get rid of rc and massratio from simState, creat cutoff group forevery atom which does not belong to cutoff group defined at mdl file
bug fixes for cutoffGroups
adding cutoffGroup into OOPSE
Fixes to libmdtools to use the simplified cutoff stuff in the BASS library
Adding molecular cutoffs
fixed two bugs in MPI version of InitfromFile and one unmatch MPI command in DumpWriter
fix a bug in setting exclude list
fix whole bunch of bugs :-)
Change DumpWriter and InitFromFile
Now molecules can keep track of their own IntegrableObjects (and RigidBodies). Also a bug-fix so that SimInfo can keep track of RigidBodies (which was done incorrectly before).
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
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Using inherit instead of compose to implement Minimizer both versions are working
Stripped out the hardwired LJ_rcut
Single version of energy minimization for argon is working, need to add constraint
Add one more file into Makefile.in
Add some lines into global.cpp to make it work with energy minimization
Substantial changes. OOPSE now has a working WATER.cpp forcefield and parser. This involved changes to WATER.cpp and ForceFields amoung other files. One important note: a hardwiring of LJ_rcut was made in calc_LJ_FF.F90. This will be removed on the next commit...
Convert Eulers in degrees into radians
Changed default orientation in BASS to use Euler angles in the following order: phi, theta, psi Removed the ability to set orientation using a unit vector
Made some error messages more user-friendly
Adding warning if sample time, status time, thermal time and reset time are not divisible by dt
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
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.
added routines for the sysbuilder to work with simSetup
added eam ForceField files to the init fixed an eam mpi parmeter setup bug
added a new NPT integrator, NPTxyz. It scales the x, y, and z direction sepeartely. no box skew allowed.
added useInitTime to the BASS syntax. * useInitTime = false: sets the origin time to 0.0 regardless of the time stamp in the .init file * default=> useInitTime = true;
cleaned things with gcc -Wall and g++ -Wall
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.
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
Added: check uniqueness of molIndex
fix bug of MPI_Allreduce in ZConstraint, the MPITYPE is set to MPI_DOUBLE, however, the corret type is MPI_INT. Therefore, when we turn on the optimization flag, it causes a seg fault
Use make_sprng_seed() to generate seed and check the seed which is specified by user at least contains 9 digits
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
updated the Changelog. added some bug fixes for setting the random number generator seed value. fixed a bug where ghostbend atom b was not being set. ( recent bug from SimState conversion)
reformmating ZConstraint and fixe bug of error msg printing
Tested MPI version of Z-Constraint Method
harmonic potential & z-contraint method
fixed a really annoying bug in Directional Atom, where mu was getting written to pseudorandom memory location.
debugging globals
added harmonical potential to z-constraint method
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switched SimInfo to use a system configuration from SimState rather than arrays from Atom
stable version of Z-Constraint
add index range checking into ZConstraint
Added Z constraint.
working on the props code
Added eam to simSetup and added changecutoffeam.
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Fixed a current time initialization bug in InitFromFile.
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
cleaned up simSetup
fixed some bugs, Changed entry_plug to info where appropriate
Bugfix in NPTim, fixes for NPTfm
Checking in changes for NPTim
Bug fixing NPTi and NPTf. there is some error in the caclulation of HmatInverse.
adding in dan's NPT stuff
Fixes and merging NPTf
fixed the bugs introduced by switching the periodic box to a matrix
Changed over the bonds to Harmonic bonds in the DUFF frc file fixed constraints.
Most of the integrator and NVT seem to be working now.
finished the basics of the integrator and SimSetup.cpp
doing some work on SimSetup to clean it up / get it to work with the new Integrator.
Added Teng's parmeters fro the ghost Bend in TraPPE_Ex some work on the integrator. ( incomplete)
fixed up sysBuild to where it should now build our systems
fixed a memory bug in Fortran, where molMembershipArray was declared nLocal instead of nGlobal.
Bug fix in progress for NPT
added a globalIndex counter to Molecule
fixed a n mpi init bug in SimSetup. caused a miscalculation of nLocal.
fixes for NPT and NVT
Fixes for NPT / NVT
Fixes for NPT and NVT
bug fixes
Added ExtendedSystem infrastructure for NPT and NVT calculations
dipoles mostly work, but there is a memory leak somewhere.
Fixes in MPI force calc and in Trappe_Ex parsing.
fixed a bug where the Excludes were not being created properly
mpi fixes and debugging mpi read write from file.
MPI buggy, fixed mpiRefresh issue.
fixed a bug where excludes were not being initialized
Fixed a single processor segfault bug.
fixed a few more bugs.
fixing some compile time bugs
finished updating SimSetup to initialize and use the new MPI division of labour, and Molecule class
LJ_FF has been converted to the new Molecule model. TraPPE_Ex is currently being updated. SimSetups routines are writtten, but not yet called.
the skeleton for making the molecules is in place. ForceField needs to be updated next.
still working on the SimSetup routine. also fixed some things in Exclude.hpp
I'm overhauling the molecule class to contain it's own bonds, bends, and torsions. may god have mercy on my soul.
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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