ntt: new transformation tools for using bond graphs with Matlab
    Copyright (C) 2003  Dr. Dominic J. Diston

    This program is free software; you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation; either version 2 of the License, or
    (at your option) any later version.

    This program is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.

    You should have received a copy of the GNU General Public License
    along with this program; if not, write to the Free Software
    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
^L
		    GNU GENERAL PUBLIC LICENSE
		       Version 2, June 1991

 Copyright (C) 1989, 1991 Free Software Foundation, Inc.
     59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
 Everyone is permitted to copy and distribute verbatim copies
 of this license document, but changing it is not allowed.

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function abg = make_abg(system)
global mtt_environment

start_time = mttGetTime ;

input = [] ;
abg = [] ;


switch class(system)
case 'char',
    input = 'spec' ;
case 'struct',
    if isfield(system,'representation')
        input = system.representation ;
    end
end    


if strcmp(input,'spec')
    mttWriteNewLine ;
    mttNotify('Making "abg" representation') ;
    mttWriteNewLine ;

    if isempty(mtt_environment)
        mttNotify('...WARNING: No "env" definition => all domain references will be ignored') ;
        mttWriteNewLine ;
        mttNotify('                                => paths will not be recognised') ;
        mttWriteNewLine ;
    end
    
    abg = mttCreateAcausalBondgraph(system) ;
    input = 'abg' ;
end

mttAssert(strcmp(input,'abg'),'Input representation not recognised') ;

if isempty(abg)
    mttWriteNewLine ;
    mttNotify('Copying "abg" representation') ;
    mttWriteNewLine ;
    
    mttNotify('...INFO: Input already defined as a "abg": copying to Output') ;
    mttWriteNewLine ;
    mttWriteNewLine ;
    abg = system ;
end


elapsed_time = mttElapseTime(start_time) ;
cpu_utilisation = round(100*elapsed_time.cpu/elapsed_time.clock) ;

mttWriteNewLine ;    
mttNotify(['Completed in ',num2str(elapsed_time.clock),' seconds']) ;
mttNotify([' (',num2str(cpu_utilisation),'%% cpu)']) ;
mttWriteNewLine ;    
mttWriteNewLine ;

function cbg = make_cbg(system)
global mtt_environment

start_time = mttGetTime ;

input = [] ;
abg = [] ;
cbg = [] ;


switch class(system)
case 'char',
    input = 'spec' ;
case 'struct',
    if isfield(system,'representation')
        input = system.representation ;
    end
end    


if strcmp(input,'spec')
    mttWriteNewLine ;
    mttNotify('Making "abg" representation') ;
    mttWriteNewLine ;

    if isempty(mtt_environment)
        mttNotify('...WARNING: No "env" definition => all domain references will be ignored') ;
        mttWriteNewLine ;
        mttNotify('                                => paths will not be recognised') ;
        mttWriteNewLine ;
    end
    
    abg = mttCreateAcausalBondgraph(system) ;
    input = 'abg' ;
end

if strcmp(input,'abg')
    if isempty(abg)
        abg = system ;
    end
    
    mttWriteNewLine ;
    mttNotify('Transforming from "abg" to "cbg"') ;
    mttWriteNewLine ;
    cbg = mttCreateCausalBondgraph(abg) ;
    input = 'cbg' ;
end

mttAssert(strcmp(input,'cbg'),'Input representation not recognised') ;

if isempty(cbg)
    mttWriteNewLine ;
    mttNotify('Copying "cbg" representation') ;
    mttWriteNewLine ;

    mttNotify('...INFO: Input already defined as a "cbg": copying to Output') ;
    mttWriteNewLine ;
    mttWriteNewLine ;
    cbg = system ;
end


elapsed_time = mttElapseTime(start_time) ;
cpu_utilisation = round(100*elapsed_time.cpu/elapsed_time.clock) ;

mttWriteNewLine ;    
mttNotify(['Completed in ',num2str(elapsed_time.clock),' seconds']) ;
mttNotify([' (',num2str(cpu_utilisation),'%% cpu)']) ;
mttWriteNewLine ;    
mttWriteNewLine ;

function make_env(system)
global mtt_environment

start_time = mttGetTime ;

input = [] ;
env = [] ;


switch class(system)
case 'char',
    input = 'spec' ;
case 'struct',
    if isfield(system,'representation')
        input = system.representation ;
    end
end    

if strcmp(input,'spec')
    mttWriteNewLine ;
    mttNotify('Making "env" representation') ;
    mttWriteNewLine ;

    env = mttCreateEnvironment(system) ;
    input = 'env' ;
end

mttAssert(strcmp(input,'env'),'Input representation not recognised') ;

if isempty(env)
    mttWriteNewLine ;
    mttNotify('Copying "env" representation') ;
    mttWriteNewLine ;

    mttNotify('...INFO: Input already defined as a "env": copying to Output') ;
    mttWriteNewLine ;
    mttWriteNewLine ;
    env = system ;
end


elapsed_time = mttElapseTime(start_time) ;
cpu_utilisation = round(100*elapsed_time.cpu/elapsed_time.clock) ;

mttWriteNewLine ;    
mttNotify(['Completed in ',num2str(elapsed_time.clock),' seconds']) ;
mttNotify([' (',num2str(cpu_utilisation),'%% cpu)']) ;
mttWriteNewLine ;    
mttWriteNewLine ;


mtt_environment = env ;

function ese = make_ese(system,sorter_on)
global mtt_environment

if nargin<2
    sorter_on = 1 ;
end

switch class(system)
case 'char',
    input = 'spec' ;
case 'struct',
    if isfield(system,'representation')
        input = system.representation ;
    end
end    

start_time = mttGetTime ;

abg = [] ;
cbg = [] ;
ese = [] ;

if strcmp(input,'spec')
 	mttWriteNewLine ;
    mttNotify('Making "abg" representation') ;
    mttWriteNewLine ;
    
    if isempty(mtt_environment)
        mttNotify('...WARNING: No "env" definition => all domain references will be ignored') ;
        mttWriteNewLine ;
        mttNotify('                                => paths will not be recognised') ;
        mttWriteNewLine ;
    end
    
    abg = mttCreateAcausalBondgraph(system) ;
    input = 'abg' ;
end

if strcmp(input,'abg')
    if isempty(abg)
        abg = system ;
    end
    
    mttWriteNewLine ;
    mttNotify('Transforming from "abg" to "cbg"') ;
    mttWriteNewLine ;
    cbg = mttCreateCausalBondgraph(abg) ;
    input = 'cbg' ;
end

if strcmp(input,'cbg')
    if isempty(cbg)
        cbg = system ;
    end
    
    mttWriteNewLine ;
    mttNotify('Transforming from "cbg" to "ese"') ;
    mttWriteNewLine ;
    ese = mttCreateElementaryEquations(cbg,sorter_on) ;
    input = 'ese' ;
end

mttAssert(strcmp(input,'ese'),'Input representation not recognised') ;

if isempty(ese)
    mttWriteNewLine ;
    mttNotify('Making "ese" representation') ;
    mttWriteNewLine ;

    mttNotify('Input already defined as a "ese": copying to Output') ;
    mttWriteNewLine ;
    mttWriteNewLine ;
    ese = system ;
end


elapsed_time = mttElapseTime(start_time) ;
cpu_utilisation = round(100*elapsed_time.cpu/elapsed_time.clock) ;

mttWriteNewLine ;    
mttNotify(['Completed in ',num2str(elapsed_time.clock),' seconds']) ;
mttNotify([' (',num2str(cpu_utilisation),'%% cpu)']) ;
mttWriteNewLine ;    
mttWriteNewLine ;

function make_sfun(system,sorter_on)
global mtt_environment

if nargin<2
    sorter_on = 1 ;
end

switch class(system)
case 'char',
    input = 'spec' ;
case 'struct',
    if isfield(system,'representation')
        input = system.representation ;
    end
end    

start_time = mttGetTime ;

abg = [] ;
cbg = [] ;
ese = [] ;

if strcmp(input,'spec')
 	mttWriteNewLine ;
    mttNotify('Making "abg" representation') ;
    mttWriteNewLine ;
    
    if isempty(mtt_environment)
        mttNotify('...WARNING: No "env" definition => all domain references will be ignored') ;
        mttWriteNewLine ;
        mttNotify('                                => paths will not be recognised') ;
        mttWriteNewLine ;
    end
    
    abg = mttCreateAcausalBondgraph(system) ;
    input = 'abg' ;
end

if strcmp(input,'abg')
    if isempty(abg)
        abg = system ;
    end
    
    mttWriteNewLine ;
    mttNotify('Transforming from "abg" to "cbg"') ;
    mttWriteNewLine ;
    cbg = mttCreateCausalBondgraph(abg) ;
    input = 'cbg' ;
end

if strcmp(input,'cbg')
    if isempty(cbg)
        cbg = system ;
    end
    
    mttWriteNewLine ;
    mttNotify('Transforming from "cbg" to "ese"') ;
    mttWriteNewLine ;
    ese = mttCreateElementaryEquations(cbg,sorter_on) ;
    input = 'ese' ;
end

mttAssert(strcmp(input,'ese'),'Input representation not recognised') ;

if isempty(ese)
    ese = system ;
end
mttCreateSystemMdl(ese) ;
    

elapsed_time = mttElapseTime(start_time) ;
cpu_utilisation = round(100*elapsed_time.cpu/elapsed_time.clock) ;

mttWriteNewLine ;    
mttNotify(['Completed in ',num2str(elapsed_time.clock),' seconds']) ;
mttNotify([' (',num2str(cpu_utilisation),'%% cpu)']) ;
mttWriteNewLine ;    
mttWriteNewLine ;

function make_sfun(system,sorter_on)
global mtt_environment

if nargin<2
    sorter_on = 1 ;
end

switch class(system)
case 'char',
    input = 'spec' ;
case 'struct',
    if isfield(system,'representation')
        input = system.representation ;
    end
end    

start_time = mttGetTime ;

abg = [] ;
cbg = [] ;
ese = [] ;

if strcmp(input,'spec')
 	mttWriteNewLine ;
    mttNotify('Making "abg" representation') ;
    mttWriteNewLine ;
    
    if isempty(mtt_environment)
        mttNotify('...WARNING: No "env" definition => all domain references will be ignored') ;
        mttWriteNewLine ;
        mttNotify('                                => paths will not be recognised') ;
        mttWriteNewLine ;
    end
    
    abg = mttCreateAcausalBondgraph(system) ;
    input = 'abg' ;
end

if strcmp(input,'abg')
    if isempty(abg)
        abg = system ;
    end
    
    mttWriteNewLine ;
    mttNotify('Transforming from "abg" to "cbg"') ;
    mttWriteNewLine ;
    cbg = mttCreateCausalBondgraph(abg) ;
    input = 'cbg' ;
end

if strcmp(input,'cbg')
    if isempty(cbg)
        cbg = system ;
    end
    
    mttWriteNewLine ;
    mttNotify('Transforming from "cbg" to "ese"') ;
    mttWriteNewLine ;
    ese = mttCreateElementaryEquations(cbg,sorter_on) ;
    input = 'ese' ;
end

mttAssert(strcmp(input,'ese'),'Input representation not recognised') ;

if isempty(ese)
    ese = system ;
end
mttWriteSystemEquations(ese) ;
mttWriteSystemDefinitions(ese) ;
mttWriteSystemInitialisation(ese) ;
mttWriteSystemMapping(ese) ;

ese = mttCreateApps(ese) ;
mttWriteSystemApps(ese) ;
mttWriteSystemSfun(ese) ;
    

elapsed_time = mttElapseTime(start_time) ;
cpu_utilisation = round(100*elapsed_time.cpu/elapsed_time.clock) ;

mttWriteNewLine ;    
mttNotify(['Completed in ',num2str(elapsed_time.clock),' seconds']) ;
mttNotify([' (',num2str(cpu_utilisation),'%% cpu)']) ;
mttWriteNewLine ;    
mttWriteNewLine ;

function model = mttApplyInterfaceCausality(model,specified_rule,branch) ;
    is_root_model = (nargin==2) ;
    
	objects = mttGetFieldNames(model,'obj') ;
    
    for i = 1:length(objects)
        object_name = objects{i} ;
        object = getfield(model,'obj',object_name) ;
        
        if isfield(object,'obj')
            if is_root_model
                branch = object_name ;
            else
                branch = [branch,'/',object_name] ;
            end
            
            object = mttApplyInterfaceCausality(object,specified_rule,branch) ;
            model = setfield(model,'obj',object_name,object) ;
            
        else
            if ~isempty(object.cr)
                if is_root_model
                    branch = mttDetachText(model.source,'/') ;
                end
                here = [branch,':',object_name] ;
                
                port_names = mttGetFieldNames(object.cr.interface,'port') ;
                
                for j = 1:length(port_names)
                    port_name = port_names{j} ;
                    port = getfield(object.cr.interface,'port',port_name) ;
                    
                    inbond = port.in ;
                    outbond = port.out ;
                    
                    for k = 1:mttGetFieldLength(port,'causality')
                        rule = port.causality(k).rule ;
                        definition = port.causality(k).def ;
                        association = port.causality(k).with ;
                        not_applied = ~port.causality(k).applied ;
                        
                        switch rule
                        case 'assert',  is_assertion = 1 ;
                        case 'prefer',  is_assertion = 0 ;
                        otherwise
                            error(['Unrecognised rule "',port_causality.rule,'" in ',here]) ;
                        end
                        
                        apply_rule = strcmp(specified_rule,rule) & not_applied ;
                        if apply_rule
                            
                            switch definition
%                            case 'effort_state',
%                                mttAssert(mttIsEqual(port.is_flow_state,0),...
%                                    ['Attempt to overwrite state assignment at port "',port_name,'" in ',here]) ;
%                                port.is_effort_state = 1 ;
                                
%                            case 'flow_state',
%                                mttAssert(mttIsEqual(port.is_effort_state,0),...
%                                    ['Attempt to overwrite state assignment at port "',port_name,'" in ',here]) ;
%                                port.is_flow_state = 1 ;
                                
                            case {'effort_in_flow_out','flow_in_effort_out','flow_out_effort_in','effort_out_flow_in'}
                                mttAssert(isempty(association),...
                                    ['Over-constraint at port "',port_name,'" in ',here]) ;
                                
                                switch definition
                                case {'effort_in_flow_out','flow_out_effort_in'},
                                    [model,inbond_ok] = mttUpdateBondCausality(model,inbond,1,1,1) ; 
                                    [model,outbond_ok] = mttUpdateBondCausality(model,outbond,0,0,1) ;
                                case {'flow_in_effort_out','effort_out_flow_in'},
                                    [model,inbond_ok] = mttUpdateBondCausality(model,inbond,0,0,1) ; 
                                    [model,outbond_ok] = mttUpdateBondCausality(model,outbond,1,1,1) ;
                                end

                                ok = inbond_ok & outbond_ok ;
                                if is_assertion
                                    mttAssert(ok,['Causal conflict at port "',port_name,'" in ',here]) ;
                                end
                                
                            case 'effort_in'
                                mttAssert(isempty(association),...
                                    ['Over-constraint at port "',port_name,'" in ',here]) ;
                                
                                [model,inbond_ok] = mttUpdateBondCausality(model,inbond,1,[],1) ; 
                                [model,outbond_ok] = mttUpdateBondCausality(model,outbond,0,[],1) ;

                                ok = inbond_ok & outbond_ok ;
                                if is_assertion
                                    mttAssert(ok,['Causal conflict at port "',port_name,'" in ',here]) ;
                                end
                                
                            case 'effort_out'
                                mttAssert(isempty(association),...
                                    ['Over-constraint at port "',port_name,'" in ',here]) ;
                                
                                [model,inbond_ok] = mttUpdateBondCausality(model,inbond,0,[],1) ; 
                                [model,outbond_ok] = mttUpdateBondCausality(model,outbond,1,[],1) ;

                                ok = inbond_ok & outbond_ok ;
                                if is_assertion
                                    mttAssert(ok,['Causal conflict at port "',port_name,'" in ',here]) ;
                                end
                                
                            case 'flow_in'
                                mttAssert(isempty(association),...
                                    ['Over-constraint at port "',port_name,'" in ',here]) ;
                                
                                [model,inbond_ok] = mttUpdateBondCausality(model,inbond,[],0,1) ; 
                                [model,outbond_ok] = mttUpdateBondCausality(model,outbond,[],1,1) ;

                                ok = inbond_ok & outbond_ok ;
                                if is_assertion
                                    mttAssert(ok,['Causal conflict at port "',port_name,'" in ',here]) ;
                                end
                                
                            case 'flow_out'
                                mttAssert(isempty(association),...
                                    ['Over-constraint at port "',port_name,'" in ',here]) ;
                                
                                [model,inbond_ok] = mttUpdateBondCausality(model,inbond,[],1,1) ; 
                                [model,outbond_ok] = mttUpdateBondCausality(model,outbond,[],0,1) ;

                                ok = inbond_ok & outbond_ok ;
                                if is_assertion
                                    mttAssert(ok,['Causal conflict at port "',port_name,'" in ',here]) ;
                                end
                                
                            case 'unicausal',
                                mttAssert(isempty(association),...
                                    ['Over-constraint at port "',port_name,'" in ',here]) ;
                                
                                [model,inbond_ok] = mttUpdateBondCausality(model,inbond,[],[],1) ; 
                                [model,outbond_ok] = mttUpdateBondCausality(model,outbond,[],[],1) ;
                                
                                ok = inbond_ok & outbond_ok ;
                                if is_assertion
                                    mttAssert(ok,['Causal conflict at port "',port_name,'" in ',here]) ;
                                end
                                
                            case {'equicausal','anticausal'}
                                mttAssert(length(association)==1,...
                                    ['Incorrect constraint at port "',port_name,'" in ',here]) ;
                                
                                associated_port_name = association{1} ;
                                associated_port = getfield(cr.interface,'port',associated_port_name) ;
                                
                                associated_inbond = associated_port.in ;
                                associated_outbond = associated_port.out ;
                                
                                mttAsert(xor(isempty(inbond),isempty(outbond)),...
                                    ['Causal rule expects unique bond at port "',port_name,'" in ',here]) ;
                                mttAsert(xor(isempty(associated_inbond),isempty(associated_outbond)),...
                                    ['Causal rule expects unique bond at port "',associated_port_name,'" in ',here]) ;
                                
                                if isempty(associated_inbond)
                                    a = associated_outbond ;
                                else
                                    a = associated_inbond ;
                                end
                                
                                if isempty(inbond)
                                    b = outbond ;
                                else
                                    b = inbond ;
                                end
                                
                                switch definition
                                case 'equicausal',
                                    [model,bond_ok] = mttUpdateBondCausality(model,b,...
                                        model.bond(a).effort,model.bond(a).flow,model.bond(a).unicausal) ; 
                                    [model,associated_bond_ok] = mttUpdateBondCausality(model,a,...
                                        model.bond(b).effort,~model.bond(b).flow,model.bond(b).unicausal) ;
                                case 'anticausal',
                                    [model,bond_ok] = mttUpdateBondCausality(model,b,...
                                        ~model.bond(a).effort,model.bond(a).flow,model.bond(a).unicausal) ; 
                                    [model,associated_bond_ok] = mttUpdateBondCausality(model,a,...
                                        ~model.bond(b).effort,~model.bond(b).flow,model.bond(b).unicausal) ;
                                end
                                
                                ok = bond_ok & associated_bond_ok ;
                                if is_assertion
                                    mttAssert(ok,['Causal conflict between ports "',port_name,...
                                            'and',associated_port_name,'" in ',here]) ;
                                end
                                
                            otherwise,
                                error(['Unrecognised constraint "',definition,'" in ',here]) ;
                            end
                            
                            port.causality(k).applied = 1 ;
                            object = setfield(object,'cr','interface','port',port_name,port) ;
                            model = setfield(model,'obj',object_name,object) ;
                        end                    
                    end
                end
            end
        end
    end
    

function model = mttApplyInterfaceDomains(model,branch) ;
    is_root_model = (nargin==1) ;
    
	objects = mttGetFieldNames(model,'obj') ;
    
    for i = 1:length(objects)
        object_name = objects{i} ;
        object = getfield(model,'obj',object_name) ;
        
        if isfield(object,'obj')
            if is_root_model
                branch = object_name ;
            else
                branch = [branch,'/',object_name] ;
            end
            
            object = mttApplyInterfaceDomains(object,branch) ;
            model = setfield(model,'obj',object_name,object) ;
            
        else
            if ~isempty(object.cr)
                if is_root_model
                    branch = mttDetachText(model.source,'/') ;
                end
                here = [branch,':',object_name] ;
                
                port_names = mttGetFieldNames(object.cr.interface,'port') ;
                
                for j = 1:length(port_names)
                    port_name = port_names{j} ;
                    port = getfield(object.cr.interface,'port',port_name) ;
                    
                    predefined_domain = port.domain ;
                    predefined_domain_item = port.domain_item ;
                    
                    inbond = port.in ;
                    outbond = port.out ;
                    
                    if isempty(inbond)
                        bond_number = outbond ;
                    else
                        bond_number = inbond ;
                    end
                    
                    [model,ok] = mttUpdateBondDomain(model,bond_number,predefined_domain,predefined_domain_item) ;
                    
                    mttAssert(ok,['Domain conflict at port "',port_name,'" in ',here]) ;
                end
            end
        end
    end
    

function model = mttCreateAcausalBondgraph(system,root)
global mtt_environment


switch nargin
case 0,
    model = [] ; return ;
case 1,
    root = [] ;
    is_root_model = 1 ;
otherwise,
    is_root_model = 0 ;
end

if is_root_model
    model = intialise_model(system) ;
    
    directory_name = identify_directory_name(system) ;
    source_name = identify_source_name(system,directory_name) ;
    
    mttNotify('...acquiring "abg" source definitions') ;
    mttWriteNewLine ;
else
    model = propagate_root_data(root) ;
    source_name = system ;
end

specification_filename = [source_name,'_abg.txt'] ;
specification = mttFetchSpecification(specification_filename) ;
specification = mttSetFieldDefault(specification,'bondgraph',system) ;
    
[local_system_name,rubbish] = mttDetachText(system,'/') ;
if isempty(local_system_name)
    local_system_name = system ;
end


if is_root_model
    source_name = identify_source_name(specification.bondgraph,directory_name) ;
else
    source_name = specification.bondgraph ;
end
source_name = mttCutText(source_name,'_abg.fig') ;

bondgraph_filename = [source_name,'_abg.fig'] ;
bondgraph = mttFetchBondgraph(bondgraph_filename) ;

model = mttCreateUnifiedModel(model,bondgraph,specification) ;
model = mttDeleteField(model,'branch') ;
model = mttDeleteField(model,'leaf') ;


if is_root_model
    mttWriteNewLine ;
    mttNotify('...acquiring "cr" source definitions') ;
    mttWriteNewLine ;
    
    for n = 1:length(model.crs)
        source_name = model.crs{n} ;
        cr_filename = [source_name,'_cr.txt'] ;
        
        if ~mttFileExists(cr_filename)
            cr_short_name = mttDetachText(source_name,'/') ;
            
            mttNotify(['   ...ERROR: "',cr_short_name,'_cr" source does not exist']) ;
            mttWriteNewLine ;
            mttNotify(['   ...finding dependencies for ',source_name,':']) ;
            mttWriteNewLine ;
            
            prefix = mttDetachText(system,'/') ;
            if isempty(prefix)
                prefix = system ;
            end
            
            cr_user = model.cr_usage(n).obj ;
            for i = 1:length(cr_user)
                mttNotify(['         ',prefix,'/',cr_user{i}]) ;
                mttWriteNewLine ;
            end
        end
        
        model.cr(n) = mttFetchInterfaceDefinition(cr_filename) ;
    end
    
    model = mttDeleteField(model,'cr_usage') ;
    model = mttDeleteField(model,'crs') ;
    model = mttDeleteField(model,'abgs') ;
end

model.env = mtt_environment ;



function model = intialise_model(system)
    model.representation = 'abg' ;
    model.abgs = [] ;
    model.crs = [] ;
    model.cr_usage = [] ;
    model.branch = [] ;
    model.leaf = [] ;
    
function model = propagate_root_data(root)
    model.abgs = root.abgs ;
    model.crs = root.crs ;
    model.cr_usage = root.cr_usage ;
    model.branch = root.branch ;
    model.leaf = root.leaf ;

function directory = identify_directory_name(system)
    mttAssert(ischar(system),'System must be specified by name') ;
    working_directory  = pwd ;
    working_directory = strrep(working_directory,'\','/') ;
    
    [system_name,local_directory] = mttDetachText(system,'/') ;
    if isempty(system_name)
        local_directory = [] ;
    end
    
    if isempty(local_directory)
        directory = working_directory ;
    else
        directory = mttLocateDirectory(working_directory,local_directory) ;
    end
    
function source = identify_source_name(system,directory)
    [system_name,local_directory] = mttDetachText(system,'/') ;
    if isempty(system_name)
        system_name = system ;
        local_directory = [] ;
    end
    source = [directory,'/',system_name] ;

function model = mttCreateApps(model)

apps_filename = [model.source,'_apps.txt'] ;
apps = mttFetchApps(apps_filename) ;

if isempty(apps)
    return ;
end

for i = 1:length(apps.app)
    app_source = apps.app{i} ;
    
    [rubbish,working_directory] = mttDetachText(model.source,'/') ;
    [name,path_spec] = mttDetachText(app_source,'/') ;
    
    if isempty(name)
        source_name = [working_directory,'/',domain_source] ;
    else
        directory = identify_directory(working_directory,path_spec,model) ;
        source_name = [directory,'/',name] ;
    end
    
    app_filename = [source_name,'_app.h'] ;
    model.app{i} = app_filename ;
end

    
function directory = identify_directory(working_directory,path_spec,model)
	path_names = mttGetFieldNames(model.env,'path') ;

    if isempty(path_spec)
		directory = [] ;
    else
        if path_spec(1)=='$'
            [path_alias,path_branch] = mttCutText(path_spec,'/') ;
            path_alias(1) = [] ;
            
            mttAssert(ismember(path_alias,path_names),...
                ['Path "',path_alias,'" not recognised']) ;
            
            path_root = getfield(model.env,'path',path_alias) ;
            
            if isempty(path_branch)
                directory = path_root ;
            else
                directory = [path_root,'/',path_branch] ;
            end
        else
            [name,local_directory] = mttDetachText(path_spec,'/') ;
            
            directory_located = 0 ;
            if strcmp(local_directory,'.')
                if isempty(name)
                    directory = working_directory ;
                    directory_located = 1 ;
                else
                    local_directory = name ;
                end
            else
                local_directory = path_spec ;
            end
            
            if ~directory_located
                directory = mttLocateDirectory(working_directory,local_directory) ;
            end
        end
    end
    

function model = mttCreateCausalBondgraph(model)

model.representation = 'cbg' ;

model = incorporate_interface_definitions(model) ;
model = establish_abg_dependencies(model) ;
model = create_object_hierarchy(model) ;
model = assign_sympar_values(model) ;
model = complete_causal_assignment(model) ;
model = complete_domain_assignment(model) ;
model = overwrite_implicit_domains(model) ;


function model = incorporate_interface_definitions(model)
	mttNotify('...incorporating "cr" definitions') ;
    mttWriteNewLine ;
    
    mttNotify(['   ...processing ',model.source]) ;
    mttWriteNewLine ;
    
    objects = mttGetFieldNames(model,'obj') ;
    for i = 1:length(objects)
        object_name = objects{i} ;
        object = getfield(model,'obj',object_name) ;
        
        if ~mttIsFoundationClass(object.class)
            mttAssert(xor(isempty(object.abg),isempty(object.cr)),...
                ['"',object_name,'" must exclusively have a "cr" or an "abg" representation']) ;
        end
        
        if isempty(object.cr)
            object = mttDeleteField(object,'cr_item') ;
            model = setfield(model,'obj',object_name,object) ;
        else
            model = mttEmbedInterfaceDefinition(model,object_name) ;
        end
    end
    
    for i = 1:mttGetFieldLength(model,'abg')
        component_type = mttDetachText(model.abg(i).source,'/') ;
        mttNotify(['   ...processing "#',num2str(i),':',component_type,'" ',model.abg(i).source]) ;
        mttWriteNewLine ;
        
        objects = mttGetFieldNames(model.abg(i),'obj') ;
        for j = 1:length(objects)
	        object_name = objects{j} ;
            object = getfield(model,'abg',{i},'obj',object_name) ;
            
    	    if ~mttIsFoundationClass(object.class)
	            mttAssert(xor(isempty(object.abg),isempty(object.cr)),...
        	        ['abg[',num2str(i),']: "',object_name,'" must exclusively have a "cr" or an "abg" representation']) ;
            end
            
            if isempty(object.cr)
                object = mttDeleteField(object,'cr_item') ;
                model = setfield(model,'abg',{i},'obj',object_name,object) ;
            else
                model.abg(i) = mttEmbedInterfaceDefinition(model.abg(i),object_name,model) ;
            end
        end
        model.abg(i).invokes = [] ;
        model.abg(i).invoked_by = [] ;
    end
    model = mttDeleteField(model,'cr') ;
    
    
function model = establish_abg_dependencies(model)
	mttNotify('...establishing "abg" dependencies') ;
    mttWriteNewLine ;
    
    for i = 1:mttGetFieldLength(model,'abg')
        objects = mttGetFieldNames(model.abg(i),'obj') ;
        for j = 1:length(objects)
            object_name = objects{j} ;
            object = getfield(model.abg(i).obj,object_name) ;
            
            if isempty(object.cr)	%... still within object hierarchy
                if ~mttIsFoundationClass(object.class)
                    existing_dependencies = model.abg(i).invokes ;
                    
                    if isempty(existing_dependencies)
                        new_dependency = 1 ;
                    else
                        new_dependency = isempty(find(existing_dependencies==object.abg)) ;
                    end
                    
                    if new_dependency
                        model.abg(i).invokes = [existing_dependencies,object.abg] ;
                    end
                    
                    existing_dependencies = model.abg(object.abg).invoked_by ;
                    if isempty(existing_dependencies)
                        new_dependency = 1 ;
                    else
                        new_dependency = isempty(find(existing_dependencies==i)) ;
                    end
                    
                    if new_dependency
                        model.abg(object.abg).invoked_by = [existing_dependencies,i] ;
                    end
                end
            end
        end
    end
    
    model.invokes = [] ;
    
    objects = mttGetFieldNames(model,'obj') ;
    for j = 1:length(objects)
        object_name = objects{j} ;
        object = getfield(model.obj,object_name) ;
        
        if ~isempty(object.abg)
            if ~mttIsFoundationClass(object.class)
                existing_dependencies = model.invokes ;
                
                if isempty(existing_dependencies)
                    new_dependency = 1 ;
                else
                    new_dependency = isempty(find(existing_dependencies==object.abg)) ;
                end
                
                if new_dependency
                    model.invokes = [existing_dependencies,object.abg] ;
                end
            end
        end
    end
    
    
function model = create_object_hierarchy(model) ;
	mttNotify('...creating object hierarchy') ;
    mttWriteNewLine ;
    
    top_level_model = mttDetachText(model.source,'/') ;
    
    if isfield(model,'abg')
        is_embedded = zeros(1,length(model.abg)) ;
        embedding = 1 ;
    else
        embedding = 0 ;
    end
    
    component = 0 ;

    embedding = isfield(model,'abg') ;
    while embedding
        component = 1 + mod(component,length(model.abg)) ;
        if ~is_embedded(component)            
            if isempty(model.abg(component).invokes)
                number_of_systems = length(model.abg(component).invoked_by) ;
                
                for n = 1:number_of_systems
                    system = model.abg(component).invoked_by(n) ;
                    component_type = mttDetachText(model.abg(component).source,'/') ;
                    system_type = mttDetachText(model.abg(system).source,'/') ;
                    mttNotify(['   ...embedding "#',num2str(component),':',component_type,...
                            '" definition within "#',num2str(system),':',system_type,'" objects']) ;
                    mttWriteNewLine ;
                    
                    model = mttEmbedAcausalBondgraph(model,component,system) ;
                end
                model.abg(component).invoked_by = [] ;
                
                if ~isempty(find(model.invokes==component))
                    component_type = mttDetachText(model.abg(component).source,'/') ;
                    mttNotify(['   ...embedding "#',num2str(component),':',component_type,...
                            '" definition within "',top_level_model,'"']) ;
                    mttWriteNewLine ;
                    
                    model = mttEmbedAcausalBondgraph(model,component) ;
                end
                is_embedded(component) = 1 ;
            end
        end
        embedding = any(~is_embedded) ;
    end
    
    model = mttDeleteField(model,'abg') ;
    model = mttDeleteField(model,'invokes') ;
    
    
function model = assign_sympar_values(model) 
	mttNotify('...assigning "sympar" values') ;
    mttWriteNewLine ;
    
    model_name = mttDetachText(model.source,'/') ;
    current_branch = model_name ;
    
    sympars = model.sympar ;
    defaults = model.sympar_default ;
    
    objects = mttGetFieldNames(model,'obj') ;
    for i = 1:length(objects)
        object_name = objects{i} ;
        object = getfield(model,'obj',object_name) ;
        
        if ~mttIsPassiveClass(object.class)
            for j = 1:length(object.parameter)
                object_parameter = object.parameter{j} ;
                if ischar(object_parameter)
                    index = strmatch(object_parameter,sympars,'exact') ;
                    
                    new_parameter = 0 ;
                    
                    if isempty(index)
                        new_parameter = 1 ;
                    else
                        default_value = defaults{index} ;
                        if isempty(default_value)
                            new_parameter = 1 ;
                        else
                            object.parameter{j} = default_value ;
                        end
                    end
                    
                    if new_parameter
                        object.parameter{j} = [current_branch,'___',object_parameter] ;
                    end
                end
            end
            
            branch = [model_name,'__',object_name] ;
            object = assign_object_sympar_values(object,branch) ;
            
            model = setfield(model,'obj',object_name,object) ;
        end
    end
    
    
function model = assign_object_sympar_values(model,branch)
    current_branch = branch ;
    
	sympars = model.sympar ;
    parameters = model.parameter ;
    
    if ~isempty(model.abg)
        objects = mttGetFieldNames(model,'obj') ;
        for i = 1:length(objects)
            object_name = objects{i} ;
            object = getfield(model,'obj',object_name) ;
            
            if ~mttIsPassiveClass(object.class)
                for j = 1:length(object.parameter)
                    object_parameter = object.parameter{j} ;
                    if ischar(object_parameter)
                        index = strmatch(object_parameter,sympars,'exact') ;
                        if isempty(index)
                            object.parameter{j} = [current_branch,'___',object_parameter] ;
                        else
                            object.parameter{j} = parameters{index} ;
                        end
                    end
                end
                
                branch = [current_branch,'__',object_name] ;
                object = assign_object_sympar_values(object,branch) ;
                
                model = setfield(model,'obj',object_name,object) ;
            end
        end
    elseif ~isempty(model.cr)
        model.cr.parameter = model.parameter ;
    end
    
    
function model = complete_causal_assignment(model)
    mttWriteNewLine ;
	mttNotify('...summarising model content') ;
    mttWriteNewLine ;
    
    model = mttCountObjects(model) ;
    mttNotifyNumberOfObjects(model) ;
    mttWriteNewLine ;
    model = mttDeleteField(model,'count') ;
    
    model = mttMeasureCausalCompletion(model) ;
	mttNotifyNumberOfBonds(model) ;
    mttWriteNewLine ;
    
    mttWriteNewLine ;
	mttNotify('...analysing predefined causality') ;
    mttWriteNewLine ;
    
	mttNotifyCausalCompletion(model) ;
    mttWriteNewLine ;
    
	if model.causal_completion.is_causal
        mttNotify('...applying CR constraints') ;
        mttWriteNewLine ;
        model = incorporate_cr_rules(model,'assert') ;
    else    
        mttNotify('...completing causality') ;
        mttWriteNewLine ;
        
        iterations = 0 ;
        
        propagating = 1 ;
        while propagating
            iterations = iterations + 1 ;
            previous_causal_completion = model.causal_completion ;
            
            model = mttApplyInterfaceCausality(model,'assert') ;
            model = mttPropagateCausality(model) ;
            model = mttApplyInterfaceCausality(model,'prefer') ;
            model = mttPropagateCausality(model) ;
            model = mttMeasureCausalCompletion(model) ;
            
            is_stable = mttCompareCausalCompletion(model.causal_completion,previous_causal_completion) ;
            propagating = (~is_stable) ;
            
            if propagating
                mttNotify(['...iteration ',num2str(iterations)]) ;
                mttWriteNewLine ;
                mttNotifyCausalCompletion(model) ;
            end
            
            propagating = propagating & (~model.causal_completion.is_causal) ;
        end
    end
    
    
    if ~model.causal_completion.is_causal
        mttWriteNewLine ;
        mttNotify('...causality not complete') ;
        mttWriteNewLine ;
        mttWriteNewLine ;
        
        mttIdentifyUndercausalBonds(model) ;
    end
    
    model = mttDeleteField(model,'causal_completion') ;
    
    
function model = complete_domain_assignment(model)
    mttWriteNewLine ;
	mttNotify('...allocating domain definitions') ;
    mttWriteNewLine ;
    
    model = mttMeasureDomainCompletion(model) ;
    
    iterations = 0 ;
    
    propagating = 1 ;
    while propagating
        iterations = iterations + 1 ;
        previous_domain_completion = model.domain_completion ;
        
        model = mttApplyInterfaceDomains(model) ;
        model = mttPropagateDomains(model) ;
        model = mttMeasureDomainCompletion(model) ;
        
        is_stable = mttCompareDomainCompletion(model.domain_completion,previous_domain_completion) ;
        propagating = (~is_stable) ;
        
        if propagating
            mttNotify(['...iteration ',num2str(iterations)]) ;
            mttWriteNewLine ;
            mttNotifyDomainCompletion(model) ;
        end
        
        propagating = propagating & (~model.domain_completion.is_done) ;
    end
    
    model = mttDeleteField(model,'domain_completion') ;
    
    
function model = overwrite_implicit_domains(model)
    mttWriteNewLine ;
	mttNotify('...overwriting implicit domain definitions') ;
    mttWriteNewLine ;
    
    model = mttOverwriteImplicitDomains(model) ;
    
    
function model = mttOverwriteImplicitDomains(root,model,env)
    is_root_model = nargin==1 ;
    
    if is_root_model
        model = root ;
        env = root.env ;
    end
        
    objects = mttGetFieldNames(model,'obj') ;
    for i = 1:length(objects)
        object_name = objects{i} ;
        object = getfield(model,'obj',object_name) ;
        
        if ~isempty(object.abg)
            object = mttOverwriteImplicitDomains(model,object,env) ;
        end
        
        if ~isempty(object.cr)
            interface_ports = mttGetFieldNames(object.cr.interface,'port') ;
            for j = 1:length(interface_ports)
                port_name = interface_ports{j} ;
                port = getfield(object.cr.interface,'port',port_name) ;
                
                if isempty(port.domain)
                    if isempty(port.in)
                        bond_number = port.out ;
                    else
                        bond_number = port.in ;
                    end
                    
                    actual_domain = model.bond(bond_number).domain ;
                    actual_domain_item = model.bond(bond_number).domain_item ;
                    
                    port.domain = actual_domain ;
                    port.domain_item = actual_domain_item ;
	                object.cr.interface = setfield(object.cr.interface,'port',port_name,port) ;
                    
                    number_of_operators = mttGetFieldLength(object.cr,'operator') ;
                    for op_counter = 1:number_of_operators
                        operator = object.cr.operator(op_counter) ;
                        
                        matching_links = strmatch(port_name,{operator.link.name},'exact') ;
                        
                        number_of_equations = mttGetFieldLength(operator,'equation') ;
                        
                        for eq_counter = 1:number_of_equations
                            equation = operator.equation(eq_counter) ;
%                            if isempty(equation.domain)
                                
                                number_of_chunks = mttGetFieldLength(equation,'chunk') ;
                                for chunk_counter = 1:number_of_chunks
                                    chunk = equation.chunk{chunk_counter} ;
                                    
                                    if iscell(chunk)
                                        if strcmp(chunk{1},'link')
                                            link = chunk{2} ;
                                            
                                            if any(link==matching_links)
                                                covar = chunk{3} ;
                                                chunk{3} = ['generic___',covar] ;
                                            end
                                        end
	                                    equation.chunk{chunk_counter} = chunk ;
                                    end
                                end
                                operator.equation(eq_counter) = equation ;
%                            end
                        end
                        object.cr.operator(op_counter) = operator ;
                    end
                end
            end
        end
        
        model = setfield(model,'obj',object_name,object) ;
    end