From e4f2acaf3d1a3153d2a7783ec16d6b6c053f2f93 Mon Sep 17 00:00:00 2001
From: Ray Speth <speth@mit.edu>
Date: Thu, 15 Mar 2012 19:54:41 +0000
Subject: [PATCH] Fixed issues with Matlab toolbox identified by the code
 analyzer

---
 .../toolbox/1D/@Domain1D/componentName.m      |  1 +
 .../matlab/toolbox/1D/@Domain1D/gridPoints.m  |  2 ++
 .../toolbox/1D/@Domain1D/setCoverageEqs.m     |  4 +--
 interfaces/matlab/toolbox/1D/@Domain1D/z.m    |  2 ++
 interfaces/matlab/toolbox/1D/@Stack/Stack.m   |  1 +
 .../matlab/toolbox/1D/@Stack/domainIndex.m    |  2 +-
 interfaces/matlab/toolbox/1D/@Stack/save.m    |  2 +-
 .../matlab/toolbox/1D/@Stack/setProfile.m     |  2 +-
 .../matlab/toolbox/1D/@Stack/solution.m       |  7 +++--
 interfaces/matlab/toolbox/1D/Surface.m        |  2 +-
 interfaces/matlab/toolbox/1D/nComponents.m    |  2 +-
 interfaces/matlab/toolbox/1D/npflame_init.m   |  9 +++++-
 .../matlab/toolbox/@FlowDevice/install.m      |  2 +-
 interfaces/matlab/toolbox/@Func/char.m        |  5 ++--
 interfaces/matlab/toolbox/@Func/display.m     |  2 +-
 interfaces/matlab/toolbox/@Func/subsref.m     |  1 +
 .../matlab/toolbox/@Kinetics/reactionEqn.m    |  6 ++--
 interfaces/matlab/toolbox/@Kinetics/rop.m     |  6 ++--
 interfaces/matlab/toolbox/@Kinetics/rxnEqs.m  |  6 ++--
 .../matlab/toolbox/@Kinetics/setMultiplier.m  |  2 +-
 .../matlab/toolbox/@Kinetics/stoich_net.m     |  2 +-
 .../matlab/toolbox/@Mixture/phaseMoles.m      |  1 +
 .../matlab/toolbox/@Reactor/massFractions.m   |  4 +--
 .../matlab/toolbox/@Reactor/setEnergy.m       |  2 +-
 .../toolbox/@ReactorNet/reactornet_hndl.m     |  2 +-
 interfaces/matlab/toolbox/@Solution/set.m     | 16 +++++-----
 .../matlab/toolbox/@ThermoPhase/elementName.m |  2 +-
 .../matlab/toolbox/@ThermoPhase/equilibrate.m | 29 -------------------
 .../matlab/toolbox/@ThermoPhase/gibbs_RT.m    |  2 +-
 .../toolbox/@ThermoPhase/massFraction.m       |  1 +
 .../toolbox/@ThermoPhase/moleFraction.m       |  1 +
 .../matlab/toolbox/@ThermoPhase/setState.m    |  2 +-
 .../matlab/toolbox/@ThermoPhase/speciesName.m |  2 +-
 .../matlab/toolbox/@Transport/Transport.m     |  2 +-
 interfaces/matlab/toolbox/@Wall/area.m        |  2 +-
 interfaces/matlab/toolbox/@XML_Node/attrib.m  |  2 +-
 interfaces/matlab/toolbox/@XML_Node/build.m   |  8 ++---
 interfaces/matlab/toolbox/conhp.m             |  2 +-
 interfaces/matlab/toolbox/conuv.m             |  2 +-
 interfaces/matlab/toolbox/geterr.m            |  6 ++--
 40 files changed, 72 insertions(+), 84 deletions(-)

diff --git a/interfaces/matlab/toolbox/1D/@Domain1D/componentName.m b/interfaces/matlab/toolbox/1D/@Domain1D/componentName.m
index de03989e9..8493ca566 100644
--- a/interfaces/matlab/toolbox/1D/@Domain1D/componentName.m
+++ b/interfaces/matlab/toolbox/1D/@Domain1D/componentName.m
@@ -2,6 +2,7 @@ function s = componentName(d, n)
 % COMPONENTNAME - Name of component n.
 %
 m = length(n);
+s = cell(m);
 for i = 1:m
     s{i} = domain_methods(d.dom_id, 40, n(i));
 end
diff --git a/interfaces/matlab/toolbox/1D/@Domain1D/gridPoints.m b/interfaces/matlab/toolbox/1D/@Domain1D/gridPoints.m
index 38d5d854a..756542688 100644
--- a/interfaces/matlab/toolbox/1D/@Domain1D/gridPoints.m
+++ b/interfaces/matlab/toolbox/1D/@Domain1D/gridPoints.m
@@ -2,11 +2,13 @@ function zz = gridPoints(d, n)
 % GRID -
 %
 if nargin == 1
+    zz = zeros(1, nPoints(d));
     for i = 1:nPoints(d)
         zz(i) = domain_methods(d.dom_id, 19, i);
     end
 else
     m = length(n);
+    zz = zeros(1, m);
     for i = 1:m
         zz(i) = domain_methods(d.dom_id, 19, n(i));
     end
diff --git a/interfaces/matlab/toolbox/1D/@Domain1D/setCoverageEqs.m b/interfaces/matlab/toolbox/1D/@Domain1D/setCoverageEqs.m
index b1bb2699f..91d982e88 100644
--- a/interfaces/matlab/toolbox/1D/@Domain1D/setCoverageEqs.m
+++ b/interfaces/matlab/toolbox/1D/@Domain1D/setCoverageEqs.m
@@ -7,9 +7,9 @@ end
 
 ion = -1;
 if isa(onoff,'char')
-    if strcmp(onoff,'on') | strcmp(onoff,'yes')
+    if strcmp(onoff,'on') || strcmp(onoff,'yes')
         ion = 1;
-    elseif strcmp(onoff,'off') | strcmp(onoff,'no')
+    elseif strcmp(onoff,'off') || strcmp(onoff,'no')
         ion = 0;
     else
         error(strcat('unknown option: ',onoff))
diff --git a/interfaces/matlab/toolbox/1D/@Domain1D/z.m b/interfaces/matlab/toolbox/1D/@Domain1D/z.m
index 22ff3a699..4d9c5cdc4 100644
--- a/interfaces/matlab/toolbox/1D/@Domain1D/z.m
+++ b/interfaces/matlab/toolbox/1D/@Domain1D/z.m
@@ -2,11 +2,13 @@ function zz = z(d, n)
 % GRID -
 %
 if nargin == 1
+    zz = zeros(1, nPoints(d));
     for i = 1:nPoints(d)
         zz(i) = domain_methods(d.dom_id, 19, i);
     end
 else
     m = length(n);
+    zz = zeros(1, m);
     for i = 1:m
         zz(i) = domain_methods(d.dom_id, 19, n(i));
     end
diff --git a/interfaces/matlab/toolbox/1D/@Stack/Stack.m b/interfaces/matlab/toolbox/1D/@Stack/Stack.m
index 9da6845f9..a016efb5f 100644
--- a/interfaces/matlab/toolbox/1D/@Stack/Stack.m
+++ b/interfaces/matlab/toolbox/1D/@Stack/Stack.m
@@ -10,6 +10,7 @@ s.stack_id = -1;
 s.domains = domains;
 if nargin == 1
     nd = length(domains);
+    ids = zeros(1, nd);
     for n=1:nd
         ids(n) = domain_hndl(domains(n));
     end
diff --git a/interfaces/matlab/toolbox/1D/@Stack/domainIndex.m b/interfaces/matlab/toolbox/1D/@Stack/domainIndex.m
index 1cbd9a147..ff10f8b37 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);
 end
diff --git a/interfaces/matlab/toolbox/1D/@Stack/save.m b/interfaces/matlab/toolbox/1D/@Stack/save.m
index 2ce2bfd50..bf49d0a6e 100644
--- a/interfaces/matlab/toolbox/1D/@Stack/save.m
+++ b/interfaces/matlab/toolbox/1D/@Stack/save.m
@@ -1,4 +1,4 @@
-function saveSoln(s, fname, id, desc)
+function save(s, fname, id, desc)
 % SAVE -
 %
 if nargin == 2
diff --git a/interfaces/matlab/toolbox/1D/@Stack/setProfile.m b/interfaces/matlab/toolbox/1D/@Stack/setProfile.m
index 2822c3ef8..04e07d037 100644
--- a/interfaces/matlab/toolbox/1D/@Stack/setProfile.m
+++ b/interfaces/matlab/toolbox/1D/@Stack/setProfile.m
@@ -27,7 +27,7 @@ end
 
 d = s.domains(n);
 
-if isa(comp,'double') | isa(comp,'cell')
+if isa(comp,'double') || isa(comp,'cell')
     c = comp;
 elseif isa(comp,'char')
     c = {comp};
diff --git a/interfaces/matlab/toolbox/1D/@Stack/solution.m b/interfaces/matlab/toolbox/1D/@Stack/solution.m
index e4381eff5..fb7851fc3 100644
--- a/interfaces/matlab/toolbox/1D/@Stack/solution.m
+++ b/interfaces/matlab/toolbox/1D/@Stack/solution.m
@@ -6,15 +6,16 @@ function x = solution(s, domain, component)
 %
 idom = domainIndex(s, domain);
 d = s.domains(idom);
-
+np = nPoints(d);
 if nargin == 3
     icomp = componentIndex(d, component);
-    for n = 1:nPoints(d)
+    x = zeros(1, np);
+    for n = 1:np
         x(n) = stack_methods(s.stack_id, 30, idom, icomp, n);
     end
 else
     nc = nComponents(d);
-    np = nPoints(d);
+    x = zeros(nc, np);
     for m = 1:nc
         for n = 1:np
             x(m,n) = stack_methods(s.stack_id, 30, idom, m, n);
diff --git a/interfaces/matlab/toolbox/1D/Surface.m b/interfaces/matlab/toolbox/1D/Surface.m
index 3eb1f7c8c..228458e1d 100644
--- a/interfaces/matlab/toolbox/1D/Surface.m
+++ b/interfaces/matlab/toolbox/1D/Surface.m
@@ -9,6 +9,6 @@ if nargin < 2
         setID(m,id);
     end
 else
-    m = Domain1D(6, surface_mech)
+    m = Domain1D(6, surface_mech);
     setID(m,id);
 end
diff --git a/interfaces/matlab/toolbox/1D/nComponents.m b/interfaces/matlab/toolbox/1D/nComponents.m
index b2ff8269e..0baa8aefb 100644
--- a/interfaces/matlab/toolbox/1D/nComponents.m
+++ b/interfaces/matlab/toolbox/1D/nComponents.m
@@ -1,2 +1,2 @@
 function n = nComponents(d)
-n = domain_methods(d.dom_id, 11)
+n = domain_methods(d.dom_id, 11);
diff --git a/interfaces/matlab/toolbox/1D/npflame_init.m b/interfaces/matlab/toolbox/1D/npflame_init.m
index 64ba1a200..7c4e16fb0 100644
--- a/interfaces/matlab/toolbox/1D/npflame_init.m
+++ b/interfaces/matlab/toolbox/1D/npflame_init.m
@@ -46,7 +46,6 @@ wt = molecularWeights(gas);
 % find the fuel and oxidizer
 ifuel = speciesIndex(gas,fuel);
 ioxidizer = speciesIndex(gas,oxidizer);
-ih = speciesIndex(gas,'H');
 
 s = nuox*wt(ioxidizer)/wt(ifuel);
 y0f = massFraction(left,ifuel);
@@ -59,6 +58,9 @@ nsp = nSpecies(gas);
 tf = temperature(left);
 tox = temperature(right);
 
+yox = zeros(1, nsp);
+yf = zeros(1, nsp);
+ystoich = zeros(1, nsp);
 for n = 1:nsp
     yox(n) = massFraction(right,n);
     yf(n) = massFraction(left,n);
@@ -82,6 +84,11 @@ f = sqrt(a/(2.0*diff(ioxidizer)));
 x0 = massFlux(left)*dz/(massFlux(left) + massFlux(right));
 
 nz = nPoints(flow);
+zm = zeros(1,nz);
+u = zeros(1,nz);
+v = zeros(1,nz);
+y = zeros(nz,nsp);
+t = zeros(1,nz);
 for j = 1:nz
     x = zz(j);
     zeta = f*(x - x0);
diff --git a/interfaces/matlab/toolbox/@FlowDevice/install.m b/interfaces/matlab/toolbox/@FlowDevice/install.m
index 273aa337f..1f31db342 100644
--- a/interfaces/matlab/toolbox/@FlowDevice/install.m
+++ b/interfaces/matlab/toolbox/@FlowDevice/install.m
@@ -1,7 +1,7 @@
 function install(f, upstream, downstream)
 
 if nargin == 3
-    if ~isa(upstream,'Reactor') | ~isa(downstream,'Reactor')
+    if ~isa(upstream,'Reactor') || ~isa(downstream,'Reactor')
         error(['Flow devices can only be installed between reactors or' ...
             ' reservoirs'])
     end
diff --git a/interfaces/matlab/toolbox/@Func/char.m b/interfaces/matlab/toolbox/@Func/char.m
index 59c70bafe..f49e56daa 100644
--- a/interfaces/matlab/toolbox/@Func/char.m
+++ b/interfaces/matlab/toolbox/@Func/char.m
@@ -30,7 +30,7 @@ else
                         a = -a;
                     end
                 end
-                if a ~= 1 | d == 0
+                if a ~= 1 || d == 0
                     s = [s num2str(a)];
                     if d > 0
                         s = [s '*'];
@@ -45,7 +45,6 @@ else
             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)) ')'];
@@ -57,7 +56,7 @@ else
         B = c(2:end,2);
         N = size(c,1)-1;
         if Ao ~= 0
-            s = [num2str(Ao/2)];
+            s = num2str(Ao/2);
         else
             s = '';
         end
diff --git a/interfaces/matlab/toolbox/@Func/display.m b/interfaces/matlab/toolbox/@Func/display.m
index f755a1f64..5bcd88136 100644
--- a/interfaces/matlab/toolbox/@Func/display.m
+++ b/interfaces/matlab/toolbox/@Func/display.m
@@ -1,4 +1,4 @@
-function d = display(a)
+function display(a)
 % DISPLAY -
 %
 disp(' ');
diff --git a/interfaces/matlab/toolbox/@Func/subsref.m b/interfaces/matlab/toolbox/@Func/subsref.m
index 8c65e9009..ac90c99ea 100644
--- a/interfaces/matlab/toolbox/@Func/subsref.m
+++ b/interfaces/matlab/toolbox/@Func/subsref.m
@@ -3,6 +3,7 @@ function b = subsref(a,s)
 switch s.type
     case '()'
         ind = s.subs{:};
+        b = zeros(1, length(ind));
         for k = 1:length(ind)
             b(k) = funcmethods(2,a.index,ind(k));
         end
diff --git a/interfaces/matlab/toolbox/@Kinetics/reactionEqn.m b/interfaces/matlab/toolbox/@Kinetics/reactionEqn.m
index 2b3a6aafd..f78b47b4a 100644
--- a/interfaces/matlab/toolbox/@Kinetics/reactionEqn.m
+++ b/interfaces/matlab/toolbox/@Kinetics/reactionEqn.m
@@ -4,7 +4,7 @@ function e = reactionEqn(a, irxn)
 if nargin == 1
     m = nReactions(a);
     n = 1;
-    irxn = [1:m]';
+    irxn = (1:m)';
 elseif nargin == 2
     if isa(irxn,'double')
         [m, n] = size(irxn);
@@ -13,10 +13,10 @@ elseif nargin == 2
     end
 end
 
-if m == 1 & n == 1
+if m == 1 && n == 1
     e = kinetics_get(a.id, 31, irxn); % rxnstring(a.id, irxn);
 else
-    e = {};
+    e = cell(m,n);
     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));
diff --git a/interfaces/matlab/toolbox/@Kinetics/rop.m b/interfaces/matlab/toolbox/@Kinetics/rop.m
index 3399814b8..ca060d4e3 100644
--- a/interfaces/matlab/toolbox/@Kinetics/rop.m
+++ b/interfaces/matlab/toolbox/@Kinetics/rop.m
@@ -6,9 +6,9 @@ function rop = rop(k)
 %    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)
-r = rop_r(k)
-rop = [f r]
+f = rop_f(k);
+r = rop_r(k);
+rop = [f r];
 if nargout == 0
     figure
     set(gcf,'Name','Rates of Progress');
diff --git a/interfaces/matlab/toolbox/@Kinetics/rxnEqs.m b/interfaces/matlab/toolbox/@Kinetics/rxnEqs.m
index 77c0fcf38..755a749b6 100644
--- a/interfaces/matlab/toolbox/@Kinetics/rxnEqs.m
+++ b/interfaces/matlab/toolbox/@Kinetics/rxnEqs.m
@@ -4,7 +4,7 @@ function e = rxnEqs(a, irxn)
 if nargin == 1
     m = nReactions(a);
     n = 1;
-    irxn = [1:m]'
+    irxn = (1:m)';
 elseif nargin == 2
     if isa(irxn,'double')
         [m, n] = size(irxn);
@@ -13,10 +13,10 @@ elseif nargin == 2
     end
 end
 
-if m == 1 & n == 1
+if m == 1 && n == 1
     e = rxnstring(a.id, irxn);
 else
-    e = {};
+    e = cell(m,n);
     for i = 1:m
         for j = 1:n
             e{i,j} = rxnstring(a.id, irxn(i,j));
diff --git a/interfaces/matlab/toolbox/@Kinetics/setMultiplier.m b/interfaces/matlab/toolbox/@Kinetics/setMultiplier.m
index dd2893db4..67b376edc 100644
--- a/interfaces/matlab/toolbox/@Kinetics/setMultiplier.m
+++ b/interfaces/matlab/toolbox/@Kinetics/setMultiplier.m
@@ -9,7 +9,7 @@ function setMultiplier(a,irxn,v)
 if nargin == 2
     v = irxn;
     m = nReactions(a);
-    irxn = [1:m]';
+    irxn = (1:m)';
     n = 1;
 else
     [m, n] = size(irxn);
diff --git a/interfaces/matlab/toolbox/@Kinetics/stoich_net.m b/interfaces/matlab/toolbox/@Kinetics/stoich_net.m
index 84f4c536a..0753ed428 100644
--- a/interfaces/matlab/toolbox/@Kinetics/stoich_net.m
+++ b/interfaces/matlab/toolbox/@Kinetics/stoich_net.m
@@ -21,7 +21,7 @@ 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);
 else
diff --git a/interfaces/matlab/toolbox/@Mixture/phaseMoles.m b/interfaces/matlab/toolbox/@Mixture/phaseMoles.m
index 5e06e656c..9c319e973 100644
--- a/interfaces/matlab/toolbox/@Mixture/phaseMoles.m
+++ b/interfaces/matlab/toolbox/@Mixture/phaseMoles.m
@@ -5,6 +5,7 @@ if nargin == 2
     moles = mixturemethods(28, mix_hndl(self), n);
 elseif nargin == 1
     np = nPhases(self);
+    m = zeros(1,np);
     for n = 1:np
         m(n) = mixturemethods(28, mix_hndl(self), n);
     end
diff --git a/interfaces/matlab/toolbox/@Reactor/massFractions.m b/interfaces/matlab/toolbox/@Reactor/massFractions.m
index 96fa12184..e5aea925d 100644
--- a/interfaces/matlab/toolbox/@Reactor/massFractions.m
+++ b/interfaces/matlab/toolbox/@Reactor/massFractions.m
@@ -4,7 +4,7 @@ function y = massFractions(r)
 %
 nsp = nSpecies(r.contents);
 ir = reactor_hndl(r);
+y = zeros(1, nsp);
 for k = 1:nsp
-    yy(k) = reactormethods(30, ir, k-1);
+    y(k) = reactormethods(30, ir, k-1);
 end
-y = yy;
diff --git a/interfaces/matlab/toolbox/@Reactor/setEnergy.m b/interfaces/matlab/toolbox/@Reactor/setEnergy.m
index 88d620e4f..7e9c53f81 100644
--- a/interfaces/matlab/toolbox/@Reactor/setEnergy.m
+++ b/interfaces/matlab/toolbox/@Reactor/setEnergy.m
@@ -11,7 +11,7 @@ function setEnergy(f, flag)
 % >>> setEnergy(r, 'on');
 % >>> setEnergy(r, 'off');
 %
-iflag = -1
+iflag = -1;
 if strcmp(flag,{'on'})
     iflag = 1;
 elseif strcmp(flag,{'off'})
diff --git a/interfaces/matlab/toolbox/@ReactorNet/reactornet_hndl.m b/interfaces/matlab/toolbox/@ReactorNet/reactornet_hndl.m
index aa39d5350..f6230aded 100644
--- a/interfaces/matlab/toolbox/@ReactorNet/reactornet_hndl.m
+++ b/interfaces/matlab/toolbox/@ReactorNet/reactornet_hndl.m
@@ -1,2 +1,2 @@
-function i = reactor_hndl(r)
+function i = reactornet_hndl(r)
 i = r.index;
diff --git a/interfaces/matlab/toolbox/@Solution/set.m b/interfaces/matlab/toolbox/@Solution/set.m
index c312b9025..d723de461 100644
--- a/interfaces/matlab/toolbox/@Solution/set.m
+++ b/interfaces/matlab/toolbox/@Solution/set.m
@@ -148,23 +148,23 @@ elseif ntot == 2
     %
     % set property pairs
     %
-    if nt == 1 & nv == 1
+    if nt == 1 && nv == 1
         setTemperature(a,tval);
         setDensity(a,1.0/vval);
-    elseif nt == 1 & np == 1
+    elseif nt == 1 && np == 1
         setTemperature(a,tval);
         setPressure(a, pval);
-    elseif nt == 1 & nq == 1
+    elseif nt == 1 && nq == 1
         setState_Tsat(a, [tval,qval]);
-    elseif np == 1 & nq == 1
+    elseif np == 1 && nq == 1
         setState_Psat(a, [pval,qval]);
-    elseif np == 1 & nh == 1
+    elseif np == 1 && nh == 1
         setState_HP(a,[hval,pval]);
-    elseif nu == 1 & nv == 1
+    elseif nu == 1 && nv == 1
         setState_UV(a,[uval,vval]);
-    elseif ns == 1 & np == 1
+    elseif ns == 1 && np == 1
         setState_SP(a,[sval,pval]);
-    elseif ns == 1 & nv == 1
+    elseif ns == 1 && nv == 1
         setState_SV(a,[sval,vval]);
     else
         error('unimplemented property pair');
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/elementName.m b/interfaces/matlab/toolbox/@ThermoPhase/elementName.m
index 28efa0292..fe63b4980 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/elementName.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/elementName.m
@@ -7,7 +7,7 @@ function nm = elementName(a, m)
 %    the same shape containing the name strings.
 %
 [mm, nn] = size(m);
-nm = {};
+nm = cell(mm,nn);
 for i = 1:mm
     for j = 1:nn
         nm{i,j} = phase_get(a.tp_id, 41, m(i,j));
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/equilibrate.m b/interfaces/matlab/toolbox/@ThermoPhase/equilibrate.m
index 6987b8c50..5f7067467 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/equilibrate.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/equilibrate.m
@@ -48,36 +48,7 @@ if nargin < 7
     loglevel = 0;
 end
 
-iok = 0;
 iok = thermo_set(a.tp_id, 50, xy, solver, rtol, maxsteps, maxiter, loglevel);
-% $$$ switch xy
-% $$$  case 'TP'
-% $$$   iok = thermo_set(a.tp_id, 50, 104, solver, rtol, maxsteps, loglevel);
-% $$$  case 'TV'
-% $$$   iok = thermo_set(a.tp_id, 50, 100, solver, rtol, maxsteps, loglevel);
-% $$$  case 'HP'
-% $$$   iok = thermo_set(a.tp_id, 50, 101, solver, rtol, maxsteps, loglevel);
-% $$$  case 'SP'
-% $$$   iok = thermo_set(a.tp_id, 50, 102, solver, rtol, maxsteps, loglevel);
-% $$$  case 'SV'
-% $$$   iok = thermo_set(a.tp_id, 50, 107, solver, rtol, maxsteps, loglevel);
-% $$$  case 'UV'
-% $$$   iok = thermo_set(a.tp_id, 50, 105, solver, rtol, maxsteps, loglevel);
-% $$$  case 'PT'
-% $$$   iok = thermo_set(a.tp_id, 50, 104, solver, rtol, maxsteps, loglevel);
-% $$$  case 'VT'
-% $$$   iok = thermo_set(a.tp_id, 50, 100, solver, rtol, maxsteps, loglevel);
-% $$$  case 'PH'
-% $$$   iok = thermo_set(a.tp_id, 50, 101, solver, rtol, maxsteps, loglevel);
-% $$$  case 'PS'
-% $$$   iok = thermo_set(a.tp_id, 50, 102, solver, rtol, maxsteps, loglevel);
-% $$$  case 'VS'
-% $$$   iok = thermo_set(a.tp_id, 50, 107, solver, rtol, maxsteps, loglevel);
-% $$$  case 'VU'
-% $$$   iok = thermo_set(a.tp_id, 50, 105, solver, rtol, maxsteps, loglevel);
-% $$$  otherwise
-% $$$   error('unsupported option')
-% $$$ end
 if iok < 0
     e = geterr;
     if e == 0
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/gibbs_RT.m b/interfaces/matlab/toolbox/@ThermoPhase/gibbs_RT.m
index 78b082c58..754b0a086 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/gibbs_RT.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/gibbs_RT.m
@@ -4,4 +4,4 @@ function g_RT = gibbs_RT(p)
 %        This method returns an array containing the pure species
 %        standard-state Gibbs free energies.
 %
-g_RT = enthalpies_RT(g) - entropies_R(g);
+g_RT = enthalpies_RT(p) - entropies_R(p);
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/massFraction.m b/interfaces/matlab/toolbox/@ThermoPhase/massFraction.m
index 90dbaed50..2e193f9ad 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/massFraction.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/massFraction.m
@@ -10,6 +10,7 @@ if isa(species,'char')
 
 elseif isa(species,'cell')
     n = length(species);
+    y = zeros(1, n);
     for j = 1:n
         k = speciesIndex(s, species{j});
         if k > 0
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/moleFraction.m b/interfaces/matlab/toolbox/@ThermoPhase/moleFraction.m
index adf0e5912..e01efb07c 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/moleFraction.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/moleFraction.m
@@ -10,6 +10,7 @@ if isa(species,'char')
 
 elseif isa(species,'cell')
     n = length(species);
+    x = zeros(1, n);
     for j = 1:n
         k = speciesIndex(s, species{j});
         if k > 0
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/setState.m b/interfaces/matlab/toolbox/@ThermoPhase/setState.m
index 3ef8e812a..6cba9fb42 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/setState.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/setState.m
@@ -1,6 +1,6 @@
 function a = setState(a,job,values)
 disp('deprecated')
-if nargin ~= 3 | ~isa(job,'char')
+if nargin ~= 3 || ~isa(job,'char')
     error('Syntax error. Type "help setState" for more information.')
 end
 
diff --git a/interfaces/matlab/toolbox/@ThermoPhase/speciesName.m b/interfaces/matlab/toolbox/@ThermoPhase/speciesName.m
index 5e6d00e1a..2acab7352 100644
--- a/interfaces/matlab/toolbox/@ThermoPhase/speciesName.m
+++ b/interfaces/matlab/toolbox/@ThermoPhase/speciesName.m
@@ -6,7 +6,7 @@ function nm = speciesName(a, k)
 %    the same shape containing the name strings.
 %
 [m, n] = size(k);
-nm = {};
+nm = cell(m,n);
 for i = 1:m
     for j = 1:n
         nm{i,j} = phase_get(a.tp_id, 40, k(i,j));
diff --git a/interfaces/matlab/toolbox/@Transport/Transport.m b/interfaces/matlab/toolbox/@Transport/Transport.m
index 4125e18dc..4318efa58 100644
--- a/interfaces/matlab/toolbox/@Transport/Transport.m
+++ b/interfaces/matlab/toolbox/@Transport/Transport.m
@@ -10,7 +10,7 @@ function tr = Transport(xml_phase, th, model, loglevel)
 tr.id = 0;
 if nargin == 4
     tr.th = th;
-    if model == 'default'
+    if strcmp(model, 'default')
         try
             node = child(xml_phase,'transport');
             tr.model = attrib(node,'model');
diff --git a/interfaces/matlab/toolbox/@Wall/area.m b/interfaces/matlab/toolbox/@Wall/area.m
index eab0ded34..ed6c6f83a 100644
--- a/interfaces/matlab/toolbox/@Wall/area.m
+++ b/interfaces/matlab/toolbox/@Wall/area.m
@@ -1,4 +1,4 @@
 function a = area(w)
 % AREA -
 %
-a = wallmethods(23, wall_hndl(w))
+a = wallmethods(23, wall_hndl(w));
diff --git a/interfaces/matlab/toolbox/@XML_Node/attrib.m b/interfaces/matlab/toolbox/@XML_Node/attrib.m
index 3b632f5b5..526e408e2 100644
--- a/interfaces/matlab/toolbox/@XML_Node/attrib.m
+++ b/interfaces/matlab/toolbox/@XML_Node/attrib.m
@@ -1,6 +1,6 @@
 function a = attrib(x, key)
 
-if nargin ~= 2 | ~isa(key,'char')
+if nargin ~= 2 || ~isa(key,'char')
     error('Syntax error. Type "help attrib" for more information.')
 end
 
diff --git a/interfaces/matlab/toolbox/@XML_Node/build.m b/interfaces/matlab/toolbox/@XML_Node/build.m
index e1ec2207a..4e3d3bafa 100644
--- a/interfaces/matlab/toolbox/@XML_Node/build.m
+++ b/interfaces/matlab/toolbox/@XML_Node/build.m
@@ -1,11 +1,11 @@
 function x = build(x, file, pre)
 
-if nargin < 2 | ~isa(file,'char')
+if nargin < 2 || ~isa(file,'char')
     error('Syntax error. Type "help build" for more information.')
 end
 
-if nargin == 3 & pre > 0
-    iok = ctmethods(10, 15, x.id, file)
+if nargin == 3 && pre > 0
+    ctmethods(10, 15, x.id, file)
 else
-    iok = ctmethods(10, 4, x.id, file)
+    ctmethods(10, 4, x.id, file)
 end
diff --git a/interfaces/matlab/toolbox/conhp.m b/interfaces/matlab/toolbox/conhp.m
index 5241cf841..d5b5f5b7f 100755
--- a/interfaces/matlab/toolbox/conhp.m
+++ b/interfaces/matlab/toolbox/conhp.m
@@ -1,4 +1,4 @@
-function dydt = conhp(t,y,gas,mw)
+function dydt = conhp(t,y,gas,mw) %#ok<INUSL>
 % CONHP ODE system for a constant-pressure, adiabatic reactor.
 %
 %    Function CONHP evaluates the system of ordinary differential
diff --git a/interfaces/matlab/toolbox/conuv.m b/interfaces/matlab/toolbox/conuv.m
index cc8b1972c..8b060881b 100755
--- a/interfaces/matlab/toolbox/conuv.m
+++ b/interfaces/matlab/toolbox/conuv.m
@@ -1,4 +1,4 @@
-function dydt = conuv(t,y,gas,mw)
+function dydt = conuv(t,y,gas,mw) %#ok<INUSL>
 % CONUV ODE system for a constant-volume, adiabatic reactor.
 %
 %    Function CONUV evaluates the system of ordinary differential
diff --git a/interfaces/matlab/toolbox/geterr.m b/interfaces/matlab/toolbox/geterr.m
index ec9187753..a530daffd 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;
-catch
-    e = ' ';
-end
\ No newline at end of file
+catch ME
+    e = getReport(ME);
+end