October 16th, 2012
· Ruby: Dialog#filter_kit is implemented.
· Crash when loading a new molecule was fixed.
· ORTEP export did not generate the same orientation as in the screen. Fixed.
· Ruby: Molecule#bond_par, angle_par, dihedral_par, improper_par, vdw_par are made obsolete, and instead MDArena#bond_par, angle_par, dihedral_par, improper_par, vdw_par are implemented. These methods returns the 'cached' parameters in the MDArena. The ParameterRef record for these parameters have a negative index, which represents the parameter belongs to the MDArena instead of the molecule.
· Opening bond/angle/dihedral/improper table now triggers search of MD parameters (but not rebuilding angle/dihedral/improper tables from bond information)
· Handling of view-related attributes of Molecule is improved (specifically, methods like Molecule#show_periodic_image= now work).
· Best-fit plane dialog is not working in Windows; fixed.
· Some fields in md_arena were not properly copied when a molecule is duplicated. Fixed.
· 'Show Graphite' command was using wrong C-C bond length. Fixed.
· Some unused fields of Molecule were removed.
· LAMatrix#svd (singular value decomposition) was implemented.
· Ruby: create_graphic was not working correctly when :ellipsoid is given with a single radius.
· Loading multiple-frame mbsf sometimes fails to load the cell parameter for the last frame. Fixed.
· Property table can now list the unit cell parameters.
· Documents for Dialog#show, Dialog#hide are written. (These were somehow missing)
· Cell minimization was not working correctly when no symmetry operations are defined. Fixed.
· MDArena#prepare was not working correctly when unit cell is added/created after initialization of MDArena. Fixed.
· Handling of selection from Ruby script was partially broken. Fixed.
· Best fit plane dialog was behaving strangely Fixed.
· Handling of Molecule object was not consistent. Hopefully fixed...
· Export ORTEP (improved) and best-fit plane calculations are implemented in Scripts/crystal.rb.
· The revision number is displayed in the about dialog (and is used for labeling clipboard contents)
· Copy/paste of molecules was broken when it had atoms with more than ATOMS_CONNECTS_LIMIT bonds. Fixed.
· Documents for some missing Ruby methods are written.
· Cell minimization is improved (hopefully...)
· Remove printf() for debugging cell minimization
· Implemented minimization of cell parameters. Looks like working...
· Handling of flexible cells were still inconsistent.
· Molecule#cell_flexibility and set_cell_flexibility are implemented, and enable/disable_cell_flexibility are removed.
· Figures for the Ruby tutorial are added to the repository.
· Handling of periodic box during MD is being reworked.
· Ruby: Molecule#box= was not working as expected. Fixed.
· Memory leak bugs are examined and removed.
· amend_by_symmetry in MD was still broken. Hopefully fixed.
· Tutorial for the Ruby interpreter was (finally) written.
· amend_by_symmetry during MD run was causing crash. Fixed.
· Graphite potential calculation is further modified (hope this is complete now!)
· When no molecule is open, Ruby scripts are evaluated in the context of 'main' (the toplevel object)
· Graphite potential calculation is improved.
· The current working directory is set to the document home on startup.
· The anisotropic parameters for the symmetry expanded atoms are now correctly handled.
· Pressure control and surface potential are removed from the GUI; they are not well tested and should be used with great care.
· The load commands can now include error messages in Ruby exception.
· MD minimize was not working properly (especially for the second run with the same molecule). Fixed.
· Symmetry expansion in CIF import is improved. (May not be complete yet)
· Molecule#expand_by_symmetry now returns an array of atom indices instead of IntGroup.
· Molecule#symop_for_transform and transform_for_symop are implemented. The symmetry expansion of CIF import is being reworked, but still incomplete.
· Molecule#is_atom_hidden and AtomRef#hidden, hidden= are implemented, and Molecule#hidden_atoms and hidden_atoms= are made obsolete.
· Molecule#set/get_view_rotation: the sign of the angle is made opposite (left-hand screw in respect to the axis), so that it is consistent with Transform#rotation. This is opposite to the convention of the OpenGL rotator.
· The restriction on the number of bonds (12) is removed (modified so heavily, that it is likely that there is still some bugs left...)
· Include periodicity flags in the 'define unit cell' dialog
· Problem on guessing UFF angle parameter was fixed.
· Fixed a very stupid bug in drawing unit cell.
· Handling of frame-specific cell parameters was very inconsistent. Hopefully fixed, but may be still incomplete.
· Graphite potential in MM/MD gets recalculated much less frequently now.
· Building verlet list was reworked to implement complete search of the periodic lattice points. Still in progress.
· Symmetry operations from the CIF file were not read correctly for hexagonal system. Fixed.
· Mac (only 10.6?): when the graphite display is on, the lighting of the molecule model looks strange. Fixed.
June 19th, 2012
· Features of Molecule cell and Molecule box are modified so that the handling of the sigma values of the cell parameters looks more consistent.
· Mbsf format now retains anisotropic parameters and sigma (for crystallographic data)
· Crash during creating bonds when ellipsoid display is on is fixed.
· Ruby: Moleculefit_coordinates is implemented.
· LAMatrixnew, zero, submatrix now accept arguments in 'column,row' order.
· MM forces are updated after 'run(0)'
· Load/save mbsf files were broken when atom type variants were used for atom types with 3 or 4 characters. Fixed.
· The order of parameters in cmd_edit_local_parameter_in_main view dialog was inconsistent. Fixed. Also fixed Ruby exception in UFF guess dialog.
· Moleculetransform, rotate, invert, etc. are now aware of symmetry related atoms. That is, the symmetry operation is updated so that the atoms are also symmetry related after transformation.
· Ruby: AtomRefsymop can now be set from script.
· Ruby: Moleculeamend_by_symmetry is implemented.
· Ruby: Moleculeset(get)_view_translation is now obsolete and replaced by set(get)_view_center.
· The order of the anisotropic thermal parameters is changed to 'b11, b22, b33, b12, b13, b23'. Inconsistency in some of the codes is fixed. TODO: when symmetry expansion is done, the anisotropic thermal parameters should be correctly converted.
· Ruby: Moleculehidden_atoms and Moleculeset_hidden_atoms are implemented.
· The order of columns for MD parameters in the bond/angle/dihedral tables are changed, so that the columns appear in the same order as in the parameter table.
· UFF parameter guess is implemented.
· Moleculeneutralize was not working correctly. Fixed, and Moleculecharge was implemented.
· The load/unload global parameters dialog is sometimes out of the screen. Fixed.
· Windows version does not display last build date in the about dialog. Fixed.
· Parameters now can be specified by using both explicit indices and atom types, like '7-ca-8'.
· Parameter editing is improved.
· Restructure MolAction.c.
· Atom range specification for the vdw cutoff parameter is now made obsolete.
· Vector3D and Transform are modified to accept an LAMatrix argument. The document is written for LAMatrix.
· Load Script Menu caused crash when no window is open. Fixed.
· Ruby: Kernellookup_menu is implemented.
· Document is written for LAMatrix.
· LAMatrixmultiply was not working correctly when on-the-fly size conversion was required. Fixed.
· Execute Script command was broken. Fixed.
· CIF import may fail when _geom_bond_site_symmetry_1 field is missing. Fixed.
· Document was written for the collaboration with other quantum chemistry softwares.
· .log and .out are both accepted as the extension of the Gaussian and GAMESS log files.
· update_version.rb is improved.
January 11th, 2012
· Ring fusion can be performed by copy-paste or "double-click and type-in".
· Various ring structures (cycloalkanes, aromatics) and solvent boxes are accessible from "Open Predefined" menu.
· CIF import is improved, so that bonds including the calculated hydrogen atoms are created by guess.
· Import/export of dcd trajectory files is implemented.
· Creating AMBER input now allows to select between AMBER8 (also for NAMD) and AMBER11 formats.
August 23rd, 2011
· Fchk import was broken (enbug in 0.5.6.1); fixed.
· Final compile date/time is now shown in the 'About' window.
· Fix mdcrd import to allow coordinates using full 8 digits (like -123.456 or 1234.567).
· Occasional crash during minimization is fixed.
August 4th, 2011
· Crash on running antechamber/parmchk on PPC Mac is (hopefully) fixed.
· Mac: resp and sqm (semiempirial QM calculation invoked by antechamber) caused crash unless gfortran is installed. To fix this, config.h/Makefiles for AmberTools is modified so that gfortran library is statically linked.
· Occasionally, termination of the subprocess (like antechamber) was not detected properly, and the subprocess was left as a zombie. Improved, but may not be completely fixed.
· Loading GAMESS dat file now can be interrupted by ESC.
· Disable close box of RubyDialogFrame.
· On importing frcmod, atom type with a single character (like "c") was not recognized properly. Fixed.
· MO import from GAMESS log/dat files are implemented.