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Molby Changelog

What's new in Molby 1.0 b02

Apr 26, 2014
  • Common "Scratch" directory is used for all external programs, namely antechamber, resp, gamess and ortep. Note: the scratch directory cannot contain whitespace characters.
  • In reading MM/MD parameters, check criteria for duplicate parameters are somewhat relaxed (i.e. comparison of floating numbers is allowed for rounding errors)
  • Symmetry Operations dialog was not working for setting new symmetry. Fixed.
  • GAMESS dialog is modified so that manual editing is possible.
  • Mac: 'Window' menu is implemented.

New in Molby 0.6.5 (Jun 21, 2013)

  • New Features:
  • Local execution of GAMESS is implemented.
  • For X-ray data (with standard deviations), calculation of bonds and angles with standard deviation is implemented.
  • GAMESS log containing F and G type orbitals can now be imported (cube calculation is not yet implemented).
  • In the 'GAMESS export' dialog, new basis sets can be loaded from external files.
  • Particle mesh Ewald calculation is implemented (experimentally).
  • "Pi-anchor" atoms (i.e. dummy atoms for cyclopentadienyl-metal bonds etc.) are implemented (experimentally).
  • The Ruby console now has history capability.
  • Bug Fix:
  • CIF files from old TeXsan software cannot be loaded. Fixed.
  • Symmetry expansion in CIF import is improved (may not be complete yet).
  • Deleting bonds was causing bus error. Fixed.
  • Two subsequent dragging of different atoms was causing undo failure. Fixed.
  • Merging/unmerging molecules are revised, so that undo works more consistently.
  • And many others.

New in Molby 0.6.4 (Oct 16, 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.

New in Molby 0.6.3 (Jun 19, 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.

New in Molby 0.6.1 (Jan 11, 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.

New in Molby 0.5.6.2 (Aug 23, 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.

New in Molby 0.5.6.1 (Aug 4, 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.