Made init files more OOPSE like.

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Minor changes

Added the SPC water model

Added TIP4P water sample

Good ssde simulation sample added

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fixed a bug in Mat3x3d.cpp

roll in progress

Fixed dependency bug (we hope)

Sample now does variant

Converted D's to E's in the funcfl files so that C can read them.

Added a bunch of files for EAM variants

Modified EAM to use forceFieldVariant

reorg of EAM force fields to have variants

Removed debugging printf statements

Roll in progress

Fixed a bug in NPTf (vScale was declared in the cpp file in addition
to the declaration in Integrator.hpp file)

Dan cleaned up the pressure calculation a bit...  Got rid of some unnecessary lines of code in Thermo.cpp

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Moved to SHAPES

More work on Fortran side of error handler

Unifying the error handlers

forgot to add these

Config changes for fortran access to SimError

fixed a bug which only writes out the first atom of a molecule

Fixed groupOffset bug

Shouldn't have been in CVS

Why is this in CVS?

starting fortran-usable version of simError

Formatting Changes, removed writeRaw

Bug in Makefile.in

Bug fix (fixes of skipList and neighbor list under MPI)

Testing

Fixed bug in useLiquidThermInt routine in ForceFields.cpp

cutoff group in progress

Paving the way for separate solid and liquid thermodynamic integration routines

Fixed a bug in Integrator.cpp where it called writeRaw() when useThermInt = false...

Makefile doesn't belong in CVS

Cutoff group changes under MPI

groupList new bases on global index of atoms

Fixed off-by-one error in groupStartRow and groupStartCol

Compacted all of the 8 copies of the force loop into one.

pressure tensor fixes

Fixes for stress / pressure tensor by cutoff group

Added Bass keyword useThermInt.

Got PDB reading working, and matching atom types too!

Changes for SHAPES potential

Several additions... Restraints.cpp and .hpp were included for restraining particles in thermodynamic integration.  By including these, changes were made in Integrator, SimInfo, ForceFeilds, SimSetup, StatWriter, and possibly some other files.  Two bass keywords were also added for performing thermodynamic integration: a lambda value one and a k power one.

add minimizer sample

Fixes for compilation under Mac OS X with IBM's xl compilers

Removed an extraneous write

const char* fix

get rid of rc and massratio from simState, creat cutoff group forevery atom
which does not belong to
cutoff group defined at mdl file

Added the cutoff Groups to the default water.mdl file

bug fixes for cutoffGroups

adding instantiation of Integrator<BaseIntegrator> in order to make OOPSE compiled by icc8

adding CutoffGroup.hpp

adding cutoffGroup into OOPSE

Fixes to libmdtools to use the simplified cutoff stuff in the BASS library

optimize DumpWriter

Many changes to get group-based cutoffs to work

fixed two bugs in calc_charge_charge when using molecular cutoff

keep the previous position of cantilever in SMD

Adding molecular cutoffs

useMolecularCutoffs added to Globals

modified the defaults for the system init time and system init state.

add reaction field correction to charge-charge interaction

fixed another bug in InitFromFile. MPI verion of OOPSE is working again

remove some useless files

DUMP2XYZ 0.99 version

fixed a bug in CompositeVisitor which cause the double counting problem

new implement of quickLate using visitor and composite pattern

fix whole bunch of bugs :-)

fixed for get_potential

Now molecules can keep track of their own IntegrableObjects (and
RigidBodies).  Also a bug-fix so that SimInfo can keep track of
RigidBodies (which was done incorrectly before).

Oops.  Those were old.

Adding RigidBody code

Slightly longer test run

incorporate SMD into ZConstraint,it does not sound a good choice, next commit will seperate SMD and ZConstraint

add LARGEFILE_SOURCE64 macro to support large file

Adding zsub, a program which can be used to replace atom type for zconstraint into OOPSE

remove the old implement of minimizer from cvs tree

adding function shakeF in order to remove the constraint force along bond direction

 started a bug fix on the massive memory overusage by OOPSE

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Add one more file into Makefile.in

Fix a bunch of bugs   :-)
Single version of conjugate gradient with golden search linesearch pass a couple of
functions test. Brent's  algorithm is still broken

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Functor.hpp pass unit test

Adding GoldenSection and Brent LineSearch Method

Substantial changes. OOPSE now has a working WATER.cpp forcefield and parser.
This involved changes to WATER.cpp and ForceFields amoung other files. One important
note: a hardwiring of LJ_rcut was made in calc_LJ_FF.F90. This will be removed on
the next commit...

Adding MinimizerParameterSet class.

revision of NLModel

Fix to new RigidBody stuff

Longer run time to test gold in MPI

More BASS changes to do new rigidBody scheme
a copy of WATER.cpp from this morning

revision of constraint for Nonlinear Optimization Model

Changed orientation lines from unit vectors to euler angles

Changed default orientation in BASS to use Euler angles in the
following order: phi, theta, psi
Removed the ability to set orientation using a unit vector

Fix broken atom assignment for rigid bodies

constraint class in energy minimization

Energy Minimizer

Updated the default water to SSD/E

Added a bunch of dummy targets so make won't complain

BASS changes to add RigidBodies required a change in
how the MoleculeStamps are used by divideLabor in mpiSimulation.cpp

fix a bug in creating eor file

fixed an struct mismatch error in the mpi initialization of the AtomStruct

Changes for altivec

changes for charge charge interactions

autoconf fixes

autoconf compatibility changes for icc8

Some changes for new MPI organization and direct charge-charge interactions

Energy Minimization method

change the interface of writeFrame

fix a bug in copying string

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

New DumpWriter (Attempt #4)

null terminate some strings just in case

added strncpy to DumpWriter

First Stab at fixing DumpWriter

Fixed a bug of sending message from master node to itself in DumpWriter.cpp
and InitializeFromFile.cpp

Making do_Forces a little more sane

mangling forces even further

mangled do_forces...

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.

More profiling fixes.

Small update to timing in MPI

added some profiling routines

working on adding GofRtheta and GofRomega

Added functions for simple profiling in fortran.

finished gofRtheta and added gofRomega. both need to be debugged and tested.

 removed the randombilayer header

backed up the old DUFF.frc to backup.DUFF.frc alte4red masses and epsilons of TB2 and TB3 in DUFF.frc

begun work on add ing in the GofR,CosTheta

added a routine to SimInfo.cpp to inline a min function.

Added support for compiling fortran without use of mpich modules. We use mpif.h instead.:

added the following parameters to BASS:
   * useInitialExtendedSystemState
   * orthoBoxTolerance
   * useIntiTime => useInitialTime

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

added template stuff to the Maikefile template

little changes to some printf format statements

bug fixes for rList problems

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

som efixes to the way rcut is setup, as well as additional debugging comments.

Refixed broken makefile

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