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sawsim.git
2010-10-23 W. Trevor KingStart fleshing out "Related work" section in the manual. commit | commitdiff | tree | snapshot
2010-10-23 W. Trevor KingFix some long URLs that had been wrapped by pybtex. commit | commitdiff | tree | snapshot
2010-10-23 W. Trevor KingUpdate the README with more information about the pysaw... commit | commitdiff | tree | snapshot
2010-10-23 W. Trevor KingAdd namedtuple definition from Python 2.6's collections... commit | commitdiff | tree | snapshot
2010-10-23 W. Trevor KingMove `import with_statement` from sawsim_histogram... commit | commitdiff | tree | snapshot
2010-10-23 W. Trevor KingReplace EXAMPLE_HISTOGRAM_FILE_CONTENTS histograms... commit | commitdiff | tree | snapshot
2010-10-23 W. Trevor KingAdd epilogs to each OptionParser in pysawsim. commit | commitdiff | tree | snapshot
2010-10-23 W. Trevor KingMove sawsim running into a new pysawsim.sawsim.SawsimRu... commit | commitdiff | tree | snapshot
2010-10-21 W. Trevor KingAdd 'mpi' to pysawsim.manager.MANAGERS. commit | commitdiff | tree | snapshot
2010-10-21 W. Trevor KingRelax command-not-found doctest messages. commit | commitdiff | tree | snapshot
2010-10-21 W. Trevor KingMerge branch 'master' of physics.drexel.edu/~wking... commit | commitdiff | tree | snapshot
2010-10-21 W. Trevor KingFix dropped receive during ThreadManager._spawn_jobs. commit | commitdiff | tree | snapshot
2010-10-20 W. Trevor KingAdd autogenerated .be/id-cache to .gitignore. commit | commitdiff | tree | snapshot
2010-10-20 W. Trevor KingMerge branch 'master' of ssh://wking@einstein/~/public_... commit | commitdiff | tree | snapshot
2010-10-20 W. Trevor KingUpgrade .be bug cache to Bugs Everywhere Directory... commit | commitdiff | tree | snapshot
2010-10-20 W. Trevor KingDisable pysawsim.manager.subproc is multiprocessing... commit | commitdiff | tree | snapshot
2010-10-20 W. Trevor KingWork around namedtuple import for Pythons < 2.6. commit | commitdiff | tree | snapshot
2010-10-20 W. Trevor KingAlso cleanup local mpd if the pysawsim nosetests fail. commit | commitdiff | tree | snapshot
2010-10-20 W. Trevor KingAdd CC, CFLAGS, and LDFLAGS to the Makefile for easy... commit | commitdiff | tree | snapshot
2010-10-20 W. Trevor KingWork around missing MPD with a more elaborate pysawsim... commit | commitdiff | tree | snapshot
2010-10-20 W. Trevor KingKill off worker-node implementations of master code. commit | commitdiff | tree | snapshot
2010-10-20 W. Trevor KingAdd pysawsim.manager.mpi with an mpi4py-based manager. commit | commitdiff | tree | snapshot
2010-10-20 W. Trevor KingAdd link to Python wiki's parallel processing page. commit | commitdiff | tree | snapshot
2010-10-20 W. Trevor KingAdjust pysawsim.manager.pbs to skip most doctests if... commit | commitdiff | tree | snapshot
2010-10-20 W. Trevor KingRemove execute permission from pysawsim/manager/pbs.py. commit | commitdiff | tree | snapshot
2010-10-20 W. Trevor KingAdd pysawsim.manager.subproc using subprocessing. commit | commitdiff | tree | snapshot
2010-10-20 W. Trevor KingAdd pysawsim.sawsim.main() and bin/sawsim_hist.py calli... commit | commitdiff | tree | snapshot
2010-10-20 W. Trevor KingAdd Histogram.to_stream() and .headings. commit | commitdiff | tree | snapshot
2010-10-20 W. Trevor KingFix 'intil_state' -> 'initial_state' typo in pysawsim... commit | commitdiff | tree | snapshot
2010-10-20 W. Trevor KingAdd Histogram.calculate_bin_edges(). commit | commitdiff | tree | snapshot
2010-10-20 W. Trevor KingReduce ThreadManager default worker_thread to 2. commit | commitdiff | tree | snapshot
2010-10-20 W. Trevor KingAdd --sawsim option to velocity_dependant_scan.main(). commit | commitdiff | tree | snapshot
2010-10-20 W. Trevor KingAllow Job status logging when .status is an Exception. commit | commitdiff | tree | snapshot
2010-10-20 W. Trevor KingAllow Job.__str__() to work when .id == None. commit | commitdiff | tree | snapshot
2010-10-20 W. Trevor KingTeardown manager after use in velocity_dependant_scan... commit | commitdiff | tree | snapshot
2010-10-20 W. Trevor KingAdd --clean-cache option to velocity_dependant_scan... commit | commitdiff | tree | snapshot
2010-10-20 W. Trevor KingNo need for `if __name__ == '__main__'` in velocity_dep... commit | commitdiff | tree | snapshot
2010-10-20 W. Trevor KingRearrange velocity_dependant_scan.main() to group resid... commit | commitdiff | tree | snapshot
2010-10-20 W. Trevor KingPass velocity_dependant_scan.main() --manager through... commit | commitdiff | tree | snapshot
2010-10-20 W. Trevor KingReposition matplotlib.use() call in velocity_dependant_... commit | commitdiff | tree | snapshot
2010-10-20 W. Trevor KingFix sawsim_histogram imports in velocity_dependant_scan.py. commit | commitdiff | tree | snapshot
2010-10-20 W. Trevor KingAdd bin/vel_dep_scan.py calling pysawsim.velocity_depen... commit | commitdiff | tree | snapshot
2010-10-20 W. Trevor KingAdd --manager option to velocity_dependant_scan.py. commit | commitdiff | tree | snapshot
2010-10-20 W. Trevor KingAdd pysawsim.manager.SUBMODS and .IsSubclass and .get_m... commit | commitdiff | tree | snapshot
2010-10-20 W. Trevor KingTransition more of the pysawsim framework into Python. commit | commitdiff | tree | snapshot
2010-10-20 W. Trevor KingAdd pysawsim.sawsim module. commit | commitdiff | tree | snapshot
2010-10-19 W. Trevor KingMove 'qwait' to pysawsim.manager.pbs and add the rest... commit | commitdiff | tree | snapshot
2010-10-19 W. Trevor KingFix a few deadlock errors in pysawsim.manager.thread. commit | commitdiff | tree | snapshot
2010-10-19 W. Trevor KingMove Histogram class from fit_force_histogram to new... commit | commitdiff | tree | snapshot
2010-10-19 W. Trevor KingJobManager.async_invoke() should accept Job instances. commit | commitdiff | tree | snapshot
2010-10-19 W. Trevor KingAdd pysawsim.manager and pysawsim.manager.thread for... commit | commitdiff | tree | snapshot
2010-10-18 W. Trevor KingAdd pysawsim/__init__.py and break invoke out into... commit | commitdiff | tree | snapshot
2010-10-18 W. Trevor KingAdd nosetests line to misc/hooks/REAMDE for pre-commit... commit | commitdiff | tree | snapshot
2010-10-18 W. Trevor KingIntroduce pysawsim in the README and add fit_force_hist... commit | commitdiff | tree | snapshot
2010-10-18 W. Trevor KingDocument suggested Git hooks. commit | commitdiff | tree | snapshot
2010-10-18 W. Trevor King"% pop. per s" -> "%% pop. per s" in printf() for k_mod... commit | commitdiff | tree | snapshot
2010-10-18 W. Trevor KingAdd prelimiary check_* code for each *.h file in sawsim.nw. commit | commitdiff | tree | snapshot
2010-10-18 W. Trevor KingCorrections to sawsim.bib after earlier pybtex run. commit | commitdiff | tree | snapshot
2010-10-18 W. Trevor KingAdd missing comma between references to tension and... commit | commitdiff | tree | snapshot
2010-10-17 W. Trevor KingAdd Tame the BeaST link and von-naming blurbs to README... commit | commitdiff | tree | snapshot
2010-10-16 W. Trevor KingPreserve space after \copy macro in sawsim.bib. commit | commitdiff | tree | snapshot
2010-10-16 W. Trevor KingConsolidated ...X macros and abbreviated journal/publis... commit | commitdiff | tree | snapshot
2010-10-16 W. Trevor KingPassed sawsim.bib through pybtex and updated keys in... commit | commitdiff | tree | snapshot
2010-10-16 W. Trevor KingCorrections to saswim.bib before reformating with pybtex. commit | commitdiff | tree | snapshot
2010-10-16 W. Trevor KingMoved BibTeX comments from src/sawsim.bib to README... commit | commitdiff | tree | snapshot
2010-10-14 W. Trevor KingAdd examples/Marszalek_Fernandez_1999/titin_intermediat... commit | commitdiff | tree | snapshot
2010-10-14 W. Trevor KingUpdate copyright/licensing blurbs with newer GPLv3+. commit | commitdiff | tree | snapshot
2010-10-14 W. Trevor KingAdded README.git to point Git newbies towards good... commit | commitdiff | tree | snapshot
2009-10-13 W. Trevor KingAdded inverse piston comments + whitespace in tension_b... commit | commitdiff | tree | snapshot
2009-09-25 W. Trevor KingFixed mispelled 'sec.transtion_rate' reference commit | commitdiff | tree | snapshot
2009-09-25 W. Trevor KingAdded cased equation to piston tension model description commit | commitdiff | tree | snapshot
2009-09-25 W. Trevor KingFixed typo in "Transition rate" section equation commit | commitdiff | tree | snapshot
2009-09-13 W. Trevor KingBumped to version 0.10. v0.10 commit | commitdiff | tree | snapshot
2009-09-13 W. Trevor KingAdded max dF "-F" option to sawsim. commit | commitdiff | tree | snapshot
2009-09-13 W. Trevor KingAdded full_chain_stiffness() to handle stiffness with... commit | commitdiff | tree | snapshot
2009-09-13 W. Trevor KingAdded piston tension model. commit | commitdiff | tree | snapshot
2009-08-21 W. Trevor King-P option now sets target P_N, not P_1. Bumped to... v0.9 commit | commitdiff | tree | snapshot
2009-08-19 W. Trevor KingExtended bell and const rate tests to multi-domain... commit | commitdiff | tree | snapshot
2009-08-13 W. Trevor KingThe (P_N = NP_1) bug that triggered 0.7 -> 0.8 isn... commit | commitdiff | tree | snapshot
2009-08-13 W. Trevor Kingsafe_strto*() now also checks for empty input commit | commitdiff | tree | snapshot
2009-08-13 W. Trevor KingSafer string to number conversion with ato*() -> safe_s... commit | commitdiff | tree | snapshot
2009-08-13 W. Trevor KingRemoved TODO in favor of BugsEverywhere bugtracking. commit | commitdiff | tree | snapshot
2009-08-13 W. Trevor KingFixed _major_ bug in multi-domain unfolding calculation... v0.8 commit | commitdiff | tree | snapshot
2009-08-03 W. Trevor Kinginverse_wlc now handles F=HUGE_VAL. commit | commitdiff | tree | snapshot
2009-03-24 W. Trevor KingAdded inverse tension functions for speed. Bumped... v0.7 commit | commitdiff | tree | snapshot
2009-03-09 W. Trevor KingFixed up the guts to support the new multi-state capabi... commit | commitdiff | tree | snapshot
2009-03-05 W. Trevor KingStarting on version 0.6, with generalized discrete... v0.6 commit | commitdiff | tree | snapshot
2009-02-25 W. Trevor KingAdded stiffness env. parameter and stiffness-corrected... v0.5 commit | commitdiff | tree | snapshot
2009-02-24 W. Trevor KingIncreased verbose output from tension_model_utils. commit | commitdiff | tree | snapshot
2009-02-24 W. Trevor KingCorrected some strings for tension_model_utils. commit | commitdiff | tree | snapshot
2009-02-02 W. Trevor KingFixed a few minor typos. commit | commitdiff | tree | snapshot
2008-11-11 W. Trevor KingAdded Fmax and Xmax options to tension_model_utils commit | commitdiff | tree | snapshot
2008-09-09 W. Trevor KingAdded testing scripts, comparing sawsim with theory commit | commitdiff | tree | snapshot
2008-09-07 W. Trevor KingRemoved debugging printfs from sawsim.c stepping commit | commitdiff | tree | snapshot
2008-09-06 W. Trevor KingAdded the option to make discrete steps in x. commit | commitdiff | tree | snapshot
2008-09-02 W. Trevor KingMade directory prerequisites order-only prerequisites. commit | commitdiff | tree | snapshot
2008-09-02 W. Trevor KingAdded a better introduction and UTF-8 capability in... commit | commitdiff | tree | snapshot
2008-09-02 W. Trevor KingFixed linker error running wlc check in check_sawsim. commit | commitdiff | tree | snapshot
2008-09-01 W. Trevor KingFixed some bugs with `make clean' commit | commitdiff | tree | snapshot
2008-09-01 W. Trevor KingMajor rewrite of the build system/Makefile reorganized. commit | commitdiff | tree | snapshot
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Sawsim, a Monte Carlo, mechanical protein unfolding simulator.