Index: mttroot/mtt/bin/trans/m/abg2cbg.m
==================================================================
--- mttroot/mtt/bin/trans/m/abg2cbg.m
+++ mttroot/mtt/bin/trans/m/abg2cbg.m
@@ -2,450 +2,477 @@
 					port_bonds,
 					port_bond_direction,
 					port_status,
 					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 1.33  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
-% %%
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-pc = '%';
-if nargin<1
-  system_name = 'no_name';
-end;
-
-if nargin<4
-  port_bonds = [];
-end;
-
-if nargin<5
-  infofile = 'stdout';
-end;
-
-% 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
-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 on %s\n\n', date);
-end;
-
-% 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
-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 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, ';']);
-
-% Find number of bonds
-[n_bonds,columns] = size(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;
-
-port_bond_direction
-
-% Coerce the port (SS:[]) component bonds to have the same direction as
-% of the bonds in the encapsulating system -- but not at top level
-if (n_ports>0)&&(~at_top_level)
-  port_bond_index = abs(components(1:n_ports,1:m_components))# relevant
-							     # bond
-							     # numbers
-  port_bond_index = nozeros(reshape(\
-                          port_bond_index',n_ports*m_components,1))'# vectorise
-
-  for i=1:n_ports
-    % Is the direction different?
-    if (sign(components(i,1))~=port_bond_direction(i))
-      mtt_info(sprintf("Flip port %i",i),infofile);
-      % Flip direction at port
-      components(i,1) = - components(i,1);
-      % and at the other end
-      for j=n_ports+1:n_components
-	for k=1:m_components
-	  if (abs(components(j,k))==port_bond_index(i))
-	    components(j,k) = - components(j,k);
-	  end
-	end
-      end;
-      % Flip the bond causalities (these are arrow-orientated)
-      bonds(port_bond_index(i),:) = -bonds(port_bond_index(i),:);
-    end
-  end
-end
-
-
-
-% Set initial status
-status = -ones(n_components,1);
-
-% If not at top level, then copy the port bonds.
-if ~at_top_level 
-  % Find number of port bonds
-  [n_port_bonds,columns] = size(port_bonds);
-
-  % Check compatibility - if ok copy port bonds to the internal bonds list.
-  if n_port_bonds~=N_ports
-  mtt_error(sprintf('%s: %1.0f port bonds incompatible with %1.0f ports', ...
-               full_name, n_port_bonds, n_ports), errorfile);
-
-  else % Copy the port bonds & status
-    for j = 1:n_port_bonds
-      jj = port_bond_index(j);
-      for k = 1:2
-	if bonds(jj,k)==0 % only copy if not already set
-	bonds(jj,k) = port_bonds(j,k);
-	end;
-      end;
-#      status(1:N_ports) = port_status;
-    end
-  end
-else
-  n_port_bonds=0;
-end;
-% bonds,port_bonds
-
-% Causality indicator
-total = 2*n_bonds;
-done = sum(sum(abs(bonds)))/total*100;
-
-% Outer while loop sets preferred causality
-ci_index=1;
-
-while( ci_index>0)
-  ci_index
-  old_done = inf;
-  % Inner loop propagates causality
-  while done~=old_done
-   % disp(sprintf('Causality is %3.0f%s complete.', done, pc));
-    old_done = done;
-done,ci_index  
-    for i = n_ports+1:n_components % Miss out the ports 
-      if status(i) ~= 0 % only do this if causality not yet complete
-
-	% Get the bonds on this component
-	comp = nozeros(components(i,:));
-	bond_list = abs(comp);
-	direction = sign(comp)'*[1 1];
-        n_bonds = length(bond_list);
-
-	% Get the component details
-	eval([ '[comp_type,name,cr,arg] = ', system_type, '_cmp(i);' ]);
-
-	% Change name of 0 and 1 components -- matlab doesn't like numbers here
-	if strcmp(comp_type,'0')
-	  comp_type = 'zero';
-	end;
-	if strcmp(comp_type,'1')
-	  comp_type = 'one';
-	end;
-      
-	% Component causality procedure name
-	cause_name = [comp_type, '_cause'];
-
-	% Component equation procedure name
-	eqn_name = [comp_type, '_eqn'];
-	
-        % Bonds on this component (arrow-orientated) -- these become the
-        % port bonds on the ith component of this subsystem.
-	
-	comp_bonds=[];
-	for kk = 1:n_bonds
-	  comp_bonds(kk,:) = bonds(bond_list(kk),:);
-	end;
-	
-
-      % Invoke  the appropriate causality procedure
-      if exist(eqn_name)~=2 % Try a compound component
-        % 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;
-
-	% Direction of bonds on the ports (0 if next to port)
-	port_bond_direction = -sign(components(i,1:n_bonds))';
-
-	% If there is a predefined causality function; use it
-        if exist(cause_name)==2
-    	  % Convert from arrow orientated to component orientated causality
-	  comp_bonds = comp_bonds.*(port_bond_direction*[1 1]);
-	
-          % Evaluate the built-in causality procedure
-	  eval([ '[comp_bonds] = ', cause_name, '(comp_bonds);' ]);
-
-         % and convert from component orientated to arrow orientated causality
-         comp_bonds = comp_bonds.*(port_bond_direction*[1 1]); 
-        end;
-
-	[comp_bonds,s] = abg2cbg(name, comp_type, full_name, 
-            comp_bonds, port_bond_direction, port_status, ...
-	    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
-	disp(['---', name, ' (', cause_name, ') ---']);
-	comp_bonds_in = comp_bonds
-
-	% 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);' ]);
-
-        % and convert from component orientated to arrow orientated causality
-        comp_bonds = comp_bonds.*direction; 
-       
-       comp_bonds_out = comp_bonds
-      end;
-
-      bonds,bond_list,comp_bonds
-      % Update the full bonds list
-      bonds(bond_list,:) = comp_bonds;
-    end;
-    end;
-    
-    done = sum(sum(abs(bonds)))/total*100;
-    %disp(sprintf('Causality is %3.0f%s complete.', done, pc), infofile));
-    
-  end;
-  
-  % Set causality of a C or I which is not already set
-  [ci_index,prefered] = getdynamic(status,system_type)
-  if ci_index>0
-    disp('Set causality of a C or I which is not already set')
-    ci_bond_index = nozeros(components(ci_index,:)); # Get all bonds
-    ci_direction = sign(ci_bond_index);
-    ci_bond_index = abs(ci_bond_index);
-    bonds(ci_bond_index,1:2) = prefered*ci_direction'*[1 1];
-  end;
-  
-end;
-
-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;
-
-if at_top_level
-  mtt_info(sprintf('Final causality of %s is %3.0f%s complete.', ...
-      full_name, final_done, pc), infofile);
-
-  if final_done<100
-	  mtt_error(sprintf("Unable to complete causality"),errorfile);
-  end;
- 
-  % List overcausal bonds
-  [over_causal_bonds,n] = getindex(status,1);
-  if n>0
-    for i=over_causal_bonds'
-      eval([ '[comp_type,name] = ', system_type, '_cmp(i);' ]);
-      mtt_info(sprintf('Component %s (%s) is overcausal', name, comp_type), ...
-	  infofile);
-    end;
-  end;
-  
-  % List undercausal bonds
-  [under_causal_bonds,n] = getindex(status,-1);
-  if n>0
-    for i=under_causal_bonds'
-      eval([ '[comp_type,name] = ', system_type, '_cmp(i);' ]);
-      mtt_info(sprintf('Component %s (%s) is undercausal', name, comp_type), ...
-	  infofile);
-    end;
-  end;
-end;
-
-% $$$ file_name = [full_name, '_', system_type]
-file_name = [full_name, '_cbg.m'];
-disp(['Writing ', file_name]);
-cbgfilenum = fopen(file_name,'w');
-write_cbg(cbgfilenum,full_name,system_type,bonds,status,components);
-fclose(cbgfilenum);
-
-% Return the port bonds - arrow orientated causality - and the direction 
-if ~at_top_level % Not at top level
-  port_bonds = bonds(port_bond_index,:) # Return port bonds
-end;
-
-disp('====================================');
-disp(['END: ', full_name, ' (', fun_name, ')']);
-disp('====================================');
+# 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 1.34  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
+# ##
+# ###############################################################
+
+  pc = '%';
+  if nargin<1
+    system_name = 'no_name';
+  end;
+
+  if nargin<4
+    port_bonds = [];
+  end;
+
+  if nargin<5
+    infofile = 'stdout';
+  end;
+
+# 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
+  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 on #s\n\n", date);
+  end;
+
+# 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
+  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 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, ";"]);
+  eval(["[ABG]=", fun_name, ";"]);
+  bonds = ABG.bonds;
+  n_ports=0;
+  if !struct_contains(ABG,"subsystems")# Are there any subsystems
+    return;			# Nothing to do
+  else
+    [n_subsystems,junk] = size(struct_elements(ABG.subsystems));
+  endif
+  
+					   
+
+				
+  [n_bonds,columns] = size(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;
+
+  port_bond_direction
+
+# Coerce the port (SS:[]) component bonds to have the same direction as
+# of the bonds in the encapsulating system -- but not at top level
+  if (n_ports>0)&&(~at_top_level)
+    port_bond_index = abs(components(1:n_ports,1:m_components))# relevant
+							     # bond
+							     # numbers
+    port_bond_index = nozeros(reshape(\
+				      port_bond_index',n_ports*m_components,1))'# vectorise
+    
+    for i=1:n_ports
+				# Is the direction different?
+      if (sign(components(i,1))~=port_bond_direction(i))
+      	mtt_info(sprintf("Flip port #i",i),infofile);
+				# Flip direction at port
+      	components(i,1) = - components(i,1);
+				# and at the other end
+      	for j=n_ports+1:n_components
+	  for k=1:m_components
+	    if (abs(components(j,k))==port_bond_index(i))
+	      components(j,k) = - components(j,k);
+	    end
+	  end
+      	end;
+				# Flip the bond causalities (these are arrow-orientated)
+      	bonds(port_bond_index(i),:) = -bonds(port_bond_index(i),:);
+      end
+    end
+  end
+
+
+
+# Set initial status
+  status = -ones(n_subsystems,1);
+
+# If not at top level, then copy the port bonds.
+  if ~at_top_level 
+  # Find number of port bonds
+    [n_port_bonds,columns] = size(port_bonds);
+
+  # Check compatibility - if ok copy port bonds to the internal bonds list.
+    if n_port_bonds~=N_ports
+      mtt_error(sprintf("#s: #1.0f port bonds incompatible with #1.0f ports", ...
+			full_name, n_port_bonds, n_ports), errorfile);
+
+    else # Copy the port bonds & status
+      for j = 1:n_port_bonds
+      	jj = port_bond_index(j);
+      	for k = 1:2
+	  if bonds(jj,k)==0 # only copy if not already set
+	    bonds(jj,k) = port_bonds(j,k);
+	  end;
+      	end;
+#      status(1:N_ports) = port_status;
+      end
+    end
+  else
+    n_port_bonds=0;
+  end;
+# bonds,port_bonds
+
+# Causality indicator
+  total = 2*n_bonds;
+  done = sum(sum(abs(bonds)))/total*100;
+
+# Outer while loop sets preferred causality
+  ci_index=1;
+
+  for [subsystem,name] = ABG.subsystems# Set new status field to -1
+    eval(["ABG.subsystems.",name,".status=-1;"]);
+  endfor;
+  
+  while( ci_index>0)
+    old_done = inf;
+				
+    while done~=old_done	# Inner loop propagates causality
+      old_done = done;
+      for [subsystem,name] = ABG.subsystems
+      	if subsystem.status ~= 0 # only do this if causality not yet complete
+
+	# Get the bonds on this component
+	  comp = subsystem.connections;
+	  bond_list = abs(comp);
+	  direction = sign(comp)'*[1 1];
+          n_bonds = length(bond_list);
+
+	# Get the component details
+	  #eval([ "[comp_type,name,cr,arg] = ", system_type, "_cmp(i);" ]);
+	  
+				# Change name of 0 and 1 components -- matlab doesn't like numbers here
+	  if strcmp(subsystem.type,"0")
+	    subsystem.type = "zero";
+	  end;
+	  if strcmp(subsystem.type,"1")
+	    subsystem.type = "one";
+	  end;
+      
+	# Component causality procedure name
+	  cause_name = [subsystem.type, "_cause"];
+
+	# Component equation procedure name
+	  eqn_name = [subsystem.type, "_eqn"];
+	
+        # Bonds on this component (arrow-orientated) -- these become the
+        # port bonds on the ith component of this subsystem.
+	
+	  comp_bonds=[];
+	  for kk = 1:n_bonds
+	    comp_bonds(kk,:) = bonds(bond_list(kk),:);
+	  end;
+	
+
+      # Invoke  the appropriate causality procedure
+	  if exist(eqn_name)~=2 # Try a compound component
+        # 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;
+
+	# Direction of bonds on the ports (0 if next to port)
+	    port_bond_direction = -sign(components(i,1:n_bonds))';
+
+	# If there is a predefined causality function; use it
+            if exist(cause_name)==2
+    	  # Convert from arrow orientated to component orientated causality
+	      comp_bonds = comp_bonds.*(port_bond_direction*[1 1]);
+	
+          # Evaluate the built-in causality procedure
+	      eval([ "[comp_bonds] = ", cause_name, "(comp_bonds);" ]);
+
+         # and convert from component orientated to arrow orientated causality
+              comp_bonds = comp_bonds.*(port_bond_direction*[1 1]); 
+            end;
+
+	    [comp_bonds,s] = abg2cbg(name, subsystem.type, full_name, 
+				     comp_bonds, port_bond_direction, port_status, ...
+				     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
+	    disp(["---", name, " (", cause_name, ") ---"]);
+	    comp_bonds_in = comp_bonds
+	    
+				# 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);" ]);
+	    eval([ "[comp_bonds,subsystem.status] = ", cause_name, "(comp_bonds);" ]);
+        # and convert from component orientated to arrow orientated causality
+            comp_bonds = comp_bonds.*direction; 
+       
+	    comp_bonds_out = comp_bonds
+	  end;
+
+	  bonds,bond_list,comp_bonds
+				# Update the full bonds list
+	  bonds(bond_list,:) = comp_bonds;
+    	end;
+      end;
+    
+      done = sum(sum(abs(bonds)))/total*100;
+    #disp(sprintf("Causality is #3.0f#s complete.", done, pc), infofile));
+    
+    end;
+  
+  # Set causality of a C or I which is not already set
+    [name,prefered] = getdynamic(ABG.subsystems)
+    if prefered==0
+      ci_index=0;
+    else
+      disp("Set causality of a C or I which is not already set")
+      eval(["ci_bond_index = ABG.subsystems.",name,".connections;"]); # Get all bonds
+      ci_direction = sign(ci_bond_index);
+      ci_bond_index = abs(ci_bond_index);
+      bonds(ci_bond_index,1:2) = prefered*ci_direction'*[1 1];
+      eval(["ABG.subsystems.",name,".status=0"]); #set status of the C or I
+    endif;
+  end;
+
+  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;
+
+if at_top_level
+  mtt_info(sprintf("Final causality of #s is #3.0f#s complete.", ...
+      full_name, done, pc), infofile);
+
+  if done<100
+	  mtt_error(sprintf("Unable to complete causality"),errorfile);
+  end;
+ 
+  # List overcausal bonds
+  [over_causal_bonds,n] = getindex(status,1);
+  if n>0
+    for i=over_causal_bonds'
+      eval([ "[comp_type,name] = ", system_type, "_cmp(i);" ]);
+      mtt_info(sprintf("Component #s (#s) is overcausal", name, subsystem.type), ...
+	  infofile);
+    end;
+  end;
+  
+  # List undercausal bonds
+  [under_causal_bonds,n] = getindex(status,-1);
+  if n>0
+    for i=under_causal_bonds'
+      eval([ "[comp_type,name] = ", system_type, "_cmp(i);" ]);
+      mtt_info(sprintf("Component #s (#s) is undercausal", name, subsystem.type), ...
+	  infofile);
+    end;
+  end;
+end;
+
+# $$$ file_name = [full_name, "_", system_type]
+file_name = [full_name, "_cbg.m"];
+disp(["Writing ", file_name]);
+cbgfilenum = fopen(file_name,"w");
+
+components=[];
+for [subsystem,name] = ABG.subsystems
+  components=add_row(components,subsystem.connections);
+endfor
+
+write_cbg(cbgfilenum,full_name,system_type,bonds,status,components);
+fclose(cbgfilenum);
+
+# Return the port bonds - arrow orientated causality - and the direction 
+if ~at_top_level # Not at top level
+  port_bonds = bonds(port_bond_index,:) # Return port bonds
+end;
+
+disp("====================================");
+disp(["END: ", full_name, " (", fun_name, ")"]);
+disp("====================================");
+
+
+
+
+