Several additions... Restraints.cpp and .hpp were included for restraining particles in thermodynamic integration. By including these, changes were made in Integrator, SimInfo, ForceFeilds, SimSetup, StatWriter, and possibly some other files. Two bass keywords were also added for performing thermodynamic integration: a lambda value one and a k power one.
get rid of rc and massratio from simState, creat cutoff group forevery atom which does not belong to cutoff group defined at mdl file
fix two bugs in siminfo which cause infinite loop; fix anoter one in CutoffGroup which causes seg fault
adding cutoffGroup into OOPSE
Many changes to get group-based cutoffs to work
C++ pass groupList to fortran
fix an unmatched c/fortran interface
add center of mass of the molecule and massRation into atom class
Changes for RigidBody dynamics (Somewhat extensive)
Fixes to profile code.
fixed a stdlib.h include error in bass.l fixed a little bug in the first time step, regarding the setting of ecr and est in fortran
som efixes to the way rcut is setup, as well as additional debugging comments.
replace c++ header stuff with more portable c header stuff Also, mod file fixes and portability changes Some fortran changes will need to be reversed.
cleaned things with gcc -Wall and g++ -Wall
fix bug in calculating maxCutoff
switched SimInfo to use a system configuration from SimState rather than arrays from Atom
Changed how cutoffs were handled from C. Now notifyCutoffs in Fortran notifies those who need the information of any changes to cutoffs.
more fixes for box changes
found a bug. Unit vectors were not being updated
fixed the bugs introduced by switching the periodic box to a matrix
Most of the integrator and NVT seem to be working now.
Added volume and enthalpy to status file
fixes for NVT
doing some testing in sticky through Symplectic.
fixed some small things with simError.h
dipoles mostly work, but there is a memory leak somewhere.
Fixes in MPI force calc and in Trappe_Ex parsing.
fixed the compile time bugs, Source builds and links
fixing some compile time bugs
I have implemeted Molecules everywhere I could remember to. will now attempt to compile.
LJ_FF has been converted to the new Molecule model. TraPPE_Ex is currently being updated. SimSetups routines are writtten, but not yet called.
little bug fixes here and there
fixed bug where short range interactions were not being calculated. removed some debug print statements
This commit was generated by cvs2svn to compensate for changes in r377, which included commits to RCS files with non-trunk default branches.
New OOPSE Tree
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