DELETED CVSROOT/checkoutlist
Index: CVSROOT/checkoutlist
==================================================================
--- CVSROOT/checkoutlist
+++ /dev/null
@@ -1,14 +0,0 @@
-# The "checkoutlist" file is used to support additional version controlled
-# administrative files in $CVSROOT/CVSROOT, such as template files.
-#
-# The first entry on a line is a filename which will be checked out from
-# the corresponding RCS file in the $CVSROOT/CVSROOT directory.
-# The remainder of the line is an error message to use if the file cannot
-# be checked out.
-#
-# File format:
-#
-#	[<whitespace>]<filename><whitespace><error message><end-of-line>
-#
-# comment lines begin with '#'
-syncmail

DELETED CVSROOT/commitinfo
Index: CVSROOT/commitinfo
==================================================================
--- CVSROOT/commitinfo
+++ /dev/null
@@ -1,15 +0,0 @@
-# The "commitinfo" file is used to control pre-commit checks.
-# The filter on the right is invoked with the repository and a list 
-# of files to check.  A non-zero exit of the filter program will 
-# cause the commit to be aborted.
-#
-# The first entry on a line is a regular expression which is tested
-# against the directory that the change is being committed to, relative
-# to the $CVSROOT.  For the first match that is found, then the remainder
-# of the line is the name of the filter to run.
-#
-# If the repository name does not match any of the regular expressions in this
-# file, the "DEFAULT" line is used, if it is specified.
-#
-# If the name "ALL" appears as a regular expression it is always used
-# in addition to the first matching regex or "DEFAULT".

DELETED CVSROOT/config
Index: CVSROOT/config
==================================================================
--- CVSROOT/config
+++ /dev/null
@@ -1,11 +0,0 @@
-# Set this to "no" if pserver shouldn't check system users/passwords
-#SystemAuth=no
-
-# Set `PreservePermissions' to `yes' to save file status information
-# in the repository.
-#PreservePermissions=no
-
-# Set `TopLevelAdmin' to `yes' to create a CVS directory at the top
-# level of the new working directory when using the `cvs checkout'
-# command.
-#TopLevelAdmin=no

DELETED CVSROOT/cvswrappers
Index: CVSROOT/cvswrappers
==================================================================
--- CVSROOT/cvswrappers
+++ /dev/null
@@ -1,23 +0,0 @@
-# This file affects handling of files based on their names.
-#
-# The -t/-f options allow one to treat directories of files
-# as a single file, or to transform a file in other ways on
-# its way in and out of CVS.
-#
-# The -m option specifies whether CVS attempts to merge files.
-#
-# The -k option specifies keyword expansion (e.g. -kb for binary).
-#
-# Format of wrapper file ($CVSROOT/CVSROOT/cvswrappers or .cvswrappers)
-#
-#  wildcard	[option value][option value]...
-#
-#  where option is one of
-#  -f		from cvs filter		value: path to filter
-#  -t		to cvs filter		value: path to filter
-#  -m		update methodology	value: MERGE or COPY
-#  -k		expansion mode		value: b, o, kkv, &c
-#
-#  and value is a single-quote delimited value.
-# For example:
-#*.gif -k 'b'

DELETED CVSROOT/editinfo
Index: CVSROOT/editinfo
==================================================================
--- CVSROOT/editinfo
+++ /dev/null
@@ -1,21 +0,0 @@
-# The "editinfo" file is used to allow verification of logging
-# information.  It works best when a template (as specified in the
-# rcsinfo file) is provided for the logging procedure.  Given a
-# template with locations for, a bug-id number, a list of people who
-# reviewed the code before it can be checked in, and an external
-# process to catalog the differences that were code reviewed, the
-# following test can be applied to the code:
-#
-#   Making sure that the entered bug-id number is correct.
-#   Validating that the code that was reviewed is indeed the code being
-#       checked in (using the bug-id number or a seperate review
-#       number to identify this particular code set.).
-#
-# If any of the above test failed, then the commit would be aborted.
-#
-# Actions such as mailing a copy of the report to each reviewer are
-# better handled by an entry in the loginfo file.
-#
-# One thing that should be noted is the the ALL keyword is not
-# supported.  There can be only one entry that matches a given
-# repository.

DELETED CVSROOT/loginfo
Index: CVSROOT/loginfo
==================================================================
--- CVSROOT/loginfo
+++ /dev/null
@@ -1,30 +0,0 @@
-# The "loginfo" file controls where "cvs commit" log information
-# is sent.  The first entry on a line is a regular expression which must match
-# the directory that the change is being made to, relative to the
-# $CVSROOT.  If a match is found, then the remainder of the line is a filter
-# program that should expect log information on its standard input.
-#
-# If the repository name does not match any of the regular expressions in this
-# file, the "DEFAULT" line is used, if it is specified.
-#
-# If the name ALL appears as a regular expression it is always used
-# in addition to the first matching regex or DEFAULT.
-#
-# You may specify a format string as part of the
-# filter.  The string is composed of a `%' followed
-# by a single format character, or followed by a set of format
-# characters surrounded by `{' and `}' as separators.  The format
-# characters are:
-#
-#   s = file name
-#   V = old version number (pre-checkin)
-#   v = new version number (post-checkin)
-#
-# For example:
-#DEFAULT (echo ""; id; echo %s; date; cat) >> $CVSROOT/CVSROOT/commitlog
-# or
-#DEFAULT (echo ""; id; echo %{sVv}; date; cat) >> $CVSROOT/CVSROOT/commitlog
-
-# Lines to mail changes
-CVSROOT $CVSROOT/CVSROOT/syncmail %{sVv} gawthrop@users.sourceforge.net
-DEFAULT $CVSROOT/CVSROOT/syncmail %{sVv} mtt-checkins@lists.sourceforge.net

DELETED CVSROOT/modules
Index: CVSROOT/modules
==================================================================
--- CVSROOT/modules
+++ /dev/null
@@ -1,26 +0,0 @@
-# Three different line formats are valid:
-#	key	-a    aliases...
-#	key [options] directory
-#	key [options] directory files...
-#
-# Where "options" are composed of:
-#	-i prog		Run "prog" on "cvs commit" from top-level of module.
-#	-o prog		Run "prog" on "cvs checkout" of module.
-#	-e prog		Run "prog" on "cvs export" of module.
-#	-t prog		Run "prog" on "cvs rtag" of module.
-#	-u prog		Run "prog" on "cvs update" of module.
-#	-d dir		Place module in directory "dir" instead of module name.
-#	-l		Top-level directory only -- do not recurse.
-#
-# NOTE:  If you change any of the "Run" options above, you'll have to
-# release and re-checkout any working directories of these modules.
-#
-# And "directory" is a path to a directory relative to $CVSROOT.
-#
-# The "-a" option specifies an alias.  An alias is interpreted as if
-# everything on the right of the "-a" had been typed on the command line.
-#
-# You can encode a module within a module by using the special '&'
-# character to interpose another module into the current module.  This
-# can be useful for creating a module that consists of many directories
-# spread out over the entire source repository.

DELETED CVSROOT/notify
Index: CVSROOT/notify
==================================================================
--- CVSROOT/notify
+++ /dev/null
@@ -1,12 +0,0 @@
-# The "notify" file controls where notifications from watches set by
-# "cvs watch add" or "cvs edit" are sent.  The first entry on a line is
-# a regular expression which is tested against the directory that the
-# change is being made to, relative to the $CVSROOT.  If it matches,
-# then the remainder of the line is a filter program that should contain
-# one occurrence of %s for the user to notify, and information on its
-# standard input.
-#
-# "ALL" or "DEFAULT" can be used in place of the regular expression.
-#
-# For example:
-#ALL mail %s -s "CVS notification"

DELETED CVSROOT/rcsinfo
Index: CVSROOT/rcsinfo
==================================================================
--- CVSROOT/rcsinfo
+++ /dev/null
@@ -1,13 +0,0 @@
-# The "rcsinfo" file is used to control templates with which the editor
-# is invoked on commit and import.
-#
-# The first entry on a line is a regular expression which is tested
-# against the directory that the change is being made to, relative to the
-# $CVSROOT.  For the first match that is found, then the remainder of the
-# line is the name of the file that contains the template.
-#
-# If the repository name does not match any of the regular expressions in this
-# file, the "DEFAULT" line is used, if it is specified.
-#
-# If the name "ALL" appears as a regular expression it is always used
-# in addition to the first matching regex or "DEFAULT".

DELETED CVSROOT/syncmail
Index: CVSROOT/syncmail
==================================================================
--- CVSROOT/syncmail
+++ /dev/null
@@ -1,287 +0,0 @@
-#! /usr/bin/python
-
-# NOTE: Until SourceForge installs a modern version of Python on the cvs
-# servers, this script MUST be compatible with Python 1.5.2.
-
-"""Complicated notification for CVS checkins.
-
-This script is used to provide email notifications of changes to the CVS
-repository.  These email changes will include context diffs of the changes.
-Really big diffs will be trimmed.
-
-This script is run from a CVS loginfo file (see $CVSROOT/CVSROOT/loginfo).  To
-set this up, create a loginfo entry that looks something like this:
-
-    mymodule /path/to/this/script %%s some-email-addr@your.domain
-
-In this example, whenever a checkin that matches `mymodule' is made, this
-script is invoked, which will generate the diff containing email, and send it
-to some-email-addr@your.domain.
-
-    Note: This module used to also do repository synchronizations via
-    rsync-over-ssh, but since the repository has been moved to SourceForge,
-    this is no longer necessary.  The syncing functionality has been ripped
-    out in the 3.0, which simplifies it considerably.  Access the 2.x versions
-    to refer to this functionality.  Because of this, the script is misnamed.
-
-It no longer makes sense to run this script from the command line.  Doing so
-will only print out this usage information.
-
-Usage:
-
-    %(PROGRAM)s [options] <%%S> email-addr [email-addr ...]
-
-Where options is:
-
-    --cvsroot=<path>
-    	Use <path> as the environment variable CVSROOT.  Otherwise this
-    	variable must exist in the environment.
-
-    --help / -h
-        Print this text.
-
-    --context=#
-    -C #
-        Include # lines of context around lines that differ (default: 2).
-
-    -c
-        Produce a context diff (default).
-
-    -u
-        Produce a unified diff (smaller).
-
-    --quiet/-q
-        Don't print as much status to stdout.
-
-    <%%S>
-        CVS %%s loginfo expansion.  When invoked by CVS, this will be a single
-        string containing the directory the checkin is being made in, relative
-        to $CVSROOT, followed by the list of files that are changing.  If the
-        %%s in the loginfo file is %%{sVv}, context diffs for each of the
-        modified files are included in any email messages that are generated.
-
-    email-addrs
-        At least one email address.
-"""
-import os
-import sys
-import time
-import string
-import getopt
-import smtplib
-import pwd
-import socket
-
-from cStringIO import StringIO
-
-# Which SMTP server to do we connect to?  Empty string means localhost.
-MAILHOST = ''
-MAILPORT = 25
-
-# Diff trimming stuff
-DIFF_HEAD_LINES = 20
-DIFF_TAIL_LINES = 20
-DIFF_TRUNCATE_IF_LARGER = 1000
-
-EMPTYSTRING = ''
-SPACE = ' '
-DOT = '.'
-COMMASPACE = ', '
-
-PROGRAM = sys.argv[0]
-
-BINARY_EXPLANATION_LINES = [
-    "(This appears to be a binary file; contents omitted.)\n"
-    ]
-
-
-def usage(code, msg=''):
-    print __doc__ % globals()
-    if msg:
-        print msg
-    sys.exit(code)
-
-
-
-def calculate_diff(filespec, contextlines):
-    try:
-        file, oldrev, newrev = string.split(filespec, ',')
-    except ValueError:
-        # No diff to report
-        return '***** Bogus filespec: %s' % filespec
-    if oldrev == 'NONE':
-        try:
-            if os.path.exists(file):
-                fp = open(file)
-            else:
-                update_cmd = 'cvs -fn update -r %s -p %s' % (newrev, file)
-                fp = os.popen(update_cmd)
-            lines = fp.readlines()
-            fp.close()
-            # Is this a binary file?  Let's look at the first few
-            # lines to figure it out:
-            for line in lines[:5]:
-                for c in string.rstrip(line):
-                    if c in string.whitespace:
-                        continue
-                    if c < ' ' or c > chr(127):
-                        lines = BINARY_EXPLANATION_LINES[:]
-                        break
-            lines.insert(0, '--- NEW FILE: %s ---\n' % file)
-        except IOError, e:
-            lines = ['***** Error reading new file: ',
-                     str(e), '\n***** file: ', file, ' cwd: ', os.getcwd()]
-    elif newrev == 'NONE':
-        lines = ['--- %s DELETED ---\n' % file]
-    else:
-        # This /has/ to happen in the background, otherwise we'll run into CVS
-        # lock contention.  What a crock.
-        if contextlines > 0:
-            difftype = "-C " + str(contextlines)
-        else:
-            difftype = "-u"
-        diffcmd = "/usr/bin/cvs -f diff -kk %s --minimal -r %s -r %s '%s'" % (
-            difftype, oldrev, newrev, file)
-        fp = os.popen(diffcmd)
-        lines = fp.readlines()
-        sts = fp.close()
-        # ignore the error code, it always seems to be 1 :(
-##        if sts:
-##            return 'Error code %d occurred during diff\n' % (sts >> 8)
-    if len(lines) > DIFF_TRUNCATE_IF_LARGER:
-        removedlines = len(lines) - DIFF_HEAD_LINES - DIFF_TAIL_LINES
-        del lines[DIFF_HEAD_LINES:-DIFF_TAIL_LINES]
-        lines.insert(DIFF_HEAD_LINES,
-                     '[...%d lines suppressed...]\n' % removedlines)
-    return string.join(lines, '')
-
-
-
-def getdomain():
-    try:
-        fqdn = socket.getfqdn()
-    except AttributeError:
-        # Python 1.5.2 :(
-        hostname = socket.gethostname()
-        byaddr = socket.gethostbyaddr(socket.gethostbyname(hostname))
-        aliases = byaddr[1]
-        aliases.insert(0, byaddr[0])
-        aliases.insert(0, hostname)
-        for fqdn in aliases:
-            if '.' in fqdn:
-                break
-        else:
-            fqdn = 'localhost.localdomain'
-    parts = string.split(fqdn, DOT)
-    return string.join(parts[1:], DOT)
-
-
-
-def blast_mail(subject, people, filestodiff, contextlines):
-    # cannot wait for child process or that will cause parent to retain cvs
-    # lock for too long.  Urg!
-    if not os.fork():
-        # in the child
-        # give up the lock you cvs thang!
-        time.sleep(2)
-        # Create the smtp connection to the localhost
-        conn = smtplib.SMTP()
-        conn.connect(MAILHOST, MAILPORT)
-        user = pwd.getpwuid(os.getuid())[0]
-        domain = getdomain()
-        author = '%s@%s' % (user, domain)
-        s = StringIO()
-        sys.stdout = s
-        try:
-            print '''\
-From: %(author)s
-To: %(people)s
-Subject: %(subject)s
-''' % {'author' : author,
-       'people' : string.join(people, COMMASPACE),
-       'subject': subject,
-       }
-            s.write(sys.stdin.read())
-            # append the diffs if available
-            print
-            for file in filestodiff:
-                print calculate_diff(file, contextlines)
-        finally:
-            sys.stdout = sys.__stdout__
-        resp = conn.sendmail(author, people, s.getvalue())
-        conn.close()
-        os._exit(0)
-
-
-
-# scan args for options
-def main():
-    try:
-        opts, args = getopt.getopt(sys.argv[1:], 'hC:cuq',
-                                   ['context=', 'cvsroot=', 'help', 'quiet'])
-    except getopt.error, msg:
-        usage(1, msg)
-
-    # parse the options
-    contextlines = 2
-    verbose = 1
-    for opt, arg in opts:
-        if opt in ('-h', '--help'):
-            usage(0)
-        elif opt == '--cvsroot':
-            os.environ['CVSROOT'] = arg
-        elif opt in ('-C', '--context'):
-            contextlines = int(arg)
-        elif opt == '-c':
-            if contextlines <= 0:
-                contextlines = 2
-        elif opt == '-u':
-            contextlines = 0
-        elif opt in ('-q', '--quiet'):
-            verbose = 0
-
-    # What follows is the specification containing the files that were
-    # modified.  The argument actually must be split, with the first component
-    # containing the directory the checkin is being made in, relative to
-    # $CVSROOT, followed by the list of files that are changing.
-    if not args:
-        usage(1, 'No CVS module specified')
-    subject = args[0]
-    specs = string.split(args[0])
-    del args[0]
-
-    # The remaining args should be the email addresses
-    if not args:
-        usage(1, 'No recipients specified')
-
-    # Now do the mail command
-    people = args
-
-    if verbose:
-        print 'Mailing %s...' % string.join(people, COMMASPACE)
-
-    if specs == ['-', 'Imported', 'sources']:
-        return
-    if specs[-3:] == ['-', 'New', 'directory']:
-        del specs[-3:]
-    elif len(specs) > 2:
-        L = specs[:2]
-        for s in specs[2:]:
-            prev = L[-1]
-            if string.count(prev, ',') < 2:
-                L[-1] = "%s %s" % (prev, s)
-            else:
-                L.append(s)
-        specs = L
-
-    if verbose:
-        print 'Generating notification message...'
-    blast_mail(subject, people, specs[1:], contextlines)
-    if verbose:
-        print 'Generating notification message... done.'
-
-
-
-if __name__ == '__main__':
-    main()
-    sys.exit(0)

DELETED CVSROOT/taginfo
Index: CVSROOT/taginfo
==================================================================
--- CVSROOT/taginfo
+++ /dev/null
@@ -1,20 +0,0 @@
-# The "taginfo" file is used to control pre-tag checks.
-# The filter on the right is invoked with the following arguments:
-#
-# $1 -- tagname
-# $2 -- operation "add" for tag, "mov" for tag -F, and "del" for tag -d
-# $3 -- repository
-# $4->  file revision [file revision ...]
-#
-# A non-zero exit of the filter program will cause the tag to be aborted.
-#
-# The first entry on a line is a regular expression which is tested
-# against the directory that the change is being committed to, relative
-# to the $CVSROOT.  For the first match that is found, then the remainder
-# of the line is the name of the filter to run.
-#
-# If the repository name does not match any of the regular expressions in this
-# file, the "DEFAULT" line is used, if it is specified.
-#
-# If the name "ALL" appears as a regular expression it is always used
-# in addition to the first matching regex or "DEFAULT".

DELETED CVSROOT/verifymsg
Index: CVSROOT/verifymsg
==================================================================
--- CVSROOT/verifymsg
+++ /dev/null
@@ -1,21 +0,0 @@
-# The "verifymsg" file is used to allow verification of logging
-# information.  It works best when a template (as specified in the
-# rcsinfo file) is provided for the logging procedure.  Given a
-# template with locations for, a bug-id number, a list of people who
-# reviewed the code before it can be checked in, and an external
-# process to catalog the differences that were code reviewed, the
-# following test can be applied to the code:
-#
-#   Making sure that the entered bug-id number is correct.
-#   Validating that the code that was reviewed is indeed the code being
-#       checked in (using the bug-id number or a seperate review
-#       number to identify this particular code set.).
-#
-# If any of the above test failed, then the commit would be aborted.
-#
-# Actions such as mailing a copy of the report to each reviewer are
-# better handled by an entry in the loginfo file.
-#
-# One thing that should be noted is the the ALL keyword is not
-# supported.  There can be only one entry that matches a given
-# repository.

Index: mttroot/mtt/bin/mtt
==================================================================
--- mttroot/mtt/bin/mtt
+++ mttroot/mtt/bin/mtt
@@ -15,10 +15,13 @@
 ###############################################################
 ## Version control history
 ###############################################################
 ## $Header$
 ## $Log$
+## Revision 1.353  2002/05/28 18:08:38  geraint
+## Fixed [ 547294 ] CRs are not sought from MTT_CRS.
+##
 ## Revision 1.352  2002/05/24 11:04:10  geraint
 ## Removed unnecessary message about *.log file not existing when -D option is used.
 ##
 ## Revision 1.351  2002/05/23 17:08:20  geraint
 ## `mtt sys sfun zip` now produces an input block and an interface block for MTT models.
@@ -2701,11 +2704,11 @@
 ifneq ($partition,)
 	echo Doing subsystems
 	mtt_make_subsystems  ${sys} rdae r
 endif
 	mtt_prepend.sh -p $1_modpar.r $1_ese.r # Add modulated parameters to start
-	ese2rdae_r ${cr_first} ${Subsystem}; tidy ${Subsystem}_rdae.r
+	ese2rdae_r ${cr_first} ${fixcc} ${Subsystem}; tidy ${Subsystem}_rdae.r
 
 ${sys}_dae.r: ${Subsystem}_rdae.r ${Subsystem}_def.r ${Subsystem}_subs.r ${Subsystem}_cr.r
 ifneq ($partition,)
 	echo Doing subsystems
 	mtt_make_subsystems  ${sys} dae r

Index: mttroot/mtt/bin/trans/dae2cse_r
==================================================================
--- mttroot/mtt/bin/trans/dae2cse_r
+++ mttroot/mtt/bin/trans/dae2cse_r
@@ -13,10 +13,14 @@
 ###############################################################
 ## Version control history
 ###############################################################
 ## $Id$
 ## $Log$
+## Revision 1.20  2002/04/28 18:41:26  geraint
+## Fixed [ 549658 ] awk should be gawk.
+## Replaced calls to awk with call to gawk.
+##
 ## Revision 1.19  2001/10/26 01:01:49  geraint
 ## fixcc when rdae_is_dae (-cr).
 ##
 ## Revision 1.18  2001/10/05 23:37:32  geraint
 ## Fixed assignment statement in ae.r when RHS=0.
@@ -127,23 +131,25 @@
   esac
   shift
 done
 
 # Create the reduce output code
+def2write_r $optimise $1 ae
 def2write_r $optimise $1 cse 
 def2write_r $optimise $1 csex # Version without E matrix
 def2write_r $optimise $1 cseo
 
+echo "Creating $1_ae.r $optimise_msg"
 echo "Creating $1_cse.r $solve_msg $optimise_msg $fix_msg"
 echo "Creating $1_csex.r $optimise_msg"
 echo "Creating $1_cseo.r $optimise_msg"
 
 # Remove the old log file
 rm -f dae2cse_r.log
 
 # Remove some files
-rm -f $1_cse.r? $1_cseo.r?
+rm -f $1_ae.r? $1_cse.r? $1_cseo.r?
 
 # Use reduce to accomplish the transformation
 $SYMBOLIC >dae2cse_r.log << EOF
 
 %Read the formatting function
@@ -319,21 +325,10 @@
 
   % No algebraic variables left!
   MTTNYz := 0;
 END; % IF MTTNyz>0 and $solve
 
-OUT "$1_ae.r";
-IF (MTTNyz>0) THEN % not $solve (or perhaps solution failed?)
-BEGIN
-    WRITE "MATRIX MTTyz(",MTTNyz,",1)";
-    WRITE "%File: $1_ae.r";
-    FOR i := 1:MTTNyz DO
-	WRITE "MTTyz(",i,",1) := ",MTTyz(i,1)," +0";
-END; % if MTTNyz>0 (and !$solve)
-WRITE ";END;";
-SHUT "$1_ae.r";
-
 OUT "$1_aej.r";
 IF (MTTNyz>0) THEN % as above
 BEGIN
     WRITE "MATRIX MTTyzj(",MTTNyz,",",MTTNyz,")";
     WRITE "%File: $1_aej.r";
@@ -345,10 +340,22 @@
 	      WRITE "MTTyzj(",i,",",j,") := ",didj," +0";
 	END;
 END;
 WRITE ";END;";
 SHUT "$1_aej.r";
+
+IF MTTNyz>0 THEN % not $solve or solution failed
+BEGIN
+OUT "$1_ae.r1";
+write "MATRIX MTTYZ(", MTTNyz, ",", 1, ")$";
+SHUT "$1_ae.r1";
+OUT "$1_ae.r2";
+write "%File: $1_ae.r";
+in ("$1_ae_write.r");
+write "END;";
+SHUT "$1_ae.r2";
+END;
 
 % Create the matrix declarations
 OUT "$1_cse.r1";
 write "%";
 IF (MTTNx > 0) THEN
@@ -445,12 +452,14 @@
 SHUT "$1_cseo.r2";
 END;
 quit;
 EOF
 
+touch $1_ae.r1 $1_ae.r2
 touch $1_cseo.r1
 touch $1_cseo.r2
+cat $1_ae.r1 $1_ae.r2 > $1_ae.r
 cat $1_cse.r1 $1_cse.r2  > $1_cse.r
 cat $1_csex.r1 $1_csex.r2  > $1_csex.r
 cat $1_cseo.r1 $1_cseo.r2  > $1_cseo.r
 
 if [ "$solve" = "1" ]; then

Index: mttroot/mtt/bin/trans/def2write_r
==================================================================
--- mttroot/mtt/bin/trans/def2write_r
+++ mttroot/mtt/bin/trans/def2write_r
@@ -11,10 +11,22 @@
 ###############################################################
 ## Version control history
 ###############################################################
 ## $Id$
 ## $Log$
+## Revision 1.11.2.1  2002/06/05 11:14:51  geraint
+## ae.r now generated using def2write_r like cse?.r
+## fix_c.r called at ese2rdae stage so that pow gets fixed in ae.r.
+##
+## These changes produce the desired result (optimised algebraic equations) but
+## have highlighted a problem; when optimisation fails, Reduce does not write
+## a result. For complicated systems, this can lead to missing assignments in
+## the resultant code.
+##
+## Revision 1.11  2002/05/17 09:14:58  geraint
+## Optimises each line in a separate session. Allows larger models to be built.
+##
 ## Revision 1.10  2002/04/28 18:41:27  geraint
 ## Fixed [ 549658 ] awk should be gawk.
 ## Replaced calls to awk with call to gawk.
 ##
 ## Revision 1.9  2001/07/27 23:29:10  geraint
@@ -79,10 +91,15 @@
 Nyz=`mtt_getsize $sys yz` # Zero outputs
 #Npar=`wc -l $sys\_sympar.txt | gawk '{print $1}'`
 
 # Set up representation-specific stuff
 case $rep in
+ae)
+matrices='Yz'
+ns="$Nyz"
+ms="1"
+;;
     cse)
         matrices='EdX E'
         ns="$Nx $Nx"
         ms="1 $Nx"
 	;;
@@ -144,47 +161,23 @@
 
 mtt_optimise ()
 {
     sys="$1"
     lhs="$2"
-    rhs="$3"
+
+    lhs=`echo $lhs | sed 's/MTTEdX/MTTdX/'`
     
-    crr="${sys}_cr.r"
     dae="${sys}_dae.r"
-    tmp="mtt_optimise.tmp"
-    tmp2="mtt_optimise2.tmp"
-    tmp3="mtt_optimise3.tmp"
-    
-    {
-	cat <<EOF
-off echo$
-load scope$
-on double$
-on noconvert$
-on rounded$
-off int$
-off nat$
-
-out "$tmp2"$
-EOF
-    } > $tmp
-    
-    echo "optimize" >> $tmp
-    grep -i -e "^$lhs" $dae |\
-	sed -e 's/;/\ INAME\ mtt_tmp/g' |\
-	sed -e 's/:=/:=/g' >> $tmp
-    {
-	cat <<EOF
-
-shut "$tmp2"$
-EOF
-    } >> $tmp
- 
-    ${SYMBOLIC:-reduce} < $tmp >> def2write_r1.log 2>> def2write_r2.log
-    cat $tmp2 | gawk -v RS=';' '($2 == ":=") {print $0}' > $tmp3
-    cat $tmp3 | mtt_fix_integers
-    rm -f $tmp $tmp2 $tmp3
+
+    exp=`grep -i -e "^$lhs" $dae`
+    rhs=`echo $exp | sed 's/.*:=\ \(.*\)/\1/'`
+    rhs=`echo $rhs | sed 's/[;$]*$//'`
+
+    if [ ! -z "${rhs}" ]; then
+	mtt_optimise.sh "$lhs" "$rhs" | mtt_fix_integers
+    fi
+
     return
 }
 
 
 # Remove log files
@@ -208,11 +201,11 @@
     js=`n2m 1 $m`; 
     for i in $is; do
       for j in $js; do
 	if [ ${opt:-""} = "-optimise" ]; then
 	    name=`echo MTT$matrix'('$i','$j')'`
-	    mtt_optimise $1 "$comma$name" "$name"
+	    mtt_optimise $1 "$comma$name"
 	    comma=''
 	else
 	    echo 'write'
 	    name=`echo MTT$matrix'('$i','$j')'`
 	    echo '  '$comma$name ':=' $name '$'

Index: mttroot/mtt/bin/trans/ese2rdae_r
==================================================================
--- mttroot/mtt/bin/trans/ese2rdae_r
+++ mttroot/mtt/bin/trans/ese2rdae_r
@@ -12,10 +12,23 @@
 ###############################################################
 ## Version control history
 ###############################################################
 ## $Id$
 ## $Log$
+## Revision 1.12.2.1  2002/06/05 11:14:51  geraint
+## ae.r now generated using def2write_r like cse?.r
+## fix_c.r called at ese2rdae stage so that pow gets fixed in ae.r.
+##
+## These changes produce the desired result (optimised algebraic equations) but
+## have highlighted a problem; when optimisation fails, Reduce does not write
+## a result. For complicated systems, this can lead to missing assignments in
+## the resultant code.
+##
+## Revision 1.12  2001/07/23 23:31:17  gawthrop
+## Added -cr option to load CRs first - avoids alg. loops with R
+## implementation of mutiports.
+##
 ## Revision 1.11  2001/07/06 00:46:50  gawthrop
 ## Added -cr option -- forces cr to be loaded before the ese.r file
 ## This avoids causality problems when using multi-port Rs to represent
 ## arbitary equations
 ##
@@ -98,10 +111,14 @@
                 info=info;;
 	-cr )
                 load_cr=yes;
                 blurb2=' using cr and subs first';
                 ;;
+      -fixcc )
+		include=`echo 'in "'$MTT_LIB'/reduce/fix_c.r";'`
+		blurb3='fixing c and cc code';
+		;;
 	-partition )
                 partition=yes;
                 blurb='with partitioning';
 		;;
 	*)
@@ -134,11 +151,11 @@
     load_cr_comm="in \"${crname}\";"
     load_subs_comm="in \"${subsname}\";"
 fi
 
 # Inform user
-echo Creating $daename $blurb $blurb2
+echo Creating $daename $blurb $blurb2 $blurb3
 
 # Remove the old log file
 rm -f $logname
 
 # Use symbolic algebra to accomplish the transformation
@@ -154,10 +171,13 @@
 % Definitions
 in "$defname";
 
 % Elementary system equations
 in "$esename";
+
+% Fix c code if required
+$include
 
 OFF Echo;
 OFF Nat;
 
 %Create the output file

Index: mttroot/mtt/bin/trans/m/args2arg.m
==================================================================
--- mttroot/mtt/bin/trans/m/args2arg.m
+++ mttroot/mtt/bin/trans/m/args2arg.m
@@ -26,6 +26,28 @@
 
 % Field separator
 if nargin<3
   FS = ';';
 end;
+
+arg = '';
+if strcmp(args, '')==0
+  L = length(args);
+  args_count = 0;
+  for i=1:n
+    arg_count = 0;
+    arg = '';
+    if args_count == L
+      break;
+    end;  
+    while args_count < L
+      args_count = args_count+1;
+      arg_count = arg_count+1;
+      ch = str2ch(args,args_count);
+      if ch==FS
+	break;
+      end;
+      arg = [arg ch];
+    end;
+  end;
+end;
 

ADDED   mttroot/mtt/bin/trans/mtt_optimise.sh
Index: mttroot/mtt/bin/trans/mtt_optimise.sh
==================================================================
--- /dev/null
+++ mttroot/mtt/bin/trans/mtt_optimise.sh
@@ -0,0 +1,45 @@
+#! /bin/sh
+
+set -e
+
+# get expression to optimise
+
+lhs="$1"
+rhs="$2"
+
+create_reduce_script ()
+{
+    lhs="$1"
+    rhs="$2"
+
+    cat <<EOF
+off echo$
+load scope$
+on double$
+on noconvert$
+on rounded$
+off int$
+off nat$
+
+out "${tmp}"$
+optimize mtt_tmp0 :=: ${rhs} iname mtt_tmp$
+write "${lhs} := mtt_tmp0 $"$
+shut "${tmp}"$
+
+;end;
+EOF
+    return
+}
+
+
+# set work file names
+
+tmp="$0.tmp"
+log="$0.log"
+
+create_reduce_script "${lhs}" "${rhs}" | reduce > ${log}
+
+cat ${tmp}
+rm -f ${tmp}
+
+exit 0

DELETED mttroot/mtt/doc/mtt.texi
Index: mttroot/mtt/doc/mtt.texi
==================================================================
--- mttroot/mtt/doc/mtt.texi
+++ /dev/null
@@ -1,6138 +0,0 @@
-\input texinfo  
-@c %**start of header
-@setfilename mtt.info
-@settitle MTT: Model Transformation Tools
-@c %**end of header
-
-@finalout
-
-@c Here is what I use in the Info `dir' file:
-@c * Mtt: (mtt).                Model transformation tools.
-
-
-
-@comment %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-@comment  Version control history
-@comment %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-@comment  $Id$
-@comment  $Log$
-@comment  Revision 1.6  2001/10/15 14:29:50  gawthrop
-@comment  Added documentaton on  [1:N] style port labels
-@comment
-@comment  Revision 1.5  2001/07/23 03:35:29  geraint
-@comment  Updated file structure (mtt/bin).
-@comment
-@comment  Revision 1.4  2001/07/23 03:25:02  geraint
-@comment  Added notes on -ae hybrd, rk4, ode2odes.cc, .oct dependencies.
-@comment
-@comment  Revision 1.3  2001/07/13 03:02:38  geraint
-@comment  Added notes on #ICD, gnuplot.txt and odes.sg rep.
-@comment
-@comment  Revision 1.2  2001/07/03 22:59:10  gawthrop
-@comment  Fixed problems with argument passing for CRs
-@comment
-@comment  Revision 1.1  2001/06/04 08:18:52  gawthrop
-@comment  Putting documentation under CVS
-@comment
-@comment  Revision 1.66  2000/12/05 14:20:55  peterg
-@comment  Added the c++  anf m CR info.
-@comment
-@comment  Revision 1.65  2000/11/27 15:36:15  peterg
-@comment  NOPAR --> NOTPAR
-@comment
-@comment  Revision 1.64  2000/11/16 14:22:48  peterg
-@comment  added UNITS declaration
-@comment
-@comment  Revision 1.63  2000/11/03 14:41:08  peterg
-@comment  Added PAR and NOPAR stuff
-@comment
-@comment  Revision 1.62  2000/10/17 17:53:34  peterg
-@comment  Added some simulation details
-@comment
-@comment  Revision 1.61  2000/09/14 17:13:06  peterg
-@comment  New options table
-@comment
-@comment  Revision 1.60  2000/09/14 17:09:20  peterg
-@comment  Tidied up valid name sections
-@comment  Tidied up defining represnetations table
-@comment  Verion 4.6
-@comment
-@comment  Revision 1.59  2000/08/30 13:09:00  peterg
-@comment  Updated option table
-@comment
-@comment  Revision 1.58  2000/08/01 13:30:19  peterg
-@comment  Version 4.4
-@comment  updated STEPFACTOR info
-@comment  describes octave and OCST interfaces
-@comment
-@comment  Revision 1.57  2000/07/20 07:55:44  peterg
-@comment  Version 4.3
-@comment
-@comment  Revision 1.56  2000/05/19 17:49:17  peterg
-@comment  Extended the user defined representation section -- new nppp rep.
-@comment
-@comment  Revision 1.55  2000/03/16 13:53:31  peterg
-@comment  Correct date
-@comment
-@comment  Revision 1.54  2000/03/15 21:22:57  peterg
-@comment  Updated to 4.1 -- old style SS no longer supported
-@comment
-@comment  Revision 1.53  1999/12/22 05:33:10  peterg
-@comment  Updated for 4.0
-@comment
-@comment  Revision 1.52  1999/11/23 00:25:11  peterg
-@comment  Added the sensitivity reps
-@comment
-@comment  Revision 1.51  1999/11/16 04:43:47  peterg
-@comment  Added start of sensitivity section
-@comment
-@comment  Revision 1.50  1999/11/16 00:30:35  peterg
-@comment  Updated simulation section
-@comment  Added vector components
-@comment
-@comment  Revision 1.49  1999/07/20 23:44:58  peterg
-@comment  V 3.8
-@comment
-@comment  Revision 1.48  1999/07/19 03:08:33  peterg
-@comment  Added documentation for (new) SS lbl fields
-@comment
-@comment  Revision 1.47  1999/03/09 01:42:22  peterg
-@comment  Rearranged the User interface section
-@comment
-@comment  Revision 1.46  1999/03/09 01:18:01  peterg
-@comment  Updated for 3.5 including xmtt
-@comment
-@comment  Revision 1.45  1999/03/03 02:39:26  peterg
-@comment  Minor updates
-@comment
-@comment  Revision 1.44  1999/02/17 06:52:14  peterg
-@comment  New level formula dor artwork
-@comment
-@comment  Revision 1.43  1998/11/25 16:49:24  peterg
-@comment  Put in subs.r documentation (was called params.r)
-@comment
-@comment  Revision 1.42  1998/11/24 12:24:59  peterg
-@comment  Added section on simulation output
-@comment  Version 3.4
-@comment
-@comment  Revision 1.41  1998/09/02 12:04:15  peterg
-@comment  Version 3.2
-@comment
-@comment  Revision 1.40  1998/08/27 08:36:39  peterg
-@comment  Removed in. methods except Euler anf implicit
-@comment
-@comment  Revision 1.39  1998/08/18 10:44:28  peterg
-@comment  Typo
-@comment
-@comment  Revision 1.38  1998/08/18 09:16:38  peterg
-@comment  Version 3.1
-@comment
-@comment  Revision 1.37  1998/08/17 16:14:30  peterg
-@comment  Version 3.1 - includes documentation on METHOD=IMPLICIT
-@comment
-@comment  Revision 1.36  1998/07/30 17:33:15  peterg
-@comment  VERSION 3.0
-@comment
-@comment  Revision 1.35  1998/07/22 11:00:53  peterg
-@comment  Correct date!
-@comment
-@comment  Revision 1.34  1998/07/22 11:00:13  peterg
-@comment  Version to BAe
-@comment
-@comment  Revision 1.33  1998/07/17 19:32:19  peterg
-@comment  Added more about aliases
-@comment
-@comment  Revision 1.32  1998/07/05 14:21:56  peterg
-@comment  Further additions (Carlisle-Glasgow)
-@comment
-@comment  Revision 1.31  1998/07/04 11:35:57  peterg
-@comment  Strarted new lbl description
-@comment
-@comment  Revision 1.30  1998/07/02 18:39:20  peterg
-@comment  Started 3.0
-@comment  Added alias and default sections.
-@comment
-@comment  Revision 1.29  1998/05/19 19:46:58  peterg
-@comment  Added the odess description
-@comment
-@comment  Revision 1.28  1998/05/14 09:17:22  peterg
-@comment  Added METHOD variable to the simpar file
-@comment
-@comment  Revision 1.27  1998/05/13 10:03:09  peterg
-@comment  Added unknown/zero SS label documentation.
-@comment
-@comment  Revision 1.26  1998/04/29 15:12:46  peterg
-@comment  Version 2.9.
-@comment
-@comment  Revision 1.25  1998/04/12 17:00:26  peterg
-@comment  Added new port features: coerced direction and top-level behaviour.
-@comment
-@comment  Revision 1.24  1998/04/05 18:27:20  peterg
-@comment  This was the 2.6 version
-@comment
-@comment Revision 1.23  1997/08/24  11:17:51  peterg
-@comment This is the released  version 2.5
-@comment
-@comment  Revision 1.22  1997/08/23 19:38:53  peterg
-@comment  Added simulation chapter.
-@comment
-@comment  Revision 1.21  1997/08/23 16:50:10  peterg
-@comment  Added desc section.
-@comment  Included named and vector ports
-@comment  Completed list of representations.
-@comment
-@comment Revision 1.20  1997/06/16  15:39:24  peterg
-@comment THis is the released 2.4 document.
-@comment
-@comment Revision 1.19  1997/06/16  09:48:23  peterg
-@comment Back under revision control (elm)
-@comment
-@comment  Revision 1.18  1997/06/14 20:27:41  peterg
-@comment  Added complex example section.
-@comment
-@comment  Revision 1.18  1997/06/13  14:51:07  peterg
-@comment  Added report section
-@comment 
-@comment  Revision 1.17  1997/05/09 15:06:02  peterg
-@comment  Changed to version 2.4.
-@comment
-@comment  Revision 1.16  1996/12/05 10:06:25  peterg
-@comment  Modified .octaverc : 'true' --> 1
-@comment
-@comment  Revision 1.15  1996/11/20 19:02:28  peterg
-@comment  Added some system admin stuff.
-@comment  Added section on simple models.
-@comment
-@comment Revision 1.14  1996/11/12  13:19:04  peterg
-@comment Put paths as section, not subsection.
-@comment
-@comment Revision 1.13  1996/11/11  16:53:14  peterg
-@comment Added params documentation
-@comment Sorted out table bug.
-@comment
-@comment  Revision 1.12  1996/11/10 20:29:31  peterg
-@comment  Added section on help -- needs more
-@comment
-@comment  Revision 1.11  1996/11/09 21:15:28  peterg
-@comment  Rewrite of quick start.
-@comment  Update of file structure.
-@comment
-@comment  Revision 1.10  1996/11/09 20:25:54  peterg
-@comment  Final v2.0.
-@comment
-@comment  Revision 1.9  1996/10/01 10:33:02  peter
-@comment  Cleaned up cross references.
-@comment
-@comment  Revision 1.8  1996/10/01 09:31:00  peter
-@comment  Added sections written in Hong Kong.
-@comment
-@comment  Revision 1.7  1996/09/16 09:49:47  peter
-@comment  Added ese section
-@comment
-@comment  Revision 1.6  1996/09/16 08:33:53  peter
-@comment  Added constitutive relationship section etc.
-@comment
-@comment  Revision 1.5  1996/09/15 20:20:56  peter
-@comment  Added abg and rbg stuff
-@comment
-@comment  Revision 1.4  1996/08/30 19:07:40  peter
-@comment  Added some admin stuff.
-@comment
-@comment  Revision 1.3  1996/08/30 07:50:16  peter
-@comment  Added file structure section.
-@comment
-@comment  Revision 1.2  1996/08/22 14:28:50  peter
-@comment  Added stuff about labels.
-@comment
-@comment  Revision 1.1  1996/08/22 11:52:59  peter
-@comment  Initial revision
-@comment %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-
-@ifinfo
-This file documents MTT a set of Model Transformation Tools.
-
-
-Copyright (C) Peter J. Gawthrop 1996, 1997, 1998, 1999
-
-Permission is granted to make and distribute verbatim copies of this
-manual provided the copyright notice and this permission notice are
-preserved on all copies.
-
-@ignore
-Permission is granted to process this file through TeX and print the
-results, provided the printed document carries copying permission
-notice identical to this one except for the removal of this paragraph
-(this paragraph not being relevant to the printed manual).
-@end ignore
-
-Permission is granted to copy and distribute modified versions of this
-manual under the conditions for verbatim copying, provided also that the
-section entitled ``GNU General Public License'' is included exactly as
-in the original, and provided that the entire resulting derived work is
-distributed under the terms of a permission notice identical to this one.
-
-Permission is granted to copy and distribute translations of this manual
-into another language, under the above conditions for modified versions,
-except that the section entitled ``GNU General Public License'' may be
-included in a translation approved by the author instead of in the
-original English.
-@end ifinfo
-
-
-@titlepage
-@title MTT: Model Transformation Tools
-@subtitle December 2000
-@subtitle For version 4.9.
-@author Peter Gawthrop
-@page
-@vskip 0pt plus 1filll
-Copyright @copyright{} 1996,1997,1998,1999,2000 Peter J. Gawthrop
-
-Permission is granted to make and distribute verbatim copies of
-this manual provided the copyright notice and this permission notice
-are preserved on all copies.
-
-Permission is granted to copy and distribute modified versions of this
-manual under the conditions for verbatim copying, provided also that the
-section entitled ``GNU General Public License'' is included exactly in
-the original, and provided that the entire resulting derived work is
-distributed under the terms of a permission notice identical to this
-one.
-
-Permission is granted to copy and distribute translations of this manual
-into another language, under the above conditions for modified versions,
-except that the section entitled ``GNU General Public License'' may be
-included in a translation approved by the author instead of in the
-original English.
-
-General information  about MTT is available at URL
-@example
-http://mtt.sourceforge.net
-@end example
-@ifhtml
-<A
-HREF="http://mtt.sourceforge.net"> here</A>.
-@end ifhtml
-
-@end titlepage
-
-
-@ifinfo
-@node Top, Introduction, (dir), (dir)
-@top MTT
-@strong{MTT} is a set of Model Transformation Tools based on bond graphs.
-@strong{MTT} implements the theory to be found in the book ``Metamodelling: Bond
-Graphs and Dynamic Systems'' by Peter Gawthrop and Lorcan Smith
-published by Prentice Hall in 1996 (ISBN 0-13-489824-9).
-
-It implements two features not discussed in that book:
-@itemize @bullet
-@item 
-bicausal bond graphs and
-@item
-hierarchical bond graphs.
-@end itemize
-
-
-
-@contents
-
-@end ifinfo
-
-
-@c @include intro.texi
-@c Copyright (C) 1996 Peter J. Gawthrop
-@c This is part of the MTT manual.
-@c For copying conditions, see the file MTT.texi.
-
-@menu
-* Introduction::                
-* User interface::              
-* Creating Models::             
-* Simulation::                  
-* Sensitivity models::          
-* Representations::             
-* Extending MTT::               
-* Languages::                   
-* Language tools::              
-* Administration::              
-* Glossary::                    
-* Index::                       
-
-@detailmenu
- --- The Detailed Node Listing ---
-
-Introduction
-
-* What is a Representation?::   
-* What is a Transformation?::   
-* Bond graphs::                 What is a bond graph?                
-* Variables::                   
-* Bonds::                       
-* Components::                  
-* Algebraic loops::             
-* Switched systems::            
-
-Components
-
-* Ports::                       
-* Constitutive relationship::   
-* Symbolic parameters::         
-* Numeric parameters::          
-
-User interface
-
-* Menu-driven interface::       
-* Command line interface::      
-* Options::                     
-* Utilities::                   
-
-Utilities
-
-* Help::                        
-* Copy::                        
-* Clean::                       
-* Version control::             
-
-Help
-
-* help representations::        
-* help components::             
-* help examples::               
-* help crs::                    
-* help <name>::                 
-
-Creating Models
-
-* Quick start::                 
-* Creating simple models::      
-* Creating complex models::     
-
-Creating complex models
-
-* Top level::                   
-
-Simulation
-
-* Steady-state solutions::      
-* Simulation parameters::       
-* Simulation input::            
-* Simulation logic::            
-* Simulation initial state::    
-* Simulation code::             
-* Simulation output::           
-
-Steady-state solutions 
-
-* Steady-state solutions - numerical(odess)::  
-* Steady-state solutions - symbolic (ss)::  
-
-Simulation parameters
-
-* Euler integration::           
-* Implicit integration::        
-* Runge Kutta IV integration::  
-* Hybrd algebraic solver::      
-
-Simulation output
-
-* Viewing results with gnuplot::  
-* Exporting results to SciGraphica::  
-
-Representations
-
-* Representation summary::      
-* Defining representations::    
-* Verbal description (desc)::   
-* Acausal bond graph (abg)::    
-* Stripped acausal bond graph (sabg)::  
-* Labels (lbl)::                
-* Description (desc)::          
-* Structure (struc)::           
-* Constitutive Relationship (cr)::  
-* Parameters::                  
-* Causal bond graph (cbg)::     
-* Elementary system equations::  
-* Differential-Algebraic Equations::  
-* Constrained-state Equations::  
-* Ordinary Differential Equations::  
-* Descriptor matrices::         
-* Report::                      
-
-Acausal bond graph (abg)
-
-* Language fig (abg.fig)::      
-* Language m (rbg.m)::          
-* Language m (abg.m)::          
-* Language tex (abg.tex)::      
-
-Language fig (abg.fig) 
-
-* icon library::                
-* bonds::                       
-* strokes::                     
-* components::                  
-* Simple components::           
-* SS components::               
-* Simple components - implementation::  
-* Compound components::         
-* Named SS components::         
-* Coerced bond direction::      
-* Port labels::                 
-* Vector port labels::          
-* Port label defaults::         
-* Vector components::           
-* artwork::                     
-* Valid names::                 
-
-Simple components
-
-* SS components::               
-* Simple components - implementation::  
-
-Compound components
-
-* Named SS components::      
-
-Language m (rbg.m)
-
-* Transformation abg2rbg_fig2m::  
-
-Language m (abg.m)
-
-* Arrow-orientated causality::  
-* Component-orientated causality::  
-* Transformation rbg2abg_m::    
-
-Stripped acausal bond graph (sabg)
-
-* Language fig (sabg.fig)::     
-* Stripped acausal bond graph (view)::  
-
-Labels (lbl)
-
-* SS component labels ::        
-* Other component labels ::     
-* Component names::             
-* Component constitutive relationship::  
-* Component arguments::         
-* Parameter declarations::      
-* Units declarations::          
-* Interface Control Definition::  
-* Aliases::                     
-* Parameter passing::           
-* Old-style labels (lbl)::      
-
-Other component labels 
-
-* Component names::             
-* Component constitutive relationship::  
-* Component arguments::         
-* Aliases::                     
-* Parameter passing::           
-* Old-style labels (lbl)::      
-
-Aliases
-
-* Port aliases::                
-* Parameter aliases::           
-* CR aliases::                  
-* Component aliases::           
-
-Old-style labels (lbl)
-
-* SS component labels (old-style)::  
-* Other component labels (old-style)::  
-* Parameter passing (old-style)::  
-
-Description (desc)
-
-* Language tex (desc.tex)::     
-
-Structure (struc)
-
-* Language txt (struc.txt)::    
-* Language tex (struc.tex)::    
-* Structure (view)::            
-
-Constitutive relationship (cr)
-
-* Predefined constitutive relationships::  
-* DIY constitutive relationships::  
-* Unresolved constitutive relationships::  
-* Unresolved constitutive relationships - Octave::  
-* Unresolved constitutive relationships - c++::  
-
-Predefined constitutive relationships
-
-* lin::                         
-* exotherm::                    
-
-Parameters
-
-* Symbolic parameters (subs.r)::  
-* Symbolic parameters for simplification (simp.r)::  
-* Numeric parameters (numpar)::  
-
-Numeric parameters (numpar)
-
-* Text form (numpar.txt)::      
-
-Causal bond graph (cbg)
-
-* Language fig (cbg.fig)::      
-* Language m (cbg.m)::          
-
-Language m (cbg.m)
-
-* Transformation abg2cbg_m::    
-
-Elementary system equations (ese)
-
-* Transformation cbg2ese_m2r::  
-
-Differential-Algebraic Equations (dae)
-
-* Differential-Algebraic Equations (reduce)::  
-* Differential-Algebraic Equations (m)::  
-
-Language reduce (dae.r)
-
-* Transformation ese2dae_r::    
-
-Language m (dae.m)
-
-* Transformation dae_r2m::      
-
-Constrained-state Equations (cse)
-
-* Constrained-state Equations (reduce)::  
-* Constrained-state Equations (view)::  
-
-Language reduce (cse.r)
-
-* Transformation dae2cse_r::    
-
-Ordinary Differential Equations
-
-* Ordinary Differential Equations (reduce)::  
-* Ordinary Differential Equations (m)::  
-* Ordinary Differential Equations (view)::  
-
-Language reduce (ode.r)
-
-* Transformation cse2ode_r::    
-
-Language m (ode.m)
-
-* Transformation ode_r2m::      
-
-Descriptor matrices (dm)
-
-* Descriptor matrices (reduce)::  
-* Descriptor matrices (m)::     
-
-Report (rep)
-
-* Report (text)::               
-* Report (view)::               
-
-Extending MTT
-
-* Makefiles::                   
-* New representations::         
-* Component library ::          
-
-Languages
-
-* Fig::                         r
-* m::                           
-* Reduce::                      
-* c::                           
-
-Language tools
-
-* Views::                       
-* Xfig::                        
-* Text editors::                
-* Octave::                      
-* LaTeX::                       
-
-Octave
-
-* Octave control system toolbox (OCST)::  
-
-Administration
-
-* Software components::         
-* REDUCE setup::                
-* Octave setup::                
-* Paths::                       
-* File structure::              
-
-Octave setup
-
-* .octaverc::                   
-* .oct file dependencies::      
-
-Paths
-
-* $MTTPATH::                    
-* $MTT_COMPONENTS::             
-* $MTT_CRS::                    
-* $MTT_EXAMPLES::               
-* $OCTAVE_PATH::                
-
-@end detailmenu
-@end menu
-
-@node Introduction, User interface, Top, Top
-@chapter Introduction
-
-@cindex MTT, purpose of
-
-@pindex MTT
-
-@strong{MTT} is a set of Model Transformation Tools based on bond
-graphs.  @strong{MTT} implements the theory to be found in the book
-``Metamodelling: Bond Graphs and Dynamic Systems'' by Peter Gawthrop and
-Lorcan Smith published by Prentice Hall in 1996 (ISBN 0-13-489824-9).
-
-It implements two features not discussed in that book:
-@itemize @bullet
-@item 
-bicausal bond graphs and
-@item
-hierarchical bond graphs.
-@end itemize
-
-In the context of software, it has been said that one good tool is worth many
-packages. UNIX is a good example of this philosophy: the user can put together
-applications from a range of ready made tools.
-This manual describes the application of this philosophy to dynamic
-system modeling embodied in @strong{MTT} - a set of Model Transformation Tools
-each of which implements a single transformation between system
-representations.
-
-
-System representations have two attributes. 
-@itemize @bullet
-@item
- A Form: e.g. acausal bond graph, differential algebraic, linear
-                state-space etc.
-@item
-A Language: e.g. Fig, Matlab, LaTeX, Reduce, postscript etc.
-@end itemize
-
-Transformations in @strong{MTT} are accomplished using appropriate software (e.g.
-Octave/Matlab, Reduce) encapsulated in UNIX Bourne shell scripts. The
-relationships between the tools are encoded in a Make File; thus the
-user can specify a final representation and all the necessary
-intermediate transformations are automatically generated.
-
-@menu
-* What is a Representation?::   
-* What is a Transformation?::   
-* Bond graphs::                 What is a bond graph?                
-* Variables::                   
-* Bonds::                       
-* Components::                  
-* Algebraic loops::             
-* Switched systems::            
-@end menu
-
-
-@node What is a Representation?, What is a Transformation?, Introduction, Introduction
-@section What is a representation?
-
-@cindex Representations, what are they?
-
-@pindex Representations
-
-Physical systems have many representations. These include
-@itemize @bullet
-@item
-a schematic diagram,
-@item
-a block diagram,
-@item
-a bunch of equations,
-@item
-a single differential(-algebraic) equation,
-@item
-simulation code,
-@item
-linearised state-space (or descriptor) equations,
-@item
-transfer function (of the linearised system),
-@item
-frequency response  (of the linearised system),
-@item
-etc...
-@end itemize
-
-Each of these representations is related to other representations by an
-appropriate transformation (@pxref{What is a Transformation?}. In many cases, a
-modeler is presented with a physical system and needs to make a
-model. In particular, a model, in this context, is a representation of
-the system appropriate to a particular use, for example:
-@itemize @bullet
-@item
-simulation,
-@item
-control system design,
-@item
-optimisation
-@item
-etc.
-@end itemize
-
-Indeed, for a given physical system, the modeler would need to derive
-a number of models. This process can be viewed as a series of steps;
-each involving a transformation between representations (@pxref{What is a Transformation?}.
-
-
-In this context, the following considerations are relevant.
-@itemize @bullet
-@item
-There is a unique `core' representation of any system.
-There are many routes  from this core representation, each leading to
-an appropriate model.
-There are many possible routes  to this core representation
-from the physical system: the route chosen is a matter of convenience.
-@item
-Because the core representation is unique, it is easy to expand the
-tool-box to include additional transformations from the physical system
-to the core representation and additional transformations from the core
-representation to the mode.
-@item
-Transformation_1 probably cannot, and certainly should not, be
-completely automated.  Engineering insight, knowledge and experience is
-essential to capture the essence (with respect to the particular use) of
-the physical system whilst discarding irrelevant form.
-@item
-Representation_1 should be `close' in some sense to the Physical system.
-@item
-The core representation, and hence the representations leading to it,
-must contain enough information to generate all of the required models.
-@item
-Representations must be easily extensible: it must be possible to add
-extra components or attributes without restructuring the representation.
-@end itemize
-
-I happen to believe that Bond graphs (@pxref{Bond graphs}) provide the
-most convenient and powerful basis for the core representation.
-
-@node What is a Transformation?, Bond graphs, What is a Representation?, Introduction
-@comment  node-name,  next,  previous,  up
-@section What is a transformation?
-@cindex Transformations
-
-
-Each system representation  (@pxref{What is a Representation?} is related to other representations by an
-appropriate transformation as follows:
-@itemize @bullet 
-@item
- Physical system
-@item
- Transformation_1 ---> Representation_1
-@item
- Transformation_2 ---> Representation_2
-@item
- ...
-@item
- Transformation_N ---> Core representation
-@item
- Transformation_N+1 ---> Representation_N+1
-@item
- Transformation_N+2 ---> Representation_N+2
-@item
- ...
-@item
- Transformation_N+M ---> Model
-@end itemize
-Thus modeling is seen as a sequence of transformations between
-representations.
-
-
-
-@node Bond graphs, Variables, What is a Transformation?, Introduction
-@section What is a bond graph?
-
-@cindex Bond graphs, what are they?
-
-@pindex Bond graphs
-
-Bond graphs provide a graphical high-level language for describing
-dynamic systems in a precise and unambiguous fashion. 
-They make a clear distinction between structure (how components are
-connected together), and behavior (the particular constitutive
-relationships, or physical laws, describing each component.
-
-They can describe a range of physical systems including:
-@itemize @bullet
-@item
-Electrical systems
-@item
-Mechanical systems
-@item
-Hydraulic systems
-@item
-Chemical process systems
-@end itemize
-
-More importantly, they can describe systems which contain subsystems
-drawn from all of these domains in a uniform manner.
-
-Bond graphs are made up of components (@pxref{Components}) connected by
-bonds (@pxref{Bonds}) which define the relationship between
-variables (@pxref{Variables}).
-
-@node Variables, Bonds, Bond graphs, Introduction
-@comment  node-name,  next,  previous,  up
-@section Variables
-@cindex Variables
-In bond graph terminology there are four sorts of variables:
-@itemize @bullet
-@item  @emph{effort} variables
-@item  @emph{flow} variables
-@item  @emph{integrated effort} variables
-@item  @emph{integrated flow} variables
-@end itemize
-
-Examples of  @emph{effort} variables are
-@itemize @bullet
-@item 
-voltage
-@item 
-pressure
-@item
-force
-@item
-torque
-@item
-temperature
-@end itemize
-
-Examples of  @emph{flow} variables are
-@itemize @bullet
-@item 
-current
-@item 
-volumetric flow rate
-@item
-velocity
-@item
-angular velocity
-@item
-heat flow
-@end itemize
-
-
-
-Examples of integrated  @emph{flow} variables are
-@itemize @bullet
-@item 
-charge
-@item 
-volume
-@item
-momentum
-@item
-angular momentum
-@item
-heat
-@end itemize
-
-
-
-@node Bonds, Components, Variables, Introduction
-@comment  node-name,  next,  previous,  up
-@section Bonds
-@cindex Bonds
-Bonds connect components (@pxref{Components}) together. Each bond
-carries two variables:
-@itemize @bullet
-@item an effort (@pxref{Variables}) variable and 
-@item a flow (@pxref{Variables}) variable.
-@end itemize
-Each bond has three notations associated with it:
-@itemize @bullet
-@item a half-arrow,
-@item a causal stroke and
-@item a causal half-stroke.
-@end itemize
-
-The half-arrow indicates two things:
-@itemize @bullet
-@item the direction of power (or pseudo power) flow and
-@item the side of the bond associated with the flow variable.
-@end itemize
-
-The causal stroke indicates two things:
-@itemize @bullet
-@item the effort variable is imposed at the same end as the stroke and
-@item the flow variable is imposed at the opposite end to the stroke.
-@end itemize
-
-The causal half-stoke indicates one thing:
-@itemize @bullet
-@item if it is on the effort side of the bond, the effort variable is 
-imposed at the same end as the stroke or
-@item if it is on the flow side of the bond, the flow variable is 
-imposed at the opposite end to the stroke.
-@end itemize
-
-
-
-@node Components, Algebraic loops, Bonds, Introduction
-@comment  node-name,  next,  previous,  up
-@section  Components
-@cindex Components
-
-Components provide the building blocks of a dynamic system when
-connected by bonds (@pxref{bonds}).
-Components have the following attributes:
-@vtable @code
-@item ports 
-        provide the connections to other components (@pxref{Ports})
-@item constitutive relationships
-        define how the port-variables are related (@pxref{Constitutive
-relationship})
-@end vtable
-
-
-@menu
-* Ports::                       
-* Constitutive relationship::   
-* Symbolic parameters::         
-* Numeric parameters::          
-@end menu
-
-@node Ports, Constitutive relationship, Components, Components
-@comment  node-name,  next,  previous,  up
-@subsection Ports
-@cindex ports
-Components have one or more ports. Each port carries two variables,
-and effort and a flow variable (@pxref{Variables}). Any pair of ports
-can be connected by a bond (@pxref{Bonds}); this connection is
-equivalent to saying that the effort variables at each port are
-identical and that the flow variables at each port are
-identical.
-
-Ports are implemented in @strong{MTT} using named SS components.
-(@pxref{Named SS components}).
-
-The direction of the named SS components.
-(@pxref{Named SS components}) 
-is coerced (@pxref{Coerced bond direction}) to have the same direction
-as the bons connected to the corresponding port. Thus the direction of
-the  direction of the named SS components has no significance unless the
-component is at the top level.
-
-@node Constitutive relationship, Symbolic parameters, Ports, Components
-@comment  node-name,  next,  previous,  up
-@subsection  Constitutive relationship
-@cindex Constitutive Relationship
-
-The constitutive relationship of a component defines how the port
-variables are related. This relationship may be linear
-or non-linear. This typically contains symbolic parameters
-(@pxref{Symbolic parameters}) which may be replaced, for the purposes
-of numerical analysis by numeric parameters
-(@pxref{Numeric parameters}).
-
-@node Symbolic parameters, Numeric parameters, Constitutive relationship, Components
-@comment  node-name,  next,  previous,  up
-@subsection Symbolic parameters
-@cindex Symbolic parameters
-The constitutive relationship of a system component (@pxref{Components})
-typically contains  symbolic parameters. For example a resistor may have
-a symbolic resistance r. It is convenient to leave such parameters as
-symbols when viewing equations or when performing symbolic analysis such
-as differentiation.
-
-However, @strong{MTT} allows replacement of symbolic parameters by
-numeric parameters (@pxref{Numeric parameters}) when appropriate.
-
-@node Numeric parameters,  , Symbolic parameters, Components
-@comment  node-name,  next,  previous,  up
-@subsection Numeric parameters
-@cindex Numeric parameters
-Numerical parameters are needed to give specific values to symbolic
-parameters (@pxref{Symbolic parameters}) for the purposes of numeric
-analysis;
-for example: simulation, graph plotting or use within a numerical
-package such as Octave (@pxref{Octave}).
-
-
-@node Algebraic loops, Switched systems, Components, Introduction
-@section Algebraic loops
-@cindex Algebraic loops
-Following Chapter 3 of the book, algebraic loops appear as under-causal
-components in the bond graph. It is up to the modeler to indicate how these loops
-are to be resolved by adding appropriate SS elements.
-
-For more information, refer to:
-``Metamodelling: Bond Graphs and Dynamic Systems'' by Peter Gawthrop and
-Lorcan Smith published by Prentice Hall in 1996 (ISBN 0-13-489824-9).
-
-@node Switched systems,  , Algebraic loops, Introduction
-@comment  node-name,  next,  previous,  up
-@section Switched systems
-@cindex Switched systems
-@cindex Hybrid systems
-@cindex logic
-
-Some systems contain switch-like components. For example an electrical
-system may contain on-off switches and diodes and a hydraulic system may
-shut-off valves and non-return valves. 
-
-Such systems are sometimes called hybrid systems. The modelling an
-simulation of such systems is the subject of current research.
-@strong{MTT} implements a simple pragmatic approach to the modelling and
-simulation of such systems via two new Bond Graph components:
-@vtable @code
-@item ISW     
-        a switched @code{I} component
-@item CSW     
-        a switched @code{C} component
-@end vtable
-
-These switches are user controlled through the logic representation
-(@pxref{Simulation logic}).
-
-@node User interface, Creating Models, Introduction, Top
-@comment  node-name,  next,  previous,  up
-@chapter User interface
-@cindex User interface
-@pindex User interface
-There are two user interfaces to  @strong{MTT}: a command line interface
-(@pxref{Command line interface}) and a menu-driven interface
-(@pxref{Menu-driven interface}).
-
-@menu
-* Menu-driven interface::       
-* Command line interface::      
-* Options::                     
-* Utilities::                   
-@end menu
-
-@node Menu-driven interface, Command line interface, User interface, User interface
-@comment  node-name,  next,  previous,  up
-@section Menu-driven interface
-@cindex Menu-driven interface
-@pindex Menu-driven interface
-The Menu-driven interface for @strong{MTT} is invoked as:
-@example
-xmtt
-@end example
-This will bring up a menu which should be self explanatory :-).
-Various messages will be echoed in the window from whence @strong{xMTT}
-was invoked.
-
-@node Command line interface, Options, Menu-driven interface, User interface
-@comment  node-name,  next,  previous,  up
-@section Command line interface
-@cindex Command line interface
-@pindex Command line interface
-The command line interface for @strong{MTT} is of the form:
-@example
-mtt [options] <system_name> <representation> <language>
-@end example
-@vtable @code
-@item [options]
-        the (optional) option switches  (@pxref{Options})
-@item <system_name>    
-        the name of the system being transformed 
-@item <representation>    
-        the mnemonic for the system representation (@pxref{Representation summary})
-@item <language>    
-        the mnemonic for language for the representation (@pxref{Languages})
-@end vtable
-for example
-@example
-mtt rc rep view
-@end example
-creates a view of the report describing system rc and
-@example
-mtt rc sm m
-@end example
-creates an m file (suitlable for Octave or Matlab) containing state
-matrices describing the system rc.
-@node Options, Utilities, Command line interface, User interface
-@comment  node-name,  next,  previous,  up
-@section Options
-@cindex Options
-
-@strong{MTT} has a number of optional switches to control its
-operation. These are invoked immediately after `mtt' on the command
-line; for example:
-@example
-mtt -o -s -c syst cbg view
-@end example
-invokes the @code{-o}, @code{-s}, and @code{-c} options.
-
-The available options are:
-@vtable @code
-@item -q
-        quiet mode -- suppress MTT banner
-@item -A 
-        solve algebraic equations symbolically
-@item -ae 
-        <hybrd> solve algebraic equations numerically
- (this option requires -cc or -oct)
-@item -D 
-        debug -- leave log files etc
-@item -I 
-        prints more information
-@item -abg 
-       start at abg.m representation
-@item -c 
-        c-code generation
-@item -cc
-       C++ code generation
-@item -d 
-        <dir>  use directory <dir>
-@item -dc 
-       Maximise derivative (not integral) causality
-@item -dc 
-       Maximise derivative (not integral) causality
-@item -i 
-       <implicit|euler|rk4>   Use implicit, euler or Runge Kutta IVintegration
-@item -o 
-       ode is same as dae
-@item -oct 
-       use oct files in place of m files where appropriate
-@item -opt 
-       optimise code generation
-@item -p 
-        print environment variables
-@item -partition 
-       partition hierachical system
-@item -r 
-        reset time stamp on representation
-@item -s 
-        try to generate sensitivity BG (experimental)
-@item -ss 
-       use steady-state info to initialise simulations
-@item -stdin 
-       read input data from standard input for  simulations
-@item -sub 
-       <subsystem> operate on this subsystem
-@item -t 
-        tidy mode (default)
-@item -u 
-        untidy mode (leaves files in current dir)
-@item -v 
-        verbose mode (multiple uses increase the verbosity)
-@item -viewlevel 
-       <N> View N levels of hierachy
-@item --version 
-       print version and exit
-@item --versions 
-       print version of mtt and components and exit
-@end vtable
-
-@node Utilities,  , Options, User interface
-@comment  node-name,  next,  previous,  up
-@section Utilities
-@cindex Utilities
-@pindex Utilities
-@strong{MTT} provides some utilities to help you keep track of model
-building and to keep things clean and tidy. The commands, and there
-purpose are:
-@ftable @code
-@item mtt help
-        Lists the help/browser commands
-@item mtt copy <system>
-        Copies the system (ie directory and enclosed files) to the
-current working directory.
-@item mtt rename <old_name> <new_name>
-        Renames all of the defining representations (@pxref{Defining
-representations}) and textually changes each file appropriately.
-@item mtt <system> clean
-        Remove all files generated by @strong{MTT} associated with
-system `system'.
-@item mtt clean
-        Remove all files generated by @strong{MTT} associated with
-all systems within the current directory.
-@item mtt system representation vc
-        Apply version control to representation `representation' of
-system `system'.
-@item mtt system vc
-        Apply version control to all representations (under version control)
-system `system'.
-@end ftable
-These are described in more detail in the following sections.
-
-@menu
-* Help::                        
-* Copy::                        
-* Clean::                       
-* Version control::             
-@end menu
-
-@node Help, Copy, Utilities, Utilities
-@comment  node-name,  next,  previous,  up
-@subsection Help
-@cindex Help
-@cindex browser
-@strong{MTT} implements a browser to keep track of all the systems,
-subsystems and constitutive relationships that you, and others may
-write. It is invoked in the following ways:
-@example
-       mtt help representations
-       mtt help components
-       mtt help examples 
-       mtt help crs
-       mtt help representations <match_string>
-       mtt help components <match_string>
-       mtt help examples  <match_string>
-       mtt help crs <match_string>
-       mtt help <component_or_example_or_CR_name>
-@end example
-
-@menu
-* help representations::        
-* help components::             
-* help examples::               
-* help crs::                    
-* help <name>::                 
-@end menu
-
-@node help representations, help components, Help, Help
-@comment  node-name,  next,  previous,  up
-@subsubsection help representations
-@cindex help
-@cindex representations
-
-The command 
-@example
-mtt help representations
-@end example
-lists all of the representations  (@pxref{Representations}) available in
-@strong{MTT}. These may change as the version number of @strong{MTT}
-increases.
-
-The command 
-@example
-mtt help representations <match_string>
-@end example
-lists those representation which contain the string @code{match_string}.
-This string can be any regular expression  (see standard Linux
-documentation under @code{awk}).
-For example
-@example
-mtt help representations descriptor
-@end example
-gives all representations containing the word @code{descriptor}.
-
-@node help components, help examples, help representations, Help
-@comment  node-name,  next,  previous,  up
-@subsubsection help components
-@cindex help
-@cindex components
-
-The command 
-@example
-mtt help components
-@end example
-lists all of the components  (@pxref{Components}) available in
-@strong{MTT}. These may change as the version number of @strong{MTT}
-increases.
-
-The command 
-@example
-mtt help components <match_string>
-@end example
-lists those component which contain the string @code{match_string}.
-This string can be any regular expression  (see standard Linux
-documentation under @code{awk}).
-For example
-@example
-mtt help components source
-@end example
-gives all components containing the word @code{component}.
-
-@node help examples, help crs, help components, Help
-@comment  node-name,  next,  previous,  up
-@subsubsection help examples
-@cindex help
-@cindex examples
-
-This command provides a good way to get started in @strong{MTT}. having
-found an interesting example, copy it to your working directory using
-@example
-mtt copy <example_name>
-@end example
-(@pxref{Copy})
-
-@example
-mtt help examples
-@end example
-lists all of the examples  available in
-@strong{MTT}. 
-This list will change as more examples are added.
-
-The command 
-@example
-mtt help examples <match_string>
-@end example
-lists those component which contain the string @code{match_string}.
-This string can be any regular expression  (see standard Linux
-documentation under @code{awk}).
-For example
-@example
-mtt help examples pharmokinetic
-@end example
-gives all examples containing the word @code{pharmokinetic}.
-
-@node help crs, help <name>, help examples, Help
-@comment  node-name,  next,  previous,  up
-@subsubsection help crs
-@cindex help
-@cindex crs
-
-The command 
-@example
-mtt help crs
-@end example
-lists all of the constitutive relationships   (@pxref{Constitutive
-relationship}) available in
-@strong{MTT}. These may change as the version number of @strong{MTT}
-increases.
-
-The command 
-@example
-mtt help crs <match_string>
-@end example
-lists those constitutive relationships which contain the string @code{match_string}.
-This string can be any regular expression  (see standard Linux
-documentation under @code{awk}).
-For example
-@example
-mtt help crs sin
-@end example
-gives all crs containing the word @code{sin}.
-
-@node help <name>,  , help crs, Help
-@comment  node-name,  next,  previous,  up
-@subsubsection help <name>
-@cindex help
-@cindex <name>
-
-The command 
-@example
-mtt help <name>
-@end example
-gives a detailed description of the entity called @code{name}.
-
-@node Copy, Clean, Help, Utilities
-@comment  node-name,  next,  previous,  up
-@subsection Copy
-@cindex Copy
-
-@strong{MTT} provides a way of copying examples to your working directory:
-@example
-mtt copy <example_name>
-@end example
-
-Use the  command
-@example
-mtt help examples
-@end example
-(@pxref{help examples}) to find something of interest.
-
-Note that components and constitutive relationships are automatically
-copied when required.
-
-@node Clean, Version control, Copy, Utilities
-@comment  node-name,  next,  previous,  up
-@subsection Clean
-@cindex Clean
-@strong{MTT} generates a lot of representations in a number of
-languages.
-Some of these you will edit yourself; others can always be recreated by
-@strong{MTT}. It makes sense, therefore to have a utility that removes
-all of these other files when you have finished actively working with a
-particular system. These are two versions:
-@enumerate
-@item
-@code{mtt system clean}
-@item
-@code{mtt clean}
-@end enumerate
-The first removes all files that can be regenerated with @strong{MTT}
-associated with system `system'; the second removes all such files
-associated with all systems in the current working directory.
-
-The files which remain after such a clean are the Defining
-representations (@pxref{Defining representations}).
-
-@node Version control,  , Clean, Utilities
-@comment  node-name,  next,  previous,  up
-@subsection Version control
-@cindex Version control
-
-When you are working on a modeling project, it is easy to forget what
-changes you made to a system and why you made them. Sometimes, you may
-regret some changes and wish to revert to an earlier version: even if
-you use .old files this may be difficult to achieve safely.
-
-These are very similar problems to those faced by software developers
-and can be solved in the same way: using version control.@strong{MTT}
-provides version control using the standard GNU Revision Control System
-(RCS). This is hidden from the user, but is fully complementary to
-direct use of RCS (e.g. via emacs vc commands) to the more experienced
-user who wishes to do so.
-
-The only files that you should ever change (i.e. the ones never
-overwritten by @strong{MTT}) are the Defining representations
-(@pxref{Defining representations}).
-
-All of the files, with the exception of @code{system_abg.fig}, 
-are initially created by @strong{MTT} and contain the RCS header for
-version control.
-
-
-The @strong{MTT} version control will automatically expand this part of
-the text to include all change comments that you give it -- so will
-direct use of RCS (e.g. via emacs vc commands)
-
-The @strong{MTT} version commands are as follows:
-@ftable @code
-@item mtt system representation vc
-        Apply version control to representation `representation' of
-system `system'.
-@item mtt system vc
-        Apply version control to all representations (under version control)
-system `system'.
-@end ftable
-
-The first is appropriate after you have made a revision to a single
-file.  It will prompt you for a change comment; this will be
-automatically included in the file header. In addition, enough
-information will be saved to enable any  version to be retrieved via
-RCS.
-
-The second is appropriate to record the state of the entire model. This
-assumes that all relevant files have been recorded by the first version
-of the command.  Once again, old versions of the entire model can be
-retrieved using the relevant RCS commands.
-
-A subdirectory `RCS' is created to hold this information. You need not
-bother about the contents, except that you must not delete any files
-within `RCS'.
-
-@node Creating Models, Simulation, User interface, Top
-@comment  node-name,  next,  previous,  up
-@chapter Creating Models
-@cindex  Creating Models
-
-@strong{MTT} helps you to analyse and transform system models --
-ultimately the process of capturing the real world in a model is up to
-you.  This chapter discusses the @strong{MTT} aspects of creating a
-model. For convenience, this is divided into creating simple models and
-creating complex models.
-
-@menu
-* Quick start::                 
-* Creating simple models::      
-* Creating complex models::     
-@end menu
-
-@node Quick start, Creating simple models, Creating Models, Creating Models
-@section Quick start
-@cindex Quick start
-@pindex Quick start
-
-It is probably worth a quick skim though @strong{MTT} to get a flavour of
-what it can do before plunging into the detail of the rest of this
-document. Here is a series of commands to do this.
-
-Copy an initial set of files describing the bond graph.
-@example
-mtt copy rc
-@end example
-@noindent 
-Move to it.
-@example
-cd rc
-@end example
-@noindent 
-@noindent 
-View the acausal bond graph (the system is called ``rc'').
-@example
-mtt rc abg view
-@end example
-@noindent 
-View the causal bond graph of the system.
-@example
-mtt rc cbg view
-@end example
-@noindent 
-View the corresponding ordinary differential equations (ode).
-@example
-mtt rc ode view
-@end example
-@noindent 
-View the system (output) step response
-@example
-mtt rc sro view
-@end example
-
-@noindent 
-An alternative (but more general) way of achieving the same result is
-@example
-mtt -c rc odeso view
-@end example
-
-@noindent 
-View the system transfer function
-@example
-mtt rc tf view
-@end example
-@noindent 
-View the log modulus frequency response of the system.
-@example
-mtt rc lmfr view
-@end example
-
-@noindent 
-View the log modulus frequency response of the system for 100
-logarithmically spaced frequencies in the range 0.1 to 10
-radians per second.
-@example
-mtt rc lmfr view 'W=logspace(-1,1,100);'
-@end example
-
-@strong{MTT} has a report generation ((@pxref{Report}) facility which
-can generate a hypertext description of the system.
-@example
-mtt rc rep hview
-@end example
-
-The report contents are specified by the rep representation
-(@pxref{Report}), in this case the corresponding file is:
-@example
-% %% Outline report file for system rc (rc_rep.txt)
-
-mtt rc abg tex
-mtt rc struc tex
-mtt rc cbg ps
-mtt rc ode tex
-mtt rc ode dvi
-mtt rc sm tex
-mtt rc tf tex
-mtt rc tf dvi
-mtt rc sro ps
-mtt rc lmfr ps
-mtt rc odes h
-mtt rc numpar txt
-mtt rc input txt
-mtt -c rc odeso ps
-mtt rc rep txt
-@end example
-A non-hypertext version can be viewed using:
-@example
-mtt rc rep view
-@end example
-
-Now have a go at modifying the bond graph.
-@example
-mtt rc abg fig
-@end example
-This brings up the bond graph in Xfig (@pxref{Xfig}).  Try creating a
-system with two rs and 2 cs.
-
-More examples can be found using
-@example
-mtt help examples
-@end example
-Details of an example can be found using
-@example
-mtt help <example_name>
-@end example
-and copied using
-@example
-mtt copy <example_name>
-@end example
-
-Lots of examples are available.
-@example
-mtt help examples
-@end example
-lists them and
-@example
-mtt copy <name>
-@end example
-gets you an example.
-
-@ifhtml
-A number of examples are to be found
-<A
-HREF="http://www.mech.gla.ac.uk/~peterg/software/MTT/examples/Examples/Examples.html"> here</A>.
-@end ifhtml
-
-@node Creating simple models, Creating complex models, Quick start, Creating Models
-@comment  node-name,  next,  previous,  up
-@section Creating simple models
-@cindex Creating simple models
-
-For then purposes of this section, simple models are those which are
-built up from bond graphs involving predefined components. In contrast,
-more complex systems (@pxref{Creating complex models}) need to be built
-up hierarchically.
-
-The recommended sequence of steps to create a simple model is:
-@enumerate
-@item Decide on a name for the system; let us call it `syst' for the
-  purposes of this discussion. 
-@item Invoke the Bond Graph editor to draw the acausal Bond Graph.
-@example
-  mtt syst abg fig
-@end example
-@item Draw the Bond Graph  (@pxref{Language fig (abg.fig)}), including
-  the bonds (@pxref{Bonds}), the components (@pxref{Components}) and any
-  artwork (@pxref{artwork}) to make the Bond Graph more readable. The
-  graphical editor xfig is (@pxref{Xfig}) is self-explanatory.
-  The icon library is helpful here (see @pxref{icon library}).
-@item Add causal strokes (@pxref{strokes}) where needed to define
-  causality. As a general rule, use the minimum number of strokes needed
-  to define the problem; this will often be only on the @code{SS} components.
-  (@pxref{SS components}).
-  
-  Save the bond graph.
-  
-@item View the corresponding causal bond graph.
-@example
-  mtt syst cbg view
-@end example
-@enumerate
-@item 
-    At this stage, @strong{MTT} will warn you that the labeled components do
-    not appear in the label file - this can safely be ignored.
-@item
-  @strong{MTT} will indicate the percentage of components which are
-    causally complete -- ideally this will be 100\%. Components which are
-    not causally complete will be listed.
-@item
-    A view of the causal bond graph will be created. The added causal
-    strokes are indicated in blue, undercausal components in green and
-    overcausal components in red.
-@item
-    If the bond graph is causally complete, proceed to the next step,
-    otherwise think hard and return to the first step.
-@end enumerate
-
-@item
-At this stage, no constitutive relationships have been
-defined. Nevertheless, @strong{MTT} will proceed in a semi-qualitative
-fashion by assuming that all constitutive relationships are unity (and
-therefore linear). It may be useful at this stage to view various
-derived representations to check the overall model properties before
-proceeding further. For example:
-@enumerate
-@item
-View the system Differential-algebraic equations
-@example
-mtt syst dae view
-@end example
-@item
-View the system state matrices
-@example
-mtt syst sm view
-@end example
-@item
-View the system transfer function
-@example
-mtt syst tf view
-@end example
-@item
-View the system step response
-@example
-mtt syst sro view
-@end example
-@end enumerate
-
-@item
-As well as creating the causal bond graph, @strong{MTT} has also
-generated templates for other text files 
-(@pxref{Defining representations})
-used to further specify the
-system.
-These can now be edited using your favorite text editor (@pxref{Text
-editors}).
-
-@item @strong{MTT} will now generate the representations
-(@pxref{Representation summary})that you desire.
-For example the system can be simulated by
-@example
-mtt syst odeso view
-@end example
-@strong{MTT} will complain if a component is named in the bond graph but
-not in the label file and vice versa. This mainly to catch typing errors.
-
-@end enumerate
-
-@node Creating complex models,  , Creating simple models, Creating Models
-@comment  node-name,  next,  previous,  up
-@section Creating complex models
-@cindex Creating complex models
-
-Complex models -- in distinction to simple models (@pxref{Creating
-simple models}) -- have a hierarchical structure. In particular, bond
-graph components can be created by specifying their bond
-graph. Typically, such components will have more than one port
-(@pxref{Ports}); within each component, ports are represented by
-named SS components (@pxref{Named SS components}); outwith
-each component, ports are unambiguously identified by 
-labels (@pxref{Port labels}) and vector labels (@pxref{Vector port labels}).
-
-Complex models are thus created by conceptually decomposing the system
-into simple subsystems, and then creating the corresponding bond graphs.
-The procedure for simple systems (@pxref{Creating simple models}) is
-then followed using the top level system (@pxref{Top level}); @strong{MTT} then recursively
-operates on the lower level systems.
-
-The report representation (@pxref{Report}) provides a convenient way of
-viewing a complex system.
-
-An example of such a system can be created as follows:
-@example
-mtt copy twolink
-mtt twolink rep hview
-@end example
-
-@ifhtml
-The result is <A
-HREF="./examples/twolink/twolink_rep/twolink_rep.html"> here</A>.
-@end ifhtml
-
-@menu
-* Top level::                   
-@end menu
-
-@node Top level,  , Creating complex models, Creating complex models
-@comment  node-name,  next,  previous,  up
-@subsection Top level
-@cindex Top level
-The top level of a complex model contains subsystems but is not, itself,
-contained by other systems. 
-It has the following special features:
-@itemize @bullet
-@item
-its name is used in the mtt command as the system name.
-@item
-all named SS componenents (@pxref{Named SS components}) are treated as
-ordinary SS components (@pxref{SS components}).
-@end itemize
-
-
-
-@c      node   next  prev  up
-@node Simulation, Sensitivity models, Creating Models, Top
-@chapter Simulation
-@cindex Simulation
-@pindex Simulation
-One purpose of modelling is to simulate the modeled dynamic
-system. Although this is just another transformation (@pxref{What is a
-Transformation?}) and therefore is covered in the appropriate chapter
-(@pxref{Representations}), it is important enough to be given its own
-chapter.
-
-Simulation is typically performed using an appropriate simulation
-language (which is often inappropriately conflated with modelling
-tools). @strong{MTT} provides a number of alternative routes to
-simulation based on the following representations (@pxref{Representations}):
-@ftable @code
-@item cse
-        constrained-state differential equation form
-@item ode
-        ordinary differential (or state-space) equations
-@c  @item dae
-@c          differential-algebraic (or generalised state-space) equations --
-@c  these may be linear or nonlinear.
-@end ftable
-in each case these equations may be
-linear or nonlinear.
-
-Special cases of numerical simulation, appropriate to @emph{linear}
-systems, are:
-@ftable @code
-@item   ir
-        impulse response - state 
-@item   iro
-        impulse response - output 
-@item   sr
-        impulse response - state 
-@item   sro
-        impulse response - output 
-@end ftable
-
-There are a number of languages (@pxref{Languages}) which can be used to describe these
-representations for the purposes of numerical simulation:
-@ftable @code
-@item m
-        @code{octave} a high-level interactive language for numerical
-        computation.
-@item c
-        @code{gcc} a c compiler.
-@item cc
-        @code{g++} a C++ front-end to gcc.
-@end ftable
-
-There are a number solution algorithms available:
-@itemize @bullet
-@item
-explicit solution via the matrix exponential
-@item
-backward Euler integration (explicit)
-@item
-forward Euler integration (implicit)
-@item
-Runge Kutta IV integration (explicit, fixed step)
-@item
-Hybrd algebraic solver (MINPACK, Octave fsolve)
-@c  @item
-@c  LSODE (Hindmarsh's ODE solver as implemented in Octave)
-@c  @item
-@c  DASSL (Petzold's DAE solver as implemented in Octave) (Unavailable just now)
-@end itemize
-
- However, all combinations of representation, language and solution
-method are not supported by @strong{MTT} at the moment. Given a system
-`system', some recommended commands are:
-@ftable @code
-@item mtt system iro view
-        creates the impulse response of a @emph{linear} system via the
-system_sm.m representation using explicit solution via the matrix exponential.
-@item mtt system sro view
-        creates the step response of a @emph{linear} system via the system_sm.m
-representation using explicit solution via the matrix exponential.
-@c  @item mtt system odeso view
-@c          creates the step response of a @emph{nonlinear} system via the
-@c  system_ode.m representation using either METHOD=Euler or
-@c  METHOD=LSODE in the parameter file (@pxref{Simulation parameters}).
-@item mtt -c system odeso view
-        creates the response of a @emph{nonlinear} system via the
-system_ode.c representation using implicit integration.
-@item mtt -c -i euler system odeso view
-        creates the response of a @emph{nonlinear} system via the
-system_ode.c representation using euler integration.
-@end ftable
-
-Simulation parameters are described in the system_simpar.txt file
-(@pxref{Simulation parameters}).
-
-The steady-state solution of a system can also be
-``simulated''(@pxref{Steady-state solutions}).
-@menu
-* Steady-state solutions::      
-* Simulation parameters::       
-* Simulation input::            
-* Simulation logic::            
-* Simulation initial state::    
-* Simulation code::             
-* Simulation output::           
-@end menu
-
-@node Steady-state solutions, Simulation parameters, Simulation, Simulation
-@comment  node-name,  next,  previous,  up
-@section Steady-state solutions 
-@cindex Steady-state solutions
-
-@menu
-* Steady-state solutions - numerical(odess)::  
-* Steady-state solutions - symbolic (ss)::  
-@end menu
-
-@node Steady-state solutions - numerical(odess), Steady-state solutions - symbolic (ss), Steady-state solutions, Steady-state solutions
-@comment  node-name,  next,  previous,  up
-@subsection Steady-state solutions (odess)
-@cindex Steady-state solutions - numerical
-
-@strong{MTT} can compute the steady-state solutions of an ordinary
-differential equation; this used the octave function `fsolve'. The
-solution is computed as a function of time using the input specified in
-the input file. The simulation parameter file (@pxref{Simulation
-parameters}) is used to provide the time scales.
-
-For example
-@example
-mtt copy rc
-cd rc
-mtt rc odess view
-@end example
-
-@node Steady-state solutions - symbolic (ss),  , Steady-state solutions - numerical(odess), Steady-state solutions
-@comment  node-name,  next,  previous,  up
-@subsection Steady-state solutions (ss) 
-@cindex Steady-state solutions - symbolic
-A rudimentary form of steady-state solution exists in mtt.
-The steady states and inouts are supplied by the user in the file
-system_simpar.r and the corresponding output and sate derivative
-computed by @strong{MTT} using
-@example
-mtt system ss view
-@end example
-
-For example
-@example
-mtt copy rc
-cd rc
-mtt rc sspar view
-mtt rc ss view
-@end example
-
-
-@node Simulation parameters, Simulation input, Steady-state solutions, Simulation
-@comment  node-name,  next,  previous,  up
-@section Simulation parameters
-@cindex Simulation parameters
-
-Simulation parameters are set in the system_simpar.txt file. At the
-moment this sets the following variables:
-@itemize @bullet
-@item LAST
-        the last simulation time
-@item DT
-        the incremental time (for plotting)
-@item STEPFACTOR
-        the number of integration steps per DT -- thus the integration
-        interval is DT/STEPFACTOR
-@c ; for sparse implicit integration (@pxref{Sparse
-@c implicit integration}) the number of conjugate-gradient minimisation
-@c steps.
-@c  @item METHOD
-@c          The integration methods available appear in the following table
-@item WMIN
-        Minimum frequency = 10^WMIN
-@item WMAX
-        Maximum frequency = 10^WMAX
-@item WSTEPS
-        Number of Frequency steps.
-@item INPUT
-        The input index for frequency response
-@end itemize
-
-There are a number of solution algorithms
-@itemize @bullet
-@item Euler
-        basic Euler integration (@pxref{Euler integration}). This method
-is simple, but not recommended for stiff systems.
-@item Implicit
-        semi-implicit integration  (@pxref{Implicit integration}) - uses the smx representation to give
-        stability.
-@item Runge Kutta IV
-        fixed step Runge Kutta fourth order integration (@pxref{Runge Kutta IV integration}).
-@item Hybrd
-        numerical algebraic equation solver
-        
-
-@c @item ImplicitS
-@c         Sparse semi-implicit integration  (@pxref{Sparse implicit integration})
-@c -- takes advantage of the sparsity of the A matrix.
-@c @item LSODE
-@c         the variable step-size method that comes with Octave (@pxref{Octave}).
-@end itemize
-
-@menu
-* Euler integration::           
-* Implicit integration::        
-* Runge Kutta IV integration::  
-* Hybrd algebraic solver::      
-@end menu
-
-@node Euler integration, Implicit integration, Simulation parameters, Simulation parameters
-@comment  node-name,  next,  previous,  up
-@subsection Euler integration
-@cindex Euler integration
-Euler integration approximates the solution of the Ordinary Differential Equation 
-@example
-dx/dt = f(x,u)
-@end example
-by
-@example
-x := x + f(x,u)*DDT
-@end example
-where
-@example
-DDT = DT/STEPFACTOR
-@end example
-If the system is linear, stability is ensured if the integer STEPFACTOR
-is chosen to be greater than the real number
-@example
-(maximum eigenvalue of -A)*DT/2
-@end example
-where A is the nxn matrix appearing in
-@example
-f(x,u) = Ax + Bu
-@end example
-If the system is non linear, the linearised system matrix A should act
-as a guide to the choice of STEPFACTOR.
-
-@node Implicit integration, Runge Kutta IV integration, Euler integration, Simulation parameters
-@comment  node-name,  next,  previous,  up
-@subsection Implicit integration
-@cindex Implicit integration
-Implicit integration approximates the solution of the Ordinary Differential Equation 
-@example
-dx/dt = f(x,u)
-@end example
-by
-@example
-(I-A*DT)x := (I-A*DT)x + f(x,u)DT
-@end example
-where A is the linearised system matrix. This implies the solution of N
-(=number of states) linear equations at each sample interval. The OCTAVE
-version used the `\' operator to solve the set of linear equations, the
-C version uses LU decomposition.
-
-If the system is linear, stability is ensured unconditionaly. If the
-system is non-linear, then the method still works well.
-
-This method is nice in that choice of DT trades of accuracy against
-computation time without compromising stability. In addition, the
-correct stready-state values are achieved.
-
-This approach can also be used for constrained state equations of the
-form:
-@example
-E(x) dx/dt = f(x,u)
-@end example
-where E(x) is a state-dependent matrix. The approximate solution is then
-given by:
-@example
-(E(x)-A*DT)x := (E(x)-A*DT)x + f(x,u)DT
-@end example
-which reduces to the ordinary differential equation case when E(x)=I.
-
-The _smx representation includes the E matrix.
-
-@node Runge Kutta IV integration, Hybrd algebraic solver, Implicit integration, Simulation parameters
-@comment  node-name,  next,  previous,  up
-@subsection Runge Kutta IV integration
-Runge Kutta IV approximates the solution of the Ordinary Differential Equation
-
-@example
-dx/dt = f(x,t)
-@end example
-
-by
-
-@example
-x := x + (DT/6)*(k1 + 2*k2 + 2*k3 + k4)
-@end example
-
-where
-
-@example
-k1 := f(x,t)
-k2 := f(x+(1/2)*k1,t+(1/2)*DT)
-k3 := f(x+(1/2)*k2,t+(1/2)*DT)
-k4 := f(x+k3,t+DT)
-@end example
-
-The @strong{MTT} implementation of Runge-Kutta integration
-is a fourth order, fixed-step, explicit integration method.
-
-For some systems of equations, the increased accuracy of using a fourth order
-method can allow larger step-lengths to be used than would allowed by the
- lower order Euler integration method.
-
-It should be noted that during the interemediate calculations (k1...k4),
- the input vector @code{u} is not advanced w.r.t. time; the system inputs are
-assumed to be constant over the period of the integration step-length.
-
-@node Hybrd algebraic solver,  , Runge Kutta IV integration, Simulation parameters
-@comment  node-name,  next,  previous,  up
-@subsection Hybrd algebraic solver
-
-The hybrd algebraic solver of @uref{http://www.netlib.org/minpack/hybrd.f,MINPACK},
-which is used by Octave in the @code{fsolve} routine, may be used in conjunction
-with one of the other integration methods to solve semi-explicit, index 1, differential
-algebraic equations; these may be generated in @strong{MTT} models by use of 
-@code{unknown} SS Components @pxref{SS component labels}.
-
-This method requires that compiled simulation code is used; either -cc or -oct.
-To perform a simulation based on a model @code{sys},
-
-@example
-mtt -cc -ae hybrd -i euler sys odeso view
-@c XXX: should be daeso view?
-@end example
-
-@strong{MTT} will attempt to minimise the residual error at each integration time-step
-using the hybrd routine.
-
-This method of simulation is particularly well suited to stiff systems where very fast
-dynamics are of little interest. Care must be taken to ensure that an acceptable level
-of convergence is achieved by the solver for the system under investigation.
-@c XXX: tolerance option
-
-@c @node Sparse implicit integration,  , Implicit integration, Simulation parameters
-@c @comment  node-name,  next,  previous,  up
-@c @subsection Sparse implicit integration
-@c @cindex Sparse implicit integration
-@c This is an experimental approach for large (N>50) systems.
-
-@c Implicit integration (@pxref{Implicit integration}) requires the
-@c solution of N linear equations at each step. This is an O(N^3) operation
-@c which can be time consuming for large (N>50) systems. However, the A
-@c matrix (and hence the (I-A*DT) matrix) is often sparse - most elements
-@c are zero.
-
-@c This method uses a conjugate-gradient optimisation method to solve the
-@c linear equations
-@c @example
-@c (I-A*DT)x := (I-A*DT)x + f(x,u)DT
-@c @end example
-@c by recasting them as the minimisation of the quadratic function
-@c @example
-@c [(I-A*DT)x_new - (I-A*DT)x_old + f(x,u)DT]^2
-@c @end example
-@c with respect to x_new. This is solved by the conjugate gradient method.
-@c MTT generates two representations _smxx.m and _smxtx to compute
-@c (I-A*DT)x and (I-A*DT)'x respectively making full use of the sparsity of
-@c the (I-A*DT) matrices to speed up the minimisation procedure.
-
-@c A fixed number of iterations (STEPFACTOR) are used in each optimisation
-@c to give a fixed simulation time. This must be chosen by the user, but
-@c between 5N and 10N seems ok. Note that the initial value of the
-@c optimisation is x_old.
-
-@node Simulation input, Simulation logic, Simulation parameters, Simulation
-@comment  node-name,  next,  previous,  up
-@section Simulation input
-@cindex Simulation input
-This is defined in the system_input.txt file. A default file is created
-automatically by @strong{MTT}. This is done explicitly by
-@example
-mtt system input txt
-@end example
-If the file already exists, the same command checks that all inputs are
-defined and that all defined inputs exist in the system and promts the
-user to correct discrepancies.
-
-Inputs are defined by the full system name appearing in the structure
-file (@pxref{Structure (struc)}). They can depend on states (again defined by
-name), time (defined by t) and parameters
-
-For example:
-@example
-system_pump_l_1_u	= 4e5*atm;
-system_pump_r_1_u	= 4e5*(t<10)*atm;
-system_ss_i	        = 0*kg;
-system_ss_o	        = 3e-3*kg;
-system_v_1_u	        = (t>10);
-system_v_ll_1_u         = 1;
-system_v_lr_1_u         = (t<10);
-system_v_ul_1_u         = 0;
-system_v_ur_1_u         = (t>10);
-@end example
-
-@node Simulation logic, Simulation initial state, Simulation input, Simulation
-@comment  node-name,  next,  previous,  up
-@section Simulation logic
-@cindex Simulation logic
-This is defined in the system_logic.txt file. A default file is created
-automatically by @strong{MTT}. This is done explicitly by
-@example
-mtt system logic txt
-@end example
-If the file already exists, the same command checks that the logic
-corresponding to all switch states (@pxref{Switched systems}) are
-defined and that all defined logic exists in the system and promts the
-user to correct discrepancies.
-
-Logical inputs are defined by the full system name corresponding to
-MTT_switch components appearing in the structure file (@pxref{Structure
-(struc)}) @emph{with `_logic' appended}. They can depend on states (again defined by name), time
-(defined by t) and parameters
-
-For example:
-@example
-bounce_ground_1_mtt_switch_logic	= bounce_intf_1_mtt3<0;
-@end example
-
-@node Simulation initial state, Simulation code, Simulation logic, Simulation
-@comment  node-name,  next,  previous,  up
-@section Simulation initial state
-@cindex Simulation initial state
-This is defined in the system_state.txt file. A default file is created
-automatically by @strong{MTT}. This is done explicitly by
-@example
-mtt system state txt
-@end example
-If the file already exists, the same command checks that all states are
-defined and that all defined states exist in the system and prompts the
-user to correct discrepancies.
-
-States are defined by the full system name appearing in the structure
-file (@pxref{Structure (struc)}). They can depend on parameters.
-For example
-@example
-system_c_l	= (1e4/k_l)/kg;
-system_c_ll	= (1e4/k_s)/kg;
-system_c_lr	= (1e4/k_s)/kg;
-system_c_u	= (1e4/k_l)/kg;
-@end example
-
-
-@c  The initial state of a simulation of is set in the @code{state}
-@c  representation with the language @code{txt}.
-
-@c  As usual, @strong{MTT} defaults this for you. There are two
-@c  possibilities
-@c  @itemize @bullet
-@c  @item
-@c  The -ss switch is not present: the states default to zero
-@c  @item
-@c  The -ss switch is present: the states default to those set in the
-@c  sspar.r file.
-@c  @end itemize
-
-@node Simulation code, Simulation output, Simulation initial state, Simulation
-@comment  node-name,  next,  previous,  up
-@section Simulation code
-simulation code can be generated by @strong{MTT} in the form
-of the @code{ode2odes} transformation. This can be produced in a number
-of languages, including .m, .oct, C and C++ @pxref{Languages}.
-
-To generate simulation code in C:
-@example
-mtt -c [options] sys ode2odes c
-@end example
-
-Similarly, to generate C++ code:
-@example
-mtt -cc [options] sys ode2odes cc
-@end example
-
-To generate an executable based on the C++ representation:
-@example
-mtt -cc [options] sys ode2odes exe
-@end example
-
-@node Simulation output,  , Simulation code, Simulation
-@comment  node-name,  next,  previous,  up
-@section Simulation output
-@cindex Simulation output
-The view (@pxref{Views}) representation provides a graphical
-representation of the results of a simulation; the postscript language
-provides the same thing in a form that can be included in a document.
-
-These are two simulation output representations
-@ftable @code
-@item odes 
-        ordinary differential equation solution (states)
-@item odeso
-         ordinary differential equation solution (output)
-@end ftable    
-
-Particular output variables can be selected by adding a fourth argument
-in one of 2 forms
-@ftable @code
-@item 'name1;name2;..;namen' 
-        plot the variables with names na1 .. namen against time
-@item 'name1:name2'
-                plot the variable with  name2 against that with name 1
-@end ftable    
-
-An example of plotting a single variable against time is:
-@example
-mtt -o -c -ss OttoCycle odeso ps 'OttoCycle_cycle_V'
-@end example
-An example of plotting one variable against another is:
-@example
-mtt -o -c -ss OttoCycle odeso ps 'OttoCycle_cycle_V:OttoCycle_cycle_P'
-@end example
-
-@menu
-* Viewing results with gnuplot::  
-* Exporting results to SciGraphica::  
-@end menu
-
-@node Viewing results with gnuplot, Exporting results to SciGraphica, Simulation output, Simulation output
-@comment  node-name,  next,  previous,  up@subsection
-@subsection Viewing results with gnuplot
-@cindex gnuplot
-
-Simulation results may be viewed in
-@uref{http://www.gnuplot.org,gnuplot} with the command
-
-@example
-mtt [options] rc gnuplot view
-@end example
-
-The plot format is controlled by the file @emph{sys_gnuplot.txt}. A default version
-of this file, which will cause gnuplot to plot the time-history of each state
-and each output individually, may be created with the command
-
-@example
-mtt rc gnuplot txt
-@end example
-
-resulting in
-
-@example
-wait=-1
-set data style lines
-set xlabel "time"
-set grid
-set term X11
-
-plot "rc_odes.dat2" using 1:4 axes x1y1 title "rc_c_c;
-pause(wait);
-plot "rc_odes.dat2" using 1:2 axes x1y1 title "rc_e2_e2
-; pause(wait);
-@end example
-
-The file is used as an input to the gnuplot program and may therefore be
-edited to contain any valid gnuplot commands.
-
-@node Exporting results to SciGraphica,  , Viewing results with gnuplot, Simulation output
-@comment  node-name,  next,  previous,  up
-@subsection Exporting results to SciGraphica
-@cindex SciGraphica
-
-Simulation results can be converted into an XML-format
-@uref{http://scigraphica.sourceforge.net,SciGraphica} (version 0.61)
-@emph{.sg} file with the command
-
-@example
-mtt [options] sys odes sg
-@end example
-
-The SciGraphica file will contain two worksheets, X_sys and Y_sys, containing
-the state and output time-histories from the simulation.
-
-@c      node   next  prev  up
-@node   Sensitivity models, Representations, Simulation, Top
-@chapter Sensitivity models
-@cindex Sensitivity models
-@pindex Sensitivity models
-
-The sensitivity model of a system is a set of equations giving the
-sensitivity of the system outputs with respect to system parameters.
-@strong{MTT} has built in methods for assisting with the development of
-such models.
-
-This feature is experimental at the moment, but the following example
-gives an idea of what can be achieved.
-@example
-mtt copy rc
-cd rc
-mtt -s src ode view
-mtt -s src odeso view
-@end example
-The sensitivity system src is automatically created from the system rc
-using the predefined sR and sC components together with vector junctions
-(@pxref{Vector components}).  The four outputs are the two system
-outputs plus the two sensitivity functions.
-
-An alternative route is to create the sensitivity functions by symbolic
-differentiation.
-The following sensitivity representations are available:
-@ftable @code
-@item   scse
-        sensitivity constrained-state equations
-@item   sm
-        sensitivity state matrices
-@item   scsm
-        sensitivity constrained-state matrices
-@end ftable
-
-
-
-@c      node   next  prev  up
-@node   Representations, Extending MTT, Sensitivity models, Top
-@chapter Representations
-@cindex Representations
-@pindex Representations
-@cindex Defining representations
-@cindex Representations, defining
-
-As discussed in @ref{What is a Representation?}, a system has many
-representations. The purpose of @strong{MTT} is to provide an easy way to
-generate such representation by applying the appropriate sequence of 
-transformations. The representations supported by @strong{MTT} are
-summarised in @ref{Representation summary}.
-
-There is a two-fold division of representations into those with which the user
-defines the system and its various attributes, and those which are
-derived from these. The @emph{defining representations} are listed in
-@ref{Defining representations}. 
-
-Each representation is implemented in one or more languages depending on
-its use. These languages are discussed in @ref{Languages} and are
-associated with appropriate tools for modifying or viewing the
-representations. 
-
-@menu
-* Representation summary::      
-* Defining representations::    
-* Verbal description (desc)::   
-* Acausal bond graph (abg)::    
-* Stripped acausal bond graph (sabg)::  
-* Labels (lbl)::                
-* Description (desc)::          
-* Structure (struc)::           
-* Constitutive Relationship (cr)::  
-* Parameters::                  
-* Causal bond graph (cbg)::     
-* Elementary system equations::  
-* Differential-Algebraic Equations::  
-* Constrained-state Equations::  
-* Ordinary Differential Equations::  
-* Descriptor matrices::         
-* Report::                      
-@end menu
-
-@node Representation summary, Defining representations, Representations, Representations
-@comment  node-name,  next,  previous,  up
-@section Representation summary
-@cindex Representation summary
-
-Some of the the representations 
-available in @strong{MTT} are (in alphabetical order):
-@ftable @code
-@item   abg
-        acausal bond graph 
-@item   cbg
-        causal bond graph 
-@item   cr
-        constitutive relationship for each subsystem 
-@item   cse
-        constrained-state equations 
-@item   csm
-        constrained-state matrices 
-@item   dae
-        differential-algebraic equations 
-@item   daes
-        dae solution - state 
-@item   daeso
-        dae solution - output 
-@item   def
-        definitions - system orders etc. 
-@item   desc
-        Verbal description of system 
-@item   dm
-        descriptor matrices 
-@item   ese
-        elementary system equations 
-@item   fr
-        frequency response 
-@item   input        
-        numerical input declaration 
-@item   ir
-        impulse response - state 
-@item   iro
-        impulse response - output 
-@item   lbl
-        label file 
-@item   lmfr
-        loglog modulus frequency response 
-@item   lpfr
-        semilog phase frequency response 
-@item   nifr
-        Nichols style frequency response 
-@item   numpar
-        numerical parameter declaration 
-@item   nyfr
-        Nyquist style frequency response 
-@item   obs
-        observer equations for CGPC 
-@item   ode
-        ordinary differential equations 
-@item   odes
-        ode solution - state 
-@item   odes
-        ODE simulation header file 
-@item   odeso
-        ode solution - output 
-@item   odess
-        ode numerical steady-states - states 
-@item   odesso
-        ode numerical steady-states - outputs 
-@item   rbg
-        raw bond graph 
-@item   rep
-        report 
-@item   rfe
-        robot-form equations 
-@item   sabg
-        stripped acausal bond graph 
-@item   simp
-        simplification information 
-@item   sm
-        state matrices 
-@item   smx
-        state matrices containing explicit states and inputs
-@item   sms
-        ode 
-@item   smss
-        SM simulation header file 
-@item   sr
-        step response - state 
-@item   sro
-        step response - output 
-@item   ss
-        steady-state equations 
-@item   sspar
-        steady-state definition 
-@item   struc
-        structure - list of inputs, outputs and states 
-@item   sub
-        Executable subsystem list 
-@item   sub
-        LaTeX subsystem list 
-@item   sympar
-        symbolic parameters 
-@item   tf
-        transfer function 
-@end ftable
-A complete list can be found via the @code{help representations} command
-(@pxref{help representations}). 
-
-Many of these representations have more than one language (@pxref{Representations}) associated
-with them.
-
-Some of these representations define the system (@pxref{Defining
-representations}).
-
-@node Defining representations, Verbal description (desc), Representation summary, Representations
-@comment  node-name,  next,  previous,  up
-@section Defining representations
-@cindex Defining representations
-
-The following representations define the system and therefore must,
-ultimately, be defined by the user. However, all of these are assigned
-default values by @strong{MTT} and may then be subsequently edited
-(@pxref{Text editors}) viewed or operated on by the appropriate tools
-(@pxref{Language tools}).
-@vtable @code
-@item system_abg.fig
-        the acausal bond graph (@pxref{Acausal bond graph (abg)})
-@item system_lbl.txt
-        the label file (@pxref{Labels (lbl)})
-@item system_desc.tex
-        the description file (@pxref{Description (desc)})
-@item system_simp.r
-        algebraic simplifications to make output more readable
-        (@pxref{Symbolic parameters for simplification (simp.r)})
-@item system_subs.r
-        algebraic substitutions to resolve, eq trig. identities
-        (@pxref{Symbolic parameters (subs.r)})
-@item system_simpar.txt
-        simulation parameters (@pxref{Simulation parameters})
-@item system_numpar.txt
-        numerical parameters (@pxref{Numeric parameters (numpar)})
-@item system_input.txt
-        the system input for simulations (@pxref{Simulation input})
-@item system_logic.txt
-        the  switching logic for simulations (@pxref{Simulation logic})
-@item system_sspar.r
-        defines the system steady-state (@pxref{Steady-state solutions - symbolic (ss)})
-@end vtable
-
-@node Verbal description (desc), Acausal bond graph (abg), Defining representations, Representations
-@comment  node-name,  next,  previous,  up
-@section Verbal description (desc)
-@cindex Verbal description (desc)
-
-Systems can be documented in LaTeX using the _desc.tex file. This file
-is included in the report (@pxref{Report}) if the abg tex option
-is included in the rep.txt file.  As usual, @strong{MTT} provides a
-default text file to be edited by the user (@pxref{Text editors}).
-
-
-@c      node   next  prev  up
-@node   Acausal bond graph (abg), Stripped acausal bond graph (sabg), Verbal description (desc), Representations
-@section Acausal bond graph (abg)
-@cindex Acausal bond graph (abg)
-@pindex Acausal bond graph (abg)
-
-The acausal bond graph is the main input to @strong{MTT}. It is up to you, as a
-system modeler, to distill the essential aspects of the system that you
-wish to model and capture this information in the form of a bond graph.
-
-The inexperienced modeler may wish to look in one of the standard
-textbooks and copy some bond graphs of  systems to get going.
-
-
-To create the acausal bond graph of system `sys' in language fig type:
-@example
-mtt sys abg fig
-@end example
-To create the acausal bond graph of system `sys' in language m type:
-@example
-mtt sys abg m
-@end example
-To view the acausal bond graph of system `sys' type:
-@example
-mtt sys abg view
-@end example
-
-@menu
-* Language fig (abg.fig)::      
-* Language m (rbg.m)::          
-* Language m (abg.m)::          
-* Language tex (abg.tex)::      
-@end menu
-
-@node Language fig (abg.fig), Language m (rbg.m), Acausal bond graph (abg), Acausal bond graph (abg)
-@subsection Language fig (abg.fig) 
-@cindex Language fig (abg.fig) 
-@pindex Language fig (abg.fig) 
-
-A bond graph is made up of:
-@ftable @code
-@item bonds
-        To connect components together.
-@item strokes
-        To indicate causality.
-@item components
-        Either simple or compound.
-@item artwork
-        Irrelevant to the system but useful to the user.
-@end ftable
-
-An icon library of bonds, components and other symbols is available
-within xfig (@pxref{icon library}).
-
-
-
-
-@menu
-* icon library::                
-* bonds::                       
-* strokes::                     
-* components::                  
-* Simple components::           
-* SS components::               
-* Simple components - implementation::  
-* Compound components::         
-* Named SS components::         
-* Coerced bond direction::      
-* Port labels::                 
-* Vector port labels::          
-* Port label defaults::         
-* Vector components::           
-* artwork::                     
-* Valid names::                 
-@end menu
-
-@node icon library, bonds, Language fig (abg.fig), Language fig (abg.fig)
-@subsubsection Icon library
-@cindex Icon
-@cindex library
-A number of predefined iconic symbols are available within xfig. 
-@example
-Click onto the library icon
-Click onto the library pull-down menu and select BondGraph
-Select iconic symbols from the presented list
-@end example
-
-@node bonds, strokes, icon library, Language fig (abg.fig)
-@subsubsection Bonds
-@cindex bonds
-@pindex bonds
-
-Bonds are represented by polylines with two segments. They must be the
-default style (i.e. plain not dashed or dotted). The shortest segment is
-taken to be the half-arrow. its positioning is significant because:
-@itemize @bullet
-@item
-It points in the direction of power flow; thus a bond normally points
-towards C, I and R components.
-@item
-the corresponding side of the bond indicates flow causality; the other
-side represents effort causality. This is significant when using casual
-half-strokes (@pxref{strokes}). Please adopt the convention of having
-the half-arrows below horizontal bonds and to the right of vertical bonds.
-@end itemize
-
-
-
-@c      node   next  prev  up
-@node strokes, components, bonds, Language fig (abg.fig)
-@subsubsection Strokes
-@cindex strokes
-@pindex strokes
-
-Causal strokes are represented by single-segment polylines.
-There are two sorts of strokes:
-@itemize @bullet
-@item
-@emph{Full} strokes: these are the usual bond-graph strokes and determine
-both the effort and flow causality in the usual way. The @emph{centre} of the
-stroke should be at about one end of the bond and be at right angles to
-it.
-@item
-@emph{Half} strokes: these are an innovation in @strong{MTT} and allow you to
-specify the effort and flow causality independently. The @emph{end} of the
-stroke should be at about one end of the bond and be at right angles to
-it. If the causal half-stroke is on the @emph{same} side as the half-arrow
-(@pxref{bonds}) then it determines @emph{flow} causality; if, on the other
-hand, it is on the @emph{opposite} side to the half-arrow
-(@pxref{bonds}) then it determines @emph{effort} causality.
-Two half strokes on the @emph{same}, but on @emph{opposite} sides of the
-bond are equivalent to a a full stroke at the same end of the bond.
-@end itemize
-
-@strong{MTT} is reasonably forgiving; but a neat diagram will be less ambiguous to
-you as well as to @strong{MTT}.
-
-Causality is indicated as follows:
-@itemize @bullet
-@item 
-@emph{Effort} is imposed at the @emph{same} end as the stroke.
-@item 
-@emph{Flow} is imposed at the @emph{opposite} end as the stroke.
-@end itemize
-
-
-
-@c      node   next  prev  up
-@node components, Simple components, strokes, Language fig (abg.fig)
-@subsubsection Components
-@cindex components
-@pindex components
-
-Components are represented by a text string in fig.  The recommended
-style is: 20pt, Times-Roman and centre justified.
-
-The component text string can be of the following forms:
-@ftable @code
-@item type
-Just the type of the component is indicated. Components may be either
-Simple components (@pxref{Simple components}) or Compound components
-(@pxref{Compound components}).  For example:
-@example
-R
-@end example
-@item type:label
-Both the type and the label of the component are given. The type must be
-a valid name (@pxref{Valid names}.The name provides a link to more
-information to be found in @xref{Labels (lbl)}. For example:
-@example
-R:r
-@end example
-@item type:label:cr
-Not only are the type and the label of the component given, but also the
-component cr argument. The type must be
-a valid name (@pxref{Valid names}.The name provides a link to more
-information to be found in @xref{Labels (lbl)}. For example:
-@example
-R:r:flow,r
-@end example
-@item type:label:expression
-Expression is a mathematical expression relating the effort (called
-mtt_e) to the flow (called mtt_f).
-For example the following three forms are equivalent
-@example
-R:r:mtt_e=r*mtt_f
-R:r:mtt_e-r*mtt_f=0
-R:r:mtt_f=mtt_e/r
-@end example
-A non-linear example is:
-@example
-R:r:mtt_e = sin(mtt_f)
-@end example
-
-@item type*n
-The name, together with the number @samp{n} of repetitions of the
-component, are given. This repetition only makes sense if the component
-has an even number of ports (@pxref{Port labels}); n copies of the component
-are concatenated with odd Named ports (@pxref{Port labels}) of the
-component being connected to the even Named ports of the previous
-component in the chain in numerical order.  This feature is particularly
-useful if the component is compound and can be used for, example to give
-a lumped approximation of a distributed system. For example:
-@example
-MySystem*25
-@end example
-@item type:label*n
-This complete form and is a combination of the simpler forms. For
-example:
-@example
-MySystem:MyLabel*25
-@end example
-
-@end ftable
-
-@node Simple components, SS components, components, Language fig (abg.fig)
-@comment  node-name,  next,  previous,  up
-@subsubsection Simple components
-@cindex Simple components
-
-The following simple components are defined in MTT.
-
-@ftable @code
-@item R
-         Standard one-port R
-@item C
-         Standard one-port I
-@item I
-         Standard one-port I
-@item SS
-        Source-sensor
-@item TF
-        Transformer
-@item GY
-        Gyrator
-@item AE
-        Effort amplifier
-@item AF
-        Flow amplifier
-@item CSW
-         Switched one-port I
-@item ISW
-         Switched one-port I
-@end ftable
-
-@menu
-* SS components::               
-* Simple components - implementation::  
-@end menu
-
-@node SS components, Simple components - implementation, Simple components, Language fig (abg.fig)
-@comment  node-name,  next,  previous,  up
-@subsubsection SS components
-@cindex SS components
-
-@iftex
-$$
-
-@end iftex
-
-
-@code{SS} components provide input and output variables for a system;
-Named SS components (@pxref{Named SS components}) provide this for
-subsystems.
-
-@node Simple components - implementation, Compound components, SS components, Language fig (abg.fig)
-@comment  node-name,  next,  previous,  up
-@subsubsection Simple components - implementation
-@cindex  Simple components - implementation
-
-Each simple component, with name NAME, is defined by two m files:
-@ftable @code
-@item NAME_cause.m
-        defines the possible causal patterns for the component
-@item NAME_eqn.m
-        defines the equations generated 
-@end ftable
-Only the experienced user would normally define simple components -
-Compound components (@pxref{Compound components}) are recommended for
-DIY components.
-
-@node Compound components, Named SS components, Simple components - implementation, Language fig (abg.fig)
-@comment  node-name,  next,  previous,  up
-@subsubsection Compound components
-@cindex  Compound components
-@cindex Named SS
-Compound components are systems described by bond graphs and implemented
-by MTT. They have special SS components, Named SS components
-(@pxref{Named SS components}), to indicate connections to the
-encapsulating system.
-
-Like any other system, they are described by a graphical Bond Graph description
-(@pxref{Language fig (abg.fig) }), and a label file (@pxref{Labels (lbl)}).
-
-By convention, all of the files describing a component live in a
-directory with the same name as the component.
-
-@menu
-* Named SS components::      
-@end menu
-
-@node Named SS components, Coerced bond direction, Compound components, Language fig (abg.fig)
-@comment  node-name,  next,  previous,  up
-@subsubsection Named SS components
-@cindex Named SS components
-
-Named SS components provide the link from the system which @emph{defines} 
-compound component to the system which @emph{uses} a compound
-component @pxref{Compound components}.
-A named SS components is of the form
-@code{SS:[name]};
-
-Where `name' is a name consisting of alphanumeric characters and
-underscore; for example:
-@example
-SS:[Mechanical_1]
-@end example
-Each such named SS provides one of the ports
-(@pxref{Ports}).
-The direction of the named SS components.
-(@pxref{Named SS components}) 
-is coerced (@pxref{Coerced bond direction}) to have the same direction
-as the bond connected to the corresponding port. Thus the direction of
-the  direction of the named SS components has no significance unless the
-component is at the top level of a system.
-
-If a named SS component exists at the top level (@pxref{Top level})
-and is treated as an
-ordinary SS component with the given direction and with the attributes
-specified in the label file (@pxref{Labels (lbl)}).
-
-@node Coerced bond direction, Port labels, Named SS components, Language fig (abg.fig)
-@comment  node-name,  next,  previous,  up
-@subsubsection Coerced bond direction
-@cindex Coerced bond direction
-@pindex Coerced bond direction
-Named SS components (@pxref{Named SS components}) provide the mechanism
-for declaring the ports (@pxref{Ports}) of a component. The
-corresponding bond has a direction. However, under some circumstances,
-it may be useful to reverse this direction. @strong{MTT} provides a
-coercion mechanism for this: the the direction of the bond attached to
-the named SS component (@pxref{Named SS components}) is replaced by the
-direction of the bond attached to the component port.
-
-@node Port labels, Vector port labels, Coerced bond direction, Language fig (abg.fig)
-@comment  node-name,  next,  previous,  up
-@subsubsection Port labels
-@cindex ports
-@pindex ports
-Most multi-port components have ports 
-@pxref{Ports})which display different
-behaviors; the exception to this is the junction (@code{0} and @code{1})
-components. For this reason, @strong{MTT} provides a method for unambiguously
-identifying the ports of a multi-port component by port labels.
-
-A port label is indicated by a name within parentheses of the form
-@code{[name]}, where `name' is a name consisting of alphanumeric
-characters and underscore; for example:
-@example
-[Mechanical_1]
-@end example
-This provides a label for corresponding to the component to which the
-nearest bond-end is attached.
-
-The following rules must be be obeyed:
-@itemize @bullet
-@item
-If a component has any port labels at all, there must be one for each
-port of the component.
-@c @item
-@c If a component is to be used repetitively (see @ref{components}), it
-@c must have an even number of ports and the odd ports are connected to the
-@c even points within the chain of components.
-@end itemize
-
-Port labels may be grouped into vector port labels (@pxref{Vector port
-labels}). Components with compatible (ie containing the same number of ports)
-vector ports may be connected by a @emph{single} bond
-(@pxref{Bonds}); such a bond implies the corresponding number of bonds
-(one for each element of the vector port label). All such bonds inherit
-the same direction and any @emph{explicit} causal strokes (@pxref{strokes})
-
-@node Vector port labels, Port label defaults, Port labels, Language fig (abg.fig)
-@comment  node-name,  next,  previous,  up
-@subsubsection Vector port labels
-@cindex vector port labels
-@cindex port labels
-Port labels (@pxref{Port labels}) may be grouped into vector port
-labels of the form @code{[name1,name2,name3]}. 
-@example
-[Mechanical_1,Electrical,Hydraulic_5]
-@end example
-
-@node Port label defaults, Vector components, Vector port labels, Language fig (abg.fig)
-@comment  node-name,  next,  previous,  up
-@subsubsection Port label defaults
-@cindex Port label defaults
-@pindex Port label defaults
-Whether impicitly or explicity, all ports of components (with the
-exception of 0 and 1 junctions) must have lables  (@pxref{Port
-labels}). However, these can be omitted from the bond graph in the
-following circumstances and default labels are supplied by @strong{MTT}.
-@enumerate
-@item A single unlabled inport defaults to [in]
-@item A single unlabled outport defaults to [out]
-@end enumerate
-
-These defaults may, in turn be aliases (@pxref{Aliases}) for port labels
-(@pxref{Port labels}) or vector port labels (@pxref{Vector port
-labels}).  Combining the default and alias mechanism is a powerful tool
-for creating uncluttered, yet complex, bond graph models.
-
-@node Vector components, artwork, Port label defaults, Language fig (abg.fig)
-@subsubsection Vector Components
-@cindex Vector components
-@pindex Vector components
-Vectors of components can be created in four cases:
-@code{0} junctions,
-@code{1} junctions,
-@code{SS} components and
-@code{SS} port components.
-
-
-In each case, the presence of a vector component is indicated by a
-single port label  (@pxref{Port labels}) of one of two forms:
-@enumerate
-@item containing numerals from 1 to
-the order of the vector. Thus a vector of 3 components is indicated by a
-port label of the form [1,2,3].
-@item  1: followed by
-the order of the vector. Thus a vector of 3 components is indicated by a
-port label of the form [1:3].
-@end enumerate
-
-
-Within the corresponding label file (@pxref{Labels (lbl)}), the
-components of a vector port can be accessed using _i where i is the
-corresponding index. Thus a port SS:[Electrical] appearing near the port
-label  [1,2,3] could contain the port alias (@pxref{Port aliases})
-@example
-%ALIAS  in Electrical_1,Electrical_2,Electrical_3
-@end example
-
-@node artwork, Valid names, Vector components, Language fig (abg.fig)
-@subsubsection Artwork
-@cindex artwork
-@pindex artwork
-You are encouraged to annotate your bond graphs extensively - this makes
-them an immediately readable document whilst retaining the precise and
-unambiguous expressive power of the bond graph.
-
-You may add any Fig (@pxref{Fig}) object to the bond graph as long as it
-will not be interpreted as part of the bond graph.  
-The reccommended way to acheive this is to put the  Bond Graph at depth
-0,10,20 etc (ie depth modulo 10 is zero) and artwork at any other depth. 
-@c  The recommended way to do this is to @emph{put all artwork at or below
-@c  Depth 1} in the figure. @strong{MTT} ignores all objects not at depth 0.
-
-
-For compatibility with earlier versions of @strong{MTT}, the following
-objects are ignored even at level 0. However, their use is strongly
-discouraged.
-@itemize @bullet
-@item
-Adding text is OK as long as it cannot be confused with components
-(@pxref{components}). In particular, you can include invalid component
-characters such as white space, @code{"}, @code{'}, @code{!} etc.
-@item
-Adding boxes, arcs etc is always OK.
-@item
-Adding dotted or dashes lines is always OK.
-@end itemize
-
-The stripped abg file (sabg) (@pxref{Stripped acausal bond graph
-(sabg)})
-shows only those parts of the diagram recognised by @strong{MTT} and is
-therefore useful for distinguishing artwork.
- 
-@node Valid names,  , artwork, Language fig (abg.fig)
-@subsubsection Valid Names
-@cindex valid name
-@pindex valid name
-A valid name is a text string containing alphanumeric characters.  It
-must @strong{NOT} contain underscore @samp{_}, hyphen @samp{-}, @samp{:}
-or @samp{*}.
-
-The following reserved words in reduce should also be avoided (with any case)
-@example
-
-Commands ALGEBRAIC ANTISYMMETRIC ARRAY BYE CLEAR CLEARRULES COMMENT
-CONT DECOMPOSE DEFINE DEPEND DISPLAY ED EDITDEF END EVEN FACTOR FOR
-FORALL FOREACH GO GOTO IF IN INDEX INFIX INPUT INTEGER KORDER LET
-LINEAR LISP LISTARGP LOAD LOAD PACKAGE MASS MATCH MATRIX MSHELL
-NODEPEND NONCOM NONZERO NOSPUR ODD OFF ON OPERATOR ORDER OUT PAUSE
-PRECEDENCE PRINT PRECISION PROCEDURE QUIT REAL REMFAC REMIND RETRY
-RETURN SAVEAS SCALAR SETMOD SHARE SHOWTIME SHUT SPUR SYMBOLIC
-SYMMETRIC VECDIM VECTOR WEIGHT WRITE WTLEVEL
-
-Boolean Operators EVENP FIXP FREEOF NUMBERP ORDP PRIMEP
-
-Infix Operators := = >= > <= < => + * / ^ ** . WHERE SETQ OR AND
-MEMBER MEMQ EQUAL NEQ EQ GEQ GREATERP LEQ LESSP PLUS DIFFERENCE MINUS
-TIMES QUOTIENT EXPT CONS Numerical Operators ABS ACOS ACOSH ACOT ACOTH
-ACSC ACSCH ASEC ASECH ASIN ASINH ATAN ATANH ATAN2 COS COSH COT COTH
-CSC CSCH EXP FACTORIAL FIX FLOOR HYPOT LN LOG LOGB LOG10 NEXTPRIME
-ROUND SEC SECH SIN SINH SQRT TAN TANH
-
-Prefix Operators APPEND ARGLENGTH CEILING COEFF COEFFN COFACTOR CONJ
-DEG DEN DET DF DILOG EI EPS ERF FACTORIZE FIRST GCD G IMPART INT
-INTERPOL LCM LCOF LENGTH LHS LINELENGTH LTERM MAINVAR MAT MATEIGEN MAX
-MIN MKID NULLSPACE NUM PART PF PRECISION RANDOM RANDOM NEW SEED RANK
-REDERR REDUCT REMAINDER REPART REST RESULTANT REVERSE RHS SECOND SET
-SHOWRULES SIGN SOLVE STRUCTR SUB SUM THIRD TP TRACE VARNAME
-
-Reserved Variables CARD NO E EVAL MODE FORT WIDTH HIGH POW I INFINITY
-K!* LOW POW NIL PI ROOT MULTIPLICITY T
-
-Switches ADJPREC ALGINT ALLBRANCH ALLFAC BFSPACE COMBINEEXPT
-COMBINELOGS COMP COMPLEX CRAMER CREF DEFN DEMO DIV ECHO ERRCONT
-EVALLHSEQP EXP EXPANDLOGS EZGCD FACTOR FORT FULLROOTS GCD IFACTOR INT
-INTSTR LCM LIST LISTARGS MCD MODULAR MSG MULTIPLICITIES NAT NERO
-NOSPLIT OUTPUT PERIOD PRECISE PRET PRI RAT RATARG RATIONAL RATIONALIZE
-RATPRI REVPRI RLISP88 ROUNDALL ROUNDBF ROUNDED SAVESTRUCTR
-SOLVESINGULAR TIME TRA TRFAC TRIGFORM TRINT
-
-Other Reserved Ids BEGIN DO EXPR FEXPR INPUT LAMBDA LISP MACRO PRODUCT
-REPEAT SMACRO SUM UNTIL WHEN WHILE WS
-
-
-@end example
-
-
-
-@node Language m (rbg.m), Language m (abg.m), Language fig (abg.fig), Acausal bond graph (abg)
-@comment  node-name,  next,  previous,  up
-@subsection Language m (rbg.m)
-The raw bond graph of system `sys' is represented as
- an m file with heading:
-@example
-function [rbonds, rstrokes,rcomponents,rports,n_ports] = sys_rbg
-@end example
-This representation is a half-way house between the fig 
-(@pxref{Language fig (abg.fig)}) and m 
-(@pxref{Language m (abg.m)}) representations. It contains the
-geometric information from the fig file in a form digestible by Octave
-(@pxref{Octave}).
-
-The five outputs of this function are:
-@itemize @bullet
-@item
-rbonds
-@item
-rstrokes
-@item
-rcomponents
-@item
-rports
-@item
-n_ports
-@end itemize
-
-@emph{rbonds} is  a matrix with
-@itemize @bullet
-@item
-one row for each bond (@pxref{bonds})
-@item
-columns 1 and 2 containing the x,y coordinates for one end of the bond
-@item
-columns 3 and 4 containing the x,y coordinates for the corner of the bond
-@item
-columns 5 and 6 containing the x,y coordinates for the other end of the bond
-@end itemize
-
-@emph{rstrokes} is  a matrix with (@pxref{strokes})
-@itemize @bullet
-@item
-one row for each stroke or half-stroke
-@item
-columns 1 and 2 containing the x,y coordinates for one end of the stroke
-@item
-columns 3 and 4 containing the x,y coordinates for the other end of the stroke
-@end itemize
-
-@emph{rcomponents} is  a matrix with (@pxref{components})
-@itemize @bullet
-@item
-one row for each component
-@item
-columns 1 and 2 containing the x,y coordinates of the component
-@item
-the remaining columns containing fig file information
-@end itemize
-
-@emph{rports} is  a matrix with (@pxref{Port labels})
-@itemize @bullet
-@item
-one row for each component port that is explicitly labeled
-@item
-columns 1 and 2 containing the x,y coordinates of the port label
-@item
-column 3 contains the port number.
-@end itemize
-
-@emph{n_ports} is the number of ports associated with the system -- i.e. the
-number of Named SS components (@pxref{Named SS components}).
-
-@menu
-* Transformation abg2rbg_fig2m::  
-@end menu
-
-@node Transformation abg2rbg_fig2m,  , Language m (rbg.m), Language m (rbg.m)
-@comment  node-name,  next,  previous,  up
-@subsubsection Transformation abg2rbg_fig2m
-@cindex Transformation abg2rbg_fig2m
-
-This transformation takes the acausal bond graph as a fig file 
-(@pxref{Language fig (abg.fig)}) and transforms it into a raw bond graph in
-m-file format (@pxref{Language m (rbg.m)}).
-
-This transformation is implemented in GNU awk (gawk).
-It scans both the fig file (@pxref{Language fig (abg.fig)})
-and the label file (@pxref{Labels (lbl)}) and generates the rbg
- (@pxref{Language m (rbg.m)}) with components sorted according to the
-label file.
-It also generates a file sys_fig.fig containing details of the bond
-graph with the components removed.
-
-
-@node Language m (abg.m), Language tex (abg.tex), Language m (rbg.m), Acausal bond graph (abg)
-@comment  node-name,  next,  previous,  up
-@subsection Language m (abg.m)
-@cindex Language m (abg.m) 
-@cindex bonds
-@cindex components
-@cindex n_ports
-
-The acausal bond graph of system `sys' is represented as
- an m file with heading:
-@example
-function [bonds,components,n_ports] = sys_abg
-@end example
-The three outputs of this function are:
-@itemize @bullet
-@item
-bonds
-@item
-components
-@item
-n_ports
-@end itemize
-
-@emph{bonds} is  a matrix with
-@itemize @bullet
-@item
-one row for each bond
-@item
-the first column contains the arrow-orientated 
-(@pxref{Arrow-orientated causality}) 
-causality of the @emph{effort} variable.
-@item
-the second column contains the arrow-orientated 
-(@pxref{Arrow-orientated causality}) 
-causality of the @emph{flow} variable.
-@end itemize
-
-@emph{components} is  a matrix with
-@itemize @bullet
-@item
-one row for each component
-@item
-one column for each bond impinging on the component. The
-@emph{magnitude} of each entry corresponds to the bond number (the
-appropriate row index of` bonds'); the sign is positive if the bond
-arrow points into the component and negative otherwise.
-@end itemize
-
-@emph{n_ports} is the number of ports associated with the system -- i.e. the
-number of Named SS components (@pxref{Named SS components}).
-
-@menu
-* Arrow-orientated causality::  
-* Component-orientated causality::  
-* Transformation rbg2abg_m::    
-@end menu
-
-@node  Arrow-orientated causality, Component-orientated causality, Language m (abg.m), Language m (abg.m)
-@comment  node-name,  next,  previous,  up
-@subsubsection  Arrow-orientated causality
-@cindex Arrow-orientated causality
-
-The  arrow-orientated causality convention assigns -1, 0 or 1 
-to both the effort and flow (@pxref{Variables}) sides of a bond 
-to represent the causal stroke (@pxref{strokes})
-as follows:
-@vtable @code
-@item 0
-        if there is no causality set.
-@item 1
-       if the causal stroke is at the arrow end of the bond.
-@item -1 
-     if the causal stroke is at the other end of the bond.
-@end vtable
-@pxref{Component-orientated causality}.
-
-@node  Component-orientated causality, Transformation rbg2abg_m, Arrow-orientated causality, Language m (abg.m)
-@comment  node-name,  next,  previous,  up
-@subsubsection  Component-orientated causality
-@cindex Component-orientated causality
-
-The  component-orientated causality convention assigns -1, 0 or 1 
-to both the effort and flow (@pxref{Variables}) sides of a bond 
-to represent the causal stroke (@pxref{strokes})
-as follows:
-@vtable @code
-@item 0
-        if there is no causality set.
-@item 1 
-      if the causal stroke is at the component end of the bond.
-@item -1
-      if the causal stroke is at the other end of the bond.
-
-@end vtable
-@pxref{Arrow-orientated causality}.
-
-@node Transformation rbg2abg_m,  , Component-orientated causality, Language m (abg.m)
-@comment  node-name,  next,  previous,  up
-@subsubsection Transformation rbg2abg_m
-@cindex Transformation rbg2abg_m
-This transformation takes the raw bond graph and, by doing some
-geometrical computation, determines the topology of the bond graph -- ie
-what is close to what.
-
-@node Language tex (abg.tex),  , Language m (abg.m), Acausal bond graph (abg)
-@comment  node-name,  next,  previous,  up
-@subsection Language tex (abg.tex)
-@cindex Language tex (abg.tex)
-
-For the purpose of producing a report (@pxref{Report}), @strong{MTT}
-generates a LaTeX (@pxref{LaTeX}) file describing the bond graph and its
-subsystems. Additional information may be supplied using the description
-representation (@pxref{Description (desc)}).
-
-@c      node   next  prev  up
-@node   Stripped acausal bond graph (sabg), Labels (lbl), Acausal bond graph (abg), Representations
-@section Stripped acausal bond graph (sabg)
-@cindex Stripped acausal bond graph (sabg)
-@pindex Stripped acausal bond graph (sabg)
-The stripped acausal bond graph is the acausal bond graph representation
-(@pxref{Acausal bond graph (abg)}) without the artwork
-(@pxref{artwork}). It is useful to check for mistakes by showing
-precisely what is recognised by @strong{MTT}.
-
-@menu
-* Language fig (sabg.fig)::     
-* Stripped acausal bond graph (view)::  
-@end menu
-
-@node Language fig (sabg.fig), Stripped acausal bond graph (view), Stripped acausal bond graph (sabg), Stripped acausal bond graph (sabg)
-@subsection Language fig (sabg.fig) 
-@cindex Language fig (sabg.fig) 
-@pindex Language fig (sabg.fig) 
-The stripped acausal bond graph can be generated as a fig (@pxref{Fig})
-file using
-@example
-mtt syst sabg fig
-@end example
-
-@node Stripped acausal bond graph (view),  , Language fig (sabg.fig), Stripped acausal bond graph (sabg)
-@subsection Stripped acausal bond graph (view)
-@cindex Language m (view)
-@cindex view  Constrained-state Equations
-This representation has the standard text view
-(@pxref{Views}).
-
-
-@node Labels (lbl), Description (desc), Stripped acausal bond graph (sabg), Representations
-@comment  node-name,  next,  previous,  up
-@section Labels (lbl)
-@cindex Labels
-@cindex lbl
-Bond graph components have optional labels. These provide pointers to
-further information relating to the component; this avoids clutter on
-the bond graph.
-
-The label file contains the following non-blank lines (blank lines are ignored)
-@itemize @bullet
-@item Summary - lines beginning with %SUMMARY
-@item Description - lines beginning with %DESCRIPTION
-@item Alias - lines beginning with %ALIAS
-@item Comments - lines beginning with % 
-@item Labels - other non-blank lines
-@end itemize
-
-Each lable contains three fields (in the following order) separated by
-white space and on one line:
-@enumerate
-@item The component name @pxref{Component names}. This must be a valid
-name  (@pxref{Valid names}.
-@item The component constitutive relationship @pxref{Component constitutive relationship}
-@item The component arguments @pxref{Component arguments}
-@end enumerate
-
-Not each component @pxref{components} needs a label, only those which are explicitly
-labeled on the Bond Graph @pxref{Acausal bond graph (abg)}.
-@strong{MTT} checks whether all  components labelled on the bond graph
-have labels and vice versa.
-
-If no lbl file exists, @strong{MTT} will create a valid one for you;
-including a default set of arguments and crs for both simplae and
-compound components.
-
-If wish to create one to edit yourself, type
-@example
-mtt system_name lbl txt
-@end example
-An example lbl file (for the RC system is):
-@example
-%% Label file for system RC (RC_lbl.txt)
-%SUMMARY RC
-%DESCRIPTION <Detailed description here>
-% Port aliases
-%ALIAS  in      in
-%ALIAS  out     out
-
-% Argument aliases
-%ALIAS  $1      c
-%ALIAS  $2      r
-
-%% Each line should be of one of the following forms:
-%            a comment (ie starting with %)
-%            component-name     cr_name arg1,arg2,..argn
-%            blank
-
-% ---- Component labels ----
-
-% Component type C
-        c               lin     effort,c
-
-% Component type R
-        r               lin     flow,r
-
-% Component type SS
-        [in]    SS              external,external
-        [out]   SS              external,external
-
-@end example
-
-
-The old-style lbl files (@pxref{Old-style labels (lbl)}) are NO LONGER
-supported -- you are encouraged to convert them ASAP.
-
-@menu
-* SS component labels ::        
-* Other component labels ::     
-* Component names::             
-* Component constitutive relationship::  
-* Component arguments::         
-* Parameter declarations::      
-* Units declarations::          
-* Interface Control Definition::  
-* Aliases::                     
-* Parameter passing::           
-* Old-style labels (lbl)::      
-@end menu
-
-@node SS component labels , Other component labels , Labels (lbl), Labels (lbl)
-@comment  node-name,  next,  previous,  up
-@subsection SS component labels 
-@cindex SS component labels 
-In addition to the label there are two information fields, @pxref{Labels
-(lbl)}. The first must be `SS', the second contains two information
-fields of the form info_field_1,info_field_2.
-
-These two information
-fields correspond to the effort and flow variables of the of the SS components as follows
-@vtable @code
-@item info_field_1
-        effort
-@item info_field_2
-        flow
-@end vtable
-Each of these two fields contains one of the following @emph{attributes}:
-@vtable @code
-@item external
-        indicates that the corresponding variable is a system input or
-output
-@item internal
-        indicates that the variable does not appear as a system output;
-        it is an error to label an input in this way.
-@item a number
-        the value of the input; or the value of the (imposed) output
-@item a symbol
-        the symbolic value of the input; or the value of the (imposed) output
-@item unknown
-        used for the SS method of solving algebraic loops. This
-        indicates that the corresponding system input (SS output) is to
-        be chosen to set the corresponding system output (SS input) to zero.
-@item zero
-        used for the SS method of solving algebraic loops. This
-        indicates that the corresponding system output (SS input) is to
-        be set to zero using the variable indicted by the corresponding
-        `unknown' label.
-@end vtable
-
-Some examples are:
-@example
-%% ss1 is both a source and sensor
-ss1     SS              external,external
-%% ss1 acts as a flow sensor - it imposes zero effort.
-ss2     SS              0,external
-@end example
-
-
-@node Other component labels , Component names, SS component labels , Labels (lbl)
-@comment  node-name,  next,  previous,  up
-@subsection Other component labels 
-@cindex Other component labels 
-
-In addition to the label there are two information fields,
-@pxref{Labels (lbl)}.
-They correspond to the constitutive relationship 
-(see @pxref{Constitutive relationship} and arguments of the
-component as follows
-@vtable @code
-@item info_field_1
-        constitutive relationship 
-@item info_field_2
-        parameters
-@end vtable
-
-Some examples are:
-@example
-%Armature resistance
-r_a     lin     effort,r_a
-
-%Gearbox ratio
-n       lin     effort,n
-@end example
-
-@strong{MTT} supports parameter-passing to  (@pxref{Parameter passing })
-subsystems.
-
-@menu
-* Component names::             
-* Component constitutive relationship::  
-* Component arguments::         
-* Aliases::                     
-* Parameter passing::           
-* Old-style labels (lbl)::      
-@end menu
-
-@node Component names, Component constitutive relationship, Other component labels , Labels (lbl)
-@comment  node-name,  next,  previous,  up
-@subsection Component names
-@cindex  Component names
-The component name field must contain a valid name  (@pxref{Valid names} corresponding to the
-name (the bit after the :) of each named component (@pxref{components})
-on  the bond graph (@pxref{Acausal bond graph (abg)}).
-
-@node Component constitutive relationship, Component arguments, Component names, Labels (lbl)
-@comment  node-name,  next,  previous,  up
-@subsection Component constitutive relationship
-@cindex  Component constitutive relationship
-The constitutive relationship field contains the name of a constitutive
-relationship for the component. There are three sorts of constitutive
-relationship recognised by @strong{MTT}:
-@enumerate
-@item A generic constitutive relationship such as @var{lin} (the generic
-linear constitutive relationship.
-@item A local constitutive relationship with the same name as the
-component type
-@item The @var{SS} constitutive relationship reserved for @var{SS}
-components.
-All labels for @var{SS} components must contain SS in this field.
-@end enumerate
-
-
-@node Component arguments, Parameter declarations, Component constitutive relationship, Labels (lbl)
-@comment  node-name,  next,  previous,  up
-@subsection Component arguments
-@cindex  Component arguments
-
-@node Parameter declarations, Units declarations, Component arguments, Labels (lbl)
-@comment  node-name,  next,  previous,  up
-@subsection Parameter declarations
-@cindex parameter declarations
-@pindex parameter declarations
-@pindex PAR 
-@pindex NOTPAR 
-@pindex VAR 
-@pindex NOTVAR 
-
-It is sometimes useful to use parameters (in addition to those implied by
-the Component arguments @pxref{Component arguments}) to compute values
-in, for example the numpar file. These can be declared in the label
-file;
-for examples , the two parameters par1 and par 2 can be declared as:
-@example
-#PAR par1
-#PAR par2
-@end example
-
-On the other hand, some CR arguments (eg foo and bar) may not correspond to
-parameters. These can be excluded from the sympar list  using
-the NOTPAR declaration
-@example
-#NOTPAR foo
-#NOTPAR bar
-@end example
-
-For comapability with old code, VAR may be used in place of PAR, but
-this usage is deprecated.
-
-@node Units declarations, Interface Control Definition, Parameter declarations, Labels (lbl)
-@comment  node-name,  next,  previous,  up
-@subsection Units declarations
-@cindex units declarations
-@pindex units declarations
-@pindex UNITS
-The units and domains of ports (@pxref{Ports}) are declared as:
-@example
-#UNITS Port_name domain effort_units flow_units
-@end example
-where "Port_name" is the name of the port, domain is one of:
-@vtable @code
-@item electrical
-         the electrical domain
-@item translational
-         the translational mechanical domain
-@item rotational
-         the rotational mechanical domain
-@item fluid
-         the fluid domain
-@item thermal
-         the thermal domain 
-@end vtable
-and effort_units and flow_units are corresponding units for the effort
-and the flow.
-
-Allowed units are those defined in the @strong{units} package.
-
-
-
-@strong{MTT} checks that units are 
-@itemize  @bullet
-@item defined consistently with the domain
-@item the same for connected ports when both ports have defined units.
-@end itemize
-No checks are done if one or both ends of a bond are not connected to a
-port with defined units.
-
-
-
-@node Interface Control Definition, Aliases, Units declarations, Labels (lbl)
-@comment  node-name,  next,  previous,  up
-@subsection Interface Control Definition
-@cindex ICD (label file directive)
-It is sometimes useful to be able to automatically generate a set of 
-assignments mapping @strong{MTT} inputs and outputs to an external interface
-definition. This can be achieved with use of the @emph{#ICD} directive.
-
-@example
-#ICD    PressureSensor		PUMP1_PRESSURE_SENSOR,Pa;null,none
-#ICD    Electrical		PUMP1_VOLTAGE,volt;PUMP1_CURRENT,amp
-
-% Component type De
-	PressureSensor	SS      external
-
-% Component type SS
-	Electrical	SS	external,external
-@end example
-
-
-The ICD directive consists of 3 whitespace delimited fields:
-
-@enumerate
-@item [%|#]ICD
-@item component name
-@item Four comma (,) or semi-colon (;) delimited fields:
-
-@enumerate
-@item name of effort parameter
-@item unit of effort parameter
-@item name of flow parameter
-@item unit of flow parameter
-@end enumerate
-@end enumerate
-
-If no parameter name is required, a value of "null" should be used.
-If the parameter does not have any units, a value of "none" should be used.
-
-ICD parameters may be aliased @pxref{Aliases} in the same way as normal
-parameters, thus it is possible to define some or all of the ICD in higher
-level components.
-
-The command
-
-@example
-mtt sys ICD txt
-@end example
-
-will generate a text file containing a list of mappings:
-
-@example
-## Interface Control Definition for System sys
-## sys_ICD.txt: Generated by MTT Thu Jul 12 21:21:21 CDT 2001
-
-Input:  PUMP1_VOLTAGE           sys_P1_1_Electrical      Causality: Effort   Units: volt
-Output: PUMP1_CURRENT           sys_P1_1_Electrical      Causality: Flow     Units: amp
-Output: PUMP1_PRESSURE_SENSOR   sys_P1_1_PressureSensor  Causality: Effort   Units: Pa
-@end example
-
-A set of assignments can be generated with the command
-@example
-mtt sys ICD m
-@end example
-
-resulting in:
-
-@example
-# Interface Control Definition mappings for system sys
-# sys_ICD.m: Generated by MTT Thu Jul 12 21:26:56 CDT 2001
-
-# Inputs
-
-        mttu(1) = PUMP1_VOLTAGE;
-
-# Outputs
-
-        PUMP1_CURRENT                  = mtty(1);
-        PUMP1_PRESSURE_SENSOR          = mtty(2);
-@end example
-
-A similar file will be generated by the command
-@example
-mtt sys ICD cc
-@end example
-
-
-
-@node Aliases, Parameter passing, Interface Control Definition, Labels (lbl)
-@comment  node-name,  next,  previous,  up
-@subsection Aliases
-@cindex aliases
-@pindex aliases
-
-Aliases provide a convenient mechanism for relabelling words appearing
-in the label file (@pxref{Labels (lbl)}). There are three contexts in
-which the alias mechanism is used:
-
-@enumerate
-@item renaming ports (@pxref{Port aliases}),
-@item renaming parameters (@pxref{Parameter aliases}) and
-@item renaming components (@pxref{Component aliases}).
-@end enumerate
-
-All three mechanisms use the same form of statement within the label
-file
-@example
-%ALIAS short_label       real_label
-@end example
-
-@strong{MTT} distinguishes between the three forms as follows:
-
-@itemize @bullet
-@item Parameter aliases: `short_label' starts with a `$'
-@item Component aliases: `real_label' contains the directory separator
-`/'
-@item Port aliases: neither of the above
-@end itemize
-
-@menu
-* Port aliases::                
-* Parameter aliases::           
-* CR aliases::                  
-* Component aliases::           
-@end menu
-
-
-@node Port aliases, Parameter aliases, Aliases, Aliases
-@comment  node-name,  next,  previous,  up
-@subsubsection Port aliases
-@cindex port aliases
-@pindex port aliases
-Aliases provide a way of refering to (@pxref{Port labels}) or vector port labels (@pxref{Vector
-port labels}) on the bond graph using a short-hand notation. With in a
-component label file (@pxref{Labels (lbl)}) statements of the following
-forms can occur 
-
-@example
-%ALIAS short_label       real_label
-@end example
-
-When the component is used within another component, the short_lable may
-be used in place of the real_label.
-More than one alias per label can be used, for example
-
-@example
-%ALIAS short_label_1       real_label
-%ALIAS short_label_2       real_label
-%ALIAS short_label_3       real_label
-@end example
-
-The port can then be refered to in four ways: as real_label,
-short_label_1, short_label_2 or short_label_3.
-An alternative notation for the ALIAS statement in this case is
-
-@example
-%ALIAS short_label_1|short_label_2|short_label_3       real_label
-@end example
-
-The alias feature is particularly powerful in conjunction with vector
-port labels (@pxref{Vector port labels}) and the port label default 
-(@pxref{Port label defaults}) mechanisms. For example, a component with
-5 ports appearing in the lbl file as:
-
-@example
-        [Hydraulic_in]  external        external
-        [Hydraulic_out] external        external
-        [Power_Shaft]           external        external
-        [Thermal_in]    external        external
-        [Thermal_out]   external        external
-@end example
-
-together with the following statements in the label file:
-
-@example
-%ALIAS  in              Thermal_in,Hyydraulic_in
-%ALIAS  out             Thermal_out,Hydraulic_out
-%ALIAS  shaft|power     Power_Shaft
-@end example
-
-can appear in the bond graph containing that component with one bond
-labeled either [shaft] or [power] or [Power_Shaft], one unlabeled vector
-bond pointing in and one unlabeled vector bond pointing out.
-
-@node Parameter aliases, CR aliases, Port aliases, Aliases
-@comment  node-name,  next,  previous,  up
-@subsubsection Parameter aliases
-@cindex parameter aliases
-@pindex parameter aliases
-
-Parameter aliases are of the form
-@example
-%ALIAS $n       actual parameter
-@end example
-where n is an integer (unique within the label file).
-For example
-
-@example
-%ALIAS  $1              c_v
-%ALIAS  $2              density,ideal_gas,r
-%ALIAS  $3              alpha
-%ALIAS  $4              flow,k_p
-@end example
-
-Assigns four symbolic parameters to the corresponding strings These four
-parameters (@code{$1}--@code{$4}) can then be used for parameter
-passing(@pxref{Parameter passing}).
-
-@node CR aliases, Component aliases, Parameter aliases, Aliases
-@comment  node-name,  next,  previous,  up
-@subsubsection CR aliases
-@cindex CR aliases
-@pindex CR aliases
-
-CR aliases are of the form
-@example
-%ALIAS $an       actual parameter
-@end example
-where n is an integer (unique within the label file).
-For example
-@example
-%ALIAS  $a1  lin           
-@end example
-assigns the symbolic parameter to be lin. This parameter @code{$1} can
-then be used for passing a diofferent cr to the
-component (@pxref{Parameter passing}).
-
-@node Component aliases,  , CR aliases, Aliases
-@comment  node-name,  next,  previous,  up
-@subsubsection Component aliases
-@cindex component aliases
-@pindex component aliases
-
-Component aliases are of the form
-@example
-%ALIAS Component_name   Component_location       
-@end example
-
-An example appears in the following label file fragment
-@example
-...
-%ALIAS  wPipe   CompressibleFlow/wPipe
-%ALIAS  Poly    CompressibleFlow/Poly
-....
-
-@end example
-The two components `wPipe' and `Poly' are both to be found within the
-library `Compressible flow' and the respective subdirectories. This
-follows the @strong{MTT} convention that compound components
-(@pxref{Compound components}) live within a directory of the same name.
- 
-
-@node Parameter passing, Old-style labels (lbl), Aliases, Labels (lbl)
-@comment  node-name,  next,  previous,  up
-@subsection Parameter passing
-@cindex Parameter passing
-@strong{MTT} supports parameter-passing to subsystems within label files
-(@pxref{Labels (lbl)}). Within a subsystem, explicit constitutive
-relationships and parameters (or groups thereof) can be replaced by
-postitional parameters such as @code{$1}, @code{$2} etc.  Although this
-can be done directly, it is recommended that this is done via the alias
-mechanism (@pxref{Parameter aliases}).
-
-In a subsystem
-@code{$i}, is replaced by the ith field of a colon @code{;} separated
-field in the calling label file. This field may include commas @code{,}
-and the four arithmetic operators @code{+}, @code{-}, @code{*} and
-@code{/}.
-
-For example, consider the following example label file fragment (associated with a
-component called Pump:
-@example
-...
-
-%ALIAS  $1              c_v
-%ALIAS  $2              density,ideal_gas,r
-%ALIAS  $3              alpha
-%ALIAS  $4              flow,k_p
-
-%ALIAS  wPipe   CompressibleFlow/wPipe
-%ALIAS  Poly    CompressibleFlow/Poly
-
-% Component type wPipe
-        pipe    none                    c_v;density,ideal_gas,r
-
-% Component type Poly
-        poly            Poly            alpha
-
-@end example
-
-The 4 parameters @code{$1}, @code{$2}, @code{$3}, and @code{$4} can be
-passed from a higher level component as in the following label file
-fragment:
-
-@example
-% Component type Pump
-        comp            none            c_v;rho,ideal_gas,r;alpha;effort,k_c
-        turb            none            c_v;rho,ideal_gas,r;alpha;effort,k_t
-@end example
-
-Thus in component `comp':
-@itemize @bullet
-@item @code{$1} is replaced by c_v
-@item @code{$2} is replaced by rho,ideal_gas
-@item @code{$3} is replaced by alpha
-@item @code{$4} is replaced by effort,k_c
-@end itemize
-whereas in component `turb' the first three parameters are the same but
-@itemize @bullet
-@item @code{$4} is replaced by effort,k_t
-@end itemize
-
-
-
-@node Old-style labels (lbl),  , Parameter passing, Labels (lbl)
-@comment  node-name,  next,  previous,  up
-@subsection Old-style labels (lbl)
-@cindex Old-style labels
-@cindex lbl
-
-Old syle labels (mtt version 2.x) are supported by mtt version
-3.x. However, you are advised to use the new form (@pxref{Labels
-(lbl)}).
-
-Each line of the @code{_label.txt} file is of one of three forms:
-@enumerate
-@item
-Contains three fields (separated by white space) of the form
-@example
-label   field_1   field_2
-@end example
-@item
-Blank
-@item
-Preceded by %
-@end enumerate
-Only the first is noticed by @strong{MTT}; the second and third are for
-providing helpful commenting.
-
-The role of the two information fields depends on the component with the
-corresponding label. In particular the classes of components are:
-@itemize @bullet
-@item
-SS components, @pxref{SS components}.
-@item
-Other components,  @pxref{components}.
-@end itemize
-Named SS component, @pxref{Named SS components} never have labels.
-@menu
-* SS component labels (old-style)::  
-* Other component labels (old-style)::  
-* Parameter passing (old-style)::  
-@end menu
-
-
-@node SS component labels (old-style), Other component labels (old-style), Old-style labels (lbl), Old-style labels (lbl)
-@comment  node-name,  next,  previous,  up
-@subsubsection SS component labels (old-style)
-@cindex SS component labels (old-style)
-In addition to the label there are two information fields,
-@pxref{Labels (lbl)}.
-They correspond to the effort and flow of the components as follows
-@vtable @code
-@item info_field_1
-        effort
-@item info_field_2
-        flow
-@end vtable
-Each of these two fields contains one of the following @emph{attributes}:
-@vtable @code
-@item
-external
-        indicates that the corresponding variable is a system input or
-output
-@item internal
-        indicates that the variable does not appear as a system output;
-        it is an error to label an input in this way.
-@item a number
-        the value of the input; or the value of the (imposed) output
-@item a symbol
-        the symbolic value of the input; or the value of the (imposed) output
-@item unknown
-        used for the SS method of solving algebraic loops. This
-        indicates that the corresponding system input (SS output) is to
-        be chosen to set the corresponding system output (SS input) to zero.
-@item zero
-        used for the SS method of solving algebraic loops. This
-        indicates that the corresponding system output (SS input) is to
-        be set to zero using the variable indicted by the corresponding
-        `unknown' label.
-@end vtable
-
-Some examples are:
-@example
-%Label  field1          field2
-ss1     external        external
-ss2     0               external
-@end example
-
-
-@node Other component labels (old-style), Parameter passing (old-style), SS component labels (old-style), Old-style labels (lbl)
-@comment  node-name,  next,  previous,  up
-@subsubsection Other component labels (old-style)
-@cindex Other component labels (old-style)
-
-In addition to the label there are two information fields,
-@pxref{Labels (lbl)}.
-They correspond to the constitutive relationship 
-(see @pxref{Constitutive relationship} and arguments of the
-component as follows
-@vtable @code
-@item info_field_1
-        constitutive relationship 
-@item info_field_2
-        parameters
-@end vtable
-
-Some examples are:
-@example
-%Armature resistance
-r_a     lin     effort,r_a
-
-%Gearbox ratio
-n       lin     effort,n
-@end example
-
-@strong{MTT} supports parameter-passing to  (@pxref{Parameter passing (old-style)})
-subsystems.
-
-
-@node Parameter passing (old-style),  , Other component labels (old-style), Old-style labels (lbl)
-@comment  node-name,  next,  previous,  up
-@subsubsection Parameter passing (old-style)
-@cindex Parameter passing (old-style)
-@strong{MTT} supports parameter-passing to  (@pxref{Parameter passing (old-style)})
-subsystems within label files (@pxref{Labels (lbl)}). Within a subsystem,
-explicit constitutive relationships and parameters (or groups thereof)
-can be replaced by 
-@code{$1}, @code{$2}, etc.
-
-In a subsystem
-@code{$i}, is replaced by the ith field of a colon @code{;} separated
-field in the calling label file. This field may include commas @code{,}.
-
-For example subsystem ROD contains the following lines in the label
-file:
-@example
-
-%DESCRIPTION    Parameter 1:    length from end 1 to mass centre
-%DESCRIPTION    Parameter 2:    length from end 2 to mass centre
-%DESCRIPTION    Parameter 3:    inertia about mass centre
-%DESCRIPTION    Parameter 4:    mass
-%DESCRIPTION    See Section 10.2 of "Metamodelling"
-
-
-%Inertias
-J       lin     flow,$3
-m_x     lin     flow,$4
-m_y     lin     flow,$4
-
-%Integrate angular velocity to get angle
-th
-
-%Modulated transformers
-s1      lsin    flow,$1
-s2      lsin    flow,$2
-c1      lcos    flow,$1
-c2      lcos    flow,$2
-
-@end example
-
-This can be used in a higher-level lbl (@pxref{Labels (lbl)}) file as:
-@example
-%SUMMARY Pendulum example from Section 10.3 of "Metamodelling"
-
-%Rod parameters
-rod     none    l;l;j;m
-
-@end example
-
-@node Description (desc), Structure (struc), Labels (lbl), Representations
-@comment  node-name,  next,  previous,  up
-@section Description (desc)
-@cindex Description
-@cindex desc
-
-The bond graph can be described textually in LaTeX (.tex) description
-file; this is the only language for this representation. This
-representation is used by the LaTeX language version (@pxref{Language tex
-(abg.tex)}) of the acausal bond graph representation (@pxref{Acausal
-bond graph (abg)}).
-
-@menu
-* Language tex (desc.tex)::     
-@end menu
-
-@node Language tex (desc.tex),  , Description (desc), Description (desc)
-@comment  node-name,  next,  previous,  up
-@subsection Language tex (desc.tex)
-@cindex Language tex (desc.tex)
-This file may contain any LaTeX compatible commands. Any mathematics
-should conform to the AMSmath package.
-
-@node Structure (struc), Constitutive Relationship (cr), Description (desc), Representations
-@comment  node-name,  next,  previous,  up
-@section Structure (struc)
-@cindex Structure
-@cindex struc
-
-The causal bond graph implies a set of equations describing the
-system. The Structure (struc) representation describes the structure of
-these equations in terms of the input, outputs, states and non-states of
-the system.
-
-@menu
-* Language txt (struc.txt)::    
-* Language tex (struc.tex)::    
-* Structure (view)::            
-@end menu
-
-@node Language txt (struc.txt), Language tex (struc.tex), Structure (struc), Structure (struc)
-@comment  node-name,  next,  previous,  up
-@subsection Language txt (struc.txt)
-@cindex Language txt (struc.txt)
-This text tile contains a description of the system structure
-(@pxref{Structure (struc)} with 5 tab-separated columns containing the
-following information:
-@vtable @code
-@item type
-        input, output state or nonstate
-@item   
-index
-        an integer corresponding to the array index
-@item 
-component name
-        the name of the component corresponding to the variable
-@item system name
-        the name of the system containing the component
-@item repetition
-        an integer corresponding to the repetition of a repeated subsystem.
-@end vtable
-
-An example of such a file (corresponding to rc) (@pxref{Quick start}) is:
-@example
-input           1       e1      rc      1
-output          1       e2      rc      1
-state           1       c       rc      1
-@end example
-
-
-@node Language tex (struc.tex), Structure (view), Language txt (struc.txt), Structure (struc)
-@comment  node-name,  next,  previous,  up
-@subsection Language tex (struc.tex)
-@cindex Language tex (struc.tex)
-This LaTeX  (@pxref{LaTeX}) file contains  a description of the system structure
-(@pxref{Structure (struc)} in @code{longtable} format. It is a useful
-item to include in a report(@pxref{Report}).
-
-@node Structure (view),  , Language tex (struc.tex), Structure (struc)
-@subsection Language tex (view)
-@cindex Structure (view)
-@cindex view Structure
-This representation has the standard text view
-(@pxref{Views}).
-
-@node Constitutive Relationship (cr), Parameters, Structure (struc), Representations
-@comment  node-name,  next,  previous,  up
-@section Constitutive relationship (cr)
-@cindex Constitutive relationship
-
-The constitutive relationship (@pxref{Constitutive relationship})
-of a simple component (@pxref{Simple components} is
-defined in the symbolic algebra language Reduce (@pxref{Reduce}).
-The constitutive relationship of a compound components 
-(@pxref{Compound components})
-is implied by the constitutive relationships of its constituent components.
-
-@menu
-* Predefined constitutive relationships::  
-* DIY constitutive relationships::  
-* Unresolved constitutive relationships::  
-* Unresolved constitutive relationships - Octave::  
-* Unresolved constitutive relationships - c++::  
-@end menu
-
-@node Predefined constitutive relationships, DIY constitutive relationships, Constitutive Relationship (cr), Constitutive Relationship (cr)
-@comment  node-name,  next,  previous,  up
-@subsection  Predefined constitutive relationships
-@cindex Predefined constitutive relationships
-
-Some common cr's are predefined by MTT; these are:
-@vtable @code
-@item lin
-        a linear constitutive relationship   
-@item exotherm
-        an exothermic reaction
-@end vtable
-
-@menu
-* lin::                         
-* exotherm::                    
-@end menu
-
-@node lin, exotherm, Predefined constitutive relationships, Predefined constitutive relationships
-@comment  node-name,  next,  previous,  up
-@subsubsection lin
-@findex lin
-The constitutive relationship @code{lin} is predefined for the following
-components.
-@vtable @code
-@item R
-        (one-port) R component
-@item TF
-        transformer
-@item GY
-        gyrator
-@item MTF
-        modulated transformer
-@item MGY
-        modulated gyrator
-@item FMR
-        flow-modulated resistor
-@end vtable
-Lin takes two arguments in the form causality,gain
-@vtable @code
-@item causality
-        the causality (effort or flow) of the @emph{input} to the
-constitutive relationship
-@item gain
-        the gain of the component when the input causality is as
-specified in the first argument.
-@end vtable
-For example the arguments
-@example
-flow,r
-@end example
-given to an R component corresponds to
-@example
-e = rf
-@end example
-if if the input causality is flow
-or
-@example
-f = e/r
-@end example
-if if the input causality is effort.
-
-@node exotherm,  , lin, Predefined constitutive relationships
-@comment  node-name,  next,  previous,  up
-@subsubsection exotherm
-@findex exotherm
-
-@node DIY constitutive relationships, Unresolved constitutive relationships, Predefined constitutive relationships, Constitutive Relationship (cr)
-@comment  node-name,  next,  previous,  up
-@subsection  DIY constitutive relationships
-@cindex DIY constitutive relationships
-You can write your own constitutive relationships using Reduce
-(@pxref{Reduce}). This requires some understanding as to how
-@strong{MTT} represent the elementary system equations
-(@pxref{Elementary system equations}). Looking at the predefined
-constitutive relationships is a good way to get started
-(@pxref{File structure}).
-
-@node Unresolved constitutive relationships, Unresolved constitutive relationships - Octave, DIY constitutive relationships, Constitutive Relationship (cr)
-@subsection Unresolved constitutive relationships
-@cindex Unresolved constitutive relationships
-
-Consider the following CR file.
-@example
-FOR ALL rho,g,vol,h,topt,bott,flowin,press
-LET tktf2(rho,g,vol,h,topt,bott,effort,2,press,effort,1)
-        = tank(rho,g,vol,h,topt,bott,press);      
-@end example
-Assuming that `tank' is not defined in a
-reduce file, MTT will leave it unresolved when generating m or c code.
-
-The resulting function can then be expressed as octave
-(@pxref{Unresolved constitutive relationships - Octave}) or c++ code as
-(@pxref{Unresolved constitutive relationships - c++}) appropriate.
-
-@node Unresolved constitutive relationships - Octave, Unresolved constitutive relationships - c++, Unresolved constitutive relationships, Constitutive Relationship (cr)
-@subsection  Unresolved constitutive relationships - Octave
-@cindex Unresolved constitutive relationships - Octave
-Following the example of the previous section, the unresolved CR `tank'
-can be expressed as an Octave m-file. For example:
-@example
-function p = tank (rho,g,vol,h,topt,bott,press)
-
-  ## usage:  p = tank (vol,h,topt,bott,press)
-  ##
-  ## 
-
-   val = press; zt = topt; zb = bott; 
-   zval = 0.5*(abs(zb+(zt-zb)*val-h)+(zb+(zt-zb)*val-h));
-
-   p = rho*g*zval + 0.5*(1+tanh((press-0.98)*500))*100000;
-
-endfunction
-@end example
-This will be automatically loaded into octave.
-
-@node Unresolved constitutive relationships - c++,  , Unresolved constitutive relationships - Octave, Constitutive Relationship (cr)
-@subsection  Unresolved constitutive relationships - c++
-@cindex Unresolved constitutive relationships - Octave
-Following the example of the previous section, the unresolved CR `tank'
-can be expressed in c++ code. For example:
-@example
-inline double tank(const double rho, 
-		   const double g, 
-		   const double vol, 
-		   const double h, 
-		   const double topt, 
-		   const double bott, 
-		   const double press)
-
-
-  /*  ## usage:  p = tank (vol,h,topt,bott,press)
-    ##
-    ##
-  */
-  double p, val, zval, zt, zb;
-
-  val = press;
-  zt = topt;
-  zb = bott;
-  zval = 0.5 * (abs(zb + (zt - zb) * val - h) + zb + (zt - zb) * val - h);
-
-  p = rho * g * zval + 0.5 * (1 + tanh((press - 0.98) * 500)) * 100000L;
-
-  return p;
-
-@end example
-
-To make sure that this is used in system `model', the model_cr.h file
-must be as follows:
-@example
-// CR headers for system model
-#include "tank.c"
-@end example
-
-@node Parameters, Causal bond graph (cbg), Constitutive Relationship (cr), Representations
-@comment  node-name,  next,  previous,  up
-@section Parameters
-@cindex Parameters
-
-In general, lbl (@pxref{Labels (lbl)}) files contain symbolic
-parameters. @strong{MTT} provides three ways of substituting for these
-parameters:
-@itemize @bullet
-@item
-symbolic substitution
-@item
-symbolic substitution for simplification of displayed equations
-@item
-numeric
-@end itemize
-
-@menu
-* Symbolic parameters (subs.r)::  
-* Symbolic parameters for simplification (simp.r)::  
-* Numeric parameters (numpar)::  
-@end menu
-
-@node Symbolic parameters (subs.r), Symbolic parameters for simplification (simp.r), Parameters, Parameters
-@comment  node-name,  next,  previous,  up
-@subsection Symbolic parameters (subs.r)
-@cindex  Symbolic parameters
-@vindex subs.r
-This file contains reduce statements to symbolically change the
-expressions describing the system.
-For example, a useful set of trig substitutions is:
-@example
-LET cos(~x)*cos(~y) = (cos(x+y)+cos(x-y))/2;
-LET cos(~x)*sin(~y) = (sin(x+y)-sin(x-y))/2;
-LET sin(~x)*sin(~y) = (cos(x-y)-cos(x+y))/2;
-LET cos(~x)^2       = (1+cos(2*x))/2;
-LET sin(~x)^2       = (1-cos(2*x));
-@end example
-
-@node Symbolic parameters for simplification (simp.r), Numeric parameters (numpar), Symbolic parameters (subs.r), Parameters
-@comment  node-name,  next,  previous,  up
-@subsection Symbolic parameters for simplification  (simp.r)
-@cindex  Symbolic parameters for simplification 
-@vindex simp.r
-This file contains reduce statements to symbolically change the
-expressions describing the system. Unlike the subs.r file
-(@pxref{Symbolic parameters (subs.r)}) it does not affect all system
-transformations; only those converting to LaTeX form.
-
-@node Numeric parameters (numpar),  , Symbolic parameters for simplification (simp.r), Parameters
-@comment  node-name,  next,  previous,  up
-@subsection Numeric parameters (numpar)
-@cindex  Numeric parameters
-
-When computing time and frequency responses; or when evaluating
-functions in Octave (@pxref{Octave}); symbolic parameters need numerical
-instantiations. 
-
-The numpar representation provides the relevant @emph{numerical}
-information. It comes in a number of languages:
-@ftable @code
-@item txt
-        a textual description of the parameter values -- this is the
-defining representation (@pxref{Defining representations}).
-@item m
-        readable by @code{octave} a high-level interactive language for numerical
-        computation -- translated by @strong{mtt} from the txt version.
-@item c
-        readable by @code{gcc} a c compiler -- translated by @strong{mtt} from the txt version.
-
-@end ftable
-
-@menu
-* Text form (numpar.txt)::      
-@end menu
-
-@node Text form (numpar.txt),  , Numeric parameters (numpar), Numeric parameters (numpar)
-@comment  node-name,  next,  previous,  up
-@subsubsection Text form (numpar.txt)
-@cindex  Numeric parameters
-This is the textual form of the numerical parameters representation
-(@pxref{Numeric parameters (numpar)}). Lines are either
-@ftable @code
-@item assignment statements
-        variable = value
-@item comments
-        lines beginning with #
-@item commented assignment statements
-        variable = value # comments
-@end ftable
-An example file is:
-@example
-# Numerical parameter file (rc_numpar.txt)
-# Generated by MTT at Mon Jun 16 15:10:17 BST 1997
-
-# %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-# %% Version control history
-# %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-# %% $Id$
-# %% $Log$
-# %% Revision 1.6  2001/10/15 14:29:50  gawthrop
-# %% Added documentaton on  [1:N] style port labels
-# %%
-# %% Revision 1.5  2001/07/23 03:35:29  geraint
-# %% Updated file structure (mtt/bin).
-# %%
-# %% Revision 1.4  2001/07/23 03:25:02  geraint
-# %% Added notes on -ae hybrd, rk4, ode2odes.cc, .oct dependencies.
-# %%
-# %% Revision 1.3  2001/07/13 03:02:38  geraint
-# %% Added notes on #ICD, gnuplot.txt and odes.sg rep.
-# %%
-# %% Revision 1.2  2001/07/03 22:59:10  gawthrop
-# %% Fixed problems with argument passing for CRs
-# %%
-# %% Revision 1.1  2001/06/04 08:18:52  gawthrop
-# %% Putting documentation under CVS
-# %%
-# %% Revision 1.66  2000/12/05 14:20:55  peterg
-# %% Added the c++  anf m CR info.
-# %%
-# %% Revision 1.65  2000/11/27 15:36:15  peterg
-# %% NOPAR --> NOTPAR
-# %%
-# %% Revision 1.64  2000/11/16 14:22:48  peterg
-# %% added UNITS declaration
-# %%
-# %% Revision 1.63  2000/11/03 14:41:08  peterg
-# %% Added PAR and NOTPAR stuff
-# %%
-# %% Revision 1.62  2000/10/17 17:53:34  peterg
-# %% Added some simulation details
-# %%
-# %% Revision 1.61  2000/09/14 17:13:06  peterg
-# %% New options table
-# %%
-# %% Revision 1.60  2000/09/14 17:09:20  peterg
-# %% Tidied up valid name sections
-# %% Tidied up defining represnetations table
-# %% Verion 4.6
-# %%
-# %% Revision 1.59  2000/08/30 13:09:00  peterg
-# %% Updated option table
-# %%
-# %% Revision 1.58  2000/08/01 13:30:19  peterg
-# %% Version 4.4
-# %% updated STEPFACTOR info
-# %% describes octave and OCST interfaces
-# %%
-# %% Revision 1.57  2000/07/20 07:55:44  peterg
-# %% Version 4.3
-# %%
-# %% Revision 1.56  2000/05/19 17:49:17  peterg
-# %% Extended the user defined representation section -- new nppp rep.
-# %%
-# %% Revision 1.55  2000/03/16 13:53:31  peterg
-# %% Correct date
-# %%
-# %% Revision 1.54  2000/03/15 21:22:57  peterg
-# %% Updated to 4.1 -- old style SS no longer supported
-# %%
-# %% Revision 1.53  1999/12/22 05:33:10  peterg
-# %% Updated for 4.0
-# %%
-# %% Revision 1.52  1999/11/23 00:25:11  peterg
-# %% Added the sensitivity reps
-# %%
-# %% Revision 1.51  1999/11/16 04:43:47  peterg
-# %% Added start of sensitivity section
-# %%
-# %% Revision 1.50  1999/11/16 00:30:35  peterg
-# %% Updated simulation section
-# %% Added vector components
-# %%
-# %% Revision 1.49  1999/07/20 23:44:58  peterg
-# %% V 3.8
-# %%
-# %% Revision 1.48  1999/07/19 03:08:33  peterg
-# %% Added documentation for (new) SS lbl fields
-# %%
-# %% Revision 1.47  1999/03/09 01:42:22  peterg
-# %% Rearranged the User interface section
-# %%
-# %% Revision 1.46  1999/03/09 01:18:01  peterg
-# %% Updated for 3.5 including xmtt
-# %%
-# %% Revision 1.45  1999/03/03 02:39:26  peterg
-# %% Minor updates
-# %%
-# %% Revision 1.44  1999/02/17 06:52:14  peterg
-# %% New level formula dor artwork
-# %%
-# %% Revision 1.43  1998/11/25 16:49:24  peterg
-# %% Put in subs.r documentation (was called params.r)
-# %%
-# %% Revision 1.42  1998/11/24 12:24:59  peterg
-# %% Added section on simulation output
-# %% Version 3.4
-# %%
-# %% Revision 1.41  1998/09/02 12:04:15  peterg
-# %% Version 3.2
-# %%
-# %% Revision 1.40  1998/08/27 08:36:39  peterg
-# %% Removed in. methods except Euler anf implicit
-# %%
-# %% Revision 1.39  1998/08/18 10:44:28  peterg
-# %% Typo
-# %%
-# %% Revision 1.38  1998/08/18 09:16:38  peterg
-# %% Version 3.1
-# %%
-# %% Revision 1.37  1998/08/17 16:14:30  peterg
-# %% Version 3.1 - includes documentation on METHOD=IMPLICIT
-# %%
-# %% Revision 1.36  1998/07/30 17:33:15  peterg
-# %% VERSION 3.0
-# %%
-# %% Revision 1.35  1998/07/22 11:00:53  peterg
-# %% Correct date!
-# %%
-# %% Revision 1.34  1998/07/22 11:00:13  peterg
-# %% Version to BAe
-# %%
-# %% Revision 1.33  1998/07/17 19:32:19  peterg
-# %% Added more about aliases
-# %%
-# %% Revision 1.32  1998/07/05 14:21:56  peterg
-# %% Further additions (Carlisle-Glasgow)
-# %%
-# %% Revision 1.31  1998/07/04 11:35:57  peterg
-# %% Strarted new lbl description
-# %%
-# %% Revision 1.30  1998/07/02 18:39:20  peterg
-# %% Started 3.0
-# %% Added alias and default sections.
-# %%
-# %% Revision 1.29  1998/05/19 19:46:58  peterg
-# %% Added the odess description
-# %%
-# %% Revision 1.28  1998/05/14 09:17:22  peterg
-# %% Added METHOD variable to the simpar file
-# %%
-# %% Revision 1.27  1998/05/13 10:03:09  peterg
-# %% Added unknown/zero SS label documentation.
-# %%
-# %% Revision 1.26  1998/04/29 15:12:46  peterg
-# %% Version 2.9.
-# %%
-# %% Revision 1.25  1998/04/12 17:00:26  peterg
-# %% Added new port features: coerced direction and top-level behaviour.
-# %%
-# %% Revision 1.24  1998/04/05 18:27:20  peterg
-# %% This was the 2.6 version
-# %%
-# Revision 1.23  1997/08/24  11:17:51  peterg
-# This is the released  version 2.5
-#
-# %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-# Parameters
-c =     1.0; # Default value
-r =     1.0; # Default value
-# Initial states
-x(1) =  0.0; # Initial state for rc (c)
-@end example
-As usual, @strong{MTT} provides a default text file to be edited by the
-user (@pxref{Text editors}).
-
-@node Causal bond graph (cbg), Elementary system equations, Parameters, Representations
-@comment  node-name,  next,  previous,  up
-@section Causal bond graph (cbg)
-@cindex Causal bond graph (cbg)
-The causal bond graph is the causally complete version of the
-Acausal bond graph (@pxref{Acausal bond graph (abg)}).
-
-To create the causal bond graph of system `sys' in language fig type:
-@example
-mtt sys cbg fig
-@end example
-To create the causal bond graph of system `sys' in language m type:
-@example
-mtt sys cbg m
-@end example
-To view the causal bond graph of system `sys' type:
-@example
-mtt sys cbg view
-@end example
-
-@menu
-* Language fig (cbg.fig)::      
-* Language m (cbg.m)::          
-@end menu
-
-@node Language fig (cbg.fig), Language m (cbg.m), Causal bond graph (cbg), Causal bond graph (cbg)
-@subsection Language fig (cbg.fig) 
-@cindex Language fig (cbg.fig) 
-@pindex Language fig (cbg.fig) 
-The fig file is created by @strong{MTT}. It is identical to the
-corresponding acausal representation (@pxref{Language fig (abg.fig)})
-except that
-@itemize @bullet
-@item
-the new causal strokes are added (using a double thickness line in blue)
-@item
-components that are undercausal are bold and green
-@item
-components that are overcausal are bold and red
-@end itemize
-
-@node Language m (cbg.m),  , Language fig (cbg.fig), Causal bond graph (cbg)
-@comment  node-name,  next,  previous,  up
-@subsection Language m (cbg.m)
-@cindex Language m (cbg.m) 
-@cindex cbonds
-@cindex status
-
-
-The causal bond graph of system `sys' is represented as
- an m file with heading:
-@example
-function [cbonds,status] = sys_cbg
-@end example
-The two outputs of this function are:
-@itemize @bullet
-@item
-cbonds
-@item
-status
-@end itemize
-
-@emph{cbonds} is  a matrix with
-@itemize @bullet
-@item
-one row for each bond
-@item
-the first column contains the arrow-orientated 
-(@pxref{Arrow-orientated causality}) 
-causality of the @emph{effort} variable.
-@item
-the second column contains the arrow-orientated 
-(@pxref{Arrow-orientated causality}) 
-causality of the @emph{flow} variable.
-@end itemize
-
-@emph{status} is  a matrix with
-@itemize @bullet
-@item
-one row for each component
-@item
-the first column contains 1 if the component is overcausal; 0 if the
-component is causally complete and -1 if the component is undercausal.
-@end itemize
-A successful model would therefore have all zeros in the status matrix.
-
-@menu
-* Transformation abg2cbg_m::    
-@end menu
-
-@node Transformation abg2cbg_m,  , Language m (cbg.m), Language m (cbg.m)
-@comment  node-name,  next,  previous,  up
-@subsubsection Transformation abg2cbg_m
-@cindex Transformation abg2cbg_m
-
-This transformation takes the acausal bond graph as an m file 
-(@pxref{Language m (abg.m)}) and transforms it into a causal bond graph in
-m-file format (@pxref{Language m (cbg.m)}).
-
-It is based on the m-function abg2cbg.m which iteratively tries to
-complete causality whilst recursively searching the bond graph
-structure.
-If causality is incomplete, it picks the first acausal dynamic (C or I)
-component, asserts integral causality, and tries again.
-
-This is essentially the sequential causality assignment procedure of
-Karnopp and Rosenberg.
-
-The transformation informs the user of the final status in terms of the
-percentage of causally complete components; a successful model will
-yield 100% here.
-
-@node Elementary system equations, Differential-Algebraic Equations, Causal bond graph (cbg), Representations
-@comment  node-name,  next,  previous,  up
-@section Elementary system equations (ese)
-@cindex Elementary system equations
-
-The elementary system equations are a complete set of assignment statements
-describing the dynamic system corresponding to the bond graph.
-They are in the Reduce (@pxref{Reduce}) language.
-
-Because these are based on a causally complete system, these assignment
-statements are directly soluble by substitution.
-
-Unlike early versions of @strong{MTT}, @strong{MTT} does @emph{not} sort
-the equations in order of solution, but rather leaves them sorted by
-component and subsystem.
-
-These are not supposed to be read by the user, so there is no view
-facility as such. However, you may read these with your favourite text
-editor and, to this end,  helpful comment lines have been added.
-
-Wherever components have an explicit constitutive relationship, the
-corresponding RHS of the equation has a standard form.
-
-@example
-cr(arguments,out_causality,outport,
-        input_1, causality_1, port_1,
-        ....
-        input_i, causality_i, port_i,
-        ....
-        input_n, causality_n, port_n
-        );
-@end example
-where the symbols have the following meaning
-@vtable @code
-@item arguments
-        the constitutive relationship arguments
-@item out_causality
-        the causality (effort or flow) of the output variable
-        (@pxref{Variables})
-@item outport
-        the number (integer) of the output port of the system
-@item input_i
-        the ith input to the component
-@item causality_i
-        the causality (effort or flow) of the ith input variable
-        (@pxref{Variables})
-@item port_i
-        the number (integer) of the ith input port of the system
-@end vtable
-
-An example for a resistor with linear constitutive relationship is:
-@example
-rc_1_bond4_flow := lin(flow,r,flow,1,
-        rc_1_bond4_effort,effort,1
-        );
-@end example
-
-@menu
-* Transformation cbg2ese_m2r::  
-@end menu
-
-@node Transformation cbg2ese_m2r,  , Elementary system equations, Elementary system equations
-@comment  node-name,  next,  previous,  up
-@subsubsection Transformation cbg2ese_m2r
-@cindex Transformation cbg2ese_m2r
-@cindex Structure
-@cindex def.r
-This transformation takes the causal bond graph as an m file 
-(@pxref{Language m (cbg.m)}) and transforms it into elementary system
-equations
-in Reduce (@pxref{Reduce})
-form.
-
-It is based on the m-function cbg2ese.m which iteratively traverses the
-causal bond graph writing equations as it goes.
-
-It also writes out the system structure as the file @file{sys_def.r}.
-
-
-@node Differential-Algebraic Equations, Constrained-state Equations, Elementary system equations, Representations
-@section Differential-Algebraic Equations (dae)
-@cindex Differential-Algebraic Equations
-@cindex DAE
-
-The system differential algebraic equations describe the system dynamics together 
-together with any algebraic constraints. 
-
-They are generated in language @code{lang} for system 
-@code{sys} by:
-@example
-mtt sys dae lang
-@end example
-Valid languages are:
-@vtable @code
-@item r
-        reduce (@pxref{Reduce}).
-@item m
-        m  (@pxref{m}).
-@item view
-        reduce (@pxref{Views}).
-@end vtable
-
-
-There are five sets of variables describing the system:
-@vtable @code
-@item x
-        the system states (corresponding to C and I components with integral
-        causality.
-@item z
-        the system nonstates (corresponding to C and I components with derivative
-        causality.
-@item u
-        the system inputs  (corresponding to SS components
-        with external attribute).
-@item ui
-        the @emph{internal} system inputs (corresponding to SS components
-        with internal attribute) used to solve algebraic loops
-        (@pxref{Algebraic loops}).
-@item y
-        the  system outputs (corresponding to SS components
-        with external attribute).
-        @end vtable
-
-In general there are four sets of equations. The right-hand side of
- each is a function of x, dz/dt,  u and ui and the left hand sides are:
-@enumerate
-@item
-the derivative of x (dx/dt)
-@item
-z
-@item
-w=0 (the algebraic equations)
-@item
-y
-@end enumerate
-
-@menu
-* Differential-Algebraic Equations (reduce)::  
-* Differential-Algebraic Equations (m)::  
-@end menu
-
-@node Differential-Algebraic Equations (reduce), Differential-Algebraic Equations (m), Differential-Algebraic Equations, Differential-Algebraic Equations
-@subsection Language reduce (dae.r)
-@cindex Differential-Algebraic Equations (reduce)
-@cindex dae.r 
-
-The system DAEs (@pxref{Differential-Algebraic Equations})
-are represented in the reduce  (@pxref{Reduce}) language as 
-arrays containing the algebraic expressions for the 
-right hand sides of each set of equations. The arrays are:
-@vtable @code
-@item MTTx
-        x -- the system states (corresponding to C and I components with integral
-        causality.
-
-@item MTTz
-        z -- the system nonstates (corresponding to C and I components with derivative
-        causality.
-@item MTTu
-        u -- the system inputs  (corresponding to SS components
-        with external attribute).
-@item mttv
-        ui -- the @emph{internal} system inputs (corresponding to SS components
-        with internal attribute) used to solve algebraic loops
-        (@pxref{Algebraic loops}).
-@item MTTy
-        y -- the  system outputs (corresponding to SS components
-        with external attribute).
-        @end vtable
-
-@menu
-* Transformation ese2dae_r::    
-@end menu
-
-@node Transformation ese2dae_r,  , Differential-Algebraic Equations (reduce), Differential-Algebraic Equations (reduce)
-@subsubsection Transformation ese2dae_r
-@cindex Transformation ese2dae_r
-@pindex  ese2dae_r
-
-This transformation (@pxref{What is a Transformation?}) 
-uses Reduce (@pxref{Reduce}) to combine the elementary system
-equations (@pxref{Elementary system equations}) with the
-constitutive relationships (@pxref{Constitutive relationship})
-and simplify the result. 
-
-@node Differential-Algebraic Equations (m),  , Differential-Algebraic Equations (reduce), Differential-Algebraic Equations
-@subsection Language m (dae.m)
-@cindex Differential-Algebraic Equations (m)
-@cindex dae.m
-The system DAEs (@pxref{Differential-Algebraic Equations})
-are represented in the m (@pxref{m}) language as  
-two m-functions of the form:
-
-@example
-function resid = sys_dae(dx,x,t)
-function y  = sys_dae(dx,x,t)
-@end example
-Where x is the dae @emph{descriptor} vector and dx its 
-time derivative; t is the time.
-The first function is of a form suitable for solution by DASSL;  
-the second function can then be used to find the coresponding system
-output.
-
-@menu
-* Transformation dae_r2m::      
-@end menu
-
-@node Transformation dae_r2m,  , Differential-Algebraic Equations (m), Differential-Algebraic Equations (m)
-@subsubsection Transformation dae_r2m
-@cindex Transformation dae_r2m
-@pindex  dae_r2m
-
-This transformation (@pxref{What is a Transformation?}) 
-uses Reduce (@pxref{Reduce}) to rewrite the elementary system
-equations (@pxref{Elementary system equations}) in m-file 
-format  (@pxref{m}) . Numerical parameters are declared as global.
-
-
-@node Constrained-state Equations, Ordinary Differential Equations, Differential-Algebraic Equations, Representations
-@section Constrained-state Equations (cse)
-@cindex Constrained-state Equations
-@cindex ODE
-
-The system constrained-state equations describe the system dynamics for
-a special class of systems (see the book for details). The resuting
-equations are of the form:
-@example
-E(x) dx/dt = f(x,u)
-y = g(x,u)
-@end example
-They typically occure where two or more states are constrained to be equal, or
-proportional, to each other. For example, two capacitors in parallel or
-two inertias connected by a stiff shaft.
-
-
-They are generated in language @code{lang} for system 
-@code{sys} by:
-@example
-mtt sys cse lang
-@end example
-Valid languages are:
-@vtable @code
-@item r
-        reduce (@pxref{Reduce}).
-@item m
-        m  (@pxref{m}).
-@item view
-        reduce (@pxref{Views}).
-@end vtable
-
-There are three sets of variables describing the system:
-@vtable @code
-@item x
-        the system states (corresponding to C and I components with integral
-        causality.
-@item u
-        the system inputs  (corresponding to SS components
-        with external attribute).
-@item y
-        the  system outputs (corresponding to SS components
-        with external attribute).
-        @end vtable
-
-In general there are two sets of equations. The right-hand side of
- each is a function of x and  u  and the left hand sides are:
-@enumerate
-@item
-the derivative of x (dx/dt)
-y
-@end enumerate
-
-@menu
-* Constrained-state Equations (reduce)::  
-* Constrained-state Equations (view)::  
-@end menu
-
-@node Constrained-state Equations (reduce), Constrained-state Equations (view), Constrained-state Equations, Constrained-state Equations
-@subsection Language reduce (cse.r)
-@cindex Constrained-state Equations (reduce)
-@cindex cse.r 
-
-The system CSEs (@pxref{Constrained-state Equations})
-are represented in the reduce  (@pxref{Reduce}) language as 
-arrays containing the algebraic expressions for the 
-right hand sides of each set of equations. The arrays are:
-@vtable @code
-@item MTTx
-        x -- the system states (corresponding to C and I components with integral
-        causality.
-@item MTTu
-        u -- the system inputs  (corresponding to SS components
-        with external attribute).
-@item MTTy
-        y -- the  system outputs (corresponding to SS components
-        with external attribute).
-@end vtable
-together with the array containing the elements of the E matrix.
-@menu
-* Transformation dae2cse_r::    
-@end menu
-
-@node Transformation dae2cse_r,  , Constrained-state Equations (reduce), Constrained-state Equations (reduce)
-@subsubsection Transformation dae2cse_r
-@cindex Transformation dae2cse_r
-@pindex  dae2cse_r
-
-This transformation (@pxref{What is a Transformation?}) 
-Reduce (@pxref{Reduce}) to find various Jacobians which are combined to
-find the E matrix and the
-constrained-state equations (@pxref{Constrained-state Equations}).
-
-@node Constrained-state Equations (view),  , Constrained-state Equations (reduce), Constrained-state Equations
-@subsection Language m (view)
-@cindex Constrained-state Equations (view)
-@cindex view Constrained-state Equations
-This representation has the standard text view
-(@pxref{Views}).
-
-@node Ordinary Differential Equations, Descriptor matrices, Constrained-state Equations, Representations
-@section Ordinary Differential Equations
-@cindex Ordinary Differential Equations
-@cindex ODE
-
-The system ordinary differential equations describe the system dynamics.
-
-They are generated in language @code{lang} for system 
-@code{sys} by:
-@example
-mtt sys ode lang
-@end example
-Valid languages are:
-@vtable @code
-@item r
-        reduce (@pxref{Reduce}).
-@item m
-        m  (@pxref{m}).
-@item view
-        reduce (@pxref{Views}).
-@end vtable
-
-There are three sets of variables describing the system:
-@vtable @code
-@item x
-        the system states (corresponding to C and I components with integral
-        causality.
-@item u
-        the system inputs  (corresponding to SS components
-        with external attribute).
-@item y
-        the  system outputs (corresponding to SS components
-        with external attribute).
-        @end vtable
-
-In general there are two sets of equations. The right-hand side of
- each is a function of x and  u  and the left hand sides are:
-@enumerate
-@item
-the derivative of x (dx/dt)
-y
-@end enumerate
-
-@menu
-* Ordinary Differential Equations (reduce)::  
-* Ordinary Differential Equations (m)::  
-* Ordinary Differential Equations (view)::  
-@end menu
-
-@node Ordinary Differential Equations (reduce), Ordinary Differential Equations (m), Ordinary Differential Equations, Ordinary Differential Equations
-@subsection Language reduce (ode.r)
-@cindex Ordinary Differential Equations (reduce)
-@cindex ode.r 
-
-The system ODEs (@pxref{Ordinary Differential Equations})
-are represented in the reduce  (@pxref{Reduce}) language as 
-arrays containing the algebraic expressions for the 
-right hand sides of each set of equations. The arrays are:
-@vtable @code
-@item MTTx
-        x -- the system states (corresponding to C and I components with integral
-        causality.
-@item MTTu
-        u -- the system inputs  (corresponding to SS components
-        with external attribute).
-@item MTTy
-        y -- the  system outputs (corresponding to SS components
-        with external attribute).
-        @end vtable
-
-@menu
-* Transformation cse2ode_r::    
-@end menu
-
-@node Transformation cse2ode_r,  , Ordinary Differential Equations (reduce), Ordinary Differential Equations (reduce)
-@subsubsection Transformation cse2ode_r
-@cindex Transformation cse2ode_r
-@pindex  cse2ode_r
-
-This transformation (@pxref{What is a Transformation?}) 
-uses Reduce (@pxref{Reduce}) to invert the E matrix of the 
-constrained-state equations (@pxref{Constrained-state Equations})
-and simplify the result. 
-
-@node Ordinary Differential Equations (m), Ordinary Differential Equations (view), Ordinary Differential Equations (reduce), Ordinary Differential Equations
-@subsection Language m (ode.m)
-@cindex Ordinary Differential Equations (m)
-@cindex ode.m
-The system ODEs (@pxref{Ordinary Differential Equations})
-are represented in the m (@pxref{m}) language as  
-two m-functions of the form:
-
-@example
-function dx = sys_ODE(x,t)
-function y  = sys_ODE(dx,x,t)
-@end example
-Where x is the ODE @emph{state} vector and dx its 
-time derivative; t is the time.
-The first function is of a form suitable for solution by odesol;  
-the second function can then be used to find the corresponding system
-output.
-
-@menu
-* Transformation ode_r2m::      
-@end menu
-
-@node Transformation ode_r2m,  , Ordinary Differential Equations (m), Ordinary Differential Equations (m)
-@subsubsection Transformation ode_r2m
-@cindex Transformation ode_r2m
-@pindex  ode_r2m
-
-This transformation (@pxref{What is a Transformation?}) 
-uses Reduce (@pxref{Reduce}) to rewrite the
-ordinary differential equations
-(@pxref{Ordinary Differential Equations}) in m-file 
-format  (@pxref{m}) . Numerical parameters are declared as global.
-
-@node Ordinary Differential Equations (view),  , Ordinary Differential Equations (m), Ordinary Differential Equations
-@subsection Language m (view)
-@cindex Ordinary Differential Equations (view)
-@cindex view Ordinary Differential Equations
-This representation has the standard text view
-(@pxref{Views}).
-
-@node Descriptor matrices, Report, Ordinary Differential Equations, Representations
-@section Descriptor matrices (dm)
-@cindex Descriptor matrices
-@cindex dm
-
-The system descriptor matrices A, B, C, D and E describe the 
-@emph{linearised} system dynamics in the form
-@example
-E dx/dt = Ax + Bu
-y = Cx + Du
-@end example
-
-They are generated in language @code{lang} for system 
-@code{sys} by:
-@example
-mtt sys dm lang
-@end example
-Valid languages are:
-@vtable @code
-@item r
-        reduce (@pxref{Reduce}).
-@item m
-        m  (@pxref{m}).
-@item view
-        reduce (@pxref{Views}).
-@end vtable
-
-
-@menu
-* Descriptor matrices (reduce)::  
-* Descriptor matrices (m)::     
-@end menu
-
-@node Descriptor matrices (reduce), Descriptor matrices (m), Descriptor matrices, Descriptor matrices
-@subsection Language reduce (dm.r)
-@cindex Descriptor matrices (reduce)
-@cindex dm.r 
-
-The system  descriptor matrices (@pxref{Descriptor matrices})
-are represented in the reduce  (@pxref{Reduce}) language as 
-arrays containing the four matrices. The arrays are:
-@vtable @code
-@item MTTA
-        A 
-@item MTTB
-        B 
-@item MTTA
-        C
-@item MTTD
-        D
-@item MTTE
-        E
-@end vtable
-
-@node Descriptor matrices (m),  , Descriptor matrices (reduce), Descriptor matrices
-@subsection Language m (dm.m)
-@cindex Descriptor matrices (m)
-@cindex dm.m
-The system descriptor matrices (@pxref{Descriptor matrices})
-are represented in the m (@pxref{m}) language as  
-an m-function of the form:
-
-@example
-function [A,B,C,D,E] = sys_dm
-@end example
-
-System numeric parameters (@pxref{Numeric parameters})
-are passed via global variables defined in the _numpar.m file.
-@c (@pxref{numpar.m}). 
-Thus the system descriptor matrices are
-typically generated in Octave (@pxref{Octave}) as follows:
-
-@example
-sys_numpar
-[A,B,C,D,E] = sys_dm
-@end example
-
-Parameters can be changed from their default values by entering
-their values directly into Octave (@pxref{Octave})  and then invoking
-@code{sys_dm}; for example
-@example
-sys_numpar
-par_1 = 25
-par_2 = par_1 + 3
-[A,B,C,D,E] = sys_dm
-@end example
-
-
-@node Report,  , Descriptor matrices, Representations
-@section Report (rep)
-@cindex Report
-@cindex rep
-
-@strong{MTT} has a report-generator feature. The user specifies the
-report contents in a text file (@pxref{Report (text)}) using an
-appropriate text editor (@pxref{Text editors}).
-
-For example, the report can be viewed by typing
-@example
-mtt system rep view
-@end example
-
-
-@menu
-* Report (text)::               
-* Report (view)::               
-@end menu
-
-@node Report (text), Report (view), Report, Report
-@subsection Language text (rep.txt)
-@cindex Report (text)
-@cindex rep.txt 
-
-The user specifies the report contents in a text file (@pxref{Report
-(text)}) using an appropriate text editor (@pxref{Text editors}).
-The text file contains lines which are either comments (indicated by %)
-or valid @strong{MTT} commands. The report will then contain appropriate
-sections. The following languages are supported by the report generator:
-@ftable @code
-@item m
-        @code{octave} a high-level interactive language for numerical
-        computation.
-@item r
-        @code{reduce}  a high-level interactive language for symbolic
-        computation.
-@item tex
-        @code{latex} a text processor.
-@item ps
-        @code{ghostview} another document viewer.
-@item c
-        @code{gcc} a c compiler.
-@end ftable
-For example:
-@example
-mtt rc abg tex
-mtt rc cbg ps
-mtt rc struc tex
-mtt rc ode tex
-mtt rc sro ps
-mtt rc tf tex
-mtt rc lmfr ps
-@end example
-
-The acausal bond graph (abg) (@pxref{Acausal bond graph (abg)}) with the
-tex language is handled in a special way: the acausal Bond Graph  in
-fig format (@pxref{Language fig (abg.fig)}), the label file (@pxref{Labels (lbl)})
-the description file (@pxref{Description (desc)}), together with
-corresponding subsystems are included in the report. It is recommended
-that the first (non-comment line) in the file should be:
-@example
-mtt <system> abg tex
-@end example
-where @code{<system>} is the name of the (top-level) system.
-
-As usual, @strong{MTT} provides a default text file to be edited by the
-user (@pxref{Text editors}).
-
-In the special case that the first argument to mtt (normally the system)
-is a directory, a default text file is provided which generates a report
-for all systems to be found in that directory tree.
-
-@node Report (view),  , Report (text), Report
-@subsection Language view
-@cindex Report (view)
-@cindex view Report
-This representation has the standard text view
-(@pxref{Views}).
-
-@node Extending MTT, Languages, Representations, Top
-@comment  node-name,  next,  previous,  up
-@chapter Extending MTT
-@cindex Extending MTT
-@cindex Make
-
-@strong{MTT} has a number of built-in mechanisms for the user to extend
-its capabilities. As @strong{MTT} is based on `Make' it is unsurprising
-that some of these  involve the creation of `make files'. 
-
-@menu
-* Makefiles::                   
-* New representations::         
-* Component library ::          
-@end menu
-
-@node Makefiles, New representations, Extending MTT, Extending MTT
-@comment  node-name,  next,  previous,  up
-@section Makefiles
-@cindex Makefiles
-
-If a file called `Makefile' exists in the current directory,
-@strong{MTT} executes it using make before doing anything else. This is
-useful if one of the .txt files contains a reference to, for example, an
-octave function of which @strong{MTT} unaware. Such a function can be
-created using the makefile. An example `Makefile' is
-@example
-# Makefile for the Two link GMV example
-
-all: msdP_tf.m TwoLinkP_obs.m TwoLinkP_sm.m twolinkp_sm.m TwoLinkGMV_numpar.m 
-
-msdP_tf.m: msdP_abg.fig 
-        mtt -q msdP tf m
-
-TwoLinkP_obs.m: TwoLinkP_abg.fig TwoLinkP_lbl.txt
-        mtt -q TwoLinkP obs m
-
-TwoLinkP_sm.m: TwoLinkP_abg.fig TwoLinkP_lbl.txt
-        mtt -q TwoLinkP sm m
-
-twolinkp_sm.m: TwoLinkP_sm.m
-        cp -v TwoLinkP_sm.m twolinkp_sm.m
-
-TwoLinkGMV_numpar.m: TwoLinkGMV_numpar.txt
-        mtt -q TwoLinkGMV numpar m
-@end example
-All of the files in the line stating `all:' are created when
-@strong{MTT} is executed (if they don't already exist).
-
-@node New representations, Component library , Makefiles, Extending MTT
-@comment  node-name,  next,  previous,  up
-@section New representations
-@cindex New representations
-
-It may be convenient to create new representations for @strong{MTT}; in
-particular, it is nice to be able to include the result of some
-numerical or symbolic computations within an @strong{MTT} report
-(@pxref{Report}).
-
-To create a new representation `myrep' in a language `mylang', create a
-file with the name
-@example
-myrep_rep.make
-@end example
-This file must contain text in `make' syntax. It is executed by
-@strong{MTT} and the two arguments `SYS' (the system name) and `LANG'
-(the language) are passed to it by @strong{MTT}. Note that @strong{MTT}
-cannot know of any prerequisites, but these can be explicitly included in
-the makefile (which may include execution of @strong{MTT} itself.
-
-The following example declares the new representation `nppp' which is
-created with the Octave script sys_nppp.m where `sys' is the system
-name.  This needs a number of files (for exaample `sys_ode2odes.out')
-which are themselves created by @strong{MTT}.
-@example
-# -*-makefile-*-
-# Makefile for representation nppp
-# File nppp_rep.make
-
-#Copyright (C) 2000 by Peter J. Gawthrop
-
-all: $(SYS)_nppp.$(LANG)
-
-$(SYS)_nppp.view: $(SYS)_nppp.ps
-        echo Viewing $(SYS)_nppp.ps; ghostview $(SYS)_nppp.ps&
-
-$(SYS)_nppp.ps: $(SYS)_ode2odes.out s$(SYS)_ode2odes.out \
-                $(SYS)_sim.m s$(SYS)_sim.m \
-                $(SYS)_state.m $(SYS)_sympar.m $(SYS)_numpar.m  \
-                s$(SYS)_state.m s$(SYS)_sympar.m s$(SYS)_numpar.m \
-                $(SYS)_sm.m $(SYS)_def.m  s$(SYS)_def.m
-        octave $(SYS)_nppp.m
-
-$(SYS)_ode2odes.out: 
-        mtt -q -c -stdin $(SYS) ode2odes out
-
-s$(SYS)_ode2odes.out:
-        mtt -q -c -stdin -s s$(SYS) ode2odes out
-
-$(SYS)_sim.m:
-        mtt -q -c $(SYS) sim m
-
-s$(SYS)_sim.m:
-        mtt -q -c -s s$(SYS) sim m
-
-$(SYS)_state.m:
-        mtt -q $(SYS) state m
-
-$(SYS)_sympar.m :
-        mtt -q $(SYS) sympar m 
-
-$(SYS)_numpar.m:
-        mtt -q $(SYS) numpar m
-
-s$(SYS)_state.m:
-        mtt -q -s s$(SYS) state m
-
-s$(SYS)_sympar.m :
-        mtt -q -s s$(SYS) sympar m 
-
-s$(SYS)_numpar.m:
-        mtt -q -s s$(SYS) numpar m
-
-$(SYS)_sm.m:
-        mtt -q $(SYS) sm m
-
-$(SYS)_def.m:
-        mtt -q $(SYS) def m
-
-s$(SYS)_def.m:
-        mtt -q -s s$(SYS) def m
-
-@end example
-
-Future extensions of @strong{MTT} will use such representations stored
-in $MTT_REP.
-
-@node Component library ,  , New representations, Extending MTT
-@comment  node-name,  next,  previous,  up
-@section Component library
-@cindex Component library
-@cindex component
-@cindex Component library
-
-If @strong{MTT} does not recognise a component (eg named MyComponent) as
-a simple component (@pxref{Simple components}) or as already existing,
-it searches the library search path $MTT_COMPONENTS
-(@pxref{$MTT_COMPONENTS}) for a directory called MyComponent containing
-MyComponent_lbl.txt. It then copies the @emph{entire} directory into the
-current working directory. Thus, for example, the directory could
-contain MyComponent_desc.tex MyComponent_abg.fig MyComponent_lbl.txt and MyComponent_cr.r in
-addition to MyComponent_lbl.txt.
-
-@c      node   next  prev  up
-@node   Languages, Language tools, Extending MTT, Top
-@chapter Languages
-@cindex Languages
-@pindex Languages
-
-
-@c      node   next  prev  up
-@menu
-* Fig::                         r
-* m::                           
-* Reduce::                      
-* c::                           
-@end menu
-
-These are a number of languages used by @strong{MTT} to implement the
-various representations.
-Each has associated Language tools (@pxref{Language tools}) to
-manipulate and/or view the representation.
-
-@ftable @code
-@item fig
-        @code{Fig} a graphical description language.
-@item m
-        @code{octave} a high-level interactive language for numerical
-        computation.
-@item r
-        @code{reduce}  a high-level interactive language for symbolic
-        computation.
-@item tex
-        @code{latex} a text processor.
-@item dvi
-        @code{xdvi} a document viewer.
-@item ps
-        @code{ghostview} another document viewer.
-@item gdat
-        @code{gnuplot} a data viewer.
-@item c
-        @code{gcc} a c compiler.
-@item sg
-	@code{scigraphica} a plotting package.
-@end ftable
-
-These tools are automatically invoked as appropriate by @strong{MTT};
-but for more advanced use, these tools can be used directly on files
-(with the appropriate suffix) generated by @strong{MTT}.
-
-
-
-@node   Fig, m, Languages, Languages
-@section Fig
-@cindex Fig
-@pindex Fig
-Please see xfig documentation.
-
-@node   m, Reduce, Fig, Languages
-@section m
-@cindex m
-@pindex m
-Please see Octave documentation 
-@ifhtml
-<A HREF="http://www.che.wisc.edu/octave/">Octave</A> documentation.
-<A HREF="http://www.mathworks.com/homepage.html">Matlab</A> documentation.
-@end ifhtml
-
-
-@node   Reduce, c, m, Languages
-@section Reduce
-@cindex Reduce
-@pindex Reduce
-Please see the reduce documentation.
-
-@node c,  , Reduce, Languages
-@comment  node-name,  next,  previous,  up
-@section c
-@cindex c
-@pindex c
-Please see the gcc documentation.
-@node Language tools, Administration, Languages, Top
-@comment  node-name,  next,  previous,  up
-@chapter Language tools
-@cindex  Language tools
-
-@menu
-* Views::                       
-* Xfig::                        
-* Text editors::                
-* Octave::                      
-* LaTeX::                       
-@end menu
-
-@node Views, Xfig, Language tools, Language tools
-@comment  node-name,  next,  previous,  up
-@section Views
-@cindex views
-
-A number of representations (@pxref{Representations}) have a language
-representation which is particularly useful for viewing by the
-user. These views are
-invoked, where appropriate by the command:
-@example
-mtt sys rep view
-@end example
-where @code{sys} is the system name and @code{rep} a corresponding representation.
-
-@node Xfig, Text editors, Views, Language tools
-@comment  node-name,  next,  previous,  up
-@section Xfig
-@cindex Xfig
-
-@node Text editors, Octave, Xfig, Language tools
-@comment  node-name,  next,  previous,  up
-@section Text editors
-@cindex Text editors
-All representations live in text files and thus may be edited using your
-favourite text editor; however, the Fig (@pxref{Fig}) representation is
-pretty meaningless in this form and so you should use Xfig
-(@pxref{Xfig}) for representation in this language.
-
-Its up to you which text editor to use. I recommend emacs, but simpler
-(and less powerful) editors such as xedit, textedit and vi are also ok.
-
-I usually run @strong{MTT} out of an emacs shell window and keep the
-rest of the files in emacs buffers.
-
-@node Octave, LaTeX, Text editors, Language tools
-@comment  node-name,  next,  previous,  up
-@section Octave
-@cindex Octave
-@cindex Matlab
-@cindex m-files
-@cindex Octave interface
-@cindex mtt.m
-
-Octave is a numerical matrix-based language @xref{Top,
-,Octave,Octave,Octave}.  It is similar to Matlab in many ways. In most
-cases, m-files generated by @strong{MTT} can be understood by both
-Matlab and Octave (and no doubt other Matlab lookalikes).
-
- @strong{MTT} provides the octave function @code{mtt}. The octave
- command
-@example
-help mtt
-@end example
-gives the following information:
-@example
- usage:  mtt (system[,representation,language])
-
- Invokes mtt from octave to generate system_representation.language
- Ie equivalent to "mtt system representation language" at the shell
- Representation and language defualt to "sm" and "m" respectively
-
-@end example
-
-Thus for example, if octave is in the directory containing the system
-rc the following session generates the state matrices of the system "rc"
-with the defaut capacitance but resitance r=0.1.
-@example
-octave> mtt("rc");
-Creating rc_rbg.m
-Creating rc_cmp.m
-Creating rc_fig.fig
-Creating rc_sabg.fig
-Creating rc_alias.txt
-Creating rc_alias.m
-Creating rc_sub.sh
-Creating rc_abg.m
-Creating rc_cbg.m (maximise integral causality)
-Creating rc_type.sh
-Creating rc_ese.r
-Creating rc_def.r
-Creating rc_struc.txt
-Creating rc_rdae.r
-Creating rc_subs.r
-Creating rc_cr.txt
-Creating rc_cr.r
-Copying CR SS to here from
-Copying CR lin to here from
-Creating rc_dae.r
-Creating rc_sympar.txt
-Creating rc_sympar.r
-Creating rc_cse.r
-Creating rc_sspar.r
-Creating rc_csm.r
-Creating rc_ode.r
-Creating rc_ss.r
-Creating rc_sm.r
-Creating rc_switch.txt
-0 switches found
-Creating rc_sympars.txt
-Creating rc_sm.m
-Copying rc_sm.m
-octave> mtt("rc","numpar");
-Creating rc_numpar.txt
-Creating rc_numpar.m
-Copying rc_numpar.m
-octave> mtt("rc","sympar");
-Creating rc_sympar.m
-Copying rc_sympar.m
-octave> par = rc_numpar
-par =
-
-  1
-  1
-
-octave> sym = rc_sympar;
-
-octave> par(sym.r) = 0.1;
-octave> [A,B,C,D] = rc_sm(par)
-A = -10
-
-B = 10
-
-C = 1
-
-D = 0
-
-octave> 
-@end example
-generates the data structure rc corresponding the the bond graph of the
-system called `rc'.
-The following octave commands then generate the step reponse and bode
-diagram respectively:
-@example
-step(rc);
-bode(rc);
-@end example
-
-
-@menu
-* Octave control system toolbox (OCST)::  
-@end menu
-
-@node Octave control system toolbox (OCST),  , Octave, Octave
-@comment  node-name,  next,  previous,  up
-@subsection Octave control system toolbox (OCST)
-@cindex Octave
-@cindex toolbox
-@cindex OCST
-@cindex control systems
-@cindex mtt2sys
-
-@strong{MTT} provides an interface to the Octave control system toolbox
-(OCST) using the mfile @code{mtt2sys}. the octave command
-@example
-help mtt2sys
-@end example
-gives the following information.
-@example
- usage:  sys = mtt2sys (Name[,par])
-
- Creates a sys structure for the Octave Control Systems Toolbox
- from an MTT system with name "Name"
- Optional second argument is system parameter list
- Assumes that Name_sm.m, Name_struc.m and Name_numpar.m exist
-@end example
-
-Thus for example, if octave is in the directory containing the system
-rc:
-@example
-rc = mtt2sys("rc");
-@end example
-generates the data structure rc corresponding the the bond graph of the
-system called `rc'.
-The following octave commands then generate the step reponse and bode
-diagram respectively:
-@example
-step(rc);
-bode(rc);
-@end example
-
- 
-
-@node LaTeX,  , Octave, Language tools
-@comment  node-name,  next,  previous,  up
-@section LaTeX
-@cindex LaTeX
-
-LaTeX is a powerful text processor which @strong{MTT} uses to provide
-visual output.
-
-@node Administration, Glossary, Language tools, Top
-@comment  node-name,  next,  previous,  up
-@chapter  Administration
-@cindex  Administration
-
-@menu
-* Software components::         
-* REDUCE setup::                
-* Octave setup::                
-* Paths::                       
-* File structure::              
-@end menu
-
-@node Software components, REDUCE setup, Administration, Administration
-@comment  node-name,  next,  previous,  up
-@section  Software components
-@cindex  Software components
-
-@strong{MTT} is built from a set of readily-available  software tools.
-These are:
-@itemize @bullet
-@item General purpose software tools.
-@item Octave (@pxref{Octave setup})
-@item REDUCE  (@pxref{REDUCE setup})
-@end itemize
-
-The General purpose tools are (these will all be available with a
-standard Linux distribution):
-@vtable @code
-@item sh
-        Bourne shell
-@item gmake
-        Gnu make
-@item gawk
-        Gnu awk
-@item sed
-        Gnu sed
-@item grep
-        Gnu grep
-@item comm
-        Gnu Compare sorted files by line
-@item xfig
-        Figure editor, version 3 or greater.        
-@item fig2dev
-        Fig file conversion, version 3 or greater. 
-@item ghostview
-        postscript viewer
-@item xdvi
-        dvi viewer
-@item dvips
-        dvi to postscript conversion
-@item latex
-        the text processor (LaTeX2e needed)
-@item latex2html
-        converts latex to html
-@item perl
-        needed for latex2html
-@item gnuplot
-        a graph plotting program
-@item gnuscape
-        or other web/html browser such as netscape, Red Baron etc.
-@item gcc
-        GNU c compiler
-@end vtable
-
-@ifhtml
-<A HREF="http://home.pages.de/~GNU/">GNU</A> documentation.
-@end ifhtml
-
-
-
-@node REDUCE setup, Octave setup, Software components, Administration
-@comment  node-name,  next,  previous,  up
-@section  REDUCE setup
-@cindex REDUCE setup
-
-Symbolic algebra is performed by REDUCE, which although not free
-software is the the result of international collaboration. The version I
-use is obtained from:
-@quotation
-ZIB ( http://www.zib.de )
-@end quotation
-@ifhtml
-<A HREF="http://www.rrz.uni-koeln.de/REDUCE/">REDUCE</A> documentation.
-<A HREF="http://www.zib.de">ZIB</A> documentation.
-@end ifhtml
-
-@node Octave setup, Paths, REDUCE setup, Administration
-@comment  node-name,  next,  previous,  up
-@section Octave setup
-@cindex  Octave setup
-
-Octave is available at various web sites including:
-@uref{http://www.octave.org}
-
-@menu
-* .octaverc::                   
-* .oct file dependencies::      
-@end menu
-
-@node .octaverc, .oct file dependencies, Octave setup, Octave setup
-@comment  node-name,  next,  previous,  up
-@subsection .octaverc
-@vindex  .octaverc
-
-
-The @file{.octaverc} file should contain the following lines:
-@example
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%% Startup file for Octave for use with MTT
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-implicit_str_to_num_ok = 1;
-empty_list_elements_ok = 1;
-
-@end example
-
-@node .oct file dependencies,  , .octaverc, Octave setup
-@comment  node-name,  next,  previous,  up Additionally, it is necessary to
-@subsection .oct file dependencies
-Successful compilation of .oct code requires that Octave has been configured
-to use dynamically linked libraries and that the Octave library @code{liboctave}
-and the Octave modified version of @code{libkpathsea} are available on the
- system.
-
-This can be acheived by compiling Octave from the source code, configured
-with the options @code{--enable-shared} and @code{--enable-dl}.
-
-Further information on configuring and installing Octave to handle dynamic
-libraries (DLDs) can be found in the
-@uref{http://www.octave.org/docs.html,Octave documentation}.
-
-
-@node Paths, File structure, Octave setup, Administration
-@comment  node-name,  next,  previous,  up
-@section Paths
-@cindex paths
-@cindex mttrc
-
-There are a number of paths that must be set correctely for @strong{MTT}
-to work. These are normally set up by sourcing the file @code{mttrc} that
-lives in the @strong{MTT} home directory.
-
-@menu
-* $MTTPATH::                    
-* $MTT_COMPONENTS::             
-* $MTT_CRS::                    
-* $MTT_EXAMPLES::               
-* $OCTAVE_PATH::                
-@end menu
-
-@node $MTTPATH, $MTT_COMPONENTS, Paths, Paths
-@comment  node-name,  next,  previous,  up
-@subsection $MTTPATH
-@vindex $MTTPATH
-The environment variable $MTTPATH points to the mtt home directory.
-This is usually @code{/usr/local/lib/mtt}.
-
-@node $MTT_COMPONENTS, $MTT_CRS, $MTTPATH, Paths
-@comment  node-name,  next,  previous,  up
-@subsection $MTT_COMPONENTS
-@vindex $MTT_COMPONENTS
-The environment variable $MTT_COMPONENTS is a colon-separated path
-pointing to directories containing components and subsystems.
-By default
-@example
-MTT_COMPONENTS=.:$MTT_LIB/lib/comp/
-@end example
-but you may wish to add your own component libraries:
-@example
-MTT_COMPONENTS=my_library_path:$MTT_COMPONENTS
-@end example
-
-@node $MTT_CRS, $MTT_EXAMPLES, $MTT_COMPONENTS, Paths
-@comment  node-name,  next,  previous,  up
-@subsection $MTT_CRS
-@vindex $MTT_CRS
-The environment variable $MTT_CRS is a colon-separated path
-pointing to directories containing constitutive relationships.
-By default
-@example
-MTT_CRS=$MTTPATH/lib/cr
-@end example
-but you may wish to add your own component libraries:
-@example
-MTT_CRS=my_cr_path:$MTT_CRS
-@end example
-
-@node $MTT_EXAMPLES, $OCTAVE_PATH, $MTT_CRS, Paths
-@comment  node-name,  next,  previous,  up
-@subsection $MTT_EXAMPLES
-@vindex $MTT_EXAMPLES
-The environment variable $MTT_EXAMPLES is a colon-separated path
-pointing to directories containing EXAMPLES and subsystems.
-By default
-@example
-MTT_EXAMPLES=$MTTPATH/lib/examples
-@end example
-but you may wish to add your own component libraries:
-@example
-MTT_EXAMPLES=my_examples_path:$MTT_EXAMPLES
-@end example
-
-@node $OCTAVE_PATH,  , $MTT_EXAMPLES, Paths
-@comment  node-name,  next,  previous,  up
-@subsection $OCTAVE_PATH
-@vindex $OCTAVE_PATH
-
-The @code{$OCTAVE_PATH} path must include the relevant paths for mtt to
-work properly. In particular, it must include:
-@example
-$MTTPATH/trans/m
-$MTTPATH/lib/comp/simple
-$MTTPATH/lib/comp/compound
-@end example
-
-@node File structure,  , Paths, Administration
-@comment  node-name,  next,  previous,  up
-@section  File structure
-@cindex File structure
-The recommended installation of @strong{MTT} uses the following
-directory structure with corresponding contents. Normally, each of the
-listed directories is a subdirectory of @file{/usr/local}. The directory
-@code{mtt} is pointed to by $MTTPATH (@pxref{$MTTPATH}).
-
-@vtable @file
-@item mtt/bin
-        This is the home directory for @strong{MTT}. @strong{MTT}  itself lives
-        here along with @file{mttrc}.
-@item mtt/bin/trans
-        The transformations executed by @strong{MTT}.
-@item mtt/bin/trans/m
-        The  @code{m-files} associated with the transformations.
-@item mtt/bin/trans/awk
-        The  @code{awk} scripts associated with the transformations.
-@item mtt/lib
-        The place for components, examples and CRs which will be updated.
-@item mtt/lib/comp/simple
-@cindex simple components
-        The  @code{m-files} defining the simple components.
-@cindex compound components
-@item mtt/lib/comp/compound
-        The  @code{m-files} defining the compound components.
-@item mtt/lib/cr/r
-        constitutive relationship definitions
-@item mtt/lib/examples
-        Some examples. 
-@item mtt/examples/metamodelling
-        Examples from the book.
-@item mtt/doc
-        The  documentation files for @strong{MTT}.
-@item mtt/doc/Examples
-        Examples used in the documentation.
-@end vtable
-
-@node Glossary, Index, Administration, Top
-@comment  node-name,  next,  previous,  up
-@unnumbered Glossary
-@printindex fn
-
-@node Index,  , Glossary, Top
-@comment      node-name, next,       previous, up
-@unnumbered Index
-@printindex cp
-
-@contents
-
-@bye
-
-

Index: mttroot/mtt/lib/rep/sfun_rep.sh
==================================================================
--- mttroot/mtt/lib/rep/sfun_rep.sh
+++ mttroot/mtt/lib/rep/sfun_rep.sh
@@ -1377,10 +1377,10 @@
 
 
 
 ### main program
 
-set_debug 0
-check_for_valid_input "$*"
+#set_debug 0
+#check_for_valid_input "$*"
 
 OPTS="$1" SYS="$2" REP="$3" LANG="$4" make $make_debug -f ${MTT_REP}/sfun_rep/Makefile ${2}_${3}.${4}
 exit 0