File Release Notes and Changelog
Release Name: xmds-1.6-1
Notes: This is a bugfix and minor tweak release of xmds, to correspond with the new documentation release.
Changes: 2007-05-08 06:52 grahamdennis * trunk/xmds-devel/source/Makefile.am: Moving the version.h make target to the top of the automake file so that maybe make will be able to find it... 2007-05-07 10:51 grahamdennis * trunk/xmds-devel/source/Makefile.am, trunk/xmds-devel/source/version.sh: I forgot that the version.h file wouldn't get updated once it existed. So I've made version.h depend on all of the other xmds sources in the automake file. There's probably a cleaner way, but I can't think of one. 2007-05-07 10:31 grahamdennis * trunk/xmds-devel/source/Makefile.am, trunk/xmds-devel/source/main.cc, trunk/xmds-devel/source/version.sh, trunk/xmds-devel/source/xmdsbreakpoint.cc, trunk/xmds-devel/source/xmdsclasses.h, trunk/xmds-devel/source/xmdsoutput.cc, trunk/xmds-devel/source/xmdssimulation.cc: Add the subversion revision number to the end of the version number reported by the application, and saved to XSIL files. This makes it easier for those of us living on the bleeding edge to track down exactly which revision number was used to create a script (for example, for tracking performance regressions). 2007-05-05 09:10 grahamdennis * trunk/xmds-devel/source/xmdsclasses.h, trunk/xmds-devel/source/xmdsintegrate.cc, trunk/xmds-devel/source/xmdsintegrateex.cc, trunk/xmds-devel/source/xmdsintegrateip.cc, trunk/xmds-devel/source/xmdssegment.cc, trunk/xmds-devel/source/xmdssequence.cc: Move allocation of k_operator_field's to one place in both the xmds source, and the source generated from scripts. This makes it easier to control when the fields are allocated, so that they are allocated only while they are needed, and are free'd after the segment they belong to has completed. Previously, the k_operator_field's were leaked. 2007-05-03 08:08 grahamdennis * trunk/xmds-devel/source/xmdsvectorelement.cc: For large data files, the size of each component could be larger than can fit into a long, so an off_t should be used. 2007-05-03 02:14 joehope * trunk/xmds-devel/source/xmdsclasses.h, trunk/xmds-devel/source/xmdsintegrate.cc, trunk/xmds-devel/source/xmdsintegrateark45.cc, trunk/xmds-devel/source/xmdsintegrateark89.cc, trunk/xmds-devel/source/xmdsintegraterk4.cc, trunk/xmds-devel/source/xmdsintegraterk9.cc, trunk/xmds-devel/source/xmdsintegratesiex.cc: Multiple bugfixes. SIEX is now restored in the post FFTW 3 age. Cross-propagation now works with stochastic equations. 2007-05-03 00:59 joehope * trunk/xmds-devel/admin/xmdsReleaseProcedure.pod: Quick update to the release procedures. 2007-05-03 00:58 joehope * trunk/xmds-devel/source/xmdsintegrate.cc, trunk/xmds-devel/source/xmdsintegratesiex.cc: Start of another bugfix. 2007-05-02 10:22 joehope * trunk/xmds-devel/source/xmdsclasses.h, trunk/xmds-devel/source/xmdsmomentgroup.cc, trunk/xmds-devel/source/xmdssequence.cc: Force initialisation of moment group data if post-propagation is performed. Most importantly, this initialises the Fourier space tag. Strictly speaking, the rest of the initialisation is unnecessary unless at least one transverse dimension is integrated, or the system is stochastic with multiple paths, but it is always safe to do, and should have approximately zero impact on speed. 2007-05-02 07:18 joehope * trunk/xmds-devel/source/xsilfield.cc: Suppress unnecessary output when loading data into Mathematica. 2007-04-26 07:46 grahamdennis * trunk/xmds-devel/source/xmdsvectorelement.cc: When I added the noises to the XSIL loading code, I forgot to make sure they were deleted at the end. 2007-04-24 05:45 grahamdennis * trunk/xmds-devel/source/xmdssimulation.cc: Just because there's a use_openmp tag, and use_mpi is true doesn't mean that someone actually wants to use both OpenMP and MPI... 2007-04-23 03:33 grahamdennis * trunk/xmds-devel/source/xmdsvectorelement.cc: It wasn't possible to use noises in the CDATA section when initialising a vector from an XSIL file. 2007-04-05 13:17 paultcochrane * trunk/xmds-devel/examples/groundstate.xmds: Added groundstate.xmds back in. 2007-04-05 13:17 paultcochrane * trunk/xmds-devel/examples/groundstate.xmds: Temporarily deleting groundstate.xmds to see if can remove the executable bit from the file as it stands in the repository. 2007-04-05 12:58 paultcochrane * ., trunk/xmds-devel/examples/groundstate.xmds: Changed the copyright info in an attempt to change the executable mode on the file (causes problems when building the Debian package). Can only see if this will work... 2007-04-02 00:28 grahamdennis * trunk/xmds-devel/source/loadxsil.m: loadxsil couldn't load 4-dimensional (or higher) arrays (correctly). xsil2graphics generated correct code, just loadxsil didn't. 2007-03-28 07:17 grahamdennis * trunk/xmds-devel/source/xmdsfield.cc, trunk/xmds-devel/source/xmdsmomentgroup.cc: Increase precision of field limits so that when changing the size of fields which don't have nice round sizes we don't confuse the XSIL loading code which expects the grids to line up almost exactly. 2007-03-22 03:43 joehope * trunk/xmds-devel/examples/nlse.xmds: Give an example with the adaptive 9(8) RK algorithm. 2007-03-22 03:41 joehope * trunk/xmds-devel/MANIFEST, trunk/xmds-devel/admin/svn2cl.xsl: Still updating for 1.6 release. 2007-03-22 03:34 joehope * trunk/xmds-devel/ChangeLog, trunk/xmds-devel/README, trunk/xmds-devel/admin/xmdsReleaseProcedure.pod, trunk/xmds-devel/configure.in: Preparing for release of version 1.6. 2007-03-20 01:26 michaelhush * trunk/xmds-devel/source/xmdsintegrateark89.cc, trunk/xmds-devel/source/xmdssimulation.cc: Fixed memory leak in ARK89EX and ARK89IP methods for stochastic problem 2007-03-12 00:58 joehope * trunk/xmds-devel/source/xmdssequence.cc: Fixed a bug where the scheduler didn't handle lack of error checking properly. 2007-02-23 05:55 michaelhush * trunk/xmds-devel/source/xmdsintegrateark89.cc, trunk/xmds-devel/source/xmdssequence.cc, trunk/xmds-devel/source/xmdssimulation.cc: Fixed bug triggered when multiple segements were created using the ARK89 methods 2007-02-14 13:59 paultcochrane * ., trunk/xmds-devel/source/Makefile.am, trunk/xmds-devel/source/xmds_arg.cc, trunk/xmds-devel/source/xmds_arg_element.cc, trunk/xmds-devel/source/xmds_argv.cc, trunk/xmds-devel/source/xmdsarg.cc, trunk/xmds-devel/source/xmdsargelement.cc, trunk/xmds-devel/source/xmdsargv.cc: Moved argument parsing sources to filenames with names a bit easier to read. 2007-02-14 13:58 paultcochrane * ., trunk/xmds-devel/source/Makefile.am: Swapped the names of two source files to group the names better 2007-02-14 13:58 paultcochrane * ., trunk/xmds-devel/source/Makefile.am: Moved XML parsing sources and argument parsing sources into their own variable. 2007-02-14 13:58 paultcochrane * ., trunk/xmds-devel/source/Makefile.am: Separated the sources specific to algorithm processing into its own variable. 2007-02-14 13:58 paultcochrane * ., trunk/xmds-devel/source/Makefile.am: Expanded source listing so makes it easier to add files as needed 2007-02-12 03:40 grahamdennis * trunk/xmds-devel/source/main.cc: Adding -openmp to compile options when compiling a threaded OpenMP simulation 2007-02-12 03:20 grahamdennis * trunk/xmds-devel/source/xmdsbreakpoint.cc: Breakpoints would be written incorrectly when writing more than one field when one of the fields was of type complex. Oops. 2007-02-12 03:02 grahamdennis * trunk/xmds-devel/source/loadxsil.m: Enable loadxsil.m to work with XSIL files produced from breakpoints. 2007-02-11 03:43 andyferris * trunk/xmds-devel/configure.in: Reverted my change to the configure script. The previous problem was misdiagnosed. Note that the libraries are tested by configure using the "cc" command, and thus uses the CC=... option. However, these libraries are only ever linked to programs compiled by the XMDS_CC=... In this case my fftw3_threads library was incompatible with gcc on my computer, when I set XMDS_CC=icc. 2007-02-08 06:35 andyferris * trunk/xmds-devel/configure.in: Changed configure.in to use the fftw library path when searching for or using the fftw3_threads library. 2007-02-08 03:18 grahamdennis * trunk/xmds-devel/source/xmdsvector.cc: Unbreak moment groups for MPI (broken yesterday when fixing buffer overflow bug). 2007-02-07 03:58 grahamdennis * trunk/xmds-devel/source/xmdsvector.cc: There was a bug in xmdsVector initialisation (not xmdsVectorElement initialisation) that caused a buffer overflow. I think this only affected MPI simulations that used explicit picture integration algorithms (e.g. RK4EX). It certainly only affected MPI simulations. 2007-02-05 06:46 grahamdennis * trunk/xmds-devel/source/xmdsfield.cc: Make deterministic simulations that use MPI but not fourier transforms work. 2007-02-05 05:08 grahamdennis * trunk/xmds-devel/source/loadxsil.m: Make loadxsil work for zero-dimensional variables stored in XSIL files. 2007-02-05 01:30 grahamdennis * trunk/xmds-devel/source/xmdsvectorelement.cc: Output more information for debugging when input grids don't match simulation grids. 2007-01-31 02:51 grahamdennis * trunk/xmds-devel/examples/Makefile: Actually cause 'make run' in the examples directory to run the examples instead of just pretending to do so. 2007-01-30 20:43 paultcochrane * ., trunk/xmds-devel/admin/build-and-test.sh: Initial import to repository. An initial first cut at a build and test script to run on the sourceforge compile farm. 2007-01-29 21:42 paultcochrane * ., trunk/xmds-devel/examples: Updated svn:ignore property to ignore gcov-generated files. 2007-01-29 21:42 paultcochrane * ., trunk/xmds-devel/examples/Makefile: Added a default target. Added a run target so that can run all simulations as well as just build them. 2007-01-29 21:42 paultcochrane * ., trunk/xmds-devel/source/getopt_xmds.h, trunk/xmds-devel/source/kissdom.cc, trunk/xmds-devel/source/main.cc, trunk/xmds-devel/source/xmdsarg.cc, trunk/xmds-devel/source/xmdsargelement.cc, trunk/xmds-devel/source/xmdsargv.cc, trunk/xmds-devel/source/xmdsbreakpoint.cc, trunk/xmds-devel/source/xmdselement.cc, trunk/xmds-devel/source/xmdsfield.cc, trunk/xmds-devel/source/xmdsfilter.cc, trunk/xmds-devel/source/xmdsglobals.cc, trunk/xmds-devel/source/xmdsintegrate.cc, trunk/xmds-devel/source/xmdsintegrateark45.cc, trunk/xmds-devel/source/xmdsintegrateark45ex.cc, trunk/xmds-devel/source/xmdsintegrateark45ip.cc, trunk/xmds-devel/source/xmdsintegrateark89.cc, trunk/xmds-devel/source/xmdsintegrateark89ex.cc, trunk/xmds-devel/source/xmdsintegrateark89ip.cc, trunk/xmds-devel/source/xmdsintegrateex.cc, trunk/xmds-devel/source/xmdsintegrateip.cc, trunk/xmds-devel/source/xmdsintegraterk4.cc, trunk/xmds-devel/source/xmdsintegraterk4ex.cc, trunk/xmds-devel/source/xmdsintegraterk4ip.cc, trunk/xmds-devel/source/xmdsintegraterk9.cc, trunk/xmds-devel/source/xmdsintegraterk9ex.cc, trunk/xmds-devel/source/xmdsintegraterk9ip.cc, trunk/xmds-devel/source/xmdsintegratesi.cc, trunk/xmds-devel/source/xmdsintegratesiex.cc, trunk/xmds-devel/source/xmdsintegratesiip.cc, trunk/xmds-devel/source/xmdsmomentgroup.cc, trunk/xmds-devel/source/xmdsoutput.cc, trunk/xmds-devel/source/xmdssegment.cc, trunk/xmds-devel/source/xmdssequence.cc, trunk/xmds-devel/source/xmdssimulation.cc, trunk/xmds-devel/source/xmdsutils.cc, trunk/xmds-devel/source/xmdsutils.h, trunk/xmds-devel/source/xmdsvector.cc, trunk/xmds-devel/source/xmdsvectorelement.cc, trunk/xmds-devel/source/xmlbasics.cc, trunk/xmds-devel/source/xmlparser.cc, trunk/xmds-devel/source/xsil2graphics.cc, trunk/xmds-devel/source/xsilfield.cc: Banishing hard tabs from the source. Replaced with relevant number of spaces. 2007-01-29 21:40 paultcochrane * ., trunk/xmds-devel/source: Updated svn:ignore property to ignore *.bak files 2007-01-29 21:40 paultcochrane * ., trunk/xmds-devel/source/xmdsintegraterk9.cc, trunk/xmds-devel/source/xmdsintegraterk9ex.cc, trunk/xmds-devel/source/xmdsintegraterk9ip.cc: Added emacs/vim coda to load common editor settings 2007-01-29 21:39 paultcochrane * ., trunk/xmds-devel/Makefile.am: Removed latexdocs variable 2007-01-25 05:46 michaelhush * trunk/xmds-devel/source/xmdsintegrateark89.cc: Changed adaptive time step algorithm, so step size is halved after a failure to improve stability 2007-01-18 03:31 michaelhush * trunk/xmds-devel/source/xmdssequence.cc: fixed problem with benchmark changes I made 2007-01-18 02:50 michaelhush * trunk/xmds-devel/examples/diffusion.xmds, trunk/xmds-devel/examples/kubo.xmds, trunk/xmds-devel/source/xmdsintegrateark89.cc, trunk/xmds-devel/source/xmdssequence.cc: Fixed time step for ARK89EX and IP for non stochastic problems and changed bemchmark so it displays a more accurate time 2007-01-16 03:03 joehope * trunk/xmds-devel/Makefile.am: Adding the missing examples into the distribution packages 2007-01-11 08:07 michaelhush * trunk/xmds-devel/source/xmdsintegrateark89.cc, trunk/xmds-devel/source/xmdsintegrateark89ip.cc: ARK89EX and ARK89IP both now work for normal and simple stochastic problems 2007-01-11 04:35 michaelhush * trunk/xmds-devel/source/xmdsclasses.h, trunk/xmds-devel/source/xmdsintegrateark89.cc, trunk/xmds-devel/source/xmdsintegrateark89ex.cc: ARK89EX now working and convergerges on diffusion.xmds and a simple stochastic problem 2007-01-07 23:52 paultcochrane * ., trunk/xmds-devel/source/xmdsintegraterk9.cc: Corrected docstring; was throwing a warning from doxygen. 2007-01-07 23:52 paultcochrane * ., trunk/xmds-devel/source/Doxyfile: Explicitly specifying the patterns to look for when searching for source files. 2007-01-07 23:51 paultcochrane * ., trunk/xmds-devel/source/dom3.h: Reformatted docstrings and made most of the lines of code within 80 character limits. 2007-01-07 19:34 paultcochrane * ., trunk/xmds-devel/source/Makefile.am: Building the pdf as well as the html version of the api when running 'make api' 2007-01-07 19:34 paultcochrane * ., trunk/xmds-devel/source/Doxyfile: CALL_GRAPH and CALLER_GRAPH set to YES 2007-01-07 19:33 paultcochrane * ., trunk/xmds-devel/source/Doxyfile: GENERATE_MAN set to NO 2007-01-07 19:33 paultcochrane * ., trunk/xmds-devel/source/Doxyfile: WARN_NO_PARAMDOC set to YES 2007-01-07 19:33 paultcochrane * ., trunk/xmds-devel/source/Doxyfile: Tab size set to 4. 2007-01-07 19:33 paultcochrane * ., trunk/xmds-devel/source/Doxyfile: Updated to current version of doxygen (1.5.1) 2007-01-07 19:32 paultcochrane * ., trunk/xmds-devel/source/Doxyfile: Moved link to where documentation should be output to be in the xmds.org directory. 2007-01-05 01:21 michaelhush * trunk/xmds-devel/source/xmdsintegrateark89.cc: Another file I forgot to add for ARK89 methods 2007-01-04 06:48 michaelhush * trunk/xmds-devel/source/xmdsintegrateark89ex.cc, trunk/xmds-devel/source/xmdsintegrateark89ip.cc: Added ARK89 classes I forgot 2007-01-04 06:46 michaelhush * trunk/xmds-devel/examples/sech_soliton.xmds, trunk/xmds-devel/source/Makefile.am, trunk/xmds-devel/source/xmdsclasses.h, trunk/xmds-devel/source/xmdsintegrate.cc, trunk/xmds-devel/source/xmdsintegrateark45.cc, trunk/xmds-devel/source/xmdsintegrateark45ex.cc, trunk/xmds-devel/source/xmdsintegrateark45ip.cc, trunk/xmds-devel/source/xmdsintegrateex.cc, trunk/xmds-devel/source/xmdsintegrateip.cc, trunk/xmds-devel/source/xmdsintegraterk4.cc, trunk/xmds-devel/source/xmdsintegraterk4ex.cc, trunk/xmds-devel/source/xmdsintegraterk4ip.cc, trunk/xmds-devel/source/xmdsintegraterk9.cc, trunk/xmds-devel/source/xmdsintegraterk9ex.cc, trunk/xmds-devel/source/xmdsintegraterk9ip.cc, trunk/xmds-devel/source/xmdsintegratesi.cc, trunk/xmds-devel/source/xmdsintegratesiex.cc, trunk/xmds-devel/source/xmdsintegratesiip.cc, trunk/xmds-devel/source/xmdssequence.cc: RK9IP now works with diffusion and sech_soliton examples, added ARK89EX and ARK89IP classes but functionality still to come 2006-12-28 15:58 paultcochrane * ., trunk/xmds-devel/configure.in: A test was missing for the fftw3.h header file (which is what fftw installs this header as by default, I would guess so that one can run fftw2 and fftw3 on the same system), this hopefully fixes bug #1600319 2006-12-28 15:58 paultcochrane * ., trunk/xmds-devel/examples/Makefile: Added the xmds binary as a dependency so that when xmds is rebuilt, one doesn't have to run 'make examples-clean; make examples' one can just run 'make examples' 2006-12-28 15:58 paultcochrane * ., trunk/xmds-devel/examples/pendulum.xmds: Fixed typo. 2006-12-25 21:05 paultcochrane * ., trunk/xmds-devel/source/main.cc: Changed some output info and added some more todo items. 2006-12-25 21:05 paultcochrane * ., trunk/xmds-devel/source/main.cc: Minor formatting changes. 2006-12-25 21:05 paultcochrane * ., trunk/xmds-devel/source/main.cc: Changed some more printf statements to cout. 2006-12-25 21:05 paultcochrane * ., trunk/xmds-devel/source/main.cc: Converted many printf statements to cout statements (more C++ like). Generic code formatting and tidying. 2006-12-25 21:04 paultcochrane * ., trunk/xmds-devel/source/main.cc: Added a todo item to improve an if-elseif sequence (no book handy atm to make it properly clean). 2006-12-25 21:04 paultcochrane * ., trunk/xmds-devel/source/main.cc: Added a note to the parsePrefs() routine about possibly making it more object oriented to reduce the number of params passed to the routine. 2006-12-25 21:04 paultcochrane * ., trunk/xmds-devel/source: Updated svn:ignore property. 2006-12-25 21:04 paultcochrane * ., trunk/xmds-devel/source/kissdom.cc, trunk/xmds-devel/source/xmdsarg.cc, trunk/xmds-devel/source/xmdsargelement.cc, trunk/xmds-devel/source/xmdsargv.cc, trunk/xmds-devel/source/xmdsbreakpoint.cc, trunk/xmds-devel/source/xmdselement.cc, trunk/xmds-devel/source/xmdsfield.cc, trunk/xmds-devel/source/xmdsfilter.cc, trunk/xmds-devel/source/xmdsglobals.cc, trunk/xmds-devel/source/xmdsintegrate.cc, trunk/xmds-devel/source/xmdsintegrateark45.cc, trunk/xmds-devel/source/xmdsintegrateark45ex.cc, trunk/xmds-devel/source/xmdsintegrateark45ip.cc, trunk/xmds-devel/source/xmdsintegrateex.cc, trunk/xmds-devel/source/xmdsintegrateip.cc, trunk/xmds-devel/source/xmdsintegraterk4.cc, trunk/xmds-devel/source/xmdsintegraterk4ex.cc, trunk/xmds-devel/source/xmdsintegraterk4ip.cc, trunk/xmds-devel/source/xmdsintegraterk9.cc, trunk/xmds-devel/source/xmdsintegraterk9ex.cc, trunk/xmds-devel/source/xmdsintegraterk9ip.cc, trunk/xmds-devel/source/xmdsintegratesi.cc, trunk/xmds-devel/source/xmdsintegratesiex.cc, trunk/xmds-devel/source/xmdsintegratesiip.cc, trunk/xmds-devel/source/xmdsmomentgroup.cc, trunk/xmds-devel/source/xmdsoutput.cc, trunk/xmds-devel/source/xmdssegment.cc, trunk/xmds-devel/source/xmdssequence.cc, trunk/xmds-devel/source/xmdssimulation.cc, trunk/xmds-devel/source/xmdsutils.cc, trunk/xmds-devel/source/xmdsvector.cc, trunk/xmds-devel/source/xmdsvectorelement.cc, trunk/xmds-devel/source/xmlbasics.cc, trunk/xmds-devel/source/xmlparser.cc, trunk/xmds-devel/source/xsilfield.cc: Reduced length of comments used as spacers between code sections (it fits within an 80 character window nicely now). 2006-12-25 21:03 paultcochrane * ., trunk/xmds-devel/examples/Makefile: Allowing all examples to run even if one fails. This is useful if one hasn't compiled xmds for mpi, and in which case highdim will fail. 2006-12-25 21:03 paultcochrane * ., trunk/xmds-devel/Makefile.am: Added "examples" and "examples-clean" rules for running the examples from the base xmds-devel directory. 2006-12-25 21:02 paultcochrane * ., trunk/xmds-devel/Makefile.am, trunk/xmds-devel/source/Makefile.am: Added an api rule to the makefiles so that one can build the Doxygen-generated api docs using "make api" 2006-12-25 21:02 paultcochrane * ., trunk/xmds-devel/source/Doxyfile: Updated the version number of xmds for the api documentation. 2006-12-25 21:02 paultcochrane * ., trunk/xmds-devel/source/main.cc: Changed the variable c to currentChar in parsePrefs() Some more basic reformatting of code for readability. 2006-12-25 21:02 paultcochrane * ., trunk/xmds-devel/source/main.cc: Some basic code reformatting in parsePrefs() 2006-12-25 21:02 paultcochrane * ., trunk/xmds-devel/source/main.cc: Basic reformat of parsePrefs() argument list to try to improve readability. Also reformatted some comments. 2006-12-25 21:01 paultcochrane * ., trunk/xmds-devel/source/main.cc: Tried to improve the display_usage() code formatting both internally, and that of the text printed to the screen. 2006-12-25 21:01 paultcochrane * ., trunk/xmds-devel/source/main.cc: Reformatted some of the comment/documentation text. 2006-12-20 07:26 paultcochrane * ., trunk/xmds-devel/admin/xmdsNewsPost.pl, trunk/xmds-devel/admin/xmdsNewsPost.txt: Deleted. No longer necessary, or a good idea. 2006-12-20 05:35 michaelhush * trunk/xmds-devel/source/Makefile.am, trunk/xmds-devel/source/xmdsclasses.h, trunk/xmds-devel/source/xmdsintegrateip.cc, trunk/xmds-devel/source/xmdsintegraterk9.cc, trunk/xmds-devel/source/xmdsintegraterk9ex.cc, trunk/xmds-devel/source/xmdsintegraterk9ip.cc, trunk/xmds-devel/source/xmdssequence.cc: Classes added for the 9th order stochastically safe rk method, ex is working but ip is still being completed 2006-12-18 13:03 paultcochrane * ., trunk/xmds-devel/.cvsignore, trunk/xmds-devel/examples/.cvsignore, trunk/xmds-devel/source/.cvsignore, trunk/xmds-devel/testsuite/.cvsignore, trunk/xmds-doc/latex/.cvsignore, trunk/xmds-doc/latex/figures/.cvsignore: Removed old .cvsignore files. 2006-12-18 12:59 paultcochrane * ., trunk/xmds-devel/AUTHORS, trunk/xmds-devel/INSTALL, trunk/xmds-devel/Makefile.am, trunk/xmds-devel/NEWS, trunk/xmds-devel/README, trunk/xmds-devel/README.Windows, trunk/xmds-devel/acinclude.m4, trunk/xmds-devel/acx_mpi.m4, trunk/xmds-devel/acx_pthread.m4, trunk/xmds-devel/admin/xmdsNewsPost.pl, trunk/xmds-devel/admin/xmdsReleaseProcedure.pod, trunk/xmds-devel/benchmark/bench, trunk/xmds-devel/benchmark/fullpos3D_16.xmds, trunk/xmds-devel/benchmark/fullpos3D_32.xmds, trunk/xmds-devel/benchmark/fullpos3D_64.xmds, trunk/xmds-devel/benchmark/gaugeatomlaser.xmds, trunk/xmds-devel/benchmark/gaugeatomlaser_128.xmds, trunk/xmds-devel/benchmark/ndparamp_100.xmds, trunk/xmds-devel/benchmark/ndparamp_200.xmds, trunk/xmds-devel/benchmark/ndparamp_50.xmds, trunk/xmds-devel/benchmark/ndparamp_500.xmds, trunk/xmds-devel/benchmark/nlse_100.xmds, trunk/xmds-devel/benchmark/nlse_1000.xmds, trunk/xmds-devel/benchmark/nlse_10000.xmds, trunk/xmds-devel/benchmark/nlse_500.xmds, trunk/xmds-devel/benchmark/nlse_5000.xmds, trunk/xmds-devel/benchmark/runbenchmarks, trunk/xmds-devel/configure.in, trunk/xmds-devel/examples/atomlaser.xmds, trunk/xmds-devel/examples/branch.xmds, trunk/xmds-devel/examples/brusselator.xmds, trunk/xmds-devel/examples/catcycle.xmds, trunk/xmds-devel/examples/chain.xmds, trunk/xmds-devel/examples/chemkin.xmds, trunk/xmds-devel/examples/diffusion.xmds, trunk/xmds-devel/examples/diffusion2.xmds, trunk/xmds-devel/examples/duffing.xmds, trunk/xmds-devel/examples/fibre.xmds, trunk/xmds-devel/examples/fisher_reaction_diffusion.xmds, trunk/xmds-devel/examples/fullpos3D.xmds, trunk/xmds-devel/examples/gaugeatomlaser.xmds, trunk/xmds-devel/examples/highdim.xmds, trunk/xmds-devel/examples/hires.xmds, trunk/xmds-devel/examples/krebs.xmds, trunk/xmds-devel/examples/kubo.xmds, trunk/xmds-devel/examples/lane_emden.xmds, trunk/xmds-devel/examples/lorenz.xmds, trunk/xmds-devel/examples/lotka_volterra.xmds, trunk/xmds-devel/examples/ndparamp.xmds, trunk/xmds-devel/examples/nlse.xmds, trunk/xmds-devel/examples/oregonator.xmds, trunk/xmds-devel/examples/paraxial_wave.xmds, trunk/xmds-devel/examples/pendulum.xmds, trunk/xmds-devel/examples/ring_modulator.xmds, trunk/xmds-devel/examples/sine.xmds, trunk/xmds-devel/examples/soliton.xmds, trunk/xmds-devel/examples/thermkin.xmds, trunk/xmds-devel/examples/tla.xmds, trunk/xmds-devel/examples/van_der_pol.xmds, trunk/xmds-devel/examples/vibstring.xmds, trunk/xmds-devel/source/Doxyfile, trunk/xmds-devel/source/Makefile.am, trunk/xmds-devel/source/dom3.h, trunk/xmds-devel/source/getopt_xmds.c, trunk/xmds-devel/source/getopt_xmds.h, trunk/xmds-devel/source/getopt_xmds1.c, trunk/xmds-devel/source/getopt_xmds_init.c, trunk/xmds-devel/source/kissdom.cc, trunk/xmds-devel/source/kissdom.h, trunk/xmds-devel/source/loadxsil.m, trunk/xmds-devel/source/main.cc, trunk/xmds-devel/source/xmdsarg.cc, trunk/xmds-devel/source/xmdsargelement.cc, trunk/xmds-devel/source/xmdsargv.cc, trunk/xmds-devel/source/xmdsbreakpoint.cc, trunk/xmds-devel/source/xmdsclasses.h, trunk/xmds-devel/source/xmdscomplex.h, trunk/xmds-devel/source/xmdselement.cc, trunk/xmds-devel/source/xmdsfield.cc, trunk/xmds-devel/source/xmdsfilter.cc, trunk/xmds-devel/source/xmdsglobals.cc, trunk/xmds-devel/source/xmdsintegrate.cc, trunk/xmds-devel/source/xmdsintegrateark45.cc, trunk/xmds-devel/source/xmdsintegrateark45ex.cc, trunk/xmds-devel/source/xmdsintegrateark45ip.cc, trunk/xmds-devel/source/xmdsintegrateex.cc, trunk/xmds-devel/source/xmdsintegrateip.cc, trunk/xmds-devel/source/xmdsintegraterk4.cc, trunk/xmds-devel/source/xmdsintegraterk4ex.cc, trunk/xmds-devel/source/xmdsintegraterk4ip.cc, trunk/xmds-devel/source/xmdsintegratesi.cc, trunk/xmds-devel/source/xmdsintegratesiex.cc, trunk/xmds-devel/source/xmdsintegratesiip.cc, trunk/xmds-devel/source/xmdsmomentgroup.cc, trunk/xmds-devel/source/xmdsoutput.cc, trunk/xmds-devel/source/xmdssegment.cc, trunk/xmds-devel/source/xmdssequence.cc, trunk/xmds-devel/source/xmdssimulation.cc, trunk/xmds-devel/source/xmdsutils.cc, trunk/xmds-devel/source/xmdsutils.h, trunk/xmds-devel/source/xmdsvector.cc, trunk/xmds-devel/source/xmdsvectorelement.cc, trunk/xmds-devel/source/xmlbasics.cc, trunk/xmds-devel/source/xmlbasics.h, trunk/xmds-devel/source/xmlparser.cc, trunk/xmds-devel/source/xmlparser.h, trunk/xmds-devel/source/xsil2graphics.cc, trunk/xmds-devel/source/xsilfield.cc, trunk/xmds-devel/source/xsilfield.h, trunk/xmds-devel/testsuite/atomlaser.xmds, trunk/xmds-devel/testsuite/fibre.xmds, trunk/xmds-devel/testsuite/fullpos3D.xmds, trunk/xmds-devel/testsuite/gaugeatomlaser.xmds, trunk/xmds-devel/testsuite/kubo.xmds, trunk/xmds-devel/testsuite/ndparamp.xmds, trunk/xmds-devel/testsuite/nlse.xmds, trunk/xmds-devel/testsuite/sine.xmds, trunk/xmds-devel/testsuite/soliton.xmds, trunk/xmds-devel/testsuite/test_xmds.pl, trunk/xmds-devel/testsuite/tla.xmds: Updated svn keywords property to make the "Id" keyword be expanded in source files. 2006-12-17 15:31 paultcochrane * ., trunk/xmds-devel/configure.in, trunk/xmds-devel/examples/atomlaser.xmds, trunk/xmds-devel/examples/branch.xmds, trunk/xmds-devel/examples/brusselator.xmds, trunk/xmds-devel/examples/catcycle.xmds, trunk/xmds-devel/examples/chain.xmds, trunk/xmds-devel/examples/chemkin.xmds, trunk/xmds-devel/examples/diffusion.xmds, trunk/xmds-devel/examples/diffusion2.xmds, trunk/xmds-devel/examples/duffing.xmds, trunk/xmds-devel/examples/fibre.xmds, trunk/xmds-devel/examples/fisher_reaction_diffusion.xmds, trunk/xmds-devel/examples/fullpos3D.xmds, trunk/xmds-devel/examples/gaugeatomlaser.xmds, trunk/xmds-devel/examples/groundstate.xmds, trunk/xmds-devel/examples/highdim.xmds, trunk/xmds-devel/examples/hires.xmds, trunk/xmds-devel/examples/krebs.xmds, trunk/xmds-devel/examples/kubo.xmds, trunk/xmds-devel/examples/lane_emden.xmds, trunk/xmds-devel/examples/lorenz.xmds, trunk/xmds-devel/examples/lotka_volterra.xmds, trunk/xmds-devel/examples/ndparamp.xmds, trunk/xmds-devel/examples/nlse.xmds, trunk/xmds-devel/examples/oregonator.xmds, trunk/xmds-devel/examples/paraxial_wave.xmds, trunk/xmds-devel/examples/pendulum.xmds, trunk/xmds-devel/examples/ring_modulator.xmds, trunk/xmds-devel/examples/sech_soliton.xmds, trunk/xmds-devel/examples/sech_soliton_tdepk.xmds, trunk/xmds-devel/examples/sine.xmds, trunk/xmds-devel/examples/soliton.xmds, trunk/xmds-devel/examples/thermkin.xmds, trunk/xmds-devel/examples/tla.xmds, trunk/xmds-devel/examples/van_der_pol.xmds, trunk/xmds-devel/examples/vibstring.xmds, trunk/xmds-devel/source/dom3.h, trunk/xmds-devel/source/kissdom.cc, trunk/xmds-devel/source/kissdom.h, trunk/xmds-devel/source/main.cc, trunk/xmds-devel/source/xmdsarg.cc, trunk/xmds-devel/source/xmdsargelement.cc, trunk/xmds-devel/source/xmdsargv.cc, trunk/xmds-devel/source/xmdsbreakpoint.cc, trunk/xmds-devel/source/xmdsclasses.h, trunk/xmds-devel/source/xmdscomplex.h, trunk/xmds-devel/source/xmdselement.cc, trunk/xmds-devel/source/xmdsfield.cc, trunk/xmds-devel/source/xmdsfilter.cc, trunk/xmds-devel/source/xmdsglobals.cc, trunk/xmds-devel/source/xmdsintegrate.cc, trunk/xmds-devel/source/xmdsintegrateark45.cc, trunk/xmds-devel/source/xmdsintegrateark45ex.cc, trunk/xmds-devel/source/xmdsintegrateark45ip.cc, trunk/xmds-devel/source/xmdsintegrateex.cc, trunk/xmds-devel/source/xmdsintegrateip.cc, trunk/xmds-devel/source/xmdsintegraterk4.cc, trunk/xmds-devel/source/xmdsintegraterk4ex.cc, trunk/xmds-devel/source/xmdsintegraterk4ip.cc, trunk/xmds-devel/source/xmdsintegratesi.cc, trunk/xmds-devel/source/xmdsintegratesiex.cc, trunk/xmds-devel/source/xmdsintegratesiip.cc, trunk/xmds-devel/source/xmdsmomentgroup.cc, trunk/xmds-devel/source/xmdsoutput.cc, trunk/xmds-devel/source/xmdssegment.cc, trunk/xmds-devel/source/xmdssequence.cc, trunk/xmds-devel/source/xmdssimulation.cc, trunk/xmds-devel/source/xmdsutils.cc, trunk/xmds-devel/source/xmdsutils.h, trunk/xmds-devel/source/xmdsvector.cc, trunk/xmds-devel/source/xmdsvectorelement.cc, trunk/xmds-devel/source/xmlbasics.cc, trunk/xmds-devel/source/xmlbasics.h, trunk/xmds-devel/source/xmlparser.cc, trunk/xmds-devel/source/xmlparser.h, trunk/xmds-devel/source/xsil2graphics.cc, trunk/xmds-devel/source/xsilfield.cc, trunk/xmds-devel/source/xsilfield.h: Updated copyright date information. 2006-12-17 15:29 paultcochrane * ., trunk/xmds-devel/configure.in, trunk/xmds-devel/source/main.cc: Updated revision number (1.5-3 has been released) 2006-12-17 15:00 paultcochrane * ., trunk/xmds-devel/examples/sech_soliton.xmds, trunk/xmds-devel/examples/sech_soliton_tdepk.xmds: Added copyright notice. 2006-12-17 15:00 paultcochrane * ., trunk/xmds-devel/examples/fullpos3D.xmds, trunk/xmds-devel/examples/gaugeatomlaser.xmds: The line at the top of each xmds file should read: <?xml version="1.0"?> not <?xmds version="1.0"?> for the file to be a well formed xml document. 2006-12-17 11:17 paultcochrane * trunk/xmds-devel/source/kissdom.cc, trunk/xmds-devel/source/main.cc, trunk/xmds-devel/source/xmdsarg.cc, trunk/xmds-devel/source/xmdsargelement.cc, trunk/xmds-devel/source/xmdsargv.cc, trunk/xmds-devel/source/xmdsbreakpoint.cc, trunk/xmds-devel/source/xmdselement.cc, trunk/xmds-devel/source/xmdsfield.cc, trunk/xmds-devel/source/xmdsfilter.cc, trunk/xmds-devel/source/xmdsglobals.cc, trunk/xmds-devel/source/xmdsintegrate.cc, trunk/xmds-devel/source/xmdsintegrateark45.cc, trunk/xmds-devel/source/xmdsintegrateark45ex.cc, trunk/xmds-devel/source/xmdsintegrateark45ip.cc, trunk/xmds-devel/source/xmdsintegrateex.cc, trunk/xmds-devel/source/xmdsintegrateip.cc, trunk/xmds-devel/source/xmdsintegraterk4.cc, trunk/xmds-devel/source/xmdsintegraterk4ex.cc, trunk/xmds-devel/source/xmdsintegraterk4ip.cc, trunk/xmds-devel/source/xmdsintegratesi.cc, trunk/xmds-devel/source/xmdsintegratesiex.cc, trunk/xmds-devel/source/xmdsintegratesiip.cc, trunk/xmds-devel/source/xmdsmomentgroup.cc, trunk/xmds-devel/source/xmdsoutput.cc, trunk/xmds-devel/source/xmdssegment.cc, trunk/xmds-devel/source/xmdssequence.cc, trunk/xmds-devel/source/xmdssimulation.cc, trunk/xmds-devel/source/xmdsutils.cc, trunk/xmds-devel/source/xmdsvector.cc, trunk/xmds-devel/source/xmdsvectorelement.cc, trunk/xmds-devel/source/xmlbasics.cc, trunk/xmds-devel/source/xmlparser.cc, trunk/xmds-devel/source/xsil2graphics.cc, trunk/xmds-devel/source/xsilfield.cc: Added emacs/vim coda to help with formatting of code. 2006-12-17 11:15 paultcochrane * trunk/xmds-devel/examples/groundstate.xmds: Changed simulation name to match filename: this helps the examples makefile correctly work out dependencies. 2006-12-17 11:15 paultcochrane * trunk/xmds-devel/examples/Makefile: Initial import to repository. This makefile is used to build the examples. We probably need to add this as part of autoconf, however, this does the job at present. 2006-12-16 18:16 paultcochrane * trunk/xmds-devel/preconf: Removed; this command would have worked nicely for older versions of the autoconf suite (i.e. those used when the original scripts were written), however now there exists the autoreconf program which comes with the autoconf suite, and so makes the preconf script obsolete. 2006-12-14 09:17 sebwuester * trunk/xmds-devel/examples/sech_soliton.xmds, trunk/xmds-devel/source/xmdsintegrateark45.cc, trunk/xmds-devel/source/xmdsintegrateark45ex.cc, trunk/xmds-devel/source/xmdsintegrateark45ip.cc, trunk/xmds-devel/source/xmdsintegrateip.cc, trunk/xmds-devel/source/xmdsintegraterk4.cc, trunk/xmds-devel/source/xmdsintegraterk4ex.cc, trunk/xmds-devel/source/xmdsintegraterk4ip.cc, trunk/xmds-devel/source/xmdsintegratesiex.cc: added underscores to some variables in ark45 which didn't have them; also added underscores to akfield etc. in rk4 and siip siex 2006-12-14 08:00 grahamdennis * trunk/xmds-devel/source/xmdsvectorelement.cc: Fix bug in earlier commit causing some simulations to not compile (those that use XSIL files to initialise non-main fields). 2006-12-14 07:46 grahamdennis * trunk/xmds-devel/source/xmdsbreakpoint.cc: Significantly sped up writing breakpoints when using MPI (removed unnecessary fseeks). For an example of the reduction, in examples/fullpos3D.xmds, the number of fseeks when writing the field data (in a breakpoint) was reduced from 393216 to 48. Also caught a bug where the data was being sent as the incorrect type when using MPI breakpoints. I continue to be astonished that this has worked in the past on the AC. 2006-12-14 05:39 joehope * trunk/xmds-devel/configure.in: Recovering 'out of the box' compilation for Mac OS X by defaulting to c++ compiler Still to achieve this for OPENMPI without passing MPI compiler explicitly as mpic++ 2006-12-14 01:57 grahamdennis * trunk/xmds-devel/source/xmdsvectorelement.cc: Significantly reduced the number of fseeks during loading of XSIL files. This is particularly important for large simulations as fseeks significantly slow down the loading procedure. 2006-12-01 05:44 paultcochrane * trunk/xmds-devel/configure.in: No longer automatically checking for icc during the configuration stage. If the user wants to use icc they can use the syntax: XMDS_CC=icc ./configure --with-user --enable-mpi (for example) 2006-12-01 04:54 paultcochrane * trunk/xmds-devel/preconf: Initial import to repository. This is a script to run to perform the autoconf preconfiguration dance before running ./configure after one has changed the configure.in or Makefile.am files. Maybe this will save some hands from RSI. 2006-12-01 04:39 paultcochrane * trunk/xmds-devel/Makefile.am: Removed trailing space. This was causing a warning from automake. 2006-12-01 04:33 paultcochrane * trunk/xmds-devel/testsuite/test_xmds.pl: Corrected a typo, and added cvs Id keyword. 2006-12-01 04:20 paultcochrane * trunk/xmds-devel, trunk/xmds-devel/.cvsignore: Initial import to repository. Getting cvs to ignore some of the autogenerated files in the root xmds-devel directory. 2006-11-30 00:13 joehope * trunk/xmds-devel/configure.in: Changing PREFIX behaviour on installation. This is one less patch separating the CVS from the Debian version. 2006-11-27 13:41 paultcochrane * trunk/xmds-devel/testsuite, trunk/xmds-devel/testsuite/.cvsignore: Initial import to repository. This file helps 'cvs status' ignore several files in the testsuite/ directory. 2006-11-27 00:05 joehope * trunk/xmds-devel/Makefile.am: Including lorentzInput.dat in the distribution tarball, as posted by Rafael Laboissiere 2006-11-24 13:08 paultcochrane * trunk/xmds-devel/source/main.cc: Updated copyright information (2004 -> 2006) 2006-11-24 13:07 paultcochrane * trunk/xmds-devel/source, trunk/xmds-devel/source/.cvsignore: Ignoring automatically generated files. 2006-11-24 12:44 paultcochrane * trunk/xmds-devel/examples, trunk/xmds-devel/examples/.cvsignore: Added .wisdom files to list to ignore, and the names of the output example executables. 2006-11-24 12:31 paultcochrane * trunk/xmds-devel/examples, trunk/xmds-devel/examples/.cvsignore: Added a .cvsignore file so that cvs status doesn't generate so much unwanted output. 2006-11-21 04:41 grahamdennis * trunk/xmds-devel/source/xmdsbreakpoint.cc: Significantly sped up writing breakpoints to disk by reordering the fwrites so that fseeks are mostly not needed. 2006-11-18 08:57 grahamdennis * trunk/xmds-devel/source/xmdsfield.cc, trunk/xmds-devel/source/xmdsintegrateip.cc: I hereby swear to try to make sure my xmds variables start with an underscore. Fixed OpenMP slowdown 2006-11-17 07:18 grahamdennis * trunk/xmds-devel/source/xmdsintegrateip.cc: I forgot to mark the k operators as thread-private in my previous commit. 2006-11-17 05:26 grahamdennis * trunk/xmds-devel/source/xmdsintegrateip.cc: Loop index variables must be signed for OpenMP to work 2006-11-17 05:21 grahamdennis * trunk/xmds-devel/source/xmdsintegrateip.cc: Parallelised (OpenMP) k_propagate and calculate_k_operator_field for ARK45. This should have a decent effect on performance with OpenMP 2006-11-17 04:19 grahamdennis * trunk/xmds-devel/source/xmdsintegrateark45ip.cc: It worked on my machine... Fix crash 2006-11-17 04:15 grahamdennis * trunk/xmds-devel/source/xmdsintegrateark45ip.cc: Combined ARK45IP for loops for cleaner code and better OpenMP compatibility This can be done for all algorithms, I'll do it as I go 2006-11-17 02:49 grahamdennis * trunk/xmds-devel/source/xmdsvectorelement.cc: One day I will remember to use underscores in variable names written by XMDS. (Fix compile warning for scripts using XSIL input) 2006-11-03 18:57 paultcochrane * trunk/xmds-devel/NEWS: Updated to the current version of xmds, and added all news items from between xmds-1.3-2 and xmds-1.5-3. 2006-11-03 18:28 paultcochrane * trunk/xmds-devel/AUTHORS: Updated the author list, and reordered all names (except for Greg's - he wrote it to start with, well, that's my reasoning) in alphabetical order by last name. 2006-11-03 14:02 paultcochrane * trunk/xmds-devel/configure.in: Moved fftw3-path help information over a bit so that it lines up with the other text when one does ./configure --help. (yes, I'm pedantic) 2006-10-17 04:59 grahamdennis * trunk/xmds-devel/source/xmdssimulation.cc, trunk/xmds-devel/source/xmdsutils.cc: Fixed a problem with how description elements were being read which caused xmds to crash when reading certain examples (e.g. branch.xmds) 2006-10-05 00:57 grahamdennis * trunk/xmds-devel/examples/lorenz.xmds, trunk/xmds-devel/source/xmdssimulation.cc: Changing the example lorenz.xmds not to require an input file as the options can be supplied on the command line Fix a bug in the byte-swapping routines due to a choice in the variable name which would result in problems for simulations that define the variable 'x'. 2006-09-19 04:49 joehope * trunk/xmds-devel/ChangeLog, trunk/xmds-devel/MANIFEST: Update of MANIFEST and ChangeLog 2006-09-19 04:46 joehope * trunk/xmds-devel/README, trunk/xmds-devel/README.Windows, trunk/xmds-devel/configure.in: Version updates prior to release 2006-09-19 04:01 joehope * trunk/xmds-devel/ChangeLog, trunk/xmds-devel/examples/kubo.xmds, trunk/xmds-devel/source/xmdssequence.cc, trunk/xmds-devel/source/xmdssimulation.cc: Fixes for a collection of MPI scheduler bugs (1558333,1551791,1551790). Single path runs are now handled by the "Uniform" scheduler automatically. Trying to run stochastic simulations without MPI no longer bombs. 2006-08-30 03:33 grahamdennis * trunk/xmds-devel/source/xmdssequence.cc: Flushing output after each path for stochastic simulations at Mattias' request. 2006-08-24 00:54 grahamdennis * trunk/xmds-devel/source/xmdsbreakpoint.cc: For MPI breakpoints, I was sending and receiving some values with the wrong datatype (double instead of int). I'm honestly surprised that this even worked for some systems before. 2006-08-23 23:50 grahamdennis * trunk/xmds-devel/examples/atomlaser.xmds: Removed the old-style breakpoint element from the example atomlaser.xmds as that style breakpoint was never implemented. And we don't want any confusion arising with new-style breakpoints. 2006-08-22 05:52 matt0064 * trunk/xmds-devel/source/loadxsil.m: Added code to loadxsil.m to initialise multi-dimensional arrays when loading in binary data. This can be a significant speed up. 2006-08-09 00:54 grahamdennis * trunk/xmds-devel/source/main.cc: Fixing a compile bug for stochastic MPI simulations with FFTW3. Thanks Andy! 2006-08-03 06:17 grahamdennis * trunk/xmds-devel/source/xsilfield.cc: Fixing a bug in the matlab output of xsil2graphics that would cause the script not to load the data from a binary file if the data is a scalar (zero dimensional) 2006-07-31 01:50 grahamdennis * trunk/xmds-devel/source/xmdsbreakpoint.cc, trunk/xmds-devel/source/xmdsvectorelement.cc: Fixing bugs with the breakpoint code. I'm fairly sure that it works now. 2006-07-28 05:09 grahamdennis * trunk/xmds-devel/source/xmdsvectorelement.cc: Adding rank number to diagnostic output when an error occurs while loading an XSIL file (with MPI). 2006-07-21 03:39 grahamdennis * trunk/xmds-devel/examples/diffusion.xmds, trunk/xmds-devel/examples/diffusion2.xmds, trunk/xmds-devel/source/xmdsbreakpoint.cc: I have fixed the breakpoint code for non-MPI simulations, and breakpoints should now also work for deterministic MPI simulations (it makes no sense to use breakpoints for stochastic MPI simulations). I have also modified the diffusion example to use a breakpoint and then to continue from that breakpoint (with a larger simulation grid) in a second diffusion example. 2006-07-19 03:28 joehope * trunk/xmds-devel/source/xmdsintegrateex.cc: Fix for a tiny bug temporarily introduced with the openMP code, which broke compilation of *EX algorithms. 2006-06-29 07:33 grahamdennis * trunk/xmds-devel/examples/nlse.xmds, trunk/xmds-devel/source/xmdssimulation.cc: Fixing a bug where a simulation with ascii output and a breakpoint element would not compile 2006-06-29 07:24 grahamdennis * trunk/xmds-devel/source/xmdsbreakpoint.cc, trunk/xmds-devel/source/xmdsclasses.h, trunk/xmds-devel/source/xmdsoutput.cc, trunk/xmds-devel/source/xmdssequence.cc, trunk/xmds-devel/source/xmdsvectorelement.cc, trunk/xmds-devel/source/xsilfield.cc: First crack at the breakpoint code. Currently it only works for simulations that aren't both deterministic and use MPI. Of course, the whole point of this code is for the deterministic MPI case, but for the moment, the vast majority of the helper code has been written. Changes to behaviour: when loading double-type variables with the XSIL loading code, it looks for a variable with an 'R' suffix instead of a variable of the same name. As it is impossible to have an output moment group variable of the same name as a field variable. 2006-06-23 01:54 grahamdennis * trunk/xmds-devel/source/xsilfield.cc: Increased verbosity of some errors when loading XSIL files to mention what the probable cause of the error was. 2006-06-21 07:33 grahamdennis * trunk/xmds-devel/source/xmdsvector.cc: Parallelised the multiplication loop at the end of the *go_space routines. This was causing a massive slowdown on NUMA architecture machines because the whole field was accessed from a single node. 2006-06-20 02:20 grahamdennis * trunk/xmds-devel/source/xmdssequence.cc: Added a fflush() after the 'beginning integration ...' printf lines to better keep track of simulations run with a buffered output stream (e.g. simulations run through batch queueing systems) 2006-06-20 01:59 grahamdennis * trunk/xmds-devel/source/xsilfield.cc: Increased the verbosity of one of the error shown when loading XSIL files when none of the variables to be loaded have been found. This is typically due to the wrong moment group being set. 2006-06-16 04:17 joehope * trunk/xmds-devel/source/xmdsvector.cc: Fix for the MPI version of mixed space Fourier transforms. It was simply wrong previously. 2006-06-07 06:40 joehope * trunk/xmds-devel/ChangeLog, trunk/xmds-devel/README.Windows, trunk/xmds-devel/configure.in, trunk/xmds-devel/source/main.cc, trunk/xmds-devel/source/xmdsfilter.cc, trunk/xmds-devel/source/xmdsintegrate.cc, trunk/xmds-devel/source/xmdsintegratesiip.cc: Fix for multiple bugs when using moment groups in filter and integrate blocks. The bugs were all specific to MPI specific code implementation. 2006-05-28 10:34 grahamdennis * trunk/xmds-devel/source/xmdsvectorelement.cc: Correction to my previous commit: It helps to actually set the field to zero instead of just looping over it. 2006-05-28 10:24 grahamdennis * trunk/xmds-devel/source/xmdsvectorelement.cc: Fix for OpenMP so that each field is initialised by the thread that will use it. This is important for NUMA-architecture supercomputers (e.g. ANU's ac) 2006-05-25 03:19 grahamdennis * trunk/xmds-devel/source/xmdsclasses.h, trunk/xmds-devel/source/xmdsfield.cc, trunk/xmds-devel/source/xmdsintegrate.cc, trunk/xmds-devel/source/xmdsintegrateark45ex.cc, trunk/xmds-devel/source/xmdsintegrateark45ip.cc, trunk/xmds-devel/source/xmdsintegrateex.cc, trunk/xmds-devel/source/xmdsintegrateip.cc, trunk/xmds-devel/source/xmdsintegraterk4ex.cc, trunk/xmds-devel/source/xmdsintegraterk4ip.cc, trunk/xmds-devel/source/xmdssimulation.cc, trunk/xmds-devel/source/xmdsvectorelement.cc: OpenMP support. Use the tag <use_openmp> yes </use_openmp> in the simulation element to use this. This does not work with deterministic MPI simulations, and doesn't really make sense to use it with stochastic MPI simulations. To make use of this, you will need a compiler that supports OpenMP such as icc or gcc 4.4 (currently unreleased). Note that one will get best performance if FFTW is compiled using OpenMP threads instead of pthreads. 2006-05-13 01:12 grahamdennis * trunk/xmds-devel/source/xmdsmomentgroup.cc: Forcing a fflush() after writing the 'sampled field...' lines. This way, it is easier to keep track of the progress of jobs on supercomputers 2006-05-12 07:49 grahamdennis * trunk/xmds-devel/source/xmdsvectorelement.cc: Fixed binary importing to not load the entire file into memory. This is needed for MPI situations where the initialisation data won't fit into memory. Also, previously, it was just plain wrong when used with deterministic MPI simulations. 2006-05-12 06:54 grahamdennis * trunk/xmds-devel/source/xsilfield.cc: Removing text claiming that the XSIL loading code does not support byte-swapping (it does) 2006-05-12 06:27 grahamdennis * trunk/xmds-devel/configure.in, trunk/xmds-devel/source/xmdsvectorelement.cc: Reducing the verbosity of the XSIL loading code Adding a --with-fftw3-path to the configure script so that the location of fftw3 can be specified independently of fftw2. Note that the path for fftw3 defaults to the path for fftw2 2006-05-12 04:23 grahamdennis * trunk/xmds-devel/source/xmdssimulation.cc: Fixing a missing \n in a printf statement 2006-05-12 01:48 grahamdennis * trunk/xmds-devel/source/Makefile.am, trunk/xmds-devel/source/main.cc, trunk/xmds-devel/source/xmdsclasses.h, trunk/xmds-devel/source/xmdscomplex.h, trunk/xmds-devel/source/xmdssimulation.cc, trunk/xmds-devel/source/xmdsvectorelement.cc, trunk/xmds-devel/source/xsilfield.cc, trunk/xmds-devel/source/xsilfield.h: Vector initialisation from XSIL moment groups (binary format only) This should work for MPI simulations (it doesn't load the entire binary file into memory, this is why the this code does not support importing data in ASCII format from XSIL files) This should deal with byte-swapping if necessary. (Not tested, but I'm going to). The input moment group grid does not have to match up exactly with the simulation grid, there are two modes for importing, 'strict' mode and 'loose' mode. In 'strict' mode, the initialisation geometry must match the simulation geometry to within 1% of the step size in each dimension. In 'loose' mode, the step size in each initialisation dimension (you may initialise from a mix of x- and k-space) must match the simulation step size in each dimension, but the start and end points (and the number of points) may be different. Documentation is forthcoming after I have given this a bit more testing. 2006-05-07 09:39 pharaoh84 * trunk/xmds-devel/configure.in, trunk/xmds-devel/source/main.cc: Fixing threads for fftw3 2006-05-07 03:10 pharaoh84 * trunk/xmds-devel/configure.in: Fixing my previous fix for systems with requiring explicit linking of the thread libraries. Also, the agressive CFLAGS are now used for systems that don't require explicit linking of the thread libraries (removed a pointless test) I hate autoconf. 2006-05-07 02:48 pharaoh84 * trunk/xmds-devel/configure.in: Fixing configure.in for fftw3 for systems that require explicit linking of thread libraries 2006-05-05 06:20 pharaoh84 * trunk/xmds-devel/configure.in: Fixing the configure.in script... I hate autoconf. 2006-05-05 06:10 pharaoh84 * trunk/xmds-devel/configure.in, trunk/xmds-devel/source/main.cc: configure.in has been modified to support fftw3. Now you need to provide the option --enable-fftw3 in order to get fftw3 support. One thing I forgot to mention in my previous commit comment was that the tag required to use fftw3 is <fftw_version>. This tag belongs in the simulation element. The default is 2 (fftw2), and set it to 3 to use fftw3. 2006-05-04 07:53 pharaoh84 * trunk/xmds-devel/source/main.cc, trunk/xmds-devel/source/xmdsclasses.h, trunk/xmds-devel/source/xmdscomplex.h, trunk/xmds-devel/source/xmdsfield.cc, trunk/xmds-devel/source/xmdsintegrateark45.cc, trunk/xmds-devel/source/xmdsintegraterk4.cc, trunk/xmds-devel/source/xmdsintegratesiex.cc, trunk/xmds-devel/source/xmdsintegratesiip.cc, trunk/xmds-devel/source/xmdssequence.cc, trunk/xmds-devel/source/xmdssimulation.cc, trunk/xmds-devel/source/xmdsvector.cc: Initial support for fftw3. It should work for simulations that are not deterministic MPI simulations with the following caveats: You are not permitted to use fftw_complex in your simulation script (fftw3 uses a different format for their fftw_complex type than is used by fftw2), instead you should be using the 'complex' type. autoconf does not yet detect fftw3, so to get your scripts to compile, you will need to insert a 'FFTW3_LIBS = ' line defining the fftw3 libraries to link in (-lfftw3 and optionally -lfftw3_threads) and the path to find the library if needed. Note that fftw3 uses a different format for wisdom, and this is stored under the new filename ~/.xmds/wisdom/hostname.wisdom.fftw3 or ~/.xmds/wisdom/hostname.wisdom.fftw3_threads for threaded-simulations. I have tested threaded, non-threaded, deterministic and stochastic simulations. I have not tested MPI-based stochastic simulations yet, however the scripts do compile. 2006-04-20 00:47 pharaoh84 * trunk/xmds-devel/examples/groundstate.xmds: Modifying this example to use the new <type> tag for output groups 2006-04-18 07:15 pharaoh84 * trunk/xmds-devel/source/xmdsmomentgroup.cc, trunk/xmds-doc/latex/languageReference.tex: Added a <type> tag to the <sampling> element for outputs. If this is set to 'double' then the output type is forced to type double. It defaults to 'complex' 2006-04-07 04:17 pharaoh84 * trunk/xmds-devel/source/xmdssequence.cc: Fixing the elapsed time for non-MPI simulations 2006-04-07 03:35 pharaoh84 * trunk/xmds-devel/source/xsil2graphics.cc: Fix spelling mistake 'Proccessing...' --> 'Processing..' 2006-03-29 00:34 athiator * trunk/xmds-devel/source/xsilfield.cc: Also prints created variables to screen when executing Mathematica instructions 2006-03-15 04:27 athiator * trunk/xmds-devel/source/xmlbasics.cc, trunk/xmds-devel/source/xmlbasics.h, trunk/xmds-devel/source/xsil2graphics.cc, trunk/xmds-devel/source/xsilfield.cc, trunk/xmds-devel/source/xsilfield.h: Changes to xsil2graphics to output a file with commands to read simulation data into Mathematica 2006-01-27 01:04 joehope * trunk/xmds-devel/source/xmdsmomentgroup.cc: Fixed error in MPI reduction for deterministic systems. The problem only affected some moment groups that used post_propagation. 2005-11-23 23:44 joehope * trunk/xmds-devel/examples/gaugeatomlaser.xmds, trunk/xmds-devel/examples/groundstate.xmds: Adding imaginary time evolution algorithm to the examples. It is often requested, demonstrates filters and moment_groups, and saves mailing it regularly. 2005-10-31 00:34 joehope * trunk/xmds-devel/source/xmdsintegraterk4ip.cc: Avoid warning for one case where it does not apply. 2005-10-27 07:01 joehope * trunk/xmds-devel/ChangeLog, trunk/xmds-devel/MANIFEST, trunk/xmds-devel/admin/xmds.spec: Final updates before 1.5-2 release 2005-10-27 00:58 joehope * trunk/xmds-devel/ChangeLog, trunk/xmds-devel/source/xmdssequence.cc, trunk/xmds-devel/source/xmdssimulation.cc: Fixed adaptive scheduler to compile cleanly on other systems. 2005-10-26 03:46 joehope * trunk/xmds-devel/ChangeLog, trunk/xmds-devel/README, trunk/xmds-devel/README.Windows, trunk/xmds-devel/configure.in, trunk/xmds-devel/examples/kubo.xmds, trunk/xmds-devel/source/main.cc, trunk/xmds-devel/source/xmdssequence.cc, trunk/xmds-devel/source/xmdssimulation.cc: Added new scheduling option for stochastic MPI calculations. It uses an adaptive scheduler to allocate batches of work to individual nodes, making for large speed increases on heterogenous systems. Bumped version numbers. 2005-10-24 22:40 joehope * trunk/xmds-devel/source/xmdssequence.cc: Fix for new timer. 2005-10-24 04:11 joehope * trunk/xmds-devel/source/xmdssequence.cc, trunk/xmds-devel/source/xmdssimulation.cc: Changed timer to work better on MPI systems. 2005-10-18 23:33 joehope * trunk/xmds-devel/examples/kubo.xmds, trunk/xmds-devel/examples/tla.xmds, trunk/xmds-devel/source/xmdsclasses.h, trunk/xmds-devel/source/xmdssimulation.cc, trunk/xmds-devel/source/xmdsvectorelement.cc: Fix for stack overflow in binary read from file. Preliminary support for MPI Scheduling options. 2005-10-13 00:45 joehope * trunk/xmds-devel/source/xmdssequence.cc: MPI runs only print out the benchmark time from the master node. 2005-10-12 04:34 joehope * trunk/xmds-devel/source/xmdsvectorelement.cc: Fix for crashing bug when loading from file in stochastic simulations. 2005-09-29 05:35 joehope * trunk/xmds-devel/ChangeLog, trunk/xmds-devel/source/xmdsmomentgroup.cc: Fix compile error for error-free stochastic binary output. 2005-08-12 05:46 sebwuester * trunk/xmds-devel/examples/sech_soliton.xmds, trunk/xmds-devel/source/xmdsclasses.h, trunk/xmds-devel/source/xmdsintegrateark45.cc: -Bugfixes in ARK45: -current step now states last accepted step instead of current forecast -fixed problems with timescales <10^-24 -fixed problem with N_samples=N_steps -Cosmetic in ARK45 - rephrased "cutoff defaulting to" not to contain the word error 2005-07-27 06:57 joehope * trunk/xmds-devel/source/xmdsintegratesiip.cc: Fixed an error in the cross propagation routines of the SIIP algorithm. Boundary conditions that are independent of the propagation dimension are now correct. 2005-07-05 10:13 joehope * trunk/xmds-devel/ChangeLog, trunk/xmds-devel/MANIFEST: Updating Changelog and MANIFEST prior to release 2005-07-05 09:37 joehope * trunk/xmds-devel/README, trunk/xmds-devel/README.Windows, trunk/xmds-devel/examples/highdim.xmds: Adjusting READMEs and examples for version 1.5-1x 2005-06-30 07:44 sebwuester * trunk/xmds-devel/source/xmdsintegrateark45.cc: Minor Bugfixes: Corrected typo in on-screen message and call to noise generator in the case of errorchecking 2005-05-25 03:33 paultcochrane * trunk/xmds-devel/examples/highdim.xmds: Fixed xml header. 2005-05-24 03:54 paultcochrane * trunk/xmds-devel/configure.in: Doing a check to see if the library lammpi++ exists in the mpicc -showme output, and if not adds -llammpi++ to the MPI_LIBS variable. This should only affect users of lam 7.x.x, this problem didn't occur in 6.x.x. 2005-05-19 05:46 paultcochrane * trunk/xmds-devel/source/xmdssequence.cc: Outputting standard C argument stuff even when <argv> is not defined. This fixes a problem where I didn't check for all possible paths in an if loop 2005-05-19 03:50 joehope * trunk/xmds-devel/ChangeLog: Update of ChangeLog 2005-05-19 03:42 joehope * trunk/xmds-devel/source/xsilfield.cc: The m file now closes files when it is done to avoid excess file pointer usage in Matlab. 2005-05-17 06:01 sebwuester * trunk/xmds-devel/source/xmdsintegrateark45.cc, trunk/xmds-devel/source/xmdsintegraterk4ip.cc: Fixed bug in warning about RK4IP and t-dep k operators. Made ARK45 error determination routine more efficient for ODEs 2005-05-10 03:40 paultcochrane * trunk/xmds-devel/source/main.cc: Moved -o <simulation_name> <simulation_name>.cc to just behind the mpicc call in the mpi compilation calls. This gets around problems with mpicc not finding various libraries. In particular, when getopt was turned on for mpi problems, mpicc wasn't finding -lxmds. 2005-05-10 01:23 paultcochrane * trunk/xmds-devel/configure.in: Changed ordering of MPICCFLAGS so that XMDS_LIBS is at the end. This should stop problems with mpicc not finding the xmds libraries. 2005-05-05 09:34 paultcochrane * trunk/xmds-devel/source/xmdssequence.cc: Hopefully fixed problem with mpi not being able to make use of the arugment parsing code. Added -h as a valid option; --help was only possible before. 2005-05-02 05:42 sebwuester * trunk/xmds-devel/examples/sech_soliton.xmds, trunk/xmds-devel/examples/sech_soliton_tdepk.xmds, trunk/xmds-devel/source/xmdsintegrateark45.cc: Fixed float precision issue in ARK45 sampling and typos in examples. 2005-05-02 02:35 sebwuester * trunk/xmds-devel/examples/sech_soliton.xmds, trunk/xmds-devel/examples/sech_soliton_tdepk.xmds, trunk/xmds-devel/source/xmdsclasses.h, trunk/xmds-devel/source/xmdsintegrate.cc, trunk/xmds-devel/source/xmdsintegrateark45.cc, trunk/xmds-devel/source/xmdsintegrateark45ex.cc, trunk/xmds-devel/source/xmdsintegrateark45ip.cc, trunk/xmds-devel/source/xmdsintegrateip.cc, trunk/xmds-devel/source/xmdsintegraterk4ip.cc, trunk/xmds-devel/source/xmdsvectorelement.cc: Added ARK45IP and ARK45EX adaptive timestep algorithms. Added example files sech_soliton.xmds, sech_soliton_tdepk.xmds Added parallel initialisation from file (ascii only) 2005-04-28 05:21 joehope * trunk/xmds-devel/source/loadxsil.m: Fix for loadxsil loading of 64 bit binaries 2005-04-27 05:44 joehope * trunk/xmds-devel/source/xmdsfield.cc: Andy's fix for cluster nodes testing the same filesystem simultaneously with the same files. 2005-04-24 04:31 joehope * trunk/xmds-devel/source/xsilfield.h: Final commit for previous fix. 2005-04-21 06:32 joehope * trunk/xmds-devel/configure.in, trunk/xmds-devel/source/xmdsmomentgroup.cc, trunk/xmds-devel/source/xsilfield.cc: Added test for the size of unsigned longs in the configure script. This, like endianness, is stored in the xsil file for binary output, and then used when generating the MATLAB script. Fixes bug with moving binary data between machines. 2005-04-12 07:25 joehope * trunk/xmds-devel/source/xmdsclasses.h, trunk/xmds-devel/source/xmdsintegrate.cc, trunk/xmds-devel/source/xmdsintegrateark45ex.cc, trunk/xmds-devel/source/xmdsintegrateark45ip.cc: Set up template for passing the adaptive boolean to the xmdsintegrate class. 2005-04-12 05:44 joehope * trunk/xmds-devel/source/xsilfield.cc: Fixed matlab error message when using binary files without the output file 2005-04-06 06:41 paultcochrane * trunk/xmds-devel/examples/lorenzInput.dat: Initial import to repository. This is the data file associated with the lorenz.xmds example. 2005-04-06 05:54 joehope * trunk/xmds-devel/examples/branch.xmds, trunk/xmds-devel/examples/brusselator.xmds, trunk/xmds-devel/examples/catcycle.xmds, trunk/xmds-devel/examples/chain.xmds, trunk/xmds-devel/examples/chemkin.xmds, trunk/xmds-devel/examples/duffing.xmds, trunk/xmds-devel/examples/fibre.xmds, trunk/xmds-devel/examples/fisher_reaction_diffusion.xmds, trunk/xmds-devel/examples/highdim.xmds, trunk/xmds-devel/examples/hires.xmds, trunk/xmds-devel/examples/krebs.xmds, trunk/xmds-devel/examples/lane_emden.xmds, trunk/xmds-devel/examples/lorenz.xmds, trunk/xmds-devel/examples/lotka_volterra.xmds, trunk/xmds-devel/examples/oregonator.xmds, trunk/xmds-devel/examples/pendulum.xmds, trunk/xmds-devel/examples/ring_modulator.xmds, trunk/xmds-devel/examples/sine.xmds, trunk/xmds-devel/examples/soliton.xmds, trunk/xmds-devel/examples/thermkin.xmds, trunk/xmds-devel/examples/van_der_pol.xmds: Fixing all examples to conform with the (post 1.4-1) rule to always specify the used vectors in integrate blocks. 2005-04-06 02:22 joehope * trunk/xmds-devel/source/xmdsmomentgroup.cc: Fix for potential problem with handling sample spaces when there are no transverse dimensions. 2005-04-06 01:43 joehope * trunk/xmds-devel/source/xmdsmomentgroup.cc: Made verbose output on the moment groups more consistent with the numbering of the groups. 2005-04-05 23:23 joehope * trunk/xmds-devel/ChangeLog, trunk/xmds-devel/configure.in: Version bump 2005-04-05 07:23 joehope * trunk/xmds-devel/source/Makefile.am, trunk/xmds-devel/source/main.cc, trunk/xmds-devel/source/xmdsclasses.h, trunk/xmds-devel/source/xmdsintegrateark45.cc, trunk/xmds-devel/source/xmdsintegrateark45ex.cc, trunk/xmds-devel/source/xmdsintegrateark45ip.cc, trunk/xmds-devel/source/xmdssequence.cc: Adding in shell files for new ARK45 algorithms and bumping versions. 2005-04-05 05:32 joehope * trunk/xmds-devel/examples/diffusion.xmds: Fixed sampling in example. 2004-12-06 04:58 paultcochrane * trunk/xmds-devel/source/xsilfield.cc: Now orienting independent variable vectors for binary input to agree with that from ascii input. 2004-12-06 04:42 paultcochrane * trunk/xmds-devel/source/xsilfield.cc: Changed ordering of variables in binary input to matlab. Should work the same as ascii now. Some changes to comments. 2004-11-17 23:35 joehope * trunk/xmds-devel/source/xsilfield.cc: Fixed a bug when using MATLAB import of output moment groups of >2 dimensions in binary format. 2004-11-17 04:54 joehope * trunk/xmds-devel/source/xsilfield.cc: Adding explicit include line to avoid problem with non-standard compilers. 2004-11-02 22:51 joehope * trunk/xmds-devel/examples/atomlaser.xmds: Changing this example to demo binary output, now that it works without explosions. 2004-11-02 22:48 joehope * trunk/xmds-devel/ChangeLog: New ChangeLog for the new version 2004-11-02 22:47 joehope * trunk/xmds-devel/MANIFEST: New manifest for the new version. 2004-11-02 22:43 joehope * trunk/xmds-devel/source/xsilfield.cc: Fix for an error where an integer overflow lead to dramatic problems with bianry output. 2004-10-25 06:02 joehope * trunk/xmds-devel/configure.in, trunk/xmds-devel/source/main.cc: Bumping the release version in preparation for a new release. 2004-10-22 08:04 paultcochrane * trunk/xmds-devel/admin/xmdsReleaseProcedure.pod: Made mention that one should update the xmds version and release numbers in configure.in. Gave a more complete explanation of generating a distribution, including checking out a temporary copy of the xmds-devel repository and going through the relevant steps to be able to do a make dist. 2004-10-22 01:16 paultcochrane * trunk/xmds-devel/source/xsilfield.cc: Added some error text for when a user tries to use binary output and then load the data using scilab. Also put in some hopefully helpful information about how to use scilab and data that comes out of xmds. Basically this means just using ascii output. 2004-10-21 10:01 paultcochrane * trunk/xmds-devel/source/xsilfield.h: Correction log for previously stuffed up commit without a log. Added extra variables to implement binary data handling of xsil2graphics. 2004-10-21 10:00 paultcochrane * trunk/xmds-devel/source/xsilfield.cc: Simple commit to actually add a log for the previous commit, because I stuffed up. Major changes. Binary files are now handled by xsil2graphics. Unfortunately, only the matlab script is produced at this stage. The scilab version is to come. 2004-10-21 09:51 paultcochrane * trunk/xmds-devel/source/xsilfield.cc, trunk/xmds-devel/source/xsilfield.h: xsilfield.cc 2004-10-21 09:51 paultcochrane * trunk/xmds-devel/source/xmdsvectorelement.cc: Changed some return statements to exit statements. Basically, the program could keep going at this point as opposed to barfing which would be far more logical in the circumstances. 2004-10-21 09:50 paultcochrane * trunk/xmds-devel/source/xmdsvector.cc: Changed unsigned long to unsigned long int. I must have been in a pedantic mood. 2004-10-21 09:49 paultcochrane * trunk/xmds-devel/source/xmdsoutput.cc: Added xmdsOutputFileName() function. This is so that I can properly determine what the output binary data filename should be, and base that upon the name of the xsil filename as opposed to the simulation filename. 2004-10-21 09:48 paultcochrane * trunk/xmds-devel/source/xmdsmomentgroup.cc: Major changes. Added more attributes to the Metalink tag of the xsil file that gets output so that can load binary data properly using xsil2graphics. Implemented a better way of constructing the output binary data filename. It is now based upon the xsilFilename rather than the simulation name (these can be different). Fixed major bug where if there is only one sample in the entire simulation (possible but not common) then data was being written over as an array was incorrectly sized. This is all happy now, and I even tested it. Yay. 2004-10-21 09:42 paultcochrane * trunk/xmds-devel/source/xmdsfilter.cc: Added a Doxygen docstring. 2004-10-21 09:41 paultcochrane * trunk/xmds-devel/source/xmdscomplex.h: Fixed problem with there being no newline at the end of the file. 2004-10-21 09:40 paultcochrane * trunk/xmds-devel/source/xmdsclasses.h: Was pedantic again and changed some unsigned constants to long unsigned ints. Added the getOutputFileName() function, and its Doxygen docstring. 2004-10-21 09:39 paultcochrane * trunk/xmds-devel/source/loadxsil.m: Removed some superfluous code in the binary loading section. Made loading of the binary data file part of the eval, as opposed to running it here. Added some strings to say that the text that follows isn't actually just informative, it is actually the code that is being executed. 2004-10-21 09:37 paultcochrane * trunk/xmds-devel/source/getopt_xmds1.c, trunk/xmds-devel/source/getopt_xmds_init.c: Added some Doxygen docstrings. 2004-10-21 09:36 paultcochrane * trunk/xmds-devel/source/getopt_xmds.c: Reformat of the C code. Documentation with Doxygen docstrings. 2004-10-21 09:34 paultcochrane * trunk/xmds-devel/configure.in: Updated version number to interim release number. 2004-10-15 07:53 joehope * trunk/xmds-devel/configure.in: Various fixes to the mpi autoconf testing. It now works with non-gcc mpi. 2004-10-11 04:06 joehope * trunk/xmds-devel/configure.in: Removed a "-Wall -pedantic" check that broke compilation when cc/mpicc were gnu/non-gnu compilers. 2004-10-06 07:52 joehope * trunk/xmds-devel/source/xmdsfilter.cc, trunk/xmds-devel/source/xmdsintegrate.cc, trunk/xmds-devel/source/xmdsintegraterk4.cc, trunk/xmds-devel/source/xmdsintegratesiex.cc, trunk/xmds-devel/source/xmdsintegratesiip.cc, trunk/xmds-devel/source/xmdsmomentgroup.cc, trunk/xmds-devel/source/xmdssequence.cc, trunk/xmds-devel/source/xmdsvectorelement.cc: Fixed a memory leak on strict compilers that didn't know that "delete(pointer)" means "delete[] pointer" for pointer arrays. 2004-10-06 07:50 joehope * trunk/xmds-devel/examples/kubo.xmds, trunk/xmds-devel/examples/van_der_pol.xmds: These, and possibly others, now need <vectors> elements in the integrate blocks. 2004-09-30 03:27 paultcochrane * trunk/xmds-devel/source/loadxsil.m: Fixed binary loading support. This now works for mutli-dimensional matrices (ie greater than two dims). Probably should be tested a bit more extensively than I've tested it, but it seems to go well in the tests that I've done. The ascii loading takes ages, especially for large output data files, so I've added a message saying that it will take ages, and have added progress output to keep the user amused while they're waiting. Realistically for large files people should use binary as it loads a couple of orders of magnitude faster than ascii. I've also implemented preallocation of matrices to help the ascii loading to run more quickly. Using this script turns out to be a better option for very large files as it doesn't use up as much memory as xsil2graphics does. For some sims I've been doing recently, xsil2graphics maxes out the memory on my machine when it's trying to generate the matlab file and data file, however, loadxsil sits there quite happily and doesn't even bother making the machine page to disk. This implies that there could be a memory leak in xsil2graphics, or that something could be done a bit more carefully concerning memory useage. 2004-09-24 03:29 paultcochrane * trunk/xmds-devel/Makefile.am: Fixed typo in orgeonator name. 2004-09-15 06:01 joehope * trunk/xmds-devel/source/xmdsintegraterk4ex.cc, trunk/xmds-devel/source/xmdsintegraterk4ip.cc: Fix for <no_noise> flag in RK4 algorithms. 2004-09-15 04:46 joehope * trunk/xmds-devel/source/xmdsclasses.h, trunk/xmds-devel/source/xmdsfilter.cc, trunk/xmds-devel/source/xmdsintegrate.cc, trunk/xmds-devel/source/xmdsintegraterk4.cc, trunk/xmds-devel/source/xmdsintegratesiex.cc, trunk/xmds-devel/source/xmdsintegratesiip.cc: Added flag that turns off the noise generation in an integration or filter element. This allows deterministic elements in stochastic simulations (e.g. the noise is in the initial state only) to run faster. Activated by the flag <no_noise>yes</no_noise>, and the default is to turn off this feature. 2004-09-15 04:27 joehope * trunk/xmds-devel/ChangeLog: Updated with cvs2cl.pl 2004-08-03 05:29 paultcochrane * trunk/xmds-devel/examples/brusselator.xmds, trunk/xmds-devel/examples/chain.xmds, trunk/xmds-devel/examples/oregonator.xmds, trunk/xmds-devel/examples/thermkin.xmds: Added GPL header. 2004-08-02 10:04 paultcochrane * trunk/xmds-devel/source/xmdsoutput.cc: Changed long to long unsigned int, which gets rid of a compiler warning, and appears only because compilers can choose which sign ints can take, hence being pedantic is the way to go. 2004-08-02 10:02 paultcochrane * trunk/xmds-devel/source/xmdsfilter.cc, trunk/xmds-devel/source/xmdsintegrate.cc, trunk/xmds-devel/source/xmdsintegratesiip.cc: Changed longs to long unsigned ints. Also fixed warnings that appear due to a .size() call on a list (which returns int) being given a format in a printf statement as being a long int. If this isn't quite the right thing to do then one probably needs to overload/override the .size() method to return long ints as opposed to just ints. 2004-08-02 09:59 paultcochrane * trunk/xmds-devel/source/xmdsclasses.h: Changed longs to long unsigned ints. 2004-08-02 09:57 paultcochrane * trunk/xmds-devel/Makefile.am: Added new example simulations to list of files to be added when doing a make dist. 2004-08-02 08:50 paultcochrane * trunk/xmds-devel/source/xmdsfilter.cc, trunk/xmds-devel/source/xmdsintegrate.cc, trunk/xmds-devel/source/xmdsintegratesiip.cc: Reformatted code so it looks nicer. 2004-08-02 08:47 paultcochrane * trunk/xmds-devel/source/xmdsfield.cc: Changed long to long unsigned int. This is a really pedantic change I know, but we need to be really explicit so that the code is really pedantically ansi compliant, and hopefully therefore more portable. 2004-08-02 08:45 paultcochrane * trunk/xmds-devel/source/xmdsclasses.h: Changed variables declared as longs to be long unsigned ints. This gets rid of some compiler warnings, especially between compilers that define ints to be signed or unsigned on their whim. 2004-08-02 08:16 paultcochrane * trunk/xmds-devel/examples/chain.xmds: Initial import to repository. This is another chemical kinetics reaction I found lying around in my sandbox. 2004-08-02 08:10 paultcochrane * trunk/xmds-devel/examples/brusselator.xmds, trunk/xmds-devel/examples/oregonator.xmds, trunk/xmds-devel/examples/thermkin.xmds: Initial import to repository. These are some more example simulations of chemical kinetics type reactions. 2004-08-02 08:04 paultcochrane * trunk/xmds-devel/benchmark/ndparamp_100.xmds, trunk/xmds-devel/benchmark/ndparamp_200.xmds, trunk/xmds-devel/benchmark/ndparamp_50.xmds, trunk/xmds-devel/benchmark/ndparamp_500.xmds, trunk/xmds-devel/benchmark/nlse_100.xmds, trunk/xmds-devel/benchmark/nlse_1000.xmds, trunk/xmds-devel/benchmark/nlse_10000.xmds, trunk/xmds-devel/benchmark/nlse_500.xmds, trunk/xmds-devel/benchmark/nlse_5000.xmds: Removed the binary_output tag as it is now obsolete. 2004-08-02 08:02 paultcochrane * trunk/xmds-devel/source/xmdssimulation.cc: Stopped storing all of the description text; we weren't using it anyway. There is now a message added to say that the description has been found, and to look in the xmds file for more info. The reason for this change is because if the description is too big, then this causes a buffer overflow and all kinds of wierd things can happen. I have commented out the original code that read the description in. 2004-07-30 07:43 joehope * trunk/xmds-devel/source/xmdsfilter.cc, trunk/xmds-devel/source/xmdsvector.cc: Allowed integrate moment groups to deal with mixed spaces and MPI transposed spaces properly. 2004-07-30 06:56 joehope * trunk/xmds-devel/source/xmdsfield.cc: Fixed the close_loops function which used to be simply wrong for mixed spaces. 2004-07-30 06:02 joehope * trunk/xmds-devel/source/xmdsfield.cc, trunk/xmds-devel/source/xmdsvector.cc: Fixed a bug where some mixed spaces were incorrectly recognised as being in the transposed order for deterministic MPI solutions. 2004-07-29 08:28 joehope * trunk/xmds-devel/examples/highdim.xmds: Added example syntax for the new <moment_group> elements in the evolution. 2004-07-29 08:27 joehope * trunk/xmds-devel/source/xmdsclasses.h, trunk/xmds-devel/source/xmdsfilter.cc, trunk/xmds-devel/source/xmdsintegrate.cc, trunk/xmds-devel/source/xmdsintegratesiip.cc, trunk/xmds-devel/source/xmdssequence.cc, trunk/xmds-devel/source/xmdssimulation.cc: Added the option of putting <moment_group> elements as well as <functions> elements in <integrate> blocks. <moment_group> elements let you define moments that are integrated through any number of transverse dimensions, so XMDS can now evolve equations that depend on integrals of the fields. Also added <moment_group> and <functions> elements to <filter> elements. You can put as many as you like, of any dimension, in any order. The <vectors> element defines the position of the <integrate> or <filter> code, so it is now mandatory. Sample syntax will be added to an example. 2004-07-27 07:33 paultcochrane * trunk/xmds-devel/source/xmlparser.cc: Cast a variable as unsigned. This stopped a warning message turning up in the compiler output due to an integer which should have been cast as unsigned. 2004-07-27 07:31 paultcochrane * trunk/xmds-devel/source/xmdsvectorelement.cc: Fixed error whereby an extra comma was added to a fprintf statement, and hence caused incorrect output when generating the code for reading in an input file. 2004-07-27 06:45 paultcochrane * trunk/xmds-devel/source/getopt_xmds_init.c: Replaced C++ comments with C-style comments. This stops some compilers complaining. 2004-07-23 07:27 joehope * trunk/xmds-devel/source/xmdsfield.cc: Fixes problem when multiple FFTW plans were created using wisdom. The variables used for the wisdom manipulation are all now local variables, so there are no more multiple definitions. 2004-07-21 05:45 joehope * trunk/xmds-devel/source/xmdsoutput.cc: Added the command line variables to the <info> element in the output tag. This will make the xsil file completely self documenting. 2004-07-19 03:59 paultcochrane * trunk/xmds-devel/admin/xmdsReleaseProcedure.pod: Found a command to put on its own line that I'd missed. 2004-07-19 03:57 paultcochrane * trunk/xmds-devel/MANIFEST: Updated manifest to xmds-1.3-5. 2004-07-19 03:56 paultcochrane * trunk/xmds-devel/admin/xmdsReleaseProcedure.pod: Put all of the commands to run on their own line. 2004-07-19 03:53 paultcochrane * trunk/xmds-devel/ChangeLog: Updated with cvs2cl.pl 2004-07-19 03:52 paultcochrane * trunk/xmds-devel/README, trunk/xmds-devel/README.Windows: Changed xmds-1.3-4 to xmds 1.3-5. 2004-07-19 03:43 paultcochrane * trunk/xmds-devel/ChangeLog: Updated with cvs2cl.pl 2004-07-19 03:42 paultcochrane * trunk/xmds-devel/source/loadxsil.m: Now detecting when there are more than two independent variables when loading binary data and output an error saying that one should use ascii data and xsil2graphics to get around the problem. The file still works for less than two independent variables (or less) with binary data and for any number of variables with ascii data (but one might as well just use xsil2graphics in that case). 2004-07-19 03:40 paultcochrane * trunk/xmds-devel/source/getopt_xmds.h: Fixed warnings that were produced as a result of having C++ comments within a C file (and when using -pedantic and -ansi). Having C++ style comments isn't a problem with modern compilers, however it's nice for users to not have warnings come up when xmds compiles. 2004-07-16 04:02 paultcochrane * trunk/xmds-devel/examples/atomlaser.xmds: Removed precision=single bit from output tag. 2004-07-16 03:46 paultcochrane * trunk/xmds-devel/admin/xmdsReleaseProcedure.pod: Added more detailed info about how to perform a release of the xmds documentation. Put the tagging commands earlier in the list of things to do before making a release, and mentioned the format of the tag to use. Also added the actual commands to use. 2004-07-16 03:25 paultcochrane * trunk/xmds-devel/admin/xmdsReleaseProcedure.pod: Changed the order of when the Readmes are updated and when the ChangeLog is updated. Added a line explaining how one should check to see if the cvs and/or the local repository needs updating before running a make dist. 2004-07-16 03:20 paultcochrane * trunk/xmds-devel/ChangeLog: Updated to current output of cvs2cl.pl. 2004-07-16 03:19 paultcochrane * trunk/xmds-devel/admin/xmdsReleaseProcedure.pod: We're now automatically generating the ChangeLog with cvs2cl.pl, so have changed what to do as far as that is concerned. 2004-07-16 03:16 paultcochrane * trunk/xmds-devel/ChangeLog: Updated to current output of cvs2cl.pl. 2004-07-16 03:12 paultcochrane * trunk/xmds-devel/README.Windows: Made mention of the fact that fftw must be installed after cygwin is installed. Also added a description of the steps required to build and install fftw. Fixed up the step numbering as necessary. Added --with-fftw-path=/usr/local to the configure option to the xmds build procedure, as this *should* be where fftw is installed, assuming that the user followed the instructions higher up in the file. Removed some comments reminding me to do stuff. 2004-07-16 01:27 paultcochrane * trunk/xmds-devel/admin/cvs2cl.pl: Initial import to repository. This is the cvs to ChangeLog script that generates the ChangeLog. 2004-07-15 07:27 joehope * trunk/xmds-devel/source/xmdsoutput.cc: Moved <info> tags down above the data to make the XSIL file valid XML. This fixed a parsing error from xsil2graphics. 2004-07-14 11:48 paultcochrane * trunk/xmds-devel/source/main.cc, trunk/xmds-devel/source/xmdsoutput.cc: Finally got grabbing and splitting up and escaping quote issues in the script code grabbing code. This is quite a big change, and means that xmds produced scripts now compile ok on linux and the APAC sc. I haven't tested anything else, but it's 10pm, and I've finally fixed the damned thing, and I'm going home (yay). 2004-07-14 06:37 joehope * trunk/xmds-devel/ChangeLog, trunk/xmds-devel/examples/atomlaser.xmds, trunk/xmds-devel/examples/fibre.xmds, trunk/xmds-devel/examples/fisher_reaction_diffusion.xmds, trunk/xmds-devel/examples/fullpos3D.xmds, trunk/xmds-devel/examples/gaugeatomlaser.xmds, trunk/xmds-devel/examples/highdim.xmds, trunk/xmds-devel/examples/hires.xmds, trunk/xmds-devel/examples/kubo.xmds, trunk/xmds-devel/examples/lorenz.xmds, trunk/xmds-devel/examples/ndparamp.xmds, trunk/xmds-devel/examples/nlse.xmds, trunk/xmds-devel/examples/pendulum.xmds, trunk/xmds-devel/examples/ring_modulator.xmds, trunk/xmds-devel/examples/sine.xmds, trunk/xmds-devel/examples/soliton.xmds, trunk/xmds-devel/examples/tla.xmds, trunk/xmds-devel/examples/vibstring.xmds, trunk/xmds-devel/source/main.cc: Changed the examples and template to ascii output until binary output is robust. 2004-07-14 04:27 joehope * trunk/xmds-devel/source/xmdssequence.cc, trunk/xmds-devel/source/xmdssimulation.cc: Fixed bug where nested subsequences could count moment samples incorrectly. The field moment samples were being counted at the start of each sequence rather than at the start of the simulation. 2004-07-14 01:32 joehope * trunk/xmds-devel/source/xmdsmomentgroup.cc: Verbose mode now mentions the addition of samples to the moment groups. 2004-07-13 08:46 paultcochrane * trunk/xmds-devel/source/xmdsargelement.cc: Removed a trigraph. Added a test to see if a short option was actually found, and if no short option could be worked out, then xmds barfs with a reasonably helpful error message. Also fixed a typo in one of the comments. 2004-07-13 07:52 paultcochrane * trunk/xmds-devel/configure.in: Added the threads checking stuff back in. However, to enable this option, one needs to use --enable-threads at the configuration step. I put this back in so that if someone does want to use threads, then at least the checking and configuration is built in. The code that was originally there is now wrapped in an if loop, and is only executed if --enable-threads is set. 2004-07-13 07:25 paultcochrane * trunk/xmds-devel/configure.in: added -pedantic flag to CFLAGS and CXXFLAGS variables for building of xmds and the -ansi flag to the CXXFLAGS variable. 2004-07-13 07:24 paultcochrane * trunk/xmds-devel/source/kissdom.h, trunk/xmds-devel/source/xmdsclasses.h, trunk/xmds-devel/source/xmlbasics.h: Removed fake trigraphs (obsolecent feature of C) that were in the comments. 2004-07-13 06:16 paultcochrane * trunk/xmds-devel/source/xmdsutils.h: Fixed problem with trailing comma in enumeration. This was found by using the -pedantic flag to gcc. 2004-07-13 05:29 paultcochrane * trunk/xmds-devel/source/kissdom.cc, trunk/xmds-devel/source/main.cc, trunk/xmds-devel/source/xmdsarg.cc, trunk/xmds-devel/source/xmdsargelement.cc, trunk/xmds-devel/source/xmdsargv.cc, trunk/xmds-devel/source/xmdsbreakpoint.cc, trunk/xmds-devel/source/xmdselement.cc, trunk/xmds-devel/source/xmdsfield.cc, trunk/xmds-devel/source/xmdsfilter.cc, trunk/xmds-devel/source/xmdsglobals.cc, trunk/xmds-devel/source/xmdsintegrate.cc, trunk/xmds-devel/source/xmdsintegrateex.cc, trunk/xmds-devel/source/xmdsintegrateip.cc, trunk/xmds-devel/source/xmdsintegraterk4.cc, trunk/xmds-devel/source/xmdsintegraterk4ex.cc, trunk/xmds-devel/source/xmdsintegraterk4ip.cc, trunk/xmds-devel/source/xmdsintegratesi.cc, trunk/xmds-devel/source/xmdsintegratesiex.cc, trunk/xmds-devel/source/xmdsintegratesiip.cc, trunk/xmds-devel/source/xmdsmomentgroup.cc, trunk/xmds-devel/source/xmdsoutput.cc, trunk/xmds-devel/source/xmdssegment.cc, trunk/xmds-devel/source/xmdssequence.cc, trunk/xmds-devel/source/xmdssimulation.cc, trunk/xmds-devel/source/xmdsutils.cc, trunk/xmds-devel/source/xmdsvector.cc, trunk/xmds-devel/source/xmdsvectorelement.cc, trunk/xmds-devel/source/xmlbasics.cc, trunk/xmds-devel/source/xmlparser.cc, trunk/xmds-devel/source/xsil2graphics.cc, trunk/xmds-devel/source/xsilfield.cc: Added braces to if, while and for statements. They weren't necessary, however, it does make the code a bit nicer, in terms of style, it might save a few bugs in the future, and it really should be used when the if, while or for has nested if, while or for statements. I hope this reduces someone's pain in the future. 2004-07-09 06:47 joehope * trunk/xmds-devel/source/xmdsfield.cc: cstr() should be c_str() 2004-07-09 06:35 joehope * trunk/xmds-devel/source/xmdsfield.cc: Attempt to stop a very rare crash when a deterministic MPI script is written without any Fourier space elements anywhere. Forces plans to always be written. This could be done with slightly greater finesse by testing for the existence of "main_forward_plan" and setting the appropriate variables manually if it doesn't exist. 2004-07-09 05:29 joehope * trunk/xmds-devel/source/xmdsvectorelement.cc: Forcing abort when input file is misread. 2004-07-01 05:26 paultcochrane * trunk/xmds-devel/source/kissdom.cc, trunk/xmds-devel/source/main.cc: Added braces to if, while and for statements. They weren't necessary, however, it does make the code a bit nicer, in terms of style, it might save a few bugs in the future, and it really should be used when the if, while or for has nested if, while or for statements. This exercise fixed two possible bugs where there was a trailing semicolon on the statement. I hope this reduces someone's pain in the future. 2004-06-30 10:23 paultcochrane * trunk/xmds-devel/source/xmdssimulation.cc: Commented out some legacy code that's not doing anything anymore. I'm keeping it around for a while before I delete it (doesn't hurt). 2004-06-30 10:22 paultcochrane * trunk/xmds-devel/source/main.cc: Updated the documentation version numbering output from xmds-1.3-4 to xmds-1.3-5. 2004-06-30 10:20 paultcochrane * trunk/xmds-devel/source/getopt_xmds_init.c: Added a dummy statement to avoid a warning that some compilers throw up when the ifdef isn't executed, and hence there aren't any executable statements in the file. Also added some comments explaining this. 2004-06-30 10:18 paultcochrane * trunk/xmds-devel/configure.in: Changed the release number from 4 to 5. Added a check for the Tru64 compiler and then set the __USE_STD_IOSTREAM appropriately if it is. Added a check for if mpicc is *not* set, but mpi is enabled and then if so, setting MPICC to the system C++ compiler. Fixed bug whereby LIBS variable should have been XMDS_LIBS, and CFLAGS should have been XMDS_CFLAGS. Hopefully this stuff gets xmds configuring and compiling better on Tru64 machines. 2004-06-30 10:15 paultcochrane * trunk/xmds-devel/README.Windows: Added some more helpful comments about how to use the configure script, where to look for more information, and how to solve the common fftw path problem. 2004-06-30 10:14 paultcochrane * trunk/xmds-devel/README: Tidied up the formatting of the text somewhat. Hopefully made a bit clearer that the switches are directly to do with the configure command. 2004-06-30 07:26 paultcochrane * trunk/xmds-devel/man, trunk/xmds-devel/man/loadxsil.1, trunk/xmds-devel/man/xmds.1, trunk/xmds-devel/man/xsil2graphics.1: Initial import to repository. These are the automatically generated man pages from the pod in the xmds-doc project. 2004-06-30 07:20 paultcochrane * trunk/xmds-devel/source/xmdssimulation.cc: Removed some whitespace. 2004-06-30 07:19 paultcochrane * trunk/xmds-devel/source/xmdsoutput.cc: Implemented breakup of simulation text into header, body and footer. I reconstruct this text here. A lot of the changes in this commit are commenting out lines of code in the generated code (ie the stuff that is generated isn't actually executed and is in fact ignored by the compiler). I left the code in at this stage as this is still an experimental process and it will be easier to back out the changes by leaving the legacy stuff in there. This change has removed the need for xmds simulations to use the system() call and the split system command to be able to write the output. I also put some info text into the output xml/xsil which tells which version of xmds produced the file. 2004-06-30 07:15 paultcochrane * trunk/xmds-devel/source/xmdsmomentgroup.cc: Fixed error whereby the Metalink xml tag should have had a /> at the end instead of just >. 2004-06-30 07:14 paultcochrane * trunk/xmds-devel/source/main.cc: Implemented the splitting up of the xmds simulation text before the parsing starts. I split the text into a header, body and footer, and then recombine these later when getting the simulation to write the xsil file. This removes the need to use the split system command, and removes some more of the system() calls in the xmds engine. Added heaps of comments of how I'm going about stuff, and added some verbose output to make sure it's doing what it should be doing. At present I'm implementing this as global variables; perhaps this really should be done through and object interface, however, this is easy and it works, we just have to be careful. Also updated the documentation version number to xmds-1.3-4. 2004-06-29 07:21 joehope * trunk/xmds-devel/source/xmdsintegraterk4.cc, trunk/xmds-devel/source/xmdsintegratesiex.cc, trunk/xmds-devel/source/xmdsintegratesiip.cc: Fix for problem in if statements. 2004-06-29 07:13 joehope * trunk/xmds-devel/source/xmdsintegraterk4.cc, trunk/xmds-devel/source/xmdsintegratesiex.cc, trunk/xmds-devel/source/xmdsintegratesiip.cc: Allows number of samples in an integrate block to be zero without trouble. 2004-06-26 05:29 paultcochrane * trunk/xmds-devel/source/main.cc: Grabbing the simulation text for splitting up the xmds script for later use at the output stage. 2004-06-25 05:28 joehope * trunk/xmds-devel/configure.in, trunk/xmds-devel/examples/atomlaser.xmds: Removed redundant code to do with choosing thread-compliant compilers for the code generator. 2004-06-24 08:12 joehope * trunk/xmds-devel/source/getopt_xmds.c, trunk/xmds-devel/source/getopt_xmds.h, trunk/xmds-devel/source/getopt_xmds1.c, trunk/xmds-devel/source/main.cc, trunk/xmds-devel/source/xmdssequence.cc, trunk/xmds-devel/source/xsil2graphics.cc: Changing names of extern variables in getopt functions. Removes further conflicts. 2004-06-24 07:19 joehope * trunk/xmds-devel/source/xmdscomplex.h: Forcing the operator overloads to be C++. This was not automatic for all compilers. 2004-06-24 06:42 joehope * trunk/xmds-devel/ChangeLog, trunk/xmds-devel/MANIFEST, trunk/xmds-devel/admin/xmds.spec, trunk/xmds-devel/source/Makefile.am, trunk/xmds-devel/source/getopt_xmds.c, trunk/xmds-devel/source/getopt_xmds.h, trunk/xmds-devel/source/getopt_xmds1.c, trunk/xmds-devel/source/getopt_xmds_init.c, trunk/xmds-devel/source/main.cc, trunk/xmds-devel/source/xmdssequence.cc, trunk/xmds-devel/source/xmdssimulation.cc, trunk/xmds-devel/source/xsil2graphics.cc: Adjusted getopt to getopt_xmds to remove conflicts with predefined functions in the standard libraries of some systems 2004-06-23 08:21 paultcochrane * trunk/xmds-devel/admin/xmdsReleaseProcedure.pod: Removed newsgroup posting instruction, because this is not a good thing to do, and I got a bit stung from doing it this time. 2004-06-22 10:44 paultcochrane * trunk/xmds-devel/Makefile.am: Added new examples to be added at make dist time. 2004-06-22 10:18 paultcochrane * trunk/xmds-devel/examples/duffing.xmds: Intitial import to repository. This is an example simulation of Duffing's equations. 2004-06-22 10:18 paultcochrane * trunk/xmds-devel/examples/krebs.xmds: Initial import to repository. This is an example simulation of a simplified Krebs cycle of biochemical reations. 2004-06-22 10:17 paultcochrane * trunk/xmds-devel/examples/chemkin.xmds: Initial import to repository. This is an example simulation of a chemical kinetic reation in chemistry. 2004-06-22 10:16 paultcochrane * trunk/xmds-devel/examples/catcycle.xmds: Initial import to repository. This is an example simulation of a catalytical cycle reation in chemistry. 2004-06-22 10:16 paultcochrane * trunk/xmds-devel/examples/branch.xmds: Initial import to repository. This is an example simulation of a branching reaction in chemistry. 2004-06-21 09:28 paultcochrane * trunk/xmds-devel/admin/xmds.spec: Still trying to get the .spec file to work. Tried changing the prefix sent to configure. I think I need to rework the configuration step of xmds to iron out these wrinkles. 2004-06-20 23:48 paultcochrane * trunk/xmds-devel/admin/xmdsNewsPost.pl: Removed sci.math.research as this is a moderated group, and posting xmds announcements isn't appropriate. 2004-06-18 06:51 paultcochrane * trunk/xmds-devel/admin/xmds.spec: Initial import to repository. This is the rpm .spec file that Greg Collecutt used to use to build xmds. I'm now trying to hack it to build the current version(s). 2004-06-18 06:28 paultcochrane * trunk/xmds-devel/admin/xmdsReleaseProcedure.pod: Added comment that the source files should be tagged appropriately. That xmds.org needs updating. That an email to xmds-announce is a good idea. And that sending a post to the relevant newsgroups, by using the xmdsNewsPost.pl script would be a (possibly) good idea. 2004-06-18 06:25 paultcochrane * trunk/xmds-devel/admin/xmdsNewsPost.pl: Fixed a bug whereby the subject and newsgroup kept getting prepended to the message text, so eventually everyone in the last newsgroup to be posted to, could tell where else I'd posted the message. Not happy that this happened. Really not happy. 2004-06-18 06:09 paultcochrane * trunk/xmds-devel/admin/xmdsNewsPost.txt: Initial import to repository. This file is the news post sent as a result of running the xmdsNewsPost.pl script. This file needs to be updated whenever a new xmds version is released, and posted appropriately. 2004-06-18 06:08 paultcochrane * trunk/xmds-devel/admin/xmdsNewsPost.pl: Initial import to repository. This is a perl script to automatically post the xmds release announcement to a list of possibly interested newsgroups. 2004-06-18 01:58 paultcochrane * trunk/xmds-devel/admin/xmdsReleaseProcedure.pod: Initial import to repository. This is the procedure one should perform to properly release xmds onto the sourceforge site (and the world in general). 2004-06-18 01:31 paultcochrane * trunk/xmds-devel/README.Windows: Converted from dos format to unix format. Updated to xmds-1.3-4, and to new syntax for xsil2graphics. 2004-06-18 01:26 paultcochrane * trunk/xmds-devel/README: Updated to current version of xmds (1.3-4). Added a comment on how to access the man pages that are now installed as part of xmds. Updated the xsil2graphics syntax in the example given. Expanded the description of what xmds is at the top of the file. 2004-06-17 07:18 paultcochrane * trunk/xmds-devel/ChangeLog: Updated changelog to current version of xmds, highlighting the current set of major changes to the code base. 2004-06-17 06:00 paultcochrane * trunk/xmds-devel/MANIFEST: Updated to current version of xmds (1.3-4). 2004-06-17 05:45 paultcochrane * trunk/xmds-devel/source/xsil2graphics.cc: Added a mention of the xmds web site in the usage output. Also tidied some of the text in the display_usage function. 2004-06-16 03:49 paultcochrane * trunk/xmds-devel/source/xsil2graphics.cc: Changed display usage to use less printf calls. Also makes the code look better 2004-06-16 02:04 paultcochrane * trunk/xmds-devel/source/main.cc: Changed an exit statement to a return 0 to be more consistent with the other returning conventions. Don't know if the current convention is that great as it reports that everything went ok, as opposed to if something went wrong. Again, this is something to chuck into the todo list. 2004-06-16 02:02 paultcochrane * trunk/xmds-devel/source/xsil2graphics.cc: converted xsil2graphics argument parsing to the gnu getopt form. It therefore changes the old style arguments of -matlab and -scilab to --matlab and --scilab respectively. Also, it requires -o or --outfile if one wants to specify and alternative output filename, so one can't do xsil2graphics blah.xsil moo.m anymore, it must be xsil2graphics blah.xsil --output moo.m. Also added some more helpful output information. 2004-06-15 12:22 paultcochrane * trunk/xmds-devel/source/main.cc: Converted the command line argument parsing code to use the getopt library. Now we have long and short options and a mix if we so desire. Also changed some of the formatting of the template code, and changed the display_usage() output so that it is a bit more accurate, informative and a little better looking. One big thing to note here is the change of the compilation flag, this is now either -n or --nocompile, note that previously this was -c, although I don't think that many people actually used it. 2004-06-15 12:19 paultcochrane * trunk/xmds-devel/configure.in: Added -lxmds and -L. to the LIBS variable, so that xmds gets built with libxmds and so it can see the getopt libraries within libxmds. 2004-06-15 09:18 paultcochrane * trunk/xmds-devel/source/xmdsmomentgroup.cc: Tidied up a problem I found with the xsil output when using binary. I'd just changed the output filename of binary files for more consistent naming wrt moment group output, and hadn't set the correct filename in the .xsil output. 2004-06-15 09:08 paultcochrane * trunk/xmds-devel/source/xmdsmomentgroup.cc: Made the output moment group number for binary output data files agree with what the moment group number actually is. 2004-06-15 09:06 paultcochrane * trunk/xmds-devel/source/Makefile.am: Added a target for loadxsil.m to be automatically installed at make install time for xmds. It goes in the bindir at this stage, so will get installed in the user's bin directory (if --with-users is set) or in the /usr/local/bin directory if root is doing the installing. 2004-06-15 09:05 paultcochrane * trunk/xmds-devel/Makefile.am: Moved position of loadxsil.m entry. The only reason I did this was so that I could comment it out when testing some code. 2004-06-15 06:46 paultcochrane * trunk/xmds-devel/source/xmdssimulation.cc: Fixed bug with incorrect parsing of noises tag. I'd used a suite of if statements instead of an if-else if-else loop construction. Added some debugging code as well, for when xmds -d is used. 2004-06-15 01:30 paultcochrane * trunk/xmds-devel/examples/diffusion.xmds: Made the lattice size of the transverse dimension a multiple of two so that the numerics are faster 2004-06-15 01:29 paultcochrane * trunk/xmds-devel/examples/atomlaser.xmds, trunk/xmds-devel/examples/fibre.xmds, trunk/xmds-devel/examples/ndparamp.xmds, trunk/xmds-devel/examples/nlse.xmds: Removed text about deprecated feature of binary_output and use_double tags. This is actually now an obsolete syntax 2004-06-15 01:16 paultcochrane * trunk/xmds-devel/source/loadxsil.m: Tidied up the text that is printed to screen. Some of output enclosed in an if loop controlled by the new debug variable. More informative output as to whether data is single or double precision. 2004-06-14 10:22 paultcochrane * trunk/xmds-devel/configure.in: Added mandir assignments so that the man pages are installed in the correct locations depending upon whether the defaults are given, a prefix, or xmds is being user installed 2004-06-14 10:21 paultcochrane * trunk/xmds-devel/Makefile.am: Added fisher_reaction_diffusion.xmds to list of examples to distribute. Added a manfiles variable with the man pages to be installed. Added the manfiles variable to the EXTRA_DIST variable so that the files are added to the distro and installed with make install 2004-06-14 10:07 paultcochrane * trunk/xmds-devel/examples/fisher_reaction_diffusion.xmds: Initial import to repository. This is an example simulation of the Fisher reaction diffusion equation for use in theoretical population genetics. 2004-06-14 06:41 paultcochrane * trunk/xmds-devel/source/xmdssequence.cc: Added code to print an audible bell character at the end of a simulation if the <bing> tag is set to yes. This is a tag to optionally add a noise letting the user know when the simulation is complete. 2004-06-14 06:40 paultcochrane * trunk/xmds-devel/source/xmdsclasses.h: Added boolean variable holding value of whether or not the <bing> tag is set to yes or no. This is a tag to optionally add a noise letting the user know when the simulation is complete. 2004-06-14 06:39 paultcochrane * trunk/xmds-devel/source/xmdssimulation.cc: Added parsing code for the <bing> tag. This is a tag to optionally add a noise letting the user know when the simulation is complete. 2004-06-14 06:37 paultcochrane * trunk/xmds-devel/MANIFEST: Updated to current list of files in xmds-1.3-3 release 2004-06-14 06:37 paultcochrane * trunk/xmds-devel/configure.in: Updated release number to current (pre) release number of 1.3-4 2004-06-14 06:36 paultcochrane * trunk/xmds-devel/Makefile.am: Added hires, lane_emden, paraxial_wave, ring_modulator and van_der_pol examples to list of examples to add to distribution. Removed dependence of latexdocs and apifiles for EXTRA_DIST variable since they are in separate parts of the overall xmds project now 2004-06-14 06:32 paultcochrane * trunk/xmds-devel/examples/hires.xmds: Initial import to repository. This is the high irradiance response in photomorphogenesis example simulation. 2004-06-14 05:57 paultcochrane * trunk/xmds-devel/examples/ring_modulator.xmds: Initial import to repository. This is an example simulation of the ring modulator circuit of electronics. 2004-06-12 09:42 paultcochrane * trunk/xmds-devel/source/xmdsoutput.cc: Added a comment so that users know when output is being generated. This can be handy to know when large files are being output, so that one can wait and not think that the process has hung. 2004-06-12 09:41 paultcochrane * trunk/xmds-devel/source/main.cc: Fixed error whereby the CC variable was used as the C compiler that xmds uses, whereas should have been XMDS_CC. The MPICC variable being printf-ed separately caused a warning message to come up in compilation of xmds. I moved this into one of the other statements so that when MPICC was a null variable, no warning is printed. 2004-06-05 05:40 paultcochrane * trunk/xmds-devel/examples/paraxial_wave.xmds: Fixed up some of the numbers and the equations defining the slits etc. 2004-06-04 03:35 paultcochrane * trunk/xmds-devel/examples/paraxial_wave.xmds: Fixed minor bug. I had a superfluous y variable floating around. 2004-06-04 03:33 paultcochrane * trunk/xmds-devel/examples/paraxial_wave.xmds: Initial import to repository. This is an example simulation of the paraxial wave equation for double slit interference. 2004-05-31 06:01 paultcochrane * trunk/xmds-devel/ChangeLog: Updated to current version of xmds; namely 1.3-3. Described new features in this version. 2004-05-31 04:08 paultcochrane * trunk/xmds-devel/source/loadxsil.m: Fixed problem with loadxsil associated with change made a few versions of xmds ago to deprecate the use of <binary_output> and <use_double> which are now implemented as attributes of the <output> tag. 2004-05-31 03:26 paultcochrane * trunk/xmds-devel/examples/van_der_pol.xmds: Initial import to repository. This is an example simulation of the Van der Pol oscillator. 2004-05-31 03:15 paultcochrane * trunk/xmds-devel/examples/lane_emden.xmds: Initial import to repository. This is an example simulation of the Lane-Emden equation in astrophysics. 2004-05-19 10:07 paultcochrane * trunk/xmds-devel/source/xmdssimulation.cc: Now barfing when xmds finds the binary_output and/or use_double tags and prints a message telling the user how to fix the problem (basically to use the new/right syntax). Thanks to Joe Hope for the idea. 2004-05-18 10:25 paultcochrane * trunk/xmds-devel/source/xmdsutils.cc: Implemented throwing an exception when the poissonian attribute is given but no mean attribute given. Also noticed that the implementation of getAttributeStrings is suboptimal in that it borrows far too much from getAssignmentStrings and doesn't actually check everything properly. This needs to be tidied. The code works atm, but it is ugly and needs to be improved. This issue has been added to the todo list for output into doxygen 2004-05-18 10:22 paultcochrane * trunk/xmds-devel/source/xmdssimulation.cc: Implemented a Poissonian noise distribution based on that in chapter 7 of Numerical Recipes. The output looks good at this stage, but more testing is necessary. Added the correct prototype declarations for each of the noise options as well, and made sure that when the poissonian noise is called, that the mean attribute is also specified. 2004-05-18 10:19 paultcochrane * trunk/xmds-devel/source/xmdsclasses.h: Added a declaration for the mean of a poissonian noise distribution 2004-05-18 10:18 paultcochrane * trunk/xmds-devel/examples/kubo.xmds: Switched off mpi, and implemented the kind attribute of the noises tag. 2004-05-18 10:02 paultcochrane * trunk/xmds-devel/configure.in: Updated the version and release numbers to their current values (1.3-3). 2004-05-18 07:46 paultcochrane * trunk/xmds-devel/source/xmdssimulation.cc: Implemented parsing code for having a kind attribute to the noises tag. This at present accepts gaussian, poissonian (not yet implemented), gaussFast (a slightly faster version of the gaussian generation routines) and uniform. Gaussian, gaussFast and uniform have been implemented and tested and seem to go alright. Tests show between 7 and 20 percent increase in speed if gaussFast is used. 2004-05-18 07:42 paultcochrane * trunk/xmds-devel/source/xmdsclasses.h: Added declaration for the XMLString holding the variable that defines the kind of noise to generate 2004-05-12 06:18 paultcochrane * trunk/xmds-devel/MANIFEST: Updated manifest to current release version (1.3-2). 2004-05-12 06:16 paultcochrane * trunk/xmds-devel/NEWS: Updated to current version of xmds, ready for release 2004-05-12 06:11 paultcochrane * trunk/xmds-devel/ChangeLog: Trivial change 2004-05-12 06:08 paultcochrane * trunk/xmds-devel/ChangeLog: Added changes to xmds since last release 2004-05-12 05:31 paultcochrane * trunk/xmds-devel/Makefile.am: Made an explicit list of the example xmds files to include in the distribution. Previously all of my test xmds scripts were added, and that just didn't look good 2004-04-29 03:23 paultcochrane * trunk/xmds-devel/source/kissdom.cc, trunk/xmds-devel/source/kissdom.h, trunk/xmds-devel/source/xmdsarg.cc, trunk/xmds-devel/source/xmdsargelement.cc, trunk/xmds-devel/source/xmdsbreakpoint.cc, trunk/xmds-devel/source/xmdsclasses.h, trunk/xmds-devel/source/xmdselement.cc, trunk/xmds-devel/source/xmdsfield.cc, trunk/xmds-devel/source/xmdsfilter.cc, trunk/xmds-devel/source/xmdsglobals.cc, trunk/xmds-devel/source/xmdsintegrate.cc, trunk/xmds-devel/source/xmdsintegrateex.cc, trunk/xmds-devel/source/xmdsintegrateip.cc, trunk/xmds-devel/source/xmdsintegraterk4.cc, trunk/xmds-devel/source/xmdsintegraterk4ex.cc, trunk/xmds-devel/source/xmdsintegraterk4ip.cc, trunk/xmds-devel/source/xmdsintegratesi.cc, trunk/xmds-devel/source/xmdsintegratesiex.cc, trunk/xmds-devel/source/xmdsintegratesiip.cc, trunk/xmds-devel/source/xmdsmomentgroup.cc, trunk/xmds-devel/source/xmdsoutput.cc, trunk/xmds-devel/source/xmdssegment.cc, trunk/xmds-devel/source/xmdssequence.cc, trunk/xmds-devel/source/xmdssimulation.cc, trunk/xmds-devel/source/xmdsutils.cc, trunk/xmds-devel/source/xmdsutils.h, trunk/xmds-devel/source/xmdsvector.cc, trunk/xmds-devel/source/xmdsvectorelement.cc, trunk/xmds-devel/source/xmlbasics.cc, trunk/xmds-devel/source/xmlbasics.h, trunk/xmds-devel/source/xmlparser.cc, trunk/xmds-devel/source/xmlparser.h, trunk/xmds-devel/source/xsil2graphics.cc, trunk/xmds-devel/source/xsilfield.cc, trunk/xmds-devel/source/xsilfield.h: More completely documented the code using doxygen. Still lots of stuff that needs doing, some stuff isn't documented at all, just marked as Undocumented and a todo command left also signifying that this needs work. Most of the functions and variables, however, have at least a brief description of what they are (or what they look like the could be, as it is quite often *not* obvious as to what a function or variable does or means. 2004-04-29 03:19 paultcochrane * trunk/xmds-devel/source/main.cc: Documented the code using doxygen. Fixed up some of the spacing in the template output code. 2004-04-28 05:31 paultcochrane * trunk/xmds-devel/source/main.cc: Moved the comment regarding global system parameters and system functionality (for generation of a template code) to just below the name and description elements 2004-04-28 05:12 paultcochrane * trunk/xmds-devel/examples/lotka_volterra.xmds: Initial import to repository. This is an example simulation of the Lotka-Volterra system used as a model of undamped oscillations in autocatalytic chemical reactions. From initial reading of (mathematical chemistry) paper to completed xmds script was about 10 minutes! Wow. Ok, now I'm impressed. 2004-04-28 01:04 paultcochrane * trunk/xmds-devel/examples/atomlaser.xmds, trunk/xmds-devel/examples/diffusion.xmds, trunk/xmds-devel/examples/fibre.xmds, trunk/xmds-devel/examples/fullpos3D.xmds, trunk/xmds-devel/examples/gaugeatomlaser.xmds, trunk/xmds-devel/examples/highdim.xmds, trunk/xmds-devel/examples/kubo.xmds, trunk/xmds-devel/examples/lorenz.xmds, trunk/xmds-devel/examples/ndparamp.xmds, trunk/xmds-devel/examples/nlse.xmds, trunk/xmds-devel/examples/pendulum.xmds, trunk/xmds-devel/examples/sine.xmds, trunk/xmds-devel/examples/soliton.xmds, trunk/xmds-devel/examples/tla.xmds, trunk/xmds-devel/examples/vibstring.xmds: Fixed up author and description tags so that is a bit more uniform over all of the examples 2004-04-28 00:58 paultcochrane * trunk/xmds-devel/examples/atomlaser.xmds, trunk/xmds-devel/examples/diffusion.xmds, trunk/xmds-devel/examples/fibre.xmds, trunk/xmds-devel/examples/fullpos3D.xmds, trunk/xmds-devel/examples/gaugeatomlaser.xmds, trunk/xmds-devel/examples/highdim.xmds, trunk/xmds-devel/examples/kubo.xmds, trunk/xmds-devel/examples/lorenz.xmds, trunk/xmds-devel/examples/ndparamp.xmds, trunk/xmds-devel/examples/nlse.xmds, trunk/xmds-devel/examples/pendulum.xmds, trunk/xmds-devel/examples/sine.xmds, trunk/xmds-devel/examples/soliton.xmds, trunk/xmds-devel/examples/tla.xmds, trunk/xmds-devel/examples/vibstring.xmds: Added CVS Id tag. 2004-04-28 00:56 paultcochrane * trunk/xmds-devel/examples/atomlaser.xmds, trunk/xmds-devel/examples/diffusion.xmds, trunk/xmds-devel/examples/fibre.xmds, trunk/xmds-devel/examples/fullpos3D.xmds, trunk/xmds-devel/examples/gaugeatomlaser.xmds, trunk/xmds-devel/examples/highdim.xmds, trunk/xmds-devel/examples/kubo.xmds, trunk/xmds-devel/examples/lorenz.xmds, trunk/xmds-devel/examples/ndparamp.xmds, trunk/xmds-devel/examples/nlse.xmds, trunk/xmds-devel/examples/pendulum.xmds, trunk/xmds-devel/examples/sine.xmds, trunk/xmds-devel/examples/soliton.xmds, trunk/xmds-devel/examples/tla.xmds, trunk/xmds-devel/examples/vibstring.xmds: Added copyright statement to example files 2004-04-28 00:43 paultcochrane * trunk/xmds-devel/configure.in: Added copyright statement. 2004-04-28 00:29 paultcochrane * trunk/xmds-devel/source/dom3.h, trunk/xmds-devel/source/kissdom.cc, trunk/xmds-devel/source/kissdom.h, trunk/xmds-devel/source/main.cc, trunk/xmds-devel/source/xmdsarg.cc, trunk/xmds-devel/source/xmdsargelement.cc, trunk/xmds-devel/source/xmdsargv.cc, trunk/xmds-devel/source/xmdsbreakpoint.cc, trunk/xmds-devel/source/xmdsclasses.h, trunk/xmds-devel/source/xmdscomplex.h, trunk/xmds-devel/source/xmdselement.cc, trunk/xmds-devel/source/xmdsfield.cc, trunk/xmds-devel/source/xmdsfilter.cc, trunk/xmds-devel/source/xmdsglobals.cc, trunk/xmds-devel/source/xmdsintegrate.cc, trunk/xmds-devel/source/xmdsintegrateex.cc, trunk/xmds-devel/source/xmdsintegrateip.cc, trunk/xmds-devel/source/xmdsintegraterk4.cc, trunk/xmds-devel/source/xmdsintegraterk4ex.cc, trunk/xmds-devel/source/xmdsintegraterk4ip.cc, trunk/xmds-devel/source/xmdsintegratesi.cc, trunk/xmds-devel/source/xmdsintegratesiex.cc, trunk/xmds-devel/source/xmdsintegratesiip.cc, trunk/xmds-devel/source/xmdsmomentgroup.cc, trunk/xmds-devel/source/xmdsoutput.cc, trunk/xmds-devel/source/xmdssegment.cc, trunk/xmds-devel/source/xmdssequence.cc, trunk/xmds-devel/source/xmdssimulation.cc, trunk/xmds-devel/source/xmdsutils.cc, trunk/xmds-devel/source/xmdsutils.h, trunk/xmds-devel/source/xmdsvector.cc, trunk/xmds-devel/source/xmdsvectorelement.cc, trunk/xmds-devel/source/xmlbasics.cc, trunk/xmds-devel/source/xmlbasics.h, trunk/xmds-devel/source/xmlparser.cc, trunk/xmds-devel/source/xmlparser.h, trunk/xmds-devel/source/xsil2graphics.cc, trunk/xmds-devel/source/xsilfield.cc, trunk/xmds-devel/source/xsilfield.h: Updated copyright statement to current year 2004-04-28 00:01 paultcochrane * trunk/xmds-devel/benchmark/runbenchmarks: Fixed format of procTime output. Moved masterData assignment into file test if loop. Removed use warnings pragma as not supported in older versions of perl, and the warnings aren't really needed atm. Also added a variable for the progInfoFname. 2004-04-27 23:56 paultcochrane * trunk/xmds-devel/source/kissdom.cc, trunk/xmds-devel/source/main.cc, trunk/xmds-devel/source/xmdsarg.cc, trunk/xmds-devel/source/xmdsargelement.cc, trunk/xmds-devel/source/xmdsargv.cc, trunk/xmds-devel/source/xmdsbreakpoint.cc, trunk/xmds-devel/source/xmdselement.cc, trunk/xmds-devel/source/xmdsfield.cc, trunk/xmds-devel/source/xmdsfilter.cc, trunk/xmds-devel/source/xmdsglobals.cc, trunk/xmds-devel/source/xmdsintegrate.cc, trunk/xmds-devel/source/xmdsintegrateex.cc, trunk/xmds-devel/source/xmdsintegrateip.cc, trunk/xmds-devel/source/xmdsintegraterk4.cc, trunk/xmds-devel/source/xmdsintegraterk4ex.cc, trunk/xmds-devel/source/xmdsintegraterk4ip.cc, trunk/xmds-devel/source/xmdsintegratesi.cc, trunk/xmds-devel/source/xmdsintegratesiex.cc, trunk/xmds-devel/source/xmdsintegratesiip.cc, trunk/xmds-devel/source/xmdsmomentgroup.cc, trunk/xmds-devel/source/xmdsoutput.cc, trunk/xmds-devel/source/xmdssegment.cc, trunk/xmds-devel/source/xmdssequence.cc, trunk/xmds-devel/source/xmdssimulation.cc, trunk/xmds-devel/source/xmdsutils.cc, trunk/xmds-devel/source/xmdsvector.cc, trunk/xmds-devel/source/xmdsvectorelement.cc, trunk/xmds-devel/source/xmlbasics.cc, trunk/xmds-devel/source/xmlparser.cc, trunk/xmds-devel/source/xsil2graphics.cc, trunk/xmds-devel/source/xsilfield.cc: Added an @file command so that doxygen finds and documents the stuff in the file 2004-04-27 23:55 paultcochrane * trunk/xmds-devel/source/Doxyfile: Changed some of the functionality of the Doxyfile. Added more explicit warnings and more in-depth documentation of the code (including private bits, which I don't know if that's a good idea or not). 2004-04-20 03:51 paultcochrane * trunk/xmds-devel/source/main.cc: Added some nice intro text so that one knows that one has just executed xmds, and that a template is being output and what the filename is. 2004-04-20 03:44 paultcochrane * trunk/xmds-devel/source/main.cc: Implemented the use of a template output option of xmds. One merely has to use the -t flag at the command line for a template xmds script to be output to stdout. If a filename is given, then the script is sent to that file, and xmds returns. This is to help those who want to write a script basically from scratch, but don't want to have to remember where everything goes and the exact set of tags that are necessary. The template is currently the one in the tutTemplateStart.tex file of the latex documentation, and has more tags than necessary to make a simulation. 2004-04-19 09:22 paultcochrane * trunk/xmds-devel/configure.in: Updated version and release numbers 2004-04-19 09:14 paultcochrane * trunk/xmds-devel/source/xmdsmomentgroup.cc, trunk/xmds-devel/source/xmdsoutput.cc, trunk/xmds-devel/source/xmdssequence.cc: I finally got sick of seeing 042's everywhere, and replaced them with double quotes. It does make things easier to read. 2004-04-19 08:59 paultcochrane * trunk/xmds-devel/source/xmdsoutput.cc: Stuff it, I might as well chuck in an info footer as well as a header, it doesn't increase the file size that much. So, I did. 2004-04-19 08:51 paultcochrane * trunk/xmds-devel/source/xmdsoutput.cc: Moved nice version information stuff that is to be put into the .xsil file here as opposed to in xmdsmomentgroup.cc. This way it's only mentioned the once, as opposed to each time a moment group is written out to file. Also moved where the <simulation> tag is written, and added some comments (my God! comments!) to the code. 2004-04-19 08:48 paultcochrane * trunk/xmds-devel/source/xmdsmomentgroup.cc: Moved nice version information stuff into a better location (namely xmdsoutput.cc) 2004-04-19 08:40 paultcochrane * trunk/xmds-devel/source/xmdssimulation.cc: Added the version and release numbers to the list of simulation parameters. Can now pass these bits of info around so that can generate xmds version information at parsing and compiling, and in the output .xsil file. 2004-04-19 08:37 paultcochrane * trunk/xmds-devel/source/xmdsmomentgroup.cc: Added an information section using <info> tags in the moment group output. This is so that it is documented which version of xmds generated the output .xsil file, and so that xmds and its web page get another plug. 2004-04-19 08:32 paultcochrane * trunk/xmds-devel/source/xmdsclasses.h: Added the version and release numbers to the list of simulation parameters so that can use these values in the output at the start of parsing and compiling a simulation, and at the end in the output of the simulations. 2004-04-19 08:31 paultcochrane * trunk/xmds-devel/source/main.cc: Printing out some info about xmds at the start of parsing and compiling a simulation. Also tidied some of the output when parsing and compiling a simulation. 2004-04-19 08:28 paultcochrane * trunk/xmds-devel/depcomp, trunk/xmds-devel/ltmain.sh: Updated. 2004-04-06 11:10 paultcochrane * trunk/xmds-devel/benchmark/gaugeatomlaser_128.xmds: Initial import to repository. This is now the correct file to use instead of gaugeatomlaser.xmds, as the benchmarking code is now much more general. 2004-04-06 11:09 paultcochrane * trunk/xmds-devel/benchmark/runbenchmarks: I think I've got it all working now. The masterData variable is being updated properly, and output to file properly, and then reread properly, so all good there. Tested on G3, AMD, and P4. Have now changed the test bench subroutine to bench_test and the bench2 subroutine is now bench, so have to do a proper run now... 2004-04-06 10:45 paultcochrane * trunk/xmds-devel/benchmark/runbenchmarks: The last message was a stuff up, however, this one is ok. Now printing all cpus listed in masterData hash 2004-04-06 10:42 paultcochrane * trunk/xmds-devel/benchmark/runbenchmarks: Added cpu information to master data hash table 2004-04-06 10:40 paultcochrane * trunk/xmds-devel/benchmark/runbenchmarks: Added cpu information to master data hash table 2004-04-06 10:29 paultcochrane * trunk/xmds-devel/benchmark/runbenchmarks: Implemented output of html of benchmark data. Implemented dumping of data using Data::Dumper, and reading the data back in (hopefully). Implemented html output of the verbose cpu information, which is linked to the main benchmarks html file. 2004-04-06 08:26 paultcochrane * trunk/xmds-devel/benchmark/runbenchmarks: Added some comments and removed some superfluous code. 2004-04-06 08:20 paultcochrane * trunk/xmds-devel/benchmark/runbenchmarks: Added the code of bench as a subroutine to runbenchmarks. Also added a testing subroutine so that I don't have to wait for all of the sims to finish before I can make sure that the code works. Implemented the use of the bench subroutine and collection of the average time into the benchData hash. 2004-04-06 07:51 paultcochrane * trunk/xmds-devel/benchmark/runbenchmarks: Added a check for linux, if so, then cpuinfo is obtained (which is slightly different for LinuxPPC and for LinuxX86) and then a shorter version of this information is kept. If not linux, then the system info is determined by using the Config module of Perl and the info that configured Perl on that system. 2004-04-06 06:58 paultcochrane * trunk/xmds-devel/benchmark/bench: Implemented shorter version of previous code using timeit instead of the Benchmark objects 2004-04-06 06:53 paultcochrane * trunk/xmds-devel/benchmark/runbenchmarks: Initial import to repository. This is the wrapper script that runs the bench script on all of the various xmds scripts. 2004-04-06 06:52 paultcochrane * trunk/xmds-devel/benchmark/nlse_100.xmds, trunk/xmds-devel/benchmark/nlse_1000.xmds, trunk/xmds-devel/benchmark/nlse_10000.xmds, trunk/xmds-devel/benchmark/nlse_500.xmds, trunk/xmds-devel/benchmark/nlse_5000.xmds: Initial import to repository. This is the nonlinear Schroedinger equation simulation for various lattice sizes. 2004-04-06 06:51 paultcochrane * trunk/xmds-devel/benchmark/ndparamp_100.xmds, trunk/xmds-devel/benchmark/ndparamp_200.xmds, trunk/xmds-devel/benchmark/ndparamp_50.xmds, trunk/xmds-devel/benchmark/ndparamp_500.xmds: Initial import to repository. This is the N-dimensional parametric oscillator simulation for various lattice sizes. 2004-04-06 06:50 paultcochrane * trunk/xmds-devel/benchmark/gaugeatomlaser.xmds: Initial import to repository. This is the gaugeatomlaser simulation which is used to really test how hard the cpu can go (sims take about three hours on new 64 bit AMD machines). 2004-04-06 06:49 paultcochrane * trunk/xmds-devel/benchmark/fullpos3D_16.xmds, trunk/xmds-devel/benchmark/fullpos3D_32.xmds, trunk/xmds-devel/benchmark/fullpos3D_64.xmds: Initial import to repository. This is the fullpos3D simulation for various lattice sizes. 2004-04-06 06:45 paultcochrane * trunk/xmds-devel/benchmark, trunk/xmds-devel/benchmark/bench: Initial import to repository. This is the basic script that compiles, runs a first go of a simulation and then runs the simulation a few times (at present three) giving an output of the average time for the simulation. 2004-03-08 10:14 paultcochrane * trunk/xmds-devel/source/xmdssimulation.cc: Added a check for the author and description tags. If they aren't found, then a warning is issued to the effect that adding such a tag would be a good idea. This is just to get users to document their code better. We might have to back this out someday... 2004-03-08 10:12 paultcochrane * trunk/xmds-devel/source/xmdsclasses.h: Added authorName and description to the list of simulation parameters. Not exactly necessary, since they are likely never to be used in a simulation as such, but they do help document the simulation source code better. Whether or not actually storing them in xmds is a good question... 2004-03-05 05:06 paultcochrane * trunk/xmds-devel/source/loadxsil.m: Added copyright statement. 2004-03-05 05:05 paultcochrane * trunk/xmds-devel/source/Doxyfile: Updated file to current version of Doxygen (some stuff was obsolete etc). 2004-03-05 05:04 paultcochrane * trunk/xmds-devel/source/xsilfield.cc: Fixed bug whereby the output from xsil2graphics didn't include the correct variable name when calling fscanfMat in the generated scilab script file. 2004-01-30 04:31 paultcochrane * trunk/xmds-devel/examples/fibre.xmds, trunk/xmds-devel/examples/fullpos3D.xmds: Fixed spelling error. 2004-01-30 04:21 paultcochrane * trunk/xmds-devel/source/xmdssimulation.cc: Fixed bug whereby attributes were parsed incorrectly. 2004-01-30 03:48 paultcochrane * trunk/xmds-devel/source/xmdssimulation.cc: Now reports errors in parsing <output> element correctly. 2004-01-30 02:10 paultcochrane * trunk/xmds-devel/testsuite/fibre.xmds, trunk/xmds-devel/testsuite/fullpos3D.xmds, trunk/xmds-devel/testsuite/gaugeatomlaser.xmds, trunk/xmds-devel/testsuite/ndparamp.xmds, trunk/xmds-devel/testsuite/nlse.xmds, trunk/xmds-devel/testsuite/soliton.xmds: Fixed problems concerning gcc 3.x needing floats inside such functions as log and sqrt instead of ints. Just a problem of adding .0 ad the end of what was previously an integer. 2004-01-30 02:04 paultcochrane * trunk/xmds-devel/testsuite/atomlaser.xmds, trunk/xmds-devel/testsuite/fibre.xmds, trunk/xmds-devel/testsuite/fullpos3D.xmds, trunk/xmds-devel/testsuite/gaugeatomlaser.xmds, trunk/xmds-devel/testsuite/kubo.xmds, trunk/xmds-devel/testsuite/ndparamp.xmds, trunk/xmds-devel/testsuite/nlse.xmds, trunk/xmds-devel/testsuite/sine.xmds, trunk/xmds-devel/testsuite/soliton.xmds, trunk/xmds-devel/testsuite/tla.xmds: Fixed up formatting of files using HTML tidy. Command used: tidy -im -xml <filename>.xmds Then some hand-tidying of the files. 2004-01-30 01:38 paultcochrane * trunk/xmds-devel/AUTHORS, trunk/xmds-devel/INSTALL, trunk/xmds-devel/Makefile.am, trunk/xmds-devel/NEWS, trunk/xmds-devel/README, trunk/xmds-devel/README.Windows, trunk/xmds-devel/acinclude.m4, trunk/xmds-devel/configure.in, trunk/xmds-devel/testsuite/atomlaser.xmds, trunk/xmds-devel/testsuite/fibre.xmds, trunk/xmds-devel/testsuite/fullpos3D.xmds, trunk/xmds-devel/testsuite/gaugeatomlaser.xmds, trunk/xmds-devel/testsuite/kubo.xmds, trunk/xmds-devel/testsuite/ndparamp.xmds, trunk/xmds-devel/testsuite/nlse.xmds, trunk/xmds-devel/testsuite/sine.xmds, trunk/xmds-devel/testsuite/soliton.xmds, trunk/xmds-devel/testsuite/tla.xmds: Added CVS Id keyword. 2004-01-30 01:25 paultcochrane * trunk/xmds-devel/source/loadxsil.m: Added CVS Id keyword. 2004-01-28 04:44 paultcochrane * trunk/xmds-devel/source/Doxyfile, trunk/xmds-devel/source/Makefile.am, trunk/xmds-devel/source/dom3.h, trunk/xmds-devel/source/kissdom.cc, trunk/xmds-devel/source/kissdom.h, trunk/xmds-devel/source/main.cc, trunk/xmds-devel/source/xmdsarg.cc, trunk/xmds-devel/source/xmdsargelement.cc, trunk/xmds-devel/source/xmdsargv.cc, trunk/xmds-devel/source/xmdsbreakpoint.cc, trunk/xmds-devel/source/xmdsclasses.h, trunk/xmds-devel/source/xmdscomplex.h, trunk/xmds-devel/source/xmdselement.cc, trunk/xmds-devel/source/xmdsfield.cc, trunk/xmds-devel/source/xmdsfilter.cc, trunk/xmds-devel/source/xmdsglobals.cc, trunk/xmds-devel/source/xmdsintegrate.cc, trunk/xmds-devel/source/xmdsintegrateex.cc, trunk/xmds-devel/source/xmdsintegrateip.cc, trunk/xmds-devel/source/xmdsintegraterk4.cc, trunk/xmds-devel/source/xmdsintegraterk4ex.cc, trunk/xmds-devel/source/xmdsintegraterk4ip.cc, trunk/xmds-devel/source/xmdsintegratesi.cc, trunk/xmds-devel/source/xmdsintegratesiex.cc, trunk/xmds-devel/source/xmdsintegratesiip.cc, trunk/xmds-devel/source/xmdsmomentgroup.cc, trunk/xmds-devel/source/xmdsoutput.cc, trunk/xmds-devel/source/xmdssegment.cc, trunk/xmds-devel/source/xmdssequence.cc, trunk/xmds-devel/source/xmdsutils.cc, trunk/xmds-devel/source/xmdsutils.h, trunk/xmds-devel/source/xmdsvector.cc, trunk/xmds-devel/source/xmdsvectorelement.cc, trunk/xmds-devel/source/xmlbasics.cc, trunk/xmds-devel/source/xmlbasics.h, trunk/xmds-devel/source/xmlparser.cc, trunk/xmds-devel/source/xmlparser.h, trunk/xmds-devel/source/xsil2graphics.cc, trunk/xmds-devel/source/xsilfield.cc, trunk/xmds-devel/source/xsilfield.h: Added CVS Id keyword. 2004-01-28 04:37 paultcochrane * trunk/xmds-devel/source/xmdssimulation.cc: Still testing the CVS Id keyword expansion. 2004-01-28 04:35 paultcochrane * trunk/xmds-devel/source/xmdssimulation.cc: Testing adding the CVS Id keyword. 2004-01-27 07:02 paultcochrane * trunk/xmds-devel/examples/atomlaser.xmds: Updated to new <output> element syntax: output format and output precision now being given as attributes of <output> element rather than in simulation options section. Also added syntax for the break point feature to come. 2004-01-27 07:00 paultcochrane * trunk/xmds-devel/examples/diffusion.xmds, trunk/xmds-devel/examples/fibre.xmds, trunk/xmds-devel/examples/fullpos3D.xmds, trunk/xmds-devel/examples/gaugeatomlaser.xmds, trunk/xmds-devel/examples/highdim.xmds, trunk/xmds-devel/examples/kubo.xmds, trunk/xmds-devel/examples/lorenz.xmds, trunk/xmds-devel/examples/ndparamp.xmds, trunk/xmds-devel/examples/nlse.xmds, trunk/xmds-devel/examples/pendulum.xmds, trunk/xmds-devel/examples/sine.xmds, trunk/xmds-devel/examples/soliton.xmds, trunk/xmds-devel/examples/tla.xmds, trunk/xmds-devel/examples/vibstring.xmds: Updated to new <output> element syntax: output format and output precision now being given as attributes of <output> element rather than in simulation options section. 2004-01-27 06:29 paultcochrane * trunk/xmds-devel/source/xmdssimulation.cc: Added attributes to <output> element to control whether output format is binary or ascii (ascii still default), and whether the output precision is double or single (double is still default). These are to replace the <binary_output> and <use_double> tags. The new syntax is <output format="ascii|binary" precision="double|single">, which is a lot more logical. 2004-01-27 06:26 paultcochrane * trunk/xmds-devel/source/Doxyfile: Changed option so that man pages are now generated. 2004-01-14 08:34 paultcochrane * trunk/xmds-devel/examples/fullpos3D.xmds: Fixed problem whereby gcc/g++ see sqrt(2) as the sqrt of an integer which doesn't work in C++, these have been changed to sqrt(2.0) so that the input is float/double. 2004-01-13 10:16 paultcochrane * trunk/xmds-devel/source/xmdsutils.h: Trivial change made during code testing. 2004-01-13 10:15 paultcochrane * trunk/xmds-devel/source/xmdsutils.cc: Fixed bug in getAttributeBools where the string comparison was being performed incorrectly. 2004-01-13 10:14 paultcochrane * trunk/xmds-devel/source/xmdsoutput.cc: Implemented parsing of enabled attribute of breakpoint element correctly. 2004-01-13 10:13 paultcochrane * trunk/xmds-devel/source/xmdsclasses.h: Changed some formatting. 2004-01-13 10:11 paultcochrane * trunk/xmds-devel/source/xmdsbreakpoint.cc: Removed some legacy code that was commented out anyway. Polished and tested the breakpoint parsing code. Now do a test to see if a file exists at the parsing stage when the file status is set to "old", and barf with an error message if not found. 2004-01-13 02:03 paultcochrane * trunk/xmds-devel/source/xmdsutils.h: Corrected one of the documentation strings. 2004-01-13 01:28 paultcochrane * trunk/xmds-devel/source/main.cc: Added a debug option to parsePrefs(), and changed the output generated so that stuff that should be in the debugging output is not in the verbose output. 2004-01-12 09:10 paultcochrane * trunk/xmds-devel/source/xmdsutils.h: Added the DEEP and NOT_DEEP variables to the global anonymous enum. 2004-01-12 09:09 paultcochrane * trunk/xmds-devel/source/xmdsoutput.cc: Added stuff to find and process the <breakpoint> tag. Started to implement the use of DEEP and NOT_DEEP variables in getElementsByTagName() and friends as opposed to just 1 and 0 respectively (it makes the code more readable). 2004-01-12 09:07 paultcochrane * trunk/xmds-devel/source/xmdsbreakpoint.cc: Initial import to repository. Basic stuff at this stage, actually does nothing other than report what the settings are as found in the .xmds script. 2004-01-12 09:06 paultcochrane * trunk/xmds-devel/source/xmdsclasses.h: Added xmdsBreakPoint object declarations (just basic stuff at this stage). Added (to xmdsOutput) a bpEnabledFlag variable to note if breakpoints are enabled, and declaration of a function to create an xmdsBreakPoint object. 2004-01-12 09:03 paultcochrane * trunk/xmds-devel/source/Makefile.am: Added xmdsbreakpoint.cc 2003-12-30 10:38 paultcochrane * trunk/xmds-devel/examples/fibre.xmds, trunk/xmds-devel/examples/fullpos3D.xmds, trunk/xmds-devel/examples/gaugeatomlaser.xmds, trunk/xmds-devel/examples/highdim.xmds, trunk/xmds-devel/examples/kubo.xmds, trunk/xmds-devel/examples/lorenz.xmds, trunk/xmds-devel/examples/ndparamp.xmds, trunk/xmds-devel/examples/nlse.xmds, trunk/xmds-devel/examples/pendulum.xmds, trunk/xmds-devel/examples/sine.xmds, trunk/xmds-devel/examples/soliton.xmds, trunk/xmds-devel/examples/tla.xmds, trunk/xmds-devel/examples/vibstring.xmds: Updated <name>, <author> and <description> tags where appropriate. 2003-12-23 04:01 paultcochrane * trunk/xmds-devel/ChangeLog, trunk/xmds-devel/MANIFEST, trunk/xmds-devel/NEWS, trunk/xmds-devel/README: Updated to reflect changes in current release (1.3-1) 2003-12-23 03:47 paultcochrane * trunk/xmds-devel/examples/atomlaser.xmds, trunk/xmds-devel/examples/diffusion.xmds, trunk/xmds-devel/examples/fibre.xmds, trunk/xmds-devel/examples/fullpos3D.xmds, trunk/xmds-devel/examples/gaugeatomlaser.xmds, trunk/xmds-devel/examples/highdim.xmds, trunk/xmds-devel/examples/kubo.xmds, trunk/xmds-devel/examples/lorenz.xmds, trunk/xmds-devel/examples/ndparamp.xmds, trunk/xmds-devel/examples/nlse.xmds, trunk/xmds-devel/examples/pendulum.xmds, trunk/xmds-devel/examples/sine.xmds, trunk/xmds-devel/examples/soliton.xmds, trunk/xmds-devel/examples/tla.xmds, trunk/xmds-devel/examples/vibstring.xmds: Tidied formatting, added some comments. 2003-12-23 01:15 paultcochrane * trunk/xmds-devel/examples/atomlaser.xmds: Commented out using of binary input file. Now is back to being initialised by code. Better this way since it's an example file. 2003-12-23 01:13 paultcochrane * trunk/xmds-devel/source/main.cc: Put preferences parsing code into a function. It's a bit neater, and only one section of code to modify instead of two. Also changed a couple of warnings to only be printed out when verbose flag is set. 2003-12-22 06:56 paultcochrane * trunk/xmds-devel/Makefile.am: Updated to include the README.Windows file in the distribution. 2003-12-22 06:55 paultcochrane * trunk/xmds-devel/README.Windows: Initial import to repository. 2003-12-22 06:01 paultcochrane * trunk/xmds-devel/examples/tla.xmds: Minor formatting improvement. 2003-12-22 06:00 paultcochrane * trunk/xmds-devel/examples/nlse.xmds: Added test code for output arguments. This needs to be fixed up, not a good example file really. 2003-12-22 05:59 paultcochrane * trunk/xmds-devel/examples/ndparamp.xmds: Added binary output and benchmark tags. 2003-12-22 05:58 paultcochrane * trunk/xmds-devel/examples/highdim.xmds: Fixed integer where float should be problem. 2003-12-22 05:57 paultcochrane * trunk/xmds-devel/examples/gaugeatomlaser.xmds: Renamed simulation and .xsil file to reflect name of "gaugeatomlaser". 2003-12-22 05:56 paultcochrane * trunk/xmds-devel/examples/fullpos3D.xmds: Some minor reformatting. 2003-12-22 05:55 paultcochrane * trunk/xmds-devel/examples/fibre.xmds: Fixed a divide by integer problem which has only really become evident since gcc3. Added <binary_output> and <use_double> tags. 2003-12-22 05:52 paultcochrane * trunk/xmds-devel/examples/atomlaser.xmds: Tidied the code slightly. Added an <author> and <description> element (may be used in the future. Added some comments to the file. Removed test code, and now acually use variables in the simulation as command line arguments. Also added some new syntax to work in xmds-1.3-1. 2003-12-22 05:49 paultcochrane * trunk/xmds-devel/testsuite/atomlaser_reference.xsil, trunk/xmds-devel/testsuite/ndparamp_reference.xsil, trunk/xmds-devel/testsuite/nlse_reference.xsil, trunk/xmds-devel/testsuite/soliton_reference.xsil, trunk/xmds-devel/testsuite/tla_reference.xsil: Updated the <simname>_reference.xsil files. 2003-12-22 05:40 paultcochrane * trunk/xmds-devel/source/main.cc: Added some documentation as introduction to xmds for output to api documentation. Also added some installation instructions as well. 2003-12-22 04:42 paultcochrane * trunk/xmds-devel/source/Doxyfile: Updated to refelect the current project number. Also removed some obsolete Doxygen commands. 2003-12-22 04:39 paultcochrane * trunk/xmds-devel/source/dom3.h: Completed documenting the DOM functions and classes as they are outlined in the W3C Working Draft of 05 June 2001. No functional changes, although the big difference is that the api documentation is now significantly better than it was before. 2003-12-19 07:17 paultcochrane * trunk/xmds-devel/source/dom3.h: Started documenting the DOM functions and classes as they are outlined in the W3C Working Draft of 05 June 2001. No functional changes, although the big difference is that the api documentation is now significantly better than it was before (and I haven't finished yet!). 2003-12-17 09:35 paultcochrane * trunk/xmds-devel/source/xmdsvectorelement.cc: Implemented binary input for use in the <filename> tag of the <vector> element. 2003-12-17 09:33 paultcochrane * trunk/xmds-devel/source/xmdsutils.h: Added an enum to specify two booleans, REQD and NOT_REQD. I will eventually implement this further so that some of the calls used of getAssignmentStrings() etc are a little more understandable. Also added declarations for getAttributeStrings() and getAttributeBools(). 2003-12-17 09:31 paultcochrane * trunk/xmds-devel/source/xmdsutils.cc: Added two new functions: getAttributeStrings() and getAttributeBools(). This was in order to implement binary and ascii input of data files (in <filename> tag of <vector> element). However, this is a more general addition, the two functions being used to get strings and booleans out of attributes of element tags respectively. 2003-12-17 09:29 paultcochrane * trunk/xmds-devel/source/xmdsclasses.h: Minor change to the xmdsVectorElement class to implement binary and ascii input files. 2003-12-17 06:18 paultcochrane * trunk/xmds-devel/source/kissdom.cc, trunk/xmds-devel/source/xmdssequence.cc, trunk/xmds-devel/source/xmdssimulation.cc, trunk/xmds-devel/source/xmdsvectorelement.cc, trunk/xmds-devel/source/xsilfield.cc: Fixed bug whereby temp<x>.dat was still being used instead of <xsilfilenamebase>x.dat for input data to matlab/scilab. 2003-12-17 06:17 paultcochrane * trunk/xmds-devel/source/xmdsvector.cc: Fixed formatting a bit. No real changes to code. 2003-12-17 06:16 paultcochrane * trunk/xmds-devel/source/xmdsmomentgroup.cc, trunk/xmds-devel/source/xmdsoutput.cc: Tidied some fprintf statements. 2003-12-17 06:15 paultcochrane * trunk/xmds-devel/source/xmdsutils.cc: Fixed some spelling errors and debugging reporting information. 2003-12-17 06:12 paultcochrane * trunk/xmds-devel/source/xmdsfield.cc: Tidied some fprintf statements by combining most of the text (and hence removing heaps of fprintf statements and making the code easier to read). 2003-12-17 06:09 paultcochrane * trunk/xmds-devel/source/xmdsclasses.h: Added a usePrefs variable to the simulationParamtersStruct in order to implement preferences. 2003-12-17 06:08 paultcochrane * trunk/xmds-devel/source/main.cc: Implemented a first go at preferences for xmds. It can be tidied a lot, but it works at present. One needs a ~/.xmds/xmds.prefs file or an xmds.prefs file in the local directory to the script one is trying to compile. The prefs file format is <compiler macro name> = <compilation variable>, e.g. XMDS_CC = gcc. One can also use comments. All text after (and including) a hash character (#) is ignored. 2003-12-17 06:03 paultcochrane * trunk/xmds-devel/configure.in: Updated to show version information as 1.3-1. 2003-12-07 03:25 paultcochrane * trunk/xmds-devel/ChangeLog: Added comments about current changes to xmds. 2003-12-07 03:24 paultcochrane * trunk/xmds-devel/configure.in: Altered release number to current release: 1.2-2 2003-11-27 05:50 paultcochrane * trunk/xmds-devel/source/xmdssimulation.cc: Added the inclusion of the sstream (string streams) header. 2003-11-27 05:49 paultcochrane * trunk/xmds-devel/source/xmdsfield.cc: Fixed segfaulting of mpi programs using wisdom. Now have more C++ type code to implement creation of the host_rank_%i.stuff etc files and for their deletion. Writing and reading from these files was causing the segfault. 2003-11-27 01:33 paultcochrane * trunk/xmds-devel/source/xmdssequence.cc: Fixed bug whereby the useWisdom option wasn't passed through to writePlanCreationCalls properly. 2003-11-27 01:14 paultcochrane * trunk/xmds-devel/configure.in: Changed way that mpiccTest was checked for the compiler running mpicc. 2003-11-25 08:19 paultcochrane * trunk/xmds-devel/ChangeLog: Added comments advising of changes up to current version of xmds. 2003-11-25 08:18 paultcochrane * trunk/xmds-devel/configure.in: Corrected version numbers to agree with current release. 2003-11-25 08:17 paultcochrane * trunk/xmds-devel/source/xmdsfield.cc: Fixed host.stuff and home.stuff file writing with mpi, I'd fixed this before in one place in the code but missed this extra place. 2003-11-25 01:37 paultcochrane * trunk/xmds-devel/source/xmdsmomentgroup.cc: Modified moment group number reporting at the terminal, so matches what is given in xsil2graphics and output files. 2003-11-24 10:10 paultcochrane * trunk/xmds-devel/configure.in: Fixed problem with optimisation settings not flowing through for script compilation when using gcc. Now check if $ac_compiler_gnu is "yes" instead of if XMDS_CC is gcc (can be g++, for example). 2003-11-24 10:07 paultcochrane * trunk/xmds-devel/source/xmdsmomentgroup.cc: Fixed binary output bug where k-space variables weren't ordered correctly before output. 2003-11-20 06:00 paultcochrane * trunk/xmds-devel/source/xmdsmomentgroup.cc: Fixed misreporting of filename if unable to open the output file for binary output. 2003-11-07 00:28 paultcochrane * trunk/xmds-devel/configure.in: Changed release number to pre1, ready for the pre1 release. (funnily enough...) 2003-11-06 10:18 paultcochrane * trunk/xmds-devel/source/loadxsil.m: Hopefully fixed problem with loading data in more than one moment group by appending _[momentGroupNumber] to variable names as is done in xsil2graphics. 2003-11-06 09:59 paultcochrane * trunk/xmds-devel/configure.in: Now pointing XMDS_CC to CXX if necessary. 2003-11-06 06:02 paultcochrane * trunk/xmds-devel/configure.in: Fixed bug where a test for null should have been non-null. 2003-11-06 01:47 paultcochrane * trunk/xmds-devel/source/xsilfield.h: Altered call to writeAsFormat so can implement writing data files as xsil filename_momentGroup.dat as opposed to temp_momentGroup.dat as before. 2003-11-06 01:46 paultcochrane * trunk/xmds-devel/source/xsilfield.cc: The output filename is the xsil base filename (the bit without the .xsil on the end) with the moment group number plus .dat, instead of just temp1.dat, temp2.dat. Not a great comment, but I implemented this idea anyway... 2003-11-06 01:44 paultcochrane * trunk/xmds-devel/source/xsil2graphics.cc: Some reformatting of code. Main change being the altering of the xsilField::writeAsFormat call, by passing through the xsil filename's base name (ie that bit without the .xsil on the end). 2003-11-06 01:42 paultcochrane * trunk/xmds-devel/source/xmdssimulation.cc: Removed the output of the (commented out in the final code anyway) unistd.h statement. 2003-11-06 01:41 paultcochrane * trunk/xmds-devel/source/xmdsfield.cc: (Hopefully) fixed problem with writing, reading and deleting host.stuff and home.stuff files when using mpi. The files now append the rank to the file name, so this problem should be fixed. 2003-11-06 01:38 paultcochrane * trunk/xmds-devel/source/main.cc: Removed XMDS_CXX stuff. Removed clibs being added to one of mpicc compile strings. This produced inconsistent compilation flags when mpicc uses a different compiler to XMDS_CC. 2003-11-06 01:16 paultcochrane * trunk/xmds-devel/admin/manifestGen.pl: Documented a far simpler way of generating the manifest. 2003-11-06 01:15 paultcochrane * trunk/xmds-devel/configure.in: Removed references to XMDS_CXX* variables, they were superfluous and caused confusion. Made some tests more stringent, so that user supplied arguments at the command line to configure can be passed through properly. If the user has specified command line options to xmds, the script now also checks if some required flags are missing from these options and appends them if necessary. 2003-11-06 01:11 paultcochrane * trunk/xmds-devel/README: Added description of configuration options that are now available in xmds-1.2, and tidied up the text a bit. Also fixed a couple of bugs with the scilab execution of the xsil file. 2003-11-06 01:09 paultcochrane * trunk/xmds-devel/Makefile.am: Removed latexdocs from being included in distribution temporarily. Will probably add back in when docs catch up to current version of xmds. 2003-11-06 01:08 paultcochrane * trunk/xmds-devel/MANIFEST: Updated to reflect current list of files for distribution. 2003-11-04 08:27 paultcochrane * trunk/xmds-devel/Makefile.am: No change, just added something and took it away, but it wants to be updated nevertheless. 2003-11-04 08:22 paultcochrane * trunk/xmds-devel/MANIFEST: Initial import to repository. 2003-11-04 08:18 paultcochrane * trunk/xmds-devel/ChangeLog: Updated to reflect changes that have happened so far since xmds-1.1. 2003-11-04 07:54 paultcochrane * trunk/xmds-devel/README: Updated to agree with current configuration options. 2003-11-04 07:53 paultcochrane * trunk/xmds-devel/AUTHORS: Updated email addresses of authors. 2003-11-04 06:59 paultcochrane * trunk/xmds-devel/configure.in: MPICCFLAGS needs $PTHREADS_CFLAGS as well. Tidied XMDS_CFLAGS and XMDS_CXXFLAGS by putting AGGRESSIVE_* instead of the explicit declaration. Removed the check for enable_mpicc_aggressive. Removed --enable-*-aggressive options. 2003-11-04 06:32 paultcochrane * trunk/xmds-devel/configure.in: Fixed bug where one actually needs the $PTHREAD_CFLAGS variable inserted into XMDS_CFLAGS. 2003-11-04 05:20 paultcochrane * trunk/xmds-devel/configure.in: Removed explicit check for MPI_Init in -lmpi since -lmpi must work if passed -llam test, AND the library arguments be in the right order. This simplifies the checking slightly. 2003-11-03 04:46 paultcochrane * trunk/xmds-devel/configure.in: The flags for gcc, icc, g++ etc all now default to the aggressive version. If the user wants other flags, they should set them at the command line at build time. 2003-11-03 04:03 paultcochrane * trunk/xmds-devel/configure.in: Changed implementation of how xmdsconfig.h is made. It's now a cp from config.h. 2003-11-03 04:01 paultcochrane * trunk/xmds-devel/Makefile.am: Added the m4 files acx_mpi.m4 and acx_pthread.m4 so that will be added to distribution output. 2003-11-03 03:58 paultcochrane * trunk/xmds-devel/examples/diffusion.xmds, trunk/xmds-devel/examples/lorenz.xmds, trunk/xmds-devel/examples/pendulum.xmds, trunk/xmds-devel/examples/vibstring.xmds: Initial import to repository. 2003-10-31 07:04 joehope * trunk/xmds-devel/configure.in, trunk/xmds-devel/examples/fibre.xmds: Making stable autoconf on MacOSX 2003-10-30 07:07 paultcochrane * trunk/xmds-devel/source/Doxyfile: Now set to produce pdf documentation as well. 2003-10-30 07:05 paultcochrane * trunk/xmds-devel/configure.in: Fixed problem with not finding lam properly. Fixed bug whereby forgot to add -lxmds to XMDS_LIBS variable. 2003-10-30 03:40 paultcochrane * trunk/xmds-devel/configure.in: No longer assuming lam, nor does one need to put --with-mpi-libs="-llam" on the command line for the script to find either the lam or mpich implementations of mpi. Fixed minor big with -I in wrong place. Now determines how mpicc is run, which in itself is dependent upon the mpi implementation, but the script detects the differences between lam and mpi and is still able to check what CC is used for mpicc. 2003-10-30 03:35 paultcochrane * trunk/xmds-devel/source/dom3.h, trunk/xmds-devel/source/kissdom.h, trunk/xmds-devel/source/xmdsclasses.h: Did some reformatting and updated docstrings. 2003-10-28 01:42 paultcochrane * trunk/xmds-devel/configure.in: Added a check for how mpicc is run, and then alter MPICCFLAGS accordingly. Also added a check for mpicc-aggressive and if on, then uses the icc-aggressive or gcc-aggressive flags if mpicc is run by icc or gcc. 2003-10-28 00:48 paultcochrane * trunk/xmds-devel/admin, trunk/xmds-devel/admin/manifestGen.pl: Initial import to repository. 2003-10-27 10:50 paultcochrane * trunk/xmds-devel/configure.in: Implemented the --with-mpi-path option better. Used the MPI_LIB_PATH to help configure look for fftw_mpi. Added the MPI_LIB_PATH to the MPICCFLAGS. 2003-10-27 10:47 paultcochrane * trunk/xmds-devel/Makefile.am: Added loadxsil.m to EXTRA_DIST files. 2003-10-27 08:13 paultcochrane * trunk/xmds-devel/source/kissdom.cc, trunk/xmds-devel/source/kissdom.h, trunk/xmds-devel/source/main.cc, trunk/xmds-devel/source/xmdsarg.cc, trunk/xmds-devel/source/xmdsargelement.cc, trunk/xmds-devel/source/xmdsargv.cc, trunk/xmds-devel/source/xmdsclasses.h, trunk/xmds-devel/source/xmdscomplex.h, trunk/xmds-devel/source/xmdselement.cc, trunk/xmds-devel/source/xmdsfield.cc, trunk/xmds-devel/source/xmdsfilter.cc, trunk/xmds-devel/source/xmdsglobals.cc, trunk/xmds-devel/source/xmdsintegrate.cc, trunk/xmds-devel/source/xmdsintegrateex.cc, trunk/xmds-devel/source/xmdsintegrateip.cc, trunk/xmds-devel/source/xmdsintegraterk4.cc, trunk/xmds-devel/source/xmdsintegraterk4ex.cc, trunk/xmds-devel/source/xmdsintegraterk4ip.cc, trunk/xmds-devel/source/xmdsintegratesi.cc, trunk/xmds-devel/source/xmdsintegratesiex.cc, trunk/xmds-devel/source/xmdsintegratesiip.cc, trunk/xmds-devel/source/xmdsmomentgroup.cc, trunk/xmds-devel/source/xmdsoutput.cc, trunk/xmds-devel/source/xmdssegment.cc, trunk/xmds-devel/source/xmdssequence.cc, trunk/xmds-devel/source/xmdssimulation.cc, trunk/xmds-devel/source/xmdsutils.cc, trunk/xmds-devel/source/xmdsutils.h, trunk/xmds-devel/source/xmdsvector.cc, trunk/xmds-devel/source/xmdsvectorelement.cc, trunk/xmds-devel/source/xmlbasics.cc, trunk/xmds-devel/source/xmlbasics.h, trunk/xmds-devel/source/xmlparser.cc, trunk/xmds-devel/source/xmlparser.h, trunk/xmds-devel/source/xsil2graphics.cc, trunk/xmds-devel/source/xsilfield.cc, trunk/xmds-devel/source/xsilfield.h: Added GPL statement. 2003-10-27 08:01 paultcochrane * trunk/xmds-devel/source/dom3.h: Changed some docstrings. Added GPL statement. 2003-10-27 07:52 paultcochrane * trunk/xmds-devel/configure.in: Hopefully fixed bloody headers problem this time!! Fixed other problems wrt getting mpi to get the correct options. Seems to go on the SC now, so that's good. 2003-10-24 01:50 paultcochrane * trunk/xmds-devel/source/xmdssequence.cc: Added more helpful (ie usage) output for when arguments to simulation binary are incorrect. 2003-10-24 01:46 paultcochrane * trunk/xmds-devel/source/main.cc: Fixed bug where insufficient number of format specifiers in a string for number of arguments to sprintf. This caused a problem with mpi not seeing the fftw libraries. 2003-10-23 10:36 paultcochrane * trunk/xmds-devel/configure.in: Now handling the case when someone uses --prefix better now. Basically I just make the USER_* and *dir variables point to the directory pointed to by the $prefix. 2003-10-23 10:11 paultcochrane * trunk/xmds-devel/source/xmdssimulation.cc: Minor terminal output touch up. 2003-10-23 10:11 paultcochrane * trunk/xmds-devel/source/main.cc: Now using XMDS_CC, XMDS_CXX, and XMDS_CFLAGS instead of the non-XMDS_* versions. 2003-10-23 10:07 paultcochrane * trunk/xmds-devel/configure.in: Hopefully now fixed the config headers not recreating themselves problem. Did some reformatting of help output. Added --with-mpi-compiler so that the user can choose what compiler to use for mpi, --enable-mpi (not default option) so that mpi is checked for and added to variables, --enable-icc-aggressive, so that aggressive optimisation settings are chosen when using icc, --enable-gcc-aggressive so that both gcc and g++ use aggressive optimisation settings, --enable-mpicc-aggressive so that mpicc will use the gcc-aggressive compiler settings. Fixed a bug where CXXFLAGS lacked an S. Needed to add the PTHREAD_CFLAGS variable to XMDS_CFLAGS and XMDS_CXXFLAGS. Removed old (and commented anyway) mpi checking code. Put mpi stuff into an if loop, and is processed only when --enable-mpi is used. Am now actually using XMDS_CFLAGS and XMDS_CXXFLAGS. Now configure script outputs nicely formatted option and variable information once configuration is complete. 2003-10-22 06:13 paultcochrane * trunk/xmds-devel/source/xmdssimulation.cc: Minor change to terminal output. 2003-10-22 06:12 paultcochrane * trunk/xmds-devel/source/main.cc: Changed INCLUDES and LIBS to be XMDS_INCLUDES and XMDS_LIBS, so is specific to the xmds simulations rather than xmds itself. 2003-10-22 06:10 paultcochrane * trunk/xmds-devel/configure.in: Corrected some *config.h errors. Relabelled some of the variables to be specific to the xmds simulations as opposed to xmds itself. Removed some superfluous function checks. Got MPI running cleaner and better. 2003-10-22 03:25 paultcochrane * trunk/xmds-devel/acx_mpi.m4: Initial import to repository. 2003-10-22 00:39 paultcochrane * trunk/xmds-devel/source/Makefile.am: Changed config.h to xmdsconfig.h 2003-10-22 00:39 paultcochrane * trunk/xmds-devel/source/xmdssimulation.cc: Changed inclusion of config.h to inclusion of xmdsconfig.h to stop possible name clashes when installing on the system instead of in the user's directory. 2003-10-22 00:38 paultcochrane * trunk/xmds-devel/source/xmdsmomentgroup.cc: Fixed minor error with incorrect format in printf statement. 2003-10-22 00:23 paultcochrane * trunk/xmds-devel/source/main.cc: Improved mpi flag handling, and added a FFTW_MPI_LIBS variable. 2003-10-22 00:22 paultcochrane * trunk/xmds-devel/configure.in: Removed some superfluous variables, and some superfluous output at configure time. Improved the ordering and determination of flags for use with mpi. 2003-10-21 23:27 paultcochrane * trunk/xmds-devel/configure.in: Now generating source/xmdsconfig.h as well as source/config.h so that simulation binaries can have more benefit from configuration headers. Added -lxmds to LIBS variable (this isn't the right thing to do, and will be fixed shortly). 2003-10-20 01:14 joehope * trunk/xmds-devel/examples/highdim.xmds: Trivial fix for occasional, minor compiler confusion: sqrt(int) 2003-10-18 10:55 paultcochrane * trunk/xmds-devel/source/xmdssimulation.cc: Removed inclusion of endian.h for binaryOutput. Now including config.h when binaryOutput is true. 2003-10-18 10:54 paultcochrane * trunk/xmds-devel/source/xmdssequence.cc: Changed checks for FLOAT_WORD_ORDER etc to CPU_IS_BIG_ENDIAN etc. 2003-10-18 10:53 paultcochrane * trunk/xmds-devel/source/xmdsmomentgroup.cc: Now determining endian-ness by the variables CPU_IS_BIG_ENDIAN and CPU_IS_LITTLE_ENDIAN. 2003-10-18 10:51 paultcochrane * trunk/xmds-devel/source/Makefile.am: Now adding the config.h generated in the configuration of xmds. This adds the variables CPU_IS_BIG_ENDIAN and CPU_IS_LITTLE_ENDIAN to check for endian-ness of the processor. 2003-10-18 10:48 paultcochrane * trunk/xmds-devel/configure.in: Removed check for endian.h and added code to search for endian-ness of processor copied from configure.ac in libsndfile. Also am now including the acinclude.m4 of libsndfile. 2003-10-18 10:07 paultcochrane * trunk/xmds-devel/acinclude.m4: Initial import to repository. 2003-10-17 04:53 paultcochrane * trunk/xmds-devel/source/xmdssimulation.cc: Instead of adding "#include getopt.h" every time a simulation code is written, it is only added now when the .xmds script contains an argv tag set, and therefore the simulation can take arguments at the command line. 2003-10-17 04:50 paultcochrane * trunk/xmds-devel/source/xmdssequence.cc: Changed getopt_long_only to getopt_long. 2003-10-17 04:49 paultcochrane * trunk/xmds-devel/source/main.cc: Removed FFTWMPILIBS variable (now superfluous). Removed superfluous %s formatting string. 2003-10-17 04:48 paultcochrane * trunk/xmds-devel/source/Makefile.am: Added the getopt sources and headers to make the libxmds library. 2003-10-17 04:36 paultcochrane * trunk/xmds-devel/config.guess, trunk/xmds-devel/depcomp, trunk/xmds-devel/ltmain.sh: Updated to current version. 2003-10-17 04:32 paultcochrane * trunk/xmds-devel/configure.in: Added underscores to some variables to improve readability. Made sure that the directory libxmds.a is put in is the same as xmdscomplex.h (on installation). Made sure that script doesn't write over previously defined (eg in the user's shell) any environment variables used (eg CFLAGS). Made sure that gcc gets the -Wall option (don't really know why... historical I guess). Changed FFTW_THREADS_* to XMDS_THREADS_*. These may be deleted in the future. Cleaned up the flags that mpi gets eventually. Further cleaning will ensue however. icc currently only used if set as CC and or CXX flags in the shell. Moved the AC_SUBSTs at the end of the script to before all of the AC_DEFINES. Made sure that -lxmds is added to LIBS. Some echos added for testing purposes. 2003-10-17 04:24 paultcochrane * trunk/xmds-devel/Makefile.am: Commented out the inclusion of xmds api documentation. 2003-10-10 05:02 joehope * trunk/xmds-devel/source/dom3.h, trunk/xmds-devel/source/kissdom.cc, trunk/xmds-devel/source/kissdom.h, trunk/xmds-devel/source/xmdsarg.cc, trunk/xmds-devel/source/xmdsargelement.cc, trunk/xmds-devel/source/xmdsargv.cc, trunk/xmds-devel/source/xmdsclasses.h, trunk/xmds-devel/source/xmdselement.cc, trunk/xmds-devel/source/xmdsfield.cc, trunk/xmds-devel/source/xmdsfilter.cc, trunk/xmds-devel/source/xmdsglobals.cc, trunk/xmds-devel/source/xmdsintegrate.cc, trunk/xmds-devel/source/xmdsintegrateex.cc, trunk/xmds-devel/source/xmdsintegrateip.cc, trunk/xmds-devel/source/xmdsintegraterk4.cc, trunk/xmds-devel/source/xmdsintegraterk4ex.cc, trunk/xmds-devel/source/xmdsintegraterk4ip.cc, trunk/xmds-devel/source/xmdsintegratesi.cc, trunk/xmds-devel/source/xmdsintegratesiex.cc, trunk/xmds-devel/source/xmdsintegratesiip.cc, trunk/xmds-devel/source/xmdsmomentgroup.cc, trunk/xmds-devel/source/xmdsoutput.cc, trunk/xmds-devel/source/xmdssegment.cc, trunk/xmds-devel/source/xmdssequence.cc, trunk/xmds-devel/source/xmdssimulation.cc, trunk/xmds-devel/source/xmdsutils.cc, trunk/xmds-devel/source/xmdsutils.h, trunk/xmds-devel/source/xmdsvector.cc, trunk/xmds-devel/source/xmdsvectorelement.cc, trunk/xmds-devel/source/xmlbasics.cc, trunk/xmds-devel/source/xmlbasics.h, trunk/xmds-devel/source/xmlparser.cc, trunk/xmds-devel/source/xmlparser.h, trunk/xmds-devel/source/xsil2graphics.cc, trunk/xmds-devel/source/xsilfield.cc, trunk/xmds-devel/source/xsilfield.h: Replace //** with // ** (often allows proper syntax colouring) 2003-10-09 06:29 paultcochrane * trunk/xmds-devel/testsuite, trunk/xmds-devel/testsuite/atomlaser.xmds, trunk/xmds-devel/testsuite/atomlaser_reference.xsil, trunk/xmds-devel/testsuite/fibre.xmds, trunk/xmds-devel/testsuite/fibre_reference.xsil, trunk/xmds-devel/testsuite/fullpos3D.xmds, trunk/xmds-devel/testsuite/fullpos3D_reference.xsil, trunk/xmds-devel/testsuite/gaugeatomlaser.xmds, trunk/xmds-devel/testsuite/gaugeatomlaser_reference.xsil, trunk/xmds-devel/testsuite/genRefData.pl, trunk/xmds-devel/testsuite/kubo.xmds, trunk/xmds-devel/testsuite/kubo_reference.xsil, trunk/xmds-devel/testsuite/ndparamp.xmds, trunk/xmds-devel/testsuite/ndparamp_reference.xsil, trunk/xmds-devel/testsuite/nlse.xmds, trunk/xmds-devel/testsuite/nlse_reference.xsil, trunk/xmds-devel/testsuite/sine.xmds, trunk/xmds-devel/testsuite/sine_reference.xsil, trunk/xmds-devel/testsuite/soliton.xmds, trunk/xmds-devel/testsuite/soliton_reference.xsil, trunk/xmds-devel/testsuite/test_xmds.pl, trunk/xmds-devel/testsuite/tla.xmds, trunk/xmds-devel/testsuite/tla_reference.xsil: Initial import to repository. 2003-10-09 02:18 offaxis * trunk/xmds-devel/source/xmdsglobals.cc: Globals from <arg> elements now read in _before_ those from the <globals> element. 2003-10-07 05:28 paultcochrane * trunk/xmds-devel/depcomp: Initial import to repository. 2003-10-07 05:01 paultcochrane * trunk/xmds-devel/acx_pthread.m4: Initial import to repository. Copied from the fftw distribution (many thanks). 2003-10-07 04:59 paultcochrane * trunk/xmds-devel/configure.in: Many, many changes. Updated to call xmds version 1.2. Added a path to one's mpi distribution if different from /usr or /usr/local. Added a check for vendor's cc and c++ compiler, and using them to compile both xmds and the simulation binaries. If the compiler is gcc then adds the -Wall compiler flag. Checks for getopt and getopt_long. Checks for the various thread libraries (code copied and modified from the fftw configure.in). Added a FFTW_LIBS variable. This may be used a bit better in the future. Checks for the Intel c compiler and if so then uses that compiler for xmds and the simulation binaries. Removed some superfluous definitions and subst's. 2003-10-07 04:52 paultcochrane * trunk/xmds-devel/examples/nlse.xmds: Removed <binary_output> tag, just for testing purposes. Fixed problem with log(2) being incorrect for more recent versions of c++: one must now use log(2.0). 2003-10-07 04:50 paultcochrane * trunk/xmds-devel/source/xmdssimulation.cc: Added config.h to headers list. Using the HAVE_ENDIAN_H variable defined therein to specify what the __BYTE_ORDER and __FLOAT_WORD_ORDER macros should be equal to. Hopefully this fixes the endian issues xmds could have, although I'm not sure yet. 2003-10-07 04:48 paultcochrane * trunk/xmds-devel/source/main.cc: Added cxx variable set equal to the CXX variable found by the configure script. This is then used for compilation of the simulation binary. Also specifying the FFTW_LIBS variable as well. Added the fftwlibs variable to the compilation of the simulation binary. 2003-10-07 04:45 paultcochrane * trunk/xmds-devel/source/loadxsil.m: Fixed a line that was missing a . 2003-10-06 04:21 paultcochrane * trunk/xmds-devel/source/xmdsmomentgroup.cc: Removed multiline string literals by adding heaps of fprintf statements. This caused problems with some compilers. 2003-10-06 04:20 paultcochrane * trunk/xmds-devel/source/xmdsfield.cc: Removed multiline string literals by adding heaps of fprintf statements. 2003-09-30 11:50 paultcochrane * trunk/xmds-devel/examples/atomlaser.xmds: Now contains more <argv> tags test code. Doesn't actually do anything... 2003-09-30 11:48 paultcochrane * trunk/xmds-devel/source/xmdsutils.h: Reformatted the text. 2003-09-30 11:47 paultcochrane * trunk/xmds-devel/source/xmdssimulation.cc: Removed test code. Fixed code to implement the gnu getopt library for command line options for the simulation binary. 2003-09-30 11:46 paultcochrane * trunk/xmds-devel/source/xmdssequence.cc: Completed code to implement gnu getopt command line options for the simulation binary. 2003-09-30 11:44 paultcochrane * trunk/xmds-devel/source/xmdsglobals.cc: Added global variables code to be output for when command line arguments are specified in the .xmds file. 2003-09-30 11:42 paultcochrane * trunk/xmds-devel/source/xmdscomplex.h: Reformatted text. 2003-09-30 11:42 paultcochrane * trunk/xmds-devel/source/xmdsclasses.h: Deleted some superfluous code (eg writeArgvIntialisationCode, writeArgvFinalisationCode). Removed test object: argvList. Fixed header so that can use an argvStruct to store information about the command line arguments specified in <argv> tags. 2003-09-30 11:39 paultcochrane * trunk/xmds-devel/source/xmdsargv.cc: Deleted some superfluous code (eg writeArgvIntialisationCode, writeArgvFinalisationCode). 2003-09-30 11:38 paultcochrane * trunk/xmds-devel/source/xmdsargelement.cc: Finally worked out how to get the argument names, short options, types, default_values etc into the simulation object. Deleted some superfluous code (eg writeArgDeclaration, writeArgCode). 2003-09-30 11:36 paultcochrane * trunk/xmds-devel/source/xmdsarg.cc: Removed some superfluous function definitions. Namely type(), setType(), default_value() and setDefaultValue() 2003-09-30 11:34 paultcochrane * trunk/xmds-devel/source/dom3.h, trunk/xmds-devel/source/kissdom.h: Reformatted text nicely. 2003-09-29 09:57 paultcochrane * trunk/xmds-devel/Makefile.am: Removed superfluous files from being added when performing a make dist. Needs to be improved further. 2003-09-29 09:56 paultcochrane * trunk/xmds-devel/configure.in: Better checking, and some testing done on platforms other than linux. 2003-09-29 08:00 paultcochrane * trunk/xmds-devel/configure.in: Actually fixed the checks now, instead of not (aarrgghh). 2003-09-29 03:28 paultcochrane * trunk/xmds-devel/configure.in: Fixed some more checks and added a check for fftw_mpi. 2003-09-29 02:02 paultcochrane * trunk/xmds-devel/configure.in: Fixed bug with incorrectly using alternative paths to fftw. 2003-09-15 10:16 paultcochrane * trunk/xmds-devel/source/xmdsarg.cc, trunk/xmds-devel/source/xmdsargelement.cc, trunk/xmds-devel/source/xmdsargv.cc, trunk/xmds-devel/source/xmdselement.cc, trunk/xmds-devel/source/xmdsfield.cc, trunk/xmds-devel/source/xmdsfilter.cc, trunk/xmds-devel/source/xmdsglobals.cc, trunk/xmds-devel/source/xmdsintegrate.cc, trunk/xmds-devel/source/xmdsintegrateex.cc, trunk/xmds-devel/source/xmdsintegrateip.cc, trunk/xmds-devel/source/xmdsintegraterk4.cc, trunk/xmds-devel/source/xmdsintegraterk4ex.cc, trunk/xmds-devel/source/xmdsintegraterk4ip.cc, trunk/xmds-devel/source/xmdsintegratesi.cc, trunk/xmds-devel/source/xmdsintegratesiex.cc, trunk/xmds-devel/source/xmdsintegratesiip.cc, trunk/xmds-devel/source/xmdsmomentgroup.cc, trunk/xmds-devel/source/xmdsoutput.cc, trunk/xmds-devel/source/xmdssegment.cc, trunk/xmds-devel/source/xmdssequence.cc, trunk/xmds-devel/source/xmdssimulation.cc, trunk/xmds-devel/source/xmdsutils.cc, trunk/xmds-devel/source/xmdsvector.cc, trunk/xmds-devel/source/xmdsvectorelement.cc: Implemented the use of a command line flag to xmds for toggling debugging information output (-d). 2003-09-15 10:14 paultcochrane * trunk/xmds-devel/source/xsil2graphics.cc: Modified to implement the -d xmds debugging flag and -x the xml debugging flag. 2003-09-15 10:13 paultcochrane * trunk/xmds-devel/source/xmlbasics.cc: Removed DEBUG macro. This is now implemented as a command line switch to xmds. Specifically -x, for xml debugging information. This change is really only useful for developers. 2003-09-15 10:12 paultcochrane * trunk/xmds-devel/source/xmdsclasses.h: Removed DEBUG macro. This is now implemented as a command line switch to xmds. 2003-09-15 10:10 paultcochrane * trunk/xmds-devel/source/main.cc: Implemented some new command line options to xmds the program. -c switches compilation of the output binary OFF. This is useful for checking is xmds outputs the correct code, or if one wants to hack the output source and not have to worry about compilation, or even if the output code is not to be used on a unix system and therefore needs some hacking to work on another system. -d switches debugging output on excluding xml parsing debugging output (same as setting the DEBUG macro in the code, except that xmds doesn't have to be recompiled every time one wants to change that). -x switches debugging output of just the xml parsing on. 2003-09-15 09:57 paultcochrane * trunk/xmds-devel/examples/atomlaser.xmds: Improved indentation of xml. Added code to test the <argv> tag set. 2003-09-15 06:56 paultcochrane * trunk/xmds-devel/ChangeLog: Initial import to repository. 2003-09-15 06:49 paultcochrane * trunk/xmds-devel/source/xmdsarg.cc, trunk/xmds-devel/source/xmdsargelement.cc, trunk/xmds-devel/source/xmdsargv.cc: Initial import to repository. 2003-09-15 06:48 paultcochrane * trunk/xmds-devel/source/xmdssimulation.cc: Improved indentation of source code. Added some code for the parsing of the <argv> element. 2003-09-15 06:45 paultcochrane * trunk/xmds-devel/source/xmdssequence.cc: Improved indentation of source code, no functional changes. 2003-09-15 06:43 paultcochrane * trunk/xmds-devel/source/xmdsclasses.h: Added declarations for xmdsArgv, xmdsArg, and xmdsArgElement classes. Also added an argvStruct structure to store the relevant information found by parsing the new <argv> etc syntax. This may or may not be used at this stage, so consider this commit as strictly temporary. 2003-09-15 06:38 paultcochrane * trunk/xmds-devel/source/dom3.h, trunk/xmds-devel/source/kissdom.cc, trunk/xmds-devel/source/kissdom.h, trunk/xmds-devel/source/main.cc, trunk/xmds-devel/source/xmdscomplex.h, trunk/xmds-devel/source/xmdsfield.cc, trunk/xmds-devel/source/xmdsfilter.cc, trunk/xmds-devel/source/xmdsglobals.cc, trunk/xmds-devel/source/xmdsintegrate.cc, trunk/xmds-devel/source/xmdsintegrateex.cc, trunk/xmds-devel/source/xmdsintegrateip.cc, trunk/xmds-devel/source/xmdsintegraterk4.cc, trunk/xmds-devel/source/xmdsintegraterk4ex.cc, trunk/xmds-devel/source/xmdsintegraterk4ip.cc, trunk/xmds-devel/source/xmdsintegratesi.cc, trunk/xmds-devel/source/xmdsintegratesiex.cc, trunk/xmds-devel/source/xmdsintegratesiip.cc, trunk/xmds-devel/source/xmdsmomentgroup.cc, trunk/xmds-devel/source/xmdsoutput.cc, trunk/xmds-devel/source/xmdssegment.cc, trunk/xmds-devel/source/xmdsutils.cc, trunk/xmds-devel/source/xmdsutils.h, trunk/xmds-devel/source/xmdsvector.cc, trunk/xmds-devel/source/xmdsvectorelement.cc, trunk/xmds-devel/source/xmlbasics.cc, trunk/xmds-devel/source/xmlbasics.h, trunk/xmds-devel/source/xmlparser.cc, trunk/xmds-devel/source/xmlparser.h: No functional changes, just indented the source code nicely 2003-09-15 06:31 paultcochrane * trunk/xmds-devel/source/Makefile.am: Added xmdsargv.cc xmdsarg.cc and xmdsargelement.cc to the list of xmds sources 2003-09-09 04:30 paultcochrane * trunk/xmds-devel/config.guess, trunk/xmds-devel/config.sub: Initial import to repository 2003-08-06 05:38 paultcochrane * trunk/xmds-devel/configure.in: Added a check for the endian.h header file. 2003-08-06 04:42 paultcochrane * trunk/xmds-devel/source/xmdssimulation.cc: If binary output is specified, then include the <endian.h> header. 2003-08-06 04:41 paultcochrane * trunk/xmds-devel/source/xmdssequence.cc: Added code to output C code to check for the definitions of __FLOAT_WORD_ORDER and __BYTE_WORD order. If the first doesn't exist, then it uses the next, if that doesn't exist, then the program exits. 2003-08-06 04:38 paultcochrane * trunk/xmds-devel/source/xmdsmomentgroup.cc: Added code to output C code that checks for littleendian or bigendian binary format, and assigns the string encodingStr accordingly, for then use in the .xsil output file of the simulation. 2003-08-06 04:35 paultcochrane * trunk/xmds-devel/source/loadxsil.m: Modified to allow for reading of bigendian or littleendian binary, as specified in the .xsil file. 2003-08-05 07:54 paultcochrane * trunk/xmds-devel/source/xmdssimulation.cc: Added argvList to myParameters assignment block in xmdsSimulation constructor. Added code to process the argv element and put the command line arguments into the argvList for use in xmdsglobals.cc. 2003-08-05 07:51 paultcochrane * trunk/xmds-devel/source/xmdssequence.cc: Added code to accept arguments on the command line for the xmds executable, only if the argvList defined via the <argv> tag is non-zero. If the incorrect number of arguments, the program gives a usage output and exits. 2003-08-05 07:49 paultcochrane * trunk/xmds-devel/source/xmdsglobals.cc: Added code to look for <argv> tag in <globals> section and append the relevant code to the myGlobalCode variable, to be output in the globals definition section of the .cc file. This implements part of allowing arguments to be passed to the executable at the command line. 2003-08-05 07:47 paultcochrane * trunk/xmds-devel/source/xmdsclasses.h: Included <string> header. Added argvList string list to parametersStruct to implement the passing of arguments to the output binary at the command line. 2003-08-04 10:27 paultcochrane * trunk/xmds-devel/source/xmdssimulation.cc: Included the vector header. Now "using namespace std" by default. 2003-08-04 10:26 paultcochrane * trunk/xmds-devel/source/xmdsoutput.cc: Fixed a spelling error in console output. 2003-08-04 10:24 paultcochrane * trunk/xmds-devel/source/xmdsmomentgroup.cc: Output binary files now have the moment group field name appended. This stops output binary files writing all over one another. Implemented a better technique of binary output: redundancy inherent in ascii output format has been removed. 2003-08-04 10:20 paultcochrane * trunk/xmds-devel/source/xmdsfield.cc: The std:: namespace is now "used". The temporary files host.stuff and home.stuff are removed after being used. 2003-08-04 10:18 paultcochrane * trunk/xmds-devel/source/loadxsil.m: Modified to allow for changes in binary output format. 2003-07-28 09:42 paultcochrane * trunk/xmds-devel/Makefile.am: examples directory is now included in EXTRA_DIST instead of SUBDIRS. This stops examples from being compiled at build time. 2003-07-28 09:41 paultcochrane * trunk/xmds-devel/configure.in: No longer produces Makefile in examples directory. 2003-07-28 09:13 paultcochrane * trunk/xmds-devel/source/Doxyfile: Initial import to repository 2003-07-28 09:12 paultcochrane * trunk/xmds-devel/source/dom3.h, trunk/xmds-devel/source/kissdom.h, trunk/xmds-devel/source/xmdsclasses.h, trunk/xmds-devel/source/xmdscomplex.h, trunk/xmds-devel/source/xmdsutils.h, trunk/xmds-devel/source/xmlbasics.h, trunk/xmds-devel/source/xmlparser.h, trunk/xmds-devel/source/xsilfield.h: Documented for use with Doxygen. Quite basic and incomplete, but with placeholders where necessary for further addition and improvement of the api documentation. 2003-07-28 09:08 paultcochrane * trunk/xmds-devel/source/main.cc, trunk/xmds-devel/source/xmdssequence.cc: Added some documentation to the file. Mainly just to test out Doxygen, automatic api documentation generator. 2003-07-23 04:24 paultcochrane * trunk/xmds-devel/examples/atomlaser.xmds, trunk/xmds-devel/examples/fibre.xmds: Added <benchmark> tag 2003-07-23 04:23 paultcochrane * trunk/xmds-devel/source/xmdssimulation.cc: Implemented code to process <benchmark> tag properly. Added <ctime> header so that can actually do the benchmarking. 2003-07-23 04:21 paultcochrane * trunk/xmds-devel/source/xmdssequence.cc: Added output code to implement <benchmark> boolean 2003-07-23 04:20 paultcochrane * trunk/xmds-devel/source/xmdsfield.cc: Fixed issues with gcc 3+ not finding ifstream, ofstream, string etc. Need to prepend with std:: to use the correct namespace. 2003-07-23 04:19 paultcochrane * trunk/xmds-devel/source/xmdsclasses.h: Added benchmark boolean to simulationParametersStruct 2003-07-23 04:17 paultcochrane * trunk/xmds-devel/configure.in: Fixed problems with not getting flags passed to mpicc right. Still not perfect though... 2003-07-23 04:16 paultcochrane * trunk/xmds-devel/Makefile.am: Altered to allow building of example binaries in the examples subdirectory 2003-07-12 05:19 paultcochrane * trunk/xmds-devel/source/loadxsil.m: Loads binary data, and ascii data. Is now callable as a function and returns variables into calling script or functions variable space. Handles multiple moment groups. 2003-07-11 05:03 paultcochrane * trunk/xmds-devel/source/loadxsil.m: Initial import to repository. Is able to parse .xsil files and automatically generate the code to load binary data in from file. This is still under heavy development, need to be able to load ascii data from .xsil files and need to actually implement as a function as opposed to a script. Nevertheless, the checkin was necessary/ 2003-07-09 04:44 paultcochrane * trunk/xmds-devel/source/xmdssimulation.cc: Added useDouble boolean to myParameters. Implemented finding use_double element in xmds file, and setting accordingly if found. 2003-07-09 04:43 paultcochrane * trunk/xmds-devel/source/xmdsmomentgroup.cc: Added <string> C++ header. Added a check for the value of the useDouble boolean, if so, set output precison and cast (if necessary) accordingly. Implemented single or double precision for output of binary data depending on value of useDouble boolean. Default is to use double. 2003-07-09 04:40 paultcochrane * trunk/xmds-devel/source/xmdsclasses.h: Added useDouble boolean to simulationParametersStruct (to implement the choice of using double or single precision in binary output. 2003-07-09 03:57 paultcochrane * trunk/xmds-devel/source/xmdssimulation.cc: Implemented binaryOutput boolean. Implemented checking for <binary_output> element in xmds code. Added some more headers to xmds generated cc file so that can use more C++ features. 2003-07-09 03:55 paultcochrane * trunk/xmds-devel/source/xmdsoutput.cc: Addition of myBoolList variable in order to implement binary output 2003-07-09 03:54 paultcochrane * trunk/xmds-devel/source/xmdsmomentgroup.cc: Implemented binary output of data if <binary_output> boolean set to yes. 2003-07-09 03:53 paultcochrane * trunk/xmds-devel/source/xmdsfield.cc: Added some informative messages to output concerning what program is doing. Changed dodgy C-like implementation of wisdom and hostName/homeDir to a more robust C++ implementation. 2003-07-09 03:50 paultcochrane * trunk/xmds-devel/source/xmdsclasses.h: Modified to turn debugging on. Modified to add binaryOutput boolean to myParameters. 2003-07-09 03:49 paultcochrane * trunk/xmds-devel/examples/atomlaser.xmds: Added <use_wisdom> and <binary_output> flags to file. 2003-07-07 06:02 paultcochrane * trunk/xmds-devel/examples/atomlaser.xmds: Made minor changes to formatting of file. 2003-07-07 06:01 paultcochrane * trunk/xmds-devel/source/xmdssimulation.cc: Added code to look for <use_wisdom> tag in .xmds file, and implement if necessary. 2003-07-07 05:59 paultcochrane * trunk/xmds-devel/source/xmdssequence.cc: Updated writePlanCreationCalls() call so that includes new arguments due to inclusion of wisdom 2003-07-07 05:57 paultcochrane * trunk/xmds-devel/source/xmdsoutput.cc: Changed writePlanCreationCalls() to allow for wisdom implementation 2003-07-07 05:56 paultcochrane * trunk/xmds-devel/source/xmdsfield.cc: Implemented the use of wisdom via the <use_wisdom> tag. xmds simulation binary now outputs more progress information: when building forward and backward plans for fftw; when importing wisdom; when exporting wisdom; when using current directory instead of ~/.xmds/wisdom for .wisdom files. Simulation binary now checks for the existence of ~/.xmds/wisdom directory for storage of .wisdom files. 2003-07-07 05:52 paultcochrane * trunk/xmds-devel/source/xmdsclasses.h: Changed simulationParametersStruct to include useWisdom boolean. Updated writePlanCreationCalls to include useWisdom in function call. 2003-07-07 05:49 paultcochrane * trunk/xmds-devel/configure.in: Added checking for icc. Removed superfluous AC_SUBST calls. Fixed some issues with building and running xmds on machines with icc, the only problem being that configure script is now becoming a bit ugly. 2003-07-03 04:15 paultcochrane * trunk/xmds-devel/source/xmlparser.cc, trunk/xmds-devel/source/xmlparser.h: Fixed xml parsing so compiles and works on LinuxPPC. Problem was to do with different implementations of char for different compilers. Basically, the PPC gcc was setting some comparisons to always true or always false, because the char data type was really unsigned char. What was actually desired (and I believe used by Linux_x86 gcc) was signed char, but this only affected a few cases. XML files are now parsed properly and produce correct output (although there are subtle differences in numerical output at the e-12 level between LinuxPPC and LinuxI386, and I haven't checked that in depth as yet). 2003-07-03 04:11 paultcochrane * trunk/xmds-devel/source/Makefile.am: Initial import to repository 2003-07-01 08:56 paultcochrane * trunk/xmds-devel/AUTHORS, trunk/xmds-devel/COPYING, trunk/xmds-devel/INSTALL, trunk/xmds-devel/Makefile.am, trunk/xmds-devel/NEWS, trunk/xmds-devel/README, trunk/xmds-devel/configure.in, trunk/xmds-devel/install-sh, trunk/xmds-devel/ltmain.sh, trunk/xmds-devel/missing, trunk/xmds-devel/mkinstalldirs: Added initial version to repository 2003-07-01 08:55 paultcochrane * trunk/xmds-devel/source/main.cc, trunk/xmds-devel/source/xsil2graphics.cc: Minor alterations to standardise the naming conventions (e.g. VER is now VERSION) 2003-06-25 02:30 joehope * trunk/xmds-devel/source/xmdssequence.cc, trunk/xmds-devel/source/xmdssimulation.cc: Making (MPI) size a global variable. Good for debugging. 2003-06-03 02:30 joehope * trunk/xmds-devel/source/xmdsintegrate.cc: Fixing case sensitive TRUE and FALSE 2003-05-31 08:21 joehope * trunk/xmds-devel/source/xmdsclasses.h, trunk/xmds-devel/source/xmdsintegrate.cc, trunk/xmds-devel/source/xmdsintegratesiip.cc: Added <functions> element in <integrate>. Places code before the integration loop. This is good for time dependent functions. 2003-05-31 05:53 joehope * trunk/xmds-devel/source/xmdsfield.cc, trunk/xmds-devel/source/xmdsmomentgroup.cc, trunk/xmds-devel/source/xmdssequence.cc: Fixing two bugs for 0D systems with post-propagation output in fourier space. Allowing FFTWPLANS all the time, and fixing a verbose range check. 2003-04-17 06:22 joehope * trunk/xmds-devel/source/xmdsmomentgroup.cc: Fix range on if statement for x-space moment group with a cross-section in the first transverse dimension (deterministic MPI only) 2003-04-17 04:52 joehope * trunk/xmds-devel/source/xmdssequence.cc, trunk/xmds-devel/source/xmdssimulation.cc: Made rank a global variable. Good for debugging. 2003-04-17 01:55 joehope * trunk/xmds-devel/source/xmdsmomentgroup.cc: Fixed pointer initialisation in moment groups for a deterministic MPI simulation with a cross section in normal space for the first transverse dimension. 2003-04-16 07:05 joehope * trunk/xmds-devel/source/xmdsvector.cc: Fixed a compiler warning in renormalisation for deterministic MPI. 2003-04-16 05:43 joehope * trunk/xmds-devel/source/xmdsintegraterk4.cc, trunk/xmds-devel/source/xmdsvector.cc: Two range fixes for deterministic MPI. 2003-04-16 02:49 joehope * trunk/xmds-devel/source/xmdscomplex.h: Made the promotion of complex to fftw_complex non-explicit. Less warnings, and it should be safe. 2003-04-16 02:46 joehope * trunk/xmds-devel/source/xmdscomplex.h: Fixed three errors in the algebra for the complex overload operators. Specifically: - (z), z*=double and z/=double were all broken! 2003-04-04 00:23 joehope * trunk/xmds-devel/examples/highdim.xmds: Making highdim.xmds an MPI-enabled script with fewer outputs. 2003-04-04 00:22 joehope * trunk/xmds-devel/examples/gaugeatomlaser.xmds: Reverted stochastic Fourier-space output to local-in-x form. 2003-04-04 00:01 joehope * trunk/xmds-devel/examples/ndparamp.xmds: Pre-version 1.0 cruft removal from examples 2003-03-28 03:03 joehope * trunk/xmds-devel/source/xmdsvector.cc: Extra print variable cruft removed 2003-03-27 07:43 joehope * trunk/xmds-devel/examples/highdim.xmds, trunk/xmds-devel/source/xmdssequence.cc: Nested subsequences now call their initialisation functions. 2003-03-27 07:29 joehope * trunk/xmds-devel/examples/highdim.xmds, trunk/xmds-devel/source/xmdsvector.cc: Mixed space transforms added for deterministic MPI. 2003-03-27 02:45 joehope * trunk/xmds-devel/source/xmdsfield.cc, trunk/xmds-devel/source/xmdsmomentgroup.cc, trunk/xmds-devel/source/xmdsvector.cc: Put TRUE and FALSE into lowercase. Needed for linux (for icc, at least). 2003-03-26 06:07 joehope * trunk/xmds-devel/examples/highdim.xmds, trunk/xmds-devel/source/xmdsintegrate.cc, trunk/xmds-devel/source/xmdsintegraterk4ex.cc, trunk/xmds-devel/source/xmdsintegraterk4ip.cc, trunk/xmds-devel/source/xmdsintegratesiex.cc, trunk/xmds-devel/source/xmdsintegratesiip.cc: Passed cycle number right through to the integrate loops 2003-03-26 05:37 joehope * trunk/xmds-devel/examples/highdim.xmds, trunk/xmds-devel/source/xmdsmomentgroup.cc: Deterministic MPI nows works with all moment groups. Mixed space transforms still broken. 2003-03-25 04:26 joehope * trunk/xmds-devel/source/xmdsfield.cc, trunk/xmds-devel/source/xmdsfilter.cc, trunk/xmds-devel/source/xmdsintegraterk4.cc, trunk/xmds-devel/source/xmdsintegratesiex.cc, trunk/xmds-devel/source/xmdsintegratesiip.cc, trunk/xmds-devel/source/xmdsmomentgroup.cc, trunk/xmds-devel/source/xmdssequence.cc: Fixed cycles. Made all segments have access to the cycle number. Partial implementation of k-space output groups for deterministic MPI. 2003-03-24 23:38 joehope * trunk/xmds-devel/examples/atomlaser.xmds, trunk/xmds-devel/examples/kubo.xmds, trunk/xmds-devel/source/xmdsclasses.h, trunk/xmds-devel/source/xsil2graphics.cc: Fixed xsil2graphics bug 708629. Added MPI changes to class definitions. 2003-03-24 09:13 joehope * trunk/xmds-devel/source/main.cc, trunk/xmds-devel/source/xmdsfield.cc, trunk/xmds-devel/source/xmdsintegrate.cc, trunk/xmds-devel/source/xmdsintegrateex.cc, trunk/xmds-devel/source/xmdsintegrateip.cc, trunk/xmds-devel/source/xmdsintegraterk4.cc, trunk/xmds-devel/source/xmdsintegraterk4ex.cc, trunk/xmds-devel/source/xmdsintegraterk4ip.cc, trunk/xmds-devel/source/xmdsintegratesiex.cc, trunk/xmds-devel/source/xmdsintegratesiip.cc, trunk/xmds-devel/source/xmdsmomentgroup.cc, trunk/xmds-devel/source/xmdssequence.cc, trunk/xmds-devel/source/xmdssimulation.cc, trunk/xmds-devel/source/xmdsvector.cc: Reversion to local-in-x tag with addition of the ability to use MPI on deterministic problems with >1 transverse dimensions. k-space moment groups and mixed space transforms currently broken. Simply compile with <use_mpi> element as for stochastic problems. 2003-03-12 23:25 joehope * trunk/xmds-devel/source/xmdsintegraterk4.cc, trunk/xmds-devel/source/xmdsintegratesiex.cc, trunk/xmds-devel/source/xmdsintegratesiip.cc: Memory reordering now complete. Cross-propagation should now be fully operational. 2003-03-11 06:23 joehope * trunk/xmds-devel/examples/fullpos3D.xmds, trunk/xmds-devel/examples/gaugeatomlaser.xmds, trunk/xmds-devel/source/xmdsfield.cc, trunk/xmds-devel/source/xmdsintegrate.cc, trunk/xmds-devel/source/xmdsintegrateex.cc, trunk/xmds-devel/source/xmdsintegrateip.cc, trunk/xmds-devel/source/xmdsintegratesiip.cc, trunk/xmds-devel/source/xmdsmomentgroup.cc, trunk/xmds-devel/source/xmdsvector.cc: Reordered all the fields so that they are contiguous in memory when running through the FFTs rather than when going through x-space loops. This is in preparation for parallelisation. x-space heavy algorithms are slower and k-space heavy algorithms are faster. I have tested all the algorithms on gaugeatomlaser.xmds, and they all work identically to the stable branch. Cross-propagation is definitely broken - but fixable with effort. Mixed transforms should still work, but I haven't tested them on anything. Input files must now be reordered - components are now the slowest changing index rather than the fastest. 2003-03-10 03:55 joehope * trunk/xmds-devel/examples/atomlaser.xmds, trunk/xmds-devel/examples/gaugeatomlaser.xmds: Updating the examples to make a tagged version. I want to have a "pre-reordering" version, as I'm about to rearrange the memory management of the main fields. 2003-03-04 02:35 joehope * trunk/xmds-devel/source/xmdsintegrateex.cc: Fixed missing segment name in xmdsintegrateex.cc (from previous speedup patch) 2003-03-03 03:58 joehope * trunk/xmds-devel/examples/atomlaser.xmds, trunk/xmds-devel/examples/gaugeatomlaser.xmds, trunk/xmds-devel/source/xmdsintegrateex.cc, trunk/xmds-devel/source/xmdsintegrateip.cc: Replaced various operations in the K_operater routines with index pointers. Provided detectable speedup. Modified Files: source/xmdsintegrateex.cc source/xmdsintegrateip.cc 2003-02-23 23:53 joehope * trunk/xmds-devel/examples/fullpos3D.xmds, trunk/xmds-devel/source/main.cc, trunk/xmds-devel/source/xmdsclasses.h, trunk/xmds-devel/source/xmdssequence.cc, trunk/xmds-devel/source/xmdssimulation.cc, trunk/xmds-devel/source/xmdsvector.cc: Added partial support for threading. Placement of a <threads>15</threads> element in the simulation element will make the FFT use 15 threads. Further threading to follow. Default, and <threads>1</threads> is equivalent to the non-threaded code. Note that fftw must be compiled with the --enable-threads option. Modified Files: Configure examples/fullpos3D.xmds source/main.cc source/xmdsclasses.h source/xmdssequence.cc source/xmdssimulation.cc source/xmdsvector.cc 2003-02-03 04:42 joehope * trunk/xmds-devel/source/kissdom.cc, trunk/xmds-devel/source/xmdsfield.cc, trunk/xmds-devel/source/xmdsintegrate.cc, trunk/xmds-devel/source/xmdsintegraterk4.cc, trunk/xmds-devel/source/xmdsintegratesiex.cc, trunk/xmds-devel/source/xmdsintegratesiip.cc, trunk/xmds-devel/source/xmdsmomentgroup.cc, trunk/xmds-devel/source/xmdsvector.cc, trunk/xmds-devel/source/xmdsvectorelement.cc, trunk/xmds-devel/source/xmlbasics.cc: Makefile has different options for different systems (different option order required) Stack no longer used for main fields (Simon) logical and rather than bitwise and (Simon) Details in changes.log 2003-02-03 01:23 joehope * trunk/xmds-devel, trunk/xmds-devel/examples, trunk/xmds-devel/examples/atomlaser.xmds, trunk/xmds-devel/examples/fibre.xmds, trunk/xmds-devel/examples/fullpos3D.xmds, trunk/xmds-devel/examples/gaugeatomlaser.xmds, trunk/xmds-devel/examples/kubo.xmds, trunk/xmds-devel/examples/ndparamp.xmds, trunk/xmds-devel/examples/nlse.xmds, trunk/xmds-devel/examples/sine.xmds, trunk/xmds-devel/examples/soliton.xmds, trunk/xmds-devel/examples/tla.xmds, trunk/xmds-devel/source, trunk/xmds-devel/source/dom3.h, trunk/xmds-devel/source/kissdom.cc, trunk/xmds-devel/source/kissdom.h, trunk/xmds-devel/source/main.cc, trunk/xmds-devel/source/xmdsclasses.h, trunk/xmds-devel/source/xmdscomplex.h, trunk/xmds-devel/source/xmdselement.cc, trunk/xmds-devel/source/xmdsfield.cc, trunk/xmds-devel/source/xmdsfilter.cc, trunk/xmds-devel/source/xmdsglobals.cc, trunk/xmds-devel/source/xmdsintegrate.cc, trunk/xmds-devel/source/xmdsintegrateex.cc, trunk/xmds-devel/source/xmdsintegrateip.cc, trunk/xmds-devel/source/xmdsintegraterk4.cc, trunk/xmds-devel/source/xmdsintegraterk4ex.cc, trunk/xmds-devel/source/xmdsintegraterk4ip.cc, trunk/xmds-devel/source/xmdsintegratesi.cc, trunk/xmds-devel/source/xmdsintegratesiex.cc, trunk/xmds-devel/source/xmdsintegratesiip.cc, trunk/xmds-devel/source/xmdsmomentgroup.cc, trunk/xmds-devel/source/xmdsoutput.cc, trunk/xmds-devel/source/xmdssegment.cc, trunk/xmds-devel/source/xmdssequence.cc, trunk/xmds-devel/source/xmdssimulation.cc, trunk/xmds-devel/source/xmdsutils.cc, trunk/xmds-devel/source/xmdsutils.h, trunk/xmds-devel/source/xmdsvector.cc, trunk/xmds-devel/source/xmdsvectorelement.cc, trunk/xmds-devel/source/xmlbasics.cc, trunk/xmds-devel/source/xmlbasics.h, trunk/xmds-devel/source/xmlparser.cc, trunk/xmds-devel/source/xmlparser.h, trunk/xmds-devel/source/xsil2graphics.cc, trunk/xmds-devel/source/xsilfield.cc, trunk/xmds-devel/source/xsilfield.h: Initial revision
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