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Support load/save of NBO info
[molby/Molby.git]
/
MolLib
/ Molecule.c
2022-11-15
Toshi Nagata
Support load/save of NBO info
master
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commitdiff
2022-10-30
Toshi Nagata
MO surface display is improved
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commitdiff
2022-10-16
Toshi Nagata
Importing JANPA log is improved
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commitdiff
2022-10-16
Toshi Nagata
F/F7/G/G9 orbitals are implemented
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commitdiff
2022-10-16
Toshi Nagata
Start implementing 'additional exponent' for JANPA...
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commitdiff
2022-09-19
Toshi Nagata
Compiler warnings are mostly removed.
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commitdiff
2021-12-25
Toshi Nagata
ORTEP silently fails with non positive-definite B....
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commitdiff
2019-08-17
toshinagata1964
About dialog is improved.
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2016-09-09
toshinagata1964
Creating cube file failed when very small electron...
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commitdiff
2014-11-16
toshinagata1964
Handling of the surface normals was incomplete. Fixed.
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commitdiff
2014-09-12
toshinagata1964
Implement loading/saving of graphiobjects from/to mbsf...
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commitdiff
2014-07-01
toshinagata1964
Fix crash in MO surface window when F orbitals are...
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commitdiff
2014-06-29
toshinagata1964
The electron density surface can be drawn by create_sur...
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commitdiff
2014-06-26
toshinagata1964
The MO information is now stored in the mbsf file.
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commitdiff
2014-06-25
toshinagata1964
The extra property values are now saved into the mbsf...
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commitdiff
2014-06-19
toshinagata1964
Show MO Surface dialog is updated (hopefully improved)
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commitdiff
2014-06-19
toshinagata1964
Show MO Surface dialog is implemented.
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commitdiff
2014-06-14
toshinagata1964
On importing Gamess output, the energy values are read...
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commitdiff
2014-06-13
toshinagata1964
Extra properties (assignable for each frame) are introd...
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commitdiff
2014-06-08
toshinagata1964
set_surface_attr now accepts attributes :color and...
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commitdiff
2014-06-05
toshinagata1964
The atomic radii for graphical display are corrected...
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commitdiff
2014-05-27
toshinagata1964
create_surface is somewhat improved (looks like working)
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commitdiff
2014-05-22
toshinagata1964
Handling of Gaussian fchk files was causing problems...
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commitdiff
2014-05-21
toshinagata1964
Creating MO surface is improved (not much tested yet)
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commitdiff
2014-05-20
toshinagata1964
Start implementing MO surface display: Molecule.create_...
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commitdiff
2014-04-26
toshinagata1964
Ruby: get_mo_coefficients and get_mo_energy are impleme...
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commitdiff
2014-03-23
toshinagata1964
Some add/delete operation caused unexpected termination.
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commitdiff
2014-03-21
toshinagata1964
Obsolete codes are removed
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commitdiff
2014-03-17
toshinagata1964
Line/Ball-and-stick/Space-filling modes are implemented
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commitdiff
2014-02-27
toshinagata1964
expand_by_symmetry was causing strange bonds when expan...
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commitdiff
2014-01-30
toshinagata1964
Ruby: Molecule#find_close_atoms is modified so that...
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commitdiff
2013-11-15
toshinagata1964
Minimizing structure including pi-anchor atoms was...
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commitdiff
2013-11-14
toshinagata1964
Handling of pi-anchor atoms is slightly modified
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commitdiff
2013-08-10
toshinagata1964
Implement load/save/set/get of bond order information.
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commitdiff
2013-08-02
toshinagata1964
On calling antechamber, atom names are modified so...
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commitdiff
2013-08-01
toshinagata1964
Resize of the Ruby Dialog is improved (still experiment...
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commitdiff
2013-06-11
toshinagata1964
r356 modification was not correct. Updated.
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commitdiff
2013-06-11
toshinagata1964
Importing PM3/GAMESS log is improved. (The atomic infor...
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commitdiff
2013-01-21
toshinagata1964
GAMESS log containing F and G type orbitals can now...
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commitdiff
2012-11-27
toshinagata1964
Bond creation is updated so that duplicate bond/angle...
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commitdiff
2012-11-27
toshinagata1964
Deleting bonds was causing bus error. Fixed.
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commitdiff
2012-11-22
toshinagata1964
Calculation of reciprocal cell parameter was incorrect...
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commitdiff
2012-11-14
toshinagata1964
(Re-retry committing) expand_by_symmetry was not workin...
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commitdiff
2012-11-14
toshinagata1964
(Retry committing) expand_by_symmetry was not working...
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commitdiff
2012-11-14
toshinagata1964
expand_by_symmetry was not working correctly when no...
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commitdiff
2012-11-11
toshinagata1964
Particle Mesh Ewald is being implemented (still not...
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commitdiff
2012-11-01
toshinagata1964
When new bonds are created, angles of type X-##-##...
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2012-10-30
toshinagata1964
Expanding by symmetry (and loading cif file) was not...
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commitdiff
2012-10-30
toshinagata1964
Attribute table was not updated correctly after revert...
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commitdiff
2012-10-30
toshinagata1964
Atom renumbering was not working for pi anchor table...
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commitdiff
2012-10-29
toshinagata1964
Remove previous pi-anchor codes.
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commitdiff
2012-10-29
toshinagata1964
Pi anchor implementation is done.
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commitdiff
2012-10-29
toshinagata1964
New implementation of pi anchor atoms is close to compl...
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commitdiff
2012-10-28
toshinagata1964
The load/save codes are rewritten, so that the error...
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commitdiff
2012-10-26
toshinagata1964
Another implementation of pi-anchor is being tried...
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commitdiff
2012-10-25
toshinagata1964
Pi atom positions are now cached within the piatom...
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commitdiff
2012-10-25
toshinagata1964
Merging/unmerging molecules are extensively revised...
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2012-10-24
toshinagata1964
Connection check is rewritten to include the pi anchor...
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2012-10-23
toshinagata1964
Molecule#get_coord_from_frame now always tries to copy...
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2012-10-19
toshinagata1964
Molecule#cell_flexibility, set_cell_flexibility are...
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2012-10-11
toshinagata1964
Filter mode (development continued)
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2012-09-01
toshinagata1964
Handling of view-related attributes of Molecule is...
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2012-08-22
toshinagata1964
Experimental feature: dummy atoms to represent pi-metal...
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2012-08-12
toshinagata1964
Some unused fields of Molecule were removed.
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commitdiff
2012-08-04
toshinagata1964
Loading multiple-frame mbsf sometimes fails to load...
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commitdiff
2012-08-03
toshinagata1964
Some cleanup of the internal structure; unused fields...
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2012-08-02
toshinagata1964
Property table can now list the unit cell parameters.
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commitdiff
2012-07-26
toshinagata1964
Cell minimization was not working correctly when no...
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2012-07-25
toshinagata1964
MDArena#prepare was not working correctly when unit...
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commitdiff
2012-07-24
toshinagata1964
Handling of Molecule object was not consistent. Hopeful...
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commitdiff
2012-07-24
toshinagata1964
The revision number is displayed in the about dialog...
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commitdiff
2012-07-24
toshinagata1964
Copy/paste of molecules was broken when it had atoms...
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commitdiff
2012-07-06
toshinagata1964
Cell minimization is improved (hopefully...)
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commitdiff
2012-07-05
toshinagata1964
Handling of flexible cells were still inconsistent.
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commitdiff
2012-07-04
toshinagata1964
Molecule#cell_flexibility and set_cell_flexibility...
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commitdiff
2012-07-04
toshinagata1964
Memory leak bugs are examined and removed.
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2012-06-29
toshinagata1964
The anisotropic parameters for the symmetry expanded...
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2012-06-27
toshinagata1964
Molecule#expand_by_symmetry now returns an array of...
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2012-06-27
toshinagata1964
Molecule#symop_for_transform and transform_for_symop...
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2012-06-25
toshinagata1964
The restriction on the number of bonds (12) is removed...
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commitdiff
2012-06-21
toshinagata1964
Handling of frame-specific cell parameters was very...
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commitdiff
2012-06-20
toshinagata1964
Building verlet list seems to be working. Handling...
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commitdiff
2012-06-18
toshinagata1964
Features of Molecule#cell and Molecule#box are modified...
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commitdiff
2012-06-18
toshinagata1964
Mbsf format now retains anisotropic parameters and...
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commitdiff
2012-06-14
toshinagata1964
Load/save mbsf files were broken when atom type variant...
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2012-06-07
toshinagata1964
Molecule#transform, rotate, invert, etc. are now aware...
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2012-06-06
toshinagata1964
MoleculeGetTransformForSymop() and MoleculeGetSymopForT...
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2012-06-04
toshinagata1964
The order of the anisotropic thermal parameters is...
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commitdiff
2012-05-08
toshinagata1964
Parameters now can be specified by using both explicit...
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commitdiff
2012-05-08
toshinagata1964
Parameter editing is under overhaul.
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commitdiff
2012-05-07
toshinagata1964
Handling of parameters are being improved, but still...
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commitdiff
2012-05-07
toshinagata1964
Handling of parameters is being reworked (still going on)
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commitdiff
2011-12-07
toshinagata1964
The structure Mat33 and Transform are now column-first...
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commitdiff
2011-11-30
toshinagata1964
Rms of crystallographic parameters (from the CIF file...
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commitdiff
2011-11-26
toshinagata1964
Some typical cyclic structures as well as solvent boxes...
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2011-11-25
toshinagata1964
Ruby: Molecule object is now unique to each open molecu...
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commitdiff
2011-10-31
toshinagata1964
Ruby: Molecule#find_close_atoms is implemented.
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commitdiff
2011-10-21
toshinagata1964
Enable undo for importing pdb and dcd.
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commitdiff
2011-10-19
toshinagata1964
Import/export of dcd format is implemented.
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commitdiff
2011-10-12
toshinagata1964
Merging molecule was resulting in strange order of...
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