OpenMD

Updating configure for qhull with c++

fixing atom2md and bringing it up to speed with OpenBabel 2.2.3

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

fixing make install process

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

missing shtool for build

Removing CGAL, cleaning up ac-tools directory

fixing mpi configure

Fixed a bug in QHULL autoconf logic

integrators/Makefile needs to be created

fixed compile flags for mac

fixing configure process

updating configure process

fixing a configure script error

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.

Changes to optimization flags.

Define USE_QHULL.

New configure

Added CGAL test

Added configure for CGAL.

Added m4 file for qhull

Fixed more bugs and removed more CGAL.

Removed CGAL from OOPSE and replaced it with qhull.

fixed a configuration error

Changes to nanorod builder for new dump format. Changes to configure to test for new version of cgal.

oops with the affineScale

changing configure script to process the new utilities

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.

added perl substitution for affineScale script

Fixed a bug in the fftw part of the configure script.

removed icc from C++ search lines, did some formatting work
on GB module, mucked around with a GB example

added mpi compilers, demoted pg compilers after pathscale

more changes

more changes for MPICH with profiling libraries required

MPI stuff

fixes for Hydrodynamics

Adding single precision capabilities to the fortran side

adding --enable-single to configure script

Getting fortran side prepped for single precision...

zlib fixes

Autoconf fixes for FFTW.  Multiple FFTW version support.

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finding ifort arguments that won't die under two different versions
of the intel fortran compiler

Adding spherical boundary conditions to LD integrator

Many performance improvements

Added status module to simParallel for error reporting.

changed compiler search order

added some missing checks for header files (particularly zlib.h)

autoconf modernization and cruft-removal

changed __FUNCTION__ to __func__ to match C99 standard, and then added
an autoconf test to check for __func__ usability.  Changed some default
compile flags for the Sun architecture

added the STL check

Adding checks for various features used by ANTLR

added some checks for pathscale compiler

added pathscale

added check for egrep (grep -E) needed for new build of libOOPSE.a

added checks for some functions to configure script

Adding some checks for OpenBabel code

added check for zlib in configure

fixed ACX_MPI to ignore some text error messages from pathscale compiler

Jedi mind-trick warning messages have been added to
make users ignore CGAL.

configure now searches for perl to use with filepp

added CGAL checks

SPRNG eradication project

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bugfixing residentMem

bugfixes for residentMem on LINUX

modifications to estimate memory in use by other processes
autoconf fixes
ps syntax checking
config.h file cleaning

ps niceness

ps strangeness

adding supprot for physmem

more fixes for gnugetopt

fixing for gnugetopt

Fortran/C++ interface de-obfuscation project appears to be complete!  Woo hoo!

Changed optimization flags for XLF and XLC.

more build fixes

cleaning up build process

A few minor build changes

updates

starting a configure version

Import of OOPSE v. 2.0