Added new restraint infrastructure Added MolecularRestraints Added ObjectRestraints Added RestraintStamp Updated thermodynamic integration to use ObjectRestraints Added Quaternion mathematics for twist swing decompositions Significantly updated RestWriter and RestReader to use dump-like files Added selections for x, y, and z coordinates of atoms Removed monolithic Restraints class Fixed a few bugs in gradients of Euler angles in DirectionalAtom and RigidBody Added some rotational capabilities to prinicpalAxisCalculator
Changes required for Inversions and Base Atom types. This will break OOPSE badly for a few days or so...
Adding infrastructure for Amber force field.
updating configure process
Non-bonded interactions added.
Addition of section parser for Spohr water-metal potential.
Fix parsing error in OptionSectionParser
End of the Link --> List Return of the Oject-Oriented replace yacc/lex parser with antlr parser
OptionSectionParser get compiled
Missed makefile for sutton-chen.
adding zlib support for DumpWriter
help
added gb
OOPSE setup for TAP water. It's not parametrized, but OOPSE will now let me run it...
Shapes is limping along with a array bounds overwrite (I think...). At least the parser loads the forcefield fine...
LinkedList removal project starts now
First commit of the new restraints code
adding IndexFinder which is used to select the molecules; Seperate ElectrostaticAtomTypesSectionParser into ChargeAtomTypesSectionParser and MultipoleAtomTypesSectionParser;remove print dipole option from Dump2XYZ;
moved Package variable into subdirectory makefiles to speed up the building process
port to SGI platform
merging new_design branch into OOPSE-2.0
Improvements to restraints
define DEV_ROOT as relative path
change Makefile to relative path
add yacc and lex rules
Import of OOPSE v. 2.0
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