diff --git a/interfaces/matlab/toolbox/1D/@Domain1D/Domain1D.m b/interfaces/matlab/toolbox/1D/@Domain1D/Domain1D.m
index 7fd2e2680..be9631872 100755
--- a/interfaces/matlab/toolbox/1D/@Domain1D/Domain1D.m
+++ b/interfaces/matlab/toolbox/1D/@Domain1D/Domain1D.m
@@ -1,42 +1,42 @@
 function d = Domain1D(a, b, c, d, e)
-% DOMAIN1D - Create a new one-dimensional domain. 
+% DOMAIN1D - Create a new one-dimensional domain.
 %
 d.dom_id = -1;
 
 if nargin == 1
-  d.dom_id = domain_methods(0, a);
+    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), 1);
+    % 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), 1);
+        else
+            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 argument type. Expecting instance of class Solution.');
+        error('wrong object type');
     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
 elseif nargin == 3
-  if a == 1
-    if isa(b,'Solution')
-      d.dom_id = domain_methods(0, 1, thermo_hndl(b), kinetics_hndl(b), ...
-				trans_hndl(b), c);
+    if a == 1
+        if isa(b,'Solution')
+            d.dom_id = domain_methods(0, 1, thermo_hndl(b), kinetics_hndl(b), ...
+                trans_hndl(b), c);
+        else
+            error('Wrong argument type. Expecting instance of class Solution.');
+        end
     else
-      error('Wrong argument type. Expecting instance of class Solution.');
+        error('unknown domain type');
     end
-  else
-    error('unknown domain type');
-  end
 end
 if d.dom_id < 0
-  error(geterr);
+    error(geterr);
 end
 d.domain_type = a;
 d = class(d, 'Domain1D');
diff --git a/interfaces/matlab/toolbox/1D/@Domain1D/componentIndex.m b/interfaces/matlab/toolbox/1D/@Domain1D/componentIndex.m
index cfc223ed6..c3a357ae8 100644
--- a/interfaces/matlab/toolbox/1D/@Domain1D/componentIndex.m
+++ b/interfaces/matlab/toolbox/1D/@Domain1D/componentIndex.m
@@ -1,9 +1,8 @@
 function n = componentIndex(d, name)
-% COMPONENTINDEX - 
-%   
+% COMPONENTINDEX -
+%
 if isa(name,'double')
-  n = name;
+    n = name;
 else
-  n = domain_methods(d.dom_id, 18, name);
+    n = domain_methods(d.dom_id, 18, name);
 end
-
diff --git a/interfaces/matlab/toolbox/1D/@Domain1D/componentName.m b/interfaces/matlab/toolbox/1D/@Domain1D/componentName.m
index 91eb86d6d..de03989e9 100644
--- a/interfaces/matlab/toolbox/1D/@Domain1D/componentName.m
+++ b/interfaces/matlab/toolbox/1D/@Domain1D/componentName.m
@@ -1,7 +1,7 @@
 function s = componentName(d, n)
 % COMPONENTNAME - Name of component n.
-%   
+%
 m = length(n);
 for i = 1:m
-  s{i} = domain_methods(d.dom_id, 40, n(i));
+    s{i} = domain_methods(d.dom_id, 40, n(i));
 end
diff --git a/interfaces/matlab/toolbox/1D/@Domain1D/disableEnergy.m b/interfaces/matlab/toolbox/1D/@Domain1D/disableEnergy.m
index f60bede4d..708e258b8 100644
--- a/interfaces/matlab/toolbox/1D/@Domain1D/disableEnergy.m
+++ b/interfaces/matlab/toolbox/1D/@Domain1D/disableEnergy.m
@@ -1,4 +1,4 @@
 function d = disableEnergy(d)
 % ENABLEENERGY - enable the energy equation
-%   
+%
 domain_methods(d.dom_id, 66, 0);
diff --git a/interfaces/matlab/toolbox/1D/@Domain1D/domainIndex.m b/interfaces/matlab/toolbox/1D/@Domain1D/domainIndex.m
index 687c29008..0b5892064 100644
--- a/interfaces/matlab/toolbox/1D/@Domain1D/domainIndex.m
+++ b/interfaces/matlab/toolbox/1D/@Domain1D/domainIndex.m
@@ -1,6 +1,6 @@
 function i = domainIndex(d)
 % DOMAININDEX - domain index.
-%   
+%
 %     This function returns an integer flag denoting the location
 %     of the domain, beginning with 1 at the left.
 %
diff --git a/interfaces/matlab/toolbox/1D/@Domain1D/domainType.m b/interfaces/matlab/toolbox/1D/@Domain1D/domainType.m
index 6902ec7af..48e35ddc9 100644
--- a/interfaces/matlab/toolbox/1D/@Domain1D/domainType.m
+++ b/interfaces/matlab/toolbox/1D/@Domain1D/domainType.m
@@ -1,6 +1,6 @@
 function i = domainType(d)
 % DOMAINTYPE - Type of domain.
-%   
+%
 %     This function returns an integer flag denoting the domain
 %     type.
 i = domain_methods(d.dom_id, 12);
diff --git a/interfaces/matlab/toolbox/1D/@Domain1D/domain_hndl.m b/interfaces/matlab/toolbox/1D/@Domain1D/domain_hndl.m
index 17ca3d452..4632d3545 100644
--- a/interfaces/matlab/toolbox/1D/@Domain1D/domain_hndl.m
+++ b/interfaces/matlab/toolbox/1D/@Domain1D/domain_hndl.m
@@ -1,5 +1,5 @@
 function n = domain_hndl(d)
 % DOMAIN_HNDL - Integer used to access kernel object.
-%   
+%
 n = d.dom_id;
 
diff --git a/interfaces/matlab/toolbox/1D/@Domain1D/gridPoints.m b/interfaces/matlab/toolbox/1D/@Domain1D/gridPoints.m
index 83385236d..38d5d854a 100644
--- a/interfaces/matlab/toolbox/1D/@Domain1D/gridPoints.m
+++ b/interfaces/matlab/toolbox/1D/@Domain1D/gridPoints.m
@@ -1,15 +1,13 @@
 function zz = gridPoints(d, n)
-% GRID - 
-%   
+% GRID -
+%
 if nargin == 1
-  for i = 1:nPoints(d)
-    zz(i) = domain_methods(d.dom_id, 19, i);
-  end
+    for i = 1:nPoints(d)
+        zz(i) = domain_methods(d.dom_id, 19, i);
+    end
 else
-  m = length(n);
-  for i = 1:m
-    zz(i) = domain_methods(d.dom_id, 19, n(i));
-  end
+    m = length(n);
+    for i = 1:m
+        zz(i) = domain_methods(d.dom_id, 19, n(i));
+    end
 end
-
-
diff --git a/interfaces/matlab/toolbox/1D/@Domain1D/isFlow.m b/interfaces/matlab/toolbox/1D/@Domain1D/isFlow.m
index fc4c6fd29..2aa39a211 100644
--- a/interfaces/matlab/toolbox/1D/@Domain1D/isFlow.m
+++ b/interfaces/matlab/toolbox/1D/@Domain1D/isFlow.m
@@ -1,10 +1,9 @@
 function a = isFlow(d)
 % ISFLOW - Returns 1 if the domain is a flow domain, and 0 otherwise.
-%   
+%
 t = domainType(d);
 if t == 50
-  a = 1;
+    a = 1;
 else
-  a = 0;
+    a = 0;
 end
-
diff --git a/interfaces/matlab/toolbox/1D/@Domain1D/isInlet.m b/interfaces/matlab/toolbox/1D/@Domain1D/isInlet.m
index 9daac3580..664e88730 100644
--- a/interfaces/matlab/toolbox/1D/@Domain1D/isInlet.m
+++ b/interfaces/matlab/toolbox/1D/@Domain1D/isInlet.m
@@ -7,4 +7,3 @@ if t == 104
 else
   a = 0;
 end
-
diff --git a/interfaces/matlab/toolbox/1D/@Domain1D/isSurface.m b/interfaces/matlab/toolbox/1D/@Domain1D/isSurface.m
index 4c82a94d6..df3fc8c53 100644
--- a/interfaces/matlab/toolbox/1D/@Domain1D/isSurface.m
+++ b/interfaces/matlab/toolbox/1D/@Domain1D/isSurface.m
@@ -1,10 +1,9 @@
 function a = isSurface(d)
 % ISSURFACE - Returns 1 if the domain is a surface, and 0 otherwise.
-%   
+%
 t = domainType(d);
 if t == 102
-  a = 1;
+    a = 1;
 else
-  a = 0;
+    a = 0;
 end
-
diff --git a/interfaces/matlab/toolbox/1D/@Domain1D/massFlux.m b/interfaces/matlab/toolbox/1D/@Domain1D/massFlux.m
index c6e391cf4..58f06674d 100644
--- a/interfaces/matlab/toolbox/1D/@Domain1D/massFlux.m
+++ b/interfaces/matlab/toolbox/1D/@Domain1D/massFlux.m
@@ -1,5 +1,4 @@
 function mdot = massFlux(d)
-% MASSFLUX - 
-%   
+% MASSFLUX -
+%
 mdot = domain_methods(d.dom_id, 17);
-
diff --git a/interfaces/matlab/toolbox/1D/@Domain1D/massFraction.m b/interfaces/matlab/toolbox/1D/@Domain1D/massFraction.m
index f5864dd78..c76c6373c 100644
--- a/interfaces/matlab/toolbox/1D/@Domain1D/massFraction.m
+++ b/interfaces/matlab/toolbox/1D/@Domain1D/massFraction.m
@@ -1,17 +1,16 @@
 function y = massFraction(d, k)
 % MASSFRACTION - Mass fraction of species k.
-%   
+%
 %    This method returns the mass fraction of species k, where
 %    k is the integer index of the species in the flow domain
 %    to which the boundary domain is attached.
 %
 if domainIndex(d) == 0
-  error('no flow domain attached!')
+    error('no flow domain attached!')
 end
 
 if isInlet(d)
-  y = domain_methods(d.dom_id,16,k-1);
+    y = domain_methods(d.dom_id,16,k-1);
 else
-  error('not yet...');
+    error('not yet...');
 end
-
diff --git a/interfaces/matlab/toolbox/1D/@Domain1D/nComponents.m b/interfaces/matlab/toolbox/1D/@Domain1D/nComponents.m
index b1ec5d366..bc46e423a 100644
--- a/interfaces/matlab/toolbox/1D/@Domain1D/nComponents.m
+++ b/interfaces/matlab/toolbox/1D/@Domain1D/nComponents.m
@@ -1,4 +1,4 @@
 function n = nComponents(d)
 % NCOMPONENTS - number of components
-%   
+%
 n = domain_methods(d.dom_id, 11);
diff --git a/interfaces/matlab/toolbox/1D/@Domain1D/nPoints.m b/interfaces/matlab/toolbox/1D/@Domain1D/nPoints.m
index d2c7da4e6..489c4f940 100644
--- a/interfaces/matlab/toolbox/1D/@Domain1D/nPoints.m
+++ b/interfaces/matlab/toolbox/1D/@Domain1D/nPoints.m
@@ -2,4 +2,3 @@ function npts = nPoints(d)
 % NPOINTS - Number of grid points.
 %   
 npts = domain_methods(d.dom_id, 14);
-
diff --git a/interfaces/matlab/toolbox/1D/@Domain1D/private/domain_methods.m b/interfaces/matlab/toolbox/1D/@Domain1D/private/domain_methods.m
index bc5e68afa..31e33ab5a 100644
--- a/interfaces/matlab/toolbox/1D/@Domain1D/private/domain_methods.m
+++ b/interfaces/matlab/toolbox/1D/@Domain1D/private/domain_methods.m
@@ -1,15 +1,15 @@
 function v = domain_methods(n, job, a, b, c, d)
 %
 if nargin == 2
-  v = ctmethods(90, n, job);
+    v = ctmethods(90, n, job);
 elseif nargin == 3
-  v = ctmethods(90, n, job, a);  
+    v = ctmethods(90, n, job, a);
 elseif nargin == 4
-  v = ctmethods(90, n, job, a, b);    
+    v = ctmethods(90, n, job, a, b);
 elseif nargin == 5
-  v = ctmethods(90, n, job, a, b, c);  
+    v = ctmethods(90, n, job, a, b, c);
 elseif nargin == 6
-  v = ctmethods(90, n, job, a, b, c, d); 
+    v = ctmethods(90, n, job, a, b, c, d);
 elseif nargin == 7
-  v = ctmethods(90, n, job, a, b, c, d, e);   
+    v = ctmethods(90, n, job, a, b, c, d, e);
 end
diff --git a/interfaces/matlab/toolbox/1D/@Domain1D/set.m b/interfaces/matlab/toolbox/1D/@Domain1D/set.m
index 8d7019b23..86f9cbd95 100644
--- a/interfaces/matlab/toolbox/1D/@Domain1D/set.m
+++ b/interfaces/matlab/toolbox/1D/@Domain1D/set.m
@@ -1,8 +1,8 @@
 function a = set(a,varargin)
 % SET -  Set properties.
 %
-%   The properties that may be set are 
-%    
+%   The properties that may be set are
+%
 %   Either the full property name or the symbol may be
 %   specified. For the extensive properties (V,H,U,S), the values
 %   must be given per unit mass. H, U, and S must be set in
@@ -25,62 +25,62 @@ function a = set(a,varargin)
 %
 
 property_argin = varargin;
-  
+
 while length(property_argin) >= 2,
-   prop = property_argin{1};
-   val = property_argin{2};
-   property_argin = property_argin(3:end);
-   switch prop
-     case 'Temperature'
-       setTemperature(a,val);
-     case 'T'
-       setTemperature(a,val);       
-     case 'MassFractions'
-       setMassFractions(a,val);       
-     case 'Y'
-       setMassFractions(a,val);              
-    case 'mdot'
-       setMdot(a,val);
-    case 'MassFlux'
-       setMdot(a,val);       
-    case 'P'
-       setPressure(a,val);
-    case 'Pressure'
-       setPressure(a,val);       
-    case 'tol'
-       sz = size(val);
-       if sz == nComponents(a)
-	 setTolerances(a, val(1,:), val(2,:));
-       elseif length(val) == 2
-	 setTolerances(a, 'default', val(1), val(2));
-       else
-	 error('wrong array size for error tolerances');
-       end
-    case 'tol-time'
-       sz = size(val);
-       if sz == nComponents(a)
-	 setTolerances(a, val(1,:), val(2,:));
-       elseif length(val) == 2
-	 rt = val(1);
-	 at = val(2);
-	 setTolerances(a, 'default', rt, at, 'ts');	 
-       else
-	 error('wrong array size for error tolerances');
-       end       
-    case 'grid'
-       setupGrid(a, val);
-    case 'bounds'
-       setBounds(a, val(1,:), val(2,:));
-    case 'X'
-       setMoleFractions(a, val);
-    case 'MoleFractions'
-       setMoleFractions(a, val);
-    case 'T_fixed'
-       setFixedTempProfile(a, val);
-    case 'ID'
-       setID(a, val);
-     otherwise
-       error(['unknown property ' char(prop)]);
-   end
+    prop = property_argin{1};
+    val = property_argin{2};
+    property_argin = property_argin(3:end);
+    switch prop
+        case 'Temperature'
+            setTemperature(a,val);
+        case 'T'
+            setTemperature(a,val);
+        case 'MassFractions'
+            setMassFractions(a,val);
+        case 'Y'
+            setMassFractions(a,val);
+        case 'mdot'
+            setMdot(a,val);
+        case 'MassFlux'
+            setMdot(a,val);
+        case 'P'
+            setPressure(a,val);
+        case 'Pressure'
+            setPressure(a,val);
+        case 'tol'
+            sz = size(val);
+            if sz == nComponents(a)
+                setTolerances(a, val(1,:), val(2,:));
+            elseif length(val) == 2
+                setTolerances(a, 'default', val(1), val(2));
+            else
+                error('wrong array size for error tolerances');
+            end
+        case 'tol-time'
+            sz = size(val);
+            if sz == nComponents(a)
+                setTolerances(a, val(1,:), val(2,:));
+            elseif length(val) == 2
+                rt = val(1);
+                at = val(2);
+                setTolerances(a, 'default', rt, at, 'ts');
+            else
+                error('wrong array size for error tolerances');
+            end
+        case 'grid'
+            setupGrid(a, val);
+        case 'bounds'
+            setBounds(a, val(1,:), val(2,:));
+        case 'X'
+            setMoleFractions(a, val);
+        case 'MoleFractions'
+            setMoleFractions(a, val);
+        case 'T_fixed'
+            setFixedTempProfile(a, val);
+        case 'ID'
+            setID(a, val);
+        otherwise
+            error(['unknown property ' char(prop)]);
+    end
 end
 
diff --git a/interfaces/matlab/toolbox/1D/@Domain1D/setBounds.m b/interfaces/matlab/toolbox/1D/@Domain1D/setBounds.m
index 078e91576..08762d61e 100644
--- a/interfaces/matlab/toolbox/1D/@Domain1D/setBounds.m
+++ b/interfaces/matlab/toolbox/1D/@Domain1D/setBounds.m
@@ -1,5 +1,5 @@
 function d = setBounds(d, component, lower, upper)
-% SETBOUNDS - 
-%   
+% SETBOUNDS -
+%
 n = componentIndex(d,component);
 domain_methods(d.dom_id, 51, n, lower, upper);
diff --git a/interfaces/matlab/toolbox/1D/@Domain1D/setCoverageEqs.m b/interfaces/matlab/toolbox/1D/@Domain1D/setCoverageEqs.m
index 6ea7c4d9d..b1bb2699f 100644
--- a/interfaces/matlab/toolbox/1D/@Domain1D/setCoverageEqs.m
+++ b/interfaces/matlab/toolbox/1D/@Domain1D/setCoverageEqs.m
@@ -1,20 +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.')
+    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
+    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;
+    ion = onoff;
 end
-domain_methods(d.dom_id, 120, ion);
\ No newline at end of file
+domain_methods(d.dom_id, 120, ion);
diff --git a/interfaces/matlab/toolbox/1D/@Domain1D/setID.m b/interfaces/matlab/toolbox/1D/@Domain1D/setID.m
index 4a325d0f0..d83241be6 100644
--- a/interfaces/matlab/toolbox/1D/@Domain1D/setID.m
+++ b/interfaces/matlab/toolbox/1D/@Domain1D/setID.m
@@ -1,4 +1,4 @@
 function d = setID(d, id)
 % SETID - Set the ID tag for the domain.
-%   
+%
 domain_methods(d.dom_id, 54, id);
diff --git a/interfaces/matlab/toolbox/1D/@Domain1D/setMdot.m b/interfaces/matlab/toolbox/1D/@Domain1D/setMdot.m
index 98647488a..49a575b11 100644
--- a/interfaces/matlab/toolbox/1D/@Domain1D/setMdot.m
+++ b/interfaces/matlab/toolbox/1D/@Domain1D/setMdot.m
@@ -1,4 +1,4 @@
 function d = setMdot(d, mdot)
-% SETMDOT - 
-%   
+% SETMDOT -
+%
 domain_methods(d.dom_id, 60, mdot);
diff --git a/interfaces/matlab/toolbox/1D/@Domain1D/setMoleFractions.m b/interfaces/matlab/toolbox/1D/@Domain1D/setMoleFractions.m
index ac9d7b5b7..03e5f22a5 100644
--- a/interfaces/matlab/toolbox/1D/@Domain1D/setMoleFractions.m
+++ b/interfaces/matlab/toolbox/1D/@Domain1D/setMoleFractions.m
@@ -1,4 +1,4 @@
 function d = setMoleFractions(d, x)
-% SETMOLEFRACTIONS - 
-%   
+% SETMOLEFRACTIONS -
+%
 domain_methods(d.dom_id, 62, x);
diff --git a/interfaces/matlab/toolbox/1D/@Domain1D/setPressure.m b/interfaces/matlab/toolbox/1D/@Domain1D/setPressure.m
index 02df91ed4..7e5a09f2e 100644
--- a/interfaces/matlab/toolbox/1D/@Domain1D/setPressure.m
+++ b/interfaces/matlab/toolbox/1D/@Domain1D/setPressure.m
@@ -1,5 +1,4 @@
 function d = setPressure(d, p)
-% SETPRESSURE - 
-%   
+% SETPRESSURE -
+%
 domain_methods(d.dom_id, 63, p);
-
diff --git a/interfaces/matlab/toolbox/1D/@Domain1D/setProfile.m b/interfaces/matlab/toolbox/1D/@Domain1D/setProfile.m
index 9abdfbec3..8ce7a5ac0 100644
--- a/interfaces/matlab/toolbox/1D/@Domain1D/setProfile.m
+++ b/interfaces/matlab/toolbox/1D/@Domain1D/setProfile.m
@@ -1,9 +1,8 @@
 function d = setProfile(d, n, p)
-% SETPROFILE - 
-%   
+% SETPROFILE -
+%
 if d.stack == 0
-  error('install domain in stack before calling setProfile.');
+    error('install domain in stack before calling setProfile.');
 end
 
 setProfile(d.stack,domainIndex(d),n,p);
-
diff --git a/interfaces/matlab/toolbox/1D/@Domain1D/setTemperature.m b/interfaces/matlab/toolbox/1D/@Domain1D/setTemperature.m
index 1a23e7058..d2412586f 100644
--- a/interfaces/matlab/toolbox/1D/@Domain1D/setTemperature.m
+++ b/interfaces/matlab/toolbox/1D/@Domain1D/setTemperature.m
@@ -1,4 +1,4 @@
 function d = setTemperature(d, t)
 % SETTEMPERATURE - Set the temperature [K].
-%   
+%
 domain_methods(d.dom_id, 61, t);
diff --git a/interfaces/matlab/toolbox/1D/@Domain1D/setTolerances.m b/interfaces/matlab/toolbox/1D/@Domain1D/setTolerances.m
index 28cd490ed..2592c5edb 100644
--- a/interfaces/matlab/toolbox/1D/@Domain1D/setTolerances.m
+++ b/interfaces/matlab/toolbox/1D/@Domain1D/setTolerances.m
@@ -1,35 +1,35 @@
 function d = setTolerances(d, component, rtol, atol, typ)
-% SETTOLERANCES - 
-%   
+% SETTOLERANCES -
+%
 ityp = 0;
 if nargin == 5
-  switch typ
-   case 'ts'
-    ityp = -1;
-   case 'time'
-    ityp = -1;
-   case 'ss'
-    ityp = 1;
-   case 'steady'
-    ityp = 1;
-  end
+    switch typ
+        case 'ts'
+            ityp = -1;
+        case 'time'
+            ityp = -1;
+        case 'ss'
+            ityp = 1;
+        case 'steady'
+            ityp = 1;
+    end
 end
 
 if strcmp(component,'default')
-  nc = nComponents(d);
-  for ii = 1:nc
-    domain_methods(d.dom_id, 52, ii, rtol, atol, ityp);
-  end
-  return
+    nc = nComponents(d);
+    for ii = 1:nc
+        domain_methods(d.dom_id, 52, ii, rtol, atol, ityp);
+    end
+    return
 end
-  
+
 if iscell(component)
-  nc = length(component);
-  for ii = 1:nc
-    n = componentIndex(d, component{ii});
-    domain_methods(d.dom_id, 52, n, rtol, atol, ityp);
-  end
+    nc = length(component);
+    for ii = 1:nc
+        n = componentIndex(d, component{ii});
+        domain_methods(d.dom_id, 52, n, rtol, atol, ityp);
+    end
 else
-  n = componentIndex(d, component);
-  domain_methods(d.dom_id, 52, n, rtol, atol, ityp);
+    n = componentIndex(d, component);
+    domain_methods(d.dom_id, 52, n, rtol, atol, ityp);
 end
diff --git a/interfaces/matlab/toolbox/1D/@Domain1D/setupGrid.m b/interfaces/matlab/toolbox/1D/@Domain1D/setupGrid.m
index 0922f24dc..bf50c5706 100644
--- a/interfaces/matlab/toolbox/1D/@Domain1D/setupGrid.m
+++ b/interfaces/matlab/toolbox/1D/@Domain1D/setupGrid.m
@@ -1,5 +1,4 @@
 function d = setupGrid(d, grid)
-% SETUPGRID - 
-%   
+% SETUPGRID -
+%
 domain_methods(d.dom_id, 53, grid);
-
diff --git a/interfaces/matlab/toolbox/1D/@Domain1D/temperature.m b/interfaces/matlab/toolbox/1D/@Domain1D/temperature.m
index d91e5e332..284e78d4e 100644
--- a/interfaces/matlab/toolbox/1D/@Domain1D/temperature.m
+++ b/interfaces/matlab/toolbox/1D/@Domain1D/temperature.m
@@ -1,5 +1,4 @@
 function t = temperature(d)
 % TEMPERATURE - Temperature [K].
-%   
+%
 t = domain_methods(d.dom_id, 15);
-
diff --git a/interfaces/matlab/toolbox/1D/@Domain1D/z.m b/interfaces/matlab/toolbox/1D/@Domain1D/z.m
index 3da29ffe2..22ff3a699 100644
--- a/interfaces/matlab/toolbox/1D/@Domain1D/z.m
+++ b/interfaces/matlab/toolbox/1D/@Domain1D/z.m
@@ -1,15 +1,13 @@
 function zz = z(d, n)
-% GRID - 
-%   
+% GRID -
+%
 if nargin == 1
-  for i = 1:nPoints(d)
-    zz(i) = domain_methods(d.dom_id, 19, i);
-  end
+    for i = 1:nPoints(d)
+        zz(i) = domain_methods(d.dom_id, 19, i);
+    end
 else
-  m = length(n);
-  for i = 1:m
-    zz(i) = domain_methods(d.dom_id, 19, n(i));
-  end
+    m = length(n);
+    for i = 1:m
+        zz(i) = domain_methods(d.dom_id, 19, n(i));
+    end
 end
-
-
diff --git a/interfaces/matlab/toolbox/1D/@Stack/Stack.m b/interfaces/matlab/toolbox/1D/@Stack/Stack.m
index e19c49134..9da6845f9 100644
--- a/interfaces/matlab/toolbox/1D/@Stack/Stack.m
+++ b/interfaces/matlab/toolbox/1D/@Stack/Stack.m
@@ -1,25 +1,24 @@
 function s = Stack(domains)
 %
-% STACK - A one-dimensional 'stack' of domains. 
-% 
+% STACK - A one-dimensional 'stack' of domains.
+%
 %    A stack object is a container for one-dimensional domains,
 %    which are instances of class Domain1D. The domains are of two
-%    types - extended domains, and connector domains. 
+%    types - extended domains, and connector domains.
 %
 s.stack_id = -1;
 s.domains = domains;
 if nargin == 1
-  nd = length(domains);
-  for n=1:nd
-    ids(n) = domain_hndl(domains(n));
-  end
-  s.stack_id = stack_methods(0, 8, nd, ids);
+    nd = length(domains);
+    for n=1:nd
+        ids(n) = domain_hndl(domains(n));
+    end
+    s.stack_id = stack_methods(0, 8, nd, ids);
 else
-  help(Stack);
-  error('wrong number of parameters');
+    help(Stack);
+    error('wrong number of parameters');
 end
 if s.stack_id < 0
-  error(geterr);
+    error(geterr);
 end
 s = class(s, 'Stack');
-
diff --git a/interfaces/matlab/toolbox/1D/@Stack/display.m b/interfaces/matlab/toolbox/1D/@Stack/display.m
index 368ba7333..6fea51b15 100644
--- a/interfaces/matlab/toolbox/1D/@Stack/display.m
+++ b/interfaces/matlab/toolbox/1D/@Stack/display.m
@@ -1,10 +1,9 @@
 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 = '-';
+    fname = '-';
 end
 stack_methods(s.stack_id, 103, fname);
-
diff --git a/interfaces/matlab/toolbox/1D/@Stack/domainIndex.m b/interfaces/matlab/toolbox/1D/@Stack/domainIndex.m
index 7beff60e0..1cbd9a147 100644
--- a/interfaces/matlab/toolbox/1D/@Stack/domainIndex.m
+++ b/interfaces/matlab/toolbox/1D/@Stack/domainIndex.m
@@ -1,7 +1,7 @@
 function n = domainIndex(d, name)
 % DOMAININDEX - Index of the domain with a specified name.
 if isa(name,'double')
-  n = name
+    n = name
 else
-  n = stack_methods(d.stack_id, 109, name);
+    n = stack_methods(d.stack_id, 109, name);
 end
diff --git a/interfaces/matlab/toolbox/1D/@Stack/grid.m b/interfaces/matlab/toolbox/1D/@Stack/grid.m
index 0ffde0e29..e451b8005 100644
--- a/interfaces/matlab/toolbox/1D/@Stack/grid.m
+++ b/interfaces/matlab/toolbox/1D/@Stack/grid.m
@@ -1,6 +1,6 @@
 function z = grid(s, d)
 % GRID - the grid in one domain.
-%   
+%
 n = domainIndex(s,d);
 d = s.domains(n);
 z = gridPoints(d);
diff --git a/interfaces/matlab/toolbox/1D/@Stack/plotSolution.m b/interfaces/matlab/toolbox/1D/@Stack/plotSolution.m
index 856278c3f..c925497fd 100644
--- a/interfaces/matlab/toolbox/1D/@Stack/plotSolution.m
+++ b/interfaces/matlab/toolbox/1D/@Stack/plotSolution.m
@@ -10,4 +10,3 @@ x = solution(s, domain, component);
 plot(z, x);
 xlabel('z (m)');
 ylabel(component);
-
diff --git a/interfaces/matlab/toolbox/1D/@Stack/private/stack_methods.m b/interfaces/matlab/toolbox/1D/@Stack/private/stack_methods.m
index b4df11529..624b6d63d 100644
--- a/interfaces/matlab/toolbox/1D/@Stack/private/stack_methods.m
+++ b/interfaces/matlab/toolbox/1D/@Stack/private/stack_methods.m
@@ -6,20 +6,19 @@ function v = stack_methods(n, job, a, b, c, d, e, f)
 %    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(90, n, job);
+    v = ctmethods(90, n, job);
 elseif nargin == 3
-  v = ctmethods(90, n, job, a);  
+    v = ctmethods(90, n, job, a);
 elseif nargin == 4
-  v = ctmethods(90, n, job, a, b);    
+    v = ctmethods(90, n, job, a, b);
 elseif nargin == 5
-  v = ctmethods(90, n, job, a, b, c);
+    v = ctmethods(90, n, job, a, b, c);
 elseif nargin == 6
-  v = ctmethods(90, n, job, a, b, c, d); 
+    v = ctmethods(90, n, job, a, b, c, d);
 elseif nargin == 7
-  v = ctmethods(90, n, job, a, b, c, d, e); 
+    v = ctmethods(90, n, job, a, b, c, d, e);
 elseif nargin == 8
-  v = ctmethods(90, n, job, a, b, c, d, e, f); 
+    v = ctmethods(90, n, job, a, b, c, d, e, f);
 else
-  error('too many arguments');
+    error('too many arguments');
 end
- 
\ No newline at end of file
diff --git a/interfaces/matlab/toolbox/1D/@Stack/resid.m b/interfaces/matlab/toolbox/1D/@Stack/resid.m
index b6764e42d..1707dc2b7 100644
--- a/interfaces/matlab/toolbox/1D/@Stack/resid.m
+++ b/interfaces/matlab/toolbox/1D/@Stack/resid.m
@@ -1,7 +1,7 @@
 function r = resid(s, domain, rdt, count)
 if nargin == 2
-  rdt = 0.0;
-  count = 0;
+    rdt = 0.0;
+    count = 0;
 end
 
 idom = domainIndex(s, domain);
@@ -10,7 +10,7 @@ d = s.domains(idom);
 r = zeros(nComponents(d), nPoints(d));
 stack_methods(s.stack_id, 113, rdt, count);
 for m = 1:nComponents(d)
-  for n = 1:nPoints(d)
-    r(m,n) = stack_methods(s.stack_id, 31, idom, m, n);
-  end
+    for n = 1:nPoints(d)
+        r(m,n) = stack_methods(s.stack_id, 31, idom, m, n);
+    end
 end
diff --git a/interfaces/matlab/toolbox/1D/@Stack/restore.m b/interfaces/matlab/toolbox/1D/@Stack/restore.m
index 90e6718fa..e9349259e 100644
--- a/interfaces/matlab/toolbox/1D/@Stack/restore.m
+++ b/interfaces/matlab/toolbox/1D/@Stack/restore.m
@@ -1,6 +1,6 @@
 function restore(s, fname, id)
 % RESTORE - Restore a previously-saved solution.
-%   
+%
 %   This method can be used to provide an initial guess for the
-%   solution. 
+%   solution.
 stack_methods(s.stack_id, 111, fname, id);
diff --git a/interfaces/matlab/toolbox/1D/@Stack/save.m b/interfaces/matlab/toolbox/1D/@Stack/save.m
index 7dfd2d5f4..2ce2bfd50 100644
--- a/interfaces/matlab/toolbox/1D/@Stack/save.m
+++ b/interfaces/matlab/toolbox/1D/@Stack/save.m
@@ -1,10 +1,10 @@
 function saveSoln(s, fname, id, desc)
-% SAVE - 
-%   
+% SAVE -
+%
 if nargin == 2
-  id = 'solution';
-  desc = '-';
+    id = 'solution';
+    desc = '-';
 elseif nargin == 3
-  desc = '-';
+    desc = '-';
 end
 stack_methods(s.stack_id, 107, fname, id, desc);
diff --git a/interfaces/matlab/toolbox/1D/@Stack/saveSoln.m b/interfaces/matlab/toolbox/1D/@Stack/saveSoln.m
index edad98dec..c9c3d417e 100644
--- a/interfaces/matlab/toolbox/1D/@Stack/saveSoln.m
+++ b/interfaces/matlab/toolbox/1D/@Stack/saveSoln.m
@@ -1,14 +1,14 @@
 function saveSoln(s, fname, id, desc)
 % SAVE - Save solution.
-%   
+%
 if nargin == 1
-  fname = 'soln.xml';
-  id = 'solution';
-  desc = '--';  
+    fname = 'soln.xml';
+    id = 'solution';
+    desc = '--';
 elseif nargin == 2
-  id = 'solution';
-  desc = '--';
+    id = 'solution';
+    desc = '--';
 elseif nargin == 3
-  desc = '--';
+    desc = '--';
 end
 stack_methods(s.stack_id, 107, fname, id, desc);
diff --git a/interfaces/matlab/toolbox/1D/@Stack/setFlatProfile.m b/interfaces/matlab/toolbox/1D/@Stack/setFlatProfile.m
index 8c58e46ad..06b7cbb7d 100644
--- a/interfaces/matlab/toolbox/1D/@Stack/setFlatProfile.m
+++ b/interfaces/matlab/toolbox/1D/@Stack/setFlatProfile.m
@@ -1,5 +1,4 @@
 function setFlatProfile(s, n, comp, v)
-% SETFLATPROFILE - 
-%   
+% SETFLATPROFILE -
+%
 stack_methods(s.stack_id, 102, n, comp, v);
-
diff --git a/interfaces/matlab/toolbox/1D/@Stack/setMaxJacAge.m b/interfaces/matlab/toolbox/1D/@Stack/setMaxJacAge.m
index 1bba4127b..5e3148a8b 100644
--- a/interfaces/matlab/toolbox/1D/@Stack/setMaxJacAge.m
+++ b/interfaces/matlab/toolbox/1D/@Stack/setMaxJacAge.m
@@ -1,8 +1,8 @@
 function setMaxJacAge(s, ss_age, ts_age)
-% SETMAXJACAGE - Set the number of times the Jacobian will be used 
+% SETMAXJACAGE - Set the number of times the Jacobian will be used
 % before it is recomputed.
-%   
+%
 if nargin == 2
-  ts_age = ss_age;
+    ts_age = ss_age;
 end
 stack_methods(s.stack_id, 114, ss_age, ts_age);
diff --git a/interfaces/matlab/toolbox/1D/@Stack/setProfile.m b/interfaces/matlab/toolbox/1D/@Stack/setProfile.m
index 5459ca12c..2822c3ef8 100644
--- a/interfaces/matlab/toolbox/1D/@Stack/setProfile.m
+++ b/interfaces/matlab/toolbox/1D/@Stack/setProfile.m
@@ -7,46 +7,44 @@ function setProfile(s, name, comp, p)
 %   v      --   array of values
 %
 %   The solution vector values for this component will be linearly
-%   interpolated from the discrete function defined by v vs. zr. 
+%   interpolated from the discrete function defined by v vs. zr.
 %   Note that zr = 0.0 corresponds to the leftmost grid point in
 %   the specified domain, and zr = 1.0 corresponds to the rightmost
 %   grid point. This method can be called at any time, but is
 %   usually used to set the initial guess for the solution.
 %
 %   Example:
-%      
+%
 %      zr = [0 0.1 0.2 0.4 0.8 1];
 %      v  = [500 650 700 730 800 900];
 %      setProfile(1, 2, zr, v);
 %
 if isa(name,'double')
-  n = name;
+    n = name;
 else
-  n = domainIndex(s, name);
+    n = domainIndex(s, name);
 end
 
 d = s.domains(n);
 
 if isa(comp,'double') | isa(comp,'cell')
-  c = comp;
+    c = comp;
 elseif isa(comp,'char')
-  c = {comp};
+    c = {comp};
 else
-  error('wrong type');
+    error('wrong type');
 end
 
 np = length(c);
 sz = size(p);
 if sz(1) == np + 1;
-  for j = 1:np
-    ic = componentIndex(d,c{j});
-    stack_methods(s.stack_id, 101, n, ic, p(1,:), p(j+1,:));
-  end
+    for j = 1:np
+        ic = componentIndex(d,c{j});
+        stack_methods(s.stack_id, 101, n, ic, p(1,:), p(j+1,:));
+    end
 elseif sz(2) == np + 1;
-  ic = componentIndex(d,c{j});
-  stack_methods(s.stack_id, 101, n, ic, p(:,1), p(:,j+1));
+    ic = componentIndex(d,c{j});
+    stack_methods(s.stack_id, 101, n, ic, p(:,1), p(:,j+1));
 else
-  error('wrong profile shape');
+    error('wrong profile shape');
 end
-
-
diff --git a/interfaces/matlab/toolbox/1D/@Stack/setRefineCriteria.m b/interfaces/matlab/toolbox/1D/@Stack/setRefineCriteria.m
index 41cb4b173..a064bb33e 100644
--- a/interfaces/matlab/toolbox/1D/@Stack/setRefineCriteria.m
+++ b/interfaces/matlab/toolbox/1D/@Stack/setRefineCriteria.m
@@ -11,20 +11,19 @@ function d = setRefineCriteria(d, n, ratio, slope, curve, prune)
 %                 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. 
-%   
+%                 neighboring point is already marked for deletion.
+%
 if nargin < 3
-  ratio = 10.0;
+    ratio = 10.0;
 end
 if nargin < 4
-  slope = 0.8;
+    slope = 0.8;
 end
 if nargin < 5
-  curve = 0.8;
+    curve = 0.8;
 end
 if nargin < 6
-  prune = -0.1;
+    prune = -0.1;
 end
 
 stack_methods(d.stack_id, 106, n, ratio, slope, curve, prune);
-
diff --git a/interfaces/matlab/toolbox/1D/@Stack/setValue.m b/interfaces/matlab/toolbox/1D/@Stack/setValue.m
index 4c95d238a..200e6f2fa 100644
--- a/interfaces/matlab/toolbox/1D/@Stack/setValue.m
+++ b/interfaces/matlab/toolbox/1D/@Stack/setValue.m
@@ -1,6 +1,6 @@
 function setValue(s, n, comp, localPoint, v)
 % SETVALUE - Set the value of a single entry in the solution vector.
-%   
+%
 %    n           -- domain number
 %    comp        -- component number
 %    localPoint  -- local index of the grid point in the domain
@@ -17,4 +17,3 @@ function setValue(s, n, comp, localPoint, v)
 %    stack.
 %
 stack_methods(s.stack_id, 100, n, comp, localPoint, v);
-
diff --git a/interfaces/matlab/toolbox/1D/@Stack/solution.m b/interfaces/matlab/toolbox/1D/@Stack/solution.m
index a7f3a4129..e4381eff5 100644
--- a/interfaces/matlab/toolbox/1D/@Stack/solution.m
+++ b/interfaces/matlab/toolbox/1D/@Stack/solution.m
@@ -3,21 +3,21 @@ function x = solution(s, domain, component)
 %
 %    x = solution(s, 'flow', 'T') returns in vector x the values of
 %    solution component 'T' in domain 'flow'.
-%   
+%
 idom = domainIndex(s, domain);
 d = s.domains(idom);
 
 if nargin == 3
-  icomp = componentIndex(d, component);
-  for n = 1:nPoints(d)
-    x(n) = stack_methods(s.stack_id, 30, idom, icomp, n);
-  end
+    icomp = componentIndex(d, component);
+    for n = 1:nPoints(d)
+        x(n) = stack_methods(s.stack_id, 30, idom, icomp, n);
+    end
 else
-  nc = nComponents(d);
-  np = nPoints(d);
-  for m = 1:nc
-    for n = 1:np
-      x(m,n) = stack_methods(s.stack_id, 30, idom, m, n);
-    end    
-  end
+    nc = nComponents(d);
+    np = nPoints(d);
+    for m = 1:nc
+        for n = 1:np
+            x(m,n) = stack_methods(s.stack_id, 30, idom, m, n);
+        end
+    end
 end
diff --git a/interfaces/matlab/toolbox/1D/@Stack/solve.m b/interfaces/matlab/toolbox/1D/@Stack/solve.m
index 0481024e3..e8088dad3 100644
--- a/interfaces/matlab/toolbox/1D/@Stack/solve.m
+++ b/interfaces/matlab/toolbox/1D/@Stack/solve.m
@@ -1,5 +1,4 @@
 function solve(s, loglevel, refine_grid)
-% SOLVE - 
-%   
+% SOLVE -
+%
 stack_methods(s.stack_id, 104, loglevel, refine_grid);
-
diff --git a/interfaces/matlab/toolbox/1D/@Stack/subsref.m b/interfaces/matlab/toolbox/1D/@Stack/subsref.m
index edb54ce5a..6bd884411 100644
--- a/interfaces/matlab/toolbox/1D/@Stack/subsref.m
+++ b/interfaces/matlab/toolbox/1D/@Stack/subsref.m
@@ -1,11 +1,11 @@
 function b = subsref(s,index)
-% SUBSREF - 
+% SUBSREF -
 switch index.type
- case '()'
-  b = s.domains(index.subs{:});
- case '.'
-  n = domainIndex(s, index.subs);
-  b = s.domains(n);
- otherwise
-  error('syntax error');
+    case '()'
+        b = s.domains(index.subs{:});
+    case '.'
+        n = domainIndex(s, index.subs);
+        b = s.domains(n);
+    otherwise
+        error('syntax error');
 end
diff --git a/interfaces/matlab/toolbox/1D/@Stack/writeStats.m b/interfaces/matlab/toolbox/1D/@Stack/writeStats.m
index 683ddcef1..e69787a1a 100644
--- a/interfaces/matlab/toolbox/1D/@Stack/writeStats.m
+++ b/interfaces/matlab/toolbox/1D/@Stack/writeStats.m
@@ -1,10 +1,8 @@
 function writeStats(s)
 % WRITESTATS - Print statistics for the current solution.
-%   
+%
 %     writeStats(s) prints a summary of the number of function and
 %     Jacobian evaluations for each grid, and the CPU time spent on
 %     each one.
 %
 stack_methods(s.stack_id, 108);
-
-
diff --git a/interfaces/matlab/toolbox/1D/AxiStagnFlow.m b/interfaces/matlab/toolbox/1D/AxiStagnFlow.m
index 1f675538b..dd14b711b 100644
--- a/interfaces/matlab/toolbox/1D/AxiStagnFlow.m
+++ b/interfaces/matlab/toolbox/1D/AxiStagnFlow.m
@@ -2,5 +2,5 @@ function m = AxiStagnFlow(gas)
 % AXISTAGNFLOW - Axisymmetric stagnation flow.
 %
 %    Return a Domain1D instance representing an axisymmetric
-%    stagnation flow. 
+%    stagnation flow.
 m = Domain1D(1, gas);
diff --git a/interfaces/matlab/toolbox/1D/AxisymmetricFlow.m b/interfaces/matlab/toolbox/1D/AxisymmetricFlow.m
index 8c423e9d6..945148015 100644
--- a/interfaces/matlab/toolbox/1D/AxisymmetricFlow.m
+++ b/interfaces/matlab/toolbox/1D/AxisymmetricFlow.m
@@ -5,7 +5,7 @@ function m = AxisymmetricFlow(gas, id)
 %
 m = Domain1D(1, gas);
 if nargin == 1
-  setID(m,'flow');
+    setID(m,'flow');
 else
-  setID(m,id);
-end
\ No newline at end of file
+    setID(m,id);
+end
diff --git a/interfaces/matlab/toolbox/1D/FreeFlame.m b/interfaces/matlab/toolbox/1D/FreeFlame.m
index 643c9a24f..a421d5b43 100644
--- a/interfaces/matlab/toolbox/1D/FreeFlame.m
+++ b/interfaces/matlab/toolbox/1D/FreeFlame.m
@@ -6,7 +6,7 @@ function m = FreeFlame(gas, id)
 %
 m = Domain1D(1, gas, 2);
 if nargin == 1
-  setID(m,'flame');
+    setID(m,'flame');
 else
-  setID(m,id);
-end
\ No newline at end of file
+    setID(m,id);
+end
diff --git a/interfaces/matlab/toolbox/1D/Inlet.m b/interfaces/matlab/toolbox/1D/Inlet.m
index 07ae84fc7..607668d52 100644
--- a/interfaces/matlab/toolbox/1D/Inlet.m
+++ b/interfaces/matlab/toolbox/1D/Inlet.m
@@ -5,9 +5,7 @@ function m = Inlet(id)
 %   either the leftmost or rightmost domain in a stack.
 m = Domain1D(2);
 if nargin == 0
-  setID(m,'inlet');
+    setID(m,'inlet');
 else
-  setID(m,id);
+    setID(m,id);
 end
-
-
diff --git a/interfaces/matlab/toolbox/1D/Outlet.m b/interfaces/matlab/toolbox/1D/Outlet.m
index 4fbe4a967..80d66b9c3 100644
--- a/interfaces/matlab/toolbox/1D/Outlet.m
+++ b/interfaces/matlab/toolbox/1D/Outlet.m
@@ -3,9 +3,7 @@ function m = Outlet(id)
 %
 m = Domain1D(5);
 if nargin == 0
-  setID(m,'outlet');
+    setID(m,'outlet');
 else
-  setID(m,id);
+    setID(m,id);
 end
-
-
diff --git a/interfaces/matlab/toolbox/1D/OutletRes.m b/interfaces/matlab/toolbox/1D/OutletRes.m
index 908501fe9..8139b72ac 100644
--- a/interfaces/matlab/toolbox/1D/OutletRes.m
+++ b/interfaces/matlab/toolbox/1D/OutletRes.m
@@ -3,9 +3,7 @@ function m = OutletRes(id)
 %
 m = Domain1D(-2);
 if nargin == 0
-  setID(m,'outletres');
+    setID(m,'outletres');
 else
-  setID(m,id);
+    setID(m,id);
 end
-
-
diff --git a/interfaces/matlab/toolbox/1D/Surface.m b/interfaces/matlab/toolbox/1D/Surface.m
index dfcf3cf5f..3eb1f7c8c 100644
--- a/interfaces/matlab/toolbox/1D/Surface.m
+++ b/interfaces/matlab/toolbox/1D/Surface.m
@@ -2,14 +2,13 @@ function m = Surface(id, surface_mech)
 % SURFACE - Return a Domain1D instance representing a non-reacting
 % or reacting surface.
 if nargin < 2
-  m = Domain1D(3);
-  if nargin == 0
-    setID(m,'surface');
-  elseif nargin == 1
-    setID(m,id);
-  end
+    m = Domain1D(3);
+    if nargin == 0
+        setID(m,'surface');
+    elseif nargin == 1
+        setID(m,id);
+    end
 else
-  m = Domain1D(6, surface_mech)
-  setID(m,id);
+    m = Domain1D(6, surface_mech)
+    setID(m,id);
 end
-
diff --git a/interfaces/matlab/toolbox/1D/SymmPlane.m b/interfaces/matlab/toolbox/1D/SymmPlane.m
index 8e164e5d5..c517c7d7d 100644
--- a/interfaces/matlab/toolbox/1D/SymmPlane.m
+++ b/interfaces/matlab/toolbox/1D/SymmPlane.m
@@ -3,9 +3,7 @@ function m = SymmPlane(id)
 %
 m = Domain1D(4);
 if nargin == 0
-  setID(m,'symmetry_plane');
+    setID(m,'symmetry_plane');
 else
-  setID(m,id);
+    setID(m,id);
 end
-
-
diff --git a/interfaces/matlab/toolbox/1D/npflame_init.m b/interfaces/matlab/toolbox/1D/npflame_init.m
index ce6467348..64ba1a200 100644
--- a/interfaces/matlab/toolbox/1D/npflame_init.m
+++ b/interfaces/matlab/toolbox/1D/npflame_init.m
@@ -19,20 +19,20 @@ function flame = npflame_init(gas, left, flow, right, fuel, oxidizer, nuox)
 
 % Check input parameters
 if nargin ~= 7
-  error('wrong number of input arguments.');
+    error('wrong number of input arguments.');
 end
 
 if ~isIdealGas(gas)
-  error('gas object must represent an ideal gas mixture.');
+    error('gas object must represent an ideal gas mixture.');
 end
 if ~isInlet(left)
-  error('left inlet object of wrong type.');
+    error('left inlet object of wrong type.');
 end
 if ~isFlow(flow)
-  error('flow object of wrong type.');
+    error('flow object of wrong type.');
 end
 if ~isInlet(right)
-  error('right inlet object of wrong type.');
+    error('right inlet object of wrong type.');
 end
 
 % create the container object
@@ -60,9 +60,9 @@ 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);
+    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);
@@ -83,23 +83,23 @@ 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);
+    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
-    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;
@@ -109,9 +109,9 @@ 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))])
+    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);
\ No newline at end of file
+% set minimal grid refinement criteria
+setRefineCriteria(flame, 2, 10.0, 0.99, 0.99);
diff --git a/interfaces/matlab/toolbox/@FlowDevice/FlowDevice.m b/interfaces/matlab/toolbox/@FlowDevice/FlowDevice.m
index fdb8d8618..2da5eb513 100644
--- a/interfaces/matlab/toolbox/@FlowDevice/FlowDevice.m
+++ b/interfaces/matlab/toolbox/@FlowDevice/FlowDevice.m
@@ -1,15 +1,13 @@
 function x = FlowDevice(typ)
 %
 if nargin == 0
-  typ = 1;
+    typ = 1;
 end
 x.index = flowdevicemethods(0,typ);
 if x.index < 0
-  error(geterr);
+    error(geterr);
 end
 x.type = typ;
 x.upstream = -1;
 x.downstream = -1;
 x = class(x,'FlowDevice');
-
-
diff --git a/interfaces/matlab/toolbox/@FlowDevice/clear.m b/interfaces/matlab/toolbox/@FlowDevice/clear.m
index 7a2fc11e2..6b922d203 100644
--- a/interfaces/matlab/toolbox/@FlowDevice/clear.m
+++ b/interfaces/matlab/toolbox/@FlowDevice/clear.m
@@ -1,4 +1,4 @@
 function clear(f)
-% CLEAR - 
-%   
+% CLEAR -
+%
 flowdevicemethods(1, f.index)
diff --git a/interfaces/matlab/toolbox/@FlowDevice/install.m b/interfaces/matlab/toolbox/@FlowDevice/install.m
index f7349f0a2..273aa337f 100644
--- a/interfaces/matlab/toolbox/@FlowDevice/install.m
+++ b/interfaces/matlab/toolbox/@FlowDevice/install.m
@@ -1,16 +1,16 @@
 function install(f, upstream, downstream)
 
 if nargin == 3
-  if ~isa(upstream,'Reactor') | ~isa(downstream,'Reactor')
-    error(['Flow devices can only be installed between reactors or' ...
-	   ' reservoirs'])
-  end
-  i = hndl(upstream);
-  j = hndl(downstream);
-  ok = flowdevicemethods(2, f.index, i, j); 
-  if ok < 0
-    error(geterr)
-  end
+    if ~isa(upstream,'Reactor') | ~isa(downstream,'Reactor')
+        error(['Flow devices can only be installed between reactors or' ...
+            ' reservoirs'])
+    end
+    i = hndl(upstream);
+    j = hndl(downstream);
+    ok = flowdevicemethods(2, f.index, i, j);
+    if ok < 0
+        error(geterr)
+    end
 else
-  error('install requires 3 arguments')
-end
\ No newline at end of file
+    error('install requires 3 arguments')
+end
diff --git a/interfaces/matlab/toolbox/@FlowDevice/massFlowRate.m b/interfaces/matlab/toolbox/@FlowDevice/massFlowRate.m
index 967bf21e0..5094a2e66 100644
--- a/interfaces/matlab/toolbox/@FlowDevice/massFlowRate.m
+++ b/interfaces/matlab/toolbox/@FlowDevice/massFlowRate.m
@@ -1,5 +1,4 @@
 function mdot = massFlowRate(f, time)
 % MASSFLOWRATE - mass flow rate in kg/s
-%   
+%
 mdot = flowdevicemethods(21, f.index, time);
-
diff --git a/interfaces/matlab/toolbox/@FlowDevice/private/flowdevicemethods.m b/interfaces/matlab/toolbox/@FlowDevice/private/flowdevicemethods.m
index b537c9290..ab0e7101b 100644
--- a/interfaces/matlab/toolbox/@FlowDevice/private/flowdevicemethods.m
+++ b/interfaces/matlab/toolbox/@FlowDevice/private/flowdevicemethods.m
@@ -1,13 +1,13 @@
 function v = flowdevicemethods(n, job, a, b, c, d)
-%   
+%
 if nargin == 2
-  v = ctmethods(80, n, job);
+    v = ctmethods(80, n, job);
 elseif nargin == 3
-  v = ctmethods(80, n, job, a);  
+    v = ctmethods(80, n, job, a);
 elseif nargin == 4
-  v = ctmethods(80, n, job, a, b);    
+    v = ctmethods(80, n, job, a, b);
 elseif nargin == 5
-  v = ctmethods(80, n, job, a, b, c);  
+    v = ctmethods(80, n, job, a, b, c);
 elseif nargin == 6
-  v = ctmethods(80, n, job, a, b, c, d); 
-end
\ No newline at end of file
+    v = ctmethods(80, n, job, a, b, c, d);
+end
diff --git a/interfaces/matlab/toolbox/@FlowDevice/setFunction.m b/interfaces/matlab/toolbox/@FlowDevice/setFunction.m
index 764077053..96fdc0ecc 100644
--- a/interfaces/matlab/toolbox/@FlowDevice/setFunction.m
+++ b/interfaces/matlab/toolbox/@FlowDevice/setFunction.m
@@ -2,11 +2,10 @@ function setFunction(f, mf)
 % SETMASSFLOWRATE -
 %
 if f.type == 1
-  k = flowdevicemethods(5, f.index, func_hndl(mf));
-  if k < 0
-    error(geterr);
-  end
+    k = flowdevicemethods(5, f.index, func_hndl(mf));
+    if k < 0
+        error(geterr);
+    end
 else
-  error('Mass flow rate can only be set for mass flow controllers')
+    error('Mass flow rate can only be set for mass flow controllers')
 end
-
diff --git a/interfaces/matlab/toolbox/@FlowDevice/setMassFlowRate.m b/interfaces/matlab/toolbox/@FlowDevice/setMassFlowRate.m
index f4e69ce7b..315b20c50 100644
--- a/interfaces/matlab/toolbox/@FlowDevice/setMassFlowRate.m
+++ b/interfaces/matlab/toolbox/@FlowDevice/setMassFlowRate.m
@@ -1,12 +1,11 @@
 function setMassFlowRate(f, mdot)
-% SETMASSFLOWRATE - 
-%   
+% SETMASSFLOWRATE -
+%
 if f.type == 1
-  k = flowdevicemethods(3, f.index, mdot);
-  if k < 0
-    error(geterr);
-  end
+    k = flowdevicemethods(3, f.index, mdot);
+    if k < 0
+        error(geterr);
+    end
 else
-  error('Mass flow rate can only be set for mass flow controllers')
+    error('Mass flow rate can only be set for mass flow controllers')
 end
-
diff --git a/interfaces/matlab/toolbox/@FlowDevice/setValveCoeff.m b/interfaces/matlab/toolbox/@FlowDevice/setValveCoeff.m
index 18381cc42..de55990b2 100644
--- a/interfaces/matlab/toolbox/@FlowDevice/setValveCoeff.m
+++ b/interfaces/matlab/toolbox/@FlowDevice/setValveCoeff.m
@@ -1,10 +1,10 @@
 function setValveCoeff(f, k)
 % SETVALVECOEFF - set valve coefficient
-%   
+%
 if f.type ~= 3
-  error('Valve coefficient can only be set for valves')
+    error('Valve coefficient can only be set for valves')
 end
 ok = flowdevicemethods(4, f.index, k);
 if ok < 0
-  error(geterr);
-end
\ No newline at end of file
+    error(geterr);
+end
diff --git a/interfaces/matlab/toolbox/@Func/Func.m b/interfaces/matlab/toolbox/@Func/Func.m
index b892f9ff7..38a76e0ae 100644
--- a/interfaces/matlab/toolbox/@Func/Func.m
+++ b/interfaces/matlab/toolbox/@Func/Func.m
@@ -1,12 +1,12 @@
 function x = Func(typ, n, p)
 %
 % Func - a class for functors.
-% 
+%
 % A functor is an object that behaves like a function. Cantera
 % defines a set of functors to use to create arbitrary functions to
 % specify things like heat fluxes, piston speeds, etc., in reactor
 % network simulations. Of course, they can be used for other things
-% too. 
+% too.
 %
 % The main feature of a functor class is that it overloads the '()'
 % operator to evaluate the function. For example, suppose object
@@ -27,7 +27,7 @@ function x = Func(typ, n, p)
 % "Func1". See the Cantera C++ documentation for more details.
 %
 if ~isa(typ, 'char')
-  error('Function type must be a string')
+    error('Function type must be a string')
 end
 
 x.f1 = 0;
@@ -36,41 +36,39 @@ x.coeffs = 0;
 
 itype = -1;
 if strcmp(typ, 'polynomial')
-  itype = 2;
+    itype = 2;
 elseif strcmp(typ,'fourier')
-  itype = 1;
+    itype = 1;
 elseif strcmp(typ,'arrhenius')
-  itype = 3;
+    itype = 3;
 elseif strcmp(typ,'gaussian')
-  itype = 4;  
+    itype = 4;
 end
 
 if itype > 0
-  x.coeffs = p;
-  x.index = funcmethods(0,itype,n,p);  
+    x.coeffs = p;
+    x.index = funcmethods(0,itype,n,p);
 elseif strcmp(typ,'periodic')
-  itype = 50;    
-  x.f1 = n;
-  x.coeffs = p;
-  x.index = funcmethods(0,itype,n.index,p);
+    itype = 50;
+    x.f1 = n;
+    x.coeffs = p;
+    x.index = funcmethods(0,itype,n.index,p);
 else
-  if strcmp(typ,'sum')
-    itype = 20;
-  elseif strcmp(typ,'diff')
-    itype = 25;    
-  elseif strcmp(typ,'prod')
-    itype = 30;
-  elseif strcmp(typ,'ratio')
-    itype = 40;
-  elseif strcmp(typ,'composite')
-    itype = 60;
-  end
-  x.f1 = n;
-  x.f2 = p;
-  x.index = funcmethods(0,itype,n.index,p.index);
+    if strcmp(typ,'sum')
+        itype = 20;
+    elseif strcmp(typ,'diff')
+        itype = 25;
+    elseif strcmp(typ,'prod')
+        itype = 30;
+    elseif strcmp(typ,'ratio')
+        itype = 40;
+    elseif strcmp(typ,'composite')
+        itype = 60;
+    end
+    x.f1 = n;
+    x.f2 = p;
+    x.index = funcmethods(0,itype,n.index,p.index);
 end
 
 x.typ = typ;
 x = class(x,'Func');
-
-
diff --git a/interfaces/matlab/toolbox/@Func/char.m b/interfaces/matlab/toolbox/@Func/char.m
index b4ff878c3..59c70bafe 100644
--- a/interfaces/matlab/toolbox/@Func/char.m
+++ b/interfaces/matlab/toolbox/@Func/char.m
@@ -1,92 +1,92 @@
 function s = char(p)
-% CHAR - 
-%   
+% CHAR -
+%
 if strcmp(p.typ,'sum')
-  s = ['(' char(p.f1) ') + (' char(p.f2) ')'];
+    s = ['(' char(p.f1) ') + (' char(p.f2) ')'];
 elseif strcmp(p.typ,'diff')
-  s = ['(' char(p.f1) ') - (' char(p.f2) ')'];  
+    s = ['(' char(p.f1) ') - (' char(p.f2) ')'];
 elseif strcmp(p.typ,'prod')
-  s = ['(' char(p.f1) ') * (' char(p.f2) ')'];    
+    s = ['(' char(p.f1) ') * (' char(p.f2) ')'];
 elseif strcmp(p.typ,'ratio')
-  s = ['(' char(p.f1) ') / (' char(p.f2) ')'];    
+    s = ['(' char(p.f1) ') / (' char(p.f2) ')'];
 elseif all(p.coeffs == 0)
-  s = '0';
+    s = '0';
 else
-  if strcmp(p.typ,'polynomial')
-    d = length(p.coeffs) - 1;
-    s = [];
-    nn = 0;
-    for b = p.coeffs;
-      cc(d+1-nn) = b;
-      nn = nn + 1;
+    if strcmp(p.typ,'polynomial')
+        d = length(p.coeffs) - 1;
+        s = [];
+        nn = 0;
+        for b = p.coeffs;
+            cc(d+1-nn) = b;
+            nn = nn + 1;
+        end
+        for a = cc;
+            if a ~= 0;
+                if ~isempty(s)
+                    if a > 0
+                        s = [s ' + '];
+                    else
+                        s = [s ' - '];
+                        a = -a;
+                    end
+                end
+                if a ~= 1 | d == 0
+                    s = [s num2str(a)];
+                    if d > 0
+                        s = [s '*'];
+                    end
+                end
+                if d >= 2
+                    s = [s 'x^' int2str(d)];
+                elseif d == 1
+                    s = [s 'x'];
+                end
+            end
+            d = d - 1;
+        end
+    elseif strcmp(p.typ,'gaussian')
+        s = num2str(p.coeffs(1));
+        s = ['Gaussian(' num2str(p.coeffs(1)) ',' ...
+            num2str(p.coeffs(2)) ',' ...
+            num2str(p.coeffs(3)) ')'];
+    elseif strcmp(p.typ,'fourier')
+        c = reshape(p.coeffs, [],2);
+        Ao = c(1,1);
+        w = c(1,2);
+        A = c(2:end,1);
+        B = c(2:end,2);
+        N = size(c,1)-1;
+        if Ao ~= 0
+            s = [num2str(Ao/2)];
+        else
+            s = '';
+        end
+        for n=1:N
+            if A(n) ~= 0
+                if A(n) < 0
+                    prefix = ' - ';
+                elseif s
+                    prefix = ' + ';
+                else
+                    prefix = '';
+                end
+
+                s = [s prefix num2str(abs(A(n))) '*cos(' num2str(n*w) '*x)'];
+            end
+
+            if B(n) ~= 0
+                if B(n) < 0
+                    prefix = ' - ';
+                elseif s
+                    prefix = ' + ';
+                else
+                    prefix = '';
+                end
+
+                s = [s prefix num2str(abs(B(n))) '*sin(' num2str(n*w) '*x)'];
+            end
+        end
+    else
+        s = ['*** char not yet implemented for' p.typ ' ***'];
     end
-    for a = cc;
-      if a ~= 0;
-	if ~isempty(s)
-	  if a > 0
-	    s = [s ' + '];
-	  else
-	    s = [s ' - '];
-	    a = -a;
-	  end
-	end
-	if a ~= 1 | d == 0
-	  s = [s num2str(a)];
-	  if d > 0
-	    s = [s '*'];
-	  end
-	end
-	if d >= 2
-	  s = [s 'x^' int2str(d)];
-	elseif d == 1
-	  s = [s 'x'];
-	end
-      end
-      d = d - 1;
-    end
-  elseif strcmp(p.typ,'gaussian')
-    s = num2str(p.coeffs(1));
-    s = ['Gaussian(' num2str(p.coeffs(1)) ',' ...
-	 num2str(p.coeffs(2)) ',' ...
-	 num2str(p.coeffs(3)) ')'];
-  elseif strcmp(p.typ,'fourier')
-      c = reshape(p.coeffs, [],2);
-      Ao = c(1,1);
-      w = c(1,2);
-      A = c(2:end,1);
-      B = c(2:end,2);
-      N = size(c,1)-1;
-      if Ao ~= 0
-          s = [num2str(Ao/2)];
-      else
-          s = '';
-      end
-      for n=1:N
-          if A(n) ~= 0
-              if A(n) < 0
-                  prefix = ' - ';
-              elseif s
-                  prefix = ' + ';
-              else
-                  prefix = '';
-              end
-
-              s = [s prefix num2str(abs(A(n))) '*cos(' num2str(n*w) '*x)'];
-          end
-
-          if B(n) ~= 0
-              if B(n) < 0
-                  prefix = ' - ';
-              elseif s
-                  prefix = ' + ';
-              else
-                  prefix = '';
-              end
-
-              s = [s prefix num2str(abs(B(n))) '*sin(' num2str(n*w) '*x)'];
-          end
-      end
-  else
-    s = ['*** char not yet implemented for' p.typ ' ***'];
-  end    
 end
diff --git a/interfaces/matlab/toolbox/@Func/display.m b/interfaces/matlab/toolbox/@Func/display.m
index d778a9a0b..f755a1f64 100644
--- a/interfaces/matlab/toolbox/@Func/display.m
+++ b/interfaces/matlab/toolbox/@Func/display.m
@@ -1,9 +1,8 @@
 function d = display(a)
-% DISPLAY - 
+% DISPLAY -
 %
 disp(' ');
 disp([inputname(1),' = '])
 disp(' ');
 disp(['   ' char(a)])
 disp(' ');
-
diff --git a/interfaces/matlab/toolbox/@Func/plus.m b/interfaces/matlab/toolbox/@Func/plus.m
index 6433b817c..fb4309620 100644
--- a/interfaces/matlab/toolbox/@Func/plus.m
+++ b/interfaces/matlab/toolbox/@Func/plus.m
@@ -2,7 +2,5 @@ function r = plus(a, b)
 %
 % PLUS - Return a functor representing the sum of two functors a
 % and b.
-%   
+%
 r = Func('sum',a,b);
-
-
diff --git a/interfaces/matlab/toolbox/@Func/private/funcmethods.m b/interfaces/matlab/toolbox/@Func/private/funcmethods.m
index 335489500..89640c0a9 100644
--- a/interfaces/matlab/toolbox/@Func/private/funcmethods.m
+++ b/interfaces/matlab/toolbox/@Func/private/funcmethods.m
@@ -1,13 +1,13 @@
 function v = funcmethods(n, job, a, b, c, d)
-%   
+%
 if nargin == 2
-  v = ctmethods(110, n, job);
+    v = ctmethods(110, n, job);
 elseif nargin == 3
-  v = ctmethods(110, n, job, a);  
+    v = ctmethods(110, n, job, a);
 elseif nargin == 4
-  v = ctmethods(110, n, job, a, b);    
+    v = ctmethods(110, n, job, a, b);
 elseif nargin == 5
-  v = ctmethods(110, n, job, a, b, c);  
+    v = ctmethods(110, n, job, a, b, c);
 elseif nargin == 6
-  v = ctmethods(110, n, job, a, b, c, d); 
-end
\ No newline at end of file
+    v = ctmethods(110, n, job, a, b, c, d);
+end
diff --git a/interfaces/matlab/toolbox/@Func/rdivide.m b/interfaces/matlab/toolbox/@Func/rdivide.m
index 517baffe5..8f48f8dc1 100644
--- a/interfaces/matlab/toolbox/@Func/rdivide.m
+++ b/interfaces/matlab/toolbox/@Func/rdivide.m
@@ -1,5 +1,4 @@
 function r = rdivide(a,b)
-% RDIVIDE - 
-%   
+% RDIVIDE -
+%
 r = Func('ratio',a,b);
-
diff --git a/interfaces/matlab/toolbox/@Func/subsref.m b/interfaces/matlab/toolbox/@Func/subsref.m
index c7ba4c736..8c65e9009 100644
--- a/interfaces/matlab/toolbox/@Func/subsref.m
+++ b/interfaces/matlab/toolbox/@Func/subsref.m
@@ -1,11 +1,11 @@
 function b = subsref(a,s)
-% SUBSREF 
+% SUBSREF
 switch s.type
-case '()'
-    ind = s.subs{:};
-    for k = 1:length(ind)
-        b(k) = funcmethods(2,a.index,ind(k));
-    end
-otherwise
-   error('Specify value for x as p(x)')
+    case '()'
+        ind = s.subs{:};
+        for k = 1:length(ind)
+            b(k) = funcmethods(2,a.index,ind(k));
+        end
+    otherwise
+        error('Specify value for x as p(x)')
 end
diff --git a/interfaces/matlab/toolbox/@Func/times.m b/interfaces/matlab/toolbox/@Func/times.m
index 348f9c1ac..ca841863a 100644
--- a/interfaces/matlab/toolbox/@Func/times.m
+++ b/interfaces/matlab/toolbox/@Func/times.m
@@ -1,5 +1,4 @@
 function r = times(a,b)
-% TIMES - 
-%   
+% TIMES -
+%
 r = Func('prod',a,b);
-
diff --git a/interfaces/matlab/toolbox/@Interface/Interface.m b/interfaces/matlab/toolbox/@Interface/Interface.m
index b8f63259b..8b7cb429d 100644
--- a/interfaces/matlab/toolbox/@Interface/Interface.m
+++ b/interfaces/matlab/toolbox/@Interface/Interface.m
@@ -5,19 +5,17 @@ doc = XML_Node('doc',src);
 node = findByID(doc,id);
 t = ThermoPhase(node);
 if nargin == 2
-  k = Kinetics(node,t);
+    k = Kinetics(node,t);
 elseif nargin == 3
-  k = Kinetics(node,t,p1);
+    k = Kinetics(node,t,p1);
 elseif nargin == 4
-  k = Kinetics(node,t,p1,p2);
+    k = Kinetics(node,t,p1,p2);
 elseif nargin == 5
-  k = Kinetics(node,t,p1,p2,p3);
+    k = Kinetics(node,t,p1,p2,p3);
 elseif nargin == 6
-  k = Kinetics(node,t,p1,p2,p3,p4);  
+    k = Kinetics(node,t,p1,p2,p3,p4);
 end
 
 s.kin = k;
 s.th = t;
 s = class(s,'Interface',t,k);
-
-
diff --git a/interfaces/matlab/toolbox/@Interface/concentrations.m b/interfaces/matlab/toolbox/@Interface/concentrations.m
index 63f3e297a..c03dd5042 100644
--- a/interfaces/matlab/toolbox/@Interface/concentrations.m
+++ b/interfaces/matlab/toolbox/@Interface/concentrations.m
@@ -1,17 +1,15 @@
 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');
+    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
-
-
diff --git a/interfaces/matlab/toolbox/@Interface/coverages.m b/interfaces/matlab/toolbox/@Interface/coverages.m
index ea5b9dec1..67f2a9766 100644
--- a/interfaces/matlab/toolbox/@Interface/coverages.m
+++ b/interfaces/matlab/toolbox/@Interface/coverages.m
@@ -1,17 +1,15 @@
 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');
+    figure
+    set(gcf,'Name','Coverages')
+    bar(c);
+    colormap(summer);
+    nm = speciesNames(s);
+    legend(nm);
+    xlabel('Species Number');
+    ylabel('Coverage');
+    title('Surface Species Coverages');
 end
-
-
diff --git a/interfaces/matlab/toolbox/@Interface/private/surfmethods.m b/interfaces/matlab/toolbox/@Interface/private/surfmethods.m
index e62c740f4..3c9fa8ff0 100644
--- a/interfaces/matlab/toolbox/@Interface/private/surfmethods.m
+++ b/interfaces/matlab/toolbox/@Interface/private/surfmethods.m
@@ -6,20 +6,19 @@ function v = surfmethods(n, job, a, b, c, d, e, f)
 %    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);
+    v = ctmethods(100, n, job);
 elseif nargin == 3
-  v = ctmethods(100, n, job, a);  
+    v = ctmethods(100, n, job, a);
 elseif nargin == 4
-  v = ctmethods(100, n, job, a, b);    
+    v = ctmethods(100, n, job, a, b);
 elseif nargin == 5
-  v = ctmethods(100, n, job, a, b, c);
+    v = ctmethods(100, n, job, a, b, c);
 elseif nargin == 6
-  v = ctmethods(100, n, job, a, b, c, d); 
+    v = ctmethods(100, n, job, a, b, c, d);
 elseif nargin == 7
-  v = ctmethods(100, n, job, a, b, c, d, e); 
+    v = ctmethods(100, n, job, a, b, c, d, e);
 elseif nargin == 8
-  v = ctmethods(100, n, job, a, b, c, d, e, f); 
+    v = ctmethods(100, n, job, a, b, c, d, e, f);
 else
-  error('too many arguments');
+    error('too many arguments');
 end
- 
\ No newline at end of file
diff --git a/interfaces/matlab/toolbox/@Interface/setCoverages.m b/interfaces/matlab/toolbox/@Interface/setCoverages.m
index 637c5847b..a65064222 100644
--- a/interfaces/matlab/toolbox/@Interface/setCoverages.m
+++ b/interfaces/matlab/toolbox/@Interface/setCoverages.m
@@ -1,17 +1,13 @@
 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
+    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);
+    surfmethods(thermo_hndl(s), 5, cov);
 end
-
-
-
-
diff --git a/interfaces/matlab/toolbox/@Kinetics/Kinetics.m b/interfaces/matlab/toolbox/@Kinetics/Kinetics.m
index e4572a710..14b5309e0 100644
--- a/interfaces/matlab/toolbox/@Kinetics/Kinetics.m
+++ b/interfaces/matlab/toolbox/@Kinetics/Kinetics.m
@@ -1,10 +1,10 @@
 function k = Kinetics(r, ph, neighbor1, neighbor2, neighbor3, neighbor4)
 %
-% KINETICS - Kinetics class constructor. 
+% KINETICS - Kinetics class constructor.
 %
 %   Class Kinetics represents kinetics managers, which are classes
 %   that manage reaction mechanisms.  The reaction mechanism
-%   attributes are specified in a CTML file. 
+%   attributes are specified in a CTML file.
 %
 
 % indices for bulk phases in a heterogeneous mechanism.
@@ -17,42 +17,42 @@ ineighbor4 = -1;
 % if only one argument is supplied, and it is an instance of
 % 'Kinetics', return a copy of this instance
 if nargin == 1
-   if isa(r,'Kinetics')
-      k = r;
-      return
-   else
-     error('wrong number of arguments')
-   end
+    if isa(r,'Kinetics')
+        k = r;
+        return
+    else
+        error('wrong number of arguments')
+    end
 end
 
 % if more than one arguement, first one must be an XML_Node
 % instance representing the XML tree
 if ~isa(r,'XML_Node')
-  error('first argument must be an XML_Node object')
+    error('first argument must be an XML_Node object')
 end
 
 k.owner = 1;
 ixml = hndl(r);
 
 % get the integer indices used to find the stored objects
-% representing the phases participating in the mechanism. 
+% representing the phases participating in the mechanism.
 iphase = thermo_hndl(ph);
 if nargin > 2
-  ineighbor1 = thermo_hndl(neighbor1);
-  if nargin > 3
-    ineighbor2 = thermo_hndl(neighbor2);
-    if nargin > 4
-      ineighbor3 = thermo_hndl(neighbor3);
-      if nargin > 5
-	ineighbor4 = thermo_hndl(neighbor4);
-      end
+    ineighbor1 = thermo_hndl(neighbor1);
+    if nargin > 3
+        ineighbor2 = thermo_hndl(neighbor2);
+        if nargin > 4
+            ineighbor3 = thermo_hndl(neighbor3);
+            if nargin > 5
+                ineighbor4 = thermo_hndl(neighbor4);
+            end
+        end
     end
-  end
 end
 k.id = kinetics_get(ixml,0,iphase,ineighbor1,ineighbor2,ineighbor3, ...
-		    ineighbor4);
+    ineighbor4);
 if k.id < 0
-  error(geterr);
+    error(geterr);
 end
 
 k = class(k,'Kinetics');
diff --git a/interfaces/matlab/toolbox/@Kinetics/advanceCoverages.m b/interfaces/matlab/toolbox/@Kinetics/advanceCoverages.m
index e8a818de0..8e334cf45 100644
--- a/interfaces/matlab/toolbox/@Kinetics/advanceCoverages.m
+++ b/interfaces/matlab/toolbox/@Kinetics/advanceCoverages.m
@@ -1,5 +1,4 @@
 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);
-
diff --git a/interfaces/matlab/toolbox/@Kinetics/clear.m b/interfaces/matlab/toolbox/@Kinetics/clear.m
index 539837d29..d49c626ba 100644
--- a/interfaces/matlab/toolbox/@Kinetics/clear.m
+++ b/interfaces/matlab/toolbox/@Kinetics/clear.m
@@ -1,5 +1,4 @@
 function clear(k)
 % CLEAR - delete the Kinetics instance.
-%   
+%
 kinetics_set(k.id,3);
-
diff --git a/interfaces/matlab/toolbox/@Kinetics/creationRates.m b/interfaces/matlab/toolbox/@Kinetics/creationRates.m
index 1336f86f2..4f39a72ba 100644
--- a/interfaces/matlab/toolbox/@Kinetics/creationRates.m
+++ b/interfaces/matlab/toolbox/@Kinetics/creationRates.m
@@ -5,19 +5,16 @@ function cdot = creationRates(a)
 %
 %        Returns a column vector of the creation rates of all
 %        species. If the output is not assigned to a variable, a
-%        bar graph is produced. 
+%        bar graph is produced.
 %
 %    See also: destructionRates, netProdRates.
 %
 cdot = kinetics_get(a.id,21,0);
 if nargout == 0
-  figure
-  set(gcf,'Name','Creation Rates')
-  bar(cdot)
-  xlabel('Species Number')
-  ylabel('Creation Rate (kmol/m^3-s)')
-  title('Species Chemical Creation Rates')
+    figure
+    set(gcf,'Name','Creation Rates')
+    bar(cdot)
+    xlabel('Species Number')
+    ylabel('Creation Rate (kmol/m^3-s)')
+    title('Species Chemical Creation Rates')
 end
-
-
-
diff --git a/interfaces/matlab/toolbox/@Kinetics/destructionRates.m b/interfaces/matlab/toolbox/@Kinetics/destructionRates.m
index 45d35331a..c18319f2f 100644
--- a/interfaces/matlab/toolbox/@Kinetics/destructionRates.m
+++ b/interfaces/matlab/toolbox/@Kinetics/destructionRates.m
@@ -5,19 +5,16 @@ function ddot = destructionRates(a)
 %
 %        Returns a column vector of the destruction rates of all
 %        species. If the output is not assigned to a variable, a
-%        bar graph is produced. 
+%        bar graph is produced.
 %
 %    See also: creationRates, netProdRates.
 %
 ddot = kinetics_get(a.id,22,0);
 if nargout == 0
-  figure
-  set(gcf,'Name','Destruction Rates')
-  bar(ddot)
-  xlabel('Species Number')
-  ylabel('Destruction Rate (kmol/m^3/s)')
-  title('Species Chemical Destruction Rates')
+    figure
+    set(gcf,'Name','Destruction Rates')
+    bar(ddot)
+    xlabel('Species Number')
+    ylabel('Destruction Rate (kmol/m^3/s)')
+    title('Species Chemical Destruction Rates')
 end
-
-
-
diff --git a/interfaces/matlab/toolbox/@Kinetics/destruction_rates.m b/interfaces/matlab/toolbox/@Kinetics/destruction_rates.m
index f6913e0d4..64c036a5b 100644
--- a/interfaces/matlab/toolbox/@Kinetics/destruction_rates.m
+++ b/interfaces/matlab/toolbox/@Kinetics/destruction_rates.m
@@ -3,18 +3,16 @@ function q = destruction_rates(a)
 %
 %    q = destruction_rates(a)
 %
-%        Returns a column vector of the destruction rates of all species. 
+%        Returns a column vector of the destruction rates of all species.
 %
 %    See also: creation_rates, net_production_rates.
 %
 q = production(a.id,nSpecies(a.ph),1);
 if nargout == 0
-  figure
-  set(gcf,'Name','Destruction Rates')
-  bar(q)
-  xlabel('Species Number')
-  ylabel('Destruction Rate (kmol/m^3/s)')
-  title('Species Chemical Destruction Rates')
+    figure
+    set(gcf,'Name','Destruction Rates')
+    bar(q)
+    xlabel('Species Number')
+    ylabel('Destruction Rate (kmol/m^3/s)')
+    title('Species Chemical Destruction Rates')
 end
-
-
diff --git a/interfaces/matlab/toolbox/@Kinetics/equil_Kc.m b/interfaces/matlab/toolbox/@Kinetics/equil_Kc.m
index e6df2a544..e15ae17c7 100644
--- a/interfaces/matlab/toolbox/@Kinetics/equil_Kc.m
+++ b/interfaces/matlab/toolbox/@Kinetics/equil_Kc.m
@@ -11,12 +11,10 @@ function kc = equil_Kc(a)
 %
 kc = kinetics_get(a.id,14,0);
 if nargout == 0
-  figure
-  set(gcf,'Name','Equilibrium Constants')
-  bar(log10(kc))
-  xlabel('Reaction Number')
-  ylabel('log_1_0 Kc [kmol, m, s]')
-  title('Equilibrium Constants Kc')
+    figure
+    set(gcf,'Name','Equilibrium Constants')
+    bar(log10(kc))
+    xlabel('Reaction Number')
+    ylabel('log_1_0 Kc [kmol, m, s]')
+    title('Equilibrium Constants Kc')
 end
-
-
diff --git a/interfaces/matlab/toolbox/@Kinetics/kinetics_hndl.m b/interfaces/matlab/toolbox/@Kinetics/kinetics_hndl.m
index 84735db8e..1271e64fe 100644
--- a/interfaces/matlab/toolbox/@Kinetics/kinetics_hndl.m
+++ b/interfaces/matlab/toolbox/@Kinetics/kinetics_hndl.m
@@ -1,6 +1,4 @@
 function i = kinetics_hndl(k)
 % KINETICS_HNDL - integer used to access kernel object
-%   
+%
 i = k.id;
-
-
diff --git a/interfaces/matlab/toolbox/@Kinetics/multiplier.m b/interfaces/matlab/toolbox/@Kinetics/multiplier.m
index 966f23421..2c368da2d 100644
--- a/interfaces/matlab/toolbox/@Kinetics/multiplier.m
+++ b/interfaces/matlab/toolbox/@Kinetics/multiplier.m
@@ -6,9 +6,8 @@ function n = multiplier(a,irxn)
 %    disable reactions.  For reversible reactions, it multiplies both
 %    the forward and reverse rates. By default, the multiplier value
 %    is 1.0, but it may be set to any other value by calling method
-%    setMultiplier. 
+%    setMultiplier.
 %
 %       MULTIPLIER(K, IRXN)   Multiplier for reaction number IRXN
 %
 n = kinetics_get(a.id,2,irxn);
-
diff --git a/interfaces/matlab/toolbox/@Kinetics/nReactions.m b/interfaces/matlab/toolbox/@Kinetics/nReactions.m
index 63529214a..5ef868a10 100644
--- a/interfaces/matlab/toolbox/@Kinetics/nReactions.m
+++ b/interfaces/matlab/toolbox/@Kinetics/nReactions.m
@@ -2,4 +2,3 @@ function n = nReactions(a)
 % NREACTIONS -  Number of reactions.
 %
 n = kinetics_get(a.id,1,0);
-
diff --git a/interfaces/matlab/toolbox/@Kinetics/nTotalSpecies.m b/interfaces/matlab/toolbox/@Kinetics/nTotalSpecies.m
index 29cde000b..262efaaf7 100644
--- a/interfaces/matlab/toolbox/@Kinetics/nTotalSpecies.m
+++ b/interfaces/matlab/toolbox/@Kinetics/nTotalSpecies.m
@@ -1,5 +1,5 @@
 function nsp = nTotalSpecies(a)
 % NTOTALSPECIES - The total number of species, summed over all
-% participating phases. 
-%   
+% participating phases.
+%
 nsp = kinetics_get(a.id, 3, 0);
diff --git a/interfaces/matlab/toolbox/@Kinetics/netProdRates.m b/interfaces/matlab/toolbox/@Kinetics/netProdRates.m
index 8d6b4e032..a7b4b9c62 100644
--- a/interfaces/matlab/toolbox/@Kinetics/netProdRates.m
+++ b/interfaces/matlab/toolbox/@Kinetics/netProdRates.m
@@ -11,12 +11,10 @@ function wdot = netProdRates(a)
 %
 wdot = kinetics_get(a.id,23,0);
 if nargout == 0
-  figure
-  set(gcf,'Name','Production Rates')
-  bar(wdot)
-  xlabel('Species Number')
-  ylabel('Net Production Rate (kmol/m^3/s)')
-  title('Species Net Chemical Production Rates')
+    figure
+    set(gcf,'Name','Production Rates')
+    bar(wdot)
+    xlabel('Species Number')
+    ylabel('Net Production Rate (kmol/m^3/s)')
+    title('Species Net Chemical Production Rates')
 end
-
-
diff --git a/interfaces/matlab/toolbox/@Kinetics/private/kinetics_get.m b/interfaces/matlab/toolbox/@Kinetics/private/kinetics_get.m
index 72c8d54d6..0131ac66e 100644
--- a/interfaces/matlab/toolbox/@Kinetics/private/kinetics_get.m
+++ b/interfaces/matlab/toolbox/@Kinetics/private/kinetics_get.m
@@ -1,18 +1,18 @@
 function v = kinetics_get(n, job, a, b, c, d, e, f)
-% KINETICS_GET - get kinetics attributes 
-%   
+% KINETICS_GET - get kinetics attributes
+%
 if nargin == 2
-  v = ctmethods(40, n, job);
+    v = ctmethods(40, n, job);
 elseif nargin == 3
-  v = ctmethods(40, n, job, a);  
+    v = ctmethods(40, n, job, a);
 elseif nargin == 4
-  v = ctmethods(40, n, job, a, b);    
+    v = ctmethods(40, n, job, a, b);
 elseif nargin == 5
-  v = ctmethods(40, n, job, a, b, c);  
+    v = ctmethods(40, n, job, a, b, c);
 elseif nargin == 6
-  v = ctmethods(40, n, job, a, b, c, d); 
+    v = ctmethods(40, n, job, a, b, c, d);
 elseif nargin == 7
-  v = ctmethods(40, n, job, a, b, c, d, e);
+    v = ctmethods(40, n, job, a, b, c, d, e);
 elseif nargin == 8
-  v = ctmethods(40, n, job, a, b, c, d, e, f); 
-end
\ No newline at end of file
+    v = ctmethods(40, n, job, a, b, c, d, e, f);
+end
diff --git a/interfaces/matlab/toolbox/@Kinetics/private/kinetics_set.m b/interfaces/matlab/toolbox/@Kinetics/private/kinetics_set.m
index 1ac0019f1..2634394dc 100644
--- a/interfaces/matlab/toolbox/@Kinetics/private/kinetics_set.m
+++ b/interfaces/matlab/toolbox/@Kinetics/private/kinetics_set.m
@@ -1,6 +1,4 @@
 function kinetics_set(n, job, a, b)
-% KINETICS_SET - get kinetics attributes 
-%   
+% KINETICS_SET - get kinetics attributes
+%
 ctmethods(40, n, -job, a, b)
-
-
diff --git a/interfaces/matlab/toolbox/@Kinetics/reactionEqn.m b/interfaces/matlab/toolbox/@Kinetics/reactionEqn.m
index 331631be1..2b3a6aafd 100644
--- a/interfaces/matlab/toolbox/@Kinetics/reactionEqn.m
+++ b/interfaces/matlab/toolbox/@Kinetics/reactionEqn.m
@@ -2,28 +2,24 @@ function e = reactionEqn(a, irxn)
 % reactionEqn  Reaction equation of reaction irxn.
 %
 if nargin == 1
-   m = nReactions(a);
-   n = 1;
-   irxn = [1:m]';
+    m = nReactions(a);
+    n = 1;
+    irxn = [1:m]';
 elseif nargin == 2
-   if isa(irxn,'double')
-      [m, n] = size(irxn);
-   else
-      error('reaction number(s) must be numeric');
-   end
+    if isa(irxn,'double')
+        [m, n] = size(irxn);
+    else
+        error('reaction number(s) must be numeric');
+    end
 end
 
 if m == 1 & n == 1
-   e = kinetics_get(a.id, 31, irxn); % rxnstring(a.id, irxn);
+    e = kinetics_get(a.id, 31, irxn); % rxnstring(a.id, irxn);
 else
-   e = {};
-   for i = 1:m
-      for j = 1:n
-	 e{i,j} = kinetics_get(a.id, 31, irxn(i,j)); % rxnstring(a.id, irxn(i,j));
-      end
-   end
+    e = {};
+    for i = 1:m
+        for j = 1:n
+            e{i,j} = kinetics_get(a.id, 31, irxn(i,j)); % rxnstring(a.id, irxn(i,j));
+        end
+    end
 end
-
-
-
-
diff --git a/interfaces/matlab/toolbox/@Kinetics/rop.m b/interfaces/matlab/toolbox/@Kinetics/rop.m
index fa1c33bbf..3399814b8 100644
--- a/interfaces/matlab/toolbox/@Kinetics/rop.m
+++ b/interfaces/matlab/toolbox/@Kinetics/rop.m
@@ -5,16 +5,16 @@ function rop = rop(k)
 %    progress. The first column contains the forward rates of progress,
 %    and the second column the reverse rates. If this function
 %    is called with no output argument, a bar graph is produced.
-%   
-f = rop_f(k) 
+%
+f = rop_f(k)
 r = rop_r(k)
 rop = [f r]
 if nargout == 0
-  figure
-  set(gcf,'Name','Rates of Progress');
-  bar(rop);
-  xlabel('Reaction Number');
-  ylabel('Rate of Progress [kmol/m^3-s]');
-  title('Rates of Progress');
-  legend('Forward', 'Reverse');
+    figure
+    set(gcf,'Name','Rates of Progress');
+    bar(rop);
+    xlabel('Reaction Number');
+    ylabel('Rate of Progress [kmol/m^3-s]');
+    title('Rates of Progress');
+    legend('Forward', 'Reverse');
 end
diff --git a/interfaces/matlab/toolbox/@Kinetics/rop_f.m b/interfaces/matlab/toolbox/@Kinetics/rop_f.m
index 1a578f1a8..d73a4f36f 100644
--- a/interfaces/matlab/toolbox/@Kinetics/rop_f.m
+++ b/interfaces/matlab/toolbox/@Kinetics/rop_f.m
@@ -10,11 +10,10 @@ function q = rop_f(a)
 %
 q = kinetics_get(a.id,11,0);
 if nargout == 0
-  figure
-  set(gcf,'Name','Rates of Progress')
-  bar(q)
-  xlabel('Reaction Number')
-  ylabel('Forward Rate of Progress [kmol/m^3]')
-  title('Forward Rates of Progress')
+    figure
+    set(gcf,'Name','Rates of Progress')
+    bar(q)
+    xlabel('Reaction Number')
+    ylabel('Forward Rate of Progress [kmol/m^3]')
+    title('Forward Rates of Progress')
 end
-
diff --git a/interfaces/matlab/toolbox/@Kinetics/rop_net.m b/interfaces/matlab/toolbox/@Kinetics/rop_net.m
index ac9a42029..1c754f2a6 100644
--- a/interfaces/matlab/toolbox/@Kinetics/rop_net.m
+++ b/interfaces/matlab/toolbox/@Kinetics/rop_net.m
@@ -10,11 +10,10 @@ function q = rop_net(a)
 %
 q = kinetics_get(a.id,13,0);
 if nargout == 0
-  figure
-  set(gcf,'Name','Rates of Progress')
-  bar(q)
-  xlabel('Reaction Number')
-  ylabel('Net Rate of Progress [kmol/m^3]')
-  title('Net Rates of Progress')
+    figure
+    set(gcf,'Name','Rates of Progress')
+    bar(q)
+    xlabel('Reaction Number')
+    ylabel('Net Rate of Progress [kmol/m^3]')
+    title('Net Rates of Progress')
 end
-
diff --git a/interfaces/matlab/toolbox/@Kinetics/rop_r.m b/interfaces/matlab/toolbox/@Kinetics/rop_r.m
index 7cc3fb907..abce56868 100644
--- a/interfaces/matlab/toolbox/@Kinetics/rop_r.m
+++ b/interfaces/matlab/toolbox/@Kinetics/rop_r.m
@@ -5,9 +5,8 @@ function q = rop_r(a)
 %
 %        Returns a column vector of the reverse rates of progress
 %        for all reactions. The value is zero for irreversible
-%        reactions. 
+%        reactions.
 %
 %    See also: rop_r, rop_net.
 %
 q = kinetics_get(a.id,12,0);
-
diff --git a/interfaces/matlab/toolbox/@Kinetics/rxnEqs.m b/interfaces/matlab/toolbox/@Kinetics/rxnEqs.m
index 76697557b..77c0fcf38 100644
--- a/interfaces/matlab/toolbox/@Kinetics/rxnEqs.m
+++ b/interfaces/matlab/toolbox/@Kinetics/rxnEqs.m
@@ -1,29 +1,25 @@
 function e = rxnEqs(a, irxn)
-% rxnEqs 
+% rxnEqs
 %
 if nargin == 1
-   m = nReactions(a);
-   n = 1;
-   irxn = [1:m]'
+    m = nReactions(a);
+    n = 1;
+    irxn = [1:m]'
 elseif nargin == 2
-   if isa(irxn,'double')
-      [m, n] = size(irxn);
-   else
-      error('reaction number(s) must be numeric');
-   end
+    if isa(irxn,'double')
+        [m, n] = size(irxn);
+    else
+        error('reaction number(s) must be numeric');
+    end
 end
 
 if m == 1 & n == 1
-   e = rxnstring(a.id, irxn);
+    e = rxnstring(a.id, irxn);
 else
-   e = {};
-   for i = 1:m
-      for j = 1:n
-	 e{i,j} = rxnstring(a.id, irxn(i,j));
-      end
-   end
+    e = {};
+    for i = 1:m
+        for j = 1:n
+            e{i,j} = rxnstring(a.id, irxn(i,j));
+        end
+    end
 end
-
-
-
-
diff --git a/interfaces/matlab/toolbox/@Kinetics/setMultiplier.m b/interfaces/matlab/toolbox/@Kinetics/setMultiplier.m
index f3d9890e1..dd2893db4 100644
--- a/interfaces/matlab/toolbox/@Kinetics/setMultiplier.m
+++ b/interfaces/matlab/toolbox/@Kinetics/setMultiplier.m
@@ -7,18 +7,16 @@ function setMultiplier(a,irxn,v)
 %    see also: MULTIPLIER
 %
 if nargin == 2
-  v = irxn;
-  m = nReactions(a);
-  irxn = [1:m]';
-  n = 1;
+    v = irxn;
+    m = nReactions(a);
+    irxn = [1:m]';
+    n = 1;
 else
-  [m, n] = size(irxn);
+    [m, n] = size(irxn);
 end
 
 for jm = 1:m
-  for jn = 1:n
-    kinetics_set(a.id,1,irxn(jm,jn),v);
-  end
+    for jn = 1:n
+        kinetics_set(a.id,1,irxn(jm,jn),v);
+    end
 end
-
-
diff --git a/interfaces/matlab/toolbox/@Kinetics/stoich_net.m b/interfaces/matlab/toolbox/@Kinetics/stoich_net.m
index 39631d4e3..84f4c536a 100644
--- a/interfaces/matlab/toolbox/@Kinetics/stoich_net.m
+++ b/interfaces/matlab/toolbox/@Kinetics/stoich_net.m
@@ -21,10 +21,10 @@ function nu = stoich_net(a,species,rxns)
 %    See also: stoich_r, stoich_p.
 %
 if nargin == 1
-  nu = stoich_p(a) - stoich_r(a)
+    nu = stoich_p(a) - stoich_r(a)
 elseif nargin == 3
-  nu = stoich_p(a,species,rxns) - stoich_r(a,species,rxns);
+    nu = stoich_p(a,species,rxns) - stoich_r(a,species,rxns);
 else
-  error(['syntax error. Type ''help stoich_net'' for more' ...
-	 ' information.'])
+    error(['syntax error. Type ''help stoich_net'' for more' ...
+        ' information.'])
 end
diff --git a/interfaces/matlab/toolbox/@Kinetics/stoich_p.m b/interfaces/matlab/toolbox/@Kinetics/stoich_p.m
index 3909df001..0c2b5d0f9 100644
--- a/interfaces/matlab/toolbox/@Kinetics/stoich_p.m
+++ b/interfaces/matlab/toolbox/@Kinetics/stoich_p.m
@@ -23,21 +23,21 @@ nr =nReactions(a);
 b = sparse(nsp,nr);
 f = @kinetics_get;
 if nargin == 1
-  kvals = 1:nsp;
-  ivals = 1:nr;
+    kvals = 1:nsp;
+    ivals = 1:nr;
 elseif nargin == 3
-  kvals = species;
-  ivals = rxns;
+    kvals = species;
+    ivals = rxns;
 else
-  error('Syntax error. type ''help stoich_r'' for more information.')
+    error('Syntax error. type ''help stoich_r'' for more information.')
 end
 
 for k = kvals
-  for i = ivals
-    nu = feval(f,a.id,6,i,k);
-    if nu ~= 0.0
-      b(k,i) = nu;
+    for i = ivals
+        nu = feval(f,a.id,6,i,k);
+        if nu ~= 0.0
+            b(k,i) = nu;
+        end
     end
-  end
 end
-nu_p = b;
\ No newline at end of file
+nu_p = b;
diff --git a/interfaces/matlab/toolbox/@Kinetics/stoich_r.m b/interfaces/matlab/toolbox/@Kinetics/stoich_r.m
index ee5ebd39f..1828495ec 100644
--- a/interfaces/matlab/toolbox/@Kinetics/stoich_r.m
+++ b/interfaces/matlab/toolbox/@Kinetics/stoich_r.m
@@ -23,21 +23,21 @@ nr =nReactions(a);
 b = sparse(nsp,nr);
 f = @kinetics_get;
 if nargin == 1
-  kvals = 1:nsp;
-  ivals = 1:nr;
+    kvals = 1:nsp;
+    ivals = 1:nr;
 elseif nargin == 3
-  kvals = species;
-  ivals = rxns;
+    kvals = species;
+    ivals = rxns;
 else
-  error('Syntax error. type ''help stoich_r'' for more information.')
+    error('Syntax error. type ''help stoich_r'' for more information.')
 end
 
 for k = kvals
-  for i = ivals
-    nu = feval(f,a.id,5,i,k);
-    if nu ~= 0.0
-      b(k,i) = nu;
+    for i = ivals
+        nu = feval(f,a.id,5,i,k);
+        if nu ~= 0.0
+            b(k,i) = nu;
+        end
     end
-  end
 end
-nu_r = b;
\ No newline at end of file
+nu_r = b;
diff --git a/interfaces/matlab/toolbox/@Kinetics/ydot.m b/interfaces/matlab/toolbox/@Kinetics/ydot.m
index d90c5571b..6c2be7ded 100644
--- a/interfaces/matlab/toolbox/@Kinetics/ydot.m
+++ b/interfaces/matlab/toolbox/@Kinetics/ydot.m
@@ -1,4 +1,4 @@
 function v = ydot(a)
 % YDOT - Evaluates wdot_k M_k / (density)
 %
-v = kinetics_get(a.id,24,0);
\ No newline at end of file
+v = kinetics_get(a.id,24,0);
diff --git a/interfaces/matlab/toolbox/@Mixture/Mixture.m b/interfaces/matlab/toolbox/@Mixture/Mixture.m
index 2a27d34aa..fffb76868 100644
--- a/interfaces/matlab/toolbox/@Mixture/Mixture.m
+++ b/interfaces/matlab/toolbox/@Mixture/Mixture.m
@@ -5,7 +5,7 @@ function m = Mixture(phases)
 %    Class Mixture represents
 %    mixtures of one or more phases of matter.  To construct a mixture,
 %    supply a cell array of phases and mole numbers:
-%    
+%
 %    >> gas = importPhase('gas.cti');
 %    >> graphite = importPhase('graphite.cti');
 %    >> mix = Mixture({gas, 1.0; graphite, 0.1});
@@ -29,7 +29,7 @@ function m = Mixture(phases)
 %    objects whenever it requires phase properties.
 %
 if nargin > 1
-  error('Mixture: wrong number of arguments');
+    error('Mixture: wrong number of arguments');
 end
 
 % create an empty mixture
@@ -40,22 +40,19 @@ m = class(m,'Mixture');
 
 % if phases are supplied, add them
 if nargin == 1
-  if ~isa(phases,'cell')
-    error('enter phases as a cell array');
-  end
-  
-  % first column contains the phase objects, and the second column
-  % the mole numbers of each phase
-  [np nc] = size(phases);
-  if nc ~= 2
-    error('wrong size for phases cell array');
-  end
-  for n = 1:np
-    addPhase(m, phases{n,1}, phases{n,2});
-  end
-  setTemperature(m, temperature(phases{n,1}));
-  setPressure(m, pressure(phases{n,1}));
+    if ~isa(phases,'cell')
+        error('enter phases as a cell array');
+    end
+
+    % first column contains the phase objects, and the second column
+    % the mole numbers of each phase
+    [np nc] = size(phases);
+    if nc ~= 2
+        error('wrong size for phases cell array');
+    end
+    for n = 1:np
+        addPhase(m, phases{n,1}, phases{n,2});
+    end
+    setTemperature(m, temperature(phases{n,1}));
+    setPressure(m, pressure(phases{n,1}));
 end
-
-  
-
diff --git a/interfaces/matlab/toolbox/@Mixture/addPhase.m b/interfaces/matlab/toolbox/@Mixture/addPhase.m
index 6eff96515..ee91e1eab 100644
--- a/interfaces/matlab/toolbox/@Mixture/addPhase.m
+++ b/interfaces/matlab/toolbox/@Mixture/addPhase.m
@@ -1,21 +1,21 @@
 function addPhase(self, phase, moles)
 % ADDPHASE - Add a phase to the mixture.
 %
-%            carbon = importPhase('graphite.cti'); 
+%            carbon = importPhase('graphite.cti');
 %            addPhase(mix, carbon, 1.0);
 %
 if ~isa(phase,'ThermoPhase')
-  error('phase object of wrong type.');
+    error('phase object of wrong type.');
 end
 if ~isa(moles,'numeric')
-  error('number of moles must be numeric.');
+    error('number of moles must be numeric.');
 end
 if moles < 0.0
-  error('negative moles!');
+    error('negative moles!');
 end
 
 iphase = thermo_hndl(phase);
 iok = mixturemethods(4, mix_hndl(self), iphase, moles);
 if iok < 0
-  error('error adding phase');
+    error('error adding phase');
 end
diff --git a/interfaces/matlab/toolbox/@Mixture/display.m b/interfaces/matlab/toolbox/@Mixture/display.m
index 1fa900830..6fd0ab7b6 100644
--- a/interfaces/matlab/toolbox/@Mixture/display.m
+++ b/interfaces/matlab/toolbox/@Mixture/display.m
@@ -1,8 +1,8 @@
 function display(self)
 [np nc] = size(self.phases);
 for n = 1:np
-  s = [sprintf('\n*******************    Phase %d', n) ...
-       sprintf('    ******************************\n\n Moles: %12.6g',  phaseMoles(self,n))];
-  disp(s);
-  display(self.phases{n,1});
+    s = [sprintf('\n*******************    Phase %d', n) ...
+        sprintf('    ******************************\n\n Moles: %12.6g',  phaseMoles(self,n))];
+    disp(s);
+    display(self.phases{n,1});
 end
diff --git a/interfaces/matlab/toolbox/@Mixture/elementIndex.m b/interfaces/matlab/toolbox/@Mixture/elementIndex.m
index 40a80f929..550b1eeea 100644
--- a/interfaces/matlab/toolbox/@Mixture/elementIndex.m
+++ b/interfaces/matlab/toolbox/@Mixture/elementIndex.m
@@ -1,5 +1,4 @@
 function n = elementIndex(self, name)
 % ELEMENTINDEX - index of element with name 'name'
-%   
+%
 n = mixturemethods(22, mix_hndl(self), name);
-
diff --git a/interfaces/matlab/toolbox/@Mixture/equilibrate.m b/interfaces/matlab/toolbox/@Mixture/equilibrate.m
index 04fde1593..0d06a31f8 100644
--- a/interfaces/matlab/toolbox/@Mixture/equilibrate.m
+++ b/interfaces/matlab/toolbox/@Mixture/equilibrate.m
@@ -1,5 +1,5 @@
 function r = equilibrate(self, XY, err, maxsteps, maxiter, ...
-			 loglevel)
+    loglevel)
 %
 % EQUILIBRATE - Set the mixture to a state of chemical equilibrium.
 %
@@ -15,29 +15,29 @@ function r = equilibrate(self, XY, err, maxsteps, maxiter, ...
 %       other than "TP" is specified, then an outer iteration loop is
 %       used to adjust T and/or P so that the specified property
 %       values are obtained.
-%          
+%
 %       XY - Two-letter string specifying the two properties to hold
 %       fixed.  Currently, 'TP', 'HP', and 'SP' are
 %       implemented. Default: 'TP'.
-%          
+%
 %       err - Error tolerance. Iteration will continue until (Delta
 %       mu)/RT is less than this value for each reaction. Default:
 %       1.0e-9. Note that this default is very conservative, and good
 %       equilibrium solutions may be obtained with larger error
 %       tolerances.
-%  
+%
 %       maxsteps - Maximum number of steps to take while solving the
 %       equilibrium problem for specified T and P. Default: 1000.
-%  
+%
 %       maxiter - Maximum number of temperature and/or pressure
 %       iterations.  This is only relevant if a property pair other
 %       than (T,P) is specified. Default: 200.
-%  
+%
 %       loglevel - Controls the amount of diagnostic output. If
 %       loglevel = 0, no diagnostic output is written. For values > 0,
 %       more detailed information is written to the log file as
 %       loglevel increases. The default is loglevel = 0.
-%  
+%
 %       The logfile is written in HTML format, and may be viewed with
 %       any web browser. The default log file name is
 %       "equilibrium_log.html", but if this file exists, the log
@@ -47,24 +47,24 @@ function r = equilibrate(self, XY, err, maxsteps, maxiter, ...
 %       times, multiple log files will be written, with names
 %       "equilibrate_log.html", "equilibrate_log1.html",
 %       "equilibrate_log2.html", and so on. Existing log files will
-%       not be overwritten.   
-%  
+%       not be overwritten.
+%
 %          >> equilibrate(mix, 'TP')
 %          >> equilibrate('TP', 1.0e-6, 500)
-%          
+%
 if nargin < 6
-  loglevel = 0;
+    loglevel = 0;
 end
-if nargin < 5 
-  maxiter = 200;
+if nargin < 5
+    maxiter = 200;
 end
 if nargin < 4
-  maxsteps = 1000;
+    maxsteps = 1000;
 end
 if nargin < 3
-  err = 1.0e-9;
+    err = 1.0e-9;
 end
 if nargin < 2
-  XY = 'TP';
+    XY = 'TP';
 end
 r = mixturemethods(31, mix_hndl(self), XY, err, maxsteps, maxiter, loglevel);
diff --git a/interfaces/matlab/toolbox/@Mixture/mix_hndl.m b/interfaces/matlab/toolbox/@Mixture/mix_hndl.m
index 0e32fedb3..5a1436ca7 100644
--- a/interfaces/matlab/toolbox/@Mixture/mix_hndl.m
+++ b/interfaces/matlab/toolbox/@Mixture/mix_hndl.m
@@ -1,6 +1,4 @@
 function i = mix_hndl(self)
 % MIX_HNDL - integer used to access kernel object
-%   
+%
 i = self.mixindex;
-
-
diff --git a/interfaces/matlab/toolbox/@Mixture/nElements.m b/interfaces/matlab/toolbox/@Mixture/nElements.m
index 0c2ba5de1..2a967de9b 100644
--- a/interfaces/matlab/toolbox/@Mixture/nElements.m
+++ b/interfaces/matlab/toolbox/@Mixture/nElements.m
@@ -1,5 +1,4 @@
 function n = nElements(self)
 % NELEMENTS - number of elements
-%   
+%
 n = mixturemethods(21, mix_hndl(self));
-
diff --git a/interfaces/matlab/toolbox/@Mixture/nPhases.m b/interfaces/matlab/toolbox/@Mixture/nPhases.m
index 49d8b89fb..04803a7fb 100644
--- a/interfaces/matlab/toolbox/@Mixture/nPhases.m
+++ b/interfaces/matlab/toolbox/@Mixture/nPhases.m
@@ -1,5 +1,4 @@
 function n = nPhases(self)
 % NPHASES - number of phases
-%   
+%
 n = mixturemethods(19, mix_hndl(self));
-
diff --git a/interfaces/matlab/toolbox/@Mixture/nSpecies.m b/interfaces/matlab/toolbox/@Mixture/nSpecies.m
index e747a5aa9..989d44077 100644
--- a/interfaces/matlab/toolbox/@Mixture/nSpecies.m
+++ b/interfaces/matlab/toolbox/@Mixture/nSpecies.m
@@ -1,5 +1,4 @@
 function n = nSpecies(self)
 % NSPECIES - number of species
-%   
+%
 n = mixturemethods(24, mix_hndl(self));
-
diff --git a/interfaces/matlab/toolbox/@Mixture/phaseMoles.m b/interfaces/matlab/toolbox/@Mixture/phaseMoles.m
index 487178a2b..5e06e656c 100644
--- a/interfaces/matlab/toolbox/@Mixture/phaseMoles.m
+++ b/interfaces/matlab/toolbox/@Mixture/phaseMoles.m
@@ -1,15 +1,14 @@
 function moles = phaseMoles(self, n)
 % PHASEMOLES - moles of phase number 'n' (kmol).
-%   
+%
 if nargin == 2
-  moles = mixturemethods(28, mix_hndl(self), n);
+    moles = mixturemethods(28, mix_hndl(self), n);
 elseif nargin == 1
     np = nPhases(self);
     for n = 1:np
-      m(n) = mixturemethods(28, mix_hndl(self), n);
+        m(n) = mixturemethods(28, mix_hndl(self), n);
     end
     moles = m;
 else
-  error('wrong number of arguments');
+    error('wrong number of arguments');
 end
-
diff --git a/interfaces/matlab/toolbox/@Mixture/pressure.m b/interfaces/matlab/toolbox/@Mixture/pressure.m
index 84dda17ee..d254a5504 100644
--- a/interfaces/matlab/toolbox/@Mixture/pressure.m
+++ b/interfaces/matlab/toolbox/@Mixture/pressure.m
@@ -1,5 +1,4 @@
 function n = pressure(self)
 % PRESSURE - pressure (Pa)
-%   
+%
 n = mixturemethods(26, mix_hndl(self));
-
diff --git a/interfaces/matlab/toolbox/@Mixture/private/mixturemethods.m b/interfaces/matlab/toolbox/@Mixture/private/mixturemethods.m
index 8978e7337..5d47e20ea 100644
--- a/interfaces/matlab/toolbox/@Mixture/private/mixturemethods.m
+++ b/interfaces/matlab/toolbox/@Mixture/private/mixturemethods.m
@@ -1,17 +1,17 @@
 function v = mixturemethods(n, job, a, b, c, d, e, f)
-%   
+%
 if nargin == 2
-  v = ctmethods(120, n, job);
+    v = ctmethods(120, n, job);
 elseif nargin == 3
-  v = ctmethods(120, n, job, a);  
+    v = ctmethods(120, n, job, a);
 elseif nargin == 4
-  v = ctmethods(120, n, job, a, b);    
+    v = ctmethods(120, n, job, a, b);
 elseif nargin == 5
-  v = ctmethods(120, n, job, a, b, c);  
+    v = ctmethods(120, n, job, a, b, c);
 elseif nargin == 6
-  v = ctmethods(120, n, job, a, b, c, d); 
+    v = ctmethods(120, n, job, a, b, c, d);
 elseif nargin == 7
-  v = ctmethods(120, n, job, a, b, c, d, e);
+    v = ctmethods(120, n, job, a, b, c, d, e);
 elseif nargin == 8
-  v = ctmethods(120, n, job, a, b, c, d, e, f);   
-end
\ No newline at end of file
+    v = ctmethods(120, n, job, a, b, c, d, e, f);
+end
diff --git a/interfaces/matlab/toolbox/@Mixture/setPhaseMoles.m b/interfaces/matlab/toolbox/@Mixture/setPhaseMoles.m
index a91c801ad..70b494d79 100644
--- a/interfaces/matlab/toolbox/@Mixture/setPhaseMoles.m
+++ b/interfaces/matlab/toolbox/@Mixture/setPhaseMoles.m
@@ -1,7 +1,5 @@
 function setPhaseMoles(self, n, moles)
 % SETPHASEMOLES - set the number of moles of phase number 'n' to
 % 'moles' (kmol).
-%   
+%
 mixturemethods(7, mix_hndl(self), n, moles);
-
-
diff --git a/interfaces/matlab/toolbox/@Mixture/setPressure.m b/interfaces/matlab/toolbox/@Mixture/setPressure.m
index 066fb30af..d3a586e7d 100644
--- a/interfaces/matlab/toolbox/@Mixture/setPressure.m
+++ b/interfaces/matlab/toolbox/@Mixture/setPressure.m
@@ -1,6 +1,4 @@
 function setPressure(self, P)
 % SETPRESSURE - set the mixture pressure (Pa)
-%   
+%
 mixturemethods(6, mix_hndl(self), P);
-
-
diff --git a/interfaces/matlab/toolbox/@Mixture/setSpeciesMoles.m b/interfaces/matlab/toolbox/@Mixture/setSpeciesMoles.m
index f519863bb..15383475e 100644
--- a/interfaces/matlab/toolbox/@Mixture/setSpeciesMoles.m
+++ b/interfaces/matlab/toolbox/@Mixture/setSpeciesMoles.m
@@ -6,7 +6,5 @@ function setSpeciesMoles(self, moles)
 % phase, and unspecified species are set to zero.
 %
 %     >> setSpeciesMoles(mix, 'C(s):1.0, CH4:2.0, O2:0.2');
-%   
+%
 mixturemethods(8, mix_hndl(self), moles);
-
-
diff --git a/interfaces/matlab/toolbox/@Mixture/setTemperature.m b/interfaces/matlab/toolbox/@Mixture/setTemperature.m
index a4aef15e9..c0e0e726e 100644
--- a/interfaces/matlab/toolbox/@Mixture/setTemperature.m
+++ b/interfaces/matlab/toolbox/@Mixture/setTemperature.m
@@ -1,6 +1,4 @@
 function setTemperature(self, T)
 % SETTEMPERATURE - set the mixture temperature
-%   
+%
 mixturemethods(5, mix_hndl(self), T);
-
-
diff --git a/interfaces/matlab/toolbox/@Mixture/speciesIndex.m b/interfaces/matlab/toolbox/@Mixture/speciesIndex.m
index e005f9ecc..e8ea3837d 100644
--- a/interfaces/matlab/toolbox/@Mixture/speciesIndex.m
+++ b/interfaces/matlab/toolbox/@Mixture/speciesIndex.m
@@ -1,5 +1,4 @@
 function n = speciesIndex(self, k, p)
 % SPECIESINDEX - index of species with name 'name'
-%   
+%
 n = mixturemethods(23, mix_hndl(self), k, p);
-
diff --git a/interfaces/matlab/toolbox/@Mixture/temperature.m b/interfaces/matlab/toolbox/@Mixture/temperature.m
index 9d1f25388..e7c953fb7 100644
--- a/interfaces/matlab/toolbox/@Mixture/temperature.m
+++ b/interfaces/matlab/toolbox/@Mixture/temperature.m
@@ -1,5 +1,4 @@
 function n = temperature(self)
 % TEMPERATURE - temperature (K)
-%   
+%
 n = mixturemethods(25, mix_hndl(self));
-
diff --git a/interfaces/matlab/toolbox/@Reactor/Reactor.m b/interfaces/matlab/toolbox/@Reactor/Reactor.m
index c672e8aad..c98938d01 100644
--- a/interfaces/matlab/toolbox/@Reactor/Reactor.m
+++ b/interfaces/matlab/toolbox/@Reactor/Reactor.m
@@ -4,7 +4,7 @@ function x = Reactor(contents, typ)
 %    A Reactor object simulates a perfectly-stirred reactor. It has
 %    a time-dependent state, and may be coupled to other reactors
 %    through flow lines or through walls that may expand or
-%    contract and/or conduct heat. 
+%    contract and/or conduct heat.
 %
 %        r1 = Reactor           % an empty reactor
 %        r2 = Reactor(gas)      % a reactor containing a gas
@@ -12,24 +12,21 @@ function x = Reactor(contents, typ)
 %   See also: Reservoir
 %
 if nargin == 0
-  contents = 0;
-  typ = 2;
+    contents = 0;
+    typ = 2;
 elseif nargin == 1
-  typ = 2;
+    typ = 2;
 elseif nargin > 2
-  error('too many arguments');
+    error('too many arguments');
 end
 
 x.index = reactormethods(0,typ);
 if x.index < 0
-  error(geterr);
+    error(geterr);
 end
 x.contents = contents;
 x = class(x,'Reactor');
 
 if isa(contents,'Solution')
-  insert(x, contents);
+    insert(x, contents);
 end
-
-
-
diff --git a/interfaces/matlab/toolbox/@Reactor/advance.m b/interfaces/matlab/toolbox/@Reactor/advance.m
index 2a4310949..93f925ab3 100644
--- a/interfaces/matlab/toolbox/@Reactor/advance.m
+++ b/interfaces/matlab/toolbox/@Reactor/advance.m
@@ -1,5 +1,5 @@
 function advance(r, tout)
-% ADVANCE - Advance the state of the reactor in time. 
+% ADVANCE - Advance the state of the reactor in time.
 %
 %    Method advance integrates the system of ordinary differential
 %    equations that determine the rate of change of the reactor
@@ -7,7 +7,7 @@ function advance(r, tout)
 %    integration is carried out from the current reactor time to time
 %    'tout.' (Note 'tout' is an absolute time, not a time interval.)  The
 %    integrator may take many internal time steps before reaching
-%    tout. 
+%    tout.
 %
 %       for i in 1:10
 %          tout = 0.1*i
diff --git a/interfaces/matlab/toolbox/@Reactor/clear.m b/interfaces/matlab/toolbox/@Reactor/clear.m
index 921177729..89f15641a 100644
--- a/interfaces/matlab/toolbox/@Reactor/clear.m
+++ b/interfaces/matlab/toolbox/@Reactor/clear.m
@@ -1,5 +1,4 @@
 function clear(r)
-% CLEAR - 
-%   
+% CLEAR -
+%
 reactormethods(2, reactor_hndl(r));
-
diff --git a/interfaces/matlab/toolbox/@Reactor/density.m b/interfaces/matlab/toolbox/@Reactor/density.m
index 9ae85dee2..5f7de3cf4 100644
--- a/interfaces/matlab/toolbox/@Reactor/density.m
+++ b/interfaces/matlab/toolbox/@Reactor/density.m
@@ -1,4 +1,4 @@
 function rho = density(r)
 % DENSITY - density
-%   
+%
 rho = reactormethods(25, reactor_hndl(r));
diff --git a/interfaces/matlab/toolbox/@Reactor/enthalpy_mass.m b/interfaces/matlab/toolbox/@Reactor/enthalpy_mass.m
index 945cc72d4..ef1ac7b69 100644
--- a/interfaces/matlab/toolbox/@Reactor/enthalpy_mass.m
+++ b/interfaces/matlab/toolbox/@Reactor/enthalpy_mass.m
@@ -1,12 +1,12 @@
 function h = enthalpy_mass(r)
 % ENTHALPY_MASS - the specific enthalpy [J/kg].
-%   
+%
 %       h = enthalpy_mass(r)
 %
 %    returns the specific enthalpy of the reactor contents at the
 %    end of the last call to 'advance' or 'step.'
 %
 %    See also: Reactor/intEnergy_mass, Reactor/entropy_mass,
-%    Reactor/enthalpy_mole 
+%    Reactor/enthalpy_mole
 %
 h = reactormethods(27, reactor_hndl(r));
diff --git a/interfaces/matlab/toolbox/@Reactor/insert.m b/interfaces/matlab/toolbox/@Reactor/insert.m
index f4e7277b5..1c4d978d8 100644
--- a/interfaces/matlab/toolbox/@Reactor/insert.m
+++ b/interfaces/matlab/toolbox/@Reactor/insert.m
@@ -1,8 +1,6 @@
 function insert(r, gas)
 % INSERT - insert a mixture into the reactor
-%   
+%
 r.contents = gas;
 setThermoMgr(r, gas);
 setKineticsMgr(r, gas);
-
-
diff --git a/interfaces/matlab/toolbox/@Reactor/intEnergy_mass.m b/interfaces/matlab/toolbox/@Reactor/intEnergy_mass.m
index 1ec99b75e..f5f01270b 100644
--- a/interfaces/matlab/toolbox/@Reactor/intEnergy_mass.m
+++ b/interfaces/matlab/toolbox/@Reactor/intEnergy_mass.m
@@ -1,12 +1,12 @@
 function u = intEnergy_mass(r)
 % INTENERGY_MASS - the specific internal energy [J/kg].
-%   
+%
 %       u = intEnergy_mass(r)
 %
 %    returns the specific internal energy of the reactor contents at
 %    the end of the last call to 'advance' or 'step.'
 %
 %    See also: Reactor/enthalpy_mass, Reactor/entropy_mass,
-%    Reactor/enthalpy_mole 
-%   
+%    Reactor/enthalpy_mole
+%
 u = reactormethods(28, reactor_hndl(r));
diff --git a/interfaces/matlab/toolbox/@Reactor/mass.m b/interfaces/matlab/toolbox/@Reactor/mass.m
index 1ec85c620..52f274b46 100644
--- a/interfaces/matlab/toolbox/@Reactor/mass.m
+++ b/interfaces/matlab/toolbox/@Reactor/mass.m
@@ -1,5 +1,4 @@
 function m = mass(r)
-% MASS - 
-%   
+% MASS -
+%
 m = reactormethods(23, reactor_hndl(r));
-
diff --git a/interfaces/matlab/toolbox/@Reactor/massFraction.m b/interfaces/matlab/toolbox/@Reactor/massFraction.m
index ad6ecc93c..51e51b2dd 100644
--- a/interfaces/matlab/toolbox/@Reactor/massFraction.m
+++ b/interfaces/matlab/toolbox/@Reactor/massFraction.m
@@ -1,5 +1,5 @@
 function y = massFraction(r, species)
-% MASSFRACTION - Mass fraction of species with name 'species'. 
-%   
+% MASSFRACTION - Mass fraction of species with name 'species'.
+%
 k = speciesIndex(r.contents, species) - 1;
 y = reactormethods(30, reactor_hndl(r), k);
diff --git a/interfaces/matlab/toolbox/@Reactor/massFractions.m b/interfaces/matlab/toolbox/@Reactor/massFractions.m
index 8381ccece..96fa12184 100644
--- a/interfaces/matlab/toolbox/@Reactor/massFractions.m
+++ b/interfaces/matlab/toolbox/@Reactor/massFractions.m
@@ -1,11 +1,10 @@
 function y = massFractions(r)
 % MASSFRACTION - Mass fractions of reactor contents after last call
-% to 'advance' or 'step'. 
-%   
+% to 'advance' or 'step'.
+%
 nsp = nSpecies(r.contents);
 ir = reactor_hndl(r);
 for k = 1:nsp
-  yy(k) = reactormethods(30, ir, k-1);
+    yy(k) = reactormethods(30, ir, k-1);
 end
 y = yy;
-
diff --git a/interfaces/matlab/toolbox/@Reactor/pressure.m b/interfaces/matlab/toolbox/@Reactor/pressure.m
index a97dc663f..1e262ec0b 100644
--- a/interfaces/matlab/toolbox/@Reactor/pressure.m
+++ b/interfaces/matlab/toolbox/@Reactor/pressure.m
@@ -1,4 +1,4 @@
 function p = pressure(r)
 % PRESSURE - pressure
-%   
+%
 p = reactormethods(29, reactor_hndl(r));
diff --git a/interfaces/matlab/toolbox/@Reactor/private/reactormethods.m b/interfaces/matlab/toolbox/@Reactor/private/reactormethods.m
index 5c4b9b7f6..4fa794e6d 100644
--- a/interfaces/matlab/toolbox/@Reactor/private/reactormethods.m
+++ b/interfaces/matlab/toolbox/@Reactor/private/reactormethods.m
@@ -1,13 +1,13 @@
 function v = reactormethods(n, job, a, b, c, d)
-%   
+%
 if nargin == 2
-  v = ctmethods(60, n, job);
+    v = ctmethods(60, n, job);
 elseif nargin == 3
-  v = ctmethods(60, n, job, a);  
+    v = ctmethods(60, n, job, a);
 elseif nargin == 4
-  v = ctmethods(60, n, job, a, b);    
+    v = ctmethods(60, n, job, a, b);
 elseif nargin == 5
-  v = ctmethods(60, n, job, a, b, c);  
+    v = ctmethods(60, n, job, a, b, c);
 elseif nargin == 6
-  v = ctmethods(60, n, job, a, b, c, d); 
-end
\ No newline at end of file
+    v = ctmethods(60, n, job, a, b, c, d);
+end
diff --git a/interfaces/matlab/toolbox/@Reactor/setEnergy.m b/interfaces/matlab/toolbox/@Reactor/setEnergy.m
index d8714e479..88d620e4f 100644
--- a/interfaces/matlab/toolbox/@Reactor/setEnergy.m
+++ b/interfaces/matlab/toolbox/@Reactor/setEnergy.m
@@ -3,22 +3,22 @@ function setEnergy(f, flag)
 % energy equation is disabled, then the reactor temperature is
 % constant. The parameter should be the string 'on' to enable the
 % energy equation, or 'off' to disable it.
-% 
+%
 % By default, Reactor objects are created with the energy equation
 % enabled, so usually this method is only needed to disable the
 % energy equation for isothermal simulations.
 %
 % >>> setEnergy(r, 'on');
 % >>> setEnergy(r, 'off');
-%   
+%
 iflag = -1
 if strcmp(flag,{'on'})
-  iflag = 1;
+    iflag = 1;
 elseif strcmp(flag,{'off'})
-  iflag = 0;
+    iflag = 0;
 end
 if iflag >= 0
-  reactormethods(9, f.index, iflag)
+    reactormethods(9, f.index, iflag)
 else
-  error('input to setEnergy not understood');
+    error('input to setEnergy not understood');
 end
diff --git a/interfaces/matlab/toolbox/@Reactor/setInitialTime.m b/interfaces/matlab/toolbox/@Reactor/setInitialTime.m
index 7ff0c934e..1a83b7906 100644
--- a/interfaces/matlab/toolbox/@Reactor/setInitialTime.m
+++ b/interfaces/matlab/toolbox/@Reactor/setInitialTime.m
@@ -1,5 +1,4 @@
 function setInitialTime(r, t0)
 % SETINITIALTIME - set the initial time. Deprecated.
-%   
+%
 reactormethods(5, reactor_hndl(r), t0);
-
diff --git a/interfaces/matlab/toolbox/@Reactor/setInitialVolume.m b/interfaces/matlab/toolbox/@Reactor/setInitialVolume.m
index ee0b3fe3c..f78e0682b 100644
--- a/interfaces/matlab/toolbox/@Reactor/setInitialVolume.m
+++ b/interfaces/matlab/toolbox/@Reactor/setInitialVolume.m
@@ -1,5 +1,4 @@
 function setInitialVolume(r, t0)
-% SETINITIALVOLUME - 
-%   
+% SETINITIALVOLUME -
+%
 reactormethods(4, reactor_hndl(r), t0);
-
diff --git a/interfaces/matlab/toolbox/@Reactor/setKineticsMgr.m b/interfaces/matlab/toolbox/@Reactor/setKineticsMgr.m
index 15c85ff63..873e6f661 100644
--- a/interfaces/matlab/toolbox/@Reactor/setKineticsMgr.m
+++ b/interfaces/matlab/toolbox/@Reactor/setKineticsMgr.m
@@ -4,8 +4,7 @@ function setKineticsMgr(r, k)
 % called by users.
 %
 if ~isa(k,'Kinetics')
-  error('wrong object type');
+    error('wrong object type');
 end
 
 reactormethods(7, reactor_hndl(r), kinetics_hndl(k));
-
diff --git a/interfaces/matlab/toolbox/@Reactor/setThermoMgr.m b/interfaces/matlab/toolbox/@Reactor/setThermoMgr.m
index f2d8ecfad..ab07272ca 100644
--- a/interfaces/matlab/toolbox/@Reactor/setThermoMgr.m
+++ b/interfaces/matlab/toolbox/@Reactor/setThermoMgr.m
@@ -2,8 +2,7 @@ function setThermoMgr(r, t)
 % SETTHERMOMGR - set the thermo manager
 %
 if ~isa(t,'ThermoPhase')
-  error('wrong object type');
+    error('wrong object type');
 end
 
 reactormethods(6, reactor_hndl(r), thermo_hndl(t));
-
diff --git a/interfaces/matlab/toolbox/@Reactor/step.m b/interfaces/matlab/toolbox/@Reactor/step.m
index 4e299682c..d4e4a410d 100644
--- a/interfaces/matlab/toolbox/@Reactor/step.m
+++ b/interfaces/matlab/toolbox/@Reactor/step.m
@@ -1,11 +1,11 @@
 function t = step(r, tout)
 % STEP - Take one internal time step toward tout.
-%   
+%
 %    The integrator used to integrate the ODEs (CVODE) takes
 %    variable-size steps, chosen so that a specified error
 %    tolerance is maintained. At times when the solution is rapidly
 %    changing, the time step becomes smaller to resolve the
-%    solution. 
+%    solution.
 %
 %    Method 'step' takes one internal time step and returns. This
 %    can be useful when it is desired to resolve a rapidly-changing
@@ -25,4 +25,3 @@ function t = step(r, tout)
 %    See also: Reactor/advance
 %
 t = reactormethods(21, reactor_hndl(r), tout);
-
diff --git a/interfaces/matlab/toolbox/@Reactor/temperature.m b/interfaces/matlab/toolbox/@Reactor/temperature.m
index 07e1b0053..e99ccaebc 100644
--- a/interfaces/matlab/toolbox/@Reactor/temperature.m
+++ b/interfaces/matlab/toolbox/@Reactor/temperature.m
@@ -1,5 +1,4 @@
 function t = temperature(r)
 % TEMPERATURE - temperature
-%   
+%
 t = reactormethods(26, reactor_hndl(r));
-
diff --git a/interfaces/matlab/toolbox/@Reactor/time.m b/interfaces/matlab/toolbox/@Reactor/time.m
index d6943d4f6..7db5f4595 100644
--- a/interfaces/matlab/toolbox/@Reactor/time.m
+++ b/interfaces/matlab/toolbox/@Reactor/time.m
@@ -1,4 +1,4 @@
 function t = time(r)
 % TIME - time
-%   
+%
 t = reactormethods(22, reactor_hndl(r));
diff --git a/interfaces/matlab/toolbox/@Reactor/volume.m b/interfaces/matlab/toolbox/@Reactor/volume.m
index 2febc87ae..aa2b15906 100644
--- a/interfaces/matlab/toolbox/@Reactor/volume.m
+++ b/interfaces/matlab/toolbox/@Reactor/volume.m
@@ -1,4 +1,4 @@
 function v = volume(r)
 % VOLUME - volume
-%   
+%
 v = reactormethods(24, reactor_hndl(r));
diff --git a/interfaces/matlab/toolbox/@ReactorNet/ReactorNet.m b/interfaces/matlab/toolbox/@ReactorNet/ReactorNet.m
index fd94174aa..90cbccf14 100644
--- a/interfaces/matlab/toolbox/@ReactorNet/ReactorNet.m
+++ b/interfaces/matlab/toolbox/@ReactorNet/ReactorNet.m
@@ -2,23 +2,23 @@ function x = ReactorNet(reactors)
 % REACTOR - Create a ReactorNet object.
 %
 %    A ReactorNet object is a container that holds one or more
-%    Reactor objects. 
+%    Reactor objects.
 %
 if nargin == 1
 else
-  error('wrong number of arguments to ReactorNet constructor');
+    error('wrong number of arguments to ReactorNet constructor');
 end
 
 x.index = reactornetmethods(0,0);
 if x.index < 0
-  error(geterr);
+    error(geterr);
 end
 x = class(x,'ReactorNet');
 
 % add reactors
 nr = length(reactors);
 for i = 1:nr
-  addReactor(x,reactors{i});
+    addReactor(x,reactors{i});
 end
 
 
diff --git a/interfaces/matlab/toolbox/@ReactorNet/advance.m b/interfaces/matlab/toolbox/@ReactorNet/advance.m
index 6bd7be98e..1b59b6c99 100644
--- a/interfaces/matlab/toolbox/@ReactorNet/advance.m
+++ b/interfaces/matlab/toolbox/@ReactorNet/advance.m
@@ -1,5 +1,5 @@
 function advance(n, tout)
-% ADVANCE - Advance the state of the reactor network in time. 
+% ADVANCE - Advance the state of the reactor network in time.
 %
 %    Method advance integrates the system of ordinary differential
 %    equations that determine the rate of change of the volume, the
diff --git a/interfaces/matlab/toolbox/@ReactorNet/atol.m b/interfaces/matlab/toolbox/@ReactorNet/atol.m
index 388cd3145..f93415961 100644
--- a/interfaces/matlab/toolbox/@ReactorNet/atol.m
+++ b/interfaces/matlab/toolbox/@ReactorNet/atol.m
@@ -1,5 +1,5 @@
 function t = atol(r)
 % ATOL - absolute error tolerance
-%   
+%
 t = reactornetmethods(24, reactornet_hndl(r));
 
diff --git a/interfaces/matlab/toolbox/@ReactorNet/private/reactornetmethods.m b/interfaces/matlab/toolbox/@ReactorNet/private/reactornetmethods.m
index 6adfd86f7..241fb726d 100644
--- a/interfaces/matlab/toolbox/@ReactorNet/private/reactornetmethods.m
+++ b/interfaces/matlab/toolbox/@ReactorNet/private/reactornetmethods.m
@@ -1,13 +1,13 @@
 function v = reactornetmethods(n, job, a, b, c, d)
-%   
+%
 if nargin == 2
-  v = ctmethods(65, n, job);
+    v = ctmethods(65, n, job);
 elseif nargin == 3
-  v = ctmethods(65, n, job, a);  
+    v = ctmethods(65, n, job, a);
 elseif nargin == 4
-  v = ctmethods(65, n, job, a, b);    
+    v = ctmethods(65, n, job, a, b);
 elseif nargin == 5
-  v = ctmethods(65, n, job, a, b, c);  
+    v = ctmethods(65, n, job, a, b, c);
 elseif nargin == 6
-  v = ctmethods(65, n, job, a, b, c, d); 
-end
\ No newline at end of file
+    v = ctmethods(65, n, job, a, b, c, d);
+end
diff --git a/interfaces/matlab/toolbox/@ReactorNet/rtol.m b/interfaces/matlab/toolbox/@ReactorNet/rtol.m
index 6cf9e7690..22423698c 100644
--- a/interfaces/matlab/toolbox/@ReactorNet/rtol.m
+++ b/interfaces/matlab/toolbox/@ReactorNet/rtol.m
@@ -1,5 +1,4 @@
 function t = rtol(r)
 % RTOL - relative error tolerance
-%   
+%
 t = reactornetmethods(23, reactornet_hndl(r));
-
diff --git a/interfaces/matlab/toolbox/@ReactorNet/setInitialTime.m b/interfaces/matlab/toolbox/@ReactorNet/setInitialTime.m
index 12cd32669..052fe71e2 100644
--- a/interfaces/matlab/toolbox/@ReactorNet/setInitialTime.m
+++ b/interfaces/matlab/toolbox/@ReactorNet/setInitialTime.m
@@ -1,7 +1,7 @@
 function setInitialTime(r, t)
 % SETINITIALTIME - Set the initial time at which to begin the time
-% integration. 
-% 
+% integration.
+%
 % If the time integration has already begun, this restarts the
 % integrator using the current solution as the initial condition,
 % setting the time to 't'.
diff --git a/interfaces/matlab/toolbox/@ReactorNet/setMaxTimeStep.m b/interfaces/matlab/toolbox/@ReactorNet/setMaxTimeStep.m
index 3ea28a02d..8ae99c71c 100644
--- a/interfaces/matlab/toolbox/@ReactorNet/setMaxTimeStep.m
+++ b/interfaces/matlab/toolbox/@ReactorNet/setMaxTimeStep.m
@@ -1,6 +1,6 @@
 function setMaxTimeStep(r, maxstep)
 % SETMAXTIMESTEP - Set the maximum time step.
-% 
+%
 % The integrator chooses a step size based on the desired error
 % tolerances and the rate at which the solution is changing. In
 % some cases, the solution changes very slowly at first, then very
diff --git a/interfaces/matlab/toolbox/@ReactorNet/step.m b/interfaces/matlab/toolbox/@ReactorNet/step.m
index 13ebe1380..c5c86c670 100644
--- a/interfaces/matlab/toolbox/@ReactorNet/step.m
+++ b/interfaces/matlab/toolbox/@ReactorNet/step.m
@@ -1,11 +1,11 @@
 function t = step(r, tout)
 % STEP - Take one internal time step toward tout.
-%   
+%
 %    The integrator used to integrate the ODEs (CVODE) takes
 %    variable-size steps, chosen so that a specified error
 %    tolerance is maintained. At times when the solution is rapidly
 %    changing, the time step becomes smaller to resolve the
-%    solution. 
+%    solution.
 %
 %    Method 'step' takes one internal time step and returns. This
 %    can be useful when it is desired to resolve a rapidly-changing
@@ -25,4 +25,3 @@ function t = step(r, tout)
 %    See also: Reactor/advance
 %
 t = reactornetmethods(21, reactornet_hndl(r), tout);
-
diff --git a/interfaces/matlab/toolbox/@ReactorNet/time.m b/interfaces/matlab/toolbox/@ReactorNet/time.m
index b93b94564..e51f7253f 100644
--- a/interfaces/matlab/toolbox/@ReactorNet/time.m
+++ b/interfaces/matlab/toolbox/@ReactorNet/time.m
@@ -1,5 +1,4 @@
 function t = time(r)
 % TIME - current value of the time.
-%   
+%
 t = reactornetmethods(22, reactornet_hndl(r));
-
diff --git a/interfaces/matlab/toolbox/@Solution/Solution.m b/interfaces/matlab/toolbox/@Solution/Solution.m
index 3cc477ae7..7e446f1c4 100644
--- a/interfaces/matlab/toolbox/@Solution/Solution.m
+++ b/interfaces/matlab/toolbox/@Solution/Solution.m
@@ -29,9 +29,9 @@ function s = Solution(src, id)
 %
 doc = XML_Node('doc',src);
 if nargin == 1
-  node = findByName(doc,'phase');
+    node = findByName(doc,'phase');
 else
-  node = findByID(doc,id);
+    node = findByID(doc,id);
 end
 t = ThermoPhase(node);
 k = Kinetics(node,t);
diff --git a/interfaces/matlab/toolbox/@Solution/clear.m b/interfaces/matlab/toolbox/@Solution/clear.m
index 27723ae8c..777502203 100644
--- a/interfaces/matlab/toolbox/@Solution/clear.m
+++ b/interfaces/matlab/toolbox/@Solution/clear.m
@@ -1,9 +1,7 @@
 function clear(s)
-% CLEAR - Delete the kernel object. 
+% CLEAR - Delete the kernel object.
 %
 clear(s.th);
 clear(s.kin);
 disp('Solution.clear: skipping clearing the transport object... check this!')
-%clear(s.tr);    
-
-
+%clear(s.tr);
diff --git a/interfaces/matlab/toolbox/@Solution/set.m b/interfaces/matlab/toolbox/@Solution/set.m
index c7226c4c1..c312b9025 100644
--- a/interfaces/matlab/toolbox/@Solution/set.m
+++ b/interfaces/matlab/toolbox/@Solution/set.m
@@ -1,8 +1,8 @@
 function a = set(a,varargin)
 % SET -  Set properties.
 %
-%   The properties that may be set are 
-%    
+%   The properties that may be set are
+%
 %   Temperature    (T)
 %   Density        (Rho)
 %   Volume         (V)
@@ -13,7 +13,7 @@ function a = set(a,varargin)
 %   MassFractions  (Y)
 %   Vapor Fraction (Vapor)
 %   Liquid Fractio (Liquid)
-% 
+%
 %   Either the full property name or the symbol may be
 %   specified. For the extensive properties (V,H,U,S), the values
 %   must be given per unit mass. H, U, and S must be set in
@@ -39,7 +39,7 @@ function a = set(a,varargin)
 property_argin = varargin;
 tval = -999;
 pval = -999;
-hval = -999; 
+hval = -999;
 uval = -999;
 sval = -999;
 vval = -999;
@@ -56,119 +56,119 @@ nu = 0;
 nq = 0;
 
 while length(property_argin) >= 2,
-  prop = property_argin{1};
-  val = property_argin{2};
-  property_argin = property_argin(3:end);
-  switch prop
-   case 'Temperature'
-    nt = nt + 1;
-    tval = val;
-   case 'T'
-    nt = nt + 1;
-    tval = val;       
-   case 'Density'
-    nv = nv + 1;
-    vval = 1.0/val;
-   case 'Rho'
-    nv = nv + 1;
-    vval = 1.0/val;
-   case 'V'
-    nv = nv + 1;
-    vval = val;
-   case 'MoleFractions'
-    nx = nx + 1;
-    setMoleFractions(a,val);
-   case 'X'
-    nx = nx + 1;
-    setMoleFractions(a,val);       
-   case 'MassFractions'
-    ny = ny + 1;
-    setMassFractions(a,val);       
-   case 'Y'
-    ny = ny + 1;
-    setMassFractions(a,val);              
-   case 'Pressure'
-    pval = val;
-    np = np + 1;
-   case 'P'
-    pval = val; 
-    np = np + 1;       
-   case 'Enthalpy'
-    hval = val;
-    nh = nh + 1;       
-   case 'H'
-    hval = val; 
-    nh = nh + 1;       
-   case 'IntEnergy'
-    uval = val;
-    nu = nu + 1;       
-   case 'U'
-    uval = val; 
-    nu = nu + 1;       
-   case 'Entropy'
-    sval = val;
-    ns = ns + 1;       
-   case 'S'
-    sval = val; 
-    ns = ns + 1;       
-   case 'Sat'
-    qval = val;
-    nq = nq + 1;
-   case 'Vapor'
-    qval = val;
-    nq = nq + 1;
-   case 'Liquid'
-    qval = 1.0 - val;
-    nq = nq + 1;
-   otherwise
-    error(['unknown property ' char(prop)])
-  end
+    prop = property_argin{1};
+    val = property_argin{2};
+    property_argin = property_argin(3:end);
+    switch prop
+        case 'Temperature'
+            nt = nt + 1;
+            tval = val;
+        case 'T'
+            nt = nt + 1;
+            tval = val;
+        case 'Density'
+            nv = nv + 1;
+            vval = 1.0/val;
+        case 'Rho'
+            nv = nv + 1;
+            vval = 1.0/val;
+        case 'V'
+            nv = nv + 1;
+            vval = val;
+        case 'MoleFractions'
+            nx = nx + 1;
+            setMoleFractions(a,val);
+        case 'X'
+            nx = nx + 1;
+            setMoleFractions(a,val);
+        case 'MassFractions'
+            ny = ny + 1;
+            setMassFractions(a,val);
+        case 'Y'
+            ny = ny + 1;
+            setMassFractions(a,val);
+        case 'Pressure'
+            pval = val;
+            np = np + 1;
+        case 'P'
+            pval = val;
+            np = np + 1;
+        case 'Enthalpy'
+            hval = val;
+            nh = nh + 1;
+        case 'H'
+            hval = val;
+            nh = nh + 1;
+        case 'IntEnergy'
+            uval = val;
+            nu = nu + 1;
+        case 'U'
+            uval = val;
+            nu = nu + 1;
+        case 'Entropy'
+            sval = val;
+            ns = ns + 1;
+        case 'S'
+            sval = val;
+            ns = ns + 1;
+        case 'Sat'
+            qval = val;
+            nq = nq + 1;
+        case 'Vapor'
+            qval = val;
+            nq = nq + 1;
+        case 'Liquid'
+            qval = 1.0 - val;
+            nq = nq + 1;
+        otherwise
+            error(['unknown property ' char(prop)])
+    end
 end
 
 if nx + ny > 1
-  error('composition specified multiple times');
+    error('composition specified multiple times');
 end
 
 ntot = nt + np + nv + ns + nh + nu + nq;
 
 if ntot == 1
-  %
-  % set T, v, or P individually
-  %
-  if nt == 1
-    setTemperature(a,tval);   % density held fixed
-  elseif nv == 1
-    setDensity(a,1.0/vval);   % temperature held fixed
-  elseif np == 1
-    setPressure(a, pval);     % temperature held fixed
-  else
-    error('pressure, volume, or density must also be specified');
-  end
-elseif ntot == 2 
-  %
-  % set property pairs
-  %
-  if nt == 1 & nv == 1
-    setTemperature(a,tval);
-    setDensity(a,1.0/vval); 
-  elseif nt == 1 & np == 1
-    setTemperature(a,tval);
-    setPressure(a, pval);
-  elseif nt == 1 & nq == 1
-    setState_Tsat(a, [tval,qval]);
-  elseif np == 1 & nq == 1
-    setState_Psat(a, [pval,qval]);
-  elseif np == 1 & nh == 1
-    setState_HP(a,[hval,pval]);
-  elseif nu == 1 & nv == 1
-    setState_UV(a,[uval,vval]);
-  elseif ns == 1 & np == 1
-    setState_SP(a,[sval,pval]);   
-  elseif ns == 1 & nv == 1
-    setState_SV(a,[sval,vval]);      
-  else
-    error('unimplemented property pair');
-  end
+    %
+    % set T, v, or P individually
+    %
+    if nt == 1
+        setTemperature(a,tval);   % density held fixed
+    elseif nv == 1
+        setDensity(a,1.0/vval);   % temperature held fixed
+    elseif np == 1
+        setPressure(a, pval);     % temperature held fixed
+    else
+        error('pressure, volume, or density must also be specified');
+    end
+elseif ntot == 2
+    %
+    % set property pairs
+    %
+    if nt == 1 & nv == 1
+        setTemperature(a,tval);
+        setDensity(a,1.0/vval);
+    elseif nt == 1 & np == 1
+        setTemperature(a,tval);
+        setPressure(a, pval);
+    elseif nt == 1 & nq == 1
+        setState_Tsat(a, [tval,qval]);
+    elseif np == 1 & nq == 1
+        setState_Psat(a, [pval,qval]);
+    elseif np == 1 & nh == 1
+        setState_HP(a,[hval,pval]);
+    elseif nu == 1 & nv == 1
+        setState_UV(a,[uval,vval]);
+    elseif ns == 1 & np == 1
+        setState_SP(a,[sval,pval]);
+    elseif ns == 1 & nv == 1
+        setState_SV(a,[sval,vval]);
+    else
+        error('unimplemented property pair');
+    end
 elseif ntot > 2
-  error('too many properties specified');
+    error('too many properties specified');
 end
diff --git a/interfaces/matlab/toolbox/@Solution/soundspeed.m b/interfaces/matlab/toolbox/@Solution/soundspeed.m
index 2648c3481..cfd564935 100644
--- a/interfaces/matlab/toolbox/@Solution/soundspeed.m
+++ b/interfaces/matlab/toolbox/@Solution/soundspeed.m
@@ -2,17 +2,17 @@ function b = soundspeed(a)
 %  SOUNDSPEED  - Speed of sound (m/s).
 
 if isIdealGas(a)
-   gamma = cp_mass(a)/cv_mass(a);
-   wtm = meanMolecularWeight(a);
-   r = gasconstant/wtm;
-   b = sqrt(gamma * r * temperature(a));
+    gamma = cp_mass(a)/cv_mass(a);
+    wtm = meanMolecularWeight(a);
+    r = gasconstant/wtm;
+    b = sqrt(gamma * r * temperature(a));
 else
-   rho0 = density(a);
-   p0 = pressure(a);
-   s0 = entropy_mass(a);
-   rho1 = 1.001*rho0;
-   set(gas,'Density',rho1,'Entropy',s0);
-   p1 = pressure(a);
-   dpdrho_s = (p1 - p0)/(rho1 - rho0);
-   b = sqrt(dpdrho_s);
+    rho0 = density(a);
+    p0 = pressure(a);
+    s0 = entropy_mass(a);
+    rho1 = 1.001*rho0;
+    set(gas,'Density',rho1,'Entropy',s0);
+    p1 = pressure(a);
+    dpdrho_s = (p1 - p0)/(rho1 - rho0);
+    b = sqrt(dpdrho_s);
 end
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/ThermoPhase.m b/interfaces/matlab/toolbox/@ThermoPhase/ThermoPhase.m
index 7bb775a9d..0aea31fde 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/ThermoPhase.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/ThermoPhase.m
@@ -2,22 +2,22 @@ function t = ThermoPhase(r)
 %THERMOPHASE Cantera ThermoPhase class constructor
 %
 if nargin == 1
-   if isa(r,'ThermoPhase')
-      % create a copy
-      t = r;
-      return   
-   elseif isa(r,'XML_Node')
-      t.owner = 1;
-      hr = hndl(r);
-      t.tp_id = thermo_get(hr,0);
-      if t.tp_id < 0
-	 error(geterr);
-      end
-   else
-      t.owner = 0;
-      t.tp_id = r;
-   end
-   t = class(t,'ThermoPhase');
+    if isa(r,'ThermoPhase')
+        % create a copy
+        t = r;
+        return
+    elseif isa(r,'XML_Node')
+        t.owner = 1;
+        hr = hndl(r);
+        t.tp_id = thermo_get(hr,0);
+        if t.tp_id < 0
+            error(geterr);
+        end
+    else
+        t.owner = 0;
+        t.tp_id = r;
+    end
+    t = class(t,'ThermoPhase');
 else
-   error('wrong number of arguments');
+    error('wrong number of arguments');
 end
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/atomicMasses.m b/interfaces/matlab/toolbox/@ThermoPhase/atomicMasses.m
index ebbbcec96..279221c8a 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/atomicMasses.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/atomicMasses.m
@@ -1,4 +1,4 @@
 function x = atomicMasses(a)
 % ATOMICMASSES - Array of element atomic masses [kg/kmol].
-% 
-  x = phase_get(a.tp_id,30);
+%
+x = phase_get(a.tp_id,30);
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/chemPotentials.m b/interfaces/matlab/toolbox/@ThermoPhase/chemPotentials.m
index d7b4a14d9..bc9a567f8 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/chemPotentials.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/chemPotentials.m
@@ -1,9 +1,9 @@
 function mu = chemPotentials(p)
 % CHEMPOTENTIALS - Species chemical potentials.
-%        
+%
 %        This method returns an array containing the species
 %        chemical potentials [J/kmol]. The expressions used to
 %        compute these depend on the model implemented by the
 %        underlying kernel thermo manager."""
-  mu = thermo_get(p.tp_id,34);
+mu = thermo_get(p.tp_id,34);
 
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/clear.m b/interfaces/matlab/toolbox/@ThermoPhase/clear.m
index e69ad8729..bf08abdc8 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/clear.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/clear.m
@@ -1,5 +1,5 @@
 function clear(t)
 % CLEAR - Delete the kernel object.
-%   
+%
 thermo_set(t.tp_id,0,10);
 
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/cp_R.m b/interfaces/matlab/toolbox/@ThermoPhase/cp_R.m
index 5dca044c8..660f83386 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/cp_R.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/cp_R.m
@@ -1,8 +1,7 @@
 function v = cp_R(p)
 % CP_R - Species non-dimensional heat capacities.
-%        
-%        This method returns an array containing the pure species
-%        standard-state heat capacities at constant pressure. 
 %
-  v = thermo_get(p.tp_id,38);
-
+%        This method returns an array containing the pure species
+%        standard-state heat capacities at constant pressure.
+%
+v = thermo_get(p.tp_id,38);
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/cp_mass.m b/interfaces/matlab/toolbox/@ThermoPhase/cp_mass.m
index e03ed2957..77923ac11 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/cp_mass.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/cp_mass.m
@@ -1,3 +1,3 @@
 function v = cp_mass(a)
 % CP_MASS - Specific heat at constant pressure [J/kg-K].
-  v = thermo_get(a.tp_id,13);
+v = thermo_get(a.tp_id,13);
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/cp_mole.m b/interfaces/matlab/toolbox/@ThermoPhase/cp_mole.m
index 4acbd378e..ab6114e4a 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/cp_mole.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/cp_mole.m
@@ -1,3 +1,3 @@
 function v = cp_mole(a)
 % CP_MOLE - Molar heat capacity at constant pressure [J/kmol-K].
-  v = thermo_get(a.tp_id,6);
+v = thermo_get(a.tp_id,6);
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/critDensity.m b/interfaces/matlab/toolbox/@ThermoPhase/critDensity.m
index ebb1d8edf..36fe010a1 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/critDensity.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/critDensity.m
@@ -1,4 +1,4 @@
 function v = critDensity(a)
 % CRITDENSITY - Critical density [kg/m3].
 %
-  v = thermo_get(a.tp_id,21);
+v = thermo_get(a.tp_id,21);
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/critPressure.m b/interfaces/matlab/toolbox/@ThermoPhase/critPressure.m
index e0e3945b7..fd08a9df9 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/critPressure.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/critPressure.m
@@ -1,4 +1,4 @@
 function v = critPressure(a)
 % CRITPRESSURE - Critical pressure [Pa].
 %
-  v = thermo_get(a.tp_id,20);
+v = thermo_get(a.tp_id,20);
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/critTemperature.m b/interfaces/matlab/toolbox/@ThermoPhase/critTemperature.m
index e0c9f153f..6f7e27a0d 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/critTemperature.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/critTemperature.m
@@ -1,4 +1,4 @@
 function v = critTemperature(a)
 % CRITTEMPERATURE - Critical temperature [K].
 %
-  v = thermo_get(a.tp_id,19);
+v = thermo_get(a.tp_id,19);
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/cv_mass.m b/interfaces/matlab/toolbox/@ThermoPhase/cv_mass.m
index f9e12826a..a0c0130a3 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/cv_mass.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/cv_mass.m
@@ -1,3 +1,3 @@
 function v = cv_mass(a)
 % CV_MASS - Specific heat at constant volume [J/kg-K].
-  v = thermo_get(a.tp_id,14);
+v = thermo_get(a.tp_id,14);
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/cv_mole.m b/interfaces/matlab/toolbox/@ThermoPhase/cv_mole.m
index 092594b83..422ef36ec 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/cv_mole.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/cv_mole.m
@@ -1,3 +1,3 @@
 function v = cv_mole(a)
 % CV_MOLE - Molar heat capacity at constant volume [J/kmol-K].
-  v = thermo_get(a.tp_id,7);
+v = thermo_get(a.tp_id,7);
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/density.m b/interfaces/matlab/toolbox/@ThermoPhase/density.m
index efab882bc..c1948027a 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/density.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/density.m
@@ -1,4 +1,4 @@
 function rho = density(p)
 % DENSITY - Mass density [kg/m^3].
-% 
-  rho = phase_get(p.tp_id,2);
+%
+rho = phase_get(p.tp_id,2);
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/display.m b/interfaces/matlab/toolbox/@ThermoPhase/display.m
index 43e3c357c..c54572ff3 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/display.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/display.m
@@ -1,3 +1,2 @@
 function display(self)
 phase_get(thermo_hndl(self), 15, 1);
-
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/elementIndex.m b/interfaces/matlab/toolbox/@ThermoPhase/elementIndex.m
index 0d8ff1d24..fceab84e5 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/elementIndex.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/elementIndex.m
@@ -1,7 +1,7 @@
 function k = elementIndex(a,name)
 % ELEMENTINDEX -  The element index of the element with name
-% 'name'. 
-% 
+% 'name'.
+%
 %   The index is an integer assigned to each element in sequence as it
 %   is read in from the input file.
 %
@@ -20,13 +20,13 @@ function k = elementIndex(a,name)
 %
 
 if iscell(name)
-  [m, n] = size(name);
-  k = zeros(m,n);
-  for i = 1:m
-    for j = 1:n
-      k(i,j) = phase_get(a.tp_id,13,name{i,j});
+    [m, n] = size(name);
+    k = zeros(m,n);
+    for i = 1:m
+        for j = 1:n
+            k(i,j) = phase_get(a.tp_id,13,name{i,j});
+        end
     end
-  end
 else
-  k = phase_get(a.tp_id,13,name);
+    k = phase_get(a.tp_id,13,name);
 end
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/elementName.m b/interfaces/matlab/toolbox/@ThermoPhase/elementName.m
index 6148e3f44..28efa0292 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/elementName.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/elementName.m
@@ -9,9 +9,7 @@ function nm = elementName(a, m)
 [mm, nn] = size(m);
 nm = {};
 for i = 1:mm
-  for j = 1:nn
-    nm{i,j} = phase_get(a.tp_id, 41, m(i,j));
-  end
+    for j = 1:nn
+        nm{i,j} = phase_get(a.tp_id, 41, m(i,j));
+    end
 end
-
-
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/enthalpies_RT.m b/interfaces/matlab/toolbox/@ThermoPhase/enthalpies_RT.m
index 72c7234f3..4d1beb104 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/enthalpies_RT.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/enthalpies_RT.m
@@ -1,12 +1,12 @@
 function v = enthalpies_RT(p)
 % ENTHALPIES_RT - Pure species non-dimensional enthalpies.
 %
-%      h_rt = enthalpies_RT(phase) 
-%    
+%      h_rt = enthalpies_RT(phase)
+%
 %    sets array h_rt to the array of standard-state species enthalpies
 %    for phase 'phase' divided by RT, where R is the universal gas
 %    constant and T is the temperature.  For gaseous species, these
 %    values are ideal gas enthalpies.
 %
-%  
-  v = thermo_get(p.tp_id,32);
+%
+v = thermo_get(p.tp_id,32);
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/enthalpy_mass.m b/interfaces/matlab/toolbox/@ThermoPhase/enthalpy_mass.m
index 5c7849471..612899621 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/enthalpy_mass.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/enthalpy_mass.m
@@ -1,4 +1,4 @@
 function v = enthalpy_mass(a)
 % ENTHALPY_MASS - Specific enthalpy [J/kg].
 %
-  v = thermo_get(a.tp_id,9);
+v = thermo_get(a.tp_id,9);
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/enthalpy_mole.m b/interfaces/matlab/toolbox/@ThermoPhase/enthalpy_mole.m
index 22cca043d..6cc02921a 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/enthalpy_mole.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/enthalpy_mole.m
@@ -1,4 +1,4 @@
 function v = enthalpy_mole(a)
 % ENTHALPY_MOLE - Molar enthalpy [J/kmol].
 %
-  v = thermo_get(a.tp_id,2);
+v = thermo_get(a.tp_id,2);
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/entropies_R.m b/interfaces/matlab/toolbox/@ThermoPhase/entropies_R.m
index b041fe480..c2fa78d7a 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/entropies_R.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/entropies_R.m
@@ -1,7 +1,7 @@
 function v = entropies_R(p)
 % ENTROPIES_R - Species non-dimensional entropies.
-%        
-%        This method returns an array containing the pure species
-%        standard-state entropies. 
 %
-  v = thermo_get(p.tp_id,36);
+%        This method returns an array containing the pure species
+%        standard-state entropies.
+%
+v = thermo_get(p.tp_id,36);
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/eosType.m b/interfaces/matlab/toolbox/@ThermoPhase/eosType.m
index 8747a9c60..e19a61cb8 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/eosType.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/eosType.m
@@ -3,5 +3,5 @@ function e = eosType(a)
 %
 %    This method returns an integer flag identifying the type of
 %    equation of state.
-% 
+%
 e = thermo_get(a.tp_id, 18);
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/equilibrate.m b/interfaces/matlab/toolbox/@ThermoPhase/equilibrate.m
index 38edd338b..6987b8c50 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/equilibrate.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/equilibrate.m
@@ -12,40 +12,40 @@ function a = equilibrate(a, xy, solver, rtol, maxsteps, maxiter, loglevel)
 %        minimization solver will be used. If solver < 0 or is
 %        unspecified, the fast solver will be tried first, then if it
 %        fails the other will be tried.
-%  
+%
 %        rtol -- the relative error tolerance.
-%  
+%
 %        maxsteps -- maximum number of steps in composition to take to
 %        find a converged solution.
-%  
+%
 %        maxiter -- for the Gibbs minimization solver only, this
 %        specifies the number of 'outer' iterations on T or P when
 %        some property pair other than TP is specified.
-%  
+%
 %        loglevel -- set to a value > 0 to write diagnostic output to
 %        a file in HTML format. Larger values generate more detailed
 %        information. The file will be named 'equilibrate_log.html.'
 %        Subsequent files will be named 'equilibrate_log1.html',
 %        'equilibrate_log2.html', etc., so that log files are not
 %        overwritten.
-%          
+%
 %
 
 % use the ChemEquil solver by default
 if nargin < 3
-  solver = -1;
+    solver = -1;
 end
 if nargin < 4
-  rtol = 1.0e-9;
+    rtol = 1.0e-9;
 end
 if nargin < 5
-  maxsteps = 1000;
+    maxsteps = 1000;
 end
 if nargin < 6
-  maxiter = 100;
+    maxiter = 100;
 end
 if nargin < 7
-  loglevel = 0;
+    loglevel = 0;
 end
 
 iok = 0;
@@ -60,7 +60,7 @@ iok = thermo_set(a.tp_id, 50, xy, solver, rtol, maxsteps, maxiter, loglevel);
 % $$$  case 'SP'
 % $$$   iok = thermo_set(a.tp_id, 50, 102, solver, rtol, maxsteps, loglevel);
 % $$$  case 'SV'
-% $$$   iok = thermo_set(a.tp_id, 50, 107, solver, rtol, maxsteps, loglevel); 
+% $$$   iok = thermo_set(a.tp_id, 50, 107, solver, rtol, maxsteps, loglevel);
 % $$$  case 'UV'
 % $$$   iok = thermo_set(a.tp_id, 50, 105, solver, rtol, maxsteps, loglevel);
 % $$$  case 'PT'
@@ -72,17 +72,17 @@ iok = thermo_set(a.tp_id, 50, xy, solver, rtol, maxsteps, maxiter, loglevel);
 % $$$  case 'PS'
 % $$$   iok = thermo_set(a.tp_id, 50, 102, solver, rtol, maxsteps, loglevel);
 % $$$  case 'VS'
-% $$$   iok = thermo_set(a.tp_id, 50, 107, solver, rtol, maxsteps, loglevel); 
+% $$$   iok = thermo_set(a.tp_id, 50, 107, solver, rtol, maxsteps, loglevel);
 % $$$  case 'VU'
-% $$$   iok = thermo_set(a.tp_id, 50, 105, solver, rtol, maxsteps, loglevel); 
+% $$$   iok = thermo_set(a.tp_id, 50, 105, solver, rtol, maxsteps, loglevel);
 % $$$  otherwise
 % $$$   error('unsupported option')
 % $$$ end
 if iok < 0
-  e = geterr;
-  if e == 0
-    e = 'unknown error';
-  end
-   error(e);
+    e = geterr;
+    if e == 0
+        e = 'unknown error';
+    end
+    error(e);
 end
 
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/gibbs_RT.m b/interfaces/matlab/toolbox/@ThermoPhase/gibbs_RT.m
index b6ac1b187..78b082c58 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/gibbs_RT.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/gibbs_RT.m
@@ -1,8 +1,7 @@
 function g_RT = gibbs_RT(p)
 % GIBBS_RT - Species non-dimensional Gibbs free energies.
-%        
+%
 %        This method returns an array containing the pure species
-%        standard-state Gibbs free energies. 
+%        standard-state Gibbs free energies.
 %
 g_RT = enthalpies_RT(g) - entropies_R(g);
-
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/gibbs_mass.m b/interfaces/matlab/toolbox/@ThermoPhase/gibbs_mass.m
index 0e268fda7..a6c587d2c 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/gibbs_mass.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/gibbs_mass.m
@@ -1,3 +1,3 @@
 function v = gibbs_mass(a)
 % GIBBS_MASS - Specific Gibbs function [J/kg].
-  v = thermo_get(a.tp_id,12);
+v = thermo_get(a.tp_id,12);
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/gibbs_mole.m b/interfaces/matlab/toolbox/@ThermoPhase/gibbs_mole.m
index 604d260e2..9f35c223b 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/gibbs_mole.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/gibbs_mole.m
@@ -1,3 +1,3 @@
 function v = gibbs_mole(a)
 % GIBBS_MOLE - Molar Gibbs function [J/kmol].
-  v = thermo_get(a.tp_id,5);
+v = thermo_get(a.tp_id,5);
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/intEnergy_mass.m b/interfaces/matlab/toolbox/@ThermoPhase/intEnergy_mass.m
index 93697d3ee..50aff6bf6 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/intEnergy_mass.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/intEnergy_mass.m
@@ -1,3 +1,3 @@
 function v = intEnergy_mass(a)
 % INTENERGY_MASS - Specific internal energy [J/kg].
-  v = thermo_get(a.tp_id,10);
+v = thermo_get(a.tp_id,10);
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/intEnergy_mole.m b/interfaces/matlab/toolbox/@ThermoPhase/intEnergy_mole.m
index 568558c7a..fbf5bf3ae 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/intEnergy_mole.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/intEnergy_mole.m
@@ -1,3 +1,3 @@
 function v = intEnergy_mole(a)
 % INTENERGY_MOLE - Molar internal energy [J/kmol].
-  v = thermo_get(a.tp_id,3);
+v = thermo_get(a.tp_id,3);
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/isIdealGas.m b/interfaces/matlab/toolbox/@ThermoPhase/isIdealGas.m
index 516bcff4d..b1f8234f7 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/isIdealGas.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/isIdealGas.m
@@ -2,8 +2,8 @@ function v = isIdealGas(a)
 % ISIDEALGAS - True if the phase is an ideal gas or ideal gas
 % mixture, and false otherwise.
 %
-  if eosType(a) == 1
-   v = 1;
+if eosType(a) == 1
+    v = 1;
 else
-   v = 0;
+    v = 0;
 end
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/massFraction.m b/interfaces/matlab/toolbox/@ThermoPhase/massFraction.m
index 34b1dbb45..90dbaed50 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/massFraction.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/massFraction.m
@@ -3,17 +3,17 @@ function y = massFraction(s, species)
 y = 0.0;
 yarray = massFractions(s);
 if isa(species,'char')
-  k = speciesIndex(s, species);
-  if  k > 0
-    y = yarray(k);
-  end
+    k = speciesIndex(s, species);
+    if  k > 0
+        y = yarray(k);
+    end
 
 elseif isa(species,'cell')
-  n = length(species);
-  for j = 1:n
-    k = speciesIndex(s, species{j});
-    if k > 0
-      y(j) = yarray(k);
+    n = length(species);
+    for j = 1:n
+        k = speciesIndex(s, species{j});
+        if k > 0
+            y(j) = yarray(k);
+        end
     end
-  end
 end
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/massFractions.m b/interfaces/matlab/toolbox/@ThermoPhase/massFractions.m
index 7887e4697..0dd5b2ad7 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/massFractions.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/massFractions.m
@@ -6,12 +6,12 @@ function x = massFractions(a)
 %   returns the array of species mass fractions for phase 'phase'.  If
 %   no output argument is specified, a bar plot is produced.
 %
-  x = phase_get(a.tp_id,21);
-  if nargout == 0
+x = phase_get(a.tp_id,21);
+if nargout == 0
     figure
     set(gcf,'Name','Mass Fractions')
     bar(x)
     xlabel('Species Number')
     ylabel('Mass Fraction')
     title('Species Mass Fractions')
-  end
\ No newline at end of file
+end
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/maxTemp.m b/interfaces/matlab/toolbox/@ThermoPhase/maxTemp.m
index 2380cecae..7ad60e7aa 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/maxTemp.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/maxTemp.m
@@ -1,6 +1,6 @@
 function v = maxTemp(p)
 % MAXTEMP - Maximum temperature.
-% 
+%
 %   The parameterizations used to represent the temperature-dependent
 %   species thermodynamic properties are generally only valid in some
 %   finite temperature range, which may be different for each species
@@ -8,5 +8,5 @@ function v = maxTemp(p)
 %   the parameterizations are valid for all species in the phase.
 %
 %   See also: minTemp
-%  
-  v = thermo_get(p.tp_id,17);
+%
+v = thermo_get(p.tp_id,17);
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/meanMolarMass.m b/interfaces/matlab/toolbox/@ThermoPhase/meanMolarMass.m
index a9a6392de..e35e602ae 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/meanMolarMass.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/meanMolarMass.m
@@ -5,4 +5,3 @@ function wtm = meanMolarMass(p)
 %   molar masses of the individual species in the phase.
 %
 wtm = phase_get(p.tp_id,4);
-  
\ No newline at end of file
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/meanMolecularWeight.m b/interfaces/matlab/toolbox/@ThermoPhase/meanMolecularWeight.m
index faee89b0d..19f73acd9 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/meanMolecularWeight.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/meanMolecularWeight.m
@@ -1,9 +1,9 @@
 function wtm = meanMolecularWeight(p)
-% MEANMOLECULARWEIGHT - Mean molecular weight. 
+% MEANMOLECULARWEIGHT - Mean molecular weight.
 %
 %    This method is a synonym for method meanMolarMass and is
 %    provided for backward compatibility.
 %
 %    See also; meanMolarMass
 %
-  wtm = meanMolarMass(p);
\ No newline at end of file
+wtm = meanMolarMass(p);
\ No newline at end of file
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/minTemp.m b/interfaces/matlab/toolbox/@ThermoPhase/minTemp.m
index aa51949c1..5fad28579 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/minTemp.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/minTemp.m
@@ -1,6 +1,6 @@
 function v = minTemp(p)
 % MINTEMP - Minimum temperature.
-% 
+%
 %   The parameterizations used to represent the temperature-dependent
 %   species thermodynamic properties are generally only valid in some
 %   finite temperature range, which may be different for each species
@@ -8,6 +8,5 @@ function v = minTemp(p)
 %   the parameterizations are valid for all species in the phase.
 %
 %   See also: maxTemp
-%  
-  v = thermo_get(p.tp_id,16);
-
+%
+v = thermo_get(p.tp_id,16);
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/molarDensity.m b/interfaces/matlab/toolbox/@ThermoPhase/molarDensity.m
index 8ab6664d0..117e86d0c 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/molarDensity.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/molarDensity.m
@@ -1,4 +1,4 @@
 function n = molarDensity(p)
 % MOLARDENSITY - Molar density [kmol/m^3].
 %
-  n = phase_get(p.tp_id,3);
+n = phase_get(p.tp_id,3);
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/molarMasses.m b/interfaces/matlab/toolbox/@ThermoPhase/molarMasses.m
index 390c0281c..4ad4826c4 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/molarMasses.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/molarMasses.m
@@ -1,4 +1,4 @@
 function x = molarMasses(a)
 % MOLARMASSES - Array of species molar masses [kg/kmol].
-% 
-  x = phase_get(a.tp_id,22);
+%
+x = phase_get(a.tp_id,22);
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/moleFraction.m b/interfaces/matlab/toolbox/@ThermoPhase/moleFraction.m
index 1c1f982fa..adf0e5912 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/moleFraction.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/moleFraction.m
@@ -3,17 +3,17 @@ 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);
+    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
 end
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/moleFractions.m b/interfaces/matlab/toolbox/@ThermoPhase/moleFractions.m
index 8dbaa0169..3529ba044 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/moleFractions.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/moleFractions.m
@@ -6,12 +6,12 @@ function x = moleFractions(a)
 %   returns the array of species mole fractions for phase 'phase'.  If
 %   no output argument is specified, a bar plot is produced.
 %
-  x = phase_get(a.tp_id,20);
-  if nargout == 0
+x = phase_get(a.tp_id,20);
+if nargout == 0
     figure
     set(gcf,'Name','Mole Fractions')
     bar(x)
     xlabel('Species Number')
     ylabel('Mole Fraction')
     title('Species Mole Fractions')
-  end
+end
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/molecularWeights.m b/interfaces/matlab/toolbox/@ThermoPhase/molecularWeights.m
index f073220c6..58d91f399 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/molecularWeights.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/molecularWeights.m
@@ -1,9 +1,8 @@
 function x = molecularWeights(a)
 % MOLECULARWEIGHTS - Array of species molar masses [kg/kmol].
-% 
+%
 %   This method is deprecated - use molarMasses instead.
 %
 %   See also: molarMasses
 %
-  x = molarMasses(a);
-
+x = molarMasses(a);
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/nAtoms.m b/interfaces/matlab/toolbox/@ThermoPhase/nAtoms.m
index 30e1e2e51..154673be2 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/nAtoms.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/nAtoms.m
@@ -1,7 +1,7 @@
 function n = nAtoms(a,k,m)
 % NATOMS - Number of atoms of element m in species k.
 if nargin == 3
-  n = phase_get(a.tp_id,14,k,m);
+    n = phase_get(a.tp_id,14,k,m);
 else
-  error('usage: nAtoms(phase, k, m)')
-end
\ No newline at end of file
+    error('usage: nAtoms(phase, k, m)')
+end
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/nElements.m b/interfaces/matlab/toolbox/@ThermoPhase/nElements.m
index 4ec6b7991..259f87373 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/nElements.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/nElements.m
@@ -1,4 +1,4 @@
 function n = nElements(a)
 % NELEMENTS - Number of elements in the phase.
 %
-n = phase_get(a.tp_id,10);
\ No newline at end of file
+n = phase_get(a.tp_id,10);
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/nSpecies.m b/interfaces/matlab/toolbox/@ThermoPhase/nSpecies.m
index cec4fb0b4..d5a0fbd94 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/nSpecies.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/nSpecies.m
@@ -1,4 +1,4 @@
 function n = nSpecies(a)
 % NSPECIES - Number of species in the phase.
 %
-n = phase_get(a.tp_id,11);
\ No newline at end of file
+n = phase_get(a.tp_id,11);
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/name.m b/interfaces/matlab/toolbox/@ThermoPhase/name.m
index 07942f411..56bd71bf3 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/name.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/name.m
@@ -1,6 +1,3 @@
 function nm = name(self)
-% NAME - user-specified phase name. 
+% NAME - user-specified phase name.
 nm = phase_get(thermo_hndl(self), 42);
-
-
-
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/private/phase_get.m b/interfaces/matlab/toolbox/@ThermoPhase/private/phase_get.m
index 5dc316adb..0d963e4b6 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/private/phase_get.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/private/phase_get.m
@@ -1,8 +1,8 @@
-function i = phase_get(n, job, a, b) 
+function i = phase_get(n, job, a, b)
 if nargin == 2
-  i = ctmethods(30,n,job);
+    i = ctmethods(30,n,job);
 elseif nargin == 3
-  i = ctmethods(30,n,job,a);
+    i = ctmethods(30,n,job,a);
 else
-  i = ctmethods(30, n, job, a, b);
+    i = ctmethods(30, n, job, a, b);
 end
\ No newline at end of file
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/private/phase_set.m b/interfaces/matlab/toolbox/@ThermoPhase/private/phase_set.m
index 2cbc21eff..0ce4e9010 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/private/phase_set.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/private/phase_set.m
@@ -1,8 +1,8 @@
-function phase_set(n, job, a, b) 
+function phase_set(n, job, a, b)
 if nargin == 2
-  ctmethods(30,n,-job);
+    ctmethods(30,n,-job);
 elseif nargin == 3
-  ctmethods(30,n,-job,a);
+    ctmethods(30,n,-job,a);
 else
-  ctmethods(30, n,-job, a, b);
+    ctmethods(30, n,-job, a, b);
 end
\ No newline at end of file
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/private/thermo_get.m b/interfaces/matlab/toolbox/@ThermoPhase/private/thermo_get.m
index 984282169..8be76892b 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/private/thermo_get.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/private/thermo_get.m
@@ -1,8 +1,8 @@
-function i = thermo_get(n, job, a, b) 
+function i = thermo_get(n, job, a, b)
 if nargin == 2
-  i = ctmethods(20,n, job);
+    i = ctmethods(20,n, job);
 elseif nargin == 3
-  i = ctmethods(20,n, job,a);
+    i = ctmethods(20,n, job,a);
 else
-  i = ctmethods(20, n, job, a, b);
+    i = ctmethods(20, n, job, a, b);
 end
\ No newline at end of file
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/private/thermo_set.m b/interfaces/matlab/toolbox/@ThermoPhase/private/thermo_set.m
index a9f8394ba..516f1c4a6 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/private/thermo_set.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/private/thermo_set.m
@@ -1,16 +1,16 @@
-function i = thermo_set(n, job, a, b, c, d, e, f) 
+function i = thermo_set(n, job, a, b, c, d, e, f)
 if nargin == 2
-  i = ctmethods(20,n,-job);
+    i = ctmethods(20,n,-job);
 elseif nargin == 3
-  i = ctmethods(20,n,-job,a);
+    i = ctmethods(20,n,-job,a);
 elseif nargin == 4
-  i = ctmethods(20, n,-job, a, b);
+    i = ctmethods(20, n,-job, a, b);
 elseif nargin == 5
-  i = ctmethods(20, n,-job, a, b, c);
+    i = ctmethods(20, n,-job, a, b, c);
 elseif nargin == 6
-  i = ctmethods(20, n,-job, a, b, c, d);
+    i = ctmethods(20, n,-job, a, b, c, d);
 elseif nargin == 7
-  i = ctmethods(20, n,-job, a, b, c, d, e);  
+    i = ctmethods(20, n,-job, a, b, c, d, e);
 elseif nargin == 8
-  i = ctmethods(20, n,-job, a, b, c, d, e, f);  
+    i = ctmethods(20, n,-job, a, b, c, d, e, f);
 end
\ No newline at end of file
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/satPressure.m b/interfaces/matlab/toolbox/@ThermoPhase/satPressure.m
index 0131adb40..dd194200d 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/satPressure.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/satPressure.m
@@ -1,3 +1,3 @@
 function v = satPressure(a, T)
 % SATPRESSURE - Saturation pressure for temperature T.
-  v = thermo_get(a.tp_id,24,T);
+v = thermo_get(a.tp_id,24,T);
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/satTemperature.m b/interfaces/matlab/toolbox/@ThermoPhase/satTemperature.m
index 0a0b3d473..86b5a2e00 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/satTemperature.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/satTemperature.m
@@ -1,3 +1,3 @@
 function v = satTemperature(a, p)
 % SATTEMPERATURE - Saturation temperature for pressure p.
-  v = thermo_get(a.tp_id,23,p);
+v = thermo_get(a.tp_id,23,p);
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/set.m b/interfaces/matlab/toolbox/@ThermoPhase/set.m
index 9a2deaca4..cc1b10e77 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/set.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/set.m
@@ -6,11 +6,11 @@ while length(property_argin) >= 2,
     val = property_argin{2};
     property_argin = property_argin(3:end);
     switch prop
-    case 'Temperature'
-        phase_set(a.tp_id,1,val);
-    case 'Density'
-        phase_set(a.tp_id,2,val);
-    otherwise
-        error('Phase properties: Temperature, Density')
+        case 'Temperature'
+            phase_set(a.tp_id,1,val);
+        case 'Density'
+            phase_set(a.tp_id,2,val);
+        otherwise
+            error('Phase properties: Temperature, Density')
     end
-end
\ No newline at end of file
+end
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/setDensity.m b/interfaces/matlab/toolbox/@ThermoPhase/setDensity.m
index 9a902187a..de4e2e0cd 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/setDensity.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/setDensity.m
@@ -4,7 +4,7 @@ function a = setDensity(a,rho)
 %   setDensity(phase, 0.01);
 %
 if rho <= 0.0
-   error('the density must be positive');
+    error('the density must be positive');
 end
 
 phase_set(a.tp_id,2,rho);
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/setElectricPotential.m b/interfaces/matlab/toolbox/@ThermoPhase/setElectricPotential.m
index 83a4ef6da..8960a8c57 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/setElectricPotential.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/setElectricPotential.m
@@ -1,4 +1,4 @@
 function a = setElectricPotential(a,phi)
 % SETELECTRICPOTENTIAL  Set the electric potential [V].
 %
-thermo_set(a.tp_id,2,phi);
\ No newline at end of file
+thermo_set(a.tp_id,2,phi);
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/setMassFractions.m b/interfaces/matlab/toolbox/@ThermoPhase/setMassFractions.m
index 47001616c..5d10be648 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/setMassFractions.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/setMassFractions.m
@@ -1,7 +1,7 @@
 function a = setMassFractions(a, y, norm)
 % SETMASSFRACTIONS  Set the species mass fractions.
 %
-%   setMassFractions(a,y) 
+%   setMassFractions(a,y)
 %
 %      If y is a vector of doubles, this call sets the species mass
 %      fractions to the values in y and then scales them so that they
@@ -30,19 +30,18 @@ function a = setMassFractions(a, y, norm)
 %  instead, or call setPressure after calling setMassFractions.
 %
 if isa(y,'double')
-  if nargin == 3
-    if strcmp(norm,'nonorm')
-      phase_set(a.tp_id,23,y);
+    if nargin == 3
+        if strcmp(norm,'nonorm')
+            phase_set(a.tp_id,23,y);
+        else
+            phase_set(a.tp_id,21,y);
+        end
     else
-      phase_set(a.tp_id,21,y);
+        phase_set(a.tp_id,21,y);
     end
-  else
-    phase_set(a.tp_id,21,y);
-  end
-%
-% string input
-%
+    %
+    % string input
+    %
 elseif isa(y,'char')
-  phase_set(a.tp_id,31,y);
+    phase_set(a.tp_id,31,y);
 end
-
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/setMoleFractions.m b/interfaces/matlab/toolbox/@ThermoPhase/setMoleFractions.m
index 7f332942d..4571c30cb 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/setMoleFractions.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/setMoleFractions.m
@@ -1,7 +1,7 @@
 function a = setMoleFractions(a,x,norm)
 % SETMOLEFRACTIONS  Set the species mole fractions.
 %
-%   setMoleFractions(a,x) 
+%   setMoleFractions(a,x)
 %
 %      If x is a vector of doubles, this call sets the species mole
 %      fractions to the values in x and then scales them so that they
@@ -30,18 +30,18 @@ function a = setMoleFractions(a,x,norm)
 %  instead, or call setPressure after calling setMoleFractions.
 
 if isa(x,'double')
-  if nargin == 3
-    if strcmp(norm,'nonorm')
-      phase_set(a.tp_id,22,x);
+    if nargin == 3
+        if strcmp(norm,'nonorm')
+            phase_set(a.tp_id,22,x);
+        else
+            phase_set(a.tp_id,20,x);
+        end
     else
-      phase_set(a.tp_id,20,x);
+        phase_set(a.tp_id,20,x);
     end
-  else
-    phase_set(a.tp_id,20,x);
-  end
-%
-% string input
-%
+    %
+    % string input
+    %
 elseif isa(x,'char')
-  phase_set(a.tp_id,30,x);
+    phase_set(a.tp_id,30,x);
 end
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/setName.m b/interfaces/matlab/toolbox/@ThermoPhase/setName.m
index 283583d98..feebd8556 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/setName.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/setName.m
@@ -1,9 +1,8 @@
 function setName(self, name)
 % SETNAME - Set the name of the phase.
-%   
+%
 if isa(name,'char')
-  phase_set(thermo_hndl(self), 32, name);
+    phase_set(thermo_hndl(self), 32, name);
 else
-  error('name must be a string.');
+    error('name must be a string.');
 end
-
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/setPressure.m b/interfaces/matlab/toolbox/@ThermoPhase/setPressure.m
index cf6e41887..d2dd4220b 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/setPressure.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/setPressure.m
@@ -5,7 +5,7 @@ function a = setPressure(a,p)
 %    temperature and chemical composition fixed.
 %
 if p <= 0.0
-   error('the pressure must be positive')
+    error('the pressure must be positive')
 end
 
-thermo_set(a.tp_id,1,p);
\ No newline at end of file
+thermo_set(a.tp_id,1,p);
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/setState.m b/interfaces/matlab/toolbox/@ThermoPhase/setState.m
index 83b3d2961..3ef8e812a 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/setState.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/setState.m
@@ -1,12 +1,12 @@
 function a = setState(a,job,values)
 disp('deprecated')
 if nargin ~= 3 | ~isa(job,'char')
-  error('Syntax error. Type "help setState" for more information.')
+    error('Syntax error. Type "help setState" for more information.')
 end
 
 switch job
- case 'T'
-  setTemperature(a,values)
- otherwise
-  error(['unknown flag: ' job])
+    case 'T'
+        setTemperature(a,values)
+    otherwise
+        error(['unknown flag: ' job])
 end
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/setState_HP.m b/interfaces/matlab/toolbox/@ThermoPhase/setState_HP.m
index 257645959..7042e49ab 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/setState_HP.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/setState_HP.m
@@ -1,13 +1,13 @@
 function a = setState_HP(a,hp)
 % SETSTATE_HP - Set the specific enthalpy [J/kg] and pressure [Pa].
-%  
+%
 %    setState_HP(a, hp) sets the specific enthalpy and pressure
 %    of object a, holding its composition fixed. Argument 'hp' must
 %    be a vector of length 2 containing the desired values for the specific
 %    enthalpy (J/kg) and pressure (Pa).
 %
 if hp(2) <= 0.0
-   error('the pressure must be positive');
+    error('the pressure must be positive');
 end
 
 thermo_set(a.tp_id,20,hp);
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/setState_Psat.m b/interfaces/matlab/toolbox/@ThermoPhase/setState_Psat.m
index ec7b77190..d81617960 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/setState_Psat.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/setState_Psat.m
@@ -1,5 +1,5 @@
 function a = setState_Psat(a,px)
 % SETSTATE_PSAT    Set the fluid to a saturated state at
 % pressure P
-%  
+%
 thermo_set(a.tp_id,24,px);
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/setState_SP.m b/interfaces/matlab/toolbox/@ThermoPhase/setState_SP.m
index fa8899aed..2b14d7696 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/setState_SP.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/setState_SP.m
@@ -1,15 +1,15 @@
 function a = setState_SP(a,sp)
 % SETSTATE_SP    Set the specific entropy [J/kg/K] and pressure [Pa].
-%  
+%
 %    setState_SP(a, sp) sets the specific entropy and pressure
 %    of object a, holding its composition fixed. Argument 'sp' must
 %    be a vector of length 2 containing the desired values for the specific
 %    entropy (J/kg/K) and pressure (Pa).
 %
 if sp(1) <= 0.0
-   error('the pressure must be positive');
+    error('the pressure must be positive');
 end
 if sp(2) <= 0.0
-  error('the specific entropy must be positive');
+    error('the specific entropy must be positive');
 end
 thermo_set(a.tp_id,23,sp);
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/setState_SV.m b/interfaces/matlab/toolbox/@ThermoPhase/setState_SV.m
index ddbcf4e5d..9c1e25827 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/setState_SV.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/setState_SV.m
@@ -1,16 +1,16 @@
 function a = setState_SV(a,sv)
 % SETSTATE_SV    Set the specific entropy [J/kg/K] and specific
 % volume [m3/kg].
-%  
+%
 %    setState_SV(a, sv) sets the specific entropy and specific volume
 %    of object a, holding its composition fixed. Argument 'sv' must
 %    be a vector of length 2 containing the desired values for the specific
 %    entropy (J/kg/K) and specific volume (m3/kg).
 %
 if sv(1) <= 0.0
-   error('the specific entropy must be positive');
+    error('the specific entropy must be positive');
 end
 if sv(2) <= 0.0
-  error('the specific volume must be positive');
+    error('the specific volume must be positive');
 end
 thermo_set(a.tp_id,22,sv);
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/setState_Tsat.m b/interfaces/matlab/toolbox/@ThermoPhase/setState_Tsat.m
index 4758aa392..79897fed5 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/setState_Tsat.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/setState_Tsat.m
@@ -1,5 +1,5 @@
 function a = setState_Tsat(a,tx)
 % SETSTATE_TSAT    Set the fluid to a saturated state at
 % temperature t
-%  
+%
 thermo_set(a.tp_id,25,tx);
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/setState_UV.m b/interfaces/matlab/toolbox/@ThermoPhase/setState_UV.m
index 3f425a7a0..5f6f885f2 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/setState_UV.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/setState_UV.m
@@ -1,7 +1,7 @@
 function a = setState_UV(a,uv)
 % SETSTATE_UV    Set the specific internal energy [J/kg] and
 % specific volume [m^3/kg].
-%  
+%
 %    setState_UV(a, uv) sets the specific internal energy and
 %    specific volume of object a, holding its composition
 %    fixed. Argument 'uv' must be a vector of length 2 containing
@@ -9,6 +9,6 @@ function a = setState_UV(a,uv)
 %    specific volume (m^3/kg).
 %
 if uv(2) <= 0.0
-  error('the specific volume must be positive');
+    error('the specific volume must be positive');
 end
 thermo_set(a.tp_id,21,uv);
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/setState_satLiquid.m b/interfaces/matlab/toolbox/@ThermoPhase/setState_satLiquid.m
index 805b7bf7f..22578f508 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/setState_satLiquid.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/setState_satLiquid.m
@@ -1,5 +1,5 @@
 function a = setState_satLiquid(a)
 % SETSTATE_SATLIQUID    Set the fluid to the saturated liquid state
-% at the current temperature. 
-%  
+% at the current temperature.
+%
 thermo_set(a.tp_id,2,0);
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/setState_satVapor.m b/interfaces/matlab/toolbox/@ThermoPhase/setState_satVapor.m
index ed0cb89f2..33e1c6568 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/setState_satVapor.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/setState_satVapor.m
@@ -1,5 +1,5 @@
 function a = setState_satVapor(a)
 % SETSTATE_SATVAPOR    Set the fluid to the saturated vapor state at the
-% current temperature. 
-%  
+% current temperature.
+%
 thermo_set(a.tp_id,3,0);
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/setTemperature.m b/interfaces/matlab/toolbox/@ThermoPhase/setTemperature.m
index e2cdec900..0884f858a 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/setTemperature.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/setTemperature.m
@@ -2,6 +2,6 @@ function a = setTemperature(a,t)
 % SETTEMPERATURE  Set the temperature [K].
 %
 if (t <= 0)
-   error('the temperature must be positive');
+    error('the temperature must be positive');
 end
 phase_set(a.tp_id,1,t);
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/speciesIndex.m b/interfaces/matlab/toolbox/@ThermoPhase/speciesIndex.m
index ddea97d1e..819f76dc5 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/speciesIndex.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/speciesIndex.m
@@ -1,5 +1,5 @@
 function k = speciesIndex(a,name)
-% SPECIESINDEX -  The species index of species with name 'name'. 
+% SPECIESINDEX -  The species index of species with name 'name'.
 %
 %   The index is an integer assigned to each species in sequence as it
 %   is read in from the input file.
@@ -20,13 +20,13 @@ function k = speciesIndex(a,name)
 %
 
 if iscell(name)
-  [m, n] = size(name);
-  k = zeros(m,n);
-  for i = 1:m
-    for j = 1:n
-      k(i,j) = phase_get(a.tp_id,12,name{i,j});
+    [m, n] = size(name);
+    k = zeros(m,n);
+    for i = 1:m
+        for j = 1:n
+            k(i,j) = phase_get(a.tp_id,12,name{i,j});
+        end
     end
-  end
 else
-  k = phase_get(a.tp_id,12,name);
-end
\ No newline at end of file
+    k = phase_get(a.tp_id,12,name);
+end
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/speciesName.m b/interfaces/matlab/toolbox/@ThermoPhase/speciesName.m
index 9d057c6e1..5e6d00e1a 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/speciesName.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/speciesName.m
@@ -8,9 +8,7 @@ function nm = speciesName(a, k)
 [m, n] = size(k);
 nm = {};
 for i = 1:m
-  for j = 1:n
-    nm{i,j} = phase_get(a.tp_id, 40, k(i,j));
-  end
+    for j = 1:n
+        nm{i,j} = phase_get(a.tp_id, 40, k(i,j));
+    end
 end
-
-
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/vaporFraction.m b/interfaces/matlab/toolbox/@ThermoPhase/vaporFraction.m
index 64c4acd3f..c45e38750 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/vaporFraction.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/vaporFraction.m
@@ -1,5 +1,5 @@
 function v = vaporFraction(a)
 % VAPORFRACTION - Vapor fraction.
 %   If object 'a' represents a liquid/vapor mixture, this method
-%   returns the vapor fraction. 
-  v = thermo_get(a.tp_id,22);
+%   returns the vapor fraction.
+v = thermo_get(a.tp_id,22);
diff --git a/interfaces/matlab/toolbox/@Transport/Transport.m b/interfaces/matlab/toolbox/@Transport/Transport.m
index a1cb3abcc..4125e18dc 100644
--- a/interfaces/matlab/toolbox/@Transport/Transport.m
+++ b/interfaces/matlab/toolbox/@Transport/Transport.m
@@ -2,29 +2,28 @@ function tr = Transport(xml_phase, th, model, loglevel)
 %TRANSPORT  Transport class constructor.
 %
 %  k = TRANSPORT(model, p, loglevel) creates a transport
-%  manager for phase object p. 
+%  manager for phase object p.
 %
 %  The 'model' parameter is a string that specifies the transport
 %  model. The phase object must have already been created.
 %
 tr.id = 0;
 if nargin == 4
-  tr.th = th;
-  if model == 'default'
-    try
-      node = child(xml_phase,'transport');
-      tr.model = attrib(node,'model');
-    catch
-      tr.model = 'None';
+    tr.th = th;
+    if model == 'default'
+        try
+            node = child(xml_phase,'transport');
+            tr.model = attrib(node,'model');
+        catch
+            tr.model = 'None';
+        end
+    else
+        tr.model = model;
     end
-  else
-    tr.model = model;
-  end
-  tr.id = trans_get(hndl(th), -1, tr.model, loglevel) ;
-  tr = class(tr,'Transport');
+    tr.id = trans_get(hndl(th), -1, tr.model, loglevel) ;
+    tr = class(tr,'Transport');
 elseif isa(model,'Transport')
-  tr = model;
+    tr = model;
 else
-  error('syntax error');
+    error('syntax error');
 end
-
diff --git a/interfaces/matlab/toolbox/@Transport/binDiffCoeffs.m b/interfaces/matlab/toolbox/@Transport/binDiffCoeffs.m
index 2eceb18ed..9a2c31d6b 100644
--- a/interfaces/matlab/toolbox/@Transport/binDiffCoeffs.m
+++ b/interfaces/matlab/toolbox/@Transport/binDiffCoeffs.m
@@ -1,10 +1,9 @@
 function v = binDiffCoeffs(a)
 %BINDIFFCOEFFS  Binary diffusion coefficients (m^2/s).
 %
-%      d = binDiffCoeffs(gas) 
+%      d = binDiffCoeffs(gas)
 %
 %      returns the matrix of binary diffusion coefficients in array
 %      d. The matrix is symmetric: d(i,j) = d(j,i).
 %
 v = trans_get(a.id, 21, nSpecies(a.th));
-
diff --git a/interfaces/matlab/toolbox/@Transport/mixDiffCoeffs.m b/interfaces/matlab/toolbox/@Transport/mixDiffCoeffs.m
index 8ca7074f4..dfa7d1ddb 100644
--- a/interfaces/matlab/toolbox/@Transport/mixDiffCoeffs.m
+++ b/interfaces/matlab/toolbox/@Transport/mixDiffCoeffs.m
@@ -1,7 +1,7 @@
 function v = mixDiffCoeffs(a)
 %MIXDIFFCOEFFS  Mixture-averaged diffusion coefficients (m^2/s).
-%  
-%    d = mixDiffCoeffs(gas) 
+%
+%    d = mixDiffCoeffs(gas)
 %
 %    returns in column vector d the mixture-averaged diffusion
 %    coefficients. Object 'gas' must belong to a class derived from
@@ -17,4 +17,3 @@ function v = mixDiffCoeffs(a)
 %        gas = GRI30('Mix')
 %
 v = trans_get(a.id, 11, nSpecies(a.th));
-
diff --git a/interfaces/matlab/toolbox/@Transport/multiDiffCoeffs.m b/interfaces/matlab/toolbox/@Transport/multiDiffCoeffs.m
index 4f6cf3cd3..915705443 100644
--- a/interfaces/matlab/toolbox/@Transport/multiDiffCoeffs.m
+++ b/interfaces/matlab/toolbox/@Transport/multiDiffCoeffs.m
@@ -1,7 +1,7 @@
 function v = multiDiffCoeffs(a)
 %MULTIDIFFCOEFFS  Multicomponent diffusion coefficients (m^2/s).
-%  
-%    d = multiDiffCoeffs(gas) 
+%
+%    d = multiDiffCoeffs(gas)
 %
 %    returns in d the array of multicomponent diffusion
 %    coefficients. Object 'gas' must belong to a class derived from
diff --git a/interfaces/matlab/toolbox/@Transport/private/trans_get.m b/interfaces/matlab/toolbox/@Transport/private/trans_get.m
index f3848e593..a7e06fff2 100644
--- a/interfaces/matlab/toolbox/@Transport/private/trans_get.m
+++ b/interfaces/matlab/toolbox/@Transport/private/trans_get.m
@@ -1,14 +1,14 @@
 function v = trans_get(n, job, a, b, c, d)
-% TRANS_GET - get transport attributes 
+% TRANS_GET - get transport attributes
 %
 if nargin == 2
-  v = ctmethods(50, n, job);
+    v = ctmethods(50, n, job);
 elseif nargin == 3
-  v = ctmethods(50, n, job, a);  
+    v = ctmethods(50, n, job, a);
 elseif nargin == 4
-  v = ctmethods(50, n, job, a, b);    
+    v = ctmethods(50, n, job, a, b);
 elseif nargin == 5
-  v = ctmethods(50, n, job, a, b, c);  
+    v = ctmethods(50, n, job, a, b, c);
 elseif nargin == 6
-  v = ctmethods(50, n, job, a, b, c, d); 
+    v = ctmethods(50, n, job, a, b, c, d);
 end
diff --git a/interfaces/matlab/toolbox/@Transport/setParameters.m b/interfaces/matlab/toolbox/@Transport/setParameters.m
index 8e254aae7..a3d347c9d 100644
--- a/interfaces/matlab/toolbox/@Transport/setParameters.m
+++ b/interfaces/matlab/toolbox/@Transport/setParameters.m
@@ -1,5 +1,4 @@
 function setParameters(tr, type, k, p)
 % SETPARAMETERS - set parameters.
-%   
+%
 v = trans_get(tr.id, 31, type, k, p);
-
diff --git a/interfaces/matlab/toolbox/@Transport/setThermalConductivity.m b/interfaces/matlab/toolbox/@Transport/setThermalConductivity.m
index ce698b79a..2f802acad 100644
--- a/interfaces/matlab/toolbox/@Transport/setThermalConductivity.m
+++ b/interfaces/matlab/toolbox/@Transport/setThermalConductivity.m
@@ -1,9 +1,8 @@
 function setThermalConductivity(tr, lam)
 % SETTHERMALCONDUCTIVITY - Set the thermal conductivity.
-%   
+%
 %    This method can only be used with transport models that
 %    support directly setting the value of the thermal
-%    conductivity. 
+%    conductivity.
 %
 setParameters(tr, 1, 0, lam);
-
diff --git a/interfaces/matlab/toolbox/@Transport/thermalConductivity.m b/interfaces/matlab/toolbox/@Transport/thermalConductivity.m
index 4dddfe2ac..77b5ba19c 100644
--- a/interfaces/matlab/toolbox/@Transport/thermalConductivity.m
+++ b/interfaces/matlab/toolbox/@Transport/thermalConductivity.m
@@ -1,8 +1,8 @@
 function v = thermalConductivity(a)
 % THERMALCONDUCTIVITY  Thermal conductivity in W/m^2/K.
 v = trans_get(a.id, 2);
-if v == -1.0 
-   error(geterr);
+if v == -1.0
+    error(geterr);
 elseif v < 0.0
-   error('exception raised');
-end   
\ No newline at end of file
+    error('exception raised');
+end
diff --git a/interfaces/matlab/toolbox/@Transport/thermalDiffCoeffs.m b/interfaces/matlab/toolbox/@Transport/thermalDiffCoeffs.m
index 0d591433f..648063525 100644
--- a/interfaces/matlab/toolbox/@Transport/thermalDiffCoeffs.m
+++ b/interfaces/matlab/toolbox/@Transport/thermalDiffCoeffs.m
@@ -1,7 +1,7 @@
 function v = thermalDiffCoeffs(a)
 %THERMALDIFFCOEFFS  Thermal diffusion coefficients.
-%  
-%    dt = thermalDiffCoeffs(gas) 
+%
+%    dt = thermalDiffCoeffs(gas)
 %
 %    returns in column vector dt the thermal diffusion
 %    coefficients. Object 'gas' must belong to a class derived from
@@ -10,4 +10,3 @@ function v = thermalDiffCoeffs(a)
 %    all be zero.
 %
 v = trans_get(a.id, 12, nSpecies(a.th));
-
diff --git a/interfaces/matlab/toolbox/@Transport/viscosity.m b/interfaces/matlab/toolbox/@Transport/viscosity.m
index 87a4bd509..d732cebbc 100644
--- a/interfaces/matlab/toolbox/@Transport/viscosity.m
+++ b/interfaces/matlab/toolbox/@Transport/viscosity.m
@@ -1,8 +1,7 @@
 function v = viscosity(a)
 v = trans_get(a.id, 1);
-if v == -1.0 
-   error(geterr);
+if v == -1.0
+    error(geterr);
 elseif v < 0.0
-   error('exception raised');
+    error('exception raised');
 end
-
diff --git a/interfaces/matlab/toolbox/@Wall/Wall.m b/interfaces/matlab/toolbox/@Wall/Wall.m
index d4c6fc054..cab69982e 100644
--- a/interfaces/matlab/toolbox/@Wall/Wall.m
+++ b/interfaces/matlab/toolbox/@Wall/Wall.m
@@ -1,14 +1,12 @@
 function x = Wall(typ)
 %
 if nargin == 0
-  typ = 1;
+    typ = 1;
 end
 x.index = wallmethods(0,typ);
 if x.index < 0
-  error(geterr);
+    error(geterr);
 end
 x.left = -1;
 x.right = -1;
 x = class(x,'Wall');
-
-
diff --git a/interfaces/matlab/toolbox/@Wall/area.m b/interfaces/matlab/toolbox/@Wall/area.m
index d9263e1d4..eab0ded34 100644
--- a/interfaces/matlab/toolbox/@Wall/area.m
+++ b/interfaces/matlab/toolbox/@Wall/area.m
@@ -1,5 +1,4 @@
 function a = area(w)
-% AREA - 
-%   
+% AREA -
+%
 a = wallmethods(23, wall_hndl(w))
-
diff --git a/interfaces/matlab/toolbox/@Wall/install.m b/interfaces/matlab/toolbox/@Wall/install.m
index b34ad5590..b42c6e500 100644
--- a/interfaces/matlab/toolbox/@Wall/install.m
+++ b/interfaces/matlab/toolbox/@Wall/install.m
@@ -1,8 +1,7 @@
 function install(w, left, right)
-% INSTALL - 
-%   
+% INSTALL -
+%
 w.left = left;
 w.right = right;
 wallmethods(4, wall_hndl(w), reactor_hndl(left), ...
-	    reactor_hndl(right));
-
+    reactor_hndl(right));
diff --git a/interfaces/matlab/toolbox/@Wall/private/wallmethods.m b/interfaces/matlab/toolbox/@Wall/private/wallmethods.m
index 188f50e9a..fd059cffc 100644
--- a/interfaces/matlab/toolbox/@Wall/private/wallmethods.m
+++ b/interfaces/matlab/toolbox/@Wall/private/wallmethods.m
@@ -1,13 +1,13 @@
 function v = wallmethods(n, job, a, b, c, d)
-%   
+%
 if nargin == 2
-  v = ctmethods(70, n, job);
+    v = ctmethods(70, n, job);
 elseif nargin == 3
-  v = ctmethods(70, n, job, a);  
+    v = ctmethods(70, n, job, a);
 elseif nargin == 4
-  v = ctmethods(70, n, job, a, b);    
+    v = ctmethods(70, n, job, a, b);
 elseif nargin == 5
-  v = ctmethods(70, n, job, a, b, c);  
+    v = ctmethods(70, n, job, a, b, c);
 elseif nargin == 6
-  v = ctmethods(70, n, job, a, b, c, d); 
-end
\ No newline at end of file
+    v = ctmethods(70, n, job, a, b, c, d);
+end
diff --git a/interfaces/matlab/toolbox/@Wall/ready.m b/interfaces/matlab/toolbox/@Wall/ready.m
index 25ab582e4..a1fe512c6 100644
--- a/interfaces/matlab/toolbox/@Wall/ready.m
+++ b/interfaces/matlab/toolbox/@Wall/ready.m
@@ -1,5 +1,4 @@
 function ok = ready(w)
-% READY - 
-%   
+% READY -
+%
 ok = wallmethods(11, wall_hndl(w));
-
diff --git a/interfaces/matlab/toolbox/@Wall/setArea.m b/interfaces/matlab/toolbox/@Wall/setArea.m
index ede46e58c..cfd6762e8 100644
--- a/interfaces/matlab/toolbox/@Wall/setArea.m
+++ b/interfaces/matlab/toolbox/@Wall/setArea.m
@@ -1,5 +1,4 @@
 function setArea(w, a)
-% SETAREA - 
-%   
+% SETAREA -
+%
 wallmethods(5, wall_hndl(w), a);
-
diff --git a/interfaces/matlab/toolbox/@Wall/setExpansionRateCoeff.m b/interfaces/matlab/toolbox/@Wall/setExpansionRateCoeff.m
index 66e6bc300..0fd625e30 100644
--- a/interfaces/matlab/toolbox/@Wall/setExpansionRateCoeff.m
+++ b/interfaces/matlab/toolbox/@Wall/setExpansionRateCoeff.m
@@ -1,5 +1,4 @@
 function setExpansionRateCoeff(w, k)
-% SETEXPANSIONRATECOEFF - 
-%   
+% SETEXPANSIONRATECOEFF -
+%
 wallmethods(9, wall_hndl(w), k);
-
diff --git a/interfaces/matlab/toolbox/@Wall/setHeatTransferCoeff.m b/interfaces/matlab/toolbox/@Wall/setHeatTransferCoeff.m
index eed158c2e..3416ce6e5 100644
--- a/interfaces/matlab/toolbox/@Wall/setHeatTransferCoeff.m
+++ b/interfaces/matlab/toolbox/@Wall/setHeatTransferCoeff.m
@@ -1,5 +1,4 @@
 function setHeatTransferCoeff(w, u)
-% SETHEATTRANSFERCOEFF - 
-%   
+% SETHEATTRANSFERCOEFF -
+%
 wallmethods(7, wall_hndl(w), u);
-
diff --git a/interfaces/matlab/toolbox/@Wall/setKinetics.m b/interfaces/matlab/toolbox/@Wall/setKinetics.m
index dd78dd3d7..fcbd09ca8 100644
--- a/interfaces/matlab/toolbox/@Wall/setKinetics.m
+++ b/interfaces/matlab/toolbox/@Wall/setKinetics.m
@@ -1,14 +1,13 @@
 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);
+    ileft = kinetics_hndl(left);
 end
 
 if isa(right,'Kinetics')
-  iright = kinetics_hndl(right);
+    iright = kinetics_hndl(right);
 end
 wallmethods(12, wall_hndl(w), ileft, iright);
-
diff --git a/interfaces/matlab/toolbox/@Wall/setThermalResistance.m b/interfaces/matlab/toolbox/@Wall/setThermalResistance.m
index 1b9aed568..94d8cbc2b 100644
--- a/interfaces/matlab/toolbox/@Wall/setThermalResistance.m
+++ b/interfaces/matlab/toolbox/@Wall/setThermalResistance.m
@@ -1,5 +1,4 @@
 function setThermalResistance(w, r)
-% SETTHERMALRESISTANCE - 
-%   
+% SETTHERMALRESISTANCE -
+%
 wallmethods(6, wall_hndl(w), r)
-
diff --git a/interfaces/matlab/toolbox/@Wall/wall_hndl.m b/interfaces/matlab/toolbox/@Wall/wall_hndl.m
index 6d1ed3d96..808b4163d 100644
--- a/interfaces/matlab/toolbox/@Wall/wall_hndl.m
+++ b/interfaces/matlab/toolbox/@Wall/wall_hndl.m
@@ -1,4 +1,4 @@
 function i = wall_hndl(w)
-% WALL_HNDL - 
-%   
-i = w.index;
\ No newline at end of file
+% WALL_HNDL -
+%
+i = w.index;
diff --git a/interfaces/matlab/toolbox/@XML_Node/XML_Node.m b/interfaces/matlab/toolbox/@XML_Node/XML_Node.m
index d6907e460..d121fa2aa 100644
--- a/interfaces/matlab/toolbox/@XML_Node/XML_Node.m
+++ b/interfaces/matlab/toolbox/@XML_Node/XML_Node.m
@@ -5,16 +5,15 @@ function x = XML_Node(name, src, wrap)
 
 x.id = 0;
 if nargin == 3
-   x.id = wrap;
+    x.id = wrap;
 elseif nargin == 2
-   % read tree from a file
-   x.id = ctmethods(10,15,0,src); % newxml(name)
-   if x.id < 0
-      error(geterr);
-   end
+    % read tree from a file
+    x.id = ctmethods(10,15,0,src); % newxml(name)
+    if x.id < 0
+        error(geterr);
+    end
 elseif nargin == 1
-  x.id = ctmethods(10,0,0,name);
+    x.id = ctmethods(10,0,0,name);
 end
 
 x = class(x,'XML_Node');
-
diff --git a/interfaces/matlab/toolbox/@XML_Node/addChild.m b/interfaces/matlab/toolbox/@XML_Node/addChild.m
index 77d294abf..573376e13 100644
--- a/interfaces/matlab/toolbox/@XML_Node/addChild.m
+++ b/interfaces/matlab/toolbox/@XML_Node/addChild.m
@@ -1,3 +1,3 @@
 function n = addChild(root, id)
-%   
+%
 n = ctmethods(10, 10, root.id, id);
diff --git a/interfaces/matlab/toolbox/@XML_Node/attrib.m b/interfaces/matlab/toolbox/@XML_Node/attrib.m
index d86d93f9b..3b632f5b5 100644
--- a/interfaces/matlab/toolbox/@XML_Node/attrib.m
+++ b/interfaces/matlab/toolbox/@XML_Node/attrib.m
@@ -1,9 +1,7 @@
 function a = attrib(x, key)
 
 if nargin ~= 2 | ~isa(key,'char')
-  error('Syntax error. Type "help attrib" for more information.')
+    error('Syntax error. Type "help attrib" for more information.')
 end
 
 a = ctmethods(10, 20, x.id, key);
-
-
diff --git a/interfaces/matlab/toolbox/@XML_Node/build.m b/interfaces/matlab/toolbox/@XML_Node/build.m
index 280dcf109..e1ec2207a 100644
--- a/interfaces/matlab/toolbox/@XML_Node/build.m
+++ b/interfaces/matlab/toolbox/@XML_Node/build.m
@@ -1,13 +1,11 @@
 function x = build(x, file, pre)
 
 if nargin < 2 | ~isa(file,'char')
-  error('Syntax error. Type "help build" for more information.')
+    error('Syntax error. Type "help build" for more information.')
 end
 
 if nargin == 3 & pre > 0
-  iok = ctmethods(10, 15, x.id, file)
+    iok = ctmethods(10, 15, x.id, file)
 else
-  iok = ctmethods(10, 4, x.id, file)
+    iok = ctmethods(10, 4, x.id, file)
 end
-
-
diff --git a/interfaces/matlab/toolbox/@XML_Node/child.m b/interfaces/matlab/toolbox/@XML_Node/child.m
index c358cbcc8..72c076fb5 100644
--- a/interfaces/matlab/toolbox/@XML_Node/child.m
+++ b/interfaces/matlab/toolbox/@XML_Node/child.m
@@ -2,5 +2,3 @@ function v = child(x, loc)
 
 id = ctmethods(10, 6, x.id, loc);
 v = XML_Node('', '', id);
-
-
diff --git a/interfaces/matlab/toolbox/@XML_Node/findByID.m b/interfaces/matlab/toolbox/@XML_Node/findByID.m
index bf0fa6e2e..c3ebc8dc1 100644
--- a/interfaces/matlab/toolbox/@XML_Node/findByID.m
+++ b/interfaces/matlab/toolbox/@XML_Node/findByID.m
@@ -1,6 +1,5 @@
 function x = findByID(root, id)
 % FINDBYID - Find an XML element by ID
-%   
+%
 index = ctmethods(10, 8, root.id, id);
 x = XML_Node('','', index);
-
diff --git a/interfaces/matlab/toolbox/@XML_Node/findByName.m b/interfaces/matlab/toolbox/@XML_Node/findByName.m
index b3239347e..5e6a0aa5d 100644
--- a/interfaces/matlab/toolbox/@XML_Node/findByName.m
+++ b/interfaces/matlab/toolbox/@XML_Node/findByName.m
@@ -1,6 +1,5 @@
 function x = findByName(root, name)
 % FINDBYNAME - Find an XML element by name
-%   
+%
 index = ctmethods(10, 9, root.id, name);
 x = XML_Node('','', index);
-
diff --git a/interfaces/matlab/toolbox/@XML_Node/nChildren.m b/interfaces/matlab/toolbox/@XML_Node/nChildren.m
index fd5dd22b0..b8d4bd223 100644
--- a/interfaces/matlab/toolbox/@XML_Node/nChildren.m
+++ b/interfaces/matlab/toolbox/@XML_Node/nChildren.m
@@ -1,3 +1,3 @@
 function n = nChildren(root, id)
-%   
+%
 n = ctmethods(10, 10, root.id, id);
diff --git a/interfaces/matlab/toolbox/@XML_Node/value.m b/interfaces/matlab/toolbox/@XML_Node/value.m
index d943dc1a9..62788f41d 100644
--- a/interfaces/matlab/toolbox/@XML_Node/value.m
+++ b/interfaces/matlab/toolbox/@XML_Node/value.m
@@ -1,13 +1,12 @@
 function v = value(x,loc)
-% VALUE - value(x) returns the value of the XML element. 
+% VALUE - value(x) returns the value of the XML element.
 %         value(x, loc) is shorthand for value(child(x,loc))
 %
 if nargin == 2
-   c = child(x, loc);
-   id = c.id;
+    c = child(x, loc);
+    id = c.id;
 else
-   id = x.id;
+    id = x.id;
 end
 
 v = ctmethods(10, 21, id);
-
diff --git a/interfaces/matlab/toolbox/@XML_Node/write.m b/interfaces/matlab/toolbox/@XML_Node/write.m
index 5acb3a71f..39034216a 100644
--- a/interfaces/matlab/toolbox/@XML_Node/write.m
+++ b/interfaces/matlab/toolbox/@XML_Node/write.m
@@ -1,4 +1,3 @@
 function write(x, file)
 
 ctmethods(10, 13, x.id, file);
-
diff --git a/interfaces/matlab/toolbox/GRI30.m b/interfaces/matlab/toolbox/GRI30.m
index 5d6c0f985..7b0c23f93 100755
--- a/interfaces/matlab/toolbox/GRI30.m
+++ b/interfaces/matlab/toolbox/GRI30.m
@@ -19,13 +19,13 @@ function s = GRI30(tr)
 %     g3 = GRI30('Multi')  % miulticomponent transport properties
 %
 if nargin == 0
-  s = Solution('gri30.cti','gri30');
+    s = Solution('gri30.cti','gri30');
 elseif nargin == 1
-  if strcmp(tr,'Mix')
-    s = Solution('gri30.cti','gri30_mix');
-  elseif strcmp(tr,'Multi')
-    s = Solution('gri30.cti','gri30_multi');
-  end
+    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
diff --git a/interfaces/matlab/toolbox/Hydrogen.m b/interfaces/matlab/toolbox/Hydrogen.m
index 3c20c2215..5b7ad4cad 100644
--- a/interfaces/matlab/toolbox/Hydrogen.m
+++ b/interfaces/matlab/toolbox/Hydrogen.m
@@ -11,4 +11,3 @@ function n = Hydrogen()
 %   Cantera C++ source code documentation.
 %
 n = importPhase('liquidvapor.cti','hydrogen');
-
diff --git a/interfaces/matlab/toolbox/IdealGasMix.m b/interfaces/matlab/toolbox/IdealGasMix.m
index b7c12a7b3..2e0cf48dd 100755
--- a/interfaces/matlab/toolbox/IdealGasMix.m
+++ b/interfaces/matlab/toolbox/IdealGasMix.m
@@ -1,8 +1,8 @@
 function s = IdealGasMix(a,b,c)
 % IDEALGASMIX - Create a Solution instance representing an ideal gas mixture.
 %
-%      gas1 = IdealGasMix('ctml_file'[,'transport_model']) 
-%      gas2 = IdealGasMix('ck_file'[,'thermo_db'[,'tran_db'[,'transport_model']]]) 
+%      gas1 = IdealGasMix('ctml_file'[,'transport_model'])
+%      gas2 = IdealGasMix('ck_file'[,'thermo_db'[,'tran_db'[,'transport_model']]])
 %
 %   creates an object that represents an ideal gas mixture. The
 %   species in the mixture, their properties, and the reactions among
@@ -33,22 +33,22 @@ function s = IdealGasMix(a,b,c)
 %
 dotloc = findstr(a,'.');
 if dotloc(end) > 1
-   ext = a(dotloc(end):end);
-   if ~strcmp(ext,'.inp')
-     if nargin == 1
-       s = Solution(a);
-     elseif nargin == 2 
-       s = Solution(a, b);
-     end
-     return
-   end
+    ext = a(dotloc(end):end);
+    if ~strcmp(ext,'.inp')
+        if nargin == 1
+            s = Solution(a);
+        elseif nargin == 2
+            s = Solution(a, b);
+        end
+        return
+    end
 end
 
 if nargin == 1
-  b = '-';
-  c = '-';
+    b = '-';
+    c = '-';
 elseif nargin == 2
-  c = '-';
+    c = '-';
 end
 xml = ck2cti(a,b,c);
 s = Solution(xml);
diff --git a/interfaces/matlab/toolbox/MassFlowController.m b/interfaces/matlab/toolbox/MassFlowController.m
index 16c00a07e..1e6ae5cf8 100644
--- a/interfaces/matlab/toolbox/MassFlowController.m
+++ b/interfaces/matlab/toolbox/MassFlowController.m
@@ -3,17 +3,17 @@ function m = MassFlowController(upstream, downstream)
 % MASSFLOWCONTROLLER - Create a mass flow controller connecting two
 % reactors / reservoirs.
 %
-%    m = MassFlowController(upstream, downstream) 
+%    m = MassFlowController(upstream, downstream)
 %
 %    creates an instance of class FlowDevice configured to simulate a
 %    mass flow controller that maintains a constant mass flow rate
 %    independent of upstream or downstream conditions. If two reactor
 %    objects are supplied as arguments, the controller is installed
-%    between the two reactors. 
+%    between the two reactors.
 %
 %    see also: FlowDevice
 %
 m = FlowDevice(1);
 if nargin == 2
-  install(m, upstream, downstream)
-end
\ No newline at end of file
+    install(m, upstream, downstream)
+end
diff --git a/interfaces/matlab/toolbox/Methane.m b/interfaces/matlab/toolbox/Methane.m
index cc55c1eaf..96010083d 100644
--- a/interfaces/matlab/toolbox/Methane.m
+++ b/interfaces/matlab/toolbox/Methane.m
@@ -8,4 +8,3 @@ function n = Methane()
 %   Properties in SI."
 %
 n = importPhase('liquidvapor.cti','methane');
-
diff --git a/interfaces/matlab/toolbox/Nitrogen.m b/interfaces/matlab/toolbox/Nitrogen.m
index 011a086be..b73d2bf87 100644
--- a/interfaces/matlab/toolbox/Nitrogen.m
+++ b/interfaces/matlab/toolbox/Nitrogen.m
@@ -8,4 +8,3 @@ function n = Nitrogen()
 %   Properties in SI."
 %
 n = importPhase('liquidvapor.cti','nitrogen');
-
diff --git a/interfaces/matlab/toolbox/Oxygen.m b/interfaces/matlab/toolbox/Oxygen.m
index 90d82dea9..b8dda0eba 100644
--- a/interfaces/matlab/toolbox/Oxygen.m
+++ b/interfaces/matlab/toolbox/Oxygen.m
@@ -8,4 +8,3 @@ function n = Oxygen()
 %   Properties in SI."
 %
 n = importPhase('liquidvapor.cti','oxygen');
-
diff --git a/interfaces/matlab/toolbox/Reservoir.m b/interfaces/matlab/toolbox/Reservoir.m
index cfe648231..e04998487 100644
--- a/interfaces/matlab/toolbox/Reservoir.m
+++ b/interfaces/matlab/toolbox/Reservoir.m
@@ -8,7 +8,7 @@ function r = Reservoir(contents)
 %    changing the composition or thermodynamic state. Note that even
 %    if the reaction mechanism associated with the fluid in the
 %    reactor defines reactions, they are disabled within
-%    reservoirs. 
+%    reservoirs.
 %
 %        r1 = Reservoir         % an empty reservoir
 %        r2 = Reservoir(gas)    % a reservoir containing a gas
@@ -16,6 +16,6 @@ function r = Reservoir(contents)
 %   See also: Reactor
 %
 if nargin == 0
-  contents = 0;
+    contents = 0;
 end
 r = Reactor(contents, 1);
diff --git a/interfaces/matlab/toolbox/Valve.m b/interfaces/matlab/toolbox/Valve.m
index 08bcc2e44..901f16d11 100644
--- a/interfaces/matlab/toolbox/Valve.m
+++ b/interfaces/matlab/toolbox/Valve.m
@@ -2,7 +2,7 @@ function m = Valve(upstream, downstream)
 %
 % VALVE - Create a valve connecting two reactors / reservoirs.
 %
-%    m = Valve(upstream, downstream) 
+%    m = Valve(upstream, downstream)
 %
 %    creates an instance of class FlowDevice configured to simulate a
 %    valve that produces a flow rate proportional to the pressure
@@ -12,7 +12,7 @@ function m = Valve(upstream, downstream)
 %
 %    The mass flow rate [kg/s] is computed from the expression
 %
-%        mdot = K ( P_upstream - P_downstream ) 
+%        mdot = K ( P_upstream - P_downstream )
 %
 %    as long as this produces a positive value.  If this expression is
 %    negative, zero is returned. Therefore, the Valve object acts as a
@@ -23,10 +23,10 @@ function m = Valve(upstream, downstream)
 %    to be linearly proportional to the mass flow rate, no matter how
 %    large the pressure difference. THIS MAY CHANGE IN A FUTURE
 %    RELEASE.
-%    
+%
 %    see also: FlowDevice, MassFlowController
 %
 m = FlowDevice(3);
 if nargin == 2
-  install(m, upstream, downstream)
-end
\ No newline at end of file
+    install(m, upstream, downstream)
+end
diff --git a/interfaces/matlab/toolbox/Water.m b/interfaces/matlab/toolbox/Water.m
index 3aa9fdfe9..26af2b1c4 100644
--- a/interfaces/matlab/toolbox/Water.m
+++ b/interfaces/matlab/toolbox/Water.m
@@ -11,4 +11,3 @@ function w = Water()
 %   Cantera C++ source code documentation.
 %
 w = importPhase('liquidvapor.cti','water');
-
diff --git a/interfaces/matlab/toolbox/adddir.m b/interfaces/matlab/toolbox/adddir.m
index 97dee1dce..729d7d71a 100755
--- a/interfaces/matlab/toolbox/adddir.m
+++ b/interfaces/matlab/toolbox/adddir.m
@@ -1,7 +1,7 @@
 function adddir(d)
 % ADDDIR  Add a directory to the Cantera search path.
-%  
-%     adddir('directory') 
+%
+%     adddir('directory')
 %
 %   adds 'directory' to the set of directories where Cantera looks for
 %   input and data files.
diff --git a/interfaces/matlab/toolbox/ck2cti.m b/interfaces/matlab/toolbox/ck2cti.m
index fa4315ebe..4d2fefafb 100644
--- a/interfaces/matlab/toolbox/ck2cti.m
+++ b/interfaces/matlab/toolbox/ck2cti.m
@@ -1,6 +1,6 @@
 function f = ck2cti(infile, thermo, transport)
 % CK2CTI - Convert a Chemkin-compatible reaction mechanism file to
-%           Cantera format. 
+%           Cantera format.
 %
 %       f = ck2cti('chem.inp')
 %       f = ck2cti('chem.inp', 'therm.dat')
@@ -19,40 +19,40 @@ function f = ck2cti(infile, thermo, transport)
 % set this to zero to turn off mechanism validation
 validate = 1;
 
-% set this to one to turn on debugging.  Use only if ck2cti 
+% set this to one to turn on debugging.  Use only if ck2cti
 % fails, and you want to see how the parser is parsing the input file.
 debug = 0;
 
 if nargin == 0
-  error('input file name must be supplied')
+    error('input file name must be supplied')
 elseif nargin == 1
-  thermo = '-';
-  transport = '-';
+    thermo = '-';
+    transport = '-';
 elseif nargin == 2
     transport = '-';
 end
-    
+
 dotloc = findstr(infile,'.');
 if dotloc(end) > 1
-   idtag = infile(1:dotloc(end)-1);
-   outfile = [idtag '.cti'];
+    idtag = infile(1:dotloc(end)-1);
+    outfile = [idtag '.cti'];
 else
-   idtag = infile;
-   outfile = [infile '.cti'];
+    idtag = infile;
+    outfile = [infile '.cti'];
 end
 
 iok = ctmethods(0,1, infile, thermo, transport, idtag, debug, validate);
-  
+
 %iok = system([prog,' -i ',infile,' -t ',thermo,' -tr ',transport, ...
 %	      ' -id ',idtag,' > ',outfile]);
 if iok
-  %ierr2 = system([prog,' > log'])
-  %if ierr2
-  %  error(['Program ck2cti is not found at ',prog,['. Edit file' ...
-  %		    [' ctbin.m to point to the Cantera bin directory.']]])
- % else
- error(['Error occurred while running ck2cti. Check file ck2cti.log' ...
-	' for error messages.']);
-  %end
+    %ierr2 = system([prog,' > log'])
+    %if ierr2
+    %  error(['Program ck2cti is not found at ',prog,['. Edit file' ...
+    %		    [' ctbin.m to point to the Cantera bin directory.']]])
+    % else
+    error(['Error occurred while running ck2cti. Check file ck2cti.log' ...
+        ' for error messages.']);
+    %end
 end
 f = outfile;
diff --git a/interfaces/matlab/toolbox/ck2ctml.m b/interfaces/matlab/toolbox/ck2ctml.m
index 3aef53dc9..47f136be6 100644
--- a/interfaces/matlab/toolbox/ck2ctml.m
+++ b/interfaces/matlab/toolbox/ck2ctml.m
@@ -1,6 +1,6 @@
 function f = ck2ctml(infile, thermo, transport)
 % CK2CTML - Convert a Chemkin-compatible reaction mechanism file to
-%           CTML. 
+%           CTML.
 %
 %    Cantera uses an XML-based file format (CTML) for specifying input
 %    parameters of any type, including specifying reaction mechanism
@@ -18,28 +18,28 @@ function f = ck2ctml(infile, thermo, transport)
 %    read from file 'therm.dat.' In the third form, the CTML file
 %    created will also contain transport property parameters. The
 %    function return value is a string containing the output file
-%    name. 
+%    name.
 %
 if nargin == 0
-  error('input file name must be supplied')
+    error('input file name must be supplied')
 elseif nargin == 1
-  thermo = '-';
-  transport = '-';
+    thermo = '-';
+    transport = '-';
 elseif nargin == 2
     transport = '-';
 end
-    
+
 dotloc = findstr(infile,'.');
 if dotloc(end) > 1
-   idtag = infile(1:dotloc(end)-1);
-   outfile = [idtag '.xml'];
+    idtag = infile(1:dotloc(end)-1);
+    outfile = [idtag '.xml'];
 else
-   idtag = infile;
-   outfile = [infile '.xml'];
+    idtag = infile;
+    outfile = [infile '.xml'];
 end
 
 iok = ctmethods(0, 1, infile, thermo, transport, outfile, idtag);
 if iok
-  error(geterr);
+    error(geterr);
 end
 f = outfile;
diff --git a/interfaces/matlab/toolbox/cleanup.m b/interfaces/matlab/toolbox/cleanup.m
index 5cbe90607..4a7b0d9be 100644
--- a/interfaces/matlab/toolbox/cleanup.m
+++ b/interfaces/matlab/toolbox/cleanup.m
@@ -1,4 +1,4 @@
 function cleanup()
-% CLEANUP - Delete all stored Cantera objects and reclaim memory 
-%   
+% CLEANUP - Delete all stored Cantera objects and reclaim memory
+%
 ctmethods(0, 4);
diff --git a/interfaces/matlab/toolbox/conhp.m b/interfaces/matlab/toolbox/conhp.m
index e68a1ef3e..5241cf841 100755
--- a/interfaces/matlab/toolbox/conhp.m
+++ b/interfaces/matlab/toolbox/conhp.m
@@ -4,7 +4,7 @@ function dydt = conhp(t,y,gas,mw)
 %    Function CONHP evaluates the system of ordinary differential
 %    equations for an adiabatic, constant-pressure,
 %    zero-dimensional reactor. It assumes that the 'gas' object
-%    represents a reacting ideal gas mixture. 
+%    represents a reacting ideal gas mixture.
 
 
 % Set the state of the gas, based on the current solution vector.
@@ -13,15 +13,15 @@ set(gas, 'T', y(1), 'P', pressure(gas), 'Y', y(2:end));
 % energy equation
 wdot = netProdRates(gas);
 tdot = - temperature(gas) * gasconstant * enthalpies_RT(gas)' ...
-       * wdot / (density(gas)*cp_mass(gas));
+    * wdot / (density(gas)*cp_mass(gas));
 
 % set up column vector for dydt
 dydt = [ tdot
-	 zeros(53,1) ];
+    zeros(53,1) ];
 
 % species equations
 rrho = 1.0/density(gas);
 nsp = nSpecies(gas);
 for i = 1:nsp
-  dydt(i+1) = rrho*mw(i)*wdot(i);
+    dydt(i+1) = rrho*mw(i)*wdot(i);
 end
diff --git a/interfaces/matlab/toolbox/conuv.m b/interfaces/matlab/toolbox/conuv.m
index 7f35b569d..cc8b1972c 100755
--- a/interfaces/matlab/toolbox/conuv.m
+++ b/interfaces/matlab/toolbox/conuv.m
@@ -4,7 +4,7 @@ function dydt = conuv(t,y,gas,mw)
 %    Function CONUV evaluates the system of ordinary differential
 %    equations for an adiabatic, constant-volume,
 %    zero-dimensional reactor. It assumes that the 'gas' object
-%    represents a reacting ideal gas mixture. 
+%    represents a reacting ideal gas mixture.
 
 
 % Set the state of the gas, based on the current solution vector.
@@ -14,14 +14,14 @@ nsp = nSpecies(gas);
 % energy equation
 wdot = netProdRates(gas);
 tdot = - temperature(gas) * gasconstant * (enthalpies_RT(gas) - ones(nsp,1))' ...
-       * wdot / (density(gas)*cv_mass(gas));
+    * wdot / (density(gas)*cv_mass(gas));
 
 % set up column vector for dydt
 dydt = [ tdot
-	 zeros(53,1) ];
+    zeros(53,1) ];
 
 % species equations
 rrho = 1.0/density(gas);
 for i = 1:nsp
-  dydt(i+1) = rrho*mw(i)*wdot(i);
+    dydt(i+1) = rrho*mw(i)*wdot(i);
 end
diff --git a/interfaces/matlab/toolbox/gaussian.m b/interfaces/matlab/toolbox/gaussian.m
index c3fabff59..47591460f 100644
--- a/interfaces/matlab/toolbox/gaussian.m
+++ b/interfaces/matlab/toolbox/gaussian.m
@@ -1,16 +1,13 @@
 function g = gaussian(peak, center, width)
 %
 % GAUSSIAN - create a Gaussian Func instance
-%        
+%
 %       gaussian(peak, center, width)
-%       
+%
 %          peak      - the peak value
 %          center    - value of x at which the peak is located
 %          width     - full width at half-maximum. The value of the
-%                      function at center +/- (width)/2 is one-half 
+%                      function at center +/- (width)/2 is one-half
 %                      the peak value.
 %
 g = Func('gaussian', 0, [peak, center, width]);
-
-
-
diff --git a/interfaces/matlab/toolbox/geterr.m b/interfaces/matlab/toolbox/geterr.m
index e06985f3a..ec9187753 100755
--- a/interfaces/matlab/toolbox/geterr.m
+++ b/interfaces/matlab/toolbox/geterr.m
@@ -1,6 +1,6 @@
 function e = geterr
 try
-  e = ctmethods(0,2); % getCanteraError;
+    e = ctmethods(0,2); % getCanteraError;
 catch
-  e = ' ';
+    e = ' ';
 end
\ No newline at end of file
diff --git a/interfaces/matlab/toolbox/importEdge.m b/interfaces/matlab/toolbox/importEdge.m
index 487978350..d0e27cd84 100644
--- a/interfaces/matlab/toolbox/importEdge.m
+++ b/interfaces/matlab/toolbox/importEdge.m
@@ -1,14 +1,14 @@
 function s = importEdge(file, name, phase1, phase2, phase3, phase4)
 % IMPORTINTERFACE - import an interface
-%   
+%
 if nargin == 3
-  s = Interface(file, name, phase1);
+    s = Interface(file, name, phase1);
 elseif nargin == 4
-  s = Interface(file, name, phase1, phase2);   
+    s = Interface(file, name, phase1, phase2);
 elseif nargin == 5
-  s = Interface(file, name, phase1, phase2, phase3);
+    s = Interface(file, name, phase1, phase2, phase3);
 elseif nargin == 6
-  s = Interface(file, name, phase1, phase2, phase3, phase4);  
-else 
-  error('importEdge only supports 4 neighbor phases');
+    s = Interface(file, name, phase1, phase2, phase3, phase4);
+else
+    error('importEdge only supports 4 neighbor phases');
 end
diff --git a/interfaces/matlab/toolbox/importInterface.m b/interfaces/matlab/toolbox/importInterface.m
index c71b44c22..922317757 100644
--- a/interfaces/matlab/toolbox/importInterface.m
+++ b/interfaces/matlab/toolbox/importInterface.m
@@ -1,10 +1,10 @@
 function s = importInterface(file, name, phase1, phase2)
 % IMPORTINTERFACE - import an interface
-%   
+%
 if nargin == 3
-  s = Interface(file, name, phase1);
+    s = Interface(file, name, phase1);
 elseif nargin == 4
-  s = Interface(file, name, phase1, phase2);  
+    s = Interface(file, name, phase1, phase2);
 else
-  error('importInterface only supports 2 bulk phases');
+    error('importInterface only supports 2 bulk phases');
 end
diff --git a/interfaces/matlab/toolbox/importPhase.m b/interfaces/matlab/toolbox/importPhase.m
index 19bad1cb1..2fc168956 100644
--- a/interfaces/matlab/toolbox/importPhase.m
+++ b/interfaces/matlab/toolbox/importPhase.m
@@ -1,8 +1,8 @@
 function s = importPhase(file, name)
 % IMPORTPHASE - import a phase from a CTI file
-%   
+%
 if nargin == 1
-  s = Solution(file);
-elseif nargin == 2 
-  s = Solution(file, name);
+    s = Solution(file);
+elseif nargin == 2
+    s = Solution(file, name);
 end
diff --git a/interfaces/matlab/toolbox/polynom.m b/interfaces/matlab/toolbox/polynom.m
index 5b6f5c0bd..10f19c74f 100644
--- a/interfaces/matlab/toolbox/polynom.m
+++ b/interfaces/matlab/toolbox/polynom.m
@@ -1,7 +1,7 @@
 function poly = polynom(coeffs)
 %
 % POLY - create an instance of class 'Func' representing a polynomial.
-%        
+%
 %   The polynomial coefficients are specified by a one-dimensional
 %   array [a0 a1 .... aN].
 %
@@ -10,10 +10,9 @@ function poly = polynom(coeffs)
 %
 [n m] = size(coeffs);
 if n == 1
-  poly = Func('polynomial',m - 1,coeffs);
+    poly = Func('polynomial',m - 1,coeffs);
 elseif m == 1
-  poly = Func('polynomial',n - 1,coeffs);
+    poly = Func('polynomial',n - 1,coeffs);
 else
-  error('wrong shape for coefficient array');
+    error('wrong shape for coefficient array');
 end
-
diff --git a/interfaces/matlab/toolbox/reactor_ode.m b/interfaces/matlab/toolbox/reactor_ode.m
index 718d31079..000ae58d7 100644
--- a/interfaces/matlab/toolbox/reactor_ode.m
+++ b/interfaces/matlab/toolbox/reactor_ode.m
@@ -3,7 +3,7 @@ function dydt = reactor_ode(t,y,gas,vdot,area,heatflux)
 %
 %    Function REACTOR evaluates the system of ordinary differential
 %    equations for a zero-dimensional reactor with arbitrary heat
-%    transfer and  volume change. 
+%    transfer and  volume change.
 %
 % Solution vector components:
 %    y(1)   Total internal energy U
@@ -17,35 +17,34 @@ function dydt = reactor_ode(t,y,gas,vdot,area,heatflux)
 dydt = zeros(m,n);
 
 for j = 1:n
-  
-  this_y = y(:,j);
-  int_energy = this_y(1);
-  vol = this_y(2);
-  masses = this_y(3:end);
-  
-  % evaluate the total mass, and the specific internal energy and volume.
-  total_mass = sum(masses);
-  u_mass = int_energy/total_mass;
-  v_mass = vol/total_mass;
+    this_y = y(:,j);
+    int_energy = this_y(1);
+    vol = this_y(2);
+    masses = this_y(3:end);
 
-  % set the state of the gas by specifying (u,v,{Y_k})
-  setMassFractions(gas,masses);
-  setState_UV(gas, [u_mass v_mass]);
-  p = pressure(gas);
+    % evaluate the total mass, and the specific internal energy and volume.
+    total_mass = sum(masses);
+    u_mass = int_energy/total_mass;
+    v_mass = vol/total_mass;
 
-  % volume equation
-  vdt = feval(vdot, t, vol, gas);
+    % set the state of the gas by specifying (u,v,{Y_k})
+    setMassFractions(gas,masses);
+    setState_UV(gas, [u_mass v_mass]);
+    p = pressure(gas);
 
-  % energy equation
-  a = feval(area, t, vol);
-  q = feval(heatflux, t, gas);  
-  udt = -p * vdt + a * q;
+    % volume equation
+    vdt = feval(vdot, t, vol, gas);
 
-  % species equations
-  ydt = total_mass * ydot(gas);
+    % energy equation
+    a = feval(area, t, vol);
+    q = feval(heatflux, t, gas);
+    udt = -p * vdt + a * q;
 
-  % set up column vector for dydt
-  dydt(:,j) = [ udt
-		vdt
-		ydt ];
+    % species equations
+    ydt = total_mass * ydot(gas);
+
+    % set up column vector for dydt
+    dydt(:,j) = [udt
+        vdt
+        ydt ];
 end