Single version of energy minimization for argon is working, need to add constraint

Add some lines into global.cpp to make it work with energy minimization

NLModel0, NLModel1 pass uit test

to avoid cyclic depency, refactory constraint class

begin unit test of minimizer

using class  Minimizer1D derived from MinimizerBase instead of a functor to do line seach

member list fixes for rigid bodies

Revision of NLModel0 and NLModel1

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

Convert Eulers in degrees into radians

Corrected spelling in several directories, and stated WATER.cpp

Adding energy minimization

Made some error messages more user-friendly

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

fixed a bug where only MPI jobs could write eor files

Fixes for Dumps

changes for charge charge interactions

Changes for adding direct charge-charge interactions (with switching function)

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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

Added bitmask to do_forces property lookup

More profiling fixes.

Small update to timing in MPI

added some profiling routines

Added functions for simple profiling in fortran.

Changes for gradients (to do minimizations)

Fixed a bug in SimInfo ordering of radii

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.

moved the velocity scale matrix calculation outside of the atom loop in the NPT family of integrators.

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

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

C++ compatibility for templates

did a complete overhaul of how c calls fortran. All function pointers and fortran calls are rigidly typecast now.

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.

added routines for the sysbuilder to work with simSetup

added a new NPT integrator, NPTxyz. It scales the x, y, and z direction sepeartely. no box skew allowed.

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.

Fixed bug in calc_eam.

changed the formating ogf the error statements in simError

added a function to get the maxCutoff

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

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

fixes for configure

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

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

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fixed ecr grow in SimInfo

fixed conserved quantity in NPT (Still some small bug)

NPTi appears very stable.

Added integrators to Makefile.in

dependency on config.h

added resetTime to the Global namespace.

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

Added: check uniqueness of molIndex

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

changed the Makefiel a litle.

Fixed a bug in MPI_DUFF. The atom block type was not being properly constucted in MPI. (The MPI struct had 6 doubles declared versus the actual 11)

small bug fix on frequency of output dumps.

updated the Changelog.

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

fixed a bug where ghostbend atom b was not being set. ( recent bug from SimState conversion)

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Tested MPI version of Z-Constraint Method

Added some profiling code -DPROFILE.

fixed a really annoying bug in Directional Atom, where mu was getting written to pseudorandom memory location.

added harmonical potential to z-constraint method

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changed the number of degrees of freedom to account for zConstreints

 fixed a deprcated instance of Atom::setZ and Atom::getZ in ZConstaint.

Bug fixes for eam...

add index range checking into ZConstraint

More bug fixes for eam.

Added eam to simSetup and added changecutoffeam.

Finished most code for eam....

making some changes to read dump files

Fixed a current time initialization bug in InitFromFile.

Initialized currentTime to 0, in case no one sets it.

Started work on a DumpReader

Changes for SSD/E

fixed spelling issue

Added massive changes for eam....

Changed how cutoffs were handled from C. Now notifyCutoffs in Fortran notifies those who need the information of any changes to cutoffs.

more fixes for box changes

fixed a long lived bug in do_forces. Rrf was not being used in the neighborlist correctly. rcut was conssistently being set lowere than Rrf causing the dipole cutoff region to be to small. Also led to the removal of the taper region to buffer the dipole cutoff.

Fixes for the NPT ensembles

fixed some bugs, Changed entry_plug to info where appropriate

more archaic code fixes

fixes to get rid of get_vx and set_vx

Added NPTfm

Checking in changes for NPTim

Fixes for get and set routines in Atom and DirectionalAtom

found a bug. Unit vectors were not being updated

working on som integrator bugs

Fixed hmat in DumpWriter (MPI) and eor.

Bunch of 1-d array -> 2-d array stuff

adding in dan's NPT stuff

Fixes for both NPTf and NPTi

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NPTi

fixed the bugs introduced by switching the periodic box to a matrix

Fixes for flexi-BOX

Updated the ChangeLog, and Converted most of the SImInfo to use non-Isotropic
boxes. wrapVector needs to be finished.

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)

currently modifiying Symplectic to become the basic integrator.

changed how NVT is now derived from Integrator

optimized the ssd calc loop

fixed up sysBuild to where it should now build our systems

More eam work.

Fixed ordering on NVT calculation in integrators.

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.

fixes for NPT and NVT

Fixes for NPT / NVT

fixes for NVT

dt/2 fix in nvt

Changes to integrate the NVT and NPT ensembles

fixed a sign error in the radial portion of SSD.

Working on NVT

bug fixes

Added ExtendedSystem infrastructure for NPT and NVT calculations

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

Starting work on NPT

Changed Readme, added some files

Fixed a bug where MPI was not getting the proper atomIdents.

Fixed DumpWriter to be more robust to errors. also added a little namespace to InitFromFile to wrap it's helper functions in MPI

Fixes in MPI force calc and in Trappe_Ex parsing.

Bug fixes in read-write routines.

mpi fixes and debugging mpi read write from file.

MPI buggy, fixed mpiRefresh issue.

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.

electrostatic changes for dipole / RF separation

fixed bug where short range interactions were not being calculated.

removed some debug print statements

Fixed F_MACH_DEP bug

Makefile fixes for depends