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Revision 1877 - Directory Listing - [select for diffs]
Modified Thu Jun 6 15:43:35 2013 UTC (12 years, 1 month ago) by gezelter
Diff to previous 1875
New electrostatic method, starting to do some performance tuning.

Revision 1875 - Directory Listing - [select for diffs]
Modified Fri May 17 14:41:42 2013 UTC (12 years, 1 month ago) by gezelter
Diff to previous 1874
Fixed a bunch of stylistic and performance issues discovered via cppcheck.

Revision 1874 - Directory Listing - [select for diffs]
Modified Wed May 15 15:09:35 2013 UTC (12 years, 1 month ago) by gezelter
Diff to previous 1869
Fixed a bunch of cppcheck warnings.

Revision 1869 - Directory Listing - [select for diffs]
Modified Tue Apr 30 17:03:03 2013 UTC (12 years, 2 months ago) by gezelter
Diff to previous 1868
Fixed a de-allocation problem in Sutton Chen

Revision 1868 - Directory Listing - [select for diffs]
Modified Tue Apr 30 15:56:54 2013 UTC (12 years, 2 months ago) by gezelter
Diff to previous 1850
CLearing out some memory leaks

Revision 1850 - Directory Listing - [select for diffs]
Modified Wed Feb 20 15:39:39 2013 UTC (12 years, 4 months ago) by gezelter
Diff to previous 1842
Fixed a widespread typo in the license 

Revision 1842 - Directory Listing - [select for diffs]
Modified Tue Jan 29 19:10:04 2013 UTC (12 years, 5 months ago) by gezelter
Diff to previous 1840
Only compute field for sites not excluded from the pairwise electrostatic contribution.
Also, now compute the mean field felt by the sites in a rigid body, and report that as
the rigid body's field.

Revision 1840 - Directory Listing - [select for diffs]
Modified Mon Jan 28 15:44:32 2013 UTC (12 years, 5 months ago) by gezelter
Diff to previous 1833
Merging trunk changes back to development branch

Revision 1833 - Directory Listing - [select for diffs]
Modified Tue Jan 15 16:28:22 2013 UTC (12 years, 5 months ago) by gezelter
Diff to previous 1826
Bug fix in Sticky potential, column label in stats

Revision 1826 - Directory Listing - [select for diffs]
Modified Wed Jan 9 19:41:48 2013 UTC (12 years, 5 months ago) by gezelter
Diff to previous 1825
Cleaning more cruft and unused variables.

Revision 1825 - Directory Listing - [select for diffs]
Modified Wed Jan 9 19:27:52 2013 UTC (12 years, 5 months ago) by gezelter
Diff to previous 1823
Deleting unused variables

Revision 1823 - Directory Listing - [select for diffs]
Modified Tue Jan 8 21:02:27 2013 UTC (12 years, 5 months ago) by gezelter
Diff to previous 1822
Fixed  a bug

Revision 1822 - Directory Listing - [select for diffs]
Modified Tue Jan 8 15:29:03 2013 UTC (12 years, 5 months ago) by gezelter
Diff to previous 1821
Performance boosts, cleaning up debugging cruft

Revision 1821 - Directory Listing - [select for diffs]
Modified Mon Jan 7 20:05:43 2013 UTC (12 years, 6 months ago) by gezelter
Diff to previous 1820
Fixed a bug in Matrix-Matrix cross product

Revision 1820 - Directory Listing - [select for diffs]
Modified Tue Dec 18 16:23:13 2012 UTC (12 years, 6 months ago) by gezelter
Diff to previous 1814
New electrostatic bug fixes.

Revision 1814 - Directory Listing - [select for diffs]
Modified Tue Nov 27 21:13:48 2012 UTC (12 years, 7 months ago) by gezelter
Diff to previous 1808
Fixed some torque bugs (I think), added a unit vector for Quadrupolar atoms.

Revision 1808 - Directory Listing - [select for diffs]
Modified Mon Oct 22 20:42:10 2012 UTC (12 years, 8 months ago) by gezelter
Diff to previous 1787
A bug fix in the electric field for the new electrostatic code.  Also comment fixes for Doxygen 

Revision 1787 - Directory Listing - [select for diffs]
Modified Wed Aug 29 18:13:11 2012 UTC (12 years, 10 months ago) by gezelter
Diff to previous 1767
Massive multipole rewrite

Revision 1767 - Directory Listing - [select for diffs]
Modified Fri Jul 6 22:01:58 2012 UTC (13 years ago) by gezelter
Diff to previous 1766
Various fixes required to compile OpenMD with the MS Visual C++ compiler

Revision 1766 - Directory Listing - [select for diffs]
Modified Thu Jul 5 17:08:25 2012 UTC (13 years ago) by gezelter
Diff to previous 1761
Added Fluctuating Charge Langevin propagator, and made it the default
fixed some errors on the one-center slater coulomb integrals, and some
parameters in PhysicalConstants.


Revision 1761 - Directory Listing - [select for diffs]
Modified Fri Jun 22 20:01:37 2012 UTC (13 years ago) by gezelter
Diff to previous 1760
fixes for fluctuating charges

Revision 1760 - Directory Listing - [select for diffs]
Modified Thu Jun 21 19:26:46 2012 UTC (13 years ago) by gezelter
Diff to previous 1756
Some bugfixes (CholeskyDecomposition), more work on fluctuating charges,
migrating stats stuff into frameData

Revision 1756 - Directory Listing - [select for diffs]
Modified Mon Jun 18 18:23:20 2012 UTC (13 years ago) by gezelter
Diff to previous 1755
bugfixes for self interactions (particularly in parallel)

Revision 1755 - Directory Listing - [select for diffs]
Modified Thu Jun 14 01:58:35 2012 UTC (13 years ago) by gezelter
Diff to previous 1750
general bugfixes

Revision 1750 - Directory Listing - [select for diffs]
Modified Thu Jun 7 12:53:46 2012 UTC (13 years, 1 month ago) by gezelter
Diff to previous 1749
Fixing some bugs in optimization, fixing status functions so that they
dump correctly (although some things are deferred until the Stats is
accumulator-based).

Revision 1749 - Directory Listing - [select for diffs]
Modified Thu Jun 7 02:47:21 2012 UTC (13 years, 1 month ago) by gezelter
Diff to previous 1734
fixed an uninitialized option bug, fixed gcc 4.6 compilation problems

Revision 1734 - Directory Listing - [select for diffs]
Modified Tue Jun 5 17:49:36 2012 UTC (13 years, 1 month ago) by jmichalk
Diff to previous 1730
Fixed the Slater overlap integral code, added dVdFq to the self interaction.

Revision 1730 - Directory Listing - [select for diffs]
Modified Wed May 30 17:19:13 2012 UTC (13 years, 1 month ago) by gezelter
Diff to previous 1725
Fixed compilation issues

Revision 1725 - Directory Listing - [select for diffs]
Modified Sat May 26 18:13:43 2012 UTC (13 years, 1 month ago) by gezelter
Diff to previous 1723
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.  


Revision 1723 - Directory Listing - [select for diffs]
Modified Thu May 24 20:59:54 2012 UTC (13 years, 1 month ago) by gezelter
Diff to previous 1721
Bug fixes for heat flux import

Revision 1721 - Directory Listing - [select for diffs]
Modified Thu May 24 14:17:42 2012 UTC (13 years, 1 month ago) by gezelter
Diff to previous 1720
Fixing some bugs

Revision 1720 - Directory Listing - [select for diffs]
Modified Thu May 24 01:48:29 2012 UTC (13 years, 1 month ago) by gezelter
Diff to previous 1718
Fixed a few bugs in that last commit

Revision 1718 - Directory Listing - [select for diffs]
Modified Thu May 24 01:29:59 2012 UTC (13 years, 1 month ago) by gezelter
Diff to previous 1711
Adding fluctuating charges, still a work in progress

Revision 1711 - Directory Listing - [select for diffs]
Modified Sat May 19 02:58:35 2012 UTC (13 years, 1 month ago) by gezelter
Diff to previous 1710
Some fixes for DataStorage issues.  Removed outdated zangle stuff that
has been replaced by the more modern restraints.

Revision 1710 - Directory Listing - [select for diffs]
Modified Fri May 18 21:44:02 2012 UTC (13 years, 1 month ago) by gezelter
Diff to previous 1688
Added an adapter layer between the AtomType and the rest of the code to 
handle the bolt-on capabilities of new types. 

Fixed a long-standing bug in how storageLayout was being set to the maximum
possible value.

Started to add infrastructure for Polarizable and fluc-Q calculations.

Revision 1688 - Directory Listing - [select for diffs]
Modified Wed Mar 14 17:56:01 2012 UTC (13 years, 3 months ago) by gezelter
Diff to previous 1686
Bug fixes for GB.  Now using strength parameter mixing ideas from Wu
et al. [J. Chem. Phys. 135, 155104 (2011)].  This helps get the
dissimilar particle mixing behavior to be the same whichever order the
two particles come in.  This does require that the force field file to
specify explicitly the values for epsilon in the cross (X), side-by-side (S), 
and end-to-end (E) configurations.


Revision 1686 - Directory Listing - [select for diffs]
Modified Sat Mar 10 04:21:44 2012 UTC (13 years, 3 months ago) by gezelter
Diff to previous 1683
Fixes for compilation under LLVM compiler
Bug-fix for switching function in Gay-Berne

Revision 1683 - Directory Listing - [select for diffs]
Modified Wed Feb 29 20:33:01 2012 UTC (13 years, 4 months ago) by jmichalk
Diff to previous 1674
LJ.cpp has been updated to more correctly deal with nonbonded interactions
(i.e. explicit interactions where the species are not necessarily defined
to be lennardJones type atoms)

Revision 1674 - Directory Listing - [select for diffs]
Modified Thu Feb 16 15:59:20 2012 UTC (13 years, 4 months ago) by gezelter
Diff to previous 1668
Fixed two bugs in new Gay-Berne module.  Torque 2 had a sign error, and there
was a subtle mixing bug for dissimilar particles in different orderings.

Revision 1668 - Directory Listing - [select for diffs]
Modified Fri Jan 6 19:03:05 2012 UTC (13 years, 6 months ago) by gezelter
Diff to previous 1665
Some fixes for CMake and single precision builds

Revision 1665 - Directory Listing - [select for diffs]
Modified Tue Nov 22 20:38:56 2011 UTC (13 years, 7 months ago) by gezelter
Diff to previous 1664
updated copyright notices

Revision 1664 - Directory Listing - [select for diffs]
Modified Tue Nov 22 14:37:41 2011 UTC (13 years, 7 months ago) by gezelter
Diff to previous 1656
Modified some of the nonbonded interactions and types

Revision 1656 - Directory Listing - [select for diffs]
Modified Tue Oct 11 19:46:51 2011 UTC (13 years, 8 months ago) by jmichalk
Diff to previous 1653
First few fixes for explicit interactions.

Revision 1653 - Directory Listing - [select for diffs]
Modified Wed Sep 28 19:37:06 2011 UTC (13 years, 9 months ago) by gezelter
Diff to previous 1647
fixing compilation bugs on gcc-4.4

Revision 1647 - Directory Listing - [select for diffs]
Modified Mon Sep 26 21:20:11 2011 UTC (13 years, 9 months ago) by gezelter
Diff to previous 1635
fixing the build system

Revision 1635 - Directory Listing - [select for diffs]
Modified Thu Sep 15 16:24:03 2011 UTC (13 years, 9 months ago) by gezelter
Diff to previous 1629
cleaning up the development branch a bit, removing cruft, etc.

Revision 1629 - Directory Listing - [select for diffs]
Modified Wed Sep 14 21:15:17 2011 UTC (13 years, 9 months ago) by gezelter
Diff to previous 1624
Merging changes from old branch into development branch

Revision 1624 - Directory Listing - [select for diffs]
Modified Tue Sep 13 14:12:54 2011 UTC (13 years, 9 months ago) by gezelter
Diff to previous 1616
Adding RepulsivePower interaction to the development branch

Revision 1616 - Directory Listing - [select for diffs]
Modified Tue Aug 30 15:45:35 2011 UTC (13 years, 10 months ago) by gezelter
Diff to previous 1613
Fixing cutoff groups

Revision 1613 - Directory Listing - [select for diffs]
Modified Thu Aug 18 20:18:19 2011 UTC (13 years, 10 months ago) by gezelter
Diff to previous 1601
Fixed a parallel bug in computing exclude lists.
Added file versioning information in MD files.
Still tracking down cutoff group bugs.

Revision 1601 - Directory Listing - [select for diffs]
Modified Thu Aug 4 20:04:35 2011 UTC (13 years, 11 months ago) by gezelter
Diff to previous 1587
removed spurious prints, fixed one bug, but there's still a parallel problem

Revision 1587 - Directory Listing - [select for diffs]
Modified Fri Jul 8 20:25:32 2011 UTC (14 years ago) by gezelter
Diff to previous 1586
Fixes

Revision 1586 - Directory Listing - [select for diffs]
Modified Tue Jun 21 06:34:35 2011 UTC (14 years ago) by gezelter
Diff to previous 1584
bug fixes

Revision 1584 - Directory Listing - [select for diffs]
Modified Fri Jun 17 20:16:35 2011 UTC (14 years ago) by gezelter
Diff to previous 1583
bug fixes.

Revision 1583 - Directory Listing - [select for diffs]
Modified Thu Jun 16 22:00:08 2011 UTC (14 years ago) by gezelter
Diff to previous 1582
Bug squashing

Revision 1582 - Directory Listing - [select for diffs]
Modified Tue Jun 14 20:41:44 2011 UTC (14 years ago) by gezelter
Diff to previous 1581
Well, the potential energy values are still garbage, but the LJ sample
runs.

Revision 1581 - Directory Listing - [select for diffs]
Modified Mon Jun 13 22:13:12 2011 UTC (14 years ago) by gezelter
Diff to previous 1579
bug fixes

Revision 1579 - Directory Listing - [select for diffs]
Modified Thu Jun 9 20:26:29 2011 UTC (14 years, 1 month ago) by gezelter
Diff to previous 1576
bug fixes (not done yet)

Revision 1576 - Directory Listing - [select for diffs]
Modified Wed Jun 8 16:05:07 2011 UTC (14 years, 1 month ago) by gezelter
Diff to previous 1575
migrating cutoff information from InteractionManager to ForceManager

Revision 1575 - Directory Listing - [select for diffs]
Modified Fri Jun 3 21:39:49 2011 UTC (14 years, 1 month ago) by gezelter
Diff to previous 1571
more parallel fixes

Revision 1571 - Directory Listing - [select for diffs]
Modified Fri May 27 16:45:44 2011 UTC (14 years, 1 month ago) by gezelter
Diff to previous 1568
Added Atypes to new C++ force decomposition.

Revision 1568 - Directory Listing - [select for diffs]
Modified Wed May 25 16:20:37 2011 UTC (14 years, 1 month ago) by gezelter
Diff to previous 1554
Added neighbor list check, and migrated skinThickness into
ForceDecomposition (and out of the InteractionManager).  Removed a
spurious inline.


Revision 1554 - Directory Listing - [select for diffs]
Modified Sat Apr 30 02:54:02 2011 UTC (14 years, 2 months ago) by gezelter
Diff to previous 1550
For efficiency, pointers instead of objects will be passed during main
force loop. 


Revision 1550 - Directory Listing - [select for diffs]
Modified Wed Apr 27 21:49:59 2011 UTC (14 years, 2 months ago) by gezelter
Diff to previous 1549
more fortran removal

Revision 1549 - Directory Listing - [select for diffs]
Modified Wed Apr 27 18:38:15 2011 UTC (14 years, 2 months ago) by gezelter
Diff to previous 1545
a few more tweaks   We're getting somewhat closer to deleting fortran.

Revision 1545 - Directory Listing - [select for diffs]
Modified Fri Apr 8 21:25:19 2011 UTC (14 years, 3 months ago) by gezelter
Diff to previous 1544
still busted, but much progress

Revision 1544 - Directory Listing - [select for diffs]
Modified Fri Mar 18 19:31:52 2011 UTC (14 years, 3 months ago) by gezelter
Diff to previous 1537
More modifications for paralllel rewrite

Revision 1537 - Directory Listing - [select for diffs]
Modified Thu Jan 6 17:42:20 2011 UTC (14 years, 6 months ago) by gezelter
Diff to previous 1536
forgot one method

Revision 1536 - Directory Listing - [select for diffs]
Modified Wed Jan 5 14:49:05 2011 UTC (14 years, 6 months ago) by gezelter
Diff to previous 1535
compiles, builds and runs, but is very slow

Revision 1535 - Directory Listing - [select for diffs]
Modified Fri Dec 31 18:31:56 2010 UTC (14 years, 6 months ago) by gezelter
Diff to previous 1532
Well, it compiles and builds, but still has a bus error at runtime.

Revision 1532 - Directory Listing - [select for diffs]
Modified Wed Dec 29 19:59:21 2010 UTC (14 years, 6 months ago) by gezelter
Diff to previous 1530
Added MAW to the C++ side, removed a whole bunch more fortran. 

Revision 1530 - Directory Listing - [select for diffs]
Modified Tue Dec 28 21:47:55 2010 UTC (14 years, 6 months ago) by gezelter
Diff to previous 1529
Moved switching functions and force options over to the C++ side, and
removed them from Fortran.

Revision 1529 - Directory Listing - [select for diffs]
Modified Mon Dec 27 18:35:59 2010 UTC (14 years, 6 months ago) by gezelter
Diff to previous 1528
fixes

Revision 1528 - Directory Listing - [select for diffs]
Modified Fri Dec 17 20:11:05 2010 UTC (14 years, 6 months ago) by gezelter
Diff to previous 1505
Doesn't build yet, but getting much closer...


Revision 1505 - Directory Listing - [select for diffs]
Modified Sun Oct 3 22:18:59 2010 UTC (14 years, 9 months ago) by gezelter
Diff to previous 1504
Less busted than it was on last check-in, but still won't completely
build.


Revision 1504 - Directory Listing - [select for diffs]
Modified Sat Oct 2 20:41:53 2010 UTC (14 years, 9 months ago) by gezelter
Diff to previous 1502
The C++ side now compiles.  Moving on to doForces

Revision 1502 - Directory Listing - [select for diffs]
Modified Sat Oct 2 19:53:32 2010 UTC (14 years, 9 months ago) by gezelter
Diff to previous 1501
Many changes, and we're not quite done with this phase yet.

Revision 1501 - Directory Listing - [select for diffs]
Modified Wed Sep 15 19:32:10 2010 UTC (14 years, 9 months ago) by gezelter
Diff to previous 1489
Starting migration of Morse to C++

Revision 1489 - Directory Listing - [select for diffs]
Modified Tue Aug 10 18:34:59 2010 UTC (14 years, 10 months ago) by gezelter
Diff to previous 1485
Migrating Sutton-Chen from Fortran over to C++

Revision 1485 - Directory Listing - [select for diffs]
Modified Wed Jul 28 19:52:00 2010 UTC (14 years, 11 months ago) by gezelter
Diff to previous 1483
Converting Sticky over to C++

Revision 1483 - Directory Listing - [select for diffs]
Modified Tue Jul 27 21:17:31 2010 UTC (14 years, 11 months ago) by gezelter
Diff to previous 1482
Added GB module to the C++ side, got rid of it on the fortran side.

Revision 1482 - Directory Listing - [select for diffs]
Modified Tue Jul 27 14:55:15 2010 UTC (14 years, 11 months ago) by gezelter
Diff to previous 1481
Fixed a bug in EAM.  Seems to work now!

Revision 1481 - Directory Listing - [select for diffs]
Modified Mon Jul 26 21:55:18 2010 UTC (14 years, 11 months ago) by gezelter
Diff to previous 1480
fixed phi mixing

Revision 1480 - Directory Listing - [select for diffs]
Modified Mon Jul 26 19:50:53 2010 UTC (14 years, 11 months ago) by gezelter
Diff to previous 1479
no longer segfaults

Revision 1479 - Directory Listing - [select for diffs]
Modified Mon Jul 26 19:00:48 2010 UTC (14 years, 11 months ago) by gezelter
Diff to previous 1478
Added EAM.  Still segfaults but compiles.

Revision 1478 - Directory Listing - [select for diffs]
Modified Fri Jul 23 20:45:40 2010 UTC (14 years, 11 months ago) by gezelter
Diff to previous 1476
busticated EAM

Revision 1476 - Directory Listing - [select for diffs]
Modified Wed Jul 21 18:31:05 2010 UTC (14 years, 11 months ago) by gezelter
Diff to previous 1473
fixed some destructor bugs dealing with the TypeContainers

Revision 1473 - Directory Listing - [select for diffs]
Modified Tue Jul 20 15:43:00 2010 UTC (14 years, 11 months ago) by gezelter
Diff to previous 1472
fixing c/fortran bugs

Revision 1472 - Directory Listing - [select for diffs]
Modified Mon Jul 19 20:42:55 2010 UTC (14 years, 11 months ago) by gezelter
Diff to previous 1471
fixing calls

Revision 1471 - Directory Listing - [select for diffs]
Added Mon Jul 19 18:59:59 2010 UTC (14 years, 11 months ago) by gezelter
Added nonbonded directory.  Compiles, links, runs, but gives incorrect
answer.

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