Fixes to libmdtools to use the simplified cutoff stuff in the BASS library
Many changes to get group-based cutoffs to work
C++ pass groupList to fortran
Adding molecular cutoffs
change the calculation of pressure tensor
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)
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...
Made some error messages more user-friendly
Changes for adding direct charge-charge interactions (with switching function)
added a more verbose error message in SimInfo. Added a more informative error message in InitializeFromFile
Fixed a bug in SimInfo ordering of radii
added a routine to SimInfo.cpp to inline a min 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
did a merge by hand from the new-templateless branch to the main trunk.
bug Fixes include:
* fixed the switching function from ortho to non-ortho box.
!!!!! THis was responsible for all of the sudden deaths we saw.
* some formating in the string when we write out the extended system state.
* added NPT.cpp to the makefile.in
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.
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
*** empty log message ***
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
Tested MPI version of Z-Constraint Method
fixed a really annoying bug in Directional Atom, where mu was getting written to pseudorandom memory location.
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
Bug fixes for eam...
add index range checking into ZConstraint
Added Z constraint.
Initialized currentTime to 0, in case no one sets it.
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
fixed a long lived bug in do_forces. Rrf was not being used in the neighborlist correctly. rcut was conssistently being set lowere than Rrf causing the dipole cutoff region to be to small. Also led to the removal of the taper region to buffer the dipole cutoff.
working on fixing ssd bug
Fixes for the NPT ensembles
found a bug. Unit vectors were not being updated
fixed some bugs
Bunch of 1-d array -> 2-d array stuff
Bug fixing NPTi and NPTf. there is some error in the caclulation of HmatInverse.
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.
Bug fix in progress for NPT
fixes for NPT and NVT
It works (kinda)...
Fixes for NPT and NVT
bug fixes
Bug fixes for simulation module rewrites
Changes for Extended System
Fixes for ExtendedSystem
dipoles mostly work, but there is a memory leak somewhere.
more bug fixes....
Fixed bug with pot_local not zeroed.
Fixes in MPI force calc and in Trappe_Ex parsing.
fixing some compile time bugs
LJ_FF has been converted to the new Molecule model. TraPPE_Ex is currently being updated. SimSetups routines are writtten, but not yet called.
fixed an mpi include bug in THermo.cpp
electrostatic changes for dipole / RF separation
little bug fixes here and there
This commit was generated by cvs2svn to compensate for changes in r377, which included commits to RCS files with non-trunk default branches.
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