Adjusted aten.dsc so its ripe for sedding.

Fix to commit script to ensure proper (global) revision renumbering.

Update debian build files.

Colourscale-based colouring of Grid data was not working properly (some flags were not set correctly) - fixed.

Density-type Grids are now rendered in the colourscale colours (if one is assigned).

Added 'gridvisible' command, and fixed 'getgrid' and 'grid' (variable creation) commands.

Minor (but important) change to DL_POLY model export filter.

Fixed formatting of spacegroup names.

Added 'nselected' to ModelAccessors.

Added 'normalise', 'selectioncog' and 'selectioncom' commands.

Added Model::selectionCom().

New bonding code was still missing some bonds at the edges of unit cells - fixed.

Fixed inhibition of atom trimming in cell replication.

Added more verbose output to 'replicatefold' and 'replicatetrim' commands.

Fixed badly written Atom::nextSelected() causing endless loops or crashes in some parts of the code.

Added '-n' switch to create new model (equivalent to -c "newmodel x").

Better axis handling in 'pdens' filter.

Removed Model::firstMarked() in favour of extending Model::firstSelected() with optional 'bool markonly' argument (also related function in Atom).

Added 'rotatecell' command to rotate cell and its contents about one of the Cartesian axes - final action as yet undecided.

Fixed bug in new bonding code.

New rebonding code - approx 100 times faster for large systems.

Added assignment operator=T to Vec3<T>.

Fixed bug in Model::resetCamera() which meant that 'setview' would result in the wrong camera y-position (inverted).

Renamed 'OnImage' properties in Prefs to OffScreen for clarity.

Added flag in Canvas to specify whether off-screen rendering is being performed (for image saving).

Grids now create a separate new display list when being rendered for an offscreen image (i.e.

in a new context).

Fixed bug with image saving from the GUI where grid data was not drawn (command-line usage was ok).

Fixed 'gridcolournegative' which cause a crash.

Added 'reorder' command and Model::reorderSelectedAtoms() to reorder (collapse) bound atoms so that they have consecutive IDs.

Save bitmap is now a little more informative.

Transform window now starts in sensible size.

Some unfinished updates to GUI in this revision.

-- AtomList now lists by pattern as a separate 'mode' (selection / shift actions not fully re-implemented).

-- CellTransform has widgets for cell rotation (but no attached functions).

Undo state in 'expand' command closed in wrong place - fixed.

Corrected orthographic view which was being drawn back to front.

Added 'singlealpha' zmapping type, which uses the first alpha character.

Removed explicit 'zmap ff' command from DL_POLY model filter.

Fixed small bugs in some commands that required element conversion and used the current zmapping style to convert names (it should have demanded the 'alpha' style).

Added missing undo state creation for some select commands.

Added 'deselecttype' command.

Adjusted tab order in Transform Window.

Changed copyright notice to include this year.

More improvements to selecting in Atomlist - undo/redo and select by pattern enabled.

Fixed small bug in Pattern::angleEnergy() which wrongly reported the lack of implemented terms for 1-3 constraint angles.

Small fixes to supplied example scripts.

Added 'mag' (magnitude) accessor to VectorAccess.

New command 'insertatom' which creates a new atom with the ID specified (moving atoms after it to higher IDs).

Transform commands 'matrixconvert' and 'matrixtransform' should have been taking minimum image coordinates when working out vectors from atom IDs - fixed.

Updated Model::selectPattern().

'select' and 'deselect' commands now accept pattern pointers as targets.

Potential crash when undoing atom deletion, related to atom / bond creation order - rewrote Model::selectionDelete() to be more efficient and fix issue.

Added new variable type 'vector' providing a 3-vector {x,y,z}.

Accessors added to provide retrieval/setting of quantities with vector variables where appropriate.

Added 'position', 'force', and 'velocity' accessors to AtomAccess.

Added 'cog' and 'com' accessors to PatternAccess.

Fixed CA_ATOMSTYLE which was using the wrong atom id (if one was provided).

The 'map' command now accepts unquoted mappings.

Adjusted definition of axes with atom IDs in 'matrixconvert' to accept a pair of zeroes for the z-axis, meaning that the cross-product of x and y axes will be used instead.

Fixed bug in 'getpattern' which was not using pattern IDs in the range 0->(N-1).

Tweaked the argument lists for Pattern::calculateCom/Cog() to allow for optional Model pointer.

Commands 'toend' and 'tostart' should have been 'movetoend' and 'movetostart' - fixed.

Some test code in surface rendering routines had been inadvertently committed - repaired in this revision.

Removed debug output from AtenTransform::on_ConvertRotateIntoButton_clicked().

Axis vectors were not normalised in Matrix Convert in Transform Window (fixed).

Fixed generation of rotation matrix in Matrix Convert in Transform window.

Added CA_AXISROTATE, CA_MATRIXTRANSFORM, and CA_MATRIXCONVERT commands.

Fixed crashes when applying atom style/label changes from the Selection menu.

First part of Atomlist retrofit - undo and shift-selection from the Atomlist Window are not yet re-implemented.

Added new ring typing commands - aromatic, aliphatic, nonaromatic.

Added preliminary detection of ring types.

Fixed 'acyclic' atom typing keyword (it was ignored).

Fixed critical bug in Save Model As which was not properly using the selected filename.

Overhauled file dialog usage for better uniformity - last directory now stored for all dialogs.

Positive / negative colour controls in Grids window were the wrong way around.

Rendering of grid data with an alpha component was broken - fixed.

Implemented forgotten functions to cut, copy, and paste grids from one model to another.

Fixed more odd actions of atom context menu.

Measure distances in selection did not work from the Measure Toolbar ('distances' command was ok).

Undo/redo was not set for Measure in Selection tools on the Measure Toolbar.

Text is now copyable from message box.

Fixed some odd actions of atom context menu.

Minor changes to layout of status bar.

Fixed deselection modifier for tree selection.

Better statusbar texts.

Fixed small memory leak in Canvas::endMode().

Improved statusbar usefulness.

Better modified selections - added optional parameter to atom selection functions in Model to request deselection instead (tree deselect [+ctrl] dysfunctional in this revision).

Added Prefs::zoomThrottle_ to manage speed of zooming (added CA_ZOOMTHROTTLE) and scaled zoom factor relative to camera distance.

Removed Model::orthoSize_ - transitions (i.e.

zoom distance) between orthographic and perspective projections now match correctly.

Added help messages to status bar for current mode (partial implementation).

Adjusted main() to search for HOMEPATH variable (Windows) if HOME (others) was not found.

Added call to app->exit() in AtenForm::closeEvent() to properly exit on Windows.

Added 'random' implicit variable into all VariableLists.

Fixed some comparisons in FFBoundAccessors::set().

Small fix to Windows build.

Fixed back face culling (now culling GL_FRONT instead of GL_BACK) and enabled by default to inmprove speed - fixes transparency rendering artefacts.

Converted Prefs::GlOption enum to use bitshifting.

Fixed twister in text-based progress indicator.

Significantly improved speed when deleting selections of atoms.

Mostly implemented new SpecialVariable structure - random number generator still inaccessible.

Finished set/get for FFBoundAccess.

Finalised loops of Models in command lists.

Added extra model management commands: CA_FIRSTMODEL, CA_LASTMODEL, and CA_CURRENTMODEL.

Fixes to Coulomb sum energies and forces.

Tweaked CA_AFTERCHAR to work properly when multiple occurrences of the same character were present in the source string (doh!).

Fixed interactive mode which would execute the cached command even if the command arguments were wrong.

Fixed '+=' (string concatenation) operator in CA_LETCHAR (and improved Dnchar::cat()).

Added string functions CA_STRIPCHARS, CA_AFTERCHAR, and CA_BEFORECHAR.

Minor adjustment to cif filter to strip spaces from HM spacegroup name.

Tweaked pdb filter to stop complaining (wrongly) that the HEADER record wasn't supplied.

Tweaked CA_FINALISEMODEL which wasn't saving the filename/path if a partner filter wasn't available.

Adjusted layout of fdf filter to correctly report the number of chemical species.

Setting an array value without an index now sets all array items to this value (a la Fortran).

Removed debug output from GuiQt::saveImage().

Renamed CA_GRIDTRANSPARENCY to CA_GRIDALPHA, and Grid::setTransparency() and Grid::transparency() to Grid::setAlpha() and Grid::alpha() to make more sense.

Converted Prefs::ViewObject enum back into sequential ints, and adjusted related set/get to use bitshifting.

Fixed CA_SHOWONSCREEN and CA_SHOWONIMAGE crashes.

CA_LOADFF now returns a fail when the forcefield couldn't be loaded (corrected bug in Aten::loadForcefield()).

In PatternAccess, 'firstatomid' and 'lastatomid' were returning the internal index [0 to N-1] rather than [1-N] - fixed.

Corrected About dialog for new website.

Adjusted changeversion script and updated debian-related build files.