const char* fix
adding generic Vector3 class
remove some useless files
DUMP2XYZ 0.99 version
fixed a bug in CompositeVisitor which cause the double counting problem
Dump2XYZ is almost working except atoms in rigidbody are double counted
new implement of quickLate using visitor and composite pattern
fix a bug in setting exclude list
Change DumpWriter and InitFromFile
Changes for RigidBody dynamics
Fix a couple of bugs in zsub
Adding zsub, a program which can be used to replace atom type for zconstraint into OOPSE
Changes to BASS reader to use Euler angles for orientation instead of unit vectors required changes in MoLocator
fixed a periodic box bug
working on adding GofRtheta and GofRomega additional work on randomBilayer
removed the randombilayer header
edited the makefile to add randomBilayer to the build. Also move the random bilayer builder from bilayerSys to randomBilayer
added a more verbose error message in SimInfo. Added a more informative error message in InitializeFromFile
added the following parameters to BASS: * useInitialExtendedSystemState * orthoBoxTolerance * useIntiTime => useInitialTime
some work on trying to find the compression bug
Portability fixes
added routines for the sysbuilder to work with simSetup remved the QuickBass routines, and had all parsing go through SimSetup. LatticeBilayer is in complete working order now.
fixes for configure, sysBuild
put QuickBass, MoLocator, and latticeBuilder into a Builder Library overhauled latticeBilayer into its own program. Removed sysBuild from the Makefile
work on bilayer builder
fixes for configure
Added a bunch of Make.dep files to CVS
removed mpi++ from the makefile
fixed a typo in the makefile.
add conserved quantity to statWriter fix bug of vector wrapping at NPTi
Changes to autoconf / configure method of configuring OOPSE
added define statemewnt to Statwriter and Dumpwriter to handle files larger than 2 gb. commented out some print statements in Zconstraint hard coding some system init into bilayer.sys
More FreeBSD fixes
updated the Changelog. added some bug fixes for setting the random number generator seed value. fixed a bug where ghostbend atom b was not being set. ( recent bug from SimState conversion)
quick makefile fix, in make links. added -f to ln -s.
Fixed sysBuild -bilayer works. Nanobuilder still broke.
Added comment line for getgetopt.
Missed del of files before.
*** empty log message ***
commit makefile
Changed makefile to only build quicklate.
Arranged sysbuilder into a subdirectory. Fixed some of sysbuilder to work with new atom allocation in libmdtools.
Made quickLate aware of Hmat. quickLate is now somewhat more intelligent about periodic boundaries and wrapping.
added more command line arguments
Broken SysBuilder
added a nanoSysBuilder that takes different cmd line arguments.
Fixed Hmat and some namespace strangeness
Added nanoBuilder and a general Lattice builder.
cleaned up the dependecy scripts in the makefiles
fixed the bugs introduced by switching the periodic box to a matrix
Most of the integrator and NVT seem to be working now.
currently modifiying Symplectic to become the basic integrator. bilayerSys.cpp altered for building tb3.
all seems to be working
still working on the bilayer code
doing some work to overhaul sysbuild.
i quick fix to th distance in the random bilayer builder
fixed up sysBuild to where it should now build our systems
almost finished.
bilayerSys and sysBuild both will build now. woot!
finished bilayerSys.cpp sysBuild still need to write the bass file. MoLocator.cpp is currently empty
working on the system builder
working on a system builder
added Ghost bends to the TraPPE_Ex forceField added sysBuild to the utils Makefile
Changed Readme, added some files