From a7e60c5e889d4ddb74b1c81b32580563e51c369c Mon Sep 17 00:00:00 2001
From: Dave Goodwin <dgg@caltech.edu>
Date: Fri, 4 May 2007 15:15:19 +0000
Subject: [PATCH] moved base files

---
 Cantera/src/{ => base}/Array.h         |   0
 Cantera/src/{ => base}/XML_Writer.h    |   0
 Cantera/src/{ => base}/config.h        |   4 +-
 Cantera/src/{ => base}/ct2ctml.cpp     |   0
 Cantera/src/{ => base}/ct_defs.h       |   0
 Cantera/src/{ => base}/ctexceptions.h  |   0
 Cantera/src/{ => base}/ctml.cpp        |   0
 Cantera/src/{ => base}/ctml.h          |   0
 Cantera/src/{ => base}/global.h        |  98 ++++++++++++++++++++
 Cantera/src/{ => base}/logger.h        |   0
 Cantera/src/{ => base}/misc.cpp        | 118 +++++++++++++++++++++++++
 Cantera/src/{ => base}/plots.cpp       |   0
 Cantera/src/{ => base}/plots.h         |   0
 Cantera/src/{ => base}/stringUtils.cpp |   0
 Cantera/src/{ => base}/stringUtils.h   |   0
 Cantera/src/{ => base}/units.h         |   0
 Cantera/src/{ => base}/utilities.h     |  36 ++++++++
 Cantera/src/{ => base}/vec_functions.h |   0
 Cantera/src/{ => base}/xml.cpp         |   0
 Cantera/src/{ => base}/xml.h           |   0
 20 files changed, 254 insertions(+), 2 deletions(-)
 rename Cantera/src/{ => base}/Array.h (100%)
 rename Cantera/src/{ => base}/XML_Writer.h (100%)
 rename Cantera/src/{ => base}/config.h (79%)
 rename Cantera/src/{ => base}/ct2ctml.cpp (100%)
 rename Cantera/src/{ => base}/ct_defs.h (100%)
 rename Cantera/src/{ => base}/ctexceptions.h (100%)
 rename Cantera/src/{ => base}/ctml.cpp (100%)
 rename Cantera/src/{ => base}/ctml.h (100%)
 rename Cantera/src/{ => base}/global.h (79%)
 rename Cantera/src/{ => base}/logger.h (100%)
 rename Cantera/src/{ => base}/misc.cpp (88%)
 rename Cantera/src/{ => base}/plots.cpp (100%)
 rename Cantera/src/{ => base}/plots.h (100%)
 rename Cantera/src/{ => base}/stringUtils.cpp (100%)
 rename Cantera/src/{ => base}/stringUtils.h (100%)
 rename Cantera/src/{ => base}/units.h (100%)
 rename Cantera/src/{ => base}/utilities.h (95%)
 rename Cantera/src/{ => base}/vec_functions.h (100%)
 rename Cantera/src/{ => base}/xml.cpp (100%)
 rename Cantera/src/{ => base}/xml.h (100%)

diff --git a/Cantera/src/Array.h b/Cantera/src/base/Array.h
similarity index 100%
rename from Cantera/src/Array.h
rename to Cantera/src/base/Array.h
diff --git a/Cantera/src/XML_Writer.h b/Cantera/src/base/XML_Writer.h
similarity index 100%
rename from Cantera/src/XML_Writer.h
rename to Cantera/src/base/XML_Writer.h
diff --git a/Cantera/src/config.h b/Cantera/src/base/config.h
similarity index 79%
rename from Cantera/src/config.h
rename to Cantera/src/base/config.h
index db96ab2c9..00042f57f 100755
--- a/Cantera/src/config.h
+++ b/Cantera/src/base/config.h
@@ -8,13 +8,13 @@
 #ifdef CANTERA_APP
 #include "../winconfig.h"
 #else
-#include "../../winconfig.h"
+#include "../../../winconfig.h"
 #endif
 #else
 #ifdef CANTERA_APP
 #include "../config.h"
 #else
-#include "../../config.h"
+#include "../../../config.h"
 #endif
 #endif
 #endif
diff --git a/Cantera/src/ct2ctml.cpp b/Cantera/src/base/ct2ctml.cpp
similarity index 100%
rename from Cantera/src/ct2ctml.cpp
rename to Cantera/src/base/ct2ctml.cpp
diff --git a/Cantera/src/ct_defs.h b/Cantera/src/base/ct_defs.h
similarity index 100%
rename from Cantera/src/ct_defs.h
rename to Cantera/src/base/ct_defs.h
diff --git a/Cantera/src/ctexceptions.h b/Cantera/src/base/ctexceptions.h
similarity index 100%
rename from Cantera/src/ctexceptions.h
rename to Cantera/src/base/ctexceptions.h
diff --git a/Cantera/src/ctml.cpp b/Cantera/src/base/ctml.cpp
similarity index 100%
rename from Cantera/src/ctml.cpp
rename to Cantera/src/base/ctml.cpp
diff --git a/Cantera/src/ctml.h b/Cantera/src/base/ctml.h
similarity index 100%
rename from Cantera/src/ctml.h
rename to Cantera/src/base/ctml.h
diff --git a/Cantera/src/global.h b/Cantera/src/base/global.h
similarity index 79%
rename from Cantera/src/global.h
rename to Cantera/src/base/global.h
index cf848b94d..f1c695769 100755
--- a/Cantera/src/global.h
+++ b/Cantera/src/base/global.h
@@ -452,6 +452,104 @@ namespace Cantera {
   inline void write_logfile(std::string file = "log.html") {}
 #endif
 
+
+  //! Search for an XML_Node either wiithin an existing XML tree structure, or in another file,
+  //! based on the file name or the XML id attribute.
+  /*!
+   * This routine will locate an XML node in either the input
+   * XML tree or in another input file specified by the file
+   * part of the file_ID string. Searches are based on the
+   * ID attribute of the XML element only.
+   *
+   * @param file_ID This is a concatenation of two strings seperated
+   *                by the "#" character. The string before the
+   *                pound character is the file name of an xml
+   *                file to carry out the search. The string after
+   *                the # character is the ID attribute 
+   *                of the xml element to search for. 
+   *                The string is interpreted as a file string if
+   *                no # character is in the string.
+   *
+   * @param root    If the file string is empty, searches for the
+   *                xml element with matching ID attribute are
+   *                carried out from this XML node.
+   *
+   * @return
+   *      This routine will process the XML file, creating an XML
+   *      tree structure. It returns a pointer to the top of the tree.
+   *
+   *
+   * For example,
+   * @code
+   *
+   * XML_Node* xn = get_XML_Node("phase", "gri30.xml#gri30_mix", 0);
+   *
+   * @endcode
+   *		  
+   * will search in the file gri30.xml for an XML element of the following form, where
+   * the XML element name, phase, is an optional hit:
+   * @verbatim
+          <phase id="gri30_mix>
+             . . .
+          </phase>
+   * @endverbatim
+   *
+   * It will return a pointer to an xml tree for the XML phase element.
+   *
+   * @ingroup inputfiles
+   */
+  XML_Node* get_XML_Node(const std::string& file_ID, XML_Node* root);
+  
+  //! Search for an XML node based on the XML element name, file name, or XML id attribute.
+  /**
+   * This routine will locate an XML node in either the input
+   * XML tree or in another input file specified by the file
+   * part of the file_ID string. Searches are based on the
+   * XML element name and the ID attribute of the XML element.
+   * An exact match of both is usually required. However, the
+   * ID attribute may be set to "", in which case the first
+   * xml element with the correct XML element name will be returned.
+   *
+   * @param nameTarget This is the XML element name to look for.
+   *                   
+   * @param file_ID This is a concatenation of two strings seperated
+   *                by the "#" character. The string before the
+   *                pound character is the file name of an xml
+   *                file to carry out the search. The string after
+   *                the # character is the ID attribute 
+   *                of the xml element to search for. 
+   *                The string is interpreted as a file string if
+   *                no # character is in the string.
+   *
+   * @param root    If the file string is empty, searches for the
+   *                xml element with matching ID attribute are
+   *                carried out from this XML node.
+   *
+   * @return
+   *      This routine will process the XML file, possibly creating an XML
+   *      tree structure. It returns a pointer to the XML node searched for.
+   *
+   * For example,
+   * @code
+   *
+   * XML_Node* xn = get_XML_NameID("phase", "gri30.xml#gri30_mix", 0);
+   *
+   * @endcode
+   *		  
+   * will search in the file gri30.xml for an XML element of the following form:
+   * @verbatim
+   *      <phase id="gri30_mix>
+   *         . . .
+   *      </phase>
+   * @endverbatim
+   *
+   * It will return a pointer to an xml tree for the XML phase element.
+   *
+   * @ingroup inputfiles
+   */
+  XML_Node* get_XML_NameID(const std::string& nameTarget,
+			   const std::string& file_ID, XML_Node* root);
+
 }
 
 #endif
diff --git a/Cantera/src/logger.h b/Cantera/src/base/logger.h
similarity index 100%
rename from Cantera/src/logger.h
rename to Cantera/src/base/logger.h
diff --git a/Cantera/src/misc.cpp b/Cantera/src/base/misc.cpp
similarity index 88%
rename from Cantera/src/misc.cpp
rename to Cantera/src/base/misc.cpp
index 77be5c3f9..8056d205e 100755
--- a/Cantera/src/misc.cpp
+++ b/Cantera/src/base/misc.cpp
@@ -24,9 +24,14 @@
 #include "units.h"
 #include "xml.h"
 #include "ctml.h"
+
+#define DGG_MOD
+#ifndef DGG_MOD
 #include "SpeciesThermoFactory.h"
 #include "ThermoFactory.h"
 #include "FalloffFactory.h"
+#endif
+
 #include "logger.h"
 
 #undef DEBUG_PATHS
@@ -178,10 +183,12 @@ namespace Cantera {
             delete s_app;
             s_app = 0;
         }
+#ifndef DGG_MOD
         SpeciesThermoFactory::deleteFactory();
         ThermoFactory::deleteFactory();
         FalloffFactory::deleteFalloffFactory();
         Unit::deleteUnit();
+#endif
     }
 
     Application* app() {
@@ -904,5 +911,116 @@ namespace Cantera {
     }
 
 #endif // WITH_HTML_LOGS
+
+
+
+  /*
+   * First we define a couple of typedefs that will
+   * be used throught this file
+   */
+  //! typedef for a pointer to an XML_Node
+  typedef const vector<XML_Node*>    nodeset_t;
+  //! typedef for an XML_Node
+  typedef XML_Node                   node_t;
+
+
+  /// split a string at a '#' sign. Used to separate a file name
+  /// from an id string.
+  static void split(const std::string& src, std::string& file, std::string& id) { 
+    string::size_type ipound = src.find('#');
+    if (ipound != string::npos) {
+      id = src.substr(ipound+1,src.size());
+      file = src.substr(0,ipound);
+    }
+    else {
+      id = "";
+      file = src;
+    }
+  }
+
+  /*
+   * This routine will locate an XML node in either the input
+   * XML tree or in another input file specified by the file
+   * part of the file_ID string. Searches are based on the
+   * ID attribute of the XML element only.
+   *
+   * param file_ID This is a concatenation of two strings seperated
+   *                by the "#" character. The string before the
+   *                pound character is the file name of an xml
+   *                file to carry out the search. The string after
+   *                the # character is the ID attribute 
+   *                of the xml element to search for. 
+   *                The string is interpreted as a file string if
+   *                no # character is in the string.
+   *
+   * param root    If the file string is empty, searches for the
+   *                xml element with matching ID attribute are
+   *                carried out from this XML node.
+   */
+  XML_Node* get_XML_Node(const std::string& file_ID, XML_Node* root) {
+    string fname, idstr;
+    XML_Node *db, *doc;
+    split(file_ID, fname, idstr);
+    if (fname == "") {
+      if (!root) throw CanteraError("get_XML_Node",
+				    "no file name given. file_ID = "+file_ID);
+      db = root->findID(idstr, 3);
+    } 
+    else {
+      doc = get_XML_File(fname);
+      if (!doc) throw CanteraError("get_XML_Node", 
+				   "get_XML_File failed trying to open "+fname);
+      db = doc->findID(idstr, 3);
+    }
+    if (!db) {
+      throw CanteraError("get_XML_Node", 
+			 "id tag '"+idstr+"' not found.");
+    }
+    return db;
+  }
+
+
+  /*
+   * This routine will locate an XML node in either the input
+   * XML tree or in another input file specified by the file
+   * part of the file_ID string. Searches are based on the
+   * XML element name and the ID attribute of the XML element.
+   * An exact match of both is usually required. However, the
+   * ID attribute may be set to "", in which case the first
+   * xml element with the correct element name will be returned.
+   *
+   * @param nameTarget This is the XML element name to look for.
+   *                   
+   * @param file_ID This is a concatenation of two strings seperated
+   *                by the "#" character. The string before the
+   *                pound character is the file name of an xml
+   *                file to carry out the search. The string after
+   *                the # character is the ID attribute 
+   *                of the xml element to search for. 
+   *                The string is interpreted as a file string if
+   *                no # character is in the string.
+   *
+   * @param root    If the file string is empty, searches for the
+   *                xml element with matching ID attribute are
+   *                carried out from this XML node.
+   */
+  XML_Node* get_XML_NameID(const std::string& nameTarget,
+			   const std::string& file_ID, 
+			   XML_Node* root) {
+    string fname, idTarget;
+    XML_Node *db, *doc;
+    split(file_ID, fname, idTarget);
+    if (fname == "") {
+      if (!root) return 0;
+      db = root->findNameID(nameTarget, idTarget);
+    } else {
+      doc = get_XML_File(fname);
+      if (!doc) return 0;
+      db = doc->findNameID(nameTarget, idTarget);
+    }
+    return db;
+  }
+
+
 }
 
diff --git a/Cantera/src/plots.cpp b/Cantera/src/base/plots.cpp
similarity index 100%
rename from Cantera/src/plots.cpp
rename to Cantera/src/base/plots.cpp
diff --git a/Cantera/src/plots.h b/Cantera/src/base/plots.h
similarity index 100%
rename from Cantera/src/plots.h
rename to Cantera/src/base/plots.h
diff --git a/Cantera/src/stringUtils.cpp b/Cantera/src/base/stringUtils.cpp
similarity index 100%
rename from Cantera/src/stringUtils.cpp
rename to Cantera/src/base/stringUtils.cpp
diff --git a/Cantera/src/stringUtils.h b/Cantera/src/base/stringUtils.h
similarity index 100%
rename from Cantera/src/stringUtils.h
rename to Cantera/src/base/stringUtils.h
diff --git a/Cantera/src/units.h b/Cantera/src/base/units.h
similarity index 100%
rename from Cantera/src/units.h
rename to Cantera/src/base/units.h
diff --git a/Cantera/src/utilities.h b/Cantera/src/base/utilities.h
similarity index 95%
rename from Cantera/src/utilities.h
rename to Cantera/src/base/utilities.h
index fdbd81329..815c22d94 100755
--- a/Cantera/src/utilities.h
+++ b/Cantera/src/base/utilities.h
@@ -563,6 +563,42 @@ namespace Cantera {
   
   //@}
 
+    template<class D, class R>
+    R poly6(D x, R* c) {
+        return ((((((c[6]*x + c[5])*x + c[4])*x + c[3])*x + 
+                     c[2])*x + c[1])*x + c[0]);
+    }
+
+    template<class D, class R>
+    R poly8(D x, R* c) {
+        return ((((((((c[8]*x + c[7])*x + c[6])*x + c[5])*x + c[4])*x + c[3])*x + 
+                     c[2])*x + c[1])*x + c[0]);
+    }
+
+    template<class D, class R>
+    R poly10(D x, R* c) {
+        return ((((((((((c[10]*x + c[9])*x + c[8])*x + c[7])*x 
+                         + c[6])*x + c[5])*x + c[4])*x + c[3])*x 
+                     + c[2])*x + c[1])*x + c[0]);
+    }
+    
+    template<class D, class R>
+    R poly5(D x, R* c) {
+        return (((((c[5]*x + c[4])*x + c[3])*x + 
+                     c[2])*x + c[1])*x + c[0]);
+    }
+    
+    template<class D, class R>
+    R poly4(D x, R* c) {
+        return ((((c[4]*x + c[3])*x + 
+                     c[2])*x + c[1])*x + c[0]);
+    }
+    
+    template<class D, class R>
+    R poly3(D x, R* c) {
+        return (((c[3]*x + c[2])*x + c[1])*x + c[0]);
+    }
+
 }
 
 
diff --git a/Cantera/src/vec_functions.h b/Cantera/src/base/vec_functions.h
similarity index 100%
rename from Cantera/src/vec_functions.h
rename to Cantera/src/base/vec_functions.h
diff --git a/Cantera/src/xml.cpp b/Cantera/src/base/xml.cpp
similarity index 100%
rename from Cantera/src/xml.cpp
rename to Cantera/src/base/xml.cpp
diff --git a/Cantera/src/xml.h b/Cantera/src/base/xml.h
similarity index 100%
rename from Cantera/src/xml.h
rename to Cantera/src/base/xml.h