Index: mttroot/mtt/bin/mtt
==================================================================
--- mttroot/mtt/bin/mtt
+++ mttroot/mtt/bin/mtt
@@ -15,10 +15,13 @@
 ###############################################################
 ## Version control history
 ###############################################################
 ## $Header$
 ## $Log$
+## Revision 1.367  2002/12/09 00:14:08  geraint
+## Hierarchical dia and mixed dia/fig bond graphs now working.
+##
 ## Revision 1.366  2002/12/06 21:56:21  geraint
 ## Cosmetic change: removed commented-out lines.
 ##
 ## Revision 1.365  2002/12/06 12:45:25  gawthrop
 ## Simplified rule for sub.sh: both fig and dia go via cmp.txt now.
@@ -2207,13 +2210,13 @@
     
    #if [ -f "$filename" ]; then
    #   echo $filename exists
    #else
      if [ -n "$Verbose" ]; then
-      echo make -s -f $2_rep.make "SYS=$1" "LANG=$3" "ARG=$4" "OPTS=$mtt_switches" 
+      echo make -s -f $2_rep.make "MTT_SYS=$1" "MTT_LANG=$3" "MTT_ARG=$4" "MTT_OPTS=$mtt_switches" 
      fi
-      make -s -f $2_rep.make "SYS=$1" "LANG=$3" "ARG=$4" "OPTS=$mtt_switches"
+      make -s -f $2_rep.make "MTT_SYS=$1" "MTT_LANG=$3" "MTT_ARG=$4" "MTT_OPTS=$mtt_switches"
       if [ -n "$4" ]; then
          echo Copying  $1_$2$__ARGS.$ps
          cp  $1_$2$__ARGS.$ps ..
       fi
    #fi

Index: mttroot/mtt/lib/rep/cxxsim_rep.make
==================================================================
--- mttroot/mtt/lib/rep/cxxsim_rep.make
+++ mttroot/mtt/lib/rep/cxxsim_rep.make
@@ -18,48 +18,48 @@
 INCLUDE=-I. -I${MTT_LIB}/cr/hh
 OPTIMISE=-O0
 WARNINGS=-Wall -ansi -pedantic
 
 
-all: $(SYS)_cxxsim.$(LANG)
+all: $(MTT_SYS)_cxxsim.$(MTT_LANG)
 
 # view rule copied from gnuplot_rep.make
 # need it here to prevent MTT using the default route (via dae)
-$(SYS)_cxxsim.view: $(SYS)_gnuplot.wish $(SYS)_cxxsim.exe
-	./$(SYS)_cxxsim.exe > $(SYS)_odes.dat2
-	sh $(SYS)_gnuplot.wish			|\
+$(MTT_SYS)_cxxsim.view: $(MTT_SYS)_gnuplot.wish $(MTT_SYS)_cxxsim.exe
+	./$(MTT_SYS)_cxxsim.exe > $(MTT_SYS)_odes.dat2
+	sh $(MTT_SYS)_gnuplot.wish		|\
 		tee gnuplot_in.log		|\
 		 gnuplot -geometry 400x300	\
 		 > gnuplot_out.log 2> gnuplot_err.log &
 
-$(SYS)_cxxsim.exe: $(SYS)_cxxsim.cc
-	echo Creating $(SYS)_cxxsim.exe
+$(MTT_SYS)_cxxsim.exe: $(MTT_SYS)_cxxsim.cc
+	echo Creating $(MTT_SYS)_cxxsim.exe
 	$(CC) -o $@ $^ $(OPTIMISE) $(WARNINGS) $(INCLUDE)
 
-$(SYS)_cxxsim.cc: $(SYS)_cr.txt $(SYS)_ese.r $(SYS)_struc.txt $(SYS)_sympar.txt cxxsim
-	./cxxsim $(SYS)
+$(MTT_SYS)_cxxsim.cc: $(MTT_SYS)_cr.txt $(MTT_SYS)_ese.r $(MTT_SYS)_struc.txt $(MTT_SYS)_sympar.txt cxxsim
+	./cxxsim $(MTT_SYS)
 	cp $@ ..
 
 cxxsim: ${MTT_LIB}/rep/cxxsim.cc
 	echo creating $@
 	echo Compiling $^
 	$(CC) -o $@ $^ $(OPTIMISE) $(WARNINGS) $(INCLUDE)
 
 # list of constitutive relationships
-$(SYS)_cr.txt:
-	mtt -q $(OPTS) $(SYS) cr txt
+$(MTT_SYS)_cr.txt:
+	mtt -q $(MTT_OPTS) $(MTT_SYS) cr txt
 
 # elementary system equations
-$(SYS)_ese.r:
-	mtt -q $(OPTS) $(SYS) ese r
+$(MTT_SYS)_ese.r:
+	mtt -q $(MTT_OPTS) $(MTT_SYS) ese r
 
 # system structure
-$(SYS)_struc.txt:
-	mtt -q $(OPTS) $(SYS) struc txt
+$(MTT_SYS)_struc.txt:
+	mtt -q $(MTT_OPTS) $(MTT_SYS) struc txt
 
 # list of symbolic parameters
-$(SYS)_sympar.txt:
-	mtt -q $(OPTS) $(SYS) sympar txt
+$(MTT_SYS)_sympar.txt:
+	mtt -q $(MTT_OPTS) $(MTT_SYS) sympar txt
 
 # gnuplot script
-$(SYS)_gnuplot.wish:
-	mtt -q $(OPTS) $(SYS) gnuplot wish
+$(MTT_SYS)_gnuplot.wish:
+	mtt -q $(MTT_OPTS) $(MTT_SYS) gnuplot wish

Index: mttroot/mtt/lib/rep/gnuplot_rep.make
==================================================================
--- mttroot/mtt/lib/rep/gnuplot_rep.make
+++ mttroot/mtt/lib/rep/gnuplot_rep.make
@@ -1,21 +1,21 @@
 # -*-makefile-*-
 # create a gnuplot input file
 
-MTTFLAGS	= $(OPTS)
+MTTFLAGS	= $(MTT_OPTS)
 
-all: $(SYS)_gnuplot.$(LANG)
+all: $(MTT_SYS)_gnuplot.$(MTT_LANG)
 
-$(SYS)_gnuplot.view: $(SYS)_gnuplot.wish
-	mtt $(OPTS) $(SYS) odes dat2
-	sh $(SYS)_gnuplot.wish			|\
+$(MTT_SYS)_gnuplot.view: $(MTT_SYS)_gnuplot.wish
+	mtt $(MTT_OPTS) $(MTT_SYS) odes dat2
+	sh $(MTT_SYS)_gnuplot.wish			|\
 		tee gnuplot_in.log		|\
 		 gnuplot -geometry 400x300	\
 		 > gnuplot_out.log 2> gnuplot_err.log &
 
-$(SYS)_gnuplot.wish: $(SYS)_struc.txt
-	$(MTTPATH)/trans/struc2gnuplot_txt2wish $(SYS)
+$(MTT_SYS)_gnuplot.wish: $(MTT_SYS)_struc.txt
+	$(MTTPATH)/trans/struc2gnuplot_txt2wish $(MTT_SYS)
 
-$(SYS)_struc.txt:
-	mtt $(MTTFLAGS) $(SYS) struc txt
+$(MTT_SYS)_struc.txt:
+	mtt $(MTTFLAGS) $(MTT_SYS) struc txt
 
 

Index: mttroot/mtt/lib/rep/ident_rep.make
==================================================================
--- mttroot/mtt/lib/rep/ident_rep.make
+++ mttroot/mtt/lib/rep/ident_rep.make
@@ -8,130 +8,130 @@
 # File ident_rep.make
 
 #Copyright (C) 2000,2001,2002 by Peter J. Gawthrop
 
 ## Model targets
-model_reps =  ${SYS}_sympar.m ${SYS}_simpar.m ${SYS}_state.m 
-model_reps += ${SYS}_numpar.m ${SYS}_input.m ${SYS}_ode2odes.m  
-model_reps += ${SYS}_def.m 
+model_reps =  ${MTT_SYS}_sympar.m ${MTT_SYS}_simpar.m ${MTT_SYS}_state.m 
+model_reps += ${MTT_SYS}_numpar.m ${MTT_SYS}_input.m ${MTT_SYS}_ode2odes.m  
+model_reps += ${MTT_SYS}_def.m 
 
 ## Prepend s to get the sensitivity targets
 sensitivity_reps = ${model_reps:%=s%}
 
 ## Model prerequisites
-model_pre =  ${SYS}_abg.fig ${SYS}_lbl.txt 
-model_pre += ${SYS}_rdae.r ${SYS}_numpar.txt
+model_pre =  ${MTT_SYS}_abg.fig ${MTT_SYS}_lbl.txt 
+model_pre += ${MTT_SYS}_rdae.r ${MTT_SYS}_numpar.txt
 
 ## Prepend s to get the sensitivity targets
 sensitivity_pre = ${model_pre:%=s%}
 
 
 ## Simulation targets
-sims = ${SYS}_sim.m s${SYS}_ssim.m
+sims = ${MTT_SYS}_sim.m s${MTT_SYS}_ssim.m
 
 ## m-files needed for ident
-ident_m = ${SYS}_ident.m ${SYS}_ident_numpar.m 
+ident_m = ${MTT_SYS}_ident.m ${MTT_SYS}_ident_numpar.m 
 
 ## Targets for the ident simulation
 ident_reps = ${ident_m} ${sims} ${model_reps} ${sensitivity_reps}
 
 ## ps output files etc
-psfiles = ${SYS}_ident.ps ${SYS}_ident.comparison.ps
+psfiles = ${MTT_SYS}_ident.ps ${MTT_SYS}_ident.comparison.ps
 figfiles = ${psfiles:%.ps=%.fig}
 gdatfiles = ${psfiles:%.ps=%.gdat}
 datfiles = ${psfiles:%.ps=%.dat2}
 
 ## LaTeX files etc
-latexfiles = ${SYS}_ident_par.tex
+latexfiles = ${MTT_SYS}_ident_par.tex
 
-all: ${SYS}_ident.${LANG}
+all: ${MTT_SYS}_ident.${MTT_LANG}
 
 echo:
 	echo "sims: ${sims}"
 	echo "model_reps: ${model_reps}"
 	echo "sensitivity_reps: ${sensitivity_reps}"
 	echo "ident_reps: ${ident_reps}"
 
-${SYS}_ident.view: ${psfiles}
-	ident_rep.sh ${SYS} view
+${MTT_SYS}_ident.view: ${psfiles}
+	ident_rep.sh ${MTT_SYS} view
 
 ${psfiles}: ${figfiles}
-	ident_rep.sh ${SYS} ps
+	ident_rep.sh ${MTT_SYS} ps
 
 ${figfiles}: ${gdatfiles}
-	ident_rep.sh ${SYS} fig
+	ident_rep.sh ${MTT_SYS} fig
 
 ${gdatfiles}: ${datfiles}
-	ident_rep.sh ${SYS} gdat
+	ident_rep.sh ${MTT_SYS} gdat
 
 ${datfiles} ${latexfiles}: ${ident_reps}
-	ident_rep.sh ${SYS} dat2
+	ident_rep.sh ${MTT_SYS} dat2
 
-${SYS}_ident.m: 
-	ident_rep.sh ${SYS} m
+${MTT_SYS}_ident.m: 
+	ident_rep.sh ${MTT_SYS} m
 
-${SYS}_ident_numpar.m:
-	ident_rep.sh ${SYS} numpar.m
+${MTT_SYS}_ident_numpar.m:
+	ident_rep.sh ${MTT_SYS} numpar.m
 
 ## System model reps
 ## Generic txt files 
-${SYS}_%.txt:
-	mtt ${OPTS} -q -stdin ${SYS} $* txt
+${MTT_SYS}_%.txt:
+	mtt ${MTT_OPTS} -q -stdin ${MTT_SYS} $* txt
 
 ## Specific m files
-${SYS}_ode2odes.m: ${model_pre}
-	mtt -q -stdin ${OPTS} ${SYS} ode2odes m
+${MTT_SYS}_ode2odes.m: ${model_pre}
+	mtt -q -stdin ${MTT_OPTS} ${MTT_SYS} ode2odes m
 
-${SYS}_sim.m: ${SYS}_ode2odes.m
-	mtt ${OPTS} -q -stdin ${SYS} sim m
+${MTT_SYS}_sim.m: ${MTT_SYS}_ode2odes.m
+	mtt ${MTT_OPTS} -q -stdin ${MTT_SYS} sim m
 
 ## Numpar files
-${SYS}_numpar.m:
-	mtt ${SYS} numpar m
+${MTT_SYS}_numpar.m:
+	mtt ${MTT_SYS} numpar m
 
 ## Sympar files
-${SYS}_sympar.m:
-	mtt ${SYS} sympar m
+${MTT_SYS}_sympar.m:
+	mtt ${MTT_SYS} sympar m
 
 ## Generic txt to m
-${SYS}_%.m: ${SYS}_%.txt
-	mtt ${OPTS} -q -stdin ${SYS} $* m
+${MTT_SYS}_%.m: ${MTT_SYS}_%.txt
+	mtt ${MTT_OPTS} -q -stdin ${MTT_SYS} $* m
 
 ## r files
-${SYS}_def.r: ${SYS}_abg.fig
-	mtt ${OPTS} -q -stdin ${SYS} def r
+${MTT_SYS}_def.r: ${MTT_SYS}_abg.fig
+	mtt ${MTT_OPTS} -q -stdin ${MTT_SYS} def r
 
-${SYS}_rdae.r: 
-	mtt ${OPTS} -q -stdin ${SYS} rdae r
+${MTT_SYS}_rdae.r: 
+	mtt ${MTT_OPTS} -q -stdin ${MTT_SYS} rdae r
 
 ## Sensitivity model reps
 ## Generic txt files 
-s${SYS}_%.txt:
-	mtt ${OPTS} -q -stdin -s s${SYS} $* txt
+s${MTT_SYS}_%.txt:
+	mtt ${MTT_OPTS} -q -stdin -s s${MTT_SYS} $* txt
 
 ## Specific m files
 ## Numpar files
-s${SYS}_numpar.m:
-	mtt -s s${SYS} numpar m
+s${MTT_SYS}_numpar.m:
+	mtt -s s${MTT_SYS} numpar m
 
 ## Sympar files
-s${SYS}_sympar.m:
-	mtt -s s${SYS} sympar m
-
-s${SYS}_ode2odes.m: ${sensitivity_pre}
-	mtt -q -stdin ${OPTS} -s s${SYS} ode2odes m
-
-s${SYS}_ssim.m:
-	mtt -q -stdin ${OPTS} -s s${SYS} ssim m
-
-s${SYS}_def.m:
-	mtt -q -stdin ${OPTS} -s s${SYS} def m
+s${MTT_SYS}_sympar.m:
+	mtt -s s${MTT_SYS} sympar m
+
+s${MTT_SYS}_ode2odes.m: ${sensitivity_pre}
+	mtt -q -stdin ${MTT_OPTS} -s s${MTT_SYS} ode2odes m
+
+s${MTT_SYS}_ssim.m:
+	mtt -q -stdin ${MTT_OPTS} -s s${MTT_SYS} ssim m
+
+s${MTT_SYS}_def.m:
+	mtt -q -stdin ${MTT_OPTS} -s s${MTT_SYS} def m
 
 
 ## Generic txt to m
-s${SYS}_%.m: s${SYS}_%.txt
-	mtt ${OPTS} -q -stdin s${SYS} $* m
+s${MTT_SYS}_%.m: s${MTT_SYS}_%.txt
+	mtt ${MTT_OPTS} -q -stdin s${MTT_SYS} $* m
 
 ## r files
-s${SYS}_rdae.r: 
-	mtt ${OPTS} -q -stdin -s s${SYS} rdae r
+s${MTT_SYS}_rdae.r: 
+	mtt ${MTT_OPTS} -q -stdin -s s${MTT_SYS} rdae r
 

Index: mttroot/mtt/lib/rep/ippp_rep.make
==================================================================
--- mttroot/mtt/lib/rep/ippp_rep.make
+++ mttroot/mtt/lib/rep/ippp_rep.make
@@ -9,10 +9,13 @@
   ###############################################################
   ## Version control history
   ###############################################################
   ## $Id$
   ## $Log$
+  ## Revision 1.4  2001/04/23 15:06:21  gawthrop
+  ## Removed stdin bug workaround
+  ##
   ## Revision 1.3  2001/04/11 07:52:45  gawthrop
   ## Temporary fix to avoid incorrect _input.cc with stdin
   ##
   ## Revision 1.2  2001/04/05 11:49:07  gawthrop
   ## Fixed a number of bugs to as to work with reports.
@@ -22,50 +25,50 @@
   ##
   ###############################################################
 
 #Copyright (C) 2000 by Peter J. Gawthrop
 
-all: $(SYS)_ippp.$(LANG)
+all: $(MTT_SYS)_ippp.$(MTT_LANG)
 
-$(SYS)_ippp.view:  $(SYS)_ippp.pdf
+$(MTT_SYS)_ippp.view:  $(MTT_SYS)_ippp.pdf
 	acroread *.pdf
 
-$(SYS)_ippp.ps: $(SYS)_parameters.ps $(SYS)_error.ps $(SYS)_outputs.ps $(SYS)_ippp.pdf
-	cp $(SYS)_parameters.ps $(SYS)_ippp.ps
-
-$(SYS)_ippp.pdf: $(SYS)_parameters.pdf $(SYS)_error.pdf $(SYS)_outputs.pdf
-	cp $(SYS)_parameters.pdf $(SYS)_ippp.pdf
-
-$(SYS)_parameters.ps: s$(SYS)_ode2odes.m s$(SYS)_ssim.m $(SYS)_ippp.m s$(SYS)_sympar.m s$(SYS)_simpar.m
-	octave $(SYS)_ippp.m
-
-$(SYS)_error.ps: $(SYS)_parameters.ps
-	touch $(SYS)_error.ps
-
-$(SYS)_outputs.ps: $(SYS)_parameters.ps
-	touch $(SYS)_outputs.ps
-
-$(SYS)_parameters.pdf: s$(SYS)_ode2odes.m s$(SYS)_ssim.m $(SYS)_ippp.m s$(SYS)_sympar.m s$(SYS)_simpar.m
-	octave $(SYS)_ippp.m
-
-$(SYS)_error.pdf: $(SYS)_parameters.pdf
-	touch $(SYS)_error.pdf
-
-$(SYS)_outputs.pdf: $(SYS)_parameters.pdf
-	touch $(SYS)_outputs.pdf
-
-s$(SYS)_ode2odes.m: 
-	echo Starting creation of s$(SYS)_ode2odes.m with options $(OPTS)
-	mtt -q $(OPTS) -stdin -s s$(SYS) ode2odes oct
-
-s$(SYS)_ssim.m: s$(SYS)_def.m
-	mtt -q $(OPTS) -s s$(SYS) ssim m
-
-s$(SYS)_sympar.m:
-	mtt -q $(OPTS) -s s$(SYS) sympar m
-
-s$(SYS)_simpar.m:
-	mtt -q $(OPTS) -s s$(SYS) simpar m
-
-s$(SYS)_def.m:
-	mtt -q $(OPTS) -s s$(SYS) def m
+$(MTT_SYS)_ippp.ps: $(MTT_SYS)_parameters.ps $(MTT_SYS)_error.ps $(MTT_SYS)_outputs.ps $(MTT_SYS)_ippp.pdf
+	cp $(MTT_SYS)_parameters.ps $(MTT_SYS)_ippp.ps
+
+$(MTT_SYS)_ippp.pdf: $(MTT_SYS)_parameters.pdf $(MTT_SYS)_error.pdf $(MTT_SYS)_outputs.pdf
+	cp $(MTT_SYS)_parameters.pdf $(MTT_SYS)_ippp.pdf
+
+$(MTT_SYS)_parameters.ps: s$(MTT_SYS)_ode2odes.m s$(MTT_SYS)_ssim.m $(MTT_SYS)_ippp.m s$(MTT_SYS)_sympar.m s$(MTT_SYS)_simpar.m
+	octave $(MTT_SYS)_ippp.m
+
+$(MTT_SYS)_error.ps: $(MTT_SYS)_parameters.ps
+	touch $(MTT_SYS)_error.ps
+
+$(MTT_SYS)_outputs.ps: $(MTT_SYS)_parameters.ps
+	touch $(MTT_SYS)_outputs.ps
+
+$(MTT_SYS)_parameters.pdf: s$(MTT_SYS)_ode2odes.m s$(MTT_SYS)_ssim.m $(MTT_SYS)_ippp.m s$(MTT_SYS)_sympar.m s$(MTT_SYS)_simpar.m
+	octave $(MTT_SYS)_ippp.m
+
+$(MTT_SYS)_error.pdf: $(MTT_SYS)_parameters.pdf
+	touch $(MTT_SYS)_error.pdf
+
+$(MTT_SYS)_outputs.pdf: $(MTT_SYS)_parameters.pdf
+	touch $(MTT_SYS)_outputs.pdf
+
+s$(MTT_SYS)_ode2odes.m: 
+	echo Starting creation of s$(MTT_SYS)_ode2odes.m with options $(MTT_OPTS)
+	mtt -q $(MTT_OPTS) -stdin -s s$(MTT_SYS) ode2odes oct
+
+s$(MTT_SYS)_ssim.m: s$(MTT_SYS)_def.m
+	mtt -q $(MTT_OPTS) -s s$(MTT_SYS) ssim m
+
+s$(MTT_SYS)_sympar.m:
+	mtt -q $(MTT_OPTS) -s s$(MTT_SYS) sympar m
+
+s$(MTT_SYS)_simpar.m:
+	mtt -q $(MTT_OPTS) -s s$(MTT_SYS) simpar m
+
+s$(MTT_SYS)_def.m:
+	mtt -q $(MTT_OPTS) -s s$(MTT_SYS) def m
 

Index: mttroot/mtt/lib/rep/nppp_rep.make
==================================================================
--- mttroot/mtt/lib/rep/nppp_rep.make
+++ mttroot/mtt/lib/rep/nppp_rep.make
@@ -7,100 +7,100 @@
 # File nppp_rep.make
 
 #Copyright (C) 2000,2001,2002 by Peter J. Gawthrop
 
 ## Model targets
-model_reps =  ${SYS}_sympar.m ${SYS}_simpar.m ${SYS}_state.m 
-model_reps += ${SYS}_numpar.m ${SYS}_input.m ${SYS}_ode2odes.m  
-model_reps += ${SYS}_def.m
+model_reps =  ${MTT_SYS}_sympar.m ${MTT_SYS}_simpar.m ${MTT_SYS}_state.m 
+model_reps += ${MTT_SYS}_numpar.m ${MTT_SYS}_input.m ${MTT_SYS}_ode2odes.m  
+model_reps += ${MTT_SYS}_def.m
 
 ## Prepend s to get the sensitivity targets
 sensitivity_reps = ${model_reps:%=s%}
 
 ## Simulation targets
-sims = ${SYS}_sim.m s${SYS}_ssim.m
+sims = ${MTT_SYS}_sim.m s${MTT_SYS}_ssim.m
 
 ## m-files needed for nppp
-nppp_m = ${SYS}_nppp.m ${SYS}_nppp_numpar.m 
+nppp_m = ${MTT_SYS}_nppp.m ${MTT_SYS}_nppp_numpar.m 
 
 ## Targets for the nppp simulation
 nppp_reps = ${nppp_m} ${sims} ${model_reps} ${sensitivity_reps}
 
 ## ps output files
-psfiles = ${SYS}_nppp.ps ${SYS}_nppp.basis.ps ${SYS}_nppp.par.ps ${SYS}_nppp.U.ps
+psfiles = ${MTT_SYS}_nppp.ps ${MTT_SYS}_nppp.basis.ps ${MTT_SYS}_nppp.par.ps ${MTT_SYS}_nppp.U.ps
 figfiles = ${psfiles:%.ps=%.fig}
 
-all: ${SYS}_nppp.${LANG}
+all: ${MTT_SYS}_nppp.${MTT_LANG}
 
 echo:
 	echo "sims: ${sims}"
 	echo "model_reps: ${model_reps}"
 	echo "sensitivity_reps: ${sensitivity_reps}"
 	echo "nppp_reps: ${nppp_reps}"
 
-${SYS}_nppp.view: ${SYS}_nppp.ps
-	nppp_rep.sh ${SYS} view
-
-${psfiles}: ${SYS}_nppp.fig
-	nppp_rep.sh ${SYS} ps
-
-${SYS}_nppp.gdat: ${SYS}_nppp.dat2
-	nppp_rep.sh ${SYS} gdat
-
-${SYS}_nppp.fig ${SYS}_nppp.dat2: ${nppp_reps}
-	nppp_rep.sh ${SYS} dat2
-
-${SYS}_nppp.m: 
-	nppp_rep.sh ${SYS} m
-
-${SYS}_nppp_numpar.m:
-	nppp_rep.sh ${SYS} numpar.m
+${MTT_SYS}_nppp.view: ${MTT_SYS}_nppp.ps
+	nppp_rep.sh ${MTT_SYS} view
+
+${psfiles}: ${MTT_SYS}_nppp.fig
+	nppp_rep.sh ${MTT_SYS} ps
+
+${MTT_SYS}_nppp.gdat: ${MTT_SYS}_nppp.dat2
+	nppp_rep.sh ${MTT_SYS} gdat
+
+${MTT_SYS}_nppp.fig ${MTT_SYS}_nppp.dat2: ${nppp_reps}
+	nppp_rep.sh ${MTT_SYS} dat2
+
+${MTT_SYS}_nppp.m: 
+	nppp_rep.sh ${MTT_SYS} m
+
+${MTT_SYS}_nppp_numpar.m:
+	nppp_rep.sh ${MTT_SYS} numpar.m
 
 ## System model reps
 ## Generic txt files 
-${SYS}_%.txt:
-	mtt ${OPTS} -q -stdin ${SYS} $* txt
+${MTT_SYS}_%.txt:
+	mtt ${MTT_OPTS} -q -stdin ${MTT_SYS} $* txt
 
 ## Specific m files
-${SYS}_ode2odes.m: ${SYS}_rdae.r
-	mtt -q -stdin ${OPTS} ${SYS} ode2odes m
+${MTT_SYS}_ode2odes.m: ${MTT_SYS}_rdae.r
+	mtt -q -stdin ${MTT_OPTS} ${MTT_SYS} ode2odes m
 
-${SYS}_sim.m: ${SYS}_ode2odes.m
-	mtt ${OPTS} -q -stdin ${SYS} sim m
+${MTT_SYS}_sim.m: ${MTT_SYS}_ode2odes.m
+	mtt ${MTT_OPTS} -q -stdin ${MTT_SYS} sim m
 
 ## Generic txt to m
-${SYS}_%.m: ${SYS}_%.txt
-	mtt ${OPTS} -q -stdin ${SYS} $* m
+${MTT_SYS}_%.m: ${MTT_SYS}_%.txt
+	mtt ${MTT_OPTS} -q -stdin ${MTT_SYS} $* m
 
 ## r files
-${SYS}_def.r: ${SYS}_abg.fig
-	mtt ${OPTS} -q -stdin ${SYS} def r
+${MTT_SYS}_def.r: ${MTT_SYS}_abg.fig
+	mtt ${MTT_OPTS} -q -stdin ${MTT_SYS} def r
 
-${SYS}_rdae.r: 
-	mtt ${OPTS} -q -stdin ${SYS} rdae r
+${MTT_SYS}_rdae.r: 
+	mtt ${MTT_OPTS} -q -stdin ${MTT_SYS} rdae r
 
 ## Sensitivity model reps
 ## Generic txt files 
-s${SYS}_%.txt:
-	mtt ${OPTS} -q -stdin s${SYS} $* txt
+s${MTT_SYS}_%.txt:
+	mtt ${MTT_OPTS} -q -stdin s${MTT_SYS} $* txt
 
 ## Specific m files
-s${SYS}_ode2odes.m: s${SYS}_rdae.r
-	mtt -q -stdin ${OPTS} -s s${SYS} ode2odes m
-
-s${SYS}_ssim.m:
-	mtt -q -stdin ${OPTS} -s s${SYS} ssim m
-
-s${SYS}_def.m:
-	mtt -q -stdin ${OPTS} -s s${SYS} def m
+s${MTT_SYS}_ode2odes.m: s${MTT_SYS}_rdae.r
+	mtt -q -stdin ${MTT_OPTS} -s s${MTT_SYS} ode2odes m
+
+s${MTT_SYS}_ssim.m:
+	mtt -q -stdin ${MTT_OPTS} -s s${MTT_SYS} ssim m
+
+s${MTT_SYS}_def.m:
+	mtt -q -stdin ${MTT_OPTS} -s s${MTT_SYS} def m
 
 
 ## Generic txt to m
-s${SYS}_%.m: s${SYS}_%.txt
-	mtt ${OPTS} -q -stdin s${SYS} $* m
+s${MTT_SYS}_%.m: s${MTT_SYS}_%.txt
+	mtt ${MTT_OPTS} -q -stdin s${MTT_SYS} $* m
 
 
 ## r files
-s${SYS}_rdae.r: 
-	mtt ${OPTS} -q -stdin -s s${SYS} rdae r
+s${MTT_SYS}_rdae.r: 
+	mtt ${MTT_OPTS} -q -stdin -s s${MTT_SYS} rdae r
 
 

Index: mttroot/mtt/lib/rep/sfun_rep.make
==================================================================
--- mttroot/mtt/lib/rep/sfun_rep.make
+++ mttroot/mtt/lib/rep/sfun_rep.make
@@ -1,6 +1,4 @@
 # -*-makefile-*-
 
-REP ?= "sfun"
-
 all:
-	${MTT_REP}/sfun_rep.sh "$(OPTS)" "$(SYS)" "$(REP)" "$(LANG)"
+	${MTT_REP}/sfun_rep.sh "$(MTT_OPTS)" "$(MTT_SYS)" "$(MTT_LANG)"

Index: mttroot/mtt/lib/rep/sfun_rep.sh
==================================================================
--- mttroot/mtt/lib/rep/sfun_rep.sh
+++ mttroot/mtt/lib/rep/sfun_rep.sh
@@ -1377,7 +1377,7 @@
 ### main program
 
 set_debug false
 check_for_valid_input "$*"
 
-OPTS="$1" SYS="$2" REP="$3" LANG="$4" make $make_debug -f ${MTT_REP}/sfun_rep/Makefile ${2}_${3}.${4}
+MTT_OPTS="$1" MTT_SYS="$2" MTT_LANG="$3" make $make_debug -f ${MTT_REP}/sfun_rep/Makefile ${2}_sfun.${3}
 exit 0

Index: mttroot/mtt/lib/rep/sfun_rep/Makefile
==================================================================
--- mttroot/mtt/lib/rep/sfun_rep/Makefile
+++ mttroot/mtt/lib/rep/sfun_rep/Makefile
@@ -1,90 +1,90 @@
 #! /usr/bin/make -f
 
-all: $(SYS)_sfun.mexglx
-
-$(SYS)_sfun.mexglx: $(SYS)_sfun.c sfun_debug.h useful-functions.hh $(SYS)_def.h $(SYS)_sympar.h $(SYS)_cr.h $(SYS)_numpar.c $(SYS)_ode.c $(SYS)_odeo.c $(SYS)_state.c $(SYS)_sfun_ae.mexglx $(SYS)_sfun_input.mexglx $(SYS)_sfun_interface.mexglx $(SYS).mdl
-	echo Creating $@
-	mex $(SYS)_sfun.c
-	cp *_sfun*mexglx $(SYS).mdl ..
-
-$(SYS)_sfun.c:: ${MTT_REP}/sfun_rep/sfun.c.tmpl
-	echo Creating $@
-	cat $^ | sed 's/<mtt_model_name>/$(SYS)/g' > $@
-
-$(SYS)_sfun_ae.mexglx: $(SYS)_sfun_ae.c sfun_debug.h useful-functions.hh $(SYS)_def.h $(SYS)_sympar.h $(SYS)_cr.h $(SYS)_ae.c
-	echo Creating $@
-	mex $(SYS)_sfun_ae.c
-
-$(SYS)_sfun_ae.c:: ${MTT_REP}/sfun_rep/mex_ae.c.tmpl
-	echo Creating $@
-	cat $^ | sed 's/<mtt_model_name>/$(SYS)/g' > $@
-
-$(SYS)_sfun_input.mexglx: $(SYS)_sfun_input.c sfun_debug.h useful-functions.hh $(SYS)_def.h $(SYS)_sympar.h $(SYS)_cr.h $(SYS)_input.c $(SYS)_numpar.c
-	echo Creating $@
-	mex $(SYS)_sfun_input.c
-
-$(SYS)_sfun_input.c:: ${MTT_REP}/sfun_rep/sfun_input.c.tmpl
-	echo Creating $@
-	cat $^ | sed 's/<mtt_model_name>/$(SYS)/g' > $@
-
-$(SYS)_sfun_interface.mexglx: $(SYS)_sfun_interface.c sfun_debug.h useful-functions.hh $(SYS)_def.h $(SYS)_sympar.h $(SYS)_numpar.c
-	echo Creating $@
-	mex $(SYS)_sfun_interface.c
-
-$(SYS)_sfun_interface.c: ${MTT_REP}/sfun_rep/sfun_interface.c.tmpl $(SYS)_struc.c
+all: $(MTT_SYS)_sfun.mexglx
+
+$(MTT_SYS)_sfun.mexglx: $(MTT_SYS)_sfun.c sfun_debug.h useful-functions.hh $(MTT_SYS)_def.h $(MTT_SYS)_sympar.h $(MTT_SYS)_cr.h $(MTT_SYS)_numpar.c $(MTT_SYS)_ode.c $(MTT_SYS)_odeo.c $(MTT_SYS)_state.c $(MTT_SYS)_sfun_ae.mexglx $(MTT_SYS)_sfun_input.mexglx $(MTT_SYS)_sfun_interface.mexglx $(MTT_SYS).mdl
+	echo Creating $@
+	mex $(MTT_SYS)_sfun.c
+	cp *_sfun*mexglx $(MTT_SYS).mdl ..
+
+$(MTT_SYS)_sfun.c:: ${MTT_REP}/sfun_rep/sfun.c.tmpl
+	echo Creating $@
+	cat $^ | sed 's/<mtt_model_name>/$(MTT_SYS)/g' > $@
+
+$(MTT_SYS)_sfun_ae.mexglx: $(MTT_SYS)_sfun_ae.c sfun_debug.h useful-functions.hh $(MTT_SYS)_def.h $(MTT_SYS)_sympar.h $(MTT_SYS)_cr.h $(MTT_SYS)_ae.c
+	echo Creating $@
+	mex $(MTT_SYS)_sfun_ae.c
+
+$(MTT_SYS)_sfun_ae.c:: ${MTT_REP}/sfun_rep/mex_ae.c.tmpl
+	echo Creating $@
+	cat $^ | sed 's/<mtt_model_name>/$(MTT_SYS)/g' > $@
+
+$(MTT_SYS)_sfun_input.mexglx: $(MTT_SYS)_sfun_input.c sfun_debug.h useful-functions.hh $(MTT_SYS)_def.h $(MTT_SYS)_sympar.h $(MTT_SYS)_cr.h $(MTT_SYS)_input.c $(MTT_SYS)_numpar.c
+	echo Creating $@
+	mex $(MTT_SYS)_sfun_input.c
+
+$(MTT_SYS)_sfun_input.c:: ${MTT_REP}/sfun_rep/sfun_input.c.tmpl
+	echo Creating $@
+	cat $^ | sed 's/<mtt_model_name>/$(MTT_SYS)/g' > $@
+
+$(MTT_SYS)_sfun_interface.mexglx: $(MTT_SYS)_sfun_interface.c sfun_debug.h useful-functions.hh $(MTT_SYS)_def.h $(MTT_SYS)_sympar.h $(MTT_SYS)_numpar.c
+	echo Creating $@
+	mex $(MTT_SYS)_sfun_interface.c
+
+$(MTT_SYS)_sfun_interface.c: ${MTT_REP}/sfun_rep/sfun_interface.c.tmpl $(MTT_SYS)_struc.c
 	echo Creating $@
 	cat ${MTT_REP}/sfun_rep/sfun_interface.c.tmpl	|\
-	 sed 's/<mtt_model_name>/$(SYS)/g'		|\
+	 sed 's/<mtt_model_name>/$(MTT_SYS)/g'		|\
 	 ${MTT_REP}/sfun_rep/insert_file.sh > $@
 
-$(SYS)_sfun.zip: $(SYS)_sfun.c sfun_debug.h useful-functions.hh $(SYS)_sfun_ae.c $(SYS)_sfun_input.c $(SYS)_sfun_interface.c \
-	 $(SYS)_def.h $(SYS)_sympar.h $(SYS)_cr.h\
-	 $(SYS)_ae.c $(SYS)_input.c $(SYS)_numpar.c $(SYS)_ode.c $(SYS)_odeo.c $(SYS)_state.c \
-	 $(SYS).mdl README
+$(MTT_SYS)_sfun.zip: $(MTT_SYS)_sfun.c sfun_debug.h useful-functions.hh $(MTT_SYS)_sfun_ae.c $(MTT_SYS)_sfun_input.c $(MTT_SYS)_sfun_interface.c \
+	 $(MTT_SYS)_def.h $(MTT_SYS)_sympar.h $(MTT_SYS)_cr.h\
+	 $(MTT_SYS)_ae.c $(MTT_SYS)_input.c $(MTT_SYS)_numpar.c $(MTT_SYS)_ode.c $(MTT_SYS)_odeo.c $(MTT_SYS)_state.c \
+	 $(MTT_SYS).mdl README
 	echo Creating $@
 	zip $@ $^
 
-$(SYS).mdl: ${MTT_REP}/sfun_rep/mdl.tmpl
+$(MTT_SYS).mdl: ${MTT_REP}/sfun_rep/mdl.tmpl
 	echo Creating $@
-	cat $^ | sed 's/<mtt_model_name>/$(SYS)/g' > $@
+	cat $^ | sed 's/<mtt_model_name>/$(MTT_SYS)/g' > $@
 
 README:: ${MTT_REP}/sfun_rep/README.tmpl README.CVS
 	echo Creating $@
-	cat $^ | sed 's/<mtt_model_name>/$(SYS)/g' > $@
+	cat $^ | sed 's/<mtt_model_name>/$(MTT_SYS)/g' > $@
 	rm -f README.CVS
 
 README.CVS:
 	echo Getting CVS status
-	cvs status ../$(SYS)_abg.fig > $@ 2>1
+	cvs status ../$(MTT_SYS)_abg.fig > $@ 2>1
 	date >> $@
 
-$(SYS)_ae.c: $(SYS)_ae.m
-	echo Creating $@
-	${MTT_CC}/mtt_m2cc.sh $(SYS) ae c cat 
-
-$(SYS)_input.c: $(SYS)_input.m
-	echo Creating $@
-	${MTT_CC}/mtt_m2cc.sh $(SYS) input c cat 
-
-$(SYS)_numpar.c: $(SYS)_numpar.m
-	echo Creating $@
-	${MTT_CC}/mtt_m2cc.sh $(SYS) numpar c cat
-
-$(SYS)_ode.c: $(SYS)_ode.m
-	echo Creating $@
-	${MTT_CC}/mtt_m2cc.sh $(SYS) ode c cat
-
-$(SYS)_odeo.c: $(SYS)_odeo.m
-	echo Creating $@
-	${MTT_CC}/mtt_m2cc.sh $(SYS) odeo c cat
-
-$(SYS)_state.c: $(SYS)_state.m
-	echo Creating $@
-	${MTT_CC}/mtt_m2cc.sh $(SYS) state c cat
-
-$(SYS)_struc.c: $(SYS)_struc.txt
+$(MTT_SYS)_ae.c: $(MTT_SYS)_ae.m
+	echo Creating $@
+	${MTT_CC}/mtt_m2cc.sh $(MTT_SYS) ae c cat 
+
+$(MTT_SYS)_input.c: $(MTT_SYS)_input.m
+	echo Creating $@
+	${MTT_CC}/mtt_m2cc.sh $(MTT_SYS) input c cat 
+
+$(MTT_SYS)_numpar.c: $(MTT_SYS)_numpar.m
+	echo Creating $@
+	${MTT_CC}/mtt_m2cc.sh $(MTT_SYS) numpar c cat
+
+$(MTT_SYS)_ode.c: $(MTT_SYS)_ode.m
+	echo Creating $@
+	${MTT_CC}/mtt_m2cc.sh $(MTT_SYS) ode c cat
+
+$(MTT_SYS)_odeo.c: $(MTT_SYS)_odeo.m
+	echo Creating $@
+	${MTT_CC}/mtt_m2cc.sh $(MTT_SYS) odeo c cat
+
+$(MTT_SYS)_state.c: $(MTT_SYS)_state.m
+	echo Creating $@
+	${MTT_CC}/mtt_m2cc.sh $(MTT_SYS) state c cat
+
+$(MTT_SYS)_struc.c: $(MTT_SYS)_struc.txt
 	echo Creating $@
 	gawk '\
 ($$1 == "input")  { printf "         double *%s\t= &(mttu[%d]);\t/* input and output */\n", $$4, $$2-1 }\
 ($$1 == "state")  { printf "   const double *_%s\t= &(mttx[%d]);\t/* input */\n", $$4, $$2-1 }\
 ($$1 == "output") { printf "   const double *_%s\t= &(mtty[%d]);\t/* input */\n", $$4, $$2-1 }\
@@ -98,6 +98,6 @@
 useful-functions.hh:: ${MTT_CC}/include/useful-functions.hh
 	echo Copying $@
 	cp $^ $@
 
 %::
-	mtt -q $(OPTS) `echo $* | sed 's/\(.*\)_\(.*\)\.\(.*\)/\1 \2 \3/'`
+	mtt -q $(MTT_OPTS) `echo $* | sed 's/\(.*\)_\(.*\)\.\(.*\)/\1 \2 \3/'`