--- trunk/OOPSE-4/ChangeLog	2005/04/15 22:22:10	2205
+++ trunk/OOPSE-4/ChangeLog	2005/09/28 18:46:04	2337
@@ -1,3 +1,782 @@
+2005-09-28 11:55  tim
+
+	* src/math/SquareMatrix3.hpp: using epsilon instead of 0.0 to avoid
+	divergence in rotation matrix to quaternion transformation
+
+2005-09-28 11:32  gezelter
+
+	* src/primitives/RigidBody.cpp: Rotation matrix multiplication
+	order error
+
+2005-09-28 11:32  gezelter
+
+	* src/io/DumpReader.cpp: tracking down quaternion bug
+
+2005-09-28 11:32  gezelter
+
+	* forceFields/DUFF2.frc: Added DIP atom types for 2-point water
+	model
+
+2005-09-27 15:02  tim
+
+	* src/math/SquareMatrix3.hpp: fix a bug in convert rotation matrix
+	to quaternion
+
+2005-09-26 13:38  chuckv
+
+	* src/UseTheForce/DarkSide/electrostatic.F90: Added define for ifc
+	7 so derfc is external. Other compilers should treat erfc as
+	intrinsic.
+
+2005-09-26 12:07  chuckv
+
+	* src/UseTheForce/DarkSide/electrostatic.F90: Changed erfc to derfc
+	and declared it to be external to fix issure with ifc7. Hopefully
+	this will not cause a problem with other compilers where derfc is
+	an intrinsic function.
+
+2005-09-26 11:42  chuckv
+
+	* src/UseTheForce/DarkSide/simulation.F90: MPI fix for SimHasAtype
+	in simulation module. We needed a seperate receive buffer.
+
+2005-09-26 10:58  chuckv
+
+	* src/: brains/SimInfo.cpp, io/Globals.cpp, io/Globals.hpp: Added
+	support for skinThickness keyword to Globals.
+
+2005-09-26 10:56  tim
+
+	* src/io/DumpReader.cpp: fix a typo in DumpReader
+
+2005-09-26 09:27  chrisfen
+
+	* samples/: minimizer/tip4p_two.md,
+	thermoIntegration/liquid/ssde.md, thermoIntegration/solid/ssde.md,
+	water/dimer/cl.md, water/dimer/mix.md, water/dimer/mix2.md,
+	water/dimer/ssd.md, water/dimer/tap.md, water/dimer/two.md,
+	water/spce/spce.md, water/ssd/ssd.md, water/ssd-ion/ssdCl.md,
+	water/ssde/ssde.md, water/tap/tap.md, water/tip3p_ice/tp3.md,
+	water/tip4p/tp4.md: fixing up some samples
+
+2005-09-24 12:39  chrisfen
+
+	* src/UseTheForce/DarkSide/electrostatic.F90: slowdown fixed - now
+	roughly the same speed as the old version when using dipoles
+	
+	energies are now exactly the same between the old version of OOPSE
+	and this version
+
+2005-09-24 12:38  chrisfen
+
+	* samples/water/ssdrf/ssdrf.md: turned rf on
+
+2005-09-23 15:31  chuckv
+
+	* src/UseTheForce/doForces.F90: Fixed "dum-dum" where we ignore the
+	skin thickness and hardcode listSkin to be 1.0. We now get listskin
+	from skin. This will get fixed to where we can manually set skin
+	thickness.
+
+2005-09-22 13:50  gezelter
+
+	* src/math/derfc.F90: added error function
+
+2005-09-21 19:08  chuckv
+
+	* src/integrators/Velocitizer.cpp: Removed print statement for
+	angular momentum and inertia tensor from velocitizer.
+
+2005-09-21 19:04  chuckv
+
+	* src/integrators/Velocitizer.cpp: Removed print statements for
+	remove angular momentum.
+
+2005-09-21 18:45  chuckv
+
+	* src/UseTheForce/DarkSide/LJ.F90: Bug fix: If we are not using LJ
+	(say we are using EAM), we probably shouldn't rebuild the LJ mixing
+	map.
+
+2005-09-21 15:59  tim
+
+	* src/io/: DumpReader.cpp, DumpReader.hpp, DumpWriter.cpp:
+	DumpReader using pure c++ io
+
+2005-09-21 12:20  chrisfen
+
+	* src/UseTheForce/: doForces.F90, DarkSide/LJ.F90: Fixed a
+	defaultCutoff bug (HEMES!)
+
+2005-09-20 17:13  gezelter
+
+	* make/Makefile.in: libz additions
+
+2005-09-20 17:03  gezelter
+
+	* configure, ac-tools/aclocal.m4, ac-tools/configure.in,
+	src/config.h.in: added check for zlib in configure
+
+2005-09-20 16:22  tim
+
+	* src/io/: DumpWriter.cpp, DumpWriter.hpp, Makefile, gzstream.cpp,
+	gzstream.hpp, zipstream.hpp: adding zlib support for DumpWriter
+
+2005-09-20 11:22  tim
+
+	* test/io/: ZipstreamTestCase.cpp, ZipstreamTestCase.hpp: adding
+	testcase for zipstream
+
+2005-09-20 10:41  tim
+
+	* src/io/zipstream.hpp: adding zipstream.hpp
+
+2005-09-20 10:34  chrisfen
+
+	* samples/: dipole/splitInWater.md, dipole/split_SSD.md,
+	dipole/twoSplitDipole.md, minimizer/ssdEM.md,
+	minimizer/tip4p_two.md, water/ssdrf/ssdrf.md, zcons/zconsFixed.md,
+	zcons/zconsMoving.md: fixed up some sample md files
+
+2005-09-19 18:21  chrisfen
+
+	* ChangeLog, samples/water/ssdrf/ssdrf.md,
+	src/UseTheForce/doForces.F90,
+	src/UseTheForce/DarkSide/electrostatic.F90,
+	src/UseTheForce/DarkSide/simulation.F90, src/brains/SimInfo.cpp,
+	src/brains/fSimulation.h: Fixed bugs in reaction field, now it
+	appears as though it really is working...
+
+2005-09-18 15:45  chrisfen
+
+	* ChangeLog, samples/water/ssdrf/ssdrf.md,
+	src/UseTheForce/doForces.F90,
+	src/UseTheForce/doForces_interface.F90,
+	src/UseTheForce/doForces_interface.h,
+	src/UseTheForce/DarkSide/electrostatic.F90,
+	src/UseTheForce/DarkSide/electrostatic_interface.h,
+	src/brains/SimInfo.cpp: reaction field seems to work now, still
+	need to do some testing...
+
+2005-09-16 18:04  chuckv
+
+	* src/io/: Globals.cpp, Globals.hpp: Added keywords for compressed
+	dump files.
+
+2005-09-16 16:07  chrisfen
+
+	* src/: UseTheForce/doForces_interface.F90,
+	UseTheForce/doForces_interface.h, brains/SimInfo.cpp: xlf found a
+	bug that ifc missed...
+
+2005-09-16 15:36  chrisfen
+
+	* src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90:
+	fixing some summation method issues
+
+2005-09-16 14:35  chrisfen
+
+	* src/brains/SimInfo.cpp: fixed a capitalization error
+
+2005-09-16 14:34  chrisfen
+
+	* src/UseTheForce/: fElectrostaticSummationMethod.h,
+	DarkSide/fElectrostaticSummationMethod.h: moved a header file
+	around
+
+2005-09-16 14:00  chrisfen
+
+	* src/: UseTheForce/DarkSide/electrostatic_interface.F90,
+	brains/SimInfo.cpp, brains/SimInfo.hpp: it builds now, but there
+	are known issues - particularly with reaction field...
+
+2005-09-16 11:07  chrisfen
+
+	* src/: UseTheForce/DarkSide/electrostatic.F90, brains/SimInfo.cpp,
+	io/Globals.cpp, io/Globals.hpp: some fixes but even more breaking
+	(cutting out the old way to do reaction field)
+
+2005-09-15 17:05  gezelter
+
+	* src/UseTheForce/: doForces.F90, fCoulombicCorrection.h,
+	fElectrostaticSummationMethod.h, DarkSide/electrostatic.F90,
+	DarkSide/electrostatic_interface.F90,
+	DarkSide/electrostatic_interface.h: Working on adding WOLF
+
+2005-09-15 14:17  tim
+
+	* src/io/DumpReader.cpp: Fix a bug in DumpReader in case readFrame
+	is called without calling getNFrames
+
+2005-09-15 08:47  chrisfen
+
+	* src/UseTheForce/fCoulombicCorrection.h: forgot to add a header
+
+2005-09-14 21:48  chuckv
+
+	* src/UseTheForce/doForces.F90: Fixed bug where gtypeMaxCutoff was
+	not initialized after creation. When maxval(gtypeMaxCutoff) was
+	called, the largest random garbage value was returned from the
+	array.
+
+2005-09-14 19:14  chrisfen
+
+	* src/: brains/SimInfo.cpp, brains/SimInfo.hpp, io/Globals.cpp,
+	io/Globals.hpp: changes to include the coulombicCorrection selector
+
+2005-09-14 19:13  chrisfen
+
+	* src/UseTheForce/DarkSide/: Makefile, electrostatic.F90,
+	reactionField.F90: added in the undamped wolf, in the process of
+	doing the damped wolf
+
+2005-09-14 19:13  chrisfen
+
+	* src/UseTheForce/: doForces.F90, doForces_interface.F90,
+	doForces_interface.h, notifyCutoffs.F90: some changes to activate
+	the coulombicCorrection selector
+
+2005-09-14 19:11  chrisfen
+
+	* samples/water/dimer/: cl.in, cl.md, water.md: just some testing
+
+2005-09-14 19:11  chrisfen
+
+	* samples/argon/: 500.in, 500.md: Equilibrated the sample
+
+2005-09-14 19:10  chrisfen
+
+	* forceFields/DUFF2.frc: re-added Cl- and Na+
+
+2005-09-14 15:31  chuckv
+
+	* src/UseTheForce/DarkSide/eam.F90: EAM now uses eamlist to lookup
+	eamAtypes instead of assuming a 1-1 correspondence to atypes.
+
+2005-09-14 15:28  gezelter
+
+	* src/UseTheForce/doForces.F90: fix to put back calculation of r in
+	do_prepair
+
+2005-09-14 14:02  gezelter
+
+	* src/UseTheForce/DarkSide/LJ.F90: fixed a bug in the
+	createMixingMap routine.  It should now set doShift correctly
+
+2005-09-07 17:44  chuckv
+
+	* src/UseTheForce/doForces.F90: Added nGroupsInRow for mpi build.
+
+2005-09-07 17:23  chuckv
+
+	* src/UseTheForce/DarkSide/simParallel.F90: Added access to mpi
+	logical variables
+
+2005-09-07 17:08  gezelter
+
+	* src/UseTheForce/doForces.F90: bugfix on the grouptype finding
+	algorithm
+
+2005-09-07 15:46  gezelter
+
+	* src/: UseTheForce/doForces.F90,
+	UseTheForce/doForces_interface.F90, UseTheForce/notifyCutoffs.F90,
+	UseTheForce/notifyCutoffs_interface.F90,
+	UseTheForce/notifyCutoffs_interface.h, brains/SimInfo.cpp,
+	io/Globals.cpp, io/Globals.hpp: adding c-side interface to change
+	cutoff Policy
+
+2005-09-07 14:18  gezelter
+
+	* src/UseTheForce/doForces.F90: Some bug hunting
+
+2005-09-07 14:18  gezelter
+
+	* samples/argon/argonNVT.md: Just a longer test
+
+2005-09-06 12:32  chuckv
+
+	* src/UseTheForce/doForces.F90: Added allocation for gtypeCutoffmap
+	etc..
+
+2005-09-01 17:56  gezelter
+
+	* src/UseTheForce/doForces.F90: initialized atomTypeMaxCutoff(i) to
+	zero
+
+2005-09-01 15:17  gezelter
+
+	* src/UseTheForce/: doForces.F90, doForces_interface.F90: wrote
+	createGtypeCutoffMap
+
+2005-08-30 13:23  chrisfen
+
+	* src/: UseTheForce/doForces.F90,
+	UseTheForce/doForces_interface.F90,
+	UseTheForce/doForces_interface.h,
+	UseTheForce/DarkSide/electrostatic.F90,
+	UseTheForce/DarkSide/gb.F90, brains/SimInfo.cpp,
+	brains/fSimulation.h, io/Globals.cpp, io/Globals.hpp: made some
+	changes for implementing the wolf potential
+
+2005-08-26 17:39  chrisfen
+
+	* src/UseTheForce/DarkSide/eam.F90: updated getEAMCut
+
+2005-08-26 16:30  chrisfen
+
+	* src/UseTheForce/: doForces.F90, DarkSide/eam.F90,
+	DarkSide/gb.F90, DarkSide/shapes.F90, DarkSide/sticky.F90: added
+	some probably nonfunctional get*cut routines
+
+2005-08-26 15:34  chuckv
+
+	* src/UseTheForce/DarkSide/eam.F90: Added eamType map to atid map.
+
+2005-08-26 11:36  gezelter
+
+	* src/UseTheForce/doForces.F90: fixing some of the problems in the
+	interactionHash and gtypeCutoff routines
+
+2005-08-17 10:26  gezelter
+
+	* src/UseTheForce/: doForces.F90, fCutoffPolicy.h,
+	DarkSide/simulation.F90: added fCutoffPolicy.h
+
+2005-08-11 16:04  gezelter
+
+	* src/UseTheForce/: doForces.F90, notifyCutoffs.F90: breakage in
+	progress
+
+2005-08-10 14:17  gezelter
+
+	* src/primitives/StuntDouble.hpp: putting spaceballs back where
+	they belong
+
+2005-08-09 17:33  gezelter
+
+	* src/UseTheForce/DarkSide/LJ.F90: Complete rewrite of Lennard
+	Jones module
+
+2005-08-09 17:33  gezelter
+
+	* src/UseTheForce/doForces.F90: Breaky Breaky BREAKY breaky breaky
+
+2005-08-09 14:40  chuckv
+
+	* src/UseTheForce/doForces.F90: In process of re-write for group
+	based cutoff....
+
+2005-07-29 14:38  gezelter
+
+	* src/UseTheForce/doForces.F90: fixes in progress
+
+2005-07-29 12:34  tim
+
+	* src/UseTheForce/doForces.F90: fix a bug which does not update
+	me_i and me_j correctly
+
+2005-07-28 17:12  chuckv
+
+	* src/UseTheForce/: doForces.F90, notifyCutoffs.F90: Changed
+	cutoffs... Segfaults nicely now...
+
+2005-07-20 12:04  gezelter
+
+	* configure, ac-tools/aclocal.m4: fixed ACX_MPI to ignore some text
+	error messages from pathscale compiler
+
+2005-07-13 11:48  tim
+
+	* src/applications/staticProps/DensityPlot.cpp: std::bind2nd is in
+	<functional>
+
+2005-07-13 10:54  tim
+
+	* src/: UseTheForce/fSwitchingFunction.h,
+	UseTheForce/mpiComponentPlan.h,
+	UseTheForce/DarkSide/fInteractionMap.h, brains/fSimulation.h,
+	io/BASS_interface.h, io/BASS_parse.c, io/BASS_parse.h,
+	io/BASSlex.l, io/BASSyacc.y, io/interface.c, io/make_nodes.c,
+	io/mpiBASS.c, io/mpiBASS.h, io/node_list.h, io/parse_tree.c,
+	io/parse_tree.h, math/MatVec3.c, utils/residentMem.c,
+	utils/simError.c, utils/simError.h: replace c++ style comment in c
+	files
+
+2005-07-03 15:53  chuckv
+
+	* src/: UseTheForce/doForces.F90, UseTheForce/notifyCutoffs.F90,
+	UseTheForce/DarkSide/simulation.F90, utils/oopseMPI.F90: Added
+	subroutine to set cuttoff for Interaction map and function in
+	simulation.F90 to determine if a particular atype is present in a
+	simulation.
+
+2005-06-28 08:58  gezelter
+
+	* src/UseTheForce/doForces.F90: [no log message]
+
+2005-06-27 17:21  chuckv
+
+	* src/UseTheForce/doForces.F90: More breaking and destruction of
+	force code. Does not build at this point...
+
+2005-06-27 16:01  gezelter
+
+	* src/: UseTheForce/doForces.F90, UseTheForce/DarkSide/atype.F90,
+	UseTheForce/DarkSide/fInteractionMap.h,
+	UseTheForce/DarkSide/interactions.F90, utils/definitions.F90:
+	Breaky breaky!
+
+2005-06-20 11:03  gezelter
+
+	* samples/water/ssd/ssd.md,
+	src/applications/staticProps/DensityPlot.cpp: fixed a bug and ran a
+	simulation
+
+2005-06-13 13:25  tim
+
+	* src/: applications/staticProps/DensityPlot.cpp,
+	applications/staticProps/DensityPlot.hpp,
+	applications/staticProps/SCDOrderParameter.cpp,
+	applications/staticProps/StaticProps.cpp,
+	io/AtomTypesSectionParser.cpp: working version of DensityPlot
+
+2005-05-31 17:31  chuckv
+
+	* src/: brains/SimInfo.cpp, integrators/Velocitizer.cpp: Changes to
+	remove angular momentum.
+
+2005-05-31 12:34  chuckv
+
+	* src/applications/nanoRodBuilder/nanorodBuilder.cpp: Fixed bug in
+	typo in nanorodBuilder.
+
+2005-05-30 09:01  chuckv
+
+	* src/: applications/nanoRodBuilder/nanorodBuilder.cpp,
+	brains/SimInfo.cpp, brains/SimInfo.hpp, brains/Stats.cpp,
+	brains/Stats.hpp, integrators/Velocitizer.cpp,
+	integrators/Velocitizer.hpp: Added method to remove system angular
+	momentum to velocitizer and added method to calculate system
+	angular momentum to siminfo.
+
+2005-05-29 16:16  chrisfen
+
+	* src/UseTheForce/DarkSide/: electrostatic.F90, sticky.F90: Removed
+	balance from the Darkside (files)
+
+2005-05-29 16:15  chrisfen
+
+	* src/UseTheForce/doForces.F90: Removed balance from doForces
+
+2005-05-29 16:15  chrisfen
+
+	* samples/water/tap/: tap.in, tap.md: Updated tap sample
+
+2005-05-29 16:15  chrisfen
+
+	* samples/water/dimer/: Makefile, tap.in, tap.md: Included a tap
+	dimer for testing purposes
+
+2005-05-29 16:14  chrisfen
+
+	* forceFields/DUFF2.frc: Re-entered the TIP4P-Ew water model. It
+	was apparently wiped earlier this month...
+
+2005-05-29 16:13  chrisfen
+
+	* ChangeLog: ran make cvslog
+
+2005-05-28 19:16  tim
+
+	* src/visitors/: AtomNameVisitor.cpp, AtomNameVisitor.hpp: adding
+	AtomNameVisitor
+
+2005-05-28 19:09  tim
+
+	* src/integrators/Integrator.cpp: dding resetIntegrator
+
+2005-05-28 19:06  tim
+
+	* src/integrators/: Integrator.cpp, Integrator.hpp, NPT.cpp,
+	NPT.hpp, NPTi.cpp, NPTi.hpp, NVT.cpp, NVT.hpp,
+	VelocityVerletIntegrator.cpp, VelocityVerletIntegrator.hpp: adding
+	resetIntegrator
+
+2005-05-27 16:11  tim
+
+	* src/applications/staticProps/: DensityPlot.cpp, DensityPlot.hpp,
+	Makefile, P2OrderParameter.cpp, SCDOrderParameter.cpp,
+	SCDOrderParameter.hpp, StaticProps.cpp, StaticProps.ggo,
+	StaticPropsCmd.c, StaticPropsCmd.h: adding DensityPlot into
+	StaticProps
+
+2005-05-26 23:41  tim
+
+	* src/: applications/staticProps/Makefile,
+	applications/staticProps/P2OrderParameter.cpp,
+	applications/staticProps/P2OrderParameter.hpp,
+	applications/staticProps/StaticProps.cpp,
+	applications/staticProps/StaticProps.ggo,
+	applications/staticProps/StaticPropsCmd.c,
+	applications/staticProps/StaticPropsCmd.h, utils/StringUtils.cpp,
+	utils/StringUtils.hpp: adding SCDOrderParameter into StaticProps
+
+2005-05-26 17:45  tim
+
+	* src/: applications/dump2Xyz/Dump2XYZ.cpp,
+	applications/dump2Xyz/Dump2XYZCmd.c,
+	applications/dump2Xyz/Dump2XYZCmd.h,
+	applications/staticProps/Makefile,
+	applications/staticProps/P2OrderParameter.cpp,
+	applications/staticProps/P2OrderParameter.hpp,
+	applications/staticProps/RadialDistrFunc.cpp,
+	applications/staticProps/RadialDistrFunc.hpp,
+	applications/staticProps/StaticAnalyser.hpp,
+	applications/staticProps/StaticProps.cpp,
+	applications/staticProps/StaticProps.ggo,
+	applications/staticProps/StaticPropsCmd.c,
+	applications/staticProps/StaticPropsCmd.h, visitors/Makefile,
+	visitors/OtherVisitor.cpp, visitors/OtherVisitor.hpp: adding
+	AtomNameVisitor to convert atom name to its base name;
+	wrappingvisitor now wrap back to the center of the mass; adding
+	P2OrderParameter into StaticProps
+
+2005-05-22 16:36  chuckv
+
+	* samples/metals/nanorod/Au_nanoparticle_FCC.md,
+	src/applications/nanoRodBuilder/Geometry.cpp,
+	src/applications/nanoRodBuilder/GeometryBuilder.cpp,
+	src/applications/nanoRodBuilder/GeometryFactory.cpp,
+	src/applications/nanoRodBuilder/GeometryFactory.hpp,
+	src/applications/nanoRodBuilder/nanorodBuilder.cpp,
+	src/integrators/VelocityVerletIntegrator.cpp: Fix to print pressure
+	tensor.
+
+2005-05-22 16:05  tim
+
+	* src/: brains/Stats.cpp, brains/Stats.hpp, brains/Thermo.cpp,
+	integrators/VelocityVerletIntegrator.cpp, io/Globals.cpp,
+	io/Globals.hpp, io/SectionParserManager.cpp: adding keyword
+	printPressureTensor
+
+2005-05-20 14:27  tim
+
+	* src/integrators/NPrT.cpp: NPrT in progress
+
+2005-05-20 11:01  tim
+
+	* src/: integrators/NPrT.cpp, io/Globals.cpp,
+	utils/OOPSEConstant.hpp: NPrT in progress
+
+2005-05-19 16:31  tim
+
+	* src/: brains/Thermo.cpp, brains/Thermo.hpp, integrators/NPAT.cpp,
+	integrators/NPrT.cpp, integrators/NPrT.hpp, io/Globals.cpp,
+	io/Globals.hpp: NPAT is working
+
+2005-05-19 10:49  tim
+
+	* src/: UseTheForce/DarkSide/LJ.F90, integrators/Makefile,
+	integrators/NPrT.cpp, io/Globals.cpp: fix bug in NPAT and NPrT
+
+2005-05-18 23:28  tim
+
+	* src/: brains/Register.cpp, integrators/NPAT.cpp,
+	integrators/NPAT.hpp, integrators/NPrT.cpp, integrators/NPrT.hpp,
+	io/Globals.cpp, io/Globals.hpp: adding NPAT and NPrT integrators
+
+2005-05-18 14:06  chrisfen
+
+	* forceFields/DUFF2.frc, src/UseTheForce/DarkSide/sticky.F90: just
+	some tap changes
+
+2005-05-18 13:31  chrisfen
+
+	* src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90,
+	DarkSide/sticky.F90: Modifications to temper the dipolar strength
+	in the first solvation shell for tap
+
+2005-05-18 07:35  chrisfen
+
+	* samples/water/tap/: tap.in, tap.md, water.md: added a tap example
+	for testing purposes
+
+2005-05-17 17:35  chrisfen
+
+	* ChangeLog, forceFields/DUFF2.frc, samples/water/dimer/ssd.md,
+	samples/water/dimer/water.md, src/UseTheForce/DUFF.cpp,
+	src/UseTheForce/doForces.F90,
+	src/UseTheForce/DarkSide/electrostatic.F90,
+	src/UseTheForce/DarkSide/electrostatic_interface.F90,
+	src/UseTheForce/DarkSide/sticky.F90: Modifications to tap.  Also
+	correcting changes to the previous merge that were not caught
+
+2005-05-16 23:20  chuckv
+
+	* src/types/: DirectionalAtomType.cpp, DirectionalAtomType.hpp:
+	Fixed merge issues between Kyle and Chris so OOPSE will actually
+	build.
+
+2005-05-16 22:46  kdaily
+
+	* src/io/: GayBerneAtomTypesSectionParser.cpp,
+	GayBerneAtomTypesSectionParser.hpp, Makefile: help
+
+2005-05-16 21:08  kdaily
+
+	* forceFields/DUFF2.frc, src/UseTheForce/doForces.F90,
+	src/UseTheForce/DarkSide/gb.F90, src/io/Makefile,
+	src/types/DirectionalAtomType.cpp,
+	src/types/DirectionalAtomType.hpp: added gb
+
+2005-05-13 15:36  chrisfen
+
+	* forceFields/DUFF2.frc: Better tap
+
+2005-05-12 14:43  chrisfen
+
+	* forceFields/DUFF2.frc, samples/water/dimer/ssd.in,
+	samples/water/dimer/ssd.md, src/UseTheForce/DarkSide/sticky.F90,
+	src/applications/dump2Xyz/Dump2XYZ.cpp,
+	src/visitors/AtomVisitor.hpp: Couple of changes for TAP water. 
+	Need to parametrize.
+
+2005-05-11 18:15  chuckv
+
+	* src/: io/ShapeAtomTypesSectionParser.cpp,
+	math/RealSphericalHarmonic.cpp, utils/CaseConversion.hpp: Fixed
+	build issues under ifc7.
+
+2005-05-09 17:07  chuckv
+
+	* src/applications/nanoRodBuilder/Geometry.hpp: More geometry
+	builder changes.
+
+2005-05-05 10:06  chrisfen
+
+	* forceFields/DUFF2.frc, samples/water/ssde/water.md: Changed SHED
+	to TAP
+
+2005-05-05 09:47  chrisfen
+
+	* forceFields/DUFF2.frc, samples/water/ssde/ssde.md,
+	samples/water/ssde/water.md, src/UseTheForce/DUFF.cpp,
+	src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/Makefile,
+	src/UseTheForce/DarkSide/atype.F90,
+	src/UseTheForce/DarkSide/atype_interface.F90,
+	src/UseTheForce/DarkSide/simulation.F90,
+	src/UseTheForce/DarkSide/sticky.F90, src/brains/SimInfo.cpp,
+	src/brains/fSimulation.h, src/io/Makefile,
+	src/io/StickyAtomTypesSectionParser.cpp,
+	src/io/StickyPowerAtomTypesSectionParser.cpp,
+	src/io/StickyPowerAtomTypesSectionParser.hpp,
+	src/types/AtomType.cpp, src/types/AtomType.hpp,
+	src/types/AtomTypeProperties.h, src/types/DirectionalAtomType.cpp,
+	src/types/DirectionalAtomType.hpp: OOPSE setup for TAP water.  It's
+	not parametrized, but OOPSE will now let me run it...
+
+2005-05-03 17:55  chuckv
+
+	* src/applications/nanoRodBuilder/: Geometry.cpp, Geometry.hpp,
+	GeometryCreator.hpp, GeometryFactory.cpp, GeometryFactory.hpp:
+	Adding support for generic geometry to nanorodbuilder.
+
+2005-05-03 12:55  chuckv
+
+	* src/applications/nanoRodBuilder/: GeometryBuilder.cpp,
+	nanorodBuilder.cpp, nanorodBuilder.ggo, nanorodBuilderCmd.c,
+	nanorodBuilderCmd.h: More changes to nanoRodBuilder....
+
+2005-04-29 14:16  gezelter
+
+	* make/Makefile.in: [no log message]
+
+2005-04-29 11:26  chrisfen
+
+	* forceFields/DUFF2.frc, samples/water/spce/water.md,
+	samples/water/ssd/water.md, samples/water/ssd-ion/ssdCl.md,
+	samples/water/ssd-ion/water.md, samples/water/ssde/water.md,
+	samples/water/ssdrf/water.md, samples/water/tip3p_ice/water.md,
+	samples/water/tip4p/water.md: Added TIP4P-Ew
+
+2005-04-27 19:24  chuckv
+
+	* src/applications/nanoRodBuilder/: GeometryBuilder.cpp,
+	GeometryBuilder.hpp, nanorodBuilder.cpp, nanorodBuilder.ggo,
+	nanorodBuilderCmd.c, nanorodBuilderCmd.h: Fixed issues with
+	nanoRodBuilder....
+
+2005-04-27 15:13  chrisfen
+
+	* samples/shape/Shapes.frc, samples/shape/linear.shape,
+	src/UseTheForce/DarkSide/atype.F90,
+	src/UseTheForce/DarkSide/shapes.F90,
+	src/UseTheForce/DarkSide/shapes_interface.F90,
+	src/types/AtomType.cpp, src/types/ShapeAtomType.cpp: Got rid of
+	write statements and am closer to a working shapes
+
+2005-04-22 16:57  chuckv
+
+	* src/utils/Predicate.hpp: Fixed gcc4 bug...
+
+2005-04-22 16:52  tim
+
+	* src/utils/: CaseConversion.hpp, Predicate.hpp, Trim.cpp,
+	Trim.hpp: adding CharClassificationFunctor to fix the locale
+	problem  of c++
+
+2005-04-21 09:12  chrisfen
+
+	* samples/shape/Shapes.frc, samples/shape/linear.in,
+	samples/shape/linear.md, src/UseTheForce/ForceField.hpp,
+	src/UseTheForce/ForceFieldFactory.hpp, src/UseTheForce/Makefile,
+	src/UseTheForce/SHAPES_FF.cpp, src/UseTheForce/SHAPES_FF.hpp,
+	src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/atype.F90,
+	src/UseTheForce/DarkSide/shapes.F90,
+	src/UseTheForce/DarkSide/shapes_interface.F90,
+	src/UseTheForce/DarkSide/shapes_interface.h,
+	src/brains/Register.cpp, src/brains/SimCreator.cpp,
+	src/io/Makefile, src/io/SectionParser.cpp,
+	src/io/SectionParser.hpp, src/io/SectionParserManager.cpp,
+	src/io/ShapeAtomTypesSectionParser.cpp,
+	src/io/ShapeAtomTypesSectionParser.hpp, src/math/Makefile,
+	src/types/AtomType.cpp, src/types/ShapeAtomType.cpp,
+	src/types/ShapeAtomType.hpp: Shapes is limping along with a array
+	bounds overwrite (I think...). At least the parser loads the
+	forcefield fine...
+
+2005-04-18 10:44  chrisfen
+
+	* src/UseTheForce/Shapes_FF.cpp: axed because file causes havoc on
+	Mac (capitalization confusion of filenames)
+
+2005-04-17 22:50  chrisfen
+
+	* src/: UseTheForce/SHAPES_FF.cpp, UseTheForce/SHAPES_FF.hpp,
+	UseTheForce/Shapes_FF.cpp,
+	io/DirectionalAtomTypesSectionParser.cpp,
+	io/ShapeAtomTypesSectionParser.cpp,
+	io/ShapeAtomTypesSectionParser.hpp: Working on the shapes parser...
+
+2005-04-15 17:43  gezelter
+
+	* README: gmake in case people forget
+
+2005-04-15 17:40  gezelter
+
+	* src/applications/oopse/oopse.cpp: fixed the spacing on the
+	banner.  Vanity.
+
+2005-04-15 17:22  gezelter
+
+	* src/: config.h.in, applications/oopse/oopse.cpp: Version string
+	in banner (and version numbers in config.h)
+
+2005-04-15 17:22  gezelter
+
+	* ChangeLog, LICENSE, README: Documentation changes
+
 2005-04-15 17:03  gezelter
 
 	* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,