2008-04-28 20:40 vincefn * [r996] Fox/ChangeLog, Fox/example/Cimetidine-powder.xml, Fox/example/ktartrate.xml, Fox/src/Fox.cpp: Release 1.7.6.2. Update cimetidine and K tartrate files with new format for extracted data. 2008-04-28 19:21 vincefn * [r995] ObjCryst/wxCryst/wxPowderPattern.cpp: Set primitive centering before launching manual indexing. Use normal peaklist (with a maximum of 30 peaks) instead of a copy. 2008-04-27 23:09 vincefn * [r994] ObjCryst/ObjCryst/PowderPattern.cpp: Don't create Le Bail-extracted single crystal data if no extraction actually took place. 2008-04-27 22:08 vincefn * [r993] ObjCryst/ObjCryst/DiffractionDataSingleCrystal.cpp, ObjCryst/ObjCryst/DiffractionDataSingleCrystal.h, ObjCryst/ObjCryst/IO.cpp, ObjCryst/ObjCryst/PowderPattern.cpp, ObjCryst/ObjCryst/PowderPattern.h, ObjCryst/ObjCryst/ScatteringData.cpp, ObjCryst/ObjCryst/ScatteringData.h, ObjCryst/wxCryst/wxCrystal.cpp: Fourier maps: store extracted structure factors in a single crystal data object, allowing to calculate Fourier maps at a fixed resolution (keep high resolution to display maps, use lower to optimize the powder pattern). 2008-04-26 23:29 vincefn * [r992] ObjCryst/wxCryst/wxCrystal.cpp: Use wxWakeUpIdle() when OpenGL update does not take place fast enough 2008-04-24 21:32 vincefn * [r991] ObjCryst/ObjCryst/DiffractionDataSingleCrystal.cpp: Copy observed intensity to mFhklObsSq to enable drawing Fourier maps for single crystal data - also when importing or copying data. 2008-04-24 20:00 vincefn * [r990] ObjCryst/wxCryst/wxCrystal.cpp: Make sure there are reflections before computing calc Fourier map. 2008-04-23 21:11 vincefn * [r989] ObjCryst/ObjCryst/DiffractionDataSingleCrystal.cpp: Copy observed intensity to mFhklObsSq to enable drawing Fourier maps for single crystal data. 2008-04-23 21:10 vincefn * [r988] ObjCryst/wxCryst/wxCrystal.cpp: Auto-scale observed scale factors to get better Fourier maps. 2008-04-22 19:18 vincefn * [r987] Fox/Fox.sln, Fox/src/Fox.vcproj: Update vc++ project files. 2008-04-13 22:31 vincefn * [r986] Fox/ChangeLog, Fox/src/Fox.cpp, ObjCryst/ObjCryst/Molecule.cpp: Release 1.7.6.1. Make sure rigid groups stay rigid during a steepest descent optimization. 2008-04-13 19:48 vincefn * [r985] Fox/ChangeLog, Fox/src/Fox.cpp: Release 1.7.6 2008-04-13 19:26 vincefn * [r984] ObjCryst/wxCryst/wxCryst.cpp, ObjCryst/wxCryst/wxCryst.h, ObjCryst/wxCryst/wxRefinableObj.cpp, ObjCryst/wxCryst/wxRefinableObj.h: Nicer formatting for floating-point values when between 0.01 and 100 2008-04-13 19:20 vincefn * [r983] ObjCryst/ObjCryst/PowderPattern.cpp, ObjCryst/ObjCryst/PowderPattern.h: Correct peak shift due to sample displacement. 2008-04-13 16:01 vincefn * [r982] ObjCryst/wxCryst/wxCrystal.cpp, ObjCryst/wxCryst/wxCrystal.h: Force using double-buffering. Use a timeout for the wxcondition update to avoid locking optimisation (wx/gtk idle problem ?). Added (commented out) PDF display functions. 2008-04-13 15:42 vincefn * [r981] ObjCryst/wxCryst/wxGlobalOptimObj.cpp, ObjCryst/wxCryst/wxGlobalOptimObj.h: Catch exception when a parameter set cannot be restored. 2008-04-13 15:24 vincefn * [r980] ObjCryst/ObjCryst/Molecule.cpp, ObjCryst/ObjCryst/Molecule.h, ObjCryst/wxCryst/wxMolecule.cpp: Add a steepest descent algorithm for the molecule conformation. Use it from time to time to avoid that the molecule drifts too far away from a reasonable conformation - useful for long (>40 million trials) optimization. Set a maximum value for base angular rotations. 2008-04-13 15:20 vincefn * [r979] ObjCryst/ObjCryst/SpaceGroup.cpp: Be less verbose except for debug builds. 2008-04-13 15:15 vincefn * [r978] ObjCryst/RefinableObj/RefinableObj.cpp: Throw an exception rather than exit when a saved parameter set cannot be found. 2008-04-11 17:46 vincefn * [r977] ObjCryst/ObjCryst/Indexing.cpp: Use correct steps for monoclinic indexing 2008-04-10 20:43 vincefn * [r976] ObjCryst/ObjCryst/PowderPattern.cpp: Avoid NaN values for extracted intensities beyond max resolution. 2008-04-10 19:03 vincefn * [r975] ObjCryst/RefinableObj/GlobalOptimObj.cpp: Slower temperature changes for ANNEALING_SMART. 2008-04-01 20:00 vincefn * [r974] Fox/ChangeLog: Fix Changelog dates 2008-03-26 21:53 vincefn * [r973] Fox/src/Fox.cpp: Fox 1.7.5.3, revision 973 2008-03-26 21:49 vincefn * [r972] ObjCryst/CrystVector/CrystVector.cpp, ObjCryst/CrystVector/CrystVector.h: Add operator/= for vectors. 2008-03-26 21:16 vincefn * [r971] ObjCryst/rules-gnu.mak: Fix compilation for fftw when using shared=1. 2008-03-25 22:17 vincefn * [r970] ObjCryst/ObjCryst/PDF.cpp, ObjCryst/ObjCryst/PDF.h: First embryo of PDF classes. 2008-03-08 21:00 vincefn * [r969] Fox/gnu.mak, ObjCryst/rules-gnu.mak: Fix compilation order... 2008-03-08 20:41 vincefn * [r968] Fox/gnu.mak, Fox/src/gnu.mak, ObjCryst/rules-gnu.mak: Build libraries in order, allowing 'make -jN', also for Fox-nogui... 2008-03-07 20:52 vincefn * [r967] Fox/gnu.mak, ObjCryst/rules-gnu.mak: Build libraries in order, allowing 'make -jN' 2008-03-07 20:48 vincefn * [r966] ObjCryst/ObjCryst/PowderPattern.cpp: Avoid using unsigned integers in ::FindPeaks() so that some tests (e.g. i<0) actually mean something... 2008-03-07 20:35 vincefn * [r965] ObjCryst/ObjCryst/Atom.cpp, ObjCryst/ObjCryst/Molecule.cpp: Nicer atoms drawn in OpenGL window, using 10 layers. 2008-02-28 08:53 vincefn * [r964] Fox/src/Fox.cpp: Release 964, 1.7.5.2 2008-02-28 08:52 vincefn * [r963] Fox/src/Fox.cpp, ObjCryst/ObjCryst/PowderPattern.cpp, ObjCryst/ObjCryst/PowderPattern.h, ObjCryst/RefinableObj/LSQNumObj.cpp: Release 963. Make sure reflection profiles are correctly reported even if they start before the pattern. Handle NaN and Inf during least squares refinement. 2008-02-23 22:23 vincefn * [r962] Fox/src/Fox.cpp: Update Fox version to release 1.7.5.1 - revision 962. 2008-02-23 22:07 vincefn * [r961] ObjCryst/ObjCryst/PowderPattern.cpp: Remove CalcNbPointUsed from BeinOptimization() since it will be called anyway when preparing the powder pattern. 2008-02-21 07:34 vincefn * [r960] ObjCryst/ObjCryst/PowderPattern.cpp, ObjCryst/ObjCryst/PowderPattern.h: Use the clock on the number of pattern points used rather than the number of reflections used to recompute profiles. 2008-02-21 00:54 vincefn * [r959] ObjCryst/ObjCryst/PowderPattern.cpp: Correctly compute & use the number of reflections below the max[sin(theta)/lambda] 2008-02-20 21:43 vincefn * [r958] Fox/ChangeLog: update ChangeLog for release 2008-02-20 21:41 vincefn * [r957] ObjCryst/rules-gnu.mak: Make sure fftw is compiled before LibCryst 2008-02-20 19:06 vincefn * [r956] Fox/src/Fox.cpp: New release version 2008-02-19 22:21 vincefn * [r955] Fox/src/Fox.cpp, ObjCryst/ObjCryst/IO.cpp, ObjCryst/ObjCryst/ScatteringData.cpp: Save extracted intensities in xml files and try to keep them in memory as long as the lattice has not changed. 2008-02-17 23:37 vincefn * [r954] ObjCryst/wxCryst/wxPowderPattern.cpp: Correctly apply centering choice for monoclinic lattices. 2008-02-17 22:47 vincefn * [r953] Fox/src/Fox.cpp: Update revision. Add --index command-line argument, for triclinic tests (undocumented). 2008-02-17 22:12 vincefn * [r952] ObjCryst/ObjCryst/Indexing.cpp, ObjCryst/ObjCryst/Indexing.h, ObjCryst/wxCryst/wxPowderPattern.cpp: Improve indexing, allow searching centered lattices. 2008-02-17 22:04 vincefn * [r951] ObjCryst/ObjCryst/Molecule.cpp, ObjCryst/ObjCryst/PowderPattern.cpp, ObjCryst/wxCryst/wxMolecule.cpp: Avoid using --pos with iterators. 2008-02-15 21:02 vincefn * [r950] ObjCryst/wxCryst/wxCrystal.cpp: During optimization, only update Fourier maps if one is displayed or the Fourier win is opened. 2008-02-15 21:01 vincefn * [r949] ObjCryst/RefinableObj/GlobalOptimObj.cpp: Trigger a refresh of the display every *10* s even if no new best cost has been reached. 2008-02-15 20:29 vincefn * [r948] ObjCryst/RefinableObj/GlobalOptimObj.cpp, ObjCryst/wxCryst/wxCrystal.cpp: Inhibit immediate update of 3D display when the crystal structure is being updated. Trigger a refresh of the 3D display every 5s even if no new best cost has been reached. 2008-02-15 20:21 vincefn * [r947] ObjCryst/wxCryst/wxMultiGraph.cpp: Call event.skip() to make sure the default handler is called for mouse & key events. This makes sure the window gets the focus from a mouse event. 2008-02-15 19:47 vincefn * [r946] ObjCryst/ObjCryst/Crystal.cpp: Correct calculation of distance table. 2008-02-14 20:09 vincefn * [r945] ObjCryst/ObjCryst/Indexing.cpp, ObjCryst/ObjCryst/Indexing.h: Improve indexing in triclinic case. 2008-02-06 21:35 vincefn * [r944] ObjCryst/wxCryst/wxPowderPattern.cpp: Inhibit profile fitting mode after closing cell explorer window 2008-02-05 19:50 vincefn * [r943] ObjCryst/wxCryst/wxCrystal.cpp, ObjCryst/wxCryst/wxPowderPattern.cpp: Call event.skip() so that events are passed to the default handlers. Most notably, this ensures left-clicking will switch the focus to the window. 2008-02-03 19:53 vincefn * [r942] ObjCryst/wxCryst/wxPowderPattern.cpp: Catch exceptions thrown during LSQ refinement. Launch Le Bail + profile fitting when the automatic box is checked, if a cell has been already highlighted. Increase maximum angle value for auto-indexing. Hide differential evolution algorithm. 2008-02-03 11:26 vincefn * [r941] ObjCryst/ObjCryst/PowderPattern.cpp, ObjCryst/ObjCryst/PowderPattern.h, ObjCryst/ObjCryst/ScatteringData.cpp, ObjCryst/ObjCryst/ScatteringData.h: Make sure the pattern is computed up to the supplied maximum resolution, also computing reflections centered above the limit but with a profile extending below the limit... Prevent NaN values during LeBail extraction. 2008-02-03 11:22 vincefn * [r940] ObjCryst/wxCryst/wxCrystal.cpp: Prevent opening the Fourier maps dialog during an optimization. 2008-02-03 11:21 vincefn * [r939] ObjCryst/RefinableObj/LSQNumObj.cpp, ObjCryst/RefinableObj/LSQNumObj.h: Add access to the compilation of all parameters. Restore initial configuration before throwing an exception during a refinement. 2008-01-15 20:25 vincefn * [r937] Fox/macosx.mak, Fox/src/Fox.cpp: Do not include Fox-nogui in the disk image 2008-01-14 22:58 vincefn * [r936] Fox/src/Fox.cpp: Never update status text from outside the main thread. 2008-01-07 21:52 vincefn * [r934] Fox/Fox.xcodeproj/project.pbxproj: Disable ZeroLink 2008-01-05 21:12 vincefn * [r933] Fox/macosx.mak: Uncompress cctbx and newmat packages as needed 2008-01-05 20:58 vincefn * [r932] Fox/Fox.xcodeproj/project.pbxproj: Remove unwanted test files from newmat 2008-01-04 12:07 vincefn * [r931] Fox/src/gnu.mak, ObjCryst/rules-gnu.mak: Compile fftw as needed 2008-01-03 22:48 vincefn * [r930] ObjCryst/wxCryst/wxCrystal.cpp, ObjCryst/wxCryst/wxCrystal.h: Correct position of Fourier maps when atom names are displayed. Add some code to automatically save POVRay files when optimising structures. 2008-01-02 22:12 vincefn * [r929] Fox/example/Cimetidine-powder.xml: Update Cimetidine powder data example with full data. 2008-01-02 21:54 vincefn * [r928] Fox/src/Fox.cpp, ObjCryst/ObjCryst/ScatteringData.cpp, ObjCryst/ObjCryst/ScatteringData.h, ObjCryst/wxCryst/wxCrystal.cpp, ObjCryst/wxCryst/wxCrystal.h: Allow using sharpened Fourier maps. Use fobs-fcalc (and not fcalc-fobs) for difference maps. Use more meaningful names for available maps. 2008-01-01 23:08 vincefn * [r927] ObjCryst/wxCryst/wxCrystal.cpp: Display Fourier maps from *all* available diffraction data. 2008-01-01 21:45 vincefn * [r926] Fox/Fox-Info.plist, Fox/macosx.mak, ObjCryst/rules-gnu.mak: Update makefiles for OSX 2008-01-01 21:43 vincefn * [r925] Fox/Fox.xcodeproj/project.pbxproj: Update project for XCode 3.0, single arch building 2008-01-01 17:55 vincefn * [r924] ObjCryst/wxCryst/wxCrystal.cpp: Really update Fourier maps... 2008-01-01 00:37 vincefn * [r923] Fox/src/Fox.cpp: Fix display of Fox revision 2008-01-01 00:37 vincefn * [r922] ObjCryst/wxCryst/wxCrystal.cpp: Correctly add calculated Fourier maps. 2007-12-31 22:50 vincefn * [r921] ObjCryst/wxCryst/wxPowderPattern.cpp, ObjCryst/wxCryst/wxPowderPattern.h: Add direct access to profile fitting from powder pattern graph and powder pattern object. 2007-12-31 22:48 vincefn * [r920] ObjCryst/wxCryst/wxCrystal.cpp: Use floor(x+.5) rather than nons-standard round() function 2007-12-29 20:39 vincefn * [r919] ObjCryst/ObjCryst/IO.cpp: Include a revision number in the ObjCryst file, for future use. 2007-12-29 20:37 vincefn * [r918] Fox/src/Fox.cpp: Make About Box modal. Only create wxInternetFSHandler if necessary. 2007-12-29 11:23 vincefn * [r917] ObjCryst/wxCryst/wxCrystal.cpp: Use powers of 2,3,5 to compute an optimal size for the fast Fourier transforms. 2007-12-28 23:53 vincefn * [r916] ObjCryst/wxCryst/wxCrystal.cpp: Optimize Fourier maps resolution depending on unit cell parameters. 2007-12-28 22:23 vincefn * [r915] ObjCryst/wxCryst/wxCrystal.cpp: More thread-safe Fourier maps modifications. 2007-12-26 22:33 vincefn * [r914] ObjCryst/wxCryst/wxCrystal.cpp: Thread-safe Fourier maps modifications. 2007-12-26 22:03 vincefn * [r913] ObjCryst/wxCryst/wxCrystal.cpp, ObjCryst/wxCryst/wxMolecule.cpp: Fix conversion of std::string to wxString 2007-12-24 11:05 vincefn * [r912] ObjCryst/wxCryst/wxCrystal.cpp: Use depth mask also when displaying Fourier maps... 2007-12-23 23:20 vincefn * [r911] ObjCryst/wxCryst/wxCrystal.cpp: Coorectly display wxMiniFrame under windows by adding wxSystemMenu (wx bug). Don't stay on top 2007-12-23 23:08 vincefn * [r910] Fox/src/Fox.cpp: Check for updates in a separate thread. 2007-12-23 19:56 vincefn * [r909] ObjCryst/rules-gnu.mak, ObjCryst/wxCryst/wxCrystal.cpp, ObjCryst/wxCryst/wxCrystal.h: Change the user interface for Fourier maps ; add support for calculated, observed and difference Fourier maps, live updated. 2007-12-23 19:44 vincefn * [r908] Fox/src/Fox.cpp: Include mechanism to check for updates, automatically or not. 2007-12-04 22:57 vincefn * [r905] Fox/src/Fox.cpp: 1.7.1.1 2007-12-04 22:56 vincefn * [r904] ObjCryst/ObjCryst/Crystal.cpp: Sanitize distance calculations. Should now also work with all combinations of lattice translations 2007-12-03 21:11 vincefn * [r903] Fox/ChangeLog: 1.7.1 Changelog. 2007-12-03 21:01 vincefn * [r902] ObjCryst/ObjCryst/PowderPattern.cpp: When importing a pattern from a CIF file, only set weight to 1/sigma^2 when _all_ points have been read. 2007-12-03 20:27 vincefn * [r901] Fox/src/Fox.cpp: Fox version 1.7.1. Report statistics with TAU. 2007-12-03 19:49 vincefn * [r900] ObjCryst/ObjCryst/CIF.cpp: Accept DDL2 type tags as if they were DDL1... Back-ported from openbabel. 2007-12-03 19:39 vincefn * [r899] ObjCryst/ObjCryst/Crystal.cpp: Do take into account translations to compute distance tables. 2007-11-06 22:46 vincefn * [r898] ObjCryst/wxCryst/wxMolecule.cpp: Reduce back the number of dihedral angles listed, but give choices about atoms to be rotated. 2007-11-06 21:23 vincefn * [r897] ObjCryst/wxCryst/wxMolecule.cpp: Give more choice to the user to set dihedral angles in the molecule. 2007-10-31 22:08 vincefn * [r896] ObjCryst/wxCryst/wxMolecule.cpp: Make sure frame is displayed with close box also under windows. 2007-10-26 22:00 vincefn * [r895] ObjCryst/wxCryst/wxMolecule.cpp: Allow user to change manually a dihedral angle. 2007-10-25 19:36 vincefn * [r894] ObjCryst/wxCryst/wxMolecule.cpp, ObjCryst/wxCryst/wxMolecule.h: Add user-controlled rotation of atoms around any existing bond 2007-10-25 19:12 vincefn * [r893] ObjCryst/ObjCryst/Molecule.cpp, ObjCryst/ObjCryst/Molecule.h: Move ExpandAtomGroupRecursive() declaration to Molecule.h. 2007-10-25 19:04 vincefn * [r892] ObjCryst/Quirks/Chronometer.h: Use boost for a more precise measure of time. Requires boost/date_time/posix_time/posix_time_types.hpp 2007-09-30 20:58 vincefn * [r891] ObjCryst/wxCryst/wxPowderPattern.cpp: Disable profile fitting after closing the profile fitting window. 2007-09-30 20:42 vincefn * [r890] ObjCryst/ObjCryst/PowderPattern.cpp, ObjCryst/ObjCryst/PowderPattern.h, ObjCryst/ObjCryst/ScatteringData.cpp, ObjCryst/ObjCryst/ScatteringData.h: Add a base access (in ScatteringData) to observed intensities. For powder patterns this corresponds to extracted (Le Bail, etc...) intensities. 2007-09-30 20:08 vincefn * [r889] ObjCryst/ObjCryst/SpaceGroup.cpp, ObjCryst/ObjCryst/SpaceGroup.h: Add computing of equivalent reflections from a given structure factor. 2007-09-30 20:02 vincefn * [r888] ObjCryst/RefinableObj/RefinableObj.cpp, ObjCryst/RefinableObj/RefinableObj.h: Add access functions to objects in registries. 2007-09-30 20:01 vincefn * [r887] ObjCryst/RefinableObj/GlobalOptimObj.cpp: Use min and max delays in seconds between display updates. 2007-07-06 21:49 vincefn * [r886] ObjCryst/Quirks/VFNStreamFormat.cpp: Use a more correct formatting 2007-07-05 22:24 vincefn * [r885] Fox/src/Fox.cpp: Add --cif2pattern option to Fox, auto-generating a powder pattern for every crystal structure loaded from an xml or CIF file. 2007-07-04 22:20 vincefn * [r884] ObjCryst/ObjCryst/PowderPattern.cpp, ObjCryst/ObjCryst/ReflectionProfile.cpp, ObjCryst/wxCryst/wxPowderPattern.cpp: Do not update the display of a powder pattern too quickly. This avoids actually calculating the powder pattern before we got the chance to switch from pseudo-voigt to DE-PV, when using TOF data. 2007-06-22 22:31 vincefn * [r883] ObjCryst/ObjCryst/PowderPattern.cpp, ObjCryst/ObjCryst/ScatteringData.cpp, ObjCryst/wxCryst/wxPowderPattern.cpp: Small changes for a more stable indexing and associated Le Bail extraction. 2007-06-22 22:28 vincefn * [r882] ObjCryst/wxCryst/wxCrystal.cpp: Initial files for FOx Grid, (c) Jan Rohlicek. 2007-06-06 19:26 vincefn * [r879] ObjCryst/ObjCryst/PowderPattern.cpp, ObjCryst/RefinableObj/LSQNumObj.cpp, ObjCryst/wxCryst/wxPowderPattern.cpp: Better profile-fitting, less verbose. 2007-06-06 19:25 vincefn * [r878] ObjCryst/ObjCryst/ReflectionProfile.cpp: Set default width to 0.01° for pseudo-Voigt. 2007-06-03 20:45 vincefn * [r877] ObjCryst/ObjCryst/PowderPattern.cpp, ObjCryst/ObjCryst/PowderPattern.h, ObjCryst/wxCryst/wxPowderPattern.cpp, ObjCryst/wxCryst/wxPowderPattern.h: Allow profile-fitting of diffracting phases, either manually or automatically when indexing. 2007-06-03 20:44 vincefn * [r876] ObjCryst/RefinableObj/LSQNumObj.cpp, ObjCryst/RefinableObj/LSQNumObj.h: Allow LSQ algorithm to work on copies rather than references of parameters, to avoid changing flags for the parameter in the original object. 2007-06-03 20:42 vincefn * [r875] ObjCryst/RefinableObj/RefinableObj.cpp, ObjCryst/RefinableObj/RefinableObj.h: Allow copying rather than referencing parameters when copying all parameters from one object to another. 2007-05-28 20:53 vincefn * [r874] ObjCryst/RefinableObj/LSQNumObj.cpp: Be less verbose in silent==false mode. Always display "human" values for the report. 2007-05-28 20:51 vincefn * [r873] ObjCryst/ObjCryst/ReflectionProfile.cpp: Force using same formula even for small or no asymmetry. Fix calculation of gaussian asymmetric profile. 2007-05-15 22:58 vincefn * [r872] ObjCryst/wxCryst/wxCryst.cpp, ObjCryst/wxCryst/wxCryst.h: Add WXCrystObjBasic::SetToolTip() as a _virtual_ function, for correct inheritance since wxWindow::SetToolTip() is not virtual... 2007-05-15 21:37 vincefn * [r871] ObjCryst/ObjCryst/Indexing.cpp: In DichoIndexed, fail the dichotomy test if two successive lines have been indexed with a single identical hkl triplet. 2007-05-15 21:22 vincefn * [r870] ObjCryst/wxCryst/wxCryst.cpp, ObjCryst/wxCryst/wxCryst.h, ObjCryst/wxCryst/wxRefinableObj.cpp, ObjCryst/wxCryst/wxRefinableObj.h: Fix use of wxTooltip - on windows, static text widgets do not receive motion events which inhibits tooltips. Overload wxWindow::SetToolTip() to make sure the tooltip is always set to sub-window receiving the motion event (entry fiels, button, ..) 2007-04-28 23:21 vincefn * [r869] ObjCryst/ObjCryst/Indexing.cpp, ObjCryst/ObjCryst/Indexing.h, ObjCryst/wxCryst/wxPowderPattern.cpp: Improve indexing, particularly for triclinic cells. All cells except triclinic work well. 2007-04-17 19:36 vincefn * [r868] ObjCryst/ObjCryst/Indexing.cpp: Fix triclinic indexing 2007-04-16 20:43 vincefn * [r867] ObjCryst/ObjCryst/Indexing.cpp: Faster indexing using more strict limits, better search intervals. 2007-04-13 14:22 vincefn * [r866] ObjCryst/ObjCryst/Indexing.cpp, ObjCryst/wxCryst/wxPowderPattern.cpp: Correct buffer overflow, wrong --iterator, and radiobox vertical display. 2007-04-13 11:31 vincefn * [r865] ObjCryst/ObjCryst/Indexing.cpp, ObjCryst/ObjCryst/Indexing.h, ObjCryst/ObjCryst/PowderPattern.cpp, ObjCryst/wxCryst/wxPowderPattern.cpp, ObjCryst/wxCryst/wxPowderPattern.h: Improve indexing - more options & informations passed to the user. 2007-04-10 20:36 vincefn * [r864] ObjCryst/ObjCryst/Indexing.cpp, ObjCryst/ObjCryst/Indexing.h, ObjCryst/wxCryst/wxPowderPattern.cpp: Improve auto-indexing (automatic sweep of crystal systems, faster dichotomy). 2007-04-08 20:22 vincefn * [r863] ObjCryst/ObjCryst/Indexing.cpp, ObjCryst/ObjCryst/Indexing.h, ObjCryst/ObjCryst/PowderPattern.cpp, ObjCryst/wxCryst/wxPowderPattern.cpp: Improve peak search & auto-indexing. Menu remains hidden by default. 2007-04-07 22:27 vincefn * [r862] ObjCryst/ObjCryst/CIF.cpp, ObjCryst/ObjCryst/CIF.h: Import wavelength from CIF when possible. Correctly import weight/sigma when iobs is _pd_meas_counts_total. 2007-04-01 21:06 vincefn * [r861] ObjCryst/CrystVector/CrystVector.cpp: Correct finding index of maximum when start point>0 2007-03-31 09:25 vincefn * [r860] ObjCryst/ObjCryst/CIF.cpp: Also recognize _pd_meas_2theta_scan as 2theta value in CIF files 2007-03-25 20:59 vincefn * [r859] ObjCryst/wxCryst/wxCrystal.cpp, ObjCryst/wxCryst/wxCrystal.h: Fix editing scattering powers parameters 2007-03-25 19:57 vincefn * [r858] ObjCryst/ObjCryst/PowderPattern.cpp: Correct debugging message 2007-03-12 22:56 vincefn * [r857] ObjCryst/ObjCryst/PowderPattern.cpp, ObjCryst/ObjCryst/ReflectionProfile.cpp: Adapt the number of points for which the profile is calculated for _each_ reflection, instead of extrapolating between the beginning and the end of the pattern. 2007-03-12 20:45 vincefn * [r856] ObjCryst/ObjCryst/ReflectionProfile.cpp: Better handle negative fwhm's. 2007-03-08 23:22 vincefn * [r855] Fox/src/Fox.cpp: Fix reading from gzip-compressed file, correctly change filename when needed. 2007-03-06 23:24 vincefn * [r854] ObjCryst/wxCryst/wxDiffractionSingleCrystal.cpp, ObjCryst/wxCryst/wxDiffractionSingleCrystal.h: Add graph representing Iobs and Icalc as a function of 1/d for single crystal data. 2007-02-28 23:33 vincefn * [r853] Fox/src/Fox.cpp: Set fox version even if __FOXVERSION__ is not set. Correctly add new single crystal structure. 2007-02-25 21:23 vincefn * [r852] ObjCryst/ObjCryst/DiffractionDataSingleCrystal.cpp, ObjCryst/ObjCryst/DiffractionDataSingleCrystal.h: Compute best scale factor on each GetChi2(), not just after each global optimization random move. 2007-02-23 20:24 vincefn * [r851] Fox/ChangeLog, Fox/ObjCryst-Fox.spec: Last changes for 1.7.0 2007-02-23 11:30 vincefn * [r850] Fox/src/Fox.cpp, Fox/src/gnu.mak: Changes for release 1.7.0 : update rpm spec file, release version info, and disabled indexing functions. 2007-02-23 11:30 vincefn * [r849] Fox/ChangeLog, Fox/ObjCryst-Fox.spec, Fox/gnu.mak, ObjCryst/wxCryst/wxPowderPattern.cpp: Changes for release 1.7.0 : update rpm spec file, release version info, and disabled indexing functions. 2007-02-23 11:02 vincefn * [r848] ObjCryst/wxCryst/wxPowderPattern.cpp, ObjCryst/wxCryst/wxPowderPattern.h: Enable different scales for x and y axis in powder pattern graph - using for x either 2Theta/TOF or Q=1/d or Q=1/2d, and fot y either I or sqrt(I) or log10(I) 2007-02-20 22:24 vincefn * [r847] Fox/Fox.sln, Fox/Fox.xcodeproj/project.pbxproj, Fox/ObjCryst-Fox.spec, Fox/gnu.mak, Fox/src/Fox.vcproj, Fox/src/gnu.mak, ObjCryst/CrystVector/gnu.mak, ObjCryst/ObjCryst/ScatteringPower.cpp, ObjCryst/ObjCryst/gnu.mak, ObjCryst/Quirks/gnu.mak, ObjCryst/RefinableObj/gnu.mak, ObjCryst/example/fluorine/gnu.mak, ObjCryst/example/gnu.mak, ObjCryst/example/pbso4/gnu.mak, ObjCryst/gnu.mak, ObjCryst/rules-gnu.mak, ObjCryst/wxCryst/gnu.mak: Use a new directory layout for the Fox/ObjCryst++ distribution. All libraries are available from the top directory and respect the objcryst subversion layout, i.e. with Fox and ObjCryst in the same directory - allows updating using 'svn update' from the top directory. 2007-02-11 20:38 vincefn * [r846] CVSROOT, Fox/src-doc: Remove obsolete directories 2007-02-07 19:29 vincefn * [r845] Fox/src/Fox.cpp: Release version 1.7.0 2007-02-05 22:36 vincefn * [r844] ObjCryst/ObjCryst/CIF.cpp, ObjCryst/ObjCryst/SpaceGroup.cpp, ObjCryst/wxCryst/wxCrystal.cpp: Use Hermann-Mauguin symbol rather than Hall, when possible (avoid symbols such as with a <"> in the middle..) 2007-01-22 23:50 vincefn * [r843] ObjCryst/ObjCryst/Crystal.cpp: Correctly take into account distances >10 Angstroems (not calculated) for CIF and text output 2007-01-19 22:13 vincefn * [r842] ObjCryst/ObjCryst/UnitCell.cpp: Correct interpretation of trigonal cells, using a default hexagonal setting, and user-chosen rhomboedral setting if the ":R" extension is used (for spacegroups 146, 148, 155, 160, 161, 166 & 167 only). 2007-01-10 23:26 vincefn * [r841] ObjCryst/ObjCryst/Indexing.cpp: Use reverse_iterator instead of const_reverse_iterator to fix compilation with Xcode. 2007-01-09 23:46 vincefn * [r840] ObjCryst/ObjCryst/Crystal.cpp: Do not count atoms several times in distance table. 2007-01-09 23:29 vincefn * [r839] ObjCryst/wxCryst/wxCrystal.cpp, ObjCryst/wxCryst/wxMolecule.cpp, ObjCryst/wxCryst/wxPowderPattern.cpp: Fixes for wxWidgets 2.8.0 - include wx/notebook.h, and use wxWIndow::SetLabel() instead of SetTitle() 2007-01-09 23:27 vincefn * [r838] ObjCryst/rules-gnu.mak: Add newmat to list of linked libraries. 2007-01-09 23:27 vincefn * [r837] ObjCryst/ObjCryst/PowderPattern.cpp: Use the correct number of reflections for integrated intensities, i.e. those for which the profile has actually been computed. 2007-01-08 21:52 vincefn * [r836] ObjCryst/rules-gnu.mak: Add "-I/usr/X11R6/include" 2007-01-07 23:25 vincefn * [r835] ObjCryst/ObjCryst/Crystal.cpp, ObjCryst/ObjCryst/Crystal.h, ObjCryst/ObjCryst/ScatteringData.cpp, ObjCryst/ObjCryst/SpaceGroup.cpp, ObjCryst/ObjCryst/SpaceGroup.h: Correct interatomic distance table calculations, store floating point symmetry operations in the spacegroup object. 2007-01-04 20:53 vincefn * [r834] Fox/src/gnu.mak: Require newmat for Fox compilation, as it is used for lsq during auto-indexing. 2006-12-23 16:09 vincefn * [r833] ObjCryst/ObjCryst/Indexing.cpp, ObjCryst/ObjCryst/Indexing.h, ObjCryst/wxCryst/wxPowderPattern.cpp: In Score(), make sure to stop increasing h,k,l indices only when d2 is increasing with k or l (for cells with angles !=90°). Allow user to supply both minimum depth and minimum score to report a solution. Do not report any solution in dicvol if one has been found deeper. 2006-12-23 16:06 vincefn * [r832] ObjCryst/ObjCryst/PowderPattern.cpp: Use width/2 as sigma on peak position. 2006-12-23 02:03 vincefn * [r831] ObjCryst/ObjCryst/PowderPattern.cpp: Remove use of sigma for peak detection. 2006-12-23 01:50 vincefn * [r830] ObjCryst/ObjCryst/Indexing.cpp: Correct dmax*1.05 in Score(), and fix size of stopOnDepth vector. 2006-12-22 22:58 vincefn * [r829] ObjCryst/ObjCryst/Indexing.cpp, ObjCryst/ObjCryst/Indexing.h, ObjCryst/ObjCryst/PowderPattern.cpp, ObjCryst/wxCryst/wxPowderPattern.cpp: Allow user to specify the score and dicvol depth on which to stop the indexing. 2006-12-20 00:01 vincefn * [r828] ObjCryst/ObjCryst/PowderPattern.cpp, ObjCryst/wxCryst/wxPowderPattern.cpp: Correctly create reflection profiles. 2006-12-19 23:35 vincefn * [r827] ObjCryst/wxCryst/wxPowderPattern.cpp: Correctly auto-initialize & display double-exponential profile with TOF data. 2006-12-19 23:12 vincefn * [r826] ObjCryst/ObjCryst/PowderPattern.cpp: Correct isnan for win32.. 2006-12-19 22:35 vincefn * [r825] ObjCryst/ObjCryst/PowderPattern.cpp: Avoid NaN & infinite scale factors. 2006-12-18 21:10 vincefn * [r824] Fox/src/Fox.cpp: Correctly recognize compressed (.xml.gz) files when loading them from the top menu. 2006-12-18 20:38 vincefn * [r823] ObjCryst/ObjCryst/PowderPattern.cpp: Only compute really useful reflection profiles, below sin(theta)/lambda, and recompute profiles as needed. 2006-12-18 20:07 vincefn * [r822] Fox/src/Fox.cpp: When asked to close, just remove all objects, don't exit Fox. 2006-12-18 19:50 vincefn * [r821] ObjCryst/ObjCryst/Atom.cpp: Do not re-initialize refinable parameter list if they are already declared. 2006-12-17 22:35 vincefn * [r820] ObjCryst/wxCryst/wxPowderPattern.cpp: Update display after auto-selecting DE-PV when adding a crystalline phase. 2006-12-17 22:30 vincefn * [r819] ObjCryst/ObjCryst/PowderPattern.cpp, ObjCryst/ObjCryst/PowderPattern.h, ObjCryst/ObjCryst/ReflectionProfile.cpp, ObjCryst/ObjCryst/ReflectionProfile.h, ObjCryst/wxCryst/wxPowderPattern.cpp: Limit generated list of reflections to d_hkl>0.5A (stol<1), to avoid too large number of reflections e.g. for high resolution TOF data. Automatically choose DE-PV profile for TOF. Update unit cell in DE-PV profile object when changing crystal. 2006-12-17 00:17 vincefn * [r818] ObjCryst/wxCryst/wxPowderPattern.cpp: Move PSI format in menu with the rest of neutron data formats. 2006-12-17 00:11 vincefn * [r817] ObjCryst/ObjCryst/PowderPattern.cpp, ObjCryst/wxCryst/wxPowderPattern.cpp: Fix background computation when using TOF data. Fix order when importing gsas TOF data. Various fixes for automatic Bayesian background, updating the display of interpolation points,... 2006-12-16 09:18 vincefn * [r816] Fox/src/Fox.vcproj: Update vcproj file, including cif.cpp and indexing.cpp files. 2006-12-16 09:06 vincefn * [r815] ObjCryst/ObjCryst/PowderPattern.cpp: Correctly initialize min intensity when searching for peaks. 2006-12-16 08:51 vincefn * [r814] ObjCryst/ObjCryst/PowderPattern.cpp: Fix out-of-bound vector access. 2006-12-16 01:09 vincefn * [r813] ObjCryst/ObjCryst/Indexing.cpp: Fix std c++ errors for compilation. 2006-12-16 00:32 vincefn * [r812] ObjCryst/ObjCryst/Indexing.cpp, ObjCryst/ObjCryst/Indexing.h, ObjCryst/ObjCryst/PowderPattern.cpp, ObjCryst/ObjCryst/PowderPattern.h, ObjCryst/ObjCryst/bc32.mak, ObjCryst/ObjCryst/gnu.mak, ObjCryst/wxCryst/wxPowderPattern.cpp, ObjCryst/wxCryst/wxPowderPattern.h: Add auto-indexing algorithms (dicvol, differential evolution) and graphical interface, all still experimental... Add import of GSAS powder pattern data with bintype=RALF and TYPE=ALT for Isis data. 2006-12-09 22:36 vincefn * [r811] ObjCryst/ObjCryst/CIF.cpp: When no symbol is given, use the labels listed in the cif file to guess the atom symbol. 2006-11-17 20:04 vincefn * [r810] Fox/src/Fox.cpp: Force correct extension of filename (.xml or .xml.gz) 2006-11-14 20:32 vincefn * [r809] ObjCryst/ObjCryst/Crystal.cpp: Correctly compute interatomic distances (and therefore dynamical occupancy correction), even when parallelepipedic asymmetric unit lower corner is not (0,0,0). 2006-11-13 23:57 vincefn * [r808] ObjCryst/ObjCryst/CIF.cpp, ObjCryst/ObjCryst/CIF.h: Update CIF reading, not line-by-line anymore but directly using the stream. Allows better parsing. 2006-11-12 10:43 vincefn * [r807] Fox/Fox-Info.plist, Fox/Fox.xcodeproj/project.pbxproj: Update XCode project files for XCode 2.4.1. Added CIF.cpp and ci_string.cpp. 2006-11-12 01:42 vincefn * [r806] Fox/src/Fox.cpp: Allow importing powderCIF files, and auto-create powder pattern from it. 2006-11-12 01:40 vincefn * [r805] ObjCryst/ObjCryst/CIF.cpp, ObjCryst/ObjCryst/CIF.h, ObjCryst/ObjCryst/PowderPattern.cpp, ObjCryst/ObjCryst/PowderPattern.h, ObjCryst/wxCryst/wxPowderPattern.cpp, ObjCryst/wxCryst/wxPowderPattern.h: Add functions to read powderCIF files, and extract the pattern from it. Some functions for peak finding are also added (menu is commented out). Fixes for CIF reading of quoted and semicolon text fields. 2006-11-11 20:29 vincefn * [r804] Fox/src/Fox.cpp: Add support to read CIF: added a CIF and a CIFData classes to extract data from Crystallographic Information File. Allows creating a Crystal structure from the CIF data. Also added a case insensitive string class. 2006-11-11 20:28 vincefn * [r803] ObjCryst/ObjCryst/CIF.cpp, ObjCryst/ObjCryst/CIF.h, ObjCryst/ObjCryst/bc32.mak, ObjCryst/ObjCryst/gnu.mak, ObjCryst/Quirks/bc32.mak, ObjCryst/Quirks/ci_string.cpp, ObjCryst/Quirks/ci_string.h, ObjCryst/Quirks/gnu.mak: Add support to read CIF: added a CIF and a CIFData classes to extract data from Crystallographic Information File. Allows creating a Crystal structure from the CIF data. Also added a case insensitive string class. 2006-11-09 22:33 vincefn * [r802] ObjCryst/ObjCryst/SpaceGroup.cpp: Allow supplying Hall symbol for spacegroups. 2006-10-29 08:16 vincefn * [r801] ObjCryst/ObjCryst/DiffractionDataSingleCrystal.cpp, ObjCryst/ObjCryst/DiffractionDataSingleCrystal.h, ObjCryst/ObjCryst/IO.cpp, ObjCryst/wxCryst/wxDiffractionSingleCrystal.cpp: Add the ability to use data with observed intensities from groups of reflections, supplied by the user. Also, save the scale factor parameter so that it is correctly restored when reloading an xml file or browsing solutions from multiple runs. 2006-10-29 06:29 vincefn * [r800] Fox/src/Fox.cpp: Change view to correct notebook page each time a top-level object is created. For single crystal data, auto-select the crystal structure if only one is available. 2006-10-23 21:34 vincefn * [r799] ObjCryst/CrystVector/CrystVector.cpp, ObjCryst/CrystVector/CrystVector.h: Add search for index of maximum or minimum in a vector, with optionnaly supplied range of indices. Add Savitzky-Golay smoothing (incl. 1st and 2nd derivatives). 2006-10-23 20:29 vincefn * [r798] ObjCryst/wxCryst/wxCrystal.cpp, ObjCryst/wxCryst/wxPowderPattern.cpp: Correct initial text for popup menus, when preferences lead to non-default values. 2006-10-19 20:43 vincefn * [r797] ObjCryst/wxCryst/wxMultiGraph.cpp, ObjCryst/wxCryst/wxPowderPattern.cpp: Larger font for graphs legends on msw. 2006-10-19 20:05 vincefn * [r796] Fox/src/Fox.cpp: Handle compressed xml files when loading files on startup 2006-10-17 21:44 vincefn * [r795] ObjCryst/wxCryst/wxPowderPattern.cpp: Correct automatic opening of powder pattern graph... 2006-10-17 21:23 vincefn * [r794] ObjCryst/wxCryst/wxCryst.cpp: Use wxWindow::Freeze() and Thaw() during BottomLayout to speed up drawing, particularly for windows. 2006-10-17 21:22 vincefn * [r793] ObjCryst/wxCryst/wxPowderPattern.cpp: Enable auto-opening the powder pattern graph, also on windows (kludge needed ?) 2006-10-17 19:27 vincefn * [r792] ObjCryst/wxCryst/wxPowderPattern.cpp: Allow opening the graph window when there are no points - incidentally, enable auto-opening the powder pattern graph. 2006-10-16 21:49 vincefn * [r791] Fox/src/Fox.cpp: Correct dialog style for preferences. 2006-10-16 20:14 vincefn * [r790] ObjCryst/wxCryst/wxCrystal.cpp, ObjCryst/wxCryst/wxPowderPattern.cpp: Add preferences. 2006-10-16 20:11 vincefn * [r789] Fox/src/Fox.cpp: Add GUI for editing preferences. Plus a few cleanups.. 2006-10-14 14:28 vincefn * [r788] Fox/src/Fox.cpp: Include wx/config.h 2006-10-13 22:43 vincefn * [r787] Fox/src/Fox.cpp: Enable Preferences (configuration). Allow compressed (gzipp'ed) xml files. 2006-10-13 22:41 vincefn * [r786] ObjCryst/ObjCryst/IO.cpp, ObjCryst/ObjCryst/IO.h: Added stream reading/saving variant to XMLCrystFileSaveGlobal and XMLCrystFileLoadAllObject. 2006-10-05 21:50 vincefn * [r785] ObjCryst/ObjCryst/SpaceGroup.cpp, ObjCryst/ObjCryst/SpaceGroup.h, ObjCryst/ObjCryst/UnitCell.cpp: Correct interpretation of rhombohedral/hexagonal cell choice. 2006-10-01 20:08 vincefn * [r784] ObjCryst/ObjCryst/ScatteringData.cpp, ObjCryst/ObjCryst/ScatteringPower.cpp, ObjCryst/wxCryst/wxDiffractionSingleCrystal.cpp: Enable electron diffraction for single crystal data. 2006-09-03 22:25 vincefn * [r783] ObjCryst/wxCryst/wxCryst.cpp, ObjCryst/wxCryst/wxCryst.h, ObjCryst/wxCryst/wxCrystal.cpp, ObjCryst/wxCryst/wxDiffractionSingleCrystal.cpp, ObjCryst/wxCryst/wxGlobalOptimObj.cpp, ObjCryst/wxCryst/wxPowderPattern.cpp, ObjCryst/wxCryst/wxScatterer.cpp: Fix size of object's names. Replace spectrum by pattern in wxPowderPattern. 2006-08-03 20:30 vincefn * [r782] Fox/gnu.mak: Add --disable-clipboard to fix compilation on some linux distributions (redhat 9 ?) 2006-08-02 21:30 vincefn * [r781] ObjCryst/wxCryst/wxCryst.cpp: Fix background colour for wxGTK with GTK < 2.x 2006-07-27 09:52 vincefn * [r780] ObjCryst/rules-gnu.mak: Removed -lXmu for linking, which should not be needed any more due to the use of freeglut. Use GL_FLAGS= and not GL_FLAGS:= to have a correct include path for static libraries... 2006-07-02 23:49 vincefn * [r779] ObjCryst/wxCryst/wxCrystal.cpp: Add the ability to import a list of atoms with their symbol and reduced coordinates. 2006-05-16 19:24 vincefn * [r778] Fox/macosx.mak: Switch from CVS to SVN. 2006-05-13 23:58 vincefn * [r777] ObjCryst/ObjCryst/ZScatterer.cpp: Fix debug message. 2006-05-13 23:57 vincefn * [r776] ObjCryst/ObjCryst/Crystal.cpp: In the CIF output, only announce the list of excluded atoms if there actually is at least 1 atom excluded. 2006-05-13 23:55 vincefn * [r775] ObjCryst/ObjCryst/Molecule.cpp: Decrease size of scattering component list when removing an atom. 2006-05-13 23:53 vincefn * [r774] ObjCryst/ObjCryst/ScatteringPower.cpp, ObjCryst/ObjCryst/ScatteringPower.h: Add ScatteringComponentList::operator-- 2006-04-15 20:29 vincefn * [r773] Fox/gnu.mak: Switch Makefile commands from cvs to svn. 2006-04-15 20:22 vincefn * [r772] Fox/gnu.mak: Update for compilation with wxGTK-2.6.3. Also update rpm build commands. 2006-04-15 20:08 vincefn * [r771] Fox/Fox.xcodeproj/project.pbxproj: Fix compilation for G4 (disable auto-vectorization). 2006-04-04 18:43 vincefn * [r770] ObjCryst/ObjCryst/ScatteringCorr.cpp: Correct polarization factor, and compute cosine only once. 2006-02-27 10:06 vincefn * [r769] Fox/Fox.sln, Fox/src/Fox.vcproj: Add visual c++ 2005 express edition project and solution files. Fix corrupted icon file. 2006-02-27 09:38 vincefn * [r768] ObjCryst/wxCryst/wxCrystal.cpp: string -> wxString fix for compilation on windows. 2006-02-25 23:19 vincefn * [r767] ObjCryst/ObjCryst/ZScatterer.cpp, ObjCryst/ObjCryst/ZScatterer.h, ObjCryst/wxCryst/wxCrystal.cpp, ObjCryst/wxCryst/wxMolecule.cpp: Add export of ZScatterer objects to a z-matrix format using atom names rather than indices to refer to bond / bond angle / dihedral angle atoms. Also added import/export of Molecule from/to such a z-matrix. 2006-02-25 22:17 vincefn * [r766] ObjCryst/wxCryst/MC.cpp, ObjCryst/wxCryst/MC.h, ObjCryst/wxCryst/MCTable.h, ObjCryst/wxCryst/mpVector.cpp, ObjCryst/wxCryst/mpVector.h: Add Michael Y. Polyakov files for Fourier maps display, finally in the SVN repository. 2006-02-21 21:29 vincefn * [r765] ObjCryst/RefinableObj/GlobalOptimObj.cpp: Correctly erase temporary parameter set at the end of a SA run. 2006-02-21 21:25 vincefn * [r764] ObjCryst/CrystVector/CrystVector.cpp: Do not (wrongly) compute determinant when inverting matrix. 2006-02-11 20:13 vincefn * [r763] ObjCryst/ObjCryst/PowderPattern.cpp: Correctly delete the reflection profile. 2006-02-11 20:11 vincefn * [r762] ObjCryst/ObjCryst/ScatteringData.cpp, ObjCryst/ObjCryst/ScatteringData.h: Nifty initialization and deletion of tabulated sine, cosine and exp tables. 2006-02-11 20:10 vincefn * [r761] ObjCryst/ObjCryst/SpaceGroup.cpp: Correctly delete cctbx spacegroup object. 2006-01-26 19:30 vincefn * [r760] ObjCryst/wxCryst/wxCrystal.cpp: Only initialize (free)glut once, when opengl window is closed/reopened. 2006-01-05 20:26 vincefn * [r759] ObjCryst/wxCryst/wxCrystal.cpp: Validate user input before importing a z-matrix. 2005-12-22 20:13 vincefn * [r758] ObjCryst/wxCryst/wxPowderPattern.cpp: Add tooltips. 2005-12-20 22:51 vincefn * [r757] ObjCryst/ObjCryst/ScatteringData.cpp: Recompute geometrical structure factor when the *used* number of reflections has changed. 2005-12-20 21:12 vincefn * [r756] ObjCryst/ObjCryst/IO.cpp: Use X-Ray tube name only if there is actually one given. 2005-12-19 22:13 vincefn * [r755] Fox/src/gnu.mak, ObjCryst/CrystVector/gnu.mak, ObjCryst/ObjCryst/gnu.mak, ObjCryst/Quirks/gnu.mak, ObjCryst/RefinableObj/gnu.mak, ObjCryst/wxCryst/gnu.mak: Remove old ($objectfile).gcda ($objectfile).gcno when compiling with profile=2. 2005-12-11 19:46 vincefn * [r754] ObjCryst/rules-gnu.mak: Enable profile feedback directed optimizations with gcc. First compile using "make profile=2", then run a few typical optimizations, then "make clean" and "make profile=3". Gain around 10% on speedtest. "make profile=1" will compile using the tau profiling package. 2005-12-08 19:39 vincefn * [r753] Fox/macosx.mak: Correct "all" and "update" targets. 2005-12-07 21:43 vincefn * [r752] ObjCryst/ObjCryst/ScatteringPower.cpp, ObjCryst/ObjCryst/ScatteringPower.h: Remove static global list of scattering powers. 2005-12-01 20:15 vincefn * [r751] ObjCryst/rules-gnu.mak: Update rules with correct search paths, plus commented out compile flags to compile with auto-vectorization. 2005-11-27 22:02 vincefn * [r750] ObjCryst/ObjCryst/ScatteringData.cpp: Change declaration for compilation with gcc 3.3 2005-11-27 21:47 vincefn * [r749] Fox/gnu.mak: Disable warnings when building freeglut, enable both gtk1 and gtk2 for wxWidgets. 2005-11-25 19:59 vincefn * [r748] ObjCryst/wxCryst/wxCrystal.cpp: Correctly initialize glut. 2005-11-25 19:59 vincefn * [r747] Fox/gnu.mak, ObjCryst/rules-gnu.mak: Compile wxWidgets and freeglut as static libraries by default, to lower dependencies. 2005-11-22 23:03 vincefn * [r746] ObjCryst/ObjCryst/SpaceGroup.cpp: Avoid re-initializing spacegroup. 2005-11-13 19:39 vincefn * [r744] ObjCryst/CrystVector/CrystVector.cpp, ObjCryst/ObjCryst/General.h, ObjCryst/ObjCryst/PowderPattern.cpp, ObjCryst/ObjCryst/ScatteringData.cpp: Add "restrict" keyword to independent pointers, to enable auto-vectorization. Also make sure that loop boundaries are constant for loops to be vectorized. 2005-11-11 22:12 vincefn * [r743] Fox/Fox.xcodeproj/project.pbxproj, Fox/macosx.mak: Update Makefile and XCode project for G5 target. 2005-11-11 21:18 vincefn * [r742] Fox/Fox.xcodeproj/project.pbxproj, Fox/macosx.mak: Update XCode project (now with XCode 2.2, but should work with 2.1). Update Makefile. 2005-11-10 23:01 vincefn * [r741] ObjCryst/ObjCryst/Molecule.cpp, ObjCryst/ObjCryst/Molecule.h, ObjCryst/wxCryst/wxMolecule.cpp, ObjCryst/wxCryst/wxMolecule.h: Added export to z-matrix from a Molecule. 2005-11-07 20:06 vincefn * [r740] ObjCryst/ObjCryst/Crystal.cpp, ObjCryst/ObjCryst/IO.cpp, ObjCryst/ObjCryst/ScatteringData.cpp, ObjCryst/ObjCryst/ScatteringPower.cpp, ObjCryst/ObjCryst/ScatteringPower.h, ObjCryst/wxCryst/wxCrystal.cpp: Add the ability to use "Ghost" atoms using Maximum Likelihood - they have an unknown position, and only contribute to the variance of the structure factor, not to the modulus. 2005-11-06 14:09 vincefn * [r739] ObjCryst/ObjCryst/PowderPatternBackgroundBayesianMinimiser.cpp: Use explicit type for log() to compile with VC++. 2005-11-06 14:04 vincefn * [r738] ObjCryst/ObjCryst/Molecule.cpp: Correct typo (extra Molecule::) 2005-11-06 13:17 vincefn * [r737] Fox/macosx-wxgtk.mak, Fox/macosx.mak, Fox/src/macosx.mak, ObjCryst/rules-macosx-wxgtk.mak, ObjCryst/rules-macosx.mak: Switch to XCode rather than Makefile building, keep macosx.mak for command-line control of XCode and disk image generation. 2005-11-06 01:24 vincefn * [r736] Fox/Fox.xcodeproj/project.pbxproj: Fixed configuration Aqua-G4 for target NoGUI, cctbx, newmat. 2005-11-06 01:02 vincefn * [r735] Fox/Fox.xcodeproj/project.pbxproj: Update targets and configurations. Add NoGUI target. 2005-11-06 00:35 vincefn * [r734] ObjCryst/ObjCryst/PowderPattern.cpp, ObjCryst/ObjCryst/PowderPattern.h, ObjCryst/wxCryst/wxPowderPattern.cpp: Sort the background points, taking into account the type of radiation (TOF...) only when it is safe to do so (the powder pattern and the radiation must have been defined first). Also, update display when needed. 2005-11-04 19:39 vincefn * [r733] Fox/src/Fox.cpp: Enable direct loading of file without "-i", i.e. "Fox pbso4.xml", for a more natural use from OS. 2005-11-03 23:48 vincefn * [r732] ObjCryst/ObjCryst/Molecule.cpp: Add VFN_DEBUG_EXIT debug message. 2005-11-03 23:45 vincefn * [r731] ObjCryst/wxCryst/wxPowderPattern.cpp, ObjCryst/wxCryst/wxPowderPattern.h: Add a grid for background point edition. 2005-11-03 23:44 vincefn * [r730] ObjCryst/ObjCryst/PowderPattern.cpp, ObjCryst/ObjCryst/PowderPattern.h: Add const access to points. In PowderPatternBackground::SetInterpPoints(...), make sure the points are sorted in ascending order of the pattern's pixels. 2005-11-03 23:43 vincefn * [r729] ObjCryst/RefinableObj/Simplex.cpp: Correctly restore best configuration. 2005-11-03 19:48 vincefn * [r728] ObjCryst/ObjCryst/IO.cpp, ObjCryst/ObjCryst/PowderPattern.cpp, ObjCryst/ObjCryst/PowderPattern.h, ObjCryst/ObjCryst/PowderPatternBackgroundBayesianMinimiser.cpp: Faster Bayesian minimization of background, and better use of the CubicSpline. 2005-11-03 19:38 vincefn * [r727] ObjCryst/RefinableObj/Simplex.cpp: Exit optimization if the worst node becomes too close to the average node. 2005-11-03 19:31 vincefn * [r726] ObjCryst/ObjCryst/Molecule.cpp, ObjCryst/ObjCryst/Molecule.h, ObjCryst/wxCryst/wxMolecule.cpp: Correct edition of dihedral and rigid groups entries. Provide a direct access to the rigid groups. 2005-11-03 19:20 vincefn * [r725] ObjCryst/CrystVector/CrystVector.cpp, ObjCryst/CrystVector/CrystVector.h: Added a default constructor to CubicSpline, along with InitSpline(...) functions. Also, added a function to get the spline value for a vector of coordinates. 2005-11-01 10:55 vincefn * [r724] Fox/Fox.xcodeproj/project.pbxproj: Add Fox-NoGUI target (shell application). 2005-10-31 23:06 vincefn * [r723] Fox/Fox.xcodeproj/project.pbxproj: Update Xcode project. 2005-10-30 23:17 vincefn * [r722] Fox/Fox.xcodeproj/project.pbxproj: Update achitecture-specific compile flags. 2005-10-30 22:47 vincefn * [r721] Fox/Fox-Info.plist, Fox/Fox.xcodeproj, Fox/Fox.xcodeproj/project.pbxproj, Fox/src/Fox.icns: Added Xcode (>=2.1) project files for MacOS X compilation. 2005-10-30 00:41 vincefn * [r720] Fox/src/Fox.cpp: Enable command-line argument for multiple-runs refinement, with statistics. 2005-10-29 15:00 vincefn * [r719] ObjCryst/ObjCryst/Crystal.cpp: Do not call BeginOptimization() twice. 2005-10-29 14:57 vincefn * [r718] ObjCryst/ObjCryst/Molecule.cpp, ObjCryst/ObjCryst/Molecule.h: Faster algorithm to determine when stretch mode are breaking rigid groups or bond lengths, bond angles and dihedral angles. Only uses derivatives if necessary. 2005-10-29 14:46 vincefn * [r717] ObjCryst/wxCryst/wxZScatterer.cpp: Return after last debug message. 2005-10-29 14:43 vincefn * [r716] ObjCryst/RefinableObj/GlobalOptimObj.cpp, ObjCryst/RefinableObj/GlobalOptimObj.h, ObjCryst/wxCryst/wxGlobalOptimObj.cpp: Add access to the XMLAutoSave option and to the best cost. 2005-10-27 22:09 vincefn * [r715] ObjCryst/RefinableObj/GlobalOptimObj.cpp: Update best cost at the end of the run. 2005-10-27 22:07 vincefn * [r714] ObjCryst/RefinableObj/RefinableObj.cpp: Correctly propagate the clock value when using RefinableObjClock::operator= 2005-10-24 21:36 vincefn * [r713] ObjCryst/RefinableObj/RefinableObj.cpp: Avoid executing twice RefinableObj::BeginOptimization and RefinableObj::EndOptimization 2005-10-24 21:34 vincefn * [r712] ObjCryst/wxCryst/wxMolecule.cpp: Enable direct editing of the rigid group table. 2005-10-18 20:07 vincefn * [r711] ObjCryst/wxCryst/wxPowderPattern.cpp: Really reduce number of hkl labels & ticks displayed. 2005-10-18 19:46 vincefn * [r710] ObjCryst/ObjCryst/Molecule.cpp, ObjCryst/ObjCryst/Molecule.h, ObjCryst/wxCryst/wxMolecule.cpp: Click Molecule::mClockAtomPosition every time an atom is moved. 2005-10-18 19:16 vincefn * [r709] ObjCryst/ObjCryst/Molecule.cpp, ObjCryst/ObjCryst/Molecule.h: Differentiate MolBond/MolBondAngle/MolDihedralAngle::GetLogLikelihood() and GetLogLikelihood(bool,bool). 2005-10-17 20:31 vincefn * [r708] ObjCryst/ObjCryst/Crystal.cpp, ObjCryst/wxCryst/wxCrystal.cpp, ObjCryst/wxCryst/wxCrystal.h: Add bond valence calculations output to Crystal::Print(...). Remove extra functions in WXCrystal. 2005-10-17 18:52 vincefn * [r707] ObjCryst/ObjCryst/Molecule.cpp, ObjCryst/ObjCryst/Molecule.h, ObjCryst/wxCryst/wxMolecule.cpp: Enabled StretchModeTwist modes. 2005-10-16 20:09 vincefn * [r706] ObjCryst/RefinableObj/RefinableObj.h: Fix declaration order. 2005-10-16 20:08 vincefn * [r705] ObjCryst/ObjCryst/Molecule.cpp, ObjCryst/ObjCryst/Molecule.h, ObjCryst/wxCryst/wxMolecule.cpp: Better respect for restraints, using LLK calculations (including derivatives). 2005-10-12 22:53 vincefn * [r704] ObjCryst/wxCryst/wxCrystal.cpp, ObjCryst/wxCryst/wxCrystal.h, ObjCryst/wxCryst/wxScatteringPower.cpp: Added a window to display all properties of scattering powers, including anti-bump and bond valence parameters. 2005-10-12 22:31 vincefn * [r703] ObjCryst/ObjCryst/Crystal.cpp, ObjCryst/ObjCryst/Crystal.h, ObjCryst/ObjCryst/IO.cpp: Change interface to bond valence parameters. 2005-10-11 21:52 vincefn * [r702] ObjCryst/ObjCryst/ScatteringPower.cpp, ObjCryst/ObjCryst/ScatteringPower.h: Add ScatteringPower::SetMaximumLikelihoodPositionError(...). 2005-10-11 21:52 vincefn * [r701] ObjCryst/ObjCryst/Crystal.cpp, ObjCryst/ObjCryst/Crystal.h, ObjCryst/ObjCryst/IO.cpp: Change interface to anti-bump and bond valence parameters. Now anti-bump refer not to pairs of elements but to pairs of scattering powers, i.e. if there are two Fe scattering powers, they have different antibump parameters, same as for bond valence paramaters. 2005-10-08 19:23 vincefn * [r700] ObjCryst/ObjCryst/ZScatterer.cpp, ObjCryst/RefinableObj/GlobalOptimObj.cpp, ObjCryst/wxCryst/wxRefinableObj.cpp, ObjCryst/wxCryst/wxScatterer.cpp, ObjCryst/wxCryst/wxScatteringPower.cpp: Decrease verbosity. 2005-10-08 19:14 vincefn * [r699] ObjCryst/ObjCryst/Molecule.cpp, ObjCryst/wxCryst/wxZScatterer.cpp: Support for large molecules: faster import from Fenske-Hall z-matrix, switch to wireframe display for more than 100 atoms. 2005-10-06 20:19 vincefn * [r698] ObjCryst/ObjCryst/ScatteringData.cpp: Correctly get second wavelength for X-ray tubes. 2005-10-02 18:50 vincefn * [r697] ObjCryst/ObjCryst/Molecule.cpp: Enabled the third flexibility option for a Molecule (automatic restraints - strict). Decrease verbosity when not in debug mode. 2005-10-01 11:27 vincefn * [r696] Fox/src/Fox.cpp: Change window title & splash screen formatting to compile with VC++... 2005-10-01 09:30 vincefn * [r695] Fox/src/Fox.cpp: Update version. More graceful exit if compiled with wxWidgets but does not use the GUI. 2005-09-30 22:57 vincefn * [r694] ObjCryst/ObjCryst/ScatteringData.cpp, ObjCryst/ObjCryst/ScatteringData.h: Correctly compute multiplicity for acentric reflections when ignoring f". Also, systematically compute the multiplicity associated with each reflection, even if it is not used. 2005-09-30 22:34 vincefn * [r693] ObjCryst/wxCryst/wxPowderPattern.cpp: Avoid minimum 2theta below 1.0, when using simulation mode. 2005-09-29 22:09 vincefn * [r692] ObjCryst/wxCryst/wxMolecule.cpp: Use string::c_str() to convert std::string to wxString (done automatically with gcc, but requires the c_str() for VC++...). 2005-09-29 19:10 vincefn * [r691] ObjCryst/ObjCryst/Molecule.cpp, ObjCryst/ObjCryst/Molecule.h, ObjCryst/wxCryst/wxCryst.cpp, ObjCryst/wxCryst/wxCryst.h, ObjCryst/wxCryst/wxMolecule.cpp, ObjCryst/wxCryst/wxMolecule.h, ObjCryst/wxCryst/wxRefinableObj.cpp, ObjCryst/wxCryst/wxZScatterer.cpp: Major update to the Molecule object, which now uses "stretch modes" changing either torsion, bond angle or bond length. Also, derivative calculations (of the atomic positions and the log(likelihood) of individual restraints) are now calculated to determine conflicts between restraints. The wxWidgets graphical interface now uses a grid layout, for atoms and all restraints, which is much faster. wxWidgets >= 2.6 is required. 2005-09-13 22:11 vincefn * [r690] ObjCryst/wxCryst/wxMolecule.cpp: Do not call BottomLayout in the WXMolAtom, WXMolBond, WXMolBondAngle and WXMolDihedralAngle constructors, to reduce number of Layouts when loading a Molecule. The WXMolecule object will call the Layout. Also, increase initial size for bond/bond angle/dihedral angle windows. 2005-09-12 19:41 vincefn * [r689] ObjCryst/ObjCryst/Molecule.cpp: Correct calculation of absolute dihedral angle, and the related log(likelihood) 2005-09-02 18:47 vincefn * [r688] ObjCryst/wxCryst/wxPowderPattern.cpp: Only display the first 100 labels (per phase). 2005-09-01 23:44 vincefn * [r687] ObjCryst/wxCryst/wxPowderPattern.cpp: Correct label positions 2005-09-01 21:27 vincefn * [r686] ObjCryst/ObjCryst/PowderPattern.cpp: Safe compute of integrated Chi^2 cumul, when there are no crystalline phases, and therefore no integration areas [the Chi^2 cumul is then null]. 2005-08-19 21:46 vincefn * [r685] ObjCryst/ObjCryst/PowderPattern.cpp: Small fix for TOF data. 2005-08-14 21:26 vincefn * [r684] ObjCryst/wxCryst/wxCrystal.cpp, ObjCryst/wxCryst/wxCrystal.h: Add menu entries to show either the full unit cell or the asymmetric unit cell (+0.1) 2005-08-14 07:57 vincefn * [r683] ObjCryst/wxCryst/wxMultiGraph.cpp: Reduce number of tick labels. 2005-08-14 07:56 vincefn * [r682] ObjCryst/ObjCryst/PowderPattern.cpp, ObjCryst/ObjCryst/PowderPattern.h, ObjCryst/wxCryst/wxPowderPattern.cpp, ObjCryst/wxCryst/wxPowderPattern.h: Add computation of cumulative Chi^2, and display it in the graph. 2005-08-13 14:54 vincefn * [r681] ObjCryst/wxCryst/wxCrystal.cpp, ObjCryst/wxCryst/wxPowderPattern.cpp: Restrict some update menus when objects are being refined. 2005-08-13 14:23 vincefn * [r680] Fox/gnu.mak: Updated "dist" target. Added target to switch from anonymous to ssh-based cvs access. 2005-08-13 14:13 vincefn * [r679] ObjCryst/wxCryst/wxCrystal.cpp, ObjCryst/wxCryst/wxCrystal.h, ObjCryst/wxCryst/wxRefinableObj.cpp: Use a wxCondition to update the OpenGL display list from a background thread. Do not update titles/spacegroup name when being refined. 2005-08-13 14:11 vincefn * [r678] ObjCryst/wxCryst/wxMultiGraph.cpp: Correctly rescale taking into account *all* graphs when adding a new graph. 2005-08-13 12:54 vincefn * [r677] ObjCryst/RefinableObj/Tracker.cpp: Do not update the display of a MainTracker whenever values are added. 2005-08-13 12:53 vincefn * [r676] ObjCryst/ObjCryst/ScatteringData.cpp: Do not acess beyond mSinThetaLambda vector size. 2005-08-13 10:10 vincefn * [r675] ObjCryst/CrystVector/CrystVector.cpp: Removed the debugging CRYSTVECTOR_MEM_CHANGE macro, valgrind being much better for memory debugging. 2005-08-13 09:34 vincefn * [r674] ObjCryst/ObjCryst/ZScatterer.cpp: Make sure random move is done. 2005-08-12 19:29 vincefn * [r673] Fox/gnu.mak: Added "dist" and "rpm" targets. 2005-08-12 19:08 vincefn * [r672] ObjCryst/Quirks/VFNStreamFormat.cpp, ObjCryst/Quirks/VFNStreamFormat.h: Small fixes (std namespace, friend declarations) for ISO c++ compliance - no more friends, all members are public. 2005-07-26 21:50 vincefn * [r671] ObjCryst/ObjCryst/ScatteringData.cpp: Use cctbx to generate the list of reflection (either in the reciprocal space ASU or full space). 2005-07-25 22:16 vincefn * [r670] ObjCryst/RefinableObj/GlobalOptimObj.cpp, ObjCryst/RefinableObj/RefinableObj.cpp, ObjCryst/wxCryst/wxCryst.cpp, ObjCryst/wxCryst/wxCrystal.cpp, ObjCryst/wxCryst/wxGlobalOptimObj.cpp, ObjCryst/wxCryst/wxRefinableObj.cpp: Change mutex locking behaviour. 2005-07-25 22:01 vincefn * [r669] ObjCryst/wxCryst/wxCrystal.cpp: Show display limits in 3D Crystal view. 2005-07-25 21:58 vincefn * [r668] ObjCryst/ObjCryst/Colours.h: Add #ifdef to safely include several times this header. 2005-07-23 22:15 vincefn * [r667] ObjCryst/wxCryst/wxPowderPattern.cpp: Do not try to display graph if there are no observed or calculated points. 2005-07-23 22:10 vincefn * [r666] ObjCryst/wxCryst/wxCrystal.cpp: Fix #include of GLUT for MacOSX when using wxMac. 2005-07-23 22:08 vincefn * [r665] ObjCryst/rules-macosx.mak: Fix for compilation on MacOS X. Only partial, since compilation on MacOS X should now be done using Xcode >=2.1 2005-07-14 19:44 vincefn * [r664] ObjCryst/ObjCryst/SpaceGroup.cpp, ObjCryst/ObjCryst/SpaceGroup.h: Store spacegroup number and number of symmetries/translations for faster access. 2005-07-14 07:25 vincefn * [r663] ObjCryst/RefinableObj/GlobalOptimObj.cpp: Only update display when necessary, at most every 300 trials. 2005-07-13 23:15 vincefn * [r662] ObjCryst/ObjCryst/SpaceGroup.cpp: Correct SpaceGroup::AreReflEquiv() 2005-07-12 22:12 vincefn * [r661] ObjCryst/ObjCryst/SpaceGroup.cpp: Correct equivalent reflections test. Fix compilation for MacOS X gcc 3.3 2005-07-12 20:43 vincefn * [r660] Fox/macosx.mak: Added Fox-nogui target 2005-07-12 20:41 vincefn * [r659] Fox/src/macosx.mak: Switch makefile {atominfo+sglite}->cctbx 2005-07-12 20:32 vincefn * [r658] ObjCryst/rules-macosx-wxgtk.mak: Add rules.mak for MacOS X with wxGTK 2005-07-12 20:29 vincefn * [r657] Fox/macosx-wxgtk.mak: Makefile for MacOS X using wxGTK 2005-07-12 20:26 vincefn * [r656] ObjCryst/wxCryst/wxCrystal.cpp: Fix OpenGL #includes for MacOS X with wxGTK. 2005-07-11 17:08 vincefn * [r655] ObjCryst/RefinableObj/LSQNumObj.cpp, ObjCryst/RefinableObj/LSQNumObj.h: Use ObjCryst namespace in LSQNumObj. Give access to a variance-covariance map. 2005-07-10 13:43 vincefn * [r654] ObjCryst/rules-vc.mak: Update for wxWidgets 2.6. Enable precompiled headers. 2005-07-08 19:47 vincefn * [r653] ObjCryst/ObjCryst/ScatteringData.cpp, ObjCryst/ObjCryst/ScatteringPower.cpp, ObjCryst/ObjCryst/SpaceGroup.cpp: Catch cctbx exceptions. 2005-07-07 21:24 vincefn * [r652] Fox/src/gnu.mak, Fox/src/vc.mak, ObjCryst/ObjCryst/Atom.cpp, ObjCryst/ObjCryst/Crystal.cpp, ObjCryst/ObjCryst/ScatteringData.cpp, ObjCryst/ObjCryst/ScatteringPower.cpp, ObjCryst/ObjCryst/ScatteringPower.h, ObjCryst/ObjCryst/SpaceGroup.cpp, ObjCryst/ObjCryst/SpaceGroup.h, ObjCryst/ObjCryst/gnu.mak, ObjCryst/example/pbso4/gnu.mak, ObjCryst/gnu.mak, ObjCryst/rules-bc32.mak, ObjCryst/rules-gnu.mak, ObjCryst/rules-vc.mak: Switch from (atominfo+sglite) to cctbx (finally !). 2005-07-07 09:58 vincefn * [r651] Fox/ObjCryst-Fox.spec: First spec file for rpm generation. 2005-07-07 09:53 vincefn * [r650] ObjCryst/rules-gnu.mak: Use generic (not x86-specific) CPPFLAGS. Also recognize RPM_OPT_FLAGS, if passed to the makefile. 2005-06-29 17:33 vincefn * [r649] ObjCryst/wxCryst/wxCryst.cpp: In WXFieldName::ValidateUserInput(), correctly release mutex before notifying the modified name to the parent object. 2005-06-07 20:36 vincefn * [r648] ObjCryst/ObjCryst/Crystal.cpp: Correct bond valence cost reporting. 2005-06-07 20:14 vincefn * [r647] ObjCryst/wxCryst/wxCrystal.cpp: Reduce initial 3D display to the parallelipedic asymmetric unit cell, plus 0.1 margins 2005-05-03 11:10 vincefn * [r646] ObjCryst/rules-gnu.mak: Fixed the include paths and options. 2005-05-03 02:58 vincefn * [r645] ObjCryst/rules-gnu.mak: Added /usr/include/GL include, for when freeglut is used. 2005-04-21 20:34 vincefn * [r644] ObjCryst/wxCryst/wxPowderPattern.cpp: Add a warning when trying to add a second background. 2005-04-21 20:33 vincefn * [r643] ObjCryst/wxCryst/wxCryst.cpp: Correct height of buttons (+ debug levels). 2005-04-21 20:32 vincefn * [r642] ObjCryst/ObjCryst/PowderPattern.cpp: Correctly compute pixel position, even in case of non-constant step. 2005-04-21 20:30 vincefn * [r641] ObjCryst/ObjCryst/IO.cpp: Correctly save the AllowMerge flag for the AntiBump/Merge function. 2005-03-24 20:43 vincefn * [r640] ObjCryst/wxCryst/wxTrackerGraph.cpp: Correctly delete graphs. 2005-03-24 19:55 vincefn * [r639] ObjCryst/RefinableObj/RefinableObj.cpp, ObjCryst/wxCryst/wxTrackerGraph.cpp: Small Multithread fixes. 2005-03-24 19:51 vincefn * [r638] ObjCryst/RefinableObj/GlobalOptimObj.cpp: Correctly initialize parameter sets when doing a Parallel Tempering run. Half Worlds start from different random parameter sets, and the other half from the initial configuration. 2005-03-23 23:59 vincefn * [r637] ObjCryst/RefinableObj/GlobalOptimObj.cpp: When starting a single run, half of the Worlds (including the last) start from the last best configuration stored. 2005-03-23 22:16 vincefn * [r636] ObjCryst/RefinableObj/GlobalOptimObj.cpp, ObjCryst/RefinableObj/RefinableObj.cpp, ObjCryst/wxCryst/wxAtom.cpp, ObjCryst/wxCryst/wxAtom.h, ObjCryst/wxCryst/wxCryst.cpp, ObjCryst/wxCryst/wxCryst.h, ObjCryst/wxCryst/wxCrystal.cpp, ObjCryst/wxCryst/wxCrystal.h, ObjCryst/wxCryst/wxDiffractionSingleCrystal.cpp, ObjCryst/wxCryst/wxDiffractionSingleCrystal.h, ObjCryst/wxCryst/wxGlobalOptimObj.cpp, ObjCryst/wxCryst/wxGlobalOptimObj.h, ObjCryst/wxCryst/wxMolecule.cpp, ObjCryst/wxCryst/wxMolecule.h, ObjCryst/wxCryst/wxMultiGraph.cpp, ObjCryst/wxCryst/wxMultiGraph.h, ObjCryst/wxCryst/wxPowderPattern.cpp, ObjCryst/wxCryst/wxPowderPattern.h, ObjCryst/wxCryst/wxRadiation.h, ObjCryst/wxCryst/wxRefinableObj.cpp, ObjCryst/wxCryst/wxRefinableObj.h, ObjCryst/wxCryst/wxScatteringPower.cpp, ObjCryst/wxCryst/wxScatteringPower.h, ObjCryst/wxCryst/wxScatteringPowerSphere.cpp, ObjCryst/wxCryst/wxScatteringPowerSphere.h, ObjCryst/wxCryst/wxZScatterer.cpp, ObjCryst/wxCryst/wxZScatterer.h: Now interface for CrystUpdate(const bool updateUI,const bool mutexlock) and UpdateUI(const bool mutexlock). The rationale of this change is to use a minimum number of Mutexes to lock update of the graphical interface. In practice only "top" objects (those declared in an OptimizationObj) will use a lock, and the lock shall be maintained during the update of the children. 2005-03-20 23:24 vincefn * [r635] ObjCryst/ObjCryst/Molecule.cpp: Suppress messages 2005-03-20 21:48 vincefn * [r634] ObjCryst/wxCryst/wxRefinableObj.cpp: Thread-safe fixes for WXFieldRefPar (again)... 2005-03-20 20:02 vincefn * [r633] ObjCryst/wxCryst/wxZScatterer.cpp: Use more meaningful names for ZScatterer parameters. 2005-03-20 19:43 vincefn * [r632] ObjCryst/wxCryst/wxRefinableObj.cpp: More thread-safe changes. 2005-03-20 19:41 vincefn * [r631] ObjCryst/RefinableObj/RefinableObj.cpp, ObjCryst/RefinableObj/RefinableObj.h: Added a copy constructor for RefinablePar, which copies everything except mpWXFieldRefPar. 2005-03-20 01:12 vincefn * [r630] ObjCryst/wxCryst/wxMultiGraph.cpp, ObjCryst/wxCryst/wxTrackerGraph.cpp: Fix graph display (mutexes, axes & popup menu) 2005-03-20 01:08 vincefn * [r629] ObjCryst/RefinableObj/GlobalOptimObj.cpp, ObjCryst/RefinableObj/GlobalOptimObj.h, ObjCryst/RefinableObj/RefinableObj.cpp, ObjCryst/RefinableObj/RefinableObj.h: Removed the InitRandomSeedFromTime() functions. The random seed is initialized once when the first OptimizationObj is created. 2005-03-16 22:57 vincefn * [r628] ObjCryst/RefinableObj/GlobalOptimObj.cpp: Also restore the best parameters at the end of a single run. 2005-03-16 22:18 vincefn * [r627] ObjCryst/wxCryst/wxCryst.cpp, ObjCryst/wxCryst/wxRefinableObj.cpp: wxMutex fixes (again), using more wxMutexLocker objects. 2005-03-16 21:51 vincefn * [r626] ObjCryst/wxCryst/wxCryst.cpp: Correct typo. 2005-03-16 21:49 vincefn * [r625] ObjCryst/wxCryst/wxCryst.cpp, ObjCryst/wxCryst/wxRefinableObj.cpp: Fix wxMutex behaviour. 2005-03-16 11:01 vincefn * [r624] ObjCryst/RefinableObj/Tracker.cpp: Only use WXDelete() if __WX__CRYST__ is defined 2005-03-16 09:39 vincefn * [r623] ObjCryst/wxCryst/wxMultiGraph.cpp, ObjCryst/wxCryst/wxMultiGraph.h: Corrected Mutex locking. 2005-03-13 10:45 vincefn * [r622] ObjCryst/wxCryst/wxCryst.cpp: Fix Layout when using scrolled windows parents..again... 2005-03-13 10:25 vincefn * [r621] ObjCryst/wxCryst/wxCryst.cpp: Fix Layout when using scrolled windows parents. 2005-03-13 01:13 vincefn * [r620] ObjCryst/wxCryst/wxPowderPattern.cpp, ObjCryst/wxCryst/wxPowderPattern.h: Added a handler for a wxSizeEvent, to get a correct graph refresh. 2005-03-13 00:53 vincefn * [r619] ObjCryst/wxCryst/wxMultiGraph.cpp, ObjCryst/wxCryst/wxMultiGraph.h: Fix win32 compilation (precompiled headers, wxMSW macros) 2005-03-13 00:28 vincefn * [r618] ObjCryst/wxCryst/bc32.mak, ObjCryst/wxCryst/gnu.mak, ObjCryst/wxCryst/vc.mak: Added a wxMultiGraph class to draw y(x) graphs, with a derived wxTrackerGraph class to draw tracked data. Automatic display in wxGlobalOptimObj. 2005-03-13 00:21 vincefn * [r617] ObjCryst/RefinableObj/GlobalOptimObj.cpp, ObjCryst/RefinableObj/GlobalOptimObj.h, ObjCryst/RefinableObj/Tracker.cpp, ObjCryst/RefinableObj/Tracker.h, ObjCryst/wxCryst/wxGlobalOptimObj.cpp, ObjCryst/wxCryst/wxGlobalOptimObj.h, ObjCryst/wxCryst/wxMultiGraph.cpp, ObjCryst/wxCryst/wxMultiGraph.h, ObjCryst/wxCryst/wxTrackerGraph.cpp, ObjCryst/wxCryst/wxTrackerGraph.h: Added a wxMultiGraph class to draw y(x) graphs, with a derived wxTrackerGraph class to draw tracked data. Automatic display in wxGlobalOptimObj. 2005-03-13 00:05 vincefn * [r616] ObjCryst/ObjCryst/Crystal.cpp: Return correct bond-valence sost when already calculated. 2005-03-09 22:04 vincefn * [r615] ObjCryst/ObjCryst/ReflectionProfile.cpp, ObjCryst/ObjCryst/ReflectionProfile.h, ObjCryst/wxCryst/wxPowderPattern.cpp: Removed Bera&Baldinozzi asymmetry description for a simpler one. 2005-03-07 23:56 vincefn * [r614] ObjCryst/RefinableObj/GlobalOptimObj.cpp, ObjCryst/RefinableObj/GlobalOptimObj.h, ObjCryst/RefinableObj/Tracker.cpp, ObjCryst/RefinableObj/Tracker.h, ObjCryst/RefinableObj/bc32.mak, ObjCryst/RefinableObj/gnu.mak, ObjCryst/RefinableObj/vc.mak, ObjCryst/wxCryst/wxGlobalOptimObj.cpp: Added Tracker objects to record the evolution of cost functions, parameters, etc.. 2005-03-06 23:11 vincefn * [r613] ObjCryst/ObjCryst/PowderPattern.cpp: Correct GSAS import function, particularly for STD file without counters. 2005-03-06 21:29 vincefn * [r612] ObjCryst/ObjCryst/PowderPattern.cpp, ObjCryst/ObjCryst/PowderPattern.h, ObjCryst/wxCryst/wxPowderPattern.cpp, ObjCryst/wxCryst/wxPowderPattern.h: Added import function for GSAS data file (constant wavelength only so far). 2005-03-01 18:27 vincefn * [r611] ObjCryst/ObjCryst/Crystal.cpp, ObjCryst/wxCryst/wxCrystal.cpp: Compute BV for anions too, and correctly display the entire list of calculated BV. 2005-02-28 20:22 vincefn * [r610] ObjCryst/ObjCryst/Crystal.cpp: Do not forget mBondValenceCostScale... 2005-02-28 19:25 vincefn * [r609] ObjCryst/ObjCryst/Crystal.cpp, ObjCryst/ObjCryst/IO.cpp, ObjCryst/ObjCryst/ScatteringPower.cpp, ObjCryst/ObjCryst/ScatteringPower.h, ObjCryst/wxCryst/wxCrystal.cpp, ObjCryst/wxCryst/wxScatteringPower.cpp: Changed "VAlence" for "Formal Charge" in ScatteringPowers. Now saving formal charge and bond-valence Ro parameters in xml files. 2005-02-28 00:33 vincefn * [r608] ObjCryst/ObjCryst/Crystal.cpp, ObjCryst/ObjCryst/Crystal.h, ObjCryst/ObjCryst/ScatteringPower.cpp, ObjCryst/ObjCryst/ScatteringPower.h, ObjCryst/wxCryst/wxCrystal.cpp: Added Bond-Valence Cost for a Crystal. 2005-02-26 22:28 vincefn * [r607] ObjCryst/RefinableObj/GlobalOptimObj.h, ObjCryst/RefinableObj/Simplex.h, ObjCryst/wxCryst/wxGlobalOptimObj.h: Cannot pass a parameter with a default value as a reference. 2005-02-26 22:26 vincefn * [r606] Fox/src/Fox.cpp: Added menu entry to close all objects, check before exiting that objects have been saved. 2005-02-26 21:01 vincefn * [r605] ObjCryst/wxCryst/wxAtom.cpp, ObjCryst/wxCryst/wxAtom.h, ObjCryst/wxCryst/wxCrystal.cpp, ObjCryst/wxCryst/wxMolecule.cpp, ObjCryst/wxCryst/wxPowderPattern.cpp, ObjCryst/wxCryst/wxRadiation.h, ObjCryst/wxCryst/wxScatterer.cpp, ObjCryst/wxCryst/wxScatteringPower.cpp, ObjCryst/wxCryst/wxScatteringPowerSphere.cpp, ObjCryst/wxCryst/wxZScatterer.cpp: Exclusively use RefinablePar::WXCreate(...) to create the wx representation of a RefinablePar, so that the RefinablePar knows of its existence and can delete it. 2005-02-26 20:56 vincefn * [r604] ObjCryst/RefinableObj/RefinableObj.cpp: Correct ObjRegistry::DeleteAll() - The wx representation of objects are deleted in the object, not from the ObjRegistry. 2005-02-26 20:49 vincefn * [r603] ObjCryst/RefinableObj/GlobalOptimObj.cpp, ObjCryst/RefinableObj/GlobalOptimObj.h: Add mXMLAutoSave choice "Every Run (Recommended)". 2005-02-22 07:16 vincefn * [r602] ObjCryst/RefinableObj/RefinableObj.cpp, ObjCryst/RefinableObj/RefinableObj.h: Added RefinableObjClock::operator=(...) to correctly copy clock 'time' without the list of parent/children clocks. 2005-02-22 07:14 vincefn * [r601] ObjCryst/ObjCryst/PowderPattern.cpp: Correct deletion of mpReflectionProfile when changing profile. Change column titles and rad->deg conversion for TOF. 2005-02-20 23:09 vincefn * [r600] ObjCryst/ObjCryst/ReflectionProfile.cpp: Corrected calculation of Berar-Baldinozzi Asymmetry function. Changed the default limts for the asymmetry parameters. 2005-02-20 20:59 vincefn * [r599] ObjCryst/ObjCryst/ReflectionProfile.cpp, ObjCryst/wxCryst/wxPowderPattern.cpp: Correct DE-PV profile calculation. Remove default limits for DE-PV parameters. 2005-02-18 23:45 vincefn * [r598] ObjCryst/RefinableObj/GlobalOptimObj.cpp, ObjCryst/RefinableObj/GlobalOptimObj.h, ObjCryst/RefinableObj/Simplex.cpp, ObjCryst/RefinableObj/Simplex.h, ObjCryst/wxCryst/wxGlobalOptimObj.cpp, ObjCryst/wxCryst/wxGlobalOptimObj.h: Separated the actual optimization from the MonteCarloObj::Optimize(...) function. Added a OptimizationObj::MultiRunOptimize(...) to perform optimization with multiple runs (the configuration being randomized at the beginning of each run). Also, added the ability to store and browse through multiple solutions. 2005-02-18 12:17 vincefn * [r597] ObjCryst/ObjCryst/Crystal.h, ObjCryst/ObjCryst/UnitCell.h: Correct inheritance for gpRefParTypeCrystal and gpRefParTypeUnitCell. 2005-02-18 12:09 vincefn * [r596] ObjCryst/ObjCryst/Molecule.cpp: Correct Molecule::GlobalOptRandomMove(...), the random change of occupancy inhibited random translation changes. 2005-02-17 11:09 vincefn * [r595] ObjCryst/ObjCryst/IO.cpp, ObjCryst/ObjCryst/PowderPattern.cpp, ObjCryst/ObjCryst/ReflectionProfile.cpp, ObjCryst/ObjCryst/ReflectionProfile.h, ObjCryst/wxCryst/wxPowderPattern.cpp: Now using a single ReflectionProfile::GetProfile(...) function, for both isotropic and anisotropic profiles. Also added a ReflectionProfileDoubleExponentialPseudoVoigt::mInstrumentAlpha0 parameter, and a few tooltips. 2005-02-16 12:55 vincefn * [r594] ObjCryst/ObjCryst/Crystal.cpp, ObjCryst/ObjCryst/Crystal.h, ObjCryst/wxCryst/wxCrystal.cpp, ObjCryst/wxCryst/wxCrystal.h: Added basic bond valence analysis function and user interface. 2005-02-15 00:39 vincefn * [r593] ObjCryst/wxCryst/wxCryst.cpp: Correctly handle addition/removal of objects from a WXCrystObjBasicList, when either the list or the object is deleted. 2005-02-15 00:37 vincefn * [r592] ObjCryst/wxCryst/wxPowderPattern.cpp, ObjCryst/wxCryst/wxPowderPattern.h: Added destructors for WXProfilePseudoVoigt and WXProfileDoubleExponentialPseudoVoigt. 2005-02-15 00:34 vincefn * [r591] ObjCryst/ObjCryst/ReflectionProfile.cpp: Added erfc function for windows compiler without the C99 functions. Also, take care of destroying wx objects if necessary. 2005-02-14 22:45 vincefn * [r590] ObjCryst/ObjCryst/IO.cpp: Added a ReflectionProfile base class to define powder pattern reflection profiles in a general way. Currently defined sub-classes are ReflectionProfilePseudoVoigt, for a standard pseudo-Voigt profile( inlcuding asymmetry description), and a ReflectionProfileDoubleExponentialPseudoVoigt profile, for neutron TOF data (profile description from Mark Pitt). 2005-02-14 14:29 vincefn * [r589] ObjCryst/ObjCryst/bc32.mak, ObjCryst/ObjCryst/gnu.mak, ObjCryst/ObjCryst/vc.mak: Added a ReflectionProfile base class to define powder pattern reflection profiles in a general way. Currently defined sub-classes are ReflectionProfilePseudoVoigt, for a standard pseudo-Voigt profile( inlcuding asymmetry description), and a ReflectionProfileDoubleExponentialPseudoVoigt profile, for neutron TOF data (profile description from Mark Pitt). 2005-02-14 10:47 vincefn * [r588] ObjCryst/ObjCryst/PowderPattern.cpp, ObjCryst/ObjCryst/PowderPattern.h, ObjCryst/ObjCryst/ReflectionProfile.cpp, ObjCryst/ObjCryst/ReflectionProfile.h, ObjCryst/RefinableObj/RefinableObj.cpp, ObjCryst/wxCryst/wxPowderPattern.cpp, ObjCryst/wxCryst/wxPowderPattern.h, ObjCryst/wxCryst/wxRefinableObj.cpp: Added a ReflectionProfile base class to define powder pattern reflection profiles in a general way. Currently defined sub-classes are ReflectionProfilePseudoVoigt, for a standard pseudo-Voigt profile( inlcuding asymmetry description), and a ReflectionProfileDoubleExponentialPseudoVoigt profile, for neutron TOF data (profile description from Mark Pitt). 2005-02-11 23:55 vincefn * [r587] ObjCryst/wxCryst/wxCryst.cpp, ObjCryst/wxCryst/wxCryst.h: Use std::set and std::map to store lists of objects/menus in WXCrystObjBasicList and WXCrystMenuBar. Also, keep in each WXCrystObjBasic a list of WXCrystObjBasicList which use this object, so that they can be notified upon destruction. 2005-01-17 22:02 vincefn * [r586] ObjCryst/RefinableObj/RefinableObj.cpp, ObjCryst/RefinableObj/RefinableObj.h: Added an access to the name of saved set of parameters. 2005-01-14 09:25 vincefn * [r585] Fox/src/Fox.cpp: Allow to automatically add the cost to the output filename when running Fox in non-gui mode. 2005-01-14 08:59 vincefn * [r584] ObjCryst/RefinableObj/GlobalOptimObj.cpp, ObjCryst/RefinableObj/GlobalOptimObj.h: TagNewBestConfig marked non-const 2005-01-13 17:08 vincefn * [r583] ObjCryst/RefinableObj/GlobalOptimObj.cpp, ObjCryst/RefinableObj/GlobalOptimObj.h, ObjCryst/wxCryst/wxGlobalOptimObj.cpp: Added a gamma law for the temperature & mutation amplitude schedules. 2005-01-13 09:41 vincefn * [r582] ObjCryst/RefinableObj/GlobalOptimObj.cpp: Correct Temperature and Mutation Amplitude schedules. 2005-01-13 09:39 vincefn * [r581] ObjCryst/ObjCryst/Molecule.cpp: Increase rotation amplitude for Molecules without any free torsion angle. 2005-01-12 09:43 vincefn * [r580] ObjCryst/wxCryst/wxMolecule.cpp: Correct numbering of atoms when adding a new one. 2005-01-11 22:53 vincefn * [r579] ObjCryst/wxCryst/wxMolecule.cpp: Smart numbering of new atoms (reusing the number at the end of the previous atom). Also, re-use previous bond length/bond angle/dihderal angle value for a new restraint. 2005-01-11 13:30 vincefn * [r578] ObjCryst/ObjCryst/Molecule.cpp, ObjCryst/wxCryst/wxMolecule.cpp, ObjCryst/wxCryst/wxMolecule.h: Normalize quaternion when doing internal optimization of a Molecule. Also, allow to print the status of all restraints in wxMolecule. 2005-01-10 22:35 vincefn * [r577] ObjCryst/wxCryst/wxMolecule.cpp: Correct layout update when adding an atom. 2005-01-10 21:52 vincefn * [r576] ObjCryst/wxCryst/wxCryst.cpp, ObjCryst/wxCryst/wxCrystal.cpp, ObjCryst/wxCryst/wxRefinableObj.cpp: Correct the Event Handling macro. This allows the background to be correctly updated for wxMSW, and fixes the problem with the end of the scrolled window being below the scrollbar. 2005-01-07 21:53 vincefn * [r575] ObjCryst/RefinableObj/RefinableObj.cpp, ObjCryst/wxCryst/wxCryst.cpp, ObjCryst/wxCryst/wxCryst.h, ObjCryst/wxCryst/wxRefinableObj.cpp: Use events to call WXCrystObj::Enable() in multi-threaded context. Also, had mutexes to lock data that is shared between (notably) CrystUpdate() and UpdateUI() in the WX* classes. 2005-01-07 21:39 vincefn * [r574] ObjCryst/ObjCryst/PowderPattern.cpp: Lower debug messages level in X2Pixel. 2005-01-07 12:33 vincefn * [r573] ObjCryst/ObjCryst/Crystal.cpp, ObjCryst/ObjCryst/Crystal.h, ObjCryst/ObjCryst/Scatterer.cpp, ObjCryst/ObjCryst/Scatterer.h, ObjCryst/ObjCryst/ScatteringData.cpp, ObjCryst/ObjCryst/ScatteringData.h, ObjCryst/ObjCryst/ScatteringPower.cpp, ObjCryst/ObjCryst/ScatteringPower.h, ObjCryst/ObjCryst/UnitCell.cpp, ObjCryst/ObjCryst/UnitCell.h, ObjCryst/RefinableObj/RefinableObj.cpp, ObjCryst/RefinableObj/RefinableObj.h: Use "nifty counters" to initialize static global objects (RefParType). 2005-01-06 23:51 vincefn * [r572] ObjCryst/RefinableObj/RefinableObj.cpp, ObjCryst/RefinableObj/RefinableObj.h: Remove pointer comparison (not supported by the c++ standard). 2004-12-18 23:46 vincefn * [r571] ObjCryst/wxCryst/wxCryst.cpp, ObjCryst/wxCryst/wxPowderPattern.cpp: Correct layout of windows. 2004-12-18 23:42 vincefn * [r570] ObjCryst/ObjCryst/ScatteringCorr.cpp: Make sure no floating-point exception occurs. 2004-12-15 19:10 vincefn * [r569] Fox/ChangeLog, Fox/gnu.mak, Fox/src/Fox.cpp, Fox/src/gnu.mak: Added the option to compile Fox under Linux without a GUI (i.e. without wxGTK), using "make Fox-nogui" 2004-12-11 22:02 vincefn * [r568] ObjCryst/Quirks/VFNStreamFormat.h: Commented out "friend" declaration to fix compilation using gcc 3.4.x. (The true fix would be to move the "template ostream& operator<< (...)" declarations _before_ the friend declaration, but since the friend declaration is not actually needed, why bother...) 2004-11-01 19:24 vincefn * [r567] ObjCryst/ObjCryst/PowderPattern.cpp, ObjCryst/wxCryst/wxPowderPattern.cpp: Small fixes to recent changes for TOF support (mostly due to handling of x (2theta,tof) array). 2004-10-31 23:52 vincefn * [r566] ObjCryst/ObjCryst/General.h, ObjCryst/ObjCryst/IO.cpp, ObjCryst/ObjCryst/PowderPattern.cpp, ObjCryst/ObjCryst/PowderPattern.h, ObjCryst/ObjCryst/ScatteringCorr.cpp, ObjCryst/ObjCryst/ScatteringCorr.h, ObjCryst/ObjCryst/ScatteringData.cpp, ObjCryst/ObjCryst/ScatteringData.h, ObjCryst/wxCryst/wxPowderPattern.cpp, ObjCryst/wxCryst/wxPowderPattern.h: Added support for neutron Time Of Flight data. 2004-10-24 21:32 vincefn * [r565] ObjCryst/ObjCryst/DiffractionDataSingleCrystal.cpp, ObjCryst/ObjCryst/DiffractionDataSingleCrystal.h, ObjCryst/ObjCryst/General.h, ObjCryst/ObjCryst/IO.cpp, ObjCryst/ObjCryst/PowderPattern.cpp, ObjCryst/ObjCryst/PowderPattern.h, ObjCryst/ObjCryst/ScatteringData.cpp, ObjCryst/ObjCryst/ScatteringData.h, ObjCryst/wxCryst/wxPowderPattern.cpp, ObjCryst/wxCryst/wxPowderPattern.h: Added support for non-constant step powder patterns, to prepare for neutron TOF data. Also begun to remove assumption that patterns and reflections are recorded as a function of 2theta. Also converted PowderPattern::GenHKLFullSpace() and ScatteringData::GenHKLFullSpace() to use a maximum value in sin(theta)/lambda (STOL) rather than 2theta. Changed ScatteringData::SortReflectionByTheta(...) to ScatteringData::SortReflectionBySinThetaOverLambda(...) 2004-10-22 10:16 vincefn * [r564] ObjCryst/rules-macosx.mak: Add linked frameworks for OpenGL & OSX 10.3, and correct linking order for libs. 2004-10-21 14:28 vincefn * [r563] Fox/macosx.mak: Fix clean target for MacOS X 2004-10-14 21:27 vincefn * [r562] ObjCryst/ObjCryst/Molecule.cpp: Also optimize overall occupancy of the Molecule if asked by the user. 2004-10-14 21:24 vincefn * [r561] ObjCryst/ObjCryst/PowderPattern.cpp: Inform the user during the Bayesian optimization of the background 2004-10-12 18:05 vincefn * [r560] ObjCryst/ObjCryst/PowderPattern.cpp, ObjCryst/ObjCryst/vc.mak, ObjCryst/RefinableObj/vc.mak: Fix compilation latest changes (powder pattern background bayesian minimization) for vc++. 2004-10-09 20:29 vincefn * [r559] ObjCryst/CrystVector/CrystVector.cpp, ObjCryst/CrystVector/CrystVector.h, ObjCryst/ObjCryst/PowderPattern.cpp, ObjCryst/ObjCryst/PowderPattern.h, ObjCryst/ObjCryst/PowderPatternBackgroundBayesianMinimiser.cpp, ObjCryst/ObjCryst/PowderPatternBackgroundBayesianMinimiser.h, ObjCryst/ObjCryst/bc32.mak, ObjCryst/ObjCryst/gnu.mak, ObjCryst/RefinableObj/GlobalOptimObj.cpp, ObjCryst/RefinableObj/GlobalOptimObj.h, ObjCryst/RefinableObj/Simplex.cpp, ObjCryst/RefinableObj/Simplex.h, ObjCryst/RefinableObj/bc32.mak, ObjCryst/RefinableObj/gnu.mak, ObjCryst/wxCryst/wxGlobalOptimObj.cpp, ObjCryst/wxCryst/wxPowderPattern.cpp, ObjCryst/wxCryst/wxPowderPattern.h: Added an algorithm object for minimizing the background of a powder pattern using the David & Sivia approach. Also added a Simplex algorithm class, as well as modified the way splines are computed. 2004-09-16 20:04 vincefn * [r558] ObjCryst/ObjCryst/Molecule.cpp: Throw an exception if we cannot find an atom. 2004-09-16 18:30 vincefn * [r557] ObjCryst/RefinableObj/IO.cpp, ObjCryst/RefinableObj/IO.h: Use STL vector to store XMLCrystTag attributes. 2004-09-16 18:29 vincefn * [r556] ObjCryst/ObjCryst/SpaceGroup.cpp: Always display the size of the (parallelepipedic) asymmetric unit. 2004-09-16 18:28 vincefn * [r555] ObjCryst/ObjCryst/UnitCell.cpp, ObjCryst/ObjCryst/UnitCell.h: Add UnitCell::GetVolume() 2004-09-16 18:27 vincefn * [r554] ObjCryst/ObjCryst/IO.cpp: Change handling of antibump distances. 2004-09-16 18:26 vincefn * [r553] ObjCryst/ObjCryst/Crystal.cpp, ObjCryst/ObjCryst/Crystal.h: Simpler and correct handling of AntiBump parameters (avoid duplicate antibump distances) 2004-09-12 22:02 vincefn * [r552] ObjCryst/wxCryst/wxCryst.cpp: Every time we destroy a widget, validate all input to make sure that WXCrystValidateAllUserInput() will not try to access a destroyed window. 2004-07-31 22:04 vincefn * [r551] Fox/src/Fox.cpp: Changed the scroll rate to (hopefully) avoid windows portions "hidden" beyond the scrollable area. 2004-07-19 21:37 vincefn * [r550] ObjCryst/ObjCryst/PowderPattern.cpp: Added VC++ kludge. 2004-07-17 06:13 vincefn * [r549] ObjCryst/ObjCryst/Molecule.cpp, ObjCryst/ObjCryst/Molecule.h: The rotation amplitude used for torsion angles and rigid body rotation is now tuned so that the average displacement per atom is equal to 0.1 Angstroem. 2004-05-26 20:40 vincefn * [r548] ObjCryst/ObjCryst/test.cpp: Use pointers to delete objects in the correct order. 2004-05-20 21:53 vincefn * [r547] ObjCryst/wxCryst/wxZScatterer.cpp: Used default delta value=0.02 in ZScatterer2Molecule(...) 2004-05-19 22:08 vincefn * [r546] ObjCryst/wxCryst/wxCryst.cpp: Fixed the BottomLayout(...) process. 2004-05-19 20:42 vincefn * [r545] ObjCryst/ObjCryst/ScatteringData.cpp: Correctly request an updated ScatteringComponentList to trigger the master clock. 2004-05-19 20:38 vincefn * [r544] ObjCryst/ObjCryst/Crystal.cpp, ObjCryst/ObjCryst/PowderPattern.cpp, ObjCryst/ObjCryst/PowderPattern.h: Fixes to use Maximum Likelihood positionnal errors, with a correct iterative scaling in the powder pattern. 2004-05-19 20:35 vincefn * [r543] ObjCryst/ObjCryst/Molecule.cpp, ObjCryst/ObjCryst/Molecule.h, ObjCryst/wxCryst/wxMolecule.cpp: Changed RotateAtomGroup(...) with an added option to keep un-rotated atoms unchanged in the Crystal unit cell. 2004-05-07 19:08 vincefn * [r542] ObjCryst/wxCryst/wxAtom.cpp, ObjCryst/wxCryst/wxCryst.cpp, ObjCryst/wxCryst/wxCryst.h, ObjCryst/wxCryst/wxCrystal.cpp, ObjCryst/wxCryst/wxDiffractionSingleCrystal.cpp, ObjCryst/wxCryst/wxGlobalOptimObj.cpp, ObjCryst/wxCryst/wxMolecule.cpp, ObjCryst/wxCryst/wxMolecule.h, ObjCryst/wxCryst/wxPowderPattern.cpp, ObjCryst/wxCryst/wxPowderPattern.h, ObjCryst/wxCryst/wxRefinableObj.cpp, ObjCryst/wxCryst/wxRefinableObj.h, ObjCryst/wxCryst/wxScatterer.cpp, ObjCryst/wxCryst/wxScatteringPower.cpp, ObjCryst/wxCryst/wxZScatterer.cpp, ObjCryst/wxCryst/wxZScatterer.h: Sanitized and standardized the Layout() process for wxCryst objects, using a BottomLayout() function to trigger a new Layout() using a bottom-top approach (children window tell their parent that they have been resized). 2004-05-06 16:18 vincefn * [r541] ObjCryst/RefinableObj/LSQNumObj.cpp: More stable Levenberg-Marquardt algorithm. 2004-05-03 10:02 vincefn * [r540] ObjCryst/wxCryst/wxPowderPattern.cpp: Use double-buffering when drawing powder patterns. 2004-05-02 20:08 vincefn * [r539] Fox/src/vc.mak, Fox/vc.mak, ObjCryst/CrystVector/vc.mak, ObjCryst/ObjCryst/vc.mak, ObjCryst/Quirks/vc.mak, ObjCryst/RefinableObj/vc.mak, ObjCryst/rules-vc.mak, ObjCryst/vc.mak, ObjCryst/wxCryst/vc.mak: Added makefiles for the free (as a beer) command-line compiler M$ Visual C++ 2003. Also requires the M$ Core, Internet and MDAC SDK (althugh stripping down wxWindows options would probably reduce that to the Core SDK). 2004-05-02 12:21 vincefn * [r538] ObjCryst/CrystVector/CrystVector.h, ObjCryst/ObjCryst/DiffractionDataSingleCrystal.cpp, ObjCryst/ObjCryst/ZScatterer.cpp: Undefined "min" and "max" macros used by MS VC++.... 2004-05-02 12:19 vincefn * [r537] ObjCryst/wxCryst/wxPowderPattern.cpp: Clarified use of pow() as pow(float, float). 2004-05-02 12:18 vincefn * [r536] ObjCryst/ObjCryst/IO.cpp: Removed useless (and misplaced) std namespace reference. 2004-04-21 23:44 vincefn * [r535] ObjCryst/RefinableObj/RefinableObj.cpp: Fix RefinableObjClock deletion behaviour (creates a infinite loop only with windows bcc32 compiler ?). Also, avoid modifying & clicking RefinablePar when no change is actually made. 2004-04-21 23:37 vincefn * [r534] Fox/src/Fox.cpp: Better Layout() behaviour for custom scrolled window. 2004-03-31 18:15 vincefn * [r533] ObjCryst/ObjCryst/PowderPattern.cpp: Coorectly compute null background when using spline, before any interpolation point has been added. 2004-03-24 23:30 vincefn * [r532] ObjCryst/rules-macosx.mak: More agressive compile flags (tuned by default for a G3) 2004-03-24 22:09 vincefn * [r531] Fox/src/Fox.cpp: Make previous change (about scrollbar & Layput problems) work as well on wxGTK. 2004-03-24 21:54 vincefn * [r530] Fox/src/Fox.cpp: Fixed scrolling problem with for MacOSX. 2004-03-24 20:01 vincefn * [r529] ObjCryst/wxCryst/wxCryst.cpp: Added kludge to enable the display of labels under MacOSX. 2004-03-24 19:42 vincefn * [r528] ObjCryst/rules-macosx.mak: Change linking order, to ensure base RefParType is initialized before all others, under MacOSX. Also remove unused include and library paths. 2004-03-23 20:06 vincefn * [r527] ObjCryst/rules-macosx.mak, ObjCryst/wxCryst/wxCrystal.cpp, ObjCryst/wxCryst/wxCrystal.h, ObjCryst/wxCryst/wxGlobalOptimObj.cpp, ObjCryst/wxCryst/wxGlobalOptimObj.h, ObjCryst/wxCryst/wxPowderPattern.cpp, ObjCryst/wxCryst/wxRefinableObj.cpp, ObjCryst/wxCryst/wxRefinableObj.h: Fixed event functions prototypes to be correct and compile using wx 2.5.1+. Also fixed compilation and linking under MacOS X. 2004-03-16 20:56 vincefn * [r526] ObjCryst/wxCryst/wxPowderPattern.cpp: Added limit (500) to the number of labels displayed on a powder pattern. 2004-02-04 12:46 vincefn * [r525] ObjCryst/ObjCryst/UnitCell.cpp: Use correct values for lattice parameters (using GetLatticePar(i)) in UnitCell::Print() 2004-02-01 12:51 vincefn * [r524] ObjCryst/ObjCryst/DiffractionDataSingleCrystal.cpp, ObjCryst/ObjCryst/Molecule.cpp: Small code modifications, including a few _deactivated_ SSE instructions. Speed improvement is small except on a p3 so it is only included as an example of SSE code. 2004-01-24 22:43 vincefn * [r523] ObjCryst/wxCryst/wxRefinableObj.cpp, ObjCryst/wxCryst/wxRefinableObj.h: Use a static popup menu (to change limits) for all WXFieldRefPar, rather than one for each parameter. Much better for memory usage, and also avoids hanging the program under windows (wxMSW 2.4.2) because of the too large number of used menus. 2004-01-24 19:12 vincefn * [r522] ObjCryst/ObjCryst/PowderPattern.cpp: Change debug level for message. 2004-01-24 19:09 vincefn * [r521] ObjCryst/ObjCryst/ScatteringData.cpp: Correctly handle the case when one listed ScatteringPower is not used, when computing structure factors. 2004-01-21 22:30 vincefn * [r520] ObjCryst/wxCryst/wxZScatterer.cpp: In ZScatterer2Molecule, avoid creating H-H bonds. 2004-01-21 22:10 vincefn * [r519] Fox/src/Fox.cpp: Increase Fox version to 1.6.1CVS. Also, change the speedtest configuration to use more atoms (20 instead of 10). 2004-01-21 22:06 vincefn * [r518] ObjCryst/ObjCryst/PowderPattern.cpp: Do not go beyond last point when computing full patterns (again). 2004-01-21 22:04 vincefn * [r517] ObjCryst/ObjCryst/ScatteringData.cpp: Add crystal lattice parameters clock as a child of the Scatteringdata master clock. 2004-01-19 18:16 vincefn * [r516] ObjCryst/ObjCryst/PowderPattern.cpp: Remove out-of-bounds pointer access. 2004-01-18 20:53 vincefn * [r515] ObjCryst/wxCryst/wxPowderPattern.cpp, ObjCryst/wxCryst/wxPowderPattern.h: Add keyboard control to change the scale and the theta range of the displayed powder pattern. 2004-01-17 13:22 vincefn * [r514] ObjCryst/wxCryst/wxMolecule.cpp: Correctly display sigma on bond angles in degrees, not radians. 2004-01-08 23:50 vincefn * [r513] ObjCryst/ObjCryst/ScatteringData.cpp, ObjCryst/ObjCryst/ScatteringData.h: Updated th process to compute scattering factors. The PrepareCalcStructFactor() function has finally been removed and the recalculation of scattering factors (resonant and Thomson part), temperature factors, geometrical structure factor, ... are finally decided using the clocks. This is much simpler and efficient. 2004-01-08 23:44 vincefn * [r512] ObjCryst/ObjCryst/Crystal.cpp, ObjCryst/ObjCryst/Crystal.h: Added a MasterClockScatteringPower, to report any change in ScatteringPowers. 2004-01-04 13:35 vincefn * [r511] ObjCryst/ObjCryst/PowderPattern.cpp, ObjCryst/ObjCryst/PowderPattern.h: More efficient computation of integrated powder pattern. 2004-01-01 13:28 vincefn * [r510] ObjCryst/ObjCryst/PowderPattern.cpp: Coorectly separate successive ranges for integrated profiles. 2004-01-01 13:22 vincefn * [r509] ObjCryst/ObjCryst/ScatteringData.cpp: Only compute Luzzati factors if necessary. 2004-01-01 13:21 vincefn * [r508] ObjCryst/ObjCryst/IO.cpp, ObjCryst/ObjCryst/PowderPattern.cpp, ObjCryst/ObjCryst/PowderPattern.h, ObjCryst/ObjCryst/test.cpp: Enable cubic splines interpolation for powder pattern background. Also add a function to set interpolation points, and use it for speed tests. 2003-12-13 22:33 vincefn * [r507] Fox/src-doc/GarnetFourier-pov.png, Fox/src-doc/index.dox, Fox/src-doc/ktartrate-pov.jpg: Update download links for release version and UniGe server unavailable. 2003-12-08 19:14 vincefn * [r504] Fox/ChangeLog, Fox/src-doc/Doxyfile, Fox/src/Fox.cpp: version -> 1.6.0.2 2003-12-08 19:05 vincefn * [r503] ObjCryst/wxCryst/wxMolecule.cpp, ObjCryst/wxCryst/wxMolecule.h: Correctly notify MolAtom, MolBond, MoldBondAngle and MolDihedralAngle in the destructor of the corresponding WX objects. 2003-12-08 18:54 vincefn * [r502] ObjCryst/rules-gnu.mak: Added -lXmu for linking with RedHat 9.0 to avoid unresolved symbol with glut.so. 2003-12-07 23:43 vincefn * [r501] ObjCryst/rules-macosx.mak: Added -DHAVE_GLUT to use glut by default for font display on OSX (to be tested). 2003-12-07 10:03 vincefn * [r500] Fox/ChangeLog, Fox/src-doc/Doxyfile, Fox/src/Fox.cpp: Version is 1.6.0.1 2003-12-06 21:49 vincefn * [r499] ObjCryst/wxCryst/wxCrystal.cpp: Correct lighting for negative contour values. 2003-12-06 20:51 vincefn * [r498] Fox/ChangeLog: Updated version to 1.6.1. 2003-12-06 20:42 vincefn * [r497] Fox/src-doc/GarnetFourier-pov.png, Fox/src-doc/manual.dox, Fox/src-doc/screenshot.dox, Fox/src/Fox.cpp: Changed version to 1.6.1. Added loading of DSN6 fourier maps, and updated documentation. 2003-12-06 20:40 vincefn * [r496] ObjCryst/wxCryst/wxCrystal.cpp, ObjCryst/wxCryst/wxCrystal.h: Added import of DSN6 fourier maps, which can be created by forplot in GSAS. Also, fixed a number of issues with the 3D display of Crystal structures (coherent choice of display limits, correct display of view center coordinates). For Fourier maps with negative contour values, the negative side will now be highlighted instead of the positive side. 2003-12-05 16:44 vincefn * [r495] Fox/ChangeLog: Change release version from 1.5.1 to 1.6.0 2003-12-02 22:30 vincefn * [r494] Fox/example/Cimetidine-powder.xml, Fox/example/Cimetidine.xml, Fox/example/ktartrate-textured.xml, Fox/example/ktartrate.xml, Fox/example/pbso4-joint.xml: Change delta values for Molecular restraints to 0.02 (new default). 2003-11-29 23:15 vincefn * [r493] Fox/example/Cimetidine-powder.xml, Fox/example/brucite-textured.xml, Fox/example/ktartrate-textured.xml, Fox/example/ktartrate.xml, Fox/example/pbso4-joint.xml, Fox/src-doc/crystal.map, Fox/src-doc/manual.dox: Update powder ddiffraction example files to slightly tune the 2theta zero parameter, improving the Rwp and Rp. Integrated Chi^2 slightly changed. Also small documentation update for the AntiBump. 2003-11-29 14:14 vincefn * [r492] Fox/src-doc/Doxyfile: Update doc for Fox release 1.6 2003-11-29 14:05 vincefn * [r491] Fox/ChangeLog, Fox/src-doc/compile.dox, Fox/src-doc/crystal.jpg, Fox/src-doc/crystal.map, Fox/src-doc/gnu.mak, Fox/src-doc/index.dox, Fox/src-doc/ktartrate-pov.jpg, Fox/src-doc/manual.dox, Fox/src-doc/screenshot.dox, Fox/src/Fox.cpp: Update doc for Fox release 1.6 2003-11-29 13:57 vincefn * [r490] ObjCryst/rules-bc32.mak: Changes to support wxWindows 2.4.x. 2003-11-29 08:43 vincefn * [r489] Fox/src/Fox.cpp: Directly show Crystal tab after Fox startup. 2003-11-28 22:48 vincefn * [r488] ObjCryst/ObjCryst/Crystal.cpp, ObjCryst/wxCryst/wxCrystal.cpp, ObjCryst/wxCryst/wxCrystal.h: Added Fourier Maps support in POV-Ray output, with a few lighting changes. Also, correctly delete triangles after running MC (in OpenGL and in POV-Ray). 2003-11-28 16:40 vincefn * [r487] ObjCryst/ObjCryst/Atom.cpp, ObjCryst/ObjCryst/Crystal.cpp, ObjCryst/ObjCryst/Molecule.cpp, ObjCryst/wxCryst/wxCrystal.cpp: A few improvements to POV-Ray output, fixing translation error. 2003-11-28 00:10 vincefn * [r486] ObjCryst/ObjCryst/Atom.cpp, ObjCryst/ObjCryst/Atom.h, ObjCryst/ObjCryst/Crystal.cpp, ObjCryst/ObjCryst/Crystal.h, ObjCryst/ObjCryst/General.h, ObjCryst/ObjCryst/Molecule.cpp, ObjCryst/ObjCryst/Molecule.h, ObjCryst/ObjCryst/Scatterer.h, ObjCryst/ObjCryst/ZScatterer.cpp, ObjCryst/ObjCryst/ZScatterer.h, ObjCryst/wxCryst/wxCrystal.cpp, ObjCryst/wxCryst/wxCrystal.h: Fixed existing functions for POV-Ray output, added it for Molecule and created a menu in the 3D crystal view to export the scene to a POV-Ray script. 2003-11-25 22:33 vincefn * [r485] Fox/ChangeLog: updated ChangeLog towards 1.5.1 bug fix release. 2003-11-25 22:06 vincefn * [r484] Fox/src-doc/compile.dox, Fox/src-doc/development.dox, Fox/src-doc/faq.dox, Fox/src-doc/index.dox, Fox/src-doc/manual.dox, Fox/src-doc/screenshot.dox, Fox/src-doc/tutorial-cimetidine.dox: Updated documentation, also with formatting fixes and better use of doxygen >1.3 2003-11-25 21:11 vincefn * [r483] ObjCryst/wxCryst/wxMolecule.cpp, ObjCryst/wxCryst/wxMolecule.h: Added a menu to change globally the delta and sigma parameters for all restraints. Also added the display of the delta and sigma parameters for all restraints. 2003-11-25 21:09 vincefn * [r482] ObjCryst/ObjCryst/Molecule.cpp, ObjCryst/ObjCryst/Molecule.h: Tuned the amplitude of random rotations for the "Rigid Body" and "User-Chosen Free torsion" flexibility option. Also, added access to the delta and sigma parameters for bond and dihedral angles. 2003-11-25 21:01 vincefn * [r481] Fox/src/Fox.cpp: Added --speedtest command-line option. 2003-11-25 21:00 vincefn * [r480] ObjCryst/ObjCryst/bc32.mak, ObjCryst/ObjCryst/gnu.mak, ObjCryst/ObjCryst/test.cpp, ObjCryst/ObjCryst/test.h: Added test file with functions to test the speed of ObjCryst++/Fox. 2003-11-25 11:00 vincefn * [r479] ObjCryst/ObjCryst/Crystal.cpp: In Crystal::GetMinDistanceTable(mindist), do not use a minimum distance when mindist<0. 2003-11-21 13:38 vincefn * [r478] ObjCryst/rules-gnu.mak, ObjCryst/wxCryst/wxCrystal.cpp: Revert to using GLUT to display text in the OpenGL crystal view, under Linux. 2003-11-15 22:43 vincefn * [r477] ObjCryst/ObjCryst/PowderPattern.cpp: Take into account correctly correction to 2theta values (zero, transparency, displacement) when computing profiles. Also, compute correctly full profiles for X-Ray tube radiation, using a single profile for the two lines. 2003-11-15 15:34 vincefn * [r476] ObjCryst/ObjCryst/PowderPattern.cpp: Correctly recompute pattern when 2theta corrections parameters (zero, transparency, displacement) have been changed. 2003-11-15 14:38 vincefn * [r475] ObjCryst/wxCryst/wxPowderPattern.cpp, ObjCryst/wxCryst/wxPowderPattern.h: Improve precision of data display, especially along the x axis. 2003-11-15 14:22 vincefn * [r474] ObjCryst/ObjCryst/PowderPattern.cpp: Correct calculation of profile, which was shifted from its true position by up to 2 pixels... 2003-11-07 23:47 vincefn * [r473] ObjCryst/ObjCryst/Molecule.cpp, ObjCryst/ObjCryst/Molecule.h, ObjCryst/wxCryst/wxMolecule.cpp: Added an option to enable the optimization of the Molecule's orientation, and enabled the option to choose the flexibility model. Also, correctly read Options from an XML input. 2003-11-07 22:15 vincefn * [r472] ObjCryst/ObjCryst/IO.cpp, ObjCryst/ObjCryst/ScatteringData.cpp, ObjCryst/wxCryst/wxDiffractionSingleCrystal.cpp, ObjCryst/wxCryst/wxPowderPattern.cpp: Added Support for Cobalt X-Ray tube. Also, the delta(lambda) and Alpha2/Alpha1 ratio are now saved in the xml file for an X-Ray tube. 2003-11-01 12:32 vincefn * [r471] ObjCryst/ObjCryst/Molecule.cpp, ObjCryst/ObjCryst/Molecule.h: Add an option to automatically optimize the starting conformation of the Molecule, which is normally done in BeginOptimization(). 2003-10-31 23:36 vincefn * [r470] ObjCryst/wxCryst/wxRefinableObj.cpp: Allow any number of choices in WXDialogChooseFromRegistry(..) 2003-10-31 23:34 vincefn * [r469] ObjCryst/wxCryst/wxCryst.cpp: Do not call UpdateUI() in WXCrystObj::Layout(), to avoid very inefficient GUI update (scales as n^2 instead of expected n). 2003-10-31 17:59 vincefn * [r468] ObjCryst/ObjCryst/Molecule.cpp: In a molecule, give the full label for each atom rather than the scattering power type, in Molecule::GetComponentName(...). This is used for CIF output. 2003-10-28 21:19 vincefn * [r467] ObjCryst/ObjCryst/Molecule.cpp: Correctly set mpWXCrystObj for bond, bond angle and dihedral angle in constructors. 2003-10-24 21:12 vincefn * [r466] Fox/src/Fox.cpp: Set version to 1.5.1CVS, and remove redundant (memory leeking, too) 'new' statement. 2003-10-24 21:10 vincefn * [r465] ObjCryst/wxCryst/wxPowderPattern.cpp: Fixed display of powder pattern graph in wxMSW 2.4 2003-10-24 19:49 vincefn * [r464] ObjCryst/ObjCryst/DiffractionDataSingleCrystal.cpp, ObjCryst/ObjCryst/PowderPattern.cpp: When computing Chi2, move test to see if there is any data sooner in the code to avoid problems. 2003-10-24 18:55 vincefn * [r463] ObjCryst/wxCryst/wxCrystal.cpp: Fix behavior for wxMSW 2.4. (initial display of status bar on GL window, and avoid event when leaving the GL window). 2003-10-12 19:18 vincefn * [r462] ObjCryst/ObjCryst/Molecule.cpp, ObjCryst/wxCryst/wxCryst.cpp, ObjCryst/wxCryst/wxMolecule.cpp, ObjCryst/wxCryst/wxMolecule.h: Bugfix: correctly delete wx representations of Bond, Bond Angle and Dihedral Angle windows. 2003-10-12 13:14 vincefn * [r461] ObjCryst/ObjCryst/Molecule.cpp, ObjCryst/ObjCryst/PowderPattern.cpp: Small bugfixes. 2003-10-11 22:09 vincefn * [r460] ObjCryst/wxCryst/wxCryst.cpp, ObjCryst/wxCryst/wxCryst.h: When calling Enable(bool) for a window, also calls Enable(..) for sub-windows, so that they are effectively dis/enabled even if they are in a separete window or frame. 2003-10-11 21:31 vincefn * [r459] ObjCryst/wxCryst/wxMolecule.cpp: When removing a Bond, also offer to remove all Bond and Dihedral Angles that involve this bond. 2003-10-11 20:50 vincefn * [r458] ObjCryst/wxCryst/wxMolecule.cpp: Allow to remove multiple Atoms/Bonds/BondAngles/DihedralAngles using wxMultiChoiceDialog. 2003-10-11 09:01 vincefn * [r457] ObjCryst/ObjCryst/Crystal.cpp, ObjCryst/ObjCryst/DiffractionDataSingleCrystal.cpp, ObjCryst/ObjCryst/Molecule.cpp, ObjCryst/ObjCryst/PowderPattern.cpp, ObjCryst/ObjCryst/Scatterer.cpp, ObjCryst/ObjCryst/ScatteringData.cpp, ObjCryst/ObjCryst/ScatteringPower.cpp, ObjCryst/ObjCryst/UnitCell.cpp, ObjCryst/RefinableObj/RefinableObj.cpp, ObjCryst/RefinableObj/RefinableObj.h: Added a pzrennt/children relationship to Clocks, so that a child clock clicks it parent(s) when it is clicked itself (check is made for loops when adding a parent). This is used to bypass calculations when an object and its sub-objects has not been modified since last calculations, bypassing more complex checks to determine what needs to be recomputed. 2003-10-04 21:45 vincefn * [r456] ObjCryst/RefinableObj/GlobalOptimObj.cpp, ObjCryst/RefinableObj/GlobalOptimObj.h: Add the ability to set a mximum time for the duration of the optimization. Also, store the actual time used for the optimization, for testing purposes. 2003-09-21 12:40 vincefn * [r455] ObjCryst/ObjCryst/PowderPattern.cpp, ObjCryst/ObjCryst/PowderPattern.h, ObjCryst/wxCryst/wxPowderPattern.cpp, ObjCryst/wxCryst/wxPowderPattern.h: Added Labels on powder patterns (practically used for reflection names). 2003-09-19 22:40 vincefn * [r454] ObjCryst/ObjCryst/Molecule.cpp: To detect free torsion bonds, take into account when bond angle and dihedral angle restraints have been modified. Also, handle the case when we do not start from a minimum of a restraint when testing for torsions to break restraints. 2003-09-19 21:45 vincefn * [r453] ObjCryst/ObjCryst/ScatteringData.cpp: Take care of when the name of an X-Ray tube is not understood. 2003-08-13 11:32 vincefn * [r452] Fox/src-doc/faq.dox: Updated the FAQ regarding the use of the AntiBump in a Crystal structure. 2003-08-09 07:50 vincefn * [r451] ObjCryst/ObjCryst/Crystal.cpp, ObjCryst/ObjCryst/Crystal.h, ObjCryst/ObjCryst/IO.cpp, ObjCryst/wxCryst/wxCrystal.cpp, ObjCryst/wxCryst/wxCrystal.h: Added a scale to the AntiBump/ProMerge cost in Crystal. 2003-08-09 07:45 vincefn * [r450] ObjCryst/RefinableObj/GlobalOptimObj.cpp: Keep record of how the wolrds have been swapped during parallel tempering, and modify the printed and saved display accordingly. 2003-08-05 20:29 vincefn * [r449] ObjCryst/ObjCryst/Molecule.cpp: Do not try flipping if there are no FlipGroups (and computing modulo[0] triggers a floating-point exception). 2003-07-31 19:15 vincefn * [r448] Fox/src/Fox.cpp: Set version to 1.5.0.4 2003-07-31 19:09 vincefn * [r447] ObjCryst/ObjCryst/Molecule.cpp: Avoid asin(x) error when abs(x)>1 2003-07-23 22:04 vincefn * [r446] Fox/src-doc/index.dox: Changed fox sourceforge download link. 2003-07-20 17:31 vincefn * [r444] ObjCryst/ObjCryst/ScatteringData.cpp: Correctly recompute resonant scattering factors when the wavelength has changed. 2003-07-19 23:32 vincefn * [r443] Fox/src-doc/index.dox: Update doc about known problems. 2003-07-19 16:47 vincefn * [r442] ObjCryst/ObjCryst/Molecule.cpp, ObjCryst/ObjCryst/PowderPattern.cpp, ObjCryst/wxCryst/wxPowderPattern.cpp, ObjCryst/wxCryst/wxZScatterer.cpp: Changed all incorrect abs(...) to fabs(...) 2003-07-19 15:29 vincefn * [r441] ObjCryst/wxCryst/wxMolecule.cpp: Added a dialog to ask for the initial values of bond lengths, angles and dihedral angles. 2003-07-19 14:45 vincefn * [r440] Fox/src-doc/manual.dox, Fox/src/Fox.cpp: Updated version number to 1.5.0.3. Added the ability to profile Fox using Tau. Updated the documentation about bond, angle, dihedral angle lists, and rigid body mode. 2003-07-19 14:27 vincefn * [r439] ObjCryst/ObjCryst/Molecule.cpp, ObjCryst/ObjCryst/Molecule.h, ObjCryst/wxCryst/wxMolecule.cpp, ObjCryst/wxCryst/wxMolecule.h: Added Molecule::FindDihedralAngle(...) and Molecule::RigidifyWithDihedralAngles(). Also fixed a few display problems for the lists of bonds, angles and dihedral angles. 2003-07-19 00:04 vincefn * [r438] ObjCryst/ObjCryst/Molecule.cpp, ObjCryst/ObjCryst/Molecule.h, ObjCryst/wxCryst/wxMolecule.cpp, ObjCryst/wxCryst/wxMolecule.h: Implemented the option defining the flexibility of a Molecule, either using auto-detected free torsion angles (the default), or as a rigid body, or as a rigid body plus user-chosen torsion angles. Also, in a WXMolecule the lists of bonds, bond angles and dihedral angles are not shown by default, but can be displayed in separate windows. 2003-07-18 12:28 vincefn * [r437] ObjCryst/ObjCryst/IO.cpp: Handle situation where there are no data points for the powder pattern in an xml file. 2003-07-15 19:51 vincefn * [r436] Fox/src/Fox.cpp: Upgrade Fox version for last beta fixes. 2003-07-15 19:50 vincefn * [r435] ObjCryst/ObjCryst/PowderPattern.cpp: Fix computing powder pattern when there is no component. 2003-07-12 22:07 vincefn * [r434] ObjCryst/ObjCryst/PowderPattern.cpp: More fixes when adding powder pattern components while using integrated profiles. 2003-07-12 19:35 vincefn * [r433] ObjCryst/ObjCryst/PowderPattern.cpp, ObjCryst/wxCryst/wxPowderPattern.cpp: Handle cases when there is no observed powder pattern, or no component to calculate the powder pattern. 2003-07-12 13:29 vincefn * [r432] Fox/src/Fox.cpp: Update version to 1.5.0.1 2003-07-12 13:13 vincefn * [r431] ObjCryst/ObjCryst/ScatteringData.cpp: Correctly compute the number of reflection used below the max sin(theta)/lambda. 2003-07-12 12:52 vincefn * [r430] ObjCryst/ObjCryst/PowderPattern.cpp: Avoid computing log of weights when weight<=0. 2003-07-12 12:29 vincefn * [r429] ObjCryst/ObjCryst/PowderPattern.cpp: Avoid division by zero when computing weights of integrated profiles. 2003-07-12 12:27 vincefn * [r428] Fox/src/Fox.cpp: Workaround wxMSW 2.2.9 bug when updating scrollbars. 2003-07-10 13:43 vincefn * [r427] Fox/macosx.mak, Fox/src/Fox.cpp, Fox/src/macosx.mak, ObjCryst/ObjCryst/Atom.cpp, ObjCryst/ObjCryst/Molecule.cpp, ObjCryst/ObjCryst/ZScatterer.cpp, ObjCryst/rules-macosx.mak, ObjCryst/wxCryst/wxCrystal.cpp: Added support for MacOSX using Apple Development tools. 2003-07-09 12:47 vincefn * [r426] Fox/example/Cimetidine.xml: Set all weights to 0.01, to work in un-weighted mode since we do not have real sigmas. 2003-07-09 10:58 vincefn * [r425] Fox/src-doc/compile.dox, Fox/src-doc/index.dox: Removed refenrences to the glut library. 2003-07-08 21:45 vincefn * [r424] Fox/src-doc/manual.dox: Update doc with some information about the R and L checkboxes for refinable parameters. 2003-07-08 21:39 vincefn * [r423] ObjCryst/wxCryst/wxRefinableObj.cpp: Correct the display of R and L buttons for WXFieldRefPar. 2003-07-08 21:37 vincefn * [r422] ObjCryst/ObjCryst/PowderPattern.cpp: Correct bug with weights when using integrated profiles. 2003-07-07 19:31 vincefn * [r421] ObjCryst/ObjCryst/PowderPattern.cpp: Avoid division by zero when computing weights from null variances. 2003-07-07 00:12 vincefn * [r420] Fox/src/Fox.cpp: Created derived WXCrystScrolledWindow to dynamically adjust scrollbars to their correct values, for the Crystal, Powder Pattern, Single Crystal, and Global Optimization tabs. 2003-07-06 23:03 vincefn * [r419] ObjCryst/ObjCryst/Molecule.cpp, ObjCryst/ObjCryst/Molecule.h, ObjCryst/wxCryst/wxCryst.cpp, ObjCryst/wxCryst/wxCrystal.cpp, ObjCryst/wxCryst/wxMolecule.cpp, ObjCryst/wxCryst/wxRefinableObj.cpp, ObjCryst/wxCryst/wxZScatterer.cpp: Try to diminish the number of graphical updates, especially for large Molecules. 2003-06-29 13:51 vincefn * [r418] Fox/src-doc/compile.dox: Added compiling notes for wxWindows 2.4.1 2003-06-29 12:40 vincefn * [r417] Fox/src/Fox.cpp: Set default maximum sin(theta)/lambda to 0.4 (resolution = 1.25 Angstroem). 2003-06-29 12:39 vincefn * [r416] ObjCryst/wxCryst/wxScatteringPower.cpp: Disabled use of Maximum likelihood parameter. 2003-06-29 12:29 vincefn * [r415] ObjCryst/ObjCryst/DiffractionDataSingleCrystal.cpp, ObjCryst/wxCryst/wxDiffractionSingleCrystal.cpp: Correctly compute Chi2, and avoid division by 0 when displaying the GoF when there is no diffraction data. 2003-06-29 12:28 vincefn * [r414] ObjCryst/wxCryst/wxCrystal.cpp: Correct position of cursor in OpenGL crystal view. 2003-06-28 22:25 vincefn * [r413] ObjCryst/wxCryst/wxCrystal.cpp, ObjCryst/wxCryst/wxCrystal.h: Corrections to correctly generate and use the OpenGL font display list under windows, as well as for multiple WXGLCrystalCanvas views. 2003-06-28 18:22 vincefn * [r412] ObjCryst/ObjCryst/Atom.cpp, ObjCryst/ObjCryst/Crystal.cpp, ObjCryst/ObjCryst/General.h, ObjCryst/ObjCryst/Molecule.cpp, ObjCryst/ObjCryst/Scatterer.cpp, ObjCryst/ObjCryst/ZScatterer.cpp, ObjCryst/rules-bc32.mak, ObjCryst/rules-gnu.mak, ObjCryst/wxCryst/wxCrystal.cpp, ObjCryst/wxCryst/wxCrystal.h: Try to generate directly an OpenGL font, without need for the glut library. 2003-06-25 22:53 vincefn * [r411] Fox/ChangeLog, Fox/example/Cimetidine-powder.xml, Fox/example/Cimetidine.xml, Fox/example/ktartrate-textured.xml, Fox/example/ktartrate.xml, Fox/example/pbso4-joint.xml, Fox/src-doc/Doxyfile, Fox/src-doc/compile.dox, Fox/src-doc/example.dox, Fox/src-doc/faq.dox, Fox/src-doc/header.html, Fox/src-doc/index.dox, Fox/src-doc/manual.dox, Fox/src-doc/tutorial-cimetidine.dox, Fox/src-doc/tutorial-pbso4.dox: Updated documentation for Fox release 1.5. 2003-06-25 22:47 vincefn * [r410] ObjCryst/wxCryst/wxCrystal.cpp: Correctly generate short filenames for Fourier and Z-matrix file input. 2003-06-25 22:30 vincefn * [r409] ObjCryst/ObjCryst/Molecule.cpp: Removed (for the moment) the option to choose the flexibility type of the Molecule. 2003-06-25 22:13 vincefn * [r408] ObjCryst/wxCryst/wxCrystal.cpp: Use a shorter name for the Molecule when importing from a file with a Fenske-Hall Z-matrix. 2003-06-25 21:14 vincefn * [r407] Fox/src/Fox.cpp: Increase scroll size for crystal structures tab. 2003-06-25 21:13 vincefn * [r406] ObjCryst/wxCryst/wxCrystal.cpp, ObjCryst/wxCryst/wxCrystal.h: Added a menu to import a Molecule structure from a Fenske-Hall Z-Matrix. 2003-06-25 21:12 vincefn * [r405] ObjCryst/wxCryst/wxRefinableObj.cpp: In WXFieldRefPar, do not display tooltip or make the popup-menu to change limits available when the limits and refined buttons are not visible. 2003-06-25 21:08 vincefn * [r404] ObjCryst/ObjCryst/Molecule.cpp: Implemented copy constructor. 2003-06-25 20:38 vincefn * [r403] ObjCryst/doc/doc-main.h: Added warning about outdated documentation. 2003-06-24 20:54 vincefn * [r402] ObjCryst/ObjCryst/Molecule.cpp: Small fixes for better conformance with ISO C++, and a happier compilation with Borland bcc32. 2003-06-22 16:02 vincefn * [r401] Fox/src/Fox.cpp: et version 1.5. Added test code for Make{Polyhedron} 2003-06-22 15:47 vincefn * [r400] ObjCryst/ObjCryst/Polyhedron.cpp, ObjCryst/ObjCryst/Polyhedron.h, ObjCryst/ObjCryst/bc32.mak, ObjCryst/ObjCryst/gnu.mak, ObjCryst/wxCryst/wxCrystal.cpp: Added functions to create Molecule-based Polyhedra, MakeTetrahedron...MakeIcosahedron, etc... 2003-06-22 15:45 vincefn * [r399] ObjCryst/wxCryst/wxZScatterer.cpp: ZScatterer2Molecule will now avoid setting any DihedralAngle restraint, and will rather add every possible BondAngle restraint. 2003-06-22 15:42 vincefn * [r398] ObjCryst/ObjCryst/Molecule.cpp, ObjCryst/ObjCryst/Molecule.h: Added Molecule::FindBondAngle() and Molecule::GetConnectivityTable(). 2003-06-21 14:20 vincefn * [r397] ObjCryst/wxCryst/wxGlobalOptimObj.cpp: Always save as an xml file at the end of an optimization. 2003-06-21 14:19 vincefn * [r396] ObjCryst/ObjCryst/Molecule.cpp: Bring back the average Molecule position in internal coordinates to (0,0,0) during a global optimization, from time to time... 2003-06-21 12:11 vincefn * [r395] ObjCryst/ObjCryst/Molecule.cpp, ObjCryst/ObjCryst/Molecule.h, ObjCryst/wxCryst/wxMolecule.cpp: Changed the way special rotation groups are stored and used in the Molecule class, using sub-classes RotorGroup and FlipGroup. The latter class allows to exchange bonds around one atom, to either change the absolute configuration around that atom, or to do a 180� flip of the two bonds. 2003-06-14 21:06 vincefn * [r394] ObjCryst/wxCryst/wxCrystal.cpp: Auto-convert all newly generated ZPolyhedra to a Molecule. Removed the ability to create a ZScatterer. 2003-06-14 21:04 vincefn * [r393] ObjCryst/ObjCryst/Crystal.cpp: Exclude dummy atoms from CIF output and dynamical occupancy correction. 2003-06-14 19:10 vincefn * [r392] ObjCryst/wxCryst/wxZScatterer.cpp: Fixed ZScatterer2Molecule() so that it also works with Dummy atoms. 2003-06-14 19:08 vincefn * [r391] ObjCryst/ObjCryst/ZScatterer.cpp, ObjCryst/ObjCryst/ZScatterer.h: Added a direct access to the orthonormal coordinates of all ZAtoms, as well as to the index of the center atom. 2003-06-14 16:37 vincefn * [r390] ObjCryst/ObjCryst/Crystal.cpp, ObjCryst/ObjCryst/Molecule.cpp, ObjCryst/ObjCryst/Molecule.h, ObjCryst/ObjCryst/Scatterer.cpp, ObjCryst/ObjCryst/Scatterer.h, ObjCryst/ObjCryst/ZScatterer.cpp, ObjCryst/ObjCryst/ZScatterer.h, ObjCryst/wxCryst/wxMolecule.cpp, ObjCryst/wxCryst/wxZScatterer.cpp, ObjCryst/wxCryst/wxZScatterer.h: Added the conversion from a ZScatterer to a Molecule. 2003-06-12 21:14 vincefn * [r389] ObjCryst/ObjCryst/Molecule.cpp: Small fixes for compiling errors and a integer/float autoconversion bug, for the Borland C++ compiler bcc. 2003-06-12 18:57 vincefn * [r388] ObjCryst/ObjCryst/Crystal.cpp: In Crystal::CIFOutput(...), remove atoms that are fully overlapping with another atom (but keep it as a comment, just in case). 2003-06-06 21:46 vincefn * [r387] ObjCryst/ObjCryst/Molecule.cpp, ObjCryst/ObjCryst/Molecule.h: Made automatic the initial optimization of the Molecule conformation if the Likelihood is too high, in BeginOptimization() as well as RandomizeConformation(). 2003-06-05 22:34 vincefn * [r386] ObjCryst/ObjCryst/Molecule.cpp, ObjCryst/wxCryst/wxMolecule.cpp: The Bond and Dihedral Angles are now displayed and stored in the xml file as degrees. Also, reduced the debug output from the Molecule and derived objects. 2003-06-05 22:31 vincefn * [r385] ObjCryst/wxCryst/wxCryst.cpp, ObjCryst/wxCryst/wxCryst.h: Added the possibility of scaling the parameter for user display in WXFieldParBase (for angles). 2003-06-05 22:29 vincefn * [r384] ObjCryst/wxCryst/wxRefinableObj.cpp, ObjCryst/wxCryst/wxRefinableObj.h: WXFieldRefPar can now have "Fix" and "Limited" buttons hidden. 2003-06-05 10:21 vincefn * [r383] ObjCryst/RefinableObj/GlobalOptimObj.cpp: Make MonteCarloObj::Optimize() (slightly) more silent. 2003-06-03 22:56 vincefn * [r382] ObjCryst/ObjCryst/Molecule.cpp, ObjCryst/ObjCryst/Molecule.h, ObjCryst/wxCryst/wxMolecule.cpp, ObjCryst/wxCryst/wxMolecule.h: Implemented the functions to remove atoms, bonds and angles from a Molecule object. Also added the corresponding menus in WXMolecule. The MolBond, BondAngle and MolDihedralAngle now have a GetName() member function. 2003-06-03 22:52 vincefn * [r381] ObjCryst/RefinableObj/RefinableObj.cpp, ObjCryst/RefinableObj/RefinableObj.h: RefinableObj::RemoveRestraint(...) and RefinableObj::RemovePar(...) now return an iterator to the next position. 2003-06-03 22:51 vincefn * [r380] ObjCryst/wxCryst/wxCrystal.cpp: Added display for the Antibump cost. Removed unused variable. 2003-06-03 20:28 vincefn * [r379] ObjCryst/wxCryst/wxCryst.cpp, ObjCryst/wxCryst/wxCryst.h: Added a direct access to menus in WXCrystMenuBar. 2003-06-03 18:25 vincefn * [r378] ObjCryst/RefinableObj/RefinableObj.cpp, ObjCryst/RefinableObj/RefinableObj.h: Added RefinableObj::RemovePar(...). 2003-06-01 13:28 vincefn * [r377] ObjCryst/ObjCryst/Atom.cpp, ObjCryst/ObjCryst/Molecule.cpp, ObjCryst/ObjCryst/ZScatterer.cpp: Better colours for atom labels when their colour is bright. 2003-05-28 03:54 briantoby * [r376] ObjCryst/wxCryst/wxCrystal.cpp: Cleanup dialog header 2003-05-28 03:51 briantoby * [r375] ObjCryst/wxCryst/wxCrystal.cpp, ObjCryst/wxCryst/wxCrystal.h: Insert a dialog to set the cursor/view center coordinates 2003-05-27 07:10 vincefn * [r374] ObjCryst/wxCryst/wxCrystal.cpp: Fixed coordinates of OpenGL center of view in fractionnal coordinates. 2003-05-26 22:45 vincefn * [r373] ObjCryst/wxCryst/wxCrystal.cpp: Add different default colors for the first 3 Fourier maps to be loaded: red, blu and green. Also, make sure the short filename (i.e. no path) is used to label the Fourier Map. 2003-05-26 22:13 vincefn * [r372] Fox/src/Fox.cpp: Switched all wx unique ID to using WX_CRYSTID for a simpler approach. Also, added the ability to load several fourier maps from the command line. 2003-05-26 22:05 vincefn * [r371] ObjCryst/wxCryst/wxCrystal.cpp, ObjCryst/wxCryst/wxCrystal.h: Added a cursor (disabled by default) to point the center of the OpenGL crystal view. Also added a status line which shows the center coordinates, as well as the values of Fourier maps, if any are loaded. 2003-05-25 23:57 vincefn * [r370] ObjCryst/wxCryst/wxAtom.cpp, ObjCryst/wxCryst/wxCryst.cpp, ObjCryst/wxCryst/wxCryst.h, ObjCryst/wxCryst/wxCrystal.cpp, ObjCryst/wxCryst/wxDiffractionSingleCrystal.cpp, ObjCryst/wxCryst/wxGlobalOptimObj.cpp, ObjCryst/wxCryst/wxMolecule.cpp, ObjCryst/wxCryst/wxPowderPattern.cpp, ObjCryst/wxCryst/wxRefinableObj.cpp, ObjCryst/wxCryst/wxScatteringPower.cpp, ObjCryst/wxCryst/wxScatteringPowerSphere.cpp, ObjCryst/wxCryst/wxZScatterer.cpp: Converted most of wxWindows unique ID using WXCRYST_ID, now avoiding a global enum with all IDs. Only those that are shared between different cource files are still declared into the enum. 2003-05-25 21:21 briantoby * [r369] ObjCryst/ObjCryst/Crystal.cpp, ObjCryst/wxCryst/wxCrystal.cpp: revise CIF generation routine and include in menu 2003-05-25 21:20 briantoby * [r368] ObjCryst/wxCryst/wxMolecule.cpp: Add #include (needed to compile on my machine) 2003-05-25 15:27 vincefn * [r367] ObjCryst/ObjCryst/Atom.cpp, ObjCryst/ObjCryst/Atom.h, ObjCryst/ObjCryst/Crystal.cpp, ObjCryst/ObjCryst/Crystal.h, ObjCryst/ObjCryst/Molecule.cpp, ObjCryst/ObjCryst/Molecule.h, ObjCryst/ObjCryst/Scatterer.h, ObjCryst/ObjCryst/ZScatterer.cpp, ObjCryst/ObjCryst/ZScatterer.h, ObjCryst/wxCryst/wxCryst.cpp, ObjCryst/wxCryst/wxCryst.h, ObjCryst/wxCryst/wxCrystal.cpp, ObjCryst/wxCryst/wxCrystal.h, ObjCryst/wxCryst/wxMolecule.cpp: Moved to better lighting effects in the OpenGL display of crystal structures. Added the ability to display atm labels, in a separate display list to be easily enabled/disabled. Also added the WXCRYST_ID which will supply unique wxwindows' ID for all windows. 2003-05-24 12:21 vincefn * [r366] ObjCryst/ObjCryst/Molecule.cpp, ObjCryst/ObjCryst/Molecule.h: Update the Molecule class with better (agin) Random Moves for global optimization, using torsion angles. Added the interface to remove atoms, bonds, angles,... code to be added. 2003-05-22 19:28 vincefn * [r365] ObjCryst/ObjCryst/IO.cpp: After importing the powder pattern, update clock of powder pattern parameters. 2003-05-12 18:56 vincefn * [r364] ObjCryst/RefinableObj/GlobalOptimObj.cpp: Make auto-save of xml files use local time rather than gmt. 2003-05-09 14:24 vincefn * [r363] ObjCryst/ObjCryst/Scatterer.cpp: Correctly set type of gpRefParTypeScattConform{X,Y,Z} as gpRefParTypeScattConform. 2003-05-06 20:31 vincefn * [r362] ObjCryst/ObjCryst/Molecule.cpp: Correct formulas for the evaluation of dihedral angles, as well as avoid NaN in acos() due to rounding errors, and correctly save dihedral angles as "Angle" in xml. 2003-05-05 12:39 vincefn * [r361] ObjCryst/ObjCryst/Molecule.cpp, ObjCryst/ObjCryst/Molecule.h, ObjCryst/wxCryst/wxMolecule.cpp, ObjCryst/wxCryst/wxMolecule.h: Update to the Molecule class, especially to improve random moves using an internal Monte-Carlo test on each random move to directly avoid unacceptable conformations. Also introduced the identification of torsion angles and their use in random movements. in WXMolecule, the search for new bond/atoms/angles is disabled during an optimization, as it lead to a segmentation fault after some time, and valgrind failed to identify the problem (glibc ??). 2003-05-05 11:10 vincefn * [r360] ObjCryst/RefinableObj/GlobalOptimObj.cpp, ObjCryst/RefinableObj/GlobalOptimObj.h: Added the collection of statistical information on the Log(Likelihood) of individual objects during optimization. 2003-05-02 19:56 vincefn * [r359] ObjCryst/wxCryst/wxCryst.cpp, ObjCryst/wxCryst/wxMolecule.cpp, ObjCryst/wxCryst/wxMolecule.h: Correctly delete objects on destruction in some wx classes, and do not delete sizers as this will be done automatically by upper sizers (?). 2003-05-02 18:59 vincefn * [r358] ObjCryst/wxCryst/wxMolecule.cpp: Changed all WXDialogChooseFromVector(...) to WXDialogChooseFromVector(...) for comilation with bcc32. 2003-05-02 18:38 vincefn * [r357] ObjCryst/ObjCryst/Molecule.cpp, ObjCryst/ObjCryst/Molecule.h, ObjCryst/wxCryst/wxMolecule.cpp, ObjCryst/wxCryst/wxMolecule.h: Continued update of the Molecule class, now with the wxMolecule class. Basic functions are now working, but requires lots of optimizing and the specific handling of more complex molecules (cyclic,...), as well as more intelligent use of torsion angles, etc... 2003-04-14 12:35 vincefn * [r356] ObjCryst/ObjCryst/ScatteringData.cpp, ObjCryst/ObjCryst/ScatteringData.h, ObjCryst/Quirks/VFNStreamFormat.cpp, ObjCryst/Quirks/VFNStreamFormat.h, ObjCryst/wxCryst/wxCryst.h, ObjCryst/wxCryst/wxDiffractionSingleCrystal.cpp, ObjCryst/wxCryst/wxDiffractionSingleCrystal.h: Added a function (ScatteringData::PrintFhklCalcDetail) to output the calculated structure factors in, with detailed (non-resonant) individual structure factors for all scattering powers. Also added the ability to save this in wxDiffractionSingleCrystal. 2003-04-14 12:30 vincefn * [r355] ObjCryst/ObjCryst/ScatteringPower.cpp: Corrected ScatteringPowerAtom::GetForwardScatteringFactor() to take into account the constant C term from the international tables. 2003-04-14 09:32 vincefn * [r354] ObjCryst/ObjCryst/Crystal.cpp: Corrected comparisons in Crystal::CalcDistTable(), to correctly choose a unique position, due to approximations. 2003-04-10 22:02 vincefn * [r353] ObjCryst/ObjCryst/Crystal.cpp, ObjCryst/ObjCryst/Crystal.h, ObjCryst/ObjCryst/IO.cpp, ObjCryst/ObjCryst/Molecule.cpp, ObjCryst/ObjCryst/Molecule.h, ObjCryst/ObjCryst/gnu.mak, ObjCryst/RefinableObj/RefinableObj.cpp, ObjCryst/wxCryst/bc32.mak, ObjCryst/wxCryst/gnu.mak, ObjCryst/wxCryst/wxCryst.h, ObjCryst/wxCryst/wxCrystal.cpp: Large update to the Molecule class. Basic input of atome, bonds, angles restraints, xml input/output, display with wx and OpenGL now work. Still a lot to do. 2003-04-10 21:59 vincefn * [r352] ObjCryst/RefinableObj/GlobalOptimObj.cpp: Correctly de-register GlobalOptimObj on destruction (not just in the parent class). 2003-04-06 19:04 vincefn * [r351] ObjCryst/ObjCryst/IO.cpp, ObjCryst/ObjCryst/PowderPattern.cpp, ObjCryst/ObjCryst/PowderPattern.h, ObjCryst/ObjCryst/ScatteringData.cpp, ObjCryst/ObjCryst/ScatteringData.h, ObjCryst/ObjCryst/ScatteringPower.cpp, ObjCryst/ObjCryst/ScatteringPower.h, ObjCryst/wxCryst/wxPowderPattern.cpp, ObjCryst/wxCryst/wxPowderPattern.h, ObjCryst/wxCryst/wxScatteringPower.cpp: maximum Likelihood update. Added parameters to describe the positionnal error of atoms in the model, in each ScatteringPowerAtom. These isotropic errors are used to compute Luzzati factors and derive the 'most likely' structure factors in ScatteringData, with a variance associated to each calculated structure factor. This is used in PowderPattern to calculate the 'most likely' pattern, and associate a variance to each caculated point of the pattern, and therefore derive the overall variance (cumulating observed and model error