--- trunk/OOPSE/ChangeLog	2003/08/28 21:09:47	736
+++ trunk/OOPSE/ChangeLog	2004/01/12 22:54:42	927
@@ -1,3 +1,873 @@
+2004-01-12 15:37  tim
+
+	* ChangeLog, libmdtools/DumpWriter.cpp, samples/argon/argon.bass,
+	samples/water/ssd.bass: Dumpwriter only write out the atoms on
+	master nodes
+
+2004-01-10 04:46  tim
+
+	* ChangeLog, libmdtools/DumpWriter.cpp: tagub is not a bug. Just
+	roll it back fix a bug of copying string to a pointer Still have
+	Seg fault, it looks like a random MPI seg fault in totalview
+
+2004-01-09 21:15  tim
+
+	* libmdtools/DumpWriter.cpp: Fix a bug of declaration of tagub
+
+2004-01-09 15:29  gezelter
+
+	* libmdtools/DumpWriter.cpp: New DumpWriter (Attempt #4)
+
+2004-01-08 17:25  chuckv
+
+	* libmdtools/DumpWriter.cpp: A work in progress...
+
+2004-01-08 13:59  gezelter
+
+	* libmdtools/DumpWriter.cpp: null terminate some strings just in
+	case
+
+2004-01-08 13:13  mmeineke
+
+	* libmdtools/InitializeFromFile.cpp: refixed the NVT readin XS
+	state bug.
+
+2004-01-08 13:05  gezelter
+
+	* libmdtools/DumpWriter.cpp: added strncpy to DumpWriter
+
+2004-01-08 12:57  mmeineke
+
+	* libmdtools/InitializeFromFile.cpp: fixed the restart from NVT
+	exstended state bug
+
+2004-01-08 12:40  gezelter
+
+	* libmdtools/DumpWriter.cpp: First Stab at fixing DumpWriter
+
+2004-01-08 10:44  mmeineke
+
+	* libmdtools/InitializeFromFile.cpp: added support for the ignore
+	XS state info  flag
+
+2004-01-07 14:26  tim
+
+	* libmdtools/DumpWriter.cpp, libmdtools/InitializeFromFile.cpp,
+	samples/argon/argon.bass, samples/water/ssd.bass: Fixed a bug of
+	sending message from master node to itself in DumpWriter.cpp and
+	InitializeFromFile.cpp
+
+2004-01-06 14:49  chuckv
+
+	* libmdtools/: calc_dipole_dipole.F90, calc_reaction_field.F90:
+	performance fixes in the dipole dipole and reaction field code
+
+2004-01-06 13:54  chuckv
+
+	* libmdtools/: calc_LJ_FF.F90, do_Forces.F90: Making do_Forces a
+	little more sane
+
+2004-01-05 17:49  chuckv
+
+	* libmdtools/: calc_LJ_FF.F90, calc_dipole_dipole.F90,
+	calc_eam.F90, calc_gb.F90, calc_reaction_field.F90,
+	calc_sticky_pair.F90, do_Forces.F90: Attempting to increase
+	performance by reducing spurious function calls
+
+2004-01-05 17:18  chuckv
+
+	* libmdtools/do_Forces.F90: mangling forces even further
+
+2004-01-05 17:18  chuckv
+
+	* configure, ac-tools/configure.in: mpich mucking
+
+2004-01-05 17:12  chuckv
+
+	* libmdtools/do_Forces.F90: mangled do_forces...
+
+2004-01-05 16:00  chuckv
+
+	* ChangeLog, ac-tools/configure.in, libmdtools/atype_module.F90,
+	libmdtools/do_Forces.F90: Added bitmask to do_forces property
+	lookup
+
+2003-12-29 14:56  chuckv
+
+	* samples/metals/Au.bass, third-party/mt19937ar.c: Added
+	third-party directory for code not written by us. Also added
+	Mersenne Twister random number generator code. This will eventually
+	replace sprng as the random number generator used by OOPSE.
+
+2003-12-22 16:26  chuckv
+
+	* libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp,
+	libmdtools/mdProfile.cpp, libmdtools/timing.F90, src/oopse.cpp:
+	Fixes to profile code.
+
+2003-12-19 15:36  mmeineke
+
+	* libmdtools/: Makefile.in, do_Forces.F90, mdProfile.cpp,
+	timing.F90, timing.f90: More profiling fixes.
+
+2003-12-19 15:19  chuckv
+
+	* libmdtools/timing.f90: Another change for MPI in timing.
+
+2003-12-19 15:17  chuckv
+
+	* libmdtools/timing.f90: Small update to timing in MPI
+
+2003-12-19 13:53  mmeineke
+
+	* libmdtools/mdProfile.cpp, src/oopse.cpp, src/oose.cpp: the
+	profiling commands work now. Will start adding PROFILE ifdefs into
+	the code
+
+2003-12-19 12:25  mmeineke
+
+	* libmdtools/: Makefile.in, do_Forces.F90, mdProfile.cpp: added
+	some profiling routines
+
+2003-12-19 10:12  mmeineke
+
+	* utils/sysbuilder/randomBilayer.cpp: working on adding GofRtheta
+	and GofRomega
+	
+	additional work on randomBilayer
+
+2003-12-19 10:12  mmeineke
+
+	* staticProps/: AllCorr.cpp, GofRomega.cpp, GofRtheta.cpp,
+	PairCorrList.hpp, staticProps.cpp: working on adding GofRtheta and
+	GofRomega
+
+2003-12-18 16:47  mmeineke
+
+	* libmdtools/: Makefile.in, mdProfile.cpp, mdProfile.hpp: added
+	some profile functionality
+
+2003-12-18 15:46  chuckv
+
+	* libmdtools/: do_Forces.F90, mpiSimulation_module.F90, timing.f90:
+	Added functions for simple profiling in fortran.
+
+2003-12-17 15:13  chuckv
+
+	* libmdtools/calc_eam.F90, libmdtools/mpiSimulation_module.F90,
+	samples/metals/init_au.in: Fixed bug in parallel EAM. rho_row and
+	rho_col were scattered into the same array. Unfortunately, MPI
+	zeros the array between scatters so half of the sum was being lost.
+	Fixed by added a temp array for column scatter, then sum loop over
+	nlocal.
+
+2003-12-16 15:49  mmeineke
+
+	* staticProps/: GofRomega.cpp, GofRtheta.cpp, Makefile.in,
+	PairCorrType.cpp, PairCorrType.hpp: finished gofRtheta and added
+	gofRomega. both need to be debugged and tested.
+
+2003-12-12 10:42  gezelter
+
+	* configure, ac-tools/aclocal.m4, ac-tools/configure.in,
+	libmdtools/Atom.hpp, libmdtools/DirectionalAtom.cpp: Changes for
+	gradients (to do minimizations)
+
+2003-12-12 10:33  mmeineke
+
+	* utils/sysbuilder/randomBilayer.hpp:  removed the randombilayer
+	header
+
+2003-12-10 11:52  mmeineke
+
+	* utils/sysbuilder/: Makefile.in, bilayerSys.cpp, bilayerSys.hpp,
+	randomBilayer.cpp, randomBilayer.hpp: edited the makefile to add
+	randomBilayer to the build. Also move the random bilayer builder
+	from bilayerSys to randomBilayer
+
+2003-11-25 10:44  mmeineke
+
+	* forceFields/: DUFF.frc, backup.DUFF.frc: backed up the old
+	DUFF.frc to backup.DUFF.frc alte4red masses and epsilons of TB2 and
+	TB3 in DUFF.frc
+
+2003-11-21 15:09  mmeineke
+
+	* libmdtools/InitializeFromFile.cpp, libmdtools/SimInfo.cpp,
+	utils/sysbuilder/latticeBilayer.cpp: added a more verbose error
+	message in SimInfo. Added a more informative error message in
+	InitializeFromFile
+
+2003-11-21 15:07  mmeineke
+
+	* staticProps/: GofRtheta.cpp, PairCorrType.hpp: begun work on add
+	ing in the GofR,CosTheta
+
+2003-11-21 14:31  chrisfen
+
+	* libmdtools/: SimInfo.cpp, do_Forces.F90, neighborLists.F90: Fixed
+	a bug in SimInfo ordering of radii
+
+2003-11-11 12:20  mmeineke
+
+	* libmdtools/SimInfo.cpp: added a routine to SimInfo.cpp to inline
+	a min function.
+
+2003-11-10 16:50  mmeineke
+
+	* libmdtools/: EAM_FF.cpp, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp:
+	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.
+
+2003-11-07 16:46  chuckv
+
+	* libmdtools/: Makefile.in, mpiSimulation_module.F90,
+	oopseMPI_module.F90: Added support for compiling fortran without
+	use of mpich modules. We use mpif.h instead.:
+
+2003-11-07 12:09  mmeineke
+
+	* libmdtools/: Integrator.hpp, NPT.cpp, NPTf.cpp, NPTi.cpp,
+	NPTxyz.cpp: moved the velocity scale matrix calculation outside of
+	the atom loop in the NPT family of integrators.
+
+2003-11-06 17:01  mmeineke
+
+	* libBASS/Globals.cpp, libBASS/Globals.hpp, libmdtools/Make.dep,
+	libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp,
+	libmdtools/NVT.cpp, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp,
+	libmdtools/SimSetup.cpp, utils/sysbuilder/Make.dep,
+	utils/sysbuilder/latticeBilayer.cpp: added the following parameters
+	to BASS:    * useInitialExtendedSystemState    * orthoBoxTolerance 
+	  * useIntiTime => useInitialTime
+
+2003-11-06 14:24  mmeineke
+
+	* libBASS/: BASS_parse.c, BASSlex.l, BASSyacc.y, interface.c,
+	make_nodes.c, make_nodes.h, parse_interface.h, parse_tree.c,
+	parse_tree.h: fixed the includes in the Make.dep
+
+2003-11-06 14:11  mmeineke
+
+	* libmdtools/: Makefile.in, NPTf.cpp, NPTi.cpp, NPTxyz.cpp,
+	NVT.cpp, SimInfo.cpp, Thermo.cpp: 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
+
+2003-11-06 13:20  mmeineke
+
+	* libmdtools/: Integrator.cpp, Makefile.in, NPT.cpp, NPTf.cpp,
+	SimInfo.cpp, Thermo.cpp, do_Forces.F90: fixed the "Sudden Death"
+	bug.	The box was not switching between orthorhombic and
+	non-orthorhombic wrapping correctly.	     we added a fabs() to
+	the check.which should fix it.
+
+2003-11-05 14:16  mmeineke
+
+	* libmdtools/AbstractClasses.hpp, libmdtools/DumpReader.cpp,
+	libmdtools/GenericData.cpp, libmdtools/GenericData.hpp,
+	libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp,
+	libmdtools/Integrator.hpp, libmdtools/Make.dep, libmdtools/NPT.cpp,
+	libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp,
+	libmdtools/NVT.cpp, libmdtools/SimInfo.hpp,
+	libmdtools/SimSetup.cpp, samples/water/ssd.bass, src/Make.dep,
+	utils/sysbuilder/Make.dep, utils/sysbuilder/latticeBilayer.cpp:
+	some work on trying to find the compression bug
+
+2003-11-03 17:07  mmeineke
+
+	* libmdtools/: DumpReader.cpp, GenericData.cpp, GenericData.hpp,
+	InitializeFromFile.cpp, Integrator.hpp, Make.dep, NPT.cpp,
+	NPTf.cpp, NPTi.cpp, NPTxyz.cpp, NVT.cpp, SimInfo.cpp, SimInfo.hpp,
+	SimSetup.cpp, SimSetup.hpp: begun work on removing templates and
+	most of standard template library from OOPSE.
+
+2003-10-31 16:06  mmeineke
+
+	* libmdtools/: AllIntegrator.hpp, Integrator.cpp, Integrator.hpp,
+	Makefile.in, NPT.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, NVT.cpp,
+	SimSetup.cpp: started work on template removal.
+
+2003-10-31 13:28  mmeineke
+
+	* libmdtools/: DumpReader.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp:
+	added template stuff to the Maikefile template
+	
+	little changes to some printf format statements
+
+2003-10-31 13:28  mmeineke
+
+	* libBASS/Makefile.in: added template stuff to the Maikefile
+	template
+
+2003-10-30 13:59  gezelter
+
+	* libmdtools/: SimInfo.cpp, SimInfo.hpp, SimSetup.cpp,
+	do_Forces.F90, neighborLists.F90, notifyCutoffs.F90: bug fixes for
+	rList problems
+
+2003-10-30 09:11  gezelter
+
+	* libmdtools/neighborLists.F90: Fixed bug that size(q0) was being
+	queried before q0 was allocated.
+
+2003-10-29 15:41  mmeineke
+
+	* libmdtools/: ForceFields.cpp, Integrator.cpp, Integrator.hpp,
+	SimInfo.cpp, SimSetup.cpp, calc_dipole_dipole.F90,
+	calc_sticky_pair.F90, do_Forces.F90: 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
+
+2003-10-29 15:40  mmeineke
+
+	* libBASS/BASSlex.l: fixed a stdlib.h include error
+
+2003-10-29 12:55  mmeineke
+
+	* libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp,
+	SimInfo.hpp, SimSetup.cpp, do_Forces.F90: som efixes to the way
+	rcut is setup, as well as additional debugging comments.
+
+2003-10-29 09:28  gezelter
+
+	* configure, ac-tools/configure.in, libBASS/Makefile.in,
+	libmdtools/Makefile.in, src/Makefile.in: C++ compatibility for
+	templates
+
+2003-10-28 22:16  gezelter
+
+	* src/Makefile.in: Refixed broken makefile
+
+2003-10-28 22:06  gezelter
+
+	* configure, ac-tools/aclocal.m4, src/Makefile.in: compatibility
+	fixes
+
+2003-10-28 19:19  tim
+
+	* ChangeLog, libmdtools/AbstractClasses.hpp,
+	libmdtools/DumpWriter.cpp, libmdtools/GenericData.hpp,
+	libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp,
+	libmdtools/Integrator.hpp, libmdtools/NPT.cpp, libmdtools/NPTf.cpp,
+	libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, libmdtools/NVT.cpp,
+	libmdtools/ReadWrite.hpp, samples/argon/argon.bass,
+	samples/water/ssd.bass: add chi and eta to the comment line of dump
+	file.
+
+2003-10-28 17:25  mmeineke
+
+	* libmdtools/: ForceFields.hpp, SimInfo.hpp,
+	fortranWrapDefines.hpp, fortranWrappers.cpp, fortranWrappers.hpp,
+	mpiComponentPlan.h, mpiSimulation.hpp: did a complete overhaul of
+	how c calls fortran. All function pointers and fortran calls are
+	rigidly typecast now.
+
+2003-10-28 15:42  gezelter
+
+	* staticProps/Makefile.in, utils/sysbuilder/Makefile.in:
+	Portability fixes
+
+2003-10-28 15:09  gezelter
+
+	* libmdtools/calc_LJ_FF.F90, libmdtools/do_Forces.F90,
+	libmdtools/fForceField.h, libmdtools/mpiSimulation_module.F90,
+	src/Makefile.in: Compatibility fixes
+
+2003-10-28 12:08  mmeineke
+
+	* libmdtools/: AbstractClasses.hpp, Integrator.hpp, Makefile.in:
+	started work on template removal
+
+2003-10-28 12:04  gezelter
+
+	* libmdtools/: fortranWrappers.cpp, fortranWrappers.hpp: started
+	trying to understand extern "C" stuff for pointers
+
+2003-10-28 11:20  gezelter
+
+	* libmdtools/: InitializeFromFile.cpp, ReadWrite.hpp,
+	ZConsWriter.cpp, ZConstraint.cpp: fixes for compatibility
+
+2003-10-28 11:03  gezelter
+
+	* libmdtools/: Atom.hpp, BendExtensions.cpp, DUFF.cpp,
+	DipoleTestFF.cpp, DirectionalAtom.cpp, DumpReader.cpp,
+	DumpWriter.cpp, EAM_FF.cpp, Exclude.cpp, ForceFields.cpp,
+	ForceFields.hpp, InitializeFromFile.cpp, Integrator.cpp, LJFF.cpp,
+	Makefile.in, Molecule.cpp, NPT.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp,
+	ReadWrite.hpp, SimInfo.cpp, SimSetup.cpp, SimState.cpp,
+	StatWriter.cpp, Thermo.cpp, TraPPE_ExFF.cpp, ZConstraint.cpp,
+	calc_LJ_FF.F90, do_Forces.F90, fortranWrappers.cpp,
+	mpiSimulation.cpp, randomSPRNG.cpp: 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.
+
+2003-10-28 11:03  gezelter
+
+	* libBASS/: AtomStamp.cpp, BASS_interface.cpp, Component.cpp,
+	Globals.cpp, Globals.hpp, LinkedCommand.hpp, MakeStamps.hpp,
+	Makefile.in, MoleculeStamp.cpp: replace c++ header stuff with more
+	portable c header stuff Also, mod file fixes and portability
+	changes
+
+2003-10-28 11:02  gezelter
+
+	* configure, ac-tools/aclocal.m4: mod file fixes and portability
+	stuff
+
+2003-10-27 18:00  gezelter
+
+	* Makefile.in, configure, ac-tools/aclocal.m4,
+	ac-tools/configure.in, ac-tools/fortran90.m4,
+	libmdtools/Makefile.in: Stuff for MOD support in other compilers
+
+2003-10-27 17:08  mmeineke
+
+	* utils/sysbuilder/: Make.dep, Makefile.in, MoLocator.cpp,
+	MoLocator.hpp, QuickBass.cpp, QuickBass.hpp, latticeBilayer.cpp:
+	added routines for the sysbuilder to work with simSetup
+	
+	remved the QuickBass routines, and had all parsing go through
+	SimSetup.  LatticeBilayer is in complete working order now.
+
+2003-10-27 17:07  mmeineke
+
+	* libmdtools/: SimInfo.hpp, SimSetup.cpp, SimSetup.hpp: added
+	routines for the sysbuilder to work with simSetup
+
+2003-10-27 11:20  gezelter
+
+	* configure, ac-tools/configure.in, samples/water/ssd.bass,
+	utils/sysbuilder/sysBuild.cpp: fixes for configure, sysBuild
+
+2003-10-24 17:17  mmeineke
+
+	* utils/sysbuilder/: Make.dep, Makefile.in, MoLocator.cpp,
+	MoLocator.hpp, QuickBass.cpp, QuickBass.hpp, bilayerSys.cpp,
+	latticeBilayer.cpp, latticeBuilder.cpp, sysBuild.cpp: put
+	QuickBass, MoLocator, and latticeBuilder into a Builder Library
+	overhauled latticeBilayer into its own program. Removed sysBuild
+	from the Makefile
+
+2003-10-24 12:36  gezelter
+
+	* utils/sysbuilder/: bilayerSys.cpp, latticeBuilder.cpp,
+	latticeBuilder.hpp, sysBuild.cpp, sysBuild.hpp: work on bilayer
+	builder
+
+2003-10-24 12:35  gezelter
+
+	* configure, ac-tools/aclocal.m4, ac-tools/configure.in: fixed a
+	merge problem
+
+2003-10-23 14:57  mmeineke
+
+	* samples/metals/Makefile.in: added eam ForceField files to the
+	init
+	
+	fixed an eam mpi parmeter setup bug
+	
+	added the init file to the makefile
+
+2003-10-23 14:57  mmeineke
+
+	* libmdtools/: EAM_FF.cpp, SimSetup.cpp: added eam ForceField files
+	to the init
+	
+	fixed an eam mpi parmeter setup bug
+
+2003-10-23 14:57  mmeineke
+
+	* forceFields/Makefile.in: added eam ForceField files to the init
+
+2003-10-22 16:17  mmeineke
+
+	* libmdtools/: AllIntegrator.hpp, Integrator.hpp, Makefile.in,
+	NPTxym.cpp, NPTxyz.cpp, NPTzm.cpp, SimSetup.cpp: added a new NPT
+	integrator, NPTxyz. It scales the x, y, and z direction sepeartely.
+	no box skew allowed.
+
+2003-10-21 14:33  mmeineke
+
+	* libBASS/Globals.cpp, libBASS/Globals.hpp,
+	libmdtools/SimSetup.cpp, staticProps/GofRtheta.cpp,
+	staticProps/PairCorrType.hpp: added useInitTime to the BASS syntax.
+	    * useInitTime = false: sets the origin time to 0.0 regardless
+	of the time stamp in the .init file	* default=> useInitTime =
+	true;
+
+2003-10-17 16:19  mmeineke
+
+	* staticProps/: AllCorr.cpp, AllCorr.hpp, CorrWrap.cpp, GofR.cpp,
+	Makefile.in, PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp,
+	staticProps.cpp, obj/placeholder: added the staticProps directory
+	to the build list for both configure  and configure.in
+	
+	fixed a number of bugs in the staticProps code. gofr is now
+	working.
+
+2003-10-17 16:18  mmeineke
+
+	* ac-tools/configure.in: added the staticProps directory to the
+	build list for both configure  and configure.in
+
+2003-10-17 16:17  mmeineke
+
+	* configure: added the staticProps directory to the build list
+
+2003-10-16 14:16  mmeineke
+
+	* libmdtools/: DumpReader.cpp, DumpWriter.cpp, Exclude.cpp,
+	Integrator.cpp, Makefile.in, ReadWrite.hpp: 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.
+
+2003-10-10 12:10  mmeineke
+
+	* props/AllCorr.cpp, props/AllCorr.hpp, props/CorrWrap.cpp,
+	props/CorrWrap.hpp, props/GofR.cpp, props/PairCorrList.cpp,
+	props/PairCorrList.hpp, props/PairCorrType.cpp,
+	props/PairCorrType.hpp, props/staticProps.cpp,
+	staticProps/AllCorr.cpp, staticProps/AllCorr.hpp,
+	staticProps/CorrWrap.cpp, staticProps/CorrWrap.hpp,
+	staticProps/GofR.cpp, staticProps/Makefile.in,
+	staticProps/PairCorrList.cpp, staticProps/PairCorrList.hpp,
+	staticProps/PairCorrType.cpp, staticProps/PairCorrType.hpp,
+	staticProps/staticProps.cpp: removed the props directory, and moved
+	everything over to staticProps
+
+2003-10-09 17:09  mmeineke
+
+	* libmdtools/Atom.hpp, props/AllCorr.cpp, props/AllCorr.hpp,
+	props/CorrWrap.cpp, props/CorrWrap.hpp, props/GofR.cpp,
+	props/PairCorrType.cpp, props/PairCorrType.hpp,
+	props/staticProps.cpp: Contiuned work on staticProps. should be in
+	a position where it will compile and run first runs.
+
+2003-10-04 13:46  chuckv
+
+	* libmdtools/calc_eam.F90, libmdtools/do_Forces.F90,
+	samples/metals/Au.bass: Fixed bug in calc_eam.
+
+2003-10-04 13:08  chuckv
+
+	* samples/metals/init_au.in: added Au init file for eam.
+
+2003-10-03 17:11  mmeineke
+
+	* libmdtools/: StatWriter.cpp, Thermo.cpp, Thermo.hpp: removed
+	entahlpy from the statwriter and thermo.
+
+2003-10-03 17:02  mmeineke
+
+	* props/: AllCorr.cpp, AllCorr.hpp, PairCorrList.cpp,
+	PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp,
+	staticProps.cpp: changed the formating ogf the error statements in
+	simError
+	
+	added a function to get the maxCutoff
+	
+	near completion of the staticProps code. still needs the pair loop,
+	and the loop to allocate and read each frame.
+
+2003-10-03 17:02  mmeineke
+
+	* libmdtools/SimInfo.hpp: changed the formating ogf the error
+	statements in simError
+	
+	added a function to get the maxCutoff
+
+2003-10-03 17:01  mmeineke
+
+	* libBASS/simError.c: changed the formating ogf the error
+	statements in simError
+
+2003-10-02 17:06  mmeineke
+
+	* props/: AllCorr.cpp, AllCorr.hpp, PairCorrList.cpp,
+	PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp,
+	staticProps.cpp: finishing up the constructs needed to get this
+	program up and running
+
+2003-09-30 11:00  mmeineke
+
+	* configure, ac-tools/aclocal.m4, ac-tools/configure.in: changed
+	f90Flags so they are no longer overwritten by the compiler.
+
+2003-09-29 17:06  mmeineke
+
+	* libmdtools/fortranWrappers.cpp: added mpif90 mod check back same
+	for conifig.in
+	
+	fixed wrappers to extern "C"
+
+2003-09-29 17:06  mmeineke
+
+	* ac-tools/configure.in: added mpif90 mod check back same for
+	conifig.in
+
+2003-09-29 17:05  mmeineke
+
+	* configure: added mpif90 mod check back
+
+2003-09-29 16:16  mmeineke
+
+	* configure, ac-tools/aclocal.m4, ac-tools/configure.in,
+	libBASS/BendStamp.cpp, libBASS/BondStamp.cpp,
+	libBASS/LinkedAssign.cpp, libBASS/LinkedCommand.cpp,
+	libBASS/MakeStamps.cpp, libBASS/TorsionStamp.cpp,
+	libBASS/ZconStamp.cpp, libBASS/simError.c,
+	libmdtools/Integrator.hpp, libmdtools/SimInfo.cpp,
+	libmdtools/SimInfo.hpp, libmdtools/calc_LJ_FF.F90,
+	libmdtools/fortranWrappers.cpp: fixed a lot of warnings and errors
+	found with SUN's SUNWspro.s1s7
+
+2003-09-29 12:38  mmeineke
+
+	* libmdtools/GenericData.hpp: light change in syntax. no
+	signifigant change.
+
+2003-09-25 16:17  mmeineke
+
+	* libmdtools/: DirectionalAtom.cpp, Integrator.hpp: fixed some
+	additional remarks from icc -w3 (extra verbose output)
+
+2003-09-25 14:27  mmeineke
+
+	* libBASS/parse_tree.c, libmdtools/Atom.cpp, libmdtools/DUFF.cpp,
+	libmdtools/DirectionalAtom.cpp, libmdtools/DumpWriter.cpp,
+	libmdtools/EAM_FF.cpp, libmdtools/ForceFields.cpp,
+	libmdtools/GenericData.cpp, libmdtools/InitializeFromFile.cpp,
+	libmdtools/Integrator.cpp, libmdtools/LJFF.cpp,
+	libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTzm.cpp,
+	libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp,
+	libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp,
+	libmdtools/ZConsWriter.cpp, libmdtools/ZConstraint.cpp,
+	libmdtools/mpiSimulation.cpp, src/oopse.cpp: cleaned things with
+	gcc -Wall and g++ -Wall
+
+2003-09-25 13:54  gezelter
+
+	* configure, ac-tools/configure.in: fixed a bug in configure
+
+2003-09-25 11:42  gezelter
+
+	* Makefile.in, configure, ac-tools/aclocal.m4,
+	ac-tools/configure.in, libBASS/Makefile.in, libmdtools/Makefile.in,
+	src/Makefile.in, utils/Makefile.in, utils/sysbuilder/Makefile.in:
+	fixes for configure
+
+2003-09-24 14:34  mmeineke
+
+	* libmdtools/Integrator.cpp: moved readyCheck in the integrator so
+	that it is called before the first Statistics are written.
+
+2003-09-23 15:36  gezelter
+
+	* src/Make.dep, utils/Make.dep, utils/sysbuilder/Make.dep: Added a
+	bunch of Make.dep files to CVS
+
+2003-09-23 15:34  mmeineke
+
+	* libmdtools/: Integrator.cpp, Integrator.hpp, NPTf.cpp,
+	SimSetup.cpp: Removed NPTfm from Integrator.hpp.
+	
+	Some small syntax cleaning in NPTfm and SimSetup
+
+2003-09-22 18:07  tim
+
+	* libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp,
+	SimInfo.hpp: fix bug in calculating maxCutoff
+
+2003-09-22 16:23  mmeineke
+
+	* libmdtools/: AllIntegrator.hpp, Integrator.hpp, Make.dep,
+	Makefile.in, NPT.cpp, NPTf.cpp, NPTfm.cpp, NPTim.cpp, SimSetup.cpp:
+	Converted NPTf to work with the NPT base class.
+	
+	Removed NPTfm and NPTim from cvs
+
+2003-09-19 15:00  mmeineke
+
+	* libmdtools/: AllIntegrator.hpp, Integrator.cpp, Integrator.hpp,
+	NPT.cpp, NPTf.cpp, NPTi.cpp, NVT.cpp, SimSetup.cpp: added NPT base
+	class. NPTi is up to date. NPTf is not.
+
+2003-09-19 11:03  mmeineke
+
+	* utils/Makefile.in, src/Makefile.in: removed mpi++ from the
+	makefile
+
+2003-09-19 11:01  gezelter
+
+	* samples/water/ssd.bass: goofing off to test NPTf and NPTi
+
+2003-09-19 11:01  gezelter
+
+	* libmdtools/: NPTf.cpp, NPTi.cpp: fixed bugs in NPTf, found
+	(nearly) conserved quantities for both NPTi and NPTf
+
+2003-09-19 10:20  mmeineke
+
+	* utils/Makefile.in: fixed a typo in the makefile.
+
+2003-09-19 09:55  gezelter
+
+	* libmdtools/NPTi.cpp, libmdtools/SimInfo.cpp,
+	samples/water/ssd.bass: [no log message]
+
+2003-09-19 09:22  tim
+
+	* libmdtools/: NPTi.cpp, NVT.cpp: [no log message]
+
+2003-09-17 09:22  mmeineke
+
+	* libmdtools/: Integrator.cpp, NPTi.cpp, NVT.cpp: fixed NPTi to now
+	work with constraints.
+
+2003-09-16 15:02  tim
+
+	* libmdtools/: Integrator.hpp, NPTf.cpp, NPTfm.cpp, NPTi.cpp,
+	SimInfo.cpp, SimInfo.hpp: fixed ecr grow in SimInfo
+	
+	fixed conserved quantity in NPT (Still some small bug)
+	
+	NPTi appears very stable.
+
+2003-09-15 11:52  tim
+
+	* libmdtools/AbstractClasses.hpp, libmdtools/Integrator.cpp,
+	libmdtools/Integrator.hpp, libmdtools/NPTf.cpp,
+	libmdtools/NPTfm.cpp, libmdtools/NPTi.cpp, libmdtools/NPTim.cpp,
+	libmdtools/NVT.cpp, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp,
+	libmdtools/StatWriter.cpp, libmdtools/Thermo.cpp,
+	libmdtools/Thermo.hpp, libmdtools/ZConstraint.cpp,
+	utils/sysbuilder/bilayerSys.cpp: add conserved quantity to
+	statWriter fix bug of vector wrapping at NPTi
+
+2003-09-12 15:51  mmeineke
+
+	* props/: AllCorr.cpp, AllCorr.hpp, GofR.cpp, PairCorrType.cpp,
+	PairCorrType.hpp: added AllCorr. It eill still need some work
+
+2003-09-12 11:20  gezelter
+
+	* libmdtools/: Make.dep, Makefile.in: Added integrators to
+	Makefile.in
+
+2003-09-12 11:20  gezelter
+
+	* ChangeLog: Entered changes for configure into ChangeLog
+
+2003-09-10 16:28  mmeineke
+
+	* props/: GofR.cpp, PairCorrType.cpp, PairCorrType.hpp: added more
+	work on getting gofR working.
+
+2003-09-09 16:50  mmeineke
+
+	* props/: GofR.cpp, PairCorrType.cpp, PairCorrType.hpp: added the
+	beginings of the GofR pair correlation.
+	
+	added identification of identI in matchI.
+
+2003-09-09 15:35  mmeineke
+
+	* libmdtools/: Integrator.cpp, Integrator.hpp, NPTxym.cpp,
+	NPTzm.cpp, Thermo.cpp, Thermo.hpp: updated the ChangeLog
+	
+	added two new NPT integrators, they still need work.
+
+2003-09-09 15:34  mmeineke
+
+	* ChangeLog: updated the ChangeLog
+
+2003-09-05 17:45  gezelter
+
+	* libmdtools/Make.dep: dependency on config.h
+
+2003-09-05 17:36  gezelter
+
+	* configure, ac-tools/aclocal.m4: fixed sprng problem
+
+2003-09-05 16:29  gezelter
+
+	* samples/metals/Makefile.in: New Makefile for metals sample
+
+2003-09-05 16:27  gezelter
+
+	* Makefile, Makefile.in, ac-tools/aclocal.m4,
+	ac-tools/configure.in, ac-tools/fortran90.m4, forceFields/Makefile,
+	forceFields/Makefile.in, libBASS/Globals.cpp, libBASS/Globals.hpp,
+	libBASS/MakeStamps.cpp, libBASS/MakeStamps.hpp, libBASS/Makefile,
+	libBASS/Makefile.in, libmdtools/Integrator.hpp,
+	libmdtools/Linux_ifc_machdep.F90, libmdtools/Make.dep,
+	libmdtools/Makefile, libmdtools/Makefile.in,
+	libmdtools/calc_eam.F90, libmdtools/config.h.in,
+	libmdtools/definitions_module.F90, libmdtools/fInfo.c,
+	libmdtools/fortranWrappers.cpp,
+	libmdtools/mpiSimulation_module.F90, libmdtools/neighborLists.F90,
+	libmdtools/simulation_module.F90, samples/Makefile,
+	samples/Makefile.in, samples/alkane/Makefile,
+	samples/alkane/Makefile.in, samples/argon/Makefile,
+	samples/argon/Makefile.in, samples/argon/argon.bass,
+	samples/beadLipid/Makefile, samples/beadLipid/Makefile.in,
+	samples/lipid/Makefile, samples/lipid/Makefile.in,
+	samples/water/Makefile, samples/water/Makefile.in, src/Makefile,
+	src/Makefile.in, utils/Makefile, utils/Makefile.in,
+	utils/sysbuilder/Makefile, utils/sysbuilder/Makefile.in: Changes to
+	autoconf / configure method of configuring OOPSE
+
+2003-09-04 16:48  mmeineke
+
+	* libmdtools/Integrator.cpp, libmdtools/Integrator.hpp,
+	libmdtools/Makefile, libmdtools/NPTf.cpp, libmdtools/NPTfm.cpp,
+	libmdtools/NPTi.cpp, libmdtools/NPTim.cpp, libmdtools/NVT.cpp,
+	libmdtools/SimInfo.hpp, libmdtools/SimSetup.cpp, src/Makefile:
+	added resetTime to the Global namespace.
+	
+	added ability to reset the integrators in the NVT and NPT family.
+
+2003-09-04 16:48  mmeineke
+
+	* libBASS/: Globals.cpp, Globals.hpp: added resetTime to the Global
+	namespace.
+
+2003-09-02 09:30  tim
+
+	* libmdtools/: Integrator.hpp, Makefile, SimSetup.cpp,
+	ZConsWriter.cpp, ZConstraint.cpp: fix a bug at MPI version of
+	PolicyByMass
+
+2003-08-28 16:09  tim
+
+	* ChangeLog, libmdtools/GenericData.cpp,
+	libmdtools/GenericData.hpp, libmdtools/SimSetup.cpp,
+	libmdtools/ZConstraint.cpp: Added: check uniqueness of molIndex
+
+2003-08-28 11:59  mmeineke
+
+	* props/: PairCorrType.cpp, PairCorrType.hpp, staticProps.cpp:
+	added the first functional parts of the PairCorrType Abstract
+	classes.
+
 2003-08-27 14:23  tim
 
 	* libmdtools/: Integrator.cpp, SimSetup.cpp, ZConstraint.cpp: fix
@@ -1471,17 +2341,27 @@
 
 2003-03-24 20:07  gezelter
 
-	* samples/Makefile: moving tests to samples
+	* samples/Makefile, tests/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
+	* samples/alkane/Makefile, samples/alkane/alkanes.mdl,
+	samples/alkane/butane.bass, samples/alkane/init_butane.eor,
+	samples/argon/Makefile, samples/argon/argon.bass,
+	samples/argon/init_argon.eor, samples/argon/lj.mdl,
+	samples/lipid/5x5.bass, samples/lipid/Makefile,
+	samples/lipid/init_5x5.eor, samples/lipid/lipid.mdl,
+	samples/lipid/water.mdl, samples/water/Makefile,
+	samples/water/init_ssd.eor, samples/water/ssd.bass,
+	samples/water/water.mdl, tests/alkane/Makefile,
+	tests/alkane/alkanes.mdl, tests/alkane/butane.bass,
+	tests/alkane/init_butane.eor, tests/argon/Makefile,
+	tests/argon/argon.bass, tests/argon/init_argon.eor,
+	tests/argon/lj.mdl, tests/lipid/5x5.bass, tests/lipid/Makefile,
+	tests/lipid/init_5x5.eor, tests/lipid/lipid.mdl,
+	tests/lipid/water.mdl, tests/water/Makefile,
+	tests/water/init_ssd.eor, tests/water/ssd.bass,
+	tests/water/water.mdl: moved tests to samples
 
 2003-03-24 19:51  gezelter
 
@@ -1489,7 +2369,9 @@
 
 2003-03-24 19:46  gezelter
 
-	* ac-tools/Make.conf.in: Added makefiles in tests directories
+	* ac-tools/Make.conf.in, tests/Makefile, tests/alkane/Makefile,
+	tests/argon/Makefile, tests/lipid/Makefile, tests/water/Makefile:
+	Added makefiles in tests directories
 
 2003-03-24 16:55  gezelter
 
@@ -1506,6 +2388,22 @@
 	* libmdtools/: Atom.hpp, ForceFields.cpp, SimInfo.cpp,
 	do_Forces.F90: little bug fixes here and there
 
+2003-03-24 11:04  mmeineke
+
+	* tests/argon/: argon.bass, init_argon.eor, lj.mdl: added an argon
+	test simulation
+
+2003-03-24 11:02  mmeineke
+
+	* tests/: lipid/5x5.bass, lipid/init_5x5.eor, lipid/lipid.mdl,
+	lipid/water.mdl, water/init_ssd.eor, water/ssd.bass,
+	water/water.mdl: [no log message]
+
+2003-03-24 11:02  mmeineke
+
+	* tests/alkane/: alkanes.mdl, butane.bass, init_butane.eor: added
+	some test bass files for experimenting with
+
 2003-03-24 10:26  mmeineke
 
 	* libmdtools/: ForceFields.cpp, f_verlet_constrained.F90: fixed bug
@@ -1615,8 +2513,8 @@
 	libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90,
 	libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp,
 	libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90,
-	libmdtools/vector_class.F90, libmdtools/wrappers.F90: New OOPSE
-	Tree
+	libmdtools/vector_class.F90, libmdtools/wrappers.F90: Initial
+	revision
 
 2003-03-21 12:42  mmeineke
 
@@ -1673,6 +2571,6 @@
 	libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90,
 	libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp,
 	libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90,
-	libmdtools/vector_class.F90, libmdtools/wrappers.F90: Initial
-	revision
+	libmdtools/vector_class.F90, libmdtools/wrappers.F90: New OOPSE
+	Tree