Revision
3520 -
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Modified
Mon Sep 7 16:31:51 2009 UTC
(15 years ago)
by
cli2
Diff to
previous 3515
Added new restraint infrastructure
Added MolecularRestraints
Added ObjectRestraints
Added RestraintStamp
Updated thermodynamic integration to use ObjectRestraints
Added Quaternion mathematics for twist swing decompositions
Significantly updated RestWriter and RestReader to use dump-like files
Added selections for x, y, and z coordinates of atoms
Removed monolithic Restraints class
Fixed a few bugs in gradients of Euler angles in DirectionalAtom and RigidBody
Added some rotational capabilities to prinicpalAxisCalculator
Revision
3501 -
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Modified
Fri May 8 19:47:05 2009 UTC
(15 years, 4 months ago)
by
skuang
Diff to
previous 3490
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
3470 -
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Modified
Wed Oct 22 20:01:49 2008 UTC
(15 years, 10 months ago)
by
gezelter
Diff to
previous 3463
General bug-fixes and other changes to make particle pots work with
the Helfand Energy correlation function
Revision
3448 -
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Modified
Thu Sep 11 19:40:59 2008 UTC
(16 years ago)
by
gezelter
Diff to
previous 3446
Added some logic to print out a special pair distance as a column in
the stat file. To use this feature, use taggedAtomPair = "0, 10" and
printTaggedPairDistance = "true" in the md file. Then, the distance
between integrableObjects 0 and 10 will be computed and printed in
the stat file on each statWrite.
Revision
3432 -
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Modified
Mon Jul 14 12:35:58 2008 UTC
(16 years, 2 months ago)
by
gezelter
Diff to
previous 3430
Changes for implementing Amber force field: Added Inversions and
worked on BaseAtomTypes so that they'd function with the fortran side.
Revision
3126 -
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Modified
Fri Apr 6 21:53:43 2007 UTC
(17 years, 5 months ago)
by
gezelter
Diff to
previous 3110
Massive update to do virials (both atomic and cutoff-group) correctly.
The rigid body constraint contributions had been missing and this was
masked by the use of cutoff groups...
Revision
3102 -
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Modified
Fri Dec 29 21:43:18 2006 UTC
(17 years, 8 months ago)
by
gezelter
Diff to
previous 3080
Adding the ability to compute Center of Mass properties on
reading in a dump file. DumpReader must be told if it needs
to do this, however.
Revision
3054 -
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Modified
Wed Oct 18 21:58:48 2006 UTC
(17 years, 10 months ago)
by
gezelter
Diff to
previous 3020
fixing a wrapVector problem in staticProps, also making Shifted force
and electrostatic damping the default behavior
Revision
3013 -
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Modified
Thu Sep 21 18:25:17 2006 UTC
(17 years, 11 months ago)
by
chrisfen
Diff to
previous 3003
fixed the half self term for wolf electrostatics and OOPSE now chooses a cutoff radius dependent alpha for damped electrostatics
Revision
2982 -
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Modified
Wed Aug 30 18:42:29 2006 UTC
(18 years ago)
by
tim
Diff to
previous 2976
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.
Revision
2787 -
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Modified
Mon Jun 5 18:24:45 2006 UTC
(18 years, 3 months ago)
by
gezelter
Diff to
previous 2777
Massive changes for GB code with multiple ellipsoid types (a la
Cleaver's paper).
Also, changes in hydrodynamics code to make HydroProp a somewhat
smarter class (rather than just a struct).
Revision
2515 -
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Modified
Fri Dec 16 18:26:41 2005 UTC
(18 years, 9 months ago)
by
tim
Diff to
previous 2504
the standard library came with SUN compiler does not have a conforming std::use_facet, define a macro
to handle it. Adding exception handling to SimCreator.
Revision
2373 -
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Modified
Mon Oct 17 03:06:29 2005 UTC
(18 years, 11 months ago)
by
tim
Diff to
previous 2372
fix a seg fault when try copy a string to event's err_msg, there are still tons of memory leaking problem in Globals
Revision
2211 -
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Modified
Thu Apr 21 14:12:19 2005 UTC
(19 years, 4 months ago)
by
chrisfen
Diff to
previous 2209
Shapes is limping along with a array bounds overwrite (I think...). At least the parser loads the forcefield fine...
Revision
2097 -
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Modified
Wed Mar 9 17:30:29 2005 UTC
(19 years, 6 months ago)
by
tim
Diff to
previous 2088
adding IndexFinder which is used to select the molecules; Seperate ElectrostaticAtomTypesSectionParser into
ChargeAtomTypesSectionParser and MultipoleAtomTypesSectionParser;remove print dipole option from Dump2XYZ;
Revision
1957 -
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Modified
Tue Jan 25 17:45:23 2005 UTC
(19 years, 7 months ago)
by
tim
Diff to
previous 1951
(1) complete section parser's error message
(2) add GhostTorsion
(3) accumulate inertial tensor from the directional atoms before calculate rigidbody's inertial tensor