sdepy:sdepy.git
8 years agoMerge branch 'master' of git@gitorious.org:/sdepy/sdepy
Michał Januszewski [Tue, 15 Jun 2010 13:59:19 +0000 (15:59 +0200)]
Merge branch 'master' of git@gitorious.org:/sdepy/sdepy

8 years agoFix ANM plot scripts.
Michał Januszewski [Tue, 15 Jun 2010 13:59:06 +0000 (15:59 +0200)]
Fix ANM plot scripts.

8 years agoAdd support for the 'store' output format.
Michał Januszewski [Tue, 15 Jun 2010 13:58:44 +0000 (15:58 +0200)]
Add support for the 'store' output format.

8 years agoMerge branch 'master' of git@gitorious.org:/sdepy/sdepy
Michał Januszewski [Tue, 15 Jun 2010 13:57:20 +0000 (15:57 +0200)]
Merge branch 'master' of git@gitorious.org:/sdepy/sdepy

8 years agoMerge branch 'master' of gitorious.org:/sdepy/sdepy
Michał Januszewski [Tue, 15 Jun 2010 13:10:58 +0000 (15:10 +0200)]
Merge branch 'master' of gitorious.org:/sdepy/sdepy

8 years agoUse the inset aspect to automatically adjust the figure aspect.
Michał Januszewski [Tue, 15 Jun 2010 12:22:38 +0000 (14:22 +0200)]
Use the inset aspect to automatically adjust the figure aspect.

8 years agoAdd subplot labels.
Michał Januszewski [Tue, 15 Jun 2010 12:01:07 +0000 (14:01 +0200)]
Add subplot labels.

8 years agoAdd preliminary support for multiplots.
Michał Januszewski [Tue, 15 Jun 2010 11:49:52 +0000 (13:49 +0200)]
Add preliminary support for multiplots.

8 years agoMerge branch 'master' of git@gitorious.org:/sdepy/sdepy
Michał Januszewski [Thu, 3 Jun 2010 23:02:36 +0000 (01:02 +0200)]
Merge branch 'master' of git@gitorious.org:/sdepy/sdepy

8 years agoFix typo in the JJ2 equations.
Michał Januszewski [Thu, 3 Jun 2010 10:46:05 +0000 (12:46 +0200)]
Fix typo in the JJ2 equations.

8 years agoAdd support for --transients=0.
Michał Januszewski [Wed, 2 Jun 2010 23:43:27 +0000 (01:43 +0200)]
Add support for --transients=0.

8 years agoUse fmod instead of % for the float modulo operation.
Michał Januszewski [Tue, 1 Jun 2010 17:07:32 +0000 (19:07 +0200)]
Use fmod instead of % for the float modulo operation.

8 years agoFix double precision calculations.
Michał Januszewski [Tue, 1 Jun 2010 15:53:36 +0000 (17:53 +0200)]
Fix double precision calculations.

8 years agoDo not generate unnecessary normal variates in the SRK2 algorithm.
Michał Januszewski [Sat, 29 May 2010 21:37:03 +0000 (23:37 +0200)]
Do not generate unnecessary normal variates in the SRK2 algorithm.

8 years agoFix time and position folding.
Michał Januszewski [Sat, 29 May 2010 19:30:05 +0000 (21:30 +0200)]
Fix time and position folding.

8 years agoMake it possible to actually run the JJ3 simulation.
Michał Januszewski [Sat, 29 May 2010 00:35:46 +0000 (02:35 +0200)]
Make it possible to actually run the JJ3 simulation.

8 years agoAdd a preliminary version of the 3xJJ system.
Michał Januszewski [Sat, 29 May 2010 00:04:21 +0000 (02:04 +0200)]
Add a preliminary version of the 3xJJ system.

8 years agoSimplify initial conditions for the 2JJ simulations.
Michał Januszewski [Fri, 28 May 2010 23:49:12 +0000 (01:49 +0200)]
Simplify initial conditions for the 2JJ simulations.

8 years agoMerge branch 'master' of gitorious.org:/sdepy/sdepy
Michał Januszewski [Fri, 28 May 2010 23:46:51 +0000 (01:46 +0200)]
Merge branch 'master' of gitorious.org:/sdepy/sdepy

8 years agoAdd support for absolute velocity plots.
Michał Januszewski [Fri, 28 May 2010 23:46:37 +0000 (01:46 +0200)]
Add support for absolute velocity plots.

8 years agoAdd a function to calculate the absolute drift velocity.
Michał Januszewski [Fri, 28 May 2010 23:46:18 +0000 (01:46 +0200)]
Add a function to calculate the absolute drift velocity.

8 years agoFix initial values of x for jj1.
Michał Januszewski [Wed, 26 May 2010 22:18:35 +0000 (00:18 +0200)]
Fix initial values of x for jj1.

8 years agoDo not print 0 * noise in the code.
Michał Januszewski [Wed, 26 May 2010 20:42:58 +0000 (22:42 +0200)]
Do not print 0 * noise in the code.

8 years agoRemove spurious time update in the SDE code.
Michał Januszewski [Wed, 26 May 2010 20:34:10 +0000 (22:34 +0200)]
Remove spurious time update in the SDE code.

8 years agoMerge branch 'master' of gitorious.org:/sdepy/sdepy
Michał Januszewski [Wed, 26 May 2010 17:09:17 +0000 (19:09 +0200)]
Merge branch 'master' of gitorious.org:/sdepy/sdepy

8 years agoUse a proper code printer when generating CUDA code.
Michał Januszewski [Wed, 26 May 2010 17:08:50 +0000 (19:08 +0200)]
Use a proper code printer when generating CUDA code.

8 years agoDo not include plot title in the pdf version (ANM plots).
Michał Januszewski [Wed, 26 May 2010 17:08:11 +0000 (19:08 +0200)]
Do not include plot title in the pdf version (ANM plots).

8 years agoAdd support for generating profiles in pdf.
Michał Januszewski [Wed, 26 May 2010 17:07:52 +0000 (19:07 +0200)]
Add support for generating profiles in pdf.

8 years agoUse tex fonts for the ANM plots.
Michał Januszewski [Wed, 26 May 2010 15:47:18 +0000 (17:47 +0200)]
Use tex fonts for the ANM plots.

This commit also adds support for figure sizes and pdf output.

8 years agoAdd a script to plot (i1, <v>) profiles.
Michał Januszewski [Wed, 26 May 2010 13:45:16 +0000 (15:45 +0200)]
Add a script to plot (i1, <v>) profiles.

8 years agoAdd scripts to automatically generate (i1, <v>) and (alpha, <v>) profiles.
Michał Januszewski [Wed, 26 May 2010 13:42:52 +0000 (15:42 +0200)]
Add scripts to automatically generate (i1, <v>) and (alpha, <v>) profiles.

8 years agoAdd initial support for pretty names in anm_plot.
Michał Januszewski [Tue, 25 May 2010 23:03:11 +0000 (01:03 +0200)]
Add initial support for pretty names in anm_plot.

8 years agoUse a tight bbox for the ANM figures.
Michał Januszewski [Tue, 25 May 2010 22:56:47 +0000 (00:56 +0200)]
Use a tight bbox for the ANM figures.

8 years agoFix typos in jj2_paper.
Michał Januszewski [Wed, 19 May 2010 08:58:33 +0000 (10:58 +0200)]
Fix typos in jj2_paper.

8 years agoAdd jj2 example as defined in the paper (single AC amplitude).
Michał Januszewski [Wed, 19 May 2010 08:55:12 +0000 (10:55 +0200)]
Add jj2 example as defined in the paper (single AC amplitude).

8 years agoMerge branch 'master' of gitorious.org:/sdepy/sdepy
Michał Januszewski [Tue, 18 May 2010 23:01:36 +0000 (01:01 +0200)]
Merge branch 'master' of gitorious.org:/sdepy/sdepy

8 years agoChange AC driving from sin(t) to cos(t) as defined in the text.
Michał Januszewski [Tue, 18 May 2010 23:00:59 +0000 (01:00 +0200)]
Change AC driving from sin(t) to cos(t) as defined in the text.

8 years agoFix a typo.
Michał Januszewski [Tue, 18 May 2010 22:51:33 +0000 (00:51 +0200)]
Fix a typo.

8 years agoAdd the 'deterministic' option.
Michał Januszewski [Tue, 18 May 2010 22:44:21 +0000 (00:44 +0200)]
Add the 'deterministic' option.

8 years agoFix period_map in the jj1 example.
Michał Januszewski [Mon, 17 May 2010 23:52:59 +0000 (01:52 +0200)]
Fix period_map in the jj1 example.

8 years agoMerge branch 'master' of gitorious.org:/sdepy/sdepy
Michał Januszewski [Mon, 17 May 2010 23:51:54 +0000 (01:51 +0200)]
Merge branch 'master' of gitorious.org:/sdepy/sdepy

8 years agoChange potential in the JJ1 example.
Michał Januszewski [Mon, 17 May 2010 23:50:34 +0000 (01:50 +0200)]
Change potential in the JJ1 example.

8 years agoAdd scripts for comparison of ANM plots.
Michał Januszewski [Mon, 17 May 2010 12:50:19 +0000 (14:50 +0200)]
Add scripts for comparison of ANM plots.

8 years agoFix color scale for plots with negative values only.
Michał Januszewski [Mon, 17 May 2010 12:49:42 +0000 (14:49 +0200)]
Fix color scale for plots with negative values only.

8 years agoMake it possible to generate multiple plots in a single run of the script.
Michał Januszewski [Mon, 17 May 2010 12:45:27 +0000 (14:45 +0200)]
Make it possible to generate multiple plots in a single run of the script.

8 years agoFix color scale if only positive values are present.
Michał Januszewski [Mon, 17 May 2010 10:44:58 +0000 (12:44 +0200)]
Fix color scale if only positive values are present.

8 years agoFix the system of two identical JJs.
Michał Januszewski [Thu, 6 May 2010 20:58:32 +0000 (22:58 +0200)]
Fix the system of two identical JJs.

8 years agoAdd the full 2JJ system.
Michał Januszewski [Thu, 6 May 2010 20:58:03 +0000 (22:58 +0200)]
Add the full 2JJ system.

8 years agoAdd the 2JJ example.
Michał Januszewski [Sun, 2 May 2010 10:23:47 +0000 (12:23 +0200)]
Add the 2JJ example.

8 years agoAdd support for independent gam2 in bp2_kuramoto.
Michał Januszewski [Sun, 2 May 2010 09:26:22 +0000 (11:26 +0200)]
Add support for independent gam2 in bp2_kuramoto.

8 years agoInclude the values of parameters in the plot title.
Michał Januszewski [Fri, 30 Apr 2010 18:12:54 +0000 (20:12 +0200)]
Include the values of parameters in the plot title.

8 years agoMake it possible to use anm_plot interactively.
Michał Januszewski [Thu, 29 Apr 2010 18:43:11 +0000 (20:43 +0200)]
Make it possible to use anm_plot interactively.

8 years agoChange the default aspect ratio.
Michał Januszewski [Thu, 29 Apr 2010 18:30:25 +0000 (20:30 +0200)]
Change the default aspect ratio.

8 years agoFix ANM plots in case there are no points with v < 0.
Michał Januszewski [Thu, 29 Apr 2010 18:02:16 +0000 (20:02 +0200)]
Fix ANM plots in case there are no points with v < 0.

8 years agoFix color map scaling in the ANM plot.
Michał Januszewski [Thu, 29 Apr 2010 17:58:32 +0000 (19:58 +0200)]
Fix color map scaling in the ANM plot.

8 years agoAdd support for saving figures to a file in anm_plot.
Michał Januszewski [Thu, 29 Apr 2010 17:52:44 +0000 (19:52 +0200)]
Add support for saving figures to a file in anm_plot.

8 years agoAdd a script for ANM plots.
Michał Januszewski [Thu, 29 Apr 2010 16:35:03 +0000 (18:35 +0200)]
Add a script for ANM plots.

8 years agoAdd a two Brownian particles simulation.
Michał Januszewski [Thu, 29 Apr 2010 13:52:38 +0000 (15:52 +0200)]
Add a two Brownian particles simulation.

For now, this is a restricted case with gamma_1 = gamma_2.  It will be
later extended to the generic case of arbitrary values of both gamma
parameters.

8 years agoAdd a description of the JJ1 simulation.
Michał Januszewski [Thu, 29 Apr 2010 13:43:57 +0000 (15:43 +0200)]
Add a description of the JJ1 simulation.

8 years agoMake it possible to use the old-style velocity histogram in the text mode.
Michał Januszewski [Tue, 27 Apr 2010 22:33:14 +0000 (00:33 +0200)]
Make it possible to use the old-style velocity histogram in the text mode.

8 years agoUpdate the TODO list.
Michał Januszewski [Tue, 27 Apr 2010 18:46:10 +0000 (20:46 +0200)]
Update the TODO list.

8 years agoDo not try to scan over the frequency variable on the CUDA device.
Michał Januszewski [Tue, 27 Apr 2010 18:45:41 +0000 (20:45 +0200)]
Do not try to scan over the frequency variable on the CUDA device.

8 years agoInclude values of parameters with multiple values in the text output.
Michał Januszewski [Tue, 27 Apr 2010 18:25:16 +0000 (20:25 +0200)]
Include values of parameters with multiple values in the text output.

8 years agoRestore support for basic pure text output.
Michał Januszewski [Tue, 27 Apr 2010 18:21:21 +0000 (20:21 +0200)]
Restore support for basic pure text output.

8 years agoFix SIGUSR2 handling.
Michał Januszewski [Tue, 27 Apr 2010 17:56:35 +0000 (19:56 +0200)]
Fix SIGUSR2 handling.

8 years agoFix shape of the numpy arrays in the output.
Michał Januszewski [Fri, 23 Apr 2010 13:47:20 +0000 (15:47 +0200)]
Fix shape of the numpy arrays in the output.

8 years agoAdd a task to the TODO list.
Michał Januszewski [Mon, 19 Apr 2010 22:36:07 +0000 (00:36 +0200)]
Add a task to the TODO list.

8 years agoMajor rearchitecture.
Michał Januszewski [Mon, 19 Apr 2010 22:33:02 +0000 (00:33 +0200)]
Major rearchitecture.

1. Make npy the default (and at the moment, the only supported) output
   format.  This greatly increases efficiency, compared to the old text
   format.
2. Add support for scanning over any system parameter.
3. Make it possible to scan over multiple system parameters in CUDA.

8 years agoChange initial conditions in the JJ1 system.
Michał Januszewski [Sun, 18 Apr 2010 19:48:05 +0000 (21:48 +0200)]
Change initial conditions in the JJ1 system.

8 years agoMake it possible to plot data with multiple postfixes.
Michał Januszewski [Sat, 17 Apr 2010 12:03:20 +0000 (14:03 +0200)]
Make it possible to plot data with multiple postfixes.

8 years agoAdd the deffplot utility.
Michał Januszewski [Mon, 12 Apr 2010 17:47:23 +0000 (19:47 +0200)]
Add the deffplot utility.

8 years agoIn bistable, do not limit the velocity histogram to a 6 stddev-wide interval.
Michał Januszewski [Mon, 12 Apr 2010 17:07:01 +0000 (19:07 +0200)]
In bistable, do not limit the velocity histogram to a 6 stddev-wide interval.

8 years agoAdd a single test script.
Michał Januszewski [Mon, 12 Apr 2010 17:02:35 +0000 (19:02 +0200)]
Add a single test script.

8 years agoMake it possible to run bistable with force > 1.
Michał Januszewski [Mon, 12 Apr 2010 16:27:15 +0000 (18:27 +0200)]
Make it possible to run bistable with force > 1.

8 years agoUpdate the TODO list.
Michał Januszewski [Mon, 12 Apr 2010 16:03:19 +0000 (18:03 +0200)]
Update the TODO list.

8 years agoDon't use state_results if not dump file is specified.
Michał Januszewski [Mon, 12 Apr 2010 15:08:26 +0000 (17:08 +0200)]
Don't use state_results if not dump file is specified.

8 years agoPrint CUDA kernel stats, fix data dump in the continue mode.
Michał Januszewski [Mon, 12 Apr 2010 14:57:11 +0000 (16:57 +0200)]
Print CUDA kernel stats, fix data dump in the continue mode.

When a simulation is started in the continue mode, its state_results
list should be reinitialized, so that the dump file doesn't get
progressively bigger with each continuation.

8 years agoFix RNG init so that it works on both 32 and 64-bit systems.
Michał Januszewski [Sun, 14 Feb 2010 10:49:10 +0000 (11:49 +0100)]
Fix RNG init so that it works on both 32 and 64-bit systems.

8 years agoFix typos in the 'sde' module.
Michał Januszewski [Sun, 14 Feb 2010 09:36:27 +0000 (10:36 +0100)]
Fix typos in the 'sde' module.

8 years agoFix the jj1 example.
Michał Januszewski [Sun, 14 Feb 2010 09:36:07 +0000 (10:36 +0100)]
Fix the jj1 example.

8 years agoAdd more data in the output of bistable.
Michał Januszewski [Sat, 13 Feb 2010 22:24:28 +0000 (23:24 +0100)]
Add more data in the output of bistable.

8 years agoSupport more signals, clean up the command line options.
Michał Januszewski [Sun, 7 Feb 2010 20:07:26 +0000 (21:07 +0100)]
Support more signals, clean up the command line options.

8 years agoAdd support for state dump on SIGUSR1.
Michał Januszewski [Sun, 7 Feb 2010 19:46:23 +0000 (20:46 +0100)]
Add support for state dump on SIGUSR1.

8 years agoAdd support for the continue and resume modes.
Michał Januszewski [Sat, 6 Feb 2010 20:52:39 +0000 (21:52 +0100)]
Add support for the continue and resume modes.

8 years agoRemove the _print function. Flush the output after every block.
Michał Januszewski [Fri, 12 Feb 2010 22:10:41 +0000 (23:10 +0100)]
Remove the _print function.  Flush the output after every block.

8 years agoAdd some more TODO tasks.
Michał Januszewski [Sat, 13 Feb 2010 22:01:10 +0000 (23:01 +0100)]
Add some more TODO tasks.

8 years agoAdd support for multiple output files.
Michał Januszewski [Sat, 13 Feb 2010 22:00:33 +0000 (23:00 +0100)]
Add support for multiple output files.

8 years agoAdd support for saving text data to a file.
Michał Januszewski [Thu, 28 Jan 2010 14:30:01 +0000 (15:30 +0100)]
Add support for saving text data to a file.

8 years agoFix output in path mode when no scan var is defined.
Michał Januszewski [Thu, 28 Jan 2010 13:39:12 +0000 (14:39 +0100)]
Fix output in path mode when no scan var is defined.

8 years agoWhen running in path mode with a scan var, output block separators.
Michał Januszewski [Sat, 13 Feb 2010 21:59:34 +0000 (22:59 +0100)]
When running in path mode with a scan var, output block separators.

8 years agoMake it possible for the initial conditions to depend on the scan parameter.
Michał Januszewski [Sat, 13 Feb 2010 22:18:01 +0000 (23:18 +0100)]
Make it possible for the initial conditions to depend on the scan parameter.

8 years agoSimplify the scan variable processing code.
Michał Januszewski [Mon, 25 Jan 2010 16:38:00 +0000 (17:38 +0100)]
Simplify the scan variable processing code.

8 years agoMake it possible to turn off fast math from the command line.
Michał Januszewski [Mon, 25 Jan 2010 13:01:09 +0000 (14:01 +0100)]
Make it possible to turn off fast math from the command line.

8 years agoxorshift -> xs
Michał Januszewski [Mon, 25 Jan 2010 12:54:59 +0000 (13:54 +0100)]
xorshift -> xs

8 years agoPrint command line arguments at the top of the output.
Michał Januszewski [Sun, 24 Jan 2010 23:31:12 +0000 (00:31 +0100)]
Print command line arguments at the top of the output.

8 years agoAdd the high quality 32-bit generator from NR3.
Michał Januszewski [Sun, 24 Jan 2010 13:13:11 +0000 (14:13 +0100)]
Add the high quality 32-bit generator from NR3.

8 years agoAdd some comments and a TODO file.
Michał Januszewski [Fri, 12 Feb 2010 22:07:40 +0000 (23:07 +0100)]
Add some comments and a TODO file.

8 years agoMake it possible to use a kernel saved in an external file.
Michał Januszewski [Sun, 24 Jan 2010 09:58:58 +0000 (10:58 +0100)]
Make it possible to use a kernel saved in an external file.

8 years agoFix the BM transform in case one of the variates is 0.
Michał Januszewski [Sat, 13 Feb 2010 21:57:13 +0000 (22:57 +0100)]
Fix the BM transform in case one of the variates is 0.

8 years agoAdd an initial version of the KISS RNG.
Michał Januszewski [Fri, 12 Feb 2010 22:05:37 +0000 (23:05 +0100)]
Add an initial version of the KISS RNG.