar >> t.rot;
+
+                // get the rest of the line, in case there are comments
+                getline(s, rest);
+                if (nm != "") { 
+                    _trmap[nm] = t; // t.name] = t;
+                }
+            }
+        }
+#endif
+    }
+
+
+    // add a NASA polynomial parameterization
+    static void addNASA(  
+        const vector_fp& low, const vector_fp& high,  
+        doublereal minx, doublereal midx, 
+        doublereal maxx) {
+
+        printf("    thermo = (\n");
+        printf("       NASA( [%8.2f, %8.2f], ", minx, midx);
+        printf("[%17.9E, %17.9E, \n", low[0], low[1]);
+        printf("              %17.9E, %17.9E, %17.9E,\n", low[2], low[3], low[4]);
+        printf("              %17.9E, %17.9E] ),\n", low[5], low[6]);
+        printf("       NASA( [%8.2f, %8.2f], ", midx, maxx);
+        printf("[%17.9E, %17.9E, \n", high[0], high[1]);
+        printf("              %17.9E, %17.9E, %17.9E,\n", high[2], high[3], high[4]);
+        printf("              %17.9E, %17.9E] )\n", high[5], high[6]);
+        printf("             )");
+    }
+
+
+    static void addTransportParams(string name) {
+
+        trdata td;
+        if (_with_transport && _trmap.find(name) != _trmap.end()) {
+            td = _trmap[name];
+        }
+        else {
+            throw CanteraError("addTransportParams",
+                "no transport data for species "+name);
+        }
+
+        printf(",\n    transport = gas_transport(\n");
+        int geom = td.geom;
+        switch (geom) {
+        case 0: printf("                     geom = \"atom\",\n"); break;
+        case 1: printf("                     geom = \"linear\",\n"); break;
+        case 2: printf("                     geom = \"nonlinear\",\n"); break;
+        }
+        printf("                     diam = %8.2f,\n",td.diam);
+        printf("                     well_depth = %8.2f",td.welldepth);
+        if (td.polar != 0.0)
+            printf(",\n                     polar = %8.2f",td.polar);
+        if (td.dipole != 0.0)
+            printf(",\n                     dipole = %8.2f",td.dipole);
+        if (td.rot != 0.0)
+            printf(",\n                     rot_relax = %8.2f",td.rot);
+        printf(")");
+    }
+
+
+//     static void addShomate(XML_Node& node, 
+//         const vector_fp& low, const vector_fp& high,  
+//         doublereal minx, doublereal midx, 
+//         doublereal maxx) {
+//         XML_Node& f = node.addChild("Shomate");
+//         if (minx != -999.0) f.addAttribute("Tmin",minx);
+//         if (maxx != -999.0) f.addAttribute("Tmid",midx);
+//         if (maxx != -999.0) f.addAttribute("Tmax",maxx);
+//         addFloatArray(f,"low",low.size(),low.begin());
+//         addFloatArray(f,"high",high.size(),high.begin());
+//     }
+
+
+    static void addFalloff(string type, 
+        const vector_fp& params) {
+        if (type == "Troe") {
+            cout << ",\n         falloff = Troe(A = " 
+                 << fp2str(params[0]) << ", T3 = "
+                 << fp2str(params[1]) << ", T1 = "
+                 << fp2str(params[2]);
+            if (params.size() >= 4) {
+                cout << ", T2 = " << fp2str(params[3]);
+            }
+            cout << ")";
+        }
+        else if (type == "SRI") {
+            cout << ",\n         falloff = SRI(A = " 
+                 << fp2str(params[0]) << ", B = "
+                 << fp2str(params[1]) << ", C = "
+                 << fp2str(params[2]);
+            if (params.size() >= 5) {
+                cout << ", D = " << fp2str(params[3])
+                     << ", E = " << fp2str(params[4]);
+            }
+            cout << ")";
+        }
+    }
+
+    /**
+     * addSpecies():
+     *
+     */
+    static void addSpecies(string idtag, const ckr::Species& sp) {
+        string spname = sp.name;
+        printf("\nspecies(name = \"%s\",\n",spname.c_str());
+        int nel = sp.elements.size();
+        int m, num;
+        string nm, str="";
+        doublereal charge = 0.0;
+        for (m = 0; m < nel; m++) {
+	  /*
+	   * Copy the element name into the string, nm. Lower case the
+	   * second letter, if needed.
+	   */
+	  nm = sp.elements[m].name;
+          nm[0] = toupper(nm[0]);
+	  if (nm.size() == 2) nm[1] = tolower(nm[1]);
+	  /*
+	   *  Obtain the current number of atoms in the species.
+	   *  Linearize the number (HKM question? can we employ real values here
+	   *  instead?)
+	   */
+	  num = int(sp.elements[m].number);
+	  /*
+	   * Add the name and number to end of the string, str
+	   */
+	  str += " "+nm+":"+int2str(num)+" ";
+
+          /* if the species contains the special element E (electron),
+           * then set the charge.
+           */
+          if (nm == "E") charge = -sp.elements[m].number;
+        }
+
+	/*
+	 * Add the child element, atomArray, to the species xml node. 
+	 */
+        printf("    atoms = \"%s\",\n", str.c_str());
+        addNASA(sp.lowCoeffs, sp.highCoeffs, 
+            sp.tlow, sp.tmid, sp.thigh);
+
+        if (_with_transport)
+            addTransportParams(sp.name);
+        printf("\n       )\n");
+    }
+
+
+    static void addReaction(string idtag, int i,
+        const ckr::Reaction& rxn,
+        const ckr::ReactionUnits& runits, doublereal version) {
+
+        cout << "\n#  Reaction " << i+1 << endl;
+        string eqn = ckr::reactionEquation(rxn);
+        cout << "reaction( \"" << eqn << "\", ";
+
+        if (rxn.isFalloffRxn) {
+            if (rxn.kf.type == ckr::Arrhenius) {
+                printf("\n         k_inf = [%10.5E, %g, %g]", rxn.kf.A, rxn.kf.n, rxn.kf.E);
+            }
+            if (rxn.kf_aux.type == ckr::Arrhenius) {
+                printf(",\n         k_0   = [%10.5E, %g, %g]", rxn.kf_aux.A, rxn.kf_aux.n, rxn.kf_aux.E);
+            }
+            if (rxn.falloffType == ckr::Lindemann)
+                addFalloff("Lindemann",rxn.falloffParameters);
+            else if (rxn.falloffType == ckr::Troe)
+                addFalloff("Troe",rxn.falloffParameters);
+            else if (rxn.falloffType == ckr::SRI)
+                addFalloff("SRI",rxn.falloffParameters);
+            else 
+                throw CanteraError("addReaction","unknown falloff type");
+        }
+        else {
+            if (rxn.kf.type == ckr::Arrhenius) {
+                printf("  [%10.5E, %g, %g]", rxn.kf.A, rxn.kf.n, rxn.kf.E);
+            }
+        }
+
+
+        int ne = rxn.e3b.size();
+        if (rxn.thirdBody != "<none>") {
+            if (rxn.thirdBody != "M") {
+                ;
+            }
+            else if (ne > 0.0) {
+                map<string, double>::const_iterator b = rxn.e3b.begin(), 
+                                                    e = rxn.e3b.end();
+                string estr = "";
+                for (; b != e; ++b) {
+                    estr += " "+b->first+":"+fp2str(b->second)+" ";
+                }
+                cout << ",\n         efficiencies = \"" << estr << "\"";
+            }
+        }
+    cout << ")" << endl;
+    }
+
+    void writeline() {
+        cout << "#-------------------------------------------------------------------------------" << endl;
+    }
+
+    /*!
+     * This routine is the main routine. It
+     * 
+     * @param r reference to a ckreader object that has already read a chemkin formatted
+     *          mechanism. This is the input to the routine.
+     * @param root Reference to the root node of an XML description of the
+     *             mechanism. The node will be filled up with the description
+     *             of the mechanism. This is the output to the routine.
+     */
+    void ck2ct(string idtag, ckr::CKReader& r) {
+
+        popError();
+        doublereal version = 1.0;
+        cout << "from ctmm import *" << endl;
+
+        cout << "dataset(\"" << idtag << "\")" << endl;
+
+        cout << "\n\n";
+        writeline();
+        cout << "#\n#  The default units. These will be used for dimensional quantities" << endl
+             << "#  with unspecified units." << endl;
+        writeline();
+        
+        cout << "units(length = \"cm\", time = \"s\", quantity = \"mol\", ";
+        string e_unit;
+        int eunit = r.units.ActEnergy;
+        if (eunit == ckr::Cal_per_Mole)
+            e_unit = "cal/mol";
+        else if (eunit == ckr::Kcal_per_Mole)
+            e_unit = "kcal/mol";
+        else if (eunit == ckr::Joules_per_Mole)
+            e_unit = "J/mol";
+        else if (eunit == ckr::Kjoules_per_Mole) 
+            e_unit = "kJ/mol";
+        else if (eunit == ckr::Kelvin) 
+            e_unit = "K";
+        else if (eunit == ckr::Electron_Volts)
+            e_unit = "eV";
+        cout << "act_energy = " << "\"" << e_unit << "\")\n\n";
+
+        cout << "\n\n\n";
+        writeline();
+        cout << "#\n#  The phase definition. This specifies an ideal gas mixture that" << endl
+             << "#  includes all species and reactions defined in this file."
+             << "\n#\n";
+        writeline();
+
+
+        printf("ideal_gas(name = \"%s\",\n",idtag.c_str());
+
+        string enames;
+        int nel = r.elements.size();
+        int i;
+        map<string, string> emap;
+        string elnm;
+        for (i = 0; i < nel; i++) {
+            elnm = r.elements[i].name;
+            elnm[0] = toupper(elnm[0]);
+            if (elnm.size() == 2) elnm[1] = tolower(elnm[1]);
+            emap[r.elements[i].name] = elnm;
+            enames += " "+elnm+" ";
+            //addElement(earray, idtag, r.elements[i]);
+        }
+        printf("      elements = \"%s\",\n",enames.c_str());
+
+        string spnames = "";
+        int nsp = r.species.size();
+        for (i = 0; i < nsp; i++) {
+            spnames += " "+r.species[i].name+" ";
+            if ((i+1) % 10 == 0) spnames += "\n                  ";
+        }
+        printf("      species = \"\"\"%s\"\"\",\n", spnames.c_str());
+        printf("      reactions = \"all\"");
+        cout << "    )" << endl;
+
+        cout << "\n\n\n";
+        writeline();
+        cout << "#\n#  Species data \n#\n";
+        writeline();
+
+        for (i = 0; i < nsp; i++) {
+            addSpecies(idtag, r.species[i]);
+        }
+
+        cout << "\n\n\n";
+        writeline();
+        cout << "#\n#  Reaction data \n#\n";
+        writeline();
+
+
+        int nrxns = r.reactions.size();
+
+         int irxn = 0;
+         string idktag = idtag;
+        for (i = 0; i < nrxns; i++) {
+
+            // if krev.A is non-zero, then the reverse rate coefficient is
+            // being explicitly specified rather than being computed from 
+            // thermochemistry. In this case, convert the reaction into 
+            // two irreversible reactions.
+
+            if (r.reactions[i].krev.A != 0.0) {
+                addReaction(idktag, irxn, 
+                    ckr::forwardReaction(r.reactions[i]), r.units, version);
+                irxn++;
+                addReaction(idktag, irxn, 
+                    ckr::reverseReaction(r.reactions[i]), r.units, version);
+                irxn++;
+            }
+
+            // Otherwise, just add the whole reaction, which may or may
+            // not be reversible.
+            else {
+                addReaction(idktag, irxn, r.reactions[i], 
+                    r.units, version);
+                irxn++;
+            }
+        }
+//         incl.addAttribute("min",1);
+//         incl.addAttribute("max", irxn);
+    }
+
+
+
+    int convert_ck(const char* in_file, const char* db_file,
+        const char* tr_file, const char* id_tag) {
+        ckr::CKReader r;
+        r.validate = true;
+        //int i=1;
+
+        string infile = string(in_file);
+        string dbfile = string(db_file);
+        string trfile = string(tr_file);
+        //string outfile = string(out_file);
+        string idtag = string(id_tag);
+        string logfile;
+        if (dbfile == "-") dbfile = "";
+        if (trfile == "-") trfile = "";
+
+        struct tm *newtime;
+        time_t aclock;
+        ::time( &aclock );              /* Get time in seconds */
+        newtime = localtime( &aclock ); /* Convert time to struct tm form */
+ 
+        try {
+
+            logfile = "ck2ct.log";
+            if (!r.read(infile, dbfile, logfile)) {
+                throw CanteraError("convert_ck",
+                    "error encountered in input file " + string(infile) 
+                    + "\nsee file ck2ct.log for more information.\n");
+            }
+
+
+            cout << "#" << endl;
+            cout << "# Generated from file " 
+                 << infile << "\n# by ck2ct on " << asctime(newtime) << "#\n" << endl;
+            if (trfile != "") {
+                cout << "# Transport data from file "+trfile+"." << endl;
+                getTransportData(trfile);
+            }
+            ck2ct(idtag, r);
+            cout << "write()" << endl;
+        }
+        catch (CanteraError) {
+            return -1;
+        }
+        
+        return 0;
+    }
+
+}
+
+

Cantera/src/converters/ck2ct.h

@@ -0,0 +1,24 @@
+#ifndef CT_CK2CT_H
+#define CT_CK2CT_H
+
+#include <iostream>
+#include <string>
+#include <stdlib.h>
+
+//#include "ctml.h"
+
+namespace ckr{
+  class CKReader;
+}
+
+namespace pip {
+
+    void ck2ct(string idtag, ckr::CKReader& r);
+
+    int convert_ck(const char* in_file, const char* db_file,
+        const char* tr_file, const char* id_tag);
+
+}
+
+#endif
+

Cantera/src/converters/ck2ctml.cpp

@@ -40,10 +40,12 @@ namespace ctml {
         doublereal maxx) {
         XML_Node& f = node.addChild("NASA");
         if (minx != -999.0) f.addAttribute("Tmin",minx);
-        if (maxx != -999.0) f.addAttribute("Tmid",midx);
-        if (maxx != -999.0) f.addAttribute("Tmax",maxx);
-        addFloatArray(f,"low",low.size(),low.begin());
-        addFloatArray(f,"high",high.size(),high.begin());
+        if (midx != -999.0) f.addAttribute("Tmax",midx);
+        addFloatArray(f,"coeffs",low.size(),low.begin());
+        XML_Node& fh = node.addChild("NASA");
+        if (midx != -999.0) fh.addAttribute("Tmin",midx);
+        if (maxx != -999.0) fh.addAttribute("Tmax",maxx);
+        addFloatArray(fh,"coeffs",high.size(),high.begin());
     }
 
     /*
@@ -66,10 +68,27 @@ namespace ctml {
 
     static void addArrhenius(XML_Node& node,  
         doublereal A, doublereal b, doublereal E, int order, 
-        string unitsys, string E_units) {
+        string id, string E_units) {
+
+#ifdef OLD_VERSION
+        // versions prior to 1.4.1
         string abe = fp2str(A)+" "+fp2str(b)+" "+fp2str(E);
         XML_Node& r = node.addChild("Arrhenius",abe);
         r.addAttribute("order",order);
+#else
+        // version 1.4.1
+        XML_Node& rn = node.addChild("Arrhenius");
+        if (id != "") rn.addAttribute("name",id);
+        string units;
+        if (order == 1) units = "/s";
+        else if (order == 2) units = "cm3/mol/s";
+        else if (order == 3) units = "cm6/mol2/s";
+        else throw CanteraError("addArrhenius",
+            "unsupported rxn order: "+int2str(order));
+        addFloat(rn, "A", A,  units);
+        addFloat(rn, "b", b);
+        addFloat(rn, "E", E, E_units);
+#endif
     }
 
     /*
@@ -273,17 +292,17 @@ namespace ctml {
         
 
         XML_Node& kf = r.addChild("rateCoeff");
-        kf.addAttribute("units","mol,cm,s");
-        kf.addAttribute("Eunits",e_unit);
+        //kf.addAttribute("units","mol,cm,s");
+        //kf.addAttribute("Eunits",e_unit);
 
         //kf.addAttribute("id",r["id"]+"_kf");
         if (rxn.kf.type == ckr::Arrhenius)
             addArrhenius(kf, rxn.kf.A, rxn.kf.n, rxn.kf.E, 
-                int(order), "mol,cm,s", e_unit);
+                int(order), "", e_unit);
 
         if (rxn.isFalloffRxn) {
             addArrhenius(kf, rxn.kf_aux.A, rxn.kf_aux.n, rxn.kf_aux.E, 
-                int(order+1), "mol,cm,s", e_unit);
+                int(order+1), "k0", e_unit);
             
             if (rxn.falloffType == ckr::Lindemann)
                 addFalloff(kf,"Lindemann",rxn.falloffParameters);
@@ -426,15 +445,15 @@ namespace ctml {
                 addString(tr,"geometry","nonlinear"); break;
             default: ;
             }
-            if (t.welldepth != 0.0)
+            //if (t.welldepth != 0.0)
                 addFloat(tr,"LJ_welldepth",t.welldepth,"Kelvin");
-            if (t.diam != 0.0)
+                //if (t.diam != 0.0)
                 addFloat(tr,"LJ_diameter",t.diam,"A");
-            if (t.dipole != 0.0)
+                //if (t.dipole != 0.0)
                 addFloat(tr,"dipoleMoment",t.dipole,"Debye");
-            if (t.polar != 0.0)
+                //if (t.polar != 0.0)
                 addFloat(tr,"polarizability",t.polar,"A^3");
-            if (t.rot != 0.0)
+                //if (t.rot != 0.0)
                 addFloat(tr,"rotRelax",t.rot);
         }
     }
@@ -562,6 +581,7 @@ namespace ctml {
             }
 
             XML_Node root("ctml");
+            root["version"] = CTML_Version;
             root.addComment("generated from "+infile+" by ck2ctml.");
             if (trfile != "") 
             root.addComment("transport data from "+trfile+".");

Cantera/src/ctml.cpp

@@ -21,6 +21,8 @@
 
 #include "ctml.h"
 
+#define CTML_VERSION_1_4_1
+
 namespace ctml {
 
     static doublereal fpValue(string val) {
@@ -69,11 +71,15 @@ namespace ctml {
         string type, 
         doublereal minval,
         doublereal maxval) {
-
         string fmt = "%17.9E";
+#ifdef CTML_VERSION_1_4
         XML_Node& f = node.addChild("float",val,fmt);
         f.addAttribute("title",title);
-        if (type != "") f.addAttribute("type",type);        
+#endif
+#ifdef CTML_VERSION_1_4_1
+        XML_Node& f = node.addChild(title,val,fmt); 
+#endif
+        if (type != "") f.addAttribute("type",type);
         if (units != "") f.addAttribute("units",units);
         if (minval != Undef) f.addAttribute("min",minval);
         if (maxval != Undef) f.addAttribute("max",maxval);

Cantera/src/ctml.h

@@ -26,6 +26,8 @@ using namespace Cantera;
 
 namespace ctml {
 
+    const string CTML_Version = "1.4.1";
+
     bool isBuiltin(string nm);
 
     void addBool(XML_Node& node, 

Cantera/src/importCTML.cpp

@@ -80,37 +80,70 @@ namespace Cantera {
      * Install a NASA polynomial thermodynamic property
      * parameterization for species k.
      */
-    void installNasaThermo(SpeciesThermo& sp, int k, XML_Node& f) {
-        doublereal tmin, tmid, tmax;
-        tmin = fpValue(f["Tmin"]);
-        tmid = fpValue(f["Tmid"]);
-        tmax = fpValue(f["Tmax"]);
+    void installNasaThermo(SpeciesThermo& sp, int k, XML_Node& f0, XML_Node& f1) {
+        doublereal tmin0, tmax0, tmin1, tmax1, tmin, tmid, tmax;
+
+        tmin0 = fpValue(f0["Tmin"]);
+        tmax0 = fpValue(f0["Tmax"]);
+        tmin1 = fpValue(f1["Tmin"]);
+        tmax1 = fpValue(f1["Tmax"]);
 
-        vector<XML_Node*> fa;
-        f.getChildren("floatArray",fa);
         vector_fp c0, c1;
-        getFloatArray(*fa[0], c0, false);
-        getFloatArray(*fa[1], c1, false);
+        if (fabs(tmax0 - tmin1) < 0.01) {
+            tmin = tmin0;
+            tmid = tmax0;
+            tmax = tmax1;
+            getFloatArray(f0.child("floatArray"), c0, false);
+            getFloatArray(f1.child("floatArray"), c1, false);
+        }
+        else if (fabs(tmax1 - tmin0) < 0.01) {
+            tmin = tmin1;
+            tmid = tmax1;
+            tmax = tmax0;
+            getFloatArray(f1.child("floatArray"), c0, false);
+            getFloatArray(f0.child("floatArray"), c1, false);
+        }
+        else {
+            throw CanteraError("installNasaThermo","non-continuous temperature ranges.");
+        }
         array_fp c(15);
         c[0] = tmid;
         doublereal p0 = OneAtm;
-        if ((*fa[0])["title"] == "low") {
-            c[1] = c0[5];
-            c[2] = c0[6];
-            copy(c0.begin(), c0.begin()+5, c.begin() + 3);
-            c[8] = c1[5];
-            c[9] = c1[6];
-            copy(c1.begin(), c1.begin()+5, c.begin() + 10);
-        }
-        else {
-            c[1] = c1[5];
-            c[2] = c1[6];
-            copy(c1.begin(), c1.begin()+5, c.begin() + 3);
-            c[8] = c0[5];
-            c[9] = c0[6];
-            copy(c0.begin(), c0.begin()+5, c.begin() + 10);
-        }
+        c[1] = c0[5];
+        c[2] = c0[6];
+        copy(c0.begin(), c0.begin()+5, c.begin() + 3);
+        c[8] = c1[5];
+        c[9] = c1[6];
+        copy(c1.begin(), c1.begin()+5, c.begin() + 10);
         sp.install(k, NASA, c.begin(), tmin, tmax, p0);
+        
+//         tmax = fpValue(f["Tmax"]);
+
+//         vector<XML_Node*> fa;
+//         f.getChildren("floatArray",fa);
+//         vector_fp c0, c1;
+//         getFloatArray(*fa[0], c0, false);
+//         getFloatArray(*fa[1], c1, false);
+//         array_fp c(15);
+//         c[0] = tmid;
+//         doublereal p0 = OneAtm;
+//         if ((*fa[0])["title"] == "low") {
+//             c[1] = c0[5];
+//             c[2] = c0[6];
+//             copy(c0.begin(), c0.begin()+5, c.begin() + 3);
+//             c[8] = c1[5];
+//             c[9] = c1[6];
+//             copy(c1.begin(), c1.begin()+5, c.begin() + 10);
+//         }
+//         else {
+//             c[1] = c1[5];
+//             c[2] = c1[6];
+//             copy(c1.begin(), c1.begin()+5, c.begin() + 3);
+//             c[8] = c0[5];
+//             c[9] = c0[6];
+//             copy(c0.begin(), c0.begin()+5, c.begin() + 10);
+//         }
+//         sp.install(k, NASA, c.begin(), tmin, tmax, p0);
     }
 
     /** 
@@ -210,10 +243,10 @@ namespace Cantera {
             int nc = tp.size();
             if (nc == 1) {
                 XML_Node& f = *tp[0];
-                if (f.name() == "NASA") {
-                    installNasaThermo(spthermo, k, f);
-                }
-                else if (f.name() == "Shomate") {
+                //if (f.name() == "NASA") {
+                //    installNasaThermo(spthermo, k, f);
+                //}
+                if (f.name() == "Shomate") {
                     installShomateThermo(spthermo, k, f);
                 }
                 else if (f.name() == "const_cp") {
@@ -222,7 +255,14 @@ namespace Cantera {
                 else 
                     throw CanteraError("importCTML",
                         "Unsupported species thermo parameterization"
-                        " for species "+s["name"]);
+                        " for species "+s["name"]+": "+f.name());
+            }
+            else if (nc == 2) {
+                XML_Node& f0 = *tp[0];
+                XML_Node& f1 = *tp[1];
+                if (f0.name() == "NASA" && f1.name() == "NASA") {
+                    installNasaThermo(spthermo, k, f0, f1);
+                }
             }
             else 
                 throw CanteraError("importCTML",
@@ -276,53 +316,43 @@ namespace Cantera {
     }
 
 
-    void getArrhenius(XML_Node& node, int& order, doublereal& A, doublereal& b, 
+    void getArrhenius(XML_Node& node, int& highlow, doublereal& A, doublereal& b, 
         doublereal& E) {
         
-        // get rxn order to do unit conversion for pre-exponential
-        order = intValue(node["order"]);
+        if (node["name"] == "k0") 
+            highlow = 0;
+        else highlow = 1;
         
-        //nodeset_t c = node.children();
+        A = getFloat(node, "A", "-");
+        b = getFloat(node, "b");
+        E = getFloat(node, "E", "-");
+        E /= GasConstant;
+    }                
 
-        vector<string> abe;
-        getStringArray(node, abe);
-        A = fpValue(abe[0]);
-        b = fpValue(abe[1]);
-        E = fpValue(abe[2]);
-
-        string u = (*node.parent())["units"];
-        string eu = (*node.parent())["Eunits"];
-
-        doublereal cmult = 1.0;
-        if (u != "") {
-            if (u == "mol,cm,s") 
-                cmult = 1.0e-6 / CtMoles_per_mole; 
-            else if (u == "molec,cm,s") 
-                cmult = 1.0e-6*Avogadro;
+    void getStick(XML_Node& node, doublereal mw, Kinetics& kin,
+        ReactionData& r, doublereal& A, doublereal& b, doublereal& E) {
+        int nr = r.reactants.size();
+        int k, ns, not_surf = 0;
+        doublereal f = 1.0;
+        for (int n = 0; n < nr; n++) {
+            k = r.reactants[n];
+            ns = r.rstoich[n];
+            const ThermoPhase& p = kin.speciesPhase(k);
+            if (p.eosType() == cSurf) 
+                f /= pow(p.standardConcentration(k),ns);
             else 
-                throw CanteraError("getArrhenius","unknown units for A");
+                not_surf++;
         }
-        A *= pow(cmult, order - 1);
-
-        doublereal gasConstant = 1.0;
-        if (eu != "") {
-            if (eu == "cal/mol") 
-                gasConstant = 1.987;
-            else if (eu == "kcal/mol") 
-                gasConstant = 1.987e-3;
-            else if (eu == "J/mol") 
-                gasConstant = 8.314;
-            else if (eu == "kJ/mol") 
-                gasConstant = 8.314e-3;
-            else if (eu == "K") 
-                gasConstant = 1.0;
-            else if (eu == "eV") 
-                gasConstant = 1.0/11600.0;
-            else 
-                throw CanteraError("getArrhenius",
-                    "unknown units for activation energy: "+eu);
+        if (not_surf != 1) {
+            throw CanteraError("getStick",
+                "reaction probabilities can only be used in "
+                "reactions with exactly 1 bulk species.");
         }
-        E /= gasConstant;
+        doublereal cbar = sqrt(8.0*GasConstant/(Pi*mw));
+        A = 0.25 * getFloat(node, "A", "-") * cbar * f;
+        b = getFloat(node, "b") + 0.5;
+        E = getFloat(node, "E", "-");
+        E /= GasConstant;
     }                
 
 
@@ -384,36 +414,30 @@ namespace Cantera {
         int nc = kf.nChildren();
         const nodeset_t& kf_children = kf.children();
         vector_fp clow(3,0.0), chigh(3,0.0);
-        int nr = nReacMolecules(rdata);
+        //        int nr = nReacMolecules(rdata);
         for (int m = 0; m < nc; m++) {
             node_t& c = *kf_children[m];
             string nm = c.name();
-            int order=0;
+            int highlow=0;
 
             if (nm == "Arrhenius") {
                 vector_fp coeff(3);
-                getArrhenius(c, order, coeff[0], coeff[1], coeff[2]);
-                if (order == 0) order = nr;
-                if (order == nr || rdata.reactionType == THREE_BODY_RXN 
+                getArrhenius(c, highlow, coeff[0], coeff[1], coeff[2]);
+                if (highlow == 1 || rdata.reactionType == THREE_BODY_RXN 
                     || rdata.reactionType == ELEMENTARY_RXN) 
                     chigh = coeff;
-                else if (order == nr + 1) clow = coeff;
-                else {
-                    cerr << "\n\n\n" << endl;
-                    kf.write(cerr);
-                    throw CanteraError("importCTML",
-                        "wrong Arrhenius coeff order");
-                }
+                else clow = coeff;
             }
-//             else if (nm == "Stick") {
-//                 vector_fp coeff(3);
-//                 string spname = c["species"];
-//                 ThermoPhase& th = kin.speciesPhase(spname);
-//                 int isp = th.speciesIndex(spname);
-//                 double mw = th.molecularWeights()[isp];
-//                 cbar = sqrt((8.0*GasConstant)/(Pi*mw));
-            //                
-            //            }
+            else if (nm == "Stick") {
+                vector_fp coeff(3);
+                string spname = c["species"];
+                ThermoPhase& th = kin.speciesPhase(spname);
+                int isp = th.speciesIndex(spname);
+                double mw = th.molecularWeights()[isp];
+                getStick(c, mw, kin, rdata, coeff[0], coeff[1], coeff[2]);
+                chigh = coeff;
+            }
+
             else if (nm == "falloff") {
                 getFalloff(c, rdata);
             }
@@ -540,7 +564,7 @@ namespace Cantera {
 
 
         /*************************************************
-         *  Add the elements.
+         *  AddArrhethe elements.
          ************************************************/
 
 
@@ -578,19 +602,27 @@ namespace Cantera {
          * the species database.
          ***************************************************************/
 
-        XML_Node& species = phase.child("speciesArray");
+        vector<XML_Node*> sparrays;
+        phase.getChildren("speciesArray", sparrays);
+        int jsp, nspa = sparrays.size();
+        vector<XML_Node*> dbases;
+        vector_int sprule(nspa,0);
 
-        int sprule = 0;
-        if (species.hasChild("skip")) {
-            XML_Node& sk = species.child("skip");
-            string eskip = sk["element"];
-            if (eskip == "undeclared") {
-                sprule = 1;
+        for (jsp = 0; jsp < nspa; jsp++) {
+
+            XML_Node& species = *sparrays[jsp]; // phase.child("speciesArray");
+
+            if (species.hasChild("skip")) {
+                XML_Node& sk = species.child("skip");
+                string eskip = sk["element"];
+                if (eskip == "undeclared") {
+                    sprule[jsp] = 1;
+                }
             }
+            db = find_XML(species["datasrc"], &phase.root(), species["idRef"],
+                "","speciesData");
+            dbases.push_back(db);
         }
-            
-        db = find_XML(species["datasrc"], &phase.root(), species["idRef"],
-            "","speciesData");
 
 
         /*******************************************************
@@ -602,42 +634,55 @@ namespace Cantera {
          ******************************************************/
 
         delete &th->speciesThermo();
-        SpeciesThermo* spth = newSpeciesThermoMgr(db);
+        SpeciesThermo* spth = newSpeciesThermoMgr(dbases);
         th->setSpeciesThermo(spth);
         SpeciesThermo& spthermo = th->speciesThermo();
 
-
-        /*
-         * Get the array of species name strings.
-         */                          
-        vector<string> spnames;
-        getStringArray(species, spnames);
-        int nsp = spnames.size();
-
         map<string,bool> declared;
-        string name;
         int k = 0;
-        for (i = 0; i < nsp; i++) {
-            name = spnames[i];
-            
-            // Check that every species is only declared once
-            if (declared[name]) {
-                throw CanteraError("importPhase",
-                    "duplicate species: "+name);
-            }
-            declared[name] = true;
+        for (jsp = 0; jsp < nspa; jsp++) {
+
+            XML_Node& species = *sparrays[jsp]; 
+            db = dbases[jsp];
 
             /*
-             * Find the species in the database by name.
-             */
-            XML_Node* s = db->findByAttr("name",spnames[i]);
-            if (s) {
-                if (installSpecies(k, *s, *th, spthermo, sprule)) 
-                    ++k;
+             * Get the array of species name strings.
+             */                          
+            vector<string> spnames;
+            getStringArray(species, spnames);
+            int nsp = spnames.size();
+
+            if (nsp == 1 && spnames[0] == "all") {
+                vector<XML_Node*> allsp;
+                db->getChildren("species",allsp);
+                nsp = allsp.size();
+                spnames.resize(nsp);
+                for (int nn = 0; nn < nsp; nn++) spnames[nn] = (*allsp[nn])["name"];
             }
-            else {
-                throw CanteraError("importPhase","no data for species "
-                    +name);
+
+            string name;
+            for (i = 0; i < nsp; i++) {
+                name = spnames[i];
+            
+                // Check that every species is only declared once
+                if (declared[name]) {
+                    throw CanteraError("importPhase",
+                        "duplicate species: "+name);
+                }
+                declared[name] = true;
+
+                /*
+                 * Find the species in the database by name.
+                 */
+                XML_Node* s = db->findByAttr("name",spnames[i]);
+                if (s) {
+                    if (installSpecies(k, *s, *th, spthermo, sprule[jsp])) 
+                        ++k;
+                }
+                else {
+                    throw CanteraError("importPhase","no data for species "
+                        +name);
+                }
             }
         }
         th->freezeSpecies();
@@ -661,7 +706,11 @@ namespace Cantera {
         int nn, eqlen;
         vector_fp dummy;
 
-        eqn = r("equation");
+        if (r.hasChild("equation"))
+            eqn = r("equation");
+        else
+            eqn = "<no equation>";
+
         eqlen = eqn.size();
         for (nn = 0; nn < eqlen; nn++) {
             if (eqn[nn] == '[') eqn[nn] = '<';
@@ -677,7 +726,7 @@ namespace Cantera {
         ok = ok && getReagents(r, kin, -1, default_phase, rdata.products, 
             rdata.pstoich, dummy, rule);
         if (!ok) {
-            cout << "skipping " << eqn << endl;
+            //cout << "skipping " << eqn << endl;
             return false;
         }
 
@@ -715,9 +764,6 @@ namespace Cantera {
 
     bool installReactionArrays(XML_Node& p, Kinetics& kin, 
         string default_phase) {
-
-        writer = new GasKineticsWriter;
-
         vector<XML_Node*> rarrays;
         int itot = 0;
         p.getChildren("reactionArray",rarrays);
@@ -736,40 +782,50 @@ namespace Cantera {
                     rxnrule = 1;
                 }
             }
-
+            int i, nrxns = 0;
             vector<XML_Node*> incl;
             rxns.getChildren("include",incl);
             int ninc = incl.size();
-            for (int nii = 0; nii < ninc; nii++) {
-                int nrxns = 0;
-                XML_Node& ii = *incl[nii];
-                vector<string> rxn_ids;
-                string pref = ii["prefix"];
-                int imin = atoi(ii["min"].c_str());
-                int imax = atoi(ii["max"].c_str());
-                if (imin != 0 && imax != 0) {
-                    nrxns = imax - imin + 1;
-                    for (int nn=0; nn<nrxns; nn++) {
-                        rxn_ids.push_back(pref+int2str(imin+nn));
-                    }
-                }
-                
-                int i;
+
+            // if no 'include' directive, then include all reactions
+            if (ninc == 0) {
+                vector<XML_Node*> allrxns;
+                rdata->getChildren("reaction",allrxns);
+                nrxns = allrxns.size();
                 for (i = 0; i < nrxns; i++) {
-                    XML_Node* r = rdata->findID(rxn_ids[i],1);
+                    XML_Node* r = allrxns[i];
                     if (r) {
                         if (installReaction(itot, *r, &kin, 
                                 default_phase, rxnrule)) ++itot;
                     }
                 }
             }
+            else {
+                for (int nii = 0; nii < ninc; nii++) {
+                    nrxns = 0;
+                    XML_Node& ii = *incl[nii];
+                    vector<string> rxn_ids;
+                    string pref = ii["prefix"];
+                    int imin = atoi(ii["min"].c_str());
+                    int imax = atoi(ii["max"].c_str());
+                    if (imin != 0 && imax != 0) {
+                        nrxns = imax - imin + 1;
+                        for (int nn=0; nn<nrxns; nn++) {
+                            rxn_ids.push_back(pref+int2str(imin+nn));
+                        }
+                    }
+                    
+                    for (i = 0; i < nrxns; i++) {
+                        XML_Node* r = rdata->findID(rxn_ids[i],1);
+                        if (r) {
+                            if (installReaction(itot, *r, &kin, 
+                                    default_phase, rxnrule)) ++itot;
+                        }
+                    }
+                }
+            }
         }
         kin.finalize();
-        ofstream fwrite("mech.cpp");
-        //writer->writeGetNetProductionRates(cout, kin.nTotalSpecies(),
-        //    kin.nReactions());
-        fwrite.close();
-        delete writer;
         writer = 0;
         return true;
     }

Cantera/src/transport/MultiTransport.cpp

@@ -45,33 +45,33 @@
 namespace Cantera {
 
 
-    template<class S>
-    struct UpdateSpeciesVisc : public Updater {
-        UpdateSpeciesVisc(S& s) : Updater(), m_s(s) {}
-        void update() { m_s._update_species_visc_T(); }
-        S& m_s;
-    };
+//     template<class S>
+//     struct UpdateSpeciesVisc : public Updater {
+//         UpdateSpeciesVisc(S& s) : Updater(), m_s(s) {}
+//         void update() { m_s._update_species_visc_T(); }
+//         S& m_s;
+//     };
 
-    template<class S>
-    struct UpdateVisc_T : public Updater {
-        UpdateVisc_T(S& s) : Updater(), m_s(s) {}
-        void update() { m_s._update_visc_T(); }
-        S& m_s;
-    };
+//     template<class S>
+//     struct UpdateVisc_T : public Updater {
+//         UpdateVisc_T(S& s) : Updater(), m_s(s) {}
+//         void update() { m_s._update_visc_T(); }
+//         S& m_s;
+//     };
 
-    template<class S>
-    struct UpdateDiff_T : public Updater {
-        UpdateDiff_T(S& s) : Updater(), m_s(s) {}
-        void update() { m_s._update_diff_T(); }
-        S& m_s;
-    };
+//     template<class S>
+//     struct UpdateDiff_T : public Updater {
+//         UpdateDiff_T(S& s) : Updater(), m_s(s) {}
+//         void update() { m_s._update_diff_T(); }
+//         S& m_s;
+//     };
 
-    template<class S>
-    struct UpdateThermal_T : public Updater {
-        UpdateThermal_T(S& s) : Updater(), m_s(s) {}
-        void update() { m_s._update_thermal_T(); }
-        S& m_s;
-    };
+//     template<class S>
+//     struct UpdateThermal_T : public Updater {
+//         UpdateThermal_T(S& s) : Updater(), m_s(s) {}
+//         void update() { m_s._update_thermal_T(); }
+//         S& m_s;
+//     };
 
 
     /////////////////////////// constants //////////////////////////
@@ -189,6 +189,11 @@ namespace Cantera {
         m_l0000_ok = false;
         m_lmatrix_soln_ok = false;
 
+        m_diff_tlast = 0.0;
+        m_spvisc_tlast = 0.0;
+        m_visc_tlast = 0.0;
+        m_thermal_tlast = 0.0;
+
         // use LU decomposition by default
         m_gmres = false;
  
@@ -223,19 +228,19 @@ namespace Cantera {
                 m_sqrt_eps_k[k]/sq298);
         }
 
-        // install updaters
-        m_update_transport_T = m_thermo->installUpdater_T(
-            new UpdateTransport_T<MultiTransport>(*this));
-        m_update_transport_C = m_thermo->installUpdater_C(
-            new UpdateTransport_C<MultiTransport>(*this));
-        m_update_spvisc_T = m_thermo->installUpdater_T(
-            new UpdateSpeciesVisc<MultiTransport>(*this));
-        m_update_visc_T = m_thermo->installUpdater_T(
-            new UpdateVisc_T<MultiTransport>(*this));
-        m_update_diff_T = m_thermo->installUpdater_T(
-            new UpdateDiff_T<MultiTransport>(*this));
-        m_update_thermal_T = m_thermo->installUpdater_T(
-            new UpdateThermal_T<MultiTransport>(*this));
+//         // install updaters
+//         m_update_transport_T = m_thermo->installUpdater_T(
+//             new UpdateTransport_T<MultiTransport>(*this));
+//         m_update_transport_C = m_thermo->installUpdater_C(
+//             new UpdateTransport_C<MultiTransport>(*this));
+//         m_update_spvisc_T = m_thermo->installUpdater_T(
+//             new UpdateSpeciesVisc<MultiTransport>(*this));
+//         m_update_visc_T = m_thermo->installUpdater_T(
+//             new UpdateVisc_T<MultiTransport>(*this));
+//         m_update_diff_T = m_thermo->installUpdater_T(
+//             new UpdateDiff_T<MultiTransport>(*this));
+//         m_update_thermal_T = m_thermo->installUpdater_T(
+//             new UpdateThermal_T<MultiTransport>(*this));
 
         return true;
     }
@@ -551,14 +556,25 @@ namespace Cantera {
         }
     }
 
-                 
+              
+    void MultiTransport::updateTransport_T() {
+        //m_thermo->update_T(m_update_transport_T);
+        _update_transport_T();
+    }
+
+    void MultiTransport::updateTransport_C() {
+        // {m_thermo->update_C(m_update_transport_C);
+        _update_transport_C();
+    }
+
+   
     /**
      *  Update temperature-dependent quantities. This method is called
      *  by the temperature property updater.
      */ 
     void MultiTransport::_update_transport_T() 
     {
-        //if (m_temp == m_thermo->temperature()) return;
+        if (m_temp == m_thermo->temperature()) return;
 
         m_temp = m_thermo->temperature();
         m_logt = log(m_temp);
@@ -620,7 +636,10 @@ namespace Cantera {
      * from the polynomial fits at unit pressure (1 Pa).
      */
     void MultiTransport::updateDiff_T() {
-        m_thermo->update_T(m_update_diff_T);
+        if (m_diff_tlast == m_thermo->temperature()) return;
+        _update_diff_T();
+        m_diff_tlast = m_thermo->temperature();
+        //m_thermo->update_T(m_update_diff_T);
     }
 
     void MultiTransport::_update_diff_T() {
@@ -661,7 +680,10 @@ namespace Cantera {
      * The flag m_visc_ok is set to true.
      */
     void MultiTransport::updateSpeciesViscosities_T() {
-        m_thermo->update_T(m_update_spvisc_T);
+        if (m_spvisc_tlast == m_thermo->temperature()) return;
+        _update_species_visc_T();
+        //m_thermo->update_T(m_update_spvisc_T);
+        m_spvisc_tlast = m_thermo->temperature();
     }
 
 
@@ -687,7 +709,10 @@ namespace Cantera {
      * @internal
      */
     void MultiTransport::updateViscosity_T() {
-        m_thermo->update_T(m_update_visc_T);
+        if (m_visc_tlast == m_thermo->temperature()) return;
+        _update_visc_T(); 
+        //m_thermo->update_T(m_update_visc_T);
+        m_visc_tlast = m_thermo->temperature();
     }
 
     void MultiTransport::_update_visc_T() {
@@ -718,10 +743,14 @@ namespace Cantera {
      * thermal conductivity and thermal diffusion coefficients.
      */
     void MultiTransport::updateThermal_T() {
-        m_thermo->update_T(m_update_thermal_T);
+        if (m_thermal_tlast == m_thermo->temperature()) return;
+        _update_thermal_T(); 
+        // m_thermo->update_T(m_update_thermal_T);
+        m_thermal_tlast = m_thermo->temperature();
     }
 
     void MultiTransport::_update_thermal_T() {
+
         // we need species viscosities and binary diffusion
         // coefficients
         updateSpeciesViscosities_T();

Cantera/src/transport/MultiTransport.h

@@ -141,9 +141,8 @@ namespace Cantera {
          * are the ones with names beginning with an underscore. These
          * are only called by the property updaters.
          */
-
-        void updateTransport_T() {m_thermo->update_T(m_update_transport_T);}
-        void updateTransport_C() {m_thermo->update_C(m_update_transport_C);}
+        void updateTransport_T();
+        void updateTransport_C();
 
         void updateThermal_T();
         void updateViscosity_T();
@@ -167,13 +166,15 @@ namespace Cantera {
 
     private:
 
-        int m_update_transport_T;
-        int m_update_transport_C;
-        int m_update_spvisc_T;
-        int m_update_visc_T;
-        int m_update_diff_T;
-        int m_update_thermal_T;
+//         int m_update_transport_T;
+//         int m_update_transport_C;
+//         int m_update_spvisc_T;
+//         int m_update_visc_T;
+//         int m_update_diff_T;
+//         int m_update_thermal_T;
 
+        doublereal m_diff_tlast, m_spvisc_tlast, m_visc_tlast,
+            m_thermal_tlast;
 
         // mixture attributes
         int m_nsp;

Cantera/src/transport/TransportFactory.cpp

@@ -691,12 +691,19 @@ namespace Cantera {
             getString(tr, "geometry", val, type);
             geom = gindx[val] - 100;
             map<string, doublereal> fv;
-            getFloats(tr, fv, false);
-            welldepth = fv["LJ_welldepth"];
-            diam = fv["LJ_diameter"];
-            dipole = fv["dipoleMoment"];
-            polar = fv["polarizability"];
-            rot = fv["rotRelax"];
+
+            welldepth = getFloat(tr, "LJ_welldepth");
+            diam = getFloat(tr, "LJ_diameter");
+            dipole = getFloat(tr, "dipoleMoment");
+            polar = getFloat(tr, "polarizability");
+            rot = getFloat(tr, "rotRelax");
+
+            //getFloats(tr, fv, false);
+            //welldepth = fv["LJ_welldepth"];
+            //diam = fv["LJ_diameter"];
+            //dipole = fv["dipoleMoment"];
+            //polar = fv["polarizability"];
+            //rot = fv["rotRelax"];
 
             TransportData data;
             data.speciesName = name;

Cantera/src/units.h

@@ -25,6 +25,7 @@ namespace Cantera {
             string u = units, tok, tsub;
             int k;
             char action = '-';
+            //if (units[0] == '/') action = '/';
             while (1 > 0) {
                 k = u.find_first_of("/-");
                 if (k >= 0)
@@ -32,7 +33,9 @@ namespace Cantera {
                 else
                     tok = u;
                 tsize = tok.size();
-                if (tok[tsize - 1] == '2') {
+                if (tsize == 0) 
+                    fctr = 1.0;
+                else if (tok[tsize - 1] == '2') {
                     tsub = tok.substr(0,tsize-1);
                     fctr = m_u[tsub];
                     fctr *= fctr;
@@ -42,6 +45,21 @@ namespace Cantera {
                     fctr = m_u[tsub];
                     fctr *= fctr*fctr;
                 }
+                else if (tok[tsize - 1] == '4') {
+                    tsub = tok.substr(0,tsize-1);
+                    fctr = m_u[tsub];
+                    fctr *= fctr*fctr*fctr;
+                }
+                else if (tok[tsize - 1] == '5') {
+                    tsub = tok.substr(0,tsize-1);
+                    fctr = m_u[tsub];
+                    fctr *= fctr*fctr*fctr*fctr;
+                }
+                else if (tok[tsize - 1] == '6') {
+                    tsub = tok.substr(0,tsize-1);
+                    fctr = m_u[tsub];
+                    fctr *= fctr*fctr*fctr*fctr*fctr;
+                }
                 else {
                     tsub = tok;
                     fctr = m_u[tok];
@@ -96,6 +114,12 @@ namespace Cantera {
             m_u["atm"]      = 1.01325e5;
             m_u["bar"]      = 1.0e5;
             m_u["Pa"]       = 1.0;
+
+            // time
+            m_u["s"]        = 1.0;
+            m_u["min"]      = 60.0;
+            m_u["hr"]       = 3600.0;
+            m_u["ms"]       = 0.001;
         }
     };
 }

config/configure.in

@@ -5,6 +5,11 @@ AC_INIT(Cantera.README)
 AC_CONFIG_HEADER(../config.h)
 AC_CONFIG_AUX_DIR(.)
 
+echo
+echo "**************************************************************"
+echo "   Cantera Configuration Script "
+echo "**************************************************************"
+echo
 
 AC_DEFINE(NDEBUG)
 
@@ -16,7 +21,29 @@ local_inst=1
 if test "x${prefix}" = "xNONE"; then
          prefix=${ac_default_prefix}
          local_inst=0
+	 if test ! -d ${prefix}; then
+  echo 
+  echo "********************************************************************"
+  echo "Installation directory /usr/local does not exist. Either create it and"
+  echo "re-run configure, or specify another installation directory using the"
+  echo "prefix option:"
+  echo "    ./configure --prefix=<installation_directory>"
+  echo "********************************************************************"
+  exit 1       
 fi
+fi
+
+echo "Cantera will be installed in ${prefix}"
+if test ! -w ${prefix}; then
+echo "checking for write-access... no"
+echo
+echo "****  Since you do not have write-access to ${prefix}, you will need to"
+echo "****  run the 'make install' step as super-user."
+echo 
+else
+echo "checking for write-access... yes"
+fi
+
 AC_SUBST(prefix)
 AC_SUBST(local_inst)
 CANTERA_LIBDIR=$prefix/lib/cantera
@@ -221,24 +248,25 @@ AC_SUBST(CANTERA_DATA_DIR)
 AC_SUBST(CT_SHARED_LIB)
 
 BUILD_CLIB=0
-#
-#  Fortran 90 Interface
-#
-BUILD_F90=0
-if test "$BUILD_FORTRAN_90_INTERFACE" = "y"; then BUILD_F90=1; BUILD_CLIB=1; fi
-AC_SUBST(BUILD_F90)
-
 #       
 #     Python Interface
 #
 BUILD_PYTHON=0
-if test "$BUILD_PYTHON_INTERFACE" != "n"; then
-  if test -z "$PYTHON_CMD"; then 
+if test -z "$PYTHON_CMD"; then 
     AC_PATH_PROGS(PYTHON_CMD, python2 python, "none")
-    if test "$PYTHON_CMD" != "none"; then BUILD_PYTHON=1; BUILD_CLIB=1; fi
-  else
-    BUILD_PYTHON=1
+fi
+if test "$PYTHON_CMD" != "none"; then
+  if test "$BUILD_PYTHON_INTERFACE" != "n"; then
+    BUILD_PYTHON=1; BUILD_CLIB=1
   fi
+else
+  echo 
+  echo "********************************************************************"
+  echo "Configuration error. Python is required to build Cantera, but it"
+  echo "cannot be found. Set environment variable PYTHON_CMD to the command to"
+  echo "run the Python interpreter on your system, and run configure again."
+  echo "********************************************************************"
+  exit 1
 fi
 AC_SUBST(BUILD_PYTHON)
 
@@ -274,7 +302,6 @@ AC_SUBST(CXX_DEPENDS)
 #---------------------------------
 
 AC_PROG_F77()
-AC_SUBST(F90)
 
 # if G77 is defined, then add a flag to turn off adding a second underscore
 # to procedures that have an underscore in the name
@@ -295,17 +322,9 @@ esac
 AC_SUBST(SHARED_CTLIB)
 AC_SUBST(mex_ext)
 
-# filename extensions for Fortran 77 and Fortran 90
+# filename extensions for Fortran 77
 if test -z "$F77_EXT"; then F77_EXT=f; fi
 AC_SUBST(F77_EXT)
-if test -z "$F90_EXT"; then F90_EXT=f90; fi
-AC_SUBST(F90_EXT)
-
-
-if test -n "$FORT_MODULE_PATH_CMD"
-then FORT_MOD_PATH=$FORT_MODULE_PATH_CMD
-fi
-AC_SUBST(FORT_MOD_PATH)
 
 
 AC_LANG_CPLUSPLUS
@@ -405,6 +424,9 @@ AC_OUTPUT(../Cantera/Makefile \
           ../test_problems/silane_equil/Makefile) 
 #	)
 
+echo
+echo "Now type '${MAKE}' to build Cantera"
+echo  
 # $Log: configure.in,v
 
 

data/inputs/air.xml

@@ -1,296 +1,406 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<?xml-stylesheet type="text/xsl" href="ctml.xslt"?>
-<ctml xmlns="http://www.cantera.org"
-      xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.cantera.org  /Users/dgg/ctml.xsd">
-      <!-- generated from air.inp by ck2ctml. -->
-      <!-- transport data from ../transport/gri30_tran.dat. -->
-      <phase id="air">
-            <state>
-                  <temperature units="K">300</temperature>
-                  <pressure units="atm">1</pressure>
-                  <moleFractions>O:1.0</moleFractions>
-            </state>
-            <thermo model="IdealGas"/>
-            <elementArray datasrc="elements.xml"> O N Ar </elementArray>
-            <speciesArray datasrc="#air_species_data"> O O2 N NO NO2 N2O N2 AR </speciesArray>
-            <reactionArray datasrc="#air_rxn_data">
-                  <include max="8" min="1" prefix="air_rxn_"/>
-            </reactionArray>
-            <kinetics model="GasKinetics"/>
-      </phase>
-      <!-- species data -->
-      <speciesData id="air_species_data">
-            <!-- O -->
-            <species id="air_s_O" name="O">
-                  <note>L 1/90</note>
-                  <atomArray> O:1 </atomArray>
-                  <thermo>
-                        <NASA Tmax="3500" Tmid="1000" Tmin="200">
-                              <floatArray size="7" title="low"> 3.168267100E+00,
-                                    -3.279318840E-03, 6.643063960E-06,
-                                    -6.128066240E-09, 2.112659710E-12,
-                                    2.912225920E+04, 2.051933460E+00 </floatArray>
-                              <floatArray size="7" title="high">
-                                    2.569420780E+00, -8.597411370E-05,
-                                    4.194845890E-08, -1.001777990E-11,
-                                    1.228336910E-15, 2.921757910E+04,
-                                    4.784338640E+00 </floatArray>
-                        </NASA>
-                  </thermo>
-                  <transport>
-                        <string title="geometry">atom</string>
-                        <float title="LJ_welldepth" units="Kelvin">8.000000000E+01</float>
-                        <float title="LJ_diameter" units="A">2.750000000E+00</float>
-                  </transport>
-            </species>
-            <!-- O2 -->
-            <species id="air_s_O2" name="O2">
-                  <note>TPIS89</note>
-                  <atomArray> O:2 </atomArray>
-                  <thermo>
-                        <NASA Tmax="3500" Tmid="1000" Tmin="200">
-                              <floatArray size="7" title="low"> 3.782456360E+00,
-                                    -2.996734160E-03, 9.847302010E-06,
-                                    -9.681295090E-09, 3.243728370E-12,
-                                    -1.063943560E+03, 3.657675730E+00 </floatArray>
-                              <floatArray size="7" title="high">
-                                    3.282537840E+00, 1.483087540E-03,
-                                    -7.579666690E-07, 2.094705550E-10,
-                                    -2.167177940E-14, -1.088457720E+03,
-                                    5.453231290E+00 </floatArray>
-                        </NASA>
-                  </thermo>
-                  <transport>
-                        <string title="geometry">linear</string>
-                        <float title="LJ_welldepth" units="Kelvin">1.074000000E+02</float>
-                        <float title="LJ_diameter" units="A">3.458000000E+00</float>
-                        <float title="polarizability" units="A^3">1.600000000E+00</float>
-                        <float title="rotRelax">3.800000000E+00</float>
-                  </transport>
-            </species>
-            <!-- N -->
-            <species id="air_s_N" name="N">
-                  <note>L 6/88</note>
-                  <atomArray> N:1 </atomArray>
-                  <thermo>
-                        <NASA Tmax="6000" Tmid="1000" Tmin="200">
-                              <floatArray size="7" title="low"> 2.500000000E+00,
-                                    0.000000000E+00, 0.000000000E+00,
-                                    0.000000000E+00, 0.000000000E+00,
-                                    5.610463700E+04, 4.193908700E+00 </floatArray>
-                              <floatArray size="7" title="high">
-                                    2.415942900E+00, 1.748906500E-04,
-                                    -1.190236900E-07, 3.022624500E-11,
-                                    -2.036098200E-15, 5.613377300E+04,
-                                    4.649609600E+00 </floatArray>
-                        </NASA>
-                  </thermo>
-                  <transport>
-                        <string title="geometry">atom</string>
-                        <float title="LJ_welldepth" units="Kelvin">7.140000000E+01</float>
-                        <float title="LJ_diameter" units="A">3.298000000E+00</float>
-                  </transport>
-            </species>
-            <!-- NO -->
-            <species id="air_s_NO" name="NO">
-                  <note>RUS 78</note>
-                  <atomArray> N:1 O:1 </atomArray>
-                  <thermo>
-                        <NASA Tmax="6000" Tmid="1000" Tmin="200">
-                              <floatArray size="7" title="low"> 4.218476300E+00,
-                                    -4.638976000E-03, 1.104102200E-05,
-                                    -9.336135400E-09, 2.803577000E-12,
-                                    9.844623000E+03, 2.280846400E+00 </floatArray>
-                              <floatArray size="7" title="high">
-                                    3.260605600E+00, 1.191104300E-03,
-                                    -4.291704800E-07, 6.945766900E-11,
-                                    -4.033609900E-15, 9.920974600E+03,
-                                    6.369302700E+00 </floatArray>
-                        </NASA>
-                  </thermo>
-                  <transport>
-                        <string title="geometry">linear</string>
-                        <float title="LJ_welldepth" units="Kelvin">9.753000000E+01</float>
-                        <float title="LJ_diameter" units="A">3.621000000E+00</float>
-                        <float title="polarizability" units="A^3">1.760000000E+00</float>
-                        <float title="rotRelax">4.000000000E+00</float>
-                  </transport>
-            </species>
-            <!-- NO2 -->
-            <species id="air_s_NO2" name="NO2">
-                  <note>L 7/88</note>
-                  <atomArray> N:1 O:2 </atomArray>
-                  <thermo>
-                        <NASA Tmax="6000" Tmid="1000" Tmin="200">
-                              <floatArray size="7" title="low"> 3.944031200E+00,
-                                    -1.585429000E-03, 1.665781200E-05,
-                                    -2.047542600E-08, 7.835056400E-12,
-                                    2.896617900E+03, 6.311991700E+00 </floatArray>
-                              <floatArray size="7" title="high">
-                                    4.884754200E+00, 2.172395600E-03,
-                                    -8.280690600E-07, 1.574751000E-10,
-                                    -1.051089500E-14, 2.316498300E+03,
-                                    -1.174169500E-01 </floatArray>
-                        </NASA>
-                  </thermo>
-                  <transport>
-                        <string title="geometry">nonlinear</string>
-                        <float title="LJ_welldepth" units="Kelvin">2.000000000E+02</float>
-                        <float title="LJ_diameter" units="A">3.500000000E+00</float>
-                        <float title="rotRelax">1.000000000E+00</float>
-                  </transport>
-            </species>
-            <!-- N2O -->
-            <species id="air_s_N2O" name="N2O">
-                  <note>L 7/88</note>
-                  <atomArray> N:2 O:1 </atomArray>
-                  <thermo>
-                        <NASA Tmax="6000" Tmid="1000" Tmin="200">
-                              <floatArray size="7" title="low"> 2.257150200E+00,
-                                    1.130472800E-02, -1.367131900E-05,
-                                    9.681980600E-09, -2.930718200E-12,
-                                    8.741774400E+03, 1.075799200E+01 </floatArray>
-                              <floatArray size="7" title="high">
-                                    4.823072900E+00, 2.627025100E-03,
-                                    -9.585087400E-07, 1.600071200E-10,
-                                    -9.775230300E-15, 8.073404800E+03,
-                                    -2.201720700E+00 </floatArray>
-                        </NASA>
-                  </thermo>
-                  <transport>
-                        <string title="geometry">linear</string>
-                        <float title="LJ_welldepth" units="Kelvin">2.324000000E+02</float>
-                        <float title="LJ_diameter" units="A">3.828000000E+00</float>
-                        <float title="rotRelax">1.000000000E+00</float>
-                  </transport>
-            </species>
-            <!-- N2 -->
-            <species id="air_s_N2" name="N2">
-                  <note>121286</note>
-                  <atomArray> N:2 </atomArray>
-                  <thermo>
-                        <NASA Tmax="5000" Tmid="1000" Tmin="300">
-                              <floatArray size="7" title="low"> 3.298677000E+00,
-                                    1.408240400E-03, -3.963222000E-06,
-                                    5.641515000E-09, -2.444854000E-12,
-                                    -1.020899900E+03, 3.950372000E+00 </floatArray>
-                              <floatArray size="7" title="high">
-                                    2.926640000E+00, 1.487976800E-03,
-                                    -5.684760000E-07, 1.009703800E-10,
-                                    -6.753351000E-15, -9.227977000E+02,
-                                    5.980528000E+00 </floatArray>
-                        </NASA>
-                  </thermo>
-                  <transport>
-                        <string title="geometry">linear</string>
-                        <float title="LJ_welldepth" units="Kelvin">9.753000000E+01</float>
-                        <float title="LJ_diameter" units="A">3.621000000E+00</float>
-                        <float title="polarizability" units="A^3">1.760000000E+00</float>
-                        <float title="rotRelax">4.000000000E+00</float>
-                  </transport>
-            </species>
-            <!-- AR -->
-            <species id="air_s_AR" name="AR">
-                  <note>120186</note>
-                  <atomArray> Ar:1 </atomArray>
-                  <thermo>
-                        <NASA Tmax="5000" Tmid="1000" Tmin="300">
-                              <floatArray size="7" title="low"> 2.500000000E+00,
-                                    0.000000000E+00, 0.000000000E+00,
-                                    0.000000000E+00, 0.000000000E+00,
-                                    -7.453750000E+02, 4.366000000E+00 </floatArray>
-                              <floatArray size="7" title="high">
-                                    2.500000000E+00, 0.000000000E+00,
-                                    0.000000000E+00, 0.000000000E+00,
-                                    0.000000000E+00, -7.453750000E+02,
-                                    4.366000000E+00 </floatArray>
-                        </NASA>
-                  </thermo>
-                  <transport>
-                        <string title="geometry">atom</string>
-                        <float title="LJ_welldepth" units="Kelvin">1.365000000E+02</float>
-                        <float title="LJ_diameter" units="A">3.330000000E+00</float>
-                  </transport>
-            </species>
-      </speciesData>
-      <!-- reaction data -->
-      <reactionData id="air_rxn_data">
-            <!-- air reaction 1 -->
-            <reaction id="air_rxn_1" reversible="yes" type="threeBody">
-                  <equation>2 O + M [=] O2 + M</equation>
-                  <reactants> O:2 </reactants>
-                  <products> O2:1 </products>
-                  <rateCoeff Eunits="cal/mol" units="mol,cm,s">
-                        <Arrhenius order="3">1.2e+17 -1 0</Arrhenius>
-                        <efficiencies default="1"> AR:0.83 </efficiencies>
-                  </rateCoeff>
-            </reaction>
-            <!-- air reaction 2 -->
-            <reaction id="air_rxn_2" reversible="yes">
-                  <equation>N + NO [=] N2 + O</equation>
-                  <reactants> N:1 NO:1 </reactants>
-                  <products> N2:1 O:1 </products>
-                  <rateCoeff Eunits="cal/mol" units="mol,cm,s">
-                        <Arrhenius order="2">2.7e+13 0 355</Arrhenius>
-                  </rateCoeff>
-            </reaction>
-            <!-- air reaction 3 -->
-            <reaction id="air_rxn_3" reversible="yes">
-                  <equation>N + O2 [=] NO + O</equation>
-                  <reactants> N:1 O2:1 </reactants>
-                  <products> NO:1 O:1 </products>
-                  <rateCoeff Eunits="cal/mol" units="mol,cm,s">
-                        <Arrhenius order="2">9e+09 1 6500</Arrhenius>
-                  </rateCoeff>
-            </reaction>
-            <!-- air reaction 4 -->
-            <reaction id="air_rxn_4" reversible="yes">
-                  <equation>N2O + O [=] N2 + O2</equation>
-                  <reactants> N2O:1 O:1 </reactants>
-                  <products> N2:1 O2:1 </products>
-                  <rateCoeff Eunits="cal/mol" units="mol,cm,s">
-                        <Arrhenius order="2">1.4e+12 0 10810</Arrhenius>
-                  </rateCoeff>
-            </reaction>
-            <!-- air reaction 5 -->
-            <reaction id="air_rxn_5" reversible="yes">
-                  <equation>N2O + O [=] 2 NO</equation>
-                  <reactants> N2O:1 O:1 </reactants>
-                  <products> NO:2 </products>
-                  <rateCoeff Eunits="cal/mol" units="mol,cm,s">
-                        <Arrhenius order="2">2.9e+13 0 23150</Arrhenius>
-                  </rateCoeff>
-            </reaction>
-            <!-- air reaction 6 -->
-            <reaction id="air_rxn_6" reversible="yes" type="falloff">
-                  <equation>N2O (+ M) [=] N2 + O (+ M)</equation>
-                  <reactants> N2O:1 </reactants>
-                  <products> N2:1 O:1 </products>
-                  <rateCoeff Eunits="cal/mol" units="mol,cm,s">
-                        <Arrhenius order="1">7.91e+10 0 56020</Arrhenius>
-                        <Arrhenius order="2">6.37e+14 0 56640</Arrhenius>
-                        <falloff type="Lindemann"/>
-                        <efficiencies default="1"> AR:0.625 </efficiencies>
-                  </rateCoeff>
-            </reaction>
-            <!-- air reaction 7 -->
-            <reaction id="air_rxn_7" reversible="yes" type="threeBody">
-                  <equation>NO + O + M [=] NO2 + M</equation>
-                  <reactants> NO:1 O:1 </reactants>
-                  <products> NO2:1 </products>
-                  <rateCoeff Eunits="cal/mol" units="mol,cm,s">
-                        <Arrhenius order="3">1.06e+20 -1.41 0</Arrhenius>
-                        <efficiencies default="1"> AR:0.7 </efficiencies>
-                  </rateCoeff>
-            </reaction>
-            <!-- air reaction 8 -->
-            <reaction id="air_rxn_8" reversible="yes">
-                  <equation>NO2 + O [=] NO + O2</equation>
-                  <reactants> NO2:1 O:1 </reactants>
-                  <products> NO:1 O2:1 </products>
-                  <rateCoeff Eunits="cal/mol" units="mol,cm,s">
-                        <Arrhenius order="2">3.9e+12 0 -240</Arrhenius>
-                  </rateCoeff>
-            </reaction>
-      </reactionData>
-</ctml>
+<?xml version="1.0"?>
+<ctml>
+
+  <!-- generated from air.inp by ck2ctml. -->
+
+  <!-- transport data from ../transport/gri30_tran.dat. -->
+  <phase id="air">
+    <state>
+      <temperature units="K">300</temperature>
+      <pressure units="atm">1</pressure>
+      <moleFractions>O:1.0</moleFractions>
+    </state>
+    <thermo model="IdealGas"/>
+    <elementArray datasrc="elements.xml"> O  N  Ar </elementArray>
+    <speciesArray datasrc="#air_species_data">
+     O  O2  N  NO  NO2  N2O  N2  AR 
+    </speciesArray>
+    <reactionArray datasrc="#air_rxn_data">
+      <include max="8" min="1" prefix="air_rxn_"/>
+    </reactionArray>
+    <kinetics model="GasKinetics"/>
+  </phase>
+
+  <!-- species data -->
+  <speciesData id="air_species_data">
+
+    <!-- O -->
+    <species id="air_s_O" name="O">
+      <note>L 1/90</note>
+      <atomArray> O:1 </atomArray>
+      <charge>0.000000000E+00</charge>
+      <thermo>
+        <NASA Tmax="1000" Tmin="200">
+          <floatArray size="7" title="coeffs">
+            3.168267100E+00,  -3.279318840E-03,   6.643063960E-06,
+           -6.128066240E-09,   2.112659710E-12,   2.912225920E+04,
+            2.051933460E+00
+          </floatArray>
+        </NASA>
+        <NASA Tmax="3500" Tmin="1000">
+          <floatArray size="7" title="coeffs">
+            2.569420780E+00,  -8.597411370E-05,   4.194845890E-08,
+           -1.001777990E-11,   1.228336910E-15,   2.921757910E+04,
+            4.784338640E+00
+          </floatArray>
+        </NASA>
+      </thermo>
+      <transport>
+        <string title="geometry">atom</string>
+        <LJ_welldepth units="Kelvin">8.000000000E+01</LJ_welldepth>
+        <LJ_diameter units="A">2.750000000E+00</LJ_diameter>
+        <dipoleMoment units="Debye">0.000000000E+00</dipoleMoment>
+        <polarizability units="A^3">0.000000000E+00</polarizability>
+        <rotRelax>0.000000000E+00</rotRelax>
+      </transport>
+    </species>
+
+    <!-- O2 -->
+    <species id="air_s_O2" name="O2">
+      <note>TPIS89</note>
+      <atomArray> O:2 </atomArray>
+      <charge>0.000000000E+00</charge>
+      <thermo>
+        <NASA Tmax="1000" Tmin="200">
+          <floatArray size="7" title="coeffs">
+            3.782456360E+00,  -2.996734160E-03,   9.847302010E-06,
+           -9.681295090E-09,   3.243728370E-12,  -1.063943560E+03,
+            3.657675730E+00
+          </floatArray>
+        </NASA>
+        <NASA Tmax="3500" Tmin="1000">
+          <floatArray size="7" title="coeffs">
+            3.282537840E+00,   1.483087540E-03,  -7.579666690E-07,
+            2.094705550E-10,  -2.167177940E-14,  -1.088457720E+03,
+            5.453231290E+00
+          </floatArray>
+        </NASA>
+      </thermo>
+      <transport>
+        <string title="geometry">linear</string>
+        <LJ_welldepth units="Kelvin">1.074000000E+02</LJ_welldepth>
+        <LJ_diameter units="A">3.458000000E+00</LJ_diameter>
+        <dipoleMoment units="Debye">0.000000000E+00</dipoleMoment>
+        <polarizability units="A^3">1.600000000E+00</polarizability>
+        <rotRelax>3.800000000E+00</rotRelax>
+      </transport>
+    </species>
+
+    <!-- N -->
+    <species id="air_s_N" name="N">
+      <note>L 6/88</note>
+      <atomArray> N:1 </atomArray>
+      <charge>0.000000000E+00</charge>
+      <thermo>
+        <NASA Tmax="1000" Tmin="200">
+          <floatArray size="7" title="coeffs">
+            2.500000000E+00,   0.000000000E+00,   0.000000000E+00,
+            0.000000000E+00,   0.000000000E+00,   5.610463700E+04,
+            4.193908700E+00
+          </floatArray>
+        </NASA>
+        <NASA Tmax="6000" Tmin="1000">
+          <floatArray size="7" title="coeffs">
+            2.415942900E+00,   1.748906500E-04,  -1.190236900E-07,
+            3.022624500E-11,  -2.036098200E-15,   5.613377300E+04,
+            4.649609600E+00
+          </floatArray>
+        </NASA>
+      </thermo>
+      <transport>
+        <string title="geometry">atom</string>
+        <LJ_welldepth units="Kelvin">7.140000000E+01</LJ_welldepth>
+        <LJ_diameter units="A">3.298000000E+00</LJ_diameter>
+        <dipoleMoment units="Debye">0.000000000E+00</dipoleMoment>
+        <polarizability units="A^3">0.000000000E+00</polarizability>
+        <rotRelax>0.000000000E+00</rotRelax>
+      </transport>
+    </species>
+
+    <!-- NO -->
+    <species id="air_s_NO" name="NO">
+      <note>RUS 78</note>
+      <atomArray> N:1  O:1 </atomArray>
+      <charge>0.000000000E+00</charge>
+      <thermo>
+        <NASA Tmax="1000" Tmin="200">
+          <floatArray size="7" title="coeffs">
+            4.218476300E+00,  -4.638976000E-03,   1.104102200E-05,
+           -9.336135400E-09,   2.803577000E-12,   9.844623000E+03,
+            2.280846400E+00
+          </floatArray>
+        </NASA>
+        <NASA Tmax="6000" Tmin="1000">
+          <floatArray size="7" title="coeffs">
+            3.260605600E+00,   1.191104300E-03,  -4.291704800E-07,
+            6.945766900E-11,  -4.033609900E-15,   9.920974600E+03,
+            6.369302700E+00
+          </floatArray>
+        </NASA>
+      </thermo>
+      <transport>
+        <string title="geometry">linear</string>
+        <LJ_welldepth units="Kelvin">9.753000000E+01</LJ_welldepth>
+        <LJ_diameter units="A">3.621000000E+00</LJ_diameter>
+        <dipoleMoment units="Debye">0.000000000E+00</dipoleMoment>
+        <polarizability units="A^3">1.760000000E+00</polarizability>
+        <rotRelax>4.000000000E+00</rotRelax>
+      </transport>
+    </species>
+
+    <!-- NO2 -->
+    <species id="air_s_NO2" name="NO2">
+      <note>L 7/88</note>
+      <atomArray> N:1  O:2 </atomArray>
+      <charge>0.000000000E+00</charge>
+      <thermo>
+        <NASA Tmax="1000" Tmin="200">
+          <floatArray size="7" title="coeffs">
+            3.944031200E+00,  -1.585429000E-03,   1.665781200E-05,
+           -2.047542600E-08,   7.835056400E-12,   2.896617900E+03,
+            6.311991700E+00
+          </floatArray>
+        </NASA>
+        <NASA Tmax="6000" Tmin="1000">
+          <floatArray size="7" title="coeffs">
+            4.884754200E+00,   2.172395600E-03,  -8.280690600E-07,
+            1.574751000E-10,  -1.051089500E-14,   2.316498300E+03,
+           -1.174169500E-01
+          </floatArray>
+        </NASA>
+      </thermo>
+      <transport>
+        <string title="geometry">nonlinear</string>
+        <LJ_welldepth units="Kelvin">2.000000000E+02</LJ_welldepth>
+        <LJ_diameter units="A">3.500000000E+00</LJ_diameter>
+        <dipoleMoment units="Debye">0.000000000E+00</dipoleMoment>
+        <polarizability units="A^3">0.000000000E+00</polarizability>
+        <rotRelax>1.000000000E+00</rotRelax>
+      </transport>
+    </species>
+
+    <!-- N2O -->
+    <species id="air_s_N2O" name="N2O">
+      <note>L 7/88</note>
+      <atomArray> N:2  O:1 </atomArray>
+      <charge>0.000000000E+00</charge>
+      <thermo>
+        <NASA Tmax="1000" Tmin="200">
+          <floatArray size="7" title="coeffs">
+            2.257150200E+00,   1.130472800E-02,  -1.367131900E-05,
+            9.681980600E-09,  -2.930718200E-12,   8.741774400E+03,
+            1.075799200E+01
+          </floatArray>
+        </NASA>
+        <NASA Tmax="6000" Tmin="1000">
+          <floatArray size="7" title="coeffs">
+            4.823072900E+00,   2.627025100E-03,  -9.585087400E-07,
+            1.600071200E-10,  -9.775230300E-15,   8.073404800E+03,
+           -2.201720700E+00
+          </floatArray>
+        </NASA>
+      </thermo>
+      <transport>
+        <string title="geometry">linear</string>
+        <LJ_welldepth units="Kelvin">2.324000000E+02</LJ_welldepth>
+        <LJ_diameter units="A">3.828000000E+00</LJ_diameter>
+        <dipoleMoment units="Debye">0.000000000E+00</dipoleMoment>
+        <polarizability units="A^3">0.000000000E+00</polarizability>
+        <rotRelax>1.000000000E+00</rotRelax>
+      </transport>
+    </species>
+
+    <!-- N2 -->
+    <species id="air_s_N2" name="N2">
+      <note>121286</note>
+      <atomArray> N:2 </atomArray>
+      <charge>0.000000000E+00</charge>
+      <thermo>
+        <NASA Tmax="1000" Tmin="300">
+          <floatArray size="7" title="coeffs">
+            3.298677000E+00,   1.408240400E-03,  -3.963222000E-06,
+            5.641515000E-09,  -2.444854000E-12,  -1.020899900E+03,
+            3.950372000E+00
+          </floatArray>
+        </NASA>
+        <NASA Tmax="5000" Tmin="1000">
+          <floatArray size="7" title="coeffs">
+            2.926640000E+00,   1.487976800E-03,  -5.684760000E-07,
+            1.009703800E-10,  -6.753351000E-15,  -9.227977000E+02,
+            5.980528000E+00
+          </floatArray>
+        </NASA>
+      </thermo>
+      <transport>
+        <string title="geometry">linear</string>
+        <LJ_welldepth units="Kelvin">9.753000000E+01</LJ_welldepth>
+        <LJ_diameter units="A">3.621000000E+00</LJ_diameter>
+        <dipoleMoment units="Debye">0.000000000E+00</dipoleMoment>
+        <polarizability units="A^3">1.760000000E+00</polarizability>
+        <rotRelax>4.000000000E+00</rotRelax>
+      </transport>
+    </species>
+
+    <!-- AR -->
+    <species id="air_s_AR" name="AR">
+      <note>120186</note>
+      <atomArray> Ar:1 </atomArray>
+      <charge>0.000000000E+00</charge>
+      <thermo>
+        <NASA Tmax="1000" Tmin="300">
+          <floatArray size="7" title="coeffs">
+            2.500000000E+00,   0.000000000E+00,   0.000000000E+00,
+            0.000000000E+00,   0.000000000E+00,  -7.453750000E+02,
+            4.366000000E+00
+          </floatArray>
+        </NASA>
+        <NASA Tmax="5000" Tmin="1000">
+          <floatArray size="7" title="coeffs">
+            2.500000000E+00,   0.000000000E+00,   0.000000000E+00,
+            0.000000000E+00,   0.000000000E+00,  -7.453750000E+02,
+            4.366000000E+00
+          </floatArray>
+        </NASA>
+      </thermo>
+      <transport>
+        <string title="geometry">atom</string>
+        <LJ_welldepth units="Kelvin">1.365000000E+02</LJ_welldepth>
+        <LJ_diameter units="A">3.330000000E+00</LJ_diameter>
+        <dipoleMoment units="Debye">0.000000000E+00</dipoleMoment>
+        <polarizability units="A^3">0.000000000E+00</polarizability>
+        <rotRelax>0.000000000E+00</rotRelax>
+      </transport>
+    </species>
+  </speciesData>
+
+  <!-- reaction data -->
+  <reactionData id="air_rxn_data">
+
+    <!-- air reaction 1 -->
+    <reaction id="air_rxn_1" reversible="yes" type="threeBody">
+      <equation>2 O + M [=] O2 + M</equation>
+      <reactants> O:2 </reactants>
+      <products> O2:1 </products>
+      <rateCoeff>
+        <Arrhenius>
+          <A units="cm6/mol2/s">1.200000000E+17</A>
+          <b>-1.000000000E+00</b>
+          <E units="cal/mol">0.000000000E+00</E>
+        </Arrhenius>
+        <efficiencies default="1">
+         AR:0.83 
+        </efficiencies>
+      </rateCoeff>
+    </reaction>
+
+    <!-- air reaction 2 -->
+    <reaction id="air_rxn_2" reversible="yes">
+      <equation>N + NO [=] N2 + O</equation>
+      <reactants> N:1  NO:1 </reactants>
+      <products> N2:1  O:1 </products>
+      <rateCoeff>
+        <Arrhenius>
+          <A units="cm3/mol/s">2.700000000E+13</A>
+          <b>0.000000000E+00</b>
+          <E units="cal/mol">3.550000000E+02</E>
+        </Arrhenius>
+      </rateCoeff>
+    </reaction>
+
+    <!-- air reaction 3 -->
+    <reaction id="air_rxn_3" reversible="yes">
+      <equation>N + O2 [=] NO + O</equation>
+      <reactants> N:1  O2:1 </reactants>
+      <products> NO:1  O:1 </products>
+      <rateCoeff>
+        <Arrhenius>
+          <A units="cm3/mol/s">9.000000000E+09</A>
+          <b>1.000000000E+00</b>
+          <E units="cal/mol">6.500000000E+03</E>
+        </Arrhenius>
+      </rateCoeff>
+    </reaction>
+
+    <!-- air reaction 4 -->
+    <reaction id="air_rxn_4" reversible="yes">
+      <equation>N2O + O [=] N2 + O2</equation>
+      <reactants> N2O:1  O:1 </reactants>
+      <products> N2:1  O2:1 </products>
+      <rateCoeff>
+        <Arrhenius>
+          <A units="cm3/mol/s">1.400000000E+12</A>
+          <b>0.000000000E+00</b>
+          <E units="cal/mol">1.081000000E+04</E>
+        </Arrhenius>
+      </rateCoeff>
+    </reaction>
+
+    <!-- air reaction 5 -->
+    <reaction id="air_rxn_5" reversible="yes">
+      <equation>N2O + O [=] 2 NO</equation>
+      <reactants> N2O:1  O:1 </reactants>
+      <products> NO:2 </products>
+      <rateCoeff>
+        <Arrhenius>
+          <A units="cm3/mol/s">2.900000000E+13</A>
+          <b>0.000000000E+00</b>
+          <E units="cal/mol">2.315000000E+04</E>
+        </Arrhenius>
+      </rateCoeff>
+    </reaction>
+
+    <!-- air reaction 6 -->
+    <reaction id="air_rxn_6" reversible="yes" type="falloff">
+      <equation>N2O (+ M) [=] N2 + O (+ M)</equation>
+      <reactants> N2O:1 </reactants>
+      <products> N2:1  O:1 </products>
+      <rateCoeff>
+        <Arrhenius>
+          <A units="/s">7.910000000E+10</A>
+          <b>0.000000000E+00</b>
+          <E units="cal/mol">5.602000000E+04</E>
+        </Arrhenius>
+        <Arrhenius name="k0">
+          <A units="cm3/mol/s">6.370000000E+14</A>
+          <b>0.000000000E+00</b>
+          <E units="cal/mol">5.664000000E+04</E>
+        </Arrhenius>
+        <falloff type="Lindemann"/>
+        <efficiencies default="1">
+         AR:0.625 
+        </efficiencies>
+      </rateCoeff>
+    </reaction>
+
+    <!-- air reaction 7 -->
+    <reaction id="air_rxn_7" reversible="yes" type="threeBody">
+      <equation>NO + O + M [=] NO2 + M</equation>
+      <reactants> NO:1  O:1 </reactants>
+      <products> NO2:1 </products>
+      <rateCoeff>
+        <Arrhenius>
+          <A units="cm6/mol2/s">1.060000000E+20</A>
+          <b>-1.410000000E+00</b>
+          <E units="cal/mol">0.000000000E+00</E>
+        </Arrhenius>
+        <efficiencies default="1">
+         AR:0.7 
+        </efficiencies>
+      </rateCoeff>
+    </reaction>
+
+    <!-- air reaction 8 -->
+    <reaction id="air_rxn_8" reversible="yes">
+      <equation>NO2 + O [=] NO + O2</equation>
+      <reactants> NO2:1  O:1 </reactants>
+      <products> NO:1  O2:1 </products>
+      <rateCoeff>
+        <Arrhenius>
+          <A units="cm3/mol/s">3.900000000E+12</A>
+          <b>0.000000000E+00</b>
+          <E units="cal/mol">-2.400000000E+02</E>
+        </Arrhenius>
+      </rateCoeff>
+    </reaction>
+  </reactionData>
+</ctml>

data/inputs/argon.xml

@@ -28,24 +28,30 @@
     <species id="argon_s_AR" name="AR">
       <note>120186</note>
       <atomArray> Ar:1 </atomArray>
+      <charge>0.000000000E+00</charge>
       <thermo>
-        <NASA Tmax="5000" Tmid="1000" Tmin="300">
-          <floatArray size="7" title="low">
-           2.500000000E+000,  0.000000000E+000,  0.000000000E+000,
-           0.000000000E+000,  0.000000000E+000, -7.453750000E+002,
-           4.366000000E+000
+        <NASA Tmax="1000" Tmin="300">
+          <floatArray size="7" title="coeffs">
+            2.500000000E+00,   0.000000000E+00,   0.000000000E+00,
+            0.000000000E+00,   0.000000000E+00,  -7.453750000E+02,
+            4.366000000E+00
           </floatArray>
-          <floatArray size="7" title="high">
-           2.500000000E+000,  0.000000000E+000,  0.000000000E+000,
-           0.000000000E+000,  0.000000000E+000, -7.453750000E+002,
-           4.366000000E+000
+        </NASA>
+        <NASA Tmax="5000" Tmin="1000">
+          <floatArray size="7" title="coeffs">
+            2.500000000E+00,   0.000000000E+00,   0.000000000E+00,
+            0.000000000E+00,   0.000000000E+00,  -7.453750000E+02,
+            4.366000000E+00
           </floatArray>
         </NASA>
       </thermo>
       <transport>
         <string title="geometry">atom</string>
-        <float title="LJ_welldepth" units="Kelvin">1.365000000E+002</float>
-        <float title="LJ_diameter" units="A">3.330000000E+000</float>
+        <LJ_welldepth units="Kelvin">1.365000000E+02</LJ_welldepth>
+        <LJ_diameter units="A">3.330000000E+00</LJ_diameter>
+        <dipoleMoment units="Debye">0.000000000E+00</dipoleMoment>
+        <polarizability units="A^3">0.000000000E+00</polarizability>
+        <rotRelax>0.000000000E+00</rotRelax>
       </transport>
     </species>
   </speciesData>

data/inputs/elements.xml

@@ -1,8 +1,8 @@
 <ctml>
   <elementData caseSensitive="no">
 	<element name="H", atomicWt = "1.00794"/>
-	<element name="D", atomicWt = "2.0"/>
-	<element name="Tr", atomicWt = "3.0"/>
+	<element name="D", atomicWt = "2.0147"/>
+	<element name="Tr", atomicWt = "3.016327"/>
 	<element name="He", atomicWt = "4.002602"/>
 	<element name="Li", atomicWt = "6.941"/>
 	<element name="Be", atomicWt = "9.012182"/>

data/inputs/h2o2.xml

@@ -19,7 +19,6 @@
       <include max="27" min="1" prefix="ohmech_rxn_"/>
     </reactionArray>
     <kinetics model="GasKinetics"/>
-    <transport model="Mix"/>
   </phase>
 
   <!-- species data -->
@@ -29,14 +28,17 @@
     <species id="ohmech_s_H2" name="H2">
       <note>TPIS78</note>
       <atomArray> H:2 </atomArray>
+      <charge>0.000000000E+00</charge>
       <thermo>
-        <NASA Tmax="3500" Tmid="1000" Tmin="200">
-          <floatArray size="7" title="low">
+        <NASA Tmax="1000" Tmin="200">
+          <floatArray size="7" title="coeffs">
             2.344331120E+00,   7.980520750E-03,  -1.947815100E-05,
             2.015720940E-08,  -7.376117610E-12,  -9.179351730E+02,
             6.830102380E-01
           </floatArray>
-          <floatArray size="7" title="high">
+        </NASA>
+        <NASA Tmax="3500" Tmin="1000">
+          <floatArray size="7" title="coeffs">
             3.337279200E+00,  -4.940247310E-05,   4.994567780E-07,
            -1.795663940E-10,   2.002553760E-14,  -9.501589220E+02,
            -3.205023310E+00
@@ -45,10 +47,11 @@
       </thermo>
       <transport>
         <string title="geometry">linear</string>
-        <float title="LJ_welldepth" units="Kelvin">3.800000000E+01</float>
-        <float title="LJ_diameter" units="A">2.920000000E+00</float>
-        <float title="polarizability" units="A^3">7.900000000E-01</float>
-        <float title="rotRelax">2.800000000E+02</float>
+        <LJ_welldepth units="Kelvin">3.800000000E+01</LJ_welldepth>
+        <LJ_diameter units="A">2.920000000E+00</LJ_diameter>
+        <dipoleMoment units="Debye">0.000000000E+00</dipoleMoment>
+        <polarizability units="A^3">7.900000000E-01</polarizability>
+        <rotRelax>2.800000000E+02</rotRelax>
       </transport>
     </species>
 
@@ -56,14 +59,17 @@
     <species id="ohmech_s_H" name="H">
       <note>L 7/88</note>
       <atomArray> H:1 </atomArray>
+      <charge>0.000000000E+00</charge>
       <thermo>
-        <NASA Tmax="3500" Tmid="1000" Tmin="200">
-          <floatArray size="7" title="low">
+        <NASA Tmax="1000" Tmin="200">
+          <floatArray size="7" title="coeffs">
             2.500000000E+00,   7.053328190E-13,  -1.995919640E-15,
             2.300816320E-18,  -9.277323320E-22,   2.547365990E+04,
            -4.466828530E-01
           </floatArray>
-          <floatArray size="7" title="high">
+        </NASA>
+        <NASA Tmax="3500" Tmin="1000">
+          <floatArray size="7" title="coeffs">
             2.500000010E+00,  -2.308429730E-11,   1.615619480E-14,
            -4.735152350E-18,   4.981973570E-22,   2.547365990E+04,
            -4.466829140E-01
@@ -72,8 +78,11 @@
       </thermo>
       <transport>
         <string title="geometry">atom</string>
-        <float title="LJ_welldepth" units="Kelvin">1.450000000E+02</float>
-        <float title="LJ_diameter" units="A">2.050000000E+00</float>
+        <LJ_welldepth units="Kelvin">1.450000000E+02</LJ_welldepth>
+        <LJ_diameter units="A">2.050000000E+00</LJ_diameter>
+        <dipoleMoment units="Debye">0.000000000E+00</dipoleMoment>
+        <polarizability units="A^3">0.000000000E+00</polarizability>
+        <rotRelax>0.000000000E+00</rotRelax>
       </transport>
     </species>
 
@@ -81,14 +90,17 @@
     <species id="ohmech_s_O" name="O">
       <note>L 1/90</note>
       <atomArray> O:1 </atomArray>
+      <charge>0.000000000E+00</charge>
       <thermo>
-        <NASA Tmax="3500" Tmid="1000" Tmin="200">
-          <floatArray size="7" title="low">
+        <NASA Tmax="1000" Tmin="200">
+          <floatArray size="7" title="coeffs">
             3.168267100E+00,  -3.279318840E-03,   6.643063960E-06,
            -6.128066240E-09,   2.112659710E-12,   2.912225920E+04,
             2.051933460E+00
           </floatArray>
-          <floatArray size="7" title="high">
+        </NASA>
+        <NASA Tmax="3500" Tmin="1000">
+          <floatArray size="7" title="coeffs">
             2.569420780E+00,  -8.597411370E-05,   4.194845890E-08,
            -1.001777990E-11,   1.228336910E-15,   2.921757910E+04,
             4.784338640E+00
@@ -97,8 +109,11 @@
       </thermo>
       <transport>
         <string title="geometry">atom</string>
-        <float title="LJ_welldepth" units="Kelvin">8.000000000E+01</float>
-        <float title="LJ_diameter" units="A">2.750000000E+00</float>
+        <LJ_welldepth units="Kelvin">8.000000000E+01</LJ_welldepth>
+        <LJ_diameter units="A">2.750000000E+00</LJ_diameter>
+        <dipoleMoment units="Debye">0.000000000E+00</dipoleMoment>
+        <polarizability units="A^3">0.000000000E+00</polarizability>
+        <rotRelax>0.000000000E+00</rotRelax>
       </transport>
     </species>
 
@@ -106,14 +121,17 @@
     <species id="ohmech_s_O2" name="O2">
       <note>TPIS89</note>
       <atomArray> O:2 </atomArray>
+      <charge>0.000000000E+00</charge>
       <thermo>
-        <NASA Tmax="3500" Tmid="1000" Tmin="200">
-          <floatArray size="7" title="low">
+        <NASA Tmax="1000" Tmin="200">
+          <floatArray size="7" title="coeffs">
             3.782456360E+00,  -2.996734160E-03,   9.847302010E-06,
            -9.681295090E-09,   3.243728370E-12,  -1.063943560E+03,
             3.657675730E+00
           </floatArray>
-          <floatArray size="7" title="high">
+        </NASA>
+        <NASA Tmax="3500" Tmin="1000">
+          <floatArray size="7" title="coeffs">
             3.282537840E+00,   1.483087540E-03,  -7.579666690E-07,
             2.094705550E-10,  -2.167177940E-14,  -1.088457720E+03,
             5.453231290E+00
@@ -122,10 +140,11 @@
       </thermo>
       <transport>
         <string title="geometry">linear</string>
-        <float title="LJ_welldepth" units="Kelvin">1.074000000E+02</float>
-        <float title="LJ_diameter" units="A">3.458000000E+00</float>
-        <float title="polarizability" units="A^3">1.600000000E+00</float>
-        <float title="rotRelax">3.800000000E+00</float>
+        <LJ_welldepth units="Kelvin">1.074000000E+02</LJ_welldepth>
+        <LJ_diameter units="A">3.458000000E+00</LJ_diameter>
+        <dipoleMoment units="Debye">0.000000000E+00</dipoleMoment>
+        <polarizability units="A^3">1.600000000E+00</polarizability>
+        <rotRelax>3.800000000E+00</rotRelax>
       </transport>
     </species>
 
@@ -133,14 +152,17 @@
     <species id="ohmech_s_OH" name="OH">
       <note>RUS 78</note>
       <atomArray> O:1  H:1 </atomArray>
+      <charge>0.000000000E+00</charge>
       <thermo>
-        <NASA Tmax="3500" Tmid="1000" Tmin="200">
-          <floatArray size="7" title="low">
+        <NASA Tmax="1000" Tmin="200">
+          <floatArray size="7" title="coeffs">
             3.992015430E+00,  -2.401317520E-03,   4.617938410E-06,
            -3.881133330E-09,   1.364114700E-12,   3.615080560E+03,
            -1.039254580E-01
           </floatArray>
-          <floatArray size="7" title="high">
+        </NASA>
+        <NASA Tmax="3500" Tmin="1000">
+          <floatArray size="7" title="coeffs">
             3.092887670E+00,   5.484297160E-04,   1.265052280E-07,
            -8.794615560E-11,   1.174123760E-14,   3.858657000E+03,
             4.476696100E+00
@@ -149,8 +171,11 @@
       </thermo>
       <transport>
         <string title="geometry">linear</string>
-        <float title="LJ_welldepth" units="Kelvin">8.000000000E+01</float>
-        <float title="LJ_diameter" units="A">2.750000000E+00</float>
+        <LJ_welldepth units="Kelvin">8.000000000E+01</LJ_welldepth>
+        <LJ_diameter units="A">2.750000000E+00</LJ_diameter>
+        <dipoleMoment units="Debye">0.000000000E+00</dipoleMoment>
+        <polarizability units="A^3">0.000000000E+00</polarizability>
+        <rotRelax>0.000000000E+00</rotRelax>
       </transport>
     </species>
 
@@ -158,14 +183,17 @@
     <species id="ohmech_s_H2O" name="H2O">
       <note>L 8/89</note>
       <atomArray> H:2  O:1 </atomArray>
+      <charge>0.000000000E+00</charge>
       <thermo>
-        <NASA Tmax="3500" Tmid="1000" Tmin="200">
-          <floatArray size="7" title="low">
+        <NASA Tmax="1000" Tmin="200">
+          <floatArray size="7" title="coeffs">
             4.198640560E+00,  -2.036434100E-03,   6.520402110E-06,
            -5.487970620E-09,   1.771978170E-12,  -3.029372670E+04,
            -8.490322080E-01
           </floatArray>
-          <floatArray size="7" title="high">
+        </NASA>
+        <NASA Tmax="3500" Tmin="1000">
+          <floatArray size="7" title="coeffs">
             3.033992490E+00,   2.176918040E-03,  -1.640725180E-07,
            -9.704198700E-11,   1.682009920E-14,  -3.000429710E+04,
             4.966770100E+00
@@ -174,10 +202,11 @@
       </thermo>
       <transport>
         <string title="geometry">nonlinear</string>
-        <float title="LJ_welldepth" units="Kelvin">5.724000000E+02</float>
-        <float title="LJ_diameter" units="A">2.605000000E+00</float>
-        <float title="dipoleMoment" units="Debye">1.844000000E+00</float>
-        <float title="rotRelax">4.000000000E+00</float>
+        <LJ_welldepth units="Kelvin">5.724000000E+02</LJ_welldepth>
+        <LJ_diameter units="A">2.605000000E+00</LJ_diameter>
+        <dipoleMoment units="Debye">1.844000000E+00</dipoleMoment>
+        <polarizability units="A^3">0.000000000E+00</polarizability>
+        <rotRelax>4.000000000E+00</rotRelax>
       </transport>
     </species>
 
@@ -185,14 +214,17 @@
     <species id="ohmech_s_HO2" name="HO2">
       <note>L 5/89</note>
       <atomArray> H:1  O:2 </atomArray>
+      <charge>0.000000000E+00</charge>
       <thermo>
-        <NASA Tmax="3500" Tmid="1000" Tmin="200">
-          <floatArray size="7" title="low">
+        <NASA Tmax="1000" Tmin="200">
+          <floatArray size="7" title="coeffs">
             4.301798010E+00,  -4.749120510E-03,   2.115828910E-05,
            -2.427638940E-08,   9.292251240E-12,   2.948080400E+02,
             3.716662450E+00
           </floatArray>
-          <floatArray size="7" title="high">
+        </NASA>
+        <NASA Tmax="3500" Tmin="1000">
+          <floatArray size="7" title="coeffs">
             4.017210900E+00,   2.239820130E-03,  -6.336581500E-07,
             1.142463700E-10,  -1.079085350E-14,   1.118567130E+02,
             3.785102150E+00
@@ -201,9 +233,11 @@
       </thermo>
       <transport>
         <string title="geometry">nonlinear</string>
-        <float title="LJ_welldepth" units="Kelvin">1.074000000E+02</float>
-        <float title="LJ_diameter" units="A">3.458000000E+00</float>
-        <float title="rotRelax">1.000000000E+00</float>
+        <LJ_welldepth units="Kelvin">1.074000000E+02</LJ_welldepth>
+        <LJ_diameter units="A">3.458000000E+00</LJ_diameter>
+        <dipoleMoment units="Debye">0.000000000E+00</dipoleMoment>
+        <polarizability units="A^3">0.000000000E+00</polarizability>
+        <rotRelax>1.000000000E+00</rotRelax>
       </transport>
     </species>
 
@@ -211,14 +245,17 @@
     <species id="ohmech_s_H2O2" name="H2O2">
       <note>L 7/88</note>
       <atomArray> H:2  O:2 </atomArray>
+      <charge>0.000000000E+00</charge>
       <thermo>
-        <NASA Tmax="3500" Tmid="1000" Tmin="200">
-          <floatArray size="7" title="low">
+        <NASA Tmax="1000" Tmin="200">
+          <floatArray size="7" title="coeffs">
             4.276112690E+00,  -5.428224170E-04,   1.673357010E-05,
            -2.157708130E-08,   8.624543630E-12,  -1.770258210E+04,
             3.435050740E+00
           </floatArray>
-          <floatArray size="7" title="high">
+        </NASA>
+        <NASA Tmax="3500" Tmin="1000">
+          <floatArray size="7" title="coeffs">
             4.165002850E+00,   4.908316940E-03,  -1.901392250E-06,
             3.711859860E-10,  -2.879083050E-14,  -1.786178770E+04,
             2.916156620E+00
@@ -227,9 +264,11 @@
       </thermo>
       <transport>
         <string title="geometry">nonlinear</string>
-        <float title="LJ_welldepth" units="Kelvin">1.074000000E+02</float>
-        <float title="LJ_diameter" units="A">3.458000000E+00</float>
-        <float title="rotRelax">3.800000000E+00</float>
+        <LJ_welldepth units="Kelvin">1.074000000E+02</LJ_welldepth>
+        <LJ_diameter units="A">3.458000000E+00</LJ_diameter>
+        <dipoleMoment units="Debye">0.000000000E+00</dipoleMoment>
+        <polarizability units="A^3">0.000000000E+00</polarizability>
+        <rotRelax>3.800000000E+00</rotRelax>
       </transport>
     </species>
 
@@ -237,14 +276,17 @@
     <species id="ohmech_s_AR" name="AR">
       <note>120186</note>
       <atomArray> Ar:1 </atomArray>
+      <charge>0.000000000E+00</charge>
       <thermo>
-        <NASA Tmax="5000" Tmid="1000" Tmin="300">
-          <floatArray size="7" title="low">
+        <NASA Tmax="1000" Tmin="300">
+          <floatArray size="7" title="coeffs">
             2.500000000E+00,   0.000000000E+00,   0.000000000E+00,
             0.000000000E+00,   0.000000000E+00,  -7.453750000E+02,
             4.366000000E+00
           </floatArray>
-          <floatArray size="7" title="high">
+        </NASA>
+        <NASA Tmax="5000" Tmin="1000">
+          <floatArray size="7" title="coeffs">
             2.500000000E+00,   0.000000000E+00,   0.000000000E+00,
             0.000000000E+00,   0.000000000E+00,  -7.453750000E+02,
             4.366000000E+00
@@ -253,8 +295,11 @@
       </thermo>
       <transport>
         <string title="geometry">atom</string>
-        <float title="LJ_welldepth" units="Kelvin">1.365000000E+02</float>
-        <float title="LJ_diameter" units="A">3.330000000E+00</float>
+        <LJ_welldepth units="Kelvin">1.365000000E+02</LJ_welldepth>
+        <LJ_diameter units="A">3.330000000E+00</LJ_diameter>
+        <dipoleMoment units="Debye">0.000000000E+00</dipoleMoment>
+        <polarizability units="A^3">0.000000000E+00</polarizability>
+        <rotRelax>0.000000000E+00</rotRelax>
       </transport>
     </species>
   </speciesData>
@@ -267,8 +312,12 @@
       <equation>2 O + M [=] O2 + M</equation>
       <reactants> O:2 </reactants>
       <products> O2:1 </products>
-      <rateCoeff Eunits="cal/mol" units="mol,cm,s">
-        <Arrhenius order="3">1.2e+17 -1 0</Arrhenius>
+      <rateCoeff>
+        <Arrhenius>
+          <A units="cm6/mol2/s">1.200000000E+17</A>
+          <b>-1.000000000E+00</b>
+          <E units="cal/mol">0.000000000E+00</E>
+        </Arrhenius>
         <efficiencies default="1">
          AR:0.83  H2:2.4  H2O:15.4 
         </efficiencies>
@@ -280,8 +329,12 @@
       <equation>O + H + M [=] OH + M</equation>
       <reactants> O:1  H:1 </reactants>
       <products> OH:1 </products>
-      <rateCoeff Eunits="cal/mol" units="mol,cm,s">
-        <Arrhenius order="3">5e+17 -1 0</Arrhenius>
+      <rateCoeff>
+        <Arrhenius>
+          <A units="cm6/mol2/s">5.000000000E+17</A>
+          <b>-1.000000000E+00</b>
+          <E units="cal/mol">0.000000000E+00</E>
+        </Arrhenius>
         <efficiencies default="1">
          AR:0.7  H2:2  H2O:6 
         </efficiencies>
@@ -293,8 +346,12 @@
       <equation>O + H2 [=] H + OH</equation>
       <reactants> O:1  H2:1 </reactants>
       <products> H:1  OH:1 </products>
-      <rateCoeff Eunits="cal/mol" units="mol,cm,s">
-        <Arrhenius order="2">38700 2.7 6260</Arrhenius>
+      <rateCoeff>
+        <Arrhenius>
+          <A units="cm3/mol/s">3.870000000E+04</A>
+          <b>2.700000000E+00</b>
+          <E units="cal/mol">6.260000000E+03</E>
+        </Arrhenius>
       </rateCoeff>
     </reaction>
 
@@ -303,8 +360,12 @@
       <equation>O + HO2 [=] OH + O2</equation>
       <reactants> O:1  HO2:1 </reactants>
       <products> OH:1  O2:1 </products>
-      <rateCoeff Eunits="cal/mol" units="mol,cm,s">
-        <Arrhenius order="2">2e+13 0 0</Arrhenius>
+      <rateCoeff>
+        <Arrhenius>
+          <A units="cm3/mol/s">2.000000000E+13</A>
+          <b>0.000000000E+00</b>
+          <E units="cal/mol">0.000000000E+00</E>
+        </Arrhenius>
       </rateCoeff>
     </reaction>
 
@@ -313,8 +374,12 @@
       <equation>O + H2O2 [=] OH + HO2</equation>
       <reactants> O:1  H2O2:1 </reactants>
       <products> OH:1  HO2:1 </products>
-      <rateCoeff Eunits="cal/mol" units="mol,cm,s">
-        <Arrhenius order="2">9.63e+06 2 4000</Arrhenius>
+      <rateCoeff>
+        <Arrhenius>
+          <A units="cm3/mol/s">9.630000000E+06</A>
+          <b>2.000000000E+00</b>
+          <E units="cal/mol">4.000000000E+03</E>
+        </Arrhenius>
       </rateCoeff>
     </reaction>
 
@@ -323,8 +388,12 @@
       <equation>H + 2 O2 [=] HO2 + O2</equation>
       <reactants> H:1  O2:2 </reactants>
       <products> HO2:1  O2:1 </products>
-      <rateCoeff Eunits="cal/mol" units="mol,cm,s">
-        <Arrhenius order="3">2.08e+19 -1.24 0</Arrhenius>
+      <rateCoeff>
+        <Arrhenius>
+          <A units="cm6/mol2/s">2.080000000E+19</A>
+          <b>-1.240000000E+00</b>
+          <E units="cal/mol">0.000000000E+00</E>
+        </Arrhenius>
       </rateCoeff>
     </reaction>
 
@@ -333,8 +402,12 @@
       <equation>H + O2 + H2O [=] HO2 + H2O</equation>
       <reactants> H:1  O2:1  H2O:1 </reactants>
       <products> HO2:1  H2O:1 </products>
-      <rateCoeff Eunits="cal/mol" units="mol,cm,s">
-        <Arrhenius order="3">1.126e+19 -0.76 0</Arrhenius>
+      <rateCoeff>
+        <Arrhenius>
+          <A units="cm6/mol2/s">1.126000000E+19</A>
+          <b>-7.600000000E-01</b>
+          <E units="cal/mol">0.000000000E+00</E>
+        </Arrhenius>
       </rateCoeff>
     </reaction>
 
@@ -343,8 +416,12 @@
       <equation>H + O2 + AR [=] HO2 + AR</equation>
       <reactants> H:1  O2:1  AR:1 </reactants>
       <products> HO2:1  AR:1 </products>
-      <rateCoeff Eunits="cal/mol" units="mol,cm,s">
-        <Arrhenius order="3">7e+17 -0.8 0</Arrhenius>
+      <rateCoeff>
+        <Arrhenius>
+          <A units="cm6/mol2/s">7.000000000E+17</A>
+          <b>-8.000000000E-01</b>
+          <E units="cal/mol">0.000000000E+00</E>
+        </Arrhenius>
       </rateCoeff>
     </reaction>
 
@@ -353,8 +430,12 @@
       <equation>H + O2 [=] O + OH</equation>
       <reactants> H:1  O2:1 </reactants>
       <products> O:1  OH:1 </products>
-      <rateCoeff Eunits="cal/mol" units="mol,cm,s">
-        <Arrhenius order="2">2.65e+16 -0.6707 17041</Arrhenius>
+      <rateCoeff>
+        <Arrhenius>
+          <A units="cm3/mol/s">2.650000000E+16</A>
+          <b>-6.707000000E-01</b>
+          <E units="cal/mol">1.704100000E+04</E>
+        </Arrhenius>
       </rateCoeff>
     </reaction>
 
@@ -363,8 +444,12 @@
       <equation>2 H + M [=] H2 + M</equation>
       <reactants> H:2 </reactants>
       <products> H2:1 </products>
-      <rateCoeff Eunits="cal/mol" units="mol,cm,s">
-        <Arrhenius order="3">1e+18 -1 0</Arrhenius>
+      <rateCoeff>
+        <Arrhenius>
+          <A units="cm6/mol2/s">1.000000000E+18</A>
+          <b>-1.000000000E+00</b>
+          <E units="cal/mol">0.000000000E+00</E>
+        </Arrhenius>
         <efficiencies default="1">
          AR:0.63  H2:0  H2O:0 
         </efficiencies>
@@ -376,8 +461,12 @@
       <equation>2 H + H2 [=] 2 H2</equation>
       <reactants> H:2  H2:1 </reactants>
       <products> H2:2 </products>
-      <rateCoeff Eunits="cal/mol" units="mol,cm,s">
-        <Arrhenius order="3">9e+16 -0.6 0</Arrhenius>
+      <rateCoeff>
+        <Arrhenius>
+          <A units="cm6/mol2/s">9.000000000E+16</A>
+          <b>-6.000000000E-01</b>
+          <E units="cal/mol">0.000000000E+00</E>
+        </Arrhenius>
       </rateCoeff>
     </reaction>
 
@@ -386,8 +475,12 @@
       <equation>2 H + H2O [=] H2 + H2O</equation>
       <reactants> H:2  H2O:1 </reactants>
       <products> H2:1  H2O:1 </products>
-      <rateCoeff Eunits="cal/mol" units="mol,cm,s">
-        <Arrhenius order="3">6e+19 -1.25 0</Arrhenius>
+      <rateCoeff>
+        <Arrhenius>
+          <A units="cm6/mol2/s">6.000000000E+19</A>
+          <b>-1.250000000E+00</b>
+          <E units="cal/mol">0.000000000E+00</E>
+        </Arrhenius>
       </rateCoeff>
     </reaction>
 
@@ -396,8 +489,12 @@
       <equation>H + OH + M [=] H2O + M</equation>
       <reactants> H:1  OH:1 </reactants>
       <products> H2O:1 </products>
-      <rateCoeff Eunits="cal/mol" units="mol,cm,s">
-        <Arrhenius order="3">2.2e+22 -2 0</Arrhenius>
+      <rateCoeff>
+        <Arrhenius>
+          <A units="cm6/mol2/s">2.200000000E+22</A>
+          <b>-2.000000000E+00</b>
+          <E units="cal/mol">0.000000000E+00</E>
+        </Arrhenius>
         <efficiencies default="1">
          AR:0.38  H2:0.73  H2O:3.65 
         </efficiencies>
@@ -409,8 +506,12 @@
       <equation>H + HO2 [=] O + H2O</equation>
       <reactants> H:1  HO2:1 </reactants>
       <products> O:1  H2O:1 </products>
-      <rateCoeff Eunits="cal/mol" units="mol,cm,s">
-        <Arrhenius order="2">3.97e+12 0 671</Arrhenius>
+      <rateCoeff>
+        <Arrhenius>
+          <A units="cm3/mol/s">3.970000000E+12</A>
+          <b>0.000000000E+00</b>
+          <E units="cal/mol">6.710000000E+02</E>
+        </Arrhenius>
       </rateCoeff>
     </reaction>
 
@@ -419,8 +520,12 @@
       <equation>H + HO2 [=] O2 + H2</equation>
       <reactants> H:1  HO2:1 </reactants>
       <products> O2:1  H2:1 </products>
-      <rateCoeff Eunits="cal/mol" units="mol,cm,s">
-        <Arrhenius order="2">4.48e+13 0 1068</Arrhenius>
+      <rateCoeff>
+        <Arrhenius>
+          <A units="cm3/mol/s">4.480000000E+13</A>
+          <b>0.000000000E+00</b>
+          <E units="cal/mol">1.068000000E+03</E>
+        </Arrhenius>
       </rateCoeff>
     </reaction>
 
@@ -429,8 +534,12 @@
       <equation>H + HO2 [=] 2 OH</equation>
       <reactants> H:1  HO2:1 </reactants>
       <products> OH:2 </products>
-      <rateCoeff Eunits="cal/mol" units="mol,cm,s">
-        <Arrhenius order="2">8.4e+13 0 635</Arrhenius>
+      <rateCoeff>
+        <Arrhenius>
+          <A units="cm3/mol/s">8.400000000E+13</A>
+          <b>0.000000000E+00</b>
+          <E units="cal/mol">6.350000000E+02</E>
+        </Arrhenius>
       </rateCoeff>
     </reaction>
 
@@ -439,8 +548,12 @@
       <equation>H + H2O2 [=] HO2 + H2</equation>
       <reactants> H:1  H2O2:1 </reactants>
       <products> HO2:1  H2:1 </products>
-      <rateCoeff Eunits="cal/mol" units="mol,cm,s">
-        <Arrhenius order="2">1.21e+07 2 5200</Arrhenius>
+      <rateCoeff>
+        <Arrhenius>
+          <A units="cm3/mol/s">1.210000000E+07</A>
+          <b>2.000000000E+00</b>
+          <E units="cal/mol">5.200000000E+03</E>
+        </Arrhenius>
       </rateCoeff>
     </reaction>
 
@@ -449,8 +562,12 @@
       <equation>H + H2O2 [=] OH + H2O</equation>
       <reactants> H:1  H2O2:1 </reactants>
       <products> OH:1  H2O:1 </products>
-      <rateCoeff Eunits="cal/mol" units="mol,cm,s">
-        <Arrhenius order="2">1e+13 0 3600</Arrhenius>
+      <rateCoeff>
+        <Arrhenius>
+          <A units="cm3/mol/s">1.000000000E+13</A>
+          <b>0.000000000E+00</b>
+          <E units="cal/mol">3.600000000E+03</E>
+        </Arrhenius>
       </rateCoeff>
     </reaction>
 
@@ -459,8 +576,12 @@
       <equation>OH + H2 [=] H + H2O</equation>
       <reactants> OH:1  H2:1 </reactants>
       <products> H:1  H2O:1 </products>
-      <rateCoeff Eunits="cal/mol" units="mol,cm,s">
-        <Arrhenius order="2">2.16e+08 1.51 3430</Arrhenius>
+      <rateCoeff>
+        <Arrhenius>
+          <A units="cm3/mol/s">2.160000000E+08</A>
+          <b>1.510000000E+00</b>
+          <E units="cal/mol">3.430000000E+03</E>
+        </Arrhenius>
       </rateCoeff>
     </reaction>
 
@@ -469,9 +590,17 @@
       <equation>2 OH (+ M) [=] H2O2 (+ M)</equation>
       <reactants> OH:2 </reactants>
       <products> H2O2:1 </products>
-      <rateCoeff Eunits="cal/mol" units="mol,cm,s">
-        <Arrhenius order="2">7.4e+13 -0.37 0</Arrhenius>
-        <Arrhenius order="3">2.3e+18 -0.9 -1700</Arrhenius>
+      <rateCoeff>
+        <Arrhenius>
+          <A units="cm3/mol/s">7.400000000E+13</A>
+          <b>-3.700000000E-01</b>
+          <E units="cal/mol">0.000000000E+00</E>
+        </Arrhenius>
+        <Arrhenius name="k0">
+          <A units="cm6/mol2/s">2.300000000E+18</A>
+          <b>-9.000000000E-01</b>
+          <E units="cal/mol">-1.700000000E+03</E>
+        </Arrhenius>
         <falloff type="Troe"> 0.7346  94  1756  5182 </falloff>
         <efficiencies default="1">
          AR:0.7  H2:2  H2O:6 
@@ -484,8 +613,12 @@
       <equation>2 OH [=] O + H2O</equation>
       <reactants> OH:2 </reactants>
       <products> O:1  H2O:1 </products>
-      <rateCoeff Eunits="cal/mol" units="mol,cm,s">
-        <Arrhenius order="2">35700 2.4 -2110</Arrhenius>
+      <rateCoeff>
+        <Arrhenius>
+          <A units="cm3/mol/s">3.570000000E+04</A>
+          <b>2.400000000E+00</b>
+          <E units="cal/mol">-2.110000000E+03</E>
+        </Arrhenius>
       </rateCoeff>
     </reaction>
 
@@ -494,8 +627,12 @@
       <equation>OH + HO2 [=] O2 + H2O</equation>
       <reactants> OH:1  HO2:1 </reactants>
       <products> O2:1  H2O:1 </products>
-      <rateCoeff Eunits="cal/mol" units="mol,cm,s">
-        <Arrhenius order="2">1.45e+13 0 -500</Arrhenius>
+      <rateCoeff>
+        <Arrhenius>
+          <A units="cm3/mol/s">1.450000000E+13</A>
+          <b>0.000000000E+00</b>
+          <E units="cal/mol">-5.000000000E+02</E>
+        </Arrhenius>
       </rateCoeff>
       <duplicate>idtag_rxn_27</duplicate>
     </reaction>
@@ -505,8 +642,12 @@
       <equation>OH + H2O2 [=] HO2 + H2O</equation>
       <reactants> OH:1  H2O2:1 </reactants>
       <products> HO2:1  H2O:1 </products>
-      <rateCoeff Eunits="cal/mol" units="mol,cm,s">
-        <Arrhenius order="2">2e+12 0 427</Arrhenius>
+      <rateCoeff>
+        <Arrhenius>
+          <A units="cm3/mol/s">2.000000000E+12</A>
+          <b>0.000000000E+00</b>
+          <E units="cal/mol">4.270000000E+02</E>
+        </Arrhenius>
       </rateCoeff>
       <duplicate>idtag_rxn_24</duplicate>
     </reaction>
@@ -516,8 +657,12 @@
       <equation>OH + H2O2 [=] HO2 + H2O</equation>
       <reactants> OH:1  H2O2:1 </reactants>
       <products> HO2:1  H2O:1 </products>
-      <rateCoeff Eunits="cal/mol" units="mol,cm,s">
-        <Arrhenius order="2">1.7e+18 0 29410</Arrhenius>
+      <rateCoeff>
+        <Arrhenius>
+          <A units="cm3/mol/s">1.700000000E+18</A>
+          <b>0.000000000E+00</b>
+          <E units="cal/mol">2.941000000E+04</E>
+        </Arrhenius>
       </rateCoeff>
       <duplicate>idtag_rxn_23</duplicate>
     </reaction>
@@ -527,8 +672,12 @@
       <equation>2 HO2 [=] O2 + H2O2</equation>
       <reactants> HO2:2 </reactants>
       <products> O2:1  H2O2:1 </products>
-      <rateCoeff Eunits="cal/mol" units="mol,cm,s">
-        <Arrhenius order="2">1.3e+11 0 -1630</Arrhenius>
+      <rateCoeff>
+        <Arrhenius>
+          <A units="cm3/mol/s">1.300000000E+11</A>
+          <b>0.000000000E+00</b>
+          <E units="cal/mol">-1.630000000E+03</E>
+        </Arrhenius>
       </rateCoeff>
       <duplicate>idtag_rxn_26</duplicate>
     </reaction>
@@ -538,8 +687,12 @@
       <equation>2 HO2 [=] O2 + H2O2</equation>
       <reactants> HO2:2 </reactants>
       <products> O2:1  H2O2:1 </products>
-      <rateCoeff Eunits="cal/mol" units="mol,cm,s">
-        <Arrhenius order="2">4.2e+14 0 12000</Arrhenius>
+      <rateCoeff>
+        <Arrhenius>
+          <A units="cm3/mol/s">4.200000000E+14</A>
+          <b>0.000000000E+00</b>
+          <E units="cal/mol">1.200000000E+04</E>
+        </Arrhenius>
       </rateCoeff>
       <duplicate>idtag_rxn_25</duplicate>
     </reaction>
@@ -549,8 +702,12 @@
       <equation>OH + HO2 [=] O2 + H2O</equation>
       <reactants> OH:1  HO2:1 </reactants>
       <products> O2:1  H2O:1 </products>
-      <rateCoeff Eunits="cal/mol" units="mol,cm,s">
-        <Arrhenius order="2">5e+15 0 17330</Arrhenius>
+      <rateCoeff>
+        <Arrhenius>
+          <A units="cm3/mol/s">5.000000000E+15</A>
+          <b>0.000000000E+00</b>
+          <E units="cal/mol">1.733000000E+04</E>
+        </Arrhenius>
       </rateCoeff>
       <duplicate>idtag_rxn_22</duplicate>
     </reaction>

data/inputs/mkxml

@@ -1,7 +1,8 @@
 #!/usr/bin/env bash
 
-../../bin/ck2ctml -i gri30.inp -id gri30 -o gri30.xml -tr ../transport/gri30_tran.dat
-../../bin/ck2ctml -i air.inp -o air.xml -t gri30.inp -id air -tr ../transport/gri30_tran.dat
-../../bin/ck2ctml -i h2o2.inp -o h2o2.xml -id ohmech -tr ../transport/gri30_tran.dat
-../../bin/ck2ctml -i silane.inp -o silane.xml -id silane
-../../bin/ck2ctml -i argon.inp -o argon.xml -id argon -t gri30.inp -tr ../transport/gri30_tran.dat
+../../bin/ck2ctml -i gri30.inp -id gri30 -o gri30_data.xml -tr ../transport/gri30_tran.dat > gri30.in
+../../bin/ck2ctml -i air.inp -o air.xml -t gri30.inp -id air -tr ../transport/gri30_tran.dat > air.in
+../../bin/ck2ctml -i h2o2.inp -o h2o2.xml -id ohmech -tr ../transport/gri30_tran.dat > h2o2.in
+../../bin/ck2ctml -i silane.inp -o silane.xml -id silane > silane.in
+../../bin/ck2ctml -i argon.inp -o argon.xml -id argon -t gri30.inp -tr ../transport/gri30_tran.dat > argon.in
+

data/inputs/silane.xml

@@ -27,14 +27,17 @@
     <species id="silane_s_H2" name="H2">
       <note>TPIS78</note>
       <atomArray> H:2 </atomArray>
+      <charge>0.000000000E+00</charge>
       <thermo>
-        <NASA Tmax="3500" Tmid="1000" Tmin="200">
-          <floatArray size="7" title="low">
+        <NASA Tmax="1000" Tmin="200">
+          <floatArray size="7" title="coeffs">
             2.344331120E+00,   7.980520750E-03,  -1.947815100E-05,
             2.015720940E-08,  -7.376117610E-12,  -9.179351730E+02,
             6.830102380E-01
           </floatArray>
-          <floatArray size="7" title="high">
+        </NASA>
+        <NASA Tmax="3500" Tmin="1000">
+          <floatArray size="7" title="coeffs">
             3.337279200E+00,  -4.940247310E-05,   4.994567780E-07,
            -1.795663940E-10,   2.002553760E-14,  -9.501589220E+02,
            -3.205023310E+00
@@ -47,14 +50,17 @@
     <species id="silane_s_H" name="H">
       <note>L 7/88</note>
       <atomArray> H:1 </atomArray>
+      <charge>0.000000000E+00</charge>
       <thermo>
-        <NASA Tmax="3500" Tmid="1000" Tmin="200">
-          <floatArray size="7" title="low">
+        <NASA Tmax="1000" Tmin="200">
+          <floatArray size="7" title="coeffs">
             2.500000000E+00,   7.053328190E-13,  -1.995919640E-15,
             2.300816320E-18,  -9.277323320E-22,   2.547365990E+04,
            -4.466828530E-01
           </floatArray>
-          <floatArray size="7" title="high">
+        </NASA>
+        <NASA Tmax="3500" Tmin="1000">
+          <floatArray size="7" title="coeffs">
             2.500000010E+00,  -2.308429730E-11,   1.615619480E-14,
            -4.735152350E-18,   4.981973570E-22,   2.547365990E+04,
            -4.466829140E-01
@@ -67,14 +73,17 @@
     <species id="silane_s_HE" name="HE">
       <note>120186</note>
       <atomArray> He:1 </atomArray>
+      <charge>0.000000000E+00</charge>
       <thermo>
-        <NASA Tmax="5000" Tmid="1000" Tmin="300">
-          <floatArray size="7" title="low">
+        <NASA Tmax="1000" Tmin="300">
+          <floatArray size="7" title="coeffs">
             2.500000000E+00,   0.000000000E+00,   0.000000000E+00,
             0.000000000E+00,   0.000000000E+00,  -7.453750000E+02,
             9.153488000E-01
           </floatArray>
-          <floatArray size="7" title="high">
+        </NASA>
+        <NASA Tmax="5000" Tmin="1000">
+          <floatArray size="7" title="coeffs">
             2.500000000E+00,   0.000000000E+00,   0.000000000E+00,
             0.000000000E+00,   0.000000000E+00,  -7.453750000E+02,
             9.153489000E-01
@@ -87,14 +96,17 @@
     <species id="silane_s_SIH4" name="SIH4">
       <note>90784</note>
       <atomArray> Si:1  H:4 </atomArray>
+      <charge>0.000000000E+00</charge>
       <thermo>
-        <NASA Tmax="2000" Tmid="1000" Tmin="300">
-          <floatArray size="7" title="low">
+        <NASA Tmax="1000" Tmin="300">
+          <floatArray size="7" title="coeffs">
             1.451640400E+00,   1.398736300E-02,  -4.234563900E-06,
            -2.360614200E-09,   1.371208900E-12,   3.113410500E+03,
             1.232185500E+01
           </floatArray>
-          <floatArray size="7" title="high">
+        </NASA>
+        <NASA Tmax="2000" Tmin="1000">
+          <floatArray size="7" title="coeffs">
             7.935938000E-01,   1.767189900E-02,  -1.139800900E-05,
             3.599260400E-09,  -4.524157100E-13,   3.198212700E+03,
             1.524225700E+01
@@ -107,14 +119,17 @@
     <species id="silane_s_SI" name="SI">
       <note>J 3/67</note>
       <atomArray> Si:1 </atomArray>
+      <charge>0.000000000E+00</charge>
       <thermo>
-        <NASA Tmax="5000" Tmid="1000" Tmin="300">
-          <floatArray size="7" title="low">
+        <NASA Tmax="1000" Tmin="300">
+          <floatArray size="7" title="coeffs">
             3.179353700E+00,  -2.764699200E-03,   4.478403800E-06,
            -3.283317700E-09,   9.121363100E-13,   5.333903200E+04,
             2.727320400E+00
           </floatArray>
-          <floatArray size="7" title="high">
+        </NASA>
+        <NASA Tmax="5000" Tmin="1000">
+          <floatArray size="7" title="coeffs">
             2.650601400E+00,  -3.576385200E-04,   2.959229300E-07,
            -7.280482900E-11,   5.796332900E-15,   5.343705400E+04,
             5.220405700E+00
@@ -127,14 +142,17 @@
     <species id="silane_s_SIH" name="SIH">
       <note>121986</note>
       <atomArray> Si:1  H:1 </atomArray>
+      <charge>0.000000000E+00</charge>
       <thermo>
-        <NASA Tmax="2000" Tmid="1000" Tmin="300">
-          <floatArray size="7" title="low">
+        <NASA Tmax="1000" Tmin="300">
+          <floatArray size="7" title="coeffs">
             3.836010000E+00,  -2.702657000E-03,   6.849070000E-06,
            -5.424184000E-09,   1.472131000E-12,   4.507593000E+04,
             9.350778000E-01
           </floatArray>
-          <floatArray size="7" title="high">
+        </NASA>
+        <NASA Tmax="2000" Tmin="1000">
+          <floatArray size="7" title="coeffs">
             3.110430000E+00,   1.094946000E-03,   2.898629000E-08,
            -2.745104000E-10,   7.051799000E-14,   4.516898000E+04,
             4.193487000E+00
@@ -147,14 +165,17 @@
     <species id="silane_s_SIH2" name="SIH2">
       <note>42489</note>
       <atomArray> Si:1  H:2 </atomArray>
+      <charge>0.000000000E+00</charge>
       <thermo>
-        <NASA Tmax="3000" Tmid="1000" Tmin="300">
-          <floatArray size="7" title="low">
+        <NASA Tmax="1000" Tmin="300">
+          <floatArray size="7" title="coeffs">
             3.475092000E+00,   2.139338000E-03,   7.672306000E-07,
             5.217668000E-10,  -9.898824000E-13,   3.147397000E+04,
             4.436585000E+00
           </floatArray>
-          <floatArray size="7" title="high">
+        </NASA>
+        <NASA Tmax="3000" Tmin="1000">
+          <floatArray size="7" title="coeffs">
             4.142390000E+00,   2.150191000E-03,  -2.190730000E-07,
            -2.073725000E-10,   4.741018000E-14,   3.110484000E+04,
             2.930745000E-01
@@ -167,14 +188,17 @@
     <species id="silane_s_SIH3" name="SIH3">
       <note>42489</note>
       <atomArray> Si:1  H:3 </atomArray>
+      <charge>0.000000000E+00</charge>
       <thermo>
-        <NASA Tmax="3000" Tmid="1000" Tmin="300">
-          <floatArray size="7" title="low">
+        <NASA Tmax="1000" Tmin="300">
+          <floatArray size="7" title="coeffs">
             2.946733000E+00,   6.466764000E-03,   5.991653000E-07,
            -2.218413000E-09,   3.052670000E-13,   2.270173000E+04,
             7.347948000E+00
           </floatArray>
-          <floatArray size="7" title="high">
+        </NASA>
+        <NASA Tmax="3000" Tmin="1000">
+          <floatArray size="7" title="coeffs">
             5.015906000E+00,   3.732750000E-03,  -3.609053000E-07,
            -3.729193000E-10,   8.468490000E-14,   2.190233000E+04,
            -4.291368000E+00
@@ -187,14 +211,17 @@
     <species id="silane_s_H3SISIH" name="H3SISIH">
       <note>111191</note>
       <atomArray> H:4  Si:2 </atomArray>
+      <charge>0.000000000E+00</charge>
       <thermo>
-        <NASA Tmax="4000" Tmid="1500" Tmin="300">
-          <floatArray size="7" title="low">
+        <NASA Tmax="1500" Tmin="300">
+          <floatArray size="7" title="coeffs">
             3.698707000E+00,   1.870180000E-02,  -1.430704000E-05,
             6.005836000E-09,  -1.116293000E-12,   3.590825000E+04,
             8.825191000E+00
           </floatArray>
-          <floatArray size="7" title="high">
+        </NASA>
+        <NASA Tmax="4000" Tmin="1500">
+          <floatArray size="7" title="coeffs">
             1.127202000E+01,   2.538145000E-03,  -2.998472000E-07,
            -9.465367000E-11,   1.855053000E-14,   3.297169000E+04,
            -3.264598000E+01
@@ -207,14 +234,17 @@
     <species id="silane_s_SI2H6" name="SI2H6">
       <note>90784</note>
       <atomArray> Si:2  H:6 </atomArray>
+      <charge>0.000000000E+00</charge>
       <thermo>
-        <NASA Tmax="2000" Tmid="1000" Tmin="300">
-          <floatArray size="7" title="low">
+        <NASA Tmax="1000" Tmin="300">
+          <floatArray size="7" title="coeffs">
             6.734798300E-01,   4.093153100E-02,  -4.484125500E-05,
             2.995223200E-08,  -8.901085400E-12,   7.932787500E+03,
             1.862740300E+01
           </floatArray>
-          <floatArray size="7" title="high">
+        </NASA>
+        <NASA Tmax="2000" Tmin="1000">
+          <floatArray size="7" title="coeffs">
             3.407493600E+00,   2.720647900E-02,  -1.771320400E-05,
             5.639117700E-09,  -7.137868200E-13,   7.532184200E+03,
             6.132175400E+00
@@ -227,14 +257,17 @@
     <species id="silane_s_H2SISIH2" name="H2SISIH2">
       <note>42489</note>
       <atomArray> Si:2  H:4 </atomArray>
+      <charge>0.000000000E+00</charge>
       <thermo>
-        <NASA Tmax="3000" Tmid="1000" Tmin="300">
-          <floatArray size="7" title="low">
+        <NASA Tmax="1000" Tmin="300">
+          <floatArray size="7" title="coeffs">
             5.133186000E+00,   1.252855000E-02,  -4.620421000E-07,
            -6.606075000E-09,   2.864345000E-12,   2.956915000E+04,
             7.605133000E-01
           </floatArray>
-          <floatArray size="7" title="high">
+        </NASA>
+        <NASA Tmax="3000" Tmin="1000">
+          <floatArray size="7" title="coeffs">
             8.986817000E+00,   5.405047000E-03,  -5.214022000E-07,
            -5.313742000E-10,   1.188727000E-13,   2.832748000E+04,
            -2.004478000E+01
@@ -247,14 +280,17 @@
     <species id="silane_s_SI3H8" name="SI3H8">
       <note>90784</note>
       <atomArray> Si:3  H:8 </atomArray>
+      <charge>0.000000000E+00</charge>
       <thermo>
-        <NASA Tmax="2000" Tmid="1000" Tmin="300">
-          <floatArray size="7" title="low">
+        <NASA Tmax="1000" Tmin="300">
+          <floatArray size="7" title="coeffs">
             7.719684600E-01,   6.344274000E-02,  -7.672610900E-05,
             5.454371500E-08,  -1.661172900E-11,   1.207126300E+04,
             2.153250700E+01
           </floatArray>
-          <floatArray size="7" title="high">
+        </NASA>
+        <NASA Tmax="2000" Tmin="1000">
+          <floatArray size="7" title="coeffs">
             6.093334100E+00,   3.658011200E-02,  -2.389236100E-05,
             7.627193200E-09,  -9.676938400E-13,   1.129720500E+04,
            -2.747565400E+00
@@ -267,14 +303,17 @@
     <species id="silane_s_SI2" name="SI2">
       <note>90784</note>
       <atomArray> Si:2 </atomArray>
+      <charge>0.000000000E+00</charge>
       <thermo>
-        <NASA Tmax="2000" Tmid="1000" Tmin="300">
-          <floatArray size="7" title="low">
+        <NASA Tmax="1000" Tmin="300">
+          <floatArray size="7" title="coeffs">
             2.967197600E+00,   6.311955800E-03,  -1.097079000E-05,
             8.927868000E-09,  -2.787368900E-12,   6.987073800E+04,
             9.278950300E+00
           </floatArray>
-          <floatArray size="7" title="high">
+        </NASA>
+        <NASA Tmax="2000" Tmin="1000">
+          <floatArray size="7" title="coeffs">
             4.144677900E+00,   6.523467700E-04,  -5.010852000E-07,
             1.806284300E-10,  -2.516111100E-14,   6.969470700E+04,
             3.862736600E+00
@@ -287,14 +326,17 @@
     <species id="silane_s_SI3" name="SI3">
       <note>J 3/67</note>
       <atomArray> Si:3 </atomArray>
+      <charge>0.000000000E+00</charge>
       <thermo>
-        <NASA Tmax="5000" Tmid="1000" Tmin="300">
-          <floatArray size="7" title="low">
+        <NASA Tmax="1000" Tmin="300">
+          <floatArray size="7" title="coeffs">
             4.597912900E+00,   1.071527400E-02,  -1.610042200E-05,
             1.096920700E-08,  -2.783287500E-12,   7.476632400E+04,
             3.442167100E+00
           </floatArray>
-          <floatArray size="7" title="high">
+        </NASA>
+        <NASA Tmax="5000" Tmin="1000">
+          <floatArray size="7" title="coeffs">
             7.421336000E+00,  -1.170994800E-04,   8.982077500E-08,
             7.193596400E-12,  -2.567083700E-15,   7.414669900E+04,
            -1.036527400E+01
@@ -312,8 +354,12 @@
       <equation>SIH4 + H [=] SIH3 + H2</equation>
       <reactants> SIH4:1  H:1 </reactants>
       <products> SIH3:1  H2:1 </products>
-      <rateCoeff Eunits="cal/mol" units="mol,cm,s">
-        <Arrhenius order="2">7.8e+14 0 2260</Arrhenius>
+      <rateCoeff>
+        <Arrhenius>
+          <A units="cm3/mol/s">7.800000000E+14</A>
+          <b>0.000000000E+00</b>
+          <E units="cal/mol">2.260000000E+03</E>
+        </Arrhenius>
       </rateCoeff>
     </reaction>
 
@@ -322,8 +368,12 @@
       <equation>SIH4 + M [=] SIH3 + H + M</equation>
       <reactants> SIH4:1 </reactants>
       <products> SIH3:1  H:1 </products>
-      <rateCoeff Eunits="cal/mol" units="mol,cm,s">
-        <Arrhenius order="2">3.91e+15 0 89356</Arrhenius>
+      <rateCoeff>
+        <Arrhenius>
+          <A units="cm3/mol/s">3.910000000E+15</A>
+          <b>0.000000000E+00</b>
+          <E units="cal/mol">8.935600000E+04</E>
+        </Arrhenius>
       </rateCoeff>
     </reaction>
 
@@ -332,8 +382,12 @@
       <equation>SIH3 + H [=] SIH2 + H2</equation>
       <reactants> SIH3:1  H:1 </reactants>
       <products> SIH2:1  H2:1 </products>
-      <rateCoeff Eunits="cal/mol" units="mol,cm,s">
-        <Arrhenius order="2">7.8e+14 0 2260</Arrhenius>
+      <rateCoeff>
+        <Arrhenius>
+          <A units="cm3/mol/s">7.800000000E+14</A>
+          <b>0.000000000E+00</b>
+          <E units="cal/mol">2.260000000E+03</E>
+        </Arrhenius>
       </rateCoeff>
     </reaction>
 
@@ -342,8 +396,12 @@
       <equation>SI + SI + M [=] SI2 + M</equation>
       <reactants> SI:1  SI:1 </reactants>
       <products> SI2:1 </products>
-      <rateCoeff Eunits="cal/mol" units="mol,cm,s">
-        <Arrhenius order="3">2.47e+16 0 1178</Arrhenius>
+      <rateCoeff>
+        <Arrhenius>
+          <A units="cm6/mol2/s">2.470000000E+16</A>
+          <b>0.000000000E+00</b>
+          <E units="cal/mol">1.178000000E+03</E>
+        </Arrhenius>
       </rateCoeff>
     </reaction>
 
@@ -352,8 +410,12 @@
       <equation>SIH4 + SIH2 [=] H3SISIH + H2</equation>
       <reactants> SIH4:1  SIH2:1 </reactants>
       <products> H3SISIH:1  H2:1 </products>
-      <rateCoeff Eunits="cal/mol" units="mol,cm,s">
-        <Arrhenius order="2">1.3e+13 0 0</Arrhenius>
+      <rateCoeff>
+        <Arrhenius>
+          <A units="cm3/mol/s">1.300000000E+13</A>
+          <b>0.000000000E+00</b>
+          <E units="cal/mol">0.000000000E+00</E>
+        </Arrhenius>
       </rateCoeff>
     </reaction>
 
@@ -362,8 +424,12 @@
       <equation>SIH + H2 [=] SIH2 + H</equation>
       <reactants> SIH:1  H2:1 </reactants>
       <products> SIH2:1  H:1 </products>
-      <rateCoeff Eunits="cal/mol" units="mol,cm,s">
-        <Arrhenius order="2">4.8e+14 0 23.64</Arrhenius>
+      <rateCoeff>
+        <Arrhenius>
+          <A units="cm3/mol/s">4.800000000E+14</A>
+          <b>0.000000000E+00</b>
+          <E units="cal/mol">2.364000000E+01</E>
+        </Arrhenius>
       </rateCoeff>
     </reaction>
 
@@ -372,8 +438,12 @@
       <equation>SIH + SIH4 [=] H3SISIH + H</equation>
       <reactants> SIH:1  SIH4:1 </reactants>
       <products> H3SISIH:1  H:1 </products>
-      <rateCoeff Eunits="cal/mol" units="mol,cm,s">
-        <Arrhenius order="2">1.6e+14 0 0</Arrhenius>
+      <rateCoeff>
+        <Arrhenius>
+          <A units="cm3/mol/s">1.600000000E+14</A>
+          <b>0.000000000E+00</b>
+          <E units="cal/mol">0.000000000E+00</E>
+        </Arrhenius>
       </rateCoeff>
     </reaction>
 
@@ -382,8 +452,12 @@
       <equation>SI + H2 [=] SIH + H</equation>
       <reactants> SI:1  H2:1 </reactants>
       <products> SIH:1  H:1 </products>
-      <rateCoeff Eunits="cal/mol" units="mol,cm,s">
-        <Arrhenius order="2">1.5e+15 0 31.8</Arrhenius>
+      <rateCoeff>
+        <Arrhenius>
+          <A units="cm3/mol/s">1.500000000E+15</A>
+          <b>0.000000000E+00</b>
+          <E units="cal/mol">3.180000000E+01</E>
+        </Arrhenius>
       </rateCoeff>
     </reaction>
 
@@ -392,9 +466,17 @@
       <equation>SIH4 (+ M) [=] SIH2 + H2 (+ M)</equation>
       <reactants> SIH4:1 </reactants>
       <products> SIH2:1  H2:1 </products>
-      <rateCoeff Eunits="cal/mol" units="mol,cm,s">
-        <Arrhenius order="1">3.119e+09 1.669 54710</Arrhenius>
-        <Arrhenius order="2">5.214e+29 -3.545 57550</Arrhenius>
+      <rateCoeff>
+        <Arrhenius>
+          <A units="/s">3.119000000E+09</A>
+          <b>1.669000000E+00</b>
+          <E units="cal/mol">5.471000000E+04</E>
+        </Arrhenius>
+        <Arrhenius name="k0">
+          <A units="cm3/mol/s">5.214000000E+29</A>
+          <b>-3.545000000E+00</b>
+          <E units="cal/mol">5.755000000E+04</E>
+        </Arrhenius>
         <falloff type="Troe"> -0.4984  888.3  209.4  2760 </falloff>
         <efficiencies default="1">
          SI2H6:4  SIH4:4 
@@ -407,9 +489,17 @@
       <equation>H3SISIH (+ M) [=] H2SISIH2 (+ M)</equation>
       <reactants> H3SISIH:1 </reactants>
       <products> H2SISIH2:1 </products>
-      <rateCoeff Eunits="cal/mol" units="mol,cm,s">
-        <Arrhenius order="1">2.54e+13 -0.2239 5381</Arrhenius>
-        <Arrhenius order="2">1.099e+33 -5.765 9152</Arrhenius>
+      <rateCoeff>
+        <Arrhenius>
+          <A units="/s">2.540000000E+13</A>
+          <b>-2.239000000E-01</b>
+          <E units="cal/mol">5.381000000E+03</E>
+        </Arrhenius>
+        <Arrhenius name="k0">
+          <A units="cm3/mol/s">1.099000000E+33</A>
+          <b>-5.765000000E+00</b>
+          <E units="cal/mol">9.152000000E+03</E>
+        </Arrhenius>
         <falloff type="Troe"> -0.4202  214.5  103  136.3 </falloff>
         <efficiencies default="1">
          SI2H6:4  SIH4:4 
@@ -422,9 +512,17 @@
       <equation>SI3H8 (+ M) [=] SIH4 + H3SISIH (+ M)</equation>
       <reactants> SI3H8:1 </reactants>
       <products> SIH4:1  H3SISIH:1 </products>
-      <rateCoeff Eunits="cal/mol" units="mol,cm,s">
-        <Arrhenius order="1">3.73e+12 0.992 50850</Arrhenius>
-        <Arrhenius order="2">4.36e+76 -17.26 59303</Arrhenius>
+      <rateCoeff>
+        <Arrhenius>
+          <A units="/s">3.730000000E+12</A>
+          <b>9.920000000E-01</b>
+          <E units="cal/mol">5.085000000E+04</E>
+        </Arrhenius>
+        <Arrhenius name="k0">
+          <A units="cm3/mol/s">4.360000000E+76</A>
+          <b>-1.726000000E+01</b>
+          <E units="cal/mol">5.930300000E+04</E>
+        </Arrhenius>
         <falloff type="Troe"> 0.4157  365.3  3102  9.724 </falloff>
         <efficiencies default="1">
          SI2H6:4  SIH4:4 
@@ -437,9 +535,17 @@
       <equation>SI3H8 (+ M) [=] SIH2 + SI2H6 (+ M)</equation>
       <reactants> SI3H8:1 </reactants>
       <products> SIH2:1  SI2H6:1 </products>
-      <rateCoeff Eunits="cal/mol" units="mol,cm,s">
-        <Arrhenius order="1">6.97e+12 0.9691 52677</Arrhenius>
-        <Arrhenius order="2">1.73e+69 -15.07 60491</Arrhenius>
+      <rateCoeff>
+        <Arrhenius>
+          <A units="/s">6.970000000E+12</A>
+          <b>9.691000000E-01</b>
+          <E units="cal/mol">5.267700000E+04</E>
+        </Arrhenius>
+        <Arrhenius name="k0">
+          <A units="cm3/mol/s">1.730000000E+69</A>
+          <b>-1.507000000E+01</b>
+          <E units="cal/mol">6.049100000E+04</E>
+        </Arrhenius>
         <falloff type="Troe"> -3.47e-05  442  2412  128.3 </falloff>
         <efficiencies default="1">
          SI2H6:4  SIH4:4 
@@ -452,9 +558,17 @@
       <equation>SI2H6 (+ M) [=] H2 + H3SISIH (+ M)</equation>
       <reactants> SI2H6:1 </reactants>
       <products> H2:1  H3SISIH:1 </products>
-      <rateCoeff Eunits="cal/mol" units="mol,cm,s">
-        <Arrhenius order="1">9.086e+09 1.834 54197</Arrhenius>
-        <Arrhenius order="2">1.945e+44 -7.772 59023</Arrhenius>
+      <rateCoeff>
+        <Arrhenius>
+          <A units="/s">9.086000000E+09</A>
+          <b>1.834000000E+00</b>
+          <E units="cal/mol">5.419700000E+04</E>
+        </Arrhenius>
+        <Arrhenius name="k0">
+          <A units="cm3/mol/s">1.945000000E+44</A>
+          <b>-7.772000000E+00</b>
+          <E units="cal/mol">5.902300000E+04</E>
+        </Arrhenius>
         <falloff type="Troe"> -0.1224  793.3  2400  11.39 </falloff>
         <efficiencies default="1">
          SI2H6:4  SIH4:4 
@@ -467,9 +581,17 @@
       <equation>SI2H6 (+ M) [=] SIH4 + SIH2 (+ M)</equation>
       <reactants> SI2H6:1 </reactants>
       <products> SIH4:1  SIH2:1 </products>
-      <rateCoeff Eunits="cal/mol" units="mol,cm,s">
-        <Arrhenius order="1">1.81e+10 1.747 50203</Arrhenius>
-        <Arrhenius order="2">5.09e+53 -10.37 56034</Arrhenius>
+      <rateCoeff>
+        <Arrhenius>
+          <A units="/s">1.810000000E+10</A>
+          <b>1.747000000E+00</b>
+          <E units="cal/mol">5.020300000E+04</E>
+        </Arrhenius>
+        <Arrhenius name="k0">
+          <A units="cm3/mol/s">5.090000000E+53</A>
+          <b>-1.037000000E+01</b>
+          <E units="cal/mol">5.603400000E+04</E>
+        </Arrhenius>
         <falloff type="Troe"> 4.375e-05  438.5  2726  438.2 </falloff>
         <efficiencies default="1">
          SI2H6:4  SIH4:4 

tools/src/ck2ctml.cpp

@@ -14,6 +14,7 @@
 using namespace std;
 
 #include "converters/ck2ctml.h"
+#include "converters/ck2ct.h"
 
 using namespace ctml;
 
@@ -68,8 +69,14 @@ int main(int argc, char** argv) {
         ++i;
     }
 
+#define MAKE_CT_INPUT
+#ifdef MAKE_CT_INPUT
+    int ierr = pip::convert_ck(infile.c_str(), dbfile.c_str(), trfile.c_str(), 
+        idtag.c_str());
+#else
     int ierr = convert_ck(infile.c_str(), dbfile.c_str(), trfile.c_str(), 
         outfile.c_str(), idtag.c_str());
+#endif
     if (ierr < 0) {
         showErrors(cerr);
     }

tools/testtools/csvdiff.cpp

@@ -38,9 +38,9 @@
 #include <limits.h>
 #include <unistd.h>
 
-#ifndef CYGWIN
-#include <getopt.h>
-#endif
+//#ifndef CYGWIN
+//#include <getopt.h>
+//#endif
 
 #include "mdp_allo.h"
 #include "tok_input_util.h"