Compilation and portability fixes

Fixed a bunch of cppcheck warnings.

Adding spatial statistics analysers.

Adding nanoparticle generators, fixing a Qhull static link bug

Added a new icosahedralBuilder for single-component Mackay Icosahedron nanoparticles.

Space typos

Merging changes from trunk branch into development.

More careful with casts, fixed windows compilation issues

Windows compilation fixes

Fixed some cruft

MERGE OpenMD trunk changes 1803:1811 into development branch

Adding stat2thcond back

Merging some of the trunk changes back to the development branch,
cleaning up a datastorage bug

Code readability updates.

Refactored Snapshot and Stats to use the Accumulator classes.  Collected
a number of methods into Thermo that belonged there.

Possibly fixed the rigid body global indexing issue.  Reformatted
comments. Started work on the FrameData section of Snapshot.
        

added a minimizer parsing block

Individual ForceField classes have been removed (they were essentially
all duplicates anyway).  

ForceField has moved to brains, and since only one force field is in
play at any time, the ForceFieldFactory and Register methods have been
removed.  

fixed an initialization bug in Dump2XYZ

Added files for fcc and pentagonal nanorod builders. Updated runMe in samples/builders to include nanorod builders.

Fixed a compilation warning for CLANG compiler

Some fixes for CMake and single precision builds

Added a waterReplacer script.  A bit rough around the edges, but seems
to do the right thing for a slab of ice.

fixing the build system

changing build process

updating gengetopt runs

removed spurious prints, fixed one bug, but there's still a parallel problem

Fixes

changes for cell linked lists

Well, it compiles and builds, but still has a bus error at runtime.

Somewhat working cmake build system now. Does not yet build a parallel target. Builds all non-mpi programs.

removing cruft (atom numbers, do_pot, do_stress) from many modules and
force managers

fixed empty revision problem

revision

Updating visitor architecture to something a bit more modern

Changes to gofrz so you can specify the z length

Adding property set to svn entries

Adding a new correlation function to do slab-segregated g(r)
calculations.  This computes at g(r) for pairs while requiring the z
coordinates of the two sites to be at fixed separations.  The data
is output in:  r, z, g(r,z)  

committing a change

testing automagic

One more

fixed some md-solvator over specificity, and an install bug

updating various dates and version numbers for 1.0.1 release

Added preliminary code for Alpha Hull calculation using qhull.
Added preliminary support to SMIPD to support Alpha Hull.
Alpha Hull does not yet add the correct things to triangle to be returned to SMPID. 
Preliminary changes for shadow hamiltonian integrator.
Chages to md files so they will work in openMD. 

Parallel bugfix in RestraintForceManager
Reverted back to hydrodynamics on triangular plates for SMIPDForceManager
Removed thermalLength and thermalConductivity keywords from Globals.
Bug tracking in openmdformat (not yet resolved).

Merging changes skipped in working copies of OOPSE into the OpenMD
tree, fixing make install

Almost all of the changes necessary to create OpenMD out of our old
project (OOPSE-4)

Removing CGAL

Added new restraint infrastructure
Added MolecularRestraints
Added ObjectRestraints
Added RestraintStamp
Updated thermodynamic integration to use ObjectRestraints
Added Quaternion mathematics for twist swing decompositions
Significantly updated RestWriter and RestReader to use dump-like files
Added selections for x, y, and z coordinates of atoms
Removed monolithic Restraints class
Fixed a few bugs in gradients of Euler angles in DirectionalAtom and RigidBody
Added some rotational capabilities to prinicpalAxisCalculator

missing energyConvert in kinetic energy

Returned old LD forces to SMIPDForceManager.

Fixes for Inversions for use with Amber

Inversion fixes and amber mostly working

Many fixes

Cleaning up oopseformat and adding inversion terms

Adding infrastructure for Amber force field.

Fixed a number of bugs in slab_density calculation

More progress...

More work on python version of md-solvator. Pretty sure mol loop is busted.

Fixed a bug in BlockSnapshotManager.

More changes, still broken.

Checking in changes for Hefland moment calculations

A bunch of minor changes to make MPI compilation faster than
the double compilation we do now...

Correcting a few typos

Adding GofZ.hpp

fixed a few correlation functions

Removed older version of openbabel from our code.  We now have a
configure check to see if openbabel is installed and then we link to
the stuff we need.  Conversion to OOPSE's md format is handled by only
one application (atom2md), so most of the work went on there.
ElementsTable still needs some work to function in parallel.

Fixes for building.

Many fixes for Charmm-type torsions.

*** empty log message ***

Added: Action Correlation function (for viscosity), Directional RCorr (for
non-spherical bodies)
Modified: LCorr (for multiple axes)

Testing files for NPT Langevin dynamics convex hull calculation.

Bug fixes for non-declared objects

Build change.

Removed nanorod builder from OOPSE.

Added Bond Order Parameter as a function of radius.

fixed a bug in waterBoxer

adding md-solvator

Added thetacorr functions to dynamic props.

Remove snapshotcentroid from makefile.

More changes to mdsplit.

Changed how mdsplit gets file names. Full path is now removed from name.

bug fixing Wigner 3-j import to C++

Adding support for radial rcorr.

Fix to makefile.

Added support for nanoparticle density profile.

Support for OOPSE RealType.

more openbabel updates, also changing velocitizer to thermalizer to
avoid a filename collision on case-insensitve file systems

fixing a wrapVector problem in staticProps, also making Shifted force
and electrostatic damping the default behavior

bug fixes

More typos...

Fixed printing of OOPSE version at header and trailer.

Changed nanoparticle builder for new dump syntax.

fixing missing lattice arguments, adding a builder sample

oops with the affineScale

fixing bugs in randomBuilder

Added utility to split dump file frames into md files.

added solvator and adjusted waterBoxer

fixed a bug in waterBoxer for invalid water names

Some efficiency fixes (now computes Wigner 3-j coefficients only once
in the constructor).

fixing bond order parameter code

Following Rein ten Wolde article

more changes to BOP and SH

Bugfixes in BondOrderParameter and SphericalHarmonic

fixed bugs (mostly in BondOrderParameter)

Working on BondOrderParameter

changing configure script to process the new utilities

added the waterBoxer script

adding NgammaT integrator

removed extra file in Hydro.cpp

starting change of file formats

fixed a pvf bug

added dumpConverter

Adding a directory for scripts
Adding affineScale script

Beginnings of a order parameter.

MPI thermodynamic integration works now.

Add the RippleOP to calculate the orderparameter of the ripples.

replace double with RealType

fixed an initialization bug of Hxy.cpp.

fixed the bugs of Hxy.cpp.

Autoconf fixes for FFTW.  Multiple FFTW version support.

Changes to calculate undulation spectrum

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

*** empty log message ***

Fixed latticeOrt in shapedlatice and latticebuilder.

(1) RoughShell Model is working; (20)Adding a new option into Hydro which allows user to generate the beads only

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.

Added shaped lattice.

Fix a bug in friction calculation for ellipsoid

New version of Hydro is working now.

LagevinDynamics is working?

unit conversion for diffusion tensor is wrong

correcting the unit in HydrodynamicsModel

adding hydrodynamics module into build system

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

Bead Model is working

Changed Names of class files.

Fixing a bug which reads the wrong frame of trajectory file during analysis

Adding :LegendrePolynomial

Added Makefile for nanoparticle builder.

fixed some version info and the copyright date

fixing RhoZ

End of the Link --> List
Return of the Oject-Oriented
replace yacc/lex parser with antlr parser

compilation issue

rename mdinConverter to atom2mdin

nothing

rewrite Globals

Added code for nanoparticle builder to cvs.

fixed a bug and ran a simulation

Fixed bug in typo in nanorodBuilder.

adding DensityPlot into StaticProps

adding AtomNameVisitor to convert atom name to its base name; wrappingvisitor
now wrap back to the center of the mass; adding P2OrderParameter into StaticProps

Couple of changes for TAP water.  Need to parametrize.

Adding support for generic geometry to nanorodbuilder.

Fixed issues with nanoRodBuilder....

Version string in banner (and version numbers in config.h)

nanorodbuilder now exit's when libCGAL is not present.

more memory leak are fixed

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

refactory LatticeFactory and LatticeCreator

Changes to delete atypes...

forget to delete prepareVisitor in Dump2XYZ

avoid building parallel executable for dump2XYZ, simpleBuilder, staticProps and dynamicProps

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

adding basic_teebuf which can operate on multiple stream simutaneously.

adding LipidTransVisitor, GofXyz is working now

more bug get fixed

make processHistogram non-abstrct function

finish GofXyz

fix a bug in writing out the value of cosang

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

bug fix in StaticProps

default length for staticProps is 1/2 smallest length of first frame

refactory CorrelationFunction

more fix

fixed a bug in SimInfo::getCutoff()

dynamicProps get built

more work in dynamicProps

adding command line option to DynamicProps

adding dynamicProps

change the filenames

remove some useless files

adding GofR

update help info for Dump2XYZ

dump2Xyz now take advantage of selection library

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

formatting

merging new_design branch into OOPSE-2.0

remove old Vector3d.hpp from application/simpleBuilder

more build fixes

define DEV_ROOT as relative path

change directory structure of application. Every executable file is replaced in seperate directory

change the #include in source files