Fixed dependency bug (we hope)
1. adding some useful math classes(Mat3x3d, Vector3d, Quaternion, Euler3) these classes use anonymous union and struct to support double[3], double[3][3] and double[4] 2. adding roll constraint algorithm
Unifying the error handlers
new rattle algorithm is working
Config changes for fortran access to SimError
formatting error messages, dependency fixes
Several additions... Restraints.cpp and .hpp were included for restraining particles in thermodynamic integration. By including these, changes were made in Integrator, SimInfo, ForceFeilds, SimSetup, StatWriter, and possibly some other files. Two bass keywords were also added for performing thermodynamic integration: a lambda value one and a k power one.
Many changes to get group-based cutoffs to work
new implement of quickLate using visitor and composite pattern
Changes for RigidBody dynamics (Somewhat extensive)
Adding zsub, a program which can be used to replace atom type for zconstraint into OOPSE
Using inherit instead of compose to implement Minimizer both versions are working
Add one more file into Makefile.in
Add some lines into global.cpp to make it work with energy minimization
Substantial changes. OOPSE now has a working WATER.cpp forcefield and parser. This involved changes to WATER.cpp and ForceFields amoung other files. One important note: a hardwiring of LJ_rcut was made in calc_LJ_FF.F90. This will be removed on the next commit...
Some changes for new MPI organization and direct charge-charge interactions
More profiling fixes.
added some profiling routines
added some profile functionality
Added support for compiling fortran without use of mpich modules. We use mpif.h instead.:
did a merge by hand from the new-templateless branch to the main trunk.
bug Fixes include:
* fixed the switching function from ortho to non-ortho box.
!!!!! THis was responsible for all of the sudden deaths we saw.
* some formating in the string when we write out the extended system state.
* added NPT.cpp to the makefile.in
C++ compatibility for templates
replace c++ header stuff with more portable c header stuff Also, mod file fixes and portability changes Some fortran changes will need to be reversed.
Stuff for MOD support in other compilers
added a new NPT integrator, NPTxyz. It scales the x, y, and z direction sepeartely. no box skew allowed.
Changed DumpReader to use linked lists instead of a vector. Fixed the makefile to build DumpReader.cpp Removed a comment output in Exclude.cpp Modified DumpWriter and Integrator to write an eor file every time a frame is written. This lets the .eor file represent the last written frame of a simulation.
fixes for configure
Converted NPTf to work with the NPT base class. Removed NPTfm and NPTim from cvs
Added integrators to Makefile.in
Changes to autoconf / configure method of configuring OOPSE
This form allows you to request diffs between any two revisions of this file. For each of the two "sides" of the diff, enter a numeric revision.