function [port_bonds, status] = abg2cbg(system_name, system_type, full_name,
					port_bonds,
					port_bond_direction,
					port_status,
					typefile, infofile, errorfile)

% abg2cbg - acausal to causal bg conversion
# abg2cbg - acausal to causal bg conversion
%
%     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
%     %%%%% Model Transformation Tools %%%%%
%     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
#
#     ###################################### 
#     ##### 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)
# 
# 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
% %%
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# ###############################################################
# ## 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;
  pc = '%';
  if nargin<1
    system_name = 'no_name';
  end;

if nargin<4
  port_bonds = [];
end;
  if nargin<4
    port_bonds = [];
  end;

if nargin<5
  infofile = 'stdout';
end;
  if nargin<5
    infofile = 'stdout';
  end;

% Are we at the top level of the heirarchy?
at_top_level = strcmp(full_name, '');
# 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 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;

# 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);
# 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'];
  fun_name = [system_type, "_abg"];

disp('====================================');
disp(['BEGIN: ', full_name, ' (', fun_name, ')']);
disp('====================================');
  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;
# 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;
# 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;
## 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
  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
# 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
    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);
# 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);
# 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);
  # 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;
    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
      end
    end
  else
    n_port_bonds=0;
  end;
# bonds,port_bonds

% Causality indicator
total = 2*n_bonds;
done = sum(sum(abs(bonds)))/total*100;
# Causality indicator
  total = 2*n_bonds;
  done = sum(sum(abs(bonds)))/total*100;

% Outer while loop sets preferred causality
ci_index=1;
# 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)
  while( ci_index>0)
  ci_index
  old_done = inf;
  % Inner loop propagates causality
  while done~=old_done
    old_done = inf;
				
    while done~=old_done	# Inner loop propagates causality
   % disp(sprintf('Causality is %3.0f%s complete.', done, pc));
    old_done = done;
      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
      for [subsystem,name] = ABG.subsystems
      	if subsystem.status ~= 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 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(comp_type,'0')
	  comp_type = 'zero';
	end;
	if strcmp(comp_type,'1')
	  comp_type = 'one';
	end;
	# 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 = [comp_type, '_cause'];
	# Component causality procedure name
	  cause_name = [subsystem.type, "_cause"];

	% Component equation procedure name
	eqn_name = [comp_type, '_eqn'];
	# 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.
        # 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;
	  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;
      # 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))';
	# 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]);
	# 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);' ]);
          # 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;
         # 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);
	    [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;
	# 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; 
	  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;
	    comp_bonds_out = comp_bonds
	  end;

      bonds,bond_list,comp_bonds
      % Update the full bonds list
      bonds(bond_list,:) = comp_bonds;
    end;
    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));
      done = sum(sum(abs(bonds)))/total*100;
    #disp(sprintf("Causality is #3.0f#s complete.", done, pc), infofile));
    
  end;
    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;
  # 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;
  end;

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, final_done, pc), infofile);
  mtt_info(sprintf("Final causality of #s is #3.0f#s complete.", ...
      full_name, done, pc), infofile);

  if final_done<100
  if done<100
	  mtt_error(sprintf("Unable to complete causality"),errorfile);
  end;
 
  % List overcausal bonds
  # 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), ...
      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
  # 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), ...
      eval([ "[comp_type,name] = ", system_type, "_cmp(i);" ]);
      mtt_info(sprintf("Component #s (#s) is undercausal", name, subsystem.type), ...
	  infofile);
    end;
  end;
end;

% $$$ file_name = [full_name, '_', system_type]
file_name = [full_name, '_cbg.m'];
disp(['Writing ', file_name]);
cbgfilenum = fopen(file_name,'w');
# $$$ 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
# 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('====================================');
disp("====================================");
disp(["END: ", full_name, " (", fun_name, ")"]);
disp("====================================");