Revision
3520 -
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Modified
Mon Sep 7 16:31:51 2009 UTC
(15 years ago)
by
cli2
Diff to
previous 3466
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
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
3319 -
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Modified
Wed Jan 23 03:45:33 2008 UTC
(16 years, 7 months ago)
by
gezelter
Diff to
previous 3126
Removed older version of openbabel from our code. We now have a
configure check to see if openbabel is installed and then we link to
the stuff we need. Conversion to OOPSE's md format is handled by only
one application (atom2md), so most of the work went on there.
ElementsTable still needs some work to function in parallel.
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
2982 -
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Modified
Wed Aug 30 18:42:29 2006 UTC
(18 years ago)
by
tim
Diff to
previous 2759
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
2625 -
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Modified
Wed Mar 15 17:35:12 2006 UTC
(18 years, 6 months ago)
by
tim
Diff to
previous 2582
using setFrc in RigidBody::calcForcesAndTorques will discard if there are force and torque applied in rigid body itself. use addFrc instead.
Revision
2394 -
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Modified
Sun Oct 23 21:08:08 2005 UTC
(18 years, 10 months ago)
by
chrisfen
Diff to
previous 2391
streamlined reaction field for dipoles (now a good bit faster) and added reaction field for charges - still need to do charge-dipole RF
Revision
2345 -
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Modified
Wed Oct 5 19:12:02 2005 UTC
(18 years, 11 months ago)
by
tim
Diff to
previous 2341
fix a bug in creating cutoffGroup. When cutoffGroup is turned off, there is a mismatch between group and center of mass array
Revision
2341 -
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Modified
Mon Oct 3 15:54:23 2005 UTC
(18 years, 11 months ago)
by
tim
Diff to
previous 2340
fix a bug in projecting the inertia tensor of
directional atom in rigibody into rigidbody's body frame (previous commit is wrong)
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
Revision
1709 -
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Modified
Thu Nov 4 16:22:03 2004 UTC
(19 years, 10 months ago)
by
gezelter
Diff to
previous 1698
isLinear and linearAxis are virtual in StuntDouble,
but are implemented by DirectionalAtom and RigidBody
In StuntDouble, they should return false and "-1" but
there should be logic to figure them out in the other
two classes