added numpy headers to pyxinstall in pyspin.py. removed dead lattice tree
added function to test whether dual representation is correct for a square plaquette model
added to pySpin.py such that it can take a trjfile name to represent the output prefix
fixed pickling bug in simulation object arrising from open file handle in trj_file
Merge 192.168.100.184:reichman/glassy_dynamics/code/simulate/PyKMC
renamed input file option to mean readnig a config from spintrj and made a continuefile option instead for restarting from spinsys
update that lets simulation object be started from an initial config rather than an initial state
Merge 192.168.100.184:reichman/glassy_dynamics/code/simulate/PyKMC
added init files so that acts as a module
removed 'inital_configuration' from system object
coft now pickles results
average_coft.py
coft now counts excitations in dual representation
sped up coft by making it not read trajectory twice\!
update to import statements in coft and default histogramming in average coft
added hexagon freezing to TPM
added feature where restart runs should be able to change temperature
fixed bug where all of persistance array was being written out rather than just that for active particles in frozen simulation. this makes cavity simulations write and run much faster