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From scnakand...@apache.org
Subject [22/32] airavata-sandbox git commit: adding datacat system
Date Mon, 24 Aug 2015 19:29:00 GMT
http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/4231ac35/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/g1/G1Parser.java
----------------------------------------------------------------------
diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/g1/G1Parser.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/g1/G1Parser.java
new file mode 100644
index 0000000..9450ea9
--- /dev/null
+++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/g1/G1Parser.java
@@ -0,0 +1,539 @@
+/*
+*
+* Licensed to the Apache Software Foundation (ASF) under one
+* or more contributor license agreements.  See the NOTICE file
+* distributed with this work for additional information
+* regarding copyright ownership.  The ASF licenses this file
+* to you under the Apache License, Version 2.0 (the
+* "License"); you may not use this file except in compliance
+* with the License.  You may obtain a copy of the License at
+*
+*   http://www.apache.org/licenses/LICENSE-2.0
+*
+* Unless required by applicable law or agreed to in writing,
+* software distributed under the License is distributed on an
+* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+* KIND, either express or implied.  See the License for the
+* specific language governing permissions and limitations
+* under the License.
+*
+*/
+package org.apache.airavata.datacat.parsers.gridchem.g1;
+
+import java_cup.runtime.lr_parser;
+import org.apache.airavata.datacat.parsers.gridchem.GridChemQueueParser;
+
+import javax.swing.*;
+import java.io.FileReader;
+import java.util.ArrayList;
+import java.util.HashMap;
+
+
+public class G1Parser extends java_cup.runtime.lr_parser implements GridChemQueueParser {
+
+  /** Default constructor. */
+  public G1Parser() {super();}
+
+  /** Constructor which sets the default scanner. */
+  public G1Parser(java_cup.runtime.Scanner s) {super(s);}
+
+    /**
+     * Constructor which uses a file reader.
+     */
+    public G1Parser(final FileReader fileReader) {
+        super(new G1Lexer(fileReader));
+    }
+
+  /** Production table. */
+  protected static final short _production_table[][] = 
+    lr_parser.unpackFromStrings(new String[]{
+            "\000\025\000\002\003\007\000\002\002\004\000\002\004" +
+                    "\003\000\002\005\004\000\002\005\003\000\002\021\002" +
+                    "\000\002\006\006\000\002\022\002\000\002\007\007\000" +
+                    "\002\010\004\000\002\011\004\000\002\012\004\000\002" +
+                    "\013\003\000\002\014\004\000\002\014\003\000\002\023" +
+                    "\002\000\002\016\006\000\002\024\002\000\002\015\007" +
+                    "\000\002\017\004\000\002\020\004"});
+
+  /** Access to production table. */
+  public short[][] production_table() {return _production_table;}
+
+  /** Parse-action table. */
+  protected static final short[][] _action_table = 
+    lr_parser.unpackFromStrings(new String[]{
+            "\000\052\000\004\004\005\001\002\000\004\007\012\001" +
+                    "\002\000\004\007\uffff\001\002\000\004\002\007\001\002" +
+                    "\000\004\002\000\001\002\000\006\005\027\007\012\001" +
+                    "\002\000\006\005\ufffd\007\ufffd\001\002\000\004\022\013" +
+                    "\001\002\000\004\006\ufffc\001\002\000\004\006\016\001" +
+                    "\002\000\006\005\ufffb\007\ufffb\001\002\000\004\020\017" +
+                    "\001\002\000\004\010\ufffa\001\002\000\004\010\022\001" +
+                    "\002\000\004\011\024\001\002\000\004\023\023\001\002" +
+                    "\000\004\011\ufff8\001\002\000\004\024\026\001\002\000" +
+                    "\006\005\ufff9\007\ufff9\001\002\000\006\005\ufff7\007\ufff7" +
+                    "\001\002\000\004\012\031\001\002\000\006\005\ufffe\007" +
+                    "\ufffe\001\002\000\004\014\ufff5\001\002\000\004\017\054" +
+                    "\001\002\000\004\014\035\001\002\000\006\014\035\017" +
+                    "\ufff6\001\002\000\004\025\037\001\002\000\006\014\ufff3" +
+                    "\017\ufff3\001\002\000\004\013\ufff2\001\002\000\004\013" +
+                    "\041\001\002\000\004\021\043\001\002\000\006\014\ufff1" +
+                    "\017\ufff1\001\002\000\004\015\ufff0\001\002\000\004\015" +
+                    "\046\001\002\000\004\016\051\001\002\000\004\026\047" +
+                    "\001\002\000\004\016\uffee\001\002\000\006\014\uffef\017" +
+                    "\uffef\001\002\000\004\027\052\001\002\000\006\014\uffed" +
+                    "\017\uffed\001\002\000\006\014\ufff4\017\ufff4\001\002\000" +
+                    "\004\002\001\001\002"});
+
+  /** Access to parse-action table. */
+  public short[][] action_table() {return _action_table;}
+
+  /** <code>reduce_goto</code> table. */
+  protected static final short[][] _reduce_table = 
+    lr_parser.unpackFromStrings(new String[]{
+            "\000\052\000\006\003\005\004\003\001\001\000\006\005" +
+                    "\007\006\010\001\001\000\002\001\001\000\002\001\001" +
+                    "\000\002\001\001\000\004\006\027\001\001\000\002\001" +
+                    "\001\000\002\001\001\000\004\021\013\001\001\000\004" +
+                    "\007\014\001\001\000\002\001\001\000\002\001\001\000" +
+                    "\004\022\017\001\001\000\004\010\020\001\001\000\004" +
+                    "\011\024\001\001\000\002\001\001\000\002\001\001\000" +
+                    "\002\001\001\000\002\001\001\000\002\001\001\000\006" +
+                    "\012\031\013\032\001\001\000\002\001\001\000\002\001" +
+                    "\001\000\002\001\001\000\006\014\033\016\035\001\001" +
+                    "\000\004\016\052\001\001\000\002\001\001\000\002\001" +
+                    "\001\000\004\023\037\001\001\000\004\015\041\001\001" +
+                    "\000\002\001\001\000\002\001\001\000\004\024\043\001" +
+                    "\001\000\004\017\044\001\001\000\004\020\047\001\001" +
+                    "\000\002\001\001\000\002\001\001\000\002\001\001\000" +
+                    "\002\001\001\000\002\001\001\000\002\001\001\000\002" +
+                    "\001\001"});
+
+  /** Access to <code>reduce_goto</code> table. */
+  public short[][] reduce_table() {return _reduce_table;}
+
+  /** Instance of action encapsulation class. */
+  protected CUP$parser$actions action_obj;
+
+    //Each string is of the format
+    //rmsForce, maximum force, iteration and energy
+    private ArrayList<String> result = new ArrayList<String>();
+    private String tempStr = "";
+
+
+    public ArrayList<String> getResult() {
+        return result;
+    }
+
+
+    public void addToResult(String value) {
+        result.add(value);
+    }
+
+    public String getTempStr() {
+        return tempStr;
+    }
+
+    public void setTempStr(String s) {
+        this.tempStr = s;
+    }
+
+    /*Adding the parsed data to the hash map */
+    @Override
+    public HashMap<String, String> getParsedData() throws Exception {
+        parse();
+        HashMap<String,String> results= new HashMap<String,String>();
+        int mpRMSForceCount=0;
+        int mpMaximumForceCount=0;
+        int mpIterationCount=0;
+        int energyCount=0;
+        int rmsForceCount=0;
+        int maximumForceCount=0;
+        int iterationCount=0;
+        for(int i=0;i<result.size();i++){
+            String singleString= result.get(i);
+            String[] temp = singleString.split(" ");
+            String secondElement=temp[1];
+            String thirdElement=temp[2];
+            if(thirdElement.equals("RMS")){
+                results.put("G1_Mp_RMS_Force_"+mpRMSForceCount,temp[4]);
+                mpRMSForceCount++;
+            }else if (thirdElement.equals("Maximum")){
+                results.put("G1_MP_Maximum_Force_"+mpMaximumForceCount,temp[4]);
+                mpMaximumForceCount++;
+            }else if (temp[3].equals("ITERATION")&&temp[2].equals("MP")){
+                results.put("G1_MP_Iteration_"+mpIterationCount,temp[3]);
+                mpIterationCount++;
+            }else if(thirdElement.equals("ENERGY")){
+                results.put("G1_Energy_"+energyCount,temp[3]);
+                energyCount++;
+            }else if(secondElement.equals("RMS")){
+                results.put("G1_RMS_Force"+rmsForceCount,temp[3]);
+                rmsForceCount++;
+            }else if(secondElement.equals("Maximum")){
+                results.put("G1_Maximum_Force"+maximumForceCount,temp[3]);
+                maximumForceCount++;
+            }else if(thirdElement.equals("ITERATION")){
+                results.put("G1_Iteration_"+iterationCount,temp[3]);
+                iterationCount++;
+            }
+        }
+
+        return results;
+    }
+
+  /** Action encapsulation object initializer. */
+  protected void init_actions()
+    {
+      action_obj = new CUP$parser$actions(this);
+    }
+
+  /** Invoke a user supplied parse action. */
+  public java_cup.runtime.Symbol do_action(
+    int                        act_num,
+    java_cup.runtime.lr_parser parser,
+    java.util.Stack            stack,
+    int                        top)
+    throws java.lang.Exception
+  {
+    /* call code in generated class */
+    return action_obj.CUP$parser$do_action(act_num, parser, stack, top);
+  }
+
+  /** Indicates start state. */
+  public int start_state() {return 0;}
+  /** Indicates start production. */
+  public int start_production() {return 1;}
+
+  /** <code>EOF</code> Symbol index. */
+  public int EOF_sym() {return 0;}
+
+  /** <code>error</code> Symbol index. */
+  public int error_sym() {return 1;}
+
+
+}
+
+/** Cup generated class to encapsulate user supplied action code.*/
+class CUP$parser$actions {
+
+ 
+  //__________________________________
+  public static boolean DEBUG = true;
+  private static JTable table;               
+  private static final String tableLabel = "SCF Intermediate Results:";
+// private static String cycle = "0";
+ 
+  
+  public static JTable getTable() {
+    return table;
+  }
+
+  public static String getTableLabel() {
+    return tableLabel;
+  }
+
+//   }
+
+  private final G1Parser G1Parser;
+
+  /** Constructor */
+  CUP$parser$actions(G1Parser G1Parser) {
+    this.G1Parser = G1Parser;
+  }
+
+  /** Method with the actual generated action code. */
+  public final java_cup.runtime.Symbol CUP$parser$do_action(
+    int                        CUP$parser$act_num,
+    java_cup.runtime.lr_parser CUP$parser$parser,
+    java.util.Stack            CUP$parser$stack,
+    int                        CUP$parser$top)
+    throws java.lang.Exception
+    {
+      /* Symbol object for return from actions */
+      java_cup.runtime.Symbol CUP$parser$result;
+
+      /* select the action based on the action number */
+      switch (CUP$parser$act_num)
+        {
+          /*. . . . . . . . . . . . . . . . . . . .*/
+          case 20: // force2 ::= MPRms MPRGRAD 
+            {
+              Object RESULT = null;
+		int mprgleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left;
+		int mprgright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right;
+		Float mprg = (Float)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-0)).value;
+		 //___________________________________________________________________
+   if (DEBUG) System.out.println("CUP:g1: MP RMS Force "+mprg);
+   G1Parser.addToResult("CUP:g1: MP RMS Force "+mprg);
+ 
+              CUP$parser$result = new java_cup.runtime.Symbol(14/*force2*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-1)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT);
+            }
+          return CUP$parser$result;
+
+          /*. . . . . . . . . . . . . . . . . . . .*/
+          case 19: // force1 ::= MPMax MPMGRAD 
+            {
+              Object RESULT = null;
+		int mpmgleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left;
+		int mpmgright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right;
+		Float mpmg = (Float)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-0)).value;
+		 //___________________________________________________________________
+   if (DEBUG) System.out.println("CUP:g1: MP Maximum Force "+mpmg);
+   G1Parser.addToResult("CUP:g1: MP Maximum Force "+mpmg);
+ 
+              CUP$parser$result = new java_cup.runtime.Symbol(13/*force1*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-1)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT);
+            }
+          return CUP$parser$result;
+
+          /*. . . . . . . . . . . . . . . . . . . .*/
+          case 18: // mpcycle ::= NMP MPITER NT$3 force1 force2 
+            {
+              Object RESULT = null;
+              // propagate RESULT from NT$3
+              if ( ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-2)).value != null )
+                RESULT = (Object) ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-2)).value;
+		int itleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-3)).left;
+		int itright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-3)).right;
+		Integer it = (Integer)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-3)).value;
+
+              CUP$parser$result = new java_cup.runtime.Symbol(11/*mpcycle*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-4)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT);
+            }
+          return CUP$parser$result;
+
+          /*. . . . . . . . . . . . . . . . . . . .*/
+          case 17: // NT$3 ::= 
+            {
+              Object RESULT = null;
+		int itleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left;
+		int itright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right;
+		Integer it = (Integer)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-0)).value;
+ //___________________________________________________________________
+   if (DEBUG) System.out.println("CUP:g1:  MP ITERATION "+it);
+   G1Parser.addToResult("CUP:g1:  MP ITERATION "+it);
+ 
+              CUP$parser$result = new java_cup.runtime.Symbol(18/*NT$3*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT);
+            }
+          return CUP$parser$result;
+
+          /*. . . . . . . . . . . . . . . . . . . .*/
+          case 16: // mpcycle1 ::= MPEnerg MPENERGY NT$2 mpcycle 
+            {
+              Object RESULT = null;
+              // propagate RESULT from NT$2
+              if ( ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-1)).value != null )
+                RESULT = (Object) ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-1)).value;
+		int mpenleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-2)).left;
+		int mpenright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-2)).right;
+		Float mpen = (Float)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-2)).value;
+
+              CUP$parser$result = new java_cup.runtime.Symbol(12/*mpcycle1*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-3)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT);
+            }
+          return CUP$parser$result;
+
+          /*. . . . . . . . . . . . . . . . . . . .*/
+          case 15: // NT$2 ::= 
+            {
+              Object RESULT = null;
+		int mpenleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left;
+		int mpenright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right;
+		Float mpen = (Float)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-0)).value;
+ //___________________________________________________________________
+   if (DEBUG) System.out.println("CUP:g1:  ENERGY "+mpen);
+   G1Parser.addToResult("CUP:g1:  ENERGY "+mpen);
+ 
+              CUP$parser$result = new java_cup.runtime.Symbol(17/*NT$2*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT);
+            }
+          return CUP$parser$result;
+
+          /*. . . . . . . . . . . . . . . . . . . .*/
+          case 14: // mppat ::= mpcycle1 
+            {
+              Object RESULT = null;
+
+              CUP$parser$result = new java_cup.runtime.Symbol(10/*mppat*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT);
+            }
+          return CUP$parser$result;
+
+          /*. . . . . . . . . . . . . . . . . . . .*/
+          case 13: // mppat ::= mppat mpcycle1 
+            {
+              Object RESULT = null;
+		
+  if (DEBUG) System.out.println("CUP:g1: in mppat");
+ 
+              CUP$parser$result = new java_cup.runtime.Symbol(10/*mppat*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-1)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT);
+            }
+          return CUP$parser$result;
+
+          /*. . . . . . . . . . . . . . . . . . . .*/
+          case 12: // mpintro ::= MPStart 
+            {
+              Object RESULT = null;
+		
+   if (DEBUG) System.out.println("CUP:g1: MPSTart ");
+ 
+              CUP$parser$result = new java_cup.runtime.Symbol(9/*mpintro*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT);
+            }
+          return CUP$parser$result;
+
+          /*. . . . . . . . . . . . . . . . . . . .*/
+          case 11: // mp2 ::= mpintro mppat 
+            {
+              Object RESULT = null;
+		
+    if (DEBUG) System.out.println("CUP:g1: in mp2 mpintro mppat");
+ 
+              CUP$parser$result = new java_cup.runtime.Symbol(8/*mp2*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-1)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT);
+            }
+          return CUP$parser$result;
+
+          /*. . . . . . . . . . . . . . . . . . . .*/
+          case 10: // grad2 ::= RmsGrad1 RGRAD1 
+            {
+              Object RESULT = null;
+		int rgleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left;
+		int rgright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right;
+		Float rg = (Float)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-0)).value;
+		 //___________________________________________________________________
+   if (DEBUG) System.out.println("CUP:gopt: RMS Force "+rg);
+   G1Parser.addToResult("CUP:gopt: RMS Force "+rg);
+ 
+              CUP$parser$result = new java_cup.runtime.Symbol(7/*grad2*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-1)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT);
+            }
+          return CUP$parser$result;
+
+          /*. . . . . . . . . . . . . . . . . . . .*/
+          case 9: // grad1 ::= MaxGrad1 MGRAD1 
+            {
+              Object RESULT = null;
+		int mgleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left;
+		int mgright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right;
+		Float mg = (Float)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-0)).value;
+		 //___________________________________________________________________
+   if (DEBUG) System.out.println("CUP:gopt: Maximum Force "+mg);
+   G1Parser.addToResult("CUP:gopt: Maximum Force "+mg);
+ 
+              CUP$parser$result = new java_cup.runtime.Symbol(6/*grad1*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-1)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT);
+            }
+          return CUP$parser$result;
+
+          /*. . . . . . . . . . . . . . . . . . . .*/
+          case 8: // cycle ::= NSearch1 ITERATION1 NT$1 grad1 grad2 
+            {
+              Object RESULT = null;
+              // propagate RESULT from NT$1
+              if ( ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-2)).value != null )
+                RESULT = (Object) ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-2)).value;
+		int cleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-3)).left;
+		int cright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-3)).right;
+		Integer c = (Integer)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-3)).value;
+
+              CUP$parser$result = new java_cup.runtime.Symbol(5/*cycle*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-4)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT);
+            }
+          return CUP$parser$result;
+
+          /*. . . . . . . . . . . . . . . . . . . .*/
+          case 7: // NT$1 ::= 
+            {
+              Object RESULT = null;
+		int cleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left;
+		int cright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right;
+		Integer c = (Integer)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-0)).value;
+ //___________________________________________________________________
+   if (DEBUG) System.out.println("CUP:gopt:  ITERATION "+c);
+   G1Parser.addToResult("CUP:gopt:  ITERATION "+c);
+ 
+              CUP$parser$result = new java_cup.runtime.Symbol(16/*NT$1*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT);
+            }
+          return CUP$parser$result;
+
+          /*. . . . . . . . . . . . . . . . . . . .*/
+          case 6: // scfcycle ::= Energ1 ENERGY1 NT$0 cycle 
+            {
+              Object RESULT = null;
+              // propagate RESULT from NT$0
+              if ( ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-1)).value != null )
+                RESULT = (Object) ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-1)).value;
+		int eleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-2)).left;
+		int eright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-2)).right;
+		Float e = (Float)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-2)).value;
+
+              CUP$parser$result = new java_cup.runtime.Symbol(4/*scfcycle*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-3)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT);
+            }
+          return CUP$parser$result;
+
+          /*. . . . . . . . . . . . . . . . . . . .*/
+          case 5: // NT$0 ::= 
+            {
+              Object RESULT = null;
+		int eleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left;
+		int eright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right;
+		Float e = (Float)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-0)).value;
+ //___________________________________________________________________
+   if (DEBUG) System.out.println("CUP:gopt:  ENERGY "+e);
+   G1Parser.addToResult("CUP:gopt:  ENERGY "+e);
+ 
+              CUP$parser$result = new java_cup.runtime.Symbol(15/*NT$0*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT);
+            }
+          return CUP$parser$result;
+
+          /*. . . . . . . . . . . . . . . . . . . .*/
+          case 4: // scfpat ::= scfcycle 
+            {
+              Object RESULT = null;
+
+              CUP$parser$result = new java_cup.runtime.Symbol(3/*scfpat*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT);
+            }
+          return CUP$parser$result;
+
+          /*. . . . . . . . . . . . . . . . . . . .*/
+          case 3: // scfpat ::= scfpat scfcycle 
+            {
+              Object RESULT = null;
+		 if (DEBUG) System.out.println("CUP:gopt: in scfpat"); 
+              CUP$parser$result = new java_cup.runtime.Symbol(3/*scfpat*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-1)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT);
+            }
+          return CUP$parser$result;
+
+          /*. . . . . . . . . . . . . . . . . . . .*/
+          case 2: // scfintro ::= FOUNDITER1 
+            {
+              Object RESULT = null;
+		 if (DEBUG) System.out.println("CUP:gopt:  found the start of Iteration"); 
+              CUP$parser$result = new java_cup.runtime.Symbol(2/*scfintro*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT);
+            }
+          return CUP$parser$result;
+
+          /*. . . . . . . . . . . . . . . . . . . .*/
+          case 1: // $START ::= startpt EOF 
+            {
+              Object RESULT = null;
+		int start_valleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-1)).left;
+		int start_valright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-1)).right;
+		Object start_val = (Object)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-1)).value;
+		RESULT = start_val;
+              CUP$parser$result = new java_cup.runtime.Symbol(0/*$START*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-1)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT);
+            }
+          /* ACCEPT */
+          CUP$parser$parser.done_parsing();
+          return CUP$parser$result;
+
+          /*. . . . . . . . . . . . . . . . . . . .*/
+          case 0: // startpt ::= scfintro scfpat SCFDONE1 mp2 MPDONE 
+            {
+              Object RESULT = null;
+		 if (DEBUG) System.out.println("CUP:gopt:  end of parse tree "); 
+ 	     
+              CUP$parser$result = new java_cup.runtime.Symbol(1/*startpt*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-4)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT);
+            }
+          return CUP$parser$result;
+
+          /* . . . . . .*/
+          default:
+            throw new Exception(
+               "Invalid action number found in internal parse table");
+
+        }
+    }
+}
+

http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/4231ac35/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/g1/G1Sym.java
----------------------------------------------------------------------
diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/g1/G1Sym.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/g1/G1Sym.java
new file mode 100644
index 0000000..f0e5e06
--- /dev/null
+++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/g1/G1Sym.java
@@ -0,0 +1,54 @@
+
+/*
+*
+* Licensed to the Apache Software Foundation (ASF) under one
+* or more contributor license agreements.  See the NOTICE file
+* distributed with this work for additional information
+* regarding copyright ownership.  The ASF licenses this file
+* to you under the Apache License, Version 2.0 (the
+* "License"); you may not use this file except in compliance
+* with the License.  You may obtain a copy of the License at
+*
+*   http://www.apache.org/licenses/LICENSE-2.0
+*
+* Unless required by applicable law or agreed to in writing,
+* software distributed under the License is distributed on an
+* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+* KIND, either express or implied.  See the License for the
+* specific language governing permissions and limitations
+* under the License.
+*
+*/
+package org.apache.airavata.datacat.parsers.gridchem.g1;
+//----------------------------------------------------
+// The following code was generated by CUP v0.10k
+// Wed Sep 10 08:33:37 IST 2014
+//----------------------------------------------------
+
+/** CUP generated class containing symbol constants. */
+public class G1Sym {
+  /* terminals */
+  public static final int ENERGY1 = 16;
+  public static final int MPMGRAD = 20;
+  public static final int MGRAD1 = 17;
+  public static final int MaxGrad1 = 6;
+  public static final int NSearch1 = 4;
+  public static final int MPRGRAD = 21;
+  public static final int MPRms = 12;
+  public static final int RmsGrad1 = 7;
+  public static final int MPMax = 11;
+  public static final int MPDONE = 13;
+  public static final int EOF = 0;
+  public static final int MPENERGY = 19;
+  public static final int ITERATION1 = 14;
+  public static final int NMP = 9;
+  public static final int MPEnerg = 10;
+  public static final int error = 1;
+  public static final int MPITER = 15;
+  public static final int MPStart = 8;
+  public static final int FOUNDITER1 = 2;
+  public static final int Energ1 = 5;
+  public static final int SCFDONE1 = 3;
+  public static final int RGRAD1 = 18;
+}
+

http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/4231ac35/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/gaussian/GaussianLexer.java
----------------------------------------------------------------------
diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/gaussian/GaussianLexer.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/gaussian/GaussianLexer.java
new file mode 100644
index 0000000..9801a99
--- /dev/null
+++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/gaussian/GaussianLexer.java
@@ -0,0 +1,864 @@
+/*
+*
+* Licensed to the Apache Software Foundation (ASF) under one
+* or more contributor license agreements.  See the NOTICE file
+* distributed with this work for additional information
+* regarding copyright ownership.  The ASF licenses this file
+* to you under the Apache License, Version 2.0 (the
+* "License"); you may not use this file except in compliance
+* with the License.  You may obtain a copy of the License at
+*
+*   http://www.apache.org/licenses/LICENSE-2.0
+*
+* Unless required by applicable law or agreed to in writing,
+* software distributed under the License is distributed on an
+* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+* KIND, either express or implied.  See the License for the
+* specific language governing permissions and limitations
+* under the License.
+*
+*/
+package org.apache.airavata.datacat.parsers.gridchem.gaussian;/* The following code was generated by JFlex 1.4.3 on 9/10/14 9:00 AM */
+
+import java_cup.runtime.Symbol;
+import org.apache.airavata.datacat.parsers.gridchem.Settings;
+
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.PrintStream;
+
+
+/**
+ * This class is a scanner generated by 
+ * <a href="http://www.jflex.de/">JFlex</a> 1.4.3
+ * on 9/10/14 9:00 AM from the specification file
+ * <tt>gaussian.flex</tt>
+ */
+public class GaussianLexer implements java_cup.runtime.Scanner {
+
+  /** This character denotes the end of file */
+  public static final int YYEOF = -1;
+
+  /** initial size of the lookahead buffer */
+  private static final int ZZ_BUFFERSIZE = 16384;
+
+  /** lexical states */
+  public static final int IGNOREALL = 6;
+  public static final int ITER1 = 4;
+  public static final int YYINITIAL = 0;
+  public static final int ITER = 2;
+
+  /**
+   * ZZ_LEXSTATE[l] is the state in the DFA for the lexical state l
+   * ZZ_LEXSTATE[l+1] is the state in the DFA for the lexical state l
+   *                  at the beginning of a line
+   * l is of the form l = 2*k, k a non negative integer
+   */
+  private static final int ZZ_LEXSTATE[] = { 
+     0,  0,  1,  1,  2,  2,  3, 3
+  };
+
+  /** 
+   * Translates characters to character classes
+   */
+  private static final char [] ZZ_CMAP = {
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, 
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, 
+     6,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  2,  0,  0, 
+     0, 19,  9,  0, 10,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0, 
+     0,  0,  0,  0,  0,  0, 13, 18, 12,  0,  0,  0,  0,  7,  0,  0, 
+     8,  0, 11,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, 
+     0,  0,  0, 21,  0, 23, 15, 22, 14,  0,  0,  0,  0, 24,  0,  3, 
+     4,  0, 16, 20,  5, 17,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, 
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, 
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, 
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, 
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, 
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, 
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, 
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, 
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0
+  };
+
+  /** 
+   * Translates DFA states to action switch labels.
+   */
+  private static final int [] ZZ_ACTION = zzUnpackAction();
+
+  private static final String ZZ_ACTION_PACKED_0 =
+    "\4\0\22\1\4\0\1\2\2\0\1\3\4\0\1\4"+
+    "\6\0\1\5\1\6\1\7\1\10\1\11\1\0\1\12"+
+    "\1\13\1\14\1\15\3\0\1\16\1\0\1\17\1\20"+
+    "\42\0\1\21\1\22";
+
+  private static int [] zzUnpackAction() {
+    int [] result = new int[94];
+    int offset = 0;
+    offset = zzUnpackAction(ZZ_ACTION_PACKED_0, offset, result);
+    return result;
+  }
+
+  private static int zzUnpackAction(String packed, int offset, int [] result) {
+    int i = 0;       /* index in packed string  */
+    int j = offset;  /* index in unpacked array */
+    int l = packed.length();
+    while (i < l) {
+      int count = packed.charAt(i++);
+      int value = packed.charAt(i++);
+      do result[j++] = value; while (--count > 0);
+    }
+    return j;
+  }
+
+
+  /** 
+   * Translates a state to a row index in the transition table
+   */
+  private static final int [] ZZ_ROWMAP = zzUnpackRowMap();
+
+  private static final String ZZ_ROWMAP_PACKED_0 =
+    "\0\0\0\31\0\62\0\113\0\144\0\175\0\226\0\257"+
+    "\0\310\0\341\0\372\0\u0113\0\u012c\0\u0145\0\u015e\0\u0177"+
+    "\0\u0190\0\u01a9\0\u01c2\0\u01db\0\u01f4\0\u020d\0\u0226\0\u023f"+
+    "\0\u0258\0\u0271\0\144\0\u028a\0\u02a3\0\144\0\u02bc\0\u02d5"+
+    "\0\u02ee\0\u0307\0\144\0\u01a9\0\u0320\0\u0339\0\u0352\0\u036b"+
+    "\0\u0384\0\144\0\144\0\144\0\144\0\144\0\u039d\0\144"+
+    "\0\144\0\144\0\144\0\u03b6\0\u03cf\0\u03e8\0\144\0\u0401"+
+    "\0\144\0\144\0\u041a\0\u0433\0\u044c\0\u0465\0\u047e\0\u0497"+
+    "\0\u04b0\0\u04c9\0\u04e2\0\u04fb\0\u0514\0\u052d\0\u0546\0\u055f"+
+    "\0\u0578\0\u0591\0\u05aa\0\u05c3\0\u05dc\0\u05f5\0\u060e\0\u0627"+
+    "\0\u0640\0\u0659\0\u0672\0\u068b\0\u06a4\0\u06bd\0\u06d6\0\u06ef"+
+    "\0\u0708\0\u0721\0\u073a\0\u0753\0\144\0\144";
+
+  private static int [] zzUnpackRowMap() {
+    int [] result = new int[94];
+    int offset = 0;
+    offset = zzUnpackRowMap(ZZ_ROWMAP_PACKED_0, offset, result);
+    return result;
+  }
+
+  private static int zzUnpackRowMap(String packed, int offset, int [] result) {
+    int i = 0;  /* index in packed string  */
+    int j = offset;  /* index in unpacked array */
+    int l = packed.length();
+    while (i < l) {
+      int high = packed.charAt(i++) << 16;
+      result[j++] = high | packed.charAt(i++);
+    }
+    return j;
+  }
+
+  /** 
+   * The transition table of the DFA
+   */
+  private static final int [] ZZ_TRANS = zzUnpackTrans();
+
+  private static final String ZZ_TRANS_PACKED_0 =
+    "\2\5\1\6\31\5\1\7\3\5\1\10\3\5\1\11"+
+    "\2\5\1\12\1\5\1\13\1\14\1\15\10\5\1\16"+
+    "\1\17\3\5\1\20\3\5\1\21\2\5\1\22\1\5"+
+    "\1\23\1\24\2\5\1\25\1\5\1\26\33\5\33\0"+
+    "\1\27\32\0\1\30\34\0\1\31\34\0\1\32\33\0"+
+    "\1\33\27\0\1\34\30\0\1\35\35\0\1\36\7\0"+
+    "\1\37\32\0\1\40\34\0\1\41\34\0\1\42\33\0"+
+    "\1\43\27\0\1\44\30\0\1\45\37\0\1\46\32\0"+
+    "\1\47\3\0\1\50\33\0\1\51\34\0\1\52\1\53"+
+    "\33\0\1\54\32\0\1\55\30\0\1\56\13\0\1\57"+
+    "\33\0\1\60\34\0\1\61\34\0\1\62\32\0\1\63"+
+    "\30\0\1\64\14\0\1\65\27\0\1\66\34\0\1\67"+
+    "\24\0\1\70\27\0\1\71\57\0\1\72\2\0\1\73"+
+    "\30\0\1\74\30\0\1\75\30\0\1\76\30\0\1\77"+
+    "\30\0\1\100\30\0\1\101\30\0\1\102\30\0\1\103"+
+    "\30\0\1\104\30\0\1\105\30\0\1\106\30\0\1\107"+
+    "\30\0\1\110\30\0\1\111\30\0\1\112\30\0\1\113"+
+    "\30\0\1\114\30\0\1\115\30\0\1\116\30\0\1\117"+
+    "\30\0\1\120\30\0\1\121\30\0\1\122\30\0\1\123"+
+    "\30\0\1\124\30\0\1\125\30\0\1\126\30\0\1\127"+
+    "\30\0\1\130\30\0\1\131\30\0\1\132\30\0\1\133"+
+    "\30\0\1\134\30\0\1\135\30\0\1\136\26\0";
+
+  private static int [] zzUnpackTrans() {
+    int [] result = new int[1900];
+    int offset = 0;
+    offset = zzUnpackTrans(ZZ_TRANS_PACKED_0, offset, result);
+    return result;
+  }
+
+  private static int zzUnpackTrans(String packed, int offset, int [] result) {
+    int i = 0;       /* index in packed string  */
+    int j = offset;  /* index in unpacked array */
+    int l = packed.length();
+    while (i < l) {
+      int count = packed.charAt(i++);
+      int value = packed.charAt(i++);
+      value--;
+      do result[j++] = value; while (--count > 0);
+    }
+    return j;
+  }
+
+
+  /* error codes */
+  private static final int ZZ_UNKNOWN_ERROR = 0;
+  private static final int ZZ_NO_MATCH = 1;
+  private static final int ZZ_PUSHBACK_2BIG = 2;
+
+  /* error messages for the codes above */
+  private static final String ZZ_ERROR_MSG[] = {
+    "Unkown internal scanner error",
+    "Error: could not match input",
+    "Error: pushback value was too large"
+  };
+
+  /**
+   * ZZ_ATTRIBUTE[aState] contains the attributes of state <code>aState</code>
+   */
+  private static final int [] ZZ_ATTRIBUTE = zzUnpackAttribute();
+
+  private static final String ZZ_ATTRIBUTE_PACKED_0 =
+    "\4\0\1\11\21\1\4\0\1\11\2\0\1\11\4\0"+
+    "\1\11\6\0\5\11\1\0\4\11\3\0\1\11\1\0"+
+    "\2\11\42\0\2\11";
+
+  private static int [] zzUnpackAttribute() {
+    int [] result = new int[94];
+    int offset = 0;
+    offset = zzUnpackAttribute(ZZ_ATTRIBUTE_PACKED_0, offset, result);
+    return result;
+  }
+
+  private static int zzUnpackAttribute(String packed, int offset, int [] result) {
+    int i = 0;       /* index in packed string  */
+    int j = offset;  /* index in unpacked array */
+    int l = packed.length();
+    while (i < l) {
+      int count = packed.charAt(i++);
+      int value = packed.charAt(i++);
+      do result[j++] = value; while (--count > 0);
+    }
+    return j;
+  }
+
+  /** the input device */
+  private java.io.Reader zzReader;
+
+  /** the current state of the DFA */
+  private int zzState;
+
+  /** the current lexical state */
+  private int zzLexicalState = YYINITIAL;
+
+  /** this buffer contains the current text to be matched and is
+      the source of the yytext() string */
+  private char zzBuffer[] = new char[ZZ_BUFFERSIZE];
+
+  /** the textposition at the last accepting state */
+  private int zzMarkedPos;
+
+  /** the current text position in the buffer */
+  private int zzCurrentPos;
+
+  /** startRead marks the beginning of the yytext() string in the buffer */
+  private int zzStartRead;
+
+  /** endRead marks the last character in the buffer, that has been read
+      from input */
+  private int zzEndRead;
+
+  /** number of newlines encountered up to the start of the matched text */
+  private int yyline;
+
+  /** the number of characters up to the start of the matched text */
+  private int yychar;
+
+  /**
+   * the number of characters from the last newline up to the start of the 
+   * matched text
+   */
+  private int yycolumn;
+
+  /** 
+   * zzAtBOL == true <=> the scanner is currently at the beginning of a line
+   */
+  private boolean zzAtBOL = true;
+
+  /** zzAtEOF == true <=> the scanner is at the EOF */
+  private boolean zzAtEOF;
+
+  /** denotes if the user-EOF-code has already been executed */
+  private boolean zzEOFDone;
+
+  /* user code: */
+  public static boolean DEBUG = false;
+
+
+  /**
+   * Creates a new scanner
+   * There is also a java.io.InputStream version of this constructor.
+   *
+   * @param   in  the java.io.Reader to read input from.
+   */
+  public GaussianLexer(java.io.Reader in) {
+    this.zzReader = in;
+  }
+
+  /**
+   * Creates a new scanner.
+   * There is also java.io.Reader version of this constructor.
+   *
+   * @param   in  the java.io.Inputstream to read input from.
+   */
+  public GaussianLexer(java.io.InputStream in) {
+    this(new java.io.InputStreamReader(in));
+  }
+
+
+  /**
+   * Refills the input buffer.
+   *
+   * @return      <code>false</code>, iff there was new input.
+   * 
+   * @exception   java.io.IOException  if any I/O-Error occurs
+   */
+  private boolean zzRefill() throws java.io.IOException {
+
+    /* first: make room (if you can) */
+    if (zzStartRead > 0) {
+      System.arraycopy(zzBuffer, zzStartRead,
+                       zzBuffer, 0,
+                       zzEndRead-zzStartRead);
+
+      /* translate stored positions */
+      zzEndRead-= zzStartRead;
+      zzCurrentPos-= zzStartRead;
+      zzMarkedPos-= zzStartRead;
+      zzStartRead = 0;
+    }
+
+    /* is the buffer big enough? */
+    if (zzCurrentPos >= zzBuffer.length) {
+      /* if not: blow it up */
+      char newBuffer[] = new char[zzCurrentPos*2];
+      System.arraycopy(zzBuffer, 0, newBuffer, 0, zzBuffer.length);
+      zzBuffer = newBuffer;
+    }
+
+    /* finally: fill the buffer with new input */
+    int numRead = zzReader.read(zzBuffer, zzEndRead,
+                                            zzBuffer.length-zzEndRead);
+
+    if (numRead > 0) {
+      zzEndRead+= numRead;
+      return false;
+    }
+    // unlikely but not impossible: read 0 characters, but not at end of stream    
+    if (numRead == 0) {
+      int c = zzReader.read();
+      if (c == -1) {
+        return true;
+      } else {
+        zzBuffer[zzEndRead++] = (char) c;
+        return false;
+      }     
+    }
+
+	// numRead < 0
+    return true;
+  }
+
+    
+  /**
+   * Closes the input stream.
+   */
+  public final void yyclose() throws java.io.IOException {
+    zzAtEOF = true;            /* indicate end of file */
+    zzEndRead = zzStartRead;  /* invalidate buffer    */
+
+    if (zzReader != null)
+      zzReader.close();
+  }
+
+
+  /**
+   * Resets the scanner to read from a new input stream.
+   * Does not close the old reader.
+   *
+   * All internal variables are reset, the old input stream 
+   * <b>cannot</b> be reused (internal buffer is discarded and lost).
+   * Lexical state is set to <tt>ZZ_INITIAL</tt>.
+   *
+   * @param reader   the new input stream 
+   */
+  public final void yyreset(java.io.Reader reader) {
+    zzReader = reader;
+    zzAtBOL  = true;
+    zzAtEOF  = false;
+    zzEOFDone = false;
+    zzEndRead = zzStartRead = 0;
+    zzCurrentPos = zzMarkedPos = 0;
+    yyline = yychar = yycolumn = 0;
+    zzLexicalState = YYINITIAL;
+  }
+
+
+  /**
+   * Returns the current lexical state.
+   */
+  public final int yystate() {
+    return zzLexicalState;
+  }
+
+
+  /**
+   * Enters a new lexical state
+   *
+   * @param newState the new lexical state
+   */
+  public final void yybegin(int newState) {
+    zzLexicalState = newState;
+  }
+
+
+  /**
+   * Returns the text matched by the current regular expression.
+   */
+  public final String yytext() {
+    return new String( zzBuffer, zzStartRead, zzMarkedPos-zzStartRead );
+  }
+
+
+  /**
+   * Returns the character at position <tt>pos</tt> from the 
+   * matched text. 
+   * 
+   * It is equivalent to yytext().charAt(pos), but faster
+   *
+   * @param pos the position of the character to fetch. 
+   *            A value from 0 to yylength()-1.
+   *
+   * @return the character at position pos
+   */
+  public final char yycharat(int pos) {
+    return zzBuffer[zzStartRead+pos];
+  }
+
+
+  /**
+   * Returns the length of the matched text region.
+   */
+  public final int yylength() {
+    return zzMarkedPos-zzStartRead;
+  }
+
+
+  /**
+   * Reports an error that occured while scanning.
+   *
+   * In a wellformed scanner (no or only correct usage of 
+   * yypushback(int) and a match-all fallback rule) this method 
+   * will only be called with things that "Can't Possibly Happen".
+   * If this method is called, something is seriously wrong
+   * (e.g. a JFlex bug producing a faulty scanner etc.).
+   *
+   * Usual syntax/scanner level error handling should be done
+   * in error fallback rules.
+   *
+   * @param   errorCode  the code of the errormessage to display
+   */
+  private void zzScanError(int errorCode) {
+    String message;
+    try {
+      message = ZZ_ERROR_MSG[errorCode];
+    }
+    catch (ArrayIndexOutOfBoundsException e) {
+      message = ZZ_ERROR_MSG[ZZ_UNKNOWN_ERROR];
+    }
+
+    throw new Error(message);
+  } 
+
+
+  /**
+   * Pushes the specified amount of characters back into the input stream.
+   *
+   * They will be read again by then next call of the scanning method
+   *
+   * @param number  the number of characters to be read again.
+   *                This number must not be greater than yylength()!
+   */
+  public void yypushback(int number)  {
+    if ( number > yylength() )
+      zzScanError(ZZ_PUSHBACK_2BIG);
+
+    zzMarkedPos -= number;
+  }
+
+
+  /**
+   * Contains user EOF-code, which will be executed exactly once,
+   * when the end of file is reached
+   */
+  private void zzDoEOF() throws java.io.IOException {
+    if (!zzEOFDone) {
+      zzEOFDone = true;
+      yyclose();
+    }
+  }
+
+
+  /**
+   * Resumes scanning until the next regular expression is matched,
+   * the end of input is encountered or an I/O-Error occurs.
+   *
+   * @return      the next token
+   * @exception   java.io.IOException  if any I/O-Error occurs
+   */
+  public java_cup.runtime.Symbol next_token() throws java.io.IOException {
+    int zzInput;
+    int zzAction;
+
+    // cached fields:
+    int zzCurrentPosL;
+    int zzMarkedPosL;
+    int zzEndReadL = zzEndRead;
+    char [] zzBufferL = zzBuffer;
+    char [] zzCMapL = ZZ_CMAP;
+
+    int [] zzTransL = ZZ_TRANS;
+    int [] zzRowMapL = ZZ_ROWMAP;
+    int [] zzAttrL = ZZ_ATTRIBUTE;
+
+    while (true) {
+      zzMarkedPosL = zzMarkedPos;
+
+      zzAction = -1;
+
+      zzCurrentPosL = zzCurrentPos = zzStartRead = zzMarkedPosL;
+  
+      zzState = ZZ_LEXSTATE[zzLexicalState];
+
+
+      zzForAction: {
+        while (true) {
+    
+          if (zzCurrentPosL < zzEndReadL)
+            zzInput = zzBufferL[zzCurrentPosL++];
+          else if (zzAtEOF) {
+            zzInput = YYEOF;
+            break zzForAction;
+          }
+          else {
+            // store back cached positions
+            zzCurrentPos  = zzCurrentPosL;
+            zzMarkedPos   = zzMarkedPosL;
+            boolean eof = zzRefill();
+            // get translated positions and possibly new buffer
+            zzCurrentPosL  = zzCurrentPos;
+            zzMarkedPosL   = zzMarkedPos;
+            zzBufferL      = zzBuffer;
+            zzEndReadL     = zzEndRead;
+            if (eof) {
+              zzInput = YYEOF;
+              break zzForAction;
+            }
+            else {
+              zzInput = zzBufferL[zzCurrentPosL++];
+            }
+          }
+          int zzNext = zzTransL[ zzRowMapL[zzState] + zzCMapL[zzInput] ];
+          if (zzNext == -1) break zzForAction;
+          zzState = zzNext;
+
+          int zzAttributes = zzAttrL[zzState];
+          if ( (zzAttributes & 1) == 1 ) {
+            zzAction = zzState;
+            zzMarkedPosL = zzCurrentPosL;
+            if ( (zzAttributes & 8) == 8 ) break zzForAction;
+          }
+
+        }
+      }
+
+      // store back cached position
+      zzMarkedPos = zzMarkedPosL;
+
+      switch (zzAction < 0 ? zzAction : ZZ_ACTION[zzAction]) {
+        case 17: 
+          { if (Settings.DEBUG) System.out.println("GaussianFlex: Found Gaussian 98");
+           yybegin(ITER);
+	   return new Symbol(GaussianSym.FOUNDITER);
+          }
+        case 19: break;
+        case 12: 
+          { if (Settings.DEBUG) System.out.println("GaussianFlex: Found RHF");
+   if (Settings.DEBUG) System.out.println(yytext());
+ try{
+     PrintStream temp = new PrintStream(new FileOutputStream("runtype2"));
+     temp.print(yytext());
+     System.out.println(yytext());}
+   catch (IOException ie){ System.out.println("Error in Gaussian Lexer");}
+      yybegin(IGNOREALL);
+     return new Symbol(GaussianSym.RUNTYP1);
+          }
+        case 20: break;
+        case 8: 
+          { if (Settings.DEBUG) System.out.println("GaussianFlex: Found rhf");
+   if (Settings.DEBUG) System.out.println(yytext());
+ try{
+     PrintStream temp = new PrintStream(new FileOutputStream("runtype1"));
+     temp.print(yytext());
+     System.out.println(yytext());}
+   catch (IOException ie){ System.out.println("Error in Gaussian Lexer");}
+     yybegin(ITER1);
+     return new Symbol(GaussianSym.RUNTYP);
+          }
+        case 21: break;
+        case 2: 
+          { if (Settings.DEBUG) System.out.println("GaussianFlex: Found hf");
+   if (Settings.DEBUG) System.out.println(yytext());
+ try{
+     PrintStream temp = new PrintStream(new FileOutputStream("runtype1"));
+     temp.print(yytext());
+     System.out.println(yytext());}
+   catch (IOException ie){ System.out.println("Error in Gaussian Lexer");}
+     yybegin(ITER1);
+     return new Symbol(GaussianSym.RUNTYP);
+          }
+        case 22: break;
+        case 16: 
+          { if (Settings.DEBUG) System.out.println("GaussianFlex: Found geom");
+   if (Settings.DEBUG) System.out.println(yytext());
+ try{
+     PrintStream temp = new PrintStream(new FileOutputStream("runtype2"));
+     temp.print(yytext());
+     System.out.println(yytext());}
+   catch (IOException ie){ System.out.println("Error in Gaussian Lexer");}
+     yybegin(IGNOREALL);
+     return new Symbol(GaussianSym.RUNTYP1);
+          }
+        case 23: break;
+        case 10: 
+          { if  (Settings.DEBUG) System.out.println("GaussianFlex: Found opt ");
+   if (Settings.DEBUG) System.out.println(yytext());
+ try{
+     PrintStream temp = new PrintStream(new FileOutputStream("runtype2"));
+     temp.print(yytext());
+     System.out.println(yytext());}
+   catch (IOException ie){ System.out.println("Error in Gaussian Lexer");}
+     yybegin(IGNOREALL);   
+     return new Symbol(GaussianSym.RUNTYP1);
+          }
+        case 24: break;
+        case 7: 
+          { if (Settings.DEBUG) System.out.println("GaussianFlex: Found RHF");
+   if (Settings.DEBUG) System.out.println(yytext());
+ try{
+     PrintStream temp = new PrintStream(new FileOutputStream("runtype1"));
+     temp.print(yytext());
+     System.out.println(yytext());}
+   catch (IOException ie){ System.out.println("Error in Gaussian Lexer");}
+     yybegin(ITER1);
+     return new Symbol(GaussianSym.RUNTYP);
+          }
+        case 25: break;
+        case 3: 
+          { if (Settings.DEBUG) System.out.println("GaussianFlex: Found G1");
+   if (Settings.DEBUG) System.out.println(yytext());
+ try{
+     PrintStream temp = new PrintStream(new FileOutputStream("runtype1"));
+     temp.print(yytext());
+     System.out.println(yytext());}
+   catch (IOException ie){ System.out.println("Error in Gaussian Lexer");}
+     yybegin(ITER1);
+     return new Symbol(GaussianSym.RUNTYP);
+          }
+        case 26: break;
+        case 18: 
+          { yybegin(IGNOREALL);
+    return new Symbol(GaussianSym.SCFDONE);
+          }
+        case 27: break;
+        case 13: 
+          { if (Settings.DEBUG) System.out.println("GaussianFlex: Found uhf");
+   if (Settings.DEBUG) System.out.println(yytext());
+ try{
+     PrintStream temp = new PrintStream(new FileOutputStream("runtype2"));
+     temp.print(yytext());
+     System.out.println(yytext());}
+   catch (IOException ie){ System.out.println("Error in Gaussian Lexer");}
+     yybegin(IGNOREALL);
+     return new Symbol(GaussianSym.RUNTYP1);
+          }
+        case 28: break;
+        case 9: 
+          { if (Settings.DEBUG) System.out.println("GaussianFlex: Found uhf");
+   if (Settings.DEBUG) System.out.println(yytext());
+ try{
+     PrintStream temp = new PrintStream(new FileOutputStream("runtype1"));
+     temp.print(yytext());
+     System.out.println(yytext());}
+   catch (IOException ie){ System.out.println("Error in Gaussian Lexer");}
+     yybegin(ITER1);
+     return new Symbol(GaussianSym.RUNTYP);
+          }
+        case 29: break;
+        case 11: 
+          { if (Settings.DEBUG) System.out.println("GaussianFlex: Found MP2");
+   if (Settings.DEBUG) System.out.println(yytext());
+ try{
+     PrintStream temp = new PrintStream(new FileOutputStream("runtype2"));
+     temp.print(yytext());
+     System.out.println(yytext());}
+   catch (IOException ie){ System.out.println("Error in Gaussian Lexer");}
+     yybegin(IGNOREALL);   
+     return new Symbol(GaussianSym.RUNTYP1);
+          }
+        case 30: break;
+        case 4: 
+          { if (Settings.DEBUG) System.out.println("GaussianFlex: Found rhf");
+   if (Settings.DEBUG) System.out.println(yytext());
+ try{
+     PrintStream temp = new PrintStream(new FileOutputStream("runtype2"));
+     temp.print(yytext());
+     System.out.println(yytext());}
+   catch (IOException ie){ System.out.println("Error in Gaussian Lexer");}
+     yybegin(IGNOREALL);
+     return new Symbol(GaussianSym.RUNTYP1);
+          }
+        case 31: break;
+        case 15: 
+          { if (Settings.DEBUG) System.out.println("GaussianFlex: Found scf=");
+   if (Settings.DEBUG) System.out.println(yytext());
+ try{
+     PrintStream temp = new PrintStream(new FileOutputStream("runtype2"));
+     temp.print(yytext());
+     System.out.println(yytext());}
+   catch (IOException ie){ System.out.println("Error in Gaussian Lexer");}
+      yybegin(IGNOREALL);
+     return new Symbol(GaussianSym.RUNTYP1);
+          }
+        case 32: break;
+        case 6: 
+          { if (Settings.DEBUG) System.out.println("GaussianFlex: Found MP4");
+   if (Settings.DEBUG) System.out.println(yytext());
+ try{
+     PrintStream temp = new PrintStream(new FileOutputStream("runtype1"));
+     temp.print(yytext());
+     System.out.println(yytext());}
+   catch (IOException ie){ System.out.println("Error in Gaussian Lexer");}
+     yybegin(ITER1);
+     return new Symbol(GaussianSym.RUNTYP);
+          }
+        case 33: break;
+        case 5: 
+          { if (Settings.DEBUG) System.out.println("GaussianFlex: Found MP2");
+   if (Settings.DEBUG) System.out.println(yytext());
+ try{
+     PrintStream temp = new PrintStream(new FileOutputStream("runtype1"));
+     temp.print(yytext());
+     System.out.println(yytext());}
+   catch (IOException ie){ System.out.println("Error in Gaussian Lexer");}
+     yybegin(ITER1);
+     return new Symbol(GaussianSym.RUNTYP);
+          }
+        case 34: break;
+        case 14: 
+          { if  (Settings.DEBUG) System.out.println("GaussianFlex: Found opt ");
+   if (Settings.DEBUG) System.out.println(yytext());
+ try{
+     PrintStream temp = new PrintStream(new FileOutputStream("runtype1"));
+     temp.print(yytext());
+     System.out.println(yytext());}
+   catch (IOException ie){ System.out.println("Error in Gaussian Lexer");}
+
+     yybegin(ITER1);
+     return new Symbol(GaussianSym.RUNTYP);
+          }
+        case 35: break;
+        case 1: 
+          { 
+          }
+        case 36: break;
+        default: 
+          if (zzInput == YYEOF && zzStartRead == zzCurrentPos) {
+            zzAtEOF = true;
+            zzDoEOF();
+              { return new java_cup.runtime.Symbol(GaussianSym.EOF); }
+          } 
+          else {
+            zzScanError(ZZ_NO_MATCH);
+          }
+      }
+    }
+  }
+
+  /**
+   * Converts an int token code into the name of the
+   * token by reflection on the cup symbol class/interface sym
+   *
+   * This code was contributed by Karl Meissner <meissnersd@yahoo.com>
+   */
+  private String getTokenName(int token) {
+    try {
+      java.lang.reflect.Field [] classFields = GaussianSym.class.getFields();
+      for (int i = 0; i < classFields.length; i++) {
+        if (classFields[i].getInt(null) == token) {
+          return classFields[i].getName();
+        }
+      }
+    } catch (Exception e) {
+      e.printStackTrace(System.err);
+    }
+
+    return "UNKNOWN TOKEN";
+  }
+
+  /**
+   * Same as next_token but also prints the token to standard out
+   * for debugging.
+   *
+   * This code was contributed by Karl Meissner <meissnersd@yahoo.com>
+   */
+  public java_cup.runtime.Symbol debug_next_token() throws java.io.IOException {
+    java_cup.runtime.Symbol s = next_token();
+    System.out.println( " --"+ yytext() + "--" + getTokenName(s.sym) + "--");
+    return s;
+  }
+
+  /**
+   * Runs the scanner on input files.
+   *
+   * This is a standalone scanner, it will print any unmatched
+   * text to System.out unchanged.
+   *
+   * @param argv   the command line, contains the filenames to run
+   *               the scanner on.
+   */
+  public static void main(String argv[]) {
+    if (argv.length == 0) {
+      System.out.println("Usage : java GaussianLexer <inputfile>");
+    }
+    else {
+      for (int i = 0; i < argv.length; i++) {
+        GaussianLexer scanner = null;
+        try {
+          scanner = new GaussianLexer( new java.io.FileReader(argv[i]) );
+          while ( !scanner.zzAtEOF ) scanner.next_token();
+        }
+        catch (java.io.FileNotFoundException e) {
+          System.out.println("File not found : \""+argv[i]+"\"");
+        }
+        catch (java.io.IOException e) {
+          System.out.println("IO error scanning file \""+argv[i]+"\"");
+          System.out.println(e);
+        }
+        catch (Exception e) {
+          System.out.println("Unexpected exception:");
+          e.printStackTrace();
+        }
+      }
+    }
+  }
+
+
+}

http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/4231ac35/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/gaussian/GaussianParser.java
----------------------------------------------------------------------
diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/gaussian/GaussianParser.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/gaussian/GaussianParser.java
new file mode 100644
index 0000000..ea61ef8
--- /dev/null
+++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/gaussian/GaussianParser.java
@@ -0,0 +1,187 @@
+/*
+*
+* Licensed to the Apache Software Foundation (ASF) under one
+* or more contributor license agreements.  See the NOTICE file
+* distributed with this work for additional information
+* regarding copyright ownership.  The ASF licenses this file
+* to you under the Apache License, Version 2.0 (the
+* "License"); you may not use this file except in compliance
+* with the License.  You may obtain a copy of the License at
+*
+*   http://www.apache.org/licenses/LICENSE-2.0
+*
+* Unless required by applicable law or agreed to in writing,
+* software distributed under the License is distributed on an
+* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+* KIND, either express or implied.  See the License for the
+* specific language governing permissions and limitations
+* under the License.
+*
+*/
+package org.apache.airavata.datacat.parsers.gridchem.gaussian;
+
+
+import java_cup.runtime.lr_parser;
+import org.apache.airavata.datacat.parsers.gridchem.GridChemQueueParser;
+
+import java.io.FileReader;
+import java.util.HashMap;
+
+
+public class GaussianParser extends java_cup.runtime.lr_parser implements GridChemQueueParser {
+
+  /** Default constructor. */
+  public GaussianParser() {super();}
+
+  /** Constructor which sets the default scanner. */
+  public GaussianParser(java_cup.runtime.Scanner s) {super(s);}
+
+    /**
+     * Constructor which uses a file reader.
+     */
+    public GaussianParser(final FileReader fileReader) {
+        super(new GaussianLexer(fileReader));
+    }
+
+
+    /** Production table. */
+  protected static final short _production_table[][] = 
+    lr_parser.unpackFromStrings(new String[]{
+            "\000\003\000\002\003\003\000\002\002\004\000\002\004" +
+                    "\005"});
+
+  /** Access to production table. */
+  public short[][] production_table() {return _production_table;}
+
+  /** Parse-action table. */
+  protected static final short[][] _action_table = 
+    lr_parser.unpackFromStrings(new String[]{
+            "\000\007\000\004\004\005\001\002\000\004\002\001\001" +
+                    "\002\000\004\006\010\001\002\000\004\002\007\001\002" +
+                    "\000\004\002\000\001\002\000\004\007\011\001\002\000" +
+                    "\004\002\uffff\001\002"});
+
+  /** Access to parse-action table. */
+  public short[][] action_table() {return _action_table;}
+
+  /** <code>reduce_goto</code> table. */
+  protected static final short[][] _reduce_table = 
+    lr_parser.unpackFromStrings(new String[]{
+            "\000\007\000\006\003\005\004\003\001\001\000\002\001" +
+                    "\001\000\002\001\001\000\002\001\001\000\002\001\001" +
+                    "\000\002\001\001\000\002\001\001"});
+
+  /** Access to <code>reduce_goto</code> table. */
+  public short[][] reduce_table() {return _reduce_table;}
+
+  /** Instance of action encapsulation class. */
+  protected CUP$parser$actions action_obj;
+
+  /** Action encapsulation object initializer. */
+  protected void init_actions()
+    {
+      action_obj = new CUP$parser$actions(this);
+    }
+
+  /** Invoke a user supplied parse action. */
+  public java_cup.runtime.Symbol do_action(
+    int                        act_num,
+    java_cup.runtime.lr_parser parser,
+    java.util.Stack            stack,
+    int                        top)
+    throws java.lang.Exception
+  {
+    /* call code in generated class */
+    return action_obj.CUP$parser$do_action(act_num, parser, stack, top);
+  }
+
+  /** Indicates start state. */
+  public int start_state() {return 0;}
+  /** Indicates start production. */
+  public int start_production() {return 1;}
+
+  /** <code>EOF</code> Symbol index. */
+  public int EOF_sym() {return 0;}
+
+  /** <code>error</code> Symbol index. */
+  public int error_sym() {return 1;}
+
+    @Override
+    public HashMap<String, String> getParsedData() throws Exception {
+        parse();
+        return null;
+    }
+}
+
+/** Cup generated class to encapsulate user supplied action code.*/
+class CUP$parser$actions {
+
+ 
+  //__________________________________
+  public static boolean DEBUG = true;
+ 
+
+  private final GaussianParser GaussianParser;
+
+  /** Constructor */
+  CUP$parser$actions(GaussianParser GaussianParser) {
+    this.GaussianParser = GaussianParser;
+  }
+
+  /** Method with the actual generated action code. */
+  public final java_cup.runtime.Symbol CUP$parser$do_action(
+    int                        CUP$parser$act_num,
+    java_cup.runtime.lr_parser CUP$parser$parser,
+    java.util.Stack            CUP$parser$stack,
+    int                        CUP$parser$top)
+    throws java.lang.Exception
+    {
+      /* Symbol object for return from actions */
+      java_cup.runtime.Symbol CUP$parser$result;
+
+      /* select the action based on the action number */
+      switch (CUP$parser$act_num)
+        {
+          /*. . . . . . . . . . . . . . . . . . . .*/
+          case 2: // scfintro ::= FOUNDITER RUNTYP RUNTYP1 
+            {
+              Object RESULT = null;
+		 if (DEBUG) System.out.println("CUP:gaussian:  found FOUNDITER "); 
+              CUP$parser$result = new java_cup.runtime.Symbol(2/*scfintro*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-2)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT);
+            }
+          return CUP$parser$result;
+
+          /*. . . . . . . . . . . . . . . . . . . .*/
+          case 1: // $START ::= startpt EOF 
+            {
+              Object RESULT = null;
+		int start_valleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-1)).left;
+		int start_valright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-1)).right;
+		Object start_val = (Object)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-1)).value;
+		RESULT = start_val;
+              CUP$parser$result = new java_cup.runtime.Symbol(0/*$START*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-1)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT);
+            }
+          /* ACCEPT */
+          CUP$parser$parser.done_parsing();
+          return CUP$parser$result;
+
+          /*. . . . . . . . . . . . . . . . . . . .*/
+          case 0: // startpt ::= scfintro 
+            {
+              Object RESULT = null;
+		 if (DEBUG) System.out.println("CUP:gaussian:  end of parse tree "); 
+	
+ 	     
+              CUP$parser$result = new java_cup.runtime.Symbol(1/*startpt*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT);
+            }
+          return CUP$parser$result;
+
+          /* . . . . . .*/
+          default:
+            throw new Exception(
+               "Invalid action number found in internal parse table");
+
+        }
+    }
+}
+

http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/4231ac35/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/gaussian/GaussianSym.java
----------------------------------------------------------------------
diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/gaussian/GaussianSym.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/gaussian/GaussianSym.java
new file mode 100644
index 0000000..25f22f0
--- /dev/null
+++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/gaussian/GaussianSym.java
@@ -0,0 +1,37 @@
+/*
+*
+* Licensed to the Apache Software Foundation (ASF) under one
+* or more contributor license agreements.  See the NOTICE file
+* distributed with this work for additional information
+* regarding copyright ownership.  The ASF licenses this file
+* to you under the Apache License, Version 2.0 (the
+* "License"); you may not use this file except in compliance
+* with the License.  You may obtain a copy of the License at
+*
+*   http://www.apache.org/licenses/LICENSE-2.0
+*
+* Unless required by applicable law or agreed to in writing,
+* software distributed under the License is distributed on an
+* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+* KIND, either express or implied.  See the License for the
+* specific language governing permissions and limitations
+* under the License.
+*
+*/
+package org.apache.airavata.datacat.parsers.gridchem.gaussian;
+//----------------------------------------------------
+// The following code was generated by CUP v0.10k
+// Wed Sep 10 09:00:14 IST 2014
+//----------------------------------------------------
+
+/** CUP generated class containing symbol constants. */
+public class GaussianSym {
+  /* terminals */
+  public static final int RUNTYP = 4;
+  public static final int SCFDONE = 3;
+  public static final int error = 1;
+  public static final int FOUNDITER = 2;
+  public static final int RUNTYP1 = 5;
+  public static final int EOF = 0;
+}
+


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