add chi and eta to the comment line of dump file.

Portability fixes

started trying to understand extern "C" stuff for pointers

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.

mod file fixes and portability stuff

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.

fixes for configure, sysBuild

work on bilayer builder

added eam ForceField files to the init

fixed an eam mpi parmeter setup bug

added the init file to the makefile

added eam ForceField files to the init

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;

added the staticProps directory to the build list
for both configure  and configure.in

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.

Contiuned work on staticProps. should be in a position where it will compile and run first runs.

added Au init file for eam.

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.

changed the formating ogf the error statements in simError

changed f90Flags so they are no longer overwritten by the compiler.

added mpif90 mod check back
same for conifig.in

fixed a lot of warnings and errors found with SUN's SUNWspro.s1s7

fixed some additional remarks from icc -w3 (extra verbose output)

fixed a bug in configure

moved readyCheck in the integrator so that it is called before the first Statistics are written.

Removed NPTfm from Integrator.hpp.

Some small syntax cleaning in NPTfm and SimSetup

Converted NPTf to work with the NPT base class.

Removed NPTfm and NPTim from cvs

removed mpi++ from the makefile

fixed bugs in NPTf, found (nearly) conserved quantities for both NPTi
and NPTf

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fixed NPTi to now work with constraints.

add conserved quantity to statWriter
fix bug of vector wrapping at NPTi

Added integrators to Makefile.in

added more work on getting gofR working.

updated the ChangeLog

added two new NPT integrators, they still need work.

dependency on config.h

New Makefile for metals sample

added resetTime to the Global namespace.

added ability to reset the integrators in the NVT and NPT family.

fix a bug at MPI version of PolicyByMass

added the first functional parts of the PairCorrType Abstract classes.

More fixes for stress tensor parallel bug.

set default force substraction policy to PolicyByMass

added define statemewnt to Statwriter and Dumpwriter to handle files larger than 2 gb.

commented out some print statements in Zconstraint

hard coding some system init into bilayer.sys

Use make_sprng_seed() to generate seed and check the seed which is specified by user at least contains 9 digits

changed the Makefiel a litle.

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user can setup seed in bass file now, if he does not specify any value for
seed, oopse will take the value of seconds of system time as seed

updated the Changelog.

added some bug fixes for setting the random number generator seed value.

bug fixed in ghost bend class

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Fixed sysBuild -bilayer works. Nanobuilder still broke.

Stable ZConstraint with average force substraction strategy

harmonic potential & z-contraint method

debugging globals

fixed a few references to older stuff...

Missed del of files before.

commit makefile

Changed makefile to only build quicklate.

Arranged sysbuilder into a subdirectory. Fixed some of sysbuilder to work with new
atom allocation in libmdtools.

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changed the number of degrees of freedom to account for zConstreints

moved frameCount's functionality into DumpReader. also split props into staticProps and dynamicProps. (currently only have staticProps)

switched SimInfo to use a system configuration from SimState rather than arrays from Atom

stable version of Z-Constraint

added z-constraint parameters to the globals

More bug fixes for eam.

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Added eam to simSetup and added changecutoffeam.

module use fixes for eam and do_forces.

added the scan function to the DumpReader. It should now save the start of each frame in a vector.

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some initial changes to Dumpwriter and friends to accomadate random file access

fixed Initializefrom file to start the simulation from the time specified in the init file.

Fixes for SSD/E

commented out an eam line

added info module

More up to date version of EAM_FF

Made quickLate aware of Hmat.  quickLate is now somewhat more
intelligent about periodic boundaries and wrapping.

added a quick wipe-and-update script for quick rebuilds on BoB

removed some debugging print statements.

working on fixing ssd bug

cleaned up simSetup

added more command line arguments

Fixing  pressure tensor

removed old outdated code

removing get_vx

Bugfix in NPTim, fixes for NPTfm

Broken SysBuilder

Removed some debugging write statements

added get and set routines to Atom and DirectionalAtom

found a bug. Unit vectors were not being updated

Switched the bond in the force field back to constrained, to preserve energy

Starting to worry about all the strtok() calls in our code

Fixed hmat in DumpWriter (MPI) and eor.

Added nanoBuilder and a general Lattice builder.

Bug fixing NPTi and NPTf. there is some error in the caclulation of HmatInverse.

adding in dan's NPT stuff

Removed Qmass

Fixes in NPTi migrated into NPTf

fixed box scaling

 cleaned up the dependecy scripts in the makefiles

Fortran flexi-BOX

working on adding the box matrix to everything.

Changed over the bonds to Harmonic bonds in the DUFF frc file

fixed constraints.

Fixes to NVT.  Check them!

Doing some work to debug the constraint code.

Most of the integrator and NVT seem to be working now.

slowly converting to new integrator and forcefield names.

 doing some work on SimSetup to clean it up / get it to work with the new Integrator.

Added Teng's parmeters fro the ghost Bend in TraPPE_Ex

some work on the integrator. ( incomplete)

added constrainA and constrainB to the Symplectic integrator

currently modifiying Symplectic to become the basic integrator.

changed how NVT is now derived from Integrator

all seems to be working

doing some work to overhaul sysbuild.

Added bead lipid model to the sample directory

added the TailBead atom types to the TraPPe_Ex forceField

fixed up the TraPPE_Ex force field. there were some duplicate entries

added the utils subdirectory to the configure script

added a new test for constraint failure

almost finished.

finished bilayerSys.cpp

sysBuild still need to write the bass file.

MoLocator.cpp is currently empty

More eam work.

Fixed ordering on NVT calculation in integrators.

added Ghost bends to the TraPPE_Ex forceField

added sysBuild to the utils Makefile

Added first mangling of EAM.

Bug fix in progress for NPT

Working on ConstantStress

fixed a bug in symplectic, where presure was only being calculated the first time through.

Added volume and enthalpy to status file

It works (kinda)...

Moved expand neighborlist to init_FF.

fixes for nvt / npt

Fixes for affine transform

Fixes for NPT and NVT

doing some testing in sticky through Symplectic.

Fixed transpose bug in mpi reduce for tau and virial.

Many fixes to add extended system

Added ExtendedSystem infrastructure for NPT and NVT calculations

final mods to try a fortran compiler

bug fixes for compilation

Breaking c and fortran, c gets smarter, fortran gets dumber...

Changes for Extended System

Added extended system header

renamed nvt to extendedsystem

fixed a possible call before initialize bug.

a few fixes to simError.h
also some fixes to Molecule.hpp

fixed some small things with simError.h

Added NVT file (very broken for now)

dipoles mostly work, but there is a memory leak somewhere.

more bug fixes....

Fixed bug with pot_local not zeroed.

bug fix in DumpWriter.cpp

fixed a bug where the Excludes were not being created properly

fixed long range interactions in Trappe

fixed a bug where excludes were not being initialized

Fixed a single processor segfault bug.

fixed a few more bugs.

 fixed the makefile

I have implemeted Molecules everywhere I could remember to.
will now attempt to compile.

finished conversion of TraPPE_ExFF to use Molecule

fixes for local->global atom numbering in MPI

Fixes to fileio for MPI

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.

fixed a couple of the "static" bugs in  Atom and Exclude

Added Atom.cpp and Exclude.cpp

Make Atom.cpp able to add and delete ranges of atoms

I'm overhauling the molecule class to contain it's own bonds, bends, and torsions.

may god have mercy on my soul.

MPI stuff for passing out molecules

Fixes for Parallel thermalization

Fixed bugs with calculation of potential energy and temperature.

added dummy files to keep the build deirectories from being pruned.

moved tests to samples

Added makefiles in tests directories

little bug fixes here and there

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fixed bug where short range interactions were not being calculated.

removed some debug print statements

added links to the makefile in forceFields

Makefile fixes, directory re-org, autoconf fixes

Fixed makefile

Readme changes

Makefile fixes for depends