File: ChangeLog

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2008-07-02 08:46  grahamdennis

	* trunk/xmds-devel/source/xmds_complex.h,
	  trunk/xpdeint/xpdeint/includes/xpdeint_complex.h: xmds & xpdeint:
	  CRITICAL BUG FIX to complex arithmetic.
	  
	  The unary negation operator was incorrectly overloaded to modify
	  the complex variable that was being negated.
	  Note that this bug only applies to the 'complex' class and not to
	  the 'fftw_complex' class.
	  
	  In more detail: Whenever code is written that requires the
	  negative of a complex variable (of type complex,
	  this bug is not present for the fftw_complex type), instead of
	  simply returning the negative of that variable,
	  the variable itself was modified to be the negative as well.
	  Consider the following code:
	  
	  complex a = 7.0 + 3*i; // a = 7 + 3i, everything is fine
	  complex b = -a;
	  // b = -7 - 3i as expected, but additionally
	  // a = -7 - 3i
	  
	  Note that this bug will not be triggered by a subtraction
	  operation. b = a-c will have been correct.
	  Additionally, if the complex number is part of a larger
	  expression, this bug will only matter if the
	  complex variable is first. i.e. z = -0.5*a would have been fine,
	  but z = -a*0.5 would not. Note that
	  the variable 'i' was not affected by this because it is defined
	  as 'const', so expressions like
	  z = -i*a were safe. Likewise any other 'const' complex constants
	  would have also been safe.
	  
	  From what I can gather from the repository logs, this bug has
	  been present in xmds (and xpdeint) since the original
	  commit, i.e. February 3, 2003. This bug could have affected any
	  simulation since then, though you would need
	  to be unlucky to hit it. Most simulations would be fine as the
	  evolution equations are typically written in the form:
	  dphi_dt = L[phi] + stuff;
	  The L[phi] term will prevent the unary negation operation from
	  being called. Unfortunately, some simulations will have hit
	  this. The only example script that hit this was the xmds
	  van_der_pol.xmds script where its evolution equations are:
	  dx_dt = xdot;
	  dxdot_dt = -x - epsilon*(x*x - 1)*xdot;
	  
	  The '-x' term in the second line triggered the bug, but the
	  calculation of the x*x term is safe as although x is a complex
	  variable, its imaginary part is zero, and the memory that 'x' is
	  stored in is immediately overwritten after this line with
	  the value of 'dx_dt * _step', and so although this simulation did
	  hit the bug, due to a coincidence it did not affect the results.
	  
	  This update should be considered critical and anyone following
	  the development versions should update both xmds and xpdeint.
	  
	  Joe: Can we do an xmds-1 release?

2008-04-22 03:49  andyferris

	* trunk/xmds-devel/source/xmds_moment_group.cc,
	  trunk/xmds-devel/source/xmds_output.cc: xmds: Output fixes.
	  * Now when using binary and the -o option the .dat files are
	  stored with the prefix given by -o and not the one in the .xmds
	  file.
	  * Removed a few compiler warnings by removing excess arguments
	  passed to printf.

2008-04-16 23:59  andyferris

	* trunk/xmds-devel/source/xsil2graphics.cc: xsil2graphics: Allow
	  multiple input file names.
	  e.g. "xsil2graphics *.xsil" now works.

2008-04-11 05:40  paultcochrane

	* trunk/xmds-devel/admin/cygwin/xmds.README: Updated the version
	  information for building and installing xmds for cygwin

2008-04-11 05:24  paultcochrane

	* trunk/xmds-devel/admin/cygwin/xmds-1.6.5-1.sh: Updated the cygwin
	  configure options to enable fftw3

2008-04-11 04:32  paultcochrane

	* trunk/xmds-devel/admin/cygwin/xmds-1.6.5-1.sh: Added the generic
	  xmds build script for building on cygwin. This hasn't yet
	  been adjusted for xmds-specfics yet.

2008-04-11 04:29  paultcochrane

	* trunk/xmds-devel/admin/cygwin/setup.hint: Added the setup.hint
	  file for use with cygwin's setup.exe

2008-04-11 04:28  paultcochrane

	* trunk/xmds-devel/admin/cygwin/xmds.README: Added the cygwin
	  readme file for the cygwin xmds package.

2008-04-11 04:19  paultcochrane

	* trunk/xmds-devel/admin/cygwin: Added a cygwin subdirectory for
	  cygwin-port related files

2008-04-09 10:55  paultcochrane

	* ., trunk/xmds-devel/admin/xmds-1.6.5-r1.ebuild: Added the Gentoo
	  ebuild used to build xmds on that distro

2008-04-09 10:44  paultcochrane

	* ., trunk/xmds-devel/admin/xmds-1.6.5-Makefile_DATA.patch,
	  trunk/xmds-devel/configure.in,
	  trunk/xmds-devel/xmds-1.6.5-Makefile_DATA.patch: Added patch to
	  the wrong directory, duh.

2008-04-09 10:42  paultcochrane

	* ., trunk/xmds-devel/configure.in:

2008-04-09 10:41  paultcochrane

	* ., trunk/xmds-devel/configure.in: - replaced hard tabs with
	  spaces
	  - added a coda for emacs and vim so that formatting is
	  automatically
	  consistent in these editors
	  - indented the code a bit more consistently

2008-04-09 10:34  paultcochrane

	* trunk/xmds-devel/xmds-1.6.5-Makefile_DATA.patch: Added the actual
	  patch to Makefile.am which I used to build the Fedora 8 RPM

2008-04-09 09:05  paultcochrane

	* trunk/xmds-devel/admin/Makefile_in_update.patch,
	  trunk/xmds-devel/admin/aclocal_update.patch,
	  trunk/xmds-devel/admin/configure_update.patch: Added the patches
	  which enabled me to get xmds to build on openSuSE's
	  build service

2008-04-09 00:51  paultcochrane

	* trunk/xmds-devel/admin/xmds_suse.spec: Added a spec file which
	  enables xmds to build SuSE Linux RPMs. This was
	  developed with the help of the openSuSE build service:
	  http://build.opensuse.org

2008-04-09 00:42  paultcochrane

	* trunk/xmds-devel/source/xmds_integrate_ark45.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark89.cc,
	  trunk/xmds-devel/source/xmds_simulation.h,
	  trunk/xmds-devel/source/xsil2graphics.cc: Applied patch courtesy
	  of Rafael Laboissiere from Debian which fixes a
	  build error when using gcc 4.3 (yay the Debian automated build
	  service!)

2008-04-08 05:55  paultcochrane

	* trunk/xmds-devel/admin/xmds.spec: Reverted incorrect
	  BuildRequires option accidentally commited in the
	  last commit

2008-04-08 05:42  paultcochrane

	* trunk/xmds-devel/admin/xmds.spec: Corrected the spec file's
	  release number information

2008-04-07 09:54  paultcochrane

	* trunk/xmds-devel/source/xsil_field.cc: Added a title to plots
	  generated with the xsil2graphics '-p' option.
	  This effectively closes the long overdue ticket (feature request
	  tracker
	  item) #1600312.

2008-04-07 09:19  paultcochrane

	* trunk/xmds-devel/admin/Makefile_DATA.patch: Added (for future
	  reference) the patch, used to get the 1.6.5 xmds version
	  able to build the rpm properly, to the repository

2008-04-07 09:09  paultcochrane

	* trunk/xmds-devel/admin/xmds.spec: Updates to get the rpm spec
	  file buildign again. A patch had to be added
	  to modify the root Makefile.am in order to fix a problem where we
	  were
	  using automake 1.10 version features, however rpmbuild requires
	  version
	  automake version 1.6.
	  Updated the file list, and made it more generic (replaced "xmds"
	  with
	  %{name}-%{version} which is more flexible.
	  Updated the changelog and header appropriately

2008-03-28 02:23  grahamdennis

	* trunk/xmds-devel/source/xmds_integrate_ex.cc: xmds (not
	  xpdeint!): Using OpenMP with an EX algorithm was broken. Oops.
	  
	  This bug is not present in xpdeint.

2008-03-27 03:15  grahamdennis

	* trunk/xmds-devel/source/xmds_simulation.cc: xmds (not xpdeint!):
	  Fixed bug Paul introduced in r1760 where the output filename
	  would be determined by the simulation name, not by the filename
	  specified in the
	  <output> tag.

2008-03-18 16:07  paultcochrane

	* trunk/xmds-devel/admin/xmdsReleaseProcedure.pod: Added a note of
	  where one can pick up a copy of xsltproc for those who
	  don't have Gnome installed by default

2008-03-18 16:03  paultcochrane

	* trunk/xmds-devel: Added ChangeLog to svn:ignore list

2008-03-18 15:54  paultcochrane

	* trunk/xmds-devel/ChangeLog: Removed the ChangeLog file from the
	  repository: it's now automatically
	  generated. See admin/xmdsReleaseProcedure.pod for details of how
	  to generate
	  this file.

2008-03-18 15:53  paultcochrane

	* trunk/xmds-devel/admin/xmdsReleaseProcedure.pod: Updated the
	  release procedure text to reflect that ChangeLog is now
	  automatically generated. Also tidied up the text a little.

2008-03-18 15:50  paultcochrane

	* trunk/xmds-devel/admin/xmdsReleaseProcedure.pod: Having thought
	  about the ChangeLog usage somewhat more (and having noticed
	  that we actually have a NEWS file in the distro), we should
	  really use
	  ChangeLog as we had been using it, and that's essentially as a
	  list of
	  svn log entries hence effectively reverting Joe's FullChangeLog
	  change of
	  quite a while ago.

2008-03-18 15:48  paultcochrane

	* trunk/xmds-devel/NEWS: Added recent news items to the news file
	  (duh, paul...)

2008-03-18 15:41  paultcochrane

	* trunk/xmds-devel/README, trunk/xmds-devel/configure.in,
	  trunk/xmds-devel/source/Doxyfile: Updated the version information
	  to 1.6.6 (we've already released 1.6.5)

2008-03-18 15:29  paultcochrane

	* trunk/xmds-devel/examples, trunk/xmds-devel/source: Updated the
	  svn:ignore property to ignore .exe (for cygwin) and Makefiles

2008-03-18 15:25  paultcochrane

	* trunk/xmds-devel/examples/Makefile.am: Updated the clean target
	  within the examples/ subdirectory

2008-03-18 15:24  paultcochrane

	* trunk/xmds-devel/source/kissdom.cc,
	  trunk/xmds-devel/source/main.cc,
	  trunk/xmds-devel/source/xmds_arg.cc,
	  trunk/xmds-devel/source/xmds_arg_element.cc,
	  trunk/xmds-devel/source/xmds_argv.cc,
	  trunk/xmds-devel/source/xmds_breakpoint.cc,
	  trunk/xmds-devel/source/xmds_element.cc,
	  trunk/xmds-devel/source/xmds_field.cc,
	  trunk/xmds-devel/source/xmds_filter.cc,
	  trunk/xmds-devel/source/xmds_globals.cc,
	  trunk/xmds-devel/source/xmds_integrate.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark45.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark45ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark45ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark89.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark89ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark89ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk4.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk4ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk4ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk9.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk9ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk9ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_si.cc,
	  trunk/xmds-devel/source/xmds_integrate_siex.cc,
	  trunk/xmds-devel/source/xmds_integrate_siip.cc,
	  trunk/xmds-devel/source/xmds_moment_group.cc,
	  trunk/xmds-devel/source/xmds_output.cc,
	  trunk/xmds-devel/source/xmds_segment.cc,
	  trunk/xmds-devel/source/xmds_sequence.cc,
	  trunk/xmds-devel/source/xmds_simulation.cc,
	  trunk/xmds-devel/source/xmds_utils.cc,
	  trunk/xmds-devel/source/xmds_vector.cc,
	  trunk/xmds-devel/source/xmds_vector_element.cc,
	  trunk/xmds-devel/source/xml_basics.cc,
	  trunk/xmds-devel/source/xml_parser.cc,
	  trunk/xmds-devel/source/xsil2graphics.cc,
	  trunk/xmds-devel/source/xsil_field.cc: Updated the copyright date
	  information

2008-03-18 13:32  paultcochrane

	* trunk/xmds-devel/configure.in: When building with --with-user,
	  the examples were set to be installed in
	  /usr/local/share/doc which of course a user can't do. This
	  updates the
	  location of the installed example files to $HOME/doc/xmds, which
	  hopefully
	  is a much better location, and will avoid users getting nasty
	  errors when
	  installing xmds locally.

2008-03-04 06:36  grahamdennis

	* trunk/xmds-devel/source/xmds_complex.h,
	  trunk/xpdeint/source/FieldElement.tmpl,
	  trunk/xpdeint/source/ScriptElement.tmpl: Add in operator
	  overloads for the complex type multiplied by longs...
	  ... and don't multiply them by longs when integrating over
	  integer-valued dimensions (in xpdeint).

2008-02-26 10:08  paultcochrane

	* trunk/xmds-devel/admin/release_notification.txt: Added the
	  release notification text used to inform the various newsgroups
	  about the current release.

2008-02-26 03:35  joehope

	* trunk/xmds-devel/MANIFEST: Update for new version.

2008-02-26 03:31  joehope

	* trunk/xmds-devel/ChangeLog, trunk/xmds-devel/README: Updating for
	  new version release.

2008-02-06 21:48  paultcochrane

	* trunk/xmds-devel/ChangeLog: Removed some old ChangeLog entries
	  which got added in for some reason.
	  Added a summary of recent changes to repository. Would others be
	  able to
	  summarise their changes here as well? Please?

2008-02-06 21:43  paultcochrane

	* trunk/xmds-devel/source/xmds_output.cc,
	  trunk/xmds-devel/source/xmds_sequence.cc,
	  trunk/xmds-devel/source/xmds_simulation.cc: One can now specify
	  the output data filename at the command line with the
	  -o/--outfilename simulation command line argument. This provides
	  the
	  feature requested by Christopher Coleman-Smith on the xmds-user
	  mailing
	  list.

2008-02-06 21:37  paultcochrane

	* trunk/xmds-devel/source/xsil2graphics.cc,
	  trunk/xmds-devel/source/xsil_field.cc,
	  trunk/xmds-devel/source/xsil_field.h: Implemented automatically
	  generating matlab/octave plot commands when
	  running xsil2graphics. When the user uses the -p (--plot) command
	  line
	  argument to xsil2graphics (and when the number of independent
	  variables is
	  either 1 or 2) then basic plotting output is generated.
	  This commit also corrects some typos in the help output of
	  xsil2graphics,
	  updates some error messages, and adds some comments and todo
	  items.

2008-02-06 21:30  paultcochrane

	* trunk/xmds-devel/examples/Makefile.am: Extending the clean target
	  to clean up more files.

2008-02-06 07:03  grahamdennis

	* trunk/xmds-devel/source/xmds_breakpoint.cc: xmds: Revert Paul's
	  r1607 commit.
	  
	  In Paul's commit, he changed the order of a couple of operations.
	  This caused
	  the first coordinate value not to be written, and instead the
	  second was the
	  first written, and the end point was written when it shouldn't
	  be. The upshot
	  of this is that you could not use the XSIL file for initialising
	  another
	  simulation. At least I know my sanity-checking code for XSIL
	  loading works.
	  
	  While I'm at it, make sure that the revision number for XMDS is
	  put in
	  breakpoint XSIL files as well as XSIL files created from moment
	  groups.

2008-01-31 06:00  michaelhush

	* trunk/xmds-devel/ChangeLog, trunk/xmds-devel/examples/fibre.xmds,
	  trunk/xmds-devel/source/xmds_integrate_ark45.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark89.cc: Fixed error
	  estimation in adaptive algorithms so zero valued functions no
	  longer cause nan errors and thus time steps

2008-01-30 07:19  gmcmanus

	* trunk/xmds-devel/BUGS, trunk/xmds-devel/source/main.cc,
	  trunk/xmds-devel/source/xmds_breakpoint.cc,
	  trunk/xmds-devel/source/xmds_output.cc: fix bug: properly escape
	  strings when outputting xmds file
	  
	  - we need to escape backslashes \ and quotation marks ",
	  which we do with escapeStringC on sim{Header,Footer,Body}Text
	  (these are only used for source generation, so they are the right
	  variables to escape).
	  We no longer escape quotation marks in simulationText.
	  
	  - we also need to avoid percentage signs, so generate code like:
	  printf("%s", "...");
	  instead of
	  printf("...");
	  
	  - similar bugs probably exist, so create a BUGS file and note it.

2008-01-30 07:18  gmcmanus

	* trunk/xmds-devel/source/main.cc: new function in main:
	  escapeStringC
	  
	  - given a string, escape backslashes and quotation marks in the
	  string
	  with a backslash.
	  This allows the string to be read properly in C source.
	  
	  - To do: for strict correctness, perhaps more characters should
	  be escaped
	  (e.g. non-printable characters)?

2008-01-30 06:53  grahamdennis

	* trunk/xmds-devel/source/xmds_integrate_rk4.cc: Increase the order
	  of the cross-propagation integration from 2nd order to 4th by
	  calculating midpoints more correctly.

2008-01-29 23:21  paultcochrane

	* trunk/xmds-devel/source/Doxyfile: The api docs don't get dumped
	  into the documentation directory of xmds.org
	  anymore. So put them locally.

2008-01-29 22:06  paultcochrane

	* trunk/xmds-devel/source/xmds_output.cc: Removed a lot of
	  auto-generate code which produced only commented out code.

2008-01-29 04:42  gmcmanus

	* trunk/xmds-devel/examples/infinite.xmds: New example: ODE with
	  singularity in derivative
	  
	  - to test min_time_step feature

2008-01-29 04:42  gmcmanus

	* trunk/xmds-devel/source/xmds_integrate.cc,
	  trunk/xmds-devel/source/xmds_integrate.h,
	  trunk/xmds-devel/source/xmds_integrate_ark45.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark89.cc: min_time_step:
	  halt adaptive integration pass if time step becomes too small
	  
	  - by default, have a min_time_step of 1e-13
	  - the checking can be disabled if min_time_step = 0
	  
	  - Implemented by adding the writeStepCheckingCode method to
	  xmdsIntegrate.
	  This is not ideal, but reduces code duplication;
	  see comments in the source.
	  - we only check the size of the step when the error is
	  intolerable,
	  so there is no cost when the integration is running successfully.
	  
	  - writeHaltCode can now print more verbose warning messages;
	  however, the caller needs to be careful about escaped characters.
	  It's easiest to avoid them altogether rather than double-quoting
	  them.
	  A function to quote raw strings with C escape codes would be
	  useful.
	  
	  - also, use doxygen style comments in xmds_integrate.h

2008-01-29 04:42  gmcmanus

	* trunk/xmds-devel/source/xmds_integrate.cc,
	  trunk/xmds-devel/source/xmds_integrate.h: xmdsIntegrate: separate
	  function to write halting code
	  
	  This is in preparation of the minimum step-size check,
	  and leads to less code duplication in the generation code.
	  It does lead to more code duplication in the generated code,
	  but in non-critical areas (it is code to halt the integration).

2008-01-29 04:41  gmcmanus

	* trunk/xmds-devel/source/xmds_integrate.cc: more accurate comment
	  for non-finite number check
	  
	  In most simulations, the components of the main vector
	  are coupled together. So even if there is no Fourier transform,
	  the components are quickly mixed together.
	  
	  Also, we check for any non-finite numbers (not just NaNs).

2008-01-29 04:40  gmcmanus

	* trunk/xmds-devel/examples/nan.xmds: remove left over comment in
	  nan example

2008-01-26 23:07  paultcochrane

	* trunk/xmds-devel/Makefile.am: Improvement of the make examples
	  target so that we can finally build
	  the examples properly on OpenSolaris.

2008-01-26 22:55  paultcochrane

	* trunk/xmds-devel/Makefile.am: Updated the base Makefile.am to
	  build the examples directory with the same
	  interface as previously. make examples and make examples-clean
	  works as
	  expected.

2008-01-26 22:52  paultcochrane

	* trunk/xmds-devel/configure.in: Added examples/Makefile to list of
	  Makefiles to be automatically built

2008-01-26 22:52  paultcochrane

	* trunk/xmds-devel/examples/Makefile.am: Added an automake Makefile
	  template to build the examples scripts.

2008-01-26 22:51  paultcochrane

	* trunk/xmds-devel/examples: Updated the svn:ignore property on the
	  examples/ subdirectory

2008-01-26 22:50  paultcochrane

	* trunk/xmds-devel/examples/Makefile: Removed examples Makefile as
	  this is now created by a Makefile.am (autoconf
	  tools)

2008-01-25 02:47  gmcmanus

	* trunk/xmds-devel/source/xmds_integrate_ark45.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark89.cc: fix bug: check
	  to halt before resetting the segment in adaptive integration
	  
	  - otherwise, the segment may always be reset to before a NaN,
	  which would then never be detected and the integration would
	  enter an infinite loop.

2008-01-25 02:06  joehope

	* trunk/xmds-devel/Makefile.am: Fix for namespace issue with
	  certain compilers.

2008-01-25 01:04  gmcmanus

	* trunk/xmds-devel/source/xmds_integrate_siip.cc: fix syntax error
	  in generated code for SIIP
	  
	  - C requires a statement after every label,
	  so we insert an empty statemeny after the _SEGMENT*_END label
	  - This bug was revealed by always printing the labels.
	  Previously it was a bug when using both SIIP and runtime_limit.

2008-01-25 00:25  gmcmanus

	* trunk/xmds-devel/source/xmds_integrate.cc: only print default
	  value message if verbose
	  
	  - fix indentation too

2008-01-25 00:22  gmcmanus

	* trunk/xmds-devel/Makefile.am: added nan.xmds to examples in
	  Makefile.am
	  
	  - removed trailing and leading spaces too

2008-01-24 23:44  gmcmanus

	* trunk/xmds-devel/examples/nan.xmds: example that has a NaN in the
	  derivative

2008-01-24 23:43  gmcmanus

	* trunk/xmds-devel/source/xmds_integrate.cc: read halt_non_finite
	  tag in xmdsIntegrate
	  
	  - the task of reading a bool from a tag,
	  reading the list<bool> and printing messages accordingly
	  should be a separate function

2008-01-24 23:43  gmcmanus

	* trunk/xmds-devel/source/xmds_integrate.cc,
	  trunk/xmds-devel/source/xmds_integrate.h: Add the non-finite
	  number checking and halting code
	  
	  - modify writeHaltCheckingCode to check the main vector for
	  non-finite numbers
	  
	  - non-finite numbers are the infinities (e.g. 1/0)
	  and NaN (e.g. 0/0).
	  - The Fourier transform will mix together all the elements
	  of the main vector, so we only need to check one component
	  - we exit the same as if overtime
	  - print useful notices when stopping the integration
	  
	  - new parameter in xmdsIntegrate: myHaltNonFinite (set to false
	  for now)

2008-01-24 23:42  gmcmanus

	* trunk/xmds-devel/source/xmds_integrate.cc,
	  trunk/xmds-devel/source/xmds_integrate.h,
	  trunk/xmds-devel/source/xmds_integrate_ark45.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark89.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk4.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk9.cc,
	  trunk/xmds-devel/source/xmds_integrate_siex.cc,
	  trunk/xmds-devel/source/xmds_integrate_siip.cc: prepare for check
	  to halt on non-finite numbers
	  
	  - generalize writeRuntimeCheckingCode to writeHaltCheckingCode,
	  and slightly rewrite it.
	  - print a notice if the simulation is halted prematurely
	  - in non-adaptive integration, move halt checks to just before
	  samples.
	  - in adaptive integration, move halt checks to end of time-step
	  loop.
	  - write SEGMENT*_END label unconditionally

2008-01-24 23:42  gmcmanus

	* trunk/xmds-devel/source/xmds_integrate_ark45.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark89.cc: small
	  refactoring: use && instead of nested ifs

2008-01-24 23:41  gmcmanus

	* trunk/xmds-devel/source/xmds_integrate.cc: improve verbose
	  messages
	  
	  - more consistency
	  - fix spelling errors
	  - fix spacing

2008-01-24 23:41  gmcmanus

	* trunk/xmds-devel/source/xmds_integrate_rk4.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk4ex.cc: indentation to
	  shorten lines

2008-01-22 06:31  gmcmanus

	* trunk/xmds-devel/source/xmds_integrate_rk4.cc: Comments about
	  sampling code
	  
	  - Code is repeated in other integrate classes.
	  - Why use multiplication and division instead of mod (%)?
	  Perhaps former is faster, depending on architecture.

2008-01-22 06:31  gmcmanus

	* trunk/xmds-devel/source/xmds_integrate.h: Why pass a reference to
	  a constant int?
	  
	  It makes some sense to pass references to constant objects,
	  so that the entire object doesn't have to be copied onto the
	  stack.
	  But ints are (about) the same size as pointers.

2008-01-22 06:31  gmcmanus

	* trunk/xmds-devel/source/xmds_integrate.h: improved documentation
	  for xmdsIntegrate methods
	  
	  - completed documentation for methods that return bool
	  - added documentation for writeRuntimeCheckingCode

2008-01-21 23:13  paultcochrane

	* trunk/xmds-devel/admin/xmds.spec: Realistically this is the spec
	  for xmds-1.6.5. Changed the comment to reflect this. Also, in the
	  last commit, I updated the comments for the given xmds.spec
	  version to document what has been altered.

2008-01-21 23:11  paultcochrane

	* trunk/xmds-devel/admin/xmds.spec: Updated the name of the pdf
	  documentation to add into the rpm
	  Added relevant files which are now installed to list of files to
	  include in the rpm

2008-01-21 22:55  paultcochrane

	* trunk/xmds-devel/admin/xmds.spec: We're now packaging for
	  xmds-1.6.5 so changed the version number to reflect this.
	  We're not able to install the files into /usr/lib/xmds and
	  /usr/include/xmds due to the fact that we determine where the
	  libraries and headers go at configure time, so revert back to
	  using the standard locations.

2008-01-21 22:44  paultcochrane

	* trunk/xmds-devel/ChangeLog: Added a note about new configuration
	  and installation changes.

2008-01-21 22:26  paultcochrane

	* trunk/xmds-devel/admin/xmds.spec: The patches for Fedora are no
	  longer necessary as the issues they addressed
	  have now been applied in the trunk.

2008-01-21 22:23  paultcochrane

	* trunk/xmds-devel/Makefile.am: The examples now go into an
	  examples/ subdirectory of the doc/xmds directory
	  when installed.

2008-01-21 22:15  paultcochrane

	* trunk/xmds-devel/Makefile.am: Actually, come to think of it, the
	  examples, NEWS, COPYING and AUTHORS
	  should also go into the /usr/share/doc/xmds dir.

2008-01-21 22:12  paultcochrane

	* trunk/xmds-devel/Makefile.am,
	  trunk/xmds-devel/source/Makefile.am: Changing the location of
	  where loadxsil.m is installed. It now goes in
	  /usr/local/share/doc/xmds/ (or equivalent). The README and
	  README.Windows
	  now also go into this directory when make install is run.

2008-01-21 21:43  paultcochrane

	* trunk/xmds-devel/admin/xmds.spec: Now using the correct version
	  information for finding the xmds source, and
	  for the release number of the .rpm

2008-01-21 19:28  paultcochrane

	* trunk/xmds-devel/TODO: Minor textual cleanup to fit with my
	  old-fashioned tastes ;-)

2008-01-21 03:52  joehope

	* trunk/xmds-devel/admin/xmdsReleaseProcedure.pod: Added in the
	  command for auto-ChangeLog generation. Even if it isn't our
	  officially released set of changes, it's a useful document.

2008-01-21 03:39  joehope

	* trunk/xmds-devel/TODO: Removing trailing space.

2008-01-21 03:03  joehope

	* trunk/xmds-devel/TODO: Updated TODO before discussion with
	  Gabriel.

2008-01-21 00:14  joehope

	* trunk/xmds-devel/source/xmds_integrate_ip.cc: Fixed bug from
	  interaction picture replacements. Have to watch people using the
	  vector version incorrectly, and my cleanup test was buggy.

2008-01-20 14:35  paultcochrane

	* trunk/xmds-devel/source/xmds_integrate.cc: Reformatted code, and
	  made indenting more consistent. No functional
	  improvements but hopefully reads a bit more easily. Also made
	  some notes on
	  places where the code could be refactored

2008-01-19 16:16  paultcochrane

	* trunk/xmds-devel/source/xmds_breakpoint.cc,
	  trunk/xmds-devel/source/xmds_integrate.cc,
	  trunk/xmds-devel/source/xmds_integrate_ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_siip.cc,
	  trunk/xmds-devel/source/xmds_vector.cc: Adding spacing around
	  parentheses for readability

2008-01-19 16:11  paultcochrane

	* trunk/xmds-devel/source/xmds_field.cc,
	  trunk/xmds-devel/source/xmds_integrate.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark45.cc,
	  trunk/xmds-devel/source/xmds_integrate_ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_siip.cc,
	  trunk/xmds-devel/source/xmds_utils.cc,
	  trunk/xmds-devel/source/xmds_utils.h,
	  trunk/xmds-devel/source/xmds_vector.cc,
	  trunk/xmds-devel/source/xmds_vector_element.cc,
	  trunk/xmds-devel/source/xml_basics.cc: Banishing hard tabs.

2008-01-19 16:03  paultcochrane

	* trunk/xmds-devel/admin/xmdsReleaseProcedure.pod: Updated release
	  procedure to reflect the change in the way the ChangeLog is
	  handled.

2008-01-19 16:02  paultcochrane

	* trunk/xmds-devel/source/kissdom.cc,
	  trunk/xmds-devel/source/xmds_breakpoint.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark45.cc,
	  trunk/xmds-devel/source/xmds_integrate_ex.cc,
	  trunk/xmds-devel/source/xmds_utils.cc,
	  trunk/xmds-devel/source/xmds_vector.cc,
	  trunk/xmds-devel/source/xsil_field.cc: Removed trailing space.

2008-01-19 16:01  paultcochrane

	* trunk/xmds-devel/configure.in: Updated xmds version number to the
	  current development version (xmds-1.6.4 has been released)

2008-01-19 16:01  paultcochrane

	* trunk/xmds-devel/source/Doxyfile: Updated the xmds version number
	  to 1.6.5 which is what we're working on now.

2008-01-19 14:54  paultcochrane

	* trunk/xmds-devel/ChangeLog: Added a list of recent changes to the
	  change log

2008-01-19 14:52  paultcochrane

	* trunk/xmds-devel/ChangeLog: Completely altered the ChangeLog. The
	  file now gives a summary of the changes
	  for each version of xmds. This is a far better overview of what
	  has been
	  happening in xmds than the overly detailed change log we used to
	  have. If
	  anyone is interested in the detailed version, they can just go
	  'svn log'.

2008-01-19 14:20  paultcochrane

	* trunk/xmds-devel/source/xmds_vector_element.cc: consting constant
	  charater arrays as per patch courtesy of Rafael Laboissiere.

2008-01-19 14:18  paultcochrane

	* trunk/xmds-devel/source/xsil_field.cc: Applying patch for
	  C-string to C++-string casts comparison courtesy of
	  Rafael Laboissiere.

2008-01-19 14:15  paultcochrane

	* trunk/xmds-devel/source: Ignoring TAGS files in svn status output

2008-01-19 12:40  paultcochrane

	* trunk/xmds-devel/source/xsil_field.cc: *This* time converted tabs
	  to spaces

2008-01-19 12:38  paultcochrane

	* trunk/xmds-devel/source/xsil_field.cc: Converted hard tabs to
	  spaces

2008-01-18 14:18  paultcochrane

	* trunk/xmds-devel/source/Makefile.am: Applying patch supplied by
	  Rafael Laboissiere to remove the xmds_config.h
	  file from the release tarball and to remove the file when running
	  make distclean

2008-01-16 00:12  joehope

	* trunk/xmds-devel/Makefile.am: Fix for the missing examples.

2008-01-15 02:03  joehope

	* trunk/xmds-devel/admin/xmdsReleaseProcedure.pod: More direct way
	  of moving the files onto the website. Must change privileges as
	  well, apparently.

2008-01-10 04:20  joehope

	* trunk/xmds-devel/MANIFEST, trunk/xmds-devel/Makefile.am: More
	  version 1.6.4 release preparation.

2008-01-10 04:13  joehope

	* trunk/xmds-devel/ChangeLog, trunk/xmds-devel/README,
	  trunk/xmds-devel/README.Windows: Preparing for new version
	  release.

2008-01-10 02:55  joehope

	* trunk/xmds-devel/examples/highdim.xmds,
	  trunk/xmds-doc/latex/functionality.tex,
	  trunk/xmds-doc/latex/languageReference.tex,
	  trunk/xmds-doc/latex/misc_defs.tex,
	  trunk/xmds-doc/latex/moreExamples.tex,
	  trunk/xmds-doc/latex/tutFromScratch.tex,
	  trunk/xmds-doc/latex/xmds_doc.tex,
	  trunk/xmds-doc/latex/xsil2graphics.tex: Update of the
	  documentation for the new version. Some older bits were updated,
	  though not thoroughly, and the new component array abilities are
	  mentioned, referenced, and included in the examples.

2008-01-10 00:11  joehope

	* trunk/xmds-devel/examples/HighdimPlotExample.nb,
	  trunk/xmds-devel/examples/highdim.xmds,
	  trunk/xmds-devel/examples/highdim_vector_version.xmds,
	  trunk/xmds-devel/source/xmds_integrate.cc,
	  trunk/xmds-devel/source/xmds_integrate.h,
	  trunk/xmds-devel/source/xmds_integrate_ark45.cc,
	  trunk/xmds-devel/source/xmds_integrate_ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_siip.cc,
	  trunk/xmds-devel/source/xmds_vector.cc: Added vector
	  functionality for the fields in XMDS. This only works for the
	  main fields, as I believe that is the only time it is required.
	  
	  highdim_vector_version.xmds has been added as a shorthand to the
	  syntax. It is an identical program to highdim.xmds, but written
	  using the new syntax. Essentially, components can be described as
	  vectors by adding their length in parentheses: phi(200)
	  
	  They are then addressed by phi(j), where j may range from 1 to
	  the maximum value. Values for j are not range checked, so be
	  careful.
	  
	  Propagation and transverse derivatives are described by
	  dphi_dt(j) and Loperator[phi](j) respectively.
	  
	  Disadvantages of using vector syntax: If the k-space operator of
	  any of the components of a vector are required, all of them are
	  calculated. This makes, for example, highdim_vector_version.xmds
	  slower than the old version.
	  
	  IMPORTANT: For interaction picture algorithms, if a k-space
	  operator is applied to any component of a vector, then it is
	  applied to ALL OF THEM. This means that
	  highdim_vector_version.xmds only solves the correct equations
	  when used with an EX algorithm.
	  
	  Noises do not currently have a vector option, but it would be
	  easy to add if anyone was interested.

2008-01-07 00:02  joehope

	* trunk/xmds-devel/source/xmds_integrate_ex.cc,
	  trunk/xmds-devel/source/xmds_utils.cc,
	  trunk/xmds-devel/source/xmds_vector.cc: Processing for vector
	  components. More to be done, but this is a transparent milestone.

2008-01-01 06:07  joehope

	* trunk/xmds-devel/configure.in: Replacing Paul's fix. Was I
	  imagining problems?

2007-12-31 04:00  joehope

	* trunk/xmds-devel/configure.in, trunk/xmds-devel/source/kissdom.h,
	  trunk/xmds-devel/source/xmds_field.cc,
	  trunk/xmds-devel/source/xmds_utils.cc,
	  trunk/xmds-devel/source/xmds_utils.h,
	  trunk/xmds-devel/source/xmds_vector.cc,
	  trunk/xmds-devel/source/xmds_vector.h,
	  trunk/xmds-devel/source/xmds_vector_element.cc: Preliminary
	  structures for definition of vector components. These changes
	  currently have no functional effect at all. Also includes a
	  backout of Paul's recent configure.in changes. We need to find a
	  script that works on all systems.

2007-12-30 17:34  paultcochrane

	* ., trunk/xmds-devel/configure.in: Converted 'test x$var != x'
	  tests to use 'test -n' instead. This is to try
	  to fix Joe's current configuration problems. It seems that for
	  some reason
	  even though FFTW_LIB_PATH and FFTW3_LIB_PATH aren't set taht the
	  true paths
	  of the if statements were still being taken and therefore -L was
	  being
	  incorrectly added to the LDFLAGS variable at configuration check
	  time.

2007-12-30 17:34  paultcochrane

	* ., trunk/xmds-devel/source/xmds_globals.cc: Minor tidyups to try
	  to improve code readability

2007-12-30 17:34  paultcochrane

	* ., trunk/xmds-devel/source/xmds_filter.cc: Tidy up code a bit,
	  add spacing and try to make autogenerated code a bit
	  easier to read.

2007-12-22 15:19  paultcochrane

	* trunk/xmds-devel/configure.in: Removed FFTW_LIB_PATH from
	  arguments to AC_CHECK_LIB() where extra libraries
	  are required, rather than extra paths to libraries. The paths to
	  libraries
	  should already have been set in LDFLAGS if we have them in some
	  non-standard
	  location.

2007-12-22 14:57  paultcochrane

	* trunk/xmds-devel/configure.in: Only appending to the LDFLAGS when
	  the FFTW*_LIB_PATH variable is set

2007-12-22 12:56  joehope

	* trunk/xmds-devel/examples/HighdimPlotExample.nb,
	  trunk/xmds-devel/source/xsil2graphics.cc,
	  trunk/xmds-devel/source/xsil_field.cc: The new version of
	  Mathematica now inputs all files. The structure of that data is
	  tidied up as well.

2007-12-21 18:51  paultcochrane

	* trunk/xmds-devel/source/xmds_integrate_ark45.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark89.cc: Fixed a bug
	  where a comparison between a C string and a character array
	  caused
	  the incorrect path to be taken.
	  The long version of the story is this: we had instances of
	  typeName == "complex"
	  which works in C++, but not when typeName is a const char * (i.e.
	  not a C++
	  string object). The correct thing to do here is to use strcmp()
	  (or make
	  typeName into a string object). So, I took the shorter path and
	  added strcmp()
	  comparisons instead. This was picked up by the Sun C++ compiler
	  (why didn't
	  gcc or icc pick this up?), and flagged as an error.

2007-12-21 18:26  paultcochrane

	* trunk/xmds-devel/source/xmds_simulation.cc: The math.h in Sun's
	  CC doesn't define INFINITY. However, it does define
	  HUGE_VAL, so use this instead of INFINITY if INFINITY isn't
	  defined.

2007-12-21 17:46  paultcochrane

	* trunk/xmds-devel/configure.in: Configuring xmds with Sun's C
	  compiler on Open Solaris means that we need to
	  have the library paths *before* the libraries. Also we need to
	  set the LDFLAGS
	  variable so that configure is able to find the appropriate
	  libraries when
	  we use --with-fftw-path.

2007-12-21 17:05  paultcochrane

	* trunk/xmds-devel/configure.in: Sun's C compiler doesn't handle
	  -Wall, hence only turning on warnings flags
	  for gcc.

2007-12-21 16:14  paultcochrane

	* trunk/xmds-devel/configure.in: Correcting a piece of error text
	  when fftw3 isn't found.

2007-12-16 04:01  joehope

	* trunk/xmds-devel/examples/HighdimPlotExample.nb,
	  trunk/xmds-devel/examples/highdim.xmds: Plotting examples for the
	  Mathematica input.

2007-12-16 04:00  joehope

	* trunk/xmds-devel/source/xml_basics.cc,
	  trunk/xmds-devel/source/xsil2graphics.cc,
	  trunk/xmds-devel/source/xsil_field.cc,
	  trunk/xmds-devel/source/xsil_field.h: Support for binary input
	  into the lastest version of Mathematica. ASCII support for latest
	  version and binary support for old version are not yet
	  implemented.

2007-12-15 19:52  joehope

	* trunk/xmds-devel/source/xmds_integrate_ark45.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark89.cc: Never say final:
	  This is the ultimate fix for the multi-block error.

2007-12-14 02:42  michaelhush

	* trunk/xmds-devel/source/xmds_integrate_ark89.cc: fixed problem
	  with cycle tag when using ark89

2007-12-12 07:23  joehope

	* trunk/xmds-devel/source/xmds_integrate_ark45.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark89.cc: When multiple
	  sequence elements are used for any reason, the sample times were
	  wrong for the adaptive algorithms. Fixed.
	  I can't believe no-one noticed this one. Further bugs to come.

2007-11-26 04:11  grahamdennis

	* trunk/xmds-devel/source/xmds_breakpoint.cc: Correct compiler
	  warning when compiling scripts that use the breakpoint
	  auto-naming feature.

2007-11-25 03:52  grahamdennis

	* trunk/xmds-devel/source/xmds_breakpoint.cc,
	  trunk/xmds-devel/source/xmds_breakpoint.h,
	  trunk/xmds-devel/source/xmds_simulation.cc: If there isn't a
	  filename tag for a breakpoint element, then the breakpoints will
	  be named 1.xsil, 2.xsil, 3.xsil etc. Note that this is not reset
	  for half-step integration. The naming increments for all
	  breakpoints in the simulation that lack a filename tag.

2007-11-18 23:17  paultcochrane

	* ., trunk/xmds-devel/source/xmds_field.cc: Merged more fprintf
	  statements together.

2007-11-18 23:17  paultcochrane

	* ., trunk/xmds-devel/source/xmds_field.cc: Changed the following
	  variables in xmdsField::writeDefines():
	  dimI->domain.begin.c_str() and dimI->domain.end.c_str()
	  to use shorter, but as descriptive, names.

2007-11-18 23:17  paultcochrane

	* ., trunk/xmds-devel/source/xmds_field.cc: Replaced occurrences of
	  myName.c_str() with a constant fieldName variable in
	  xmdsField::writeDefines()

2007-11-18 23:16  paultcochrane

	* ., trunk/xmds-devel/source/xmds_field.cc: Compacted more fprintf
	  statements into fewer. Attempting to make the
	  generated code look as "normal" as possible.

2007-11-18 23:16  paultcochrane

	* ., trunk/xmds-devel/source/xmds_field.cc: More spacing-out of
	  code and compression of fprintf statements into one.

2007-11-18 23:16  paultcochrane

	* ., trunk/xmds-devel/source/xmds_element.cc: Minor formatting
	  changes. Dunno if it helped readability that much ...

2007-11-18 20:20  paultcochrane

	* ., trunk/xmds-devel/source/xmds_breakpoint.cc: Further expansion
	  of generated code.
	  Some more formatting changes.

2007-11-18 20:19  paultcochrane

	* ., trunk/xmds-devel/source/xmds_breakpoint.cc: Wrote some of the
	  generated code a bit more longhand so that it's easier to
	  read in the xmds code.

2007-11-18 20:19  paultcochrane

	* ., trunk/xmds-devel/source/xmds_breakpoint.cc: Further
	  compression of code to be generated into single fprintf
	  statements

2007-11-18 20:19  paultcochrane

	* ., trunk/xmds-devel/source/xmds_breakpoint.cc: Caught a mistake
	  in one of the format strings.

2007-11-18 20:19  paultcochrane

	* ., trunk/xmds-devel/source/xmds_breakpoint.cc: Merged some
	  fprintf statements into one, to try to make code to be generated
	  easier to read.

2007-11-18 20:19  paultcochrane

	* ., trunk/xmds-devel/source/xmds_breakpoint.cc: Moved 'coordinate'
	  variable increment into body of 'for' loop instead of
	  residing in 'for' loop header itself. This is in the generated
	  code.
	  BTW: the last commit added braces around this 'for' loop.

2007-11-18 20:19  paultcochrane

	* ., trunk/xmds-devel/source/xmds_breakpoint.cc: More formatting
	  changes. I'm doing this in little bits on this file to try
	  enable us to pinpoint where something went wrong if at all.

2007-11-18 18:47  paultcochrane

	* ., trunk/xmds-devel/source/xmds_breakpoint.cc: Code formatting
	  improvements. Hopefully a bit easier to read now.

2007-11-18 18:47  paultcochrane

	* ., trunk/xmds-devel/source/xmds_complex.h,
	  trunk/xmds-devel/source/xmds_field.h: Putting declaration of
	  initialiseFieldFromXSILFile() back in xmds_complex.h
	  so that diffusion2.xmds can build again. Maybe we need an
	  xmds_utils.h
	  header?

2007-11-18 18:47  paultcochrane

	* ., trunk/xmds-devel/source/xmds_argv.cc: Minor code format
	  change.

2007-11-18 18:47  paultcochrane

	* ., trunk/xmds-devel/source/xmds_arg_element.cc: Minor textual
	  changes; code readability improvements.

2007-11-18 18:46  paultcochrane

	* ., trunk/xmds-devel/source/kissdom.cc: Minor code tidyups; trying
	  to improve readability a bit.

2007-11-17 14:15  paultcochrane

	* ., trunk/xmds-devel/TODO: Minor textual tidyups

2007-11-17 13:42  paultcochrane

	* ., trunk/xmds-devel/source/kissdom.cc,
	  trunk/xmds-devel/source/xmds_arg.cc,
	  trunk/xmds-devel/source/xmds_complex.h,
	  trunk/xmds-devel/source/xmds_element.cc,
	  trunk/xmds-devel/source/xmds_field.cc,
	  trunk/xmds-devel/source/xmds_filter.cc,
	  trunk/xmds-devel/source/xmds_globals.cc,
	  trunk/xmds-devel/source/xmds_integrate.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark45.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark45ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark45ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark89.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark89ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark89ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk4.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk4ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk4ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk9.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk9ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk9ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_si.cc,
	  trunk/xmds-devel/source/xmds_integrate_siex.cc,
	  trunk/xmds-devel/source/xmds_integrate_siip.cc,
	  trunk/xmds-devel/source/xmds_moment_group.cc,
	  trunk/xmds-devel/source/xmds_output.cc,
	  trunk/xmds-devel/source/xmds_segment.cc,
	  trunk/xmds-devel/source/xmds_sequence.cc,
	  trunk/xmds-devel/source/xmds_utils.cc,
	  trunk/xmds-devel/source/xmds_vector.cc,
	  trunk/xmds-devel/source/xmds_vector_element.cc,
	  trunk/xmds-devel/source/xml_parser.h: Spacing code out a bit more
	  for readability.

2007-11-17 13:41  paultcochrane

	* ., trunk/xmds-devel/source/xmds_simulation.cc: - Added spaces
	  around commas and semicolons
	  - Removed superfluous trailing semicolon in _dtdWstore struct in
	  generated
	  code.

2007-11-17 13:41  paultcochrane

	* ., trunk/xmds-devel/source/main.cc,
	  trunk/xmds-devel/source/xmds_breakpoint.cc,
	  trunk/xmds-devel/source/xml_basics.cc,
	  trunk/xmds-devel/source/xml_parser.cc,
	  trunk/xmds-devel/source/xsil_field.cc: Adding spacing around
	  commas and semicolons to try to improve readability

2007-11-17 13:41  paultcochrane

	* ., trunk/xmds-devel/source/xmds_integrate_ark45.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark89.cc: Rolled lots of
	  fprintf statements into one fprintf statement where possible.
	  Hopefully this makes the code to be generated easier to read.

2007-11-17 13:41  paultcochrane

	* ., trunk/xmds-devel/source/xml_basics.h: Removed unused XMLBASICS
	  define.
	  Minor docstring tidyups

2007-11-17 13:40  paultcochrane

	* ., trunk/xmds-devel/source/xmds_vector.h,
	  trunk/xmds-devel/source/xml_basics.cc,
	  trunk/xmds-devel/source/xsil_field.cc,
	  trunk/xmds-devel/source/xsil_field.h: Updated some Doxygen docs.

2007-11-17 13:40  paultcochrane

	* ., trunk/xmds-devel/source/kissdom.h: Removed unused #define
	  variable.

2007-11-17 13:40  paultcochrane

	* ., trunk/xmds-devel/source/xmds_complex.h,
	  trunk/xmds-devel/source/xmds_field.h: Moved declaration of
	  initialiseFieldFromXSILFile to xmds_field.h. Updated
	  some of the doxygen docs in xmds_field.h

2007-11-13 07:49  paultcochrane

	* ., trunk/xmds-devel/source/kissdom.cc,
	  trunk/xmds-devel/source/xmds_breakpoint.cc,
	  trunk/xmds-devel/source/xmds_complex.h,
	  trunk/xmds-devel/source/xmds_element.cc,
	  trunk/xmds-devel/source/xmds_field.cc,
	  trunk/xmds-devel/source/xmds_filter.cc,
	  trunk/xmds-devel/source/xmds_globals.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark45ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark45ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark89.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark89ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark89ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk4.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk4ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk4ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk9.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk9ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk9ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_si.cc,
	  trunk/xmds-devel/source/xmds_integrate_siex.cc,
	  trunk/xmds-devel/source/xmds_integrate_siip.cc,
	  trunk/xmds-devel/source/xmds_moment_group.cc,
	  trunk/xmds-devel/source/xmds_output.cc,
	  trunk/xmds-devel/source/xmds_segment.cc,
	  trunk/xmds-devel/source/xmds_sequence.cc,
	  trunk/xmds-devel/source/xmds_utils.cc,
	  trunk/xmds-devel/source/xmds_vector.cc,
	  trunk/xmds-devel/source/xmds_vector_element.cc,
	  trunk/xmds-devel/source/xml_basics.cc,
	  trunk/xmds-devel/source/xml_parser.cc: Adjusted spacing around
	  parentheses for consistency and readability

2007-11-13 07:48  paultcochrane

	* ., trunk/xmds-devel/source/xmds_moment_group.h,
	  trunk/xmds-devel/source/xml_parser.h,
	  trunk/xmds-devel/source/xsil_field.h: Correcting filenames in
	  doxygen documentation.

2007-11-13 07:47  paultcochrane

	* ., trunk/xmds-devel/source/Doxyfile: Updated Doxyfile format.

2007-11-11 22:01  paultcochrane

	* trunk/xmds-devel/test/coding_stds/c_parens.t: Added C-language
	  parenthesis spacing coding standards test from the Parrot
	  project: www.parrotcode.org. Adjusted the test for the xmds
	  source.

2007-11-11 21:55  paultcochrane

	* ., trunk/xmds-devel/source/dom3.h,
	  trunk/xmds-devel/source/kissdom.cc,
	  trunk/xmds-devel/source/main.cc,
	  trunk/xmds-devel/source/xmds_arg_element.cc,
	  trunk/xmds-devel/source/xmds_argv.cc,
	  trunk/xmds-devel/source/xmds_breakpoint.cc,
	  trunk/xmds-devel/source/xmds_field.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark45.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark89.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark89ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark89ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk9ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk9ip.cc,
	  trunk/xmds-devel/source/xmds_output.cc,
	  trunk/xmds-devel/source/xmds_simulation.cc,
	  trunk/xmds-devel/source/xmds_vector.cc,
	  trunk/xmds-devel/source/xml_basics.cc,
	  trunk/xmds-devel/source/xml_parser.cc,
	  trunk/xmds-devel/source/xsil_field.cc: Adjusted parenthesis
	  spacing for more consistent formatting.

2007-11-11 21:55  paultcochrane

	* ., trunk/xmds-devel/test/coding_stds/cuddled_else.t,
	  trunk/xmds-devel/test/coding_stds/tabs.t,
	  trunk/xmds-devel/test/coding_stds/trailing_space.t: Removed old
	  Parrot-specific comments from coding standards test files.

2007-11-11 21:06  paultcochrane

	* ., trunk/xmds-devel/source/xmds_argv.cc,
	  trunk/xmds-devel/source/xmds_field.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark45.cc,
	  trunk/xmds-devel/source/xmds_moment_group.cc,
	  trunk/xmds-devel/source/xmds_simulation.cc,
	  trunk/xmds-devel/source/xmds_utils.cc,
	  trunk/xmds-devel/source/xsil2graphics.cc,
	  trunk/xmds-devel/source/xsil_field.cc,
	  trunk/xmds-devel/source/xsil_field.h: Removed trailing whitespace

2007-11-11 21:05  paultcochrane

	* ., trunk/xmds-devel/source/xmds_breakpoint.cc,
	  trunk/xmds-devel/source/xmds_integrate_ip.cc,
	  trunk/xmds-devel/source/xmds_simulation.cc,
	  trunk/xmds-devel/source/xmds_vector_element.cc: Removed cuddled
	  else instances.

2007-11-11 21:05  paultcochrane

	* ., trunk/xmds-devel/test/coding_stds/cuddled_else.t,
	  trunk/xmds-devel/test/coding_stds/trailing_space.t: Removed
	  non-existent filename from list of files to test coding
	  standards.

2007-11-11 20:21  paultcochrane

	* ., trunk/xmds-devel/source/xmds_integrate_ark45.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark89.cc,
	  trunk/xmds-devel/source/xmds_moment_group.cc: Converted hard tabs
	  into spaces

2007-11-11 20:21  paultcochrane

	* ., trunk/xmds-devel/test/coding_stds/tabs.t: Removed now
	  non-existent file from coding standards test

2007-11-11 20:20  paultcochrane

	* ., trunk/xmds-devel/configure.in: Rolled xmds version information
	  into a variable. Updated the variable to be
	  xmds-1.6.4 as we've already released xmds-1.6.3.

2007-11-11 20:20  paultcochrane

	* ., trunk/xmds-devel/source/xmds_breakpoint.cc,
	  trunk/xmds-devel/source/xmds_output.cc: Removed superfluous comma
	  in xmds output info text.

2007-11-11 20:19  paultcochrane

	* ., trunk/xmds-devel/source/Doxyfile,
	  trunk/xmds-devel/source/main.cc,
	  trunk/xmds-devel/source/xmds_breakpoint.cc,
	  trunk/xmds-devel/source/xmds_output.cc,
	  trunk/xmds-devel/source/xmds_simulation.cc,
	  trunk/xmds-devel/source/xmds_simulation.h,
	  trunk/xmds-devel/source/xsil2graphics.cc: Realistically speaking,
	  we don't need the RELEASE variable as a part of the
	  xmds version information; it's superfluous. Hence, I've removed
	  it, and we
	  can just define minor releases of xmds (i.e. xmds-x.x.y) with
	  just the
	  VERSION variable. This has the positive side effect of removing
	  some
	  superfluous code to handle the RELEASE information, and making
	  sure that in
	  each location where xmds version info is printed that the format
	  is the
	  same. Also, it makes packaging xmds easier for downstream
	  packagers, and
	  when we make a release ourselves (with 'make dits') the .tar.gz
	  file comes
	  out with the full version information instead of just the major
	  version.

2007-10-23 04:28  andyferris

	* trunk/xmds-devel/source/xmds_moment_group.cc: Fixed typo "dobule"

2007-10-23 02:35  andyferris

	* trunk/xmds-devel/source/xmds_utils.cc,
	  trunk/xmds-devel/source/xml_parser.cc: * xmds now reports the
	  line number of elements and the parents when encountering an
	  xmdsException.
	  * The XML parser now assigns attributes xmdsLineNumber and
	  xmdsColumnNumber to
	  EVERY element. This isn't what I'd call XML compliant but it does
	  the job.

2007-10-22 03:51  andyferris

	* trunk/xmds-devel/TODO, trunk/xmds-devel/source/xmds_field.cc,
	  trunk/xmds-devel/source/xmds_moment_group.cc,
	  trunk/xmds-devel/source/xmds_utils.cc,
	  trunk/xmds-devel/source/xmds_utils.h: <domains> can now be
	  specified with C-code.

2007-10-19 14:27  paultcochrane

	* trunk/xmds-devel/admin/xmds.spec: Further updates to spec
	  (although not yet complete) after more comments from
	  Patrice Dumas

2007-10-19 14:25  paultcochrane

	* trunk/xmds-devel/README: Added mention of Octave to README

2007-10-17 08:39  paultcochrane

	* trunk/xmds-devel/admin/xmds.spec: Several updates to get spec
	  file to conform to Fedora guidelines.

2007-10-17 00:30  andyferris

	* trunk/xmds-devel/TODO,
	  trunk/xmds-devel/source/xmds_breakpoint.cc,
	  trunk/xmds-devel/source/xmds_integrate.h,
	  trunk/xmds-devel/source/xmds_integrate_ark45.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark89.cc,
	  trunk/xmds-devel/source/xmds_moment_group.cc,
	  trunk/xmds-devel/source/xmds_sequence.cc,
	  trunk/xmds-devel/source/xmds_simulation.cc,
	  trunk/xmds-devel/source/xmds_simulation.h: Some more tags are now
	  allowed to have C-code inside them:
	  
	  * <npaths> is now interpretted as a string and thus works. If
	  code is
	  inserted here then it assumed paths > 1 (so mean_ and sd_ data is
	  produced).
	  * <interval> used to work for non-adaptive code; now it works
	  always.
	  * <seed> now allows arbitrary code, not just command-line args.
	  * Added a discussion in TODO.

2007-09-20 12:40  grahamdennis

	* trunk/xmds-devel/source/xmds_moment_group.cc: Fix a subtle bug
	  when outputting data that has the propagation dimension
	  fourier transformed. This bug was introduced when the
	  runtime_limit code
	  was added, and occurs even without a runtime_limit.
	  I think I implemented the runtime_limit in an awful way.

2007-09-18 11:12  joehope

	* trunk/xmds-devel/source/xmds_moment_group.cc: Precision = double
	  actually increases the precision of ascii output.

2007-09-04 00:18  grahamdennis

	* trunk/xmds-devel/source/xmds_complex.h: Correct the branch cut
	  for the complex argument function (hence also fixing the branch
	  cut for the c_sqrt function). This should happen at z = -x (phi =
	  +/- pi), not at z=-i y (phi = 3pi/2, -pi/2).

2007-08-31 06:23  grahamdennis

	* trunk/xmds-devel/source/loadxsil.m: Fix loadxsil.m for matlab.
	  I'm hoping this works for Octave (Paul?)

2007-08-27 05:59  joehope

	* trunk/xmds-devel/TODO: Another feature requested. Will take a
	  day.

2007-08-24 08:54  paultcochrane

	* trunk/xmds-devel/test/generated_code/Makefile: Improved the
	  generated <-> reference comparison test by grepping out
	  changable content.

2007-08-24 02:54  grahamdennis

	* trunk/xmds-devel/source/loadxsil.m: Fix broken loadxsil.m since
	  r1543.

2007-08-24 01:13  grahamdennis

	* trunk/xmds-devel/source/xmds_simulation.cc: Instead of defining
	  an isfinite that is always true, define one that should work on
	  systems that lack a built-in isfinite.

2007-08-24 01:03  grahamdennis

	* trunk/xmds-devel/source/xmds_simulation.cc: Compile fix for
	  systems that don't have isfinite. This defines isfinite as true,
	  which is kinda hackish.

2007-08-23 22:12  paultcochrane

	* ., trunk/xmds-devel/source/loadxsil.m: Fixed another problem
	  associated with matlab handling structures in a more
	  non-standard manner than octave.
	  Also indented the generated code for eval() so that one can read
	  it a bit
	  more easily.

2007-08-23 22:01  paultcochrane

	* ., trunk/xmds-devel/source/loadxsil.m: Further spacing out of
	  code.

2007-08-23 22:00  paultcochrane

	* ., trunk/xmds-devel/source/loadxsil.m: Made if(debug) statements
	  more explicit

2007-08-23 22:00  paultcochrane

	* ., trunk/xmds-devel/source/loadxsil.m: Spaced out the code a
	  little bit.

2007-08-23 22:00  paultcochrane

	* ., trunk/xmds-devel/source/loadxsil.m: Correcting address of FSF

2007-08-23 22:00  paultcochrane

	* ., trunk/xmds-devel/source/loadxsil.m: Now just cleaning up the
	  text a bit.

2007-08-23 21:59  paultcochrane

	* ., trunk/xmds-devel/source/loadxsil.m: Unindented some
	  over-zealous indentation.

2007-08-23 21:59  paultcochrane

	* ., trunk/xmds-devel/source/loadxsil.m: Removed old commented-out
	  code

2007-08-23 21:59  paultcochrane

	* ., trunk/xmds-devel/source/loadxsil.m: Finally found the extra
	  level of indentation I was looking for.

2007-08-23 21:59  paultcochrane

	* ., trunk/xmds-devel/source/loadxsil.m: Trying to reindent the
	  code so that it makes some sense. I wish someone
	  would be able to tell me that I never wrote this code... *sigh*

2007-08-23 21:58  paultcochrane

	* ., trunk/xmds-devel/source/loadxsil.m: Replaced hard tabs with
	  spaces.

2007-08-23 21:58  paultcochrane

	* ., trunk/xmds-devel/source/loadxsil.m: Added a vim comment to set
	  tabstops and so-on properly

2007-08-23 21:58  paultcochrane

	* ., trunk/xmds-devel/source/loadxsil.m: Octave needs the return
	  character to be properly escaped when loading data
	  from ascii data files. This change means that both matlab and
	  octave can
	  load data, however the matlab informative output doesn't look as
	  nice any
	  more. We'll need to think more carefully about how to make this
	  work on
	  both systems.

2007-08-23 21:58  paultcochrane

	* ., trunk/xmds-devel/source/loadxsil.m: When debug is at a level
	  other than 0, then the assignin call doesn't need
	  to be run (this fixes a problem with running loadxsil.m with
	  debuggin on).

2007-08-23 21:58  paultcochrane

	* ., trunk/xmds-devel/source/loadxsil.m: Applied patch correcting
	  octave-related compatibility issues. Patch
	  courtesy of Rafael Laboissiere <rafael at debian dot org>

2007-08-23 10:32  paultcochrane

	* trunk/xmds-devel/source/xsil_field.cc: Corrected some superfluous
	  character output issues when generating command
	  file output for R.

2007-08-22 17:00  paultcochrane

	* trunk/xmds-devel/source/main.cc: Now exiting properly when we are
	  unable to determine the current directory.

2007-08-22 16:57  paultcochrane

	* trunk/xmds-devel/source/main.cc: Now exiting properly when we
	  aren't able to properly determine the user's
	  home directory.

2007-08-22 16:46  paultcochrane

	* trunk/xmds-devel/source/main.cc: Should have been checking for
	  .fail() instead of equality with null in file
	  opening checking code for templates.

2007-08-22 16:43  paultcochrane

	* trunk/xmds-devel/source/main.cc: The template text variable is
	  now a string instead of being assigned const
	  char *, which isn't very C++. This removes a couple of todo items
	  as
	  well...

2007-08-22 16:39  paultcochrane

	* trunk/xmds-devel/source/main.cc: Template output code now uses
	  C++ completely for output instead of a mixture
	  between standard C and C++.

2007-08-22 16:24  paultcochrane

	* trunk/xmds-devel/source/main.cc: Some cout's should have been
	  cerr's so that the output was directed to
	  stderr as opposed to just stdout

2007-08-22 15:48  paultcochrane

	* trunk/xmds-devel/source/xsil_field.cc: Removed repeated code in
	  writeAsFormat()

2007-08-22 15:47  paultcochrane

	* trunk/xmds-devel/examples: Added *.gnu and *.R to files to be
	  ignored.

2007-08-22 15:45  paultcochrane

	* trunk/xmds-devel/source/xsil2graphics.cc,
	  trunk/xmds-devel/source/xsil_field.cc,
	  trunk/xmds-devel/source/xsil_field.h: Added rudimentary support
	  for the R programming and graphics language. One
	  can now load variables into R at the R command prompt using
	  something like:
	  > source("sine.R")
	  > ls()
	  > plot(t_1, c_1)
	  At present this doesn't handle multi-dimensional data (I'm not
	  sure if R
	  handles that at all), but it's a start at least.

2007-08-22 10:55  paultcochrane

	* trunk/xmds-devel/source/xsil2graphics.cc,
	  trunk/xmds-devel/source/xsil_field.cc,
	  trunk/xmds-devel/source/xsil_field.h: Added rudimentary handling
	  of gnuplot output to xsil2graphics. This
	  basically just outputs the data file as is and doesn't generate a
	  variable
	  loading file as one doesn't require one for gnuplot to display
	  the data.
	  This is effectively the same functionality as for the other
	  display options,
	  namely: generate a data file, and optionally a variable-loading
	  command file
	  such that from within the relevant environment one can then
	  display the
	  data.

2007-08-22 07:39  paultcochrane

	* trunk/xmds-devel/source/xmds_simulation.cc: Added a check for an
	  inconsistent value of the <fftw_version> tag when xmds
	  is built with only fftw3 support. Many thanks to Graham for
	  pointing this
	  situation out.

2007-08-21 17:30  paultcochrane

	* ., trunk/xmds-devel/admin/xmdsReleaseProcedure.pod: Added some
	  notes on making the documentation (now it's possible to use make
	  instead of aap) and making a distribution of the docs.

2007-08-21 17:30  paultcochrane

	* ., trunk/xmds-devel/examples/Makefile: Now removing files
	  generated by gcov as part of clean target

2007-08-21 17:30  paultcochrane

	* ., trunk/xmds-devel/COPYING,
	  trunk/xmds-devel/examples/atomlaser.xmds,
	  trunk/xmds-devel/examples/branch.xmds,
	  trunk/xmds-devel/examples/brusselator.xmds,
	  trunk/xmds-devel/examples/catcycle.xmds,
	  trunk/xmds-devel/examples/chain.xmds,
	  trunk/xmds-devel/examples/chemkin.xmds,
	  trunk/xmds-devel/examples/diffusion.xmds,
	  trunk/xmds-devel/examples/diffusion2.xmds,
	  trunk/xmds-devel/examples/duffing.xmds,
	  trunk/xmds-devel/examples/fibre.xmds,
	  trunk/xmds-devel/examples/fisher_reaction_diffusion.xmds,
	  trunk/xmds-devel/examples/fullpos3D.xmds,
	  trunk/xmds-devel/examples/gaugeatomlaser.xmds,
	  trunk/xmds-devel/examples/groundstate.xmds,
	  trunk/xmds-devel/examples/highdim.xmds,
	  trunk/xmds-devel/examples/hires.xmds,
	  trunk/xmds-devel/examples/krebs.xmds,
	  trunk/xmds-devel/examples/kubo.xmds,
	  trunk/xmds-devel/examples/lane_emden.xmds,
	  trunk/xmds-devel/examples/lorenz.xmds,
	  trunk/xmds-devel/examples/lotka_volterra.xmds,
	  trunk/xmds-devel/examples/ndparamp.xmds,
	  trunk/xmds-devel/examples/nlse.xmds,
	  trunk/xmds-devel/examples/oregonator.xmds,
	  trunk/xmds-devel/examples/paraxial_wave.xmds,
	  trunk/xmds-devel/examples/pendulum.xmds,
	  trunk/xmds-devel/examples/ring_modulator.xmds,
	  trunk/xmds-devel/examples/sech_soliton.xmds,
	  trunk/xmds-devel/examples/sech_soliton_tdepk.xmds,
	  trunk/xmds-devel/examples/sine.xmds,
	  trunk/xmds-devel/examples/soliton.xmds,
	  trunk/xmds-devel/examples/thermkin.xmds,
	  trunk/xmds-devel/examples/tla.xmds,
	  trunk/xmds-devel/examples/van_der_pol.xmds,
	  trunk/xmds-devel/examples/vibstring.xmds: Correcting address of
	  Free Software Foundation.

2007-08-21 17:28  paultcochrane

	* ., trunk/xmds-devel/configure.in: Corrected location of
	  FFTW3_LIBS and FFTW3_THREADLIBS variables so that they
	  are seen in the proper scope

2007-08-21 14:06  paultcochrane

	* trunk/xmds-devel/source/xmds_breakpoint.h: Removed old todo item.
	  Breakpoints have already been implemented.

2007-08-21 13:47  paultcochrane

	* trunk/xmds-devel/source/xsil_field.h: Did some rearranging to
	  make the text (hopefully) a bit easier to read.

2007-08-21 13:18  paultcochrane

	* trunk/xmds-devel/source/xmds_simulation.cc: Trying to tidy up
	  further...

2007-08-21 13:04  paultcochrane

	* trunk/xmds-devel/source/xmds_simulation.cc: Removed old
	  commented-out code.

2007-08-21 13:01  paultcochrane

	* trunk/xmds-devel/source/xmds_simulation.cc: More text tidyups.

2007-08-21 12:12  paultcochrane

	* trunk/xmds-devel/test/generated_code/reference/diffusion.cc,
	  trunk/xmds-devel/test/generated_code/reference/diffusion2.cc,
	  trunk/xmds-devel/test/generated_code/reference/fibre.cc,
	  trunk/xmds-devel/test/generated_code/reference/nlse.cc,
	  trunk/xmds-devel/test/generated_code/reference/sech_soliton.cc,
	  trunk/xmds-devel/test/generated_code/reference/sech_soliton_tdepk.cc:
	  Updated fftw3 references after Graham's recent xmds bugfix.

2007-08-21 12:09  paultcochrane

	* trunk/xmds-devel/source/xmds_simulation.cc: Making use of the new
	  FFTW_THREE_ONLY #defined variable to choose fftw3 as
	  the default if fftw2 isn't detected at configure time, but fftw3
	  is. This
	  allows systems with fftw3 only to build almost completely "out of
	  the box",
	  and to build and run the examples.
	  Graham: could you confirm whether or not this breaks your build?
	  I'm not
	  able to test a dual fftw2/fftw3 system.

2007-08-21 12:07  paultcochrane

	* trunk/xmds-devel/configure.in: Trying to get fftw3-only builds
	  working properly. This change checks for
	  fftw3 in the absence of fftw2 and if so sets up the FFTW_LIBS
	  appropriately
	  and sets a flag to later tell xmds that it only has access to
	  fftw3.
	  Did some quoting tidyups at the same time. (I should really have
	  done these
	  in a separate commit...)

2007-08-21 10:09  paultcochrane

	* trunk/xmds-devel/source/xsil_field.cc: Further spacing-out of
	  code.
	  Made a note of an odd-looking for loop. If it actually does
	  anything it
	  should have a comment next to it explaining what it does.

2007-08-21 09:46  paultcochrane

	* trunk/xmds-devel/source/xsil_field.cc: More generic tidyups.
	  Added braces to if/else statements. Added space to
	  try to improve readability.

2007-08-21 08:21  paultcochrane

	* trunk/xmds-devel/source/xmds_integrate_ark45.cc: Should have been
	  using boolean AND instead of bitwise AND in some if
	  statements. Also removed some superfluous brackets and added some
	  more
	  spacing.

2007-08-21 08:17  paultcochrane

	* trunk/xmds-devel/source/xmds_integrate_ark45.cc: Minor touchups.
	  Trying to see if I can make the code to be autogenerated a
	  bit easier to read before it is generated.

2007-08-20 12:51  paultcochrane

	* trunk/xmds-devel/source/xmds_integrate_ark45.cc: Adding some
	  whitespace for readability.

2007-08-20 12:50  paultcochrane

	* trunk/xmds-devel/acinclude.m4: Removing some underquoted variable
	  warnings in generation of autoconf files.

2007-08-15 10:30  paultcochrane

	* trunk/xmds-devel/configure.in: Configure now no longer barfs on
	  fftw2 if it doesn't exist. However, it
	  will now barf if both fftw2 and fftw3 aren't available.

2007-08-15 09:47  paultcochrane

	* trunk/xmds-devel/source/xmds_arg.h,
	  trunk/xmds-devel/source/xmds_arg_element.h,
	  trunk/xmds-devel/source/xmds_argv.h,
	  trunk/xmds-devel/source/xmds_breakpoint.h,
	  trunk/xmds-devel/source/xmds_common.h,
	  trunk/xmds-devel/source/xmds_complex.h,
	  trunk/xmds-devel/source/xmds_element.h,
	  trunk/xmds-devel/source/xmds_field.h,
	  trunk/xmds-devel/source/xmds_filter.h,
	  trunk/xmds-devel/source/xmds_globals.h,
	  trunk/xmds-devel/source/xmds_integrate.h,
	  trunk/xmds-devel/source/xmds_integrate_ark45.h,
	  trunk/xmds-devel/source/xmds_integrate_ark45ex.h,
	  trunk/xmds-devel/source/xmds_integrate_ark45ip.h,
	  trunk/xmds-devel/source/xmds_integrate_ark89.h,
	  trunk/xmds-devel/source/xmds_integrate_ark89ex.h,
	  trunk/xmds-devel/source/xmds_integrate_ark89ip.h,
	  trunk/xmds-devel/source/xmds_integrate_ex.h,
	  trunk/xmds-devel/source/xmds_integrate_ip.h,
	  trunk/xmds-devel/source/xmds_integrate_rk4.h,
	  trunk/xmds-devel/source/xmds_integrate_rk4ex.h,
	  trunk/xmds-devel/source/xmds_integrate_rk4ip.h,
	  trunk/xmds-devel/source/xmds_integrate_rk9.h,
	  trunk/xmds-devel/source/xmds_integrate_rk9ex.h,
	  trunk/xmds-devel/source/xmds_integrate_rk9ip.h,
	  trunk/xmds-devel/source/xmds_integrate_si.h,
	  trunk/xmds-devel/source/xmds_integrate_siex.h,
	  trunk/xmds-devel/source/xmds_integrate_siip.h,
	  trunk/xmds-devel/source/xmds_moment_group.h,
	  trunk/xmds-devel/source/xmds_output.h,
	  trunk/xmds-devel/source/xmds_segment.h,
	  trunk/xmds-devel/source/xmds_sequence.h,
	  trunk/xmds-devel/source/xmds_simulation.h,
	  trunk/xmds-devel/source/xmds_utils.h,
	  trunk/xmds-devel/source/xmds_vector.h,
	  trunk/xmds-devel/source/xmds_vector_element.h: Added copyright
	  info to the new headers.

2007-08-15 09:31  paultcochrane

	* trunk/xmds-devel/source/xmds_arg.cc,
	  trunk/xmds-devel/source/xmds_arg_element.cc,
	  trunk/xmds-devel/source/xmds_argv.cc,
	  trunk/xmds-devel/source/xmds_breakpoint.cc,
	  trunk/xmds-devel/source/xmds_element.cc,
	  trunk/xmds-devel/source/xmds_field.cc,
	  trunk/xmds-devel/source/xmds_filter.cc,
	  trunk/xmds-devel/source/xmds_globals.cc,
	  trunk/xmds-devel/source/xmds_integrate.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark45.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark45ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark45ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark89.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark89ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark89ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk4.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk4ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk4ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk9.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk9ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk9ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_si.cc,
	  trunk/xmds-devel/source/xmds_integrate_siex.cc,
	  trunk/xmds-devel/source/xmds_integrate_siip.cc,
	  trunk/xmds-devel/source/xmds_moment_group.cc,
	  trunk/xmds-devel/source/xmds_output.cc,
	  trunk/xmds-devel/source/xmds_segment.cc,
	  trunk/xmds-devel/source/xmds_sequence.cc,
	  trunk/xmds-devel/source/xmds_simulation.cc,
	  trunk/xmds-devel/source/xmds_utils.cc,
	  trunk/xmds-devel/source/xmds_vector.cc,
	  trunk/xmds-devel/source/xmds_vector_element.cc,
	  trunk/xmds-devel/source/xml_basics.cc,
	  trunk/xmds-devel/source/xml_parser.cc,
	  trunk/xmds-devel/source/xsil_field.cc: Corrected 'file' field in
	  doxygen documentation

2007-08-15 09:28  paultcochrane

	* trunk/xmds-devel/source/main.cc: Removed superfluous text from
	  doxygen docs.

2007-08-15 09:25  paultcochrane

	* trunk/xmds-devel/source/Makefile.am: No longer building the latex
	  docs with the api target

2007-08-15 09:24  paultcochrane

	* trunk/xmds-devel/source/main.cc: Updated version information for
	  doxygen

2007-08-15 09:15  paultcochrane

	* trunk/xmds-devel/source/Doxyfile: Updated the version number to
	  be current with xmds

2007-08-15 08:49  paultcochrane

	* trunk/xmds-devel/source/xmds_arg.cc,
	  trunk/xmds-devel/source/xmds_arg_element.cc,
	  trunk/xmds-devel/source/xmds_argv.cc: More spacing and textual
	  cleanups.

2007-08-15 08:06  paultcochrane

	* trunk/xmds-devel/source/kissdom.cc: Minor textual tidyups.

2007-08-15 08:06  paultcochrane

	* trunk/xmds-devel/configure.in: The configure script shouldn't
	  barf on not finding fftw2 when --enable-fftw3
	  is set. Hence now only running the fftw2-specific checks when
	  --enable-fftw3 isn't set when running the configure script.

2007-08-15 07:52  paultcochrane

	* trunk/xmds-devel/test/generated_code/reference_fftw2/diffusion.cc,
	  trunk/xmds-devel/test/generated_code/reference_fftw2/diffusion2.cc,
	  trunk/xmds-devel/test/generated_code/reference_fftw2/fibre.cc,
	  trunk/xmds-devel/test/generated_code/reference_fftw2/nlse.cc,
	  trunk/xmds-devel/test/generated_code/reference_fftw2/sech_soliton.cc,
	  trunk/xmds-devel/test/generated_code/reference_fftw2/sech_soliton_tdepk.cc:
	  Updated reference files after recent change by grahamdennis which
	  fixed an
	  issue with error calculations in adaptive algorithms.

2007-08-15 07:50  paultcochrane

	* trunk/xmds-devel/Makefile.am, trunk/xmds-devel/test/Makefile:
	  Added test-fftw2 targets to makefiles further up the directory
	  structure.

2007-08-14 14:31  paultcochrane

	* trunk/xmds-devel/source/xsil2graphics.cc: Further code tidy-ups
	  and c++ isms.

2007-08-14 14:19  paultcochrane

	* trunk/xmds-devel/source/xsil2graphics.cc: Added some space to the
	  code to try to improve readability

2007-08-14 14:14  paultcochrane

	* trunk/xmds-devel/source/xsil2graphics.cc: Using c++ io output
	  instead of standard c. This allows us to use stdout and
	  stderr more easily. <cstring> is then no longer needed.
	  Also added usage output when no input file is specified to be
	  consistent
	  with xmds behaviour.

2007-08-14 13:57  paultcochrane

	* trunk/xmds-devel/source/main.cc,
	  trunk/xmds-devel/source/xmds_arg.cc,
	  trunk/xmds-devel/source/xmds_arg_element.cc,
	  trunk/xmds-devel/source/xmds_argv.cc,
	  trunk/xmds-devel/source/xmds_breakpoint.cc,
	  trunk/xmds-devel/source/xmds_element.cc,
	  trunk/xmds-devel/source/xmds_field.cc,
	  trunk/xmds-devel/source/xmds_filter.cc,
	  trunk/xmds-devel/source/xmds_globals.cc,
	  trunk/xmds-devel/source/xmds_integrate.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark45.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark45ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark45ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark89.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark89ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark89ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk4.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk4ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk4ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk9.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk9ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk9ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_si.cc,
	  trunk/xmds-devel/source/xmds_integrate_siex.cc,
	  trunk/xmds-devel/source/xmds_integrate_siip.cc,
	  trunk/xmds-devel/source/xmds_moment_group.cc,
	  trunk/xmds-devel/source/xmds_output.cc,
	  trunk/xmds-devel/source/xmds_segment.cc,
	  trunk/xmds-devel/source/xmds_sequence.cc,
	  trunk/xmds-devel/source/xmds_simulation.cc,
	  trunk/xmds-devel/source/xmds_utils.cc,
	  trunk/xmds-devel/source/xmds_vector.cc,
	  trunk/xmds-devel/source/xmds_vector_element.cc,
	  trunk/xmds-devel/source/xsil2graphics.cc,
	  trunk/xmds-devel/source/xsil_field.cc: Now using xmds_common.h in
	  .cc source files.

2007-08-14 13:56  paultcochrane

	* trunk/xmds-devel/source/Makefile.am: I should have added
	  xmds_common.h in the last commit. Duh.

2007-08-14 13:54  paultcochrane

	* trunk/xmds-devel/source/Makefile.am: Removing xmds_classes.h from
	  dependencies list.

2007-08-14 13:53  paultcochrane

	* trunk/xmds-devel/source/xmds_common.h: Getting the order of the
	  headers correct.

2007-08-14 13:41  paultcochrane

	* trunk/xmds-devel/source/dom3.h,
	  trunk/xmds-devel/source/getopt_xmds.h,
	  trunk/xmds-devel/source/kissdom.cc,
	  trunk/xmds-devel/source/kissdom.h,
	  trunk/xmds-devel/source/main.cc,
	  trunk/xmds-devel/source/xmds_arg.cc,
	  trunk/xmds-devel/source/xmds_arg.h,
	  trunk/xmds-devel/source/xmds_arg_element.cc,
	  trunk/xmds-devel/source/xmds_arg_element.h,
	  trunk/xmds-devel/source/xmds_argv.cc,
	  trunk/xmds-devel/source/xmds_argv.h,
	  trunk/xmds-devel/source/xmds_breakpoint.cc,
	  trunk/xmds-devel/source/xmds_breakpoint.h,
	  trunk/xmds-devel/source/xmds_common.h,
	  trunk/xmds-devel/source/xmds_complex.h,
	  trunk/xmds-devel/source/xmds_element.cc,
	  trunk/xmds-devel/source/xmds_element.h,
	  trunk/xmds-devel/source/xmds_field.cc,
	  trunk/xmds-devel/source/xmds_field.h,
	  trunk/xmds-devel/source/xmds_filter.cc,
	  trunk/xmds-devel/source/xmds_filter.h,
	  trunk/xmds-devel/source/xmds_globals.cc,
	  trunk/xmds-devel/source/xmds_globals.h,
	  trunk/xmds-devel/source/xmds_integrate.cc,
	  trunk/xmds-devel/source/xmds_integrate.h,
	  trunk/xmds-devel/source/xmds_integrate_ark45.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark45.h,
	  trunk/xmds-devel/source/xmds_integrate_ark45ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark45ex.h,
	  trunk/xmds-devel/source/xmds_integrate_ark45ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark45ip.h,
	  trunk/xmds-devel/source/xmds_integrate_ark89.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark89.h,
	  trunk/xmds-devel/source/xmds_integrate_ark89ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark89ex.h,
	  trunk/xmds-devel/source/xmds_integrate_ark89ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark89ip.h,
	  trunk/xmds-devel/source/xmds_integrate_ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_ex.h,
	  trunk/xmds-devel/source/xmds_integrate_ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_ip.h,
	  trunk/xmds-devel/source/xmds_integrate_rk4.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk4.h,
	  trunk/xmds-devel/source/xmds_integrate_rk4ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk4ex.h,
	  trunk/xmds-devel/source/xmds_integrate_rk4ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk4ip.h,
	  trunk/xmds-devel/source/xmds_integrate_rk9.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk9.h,
	  trunk/xmds-devel/source/xmds_integrate_rk9ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk9ex.h,
	  trunk/xmds-devel/source/xmds_integrate_rk9ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk9ip.h,
	  trunk/xmds-devel/source/xmds_integrate_si.cc,
	  trunk/xmds-devel/source/xmds_integrate_si.h,
	  trunk/xmds-devel/source/xmds_integrate_siex.cc,
	  trunk/xmds-devel/source/xmds_integrate_siex.h,
	  trunk/xmds-devel/source/xmds_integrate_siip.cc,
	  trunk/xmds-devel/source/xmds_integrate_siip.h,
	  trunk/xmds-devel/source/xmds_moment_group.cc,
	  trunk/xmds-devel/source/xmds_moment_group.h,
	  trunk/xmds-devel/source/xmds_output.cc,
	  trunk/xmds-devel/source/xmds_output.h,
	  trunk/xmds-devel/source/xmds_segment.cc,
	  trunk/xmds-devel/source/xmds_segment.h,
	  trunk/xmds-devel/source/xmds_sequence.cc,
	  trunk/xmds-devel/source/xmds_sequence.h,
	  trunk/xmds-devel/source/xmds_simulation.cc,
	  trunk/xmds-devel/source/xmds_simulation.h,
	  trunk/xmds-devel/source/xmds_utils.cc,
	  trunk/xmds-devel/source/xmds_utils.h,
	  trunk/xmds-devel/source/xmds_vector.cc,
	  trunk/xmds-devel/source/xmds_vector.h,
	  trunk/xmds-devel/source/xmds_vector_element.cc,
	  trunk/xmds-devel/source/xmds_vector_element.h,
	  trunk/xmds-devel/source/xml_basics.cc,
	  trunk/xmds-devel/source/xml_basics.h,
	  trunk/xmds-devel/source/xml_parser.cc,
	  trunk/xmds-devel/source/xml_parser.h,
	  trunk/xmds-devel/source/xsil2graphics.cc,
	  trunk/xmds-devel/source/xsil_field.cc,
	  trunk/xmds-devel/source/xsil_field.h: Set the svn:keywords
	  property on all .cc and .h files.

2007-08-14 13:38  paultcochrane

	* trunk/xmds-devel/source/xmds_common.h: Should have written
	  xml_basics.h. duh.

2007-08-14 13:35  paultcochrane

	* trunk/xmds-devel/source/xmds_common.h: Added a file to wrap the
	  common headers used in (almost) all xmds source
	  files. I know this seems to do the same job as what
	  xmds_classes.h did,
	  however the name is an important functional change, and we've
	  managed to
	  remove the overall dependence on <list> (which wasn't used) and
	  on <string>
	  which is only used in certain places.

2007-08-14 12:24  paultcochrane

	* trunk/xmds-devel/source/xmds_classes.h: We no longer need
	  xmds_classes.h. Deleting...

2007-08-14 12:13  paultcochrane

	* trunk/xmds-devel/source/main.cc,
	  trunk/xmds-devel/source/xmds_classes.h: main.cc no longer
	  requires xmds_classes.h

2007-08-14 12:12  paultcochrane

	* trunk/xmds-devel/source/xmds_classes.h: xmds_utils.h no longer
	  necessary in xmds_classes.h

2007-08-14 12:11  paultcochrane

	* trunk/xmds-devel/source/xmds_classes.h: xmds_element.h no longer
	  necessary in xmds_classes.h

2007-08-14 12:10  paultcochrane

	* trunk/xmds-devel/source/xmds_classes.h: xmds_globals.h no longer
	  necessary in xmds_classes.h

2007-08-14 12:10  paultcochrane

	* trunk/xmds-devel/source/xmds_classes.h,
	  trunk/xmds-devel/source/xmds_field.cc: xmds_field.h no longer
	  necessary in xmds_classes.h

2007-08-14 12:09  paultcochrane

	* trunk/xmds-devel/source/xmds_classes.h,
	  trunk/xmds-devel/source/xmds_vector.cc: xmds_vector.h no longer
	  necessary in xmds_classes.h

2007-08-14 12:08  paultcochrane

	* trunk/xmds-devel/source/xmds_classes.h,
	  trunk/xmds-devel/source/xmds_field.cc,
	  trunk/xmds-devel/source/xmds_vector_element.cc:
	  xmds_vector_element.h no longer necessary in xmds_classes.h

2007-08-14 12:07  paultcochrane

	* trunk/xmds-devel/source/xmds_argv.cc,
	  trunk/xmds-devel/source/xmds_classes.h: xmds_argv.h no longer
	  necessary in xmds_classes.h

2007-08-14 12:06  paultcochrane

	* trunk/xmds-devel/source/xmds_classes.h: xmds_arg.h no longer
	  necessary in xmds_classes.h

2007-08-14 12:05  paultcochrane

	* trunk/xmds-devel/source/xmds_arg_element.cc,
	  trunk/xmds-devel/source/xmds_argv.cc,
	  trunk/xmds-devel/source/xmds_classes.h: xmds_arg_element.h no
	  longer necessary in xmds_classes.h

2007-08-14 12:03  paultcochrane

	* trunk/xmds-devel/source/xmds_classes.h,
	  trunk/xmds-devel/source/xmds_moment_group.cc: xmds_moment_group.h
	  no longer necessary in xmds_classes.h

2007-08-14 12:02  paultcochrane

	* trunk/xmds-devel/source/xmds_classes.h,
	  trunk/xmds-devel/source/xmds_output.cc: xmds_output.h no longer
	  necessary in xmds_classes.h

2007-08-14 11:54  paultcochrane

	* trunk/xmds-devel/source/xmds_classes.h,
	  trunk/xmds-devel/source/xmds_segment.cc: xmds_segment.h no longer
	  needed in xmds_classes.h

2007-08-14 11:53  paultcochrane

	* trunk/xmds-devel/source/xmds_classes.h,
	  trunk/xmds-devel/source/xmds_filter.cc: xmds_filters.h wasn't
	  needed in xmds_classes.h

2007-08-14 11:51  paultcochrane

	* trunk/xmds-devel/source/main.cc,
	  trunk/xmds-devel/source/xmds_arg_element.cc,
	  trunk/xmds-devel/source/xmds_argv.cc,
	  trunk/xmds-devel/source/xmds_classes.h,
	  trunk/xmds-devel/source/xmds_field.cc,
	  trunk/xmds-devel/source/xmds_filter.cc,
	  trunk/xmds-devel/source/xmds_moment_group.cc,
	  trunk/xmds-devel/source/xmds_output.cc,
	  trunk/xmds-devel/source/xmds_segment.cc,
	  trunk/xmds-devel/source/xmds_simulation.cc,
	  trunk/xmds-devel/source/xmds_vector.cc,
	  trunk/xmds-devel/source/xmds_vector_element.cc: Disentangled
	  xmds_simulation.h from xmds_classes.h

2007-08-14 10:32  paultcochrane

	* trunk/xmds-devel/source/xmds_classes.h,
	  trunk/xmds-devel/source/xmds_sequence.cc: Removed xmds_sequence.h
	  from xmds_classes.h

2007-08-14 10:25  paultcochrane

	* trunk/xmds-devel/source/xmds_classes.h,
	  trunk/xmds-devel/source/xmds_integrate.cc: xmds_integrate.h
	  removed from xmds_classes.h

2007-08-14 10:23  paultcochrane

	* trunk/xmds-devel/source/xmds_breakpoint.cc,
	  trunk/xmds-devel/source/xmds_classes.h,
	  trunk/xmds-devel/source/xmds_sequence.cc: Disentangled
	  xmds_breakpoint.h from xmds_classes.h

2007-08-14 10:14  paultcochrane

	* trunk/xmds-devel/source/xmds_classes.h,
	  trunk/xmds-devel/source/xmds_integrate_ark45.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark89.cc,
	  trunk/xmds-devel/source/xmds_integrate_ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk4.cc,
	  trunk/xmds-devel/source/xmds_integrate_si.cc,
	  trunk/xmds-devel/source/xmds_integrate_siex.cc,
	  trunk/xmds-devel/source/xmds_integrate_siip.cc,
	  trunk/xmds-devel/source/xmds_sequence.cc: Removed the remaining
	  xmds_classes.h dependenices from the
	  algorithm-related class files.

2007-08-14 05:16  grahamdennis

	* trunk/xmds-devel/source/xmds_integrate_ark45.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark89.cc: Finally, the bug
	  I wanted to fix... Due to the way errors were calculated for
	  adaptive algorithms, in really bad situations (where the field
	  becomes infinite due to overly large step sizes), small errors
	  would be reported instead of really large errors. This is
	  particularly noticeable for situations with density-dependent
	  loss. This caused the rest of the simulation to fail.

2007-08-14 04:42  grahamdennis

	* trunk/xmds-devel/source/kissdom.cc,
	  trunk/xmds-devel/source/xmds_filter.cc,
	  trunk/xmds-devel/source/xmds_integrate.cc,
	  trunk/xmds-devel/source/xmds_integrate_siip.cc,
	  trunk/xmds-devel/source/xmds_sequence.cc: Fixing warnings due to
	  size_t's being passed to printf where the format specifier %i was
	  used instead of %zi.

2007-08-14 04:32  grahamdennis

	* trunk/xmds-devel/configure.in,
	  trunk/xmds-devel/source/xmds_simulation.cc: Reverting changes in
	  r1379 and 1453 (making it possible to build xmds without FFTW2)
	  because it broke the ability to build xmds with FFTW2 and FFTW3.

2007-08-14 04:16  grahamdennis

	* trunk/xmds-devel/Makefile.am: Fixing broken Makefile.am

2007-08-13 15:52  paultcochrane

	* trunk/xmds-devel/source/xmds_classes.h,
	  trunk/xmds-devel/source/xmds_integrate_rk4ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk4ip.cc,
	  trunk/xmds-devel/source/xmds_sequence.cc: RK4 subclasses now no
	  longer depend upon xmds_classes.h

2007-08-13 10:35  paultcochrane

	* trunk/xmds-devel/source/xmds_classes.h,
	  trunk/xmds-devel/source/xmds_integrate_rk9.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk9ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk9ip.cc,
	  trunk/xmds-devel/source/xmds_sequence.cc: RK9 headers
	  disentangled from xmds_classes.h

2007-08-13 10:29  paultcochrane

	* trunk/xmds-devel/source/xmds_classes.h,
	  trunk/xmds-devel/source/xmds_integrate_ark45ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark45ip.cc,
	  trunk/xmds-devel/source/xmds_sequence.cc: Removed ark45 header
	  dependencies from xmds_classes.h

2007-08-13 08:28  paultcochrane

	* trunk/xmds-devel/source/xmds_classes.h,
	  trunk/xmds-devel/source/xmds_integrate_ark89ip.cc,
	  trunk/xmds-devel/source/xmds_sequence.cc: xmds_classes.h no
	  longer depends upon xmds_integrate_ark89ip.h

2007-08-13 08:24  paultcochrane

	* trunk/xmds-devel/source/xmds_classes.h,
	  trunk/xmds-devel/source/xmds_integrate_ark89ex.cc,
	  trunk/xmds-devel/source/xmds_sequence.cc: xmds_classes.h now no
	  longer depends upon xmds_integrate_ark89ex.h

2007-08-13 08:12  paultcochrane

	* trunk/xmds-devel/source/xmds_arg_element.cc,
	  trunk/xmds-devel/source/xmds_argv.cc,
	  trunk/xmds-devel/source/xmds_breakpoint.cc,
	  trunk/xmds-devel/source/xmds_field.cc,
	  trunk/xmds-devel/source/xmds_filter.cc,
	  trunk/xmds-devel/source/xmds_filter.h,
	  trunk/xmds-devel/source/xmds_integrate.cc,
	  trunk/xmds-devel/source/xmds_integrate.h,
	  trunk/xmds-devel/source/xmds_integrate_ark45.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark45ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark45ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark89.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark89ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark89ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk4.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk4ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk4ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk9.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk9ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk9ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_si.cc,
	  trunk/xmds-devel/source/xmds_integrate_siex.cc,
	  trunk/xmds-devel/source/xmds_integrate_siip.cc,
	  trunk/xmds-devel/source/xmds_moment_group.cc,
	  trunk/xmds-devel/source/xmds_output.cc,
	  trunk/xmds-devel/source/xmds_output.h,
	  trunk/xmds-devel/source/xmds_segment.cc,
	  trunk/xmds-devel/source/xmds_sequence.cc,
	  trunk/xmds-devel/source/xmds_simulation.cc,
	  trunk/xmds-devel/source/xmds_simulation.h,
	  trunk/xmds-devel/source/xmds_vector.cc,
	  trunk/xmds-devel/source/xmds_vector.h,
	  trunk/xmds-devel/source/xmds_vector_element.cc,
	  trunk/xmds-devel/source/xmds_vector_element.h: Each .cc file now
	  includes its own header. Also needed to add some explicit
	  header dependencies to various sub headers to get things to
	  compile again.

2007-08-13 07:46  paultcochrane

	* trunk/xmds-devel/source/xmds_arg_element.h,
	  trunk/xmds-devel/source/xmds_breakpoint.h,
	  trunk/xmds-devel/source/xmds_filter.h,
	  trunk/xmds-devel/source/xmds_integrate.h,
	  trunk/xmds-devel/source/xmds_integrate_ark45.h,
	  trunk/xmds-devel/source/xmds_integrate_ark45ex.h,
	  trunk/xmds-devel/source/xmds_integrate_ark45ip.h,
	  trunk/xmds-devel/source/xmds_integrate_ark89.h,
	  trunk/xmds-devel/source/xmds_integrate_ark89ex.h,
	  trunk/xmds-devel/source/xmds_integrate_ark89ip.h,
	  trunk/xmds-devel/source/xmds_integrate_ex.h,
	  trunk/xmds-devel/source/xmds_integrate_ip.h,
	  trunk/xmds-devel/source/xmds_integrate_rk4.h,
	  trunk/xmds-devel/source/xmds_integrate_rk4ex.h,
	  trunk/xmds-devel/source/xmds_integrate_rk4ip.h,
	  trunk/xmds-devel/source/xmds_integrate_rk9.h,
	  trunk/xmds-devel/source/xmds_integrate_rk9ex.h,
	  trunk/xmds-devel/source/xmds_integrate_rk9ip.h,
	  trunk/xmds-devel/source/xmds_integrate_si.h,
	  trunk/xmds-devel/source/xmds_integrate_siex.h,
	  trunk/xmds-devel/source/xmds_integrate_siip.h,
	  trunk/xmds-devel/source/xmds_moment_group.h,
	  trunk/xmds-devel/source/xmds_output.h,
	  trunk/xmds-devel/source/xmds_segment.h,
	  trunk/xmds-devel/source/xmds_sequence.h,
	  trunk/xmds-devel/source/xmds_simulation.h,
	  trunk/xmds-devel/source/xmds_vector_element.h: Added header
	  dependencies for objects inheriting directly from other
	  objects.

2007-08-13 07:07  paultcochrane

	* trunk/xmds-devel/source/Makefile.am,
	  trunk/xmds-devel/source/xmds_classes.h,
	  trunk/xmds-devel/source/xmds_integrate_ark45ex.h,
	  trunk/xmds-devel/source/xmds_integrate_ark45ip.h,
	  trunk/xmds-devel/source/xmds_integrate_ark89ex.h,
	  trunk/xmds-devel/source/xmds_integrate_ark89ip.h,
	  trunk/xmds-devel/source/xmds_integrate_rk4ex.h,
	  trunk/xmds-devel/source/xmds_integrate_rk4ip.h,
	  trunk/xmds-devel/source/xmds_integrate_rk9ex.h,
	  trunk/xmds-devel/source/xmds_integrate_rk9ip.h,
	  trunk/xmds-devel/source/xmds_simulation.h: Moved the remaining
	  class declarations out of xmds_classes.h into their own
	  header files. Now to try and unravel the header dependencies so
	  that if
	  something changes in a header, absolutely everything needs to get
	  rebuilt...

2007-08-11 15:50  paultcochrane

	* ., trunk/xmds-devel/test/generated_code/Makefile,
	  trunk/xmds-devel/test/generated_code/reference_fftw2,
	  trunk/xmds-devel/test/generated_code/reference_fftw2/atomlaser.cc,
	  trunk/xmds-devel/test/generated_code/reference_fftw2/branch.cc,
	  trunk/xmds-devel/test/generated_code/reference_fftw2/brusselator.cc,
	  trunk/xmds-devel/test/generated_code/reference_fftw2/catcycle.cc,
	  trunk/xmds-devel/test/generated_code/reference_fftw2/chain.cc,
	  trunk/xmds-devel/test/generated_code/reference_fftw2/chemkin.cc,
	  trunk/xmds-devel/test/generated_code/reference_fftw2/diffusion.cc,
	  trunk/xmds-devel/test/generated_code/reference_fftw2/diffusion2.cc,
	  trunk/xmds-devel/test/generated_code/reference_fftw2/duffing.cc,
	  trunk/xmds-devel/test/generated_code/reference_fftw2/fibre.cc,
	  trunk/xmds-devel/test/generated_code/reference_fftw2/fisher_reaction_diffusion.cc,
	  trunk/xmds-devel/test/generated_code/reference_fftw2/fullpos3D.cc,
	  trunk/xmds-devel/test/generated_code/reference_fftw2/groundstate.cc,
	  trunk/xmds-devel/test/generated_code/reference_fftw2/hires.cc,
	  trunk/xmds-devel/test/generated_code/reference_fftw2/krebs.cc,
	  trunk/xmds-devel/test/generated_code/reference_fftw2/kubo.cc,
	  trunk/xmds-devel/test/generated_code/reference_fftw2/lane_emden.cc,
	  trunk/xmds-devel/test/generated_code/reference_fftw2/lorenz.cc,
	  trunk/xmds-devel/test/generated_code/reference_fftw2/lotka_volterra.cc,
	  trunk/xmds-devel/test/generated_code/reference_fftw2/ndparamp.cc,
	  trunk/xmds-devel/test/generated_code/reference_fftw2/nlse.cc,
	  trunk/xmds-devel/test/generated_code/reference_fftw2/oregonator.cc,
	  trunk/xmds-devel/test/generated_code/reference_fftw2/paraxial_wave.cc,
	  trunk/xmds-devel/test/generated_code/reference_fftw2/pendulum.cc,
	  trunk/xmds-devel/test/generated_code/reference_fftw2/ring_modulator.cc,
	  trunk/xmds-devel/test/generated_code/reference_fftw2/sech_soliton.cc,
	  trunk/xmds-devel/test/generated_code/reference_fftw2/sech_soliton_tdepk.cc,
	  trunk/xmds-devel/test/generated_code/reference_fftw2/sine.cc,
	  trunk/xmds-devel/test/generated_code/reference_fftw2/soliton.cc,
	  trunk/xmds-devel/test/generated_code/reference_fftw2/thermkin.cc,
	  trunk/xmds-devel/test/generated_code/reference_fftw2/tla.cc,
	  trunk/xmds-devel/test/generated_code/reference_fftw2/van_der_pol.cc,
	  trunk/xmds-devel/test/generated_code/reference_fftw2/vibstring.cc:
	  FFTW2 and FFTW3 generated output is different, so we need
	  different
	  references depending upon which version xmds is built with. Here
	  is a quick
	  hack of the test Makefile to handle this, and the appropriate
	  reference
	  files.

2007-08-10 18:41  paultcochrane

	* ., trunk/xmds-devel/configure.in: I'd failed to properly
	  initialise USING_FFTW3. This has been fixed.

2007-08-10 18:41  paultcochrane

	* ., trunk/xmds-devel/admin/cvs2cl.pl: We're using svn now, so
	  don't need the script anymore.

2007-08-10 15:34  paultcochrane

	* trunk/xmds-devel/source/Makefile.am,
	  trunk/xmds-devel/source/xmds_classes.h,
	  trunk/xmds-devel/source/xmds_integrate_ark89.h,
	  trunk/xmds-devel/source/xmds_integrate_rk4.h,
	  trunk/xmds-devel/source/xmds_integrate_rk9.h,
	  trunk/xmds-devel/source/xmds_integrate_siex.h,
	  trunk/xmds-devel/source/xmds_integrate_siip.h: I know I should do
	  these as individual commits as then one has more
	  fine-grained control over when things have broken if at all.
	  However, it
	  can't hurt to separate some of the xmdsIntegrate* declarations in
	  one go,
	  can it? ;-)

2007-08-10 15:02  paultcochrane

	* trunk/xmds-devel/source/Makefile.am,
	  trunk/xmds-devel/source/xmds_classes.h,
	  trunk/xmds-devel/source/xmds_integrate_ark45.h: Moved
	  xmdsIntegrateARK45 declarations into xmds_integrate_ark45.h

2007-08-10 14:59  paultcochrane

	* trunk/xmds-devel/source/Makefile.am,
	  trunk/xmds-devel/source/xmds_classes.h,
	  trunk/xmds-devel/source/xmds_integrate_si.h: Moved
	  xmdsIntegrateSI declarations into xmds_integrate_si.h

2007-08-10 14:55  paultcochrane

	* trunk/xmds-devel/source/Makefile.am,
	  trunk/xmds-devel/source/xmds_classes.h,
	  trunk/xmds-devel/source/xmds_integrate_ex.h: Moved
	  xmdsIntegrateEX declarations into xmds_integrate_ex.h

2007-08-10 14:45  paultcochrane

	* trunk/xmds-devel/source/Makefile.am,
	  trunk/xmds-devel/source/xmds_classes.h,
	  trunk/xmds-devel/source/xmds_integrate_ip.h: Moved
	  xmdsIntegrateIP stuff into xmds_integrate_ip.h

2007-08-10 14:33  paultcochrane

	* trunk/xmds-devel/source/Makefile.am,
	  trunk/xmds-devel/source/xmds_breakpoint.h,
	  trunk/xmds-devel/source/xmds_classes.h: Moved xmdsBreakpoint
	  declarations into xmds_breakpoint.h

2007-08-10 14:30  paultcochrane

	* trunk/xmds-devel/source/Makefile.am,
	  trunk/xmds-devel/source/xmds_classes.h,
	  trunk/xmds-devel/source/xmds_filter.h: Moved xmdsFilter
	  declarations into xmds_filter.h

2007-08-10 14:27  paultcochrane

	* trunk/xmds-devel/source/Makefile.am,
	  trunk/xmds-devel/source/xmds_classes.h,
	  trunk/xmds-devel/source/xmds_integrate.h: Moved xmdsIntegrate
	  declarations into xmds_integrate.h

2007-08-10 14:24  paultcochrane

	* trunk/xmds-devel/source/Makefile.am,
	  trunk/xmds-devel/source/xmds_classes.h,
	  trunk/xmds-devel/source/xmds_sequence.h: Moved xmdsSequence
	  declarations into xmds_sequence.h

2007-08-10 14:20  paultcochrane

	* trunk/xmds-devel/source/Makefile.am,
	  trunk/xmds-devel/source/xmds_classes.h,
	  trunk/xmds-devel/source/xmds_segment.h: Moved xmdsSegment
	  declarations into xmds_segment.h

2007-08-10 14:20  paultcochrane

	* trunk/xmds-devel/source/xmds_arg.cc,
	  trunk/xmds-devel/source/xmds_arg.h,
	  trunk/xmds-devel/source/xmds_argv.cc: Trying to improve header
	  dependencies further. Not getting far though...

2007-08-10 13:58  paultcochrane

	* trunk/xmds-devel/source/Makefile.am,
	  trunk/xmds-devel/source/xmds_classes.h,
	  trunk/xmds-devel/source/xmds_output.h: Moved xmdsOutput
	  declarations into xmds_output.h

2007-08-10 13:43  paultcochrane

	* trunk/xmds-devel/source/xmds_element.cc,
	  trunk/xmds-devel/source/xmds_globals.cc: Starting to remove
	  dependencies upon xmds_classes.h

2007-08-10 13:30  paultcochrane

	* trunk/xmds-devel/source/Makefile.am,
	  trunk/xmds-devel/source/xmds_arg_element.h,
	  trunk/xmds-devel/source/xmds_classes.h,
	  trunk/xmds-devel/source/xmds_moment_group.h: Moved xmdsArgElement
	  and xmdsMomentGroup declarations into their own
	  headers.

2007-08-10 13:20  paultcochrane

	* trunk/xmds-devel/source/Makefile.am,
	  trunk/xmds-devel/source/xmds_arg.h,
	  trunk/xmds-devel/source/xmds_classes.h: Moved xmdsArg
	  declarations into xmds_arg.h

2007-08-10 13:11  paultcochrane

	* trunk/xmds-devel/source/Makefile.am,
	  trunk/xmds-devel/source/xmds_argv.cc,
	  trunk/xmds-devel/source/xmds_argv.h,
	  trunk/xmds-devel/source/xmds_classes.h: Moved declarations of
	  xmdsArgv into xmds_argv.h

2007-08-10 13:10  paultcochrane

	* trunk/xmds-devel/source/xmds_element.h: We should have been
	  #including xmds_utils.h here... Oops. Fixed that.

2007-08-10 13:02  paultcochrane

	* trunk/xmds-devel/source/Makefile.am,
	  trunk/xmds-devel/source/xmds_classes.h,
	  trunk/xmds-devel/source/xmds_vector_element.h: Moved
	  xmdsVectorElement declarations into xmds_vector_element.h

2007-08-10 12:58  paultcochrane

	* trunk/xmds-devel/source/Makefile.am,
	  trunk/xmds-devel/source/xmds_classes.h,
	  trunk/xmds-devel/source/xmds_vector.h: Moved xmdsVector
	  declarations into xmds_vector.h

2007-08-10 08:25  paultcochrane

	* trunk/xmds-devel/source/Makefile.am,
	  trunk/xmds-devel/source/xmds_classes.h,
	  trunk/xmds-devel/source/xmds_field.h: Moved xmdsField
	  declarations int xmds_field.h

2007-08-10 08:12  paultcochrane

	* trunk/xmds-devel/source/Makefile.am,
	  trunk/xmds-devel/source/xmds_classes.h,
	  trunk/xmds-devel/source/xmds_globals.cc,
	  trunk/xmds-devel/source/xmds_globals.h: Moved xmdsGloabls
	  declarations into xmds_globals.h

2007-08-10 08:12  paultcochrane

	* trunk/xmds-devel/source/xmds_utils.cc,
	  trunk/xmds-devel/source/xml_basics.cc: Removed old commented-out
	  code.

2007-08-10 07:44  paultcochrane

	* trunk/xmds-devel/source/Makefile.am,
	  trunk/xmds-devel/source/xmds_classes.h,
	  trunk/xmds-devel/source/xmds_element.h: Moved xmdsElement
	  delcarations from xmds_classes.h into its own header.
	  Added the relevant references to the Makefile and to
	  xmds_classes.h so that
	  the other classes can find everything properly.

2007-08-10 07:42  paultcochrane

	* trunk/xmds-devel/source/xmds_utils.h: Put header guards in
	  xmds_utils.h

2007-08-10 07:22  paultcochrane

	* trunk/xmds-devel/source/xmds_classes.h: Added a guard for the
	  header, this is to protect against multiple calls of
	  the header once I've broken up the header a bit (I'm going to try
	  to
	  modularise the code a bit more).

2007-08-09 16:39  paultcochrane

	* trunk/xmds-devel/source/xmds_field.cc: Trying to get the code to
	  look ok within 80 chars.

2007-08-09 16:20  paultcochrane

	* trunk/xmds-devel/source/xmds_field.cc: Added spaces, braces and
	  other minor cleanups

2007-08-09 15:50  paultcochrane

	* trunk/xmds-devel/source/xmds_integrate.cc,
	  trunk/xmds-devel/source/xmds_utils.cc: Cleaning up after myself
	  (just removing trailing whitespace)

2007-08-09 15:46  paultcochrane

	* trunk/xmds-devel/source/xmds_integrate.cc: Trying even harder to
	  get things within 80 chars, or at least make things
	  a bit easier to work out what's going on.

2007-08-09 15:42  paultcochrane

	* trunk/xmds-devel/source/xmds_integrate.cc,
	  trunk/xmds-devel/source/xmds_utils.cc: More line-length
	  shortening...

2007-08-09 15:33  paultcochrane

	* trunk/xmds-devel/source/xmds_integrate.cc: Some bitwise ANDs
	  should have been boolean ANDs

2007-08-09 12:43  paultcochrane

	* trunk/xmds-devel/source/xmds_integrate.cc: Split long lines
	  across multiple lines; again, trying to improve the
	  readability of the code.

2007-08-09 12:39  paultcochrane

	* trunk/xmds-devel/test/generated_code/Makefile,
	  trunk/xmds-devel/test/generated_code/reference/atomlaser.cc,
	  trunk/xmds-devel/test/generated_code/reference/branch.cc,
	  trunk/xmds-devel/test/generated_code/reference/brusselator.cc,
	  trunk/xmds-devel/test/generated_code/reference/catcycle.cc,
	  trunk/xmds-devel/test/generated_code/reference/chain.cc,
	  trunk/xmds-devel/test/generated_code/reference/chemkin.cc,
	  trunk/xmds-devel/test/generated_code/reference/diffusion.cc,
	  trunk/xmds-devel/test/generated_code/reference/diffusion2.cc,
	  trunk/xmds-devel/test/generated_code/reference/duffing.cc,
	  trunk/xmds-devel/test/generated_code/reference/fibre.cc,
	  trunk/xmds-devel/test/generated_code/reference/fisher_reaction_diffusion.cc,
	  trunk/xmds-devel/test/generated_code/reference/fullpos3D.cc,
	  trunk/xmds-devel/test/generated_code/reference/groundstate.cc,
	  trunk/xmds-devel/test/generated_code/reference/hires.cc,
	  trunk/xmds-devel/test/generated_code/reference/krebs.cc,
	  trunk/xmds-devel/test/generated_code/reference/kubo.cc,
	  trunk/xmds-devel/test/generated_code/reference/lane_emden.cc,
	  trunk/xmds-devel/test/generated_code/reference/lorenz.cc,
	  trunk/xmds-devel/test/generated_code/reference/lotka_volterra.cc,
	  trunk/xmds-devel/test/generated_code/reference/ndparamp.cc,
	  trunk/xmds-devel/test/generated_code/reference/nlse.cc,
	  trunk/xmds-devel/test/generated_code/reference/oregonator.cc,
	  trunk/xmds-devel/test/generated_code/reference/paraxial_wave.cc,
	  trunk/xmds-devel/test/generated_code/reference/pendulum.cc,
	  trunk/xmds-devel/test/generated_code/reference/ring_modulator.cc,
	  trunk/xmds-devel/test/generated_code/reference/sech_soliton.cc,
	  trunk/xmds-devel/test/generated_code/reference/sech_soliton_tdepk.cc,
	  trunk/xmds-devel/test/generated_code/reference/sine.cc,
	  trunk/xmds-devel/test/generated_code/reference/soliton.cc,
	  trunk/xmds-devel/test/generated_code/reference/thermkin.cc,
	  trunk/xmds-devel/test/generated_code/reference/tla.cc,
	  trunk/xmds-devel/test/generated_code/reference/van_der_pol.cc,
	  trunk/xmds-devel/test/generated_code/reference/vibstring.cc: The
	  generated output changes as soon as the version information
	  changes.
	  Now grepping out this dynamic output, and have removed the
	  relevant lines
	  from the references.

2007-08-09 12:06  paultcochrane

	* trunk/xmds-devel/source: Updated svn:ignore property to ignore
	  files generated by gcov

2007-08-09 12:00  paultcochrane

	* trunk/xmds-devel/source/xmds_integrate.cc: Continuing with code
	  tidying. Extra spaces, more brackets in places etc.
	  etc.

2007-08-09 09:56  paultcochrane

	* trunk/xmds-devel/source/xmds_utils.cc: Whitespace *within* code,
	  however, is a good thing. It makes code easier to
	  read. Hence I've just added some...

2007-08-09 09:11  paultcochrane

	* trunk/xmds-devel/configure.in: Removed extra gcc-specific
	  warnings options (I only wanted to use them for
	  testing purposes, sorry for the extra commit)

2007-08-09 09:00  paultcochrane

	* trunk/xmds-devel/configure.in,
	  trunk/xmds-devel/source/kissdom.cc,
	  trunk/xmds-devel/source/xmds_arg.cc,
	  trunk/xmds-devel/source/xmds_arg_element.cc,
	  trunk/xmds-devel/source/xmds_argv.cc,
	  trunk/xmds-devel/source/xmds_breakpoint.cc,
	  trunk/xmds-devel/source/xmds_element.cc,
	  trunk/xmds-devel/source/xmds_field.cc,
	  trunk/xmds-devel/source/xmds_filter.cc,
	  trunk/xmds-devel/source/xmds_globals.cc,
	  trunk/xmds-devel/source/xmds_integrate.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark45.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark45ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark45ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark89.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark89ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark89ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk4.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk4ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk4ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk9.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk9ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk9ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_si.cc,
	  trunk/xmds-devel/source/xmds_integrate_siex.cc,
	  trunk/xmds-devel/source/xmds_integrate_siip.cc,
	  trunk/xmds-devel/source/xmds_moment_group.cc,
	  trunk/xmds-devel/source/xmds_output.cc,
	  trunk/xmds-devel/source/xmds_segment.cc,
	  trunk/xmds-devel/source/xmds_sequence.cc,
	  trunk/xmds-devel/source/xmds_simulation.cc,
	  trunk/xmds-devel/source/xmds_utils.cc,
	  trunk/xmds-devel/source/xmds_vector.cc,
	  trunk/xmds-devel/source/xmds_vector_element.cc,
	  trunk/xmds-devel/source/xml_basics.cc,
	  trunk/xmds-devel/source/xml_basics.h,
	  trunk/xmds-devel/source/xml_parser.cc,
	  trunk/xmds-devel/source/xsil_field.cc: There shouldn't be
	  semicolons at the end of class/function etc. definitions.
	  Hence removed them.

2007-08-09 07:30  paultcochrane

	* trunk/xmds-devel/source/dom3.h,
	  trunk/xmds-devel/source/getopt_xmds.h,
	  trunk/xmds-devel/source/kissdom.cc,
	  trunk/xmds-devel/source/kissdom.h,
	  trunk/xmds-devel/source/main.cc,
	  trunk/xmds-devel/source/xmds_arg.cc,
	  trunk/xmds-devel/source/xmds_arg_element.cc,
	  trunk/xmds-devel/source/xmds_argv.cc,
	  trunk/xmds-devel/source/xmds_breakpoint.cc,
	  trunk/xmds-devel/source/xmds_classes.h,
	  trunk/xmds-devel/source/xmds_complex.h,
	  trunk/xmds-devel/source/xmds_element.cc,
	  trunk/xmds-devel/source/xmds_field.cc,
	  trunk/xmds-devel/source/xmds_filter.cc,
	  trunk/xmds-devel/source/xmds_globals.cc,
	  trunk/xmds-devel/source/xmds_integrate.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark45.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark45ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark45ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark89.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark89ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark89ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk4.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk4ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk4ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk9.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk9ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk9ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_si.cc,
	  trunk/xmds-devel/source/xmds_integrate_siex.cc,
	  trunk/xmds-devel/source/xmds_integrate_siip.cc,
	  trunk/xmds-devel/source/xmds_moment_group.cc,
	  trunk/xmds-devel/source/xmds_output.cc,
	  trunk/xmds-devel/source/xmds_segment.cc,
	  trunk/xmds-devel/source/xmds_sequence.cc,
	  trunk/xmds-devel/source/xmds_simulation.cc,
	  trunk/xmds-devel/source/xmds_utils.cc,
	  trunk/xmds-devel/source/xmds_utils.h,
	  trunk/xmds-devel/source/xmds_vector.cc,
	  trunk/xmds-devel/source/xmds_vector_element.cc,
	  trunk/xmds-devel/source/xml_basics.cc,
	  trunk/xmds-devel/source/xml_basics.h,
	  trunk/xmds-devel/source/xml_parser.cc,
	  trunk/xmds-devel/source/xml_parser.h,
	  trunk/xmds-devel/source/xsil2graphics.cc,
	  trunk/xmds-devel/source/xsil_field.cc,
	  trunk/xmds-devel/source/xsil_field.h: Purged the source of
	  trailing whitespace

2007-08-08 16:25  paultcochrane

	* trunk/xmds-devel/test/coding_stds/trailing_space.t: This adds a
	  test for trailing spaces in source code. This is fairly aesthetic
	  but trailing spaces *are* yuckky.

2007-08-08 16:21  paultcochrane

	* trunk/xmds-devel/source/kissdom.h,
	  trunk/xmds-devel/source/xmds_classes.h,
	  trunk/xmds-devel/source/xmds_complex.h,
	  trunk/xmds-devel/source/xmds_filter.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark89.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk4.cc,
	  trunk/xmds-devel/source/xmds_sequence.cc,
	  trunk/xmds-devel/source/xmds_simulation.cc,
	  trunk/xmds-devel/source/xmds_utils.h,
	  trunk/xmds-devel/source/xmds_vector.cc,
	  trunk/xmds-devel/source/xml_basics.h,
	  trunk/xmds-devel/source/xml_parser.h,
	  trunk/xmds-devel/source/xsil_field.h: Banishing hard tabs from
	  the source.

2007-08-08 16:20  paultcochrane

	* trunk/xmds-devel/test/generated_code/reference/fibre.cc: Removing
	  hard tabs from the sources altered the fibre.cc reference. This
	  commit updates the reference.

2007-08-08 16:08  paultcochrane

	* trunk/xmds-devel/test/coding_stds/tabs.t: Added a coding
	  standards test to test for hard tabs (hard tabs aren't
	  portable across editors, however spaces are). I.e. this will help
	  ensure
	  that the source looks the same wherever you are, and what you use
	  to view it.

2007-08-08 15:57  paultcochrane

	* trunk/xmds-devel/source/xmds_breakpoint.cc,
	  trunk/xmds-devel/source/xmds_field.cc,
	  trunk/xmds-devel/source/xmds_integrate.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark45.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark45ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark89.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark89ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk9ip.cc,
	  trunk/xmds-devel/source/xmds_sequence.cc,
	  trunk/xmds-devel/source/xmds_simulation.cc,
	  trunk/xmds-devel/source/xmds_vector.cc,
	  trunk/xmds-devel/source/xmds_vector_element.cc,
	  trunk/xmds-devel/source/xsil_field.cc: Banishing cuddled else's
	  from the source (they make if/else statments harder
	  to read).

2007-08-08 15:40  paultcochrane

	* trunk/xmds-devel/test/coding_stds,
	  trunk/xmds-devel/test/coding_stds/cuddled_else.t: Added the first
	  of a set of coding standards tests which will help clean up
	  the xmds source. These tests are borrowed from the Parrot project
	  (http://www.parrotcode.org) and are licensed in a way which plays
	  with the gpl

2007-08-08 15:03  paultcochrane

	* trunk/xmds-devel/configure.in: Beginning to add warning flags to
	  gcc when building xmds to help pick up
	  common errors.

2007-08-08 14:46  paultcochrane

	* trunk/xmds-devel/source/xmds_vector_element.cc: Removed
	  superfluous argument from dollar-sign POSIX extended fprintf()
	  statement.

2007-08-08 14:45  paultcochrane

	* trunk/xmds-devel/test/generated_code/Makefile: No longer
	  compiling the test examples before comparing them with the
	  examples.
	  This saves a *lot* of time when running the tests often. The xmds
	  output is
	  compared to a reference C output anyway...

2007-08-08 14:41  paultcochrane

	* trunk/xmds-devel/source/xmds_vector_element.cc: Dollar signs were
	  missing within POSIX extended fprintf() statement

2007-08-08 14:34  paultcochrane

	* trunk/xmds-devel/source/xmds_integrate.cc: Corrected a leftover
	  comparison between signed and unsigned

2007-08-08 14:33  paultcochrane

	* trunk/xmds-devel/Makefile.am: Made the test suite dependent upon
	  xmds being built first.

2007-08-08 13:18  paultcochrane

	* trunk/xmds-devel/source/xmds_integrate_ark89.cc: Corrected
	  potential bug whereby an argument was missing to an fprintf()
	  statement.

2007-08-08 13:09  paultcochrane

	* trunk/xmds-devel/source/xmds_breakpoint.cc,
	  trunk/xmds-devel/source/xmds_vector_element.cc: Corrected more
	  integer length issues in fprintf() statements.

2007-08-08 12:23  paultcochrane

	* trunk/xmds-devel/source/xmds_breakpoint.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark45ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark45ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark89ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark89ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk9.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk9ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk9ip.cc,
	  trunk/xmds-devel/source/xmds_vector.cc,
	  trunk/xmds-devel/source/xmds_vector_element.cc: Removed remaining
	  superfluous fprintf() arguments.

2007-08-08 12:06  paultcochrane

	* trunk/xmds-devel/source/xmds_integrate_ark89.cc: Removing excess
	  arguments to fprintf() functions.

2007-08-08 10:31  paultcochrane

	* trunk/xmds-devel/source/xmds_integrate_ark45.cc: Removed extra
	  (and therefore unused) arguments to fprintf() statements.

2007-08-08 10:22  paultcochrane

	* trunk/xmds-devel/source/dom3.h: Giving a destructor to those
	  objects lacking one.

2007-08-08 10:14  paultcochrane

	* trunk/xmds-devel/source/xmds_breakpoint.cc,
	  trunk/xmds-devel/source/xmds_vector_element.cc: Removed unused
	  variables

2007-08-08 10:14  paultcochrane

	* trunk/xmds-devel/test/generated_code: Corrected svn:ignore
	  property

2007-08-08 09:57  paultcochrane

	* trunk/xmds-devel/test/generated_code: Updated svn:ignore property

2007-08-08 09:55  paultcochrane

	* trunk/xmds-devel/Makefile.am, trunk/xmds-devel/test/Makefile,
	  trunk/xmds-devel/test/generated_code/Makefile: First rough cut at
	  getting the generated code test suite to do something
	  meaningful

2007-08-08 09:13  paultcochrane

	* trunk/xmds-devel/test/generated_code,
	  trunk/xmds-devel/test/generated_code/atomlaser.xmds,
	  trunk/xmds-devel/test/generated_code/branch.xmds,
	  trunk/xmds-devel/test/generated_code/brusselator.xmds,
	  trunk/xmds-devel/test/generated_code/catcycle.xmds,
	  trunk/xmds-devel/test/generated_code/chain.xmds,
	  trunk/xmds-devel/test/generated_code/chemkin.xmds,
	  trunk/xmds-devel/test/generated_code/diffusion.xmds,
	  trunk/xmds-devel/test/generated_code/diffusion2.xmds,
	  trunk/xmds-devel/test/generated_code/duffing.xmds,
	  trunk/xmds-devel/test/generated_code/fibre.xmds,
	  trunk/xmds-devel/test/generated_code/fisher_reaction_diffusion.xmds,
	  trunk/xmds-devel/test/generated_code/fullpos3D.xmds,
	  trunk/xmds-devel/test/generated_code/groundstate.xmds,
	  trunk/xmds-devel/test/generated_code/hires.xmds,
	  trunk/xmds-devel/test/generated_code/krebs.xmds,
	  trunk/xmds-devel/test/generated_code/kubo.xmds,
	  trunk/xmds-devel/test/generated_code/lane_emden.xmds,
	  trunk/xmds-devel/test/generated_code/lorenz.xmds,
	  trunk/xmds-devel/test/generated_code/lotka_volterra.xmds,
	  trunk/xmds-devel/test/generated_code/ndparamp.xmds,
	  trunk/xmds-devel/test/generated_code/nlse.xmds,
	  trunk/xmds-devel/test/generated_code/oregonator.xmds,
	  trunk/xmds-devel/test/generated_code/paraxial_wave.xmds,
	  trunk/xmds-devel/test/generated_code/pendulum.xmds,
	  trunk/xmds-devel/test/generated_code/reference,
	  trunk/xmds-devel/test/generated_code/reference/atomlaser.cc,
	  trunk/xmds-devel/test/generated_code/reference/branch.cc,
	  trunk/xmds-devel/test/generated_code/reference/brusselator.cc,
	  trunk/xmds-devel/test/generated_code/reference/catcycle.cc,
	  trunk/xmds-devel/test/generated_code/reference/chain.cc,
	  trunk/xmds-devel/test/generated_code/reference/chemkin.cc,
	  trunk/xmds-devel/test/generated_code/reference/diffusion.cc,
	  trunk/xmds-devel/test/generated_code/reference/diffusion2.cc,
	  trunk/xmds-devel/test/generated_code/reference/duffing.cc,
	  trunk/xmds-devel/test/generated_code/reference/fibre.cc,
	  trunk/xmds-devel/test/generated_code/reference/fisher_reaction_diffusion.cc,
	  trunk/xmds-devel/test/generated_code/reference/fullpos3D.cc,
	  trunk/xmds-devel/test/generated_code/reference/groundstate.cc,
	  trunk/xmds-devel/test/generated_code/reference/hires.cc,
	  trunk/xmds-devel/test/generated_code/reference/krebs.cc,
	  trunk/xmds-devel/test/generated_code/reference/kubo.cc,
	  trunk/xmds-devel/test/generated_code/reference/lane_emden.cc,
	  trunk/xmds-devel/test/generated_code/reference/lorenz.cc,
	  trunk/xmds-devel/test/generated_code/reference/lotka_volterra.cc,
	  trunk/xmds-devel/test/generated_code/reference/ndparamp.cc,
	  trunk/xmds-devel/test/generated_code/reference/nlse.cc,
	  trunk/xmds-devel/test/generated_code/reference/oregonator.cc,
	  trunk/xmds-devel/test/generated_code/reference/paraxial_wave.cc,
	  trunk/xmds-devel/test/generated_code/reference/pendulum.cc,
	  trunk/xmds-devel/test/generated_code/reference/ring_modulator.cc,
	  trunk/xmds-devel/test/generated_code/reference/sech_soliton.cc,
	  trunk/xmds-devel/test/generated_code/reference/sech_soliton_tdepk.cc,
	  trunk/xmds-devel/test/generated_code/reference/sine.cc,
	  trunk/xmds-devel/test/generated_code/reference/soliton.cc,
	  trunk/xmds-devel/test/generated_code/reference/thermkin.cc,
	  trunk/xmds-devel/test/generated_code/reference/tla.cc,
	  trunk/xmds-devel/test/generated_code/reference/van_der_pol.cc,
	  trunk/xmds-devel/test/generated_code/reference/vibstring.cc,
	  trunk/xmds-devel/test/generated_code/ring_modulator.xmds,
	  trunk/xmds-devel/test/generated_code/sech_soliton.xmds,
	  trunk/xmds-devel/test/generated_code/sech_soliton_tdepk.xmds,
	  trunk/xmds-devel/test/generated_code/sine.xmds,
	  trunk/xmds-devel/test/generated_code/soliton.xmds,
	  trunk/xmds-devel/test/generated_code/thermkin.xmds,
	  trunk/xmds-devel/test/generated_code/tla.xmds,
	  trunk/xmds-devel/test/generated_code/van_der_pol.xmds,
	  trunk/xmds-devel/test/generated_code/vibstring.xmds: Added a
	  directory to test the generated C code of xmds. This includes
	  most of
	  the current example xmds files, and a directory of the current C
	  output
	  from an xmds run using fftw3.

2007-08-08 08:58  paultcochrane

	* trunk/xmds-devel/test: Added a test directory (as a base for a
	  more extended test suite)

2007-08-08 08:48  paultcochrane

	* trunk/xmds-devel/source/xmds_breakpoint.cc,
	  trunk/xmds-devel/source/xmds_vector_element.cc,
	  trunk/xmds-devel/source/xsil_field.cc: Correcting comparisons
	  between signed and unsigned integers

2007-08-08 08:22  paultcochrane

	* trunk/xmds-devel/source/xmds_breakpoint.cc,
	  trunk/xmds-devel/source/xmds_field.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark45.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark89.cc,
	  trunk/xmds-devel/source/xmds_sequence.cc,
	  trunk/xmds-devel/source/xmds_simulation.cc,
	  trunk/xmds-devel/source/xmds_vector.cc: Correcting format strings
	  in fprintf() statements to use the appropriate long
	  and in some cases short) format.

2007-08-07 14:09  paultcochrane

	* trunk/xmds-devel/source/main.cc: Minor code reformatting.

2007-08-07 13:54  paultcochrane

	* trunk/xmds-devel/source/kissdom.cc,
	  trunk/xmds-devel/source/kissdom.h,
	  trunk/xmds-devel/source/main.cc,
	  trunk/xmds-devel/source/xmds_arg.cc,
	  trunk/xmds-devel/source/xmds_arg_element.cc,
	  trunk/xmds-devel/source/xmds_argv.cc,
	  trunk/xmds-devel/source/xmds_breakpoint.cc,
	  trunk/xmds-devel/source/xmds_classes.h,
	  trunk/xmds-devel/source/xmds_complex.h,
	  trunk/xmds-devel/source/xmds_element.cc,
	  trunk/xmds-devel/source/xmds_field.cc,
	  trunk/xmds-devel/source/xmds_filter.cc,
	  trunk/xmds-devel/source/xmds_globals.cc,
	  trunk/xmds-devel/source/xmds_integrate.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark45.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark45ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark45ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark89.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark89ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark89ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk4.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk4ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk4ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk9.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk9ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk9ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_si.cc,
	  trunk/xmds-devel/source/xmds_integrate_siex.cc,
	  trunk/xmds-devel/source/xmds_integrate_siip.cc,
	  trunk/xmds-devel/source/xmds_moment_group.cc,
	  trunk/xmds-devel/source/xmds_output.cc,
	  trunk/xmds-devel/source/xmds_segment.cc,
	  trunk/xmds-devel/source/xmds_sequence.cc,
	  trunk/xmds-devel/source/xmds_simulation.cc,
	  trunk/xmds-devel/source/xmds_utils.cc,
	  trunk/xmds-devel/source/xmds_utils.h,
	  trunk/xmds-devel/source/xmds_vector.cc,
	  trunk/xmds-devel/source/xmds_vector_element.cc,
	  trunk/xmds-devel/source/xml_basics.cc,
	  trunk/xmds-devel/source/xml_basics.h,
	  trunk/xmds-devel/source/xml_parser.cc,
	  trunk/xmds-devel/source/xml_parser.h,
	  trunk/xmds-devel/source/xsil2graphics.cc,
	  trunk/xmds-devel/source/xsil_field.cc,
	  trunk/xmds-devel/source/xsil_field.h: Indented the code using
	  emacs' built in formatting engine.

2007-08-07 13:06  paultcochrane

	* trunk/xmds-devel/Makefile.am, trunk/xmds-devel/configure.in,
	  trunk/xmds-devel/source, trunk/xmds-devel/source/Makefile.am,
	  trunk/xmds-devel/source/kissdom.cc,
	  trunk/xmds-devel/source/main.cc,
	  trunk/xmds-devel/source/xmds_arg.cc,
	  trunk/xmds-devel/source/xmds_arg_element.cc,
	  trunk/xmds-devel/source/xmds_argv.cc,
	  trunk/xmds-devel/source/xmds_breakpoint.cc,
	  trunk/xmds-devel/source/xmds_complex.h,
	  trunk/xmds-devel/source/xmds_element.cc,
	  trunk/xmds-devel/source/xmds_field.cc,
	  trunk/xmds-devel/source/xmds_filter.cc,
	  trunk/xmds-devel/source/xmds_globals.cc,
	  trunk/xmds-devel/source/xmds_integrate.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark45.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark45ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark45ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark89.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark89ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_ark89ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk4.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk4ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk4ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk9.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk9ex.cc,
	  trunk/xmds-devel/source/xmds_integrate_rk9ip.cc,
	  trunk/xmds-devel/source/xmds_integrate_si.cc,
	  trunk/xmds-devel/source/xmds_integrate_siex.cc,
	  trunk/xmds-devel/source/xmds_integrate_siip.cc,
	  trunk/xmds-devel/source/xmds_moment_group.cc,
	  trunk/xmds-devel/source/xmds_output.cc,
	  trunk/xmds-devel/source/xmds_segment.cc,
	  trunk/xmds-devel/source/xmds_sequence.cc,
	  trunk/xmds-devel/source/xmds_simulation.cc,
	  trunk/xmds-devel/source/xmds_utils.cc,
	  trunk/xmds-devel/source/xmds_utils.h,
	  trunk/xmds-devel/source/xmds_vector.cc,
	  trunk/xmds-devel/source/xmds_vector_element.cc,
	  trunk/xmds-devel/source/xmdscomplex.h,
	  trunk/xmds-devel/source/xmdselement.cc,
	  trunk/xmds-devel/source/xmdsfield.cc,
	  trunk/xmds-devel/source/xmdsfilter.cc,
	  trunk/xmds-devel/source/xmdsglobals.cc,
	  trunk/xmds-devel/source/xmdsintegrate.cc,
	  trunk/xmds-devel/source/xmdsintegrateark45.cc,
	  trunk/xmds-devel/source/xmdsintegrateark45ex.cc,
	  trunk/xmds-devel/source/xmdsintegrateark45ip.cc,
	  trunk/xmds-devel/source/xmdsintegrateark89.cc,
	  trunk/xmds-devel/source/xmdsintegrateark89ex.cc,
	  trunk/xmds-devel/source/xmdsintegrateark89ip.cc,
	  trunk/xmds-devel/source/xmdsintegrateex.cc,
	  trunk/xmds-devel/source/xmdsintegrateip.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4ex.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4ip.cc,
	  trunk/xmds-devel/source/xmdsintegraterk9.cc,
	  trunk/xmds-devel/source/xmdsintegraterk9ex.cc,
	  trunk/xmds-devel/source/xmdsintegraterk9ip.cc,
	  trunk/xmds-devel/source/xmdsintegratesi.cc,
	  trunk/xmds-devel/source/xmdsintegratesiex.cc,
	  trunk/xmds-devel/source/xmdsintegratesiip.cc,
	  trunk/xmds-devel/source/xmdsmomentgroup.cc,
	  trunk/xmds-devel/source/xmdsoutput.cc,
	  trunk/xmds-devel/source/xmdssegment.cc,
	  trunk/xmds-devel/source/xmdssequence.cc,
	  trunk/xmds-devel/source/xmdssimulation.cc,
	  trunk/xmds-devel/source/xmdsutils.cc,
	  trunk/xmds-devel/source/xmdsutils.h,
	  trunk/xmds-devel/source/xmdsvector.cc,
	  trunk/xmds-devel/source/xmdsvectorelement.cc,
	  trunk/xmds-devel/source/xml_basics.cc,
	  trunk/xmds-devel/source/xml_basics.h,
	  trunk/xmds-devel/source/xml_parser.cc,
	  trunk/xmds-devel/source/xml_parser.h,
	  trunk/xmds-devel/source/xmlbasics.cc,
	  trunk/xmds-devel/source/xmlbasics.h,
	  trunk/xmds-devel/source/xmlparser.cc,
	  trunk/xmds-devel/source/xmlparser.h,
	  trunk/xmds-devel/source/xsil2graphics.cc,
	  trunk/xmds-devel/source/xsil_field.cc,
	  trunk/xmds-devel/source/xsil_field.h,
	  trunk/xmds-devel/source/xsilfield.cc,
	  trunk/xmds-devel/source/xsilfield.h: Added underscores to
	  remaining filenames for increased readability

2007-08-07 12:27  paultcochrane

	* trunk/xmds-devel/source/Makefile.am,
	  trunk/xmds-devel/source/main.cc,
	  trunk/xmds-devel/source/xmds_arg.cc,
	  trunk/xmds-devel/source/xmds_arg_element.cc,
	  trunk/xmds-devel/source/xmds_argv.cc,
	  trunk/xmds-devel/source/xmds_breakpoint.cc,
	  trunk/xmds-devel/source/xmds_classes.h,
	  trunk/xmds-devel/source/xmdsbreakpoint.cc,
	  trunk/xmds-devel/source/xmdsclasses.h,
	  trunk/xmds-devel/source/xmdselement.cc,
	  trunk/xmds-devel/source/xmdsfield.cc,
	  trunk/xmds-devel/source/xmdsfilter.cc,
	  trunk/xmds-devel/source/xmdsglobals.cc,
	  trunk/xmds-devel/source/xmdsintegrate.cc,
	  trunk/xmds-devel/source/xmdsintegrateark45.cc,
	  trunk/xmds-devel/source/xmdsintegrateark45ex.cc,
	  trunk/xmds-devel/source/xmdsintegrateark45ip.cc,
	  trunk/xmds-devel/source/xmdsintegrateark89.cc,
	  trunk/xmds-devel/source/xmdsintegrateark89ex.cc,
	  trunk/xmds-devel/source/xmdsintegrateark89ip.cc,
	  trunk/xmds-devel/source/xmdsintegrateex.cc,
	  trunk/xmds-devel/source/xmdsintegrateip.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4ex.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4ip.cc,
	  trunk/xmds-devel/source/xmdsintegraterk9.cc,
	  trunk/xmds-devel/source/xmdsintegraterk9ex.cc,
	  trunk/xmds-devel/source/xmdsintegraterk9ip.cc,
	  trunk/xmds-devel/source/xmdsintegratesi.cc,
	  trunk/xmds-devel/source/xmdsintegratesiex.cc,
	  trunk/xmds-devel/source/xmdsintegratesiip.cc,
	  trunk/xmds-devel/source/xmdsmomentgroup.cc,
	  trunk/xmds-devel/source/xmdsoutput.cc,
	  trunk/xmds-devel/source/xmdssegment.cc,
	  trunk/xmds-devel/source/xmdssequence.cc,
	  trunk/xmds-devel/source/xmdssimulation.cc,
	  trunk/xmds-devel/source/xmdsvector.cc,
	  trunk/xmds-devel/source/xmdsvectorelement.cc: Added underscores
	  to filenames for better readability

2007-08-07 12:15  paultcochrane

	* trunk/xmds-devel/examples/atomlaser.xmds,
	  trunk/xmds-devel/examples/branch.xmds,
	  trunk/xmds-devel/examples/brusselator.xmds,
	  trunk/xmds-devel/examples/catcycle.xmds,
	  trunk/xmds-devel/examples/chain.xmds,
	  trunk/xmds-devel/examples/chemkin.xmds,
	  trunk/xmds-devel/examples/diffusion.xmds,
	  trunk/xmds-devel/examples/diffusion2.xmds,
	  trunk/xmds-devel/examples/duffing.xmds,
	  trunk/xmds-devel/examples/fibre.xmds,
	  trunk/xmds-devel/examples/fisher_reaction_diffusion.xmds,
	  trunk/xmds-devel/examples/fullpos3D.xmds,
	  trunk/xmds-devel/examples/gaugeatomlaser.xmds,
	  trunk/xmds-devel/examples/highdim.xmds,
	  trunk/xmds-devel/examples/hires.xmds,
	  trunk/xmds-devel/examples/krebs.xmds,
	  trunk/xmds-devel/examples/kubo.xmds,
	  trunk/xmds-devel/examples/lane_emden.xmds,
	  trunk/xmds-devel/examples/lorenz.xmds,
	  trunk/xmds-devel/examples/lotka_volterra.xmds,
	  trunk/xmds-devel/examples/ndparamp.xmds,
	  trunk/xmds-devel/examples/nlse.xmds,
	  trunk/xmds-devel/examples/oregonator.xmds,
	  trunk/xmds-devel/examples/paraxial_wave.xmds,
	  trunk/xmds-devel/examples/pendulum.xmds,
	  trunk/xmds-devel/examples/ring_modulator.xmds,
	  trunk/xmds-devel/examples/sech_soliton.xmds,
	  trunk/xmds-devel/examples/sech_soliton_tdepk.xmds,
	  trunk/xmds-devel/examples/sine.xmds,
	  trunk/xmds-devel/examples/soliton.xmds,
	  trunk/xmds-devel/examples/thermkin.xmds,
	  trunk/xmds-devel/examples/tla.xmds,
	  trunk/xmds-devel/examples/van_der_pol.xmds,
	  trunk/xmds-devel/examples/vibstring.xmds: Updated more copyright
	  dates

2007-08-07 12:11  paultcochrane

	* trunk/xmds-devel/source/dom3.h,
	  trunk/xmds-devel/source/kissdom.cc,
	  trunk/xmds-devel/source/kissdom.h,
	  trunk/xmds-devel/source/loadxsil.m,
	  trunk/xmds-devel/source/main.cc,
	  trunk/xmds-devel/source/xmds_arg.cc,
	  trunk/xmds-devel/source/xmds_arg_element.cc,
	  trunk/xmds-devel/source/xmds_argv.cc,
	  trunk/xmds-devel/source/xmdsbreakpoint.cc,
	  trunk/xmds-devel/source/xmdsclasses.h,
	  trunk/xmds-devel/source/xmdscomplex.h,
	  trunk/xmds-devel/source/xmdselement.cc,
	  trunk/xmds-devel/source/xmdsfield.cc,
	  trunk/xmds-devel/source/xmdsfilter.cc,
	  trunk/xmds-devel/source/xmdsglobals.cc,
	  trunk/xmds-devel/source/xmdsintegrate.cc,
	  trunk/xmds-devel/source/xmdsintegrateark45.cc,
	  trunk/xmds-devel/source/xmdsintegrateark45ex.cc,
	  trunk/xmds-devel/source/xmdsintegrateark45ip.cc,
	  trunk/xmds-devel/source/xmdsintegrateark89.cc,
	  trunk/xmds-devel/source/xmdsintegrateark89ex.cc,
	  trunk/xmds-devel/source/xmdsintegrateark89ip.cc,
	  trunk/xmds-devel/source/xmdsintegrateex.cc,
	  trunk/xmds-devel/source/xmdsintegrateip.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4ex.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4ip.cc,
	  trunk/xmds-devel/source/xmdsintegraterk9.cc,
	  trunk/xmds-devel/source/xmdsintegraterk9ex.cc,
	  trunk/xmds-devel/source/xmdsintegraterk9ip.cc,
	  trunk/xmds-devel/source/xmdsintegratesi.cc,
	  trunk/xmds-devel/source/xmdsintegratesiex.cc,
	  trunk/xmds-devel/source/xmdsintegratesiip.cc,
	  trunk/xmds-devel/source/xmdsmomentgroup.cc,
	  trunk/xmds-devel/source/xmdsoutput.cc,
	  trunk/xmds-devel/source/xmdssegment.cc,
	  trunk/xmds-devel/source/xmdssequence.cc,
	  trunk/xmds-devel/source/xmdssimulation.cc,
	  trunk/xmds-devel/source/xmdsutils.cc,
	  trunk/xmds-devel/source/xmdsutils.h,
	  trunk/xmds-devel/source/xmdsvector.cc,
	  trunk/xmds-devel/source/xmdsvectorelement.cc,
	  trunk/xmds-devel/source/xmlbasics.cc,
	  trunk/xmds-devel/source/xmlbasics.h,
	  trunk/xmds-devel/source/xmlparser.cc,
	  trunk/xmds-devel/source/xmlparser.h,
	  trunk/xmds-devel/source/xsil2graphics.cc,
	  trunk/xmds-devel/source/xsilfield.cc,
	  trunk/xmds-devel/source/xsilfield.h: Updated copyright date

2007-08-07 11:44  paultcochrane

	* trunk/xmds-devel/source: Now ignoring the version.h file and
	  vim-generated .swp files

2007-08-07 11:42  paultcochrane

	* trunk/xmds-devel/configure.in,
	  trunk/xmds-devel/source/xmdssimulation.cc: Some first steps at
	  getting xmds to configure and work properly on systems
	  which only have fftw3 installed.

2007-08-03 07:12  joehope

	* trunk/xmds-devel/source/xmdsfilter.cc,
	  trunk/xmds-devel/source/xmdsintegrateark45.cc,
	  trunk/xmds-devel/source/xmdsintegrateark89.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4.cc,
	  trunk/xmds-devel/source/xmdsintegraterk9.cc,
	  trunk/xmds-devel/source/xmdsintegratesiex.cc,
	  trunk/xmds-devel/source/xmdsintegratesiip.cc,
	  trunk/xmds-devel/source/xmdssimulation.cc,
	  trunk/xmds-devel/source/xmdsvectorelement.cc: Making Poissonian
	  noise sources work.
	  
	  dpsi_dt = n_1
	  
	  for a poissonian noise now works like
	  
	  dpsi = dn
	  
	  Not implemented for adaptive algorithms, but there's an
	  exception.

2007-07-30 05:52  grahamdennis

	* trunk/xmds-devel/source/xmdsmomentgroup.cc: Fix for bug
	  introduced in r1350 where it was possible to cause an integer
	  overflow when writing moment groups. This only affected
	  stochastic simulations or simulations with error checking, and
	  then only those moment groups that had a very large number of
	  time samples.

2007-07-13 02:31  grahamdennis

	* trunk/xmds-devel/source/xmdsintegrateark45.cc,
	  trunk/xmds-devel/source/xmdsintegrateark89.cc,
	  trunk/xmds-devel/source/xmdssequence.cc,
	  trunk/xmds-devel/source/xmdssimulation.cc: There was a bug in the
	  adaptive timestep algorithms for deterministic MPI simulations
	  caused when the number of points in the first dimension isn't
	  divisible by the number of CPUs. The problem was that it was
	  assumed that on each rank, total_local_size was the size of the
	  grid on that node, and this is not necessarily the case, as it is
	  just the maximum of the grid size on the node (as the swapped and
	  unswapped cases can use different amounts of memory).
	  This mistake is fairly widespread but mostly it isn't a problem,
	  it's just a small wastage of CPU cycles (when the first dimension
	  isn't divisible by the number of CPUs), however the adaptive
	  timestep algorithms need to calculate the maximum of the vectors
	  on the grid and this is where it does cause a problem.

2007-07-11 06:22  grahamdennis

	* trunk/xmds-devel/source/xmdsmomentgroup.cc,
	  trunk/xmds-devel/source/xmdssequence.cc: Significantly reduce
	  memory consumption caused by output moment groups for
	  deterministic MPI simulations. (Memory consumption is only
	  reduced for ranks other than 0).

2007-07-09 04:20  grahamdennis

	* trunk/xmds-devel/source/xmds_argv.cc,
	  trunk/xmds-devel/source/xmdsclasses.h,
	  trunk/xmds-devel/source/xmdsglobals.cc: Allow <argv> elements to
	  work when you don't have a <globals> element.

2007-07-03 07:25  grahamdennis

	* trunk/xmds-devel/source/xmdssimulation.cc: Fixed bug with the
	  runtime limit for deterministic simulations using MPI where it
	  was possible for some nodes to decide they were running overtime,
	  but others could think otherwise.
	  Prevented the runtime limit code being used for stochastic
	  simulations until I work out how to do that properly.

2007-07-02 05:15  grahamdennis

	* trunk/xmds-devel/source/xmdssequence.cc: Fix for another bug
	  introduced in r1368.

2007-06-28 08:51  grahamdennis

	* trunk/xmds-devel/source/xmdsintegrateark89.cc: Fix for a serious
	  bug in ARK89 (when using MPI on more than one CPU) where ranks
	  other than 0 would sample at any time greater (potentially much
	  greater) than the sample time, but not at the sample time. Rank 0
	  was unaffected. For strongly convergent paths, this could lead to
	  the path far overshooting the entire time-range of the
	  simulation.

2007-06-28 05:17  grahamdennis

	* trunk/xmds-devel/source/xmdssequence.cc: Ooops. I made a mistake
	  in my last commit.

2007-06-28 02:01  grahamdennis

	* trunk/xmds-devel/TODO,
	  trunk/xmds-devel/source/xmdsmomentgroup.cc,
	  trunk/xmds-devel/source/xmdssequence.cc,
	  trunk/xmds-devel/source/xmdssimulation.cc: Fix for an issue when
	  using MPI to distribute a stochastic simulation that only has 1
	  path when using the Uniform MPI_Method on more than one CPU.

2007-06-27 06:55  joehope

	* trunk/xmds-devel/ChangeLog: Bump for bugfix release.

2007-06-27 06:32  joehope

	* trunk/xmds-devel/admin/xmdsReleaseProcedure.pod: Added notes for
	  the website updates.

2007-06-27 03:24  joehope

	* trunk/xmds-devel/TODO, trunk/xmds-devel/configure.in,
	  trunk/xmds-devel/source/xmdsvector.cc: Fixed a very rarely
	  occurring bug when sampling in mixed Fourier and normal space on
	  uneven grids.
	  
	  Turns out FFTW didn't work exactly as I expected, but all is
	  well, now.

2007-06-26 02:40  grahamdennis

	* trunk/xmds-devel/source/loadxsil.m: When I made loadxsil.m deal
	  with missing moment groups (produced by simulations that have hit
	  a run-time limit) it didn't work for when the last moment group
	  was missing. Fixed.

2007-06-23 13:29  joehope

	* trunk/xmds-devel/source/xmdssequence.cc,
	  trunk/xmds-devel/source/xmdsvector.cc: Minor fixes while hunting
	  for the mixed space bug.

2007-06-21 01:31  joehope

	* trunk/xmds-devel/source/main.cc,
	  trunk/xmds-devel/source/xmds_arg_element.cc,
	  trunk/xmds-devel/source/xmdsfilter.cc,
	  trunk/xmds-devel/source/xmdsintegrate.cc,
	  trunk/xmds-devel/source/xmdsintegrateark45.cc,
	  trunk/xmds-devel/source/xmdsintegrateark89.cc,
	  trunk/xmds-devel/source/xmdsintegratesiip.cc,
	  trunk/xmds-devel/source/xmdsmomentgroup.cc,
	  trunk/xmds-devel/source/xmdssimulation.cc,
	  trunk/xmds-devel/source/xmdsutils.cc,
	  trunk/xmds-devel/source/xmlparser.cc,
	  trunk/xmds-devel/source/xsil2graphics.cc,
	  trunk/xmds-devel/source/xsilfield.cc: Extra includes to allow
	  compilation with g++ 4.3
	  Submitted by Rafael Laboissiere, rafael@debian.org

2007-06-20 06:03  grahamdennis

	* trunk/xmds-devel/source/xmdsintegrateark89.cc: Bug fixes for
	  ARK89.
	  There was a bug in ARK89 where infrequently it would not sample
	  exactly at the correct sample times, but earlier (usually only
	  slightly earlier), and these incorrect sample times would not be
	  the same for all paths.
	  There was a second 'bug' due to the finite precision of doubles
	  that infrequently led to smaller-than-necessary timesteps being
	  calculated. This bug did not affect simulation results, it only
	  slightly increased the time taken for simulations.

2007-06-15 01:45  joehope

	* trunk/xmds-devel/MANIFEST,
	  trunk/xmds-devel/admin/xmdsReleaseProcedure.pod,
	  trunk/xmds-devel/configure.in: Trivial updates for the xmds-1.6-2
	  bugfix release.

2007-06-14 04:56  joehope

	* trunk/xmds-devel/ChangeLog, trunk/xmds-devel/README,
	  trunk/xmds-devel/configure.in: Version bumps for bugfix release.

2007-06-12 03:34  grahamdennis

	* trunk/xmds-devel/source/xmdsbreakpoint.cc: Breakpoints for
	  vectors of type double would be written incorrectly (the same
	  data would be written multiple times) if MPI was used for
	  deterministic simulations. This is a regression since r1179
	  (2006-12-14).

2007-06-08 07:33  grahamdennis

	* trunk/xmds-devel/source/xmdssequence.cc: Rest of Scheduling fix.

2007-06-08 07:14  joehope

	* trunk/xmds-devel/source/xmdssequence.cc,
	  trunk/xmds-devel/source/xmdssimulation.cc: Partial fix for the
	  Scheduler bug. Has to be finished for Scheduling+Error checking.
	  Fix for argv fix.
	  Fix for IntelMKL case.

2007-06-08 01:31  grahamdennis

	* trunk/xmds-devel/source/xmdssimulation.cc: Make XMDS not crash
	  when there isn't an ARGV element.

2007-06-07 05:51  grahamdennis

	* trunk/xmds-devel/TODO, trunk/xmds-devel/source/main.cc,
	  trunk/xmds-devel/source/xmdsclasses.h,
	  trunk/xmds-devel/source/xmdssequence.cc,
	  trunk/xmds-devel/source/xmdssimulation.cc: Add (optional) for
	  using the Intel MKL for generating random numbers. For Gaussian
	  numbers, Intel MKL is ~5x faster than
	  our current implementation of "gaussFast" (when generating 1000
	  numbers).
	  Note that MKL is a vector library, and so will not necessarily be
	  faster than the current implementation for single-dimensional
	  problems.
	  In terms of real-world performance, this sped up the kubo
	  oscillator by 2.5x (when using a transverse dimension for paths).
	  The tag to enable Intel MKL is <use_intel_mkl>, and it defaults
	  to 'no'.

2007-06-06 06:50  andyferris

	* trunk/xmds-devel/source/xmdsclasses.h,
	  trunk/xmds-devel/source/xmdssequence.cc,
	  trunk/xmds-devel/source/xmdssimulation.cc: * Allowed command-line
	  arguments to be used as the random seed.
	  This might be useful when analysing trajectory data using a
	  batch script rather than XMDS's internal sampling.
	  
	  * This pretty much mitigates my desire for XMDS to dump all its
	  trajectory data as the same thing can be done with a batch
	  script and without hacking the output .cc code (as I was
	  previously forced to do).
	  
	  * XMDS checks whether the seed element contains positive integers
	  or strings matching one of the <arg> names. I have now made
	  <argv> the first element to be processed to accommodate this
	  search.
	  
	  * In future, we might want to consider allowing many of the tags
	  to
	  be replaced by a command-line arg. Unfortunately, most numbers
	  are #define'd rather than initialised, making things difficult to
	  generalise...

2007-06-05 01:19  grahamdennis

	* trunk/xmds-devel/source/xmdsintegrate.cc,
	  trunk/xmds-devel/source/xmdsintegrateark45.cc,
	  trunk/xmds-devel/source/xmdsintegrateark89.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4.cc,
	  trunk/xmds-devel/source/xmdsintegraterk9.cc,
	  trunk/xmds-devel/source/xmdsintegratesiex.cc,
	  trunk/xmds-devel/source/xmdsintegratesiip.cc: Fix for compiler
	  warning caused by the runtime limit code when there is no runtime
	  limit.

2007-06-03 05:10  grahamdennis

	* trunk/xmds-devel/examples/diffusion.xmds,
	  trunk/xmds-devel/source/kissdom.cc,
	  trunk/xmds-devel/source/loadxsil.m,
	  trunk/xmds-devel/source/xmdsbreakpoint.cc,
	  trunk/xmds-devel/source/xmdsclasses.h,
	  trunk/xmds-devel/source/xmdsfilter.cc,
	  trunk/xmds-devel/source/xmdsintegrate.cc,
	  trunk/xmds-devel/source/xmdsintegrateark45.cc,
	  trunk/xmds-devel/source/xmdsintegrateark89.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4.cc,
	  trunk/xmds-devel/source/xmdsintegraterk9.cc,
	  trunk/xmds-devel/source/xmdsintegratesi.cc,
	  trunk/xmds-devel/source/xmdsintegratesiex.cc,
	  trunk/xmds-devel/source/xmdsintegratesiip.cc,
	  trunk/xmds-devel/source/xmdsmomentgroup.cc,
	  trunk/xmds-devel/source/xmdssegment.cc,
	  trunk/xmds-devel/source/xmdssequence.cc,
	  trunk/xmds-devel/source/xmdssimulation.cc,
	  trunk/xmds-devel/source/xsil2graphics.cc,
	  trunk/xmds-devel/source/xsilfield.cc,
	  trunk/xmds-devel/testsuite/test_xmds.pl: Runtime-limiting
	  support.
	  Add the tag <runtime_limit> to the simulation to specify an
	  *advisory* maximum running time.
	  The format for this string is HH:MM, HH:MM:SS or SSSS. Note that
	  HH can be greater than 24.
	  Once each timestep, the simulation will determine if it is
	  running overtime. If it is, then
	  any pending samples *for that integrate element* will be sampled,
	  and all remaining integrate
	  and filter elements will be skipped. The only elements that will
	  execute after the runtime limit
	  has been hit are breakpoint elements. Note that if a moment group
	  is never sampled, then it won't
	  get written to the XSIL file, and a .dat file will not be created
	  (for binary output).
	  
	  This patch adds support for XSIL files with 'missing' moment
	  groups and fixes a bug in loadxsil when
	  loading breakpoints from an XMDS script that uses ASCII output.

2007-06-01 05:57  joehope

	* trunk/xmds-devel/TODO: Results of the Brainstorm. This will be
	  handy later too. Andy and Grahama are great.

2007-05-22 04:14  grahamdennis

	* trunk/xmds-devel/source/main.cc: Forgot a space... oops.

2007-05-22 01:45  grahamdennis

	* trunk/xmds-devel/source/main.cc: Make sure that the revision is
	  printed when xmds processes scripts (I didn't notice this when
	  adding the revision information.

2007-05-21 05:16  grahamdennis

	* trunk/xmds-devel/source/xmdsintegrateark45.cc,
	  trunk/xmds-devel/source/xmdsintegrateark89.cc: Prevented the ARK
	  algorithms from printing large amounts of information when there
	  is more than one path, as otherwise this information will swamp
	  everything else.

2007-05-10 06:51  joehope

	* trunk/xmds-devel/admin/xmdsReleaseProcedure.pod: Whoops, and
	  again.

2007-05-10 06:50  joehope

	* trunk/xmds-devel/admin/xmdsReleaseProcedure.pod: More admin notes
	  moved to svn

2007-05-09 07:16  joehope

	* trunk/xmds-devel/configure.in: Seeding the version script so it
	  works on a clean install. It would be better to run version.sh at
	  the top of every make, if we knew how to force that through
	  autoconf.

2007-05-09 05:24  joehope

	* trunk/xmds-devel/MANIFEST: Near release adjustment.

2007-05-09 05:18  joehope

	* trunk/xmds-devel/ChangeLog, trunk/xmds-devel/README,
	  trunk/xmds-devel/README.Windows,
	  trunk/xmds-devel/admin/xmdsReleaseProcedure.pod,
	  trunk/xmds-devel/configure.in,
	  trunk/xmds-devel/examples/fibre.xmds,
	  trunk/xmds-devel/examples/sech_soliton_tdepk.xmds: Misc changes
	  before release.

2007-05-08 06:52  grahamdennis

	* trunk/xmds-devel/source/Makefile.am: Moving the version.h make
	  target to the top of the automake file so that maybe make will be
	  able to find it...

2007-05-07 10:51  grahamdennis

	* trunk/xmds-devel/source/Makefile.am,
	  trunk/xmds-devel/source/version.sh: I forgot that the version.h
	  file wouldn't get updated once it existed. So I've made version.h
	  depend on all of the other xmds sources in the automake file.
	  There's probably a cleaner way, but I can't think of one.

2007-05-07 10:31  grahamdennis

	* trunk/xmds-devel/source/Makefile.am,
	  trunk/xmds-devel/source/main.cc,
	  trunk/xmds-devel/source/version.sh,
	  trunk/xmds-devel/source/xmdsbreakpoint.cc,
	  trunk/xmds-devel/source/xmdsclasses.h,
	  trunk/xmds-devel/source/xmdsoutput.cc,
	  trunk/xmds-devel/source/xmdssimulation.cc: Add the subversion
	  revision number to the end of the version number reported by the
	  application, and saved to XSIL files. This makes it easier for
	  those of us living on the bleeding edge to track down exactly
	  which revision number was used to create a script (for example,
	  for tracking performance regressions).

2007-05-05 09:10  grahamdennis

	* trunk/xmds-devel/source/xmdsclasses.h,
	  trunk/xmds-devel/source/xmdsintegrate.cc,
	  trunk/xmds-devel/source/xmdsintegrateex.cc,
	  trunk/xmds-devel/source/xmdsintegrateip.cc,
	  trunk/xmds-devel/source/xmdssegment.cc,
	  trunk/xmds-devel/source/xmdssequence.cc: Move allocation of
	  k_operator_field's to one place in both the xmds source, and the
	  source generated from scripts. This makes it easier to control
	  when the fields are allocated, so that they are allocated only
	  while they are needed, and are free'd after the segment they
	  belong to has completed. Previously, the k_operator_field's were
	  leaked.

2007-05-03 08:08  grahamdennis

	* trunk/xmds-devel/source/xmdsvectorelement.cc: For large data
	  files, the size of each component could be larger than can fit
	  into a long, so an off_t should be used.

2007-05-03 02:14  joehope

	* trunk/xmds-devel/source/xmdsclasses.h,
	  trunk/xmds-devel/source/xmdsintegrate.cc,
	  trunk/xmds-devel/source/xmdsintegrateark45.cc,
	  trunk/xmds-devel/source/xmdsintegrateark89.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4.cc,
	  trunk/xmds-devel/source/xmdsintegraterk9.cc,
	  trunk/xmds-devel/source/xmdsintegratesiex.cc: Multiple bugfixes.
	  SIEX is now restored in the post FFTW 3 age.
	  Cross-propagation now works with stochastic equations.

2007-05-03 00:59  joehope

	* trunk/xmds-devel/admin/xmdsReleaseProcedure.pod: Quick update to
	  the release procedures.

2007-05-03 00:58  joehope

	* trunk/xmds-devel/source/xmdsintegrate.cc,
	  trunk/xmds-devel/source/xmdsintegratesiex.cc: Start of another
	  bugfix.

2007-05-02 10:22  joehope

	* trunk/xmds-devel/source/xmdsclasses.h,
	  trunk/xmds-devel/source/xmdsmomentgroup.cc,
	  trunk/xmds-devel/source/xmdssequence.cc: Force initialisation of
	  moment group data if post-propagation is performed.
	  Most importantly, this initialises the Fourier space tag.
	  Strictly speaking,
	  the rest of the initialisation is unnecessary unless at least one
	  transverse
	  dimension is integrated, or the system is stochastic with
	  multiple paths,
	  but it is always safe to do, and should have approximately zero
	  impact on speed.

2007-05-02 07:18  joehope

	* trunk/xmds-devel/source/xsilfield.cc: Suppress unnecessary output
	  when loading data into Mathematica.

2007-04-26 07:46  grahamdennis

	* trunk/xmds-devel/source/xmdsvectorelement.cc: When I added the
	  noises to the XSIL loading code, I forgot to make sure they were
	  deleted at the end.

2007-04-24 05:45  grahamdennis

	* trunk/xmds-devel/source/xmdssimulation.cc: Just because there's a
	  use_openmp tag, and use_mpi is true doesn't mean that someone
	  actually wants to use both OpenMP and MPI...

2007-04-23 03:33  grahamdennis

	* trunk/xmds-devel/source/xmdsvectorelement.cc: It wasn't possible
	  to use noises in the CDATA section when initialising a vector
	  from an XSIL file.

2007-04-05 13:17  paultcochrane

	* trunk/xmds-devel/examples/groundstate.xmds: Added
	  groundstate.xmds back in.

2007-04-05 13:17  paultcochrane

	* trunk/xmds-devel/examples/groundstate.xmds: Temporarily deleting
	  groundstate.xmds to see if can remove the executable
	  bit from the file as it stands in the repository.

2007-04-05 12:58  paultcochrane

	* ., trunk/xmds-devel/examples/groundstate.xmds: Changed the
	  copyright info in an attempt to change the executable mode on
	  the file (causes problems when building the Debian package). Can
	  only see
	  if this will work...

2007-04-02 00:28  grahamdennis

	* trunk/xmds-devel/source/loadxsil.m: loadxsil couldn't load
	  4-dimensional (or higher) arrays (correctly). xsil2graphics
	  generated correct code, just loadxsil didn't.

2007-03-28 07:17  grahamdennis

	* trunk/xmds-devel/source/xmdsfield.cc,
	  trunk/xmds-devel/source/xmdsmomentgroup.cc: Increase precision of
	  field limits so that when changing the size of fields which don't
	  have nice round sizes we don't confuse the XSIL loading code
	  which expects the grids to line up almost exactly.

2007-03-22 03:43  joehope

	* trunk/xmds-devel/examples/nlse.xmds: Give an example with the
	  adaptive 9(8) RK algorithm.

2007-03-22 03:41  joehope

	* trunk/xmds-devel/MANIFEST, trunk/xmds-devel/admin/svn2cl.xsl:
	  Still updating for 1.6 release.

2007-03-22 03:34  joehope

	* trunk/xmds-devel/ChangeLog, trunk/xmds-devel/README,
	  trunk/xmds-devel/admin/xmdsReleaseProcedure.pod,
	  trunk/xmds-devel/configure.in: Preparing for release of version
	  1.6.

2007-03-20 01:26  michaelhush

	* trunk/xmds-devel/source/xmdsintegrateark89.cc,
	  trunk/xmds-devel/source/xmdssimulation.cc: Fixed memory leak in
	  ARK89EX and ARK89IP methods for stochastic problem

2007-03-12 00:58  joehope

	* trunk/xmds-devel/source/xmdssequence.cc: Fixed a bug where the
	  scheduler didn't handle lack of error checking properly.

2007-02-23 05:55  michaelhush

	* trunk/xmds-devel/source/xmdsintegrateark89.cc,
	  trunk/xmds-devel/source/xmdssequence.cc,
	  trunk/xmds-devel/source/xmdssimulation.cc: Fixed bug triggered
	  when multiple segements were created using the ARK89 methods

2007-02-14 13:59  paultcochrane

	* ., trunk/xmds-devel/source/Makefile.am,
	  trunk/xmds-devel/source/xmds_arg.cc,
	  trunk/xmds-devel/source/xmds_arg_element.cc,
	  trunk/xmds-devel/source/xmds_argv.cc,
	  trunk/xmds-devel/source/xmdsarg.cc,
	  trunk/xmds-devel/source/xmdsargelement.cc,
	  trunk/xmds-devel/source/xmdsargv.cc: Moved argument parsing
	  sources to filenames with names a bit easier to read.

2007-02-14 13:58  paultcochrane

	* ., trunk/xmds-devel/source/Makefile.am: Swapped the names of two
	  source files to group the names better

2007-02-14 13:58  paultcochrane

	* ., trunk/xmds-devel/source/Makefile.am: Moved XML parsing sources
	  and argument parsing sources into their own
	  variable.

2007-02-14 13:58  paultcochrane

	* ., trunk/xmds-devel/source/Makefile.am: Separated the sources
	  specific to algorithm processing into its own
	  variable.

2007-02-14 13:58  paultcochrane

	* ., trunk/xmds-devel/source/Makefile.am: Expanded source listing
	  so makes it easier to add files as needed

2007-02-12 03:40  grahamdennis

	* trunk/xmds-devel/source/main.cc: Adding -openmp to compile
	  options when compiling a threaded OpenMP simulation

2007-02-12 03:20  grahamdennis

	* trunk/xmds-devel/source/xmdsbreakpoint.cc: Breakpoints would be
	  written incorrectly when writing more than one field when one of
	  the fields was of type complex. Oops.

2007-02-12 03:02  grahamdennis

	* trunk/xmds-devel/source/loadxsil.m: Enable loadxsil.m to work
	  with XSIL files produced from breakpoints.

2007-02-11 03:43  andyferris

	* trunk/xmds-devel/configure.in: Reverted my change to the
	  configure script. The previous problem was misdiagnosed. Note
	  that the libraries are tested by configure using the "cc"
	  command, and thus uses the CC=... option. However, these
	  libraries are only ever linked to programs compiled by the
	  XMDS_CC=... In this case my fftw3_threads library was
	  incompatible with gcc on my computer, when I set XMDS_CC=icc.

2007-02-08 06:35  andyferris

	* trunk/xmds-devel/configure.in: Changed configure.in to use the
	  fftw library path when searching for or using the fftw3_threads
	  library.

2007-02-08 03:18  grahamdennis

	* trunk/xmds-devel/source/xmdsvector.cc: Unbreak moment groups for
	  MPI (broken yesterday when fixing buffer overflow bug).

2007-02-07 03:58  grahamdennis

	* trunk/xmds-devel/source/xmdsvector.cc: There was a bug in
	  xmdsVector initialisation (not xmdsVectorElement initialisation)
	  that caused a buffer overflow. I think this only affected MPI
	  simulations that used explicit picture integration algorithms
	  (e.g. RK4EX). It certainly only affected MPI simulations.

2007-02-05 06:46  grahamdennis

	* trunk/xmds-devel/source/xmdsfield.cc: Make deterministic
	  simulations that use MPI but not fourier transforms work.

2007-02-05 05:08  grahamdennis

	* trunk/xmds-devel/source/loadxsil.m: Make loadxsil work for
	  zero-dimensional variables stored in XSIL files.

2007-02-05 01:30  grahamdennis

	* trunk/xmds-devel/source/xmdsvectorelement.cc: Output more
	  information for debugging when input grids don't match simulation
	  grids.

2007-01-31 02:51  grahamdennis

	* trunk/xmds-devel/examples/Makefile: Actually cause 'make run' in
	  the examples directory to run the examples instead of just
	  pretending to do so.

2007-01-30 20:43  paultcochrane

	* ., trunk/xmds-devel/admin/build-and-test.sh: Initial import to
	  repository. An initial first cut at a build and test
	  script to run on the sourceforge compile farm.

2007-01-29 21:42  paultcochrane

	* ., trunk/xmds-devel/examples: Updated svn:ignore property to
	  ignore gcov-generated files.

2007-01-29 21:42  paultcochrane

	* ., trunk/xmds-devel/examples/Makefile: Added a default target.
	  Added a run target so that can run all simulations as well as
	  just build
	  them.

2007-01-29 21:42  paultcochrane

	* ., trunk/xmds-devel/source/getopt_xmds.h,
	  trunk/xmds-devel/source/kissdom.cc,
	  trunk/xmds-devel/source/main.cc,
	  trunk/xmds-devel/source/xmdsarg.cc,
	  trunk/xmds-devel/source/xmdsargelement.cc,
	  trunk/xmds-devel/source/xmdsargv.cc,
	  trunk/xmds-devel/source/xmdsbreakpoint.cc,
	  trunk/xmds-devel/source/xmdselement.cc,
	  trunk/xmds-devel/source/xmdsfield.cc,
	  trunk/xmds-devel/source/xmdsfilter.cc,
	  trunk/xmds-devel/source/xmdsglobals.cc,
	  trunk/xmds-devel/source/xmdsintegrate.cc,
	  trunk/xmds-devel/source/xmdsintegrateark45.cc,
	  trunk/xmds-devel/source/xmdsintegrateark45ex.cc,
	  trunk/xmds-devel/source/xmdsintegrateark45ip.cc,
	  trunk/xmds-devel/source/xmdsintegrateark89.cc,
	  trunk/xmds-devel/source/xmdsintegrateark89ex.cc,
	  trunk/xmds-devel/source/xmdsintegrateark89ip.cc,
	  trunk/xmds-devel/source/xmdsintegrateex.cc,
	  trunk/xmds-devel/source/xmdsintegrateip.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4ex.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4ip.cc,
	  trunk/xmds-devel/source/xmdsintegraterk9.cc,
	  trunk/xmds-devel/source/xmdsintegraterk9ex.cc,
	  trunk/xmds-devel/source/xmdsintegraterk9ip.cc,
	  trunk/xmds-devel/source/xmdsintegratesi.cc,
	  trunk/xmds-devel/source/xmdsintegratesiex.cc,
	  trunk/xmds-devel/source/xmdsintegratesiip.cc,
	  trunk/xmds-devel/source/xmdsmomentgroup.cc,
	  trunk/xmds-devel/source/xmdsoutput.cc,
	  trunk/xmds-devel/source/xmdssegment.cc,
	  trunk/xmds-devel/source/xmdssequence.cc,
	  trunk/xmds-devel/source/xmdssimulation.cc,
	  trunk/xmds-devel/source/xmdsutils.cc,
	  trunk/xmds-devel/source/xmdsutils.h,
	  trunk/xmds-devel/source/xmdsvector.cc,
	  trunk/xmds-devel/source/xmdsvectorelement.cc,
	  trunk/xmds-devel/source/xmlbasics.cc,
	  trunk/xmds-devel/source/xmlparser.cc,
	  trunk/xmds-devel/source/xsil2graphics.cc,
	  trunk/xmds-devel/source/xsilfield.cc: Banishing hard tabs from
	  the source. Replaced with relevant number of spaces.

2007-01-29 21:40  paultcochrane

	* ., trunk/xmds-devel/source: Updated svn:ignore property to ignore
	  *.bak files

2007-01-29 21:40  paultcochrane

	* ., trunk/xmds-devel/source/xmdsintegraterk9.cc,
	  trunk/xmds-devel/source/xmdsintegraterk9ex.cc,
	  trunk/xmds-devel/source/xmdsintegraterk9ip.cc: Added emacs/vim
	  coda to load common editor settings

2007-01-29 21:39  paultcochrane

	* ., trunk/xmds-devel/Makefile.am: Removed latexdocs variable

2007-01-25 05:46  michaelhush

	* trunk/xmds-devel/source/xmdsintegrateark89.cc: Changed adaptive
	  time step algorithm, so step size is halved after a failure to
	  improve stability

2007-01-18 03:31  michaelhush

	* trunk/xmds-devel/source/xmdssequence.cc: fixed problem with
	  benchmark changes I made

2007-01-18 02:50  michaelhush

	* trunk/xmds-devel/examples/diffusion.xmds,
	  trunk/xmds-devel/examples/kubo.xmds,
	  trunk/xmds-devel/source/xmdsintegrateark89.cc,
	  trunk/xmds-devel/source/xmdssequence.cc: Fixed time step for
	  ARK89EX and IP for non stochastic problems
	  and changed bemchmark so it displays a more accurate time

2007-01-16 03:03  joehope

	* trunk/xmds-devel/Makefile.am: Adding the missing examples into
	  the distribution packages

2007-01-11 08:07  michaelhush

	* trunk/xmds-devel/source/xmdsintegrateark89.cc,
	  trunk/xmds-devel/source/xmdsintegrateark89ip.cc: ARK89EX and
	  ARK89IP both now work for normal and simple stochastic problems

2007-01-11 04:35  michaelhush

	* trunk/xmds-devel/source/xmdsclasses.h,
	  trunk/xmds-devel/source/xmdsintegrateark89.cc,
	  trunk/xmds-devel/source/xmdsintegrateark89ex.cc: ARK89EX now
	  working and convergerges on diffusion.xmds and a simple
	  stochastic problem

2007-01-07 23:52  paultcochrane

	* ., trunk/xmds-devel/source/xmdsintegraterk9.cc: Corrected
	  docstring; was throwing a warning from doxygen.

2007-01-07 23:52  paultcochrane

	* ., trunk/xmds-devel/source/Doxyfile: Explicitly specifying the
	  patterns to look for when searching for source
	  files.

2007-01-07 23:51  paultcochrane

	* ., trunk/xmds-devel/source/dom3.h: Reformatted docstrings and
	  made most of the lines of code within 80
	  character limits.

2007-01-07 19:34  paultcochrane

	* ., trunk/xmds-devel/source/Makefile.am: Building the pdf as well
	  as the html version of the api when running
	  'make api'

2007-01-07 19:34  paultcochrane

	* ., trunk/xmds-devel/source/Doxyfile: CALL_GRAPH and CALLER_GRAPH
	  set to YES

2007-01-07 19:33  paultcochrane

	* ., trunk/xmds-devel/source/Doxyfile: GENERATE_MAN set to NO

2007-01-07 19:33  paultcochrane

	* ., trunk/xmds-devel/source/Doxyfile: WARN_NO_PARAMDOC set to YES

2007-01-07 19:33  paultcochrane

	* ., trunk/xmds-devel/source/Doxyfile: Tab size set to 4.

2007-01-07 19:33  paultcochrane

	* ., trunk/xmds-devel/source/Doxyfile: Updated to current version
	  of doxygen (1.5.1)

2007-01-07 19:32  paultcochrane

	* ., trunk/xmds-devel/source/Doxyfile: Moved link to where
	  documentation should be output to be in the xmds.org
	  directory.

2007-01-05 01:21  michaelhush

	* trunk/xmds-devel/source/xmdsintegrateark89.cc: Another file I
	  forgot to add for ARK89 methods

2007-01-04 06:48  michaelhush

	* trunk/xmds-devel/source/xmdsintegrateark89ex.cc,
	  trunk/xmds-devel/source/xmdsintegrateark89ip.cc: Added ARK89
	  classes I forgot

2007-01-04 06:46  michaelhush

	* trunk/xmds-devel/examples/sech_soliton.xmds,
	  trunk/xmds-devel/source/Makefile.am,
	  trunk/xmds-devel/source/xmdsclasses.h,
	  trunk/xmds-devel/source/xmdsintegrate.cc,
	  trunk/xmds-devel/source/xmdsintegrateark45.cc,
	  trunk/xmds-devel/source/xmdsintegrateark45ex.cc,
	  trunk/xmds-devel/source/xmdsintegrateark45ip.cc,
	  trunk/xmds-devel/source/xmdsintegrateex.cc,
	  trunk/xmds-devel/source/xmdsintegrateip.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4ex.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4ip.cc,
	  trunk/xmds-devel/source/xmdsintegraterk9.cc,
	  trunk/xmds-devel/source/xmdsintegraterk9ex.cc,
	  trunk/xmds-devel/source/xmdsintegraterk9ip.cc,
	  trunk/xmds-devel/source/xmdsintegratesi.cc,
	  trunk/xmds-devel/source/xmdsintegratesiex.cc,
	  trunk/xmds-devel/source/xmdsintegratesiip.cc,
	  trunk/xmds-devel/source/xmdssequence.cc: RK9IP now works with
	  diffusion and sech_soliton examples, added ARK89EX and ARK89IP
	  classes but functionality still to come

2006-12-28 15:58  paultcochrane

	* ., trunk/xmds-devel/configure.in: A test was missing for the
	  fftw3.h header file (which is what fftw installs
	  this header as by default, I would guess so that one can run
	  fftw2 and fftw3
	  on the same system), this hopefully fixes bug #1600319

2006-12-28 15:58  paultcochrane

	* ., trunk/xmds-devel/examples/Makefile: Added the xmds binary as a
	  dependency so that when xmds is rebuilt, one
	  doesn't have to run 'make examples-clean; make examples' one can
	  just run
	  'make examples'

2006-12-28 15:58  paultcochrane

	* ., trunk/xmds-devel/examples/pendulum.xmds: Fixed typo.

2006-12-25 21:05  paultcochrane

	* ., trunk/xmds-devel/source/main.cc: Changed some output info and
	  added some more todo items.

2006-12-25 21:05  paultcochrane

	* ., trunk/xmds-devel/source/main.cc: Minor formatting changes.

2006-12-25 21:05  paultcochrane

	* ., trunk/xmds-devel/source/main.cc: Changed some more printf
	  statements to cout.

2006-12-25 21:05  paultcochrane

	* ., trunk/xmds-devel/source/main.cc: Converted many printf
	  statements to cout statements (more C++ like).
	  Generic code formatting and tidying.

2006-12-25 21:04  paultcochrane

	* ., trunk/xmds-devel/source/main.cc: Added a todo item to improve
	  an if-elseif sequence (no book handy atm to
	  make it properly clean).

2006-12-25 21:04  paultcochrane

	* ., trunk/xmds-devel/source/main.cc: Added a note to the
	  parsePrefs() routine about possibly making it more
	  object oriented to reduce the number of params passed to the
	  routine.

2006-12-25 21:04  paultcochrane

	* ., trunk/xmds-devel/source: Updated svn:ignore property.

2006-12-25 21:04  paultcochrane

	* ., trunk/xmds-devel/source/kissdom.cc,
	  trunk/xmds-devel/source/xmdsarg.cc,
	  trunk/xmds-devel/source/xmdsargelement.cc,
	  trunk/xmds-devel/source/xmdsargv.cc,
	  trunk/xmds-devel/source/xmdsbreakpoint.cc,
	  trunk/xmds-devel/source/xmdselement.cc,
	  trunk/xmds-devel/source/xmdsfield.cc,
	  trunk/xmds-devel/source/xmdsfilter.cc,
	  trunk/xmds-devel/source/xmdsglobals.cc,
	  trunk/xmds-devel/source/xmdsintegrate.cc,
	  trunk/xmds-devel/source/xmdsintegrateark45.cc,
	  trunk/xmds-devel/source/xmdsintegrateark45ex.cc,
	  trunk/xmds-devel/source/xmdsintegrateark45ip.cc,
	  trunk/xmds-devel/source/xmdsintegrateex.cc,
	  trunk/xmds-devel/source/xmdsintegrateip.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4ex.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4ip.cc,
	  trunk/xmds-devel/source/xmdsintegraterk9.cc,
	  trunk/xmds-devel/source/xmdsintegraterk9ex.cc,
	  trunk/xmds-devel/source/xmdsintegraterk9ip.cc,
	  trunk/xmds-devel/source/xmdsintegratesi.cc,
	  trunk/xmds-devel/source/xmdsintegratesiex.cc,
	  trunk/xmds-devel/source/xmdsintegratesiip.cc,
	  trunk/xmds-devel/source/xmdsmomentgroup.cc,
	  trunk/xmds-devel/source/xmdsoutput.cc,
	  trunk/xmds-devel/source/xmdssegment.cc,
	  trunk/xmds-devel/source/xmdssequence.cc,
	  trunk/xmds-devel/source/xmdssimulation.cc,
	  trunk/xmds-devel/source/xmdsutils.cc,
	  trunk/xmds-devel/source/xmdsvector.cc,
	  trunk/xmds-devel/source/xmdsvectorelement.cc,
	  trunk/xmds-devel/source/xmlbasics.cc,
	  trunk/xmds-devel/source/xmlparser.cc,
	  trunk/xmds-devel/source/xsilfield.cc: Reduced length of comments
	  used as spacers between code sections (it fits
	  within an 80 character window nicely now).

2006-12-25 21:03  paultcochrane

	* ., trunk/xmds-devel/examples/Makefile: Allowing all examples to
	  run even if one fails. This is useful if one
	  hasn't compiled xmds for mpi, and in which case highdim will
	  fail.

2006-12-25 21:03  paultcochrane

	* ., trunk/xmds-devel/Makefile.am: Added "examples" and
	  "examples-clean" rules for running the examples from
	  the base xmds-devel directory.

2006-12-25 21:02  paultcochrane

	* ., trunk/xmds-devel/Makefile.am,
	  trunk/xmds-devel/source/Makefile.am: Added an api rule to the
	  makefiles so that one can build the
	  Doxygen-generated api docs using "make api"

2006-12-25 21:02  paultcochrane

	* ., trunk/xmds-devel/source/Doxyfile: Updated the version number
	  of xmds for the api documentation.

2006-12-25 21:02  paultcochrane

	* ., trunk/xmds-devel/source/main.cc: Changed the variable c to
	  currentChar in parsePrefs()
	  Some more basic reformatting of code for readability.

2006-12-25 21:02  paultcochrane

	* ., trunk/xmds-devel/source/main.cc: Some basic code reformatting
	  in parsePrefs()

2006-12-25 21:02  paultcochrane

	* ., trunk/xmds-devel/source/main.cc: Basic reformat of
	  parsePrefs() argument list to try to improve readability.
	  Also reformatted some comments.

2006-12-25 21:01  paultcochrane

	* ., trunk/xmds-devel/source/main.cc: Tried to improve the
	  display_usage() code formatting both internally, and
	  that of the text printed to the screen.

2006-12-25 21:01  paultcochrane

	* ., trunk/xmds-devel/source/main.cc: Reformatted some of the
	  comment/documentation text.

2006-12-20 07:26  paultcochrane

	* ., trunk/xmds-devel/admin/xmdsNewsPost.pl,
	  trunk/xmds-devel/admin/xmdsNewsPost.txt: Deleted. No longer
	  necessary, or a good idea.

2006-12-20 05:35  michaelhush

	* trunk/xmds-devel/source/Makefile.am,
	  trunk/xmds-devel/source/xmdsclasses.h,
	  trunk/xmds-devel/source/xmdsintegrateip.cc,
	  trunk/xmds-devel/source/xmdsintegraterk9.cc,
	  trunk/xmds-devel/source/xmdsintegraterk9ex.cc,
	  trunk/xmds-devel/source/xmdsintegraterk9ip.cc,
	  trunk/xmds-devel/source/xmdssequence.cc: Classes added for the
	  9th order stochastically safe rk method, ex is working but ip is
	  still being completed

2006-12-18 13:03  paultcochrane

	* ., trunk/xmds-devel/.cvsignore,
	  trunk/xmds-devel/examples/.cvsignore,
	  trunk/xmds-devel/source/.cvsignore,
	  trunk/xmds-devel/testsuite/.cvsignore,
	  trunk/xmds-doc/latex/.cvsignore,
	  trunk/xmds-doc/latex/figures/.cvsignore: Removed old .cvsignore
	  files.

2006-12-18 12:59  paultcochrane

	* ., trunk/xmds-devel/AUTHORS, trunk/xmds-devel/INSTALL,
	  trunk/xmds-devel/Makefile.am, trunk/xmds-devel/NEWS,
	  trunk/xmds-devel/README, trunk/xmds-devel/README.Windows,
	  trunk/xmds-devel/acinclude.m4, trunk/xmds-devel/acx_mpi.m4,
	  trunk/xmds-devel/acx_pthread.m4,
	  trunk/xmds-devel/admin/xmdsNewsPost.pl,
	  trunk/xmds-devel/admin/xmdsReleaseProcedure.pod,
	  trunk/xmds-devel/benchmark/bench,
	  trunk/xmds-devel/benchmark/fullpos3D_16.xmds,
	  trunk/xmds-devel/benchmark/fullpos3D_32.xmds,
	  trunk/xmds-devel/benchmark/fullpos3D_64.xmds,
	  trunk/xmds-devel/benchmark/gaugeatomlaser.xmds,
	  trunk/xmds-devel/benchmark/gaugeatomlaser_128.xmds,
	  trunk/xmds-devel/benchmark/ndparamp_100.xmds,
	  trunk/xmds-devel/benchmark/ndparamp_200.xmds,
	  trunk/xmds-devel/benchmark/ndparamp_50.xmds,
	  trunk/xmds-devel/benchmark/ndparamp_500.xmds,
	  trunk/xmds-devel/benchmark/nlse_100.xmds,
	  trunk/xmds-devel/benchmark/nlse_1000.xmds,
	  trunk/xmds-devel/benchmark/nlse_10000.xmds,
	  trunk/xmds-devel/benchmark/nlse_500.xmds,
	  trunk/xmds-devel/benchmark/nlse_5000.xmds,
	  trunk/xmds-devel/benchmark/runbenchmarks,
	  trunk/xmds-devel/configure.in,
	  trunk/xmds-devel/examples/atomlaser.xmds,
	  trunk/xmds-devel/examples/branch.xmds,
	  trunk/xmds-devel/examples/brusselator.xmds,
	  trunk/xmds-devel/examples/catcycle.xmds,
	  trunk/xmds-devel/examples/chain.xmds,
	  trunk/xmds-devel/examples/chemkin.xmds,
	  trunk/xmds-devel/examples/diffusion.xmds,
	  trunk/xmds-devel/examples/diffusion2.xmds,
	  trunk/xmds-devel/examples/duffing.xmds,
	  trunk/xmds-devel/examples/fibre.xmds,
	  trunk/xmds-devel/examples/fisher_reaction_diffusion.xmds,
	  trunk/xmds-devel/examples/fullpos3D.xmds,
	  trunk/xmds-devel/examples/gaugeatomlaser.xmds,
	  trunk/xmds-devel/examples/highdim.xmds,
	  trunk/xmds-devel/examples/hires.xmds,
	  trunk/xmds-devel/examples/krebs.xmds,
	  trunk/xmds-devel/examples/kubo.xmds,
	  trunk/xmds-devel/examples/lane_emden.xmds,
	  trunk/xmds-devel/examples/lorenz.xmds,
	  trunk/xmds-devel/examples/lotka_volterra.xmds,
	  trunk/xmds-devel/examples/ndparamp.xmds,
	  trunk/xmds-devel/examples/nlse.xmds,
	  trunk/xmds-devel/examples/oregonator.xmds,
	  trunk/xmds-devel/examples/paraxial_wave.xmds,
	  trunk/xmds-devel/examples/pendulum.xmds,
	  trunk/xmds-devel/examples/ring_modulator.xmds,
	  trunk/xmds-devel/examples/sine.xmds,
	  trunk/xmds-devel/examples/soliton.xmds,
	  trunk/xmds-devel/examples/thermkin.xmds,
	  trunk/xmds-devel/examples/tla.xmds,
	  trunk/xmds-devel/examples/van_der_pol.xmds,
	  trunk/xmds-devel/examples/vibstring.xmds,
	  trunk/xmds-devel/source/Doxyfile,
	  trunk/xmds-devel/source/Makefile.am,
	  trunk/xmds-devel/source/dom3.h,
	  trunk/xmds-devel/source/getopt_xmds.c,
	  trunk/xmds-devel/source/getopt_xmds.h,
	  trunk/xmds-devel/source/getopt_xmds1.c,
	  trunk/xmds-devel/source/getopt_xmds_init.c,
	  trunk/xmds-devel/source/kissdom.cc,
	  trunk/xmds-devel/source/kissdom.h,
	  trunk/xmds-devel/source/loadxsil.m,
	  trunk/xmds-devel/source/main.cc,
	  trunk/xmds-devel/source/xmdsarg.cc,
	  trunk/xmds-devel/source/xmdsargelement.cc,
	  trunk/xmds-devel/source/xmdsargv.cc,
	  trunk/xmds-devel/source/xmdsbreakpoint.cc,
	  trunk/xmds-devel/source/xmdsclasses.h,
	  trunk/xmds-devel/source/xmdscomplex.h,
	  trunk/xmds-devel/source/xmdselement.cc,
	  trunk/xmds-devel/source/xmdsfield.cc,
	  trunk/xmds-devel/source/xmdsfilter.cc,
	  trunk/xmds-devel/source/xmdsglobals.cc,
	  trunk/xmds-devel/source/xmdsintegrate.cc,
	  trunk/xmds-devel/source/xmdsintegrateark45.cc,
	  trunk/xmds-devel/source/xmdsintegrateark45ex.cc,
	  trunk/xmds-devel/source/xmdsintegrateark45ip.cc,
	  trunk/xmds-devel/source/xmdsintegrateex.cc,
	  trunk/xmds-devel/source/xmdsintegrateip.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4ex.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4ip.cc,
	  trunk/xmds-devel/source/xmdsintegratesi.cc,
	  trunk/xmds-devel/source/xmdsintegratesiex.cc,
	  trunk/xmds-devel/source/xmdsintegratesiip.cc,
	  trunk/xmds-devel/source/xmdsmomentgroup.cc,
	  trunk/xmds-devel/source/xmdsoutput.cc,
	  trunk/xmds-devel/source/xmdssegment.cc,
	  trunk/xmds-devel/source/xmdssequence.cc,
	  trunk/xmds-devel/source/xmdssimulation.cc,
	  trunk/xmds-devel/source/xmdsutils.cc,
	  trunk/xmds-devel/source/xmdsutils.h,
	  trunk/xmds-devel/source/xmdsvector.cc,
	  trunk/xmds-devel/source/xmdsvectorelement.cc,
	  trunk/xmds-devel/source/xmlbasics.cc,
	  trunk/xmds-devel/source/xmlbasics.h,
	  trunk/xmds-devel/source/xmlparser.cc,
	  trunk/xmds-devel/source/xmlparser.h,
	  trunk/xmds-devel/source/xsil2graphics.cc,
	  trunk/xmds-devel/source/xsilfield.cc,
	  trunk/xmds-devel/source/xsilfield.h,
	  trunk/xmds-devel/testsuite/atomlaser.xmds,
	  trunk/xmds-devel/testsuite/fibre.xmds,
	  trunk/xmds-devel/testsuite/fullpos3D.xmds,
	  trunk/xmds-devel/testsuite/gaugeatomlaser.xmds,
	  trunk/xmds-devel/testsuite/kubo.xmds,
	  trunk/xmds-devel/testsuite/ndparamp.xmds,
	  trunk/xmds-devel/testsuite/nlse.xmds,
	  trunk/xmds-devel/testsuite/sine.xmds,
	  trunk/xmds-devel/testsuite/soliton.xmds,
	  trunk/xmds-devel/testsuite/test_xmds.pl,
	  trunk/xmds-devel/testsuite/tla.xmds: Updated svn keywords
	  property to make the "Id" keyword be expanded in
	  source files.

2006-12-17 15:31  paultcochrane

	* ., trunk/xmds-devel/configure.in,
	  trunk/xmds-devel/examples/atomlaser.xmds,
	  trunk/xmds-devel/examples/branch.xmds,
	  trunk/xmds-devel/examples/brusselator.xmds,
	  trunk/xmds-devel/examples/catcycle.xmds,
	  trunk/xmds-devel/examples/chain.xmds,
	  trunk/xmds-devel/examples/chemkin.xmds,
	  trunk/xmds-devel/examples/diffusion.xmds,
	  trunk/xmds-devel/examples/diffusion2.xmds,
	  trunk/xmds-devel/examples/duffing.xmds,
	  trunk/xmds-devel/examples/fibre.xmds,
	  trunk/xmds-devel/examples/fisher_reaction_diffusion.xmds,
	  trunk/xmds-devel/examples/fullpos3D.xmds,
	  trunk/xmds-devel/examples/gaugeatomlaser.xmds,
	  trunk/xmds-devel/examples/groundstate.xmds,
	  trunk/xmds-devel/examples/highdim.xmds,
	  trunk/xmds-devel/examples/hires.xmds,
	  trunk/xmds-devel/examples/krebs.xmds,
	  trunk/xmds-devel/examples/kubo.xmds,
	  trunk/xmds-devel/examples/lane_emden.xmds,
	  trunk/xmds-devel/examples/lorenz.xmds,
	  trunk/xmds-devel/examples/lotka_volterra.xmds,
	  trunk/xmds-devel/examples/ndparamp.xmds,
	  trunk/xmds-devel/examples/nlse.xmds,
	  trunk/xmds-devel/examples/oregonator.xmds,
	  trunk/xmds-devel/examples/paraxial_wave.xmds,
	  trunk/xmds-devel/examples/pendulum.xmds,
	  trunk/xmds-devel/examples/ring_modulator.xmds,
	  trunk/xmds-devel/examples/sech_soliton.xmds,
	  trunk/xmds-devel/examples/sech_soliton_tdepk.xmds,
	  trunk/xmds-devel/examples/sine.xmds,
	  trunk/xmds-devel/examples/soliton.xmds,
	  trunk/xmds-devel/examples/thermkin.xmds,
	  trunk/xmds-devel/examples/tla.xmds,
	  trunk/xmds-devel/examples/van_der_pol.xmds,
	  trunk/xmds-devel/examples/vibstring.xmds,
	  trunk/xmds-devel/source/dom3.h,
	  trunk/xmds-devel/source/kissdom.cc,
	  trunk/xmds-devel/source/kissdom.h,
	  trunk/xmds-devel/source/main.cc,
	  trunk/xmds-devel/source/xmdsarg.cc,
	  trunk/xmds-devel/source/xmdsargelement.cc,
	  trunk/xmds-devel/source/xmdsargv.cc,
	  trunk/xmds-devel/source/xmdsbreakpoint.cc,
	  trunk/xmds-devel/source/xmdsclasses.h,
	  trunk/xmds-devel/source/xmdscomplex.h,
	  trunk/xmds-devel/source/xmdselement.cc,
	  trunk/xmds-devel/source/xmdsfield.cc,
	  trunk/xmds-devel/source/xmdsfilter.cc,
	  trunk/xmds-devel/source/xmdsglobals.cc,
	  trunk/xmds-devel/source/xmdsintegrate.cc,
	  trunk/xmds-devel/source/xmdsintegrateark45.cc,
	  trunk/xmds-devel/source/xmdsintegrateark45ex.cc,
	  trunk/xmds-devel/source/xmdsintegrateark45ip.cc,
	  trunk/xmds-devel/source/xmdsintegrateex.cc,
	  trunk/xmds-devel/source/xmdsintegrateip.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4ex.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4ip.cc,
	  trunk/xmds-devel/source/xmdsintegratesi.cc,
	  trunk/xmds-devel/source/xmdsintegratesiex.cc,
	  trunk/xmds-devel/source/xmdsintegratesiip.cc,
	  trunk/xmds-devel/source/xmdsmomentgroup.cc,
	  trunk/xmds-devel/source/xmdsoutput.cc,
	  trunk/xmds-devel/source/xmdssegment.cc,
	  trunk/xmds-devel/source/xmdssequence.cc,
	  trunk/xmds-devel/source/xmdssimulation.cc,
	  trunk/xmds-devel/source/xmdsutils.cc,
	  trunk/xmds-devel/source/xmdsutils.h,
	  trunk/xmds-devel/source/xmdsvector.cc,
	  trunk/xmds-devel/source/xmdsvectorelement.cc,
	  trunk/xmds-devel/source/xmlbasics.cc,
	  trunk/xmds-devel/source/xmlbasics.h,
	  trunk/xmds-devel/source/xmlparser.cc,
	  trunk/xmds-devel/source/xmlparser.h,
	  trunk/xmds-devel/source/xsil2graphics.cc,
	  trunk/xmds-devel/source/xsilfield.cc,
	  trunk/xmds-devel/source/xsilfield.h: Updated copyright date
	  information.

2006-12-17 15:29  paultcochrane

	* ., trunk/xmds-devel/configure.in,
	  trunk/xmds-devel/source/main.cc: Updated revision number (1.5-3
	  has been released)

2006-12-17 15:00  paultcochrane

	* ., trunk/xmds-devel/examples/sech_soliton.xmds,
	  trunk/xmds-devel/examples/sech_soliton_tdepk.xmds: Added
	  copyright notice.

2006-12-17 15:00  paultcochrane

	* ., trunk/xmds-devel/examples/fullpos3D.xmds,
	  trunk/xmds-devel/examples/gaugeatomlaser.xmds: The line at the
	  top of each xmds file should read:
	  <?xml version="1.0"?>
	  not
	  <?xmds version="1.0"?>
	  for the file to be a well formed xml document.

2006-12-17 11:17  paultcochrane

	* trunk/xmds-devel/source/kissdom.cc,
	  trunk/xmds-devel/source/main.cc,
	  trunk/xmds-devel/source/xmdsarg.cc,
	  trunk/xmds-devel/source/xmdsargelement.cc,
	  trunk/xmds-devel/source/xmdsargv.cc,
	  trunk/xmds-devel/source/xmdsbreakpoint.cc,
	  trunk/xmds-devel/source/xmdselement.cc,
	  trunk/xmds-devel/source/xmdsfield.cc,
	  trunk/xmds-devel/source/xmdsfilter.cc,
	  trunk/xmds-devel/source/xmdsglobals.cc,
	  trunk/xmds-devel/source/xmdsintegrate.cc,
	  trunk/xmds-devel/source/xmdsintegrateark45.cc,
	  trunk/xmds-devel/source/xmdsintegrateark45ex.cc,
	  trunk/xmds-devel/source/xmdsintegrateark45ip.cc,
	  trunk/xmds-devel/source/xmdsintegrateex.cc,
	  trunk/xmds-devel/source/xmdsintegrateip.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4ex.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4ip.cc,
	  trunk/xmds-devel/source/xmdsintegratesi.cc,
	  trunk/xmds-devel/source/xmdsintegratesiex.cc,
	  trunk/xmds-devel/source/xmdsintegratesiip.cc,
	  trunk/xmds-devel/source/xmdsmomentgroup.cc,
	  trunk/xmds-devel/source/xmdsoutput.cc,
	  trunk/xmds-devel/source/xmdssegment.cc,
	  trunk/xmds-devel/source/xmdssequence.cc,
	  trunk/xmds-devel/source/xmdssimulation.cc,
	  trunk/xmds-devel/source/xmdsutils.cc,
	  trunk/xmds-devel/source/xmdsvector.cc,
	  trunk/xmds-devel/source/xmdsvectorelement.cc,
	  trunk/xmds-devel/source/xmlbasics.cc,
	  trunk/xmds-devel/source/xmlparser.cc,
	  trunk/xmds-devel/source/xsil2graphics.cc,
	  trunk/xmds-devel/source/xsilfield.cc: Added emacs/vim coda to
	  help with formatting of code.

2006-12-17 11:15  paultcochrane

	* trunk/xmds-devel/examples/groundstate.xmds: Changed simulation
	  name to match filename: this helps the examples makefile
	  correctly work out dependencies.

2006-12-17 11:15  paultcochrane

	* trunk/xmds-devel/examples/Makefile: Initial import to repository.
	  This makefile is used to build the examples.
	  We probably need to add this as part of autoconf, however, this
	  does the job
	  at present.

2006-12-16 18:16  paultcochrane

	* trunk/xmds-devel/preconf: Removed; this command would have worked
	  nicely for older versions of the
	  autoconf suite (i.e. those used when the original scripts were
	  written),
	  however now there exists the autoreconf program which comes with
	  the
	  autoconf suite, and so makes the preconf script obsolete.

2006-12-14 09:17  sebwuester

	* trunk/xmds-devel/examples/sech_soliton.xmds,
	  trunk/xmds-devel/source/xmdsintegrateark45.cc,
	  trunk/xmds-devel/source/xmdsintegrateark45ex.cc,
	  trunk/xmds-devel/source/xmdsintegrateark45ip.cc,
	  trunk/xmds-devel/source/xmdsintegrateip.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4ex.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4ip.cc,
	  trunk/xmds-devel/source/xmdsintegratesiex.cc: added underscores
	  to some variables in ark45 which didn't have them; also added
	  underscores to akfield etc. in rk4 and siip siex

2006-12-14 08:00  grahamdennis

	* trunk/xmds-devel/source/xmdsvectorelement.cc: Fix bug in earlier
	  commit causing some simulations to not compile (those that use
	  XSIL files to initialise non-main fields).

2006-12-14 07:46  grahamdennis

	* trunk/xmds-devel/source/xmdsbreakpoint.cc: Significantly sped up
	  writing breakpoints when using MPI (removed unnecessary fseeks).
	  For an example of the reduction, in examples/fullpos3D.xmds, the
	  number of fseeks when writing the field data (in a breakpoint)
	  was reduced from 393216 to 48.
	  
	  Also caught a bug where the data was being sent as the incorrect
	  type when using MPI breakpoints. I continue to be astonished that
	  this has worked in the past on the AC.

2006-12-14 05:39  joehope

	* trunk/xmds-devel/configure.in: Recovering 'out of the box'
	  compilation for Mac OS X by defaulting to c++ compiler
	  Still to achieve this for OPENMPI without passing MPI compiler
	  explicitly as mpic++

2006-12-14 01:57  grahamdennis

	* trunk/xmds-devel/source/xmdsvectorelement.cc: Significantly
	  reduced the number of fseeks during loading of XSIL files. This
	  is particularly important for large simulations as fseeks
	  significantly slow down the loading procedure.

2006-12-01 05:44  paultcochrane

	* trunk/xmds-devel/configure.in: No longer automatically checking
	  for icc during the configuration stage. If
	  the user wants to use icc they can use the syntax:
	  XMDS_CC=icc ./configure --with-user --enable-mpi (for example)

2006-12-01 04:54  paultcochrane

	* trunk/xmds-devel/preconf: Initial import to repository. This is a
	  script to run to perform the
	  autoconf preconfiguration dance before running ./configure after
	  one has
	  changed the configure.in or Makefile.am files. Maybe this will
	  save some
	  hands from RSI.

2006-12-01 04:39  paultcochrane

	* trunk/xmds-devel/Makefile.am: Removed trailing space. This was
	  causing a warning from automake.

2006-12-01 04:33  paultcochrane

	* trunk/xmds-devel/testsuite/test_xmds.pl: Corrected a typo, and
	  added cvs Id keyword.

2006-12-01 04:20  paultcochrane

	* trunk/xmds-devel, trunk/xmds-devel/.cvsignore: Initial import to
	  repository. Getting cvs to ignore some of the autogenerated
	  files in the root xmds-devel directory.

2006-11-30 00:13  joehope

	* trunk/xmds-devel/configure.in: Changing PREFIX behaviour on
	  installation. This is one less patch separating
	  the CVS from the Debian version.

2006-11-27 13:41  paultcochrane

	* trunk/xmds-devel/testsuite,
	  trunk/xmds-devel/testsuite/.cvsignore: Initial import to
	  repository. This file helps 'cvs status' ignore several
	  files in the testsuite/ directory.

2006-11-27 00:05  joehope

	* trunk/xmds-devel/Makefile.am: Including lorentzInput.dat in the
	  distribution tarball, as posted by Rafael Laboissiere

2006-11-24 13:08  paultcochrane

	* trunk/xmds-devel/source/main.cc: Updated copyright information
	  (2004 -> 2006)

2006-11-24 13:07  paultcochrane

	* trunk/xmds-devel/source, trunk/xmds-devel/source/.cvsignore:
	  Ignoring automatically generated files.

2006-11-24 12:44  paultcochrane

	* trunk/xmds-devel/examples, trunk/xmds-devel/examples/.cvsignore:
	  Added .wisdom files to list to ignore, and the names of the
	  output example
	  executables.

2006-11-24 12:31  paultcochrane

	* trunk/xmds-devel/examples, trunk/xmds-devel/examples/.cvsignore:
	  Added a .cvsignore file so that cvs status doesn't generate so
	  much unwanted
	  output.

2006-11-21 04:41  grahamdennis

	* trunk/xmds-devel/source/xmdsbreakpoint.cc: Significantly sped up
	  writing breakpoints to disk by reordering the fwrites
	  so that fseeks are mostly not needed.

2006-11-18 08:57  grahamdennis

	* trunk/xmds-devel/source/xmdsfield.cc,
	  trunk/xmds-devel/source/xmdsintegrateip.cc: I hereby swear to try
	  to make sure my xmds variables start with an underscore.
	  Fixed OpenMP slowdown

2006-11-17 07:18  grahamdennis

	* trunk/xmds-devel/source/xmdsintegrateip.cc: I forgot to mark the
	  k operators as thread-private in my previous commit.

2006-11-17 05:26  grahamdennis

	* trunk/xmds-devel/source/xmdsintegrateip.cc: Loop index variables
	  must be signed for OpenMP to work

2006-11-17 05:21  grahamdennis

	* trunk/xmds-devel/source/xmdsintegrateip.cc: Parallelised (OpenMP)
	  k_propagate and calculate_k_operator_field for ARK45.
	  This should have a decent effect on performance with OpenMP

2006-11-17 04:19  grahamdennis

	* trunk/xmds-devel/source/xmdsintegrateark45ip.cc: It worked on my
	  machine...
	  Fix crash

2006-11-17 04:15  grahamdennis

	* trunk/xmds-devel/source/xmdsintegrateark45ip.cc: Combined ARK45IP
	  for loops for cleaner code and better OpenMP compatibility
	  This can be done for all algorithms, I'll do it as I go

2006-11-17 02:49  grahamdennis

	* trunk/xmds-devel/source/xmdsvectorelement.cc: One day I will
	  remember to use underscores in variable names written by XMDS.
	  (Fix compile warning for scripts using XSIL input)

2006-11-03 18:57  paultcochrane

	* trunk/xmds-devel/NEWS: Updated to the current version of xmds,
	  and added all news items from
	  between xmds-1.3-2 and xmds-1.5-3.

2006-11-03 18:28  paultcochrane

	* trunk/xmds-devel/AUTHORS: Updated the author list, and reordered
	  all names (except for Greg's - he
	  wrote it to start with, well, that's my reasoning) in
	  alphabetical order by
	  last name.

2006-11-03 14:02  paultcochrane

	* trunk/xmds-devel/configure.in: Moved fftw3-path help information
	  over a bit so that it lines up with the
	  other text when one does ./configure --help. (yes, I'm pedantic)

2006-10-17 04:59  grahamdennis

	* trunk/xmds-devel/source/xmdssimulation.cc,
	  trunk/xmds-devel/source/xmdsutils.cc: Fixed a problem with how
	  description elements were being read which caused xmds to crash
	  when reading certain examples (e.g. branch.xmds)

2006-10-05 00:57  grahamdennis

	* trunk/xmds-devel/examples/lorenz.xmds,
	  trunk/xmds-devel/source/xmdssimulation.cc: Changing the example
	  lorenz.xmds not to require an input file as the options can be
	  supplied on the command line
	  Fix a bug in the byte-swapping routines due to a choice in the
	  variable name which would result in problems for
	  simulations that define the variable 'x'.

2006-09-19 04:49  joehope

	* trunk/xmds-devel/ChangeLog, trunk/xmds-devel/MANIFEST: Update of
	  MANIFEST and ChangeLog

2006-09-19 04:46  joehope

	* trunk/xmds-devel/README, trunk/xmds-devel/README.Windows,
	  trunk/xmds-devel/configure.in: Version updates prior to release

2006-09-19 04:01  joehope

	* trunk/xmds-devel/ChangeLog, trunk/xmds-devel/examples/kubo.xmds,
	  trunk/xmds-devel/source/xmdssequence.cc,
	  trunk/xmds-devel/source/xmdssimulation.cc: Fixes for a collection
	  of MPI scheduler bugs (1558333,1551791,1551790). Single path runs
	  are now handled by the "Uniform" scheduler automatically. Trying
	  to run stochastic simulations without MPI no longer
	  bombs.

2006-08-30 03:33  grahamdennis

	* trunk/xmds-devel/source/xmdssequence.cc: Flushing output after
	  each path for stochastic simulations at Mattias' request.

2006-08-24 00:54  grahamdennis

	* trunk/xmds-devel/source/xmdsbreakpoint.cc: For MPI breakpoints, I
	  was sending and receiving some values with the wrong
	  datatype (double instead of int). I'm honestly surprised that
	  this even
	  worked for some systems before.

2006-08-23 23:50  grahamdennis

	* trunk/xmds-devel/examples/atomlaser.xmds: Removed the old-style
	  breakpoint element from the example atomlaser.xmds as
	  that style breakpoint was never implemented. And we don't want
	  any confusion
	  arising with new-style breakpoints.

2006-08-22 05:52  matt0064

	* trunk/xmds-devel/source/loadxsil.m: Added code to loadxsil.m to
	  initialise multi-dimensional arrays when loading in binary data.
	  This can be a significant speed up.

2006-08-09 00:54  grahamdennis

	* trunk/xmds-devel/source/main.cc: Fixing a compile bug for
	  stochastic MPI simulations with FFTW3. Thanks Andy!

2006-08-03 06:17  grahamdennis

	* trunk/xmds-devel/source/xsilfield.cc: Fixing a bug in the matlab
	  output of xsil2graphics that would cause the script
	  not to load the data from a binary file if the data is a scalar
	  (zero dimensional)

2006-07-31 01:50  grahamdennis

	* trunk/xmds-devel/source/xmdsbreakpoint.cc,
	  trunk/xmds-devel/source/xmdsvectorelement.cc: Fixing bugs with
	  the breakpoint code. I'm fairly sure that it works now.

2006-07-28 05:09  grahamdennis

	* trunk/xmds-devel/source/xmdsvectorelement.cc: Adding rank number
	  to diagnostic output when an error occurs while loading
	  an XSIL file (with MPI).

2006-07-21 03:39  grahamdennis

	* trunk/xmds-devel/examples/diffusion.xmds,
	  trunk/xmds-devel/examples/diffusion2.xmds,
	  trunk/xmds-devel/source/xmdsbreakpoint.cc: I have fixed the
	  breakpoint code for non-MPI simulations, and breakpoints should
	  now
	  also work for deterministic MPI simulations (it makes no sense to
	  use breakpoints for
	  stochastic MPI simulations). I have also modified the diffusion
	  example to use a
	  breakpoint and then to continue from that breakpoint (with a
	  larger simulation grid) in
	  a second diffusion example.

2006-07-19 03:28  joehope

	* trunk/xmds-devel/source/xmdsintegrateex.cc: Fix for a tiny bug
	  temporarily introduced with the openMP code, which
	  broke compilation of *EX algorithms.

2006-06-29 07:33  grahamdennis

	* trunk/xmds-devel/examples/nlse.xmds,
	  trunk/xmds-devel/source/xmdssimulation.cc: Fixing a bug where a
	  simulation with ascii output and a breakpoint element
	  would not compile

2006-06-29 07:24  grahamdennis

	* trunk/xmds-devel/source/xmdsbreakpoint.cc,
	  trunk/xmds-devel/source/xmdsclasses.h,
	  trunk/xmds-devel/source/xmdsoutput.cc,
	  trunk/xmds-devel/source/xmdssequence.cc,
	  trunk/xmds-devel/source/xmdsvectorelement.cc,
	  trunk/xmds-devel/source/xsilfield.cc: First crack at the
	  breakpoint code. Currently it only works for simulations that
	  aren't both deterministic and use MPI. Of course, the whole point
	  of this code
	  is for the deterministic MPI case, but for the moment, the vast
	  majority of the helper
	  code has been written.
	  
	  Changes to behaviour: when loading double-type variables with the
	  XSIL loading code,
	  it looks for a variable with an 'R' suffix instead of a variable
	  of the same name. As it
	  is impossible to have an output moment group variable of the same
	  name as a field variable.

2006-06-23 01:54  grahamdennis

	* trunk/xmds-devel/source/xsilfield.cc: Increased verbosity of some
	  errors when loading XSIL files to mention what the
	  probable cause of the error was.

2006-06-21 07:33  grahamdennis

	* trunk/xmds-devel/source/xmdsvector.cc: Parallelised the
	  multiplication loop at the end of the *go_space routines.
	  This was causing a massive slowdown on NUMA architecture machines
	  because
	  the whole field was accessed from a single node.

2006-06-20 02:20  grahamdennis

	* trunk/xmds-devel/source/xmdssequence.cc: Added a fflush() after
	  the 'beginning integration ...' printf lines to better keep track
	  of simulations run with a buffered output stream (e.g.
	  simulations run through batch
	  queueing systems)

2006-06-20 01:59  grahamdennis

	* trunk/xmds-devel/source/xsilfield.cc: Increased the verbosity of
	  one of the error shown when loading XSIL files when none of the
	  variables to be loaded have been found. This is typically due to
	  the wrong moment group being
	  set.

2006-06-16 04:17  joehope

	* trunk/xmds-devel/source/xmdsvector.cc: Fix for the MPI version of
	  mixed space Fourier transforms. It was simply wrong previously.

2006-06-07 06:40  joehope

	* trunk/xmds-devel/ChangeLog, trunk/xmds-devel/README.Windows,
	  trunk/xmds-devel/configure.in, trunk/xmds-devel/source/main.cc,
	  trunk/xmds-devel/source/xmdsfilter.cc,
	  trunk/xmds-devel/source/xmdsintegrate.cc,
	  trunk/xmds-devel/source/xmdsintegratesiip.cc: Fix for multiple
	  bugs when using moment groups in filter and integrate blocks.
	  The bugs were all specific to MPI specific code implementation.

2006-05-28 10:34  grahamdennis

	* trunk/xmds-devel/source/xmdsvectorelement.cc: Correction to my
	  previous commit:
	  It helps to actually set the field to zero instead of just
	  looping over it.

2006-05-28 10:24  grahamdennis

	* trunk/xmds-devel/source/xmdsvectorelement.cc: Fix for OpenMP so
	  that each field is initialised by the thread that will
	  use it. This is important for NUMA-architecture supercomputers
	  (e.g. ANU's ac)

2006-05-25 03:19  grahamdennis

	* trunk/xmds-devel/source/xmdsclasses.h,
	  trunk/xmds-devel/source/xmdsfield.cc,
	  trunk/xmds-devel/source/xmdsintegrate.cc,
	  trunk/xmds-devel/source/xmdsintegrateark45ex.cc,
	  trunk/xmds-devel/source/xmdsintegrateark45ip.cc,
	  trunk/xmds-devel/source/xmdsintegrateex.cc,
	  trunk/xmds-devel/source/xmdsintegrateip.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4ex.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4ip.cc,
	  trunk/xmds-devel/source/xmdssimulation.cc,
	  trunk/xmds-devel/source/xmdsvectorelement.cc: OpenMP support. Use
	  the tag <use_openmp> yes </use_openmp> in the simulation
	  element to use this. This does not work with deterministic MPI
	  simulations,
	  and doesn't really make sense to use it with stochastic MPI
	  simulations.
	  To make use of this, you will need a compiler that supports
	  OpenMP such as icc
	  or gcc 4.4 (currently unreleased). Note that one will get best
	  performance if
	  FFTW is compiled using OpenMP threads instead of pthreads.

2006-05-13 01:12  grahamdennis

	* trunk/xmds-devel/source/xmdsmomentgroup.cc: Forcing a fflush()
	  after writing the 'sampled field...' lines.
	  This way, it is easier to keep track of the progress of jobs on
	  supercomputers

2006-05-12 07:49  grahamdennis

	* trunk/xmds-devel/source/xmdsvectorelement.cc: Fixed binary
	  importing to not load the entire file into memory. This is needed
	  for MPI situations where
	  the initialisation data won't fit into memory. Also, previously,
	  it was just plain wrong when used with
	  deterministic MPI simulations.

2006-05-12 06:54  grahamdennis

	* trunk/xmds-devel/source/xsilfield.cc: Removing text claiming that
	  the XSIL loading code does not support byte-swapping (it does)

2006-05-12 06:27  grahamdennis

	* trunk/xmds-devel/configure.in,
	  trunk/xmds-devel/source/xmdsvectorelement.cc: Reducing the
	  verbosity of the XSIL loading code
	  Adding a --with-fftw3-path to the configure script so that the
	  location of fftw3 can be specified
	  independently of fftw2. Note that the path for fftw3 defaults to
	  the path for fftw2

2006-05-12 04:23  grahamdennis

	* trunk/xmds-devel/source/xmdssimulation.cc: Fixing a missing \n in
	  a printf statement

2006-05-12 01:48  grahamdennis

	* trunk/xmds-devel/source/Makefile.am,
	  trunk/xmds-devel/source/main.cc,
	  trunk/xmds-devel/source/xmdsclasses.h,
	  trunk/xmds-devel/source/xmdscomplex.h,
	  trunk/xmds-devel/source/xmdssimulation.cc,
	  trunk/xmds-devel/source/xmdsvectorelement.cc,
	  trunk/xmds-devel/source/xsilfield.cc,
	  trunk/xmds-devel/source/xsilfield.h: Vector initialisation from
	  XSIL moment groups (binary format only)
	  This should work for MPI simulations (it doesn't load the entire
	  binary file into memory,
	  this is why the this code does not support importing data in
	  ASCII format from XSIL files)
	  This should deal with byte-swapping if necessary. (Not tested,
	  but I'm going to).
	  The input moment group grid does not have to match up exactly
	  with the simulation grid,
	  there are two modes for importing, 'strict' mode and 'loose'
	  mode.
	  
	  In 'strict' mode, the initialisation geometry must match the
	  simulation geometry to within 1%
	  of the step size in each dimension. In 'loose' mode, the step
	  size in each initialisation dimension
	  (you may initialise from a mix of x- and k-space) must match the
	  simulation step size in each dimension,
	  but the start and end points (and the number of points) may be
	  different.
	  
	  Documentation is forthcoming after I have given this a bit more
	  testing.

2006-05-07 09:39  pharaoh84

	* trunk/xmds-devel/configure.in, trunk/xmds-devel/source/main.cc:
	  Fixing threads for fftw3

2006-05-07 03:10  pharaoh84

	* trunk/xmds-devel/configure.in: Fixing my previous fix for systems
	  with requiring explicit linking
	  of the thread libraries.
	  Also, the agressive CFLAGS are now used for systems that don't
	  require
	  explicit linking of the thread libraries (removed a pointless
	  test)
	  
	  I hate autoconf.

2006-05-07 02:48  pharaoh84

	* trunk/xmds-devel/configure.in: Fixing configure.in for fftw3 for
	  systems that require explicit linking of thread
	  libraries

2006-05-05 06:20  pharaoh84

	* trunk/xmds-devel/configure.in: Fixing the configure.in script...
	  I hate autoconf.

2006-05-05 06:10  pharaoh84

	* trunk/xmds-devel/configure.in, trunk/xmds-devel/source/main.cc:
	  configure.in has been modified to support fftw3. Now you need to
	  provide the option
	  --enable-fftw3 in order to get fftw3 support.
	  One thing I forgot to mention in my previous commit comment was
	  that the tag required to use fftw3
	  is <fftw_version>. This tag belongs in the simulation element.
	  The default is 2 (fftw2), and set
	  it to 3 to use fftw3.

2006-05-04 07:53  pharaoh84

	* trunk/xmds-devel/source/main.cc,
	  trunk/xmds-devel/source/xmdsclasses.h,
	  trunk/xmds-devel/source/xmdscomplex.h,
	  trunk/xmds-devel/source/xmdsfield.cc,
	  trunk/xmds-devel/source/xmdsintegrateark45.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4.cc,
	  trunk/xmds-devel/source/xmdsintegratesiex.cc,
	  trunk/xmds-devel/source/xmdsintegratesiip.cc,
	  trunk/xmds-devel/source/xmdssequence.cc,
	  trunk/xmds-devel/source/xmdssimulation.cc,
	  trunk/xmds-devel/source/xmdsvector.cc: Initial support for fftw3.
	  It should work for simulations that are not deterministic MPI
	  simulations with the following caveats:
	  You are not permitted to use fftw_complex in your simulation
	  script (fftw3 uses a different format for their fftw_complex type
	  than
	  is used by fftw2), instead you should be using the 'complex'
	  type.
	  autoconf does not yet detect fftw3, so to get your scripts to
	  compile, you will need to insert a 'FFTW3_LIBS = ' line defining
	  the
	  fftw3 libraries to link in (-lfftw3 and optionally
	  -lfftw3_threads) and the path to find the library if needed.
	  
	  Note that fftw3 uses a different format for wisdom, and this is
	  stored under the new filename
	  ~/.xmds/wisdom/hostname.wisdom.fftw3
	  or ~/.xmds/wisdom/hostname.wisdom.fftw3_threads for
	  threaded-simulations.
	  
	  I have tested threaded, non-threaded, deterministic and
	  stochastic simulations. I have not tested MPI-based stochastic
	  simulations yet,
	  however the scripts do compile.

2006-04-20 00:47  pharaoh84

	* trunk/xmds-devel/examples/groundstate.xmds: Modifying this
	  example to use the new <type> tag for output groups

2006-04-18 07:15  pharaoh84

	* trunk/xmds-devel/source/xmdsmomentgroup.cc,
	  trunk/xmds-doc/latex/languageReference.tex: Added a <type> tag to
	  the <sampling> element for outputs.
	  If this is set to 'double' then the output type is forced to type
	  double.
	  It defaults to 'complex'

2006-04-07 04:17  pharaoh84

	* trunk/xmds-devel/source/xmdssequence.cc: Fixing the elapsed time
	  for non-MPI simulations

2006-04-07 03:35  pharaoh84

	* trunk/xmds-devel/source/xsil2graphics.cc: Fix spelling mistake
	  'Proccessing...' --> 'Processing..'

2006-03-29 00:34  athiator

	* trunk/xmds-devel/source/xsilfield.cc: Also prints created
	  variables to screen when executing Mathematica instructions

2006-03-15 04:27  athiator

	* trunk/xmds-devel/source/xmlbasics.cc,
	  trunk/xmds-devel/source/xmlbasics.h,
	  trunk/xmds-devel/source/xsil2graphics.cc,
	  trunk/xmds-devel/source/xsilfield.cc,
	  trunk/xmds-devel/source/xsilfield.h: Changes to xsil2graphics to
	  output a file with commands to read simulation data into
	  Mathematica

2006-01-27 01:04  joehope

	* trunk/xmds-devel/source/xmdsmomentgroup.cc: Fixed error in MPI
	  reduction for deterministic systems.
	  The problem only affected some moment groups that used
	  post_propagation.

2005-11-23 23:44  joehope

	* trunk/xmds-devel/examples/gaugeatomlaser.xmds,
	  trunk/xmds-devel/examples/groundstate.xmds: Adding imaginary time
	  evolution algorithm to the examples. It is often requested,
	  demonstrates
	  filters and moment_groups, and saves mailing it regularly.

2005-10-31 00:34  joehope

	* trunk/xmds-devel/source/xmdsintegraterk4ip.cc: Avoid warning for
	  one case where it does not apply.

2005-10-27 07:01  joehope

	* trunk/xmds-devel/ChangeLog, trunk/xmds-devel/MANIFEST,
	  trunk/xmds-devel/admin/xmds.spec: Final updates before 1.5-2
	  release

2005-10-27 00:58  joehope

	* trunk/xmds-devel/ChangeLog,
	  trunk/xmds-devel/source/xmdssequence.cc,
	  trunk/xmds-devel/source/xmdssimulation.cc: Fixed adaptive
	  scheduler to compile cleanly on other systems.

2005-10-26 03:46  joehope

	* trunk/xmds-devel/ChangeLog, trunk/xmds-devel/README,
	  trunk/xmds-devel/README.Windows, trunk/xmds-devel/configure.in,
	  trunk/xmds-devel/examples/kubo.xmds,
	  trunk/xmds-devel/source/main.cc,
	  trunk/xmds-devel/source/xmdssequence.cc,
	  trunk/xmds-devel/source/xmdssimulation.cc: Added new scheduling
	  option for stochastic MPI calculations. It uses
	  an adaptive scheduler to allocate batches of work to individual
	  nodes,
	  making for large speed increases on heterogenous systems. Bumped
	  version numbers.

2005-10-24 22:40  joehope

	* trunk/xmds-devel/source/xmdssequence.cc: Fix for new timer.

2005-10-24 04:11  joehope

	* trunk/xmds-devel/source/xmdssequence.cc,
	  trunk/xmds-devel/source/xmdssimulation.cc: Changed timer to work
	  better on MPI systems.

2005-10-18 23:33  joehope

	* trunk/xmds-devel/examples/kubo.xmds,
	  trunk/xmds-devel/examples/tla.xmds,
	  trunk/xmds-devel/source/xmdsclasses.h,
	  trunk/xmds-devel/source/xmdssimulation.cc,
	  trunk/xmds-devel/source/xmdsvectorelement.cc: Fix for stack
	  overflow in binary read from file.
	  Preliminary support for MPI Scheduling options.

2005-10-13 00:45  joehope

	* trunk/xmds-devel/source/xmdssequence.cc: MPI runs only print out
	  the benchmark time from the master node.

2005-10-12 04:34  joehope

	* trunk/xmds-devel/source/xmdsvectorelement.cc: Fix for crashing
	  bug when loading from file in stochastic simulations.

2005-09-29 05:35  joehope

	* trunk/xmds-devel/ChangeLog,
	  trunk/xmds-devel/source/xmdsmomentgroup.cc: Fix compile error for
	  error-free stochastic binary output.

2005-08-12 05:46  sebwuester

	* trunk/xmds-devel/examples/sech_soliton.xmds,
	  trunk/xmds-devel/source/xmdsclasses.h,
	  trunk/xmds-devel/source/xmdsintegrateark45.cc: -Bugfixes in
	  ARK45:
	  -current step now states last accepted step instead of current
	  forecast
	  -fixed problems with timescales <10^-24
	  -fixed problem with N_samples=N_steps
	  -Cosmetic in ARK45
	  - rephrased "cutoff defaulting to" not to contain the word error

2005-07-27 06:57  joehope

	* trunk/xmds-devel/source/xmdsintegratesiip.cc: Fixed an error in
	  the cross propagation routines of the SIIP algorithm.
	  Boundary conditions that are independent of the propagation
	  dimension are
	  now correct.

2005-07-05 10:13  joehope

	* trunk/xmds-devel/ChangeLog, trunk/xmds-devel/MANIFEST: Updating
	  Changelog and MANIFEST prior to release

2005-07-05 09:37  joehope

	* trunk/xmds-devel/README, trunk/xmds-devel/README.Windows,
	  trunk/xmds-devel/examples/highdim.xmds: Adjusting READMEs and
	  examples for version 1.5-1x

2005-06-30 07:44  sebwuester

	* trunk/xmds-devel/source/xmdsintegrateark45.cc: Minor Bugfixes:
	  Corrected typo in on-screen message and call to noise generator
	  in the case of errorchecking

2005-05-25 03:33  paultcochrane

	* trunk/xmds-devel/examples/highdim.xmds: Fixed xml header.

2005-05-24 03:54  paultcochrane

	* trunk/xmds-devel/configure.in: Doing a check to see if the
	  library lammpi++ exists in the mpicc -showme
	  output, and if not adds -llammpi++ to the MPI_LIBS variable. This
	  should
	  only affect users of lam 7.x.x, this problem didn't occur in
	  6.x.x.

2005-05-19 05:46  paultcochrane

	* trunk/xmds-devel/source/xmdssequence.cc: Outputting standard C
	  argument stuff even when <argv> is not defined.
	  This fixes a problem where I didn't check for all possible paths
	  in an if loop

2005-05-19 03:50  joehope

	* trunk/xmds-devel/ChangeLog: Update of ChangeLog

2005-05-19 03:42  joehope

	* trunk/xmds-devel/source/xsilfield.cc: The m file now closes files
	  when it is done to avoid excess file
	  pointer usage in Matlab.

2005-05-17 06:01  sebwuester

	* trunk/xmds-devel/source/xmdsintegrateark45.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4ip.cc: Fixed bug in
	  warning about RK4IP and t-dep k operators. Made ARK45 error
	  determination routine more efficient for ODEs

2005-05-10 03:40  paultcochrane

	* trunk/xmds-devel/source/main.cc: Moved -o <simulation_name>
	  <simulation_name>.cc to just behind the mpicc
	  call in the mpi compilation calls. This gets around problems with
	  mpicc not
	  finding various libraries. In particular, when getopt was turned
	  on for mpi
	  problems, mpicc wasn't finding -lxmds.

2005-05-10 01:23  paultcochrane

	* trunk/xmds-devel/configure.in: Changed ordering of MPICCFLAGS so
	  that XMDS_LIBS is at the end. This should stop problems with
	  mpicc not finding the xmds libraries.

2005-05-05 09:34  paultcochrane

	* trunk/xmds-devel/source/xmdssequence.cc: Hopefully fixed problem
	  with mpi not being able to make use of the arugment
	  parsing code. Added -h as a valid option; --help was only
	  possible before.

2005-05-02 05:42  sebwuester

	* trunk/xmds-devel/examples/sech_soliton.xmds,
	  trunk/xmds-devel/examples/sech_soliton_tdepk.xmds,
	  trunk/xmds-devel/source/xmdsintegrateark45.cc: Fixed float
	  precision issue in ARK45 sampling and typos in examples.

2005-05-02 02:35  sebwuester

	* trunk/xmds-devel/examples/sech_soliton.xmds,
	  trunk/xmds-devel/examples/sech_soliton_tdepk.xmds,
	  trunk/xmds-devel/source/xmdsclasses.h,
	  trunk/xmds-devel/source/xmdsintegrate.cc,
	  trunk/xmds-devel/source/xmdsintegrateark45.cc,
	  trunk/xmds-devel/source/xmdsintegrateark45ex.cc,
	  trunk/xmds-devel/source/xmdsintegrateark45ip.cc,
	  trunk/xmds-devel/source/xmdsintegrateip.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4ip.cc,
	  trunk/xmds-devel/source/xmdsvectorelement.cc: Added ARK45IP and
	  ARK45EX adaptive timestep algorithms.
	  Added example files sech_soliton.xmds, sech_soliton_tdepk.xmds
	  Added parallel initialisation from file (ascii only)

2005-04-28 05:21  joehope

	* trunk/xmds-devel/source/loadxsil.m: Fix for loadxsil loading of
	  64 bit binaries

2005-04-27 05:44  joehope

	* trunk/xmds-devel/source/xmdsfield.cc: Andy's fix for cluster
	  nodes testing the same filesystem simultaneously with the same
	  files.

2005-04-24 04:31  joehope

	* trunk/xmds-devel/source/xsilfield.h: Final commit for previous
	  fix.

2005-04-21 06:32  joehope

	* trunk/xmds-devel/configure.in,
	  trunk/xmds-devel/source/xmdsmomentgroup.cc,
	  trunk/xmds-devel/source/xsilfield.cc: Added test for the size of
	  unsigned longs in the configure script. This,
	  like endianness, is stored in the xsil file for binary output,
	  and then
	  used when generating the MATLAB script. Fixes bug with moving
	  binary
	  data between machines.

2005-04-12 07:25  joehope

	* trunk/xmds-devel/source/xmdsclasses.h,
	  trunk/xmds-devel/source/xmdsintegrate.cc,
	  trunk/xmds-devel/source/xmdsintegrateark45ex.cc,
	  trunk/xmds-devel/source/xmdsintegrateark45ip.cc: Set up template
	  for passing the adaptive boolean to the xmdsintegrate class.

2005-04-12 05:44  joehope

	* trunk/xmds-devel/source/xsilfield.cc: Fixed matlab error message
	  when using binary files without the output file

2005-04-06 06:41  paultcochrane

	* trunk/xmds-devel/examples/lorenzInput.dat: Initial import to
	  repository. This is the data file associated with the lorenz.xmds
	  example.

2005-04-06 05:54  joehope

	* trunk/xmds-devel/examples/branch.xmds,
	  trunk/xmds-devel/examples/brusselator.xmds,
	  trunk/xmds-devel/examples/catcycle.xmds,
	  trunk/xmds-devel/examples/chain.xmds,
	  trunk/xmds-devel/examples/chemkin.xmds,
	  trunk/xmds-devel/examples/duffing.xmds,
	  trunk/xmds-devel/examples/fibre.xmds,
	  trunk/xmds-devel/examples/fisher_reaction_diffusion.xmds,
	  trunk/xmds-devel/examples/highdim.xmds,
	  trunk/xmds-devel/examples/hires.xmds,
	  trunk/xmds-devel/examples/krebs.xmds,
	  trunk/xmds-devel/examples/lane_emden.xmds,
	  trunk/xmds-devel/examples/lorenz.xmds,
	  trunk/xmds-devel/examples/lotka_volterra.xmds,
	  trunk/xmds-devel/examples/oregonator.xmds,
	  trunk/xmds-devel/examples/pendulum.xmds,
	  trunk/xmds-devel/examples/ring_modulator.xmds,
	  trunk/xmds-devel/examples/sine.xmds,
	  trunk/xmds-devel/examples/soliton.xmds,
	  trunk/xmds-devel/examples/thermkin.xmds,
	  trunk/xmds-devel/examples/van_der_pol.xmds: Fixing all examples
	  to conform with the (post 1.4-1) rule to always specify the used
	  vectors in integrate blocks.

2005-04-06 02:22  joehope

	* trunk/xmds-devel/source/xmdsmomentgroup.cc: Fix for potential
	  problem with handling sample spaces when there are no transverse
	  dimensions.

2005-04-06 01:43  joehope

	* trunk/xmds-devel/source/xmdsmomentgroup.cc: Made verbose output
	  on the moment groups more consistent with the numbering of the
	  groups.

2005-04-05 23:23  joehope

	* trunk/xmds-devel/ChangeLog, trunk/xmds-devel/configure.in:
	  Version bump

2005-04-05 07:23  joehope

	* trunk/xmds-devel/source/Makefile.am,
	  trunk/xmds-devel/source/main.cc,
	  trunk/xmds-devel/source/xmdsclasses.h,
	  trunk/xmds-devel/source/xmdsintegrateark45.cc,
	  trunk/xmds-devel/source/xmdsintegrateark45ex.cc,
	  trunk/xmds-devel/source/xmdsintegrateark45ip.cc,
	  trunk/xmds-devel/source/xmdssequence.cc: Adding in shell files
	  for new ARK45 algorithms and bumping versions.

2005-04-05 05:32  joehope

	* trunk/xmds-devel/examples/diffusion.xmds: Fixed sampling in
	  example.

2004-12-06 04:58  paultcochrane

	* trunk/xmds-devel/source/xsilfield.cc: Now orienting independent
	  variable vectors for binary input to agree with that from ascii
	  input.

2004-12-06 04:42  paultcochrane

	* trunk/xmds-devel/source/xsilfield.cc: Changed ordering of
	  variables in binary input to matlab. Should work the same as
	  ascii now. Some changes to comments.

2004-11-17 23:35  joehope

	* trunk/xmds-devel/source/xsilfield.cc: Fixed a bug when using
	  MATLAB import of output moment groups of >2 dimensions in binary
	  format.

2004-11-17 04:54  joehope

	* trunk/xmds-devel/source/xsilfield.cc: Adding explicit include
	  line to avoid problem with non-standard compilers.

2004-11-02 22:51  joehope

	* trunk/xmds-devel/examples/atomlaser.xmds: Changing this example
	  to demo binary output, now that it works without explosions.

2004-11-02 22:48  joehope

	* trunk/xmds-devel/ChangeLog: New ChangeLog for the new version

2004-11-02 22:47  joehope

	* trunk/xmds-devel/MANIFEST: New manifest for the new version.

2004-11-02 22:43  joehope

	* trunk/xmds-devel/source/xsilfield.cc: Fix for an error where an
	  integer overflow lead to dramatic problems with bianry output.

2004-10-25 06:02  joehope

	* trunk/xmds-devel/configure.in, trunk/xmds-devel/source/main.cc:
	  Bumping the release version in preparation for a new release.

2004-10-22 08:04  paultcochrane

	* trunk/xmds-devel/admin/xmdsReleaseProcedure.pod: Made mention
	  that one should update the xmds version and release numbers in
	  configure.in. Gave a more complete explanation of generating a
	  distribution, including checking out a temporary copy of the
	  xmds-devel repository and going through the relevant steps to be
	  able to do a make dist.

2004-10-22 01:16  paultcochrane

	* trunk/xmds-devel/source/xsilfield.cc: Added some error text for
	  when a user tries to use binary output and then load the data
	  using scilab. Also put in some hopefully helpful information
	  about how to use scilab and data that comes out of xmds.
	  Basically this means just using ascii output.

2004-10-21 10:01  paultcochrane

	* trunk/xmds-devel/source/xsilfield.h: Correction log for
	  previously stuffed up commit without a log. Added extra variables
	  to implement binary data handling of xsil2graphics.

2004-10-21 10:00  paultcochrane

	* trunk/xmds-devel/source/xsilfield.cc: Simple commit to actually
	  add a log for the previous commit, because I stuffed up. Major
	  changes. Binary files are now handled by xsil2graphics.
	  Unfortunately, only the matlab script is produced at this stage.
	  The scilab version is to come.

2004-10-21 09:51  paultcochrane

	* trunk/xmds-devel/source/xsilfield.cc,
	  trunk/xmds-devel/source/xsilfield.h: xsilfield.cc

2004-10-21 09:51  paultcochrane

	* trunk/xmds-devel/source/xmdsvectorelement.cc: Changed some return
	  statements to exit statements. Basically, the program could keep
	  going at this point as opposed to barfing which would be far more
	  logical in the circumstances.

2004-10-21 09:50  paultcochrane

	* trunk/xmds-devel/source/xmdsvector.cc: Changed unsigned long to
	  unsigned long int. I must have been in a pedantic mood.

2004-10-21 09:49  paultcochrane

	* trunk/xmds-devel/source/xmdsoutput.cc: Added xmdsOutputFileName()
	  function. This is so that I can properly determine what the
	  output binary data filename should be, and base that upon the
	  name of the xsil filename as opposed to the simulation filename.

2004-10-21 09:48  paultcochrane

	* trunk/xmds-devel/source/xmdsmomentgroup.cc: Major changes. Added
	  more attributes to the Metalink tag of the xsil file that gets
	  output so that can load binary data properly using xsil2graphics.
	  Implemented a better way of constructing the output binary data
	  filename. It is now based upon the xsilFilename rather than the
	  simulation name (these can be different). Fixed major bug where
	  if there is only one sample in the entire simulation (possible
	  but not common) then data was being written over as an array was
	  incorrectly sized. This is all happy now, and I even tested it.
	  Yay.

2004-10-21 09:42  paultcochrane

	* trunk/xmds-devel/source/xmdsfilter.cc: Added a Doxygen docstring.

2004-10-21 09:41  paultcochrane

	* trunk/xmds-devel/source/xmdscomplex.h: Fixed problem with there
	  being no newline at the end of the file.

2004-10-21 09:40  paultcochrane

	* trunk/xmds-devel/source/xmdsclasses.h: Was pedantic again and
	  changed some unsigned constants to long unsigned ints. Added the
	  getOutputFileName() function, and its Doxygen docstring.

2004-10-21 09:39  paultcochrane

	* trunk/xmds-devel/source/loadxsil.m: Removed some superfluous code
	  in the binary loading section. Made loading of the binary data
	  file part of the eval, as opposed to running it here. Added some
	  strings to say that the text that follows isn't actually just
	  informative, it is actually the code that is being executed.

2004-10-21 09:37  paultcochrane

	* trunk/xmds-devel/source/getopt_xmds1.c,
	  trunk/xmds-devel/source/getopt_xmds_init.c: Added some Doxygen
	  docstrings.

2004-10-21 09:36  paultcochrane

	* trunk/xmds-devel/source/getopt_xmds.c: Reformat of the C code.
	  Documentation with Doxygen docstrings.

2004-10-21 09:34  paultcochrane

	* trunk/xmds-devel/configure.in: Updated version number to interim
	  release number.

2004-10-15 07:53  joehope

	* trunk/xmds-devel/configure.in: Various fixes to the mpi autoconf
	  testing. It now works with non-gcc mpi.

2004-10-11 04:06  joehope

	* trunk/xmds-devel/configure.in: Removed a "-Wall -pedantic" check
	  that broke compilation when cc/mpicc were gnu/non-gnu compilers.

2004-10-06 07:52  joehope

	* trunk/xmds-devel/source/xmdsfilter.cc,
	  trunk/xmds-devel/source/xmdsintegrate.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4.cc,
	  trunk/xmds-devel/source/xmdsintegratesiex.cc,
	  trunk/xmds-devel/source/xmdsintegratesiip.cc,
	  trunk/xmds-devel/source/xmdsmomentgroup.cc,
	  trunk/xmds-devel/source/xmdssequence.cc,
	  trunk/xmds-devel/source/xmdsvectorelement.cc: Fixed a memory leak
	  on strict compilers that didn't know that "delete(pointer)"
	  means "delete[] pointer" for pointer arrays.

2004-10-06 07:50  joehope

	* trunk/xmds-devel/examples/kubo.xmds,
	  trunk/xmds-devel/examples/van_der_pol.xmds: These, and possibly
	  others, now need <vectors> elements in the integrate blocks.

2004-09-30 03:27  paultcochrane

	* trunk/xmds-devel/source/loadxsil.m: Fixed binary loading support.
	  This now works for mutli-dimensional matrices (ie greater than
	  two dims). Probably should be tested a bit more extensively than
	  I've tested it, but it seems to go well in the tests that I've
	  done. The ascii loading takes ages, especially for large output
	  data files, so I've added a message saying that it will take
	  ages, and have added progress output to keep the user amused
	  while they're waiting. Realistically for large files people
	  should use binary as it loads a couple of orders of magnitude
	  faster than ascii. I've also implemented preallocation of
	  matrices to help the ascii loading to run more quickly. Using
	  this script turns out to be a better option for very large files
	  as it doesn't use up as much memory as xsil2graphics does. For
	  some sims I've been doing recently, xsil2graphics maxes out the
	  memory on my machine when it's trying to generate the matlab file
	  and data file, however, loadxsil sits there quite happily and
	  doesn't even bother making the machine page to disk. This implies
	  that there could be a memory leak in xsil2graphics, or that
	  something could be done a bit more carefully concerning memory
	  useage.

2004-09-24 03:29  paultcochrane

	* trunk/xmds-devel/Makefile.am: Fixed typo in orgeonator name.

2004-09-15 06:01  joehope

	* trunk/xmds-devel/source/xmdsintegraterk4ex.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4ip.cc: Fix for <no_noise>
	  flag in RK4 algorithms.

2004-09-15 04:46  joehope

	* trunk/xmds-devel/source/xmdsclasses.h,
	  trunk/xmds-devel/source/xmdsfilter.cc,
	  trunk/xmds-devel/source/xmdsintegrate.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4.cc,
	  trunk/xmds-devel/source/xmdsintegratesiex.cc,
	  trunk/xmds-devel/source/xmdsintegratesiip.cc: Added flag that
	  turns off the noise generation in an integration
	  or filter element. This allows deterministic elements in
	  stochastic
	  simulations (e.g. the noise is in the initial state only) to run
	  faster.
	  
	  Activated by the flag <no_noise>yes</no_noise>, and the default
	  is to
	  turn off this feature.

2004-09-15 04:27  joehope

	* trunk/xmds-devel/ChangeLog: Updated with cvs2cl.pl

2004-08-03 05:29  paultcochrane

	* trunk/xmds-devel/examples/brusselator.xmds,
	  trunk/xmds-devel/examples/chain.xmds,
	  trunk/xmds-devel/examples/oregonator.xmds,
	  trunk/xmds-devel/examples/thermkin.xmds: Added GPL header.

2004-08-02 10:04  paultcochrane

	* trunk/xmds-devel/source/xmdsoutput.cc: Changed long to long
	  unsigned int, which gets rid of a compiler warning, and appears
	  only because compilers can choose which sign ints can take, hence
	  being pedantic is the way to go.

2004-08-02 10:02  paultcochrane

	* trunk/xmds-devel/source/xmdsfilter.cc,
	  trunk/xmds-devel/source/xmdsintegrate.cc,
	  trunk/xmds-devel/source/xmdsintegratesiip.cc: Changed longs to
	  long unsigned ints. Also fixed warnings that appear due to a
	  .size() call on a list (which returns int) being given a format
	  in a printf statement as being a long int. If this isn't quite
	  the right thing to do then one probably needs to
	  overload/override the .size() method to return long ints as
	  opposed to just ints.

2004-08-02 09:59  paultcochrane

	* trunk/xmds-devel/source/xmdsclasses.h: Changed longs to long
	  unsigned ints.

2004-08-02 09:57  paultcochrane

	* trunk/xmds-devel/Makefile.am: Added new example simulations to
	  list of files to be added when doing a make dist.

2004-08-02 08:50  paultcochrane

	* trunk/xmds-devel/source/xmdsfilter.cc,
	  trunk/xmds-devel/source/xmdsintegrate.cc,
	  trunk/xmds-devel/source/xmdsintegratesiip.cc: Reformatted code so
	  it looks nicer.

2004-08-02 08:47  paultcochrane

	* trunk/xmds-devel/source/xmdsfield.cc: Changed long to long
	  unsigned int. This is a really pedantic change I know, but we
	  need to be really explicit so that the code is really
	  pedantically ansi compliant, and hopefully therefore more
	  portable.

2004-08-02 08:45  paultcochrane

	* trunk/xmds-devel/source/xmdsclasses.h: Changed variables declared
	  as longs to be long unsigned ints. This gets rid of some compiler
	  warnings, especially between compilers that define ints to be
	  signed or unsigned on their whim.

2004-08-02 08:16  paultcochrane

	* trunk/xmds-devel/examples/chain.xmds: Initial import to
	  repository. This is another chemical kinetics reaction I found
	  lying around in my sandbox.

2004-08-02 08:10  paultcochrane

	* trunk/xmds-devel/examples/brusselator.xmds,
	  trunk/xmds-devel/examples/oregonator.xmds,
	  trunk/xmds-devel/examples/thermkin.xmds: Initial import to
	  repository. These are some more example simulations of chemical
	  kinetics type reactions.

2004-08-02 08:04  paultcochrane

	* trunk/xmds-devel/benchmark/ndparamp_100.xmds,
	  trunk/xmds-devel/benchmark/ndparamp_200.xmds,
	  trunk/xmds-devel/benchmark/ndparamp_50.xmds,
	  trunk/xmds-devel/benchmark/ndparamp_500.xmds,
	  trunk/xmds-devel/benchmark/nlse_100.xmds,
	  trunk/xmds-devel/benchmark/nlse_1000.xmds,
	  trunk/xmds-devel/benchmark/nlse_10000.xmds,
	  trunk/xmds-devel/benchmark/nlse_500.xmds,
	  trunk/xmds-devel/benchmark/nlse_5000.xmds: Removed the
	  binary_output tag as it is now obsolete.

2004-08-02 08:02  paultcochrane

	* trunk/xmds-devel/source/xmdssimulation.cc: Stopped storing all of
	  the description text; we weren't using it anyway. There is now a
	  message added to say that the description has been found, and to
	  look in the xmds file for more info. The reason for this change
	  is because if the description is too big, then this causes a
	  buffer overflow and all kinds of wierd things can happen. I have
	  commented out the original code that read the description in.

2004-07-30 07:43  joehope

	* trunk/xmds-devel/source/xmdsfilter.cc,
	  trunk/xmds-devel/source/xmdsvector.cc: Allowed integrate moment
	  groups to deal with mixed spaces and MPI transposed spaces
	  properly.

2004-07-30 06:56  joehope

	* trunk/xmds-devel/source/xmdsfield.cc: Fixed the close_loops
	  function which used to be simply wrong for mixed spaces.

2004-07-30 06:02  joehope

	* trunk/xmds-devel/source/xmdsfield.cc,
	  trunk/xmds-devel/source/xmdsvector.cc: Fixed a bug where some
	  mixed spaces were incorrectly recognised as being in the
	  transposed order for deterministic MPI solutions.

2004-07-29 08:28  joehope

	* trunk/xmds-devel/examples/highdim.xmds: Added example syntax for
	  the new <moment_group> elements in the evolution.

2004-07-29 08:27  joehope

	* trunk/xmds-devel/source/xmdsclasses.h,
	  trunk/xmds-devel/source/xmdsfilter.cc,
	  trunk/xmds-devel/source/xmdsintegrate.cc,
	  trunk/xmds-devel/source/xmdsintegratesiip.cc,
	  trunk/xmds-devel/source/xmdssequence.cc,
	  trunk/xmds-devel/source/xmdssimulation.cc: Added the option of
	  putting <moment_group> elements as well as <functions> elements
	  in <integrate> blocks.
	  <moment_group> elements let you define moments that are
	  integrated through any number of transverse dimensions,
	  so XMDS can now evolve equations that depend on integrals of the
	  fields.
	  Also added <moment_group> and <functions> elements to <filter>
	  elements.
	  
	  You can put as many as you like, of any dimension, in any order.
	  The <vectors> element defines the position
	  of the <integrate> or <filter> code, so it is now mandatory.
	  Sample syntax will be added to an example.

2004-07-27 07:33  paultcochrane

	* trunk/xmds-devel/source/xmlparser.cc: Cast a variable as
	  unsigned. This stopped a warning message turning up in the
	  compiler output due to an integer which should have been cast as
	  unsigned.

2004-07-27 07:31  paultcochrane

	* trunk/xmds-devel/source/xmdsvectorelement.cc: Fixed error whereby
	  an extra comma was added to a fprintf statement, and hence caused
	  incorrect output when generating the code for reading in an input
	  file.

2004-07-27 06:45  paultcochrane

	* trunk/xmds-devel/source/getopt_xmds_init.c: Replaced C++ comments
	  with C-style comments. This stops some compilers complaining.

2004-07-23 07:27  joehope

	* trunk/xmds-devel/source/xmdsfield.cc: Fixes problem when multiple
	  FFTW plans were created using wisdom. The
	  variables used for the wisdom manipulation are all now local
	  variables, so there are no more multiple definitions.

2004-07-21 05:45  joehope

	* trunk/xmds-devel/source/xmdsoutput.cc: Added the command line
	  variables to the <info> element in the output tag.
	  This will make the xsil file completely self documenting.

2004-07-19 03:59  paultcochrane

	* trunk/xmds-devel/admin/xmdsReleaseProcedure.pod: Found a command
	  to put on its own line that I'd missed.

2004-07-19 03:57  paultcochrane

	* trunk/xmds-devel/MANIFEST: Updated manifest to xmds-1.3-5.

2004-07-19 03:56  paultcochrane

	* trunk/xmds-devel/admin/xmdsReleaseProcedure.pod: Put all of the
	  commands to run on their own line.

2004-07-19 03:53  paultcochrane

	* trunk/xmds-devel/ChangeLog: Updated with cvs2cl.pl

2004-07-19 03:52  paultcochrane

	* trunk/xmds-devel/README, trunk/xmds-devel/README.Windows: Changed
	  xmds-1.3-4 to xmds 1.3-5.

2004-07-19 03:43  paultcochrane

	* trunk/xmds-devel/ChangeLog: Updated with cvs2cl.pl

2004-07-19 03:42  paultcochrane

	* trunk/xmds-devel/source/loadxsil.m: Now detecting when there are
	  more than two independent variables when loading binary data and
	  output an error saying that one should use ascii data and
	  xsil2graphics to get around the problem. The file still works for
	  less than two independent variables (or less) with binary data
	  and for any number of variables with ascii data (but one might as
	  well just use xsil2graphics in that case).

2004-07-19 03:40  paultcochrane

	* trunk/xmds-devel/source/getopt_xmds.h: Fixed warnings that were
	  produced as a result of having C++ comments within a C file (and
	  when using -pedantic and -ansi). Having C++ style comments isn't
	  a problem with modern compilers, however it's nice for users to
	  not have warnings come up when xmds compiles.

2004-07-16 04:02  paultcochrane

	* trunk/xmds-devel/examples/atomlaser.xmds: Removed
	  precision=single bit from output tag.

2004-07-16 03:46  paultcochrane

	* trunk/xmds-devel/admin/xmdsReleaseProcedure.pod: Added more
	  detailed info about how to perform a release of the xmds
	  documentation. Put the tagging commands earlier in the list of
	  things to do before making a release, and mentioned the format of
	  the tag to use. Also added the actual commands to use.

2004-07-16 03:25  paultcochrane

	* trunk/xmds-devel/admin/xmdsReleaseProcedure.pod: Changed the
	  order of when the Readmes are updated and when the ChangeLog is
	  updated. Added a line explaining how one should check to see if
	  the cvs and/or the local repository needs updating before running
	  a make dist.

2004-07-16 03:20  paultcochrane

	* trunk/xmds-devel/ChangeLog: Updated to current output of
	  cvs2cl.pl.

2004-07-16 03:19  paultcochrane

	* trunk/xmds-devel/admin/xmdsReleaseProcedure.pod: We're now
	  automatically generating the ChangeLog with cvs2cl.pl, so have
	  changed what to do as far as that is concerned.

2004-07-16 03:16  paultcochrane

	* trunk/xmds-devel/ChangeLog: Updated to current output of
	  cvs2cl.pl.

2004-07-16 03:12  paultcochrane

	* trunk/xmds-devel/README.Windows: Made mention of the fact that
	  fftw must be installed after cygwin is installed. Also added a
	  description of the steps required to build and install fftw.
	  Fixed up the step numbering as necessary. Added
	  --with-fftw-path=/usr/local to the configure option to the xmds
	  build procedure, as this *should* be where fftw is installed,
	  assuming that the user followed the instructions higher up in the
	  file. Removed some comments reminding me to do stuff.

2004-07-16 01:27  paultcochrane

	* trunk/xmds-devel/admin/cvs2cl.pl: Initial import to repository.
	  This is the cvs to ChangeLog script that generates the ChangeLog.

2004-07-15 07:27  joehope

	* trunk/xmds-devel/source/xmdsoutput.cc: Moved <info> tags down
	  above the data to make the XSIL file valid XML. This fixed a
	  parsing error from xsil2graphics.

2004-07-14 11:48  paultcochrane

	* trunk/xmds-devel/source/main.cc,
	  trunk/xmds-devel/source/xmdsoutput.cc: Finally got grabbing and
	  splitting up and escaping quote issues in the script code
	  grabbing code. This is quite a big change, and means that xmds
	  produced scripts now compile ok on linux and the APAC sc. I
	  haven't tested anything else, but it's 10pm, and I've finally
	  fixed the damned thing, and I'm going home (yay).

2004-07-14 06:37  joehope

	* trunk/xmds-devel/ChangeLog,
	  trunk/xmds-devel/examples/atomlaser.xmds,
	  trunk/xmds-devel/examples/fibre.xmds,
	  trunk/xmds-devel/examples/fisher_reaction_diffusion.xmds,
	  trunk/xmds-devel/examples/fullpos3D.xmds,
	  trunk/xmds-devel/examples/gaugeatomlaser.xmds,
	  trunk/xmds-devel/examples/highdim.xmds,
	  trunk/xmds-devel/examples/hires.xmds,
	  trunk/xmds-devel/examples/kubo.xmds,
	  trunk/xmds-devel/examples/lorenz.xmds,
	  trunk/xmds-devel/examples/ndparamp.xmds,
	  trunk/xmds-devel/examples/nlse.xmds,
	  trunk/xmds-devel/examples/pendulum.xmds,
	  trunk/xmds-devel/examples/ring_modulator.xmds,
	  trunk/xmds-devel/examples/sine.xmds,
	  trunk/xmds-devel/examples/soliton.xmds,
	  trunk/xmds-devel/examples/tla.xmds,
	  trunk/xmds-devel/examples/vibstring.xmds,
	  trunk/xmds-devel/source/main.cc: Changed the examples and
	  template to ascii output until binary output is robust.

2004-07-14 04:27  joehope

	* trunk/xmds-devel/source/xmdssequence.cc,
	  trunk/xmds-devel/source/xmdssimulation.cc: Fixed bug where nested
	  subsequences could count moment samples incorrectly.
	  The field moment samples were being counted at the start of each
	  sequence
	  rather than at the start of the simulation.

2004-07-14 01:32  joehope

	* trunk/xmds-devel/source/xmdsmomentgroup.cc: Verbose mode now
	  mentions the addition of samples to the moment groups.

2004-07-13 08:46  paultcochrane

	* trunk/xmds-devel/source/xmdsargelement.cc: Removed a trigraph.
	  Added a test to see if a short option was actually found, and if
	  no short option could be worked out, then xmds barfs with a
	  reasonably helpful error message. Also fixed a typo in one of the
	  comments.

2004-07-13 07:52  paultcochrane

	* trunk/xmds-devel/configure.in: Added the threads checking stuff
	  back in. However, to enable this option, one needs to use
	  --enable-threads at the configuration step. I put this back in so
	  that if someone does want to use threads, then at least the
	  checking and configuration is built in. The code that was
	  originally there is now wrapped in an if loop, and is only
	  executed if --enable-threads is set.

2004-07-13 07:25  paultcochrane

	* trunk/xmds-devel/configure.in: added -pedantic flag to CFLAGS and
	  CXXFLAGS variables for building of xmds and the -ansi flag to the
	  CXXFLAGS variable.

2004-07-13 07:24  paultcochrane

	* trunk/xmds-devel/source/kissdom.h,
	  trunk/xmds-devel/source/xmdsclasses.h,
	  trunk/xmds-devel/source/xmlbasics.h: Removed fake trigraphs
	  (obsolecent feature of C) that were in the comments.

2004-07-13 06:16  paultcochrane

	* trunk/xmds-devel/source/xmdsutils.h: Fixed problem with trailing
	  comma in enumeration. This was found by using the -pedantic flag
	  to gcc.

2004-07-13 05:29  paultcochrane

	* trunk/xmds-devel/source/kissdom.cc,
	  trunk/xmds-devel/source/main.cc,
	  trunk/xmds-devel/source/xmdsarg.cc,
	  trunk/xmds-devel/source/xmdsargelement.cc,
	  trunk/xmds-devel/source/xmdsargv.cc,
	  trunk/xmds-devel/source/xmdsbreakpoint.cc,
	  trunk/xmds-devel/source/xmdselement.cc,
	  trunk/xmds-devel/source/xmdsfield.cc,
	  trunk/xmds-devel/source/xmdsfilter.cc,
	  trunk/xmds-devel/source/xmdsglobals.cc,
	  trunk/xmds-devel/source/xmdsintegrate.cc,
	  trunk/xmds-devel/source/xmdsintegrateex.cc,
	  trunk/xmds-devel/source/xmdsintegrateip.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4ex.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4ip.cc,
	  trunk/xmds-devel/source/xmdsintegratesi.cc,
	  trunk/xmds-devel/source/xmdsintegratesiex.cc,
	  trunk/xmds-devel/source/xmdsintegratesiip.cc,
	  trunk/xmds-devel/source/xmdsmomentgroup.cc,
	  trunk/xmds-devel/source/xmdsoutput.cc,
	  trunk/xmds-devel/source/xmdssegment.cc,
	  trunk/xmds-devel/source/xmdssequence.cc,
	  trunk/xmds-devel/source/xmdssimulation.cc,
	  trunk/xmds-devel/source/xmdsutils.cc,
	  trunk/xmds-devel/source/xmdsvector.cc,
	  trunk/xmds-devel/source/xmdsvectorelement.cc,
	  trunk/xmds-devel/source/xmlbasics.cc,
	  trunk/xmds-devel/source/xmlparser.cc,
	  trunk/xmds-devel/source/xsil2graphics.cc,
	  trunk/xmds-devel/source/xsilfield.cc: Added braces to if, while
	  and for statements. They weren't necessary, however, it does make
	  the code a bit nicer, in terms of style, it might save a few bugs
	  in the future, and it really should be used when the if, while or
	  for has nested if, while or for statements. I hope this reduces
	  someone's pain in the future.

2004-07-09 06:47  joehope

	* trunk/xmds-devel/source/xmdsfield.cc: cstr() should be c_str()

2004-07-09 06:35  joehope

	* trunk/xmds-devel/source/xmdsfield.cc: Attempt to stop a very rare
	  crash when a deterministic MPI script is written
	  without any Fourier space elements anywhere. Forces plans to
	  always be written.
	  This could be done with slightly greater finesse by testing for
	  the existence
	  of "main_forward_plan" and setting the appropriate variables
	  manually if it
	  doesn't exist.

2004-07-09 05:29  joehope

	* trunk/xmds-devel/source/xmdsvectorelement.cc: Forcing abort when
	  input file is misread.

2004-07-01 05:26  paultcochrane

	* trunk/xmds-devel/source/kissdom.cc,
	  trunk/xmds-devel/source/main.cc: Added braces to if, while and
	  for statements. They weren't necessary, however, it does make the
	  code a bit nicer, in terms of style, it might save a few bugs in
	  the future, and it really should be used when the if, while or
	  for has nested if, while or for statements. This exercise fixed
	  two possible bugs where there was a trailing semicolon on the
	  statement. I hope this reduces someone's pain in the future.

2004-06-30 10:23  paultcochrane

	* trunk/xmds-devel/source/xmdssimulation.cc: Commented out some
	  legacy code that's not doing anything anymore. I'm keeping it
	  around for a while before I delete it (doesn't hurt).

2004-06-30 10:22  paultcochrane

	* trunk/xmds-devel/source/main.cc: Updated the documentation
	  version numbering output from xmds-1.3-4 to xmds-1.3-5.

2004-06-30 10:20  paultcochrane

	* trunk/xmds-devel/source/getopt_xmds_init.c: Added a dummy
	  statement to avoid a warning that some compilers throw up when
	  the ifdef isn't executed, and hence there aren't any executable
	  statements in the file. Also added some comments explaining this.

2004-06-30 10:18  paultcochrane

	* trunk/xmds-devel/configure.in: Changed the release number from 4
	  to 5. Added a check for the Tru64 compiler and then set the
	  __USE_STD_IOSTREAM appropriately if it is. Added a check for if
	  mpicc is *not* set, but mpi is enabled and then if so, setting
	  MPICC to the system C++ compiler. Fixed bug whereby LIBS variable
	  should have been XMDS_LIBS, and CFLAGS should have been
	  XMDS_CFLAGS. Hopefully this stuff gets xmds configuring and
	  compiling better on Tru64 machines.

2004-06-30 10:15  paultcochrane

	* trunk/xmds-devel/README.Windows: Added some more helpful comments
	  about how to use the configure script, where to look for more
	  information, and how to solve the common fftw path problem.

2004-06-30 10:14  paultcochrane

	* trunk/xmds-devel/README: Tidied up the formatting of the text
	  somewhat. Hopefully made a bit clearer that the switches are
	  directly to do with the configure command.

2004-06-30 07:26  paultcochrane

	* trunk/xmds-devel/man, trunk/xmds-devel/man/loadxsil.1,
	  trunk/xmds-devel/man/xmds.1,
	  trunk/xmds-devel/man/xsil2graphics.1: Initial import to
	  repository. These are the automatically generated man pages from
	  the pod in the xmds-doc project.

2004-06-30 07:20  paultcochrane

	* trunk/xmds-devel/source/xmdssimulation.cc: Removed some
	  whitespace.

2004-06-30 07:19  paultcochrane

	* trunk/xmds-devel/source/xmdsoutput.cc: Implemented breakup of
	  simulation text into header, body and footer. I reconstruct this
	  text here. A lot of the changes in this commit are commenting out
	  lines of code in the generated code (ie the stuff that is
	  generated isn't actually executed and is in fact ignored by the
	  compiler). I left the code in at this stage as this is still an
	  experimental process and it will be easier to back out the
	  changes by leaving the legacy stuff in there. This change has
	  removed the need for xmds simulations to use the system() call
	  and the split system command to be able to write the output. I
	  also put some info text into the output xml/xsil which tells
	  which version of xmds produced the file.

2004-06-30 07:15  paultcochrane

	* trunk/xmds-devel/source/xmdsmomentgroup.cc: Fixed error whereby
	  the Metalink xml tag should have had a /> at the end instead of
	  just >.

2004-06-30 07:14  paultcochrane

	* trunk/xmds-devel/source/main.cc: Implemented the splitting up of
	  the xmds simulation text before the parsing starts. I split the
	  text into a header, body and footer, and then recombine these
	  later when getting the simulation to write the xsil file. This
	  removes the need to use the split system command, and removes
	  some more of the system() calls in the xmds engine. Added heaps
	  of comments of how I'm going about stuff, and added some verbose
	  output to make sure it's doing what it should be doing. At
	  present I'm implementing this as global variables; perhaps this
	  really should be done through and object interface, however, this
	  is easy and it works, we just have to be careful. Also updated
	  the documentation version number to xmds-1.3-4.

2004-06-29 07:21  joehope

	* trunk/xmds-devel/source/xmdsintegraterk4.cc,
	  trunk/xmds-devel/source/xmdsintegratesiex.cc,
	  trunk/xmds-devel/source/xmdsintegratesiip.cc: Fix for problem in
	  if statements.

2004-06-29 07:13  joehope

	* trunk/xmds-devel/source/xmdsintegraterk4.cc,
	  trunk/xmds-devel/source/xmdsintegratesiex.cc,
	  trunk/xmds-devel/source/xmdsintegratesiip.cc: Allows number of
	  samples in an integrate block to be zero without trouble.

2004-06-26 05:29  paultcochrane

	* trunk/xmds-devel/source/main.cc: Grabbing the simulation text for
	  splitting up the xmds script for later use at the output stage.

2004-06-25 05:28  joehope

	* trunk/xmds-devel/configure.in,
	  trunk/xmds-devel/examples/atomlaser.xmds: Removed redundant code
	  to do with choosing thread-compliant compilers
	  for the code generator.

2004-06-24 08:12  joehope

	* trunk/xmds-devel/source/getopt_xmds.c,
	  trunk/xmds-devel/source/getopt_xmds.h,
	  trunk/xmds-devel/source/getopt_xmds1.c,
	  trunk/xmds-devel/source/main.cc,
	  trunk/xmds-devel/source/xmdssequence.cc,
	  trunk/xmds-devel/source/xsil2graphics.cc: Changing names of
	  extern variables in getopt functions. Removes further conflicts.

2004-06-24 07:19  joehope

	* trunk/xmds-devel/source/xmdscomplex.h: Forcing the operator
	  overloads to be C++. This was not automatic for all compilers.

2004-06-24 06:42  joehope

	* trunk/xmds-devel/ChangeLog, trunk/xmds-devel/MANIFEST,
	  trunk/xmds-devel/admin/xmds.spec,
	  trunk/xmds-devel/source/Makefile.am,
	  trunk/xmds-devel/source/getopt_xmds.c,
	  trunk/xmds-devel/source/getopt_xmds.h,
	  trunk/xmds-devel/source/getopt_xmds1.c,
	  trunk/xmds-devel/source/getopt_xmds_init.c,
	  trunk/xmds-devel/source/main.cc,
	  trunk/xmds-devel/source/xmdssequence.cc,
	  trunk/xmds-devel/source/xmdssimulation.cc,
	  trunk/xmds-devel/source/xsil2graphics.cc: Adjusted getopt to
	  getopt_xmds to remove conflicts with
	  predefined functions in the standard libraries of some systems

2004-06-23 08:21  paultcochrane

	* trunk/xmds-devel/admin/xmdsReleaseProcedure.pod: Removed
	  newsgroup posting instruction, because this is not a good thing
	  to do, and I got a bit stung from doing it this time.

2004-06-22 10:44  paultcochrane

	* trunk/xmds-devel/Makefile.am: Added new examples to be added at
	  make dist time.

2004-06-22 10:18  paultcochrane

	* trunk/xmds-devel/examples/duffing.xmds: Intitial import to
	  repository. This is an example simulation of Duffing's equations.

2004-06-22 10:18  paultcochrane

	* trunk/xmds-devel/examples/krebs.xmds: Initial import to
	  repository. This is an example simulation of a simplified Krebs
	  cycle of biochemical reations.

2004-06-22 10:17  paultcochrane

	* trunk/xmds-devel/examples/chemkin.xmds: Initial import to
	  repository. This is an example simulation of a chemical kinetic
	  reation in chemistry.

2004-06-22 10:16  paultcochrane

	* trunk/xmds-devel/examples/catcycle.xmds: Initial import to
	  repository. This is an example simulation of a catalytical cycle
	  reation in chemistry.

2004-06-22 10:16  paultcochrane

	* trunk/xmds-devel/examples/branch.xmds: Initial import to
	  repository. This is an example simulation of a branching reaction
	  in chemistry.

2004-06-21 09:28  paultcochrane

	* trunk/xmds-devel/admin/xmds.spec: Still trying to get the .spec
	  file to work. Tried changing the prefix sent to configure. I
	  think I need to rework the configuration step of xmds to iron out
	  these wrinkles.

2004-06-20 23:48  paultcochrane

	* trunk/xmds-devel/admin/xmdsNewsPost.pl: Removed sci.math.research
	  as this is a moderated group, and posting xmds announcements
	  isn't appropriate.

2004-06-18 06:51  paultcochrane

	* trunk/xmds-devel/admin/xmds.spec: Initial import to repository.
	  This is the rpm .spec file that Greg Collecutt used to use to
	  build xmds. I'm now trying to hack it to build the current
	  version(s).

2004-06-18 06:28  paultcochrane

	* trunk/xmds-devel/admin/xmdsReleaseProcedure.pod: Added comment
	  that the source files should be tagged appropriately. That
	  xmds.org needs updating. That an email to xmds-announce is a good
	  idea. And that sending a post to the relevant newsgroups, by
	  using the xmdsNewsPost.pl script would be a (possibly) good idea.

2004-06-18 06:25  paultcochrane

	* trunk/xmds-devel/admin/xmdsNewsPost.pl: Fixed a bug whereby the
	  subject and newsgroup kept getting prepended to the message text,
	  so eventually everyone in the last newsgroup to be posted to,
	  could tell where else I'd posted the message. Not happy that this
	  happened. Really not happy.

2004-06-18 06:09  paultcochrane

	* trunk/xmds-devel/admin/xmdsNewsPost.txt: Initial import to
	  repository. This file is the news post sent as a result of
	  running the xmdsNewsPost.pl script. This file needs to be updated
	  whenever a new xmds version is released, and posted
	  appropriately.

2004-06-18 06:08  paultcochrane

	* trunk/xmds-devel/admin/xmdsNewsPost.pl: Initial import to
	  repository. This is a perl script to automatically post the xmds
	  release announcement to a list of possibly interested newsgroups.

2004-06-18 01:58  paultcochrane

	* trunk/xmds-devel/admin/xmdsReleaseProcedure.pod: Initial import
	  to repository. This is the procedure one should perform to
	  properly release xmds onto the sourceforge site (and the world in
	  general).

2004-06-18 01:31  paultcochrane

	* trunk/xmds-devel/README.Windows: Converted from dos format to
	  unix format. Updated to xmds-1.3-4, and to new syntax for
	  xsil2graphics.

2004-06-18 01:26  paultcochrane

	* trunk/xmds-devel/README: Updated to current version of xmds
	  (1.3-4). Added a comment on how to access the man pages that are
	  now installed as part of xmds. Updated the xsil2graphics syntax
	  in the example given. Expanded the description of what xmds is at
	  the top of the file.

2004-06-17 07:18  paultcochrane

	* trunk/xmds-devel/ChangeLog: Updated changelog to current version
	  of xmds, highlighting the current set of major changes to the
	  code base.

2004-06-17 06:00  paultcochrane

	* trunk/xmds-devel/MANIFEST: Updated to current version of xmds
	  (1.3-4).

2004-06-17 05:45  paultcochrane

	* trunk/xmds-devel/source/xsil2graphics.cc: Added a mention of the
	  xmds web site in the usage output. Also tidied some of the text
	  in the display_usage function.

2004-06-16 03:49  paultcochrane

	* trunk/xmds-devel/source/xsil2graphics.cc: Changed display usage
	  to use less printf calls. Also makes the code look better

2004-06-16 02:04  paultcochrane

	* trunk/xmds-devel/source/main.cc: Changed an exit statement to a
	  return 0 to be more consistent with the other returning
	  conventions. Don't know if the current convention is that great
	  as it reports that everything went ok, as opposed to if something
	  went wrong. Again, this is something to chuck into the todo list.

2004-06-16 02:02  paultcochrane

	* trunk/xmds-devel/source/xsil2graphics.cc: converted xsil2graphics
	  argument parsing to the gnu getopt form. It therefore changes the
	  old style arguments of -matlab and -scilab to --matlab and
	  --scilab respectively. Also, it requires -o or --outfile if one
	  wants to specify and alternative output filename, so one can't do
	  xsil2graphics blah.xsil moo.m anymore, it must be xsil2graphics
	  blah.xsil --output moo.m. Also added some more helpful output
	  information.

2004-06-15 12:22  paultcochrane

	* trunk/xmds-devel/source/main.cc: Converted the command line
	  argument parsing code to use the getopt library. Now we have long
	  and short options and a mix if we so desire. Also changed some of
	  the formatting of the template code, and changed the
	  display_usage() output so that it is a bit more accurate,
	  informative and a little better looking. One big thing to note
	  here is the change of the compilation flag, this is now either -n
	  or --nocompile, note that previously this was -c, although I
	  don't think that many people actually used it.

2004-06-15 12:19  paultcochrane

	* trunk/xmds-devel/configure.in: Added -lxmds and -L. to the LIBS
	  variable, so that xmds gets built with libxmds and so it can see
	  the getopt libraries within libxmds.

2004-06-15 09:18  paultcochrane

	* trunk/xmds-devel/source/xmdsmomentgroup.cc: Tidied up a problem I
	  found with the xsil output when using binary. I'd just changed
	  the output filename of binary files for more consistent naming
	  wrt moment group output, and hadn't set the correct filename in
	  the .xsil output.

2004-06-15 09:08  paultcochrane

	* trunk/xmds-devel/source/xmdsmomentgroup.cc: Made the output
	  moment group number for binary output data files agree with what
	  the moment group number actually is.

2004-06-15 09:06  paultcochrane

	* trunk/xmds-devel/source/Makefile.am: Added a target for
	  loadxsil.m to be automatically installed at make install time for
	  xmds. It goes in the bindir at this stage, so will get installed
	  in the user's bin directory (if --with-users is set) or in the
	  /usr/local/bin directory if root is doing the installing.

2004-06-15 09:05  paultcochrane

	* trunk/xmds-devel/Makefile.am: Moved position of loadxsil.m entry.
	  The only reason I did this was so that I could comment it out
	  when testing some code.

2004-06-15 06:46  paultcochrane

	* trunk/xmds-devel/source/xmdssimulation.cc: Fixed bug with
	  incorrect parsing of noises tag. I'd used a suite of if
	  statements instead of an if-else if-else loop construction. Added
	  some debugging code as well, for when xmds -d is used.

2004-06-15 01:30  paultcochrane

	* trunk/xmds-devel/examples/diffusion.xmds: Made the lattice size
	  of the transverse dimension a multiple of two so that the
	  numerics are faster

2004-06-15 01:29  paultcochrane

	* trunk/xmds-devel/examples/atomlaser.xmds,
	  trunk/xmds-devel/examples/fibre.xmds,
	  trunk/xmds-devel/examples/ndparamp.xmds,
	  trunk/xmds-devel/examples/nlse.xmds: Removed text about
	  deprecated feature of binary_output and use_double tags. This is
	  actually now an obsolete syntax

2004-06-15 01:16  paultcochrane

	* trunk/xmds-devel/source/loadxsil.m: Tidied up the text that is
	  printed to screen. Some of output enclosed in an if loop
	  controlled by the new debug variable. More informative output as
	  to whether data is single or double precision.

2004-06-14 10:22  paultcochrane

	* trunk/xmds-devel/configure.in: Added mandir assignments so that
	  the man pages are installed in the correct locations depending
	  upon whether the defaults are given, a prefix, or xmds is being
	  user installed

2004-06-14 10:21  paultcochrane

	* trunk/xmds-devel/Makefile.am: Added
	  fisher_reaction_diffusion.xmds to list of examples to distribute.
	  Added a manfiles variable with the man pages to be installed.
	  Added the manfiles variable to the EXTRA_DIST variable so that
	  the files are added to the distro and installed with make install

2004-06-14 10:07  paultcochrane

	* trunk/xmds-devel/examples/fisher_reaction_diffusion.xmds: Initial
	  import to repository. This is an example simulation of the Fisher
	  reaction diffusion equation for use in theoretical population
	  genetics.

2004-06-14 06:41  paultcochrane

	* trunk/xmds-devel/source/xmdssequence.cc: Added code to print an
	  audible bell character at the end of a simulation if the <bing>
	  tag is set to yes. This is a tag to optionally add a noise
	  letting the user know when the simulation is complete.

2004-06-14 06:40  paultcochrane

	* trunk/xmds-devel/source/xmdsclasses.h: Added boolean variable
	  holding value of whether or not the <bing> tag is set to yes or
	  no. This is a tag to optionally add a noise letting the user know
	  when the simulation is complete.

2004-06-14 06:39  paultcochrane

	* trunk/xmds-devel/source/xmdssimulation.cc: Added parsing code for
	  the <bing> tag. This is a tag to optionally add a noise letting
	  the user know when the simulation is complete.

2004-06-14 06:37  paultcochrane

	* trunk/xmds-devel/MANIFEST: Updated to current list of files in
	  xmds-1.3-3 release

2004-06-14 06:37  paultcochrane

	* trunk/xmds-devel/configure.in: Updated release number to current
	  (pre) release number of 1.3-4

2004-06-14 06:36  paultcochrane

	* trunk/xmds-devel/Makefile.am: Added hires, lane_emden,
	  paraxial_wave, ring_modulator and van_der_pol examples to list of
	  examples to add to distribution. Removed dependence of latexdocs
	  and apifiles for EXTRA_DIST variable since they are in separate
	  parts of the overall xmds project now

2004-06-14 06:32  paultcochrane

	* trunk/xmds-devel/examples/hires.xmds: Initial import to
	  repository. This is the high irradiance response in
	  photomorphogenesis example simulation.

2004-06-14 05:57  paultcochrane

	* trunk/xmds-devel/examples/ring_modulator.xmds: Initial import to
	  repository. This is an example simulation of the ring modulator
	  circuit of electronics.

2004-06-12 09:42  paultcochrane

	* trunk/xmds-devel/source/xmdsoutput.cc: Added a comment so that
	  users know when output is being generated. This can be handy to
	  know when large files are being output, so that one can wait and
	  not think that the process has hung.

2004-06-12 09:41  paultcochrane

	* trunk/xmds-devel/source/main.cc: Fixed error whereby the CC
	  variable was used as the C compiler that xmds uses, whereas
	  should have been XMDS_CC. The MPICC variable being printf-ed
	  separately caused a warning message to come up in compilation of
	  xmds. I moved this into one of the other statements so that when
	  MPICC was a null variable, no warning is printed.

2004-06-05 05:40  paultcochrane

	* trunk/xmds-devel/examples/paraxial_wave.xmds: Fixed up some of
	  the numbers and the equations defining the slits etc.

2004-06-04 03:35  paultcochrane

	* trunk/xmds-devel/examples/paraxial_wave.xmds: Fixed minor bug. I
	  had a superfluous y variable floating around.

2004-06-04 03:33  paultcochrane

	* trunk/xmds-devel/examples/paraxial_wave.xmds: Initial import to
	  repository. This is an example simulation of the paraxial wave
	  equation for double slit interference.

2004-05-31 06:01  paultcochrane

	* trunk/xmds-devel/ChangeLog: Updated to current version of xmds;
	  namely 1.3-3. Described new features in this version.

2004-05-31 04:08  paultcochrane

	* trunk/xmds-devel/source/loadxsil.m: Fixed problem with loadxsil
	  associated with change made a few versions of xmds ago to
	  deprecate the use of <binary_output> and <use_double> which are
	  now implemented as attributes of the <output> tag.

2004-05-31 03:26  paultcochrane

	* trunk/xmds-devel/examples/van_der_pol.xmds: Initial import to
	  repository. This is an example simulation of the Van der Pol
	  oscillator.

2004-05-31 03:15  paultcochrane

	* trunk/xmds-devel/examples/lane_emden.xmds: Initial import to
	  repository. This is an example simulation of the Lane-Emden
	  equation in astrophysics.

2004-05-19 10:07  paultcochrane

	* trunk/xmds-devel/source/xmdssimulation.cc: Now barfing when xmds
	  finds the binary_output and/or use_double tags and prints a
	  message telling the user how to fix the problem (basically to use
	  the new/right syntax). Thanks to Joe Hope for the idea.

2004-05-18 10:25  paultcochrane

	* trunk/xmds-devel/source/xmdsutils.cc: Implemented throwing an
	  exception when the poissonian attribute is given but no mean
	  attribute given. Also noticed that the implementation of
	  getAttributeStrings is suboptimal in that it borrows far too much
	  from getAssignmentStrings and doesn't actually check everything
	  properly. This needs to be tidied. The code works atm, but it is
	  ugly and needs to be improved. This issue has been added to the
	  todo list for output into doxygen

2004-05-18 10:22  paultcochrane

	* trunk/xmds-devel/source/xmdssimulation.cc: Implemented a
	  Poissonian noise distribution based on that in chapter 7 of
	  Numerical Recipes. The output looks good at this stage, but more
	  testing is necessary. Added the correct prototype declarations
	  for each of the noise options as well, and made sure that when
	  the poissonian noise is called, that the mean attribute is also
	  specified.

2004-05-18 10:19  paultcochrane

	* trunk/xmds-devel/source/xmdsclasses.h: Added a declaration for
	  the mean of a poissonian noise distribution

2004-05-18 10:18  paultcochrane

	* trunk/xmds-devel/examples/kubo.xmds: Switched off mpi, and
	  implemented the kind attribute of the noises tag.

2004-05-18 10:02  paultcochrane

	* trunk/xmds-devel/configure.in: Updated the version and release
	  numbers to their current values (1.3-3).

2004-05-18 07:46  paultcochrane

	* trunk/xmds-devel/source/xmdssimulation.cc: Implemented parsing
	  code for having a kind attribute to the noises tag. This at
	  present accepts gaussian, poissonian (not yet implemented),
	  gaussFast (a slightly faster version of the gaussian generation
	  routines) and uniform. Gaussian, gaussFast and uniform have been
	  implemented and tested and seem to go alright. Tests show between
	  7 and 20 percent increase in speed if gaussFast is used.

2004-05-18 07:42  paultcochrane

	* trunk/xmds-devel/source/xmdsclasses.h: Added declaration for the
	  XMLString holding the variable that defines the kind of noise to
	  generate

2004-05-12 06:18  paultcochrane

	* trunk/xmds-devel/MANIFEST: Updated manifest to current release
	  version (1.3-2).

2004-05-12 06:16  paultcochrane

	* trunk/xmds-devel/NEWS: Updated to current version of xmds, ready
	  for release

2004-05-12 06:11  paultcochrane

	* trunk/xmds-devel/ChangeLog: Trivial change

2004-05-12 06:08  paultcochrane

	* trunk/xmds-devel/ChangeLog: Added changes to xmds since last
	  release

2004-05-12 05:31  paultcochrane

	* trunk/xmds-devel/Makefile.am: Made an explicit list of the
	  example xmds files to include in the distribution. Previously all
	  of my test xmds scripts were added, and that just didn't look
	  good

2004-04-29 03:23  paultcochrane

	* trunk/xmds-devel/source/kissdom.cc,
	  trunk/xmds-devel/source/kissdom.h,
	  trunk/xmds-devel/source/xmdsarg.cc,
	  trunk/xmds-devel/source/xmdsargelement.cc,
	  trunk/xmds-devel/source/xmdsbreakpoint.cc,
	  trunk/xmds-devel/source/xmdsclasses.h,
	  trunk/xmds-devel/source/xmdselement.cc,
	  trunk/xmds-devel/source/xmdsfield.cc,
	  trunk/xmds-devel/source/xmdsfilter.cc,
	  trunk/xmds-devel/source/xmdsglobals.cc,
	  trunk/xmds-devel/source/xmdsintegrate.cc,
	  trunk/xmds-devel/source/xmdsintegrateex.cc,
	  trunk/xmds-devel/source/xmdsintegrateip.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4ex.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4ip.cc,
	  trunk/xmds-devel/source/xmdsintegratesi.cc,
	  trunk/xmds-devel/source/xmdsintegratesiex.cc,
	  trunk/xmds-devel/source/xmdsintegratesiip.cc,
	  trunk/xmds-devel/source/xmdsmomentgroup.cc,
	  trunk/xmds-devel/source/xmdsoutput.cc,
	  trunk/xmds-devel/source/xmdssegment.cc,
	  trunk/xmds-devel/source/xmdssequence.cc,
	  trunk/xmds-devel/source/xmdssimulation.cc,
	  trunk/xmds-devel/source/xmdsutils.cc,
	  trunk/xmds-devel/source/xmdsutils.h,
	  trunk/xmds-devel/source/xmdsvector.cc,
	  trunk/xmds-devel/source/xmdsvectorelement.cc,
	  trunk/xmds-devel/source/xmlbasics.cc,
	  trunk/xmds-devel/source/xmlbasics.h,
	  trunk/xmds-devel/source/xmlparser.cc,
	  trunk/xmds-devel/source/xmlparser.h,
	  trunk/xmds-devel/source/xsil2graphics.cc,
	  trunk/xmds-devel/source/xsilfield.cc,
	  trunk/xmds-devel/source/xsilfield.h: More completely documented
	  the code using doxygen. Still lots of stuff that needs doing,
	  some stuff isn't documented at all, just marked as Undocumented
	  and a todo command left also signifying that this needs work.
	  Most of the functions and variables, however, have at least a
	  brief description of what they are (or what they look like the
	  could be, as it is quite often *not* obvious as to what a
	  function or variable does or means.

2004-04-29 03:19  paultcochrane

	* trunk/xmds-devel/source/main.cc: Documented the code using
	  doxygen. Fixed up some of the spacing in the template output
	  code.

2004-04-28 05:31  paultcochrane

	* trunk/xmds-devel/source/main.cc: Moved the comment regarding
	  global system parameters and system functionality (for generation
	  of a template code) to just below the name and description
	  elements

2004-04-28 05:12  paultcochrane

	* trunk/xmds-devel/examples/lotka_volterra.xmds: Initial import to
	  repository. This is an example simulation of the Lotka-Volterra
	  system used as a model of undamped oscillations in autocatalytic
	  chemical reactions. From initial reading of (mathematical
	  chemistry) paper to completed xmds script was about 10 minutes!
	  Wow. Ok, now I'm impressed.

2004-04-28 01:04  paultcochrane

	* trunk/xmds-devel/examples/atomlaser.xmds,
	  trunk/xmds-devel/examples/diffusion.xmds,
	  trunk/xmds-devel/examples/fibre.xmds,
	  trunk/xmds-devel/examples/fullpos3D.xmds,
	  trunk/xmds-devel/examples/gaugeatomlaser.xmds,
	  trunk/xmds-devel/examples/highdim.xmds,
	  trunk/xmds-devel/examples/kubo.xmds,
	  trunk/xmds-devel/examples/lorenz.xmds,
	  trunk/xmds-devel/examples/ndparamp.xmds,
	  trunk/xmds-devel/examples/nlse.xmds,
	  trunk/xmds-devel/examples/pendulum.xmds,
	  trunk/xmds-devel/examples/sine.xmds,
	  trunk/xmds-devel/examples/soliton.xmds,
	  trunk/xmds-devel/examples/tla.xmds,
	  trunk/xmds-devel/examples/vibstring.xmds: Fixed up author and
	  description tags so that is a bit more uniform over all of the
	  examples

2004-04-28 00:58  paultcochrane

	* trunk/xmds-devel/examples/atomlaser.xmds,
	  trunk/xmds-devel/examples/diffusion.xmds,
	  trunk/xmds-devel/examples/fibre.xmds,
	  trunk/xmds-devel/examples/fullpos3D.xmds,
	  trunk/xmds-devel/examples/gaugeatomlaser.xmds,
	  trunk/xmds-devel/examples/highdim.xmds,
	  trunk/xmds-devel/examples/kubo.xmds,
	  trunk/xmds-devel/examples/lorenz.xmds,
	  trunk/xmds-devel/examples/ndparamp.xmds,
	  trunk/xmds-devel/examples/nlse.xmds,
	  trunk/xmds-devel/examples/pendulum.xmds,
	  trunk/xmds-devel/examples/sine.xmds,
	  trunk/xmds-devel/examples/soliton.xmds,
	  trunk/xmds-devel/examples/tla.xmds,
	  trunk/xmds-devel/examples/vibstring.xmds: Added CVS Id tag.

2004-04-28 00:56  paultcochrane

	* trunk/xmds-devel/examples/atomlaser.xmds,
	  trunk/xmds-devel/examples/diffusion.xmds,
	  trunk/xmds-devel/examples/fibre.xmds,
	  trunk/xmds-devel/examples/fullpos3D.xmds,
	  trunk/xmds-devel/examples/gaugeatomlaser.xmds,
	  trunk/xmds-devel/examples/highdim.xmds,
	  trunk/xmds-devel/examples/kubo.xmds,
	  trunk/xmds-devel/examples/lorenz.xmds,
	  trunk/xmds-devel/examples/ndparamp.xmds,
	  trunk/xmds-devel/examples/nlse.xmds,
	  trunk/xmds-devel/examples/pendulum.xmds,
	  trunk/xmds-devel/examples/sine.xmds,
	  trunk/xmds-devel/examples/soliton.xmds,
	  trunk/xmds-devel/examples/tla.xmds,
	  trunk/xmds-devel/examples/vibstring.xmds: Added copyright
	  statement to example files

2004-04-28 00:43  paultcochrane

	* trunk/xmds-devel/configure.in: Added copyright statement.

2004-04-28 00:29  paultcochrane

	* trunk/xmds-devel/source/dom3.h,
	  trunk/xmds-devel/source/kissdom.cc,
	  trunk/xmds-devel/source/kissdom.h,
	  trunk/xmds-devel/source/main.cc,
	  trunk/xmds-devel/source/xmdsarg.cc,
	  trunk/xmds-devel/source/xmdsargelement.cc,
	  trunk/xmds-devel/source/xmdsargv.cc,
	  trunk/xmds-devel/source/xmdsbreakpoint.cc,
	  trunk/xmds-devel/source/xmdsclasses.h,
	  trunk/xmds-devel/source/xmdscomplex.h,
	  trunk/xmds-devel/source/xmdselement.cc,
	  trunk/xmds-devel/source/xmdsfield.cc,
	  trunk/xmds-devel/source/xmdsfilter.cc,
	  trunk/xmds-devel/source/xmdsglobals.cc,
	  trunk/xmds-devel/source/xmdsintegrate.cc,
	  trunk/xmds-devel/source/xmdsintegrateex.cc,
	  trunk/xmds-devel/source/xmdsintegrateip.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4ex.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4ip.cc,
	  trunk/xmds-devel/source/xmdsintegratesi.cc,
	  trunk/xmds-devel/source/xmdsintegratesiex.cc,
	  trunk/xmds-devel/source/xmdsintegratesiip.cc,
	  trunk/xmds-devel/source/xmdsmomentgroup.cc,
	  trunk/xmds-devel/source/xmdsoutput.cc,
	  trunk/xmds-devel/source/xmdssegment.cc,
	  trunk/xmds-devel/source/xmdssequence.cc,
	  trunk/xmds-devel/source/xmdssimulation.cc,
	  trunk/xmds-devel/source/xmdsutils.cc,
	  trunk/xmds-devel/source/xmdsutils.h,
	  trunk/xmds-devel/source/xmdsvector.cc,
	  trunk/xmds-devel/source/xmdsvectorelement.cc,
	  trunk/xmds-devel/source/xmlbasics.cc,
	  trunk/xmds-devel/source/xmlbasics.h,
	  trunk/xmds-devel/source/xmlparser.cc,
	  trunk/xmds-devel/source/xmlparser.h,
	  trunk/xmds-devel/source/xsil2graphics.cc,
	  trunk/xmds-devel/source/xsilfield.cc,
	  trunk/xmds-devel/source/xsilfield.h: Updated copyright statement
	  to current year

2004-04-28 00:01  paultcochrane

	* trunk/xmds-devel/benchmark/runbenchmarks: Fixed format of
	  procTime output. Moved masterData assignment into file test if
	  loop. Removed use warnings pragma as not supported in older
	  versions of perl, and the warnings aren't really needed atm. Also
	  added a variable for the progInfoFname.

2004-04-27 23:56  paultcochrane

	* trunk/xmds-devel/source/kissdom.cc,
	  trunk/xmds-devel/source/main.cc,
	  trunk/xmds-devel/source/xmdsarg.cc,
	  trunk/xmds-devel/source/xmdsargelement.cc,
	  trunk/xmds-devel/source/xmdsargv.cc,
	  trunk/xmds-devel/source/xmdsbreakpoint.cc,
	  trunk/xmds-devel/source/xmdselement.cc,
	  trunk/xmds-devel/source/xmdsfield.cc,
	  trunk/xmds-devel/source/xmdsfilter.cc,
	  trunk/xmds-devel/source/xmdsglobals.cc,
	  trunk/xmds-devel/source/xmdsintegrate.cc,
	  trunk/xmds-devel/source/xmdsintegrateex.cc,
	  trunk/xmds-devel/source/xmdsintegrateip.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4ex.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4ip.cc,
	  trunk/xmds-devel/source/xmdsintegratesi.cc,
	  trunk/xmds-devel/source/xmdsintegratesiex.cc,
	  trunk/xmds-devel/source/xmdsintegratesiip.cc,
	  trunk/xmds-devel/source/xmdsmomentgroup.cc,
	  trunk/xmds-devel/source/xmdsoutput.cc,
	  trunk/xmds-devel/source/xmdssegment.cc,
	  trunk/xmds-devel/source/xmdssequence.cc,
	  trunk/xmds-devel/source/xmdssimulation.cc,
	  trunk/xmds-devel/source/xmdsutils.cc,
	  trunk/xmds-devel/source/xmdsvector.cc,
	  trunk/xmds-devel/source/xmdsvectorelement.cc,
	  trunk/xmds-devel/source/xmlbasics.cc,
	  trunk/xmds-devel/source/xmlparser.cc,
	  trunk/xmds-devel/source/xsil2graphics.cc,
	  trunk/xmds-devel/source/xsilfield.cc: Added an @file command so
	  that doxygen finds and documents the stuff in the file

2004-04-27 23:55  paultcochrane

	* trunk/xmds-devel/source/Doxyfile: Changed some of the
	  functionality of the Doxyfile. Added more explicit warnings and
	  more in-depth documentation of the code (including private bits,
	  which I don't know if that's a good idea or not).

2004-04-20 03:51  paultcochrane

	* trunk/xmds-devel/source/main.cc: Added some nice intro text so
	  that one knows that one has just executed xmds, and that a
	  template is being output and what the filename is.

2004-04-20 03:44  paultcochrane

	* trunk/xmds-devel/source/main.cc: Implemented the use of a
	  template output option of xmds. One merely has to use the -t flag
	  at the command line for a template xmds script to be output to
	  stdout. If a filename is given, then the script is sent to that
	  file, and xmds returns. This is to help those who want to write a
	  script basically from scratch, but don't want to have to remember
	  where everything goes and the exact set of tags that are
	  necessary. The template is currently the one in the
	  tutTemplateStart.tex file of the latex documentation, and has
	  more tags than necessary to make a simulation.

2004-04-19 09:22  paultcochrane

	* trunk/xmds-devel/configure.in: Updated version and release
	  numbers

2004-04-19 09:14  paultcochrane

	* trunk/xmds-devel/source/xmdsmomentgroup.cc,
	  trunk/xmds-devel/source/xmdsoutput.cc,
	  trunk/xmds-devel/source/xmdssequence.cc: I finally got sick of
	  seeing 042's everywhere, and replaced them with double quotes. It
	  does make things easier to read.

2004-04-19 08:59  paultcochrane

	* trunk/xmds-devel/source/xmdsoutput.cc: Stuff it, I might as well
	  chuck in an info footer as well as a header, it doesn't increase
	  the file size that much. So, I did.

2004-04-19 08:51  paultcochrane

	* trunk/xmds-devel/source/xmdsoutput.cc: Moved nice version
	  information stuff that is to be put into the .xsil file here as
	  opposed to in xmdsmomentgroup.cc. This way it's only mentioned
	  the once, as opposed to each time a moment group is written out
	  to file. Also moved where the <simulation> tag is written, and
	  added some comments (my God! comments!) to the code.

2004-04-19 08:48  paultcochrane

	* trunk/xmds-devel/source/xmdsmomentgroup.cc: Moved nice version
	  information stuff into a better location (namely xmdsoutput.cc)

2004-04-19 08:40  paultcochrane

	* trunk/xmds-devel/source/xmdssimulation.cc: Added the version and
	  release numbers to the list of simulation parameters. Can now
	  pass these bits of info around so that can generate xmds version
	  information at parsing and compiling, and in the output .xsil
	  file.

2004-04-19 08:37  paultcochrane

	* trunk/xmds-devel/source/xmdsmomentgroup.cc: Added an information
	  section using <info> tags in the moment group output. This is so
	  that it is documented which version of xmds generated the output
	  .xsil file, and so that xmds and its web page get another plug.

2004-04-19 08:32  paultcochrane

	* trunk/xmds-devel/source/xmdsclasses.h: Added the version and
	  release numbers to the list of simulation parameters so that can
	  use these values in the output at the start of parsing and
	  compiling a simulation, and at the end in the output of the
	  simulations.

2004-04-19 08:31  paultcochrane

	* trunk/xmds-devel/source/main.cc: Printing out some info about
	  xmds at the start of parsing and compiling a simulation. Also
	  tidied some of the output when parsing and compiling a
	  simulation.

2004-04-19 08:28  paultcochrane

	* trunk/xmds-devel/depcomp, trunk/xmds-devel/ltmain.sh: Updated.

2004-04-06 11:10  paultcochrane

	* trunk/xmds-devel/benchmark/gaugeatomlaser_128.xmds: Initial
	  import to repository. This is now the correct file to use instead
	  of gaugeatomlaser.xmds, as the benchmarking code is now much more
	  general.

2004-04-06 11:09  paultcochrane

	* trunk/xmds-devel/benchmark/runbenchmarks: I think I've got it all
	  working now. The masterData variable is being updated
	  properly, and output to file properly, and then reread properly,
	  so all good
	  there. Tested on G3, AMD, and P4. Have now changed the test bench
	  subroutine
	  to bench_test and the bench2 subroutine is now bench, so have to
	  do a proper
	  run now...

2004-04-06 10:45  paultcochrane

	* trunk/xmds-devel/benchmark/runbenchmarks: The last message was a
	  stuff up, however, this one is ok. Now printing all cpus listed
	  in masterData hash

2004-04-06 10:42  paultcochrane

	* trunk/xmds-devel/benchmark/runbenchmarks: Added cpu information
	  to master data hash table

2004-04-06 10:40  paultcochrane

	* trunk/xmds-devel/benchmark/runbenchmarks: Added cpu information
	  to master data hash table

2004-04-06 10:29  paultcochrane

	* trunk/xmds-devel/benchmark/runbenchmarks: Implemented output of
	  html of benchmark data. Implemented dumping of data
	  using Data::Dumper, and reading the data back in (hopefully).
	  Implemented
	  html output of the verbose cpu information, which is linked to
	  the main
	  benchmarks html file.

2004-04-06 08:26  paultcochrane

	* trunk/xmds-devel/benchmark/runbenchmarks: Added some comments and
	  removed some superfluous code.

2004-04-06 08:20  paultcochrane

	* trunk/xmds-devel/benchmark/runbenchmarks: Added the code of bench
	  as a subroutine to runbenchmarks. Also added a testing
	  subroutine so that I don't have to wait for all of the sims to
	  finish before
	  I can make sure that the code works. Implemented the use of the
	  bench
	  subroutine and collection of the average time into the benchData
	  hash.

2004-04-06 07:51  paultcochrane

	* trunk/xmds-devel/benchmark/runbenchmarks: Added a check for
	  linux, if so, then cpuinfo is obtained (which is slightly
	  different for LinuxPPC and for LinuxX86) and then a shorter
	  version of this
	  information is kept. If not linux, then the system info is
	  determined by
	  using the Config module of Perl and the info that configured Perl
	  on that
	  system.

2004-04-06 06:58  paultcochrane

	* trunk/xmds-devel/benchmark/bench: Implemented shorter version of
	  previous code using timeit instead of the Benchmark objects

2004-04-06 06:53  paultcochrane

	* trunk/xmds-devel/benchmark/runbenchmarks: Initial import to
	  repository. This is the wrapper script that runs the
	  bench script on all of the various xmds scripts.

2004-04-06 06:52  paultcochrane

	* trunk/xmds-devel/benchmark/nlse_100.xmds,
	  trunk/xmds-devel/benchmark/nlse_1000.xmds,
	  trunk/xmds-devel/benchmark/nlse_10000.xmds,
	  trunk/xmds-devel/benchmark/nlse_500.xmds,
	  trunk/xmds-devel/benchmark/nlse_5000.xmds: Initial import to
	  repository. This is the nonlinear Schroedinger equation
	  simulation for various lattice sizes.

2004-04-06 06:51  paultcochrane

	* trunk/xmds-devel/benchmark/ndparamp_100.xmds,
	  trunk/xmds-devel/benchmark/ndparamp_200.xmds,
	  trunk/xmds-devel/benchmark/ndparamp_50.xmds,
	  trunk/xmds-devel/benchmark/ndparamp_500.xmds: Initial import to
	  repository. This is the N-dimensional parametric oscillator
	  simulation for various lattice sizes.

2004-04-06 06:50  paultcochrane

	* trunk/xmds-devel/benchmark/gaugeatomlaser.xmds: Initial import to
	  repository. This is the gaugeatomlaser simulation which
	  is used to really test how hard the cpu can go (sims take about
	  three hours on
	  new 64 bit AMD machines).

2004-04-06 06:49  paultcochrane

	* trunk/xmds-devel/benchmark/fullpos3D_16.xmds,
	  trunk/xmds-devel/benchmark/fullpos3D_32.xmds,
	  trunk/xmds-devel/benchmark/fullpos3D_64.xmds: Initial import to
	  repository. This is the fullpos3D simulation for various
	  lattice sizes.

2004-04-06 06:45  paultcochrane

	* trunk/xmds-devel/benchmark, trunk/xmds-devel/benchmark/bench:
	  Initial import to repository. This is the basic script that
	  compiles, runs
	  a first go of a simulation and then runs the simulation a few
	  times (at
	  present three) giving an output of the average time for the
	  simulation.

2004-03-08 10:14  paultcochrane

	* trunk/xmds-devel/source/xmdssimulation.cc: Added a check for the
	  author and description tags. If they aren't found, then a warning
	  is issued to the effect that adding such a tag would be a good
	  idea. This is just to get users to document their code better. We
	  might have to back this out someday...

2004-03-08 10:12  paultcochrane

	* trunk/xmds-devel/source/xmdsclasses.h: Added authorName and
	  description to the list of simulation parameters. Not exactly
	  necessary, since they are likely never to be used in a simulation
	  as such, but they do help document the simulation source code
	  better. Whether or not actually storing them in xmds is a good
	  question...

2004-03-05 05:06  paultcochrane

	* trunk/xmds-devel/source/loadxsil.m: Added copyright statement.

2004-03-05 05:05  paultcochrane

	* trunk/xmds-devel/source/Doxyfile: Updated file to current version
	  of Doxygen (some stuff was obsolete etc).

2004-03-05 05:04  paultcochrane

	* trunk/xmds-devel/source/xsilfield.cc: Fixed bug whereby the
	  output from xsil2graphics didn't include the correct variable
	  name when calling fscanfMat in the generated scilab script file.

2004-01-30 04:31  paultcochrane

	* trunk/xmds-devel/examples/fibre.xmds,
	  trunk/xmds-devel/examples/fullpos3D.xmds: Fixed spelling error.

2004-01-30 04:21  paultcochrane

	* trunk/xmds-devel/source/xmdssimulation.cc: Fixed bug whereby
	  attributes were parsed incorrectly.

2004-01-30 03:48  paultcochrane

	* trunk/xmds-devel/source/xmdssimulation.cc: Now reports errors in
	  parsing <output> element correctly.

2004-01-30 02:10  paultcochrane

	* trunk/xmds-devel/testsuite/fibre.xmds,
	  trunk/xmds-devel/testsuite/fullpos3D.xmds,
	  trunk/xmds-devel/testsuite/gaugeatomlaser.xmds,
	  trunk/xmds-devel/testsuite/ndparamp.xmds,
	  trunk/xmds-devel/testsuite/nlse.xmds,
	  trunk/xmds-devel/testsuite/soliton.xmds: Fixed problems
	  concerning gcc 3.x needing floats inside such functions as log
	  and sqrt instead of ints. Just a problem of adding .0 ad the end
	  of what was
	  previously an integer.

2004-01-30 02:04  paultcochrane

	* trunk/xmds-devel/testsuite/atomlaser.xmds,
	  trunk/xmds-devel/testsuite/fibre.xmds,
	  trunk/xmds-devel/testsuite/fullpos3D.xmds,
	  trunk/xmds-devel/testsuite/gaugeatomlaser.xmds,
	  trunk/xmds-devel/testsuite/kubo.xmds,
	  trunk/xmds-devel/testsuite/ndparamp.xmds,
	  trunk/xmds-devel/testsuite/nlse.xmds,
	  trunk/xmds-devel/testsuite/sine.xmds,
	  trunk/xmds-devel/testsuite/soliton.xmds,
	  trunk/xmds-devel/testsuite/tla.xmds: Fixed up formatting of files
	  using HTML tidy.
	  Command used: tidy -im -xml <filename>.xmds
	  Then some hand-tidying of the files.

2004-01-30 01:38  paultcochrane

	* trunk/xmds-devel/AUTHORS, trunk/xmds-devel/INSTALL,
	  trunk/xmds-devel/Makefile.am, trunk/xmds-devel/NEWS,
	  trunk/xmds-devel/README, trunk/xmds-devel/README.Windows,
	  trunk/xmds-devel/acinclude.m4, trunk/xmds-devel/configure.in,
	  trunk/xmds-devel/testsuite/atomlaser.xmds,
	  trunk/xmds-devel/testsuite/fibre.xmds,
	  trunk/xmds-devel/testsuite/fullpos3D.xmds,
	  trunk/xmds-devel/testsuite/gaugeatomlaser.xmds,
	  trunk/xmds-devel/testsuite/kubo.xmds,
	  trunk/xmds-devel/testsuite/ndparamp.xmds,
	  trunk/xmds-devel/testsuite/nlse.xmds,
	  trunk/xmds-devel/testsuite/sine.xmds,
	  trunk/xmds-devel/testsuite/soliton.xmds,
	  trunk/xmds-devel/testsuite/tla.xmds: Added CVS Id keyword.

2004-01-30 01:25  paultcochrane

	* trunk/xmds-devel/source/loadxsil.m: Added CVS Id keyword.

2004-01-28 04:44  paultcochrane

	* trunk/xmds-devel/source/Doxyfile,
	  trunk/xmds-devel/source/Makefile.am,
	  trunk/xmds-devel/source/dom3.h,
	  trunk/xmds-devel/source/kissdom.cc,
	  trunk/xmds-devel/source/kissdom.h,
	  trunk/xmds-devel/source/main.cc,
	  trunk/xmds-devel/source/xmdsarg.cc,
	  trunk/xmds-devel/source/xmdsargelement.cc,
	  trunk/xmds-devel/source/xmdsargv.cc,
	  trunk/xmds-devel/source/xmdsbreakpoint.cc,
	  trunk/xmds-devel/source/xmdsclasses.h,
	  trunk/xmds-devel/source/xmdscomplex.h,
	  trunk/xmds-devel/source/xmdselement.cc,
	  trunk/xmds-devel/source/xmdsfield.cc,
	  trunk/xmds-devel/source/xmdsfilter.cc,
	  trunk/xmds-devel/source/xmdsglobals.cc,
	  trunk/xmds-devel/source/xmdsintegrate.cc,
	  trunk/xmds-devel/source/xmdsintegrateex.cc,
	  trunk/xmds-devel/source/xmdsintegrateip.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4ex.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4ip.cc,
	  trunk/xmds-devel/source/xmdsintegratesi.cc,
	  trunk/xmds-devel/source/xmdsintegratesiex.cc,
	  trunk/xmds-devel/source/xmdsintegratesiip.cc,
	  trunk/xmds-devel/source/xmdsmomentgroup.cc,
	  trunk/xmds-devel/source/xmdsoutput.cc,
	  trunk/xmds-devel/source/xmdssegment.cc,
	  trunk/xmds-devel/source/xmdssequence.cc,
	  trunk/xmds-devel/source/xmdsutils.cc,
	  trunk/xmds-devel/source/xmdsutils.h,
	  trunk/xmds-devel/source/xmdsvector.cc,
	  trunk/xmds-devel/source/xmdsvectorelement.cc,
	  trunk/xmds-devel/source/xmlbasics.cc,
	  trunk/xmds-devel/source/xmlbasics.h,
	  trunk/xmds-devel/source/xmlparser.cc,
	  trunk/xmds-devel/source/xmlparser.h,
	  trunk/xmds-devel/source/xsil2graphics.cc,
	  trunk/xmds-devel/source/xsilfield.cc,
	  trunk/xmds-devel/source/xsilfield.h: Added CVS Id keyword.

2004-01-28 04:37  paultcochrane

	* trunk/xmds-devel/source/xmdssimulation.cc: Still testing the CVS
	  Id keyword expansion.

2004-01-28 04:35  paultcochrane

	* trunk/xmds-devel/source/xmdssimulation.cc: Testing adding the CVS
	  Id keyword.

2004-01-27 07:02  paultcochrane

	* trunk/xmds-devel/examples/atomlaser.xmds: Updated to new <output>
	  element syntax: output format and output precision now being
	  given as attributes of <output> element rather than in simulation
	  options section. Also added syntax for the break point feature to
	  come.

2004-01-27 07:00  paultcochrane

	* trunk/xmds-devel/examples/diffusion.xmds,
	  trunk/xmds-devel/examples/fibre.xmds,
	  trunk/xmds-devel/examples/fullpos3D.xmds,
	  trunk/xmds-devel/examples/gaugeatomlaser.xmds,
	  trunk/xmds-devel/examples/highdim.xmds,
	  trunk/xmds-devel/examples/kubo.xmds,
	  trunk/xmds-devel/examples/lorenz.xmds,
	  trunk/xmds-devel/examples/ndparamp.xmds,
	  trunk/xmds-devel/examples/nlse.xmds,
	  trunk/xmds-devel/examples/pendulum.xmds,
	  trunk/xmds-devel/examples/sine.xmds,
	  trunk/xmds-devel/examples/soliton.xmds,
	  trunk/xmds-devel/examples/tla.xmds,
	  trunk/xmds-devel/examples/vibstring.xmds: Updated to new <output>
	  element syntax: output format and output precision now being
	  given as attributes of <output> element rather than in simulation
	  options section.

2004-01-27 06:29  paultcochrane

	* trunk/xmds-devel/source/xmdssimulation.cc: Added attributes to
	  <output> element to control whether output format is binary or
	  ascii (ascii still default), and whether the output precision is
	  double or single (double is still default). These are to replace
	  the <binary_output> and <use_double> tags. The new syntax is
	  <output format="ascii|binary" precision="double|single">, which
	  is a lot more logical.

2004-01-27 06:26  paultcochrane

	* trunk/xmds-devel/source/Doxyfile: Changed option so that man
	  pages are now generated.

2004-01-14 08:34  paultcochrane

	* trunk/xmds-devel/examples/fullpos3D.xmds: Fixed problem whereby
	  gcc/g++ see sqrt(2) as the sqrt of an integer which doesn't work
	  in C++, these have been changed to sqrt(2.0) so that the input is
	  float/double.

2004-01-13 10:16  paultcochrane

	* trunk/xmds-devel/source/xmdsutils.h: Trivial change made during
	  code testing.

2004-01-13 10:15  paultcochrane

	* trunk/xmds-devel/source/xmdsutils.cc: Fixed bug in
	  getAttributeBools where the string comparison was being performed
	  incorrectly.

2004-01-13 10:14  paultcochrane

	* trunk/xmds-devel/source/xmdsoutput.cc: Implemented parsing of
	  enabled attribute of breakpoint element correctly.

2004-01-13 10:13  paultcochrane

	* trunk/xmds-devel/source/xmdsclasses.h: Changed some formatting.

2004-01-13 10:11  paultcochrane

	* trunk/xmds-devel/source/xmdsbreakpoint.cc: Removed some legacy
	  code that was commented out anyway. Polished and tested the
	  breakpoint parsing code. Now do a test to see if a file exists at
	  the parsing stage when the file status is set to "old", and barf
	  with an error message if not found.

2004-01-13 02:03  paultcochrane

	* trunk/xmds-devel/source/xmdsutils.h: Corrected one of the
	  documentation strings.

2004-01-13 01:28  paultcochrane

	* trunk/xmds-devel/source/main.cc: Added a debug option to
	  parsePrefs(), and changed the output generated so that stuff that
	  should be in the debugging output is not in the verbose output.

2004-01-12 09:10  paultcochrane

	* trunk/xmds-devel/source/xmdsutils.h: Added the DEEP and NOT_DEEP
	  variables to the global anonymous enum.

2004-01-12 09:09  paultcochrane

	* trunk/xmds-devel/source/xmdsoutput.cc: Added stuff to find and
	  process the <breakpoint> tag. Started to implement the use of
	  DEEP and NOT_DEEP variables in getElementsByTagName() and friends
	  as opposed to just 1 and 0 respectively (it makes the code more
	  readable).

2004-01-12 09:07  paultcochrane

	* trunk/xmds-devel/source/xmdsbreakpoint.cc: Initial import to
	  repository. Basic stuff at this stage, actually does nothing
	  other than report what the settings are as found in the .xmds
	  script.

2004-01-12 09:06  paultcochrane

	* trunk/xmds-devel/source/xmdsclasses.h: Added xmdsBreakPoint
	  object declarations (just basic stuff at this stage). Added (to
	  xmdsOutput) a bpEnabledFlag variable to note if breakpoints are
	  enabled, and declaration of a function to create an
	  xmdsBreakPoint object.

2004-01-12 09:03  paultcochrane

	* trunk/xmds-devel/source/Makefile.am: Added xmdsbreakpoint.cc

2003-12-30 10:38  paultcochrane

	* trunk/xmds-devel/examples/fibre.xmds,
	  trunk/xmds-devel/examples/fullpos3D.xmds,
	  trunk/xmds-devel/examples/gaugeatomlaser.xmds,
	  trunk/xmds-devel/examples/highdim.xmds,
	  trunk/xmds-devel/examples/kubo.xmds,
	  trunk/xmds-devel/examples/lorenz.xmds,
	  trunk/xmds-devel/examples/ndparamp.xmds,
	  trunk/xmds-devel/examples/nlse.xmds,
	  trunk/xmds-devel/examples/pendulum.xmds,
	  trunk/xmds-devel/examples/sine.xmds,
	  trunk/xmds-devel/examples/soliton.xmds,
	  trunk/xmds-devel/examples/tla.xmds,
	  trunk/xmds-devel/examples/vibstring.xmds: Updated <name>,
	  <author> and <description> tags where appropriate.

2003-12-23 04:01  paultcochrane

	* trunk/xmds-devel/ChangeLog, trunk/xmds-devel/MANIFEST,
	  trunk/xmds-devel/NEWS, trunk/xmds-devel/README: Updated to
	  reflect changes in current release (1.3-1)

2003-12-23 03:47  paultcochrane

	* trunk/xmds-devel/examples/atomlaser.xmds,
	  trunk/xmds-devel/examples/diffusion.xmds,
	  trunk/xmds-devel/examples/fibre.xmds,
	  trunk/xmds-devel/examples/fullpos3D.xmds,
	  trunk/xmds-devel/examples/gaugeatomlaser.xmds,
	  trunk/xmds-devel/examples/highdim.xmds,
	  trunk/xmds-devel/examples/kubo.xmds,
	  trunk/xmds-devel/examples/lorenz.xmds,
	  trunk/xmds-devel/examples/ndparamp.xmds,
	  trunk/xmds-devel/examples/nlse.xmds,
	  trunk/xmds-devel/examples/pendulum.xmds,
	  trunk/xmds-devel/examples/sine.xmds,
	  trunk/xmds-devel/examples/soliton.xmds,
	  trunk/xmds-devel/examples/tla.xmds,
	  trunk/xmds-devel/examples/vibstring.xmds: Tidied formatting,
	  added some comments.

2003-12-23 01:15  paultcochrane

	* trunk/xmds-devel/examples/atomlaser.xmds: Commented out using of
	  binary input file. Now is back to being initialised by code.
	  Better this way since it's an example file.

2003-12-23 01:13  paultcochrane

	* trunk/xmds-devel/source/main.cc: Put preferences parsing code
	  into a function. It's a bit neater, and only one section of code
	  to modify instead of two. Also changed a couple of warnings to
	  only be printed out when verbose flag is set.

2003-12-22 06:56  paultcochrane

	* trunk/xmds-devel/Makefile.am: Updated to include the
	  README.Windows file in the distribution.

2003-12-22 06:55  paultcochrane

	* trunk/xmds-devel/README.Windows: Initial import to repository.

2003-12-22 06:01  paultcochrane

	* trunk/xmds-devel/examples/tla.xmds: Minor formatting improvement.

2003-12-22 06:00  paultcochrane

	* trunk/xmds-devel/examples/nlse.xmds: Added test code for output
	  arguments. This needs to be fixed up, not a good example file
	  really.

2003-12-22 05:59  paultcochrane

	* trunk/xmds-devel/examples/ndparamp.xmds: Added binary output and
	  benchmark tags.

2003-12-22 05:58  paultcochrane

	* trunk/xmds-devel/examples/highdim.xmds: Fixed integer where float
	  should be problem.

2003-12-22 05:57  paultcochrane

	* trunk/xmds-devel/examples/gaugeatomlaser.xmds: Renamed simulation
	  and .xsil file to reflect name of "gaugeatomlaser".

2003-12-22 05:56  paultcochrane

	* trunk/xmds-devel/examples/fullpos3D.xmds: Some minor
	  reformatting.

2003-12-22 05:55  paultcochrane

	* trunk/xmds-devel/examples/fibre.xmds: Fixed a divide by integer
	  problem which has only really become evident since gcc3. Added
	  <binary_output> and <use_double> tags.

2003-12-22 05:52  paultcochrane

	* trunk/xmds-devel/examples/atomlaser.xmds: Tidied the code
	  slightly. Added an <author> and <description> element (may be
	  used in the future. Added some comments to the file. Removed test
	  code, and now acually use variables in the simulation as command
	  line arguments. Also added some new syntax to work in xmds-1.3-1.

2003-12-22 05:49  paultcochrane

	* trunk/xmds-devel/testsuite/atomlaser_reference.xsil,
	  trunk/xmds-devel/testsuite/ndparamp_reference.xsil,
	  trunk/xmds-devel/testsuite/nlse_reference.xsil,
	  trunk/xmds-devel/testsuite/soliton_reference.xsil,
	  trunk/xmds-devel/testsuite/tla_reference.xsil: Updated the
	  <simname>_reference.xsil files.

2003-12-22 05:40  paultcochrane

	* trunk/xmds-devel/source/main.cc: Added some documentation as
	  introduction to xmds for output to api documentation. Also added
	  some installation instructions as well.

2003-12-22 04:42  paultcochrane

	* trunk/xmds-devel/source/Doxyfile: Updated to refelect the current
	  project number. Also removed some obsolete Doxygen commands.

2003-12-22 04:39  paultcochrane

	* trunk/xmds-devel/source/dom3.h: Completed documenting the DOM
	  functions and classes as they are outlined in the W3C Working
	  Draft of 05 June 2001. No functional changes, although the big
	  difference is that the api documentation is now significantly
	  better than it was before.

2003-12-19 07:17  paultcochrane

	* trunk/xmds-devel/source/dom3.h: Started documenting the DOM
	  functions and classes as they are outlined in the W3C Working
	  Draft of 05 June 2001. No functional changes, although the big
	  difference is that the api documentation is now significantly
	  better than it was before (and I haven't finished yet!).

2003-12-17 09:35  paultcochrane

	* trunk/xmds-devel/source/xmdsvectorelement.cc: Implemented binary
	  input for use in the <filename> tag of the <vector> element.

2003-12-17 09:33  paultcochrane

	* trunk/xmds-devel/source/xmdsutils.h: Added an enum to specify two
	  booleans, REQD and NOT_REQD. I will eventually implement this
	  further so that some of the calls used of getAssignmentStrings()
	  etc are a little more understandable. Also added declarations for
	  getAttributeStrings() and getAttributeBools().

2003-12-17 09:31  paultcochrane

	* trunk/xmds-devel/source/xmdsutils.cc: Added two new functions:
	  getAttributeStrings() and getAttributeBools(). This was in order
	  to implement binary and ascii input of data files (in <filename>
	  tag of <vector> element). However, this is a more general
	  addition, the two functions being used to get strings and
	  booleans out of attributes of element tags respectively.

2003-12-17 09:29  paultcochrane

	* trunk/xmds-devel/source/xmdsclasses.h: Minor change to the
	  xmdsVectorElement class to implement binary and ascii input
	  files.

2003-12-17 06:18  paultcochrane

	* trunk/xmds-devel/source/kissdom.cc,
	  trunk/xmds-devel/source/xmdssequence.cc,
	  trunk/xmds-devel/source/xmdssimulation.cc,
	  trunk/xmds-devel/source/xmdsvectorelement.cc,
	  trunk/xmds-devel/source/xsilfield.cc: Fixed bug whereby
	  temp<x>.dat was still being used instead of
	  <xsilfilenamebase>x.dat for input data to matlab/scilab.

2003-12-17 06:17  paultcochrane

	* trunk/xmds-devel/source/xmdsvector.cc: Fixed formatting a bit. No
	  real changes to code.

2003-12-17 06:16  paultcochrane

	* trunk/xmds-devel/source/xmdsmomentgroup.cc,
	  trunk/xmds-devel/source/xmdsoutput.cc: Tidied some fprintf
	  statements.

2003-12-17 06:15  paultcochrane

	* trunk/xmds-devel/source/xmdsutils.cc: Fixed some spelling errors
	  and debugging reporting information.

2003-12-17 06:12  paultcochrane

	* trunk/xmds-devel/source/xmdsfield.cc: Tidied some fprintf
	  statements by combining most of the text (and hence removing
	  heaps of fprintf statements and making the code easier to read).

2003-12-17 06:09  paultcochrane

	* trunk/xmds-devel/source/xmdsclasses.h: Added a usePrefs variable
	  to the simulationParamtersStruct in order to implement
	  preferences.

2003-12-17 06:08  paultcochrane

	* trunk/xmds-devel/source/main.cc: Implemented a first go at
	  preferences for xmds. It can be tidied a lot, but it works at
	  present. One needs a ~/.xmds/xmds.prefs file or an xmds.prefs
	  file in the local directory to the script one is trying to
	  compile. The prefs file format is <compiler macro name> =
	  <compilation variable>, e.g. XMDS_CC = gcc. One can also use
	  comments. All text after (and including) a hash character (#) is
	  ignored.

2003-12-17 06:03  paultcochrane

	* trunk/xmds-devel/configure.in: Updated to show version
	  information as 1.3-1.

2003-12-07 03:25  paultcochrane

	* trunk/xmds-devel/ChangeLog: Added comments about current changes
	  to xmds.

2003-12-07 03:24  paultcochrane

	* trunk/xmds-devel/configure.in: Altered release number to current
	  release: 1.2-2

2003-11-27 05:50  paultcochrane

	* trunk/xmds-devel/source/xmdssimulation.cc: Added the inclusion of
	  the sstream (string streams) header.

2003-11-27 05:49  paultcochrane

	* trunk/xmds-devel/source/xmdsfield.cc: Fixed segfaulting of mpi
	  programs using wisdom. Now have more C++ type code to implement
	  creation of the host_rank_%i.stuff etc files and for their
	  deletion. Writing and reading from these files was causing the
	  segfault.

2003-11-27 01:33  paultcochrane

	* trunk/xmds-devel/source/xmdssequence.cc: Fixed bug whereby the
	  useWisdom option wasn't passed through to writePlanCreationCalls
	  properly.

2003-11-27 01:14  paultcochrane

	* trunk/xmds-devel/configure.in: Changed way that mpiccTest was
	  checked for the compiler running mpicc.

2003-11-25 08:19  paultcochrane

	* trunk/xmds-devel/ChangeLog: Added comments advising of changes up
	  to current version of xmds.

2003-11-25 08:18  paultcochrane

	* trunk/xmds-devel/configure.in: Corrected version numbers to agree
	  with current release.

2003-11-25 08:17  paultcochrane

	* trunk/xmds-devel/source/xmdsfield.cc: Fixed host.stuff and
	  home.stuff file writing with mpi, I'd fixed this before in one
	  place in the code but missed this extra place.

2003-11-25 01:37  paultcochrane

	* trunk/xmds-devel/source/xmdsmomentgroup.cc: Modified moment group
	  number reporting at the terminal, so matches what is given in
	  xsil2graphics and output files.

2003-11-24 10:10  paultcochrane

	* trunk/xmds-devel/configure.in: Fixed problem with optimisation
	  settings not flowing through for script compilation when using
	  gcc. Now check if $ac_compiler_gnu is "yes" instead of if XMDS_CC
	  is gcc (can be g++, for example).

2003-11-24 10:07  paultcochrane

	* trunk/xmds-devel/source/xmdsmomentgroup.cc: Fixed binary output
	  bug where k-space variables weren't ordered correctly before
	  output.

2003-11-20 06:00  paultcochrane

	* trunk/xmds-devel/source/xmdsmomentgroup.cc: Fixed misreporting of
	  filename if unable to open the output file for binary output.

2003-11-07 00:28  paultcochrane

	* trunk/xmds-devel/configure.in: Changed release number to pre1,
	  ready for the pre1 release. (funnily enough...)

2003-11-06 10:18  paultcochrane

	* trunk/xmds-devel/source/loadxsil.m: Hopefully fixed problem with
	  loading data in more than one moment group by appending
	  _[momentGroupNumber] to variable names as is done in
	  xsil2graphics.

2003-11-06 09:59  paultcochrane

	* trunk/xmds-devel/configure.in: Now pointing XMDS_CC to CXX if
	  necessary.

2003-11-06 06:02  paultcochrane

	* trunk/xmds-devel/configure.in: Fixed bug where a test for null
	  should have been non-null.

2003-11-06 01:47  paultcochrane

	* trunk/xmds-devel/source/xsilfield.h: Altered call to
	  writeAsFormat so can implement writing data files as xsil
	  filename_momentGroup.dat as opposed to temp_momentGroup.dat as
	  before.

2003-11-06 01:46  paultcochrane

	* trunk/xmds-devel/source/xsilfield.cc: The output filename is the
	  xsil base filename (the bit without the .xsil on the end) with
	  the moment group number plus .dat, instead of just temp1.dat,
	  temp2.dat. Not a great comment, but I implemented this idea
	  anyway...

2003-11-06 01:44  paultcochrane

	* trunk/xmds-devel/source/xsil2graphics.cc: Some reformatting of
	  code. Main change being the altering of the
	  xsilField::writeAsFormat call, by passing through the xsil
	  filename's base name (ie that bit without the .xsil on the end).

2003-11-06 01:42  paultcochrane

	* trunk/xmds-devel/source/xmdssimulation.cc: Removed the output of
	  the (commented out in the final code anyway) unistd.h statement.

2003-11-06 01:41  paultcochrane

	* trunk/xmds-devel/source/xmdsfield.cc: (Hopefully) fixed problem
	  with writing, reading and deleting host.stuff and home.stuff
	  files when using mpi. The files now append the rank to the file
	  name, so this problem should be fixed.

2003-11-06 01:38  paultcochrane

	* trunk/xmds-devel/source/main.cc: Removed XMDS_CXX stuff. Removed
	  clibs being added to one of mpicc compile strings. This produced
	  inconsistent compilation flags when mpicc uses a different
	  compiler to XMDS_CC.

2003-11-06 01:16  paultcochrane

	* trunk/xmds-devel/admin/manifestGen.pl: Documented a far simpler
	  way of generating the manifest.

2003-11-06 01:15  paultcochrane

	* trunk/xmds-devel/configure.in: Removed references to XMDS_CXX*
	  variables, they were superfluous and caused confusion. Made some
	  tests more stringent, so that user supplied arguments at the
	  command line to configure can be passed through properly. If the
	  user has specified command line options to xmds, the script now
	  also checks if some required flags are missing from these options
	  and appends them if necessary.

2003-11-06 01:11  paultcochrane

	* trunk/xmds-devel/README: Added description of configuration
	  options that are now available in xmds-1.2, and tidied up the
	  text a bit. Also fixed a couple of bugs with the scilab execution
	  of the xsil file.

2003-11-06 01:09  paultcochrane

	* trunk/xmds-devel/Makefile.am: Removed latexdocs from being
	  included in distribution temporarily. Will probably add back in
	  when docs catch up to current version of xmds.

2003-11-06 01:08  paultcochrane

	* trunk/xmds-devel/MANIFEST: Updated to reflect current list of
	  files for distribution.

2003-11-04 08:27  paultcochrane

	* trunk/xmds-devel/Makefile.am: No change, just added something and
	  took it away, but it wants to be updated nevertheless.

2003-11-04 08:22  paultcochrane

	* trunk/xmds-devel/MANIFEST: Initial import to repository.

2003-11-04 08:18  paultcochrane

	* trunk/xmds-devel/ChangeLog: Updated to reflect changes that have
	  happened so far since xmds-1.1.

2003-11-04 07:54  paultcochrane

	* trunk/xmds-devel/README: Updated to agree with current
	  configuration options.

2003-11-04 07:53  paultcochrane

	* trunk/xmds-devel/AUTHORS: Updated email addresses of authors.

2003-11-04 06:59  paultcochrane

	* trunk/xmds-devel/configure.in: MPICCFLAGS needs $PTHREADS_CFLAGS
	  as well. Tidied XMDS_CFLAGS and XMDS_CXXFLAGS by putting
	  AGGRESSIVE_* instead of the explicit declaration. Removed the
	  check for enable_mpicc_aggressive. Removed --enable-*-aggressive
	  options.

2003-11-04 06:32  paultcochrane

	* trunk/xmds-devel/configure.in: Fixed bug where one actually needs
	  the $PTHREAD_CFLAGS variable inserted into XMDS_CFLAGS.

2003-11-04 05:20  paultcochrane

	* trunk/xmds-devel/configure.in: Removed explicit check for
	  MPI_Init in -lmpi since -lmpi must work if passed -llam test, AND
	  the library arguments be in the right order. This simplifies the
	  checking slightly.

2003-11-03 04:46  paultcochrane

	* trunk/xmds-devel/configure.in: The flags for gcc, icc, g++ etc
	  all now default to the aggressive version. If the user wants
	  other flags, they should set them at the command line at build
	  time.

2003-11-03 04:03  paultcochrane

	* trunk/xmds-devel/configure.in: Changed implementation of how
	  xmdsconfig.h is made. It's now a cp from config.h.

2003-11-03 04:01  paultcochrane

	* trunk/xmds-devel/Makefile.am: Added the m4 files acx_mpi.m4 and
	  acx_pthread.m4 so that will be added to distribution output.

2003-11-03 03:58  paultcochrane

	* trunk/xmds-devel/examples/diffusion.xmds,
	  trunk/xmds-devel/examples/lorenz.xmds,
	  trunk/xmds-devel/examples/pendulum.xmds,
	  trunk/xmds-devel/examples/vibstring.xmds: Initial import to
	  repository.

2003-10-31 07:04  joehope

	* trunk/xmds-devel/configure.in,
	  trunk/xmds-devel/examples/fibre.xmds: Making stable autoconf on
	  MacOSX

2003-10-30 07:07  paultcochrane

	* trunk/xmds-devel/source/Doxyfile: Now set to produce pdf
	  documentation as well.

2003-10-30 07:05  paultcochrane

	* trunk/xmds-devel/configure.in: Fixed problem with not finding lam
	  properly. Fixed bug whereby forgot to add -lxmds to XMDS_LIBS
	  variable.

2003-10-30 03:40  paultcochrane

	* trunk/xmds-devel/configure.in: No longer assuming lam, nor does
	  one need to put --with-mpi-libs="-llam" on the command line for
	  the script to find either the lam or mpich implementations of
	  mpi. Fixed minor big with -I in wrong place. Now determines how
	  mpicc is run, which in itself is dependent upon the mpi
	  implementation, but the script detects the differences between
	  lam and mpi and is still able to check what CC is used for mpicc.

2003-10-30 03:35  paultcochrane

	* trunk/xmds-devel/source/dom3.h,
	  trunk/xmds-devel/source/kissdom.h,
	  trunk/xmds-devel/source/xmdsclasses.h: Did some reformatting and
	  updated docstrings.

2003-10-28 01:42  paultcochrane

	* trunk/xmds-devel/configure.in: Added a check for how mpicc is
	  run, and then alter MPICCFLAGS accordingly. Also added a check
	  for mpicc-aggressive and if on, then uses the icc-aggressive or
	  gcc-aggressive flags if mpicc is run by icc or gcc.

2003-10-28 00:48  paultcochrane

	* trunk/xmds-devel/admin, trunk/xmds-devel/admin/manifestGen.pl:
	  Initial import to repository.

2003-10-27 10:50  paultcochrane

	* trunk/xmds-devel/configure.in: Implemented the --with-mpi-path
	  option better. Used the MPI_LIB_PATH to help configure look for
	  fftw_mpi. Added the MPI_LIB_PATH to the MPICCFLAGS.

2003-10-27 10:47  paultcochrane

	* trunk/xmds-devel/Makefile.am: Added loadxsil.m to EXTRA_DIST
	  files.

2003-10-27 08:13  paultcochrane

	* trunk/xmds-devel/source/kissdom.cc,
	  trunk/xmds-devel/source/kissdom.h,
	  trunk/xmds-devel/source/main.cc,
	  trunk/xmds-devel/source/xmdsarg.cc,
	  trunk/xmds-devel/source/xmdsargelement.cc,
	  trunk/xmds-devel/source/xmdsargv.cc,
	  trunk/xmds-devel/source/xmdsclasses.h,
	  trunk/xmds-devel/source/xmdscomplex.h,
	  trunk/xmds-devel/source/xmdselement.cc,
	  trunk/xmds-devel/source/xmdsfield.cc,
	  trunk/xmds-devel/source/xmdsfilter.cc,
	  trunk/xmds-devel/source/xmdsglobals.cc,
	  trunk/xmds-devel/source/xmdsintegrate.cc,
	  trunk/xmds-devel/source/xmdsintegrateex.cc,
	  trunk/xmds-devel/source/xmdsintegrateip.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4ex.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4ip.cc,
	  trunk/xmds-devel/source/xmdsintegratesi.cc,
	  trunk/xmds-devel/source/xmdsintegratesiex.cc,
	  trunk/xmds-devel/source/xmdsintegratesiip.cc,
	  trunk/xmds-devel/source/xmdsmomentgroup.cc,
	  trunk/xmds-devel/source/xmdsoutput.cc,
	  trunk/xmds-devel/source/xmdssegment.cc,
	  trunk/xmds-devel/source/xmdssequence.cc,
	  trunk/xmds-devel/source/xmdssimulation.cc,
	  trunk/xmds-devel/source/xmdsutils.cc,
	  trunk/xmds-devel/source/xmdsutils.h,
	  trunk/xmds-devel/source/xmdsvector.cc,
	  trunk/xmds-devel/source/xmdsvectorelement.cc,
	  trunk/xmds-devel/source/xmlbasics.cc,
	  trunk/xmds-devel/source/xmlbasics.h,
	  trunk/xmds-devel/source/xmlparser.cc,
	  trunk/xmds-devel/source/xmlparser.h,
	  trunk/xmds-devel/source/xsil2graphics.cc,
	  trunk/xmds-devel/source/xsilfield.cc,
	  trunk/xmds-devel/source/xsilfield.h: Added GPL statement.

2003-10-27 08:01  paultcochrane

	* trunk/xmds-devel/source/dom3.h: Changed some docstrings. Added
	  GPL statement.

2003-10-27 07:52  paultcochrane

	* trunk/xmds-devel/configure.in: Hopefully fixed bloody headers
	  problem this time!! Fixed other problems wrt getting mpi to get
	  the correct options. Seems to go on the SC now, so that's good.

2003-10-24 01:50  paultcochrane

	* trunk/xmds-devel/source/xmdssequence.cc: Added more helpful (ie
	  usage) output for when arguments to simulation binary are
	  incorrect.

2003-10-24 01:46  paultcochrane

	* trunk/xmds-devel/source/main.cc: Fixed bug where insufficient
	  number of format specifiers in a string for number of arguments
	  to sprintf. This caused a problem with mpi not seeing the fftw
	  libraries.

2003-10-23 10:36  paultcochrane

	* trunk/xmds-devel/configure.in: Now handling the case when someone
	  uses --prefix better now. Basically I just make the USER_* and
	  *dir variables point to the directory pointed to by the $prefix.

2003-10-23 10:11  paultcochrane

	* trunk/xmds-devel/source/xmdssimulation.cc: Minor terminal output
	  touch up.

2003-10-23 10:11  paultcochrane

	* trunk/xmds-devel/source/main.cc: Now using XMDS_CC, XMDS_CXX, and
	  XMDS_CFLAGS instead of the non-XMDS_* versions.

2003-10-23 10:07  paultcochrane

	* trunk/xmds-devel/configure.in: Hopefully now fixed the config
	  headers not recreating themselves problem. Did some reformatting
	  of help output. Added --with-mpi-compiler so that the user can
	  choose what compiler to use for mpi, --enable-mpi (not default
	  option) so that mpi is checked for and added to variables,
	  --enable-icc-aggressive, so that aggressive optimisation settings
	  are chosen when using icc, --enable-gcc-aggressive so that both
	  gcc and g++ use aggressive optimisation settings,
	  --enable-mpicc-aggressive so that mpicc will use the
	  gcc-aggressive compiler settings. Fixed a bug where CXXFLAGS
	  lacked an S. Needed to add the PTHREAD_CFLAGS variable to
	  XMDS_CFLAGS and XMDS_CXXFLAGS. Removed old (and commented anyway)
	  mpi checking code. Put mpi stuff into an if loop, and is
	  processed only when --enable-mpi is used. Am now actually using
	  XMDS_CFLAGS and XMDS_CXXFLAGS. Now configure script outputs
	  nicely formatted option and variable information once
	  configuration is complete.

2003-10-22 06:13  paultcochrane

	* trunk/xmds-devel/source/xmdssimulation.cc: Minor change to
	  terminal output.

2003-10-22 06:12  paultcochrane

	* trunk/xmds-devel/source/main.cc: Changed INCLUDES and LIBS to be
	  XMDS_INCLUDES and XMDS_LIBS, so is specific to the xmds
	  simulations rather than xmds itself.

2003-10-22 06:10  paultcochrane

	* trunk/xmds-devel/configure.in: Corrected some *config.h errors.
	  Relabelled some of the variables to be specific to the xmds
	  simulations as opposed to xmds itself. Removed some superfluous
	  function checks. Got MPI running cleaner and better.

2003-10-22 03:25  paultcochrane

	* trunk/xmds-devel/acx_mpi.m4: Initial import to repository.

2003-10-22 00:39  paultcochrane

	* trunk/xmds-devel/source/Makefile.am: Changed config.h to
	  xmdsconfig.h

2003-10-22 00:39  paultcochrane

	* trunk/xmds-devel/source/xmdssimulation.cc: Changed inclusion of
	  config.h to inclusion of xmdsconfig.h to stop possible name
	  clashes when installing on the system instead of in the user's
	  directory.

2003-10-22 00:38  paultcochrane

	* trunk/xmds-devel/source/xmdsmomentgroup.cc: Fixed minor error
	  with incorrect format in printf statement.

2003-10-22 00:23  paultcochrane

	* trunk/xmds-devel/source/main.cc: Improved mpi flag handling, and
	  added a FFTW_MPI_LIBS variable.

2003-10-22 00:22  paultcochrane

	* trunk/xmds-devel/configure.in: Removed some superfluous
	  variables, and some superfluous output at configure time.
	  Improved the ordering and determination of flags for use with
	  mpi.

2003-10-21 23:27  paultcochrane

	* trunk/xmds-devel/configure.in: Now generating source/xmdsconfig.h
	  as well as source/config.h so that simulation binaries can have
	  more benefit from configuration headers. Added -lxmds to LIBS
	  variable (this isn't the right thing to do, and will be fixed
	  shortly).

2003-10-20 01:14  joehope

	* trunk/xmds-devel/examples/highdim.xmds: Trivial fix for
	  occasional, minor compiler confusion: sqrt(int)

2003-10-18 10:55  paultcochrane

	* trunk/xmds-devel/source/xmdssimulation.cc: Removed inclusion of
	  endian.h for binaryOutput. Now including config.h when
	  binaryOutput is true.

2003-10-18 10:54  paultcochrane

	* trunk/xmds-devel/source/xmdssequence.cc: Changed checks for
	  FLOAT_WORD_ORDER etc to CPU_IS_BIG_ENDIAN etc.

2003-10-18 10:53  paultcochrane

	* trunk/xmds-devel/source/xmdsmomentgroup.cc: Now determining
	  endian-ness by the variables CPU_IS_BIG_ENDIAN and
	  CPU_IS_LITTLE_ENDIAN.

2003-10-18 10:51  paultcochrane

	* trunk/xmds-devel/source/Makefile.am: Now adding the config.h
	  generated in the configuration of xmds. This adds the variables
	  CPU_IS_BIG_ENDIAN and CPU_IS_LITTLE_ENDIAN to check for
	  endian-ness of the processor.

2003-10-18 10:48  paultcochrane

	* trunk/xmds-devel/configure.in: Removed check for endian.h and
	  added code to search for endian-ness of processor copied from
	  configure.ac in libsndfile. Also am now including the
	  acinclude.m4 of libsndfile.

2003-10-18 10:07  paultcochrane

	* trunk/xmds-devel/acinclude.m4: Initial import to repository.

2003-10-17 04:53  paultcochrane

	* trunk/xmds-devel/source/xmdssimulation.cc: Instead of adding
	  "#include getopt.h" every time a simulation code is written, it
	  is only added now when the .xmds script contains an argv tag set,
	  and therefore the simulation can take arguments at the command
	  line.

2003-10-17 04:50  paultcochrane

	* trunk/xmds-devel/source/xmdssequence.cc: Changed getopt_long_only
	  to getopt_long.

2003-10-17 04:49  paultcochrane

	* trunk/xmds-devel/source/main.cc: Removed FFTWMPILIBS variable
	  (now superfluous). Removed superfluous %s formatting string.

2003-10-17 04:48  paultcochrane

	* trunk/xmds-devel/source/Makefile.am: Added the getopt sources and
	  headers to make the libxmds library.

2003-10-17 04:36  paultcochrane

	* trunk/xmds-devel/config.guess, trunk/xmds-devel/depcomp,
	  trunk/xmds-devel/ltmain.sh: Updated to current version.

2003-10-17 04:32  paultcochrane

	* trunk/xmds-devel/configure.in: Added underscores to some
	  variables to improve readability. Made sure that the directory
	  libxmds.a is put in is the same as xmdscomplex.h (on
	  installation). Made sure that script doesn't write over
	  previously defined (eg in the user's shell) any environment
	  variables used (eg CFLAGS). Made sure that gcc gets the -Wall
	  option (don't really know why... historical I guess). Changed
	  FFTW_THREADS_* to XMDS_THREADS_*. These may be deleted in the
	  future. Cleaned up the flags that mpi gets eventually. Further
	  cleaning will ensue however. icc currently only used if set as CC
	  and or CXX flags in the shell. Moved the AC_SUBSTs at the end of
	  the script to before all of the AC_DEFINES. Made sure that -lxmds
	  is added to LIBS. Some echos added for testing purposes.

2003-10-17 04:24  paultcochrane

	* trunk/xmds-devel/Makefile.am: Commented out the inclusion of xmds
	  api documentation.

2003-10-10 05:02  joehope

	* trunk/xmds-devel/source/dom3.h,
	  trunk/xmds-devel/source/kissdom.cc,
	  trunk/xmds-devel/source/kissdom.h,
	  trunk/xmds-devel/source/xmdsarg.cc,
	  trunk/xmds-devel/source/xmdsargelement.cc,
	  trunk/xmds-devel/source/xmdsargv.cc,
	  trunk/xmds-devel/source/xmdsclasses.h,
	  trunk/xmds-devel/source/xmdselement.cc,
	  trunk/xmds-devel/source/xmdsfield.cc,
	  trunk/xmds-devel/source/xmdsfilter.cc,
	  trunk/xmds-devel/source/xmdsglobals.cc,
	  trunk/xmds-devel/source/xmdsintegrate.cc,
	  trunk/xmds-devel/source/xmdsintegrateex.cc,
	  trunk/xmds-devel/source/xmdsintegrateip.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4ex.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4ip.cc,
	  trunk/xmds-devel/source/xmdsintegratesi.cc,
	  trunk/xmds-devel/source/xmdsintegratesiex.cc,
	  trunk/xmds-devel/source/xmdsintegratesiip.cc,
	  trunk/xmds-devel/source/xmdsmomentgroup.cc,
	  trunk/xmds-devel/source/xmdsoutput.cc,
	  trunk/xmds-devel/source/xmdssegment.cc,
	  trunk/xmds-devel/source/xmdssequence.cc,
	  trunk/xmds-devel/source/xmdssimulation.cc,
	  trunk/xmds-devel/source/xmdsutils.cc,
	  trunk/xmds-devel/source/xmdsutils.h,
	  trunk/xmds-devel/source/xmdsvector.cc,
	  trunk/xmds-devel/source/xmdsvectorelement.cc,
	  trunk/xmds-devel/source/xmlbasics.cc,
	  trunk/xmds-devel/source/xmlbasics.h,
	  trunk/xmds-devel/source/xmlparser.cc,
	  trunk/xmds-devel/source/xmlparser.h,
	  trunk/xmds-devel/source/xsil2graphics.cc,
	  trunk/xmds-devel/source/xsilfield.cc,
	  trunk/xmds-devel/source/xsilfield.h: Replace //** with // **
	  (often allows proper syntax colouring)

2003-10-09 06:29  paultcochrane

	* trunk/xmds-devel/testsuite,
	  trunk/xmds-devel/testsuite/atomlaser.xmds,
	  trunk/xmds-devel/testsuite/atomlaser_reference.xsil,
	  trunk/xmds-devel/testsuite/fibre.xmds,
	  trunk/xmds-devel/testsuite/fibre_reference.xsil,
	  trunk/xmds-devel/testsuite/fullpos3D.xmds,
	  trunk/xmds-devel/testsuite/fullpos3D_reference.xsil,
	  trunk/xmds-devel/testsuite/gaugeatomlaser.xmds,
	  trunk/xmds-devel/testsuite/gaugeatomlaser_reference.xsil,
	  trunk/xmds-devel/testsuite/genRefData.pl,
	  trunk/xmds-devel/testsuite/kubo.xmds,
	  trunk/xmds-devel/testsuite/kubo_reference.xsil,
	  trunk/xmds-devel/testsuite/ndparamp.xmds,
	  trunk/xmds-devel/testsuite/ndparamp_reference.xsil,
	  trunk/xmds-devel/testsuite/nlse.xmds,
	  trunk/xmds-devel/testsuite/nlse_reference.xsil,
	  trunk/xmds-devel/testsuite/sine.xmds,
	  trunk/xmds-devel/testsuite/sine_reference.xsil,
	  trunk/xmds-devel/testsuite/soliton.xmds,
	  trunk/xmds-devel/testsuite/soliton_reference.xsil,
	  trunk/xmds-devel/testsuite/test_xmds.pl,
	  trunk/xmds-devel/testsuite/tla.xmds,
	  trunk/xmds-devel/testsuite/tla_reference.xsil: Initial import to
	  repository.

2003-10-09 02:18  offaxis

	* trunk/xmds-devel/source/xmdsglobals.cc: Globals from <arg>
	  elements now read in _before_ those from the <globals> element.

2003-10-07 05:28  paultcochrane

	* trunk/xmds-devel/depcomp: Initial import to repository.

2003-10-07 05:01  paultcochrane

	* trunk/xmds-devel/acx_pthread.m4: Initial import to repository.
	  Copied from the fftw distribution (many thanks).

2003-10-07 04:59  paultcochrane

	* trunk/xmds-devel/configure.in: Many, many changes. Updated to
	  call xmds version 1.2. Added a path to one's mpi distribution if
	  different from /usr or /usr/local. Added a check for vendor's cc
	  and c++ compiler, and using them to compile both xmds and the
	  simulation binaries. If the compiler is gcc then adds the -Wall
	  compiler flag. Checks for getopt and getopt_long. Checks for the
	  various thread libraries (code copied and modified from the fftw
	  configure.in). Added a FFTW_LIBS variable. This may be used a bit
	  better in the future. Checks for the Intel c compiler and if so
	  then uses that compiler for xmds and the simulation binaries.
	  Removed some superfluous definitions and subst's.

2003-10-07 04:52  paultcochrane

	* trunk/xmds-devel/examples/nlse.xmds: Removed <binary_output> tag,
	  just for testing purposes. Fixed problem with log(2) being
	  incorrect for more recent versions of c++: one must now use
	  log(2.0).

2003-10-07 04:50  paultcochrane

	* trunk/xmds-devel/source/xmdssimulation.cc: Added config.h to
	  headers list. Using the HAVE_ENDIAN_H variable defined therein to
	  specify what the __BYTE_ORDER and __FLOAT_WORD_ORDER macros
	  should be equal to. Hopefully this fixes the endian issues xmds
	  could have, although I'm not sure yet.

2003-10-07 04:48  paultcochrane

	* trunk/xmds-devel/source/main.cc: Added cxx variable set equal to
	  the CXX variable found by the configure script. This is then used
	  for compilation of the simulation binary. Also specifying the
	  FFTW_LIBS variable as well. Added the fftwlibs variable to the
	  compilation of the simulation binary.

2003-10-07 04:45  paultcochrane

	* trunk/xmds-devel/source/loadxsil.m: Fixed a line that was missing
	  a
	  .

2003-10-06 04:21  paultcochrane

	* trunk/xmds-devel/source/xmdsmomentgroup.cc: Removed multiline
	  string literals by adding heaps of fprintf statements. This
	  caused problems with some compilers.

2003-10-06 04:20  paultcochrane

	* trunk/xmds-devel/source/xmdsfield.cc: Removed multiline string
	  literals by adding heaps of fprintf statements.

2003-09-30 11:50  paultcochrane

	* trunk/xmds-devel/examples/atomlaser.xmds: Now contains more
	  <argv> tags test code. Doesn't actually do anything...

2003-09-30 11:48  paultcochrane

	* trunk/xmds-devel/source/xmdsutils.h: Reformatted the text.

2003-09-30 11:47  paultcochrane

	* trunk/xmds-devel/source/xmdssimulation.cc: Removed test code.
	  Fixed code to implement the gnu getopt library for command line
	  options for the simulation binary.

2003-09-30 11:46  paultcochrane

	* trunk/xmds-devel/source/xmdssequence.cc: Completed code to
	  implement gnu getopt command line options for the simulation
	  binary.

2003-09-30 11:44  paultcochrane

	* trunk/xmds-devel/source/xmdsglobals.cc: Added global variables
	  code to be output for when command line arguments are specified
	  in the .xmds file.

2003-09-30 11:42  paultcochrane

	* trunk/xmds-devel/source/xmdscomplex.h: Reformatted text.

2003-09-30 11:42  paultcochrane

	* trunk/xmds-devel/source/xmdsclasses.h: Deleted some superfluous
	  code (eg writeArgvIntialisationCode, writeArgvFinalisationCode).
	  Removed test object: argvList. Fixed header so that can use an
	  argvStruct to store information about the command line arguments
	  specified in <argv> tags.

2003-09-30 11:39  paultcochrane

	* trunk/xmds-devel/source/xmdsargv.cc: Deleted some superfluous
	  code (eg writeArgvIntialisationCode, writeArgvFinalisationCode).

2003-09-30 11:38  paultcochrane

	* trunk/xmds-devel/source/xmdsargelement.cc: Finally worked out how
	  to get the argument names, short options, types, default_values
	  etc into the simulation object. Deleted some superfluous code (eg
	  writeArgDeclaration, writeArgCode).

2003-09-30 11:36  paultcochrane

	* trunk/xmds-devel/source/xmdsarg.cc: Removed some superfluous
	  function definitions. Namely type(), setType(), default_value()
	  and setDefaultValue()

2003-09-30 11:34  paultcochrane

	* trunk/xmds-devel/source/dom3.h,
	  trunk/xmds-devel/source/kissdom.h: Reformatted text nicely.

2003-09-29 09:57  paultcochrane

	* trunk/xmds-devel/Makefile.am: Removed superfluous files from
	  being added when performing a make dist. Needs to be improved
	  further.

2003-09-29 09:56  paultcochrane

	* trunk/xmds-devel/configure.in: Better checking, and some testing
	  done on platforms other than linux.

2003-09-29 08:00  paultcochrane

	* trunk/xmds-devel/configure.in: Actually fixed the checks now,
	  instead of not (aarrgghh).

2003-09-29 03:28  paultcochrane

	* trunk/xmds-devel/configure.in: Fixed some more checks and added a
	  check for fftw_mpi.

2003-09-29 02:02  paultcochrane

	* trunk/xmds-devel/configure.in: Fixed bug with incorrectly using
	  alternative paths to fftw.

2003-09-15 10:16  paultcochrane

	* trunk/xmds-devel/source/xmdsarg.cc,
	  trunk/xmds-devel/source/xmdsargelement.cc,
	  trunk/xmds-devel/source/xmdsargv.cc,
	  trunk/xmds-devel/source/xmdselement.cc,
	  trunk/xmds-devel/source/xmdsfield.cc,
	  trunk/xmds-devel/source/xmdsfilter.cc,
	  trunk/xmds-devel/source/xmdsglobals.cc,
	  trunk/xmds-devel/source/xmdsintegrate.cc,
	  trunk/xmds-devel/source/xmdsintegrateex.cc,
	  trunk/xmds-devel/source/xmdsintegrateip.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4ex.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4ip.cc,
	  trunk/xmds-devel/source/xmdsintegratesi.cc,
	  trunk/xmds-devel/source/xmdsintegratesiex.cc,
	  trunk/xmds-devel/source/xmdsintegratesiip.cc,
	  trunk/xmds-devel/source/xmdsmomentgroup.cc,
	  trunk/xmds-devel/source/xmdsoutput.cc,
	  trunk/xmds-devel/source/xmdssegment.cc,
	  trunk/xmds-devel/source/xmdssequence.cc,
	  trunk/xmds-devel/source/xmdssimulation.cc,
	  trunk/xmds-devel/source/xmdsutils.cc,
	  trunk/xmds-devel/source/xmdsvector.cc,
	  trunk/xmds-devel/source/xmdsvectorelement.cc: Implemented the use
	  of a command line flag to xmds for toggling debugging information
	  output (-d).

2003-09-15 10:14  paultcochrane

	* trunk/xmds-devel/source/xsil2graphics.cc: Modified to implement
	  the -d xmds debugging flag and -x the xml debugging flag.

2003-09-15 10:13  paultcochrane

	* trunk/xmds-devel/source/xmlbasics.cc: Removed DEBUG macro. This
	  is now implemented as a command line switch to xmds. Specifically
	  -x, for xml debugging information. This change is really only
	  useful for developers.

2003-09-15 10:12  paultcochrane

	* trunk/xmds-devel/source/xmdsclasses.h: Removed DEBUG macro. This
	  is now implemented as a command line switch to xmds.

2003-09-15 10:10  paultcochrane

	* trunk/xmds-devel/source/main.cc: Implemented some new command
	  line options to xmds the program. -c switches compilation of the
	  output binary OFF. This is useful for checking is xmds outputs
	  the correct code, or if one wants to hack the output source and
	  not have to worry about compilation, or even if the output code
	  is not to be used on a unix system and therefore needs some
	  hacking to work on another system. -d switches debugging output
	  on excluding xml parsing debugging output (same as setting the
	  DEBUG macro in the code, except that xmds doesn't have to be
	  recompiled every time one wants to change that). -x switches
	  debugging output of just the xml parsing on.

2003-09-15 09:57  paultcochrane

	* trunk/xmds-devel/examples/atomlaser.xmds: Improved indentation of
	  xml. Added code to test the <argv> tag set.

2003-09-15 06:56  paultcochrane

	* trunk/xmds-devel/ChangeLog: Initial import to repository.

2003-09-15 06:49  paultcochrane

	* trunk/xmds-devel/source/xmdsarg.cc,
	  trunk/xmds-devel/source/xmdsargelement.cc,
	  trunk/xmds-devel/source/xmdsargv.cc: Initial import to
	  repository.

2003-09-15 06:48  paultcochrane

	* trunk/xmds-devel/source/xmdssimulation.cc: Improved indentation
	  of source code. Added some code for the parsing of the <argv>
	  element.

2003-09-15 06:45  paultcochrane

	* trunk/xmds-devel/source/xmdssequence.cc: Improved indentation of
	  source code, no functional changes.

2003-09-15 06:43  paultcochrane

	* trunk/xmds-devel/source/xmdsclasses.h: Added declarations for
	  xmdsArgv, xmdsArg, and xmdsArgElement classes. Also added an
	  argvStruct structure to store the relevant information found by
	  parsing the new <argv> etc syntax. This may or may not be used at
	  this stage, so consider this commit as strictly temporary.

2003-09-15 06:38  paultcochrane

	* trunk/xmds-devel/source/dom3.h,
	  trunk/xmds-devel/source/kissdom.cc,
	  trunk/xmds-devel/source/kissdom.h,
	  trunk/xmds-devel/source/main.cc,
	  trunk/xmds-devel/source/xmdscomplex.h,
	  trunk/xmds-devel/source/xmdsfield.cc,
	  trunk/xmds-devel/source/xmdsfilter.cc,
	  trunk/xmds-devel/source/xmdsglobals.cc,
	  trunk/xmds-devel/source/xmdsintegrate.cc,
	  trunk/xmds-devel/source/xmdsintegrateex.cc,
	  trunk/xmds-devel/source/xmdsintegrateip.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4ex.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4ip.cc,
	  trunk/xmds-devel/source/xmdsintegratesi.cc,
	  trunk/xmds-devel/source/xmdsintegratesiex.cc,
	  trunk/xmds-devel/source/xmdsintegratesiip.cc,
	  trunk/xmds-devel/source/xmdsmomentgroup.cc,
	  trunk/xmds-devel/source/xmdsoutput.cc,
	  trunk/xmds-devel/source/xmdssegment.cc,
	  trunk/xmds-devel/source/xmdsutils.cc,
	  trunk/xmds-devel/source/xmdsutils.h,
	  trunk/xmds-devel/source/xmdsvector.cc,
	  trunk/xmds-devel/source/xmdsvectorelement.cc,
	  trunk/xmds-devel/source/xmlbasics.cc,
	  trunk/xmds-devel/source/xmlbasics.h,
	  trunk/xmds-devel/source/xmlparser.cc,
	  trunk/xmds-devel/source/xmlparser.h: No functional changes, just
	  indented the source code nicely

2003-09-15 06:31  paultcochrane

	* trunk/xmds-devel/source/Makefile.am: Added xmdsargv.cc xmdsarg.cc
	  and xmdsargelement.cc to the list of xmds sources

2003-09-09 04:30  paultcochrane

	* trunk/xmds-devel/config.guess, trunk/xmds-devel/config.sub:
	  Initial import to repository

2003-08-06 05:38  paultcochrane

	* trunk/xmds-devel/configure.in: Added a check for the endian.h
	  header file.

2003-08-06 04:42  paultcochrane

	* trunk/xmds-devel/source/xmdssimulation.cc: If binary output is
	  specified, then include the <endian.h> header.

2003-08-06 04:41  paultcochrane

	* trunk/xmds-devel/source/xmdssequence.cc: Added code to output C
	  code to check for the definitions of __FLOAT_WORD_ORDER and
	  __BYTE_WORD order. If the first doesn't exist, then it uses the
	  next, if that doesn't exist, then the program exits.

2003-08-06 04:38  paultcochrane

	* trunk/xmds-devel/source/xmdsmomentgroup.cc: Added code to output
	  C code that checks for littleendian or bigendian binary format,
	  and assigns the string encodingStr accordingly, for then use in
	  the .xsil output file of the simulation.

2003-08-06 04:35  paultcochrane

	* trunk/xmds-devel/source/loadxsil.m: Modified to allow for reading
	  of bigendian or littleendian binary, as specified in the .xsil
	  file.

2003-08-05 07:54  paultcochrane

	* trunk/xmds-devel/source/xmdssimulation.cc: Added argvList to
	  myParameters assignment block in xmdsSimulation constructor.
	  Added code to process the argv element and put the command line
	  arguments into the argvList for use in xmdsglobals.cc.

2003-08-05 07:51  paultcochrane

	* trunk/xmds-devel/source/xmdssequence.cc: Added code to accept
	  arguments on the command line for the xmds executable, only if
	  the argvList defined via the <argv> tag is non-zero. If the
	  incorrect number of arguments, the program gives a usage output
	  and exits.

2003-08-05 07:49  paultcochrane

	* trunk/xmds-devel/source/xmdsglobals.cc: Added code to look for
	  <argv> tag in <globals> section and append the relevant code to
	  the myGlobalCode variable, to be output in the globals definition
	  section of the .cc file. This implements part of allowing
	  arguments to be passed to the executable at the command line.

2003-08-05 07:47  paultcochrane

	* trunk/xmds-devel/source/xmdsclasses.h: Included <string> header.
	  Added argvList string list to parametersStruct to implement the
	  passing of arguments to the output binary at the command line.

2003-08-04 10:27  paultcochrane

	* trunk/xmds-devel/source/xmdssimulation.cc: Included the vector
	  header. Now "using namespace std" by default.

2003-08-04 10:26  paultcochrane

	* trunk/xmds-devel/source/xmdsoutput.cc: Fixed a spelling error in
	  console output.

2003-08-04 10:24  paultcochrane

	* trunk/xmds-devel/source/xmdsmomentgroup.cc: Output binary files
	  now have the moment group field name appended. This stops output
	  binary files writing all over one another. Implemented a better
	  technique of binary output: redundancy inherent in ascii output
	  format has been removed.

2003-08-04 10:20  paultcochrane

	* trunk/xmds-devel/source/xmdsfield.cc: The std:: namespace is now
	  "used". The temporary files host.stuff and home.stuff are removed
	  after being used.

2003-08-04 10:18  paultcochrane

	* trunk/xmds-devel/source/loadxsil.m: Modified to allow for changes
	  in binary output format.

2003-07-28 09:42  paultcochrane

	* trunk/xmds-devel/Makefile.am: examples directory is now included
	  in EXTRA_DIST instead of SUBDIRS. This stops examples from being
	  compiled at build time.

2003-07-28 09:41  paultcochrane

	* trunk/xmds-devel/configure.in: No longer produces Makefile in
	  examples directory.

2003-07-28 09:13  paultcochrane

	* trunk/xmds-devel/source/Doxyfile: Initial import to repository

2003-07-28 09:12  paultcochrane

	* trunk/xmds-devel/source/dom3.h,
	  trunk/xmds-devel/source/kissdom.h,
	  trunk/xmds-devel/source/xmdsclasses.h,
	  trunk/xmds-devel/source/xmdscomplex.h,
	  trunk/xmds-devel/source/xmdsutils.h,
	  trunk/xmds-devel/source/xmlbasics.h,
	  trunk/xmds-devel/source/xmlparser.h,
	  trunk/xmds-devel/source/xsilfield.h: Documented for use with
	  Doxygen. Quite basic and incomplete, but with placeholders where
	  necessary for further addition and improvement of the api
	  documentation.

2003-07-28 09:08  paultcochrane

	* trunk/xmds-devel/source/main.cc,
	  trunk/xmds-devel/source/xmdssequence.cc: Added some documentation
	  to the file. Mainly just to test out Doxygen, automatic api
	  documentation generator.

2003-07-23 04:24  paultcochrane

	* trunk/xmds-devel/examples/atomlaser.xmds,
	  trunk/xmds-devel/examples/fibre.xmds: Added <benchmark> tag

2003-07-23 04:23  paultcochrane

	* trunk/xmds-devel/source/xmdssimulation.cc: Implemented code to
	  process <benchmark> tag properly. Added <ctime> header so that
	  can actually do the benchmarking.

2003-07-23 04:21  paultcochrane

	* trunk/xmds-devel/source/xmdssequence.cc: Added output code to
	  implement <benchmark> boolean

2003-07-23 04:20  paultcochrane

	* trunk/xmds-devel/source/xmdsfield.cc: Fixed issues with gcc 3+
	  not finding ifstream, ofstream, string etc. Need to prepend with
	  std:: to use the correct namespace.

2003-07-23 04:19  paultcochrane

	* trunk/xmds-devel/source/xmdsclasses.h: Added benchmark boolean to
	  simulationParametersStruct

2003-07-23 04:17  paultcochrane

	* trunk/xmds-devel/configure.in: Fixed problems with not getting
	  flags passed to mpicc right. Still not perfect though...

2003-07-23 04:16  paultcochrane

	* trunk/xmds-devel/Makefile.am: Altered to allow building of
	  example binaries in the examples subdirectory

2003-07-12 05:19  paultcochrane

	* trunk/xmds-devel/source/loadxsil.m: Loads binary data, and ascii
	  data. Is now callable as a function and returns variables into
	  calling script or functions variable space. Handles multiple
	  moment groups.

2003-07-11 05:03  paultcochrane

	* trunk/xmds-devel/source/loadxsil.m: Initial import to repository.
	  Is able to parse .xsil files and automatically generate the code
	  to load binary data in from file. This is still under heavy
	  development, need to be able to load ascii data from .xsil files
	  and need to actually implement as a function as opposed to a
	  script. Nevertheless, the checkin was necessary/

2003-07-09 04:44  paultcochrane

	* trunk/xmds-devel/source/xmdssimulation.cc: Added useDouble
	  boolean to myParameters. Implemented finding use_double element
	  in xmds file, and setting accordingly if found.

2003-07-09 04:43  paultcochrane

	* trunk/xmds-devel/source/xmdsmomentgroup.cc: Added <string> C++
	  header. Added a check for the value of the useDouble boolean, if
	  so, set output precison and cast (if necessary) accordingly.
	  Implemented single or double precision for output of binary data
	  depending on value of useDouble boolean. Default is to use
	  double.

2003-07-09 04:40  paultcochrane

	* trunk/xmds-devel/source/xmdsclasses.h: Added useDouble boolean to
	  simulationParametersStruct (to implement the choice of using
	  double or single precision in binary output.

2003-07-09 03:57  paultcochrane

	* trunk/xmds-devel/source/xmdssimulation.cc: Implemented
	  binaryOutput boolean. Implemented checking for <binary_output>
	  element in xmds code. Added some more headers to xmds generated
	  cc file so that can use more C++ features.

2003-07-09 03:55  paultcochrane

	* trunk/xmds-devel/source/xmdsoutput.cc: Addition of myBoolList
	  variable in order to implement binary output

2003-07-09 03:54  paultcochrane

	* trunk/xmds-devel/source/xmdsmomentgroup.cc: Implemented binary
	  output of data if <binary_output> boolean set to yes.

2003-07-09 03:53  paultcochrane

	* trunk/xmds-devel/source/xmdsfield.cc: Added some informative
	  messages to output concerning what program is doing. Changed
	  dodgy C-like implementation of wisdom and hostName/homeDir to a
	  more robust C++ implementation.

2003-07-09 03:50  paultcochrane

	* trunk/xmds-devel/source/xmdsclasses.h: Modified to turn debugging
	  on. Modified to add binaryOutput boolean to myParameters.

2003-07-09 03:49  paultcochrane

	* trunk/xmds-devel/examples/atomlaser.xmds: Added <use_wisdom> and
	  <binary_output> flags to file.

2003-07-07 06:02  paultcochrane

	* trunk/xmds-devel/examples/atomlaser.xmds: Made minor changes to
	  formatting of file.

2003-07-07 06:01  paultcochrane

	* trunk/xmds-devel/source/xmdssimulation.cc: Added code to look for
	  <use_wisdom> tag in .xmds file, and implement if necessary.

2003-07-07 05:59  paultcochrane

	* trunk/xmds-devel/source/xmdssequence.cc: Updated
	  writePlanCreationCalls() call so that includes new arguments due
	  to inclusion of wisdom

2003-07-07 05:57  paultcochrane

	* trunk/xmds-devel/source/xmdsoutput.cc: Changed
	  writePlanCreationCalls() to allow for wisdom implementation

2003-07-07 05:56  paultcochrane

	* trunk/xmds-devel/source/xmdsfield.cc: Implemented the use of
	  wisdom via the <use_wisdom> tag. xmds simulation binary now
	  outputs more progress information: when building forward and
	  backward plans for fftw; when importing wisdom; when exporting
	  wisdom; when using current directory instead of ~/.xmds/wisdom
	  for .wisdom files. Simulation binary now checks for the existence
	  of ~/.xmds/wisdom directory for storage of .wisdom files.

2003-07-07 05:52  paultcochrane

	* trunk/xmds-devel/source/xmdsclasses.h: Changed
	  simulationParametersStruct to include useWisdom boolean. Updated
	  writePlanCreationCalls to include useWisdom in function call.

2003-07-07 05:49  paultcochrane

	* trunk/xmds-devel/configure.in: Added checking for icc. Removed
	  superfluous AC_SUBST calls. Fixed some issues with building and
	  running xmds on machines with icc, the only problem being that
	  configure script is now becoming a bit ugly.

2003-07-03 04:15  paultcochrane

	* trunk/xmds-devel/source/xmlparser.cc,
	  trunk/xmds-devel/source/xmlparser.h: Fixed xml parsing so
	  compiles and works on LinuxPPC. Problem was to do with different
	  implementations of char for different compilers. Basically, the
	  PPC gcc was setting some comparisons to always true or always
	  false, because the char data type was really unsigned char. What
	  was actually desired (and I believe used by Linux_x86 gcc) was
	  signed char, but this only affected a few cases. XML files are
	  now parsed properly and produce correct output (although there
	  are subtle differences in numerical output at the e-12 level
	  between LinuxPPC and LinuxI386, and I haven't checked that in
	  depth as yet).

2003-07-03 04:11  paultcochrane

	* trunk/xmds-devel/source/Makefile.am: Initial import to repository

2003-07-01 08:56  paultcochrane

	* trunk/xmds-devel/AUTHORS, trunk/xmds-devel/COPYING,
	  trunk/xmds-devel/INSTALL, trunk/xmds-devel/Makefile.am,
	  trunk/xmds-devel/NEWS, trunk/xmds-devel/README,
	  trunk/xmds-devel/configure.in, trunk/xmds-devel/install-sh,
	  trunk/xmds-devel/ltmain.sh, trunk/xmds-devel/missing,
	  trunk/xmds-devel/mkinstalldirs: Added initial version to
	  repository

2003-07-01 08:55  paultcochrane

	* trunk/xmds-devel/source/main.cc,
	  trunk/xmds-devel/source/xsil2graphics.cc: Minor alterations to
	  standardise the naming conventions (e.g. VER is now VERSION)

2003-06-25 02:30  joehope

	* trunk/xmds-devel/source/xmdssequence.cc,
	  trunk/xmds-devel/source/xmdssimulation.cc: Making (MPI) size a
	  global variable. Good for debugging.

2003-06-03 02:30  joehope

	* trunk/xmds-devel/source/xmdsintegrate.cc: Fixing case sensitive
	  TRUE and FALSE

2003-05-31 08:21  joehope

	* trunk/xmds-devel/source/xmdsclasses.h,
	  trunk/xmds-devel/source/xmdsintegrate.cc,
	  trunk/xmds-devel/source/xmdsintegratesiip.cc: Added <functions>
	  element in <integrate>. Places code before the integration loop.
	  This is good for time dependent functions.

2003-05-31 05:53  joehope

	* trunk/xmds-devel/source/xmdsfield.cc,
	  trunk/xmds-devel/source/xmdsmomentgroup.cc,
	  trunk/xmds-devel/source/xmdssequence.cc: Fixing two bugs for 0D
	  systems with post-propagation output in fourier space.
	  Allowing FFTWPLANS all the time, and fixing a verbose range
	  check.

2003-04-17 06:22  joehope

	* trunk/xmds-devel/source/xmdsmomentgroup.cc: Fix range on if
	  statement for x-space moment group with a cross-section in
	  the first transverse dimension (deterministic MPI only)

2003-04-17 04:52  joehope

	* trunk/xmds-devel/source/xmdssequence.cc,
	  trunk/xmds-devel/source/xmdssimulation.cc: Made rank a global
	  variable. Good for debugging.

2003-04-17 01:55  joehope

	* trunk/xmds-devel/source/xmdsmomentgroup.cc: Fixed pointer
	  initialisation in moment groups for a deterministic MPI
	  simulation with a cross section in normal space for the first
	  transverse
	  dimension.

2003-04-16 07:05  joehope

	* trunk/xmds-devel/source/xmdsvector.cc: Fixed a compiler warning
	  in renormalisation for deterministic MPI.

2003-04-16 05:43  joehope

	* trunk/xmds-devel/source/xmdsintegraterk4.cc,
	  trunk/xmds-devel/source/xmdsvector.cc: Two range fixes for
	  deterministic MPI.

2003-04-16 02:49  joehope

	* trunk/xmds-devel/source/xmdscomplex.h: Made the promotion of
	  complex to fftw_complex non-explicit.
	  Less warnings, and it should be safe.

2003-04-16 02:46  joehope

	* trunk/xmds-devel/source/xmdscomplex.h: Fixed three errors in the
	  algebra for the complex overload operators.
	  Specifically: - (z), z*=double and z/=double were all broken!

2003-04-04 00:23  joehope

	* trunk/xmds-devel/examples/highdim.xmds: Making highdim.xmds an
	  MPI-enabled script with fewer outputs.

2003-04-04 00:22  joehope

	* trunk/xmds-devel/examples/gaugeatomlaser.xmds: Reverted
	  stochastic Fourier-space output to local-in-x form.

2003-04-04 00:01  joehope

	* trunk/xmds-devel/examples/ndparamp.xmds: Pre-version 1.0 cruft
	  removal from examples

2003-03-28 03:03  joehope

	* trunk/xmds-devel/source/xmdsvector.cc: Extra print variable cruft
	  removed

2003-03-27 07:43  joehope

	* trunk/xmds-devel/examples/highdim.xmds,
	  trunk/xmds-devel/source/xmdssequence.cc: Nested subsequences now
	  call their initialisation functions.

2003-03-27 07:29  joehope

	* trunk/xmds-devel/examples/highdim.xmds,
	  trunk/xmds-devel/source/xmdsvector.cc: Mixed space transforms
	  added for deterministic MPI.

2003-03-27 02:45  joehope

	* trunk/xmds-devel/source/xmdsfield.cc,
	  trunk/xmds-devel/source/xmdsmomentgroup.cc,
	  trunk/xmds-devel/source/xmdsvector.cc: Put TRUE and FALSE into
	  lowercase. Needed for linux (for icc, at least).

2003-03-26 06:07  joehope

	* trunk/xmds-devel/examples/highdim.xmds,
	  trunk/xmds-devel/source/xmdsintegrate.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4ex.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4ip.cc,
	  trunk/xmds-devel/source/xmdsintegratesiex.cc,
	  trunk/xmds-devel/source/xmdsintegratesiip.cc: Passed cycle number
	  right through to the integrate loops

2003-03-26 05:37  joehope

	* trunk/xmds-devel/examples/highdim.xmds,
	  trunk/xmds-devel/source/xmdsmomentgroup.cc: Deterministic MPI
	  nows works with all moment groups. Mixed space transforms still
	  broken.

2003-03-25 04:26  joehope

	* trunk/xmds-devel/source/xmdsfield.cc,
	  trunk/xmds-devel/source/xmdsfilter.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4.cc,
	  trunk/xmds-devel/source/xmdsintegratesiex.cc,
	  trunk/xmds-devel/source/xmdsintegratesiip.cc,
	  trunk/xmds-devel/source/xmdsmomentgroup.cc,
	  trunk/xmds-devel/source/xmdssequence.cc: Fixed cycles. Made all
	  segments have access to the cycle number.
	  Partial implementation of k-space output groups for deterministic
	  MPI.

2003-03-24 23:38  joehope

	* trunk/xmds-devel/examples/atomlaser.xmds,
	  trunk/xmds-devel/examples/kubo.xmds,
	  trunk/xmds-devel/source/xmdsclasses.h,
	  trunk/xmds-devel/source/xsil2graphics.cc: Fixed xsil2graphics bug
	  708629. Added MPI changes to class definitions.

2003-03-24 09:13  joehope

	* trunk/xmds-devel/source/main.cc,
	  trunk/xmds-devel/source/xmdsfield.cc,
	  trunk/xmds-devel/source/xmdsintegrate.cc,
	  trunk/xmds-devel/source/xmdsintegrateex.cc,
	  trunk/xmds-devel/source/xmdsintegrateip.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4ex.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4ip.cc,
	  trunk/xmds-devel/source/xmdsintegratesiex.cc,
	  trunk/xmds-devel/source/xmdsintegratesiip.cc,
	  trunk/xmds-devel/source/xmdsmomentgroup.cc,
	  trunk/xmds-devel/source/xmdssequence.cc,
	  trunk/xmds-devel/source/xmdssimulation.cc,
	  trunk/xmds-devel/source/xmdsvector.cc: Reversion to local-in-x
	  tag with addition of the ability to use MPI on
	  deterministic problems with >1 transverse dimensions. k-space
	  moment groups
	  and mixed space transforms currently broken. Simply compile with
	  <use_mpi>
	  element as for stochastic problems.

2003-03-12 23:25  joehope

	* trunk/xmds-devel/source/xmdsintegraterk4.cc,
	  trunk/xmds-devel/source/xmdsintegratesiex.cc,
	  trunk/xmds-devel/source/xmdsintegratesiip.cc: Memory reordering
	  now complete. Cross-propagation should now be fully operational.

2003-03-11 06:23  joehope

	* trunk/xmds-devel/examples/fullpos3D.xmds,
	  trunk/xmds-devel/examples/gaugeatomlaser.xmds,
	  trunk/xmds-devel/source/xmdsfield.cc,
	  trunk/xmds-devel/source/xmdsintegrate.cc,
	  trunk/xmds-devel/source/xmdsintegrateex.cc,
	  trunk/xmds-devel/source/xmdsintegrateip.cc,
	  trunk/xmds-devel/source/xmdsintegratesiip.cc,
	  trunk/xmds-devel/source/xmdsmomentgroup.cc,
	  trunk/xmds-devel/source/xmdsvector.cc: Reordered all the fields
	  so that they are contiguous in memory when running
	  through the FFTs rather than when going through x-space loops.
	  This is in
	  preparation for parallelisation. x-space heavy algorithms are
	  slower and
	  k-space heavy algorithms are faster. I have tested all the
	  algorithms on
	  gaugeatomlaser.xmds, and they all work identically to the stable
	  branch.
	  Cross-propagation is definitely broken - but fixable with effort.
	  Mixed transforms should still work, but I haven't tested them on
	  anything.
	  Input files must now be reordered - components are now the
	  slowest changing
	  index rather than the fastest.

2003-03-10 03:55  joehope

	* trunk/xmds-devel/examples/atomlaser.xmds,
	  trunk/xmds-devel/examples/gaugeatomlaser.xmds: Updating the
	  examples to make a tagged version. I want to have a
	  "pre-reordering" version, as I'm about to rearrange the memory
	  management of the main fields.

2003-03-04 02:35  joehope

	* trunk/xmds-devel/source/xmdsintegrateex.cc: Fixed missing segment
	  name in xmdsintegrateex.cc (from previous speedup patch)

2003-03-03 03:58  joehope

	* trunk/xmds-devel/examples/atomlaser.xmds,
	  trunk/xmds-devel/examples/gaugeatomlaser.xmds,
	  trunk/xmds-devel/source/xmdsintegrateex.cc,
	  trunk/xmds-devel/source/xmdsintegrateip.cc: Replaced various
	  operations in the K_operater routines with index pointers.
	  Provided detectable speedup.
	  Modified Files:
	  source/xmdsintegrateex.cc source/xmdsintegrateip.cc

2003-02-23 23:53  joehope

	* trunk/xmds-devel/examples/fullpos3D.xmds,
	  trunk/xmds-devel/source/main.cc,
	  trunk/xmds-devel/source/xmdsclasses.h,
	  trunk/xmds-devel/source/xmdssequence.cc,
	  trunk/xmds-devel/source/xmdssimulation.cc,
	  trunk/xmds-devel/source/xmdsvector.cc: Added partial support for
	  threading. Placement of a <threads>15</threads> element
	  in the simulation element will make the FFT use 15 threads.
	  Further threading to
	  follow. Default, and <threads>1</threads> is equivalent to the
	  non-threaded code.
	  
	  Note that fftw must be compiled with the --enable-threads option.
	  
	  Modified Files:
	  Configure examples/fullpos3D.xmds
	  source/main.cc source/xmdsclasses.h source/xmdssequence.cc
	  source/xmdssimulation.cc source/xmdsvector.cc

2003-02-03 04:42  joehope

	* trunk/xmds-devel/source/kissdom.cc,
	  trunk/xmds-devel/source/xmdsfield.cc,
	  trunk/xmds-devel/source/xmdsintegrate.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4.cc,
	  trunk/xmds-devel/source/xmdsintegratesiex.cc,
	  trunk/xmds-devel/source/xmdsintegratesiip.cc,
	  trunk/xmds-devel/source/xmdsmomentgroup.cc,
	  trunk/xmds-devel/source/xmdsvector.cc,
	  trunk/xmds-devel/source/xmdsvectorelement.cc,
	  trunk/xmds-devel/source/xmlbasics.cc: Makefile has different
	  options for different systems (different option order required)
	  
	  Stack no longer used for main fields (Simon)
	  
	  logical and rather than bitwise and (Simon)
	  
	  Details in changes.log

2003-02-03 01:23  joehope

	* trunk/xmds-devel, trunk/xmds-devel/examples,
	  trunk/xmds-devel/examples/atomlaser.xmds,
	  trunk/xmds-devel/examples/fibre.xmds,
	  trunk/xmds-devel/examples/fullpos3D.xmds,
	  trunk/xmds-devel/examples/gaugeatomlaser.xmds,
	  trunk/xmds-devel/examples/kubo.xmds,
	  trunk/xmds-devel/examples/ndparamp.xmds,
	  trunk/xmds-devel/examples/nlse.xmds,
	  trunk/xmds-devel/examples/sine.xmds,
	  trunk/xmds-devel/examples/soliton.xmds,
	  trunk/xmds-devel/examples/tla.xmds, trunk/xmds-devel/source,
	  trunk/xmds-devel/source/dom3.h,
	  trunk/xmds-devel/source/kissdom.cc,
	  trunk/xmds-devel/source/kissdom.h,
	  trunk/xmds-devel/source/main.cc,
	  trunk/xmds-devel/source/xmdsclasses.h,
	  trunk/xmds-devel/source/xmdscomplex.h,
	  trunk/xmds-devel/source/xmdselement.cc,
	  trunk/xmds-devel/source/xmdsfield.cc,
	  trunk/xmds-devel/source/xmdsfilter.cc,
	  trunk/xmds-devel/source/xmdsglobals.cc,
	  trunk/xmds-devel/source/xmdsintegrate.cc,
	  trunk/xmds-devel/source/xmdsintegrateex.cc,
	  trunk/xmds-devel/source/xmdsintegrateip.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4ex.cc,
	  trunk/xmds-devel/source/xmdsintegraterk4ip.cc,
	  trunk/xmds-devel/source/xmdsintegratesi.cc,
	  trunk/xmds-devel/source/xmdsintegratesiex.cc,
	  trunk/xmds-devel/source/xmdsintegratesiip.cc,
	  trunk/xmds-devel/source/xmdsmomentgroup.cc,
	  trunk/xmds-devel/source/xmdsoutput.cc,
	  trunk/xmds-devel/source/xmdssegment.cc,
	  trunk/xmds-devel/source/xmdssequence.cc,
	  trunk/xmds-devel/source/xmdssimulation.cc,
	  trunk/xmds-devel/source/xmdsutils.cc,
	  trunk/xmds-devel/source/xmdsutils.h,
	  trunk/xmds-devel/source/xmdsvector.cc,
	  trunk/xmds-devel/source/xmdsvectorelement.cc,
	  trunk/xmds-devel/source/xmlbasics.cc,
	  trunk/xmds-devel/source/xmlbasics.h,
	  trunk/xmds-devel/source/xmlparser.cc,
	  trunk/xmds-devel/source/xmlparser.h,
	  trunk/xmds-devel/source/xsil2graphics.cc,
	  trunk/xmds-devel/source/xsilfield.cc,
	  trunk/xmds-devel/source/xsilfield.h: Initial revision