- Molecuilder-devel

[SCM] MoleCuilder branch Candidate_v1.4.7 created. v1.4.6-34-g8e20e36
by git＠ins.uni-bonn.de 18 Aug '14

18 Aug '14

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, Candidate_v1.4.7 has been created at 8e20e36dcc35c56d5a90a9967b3b89ff17846858 (commit) - Log ----------------------------------------------------------------- commit 8e20e36dcc35c56d5a90a9967b3b89ff17846858 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Aug 14 11:05:32 2014 +0200 FIX: QtTimeLine::recieveNotification() checked falsely against AtomObserver. - publisher is always the atom, not the relay. - that's why the time line did not get updated when a molecule with more than one timestep was loaded. commit fb55065f34f19f831cc839df4504c71af959e0ca Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Aug 13 17:08:14 2014 +0200 MPQCCommandFragmentController supports FragmentationAutomationAction being a Process. - i.e. it also calls an update handler when more results have been received. commit 3df57f2e7d807f5db30f539726be285674ae8227 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Aug 13 15:59:54 2014 +0200 FIX: PdbParser would write coordinates 4.1000 instead of 5.000. - we did round in printCoordinates(), without checking for overflow, resulting in 1000 for 999.9 instead of 999. - extended ParserPdbUnitTest to test these cases. commit c7212c1d7bc21c1f8e7249d31eae711aa179115f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Aug 11 19:56:03 2014 +0200 Giving the maximum components over all force vectors in ForceAnnealing. commit 24b66db290e0f96f9b9eed3221e779ca570dc9da Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Aug 10 15:17:52 2014 +0200 FIX: typos in AtomicForceManipulator.hpp. commit 51cfda11221ab02d7db630f150d0ba120ec6dff3 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Aug 10 14:47:43 2014 +0200 FIX: CheckOrderAtSite() called PrintAtomMask() with wrong AtomCount. commit 622e44a48d1737a7ede7a36df157afdbef7f88c7 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Aug 2 18:22:46 2014 +0200 Added MakroAction StructureOptimizationAction. - performs similarly as MolecularDynamicsAction only using ForceAnnealing. commit ffa509902bdaef0fce358b99bc31165d858391c7 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Aug 16 17:40:44 2014 +0200 FIX: MolecularDynamicsAction works also without JobMarket. - since FragmentationAutomation works without. commit 75869021a53f72dfd0b76aa0d1d11b0dcae8f5f8 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Aug 2 12:05:40 2014 +0200 Added ForceAnnealingAction. - also added regression test. - added output-every-step for debugging. commit c7390ef3bc9bd50283ccac940a2ad75a4d40d33b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Aug 2 12:01:05 2014 +0200 Added CodeCheck for ensuring testsuite..at's appear in tests/regression/Makefile.am. - brought files in tests/regression/Makefile.am in alphabetical order. - FIX: testsuite-potential.at was missing. commit 8a5780b12c77470597a7d4796295943179ed98ee Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Aug 2 11:43:22 2014 +0200 Extended VerletIntegrationAction wirth Undo/Redo. - using new UndoRedoHelpers for this. - VerletForceIntegration::operator() does not return bool anymore, check for empty atom set is done in Action. - TESTFIX: Removed XFAIl from regression tests verlet-integration. commit 9c308e95470d81793fa114b4a5bee29600e534d8 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Aug 2 10:00:14 2014 +0200 Extended UndoRedoHelpers. - added removeLastStep(), addNewStep(). - FIX: some UndoRedoHelper functions did not have const arguments as they should. - FIX: AtomicInfo did not set/store force vector of atom. - added AtomInfo::removeTrajectoryStep() and BondedParticleInfo::...() to allow for removal of a time step in the course of undoing. Enhanced AtomInfo, atom, and TesselPoint by removeSteps(), similar to UpdateSteps(). commit ea2b2a3230ff75e1a00a6a3d230028d9c9ef79f7 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Aug 2 08:54:30 2014 +0200 Sorted GlobalListOfActions. - note that Redo must remain at the front due to technical reasons. commit 50f5e97ca0b56ad057decac0decb279efee916bd Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Aug 2 07:05:12 2014 +0200 Added StructuralOptimizationAction. - performs a single optimization step. commit 343c5aa67b8af4355dabe12bc32e94678574ee19 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Aug 2 06:51:13 2014 +0200 Added CorrectBondDegreeAction and fixed Calculation tests. - pdb files do have bond graph but not the right degrees. - there also lies some ambiguity in here as double bonds depend on the chosen matching. commit 5d555048c6955ac3bda0b2cb4b3e6b20ab49880e Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Jul 18 19:45:45 2014 +0200 FragmentationAction now compiles global saturation positions information. commit a1d1dd8b043f6987e14d6d37973e71bd8ccad587 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jul 30 20:50:13 2014 +0200 Added SaturationDistanceMaximizer to determine best alphas for SaturatedBonds. - also added simple unit tests that ascertains that with just degree 1 bonds nothing happens. commit bac32f93be11686cd34925f6b8ddc570e886dce7 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jul 30 20:45:14 2014 +0200 Added SaturatedBond as container for a "dangling bond" and its saturation hydrogens. - most member variables are private, this prints them for debugging. commit a8f1d258e9e7fda6f62cbc12bf57a09cb5102256 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jul 23 23:50:08 2014 +0200 Added new Vector::IsParallelTo(). commit 98a293b9263c73baadd2152296722d9dd0d401e9 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Jul 18 19:08:09 2014 +0200 SaturatedFragment can deal with a global saturation position map. - so far, we create an empty one in FragmentationAction such that nothing's changed for the moment. - similarly in StoreSaturatedFragmentAction. However, there this is intended as only local information is required (it's only a single fragment). commit bdd5a84d9caf9791ea18d3a07979dee75f9bc54e Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jul 23 11:26:42 2014 +0200 FIX: VectorContent::Normalize() had int, not double. commit 3834b60a172eb5fc5a8f0c36a9bc18ca164bb189 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jul 17 23:52:05 2014 +0200 TESTFIX: extracheck threshold is _relative_ 1e-5. commit fec597f5b80c0f86e5d9e73637b0ffff32750b57 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Jul 12 13:56:14 2014 +0200 Added new convenience library libMolecuilderTesselation. - we need this for getting the connection information between the nearest neighboring points on the sphere. commit de2cbfe9e898e38b885f3727e766bc34f57f9c60 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu May 29 12:00:26 2014 +0200 Added SaturateFragment()::saturateAtom() replacing all cut bonds at once. - so far, we have just outsourced the loop over each cut bond into this function. commit 9e3fca9793f8283b21549888452621aad9772a63 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu May 29 12:30:49 2014 +0200 FIX: BondedParticleInfo::BondList is now a typedef. - removed the define. commit 9d32646c6dd4acfd9baa5f5b17e41207adee8b18 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu May 29 11:55:28 2014 +0200 Refactored SaturatedFragment::saturate() using list of cut bonds. - this is preparatory for replacing AddHydrogenReplacementAtom(). commit 3fbdca6228d7cb54dd1ec647f23636bf048cea6d Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Aug 26 21:53:59 2013 +0200 SaturatedFragment::AddHydrogenReplacementAtom() uses degree 1 if other is missing. commit 06804b923c9b82a6dd4f7d932a21781d6e4eae6e Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Aug 26 21:49:32 2013 +0200 Removed molecule::AddHydrogenReplacement() and BreadthFirstSearchAdd. - this capability has been transfered to SaturatedFragment, and BFSAdd has not been used for a long, long time. commit 9fd44f7f53b271add9c0ff9fe035e67c63361f09 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jul 10 19:06:56 2014 +0200 Vector::Is...() functions extended for numeric threshold. - if none given we use LINALG_MYEPSILON(), otherwise given to function. - this allows for rounding-sensible IsEqualTo() checking and more. commit 74d179f0dff39a6c2ff23bdd8c5bae931bc4bd12 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jul 30 20:48:11 2014 +0200 FIX: elements db uses wrong hbondangle for degree 1. - angle is cone's opening angle and needs to be zero for degree 1 because the cone is just a line. commit 3567e21ff36698dd519060d6ddaa4ba24e65685f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jul 3 19:13:39 2014 +0200 FIX: Plane's cstor did not check for linear dependence in a numerical stable way. - we check with NormSquared() and we use Projection() instead of Angle() to check whether vectors are linear dependent. commit c77d36e7ff07e14a81c2f181349203f9d7fd8a50 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Jun 13 13:22:14 2014 +0200 FIX: VectorContent::Normalize() did not check for zero factor. commit 72eada0a916425172fc2053704f4ca36992494be Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jun 23 20:00:48 2014 +0200 FIX: CodePatterns_LIBS was introduced in AM_LDFLAGS and not in LIBS. - this might have caused problems with libtool not correctly noting down this lib as a dependency. commit 8e2779350975a8ced8c8e2d73ad3c4b62c79ab34 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jul 30 20:46:56 2014 +0200 TESTFIX: Regression test series Calculations would not run in parallel. - we have to use $(MAKE), otherwise jobobserver cannot deduce whether it calls a make and does not pass "-j4" option. - regression tests Fragmentations now give status in color. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch findBestMatching_HigherBondDegrees created. v1.4.6-35-g74c4846
by git＠ins.uni-bonn.de 17 Jul '14

17 Jul '14

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, findBestMatching_HigherBondDegrees has been created at 74c4846adeb2221e23f1677599fd7e537726cdf2 (commit) - Log ----------------------------------------------------------------- commit 74c4846adeb2221e23f1677599fd7e537726cdf2 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Jul 12 21:07:44 2014 +0200 recurseMatching() now takes connections into account. - matchSphericalPointDistribution() replaced by getRemainingPoints() as that describes what it does. match...() sounds symmetrical which the function is no longer as connection is associated with former _newpolygon. - SphericalPointDistribution now has internal points and adjacency, initialized by initSelf(). - findBestMatching() and getRemainingPoints() are no longer static functions. - all unit tests are working again, including the .._multiple() that tests for joint points due to bond degree greater than 1. - the huge case switch in SaturatedFragment::saturateAtom() now resides in initSelf(). commit 424744e3e644f5aeacf274e71e4528dac465b5d9 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Jul 12 18:19:46 2014 +0200 Removed all IsZero() checking and special cases for the triangle idea. commit d99741e38395b7ff4ad22813907b2d69aa74ecbe Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Jul 12 13:57:54 2014 +0200 Added getConnections() to SphericalPointDistribution. - we use tesselation in order to extract the connection information between nearest neighboring points from the BoundaryLines of the tesselation. The triangles are ideal as they assure that no point lies within a triangle, hence all these points may be safely combined. - functions reside in extra module as with get(). - added extensive unit tests. - TESTS: Removed XFAIL from SphericalPointDistributionUnitTest. commit 89a48b431dc2b06e1269a4ab4d444bc47f2f6156 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Jul 12 13:56:14 2014 +0200 Added new convenience library libMolecuilderTesselation. - we need this for getting the connection information between the nearest neighboring points on the sphere. commit 2056d8e9728853377fc1c7c26c1322fe2f9faa76 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jul 10 00:08:37 2014 +0200 Added calculation of center of minimum distance by bisection. - this will give us a unique a definite point independent of the (rotational) position of the point set on the unit sphere. - added unit test. commit e31d6162f4205d7cd5a9ef15371d2ebcacdae280 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jul 9 23:14:53 2014 +0200 Refactoring SphericalPointDistribution to combine point list and subset of indices. - added struct PolygonWithIndices. - TESTS: marked SphericalPointDistributionUnitTest as XFAIL. commit c13adf75d483a6cba35a02e6844ac140f65dff9b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jun 30 11:35:42 2014 +0200 SphericalPointDistribution is now working with bond degree weights. - recurseMatching() now works on IndexTupleList_t. - also rewrote calculatePairwiseDistances() and calculateErrorOfMatching(). - L1THRESHOLD in recurseMatching() moved over to class body. - increased verbosity level of ...Matching() functions by one, added note on eventually chosen matching and why. - we assert that bestL2 is not too large. - FIX: calculateErrorOfMatching() did not use absolute value of gap for L1 error. - TESTS: Regresssion test FragmentMolecule-cycles working again. commit 7fb05b0f286d0e6547b2e9b3952075af4ca1185b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jun 29 23:20:49 2014 +0200 Extracted joinPoints() function to make it accessible to tests. - added unit test. - moved some function definitions around and added documentation. commit ebe0d1969ee9703650e8a896e779d0f0a2ce1b60 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jun 29 20:02:32 2014 +0200 Extended SphericalPointDistribution::Polygon_t to WeightedPolygon_t. - contains additionally the weights from the already present points. - in order to deal sensibly with present bonds of higher degree (>1) that shift neighboring occupied orbitals even further away, we additionally pass on the bond degree. This indicates how many points of the N points have to be accumulated for this on present bond. - TESTS: Regression test FragmentMolecule-cylces failing for the moment. commit aab590c67f29ff07b8a028477c2b48a6217c7727 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jun 24 18:39:55 2014 +0200 tempcommit: Removed skipping of scripts in tests/Fragmentation again. commit bab2632197ed02c9a56f56aab6c56481f23fec62 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 12 09:23:12 2014 +0200 Using the idea of three points giving a triangle to find rotation axis. - we calculate the center of either triangle and rotate the center of the ideal point distribution to match the one from the given points. - next we have the triangles normals as axis, take the first matching point and rotate align it. - we have to deal with a lot of special cases: What if only zero, one, or two points are given ... - in general we assume that the triangle lies relatively flat on the sphere's surface but what if the origin is in the triangle plane or even the calculated center is at the origin ... - TESTS: SphericalPointDistributionUnitTest working again, regression tests FragmentMolecule-cylces and StoreSaturatedFragment working. commit 7394e32f76d37ff35939c289494f79c1f40a7cc8 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 5 19:58:13 2014 +0200 Extended SphericalPointDistributionUnitTest to two and three matching points for all functions. - marked test as XFAIL for the moment. commit 61948b3ea29f85bd0eac1b9ef6623487c3362ba3 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 5 19:42:39 2014 +0200 Dropped quaternion rotation for simple arbitrary rotation axis and angle. - with newCenter, oldCenter and the cross product we have all we need: a rotation axis and an angle. We don't need to burden ourselves with those stupid, absolutely not working quaternions. - removeMatchingPoints() now works on an array. - Orientation rotation was wrong way round, added check. - TESTFIX: removed QuaternionTest from SphericalPointDistributionTest, marked FragmentMolecule-cycle and StoreSaturatedFragment regression tests as XFAIL. commit 6e6ac8887bcd442e8f99f5617bccb5cb993b45d9 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 5 19:18:40 2014 +0200 Added "arbitrary" rotation for matchSphericalPointDistributionsTest_2(). commit 58074bd81bc53778839be4e389dfca6e6a08fd41 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 5 19:17:10 2014 +0200 Adding QuaternionTest for SphericalPointDistributionUnitTest, fixed tests. - just first two components get flipped when first point is at (0,1,0). - removed XFAIL from FragmentMolecule and StoreSaturatedFragment regression tests. commit d887b9a8e45b626ce32175d07592cc0a2c84e05e Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 5 19:16:26 2014 +0200 Implemented rotations via boost::quaternions. commit 0f99c00acc8e10b6a3fdc43633148d8f96c156d7 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jun 4 13:23:31 2014 +0200 Added more unit test functions up to N=8 to SphericalPointDistributionUnitTest. - marked unit test as XFAIL. commit 2e2ab4c0c5db85d7d08340d6a9757b60dc8d2fa8 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jun 4 13:22:49 2014 +0200 Fixes to SaturatedFragment::saturateFragment(). - properly setting up the number of points and the "old" polygon. - properly filling in the hydrogen atoms at the calculated places. - We have the number of remaining bonds plus the rest. The rest is the valence minus the number of remaining bonds each weighted with its degree. This gives the right number of places to put hydrogens and fill up the valence. - TESTS: Removed XFAIL from FragmentMolecule cycles regression test. commit 9a970729e39cd12d20109261c377a9875f9b8d7b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jun 2 16:51:33 2014 +0200 FIX: SphericalPointDistribution succeeds with unit test. - removed XFAIL from FragmentationAutomation regression tests. commit 30cd476821124282d0339ca217f42b31781a4a2e Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri May 30 15:06:25 2014 +0200 Added Logging to SphericalPointDistribution for debugging. commit 8be52eb93e07efad5c321af8f08069a6eb6e34b6 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri May 30 15:31:15 2014 +0200 Moved all code from header of SphericalPointDistribution into cpp module. commit 43cef5bdab8a49793e3bf2ab01a351923606c17f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu May 29 20:15:49 2014 +0200 SphericalPointDistribution now has full functionality. - we look for a best matching between present points and desired ideal configuration, we rotate for alignment and fill all remaining vacant points with hydrogens. - TESTS: temporarily skipping all Fragmentation regression tests, FragmentationAutomation regression tests marked as XFAIL. commit fce8c1345985e3a228b3386a565613e2b279b057 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu May 29 20:15:26 2014 +0200 Added unit tests for SphericalPointDistribution. commit 1078546931ea95529f87659dbd77106c65322055 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu May 29 13:29:27 2014 +0200 Reimplemented SaturatedFragment::saturateAtom() and added ::setHydrogenReplacement(). - this is now based on an ideal distribution of electrons around an atom via the VSPER model which we match as closely as possible with the still bound neighboring atoms and fill all remaining vacant spots with hydrogens. - SaturatedFragment sets father simply to the _given_ atom. - TEST: dimethyl_bromomalonate marked as XFAIL. commit 5e493c056cc54287b7bf9b6271f93fe8dc2ff945 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu May 29 13:29:03 2014 +0200 Added matchSphericalPointDistributions() to SphericalPointDistribution. - so far we do nothing. commit b1f0cd777ea2c2da39e74352ad4ef59f3f95c8fc Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu May 29 13:11:39 2014 +0200 Added SphericalPointDistribution for points on spherical surface according to VSEPR. - this is taken from CreateVspeShape.py from Christian Neuen. commit d1a9684753cced0c8a32d168f5d719269ee83636 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu May 29 12:00:26 2014 +0200 Added SaturateFragment()::saturateAtom() replacing all cut bonds at once. - so far, we have just outsourced the loop over each cut bond into this function. commit 29dc30eb0a9af60e3d5d95705c3dc27681e79ec1 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu May 29 12:30:49 2014 +0200 FIX: BondedParticleInfo::BondList is now a typedef. - removed the define. commit 82627213ad32b651ea7dd756756f310db41361bc Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu May 29 11:55:28 2014 +0200 Refactored SaturatedFragment::saturate() using list of cut bonds. - this is preparatory for replacing AddHydrogenReplacementAtom(). commit 9ab2fb34a97f30798bf58a15dabc522338530163 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Aug 26 21:53:59 2013 +0200 SaturatedFragment::AddHydrogenReplacementAtom() uses degree 1 if other is missing. commit ca38704916242f977db4bf7c96bb0adea7dd0593 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Aug 26 21:49:32 2013 +0200 Removed molecule::AddHydrogenReplacement() and BreadthFirstSearchAdd. - this capability has been transfered to SaturatedFragment, and BFSAdd has not been used for a long, long time. commit 030ede0ba59a8d3ccca23d71162da9db37656473 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jul 10 19:06:56 2014 +0200 Vector::Is...() functions extended for numeric threshold. - if none given we use LINALG_MYEPSILON(), otherwise given to function. - this allows for rounding-sensible IsEqualTo() checking and more. commit 73fa9ef7159349c386272c868091c9cbd2df9ffa Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jul 3 19:13:39 2014 +0200 FIX: Plane's cstor did not check for linear dependence in a numerical stable way. - we check with NormSquared() and we use Projection() instead of Angle() to check whether vectors are linear dependent. commit 0fa470da645ae2613038cd51107035cf812961a2 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Jun 13 13:22:14 2014 +0200 FIX: VectorContent::Normalize() did not check for zero factor. commit 54705ccefd926c54e18d97c6ac2433c15a322695 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jun 23 20:00:48 2014 +0200 FIX: CodePatterns_LIBS was introduced in AM_LDFLAGS and not in LIBS. - this might have caused problems with libtool not correctly noting down this lib as a dependency. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch findBestMatching_HigherBondDegrees deleted. v1.4.6-37-g8437328
by git＠ins.uni-bonn.de 17 Jul '14

17 Jul '14

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, findBestMatching_HigherBondDegrees has been deleted was 84373283aed9dfacd2c29f96607356331923b332 ----------------------------------------------------------------------- 84373283aed9dfacd2c29f96607356331923b332 recurseMatching() now takes connections into account. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch findBestMatching_HigherBondDegrees created. v1.4.6-37-g8437328
by git＠ins.uni-bonn.de 16 Jul '14

16 Jul '14

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, findBestMatching_HigherBondDegrees has been created at 84373283aed9dfacd2c29f96607356331923b332 (commit) - Log ----------------------------------------------------------------- commit 84373283aed9dfacd2c29f96607356331923b332 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Jul 12 21:07:44 2014 +0200 recurseMatching() now takes connections into account. - matchSphericalPointDistribution() replaced by getRemainingPoints() as that describes what it does. match...() sounds symmetrical which the function is no longer as connection is associated with former _newpolygon. - SphericalPointDistribution now has internal points and adjacency, initialized by initSelf(). - findBestMatching() and getRemainingPoints() are no longer static functions. - all unit tests are working again, including the .._multiple() that tests for joint points due to bond degree greater than 1. - the huge case switch in SaturatedFragment::saturateAtom() now resides in initSelf(). commit ccccd2c961ffe80db854a7902cacbcf26c44ff73 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Jul 12 18:19:46 2014 +0200 Removed all IsZero() checking and special cases for the triangle idea. commit f3234b14f3c6731657a1772d6798b8dc48d5ed02 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Jul 12 13:57:54 2014 +0200 Added getConnections() to SphericalPointDistribution. - we use tesselation in order to extract the connection information between nearest neighboring points from the BoundaryLines of the tesselation. The triangles are ideal as they assure that no point lies within a triangle, hence all these points may be safely combined. - functions reside in extra module as with get(). - added extensive unit tests. commit 299a7418d1a00dade644adc26d036813970664b7 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Jul 12 13:56:14 2014 +0200 Added new convenience library libMolecuilderTesselation. - we need this for getting the connection information between the nearest neighboring points on the sphere. commit 9bb93c279b1a6f5c62bd8e6b0ac9c67ffd7aa462 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jul 10 00:08:37 2014 +0200 Added calculation of center of minimum distance by bisection. - this will give us a unique a definite point independent of the (rotational) position of the point set on the unit sphere. commit 79c70688bd13a002a24660be2c7eccc92bd5fcdb Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jul 9 23:14:53 2014 +0200 Refactoring SphericalPointDistribution to combine point list and subset of indices. - added struct PolygonWithIndices. commit 455400b95d97c90534c16a21a700e019cf50dc68 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jul 14 22:05:51 2014 +0200 FIX: Determining angle with respect to oldCenter and not projecting anymore. commit 30e64c99c35980d249eb3de86f93b718245dba44 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jul 3 19:17:04 2014 +0200 SphericalPointDistribution is now working with bond degree weights. - L1THRESHOLD in recurseMatching() moved over to class body. - increased verbosity level of ...Matching() functions by one, added note on eventually chosen matching and why. - we assert that bestL2 is not too large. - FIX: calculateErrorOfMatching() did not use absolute value of gap for L1 error. commit 34521176aca2aeaecb4a822b1c372f38fd1978cf Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jun 30 11:35:42 2014 +0200 recurseMatching() now works on IndexTupleList_t. - also rewrote calculatePairwiseDistances() and calculateErrorOfMatching(). commit e81c43f2e7435c5688ea6faeda1bfcd437c76469 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jun 29 23:20:49 2014 +0200 Extracted joinPoints() function to make it accessible to tests. - added unit test. - moved some function definitions around and added documentation. commit 09be85056bb9145bf23af92fc25cc64ef4ccfa3f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jun 29 20:02:32 2014 +0200 Extended SphericalPointDistribution::Polygon_t to WeightedPolygon_t. - contains additionally the weights from the already present points. - in order to deal sensibly with present bonds of higher degree (>1) that shift neighboring occupied orbitals even further away, we additionally pass on the bond degree. This indicates how many points of the N points have to be accumulated for this on present bond. commit 739623e1eccbc0e0214d2ee07d09962b2b74d38b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 12 09:23:12 2014 +0200 Using the idea of three points giving a triangle to find rotation axis. - we calculate the center of either triangle and rotate the center of the ideal point distribution to match the one from the given points. - next we have the triangles normals as axis, take the first matching point and rotate align it. - we have to deal with a lot of special cases: What if only zero, one, or two points are given ... - in general we assume that the triangle lies relatively flat on the sphere's surface but what if the origin is in the triangle plane or even the calculated center is at the origin ... commit 0221dd96e476cd906da483767c0720be67aa2efa Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 5 19:58:13 2014 +0200 Extended SphericalPointDistributionUnitTest to two and three matching points for all functions. commit 459cb215c5aaff35348da26627f899d062c1bab0 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jun 24 18:39:55 2014 +0200 tempcommit: Removed skipping of scripts in tests/Fragmentation again. commit 019956cbdd1f29b2e25d6fbebd00d9ee089c883f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 5 19:42:39 2014 +0200 Dropped quaternion rotation for simple arbitrary rotation axis and angle. - with newCenter, oldCenter and the cross product we have all we need: a rotation axis and an angle. We don't need to burden ourselves with those stupid, absolutely not working quaternions. - removeMatchingPoints() now works on an array. - Orientation rotation was wrong way round, added check. - TESTFIX: removed QuaternionTest from SphericalPointDistributionTest. commit 6e6ac8887bcd442e8f99f5617bccb5cb993b45d9 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 5 19:18:40 2014 +0200 Added "arbitrary" rotation for matchSphericalPointDistributionsTest_2(). commit 58074bd81bc53778839be4e389dfca6e6a08fd41 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 5 19:17:10 2014 +0200 Adding QuaternionTest for SphericalPointDistributionUnitTest, fixed tests. - just first two components get flipped when first point is at (0,1,0). - removed XFAIL from FragmentMolecule and StoreSaturatedFragment regression tests. commit d887b9a8e45b626ce32175d07592cc0a2c84e05e Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 5 19:16:26 2014 +0200 Implemented rotations via boost::quaternions. commit 0f99c00acc8e10b6a3fdc43633148d8f96c156d7 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jun 4 13:23:31 2014 +0200 Added more unit test functions up to N=8 to SphericalPointDistributionUnitTest. - marked unit test as XFAIL. commit 2e2ab4c0c5db85d7d08340d6a9757b60dc8d2fa8 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jun 4 13:22:49 2014 +0200 Fixes to SaturatedFragment::saturateFragment(). - properly setting up the number of points and the "old" polygon. - properly filling in the hydrogen atoms at the calculated places. - We have the number of remaining bonds plus the rest. The rest is the valence minus the number of remaining bonds each weighted with its degree. This gives the right number of places to put hydrogens and fill up the valence. - TESTS: Removed XFAIL from FragmentMolecule cycles regression test. commit 9a970729e39cd12d20109261c377a9875f9b8d7b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jun 2 16:51:33 2014 +0200 FIX: SphericalPointDistribution succeeds with unit test. - removed XFAIL from FragmentationAutomation regression tests. commit 30cd476821124282d0339ca217f42b31781a4a2e Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri May 30 15:06:25 2014 +0200 Added Logging to SphericalPointDistribution for debugging. commit 8be52eb93e07efad5c321af8f08069a6eb6e34b6 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri May 30 15:31:15 2014 +0200 Moved all code from header of SphericalPointDistribution into cpp module. commit 43cef5bdab8a49793e3bf2ab01a351923606c17f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu May 29 20:15:49 2014 +0200 SphericalPointDistribution now has full functionality. - we look for a best matching between present points and desired ideal configuration, we rotate for alignment and fill all remaining vacant points with hydrogens. - TESTS: temporarily skipping all Fragmentation regression tests, FragmentationAutomation regression tests marked as XFAIL. commit fce8c1345985e3a228b3386a565613e2b279b057 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu May 29 20:15:26 2014 +0200 Added unit tests for SphericalPointDistribution. commit 1078546931ea95529f87659dbd77106c65322055 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu May 29 13:29:27 2014 +0200 Reimplemented SaturatedFragment::saturateAtom() and added ::setHydrogenReplacement(). - this is now based on an ideal distribution of electrons around an atom via the VSPER model which we match as closely as possible with the still bound neighboring atoms and fill all remaining vacant spots with hydrogens. - SaturatedFragment sets father simply to the _given_ atom. - TEST: dimethyl_bromomalonate marked as XFAIL. commit 5e493c056cc54287b7bf9b6271f93fe8dc2ff945 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu May 29 13:29:03 2014 +0200 Added matchSphericalPointDistributions() to SphericalPointDistribution. - so far we do nothing. commit b1f0cd777ea2c2da39e74352ad4ef59f3f95c8fc Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu May 29 13:11:39 2014 +0200 Added SphericalPointDistribution for points on spherical surface according to VSEPR. - this is taken from CreateVspeShape.py from Christian Neuen. commit d1a9684753cced0c8a32d168f5d719269ee83636 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu May 29 12:00:26 2014 +0200 Added SaturateFragment()::saturateAtom() replacing all cut bonds at once. - so far, we have just outsourced the loop over each cut bond into this function. commit 29dc30eb0a9af60e3d5d95705c3dc27681e79ec1 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu May 29 12:30:49 2014 +0200 FIX: BondedParticleInfo::BondList is now a typedef. - removed the define. commit 82627213ad32b651ea7dd756756f310db41361bc Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu May 29 11:55:28 2014 +0200 Refactored SaturatedFragment::saturate() using list of cut bonds. - this is preparatory for replacing AddHydrogenReplacementAtom(). commit 9ab2fb34a97f30798bf58a15dabc522338530163 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Aug 26 21:53:59 2013 +0200 SaturatedFragment::AddHydrogenReplacementAtom() uses degree 1 if other is missing. commit ca38704916242f977db4bf7c96bb0adea7dd0593 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Aug 26 21:49:32 2013 +0200 Removed molecule::AddHydrogenReplacement() and BreadthFirstSearchAdd. - this capability has been transfered to SaturatedFragment, and BFSAdd has not been used for a long, long time. commit 030ede0ba59a8d3ccca23d71162da9db37656473 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jul 10 19:06:56 2014 +0200 Vector::Is...() functions extended for numeric threshold. - if none given we use LINALG_MYEPSILON(), otherwise given to function. - this allows for rounding-sensible IsEqualTo() checking and more. commit 73fa9ef7159349c386272c868091c9cbd2df9ffa Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jul 3 19:13:39 2014 +0200 FIX: Plane's cstor did not check for linear dependence in a numerical stable way. - we check with NormSquared() and we use Projection() instead of Angle() to check whether vectors are linear dependent. commit 0fa470da645ae2613038cd51107035cf812961a2 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Jun 13 13:22:14 2014 +0200 FIX: VectorContent::Normalize() did not check for zero factor. commit 54705ccefd926c54e18d97c6ac2433c15a322695 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jun 23 20:00:48 2014 +0200 FIX: CodePatterns_LIBS was introduced in AM_LDFLAGS and not in LIBS. - this might have caused problems with libtool not correctly noting down this lib as a dependency. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch findBestMatching_HigherBondDegrees deleted. v1.4.6-37-gd5ef4a3
by git＠ins.uni-bonn.de 16 Jul '14

16 Jul '14

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, findBestMatching_HigherBondDegrees has been deleted was d5ef4a3efb4603f5f958618979480f87c699ac96 ----------------------------------------------------------------------- d5ef4a3efb4603f5f958618979480f87c699ac96 recurseMatching() now takes connections into account. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch findBestMatching_HigherBondDegrees created. v1.4.6-37-gd5ef4a3
by git＠ins.uni-bonn.de 15 Jul '14

15 Jul '14

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, findBestMatching_HigherBondDegrees has been created at d5ef4a3efb4603f5f958618979480f87c699ac96 (commit) - Log ----------------------------------------------------------------- commit d5ef4a3efb4603f5f958618979480f87c699ac96 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Jul 12 21:07:44 2014 +0200 recurseMatching() now takes connections into account. - matchSphericalPointDistribution() replaced by getRemainingPoints() as that describes what it does. match...() sounds symmetrical which the function is no longer as connection is associated with former _newpolygon. - SphericalPointDistribution now has internal points and adjacency, initialized by initSelf(). - findBestMatching() and getRemainingPoints() are no longer static functions. - all unit tests are working again, including the .._multiple() that tests for joint points due to bond degree greater than 1. - the huge case switch in SaturatedFragment::saturateAtom() now resides in initSelf(). commit 516f247b50e86779a0147f0806840bed760e81ef Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Jul 12 18:19:46 2014 +0200 Removed all IsZero() checking and special cases for the triangle idea. commit 80c0e69bca946bbf7aa0aa91d19becc674eed496 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Jul 12 13:57:54 2014 +0200 Added getConnections() to SphericalPointDistribution. - we use tesselation in order to extract the connection information between nearest neighboring points from the BoundaryLines of the tesselation. The triangles are ideal as they assure that no point lies within a triangle, hence all these points may be safely combined. - functions reside in extra module as with get(). - added extensive unit tests. commit 322b9fb06eeef35851ea58dd9182d82de79d8cd2 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Jul 12 13:56:14 2014 +0200 Added new convenience library libMolecuilderTesselation. - we need this for getting the connection information between the nearest neighboring points on the sphere. commit 79279976192bde83e603b96a6b22b49ecc6e64b6 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jul 10 00:08:37 2014 +0200 Added calculation of center of minimum distance by bisection. - this will give us a unique a definite point independent of the (rotational) position of the point set on the unit sphere. commit d30d12f54d58725d885fcf0e3f105af3533274e5 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jul 9 23:14:53 2014 +0200 Refactoring SphericalPointDistribution to combine point list and subset of indices. - added struct PolygonWithIndices. commit 9b2aeb1d66532608da2e838c6a81f9d24f5c2401 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jul 14 22:05:51 2014 +0200 FIX: Determining angle with respect to oldCenter and not projecting anymore. commit cef6f8acb60dcf60b778e078c695128f6ed805c0 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jul 3 19:17:04 2014 +0200 SphericalPointDistribution is now working with bond degree weights. - L1THRESHOLD in recurseMatching() moved over to class body. - increased verbosity level of ...Matching() functions by one, added note on eventually chosen matching and why. - we assert that bestL2 is not too large. - FIX: calculateErrorOfMatching() did not use absolute value of gap for L1 error. commit bd7b460239c2d2aca1e5922d3215cf252fedf56c Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jun 30 11:35:42 2014 +0200 recurseMatching() now works on IndexTupleList_t. - also rewrote calculatePairwiseDistances() and calculateErrorOfMatching(). commit cf74238925491e585f8d2b8a9d8096f2df237e9c Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jun 29 23:20:49 2014 +0200 Extracted joinPoints() function to make it accessible to tests. - added unit test. - moved some function definitions around and added documentation. commit cc9de47a66814cd107d00cfa6563030a6c8cf912 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jun 29 20:02:32 2014 +0200 Extended SphericalPointDistribution::Polygon_t to WeightedPolygon_t. - contains additionally the weights from the already present points. - in order to deal sensibly with present bonds of higher degree (>1) that shift neighboring occupied orbitals even further away, we additionally pass on the bond degree. This indicates how many points of the N points have to be accumulated for this on present bond. commit e0b8eda1afb868ad636f6eeaba9c3bf5d42f0935 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 12 09:23:12 2014 +0200 Using the idea of three points giving a triangle to find rotation axis. - we calculate the center of either triangle and rotate the center of the ideal point distribution to match the one from the given points. - next we have the triangles normals as axis, take the first matching point and rotate align it. - we have to deal with a lot of special cases: What if only zero, one, or two points are given ... - in general we assume that the triangle lies relatively flat on the sphere's surface but what if the origin is in the triangle plane or even the calculated center is at the origin ... commit 1106f43fb13544e557265b96c1098137801f8416 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 5 19:58:13 2014 +0200 Extended SphericalPointDistributionUnitTest to two and three matching points for all functions. commit cd22f5284aa598b1595b1d671189ce6c1618e601 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jun 24 18:39:55 2014 +0200 tempcommit: All scripts in tests/Fragmentation added again. commit e2f42c883248c6342280494dc1235a592f110163 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 5 19:42:39 2014 +0200 Dropped quaternion rotation for simple arbitrary rotation axis and angle. - with newCenter, oldCenter and the cross product we have all we need: a rotation axis and an angle. We don't need to burden ourselves with those stupid, absolutely not working quaternions. - removeMatchingPoints() now works on an array. - Orientation rotation was wrong way round, added check. - TESTFIX: removed QuaternionTest from SphericalPointDistributionTest. commit 06e27c22eed72754e7b5e3857046f247cab94243 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 5 19:18:40 2014 +0200 Added "arbitrary" rotation for matchSphericalPointDistributionsTest_2(). commit 52dd5e856d25ef628ad6e8481695c827731ad503 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 5 19:17:10 2014 +0200 Adding QuaternionTest for SphericalPointDistributionUnitTest, fixed tests. - just first two components get flipped when first point is at (0,1,0). - removed XFAIL from FragmentMolecule and StoreSaturatedFragment regression tests. commit b4076c69448732077db22aaf10c8e40cb5727167 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 5 19:16:26 2014 +0200 Implemented rotations via boost::quaternions. commit c00b533e0955ac769db7c4f3f59efdf95bb10299 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jun 4 13:23:31 2014 +0200 Added more unit test functions up to N=8 to SphericalPointDistributionUnitTest. - marked unit test as XFAIL. commit 454602b1e42f69c69f8888662574c672a306dd04 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jun 4 13:22:49 2014 +0200 Fixes to SaturatedFragment::saturateFragment(). - properly setting up the number of points and the "old" polygon. - properly filling in the hydrogen atoms at the calculated places. - We have the number of remaining bonds plus the rest. The rest is the valence minus the number of remaining bonds each weighted with its degree. This gives the right number of places to put hydrogens and fill up the valence. - marked again all tests/Fragmentation scripts as XFAIL. commit 9a970729e39cd12d20109261c377a9875f9b8d7b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jun 2 16:51:33 2014 +0200 FIX: SphericalPointDistribution succeeds with unit test. - removed XFAIL from FragmentationAutomation regression tests. commit 30cd476821124282d0339ca217f42b31781a4a2e Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri May 30 15:06:25 2014 +0200 Added Logging to SphericalPointDistribution for debugging. commit 8be52eb93e07efad5c321af8f08069a6eb6e34b6 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri May 30 15:31:15 2014 +0200 Moved all code from header of SphericalPointDistribution into cpp module. commit 43cef5bdab8a49793e3bf2ab01a351923606c17f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu May 29 20:15:49 2014 +0200 SphericalPointDistribution now has full functionality. - we look for a best matching between present points and desired ideal configuration, we rotate for alignment and fill all remaining vacant points with hydrogens. - TESTS: temporarily skipping all Fragmentation regression tests, FragmentationAutomation regression tests marked as XFAIL. commit fce8c1345985e3a228b3386a565613e2b279b057 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu May 29 20:15:26 2014 +0200 Added unit tests for SphericalPointDistribution. commit 1078546931ea95529f87659dbd77106c65322055 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu May 29 13:29:27 2014 +0200 Reimplemented SaturatedFragment::saturateAtom() and added ::setHydrogenReplacement(). - this is now based on an ideal distribution of electrons around an atom via the VSPER model which we match as closely as possible with the still bound neighboring atoms and fill all remaining vacant spots with hydrogens. - SaturatedFragment sets father simply to the _given_ atom. - TEST: dimethyl_bromomalonate marked as XFAIL. commit 5e493c056cc54287b7bf9b6271f93fe8dc2ff945 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu May 29 13:29:03 2014 +0200 Added matchSphericalPointDistributions() to SphericalPointDistribution. - so far we do nothing. commit b1f0cd777ea2c2da39e74352ad4ef59f3f95c8fc Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu May 29 13:11:39 2014 +0200 Added SphericalPointDistribution for points on spherical surface according to VSEPR. - this is taken from CreateVspeShape.py from Christian Neuen. commit d1a9684753cced0c8a32d168f5d719269ee83636 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu May 29 12:00:26 2014 +0200 Added SaturateFragment()::saturateAtom() replacing all cut bonds at once. - so far, we have just outsourced the loop over each cut bond into this function. commit 29dc30eb0a9af60e3d5d95705c3dc27681e79ec1 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu May 29 12:30:49 2014 +0200 FIX: BondedParticleInfo::BondList is now a typedef. - removed the define. commit 82627213ad32b651ea7dd756756f310db41361bc Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu May 29 11:55:28 2014 +0200 Refactored SaturatedFragment::saturate() using list of cut bonds. - this is preparatory for replacing AddHydrogenReplacementAtom(). commit 9ab2fb34a97f30798bf58a15dabc522338530163 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Aug 26 21:53:59 2013 +0200 SaturatedFragment::AddHydrogenReplacementAtom() uses degree 1 if other is missing. commit ca38704916242f977db4bf7c96bb0adea7dd0593 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Aug 26 21:49:32 2013 +0200 Removed molecule::AddHydrogenReplacement() and BreadthFirstSearchAdd. - this capability has been transfered to SaturatedFragment, and BFSAdd has not been used for a long, long time. commit 030ede0ba59a8d3ccca23d71162da9db37656473 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jul 10 19:06:56 2014 +0200 Vector::Is...() functions extended for numeric threshold. - if none given we use LINALG_MYEPSILON(), otherwise given to function. - this allows for rounding-sensible IsEqualTo() checking and more. commit 73fa9ef7159349c386272c868091c9cbd2df9ffa Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jul 3 19:13:39 2014 +0200 FIX: Plane's cstor did not check for linear dependence in a numerical stable way. - we check with NormSquared() and we use Projection() instead of Angle() to check whether vectors are linear dependent. commit 0fa470da645ae2613038cd51107035cf812961a2 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Jun 13 13:22:14 2014 +0200 FIX: VectorContent::Normalize() did not check for zero factor. commit 54705ccefd926c54e18d97c6ac2433c15a322695 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jun 23 20:00:48 2014 +0200 FIX: CodePatterns_LIBS was introduced in AM_LDFLAGS and not in LIBS. - this might have caused problems with libtool not correctly noting down this lib as a dependency. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch findBestMatching_HigherBondDegrees deleted. v1.4.6-37-g32cfaab
by git＠ins.uni-bonn.de 15 Jul '14

15 Jul '14

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, findBestMatching_HigherBondDegrees has been deleted was 32cfaab88f63a122cc5885985b96503048d92a05 ----------------------------------------------------------------------- 32cfaab88f63a122cc5885985b96503048d92a05 recurseMatching() now takes connections into account. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch findBestMatching_HigherBondDegrees created. v1.4.6-37-g32cfaab
by git＠ins.uni-bonn.de 14 Jul '14

14 Jul '14

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, findBestMatching_HigherBondDegrees has been created at 32cfaab88f63a122cc5885985b96503048d92a05 (commit) - Log ----------------------------------------------------------------- commit 32cfaab88f63a122cc5885985b96503048d92a05 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Jul 12 21:07:44 2014 +0200 recurseMatching() now takes connections into account. - matchSphericalPointDistribution() replaced by getRemainingPoints() as that describes what it does. match...() sounds symmetrical which the function is no longer as connection is associated with former _newpolygon. - SphericalPointDistribution now has internal points and adjacency, initialized by initSelf(). - findBestMatching() and getRemainingPoints() are no longer static functions. - all unit tests are working again, including the .._multiple() that tests for joint points due to bond degree greater than 1. - the huge case switch in SaturatedFragment::saturateAtom() now resides in initSelf(). commit 7c73042ce3ecfd0229d9ffc11a0d6b519f339f9c Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Jul 12 18:19:46 2014 +0200 Removed all IsZero() checking and special cases for the triangle idea. commit 6750c12cb19911e7bb5d746995ab74bc6da56e48 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Jul 12 13:57:54 2014 +0200 Added getConnections() to SphericalPointDistribution. - we use tesselation in order to extract the connection information between nearest neighboring points from the BoundaryLines of the tesselation. The triangles are ideal as they assure that no point lies within a triangle, hence all these points may be safely combined. - functions reside in extra module as with get(). - added extensive unit tests. commit 36d6d262176326d6bca5d9fa3e6c1ffbc32d218a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Jul 12 13:56:14 2014 +0200 Added new convenience library libMolecuilderTesselation. - we need this for getting the connection information between the nearest neighboring points on the sphere. commit 0582456e28195231839168d506923f51e3734958 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jul 10 00:08:37 2014 +0200 Added calculation of center of minimum distance by bisection. - this will give us a unique a definite point independent of the (rotational) position of the point set on the unit sphere. commit 2b523bd65dcce9bf7c6cc1737860fafd93b58184 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jul 9 23:14:53 2014 +0200 Refactoring SphericalPointDistribution to combine point list and subset of indices. - added struct PolygonWithIndices. commit f9596827dae2cf9bcb2b4edb5638f646bf96754f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jul 14 22:05:51 2014 +0200 FIX: Determining angle with respect to oldCenter and not projecting anymore. commit c3ec1bbeddeaf487adf754a72062e8057ad715cc Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jul 3 19:17:04 2014 +0200 SphericalPointDistribution is now working with bond degree weights. - L1THRESHOLD in recurseMatching() moved over to class body. - increased verbosity level of ...Matching() functions by one, added note on eventually chosen matching and why. - we assert that bestL2 is not too large. - FIX: calculateErrorOfMatching() did not use absolute value of gap for L1 error. commit 42651d59cf8359611afa940937b329dd955e0588 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jun 30 11:35:42 2014 +0200 recurseMatching() now works on IndexTupleList_t. - also rewrote calculatePairwiseDistances() and calculateErrorOfMatching(). commit 8327a81827f6c3b48a510b008c3ad6864116d9b3 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jun 29 23:20:49 2014 +0200 Extracted joinPoints() function to make it accessible to tests. - added unit test. - moved some function definitions around and added documentation. commit abab6cc2c35cf1f86014477bfcbfe31ceb2d5816 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jun 29 20:02:32 2014 +0200 Extended SphericalPointDistribution::Polygon_t to WeightedPolygon_t. - contains additionally the weights from the already present points. - in order to deal sensibly with present bonds of higher degree (>1) that shift neighboring occupied orbitals even further away, we additionally pass on the bond degree. This indicates how many points of the N points have to be accumulated for this on present bond. commit ea30df3279ae1c1dd3b8b5a691e756830c4cbf69 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 12 09:23:12 2014 +0200 Using the idea of three points giving a triangle to find rotation axis. - we calculate the center of either triangle and rotate the center of the ideal point distribution to match the one from the given points. - next we have the triangles normals as axis, take the first matching point and rotate align it. - we have to deal with a lot of special cases: What if only zero, one, or two points are given ... - in general we assume that the triangle lies relatively flat on the sphere's surface but what if the origin is in the triangle plane or even the calculated center is at the origin ... commit 4eb8662e9ea6e43fdb6e875574c2e8c4fe9cd157 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 5 19:58:13 2014 +0200 Extended SphericalPointDistributionUnitTest to two and three matching points for all functions. commit 07df22983d48abb8c008a57c72374069f08af7c4 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jun 24 18:39:55 2014 +0200 tempcommit: All scripts in tests/Fragmentation added again. commit d8c1bad2c68f0c8174def8f6fde0bdbec8e4140b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 5 19:42:39 2014 +0200 Dropped quaternion rotation for simple arbitrary rotation axis and angle. - with newCenter, oldCenter and the cross product we have all we need: a rotation axis and an angle. We don't need to burden ourselves with those stupid, absolutely not working quaternions. - removeMatchingPoints() now works on an array. - Orientation rotation was wrong way round, added check. - TESTFIX: removed QuaternionTest from SphericalPointDistributionTest. commit 3eec68b7518abae29e0938025a6e94dce32d69fe Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 5 19:18:40 2014 +0200 Added "arbitrary" rotation for matchSphericalPointDistributionsTest_2(). commit 37b6ab4eb7884a58087a297211e2792e8c4e20ff Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 5 19:17:10 2014 +0200 Adding QuaternionTest for SphericalPointDistributionUnitTest, fixed tests. - just first two components get flipped when first point is at (0,1,0). commit 3e675ef05b13282c13d5f66303055b61955515b1 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 5 19:16:26 2014 +0200 Implemented rotations via boost::quaternions. commit f22a9f3f5a25efd7fdea746b77e7477637465e7f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jun 4 13:23:31 2014 +0200 Added more unit test functions up to N=8 to SphericalPointDistributionUnitTest. - marked unit test as XFAIL. commit 2f9510330f2000749bd70de7a77efef928cff83c Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jun 4 13:22:49 2014 +0200 Fixes to SaturatedFragment::saturateFragment(). - properly setting up the number of points and the "old" polygon. - properly filling in the hydrogen atoms at the calculated places. - We have the number of remaining bonds plus the rest. The rest is the valence minus the number of remaining bonds each weighted with its degree. This gives the right number of places to put hydrogens and fill up the valence. - marked again all tests/Fragmentation scripts as XFAIL. commit 5ee335e69787dd65e7fe1dd2d2e8a1f59867f62a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jun 2 16:51:33 2014 +0200 FIX: SphericalPointDistribution succeeds with unit test. - removed XFAIL from tests/Fragmentation scripts again. commit b805acbb7248f6ff6d0a99b6510098b8d92bbadc Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri May 30 15:06:25 2014 +0200 Added Logging to SphericalPointDistribution for debugging. commit 9420d52eda268e085ea3c30226ac7c25c33bdbba Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri May 30 15:31:15 2014 +0200 Moved all code from header of SphericalPointDistribution into cpp module. commit d663b8dbe908b90a550d679a1c1981af0df0e269 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu May 29 20:15:49 2014 +0200 SphericalPointDistribution now has full functionality. - we look for a best matching between present points and desired ideal configuration, we rotate for alignment and fill all remaining vacant points with hydrogens. - temporarily removed all tests/Fragmentation tests. commit fff44a135d0a59ea42e78f3efc8b080438425a13 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu May 29 20:15:26 2014 +0200 Added unit tests for SphericalPointDistribution. commit 2bba27e7f7f57c25ca0b57d3615f8ebe482597e8 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu May 29 13:29:27 2014 +0200 Reimplemented SaturatedFragment::saturateAtom() and added ::setHydrogenReplacement(). - this is now based on an ideal distribution of electrons around an atom via the VSPER model which we match as closely as possible with the still bound neighboring atoms and fill all remaining vacant spots with hydrogens. - SaturatedFragment sets father simply to the _given_ atom. commit 5e493c056cc54287b7bf9b6271f93fe8dc2ff945 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu May 29 13:29:03 2014 +0200 Added matchSphericalPointDistributions() to SphericalPointDistribution. - so far we do nothing. commit b1f0cd777ea2c2da39e74352ad4ef59f3f95c8fc Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu May 29 13:11:39 2014 +0200 Added SphericalPointDistribution for points on spherical surface according to VSEPR. - this is taken from CreateVspeShape.py from Christian Neuen. commit d1a9684753cced0c8a32d168f5d719269ee83636 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu May 29 12:00:26 2014 +0200 Added SaturateFragment()::saturateAtom() replacing all cut bonds at once. - so far, we have just outsourced the loop over each cut bond into this function. commit 29dc30eb0a9af60e3d5d95705c3dc27681e79ec1 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu May 29 12:30:49 2014 +0200 FIX: BondedParticleInfo::BondList is now a typedef. - removed the define. commit 82627213ad32b651ea7dd756756f310db41361bc Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu May 29 11:55:28 2014 +0200 Refactored SaturatedFragment::saturate() using list of cut bonds. - this is preparatory for replacing AddHydrogenReplacementAtom(). commit 9ab2fb34a97f30798bf58a15dabc522338530163 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Aug 26 21:53:59 2013 +0200 SaturatedFragment::AddHydrogenReplacementAtom() uses degree 1 if other is missing. commit ca38704916242f977db4bf7c96bb0adea7dd0593 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Aug 26 21:49:32 2013 +0200 Removed molecule::AddHydrogenReplacement() and BreadthFirstSearchAdd. - this capability has been transfered to SaturatedFragment, and BFSAdd has not been used for a long, long time. commit 030ede0ba59a8d3ccca23d71162da9db37656473 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jul 10 19:06:56 2014 +0200 Vector::Is...() functions extended for numeric threshold. - if none given we use LINALG_MYEPSILON(), otherwise given to function. - this allows for rounding-sensible IsEqualTo() checking and more. commit 73fa9ef7159349c386272c868091c9cbd2df9ffa Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jul 3 19:13:39 2014 +0200 FIX: Plane's cstor did not check for linear dependence in a numerical stable way. - we check with NormSquared() and we use Projection() instead of Angle() to check whether vectors are linear dependent. commit 0fa470da645ae2613038cd51107035cf812961a2 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Jun 13 13:22:14 2014 +0200 FIX: VectorContent::Normalize() did not check for zero factor. commit 54705ccefd926c54e18d97c6ac2433c15a322695 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jun 23 20:00:48 2014 +0200 FIX: CodePatterns_LIBS was introduced in AM_LDFLAGS and not in LIBS. - this might have caused problems with libtool not correctly noting down this lib as a dependency. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch findBestMatching_HigherBondDegrees deleted. v1.4.5-37-ga528096
by git＠ins.uni-bonn.de 14 Jul '14

14 Jul '14

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, findBestMatching_HigherBondDegrees has been deleted was a52809690c9890d164d5adc3ef4d68858467ab28 ----------------------------------------------------------------------- a52809690c9890d164d5adc3ef4d68858467ab28 recurseMatching() now takes connections into account. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder annotated tag v1.4.6 created. v1.4.6
by git＠ins.uni-bonn.de 14 Jul '14

14 Jul '14

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The annotated tag, v1.4.6 has been created at d566ce18134a7468b4fe77beebec3217a14abde9 (tag) tagging 2a03b00b33c43f417fdf3452727473a2043f2638 (commit) replaces v1.4.5 tagged by Frederik Heber on Mon Jul 14 22:23:30 2014 +0200 - Log ----------------------------------------------------------------- Fragmentation now works (serially) without JobMarket. QtGUI shows clickable log of Actions. All Actions give status messages in all GUIs. This version contains the following branches: a61dbbe Fragmentation_Automation_wo_JobMarket (If compiled without JobMarket fragmentation calculations are now possible directly from within molecuilder) 26b4d62 StatusToAllActions (All Actions revised to give meaningful status and failure messages) 0ef9127 QtGUI_LogBox (QtGUI has extra widget showing the console log and allows to click on atoms for highlighting) 1b1fa57 Decrease_Testsuite_Runtime (decreased the file sizes for all regression tests that took excessively long) Frederik Heber (44): FIX: RandomNumberEngine_Encapsulation::clone() did not set the seed obtained from its prototype. TESTFIX: reduced required threshold for fit-potential regression tests to speed up. TESTFIX: FillSphericalSurface regression now with just 20 instead of 200 fill points. TESTFIX: reduced dbond file size in regression test Molecules/BondFile. TESTFIX: Reduced box size in DipoleCorrelation-DiscreteAngle regression test to speed up. TESTFIX: Reduced box size in FillRegularGrid to speed up regression test. TESTFIX: Changed size of loaded file for unselection AllMolecules regression test. TESTFIX: Reduced size of loaded file for regression test InvertMolecules to speed up. FIX: TxMenu and CommandLineWindow lacked waitQueue() in the wait-for-key loop. Added observable ActionStatusList to ActionQueue. Updated all UI's StatusIndicator classes to use ActionStatusList. ActionQueue gives caught failure of Action and success via pushStatus(). All Actions now give correct failure status via STATUS() macro. DOCU: Extended documentation on FunctionApproximation and potential fitting. Extracted function from PotentialFitPotentialAction::performCall(). Extracted associating each configuration with its L2 error into TrainingData. Removed FunctionModel::getSpecificExtractor() that is not needed anymore. FunctionModel now uses list_of_arguments to split sequence of subsets of distances. Enhanced error messages in FitParticleChargesAction. FitParticleChargesAction now averages over all fitted partial charges. Added ion class, derived from element. Changed element class and periodentafel to have and use functions from ion. FIX: lib...FragmentationAutomation was linked in outside CONDJOBMARKET. Renamed ResultContainer -> ReceivedResultContainer. Extracted ResultContainer from ReceiveResultContainer. Added FragmentJob, ..Result, JobId, SystemCommandJob, and types from JobMarket. Added inclusion switch on HAVE_JOBMARKET for files depending on JobMarket. LibJobMarket only compiled in if CONDJOBMARKET. Lib..FragmentationAutomation and lib..Jobs now also compiled without JobMarket. FIX: Need to purge FragmentationResultContainer. Added QtLogBox to QtMainWindow, using QDebugStream to display log. QtLogBox catches mousePressEvent and selects atom in log. Merge branch 'QtGUI_LogBox' into stable Merge branch 'StatusToAllActions' into stable Added MPQCCommandFragmentController. Using MPQCCommandFragmentController in FragmentationAutomationAction. Removed (very) old joiner and analyzer programs. All HAVE_VMG also check for HAVE_JOBMARKET. Specifying executable and suffix in SystemCommandJob with MPQCCommandFragmentController. FIX: Preparation of temporary filename in SystemCommandJob now working correctly. Added test for mpqc and fragmentation calculations in target extracheck. In CommandLineUI actions are skipped after failing action. Merge branch 'Fragmentation_Automation_wo_JobMarket' into stable Set version to 1.4.6. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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