 ../
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AtomTypesSectionParser.cpp
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1277
(16 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.
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AtomTypesSectionParser.hpp
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507
(20 years ago)
by gezelter:
xemacs has been drafted to perform our indentation services
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BaseAtomTypesSectionParser.cpp
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1282
(16 years ago)
by gezelter:
Many fixes
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BaseAtomTypesSectionParser.hpp
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1275
(16 years ago)
by cli2:
Changes required for Inversions and Base Atom types. This will
break OOPSE badly for a few days or so...
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BendTypesSectionParser.cpp
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963
(19 years ago)
by tim:
Adding single precision capabilities to c++ side
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BendTypesSectionParser.hpp
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802
(19 years ago)
by chuckv:
Wow thats alot o' files. Now passing forceFieldOptions to all of the parsers.
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BondTypesSectionParser.cpp
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963
(19 years ago)
by tim:
Adding single precision capabilities to c++ side
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BondTypesSectionParser.hpp
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802
(19 years ago)
by chuckv:
Wow thats alot o' files. Now passing forceFieldOptions to all of the parsers.
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ChargeAtomTypesSectionParser.cpp
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1269
(16 years ago)
by gezelter:
Adding infrastructure for Amber force field.
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ChargeAtomTypesSectionParser.hpp
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802
(19 years ago)
by chuckv:
Wow thats alot o' files. Now passing forceFieldOptions to all of the parsers.
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DirectionalAtomTypesSectionParser.cpp
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1282
(16 years ago)
by gezelter:
Many fixes
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DirectionalAtomTypesSectionParser.hpp
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802
(19 years ago)
by chuckv:
Wow thats alot o' files. Now passing forceFieldOptions to all of the parsers.
|
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DumpReader.cpp
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1313
(16 years ago)
by gezelter:
General bug-fixes and other changes to make particle pots work with
the Helfand Energy correlation function
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DumpReader.hpp
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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
|
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DumpWriter.cpp
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1313
(16 years ago)
by gezelter:
General bug-fixes and other changes to make particle pots work with
the Helfand Energy correlation function
|
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DumpWriter.hpp
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1024
(18 years ago)
by tim:
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.
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EAMAtomTypesSectionParser.cpp
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963
(19 years ago)
by tim:
Adding single precision capabilities to c++ side
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EAMAtomTypesSectionParser.hpp
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963
(19 years ago)
by tim:
Adding single precision capabilities to c++ side
|
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ForceFieldOptions.cpp
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1293
(16 years ago)
by chuckv:
Added large quantities of code for convex hull and constant pressure langevin dynamics.
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ForceFieldOptions.hpp
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1293
(16 years ago)
by chuckv:
Added large quantities of code for convex hull and constant pressure langevin dynamics.
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GayBerneAtomTypesSectionParser.cpp
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981
(19 years ago)
by gezelter:
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).
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GayBerneAtomTypesSectionParser.hpp
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981
(19 years ago)
by gezelter:
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).
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Globals.cpp
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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
|
|
Globals.hpp
|
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
|
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InversionTypesSectionParser.cpp
|
1290
(16 years ago)
by cli2:
Inversion fixes and amber mostly working
|
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InversionTypesSectionParser.hpp
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1290
(16 years ago)
by cli2:
Inversion fixes and amber mostly working
|
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LennardJonesAtomTypesSectionParser.cpp
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839
(19 years ago)
by chuckv:
Added energy scaling to section parsers.
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LennardJonesAtomTypesSectionParser.hpp
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799
(19 years ago)
by chuckv:
Added forceOptions to section parser
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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
|
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MetalNonMetalInteractionsSectionParser.cpp
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1254
(17 years ago)
by chuckv:
Removed accidental print lines.
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MetalNonMetalInteractionsSectionParser.hpp
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1238
(17 years ago)
by gezelter:
Changing functional form
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MultipoleAtomTypesSectionParser.cpp
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984
(19 years ago)
by chrisfen:
fixed some typos
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MultipoleAtomTypesSectionParser.hpp
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802
(19 years ago)
by chuckv:
Wow thats alot o' files. Now passing forceFieldOptions to all of the parsers.
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OptionSectionParser.cpp
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788
(19 years ago)
by gezelter:
Adding handler for CLAY force field
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OptionSectionParser.hpp
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749
(19 years ago)
by tim:
OptionSectionParser get compiled
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ParamConstraint.cpp
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1341
(16 years ago)
by skuang:
Bug fixes and sanity checks for RNEMD (nBins should be even), check to make
sure we aren't selecting inappropriate numbers of integrable Objects
|
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ParamConstraint.hpp
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1341
(16 years ago)
by skuang:
Bug fixes and sanity checks for RNEMD (nBins should be even), check to make
sure we aren't selecting inappropriate numbers of integrable Objects
|
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RestReader.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
|
|
RestReader.hpp
|
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
|
|
RestWriter.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
|
|
RestWriter.hpp
|
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
|
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SCAtomTypesSectionParser.cpp
|
1150
(17 years ago)
by chuckv:
Non-bonded interactions added.
|
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SCAtomTypesSectionParser.hpp
|
802
(19 years ago)
by chuckv:
Wow thats alot o' files. Now passing forceFieldOptions to all of the parsers.
|
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SectionParser.cpp
|
514
(20 years ago)
by chrisfen:
Shapes is limping along with a array bounds overwrite (I think...). At least the parser loads the forcefield fine...
|
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SectionParser.hpp
|
749
(19 years ago)
by tim:
OptionSectionParser get compiled
|
|
SectionParserManager.cpp
|
1277
(16 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.
|
|
SectionParserManager.hpp
|
507
(20 years ago)
by gezelter:
xemacs has been drafted to perform our indentation services
|
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ShapeAtomTypesSectionParser.cpp
|
1305
(16 years ago)
by skuang:
A few simple mods to remove gcc compile warnings
|
|
ShapeAtomTypesSectionParser.hpp
|
802
(19 years ago)
by chuckv:
Wow thats alot o' files. Now passing forceFieldOptions to all of the parsers.
|
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StatWriter.cpp
|
1316
(16 years ago)
by chuckv:
More attempts to get SMIPD to themostat properly
|
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StatWriter.hpp
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681
(19 years ago)
by tim:
Customized StatWriter is working
|
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StickyAtomTypesSectionParser.cpp
|
802
(19 years ago)
by chuckv:
Wow thats alot o' files. Now passing forceFieldOptions to all of the parsers.
|
|
StickyAtomTypesSectionParser.hpp
|
802
(19 years ago)
by chuckv:
Wow thats alot o' files. Now passing forceFieldOptions to all of the parsers.
|
|
StickyPowerAtomTypesSectionParser.cpp
|
802
(19 years ago)
by chuckv:
Wow thats alot o' files. Now passing forceFieldOptions to all of the parsers.
|
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StickyPowerAtomTypesSectionParser.hpp
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802
(19 years ago)
by chuckv:
Wow thats alot o' files. Now passing forceFieldOptions to all of the parsers.
|
|
TorsionTypesSectionParser.cpp
|
1293
(16 years ago)
by chuckv:
Added large quantities of code for convex hull and constant pressure langevin dynamics.
|
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TorsionTypesSectionParser.hpp
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1258
(17 years ago)
by gezelter:
Adding Trappe torsion types and fixing Opls types
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ZConsReader.cpp
|
770
(19 years ago)
by tim:
End of the Link --> List
Return of the Oject-Oriented
replace yacc/lex parser with antlr parser
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ZConsReader.hpp
|
963
(19 years ago)
by tim:
Adding single precision capabilities to c++ side
|
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ZConsWriter.cpp
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1241
(17 years ago)
by gezelter:
A bunch of minor changes to make MPI compilation faster than
the double compilation we do now...
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ZConsWriter.hpp
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1241
(17 years ago)
by gezelter:
A bunch of minor changes to make MPI compilation faster than
the double compilation we do now...
|
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basic_ifstrstream.hpp
|
1313
(16 years ago)
by gezelter:
General bug-fixes and other changes to make particle pots work with
the Helfand Energy correlation function
|
|
basic_teebuf.hpp
|
507
(20 years ago)
by gezelter:
xemacs has been drafted to perform our indentation services
|
|
gzstream.cpp
|
615
(19 years ago)
by tim:
adding zlib support for DumpWriter
|
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gzstream.hpp
|
615
(19 years ago)
by tim:
adding zlib support for DumpWriter
|
