*** empty log message ***

Cantera/clib/src/ctonedim.cpp

@@ -169,8 +169,6 @@ extern "C" {
     }
 
 
-    //------------------ inlet domains ------------------------------
-
     int DLL_EXPORT inlet_new() {
         try {
             Inlet1D* i = new Inlet1D();
@@ -189,10 +187,11 @@ extern "C" {
 
     int DLL_EXPORT reactingsurf_new() {
         try {
-            ReactingSurf1D* i = new ReactingSurf1D();
+            writelog("in reactingsurf_new\n");
+            Domain1D* i = new ReactingSurf1D();
             return Cabinet<Domain1D>::cabinet()->add(i);
         }
-        catch (CanteraError) { return -1; }
+        catch (CanteraError) { writelog("error"); return -1; }
     }
 
     int DLL_EXPORT symm_new() {
@@ -266,6 +265,16 @@ extern "C" {
         catch (CanteraError) { return -1; }
     }
 
+    int DLL_EXPORT reactingsurf_enableCoverageEqs(int i, int onoff) {
+        try {
+            ReactingSurf1D* srf = (ReactingSurf1D*)_bdry(i);
+            srf->enableCoverageEquations(onoff);
+            return 0;
+        }
+
+        catch (CanteraError) { return -1; }
+    }
+
     //------------------ stagnation flow domains --------------------
 
     int DLL_EXPORT stflow_new(int iph, int ikin, int itr) {
@@ -424,9 +433,9 @@ extern "C" {
     }
 
     int DLL_EXPORT sim1D_setRefineCriteria(int i, int dom, double ratio,
-        double slope, double curve) {
+        double slope, double curve, double prune) {
         try {
-            _sim1D(i)->setRefineCriteria(dom, ratio, slope, curve);
+            _sim1D(i)->setRefineCriteria(dom, ratio, slope, curve, prune);
             return 0;
         }
         catch (CanteraError) { return -1; }
@@ -491,4 +500,31 @@ extern "C" {
         catch (CanteraError) { return -1; }
     }
 
+    int DLL_EXPORT sim1D_setMaxJacAge(int i, int ss_age, int ts_age) {
+        try {
+            _sim1D(i)->setJacAge(ss_age, ts_age);
+            return 0;
+        }
+        catch (CanteraError) { return -1; }
+    }
+
+    int DLL_EXPORT sim1D_timeStepFactor(int i, double tfactor) {
+        try {
+            _sim1D(i)->setTimeStepFactor(tfactor);
+            return 0;
+        }
+        catch (CanteraError) { return -1; }
+    }
+
+    int DLL_EXPORT sim1D_setTimeStepLimits(int i, double tsmin, double tsmax) {
+        try {
+            if (tsmin > 0.0)
+                _sim1D(i)->setMinTimeStep(tsmin);
+            if (tsmax > 0.0)
+                _sim1D(i)->setMaxTimeStep(tsmax);
+            return 0;
+        }
+        catch (CanteraError) { return -1; }
+    }
+
 }

Cantera/clib/src/ctonedim.h

@@ -28,7 +28,9 @@ extern "C" {
     double DLL_IMPORT bdry_temperature(int i);
     double DLL_IMPORT bdry_massFraction(int i, int k);
     double DLL_IMPORT bdry_mdot(int i);
+
     int DLL_IMPORT reactingsurf_setkineticsmgr(int i, int j);
+    int DLL_IMPORT reactingsurf_enableCoverageEqs(int i, int onoff);
 
     int DLL_IMPORT inlet_new();
     int DLL_IMPORT outlet_new();
@@ -55,7 +57,7 @@ extern "C" {
     int DLL_IMPORT sim1D_solve(int i, int loglevel, int refine_grid);
     int DLL_IMPORT sim1D_refine(int i, int loglevel);
     int DLL_IMPORT sim1D_setRefineCriteria(int i, int dom, double ratio,
-        double slope, double curve);
+        double slope, double curve, double prune);
     int DLL_IMPORT sim1D_save(int i, char* fname, char* id, 
         char* desc);
     int DLL_IMPORT sim1D_restore(int i, char* fname, char* id);
@@ -65,6 +67,10 @@ extern "C" {
     double DLL_IMPORT sim1D_workValue(int i, int idom, 
         int icomp, int localPoint);
     int DLL_IMPORT sim1D_eval(int i, double rdt, int count);
+    int DLL_IMPORT sim1D_setMaxJacAge(int i, int ss_age, int ts_age);
+    int DLL_IMPORT sim1D_timeStepFactor(int i, double tfactor);
+    int DLL_IMPORT sim1D_setTimeStepLimits(int i, double tsmin, double tsmax);
+
 }
 
 

Cantera/clib/src/ctsurf.cpp

@@ -65,6 +65,11 @@ extern "C" {
         return 0;
     }
 
+    int DLL_EXPORT surf_setcoveragesbyname(int i, char* c) {
+        _surfphase(i)->setCoveragesByName(string(c));
+        return 0;
+    }
+
     int DLL_EXPORT surf_getcoverages(int i, double* c) {
         _surfphase(i)->getCoverages(c);
         return 0;

Cantera/clib/src/ctsurf.h

@@ -48,7 +48,7 @@ extern "C" {
     double DLL_IMPORT surface_temperature(int i);
     int DLL_IMPORT surface_settemperature(int i, double t);
     int DLL_IMPORT surface_setcoverages(int i, double* c);
-
+    int DLL_EXPORT surf_setcoveragesbyname(int i, char* c);
 }
 
 #endif

Cantera/matlab/Makefile.in

@@ -29,7 +29,7 @@ LIB_DEPS = $(CANTERA_LIBDIR)/libcantera.a $(CANTERA_LIBDIR)/libzeroD.a \
 all: cantera/ctmethods.@mex_ext@
 
 cantera/ctmethods.@mex_ext@: $(SRCS) $(LIB_DEPS)
-	@PYTHON_CMD@ setup_matlab.py @buildlib@ @CT_SHARED_LIB@ '$(LIBS)'
+	@PYTHON_CMD@ setup_matlab.py @prefix@/bin @buildlib@ @CT_SHARED_LIB@ '$(LIBS)'
 	(@MATLAB_CMD@ -nodesktop -nojvm -nosplash -r setup)
 	rm -f setup.m
 

Cantera/matlab/cantera/1D/@Domain1D/Domain1D.m

@@ -6,16 +6,27 @@ d.dom_id = -1;
 if nargin == 1
   d.dom_id = domain_methods(0, a);
 elseif nargin == 2
+  % a stagnation flow
   if a == 1
     if isa(b,'Solution')
       d.dom_id = domain_methods(0, 1, thermo_hndl(b), kinetics_hndl(b), ...
 				trans_hndl(b));
     else
-      error('Wrong argument type. Expecting instance of class Solution.')
+      error('Wrong argument type. Expecting instance of class Solution.');
     end
+  elseif a == 6
+    if isa(b,'Interface')
+      d.dom_id = domain_methods(0, 6, kinetics_hndl(b));
+    else
+      error('Wrong argument type. Expecting instance of class Interface.');
+    end      
+  else
+    error('wrong object type');
   end
+  
 end
 if d.dom_id < 0
   error(geterr);
 end
+d.domain_type = a;
 d = class(d, 'Domain1D');

Cantera/matlab/cantera/1D/@Domain1D/setCoverageEqs.m

@@ -0,0 +1,20 @@
+function d = setCoverageEqs(d,onoff)
+% SETCOVERAGEEQS - Enable or disable solving the coverage equations.
+%   
+if d.domain_type ~= 6
+  error('Wrong domain type. Expected a reacting surface domain.')
+end
+
+ion = -1;
+if isa(onoff,'char')
+  if strcmp(onoff,'on') | strcmp(onoff,'yes') 
+    ion = 1;
+  elseif strcmp(onoff,'off') | strcmp(onoff,'no')
+    ion = 0;
+  else
+    error(strcat('unknown option: ',onoff))
+  end
+elseif isa(onoff,'numeric')
+  ion = onoff;
+end
+domain_methods(d.dom_id, 120, ion);

Cantera/matlab/cantera/1D/@Stack/display.m

@@ -1,5 +1,7 @@
 function display(s, fname)
-% DISPLAY - show all domains.
+% DISPLAY - show all domains. 
+%
+%  fname - file to write summary to. If omitted, output is to the screen.
 %
 if nargin == 1
   fname = '-';

Cantera/matlab/cantera/1D/@Stack/private/stack_methods.m

@@ -1,4 +1,4 @@
-function v = stack_methods(n, job, a, b, c, d, e)
+function v = stack_methods(n, job, a, b, c, d, e, f)
 % STACK_METHODS - converter function for methods of class Stack
 %
 %    All Cantera functions and methods are handled by the single MEX
@@ -17,6 +17,9 @@ elseif nargin == 6
   v = ctmethods(90, n, job, a, b, c, d); 
 elseif nargin == 7
   v = ctmethods(90, n, job, a, b, c, d, e); 
+elseif nargin == 8
+  v = ctmethods(90, n, job, a, b, c, d, e, f); 
 else
-  error('wrong number of arguments');
+  error('too many arguments');
 end
+ 

Cantera/matlab/cantera/1D/@Stack/setMaxJacAge.m

@@ -0,0 +1,8 @@
+function setMaxJacAge(s, ss_age, ts_age)
+% SETMAXJACAGE - Set the number of times the Jacobian will be used 
+% before it is recomputed.
+%   
+if nargin == 2
+  ts_age = ss_age;
+end
+stack_methods(s.stack_id, 114, ss_age, ts_age);

Cantera/matlab/cantera/1D/@Stack/setRefineCriteria.m

@@ -1,5 +1,30 @@
-function d = setRefineCriteria(d, n, ratio, slope, curve)
+function d = setRefineCriteria(d, n, ratio, slope, curve, prune)
-% SETREFINECRITERIA - 
+% SETREFINECRITERIA - Set the criteria used to refine the grid.
+%
+%     n  --  domain number beginning with domain 1 at the left
+%     ratio  --   maximum size ratio between adjacent cells
+%     slope  --   maximum relative difference in value between
+%                 adjacent points
+%     curve  --   maximum relative difference in slope between
+%                 adjacent cells
+%     prune  --   minimum value for slope or curve for which points
+%                 will be retained in the grid. If the computed
+%                 slope or curve value is below prune for all
+%                 components, it will be deleted, unless either
+%                 neighboring point is already marked for deletion. 
 %   
-stack_methods(d.stack_id, 106, n, ratio, slope, curve);
+if nargin < 3
+  ratio = 10.0;
+end
+if nargin < 4
+  slope = 0.8;
+end
+if nargin < 5
+  curve = 0.8;
+end
+if nargin < 6
+  prune = -0.1;
+end
+
+stack_methods(d.stack_id, 106, n, ratio, slope, curve, prune);
 

Cantera/matlab/cantera/1D/@Stack/setTimeStep.m

@@ -0,0 +1,12 @@
+function setTimeStep(s, stepsize, steps)
+% SETTIMESTEP - Specify a sequence of time steps.
+%
+%    stepsize -      initial step size (s)
+%    steps    -      array of number of steps to take before
+%                    re-attempting solution of steady-state problem. For
+%                    example, steps = [1, 2, 5, 10] would cause one time
+%                    step to be taken first the the steady-state
+%                    solution attempted. If this failed, two time steps
+%                    would be taken, etc. 
+
+stack_methods(s.stack_id, 112, stepsize, length(steps), steps)

Cantera/matlab/cantera/1D/Surface.m

@@ -1,9 +1,15 @@
-function m = Surface(id)
+function m = Surface(id, surface_mech)
 % SURFACE - Return a Domain1D instance representing a non-reacting
-% surface.
+% or reacting surface.
-m = Domain1D(3);
+if nargin < 2
-if nargin == 0
+  m = Domain1D(3);
-  setID(m,'surface');
+  if nargin == 0
+    setID(m,'surface');
+  elseif nargin == 1
+    setID(m,id);
+  end
 else
+  m = Domain1D(6, surface_mech)
   setID(m,id);
 end
+

Cantera/matlab/cantera/1D/nComponents.m

@@ -0,0 +1,2 @@
+function n = nComponents(d)
+n = domain_methods(d.dom_id, 11)

Cantera/matlab/cantera/1D/npflame_init.m

@@ -0,0 +1,117 @@
+function flame = npflame_init(gas, left, flow, right, fuel, oxidizer, nuox)
+%  FLAME - create a non-premixed flame object.
+%
+%    gas     --  object representing the gas. This object will be used to
+%                compute all required thermodynamic, kinetic, and transport
+%                properties. The state of this object should be set
+%                to an estimate of the gas state emerging from the
+%                burner before calling StagnationFlame.
+%
+%    left    --  object representing the left inlet, which must be
+%                created using function Inlet.
+%
+%    flow    --  object representing the flow, created with
+%                function AxisymmetricFlow.
+%
+%    right   --  object representing the right inlet, which must be
+%                created using function Inlet.
+%
+
+% Check input parameters
+if nargin ~= 7
+  error('wrong number of input arguments.');
+end
+
+if ~isIdealGas(gas)
+  error('gas object must represent an ideal gas mixture.');
+end
+if ~isInlet(left)
+  error('left inlet object of wrong type.');
+end
+if ~isFlow(flow)
+  error('flow object of wrong type.');
+end
+if ~isInlet(right)
+  error('right inlet object of wrong type.');
+end
+
+% create the container object
+flame = Stack([left flow right]);
+
+% set default initial profiles.
+rho0 = density(gas);
+
+wt = molecularWeights(gas);
+
+% find the fuel and oxidizer
+ifuel = speciesIndex(gas,fuel);
+ioxidizer = speciesIndex(gas,oxidizer);
+ih = speciesIndex(gas,'H');
+
+s = nuox*wt(ioxidizer)/wt(ifuel);
+y0f = massFraction(left,ifuel);
+y0ox = massFraction(right,ioxidizer);
+phi = s*y0f/y0ox;
+zst = 1.0/(1.0 + phi);
+
+% compute stoichiometric adiabatic flame temperature
+nsp = nSpecies(gas);
+tf = temperature(left);
+tox = temperature(right);
+
+for n = 1:nsp
+  yox(n) = massFraction(right,n);
+  yf(n) = massFraction(left,n);
+  ystoich(n) = zst*yf(n) + (1.0 - zst)*yox(n);
+end
+
+set(gas,'T',temperature(left),'P',pressure(gas),'Y',ystoich);
+equilibrate(gas,'HP');
+teq = temperature(gas);
+yeq = massFractions(gas);
+
+% estimated strain rate
+zz = z(flow);
+dz = zz(end) - zz(1);
+vleft = massFlux(left)/rho0;
+vright = massFlux(right)/rho0;
+a = (abs(vleft) + abs(vright))/dz;
+diff = mixDiffCoeffs(gas);
+f = sqrt(a/(2.0*diff(ioxidizer)));
+
+x0 = massFlux(left)*dz/(massFlux(left) + massFlux(right));
+
+nz = nPoints(flow)
+for j = 1:nz
+  x = zz(j);
+  zeta = f*(x - x0);
+  zmix = 0.5*(1.0 - erf(zeta));
+  zm(j) = zmix;
+  u(j) = a*(x0 - zz(j));
+  v(j) = a;
+  if zmix > zst
+    for n = 1:nsp
+      y(j,n) = yeq(n) + (zmix - zst)*(yf(n) - yeq(n))/(1.0 - zst);
+    end
+    t(j) = teq + (tf - teq)*(zmix - zst)/(1.0 - zst);
+  else
+    for n = 1:nsp
+      y(j,n) = yox(n) + zmix*(yeq(n) - yox(n))/zst;
+    end
+    t(j) = tox + zmix*(teq - tox)/zst;
+  end
+end
+
+zrel = zz/dz;
+
+setProfile(flame, 2, {'u', 'V'}, [zrel; u; v]);
+
+setProfile(flame, 2, 'T', [zrel; t] );
+
+for n = 1:nsp
+  nm = speciesName(gas,n);
+  setProfile(flame, 2, nm, [zrel; transpose(y(:,n))])
+end
+
+% set minimal grid refinement criteria 
+setRefineCriteria(flame, 2, 10.0, 0.99, 0.99);

Cantera/matlab/cantera/@Interface/Interface.m

@@ -0,0 +1,27 @@
+function s = Interface(src, id, p1, p2, p3, p4)
+% Interface - class Interface constructor.
+%
+%
+if nargin ~= 3
+   error('wrong number of arguments');
+end
+doc = XML_Node('doc',src);
+node = findByID(doc,id);
+t = ThermoPhase(node);
+if nargin == 2
+  k = Kinetics(node,t);
+elseif nargin == 3
+  k = Kinetics(node,t,p1);
+elseif nargin == 4
+  k = Kinetics(node,t,p1,p2);
+elseif nargin == 5
+  k = Kinetics(node,t,p1,p2,p3);
+elseif nargin == 6
+  k = Kinetics(node,t,p1,p2,p3,p4);  
+end
+
+s.kin = k;
+s.th = t;
+s = class(s,'Interface',t,k);
+
+

Cantera/matlab/cantera/@Interface/concentrations.m

@@ -0,0 +1,17 @@
+function c = concentrations(s)
+% CONCENTRATIONS - Surface concentrations
+%   
+c = surfmethods(thermo_hndl(s), 101);
+if nargout == 0
+  figure
+  set(gcf,'Name','Concentrations')
+  bar(c);
+  colormap(summer);
+  nm = speciesNames(s);
+  legend(nm);
+  xlabel('Species Number');
+  ylabel('Concentration [kmol/m2]');
+  title('Surface Species Concentrations');
+end
+
+

Cantera/matlab/cantera/@Interface/coverages.m

@@ -0,0 +1,17 @@
+function c = coverages(s)
+% COVERAGES - Surface coverages
+%   
+c = surfmethods(thermo_hndl(s), 101);
+if nargout == 0
+  figure
+  set(gcf,'Name','Coverages')
+  bar(c);
+  colormap(summer);
+  nm = speciesNames(s);
+  legend(nm);
+  xlabel('Species Number');
+  ylabel('Coverage');
+  title('Surface Species Coverages');
+end
+
+

Cantera/matlab/cantera/@Interface/private/surfmethods.m

@@ -0,0 +1,25 @@
+function v = surfmethods(n, job, a, b, c, d, e, f)
+% SURFMETHODS - converter function for methods of class Stack
+%
+%    All Cantera functions and methods are handled by the single MEX
+%    file 'ctmethods.' This function is provided only for convenience,
+%    and simply calls ctmethods with a flag associated with this class
+%    as the first parameter, followed by the input arguments.
+if nargin == 2
+  v = ctmethods(100, n, job);
+elseif nargin == 3
+  v = ctmethods(100, n, job, a);  
+elseif nargin == 4
+  v = ctmethods(100, n, job, a, b);    
+elseif nargin == 5
+  v = ctmethods(100, n, job, a, b, c);
+elseif nargin == 6
+  v = ctmethods(100, n, job, a, b, c, d); 
+elseif nargin == 7
+  v = ctmethods(100, n, job, a, b, c, d, e); 
+elseif nargin == 8
+  v = ctmethods(100, n, job, a, b, c, d, e, f); 
+else
+  error('too many arguments');
+end
+ 

Cantera/matlab/cantera/@Interface/setCoverages.m

@@ -0,0 +1,17 @@
+function setCoverages(s,cov)
+% SETCOVERAGES - set surface coverages
+%   
+if isa(cov,'double')
+  sz = length(cov);
+  if sz == nSpecies(s)
+    surfmethods(thermo_hndl(s), 3, cov);
+  else
+    error('wrong size for coverage array');
+  end
+elseif isa(cov,'char')
+  surfmethods(thermo_hndl(s), 5, cov);
+end
+
+
+
+

Cantera/matlab/cantera/@Kinetics/Kinetics.m

@@ -33,15 +33,15 @@ end
 k.owner = 1;
 ixml = hndl(r);
 
-iphase = hndl(ph)
+iphase = thermo_hndl(ph);
 if nargin > 2
-  ineighbor1 = hndl(neighbor1)
+  ineighbor1 = thermo_hndl(neighbor1)
   if nargin > 3
-    ineighbor2 = hndl(neighbor2)
+    ineighbor2 = thermo_hndl(neighbor2)
     if nargin > 4
-      ineighbor3 = hndl(neighbor3)
+      ineighbor3 = thermo_hndl(neighbor3)
       if nargin > 5
-	ineighbor4 = hndl(neighbor4)
+	ineighbor4 = thermo_hndl(neighbor4)
       end
     end
   end

Cantera/matlab/cantera/@Kinetics/advanceCoverages.m

@@ -0,0 +1,5 @@
+function advanceCoverages(k, dt)
+% ADVANCECOVERAGES - advance the surface coverages forward in time holding the bulk phase concentrations fixed.
+%   
+kinetics_set(k.id, 5, 0, dt);
+

Cantera/matlab/cantera/@Kinetics/setMultiplier.m

@@ -1,4 +1,4 @@
-function setMultiplier(a,i,v)
+function setMultiplier(a,irxn,v)
 % SETMULTIPLIER  Set the rate of progress multiplier.
 %
 %    SETMULTIPLIER(K, IRXN, V) sets the multipler for reaction IRXN
@@ -6,5 +6,19 @@ function setMultiplier(a,i,v)
 %
 %    see also: MULTIPLIER
 %
-kinetics_set(a.id,1,i,v);
+if nargin == 2
+  v = irxn;
+  m = nReactions(a);
+  irxn = [1:m]';
+  n = 1;
+else
+  [m, n] = size(irxn);
+end
+
+for jm = 1:m
+  for jn = 1:n
+    kinetics_set(a.id,1,irxn(jm,jn),v);
+  end
+end
+
 

Cantera/matlab/cantera/@Solution/Solution.m

@@ -1,4 +1,4 @@
-function s = Solution(x, r)
+function s = Solution(src, id)
 % SOLUTION - class Solution constructor.
 %
 %    Class Solution represents solutions of multiple species. A
@@ -27,30 +27,17 @@ function s = Solution(x, r)
 %
 % See also: ThermoPhase, Kinetics, Transport
 %
+doc = XML_Node('doc',src);
 if nargin == 1
-  trmodel = 'None';
+  node = findByName(doc,'phase');
-elseif nargin == 2
-  trmodel = r;
 else
-   error('wrong number of arguments');
+  node = findByID(doc,id);
 end
-
+t = ThermoPhase(node);
-if isa(x,'Solution')
+k = Kinetics(node,t);
-  s = x;
-  return
-elseif isa(x,'XML_Node')
-  xp = x;
-else
-  doc = XML_Node('doc');
-  build(doc, x, 1);
-  write(doc,'xp.out');
-  xp = child(doc,'ctml/phase');
-end
-t = ThermoPhase(xp);
-k = Kinetics(xp,t);
 s.kin = k;
 s.th = t;
-tr = Transport(trmodel,t,4);
+tr = Transport(node,t,'default',4);
 s.tr = tr;
 s = class(s,'Solution',t,k,tr);
 

Cantera/matlab/cantera/@ThermoPhase/moleFraction.m

@@ -0,0 +1,19 @@
+function x = moleFraction(s, species)
+
+x = 0.0;
+xarray = moleFractions(s);
+if isa(species,'char')
+  k = speciesIndex(s, species);
+  if  k > 0
+    x = xarray(k);
+  end
+  
+elseif isa(species,'cell')
+  n = length(species);
+  for j = 1:n
+    k = speciesIndex(s, species{j});
+    if k > 0
+      x(j) = xarray(k);
+    end
+  end
+end

Cantera/matlab/cantera/@Transport/Transport.m

@@ -1,4 +1,4 @@
-function tr = Transport(model, th, loglevel)
+function tr = Transport(xml_phase, th, model, loglevel)
 %TRANSPORT  Transport class constructor.
 %
 %  k = TRANSPORT(model, p, loglevel) creates a transport
@@ -8,14 +8,23 @@ function tr = Transport(model, th, loglevel)
 %  model. The phase object must have already been created.
 %
 tr.id = 0;
-if nargin == 3
+if nargin == 4
   tr.th = th;
-  tr.model = model;
+  if model == 'default'
-  tr.id = trans_get(hndl(th), -1, model, loglevel) ;
+    try
+      node = child(xml_phase,'transport');
+      tr.model = attrib(node,'model');
+    catch
+      tr.model = '';
+    end
+  else
+    tr.model = model;
+  end
+  tr.id = trans_get(hndl(th), -1, tr.model, loglevel) ;
   tr = class(tr,'Transport');
 elseif isa(model,'Transport')
   tr = model;
 else
-  error('syntax error')
+  error('syntax error');
 end
 

Cantera/matlab/cantera/@Wall/setKinetics.m

@@ -0,0 +1,14 @@
+function setKinetics(w, left, right)
+% SETKINETICS - Specify the left and right surface reaction mechanisms.
+%   
+ileft = 0;
+iright = 0;
+if isa(left,'Kinetics')
+  ileft = kinetics_hndl(left);
+end
+
+if isa(right,'Kinetics')
+  iright = kinetics_hndl(right);
+end
+wallmethods(12, wall_hndl(w), ileft, iright);
+

Cantera/matlab/cantera/@XML_Node/XML_Node.m

@@ -1,24 +1,19 @@
-function x = XML_Node(name, src, root, wrap)
+function x = XML_Node(name, src, wrap)
-%XML_Node Cantera XML_Node class constructor
+%
+% XML_Node Cantera XML_Node class constructor
 %
 x.id = 0;
-x.root = 0;
+if nargin == 3
-if nargin == 4
    x.id = wrap;
-   x.root = root;
+elseif nargin == 2
-elseif nargin > 0
+   % read tree from a file
-   % create an empty node with name 'name'
+   x.id = ctmethods(10,15,0,src); % newxml(name)
-   x.id = ctmethods(10,0,0,name); % newxml(name)
    if x.id < 0
       error(geterr);
    end
-end
+elseif nargin == 1
-if nargin > 2
+  x.id = ctmethods(10,0,0,name);
-   x.root = root;
 end
 
 x = class(x,'XML_Node');
 
-if nargin > 1 & nargin < 4
-   build(x, src);
-end

Cantera/matlab/cantera/@XML_Node/addChild.m

@@ -0,0 +1,3 @@
+function n = addChild(root, id)
+%   
+n = ctmethods(10, 10, root.id, id);

Cantera/matlab/cantera/@XML_Node/attrib.m

@@ -1,9 +1,9 @@
-function x = attrib(x, key)
+function a = attrib(x, key)
 
 if nargin ~= 2 | ~isa(key,'char')
   error('Syntax error. Type "help attrib" for more information.')
 end
 
-iok = ctmethods(10, 20, x.id, key);
+a = ctmethods(10, 20, x.id, key);
 
 

Cantera/matlab/cantera/@XML_Node/child.m

@@ -1,6 +1,6 @@
 function v = child(x, loc)
 
 id = ctmethods(10, 6, x.id, loc);
-v = XML_Node('', '', x.root, id);
+v = XML_Node('', '', id);
 
 

Cantera/matlab/cantera/@XML_Node/findByID.m

@@ -0,0 +1,6 @@
+function x = findByID(root, id)
+% FINDBYID - Find an XML element by ID
+%   
+index = ctmethods(10, 8, root.id, id);
+x = XML_Node('','', index);
+

Cantera/matlab/cantera/@XML_Node/findByName.m

@@ -0,0 +1,6 @@
+function x = findByName(root, name)
+% FINDBYNAME - Find an XML element by name
+%   
+index = ctmethods(10, 9, root.id, name);
+x = XML_Node('','', index);
+

Cantera/matlab/cantera/@XML_Node/nChildren.m

@@ -0,0 +1,3 @@
+function n = nChildren(root, id)
+%   
+n = ctmethods(10, 10, root.id, id);

Cantera/matlab/cantera/GRI30.m

@@ -19,9 +19,13 @@ function s = GRI30(tr)
 %     g3 = GRI30('Multi')  % miulticomponent transport properties
 %
 if nargin == 0
-  s = Solution('gri30.xml');
+  s = Solution('gri30.cti','gri30');
 elseif nargin == 1
-  s = Solution('gri30.xml',tr); 
+  if strcmp(tr,'Mix')
+    s = Solution('gri30.cti','gri30_mix');
+  elseif strcmp(tr,'Multi')
+    s = Solution('gri30.cti','gri30_multi');
+  end
 else
-  error('wrong number of arguments')
+  error('wrong number of arguments');
 end

Cantera/matlab/cantera/IdealGasMix.m

@@ -1,4 +1,4 @@
-function s = IdealGasMix(a,b,c,d)
+function s = IdealGasMix(a,b,c)
 % IDEALGASMIX - Create a Solution instance representing an ideal gas mixture.
 %
 %      gas1 = IdealGasMix('ctml_file'[,'transport_model']) 
@@ -34,13 +34,12 @@ function s = IdealGasMix(a,b,c,d)
 dotloc = findstr(a,'.');
 if dotloc > 1
    ext = a(dotloc:end);
-   if ext == '.xml';
+   if ~strcmp(ext,'.inp')
      if nargin == 1
        s = Solution(a);
      elseif nargin == 2 
        s = Solution(a, b);
      end
-     set(s,'P',oneatm);
      return
    end
 end
@@ -48,13 +47,9 @@ end
 if nargin == 1
   b = '-';
   c = '-';
-  d = 'None';
 elseif nargin == 2
   c = '-';
-  d = 'None';
-elseif nargin == 3
-  d = 'None';
 end
-xml = ck2ctml(a,b,c);
+xml = ck2cti(a,b,c);
-s = Solution(xml,d);
+s = Solution(xml);
 set(s,'P',oneatm);

Cantera/matlab/cantera/ck2cti.m

@@ -0,0 +1,43 @@
+function f = ck2cti(infile, thermo, transport)
+% CK2CTI - Convert a Chemkin-compatible reaction mechanism file to
+%           Cantera format. 
+%
+%       f = ck2cti('chem.inp')
+%       f = ck2cti('chem.inp', 'therm.dat')
+%       f = ck2cti('chem.inp', 'therm.dat', 'tran.dat')
+%
+%    These 3 statements all create a Cantera input file 'chem.cti.' In
+%    the first case, the CK-format file contains all required species
+%    thermo data, while in the second case some or all thermo data is
+%    read from file 'therm.dat.' In the third form, the input file
+%    created will also contain transport property parameters. The
+%    function return value is a string containing the output file
+%    name.
+%
+prog = [ctbin,'/ck2cti'];
+
+if nargin == 0
+  error('input file name must be supplied')
+elseif nargin == 1
+  thermo = '-';
+  transport = '-';
+elseif nargin == 2
+    transport = '-';
+end
+    
+dotloc = findstr(infile,'.');
+if dotloc > 1
+   idtag = infile(1:dotloc-1);
+   outfile = [idtag '.cti'];
+else
+   idtag = infile;
+   outfile = [infile '.cti'];
+end
+
+iok = system([prog,' -i ',infile,' -t ',thermo,' -tr ',transport, ...
+	      ' -id ',idtag,' > ',outfile]);
+if iok
+  error(['Error occurred while running ck2cti. Check file ck2cti.log' ...
+	 ' for error messages.']);
+end
+f = outfile;

Cantera/matlab/cantera/cleanup.m

@@ -0,0 +1,4 @@
+function cleanup()
+% CLEANUP - Delete all stored Cantera objects and reclaim memory 
+%   
+ctmethods(0, 4);

Cantera/matlab/cantera/examples/catcomb.m

@@ -209,7 +209,7 @@ disp(e);
 
 %%%%%%%%%% make plots %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
-figure(1);
+clf;
 subplot(3,3,1);
 plotSolution(sim1D, 'flow', 'T');
 title('Temperature [K]');

Cantera/matlab/cantera/examples/diffflame.m

@@ -0,0 +1,134 @@
+% DIFFFLAME - A non-premixed opposed-jet flame.
+%
+%
+ 
+help diffflame
+disp('press any key to begin the simulation');
+pause
+
+
+t0 = cputime;  % record the starting time
+
+
+% parameter values
+p          =   oneatm;              % pressure
+tin        =   300.0;               % inlet temperature
+mdot_o     =   0.72;                % air, kg/m^2/s
+mdot_f     =   0.24;                % fuel, kg/m^2/s
+
+rxnmech    =  'gri30.xml';          % reaction mechanism file
+transport  =  'Mix';                % transport model
+comp1       =  'O2:0.21, N2:0.78, AR:0.01';  % air composition
+comp2       =  'C2H6:1';            % fuel composition
+
+initial_grid = 0.02*[0.0 0.2 0.4 0.6 0.8 1.0];  % m
+
+tol_ss    = [1.0e-5 1.0e-12];       % [rtol atol] for steady-state
+                                    % problem
+tol_ts    = [1.0e-3 1.0e-4];        % [rtol atol] for time stepping
+
+loglevel  = 1;                      % amount of diagnostic output (0
+                                    % to 5)
+				    
+refine_grid = 1;                    % 1 to enable refinement, 0 to
+                                    % disable 				   
+
+				   
+%%%%%%%%%%%%%%%% create the gas object %%%%%%%%%%%%%%%%%%%%%%%%
+%
+% This object will be used to evaluate all thermodynamic, kinetic,
+% and transport properties
+%
+gas = GRI30('Mix')
+
+% set its state to that of the  fuel (arbitrary)
+set(gas,'T', tin, 'P', p, 'X', comp2);
+
+
+
+%%%%%%%%%%%%%%%% create the flow object %%%%%%%%%%%%%%%%%%%%%%%
+
+f = AxisymmetricFlow(gas,'flow');
+
+set(f, 'P', p, 'grid', initial_grid);
+set(f, 'tol', tol_ss, 'tol-time', tol_ts);
+
+
+
+%%%%%%%%%%%%%%% create the air inlet %%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+%  The temperature, mass flux, and composition (relative molar) may be
+%  specified.
+%
+inlet_o = Inlet('air_inlet');
+set(inlet_o, 'T', tin, 'MassFlux', mdot_o, 'X', comp1);
+
+
+
+%%%%%%%%%%%%%% create the fuel inlet %%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% 
+%
+inlet_f = Inlet('fuel_inlet');
+set(inlet_f, 'T', tin, 'MassFlux', mdot_f, 'X', comp2);
+
+
+%%%%%%%%%%%%% create the flame object  %%%%%%%%%%%%
+%
+% Once the component parts have been created, they can be assembled
+% to create the flame object. Function npflame_init (in Cantera/1D) 
+% sets up the initial guess for the solution using a Burke-Schumann
+% flame. 
+%
+fl = npflame_init(gas, inlet_f, f, inlet_o, 'C2H6', 'O2', 3.5);
+
+% if the starting solution is to be read from a previously-saved
+% solution, uncomment this line and edit the file name and solution id.
+%restore(fl,'h2flame2.xml', 'energy')
+
+% solve with fixed temperature profile first
+solve(fl, loglevel, 0); %refine_grid);
+
+
+%%%%%%%%%%%% enable the energy equation %%%%%%%%%%%%%%%%%%%%%
+%
+%  The energy equation will now be solved to compute the
+%  temperature profile. We also tighten the grid refinement
+%  criteria to get an accurate final solution.
+%
+
+enableEnergy(f);
+setRefineCriteria(fl, 2, 200.0, 0.1, 0.1);
+solve(fl, loglevel, refine_grid);
+saveSoln(fl,'c2h6.xml','energy',['solution with energy' ...
+		    ' equation']);
+
+
+%%%%%%%%%% show statistics %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+writeStats(fl);
+elapsed = cputime - t0;
+e = sprintf('Elapsed CPU time: %10.4g',elapsed);
+disp(e);
+
+
+%%%%%%%%%% make plots %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+clf;
+subplot(2,3,1);
+plotSolution(fl, 'flow', 'T');
+title('Temperature [K]');
+subplot(2,3,2);
+plotSolution(fl, 'flow', 'C2H6');
+title('C2H6 Mass Fraction');
+subplot(2,3,3);
+plotSolution(fl, 'flow', 'O2');
+title('O2 Mass Fraction');
+subplot(2,3,4);
+plotSolution(fl, 'flow', 'CH');
+title('CH Mass Fraction');
+subplot(2,3,5);
+plotSolution(fl, 'flow', 'V');
+title('Radial Velocity / Radius [s^-1]');
+subplot(2,3,6);
+plotSolution(fl, 'flow', 'u');
+title('Axial Velocity [m/s]');
+

Cantera/matlab/cantera/examples/equil.m

@@ -34,14 +34,14 @@ for i = 1:50
 end
 
 % make plots
-
+clf;
-figure(1);
+subplot(1,2,1);
 plot(phi,tad);
 xlabel('Equivalence Ratio');
 ylabel('Temperature (K)');
 title('Adiabatic Flame Temperature');
 
-figure(2);
+subplot(1,2,2);
 semilogy(phi,xeq);
 axis([phi(1) phi(50) 1.0e-14 1]);
 %legend(speciesName(gas,1:nsp),1);

Cantera/matlab/cantera/examples/flame.m

@@ -58,6 +58,7 @@ mdot1 = massFlux(right);
 t0 = temperature(left);
 if flametype == 0
   t1 = teq;
+  mdot1 = -mdot0;
 else
   t1 = temperature(right);
 end
@@ -72,7 +73,7 @@ for n = 1:nSpecies(gas)
   nm = speciesName(gas,n);
   if strcmp(nm,'H') | strcmp(nm,'OH') | strcmp(nm,'O') | ...
   	strcmp(nm,'HO2')
-    yint = 3.0*yeq(n);
+    yint = 1.0*yeq(n);
   else
     yint = yeq(n);
   end

Cantera/matlab/cantera/examples/flame1.m

@@ -1,8 +1,11 @@
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% FLAME1 - A burner-stabilized flat flame
 %
-%  A burner-stabilized flat flame
+%    This script simulates a burner-stablized lean hydrogen-oxygen flame
-%
+%    at low pressure. 
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+help flame1;
+disp('press any key to begin the simulation');
+pause;
 
 t0 = cputime;  % record the starting time
 
@@ -10,16 +13,15 @@ t0 = cputime;  % record the starting time
 % parameter values
 p          =   0.05*oneatm;         % pressure
 tburner    =   373.0;               % burner temperature
-mdot       =   0.04;                % kg/m^2/s
+mdot       =   0.06;                % kg/m^2/s
 
-rxnmech    =  'h2o2.xml';           % reaction mechanism file
+rxnmech    =  'h2o2.cti';           % reaction mechanism file
-transport  =  'Mix';                % transport model
 comp       =  'H2:1.8, O2:1, AR:7'; % premixed gas composition
 
 initial_grid = [0.0 0.02 0.04 0.06 0.08 0.1 ...
-		0.15 0.2 0.49 0.5];  % m
+		0.15 0.2 0.4 0.49 0.5];  % m
 
-tol_ss    = [1.0e-5 1.0e-12];       % [rtol atol] for steady-state
+tol_ss    = [1.0e-5 1.0e-9];       % [rtol atol] for steady-state
                                     % problem
 tol_ts    = [1.0e-3 1.0e-4];        % [rtol atol] for time stepping
 
@@ -35,7 +37,7 @@ refine_grid = 1;                    % 1 to enable refinement, 0 to
 % This object will be used to evaluate all thermodynamic, kinetic,
 % and transport properties
 %
-gas = IdealGasMix(rxnmech, transport);
+gas = IdealGasMix(rxnmech);
 
 % set its state to that of the unburned gas at the burner
 set(gas,'T', tburner, 'P', p, 'X', comp);
@@ -83,8 +85,7 @@ fl = flame(gas, burner, f, s);
 %restore(fl,'h2flame2.xml', 'energy')
 
 
-solve(fl, loglevel, refine_grid);
+solve(fl, 1, refine_grid);
-
 
 
 %%%%%%%%%%%% enable the energy equation %%%%%%%%%%%%%%%%%%%%%
@@ -110,7 +111,7 @@ disp(e);
 
 %%%%%%%%%% make plots %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
-figure(1);
+clf;
 subplot(2,2,1);
 plotSolution(fl, 'flow', 'T');
 title('Temperature [K]');

Cantera/matlab/cantera/examples/flame2.m

@@ -36,7 +36,7 @@ refine_grid = 1;                    % 1 to enable refinement, 0 to
 % This object will be used to evaluate all thermodynamic, kinetic,
 % and transport properties
 %
-gas = IdealGasMix(rxnmech, transport);
+gas = GRI30('Mix'); %IdealGasMix(rxnmech, transport);
 
 % set its state to that of the  fuel (arbitrary)
 set(gas,'T', tin, 'P', p, 'X', comp2);

Cantera/matlab/cantera/examples/isentropic.m

@@ -50,7 +50,7 @@ a = a/amin;
 
 % plot results
 
-figure(1);
+clf;
 plot(mach,a);
 ylabel('Area Ratio');
 xlabel('Mach Number');

Cantera/matlab/cantera/examples/prandtl1.m

@@ -46,7 +46,7 @@ disp(['CPU time = ' num2str(cputime - t0)]);
 
 % plot results
 
-figure(1);
+clf;
 subplot(2,2,1);
 surf(xo2,t,pr);
 xlabel('Elemental O/(O+H)');

Cantera/matlab/cantera/examples/prandtl2.m

@@ -45,7 +45,7 @@ disp(['CPU time = ' num2str(cputime - t0)]);
 
 % plot results
 
-figure(1);
+clf;
 subplot(2,2,1);
 surf(xo2,t,pr);
 xlabel('Elemental O/(O+H)');

Cantera/matlab/cantera/examples/reactor1.m

@@ -21,15 +21,13 @@ nsp = nSpecies(gas);
 set(gas,'T',1001.0,'P',oneatm,'X','H2:2,O2:1,N2:4');
 
 % create a reactor, and insert the gas
-r = Reactor;
+r = Reactor(gas);
-insert(r, gas);
 
 % create a reservoir to represent the environment
-env = Reservoir;
+a = IdealGasMix('air.cti');
-a = IdealGasMix('air.xml');
+env = Reservoir(a);
-insert(env, a);
 
-% Define a wall between the reactor and the environment, and
+% Define a wall between the reactor and the environment and
 % make it flexible, so that the pressure in the reactor is held
 % at the environment pressure.
 w = Wall;
@@ -47,8 +45,28 @@ t0 = cputime;
 for n = 1:100
   t = t + dt;
   advance(r, t);
-  disp([time(r) temperature(r)]);  
+  tim(n) = time(r);
+  temp(n) = temperature(r);  
+  x(n,1:3) = moleFraction(gas,{'OH','H','H2'});
 end
 disp(['CPU time = ' num2str(cputime - t0)]);
 
+clf;
+subplot(2,2,1);
+plot(tim,temp);
+xlabel('Time (s)');
+ylabel('Temperature (K)');
+subplot(2,2,2)
+plot(tim,x(:,1));
+xlabel('Time (s)');
+ylabel('OH Mole Fraction (K)');
+subplot(2,2,3)
+plot(tim,x(:,2));
+xlabel('Time (s)');
+ylabel('H Mole Fraction (K)');
+subplot(2,2,4)
+plot(tim,x(:,3));
+xlabel('Time (s)');
+ylabel('H2 Mole Fraction (K)');
 clear all
+cleanup

Cantera/matlab/cantera/examples/reactor2.m

@@ -20,8 +20,7 @@ nsp = nSpecies(gas);
 set(gas,'T',1001.0,'P',oneatm,'X','H2:2,O2:1,N2:4');
 
 % create a reactor, and insert the gas
-r = Reactor;
+r = Reactor(gas);
-insert(r, gas);
 
 t = 0;
 dt = 1.0e-5;
@@ -29,8 +28,28 @@ t0 = cputime;
 for n = 1:100
   t = t + dt;
   advance(r, t);
-  disp([time(r) temperature(r)]);  
+  tim(n) = time(r);
+  temp(n) = temperature(r);  
+  x(n,1:3) = moleFraction(gas,{'OH','H','H2'});
 end
 disp(['CPU time = ' num2str(cputime - t0)]);
 
+clf;
+subplot(2,2,1);
+plot(tim,temp);
+xlabel('Time (s)');
+ylabel('Temperature (K)');
+subplot(2,2,2)
+plot(tim,x(:,1));
+xlabel('Time (s)');
+ylabel('OH Mole Fraction (K)');
+subplot(2,2,3)
+plot(tim,x(:,2));
+xlabel('Time (s)');
+ylabel('H Mole Fraction (K)');
+subplot(2,2,4)
+plot(tim,x(:,3));
+xlabel('Time (s)');
+ylabel('H2 Mole Fraction (K)');
 clear all
+cleanup

Cantera/matlab/cantera/examples/run_examples.m

@@ -1,44 +1,32 @@
-function run_examples(g)
-if nargin == 0 | ~isa(g,'solution')
-   gas = 0;
-end
 
 % runs all examples
-%adddir([pwd '/../data']);
+equil(0);
-equil(gas);
 disp('press any key to continue');
 pause
-set(1:2,'Visible','off');
+isentropic(0);
-isentropic(gas);
 disp('press any key to continue');
 pause
-set(1:2,'Visible','off');
+reactor1(0);
-reactor1(gas);
 disp('press any key to continue');
 pause
-set(1:2,'Visible','off');
+reactor2(0);
-reactor2(gas);
 disp('press any key to continue');
 pause
-set(1:2,'Visible','off');
+surfreactor;
-ignite(gas);
 disp('press any key to continue');
 pause
-set(1:2,'Visible','off');
+prandtl1(0);
-ignite_hp(gas);
 disp('press any key to continue');
 pause
-set(1:2,'Visible','off');
+prandtl2(0);
-ignite2(gas);
 disp('press any key to continue');
 pause
-set(1:2,'Visible','off');
+flame1
-ignite_uv(gas);
+disp('press any key to continue');
 pause
-set(1:2,'Visible','off');
+diffflame
-prandtl1(gas);
+disp('press any key to continue');
 pause
-set(1:2,'Visible','off');
+catcomb
-prandtl2(gas);
+disp('press any key to continue');
 pause
-set(1:2,'Visible','off');

Cantera/matlab/cantera/examples/surfreactor.m

@@ -0,0 +1,78 @@
+% SURFREACTOR Zero-dimensional reactor with surface chemistry
+% 
+%    This example illustrates how to use class 'Reactor' for
+%    zero-dimensional simulations including both homogeneous and
+%    heterogeneous chemistry. 
+
+help surfreactor
+
+t = 870.0;
+gas = importPhase('ptcombust.cti','gas');
+
+% set the initial conditions
+set(gas,'T',t,'P',oneatm,'X','CH4:0.01, O2:0.21, N2:0.78');
+
+surf = importInterface('ptcombust.cti','Pt_surf', gas);
+setTemperature(surf, t);
+
+nsp = nSpecies(gas);
+
+% create a reactor, and insert the gas
+r = Reactor(gas);
+setInitialVolume(r, 1.0e-6)
+
+% create a reservoir to represent the environment
+a = IdealGasMix('air.cti');
+set(a,'T',t,'P',oneatm);
+env = Reservoir(a);
+
+% Define a wall between the reactor and the environment and
+% make it flexible, so that the pressure in the reactor is held
+% at the environment pressure.
+w = Wall;
+install(w,r,env);
+
+% set the surface mechanism on the left side of the wall (facing
+% reactor 'r' to 'surf'. No surface mechanism will be installed on
+% the air side.
+setKinetics(w, surf, 0);
+
+% set the wall area and heat transfer coefficient.
+setArea(w, 1.0e-4);
+setHeatTransferCoeff(w,0.1);
+
+% set expansion parameter. dV/dt = K(P_1 - P_2)
+setExpansionRateCoeff(w, 1.0);
+
+
+t = 0;
+dt = 0.1;
+t0 = cputime;
+names = {'CH4','O2','CO','CO2','H2O'};
+for n = 1:100
+  t = t + dt;
+  advance(r, t);
+  tim(n) = t;
+  temp(n) = temperature(r);  
+  cov(n,:) = coverages(surf)';
+  x(n,:) = moleFraction(gas,names);
+end
+disp(['CPU time = ' num2str(cputime - t0)]);
+
+clf;
+subplot(2,2,1);
+plot(tim,temp);
+xlabel('Time (s)');
+ylabel('Temperature (K)');
+subplot(2,2,2);
+semilogy(tim,cov);
+xlabel('Time (s)');
+ylabel('Coverages');
+legend(speciesNames(surf));
+subplot(2,2,3);
+plot(tim,x);
+xlabel('Time (s)');
+ylabel('Mole Fractions');
+legend(names);
+clear all
+cleanup

Cantera/matlab/cantera/importInterface.m

@@ -0,0 +1,10 @@
+function s = importInterface(file, name, phase1, phase2)
+% IMPORTINTERFACE - import an interface
+%   
+if nargin == 3
+  s = Interface(file, name, phase1);
+elseif nargin == 4
+  s = Interface(file, name, phase1, phase2);  
+else
+  error('importInterface only supports 2 bulk phases');
+end

Cantera/matlab/cantera/importPhase.m

@@ -0,0 +1,8 @@
+function s = importPhase(file, name)
+% IMPORTPHASE - import a phase
+%   
+if nargin == 1
+  s = Solution(file);
+elseif nargin == 2 
+  s = Solution(file, name);
+end

Cantera/matlab/cantera/private/ctfunctions.cpp

@@ -59,7 +59,7 @@ void ctfunctions( int nlhs, mxArray *plhs[],
     case 4:
         iok = domain_clear();
         iok = sim1D_clear();
-        //iok = xml_clear();
+        iok = xml_clear();
         iok = clearStorage();
         break;
 

Cantera/matlab/cantera/private/ctmethods.cpp

@@ -27,6 +27,7 @@ const int REACTOR_CLASS = 60;
 const int WALL_CLASS = 70;
 const int FLOWDEVICE_CLASS = 80;
 const int ONEDIM_CLASS = 90;
+const int SURF_CLASS = 100;
 
 void ctfunctions( int nlhs, mxArray *plhs[], int nrhs, 
     const mxArray *prhs[] );
@@ -40,6 +41,9 @@ void thermomethods( int nlhs, mxArray *plhs[], int nrhs,
 void phasemethods( int nlhs, mxArray *plhs[], int nrhs, 
     const mxArray *prhs[] );
 
+void surfmethods( int nlhs, mxArray *plhs[], int nrhs, 
+    const mxArray *prhs[] );
+
 void kineticsmethods( int nlhs, mxArray *plhs[], int nrhs, 
     const mxArray *prhs[] );
 
@@ -94,6 +98,8 @@ extern "C" {
             flowdevicemethods(nlhs, plhs, nrhs, prhs); break;
         case ONEDIM_CLASS:
             onedimmethods(nlhs, plhs, nrhs, prhs); break;
+        case SURF_CLASS:
+            surfmethods(nlhs, plhs, nrhs, prhs); break;
         default:
             mexErrMsgTxt("unknown class");
         }

Cantera/matlab/cantera/private/kineticsmethods.cpp

@@ -146,11 +146,13 @@ void kineticsmethods( int nlhs, mxArray *plhs[],
                 iok = kin_setMultiplier(kin,irxn-1,v); break;
             case 3:
                 iok = delKinetics(kin); break;
+            case 5:
+                iok = kin_advanceCoverages(kin,v); break;
             default:
-                iok = -1;
+                mexErrMsgTxt("unknown job");
             }
         }
     
-        if (iok < 0) mexErrMsgTxt("error in kineticsmethods.");
+        if (iok < 0) reportError();
     }
 }

Cantera/matlab/cantera/private/onedimmethods.cpp

@@ -4,8 +4,15 @@
 #include "../../../clib/src/ctonedim.h"
 
 #include <iostream>
+#include <string>
 using namespace std;
 
+
+namespace Cantera {
+    void writelog(const std::string& s);
+}
+using namespace Cantera;
+
 void onedimmethods( int nlhs, mxArray *plhs[],
     int nrhs, const mxArray *prhs[] ) {
     double vv;
@@ -82,7 +89,9 @@ void onedimmethods( int nlhs, mxArray *plhs[],
             for (k = 0; k < sz; k++) {
                 ptrs[k] = int(dom_ids[k]);
             }
+            writelog("calling sim1D_new\n");
             indx = sim1D_new(sz, ptrs);
+            writelog("ret sim1D_new\n");
             delete[] ptrs;
             break;
 
@@ -197,9 +206,10 @@ void onedimmethods( int nlhs, mxArray *plhs[],
         int iok = -1;
         double *lower, *upper, *rtol, *atol, *grid, *pos, *values, 
             mdot, t, p, val, *temp, ratio, slope, curve, tstep, *dts, 
-            rdt;
+            rdt, prune;
         int nlower, nupper, nr, na, npts, np, comp, localPoint, idom,
-            loglevel, refine_grid, n, flag, itime, ns, *nsteps, icount;
+            loglevel, refine_grid, n, flag, itime, ns, *nsteps, icount,
+            onoff, ss_age, ts_age;
         char *xstr, *fname, *id, *desc, *name;
         switch (job) {
         case 51:
@@ -309,12 +319,14 @@ void onedimmethods( int nlhs, mxArray *plhs[],
             iok = sim1D_refine(dom, loglevel);
             break;
         case 106:
-            checkNArgs(7, nrhs);
+            checkNArgs(8, nrhs);
             idom = getInt(prhs[3]) - 1;
             ratio = getDouble(prhs[4]);
             slope = getDouble(prhs[5]);
             curve = getDouble(prhs[6]);
-            iok = sim1D_setRefineCriteria(dom, idom, ratio, slope, curve);
+            prune = getDouble(prhs[7]);
+            iok = sim1D_setRefineCriteria(dom, idom, 
+                ratio, slope, curve, prune);
             break;
         case 107:
             iok = 0;
@@ -362,11 +374,23 @@ void onedimmethods( int nlhs, mxArray *plhs[],
             icount = getInt(prhs[4]);
             iok = sim1D_eval(dom, rdt, icount); 
             break;
+        case 114:
+            checkNArgs(5, nrhs);
+            ss_age = getInt(prhs[3]);
+            ts_age = getInt(prhs[4]);
+            iok = sim1D_setMaxJacAge(dom, ss_age, ts_age);
+            break;
             //case 200:
             //iok = domain1D_clear();
             //iok = sim1D_clear();
             //break;
 
+        case 120:
+            checkNArgs(4, nrhs);
+            onoff = getInt(prhs[3]);
+            iok = reactingsurf_enableCoverageEqs(dom, onoff);
+            break;
+
         default:
             mexPrintf(" job = %d ",job);
             mexErrMsgTxt("unknown parameter");

Cantera/matlab/cantera/private/surfmethods.cpp

@@ -0,0 +1,102 @@
+
+#include "mex.h"
+#include "ctmatutils.h"
+#include "../../../clib/src/ctsurf.h"
+#include "../../../clib/src/ct.h"
+
+#include <iostream>
+#include <string>
+using namespace std;
+
+
+namespace Cantera {
+    void writelog(const std::string& s);
+}
+using namespace Cantera;
+
+void surfmethods( int nlhs, mxArray *plhs[],
+    int nrhs, const mxArray *prhs[] ) {
+    double vv;
+    int job = getInt(prhs[2]); 
+    int n, m, iok;
+    double* ptr;
+    char* str;
+    int surf, nsp;
+    surf = getInt(prhs[1]);    
+
+    // set parameters
+    if (job < 100) {
+
+        switch (job) {
+
+        case 1:
+            checkNArgs(4, nrhs);
+            vv = getDouble(prhs[3]);
+            iok = surf_setsitedensity(surf, vv);
+            break;
+
+        case 3:
+            checkNArgs(4, nrhs);
+            ptr = mxGetPr(prhs[3]);
+            m = mxGetM(prhs[3]);
+            n = mxGetN(prhs[3]);
+            nsp = phase_nSpecies(surf);
+            if ((m == nsp && n == 1) || (m == 1 && n == nsp)) {
+                iok = surf_setcoverages(surf, ptr);
+            }
+            else {
+                mexErrMsgTxt("wrong array size for coverages");
+            }
+            break;
+
+        case 5:
+            checkNArgs(4, nrhs);
+            str = getString(prhs[3]);
+            iok = surf_setcoveragesbyname(surf, str);
+            break;
+
+        default:
+            mexErrMsgTxt("unknown job");
+        }
+        if (iok < 0) reportError();
+        plhs[0] = mxCreateNumericMatrix(1,1,mxDOUBLE_CLASS,mxREAL);
+        double *h = mxGetPr(plhs[0]);
+        *h = double(iok);
+        return;
+    }
+
+    // return array parameters
+    else if (job < 200) {
+        nsp = phase_nSpecies(surf);
+        double* x = new double[nsp];
+
+        switch (job) {
+        case 101:
+            checkNArgs(3,nrhs);
+            iok = surf_getcoverages(surf,x);
+            break;
+        case 103:
+            iok = surf_getconcentrations(surf,x);
+            break;
+        default:
+            ;
+        }
+        plhs[0] = mxCreateNumericMatrix(nsp,1,
+            mxDOUBLE_CLASS,mxREAL);
+        double *h = mxGetPr(plhs[0]);
+        if (iok >= 0) {
+            for (int i = 0; i < nsp; i++) h[i] = x[i];
+            delete x;
+            return;
+        }
+        else {
+            for (int i = 0; i < nsp; i++) h[i] = -999.99;
+            delete x;
+            reportError();
+            return;
+        }
+    }
+    else {
+        mexErrMsgTxt("unknown job");
+    }
+}

Cantera/matlab/cantera/private/wallmethods.cpp

@@ -68,6 +68,11 @@ const double Undef = -999.123;
             case 11:
                 iok = wall_ready(i);
                 break;
+            case 12:
+                n = getInt(prhs[3]);
+                m = getInt(prhs[4]);
+                iok = wall_setkinetics(i, n, m);
+                break;
             default:
                 mexErrMsgTxt("unknown job parameter");
             }

Cantera/matlab/cantera/private/xmlmethods.cpp

@@ -105,7 +105,7 @@ void xmlmethods( int nlhs, mxArray *plhs[],
                 break;
         case 15:
             file = getString(prhs[3]);
-            iok = xml_preprocess_and_build(i, file);
+            iok = xml_get_XML_File(file); // xml_preprocess_and_build(i, file);
             break;
             default:
                 mexErrMsgTxt("unknown job parameter");

Cantera/matlab/setup_matlab.py

@@ -1,11 +1,12 @@
 
 import sys
 
-if len(sys.argv) >= 3:
+if len(sys.argv) >= 4:
-    libdir = sys.argv[1]
+    bindir = sys.argv[1]
-    libs = '-l'+sys.argv[2]+' '+sys.argv[3]
+    libdir = sys.argv[2]
+    libs = '-l'+sys.argv[3]+' '+sys.argv[4]
 else:
-    print 'usage: python setup_matlab.py <libdir> <lib>'
+    print 'usage: python setup_matlab.py <bindir> <libdir> <lib>'
     sys.exit(0)
     
 f = open('setup.m','w')
@@ -20,7 +21,14 @@ mex private/ctmethods.cpp private/ctfunctions.cpp ...
     private/thermomethods.cpp private/kineticsmethods.cpp ...
     private/transportmethods.cpp private/reactormethods.cpp ...
     private/wallmethods.cpp private/flowdevicemethods.cpp ...
-    private/onedimmethods.cpp private/write.cpp ...
+    private/onedimmethods.cpp private/surfmethods.cpp private/write.cpp ...
 """+'     -L'+libdir+' '+libs+'\n'+"""disp('done.');
 """)
 fb.close()
+
+fp = open('cantera/ctbin.m','w')
+fp.write("""function path = ctbin
+path = '"""+bindir+"""';
+""")
+fp.close()
+

Cantera/python/Cantera/ctml_writer.py

@@ -23,12 +23,6 @@ SPECIES_SET = 20
 COLLECTION = 30
 THERMO = 40
 
-# dictionary maps error conditions -> action
-_handle_error = {}
-_handle_error['undeclared_element'] = 'error'
-_handle_error['undeclared_species'] = 'error'
-_handle_error['negative_A'] = 'error'
-
 # default units
 _ulen = 'm' 
 _umol = 'kmol'
@@ -54,7 +48,7 @@ _speciesnames = []
 _phases = []
 _reactions = []
 _atw = {}
-_mw = {}
+#_mw = {}
 
 _valsp = ''
 _valrxn = ''
@@ -88,20 +82,6 @@ def standard_pressure(p0):
     global _pref
     _pref = p0
 
-def on_error(undeclared_element = '',
-             undeclared_species = '',
-             negative_A = ''):
-    """specify an action when an error condition is encountered."""
-    global _handle_error
-    
-    if undeclared_element:
-        _handle_error['undeclared_element'] = undeclared_element
-    if undeclared_species:
-        _handle_error['undeclared_species'] = undeclared_species
-    if negative_A:
-        _handle_error['negative_A'] = negative_A                
-            
-    
 def get_atomic_wts():
     """get the atomic weights from the elements database."""
     global _atw
@@ -250,19 +230,19 @@ class species(writer):
     def __init__(self,
                  name = 'missing name!',
                  atoms = '',
-                 comment = '',
+                 note = '',
                  thermo = None,
                  transport = None,
                  charge = -999):
         self._name = name
         self._atoms = getAtomicComp(atoms)
-        mw = 0.0
+        #mw = 0.0
-        for a in self._atoms.keys():
+        #for a in self._atoms.keys():
-            mw += self._atoms[a]*float(_atw[a])
+        #    mw += self._atoms[a]*float(_atw[a])
-        self._mw = mw
+        #self._mw = mw
-        global _mw
+        #global _mw
-        _mw[name] = mw
+        #_mw[name] = mw
-        self._comment = comment
+        self._comment = note
         
         if thermo:
             self._thermo = thermo
@@ -789,13 +769,15 @@ class phase(writer):
                  elements = '',
                  species = '',
                  reactions = 'none',
-                 initial_state = None):
+                 initial_state = None,
+                 options = []):
         
         self._name = name
         self._dim = dim
         self._el = elements
         self._sp = []
         self._rx = []
+        self._options = options
 
         #--------------------------------
         #        process species
@@ -888,7 +870,7 @@ class phase(writer):
             datasrc = r[0]
             ra = p.addChild('reactionArray')
             ra['datasrc'] = datasrc+'#reaction_data'
-            if _handle_error['undeclared_species'] == 'skip':
+            if 'skip_undeclared_species' in self._options:
                 rk = ra.addChild('skip')
                 rk['species'] = 'undeclared'
             
@@ -921,7 +903,7 @@ class phase(writer):
             sa = ph.addChild('speciesArray',names)
             sa['datasrc'] = datasrc+'#species_data'
 
-            if _handle_error['undeclared_element'] == 'skip':
+            if 'skip_undeclared_elements' in self._options:
                 sk = sa.addChild('skip')
                 sk['element'] = 'undeclared'
             
@@ -943,10 +925,11 @@ class ideal_gas(phase):
                  reactions = 'none',
                  kinetics = 'GasKinetics',
                  transport = 'None',
-                 initial_state = None):
+                 initial_state = None,
+                 options = []):
         
         phase.__init__(self, name, 3, elements, species, reactions,
-                       initial_state)
+                       initial_state, options)
         self._pure = 0
         self._kin = kinetics
         self._tr = transport
@@ -972,10 +955,11 @@ class pure_solid(phase):
                  species = '',
                  density = -1.0,
                  transport = 'None',
-                 initial_state = None):
+                 initial_state = None,
+                 options = []):
         
         phase.__init__(self, name, 3, elements, species, 'none',
-                       initial_state)
+                       initial_state, options)
         self._dens = density
         self._pure = 1
         if self._dens < 0.0:
@@ -1009,11 +993,12 @@ class ideal_interface(phase):
                  phases = [],
                  kinetics = 'Interface',
                  transport = 'None',
-                 initial_state = None):
+                 initial_state = None,
+                 options = []):
 
         self._type = 'surface'
         phase.__init__(self, name, 2, elements, species, reactions,
-                       initial_state)
+                       initial_state, options)
         self._pure = 0
         self._kin = kinetics
         self._tr = transport
@@ -1176,7 +1161,7 @@ class Lindemann:
 ##         tr.addChild('rotRelax',`self._params[4]`)        
 
 
-get_atomic_wts()
+#get_atomic_wts()
 validate()
 
 
@@ -1197,7 +1182,10 @@ if __name__ == "__main__":
 # $Revision$
 # $Date$
 # $Log$
-# Revision 1.18  2003-08-21 14:29:53  dggoodwin
+# Revision 1.19  2003-08-26 03:39:02  dggoodwin
+# *** empty log message ***
+#
+# Revision 1.18  2003/08/21 14:29:53  dggoodwin
 # *** empty log message ***
 #
 # Revision 1.17  2003/08/20 15:35:32  dggoodwin

data/inputs/air.cti

@@ -1,38 +1,24 @@
 #
 # Generated from file air.inp
-# by ck2ct on Fri Aug  8 20:22:22 2003
+# by ck2cti on Mon Aug 25 09:52:58 2003
 #
-
 # Transport data from file ../transport/gri30_tran.dat.
 
-
-#-------------------------------------------------------------------------------
-#
-#  The default units. These will be used for dimensional quantities
-#  with unspecified units.
-#-------------------------------------------------------------------------------
 units(length = "cm", time = "s", quantity = "mol", act_energy = "cal/mol")
 
 
-
-
-#-------------------------------------------------------------------------------
-#
-#  The phase definition. This specifies an ideal gas mixture that
-#  includes all species and reactions defined in this file.
-#
-#-------------------------------------------------------------------------------
 ideal_gas(name = "air",
       elements = " O  N  Ar ",
       species = """ O  O2  N  NO  NO2  N2O  N2  AR """,
-      reactions = "all"    )
+      reactions = "all",
+      transport = "Mix",
+      initial_state = state(temperature = 300.0,
+                        pressure = OneAtm)    )
 
 
 
 #-------------------------------------------------------------------------------
-#
 #  Species data 
-#
 #-------------------------------------------------------------------------------
 
 species(name = "O",
@@ -48,7 +34,8 @@ species(name = "O",
     transport = gas_transport(
                      geom = "atom",
                      diam =     2.75,
-                     well_depth =    80.00)
+                     well_depth =    80.00),
+    note = "L 1/90"
        )
 
 species(name = "O2",
@@ -66,7 +53,8 @@ species(name = "O2",
                      diam =     3.46,
                      well_depth =   107.40,
                      polar =     1.60,
-                     rot_relax =     3.80)
+                     rot_relax =     3.80),
+    note = "TPIS89"
        )
 
 species(name = "N",
@@ -82,7 +70,8 @@ species(name = "N",
     transport = gas_transport(
                      geom = "atom",
                      diam =     3.30,
-                     well_depth =    71.40)
+                     well_depth =    71.40),
+    note = "L 6/88"
        )
 
 species(name = "NO",
@@ -100,7 +89,8 @@ species(name = "NO",
                      diam =     3.62,
                      well_depth =    97.53,
                      polar =     1.76,
-                     rot_relax =     4.00)
+                     rot_relax =     4.00),
+    note = "RUS 78"
        )
 
 species(name = "NO2",
@@ -117,7 +107,8 @@ species(name = "NO2",
                      geom = "nonlinear",
                      diam =     3.50,
                      well_depth =   200.00,
-                     rot_relax =     1.00)
+                     rot_relax =     1.00),
+    note = "L 7/88"
        )
 
 species(name = "N2O",
@@ -134,7 +125,8 @@ species(name = "N2O",
                      geom = "linear",
                      diam =     3.83,
                      well_depth =   232.40,
-                     rot_relax =     1.00)
+                     rot_relax =     1.00),
+    note = "L 7/88"
        )
 
 species(name = "N2",
@@ -152,7 +144,8 @@ species(name = "N2",
                      diam =     3.62,
                      well_depth =    97.53,
                      polar =     1.76,
-                     rot_relax =     4.00)
+                     rot_relax =     4.00),
+    note = "121286"
        )
 
 species(name = "AR",
@@ -168,15 +161,14 @@ species(name = "AR",
     transport = gas_transport(
                      geom = "atom",
                      diam =     3.33,
-                     well_depth =   136.50)
+                     well_depth =   136.50),
+    note = "120186"
        )
 
 
 
 #-------------------------------------------------------------------------------
-#
 #  Reaction data 
-#
 #-------------------------------------------------------------------------------
 
 #  Reaction 1

data/inputs/air.xml

@@ -1,344 +0,0 @@
-<ctml>
-  <validate reactions="yes" species="yes"/>
-
-  <!--    phase air     -->
-  <phase dim="3" id="air">
-    <validation>
-      <duplicateReactions>halt</duplicateReactions>
-      <thermo>warn</thermo>
-    </validation>
-    <elementArray datasrc="elements.xml"> O  N  Ar </elementArray>
-    <speciesArray datasrc="#species_data"> O  O2  N  NO  NO2  N2O  N2  AR </speciesArray>
-    <reactionArray datasrc="#reaction_data"/>
-    <thermo model="IdealGas"/>
-    <kinetics model="GasKinetics"/>
-    <transport model="None"/>
-  </phase>
-
-  <!--     species definitions     -->
-  <speciesData id="species_data">
-
-    <!--    species O    -->
-    <species name="O">
-      <atomArray>O:1 </atomArray>
-      <thermo>
-        <NASA P0="100000.0" Tmax="1000.0" Tmin="200.0">
-          <floatArray name="coeffs" size="7">
-            3.168267100E+00,  -3.279318840E-03,   6.643063960E-06,  -6.128066240E-09, 
-            2.112659710E-12,   2.912225920E+04,   2.051933460E+00,</floatArray>
-        </NASA>
-        <NASA P0="100000.0" Tmax="3500.0" Tmin="1000.0">
-          <floatArray name="coeffs" size="7">
-            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 model="gas_transport">
-        <string title="geometry">atom</string>
-        <LJ_welldepth units="K">  80.000</LJ_welldepth>
-        <LJ_diameter units="A">   2.750</LJ_diameter>
-        <dipoleMoment units="Debye">   0.000</dipoleMoment>
-        <polarizability units="A3">   0.000</polarizability>
-        <rotRelax>   0.000</rotRelax>
-      </transport>
-    </species>
-
-    <!--    species O2    -->
-    <species name="O2">
-      <atomArray>O:2 </atomArray>
-      <thermo>
-        <NASA P0="100000.0" Tmax="1000.0" Tmin="200.0">
-          <floatArray name="coeffs" size="7">
-            3.782456360E+00,  -2.996734160E-03,   9.847302010E-06,  -9.681295090E-09, 
-            3.243728370E-12,  -1.063943560E+03,   3.657675730E+00,</floatArray>
-        </NASA>
-        <NASA P0="100000.0" Tmax="3500.0" Tmin="1000.0">
-          <floatArray name="coeffs" size="7">
-            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 model="gas_transport">
-        <string title="geometry">linear</string>
-        <LJ_welldepth units="K"> 107.400</LJ_welldepth>
-        <LJ_diameter units="A">   3.460</LJ_diameter>
-        <dipoleMoment units="Debye">   0.000</dipoleMoment>
-        <polarizability units="A3">   1.600</polarizability>
-        <rotRelax>   3.800</rotRelax>
-      </transport>
-    </species>
-
-    <!--    species N    -->
-    <species name="N">
-      <atomArray>N:1 </atomArray>
-      <thermo>
-        <NASA P0="100000.0" Tmax="1000.0" Tmin="200.0">
-          <floatArray name="coeffs" size="7">
-            2.500000000E+00,   0.000000000E+00,   0.000000000E+00,   0.000000000E+00, 
-            0.000000000E+00,   5.610463700E+04,   4.193908700E+00,</floatArray>
-        </NASA>
-        <NASA P0="100000.0" Tmax="6000.0" Tmin="1000.0">
-          <floatArray name="coeffs" size="7">
-            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 model="gas_transport">
-        <string title="geometry">atom</string>
-        <LJ_welldepth units="K">  71.400</LJ_welldepth>
-        <LJ_diameter units="A">   3.300</LJ_diameter>
-        <dipoleMoment units="Debye">   0.000</dipoleMoment>
-        <polarizability units="A3">   0.000</polarizability>
-        <rotRelax>   0.000</rotRelax>
-      </transport>
-    </species>
-
-    <!--    species NO    -->
-    <species name="NO">
-      <atomArray>O:1 N:1 </atomArray>
-      <thermo>
-        <NASA P0="100000.0" Tmax="1000.0" Tmin="200.0">
-          <floatArray name="coeffs" size="7">
-            4.218476300E+00,  -4.638976000E-03,   1.104102200E-05,  -9.336135400E-09, 
-            2.803577000E-12,   9.844623000E+03,   2.280846400E+00,</floatArray>
-        </NASA>
-        <NASA P0="100000.0" Tmax="6000.0" Tmin="1000.0">
-          <floatArray name="coeffs" size="7">
-            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 model="gas_transport">
-        <string title="geometry">linear</string>
-        <LJ_welldepth units="K">  97.530</LJ_welldepth>
-        <LJ_diameter units="A">   3.620</LJ_diameter>
-        <dipoleMoment units="Debye">   0.000</dipoleMoment>
-        <polarizability units="A3">   1.760</polarizability>
-        <rotRelax>   4.000</rotRelax>
-      </transport>
-    </species>
-
-    <!--    species NO2    -->
-    <species name="NO2">
-      <atomArray>O:2 N:1 </atomArray>
-      <thermo>
-        <NASA P0="100000.0" Tmax="1000.0" Tmin="200.0">
-          <floatArray name="coeffs" size="7">
-            3.944031200E+00,  -1.585429000E-03,   1.665781200E-05,  -2.047542600E-08, 
-            7.835056400E-12,   2.896617900E+03,   6.311991700E+00,</floatArray>
-        </NASA>
-        <NASA P0="100000.0" Tmax="6000.0" Tmin="1000.0">
-          <floatArray name="coeffs" size="7">
-            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 model="gas_transport">
-        <string title="geometry">nonlinear</string>
-        <LJ_welldepth units="K"> 200.000</LJ_welldepth>
-        <LJ_diameter units="A">   3.500</LJ_diameter>
-        <dipoleMoment units="Debye">   0.000</dipoleMoment>
-        <polarizability units="A3">   0.000</polarizability>
-        <rotRelax>   1.000</rotRelax>
-      </transport>
-    </species>
-
-    <!--    species N2O    -->
-    <species name="N2O">
-      <atomArray>O:1 N:2 </atomArray>
-      <thermo>
-        <NASA P0="100000.0" Tmax="1000.0" Tmin="200.0">
-          <floatArray name="coeffs" size="7">
-            2.257150200E+00,   1.130472800E-02,  -1.367131900E-05,   9.681980600E-09, 
-           -2.930718200E-12,   8.741774400E+03,   1.075799200E+01,</floatArray>
-        </NASA>
-        <NASA P0="100000.0" Tmax="6000.0" Tmin="1000.0">
-          <floatArray name="coeffs" size="7">
-            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 model="gas_transport">
-        <string title="geometry">linear</string>
-        <LJ_welldepth units="K"> 232.400</LJ_welldepth>
-        <LJ_diameter units="A">   3.830</LJ_diameter>
-        <dipoleMoment units="Debye">   0.000</dipoleMoment>
-        <polarizability units="A3">   0.000</polarizability>
-        <rotRelax>   1.000</rotRelax>
-      </transport>
-    </species>
-
-    <!--    species N2    -->
-    <species name="N2">
-      <atomArray>N:2 </atomArray>
-      <thermo>
-        <NASA P0="100000.0" Tmax="1000.0" Tmin="300.0">
-          <floatArray name="coeffs" size="7">
-            3.298677000E+00,   1.408240400E-03,  -3.963222000E-06,   5.641515000E-09, 
-           -2.444854000E-12,  -1.020899900E+03,   3.950372000E+00,</floatArray>
-        </NASA>
-        <NASA P0="100000.0" Tmax="5000.0" Tmin="1000.0">
-          <floatArray name="coeffs" size="7">
-            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 model="gas_transport">
-        <string title="geometry">linear</string>
-        <LJ_welldepth units="K">  97.530</LJ_welldepth>
-        <LJ_diameter units="A">   3.620</LJ_diameter>
-        <dipoleMoment units="Debye">   0.000</dipoleMoment>
-        <polarizability units="A3">   1.760</polarizability>
-        <rotRelax>   4.000</rotRelax>
-      </transport>
-    </species>
-
-    <!--    species AR    -->
-    <species name="AR">
-      <atomArray>Ar:1 </atomArray>
-      <thermo>
-        <NASA P0="100000.0" Tmax="1000.0" Tmin="300.0">
-          <floatArray name="coeffs" size="7">
-            2.500000000E+00,   0.000000000E+00,   0.000000000E+00,   0.000000000E+00, 
-            0.000000000E+00,  -7.453750000E+02,   4.366000000E+00,</floatArray>
-        </NASA>
-        <NASA P0="100000.0" Tmax="5000.0" Tmin="1000.0">
-          <floatArray name="coeffs" size="7">
-            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 model="gas_transport">
-        <string title="geometry">atom</string>
-        <LJ_welldepth units="K"> 136.500</LJ_welldepth>
-        <LJ_diameter units="A">   3.330</LJ_diameter>
-        <dipoleMoment units="Debye">   0.000</dipoleMoment>
-        <polarizability units="A3">   0.000</polarizability>
-        <rotRelax>   0.000</rotRelax>
-      </transport>
-    </species>
-  </speciesData>
-  <reactionData id="reaction_data">
-
-    <!--   reaction 0001    -->
-    <reaction id="0001" reversible="yes" type="threeBody">
-      <equation>2 O + M [=] O2 + M</equation>
-      <rateCoeff>
-        <Arrhenius>
-          <A units="cm6/mol2/s">  1.200000E+17</A>
-          <b>-1</b>
-          <E units="cal/mol">0.000000</E>
-        </Arrhenius>
-        <efficiencies default="1.0"> AR:0.83 </efficiencies>
-      </rateCoeff>
-      <reactants>O:2</reactants>
-      <products>O2:1</products>
-    </reaction>
-
-    <!--   reaction 0002    -->
-    <reaction id="0002" reversible="yes">
-      <equation>N + NO [=] N2 + O</equation>
-      <rateCoeff>
-        <Arrhenius>
-          <A units="cm3/mol/s">  2.700000E+13</A>
-          <b>0</b>
-          <E units="cal/mol">355.000000</E>
-        </Arrhenius>
-      </rateCoeff>
-      <reactants>NO:1 N:1</reactants>
-      <products>N2:1 O:1</products>
-    </reaction>
-
-    <!--   reaction 0003    -->
-    <reaction id="0003" reversible="yes">
-      <equation>N + O2 [=] NO + O</equation>
-      <rateCoeff>
-        <Arrhenius>
-          <A units="cm3/mol/s">  9.000000E+09</A>
-          <b>1</b>
-          <E units="cal/mol">6500.000000</E>
-        </Arrhenius>
-      </rateCoeff>
-      <reactants>O2:1 N:1</reactants>
-      <products>O:1 NO:1</products>
-    </reaction>
-
-    <!--   reaction 0004    -->
-    <reaction id="0004" reversible="yes">
-      <equation>N2O + O [=] N2 + O2</equation>
-      <rateCoeff>
-        <Arrhenius>
-          <A units="cm3/mol/s">  1.400000E+12</A>
-          <b>0</b>
-          <E units="cal/mol">10810.000000</E>
-        </Arrhenius>
-      </rateCoeff>
-      <reactants>N2O:1 O:1</reactants>
-      <products>N2:1 O2:1</products>
-    </reaction>
-
-    <!--   reaction 0005    -->
-    <reaction id="0005" reversible="yes">
-      <equation>N2O + O [=] 2 NO</equation>
-      <rateCoeff>
-        <Arrhenius>
-          <A units="cm3/mol/s">  2.900000E+13</A>
-          <b>0</b>
-          <E units="cal/mol">23150.000000</E>
-        </Arrhenius>
-      </rateCoeff>
-      <reactants>N2O:1 O:1</reactants>
-      <products>NO:2</products>
-    </reaction>
-
-    <!--   reaction 0006    -->
-    <reaction id="0006" reversible="yes" type="falloff">
-      <equation>N2O (+ M) [=] N2 + O (+ M)</equation>
-      <rateCoeff>
-        <Arrhenius>
-          <A units="/s">  7.910000E+10</A>
-          <b>0</b>
-          <E units="cal/mol">56020.000000</E>
-        </Arrhenius>
-        <Arrhenius name="k0">
-          <A units="cm3/mol/s">  6.370000E+14</A>
-          <b>0</b>
-          <E units="cal/mol">56640.000000</E>
-        </Arrhenius>
-        <efficiencies default="1.0"> AR:0.625 </efficiencies>
-        <falloff type="Lindemann"/>
-      </rateCoeff>
-      <reactants>N2O:1</reactants>
-      <products>N2:1 O:1</products>
-    </reaction>
-
-    <!--   reaction 0007    -->
-    <reaction id="0007" reversible="yes" type="threeBody">
-      <equation>NO + O + M [=] NO2 + M</equation>
-      <rateCoeff>
-        <Arrhenius>
-          <A units="cm6/mol2/s">  1.060000E+20</A>
-          <b>-1.4099999999999999</b>
-          <E units="cal/mol">0.000000</E>
-        </Arrhenius>
-        <efficiencies default="1.0"> AR:0.7 </efficiencies>
-      </rateCoeff>
-      <reactants>O:1 NO:1</reactants>
-      <products>NO2:1</products>
-    </reaction>
-
-    <!--   reaction 0008    -->
-    <reaction id="0008" reversible="yes">
-      <equation>NO2 + O [=] NO + O2</equation>
-      <rateCoeff>
-        <Arrhenius>
-          <A units="cm3/mol/s">  3.900000E+12</A>
-          <b>0</b>
-          <E units="cal/mol">-240.000000</E>
-        </Arrhenius>
-      </rateCoeff>
-      <reactants>O:1 NO2:1</reactants>
-      <products>O2:1 NO:1</products>
-    </reaction>
-  </reactionData>
-</ctml>

data/inputs/argon.cti

@@ -0,0 +1,45 @@
+#
+# Generated from file argon.inp
+# by ck2cti on Mon Aug 25 09:52:59 2003
+#
+# Transport data from file ../transport/gri30_tran.dat.
+
+units(length = "cm", time = "s", quantity = "mol", act_energy = "cal/mol")
+
+
+ideal_gas(name = "argon",
+      elements = " Ar ",
+      species = """ AR """,
+      reactions = "all",
+      transport = "Mix",
+      initial_state = state(temperature = 300.0,
+                        pressure = OneAtm)    )
+
+
+
+#-------------------------------------------------------------------------------
+#  Species data 
+#-------------------------------------------------------------------------------
+
+species(name = "AR",
+    atoms = " Ar:1 ",
+    thermo = (
+       NASA( [  300.00,  1000.00], [  2.500000000E+00,   0.000000000E+00, 
+                0.000000000E+00,   0.000000000E+00,   0.000000000E+00,
+               -7.453750000E+02,   4.366000000E+00] ),
+       NASA( [ 1000.00,  5000.00], [  2.500000000E+00,   0.000000000E+00, 
+                0.000000000E+00,   0.000000000E+00,   0.000000000E+00,
+               -7.453750000E+02,   4.366000000E+00] )
+             ),
+    transport = gas_transport(
+                     geom = "atom",
+                     diam =     3.33,
+                     well_depth =   136.50),
+    note = "120186"
+       )
+
+
+
+#-------------------------------------------------------------------------------
+#  Reaction data 
+#-------------------------------------------------------------------------------

data/inputs/argon.xml

@@ -1,47 +0,0 @@
-<ctml>
-  <validate reactions="yes" species="yes"/>
-
-  <!--    phase argon     -->
-  <phase dim="3" id="argon">
-    <validation>
-      <duplicateReactions>halt</duplicateReactions>
-      <thermo>warn</thermo>
-    </validation>
-    <elementArray datasrc="elements.xml"> Ar </elementArray>
-    <speciesArray datasrc="#species_data"> AR </speciesArray>
-    <reactionArray datasrc="#reaction_data"/>
-    <thermo model="IdealGas"/>
-    <kinetics model="GasKinetics"/>
-    <transport model="None"/>
-  </phase>
-
-  <!--     species definitions     -->
-  <speciesData id="species_data">
-
-    <!--    species AR    -->
-    <species name="AR">
-      <atomArray>Ar:1 </atomArray>
-      <thermo>
-        <NASA P0="100000.0" Tmax="1000.0" Tmin="300.0">
-          <floatArray name="coeffs" size="7">
-            2.500000000E+00,   0.000000000E+00,   0.000000000E+00,   0.000000000E+00, 
-            0.000000000E+00,  -7.453750000E+02,   4.366000000E+00,</floatArray>
-        </NASA>
-        <NASA P0="100000.0" Tmax="5000.0" Tmin="1000.0">
-          <floatArray name="coeffs" size="7">
-            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 model="gas_transport">
-        <string title="geometry">atom</string>
-        <LJ_welldepth units="K"> 136.500</LJ_welldepth>
-        <LJ_diameter units="A">   3.330</LJ_diameter>
-        <dipoleMoment units="Debye">   0.000</dipoleMoment>
-        <polarizability units="A3">   0.000</polarizability>
-        <rotRelax>   0.000</rotRelax>
-      </transport>
-    </species>
-  </speciesData>
-  <reactionData id="reaction_data"/>
-</ctml>

data/inputs/gri30.cti

@@ -1,27 +1,12 @@
 #
 # Generated from file gri30.inp
-# by ck2ct on Fri Aug  8 20:22:21 2003
+# by ck2cti on Mon Aug 25 09:52:57 2003
 #
-
 # Transport data from file ../transport/gri30_tran.dat.
 
-
-#-------------------------------------------------------------------------------
-#
-#  The default units. These will be used for dimensional quantities
-#  with unspecified units.
-#-------------------------------------------------------------------------------
 units(length = "cm", time = "s", quantity = "mol", act_energy = "cal/mol")
 
 
-
-
-#-------------------------------------------------------------------------------
-#
-#  The phase definition. This specifies an ideal gas mixture that
-#  includes all species and reactions defined in this file.
-#
-#-------------------------------------------------------------------------------
 ideal_gas(name = "gri30",
       elements = " O  H  C  N  Ar ",
       species = """ H2  H  O  O2  OH  H2O  HO2  H2O2  C  CH 
@@ -30,14 +15,44 @@ ideal_gas(name = "gri30",
                    N  NH  NH2  NH3  NNH  NO  NO2  N2O  HNO  CN 
                    HCN  H2CN  HCNN  HCNO  HOCN  HNCO  NCO  N2  AR  C3H7 
                    C3H8  CH2CHO  CH3CHO """,
-      reactions = "all"    )
+      reactions = "all",
+      kinetics = "GRI30",
+      initial_state = state(temperature = 300.0,
+                        pressure = OneAtm)    )
+
+ideal_gas(name = "gri30_mix",
+      elements = " O  H  C  N  Ar ",
+      species = """ H2  H  O  O2  OH  H2O  HO2  H2O2  C  CH 
+                   CH2  CH2(S)  CH3  CH4  CO  CO2  HCO  CH2O  CH2OH  CH3O 
+                   CH3OH  C2H  C2H2  C2H3  C2H4  C2H5  C2H6  HCCO  CH2CO  HCCOH 
+                   N  NH  NH2  NH3  NNH  NO  NO2  N2O  HNO  CN 
+                   HCN  H2CN  HCNN  HCNO  HOCN  HNCO  NCO  N2  AR  C3H7 
+                   C3H8  CH2CHO  CH3CHO """,
+      reactions = "all",
+      kinetics = "GRI30",
+      transport = "Mix",
+      initial_state = state(temperature = 300.0,
+                        pressure = OneAtm)    )
+
+
+ideal_gas(name = "gri30_multi",
+      elements = " O  H  C  N  Ar ",
+      species = """ H2  H  O  O2  OH  H2O  HO2  H2O2  C  CH 
+                   CH2  CH2(S)  CH3  CH4  CO  CO2  HCO  CH2O  CH2OH  CH3O 
+                   CH3OH  C2H  C2H2  C2H3  C2H4  C2H5  C2H6  HCCO  CH2CO  HCCOH 
+                   N  NH  NH2  NH3  NNH  NO  NO2  N2O  HNO  CN 
+                   HCN  H2CN  HCNN  HCNO  HOCN  HNCO  NCO  N2  AR  C3H7 
+                   C3H8  CH2CHO  CH3CHO """,
+      reactions = "all",
+      kinetics = "GRI30",
+      transport = "Multi",
+      initial_state = state(temperature = 300.0,
+                        pressure = OneAtm)    )
 
 
 
 #-------------------------------------------------------------------------------
-#
 #  Species data 
-#
 #-------------------------------------------------------------------------------
 
 species(name = "H2",
@@ -55,7 +70,8 @@ species(name = "H2",
                      diam =     2.92,
                      well_depth =    38.00,
                      polar =     0.79,
-                     rot_relax =   280.00)
+                     rot_relax =   280.00),
+    note = "TPIS78"
        )
 
 species(name = "H",
@@ -71,7 +87,8 @@ species(name = "H",
     transport = gas_transport(
                      geom = "atom",
                      diam =     2.05,
-                     well_depth =   145.00)
+                     well_depth =   145.00),
+    note = "L 7/88"
        )
 
 species(name = "O",
@@ -87,7 +104,8 @@ species(name = "O",
     transport = gas_transport(
                      geom = "atom",
                      diam =     2.75,
-                     well_depth =    80.00)
+                     well_depth =    80.00),
+    note = "L 1/90"
        )
 
 species(name = "O2",
@@ -105,7 +123,8 @@ species(name = "O2",
                      diam =     3.46,
                      well_depth =   107.40,
                      polar =     1.60,
-                     rot_relax =     3.80)
+                     rot_relax =     3.80),
+    note = "TPIS89"
        )
 
 species(name = "OH",
@@ -121,7 +140,8 @@ species(name = "OH",
     transport = gas_transport(
                      geom = "linear",
                      diam =     2.75,
-                     well_depth =    80.00)
+                     well_depth =    80.00),
+    note = "RUS 78"
        )
 
 species(name = "H2O",
@@ -139,7 +159,8 @@ species(name = "H2O",
                      diam =     2.60,
                      well_depth =   572.40,
                      dipole =     1.84,
-                     rot_relax =     4.00)
+                     rot_relax =     4.00),
+    note = "L 8/89"
        )
 
 species(name = "HO2",
@@ -156,7 +177,8 @@ species(name = "HO2",
                      geom = "nonlinear",
                      diam =     3.46,
                      well_depth =   107.40,
-                     rot_relax =     1.00)
+                     rot_relax =     1.00),
+    note = "L 5/89"
        )
 
 species(name = "H2O2",
@@ -173,7 +195,8 @@ species(name = "H2O2",
                      geom = "nonlinear",
                      diam =     3.46,
                      well_depth =   107.40,
-                     rot_relax =     3.80)
+                     rot_relax =     3.80),
+    note = "L 7/88"
        )
 
 species(name = "C",
@@ -189,7 +212,8 @@ species(name = "C",
     transport = gas_transport(
                      geom = "atom",
                      diam =     3.30,
-                     well_depth =    71.40)
+                     well_depth =    71.40),
+    note = "L11/88"
        )
 
 species(name = "CH",
@@ -205,7 +229,8 @@ species(name = "CH",
     transport = gas_transport(
                      geom = "linear",
                      diam =     2.75,
-                     well_depth =    80.00)
+                     well_depth =    80.00),
+    note = "TPIS79"
        )
 
 species(name = "CH2",
@@ -221,7 +246,8 @@ species(name = "CH2",
     transport = gas_transport(
                      geom = "linear",
                      diam =     3.80,
-                     well_depth =   144.00)
+                     well_depth =   144.00),
+    note = "L S/93"
        )
 
 species(name = "CH2(S)",
@@ -237,7 +263,8 @@ species(name = "CH2(S)",
     transport = gas_transport(
                      geom = "linear",
                      diam =     3.80,
-                     well_depth =   144.00)
+                     well_depth =   144.00),
+    note = "L S/93"
        )
 
 species(name = "CH3",
@@ -253,7 +280,8 @@ species(name = "CH3",
     transport = gas_transport(
                      geom = "linear",
                      diam =     3.80,
-                     well_depth =   144.00)
+                     well_depth =   144.00),
+    note = "L11/89"
        )
 
 species(name = "CH4",
@@ -271,7 +299,8 @@ species(name = "CH4",
                      diam =     3.75,
                      well_depth =   141.40,
                      polar =     2.60,
-                     rot_relax =    13.00)
+                     rot_relax =    13.00),
+    note = "L 8/88"
        )
 
 species(name = "CO",
@@ -289,7 +318,8 @@ species(name = "CO",
                      diam =     3.65,
                      well_depth =    98.10,
                      polar =     1.95,
-                     rot_relax =     1.80)
+                     rot_relax =     1.80),
+    note = "TPIS79"
        )
 
 species(name = "CO2",
@@ -307,7 +337,8 @@ species(name = "CO2",
                      diam =     3.76,
                      well_depth =   244.00,
                      polar =     2.65,
-                     rot_relax =     2.10)
+                     rot_relax =     2.10),
+    note = "L 7/88"
        )
 
 species(name = "HCO",
@@ -323,7 +354,8 @@ species(name = "HCO",
     transport = gas_transport(
                      geom = "nonlinear",
                      diam =     3.59,
-                     well_depth =   498.00)
+                     well_depth =   498.00),
+    note = "L12/89"
        )
 
 species(name = "CH2O",
@@ -340,7 +372,8 @@ species(name = "CH2O",
                      geom = "nonlinear",
                      diam =     3.59,
                      well_depth =   498.00,
-                     rot_relax =     2.00)
+                     rot_relax =     2.00),
+    note = "L 8/88"
        )
 
 species(name = "CH2OH",
@@ -358,7 +391,8 @@ species(name = "CH2OH",
                      diam =     3.69,
                      well_depth =   417.00,
                      dipole =     1.70,
-                     rot_relax =     2.00)
+                     rot_relax =     2.00),
+    note = "GUNL93"
        )
 
 species(name = "CH3O",
@@ -376,7 +410,8 @@ species(name = "CH3O",
                      diam =     3.69,
                      well_depth =   417.00,
                      dipole =     1.70,
-                     rot_relax =     2.00)
+                     rot_relax =     2.00),
+    note = "121686"
        )
 
 species(name = "CH3OH",
@@ -393,7 +428,8 @@ species(name = "CH3OH",
                      geom = "nonlinear",
                      diam =     3.63,
                      well_depth =   481.80,
-                     rot_relax =     1.00)
+                     rot_relax =     1.00),
+    note = "L 8/88"
        )
 
 species(name = "C2H",
@@ -410,7 +446,8 @@ species(name = "C2H",
                      geom = "linear",
                      diam =     4.10,
                      well_depth =   209.00,
-                     rot_relax =     2.50)
+                     rot_relax =     2.50),
+    note = "L 1/91"
        )
 
 species(name = "C2H2",
@@ -427,7 +464,8 @@ species(name = "C2H2",
                      geom = "linear",
                      diam =     4.10,
                      well_depth =   209.00,
-                     rot_relax =     2.50)
+                     rot_relax =     2.50),
+    note = "L 1/91"
        )
 
 species(name = "C2H3",
@@ -444,7 +482,8 @@ species(name = "C2H3",
                      geom = "nonlinear",
                      diam =     4.10,
                      well_depth =   209.00,
-                     rot_relax =     1.00)
+                     rot_relax =     1.00),
+    note = "L 2/92"
        )
 
 species(name = "C2H4",
@@ -461,7 +500,8 @@ species(name = "C2H4",
                      geom = "nonlinear",
                      diam =     3.97,
                      well_depth =   280.80,
-                     rot_relax =     1.50)
+                     rot_relax =     1.50),
+    note = "L 1/91"
        )
 
 species(name = "C2H5",
@@ -478,7 +518,8 @@ species(name = "C2H5",
                      geom = "nonlinear",
                      diam =     4.30,
                      well_depth =   252.30,
-                     rot_relax =     1.50)
+                     rot_relax =     1.50),
+    note = "L12/92"
        )
 
 species(name = "C2H6",
@@ -495,7 +536,8 @@ species(name = "C2H6",
                      geom = "nonlinear",
                      diam =     4.30,
                      well_depth =   252.30,
-                     rot_relax =     1.50)
+                     rot_relax =     1.50),
+    note = "L 8/88"
        )
 
 species(name = "HCCO",
@@ -512,7 +554,8 @@ species(name = "HCCO",
                      geom = "nonlinear",
                      diam =     2.50,
                      well_depth =   150.00,
-                     rot_relax =     1.00)
+                     rot_relax =     1.00),
+    note = "SRIC91"
        )
 
 species(name = "CH2CO",
@@ -529,7 +572,8 @@ species(name = "CH2CO",
                      geom = "nonlinear",
                      diam =     3.97,
                      well_depth =   436.00,
-                     rot_relax =     2.00)
+                     rot_relax =     2.00),
+    note = "L 5/90"
        )
 
 species(name = "HCCOH",
@@ -546,7 +590,8 @@ species(name = "HCCOH",
                      geom = "nonlinear",
                      diam =     3.97,
                      well_depth =   436.00,
-                     rot_relax =     2.00)
+                     rot_relax =     2.00),
+    note = "SRI91"
        )
 
 species(name = "N",
@@ -562,7 +607,8 @@ species(name = "N",
     transport = gas_transport(
                      geom = "atom",
                      diam =     3.30,
-                     well_depth =    71.40)
+                     well_depth =    71.40),
+    note = "L 6/88"
        )
 
 species(name = "NH",
@@ -579,7 +625,8 @@ species(name = "NH",
                      geom = "linear",
                      diam =     2.65,
                      well_depth =    80.00,
-                     rot_relax =     4.00)
+                     rot_relax =     4.00),
+    note = "And94"
        )
 
 species(name = "NH2",
@@ -597,7 +644,8 @@ species(name = "NH2",
                      diam =     2.65,
                      well_depth =    80.00,
                      polar =     2.26,
-                     rot_relax =     4.00)
+                     rot_relax =     4.00),
+    note = "And89"
        )
 
 species(name = "NH3",
@@ -615,7 +663,8 @@ species(name = "NH3",
                      diam =     2.92,
                      well_depth =   481.00,
                      dipole =     1.47,
-                     rot_relax =    10.00)
+                     rot_relax =    10.00),
+    note = "J 6/77"
        )
 
 species(name = "NNH",
@@ -632,7 +681,8 @@ species(name = "NNH",
                      geom = "nonlinear",
                      diam =     3.80,
                      well_depth =    71.40,
-                     rot_relax =     1.00)
+                     rot_relax =     1.00),
+    note = "T07/93"
        )
 
 species(name = "NO",
@@ -650,7 +700,8 @@ species(name = "NO",
                      diam =     3.62,
                      well_depth =    97.53,
                      polar =     1.76,
-                     rot_relax =     4.00)
+                     rot_relax =     4.00),
+    note = "RUS 78"
        )
 
 species(name = "NO2",
@@ -667,7 +718,8 @@ species(name = "NO2",
                      geom = "nonlinear",
                      diam =     3.50,
                      well_depth =   200.00,
-                     rot_relax =     1.00)
+                     rot_relax =     1.00),
+    note = "L 7/88"
        )
 
 species(name = "N2O",
@@ -684,7 +736,8 @@ species(name = "N2O",
                      geom = "linear",
                      diam =     3.83,
                      well_depth =   232.40,
-                     rot_relax =     1.00)
+                     rot_relax =     1.00),
+    note = "L 7/88"
        )
 
 species(name = "HNO",
@@ -701,7 +754,8 @@ species(name = "HNO",
                      geom = "nonlinear",
                      diam =     3.49,
                      well_depth =   116.70,
-                     rot_relax =     1.00)
+                     rot_relax =     1.00),
+    note = "And93"
        )
 
 species(name = "CN",
@@ -718,7 +772,8 @@ species(name = "CN",
                      geom = "linear",
                      diam =     3.86,
                      well_depth =    75.00,
-                     rot_relax =     1.00)
+                     rot_relax =     1.00),
+    note = "HBH92"
        )
 
 species(name = "HCN",
@@ -735,7 +790,8 @@ species(name = "HCN",
                      geom = "linear",
                      diam =     3.63,
                      well_depth =   569.00,
-                     rot_relax =     1.00)
+                     rot_relax =     1.00),
+    note = "GRI/98"
        )
 
 species(name = "H2CN",
@@ -752,7 +808,8 @@ species(name = "H2CN",
                      geom = "linear",
                      diam =     3.63,
                      well_depth =   569.00,
-                     rot_relax =     1.00)
+                     rot_relax =     1.00),
+    note = "41687"
        )
 
 species(name = "HCNN",
@@ -769,7 +826,8 @@ species(name = "HCNN",
                      geom = "nonlinear",
                      diam =     2.50,
                      well_depth =   150.00,
-                     rot_relax =     1.00)
+                     rot_relax =     1.00),
+    note = "SRI/94"
        )
 
 species(name = "HCNO",
@@ -786,7 +844,8 @@ species(name = "HCNO",
                      geom = "nonlinear",
                      diam =     3.83,
                      well_depth =   232.40,
-                     rot_relax =     1.00)
+                     rot_relax =     1.00),
+    note = "BDEA94"
        )
 
 species(name = "HOCN",
@@ -803,7 +862,8 @@ species(name = "HOCN",
                      geom = "nonlinear",
                      diam =     3.83,
                      well_depth =   232.40,
-                     rot_relax =     1.00)
+                     rot_relax =     1.00),
+    note = "BDEA94"
        )
 
 species(name = "HNCO",
@@ -820,7 +880,8 @@ species(name = "HNCO",
                      geom = "nonlinear",
                      diam =     3.83,
                      well_depth =   232.40,
-                     rot_relax =     1.00)
+                     rot_relax =     1.00),
+    note = "BDEA94"
        )
 
 species(name = "NCO",
@@ -837,7 +898,8 @@ species(name = "NCO",
                      geom = "linear",
                      diam =     3.83,
                      well_depth =   232.40,
-                     rot_relax =     1.00)
+                     rot_relax =     1.00),
+    note = "EA 93"
        )
 
 species(name = "N2",
@@ -855,7 +917,8 @@ species(name = "N2",
                      diam =     3.62,
                      well_depth =    97.53,
                      polar =     1.76,
-                     rot_relax =     4.00)
+                     rot_relax =     4.00),
+    note = "121286"
        )
 
 species(name = "AR",
@@ -871,7 +934,8 @@ species(name = "AR",
     transport = gas_transport(
                      geom = "atom",
                      diam =     3.33,
-                     well_depth =   136.50)
+                     well_depth =   136.50),
+    note = "120186"
        )
 
 species(name = "C3H7",
@@ -888,7 +952,8 @@ species(name = "C3H7",
                      geom = "nonlinear",
                      diam =     4.98,
                      well_depth =   266.80,
-                     rot_relax =     1.00)
+                     rot_relax =     1.00),
+    note = "L 9/84"
        )
 
 species(name = "C3H8",
@@ -905,7 +970,8 @@ species(name = "C3H8",
                      geom = "nonlinear",
                      diam =     4.98,
                      well_depth =   266.80,
-                     rot_relax =     1.00)
+                     rot_relax =     1.00),
+    note = "L 4/85"
        )
 
 species(name = "CH2CHO",
@@ -922,7 +988,8 @@ species(name = "CH2CHO",
                      geom = "nonlinear",
                      diam =     3.97,
                      well_depth =   436.00,
-                     rot_relax =     2.00)
+                     rot_relax =     2.00),
+    note = "SAND86"
        )
 
 species(name = "CH3CHO",
@@ -939,15 +1006,14 @@ species(name = "CH3CHO",
                      geom = "nonlinear",
                      diam =     3.97,
                      well_depth =   436.00,
-                     rot_relax =     2.00)
+                     rot_relax =     2.00),
+    note = "L 8/88"
        )
 
 
 
 #-------------------------------------------------------------------------------
-#
 #  Reaction data 
-#
 #-------------------------------------------------------------------------------
 
 #  Reaction 1
@@ -1273,13 +1339,16 @@ falloff_reaction( "2 OH (+ M) <=> H2O2 (+ M)",
 reaction( "2 OH <=> O + H2O",   [3.57000E+04, 2.4, -2110])
 
 #  Reaction 87
-reaction( "OH + HO2 <=> O2 + H2O",   [1.45000E+13, 0, -500])
+reaction( "OH + HO2 <=> O2 + H2O",   [1.45000E+13, 0, -500],
+         options = 'duplicate')
 
 #  Reaction 88
-reaction( "OH + H2O2 <=> HO2 + H2O",   [2.00000E+12, 0, 427])
+reaction( "OH + H2O2 <=> HO2 + H2O",   [2.00000E+12, 0, 427],
+         options = 'duplicate')
 
 #  Reaction 89
-reaction( "OH + H2O2 <=> HO2 + H2O",   [1.70000E+18, 0, 29410])
+reaction( "OH + H2O2 <=> HO2 + H2O",   [1.70000E+18, 0, 29410],
+         options = 'duplicate')
 
 #  Reaction 90
 reaction( "OH + C <=> H + CO",   [5.00000E+13, 0, 0])
@@ -1361,10 +1430,12 @@ reaction( "OH + C2H6 <=> C2H5 + H2O",   [3.54000E+06, 2.12, 870])
 reaction( "OH + CH2CO <=> HCCO + H2O",   [7.50000E+12, 0, 2000])
 
 #  Reaction 115
-reaction( "2 HO2 <=> O2 + H2O2",   [1.30000E+11, 0, -1630])
+reaction( "2 HO2 <=> O2 + H2O2",   [1.30000E+11, 0, -1630],
+         options = 'duplicate')
 
 #  Reaction 116
-reaction( "2 HO2 <=> O2 + H2O2",   [4.20000E+14, 0, 12000])
+reaction( "2 HO2 <=> O2 + H2O2",   [4.20000E+14, 0, 12000],
+         options = 'duplicate')
 
 #  Reaction 117
 reaction( "HO2 + CH2 <=> OH + CH2O",   [2.00000E+13, 0, 0])
@@ -1914,7 +1985,8 @@ reaction( "O + C2H4 <=> H + CH2CHO",   [6.70000E+06, 1.83, 220])
 reaction( "O + C2H5 <=> H + CH3CHO",   [1.09600E+14, 0, 0])
 
 #  Reaction 287
-reaction( "OH + HO2 <=> O2 + H2O",   [5.00000E+15, 0, 17330])
+reaction( "OH + HO2 <=> O2 + H2O",   [5.00000E+15, 0, 17330],
+         options = 'duplicate')
 
 #  Reaction 288
 reaction( "OH + CH3 => H2 + CH2O",   [8.00000E+09, 0.5, -1755])

data/inputs/h2o2.cti

@@ -0,0 +1,284 @@
+#
+# Generated from file h2o2.inp
+# by ck2cti on Mon Aug 25 09:52:58 2003
+#
+# Transport data from file ../transport/gri30_tran.dat.
+
+units(length = "cm", time = "s", quantity = "mol", act_energy = "cal/mol")
+
+
+ideal_gas(name = "ohmech",
+      elements = " O  H  Ar ",
+      species = """ H2  H  O  O2  OH  H2O  HO2  H2O2  AR """,
+      reactions = "all",
+      transport = "Mix",
+      initial_state = state(temperature = 300.0,
+                        pressure = OneAtm)    )
+
+
+
+#-------------------------------------------------------------------------------
+#  Species data 
+#-------------------------------------------------------------------------------
+
+species(name = "H2",
+    atoms = " H:2 ",
+    thermo = (
+       NASA( [  200.00,  1000.00], [  2.344331120E+00,   7.980520750E-03, 
+               -1.947815100E-05,   2.015720940E-08,  -7.376117610E-12,
+               -9.179351730E+02,   6.830102380E-01] ),
+       NASA( [ 1000.00,  3500.00], [  3.337279200E+00,  -4.940247310E-05, 
+                4.994567780E-07,  -1.795663940E-10,   2.002553760E-14,
+               -9.501589220E+02,  -3.205023310E+00] )
+             ),
+    transport = gas_transport(
+                     geom = "linear",
+                     diam =     2.92,
+                     well_depth =    38.00,
+                     polar =     0.79,
+                     rot_relax =   280.00),
+    note = "TPIS78"
+       )
+
+species(name = "H",
+    atoms = " H:1 ",
+    thermo = (
+       NASA( [  200.00,  1000.00], [  2.500000000E+00,   7.053328190E-13, 
+               -1.995919640E-15,   2.300816320E-18,  -9.277323320E-22,
+                2.547365990E+04,  -4.466828530E-01] ),
+       NASA( [ 1000.00,  3500.00], [  2.500000010E+00,  -2.308429730E-11, 
+                1.615619480E-14,  -4.735152350E-18,   4.981973570E-22,
+                2.547365990E+04,  -4.466829140E-01] )
+             ),
+    transport = gas_transport(
+                     geom = "atom",
+                     diam =     2.05,
+                     well_depth =   145.00),
+    note = "L 7/88"
+       )
+
+species(name = "O",
+    atoms = " O:1 ",
+    thermo = (
+       NASA( [  200.00,  1000.00], [  3.168267100E+00,  -3.279318840E-03, 
+                6.643063960E-06,  -6.128066240E-09,   2.112659710E-12,
+                2.912225920E+04,   2.051933460E+00] ),
+       NASA( [ 1000.00,  3500.00], [  2.569420780E+00,  -8.597411370E-05, 
+                4.194845890E-08,  -1.001777990E-11,   1.228336910E-15,
+                2.921757910E+04,   4.784338640E+00] )
+             ),
+    transport = gas_transport(
+                     geom = "atom",
+                     diam =     2.75,
+                     well_depth =    80.00),
+    note = "L 1/90"
+       )
+
+species(name = "O2",
+    atoms = " O:2 ",
+    thermo = (
+       NASA( [  200.00,  1000.00], [  3.782456360E+00,  -2.996734160E-03, 
+                9.847302010E-06,  -9.681295090E-09,   3.243728370E-12,
+               -1.063943560E+03,   3.657675730E+00] ),
+       NASA( [ 1000.00,  3500.00], [  3.282537840E+00,   1.483087540E-03, 
+               -7.579666690E-07,   2.094705550E-10,  -2.167177940E-14,
+               -1.088457720E+03,   5.453231290E+00] )
+             ),
+    transport = gas_transport(
+                     geom = "linear",
+                     diam =     3.46,
+                     well_depth =   107.40,
+                     polar =     1.60,
+                     rot_relax =     3.80),
+    note = "TPIS89"
+       )
+
+species(name = "OH",
+    atoms = " O:1  H:1 ",
+    thermo = (
+       NASA( [  200.00,  1000.00], [  3.992015430E+00,  -2.401317520E-03, 
+                4.617938410E-06,  -3.881133330E-09,   1.364114700E-12,
+                3.615080560E+03,  -1.039254580E-01] ),
+       NASA( [ 1000.00,  3500.00], [  3.092887670E+00,   5.484297160E-04, 
+                1.265052280E-07,  -8.794615560E-11,   1.174123760E-14,
+                3.858657000E+03,   4.476696100E+00] )
+             ),
+    transport = gas_transport(
+                     geom = "linear",
+                     diam =     2.75,
+                     well_depth =    80.00),
+    note = "RUS 78"
+       )
+
+species(name = "H2O",
+    atoms = " H:2  O:1 ",
+    thermo = (
+       NASA( [  200.00,  1000.00], [  4.198640560E+00,  -2.036434100E-03, 
+                6.520402110E-06,  -5.487970620E-09,   1.771978170E-12,
+               -3.029372670E+04,  -8.490322080E-01] ),
+       NASA( [ 1000.00,  3500.00], [  3.033992490E+00,   2.176918040E-03, 
+               -1.640725180E-07,  -9.704198700E-11,   1.682009920E-14,
+               -3.000429710E+04,   4.966770100E+00] )
+             ),
+    transport = gas_transport(
+                     geom = "nonlinear",
+                     diam =     2.60,
+                     well_depth =   572.40,
+                     dipole =     1.84,
+                     rot_relax =     4.00),
+    note = "L 8/89"
+       )
+
+species(name = "HO2",
+    atoms = " H:1  O:2 ",
+    thermo = (
+       NASA( [  200.00,  1000.00], [  4.301798010E+00,  -4.749120510E-03, 
+                2.115828910E-05,  -2.427638940E-08,   9.292251240E-12,
+                2.948080400E+02,   3.716662450E+00] ),
+       NASA( [ 1000.00,  3500.00], [  4.017210900E+00,   2.239820130E-03, 
+               -6.336581500E-07,   1.142463700E-10,  -1.079085350E-14,
+                1.118567130E+02,   3.785102150E+00] )
+             ),
+    transport = gas_transport(
+                     geom = "nonlinear",
+                     diam =     3.46,
+                     well_depth =   107.40,
+                     rot_relax =     1.00),
+    note = "L 5/89"
+       )
+
+species(name = "H2O2",
+    atoms = " H:2  O:2 ",
+    thermo = (
+       NASA( [  200.00,  1000.00], [  4.276112690E+00,  -5.428224170E-04, 
+                1.673357010E-05,  -2.157708130E-08,   8.624543630E-12,
+               -1.770258210E+04,   3.435050740E+00] ),
+       NASA( [ 1000.00,  3500.00], [  4.165002850E+00,   4.908316940E-03, 
+               -1.901392250E-06,   3.711859860E-10,  -2.879083050E-14,
+               -1.786178770E+04,   2.916156620E+00] )
+             ),
+    transport = gas_transport(
+                     geom = "nonlinear",
+                     diam =     3.46,
+                     well_depth =   107.40,
+                     rot_relax =     3.80),
+    note = "L 7/88"
+       )
+
+species(name = "AR",
+    atoms = " Ar:1 ",
+    thermo = (
+       NASA( [  300.00,  1000.00], [  2.500000000E+00,   0.000000000E+00, 
+                0.000000000E+00,   0.000000000E+00,   0.000000000E+00,
+               -7.453750000E+02,   4.366000000E+00] ),
+       NASA( [ 1000.00,  5000.00], [  2.500000000E+00,   0.000000000E+00, 
+                0.000000000E+00,   0.000000000E+00,   0.000000000E+00,
+               -7.453750000E+02,   4.366000000E+00] )
+             ),
+    transport = gas_transport(
+                     geom = "atom",
+                     diam =     3.33,
+                     well_depth =   136.50),
+    note = "120186"
+       )
+
+
+
+#-------------------------------------------------------------------------------
+#  Reaction data 
+#-------------------------------------------------------------------------------
+
+#  Reaction 1
+three_body_reaction( "2 O + M <=> O2 + M",   [1.20000E+17, -1, 0],
+         efficiencies = " AR:0.83  H2:2.4  H2O:15.4 ")
+
+#  Reaction 2
+three_body_reaction( "O + H + M <=> OH + M",   [5.00000E+17, -1, 0],
+         efficiencies = " AR:0.7  H2:2  H2O:6 ")
+
+#  Reaction 3
+reaction( "O + H2 <=> H + OH",   [3.87000E+04, 2.7, 6260])
+
+#  Reaction 4
+reaction( "O + HO2 <=> OH + O2",   [2.00000E+13, 0, 0])
+
+#  Reaction 5
+reaction( "O + H2O2 <=> OH + HO2",   [9.63000E+06, 2, 4000])
+
+#  Reaction 6
+reaction( "H + 2 O2 <=> HO2 + O2",   [2.08000E+19, -1.24, 0])
+
+#  Reaction 7
+reaction( "H + O2 + H2O <=> HO2 + H2O",   [1.12600E+19, -0.76, 0])
+
+#  Reaction 8
+reaction( "H + O2 + AR <=> HO2 + AR",   [7.00000E+17, -0.8, 0])
+
+#  Reaction 9
+reaction( "H + O2 <=> O + OH",   [2.65000E+16, -0.6707, 17041])
+
+#  Reaction 10
+three_body_reaction( "2 H + M <=> H2 + M",   [1.00000E+18, -1, 0],
+         efficiencies = " AR:0.63  H2:0  H2O:0 ")
+
+#  Reaction 11
+reaction( "2 H + H2 <=> 2 H2",   [9.00000E+16, -0.6, 0])
+
+#  Reaction 12
+reaction( "2 H + H2O <=> H2 + H2O",   [6.00000E+19, -1.25, 0])
+
+#  Reaction 13
+three_body_reaction( "H + OH + M <=> H2O + M",   [2.20000E+22, -2, 0],
+         efficiencies = " AR:0.38  H2:0.73  H2O:3.65 ")
+
+#  Reaction 14
+reaction( "H + HO2 <=> O + H2O",   [3.97000E+12, 0, 671])
+
+#  Reaction 15
+reaction( "H + HO2 <=> O2 + H2",   [4.48000E+13, 0, 1068])
+
+#  Reaction 16
+reaction( "H + HO2 <=> 2 OH",   [8.40000E+13, 0, 635])
+
+#  Reaction 17
+reaction( "H + H2O2 <=> HO2 + H2",   [1.21000E+07, 2, 5200])
+
+#  Reaction 18
+reaction( "H + H2O2 <=> OH + H2O",   [1.00000E+13, 0, 3600])
+
+#  Reaction 19
+reaction( "OH + H2 <=> H + H2O",   [2.16000E+08, 1.51, 3430])
+
+#  Reaction 20
+falloff_reaction( "2 OH (+ M) <=> H2O2 (+ M)", 
+         kf = [7.40000E+13, -0.37, 0],
+         kf0   = [2.30000E+18, -0.9, -1700],
+         falloff = Troe(A = 0.7346, T3 = 94, T1 = 1756, T2 = 5182),
+         efficiencies = " AR:0.7  H2:2  H2O:6 ")
+
+#  Reaction 21
+reaction( "2 OH <=> O + H2O",   [3.57000E+04, 2.4, -2110])
+
+#  Reaction 22
+reaction( "OH + HO2 <=> O2 + H2O",   [1.45000E+13, 0, -500],
+         options = 'duplicate')
+
+#  Reaction 23
+reaction( "OH + H2O2 <=> HO2 + H2O",   [2.00000E+12, 0, 427],
+         options = 'duplicate')
+
+#  Reaction 24
+reaction( "OH + H2O2 <=> HO2 + H2O",   [1.70000E+18, 0, 29410],
+         options = 'duplicate')
+
+#  Reaction 25
+reaction( "2 HO2 <=> O2 + H2O2",   [1.30000E+11, 0, -1630],
+         options = 'duplicate')
+
+#  Reaction 26
+reaction( "2 HO2 <=> O2 + H2O2",   [4.20000E+14, 0, 12000],
+         options = 'duplicate')
+
+#  Reaction 27
+reaction( "OH + HO2 <=> O2 + H2O",   [5.00000E+15, 0, 17330],
+         options = 'duplicate')

data/inputs/h2o2.xml

@@ -1,637 +0,0 @@
-<ctml>
-  <validate reactions="yes" species="yes"/>
-
-  <!--    phase ohmech     -->
-  <phase dim="3" id="ohmech">
-    <validation>
-      <duplicateReactions>halt</duplicateReactions>
-      <thermo>warn</thermo>
-    </validation>
-    <elementArray datasrc="elements.xml"> O  H  Ar </elementArray>
-    <speciesArray datasrc="#species_data"> H2  H  O  O2  OH  H2O  HO2  H2O2  AR </speciesArray>
-    <reactionArray datasrc="#reaction_data"/>
-    <thermo model="IdealGas"/>
-    <kinetics model="GasKinetics"/>
-    <transport model="None"/>
-  </phase>
-
-  <!--     species definitions     -->
-  <speciesData id="species_data">
-
-    <!--    species H2    -->
-    <species name="H2">
-      <atomArray>H:2 </atomArray>
-      <thermo>
-        <NASA P0="100000.0" Tmax="1000.0" Tmin="200.0">
-          <floatArray name="coeffs" size="7">
-            2.344331120E+00,   7.980520750E-03,  -1.947815100E-05,   2.015720940E-08, 
-           -7.376117610E-12,  -9.179351730E+02,   6.830102380E-01,</floatArray>
-        </NASA>
-        <NASA P0="100000.0" Tmax="3500.0" Tmin="1000.0">
-          <floatArray name="coeffs" size="7">
-            3.337279200E+00,  -4.940247310E-05,   4.994567780E-07,  -1.795663940E-10, 
-            2.002553760E-14,  -9.501589220E+02,  -3.205023310E+00,</floatArray>
-        </NASA>
-      </thermo>
-      <transport model="gas_transport">
-        <string title="geometry">linear</string>
-        <LJ_welldepth units="K">  38.000</LJ_welldepth>
-        <LJ_diameter units="A">   2.920</LJ_diameter>
-        <dipoleMoment units="Debye">   0.000</dipoleMoment>
-        <polarizability units="A3">   0.790</polarizability>
-        <rotRelax> 280.000</rotRelax>
-      </transport>
-    </species>
-
-    <!--    species H    -->
-    <species name="H">
-      <atomArray>H:1 </atomArray>
-      <thermo>
-        <NASA P0="100000.0" Tmax="1000.0" Tmin="200.0">
-          <floatArray name="coeffs" size="7">
-            2.500000000E+00,   7.053328190E-13,  -1.995919640E-15,   2.300816320E-18, 
-           -9.277323320E-22,   2.547365990E+04,  -4.466828530E-01,</floatArray>
-        </NASA>
-        <NASA P0="100000.0" Tmax="3500.0" Tmin="1000.0">
-          <floatArray name="coeffs" size="7">
-            2.500000010E+00,  -2.308429730E-11,   1.615619480E-14,  -4.735152350E-18, 
-            4.981973570E-22,   2.547365990E+04,  -4.466829140E-01,</floatArray>
-        </NASA>
-      </thermo>
-      <transport model="gas_transport">
-        <string title="geometry">atom</string>
-        <LJ_welldepth units="K"> 145.000</LJ_welldepth>
-        <LJ_diameter units="A">   2.050</LJ_diameter>
-        <dipoleMoment units="Debye">   0.000</dipoleMoment>
-        <polarizability units="A3">   0.000</polarizability>
-        <rotRelax>   0.000</rotRelax>
-      </transport>
-    </species>
-
-    <!--    species O    -->
-    <species name="O">
-      <atomArray>O:1 </atomArray>
-      <thermo>
-        <NASA P0="100000.0" Tmax="1000.0" Tmin="200.0">
-          <floatArray name="coeffs" size="7">
-            3.168267100E+00,  -3.279318840E-03,   6.643063960E-06,  -6.128066240E-09, 
-            2.112659710E-12,   2.912225920E+04,   2.051933460E+00,</floatArray>
-        </NASA>
-        <NASA P0="100000.0" Tmax="3500.0" Tmin="1000.0">
-          <floatArray name="coeffs" size="7">
-            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 model="gas_transport">
-        <string title="geometry">atom</string>
-        <LJ_welldepth units="K">  80.000</LJ_welldepth>
-        <LJ_diameter units="A">   2.750</LJ_diameter>
-        <dipoleMoment units="Debye">   0.000</dipoleMoment>
-        <polarizability units="A3">   0.000</polarizability>
-        <rotRelax>   0.000</rotRelax>
-      </transport>
-    </species>
-
-    <!--    species O2    -->
-    <species name="O2">
-      <atomArray>O:2 </atomArray>
-      <thermo>
-        <NASA P0="100000.0" Tmax="1000.0" Tmin="200.0">
-          <floatArray name="coeffs" size="7">
-            3.782456360E+00,  -2.996734160E-03,   9.847302010E-06,  -9.681295090E-09, 
-            3.243728370E-12,  -1.063943560E+03,   3.657675730E+00,</floatArray>
-        </NASA>
-        <NASA P0="100000.0" Tmax="3500.0" Tmin="1000.0">
-          <floatArray name="coeffs" size="7">
-            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 model="gas_transport">
-        <string title="geometry">linear</string>
-        <LJ_welldepth units="K"> 107.400</LJ_welldepth>
-        <LJ_diameter units="A">   3.460</LJ_diameter>
-        <dipoleMoment units="Debye">   0.000</dipoleMoment>
-        <polarizability units="A3">   1.600</polarizability>
-        <rotRelax>   3.800</rotRelax>
-      </transport>
-    </species>
-
-    <!--    species OH    -->
-    <species name="OH">
-      <atomArray>H:1 O:1 </atomArray>
-      <thermo>
-        <NASA P0="100000.0" Tmax="1000.0" Tmin="200.0">
-          <floatArray name="coeffs" size="7">
-            3.992015430E+00,  -2.401317520E-03,   4.617938410E-06,  -3.881133330E-09, 
-            1.364114700E-12,   3.615080560E+03,  -1.039254580E-01,</floatArray>
-        </NASA>
-        <NASA P0="100000.0" Tmax="3500.0" Tmin="1000.0">
-          <floatArray name="coeffs" size="7">
-            3.092887670E+00,   5.484297160E-04,   1.265052280E-07,  -8.794615560E-11, 
-            1.174123760E-14,   3.858657000E+03,   4.476696100E+00,</floatArray>
-        </NASA>
-      </thermo>
-      <transport model="gas_transport">
-        <string title="geometry">linear</string>
-        <LJ_welldepth units="K">  80.000</LJ_welldepth>
-        <LJ_diameter units="A">   2.750</LJ_diameter>
-        <dipoleMoment units="Debye">   0.000</dipoleMoment>
-        <polarizability units="A3">   0.000</polarizability>
-        <rotRelax>   0.000</rotRelax>
-      </transport>
-    </species>
-
-    <!--    species H2O    -->
-    <species name="H2O">
-      <atomArray>H:2 O:1 </atomArray>
-      <thermo>
-        <NASA P0="100000.0" Tmax="1000.0" Tmin="200.0">
-          <floatArray name="coeffs" size="7">
-            4.198640560E+00,  -2.036434100E-03,   6.520402110E-06,  -5.487970620E-09, 
-            1.771978170E-12,  -3.029372670E+04,  -8.490322080E-01,</floatArray>
-        </NASA>
-        <NASA P0="100000.0" Tmax="3500.0" Tmin="1000.0">
-          <floatArray name="coeffs" size="7">
-            3.033992490E+00,   2.176918040E-03,  -1.640725180E-07,  -9.704198700E-11, 
-            1.682009920E-14,  -3.000429710E+04,   4.966770100E+00,</floatArray>
-        </NASA>
-      </thermo>
-      <transport model="gas_transport">
-        <string title="geometry">nonlinear</string>
-        <LJ_welldepth units="K"> 572.400</LJ_welldepth>
-        <LJ_diameter units="A">   2.600</LJ_diameter>
-        <dipoleMoment units="Debye">   1.840</dipoleMoment>
-        <polarizability units="A3">   0.000</polarizability>
-        <rotRelax>   4.000</rotRelax>
-      </transport>
-    </species>
-
-    <!--    species HO2    -->
-    <species name="HO2">
-      <atomArray>H:1 O:2 </atomArray>
-      <thermo>
-        <NASA P0="100000.0" Tmax="1000.0" Tmin="200.0">
-          <floatArray name="coeffs" size="7">
-            4.301798010E+00,  -4.749120510E-03,   2.115828910E-05,  -2.427638940E-08, 
-            9.292251240E-12,   2.948080400E+02,   3.716662450E+00,</floatArray>
-        </NASA>
-        <NASA P0="100000.0" Tmax="3500.0" Tmin="1000.0">
-          <floatArray name="coeffs" size="7">
-            4.017210900E+00,   2.239820130E-03,  -6.336581500E-07,   1.142463700E-10, 
-           -1.079085350E-14,   1.118567130E+02,   3.785102150E+00,</floatArray>
-        </NASA>
-      </thermo>
-      <transport model="gas_transport">
-        <string title="geometry">nonlinear</string>
-        <LJ_welldepth units="K"> 107.400</LJ_welldepth>
-        <LJ_diameter units="A">   3.460</LJ_diameter>
-        <dipoleMoment units="Debye">   0.000</dipoleMoment>
-        <polarizability units="A3">   0.000</polarizability>
-        <rotRelax>   1.000</rotRelax>
-      </transport>
-    </species>
-
-    <!--    species H2O2    -->
-    <species name="H2O2">
-      <atomArray>H:2 O:2 </atomArray>
-      <thermo>
-        <NASA P0="100000.0" Tmax="1000.0" Tmin="200.0">
-          <floatArray name="coeffs" size="7">
-            4.276112690E+00,  -5.428224170E-04,   1.673357010E-05,  -2.157708130E-08, 
-            8.624543630E-12,  -1.770258210E+04,   3.435050740E+00,</floatArray>
-        </NASA>
-        <NASA P0="100000.0" Tmax="3500.0" Tmin="1000.0">
-          <floatArray name="coeffs" size="7">
-            4.165002850E+00,   4.908316940E-03,  -1.901392250E-06,   3.711859860E-10, 
-           -2.879083050E-14,  -1.786178770E+04,   2.916156620E+00,</floatArray>
-        </NASA>
-      </thermo>
-      <transport model="gas_transport">
-        <string title="geometry">nonlinear</string>
-        <LJ_welldepth units="K"> 107.400</LJ_welldepth>
-        <LJ_diameter units="A">   3.460</LJ_diameter>
-        <dipoleMoment units="Debye">   0.000</dipoleMoment>
-        <polarizability units="A3">   0.000</polarizability>
-        <rotRelax>   3.800</rotRelax>
-      </transport>
-    </species>
-
-    <!--    species AR    -->
-    <species name="AR">
-      <atomArray>Ar:1 </atomArray>
-      <thermo>
-        <NASA P0="100000.0" Tmax="1000.0" Tmin="300.0">
-          <floatArray name="coeffs" size="7">
-            2.500000000E+00,   0.000000000E+00,   0.000000000E+00,   0.000000000E+00, 
-            0.000000000E+00,  -7.453750000E+02,   4.366000000E+00,</floatArray>
-        </NASA>
-        <NASA P0="100000.0" Tmax="5000.0" Tmin="1000.0">
-          <floatArray name="coeffs" size="7">
-            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 model="gas_transport">
-        <string title="geometry">atom</string>
-        <LJ_welldepth units="K"> 136.500</LJ_welldepth>
-        <LJ_diameter units="A">   3.330</LJ_diameter>
-        <dipoleMoment units="Debye">   0.000</dipoleMoment>
-        <polarizability units="A3">   0.000</polarizability>
-        <rotRelax>   0.000</rotRelax>
-      </transport>
-    </species>
-  </speciesData>
-  <reactionData id="reaction_data">
-
-    <!--   reaction 0001    -->
-    <reaction id="0001" reversible="yes" type="threeBody">
-      <equation>2 O + M [=] O2 + M</equation>
-      <rateCoeff>
-        <Arrhenius>
-          <A units="cm6/mol2/s">  1.200000E+17</A>
-          <b>-1</b>
-          <E units="cal/mol">0.000000</E>
-        </Arrhenius>
-        <efficiencies default="1.0"> AR:0.83  H2:2.4  H2O:15.4 </efficiencies>
-      </rateCoeff>
-      <reactants>O:2</reactants>
-      <products>O2:1</products>
-    </reaction>
-
-    <!--   reaction 0002    -->
-    <reaction id="0002" reversible="yes" type="threeBody">
-      <equation>O + H + M [=] OH + M</equation>
-      <rateCoeff>
-        <Arrhenius>
-          <A units="cm6/mol2/s">  5.000000E+17</A>
-          <b>-1</b>
-          <E units="cal/mol">0.000000</E>
-        </Arrhenius>
-        <efficiencies default="1.0"> AR:0.7  H2:2  H2O:6 </efficiencies>
-      </rateCoeff>
-      <reactants>H:1 O:1</reactants>
-      <products>OH:1</products>
-    </reaction>
-
-    <!--   reaction 0003    -->
-    <reaction id="0003" reversible="yes">
-      <equation>O + H2 [=] H + OH</equation>
-      <rateCoeff>
-        <Arrhenius>
-          <A units="cm3/mol/s">  3.870000E+04</A>
-          <b>2.7000000000000002</b>
-          <E units="cal/mol">6260.000000</E>
-        </Arrhenius>
-      </rateCoeff>
-      <reactants>H2:1 O:1</reactants>
-      <products>H:1 OH:1</products>
-    </reaction>
-
-    <!--   reaction 0004    -->
-    <reaction id="0004" reversible="yes">
-      <equation>O + HO2 [=] OH + O2</equation>
-      <rateCoeff>
-        <Arrhenius>
-          <A units="cm3/mol/s">  2.000000E+13</A>
-          <b>0</b>
-          <E units="cal/mol">0.000000</E>
-        </Arrhenius>
-      </rateCoeff>
-      <reactants>HO2:1 O:1</reactants>
-      <products>O2:1 OH:1</products>
-    </reaction>
-
-    <!--   reaction 0005    -->
-    <reaction id="0005" reversible="yes">
-      <equation>O + H2O2 [=] OH + HO2</equation>
-      <rateCoeff>
-        <Arrhenius>
-          <A units="cm3/mol/s">  9.630000E+06</A>
-          <b>2</b>
-          <E units="cal/mol">4000.000000</E>
-        </Arrhenius>
-      </rateCoeff>
-      <reactants>H2O2:1 O:1</reactants>
-      <products>HO2:1 OH:1</products>
-    </reaction>
-
-    <!--   reaction 0006    -->
-    <reaction id="0006" reversible="yes">
-      <equation>H + 2 O2 [=] HO2 + O2</equation>
-      <rateCoeff>
-        <Arrhenius>
-          <A units="cm6/mol2/s">  2.080000E+19</A>
-          <b>-1.24</b>
-          <E units="cal/mol">0.000000</E>
-        </Arrhenius>
-      </rateCoeff>
-      <reactants>H:1 O2:2</reactants>
-      <products>HO2:1 O2:1</products>
-    </reaction>
-
-    <!--   reaction 0007    -->
-    <reaction id="0007" reversible="yes">
-      <equation>H + O2 + H2O [=] HO2 + H2O</equation>
-      <rateCoeff>
-        <Arrhenius>
-          <A units="cm6/mol2/s">  1.126000E+19</A>
-          <b>-0.76000000000000001</b>
-          <E units="cal/mol">0.000000</E>
-        </Arrhenius>
-      </rateCoeff>
-      <reactants>H:1 H2O:1 O2:1</reactants>
-      <products>H2O:1 HO2:1</products>
-    </reaction>
-
-    <!--   reaction 0008    -->
-    <reaction id="0008" reversible="yes">
-      <equation>H + O2 + AR [=] HO2 + AR</equation>
-      <rateCoeff>
-        <Arrhenius>
-          <A units="cm6/mol2/s">  7.000000E+17</A>
-          <b>-0.80000000000000004</b>
-          <E units="cal/mol">0.000000</E>
-        </Arrhenius>
-      </rateCoeff>
-      <reactants>H:1 AR:1 O2:1</reactants>
-      <products>AR:1 HO2:1</products>
-    </reaction>
-
-    <!--   reaction 0009    -->
-    <reaction id="0009" reversible="yes">
-      <equation>H + O2 [=] O + OH</equation>
-      <rateCoeff>
-        <Arrhenius>
-          <A units="cm3/mol/s">  2.650000E+16</A>
-          <b>-0.67069999999999996</b>
-          <E units="cal/mol">17041.000000</E>
-        </Arrhenius>
-      </rateCoeff>
-      <reactants>H:1 O2:1</reactants>
-      <products>O:1 OH:1</products>
-    </reaction>
-
-    <!--   reaction 0010    -->
-    <reaction id="0010" reversible="yes" type="threeBody">
-      <equation>2 H + M [=] H2 + M</equation>
-      <rateCoeff>
-        <Arrhenius>
-          <A units="cm6/mol2/s">  1.000000E+18</A>
-          <b>-1</b>
-          <E units="cal/mol">0.000000</E>
-        </Arrhenius>
-        <efficiencies default="1.0"> AR:0.63  H2:0  H2O:0 </efficiencies>
-      </rateCoeff>
-      <reactants>H:2</reactants>
-      <products>H2:1</products>
-    </reaction>
-
-    <!--   reaction 0011    -->
-    <reaction id="0011" reversible="yes">
-      <equation>2 H + H2 [=] 2 H2</equation>
-      <rateCoeff>
-        <Arrhenius>
-          <A units="cm6/mol2/s">  9.000000E+16</A>
-          <b>-0.59999999999999998</b>
-          <E units="cal/mol">0.000000</E>
-        </Arrhenius>
-      </rateCoeff>
-      <reactants>H2:1 H:2</reactants>
-      <products>H2:2</products>
-    </reaction>
-
-    <!--   reaction 0012    -->
-    <reaction id="0012" reversible="yes">
-      <equation>2 H + H2O [=] H2 + H2O</equation>
-      <rateCoeff>
-        <Arrhenius>
-          <A units="cm6/mol2/s">  6.000000E+19</A>
-          <b>-1.25</b>
-          <E units="cal/mol">0.000000</E>
-        </Arrhenius>
-      </rateCoeff>
-      <reactants>H:2 H2O:1</reactants>
-      <products>H2:1 H2O:1</products>
-    </reaction>
-
-    <!--   reaction 0013    -->
-    <reaction id="0013" reversible="yes" type="threeBody">
-      <equation>H + OH + M [=] H2O + M</equation>
-      <rateCoeff>
-        <Arrhenius>
-          <A units="cm6/mol2/s">  2.200000E+22</A>
-          <b>-2</b>
-          <E units="cal/mol">0.000000</E>
-        </Arrhenius>
-        <efficiencies default="1.0"> AR:0.38  H2:0.73  H2O:3.65 </efficiencies>
-      </rateCoeff>
-      <reactants>H:1 OH:1</reactants>
-      <products>H2O:1</products>
-    </reaction>
-
-    <!--   reaction 0014    -->
-    <reaction id="0014" reversible="yes">
-      <equation>H + HO2 [=] O + H2O</equation>
-      <rateCoeff>
-        <Arrhenius>
-          <A units="cm3/mol/s">  3.970000E+12</A>
-          <b>0</b>
-          <E units="cal/mol">671.000000</E>
-        </Arrhenius>
-      </rateCoeff>
-      <reactants>H:1 HO2:1</reactants>
-      <products>H2O:1 O:1</products>
-    </reaction>
-
-    <!--   reaction 0015    -->
-    <reaction id="0015" reversible="yes">
-      <equation>H + HO2 [=] O2 + H2</equation>
-      <rateCoeff>
-        <Arrhenius>
-          <A units="cm3/mol/s">  4.480000E+13</A>
-          <b>0</b>
-          <E units="cal/mol">1068.000000</E>
-        </Arrhenius>
-      </rateCoeff>
-      <reactants>H:1 HO2:1</reactants>
-      <products>H2:1 O2:1</products>
-    </reaction>
-
-    <!--   reaction 0016    -->
-    <reaction id="0016" reversible="yes">
-      <equation>H + HO2 [=] 2 OH</equation>
-      <rateCoeff>
-        <Arrhenius>
-          <A units="cm3/mol/s">  8.400000E+13</A>
-          <b>0</b>
-          <E units="cal/mol">635.000000</E>
-        </Arrhenius>
-      </rateCoeff>
-      <reactants>H:1 HO2:1</reactants>
-      <products>OH:2</products>
-    </reaction>
-
-    <!--   reaction 0017    -->
-    <reaction id="0017" reversible="yes">
-      <equation>H + H2O2 [=] HO2 + H2</equation>
-      <rateCoeff>
-        <Arrhenius>
-          <A units="cm3/mol/s">  1.210000E+07</A>
-          <b>2</b>
-          <E units="cal/mol">5200.000000</E>
-        </Arrhenius>
-      </rateCoeff>
-      <reactants>H:1 H2O2:1</reactants>
-      <products>H2:1 HO2:1</products>
-    </reaction>
-
-    <!--   reaction 0018    -->
-    <reaction id="0018" reversible="yes">
-      <equation>H + H2O2 [=] OH + H2O</equation>
-      <rateCoeff>
-        <Arrhenius>
-          <A units="cm3/mol/s">  1.000000E+13</A>
-          <b>0</b>
-          <E units="cal/mol">3600.000000</E>
-        </Arrhenius>
-      </rateCoeff>
-      <reactants>H:1 H2O2:1</reactants>
-      <products>H2O:1 OH:1</products>
-    </reaction>
-
-    <!--   reaction 0019    -->
-    <reaction id="0019" reversible="yes">
-      <equation>OH + H2 [=] H + H2O</equation>
-      <rateCoeff>
-        <Arrhenius>
-          <A units="cm3/mol/s">  2.160000E+08</A>
-          <b>1.51</b>
-          <E units="cal/mol">3430.000000</E>
-        </Arrhenius>
-      </rateCoeff>
-      <reactants>H2:1 OH:1</reactants>
-      <products>H:1 H2O:1</products>
-    </reaction>
-
-    <!--   reaction 0020    -->
-    <reaction id="0020" reversible="yes" type="falloff">
-      <equation>2 OH (+ M) [=] H2O2 (+ M)</equation>
-      <rateCoeff>
-        <Arrhenius>
-          <A units="cm3/mol/s">  7.400000E+13</A>
-          <b>-0.37</b>
-          <E units="cal/mol">0.000000</E>
-        </Arrhenius>
-        <Arrhenius name="k0">
-          <A units="cm6/mol2/s">  2.300000E+18</A>
-          <b>-0.90000000000000002</b>
-          <E units="cal/mol">-1700.000000</E>
-        </Arrhenius>
-        <efficiencies default="1.0"> AR:0.7  H2:2  H2O:6 </efficiencies>
-        <falloff type="Troe">0.7346 94 1756 5182 </falloff>
-      </rateCoeff>
-      <reactants>OH:2</reactants>
-      <products>H2O2:1</products>
-    </reaction>
-
-    <!--   reaction 0021    -->
-    <reaction id="0021" reversible="yes">
-      <equation>2 OH [=] O + H2O</equation>
-      <rateCoeff>
-        <Arrhenius>
-          <A units="cm3/mol/s">  3.570000E+04</A>
-          <b>2.3999999999999999</b>
-          <E units="cal/mol">-2110.000000</E>
-        </Arrhenius>
-      </rateCoeff>
-      <reactants>OH:2</reactants>
-      <products>H2O:1 O:1</products>
-    </reaction>
-
-    <!--   reaction 0022    -->
-    <reaction duplicate="yes" id="0022" reversible="yes">
-      <equation>OH + HO2 [=] O2 + H2O</equation>
-      <rateCoeff>
-        <Arrhenius>
-          <A units="cm3/mol/s">  1.450000E+13</A>
-          <b>0</b>
-          <E units="cal/mol">-500.000000</E>
-        </Arrhenius>
-      </rateCoeff>
-      <reactants>HO2:1 OH:1</reactants>
-      <products>H2O:1 O2:1</products>
-    </reaction>
-
-    <!--   reaction 0023    -->
-    <reaction duplicate="yes" id="0023" reversible="yes">
-      <equation>OH + H2O2 [=] HO2 + H2O</equation>
-      <rateCoeff>
-        <Arrhenius>
-          <A units="cm3/mol/s">  2.000000E+12</A>
-          <b>0</b>
-          <E units="cal/mol">427.000000</E>
-        </Arrhenius>
-      </rateCoeff>
-      <reactants>H2O2:1 OH:1</reactants>
-      <products>H2O:1 HO2:1</products>
-    </reaction>
-
-    <!--   reaction 0024    -->
-    <reaction duplicate="yes" id="0024" reversible="yes">
-      <equation>OH + H2O2 [=] HO2 + H2O</equation>
-      <rateCoeff>
-        <Arrhenius>
-          <A units="cm3/mol/s">  1.700000E+18</A>
-          <b>0</b>
-          <E units="cal/mol">29410.000000</E>
-        </Arrhenius>
-      </rateCoeff>
-      <reactants>H2O2:1 OH:1</reactants>
-      <products>H2O:1 HO2:1</products>
-    </reaction>
-
-    <!--   reaction 0025    -->
-    <reaction duplicate="yes" id="0025" reversible="yes">
-      <equation>2 HO2 [=] O2 + H2O2</equation>
-      <rateCoeff>
-        <Arrhenius>
-          <A units="cm3/mol/s">  1.300000E+11</A>
-          <b>0</b>
-          <E units="cal/mol">-1630.000000</E>
-        </Arrhenius>
-      </rateCoeff>
-      <reactants>HO2:2</reactants>
-      <products>O2:1 H2O2:1</products>
-    </reaction>
-
-    <!--   reaction 0026    -->
-    <reaction duplicate="yes" id="0026" reversible="yes">
-      <equation>2 HO2 [=] O2 + H2O2</equation>
-      <rateCoeff>
-        <Arrhenius>
-          <A units="cm3/mol/s">  4.200000E+14</A>
-          <b>0</b>
-          <E units="cal/mol">12000.000000</E>
-        </Arrhenius>
-      </rateCoeff>
-      <reactants>HO2:2</reactants>
-      <products>O2:1 H2O2:1</products>
-    </reaction>
-
-    <!--   reaction 0027    -->
-    <reaction duplicate="yes" id="0027" reversible="yes">
-      <equation>OH + HO2 [=] O2 + H2O</equation>
-      <rateCoeff>
-        <Arrhenius>
-          <A units="cm3/mol/s">  5.000000E+15</A>
-          <b>0</b>
-          <E units="cal/mol">17330.000000</E>
-        </Arrhenius>
-      </rateCoeff>
-      <reactants>HO2:1 OH:1</reactants>
-      <products>H2O:1 O2:1</products>
-    </reaction>
-  </reactionData>
-</ctml>

data/inputs/ptcombust.cti

@@ -0,0 +1,280 @@
+#
+# see http://reaflow.iwr.uni-heidelberg.de/~Olaf.Deutschmann/ for more about this mechanism
+#
+#---------------------------------------------------------------------!
+#***********************************************************************
+#****                                                                  *
+#****     CH4-O2 SURFACE MECHANISM  ON PT                              *
+#****                                                                  *
+#****     Version 1.2   November  1995                                 *
+#****                                                                  *
+#****     O. Deutschmann, IWR, Heidelberg University, Germany          *
+#****                                                                  *
+#****     Kinetic data:                                                *
+#****      k = A * T**b * exp (-Ea/RT)         A          b       Ea   *
+#****                                       (cm,mol,s)    -      J/mol *
+#****                                                                  *
+#****                                                                  *
+#***********************************************************************
+#
+#  Ref:- 1.) Deutschman et al., 26th Symp. (Intl.) on Combustion,1996
+#            pp. 1747-1754
+#----------------------------------------------------------------------
+#
+#  Converted to Cantera format 
+#  by ck2cti on Thu Aug 21 07:58:45 2003
+#
+#----------------------------------------------------------------------
+
+units(length = "cm", time = "s", quantity = "mol", act_energy = "J/mol")
+
+ideal_gas(name = "gas",
+         elements = "O H C N Ar",
+         species = """gri30: H2      H       O       O2      OH      H2O     HO2     H2O2 
+         C       CH      CH2     CH2(S)  CH3     CH4     CO      CO2     
+         HCO     CH2O    CH2OH   CH3O    CH3OH   C2H     C2H2    C2H3    
+         C2H4    C2H5    C2H6    HCCO    CH2CO   HCCOH AR N2""",
+          transport = 'Mix',
+          reactions = 'gri30: all',
+          options = ['skip_undeclared_elements',
+                     'skip_undeclared_species'],
+          initial_state = state(temperature = 300.0, pressure = OneAtm,
+                                mole_fractions = 'CH4:0.095, O2:0.21, AR:0.79')
+          )
+
+
+ideal_interface(name = "Pt_surf",
+                elements = " Pt  H  O  C ",
+                species = """ PT(S) H(S)
+ H2O(S)  OH(S)  CO(S)  CO2(S)  CH3(S)
+                CH2(S)s  CH(S)  C(S)  O(S) """,
+                phases = "gas",
+                site_density = 2.7063e-9,
+                reactions = "all",
+                initial_state = state(temperature = 900.0,
+                                      coverages = 'O(S):0.0, PT(S):0.5, H(S):0.5')
+                )
+
+#-------------------------------------------------------------------------------
+#  Species data
+#
+# Note that reactions 12-14 are reversible, and therefore require thermo
+# data
+#-------------------------------------------------------------------------------
+
+species(name = "PT(S)",
+    atoms = " Pt:1 ",
+    thermo = (
+       NASA( [  300.00,  1000.00], [  0.000000000E+00,   0.000000000E+00, 
+                0.000000000E+00,   0.000000000E+00,   0.000000000E+00,
+                0.000000000E+00,   0.000000000E+00] ),
+       NASA( [ 1000.00,  3000.00], [  0.000000000E+00,   0.000000000E+00, 
+                0.000000000E+00,   0.000000000E+00,   0.000000000E+00,
+                0.000000000E+00,   0.000000000E+00] )
+             )
+       )
+
+species(name = "H(S)",
+    atoms = " H:1  Pt:1 ",
+    thermo = (
+       NASA( [  300.00,  1000.00], [ -1.302987700E+00,   5.417319900E-03, 
+                3.127797200E-07,  -3.232853300E-09,   1.136282000E-12,
+               -4.227707500E+03,   5.874323800E+00] ),
+       NASA( [ 1000.00,  3000.00], [  1.069699600E+00,   1.543223000E-03, 
+               -1.550092200E-07,  -1.657316500E-10,   3.835934700E-14,
+               -5.054612800E+03,  -7.155523800E+00] )
+             )
+       )
+
+species(name = "H2O(S)",
+    atoms = " O:1  H:2  Pt:1 ",
+    thermo = (
+       NASA( [  300.00,  1000.00], [ -2.765155300E+00,   1.331511500E-02, 
+                1.012769500E-06,  -7.182008300E-09,   2.281377600E-12,
+               -3.639805500E+04,   1.209814500E+01] ),
+       NASA( [ 1000.00,  3000.00], [  2.580305100E+00,   4.957082700E-03, 
+               -4.689405600E-07,  -5.263313700E-10,   1.199832200E-13,
+               -3.830223400E+04,  -1.740632200E+01] )
+             )
+       )
+
+species(name = "OH(S)",
+    atoms = " O:1  H:1  Pt:1 ",
+    thermo = (
+       NASA( [  300.00,  1000.00], [ -2.034088100E+00,   9.366268300E-03, 
+                6.627521400E-07,  -5.207488700E-09,   1.708873500E-12,
+               -2.531994900E+04,   8.986318600E+00] ),
+       NASA( [ 1000.00,  3000.00], [  1.824997300E+00,   3.250156500E-03, 
+               -3.119754100E-07,  -3.460320600E-10,   7.917147200E-14,
+               -2.668549200E+04,  -1.228089100E+01] )
+             )
+       )
+
+species(name = "CO(S)",
+    atoms = " C:1  O:1  Pt:1 ",
+    thermo = (
+       NASA( [  300.00,  1000.00], [  4.890746600E+00,   6.813423500E-05, 
+                1.976881400E-07,   1.238866900E-09,  -9.033924900E-13,
+               -3.229783600E+04,  -1.745316100E+01] ),
+       NASA( [ 1000.00,  3000.00], [  4.708377800E+00,   9.603729700E-04, 
+               -1.180527900E-07,  -7.688382600E-11,   1.823200000E-14,
+               -3.231172300E+04,  -1.671959300E+01] )
+             )
+       )
+
+species(name = "CO2(S)",
+    atoms = " C:1  O:2  Pt:1 ",
+    thermo = (
+       NASA( [  300.00,  1000.00], [  4.690000000E-01,   6.266200000E-03, 
+                0.000000000E+00,   0.000000000E+00,   0.000000000E+00,
+               -5.045870000E+04,  -4.555000000E+00] ),
+       NASA( [ 1000.00,  3000.00], [  4.690000000E-01,   6.266000000E-03, 
+                0.000000000E+00,   0.000000000E+00,   0.000000000E+00,
+               -5.045870000E+04,  -4.555000000E+00] )
+             )
+       )
+
+species(name = "CH3(S)",
+    atoms = " C:1  H:3  Pt:1 ",
+    thermo = (
+       NASA( [  300.00,  1000.00], [  1.291921700E+00,   7.267560300E-03, 
+                9.817947600E-07,  -2.047129400E-09,   9.083271700E-14,
+               -2.574561000E+03,  -1.198303700E+00] ),
+       NASA( [ 1000.00,  3000.00], [  3.001616500E+00,   5.408450500E-03, 
+               -4.053805800E-07,  -5.342246600E-10,   1.145188700E-13,
+               -3.275272200E+03,  -1.096598400E+01] )
+             )
+       )
+
+species(name = "CH2(S)s",
+    atoms = " C:1  H:2  Pt:1 ",
+    thermo = (
+       NASA( [  300.00,  1000.00], [ -1.487640400E-01,   5.139628900E-03, 
+                1.121107500E-06,  -8.275545200E-10,  -4.457234500E-13,
+                1.087870000E+04,   5.745188200E+00] ),
+       NASA( [ 1000.00,  3000.00], [  7.407612200E-01,   4.803253300E-03, 
+               -3.282563300E-07,  -4.777978600E-10,   1.007345200E-13,
+                1.044375200E+04,   4.084208600E-01] )
+             )
+       )
+
+species(name = "CH(S)",
+    atoms = " C:1  H:1  Pt:1 ",
+    thermo = (
+       NASA( [  300.00,  1000.00], [  8.415748500E-01,   1.309538000E-03, 
+                2.846457500E-07,   6.386290400E-10,  -4.276665800E-13,
+                2.233280100E+04,   1.145230500E+00] ),
+       NASA( [ 1000.00,  3000.00], [ -4.824247200E-03,   3.044623900E-03, 
+               -1.606609900E-07,  -2.904170000E-10,   5.799992400E-14,
+                2.259521900E+04,   5.667781800E+00] )
+             )
+       )
+
+species(name = "C(S)",
+    atoms = " C:1  Pt:1 ",
+    thermo = (
+       NASA( [  300.00,  1000.00], [  5.892401900E-01,   2.501284200E-03, 
+               -3.422949800E-07,  -1.899434600E-09,   1.019040600E-12,
+                1.023692300E+04,   2.193701700E+00] ),
+       NASA( [ 1000.00,  3000.00], [  1.579282400E+00,   3.652870100E-04, 
+               -5.065767200E-08,  -3.488485500E-11,   8.808969900E-15,
+                9.953575200E+03,  -3.024049500E+00] )
+             )
+       )
+
+species(name = "O(S)",
+    atoms = " O:1  Pt:1 ",
+    thermo = (
+       NASA( [  300.00,  1000.00], [ -9.498690400E-01,   7.404230500E-03, 
+               -1.045142400E-06,  -6.112042000E-09,   3.378799200E-12,
+               -1.320991200E+04,   3.613790500E+00] ),
+       NASA( [ 1000.00,  3000.00], [  1.945418000E+00,   9.176164700E-04, 
+               -1.122671900E-07,  -9.909962400E-11,   2.430769900E-14,
+               -1.400518700E+04,  -1.153166300E+01] )
+             )
+       )
+
+
+
+#-------------------------------------------------------------------------------
+#  Reaction data 
+#-------------------------------------------------------------------------------
+
+#  Reaction 1
+surface_reaction("H2 + 2 PT(S) => 2 H(S)", [4.45790E+10, 0.5, 0], 
+		  order = "PT(S):1")
+
+#  Reaction 2
+surface_reaction( "2 H(S) => H2 + 2 PT(S)",   
+		  Arrhenius(3.70000E+21, 0, 67400, coverage = ['H(S)', 0.0, 0.0, -6000.0]))
+
+#  Reaction 3
+surface_reaction( "H + PT(S) => H(S)",   stick(1.00000E+00, 0, 0))
+
+#  Reaction 4
+surface_reaction( "O2 + 2 PT(S) => 2 O(S)",   Arrhenius(1.80000E+21, -0.5, 0),
+         options = 'duplicate')
+
+#  Reaction 5
+surface_reaction( "O2 + 2 PT(S) => 2 O(S)",   stick(2.30000E-02, 0, 0),
+         options = 'duplicate')
+
+#  Reaction 6
+surface_reaction( "2 O(S) => O2 + 2 PT(S)",   
+		  Arrhenius(3.70000E+21, 0, 213200,
+                            coverage = ['O(S)', 0.0, 0.0, -60000.0]) )
+
+#  Reaction 7
+surface_reaction( "O + PT(S) => O(S)",   stick(1.00000E+00, 0, 0))
+
+#  Reaction 8
+surface_reaction( "H2O + PT(S) => H2O(S)",   stick(7.50000E-01, 0, 0))
+
+#  Reaction 9
+surface_reaction( "H2O(S) => H2O + PT(S)",   [1.00000E+13, 0, 40300])
+
+#  Reaction 10
+surface_reaction( "OH + PT(S) => OH(S)",   stick(1.00000E+00, 0, 0))
+
+#  Reaction 11
+surface_reaction( "OH(S) => OH + PT(S)",   [1.00000E+13, 0, 192800])
+
+#  Reaction 12
+surface_reaction( "H(S) + O(S) <=> OH(S) + PT(S)",   [3.70000E+21, 0, 11500])
+
+#  Reaction 13
+surface_reaction( "H(S) + OH(S) <=> H2O(S) + PT(S)",   [3.70000E+21, 0, 17400])
+
+#  Reaction 14
+surface_reaction( "OH(S) + OH(S) <=> H2O(S) + O(S)",   [3.70000E+21, 0, 48200])
+
+#  Reaction 15
+surface_reaction( "CO + PT(S) => CO(S)",   [1.61800E+20, 0.5, 0], order = "PT(S):2")
+
+#  Reaction 16
+surface_reaction( "CO(S) => CO + PT(S)",   [1.00000E+13, 0, 125500])
+
+#  Reaction 17
+surface_reaction( "CO2(S) => CO2 + PT(S)",   [1.00000E+13, 0, 20500])
+
+#  Reaction 18
+surface_reaction( "CO(S) + O(S) => CO2(S) + PT(S)",   [3.70000E+21, 0, 105000])
+
+#  Reaction 19
+surface_reaction( "CH4 + 2 PT(S) => CH3(S) + H(S)",   [4.63340E+20, 0.5, 0],
+		  order = "PT(S):2.3")
+
+#  Reaction 20
+surface_reaction( "CH3(S) + PT(S) => CH2(S)s + H(S)",   [3.70000E+21, 0, 20000])
+
+#  Reaction 21
+surface_reaction( "CH2(S)s + PT(S) => CH(S) + H(S)",   [3.70000E+21, 0, 20000])
+
+#  Reaction 22
+surface_reaction( "CH(S) + PT(S) => C(S) + H(S)",   [3.70000E+21, 0, 20000])
+
+#  Reaction 23
+surface_reaction( "C(S) + O(S) => CO(S) + PT(S)",   [3.70000E+21, 0, 62800])
+
+#  Reaction 24
+surface_reaction( "CO(S) + PT(S) => C(S) + O(S)",   [1.00000E+18, 0, 184000])

data/inputs/silane.cti

@@ -0,0 +1,287 @@
+#
+# Generated from file silane.inp
+# by ck2cti on Mon Aug 25 09:52:58 2003
+#
+units(length = "cm", time = "s", quantity = "mol", act_energy = "cal/mol")
+
+
+ideal_gas(name = "silane",
+      elements = " Si  H  He ",
+      species = """ H2  H  HE  SIH4  SI  SIH  SIH2  SIH3  H3SISIH  SI2H6 
+                   H2SISIH2  SI3H8  SI2  SI3 """,
+      reactions = "all",
+      initial_state = state(temperature = 300.0,
+                        pressure = OneAtm)    )
+
+
+
+#-------------------------------------------------------------------------------
+#  Species data 
+#-------------------------------------------------------------------------------
+
+species(name = "H2",
+    atoms = " H:2 ",
+    thermo = (
+       NASA( [  200.00,  1000.00], [  2.344331120E+00,   7.980520750E-03, 
+               -1.947815100E-05,   2.015720940E-08,  -7.376117610E-12,
+               -9.179351730E+02,   6.830102380E-01] ),
+       NASA( [ 1000.00,  3500.00], [  3.337279200E+00,  -4.940247310E-05, 
+                4.994567780E-07,  -1.795663940E-10,   2.002553760E-14,
+               -9.501589220E+02,  -3.205023310E+00] )
+             ),
+    note = "TPIS78"
+       )
+
+species(name = "H",
+    atoms = " H:1 ",
+    thermo = (
+       NASA( [  200.00,  1000.00], [  2.500000000E+00,   7.053328190E-13, 
+               -1.995919640E-15,   2.300816320E-18,  -9.277323320E-22,
+                2.547365990E+04,  -4.466828530E-01] ),
+       NASA( [ 1000.00,  3500.00], [  2.500000010E+00,  -2.308429730E-11, 
+                1.615619480E-14,  -4.735152350E-18,   4.981973570E-22,
+                2.547365990E+04,  -4.466829140E-01] )
+             ),
+    note = "L 7/88"
+       )
+
+species(name = "HE",
+    atoms = " He:1 ",
+    thermo = (
+       NASA( [  300.00,  1000.00], [  2.500000000E+00,   0.000000000E+00, 
+                0.000000000E+00,   0.000000000E+00,   0.000000000E+00,
+               -7.453750000E+02,   9.153488000E-01] ),
+       NASA( [ 1000.00,  5000.00], [  2.500000000E+00,   0.000000000E+00, 
+                0.000000000E+00,   0.000000000E+00,   0.000000000E+00,
+               -7.453750000E+02,   9.153489000E-01] )
+             ),
+    note = "120186"
+       )
+
+species(name = "SIH4",
+    atoms = " Si:1  H:4 ",
+    thermo = (
+       NASA( [  300.00,  1000.00], [  1.451640400E+00,   1.398736300E-02, 
+               -4.234563900E-06,  -2.360614200E-09,   1.371208900E-12,
+                3.113410500E+03,   1.232185500E+01] ),
+       NASA( [ 1000.00,  2000.00], [  7.935938000E-01,   1.767189900E-02, 
+               -1.139800900E-05,   3.599260400E-09,  -4.524157100E-13,
+                3.198212700E+03,   1.524225700E+01] )
+             ),
+    note = "90784"
+       )
+
+species(name = "SI",
+    atoms = " Si:1 ",
+    thermo = (
+       NASA( [  300.00,  1000.00], [  3.179353700E+00,  -2.764699200E-03, 
+                4.478403800E-06,  -3.283317700E-09,   9.121363100E-13,
+                5.333903200E+04,   2.727320400E+00] ),
+       NASA( [ 1000.00,  5000.00], [  2.650601400E+00,  -3.576385200E-04, 
+                2.959229300E-07,  -7.280482900E-11,   5.796332900E-15,
+                5.343705400E+04,   5.220405700E+00] )
+             ),
+    note = "J 3/67"
+       )
+
+species(name = "SIH",
+    atoms = " Si:1  H:1 ",
+    thermo = (
+       NASA( [  300.00,  1000.00], [  3.836010000E+00,  -2.702657000E-03, 
+                6.849070000E-06,  -5.424184000E-09,   1.472131000E-12,
+                4.507593000E+04,   9.350778000E-01] ),
+       NASA( [ 1000.00,  2000.00], [  3.110430000E+00,   1.094946000E-03, 
+                2.898629000E-08,  -2.745104000E-10,   7.051799000E-14,
+                4.516898000E+04,   4.193487000E+00] )
+             ),
+    note = "121986"
+       )
+
+species(name = "SIH2",
+    atoms = " Si:1  H:2 ",
+    thermo = (
+       NASA( [  300.00,  1000.00], [  3.475092000E+00,   2.139338000E-03, 
+                7.672306000E-07,   5.217668000E-10,  -9.898824000E-13,
+                3.147397000E+04,   4.436585000E+00] ),
+       NASA( [ 1000.00,  3000.00], [  4.142390000E+00,   2.150191000E-03, 
+               -2.190730000E-07,  -2.073725000E-10,   4.741018000E-14,
+                3.110484000E+04,   2.930745000E-01] )
+             ),
+    note = "42489"
+       )
+
+species(name = "SIH3",
+    atoms = " Si:1  H:3 ",
+    thermo = (
+       NASA( [  300.00,  1000.00], [  2.946733000E+00,   6.466764000E-03, 
+                5.991653000E-07,  -2.218413000E-09,   3.052670000E-13,
+                2.270173000E+04,   7.347948000E+00] ),
+       NASA( [ 1000.00,  3000.00], [  5.015906000E+00,   3.732750000E-03, 
+               -3.609053000E-07,  -3.729193000E-10,   8.468490000E-14,
+                2.190233000E+04,  -4.291368000E+00] )
+             ),
+    note = "42489"
+       )
+
+species(name = "H3SISIH",
+    atoms = " H:4  Si:2 ",
+    thermo = (
+       NASA( [  300.00,  1500.00], [  3.698707000E+00,   1.870180000E-02, 
+               -1.430704000E-05,   6.005836000E-09,  -1.116293000E-12,
+                3.590825000E+04,   8.825191000E+00] ),
+       NASA( [ 1500.00,  4000.00], [  1.127202000E+01,   2.538145000E-03, 
+               -2.998472000E-07,  -9.465367000E-11,   1.855053000E-14,
+                3.297169000E+04,  -3.264598000E+01] )
+             ),
+    note = "111191"
+       )
+
+species(name = "SI2H6",
+    atoms = " Si:2  H:6 ",
+    thermo = (
+       NASA( [  300.00,  1000.00], [  6.734798300E-01,   4.093153100E-02, 
+               -4.484125500E-05,   2.995223200E-08,  -8.901085400E-12,
+                7.932787500E+03,   1.862740300E+01] ),
+       NASA( [ 1000.00,  2000.00], [  3.407493600E+00,   2.720647900E-02, 
+               -1.771320400E-05,   5.639117700E-09,  -7.137868200E-13,
+                7.532184200E+03,   6.132175400E+00] )
+             ),
+    note = "90784"
+       )
+
+species(name = "H2SISIH2",
+    atoms = " Si:2  H:4 ",
+    thermo = (
+       NASA( [  300.00,  1000.00], [  5.133186000E+00,   1.252855000E-02, 
+               -4.620421000E-07,  -6.606075000E-09,   2.864345000E-12,
+                2.956915000E+04,   7.605133000E-01] ),
+       NASA( [ 1000.00,  3000.00], [  8.986817000E+00,   5.405047000E-03, 
+               -5.214022000E-07,  -5.313742000E-10,   1.188727000E-13,
+                2.832748000E+04,  -2.004478000E+01] )
+             ),
+    note = "42489"
+       )
+
+species(name = "SI3H8",
+    atoms = " Si:3  H:8 ",
+    thermo = (
+       NASA( [  300.00,  1000.00], [  7.719684600E-01,   6.344274000E-02, 
+               -7.672610900E-05,   5.454371500E-08,  -1.661172900E-11,
+                1.207126300E+04,   2.153250700E+01] ),
+       NASA( [ 1000.00,  2000.00], [  6.093334100E+00,   3.658011200E-02, 
+               -2.389236100E-05,   7.627193200E-09,  -9.676938400E-13,
+                1.129720500E+04,  -2.747565400E+00] )
+             ),
+    note = "90784"
+       )
+
+species(name = "SI2",
+    atoms = " Si:2 ",
+    thermo = (
+       NASA( [  300.00,  1000.00], [  2.967197600E+00,   6.311955800E-03, 
+               -1.097079000E-05,   8.927868000E-09,  -2.787368900E-12,
+                6.987073800E+04,   9.278950300E+00] ),
+       NASA( [ 1000.00,  2000.00], [  4.144677900E+00,   6.523467700E-04, 
+               -5.010852000E-07,   1.806284300E-10,  -2.516111100E-14,
+                6.969470700E+04,   3.862736600E+00] )
+             ),
+    note = "90784"
+       )
+
+species(name = "SI3",
+    atoms = " Si:3 ",
+    thermo = (
+       NASA( [  300.00,  1000.00], [  4.597912900E+00,   1.071527400E-02, 
+               -1.610042200E-05,   1.096920700E-08,  -2.783287500E-12,
+                7.476632400E+04,   3.442167100E+00] ),
+       NASA( [ 1000.00,  5000.00], [  7.421336000E+00,  -1.170994800E-04, 
+                8.982077500E-08,   7.193596400E-12,  -2.567083700E-15,
+                7.414669900E+04,  -1.036527400E+01] )
+             ),
+    note = "J 3/67"
+       )
+
+
+
+#-------------------------------------------------------------------------------
+#  Reaction data 
+#-------------------------------------------------------------------------------
+
+#  Reaction 1
+#  Roth
+reaction( "SIH4 + H <=> SIH3 + H2",   [7.80000E+14, 0, 2260])
+
+#  Reaction 2
+#  94TAK/MOM   tst calc
+three_body_reaction( "SIH4 + M <=> SIH3 + H + M",   [3.91000E+15, 0, 89356])
+
+#  Reaction 3
+#  assume same as SIH4
+reaction( "SIH3 + H <=> SIH2 + H2",   [7.80000E+14, 0, 2260])
+
+#  Reaction 4
+#  90MAR/RAF
+three_body_reaction( "SI + SI + M <=> SI2 + M",   [2.47000E+16, 0, 1178])
+
+#  Reaction 5
+#  R8
+reaction( "SIH4 + SIH2 <=> H3SISIH + H2",   [1.30000E+13, 0, 0])
+
+#  Reaction 6
+#  R11
+reaction( "SIH + H2 <=> SIH2 + H",   [4.80000E+14, 0, 23.64])
+
+#  Reaction 7
+#  R12
+reaction( "SIH + SIH4 <=> H3SISIH + H",   [1.60000E+14, 0, 0])
+
+#  Reaction 8
+#  R13
+reaction( "SI + H2 <=> SIH + H",   [1.50000E+15, 0, 31.8])
+
+#  Reaction 9
+#  R1
+falloff_reaction( "SIH4 (+ M) <=> SIH2 + H2 (+ M)", 
+         kf = [3.11900E+09, 1.669, 54710],
+         kf0   = [5.21400E+29, -3.545, 57550],
+         falloff = Troe(A = -0.4984, T3 = 888.3, T1 = 209.4, T2 = 2760),
+         efficiencies = " SI2H6:4  SIH4:4 ")
+
+#  Reaction 10
+#  HF(SiH2)=64.3, anh_inc.16b,  beta(Ar,300) = 0.25 fit from 300 to 1200K
+#  A6
+falloff_reaction( "H3SISIH (+ M) <=> H2SISIH2 (+ M)", 
+         kf = [2.54000E+13, -0.2239, 5381],
+         kf0   = [1.09900E+33, -5.765, 9152],
+         falloff = Troe(A = -0.4202, T3 = 214.5, T1 = 103, T2 = 136.3),
+         efficiencies = " SI2H6:4  SIH4:4 ")
+
+#  Reaction 11
+#    RRKM fits 3/18/93 by MEC
+falloff_reaction( "SI3H8 (+ M) <=> SIH4 + H3SISIH (+ M)", 
+         kf = [3.73000E+12, 0.992, 50850],
+         kf0   = [4.36000E+76, -17.26, 59303],
+         falloff = Troe(A = 0.4157, T3 = 365.3, T1 = 3102, T2 = 9.724),
+         efficiencies = " SI2H6:4  SIH4:4 ")
+
+#  Reaction 12
+falloff_reaction( "SI3H8 (+ M) <=> SIH2 + SI2H6 (+ M)", 
+         kf = [6.97000E+12, 0.9691, 52677],
+         kf0   = [1.73000E+69, -15.07, 60491],
+         falloff = Troe(A = -3.47e-05, T3 = 442, T1 = 2412, T2 = 128.3),
+         efficiencies = " SI2H6:4  SIH4:4 ")
+
+#  Reaction 13
+falloff_reaction( "SI2H6 (+ M) <=> H2 + H3SISIH (+ M)", 
+         kf = [9.08600E+09, 1.834, 54197],
+         kf0   = [1.94500E+44, -7.772, 59023],
+         falloff = Troe(A = -0.1224, T3 = 793.3, T1 = 2400, T2 = 11.39),
+         efficiencies = " SI2H6:4  SIH4:4 ")
+
+#  Reaction 14
+#  A3
+falloff_reaction( "SI2H6 (+ M) <=> SIH4 + SIH2 (+ M)", 
+         kf = [1.81000E+10, 1.747, 50203],
+         kf0   = [5.09000E+53, -10.37, 56034],
+         falloff = Troe(A = 4.375e-05, T3 = 438.5, T1 = 2726, T2 = 438.2),
+         efficiencies = " SI2H6:4  SIH4:4 ")

data/inputs/silane.xml

@@ -1,501 +0,0 @@
-<ctml>
-  <validate reactions="yes" species="yes"/>
-
-  <!--    phase silane     -->
-  <phase dim="3" id="silane">
-    <validation>
-      <duplicateReactions>halt</duplicateReactions>
-      <thermo>warn</thermo>
-    </validation>
-    <elementArray datasrc="elements.xml"> Si  H  He </elementArray>
-    <speciesArray datasrc="#species_data">
-     H2  H  HE  SIH4  SI  SIH  SIH2  SIH3  H3SISIH  SI2H6 
-                       H2SISIH2  SI3H8  SI2  SI3 </speciesArray>
-    <reactionArray datasrc="#reaction_data"/>
-    <thermo model="IdealGas"/>
-    <kinetics model="GasKinetics"/>
-    <transport model="None"/>
-  </phase>
-
-  <!--     species definitions     -->
-  <speciesData id="species_data">
-
-    <!--    species H2    -->
-    <species name="H2">
-      <atomArray>H:2 </atomArray>
-      <thermo>
-        <NASA P0="100000.0" Tmax="1000.0" Tmin="200.0">
-          <floatArray name="coeffs" size="7">
-            2.344331120E+00,   7.980520750E-03,  -1.947815100E-05,   2.015720940E-08, 
-           -7.376117610E-12,  -9.179351730E+02,   6.830102380E-01,</floatArray>
-        </NASA>
-        <NASA P0="100000.0" Tmax="3500.0" Tmin="1000.0">
-          <floatArray name="coeffs" size="7">
-            3.337279200E+00,  -4.940247310E-05,   4.994567780E-07,  -1.795663940E-10, 
-            2.002553760E-14,  -9.501589220E+02,  -3.205023310E+00,</floatArray>
-        </NASA>
-      </thermo>
-    </species>
-
-    <!--    species H    -->
-    <species name="H">
-      <atomArray>H:1 </atomArray>
-      <thermo>
-        <NASA P0="100000.0" Tmax="1000.0" Tmin="200.0">
-          <floatArray name="coeffs" size="7">
-            2.500000000E+00,   7.053328190E-13,  -1.995919640E-15,   2.300816320E-18, 
-           -9.277323320E-22,   2.547365990E+04,  -4.466828530E-01,</floatArray>
-        </NASA>
-        <NASA P0="100000.0" Tmax="3500.0" Tmin="1000.0">
-          <floatArray name="coeffs" size="7">
-            2.500000010E+00,  -2.308429730E-11,   1.615619480E-14,  -4.735152350E-18, 
-            4.981973570E-22,   2.547365990E+04,  -4.466829140E-01,</floatArray>
-        </NASA>
-      </thermo>
-    </species>
-
-    <!--    species HE    -->
-    <species name="HE">
-      <atomArray>He:1 </atomArray>
-      <thermo>
-        <NASA P0="100000.0" Tmax="1000.0" Tmin="300.0">
-          <floatArray name="coeffs" size="7">
-            2.500000000E+00,   0.000000000E+00,   0.000000000E+00,   0.000000000E+00, 
-            0.000000000E+00,  -7.453750000E+02,   9.153488000E-01,</floatArray>
-        </NASA>
-        <NASA P0="100000.0" Tmax="5000.0" Tmin="1000.0">
-          <floatArray name="coeffs" size="7">
-            2.500000000E+00,   0.000000000E+00,   0.000000000E+00,   0.000000000E+00, 
-            0.000000000E+00,  -7.453750000E+02,   9.153489000E-01,</floatArray>
-        </NASA>
-      </thermo>
-    </species>
-
-    <!--    species SIH4    -->
-    <species name="SIH4">
-      <atomArray>H:4 Si:1 </atomArray>
-      <thermo>
-        <NASA P0="100000.0" Tmax="1000.0" Tmin="300.0">
-          <floatArray name="coeffs" size="7">
-            1.451640400E+00,   1.398736300E-02,  -4.234563900E-06,  -2.360614200E-09, 
-            1.371208900E-12,   3.113410500E+03,   1.232185500E+01,</floatArray>
-        </NASA>
-        <NASA P0="100000.0" Tmax="2000.0" Tmin="1000.0">
-          <floatArray name="coeffs" size="7">
-            7.935938000E-01,   1.767189900E-02,  -1.139800900E-05,   3.599260400E-09, 
-           -4.524157100E-13,   3.198212700E+03,   1.524225700E+01,</floatArray>
-        </NASA>
-      </thermo>
-    </species>
-
-    <!--    species SI    -->
-    <species name="SI">
-      <atomArray>Si:1 </atomArray>
-      <thermo>
-        <NASA P0="100000.0" Tmax="1000.0" Tmin="300.0">
-          <floatArray name="coeffs" size="7">
-            3.179353700E+00,  -2.764699200E-03,   4.478403800E-06,  -3.283317700E-09, 
-            9.121363100E-13,   5.333903200E+04,   2.727320400E+00,</floatArray>
-        </NASA>
-        <NASA P0="100000.0" Tmax="5000.0" Tmin="1000.0">
-          <floatArray name="coeffs" size="7">
-            2.650601400E+00,  -3.576385200E-04,   2.959229300E-07,  -7.280482900E-11, 
-            5.796332900E-15,   5.343705400E+04,   5.220405700E+00,</floatArray>
-        </NASA>
-      </thermo>
-    </species>
-
-    <!--    species SIH    -->
-    <species name="SIH">
-      <atomArray>H:1 Si:1 </atomArray>
-      <thermo>
-        <NASA P0="100000.0" Tmax="1000.0" Tmin="300.0">
-          <floatArray name="coeffs" size="7">
-            3.836010000E+00,  -2.702657000E-03,   6.849070000E-06,  -5.424184000E-09, 
-            1.472131000E-12,   4.507593000E+04,   9.350778000E-01,</floatArray>
-        </NASA>
-        <NASA P0="100000.0" Tmax="2000.0" Tmin="1000.0">
-          <floatArray name="coeffs" size="7">
-            3.110430000E+00,   1.094946000E-03,   2.898629000E-08,  -2.745104000E-10, 
-            7.051799000E-14,   4.516898000E+04,   4.193487000E+00,</floatArray>
-        </NASA>
-      </thermo>
-    </species>
-
-    <!--    species SIH2    -->
-    <species name="SIH2">
-      <atomArray>H:2 Si:1 </atomArray>
-      <thermo>
-        <NASA P0="100000.0" Tmax="1000.0" Tmin="300.0">
-          <floatArray name="coeffs" size="7">
-            3.475092000E+00,   2.139338000E-03,   7.672306000E-07,   5.217668000E-10, 
-           -9.898824000E-13,   3.147397000E+04,   4.436585000E+00,</floatArray>
-        </NASA>
-        <NASA P0="100000.0" Tmax="3000.0" Tmin="1000.0">
-          <floatArray name="coeffs" size="7">
-            4.142390000E+00,   2.150191000E-03,  -2.190730000E-07,  -2.073725000E-10, 
-            4.741018000E-14,   3.110484000E+04,   2.930745000E-01,</floatArray>
-        </NASA>
-      </thermo>
-    </species>
-
-    <!--    species SIH3    -->
-    <species name="SIH3">
-      <atomArray>H:3 Si:1 </atomArray>
-      <thermo>
-        <NASA P0="100000.0" Tmax="1000.0" Tmin="300.0">
-          <floatArray name="coeffs" size="7">
-            2.946733000E+00,   6.466764000E-03,   5.991653000E-07,  -2.218413000E-09, 
-            3.052670000E-13,   2.270173000E+04,   7.347948000E+00,</floatArray>
-        </NASA>
-        <NASA P0="100000.0" Tmax="3000.0" Tmin="1000.0">
-          <floatArray name="coeffs" size="7">
-            5.015906000E+00,   3.732750000E-03,  -3.609053000E-07,  -3.729193000E-10, 
-            8.468490000E-14,   2.190233000E+04,  -4.291368000E+00,</floatArray>
-        </NASA>
-      </thermo>
-    </species>
-
-    <!--    species H3SISIH    -->
-    <species name="H3SISIH">
-      <atomArray>H:4 Si:2 </atomArray>
-      <thermo>
-        <NASA P0="100000.0" Tmax="1500.0" Tmin="300.0">
-          <floatArray name="coeffs" size="7">
-            3.698707000E+00,   1.870180000E-02,  -1.430704000E-05,   6.005836000E-09, 
-           -1.116293000E-12,   3.590825000E+04,   8.825191000E+00,</floatArray>
-        </NASA>
-        <NASA P0="100000.0" Tmax="4000.0" Tmin="1500.0">
-          <floatArray name="coeffs" size="7">
-            1.127202000E+01,   2.538145000E-03,  -2.998472000E-07,  -9.465367000E-11, 
-            1.855053000E-14,   3.297169000E+04,  -3.264598000E+01,</floatArray>
-        </NASA>
-      </thermo>
-    </species>
-
-    <!--    species SI2H6    -->
-    <species name="SI2H6">
-      <atomArray>H:6 Si:2 </atomArray>
-      <thermo>
-        <NASA P0="100000.0" Tmax="1000.0" Tmin="300.0">
-          <floatArray name="coeffs" size="7">
-            6.734798300E-01,   4.093153100E-02,  -4.484125500E-05,   2.995223200E-08, 
-           -8.901085400E-12,   7.932787500E+03,   1.862740300E+01,</floatArray>
-        </NASA>
-        <NASA P0="100000.0" Tmax="2000.0" Tmin="1000.0">
-          <floatArray name="coeffs" size="7">
-            3.407493600E+00,   2.720647900E-02,  -1.771320400E-05,   5.639117700E-09, 
-           -7.137868200E-13,   7.532184200E+03,   6.132175400E+00,</floatArray>
-        </NASA>
-      </thermo>
-    </species>
-
-    <!--    species H2SISIH2    -->
-    <species name="H2SISIH2">
-      <atomArray>H:4 Si:2 </atomArray>
-      <thermo>
-        <NASA P0="100000.0" Tmax="1000.0" Tmin="300.0">
-          <floatArray name="coeffs" size="7">
-            5.133186000E+00,   1.252855000E-02,  -4.620421000E-07,  -6.606075000E-09, 
-            2.864345000E-12,   2.956915000E+04,   7.605133000E-01,</floatArray>
-        </NASA>
-        <NASA P0="100000.0" Tmax="3000.0" Tmin="1000.0">
-          <floatArray name="coeffs" size="7">
-            8.986817000E+00,   5.405047000E-03,  -5.214022000E-07,  -5.313742000E-10, 
-            1.188727000E-13,   2.832748000E+04,  -2.004478000E+01,</floatArray>
-        </NASA>
-      </thermo>
-    </species>
-
-    <!--    species SI3H8    -->
-    <species name="SI3H8">
-      <atomArray>H:8 Si:3 </atomArray>
-      <thermo>
-        <NASA P0="100000.0" Tmax="1000.0" Tmin="300.0">
-          <floatArray name="coeffs" size="7">
-            7.719684600E-01,   6.344274000E-02,  -7.672610900E-05,   5.454371500E-08, 
-           -1.661172900E-11,   1.207126300E+04,   2.153250700E+01,</floatArray>
-        </NASA>
-        <NASA P0="100000.0" Tmax="2000.0" Tmin="1000.0">
-          <floatArray name="coeffs" size="7">
-            6.093334100E+00,   3.658011200E-02,  -2.389236100E-05,   7.627193200E-09, 
-           -9.676938400E-13,   1.129720500E+04,  -2.747565400E+00,</floatArray>
-        </NASA>
-      </thermo>
-    </species>
-
-    <!--    species SI2    -->
-    <species name="SI2">
-      <atomArray>Si:2 </atomArray>
-      <thermo>
-        <NASA P0="100000.0" Tmax="1000.0" Tmin="300.0">
-          <floatArray name="coeffs" size="7">
-            2.967197600E+00,   6.311955800E-03,  -1.097079000E-05,   8.927868000E-09, 
-           -2.787368900E-12,   6.987073800E+04,   9.278950300E+00,</floatArray>
-        </NASA>
-        <NASA P0="100000.0" Tmax="2000.0" Tmin="1000.0">
-          <floatArray name="coeffs" size="7">
-            4.144677900E+00,   6.523467700E-04,  -5.010852000E-07,   1.806284300E-10, 
-           -2.516111100E-14,   6.969470700E+04,   3.862736600E+00,</floatArray>
-        </NASA>
-      </thermo>
-    </species>
-
-    <!--    species SI3    -->
-    <species name="SI3">
-      <atomArray>Si:3 </atomArray>
-      <thermo>
-        <NASA P0="100000.0" Tmax="1000.0" Tmin="300.0">
-          <floatArray name="coeffs" size="7">
-            4.597912900E+00,   1.071527400E-02,  -1.610042200E-05,   1.096920700E-08, 
-           -2.783287500E-12,   7.476632400E+04,   3.442167100E+00,</floatArray>
-        </NASA>
-        <NASA P0="100000.0" Tmax="5000.0" Tmin="1000.0">
-          <floatArray name="coeffs" size="7">
-            7.421336000E+00,  -1.170994800E-04,   8.982077500E-08,   7.193596400E-12, 
-           -2.567083700E-15,   7.414669900E+04,  -1.036527400E+01,</floatArray>
-        </NASA>
-      </thermo>
-    </species>
-  </speciesData>
-  <reactionData id="reaction_data">
-
-    <!--   reaction 0001    -->
-    <reaction id="0001" reversible="yes">
-      <equation>SIH4 + H [=] SIH3 + H2</equation>
-      <rateCoeff>
-        <Arrhenius>
-          <A units="cm3/mol/s">  7.800000E+14</A>
-          <b>0</b>
-          <E units="cal/mol">2260.000000</E>
-        </Arrhenius>
-      </rateCoeff>
-      <reactants>SIH4:1 H:1</reactants>
-      <products>H2:1 SIH3:1</products>
-    </reaction>
-
-    <!--   reaction 0002    -->
-    <reaction id="0002" reversible="yes" type="threeBody">
-      <equation>SIH4 + M [=] SIH3 + H + M</equation>
-      <rateCoeff>
-        <Arrhenius>
-          <A units="cm3/mol/s">  3.910000E+15</A>
-          <b>0</b>
-          <E units="cal/mol">89356.000000</E>
-        </Arrhenius>
-      </rateCoeff>
-      <reactants>SIH4:1</reactants>
-      <products>H:1 SIH3:1</products>
-    </reaction>
-
-    <!--   reaction 0003    -->
-    <reaction id="0003" reversible="yes">
-      <equation>SIH3 + H [=] SIH2 + H2</equation>
-      <rateCoeff>
-        <Arrhenius>
-          <A units="cm3/mol/s">  7.800000E+14</A>
-          <b>0</b>
-          <E units="cal/mol">2260.000000</E>
-        </Arrhenius>
-      </rateCoeff>
-      <reactants>H:1 SIH3:1</reactants>
-      <products>H2:1 SIH2:1</products>
-    </reaction>
-
-    <!--   reaction 0004    -->
-    <reaction id="0004" reversible="yes" type="threeBody">
-      <equation>SI + SI + M [=] SI2 + M</equation>
-      <rateCoeff>
-        <Arrhenius>
-          <A units="cm6/mol2/s">  2.470000E+16</A>
-          <b>0</b>
-          <E units="cal/mol">1178.000000</E>
-        </Arrhenius>
-      </rateCoeff>
-      <reactants>SI:2</reactants>
-      <products>SI2:1</products>
-    </reaction>
-
-    <!--   reaction 0005    -->
-    <reaction id="0005" reversible="yes">
-      <equation>SIH4 + SIH2 [=] H3SISIH + H2</equation>
-      <rateCoeff>
-        <Arrhenius>
-          <A units="cm3/mol/s">  1.300000E+13</A>
-          <b>0</b>
-          <E units="cal/mol">0.000000</E>
-        </Arrhenius>
-      </rateCoeff>
-      <reactants>SIH4:1 SIH2:1</reactants>
-      <products>H2:1 H3SISIH:1</products>
-    </reaction>
-
-    <!--   reaction 0006    -->
-    <reaction id="0006" reversible="yes">
-      <equation>SIH + H2 [=] SIH2 + H</equation>
-      <rateCoeff>
-        <Arrhenius>
-          <A units="cm3/mol/s">  4.800000E+14</A>
-          <b>0</b>
-          <E units="cal/mol">23.640000</E>
-        </Arrhenius>
-      </rateCoeff>
-      <reactants>H2:1 SIH:1</reactants>
-      <products>H:1 SIH2:1</products>
-    </reaction>
-
-    <!--   reaction 0007    -->
-    <reaction id="0007" reversible="yes">
-      <equation>SIH + SIH4 [=] H3SISIH + H</equation>
-      <rateCoeff>
-        <Arrhenius>
-          <A units="cm3/mol/s">  1.600000E+14</A>
-          <b>0</b>
-          <E units="cal/mol">0.000000</E>
-        </Arrhenius>
-      </rateCoeff>
-      <reactants>SIH4:1 SIH:1</reactants>
-      <products>H:1 H3SISIH:1</products>
-    </reaction>
-
-    <!--   reaction 0008    -->
-    <reaction id="0008" reversible="yes">
-      <equation>SI + H2 [=] SIH + H</equation>
-      <rateCoeff>
-        <Arrhenius>
-          <A units="cm3/mol/s">  1.500000E+15</A>
-          <b>0</b>
-          <E units="cal/mol">31.800000</E>
-        </Arrhenius>
-      </rateCoeff>
-      <reactants>H2:1 SI:1</reactants>
-      <products>H:1 SIH:1</products>
-    </reaction>
-
-    <!--   reaction 0009    -->
-    <reaction id="0009" reversible="yes" type="falloff">
-      <equation>SIH4 (+ M) [=] SIH2 + H2 (+ M)</equation>
-      <rateCoeff>
-        <Arrhenius>
-          <A units="/s">  3.119000E+09</A>
-          <b>1.669</b>
-          <E units="cal/mol">54710.000000</E>
-        </Arrhenius>
-        <Arrhenius name="k0">
-          <A units="cm3/mol/s">  5.214000E+29</A>
-          <b>-3.5449999999999999</b>
-          <E units="cal/mol">57550.000000</E>
-        </Arrhenius>
-        <efficiencies default="1.0"> SI2H6:4  SIH4:4 </efficiencies>
-        <falloff type="Troe">-0.4984 888.3 209.4 2760 </falloff>
-      </rateCoeff>
-      <reactants>SIH4:1</reactants>
-      <products>H2:1 SIH2:1</products>
-    </reaction>
-
-    <!--   reaction 0010    -->
-    <reaction id="0010" reversible="yes" type="falloff">
-      <equation>H3SISIH (+ M) [=] H2SISIH2 (+ M)</equation>
-      <rateCoeff>
-        <Arrhenius>
-          <A units="/s">  2.540000E+13</A>
-          <b>-0.22389999999999999</b>
-          <E units="cal/mol">5381.000000</E>
-        </Arrhenius>
-        <Arrhenius name="k0">
-          <A units="cm3/mol/s">  1.099000E+33</A>
-          <b>-5.7649999999999997</b>
-          <E units="cal/mol">9152.000000</E>
-        </Arrhenius>
-        <efficiencies default="1.0"> SI2H6:4  SIH4:4 </efficiencies>
-        <falloff type="Troe">-0.4202 214.5 103 136.3 </falloff>
-      </rateCoeff>
-      <reactants>H3SISIH:1</reactants>
-      <products>H2SISIH2:1</products>
-    </reaction>
-
-    <!--   reaction 0011    -->
-    <reaction id="0011" reversible="yes" type="falloff">
-      <equation>SI3H8 (+ M) [=] SIH4 + H3SISIH (+ M)</equation>
-      <rateCoeff>
-        <Arrhenius>
-          <A units="/s">  3.730000E+12</A>
-          <b>0.99199999999999999</b>
-          <E units="cal/mol">50850.000000</E>
-        </Arrhenius>
-        <Arrhenius name="k0">
-          <A units="cm3/mol/s">  4.360000E+76</A>
-          <b>-17.260000000000002</b>
-          <E units="cal/mol">59303.000000</E>
-        </Arrhenius>
-        <efficiencies default="1.0"> SI2H6:4  SIH4:4 </efficiencies>
-        <falloff type="Troe">0.4157 365.3 3102 9.724 </falloff>
-      </rateCoeff>
-      <reactants>SI3H8:1</reactants>
-      <products>SIH4:1 H3SISIH:1</products>
-    </reaction>
-
-    <!--   reaction 0012    -->
-    <reaction id="0012" reversible="yes" type="falloff">
-      <equation>SI3H8 (+ M) [=] SIH2 + SI2H6 (+ M)</equation>
-      <rateCoeff>
-        <Arrhenius>
-          <A units="/s">  6.970000E+12</A>
-          <b>0.96909999999999996</b>
-          <E units="cal/mol">52677.000000</E>
-        </Arrhenius>
-        <Arrhenius name="k0">
-          <A units="cm3/mol/s">  1.730000E+69</A>
-          <b>-15.07</b>
-          <E units="cal/mol">60491.000000</E>
-        </Arrhenius>
-        <efficiencies default="1.0"> SI2H6:4  SIH4:4 </efficiencies>
-        <falloff type="Troe">-3.47e-05 442 2412 128.3 </falloff>
-      </rateCoeff>
-      <reactants>SI3H8:1</reactants>
-      <products>SI2H6:1 SIH2:1</products>
-    </reaction>
-
-    <!--   reaction 0013    -->
-    <reaction id="0013" reversible="yes" type="falloff">
-      <equation>SI2H6 (+ M) [=] H2 + H3SISIH (+ M)</equation>
-      <rateCoeff>
-        <Arrhenius>
-          <A units="/s">  9.086000E+09</A>
-          <b>1.8340000000000001</b>
-          <E units="cal/mol">54197.000000</E>
-        </Arrhenius>
-        <Arrhenius name="k0">
-          <A units="cm3/mol/s">  1.945000E+44</A>
-          <b>-7.7720000000000002</b>
-          <E units="cal/mol">59023.000000</E>
-        </Arrhenius>
-        <efficiencies default="1.0"> SI2H6:4  SIH4:4 </efficiencies>
-        <falloff type="Troe">-0.1224 793.3 2400 11.39 </falloff>
-      </rateCoeff>
-      <reactants>SI2H6:1</reactants>
-      <products>H2:1 H3SISIH:1</products>
-    </reaction>
-
-    <!--   reaction 0014    -->
-    <reaction id="0014" reversible="yes" type="falloff">
-      <equation>SI2H6 (+ M) [=] SIH4 + SIH2 (+ M)</equation>
-      <rateCoeff>
-        <Arrhenius>
-          <A units="/s">  1.810000E+10</A>
-          <b>1.7470000000000001</b>
-          <E units="cal/mol">50203.000000</E>
-        </Arrhenius>
-        <Arrhenius name="k0">
-          <A units="cm3/mol/s">  5.090000E+53</A>
-          <b>-10.369999999999999</b>
-          <E units="cal/mol">56034.000000</E>
-        </Arrhenius>
-        <efficiencies default="1.0"> SI2H6:4  SIH4:4 </efficiencies>
-        <falloff type="Troe">4.375e-05 438.5 2726 438.2 </falloff>
-      </rateCoeff>
-      <reactants>SI2H6:1</reactants>
-      <products>SIH4:1 SIH2:1</products>
-    </reaction>
-  </reactionData>
-</ctml>

tools/Makefile.in

@@ -5,7 +5,7 @@
 #
 all: kernel 
 
-install: templates-install
+install: templates-install apps-install
 
 kernel:
 	cd src; @MAKE@
@@ -13,7 +13,7 @@ kernel:
 
 apps-install:
 	@INSTALL@ -d @prefix@/bin
-	@INSTALL@ ../bin/ck2ctml @prefix@/bin
+	@INSTALL@ ../bin/ck2cti @prefix@/bin
 
 clean:
 	$(RM) *.*~ 

tools/src/Makefile.in

@@ -20,11 +20,7 @@ CANTERALIB_DEP = @buildlib@/libcantera.a \
 .cpp.o:
 	@CXX@ -c $< @DEFS@  $(INCDIR) @CXXFLAGS@ $(CXX_FLAGS) 
 
-all: $(BINDIR)/ck2ctml $(BINDIR)/cti2ctml $(BINDIR)/ck2cti
+all: $(BINDIR)/cti2ctml $(BINDIR)/ck2cti
-
-$(BINDIR)/ck2ctml: ck2ctml.o $(CONVLIB_DEP) $(CANTERALIB_DEP)
-	@CXX@ -o $(BINDIR)/ck2ctml ck2ctml.o $(LCXX_FLAGS) -lconverters $(LOCAL_LIBS) \
-               $(LCXX_END_LIBS)
 
 $(BINDIR)/ck2cti: ck2cti.o $(CONVLIB_DEP) $(CANTERALIB_DEP)
 	@CXX@ -o $(BINDIR)/ck2cti ck2cti.o $(LCXX_FLAGS) -lconverters $(LOCAL_LIBS) \