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fixed a deprcated instance of Atom::setZ and Atom::getZ in ZConstaint.
switched SimInfo to use a system configuration from SimState rather than arrays from Atom
Added Z constraint.
Added eam to simSetup and added changecutoffeam.
Finished most code for eam....
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Added massive changes for eam....
Changed how cutoffs were handled from C. Now notifyCutoffs in Fortran notifies those who need the information of any changes to cutoffs.
cleaned up simSetup
Bugfix in NPTim, fixes for NPTfm
Checking in changes for NPTim
found a bug. Unit vectors were not being updated
Working on NPTim
Fixes for both NPTf and NPTi
NPTi
cleaned up the dependecy scripts in the makefiles
fixed the bugs introduced by switching the periodic box to a matrix
Most of the integrator and NVT seem to be working now.
slowly converting to new integrator and forcefield names.
Added ExtendedSystem infrastructure for NPT and NVT calculations
bug fixes for compilation
Breaking c and fortran, c gets smarter, fortran gets dumber...
fixed some small things with simError.h
fixed the makefile
fixing some compile time bugs
Added Atom.cpp and Exclude.cpp
Fixed F_MACH_DEP bug
Makefile fixes, directory re-org, autoconf fixes
Makefile fixes for depends
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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