Refactored Snapshot and Stats to use the Accumulator classes. Collected a number of methods into Thermo that belonged there.
Some bugfixes (CholeskyDecomposition), more work on fluctuating charges, migrating stats stuff into frameData
Reorganized source directories, added RNEMD and flucQ blocks for options parsing.
Bug fixes for heat flux import
Adding fluctuating charges, still a work in progress
Adding more support structure for Fluctuating Charges.
updated copyright notices
migrating cutoff information from InteractionManager to ForceManager
Creating busticated version of OpenMD
removing cruft (atom numbers, do_pot, do_stress) from many modules and force managers
Adding property set to svn entries
Adding a progress bar, and pAngle staticProps
Merging changes skipped in working copies of OOPSE into the OpenMD tree, fixing make install
Almost all of the changes necessary to create OpenMD out of our old project (OOPSE-4)
added RNEMD scaling
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
Bug fixes and sanity checks for RNEMD (nBins should be even), check to make sure we aren't selecting inappropriate numbers of integrable Objects
Added a getStatus routine to check the temperatures
Adding RNEMD
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.
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...
fixes to zang writing
Added simulation box dipole moment accumulation for the purposes of calculating dielectric constants
MPI thermodynamic integration works now.
Adding single precision capabilities to c++ side
Got rid of spurious printing out of timestep
End of the Link --> List Return of the Oject-Oriented replace yacc/lex parser with antlr parser
OptionSectionParser get compiled
Customized StatWriter is working
adding resetIntegrator
Fix to print pressure tensor.
adding keyword printPressureTensor
xemacs has been drafted to perform our indentation services
minor change to TI output
First commit of the new restraints code
adding basic_teebuf which can operate on multiple stream simutaneously.
fix a bug in VelocityVerletIntegrator : last frame is written twice
dynamicProps get built
forget to add eorWriter
merging new_design branch into OOPSE-2.0
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