Revision 1874 - (view) (annotate) - [select for diffs]
Modified Wed May 15 15:09:35 2013 UTC (11 years, 11 months ago) by gezelter
File length: 75117 byte(s)
Diff to previous 1868 , to selected 1629

Fixed a bunch of cppcheck warnings.

CLearing out some memory leaks

Revision 1867 - (view) (annotate) - [select for diffs]
Modified Mon Apr 29 17:53:48 2013 UTC (12 years ago) by gezelter
File length: 74787 byte(s)
Diff to previous 1866 , to selected 1629

Attempt to fix memory leak in Multiple hull calls

Fixes for Qhull static build strangeness

Revision 1861 - (view) (annotate) - [select for diffs]
Modified Tue Apr 9 19:45:54 2013 UTC (12 years ago) by gezelter
File length: 74741 byte(s)
Diff to previous 1856 , to selected 1629

Added a Harmonic Torsion Type, fixed some bugs in RNEMD and waterReplacer.

Bug fixes to get new parallel decomposition methods working without periodic boundary conditions.  
Updated volume in stats file correctly.
LangevinHull fixes for low viscosity values.

Revision 1855 - (view) (annotate) - [select for diffs]
Modified Tue Apr 2 18:31:51 2013 UTC (12 years, 1 month ago) by gezelter
File length: 73219 byte(s)
Diff to previous 1854 , to selected 1629

Fixed a bunch of bugs in CubicSpline debug sections, ForceMatrix Decomp 
computing costhetas for non-existent rotation matrices, Hidden accumulator counts, and SMIPD non-coupling

First pass at angular momentum aware version of VSS-RNEMD.

Revision 1850 - (view) (annotate) - [select for diffs]
Modified Wed Feb 20 15:39:39 2013 UTC (12 years, 2 months ago) by gezelter
File length: 56550 byte(s)
Diff to previous 1830 , to selected 1629

Fixed a widespread typo in the license 

Windows compilation fixes

Revision 1813 - (view) (annotate) - [select for diffs]
Modified Fri Nov 16 21:39:55 2012 UTC (12 years, 5 months ago) by gezelter
File length: 56529 byte(s)
Diff to previous 1812 , to selected 1629

Forgot to merge some important accumulator changes

MERGE OpenMD trunk changes 1803:1811 into development branch

Revision 1803 - (view) (annotate) - [select for diffs]
Modified Wed Oct 3 14:20:07 2012 UTC (12 years, 6 months ago) by gezelter
File length: 56472 byte(s)
Diff to previous 1777 , to selected 1629

Merging trunk changes back to development branch

Various fixes for the RNEMD output.

Revision 1776 - (view) (annotate) - [select for diffs]
Modified Thu Aug 9 15:52:59 2012 UTC (12 years, 8 months ago) by gezelter
File length: 56503 byte(s)
Diff to previous 1775 , to selected 1629

Fixes to mdParser to handle vector assignments, fixes for VelocityVerletIntegrator deleting rnemd_ when it doesn't exist yet.

Tracking down a strange bug report.   Fixing some output. Fixing some samples.

Revision 1774 - (view) (annotate) - [select for diffs]
Modified Wed Aug 8 16:03:02 2012 UTC (12 years, 8 months ago) by gezelter
File length: 56094 byte(s)
Diff to previous 1773 , to selected 1629

Cleaning up RNEMD log, adding XY area to Snapshot

Adding new RNEMD options and output file format

Revision 1769 - (view) (annotate) - [select for diffs]
Modified Mon Jul 9 14:15:52 2012 UTC (12 years, 9 months ago) by gezelter
File length: 52767 byte(s)
Diff to previous 1764 , to selected 1629

Code readability updates.

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

Revision 1731 - (view) (annotate) - [select for diffs]
Modified Thu May 31 12:25:30 2012 UTC (12 years, 11 months ago) by gezelter
File length: 52934 byte(s)
Copied from: branches/development/src/integrators/RNEMD.cpp revision 1730
Diff to previous 1728 , to selected 1629

Reorganized source directories, added RNEMD and flucQ blocks for
options parsing.

resolved

Revision 1723 - (view) (annotate) - [select for diffs]
Modified Thu May 24 20:59:54 2012 UTC (12 years, 11 months ago) by gezelter
Original Path: branches/development/src/integrators/RNEMD.cpp
File length: 49500 byte(s)
Diff to previous 1722 , to selected 1629

Bug fixes for heat flux import

Merging Shenyu's RNEMD changes from openmd-1 into the development branch.

Revision 1665 - (view) (annotate) - [select for diffs]
Modified Tue Nov 22 20:38:56 2011 UTC (13 years, 5 months ago) by gezelter
Original Path: branches/development/src/integrators/RNEMD.cpp
File length: 36168 byte(s)
Diff to previous 1629

updated copyright notices

Merging changes from old branch into development branch

Revision 1627 - (view) (annotate) - [select for diffs]
Modified Tue Sep 13 22:05:04 2011 UTC (13 years, 7 months ago) by gezelter
Original Path: branches/development/src/integrators/RNEMD.cpp
File length: 33271 byte(s)
Diff to previous 1465 , to selected 1629

Splitting out ifstrstream into a header and an implementation.  This
means that much of the code that depends on it can be compiled only
once and the parallel I/O is concentrated into a few files.  To do
this, a number of files that relied on basic_ifstrstream to load the
mpi header had to be modified to manage their own headers.

Creating busticated version of OpenMD

Revision 1442 - (view) (annotate) - [select for diffs]
Modified Mon May 10 17:28:26 2010 UTC (14 years, 11 months ago) by gezelter
Original Path: trunk/src/integrators/RNEMD.cpp
File length: 33254 byte(s)
Diff to previous 1396 , to selected 1629

Adding property set to svn entries

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

Revision 1390 - (view) (annotate) - [select for diffs]
Modified Wed Nov 25 20:02:06 2009 UTC (15 years, 5 months ago) by gezelter
Original Path: trunk/src/integrators/RNEMD.cpp
File length: 32066 byte(s)
Diff to previous 1368 , to selected 1629

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

added RNEMD scaling

Revision 1350 - (view) (annotate) - [select for diffs]
Modified Thu May 21 18:56:45 2009 UTC (15 years, 11 months ago) by gezelter
Original Path: trunk/src/integrators/RNEMD.cpp
File length: 17543 byte(s)
Diff to previous 1341 , to selected 1629

Parallel version of RNEMD

Bug fixes and sanity checks for RNEMD (nBins should be even), check to make
sure we aren't selecting inappropriate numbers of integrable Objects

Revision 1339 - (view) (annotate) - [select for diffs]
Modified Thu Apr 23 18:31:05 2009 UTC (16 years ago) by gezelter
Original Path: trunk/src/integrators/RNEMD.cpp
File length: 12603 byte(s)
Diff to previous 1338 , to selected 1629

bug fix in DLM, added temperature profiles and uniform bins to RNEMD

Added a getStatus routine to check the temperatures

Revision 1334 - (view) (annotate) - [select for diffs]
Modified Thu Apr 2 19:55:37 2009 UTC (16 years, 1 month ago) by gezelter
Original Path: trunk/src/integrators/RNEMD.cpp
File length: 7723 byte(s)
Diff to previous 1333 , to selected 1629

Bug fix

Debugging, but still unstable

Revision 1332 - (view) (annotate) - [select for diffs]
Modified Thu Apr 2 17:25:59 2009 UTC (16 years, 1 month ago) by gezelter
Original Path: trunk/src/integrators/RNEMD.cpp
File length: 7407 byte(s)
Diff to previous 1331 , to selected 1629

fixed some bugs, added some logic to sort stuntdoubles

Adding options to RNEMD for selecting particular StuntDoubles

Revision 1330 - (view) (annotate) - [select for diffs]
Modified Thu Mar 19 21:03:36 2009 UTC (16 years, 1 month ago) by skuang
Original Path: trunk/src/integrators/RNEMD.cpp
File length: 3879 byte(s)
Diff to previous 1329 , to selected 1629

Added handlers to Integrator to call RNEMD at the right times.  Added initialization
to RNEMD to make sure values from the MD file are available.

Adding RNEMD