2005-10-27 10:58 joehope * ChangeLog, source/xmdssequence.cc, source/xmdssimulation.cc: Fixed adaptive scheduler to compile cleanly on other systems. 2005-10-26 13:46 joehope * ChangeLog, README, README.Windows, configure.in, examples/kubo.xmds, source/main.cc, source/xmdssequence.cc, source/xmdssimulation.cc: Added new scheduling option for stochastic MPI calculations. It uses an adaptive scheduler to allocate batches of work to individual nodes, making for large speed increases on heterogenous systems. Bumped version numbers. 2005-10-25 08:40 joehope * source/xmdssequence.cc: Fix for new timer. 2005-10-24 14:11 joehope * source/: xmdssimulation.cc, xmdssequence.cc: Changed timer to work better on MPI systems. 2005-10-19 09:33 joehope * examples/kubo.xmds, examples/tla.xmds, source/xmdsclasses.h, source/xmdssimulation.cc, source/xmdsvectorelement.cc: Fix for stack overflow in binary read from file. Preliminary support for MPI Scheduling options. 2005-10-13 10:45 joehope * source/xmdssequence.cc: MPI runs only print out the benchmark time from the master node. 2005-10-12 14:34 joehope * source/xmdsvectorelement.cc: Fix for crashing bug when loading from file in stochastic simulations. 2005-09-29 15:35 joehope * source/xmdsmomentgroup.cc, ChangeLog: Fix compile error for error-free stochastic binary output. 2005-08-12 15:46 sebwuester * examples/sech_soliton.xmds, source/xmdsclasses.h, source/xmdsintegrateark45.cc: -Bugfixes in ARK45: -current step now states last accepted step instead of current forecast -fixed problems with timescales <10^-24 -fixed problem with N_samples=N_steps -Cosmetic in ARK45 - rephrased "cutoff defaulting to" not to contain the word error 2005-07-27 16:57 joehope * source/xmdsintegratesiip.cc: Fixed an error in the cross propagation routines of the SIIP algorithm. Boundary conditions that are independent of the propagation dimension are now correct. 2005-07-05 20:13 joehope * ChangeLog, MANIFEST: Updating Changelog and MANIFEST prior to release 2005-07-05 19:37 joehope * README, README.Windows, examples/highdim.xmds: Adjusting READMEs and examples for version 1.5-1x 2005-06-30 17:44 sebwuester * source/xmdsintegrateark45.cc: Minor Bugfixes: Corrected typo in on-screen message and call to noise generator in the case of errorchecking 2005-05-25 13:33 paultcochrane * examples/highdim.xmds: Fixed xml header. 2005-05-24 13:54 paultcochrane * configure.in: Doing a check to see if the library lammpi++ exists in the mpicc -showme output, and if not adds -llammpi++ to the MPI_LIBS variable. This should only affect users of lam 7.x.x, this problem didn't occur in 6.x.x. 2005-05-19 15:46 paultcochrane * source/xmdssequence.cc: Outputting standard C argument stuff even when is not defined. This fixes a problem where I didn't check for all possible paths in an if loop 2005-05-19 13:50 joehope * ChangeLog: Update of ChangeLog 2005-05-19 13:42 joehope * source/xsilfield.cc: The m file now closes files when it is done to avoid excess file pointer usage in Matlab. 2005-05-17 16:01 sebwuester * source/: xmdsintegrateark45.cc, xmdsintegraterk4ip.cc: Fixed bug in warning about RK4IP and t-dep k operators. Made ARK45 error determination routine more efficient for ODEs 2005-05-10 13:40 paultcochrane * source/main.cc: Moved -o .cc to just behind the mpicc call in the mpi compilation calls. This gets around problems with mpicc not finding various libraries. In particular, when getopt was turned on for mpi problems, mpicc wasn't finding -lxmds. 2005-05-10 11:23 paultcochrane * configure.in: Changed ordering of MPICCFLAGS so that XMDS_LIBS is at the end. This should stop problems with mpicc not finding the xmds libraries. 2005-05-05 19:34 paultcochrane * source/xmdssequence.cc: Hopefully fixed problem with mpi not being able to make use of the arugment parsing code. Added -h as a valid option; --help was only possible before. 2005-05-02 15:42 sebwuester * examples/sech_soliton.xmds, examples/sech_soliton_tdepk.xmds, source/xmdsintegrateark45.cc: Fixed float precision issue in ARK45 sampling and typos in examples. 2005-05-02 12:35 sebwuester * examples/sech_soliton.xmds, examples/sech_soliton_tdepk.xmds, source/xmdsclasses.h, source/xmdsintegrate.cc, source/xmdsintegrateark45.cc, source/xmdsintegrateark45ex.cc, source/xmdsintegrateark45ip.cc, source/xmdsintegrateip.cc, source/xmdsintegraterk4ip.cc, source/xmdsvectorelement.cc: Added ARK45IP and ARK45EX adaptive timestep algorithms. Added example files sech_soliton.xmds, sech_soliton_tdepk.xmds Added parallel initialisation from file (ascii only) 2005-04-28 15:21 joehope * source/loadxsil.m: Fix for loadxsil loading of 64 bit binaries 2005-04-27 15:44 joehope * source/xmdsfield.cc: Andy's fix for cluster nodes testing the same filesystem simultaneously with the same files. 2005-04-24 14:31 joehope * source/xsilfield.h: Final commit for previous fix. 2005-04-21 16:32 joehope * configure.in, source/xmdsmomentgroup.cc, source/xsilfield.cc: Added test for the size of unsigned longs in the configure script. This, like endianness, is stored in the xsil file for binary output, and then used when generating the MATLAB script. Fixes bug with moving binary data between machines. 2005-04-12 17:25 joehope * source/: xmdsclasses.h, xmdsintegrate.cc, xmdsintegrateark45ex.cc, xmdsintegrateark45ip.cc: Set up template for passing the adaptive boolean to the xmdsintegrate class. 2005-04-12 15:44 joehope * source/xsilfield.cc: Fixed matlab error message when using binary files without the output file 2005-04-06 16:41 paultcochrane * examples/lorenzInput.dat: Initial import to repository. This is the data file associated with the lorenz.xmds example. 2005-04-06 15:54 joehope * examples/: branch.xmds, brusselator.xmds, catcycle.xmds, chain.xmds, chemkin.xmds, duffing.xmds, fibre.xmds, fisher_reaction_diffusion.xmds, highdim.xmds, hires.xmds, krebs.xmds, lane_emden.xmds, lorenz.xmds, lotka_volterra.xmds, oregonator.xmds, pendulum.xmds, ring_modulator.xmds, sine.xmds, soliton.xmds, thermkin.xmds, van_der_pol.xmds: Fixing all examples to conform with the (post 1.4-1) rule to always specify the used vectors in integrate blocks. 2005-04-06 12:22 joehope * source/xmdsmomentgroup.cc: Fix for potential problem with handling sample spaces when there are no transverse dimensions. 2005-04-06 11:43 joehope * source/xmdsmomentgroup.cc: Made verbose output on the moment groups more consistent with the numbering of the groups. 2005-04-06 09:23 joehope * ChangeLog, configure.in: Version bump 2005-04-05 17:23 joehope * source/: xmdsintegrateark45.cc, xmdsclasses.h, xmdsintegrateark45ex.cc, xmdsintegrateark45ip.cc, Makefile.am, main.cc, xmdssequence.cc: Adding in shell files for new ARK45 algorithms and bumping versions. 2005-04-05 15:32 joehope * examples/diffusion.xmds: Fixed sampling in example. 2004-12-06 15:58 paultcochrane * source/xsilfield.cc: Now orienting independent variable vectors for binary input to agree with that from ascii input. 2004-12-06 15:42 paultcochrane * source/xsilfield.cc: Changed ordering of variables in binary input to matlab. Should work the same as ascii now. Some changes to comments. 2004-11-18 10:35 joehope * source/xsilfield.cc: Fixed a bug when using MATLAB import of output moment groups of >2 dimensions in binary format. 2004-11-17 15:54 joehope * source/xsilfield.cc: Adding explicit include line to avoid problem with non-standard compilers. 2004-11-03 09:51 joehope * examples/atomlaser.xmds: Changing this example to demo binary output, now that it works without explosions. 2004-11-03 09:48 joehope * ChangeLog: New ChangeLog for the new version 2004-11-03 09:47 joehope * MANIFEST: New manifest for the new version. 2004-11-03 09:43 joehope * source/xsilfield.cc: Fix for an error where an integer overflow lead to dramatic problems with bianry output. 2004-10-25 16:02 joehope * configure.in, source/main.cc: Bumping the release version in preparation for a new release. 2004-10-22 18:04 paultcochrane * admin/xmdsReleaseProcedure.pod: Made mention that one should update the xmds version and release numbers in configure.in. Gave a more complete explanation of generating a distribution, including checking out a temporary copy of the xmds-devel repository and going through the relevant steps to be able to do a make dist. 2004-10-22 11:16 paultcochrane * source/xsilfield.cc: Added some error text for when a user tries to use binary output and then load the data using scilab. Also put in some hopefully helpful information about how to use scilab and data that comes out of xmds. Basically this means just using ascii output. 2004-10-21 20:01 paultcochrane * source/xsilfield.h: Correction log for previously stuffed up commit without a log. Added extra variables to implement binary data handling of xsil2graphics. 2004-10-21 20:00 paultcochrane * source/xsilfield.cc: Simple commit to actually add a log for the previous commit, because I stuffed up. Major changes. Binary files are now handled by xsil2graphics. Unfortunately, only the matlab script is produced at this stage. The scilab version is to come. 2004-10-21 19:51 paultcochrane * source/: xsilfield.cc, xsilfield.h: xsilfield.cc 2004-10-21 19:51 paultcochrane * source/xmdsvectorelement.cc: Changed some return statements to exit statements. Basically, the program could keep going at this point as opposed to barfing which would be far more logical in the circumstances. 2004-10-21 19:50 paultcochrane * source/xmdsvector.cc: Changed unsigned long to unsigned long int. I must have been in a pedantic mood. 2004-10-21 19:49 paultcochrane * source/xmdsoutput.cc: Added xmdsOutputFileName() function. This is so that I can properly determine what the output binary data filename should be, and base that upon the name of the xsil filename as opposed to the simulation filename. 2004-10-21 19:48 paultcochrane * source/xmdsmomentgroup.cc: Major changes. Added more attributes to the Metalink tag of the xsil file that gets output so that can load binary data properly using xsil2graphics. Implemented a better way of constructing the output binary data filename. It is now based upon the xsilFilename rather than the simulation name (these can be different). Fixed major bug where if there is only one sample in the entire simulation (possible but not common) then data was being written over as an array was incorrectly sized. This is all happy now, and I even tested it. Yay. 2004-10-21 19:42 paultcochrane * source/xmdsfilter.cc: Added a Doxygen docstring. 2004-10-21 19:41 paultcochrane * source/xmdscomplex.h: Fixed problem with there being no newline at the end of the file. 2004-10-21 19:40 paultcochrane * source/xmdsclasses.h: Was pedantic again and changed some unsigned constants to long unsigned ints. Added the getOutputFileName() function, and its Doxygen docstring. 2004-10-21 19:39 paultcochrane * source/loadxsil.m: Removed some superfluous code in the binary loading section. Made loading of the binary data file part of the eval, as opposed to running it here. Added some strings to say that the text that follows isn't actually just informative, it is actually the code that is being executed. 2004-10-21 19:37 paultcochrane * source/: getopt_xmds1.c, getopt_xmds_init.c: Added some Doxygen docstrings. 2004-10-21 19:36 paultcochrane * source/getopt_xmds.c: Reformat of the C code. Documentation with Doxygen docstrings. 2004-10-21 19:34 paultcochrane * configure.in: Updated version number to interim release number. 2004-10-15 17:53 joehope * configure.in: Various fixes to the mpi autoconf testing. It now works with non-gcc mpi. 2004-10-11 14:06 joehope * configure.in: Removed a "-Wall -pedantic" check that broke compilation when cc/mpicc were gnu/non-gnu compilers. 2004-10-06 17:52 joehope * source/: xmdsfilter.cc, xmdsintegrate.cc, xmdsintegraterk4.cc, xmdsintegratesiex.cc, xmdsintegratesiip.cc, xmdsmomentgroup.cc, xmdssequence.cc, xmdsvectorelement.cc: Fixed a memory leak on strict compilers that didn't know that "delete(pointer)" means "delete[] pointer" for pointer arrays. 2004-10-06 17:50 joehope * examples/: kubo.xmds, van_der_pol.xmds: These, and possibly others, now need elements in the integrate blocks. 2004-09-30 13:27 paultcochrane * source/loadxsil.m: Fixed binary loading support. This now works for mutli-dimensional matrices (ie greater than two dims). Probably should be tested a bit more extensively than I've tested it, but it seems to go well in the tests that I've done. The ascii loading takes ages, especially for large output data files, so I've added a message saying that it will take ages, and have added progress output to keep the user amused while they're waiting. Realistically for large files people should use binary as it loads a couple of orders of magnitude faster than ascii. I've also implemented preallocation of matrices to help the ascii loading to run more quickly. Using this script turns out to be a better option for very large files as it doesn't use up as much memory as xsil2graphics does. For some sims I've been doing recently, xsil2graphics maxes out the memory on my machine when it's trying to generate the matlab file and data file, however, loadxsil sits there quite happily and doesn't even bother making the machine page to disk. This implies that there could be a memory leak in xsil2graphics, or that something could be done a bit more carefully concerning memory useage. 2004-09-24 13:29 paultcochrane * Makefile.am: Fixed typo in orgeonator name. 2004-09-15 16:01 joehope * source/: xmdsintegraterk4ex.cc, xmdsintegraterk4ip.cc: Fix for flag in RK4 algorithms. 2004-09-15 14:46 joehope * source/: xmdsclasses.h, xmdsfilter.cc, xmdsintegrate.cc, xmdsintegraterk4.cc, xmdsintegratesiex.cc, xmdsintegratesiip.cc: Added flag that turns off the noise generation in an integration or filter element. This allows deterministic elements in stochastic simulations (e.g. the noise is in the initial state only) to run faster. Activated by the flag yes, and the default is to turn off this feature. 2004-09-15 14:27 joehope * ChangeLog: Updated with cvs2cl.pl 2004-08-03 15:29 paultcochrane * examples/: brusselator.xmds, chain.xmds, oregonator.xmds, thermkin.xmds: Added GPL header. 2004-08-02 20:04 paultcochrane * source/xmdsoutput.cc: Changed long to long unsigned int, which gets rid of a compiler warning, and appears only because compilers can choose which sign ints can take, hence being pedantic is the way to go. 2004-08-02 20:01 paultcochrane * source/: xmdsfilter.cc, xmdsintegrate.cc, xmdsintegratesiip.cc: Changed longs to long unsigned ints. Also fixed warnings that appear due to a .size() call on a list (which returns int) being given a format in a printf statement as being a long int. If this isn't quite the right thing to do then one probably needs to overload/override the .size() method to return long ints as opposed to just ints. 2004-08-02 19:59 paultcochrane * source/xmdsclasses.h: Changed longs to long unsigned ints. 2004-08-02 19:57 paultcochrane * Makefile.am: Added new example simulations to list of files to be added when doing a make dist. 2004-08-02 18:48 paultcochrane * source/: xmdsfilter.cc, xmdsintegrate.cc, xmdsintegratesiip.cc: Reformatted code so it looks nicer. 2004-08-02 18:47 paultcochrane * source/xmdsfield.cc: Changed long to long unsigned int. This is a really pedantic change I know, but we need to be really explicit so that the code is really pedantically ansi compliant, and hopefully therefore more portable. 2004-08-02 18:45 paultcochrane * source/xmdsclasses.h: Changed variables declared as longs to be long unsigned ints. This gets rid of some compiler warnings, especially between compilers that define ints to be signed or unsigned on their whim. 2004-08-02 18:16 paultcochrane * examples/chain.xmds: Initial import to repository. This is another chemical kinetics reaction I found lying around in my sandbox. 2004-08-02 18:10 paultcochrane * examples/: brusselator.xmds, oregonator.xmds, thermkin.xmds: Initial import to repository. These are some more example simulations of chemical kinetics type reactions. 2004-08-02 18:04 paultcochrane * benchmark/: ndparamp_100.xmds, ndparamp_200.xmds, ndparamp_50.xmds, ndparamp_500.xmds, nlse_100.xmds, nlse_1000.xmds, nlse_10000.xmds, nlse_500.xmds, nlse_5000.xmds: Removed the binary_output tag as it is now obsolete. 2004-08-02 18:02 paultcochrane * source/xmdssimulation.cc: Stopped storing all of the description text; we weren't using it anyway. There is now a message added to say that the description has been found, and to look in the xmds file for more info. The reason for this change is because if the description is too big, then this causes a buffer overflow and all kinds of wierd things can happen. I have commented out the original code that read the description in. 2004-07-30 17:43 joehope * source/: xmdsfilter.cc, xmdsvector.cc: Allowed integrate moment groups to deal with mixed spaces and MPI transposed spaces properly. 2004-07-30 16:56 joehope * source/xmdsfield.cc: Fixed the close_loops function which used to be simply wrong for mixed spaces. 2004-07-30 16:02 joehope * source/: xmdsfield.cc, xmdsvector.cc: Fixed a bug where some mixed spaces were incorrectly recognised as being in the transposed order for deterministic MPI solutions. 2004-07-29 18:28 joehope * examples/highdim.xmds: Added example syntax for the new elements in the evolution. 2004-07-29 18:27 joehope * source/: xmdsclasses.h, xmdsfilter.cc, xmdsintegrate.cc, xmdsintegratesiip.cc, xmdssequence.cc, xmdssimulation.cc: Added the option of putting elements as well as elements in blocks. 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 and elements to elements. You can put as many as you like, of any dimension, in any order. The element defines the position of the or code, so it is now mandatory. Sample syntax will be added to an example. 2004-07-27 17:33 paultcochrane * source/xmlparser.cc: Cast a variable as unsigned. This stopped a warning message turning up in the compiler output due to an integer which should have been cast as unsigned. 2004-07-27 17:31 paultcochrane * source/xmdsvectorelement.cc: Fixed error whereby an extra comma was added to a fprintf statement, and hence caused incorrect output when generating the code for reading in an input file. 2004-07-27 16:45 paultcochrane * source/getopt_xmds_init.c: Replaced C++ comments with C-style comments. This stops some compilers complaining. 2004-07-23 17:27 joehope * source/xmdsfield.cc: Fixes problem when multiple FFTW plans were created using wisdom. The variables used for the wisdom manipulation are all now local variables, so there are no more multiple definitions. 2004-07-21 15:45 joehope * source/xmdsoutput.cc: Added the command line variables to the element in the output tag. This will make the xsil file completely self documenting. 2004-07-19 13:59 paultcochrane * admin/xmdsReleaseProcedure.pod: Found a command to put on its own line that I'd missed. 2004-07-19 13:57 paultcochrane * MANIFEST: Updated manifest to xmds-1.3-5. 2004-07-19 13:56 paultcochrane * admin/xmdsReleaseProcedure.pod: Put all of the commands to run on their own line. 2004-07-19 13:53 paultcochrane * ChangeLog: Updated with cvs2cl.pl 2004-07-19 13:52 paultcochrane * README, README.Windows: Changed xmds-1.3-4 to xmds 1.3-5. 2004-07-19 13:43 paultcochrane * ChangeLog: Updated with cvs2cl.pl 2004-07-19 13:42 paultcochrane * source/loadxsil.m: Now detecting when there are more than two independent variables when loading binary data and output an error saying that one should use ascii data and xsil2graphics to get around the problem. The file still works for less than two independent variables (or less) with binary data and for any number of variables with ascii data (but one might as well just use xsil2graphics in that case). 2004-07-19 13:40 paultcochrane * source/getopt_xmds.h: Fixed warnings that were produced as a result of having C++ comments within a C file (and when using -pedantic and -ansi). Having C++ style comments isn't a problem with modern compilers, however it's nice for users to not have warnings come up when xmds compiles. 2004-07-16 14:02 paultcochrane * examples/atomlaser.xmds: Removed precision=single bit from output tag. 2004-07-16 13:46 paultcochrane * admin/xmdsReleaseProcedure.pod: Added more detailed info about how to perform a release of the xmds documentation. Put the tagging commands earlier in the list of things to do before making a release, and mentioned the format of the tag to use. Also added the actual commands to use. 2004-07-16 13:25 paultcochrane * admin/xmdsReleaseProcedure.pod: Changed the order of when the Readmes are updated and when the ChangeLog is updated. Added a line explaining how one should check to see if the cvs and/or the local repository needs updating before running a make dist. 2004-07-16 13:20 paultcochrane * ChangeLog: Updated to current output of cvs2cl.pl. 2004-07-16 13:19 paultcochrane * admin/xmdsReleaseProcedure.pod: We're now automatically generating the ChangeLog with cvs2cl.pl, so have changed what to do as far as that is concerned. 2004-07-16 13:16 paultcochrane * ChangeLog: Updated to current output of cvs2cl.pl. 2004-07-16 13:12 paultcochrane * README.Windows: Made mention of the fact that fftw must be installed after cygwin is installed. Also added a description of the steps required to build and install fftw. Fixed up the step numbering as necessary. Added --with-fftw-path=/usr/local to the configure option to the xmds build procedure, as this *should* be where fftw is installed, assuming that the user followed the instructions higher up in the file. Removed some comments reminding me to do stuff. 2004-07-16 11:27 paultcochrane * admin/cvs2cl.pl: Initial import to repository. This is the cvs to ChangeLog script that generates the ChangeLog. 2004-07-15 17:27 joehope * source/xmdsoutput.cc: Moved tags down above the data to make the XSIL file valid XML. This fixed a parsing error from xsil2graphics. 2004-07-14 21:48 paultcochrane * source/: main.cc, xmdsoutput.cc: Finally got grabbing and splitting up and escaping quote issues in the script code grabbing code. This is quite a big change, and means that xmds produced scripts now compile ok on linux and the APAC sc. I haven't tested anything else, but it's 10pm, and I've finally fixed the damned thing, and I'm going home (yay). 2004-07-14 16:36 joehope * ChangeLog, examples/atomlaser.xmds, examples/fibre.xmds, examples/fisher_reaction_diffusion.xmds, examples/fullpos3D.xmds, examples/gaugeatomlaser.xmds, examples/highdim.xmds, examples/hires.xmds, examples/kubo.xmds, examples/lorenz.xmds, examples/ndparamp.xmds, examples/nlse.xmds, examples/pendulum.xmds, examples/ring_modulator.xmds, examples/sine.xmds, examples/soliton.xmds, examples/tla.xmds, examples/vibstring.xmds, source/main.cc: Changed the examples and template to ascii output until binary output is robust. 2004-07-14 14:27 joehope * source/: xmdssequence.cc, xmdssimulation.cc: Fixed bug where nested subsequences could count moment samples incorrectly. The field moment samples were being counted at the start of each sequence rather than at the start of the simulation. 2004-07-14 11:32 joehope * source/xmdsmomentgroup.cc: Verbose mode now mentions the addition of samples to the moment groups. 2004-07-13 18:46 paultcochrane * source/xmdsargelement.cc: Removed a trigraph. Added a test to see if a short option was actually found, and if no short option could be worked out, then xmds barfs with a reasonably helpful error message. Also fixed a typo in one of the comments. 2004-07-13 17:52 paultcochrane * configure.in: Added the threads checking stuff back in. However, to enable this option, one needs to use --enable-threads at the configuration step. I put this back in so that if someone does want to use threads, then at least the checking and configuration is built in. The code that was originally there is now wrapped in an if loop, and is only executed if --enable-threads is set. 2004-07-13 17:25 paultcochrane * configure.in: added -pedantic flag to CFLAGS and CXXFLAGS variables for building of xmds and the -ansi flag to the CXXFLAGS variable. 2004-07-13 17:24 paultcochrane * source/: kissdom.h, xmdsclasses.h, xmlbasics.h: Removed fake trigraphs (obsolecent feature of C) that were in the comments. 2004-07-13 16:16 paultcochrane * source/xmdsutils.h: Fixed problem with trailing comma in enumeration. This was found by using the -pedantic flag to gcc. 2004-07-13 15:29 paultcochrane * source/: kissdom.cc, main.cc, xmdsarg.cc, xmdsargelement.cc, xmdsargv.cc, xmdsbreakpoint.cc, xmdselement.cc, xmdsfield.cc, xmdsfilter.cc, xmdsglobals.cc, xmdsintegrate.cc, xmdsintegrateex.cc, xmdsintegrateip.cc, xmdsintegraterk4.cc, xmdsintegraterk4ex.cc, xmdsintegraterk4ip.cc, xmdsintegratesi.cc, xmdsintegratesiex.cc, xmdsintegratesiip.cc, xmdsmomentgroup.cc, xmdsoutput.cc, xmdssegment.cc, xmdssequence.cc, xmdssimulation.cc, xmdsutils.cc, xmdsvector.cc, xmdsvectorelement.cc, xmlbasics.cc, xmlparser.cc, xsil2graphics.cc, xsilfield.cc: Added braces to if, while and for statements. They weren't necessary, however, it does make the code a bit nicer, in terms of style, it might save a few bugs in the future, and it really should be used when the if, while or for has nested if, while or for statements. I hope this reduces someone's pain in the future. 2004-07-09 16:47 joehope * source/xmdsfield.cc: cstr() should be c_str() 2004-07-09 16:35 joehope * source/xmdsfield.cc: Attempt to stop a very rare crash when a deterministic MPI script is written without any Fourier space elements anywhere. Forces plans to always be written. This could be done with slightly greater finesse by testing for the existence of "main_forward_plan" and setting the appropriate variables manually if it doesn't exist. 2004-07-09 15:29 joehope * source/xmdsvectorelement.cc: Forcing abort when input file is misread. 2004-07-01 15:24 paultcochrane * source/: kissdom.cc, main.cc: Added braces to if, while and for statements. They weren't necessary, however, it does make the code a bit nicer, in terms of style, it might save a few bugs in the future, and it really should be used when the if, while or for has nested if, while or for statements. This exercise fixed two possible bugs where there was a trailing semicolon on the statement. I hope this reduces someone's pain in the future. 2004-06-30 20:23 paultcochrane * source/xmdssimulation.cc: Commented out some legacy code that's not doing anything anymore. I'm keeping it around for a while before I delete it (doesn't hurt). 2004-06-30 20:22 paultcochrane * source/main.cc: Updated the documentation version numbering output from xmds-1.3-4 to xmds-1.3-5. 2004-06-30 20:20 paultcochrane * source/getopt_xmds_init.c: Added a dummy statement to avoid a warning that some compilers throw up when the ifdef isn't executed, and hence there aren't any executable statements in the file. Also added some comments explaining this. 2004-06-30 20:18 paultcochrane * configure.in: Changed the release number from 4 to 5. Added a check for the Tru64 compiler and then set the __USE_STD_IOSTREAM appropriately if it is. Added a check for if mpicc is *not* set, but mpi is enabled and then if so, setting MPICC to the system C++ compiler. Fixed bug whereby LIBS variable should have been XMDS_LIBS, and CFLAGS should have been XMDS_CFLAGS. Hopefully this stuff gets xmds configuring and compiling better on Tru64 machines. 2004-06-30 20:15 paultcochrane * README.Windows: Added some more helpful comments about how to use the configure script, where to look for more information, and how to solve the common fftw path problem. 2004-06-30 20:14 paultcochrane * README: Tidied up the formatting of the text somewhat. Hopefully made a bit clearer that the switches are directly to do with the configure command. 2004-06-30 17:26 paultcochrane * man/: loadxsil.1, xmds.1, xsil2graphics.1: Initial import to repository. These are the automatically generated man pages from the pod in the xmds-doc project. 2004-06-30 17:20 paultcochrane * source/xmdssimulation.cc: Removed some whitespace. 2004-06-30 17:19 paultcochrane * source/xmdsoutput.cc: Implemented breakup of simulation text into header, body and footer. I reconstruct this text here. A lot of the changes in this commit are commenting out lines of code in the generated code (ie the stuff that is generated isn't actually executed and is in fact ignored by the compiler). I left the code in at this stage as this is still an experimental process and it will be easier to back out the changes by leaving the legacy stuff in there. This change has removed the need for xmds simulations to use the system() call and the split system command to be able to write the output. I also put some info text into the output xml/xsil which tells which version of xmds produced the file. 2004-06-30 17:15 paultcochrane * source/xmdsmomentgroup.cc: Fixed error whereby the Metalink xml tag should have had a /> at the end instead of just >. 2004-06-30 17:14 paultcochrane * source/main.cc: Implemented the splitting up of the xmds simulation text before the parsing starts. I split the text into a header, body and footer, and then recombine these later when getting the simulation to write the xsil file. This removes the need to use the split system command, and removes some more of the system() calls in the xmds engine. Added heaps of comments of how I'm going about stuff, and added some verbose output to make sure it's doing what it should be doing. At present I'm implementing this as global variables; perhaps this really should be done through and object interface, however, this is easy and it works, we just have to be careful. Also updated the documentation version number to xmds-1.3-4. 2004-06-29 17:21 joehope * source/: xmdsintegratesiip.cc, xmdsintegratesiex.cc, xmdsintegraterk4.cc: Fix for problem in if statements. 2004-06-29 17:13 joehope * source/: xmdsintegratesiex.cc, xmdsintegraterk4.cc, xmdsintegratesiip.cc: Allows number of samples in an integrate block to be zero without trouble. 2004-06-26 15:29 paultcochrane * source/main.cc: Grabbing the simulation text for splitting up the xmds script for later use at the output stage. 2004-06-25 15:28 joehope * configure.in, examples/atomlaser.xmds: Removed redundant code to do with choosing thread-compliant compilers for the code generator. 2004-06-24 18:12 joehope * source/: getopt.h, getopt1.c, getopt_init.c, getopt_xmds.c, getopt_xmds.h, getopt_xmds1.c, main.cc, xmdssequence.cc, xsil2graphics.cc: Changing names of extern variables in getopt functions. Removes further conflicts. 2004-06-24 17:19 joehope * source/xmdscomplex.h: Forcing the operator overloads to be C++. This was not automatic for all compilers. 2004-06-24 16:42 joehope * ChangeLog, MANIFEST, admin/xmds.spec, source/Makefile.am, source/getopt.c, source/getopt_xmds.c, source/getopt_xmds.h, source/getopt_xmds1.c, source/getopt_xmds_init.c, source/main.cc, source/xmdssequence.cc, source/xmdssimulation.cc, source/xsil2graphics.cc: Adjusted getopt to getopt_xmds to remove conflicts with predefined functions in the standard libraries of some systems 2004-06-23 18:21 paultcochrane * admin/xmdsReleaseProcedure.pod: Removed newsgroup posting instruction, because this is not a good thing to do, and I got a bit stung from doing it this time. 2004-06-22 20:44 paultcochrane * Makefile.am: Added new examples to be added at make dist time. 2004-06-22 20:18 paultcochrane * examples/duffing.xmds: Intitial import to repository. This is an example simulation of Duffing's equations. 2004-06-22 20:18 paultcochrane * examples/krebs.xmds: Initial import to repository. This is an example simulation of a simplified Krebs cycle of biochemical reations. 2004-06-22 20:17 paultcochrane * examples/chemkin.xmds: Initial import to repository. This is an example simulation of a chemical kinetic reation in chemistry. 2004-06-22 20:16 paultcochrane * examples/catcycle.xmds: Initial import to repository. This is an example simulation of a catalytical cycle reation in chemistry. 2004-06-22 20:16 paultcochrane * examples/branch.xmds: Initial import to repository. This is an example simulation of a branching reaction in chemistry. 2004-06-21 19:28 paultcochrane * admin/xmds.spec: Still trying to get the .spec file to work. Tried changing the prefix sent to configure. I think I need to rework the configuration step of xmds to iron out these wrinkles. 2004-06-21 09:48 paultcochrane * admin/xmdsNewsPost.pl: Removed sci.math.research as this is a moderated group, and posting xmds announcements isn't appropriate. 2004-06-18 16:51 paultcochrane * admin/xmds.spec: Initial import to repository. This is the rpm .spec file that Greg Collecutt used to use to build xmds. I'm now trying to hack it to build the current version(s). 2004-06-18 16:28 paultcochrane * admin/xmdsReleaseProcedure.pod: Added comment that the source files should be tagged appropriately. That xmds.org needs updating. That an email to xmds-announce is a good idea. And that sending a post to the relevant newsgroups, by using the xmdsNewsPost.pl script would be a (possibly) good idea. 2004-06-18 16:25 paultcochrane * admin/xmdsNewsPost.pl: Fixed a bug whereby the subject and newsgroup kept getting prepended to the message text, so eventually everyone in the last newsgroup to be posted to, could tell where else I'd posted the message. Not happy that this happened. Really not happy. 2004-06-18 16:09 paultcochrane * admin/xmdsNewsPost.txt: Initial import to repository. This file is the news post sent as a result of running the xmdsNewsPost.pl script. This file needs to be updated whenever a new xmds version is released, and posted appropriately. 2004-06-18 16:08 paultcochrane * admin/xmdsNewsPost.pl: Initial import to repository. This is a perl script to automatically post the xmds release announcement to a list of possibly interested newsgroups. 2004-06-18 11:58 paultcochrane * admin/xmdsReleaseProcedure.pod: Initial import to repository. This is the procedure one should perform to properly release xmds onto the sourceforge site (and the world in general). 2004-06-18 11:31 paultcochrane * README.Windows: Converted from dos format to unix format. Updated to xmds-1.3-4, and to new syntax for xsil2graphics. 2004-06-18 11:26 paultcochrane * README: Updated to current version of xmds (1.3-4). Added a comment on how to access the man pages that are now installed as part of xmds. Updated the xsil2graphics syntax in the example given. Expanded the description of what xmds is at the top of the file. 2004-06-17 17:18 paultcochrane * ChangeLog: Updated changelog to current version of xmds, highlighting the current set of major changes to the code base. 2004-06-17 16:00 paultcochrane * MANIFEST: Updated to current version of xmds (1.3-4). 2004-06-17 15:45 paultcochrane * source/xsil2graphics.cc: Added a mention of the xmds web site in the usage output. Also tidied some of the text in the display_usage function. 2004-06-16 13:49 paultcochrane * source/xsil2graphics.cc: Changed display usage to use less printf calls. Also makes the code look better 2004-06-16 12:04 paultcochrane * source/main.cc: Changed an exit statement to a return 0 to be more consistent with the other returning conventions. Don't know if the current convention is that great as it reports that everything went ok, as opposed to if something went wrong. Again, this is something to chuck into the todo list. 2004-06-16 12:02 paultcochrane * source/xsil2graphics.cc: converted xsil2graphics argument parsing to the gnu getopt form. It therefore changes the old style arguments of -matlab and -scilab to --matlab and --scilab respectively. Also, it requires -o or --outfile if one wants to specify and alternative output filename, so one can't do xsil2graphics blah.xsil moo.m anymore, it must be xsil2graphics blah.xsil --output moo.m. Also added some more helpful output information. 2004-06-15 22:22 paultcochrane * source/main.cc: Converted the command line argument parsing code to use the getopt library. Now we have long and short options and a mix if we so desire. Also changed some of the formatting of the template code, and changed the display_usage() output so that it is a bit more accurate, informative and a little better looking. One big thing to note here is the change of the compilation flag, this is now either -n or --nocompile, note that previously this was -c, although I don't think that many people actually used it. 2004-06-15 22:19 paultcochrane * configure.in: Added -lxmds and -L. to the LIBS variable, so that xmds gets built with libxmds and so it can see the getopt libraries within libxmds. 2004-06-15 19:18 paultcochrane * source/xmdsmomentgroup.cc: Tidied up a problem I found with the xsil output when using binary. I'd just changed the output filename of binary files for more consistent naming wrt moment group output, and hadn't set the correct filename in the .xsil output. 2004-06-15 19:08 paultcochrane * source/xmdsmomentgroup.cc: Made the output moment group number for binary output data files agree with what the moment group number actually is. 2004-06-15 19:06 paultcochrane * source/Makefile.am: Added a target for loadxsil.m to be automatically installed at make install time for xmds. It goes in the bindir at this stage, so will get installed in the user's bin directory (if --with-users is set) or in the /usr/local/bin directory if root is doing the installing. 2004-06-15 19:05 paultcochrane * Makefile.am: Moved position of loadxsil.m entry. The only reason I did this was so that I could comment it out when testing some code. 2004-06-15 16:46 paultcochrane * source/xmdssimulation.cc: Fixed bug with incorrect parsing of noises tag. I'd used a suite of if statements instead of an if-else if-else loop construction. Added some debugging code as well, for when xmds -d is used. 2004-06-15 11:30 paultcochrane * examples/diffusion.xmds: Made the lattice size of the transverse dimension a multiple of two so that the numerics are faster 2004-06-15 11:28 paultcochrane * examples/: atomlaser.xmds, fibre.xmds, ndparamp.xmds, nlse.xmds: Removed text about deprecated feature of binary_output and use_double tags. This is actually now an obsolete syntax 2004-06-15 11:16 paultcochrane * source/loadxsil.m: Tidied up the text that is printed to screen. Some of output enclosed in an if loop controlled by the new debug variable. More informative output as to whether data is single or double precision. 2004-06-14 20:22 paultcochrane * configure.in: Added mandir assignments so that the man pages are installed in the correct locations depending upon whether the defaults are given, a prefix, or xmds is being user installed 2004-06-14 20:21 paultcochrane * Makefile.am: Added fisher_reaction_diffusion.xmds to list of examples to distribute. Added a manfiles variable with the man pages to be installed. Added the manfiles variable to the EXTRA_DIST variable so that the files are added to the distro and installed with make install 2004-06-14 20:07 paultcochrane * examples/fisher_reaction_diffusion.xmds: Initial import to repository. This is an example simulation of the Fisher reaction diffusion equation for use in theoretical population genetics. 2004-06-14 16:41 paultcochrane * source/xmdssequence.cc: Added code to print an audible bell character at the end of a simulation if the tag is set to yes. This is a tag to optionally add a noise letting the user know when the simulation is complete. 2004-06-14 16:40 paultcochrane * source/xmdsclasses.h: Added boolean variable holding value of whether or not the tag is set to yes or no. This is a tag to optionally add a noise letting the user know when the simulation is complete. 2004-06-14 16:39 paultcochrane * source/xmdssimulation.cc: Added parsing code for the tag. This is a tag to optionally add a noise letting the user know when the simulation is complete. 2004-06-14 16:37 paultcochrane * MANIFEST: Updated to current list of files in xmds-1.3-3 release 2004-06-14 16:37 paultcochrane * configure.in: Updated release number to current (pre) release number of 1.3-4 2004-06-14 16:36 paultcochrane * Makefile.am: Added hires, lane_emden, paraxial_wave, ring_modulator and van_der_pol examples to list of examples to add to distribution. Removed dependence of latexdocs and apifiles for EXTRA_DIST variable since they are in separate parts of the overall xmds project now 2004-06-14 16:32 paultcochrane * examples/hires.xmds: Initial import to repository. This is the high irradiance response in photomorphogenesis example simulation. 2004-06-14 15:57 paultcochrane * examples/ring_modulator.xmds: Initial import to repository. This is an example simulation of the ring modulator circuit of electronics. 2004-06-12 19:42 paultcochrane * source/xmdsoutput.cc: Added a comment so that users know when output is being generated. This can be handy to know when large files are being output, so that one can wait and not think that the process has hung. 2004-06-12 19:41 paultcochrane * source/main.cc: Fixed error whereby the CC variable was used as the C compiler that xmds uses, whereas should have been XMDS_CC. The MPICC variable being printf-ed separately caused a warning message to come up in compilation of xmds. I moved this into one of the other statements so that when MPICC was a null variable, no warning is printed. 2004-06-05 15:40 paultcochrane * examples/paraxial_wave.xmds: Fixed up some of the numbers and the equations defining the slits etc. 2004-06-04 13:35 paultcochrane * examples/paraxial_wave.xmds: Fixed minor bug. I had a superfluous y variable floating around. 2004-06-04 13:33 paultcochrane * examples/paraxial_wave.xmds: Initial import to repository. This is an example simulation of the paraxial wave equation for double slit interference. 2004-05-31 16:01 paultcochrane * ChangeLog: Updated to current version of xmds; namely 1.3-3. Described new features in this version. 2004-05-31 14:08 paultcochrane * source/loadxsil.m: Fixed problem with loadxsil associated with change made a few versions of xmds ago to deprecate the use of and which are now implemented as attributes of the tag. 2004-05-31 13:26 paultcochrane * examples/van_der_pol.xmds: Initial import to repository. This is an example simulation of the Van der Pol oscillator. 2004-05-31 13:15 paultcochrane * examples/lane_emden.xmds: Initial import to repository. This is an example simulation of the Lane-Emden equation in astrophysics. 2004-05-19 20:07 paultcochrane * source/xmdssimulation.cc: Now barfing when xmds finds the binary_output and/or use_double tags and prints a message telling the user how to fix the problem (basically to use the new/right syntax). Thanks to Joe Hope for the idea. 2004-05-18 20:25 paultcochrane * source/xmdsutils.cc: Implemented throwing an exception when the poissonian attribute is given but no mean attribute given. Also noticed that the implementation of getAttributeStrings is suboptimal in that it borrows far too much from getAssignmentStrings and doesn't actually check everything properly. This needs to be tidied. The code works atm, but it is ugly and needs to be improved. This issue has been added to the todo list for output into doxygen 2004-05-18 20:22 paultcochrane * source/xmdssimulation.cc: Implemented a Poissonian noise distribution based on that in chapter 7 of Numerical Recipes. The output looks good at this stage, but more testing is necessary. Added the correct prototype declarations for each of the noise options as well, and made sure that when the poissonian noise is called, that the mean attribute is also specified. 2004-05-18 20:19 paultcochrane * source/xmdsclasses.h: Added a declaration for the mean of a poissonian noise distribution 2004-05-18 20:18 paultcochrane * examples/kubo.xmds: Switched off mpi, and implemented the kind attribute of the noises tag. 2004-05-18 20:02 paultcochrane * configure.in: Updated the version and release numbers to their current values (1.3-3). 2004-05-18 17:46 paultcochrane * source/xmdssimulation.cc: Implemented parsing code for having a kind attribute to the noises tag. This at present accepts gaussian, poissonian (not yet implemented), gaussFast (a slightly faster version of the gaussian generation routines) and uniform. Gaussian, gaussFast and uniform have been implemented and tested and seem to go alright. Tests show between 7 and 20 percent increase in speed if gaussFast is used. 2004-05-18 17:42 paultcochrane * source/xmdsclasses.h: Added declaration for the XMLString holding the variable that defines the kind of noise to generate 2004-05-12 16:18 paultcochrane * MANIFEST: Updated manifest to current release version (1.3-2). 2004-05-12 16:16 paultcochrane * NEWS: Updated to current version of xmds, ready for release 2004-05-12 16:11 paultcochrane * ChangeLog: Trivial change 2004-05-12 16:08 paultcochrane * ChangeLog: Added changes to xmds since last release 2004-05-12 15:31 paultcochrane * Makefile.am: Made an explicit list of the example xmds files to include in the distribution. Previously all of my test xmds scripts were added, and that just didn't look good 2004-04-29 13:22 paultcochrane * source/: kissdom.cc, kissdom.h, xmdsarg.cc, xmdsargelement.cc, xmdsbreakpoint.cc, xmdsclasses.h, xmdselement.cc, xmdsfield.cc, xmdsfilter.cc, xmdsglobals.cc, xmdsintegrate.cc, xmdsintegrateex.cc, xmdsintegrateip.cc, xmdsintegraterk4.cc, xmdsintegraterk4ex.cc, xmdsintegraterk4ip.cc, xmdsintegratesi.cc, xmdsintegratesiex.cc, xmdsintegratesiip.cc, xmdsmomentgroup.cc, xmdsoutput.cc, xmdssegment.cc, xmdssequence.cc, xmdssimulation.cc, xmdsutils.cc, xmdsutils.h, xmdsvector.cc, xmdsvectorelement.cc, xmlbasics.cc, xmlbasics.h, xmlparser.cc, xmlparser.h, xsil2graphics.cc, xsilfield.cc, xsilfield.h: More completely documented the code using doxygen. Still lots of stuff that needs doing, some stuff isn't documented at all, just marked as Undocumented and a todo command left also signifying that this needs work. Most of the functions and variables, however, have at least a brief description of what they are (or what they look like the could be, as it is quite often *not* obvious as to what a function or variable does or means. 2004-04-29 13:19 paultcochrane * source/main.cc: Documented the code using doxygen. Fixed up some of the spacing in the template output code. 2004-04-28 15:31 paultcochrane * source/main.cc: Moved the comment regarding global system parameters and system functionality (for generation of a template code) to just below the name and description elements 2004-04-28 15:12 paultcochrane * examples/lotka_volterra.xmds: Initial import to repository. This is an example simulation of the Lotka-Volterra system used as a model of undamped oscillations in autocatalytic chemical reactions. From initial reading of (mathematical chemistry) paper to completed xmds script was about 10 minutes! Wow. Ok, now I'm impressed. 2004-04-28 11:04 paultcochrane * examples/: atomlaser.xmds, diffusion.xmds, fibre.xmds, fullpos3D.xmds, gaugeatomlaser.xmds, highdim.xmds, kubo.xmds, lorenz.xmds, ndparamp.xmds, nlse.xmds, pendulum.xmds, sine.xmds, soliton.xmds, tla.xmds, vibstring.xmds: Fixed up author and description tags so that is a bit more uniform over all of the examples 2004-04-28 10:58 paultcochrane * examples/: atomlaser.xmds, diffusion.xmds, fibre.xmds, fullpos3D.xmds, gaugeatomlaser.xmds, highdim.xmds, kubo.xmds, lorenz.xmds, ndparamp.xmds, nlse.xmds, pendulum.xmds, sine.xmds, soliton.xmds, tla.xmds, vibstring.xmds: Added CVS Id tag. 2004-04-28 10:56 paultcochrane * examples/: atomlaser.xmds, diffusion.xmds, fibre.xmds, fullpos3D.xmds, gaugeatomlaser.xmds, highdim.xmds, kubo.xmds, lorenz.xmds, ndparamp.xmds, nlse.xmds, pendulum.xmds, sine.xmds, soliton.xmds, tla.xmds, vibstring.xmds: Added copyright statement to example files 2004-04-28 10:43 paultcochrane * configure.in: Added copyright statement. 2004-04-28 10:28 paultcochrane * source/: kissdom.cc, main.cc, xmdsarg.cc, xmdsargelement.cc, xmdsargv.cc, xmdsbreakpoint.cc, xmdselement.cc, xmdsfield.cc, xmdsfilter.cc, xmdsglobals.cc, xmdsintegrate.cc, xmdsintegrateex.cc, xmdsintegrateip.cc, xmdsintegraterk4.cc, xmdsintegraterk4ex.cc, xmdsintegraterk4ip.cc, xmdsintegratesi.cc, xmdsintegratesiex.cc, xmdsintegratesiip.cc, xmdsmomentgroup.cc, xmdsoutput.cc, xmdssegment.cc, xmdssequence.cc, xmdssimulation.cc, xmdsutils.cc, xmdsvector.cc, xmdsvectorelement.cc, xmlbasics.cc, xmlparser.cc, xsil2graphics.cc, xsilfield.cc, dom3.h, kissdom.h, xmdsclasses.h, xmdscomplex.h, xmdsutils.h, xmlbasics.h, xmlparser.h, xsilfield.h: Updated copyright statement to current year 2004-04-28 10:01 paultcochrane * benchmark/runbenchmarks: Fixed format of procTime output. Moved masterData assignment into file test if loop. Removed use warnings pragma as not supported in older versions of perl, and the warnings aren't really needed atm. Also added a variable for the progInfoFname. 2004-04-28 09:56 paultcochrane * source/: kissdom.cc, main.cc, xmdsarg.cc, xmdsargelement.cc, xmdsargv.cc, xmdsbreakpoint.cc, xmdselement.cc, xmdsfield.cc, xmdsfilter.cc, xmdsglobals.cc, xmdsintegrate.cc, xmdsintegrateex.cc, xmdsintegrateip.cc, xmdsintegraterk4.cc, xmdsintegraterk4ex.cc, xmdsintegraterk4ip.cc, xmdsintegratesi.cc, xmdsintegratesiex.cc, xmdsintegratesiip.cc, xmdsmomentgroup.cc, xmdsoutput.cc, xmdssegment.cc, xmdssequence.cc, xmdssimulation.cc, xmdsutils.cc, getopt.c, getopt1.c, getopt_init.c, xmdsvector.cc, xmdsvectorelement.cc, xmlbasics.cc, xmlparser.cc, xsil2graphics.cc, xsilfield.cc: Added an @file command so that doxygen finds and documents the stuff in the file 2004-04-28 09:55 paultcochrane * source/Doxyfile: Changed some of the functionality of the Doxyfile. Added more explicit warnings and more in-depth documentation of the code (including private bits, which I don't know if that's a good idea or not). 2004-04-20 13:51 paultcochrane * source/main.cc: Added some nice intro text so that one knows that one has just executed xmds, and that a template is being output and what the filename is. 2004-04-20 13:44 paultcochrane * source/main.cc: Implemented the use of a template output option of xmds. One merely has to use the -t flag at the command line for a template xmds script to be output to stdout. If a filename is given, then the script is sent to that file, and xmds returns. This is to help those who want to write a script basically from scratch, but don't want to have to remember where everything goes and the exact set of tags that are necessary. The template is currently the one in the tutTemplateStart.tex file of the latex documentation, and has more tags than necessary to make a simulation. 2004-04-19 19:22 paultcochrane * configure.in: Updated version and release numbers 2004-04-19 19:14 paultcochrane * source/: xmdsmomentgroup.cc, xmdsoutput.cc, xmdssequence.cc: I finally got sick of seeing 042's everywhere, and replaced them with double quotes. It does make things easier to read. 2004-04-19 18:59 paultcochrane * source/xmdsoutput.cc: Stuff it, I might as well chuck in an info footer as well as a header, it doesn't increase the file size that much. So, I did. 2004-04-19 18:51 paultcochrane * source/xmdsoutput.cc: Moved nice version information stuff that is to be put into the .xsil file here as opposed to in xmdsmomentgroup.cc. This way it's only mentioned the once, as opposed to each time a moment group is written out to file. Also moved where the tag is written, and added some comments (my God! comments!) to the code. 2004-04-19 18:48 paultcochrane * source/xmdsmomentgroup.cc: Moved nice version information stuff into a better location (namely xmdsoutput.cc) 2004-04-19 18:40 paultcochrane * source/xmdssimulation.cc: Added the version and release numbers to the list of simulation parameters. Can now pass these bits of info around so that can generate xmds version information at parsing and compiling, and in the output .xsil file. 2004-04-19 18:37 paultcochrane * source/xmdsmomentgroup.cc: Added an information section using tags in the moment group output. This is so that it is documented which version of xmds generated the output .xsil file, and so that xmds and its web page get another plug. 2004-04-19 18:32 paultcochrane * source/xmdsclasses.h: Added the version and release numbers to the list of simulation parameters so that can use these values in the output at the start of parsing and compiling a simulation, and at the end in the output of the simulations. 2004-04-19 18:31 paultcochrane * source/main.cc: Printing out some info about xmds at the start of parsing and compiling a simulation. Also tidied some of the output when parsing and compiling a simulation. 2004-04-19 18:28 paultcochrane * depcomp, ltmain.sh: Updated. 2004-04-06 21:10 paultcochrane * benchmark/gaugeatomlaser_128.xmds: Initial import to repository. This is now the correct file to use instead of gaugeatomlaser.xmds, as the benchmarking code is now much more general. 2004-04-06 21:09 paultcochrane * benchmark/runbenchmarks: I think I've got it all working now. The masterData variable is being updated properly, and output to file properly, and then reread properly, so all good there. Tested on G3, AMD, and P4. Have now changed the test bench subroutine to bench_test and the bench2 subroutine is now bench, so have to do a proper run now... 2004-04-06 20:45 paultcochrane * benchmark/runbenchmarks: The last message was a stuff up, however, this one is ok. Now printing all cpus listed in masterData hash 2004-04-06 20:40 paultcochrane * benchmark/: runbenchmarks: Added cpu information to master data hash table 2004-04-06 20:29 paultcochrane * benchmark/runbenchmarks: Implemented output of html of benchmark data. Implemented dumping of data using Data::Dumper, and reading the data back in (hopefully). Implemented html output of the verbose cpu information, which is linked to the main benchmarks html file. 2004-04-06 18:26 paultcochrane * benchmark/runbenchmarks: Added some comments and removed some superfluous code. 2004-04-06 18:20 paultcochrane * benchmark/runbenchmarks: Added the code of bench as a subroutine to runbenchmarks. Also added a testing subroutine so that I don't have to wait for all of the sims to finish before I can make sure that the code works. Implemented the use of the bench subroutine and collection of the average time into the benchData hash. 2004-04-06 17:51 paultcochrane * benchmark/runbenchmarks: Added a check for linux, if so, then cpuinfo is obtained (which is slightly different for LinuxPPC and for LinuxX86) and then a shorter version of this information is kept. If not linux, then the system info is determined by using the Config module of Perl and the info that configured Perl on that system. 2004-04-06 16:58 paultcochrane * benchmark/bench: Implemented shorter version of previous code using timeit instead of the Benchmark objects 2004-04-06 16:53 paultcochrane * benchmark/runbenchmarks: Initial import to repository. This is the wrapper script that runs the bench script on all of the various xmds scripts. 2004-04-06 16:52 paultcochrane * benchmark/: nlse_100.xmds, nlse_1000.xmds, nlse_10000.xmds, nlse_500.xmds, nlse_5000.xmds: Initial import to repository. This is the nonlinear Schroedinger equation simulation for various lattice sizes. 2004-04-06 16:51 paultcochrane * benchmark/: ndparamp_100.xmds, ndparamp_200.xmds, ndparamp_50.xmds, ndparamp_500.xmds: Initial import to repository. This is the N-dimensional parametric oscillator simulation for various lattice sizes. 2004-04-06 16:50 paultcochrane * benchmark/gaugeatomlaser.xmds: Initial import to repository. This is the gaugeatomlaser simulation which is used to really test how hard the cpu can go (sims take about three hours on new 64 bit AMD machines). 2004-04-06 16:49 paultcochrane * benchmark/: fullpos3D_16.xmds, fullpos3D_32.xmds, fullpos3D_64.xmds: Initial import to repository. This is the fullpos3D simulation for various lattice sizes. 2004-04-06 16:45 paultcochrane * benchmark/bench: Initial import to repository. This is the basic script that compiles, runs a first go of a simulation and then runs the simulation a few times (at present three) giving an output of the average time for the simulation. 2004-03-08 21:14 paultcochrane * source/xmdssimulation.cc: Added a check for the author and description tags. If they aren't found, then a warning is issued to the effect that adding such a tag would be a good idea. This is just to get users to document their code better. We might have to back this out someday... 2004-03-08 21:12 paultcochrane * source/xmdsclasses.h: Added authorName and description to the list of simulation parameters. Not exactly necessary, since they are likely never to be used in a simulation as such, but they do help document the simulation source code better. Whether or not actually storing them in xmds is a good question... 2004-03-05 16:06 paultcochrane * source/loadxsil.m: Added copyright statement. 2004-03-05 16:05 paultcochrane * source/Doxyfile: Updated file to current version of Doxygen (some stuff was obsolete etc). 2004-03-05 16:04 paultcochrane * source/xsilfield.cc: Fixed bug whereby the output from xsil2graphics didn't include the correct variable name when calling fscanfMat in the generated scilab script file. 2004-02-02 18:25 paultcochrane * frontend/tkxmds.pl: Moved file from xmds-devel/frontend to own module tkxmds. 2004-02-02 18:24 paultcochrane * frontend/tkxmds.pl: Added more functionality in terms of open file method and save file as etc. Have look to menus very similar to the xmdseditor of Doug Turk. Also have many of frontend features looking the same as the xmdseditor. Added pod documentation, but this needs to be added to. Much work needed on getting the backend working so that can actually edit, create and run xmds scripts. 2004-02-02 18:21 paultcochrane * frontend/tkxmds: Removed. This is a symlink, so doesn't really need to be in repository, and probably shouldn't be there anyway. 2004-02-02 18:20 paultcochrane * frontend/tkxmds: Updated. Silly thing to say really, since is really just a simlink to tkxmds.pl. 2004-02-02 18:17 paultcochrane * doc/latex/figures/: classes.eps, fibre2.eps, funct.eps, funct.fig, kubo2.eps, ndparamp1.eps, nlse.eps, classes.fig, defferential.eps, fibre1.eps, kubo1.eps, main.eps, main.fig, main.py, ndparamp2.eps, tla.eps: Removing files from xmds-devel/doc/latex/figures to move them into xmds-doc/latex/figures. 2004-02-02 18:10 paultcochrane * doc/latex/: abstract.tex, bibliography.tex, fancyhdr.sty, functionality.tex, lstdoc.sty, titlepage.tex, xmds_defs.tex, ccaption.sty, doc.tex, languageReference.tex, lstlang1.sty, numModellingTheory.tex, .latex2html-init, book.cls, develAndProgStructure.tex, intro.tex, listings.cfg, listings.sty, lstlang2.sty, lstlang3.sty, lstmisc.sty, lstpatch.sty, main.aap, misc_defs.tex, moreExamples.tex, outlook.tex, quotchap.sty, tutFromScratch.tex, tutTemplateStart.tex, workedExample.tex, xmds_doc.tex, xsil.tex, xsil2graphics.tex: Removing files from xmds-deve/doc/latex to move them into xmds-doc/latex. 2004-02-02 18:04 paultcochrane * doc/: xmds.1, xmds.pod: Moved xmds.pod and xmds.1 to new module xmds-doc into the man subdirectory thereof. 2004-01-31 20:41 paultcochrane * doc/latex/figures/main.py: Initial import. This file is used to generate the eps file using pyscript. 2004-01-31 20:37 paultcochrane * doc/latex/: xmds_doc.pdf, xmds_doc.ps: Automatically generated files don't need to be in the repository. If you want to generate them, use the aap recipe. 2004-01-31 20:35 paultcochrane * doc/latex/main.aap: Added comments for people who may not have aap to run the recipe file. Added the CVS Id keyword. Added a help target to print out how to use the file. 2004-01-30 15:31 paultcochrane * examples/: fibre.xmds, fullpos3D.xmds: Fixed spelling error. 2004-01-30 15:21 paultcochrane * source/xmdssimulation.cc: Fixed bug whereby attributes were parsed incorrectly. 2004-01-30 14:48 paultcochrane * source/xmdssimulation.cc: Now reports errors in parsing element correctly. 2004-01-30 13:10 paultcochrane * testsuite/: fibre.xmds, fullpos3D.xmds, gaugeatomlaser.xmds, ndparamp.xmds, nlse.xmds, soliton.xmds: Fixed problems concerning gcc 3.x needing floats inside such functions as log and sqrt instead of ints. Just a problem of adding .0 ad the end of what was previously an integer. 2004-01-30 13:04 paultcochrane * testsuite/: atomlaser.xmds, fibre.xmds, fullpos3D.xmds, gaugeatomlaser.xmds, kubo.xmds, ndparamp.xmds, nlse.xmds, sine.xmds, soliton.xmds, tla.xmds: Fixed up formatting of files using HTML tidy. Command used: tidy -im -xml .xmds Then some hand-tidying of the files. 2004-01-30 12:38 paultcochrane * testsuite/: atomlaser.xmds, fibre.xmds, fullpos3D.xmds, gaugeatomlaser.xmds, kubo.xmds, ndparamp.xmds, nlse.xmds, sine.xmds, soliton.xmds, tla.xmds: Added CVS Id keyword. 2004-01-30 12:34 paultcochrane * configure.in: Added CVS Id keyword. 2004-01-30 12:31 paultcochrane * AUTHORS, INSTALL, Makefile.am, NEWS, README, README.Windows, acinclude.m4: Added CVS Id keyword. 2004-01-30 12:25 paultcochrane * source/loadxsil.m: Added CVS Id keyword. 2004-01-30 10:44 paultcochrane * doc/latex/: xmds_doc.pdf, xmds_doc.ps: Updated. 2004-01-30 10:37 paultcochrane * doc/latex/: abstract.tex, bibliography.tex, develAndProgStructure.tex, functionality.tex, intro.tex, languageReference.tex, misc_defs.tex, moreExamples.tex, numModellingTheory.tex, outlook.tex, titlepage.tex, tutFromScratch.tex, tutTemplateStart.tex, workedExample.tex, xmds_defs.tex, xmds_doc.tex, xsil.tex, xsil2graphics.tex: Added CVS Id keyword. 2004-01-30 10:29 paultcochrane * doc/latex/.latex2html-init: Added CVS Id keyword. 2004-01-28 15:43 paultcochrane * source/: Makefile.am, dom3.h, getopt.h, kissdom.h, main.cc, xmdsarg.cc, xmdsclasses.h, xmdsglobals.cc, xmdsintegrate.cc, xmdsintegrateex.cc, xmdsintegrateip.cc, xmdsintegraterk4.cc, xmdsintegratesiex.cc, xmdssequence.cc, xmdsvectorelement.cc, xmlbasics.cc, xmlbasics.h, xmlparser.h, xsilfield.h, kissdom.cc, xmdsargelement.cc, xmdsargv.cc, xmdsbreakpoint.cc, xmdscomplex.h, xmdselement.cc, xmdsfield.cc, xmdsfilter.cc, xmdsintegraterk4ex.cc, xmdsintegraterk4ip.cc, xmdsintegratesi.cc, xmdsintegratesiip.cc, xmdsmomentgroup.cc, xmdsoutput.cc, xmdssegment.cc, xmdsutils.cc, xmdsutils.h, xmdsvector.cc, xmlparser.cc, xsil2graphics.cc, xsilfield.cc, Doxyfile, getopt.c, getopt1.c, getopt_init.c: Added CVS Id keyword. 2004-01-28 15:37 paultcochrane * source/xmdssimulation.cc: Still testing the CVS Id keyword expansion. 2004-01-28 15:35 paultcochrane * source/xmdssimulation.cc: Testing adding the CVS Id keyword. 2004-01-27 18:02 paultcochrane * examples/atomlaser.xmds: Updated to new element syntax: output format and output precision now being given as attributes of element rather than in simulation options section. Also added syntax for the break point feature to come. 2004-01-27 18:00 paultcochrane * examples/: diffusion.xmds, fibre.xmds, fullpos3D.xmds, gaugeatomlaser.xmds, highdim.xmds, kubo.xmds, lorenz.xmds, ndparamp.xmds, nlse.xmds, pendulum.xmds, sine.xmds, soliton.xmds, tla.xmds, vibstring.xmds: Updated to new element syntax: output format and output precision now being given as attributes of element rather than in simulation options section. 2004-01-27 17:29 paultcochrane * source/xmdssimulation.cc: Added attributes to 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 and tags. The new syntax is , which is a lot more logical. 2004-01-27 17:26 paultcochrane * source/Doxyfile: Changed option so that man pages are now generated. 2004-01-27 16:32 paultcochrane * Makefile.in, aclocal.m4, configure: Deleted. 2004-01-27 16:26 paultcochrane * .DS_Store, changes.log, readme, source/.DS_Store, source/stamp-h.in, source/stamp-h1.in, source/Makefile.in, source/config.h.in: Deleted. 2004-01-27 16:13 paultcochrane * doc/: img24.gif, img25.gif, img26.gif, img27.gif, img28.gif, img29.gif, img3.gif, img30.gif, img31.gif, img32.gif, img33.gif, img34.gif, img35.gif, img36.gif, img37.gif, img38.gif, img39.gif, img4.gif, img40.gif, img41.gif, img42.gif, img43.gif, img44.gif, img45.gif, img46.gif, img47.gif, img48.gif, img49.gif, img5.gif, img50.gif, img52.gif, img53.gif, img55.gif, img56.gif, img57.gif, img58.gif, img59.gif, img6.gif, img60.gif, img61.gif, img62.gif, img63.gif, img64.gif, img66.gif, img67.gif, img69.gif, img7.gif, img70.gif, img71.gif, img51.gif, img54.gif, img65.gif, img68.gif, img72.gif, img73.gif, img74.gif, img75.gif, img76.gif, img77.gif, img78.gif, img79.gif, img8.gif, img80.gif, img81.gif, img82.gif, img83.gif, img84.gif, img85.gif, img86.gif, img87.gif, img88.gif, img89.gif, img9.gif, img90.gif, img91.gif, img92.gif, img93.gif, img94.gif, img95.gif, img96.gif, img97.gif, img98.gif, img99.gif: Deleted. 2004-01-27 16:09 paultcochrane * doc/: doc.css, doc.html, img1.gif, img10.gif, img100.gif, img101.gif, img102.gif, img103.gif, img104.gif, img105.gif, img106.gif, img107.gif, img108.gif, img109.gif, img11.gif, img110.gif, img111.gif, img112.gif, img113.gif, img114.gif, img115.gif, img116.gif, img117.gif, img118.gif, img119.gif, img12.gif, img120.gif, img121.gif, img122.gif, img123.gif, img124.gif, img125.gif, img126.gif, img127.gif, img128.gif, img129.gif, img13.gif, img130.gif, img131.gif, img132.gif, img133.gif, img134.gif, img135.gif, img136.gif, img137.gif, img138.gif, img139.gif, img14.gif, img140.gif, img141.gif, img142.gif, img143.gif, img144.gif, img145.gif, img146.gif, img147.gif, img148.gif, img149.gif, img15.gif, img150.gif, img151.gif, img152.gif, img153.gif, img154.gif, img155.gif, img156.gif, img157.gif, img158.gif, img159.gif, img16.gif, img160.gif, img161.gif, img162.gif, img163.gif, img164.gif, img165.gif, img166.gif, img167.gif, img168.gif, img169.gif, img17.gif, img175.gif, img178.gif, img182.gif, img185.gif, img188.gif, img192.gif, img170.gif, img171.gif, img172.gif, img173.gif, img174.gif, img176.gif, img177.gif, img179.gif, img18.gif, img180.gif, img181.gif, img183.gif, img184.gif, img186.gif, img187.gif, img189.gif, img19.gif, img190.gif, img191.gif, img193.gif, img194.gif, img195.gif, img196.gif, img197.gif, img198.gif, img199.gif, img2.gif, img20.gif, img200.gif, img201.gif, img202.gif, img203.gif, img204.gif, img205.gif, img206.gif, img207.gif, img208.gif, img209.gif, img21.gif, img210.gif, img211.gif, img212.gif, img213.gif, img214.gif, img22.gif, img23.gif: Deleted. 2004-01-27 16:04 paultcochrane * doc/xmds.1: Updated. 2004-01-27 16:03 paultcochrane * doc/xmds.pod: Added FILES section. 2004-01-23 17:35 paultcochrane * doc/xmds.1: Initial import to repository. Automatically generated man page documentation. 2004-01-23 17:33 paultcochrane * doc/xmds.pod: Initial import to repository. Perl POD file to generate the xmds man page. 2004-01-14 19:34 paultcochrane * examples/fullpos3D.xmds: Fixed problem whereby gcc/g++ see sqrt(2) as the sqrt of an integer which doesn't work in C++, these have been changed to sqrt(2.0) so that the input is float/double. 2004-01-13 21:16 paultcochrane * source/xmdsutils.h: Trivial change made during code testing. 2004-01-13 21:15 paultcochrane * source/xmdsutils.cc: Fixed bug in getAttributeBools where the string comparison was being performed incorrectly. 2004-01-13 21:14 paultcochrane * source/xmdsoutput.cc: Implemented parsing of enabled attribute of breakpoint element correctly. 2004-01-13 21:13 paultcochrane * source/xmdsclasses.h: Changed some formatting. 2004-01-13 21:11 paultcochrane * source/xmdsbreakpoint.cc: Removed some legacy code that was commented out anyway. Polished and tested the breakpoint parsing code. Now do a test to see if a file exists at the parsing stage when the file status is set to "old", and barf with an error message if not found. 2004-01-13 13:03 paultcochrane * source/xmdsutils.h: Corrected one of the documentation strings. 2004-01-13 12:28 paultcochrane * source/main.cc: Added a debug option to parsePrefs(), and changed the output generated so that stuff that should be in the debugging output is not in the verbose output. 2004-01-12 20:10 paultcochrane * source/xmdsutils.h: Added the DEEP and NOT_DEEP variables to the global anonymous enum. 2004-01-12 20:09 paultcochrane * source/xmdsoutput.cc: Added stuff to find and process the tag. Started to implement the use of DEEP and NOT_DEEP variables in getElementsByTagName() and friends as opposed to just 1 and 0 respectively (it makes the code more readable). 2004-01-12 20:07 paultcochrane * source/xmdsbreakpoint.cc: Initial import to repository. Basic stuff at this stage, actually does nothing other than report what the settings are as found in the .xmds script. 2004-01-12 20:06 paultcochrane * source/xmdsclasses.h: Added xmdsBreakPoint object declarations (just basic stuff at this stage). Added (to xmdsOutput) a bpEnabledFlag variable to note if breakpoints are enabled, and declaration of a function to create an xmdsBreakPoint object. 2004-01-12 20:03 paultcochrane * source/Makefile.am: Added xmdsbreakpoint.cc 2004-01-08 15:34 paultcochrane * doc/latex/xmds_doc.tex: Moved the "starting from scratch" and "using a template" chapter headings into their own files and have include statements instead. 2004-01-08 15:31 paultcochrane * doc/latex/abstract.tex: Almost a complete rewrite. 2004-01-08 15:29 paultcochrane * doc/latex/tutFromScratch.tex: Extended the discussion of how to build a basic simulation. In the middle of discussing the tag. 2004-01-08 10:30 paultcochrane * doc/latex/xmds_defs.tex: Changed myhtml style to the xml language (new in current version of listings package). Added a couple of keywords to morekeywords list and found that one needs a comma at the start of the list so that all of the keywords are highlighted. 2004-01-07 15:39 paultcochrane * doc/latex/xmds_defs.tex: Added the author and description keywords to the myhtml style for the listings package. 2004-01-07 15:37 paultcochrane * doc/latex/main.aap: Made sure that latex/pdflatex are run twice in building the dvi/pdf. 2004-01-07 12:44 paultcochrane * doc/latex/misc_defs.tex: Moved some ewcommands from languageReference.tex to here. 2004-01-07 12:44 paultcochrane * doc/latex/languageReference.tex: Moved ewcommand and ewenvironment stuff into misc_defs.tex. 2004-01-07 12:05 paultcochrane * doc/latex/tutTemplateStart.tex: Initial import to repository. 2004-01-07 12:01 paultcochrane * doc/latex/tutFromScratch.tex: Initial import to repository. 2004-01-07 11:57 paultcochrane * doc/latex/numModellingTheory.tex: Fixed vector subscripting errors. 2004-01-07 11:57 paultcochrane * doc/latex/misc_defs.tex: Changed the definition of ec to be mathbf{#1} 2004-01-06 19:28 paultcochrane * doc/latex/main.aap: Intial import to repository. 2004-01-06 19:27 paultcochrane * doc/latex/: xmds_doc.ps, xmds_doc.pdf: Updated to current version of docs. 2004-01-06 19:21 paultcochrane * doc/latex/abstract.tex: Changed chapter to chapter* 2004-01-06 19:19 paultcochrane * doc/latex/xmds_doc.tex: Changed input's to include's 2004-01-06 19:16 paultcochrane * doc/latex/xmds_defs.tex: Commented out inclusion of hyperref package for pdflatex: it is already loaded. 2004-01-06 17:48 paultcochrane * doc/latex/languageReference.tex: Removed the mention of the xmds version of tags in the simulation block. Added mention of the xmds version of the argv tag. 2004-01-06 17:45 paultcochrane * doc/latex/functionality.tex: Minor change; joined two paragraphs together. 2004-01-06 17:43 paultcochrane * doc/latex/.latex2html-init: Removed [math] in the HTML_VERSION, specifying now IMAGE_TYPE = png, and have a better ADDRESS variable set. 2004-01-06 16:54 paultcochrane * doc/latex/xmds_doc.tex: Split document into parts. Added chapter headings for the Tutorial part. 2004-01-06 16:52 paultcochrane * doc/latex/xmds_defs.tex: Added another keyword to myC++ style. Made LightGrey definition lighter. 2004-01-06 16:50 paultcochrane * doc/latex/workedExample.tex: Converted document to work more nicely in latex2html. 2004-01-06 16:45 paultcochrane * doc/latex/languageReference.tex: Corrected a spelling error. Altered definition of xmdsOneTwo. Converted document for better processing in latex2html. 2004-01-06 16:36 paultcochrane * doc/latex/: listings.cfg, listings.sty, lstdoc.sty, lstlang1.sty, lstlang2.sty, lstlang3.sty, lstmisc.sty, lstpatch.sty: Initial import to repository. 2004-01-06 16:12 paultcochrane * doc/latex/.latex2html-init: Added NO_SIMPLE_MATH=1, increased MAX_SPLIT_DEPTH to 4, changed the HTML_VERSION to 4.0[math] 2004-01-06 00:23 paultcochrane * doc/latex/xmds_defs.tex: Changed file so that can use with latex2html (some conditional stuff added etc). 2004-01-05 22:32 paultcochrane * doc/latex/.latex2html-init: Changed to point the TMP variable to /var/tmp 2004-01-05 22:24 paultcochrane * doc/latex/.latex2html-init: Initial import to repository. 2004-01-05 18:27 paultcochrane * doc/latex/workedExample.tex: Reformatted some of the code examples. And changed some :'s to $ dots$. 2004-01-05 17:35 paultcochrane * doc/latex/book.cls: Initial import to repository. (implements a slight change to the standard book.cls which can't be incorporated into .tex files (uses @'s etc)) 2004-01-05 17:30 paultcochrane * doc/latex/functionality.tex: Updated and improved installation instructions, with particular emphasis on installation from tarball. 2004-01-05 16:32 paultcochrane * doc/latex/xmds_doc.tex: Extended the secnumdepth and tocdepth counters to 4 so that have numbers all the way down to paragraph in the document and in the toc. 2004-01-05 16:31 paultcochrane * doc/latex/languageReference.tex: Changed extit{required} to eqd. Changed ext{optional} to optl. Changed extsc{xmds-devel only} to $ge$ xmds-1.2 (command is xmdsOneTwo). 2003-12-30 21:38 paultcochrane * examples/: fibre.xmds, fullpos3D.xmds, gaugeatomlaser.xmds, highdim.xmds, kubo.xmds, lorenz.xmds, ndparamp.xmds, nlse.xmds, pendulum.xmds, sine.xmds, soliton.xmds, tla.xmds, vibstring.xmds: Updated , and tags where appropriate. 2003-12-23 15:01 paultcochrane * NEWS: Updated to reflect changes in current release (1.3-1) 2003-12-23 14:57 paultcochrane * ChangeLog, MANIFEST, README: Updated to reflect changes in current release (1.3-1) 2003-12-23 14:47 paultcochrane * examples/: atomlaser.xmds, diffusion.xmds, fibre.xmds, fullpos3D.xmds, gaugeatomlaser.xmds, highdim.xmds, kubo.xmds, lorenz.xmds, ndparamp.xmds, nlse.xmds, pendulum.xmds, sine.xmds, soliton.xmds, tla.xmds, vibstring.xmds: Tidied formatting, added some comments. 2003-12-23 12:15 paultcochrane * examples/atomlaser.xmds: Commented out using of binary input file. Now is back to being initialised by code. Better this way since it's an example file. 2003-12-23 12:13 paultcochrane * source/main.cc: Put preferences parsing code into a function. It's a bit neater, and only one section of code to modify instead of two. Also changed a couple of warnings to only be printed out when verbose flag is set. 2003-12-22 17:56 paultcochrane * Makefile.am: Updated to include the README.Windows file in the distribution. 2003-12-22 17:55 paultcochrane * README.Windows: Initial import to repository. 2003-12-22 17:01 paultcochrane * examples/tla.xmds: Minor formatting improvement. 2003-12-22 17:00 paultcochrane * examples/nlse.xmds: Added test code for output arguments. This needs to be fixed up, not a good example file really. 2003-12-22 16:59 paultcochrane * examples/ndparamp.xmds: Added binary output and benchmark tags. 2003-12-22 16:58 paultcochrane * examples/highdim.xmds: Fixed integer where float should be problem. 2003-12-22 16:57 paultcochrane * examples/gaugeatomlaser.xmds: Renamed simulation and .xsil file to reflect name of "gaugeatomlaser". 2003-12-22 16:56 paultcochrane * examples/fullpos3D.xmds: Some minor reformatting. 2003-12-22 16:55 paultcochrane * examples/fibre.xmds: Fixed a divide by integer problem which has only really become evident since gcc3. Added and tags. 2003-12-22 16:52 paultcochrane * examples/atomlaser.xmds: Tidied the code slightly. Added an and element (may be used in the future. Added some comments to the file. Removed test code, and now acually use variables in the simulation as command line arguments. Also added some new syntax to work in xmds-1.3-1. 2003-12-22 16:49 paultcochrane * testsuite/: atomlaser_reference.xsil, ndparamp_reference.xsil, nlse_reference.xsil, soliton_reference.xsil, tla_reference.xsil: Updated the _reference.xsil files. 2003-12-22 16:48 paultcochrane * doc/latex/xsil2graphics.tex: Removed mention of xsil2matlab (obviously an older version of xsil2graphics). Also added some docs showing how to actually use the xsil2graphics output in matlab and scilab. This needs expanding. 2003-12-22 16:46 paultcochrane * doc/latex/xmds_defs.tex: Fixed up hyperref call for generating linked dvi files. 2003-12-22 16:40 paultcochrane * source/main.cc: Added some documentation as introduction to xmds for output to api documentation. Also added some installation instructions as well. 2003-12-22 15:42 paultcochrane * source/Doxyfile: Updated to refelect the current project number. Also removed some obsolete Doxygen commands. 2003-12-22 15:39 paultcochrane * source/dom3.h: Completed documenting the DOM functions and classes as they are outlined in the W3C Working Draft of 05 June 2001. No functional changes, although the big difference is that the api documentation is now significantly better than it was before. 2003-12-19 18:17 paultcochrane * source/dom3.h: Started documenting the DOM functions and classes as they are outlined in the W3C Working Draft of 05 June 2001. No functional changes, although the big difference is that the api documentation is now significantly better than it was before (and I haven't finished yet!). 2003-12-17 20:35 paultcochrane * source/xmdsvectorelement.cc: Implemented binary input for use in the tag of the element. 2003-12-17 20:33 paultcochrane * source/xmdsutils.h: Added an enum to specify two booleans, REQD and NOT_REQD. I will eventually implement this further so that some of the calls used of getAssignmentStrings() etc are a little more understandable. Also added declarations for getAttributeStrings() and getAttributeBools(). 2003-12-17 20:31 paultcochrane * source/xmdsutils.cc: Added two new functions: getAttributeStrings() and getAttributeBools(). This was in order to implement binary and ascii input of data files (in tag of element). However, this is a more general addition, the two functions being used to get strings and booleans out of attributes of element tags respectively. 2003-12-17 20:29 paultcochrane * source/xmdsclasses.h: Minor change to the xmdsVectorElement class to implement binary and ascii input files. 2003-12-17 17:18 paultcochrane * source/: kissdom.cc, xmdssequence.cc, xmdssimulation.cc, xmdsvectorelement.cc, xsilfield.cc: Fixed bug whereby temp.dat was still being used instead of x.dat for input data to matlab/scilab. 2003-12-17 17:17 paultcochrane * source/xmdsvector.cc: Fixed formatting a bit. No real changes to code. 2003-12-17 17:16 paultcochrane * source/xmdsoutput.cc: Tidied some fprintf statements. 2003-12-17 17:15 paultcochrane * source/xmdsutils.cc: Fixed some spelling errors and debugging reporting information. 2003-12-17 17:13 paultcochrane * source/xmdsmomentgroup.cc: Tidied some fprintf statements. 2003-12-17 17:12 paultcochrane * source/xmdsfield.cc: Tidied some fprintf statements by combining most of the text (and hence removing heaps of fprintf statements and making the code easier to read). 2003-12-17 17:09 paultcochrane * source/xmdsclasses.h: Added a usePrefs variable to the simulationParamtersStruct in order to implement preferences. 2003-12-17 17:08 paultcochrane * source/main.cc: Implemented a first go at preferences for xmds. It can be tidied a lot, but it works at present. One needs a ~/.xmds/xmds.prefs file or an xmds.prefs file in the local directory to the script one is trying to compile. The prefs file format is = , e.g. XMDS_CC = gcc. One can also use comments. All text after (and including) a hash character (#) is ignored. 2003-12-17 17:03 paultcochrane * configure.in: Updated to show version information as 1.3-1. 2003-12-07 14:25 paultcochrane * ChangeLog: Added comments about current changes to xmds. 2003-12-07 14:24 paultcochrane * configure.in: Altered release number to current release: 1.2-2 2003-11-27 16:50 paultcochrane * source/xmdssimulation.cc: Added the inclusion of the sstream (string streams) header. 2003-11-27 16:49 paultcochrane * source/xmdsfield.cc: Fixed segfaulting of mpi programs using wisdom. Now have more C++ type code to implement creation of the host_rank_%i.stuff etc files and for their deletion. Writing and reading from these files was causing the segfault. 2003-11-27 12:33 paultcochrane * source/xmdssequence.cc: Fixed bug whereby the useWisdom option wasn't passed through to writePlanCreationCalls properly. 2003-11-27 12:14 paultcochrane * configure.in: Changed way that mpiccTest was checked for the compiler running mpicc. 2003-11-25 19:19 paultcochrane * ChangeLog: Added comments advising of changes up to current version of xmds. 2003-11-25 19:18 paultcochrane * configure.in: Corrected version numbers to agree with current release. 2003-11-25 19:17 paultcochrane * source/xmdsfield.cc: Fixed host.stuff and home.stuff file writing with mpi, I'd fixed this before in one place in the code but missed this extra place. 2003-11-25 12:37 paultcochrane * source/xmdsmomentgroup.cc: Modified moment group number reporting at the terminal, so matches what is given in xsil2graphics and output files. 2003-11-24 21:10 paultcochrane * configure.in: Fixed problem with optimisation settings not flowing through for script compilation when using gcc. Now check if $ac_compiler_gnu is "yes" instead of if XMDS_CC is gcc (can be g++, for example). 2003-11-24 21:07 paultcochrane * source/xmdsmomentgroup.cc: Fixed binary output bug where k-space variables weren't ordered correctly before output. 2003-11-20 17:00 paultcochrane * source/xmdsmomentgroup.cc: Fixed misreporting of filename if unable to open the output file for binary output. 2003-11-07 11:28 paultcochrane * configure.in: Changed release number to pre1, ready for the pre1 release. (funnily enough...) 2003-11-06 21:18 paultcochrane * source/loadxsil.m: Hopefully fixed problem with loading data in more than one moment group by appending _[momentGroupNumber] to variable names as is done in xsil2graphics. 2003-11-06 20:59 paultcochrane * configure.in: Now pointing XMDS_CC to CXX if necessary. 2003-11-06 17:02 paultcochrane * configure.in: Fixed bug where a test for null should have been non-null. 2003-11-06 12:47 paultcochrane * source/xsilfield.h: Altered call to writeAsFormat so can implement writing data files as xsil filename_momentGroup.dat as opposed to temp_momentGroup.dat as before. 2003-11-06 12:46 paultcochrane * source/xsilfield.cc: The output filename is the xsil base filename (the bit without the .xsil on the end) with the moment group number plus .dat, instead of just temp1.dat, temp2.dat. Not a great comment, but I implemented this idea anyway... 2003-11-06 12:44 paultcochrane * source/xsil2graphics.cc: Some reformatting of code. Main change being the altering of the xsilField::writeAsFormat call, by passing through the xsil filename's base name (ie that bit without the .xsil on the end). 2003-11-06 12:42 paultcochrane * source/xmdssimulation.cc: Removed the output of the (commented out in the final code anyway) unistd.h statement. 2003-11-06 12:41 paultcochrane * source/xmdsfield.cc: (Hopefully) fixed problem with writing, reading and deleting host.stuff and home.stuff files when using mpi. The files now append the rank to the file name, so this problem should be fixed. 2003-11-06 12:38 paultcochrane * source/main.cc: Removed XMDS_CXX stuff. Removed clibs being added to one of mpicc compile strings. This produced inconsistent compilation flags when mpicc uses a different compiler to XMDS_CC. 2003-11-06 12:34 paultcochrane * doc/latex/: xmds_doc.pdf, xmds_doc.ps: Updated. 2003-11-06 12:29 paultcochrane * doc/latex/xmds_defs.tex: Updated list of tags defined for myhtml style in listings.sty code. 2003-11-06 12:27 paultcochrane * doc/latex/workedExample.tex: Basic formatting of some xmds code. 2003-11-06 12:26 paultcochrane * doc/latex/moreExamples.tex: Basic formatting of xmds code. 2003-11-06 12:24 paultcochrane * doc/latex/languageReference.tex: Added docs for argv tagset (and subtags). 2003-11-06 12:22 paultcochrane * doc/latex/functionality.tex: Mentioned explicitly that version 2.1.x of fftw is required for xmds. Updated references to point to xmds-1.2, not xmds-1.0. 2003-11-06 12:16 paultcochrane * admin/manifestGen.pl: Documented a far simpler way of generating the manifest. 2003-11-06 12:15 paultcochrane * configure.in: Removed references to XMDS_CXX* variables, they were superfluous and caused confusion. Made some tests more stringent, so that user supplied arguments at the command line to configure can be passed through properly. If the user has specified command line options to xmds, the script now also checks if some required flags are missing from these options and appends them if necessary. 2003-11-06 12:11 paultcochrane * README: Added description of configuration options that are now available in xmds-1.2, and tidied up the text a bit. Also fixed a couple of bugs with the scilab execution of the xsil file. 2003-11-06 12:09 paultcochrane * Makefile.am: Removed latexdocs from being included in distribution temporarily. Will probably add back in when docs catch up to current version of xmds. 2003-11-06 12:08 paultcochrane * MANIFEST: Updated to reflect current list of files for distribution. 2003-11-04 19:27 paultcochrane * Makefile.am: No change, just added something and took it away, but it wants to be updated nevertheless. 2003-11-04 19:26 paultcochrane * LICENSE: Deleted: it is really the COPYING file, so it's really superfluous. 2003-11-04 19:22 paultcochrane * MANIFEST: Initial import to repository. 2003-11-04 19:18 paultcochrane * ChangeLog: Updated to reflect changes that have happened so far since xmds-1.1. 2003-11-04 18:54 paultcochrane * README: Updated to agree with current configuration options. 2003-11-04 18:53 paultcochrane * AUTHORS: Updated email addresses of authors. 2003-11-04 17:59 paultcochrane * configure.in: MPICCFLAGS needs $PTHREADS_CFLAGS as well. Tidied XMDS_CFLAGS and XMDS_CXXFLAGS by putting AGGRESSIVE_* instead of the explicit declaration. Removed the check for enable_mpicc_aggressive. Removed --enable-*-aggressive options. 2003-11-04 17:32 paultcochrane * configure.in: Fixed bug where one actually needs the $PTHREAD_CFLAGS variable inserted into XMDS_CFLAGS. 2003-11-04 16:20 paultcochrane * configure.in: Removed explicit check for MPI_Init in -lmpi since -lmpi must work if passed -llam test, AND the library arguments be in the right order. This simplifies the checking slightly. 2003-11-03 15:46 paultcochrane * configure.in: The flags for gcc, icc, g++ etc all now default to the aggressive version. If the user wants other flags, they should set them at the command line at build time. 2003-11-03 15:03 paultcochrane * configure.in: Changed implementation of how xmdsconfig.h is made. It's now a cp from config.h. 2003-11-03 15:01 paultcochrane * Makefile.am: Added the m4 files acx_mpi.m4 and acx_pthread.m4 so that will be added to distribution output. 2003-11-03 14:58 paultcochrane * examples/: diffusion.xmds, lorenz.xmds, pendulum.xmds, vibstring.xmds: Initial import to repository. 2003-11-01 16:15 paultcochrane * source/xmdsconfig.h.in: deleted 2003-10-31 18:04 joehope * configure.in, examples/fibre.xmds, source/xmdsconfig.h.in: Making stable autoconf on MacOSX 2003-10-30 18:07 paultcochrane * source/Doxyfile: Now set to produce pdf documentation as well. 2003-10-30 18:05 paultcochrane * configure.in: Fixed problem with not finding lam properly. Fixed bug whereby forgot to add -lxmds to XMDS_LIBS variable. 2003-10-30 14:40 paultcochrane * configure.in: No longer assuming lam, nor does one need to put --with-mpi-libs="-llam" on the command line for the script to find either the lam or mpich implementations of mpi. Fixed minor big with -I in wrong place. Now determines how mpicc is run, which in itself is dependent upon the mpi implementation, but the script detects the differences between lam and mpi and is still able to check what CC is used for mpicc. 2003-10-30 14:33 paultcochrane * source/: dom3.h, kissdom.h, xmdsclasses.h: Did some reformatting and updated docstrings. 2003-10-29 12:48 paultcochrane * source/xmdsconfig.h.in: Initial import to repository. 2003-10-28 12:42 paultcochrane * configure.in: Added a check for how mpicc is run, and then alter MPICCFLAGS accordingly. Also added a check for mpicc-aggressive and if on, then uses the icc-aggressive or gcc-aggressive flags if mpicc is run by icc or gcc. 2003-10-28 11:48 paultcochrane * admin/manifestGen.pl: Initial import to repository. 2003-10-27 21:50 paultcochrane * LICENSE: Initial import to repository. 2003-10-27 21:50 paultcochrane * configure.in: Implemented the --with-mpi-path option better. Used the MPI_LIB_PATH to help configure look for fftw_mpi. Added the MPI_LIB_PATH to the MPICCFLAGS. 2003-10-27 21:47 paultcochrane * Makefile.am: Added loadxsil.m to EXTRA_DIST files. 2003-10-27 19:11 paultcochrane * source/: xmdscomplex.h, xmdselement.cc, xmdsfield.cc, xmdsfilter.cc, xmdsglobals.cc, xmdsintegrate.cc, xmdsintegrateex.cc, xmdsintegrateip.cc, xmdsintegraterk4.cc, xmdsintegraterk4ex.cc, xmdsintegraterk4ip.cc, xmdsintegratesi.cc, xmdsintegratesiex.cc, xmdsintegratesiip.cc, xmdsmomentgroup.cc, xmdsoutput.cc, xmdssegment.cc, xmdssequence.cc, xmdssimulation.cc, xmdsutils.cc, xmdsutils.h, xmdsvector.cc, xmdsvectorelement.cc, xmlbasics.cc, xmlbasics.h, xmlparser.cc, xmlparser.h, xsil2graphics.cc, xsilfield.cc, xsilfield.h: Added GPL statement. 2003-10-27 19:07 paultcochrane * source/: kissdom.cc, kissdom.h, main.cc, xmdsarg.cc, xmdsargelement.cc, xmdsargv.cc, xmdsclasses.h: Added GPL statement. 2003-10-27 19:05 paultcochrane * source/getopt.h: Added some docstrings. 2003-10-27 19:01 paultcochrane * source/dom3.h: Changed some docstrings. Added GPL statement. 2003-10-27 18:52 paultcochrane * configure.in: Hopefully fixed bloody headers problem this time!! Fixed other problems wrt getting mpi to get the correct options. Seems to go on the SC now, so that's good. 2003-10-24 11:50 paultcochrane * source/xmdssequence.cc: Added more helpful (ie usage) output for when arguments to simulation binary are incorrect. 2003-10-24 11:46 paultcochrane * source/main.cc: Fixed bug where insufficient number of format specifiers in a string for number of arguments to sprintf. This caused a problem with mpi not seeing the fftw libraries. 2003-10-23 20:36 paultcochrane * configure.in: Now handling the case when someone uses --prefix better now. Basically I just make the USER_* and *dir variables point to the directory pointed to by the $prefix. 2003-10-23 20:11 paultcochrane * source/xmdssimulation.cc: Minor terminal output touch up. 2003-10-23 20:11 paultcochrane * source/main.cc: Now using XMDS_CC, XMDS_CXX, and XMDS_CFLAGS instead of the non-XMDS_* versions. 2003-10-23 20:07 paultcochrane * configure.in: Hopefully now fixed the config headers not recreating themselves problem. Did some reformatting of help output. Added --with-mpi-compiler so that the user can choose what compiler to use for mpi, --enable-mpi (not default option) so that mpi is checked for and added to variables, --enable-icc-aggressive, so that aggressive optimisation settings are chosen when using icc, --enable-gcc-aggressive so that both gcc and g++ use aggressive optimisation settings, --enable-mpicc-aggressive so that mpicc will use the gcc-aggressive compiler settings. Fixed a bug where CXXFLAGS lacked an S. Needed to add the PTHREAD_CFLAGS variable to XMDS_CFLAGS and XMDS_CXXFLAGS. Removed old (and commented anyway) mpi checking code. Put mpi stuff into an if loop, and is processed only when --enable-mpi is used. Am now actually using XMDS_CFLAGS and XMDS_CXXFLAGS. Now configure script outputs nicely formatted option and variable information once configuration is complete. 2003-10-22 16:13 paultcochrane * source/xmdssimulation.cc: Minor change to terminal output. 2003-10-22 16:12 paultcochrane * source/main.cc: Changed INCLUDES and LIBS to be XMDS_INCLUDES and XMDS_LIBS, so is specific to the xmds simulations rather than xmds itself. 2003-10-22 16:10 paultcochrane * configure.in: Corrected some *config.h errors. Relabelled some of the variables to be specific to the xmds simulations as opposed to xmds itself. Removed some superfluous function checks. Got MPI running cleaner and better. 2003-10-22 13:25 paultcochrane * acx_mpi.m4: Initial import to repository. 2003-10-22 10:39 paultcochrane * source/Makefile.am: Changed config.h to xmdsconfig.h 2003-10-22 10:39 paultcochrane * source/xmdssimulation.cc: Changed inclusion of config.h to inclusion of xmdsconfig.h to stop possible name clashes when installing on the system instead of in the user's directory. 2003-10-22 10:38 paultcochrane * source/xmdsmomentgroup.cc: Fixed minor error with incorrect format in printf statement. 2003-10-22 10:23 paultcochrane * source/main.cc: Improved mpi flag handling, and added a FFTW_MPI_LIBS variable. 2003-10-22 10:22 paultcochrane * configure.in: Removed some superfluous variables, and some superfluous output at configure time. Improved the ordering and determination of flags for use with mpi. 2003-10-22 09:27 paultcochrane * configure.in: Now generating source/xmdsconfig.h as well as source/config.h so that simulation binaries can have more benefit from configuration headers. Added -lxmds to LIBS variable (this isn't the right thing to do, and will be fixed shortly). 2003-10-20 11:14 joehope * examples/highdim.xmds: Trivial fix for occasional, minor compiler confusion: sqrt(int) 2003-10-18 20:57 paultcochrane * Makefile.in: Updated to current version. 2003-10-18 20:55 paultcochrane * source/xmdssimulation.cc: Removed inclusion of endian.h for binaryOutput. Now including config.h when binaryOutput is true. 2003-10-18 20:54 paultcochrane * source/xmdssequence.cc: Changed checks for FLOAT_WORD_ORDER etc to CPU_IS_BIG_ENDIAN etc. 2003-10-18 20:53 paultcochrane * source/xmdsmomentgroup.cc: Now determining endian-ness by the variables CPU_IS_BIG_ENDIAN and CPU_IS_LITTLE_ENDIAN. 2003-10-18 20:51 paultcochrane * source/Makefile.am: Now adding the config.h generated in the configuration of xmds. This adds the variables CPU_IS_BIG_ENDIAN and CPU_IS_LITTLE_ENDIAN to check for endian-ness of the processor. 2003-10-18 20:49 paultcochrane * aclocal.m4, configure, source/Makefile.in, source/config.h.in: Updated to current version. 2003-10-18 20:48 paultcochrane * configure.in: Removed check for endian.h and added code to search for endian-ness of processor copied from configure.ac in libsndfile. Also am now including the acinclude.m4 of libsndfile. 2003-10-18 20:07 paultcochrane * acinclude.m4: Initial import to repository. 2003-10-17 14:53 paultcochrane * source/xmdssimulation.cc: Instead of adding "#include getopt.h" every time a simulation code is written, it is only added now when the .xmds script contains an argv tag set, and therefore the simulation can take arguments at the command line. 2003-10-17 14:50 paultcochrane * source/xmdssequence.cc: Changed getopt_long_only to getopt_long. 2003-10-17 14:49 paultcochrane * source/main.cc: Removed FFTWMPILIBS variable (now superfluous). Removed superfluous %s formatting string. 2003-10-17 14:48 paultcochrane * source/Makefile.am: Added the getopt sources and headers to make the libxmds library. 2003-10-17 14:47 paultcochrane * source/: getopt.c, getopt.h, getopt1.c, getopt_init.c, stamp-h.in, stamp-h1.in: Initial import to repository. 2003-10-17 14:36 paultcochrane * configure, ltmain.sh, source/Makefile.in, source/config.h.in: Updated to current version. 2003-10-17 14:32 paultcochrane * depcomp, Makefile.in, aclocal.m4, config.guess: Updated to current version. 2003-10-17 14:32 paultcochrane * configure.in: Added underscores to some variables to improve readability. Made sure that the directory libxmds.a is put in is the same as xmdscomplex.h (on installation). Made sure that script doesn't write over previously defined (eg in the user's shell) any environment variables used (eg CFLAGS). Made sure that gcc gets the -Wall option (don't really know why... historical I guess). Changed FFTW_THREADS_* to XMDS_THREADS_*. These may be deleted in the future. Cleaned up the flags that mpi gets eventually. Further cleaning will ensue however. icc currently only used if set as CC and or CXX flags in the shell. Moved the AC_SUBSTs at the end of the script to before all of the AC_DEFINES. Made sure that -lxmds is added to LIBS. Some echos added for testing purposes. 2003-10-17 14:24 paultcochrane * Makefile.am: Commented out the inclusion of xmds api documentation. 2003-10-10 15:02 joehope * source/: dom3.h, kissdom.cc, kissdom.h, xmdsclasses.h, xmdsutils.h, xmlbasics.h, xmlparser.h, xsilfield.h, xmdsarg.cc, xmdsargelement.cc, xmdsargv.cc, xmdselement.cc, xmdsfield.cc, xmdsfilter.cc, xmdsglobals.cc, xmdsintegrate.cc, xmdsintegrateex.cc, xmdsintegrateip.cc, xmdsintegraterk4.cc, xmdsintegraterk4ex.cc, xmdsintegraterk4ip.cc, xmdsintegratesi.cc, xmdsintegratesiex.cc, xmdsintegratesiip.cc, xmdsmomentgroup.cc, xmdsoutput.cc, xmdssegment.cc, xmdssequence.cc, xmdssimulation.cc, xmdsutils.cc, xmdsvector.cc, xmdsvectorelement.cc, xmlbasics.cc, xmlparser.cc, xsil2graphics.cc, xsilfield.cc: Replace //** with // ** (often allows proper syntax colouring) 2003-10-09 16:29 paultcochrane * testsuite/atomlaser.xmds, testsuite/atomlaser_reference.xsil, testsuite/fibre.xmds, testsuite/fibre_reference.xsil, testsuite/fullpos3D.xmds, testsuite/fullpos3D_reference.xsil, testsuite/gaugeatomlaser.xmds, testsuite/gaugeatomlaser_reference.xsil, testsuite/genRefData.pl, testsuite/kubo.xmds, testsuite/kubo_reference.xsil, testsuite/ndparamp.xmds, testsuite/ndparamp_reference.xsil, testsuite/nlse.xmds, testsuite/nlse_reference.xsil, testsuite/sine.xmds, testsuite/sine_reference.xsil, testsuite/soliton.xmds, testsuite/soliton_reference.xsil, testsuite/test_xmds.pl, testsuite/tla.xmds, testsuite/tla_reference.xsil, frontend/tkxmds, frontend/tkxmds.pl: Initial import to repository. 2003-10-09 14:49 joehope * configure: Fixing link to libraries used for testing fftw_mpi 2003-10-09 12:18 offaxis * source/xmdsglobals.cc: Globals from elements now read in _before_ those from the element. 2003-10-07 15:28 paultcochrane * depcomp: Initial import to repository. 2003-10-07 15:01 paultcochrane * acx_pthread.m4: Initial import to repository. Copied from the fftw distribution (many thanks). 2003-10-07 14:59 paultcochrane * configure.in: Many, many changes. Updated to call xmds version 1.2. Added a path to one's mpi distribution if different from /usr or /usr/local. Added a check for vendor's cc and c++ compiler, and using them to compile both xmds and the simulation binaries. If the compiler is gcc then adds the -Wall compiler flag. Checks for getopt and getopt_long. Checks for the various thread libraries (code copied and modified from the fftw configure.in). Added a FFTW_LIBS variable. This may be used a bit better in the future. Checks for the Intel c compiler and if so then uses that compiler for xmds and the simulation binaries. Removed some superfluous definitions and subst's. 2003-10-07 14:55 paultcochrane * configure: Changed to agree with current version of configure.in 2003-10-07 14:53 paultcochrane * Makefile.in: Updated to agree with current version of Makefile.am 2003-10-07 14:52 paultcochrane * examples/nlse.xmds: Removed tag, just for testing purposes. Fixed problem with log(2) being incorrect for more recent versions of c++: one must now use log(2.0). 2003-10-07 14:50 paultcochrane * source/xmdssimulation.cc: Added config.h to headers list. Using the HAVE_ENDIAN_H variable defined therein to specify what the __BYTE_ORDER and __FLOAT_WORD_ORDER macros should be equal to. Hopefully this fixes the endian issues xmds could have, although I'm not sure yet. 2003-10-07 14:48 paultcochrane * source/main.cc: Added cxx variable set equal to the CXX variable found by the configure script. This is then used for compilation of the simulation binary. Also specifying the FFTW_LIBS variable as well. Added the fftwlibs variable to the compilation of the simulation binary. 2003-10-07 14:45 paultcochrane * source/loadxsil.m: Fixed a line that was missing a . 2003-10-07 14:44 paultcochrane * source/config.h.in: Updated to agree with current version of configure.in etc 2003-10-07 14:43 paultcochrane * source/Makefile.in: Updated to agree with current version of Makefile.am 2003-10-06 14:21 paultcochrane * source/xmdsmomentgroup.cc: Removed multiline string literals by adding heaps of fprintf statements. This caused problems with some compilers. 2003-10-06 14:20 paultcochrane * source/xmdsfield.cc: Removed multiline string literals by adding heaps of fprintf statements. 2003-09-30 21:50 paultcochrane * examples/atomlaser.xmds: Now contains more tags test code. Doesn't actually do anything... 2003-09-30 21:48 paultcochrane * source/xmdsutils.h: Reformatted the text. 2003-09-30 21:47 paultcochrane * source/xmdssimulation.cc: Removed test code. Fixed code to implement the gnu getopt library for command line options for the simulation binary. 2003-09-30 21:46 paultcochrane * source/xmdssequence.cc: Completed code to implement gnu getopt command line options for the simulation binary. 2003-09-30 21:44 paultcochrane * source/xmdsglobals.cc: Added global variables code to be output for when command line arguments are specified in the .xmds file. 2003-09-30 21:42 paultcochrane * source/xmdscomplex.h: Reformatted text. 2003-09-30 21:42 paultcochrane * source/xmdsclasses.h: Deleted some superfluous code (eg writeArgvIntialisationCode, writeArgvFinalisationCode). Removed test object: argvList. Fixed header so that can use an argvStruct to store information about the command line arguments specified in tags. 2003-09-30 21:39 paultcochrane * source/xmdsargv.cc: Deleted some superfluous code (eg writeArgvIntialisationCode, writeArgvFinalisationCode). 2003-09-30 21:38 paultcochrane * source/xmdsargelement.cc: Finally worked out how to get the argument names, short options, types, default_values etc into the simulation object. Deleted some superfluous code (eg writeArgDeclaration, writeArgCode). 2003-09-30 21:36 paultcochrane * source/xmdsarg.cc: Removed some superfluous function definitions. Namely type(), setType(), default_value() and setDefaultValue() 2003-09-30 21:33 paultcochrane * source/: dom3.h, kissdom.h: Reformatted text nicely. 2003-09-30 21:32 paultcochrane * source/Makefile.in: Updated to reflect changes in Makefile.am 2003-09-29 19:57 paultcochrane * Makefile.in: Updated to reflect changes in Makefile.am 2003-09-29 19:57 paultcochrane * Makefile.am: Removed superfluous files from being added when performing a make dist. Needs to be improved further. 2003-09-29 19:56 paultcochrane * aclocal.m4: Updated. 2003-09-29 19:56 paultcochrane * configure.in: Better checking, and some testing done on platforms other than linux. 2003-09-29 19:55 paultcochrane * configure: Updated to current configure.in 2003-09-29 18:03 paultcochrane * configure: Updated to current configure.in 2003-09-29 18:00 paultcochrane * configure.in: Actually fixed the checks now, instead of not (aarrgghh). 2003-09-29 13:28 paultcochrane * configure.in: Fixed some more checks and added a check for fftw_mpi. 2003-09-29 13:28 paultcochrane * configure: Updated to current version of configure.in 2003-09-29 12:03 paultcochrane * configure: Updated to current version of configure.in 2003-09-29 12:02 paultcochrane * configure.in: Fixed bug with incorrectly using alternative paths to fftw. 2003-09-24 14:32 paultcochrane * doc/latex/figures/main.eps: Redrew in PyScript, so looks much better now. 2003-09-24 14:20 paultcochrane * doc/latex/figures/defferential.eps: Initial import to repository. 2003-09-24 14:19 paultcochrane * doc/latex/xmds_doc.tex: Included language reference LaTeX source file. 2003-09-24 14:18 paultcochrane * doc/latex/xmds_defs.tex: Added more keywords to morekeywords statement for myhtml language style. 2003-09-24 14:17 paultcochrane * doc/latex/titlepage.tex: Minor change to xmds_logo LaTeX code. 2003-09-24 14:15 paultcochrane * doc/latex/languageReference.tex: Initial import to repository. 2003-09-24 14:14 paultcochrane * doc/latex/numModellingTheory.tex: Added (funny, and therefore probably superfluous) figure at start of chapter. Sundry other formatting changes. 2003-09-24 14:12 paultcochrane * doc/latex/bibliography.tex: Updated for use with hyperref package 2003-09-15 20:16 paultcochrane * source/: xmdsarg.cc, xmdsargelement.cc, xmdsargv.cc, xmdselement.cc, xmdsfield.cc, xmdsfilter.cc, xmdsglobals.cc, xmdsintegrate.cc, xmdsintegrateex.cc, xmdsintegrateip.cc, xmdsintegraterk4.cc, xmdsintegraterk4ex.cc, xmdsintegraterk4ip.cc, xmdsintegratesi.cc, xmdsintegratesiex.cc, xmdsintegratesiip.cc, xmdsmomentgroup.cc, xmdsoutput.cc, xmdssegment.cc, xmdssequence.cc, xmdssimulation.cc, xmdsutils.cc, xmdsvector.cc, xmdsvectorelement.cc: Implemented the use of a command line flag to xmds for toggling debugging information output (-d). 2003-09-15 20:14 paultcochrane * source/xsil2graphics.cc: Modified to implement the -d xmds debugging flag and -x the xml debugging flag. 2003-09-15 20:13 paultcochrane * source/xmlbasics.cc: Removed DEBUG macro. This is now implemented as a command line switch to xmds. Specifically -x, for xml debugging information. This change is really only useful for developers. 2003-09-15 20:12 paultcochrane * source/xmdsclasses.h: Removed DEBUG macro. This is now implemented as a command line switch to xmds. 2003-09-15 20:10 paultcochrane * source/main.cc: Implemented some new command line options to xmds the program. -c switches compilation of the output binary OFF. This is useful for checking is xmds outputs the correct code, or if one wants to hack the output source and not have to worry about compilation, or even if the output code is not to be used on a unix system and therefore needs some hacking to work on another system. -d switches debugging output on excluding xml parsing debugging output (same as setting the DEBUG macro in the code, except that xmds doesn't have to be recompiled every time one wants to change that). -x switches debugging output of just the xml parsing on. 2003-09-15 19:57 paultcochrane * examples/atomlaser.xmds: Improved indentation of xml. Added code to test the tag set. 2003-09-15 16:56 paultcochrane * ChangeLog: Initial import to repository. 2003-09-15 16:49 paultcochrane * source/: xmdsarg.cc, xmdsargelement.cc, xmdsargv.cc: Initial import to repository. 2003-09-15 16:48 paultcochrane * source/xmdssimulation.cc: Improved indentation of source code. Added some code for the parsing of the element. 2003-09-15 16:45 paultcochrane * source/xmdssequence.cc: Improved indentation of source code, no functional changes. 2003-09-15 16:43 paultcochrane * source/xmdsclasses.h: Added declarations for xmdsArgv, xmdsArg, and xmdsArgElement classes. Also added an argvStruct structure to store the relevant information found by parsing the new etc syntax. This may or may not be used at this stage, so consider this commit as strictly temporary. 2003-09-15 16:38 paultcochrane * source/: xmdsutils.cc, xmdsutils.h, xmdsvector.cc, xmdsvectorelement.cc: No functional changes, just indented the source code nicely 2003-09-15 16:32 paultcochrane * source/: dom3.h, kissdom.cc, kissdom.h, xmdscomplex.h, xmdsfilter.cc, xmdsglobals.cc, xmdsintegrate.cc, xmdsintegrateex.cc, xmdsintegrateip.cc, xmdsintegraterk4.cc, xmdsintegraterk4ex.cc, xmdsintegraterk4ip.cc, xmdsintegratesi.cc, xmdsintegratesiex.cc, xmdsintegratesiip.cc, xmdsmomentgroup.cc, xmdsoutput.cc, xmdssegment.cc, xmlbasics.cc, xmlbasics.h, xmlparser.cc, xmlparser.h, main.cc, xmdsfield.cc: No functional changes, just indented the source code nicely 2003-09-15 16:31 paultcochrane * source/Makefile.am: Added xmdsargv.cc xmdsarg.cc and xmdsargelement.cc to the list of xmds sources 2003-09-15 16:29 paultcochrane * Makefile.in, source/Makefile.in: Adding relevant changes made by automake and autoconf 2003-09-09 14:32 paultcochrane * source/: Makefile.in, config.h.in: Initial import to repository 2003-09-09 14:29 paultcochrane * config.sub, config.guess, Makefile.in: Initial import to repository 2003-09-04 19:54 paultcochrane * aclocal.m4: Initial import to repository 2003-09-04 19:53 paultcochrane * configure: Initial import to repository. 2003-08-25 11:44 paultcochrane * doc/latex/: abstract.tex, ccaption.sty, develAndProgStructure.tex, fancyhdr.sty, functionality.tex, intro.tex, misc_defs.tex, moreExamples.tex, numModellingTheory.tex, outlook.tex, quotchap.sty, titlepage.tex, workedExample.tex, xmds_defs.tex, xmds_doc.tex, xsil.tex, xsil2graphics.tex, xmds_doc.pdf, xmds_doc.ps: Initial import to repository 2003-08-25 11:41 paultcochrane * doc/latex/xmds.tex: Obsolete 2003-08-21 11:38 paultcochrane * doc/latex/: bibliography.tex, doc.tex, xmds.tex, figures/classes.eps, figures/classes.fig, figures/fibre1.eps, figures/fibre2.eps, figures/funct.eps, figures/funct.fig, figures/kubo1.eps, figures/kubo2.eps, figures/main.eps, figures/main.fig, figures/ndparamp1.eps, figures/ndparamp2.eps, figures/nlse.eps, figures/tla.eps: Initial commit of v1.0 latex docs to devel tree 2003-08-06 15:38 paultcochrane * configure.in: Added a check for the endian.h header file. 2003-08-06 14:42 paultcochrane * source/xmdssimulation.cc: If binary output is specified, then include the header. 2003-08-06 14:41 paultcochrane * source/xmdssequence.cc: Added code to output C code to check for the definitions of __FLOAT_WORD_ORDER and __BYTE_WORD order. If the first doesn't exist, then it uses the next, if that doesn't exist, then the program exits. 2003-08-06 14:38 paultcochrane * source/xmdsmomentgroup.cc: Added code to output C code that checks for littleendian or bigendian binary format, and assigns the string encodingStr accordingly, for then use in the .xsil output file of the simulation. 2003-08-06 14:35 paultcochrane * source/loadxsil.m: Modified to allow for reading of bigendian or littleendian binary, as specified in the .xsil file. 2003-08-05 17:54 paultcochrane * source/xmdssimulation.cc: Added argvList to myParameters assignment block in xmdsSimulation constructor. Added code to process the argv element and put the command line arguments into the argvList for use in xmdsglobals.cc. 2003-08-05 17:51 paultcochrane * source/xmdssequence.cc: Added code to accept arguments on the command line for the xmds executable, only if the argvList defined via the tag is non-zero. If the incorrect number of arguments, the program gives a usage output and exits. 2003-08-05 17:49 paultcochrane * source/xmdsglobals.cc: Added code to look for tag in section and append the relevant code to the myGlobalCode variable, to be output in the globals definition section of the .cc file. This implements part of allowing arguments to be passed to the executable at the command line. 2003-08-05 17:47 paultcochrane * source/xmdsclasses.h: Included header. Added argvList string list to parametersStruct to implement the passing of arguments to the output binary at the command line. 2003-08-04 20:29 paultcochrane * source/Makefile: Obsolete. Now automatically generated by configure script. 2003-08-04 20:28 paultcochrane * Configure: Obsolete 2003-08-04 20:27 paultcochrane * source/xmdssimulation.cc: Included the vector header. Now "using namespace std" by default. 2003-08-04 20:26 paultcochrane * source/xmdsoutput.cc: Fixed a spelling error in console output. 2003-08-04 20:24 paultcochrane * source/xmdsmomentgroup.cc: Output binary files now have the moment group field name appended. This stops output binary files writing all over one another. Implemented a better technique of binary output: redundancy inherent in ascii output format has been removed. 2003-08-04 20:20 paultcochrane * source/xmdsfield.cc: The std:: namespace is now "used". The temporary files host.stuff and home.stuff are removed after being used. 2003-08-04 20:18 paultcochrane * source/loadxsil.m: Modified to allow for changes in binary output format. 2003-07-28 19:42 paultcochrane * Makefile.am: examples directory is now included in EXTRA_DIST instead of SUBDIRS. This stops examples from being compiled at build time. 2003-07-28 19:41 paultcochrane * configure.in: No longer produces Makefile in examples directory. 2003-07-28 19:13 paultcochrane * source/Doxyfile: Initial import to repository 2003-07-28 19:12 paultcochrane * source/: dom3.h, kissdom.h, xmdsclasses.h, xmdscomplex.h, xmdsutils.h, xmlbasics.h, xmlparser.h, xsilfield.h: Documented for use with Doxygen. Quite basic and incomplete, but with placeholders where necessary for further addition and improvement of the api documentation. 2003-07-28 19:07 paultcochrane * source/: main.cc, xmdssequence.cc: Added some documentation to the file. Mainly just to test out Doxygen, automatic api documentation generator. 2003-07-23 14:23 paultcochrane * examples/: atomlaser.xmds, fibre.xmds: Added tag 2003-07-23 14:23 paultcochrane * source/xmdssimulation.cc: Implemented code to process tag properly. Added header so that can actually do the benchmarking. 2003-07-23 14:21 paultcochrane * source/xmdssequence.cc: Added output code to implement boolean 2003-07-23 14:20 paultcochrane * source/xmdsfield.cc: Fixed issues with gcc 3+ not finding ifstream, ofstream, string etc. Need to prepend with std:: to use the correct namespace. 2003-07-23 14:19 paultcochrane * source/xmdsclasses.h: Added benchmark boolean to simulationParametersStruct 2003-07-23 14:17 paultcochrane * configure.in: Fixed problems with not getting flags passed to mpicc right. Still not perfect though... 2003-07-23 14:16 paultcochrane * Makefile.am: Altered to allow building of example binaries in the examples subdirectory 2003-07-12 15:19 paultcochrane * source/loadxsil.m: Loads binary data, and ascii data. Is now callable as a function and returns variables into calling script or functions variable space. Handles multiple moment groups. 2003-07-11 15:03 paultcochrane * source/loadxsil.m: Initial import to repository. Is able to parse .xsil files and automatically generate the code to load binary data in from file. This is still under heavy development, need to be able to load ascii data from .xsil files and need to actually implement as a function as opposed to a script. Nevertheless, the checkin was necessary/ 2003-07-09 14:44 paultcochrane * source/xmdssimulation.cc: Added useDouble boolean to myParameters. Implemented finding use_double element in xmds file, and setting accordingly if found. 2003-07-09 14:43 paultcochrane * source/xmdsmomentgroup.cc: Added C++ header. Added a check for the value of the useDouble boolean, if so, set output precison and cast (if necessary) accordingly. Implemented single or double precision for output of binary data depending on value of useDouble boolean. Default is to use double. 2003-07-09 14:40 paultcochrane * source/xmdsclasses.h: Added useDouble boolean to simulationParametersStruct (to implement the choice of using double or single precision in binary output. 2003-07-09 13:57 paultcochrane * source/xmdssimulation.cc: Implemented binaryOutput boolean. Implemented checking for element in xmds code. Added some more headers to xmds generated cc file so that can use more C++ features. 2003-07-09 13:55 paultcochrane * source/xmdsoutput.cc: Addition of myBoolList variable in order to implement binary output 2003-07-09 13:54 paultcochrane * source/xmdsmomentgroup.cc: Implemented binary output of data if boolean set to yes. 2003-07-09 13:53 paultcochrane * source/xmdsfield.cc: Added some informative messages to output concerning what program is doing. Changed dodgy C-like implementation of wisdom and hostName/homeDir to a more robust C++ implementation. 2003-07-09 13:50 paultcochrane * source/xmdsclasses.h: Modified to turn debugging on. Modified to add binaryOutput boolean to myParameters. 2003-07-09 13:49 paultcochrane * examples/atomlaser.xmds: Added and flags to file. 2003-07-07 16:02 paultcochrane * examples/atomlaser.xmds: Made minor changes to formatting of file. 2003-07-07 16:01 paultcochrane * source/xmdssimulation.cc: Added code to look for tag in .xmds file, and implement if necessary. 2003-07-07 15:59 paultcochrane * source/xmdssequence.cc: Updated writePlanCreationCalls() call so that includes new arguments due to inclusion of wisdom 2003-07-07 15:57 paultcochrane * source/xmdsoutput.cc: Changed writePlanCreationCalls() to allow for wisdom implementation 2003-07-07 15:56 paultcochrane * source/xmdsfield.cc: Implemented the use of wisdom via the tag. xmds simulation binary now outputs more progress information: when building forward and backward plans for fftw; when importing wisdom; when exporting wisdom; when using current directory instead of ~/.xmds/wisdom for .wisdom files. Simulation binary now checks for the existence of ~/.xmds/wisdom directory for storage of .wisdom files. 2003-07-07 15:52 paultcochrane * source/xmdsclasses.h: Changed simulationParametersStruct to include useWisdom boolean. Updated writePlanCreationCalls to include useWisdom in function call. 2003-07-07 15:49 paultcochrane * configure.in: Added checking for icc. Removed superfluous AC_SUBST calls. Fixed some issues with building and running xmds on machines with icc, the only problem being that configure script is now becoming a bit ugly. 2003-07-03 14:15 paultcochrane * source/: xmlparser.cc, xmlparser.h: Fixed xml parsing so compiles and works on LinuxPPC. Problem was to do with different implementations of char for different compilers. Basically, the PPC gcc was setting some comparisons to always true or always false, because the char data type was really unsigned char. What was actually desired (and I believe used by Linux_x86 gcc) was signed char, but this only affected a few cases. XML files are now parsed properly and produce correct output (although there are subtle differences in numerical output at the e-12 level between LinuxPPC and LinuxI386, and I haven't checked that in depth as yet). 2003-07-03 14:11 paultcochrane * source/Makefile.am: Initial import to repository 2003-07-01 18:56 paultcochrane * AUTHORS, COPYING, INSTALL, Makefile.am, README, configure.in, install-sh, ltmain.sh, missing, mkinstalldirs, NEWS: Added initial version to repository 2003-07-01 18:54 paultcochrane * source/: main.cc, xsil2graphics.cc: Minor alterations to standardise the naming conventions (e.g. VER is now VERSION) 2003-06-25 12:30 joehope * source/: xmdssequence.cc, xmdssimulation.cc: Making (MPI) size a global variable. Good for debugging. 2003-06-03 13:53 joehope * Configure: Reset Configure to Linux by default 2003-06-03 13:51 joehope * Configure: Blank space in "release" tag in case of compiler warnings 2003-06-03 12:29 joehope * Configure, source/xmdsintegrate.cc: Fixing case sensitive TRUE and FALSE 2003-05-31 18:44 joehope * changes.log: Changes log is up to date for the version 1.1 release 2003-05-31 18:21 joehope * source/: xmdsclasses.h, xmdsintegrate.cc, xmdsintegratesiip.cc: Added element in . Places code before the integration loop. This is good for time dependent functions. 2003-05-31 15:53 joehope * source/: xmdsfield.cc, xmdsmomentgroup.cc, xmdssequence.cc: Fixing two bugs for 0D systems with post-propagation output in fourier space. Allowing FFTWPLANS all the time, and fixing a verbose range check. 2003-05-06 09:42 joehope * changes.log: New changes.log for xmds-1.1-beta2 2003-04-17 16:22 joehope * source/xmdsmomentgroup.cc: Fix range on if statement for x-space moment group with a cross-section in the first transverse dimension (deterministic MPI only) 2003-04-17 14:52 joehope * source/: xmdssequence.cc, xmdssimulation.cc: Made rank a global variable. Good for debugging. 2003-04-17 11:55 joehope * source/xmdsmomentgroup.cc: Fixed pointer initialisation in moment groups for a deterministic MPI simulation with a cross section in normal space for the first transverse dimension. 2003-04-16 17:05 joehope * source/xmdsvector.cc: Fixed a compiler warning in renormalisation for deterministic MPI. 2003-04-16 15:43 joehope * source/: xmdsintegraterk4.cc, xmdsvector.cc: Two range fixes for deterministic MPI. 2003-04-16 12:49 joehope * source/xmdscomplex.h: Made the promotion of complex to fftw_complex non-explicit. Less warnings, and it should be safe. 2003-04-16 12:46 joehope * source/xmdscomplex.h: Fixed three errors in the algebra for the complex overload operators. Specifically: - (z), z*=double and z/=double were all broken! 2003-04-04 10:23 joehope * examples/highdim.xmds: Making highdim.xmds an MPI-enabled script with fewer outputs. 2003-04-04 10:22 joehope * examples/gaugeatomlaser.xmds: Reverted stochastic Fourier-space output to local-in-x form. 2003-04-04 10:00 joehope * changes.log, examples/ndparamp.xmds: Pre-version 1.0 cruft removal from examples 2003-03-28 14:03 joehope * source/xmdsvector.cc: Extra print variable cruft removed 2003-03-28 11:43 joehope * Configure: Default Configure file settings for linux - ready for 1.1-beta release 2003-03-27 18:43 joehope * examples/highdim.xmds, source/xmdssequence.cc: Nested subsequences now call their initialisation functions. 2003-03-27 18:29 joehope * examples/highdim.xmds, source/xmdsvector.cc: Mixed space transforms added for deterministic MPI. 2003-03-27 13:45 joehope * source/: xmdsfield.cc, xmdsmomentgroup.cc, xmdsvector.cc: Put TRUE and FALSE into lowercase. Needed for linux (for icc, at least). 2003-03-26 17:07 joehope * examples/highdim.xmds, source/xmdsintegrate.cc, source/xmdsintegraterk4ex.cc, source/xmdsintegraterk4ip.cc, source/xmdsintegratesiex.cc, source/xmdsintegratesiip.cc: Passed cycle number right through to the integrate loops 2003-03-26 16:37 joehope * changes.log, examples/highdim.xmds, source/xmdsmomentgroup.cc: Deterministic MPI nows works with all moment groups. Mixed space transforms still broken. 2003-03-25 15:26 joehope * source/: xmdsfield.cc, xmdsfilter.cc, xmdsintegraterk4.cc, xmdsintegratesiex.cc, xmdsintegratesiip.cc, xmdsmomentgroup.cc, xmdssequence.cc: Fixed cycles. Made all segments have access to the cycle number. Partial implementation of k-space output groups for deterministic MPI. 2003-03-25 10:38 joehope * examples/atomlaser.xmds, examples/kubo.xmds, source/xmdsclasses.h, source/xsil2graphics.cc: Fixed xsil2graphics bug 708629. Added MPI changes to class definitions. 2003-03-24 20:13 joehope * Configure, source/main.cc, source/xmdsfield.cc, source/xmdsintegrate.cc, source/xmdsintegrateex.cc, source/xmdsintegrateip.cc, source/xmdsintegraterk4.cc, source/xmdsintegraterk4ex.cc, source/xmdsintegraterk4ip.cc, source/xmdsintegratesiex.cc, source/xmdsintegratesiip.cc, source/xmdsmomentgroup.cc, source/xmdssequence.cc, source/xmdssimulation.cc, source/xmdsvector.cc: Reversion to local-in-x tag with addition of the ability to use MPI on deterministic problems with >1 transverse dimensions. k-space moment groups and mixed space transforms currently broken. Simply compile with element as for stochastic problems. 2003-03-13 10:25 joehope * source/: xmdsintegraterk4.cc, xmdsintegratesiex.cc, xmdsintegratesiip.cc: Memory reordering now complete. Cross-propagation should now be fully operational. 2003-03-11 17:23 joehope * Configure, examples/fullpos3D.xmds, examples/gaugeatomlaser.xmds, source/xmdsfield.cc, source/xmdsintegrate.cc, source/xmdsintegrateex.cc, source/xmdsintegrateip.cc, source/xmdsintegratesiip.cc, source/xmdsmomentgroup.cc, source/xmdsvector.cc: Reordered all the fields so that they are contiguous in memory when running through the FFTs rather than when going through x-space loops. This is in preparation for parallelisation. x-space heavy algorithms are slower and k-space heavy algorithms are faster. I have tested all the algorithms on gaugeatomlaser.xmds, and they all work identically to the stable branch. Cross-propagation is definitely broken - but fixable with effort. Mixed transforms should still work, but I haven't tested them on anything. Input files must now be reordered - components are now the slowest changing index rather than the fastest. 2003-03-10 14:55 joehope * examples/: atomlaser.xmds, gaugeatomlaser.xmds: Updating the examples to make a tagged version. I want to have a "pre-reordering" version, as I'm about to rearrange the memory management of the main fields. 2003-03-04 13:35 joehope * .DS_Store, source/.DS_Store, source/xmdsintegrateex.cc: Fixed missing segment name in xmdsintegrateex.cc (from previous speedup patch) 2003-03-03 14:58 joehope * .DS_Store, examples/atomlaser.xmds, examples/gaugeatomlaser.xmds, source/xmdsintegrateex.cc, source/xmdsintegrateip.cc: Replaced various operations in the K_operater routines with index pointers. Provided detectable speedup. Modified Files: source/xmdsintegrateex.cc source/xmdsintegrateip.cc 2003-02-24 10:53 joehope * .DS_Store, Configure, examples/fullpos3D.xmds, source/.DS_Store, source/main.cc, source/xmdsclasses.h, source/xmdssequence.cc, source/xmdssimulation.cc, source/xmdsvector.cc: Added partial support for threading. Placement of a 15 element in the simulation element will make the FFT use 15 threads. Further threading to follow. Default, and 1 is equivalent to the non-threaded code. Note that fftw must be compiled with the --enable-threads option. Modified Files: Configure examples/fullpos3D.xmds source/main.cc source/xmdsclasses.h source/xmdssequence.cc source/xmdssimulation.cc source/xmdsvector.cc 2003-02-06 18:02 joehope * Configure: Spelling errors in 1.3 patch fixed. 2003-02-06 17:57 joehope * Configure, source/Makefile: Fixed ordering of -lm and -lfftw libraries Fixed misnamed XMDSCSTDLIBS in the configure file Allowing XMDSCC XMDSCFLAGS and XMDSCSTDLIBS to be set individually, with the main choices being the default for unspecified ones. Refined default compile options for True64 unix. Added warning in the installation process that tells you the system that you've chosen. 2003-02-03 15:42 joehope * Configure, changes.log, source/Makefile, source/kissdom.cc, source/xmdsfield.cc, source/xmdsintegrate.cc, source/xmdsintegraterk4.cc, source/xmdsintegratesiex.cc, source/xmdsintegratesiip.cc, source/xmdsmomentgroup.cc, source/xmdsvector.cc, source/xmdsvectorelement.cc, source/xmlbasics.cc: Makefile has different options for different systems (different option order required) Stack no longer used for main fields (Simon) logical and rather than bitwise and (Simon) Details in changes.log 2003-02-03 12:23 joehope * .DS_Store, changes.log, Configure, readme, doc/doc.css, doc/doc.html, doc/img1.gif, doc/img10.gif, doc/img100.gif, doc/img101.gif, doc/img102.gif, doc/img103.gif, doc/img104.gif, doc/img105.gif, doc/img106.gif, doc/img107.gif, doc/img108.gif, doc/img109.gif, doc/img11.gif, doc/img110.gif, doc/img111.gif, doc/img112.gif, doc/img113.gif, doc/img114.gif, 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doc/img96.gif, doc/img97.gif, doc/img98.gif, doc/img99.gif, examples/atomlaser.xmds, examples/fibre.xmds, examples/fullpos3D.xmds, examples/gaugeatomlaser.xmds, examples/kubo.xmds, examples/ndparamp.xmds, examples/nlse.xmds, examples/sine.xmds, examples/soliton.xmds, examples/tla.xmds, source/.DS_Store, source/dom3.h, source/kissdom.cc, source/Makefile, source/kissdom.h, source/main.cc, source/xmdsclasses.h, source/xmdscomplex.h, source/xmdselement.cc, source/xmdsfield.cc, source/xmdsfilter.cc, source/xmdsglobals.cc, source/xmdsintegrate.cc, source/xmdsintegrateex.cc, source/xmdsintegrateip.cc, source/xmdsintegraterk4.cc, source/xmdsintegraterk4ex.cc, source/xmdsintegraterk4ip.cc, source/xmdsintegratesi.cc, source/xmdsintegratesiex.cc, source/xmdsintegratesiip.cc, source/xmdsmomentgroup.cc, source/xmdsoutput.cc, source/xmdssegment.cc, source/xmdssequence.cc, source/xmdssimulation.cc, source/xmdsutils.cc, source/xmdsutils.h, source/xmdsvector.cc, source/xmdsvectorelement.cc, source/xmlbasics.cc, source/xmlbasics.h, source/xmlparser.cc, source/xmlparser.h, source/xsil2graphics.cc, source/xsilfield.cc, source/xsilfield.h: Import version 1.0-2 to start development branch 2003-02-03 12:23 joehope * .DS_Store, changes.log, Configure, readme, doc/doc.css, doc/doc.html, doc/img1.gif, doc/img10.gif, doc/img100.gif, doc/img101.gif, doc/img102.gif, doc/img103.gif, doc/img104.gif, doc/img105.gif, doc/img106.gif, doc/img107.gif, doc/img108.gif, doc/img109.gif, doc/img11.gif, doc/img110.gif, doc/img111.gif, doc/img112.gif, doc/img113.gif, doc/img114.gif, doc/img115.gif, doc/img116.gif, doc/img117.gif, doc/img118.gif, doc/img119.gif, doc/img12.gif, doc/img120.gif, doc/img121.gif, doc/img122.gif, doc/img123.gif, doc/img124.gif, doc/img125.gif, doc/img126.gif, doc/img127.gif, doc/img128.gif, doc/img129.gif, doc/img13.gif, doc/img130.gif, doc/img131.gif, doc/img132.gif, doc/img133.gif, doc/img134.gif, doc/img135.gif, doc/img136.gif, doc/img137.gif, doc/img138.gif, doc/img139.gif, doc/img14.gif, doc/img140.gif, doc/img141.gif, doc/img142.gif, doc/img143.gif, doc/img144.gif, doc/img145.gif, doc/img146.gif, doc/img147.gif, doc/img148.gif, doc/img149.gif, doc/img15.gif, doc/img150.gif, doc/img151.gif, doc/img152.gif, doc/img153.gif, doc/img154.gif, doc/img155.gif, doc/img156.gif, doc/img157.gif, doc/img158.gif, doc/img159.gif, doc/img16.gif, doc/img160.gif, doc/img161.gif, doc/img162.gif, doc/img163.gif, doc/img164.gif, doc/img165.gif, doc/img166.gif, doc/img167.gif, doc/img168.gif, doc/img169.gif, doc/img17.gif, doc/img170.gif, doc/img171.gif, doc/img172.gif, doc/img173.gif, doc/img174.gif, doc/img175.gif, doc/img176.gif, doc/img177.gif, doc/img178.gif, doc/img179.gif, doc/img18.gif, doc/img180.gif, doc/img181.gif, doc/img182.gif, doc/img183.gif, doc/img184.gif, doc/img185.gif, doc/img186.gif, doc/img187.gif, doc/img188.gif, doc/img189.gif, doc/img19.gif, doc/img190.gif, doc/img191.gif, doc/img192.gif, doc/img193.gif, doc/img194.gif, 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doc/img60.gif, doc/img61.gif, doc/img62.gif, doc/img63.gif, doc/img64.gif, doc/img65.gif, doc/img66.gif, doc/img67.gif, doc/img68.gif, doc/img69.gif, doc/img7.gif, doc/img70.gif, doc/img71.gif, doc/img72.gif, doc/img73.gif, doc/img74.gif, doc/img75.gif, doc/img76.gif, doc/img77.gif, doc/img78.gif, doc/img79.gif, doc/img8.gif, doc/img80.gif, doc/img81.gif, doc/img82.gif, doc/img83.gif, doc/img84.gif, doc/img85.gif, doc/img86.gif, doc/img87.gif, doc/img88.gif, doc/img89.gif, doc/img9.gif, doc/img90.gif, doc/img91.gif, doc/img92.gif, doc/img93.gif, doc/img94.gif, doc/img95.gif, doc/img96.gif, doc/img97.gif, doc/img98.gif, doc/img99.gif, examples/atomlaser.xmds, examples/fibre.xmds, examples/fullpos3D.xmds, examples/gaugeatomlaser.xmds, examples/kubo.xmds, examples/ndparamp.xmds, examples/nlse.xmds, examples/sine.xmds, examples/soliton.xmds, examples/tla.xmds, source/.DS_Store, source/dom3.h, source/kissdom.cc, source/Makefile, source/kissdom.h, source/main.cc, source/xmdsclasses.h, source/xmdscomplex.h, source/xmdselement.cc, source/xmdsfield.cc, source/xmdsfilter.cc, source/xmdsglobals.cc, source/xmdsintegrate.cc, source/xmdsintegrateex.cc, source/xmdsintegrateip.cc, source/xmdsintegraterk4.cc, source/xmdsintegraterk4ex.cc, source/xmdsintegraterk4ip.cc, source/xmdsintegratesi.cc, source/xmdsintegratesiex.cc, source/xmdsintegratesiip.cc, source/xmdsmomentgroup.cc, source/xmdsoutput.cc, source/xmdssegment.cc, source/xmdssequence.cc, source/xmdssimulation.cc, source/xmdsutils.cc, source/xmdsutils.h, source/xmdsvector.cc, source/xmdsvectorelement.cc, source/xmlbasics.cc, source/xmlbasics.h, source/xmlparser.cc, source/xmlparser.h, source/xsil2graphics.cc, source/xsilfield.cc, source/xsilfield.h: Initial revision