ChangeLog for Release v1.7

Revision 1690

Added detection of valid X11 DISPLAY, forcing Aten to run in console mode if no X-server is present.
Replaced optional renaming argument of 'loadmodel' with optional filter nickname specification to force loading of model in desired format.

Revision 1689

Added MAXIT and PCM options to GAMESS-US output filter, and adjusted output.
Fixed - Setting quoted filter options on the command line now works.
Added ability to set filter options for expression export.

Revision 1688

Added option to Build widget to adjust bond tolerance.
Doc update.
Added some main menu shortcuts, and tweaked others.
Removed old generator-related member functions and variables from ForcefieldAtom, and Forcefield::readGenerator function.
Updated Forcefield::save() - now nearly complete.

Revision 1687

Updated TODO.

Revision 1686

User action modes in tool windows are now properly deselected when the containing window is closed.
Fixed - Update of Cell Definition window after undoing/redoing a cell change.
Fixed - Mismatch of logs and crash when redoing an undone action.
Added Log::Cell type.
Switched usage of Log::Misc to Log::Camera in CellTransform functions when a redraw of the model was necessary.
Fixed - Changes to the unit cell would not affect any logs relevant to savepoint.
Fixed - Several logs were not updated on undo/redo.

Revision 1685

Fixed - Format of IFREEZ in GAMESS-US output was incorrect.

Revision 1684

Fixed - 'insertatom' was broken since Model::addAtom() would somehow mistakenly accept an id in place of a Vec3, and do nothing with it.

Revision 1683

Fixed - Argument definition for 'selectf' command was wrong, breaking command.
Doc update (many missing selection commands).
Fixed - Interactive prompt and GUI panel were broken since existing variables could not be referenced.

Revision 1682

Updated messaging on failed pattern creation.
Added check for current colour scheme after setting custom atom colours through the context menu through the context menu.

Revision 1681

Added overloaded Matrix::applyScaling() and Primitive::defineVertex() functions to accept Vec3s as arguments.
Tweaked format of header in disorder builder output.
Fixed - watermethane script.
Moved glyph rendering to separate file src/render/engine_glyph.cpp and tidied up code a little.
Reimplemented tetrahedron rendering.
Fixed - Rendering of line glyphs, and arrow bodies of vector and arrow glyphs.

Revision 1680

Fixed - Tab ordering within and sizes of several tool windows.

Revision 1679

Added menu option to allow creation of default pattern.
Removed optional argument from 'createpatterns' command which allowed default pattern to be accepted.
Combined all menu actions source filed in src/gui into one file src/gui/mainmenuactions.cpp.

Revision 1678

Broken Commit - Partial removal of automatic default pattern generation.

Revision 1677

Changed 'getview' so it prints out data in a more usable format.
Fixed - Added reset of modelview matrix to cell drawing, and fixed drawing of additional cells when Cell Replicate page is visible.
Fixed - Creating a new model removed previously-visible models from the list, but did not set the flags in the actual models.

Revision 1676

Fixed - 'newglyph' was not reporting list of valid glyph types on error.
Fixed - Initial vector now set for tubearrow glyph.

Revision 1675

Fixed - Several test scripts were broken because of removal of 'calculateelec' Prefs member.
Fixed - UFF parameters test script.
Fixed - Some issues with consistency of signs of calculated van der Waals forces.
Added script to test consistency of van der Waals force/energy calculation.
Changed ordering of van der Waals Morse potential parameters to be more logical, and corrected conversion of 'k' value.

Revision 1674

Updated TODO and manual.

Revision 1673

Fixed - Update of Select window after various toolbar/menu actions.

Revision 1672

Added KVMap::pairs() function to return first pair in list.
Removed filename argument from Forcefield::save().
Added 'Save' button to complement 'Save As' in Forcefields window.
Added List::second() function to return second item in the list.
Doc update.
Fixed - Many issues with forcefield save code, but still not complete.
Tweaked cgparticle.txt, chloroform.txt, and watermethane.txt scripts to work with new disorder builder code.
Removed regions.txt and regions2.txt from repo.
Fixed - Consistency of step number in MC output.

Revision 1671

Fixed - Update of element colours after changes in prefs window.
Added progress indicator to generation of icons in Fragments window.
Fixed - Alpha values were not honoured in element colours (e.g. when setting through prefs).
When setting custom atom colour theourh context menu, scheme is now automatically set to 'custom'.
Fixed - ZMatrix window was not updated when shown.

Revision 1670

Fixed - Tweaks in Disorder builder were never accepted since candidate molecule itself was not excluded from loop.
Moved all control variable definitions for Disorder builder to the MonteCarlo class, and added accessors.
Added method options dialog to Disorder wizard (final page).
Fixed - Disorder builder was not cancelable via the progress indicator.
Fixed - Progress indicator for Disorder builder indicated no progress.
Added recovery procedure to Disorder builder in order to help separate molecules with bad contacts at the end of the build.
Added DisorderData::sourceModel() method.
Added forcefield pointer to information copied in Model::copy().
Fixed - Crash when running Disorder builder twice, which would mistakenly try to delete the previous newly-created model (if there was one).
Disorder builder now adds on a valid pattern definition, including original forcefields assigned to component models.
Added check for no cell when Disorder building using the free cell option.
Fixed - PartitionData::clear() was not nullifying currentCellChunk_ pointer, leading to crashes when re-running disorder builder using the same scheme.

Revision 1669

Fixed - Command text for 'setupcomponent' definition stated default partition was 0 when it should be 1.
Fixed - Disorder builder would fail to find a suitable component for deletion sometimes owing to incorrect usage of recently updated AtenMath::randomi.
Reverted AtenMath::randomi() to return random number between 0 and range-1, and corrected 'randomi' command to match.
Fixed - Model::selectionDelete() would crash because previous change from atom list to selection list did not grab the atom pointer.
Added some more verbosity to Clipboard::copy*() functions, and optional quiet operation flags to some.
Fixed - Check for densities in Disorder builder now accounts for accuracy parameter.

Revision 1668

Fixed - Changes to model (e.g. selections) arising from execution of filters when writing files would fill up undo/redo lists, so now undo/redo is temporarily disabled before calling executeWrite().
Added 'random' and 'randomi' functions.
Tweaked AtenMath::random() to return 0.0 to 1.0 inclusive, and added function to return random integer between 0 and RAND_MAX.
Added CHARMM27 Pro-Na forcefield to repo, in data/fftesting.
Fixed - Interactive modes (CLI and GUI) were broken in the sense that variables were cleared from the containing Program after each command.
Fixed - Interactive panel of Command Window now resizes columns in the variable list.
Added some verbosity to Prefs file loading on startup, stating where and which file(s) were found.
Fixed - Stick line widths were not set in Preferences window.
Changed Primitive::createCross() to Primitive::plotCross() and removed level-of-detail support.
Removed RenderPrimitives::stickAtom_ in favour of plotting vertices each time.
Fixed - Unbound stick atoms did not display correctly when selected.
Ato file export now writes random number information.
Fixed - Ato file import now correctly recognises end of LJ input section.

Revision 1667

Added prefs GUI options and accessors 'chargelabelformat' to change format of atom charge label, and 'sticknormalwidth' and 'stickselectedwidth' to determine line thicknesses of stick models.
Fixed - Display of selected stick atoms with no bonds.
Fixed - Labels for atoms were drawn twice each render.

Revision 1666

Removed arrays of scaled atoms from RenderPrimitives, and made single unit and scaled atom objects, plus stick atom primitive.
Rendering of offscreen bitmaps now considerably faster owing to lighter primitive generation load.

Revision 1665

Removed progress indicator usage from Clipboard::paste(), Clipboard::copySelection(), and Clipboard::copyBonds().
Removed ability for ProgressIndicator to display secondary job information, instead allowing just a subtitle to be set if desired.
Removed storage of main context pointer in GuiQt since it was utterly pointless on Windows.
Removed simple enable/disable of drawing in TCanvas in favour of enum directing rendering target to none, screen, or pixmap.
Primitive instances are now cleared at the back end of TCanvas::paintGL if the current drawing target is PixmapTarget.
Fixed - Memory leak in Model destructor, not freeing pixelData_.

Revision 1664

Added new fragments.

Revision 1663

Fixed - Saving images of models in process/batch modes was broken since the visible models list was not cleared and reinitialised with each model.
Added Quick Command item to Edit menu (shortcut F10).

Revision 1662

Fixed - Warning message regarding element searches on blank string was not suppressed in quiet mode.
Fixed - Text labels (i.e.
primitives) are now cleared correctly on changing model.

Revision 1661

Fixed - Disorder builder would delete too many molecules when adjusting for too high density.
Tweaked progress indicator to not promote minor events to major ones (prevents excessive messages when using clipboard, and fixes lack of Disorder build progress indicator, amongst other things).
Fixed - Some icons were not in plain svg format.
Disorder build now creates an undo state on completion.

Revision 1660

Fixed - Detection of bond planes was broken due to a combination of bad logic and idiocy.

Revision 1659

Reformatted TODO.
Added --process switch to run supplied commands on all models but not save results.
Added some verbosity to program modes.
Tidied up Atom List widget a little.

Revision 1658

Added flag to RenderEngine to allow forced clearing of primitive lists in next render.
Fixed - Saving images was randomly broken from CLI since filtered primitive lists were not recreated.
Fixed - Primitive instances now free their associated OpenGL display list of VBO, but only if they are being freed from the main (permanent) context.
Fixed - Echoes of stick bonds/atoms from previous model.

Revision 1657

Removed ppc from Mac build targets in CMakeLists.txt, since latest Qt 4.7.3 seems to be incompatible.

Revision 1656

Fixed - Keeping of view through '--keepview' switch was not honoured due to badly placed reset of prefs values on GUI start.
Added 'cleartypes' command to remove all atom typing from the current model.
Updated manual.

Revision 1655

Removed debug info from code running scripts from CLI.
Fixed - Range checking for component partition was wrong in MonteCarlo::disorder().
Fixed - 'newpattern' command was not returning a pointer to the new pattern.
Reinstated verbosity of Model::addPattern command.
Fixed - Pattern detection would report wrong source atom on failure.
Removed Aten::defaultForcefield_ member and accessors since this was being confused with the forcefield stored in current.ff.
Fixed - Assigning a forcefield to a specific pattern was broken.
Fixed - Rebonding within patterns would ignore the argument specifying whether to augment if the related Prefs value was TRUE.
Removed 'defaultff' command since it was just a less-flexible duplicate of 'currentff'.
Removed ElementMap::findAlpha() and combined the two ElementMap::find() overloads into one single function for clarity.
Fixed - Setting ZMapping style on command line and then loading a forcefield

Revision 1654

Show Toolbox menu item now repositions toolbox as well, in case it was lost offscreen.
Added 'Manual Swap Buffers' option to Settings menu.
Fixed - Draw/Detect Hydrogen Bonds menu item was not updated after Prefs change.

Revision 1653

Fixed - Determination of bond plane did not take into account linear bonds, breaking bond drawing in such cases.
Updated TODO.

Revision 1652

Update pdf with links, and corrected Aten literature reference.

Revision 1651

Added new user manual to repo.

Revision 1650

Removed PrefsVariable accessor 'vdwscale' and references thereto, and MonteCarlo::vdwScale_ member, neither of which are used any more.
Final removal of old documentation detritus.
Removed references to vdwScale in vdW energy and force calculation.

Revision 1649

More removal of old documentation.

Revision 1648

Removed definition of VdwScale function left over in last commit.
Removed old documentation from repo.

Revision 1647

Changed 'loadmodel' command so that new current model is returned, rather than the number of models loaded.
Removed third argument from 'disorder' command since it was irrelevant.
Removed 'vdwscale' command since it is no longer used.

Revision 1646

Fixed - Transformation of selected atoms by matrix was broken.

Revision 1645

Updated todo.
Minor fix in mainwindow_funcs.cpp (printf format).

Revision 1644

Added saving of main window geometry to global settings.
Fixed - Toolbox position was not restored correctly on startup.

Revision 1643

Rearranged Scripts tab of Command window a little, and added button to allow selected scripts to be removed.
Fixed - Rebond (No Augment) option in Build window was still augmenting bonds.
Added menu item to toggle detection/display of H-bonds in models.
Fixed - Drawing of selected multiple stick bonds was broken.

Revision 1642

Renamed 'gridcolourprimary' command to 'gridcolour' for consistency, and renamed internal enum to match.

Revision 1641

Fixed - Disorder builder was checking for partition density for models using 'population' insertion policy.
Fixed - Model variable member 'componentpartition' was being set with ID in range 1-N as opposed to 0-N-1.
Made lower limit for disorder scalefactor a bit more generous (1.0 c.f.
1.15).

Revision 1640

Fixed - Fragments window was not updated on first showing.

Revision 1639

Corrected some spelling errors in copyright notices in a few files.

Revision 1638

Fixed - ElementO button in Build window was not in the relevant buttongroup.
Fixed - Loaded models etc. are now made the visible primary model.

Revision 1637

Fixed - Stack counters in PrimitiveInstances were never updated.
Fixed - Update of primitives after Prefs change was utterly broken.

Revision 1636

Fixed - WidgetNode::setWidgetValue() was not returning a value.

Revision 1635

Fixed - Forces for BondConstraint angles were calculated incorrectly.

Revision 1634

Fixed - Drawing of Fragments when DrawFragmentAction was active was broken.
Added extra flag to RenderEngine::render3D() to allow forcing of all lists to be updated.
Fixed - Icons were not generated for fragments created from selections.

Revision 1633

Fixed - 'addangle, 'addbond', and 'addtorsion' member functions of ForcefieldVariable now return a value of type ForcefieldBound.

Revision 1632

Removed enum member LineParser::Defaults and references thereto, and added LineParser::StripComments.
Control of comment removal is now governed by the state of the LineParser::StripComments bit.
Fixed - Always stripping comments in LineParser::readNextLine was a bad idea, and broke cds filter which needed the commented lines.
Fixed - Some read options were not passed down to commands from parent tree.

Revision 1631

Fixed - Generator::setMatrixPart was setting incorrect translation vectors because of incorrect string to number conversion.
Fixed - Model::pack() was using transpose of rotation matrix from SGinfo by mistake, breaking 'exotic' spacegroups.
Fixed - Generator::setMatrixPart() was setting the transpose of the rotation matrix.
Fixed - Generator::set() was not clearing the matrix before setting it, leaving traces of the identity matrix behind.
Changed Generator::setMatrixPart() to return void instead of bool, since it wasn't returning anything useful.
WidgetNode::setWidgetValue() now returns a bool to allow better checking of success by other routines.
Fixed - Setting a widget option (when specifying a filter) which contained an invalid combo item would not raise an error.
Added Matrix::setRow() functions.

Revision 1630

Updated Grids Widget to allow simultaneous editing of multiple grids at once, including display/editing of all grids across all models instead of just the current one.
Updated WrapInt class with more useful constructor.
Implemented different colour of multiple partitions in same scheme.

Revision 1629

Added detection and rendering of hydrogen bonds, and added Prefs GUI option and accessors to control it.
Moved Colours to separate subpage in View options in Prefs window.
Fixed - Stick primitives were not correctly cleared all the time (e.g. when starting a new model).
Removed debug output from tcanvas_funcs.cpp.

Revision 1628

Removed some style definitions from several ui files (ToolTipBase and ToolTipText) to fix build using Qt 4.3.
Added basic case code to GuiQt::pid() to fix build with Qt4.3.
Fixed - Some (all?) picking modes were broken due to the mode being reactivated in the buttongroup callback, without the number of atoms to pick supplied.

Revision 1627

Moved variable setting code from PartitionScheme::setVariable() to general Tree::setVariable().
Added ability to set filter options in 'savemodel' command and --export mode.
Removed descriptive text from DFTTYP options in GAMESS-US filter.
Fixed - Export and BatchExport modes were not setting custom option values in filters.
Fixed - Some crash-inducing pointer misuses in WidgetNode::setWidgetValue.

Revision 1626

Fixed - Default number of steps in GAMESS-US optimize runs was incorrect in filter.
Fixed - Orthographic view was flipped top to bottom.

Revision 1625

Fixed - Include paths for GL/gl.h in render/vertexchunk.h and render/primitiveinfo.h were incorrect on Mac OS X.
Minor code cleanups throughout.
Fixed - Glyph rendering was mistakenly passing colour as boolean calcCentroid values for triangle glyphs.
Fixed - Crash related to primitive updates when no previous instance was present.
Fixed - List and Reflist now do much more checking for NULL pointers in many of their member functions.
Fixed - Windows build was broken due to use of VBOs requiring extension functions to be defined.

Revision 1624

Fixed - Aromatic ring name/keyword was missing from atom colour lists.

Revision 1623

Fixed - Vector shift buttons were not connected.
More updates to Vibrations widget - control over frame delay, better checking of source data.
Moved generation of fragment icons to be first repopulation of Fragments Widget list, rather than on startup.
Removed calls to GuiQt::setInteractive() when updating and terminating progress dialog.
Fixed - TCanvas::displayModel() would potentially return a vibration frame pointer, which should never be necessary.
Added integer vibration frame index counter to Model, and frame retrieval function.
Fixed - Prefs option keepView had no effect on trajectory frames.
Fixed - keepview option is now switched off when GUI starts.
Removed usage of OpenGL calls in Model::setupView(), preferring instead to calculate projection matrices directly.
Removed wasteful Model-specific rotation globe projection matrices in favour of on-the-fly creation in RenderEngine.
Removed all references to 'savevector' command.
Added ability to save images of vibration frames (movies to follow).

Revision 1622

Fixed - Many action-related buttons in dock widgets (namely Transform) were missing from the internal button group.
Renamed some members of UserAction enum to provide better coherence with widget names in GUI.
Added data/test/axes.xyz example.
Fixed - Stick-style was 'bleeding' between models because the relevant primitives were not propery cleared.
Fixed - Update issues relating to global style changes through toolbar and View menu.

Revision 1621

Fixed - Delay value in Trajectory widget was ignored.
Added GuiQt::setInteractivity() function to allow interactivity to be turned on/off, leaving only ability to be changing camera view.
Increased maximum number of disorder cycles to 10000.
Fixed - Rendering of vibration frames was broken.
Vibrations window updated and partially improved.
Fixed - Matrix transformation of systems appeared to be broken for several reasons.

Revision 1620

Added KVTable::pairs() function to return head of pair list.
Made QButtonGroups list a private member of CustomDialog so they could be deleted properly on destruction.
Added postRedisplay() call to TCanvas::generateImage() to prevent usage of current buffer when saved image is same size as context.
Added 'selectfor' and 'deselectfor' commands, and options to do so in Select widget.
Fixed - RenderEngine::initialiseGL() was only called in TCanvas::initialiseGL(), meaning that spotlight / colour changes etc were not propagated to the main view (but were to saved images).
Made spotlight default position a little more sensible, and changed Prefs window UI widgets to allow more extreme values.

Revision 1619

Fixed - Stick rendering was incorrect and slow, and is now much better.

Revision 1618

Fixed - Changing status of grid volume outline in Grid class was not logging change in self or parent Model.
Fixed - GridPrimitives now use no instances.

Revision 1617

Added CLI option to force rendering to use direct vertex array passing only, rather than display lists.
Finished implementation of primitive instances.

Revision 1616

Updates to new rendering method.

Revision 1615

Broken commit - partial implementation of Primitive instantiation method.

Revision 1614

Reverted to old text rendering (no lists) for simplicity and sanity.
Added Reflist of text glyphs to Model and separate rendering function.

Revision 1613

Updated 'speedtest' function to provide better output.
Removed Log::Visual and replaced with Log::Camera and Log::Style.
Improved rendering engine to only recalculate primitive lists on model (rather than camera) change.
Added != operator to and isSame(Log::LogType, Log &other) functions to Log.
Glyph lineWidth_ property removed.
Removed TCanvas::isValid() function, since it was hiding a function from QGLWidget.
Disabled rendering check for now, since it didn't work.
Made some commonly-used pointer members of GuiQt private (e.g. mainWidget, mainWindow etc.).
Text object rendering broken in current commit (to be fixed subsequently).
Added (optional) use of vertex buffer objects (--vbo CLI switch).

Revision 1612

Fixed - Atom::copy was neglecting hidden status meaning, for example, that hidden atoms were not honoured in vibration frame generation.
Fixed - Vibration arrow drawing for hidden atoms fixed.

Revision 1611

Added code to allow removal of trajectory from current model.
Added additional menu items controlling propagation of style to/from parent model in trajectory frames.
Fixed - Vibrations widget is now disabled when no vibrations are available.

Revision 1610

Fixed - User includes were not loaded since wrong path was searched.
Fixed - Some user-file loading code was not using the Aten::atenDir_ variable to determine the path, meaning Windows versions would not find anything.
Fixed - Loading multiple include files was erasing previously defined global functions.
Added extra, optional argument to all Parser::generate() and Tree::generate() calls to allow clearing of previous program cnoitents to be overridden.

Revision 1609

Added many checks for NULL nodes to parser grammar.

Revision 1608

Finished basic implementation of parent style copying in trajectory playback.

Revision 1607

Partial implementation of trajectory style copying.

Revision 1606

Program and user prefs file loading now looks for 'prefs.txt' and 'user.txt' in addition to dat files.
Removed Aten::prefsCommands in favour of using local Program variables in Prefs::load().
Tweaked progress indicator to always (unless quiet) print job title in text mode.
Added prefs options for post-processing video encoder executable and arguments, and necessary accessors and GUI options.

Revision 1605

Fixed - Rotation globe was not hidden when saving bitmap images from the command-line.
Fixed - User background colour settings were lost.

Revision 1604

Fixed - --noqtsettings switch was broken.
Fixed - Grid origin group had default widget title.

Revision 1603

Fixed some issues with documentation which prevented build.

Revision 1602

Fixed - 'selectfftype' was performing inverted selection.
Fixed - Grammar would allow failed function additions to pass without aborting program.

Revision 1601

Reinstated importgrid filter for cube files, but model data is no longer loaded.
Fixed - Missing endGL() call in TCanvas::isRenderingOk() which was killing all rendering.
Made TCanvas::isRenderingOk() more robust.
Fixed - Spewing of QPainter errors when certain dock widgets were floated, related to assigned svg window icons.

Revision 1600

Added trial function to detect corrupt rendering canvas.
Changed declaration of Prefs::load() to accept no arguments - program and user preferences are both loaded from the function (if they exist).

Revision 1599

Changed Gaussian cube file filter type from 'importgrid' to 'importmodel'.

Revision 1598

Fixed - ato filter was reading rotations wrongly.
Added test file data/test/ipa.ato.
Made more of Pattern output only visible when in verbose mode.
Added progress indicators to Disorder-related functions.
Some general fixes and tweaks to progress indicators.
Fixed - Update of main view after disorder build.

Revision 1597

Renamed some functions in DisorderData and MonteCarlo::disorder() for clarity.
Implemented new GUI progress dialog.
Fixed Windows build.
Fixed - All dock widgets referred to the wrong button (AtomListButton) when setting its own state.
Fixed - Corruption and update of extra visual elements from CellTransform widget.

Revision 1596

Partial reimplementation of progress indicator.
Removed configure option --with-oldqt - propet QT_VERSION define now used instead.

Revision 1594

Merging changes from nugui branch back into trunk.

Revision 1568

Added Atom::data_ member to permit temporary storage of data associated to individual atoms (from filters, etc.) and accessors to match.
Added preliminary basis for EPSR ATO file import and export filter.
Fixed - 'nextarg' command failed with DOS-style linefeeds, since LineParser::getCharsDelim() did not recognise them.

Revision 1560

Updated changeversion script to accept alpha character minor subversion.

Revision 1557

Fixed some debug output calls in Aten::openIncludes() and Aten::openFilters().
Fixed - Checking for presence of standard input on startup failed to realise there was no input on some systems.

Revision 1529

Tweaks to aten.dsc (from 1.6 release).

Revision 1527

Reversioned to 1.7 (some files had been overwritten with 1.6 versions).

Revision 1525

Tweaked cldp-il.ff again.
Updated build files to fix some builds (from 1.6 commits).

Revision 1519

Changed definitions for dicyanamide anion in cldp-il.ff so as not to use multiple bond information.

Revision 1518

Minor change to Ring class to prevent misuse of potentially undefined value.

Revision 1512

Tweaks to changelog1.6 and doc build script (to remove aggravating xml header in single-page manual).

Revision 1510

Added 1.6 changelog to trunk.

Revision 1496

Version bump to 1.7.

latest release :	1.7
latest beta :	1.8.1786