2010-10-15 * mesh.h (Mesh): Added iterations. incrementIterations() and getIterations(). * VirtualLeaf.cpp (Plot): Replaced local frame counter with mesh.incrementIterations(). * canvas.cpp (TimeStepWrap): Replaced local counter with mesh.incrementIterations(). 2010-10-14 * VirtualLeaf.pro: Turned debug off to make all profiles must be consistant. * VirtualLeaf-install.nsi: Tweaked paths to coincide with UNIX distribution, i.e. VirtualLeaf.exe, its libraries, models, and the uninstaller all go in the bin directory. And leaves directory placed under data directory. * canvas.cpp (exportCellData): Added a check to inquire before overwritting an existing file. 2010-10-14 * mesh.cpp: In response to referees' comments, added new parameter "yield_threshold" instead of fixed parameter '4' for yield threshold. * wallitem.cpp: when clicking a wall, both the wall type was cycled and the transporterdialog popped up. Corrected this - for wall type cycling, hold the Control button while left clicking. TransporterDialog only pops up for left click. Also made sure the wall is redrawn after changing the transporter values. * cell.cpp (DivideWalls): accomodated for rename of Circumference -> WallCircumference * hull.h: added an operator< to sort Points * hull.cpp: added an operator< to sort Points * cellbase.cpp (ExactCircumference): I added a new function ExactCircumference, yielding the circumference of the cell along its wall_elements * VirtualLeaf.cpp: adjust info_string to accomodate for new name of function CellBase::Circumference -> CellBase::WallCircumference * mesh.cpp: corrected Mesh::Compactness, the boundary coordinates need to be sorted in x,y order for the convex hull algorithm (thanks Margriet!). I updated CSVExportCellData so it exports the circumferences of hull and boundary_polygon. 2010-10-14 * VirtualLeafpar.tmpl (export_fn_prefix): changed to 'cell.' * canvas.cpp (TimeStepWrap): Removed TimeStamp(). Cell data filename now incorporates iteration number. * canvas.h (MainBase): Removed TimeStamp(). 2010-10-08 * pardialog.h: * pardialog.cpp: * parameter.h: * parameter.cpp: Regenerated to include export_interval and export_fn_prefix. * VirtualLeafpar.tmpl: Appended export_interval and export_fn_prefix. * canvas.h (MainBase): Declared polymorphic exportCellData() functions. * canvas.cpp: (TimeStamp): New private TimeStamp() function. (TimeStepWrap): Added invocation of exportCellData(). (exportCellData): Created two polymorphic functions: one with a single QString argument, the other with no argument. The former is called from TimeStepWrap() while the latter is called from the "Export cell areas" item in the file menu. 2010-10-07 * canvas.cpp (exportCellData): Added a Q3FileDialog to inquire where to write the exportCellData. 2010-06-28 * VirtualLeaf-install.nsi: Grab gpl3.txt from doc directory. * canvas.cpp (gpl): gpl3.txt can be either in an ancestor doc directory (Linux) or a decedent doc directory (Windows, via the binary installer). * VirtualLeaf-install.nsi: Add VirtualLeaf doc directory. 2010-06-25 * gpl3.txt: Moved gpl3.txt from doc to src directory. * VirtualLeaf.pro: Added -Wno-write-strings and -Wno-unused-parameter to QMAKE_CXXFLAGS. * libplugin.pro: Ditto. * parameter.cpp: Result of adding datadir changes to make_parameter_source.pl. * parameter.h: Ditto. * output.h: Declared new function (AppendHomeDirIfPathRelative). * output.cpp (AppendHomeDirIfPathRelative): Added new function. * canvas.cpp (gpl): Moving gpl3.txt from doc to src obviates the need to docDir.cd("../doc"). * VirtualLeaf-install.nsi: Grab gpl3.txt from src directory. Add missing libiconv/bin, libxml2bin and libz/bin directories. Copy libiconv-2.dll, libxml2.dll and zlib1.dll from relative paths. * VirtualLeaf.pro: copy gpl3.txt as part of QMAKE_POST_LINK. 2010-06-24 * libplugin.pro: Use correct library path. * VirtualLeaf.pro: Ditto. * VirtualLeaf.cpp (DrawCell): Iterate over NChem to construct info_string. 2010-06-23 * simitembase.cpp: Removed NULL assignments to unused variables. * VirtualLeaf.cpp: Ditto. * apoplastitem.cpp: Ditto. * canvas.cpp: Ditto. * cell.cpp: Ditto. * cellbase.h: Ditto. * forwardeuler.cpp: Ditto. * mainbase.h: Ditto. * nodeitem.cpp: Ditto. * qcanvasarrow.h: Ditto. * simitembase.cpp: Ditto. * Makefile (clean): Add -f Makefile argument to each make invocation. * VirtualLeaf-install.nsi: New gpl license text. * VirtualLeaf.pro: Disabled console mode. * mesh.cpp (Clear): Added parentheses to qDebug statments. (TestIllegalWalls): Replaced qDebug(). * canvas.cpp (mouseReleaseEvent): Replaced qDebug() with cerr since qDebug complains about *node_set. * wall.cpp (CorrectWall): Rplaced gDebug() with cerr in transform call and when printing *this. 2010-06-22 * Makefile (tutorials): Add tutorials target. 2010-06-21 * parameter.cpp: Added particular reassignment of datadir. * canvas.cpp (gpl): Added GPL3 License text. Display detail text only if the source text file exists. 2010-06-18 * canvas.cpp (gpl): Added gpl slot to display GPL license. * VirtualLeaf.pro: Changed default LIBXML2DIR, LIBICONVDIR and LIBZDIR to corresponding distribution lib directories. * libplugin.pro: Ditto. * Makefile (clean): add if stmt not to `touch` on windows. 2010-06-17 * VirtualLeaf.pro: Removed perl references. * libplugin.pro: Ditto. 2010-06-15 * VirtualLeaf.pro: Removed xmlwritecode.cpp from SOURCES list. * xmlwrite.cpp (XMLSave): Removed references to XMLWriteLeafSourceCode and XMLWriteReactionsCode. * xmlwrite.h (XMLIO): Ditto! * mesh.cpp (findNextBoundaryNode): Initialize Node *next_boundary_node = NULL; * xmlwrite.cpp (XMLReadSimtime): Removed unused variable cur (XMLReadWalls): viz_flux need not be declared twice; default value of 0.0. (XMLReadCells): Removed unused count variable. (XMLReadSimtime): Removed unused cur variable. (XMLRead): Removed unused v_str variable. * simitembase.cpp (userMove): Use assignment merely to obviate compilation warning. (SimItemBase) Ditto. * qcanvasarrow.h (QGraphicsLineItem): Use assignment merely to obviate compilation warning. * output.cpp (OpenWriteFile): Removed unused par variable. * nodeitem.cpp (paint): Use assignment merely to obviate compilation warning. * forwardeuler.cpp (odeint): Use assignment merely to obviate compilation warning. * cell.cpp (DivideOverGivenLine): Use assignment merely to obviate compilation warning. * canvas.cpp (FigureEditor): Use assignments merely to obviate compilation errors. (mousePressEvent): Removed unused item variable. * apoplastitem.cpp (ApoplastItem): Removed unused par variable. (OnClick): Use NULL assignment merely to obviate compilation warning. * mainbase.h (MainBase): Use assignment merely to obviate compilation warning. * cellbase.h (CellsStaticDatamembers): Use assignment merely to obviate compilation warning. * cell.cpp: Wrapped diagnostic output in QDEBUG blocks. * VirtualLeaf.cpp ditto. * canvas.cpp ditto. * cell.cpp ditto. * data_plot.cpp ditto. * forwardeuler.cpp ditto. * mesh.cpp ditto. * mesh.h * random.cpp ditto. * wall.cpp ditto. * wallbase.cpp ditto. * wallitem.cpp ditto. 2010-06-07 * VirtualLeaf.pro: Removed explicit perl invocation to regerenerate parameter files. * libplugin.pro: ditto. 2010-06-03 * pardialog.h: Added default versions of this automatically generated file. * pardialog.cpp: ditto. * parameter.h: ditto. * parameter.cpp: ditto. * VirtualLeaf.pro: delete/generate parameter.{h,cpp}and pardialog.{h,cpp} only if perl is installed. * libplugin.pro: dito. * Makefile: Added top-level Makefile 2010-05-10 * VirtualLeaf.pro: Added -fPIC option to QMAKE_CXXFLAGS.