- The "log file" field is set to blank unless explicitly set by the user.
- The structure Mat33 and Transform are now column-first arrangement (no change on Ruby interface and mbsf file format)
- Rms of crystallographic parameters (from the CIF file) are now kept in the molecule. Copying/saving of such parameters are not yet supported.
+
+2012.6.18.
+Version 0.6.3
+
+リリースノート
+- LAMatrix クラスのドキュメントを作成。
+- 量子化学計算ソフトウェアとの連携のドキュメントを作成。
+- CIFファイルから読み込んだ座標値・異方性温度因子・セルパラメータの標準偏差を mbsf ファイルに保存するようにした。
+- Ruby コマンド新設: Molecule#fit_coordinates, Molecule#amend_by_symmetry, Molecule#set(get)_view_center, Molecule#hidden_atoms, Molecule#set_hidden_atoms, Molecule#charge, Kernel#lookup_menu
+- Bond, angle などのテーブルから分子力学パラメータを編集するとき、Universal Force Field (UFF) で力の定数を見積もる機能をつけた。
+- 分子力学パラメータを原子のインデックスで指定できるようにした（実はもともとあった機能だが、分子を編集してもパラメータが維持されるようになった）。
+- その他バグ修正（ChangeLog を参照）
+
+- Document for the LAMatrix class was written.
+- Document for the collaboration with other quantum chemistry softwares was written.
+- Mbsf files now retain sigmas for the crystallographic parameters (imported from CIF).
+- New Ruby commands: Molecule#fit_coordinates, Molecule#amend_by_symmetry, Molecule#set(get)_view_center, Molecule#hidden_atoms, Molecule#set_hidden_atoms, Molecule#charge, Kernel#lookup_menu
+- When the MM parameters are edited from the bond/angle table, the force constant can be guessed by Universal Force Field (UFF).
+- The MM parameters can now be specified by explicit atom indices.
+- Other bug fixes (see the change log).
+
+ChangeLog
+- 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: Molecule#fit_coordinates is implemented.
+- LAMatrix#new, #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_mainview dialog was inconsistent. Fixed. Also fixed Ruby exception in UFF guess dialog.
+- Molecule#transform, 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: AtomRef#symop can now be set from script.
+- Ruby: Molecule#amend_by_symmetry is implemented.
+- Ruby: Molecule#set(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: Molecule#hidden_atoms and Molecule#set_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.
+- Molecule#neutralize was not working correctly. Fixed, and Molecule#charge 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: Kernel#lookup_menu is implemented.
+- Document is written for LAMatrix.
+- LAMatrix#multiply 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.
+
+2012.10.13.
+
+Version 0.6.4
+
+リリースノート
+- bond/angle/dihedral/improper の属性テーブルを開くと、分子力学パラメータを検索するようにした（ただし、結合情報から angle/dihedral テーブルの再構成はやらない。これは MM/MD ウィンドウを開いたときに起きる）
+- 属性テーブルに単位格子を表示できるようにした。
+- "Show Graphite" コマンドが間違った C-C 結合距離を使っていたので修正。正しくは 1.42Å。
+- 最適平面計算を実装（Script メニューの Best-fit Plane）
+- リビジョン番号を About ダイアログに表示するようにした。
+- 単位格子の最適化機能を実装（まだ実験的）
+- 原子当たりの結合数の上限 (12) を撤廃した。
+- Ruby: Dialog#filter_kit を実装。使い方がドキュメントの付録に書かれている。
+- Ruby: LAMatrix#svd (singular value decomposition) を実装。
+- Ruby: bond_par, angle_par, dihedral_par, improper_par, vdw_par メソッドを Molecule から MDArena に移した。
+- その他多くのバグ修正（ChangeLog 参照）
+
+Release Note
+- Opening bond/angle/dihedral/improper table now triggers searching MD parameters (but not rebuilding angle/dihedral/improper tables).
+- Property table can now list the unit cell parameters.
+- "Show Graphite" command was using _very_ wrong C-C bond length. Now it uses correct length (1.42 angstrom).
+- Best-fit plane calculations are implemented.
+- The revision number is displayed in the about dialog.
+- Cell parameter minimization is implemented (still experimental).
+- The restriction on the number of bonds (12) is removed.
+- Ruby: Dialog#filter_kit is implemented. The how-to is described in the document (appendix).
+- Ruby: LAMatrix#svd (singular value decomposition) was implemented.
+- Ruby: The methods bond_par, angle_par, dihedral_par, improper_par, vdw_par are moved from Molecule to MDArena.
+- Bug fixes (see the ChangeLog)
+
+ChangeLog
+- 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.
+
+2012.6.15.
+ Version 0.6.5 を公開したのだが、GAMESS の構造最適化中のコンソールメッセージが変。同じ NSERCH に対応する行が複数表示されてしまう。要修正。
+ 理想的には、GAMESS も MM/MD と同じように実行中はいったん Molby に制御を戻して、表示を自由に変更できるようにするのがよい（編集は禁止）。さらに、複数の分子についてそれぞれ計算を走らせることも可能にできればなおよい。これはかなりの大改造が必要。
+
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