July 2014 - Molecuilder-devel

[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

1 0

[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

1 0

[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

1 0

[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

1 0

[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

1 0

[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

1 0

[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

1 0

[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

1 0

[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

1 0

[SCM] MoleCuilder branch stable created. v1.4.5-44-g2a03b00
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, stable has been created at 2a03b00b33c43f417fdf3452727473a2043f2638 (commit) - Log ----------------------------------------------------------------- commit 2a03b00b33c43f417fdf3452727473a2043f2638 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jun 29 04:44:41 2014 +0200 Set version to 1.4.6. - MoleCuilder library is now 13:4:1. - Codename "Robert Scott" (polar explorer, second to reach the south pole, was born 146 years ago) commit d8821e62974799dc0fa0b06ad6a9ec1bc73b57a8 Merge: c73e35f a61dbbe Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jul 14 13:16:23 2014 +0200 Merge branch 'Fragmentation_Automation_wo_JobMarket' into stable Conflicts: src/Actions/ActionQueue.cpp src/Actions/FragmentationAction/FragmentationAction.cpp src/Actions/PotentialAction/FitParticleChargesAction.cpp - in ActionQueue taking over both changes. - FragmentationAction added Status message where we don't complain for not having HAVE_JOBMARKET anymore. Removed. - FitParticleChargesAction had charge averaging and error message in case of no present fragments overlapping. commit a61dbbe03ddbe4f5f0a22574b63fb4d32e312493 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jul 13 15:03:31 2014 +0200 In CommandLineUI actions are skipped after failing action. - ActionQueue has queryable flag lastActionOk. - CommandLineWindow uses flag to check whether to queue further actions. - added regression test in the context of fragmentation-automation. commit abfc95ba5c74e7d73ba21441037391420169955e Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jul 13 09:50:39 2014 +0200 Added test for mpqc and fragmentation calculations in target extracheck. - calculations take some time, hence these tests are only executed in extracheck. - extracheck only does something in case of disable-jobmarket. commit 99692c9432d0e1c94ff5a06b6e7bc5ac1a6c1e27 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jul 13 01:17:29 2014 +0200 FIX: Preparation of temporary filename in SystemCommandJob now working correctly. commit d6a7b9066f589c9d821d442a8d23585ebd632c24 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jul 13 01:05:27 2014 +0200 Specifying executable and suffix in SystemCommandJob with MPQCCommandFragmentController. - now requiring JobMarket 1.1.5 (if given) for updated SystemCommandJob. - SystemCommandJob allows specifying a suffix to the temporary file. - this allows adding ".in" to MPQCCommandJob's temporary file name. commit 18ed8c7a1d88e9db52b1b57a548546f17406a526 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jul 7 22:43:47 2014 +0200 All HAVE_VMG also check for HAVE_JOBMARKET. - right now VMG is not activated when we lack JobMarket anyway, but this is actually safer. - FramentationLongRangeResults no longer compiled in when lacking VMG. commit 2e584e7ebd971c6cbd41f1ca6d93bb5fe7887849 Author: Frederik Heber <heber(a)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 bf0ff325add9c6c7128a5dc3877f74aa7589da2e Author: Frederik Heber <heber(a)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 1d17e57c9c64b6781a9d183fcf18872bae9cf9b9 Author: Frederik Heber <heber(a)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 c73e35f66c0f01f80b5db60d4be99c3921abcb85 Merge: 4e5bf51 26b4d62 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Jun 28 22:03:14 2014 +0200 Merge branch 'StatusToAllActions' into stable commit 4e5bf51bd8dbec42331f2d499ea6f0df4beabd08 Merge: 1b1fa57 0ef9127 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Jun 28 22:03:02 2014 +0200 Merge branch 'QtGUI_LogBox' into stable commit 0ef9127937748a00a4b5acfe70e56c991aed77b0 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 19 23:30:53 2014 +0200 QtLogBox catches mousePressEvent and selects atom in log. - this should ease graphical debugging a lot. commit e0b5f07b569ad48c9e5c6ed53968f1e215c43d1b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 19 23:00:14 2014 +0200 Added QtLogBox to QtMainWindow, using QDebugStream to display log. commit 7f8c9ad6477b6f1c9412bc613327680267c2d70f Author: Frederik Heber <heber(a)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(a)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(a)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(a)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(a)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(a)ins.uni-bonn.de> Date: Tue Apr 22 18:11:59 2014 +0200 Extracted ResultContainer from ReceiveResultContainer. commit d4eaf11f136baa85a4bdfa982418399b22a44110 Author: Frederik Heber <heber(a)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(a)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(a)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(a)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(a)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(a)ins.uni-bonn.de> Date: Wed Mar 5 22:36:44 2014 +0100 Enhanced error messages in FitParticleChargesAction. commit e1fe7e9e5ab6e5acab3403d31d4139a02a1c1754 Author: Frederik Heber <heber(a)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(a)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(a)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(a)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(a)ins.uni-bonn.de> Date: Thu Feb 27 20:07:56 2014 +0100 DOCU: Extended documentation on FunctionApproximation and potential fitting. commit 26b4d62081a948abd7e73ffa88b6aec3eb1e5234 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 19 15:56:27 2014 +0200 All Actions now give correct failure status via STATUS() macro. commit 0b6b770c3a01e40e913e85102527423a7acc09e0 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 19 15:55:01 2014 +0200 ActionQueue gives caught failure of Action and success via pushStatus(). commit 378f2d5ba8914489acde58f6de2d54c2e0ae84ba Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 19 13:02:54 2014 +0200 Updated all UI's StatusIndicator classes to use ActionStatusList. - CommandLineStatusIndicator and TextStatusIndicator just print the message. - QtStatusBar has a QTimer that updates the status message in second intervals. commit 26b4eb453c6d8c6ccdb34e5b8a56f055e76a561b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 19 11:17:06 2014 +0200 Added observable ActionStatusList to ActionQueue. - this allows to fetch Status messages from Actions at a central place. - Action::pushStatus() as befriended proxy to ActionQueue::pushStatus() added. - equipped ActionStatusList with a thread lock to protect access. commit 3ded2b779a607bf609e8dbfd11734a0b924f6597 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 19 14:28:15 2014 +0200 FIX: TxMenu and CommandLineWindow lacked waitQueue() in the wait-for-key loop. - this has occured due to queueAction() introduction. - otherwise the UI is destroyed before even the first Action has started. commit 1b1fa5704cd7e88e0af6f128b9e17b69d9aac345 Author: Frederik Heber <heber(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)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). ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

1 0