diff --git a/test_problems/diamondSurf/diamond_blessed.xml b/test_problems/diamondSurf/diamond_blessed.xml
index 47da35476..176662f96 100644
--- a/test_problems/diamondSurf/diamond_blessed.xml
+++ b/test_problems/diamondSurf/diamond_blessed.xml
@@ -1,10 +1,11 @@
+<?xml version="1.0"?>
 <ctml>
   <validate reactions="yes" species="yes"/>
 
-  <!--    phase gas     -->
+  <!-- phase gas     -->
   <phase dim="3" id="gas">
     <elementArray datasrc="elements.xml">H C</elementArray>
-    <speciesArray datasrc="gri30.xml#species_data"> H H2 CH3 CH4</speciesArray>
+    <speciesArray datasrc="gri30.xml#species_data">H H2 CH3 CH4</speciesArray>
     <state>
       <temperature units="K">1200.0</temperature>
       <pressure units="Pa">2666.4473684210525</pressure>
@@ -15,7 +16,7 @@
     <transport model="None"/>
   </phase>
 
-  <!--    phase diamond     -->
+  <!-- phase diamond     -->
   <phase dim="3" id="diamond">
     <elementArray datasrc="elements.xml">H C</elementArray>
     <speciesArray datasrc="#species_data">C(d)</speciesArray>
@@ -26,9 +27,9 @@
     <kinetics model="none"/>
   </phase>
 
-  <!--    phase diamond_100     -->
+  <!-- phase diamond_100     -->
   <phase dim="2" id="diamond_100">
-    <elementArray datasrc="elements.xml"> H C </elementArray>
+    <elementArray datasrc="elements.xml">H C </elementArray>
     <speciesArray datasrc="#species_data">c6HH c6H* c6*H c6** c6HM c6HM* c6*M c6B</speciesArray>
     <reactionArray datasrc="#reaction_data"/>
     <state>
@@ -43,402 +44,402 @@
     <phaseArray>gas diamond</phaseArray>
   </phase>
 
-  <!--     species definitions     -->
+  <!-- species definitions     -->
   <speciesData id="species_data">
 
-    <!--    species C(d)    -->
+    <!-- species C(d)    -->
     <species name="C(d)">
       <atomArray>C:1 </atomArray>
       <thermo>
         <const_cp Tmax="5000.0" Tmin="100.0">
-          <t0 units="K">298.14999999999998</t0>
-          <h0 units="J/mol">0.0</h0>
-          <s0 units="J/mol/K">0.0</s0>
-          <cp0 units="J/mol/K">0.0</cp0>
+           <t0 units="K">298.14999999999998</t0>
+           <h0 units="J/mol">0.0</h0>
+           <s0 units="J/mol/K">0.0</s0>
+           <cp0 units="J/mol/K">0.0</cp0>
         </const_cp>
       </thermo>
     </species>
 
-    <!--    species c6H*    -->
+    <!-- species c6H*    -->
     <species name="c6H*">
       <atomArray>H:1 </atomArray>
       <thermo>
         <const_cp Tmax="5000.0" Tmin="100.0">
-          <t0 units="K">298.14999999999998</t0>
-          <h0 units="kcal/mol">51.700000000000003</h0>
-          <s0 units="cal/mol/K">19.5</s0>
-          <cp0 units="J/mol/K">0.0</cp0>
+           <t0 units="K">298.14999999999998</t0>
+           <h0 units="kcal/mol">51.700000000000003</h0>
+           <s0 units="cal/mol/K">19.5</s0>
+           <cp0 units="J/mol/K">0.0</cp0>
         </const_cp>
       </thermo>
     </species>
 
-    <!--    species c6*H    -->
+    <!-- species c6*H    -->
     <species name="c6*H">
       <atomArray>H:1 </atomArray>
       <thermo>
         <const_cp Tmax="5000.0" Tmin="100.0">
-          <t0 units="K">298.14999999999998</t0>
-          <h0 units="kcal/mol">46.100000000000001</h0>
-          <s0 units="cal/mol/K">19.899999999999999</s0>
-          <cp0 units="J/mol/K">0.0</cp0>
+           <t0 units="K">298.14999999999998</t0>
+           <h0 units="kcal/mol">46.100000000000001</h0>
+           <s0 units="cal/mol/K">19.899999999999999</s0>
+           <cp0 units="J/mol/K">0.0</cp0>
         </const_cp>
       </thermo>
     </species>
 
-    <!--    species c6HH    -->
+    <!-- species c6HH    -->
     <species name="c6HH">
       <atomArray>H:2 </atomArray>
       <thermo>
         <const_cp Tmax="5000.0" Tmin="100.0">
-          <t0 units="K">298.14999999999998</t0>
-          <h0 units="kcal/mol">11.4</h0>
-          <s0 units="cal/mol/K">21.0</s0>
-          <cp0 units="J/mol/K">0.0</cp0>
+           <t0 units="K">298.14999999999998</t0>
+           <h0 units="kcal/mol">11.4</h0>
+           <s0 units="cal/mol/K">21.0</s0>
+           <cp0 units="J/mol/K">0.0</cp0>
         </const_cp>
       </thermo>
     </species>
 
-    <!--    species c6HM    -->
+    <!-- species c6HM    -->
     <species name="c6HM">
       <atomArray>H:4 C:1 </atomArray>
       <thermo>
         <const_cp Tmax="5000.0" Tmin="100.0">
-          <t0 units="K">298.14999999999998</t0>
-          <h0 units="kcal/mol">26.899999999999999</h0>
-          <s0 units="cal/mol/K">40.299999999999997</s0>
-          <cp0 units="J/mol/K">0.0</cp0>
+           <t0 units="K">298.14999999999998</t0>
+           <h0 units="kcal/mol">26.899999999999999</h0>
+           <s0 units="cal/mol/K">40.299999999999997</s0>
+           <cp0 units="J/mol/K">0.0</cp0>
         </const_cp>
       </thermo>
     </species>
 
-    <!--    species c6HM*    -->
+    <!-- species c6HM*    -->
     <species name="c6HM*">
       <atomArray>H:3 C:1 </atomArray>
       <thermo>
         <const_cp Tmax="5000.0" Tmin="100.0">
-          <t0 units="K">298.14999999999998</t0>
-          <h0 units="kcal/mol">65.799999999999997</h0>
-          <s0 units="cal/mol/K">40.100000000000001</s0>
-          <cp0 units="J/mol/K">0.0</cp0>
+           <t0 units="K">298.14999999999998</t0>
+           <h0 units="kcal/mol">65.799999999999997</h0>
+           <s0 units="cal/mol/K">40.100000000000001</s0>
+           <cp0 units="J/mol/K">0.0</cp0>
         </const_cp>
       </thermo>
     </species>
 
-    <!--    species c6*M    -->
+    <!-- species c6*M    -->
     <species name="c6*M">
       <atomArray>H:3 C:1 </atomArray>
       <thermo>
         <const_cp Tmax="5000.0" Tmin="100.0">
-          <t0 units="K">298.14999999999998</t0>
-          <h0 units="kcal/mol">53.299999999999997</h0>
-          <s0 units="cal/mol/K">38.899999999999999</s0>
-          <cp0 units="J/mol/K">0.0</cp0>
+           <t0 units="K">298.14999999999998</t0>
+           <h0 units="kcal/mol">53.299999999999997</h0>
+           <s0 units="cal/mol/K">38.899999999999999</s0>
+           <cp0 units="J/mol/K">0.0</cp0>
         </const_cp>
       </thermo>
     </species>
 
-    <!--    species c6**    -->
+    <!-- species c6**    -->
     <species name="c6**">
       <atomArray>C:0 </atomArray>
       <thermo>
         <const_cp Tmax="5000.0" Tmin="100.0">
-          <t0 units="K">298.14999999999998</t0>
-          <h0 units="kcal/mol">90.0</h0>
-          <s0 units="cal/mol/K">18.399999999999999</s0>
-          <cp0 units="J/mol/K">0.0</cp0>
+           <t0 units="K">298.14999999999998</t0>
+           <h0 units="kcal/mol">90.0</h0>
+           <s0 units="cal/mol/K">18.399999999999999</s0>
+           <cp0 units="J/mol/K">0.0</cp0>
         </const_cp>
       </thermo>
     </species>
 
-    <!--    species c6B    -->
+    <!-- species c6B    -->
     <species name="c6B">
       <atomArray>H:2 C:1 </atomArray>
       <thermo>
         <const_cp Tmax="5000.0" Tmin="100.0">
-          <t0 units="K">298.14999999999998</t0>
-          <h0 units="kcal/mol">40.899999999999999</h0>
-          <s0 units="cal/mol/K">26.899999999999999</s0>
-          <cp0 units="J/mol/K">0.0</cp0>
+           <t0 units="K">298.14999999999998</t0>
+           <h0 units="kcal/mol">40.899999999999999</h0>
+           <s0 units="cal/mol/K">26.899999999999999</s0>
+           <cp0 units="J/mol/K">0.0</cp0>
         </const_cp>
       </thermo>
     </species>
   </speciesData>
   <reactionData id="reaction_data">
 
-    <!--   reaction 0001    -->
-    <reaction id="0001" reversible="yes" type="surface">
+    <!-- reaction 0001    -->
+    <reaction reversible="yes" type="surface" id="0001">
       <equation>c6HH + H   [=] c6H* + H2</equation>
       <rateCoeff>
         <Arrhenius>
-          <A>  1.300000E+11</A>
-          <b>0.0</b>
-          <E units="kcal/mol">7.300000</E>
+           <A>1.300000E+11</A>
+           <b>0.0</b>
+           <E units="kcal/mol">7.300000</E>
         </Arrhenius>
       </rateCoeff>
       <reactants>H:1 c6HH:1</reactants>
       <products>H2:1 c6H*:1</products>
     </reaction>
 
-    <!--   reaction 0002    -->
-    <reaction id="0002" reversible="yes" type="surface">
+    <!-- reaction 0002    -->
+    <reaction reversible="yes" type="surface" id="0002">
       <equation>c6H* + H   [=] c6HH</equation>
       <rateCoeff>
         <Arrhenius>
-          <A>  1.000000E+10</A>
-          <b>0.0</b>
-          <E units="kcal/mol">0.000000</E>
+           <A>1.000000E+10</A>
+           <b>0.0</b>
+           <E units="kcal/mol">0.000000</E>
         </Arrhenius>
       </rateCoeff>
       <reactants>c6H*:1 H:1</reactants>
       <products>c6HH:1</products>
     </reaction>
 
-    <!--   reaction 0003    -->
-    <reaction id="0003" reversible="yes" type="surface">
+    <!-- reaction 0003    -->
+    <reaction reversible="yes" type="surface" id="0003">
       <equation>c6H* + CH3 [=] c6HM</equation>
       <rateCoeff>
         <Arrhenius>
-          <A>  5.000000E+09</A>
-          <b>0.0</b>
-          <E units="kcal/mol">0.000000</E>
+           <A>5.000000E+09</A>
+           <b>0.0</b>
+           <E units="kcal/mol">0.000000</E>
         </Arrhenius>
       </rateCoeff>
       <reactants>c6H*:1 CH3:1</reactants>
       <products>c6HM:1</products>
     </reaction>
 
-    <!--   reaction 0004    -->
-    <reaction id="0004" reversible="yes" type="surface">
+    <!-- reaction 0004    -->
+    <reaction reversible="yes" type="surface" id="0004">
       <equation>c6HM + H   [=] c6*M + H2</equation>
       <rateCoeff>
         <Arrhenius>
-          <A>  1.300000E+11</A>
-          <b>0.0</b>
-          <E units="kcal/mol">7.300000</E>
+           <A>1.300000E+11</A>
+           <b>0.0</b>
+           <E units="kcal/mol">7.300000</E>
         </Arrhenius>
       </rateCoeff>
       <reactants>H:1 c6HM:1</reactants>
       <products>H2:1 c6*M:1</products>
     </reaction>
 
-    <!--   reaction 0005    -->
-    <reaction id="0005" reversible="yes" type="surface">
+    <!-- reaction 0005    -->
+    <reaction reversible="yes" type="surface" id="0005">
       <equation>c6*M + H   [=] c6HM</equation>
       <rateCoeff>
         <Arrhenius>
-          <A>  1.000000E+10</A>
-          <b>0.0</b>
-          <E units="kcal/mol">0.000000</E>
+           <A>1.000000E+10</A>
+           <b>0.0</b>
+           <E units="kcal/mol">0.000000</E>
         </Arrhenius>
       </rateCoeff>
       <reactants>H:1 c6*M:1</reactants>
       <products>c6HM:1</products>
     </reaction>
 
-    <!--   reaction 0006    -->
-    <reaction id="0006" reversible="yes" type="surface">
+    <!-- reaction 0006    -->
+    <reaction reversible="yes" type="surface" id="0006">
       <equation>c6HM + H   [=] c6HM* + H2</equation>
       <rateCoeff>
         <Arrhenius>
-          <A>  2.800000E+04</A>
-          <b>0.0</b>
-          <E units="kcal/mol">7.700000</E>
+           <A>2.800000E+04</A>
+           <b>0.0</b>
+           <E units="kcal/mol">7.700000</E>
         </Arrhenius>
       </rateCoeff>
       <reactants>H:1 c6HM:1</reactants>
       <products>H2:1 c6HM*:1</products>
     </reaction>
 
-    <!--   reaction 0007    -->
-    <reaction id="0007" reversible="yes" type="surface">
+    <!-- reaction 0007    -->
+    <reaction reversible="yes" type="surface" id="0007">
       <equation>c6HM* + H  [=] c6HM</equation>
       <rateCoeff>
         <Arrhenius>
-          <A>  1.000000E+10</A>
-          <b>0.0</b>
-          <E units="kcal/mol">0.000000</E>
+           <A>1.000000E+10</A>
+           <b>0.0</b>
+           <E units="kcal/mol">0.000000</E>
         </Arrhenius>
       </rateCoeff>
       <reactants>c6HM*:1 H:1</reactants>
       <products>c6HM:1</products>
     </reaction>
 
-    <!--   reaction 0008    -->
-    <reaction id="0008" reversible="yes" type="surface">
+    <!-- reaction 0008    -->
+    <reaction reversible="yes" type="surface" id="0008">
       <equation>c6HM*      [=] c6*M</equation>
       <rateCoeff>
         <Arrhenius>
-          <A>  1.000000E+08</A>
-          <b>0.0</b>
-          <E units="kcal/mol">0.000000</E>
+           <A>1.000000E+08</A>
+           <b>0.0</b>
+           <E units="kcal/mol">0.000000</E>
         </Arrhenius>
       </rateCoeff>
       <reactants>c6HM*:1</reactants>
       <products>c6*M:1</products>
     </reaction>
 
-    <!--   reaction 0009    -->
-    <reaction id="0009" reversible="yes" type="surface">
+    <!-- reaction 0009    -->
+    <reaction reversible="yes" type="surface" id="0009">
       <equation>c6HM* + H  [=] c6H* + CH3</equation>
       <rateCoeff>
         <Arrhenius>
-          <A>  3.000000E+10</A>
-          <b>0.0</b>
-          <E units="kcal/mol">0.000000</E>
+           <A>3.000000E+10</A>
+           <b>0.0</b>
+           <E units="kcal/mol">0.000000</E>
         </Arrhenius>
       </rateCoeff>
       <reactants>c6HM*:1 H:1</reactants>
       <products>c6H*:1 CH3:1</products>
     </reaction>
 
-    <!--   reaction 0010    -->
-    <reaction id="0010" reversible="yes" type="surface">
+    <!-- reaction 0010    -->
+    <reaction reversible="yes" type="surface" id="0010">
       <equation>c6HM* + H  [=] c6B + H2</equation>
       <rateCoeff>
         <Arrhenius>
-          <A>  1.300000E+11</A>
-          <b>0.0</b>
-          <E units="kcal/mol">7.300000</E>
+           <A>1.300000E+11</A>
+           <b>0.0</b>
+           <E units="kcal/mol">7.300000</E>
         </Arrhenius>
       </rateCoeff>
       <reactants>c6HM*:1 H:1</reactants>
       <products>H2:1 c6B:1</products>
     </reaction>
 
-    <!--   reaction 0011    -->
-    <reaction id="0011" reversible="yes" type="surface">
+    <!-- reaction 0011    -->
+    <reaction reversible="yes" type="surface" id="0011">
       <equation>c6*M + H   [=] c6B + H2</equation>
       <rateCoeff>
         <Arrhenius>
-          <A>  2.800000E+04</A>
-          <b>2.0</b>
-          <E units="kcal/mol">7.700000</E>
+           <A>2.800000E+04</A>
+           <b>2.0</b>
+           <E units="kcal/mol">7.700000</E>
         </Arrhenius>
       </rateCoeff>
       <reactants>H:1 c6*M:1</reactants>
       <products>H2:1 c6B:1</products>
     </reaction>
 
-    <!--   reaction 0012    -->
-    <reaction id="0012" reversible="yes" type="surface">
+    <!-- reaction 0012    -->
+    <reaction reversible="yes" type="surface" id="0012">
       <equation>c6HH + H   [=] c6*H + H2</equation>
       <rateCoeff>
         <Arrhenius>
-          <A>  1.300000E+11</A>
-          <b>0.0</b>
-          <E units="kcal/mol">7.300000</E>
+           <A>1.300000E+11</A>
+           <b>0.0</b>
+           <E units="kcal/mol">7.300000</E>
         </Arrhenius>
       </rateCoeff>
       <reactants>H:1 c6HH:1</reactants>
       <products>H2:1 c6*H:1</products>
     </reaction>
 
-    <!--   reaction 0013    -->
-    <reaction id="0013" reversible="yes" type="surface">
+    <!-- reaction 0013    -->
+    <reaction reversible="yes" type="surface" id="0013">
       <equation>c6*H + H   [=] c6HH</equation>
       <rateCoeff>
         <Arrhenius>
-          <A>  1.000000E+10</A>
-          <b>0.0</b>
-          <E units="kcal/mol">0.000000</E>
+           <A>1.000000E+10</A>
+           <b>0.0</b>
+           <E units="kcal/mol">0.000000</E>
         </Arrhenius>
       </rateCoeff>
       <reactants>c6*H:1 H:1</reactants>
       <products>c6HH:1</products>
     </reaction>
 
-    <!--   reaction 0014    -->
-    <reaction id="0014" reversible="yes" type="surface">
+    <!-- reaction 0014    -->
+    <reaction reversible="yes" type="surface" id="0014">
       <equation>c6H* + H   [=] c6** + H2</equation>
       <rateCoeff>
         <Arrhenius>
-          <A>  1.300000E+11</A>
-          <b>0.0</b>
-          <E units="kcal/mol">7.300000</E>
+           <A>1.300000E+11</A>
+           <b>0.0</b>
+           <E units="kcal/mol">7.300000</E>
         </Arrhenius>
       </rateCoeff>
       <reactants>c6H*:1 H:1</reactants>
       <products>H2:1 c6**:1</products>
     </reaction>
 
-    <!--   reaction 0015    -->
-    <reaction id="0015" reversible="yes" type="surface">
+    <!-- reaction 0015    -->
+    <reaction reversible="yes" type="surface" id="0015">
       <equation>c6** + H   [=] c6H*</equation>
       <rateCoeff>
         <Arrhenius>
-          <A>  1.000000E+10</A>
-          <b>0.0</b>
-          <E units="kcal/mol">0.000000</E>
+           <A>1.000000E+10</A>
+           <b>0.0</b>
+           <E units="kcal/mol">0.000000</E>
         </Arrhenius>
       </rateCoeff>
       <reactants>H:1 c6**:1</reactants>
       <products>c6H*:1</products>
     </reaction>
 
-    <!--   reaction 0016    -->
-    <reaction id="0016" reversible="yes" type="surface">
+    <!-- reaction 0016    -->
+    <reaction reversible="yes" type="surface" id="0016">
       <equation>c6*H + H   [=] c6** + H2</equation>
       <rateCoeff>
         <Arrhenius>
-          <A>  4.500000E+03</A>
-          <b>2.0</b>
-          <E units="kcal/mol">5.000000</E>
+           <A>4.500000E+03</A>
+           <b>2.0</b>
+           <E units="kcal/mol">5.000000</E>
         </Arrhenius>
       </rateCoeff>
       <reactants>c6*H:1 H:1</reactants>
       <products>H2:1 c6**:1</products>
     </reaction>
 
-    <!--   reaction 0017    -->
-    <reaction id="0017" reversible="yes" type="surface">
+    <!-- reaction 0017    -->
+    <reaction reversible="yes" type="surface" id="0017">
       <equation>c6** + H   [=] c6*H</equation>
       <rateCoeff>
         <Arrhenius>
-          <A>  1.000000E+10</A>
-          <b>0.0</b>
-          <E units="kcal/mol">0.000000</E>
+           <A>1.000000E+10</A>
+           <b>0.0</b>
+           <E units="kcal/mol">0.000000</E>
         </Arrhenius>
       </rateCoeff>
       <reactants>H:1 c6**:1</reactants>
       <products>c6*H:1</products>
     </reaction>
 
-    <!--   reaction 0018    -->
-    <reaction id="0018" reversible="yes" type="surface">
+    <!-- reaction 0018    -->
+    <reaction reversible="yes" type="surface" id="0018">
       <equation>c6** + CH3 [=] c6*M</equation>
       <rateCoeff>
         <Arrhenius>
-          <A>  5.000000E+09</A>
-          <b>0.0</b>
-          <E units="kcal/mol">0.000000</E>
+           <A>5.000000E+09</A>
+           <b>0.0</b>
+           <E units="kcal/mol">0.000000</E>
         </Arrhenius>
       </rateCoeff>
       <reactants>CH3:1 c6**:1</reactants>
       <products>c6*M:1</products>
     </reaction>
 
-    <!--   reaction 0019    -->
-    <reaction id="0019" reversible="yes" type="surface">
+    <!-- reaction 0019    -->
+    <reaction reversible="yes" type="surface" id="0019">
       <equation>c6H*       [=] c6*H</equation>
       <rateCoeff>
         <Arrhenius>
-          <A>  1.000000E+08</A>
-          <b>0.0</b>
-          <E units="kcal/mol">0.000000</E>
+           <A>1.000000E+08</A>
+           <b>0.0</b>
+           <E units="kcal/mol">0.000000</E>
         </Arrhenius>
       </rateCoeff>
       <reactants>c6H*:1</reactants>
       <products>c6*H:1</products>
     </reaction>
 
-    <!--   reaction 0020    -->
-    <reaction id="0020" reversible="yes" type="surface">
+    <!-- reaction 0020    -->
+    <reaction reversible="yes" type="surface" id="0020">
       <equation>c6B       [=] c6HH + C(d)</equation>
       <rateCoeff>
         <Arrhenius>
-          <A>  1.000000E+09</A>
-          <b>0.0</b>
-          <E units="kcal/mol">0.000000</E>
+           <A>1.000000E+09</A>
+           <b>0.0</b>
+           <E units="kcal/mol">0.000000</E>
         </Arrhenius>
       </rateCoeff>
       <reactants>c6B:1</reactants>