Revision
3520 -
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Modified
Mon Sep 7 16:31:51 2009 UTC
(15 years ago)
by
cli2
Diff to
previous 3463
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
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
3439 -
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Modified
Thu Jul 31 18:40:21 2008 UTC
(16 years, 1 month ago)
by
gezelter
Diff to
previous 3437
fixed a strange compiler structure alignment problem with the
intel Mac compiler (structs that cross between C and fortran
appear to need 8-byte boundary alignment on this compiler).
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
3364 -
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Modified
Fri Mar 7 19:37:14 2008 UTC
(16 years, 6 months ago)
by
cpuglis
Diff to
previous 3356
Changed some logic in Polynomial, PolynomialTorsionType, and CharmmTorsionType
to allow for polynomials to be set via the = operator.
Revision
3129 -
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Modified
Fri Apr 20 18:15:48 2007 UTC
(17 years, 5 months ago)
by
chrisfen
Diff to
previous 2787
SF Lennard-Jones was added for everyones' enjoyment. The behavior is tethered to the electrostaticSummationMethod keyword.
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 2759
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 2507
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
2211 -
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Modified
Thu Apr 21 14:12:19 2005 UTC
(19 years, 4 months ago)
by
chrisfen
Diff to
previous 2204
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 2094
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