July 2014 - Molecuilder-devel

[SCM] MoleCuilder branch stable deleted. v1.4.5-39-g7679917
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 deleted was 7679917e5aa1ce2345802ab2c48608517aacbe8d ----------------------------------------------------------------------- 7679917e5aa1ce2345802ab2c48608517aacbe8d Set version to 1.4.6. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder annotated tag v1.4.6 deleted. v1.4.5-39-g7679917
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 deleted was 6caf27b827bcaa1a42fdea8aaaf1f72ee49bea18 ----------------------------------------------------------------------- tag v1.4.6 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: ef0dc6a 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) 7679917e5aa1ce2345802ab2c48608517aacbe8d Set version to 1.4.6. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch findBestMatching_HigherBondDegrees created. 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 created at a52809690c9890d164d5adc3ef4d68858467ab28 (commit) - Log ----------------------------------------------------------------- commit a52809690c9890d164d5adc3ef4d68858467ab28 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 9ab371329d441d507e00d0c773014931fe53b885 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 96933e4ad0480d6ddaf091cbce3b8cb91f40c1de 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 6e337eb825b876f15cc017c5dcf42c94887e2fa9 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 a357d48348d4ab1d33a547aab851e7359e69938d 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 5f27b80e1272989f1469d28a8070bee26389887f 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 fc4dabdabaf006cde45e260bd144ed916ae7f46f 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 ea7f2eaa785c39824664a05fd0199bbca9cab600 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 068d6a98b2561de75096cf2feed70f5d0b6e36e6 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 01d1633822d8cf611db8239ca8d7759695d34683 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 f393a74764cc237b373b2caa50517d264dc46104 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 6e11107f520a25d7c65dc2bb8ab091d6ae6cba4f 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 ce742321b59c93c48416d09bdbfcc0ac82112e70 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 bc0815d2311f08d93cf2cd6a74281fa4251c9675 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 7caa296033203e0ac6dce304e3fd5f588a3d72e3 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 34505299858705efb0f0d5d29fe36ef9793b890d 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 fffe3d9d682aa1a71f7e64e41dbbfce0b8846b51 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 d39cacc2fb69b8333e8b9e3d44e4d26c9af7e51e Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 5 19:16:26 2014 +0200 Implemented rotations via boost::quaternions. commit a71e9c34405db0e33eb012c59603e7ebd1f61167 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 46283ef58a03365c84f8451c3e28c22740a59f2d 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 0ea2467a134cd024391378d0822d5616fd2c62a4 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 96cfd10ca1ad1afe57b367af92101e285a75a964 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 8348951687390019138052fe80e6d2e15bf1c4cd 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 a3056142c29a56af99e8ff8b65a9fc68f9f57253 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 c73a121fefefd0d827f2a8beb5bd4f0d28f226c2 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu May 29 20:15:26 2014 +0200 Added unit tests for SphericalPointDistribution. commit 8a2639e9fff134196a43c8ce7569584f16562884 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 5870b5b1e66a76563dc034aadaaa4d645c9e83be 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 f46c4387ed4849a2b2ae189e31827a153fa65106 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 7414e5cd0fca8a4cfe755a3eb9423ccb6305b9db 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 ecf5333632140eaeb22aace2f2d10ca995c42ccd 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 65ce6501b46bf096e98a8dc363380b58c7ded4f4 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 33ea47fd820fb196d78a4545693e1273162c671c 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 e99d4f93951ff55ad8224cfa179c4804b375aeab 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 6f7f656a890de97442f4f63e64f6f086cfb6b8d9 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 84ea50df3e76dd78b71cbe859592887c56f81818 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 efeb2665aeeeb24d3497611030d993afc6a686c2 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 8c4fc3cf00fdeddea494c6eb9a3d6c86cb750ea7 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. v1.4.5-40-g2df8f03
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 2df8f03de678873fd4893bc695c15dfb2baed154 ----------------------------------------------------------------------- 2df8f03de678873fd4893bc695c15dfb2baed154 recurseMatching() now takes connections into account. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch findBestMatching_HigherBondDegrees created. v1.4.5-40-g2df8f03
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 2df8f03de678873fd4893bc695c15dfb2baed154 (commit) - Log ----------------------------------------------------------------- commit 2df8f03de678873fd4893bc695c15dfb2baed154 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 5cd0c01d3293a635c1da2bd793518ba04738eb37 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 9fc27da9dcd012345967223df0baee8879080630 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 acec70e202f4044f8d42bd6097a7f709d5f11ca9 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 9625bbfd02bb7b5b8fa07ca95aa7306a244627e0 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 844b94b994c6208cfe9f9856a5e5121d642bb6b0 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 4dc743debf9491456934d97ad37a255ca61c484f 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 2a2d8503882c4119a3e4f2966620f69c3e625958 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 340547df85785010d86e6f18436e01ff8db8af16 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 846c853264acf8d4799925a3601755226a34aafc 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 1e8c867ef68a86fdbeb4a98c7efe70b3eeae91bb 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 09ec9b7e0a368ac5cab79be100d8779e70fdfbbe Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Jul 12 13:55:44 2014 +0200 tempcommit: Extracted get() to extra module. commit 3639b9875db838404cee01dfc0b2c5c48284aa74 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jul 14 22:14:36 2014 +0200 Added case 0 and 1 to SphericalPointDistribution. commit d8167e1b6d304045dacb7222e37b5fcebb87616f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jul 14 22:14:26 2014 +0200 Added case 0 and 1 to saturateAtoms(). commit bf8c37e62015e75e80bc8e67b1045956987c5e47 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 3fbdfbe5c8eefa8f98578ee40e314821963b2a71 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 847a19cbecb25ff5e9fb700aefb5c17325fb2cd9 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 5b8d193a2b3b7a0700f232a00eabc3fa19b16cd7 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 9344a9969937b0960b1610c3d5d7df1c2a21de60 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 3ae3aa39aa73a6a83ec14400c3539d9839b0c5fe 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 e401aa70a6f25a1138e3493a693bd29a2b3a4ab7 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 5 19:16:26 2014 +0200 Implemented rotations via boost::quaternions. commit 900ee80bf6467c1da9ad01b86ea1e7a7041eb131 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 27ba2c799724cd9a6121c4e8b2a1d0865ff7d1c7 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 2a72eff1a77ee435c7dcc9e2d236de076026990d 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 cd80c552438d2363d47e01ec873c599f8c757d6e 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 22e6dac35e2644bbd09aab89dee66ffdd76627a0 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 fbb16d7138ca586231e19511978bbc20fb9975aa 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 31e59fb2b9c500d57e762be5059c1cb7ac11f675 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu May 29 20:15:26 2014 +0200 Added unit tests for SphericalPointDistribution. commit 465bc2529bae68c6028e31502ce9d336e3258808 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 5870b5b1e66a76563dc034aadaaa4d645c9e83be 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 f46c4387ed4849a2b2ae189e31827a153fa65106 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 7414e5cd0fca8a4cfe755a3eb9423ccb6305b9db 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 ecf5333632140eaeb22aace2f2d10ca995c42ccd 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 65ce6501b46bf096e98a8dc363380b58c7ded4f4 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 33ea47fd820fb196d78a4545693e1273162c671c 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 e99d4f93951ff55ad8224cfa179c4804b375aeab 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 6f7f656a890de97442f4f63e64f6f086cfb6b8d9 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 84ea50df3e76dd78b71cbe859592887c56f81818 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 efeb2665aeeeb24d3497611030d993afc6a686c2 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 8c4fc3cf00fdeddea494c6eb9a3d6c86cb750ea7 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 StatusToAllActions deleted. v1.4.5-13-g26b4d62
by git＠ins.uni-bonn.de 03 Jul '14

03 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, StatusToAllActions has been deleted was 26b4d62081a948abd7e73ffa88b6aec3eb1e5234 ----------------------------------------------------------------------- 26b4d62081a948abd7e73ffa88b6aec3eb1e5234 All Actions now give correct failure status via STATUS() macro. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch Decrease_Testsuite_Runtime deleted. v1.4.5-8-g1b1fa57
by git＠ins.uni-bonn.de 03 Jul '14

03 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, Decrease_Testsuite_Runtime has been deleted was 1b1fa5704cd7e88e0af6f128b9e17b69d9aac345 ----------------------------------------------------------------------- 1b1fa5704cd7e88e0af6f128b9e17b69d9aac345 TESTFIX: Reduced size of loaded file for regression test InvertMolecules to speed up. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch QtGUI_LogBox deleted. v1.4.5-10-g0ef9127
by git＠ins.uni-bonn.de 03 Jul '14

03 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, QtGUI_LogBox has been deleted was 0ef9127937748a00a4b5acfe70e56c991aed77b0 ----------------------------------------------------------------------- 0ef9127937748a00a4b5acfe70e56c991aed77b0 QtLogBox catches mousePressEvent and selects atom in log. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch Fragmentation_Automation_wo_JobMarket deleted. v1.4.5-28-gef0dc6a
by git＠ins.uni-bonn.de 03 Jul '14

03 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, Fragmentation_Automation_wo_JobMarket has been deleted was ef0dc6aec0daf62326d90b941f9d8b2e0cd8abfb ----------------------------------------------------------------------- ef0dc6aec0daf62326d90b941f9d8b2e0cd8abfb Removed (very) old joiner and analyzer programs. ----------------------------------------------------------------------- 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 03 Jul '14

03 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 6caf27b827bcaa1a42fdea8aaaf1f72ee49bea18 (tag) tagging 7679917e5aa1ce2345802ab2c48608517aacbe8d (commit) replaces v1.4.5 tagged by Frederik Heber on Thu Jul 3 15:36:12 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: ef0dc6a 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 (39): 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 MPQCCommandFragmentController. Using MPQCCommandFragmentController in FragmentationAutomationAction. Removed (very) old joiner and analyzer programs. 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 Merge branch 'Fragmentation_Automation_wo_JobMarket' into stable Set version to 1.4.6. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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