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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