Squash merge hacc/unify-nbody-cosmotools-halofinder

A detailed commit history of the branch follows:

commit 37919db44c20740e21b1b0f2ab704e8d7218eeaf
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Mon Apr 14 13:47:22 2014 +0000

    hacc/trunk added error description to assert in ParticleExchange2 to remind user to try increasing MEMORY_PADDING_DISPLACEMENT

    From: apope <apope@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/unify-nbody-cosmotools-halofinder@1978 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit b43a70f06320f2c6e94d0aa0f7c0cf8d2d93f995
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Mon Apr 14 13:47:20 2014 +0000

    also rem _com_ cols from sod prop in halotestp

    From: hfinkel <hfinkel@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/unify-nbody-cosmotools-halofinder@1977 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit 64b7f487e691686cd58627180f30217cf4966bca
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Fri Apr 4 18:06:52 2014 +0000

    COMP: Add rule to build halofinder programs

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/unify-nbody-cosmotools-halofinder@1970 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit 81d7a851540f84781dc8385929810bdd7df4b2e7
Merge: 3c2b3d7 446eb43
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Fri Apr 4 18:06:50 2014 +0000

    Merge branch 'master' into unify-nbody-cosmotools-halofinder

    Conflicts:
    	cosmotools/Makefile

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/unify-nbody-cosmotools-halofinder@1969 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit 3c2b3d7562da7dd2c0a6b7a714bc061c70357424
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Thu Apr 3 20:42:13 2014 +0000

    BUGFIX: Fix running in situ w/just CosmoTools

    Fixed an issue when running the code with just CosmoTools. When
    no analysisdat file is provided, m_analysisdat is NULL and the
    code would crash b/c it would attempt to access the m_analysisdat
    file to get the overload size before refreshing the particles.
    Fixed that by getting the overload size specified in the
    indat.params file.

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/unify-nbody-cosmotools-halofinder@1967 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit f6015c39969f2addc3e5fb37876fd11646676aad
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Thu Apr 3 14:22:17 2014 +0000

    BUGFIX: Fix crash when number of halos is zero.

    The code crashed when running the halofinder at an
    early time-step, wherein there were no halos found.
    Fixed that.

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/unify-nbody-cosmotools-halofinder@1966 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit 114b31d05b17ddea67d95061fac706590b5f55b8
Merge: fa0c5c4 c223923
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Fri Mar 28 02:12:50 2014 +0000

    Merge branch 'master' into unify-nbody-cosmotools-halofinder

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/unify-nbody-cosmotools-halofinder@1964 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit fa0c5c4608f2d86aae3d7968be10f766f36d73c2
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Wed Mar 26 17:52:38 2014 +0000

    Merge r1928,r1929 to unify-nbody-cosmotools-halofinder

    From: Hal Finkel <hfinkel@anl.gov>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/unify-nbody-cosmotools-halofinder@1959 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit b26404ed01e748bfa0887b00f8d51e09337b6750
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Wed Mar 26 17:52:36 2014 +0000

    Merge r1927 to unify-nbody-cosmotools-halofinder

    From: Nicholas Frontiere <nfrontiere@gmail.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/unify-nbody-cosmotools-halofinder@1958 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit 3cc95876d5d6927e4c455b4926f68960edfefbea
Merge: 76c6652 dc17aba
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Wed Mar 26 17:52:34 2014 +0000

    Merge branch 'master' into unify-nbody-cosmotools-halofinder

    Conflicts:
    	nbody/halo_finder/HaloCenterFinder.cxx
    	nbody/halo_finder/ParticleDistribute.cxx

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/unify-nbody-cosmotools-halofinder@1957 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit 76c6652c41cc0f2f38635144cd4f98fd5fcc0413
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Mon Mar 17 23:31:07 2014 +0000

    BUGFIX: Fix logic in threshold for subhalo finder

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/unify-nbody-cosmotools-halofinder@1926 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit a67ec3f16876e50d03594da240ada6f766c59cb0
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Mon Mar 17 21:32:06 2014 +0000

    ENH: Uncomment sub-halo finding via MC3Extras

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/unify-nbody-cosmotools-halofinder@1925 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit b2e917ae66462c2211de674c093639d431361f0b
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Mon Mar 17 20:25:56 2014 +0000

    ENH: Compute halofinder derived parameters

    This commit adds functionality for computing some
    halofinder parameters that are derived from the
    user-supplied parameters in the config file and the
    simulation parameters, to mimic the behavior of the
    HaloFinderInSitu class under "nbody/simulation".
    This also required the addition of one more parameter in
    the cosmotools config file to specify the minimum mass
    (M_solar/h).

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/unify-nbody-cosmotools-halofinder@1924 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit bce3ed7e9fc75b4c2e6b1971919a801f73ef6a0a
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Mon Mar 17 15:09:55 2014 +0000

    BUGFIX: Fix pointer access to FOF properties data

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/unify-nbody-cosmotools-halofinder@1923 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit ddf91ec0d8431e84ba0da0236d526766d31dd8cd
Merge: fe42683 a892674
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Sat Mar 15 20:45:07 2014 +0000

    Merge branch 'master' into unify-nbody-cosmotools-halofinder

    Conflicts:
    	nbody/cpu/Makefile

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/unify-nbody-cosmotools-halofinder@1922 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit fe42683940405854be5e0ecbd625f599a68a3501
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Sat Mar 15 20:40:15 2014 +0000

    ENH: Simplify code

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/unify-nbody-cosmotools-halofinder@1921 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit 250195d1a478fd7fabe074a64f8247a1d21094bb
Merge: babb39a 0667f22
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Fri Mar 14 14:43:12 2014 +0000

    Merge branch 'master' into unify-nbody-cosmotools-halofinder

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/unify-nbody-cosmotools-halofinder@1919 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit babb39ad66dc778850e3cf539d8d12903104064d
Merge: 8ed32b3 8c4047d
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Thu Mar 13 23:34:55 2014 +0000

    Merge branch 'master' into unify-nbody-cosmotools-halofinder

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/unify-nbody-cosmotools-halofinder@1916 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit 8ed32b386f5f78b5a2bf08d994bcede94eb6de6e
Merge: 3e9fb32 61e7a3a
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Wed Mar 12 20:53:48 2014 +0000

    Merge branch 'master' into unify-nbody-cosmotools-halofinder

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/unify-nbody-cosmotools-halofinder@1913 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit 3e9fb32fb2d07f7122a1885e808e467e7877bebc
Merge: 163f750 11c7223
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Mon Mar 3 16:53:14 2014 +0000

    Merge branch 'master' into unify-nbody-cosmotools-halofinder

    Conflicts:
    	nbody/halo_finder/Makefile

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/unify-nbody-cosmotools-halofinder@1889 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit 163f75058bc8a9a710f5ae05cf10348d7fe14623
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Tue Feb 18 16:55:24 2014 +0000

    ENH: Minor modifications to output reporting

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/unify-nbody-cosmotools-halofinder@1873 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit ecea6aa04768ad1c8805011b0abc26f3268d2a2c
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Tue Feb 18 01:55:13 2014 +0000

    BUGFIX: Fix clearSerial in call to collectHalos()

    Fixed issue wherein the code would clear the serial
    halofinder data-structures after calling collectHalos()
    eventhough, GenerateOutput() and ENABLE_PARTICLE_OUTPUS
    is true. When these flags are true, writeTaggedParticles()
    is called, which needs the serial halofinder data-structures.
    The code would SIGSEGV, since these data-structures were NULL.
    Fixed that.

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/unify-nbody-cosmotools-halofinder@1872 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit 309ad3ff39a0ed12acef194764d37f08c43ed6e9
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Tue Feb 18 01:55:11 2014 +0000

    BUGFIX: Stepping through parallel breakpoints.

    Ensure we flush std::cin, by calling "ignore()", so that
    we can step through multiple parallel breakpoints.

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/unify-nbody-cosmotools-halofinder@1871 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit b59a381e7a2b3bd94bc685e93bc8c7d5d8b28b8b
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Tue Feb 18 01:55:08 2014 +0000

    ENH: Read key-value pair followed by a comment.

    This commits modifies the cosmotools-config parser, such that,
    it can read lines consisting of key-value pairs, followed by
    a comment.

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/unify-nbody-cosmotools-halofinder@1870 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit e7dd35ad00d009d7f56a2b9372b65f3d91b876c7
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Sun Feb 16 22:32:06 2014 +0000

    ENH: config-driven output of center-of-mass vars

    This commit adds parameters to control whether the center-of-mass
    variables will be written out when generating FOF, SOD and
    subhalo summaries respectively. Previously, this was controlled
    via an #ifdef, which would require re-compiling the code.

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/unify-nbody-cosmotools-halofinder@1868 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit d02bee10a8f1a0d0faa6e7c343e0cadc6f29979d
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Sun Feb 16 22:32:03 2014 +0000

    ENH: Update CosmoTools in situ halofinder wrapper

    This commit updates the CosmoTools in situ wrapper to use the latest
    halofinder. This implementation is based on the HaloFinderInSitu
    code from "hacc/nbody/simulation" and it implements all the parameters
    therein, including support for center-finding, SOD halo finding and
    sub-halo finding.

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/unify-nbody-cosmotools-halofinder@1867 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit 081b661569d28fea71e466b990d92812fece8c10
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Sun Feb 16 22:32:01 2014 +0000

    ENH: Add sim parameters needed by center finder.

    This commit adds the hubble, omega_matter and omega_cb
    to the CosmoTools simulation parameters object, which are
    needed by the center finder. Further, it modifies the CosmoTools
    interface accordingly to propagate these parameters from
    the simulation. Last, cosmotools-driver is updated to reflect
    these changes -- it now extracts more parameters from the
    supplied indat.params file and computes omega_matter and
    omega_cb using the same logic as in "nbody/initializer/BaseData.h".

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/unify-nbody-cosmotools-halofinder@1866 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit 087684b574c1ab1b9143d4cca589b50c0fe36fee
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Sun Feb 16 22:31:55 2014 +0000

    COMP: Fix pointer arithmetic on void*.

    Cast void* to unsigned char* before doing any pointer arithmetic.

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/unify-nbody-cosmotools-halofinder@1865 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit fb8c0bc49719e0b6ec150828545284fba50c1408
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Tue Feb 11 21:05:04 2014 +0000

    COMP: Build halofinder programs

    This commit adds the ability to build halofinder executables
    using both the cmake-based and raw-makefile builds.

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/unify-nbody-cosmotools-halofinder@1864 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit ba08646c46d1e95166a11e3721c3638153a1e3a2
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Tue Feb 11 21:05:01 2014 +0000

    ENH: Use bigchunk from nbody/halo_finder

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/unify-nbody-cosmotools-halofinder@1863 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit 43058a87670526a86e835e89bb0d776ae96e72bc
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Tue Feb 11 21:04:59 2014 +0000

    ENH: Move halofinder programs into a programs dir

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/unify-nbody-cosmotools-halofinder@1862 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit 0014cb35b5629644c41f9ed73227f5c0187f635d
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Mon Feb 10 19:49:25 2014 +0000

    STYLE: Make bold font work on iTerm2

    Apparently, there are different flavors of "echo" that
    work somewhat differently. The raw Makefile build reports
    a counter and the code that is being compiled in bold font.
    That did not work on iTerm2, which is annoying. This change
    fixes that so that it works on both linux and OS X.

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/unify-nbody-cosmotools-halofinder@1861 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit 471affebec97269a5130c961d521b695455fda3c
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Mon Feb 10 19:49:23 2014 +0000

    ENH: Removed dead VTK code from nbody/halo_finder

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/unify-nbody-cosmotools-halofinder@1860 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit a35ac08d18ca8152762ba8b8b33169dec0fded63
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Mon Feb 10 19:49:21 2014 +0000

    ENH: Remove ifdef USE_VTK_COSMO

    This commit removes the ifdef USE_VTK_COSMO. This is no longer
    needed since this code does not build within ParaView/VTK.
    Instead, ParaView links to the static cosmotools library that
    is used to build CosmoTools VTK wrappers for filters and readers.

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/unify-nbody-cosmotools-halofinder@1859 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit a55e4953985ddc3be655dea3c6451499c1bbcb2a
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Mon Feb 10 19:49:16 2014 +0000

    COMP: Compile 'hacc/nbody' after moving halofinder

    This commit fixes hacc/nbody s.t. it compiles after moving
    the halofinder code into the hacc/cosmotools module.

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/unify-nbody-cosmotools-halofinder@1858 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit acaecf20cb2dd1fb19f3229d81f4dc98c134c8dd
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Mon Feb 10 19:49:12 2014 +0000

    COMP: fix nbody/initializer typedef collision

    This commit fixes a typedef collision on the "INTEGER" type between
    the 'nbody/initializer' typedefs and 'CosmoToolsDefinitions'.
    'nbody/initializer' now uses "INTTYPE" instead of "INTEGER".

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/unify-nbody-cosmotools-halofinder@1857 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit 4067a2d0e542e6b55b04468983d07e322e0c4961
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Mon Feb 10 19:49:09 2014 +0000

    COMP: Comment out older API calls to halofinder.

    This commit comments out older API calls to the
    halofinder, made from the CosmoTools in situ wrapper,
    LANLHaloFinderInSituAlgorithm. This is a temporary fix
    to get the code to compile. Soon, this implementation
    will employ HaloFinderInSitu class for interfacing with
    the halofinder, which will completely change the implementation
    of this class.

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/unify-nbody-cosmotools-halofinder@1856 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit 913db9698da40ed6eeda1770d0ccdaf33a814da1
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Mon Feb 10 19:49:06 2014 +0000

    ENH: Move SubHaloTest to testing directory

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/unify-nbody-cosmotools-halofinder@1855 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit cbdd7b0580e314c23ff3fe54c2af4862599f8a50
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Mon Feb 10 19:49:04 2014 +0000

    COMP: move dims-local-init to cosmotools

    Moved dims-local-init to cosmotools b/c it is needed by
    HaloTestP.

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/unify-nbody-cosmotools-halofinder@1854 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit 9d6d105ed4575b528eafabc59dc8da5e6c3b7ec4
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Mon Feb 10 19:49:01 2014 +0000

    COMP: Compile halofinder code within cosmotools.

    Changes to get the newly imported halofinder compiling within
    cosmotools again.

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/unify-nbody-cosmotools-halofinder@1853 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit acb3827994be62e49363cd0bbaf53b5ba82c0f20
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Mon Feb 10 19:48:55 2014 +0000

    COMP: Fix compilation issues with HaloFinder.cxx

    HaloFinder.cxx was not using correctly the current API of
    HaloCenterFinder::setParameters and HaloFinder::HistCenterFinding
    was calling HaloCenterFinder::mostBoundParticleN2 and
    HaloCenterFinder::mostBoundParticleAStar with minPotential as
    a parameter that was never passed in to the function. Fixed that.

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/unify-nbody-cosmotools-halofinder@1852 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit a487884de5d16a8f97621215357abf2d7d9a860e
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Mon Feb 10 19:48:53 2014 +0000

    ENH: Remove some dead code from blosc.

    Removed dead code -- this code is now part of the genericio module.

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/unify-nbody-cosmotools-halofinder@1851 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit 316e0f1e8239635d44dd078a6d6ba09589ba36c9
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Mon Feb 10 19:48:50 2014 +0000

    ENH: Move halofinder from nbody to cosmotools

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/unify-nbody-cosmotools-halofinder@1850 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit 267e000c07a154dab4ae31cb543a553667328729
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Mon Feb 10 19:48:40 2014 +0000

    ENH: rm legacy codes from cosmotools/halofinder.

    Remove legacy applications for redistributing
    cosmo files. These exist in nbody/halo_finder.

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/unify-nbody-cosmotools-halofinder@1849 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit e433f2bd78786d039538acec61ce1bea71c0f6a9
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Mon Feb 10 19:48:38 2014 +0000

    ENH: Remove winDirent.h

    Removed useless winDirent header file -- We don't compile/run
    on weird platforms like windows.

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/unify-nbody-cosmotools-halofinder@1848 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit 8b01318a67640f4603495304c7c53add9a14ab7c
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Mon Feb 10 19:48:36 2014 +0000

    ENH: Remove VTK classes/filters from hacc/nbody.

    Removed VTK classes/filters from hacc/nbody. Updated and
    improved versions of these codes exist within the ParaView
    source tree, which links against CosmoTools.

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/unify-nbody-cosmotools-halofinder@1847 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit 4ece383b140cdde63766f5ffeac160711935b9b2
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Mon Feb 10 19:48:33 2014 +0000

    ENH: Remove hf-redistributable from hacc/nbody.

    This commit removes the hf-redistributable directory
    from hacc/nbody. The halofinder will be re-distributable
    with cosmotools.

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/unify-nbody-cosmotools-halofinder@1846 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit 9877e39e755df105f80e3989d572ac20ffa1ceff
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Mon Feb 10 19:48:29 2014 +0000

    ENH: Fix `git svn-checkout <branch>` alias

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/unify-nbody-cosmotools-halofinder@1845 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit a4d05c8af136739d24206accfd8b15f3684829d3
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Fri Feb 7 13:49:42 2014 +0000

    Creating branch:unify-nbody-cosmotools-halofinder

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/unify-nbody-cosmotools-halofinder@1830 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

From: George Zagaris <george.zagaris@kitware.com>

git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/trunk/cosmotools@1979 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf
Merge branch 'svn/trunk'
ENH: Remove old & not needed  mergertree code
ENH: Remove old & not needed  mergertree code

From: George Zagaris <george.zagaris@kitware.com>

git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/trunk/cosmotools@1982 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf
Merge branch 'svn/trunk'
COMP: Add cmake option to enable OpenMP
COMP: Build sim interface and programs by default
ENH: Stream & density field openmp parallelization

This commit adds basic threading of the multi-stream and
density field calculation using openmp. This yields a
~2x speedup for this step, but performance can be improved
further with a bit more work.