Index: mttroot/mtt/bin/trans/m/abg2cbg.m
==================================================================
--- mttroot/mtt/bin/trans/m/abg2cbg.m
+++ mttroot/mtt/bin/trans/m/abg2cbg.m
@@ -3,192 +3,195 @@
 					port_bond_direction,
 					port_status,
 					derivative_causality,
 					typefile, infofile, errorfile)
 
-# abg2cbg - acausal to causal bg conversion
-#
-#     ###################################### 
-#     ##### Model Transformation Tools #####
-#     ######################################
-# 
-# Matlab function  abg2cbg.m
-# Acausal bond graph to causal bond graph: mfile format
-# [bonds,status] = abg2cbg(system_name, system_type, full_name, port_bonds, infofile)
-
-# ###############################################################
-# ## Version control history
-# ###############################################################
-# ## $Id$
-# ## $Log$
-# ## Revision 1.45  1999/11/01 03:17:45  peterg
-# ## Added extra info - current subsystem
-# ##
-# ## Revision 1.44  1999/03/11 23:54:11  peterg
-# ## Include possibility of vector SS when finding port_bond_index
-# ##
-# ## Revision 1.43  1998/12/14 15:19:36  peterg
-# ## Added missing "derivative_causality," argument to recursive call of
-# ## this function
-# ##
-# ## Revision 1.42  1998/12/03 14:55:40  peterg
-# ## Now uses number of components with complete causality to measure
-# ## progress of algorithm -- Done.
-# ## This replaces bond count -- done.
-# ##
-# ## Revision 1.41  1998/11/20 10:52:28  peterg
-# ## Copies port bonds if the port bonds ARE set
-# ## -- replaces Copies port bonds if the component bonds are NOT set
-# ##
-# ## Revision 1.40  1998/09/02 11:47:09  peterg
-# ## Now uses explicit ordered list of ports instead of port.index.
-# ## Note that subsystems are still treated in arbitrary order.
-# ##
-# ## Revision 1.39  1998/08/25 20:06:16  peterg
-# ## Writes flipped port info
-# ##
-# ## Revision 1.38  1998/08/25 09:15:28  peterg
-# ## Fixed couple of problems with using two copies of the one data
-# ## stucture:
-# ##
-# ## ABG_field and ABG.field
-# ##
-# ## Maybe this is conceptually wrong?
-# ##
-# ## Revision 1.37  1998/08/25 08:33:29  peterg
-# ## Now does ports as well - fixed string prob by using deblank
-# ##
-# ## Revision 1.36  1998/08/25 06:44:40  peterg
-# ## Furhter revisions
-# ##
-# ## Revision 1.35  1998/08/24 10:16:32  peterg
-# ## Coverted to new structure - still needs status sorting.
-# ##
-# ## Revision 1.34  1998/08/24 07:35:03  peterg
-# ## About to go to new abg format.
-# ##
-# ## Revision 1.33  1998/07/29 13:36:37  peterg
-# ## Don't set port status if there aren't any ports.
-# ##
-# ## Revision 1.32  1998/07/28 19:06:11  peterg
-# ## *** empty log message ***
-# ##
-# ## Revision 1.31  1998/07/28 13:15:10  peterg
-# ## Vector SS ports included.
-# ##
-# ## Revision 1.30  1998/07/27 20:29:49  peterg
-# ## Had another go at causality ....
-# ##   1. Impose external causality onto all port bonds
-# ##   2. Set C_cause.m so that it DOESN'T set causality
-# ##       -- I_cause is already ok !
-# ##
-# ## Revision 1.29  1998/07/10 09:01:42  peterg
-# ## Added error + info file in new form
-# ##
-# ## Revision 1.28  1998/07/08 09:23:42  peterg
-# ## Undid the previous change -- needs more thought.
-# ##
-# ## Revision 1.27  1998/07/03 19:03:31  peterg
-# ## Always override the causality of port bonds!
-# ##
-# ## Revision 1.26  1998/06/27 13:24:04  peterg
-# ## Causality now set correctly for:
-# ## 	multi-port C and I
-# ## 	C and I with arrows pointing in
-# ##
-# ## Revision 1.25  1998/06/25 18:53:30  peterg
-# ## Actually, the previous comment was optimistic.
-# ## The port causalities on a compound are now forced to be the same as
-# ## that specified by a a _cuase.m file (if it exists)
-# ##
-# ## Revision 1.24  1998/06/25 17:45:03  peterg
-# ## No change -- but checked that explicit causality works!
-# ##
-# ## Revision 1.23  1998/04/04 10:46:37  peterg
-# ## Coerces port bonds to have smae direction as the imposing bonds
-# ## _cbg now generates the (coerced) components as welll as the (coerced)
-# ## causality.
-# ##
-# ## Revision 1.22  1997/08/19 10:21:09  peterg
-# ## Only copy port cuaslity info if not already set within the
-# ## subsystem. I thought I'd done this already ....
-# ##
-# ## Revision 1.21  1997/08/18 16:25:25  peterg
-# ## Minor bug fixes
-# ##
-# ## Revision 1.20  1997/08/18 12:45:24  peterg
-# ## Replaced: comp_bonds = bonds(bond_list,:)
-# ## by: 	for kk = 1:n_comp
-# ## 	  comp_bonds(kk,:) = bonds(comp(kk),:);
-# ## 	end;
-# ##
-# ## to avoid an octave bug in 1.92.
-# ##
-# ## Revision 1.19  1997/08/18 11:23:59  peterg
-# ## Main component loop now misses out the ports (SS:[]) -- the causality
-# ## is merely passed through these components.
-# ##
-# ## Revision 1.18  1997/08/08 08:11:04  peterg
-# ## Suppress compoment trace.
-# ##
-# ## Revision 1.17  1997/08/07 16:10:13  peterg
-# ## Move the if status ..  to the beginning of the main loop.
-# ##
-# ## Revision 1.16  1997/08/04 13:11:19  peterg
-# ## Only change to component-orientated causality for simple components
-# ## NOT for compound components.
-# ##
-# ## Revision 1.15  1997/01/05 12:25:59  peterg
-# ## More informative message about port bonds incompatible with  ports
-# ##
-# ## Revision 1.14  1996/12/31 16:20:42  peterg
-# ## Just write causality information at top level -- it gets a bit
-# ## voluminous if written at deeper levels.
-# ##
-# ## Revision 1.13  1996/12/31 11:49:09  peterg
-# ## Don't copy port bond causality if already set -- allows subsystem
-# ## causality to be preset directely on named SS.
-# ##
-# ## Revision 1.12  1996/12/31 11:42:36  peterg
-# ## *** empty log message ***
-# ##
-# ## Revision 1.11  1996/12/07  17:10:48  peterg
-# ## Allows port SS at top level - ie takes it to be an ardianry SS at top
-# ## level.
-# ##
-# ## Revision 1.10  1996/12/04 21:48:55  peterg
-# ## Compares full-name with empty string (instead of testing for zero
-# ## length.
-# ##
-# ## Revision 1.9  1996/08/30  12:55:40  peter
-# ## More heirachical stuff added.
-# ##
-# ## Revision 1.8  1996/08/26  10:04:25  peterg
-# ## Fixed error due to a line wrap.
-# ##
-# ##Revision 1.7  1996/08/16  12:58:58  peter
-# ## Now does preferred causality of I and C.
-# ## Revision 1.6  1996/08/09 08:27:29  peter
-# ## Added a few deguging lines
-# ##
-# ## Revision 1.5  1996/08/08 18:06:18  peter
-# ## Unified file naming scheme
-# ##
-# ## Revision 1.4  1996/08/08 08:30:06  peter
-# ## The cbg filename contains the system name - this makes things easier
-# ## when setting up the m to fig translation and m to ese translation
-# ##
-# ## Revision 1.3  1996/08/05 18:53:21  peter
-# ## Fixed bug passing causality from subsystems.
-# ##
-# ## Revision 1.2  1996/08/05 15:41:41  peter
-# ## Now recursively does causality on subsystems.
-# ##
-# ## Revision 1.1  1996/08/04 17:55:55  peter
-# ## Initial revision
-# ##
-# ###############################################################
+  ## abg2cbg - acausal to causal bg conversion
+  ##
+  ##     ###################################### 
+  ##     ##### Model Transformation Tools #####
+  ##     ######################################
+  ## 
+  ## Matlab function  abg2cbg.m
+  ## Acausal bond graph to causal bond graph: mfile format
+  ## [bonds,status] = abg2cbg(system_name, system_type, full_name, port_bonds, infofile)
+
+  ## ###############################################################
+  ## ## Version control history
+  ## ###############################################################
+  ## ## $Id$
+  ## ## $Log$
+  ## ## Revision 1.46  2000/02/17 16:14:49  peterg
+  ## ## *** empty log message ***
+  ## ##
+  ## ## Revision 1.45  1999/11/01 03:17:45  peterg
+  ## ## Added extra info - current subsystem
+  ## ##
+  ## ## Revision 1.44  1999/03/11 23:54:11  peterg
+  ## ## Include possibility of vector SS when finding port_bond_index
+  ## ##
+  ## ## Revision 1.43  1998/12/14 15:19:36  peterg
+  ## ## Added missing "derivative_causality," argument to recursive call of
+  ## ## this function
+  ## ##
+  ## ## Revision 1.42  1998/12/03 14:55:40  peterg
+  ## ## Now uses number of components with complete causality to measure
+  ## ## progress of algorithm -- Done.
+  ## ## This replaces bond count -- done.
+  ## ##
+  ## ## Revision 1.41  1998/11/20 10:52:28  peterg
+  ## ## Copies port bonds if the port bonds ARE set
+  ## ## -- replaces Copies port bonds if the component bonds are NOT set
+  ## ##
+  ## ## Revision 1.40  1998/09/02 11:47:09  peterg
+  ## ## Now uses explicit ordered list of ports instead of port.index.
+  ## ## Note that subsystems are still treated in arbitrary order.
+  ## ##
+  ## ## Revision 1.39  1998/08/25 20:06:16  peterg
+  ## ## Writes flipped port info
+  ## ##
+  ## ## Revision 1.38  1998/08/25 09:15:28  peterg
+  ## ## Fixed couple of problems with using two copies of the one data
+  ## ## stucture:
+  ## ##
+  ## ## ABG_field and ABG.field
+  ## ##
+  ## ## Maybe this is conceptually wrong?
+  ## ##
+  ## ## Revision 1.37  1998/08/25 08:33:29  peterg
+  ## ## Now does ports as well - fixed string prob by using deblank
+  ## ##
+  ## ## Revision 1.36  1998/08/25 06:44:40  peterg
+  ## ## Furhter revisions
+  ## ##
+  ## ## Revision 1.35  1998/08/24 10:16:32  peterg
+  ## ## Coverted to new structure - still needs status sorting.
+  ## ##
+  ## ## Revision 1.34  1998/08/24 07:35:03  peterg
+  ## ## About to go to new abg format.
+  ## ##
+  ## ## Revision 1.33  1998/07/29 13:36:37  peterg
+  ## ## Don't set port status if there aren't any ports.
+  ## ##
+  ## ## Revision 1.32  1998/07/28 19:06:11  peterg
+  ## ## *** empty log message ***
+  ## ##
+  ## ## Revision 1.31  1998/07/28 13:15:10  peterg
+  ## ## Vector SS ports included.
+  ## ##
+  ## ## Revision 1.30  1998/07/27 20:29:49  peterg
+  ## ## Had another go at causality ....
+  ## ##   1. Impose external causality onto all port bonds
+  ## ##   2. Set C_cause.m so that it DOESN'T set causality
+  ## ##       -- I_cause is already ok !
+  ## ##
+  ## ## Revision 1.29  1998/07/10 09:01:42  peterg
+  ## ## Added error + info file in new form
+  ## ##
+  ## ## Revision 1.28  1998/07/08 09:23:42  peterg
+  ## ## Undid the previous change -- needs more thought.
+  ## ##
+  ## ## Revision 1.27  1998/07/03 19:03:31  peterg
+  ## ## Always override the causality of port bonds!
+  ## ##
+  ## ## Revision 1.26  1998/06/27 13:24:04  peterg
+  ## ## Causality now set correctly for:
+  ## ## 	multi-port C and I
+  ## ## 	C and I with arrows pointing in
+  ## ##
+  ## ## Revision 1.25  1998/06/25 18:53:30  peterg
+  ## ## Actually, the previous comment was optimistic.
+  ## ## The port causalities on a compound are now forced to be the same as
+  ## ## that specified by a a _cuase.m file (if it exists)
+  ## ##
+  ## ## Revision 1.24  1998/06/25 17:45:03  peterg
+  ## ## No change -- but checked that explicit causality works!
+  ## ##
+  ## ## Revision 1.23  1998/04/04 10:46:37  peterg
+  ## ## Coerces port bonds to have smae direction as the imposing bonds
+  ## ## _cbg now generates the (coerced) components as welll as the (coerced)
+  ## ## causality.
+  ## ##
+  ## ## Revision 1.22  1997/08/19 10:21:09  peterg
+  ## ## Only copy port cuaslity info if not already set within the
+  ## ## subsystem. I thought I'd done this already ....
+  ## ##
+  ## ## Revision 1.21  1997/08/18 16:25:25  peterg
+  ## ## Minor bug fixes
+  ## ##
+  ## ## Revision 1.20  1997/08/18 12:45:24  peterg
+  ## ## Replaced: comp_bonds = bonds(bond_list,:)
+  ## ## by: 	for kk = 1:n_comp
+  ## ## 	  comp_bonds(kk,:) = bonds(comp(kk),:);
+  ## ## 	end;
+  ## ##
+  ## ## to avoid an octave bug in 1.92.
+  ## ##
+  ## ## Revision 1.19  1997/08/18 11:23:59  peterg
+  ## ## Main component loop now misses out the ports (SS:[]) -- the causality
+  ## ## is merely passed through these components.
+  ## ##
+  ## ## Revision 1.18  1997/08/08 08:11:04  peterg
+  ## ## Suppress compoment trace.
+  ## ##
+  ## ## Revision 1.17  1997/08/07 16:10:13  peterg
+  ## ## Move the if status ..  to the beginning of the main loop.
+  ## ##
+  ## ## Revision 1.16  1997/08/04 13:11:19  peterg
+  ## ## Only change to component-orientated causality for simple components
+  ## ## NOT for compound components.
+  ## ##
+  ## ## Revision 1.15  1997/01/05 12:25:59  peterg
+  ## ## More informative message about port bonds incompatible with  ports
+  ## ##
+  ## ## Revision 1.14  1996/12/31 16:20:42  peterg
+  ## ## Just write causality information at top level -- it gets a bit
+  ## ## voluminous if written at deeper levels.
+  ## ##
+  ## ## Revision 1.13  1996/12/31 11:49:09  peterg
+  ## ## Don't copy port bond causality if already set -- allows subsystem
+  ## ## causality to be preset directely on named SS.
+  ## ##
+  ## ## Revision 1.12  1996/12/31 11:42:36  peterg
+  ## ## *** empty log message ***
+  ## ##
+  ## ## Revision 1.11  1996/12/07  17:10:48  peterg
+  ## ## Allows port SS at top level - ie takes it to be an ardianry SS at top
+  ## ## level.
+  ## ##
+  ## ## Revision 1.10  1996/12/04 21:48:55  peterg
+  ## ## Compares full-name with empty string (instead of testing for zero
+  ## ## length.
+  ## ##
+  ## ## Revision 1.9  1996/08/30  12:55:40  peter
+  ## ## More heirachical stuff added.
+  ## ##
+  ## ## Revision 1.8  1996/08/26  10:04:25  peterg
+  ## ## Fixed error due to a line wrap.
+  ## ##
+  ## ##Revision 1.7  1996/08/16  12:58:58  peter
+  ## ## Now does preferred causality of I and C.
+  ## ## Revision 1.6  1996/08/09 08:27:29  peter
+  ## ## Added a few deguging lines
+  ## ##
+  ## ## Revision 1.5  1996/08/08 18:06:18  peter
+  ## ## Unified file naming scheme
+  ## ##
+  ## ## Revision 1.4  1996/08/08 08:30:06  peter
+  ## ## The cbg filename contains the system name - this makes things easier
+  ## ## when setting up the m to fig translation and m to ese translation
+  ## ##
+  ## ## Revision 1.3  1996/08/05 18:53:21  peter
+  ## ## Fixed bug passing causality from subsystems.
+  ## ##
+  ## ## Revision 1.2  1996/08/05 15:41:41  peter
+  ## ## Now recursively does causality on subsystems.
+  ## ##
+  ## ## Revision 1.1  1996/08/04 17:55:55  peter
+  ## ## Initial revision
+  ## ##
+  ## ###############################################################
 
   mtt_info(sprintf("Completing causality for subsystem %s", system_name), infofile);
 
   pc = '%';
   if nargin<1
@@ -201,61 +204,61 @@
 
   if nargin<5
     infofile = 'stdout';
   end;
 
-# Are we at the top level of the heirarchy?
+  ## Are we at the top level of the heirarchy?
   at_top_level = strcmp(full_name, '');
 
-# Create a file to contain shell commands which map subsystem types 
-# onto components
+  ## Create a file to contain shell commands which map subsystem types 
+  ## onto components
   if at_top_level # Then at top level
     fprintf(typefile, "# Commands to map types onto subsystems\n");
     fprintf(typefile, "# File %s_type.sh\n", system_name);
     fprintf(typefile, "# Generated by MTT at %s\n\n", ctime(time));
   end;
 
-# Create the (full) system name
+  ## Create the (full) system name
   if at_top_level
     full_name = system_name;
     system_type = system_name;
   else
     full_name = [full_name, "_", system_name];
   end;
   
 
-# Add to file to contain shell commands which map subsystem types 
-# onto components
+  ## Add to file to contain shell commands which map subsystem types 
+  ## onto components
   fprintf(typefile, "$1%s$2%s$3\n", system_type, full_name);
 
   fun_name = [system_type, "_abg"];
 
   disp("====================================");
   disp(["BEGIN: ", full_name, " (", fun_name, ")"]);
   disp("====================================");
 
-# If no such function - then there is nothing to be done.
+  ## If no such function - then there is nothing to be done.
   if exist(fun_name)~=2
     mtt_error(["m-file ", fun_name, " does not exist"], errorfile);
     bonds = [];
     status = [];
     return
   end;
 
-# Evaluate the system function to get the bonds and number of ports
-#eval(["[bonds,components,n_ports,N_ports]=", fun_name, ";"]);
+  ## Evaluate the system function to get the bonds and number of ports
+  ##eval(["[bonds,components,n_ports,N_ports]=", fun_name, ";"]);
   eval(["[ABG]=", fun_name, ";"]);
-!struct_contains(ABG,"subsystems")
+  !struct_contains(ABG,"subsystems")
   if !struct_contains(ABG,"subsystems")# Are there any subsystems?
     return;			# Nothing to do
   else
     [n_subsystems,junk] = size(struct_elements(ABG.subsystems))
   endif
   
   if struct_contains(ABG,"portlist")# Are there any ports?
     [n_ports,junk] = size(ABG.portlist);
-#     port_bond_index=zeros(n_ports,1);
+    ##     port_bond_index=zeros(n_ports,1);
     i_port = 0;
     for i=1:n_ports		# Find indices of the internal ports
       name = deblank(ABG.portlist(i,:)); # Name of this port
       eval(["port = ABG.ports.",name,";"]); # Extract port info
       for j=1:length(port.connections) # Maybe vector SS
@@ -264,39 +267,39 @@
     endfor
   else
     n_ports = 0;
   endif				   
 
-				
+  
   [n_bonds,columns] = size(ABG.bonds);# Find number of bonds
   if (columns ~= 2)&(n_bonds>0)
     error("Incorrect bonds matrix: must have 2 columns");
   end;
 
- 
-## Find number of components
-#  [n_components,m_components] = size(components);
-#  if n_components==0 # there is nothing to be done
-#    return
-#  end;
+  
+  ## Find number of components
+  ##  [n_components,m_components] = size(components);
+  ##  if n_components==0 # there is nothing to be done
+  ##    return
+  ##  end;
 
 
   
-# Coerce the port (SS:[]) component bonds to have the same direction as
-# of the bonds in the encapsulating system -- but not at top level
+  ## Coerce the port (SS:[]) component bonds to have the same direction as
+  ## of the bonds in the encapsulating system -- but not at top level
   Flipped.ports="";Flipped.subs="";Flipped.cons="";
   
   if (n_ports>0)&&(!at_top_level) # Coerce directions
     for i=1:n_ports
       name = deblank(ABG.portlist(i,:)); # Name of this port
       eval(["port = ABG.ports.",name,";"]); # Extract port info
-disp ("----");
-i
-name
-port
-port_bond_direction
-port.connections
+      disp ("----");
+      i
+      name
+      port
+      port_bond_direction
+      port.connections
 
       if (sign(port.connections)!=port_bond_direction(i)) # Direction different?
       	eval(["ABG.ports.",name,".connections = - port.connections;"]); # Flip direction at port
 	Flipped.ports=[Flipped.ports;name];	# Remember which port has been flipped
         bond_index=abs(port.connections); # Index of bond on port
@@ -303,49 +306,49 @@
       	mtt_info(sprintf("Flip port %s on %s"\
 			 ,name,full_name),infofile); # And report
       	for [subsystem,name] = ABG.subsystems # and at the other end
 	  for k=1:length(subsystem.connections)
 	    if (abs(subsystem.connections(k))==bond_index) # Then flip the connection
-	    eval(["ABG.subsystems.",name,".connections(k)   = -subsystem.connections(k);"]);
-	    Flipped.subs=[Flipped.subs;name];	# Remember which subsystem has been flipped
-	    Flipped.cons=[Flipped.cons;k];	# Remember which connection has been flipped
-      	    mtt_info(sprintf("Flip subsystem %s on %s"\
-			     ,name,full_name),infofile); # And report
+	      eval(["ABG.subsystems.",name,".connections(k)   = -subsystem.connections(k);"]);
+	      Flipped.subs=[Flipped.subs;name];	# Remember which subsystem has been flipped
+	      Flipped.cons=[Flipped.cons;k];	# Remember which connection has been flipped
+      	      mtt_info(sprintf("Flip subsystem %s on %s"\
+			       ,name,full_name),infofile); # And report
 	    endif
 	  endfor
       	endfor			# subsystem = ABG.subsystems
 
       	ABG.bonds(bond_index,:) = -ABG.bonds(bond_index,:);	# Flip the bond causalities 
-				#(these are arrow-orientated)
+	##(these are arrow-orientated)
       endif			# Is the direction different?
     endfor			# port = ABG.ports
   endif				# (n_ports>0)&&(!at_top_level)
 
-# If not at top level, then copy the port bonds.
+  ## If not at top level, then copy the port bonds.
   if !at_top_level		# Find number of port bonds
 
     for j=1:n_ports
       jj = port_bond_index(j); # The index of the bond
       for k = 1:2
-#	if ABG.bonds(jj,k)==0 # only copy if not already set
-#	  ABG.bonds(jj,k) = port_bonds(j,k);
-#	endif
+	##	if ABG.bonds(jj,k)==0 # only copy if not already set
+	##	  ABG.bonds(jj,k) = port_bonds(j,k);
+	##	endif
 	if port_bonds(j,k)!=0	# only copy if port bonds are set
 	  ABG.bonds(jj,k) = port_bonds(j,k);
 	endif
       endfor
     endfor
   else
     n_port_bonds=0;
   endif
   
-# Causality indicator
+  ## Causality indicator
   total = 2*n_bonds;
   done = sum(sum(abs(ABG.bonds)))/total*100;
 
   fields=["ports";"subsystems"];	# Do for both ports and subsystems -
-				# ports first
+  ## ports first
   for i=1:2
     field=deblank(fields(i,:));
     if struct_contains(ABG,field);
       eval(["ABG_field = ABG.",field, ";"]);
       field,ABG_field
@@ -355,25 +358,25 @@
     	eval(["ok = (ABG_field.",name,".status==0);"]);
 	sum_ok = sum_ok + ok; n_comp ++;
       endfor;
       Done = sum_ok/n_comp*100
       
-# Outer while loop sets preferred causality
+      ## Outer while loop sets preferred causality
       ci_index=1;
 
-#      for [subsystem,name] = ABG_field# Set new status field to -1
-#    	eval(["ABG_field.",name,".status=-1;"]);
-#      endfor;
+      ##      for [subsystem,name] = ABG_field# Set new status field to -1
+      ##    	eval(["ABG_field.",name,".status=-1;"]);
+      ##      endfor;
       
       while( ci_index>0)
     	old_done = inf;
     	old_Done = inf;
 	
     	while Done!=old_Done	# Inner loop propagates causality
 	  old_Done = Done;
 	  for [subsystem,name] = ABG_field
-name,subsystem
+	    name,subsystem
       	    if subsystem.status != 0 # only do this if causality not yet complete
 	      comp = subsystem.connections; # Get the bonds on this component
 	      bond_list = abs(comp);
 	      direction = sign(comp)'*[1 1];
               n_bonds = length(bond_list);
@@ -382,22 +385,22 @@
 	    	subsystem.type = "zero";
 	      end;
 	      if strcmp(subsystem.type,"1")
 	    	subsystem.type = "one";
 	      end;
-				
+	      
 	      cause_name = [subsystem.type, "_cause"];# Component causality procedure name
 	      eqn_name = [subsystem.type, "_eqn"]; #Component equation procedure name
 	      
 	      comp_bonds=[];	# Bonds on this component (arrow-orientated) -- these become the
 	      for kk = 1:n_bonds # port bonds on the ith component of this subsystem.
 	    	comp_bonds(kk,:) = ABG.bonds(bond_list(kk),:);
 	      end;
 
 	      if exist(eqn_name)!=2 # Try a compound component
-				# Port status depends on whether the corresponding bonds are
-				#  fully causal at this stage.
+		## Port status depends on whether the corresponding bonds are
+		##  fully causal at this stage.
             	one = ones(n_bonds,1);
             	port_status = (sum(abs(comp_bonds'))'==2*one) - one;
 		
 	    	port_bond_direction = -sign(subsystem.connections)'; # Direction of bonds
 
@@ -406,37 +409,30 @@
 		  eval([ "[comp_bonds] = ", cause_name, "(comp_bonds);" ]); # Evaluate the built-in causality procedure
 
 		  comp_bonds = comp_bonds.*(port_bond_direction*[1 1]);	# and convert from component orientated to arrow orientated causality
             	end;
 		
-port_bond_direction,comp_bonds
+		port_bond_direction,comp_bonds
 	    	[comp_bonds,subsystem.status] = abg2cbg(name, subsystem.type, full_name, 
 							comp_bonds, port_bond_direction, port_status, ...
 							derivative_causality, ...
 						    	typefile, infofile, errorfile);
-				#	# Create a single status from the status vector s
-				#	    if max(abs(s)) == 0 # Causal
-				#	      status(i) = 0;
-				#	    else
-				#	      if max(s) == 1 # At least one component is overcausal
-				#	    	status(i) = 1;
-				#	      else           # no component is overcausal but some are undercausal
-				#	    	status(i) = -1;
-				#	      end;
-				#	    end;
+
 		
 	      else # its a simple component -- or explicit causality defined
+		mtt_info(sprintf("Completing causality for component %s (%s)",
+				 name, subsystem.type), infofile);
 	    	disp(["---", name, " (", cause_name, ") ---"]);
 	    	comp_bonds_in = comp_bonds
 	    	
-				# Convert from arrow orientated to component orientated causality
+		## Convert from arrow orientated to component orientated causality
 	    	comp_bonds = comp_bonds.*direction;
 	    	
-				# Evaluate the built-in causality procedure
-				#eval([ "[comp_bonds,status(i)] = ", cause_name, "(comp_bonds);" ]);
+		## Evaluate the built-in causality procedure
+		##eval([ "[comp_bonds,status(i)] = ", cause_name, "(comp_bonds);" ]);
 	    	eval([ "[comp_bonds,subsystem.status] = ", cause_name, "(comp_bonds)" ]);
-				# and convert from component orientated to arrow orientated causality
+		## and convert from component orientated to arrow orientated causality
             	comp_bonds = comp_bonds.*direction; 
 		
 	    	comp_bonds_out = comp_bonds
 	      end;
 	      
@@ -451,11 +447,11 @@
 	    sum_ok = sum_ok + ok; n_comp ++;
 	  endfor;
 
 	  Done = sum_ok/n_comp*100
 	  done = sum(sum(abs(ABG.bonds)))/total*100
-				#disp(sprintf("Causality is #3.0f#s complete.", done, pc), infofile));
+	  ##disp(sprintf("Causality is #3.0f#s complete.", done, pc), infofile));
 	  
     	endwhile			# done!=old_done
   	
     	[name,prefered] = getdynamic(ABG_field) # Set causality of a C or I which is not already set
     	if prefered==0
@@ -473,16 +469,16 @@
     	endif
       endwhile			# ( ci_index>0)
       eval(["ABG.",field," = ABG_field;"]); # Copy back to actual structure
     endif			# struct_contains(CBG,field(i,:));
   endfor
-#  if n_ports>0
-#    status(1:n_ports) = zeros(n_ports,1); # Port status not relevant
-#  endif;
+  ##  if n_ports>0
+  ##    status(1:n_ports) = zeros(n_ports,1); # Port status not relevant
+  ##  endif;
   
-				# Print final causality
-				#  final_done =  (sum(status==zeros(n_components,1))/n_components)*100;
+  ## Print final causality
+  ##  final_done =  (sum(status==zeros(n_components,1))/n_components)*100;
   
   if at_top_level
     mtt_info(sprintf("Final causality of %s is %3.0f%s complete.", ...
 		     full_name, Done, pc), infofile);
     
@@ -493,11 +489,11 @@
   
 
   disp(["Writing ", full_name]);
   write_cbg(full_name,system_type,ABG,Flipped);
   
-				# Return the port bonds - arrow orientated causality - and the direction 
+  ## Return the port bonds - arrow orientated causality - and the direction 
   status=0;
   if !at_top_level # Not at top level
     port_bonds = ABG.bonds(port_bond_index,:); # Return port bonds
   endif;				# at top level