 ../
|
AmberImproperTorsionType.hpp
|
1291
(16 years ago)
by gezelter:
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.
|
|
AtomStamp.cpp
|
1170
(18 years ago)
by gezelter:
removed MWM as an atom type property
|
|
AtomStamp.hpp
|
1277
(17 years ago)
by gezelter:
Changes for implementing Amber force field: Added Inversions and
worked on BaseAtomTypes so that they'd function with the fortran side.
|
|
AtomType.cpp
|
1306
(16 years ago)
by chuckv:
Returned old LD forces to SMIPDForceManager.
|
|
AtomType.hpp
|
1306
(16 years ago)
by chuckv:
Returned old LD forces to SMIPDForceManager.
|
|
AtomTypeProperties.h
|
1293
(16 years ago)
by chuckv:
Added large quantities of code for convex hull and constant pressure langevin dynamics.
|
|
BendStamp.cpp
|
1171
(18 years ago)
by gezelter:
Just some formatting fixes
|
|
BendStamp.hpp
|
1171
(18 years ago)
by gezelter:
Just some formatting fixes
|
|
BendType.hpp
|
1171
(18 years ago)
by gezelter:
Just some formatting fixes
|
|
BondStamp.cpp
|
1171
(18 years ago)
by gezelter:
Just some formatting fixes
|
|
BondStamp.hpp
|
1171
(18 years ago)
by gezelter:
Just some formatting fixes
|
|
BondType.hpp
|
1171
(18 years ago)
by gezelter:
Just some formatting fixes
|
|
CharmmTorsionType.cpp
|
1290
(16 years ago)
by cli2:
Inversion fixes and amber mostly working
|
|
CharmmTorsionType.hpp
|
1195
(17 years ago)
by cpuglis:
Many fixes for Charmm-type torsions.
|
|
Component.cpp
|
1171
(18 years ago)
by gezelter:
Just some formatting fixes
|
|
Component.hpp
|
1171
(18 years ago)
by gezelter:
Just some formatting fixes
|
|
CubicBendType.hpp
|
1171
(18 years ago)
by gezelter:
Just some formatting fixes
|
|
CubicBondType.hpp
|
1171
(18 years ago)
by gezelter:
Just some formatting fixes
|
|
CubicTorsionType.hpp
|
1171
(18 years ago)
by gezelter:
Just some formatting fixes
|
|
CutoffGroupStamp.cpp
|
1171
(18 years ago)
by gezelter:
Just some formatting fixes
|
|
CutoffGroupStamp.hpp
|
1171
(18 years ago)
by gezelter:
Just some formatting fixes
|
|
DataHolder.hpp
|
1171
(18 years ago)
by gezelter:
Just some formatting fixes
|
|
DirectionalAtomType.cpp
|
1282
(16 years ago)
by gezelter:
Many fixes
|
|
DirectionalAtomType.hpp
|
1282
(16 years ago)
by gezelter:
Many fixes
|
|
FixedBondType.hpp
|
1171
(18 years ago)
by gezelter:
Just some formatting fixes
|
|
FragmentStamp.cpp
|
1171
(18 years ago)
by gezelter:
Just some formatting fixes
|
|
FragmentStamp.hpp
|
1171
(18 years ago)
by gezelter:
Just some formatting fixes
|
|
HarmonicBendType.hpp
|
1171
(18 years ago)
by gezelter:
Just some formatting fixes
|
|
HarmonicBondType.hpp
|
1171
(18 years ago)
by gezelter:
Just some formatting fixes
|
|
ImproperCosineInversionType.cpp
|
1277
(17 years ago)
by gezelter:
Changes for implementing Amber force field: Added Inversions and
worked on BaseAtomTypes so that they'd function with the fortran side.
|
|
ImproperCosineInversionType.hpp
|
1277
(17 years ago)
by gezelter:
Changes for implementing Amber force field: Added Inversions and
worked on BaseAtomTypes so that they'd function with the fortran side.
|
|
InversionStamp.cpp
|
1275
(17 years ago)
by cli2:
Changes required for Inversions and Base Atom types. This will
break OOPSE badly for a few days or so...
|
|
InversionStamp.hpp
|
1275
(17 years ago)
by cli2:
Changes required for Inversions and Base Atom types. This will
break OOPSE badly for a few days or so...
|
|
InversionType.hpp
|
1275
(17 years ago)
by cli2:
Changes required for Inversions and Base Atom types. This will
break OOPSE badly for a few days or so...
|
|
LennardJonesInteractionType.hpp
|
1252
(17 years ago)
by chuckv:
Fixed typo in LJinteraction types. LJ-metal appears to work now.
|
|
MAWInteractionType.hpp
|
1284
(16 years ago)
by gezelter:
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).
|
|
Makefile
|
1360
(15 years ago)
by cli2:
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
|
|
MoleculeStamp.cpp
|
1277
(17 years ago)
by gezelter:
Changes for implementing Amber force field: Added Inversions and
worked on BaseAtomTypes so that they'd function with the fortran side.
|
|
MoleculeStamp.hpp
|
1275
(17 years ago)
by cli2:
Changes required for Inversions and Base Atom types. This will
break OOPSE badly for a few days or so...
|
|
MorseBondType.hpp
|
1171
(18 years ago)
by gezelter:
Just some formatting fixes
|
|
NonBondedInteractionType.hpp
|
1293
(16 years ago)
by chuckv:
Added large quantities of code for convex hull and constant pressure langevin dynamics.
|
|
OplsTorsionType.hpp
|
1290
(16 years ago)
by cli2:
Inversion fixes and amber mostly working
|
|
PolynomialBendType.hpp
|
1172
(18 years ago)
by gezelter:
Formatting to prettify the code
|
|
PolynomialBondType.hpp
|
1172
(18 years ago)
by gezelter:
Formatting to prettify the code
|
|
PolynomialInversionType.hpp
|
1290
(16 years ago)
by cli2:
Inversion fixes and amber mostly working
|
|
PolynomialTorsionType.hpp
|
1290
(16 years ago)
by cli2:
Inversion fixes and amber mostly working
|
|
QuarticBendType.hpp
|
1172
(18 years ago)
by gezelter:
Formatting to prettify the code
|
|
QuarticBondType.hpp
|
1172
(18 years ago)
by gezelter:
Formatting to prettify the code
|
|
QuarticTorsionType.hpp
|
1172
(18 years ago)
by gezelter:
Formatting to prettify the code
|
|
RepulsiveMorseInteractionType.hpp
|
1284
(16 years ago)
by gezelter:
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).
|
|
RestraintStamp.cpp
|
1364
(15 years ago)
by cli2:
Bug fixes in the SelectionEvaluator and SelectionCompiler
Added print option in Restraints
|
|
RestraintStamp.hpp
|
1364
(15 years ago)
by cli2:
Bug fixes in the SelectionEvaluator and SelectionCompiler
Added print option in Restraints
|
|
RigidBodyStamp.cpp
|
1172
(18 years ago)
by gezelter:
Formatting to prettify the code
|
|
RigidBodyStamp.hpp
|
1172
(18 years ago)
by gezelter:
Formatting to prettify the code
|
|
ShapeAtomType.cpp
|
1172
(18 years ago)
by gezelter:
Formatting to prettify the code
|
|
ShapeAtomType.hpp
|
1172
(18 years ago)
by gezelter:
Formatting to prettify the code
|
|
ShiftedMorseInteractionType.hpp
|
1284
(16 years ago)
by gezelter:
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).
|
|
TorsionStamp.cpp
|
1172
(18 years ago)
by gezelter:
Formatting to prettify the code
|
|
TorsionStamp.hpp
|
1172
(18 years ago)
by gezelter:
Formatting to prettify the code
|
|
TorsionType.hpp
|
1172
(18 years ago)
by gezelter:
Formatting to prettify the code
|
|
TrappeTorsionType.hpp
|
1258
(17 years ago)
by gezelter:
Adding Trappe torsion types and fixing Opls types
|
|
UreyBradleyBendType.hpp
|
1172
(18 years ago)
by gezelter:
Formatting to prettify the code
|
|
ZconsStamp.cpp
|
1360
(15 years ago)
by cli2:
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
|
|
ZconsStamp.hpp
|
1172
(18 years ago)
by gezelter:
Formatting to prettify the code
|
