Fixed a bunch of stylistic and performance issues discovered via cppcheck.
Fixed a bunch of cppcheck warnings.
Fixed a bug when there's no electric field being calculated.
Fixed a minor visitor bug
Bugs in the FQ samples, fixed for Dump2XYZ to print out charges and electric fields
Fixed a widespread typo in the license
Deleting unused variables
Fixed a bug in Matrix-Matrix cross product
Fixed some torque bugs (I think), added a unit vector for Quadrupolar atoms.
Massive multipole rewrite
Various fixes required to compile OpenMD with the MS Visual C++ compiler
Refactored Snapshot and Stats to use the Accumulator classes. Collected a number of methods into Thermo that belonged there.
Individual ForceField classes have been removed (they were essentially all duplicates anyway). ForceField has moved to brains, and since only one force field is in play at any time, the ForceFieldFactory and Register methods have been removed.
Un-did some changes that weren't ready to be committed.
Added files for fcc and pentagonal nanorod builders. Updated runMe in samples/builders to include nanorod builders.
updated copyright notices
fixing the build system
indenting fix
Merging changes from old branch into development branch
Creating busticated version of OpenMD
small changes
more changes to make Dump2XYZ do velocities & forces
Updating visitor architecture to something a bit more modern
Adding property set to svn entries
Fixed a missing cstdio include
Almost all of the changes necessary to create OpenMD out of our old project (OOPSE-4)
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.
Inversion fixes and amber mostly working
Committing changes made to AtomVisitor to render xyz2pov scenes
new visitors for some odd molecules
Support for printPosOnly in Dump2XYZ.
Added TRED water visitor for Dump2XYZ visualization
fixed a build problem... GB_12b_ratio no longer exists (replaced with BG_l).
output the principle axis of GB
testing GB, removing CM drift in Langevin Dynamics, fixing a memory leak, adding a visitor
Adding single precision capabilities to c++ side
adding a gay-berne switch to Dump2XYZ
Adding visitor for GBlipid atom type
End of the Link --> List Return of the Oject-Oriented replace yacc/lex parser with antlr parser
rewrite Globals
adding AtomNameVisitor
adding AtomNameVisitor to convert atom name to its base name; wrappingvisitor now wrap back to the center of the mass; adding P2OrderParameter into StaticProps
Couple of changes for TAP water. Need to parametrize.
xemacs has been drafted to perform our indentation services
fixed the wrapping
LipidTranVisitor should do the wrapping
adding IndexFinder which is used to select the molecules; Seperate ElectrostaticAtomTypesSectionParser into ChargeAtomTypesSectionParser and MultipoleAtomTypesSectionParser;remove print dipole option from Dump2XYZ;
fixing a strange icc8 bug (we think).
fix compilation problem for g++ 3.4
Fix a bug in GofRAngle
adding LipidTransVisitor, GofXyz is working now
dynamicProps get built
IgnoreVisitor and XYZVisitor now use selection library
(1)Cast wrong atom to DirectionalAtom in GhostTorsion (2)get the wrong column of electroframe
moved Package variable into subdirectory makefiles to speed up the building process
LinearVisitor get fixed
merging new_design branch into OOPSE-2.0
Added the linear visitor
replace old GebericData with new GenericData
define DEV_ROOT as relative path
change Makefile to relative path
change the #include in source files
Import of OOPSE v. 2.0