2005-10-27 10:58  joehope

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

2005-10-26 13:46  joehope

	* ChangeLog, README, README.Windows, configure.in,
	  examples/kubo.xmds, source/main.cc, source/xmdssequence.cc,
	  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.

2005-10-25 08:40  joehope

	* source/xmdssequence.cc: Fix for new timer.

2005-10-24 14:11  joehope

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

2005-10-19 09:33  joehope

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

2005-10-13 10:45  joehope

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

2005-10-12 14:34  joehope

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

2005-09-29 15:35  joehope

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

2005-08-12 15:46  sebwuester

	* examples/sech_soliton.xmds, source/xmdsclasses.h,
	  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 16:57  joehope

	* 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 20:13  joehope

	* ChangeLog, MANIFEST: Updating Changelog and MANIFEST prior to
	  release

2005-07-05 19:37  joehope

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

2005-06-30 17:44  sebwuester

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

2005-05-25 13:33  paultcochrane

	* examples/highdim.xmds: Fixed xml header.

2005-05-24 13:54  paultcochrane

	* 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 15:46  paultcochrane

	* 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 13:50  joehope

	* ChangeLog: Update of ChangeLog

2005-05-19 13:42  joehope

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

2005-05-17 16:01  sebwuester

	* source/: xmdsintegrateark45.cc, 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 13:40  paultcochrane

	* 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 11:23  paultcochrane

	* 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 19:34  paultcochrane

	* 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 15:42  sebwuester

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

2005-05-02 12:35  sebwuester

	* examples/sech_soliton.xmds, examples/sech_soliton_tdepk.xmds,
	  source/xmdsclasses.h, source/xmdsintegrate.cc,
	  source/xmdsintegrateark45.cc, source/xmdsintegrateark45ex.cc,
	  source/xmdsintegrateark45ip.cc, source/xmdsintegrateip.cc,
	  source/xmdsintegraterk4ip.cc, 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 15:21  joehope

	* source/loadxsil.m: Fix for loadxsil loading of 64 bit binaries

2005-04-27 15:44  joehope

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

2005-04-24 14:31  joehope

	* source/xsilfield.h: Final commit for previous fix.

2005-04-21 16:32  joehope

	* configure.in, source/xmdsmomentgroup.cc, 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 17:25  joehope

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

2005-04-12 15:44  joehope

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

2005-04-06 16:41  paultcochrane

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

2005-04-06 15:54  joehope

	* examples/: branch.xmds, brusselator.xmds, catcycle.xmds,
	  chain.xmds, chemkin.xmds, duffing.xmds, fibre.xmds,
	  fisher_reaction_diffusion.xmds, highdim.xmds, hires.xmds,
	  krebs.xmds, lane_emden.xmds, lorenz.xmds, lotka_volterra.xmds,
	  oregonator.xmds, pendulum.xmds, ring_modulator.xmds, sine.xmds,
	  soliton.xmds, thermkin.xmds, 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 12:22  joehope

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

2005-04-06 11:43  joehope

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

2005-04-06 09:23  joehope

	* ChangeLog, configure.in: Version bump

2005-04-05 17:23  joehope

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

2005-04-05 15:32  joehope

	* examples/diffusion.xmds: Fixed sampling in example.

2004-12-06 15:58  paultcochrane

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

2004-12-06 15:42  paultcochrane

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

2004-11-18 10:35  joehope

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

2004-11-17 15:54  joehope

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

2004-11-03 09:51  joehope

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

2004-11-03 09:48  joehope

	* ChangeLog: New ChangeLog for the new version

2004-11-03 09:47  joehope

	* MANIFEST: New manifest for the new version.

2004-11-03 09:43  joehope

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

2004-10-25 16:02  joehope

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

2004-10-22 18:04  paultcochrane

	* 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 11:16  paultcochrane

	* 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 20:01  paultcochrane

	* 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 20:00  paultcochrane

	* 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 19:51  paultcochrane

	* source/: xsilfield.cc, xsilfield.h: xsilfield.cc

2004-10-21 19:51  paultcochrane

	* 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 19:50  paultcochrane

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

2004-10-21 19:49  paultcochrane

	* 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 19:48  paultcochrane

	* 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 19:42  paultcochrane

	* source/xmdsfilter.cc: Added a Doxygen docstring.

2004-10-21 19:41  paultcochrane

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

2004-10-21 19:40  paultcochrane

	* 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 19:39  paultcochrane

	* 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 19:37  paultcochrane

	* source/: getopt_xmds1.c, getopt_xmds_init.c: Added some Doxygen
	  docstrings.

2004-10-21 19:36  paultcochrane

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

2004-10-21 19:34  paultcochrane

	* configure.in: Updated version number to interim release number.

2004-10-15 17:53  joehope

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

2004-10-11 14:06  joehope

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

2004-10-06 17:52  joehope

	* source/: xmdsfilter.cc, xmdsintegrate.cc, xmdsintegraterk4.cc,
	  xmdsintegratesiex.cc, xmdsintegratesiip.cc, xmdsmomentgroup.cc,
	  xmdssequence.cc, 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 17:50  joehope

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

2004-09-30 13:27  paultcochrane

	* 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 13:29  paultcochrane

	* Makefile.am: Fixed typo in orgeonator name.

2004-09-15 16:01  joehope

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

2004-09-15 14:46  joehope

	* source/: xmdsclasses.h, xmdsfilter.cc, xmdsintegrate.cc,
	  xmdsintegraterk4.cc, xmdsintegratesiex.cc, 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 14:27  joehope

	* ChangeLog: Updated with cvs2cl.pl

2004-08-03 15:29  paultcochrane

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

2004-08-02 20:04  paultcochrane

	* 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 20:01  paultcochrane

	* source/: xmdsfilter.cc, xmdsintegrate.cc, 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 19:59  paultcochrane

	* source/xmdsclasses.h: Changed longs to long unsigned ints.

2004-08-02 19:57  paultcochrane

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

2004-08-02 18:48  paultcochrane

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

2004-08-02 18:47  paultcochrane

	* 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 18:45  paultcochrane

	* 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 18:16  paultcochrane

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

2004-08-02 18:10  paultcochrane

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

2004-08-02 18:04  paultcochrane

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

2004-08-02 18:02  paultcochrane

	* 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 17:43  joehope

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

2004-07-30 16:56  joehope

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

2004-07-30 16:02  joehope

	* source/: xmdsfield.cc, 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 18:28  joehope

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

2004-07-29 18:27  joehope

	* source/: xmdsclasses.h, xmdsfilter.cc, xmdsintegrate.cc,
	  xmdsintegratesiip.cc, xmdssequence.cc, 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 17:33  paultcochrane

	* 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 17:31  paultcochrane

	* 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 16:45  paultcochrane

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

2004-07-23 17:27  joehope

	* 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 15:45  joehope

	* 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 13:59  paultcochrane

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

2004-07-19 13:57  paultcochrane

	* MANIFEST: Updated manifest to xmds-1.3-5.

2004-07-19 13:56  paultcochrane

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

2004-07-19 13:53  paultcochrane

	* ChangeLog: Updated with cvs2cl.pl

2004-07-19 13:52  paultcochrane

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

2004-07-19 13:43  paultcochrane

	* ChangeLog: Updated with cvs2cl.pl

2004-07-19 13:42  paultcochrane

	* 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 13:40  paultcochrane

	* 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 14:02  paultcochrane

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

2004-07-16 13:46  paultcochrane

	* 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 13:25  paultcochrane

	* 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 13:20  paultcochrane

	* ChangeLog: Updated to current output of cvs2cl.pl.

2004-07-16 13:19  paultcochrane

	* 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 13:16  paultcochrane

	* ChangeLog: Updated to current output of cvs2cl.pl.

2004-07-16 13:12  paultcochrane

	* 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 11:27  paultcochrane

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

2004-07-15 17:27  joehope

	* 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 21:48  paultcochrane

	* source/: main.cc, 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 16:36  joehope

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

2004-07-14 14:27  joehope

	* source/: xmdssequence.cc, 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 11:32  joehope

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

2004-07-13 18:46  paultcochrane

	* 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 17:52  paultcochrane

	* 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 17:25  paultcochrane

	* 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 17:24  paultcochrane

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

2004-07-13 16:16  paultcochrane

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

2004-07-13 15:29  paultcochrane

	* source/: kissdom.cc, main.cc, xmdsarg.cc, xmdsargelement.cc,
	  xmdsargv.cc, xmdsbreakpoint.cc, xmdselement.cc, xmdsfield.cc,
	  xmdsfilter.cc, xmdsglobals.cc, xmdsintegrate.cc,
	  xmdsintegrateex.cc, xmdsintegrateip.cc, xmdsintegraterk4.cc,
	  xmdsintegraterk4ex.cc, xmdsintegraterk4ip.cc, xmdsintegratesi.cc,
	  xmdsintegratesiex.cc, xmdsintegratesiip.cc, xmdsmomentgroup.cc,
	  xmdsoutput.cc, xmdssegment.cc, xmdssequence.cc,
	  xmdssimulation.cc, xmdsutils.cc, xmdsvector.cc,
	  xmdsvectorelement.cc, xmlbasics.cc, xmlparser.cc,
	  xsil2graphics.cc, 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 16:47  joehope

	* source/xmdsfield.cc: cstr()  should be c_str()

2004-07-09 16:35  joehope

	* 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 15:29  joehope

	* source/xmdsvectorelement.cc: Forcing abort when input file is
	  misread.

2004-07-01 15:24  paultcochrane

	* source/: kissdom.cc, 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 20:23  paultcochrane

	* 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 20:22  paultcochrane

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

2004-06-30 20:20  paultcochrane

	* 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 20:18  paultcochrane

	* 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 20:15  paultcochrane

	* 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 20:14  paultcochrane

	* 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 17:26  paultcochrane

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

2004-06-30 17:20  paultcochrane

	* source/xmdssimulation.cc: Removed some whitespace.

2004-06-30 17:19  paultcochrane

	* 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 17:15  paultcochrane

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

2004-06-30 17:14  paultcochrane

	* 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 17:21  joehope

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

2004-06-29 17:13  joehope

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

2004-06-26 15:29  paultcochrane

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

2004-06-25 15:28  joehope

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

2004-06-24 18:12  joehope

	* source/: getopt.h, getopt1.c, getopt_init.c, getopt_xmds.c,
	  getopt_xmds.h, getopt_xmds1.c, main.cc, xmdssequence.cc,
	  xsil2graphics.cc: Changing names of extern variables in getopt
	  functions.  Removes further conflicts.

2004-06-24 17:19  joehope

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

2004-06-24 16:42  joehope

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

2004-06-23 18:21  paultcochrane

	* 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 20:44  paultcochrane

	* Makefile.am: Added new examples to be added at make dist time.

2004-06-22 20:18  paultcochrane

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

2004-06-22 20:18  paultcochrane

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

2004-06-22 20:17  paultcochrane

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

2004-06-22 20:16  paultcochrane

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

2004-06-22 20:16  paultcochrane

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

2004-06-21 19:28  paultcochrane

	* 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.

2004-06-21 09:48  paultcochrane

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

2004-06-18 16:51  paultcochrane

	* 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 16:28  paultcochrane

	* 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 16:25  paultcochrane

	* 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 16:09  paultcochrane

	* 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 16:08  paultcochrane

	* 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 11:58  paultcochrane

	* 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 11:31  paultcochrane

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

2004-06-18 11:26  paultcochrane

	* 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 17:18  paultcochrane

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

2004-06-17 16:00  paultcochrane

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

2004-06-17 15:45  paultcochrane

	* 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 13:49  paultcochrane

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

2004-06-16 12:04  paultcochrane

	* 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 12:02  paultcochrane

	* 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 22:22  paultcochrane

	* 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 22:19  paultcochrane

	* 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 19:18  paultcochrane

	* 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 19:08  paultcochrane

	* 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 19:06  paultcochrane

	* 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 19:05  paultcochrane

	* 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 16:46  paultcochrane

	* 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 11:30  paultcochrane

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

2004-06-15 11:28  paultcochrane

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

2004-06-15 11:16  paultcochrane

	* 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 20:22  paultcochrane

	* 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 20:21  paultcochrane

	* 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 20:07  paultcochrane

	* 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 16:41  paultcochrane

	* 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 16:40  paultcochrane

	* 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 16:39  paultcochrane

	* 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 16:37  paultcochrane

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

2004-06-14 16:37  paultcochrane

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

2004-06-14 16:36  paultcochrane

	* 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 16:32  paultcochrane

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

2004-06-14 15:57  paultcochrane

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

2004-06-12 19:42  paultcochrane

	* 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 19:41  paultcochrane

	* 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 15:40  paultcochrane

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

2004-06-04 13:35  paultcochrane

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

2004-06-04 13:33  paultcochrane

	* 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 16:01  paultcochrane

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

2004-05-31 14:08  paultcochrane

	* 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 13:26  paultcochrane

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

2004-05-31 13:15  paultcochrane

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

2004-05-19 20:07  paultcochrane

	* 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 20:25  paultcochrane

	* 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 20:22  paultcochrane

	* 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 20:19  paultcochrane

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

2004-05-18 20:18  paultcochrane

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

2004-05-18 20:02  paultcochrane

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

2004-05-18 17:46  paultcochrane

	* 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 17:42  paultcochrane

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

2004-05-12 16:18  paultcochrane

	* MANIFEST: Updated manifest to current release version (1.3-2).

2004-05-12 16:16  paultcochrane

	* NEWS: Updated to current version of xmds, ready for release

2004-05-12 16:11  paultcochrane

	* ChangeLog: Trivial change

2004-05-12 16:08  paultcochrane

	* ChangeLog: Added changes to xmds since last release

2004-05-12 15:31  paultcochrane

	* 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 13:22  paultcochrane

	* source/: kissdom.cc, kissdom.h, xmdsarg.cc, xmdsargelement.cc,
	  xmdsbreakpoint.cc, xmdsclasses.h, xmdselement.cc, xmdsfield.cc,
	  xmdsfilter.cc, xmdsglobals.cc, xmdsintegrate.cc,
	  xmdsintegrateex.cc, xmdsintegrateip.cc, xmdsintegraterk4.cc,
	  xmdsintegraterk4ex.cc, xmdsintegraterk4ip.cc, xmdsintegratesi.cc,
	  xmdsintegratesiex.cc, xmdsintegratesiip.cc, xmdsmomentgroup.cc,
	  xmdsoutput.cc, xmdssegment.cc, xmdssequence.cc,
	  xmdssimulation.cc, xmdsutils.cc, xmdsutils.h, xmdsvector.cc,
	  xmdsvectorelement.cc, xmlbasics.cc, xmlbasics.h, xmlparser.cc,
	  xmlparser.h, xsil2graphics.cc, xsilfield.cc, 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 13:19  paultcochrane

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

2004-04-28 15:31  paultcochrane

	* 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 15:12  paultcochrane

	* 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 11:04  paultcochrane

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

2004-04-28 10:58  paultcochrane

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

2004-04-28 10:56  paultcochrane

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

2004-04-28 10:43  paultcochrane

	* configure.in: Added copyright statement.

2004-04-28 10:28  paultcochrane

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

2004-04-28 10:01  paultcochrane

	* 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.

2004-04-28 09:56  paultcochrane

	* source/: kissdom.cc, main.cc, xmdsarg.cc, xmdsargelement.cc,
	  xmdsargv.cc, xmdsbreakpoint.cc, xmdselement.cc, xmdsfield.cc,
	  xmdsfilter.cc, xmdsglobals.cc, xmdsintegrate.cc,
	  xmdsintegrateex.cc, xmdsintegrateip.cc, xmdsintegraterk4.cc,
	  xmdsintegraterk4ex.cc, xmdsintegraterk4ip.cc, xmdsintegratesi.cc,
	  xmdsintegratesiex.cc, xmdsintegratesiip.cc, xmdsmomentgroup.cc,
	  xmdsoutput.cc, xmdssegment.cc, xmdssequence.cc,
	  xmdssimulation.cc, xmdsutils.cc, getopt.c, getopt1.c,
	  getopt_init.c, xmdsvector.cc, xmdsvectorelement.cc, xmlbasics.cc,
	  xmlparser.cc, xsil2graphics.cc, xsilfield.cc: Added an @file
	  command so that doxygen finds and documents the stuff in the file

2004-04-28 09:55  paultcochrane

	* 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 13:51  paultcochrane

	* 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 13:44  paultcochrane

	* 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 19:22  paultcochrane

	* configure.in: Updated version and release numbers

2004-04-19 19:14  paultcochrane

	* source/: xmdsmomentgroup.cc, xmdsoutput.cc, 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 18:59  paultcochrane

	* 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 18:51  paultcochrane

	* 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 18:48  paultcochrane

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

2004-04-19 18:40  paultcochrane

	* 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 18:37  paultcochrane

	* 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 18:32  paultcochrane

	* 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 18:31  paultcochrane

	* 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 18:28  paultcochrane

	* depcomp, ltmain.sh: Updated.

2004-04-06 21:10  paultcochrane

	* 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 21:09  paultcochrane

	* 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 20:45  paultcochrane

	* 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 20:40  paultcochrane

	* benchmark/: runbenchmarks: Added cpu information to master data
	  hash table

2004-04-06 20:29  paultcochrane

	* 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 18:26  paultcochrane

	* benchmark/runbenchmarks: Added some comments and removed some
	  superfluous code.

2004-04-06 18:20  paultcochrane

	* 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 17:51  paultcochrane

	* 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 16:58  paultcochrane

	* benchmark/bench: Implemented shorter version of previous code
	  using timeit instead of the Benchmark objects

2004-04-06 16:53  paultcochrane

	* 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 16:52  paultcochrane

	* benchmark/: nlse_100.xmds, nlse_1000.xmds, nlse_10000.xmds,
	  nlse_500.xmds, nlse_5000.xmds: Initial import to repository.
	  This is the nonlinear Schroedinger equation simulation for
	  various lattice sizes.

2004-04-06 16:51  paultcochrane

	* benchmark/: ndparamp_100.xmds, ndparamp_200.xmds,
	  ndparamp_50.xmds, ndparamp_500.xmds: Initial import to
	  repository.  This is the N-dimensional parametric oscillator
	  simulation for various lattice sizes.

2004-04-06 16:50  paultcochrane

	* 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 16:49  paultcochrane

	* benchmark/: fullpos3D_16.xmds, fullpos3D_32.xmds,
	  fullpos3D_64.xmds: Initial import to repository.  This is the
	  fullpos3D simulation for various lattice sizes.

2004-04-06 16:45  paultcochrane

	* 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 21:14  paultcochrane

	* 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 21:12  paultcochrane

	* 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 16:06  paultcochrane

	* source/loadxsil.m: Added copyright statement.

2004-03-05 16:05  paultcochrane

	* source/Doxyfile: Updated file to current version of Doxygen (some
	  stuff was obsolete etc).

2004-03-05 16:04  paultcochrane

	* 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.

2004-02-02 18:25  paultcochrane

	* frontend/tkxmds.pl: Moved file from xmds-devel/frontend to own
	  module tkxmds.

2004-02-02 18:24  paultcochrane

	* frontend/tkxmds.pl: Added more functionality in terms of open
	  file method and save file as etc.  Have look to menus very
	  similar to the xmdseditor of Doug Turk.  Also have many of
	  frontend features looking the same as the xmdseditor.  Added pod
	  documentation, but this needs to be added to.  Much work needed
	  on getting the backend working so that can actually edit, create
	  and run xmds scripts.

2004-02-02 18:21  paultcochrane

	* frontend/tkxmds: Removed.  This is a symlink, so doesn't really
	  need to be in repository, and probably shouldn't be there anyway.

2004-02-02 18:20  paultcochrane

	* frontend/tkxmds: Updated.  Silly thing to say really, since is
	  really just a simlink to tkxmds.pl.

2004-02-02 18:17  paultcochrane

	* doc/latex/figures/: classes.eps, fibre2.eps, funct.eps,
	  funct.fig, kubo2.eps, ndparamp1.eps, nlse.eps, classes.fig,
	  defferential.eps, fibre1.eps, kubo1.eps, main.eps, main.fig,
	  main.py, ndparamp2.eps, tla.eps: Removing files from
	  xmds-devel/doc/latex/figures to move them into
	  xmds-doc/latex/figures.

2004-02-02 18:10  paultcochrane

	* doc/latex/: abstract.tex, bibliography.tex, fancyhdr.sty,
	  functionality.tex, lstdoc.sty, titlepage.tex, xmds_defs.tex,
	  ccaption.sty, doc.tex, languageReference.tex, lstlang1.sty,
	  numModellingTheory.tex, .latex2html-init, book.cls,
	  develAndProgStructure.tex, intro.tex, listings.cfg, listings.sty,
	  lstlang2.sty, lstlang3.sty, lstmisc.sty, lstpatch.sty, main.aap,
	  misc_defs.tex, moreExamples.tex, outlook.tex, quotchap.sty,
	  tutFromScratch.tex, tutTemplateStart.tex, workedExample.tex,
	  xmds_doc.tex, xsil.tex, xsil2graphics.tex: Removing files from
	  xmds-deve/doc/latex to move them into xmds-doc/latex.

2004-02-02 18:04  paultcochrane

	* doc/: xmds.1, xmds.pod: Moved xmds.pod and xmds.1 to new module
	  xmds-doc into the man subdirectory thereof.

2004-01-31 20:41  paultcochrane

	* doc/latex/figures/main.py: Initial import.  This file is used to
	  generate the eps file using pyscript.

2004-01-31 20:37  paultcochrane

	* doc/latex/: xmds_doc.pdf, xmds_doc.ps: Automatically generated
	  files don't need to be in the repository.  If you want to
	  generate them, use the aap recipe.

2004-01-31 20:35  paultcochrane

	* doc/latex/main.aap: Added comments for people who may not have
	  aap to run the recipe file.  Added the CVS Id keyword.  Added a
	  help target to print out how to use the file.

2004-01-30 15:31  paultcochrane

	* examples/: fibre.xmds, fullpos3D.xmds: Fixed spelling error.

2004-01-30 15:21  paultcochrane

	* source/xmdssimulation.cc: Fixed bug whereby attributes were
	  parsed incorrectly.

2004-01-30 14:48  paultcochrane

	* source/xmdssimulation.cc: Now reports errors in parsing <output>
	  element correctly.

2004-01-30 13:10  paultcochrane

	* testsuite/: fibre.xmds, fullpos3D.xmds, gaugeatomlaser.xmds,
	  ndparamp.xmds, nlse.xmds, 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 13:04  paultcochrane

	* testsuite/: atomlaser.xmds, fibre.xmds, fullpos3D.xmds,
	  gaugeatomlaser.xmds, kubo.xmds, ndparamp.xmds, nlse.xmds,
	  sine.xmds, soliton.xmds, 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 12:38  paultcochrane

	* testsuite/: atomlaser.xmds, fibre.xmds, fullpos3D.xmds,
	  gaugeatomlaser.xmds, kubo.xmds, ndparamp.xmds, nlse.xmds,
	  sine.xmds, soliton.xmds, tla.xmds: Added CVS Id keyword.

2004-01-30 12:34  paultcochrane

	* configure.in: Added CVS Id keyword.

2004-01-30 12:31  paultcochrane

	* AUTHORS, INSTALL, Makefile.am, NEWS, README, README.Windows,
	  acinclude.m4: Added CVS Id keyword.

2004-01-30 12:25  paultcochrane

	* source/loadxsil.m: Added CVS Id keyword.

2004-01-30 10:44  paultcochrane

	* doc/latex/: xmds_doc.pdf, xmds_doc.ps: Updated.

2004-01-30 10:37  paultcochrane

	* doc/latex/: abstract.tex, bibliography.tex,
	  develAndProgStructure.tex, functionality.tex, intro.tex,
	  languageReference.tex, misc_defs.tex, moreExamples.tex,
	  numModellingTheory.tex, outlook.tex, titlepage.tex,
	  tutFromScratch.tex, tutTemplateStart.tex, workedExample.tex,
	  xmds_defs.tex, xmds_doc.tex, xsil.tex, xsil2graphics.tex: Added
	  CVS Id keyword.

2004-01-30 10:29  paultcochrane

	* doc/latex/.latex2html-init: Added CVS Id keyword.

2004-01-28 15:43  paultcochrane

	* source/: Makefile.am, dom3.h, getopt.h, kissdom.h, main.cc,
	  xmdsarg.cc, xmdsclasses.h, xmdsglobals.cc, xmdsintegrate.cc,
	  xmdsintegrateex.cc, xmdsintegrateip.cc, xmdsintegraterk4.cc,
	  xmdsintegratesiex.cc, xmdssequence.cc, xmdsvectorelement.cc,
	  xmlbasics.cc, xmlbasics.h, xmlparser.h, xsilfield.h, kissdom.cc,
	  xmdsargelement.cc, xmdsargv.cc, xmdsbreakpoint.cc, xmdscomplex.h,
	  xmdselement.cc, xmdsfield.cc, xmdsfilter.cc,
	  xmdsintegraterk4ex.cc, xmdsintegraterk4ip.cc, xmdsintegratesi.cc,
	  xmdsintegratesiip.cc, xmdsmomentgroup.cc, xmdsoutput.cc,
	  xmdssegment.cc, xmdsutils.cc, xmdsutils.h, xmdsvector.cc,
	  xmlparser.cc, xsil2graphics.cc, xsilfield.cc, Doxyfile, getopt.c,
	  getopt1.c, getopt_init.c: Added CVS Id keyword.

2004-01-28 15:37  paultcochrane

	* source/xmdssimulation.cc: Still testing the CVS Id keyword
	  expansion.

2004-01-28 15:35  paultcochrane

	* source/xmdssimulation.cc: Testing adding the CVS Id keyword.

2004-01-27 18:02  paultcochrane

	* 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 18:00  paultcochrane

	* examples/: diffusion.xmds, fibre.xmds, fullpos3D.xmds,
	  gaugeatomlaser.xmds, highdim.xmds, kubo.xmds, lorenz.xmds,
	  ndparamp.xmds, nlse.xmds, pendulum.xmds, sine.xmds, soliton.xmds,
	  tla.xmds, 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 17:29  paultcochrane

	* 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 17:26  paultcochrane

	* source/Doxyfile: Changed option so that man pages are now
	  generated.

2004-01-27 16:32  paultcochrane

	* Makefile.in, aclocal.m4, configure: Deleted.

2004-01-27 16:26  paultcochrane

	* .DS_Store, changes.log, readme, source/.DS_Store,
	  source/stamp-h.in, source/stamp-h1.in, source/Makefile.in,
	  source/config.h.in: Deleted.

2004-01-27 16:13  paultcochrane

	* doc/: img24.gif, img25.gif, img26.gif, img27.gif, img28.gif,
	  img29.gif, img3.gif, img30.gif, img31.gif, img32.gif, img33.gif,
	  img34.gif, img35.gif, img36.gif, img37.gif, img38.gif, img39.gif,
	  img4.gif, img40.gif, img41.gif, img42.gif, img43.gif, img44.gif,
	  img45.gif, img46.gif, img47.gif, img48.gif, img49.gif, img5.gif,
	  img50.gif, img52.gif, img53.gif, img55.gif, img56.gif, img57.gif,
	  img58.gif, img59.gif, img6.gif, img60.gif, img61.gif, img62.gif,
	  img63.gif, img64.gif, img66.gif, img67.gif, img69.gif, img7.gif,
	  img70.gif, img71.gif, img51.gif, img54.gif, img65.gif, img68.gif,
	  img72.gif, img73.gif, img74.gif, img75.gif, img76.gif, img77.gif,
	  img78.gif, img79.gif, img8.gif, img80.gif, img81.gif, img82.gif,
	  img83.gif, img84.gif, img85.gif, img86.gif, img87.gif, img88.gif,
	  img89.gif, img9.gif, img90.gif, img91.gif, img92.gif, img93.gif,
	  img94.gif, img95.gif, img96.gif, img97.gif, img98.gif, img99.gif:
	  Deleted.

2004-01-27 16:09  paultcochrane

	* doc/: doc.css, doc.html, img1.gif, img10.gif, img100.gif,
	  img101.gif, img102.gif, img103.gif, img104.gif, img105.gif,
	  img106.gif, img107.gif, img108.gif, img109.gif, img11.gif,
	  img110.gif, img111.gif, img112.gif, img113.gif, img114.gif,
	  img115.gif, img116.gif, img117.gif, img118.gif, img119.gif,
	  img12.gif, img120.gif, img121.gif, img122.gif, img123.gif,
	  img124.gif, img125.gif, img126.gif, img127.gif, img128.gif,
	  img129.gif, img13.gif, img130.gif, img131.gif, img132.gif,
	  img133.gif, img134.gif, img135.gif, img136.gif, img137.gif,
	  img138.gif, img139.gif, img14.gif, img140.gif, img141.gif,
	  img142.gif, img143.gif, img144.gif, img145.gif, img146.gif,
	  img147.gif, img148.gif, img149.gif, img15.gif, img150.gif,
	  img151.gif, img152.gif, img153.gif, img154.gif, img155.gif,
	  img156.gif, img157.gif, img158.gif, img159.gif, img16.gif,
	  img160.gif, img161.gif, img162.gif, img163.gif, img164.gif,
	  img165.gif, img166.gif, img167.gif, img168.gif, img169.gif,
	  img17.gif, img175.gif, img178.gif, img182.gif, img185.gif,
	  img188.gif, img192.gif, img170.gif, img171.gif, img172.gif,
	  img173.gif, img174.gif, img176.gif, img177.gif, img179.gif,
	  img18.gif, img180.gif, img181.gif, img183.gif, img184.gif,
	  img186.gif, img187.gif, img189.gif, img19.gif, img190.gif,
	  img191.gif, img193.gif, img194.gif, img195.gif, img196.gif,
	  img197.gif, img198.gif, img199.gif, img2.gif, img20.gif,
	  img200.gif, img201.gif, img202.gif, img203.gif, img204.gif,
	  img205.gif, img206.gif, img207.gif, img208.gif, img209.gif,
	  img21.gif, img210.gif, img211.gif, img212.gif, img213.gif,
	  img214.gif, img22.gif, img23.gif: Deleted.

2004-01-27 16:04  paultcochrane

	* doc/xmds.1: Updated.

2004-01-27 16:03  paultcochrane

	* doc/xmds.pod: Added FILES section.

2004-01-23 17:35  paultcochrane

	* doc/xmds.1: Initial import to repository.  Automatically
	  generated man page documentation.

2004-01-23 17:33  paultcochrane

	* doc/xmds.pod: Initial import to repository.  Perl POD file to
	  generate the xmds man page.

2004-01-14 19:34  paultcochrane

	* 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 21:16  paultcochrane

	* source/xmdsutils.h: Trivial change made during code testing.

2004-01-13 21:15  paultcochrane

	* source/xmdsutils.cc: Fixed bug in getAttributeBools where the
	  string comparison was being performed incorrectly.

2004-01-13 21:14  paultcochrane

	* source/xmdsoutput.cc: Implemented parsing of enabled attribute of
	  breakpoint element correctly.

2004-01-13 21:13  paultcochrane

	* source/xmdsclasses.h: Changed some formatting.

2004-01-13 21:11  paultcochrane

	* 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 13:03  paultcochrane

	* source/xmdsutils.h: Corrected one of the documentation strings.

2004-01-13 12:28  paultcochrane

	* 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 20:10  paultcochrane

	* source/xmdsutils.h: Added the DEEP and NOT_DEEP variables to the
	  global anonymous enum.

2004-01-12 20:09  paultcochrane

	* 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 20:07  paultcochrane

	* 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 20:06  paultcochrane

	* 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 20:03  paultcochrane

	* source/Makefile.am: Added xmdsbreakpoint.cc

2004-01-08 15:34  paultcochrane

	* doc/latex/xmds_doc.tex: Moved the "starting from scratch" and
	  "using a template" chapter headings into their own files and have
	  include statements instead.

2004-01-08 15:31  paultcochrane

	* doc/latex/abstract.tex: Almost a complete rewrite.

2004-01-08 15:29  paultcochrane

	* doc/latex/tutFromScratch.tex: Extended the discussion of how to
	  build a basic simulation.  In the middle of discussing the
	  <field> tag.

2004-01-08 10:30  paultcochrane

	* doc/latex/xmds_defs.tex: Changed myhtml style to the xml language
	  (new in current version of listings package).  Added a couple of
	  keywords to morekeywords list and found that one needs a comma at
	  the start of the list so that all of the keywords are
	  highlighted.

2004-01-07 15:39  paultcochrane

	* doc/latex/xmds_defs.tex: Added the author and description
	  keywords to the myhtml style for the listings package.

2004-01-07 15:37  paultcochrane

	* doc/latex/main.aap: Made sure that latex/pdflatex are run twice
	  in building the dvi/pdf.

2004-01-07 12:44  paultcochrane

	* doc/latex/misc_defs.tex: Moved some ewcommands from
	  languageReference.tex to here.

2004-01-07 12:44  paultcochrane

	* doc/latex/languageReference.tex: Moved ewcommand and
	  ewenvironment stuff into misc_defs.tex.

2004-01-07 12:05  paultcochrane

	* doc/latex/tutTemplateStart.tex: Initial import to repository.

2004-01-07 12:01  paultcochrane

	* doc/latex/tutFromScratch.tex: Initial import to repository.

2004-01-07 11:57  paultcochrane

	* doc/latex/numModellingTheory.tex: Fixed vector subscripting
	  errors.

2004-01-07 11:57  paultcochrane

	* doc/latex/misc_defs.tex: Changed the definition of ec to be
	  mathbf{#1}

2004-01-06 19:28  paultcochrane

	* doc/latex/main.aap: Intial import to repository.

2004-01-06 19:27  paultcochrane

	* doc/latex/: xmds_doc.ps, xmds_doc.pdf: Updated to current version
	  of docs.

2004-01-06 19:21  paultcochrane

	* doc/latex/abstract.tex: Changed chapter to chapter*

2004-01-06 19:19  paultcochrane

	* doc/latex/xmds_doc.tex: Changed input's to include's

2004-01-06 19:16  paultcochrane

	* doc/latex/xmds_defs.tex: Commented out inclusion of hyperref
	  package for pdflatex: it is already loaded.

2004-01-06 17:48  paultcochrane

	* doc/latex/languageReference.tex: Removed the mention of the xmds
	  version of tags in the simulation block.  Added mention of the
	  xmds version of the argv tag.

2004-01-06 17:45  paultcochrane

	* doc/latex/functionality.tex: Minor change; joined two paragraphs
	  together.

2004-01-06 17:43  paultcochrane

	* doc/latex/.latex2html-init: Removed [math] in the HTML_VERSION,
	  specifying now IMAGE_TYPE = png, and have a better ADDRESS
	  variable set.

2004-01-06 16:54  paultcochrane

	* doc/latex/xmds_doc.tex: Split document into parts.  Added chapter
	  headings for the Tutorial part.

2004-01-06 16:52  paultcochrane

	* doc/latex/xmds_defs.tex: Added another keyword to myC++ style.
	  Made LightGrey definition lighter.

2004-01-06 16:50  paultcochrane

	* doc/latex/workedExample.tex: Converted document to work more
	  nicely in latex2html.

2004-01-06 16:45  paultcochrane

	* doc/latex/languageReference.tex: Corrected a spelling error.
	  Altered definition of xmdsOneTwo.  Converted document for better
	  processing in latex2html.

2004-01-06 16:36  paultcochrane

	* doc/latex/: listings.cfg, listings.sty, lstdoc.sty, lstlang1.sty,
	  lstlang2.sty, lstlang3.sty, lstmisc.sty, lstpatch.sty: Initial
	  import to repository.

2004-01-06 16:12  paultcochrane

	* doc/latex/.latex2html-init: Added NO_SIMPLE_MATH=1, increased
	  MAX_SPLIT_DEPTH to 4, changed the HTML_VERSION to 4.0[math]

2004-01-06 00:23  paultcochrane

	* doc/latex/xmds_defs.tex: Changed file so that can use with
	  latex2html (some conditional stuff added etc).

2004-01-05 22:32  paultcochrane

	* doc/latex/.latex2html-init: Changed to point the TMP variable to
	  /var/tmp

2004-01-05 22:24  paultcochrane

	* doc/latex/.latex2html-init: Initial import to repository.

2004-01-05 18:27  paultcochrane

	* doc/latex/workedExample.tex: Reformatted some of the code
	  examples.  And changed some :'s to $dots$.

2004-01-05 17:35  paultcochrane

	* doc/latex/book.cls: Initial import to repository.  (implements a
	  slight change to the standard book.cls which can't be
	  incorporated into .tex files (uses @'s etc))

2004-01-05 17:30  paultcochrane

	* doc/latex/functionality.tex: Updated and improved installation
	  instructions, with particular emphasis on installation from
	  tarball.

2004-01-05 16:32  paultcochrane

	* doc/latex/xmds_doc.tex: Extended the secnumdepth and tocdepth
	  counters to 4 so that have numbers all the way down to paragraph
	  in the document and in the toc.

2004-01-05 16:31  paultcochrane

	* doc/latex/languageReference.tex: Changed	extit{required} to
	  eqd.	Changed       ext{optional} to optl.  Changed
	  extsc{xmds-devel only} to $ge$ xmds-1.2 (command is xmdsOneTwo).

2003-12-30 21:38  paultcochrane

	* examples/: fibre.xmds, fullpos3D.xmds, gaugeatomlaser.xmds,
	  highdim.xmds, kubo.xmds, lorenz.xmds, ndparamp.xmds, nlse.xmds,
	  pendulum.xmds, sine.xmds, soliton.xmds, tla.xmds, vibstring.xmds:
	  Updated <name>, <author> and <description> tags where
	  appropriate.

2003-12-23 15:01  paultcochrane

	* NEWS: Updated to reflect changes in current release (1.3-1)

2003-12-23 14:57  paultcochrane

	* ChangeLog, MANIFEST, README: Updated to reflect changes in
	  current release (1.3-1)

2003-12-23 14:47  paultcochrane

	* examples/: atomlaser.xmds, diffusion.xmds, fibre.xmds,
	  fullpos3D.xmds, gaugeatomlaser.xmds, highdim.xmds, kubo.xmds,
	  lorenz.xmds, ndparamp.xmds, nlse.xmds, pendulum.xmds, sine.xmds,
	  soliton.xmds, tla.xmds, vibstring.xmds: Tidied formatting, added
	  some comments.

2003-12-23 12:15  paultcochrane

	* 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 12:13  paultcochrane

	* 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 17:56  paultcochrane

	* Makefile.am: Updated to include the README.Windows file in the
	  distribution.

2003-12-22 17:55  paultcochrane

	* README.Windows: Initial import to repository.

2003-12-22 17:01  paultcochrane

	* examples/tla.xmds: Minor formatting improvement.

2003-12-22 17:00  paultcochrane

	* examples/nlse.xmds: Added test code for output arguments.  This
	  needs to be fixed up, not a good example file really.

2003-12-22 16:59  paultcochrane

	* examples/ndparamp.xmds: Added binary output and benchmark tags.

2003-12-22 16:58  paultcochrane

	* examples/highdim.xmds: Fixed integer where float should be
	  problem.

2003-12-22 16:57  paultcochrane

	* examples/gaugeatomlaser.xmds: Renamed simulation and .xsil file
	  to reflect name of "gaugeatomlaser".

2003-12-22 16:56  paultcochrane

	* examples/fullpos3D.xmds: Some minor reformatting.

2003-12-22 16:55  paultcochrane

	* 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 16:52  paultcochrane

	* 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 16:49  paultcochrane

	* testsuite/: atomlaser_reference.xsil, ndparamp_reference.xsil,
	  nlse_reference.xsil, soliton_reference.xsil, tla_reference.xsil:
	  Updated the <simname>_reference.xsil files.

2003-12-22 16:48  paultcochrane

	* doc/latex/xsil2graphics.tex: Removed mention of xsil2matlab
	  (obviously an older version of xsil2graphics).  Also added some
	  docs showing how to actually use the xsil2graphics output in
	  matlab and scilab.  This needs expanding.

2003-12-22 16:46  paultcochrane

	* doc/latex/xmds_defs.tex: Fixed up hyperref call for generating
	  linked dvi files.

2003-12-22 16:40  paultcochrane

	* 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 15:42  paultcochrane

	* source/Doxyfile: Updated to refelect the current project number.
	  Also removed some obsolete Doxygen commands.

2003-12-22 15:39  paultcochrane

	* 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 18:17  paultcochrane

	* 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 20:35  paultcochrane

	* source/xmdsvectorelement.cc: Implemented binary input for use in
	  the <filename> tag of the <vector> element.

2003-12-17 20:33  paultcochrane

	* 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 20:31  paultcochrane

	* 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 20:29  paultcochrane

	* source/xmdsclasses.h: Minor change to the xmdsVectorElement class
	  to implement binary and ascii input files.

2003-12-17 17:18  paultcochrane

	* source/: kissdom.cc, xmdssequence.cc, xmdssimulation.cc,
	  xmdsvectorelement.cc, 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 17:17  paultcochrane

	* source/xmdsvector.cc: Fixed formatting a bit.  No real changes to
	  code.

2003-12-17 17:16  paultcochrane

	* source/xmdsoutput.cc: Tidied some fprintf statements.

2003-12-17 17:15  paultcochrane

	* source/xmdsutils.cc: Fixed some spelling errors and debugging
	  reporting information.

2003-12-17 17:13  paultcochrane

	* source/xmdsmomentgroup.cc: Tidied some fprintf statements.

2003-12-17 17:12  paultcochrane

	* 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 17:09  paultcochrane

	* source/xmdsclasses.h: Added a usePrefs variable to the
	  simulationParamtersStruct in order to implement preferences.

2003-12-17 17:08  paultcochrane

	* 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 17:03  paultcochrane

	* configure.in: Updated to show version information as 1.3-1.

2003-12-07 14:25  paultcochrane

	* ChangeLog: Added comments about current changes to xmds.

2003-12-07 14:24  paultcochrane

	* configure.in: Altered release number to current release: 1.2-2

2003-11-27 16:50  paultcochrane

	* source/xmdssimulation.cc: Added the inclusion of the sstream
	  (string streams) header.

2003-11-27 16:49  paultcochrane

	* 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 12:33  paultcochrane

	* source/xmdssequence.cc: Fixed bug whereby the useWisdom option
	  wasn't passed through to writePlanCreationCalls properly.

2003-11-27 12:14  paultcochrane

	* configure.in: Changed way that mpiccTest was checked for the
	  compiler running mpicc.

2003-11-25 19:19  paultcochrane

	* ChangeLog: Added comments advising of changes up to current
	  version of xmds.

2003-11-25 19:18  paultcochrane

	* configure.in: Corrected version numbers to agree with current
	  release.

2003-11-25 19:17  paultcochrane

	* 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 12:37  paultcochrane

	* source/xmdsmomentgroup.cc: Modified moment group number reporting
	  at the terminal, so matches what is given in xsil2graphics and
	  output files.

2003-11-24 21:10  paultcochrane

	* 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 21:07  paultcochrane

	* source/xmdsmomentgroup.cc: Fixed binary output bug where k-space
	  variables weren't ordered correctly before output.

2003-11-20 17:00  paultcochrane

	* source/xmdsmomentgroup.cc: Fixed misreporting of filename if
	  unable to open the output file for binary output.

2003-11-07 11:28  paultcochrane

	* configure.in: Changed release number to pre1, ready for the pre1
	  release. (funnily enough...)

2003-11-06 21:18  paultcochrane

	* 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 20:59  paultcochrane

	* configure.in: Now pointing XMDS_CC to CXX if necessary.

2003-11-06 17:02  paultcochrane

	* configure.in: Fixed bug where a test for null should have been
	  non-null.

2003-11-06 12:47  paultcochrane

	* 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 12:46  paultcochrane

	* 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 12:44  paultcochrane

	* 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 12:42  paultcochrane

	* source/xmdssimulation.cc: Removed the output of the (commented
	  out in the final code anyway) unistd.h statement.

2003-11-06 12:41  paultcochrane

	* 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 12:38  paultcochrane

	* 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 12:34  paultcochrane

	* doc/latex/: xmds_doc.pdf, xmds_doc.ps: Updated.

2003-11-06 12:29  paultcochrane

	* doc/latex/xmds_defs.tex: Updated list of tags defined for myhtml
	  style in listings.sty code.

2003-11-06 12:27  paultcochrane

	* doc/latex/workedExample.tex: Basic formatting of some xmds code.

2003-11-06 12:26  paultcochrane

	* doc/latex/moreExamples.tex: Basic formatting of xmds code.

2003-11-06 12:24  paultcochrane

	* doc/latex/languageReference.tex: Added docs for argv tagset (and
	  subtags).

2003-11-06 12:22  paultcochrane

	* doc/latex/functionality.tex: Mentioned explicitly that version
	  2.1.x of fftw is required for xmds.  Updated references to point
	  to xmds-1.2, not xmds-1.0.

2003-11-06 12:16  paultcochrane

	* admin/manifestGen.pl: Documented a far simpler way of generating
	  the manifest.

2003-11-06 12:15  paultcochrane

	* 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 12:11  paultcochrane

	* 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 12:09  paultcochrane

	* 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 12:08  paultcochrane

	* MANIFEST: Updated to reflect current list of files for
	  distribution.

2003-11-04 19:27  paultcochrane

	* Makefile.am: No change, just added something and took it away,
	  but it wants to be updated nevertheless.

2003-11-04 19:26  paultcochrane

	* LICENSE: Deleted: it is really the COPYING file, so it's really
	  superfluous.

2003-11-04 19:22  paultcochrane

	* MANIFEST: Initial import to repository.

2003-11-04 19:18  paultcochrane

	* ChangeLog: Updated to reflect changes that have happened so far
	  since xmds-1.1.

2003-11-04 18:54  paultcochrane

	* README: Updated to agree with current configuration options.

2003-11-04 18:53  paultcochrane

	* AUTHORS: Updated email addresses of authors.

2003-11-04 17:59  paultcochrane

	* 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 17:32  paultcochrane

	* configure.in: Fixed bug where one actually needs the
	  $PTHREAD_CFLAGS variable inserted into XMDS_CFLAGS.

2003-11-04 16:20  paultcochrane

	* 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 15:46  paultcochrane

	* 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 15:03  paultcochrane

	* configure.in: Changed implementation of how xmdsconfig.h is made.
	  It's now a cp from config.h.

2003-11-03 15:01  paultcochrane

	* Makefile.am: Added the m4 files acx_mpi.m4 and acx_pthread.m4 so
	  that will be added to distribution output.

2003-11-03 14:58  paultcochrane

	* examples/: diffusion.xmds, lorenz.xmds, pendulum.xmds,
	  vibstring.xmds: Initial import to repository.

2003-11-01 16:15  paultcochrane

	* source/xmdsconfig.h.in: deleted

2003-10-31 18:04  joehope

	* configure.in, examples/fibre.xmds, source/xmdsconfig.h.in: Making
	  stable autoconf on MacOSX

2003-10-30 18:07  paultcochrane

	* source/Doxyfile: Now set to produce pdf documentation as well.

2003-10-30 18:05  paultcochrane

	* configure.in: Fixed problem with not finding lam properly.  Fixed
	  bug whereby forgot to add -lxmds to XMDS_LIBS variable.

2003-10-30 14:40  paultcochrane

	* 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 14:33  paultcochrane

	* source/: dom3.h, kissdom.h, xmdsclasses.h: Did some reformatting
	  and updated docstrings.

2003-10-29 12:48  paultcochrane

	* source/xmdsconfig.h.in: Initial import to repository.

2003-10-28 12:42  paultcochrane

	* 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 11:48  paultcochrane

	* admin/manifestGen.pl: Initial import to repository.

2003-10-27 21:50  paultcochrane

	* LICENSE: Initial import to repository.

2003-10-27 21:50  paultcochrane

	* 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 21:47  paultcochrane

	* Makefile.am: Added loadxsil.m to EXTRA_DIST files.

2003-10-27 19:11  paultcochrane

	* source/: xmdscomplex.h, xmdselement.cc, xmdsfield.cc,
	  xmdsfilter.cc, xmdsglobals.cc, xmdsintegrate.cc,
	  xmdsintegrateex.cc, xmdsintegrateip.cc, xmdsintegraterk4.cc,
	  xmdsintegraterk4ex.cc, xmdsintegraterk4ip.cc, xmdsintegratesi.cc,
	  xmdsintegratesiex.cc, xmdsintegratesiip.cc, xmdsmomentgroup.cc,
	  xmdsoutput.cc, xmdssegment.cc, xmdssequence.cc,
	  xmdssimulation.cc, xmdsutils.cc, xmdsutils.h, xmdsvector.cc,
	  xmdsvectorelement.cc, xmlbasics.cc, xmlbasics.h, xmlparser.cc,
	  xmlparser.h, xsil2graphics.cc, xsilfield.cc, xsilfield.h: Added
	  GPL statement.

2003-10-27 19:07  paultcochrane

	* source/: kissdom.cc, kissdom.h, main.cc, xmdsarg.cc,
	  xmdsargelement.cc, xmdsargv.cc, xmdsclasses.h: Added GPL
	  statement.

2003-10-27 19:05  paultcochrane

	* source/getopt.h: Added some docstrings.

2003-10-27 19:01  paultcochrane

	* source/dom3.h: Changed some docstrings.  Added GPL statement.

2003-10-27 18:52  paultcochrane

	* 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 11:50  paultcochrane

	* source/xmdssequence.cc: Added more helpful (ie usage) output for
	  when arguments to simulation binary are incorrect.

2003-10-24 11:46  paultcochrane

	* 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 20:36  paultcochrane

	* 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 20:11  paultcochrane

	* source/xmdssimulation.cc: Minor terminal output touch up.

2003-10-23 20:11  paultcochrane

	* source/main.cc: Now using XMDS_CC, XMDS_CXX, and XMDS_CFLAGS
	  instead of the non-XMDS_* versions.

2003-10-23 20:07  paultcochrane

	* 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 16:13  paultcochrane

	* source/xmdssimulation.cc: Minor change to terminal output.

2003-10-22 16:12  paultcochrane

	* 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 16:10  paultcochrane

	* 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 13:25  paultcochrane

	* acx_mpi.m4: Initial import to repository.

2003-10-22 10:39  paultcochrane

	* source/Makefile.am: Changed config.h to xmdsconfig.h

2003-10-22 10:39  paultcochrane

	* 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 10:38  paultcochrane

	* source/xmdsmomentgroup.cc: Fixed minor error with incorrect
	  format in printf statement.

2003-10-22 10:23  paultcochrane

	* source/main.cc: Improved mpi flag handling, and added a
	  FFTW_MPI_LIBS variable.

2003-10-22 10:22  paultcochrane

	* configure.in: Removed some superfluous variables, and some
	  superfluous output at configure time.  Improved the ordering and
	  determination of flags for use with mpi.

2003-10-22 09:27  paultcochrane

	* 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 11:14  joehope

	* examples/highdim.xmds: Trivial fix for occasional, minor compiler
	  confusion: sqrt(int)

2003-10-18 20:57  paultcochrane

	* Makefile.in: Updated to current version.

2003-10-18 20:55  paultcochrane

	* source/xmdssimulation.cc: Removed inclusion of endian.h for
	  binaryOutput.  Now including config.h when binaryOutput is true.

2003-10-18 20:54  paultcochrane

	* source/xmdssequence.cc: Changed checks for FLOAT_WORD_ORDER etc
	  to CPU_IS_BIG_ENDIAN etc.

2003-10-18 20:53  paultcochrane

	* source/xmdsmomentgroup.cc: Now determining endian-ness by the
	  variables CPU_IS_BIG_ENDIAN and CPU_IS_LITTLE_ENDIAN.

2003-10-18 20:51  paultcochrane

	* 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 20:49  paultcochrane

	* aclocal.m4, configure, source/Makefile.in, source/config.h.in:
	  Updated to current version.

2003-10-18 20:48  paultcochrane

	* 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 20:07  paultcochrane

	* acinclude.m4: Initial import to repository.

2003-10-17 14:53  paultcochrane

	* 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 14:50  paultcochrane

	* source/xmdssequence.cc: Changed getopt_long_only to getopt_long.

2003-10-17 14:49  paultcochrane

	* source/main.cc: Removed FFTWMPILIBS variable (now superfluous).
	  Removed superfluous %s formatting string.

2003-10-17 14:48  paultcochrane

	* source/Makefile.am: Added the getopt sources and headers to make
	  the libxmds library.

2003-10-17 14:47  paultcochrane

	* source/: getopt.c, getopt.h, getopt1.c, getopt_init.c,
	  stamp-h.in, stamp-h1.in: Initial import to repository.

2003-10-17 14:36  paultcochrane

	* configure, ltmain.sh, source/Makefile.in, source/config.h.in:
	  Updated to current version.

2003-10-17 14:32  paultcochrane

	* depcomp, Makefile.in, aclocal.m4, config.guess: Updated to
	  current version.

2003-10-17 14:32  paultcochrane

	* 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 14:24  paultcochrane

	* Makefile.am: Commented out the inclusion of xmds api
	  documentation.

2003-10-10 15:02  joehope

	* source/: dom3.h, kissdom.cc, kissdom.h, xmdsclasses.h,
	  xmdsutils.h, xmlbasics.h, xmlparser.h, xsilfield.h, xmdsarg.cc,
	  xmdsargelement.cc, xmdsargv.cc, xmdselement.cc, xmdsfield.cc,
	  xmdsfilter.cc, xmdsglobals.cc, xmdsintegrate.cc,
	  xmdsintegrateex.cc, xmdsintegrateip.cc, xmdsintegraterk4.cc,
	  xmdsintegraterk4ex.cc, xmdsintegraterk4ip.cc, xmdsintegratesi.cc,
	  xmdsintegratesiex.cc, xmdsintegratesiip.cc, xmdsmomentgroup.cc,
	  xmdsoutput.cc, xmdssegment.cc, xmdssequence.cc,
	  xmdssimulation.cc, xmdsutils.cc, xmdsvector.cc,
	  xmdsvectorelement.cc, xmlbasics.cc, xmlparser.cc,
	  xsil2graphics.cc, xsilfield.cc: Replace //** with // **  (often
	  allows proper syntax colouring)

2003-10-09 16:29  paultcochrane

	* testsuite/atomlaser.xmds, testsuite/atomlaser_reference.xsil,
	  testsuite/fibre.xmds, testsuite/fibre_reference.xsil,
	  testsuite/fullpos3D.xmds, testsuite/fullpos3D_reference.xsil,
	  testsuite/gaugeatomlaser.xmds,
	  testsuite/gaugeatomlaser_reference.xsil, testsuite/genRefData.pl,
	  testsuite/kubo.xmds, testsuite/kubo_reference.xsil,
	  testsuite/ndparamp.xmds, testsuite/ndparamp_reference.xsil,
	  testsuite/nlse.xmds, testsuite/nlse_reference.xsil,
	  testsuite/sine.xmds, testsuite/sine_reference.xsil,
	  testsuite/soliton.xmds, testsuite/soliton_reference.xsil,
	  testsuite/test_xmds.pl, testsuite/tla.xmds,
	  testsuite/tla_reference.xsil, frontend/tkxmds,
	  frontend/tkxmds.pl: Initial import to repository.

2003-10-09 14:49  joehope

	* configure: Fixing link to libraries used for testing fftw_mpi

2003-10-09 12:18  offaxis

	* source/xmdsglobals.cc: Globals from <arg> elements now read in
	  _before_ those from the <globals> element.

2003-10-07 15:28  paultcochrane

	* depcomp: Initial import to repository.

2003-10-07 15:01  paultcochrane

	* acx_pthread.m4: Initial import to repository.  Copied from the
	  fftw distribution (many thanks).

2003-10-07 14:59  paultcochrane

	* 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 14:55  paultcochrane

	* configure: Changed to agree with current version of configure.in

2003-10-07 14:53  paultcochrane

	* Makefile.in: Updated to agree with current version of Makefile.am

2003-10-07 14:52  paultcochrane

	* 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 14:50  paultcochrane

	* 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 14:48  paultcochrane

	* 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 14:45  paultcochrane

	* source/loadxsil.m: Fixed a line that was missing a .

2003-10-07 14:44  paultcochrane

	* source/config.h.in: Updated to agree with current version of
	  configure.in etc

2003-10-07 14:43  paultcochrane

	* source/Makefile.in: Updated to agree with current version of
	  Makefile.am

2003-10-06 14:21  paultcochrane

	* source/xmdsmomentgroup.cc: Removed multiline string literals by
	  adding heaps of fprintf statements.  This caused problems with
	  some compilers.

2003-10-06 14:20  paultcochrane

	* source/xmdsfield.cc: Removed multiline string literals by adding
	  heaps of fprintf statements.

2003-09-30 21:50  paultcochrane

	* examples/atomlaser.xmds: Now contains more <argv> tags test code.
	  Doesn't actually do anything...

2003-09-30 21:48  paultcochrane

	* source/xmdsutils.h: Reformatted the text.

2003-09-30 21:47  paultcochrane

	* 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 21:46  paultcochrane

	* source/xmdssequence.cc: Completed code to implement gnu getopt
	  command line options for the simulation binary.

2003-09-30 21:44  paultcochrane

	* source/xmdsglobals.cc: Added global variables code to be output
	  for when command line arguments are specified in the .xmds file.

2003-09-30 21:42  paultcochrane

	* source/xmdscomplex.h: Reformatted text.

2003-09-30 21:42  paultcochrane

	* 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 21:39  paultcochrane

	* source/xmdsargv.cc: Deleted some superfluous code (eg
	  writeArgvIntialisationCode, writeArgvFinalisationCode).

2003-09-30 21:38  paultcochrane

	* 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 21:36  paultcochrane

	* source/xmdsarg.cc: Removed some superfluous function definitions.
	  Namely type(), setType(), default_value() and setDefaultValue()

2003-09-30 21:33  paultcochrane

	* source/: dom3.h, kissdom.h: Reformatted text nicely.

2003-09-30 21:32  paultcochrane

	* source/Makefile.in: Updated to reflect changes in Makefile.am

2003-09-29 19:57  paultcochrane

	* Makefile.in: Updated to reflect changes in Makefile.am

2003-09-29 19:57  paultcochrane

	* Makefile.am: Removed superfluous files from being added when
	  performing a make dist.  Needs to be improved further.

2003-09-29 19:56  paultcochrane

	* aclocal.m4: Updated.

2003-09-29 19:56  paultcochrane

	* configure.in: Better checking, and some testing done on platforms
	  other than linux.

2003-09-29 19:55  paultcochrane

	* configure: Updated to current configure.in

2003-09-29 18:03  paultcochrane

	* configure: Updated to current configure.in

2003-09-29 18:00  paultcochrane

	* configure.in: Actually fixed the checks now, instead of not
	  (aarrgghh).

2003-09-29 13:28  paultcochrane

	* configure.in: Fixed some more checks and added a check for
	  fftw_mpi.

2003-09-29 13:28  paultcochrane

	* configure: Updated to current version of configure.in

2003-09-29 12:03  paultcochrane

	* configure: Updated to current version of configure.in

2003-09-29 12:02  paultcochrane

	* configure.in: Fixed bug with incorrectly using alternative paths
	  to fftw.

2003-09-24 14:32  paultcochrane

	* doc/latex/figures/main.eps: Redrew in PyScript, so looks much
	  better now.

2003-09-24 14:20  paultcochrane

	* doc/latex/figures/defferential.eps: Initial import to repository.

2003-09-24 14:19  paultcochrane

	* doc/latex/xmds_doc.tex: Included language reference LaTeX source
	  file.

2003-09-24 14:18  paultcochrane

	* doc/latex/xmds_defs.tex: Added more keywords to morekeywords
	  statement for myhtml language style.

2003-09-24 14:17  paultcochrane

	* doc/latex/titlepage.tex: Minor change to xmds_logo LaTeX code.

2003-09-24 14:15  paultcochrane

	* doc/latex/languageReference.tex: Initial import to repository.

2003-09-24 14:14  paultcochrane

	* doc/latex/numModellingTheory.tex: Added (funny, and therefore
	  probably superfluous) figure at start of chapter.  Sundry other
	  formatting changes.

2003-09-24 14:12  paultcochrane

	* doc/latex/bibliography.tex: Updated for use with hyperref package

2003-09-15 20:16  paultcochrane

	* source/: xmdsarg.cc, xmdsargelement.cc, xmdsargv.cc,
	  xmdselement.cc, xmdsfield.cc, xmdsfilter.cc, xmdsglobals.cc,
	  xmdsintegrate.cc, xmdsintegrateex.cc, xmdsintegrateip.cc,
	  xmdsintegraterk4.cc, xmdsintegraterk4ex.cc,
	  xmdsintegraterk4ip.cc, xmdsintegratesi.cc, xmdsintegratesiex.cc,
	  xmdsintegratesiip.cc, xmdsmomentgroup.cc, xmdsoutput.cc,
	  xmdssegment.cc, xmdssequence.cc, xmdssimulation.cc, xmdsutils.cc,
	  xmdsvector.cc, xmdsvectorelement.cc: Implemented the use of a
	  command line flag to xmds for toggling debugging information
	  output (-d).

2003-09-15 20:14  paultcochrane

	* source/xsil2graphics.cc: Modified to implement the -d xmds
	  debugging flag and -x the xml debugging flag.

2003-09-15 20:13  paultcochrane

	* 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 20:12  paultcochrane

	* source/xmdsclasses.h: Removed DEBUG macro.  This is now
	  implemented as a command line switch to xmds.

2003-09-15 20:10  paultcochrane

	* 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 19:57  paultcochrane

	* examples/atomlaser.xmds: Improved indentation of xml.  Added code
	  to test the <argv> tag set.

2003-09-15 16:56  paultcochrane

	* ChangeLog: Initial import to repository.

2003-09-15 16:49  paultcochrane

	* source/: xmdsarg.cc, xmdsargelement.cc, xmdsargv.cc: Initial
	  import to repository.

2003-09-15 16:48  paultcochrane

	* source/xmdssimulation.cc: Improved indentation of source code.
	  Added some code for the parsing of the <argv> element.

2003-09-15 16:45  paultcochrane

	* source/xmdssequence.cc: Improved indentation of source code, no
	  functional changes.

2003-09-15 16:43  paultcochrane

	* 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 16:38  paultcochrane

	* source/: xmdsutils.cc, xmdsutils.h, xmdsvector.cc,
	  xmdsvectorelement.cc: No functional changes, just indented the
	  source code nicely

2003-09-15 16:32  paultcochrane

	* source/: dom3.h, kissdom.cc, kissdom.h, xmdscomplex.h,
	  xmdsfilter.cc, xmdsglobals.cc, xmdsintegrate.cc,
	  xmdsintegrateex.cc, xmdsintegrateip.cc, xmdsintegraterk4.cc,
	  xmdsintegraterk4ex.cc, xmdsintegraterk4ip.cc, xmdsintegratesi.cc,
	  xmdsintegratesiex.cc, xmdsintegratesiip.cc, xmdsmomentgroup.cc,
	  xmdsoutput.cc, xmdssegment.cc, xmlbasics.cc, xmlbasics.h,
	  xmlparser.cc, xmlparser.h, main.cc, xmdsfield.cc: No functional
	  changes, just indented the source code nicely

2003-09-15 16:31  paultcochrane

	* source/Makefile.am: Added xmdsargv.cc xmdsarg.cc and
	  xmdsargelement.cc to the list of xmds sources

2003-09-15 16:29  paultcochrane

	* Makefile.in, source/Makefile.in: Adding relevant changes made by
	  automake and autoconf

2003-09-09 14:32  paultcochrane

	* source/: Makefile.in, config.h.in: Initial import to repository

2003-09-09 14:29  paultcochrane

	* config.sub, config.guess, Makefile.in: Initial import to
	  repository

2003-09-04 19:54  paultcochrane

	* aclocal.m4: Initial import to repository

2003-09-04 19:53  paultcochrane

	* configure: Initial import to repository.

2003-08-25 11:44  paultcochrane

	* doc/latex/: abstract.tex, ccaption.sty,
	  develAndProgStructure.tex, fancyhdr.sty, functionality.tex,
	  intro.tex, misc_defs.tex, moreExamples.tex,
	  numModellingTheory.tex, outlook.tex, quotchap.sty, titlepage.tex,
	  workedExample.tex, xmds_defs.tex, xmds_doc.tex, xsil.tex,
	  xsil2graphics.tex, xmds_doc.pdf, xmds_doc.ps: Initial import to
	  repository

2003-08-25 11:41  paultcochrane

	* doc/latex/xmds.tex: Obsolete

2003-08-21 11:38  paultcochrane

	* doc/latex/: bibliography.tex, doc.tex, xmds.tex,
	  figures/classes.eps, figures/classes.fig, figures/fibre1.eps,
	  figures/fibre2.eps, figures/funct.eps, figures/funct.fig,
	  figures/kubo1.eps, figures/kubo2.eps, figures/main.eps,
	  figures/main.fig, figures/ndparamp1.eps, figures/ndparamp2.eps,
	  figures/nlse.eps, figures/tla.eps: Initial commit of v1.0 latex
	  docs to devel tree

2003-08-06 15:38  paultcochrane

	* configure.in: Added a check for the endian.h header file.

2003-08-06 14:42  paultcochrane

	* source/xmdssimulation.cc: If binary output is specified, then
	  include the <endian.h> header.

2003-08-06 14:41  paultcochrane

	* 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 14:38  paultcochrane

	* 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 14:35  paultcochrane

	* source/loadxsil.m: Modified to allow for reading of bigendian or
	  littleendian binary, as specified in the .xsil file.

2003-08-05 17:54  paultcochrane

	* 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 17:51  paultcochrane

	* 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 17:49  paultcochrane

	* 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 17:47  paultcochrane

	* 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 20:29  paultcochrane

	* source/Makefile: Obsolete.  Now automatically generated by
	  configure script.

2003-08-04 20:28  paultcochrane

	* Configure: Obsolete

2003-08-04 20:27  paultcochrane

	* source/xmdssimulation.cc: Included the vector header.  Now "using
	  namespace std" by default.

2003-08-04 20:26  paultcochrane

	* source/xmdsoutput.cc: Fixed a spelling error in console output.

2003-08-04 20:24  paultcochrane

	* 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 20:20  paultcochrane

	* 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 20:18  paultcochrane

	* source/loadxsil.m: Modified to allow for changes in binary output
	  format.

2003-07-28 19:42  paultcochrane

	* 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 19:41  paultcochrane

	* configure.in: No longer produces Makefile in examples directory.

2003-07-28 19:13  paultcochrane

	* source/Doxyfile: Initial import to repository

2003-07-28 19:12  paultcochrane

	* source/: dom3.h, kissdom.h, xmdsclasses.h, xmdscomplex.h,
	  xmdsutils.h, xmlbasics.h, xmlparser.h, 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 19:07  paultcochrane

	* source/: main.cc, xmdssequence.cc: Added some documentation to
	  the file.  Mainly just to test out Doxygen, automatic api
	  documentation generator.

2003-07-23 14:23  paultcochrane

	* examples/: atomlaser.xmds, fibre.xmds: Added <benchmark> tag

2003-07-23 14:23  paultcochrane

	* source/xmdssimulation.cc: Implemented code to process <benchmark>
	  tag properly.  Added <ctime> header so that can actually do the
	  benchmarking.

2003-07-23 14:21  paultcochrane

	* source/xmdssequence.cc: Added output code to implement
	  <benchmark> boolean

2003-07-23 14:20  paultcochrane

	* 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 14:19  paultcochrane

	* source/xmdsclasses.h: Added benchmark boolean to
	  simulationParametersStruct

2003-07-23 14:17  paultcochrane

	* configure.in: Fixed problems with not getting flags passed to
	  mpicc right.	Still not perfect though...

2003-07-23 14:16  paultcochrane

	* Makefile.am: Altered to allow building of example binaries in the
	  examples subdirectory

2003-07-12 15:19  paultcochrane

	* 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 15:03  paultcochrane

	* 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 14:44  paultcochrane

	* source/xmdssimulation.cc: Added useDouble boolean to
	  myParameters.  Implemented finding use_double element in xmds
	  file, and setting accordingly if found.

2003-07-09 14:43  paultcochrane

	* 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 14:40  paultcochrane

	* source/xmdsclasses.h: Added useDouble boolean to
	  simulationParametersStruct (to implement the choice of using
	  double or single precision in binary output.

2003-07-09 13:57  paultcochrane

	* 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 13:55  paultcochrane

	* source/xmdsoutput.cc: Addition of myBoolList variable in order to
	  implement binary output

2003-07-09 13:54  paultcochrane

	* source/xmdsmomentgroup.cc: Implemented binary output of data if
	  <binary_output> boolean set to yes.

2003-07-09 13:53  paultcochrane

	* 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 13:50  paultcochrane

	* source/xmdsclasses.h: Modified to turn debugging on.	Modified to
	  add binaryOutput boolean to myParameters.

2003-07-09 13:49  paultcochrane

	* examples/atomlaser.xmds: Added <use_wisdom> and <binary_output>
	  flags to file.

2003-07-07 16:02  paultcochrane

	* examples/atomlaser.xmds: Made minor changes to formatting of
	  file.

2003-07-07 16:01  paultcochrane

	* source/xmdssimulation.cc: Added code to look for <use_wisdom> tag
	  in .xmds file, and implement if necessary.

2003-07-07 15:59  paultcochrane

	* source/xmdssequence.cc: Updated writePlanCreationCalls() call so
	  that includes new arguments due to inclusion of wisdom

2003-07-07 15:57  paultcochrane

	* source/xmdsoutput.cc: Changed writePlanCreationCalls() to allow
	  for wisdom implementation

2003-07-07 15:56  paultcochrane

	* 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 15:52  paultcochrane

	* source/xmdsclasses.h: Changed simulationParametersStruct to
	  include useWisdom boolean.  Updated writePlanCreationCalls to
	  include useWisdom in function call.

2003-07-07 15:49  paultcochrane

	* 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 14:15  paultcochrane

	* source/: xmlparser.cc, 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 14:11  paultcochrane

	* source/Makefile.am: Initial import to repository

2003-07-01 18:56  paultcochrane

	* AUTHORS, COPYING, INSTALL, Makefile.am, README, configure.in,
	  install-sh, ltmain.sh, missing, mkinstalldirs, NEWS: Added
	  initial version to repository

2003-07-01 18:54  paultcochrane

	* source/: main.cc, xsil2graphics.cc: Minor alterations to
	  standardise the naming conventions (e.g. VER is now VERSION)

2003-06-25 12:30  joehope

	* source/: xmdssequence.cc, xmdssimulation.cc: Making (MPI) size a
	  global variable.  Good for debugging.

2003-06-03 13:53  joehope

	* Configure: Reset Configure to Linux by default

2003-06-03 13:51  joehope

	* Configure: Blank space in "release" tag in case of compiler
	  warnings

2003-06-03 12:29  joehope

	* Configure, source/xmdsintegrate.cc: Fixing case sensitive TRUE
	  and FALSE

2003-05-31 18:44  joehope

	* changes.log: Changes log is up to date for the version 1.1
	  release

2003-05-31 18:21  joehope

	* source/: xmdsclasses.h, xmdsintegrate.cc, xmdsintegratesiip.cc:
	  Added <functions> element in <integrate>.  Places code before the
	  integration loop.  This is good for time dependent functions.

2003-05-31 15:53  joehope

	* source/: xmdsfield.cc, xmdsmomentgroup.cc, 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.

2003-05-06 09:42  joehope

	* changes.log: New changes.log for xmds-1.1-beta2

2003-04-17 16:22  joehope

	* 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 14:52  joehope

	* source/: xmdssequence.cc, xmdssimulation.cc: Made rank a global
	  variable.  Good for debugging.

2003-04-17 11:55  joehope

	* 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 17:05  joehope

	* source/xmdsvector.cc: Fixed a compiler warning in renormalisation
	  for deterministic MPI.

2003-04-16 15:43  joehope

	* source/: xmdsintegraterk4.cc, xmdsvector.cc: Two range fixes for
	  deterministic MPI.

2003-04-16 12:49  joehope

	* source/xmdscomplex.h: Made the promotion of complex to
	  fftw_complex non-explicit.  Less warnings, and it should be safe.

2003-04-16 12:46  joehope

	* 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 10:23  joehope

	* examples/highdim.xmds: Making highdim.xmds an MPI-enabled script
	  with fewer outputs.

2003-04-04 10:22  joehope

	* examples/gaugeatomlaser.xmds: Reverted stochastic Fourier-space
	  output to local-in-x form.

2003-04-04 10:00  joehope

	* changes.log, examples/ndparamp.xmds: Pre-version 1.0 cruft
	  removal from examples

2003-03-28 14:03  joehope

	* source/xmdsvector.cc: Extra print variable cruft removed

2003-03-28 11:43  joehope

	* Configure: Default Configure file settings for linux	- ready for
	  1.1-beta release

2003-03-27 18:43  joehope

	* examples/highdim.xmds, source/xmdssequence.cc: Nested
	  subsequences now call their initialisation functions.

2003-03-27 18:29  joehope

	* examples/highdim.xmds, source/xmdsvector.cc: Mixed space
	  transforms added for deterministic MPI.

2003-03-27 13:45  joehope

	* source/: xmdsfield.cc, xmdsmomentgroup.cc, xmdsvector.cc: Put
	  TRUE and FALSE into lowercase.  Needed for linux (for icc, at
	  least).

2003-03-26 17:07  joehope

	* examples/highdim.xmds, source/xmdsintegrate.cc,
	  source/xmdsintegraterk4ex.cc, source/xmdsintegraterk4ip.cc,
	  source/xmdsintegratesiex.cc, source/xmdsintegratesiip.cc: Passed
	  cycle number right through to the integrate loops

2003-03-26 16:37  joehope

	* changes.log, examples/highdim.xmds, source/xmdsmomentgroup.cc:
	  Deterministic MPI nows works with all moment groups.	Mixed space
	  transforms still broken.

2003-03-25 15:26  joehope

	* source/: xmdsfield.cc, xmdsfilter.cc, xmdsintegraterk4.cc,
	  xmdsintegratesiex.cc, xmdsintegratesiip.cc, xmdsmomentgroup.cc,
	  xmdssequence.cc: Fixed cycles.  Made all segments have access to
	  the cycle number.  Partial implementation of k-space output
	  groups for deterministic MPI.

2003-03-25 10:38  joehope

	* examples/atomlaser.xmds, examples/kubo.xmds,
	  source/xmdsclasses.h, source/xsil2graphics.cc: Fixed
	  xsil2graphics bug 708629.  Added MPI changes to class
	  definitions.

2003-03-24 20:13  joehope

	* Configure, source/main.cc, source/xmdsfield.cc,
	  source/xmdsintegrate.cc, source/xmdsintegrateex.cc,
	  source/xmdsintegrateip.cc, source/xmdsintegraterk4.cc,
	  source/xmdsintegraterk4ex.cc, source/xmdsintegraterk4ip.cc,
	  source/xmdsintegratesiex.cc, source/xmdsintegratesiip.cc,
	  source/xmdsmomentgroup.cc, source/xmdssequence.cc,
	  source/xmdssimulation.cc, 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.

2003-03-13 10:25  joehope

	* source/: xmdsintegraterk4.cc, xmdsintegratesiex.cc,
	  xmdsintegratesiip.cc: Memory reordering now complete.
	  Cross-propagation should now be fully operational.

2003-03-11 17:23  joehope

	* Configure, examples/fullpos3D.xmds, examples/gaugeatomlaser.xmds,
	  source/xmdsfield.cc, source/xmdsintegrate.cc,
	  source/xmdsintegrateex.cc, source/xmdsintegrateip.cc,
	  source/xmdsintegratesiip.cc, source/xmdsmomentgroup.cc,
	  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 14:55  joehope

	* examples/: atomlaser.xmds, 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 13:35  joehope

	* .DS_Store, source/.DS_Store, source/xmdsintegrateex.cc: Fixed
	  missing segment name in xmdsintegrateex.cc (from previous speedup
	  patch)

2003-03-03 14:58  joehope

	* .DS_Store, examples/atomlaser.xmds, examples/gaugeatomlaser.xmds,
	  source/xmdsintegrateex.cc, 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

2003-02-24 10:53  joehope

	* .DS_Store, Configure, examples/fullpos3D.xmds, source/.DS_Store,
	  source/main.cc, source/xmdsclasses.h, source/xmdssequence.cc,
	  source/xmdssimulation.cc, 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

2003-02-06 18:02  joehope

	* Configure: Spelling errors in 1.3 patch fixed.

2003-02-06 17:57  joehope

	* Configure, source/Makefile: Fixed ordering of -lm and -lfftw
	  libraries

	  Fixed misnamed XMDSCSTDLIBS in the configure file

	  Allowing XMDSCC XMDSCFLAGS and XMDSCSTDLIBS to be set
	  individually, with the main choices being the default for
	  unspecified ones.

	  Refined default compile options for True64 unix.

	  Added warning in the installation process that tells you the
	  system that you've chosen.

2003-02-03 15:42  joehope

	* Configure, changes.log, source/Makefile, source/kissdom.cc,
	  source/xmdsfield.cc, source/xmdsintegrate.cc,
	  source/xmdsintegraterk4.cc, source/xmdsintegratesiex.cc,
	  source/xmdsintegratesiip.cc, source/xmdsmomentgroup.cc,
	  source/xmdsvector.cc, source/xmdsvectorelement.cc,
	  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 12:23  joehope

	* .DS_Store, changes.log, Configure, readme, doc/doc.css,
	  doc/doc.html, doc/img1.gif, doc/img10.gif, doc/img100.gif,
	  doc/img101.gif, doc/img102.gif, doc/img103.gif, doc/img104.gif,
	  doc/img105.gif, doc/img106.gif, doc/img107.gif, doc/img108.gif,
	  doc/img109.gif, doc/img11.gif, doc/img110.gif, doc/img111.gif,
	  doc/img112.gif, doc/img113.gif, doc/img114.gif, doc/img115.gif,
	  doc/img116.gif, doc/img117.gif, doc/img118.gif, doc/img119.gif,
	  doc/img12.gif, doc/img120.gif, doc/img121.gif, doc/img122.gif,
	  doc/img123.gif, doc/img124.gif, doc/img125.gif, doc/img126.gif,
	  doc/img127.gif, doc/img128.gif, doc/img129.gif, doc/img13.gif,
	  doc/img130.gif, doc/img131.gif, doc/img132.gif, doc/img133.gif,
	  doc/img134.gif, doc/img135.gif, doc/img136.gif, doc/img137.gif,
	  doc/img138.gif, doc/img139.gif, doc/img14.gif, doc/img140.gif,
	  doc/img141.gif, doc/img142.gif, doc/img143.gif, doc/img144.gif,
	  doc/img145.gif, doc/img146.gif, doc/img147.gif, doc/img148.gif,
	  doc/img149.gif, doc/img15.gif, doc/img150.gif, doc/img151.gif,
	  doc/img152.gif, doc/img153.gif, doc/img154.gif, doc/img155.gif,
	  doc/img156.gif, doc/img157.gif, doc/img158.gif, doc/img159.gif,
	  doc/img16.gif, doc/img160.gif, doc/img161.gif, doc/img162.gif,
	  doc/img163.gif, doc/img164.gif, doc/img165.gif, doc/img166.gif,
	  doc/img167.gif, doc/img168.gif, doc/img169.gif, doc/img17.gif,
	  doc/img170.gif, doc/img171.gif, doc/img172.gif, doc/img173.gif,
	  doc/img174.gif, doc/img175.gif, doc/img176.gif, doc/img177.gif,
	  doc/img178.gif, doc/img179.gif, doc/img18.gif, doc/img180.gif,
	  doc/img181.gif, doc/img182.gif, doc/img183.gif, doc/img184.gif,
	  doc/img185.gif, doc/img186.gif, doc/img187.gif, doc/img188.gif,
	  doc/img189.gif, doc/img19.gif, doc/img190.gif, doc/img191.gif,
	  doc/img192.gif, doc/img193.gif, doc/img194.gif, doc/img195.gif,
	  doc/img196.gif, doc/img197.gif, doc/img198.gif, doc/img199.gif,
	  doc/img2.gif, doc/img20.gif, doc/img200.gif, doc/img201.gif,
	  doc/img202.gif, doc/img203.gif, doc/img204.gif, doc/img205.gif,
	  doc/img206.gif, doc/img207.gif, doc/img208.gif, doc/img209.gif,
	  doc/img21.gif, doc/img210.gif, doc/img211.gif, doc/img212.gif,
	  doc/img213.gif, doc/img214.gif, doc/img22.gif, doc/img23.gif,
	  doc/img24.gif, doc/img25.gif, doc/img26.gif, doc/img27.gif,
	  doc/img28.gif, doc/img29.gif, doc/img3.gif, doc/img30.gif,
	  doc/img31.gif, doc/img32.gif, doc/img33.gif, doc/img34.gif,
	  doc/img35.gif, doc/img36.gif, doc/img37.gif, doc/img38.gif,
	  doc/img39.gif, doc/img4.gif, doc/img40.gif, doc/img41.gif,
	  doc/img42.gif, doc/img43.gif, doc/img44.gif, doc/img45.gif,
	  doc/img46.gif, doc/img47.gif, doc/img48.gif, doc/img49.gif,
	  doc/img5.gif, doc/img50.gif, doc/img51.gif, doc/img52.gif,
	  doc/img53.gif, doc/img54.gif, doc/img55.gif, doc/img56.gif,
	  doc/img57.gif, doc/img58.gif, doc/img59.gif, doc/img6.gif,
	  doc/img60.gif, doc/img61.gif, doc/img62.gif, doc/img63.gif,
	  doc/img64.gif, doc/img65.gif, doc/img66.gif, doc/img67.gif,
	  doc/img68.gif, doc/img69.gif, doc/img7.gif, doc/img70.gif,
	  doc/img71.gif, doc/img72.gif, doc/img73.gif, doc/img74.gif,
	  doc/img75.gif, doc/img76.gif, doc/img77.gif, doc/img78.gif,
	  doc/img79.gif, doc/img8.gif, doc/img80.gif, doc/img81.gif,
	  doc/img82.gif, doc/img83.gif, doc/img84.gif, doc/img85.gif,
	  doc/img86.gif, doc/img87.gif, doc/img88.gif, doc/img89.gif,
	  doc/img9.gif, doc/img90.gif, doc/img91.gif, doc/img92.gif,
	  doc/img93.gif, doc/img94.gif, doc/img95.gif, doc/img96.gif,
	  doc/img97.gif, doc/img98.gif, doc/img99.gif,
	  examples/atomlaser.xmds, examples/fibre.xmds,
	  examples/fullpos3D.xmds, examples/gaugeatomlaser.xmds,
	  examples/kubo.xmds, examples/ndparamp.xmds, examples/nlse.xmds,
	  examples/sine.xmds, examples/soliton.xmds, examples/tla.xmds,
	  source/.DS_Store, source/dom3.h, source/kissdom.cc,
	  source/Makefile, source/kissdom.h, source/main.cc,
	  source/xmdsclasses.h, source/xmdscomplex.h,
	  source/xmdselement.cc, source/xmdsfield.cc, source/xmdsfilter.cc,
	  source/xmdsglobals.cc, source/xmdsintegrate.cc,
	  source/xmdsintegrateex.cc, source/xmdsintegrateip.cc,
	  source/xmdsintegraterk4.cc, source/xmdsintegraterk4ex.cc,
	  source/xmdsintegraterk4ip.cc, source/xmdsintegratesi.cc,
	  source/xmdsintegratesiex.cc, source/xmdsintegratesiip.cc,
	  source/xmdsmomentgroup.cc, source/xmdsoutput.cc,
	  source/xmdssegment.cc, source/xmdssequence.cc,
	  source/xmdssimulation.cc, source/xmdsutils.cc,
	  source/xmdsutils.h, source/xmdsvector.cc,
	  source/xmdsvectorelement.cc, source/xmlbasics.cc,
	  source/xmlbasics.h, source/xmlparser.cc, source/xmlparser.h,
	  source/xsil2graphics.cc, source/xsilfield.cc, source/xsilfield.h:
	  Import version 1.0-2 to start development branch

2003-02-03 12:23  joehope

	* .DS_Store, changes.log, Configure, readme, doc/doc.css,
	  doc/doc.html, doc/img1.gif, doc/img10.gif, doc/img100.gif,
	  doc/img101.gif, doc/img102.gif, doc/img103.gif, doc/img104.gif,
	  doc/img105.gif, doc/img106.gif, doc/img107.gif, doc/img108.gif,
	  doc/img109.gif, doc/img11.gif, doc/img110.gif, doc/img111.gif,
	  doc/img112.gif, doc/img113.gif, doc/img114.gif, doc/img115.gif,
	  doc/img116.gif, doc/img117.gif, doc/img118.gif, doc/img119.gif,
	  doc/img12.gif, doc/img120.gif, doc/img121.gif, doc/img122.gif,
	  doc/img123.gif, doc/img124.gif, doc/img125.gif, doc/img126.gif,
	  doc/img127.gif, doc/img128.gif, doc/img129.gif, doc/img13.gif,
	  doc/img130.gif, doc/img131.gif, doc/img132.gif, doc/img133.gif,
	  doc/img134.gif, doc/img135.gif, doc/img136.gif, doc/img137.gif,
	  doc/img138.gif, doc/img139.gif, doc/img14.gif, doc/img140.gif,
	  doc/img141.gif, doc/img142.gif, doc/img143.gif, doc/img144.gif,
	  doc/img145.gif, doc/img146.gif, doc/img147.gif, doc/img148.gif,
	  doc/img149.gif, doc/img15.gif, doc/img150.gif, doc/img151.gif,
	  doc/img152.gif, doc/img153.gif, doc/img154.gif, doc/img155.gif,
	  doc/img156.gif, doc/img157.gif, doc/img158.gif, doc/img159.gif,
	  doc/img16.gif, doc/img160.gif, doc/img161.gif, doc/img162.gif,
	  doc/img163.gif, doc/img164.gif, doc/img165.gif, doc/img166.gif,
	  doc/img167.gif, doc/img168.gif, doc/img169.gif, doc/img17.gif,
	  doc/img170.gif, doc/img171.gif, doc/img172.gif, doc/img173.gif,
	  doc/img174.gif, doc/img175.gif, doc/img176.gif, doc/img177.gif,
	  doc/img178.gif, doc/img179.gif, doc/img18.gif, doc/img180.gif,
	  doc/img181.gif, doc/img182.gif, doc/img183.gif, doc/img184.gif,
	  doc/img185.gif, doc/img186.gif, doc/img187.gif, doc/img188.gif,
	  doc/img189.gif, doc/img19.gif, doc/img190.gif, doc/img191.gif,
	  doc/img192.gif, doc/img193.gif, doc/img194.gif, doc/img195.gif,
	  doc/img196.gif, doc/img197.gif, doc/img198.gif, doc/img199.gif,
	  doc/img2.gif, doc/img20.gif, doc/img200.gif, doc/img201.gif,
	  doc/img202.gif, doc/img203.gif, doc/img204.gif, doc/img205.gif,
	  doc/img206.gif, doc/img207.gif, doc/img208.gif, doc/img209.gif,
	  doc/img21.gif, doc/img210.gif, doc/img211.gif, doc/img212.gif,
	  doc/img213.gif, doc/img214.gif, doc/img22.gif, doc/img23.gif,
	  doc/img24.gif, doc/img25.gif, doc/img26.gif, doc/img27.gif,
	  doc/img28.gif, doc/img29.gif, doc/img3.gif, doc/img30.gif,
	  doc/img31.gif, doc/img32.gif, doc/img33.gif, doc/img34.gif,
	  doc/img35.gif, doc/img36.gif, doc/img37.gif, doc/img38.gif,
	  doc/img39.gif, doc/img4.gif, doc/img40.gif, doc/img41.gif,
	  doc/img42.gif, doc/img43.gif, doc/img44.gif, doc/img45.gif,
	  doc/img46.gif, doc/img47.gif, doc/img48.gif, doc/img49.gif,
	  doc/img5.gif, doc/img50.gif, doc/img51.gif, doc/img52.gif,
	  doc/img53.gif, doc/img54.gif, doc/img55.gif, doc/img56.gif,
	  doc/img57.gif, doc/img58.gif, doc/img59.gif, doc/img6.gif,
	  doc/img60.gif, doc/img61.gif, doc/img62.gif, doc/img63.gif,
	  doc/img64.gif, doc/img65.gif, doc/img66.gif, doc/img67.gif,
	  doc/img68.gif, doc/img69.gif, doc/img7.gif, doc/img70.gif,
	  doc/img71.gif, doc/img72.gif, doc/img73.gif, doc/img74.gif,
	  doc/img75.gif, doc/img76.gif, doc/img77.gif, doc/img78.gif,
	  doc/img79.gif, doc/img8.gif, doc/img80.gif, doc/img81.gif,
	  doc/img82.gif, doc/img83.gif, doc/img84.gif, doc/img85.gif,
	  doc/img86.gif, doc/img87.gif, doc/img88.gif, doc/img89.gif,
	  doc/img9.gif, doc/img90.gif, doc/img91.gif, doc/img92.gif,
	  doc/img93.gif, doc/img94.gif, doc/img95.gif, doc/img96.gif,
	  doc/img97.gif, doc/img98.gif, doc/img99.gif,
	  examples/atomlaser.xmds, examples/fibre.xmds,
	  examples/fullpos3D.xmds, examples/gaugeatomlaser.xmds,
	  examples/kubo.xmds, examples/ndparamp.xmds, examples/nlse.xmds,
	  examples/sine.xmds, examples/soliton.xmds, examples/tla.xmds,
	  source/.DS_Store, source/dom3.h, source/kissdom.cc,
	  source/Makefile, source/kissdom.h, source/main.cc,
	  source/xmdsclasses.h, source/xmdscomplex.h,
	  source/xmdselement.cc, source/xmdsfield.cc, source/xmdsfilter.cc,
	  source/xmdsglobals.cc, source/xmdsintegrate.cc,
	  source/xmdsintegrateex.cc, source/xmdsintegrateip.cc,
	  source/xmdsintegraterk4.cc, source/xmdsintegraterk4ex.cc,
	  source/xmdsintegraterk4ip.cc, source/xmdsintegratesi.cc,
	  source/xmdsintegratesiex.cc, source/xmdsintegratesiip.cc,
	  source/xmdsmomentgroup.cc, source/xmdsoutput.cc,
	  source/xmdssegment.cc, source/xmdssequence.cc,
	  source/xmdssimulation.cc, source/xmdsutils.cc,
	  source/xmdsutils.h, source/xmdsvector.cc,
	  source/xmdsvectorelement.cc, source/xmlbasics.cc,
	  source/xmlbasics.h, source/xmlparser.cc, source/xmlparser.h,
	  source/xsil2graphics.cc, source/xsilfield.cc, source/xsilfield.h:
	  Initial revision

