ADDED   mttroot/mtt/bin/trans/ode2obs_r
Index: mttroot/mtt/bin/trans/ode2obs_r
==================================================================
--- /dev/null
+++ mttroot/mtt/bin/trans/ode2obs_r
@@ -0,0 +1,182 @@
+#! /bin/sh
+
+     ###################################### 
+     ##### Model Transformation Tools #####
+     ######################################
+
+# Bourne shell script: ode2obs_r
+# Odrinary differential equations to observer function equations
+# P.J.Gawthrop 14 June 1991, 8 Aug 1991, 2 April 1992, 14 April 1994, 28 Dec 94,
+#		12th July 1995, April 1996
+# Copyright (c) P.J.Gawthrop 1991, 1992, 1994, 1995, 1996.
+
+###############################################################
+## Version control history
+###############################################################
+## $Id$
+## $Log$
+###############################################################
+
+#Inform user
+echo Creating $1_obs.r
+
+# Remove the old log file
+rm -f ode2obs_r.log
+
+# Use reduce to accomplish the transformation
+reduce >ode2obs_r.log << EOF
+
+OFF Echo;
+OFF Nat;
+ON NERO;
+
+in "$1_def.r";
+MTTdxs := MTTdX;  %Save the symbolic form of dX
+
+%Set default values - reset by sympar file.
+MTTGPCNy := 2;
+MTTGPCNu := 0;
+
+in "$1_sympar.r";
+in "$1_ode.r";
+
+
+%Create the U vector of input derivatives.
+MTTNuu := (MTTGPCNu+1)*MTTNu;
+MTTNuu1 := MTTGPCNu*MTTNu;
+Matrix MTTUU(MTTNuu,1);
+
+FOR i := 1:MTTNu DO
+  MTTUU(i,1) := MTTU(i,1);
+END;
+
+IF MTTGPCNu>0 THEN
+FOR i := 1:MTTNu DO
+  MTTUU(i+MTTNu,1) := MTTdU(i,1);
+END;
+
+MTTU := MTTU;
+MTTdU := MTTdU;
+MTTUU := MTTUU;
+
+%Create the Y vector of output derivatives.
+MTTNyy := (MTTGPCNy+1)*MTTNy;
+Matrix MTTYY(MTTNyy,1);
+
+FOR i := 1:MTTNy DO
+  MTTYY(i,1) := MTTY(i,1);
+END;
+
+l := MTTNy;
+FOR i := 1:MTTGPCNy DO
+    FOR j := 1:MTTNy DO
+    BEGIN
+    l := l+1;
+    MTTYY(l,1) := 0;
+    FOR k := 1:MTTNx DO %Derivatives wrt x
+    BEGIN
+      xk := MTTX(k,1);
+      MTTYY(l,1) := MTTYY(l,1) + df(MTTYY(l-MTTNy,1), xk, 1)*MTTdX(k,1);
+    END;
+    IF MTTNuu1>0 THEN
+    FOR k := 1:MTTNuu1 DO %Derivatives wrt u
+    BEGIN
+      uk := MTTUU(k,1);
+      MTTYY(l,1) := MTTYY(l,1) + df(MTTYY(l-MTTNy,1), uk, 1)*MTTUU(k+MTTNu,1);
+    END;
+  END;
+END;
+
+%Create O_x - derivative of YY wrt x
+Matrix MTTO_x(MTTNyy,MTTNx);
+FOR j := 1:MTTNx DO
+  BEGIN
+  xj := MTTX(j,1);
+  FOR i := 1:MTTNyy DO
+    BEGIN
+    MTTO_x(i,j) := df(MTTYY(i,1), xj);
+    END;
+  END;
+
+%Create O_u - derivative of YY wrt u (Assumes GPC Nu = 0)
+MTTNNu := (MTTGPCNu+1)*MTTNu;
+Matrix MTTO_u(MTTNyy,MTTNNu);
+FOR j := 1:MTTNNu DO
+  BEGIN
+  uj := MTTu(j,1);	
+  FOR i := 1:MTTNyy DO
+    BEGIN
+    MTTO_u(i,j) := df(MTTYY(i,1), uj);
+    END;
+  END;
+
+
+%Create O_uu - derivative of O_u wrt u (Assumes GPC Nu = 0)
+%This is a multi-dimensional matrix kth elements stacked sideways.
+Matrix MTTO_uu(MTTNyy,MTTNNu*MTTNNu);
+FOR k := 1:MTTNNu DO
+  BEGIN
+  uk := MTTu(k,1);	
+  FOR j := 1:MTTNNu DO
+    BEGIN
+    FOR i := 1:MTTNyy DO
+      BEGIN
+      jk := j+(k-1)*MTTNu;
+      MTTO_uu(i,jk) := df(MTTO_u(i,j), uk);
+      END;
+    END;
+  END;
+
+%Create O_ux - derivative of O_u wrt x 
+%This is a multi-dimensional matrix kth elements stacked sideways.
+Matrix MTTO_ux(MTTNyy,MTTNu*MTTNx);
+FOR k := 1:MTTNx DO
+  BEGIN
+  xk := MTTx(k,1);	
+  FOR j := 1:MTTNu DO
+    BEGIN
+    FOR i := 1:MTTNyy DO
+      BEGIN
+      jk := j+(k-1)*MTTNu;
+      MTTO_ux(i,jk) := df(MTTO_u(i,j), xk);
+      END;
+    END;
+  END;
+
+
+
+%%Create the _obs.r file
+OUT "$1_obs.r";
+
+MTTYY := MTTYY;
+MTTO_x := MTTO_x;
+MTTO_u := MTTO_u;
+MTTO_uu := MTTO_uu;
+MTTO_ux := MTTO_ux;
+
+write ";END;";
+
+SHUT "$1_obs.r";
+quit;
+
+EOF
+
+
+#Reduce writes errors to std output with ***** in front.
+grep '\*\*\*\*\*' ode2obs_r.log >mtt_error
+# Test for errors and print if any
+err_length=$(wc -c <mtt_error)
+if [ $err_length != "0" ]
+then
+  echo MTT has failed with the following errors '...'
+  cat mtt_error
+  exit 1
+else
+  exit 0
+fi
+
+
+
+
+
+