pythonification of affineScale, translate in md2md, removed spurious cutoffGroups in waterBoxer. Perhaps we need a python md-file parsing library?
fixes for surface atoms that expose multiple hydrogens, updated python set syntax
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
Added large quantities of code for convex hull and constant pressure langevin dynamics.
Hopefully md-solvator is done.
More md-solvator work.
Md solvator writes out md files now. Index problem.
More progress...
More changes to md-solvator. Still don't know if it works.
More work on python version of md-solvator. Pretty sure mol loop is busted.
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Added repeat box options to make larger systems
Adding new md2md utility program
added stat2visco
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forgot a tolerance for simple cubic lattice magic number determination
fixed a bug in waterBoxer
adding md-solvator
Added the ability of waterBoxer to deal with non-cubical boxes.
More changes to mdsplit.
Breaking more mdsplit stuff....
Changed how mdsplit gets file names. Full path is now removed from name.
More typos...
Typo in mdSplit.
Fixed printing of OOPSE version at header and trailer.
now the -n command works
oops with the affineScale
who needs .in files for perl? using env
Added utility to split dump file frames into md files.
forgot to adjust the makefile
added solvator and adjusted waterBoxer
improvements to waterBoxer
fixed a bug in waterBoxer for invalid water names
changing configure script to process the new utilities
added some features to waterBoxer
added the waterBoxer script
added comment info
modified affineScale to work with the new OOPSE files
Changing utility programs to use the new file format
fixed a pvf bug
fixed dumpConverter problems
added dumpConverter
fixed a spelling bug
Adding a directory for scripts Adding affineScale script