diff --git a/Cantera/README.txt b/Cantera/README.txt
new file mode 100644
index 000000000..06aaa8f6e
--- /dev/null
+++ b/Cantera/README.txt
@@ -0,0 +1,9 @@
+
+This directory contains the source for Cantera and its various language interfaces.
+
+clib    -  the library of C-callable functions used by the Python and Matlab interfaces.
+cxx     -  files that are only required for C++ application programs.
+matlab  -  the Cantera Matlab toolbox
+python  -  the Cantera Python package
+src     -  the Cantera kernel
+
diff --git a/Cantera/clib/README.txt b/Cantera/clib/README.txt
new file mode 100644
index 000000000..749a905c9
--- /dev/null
+++ b/Cantera/clib/README.txt
@@ -0,0 +1,5 @@
+
+This directory contains code that implements C-callable functions that
+can be used to create and use Cantera objects from languages other
+than C++. It is used by both the Python and Matlab interface packages.
+
diff --git a/Cantera/clib/src/ct.cpp b/Cantera/clib/src/ct.cpp
index ec1617df6..ae9f65d65 100755
--- a/Cantera/clib/src/ct.cpp
+++ b/Cantera/clib/src/ct.cpp
@@ -831,14 +831,15 @@ extern "C" {
 
     int DLL_EXPORT readlog(int n, char* buf) {
         string s;
-        getlog(s);
+        writelog("function readlog is deprecated!");
+        //getlog(s);
         int nlog = s.size();
         if (n < 0) return nlog; 
         int nn = min(n-1, nlog);
         copy(s.begin(), s.begin() + nn,
             buf);
         buf[min(nlog, n-1)] = '\0';
-        clearlog();
+        //clearlog();
         return 0;
 
     } 
diff --git a/Cantera/cxx/writelog.cpp b/Cantera/cxx/writelog.cpp
index 874d28f54..e51c8f6ab 100644
--- a/Cantera/cxx/writelog.cpp
+++ b/Cantera/cxx/writelog.cpp
@@ -3,7 +3,7 @@
 using namespace std;
 
 namespace Cantera {
- 
+
    void writelog(const string& s) {
         cout << s;
     }
diff --git a/Cantera/matlab/cantera/private/ctmethods.cpp b/Cantera/matlab/cantera/private/ctmethods.cpp
index 02399690b..40f17af8e 100644
--- a/Cantera/matlab/cantera/private/ctmethods.cpp
+++ b/Cantera/matlab/cantera/private/ctmethods.cpp
@@ -69,7 +69,7 @@ extern "C" {
         int iclass = getInt(prhs[0]);
         
         // specifies that function writelog should write to MATLAB
-        Cantera::setMatlabMode(true);
+        //Cantera::setMatlabMode(true);
 
         // Hand off to the appropriate routine, based on the
         // value of the first parameter
diff --git a/Cantera/python/Cantera/ctml_writer.py b/Cantera/python/Cantera/ctml_writer.py
index 9b09f3b4d..d73d316a4 100644
--- a/Cantera/python/Cantera/ctml_writer.py
+++ b/Cantera/python/Cantera/ctml_writer.py
@@ -1,8 +1,15 @@
-
 #
 # Cantera input file processor
 #
-
+# The functions and classes in this module process Cantera .cti input files and produce CTML files. #
+# usage:
+#
+# from Cantera import *
+# from Cantera.ctml_writer import *
+# execfile('infile.cti')
+# write()
+#
+from Cantera import CanteraError
 from Cantera import GasConstant
 from Cantera.XML import XML_Node
 import types, math
@@ -17,6 +24,12 @@ SKIP_UNDECLARED_ELEMENTS = 20
 SKIP_UNDECLARED_SPECIES = 30
 STOP = 0
 
+_EXCEPT = 10
+_WARN = 2
+_SKIP = 1
+_handle_undeclared_element = _EXCEPT
+_handle_undeclared_species = _EXCEPT
+
 # default units
 _ulen = 'm' 
 _umol = 'kmol'
@@ -30,18 +43,26 @@ _pref = 1.0e5    # 1 bar
 _name = 'noname'
 
 _species = []
+_speciesnames = []
 _phases = []
 _reactions = []
 _atw = {}
 _mw = {}
 
 def isnum(a):
+    """True if a is an integer or floating-point number."""
     if type(a) == types.IntType or type(a) == types.FloatType:
         return 1
     else:
         return 0
-    
+
+def is_local_species(name):
+    if name in _speciesnames:
+        return 1
+    return 0
+
 def dataset(nm):
+    "Set the dataset name"
     global _name
     _name = nm
 
@@ -49,6 +70,15 @@ def standard_pressure(p0):
     """Set the default standard-state pressure."""
     global _pref
     _pref = p0
+
+def on_error(undeclared_element = '', undeclared_species = ''):
+    global _handle_undeclared_species
+    global _handle_undeclared_element
+    
+    _handle_undeclared_species = undeclared_species
+    _handle_undeclared_element = undeclared_element
+            
+            
     
 def get_atomic_wts():
     global _atw
@@ -216,6 +246,8 @@ class species(writer):
         
         global _species
         _species.append(self)
+        global _speciesnames
+        _speciesnames.append(name)
         
 
     def build(self, p):
@@ -417,22 +449,13 @@ class reaction(writer):
             else:
                 nstr = `self._num`
             id = nstr
-        p.addComment("   reaction "+id+"    ")                
-        r = p.addChild('reaction')
-        r['id'] = id
-        if self.rev:
-            r['reversible'] = 'yes'
-        else:
-            r['reversible'] = 'no'
 
-        ee = self._e.replace('<','[')
-        ee = ee.replace('>',']')
-        r.addChild('equation',ee)
         
         mdim = 0
         ldim = 0
         str = ''
 
+            
         for s in self._r.keys():
             ns = self._r[s]
             nm = -999
@@ -446,12 +469,49 @@ class reaction(writer):
                     if ph.is_ideal_gas():
                         self._igspecies.append(s)
                     break
-            if nm < 0:
-                print self._r
-                raise 'undeclared species '+s
-            else:
-                mdim += nm*ns
-                ldim += nl*ns
+##             if nm < 0:
+##                 if _handle_undeclared_species == _WARN:
+##                     print 'Warning... skipping reaction '+self._e
+##                     print 'because species '+s+' is undeclared'
+##                 if _handle_undeclared_species <= _WARN:
+##                     return 0
+##                 else:
+##                     raise CanteraError('undeclared species '+s+' in reaction '+self._e)
+
+##             else:
+            mdim += nm*ns
+            ldim += nl*ns
+
+##         for s in self._p.keys():
+##             ns = self._p[s]
+##             ok = 0
+##             for ph in _phases:
+##                 if ph.has_species(s):
+##                     ok = 1
+##                     break
+                
+##             if not ok:
+##                 if _handle_undeclared_species == _WARN:
+##                     print 'Warning... skipping reaction '+self._e
+##                     print 'because species '+s+' is undeclared'
+##                 if _handle_undeclared_species <= _WARN:
+##                     return 0
+##                 else:
+##                     raise CanteraError('undeclared species '+s+' in reaction '+self._e)
+
+
+        p.addComment("   reaction "+id+"    ")                
+        r = p.addChild('reaction')
+        r['id'] = id
+        if self.rev:
+            r['reversible'] = 'yes'
+        else:
+            r['reversible'] = 'no'
+
+        ee = self._e.replace('<','[')
+        ee = ee.replace('>',']')
+        r.addChild('equation',ee)
+                
 
         # adjust the moles and length powers based on the dimensions of
         # the rate of progress (moles/length^2 or moles/length^3)
@@ -537,6 +597,7 @@ class three_body_reaction(reaction):
         
     def build(self, p):
         r = reaction.build(self, p)
+        if r == 0: return
         kfnode = r.child('rateCoeff')
         
         if self._eff:
@@ -591,7 +652,7 @@ class falloff_reaction(reaction):
         
     def build(self, p):
         r = reaction.build(self, p)
-
+        if r == 0: return
         kfnode = r.child('rateCoeff')
         
         if self._eff and self._effm >= 0.0:
@@ -748,6 +809,10 @@ class phase(writer):
             datasrc = r[0]
             ra = p.addChild('reactionArray')
             ra['datasrc'] = datasrc+'#reaction_data'
+            if _handle_undeclared_species == 'skip':
+                rk = ra.addChild('skip')
+                rk['species'] = 'undeclared'
+            
             rtoks = r[1].split()
             if rtoks[0] <> 'all':
                 i = ra.addChild('include')
@@ -770,10 +835,10 @@ class phase(writer):
             datasrc, names = s
             sa = ph.addChild('speciesArray',names)
             sa['datasrc'] = datasrc+'#species_data'
-            
-        if self._skip:
-            sk = sa.addChild('skip')
-            sk['element'] = 'undeclared'
+
+            if _handle_undeclared_element == 'skip':
+                sk = sa.addChild('skip')
+                sk['element'] = 'undeclared'
             
         if self._rxns <> 'none':
             self.buildrxns(ph)
diff --git a/Cantera/python/Cantera/exceptions.py b/Cantera/python/Cantera/exceptions.py
index d97b130cd..81db707f6 100755
--- a/Cantera/python/Cantera/exceptions.py
+++ b/Cantera/python/Cantera/exceptions.py
@@ -9,9 +9,9 @@ class CanteraError(Exception):
             msg = _cantera.get_Cantera_Error()
         self.msg = msg
     def __str__(self):
-        print '\n\n\n#############  CANTERA ERROR  ############\n'
+        print '\n\n\n#######################  CANTERA ERROR  ######################\n'
         print '    ',self.msg
-        print '\n##########################################\n'
+        print '\n##############################################################\n'
 
 
 class OptionError(CanteraError):
diff --git a/Cantera/python/src/writelog.cpp b/Cantera/python/src/writelog.cpp
index 5c36f3341..415a90579 100644
--- a/Cantera/python/src/writelog.cpp
+++ b/Cantera/python/src/writelog.cpp
@@ -2,7 +2,7 @@
 #include <string>
 using namespace std;
 
-static std::string ss = "print \"";
+static std::string ss = "print \"\"\" ";
 
 namespace Cantera {
 
@@ -11,9 +11,9 @@ namespace Cantera {
         int n = 0;
         while (ch != '\0') {
             if (ch =='\n') {
-                ss += "\"";
+                ss += "\"\"\"";
                 PyRun_SimpleString((char *)ss.c_str());            
-                ss = "print \"";
+                ss = "print \"\"\"";
             }
             else 
                 ss += ch;
diff --git a/Cantera/src/ChemEquil.h b/Cantera/src/ChemEquil.h
index b8087ca5b..3b02f6016 100755
--- a/Cantera/src/ChemEquil.h
+++ b/Cantera/src/ChemEquil.h
@@ -26,7 +26,7 @@ using namespace std;
 #include "ct_defs.h"
 #include "vec_functions.h"
 #include "ctexceptions.h"
-#include "Thermo.h"
+#include "ThermoPhase.h"
 #include "PropertyCalculator.h"
 #include "DenseMatrix.h"
 
diff --git a/Cantera/src/ConstDensityThermo.h b/Cantera/src/ConstDensityThermo.h
index 1438ee5e9..846687310 100755
--- a/Cantera/src/ConstDensityThermo.h
+++ b/Cantera/src/ConstDensityThermo.h
@@ -17,7 +17,7 @@
 
 #include "ct_defs.h"
 #include "mix_defs.h"
-#include "Thermo.h"
+#include "ThermoPhase.h"
 #include "SpeciesThermo.h"
 
 namespace Cantera {
diff --git a/Cantera/src/ct2ctml.cpp b/Cantera/src/ct2ctml.cpp
index 2a97448a3..e9a5682d5 100644
--- a/Cantera/src/ct2ctml.cpp
+++ b/Cantera/src/ct2ctml.cpp
@@ -39,20 +39,26 @@ namespace ctml {
         }
         f << "from Cantera import *\n";
         f.close();
+        int ierr = 0;
         string cmd = pypath() + " " + path + " &> " + tmpDir() + "/log";
-        int ierr = system(cmd.c_str());
-        if (ierr != 0) {
-            string msg;
-            msg = cmd + "\n\n########################################################################\n\n"
-                  "The Cantera Python interface is required in order to process\n"
-                  "Cantera input files, but it does not seem to be correctly installed.\n\n"
-                  "Check that you can invoke the Python interpreter with \n"
-                  "the command \"python\", and that typing \"from Cantera import *\"\n"
-                  "at the Python prompt does not produce an error. If Python on your system\n"
-                  "is invoked with some other command, set environment variable PYTHON_CMD\n"
-                  "to the full path to the Python interpreter. \n\n"
-                  "#########################################################################\n\n";
-            writelog(msg);
+        try {
+            ierr = system(cmd.c_str());
+            if (ierr != 0) {
+                string msg;
+                msg = cmd + "\n\n########################################################################\n\n"
+                      "The Cantera Python interface is required in order to process\n"
+                      "Cantera input files, but it does not seem to be correctly installed.\n\n"
+                      "Check that you can invoke the Python interpreter with \n"
+                      "the command \"python\", and that typing \"from Cantera import *\"\n"
+                      "at the Python prompt does not produce an error. If Python on your system\n"
+                      "is invoked with some other command, set environment variable PYTHON_CMD\n"
+                      "to the full path to the Python interpreter. \n\n"
+                      "#########################################################################\n\n";
+                writelog(msg);
+                return false;
+            }
+        }
+        catch (...) {
             return false;
         }
         return true;
@@ -76,19 +82,37 @@ namespace ctml {
           << "write()\n";
         f.close();
         string cmd = pypath() + " " + path + " &> ct2ctml.log";
-        int ierr = system(cmd.c_str());
-        if (ierr != 0) {
-            string msg = cmd;
+        int ierr;
+        try {
+            ierr = system(cmd.c_str());
+        }
+        catch (...) {
+            ierr = -10;
+        }
+        char line[90];
+        //if (ierr != 0) {
+        try {
+            char ch;
+            string s = "";
             ifstream ferr("ct2ctml.log");
             if (ferr) {
-                char line[80];
                 while (!ferr.eof()) {
                     //msg += "\n";
-                    ferr.getline(line, 80);
-                    writelog(string(line)+"\n");
+                    ferr.get(ch);
+                    s += ch;
+                    if (ch == '\n') {
+                        writelog(s);
+                        s = "";
+                    }
                 }
                 ferr.close();
             }
+        }
+        catch (...) {
+            ; //writelog("could not print error message.\n");
+        }
+        if (ierr != 0) {
+            string msg = cmd;
             bool pyok = checkPython();
             if (!pyok) 
                 msg += "\nError in Python installation.";
diff --git a/Cantera/src/ctml.cpp b/Cantera/src/ctml.cpp
index d4a97efe8..0c3b0434e 100755
--- a/Cantera/src/ctml.cpp
+++ b/Cantera/src/ctml.cpp
@@ -191,14 +191,14 @@ namespace ctml {
             if (vmin != "") {
                 x0 = atof(vmin.c_str());
                 if (x < x0 - Tiny) {
-                write("\nWarning: value "+fi()+" is below lower limit of "
+                writelog("\nWarning: value "+fi()+" is below lower limit of "
                     +vmin+".\n");
                 }
             }
             if (fi["max"] != "") {
                 x1 = atof(vmax.c_str());
                 if (x > x1 + Tiny) {
-                write("\nWarning: value "+fi()+" is above upper limit of "
+                writelog("\nWarning: value "+fi()+" is above upper limit of "
                     +vmax+".\n");
                 }
             }
@@ -232,14 +232,14 @@ namespace ctml {
         if (vmin != "") {
             x0 = atof(vmin.c_str());
             if (x < x0 - Tiny) {
-                write("\nWarning: value "+node()+" is below lower limit of "
+                writelog("\nWarning: value "+node()+" is below lower limit of "
                     +vmin+".\n");
                 }
             }
         if (node["max"] != "") {
             x1 = atof(vmax.c_str());
             if (x > x1 + Tiny) {
-                write("\nWarning: value "+node()+" is above upper limit of "
+                writelog("\nWarning: value "+node()+" is above upper limit of "
                     +vmax+".\n");
             }
         }
@@ -286,11 +286,11 @@ namespace ctml {
             }
             vv = v.back();
             if (vmin != Undef && vv < vmin - Tiny) {
-                write("\nWarning: value "+fp2str(vv)+
+                writelog("\nWarning: value "+fp2str(vv)+
                     " is below lower limit of " +fp2str(vmin)+".\n");
             }
             if (vmax != Undef && vv > vmax + Tiny) {
-                write("\nWarning: value "+fp2str(vv)+
+                writelog("\nWarning: value "+fp2str(vv)+
                     " is above upper limit of " +fp2str(vmin)+".\n");
             }
         }
diff --git a/Cantera/src/global.h b/Cantera/src/global.h
index c67c3ddce..5de4d01e8 100755
--- a/Cantera/src/global.h
+++ b/Cantera/src/global.h
@@ -1,5 +1,9 @@
 /**
  * @file global.h
+ *
+ * These functions handle various utility functions, and store some parameters in 
+ * global storage that are accessible at all times. 
+8
  */
 
 /* $Author$
@@ -17,7 +21,7 @@
 
 namespace Cantera {
 
-    /// Number of errors that have been encountered
+    /// Number of errors that have been encountered so far
     int nErrors();
 
     /// The last error message
@@ -26,7 +30,7 @@ namespace Cantera {
     /// Add an error message
     void setError(string r, string msg);
 
-    /// Print the error messages to f
+    /// Print the error messages to stream f
     void showErrors(ostream& f);
 
     /// Discard the last error message
@@ -38,26 +42,53 @@ namespace Cantera {
     /// Add a directory to the search path
     void addDirectory(string dir);
 
-    /// Write a message
-    void write(const string& msg);
+    // Write a message (deprecated; use writelog)
+    //void write(const string& msg);
 
-    ///  Write a message
-    void write(const char* msg);
+    //  Write a message (deprecated; use writelog)
+    //void write(const char* msg);
 
+    /// The root directory where Cantera is installed
     string canteraRoot();
 
+    /// Set the temporary file directory. Default: /tmp.
     void setTmpDir(string tmp);
+
+    /// The directory where temporary files may be created
     string tmpDir();
 
+
     /**
-     * Write a diagnostic message to an internal buffer.
-     */
+     * Write a diagnostic message to standard output.
+     *
+     * There are several versions of function writelog, each designed
+     * for a particular environment.  One version is designed for use
+     * in C++ programs, or in any environment where messages can be
+     * written to the standard output stream. Other versions are
+     * written specifically for Matlab and for Python, which call
+     * Matlab or Python functions, respectively, to display the
+     * message.  This is particularly important for Matlab, since
+     * everything written to the standard output simply
+     * disappears. For Python, the messages show up, but are not in
+     * the right order if Python scripts also print output. Hence the
+     * need for separate versions.
+     *
+     * The C++ version may be linked to an application by linking in
+     * the library libctcxx.a (-lctcxx). The Python and Matlab
+     * interfaces do not link this library, and instead link to their
+     * own versions of writelog.
+     */ 
+
     void writelog(const string& msg);
     void writelog(const char* msg);
 
     
-    void getlog(string& s);
-    void clearlog();
+    //void getlog(string& s);
+    //void clearlog();
+
+    /**
+     * Return the conversion factor to convert unit string 'unit' to SI units.
+     */ 
     doublereal toSI(string unit);
     doublereal actEnergyToSI(string unit);
     //
diff --git a/Cantera/src/misc.cpp b/Cantera/src/misc.cpp
index a1f86dbcd..8a724a28b 100755
--- a/Cantera/src/misc.cpp
+++ b/Cantera/src/misc.cpp
@@ -33,7 +33,7 @@ namespace Cantera {
     class Application {
     public:
         Application() : linelen(0), stop_on_error(false), 
-                        write_log_to_cout(true), matlab(false), tmp_dir("/tmp") {}
+                        tmp_dir("/tmp") {}
         virtual ~Application(){}
         vector<string> inputDirs;
         vector<string> errorMessage;
@@ -42,8 +42,8 @@ namespace Cantera {
         string msglog;
         size_t linelen;
         bool stop_on_error;
-        bool write_log_to_cout;
-        bool matlab;
+        //bool write_log_to_cout;
+        //bool matlab;
         map<string, string>     options;
         string tmp_dir;
     };
@@ -69,10 +69,10 @@ namespace Cantera {
         return __app;
     }
 
-    void setTmpDir(string tmp) { appinit();  __app->tmp_dir = tmp; }
-    string tmpDir() { appinit(); return __app->tmp_dir; }
+    void setTmpDir(string tmp) { app()->tmp_dir = tmp; }
+    string tmpDir() { appinit(); return app()->tmp_dir; }
 
-    int nErrors() {return __app->errorMessage.size();}
+    int nErrors() {return app()->errorMessage.size();}
 
     void popError() {
         appinit();
@@ -256,22 +256,23 @@ namespace Cantera {
         }
     }
 
-    void setMatlabMode(bool m) { 
-        appinit();
-        __app->matlab = m; 
-    }
+    //void setMatlabMode(bool m) { 
+    //    appinit();
+    //    __app->matlab = m; 
+    //}
+
+    //void write(const string& msg) {cout << msg;}
+    //void write(const char* msg) {cout << msg;}
 
-    void write(const string& msg) {cout << msg;}
-    void write(const char* msg) {cout << msg;}
     void writelog(const char* msg) {writelog(string(msg));}
-    void getlog(string& s) {
-        appinit();
-        s = __app->msglog;
-        //__app->msglog = "";
-    }
-    void clearlog() {
-        __app->msglog = "";
-    }
+    //void getlog(string& s) {
+    //    appinit();
+    //    s = __app->msglog;
+    //    //__app->msglog = "";
+    //}
+    //void clearlog() {
+    //    __app->msglog = "";
+    //}
 
     doublereal toSI(string unit) {
         doublereal f = Unit::units()->toSI(unit);