News in version 3

Difference between revisions from 2009/01/30 06:12 and 2009/01/29 10:35.
New version of cuby, Cuby3, was rewritten from scratch to be even better than the previous one. The philosophy of the code remains the same, but the implementation differs, what brings incompatibility with previous versions. However, all these changes have good reason.

!!Highlights

* '''Cuby can run without binary libraries'''{br}Everything was implemented in pure ruby to make Cuby independent. For higher performance, binary libraries can be optionaly used for some operations (i.e. matrix algebra).
* '''Cuby can run without binary libraries'''{br}Everything was implemented in pure ruby to make Cuby independent. For higher performance, binary [extensions|Extensions] can be optionaly used for some operations (i.e. matrix algebra).
* '''Input is no longer one file''', keywords and geometry are separate files{br}Reasons:
** Geometry in different formats can be read
** Keywords use standardized format (YAML)
** It is easier to run multiple calculations with the same settings
* Geometry can be either in XYZ, Z-matrix or PDB format
* Interaction energy calculation can recognize monomers automatically
* Atom selection expressions are now more powerful
* Output verbosity level can be changed