1. No more texture fetching in Covalent,Native,Pairs and Indentation
potential.
2. The code in the potentials initialization is re-orginized into
several subroutines (building map of interactions, constructing the GPU
constant)
3. The energy output is no longer in one float4* array for all the
potentials. Every potential now have float* h_energies and d_energies to
store the energy per particle and float* energies to store energy per
trajectory.
4. Several new methods regarding an access to the energy evaluation
routines are added. Each potential now returns the number of energy
terms it computes, provides routines to evaluate these values and to get
them by trajectory number.
5. Output_manager is reorganized, which lead to a slightly different
output. Now, the output manager calls eqch potential for its energy
values rather then directly compute each energy. This allows for better
extensibility (for instance if new potentials will be added). The order
of the terms in the dat file change though, which can be harmfull for
analysis scripts. 
6. Output manager now prints data fro several trajectories into the
standard output (for many-runs-per-GPU). The number of trajectories
printed is controlled by 'printruns' parameter (default = 10). The width
of columns in standard outpu can also be changed by parameter
'outputcolwidth' (default 16).
7. Temperature moved from aformentioned float4 array into the new array
called float* d_T, h_T (temperature stored per particle). The averaging
of the data is now done over the number of steps between dat outputs
(rather than over pairlist period).
8. Some comments added