Implemented a separate solid and liquid thermodynamic integration routines
Fixed Thermodynamic integration code.
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.
adding cutoffGroup into OOPSE
Fixes to libmdtools to use the simplified cutoff stuff in the BASS library
C++ pass groupList to fortran
Adding molecular cutoffs
change the calculation of pressure tensor
new implement of quickLate using visitor and composite pattern
Change DumpWriter and InitFromFile
Changes for RigidBody dynamics (Somewhat extensive)
Using inherit instead of compose to implement Minimizer both versions are working
Add some lines into global.cpp to make it work with energy minimization
Changes for adding direct charge-charge interactions (with switching function)
reordered the rcut/ecr/boxSize initialization removed the rcut/ecr shrink and grow algorithm. the simulation will now exit when it runs into rcut or ecr.
added the following parameters to BASS: * useInitialExtendedSystemState * orthoBoxTolerance * useIntiTime => useInitialTime
bug fixes for rList problems
som efixes to the way rcut is setup, as well as additional debugging comments.
did a complete overhaul of how c calls fortran. All function pointers and fortran calls are rigidly typecast now.
added routines for the sysbuilder to work with simSetup
changed the formating ogf the error statements in simError added a function to get the maxCutoff
fixed a lot of warnings and errors found with SUN's SUNWspro.s1s7
cleaned things with gcc -Wall and g++ -Wall
fix bug in calculating maxCutoff
fixed ecr grow in SimInfo fixed conserved quantity in NPT (Still some small bug) NPTi appears very stable.
add conserved quantity to statWriter fix bug of vector wrapping at NPTi
added resetTime to the Global namespace. added ability to reset the integrators in the NVT and NPT family.
user can setup seed in bass file now, if he does not specify any value for seed, oopse will take the value of seconds of system time as seed
Added zConstraint into the BASS language syntax.
changed the number of degrees of freedom to account for zConstreints
switched SimInfo to use a system configuration from SimState rather than arrays from Atom
add index range checking into ZConstraint
Added Z constraint.
Fixed a current time initialization bug in InitFromFile.
some initial changes to Dumpwriter and friends to accomadate random file access
Started work on a DumpReader
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
Bunch of 1-d array -> 2-d array stuff
NPTi
fixed the bugs introduced by switching the periodic box to a matrix
working on adding the box matrix to everything.
Updated the ChangeLog, and Converted most of the SImInfo to use non-Isotropic boxes. wrapVector needs to be finished.
currently modifiying Symplectic to become the basic integrator.
fixes for NPT and NVT
Changes for Extended System
Fixes for ExtendedSystem
fixed a few more bugs.
finished updating SimSetup to initialize and use the new MPI division of labour, and Molecule class
still working on the SimSetup routine. also fixed some things in Exclude.hpp
electrostatic changes for dipole / RF separation
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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