--- trunk/OOPSE/ChangeLog	2003/06/25 21:12:14	567
+++ trunk/OOPSE/ChangeLog	2003/06/30 22:04:01	568
@@ -1,3 +1,814 @@
+2003-06-25 16:12  mmeineke
+
+	* libmdtools/: Integrator.cpp, SimSetup.cpp: Changed over the bonds
+	to Harmonic bonds in the DUFF frc file
+	
+	fixed constraints.
+
+2003-06-25 16:11  mmeineke
+
+	* forceFields/DUFF.frc: Changed over the bonds to Harmonic bonds in
+	the DUFF frc file
+
+2003-06-24 17:51  gezelter
+
+	* libmdtools/: Integrator.hpp, NVT.cpp: Fixes to NVT.  Check them!
+
+2003-06-24 14:57  mmeineke
+
+	* forceFields/DUFF.frc, libmdtools/BondExtensions.cpp,
+	libmdtools/DUFF.cpp, libmdtools/SRI.hpp: added Harmonic bod into
+	the DUFF forcefield and BondExtensions.cpp
+
+2003-06-23 16:24  mmeineke
+
+	* libmdtools/Integrator.cpp: Doing some work to debug the
+	constraint code.
+
+2003-06-20 15:50  gezelter
+
+	* libmdtools/Integrator.hpp: NPT fix
+
+2003-06-20 15:29  mmeineke
+
+	* libmdtools/Atom.cpp, libmdtools/DUFF.cpp,
+	libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp,
+	libmdtools/Integrator.hpp, libmdtools/LJFF.cpp,
+	libmdtools/Makefile, libmdtools/NVT.cpp, libmdtools/SimSetup.cpp,
+	libmdtools/Thermo.hpp, src/Makefile, utils/Makefile: Most of the
+	integrator and NVT seem to be working now.
+
+2003-06-20 11:49  gezelter
+
+	* libmdtools/: Integrator.hpp, NVT.cpp: NVT additions
+
+2003-06-19 17:02  mmeineke
+
+	* forceFields/DUFF.frc, forceFields/LJFF.frc,
+	forceFields/LJ_FF.frc, forceFields/Makefile,
+	forceFields/TraPPE.frc, forceFields/TraPPE_Ex.frc,
+	libmdtools/DUFF.cpp, libmdtools/ForceFields.hpp,
+	libmdtools/Integrator.cpp, libmdtools/Integrator.hpp,
+	libmdtools/LJFF.cpp, libmdtools/LJ_FF.cpp, libmdtools/Makefile,
+	libmdtools/TraPPEFF.cpp: slowly converting to new integrator and
+	forcefield names.
+
+2003-06-19 14:21  mmeineke
+
+	* libmdtools/: Integrator.cpp, SimSetup.cpp, Symplectic.cpp:
+	finished the basics of the integrator and SimSetup.cpp
+
+2003-06-19 14:11  mmeineke
+
+	* libmdtools/SimSetup.cpp:  doing some work on SimSetup to clean it
+	up / get it to work with the new Integrator.
+
+2003-06-18 17:20  mmeineke
+
+	* libmdtools/Symplectic.cpp: minor changes in an attempt to fix
+	output times.
+
+2003-06-17 16:56  mmeineke
+
+	* libmdtools/: Integrator.hpp, SimSetup.cpp: Added Teng's parmeters
+	fro the ghost Bend in TraPPE_Ex
+	
+	some work on the integrator. ( incomplete)
+
+2003-06-17 16:55  mmeineke
+
+	* forceFields/TraPPE_Ex.frc: Added Teng's parmeters fro the ghost
+	Bend in TraPPE_Ex
+
+2003-06-04 16:06  mmeineke
+
+	* libmdtools/: Integrator.hpp, Symplectic.cpp: added constrainA and
+	constrainB to the Symplectic integrator
+
+2003-05-30 16:32  mmeineke
+
+	* utils/bilayerSys.cpp: currently modifiying Symplectic to become
+	the basic integrator.
+	
+	bilayerSys.cpp altered for building tb3.
+
+2003-05-30 16:31  mmeineke
+
+	* libmdtools/: Integrator.hpp, SimInfo.hpp, Symplectic.cpp,
+	TraPPE_ExFF.cpp, Verlet.cpp, f_verlet_constrained.F90: currently
+	modifiying Symplectic to become the basic integrator.
+
+2003-05-30 15:19  mmeineke
+
+	* libmdtools/Integrator.hpp: added some member variables for
+	position, velocity, etc.
+
+2003-05-30 14:07  mmeineke
+
+	* libmdtools/: AbstractClasses.hpp, Integrator.hpp: changed how NVT
+	is now derived from Integrator
+
+2003-05-20 11:44  mmeineke
+
+	* libmdtools/GhostBend.cpp: fixed an a mismatched Ghostbend bug.
+
+2003-05-17 11:57  mmeineke
+
+	* utils/: Makefile, MoLocator.cpp, bilayerSys.cpp: all seems to be
+	working
+
+2003-05-16 16:37  mmeineke
+
+	* utils/bilayerSys.cpp: still working on the bilayer code
+
+2003-05-16 09:28  mmeineke
+
+	* utils/: bilayerSys.cpp, sysBuild.cpp, sysBuild.hpp: doing some
+	work to overhaul sysbuild.
+
+2003-05-13 16:23  mmeineke
+
+	* libmdtools/calc_sticky_pair.F90: optimized the ssd calc loop
+
+2003-05-13 15:47  mmeineke
+
+	* samples/: Makefile, beadLipid/Makefile, beadLipid/beadLipid.mdl,
+	beadLipid/water.mdl: Added bead lipid model to the sample directory
+
+2003-05-13 15:34  mmeineke
+
+	* forceFields/TraPPE_Ex.frc: finished adding the Tail beads into
+	the Trappe extended force field
+
+2003-05-13 12:01  mmeineke
+
+	* forceFields/TraPPE_Ex.frc: added the TailBead atom types to the
+	TraPPe_Ex forceField
+
+2003-05-09 14:51  mmeineke
+
+	* samples/lipid/lipid.mdl: fixed up the TraPPE_Ex force field.
+	there were some duplicate entries
+	
+	added a two chain lipid to the lipid.mdl in sample
+
+2003-05-09 14:51  mmeineke
+
+	* forceFields/TraPPE_Ex.frc: fixed up the TraPPE_Ex force field.
+	there were some duplicate entries
+
+2003-05-09 11:56  mmeineke
+
+	* forceFields/TraPPE_Ex.frc: added the utils subdirectory to the
+	configure script
+	
+	added the CH branching group to the TraPPE_Ex fource field
+
+2003-05-09 11:55  mmeineke
+
+	* ac-tools/configure.in: added the utils subdirectory to the
+	configure script
+
+2003-04-25 11:02  mmeineke
+
+	* utils/bilayerSys.cpp: i quick fix to th distance in the random
+	bilayer builder
+
+2003-04-24 21:00  mmeineke
+
+	* libmdtools/f_verlet_constrained.F90: added a new test for
+	constraint failure
+
+2003-04-17 16:54  mmeineke
+
+	* libBASS/BASS_interface.h, libmdtools/SimSetup.cpp,
+	utils/Makefile, utils/MoLocator.cpp, utils/MoLocator.hpp,
+	utils/bilayerSys.cpp: fixed up sysBuild to where it should now
+	build our systems
+
+2003-04-16 16:11  mmeineke
+
+	* utils/: MoLocator.cpp, MoLocator.hpp: almost finished.
+
+2003-04-15 16:47  mmeineke
+
+	* utils/: bilayerSys.cpp, sysBuild.cpp, sysBuild.hpp: bilayerSys
+	and sysBuild both will build now. woot!
+
+2003-04-15 16:20  mmeineke
+
+	* utils/: MoLocator.cpp, MoLocator.hpp, bilayerSys.cpp,
+	bilayerSys.hpp, sysBuild.cpp, sysBuild.hpp: finished bilayerSys.cpp
+	
+	sysBuild still need to write the bass file.
+	
+	MoLocator.cpp is currently empty
+
+2003-04-15 15:40  chuckv
+
+	* forceFields/EAM_FF.frc, forceFields/agu3.eam,
+	forceFields/auu3.eam, forceFields/cuu3.eam, forceFields/niu3.eam,
+	forceFields/pdu3.eam, forceFields/ptu3.eam,
+	libmdtools/ForceFields.hpp: Added eam force files...
+
+2003-04-15 11:37  chuckv
+
+	* libmdtools/EAM_FF.cpp: More eam work.
+
+2003-04-14 16:22  mmeineke
+
+	* libmdtools/SimSetup.hpp, utils/Makefile, utils/bilayerSys.cpp,
+	utils/bilayerSys.hpp, utils/sysBuild.cpp, utils/sysBuild.hpp:
+	working on the system builder
+
+2003-04-14 16:16  chuckv
+
+	* libmdtools/: Symplectic.cpp, Verlet.cpp, calc_eam.F90: Fixed
+	ordering on NVT calculation in integrators.
+
+2003-04-14 14:51  mmeineke
+
+	* utils/: Makefile, sysBuild.cpp, MPIobj/placeHolder,
+	obj/placeHolder:  working on a system builder
+
+2003-04-14 14:04  mmeineke
+
+	* utils/Makefile: added Ghost bends to the TraPPE_Ex forceField
+	
+	added sysBuild to the utils Makefile
+
+2003-04-14 14:03  mmeineke
+
+	* forceFields/TraPPE_Ex.frc, libmdtools/TraPPE_ExFF.cpp: added
+	Ghost bends to the TraPPE_Ex forceField
+
+2003-04-14 13:19  chuckv
+
+	* libmdtools/calc_eam.F90: Added first mangling of EAM.
+
+2003-04-11 13:46  mmeineke
+
+	* libmdtools/: SimSetup.cpp, calc_LJ_FF.F90, force_globals.F90,
+	simulation_module.F90: fixed a memory bug in Fortran, where
+	molMembershipArray was declared nLocal instead of nGlobal.
+
+2003-04-11 10:16  gezelter
+
+	* libmdtools/: Molecule.cpp, Molecule.hpp, SimInfo.cpp,
+	SimSetup.cpp, calc_LJ_FF.F90, do_Forces.F90,
+	fortranWrapDefines.hpp, simulation_module.F90: Bug fix in progress
+	for NPT
+
+2003-04-10 15:08  mmeineke
+
+	* libmdtools/: Molecule.cpp, Molecule.hpp, SimSetup.cpp:  added a
+	globalIndex counter to Molecule
+
+2003-04-10 11:35  gezelter
+
+	* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp: Working on
+	ConstantStress
+
+2003-04-10 11:27  mmeineke
+
+	* libmdtools/SimSetup.cpp: fixed a n mpi init bug in SimSetup.
+	caused a miscalculation of nLocal.
+
+2003-04-10 11:21  mmeineke
+
+	* libmdtools/: Symplectic.cpp, Thermo.cpp, calc_dipole_dipole.F90,
+	do_Forces.F90: fixed a bug in symplectic, where presure was only
+	being calculated the first time through.
+
+2003-04-09 11:20  chuckv
+
+	* samples/alkane/alkanes.mdl: added pentane to the alkane model
+	file
+
+2003-04-09 08:59  gezelter
+
+	* libmdtools/: ExtendedSystem.cpp, ForceFields.cpp, StatWriter.cpp,
+	Thermo.cpp, Thermo.hpp: Added volume and enthalpy to status file
+
+2003-04-08 23:06  gezelter
+
+	* libmdtools/: DumpWriter.cpp, ExtendedSystem.cpp,
+	ExtendedSystem.hpp, Molecule.cpp, Molecule.hpp, SimInfo.cpp,
+	SimInfo.hpp, SimSetup.cpp, Symplectic.cpp, Thermo.cpp, Thermo.hpp,
+	Verlet.cpp, calc_LJ_FF.F90, calc_dipole_dipole.F90, calc_gb.F90,
+	calc_reaction_field.F90, calc_sticky_pair.F90,
+	fortranWrapDefines.hpp, simulation_module.F90: fixes for NPT and
+	NVT
+
+2003-04-08 17:38  chuckv
+
+	* libmdtools/SimInfo.cpp, libmdtools/Symplectic.cpp,
+	libmdtools/calc_LJ_FF.F90, libmdtools/calc_dipole_dipole.F90,
+	libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90,
+	libmdtools/simulation_module.F90, samples/water/ssd.bass: It works
+	(kinda)...
+
+2003-04-08 16:35  gezelter
+
+	* libBASS/Globals.cpp, libBASS/Globals.hpp,
+	libmdtools/ExtendedSystem.cpp, libmdtools/ExtendedSystem.hpp,
+	libmdtools/SimSetup.cpp: Fixes for NPT / NVT
+
+2003-04-08 12:16  chuckv
+
+	* libmdtools/: do_Forces.F90, neighborLists.F90,
+	simulation_module.F90: Moved expand neighborlist to init_FF.
+
+2003-04-08 10:20  chuckv
+
+	* libmdtools/: ForceFields.cpp, Thermo.cpp, Verlet.cpp: fixes for
+	NVT
+
+2003-04-08 09:39  gezelter
+
+	* libmdtools/Verlet.cpp: fixes for nvt / npt
+
+2003-04-08 09:34  gezelter
+
+	* libmdtools/: ExtendedSystem.cpp, StatWriter.cpp, Symplectic.cpp,
+	Thermo.cpp, Verlet.cpp: dt/2 fix in nvt
+
+2003-04-08 07:50  gezelter
+
+	* libmdtools/ExtendedSystem.cpp: Fixes for affine transform
+
+2003-04-08 07:44  gezelter
+
+	* libmdtools/: ExtendedSystem.cpp, Molecule.cpp, Molecule.hpp,
+	Symplectic.cpp, Thermo.cpp, Verlet.cpp: Changes to integrate the
+	NVT and NPT ensembles
+
+2003-04-07 16:42  gezelter
+
+	* libBASS/Globals.cpp, libBASS/Globals.hpp,
+	libmdtools/ExtendedSystem.cpp, libmdtools/SimInfo.cpp,
+	libmdtools/SimSetup.cpp: Fixes for NPT and NVT
+
+2003-04-07 16:20  mmeineke
+
+	* libmdtools/calc_sticky_pair.F90: fixed a sign error in the radial
+	portion of SSD.
+
+2003-04-07 16:16  mmeineke
+
+	* libmdtools/: ForceFields.cpp, Symplectic.cpp: 
+	doing some testing in sticky through Symplectic.
+
+2003-04-07 15:51  gezelter
+
+	* libmdtools/: ExtendedSystem.cpp, Verlet.cpp: Working on NVT
+
+2003-04-07 15:50  chuckv
+
+	* libmdtools/do_Forces.F90: Fixed transpose bug in mpi reduce for
+	tau and virial.
+
+2003-04-07 15:06  mmeineke
+
+	* libmdtools/DumpWriter.cpp, libmdtools/SimInfo.cpp,
+	libmdtools/SimSetup.cpp, libmdtools/Symplectic.cpp,
+	libmdtools/calc_dipole_dipole.F90, libmdtools/calc_sticky_pair.F90,
+	src/Makefile: bug fixes
+
+2003-04-07 11:56  gezelter
+
+	* libmdtools/: ExtendedSystem.cpp, Molecule.cpp, Molecule.hpp,
+	StatWriter.cpp, Symplectic.cpp, Thermo.cpp, Thermo.hpp, Verlet.cpp:
+	Many fixes to add extended system
+
+2003-04-07 09:30  gezelter
+
+	* src/Makefile: Fixed a bug caused by my experimentation
+
+2003-04-07 09:30  gezelter
+
+	* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp,
+	Integrator.hpp, Makefile, SimSetup.cpp, Symplectic.cpp, Verlet.cpp:
+	Added ExtendedSystem infrastructure for NPT and NVT calculations
+
+2003-04-07 09:30  gezelter
+
+	* libBASS/: Globals.cpp, Globals.hpp: Added targetPressure to BASS
+
+2003-04-04 23:07  gezelter
+
+	* src/Makefile: final mods to try a fortran compiler
+
+2003-04-04 22:39  gezelter
+
+	* libmdtools/: LJ_FF.cpp, SimInfo.cpp, TraPPE_ExFF.cpp,
+	fortranWrapDefines.hpp: Bug fixes for simulation module rewrites
+
+2003-04-04 21:56  gezelter
+
+	* libmdtools/: Makefile, atype_module.F90, do_Forces.F90,
+	fortranWrappers.cpp, wrappers.F90: bug fixes for compilation
+
+2003-04-04 21:45  gezelter
+
+	* libmdtools/: fortranWrapDefines.hpp, fortranWrappers.hpp: bug
+	fixes to fortran wrappers
+
+2003-04-04 17:22  chuckv
+
+	* libmdtools/: Makefile, calc_LJ_FF.F90, calc_dipole_dipole.F90,
+	calc_gb.F90, calc_reaction_field.F90, calc_sticky_pair.F90,
+	do_Forces.F90, fortranWrapDefines.hpp, fortranWrappers.cpp,
+	simulation_module.F90, wrappers.F90: Breaking c and fortran, c gets
+	smarter, fortran gets dumber...
+
+2003-04-04 14:57  mmeineke
+
+	* libmdtools/: calc_dipole_dipole.F90, do_Forces.F90,
+	neighborLists.F90: fixed a memory read bug in neighborlist
+
+2003-04-04 14:47  gezelter
+
+	* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, SimInfo.cpp,
+	SimInfo.hpp, Thermo.cpp: Changes for Extended System
+
+2003-04-04 14:16  gezelter
+
+	* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, SimInfo.cpp,
+	SimInfo.hpp: Fixes for ExtendedSystem
+
+2003-04-03 20:57  gezelter
+
+	* libmdtools/ExtendedSystem.hpp: Added extended system header
+
+2003-04-03 20:57  gezelter
+
+	* libmdtools/: ExtendedSystem.cpp, Thermo.cpp, Thermo.hpp: changes
+	for extended system code
+
+2003-04-03 18:49  gezelter
+
+	* libmdtools/: ExtendedSystem.cpp, NVT.cpp: renamed nvt to
+	extendedsystem
+
+2003-04-03 17:19  mmeineke
+
+	* libmdtools/Molecule.hpp: added some little fixes here and there.
+
+2003-04-03 17:01  mmeineke
+
+	* libmdtools/TraPPE_ExFF.cpp: fixed a possible call before
+	initialize bug.
+
+2003-04-03 16:12  mmeineke
+
+	* libmdtools/: DumpWriter.cpp, Molecule.cpp, randomSPRNG.hpp: just
+	little things like deleteing unused variables and such.
+
+2003-04-03 15:57  mmeineke
+
+	* libmdtools/: Molecule.cpp, Molecule.hpp: a few fixes to
+	simError.h also some fixes to Molecule.hpp
+
+2003-04-03 15:57  mmeineke
+
+	* libBASS/simError.h: a few fixes to simError.h
+
+2003-04-03 15:21  mmeineke
+
+	* libBASS/Makefile, libBASS/mpiBASS.c, libBASS/simError.c,
+	libBASS/simError.h, libmdtools/DumpWriter.cpp,
+	libmdtools/ForceFields.cpp, libmdtools/InitializeFromFile.cpp,
+	libmdtools/LJ_FF.cpp, libmdtools/Makefile, libmdtools/Thermo.cpp,
+	libmdtools/TraPPE_ExFF.cpp, libmdtools/mpiSimulation.cpp,
+	src/Makefile, src/oopse.cpp: fixed some small things with
+	simError.h
+
+2003-04-03 15:19  gezelter
+
+	* libmdtools/: Molecule.cpp, Molecule.hpp: Starting work on NPT
+
+2003-04-03 14:58  gezelter
+
+	* libmdtools/: NVT.cpp, Thermo.cpp: Added NVT file (very broken for
+	now)
+
+2003-04-03 08:42  gezelter
+
+	* README, libmdtools/Thermo.cpp, utils/Makefile, utils/quickLate.c:
+	Changed Readme, added some files
+
+2003-04-02 17:19  mmeineke
+
+	* libmdtools/: ForceFields.cpp, SimInfo.cpp, SimSetup.cpp,
+	Symplectic.cpp, calc_dipole_dipole.F90, calc_sticky_pair.F90:
+	dipoles mostly work, but there is a memory leak somewhere.
+
+2003-04-02 10:01  mmeineke
+
+	* libmdtools/TraPPE_ExFF.cpp: Fixed a bug where MPI was not getting
+	the proper atomIdents.
+
+2003-04-01 11:50  chuckv
+
+	* libmdtools/SimInfo.cpp, libmdtools/do_Forces.F90,
+	libmdtools/mpiSimulation.cpp, libmdtools/mpiSimulation_module.F90,
+	samples/argon/argon.bass: more bug fixes....
+
+2003-04-01 11:49  mmeineke
+
+	* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp: Fixed
+	DumpWriter to be more robust to errors. also added a little
+	namespace to InitFromFile to wrap it's helper functions in MPI
+
+2003-03-31 17:09  chuckv
+
+	* libmdtools/: SimInfo.cpp, do_Forces.F90: Fixed bug with pot_local
+	not zeroed.
+
+2003-03-31 16:50  chuckv
+
+	* libmdtools/BendExtensions.cpp, libmdtools/Exclude.cpp,
+	libmdtools/ForceFields.cpp, libmdtools/Molecule.cpp,
+	libmdtools/Molecule.hpp, libmdtools/SimInfo.cpp,
+	libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp,
+	libmdtools/TraPPE_ExFF.cpp, libmdtools/do_Forces.F90,
+	samples/alkane/butane.bass: Fixes in MPI force calc and in
+	Trappe_Ex parsing.
+
+2003-03-28 17:34  chuckv
+
+	* libmdtools/DumpWriter.cpp: bug fix in DumpWriter.cpp
+
+2003-03-28 16:45  chuckv
+
+	* libBASS/Makefile, libmdtools/DumpWriter.cpp,
+	libmdtools/InitializeFromFile.cpp: Bug fixes in read-write
+	routines.
+
+2003-03-28 14:33  mmeineke
+
+	* libmdtools/: Exclude.cpp, Exclude.hpp, Molecule.cpp,
+	Molecule.hpp, SRI.hpp, SimSetup.cpp, simulation_module.F90: fixed a
+	bug where the Excludes were not being created properly
+
+2003-03-28 14:30  chuckv
+
+	* libBASS/Makefile, libmdtools/DumpWriter.cpp,
+	libmdtools/LJ_FF.cpp, libmdtools/SimSetup.cpp,
+	libmdtools/TraPPE_ExFF.cpp, libmdtools/mpiSimulation.cpp: mpi fixes
+	and debugging mpi read write from file.
+
+2003-03-28 10:28  mmeineke
+
+	* libmdtools/: LJ_FF.cpp, TraPPE_ExFF.cpp: fixed long range
+	interactions in Trappe
+
+2003-03-27 18:33  chuckv
+
+	* libmdtools/: SimSetup.cpp, mpiSimulation.cpp,
+	mpiSimulation_module.F90: MPI buggy, fixed mpiRefresh issue.
+
+2003-03-27 17:16  mmeineke
+
+	* libmdtools/: Exclude.cpp, SimSetup.cpp: fixed a bug where
+	excludes were not being initialized
+
+2003-03-27 16:52  mmeineke
+
+	* src/Makefile: [no log message]
+
+2003-03-27 16:52  mmeineke
+
+	* libmdtools/SimSetup.cpp: Fixed a single processor segfault bug.
+
+2003-03-27 16:07  mmeineke
+
+	* libmdtools/: Exclude.cpp, ForceFields.cpp, LJ_FF.cpp,
+	Molecule.cpp, Symplectic.cpp, Thermo.cpp, TraPPE_ExFF.cpp,
+	Verlet.cpp: fixed the compile time bugs, Source builds and links
+
+2003-03-27 15:48  mmeineke
+
+	* libmdtools/: Molecule.cpp, SimInfo.hpp, SimSetup.cpp: fixed a few
+	more bugs.
+
+2003-03-27 15:40  mmeineke
+
+	* libmdtools/Molecule.cpp: added the Molecule.cpp file
+
+2003-03-27 15:39  mmeineke
+
+	* libmdtools/: Makefile, Molecule.hpp:	fixed the makefile
+
+2003-03-27 15:36  mmeineke
+
+	* libmdtools/: AbstractClasses.hpp, ForceFields.cpp,
+	ForceFields.hpp, LJ_FF.cpp, Makefile, Molecule.hpp, SimInfo.cpp,
+	SimSetup.cpp, SimSetup.hpp: fixing some compile time bugs
+
+2003-03-27 15:12  mmeineke
+
+	* libmdtools/: AbstractClasses.hpp, ForceFields.cpp,
+	Integrator.hpp, Molecule.hpp, Symplectic.cpp, Thermo.cpp,
+	Verlet.cpp: I have implemeted Molecules everywhere I could remember
+	to.  will now attempt to compile.
+
+2003-03-27 14:21  mmeineke
+
+	* libmdtools/: Molecule.hpp, SimInfo.hpp, SimSetup.cpp,
+	SimSetup.hpp, mpiSimulation.cpp, mpiSimulation.hpp: finished
+	updating SimSetup to initialize and use the new MPI division of
+	labour, and Molecule class
+
+2003-03-27 12:55  mmeineke
+
+	* libmdtools/TraPPE_ExFF.cpp: finished conversion of TraPPE_ExFF to
+	use Molecule
+
+2003-03-27 12:32  mmeineke
+
+	* libmdtools/: ForceFields.cpp, ForceFields.hpp, LJ_FF.cpp,
+	SimInfo.cpp, SimSetup.cpp, TraPPE_ExFF.cpp: LJ_FF has been
+	converted to the new Molecule model. TraPPE_Ex is currently being
+	updated.  SimSetups routines are writtten, but not yet called.
+
+2003-03-27 10:07  gezelter
+
+	* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp,
+	mpiSimulation.cpp, mpiSimulation.hpp: fixes for local->global atom
+	numbering in MPI
+
+2003-03-27 09:30  mmeineke
+
+	* libmdtools/mpiSimulation.cpp: little bug fixes here and there.
+
+2003-03-26 20:49  gezelter
+
+	* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp: Fixes to
+	fileio for MPI
+
+2003-03-26 18:14  gezelter
+
+	* libmdtools/: DumpWriter.cpp, Exclude.cpp, Molecule.hpp,
+	mpiSimulation.cpp, mpiSimulation.hpp, mpiSimulation_module.F90: bug
+	fixes	many bug fixes
+
+2003-03-26 17:24  gezelter
+
+	* libmdtools/DumpWriter.cpp: Making DumpWriter less dependent on
+	sequence of atoms on the other processors.  Node 0 now fires
+	potatoes at other processors to get them to send french fries back.
+
+2003-03-26 17:02  mmeineke
+
+	* libmdtools/: DirectionalAtom.cpp, SimSetup.cpp: the skeleton for
+	making the molecules is in place. ForceField needs to be updated
+	next.
+
+2003-03-26 16:54  mmeineke
+
+	* libmdtools/: Atom.cpp, Atom.hpp, Exclude.cpp: fixed a couple of
+	the "static" bugs in  Atom and Exclude
+
+2003-03-26 16:50  mmeineke
+
+	* libmdtools/: Exclude.cpp, Exclude.hpp, Molecule.hpp, SimInfo.hpp,
+	SimSetup.cpp: still working on the SimSetup routine. also fixed
+	some things in Exclude.hpp
+
+2003-03-26 16:24  gezelter
+
+	* libmdtools/Makefile: Added Atom.cpp and Exclude.cpp
+
+2003-03-26 16:23  gezelter
+
+	* libmdtools/: Atom.cpp, Exclude.cpp, Exclude.hpp: Fixes in Atom
+	and Exclude list
+
+2003-03-26 16:04  gezelter
+
+	* libmdtools/: Atom.cpp, Atom.hpp: Make Atom.cpp able to add and
+	delete ranges of atoms
+
+2003-03-26 15:45  mmeineke
+
+	* libmdtools/: Exclude.cpp, Exclude.hpp: added an Exclude class
+	with static arrays similar to the Atom class
+
+2003-03-26 15:22  mmeineke
+
+	* libmdtools/: Molecule.hpp, SimSetup.cpp, SimSetup.hpp: I'm
+	overhauling the molecule class to contain it's own bonds, bends,
+	and torsions.
+	
+	may god have mercy on my soul.
+
+2003-03-26 14:34  chuckv
+
+	* libmdtools/mpiSimulation.cpp: Finished globalIndex.
+
+2003-03-26 13:02  gezelter
+
+	* libmdtools/: mpiComponentPlan.h, mpiSimulation.cpp,
+	mpiSimulation.hpp: MPI stuff for passing out molecules
+
+2003-03-26 11:12  chuckv
+
+	* libmdtools/mpiSimulation.cpp: working on load balancing
+
+2003-03-26 10:37  chuckv
+
+	* libmdtools/Thermo.cpp, libmdtools/Thermo.hpp,
+	samples/argon/argon.bass: Fixes for Parallel thermalization
+
+2003-03-26 09:55  mmeineke
+
+	* libmdtools/: SimInfo.cpp, Thermo.cpp: fixed an mpi include bug in
+	THermo.cpp
+
+2003-03-25 17:54  chuckv
+
+	* libmdtools/: Thermo.cpp, Thermo.hpp: Fixed bugs with calculation
+	of potential energy and temperature.
+
+2003-03-25 09:29  mmeineke
+
+	* libBASS/obj/dummy, libmdtools/MPIobj/dummy, libmdtools/obj/dummy,
+	src/MPIobj/dummy, src/obj/dummy: [no log message]
+
+2003-03-25 09:29  mmeineke
+
+	* libBASS/MPIobj/dummy: added dummy files to keep the build
+	deirectories from being pruned.
+
+2003-03-24 20:07  gezelter
+
+	* samples/Makefile: moving tests to samples
+
+2003-03-24 20:06  gezelter
+
+	* samples/: alkane/Makefile, alkane/alkanes.mdl,
+	alkane/butane.bass, alkane/init_butane.eor, argon/Makefile,
+	argon/argon.bass, argon/init_argon.eor, argon/lj.mdl,
+	lipid/5x5.bass, lipid/Makefile, lipid/init_5x5.eor,
+	lipid/lipid.mdl, lipid/water.mdl, water/Makefile,
+	water/init_ssd.eor, water/ssd.bass, water/water.mdl: moved tests to
+	samples
+
+2003-03-24 19:51  gezelter
+
+	* ac-tools/configure.in: Tests are becoming samples
+
+2003-03-24 19:46  gezelter
+
+	* ac-tools/Make.conf.in: Added makefiles in tests directories
+
+2003-03-24 16:55  gezelter
+
+	* libBASS/Globals.cpp, libBASS/Globals.hpp, libmdtools/SimInfo.cpp,
+	libmdtools/SimInfo.hpp, libmdtools/SimSetup.cpp,
+	libmdtools/TraPPE_ExFF.cpp, libmdtools/calc_dipole_dipole.F90,
+	libmdtools/calc_reaction_field.F90,
+	libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90,
+	libmdtools/simulation_module.F90: electrostatic changes for dipole
+	/ RF separation
+
+2003-03-24 13:33  mmeineke
+
+	* libmdtools/: Atom.hpp, ForceFields.cpp, SimInfo.cpp,
+	do_Forces.F90: little bug fixes here and there
+
+2003-03-24 10:26  mmeineke
+
+	* libmdtools/: ForceFields.cpp, f_verlet_constrained.F90: fixed bug
+	where short range interactions were not being calculated.
+	
+	removed some debug print statements
+
+2003-03-21 17:11  chuckv
+
+	* libmdtools/: TraPPE_ExFF.cpp, calc_dipole_dipole.F90,
+	do_Forces.F90, f_verlet_constrained.F90, simulation_module.F90:
+	various write statements for debugging
+
+2003-03-21 16:26  chuckv
+
+	* forceFields/Makefile: added links to the makefile in forceFields
+
+2003-03-21 15:52  gezelter
+
+	* ac-tools/Make.conf.in, ac-tools/configure.in,
+	libmdtools/Makefile: Fixed F_MACH_DEP bug
+
+2003-03-21 15:37  gezelter
+
+	* ChangeLog, Makefile, ac-tools/Make.conf.in, ac-tools/config.h.in,
+	ac-tools/configure.in, forceFields/Makefile, libBASS/Makefile,
+	libmdtools/Makefile, scripts/cvs2cl.pl, scripts/sfmakedepend,
+	src/Makefile, utils/sfmakedepend: Makefile fixes, directory re-org,
+	autoconf fixes
+
 2003-03-21 14:58  gezelter
 
 	* LICENSE: Added license file