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
C++ compatibility for templates
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.
Stuff for MOD support in other compilers
added a new NPT integrator, NPTxyz. It scales the x, y, and z direction sepeartely. no box skew allowed.
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.
fixes for configure
Converted NPTf to work with the NPT base class. Removed NPTfm and NPTim from cvs
Added integrators to Makefile.in
Changes to autoconf / configure method of configuring OOPSE
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