[Molecuilder-devel] [SCM] MoleCuilder branch Fragmentation_Automation_wo_JobMarket created. v1.4.5-28-gef0dc6a
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The branch, Fragmentation_Automation_wo_JobMarket has been created
at ef0dc6aec0daf62326d90b941f9d8b2e0cd8abfb (commit)
- Log -----------------------------------------------------------------
commit ef0dc6aec0daf62326d90b941f9d8b2e0cd8abfb
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Sun Apr 27 16:36:58 2014 +0200
Removed (very) old joiner and analyzer programs.
- they are not needed anymore when FragmentationAutomation works also without
JobMarket now.
commit 21854c7e3d111962fab06041bc7dab5f959cccee
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Wed Apr 23 13:57:20 2014 +0200
Using MPQCCommandFragmentController in FragmentationAutomationAction.
- FragmentationAction does not lament missing JobMarket and output-types.
commit b84db242bb23b3f493f94c9fd568ac2d27ea1d19
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Wed Apr 23 13:57:57 2014 +0200
Added MPQCCommandFragmentController.
- MPQCCommandFragmentController mimicks JobMarket's FragmentController or
SpecificFragmentController, respectively, without relying on JobMarket.
- modified FragmentJob to grant MPQCCommandFragmentController access to to
setId(). In JobMarket access is granted to FragmentController which we do
not inherit from here.
commit 7f8c9ad6477b6f1c9412bc613327680267c2d70f
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Sat Apr 26 19:19:09 2014 +0200
FIX: Need to purge FragmentationResultContainer.
- otherwise molecuilder stalls on quit.
- requires JobMarket includes for pyMoleCuilder.
commit 786d28e4533ffcfc1d63d95f08f65c92dd946946
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Wed Apr 23 13:24:32 2014 +0200
Lib..FragmentationAutomation and lib..Jobs now also compiled without JobMarket.
- FragmentationAutomationAction, MolecularDynamics.., and ParseFragmentJobs..
are also compiled, makes sense with upcoming MPQCCommandFragmentController.
- must not compile SpecificFragmentController or MPQCFragmentController
without JobMarket.
- now requires libboost_iostreams.
- this is due to MPQCCommandJob fiddling with streams to convert results.
commit 2cc7faa758cecbb1c378dc72c67f25dfd7cbd323
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Wed Apr 23 13:25:58 2014 +0200
LibJobMarket only compiled in if CONDJOBMARKET.
commit 1dfe00d53becf9875c49a1c974659affcd083a2b
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Wed Apr 23 13:43:17 2014 +0200
Added inclusion switch on HAVE_JOBMARKET for files depending on JobMarket.
- this is preparatory for using MPQCCommandJob without JobMarket.
- this is possible with several basic files taken over from JobMarket project.
- changes to ExportGraph_ToJobs, needs to export MPQCCommandJob when no
HAVE_JOBMARKET is given.
commit c3de511c88d74c7dd3ee27b035ff60e0ecf0b720
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Wed Apr 23 13:19:14 2014 +0200
Added FragmentJob, ..Result, JobId, SystemCommandJob, and types from JobMarket.
- taken over from version v1.1.4 with disclaimer adapted.
- changed include paths to JobMarket -> Jobs/JobMarket.
- these files are only used when no HAVE_JOBMARKET is defined.
- SystemCommandJob had Info, causing extra Chronos entry.
commit a498c1b15125817769fd9b27a366acd471b6b413
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Tue Apr 22 18:11:59 2014 +0200
Extracted ResultContainer from ReceiveResultContainer.
commit d4eaf11f136baa85a4bdfa982418399b22a44110
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Tue Apr 22 17:59:51 2014 +0200
Renamed ResultContainer -> ReceivedResultContainer.
- this belongs to SpecificFragmentController.
- renamed _ResultContainer_impl -> _ReceiveResultContainer_impl.
- FIX: also renamed inclusion guard.
commit a42feea2484491fdb28f92c73043956e00a2d922
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Thu Apr 24 23:56:03 2014 +0200
FIX: lib...FragmentationAutomation was linked in outside CONDJOBMARKET.
commit 37ef6d9c81dd05d5433115e175bac28b62275986
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Thu Mar 20 18:29:00 2014 +0100
Changed element class and periodentafel to have and use functions from ion.
- If ionization is zero, fall back to other function.
commit 31bd9c87bb06e45f77fe0e6e5b0d8ca6a9751ae7
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Thu Mar 20 18:28:44 2014 +0100
Added ion class, derived from element.
commit 9b68fc02f36ed091c9bb88104aedd4c88c66f0dd
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Wed Mar 5 23:12:01 2014 +0100
FitParticleChargesAction now averages over all fitted partial charges.
- i.e. we iterate over all fragments and not just fit the first.
commit 550f2a98ea5244ef1fc747f6debbc4635e941f7c
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Wed Mar 5 22:36:44 2014 +0100
Enhanced error messages in FitParticleChargesAction.
commit e1fe7e9e5ab6e5acab3403d31d4139a02a1c1754
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Thu Feb 27 21:15:41 2014 +0100
FunctionModel now uses list_of_arguments to split sequence of subsets of distances.
- this fixes ambiguities with the set of distances:
Imagine the distances within a water molecule as OH (A) and HH (B).
We then may have a sequence of argument_t as AABAAB. And with the current
implementation of CompoundPotential::splitUpArgumentsByModels() we would
always choose the latter (and more complex) model. Hence, we make two calls
to TriplePotential_Angle, instead of calls twice to PairPotential_Harmonic
for A, one to PairPotential_Harmonic for B, and once to TriplePotential_Angle
for AAB.
- now, we new list looks like A,A,B,AAB where each tuple of distances can be
uniquely associated with a specific potential.
- changed signatures of EmpiricalPotential::operator(), ::derivative(),
::parameter_derivative(). This involved changing all of the current specific
potentials and CompoundPotential.
- TrainingData must discern between the InputVector_t (just all distances) and
the FilteredInputVector_t (tuples of subsets of distances).
- FunctionApproximation now has list_of_arguments_t as parameter to evaluate()
and evaluate_derivative().
- DOCU: docu change in TrainingData.
commit 16227a32089e461901d97290d3e2fb626919cf26
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Thu Feb 27 22:44:28 2014 +0100
Removed FunctionModel::getSpecificExtractor() that is not needed anymore.
- it was only used in FitPotentialAction generating WorstFragmentMap.
- strangely required to change the order of some libraries
(libMolecuilderFragmentation_Summation needed further down).
commit f4496dfa7f4fdd324a537113b0d2419c2bc7496f
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Thu Feb 27 22:26:39 2014 +0100
Extracted associating each configuration with its L2 error into TrainingData.
commit 4e009d7565cb91ce80fa628407fbf1936e23d12c
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Thu Feb 27 18:46:49 2014 +0100
Extracted function from PotentialFitPotentialAction::performCall().
- new function getNumbersFromElements().
- also added warning when take-best-of and set-threshold have both been used.
commit 1ba8a154f0c3a28438bcfafdbb90182004c65f55
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Thu Feb 27 20:07:56 2014 +0100
DOCU: Extended documentation on FunctionApproximation and potential fitting.
commit 1b1fa5704cd7e88e0af6f128b9e17b69d9aac345
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Wed Jun 25 00:16:55 2014 +0200
TESTFIX: Reduced size of loaded file for regression test InvertMolecules to speed up.
commit 89604a46c1db5a85643b922ce06b5f4b5f0c5345
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Wed Jun 25 00:14:38 2014 +0200
TESTFIX: Changed size of loaded file for unselection AllMolecules regression test.
commit f678fc41737d988593634f12c8a2a6dbb76c282f
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Wed Jun 25 00:06:02 2014 +0200
TESTFIX: Reduced box size in FillRegularGrid to speed up regression test.
commit e4157b9b9699796a9b05157d81e33042b7670e3b
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Wed Jun 25 00:02:45 2014 +0200
TESTFIX: Reduced box size in DipoleCorrelation-DiscreteAngle regression test to speed up.
- the histogram files have not yet been changed.
commit 6d3cb81a37b7c7089163a6bbf61f4c8e6874cc81
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Tue Jun 24 23:57:37 2014 +0200
TESTFIX: reduced dbond file size in regression test Molecules/BondFile.
commit 2cc1cbe98dd0605266ded20ff583bfaf6b64fb77
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Tue Jun 24 23:29:38 2014 +0200
TESTFIX: FillSphericalSurface regression now with just 20 instead of 200 fill points.
commit 1dbbebbd0643e4b6a024acbe95232cacda8a7a10
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Tue Jun 24 23:41:19 2014 +0200
TESTFIX: reduced required threshold for fit-potential regression tests to speed up.
commit 0932c2cf081d696ef9cc91e7a5183c13064994e0
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Thu Jun 26 09:41:59 2014 +0200
FIX: RandomNumberEngine_Encapsulation::clone() did not set the seed obtained from its prototype.
- this caused all engines to always start with default seed of 1, irrespective
of the set parameter. The engine is always cloned from prototypes in the
factory that can be manipulated to change their parameters. Hence, clone
needs to set the seed (the engine's only parameter).
- EmpiricalPotentials now use RandomNumberGenerator to obtain random starting
values.
- TESTFIX: fit-potential regression tests now use fixed seed in order to always
take the same amount of time (some test runs in debug mode take very long
because of ill-chosen random values).
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