new rattle algorithm is working
in the progress of fixing MPI version of cutoff group
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 instantiation of Integrator<BaseIntegrator> in order to make OOPSE compiled by icc8
keep the previous position of cantilever in SMD
Change DumpWriter and InitFromFile
Changes for RigidBody dynamics (Somewhat extensive)
incorporate SMD into ZConstraint,it does not sound a good choice, next commit will seperate SMD and ZConstraint
ZConstraint now can support sequential moving. Refactorying is needed to support SMD in ZConstraint
Using inherit instead of compose to implement Minimizer both versions are working
adding function shakeF in order to remove the constraint force along bond direction
Single version of energy minimization for argon is working, need to add constraint
Add some lines into global.cpp to make it work with energy minimization
to avoid cyclic depency, refactory constraint class
revision of constraint for Nonlinear Optimization Model
Energy Minimizer
moved the velocity scale matrix calculation outside of the atom loop in the NPT family of integrators.
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
add chi and eta to the comment line of dump file.
added a new NPT integrator, NPTxyz. It scales the x, y, and z direction sepeartely. no box skew allowed.
fixed a lot of warnings and errors found with SUN's SUNWspro.s1s7
fixed some additional remarks from icc -w3 (extra verbose output)
Removed NPTfm from Integrator.hpp. Some small syntax cleaning in NPTfm and SimSetup
Converted NPTf to work with the NPT base class. Removed NPTfm and NPTim from cvs
added NPT base class. NPTi is up to date. NPTf is not.
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
updated the ChangeLog added two new NPT integrators, they still need work.
Changes to autoconf / configure method of configuring OOPSE
added resetTime to the Global namespace. added ability to reset the integrators in the NVT and NPT family.
fix a bug at MPI version of PolicyByMass
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reformmating ZConstraint and fixe bug of error msg printing
Tested MPI version of Z-Constraint Method
Stable ZConstraint with average force substraction strategy
harmonic potential & z-contraint method
added harmonical potential to z-constraint method
added method of moving zconstraint molecules to specified positions
Added Z constraint.
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Bugfix in NPTim, fixes for NPTfm
Checking in changes for NPTim
Fixes for get and set routines in Atom and DirectionalAtom
found a bug. Unit vectors were not being updated
Working on NPTim
working on som integrator bugs
Bunch of 1-d array -> 2-d array stuff
Bug fixing NPTi and NPTf. there is some error in the caclulation of HmatInverse.
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NPTi
Fixes to NVT. Check them!
NPT fix
Most of the integrator and NVT seem to be working now.
NVT additions
slowly converting to new integrator and forcefield names.
Added Teng's parmeters fro the ghost Bend in TraPPE_Ex some work on the integrator. ( incomplete)
added constrainA and constrainB to the Symplectic integrator
currently modifiying Symplectic to become the basic integrator.
added some member variables for position, velocity, etc.
changed how NVT is now derived from Integrator
Added ExtendedSystem infrastructure for NPT and NVT calculations
I have implemeted Molecules everywhere I could remember to. will now attempt to compile.
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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