changing configure script to process the new utilities

added the waterBoxer script

adding NgammaT integrator

fixed TI MPI bug

converted samples over to the OOPSE-4 file format

Fixed an MPI bug in thermodynamic integration

Changing utility programs to use the new file format

Massive changes preparing for release of OOPSE-4: The main difference
is that the new MD file format (.md, .dump, .eor) now contains meta-data
information along with the configuration information.

fixed an ordering issue in quadrupole-charge interactions

Changing atom2mdin into atom2md to reflect new unified file format

fixed dumpConverter problems

fixed a spelling bug

fixed a getSigma bug

fixed d / sigma0 confusion

removed printing of GBN and GBM from previous debugging

Adding more changes to orientational bond order parameter.

Added the multipole interaction routine.  It doesn't work yet, so it's not included in the build.

fixed forces and torques for GB

Beginnings of a order parameter.

MPI thermodynamic integration works now.

Added support for Winger3jm coefficients.

output the principle axis of GB

damping now works for charge-quadrupole and dipole-dipole

fixed some typos

Added methods to access GB_mu and GB_nu from the force field options

Add the RippleOP to calculate the orderparameter of the ripples.

Fix a type promotion problem

fixes for Hydrodynamics

Fixed a bug when spherical boundary conditions were off.

wrapping back to PBC by molecule instead of by individual atom

Last bug showed up in 2 places, fixed the other one.

Adding single precision capabilities to c++ side

adding --enable-single to configure script

electrostatic refinement

*** empty log message ***

adding a gay-berne switch to Dump2XYZ

missing makefile was hanging up 'make clean'

Change in siminfo used in nanoparticleBuilder.

Using OpenBabel element table to pick vdw radii for hydrodynamics
if the LJ sigma can't be found.

Added EAM atom types to Hydro models

Removed sqrt splines and shape stuff (doesn't work, so why was it in there?).  Changed some of the water samples to use shifted_force.  Probably should set the defaults to use the damped version now that we sped it up.

splined up sticky

Many performance improvements

Since status.F90 is used by interpolation.F90, the former needs to be listed above the later in the Makefile.

added some logical flags

bug fixes for interpolation module

Added interpolation module.

Added status module to simParallel for error reporting.

Fixed memory leak bug where SCList capacity was not reset to zero on destruction.

Added check to make sure md file exists.

Fix the normalization problem in calculating correlation functions

Makefile for nanoparticle builder.

Debugging changes to nanoparticle builder.

Adding position correlation function. The command line option for DynamicProps is now changed. --rcorr is for position correlation and --rmsd is for mean square displacement.

remove a unknown method

Throw exception if the file can not be opened for preprocessing

fix a bug in calculating hydrodynamics tensor when the radius of beads are not the same

Verify the correctness of Ellipsoid's hydrodynamics properties

refactor Hydrodynamics module.

LagevinDynamics is working?

unit conversion for diffusion tensor is wrong

correcting the unit in HydrodynamicsModel

Adding RoughShell and BeadModel

adding Cholesky Decomposition

Fixed a double/int bug.  Surprised no one ever noticed before...

Bead Model is working

fixed a spelling error

Changed Names of class files.

fix a bug in converting integer to double

adding transpose into SquareMatrix3; fix a bug in AtomStamp where orientation is not set correctly.

Adding visitor for GBlipid atom type

Changes to cutoff radius setting to a more logical procedure - still may change...

Adding :LegendrePolynomial

Added Makefile for nanoparticle builder.

Removed MixingRule from Globals. Handled by forceField now.

fixed some version info and the copyright date

Changed formating.

filepp can not handle multiple line macro, just convert multiple line macro into single line macro.

autoconf modernization and cruft removal

instead of printing to std::cout, throwing an exception when error is found.

Sutton and Chen should be working now.

fixing RhoZ

replace isType<int> with isInteger

Sutton-Chen no longer segfaults or produces 0 potential, but rather
produces Inf for the potential. Progress....

Long range potential return from fortran is already accumulated, it should not be accumulated again;
nGroupTypesCol is not initialized; GroupMaxCutoffCol is not allocated;

Sutton-Chen bug fixes. Almost there...

More changes to forcefield options.

Force option changes.

make minor change to build oopse under solaris

replace grammar for numerical parsing

Removing compiler dependencies and replacing them with real autoconf
checks

fix a nasty negative integer parsing problem by refining the grammar

fixed compilation problem for icc7

added copyright

Wow thats alot o' files. Now passing forceFieldOptions to all of the parsers.

*** empty log message ***

Removed geometric distance mixing from individual modules and now use
force options to detemine what the deal is.

Fixed ifc public-private issue.

Fixed a bug in checkTorsion

Changes to build twinned crystal

Fix parsing error in OptionSectionParser

Fixed build bug in openbabel.

adding more checking for topology

We've made big changes.  This isn't 2.0 anymore.

Adding FragmentStamp

Got rid of spurious printing out of timestep

adding DataHolder

Code to calculate rho(Z) to calculate density profiles for water slabs.

compilation bug

Cutoff Mixing fixes

Cutoff mixing fixes have been made.

adding support for soft linking

fixed a bug

Unifying config.h stuff and making sure the OpenBabel codes can find
our default (and environment variable) Force Field directories.

OptionSectionParser get compiled

adding mdinConverter

register openbabel readers/writers

adding openbabel

cleaned up the charge-charge interactions a bit...

Made preforce calc public in suttonchen.

Added Sutton-Chen to force loop...

Missed makefile for sutton-chen.

Sutton-Chen almost done. Just need to fix do_forces to use Sutton-Chen.

added in a 5th order polynomial switching function option

Added a keyword and ability to output forces and torques

Working on shifted_force...

improvements in shifted-force

More work on suttonchen.

forgot to add the screening method header

again, changing how we deal with summation and screening methods

Added suppport to atypes for MEAM and sutton-chen

fixed a capitalization problem with NPT integrator initialization

still fixing up wolf...

changed the default switching radius to 85% of rcut

reaction field looks to be working now

streamlined reaction field for dipoles (now a good bit faster) and added reaction field for charges - still need to do charge-dipole RF

Still had some globals toUpper problems - these changes should fix those...

fix an index mismathcing between c and fortran

merged reaction field with electrostatics.F90

using notation from Cleaver paper

Another bug fix

changing GB architecture

Change error message in Globals

Add parts for the GayBerne LJ

added default restraint spring constants into Globals

Fix to forceManager to pass potential array to fortran.

simplifying long range potential array

More Change goodness for calculation of potential.

Breaky Breaky: Add Support for seperating potential contributions.

Design change for nanoRod builder --twinned.

Bug fix, undeclared local variable in MPI.

There is still something wrong with inertia tensor projection

fix a bug in creating cutoffGroup. When
cutoffGroup is turned off, there is a mismatch between group and
center of mass array

fixed an annoying mass ratio bug that results in simulation failure with massless particles

just some random changes when testing

fix a bug in projecting the inertia tensor of directional atom in rigibody into rigidbody's body frame

using epsilon instead of 0.0 to avoid divergence in rotation matrix to quaternion transformation

tracking down quaternion bug

Added define for ifc 7 so derfc is external. Other compilers should treat erfc as intrinsic.

MPI fix for SimHasAtype in simulation module. We needed a seperate receive buffer.

fix a typo in DumpReader

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.

Removed print statement for angular momentum and inertia tensor from velocitizer.

Bug fix: If we are not using LJ (say we are using EAM), we probably shouldn't rebuild the LJ mixing map.

Fixed a defaultCutoff bug (HEMES!)

adding zlib support for DumpWriter

Fixed bugs in reaction field, now it appears as though it really is working...

Added keywords for compressed dump files.

fixing some summation method issues

moved a header file around

some fixes but even more breaking (cutting out the old way to do reaction field)

Fix a bug in DumpReader in case readFrame is called without calling getNFrames

Fixed bug where gtypeMaxCutoff was not initialized after creation. When maxval(gtypeMaxCutoff) was called, the largest random garbage value was returned from the array.

added in the undamped wolf, in the process of doing the damped wolf

EAM now uses eamlist to lookup eamAtypes instead of assuming a 1-1 correspondence to atypes.

fixed a bug in the createMixingMap routine.  It should now set doShift
correctly

Added access to mpi logical variables

adding c-side interface to change cutoff Policy

Added allocation for gtypeCutoffmap etc..

wrote createGtypeCutoffMap

updated getEAMCut

Added eamType map to atid map.

added fCutoffPolicy.h

putting spaceballs back where they belong

Breaky Breaky BREAKY breaky breaky

fixes in progress

Changed cutoffs... Segfaults nicely now...

replace c++ style comment in c files

*** empty log message ***

Breaky breaky!

working version of DensityPlot

Fixed bug in typo in nanorodBuilder.

Removed balance from the Darkside (files)

adding AtomNameVisitor

adding resetIntegrator

adding SCDOrderParameter into StaticProps

Fix to print pressure tensor.

NPrT in progress

NPAT is working

adding NPAT and NPrT integrators

Modifications to temper the dipolar strength in the first solvation shell for tap

Fixed merge issues between Kyle and Chris so OOPSE will actually build.

added gb

Fixed build issues under ifc7.

OOPSE setup for TAP water.  It's not parametrized, but OOPSE will now let me run it...

More changes to nanoRodBuilder....

Got rid of write statements and am closer to a working shapes

adding CharClassificationFunctor to fix the locale problem  of c++

axed because file causes havoc on Mac (capitalization confusion of filenames)

fixed the spacing on the banner.  Vanity.

xemacs has been drafted to perform our indentation services

nanorodbuilder now exit's when libCGAL is not present.

Changed interface name for SGI Compiler

fix some warning messages

Added destroy methods for Fortran modules.

more memory leak are fixed

fix memory leak in nanorodBuilder and simpleBuilder(forget to delete lattice)

refactory LatticeFactory and LatticeCreator

refactory LatticeFactory and LatticeCreator

added lattice directory

cleaned up memory leak fix

destory atom type in fortran side

Fixed pointer memory leak in vector_class.

minor change to TI output

Added code to delete vector.

Importing nanoRodBuilder application (may not work yet).  ((Doesn't work yet.))
(((May never work....)))

fixing of the quadrupoles.  look!  it's divide by 3 like stone says!

added some stuff to clean out module files during "make clean"

Altered signs to fix charge-dipole interactions

support '+' and '-' in atom type name;clean the code a little bit

fixed the wrapping

fix a bug in getting the dimension of histogram

Make sure electrostatic_module provides data for reaction_field

VelocityVerletIntegrator already deletes and Nullifies restWriter,
so Integrator shouldn't do it.

first run at charge-quadrupole interactions

fix a typo in MultipoleAtomTypesSectionParser

settled on a unit for quadrupoles

fixed a bug in MPI restraints

fixed a doxygen problem

using map to replace link list

added fortran-side support for split dipoles

fixing restraints

First commit of the new restraints code

fix compilation issue

adding IndexFinder which is used to select the molecules; Seperate ElectrostaticAtomTypesSectionParser into
ChargeAtomTypesSectionParser and MultipoleAtomTypesSectionParser;remove print dipole option from Dump2XYZ;

added splitDipole and fixed quadrupole stuff

fixing a strange icc8 bug (we think).

Electrostatic Unification Project

Using OOPSE_itoa and checking a NULL left over from the LinkedList days

electrostatic unification project

SPRNG eradication project

avoid using const char*(hope can fixed the missing atom type problem)

info_ in Velocitizer is not initialized which causes a seg fault

fixed a file inclusion problem

fix compilation problem for g++ 3.4

Making small modifications to allow for use on MPI machines

Adding a modified version of MersenneTwister.hpp

adding basic_teebuf which can operate on multiple stream simutaneously.

Fix a bug in GofRAngle

fix for compilation on the Sun

adding LipidTransVisitor, GofXyz is working now

Updated copyright information

more bug get fixed

make processHistogram non-abstrct function

finish GofXyz

forget the const correctness for BitSet

return residentMem in byte

using PhysMem - RSSMem to estimate avaliable memory

change the suffix of output files;fix the problem of counting in staticProps

BlockSnapshotManager is using reference counting now

adding typedef to TokenMap, using TokenMapType::value_type instead of
std::make_pair to make Sun compiler happy

(1) adding #ifdef __RWSTD to make sun compiler happy
(2) fix pair density calculation problem when two selections intersect with each other

*** empty log message ***

bugfixing residentMem

added residentMem

fix a bug in BlockSnapshotManager.hpp

fix a bug in VelocityVerletIntegrator : last frame is written twice

refactory CorrelationFunction

fix a bug in calculating  bytes per stuntdouble

fixed a bug in CorrelationFunction

maximum length defaults to the cutoff radius

dynamicProps get built

more work in dynamicProps

adding command line option to DynamicProps

adding dynamicProps

adding one more constructor to Snapshot to create customized DataStorage

adding support for physmem

more work in StaticProps

adding GofRAngle

staticProps in progress

add getRigidBodyAt  function into Molecule class

support select internal index selection, for example, select DMPC.3

selection librarys added

issue commented out in wildcards

fix a bug in determing the global index for rigidbodies

selection library is working

IgnoreVisitor and XYZVisitor now use selection library

dump2Xyz now take advantage of selection library

adding missing implementation

selection library get built

remove some useless files

more work in selection library

selection library in progress, except SelectionEvaluator, other files are compiled

add SelectionCompiler.cpp

adding selection library

(1)Cast wrong atom to DirectionalAtom in GhostTorsion
(2)get the wrong column of electroframe

(1) complete section parser's error message
(2) add GhostTorsion
(3) accumulate inertial tensor from the directional atoms before calculate rigidbody's inertial tensor

forget to set maxIterNum_ in NVT

moved Package variable into subdirectory makefiles to speed up
the building process

added dummy subroutine to avoid empty unit, synchronized this dummy
routine between C and fortran

fixing for gnugetopt

no message

remove include Integrator.hpp in Minimizer

formatting

remove useless debug info

LinearVisitor get fixed

fix another bug in WATER.cpp

improved restraints - mpi should work fine

Improvements to restraints

working towards parallel restraints

Got rid of some write statements

current status of the debugging process

isLinear and linearAxis are virtual in StuntDouble,
but are implemented by DirectionalAtom and RigidBody
In StuntDouble, they should return false and "-1" but
there should be logic to figure them out in the other
two classes

Breaky Breaky

Shapes looks like it's working

shapes rcut calculator added

remove old Vector3d.hpp from application/simpleBuilder

Done with combination

ReplaceWildCard is working

Minor change

fix of setDipoles

fixed duplicate declaration foo

Adding Generic Tuple3 and Tuple4