fixed a bug in the temperature profile calculation

Revision 1941 - (view) (annotate) - [select for diffs]
Modified Tue Nov 5 16:49:04 2013 UTC (11 years, 5 months ago) by gezelter
File length: 76637 byte(s)
Diff to previous 1940

Fixing the angular momentum printout bug

Angular velocity fix in RNEMD

Revision 1938 - (view) (annotate) - [select for diffs]
Modified Thu Oct 31 15:32:17 2013 UTC (11 years, 6 months ago) by gezelter
File length: 76187 byte(s)
Diff to previous 1903

Some MPI include re-ordering to work with the Intel MPI implementation.

Test to see if we can eliminate a bug in MPI runs involving RNEMD.

Revision 1879 - (view) (annotate) - [select for diffs]
Modified Sun Jun 16 15:15:42 2013 UTC (11 years, 10 months ago) by gezelter
File length: 75700 byte(s)
Diff to previous 1804

MERGE OpenMD development 1783:1878 into trunk

Fixed a bug when the bins have no objects in them.

Revision 1801 - (view) (annotate) - [select for diffs]
Modified Mon Oct 1 18:21:15 2012 UTC (12 years, 7 months ago) by gezelter
File length: 56392 byte(s)
Diff to previous 1793

Some parallel fixes for "select all" selection scripts.  The distance finder
selection, e.g. "select within(4.0, Au)", still needs work, however.

Cleaning up some warning messages on linux

Revision 1791 - (view) (annotate) - [select for diffs]
Modified Fri Aug 31 16:48:50 2012 UTC (12 years, 8 months ago) by gezelter
File length: 57265 byte(s)
Diff to previous 1789

switched to a base accumulator to make the hidden function warnings
from the intel compiler go away.

Fixing a compilation issue on Windows

Revision 1782 - (view) (annotate) - [select for diffs]
Modified Wed Aug 22 02:28:28 2012 UTC (12 years, 8 months ago) by gezelter
File length: 57097 byte(s)
Diff to previous 1777

MERGE OpenMD development branch 1465:1781 into trunk

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
Original Path: branches/development/src/rnemd/RNEMD.cpp
File length: 56503 byte(s)
Diff to previous 1775

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
Original Path: branches/development/src/rnemd/RNEMD.cpp
File length: 56094 byte(s)
Diff to previous 1773

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
Original Path: branches/development/src/rnemd/RNEMD.cpp
File length: 52767 byte(s)
Diff to previous 1764

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
Original Path: branches/development/src/rnemd/RNEMD.cpp
File length: 52934 byte(s)
Copied from: branches/development/src/integrators/RNEMD.cpp revision 1730
Diff to previous 1728

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

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

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

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

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

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

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

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

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

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