*** empty log message ***
roll in progress
roll in progress
new rattle algorithm is working
Formatting Changes, removed writeRaw
Implemented a separate solid and liquid thermodynamic integration routines
Fixed a bug in Integrator.cpp where it called writeRaw() when useThermInt = false...
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.
fixes for skip list
Many changes to get group-based cutoffs to work
C++ pass groupList to fortran
fixed getCOMVel and velocitize at thermo
Fixed a charge bug
new implement of quickLate using visitor and composite pattern
fix whole bunch of bugs :-)
Change DumpWriter and InitFromFile
Changes for RigidBody dynamics (Somewhat extensive)
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
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...
Merge the code of writeFinal and writeDump; Adding sortingIndex into DumpWriter; Fix a bug of writing last frame twice in integrator
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.
add chi and eta to the comment line of dump file.
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.
Changed DumpReader to use linked lists instead of a vector. Fixed the makefile to build DumpReader.cpp Removed a comment output in Exclude.cpp Modified DumpWriter and Integrator to write an eor file every time a frame is written. This lets the .eor file represent the last written frame of a simulation.
cleaned things with gcc -Wall and g++ -Wall
moved readyCheck in the integrator so that it is called before the first Statistics are written.
Removed NPTfm from Integrator.hpp. Some small syntax cleaning in NPTfm and SimSetup
fix bug in calculating maxCutoff
added NPT base class. NPTi is up to date. NPTf is not.
fixed NPTi to now work with constraints.
add conserved quantity to statWriter fix bug of vector wrapping at NPTi
updated the ChangeLog added two new NPT integrators, they still need work.
added resetTime to the Global namespace. added ability to reset the integrators in the NVT and NPT family.
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
set default force substraction policy to PolicyByMass
*** empty log message ***
small bug fix on frequency of output dumps.
harmonic potential & z-contraint method
added method of moving zconstraint molecules to specified positions
*** empty log message ***
some initial changes to Dumpwriter and friends to accomadate random file access
fixed Initializefrom file to start the simulation from the time specified in the init file.
Started work on a DumpReader
fixed some bugs, Changed entry_plug to info where appropriate
Removed some debugging write statements
Fixes for get and set routines in Atom and DirectionalAtom
found a bug. Unit vectors were not being updated
working on som integrator bugs
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.
Doing some work to debug the constraint code.
Most of the integrator and NVT seem to be working now.
slowly converting to new integrator and forcefield names.
finished the basics of the integrator and SimSetup.cpp
This form allows you to request diffs between any two revisions of this file. For each of the two "sides" of the diff, enter a numeric revision.