Coding day 2015 analysis

=Instructions=

1. Chose one of the analysis commands to work on. Only take a command from a lower stage, if the previous stage is completed. 2. Identify the tcl parser for the analysis command by running grep REGISTER_ANALY.*CommandName in the src/tcl direcotry, where CommandName is the tcl analysis subcommand. The second argument of REGISTER_ANALYSIS is the name of the c-function which parses the tcl code (Example: tclcommand_parse_analyze_mindist) 3. Locate the respective c-function. Most are in src/tcl/statistics_tcl.cpp, if not, use grep in src/tcl. 4. From the tcl parser identify the actual calls to the Espresso core which carry out the analysis, and what arguments they require. (Exampel: For mindist, this is mindist(IntList*, IntList*)) 5. Expose the required c-functions in src/python/espressomd/c_analyze.pxd in the section (replace file name if not in statistics.hpp) cdef extern from "statistics.hpp", (For mindist: cdef double mindist(IntList *set1, IntList *set2)) 6. In src/python/espressomd/analyze.pyx, write a python/cython version of the tcl parser function. See distto as an example. If the tcl parser contained a call to update_part_cfg, don't forget to include it.

Conventions: Examples: import numpy as np   Numpy array: np.array(x[0],x[1],x[2]) dictionary: {"kinetic":kin,"coulomb":coulomb}
 * The first argument is an instane of teh espresso system class
 * Use keyword arguments for remaining parameters (exmpale mindist(system, p1=default,p2=default))
 * Return pythonic data types
 * Use docstrings

=Tasks=

==Stage 1
 * pressure (partially done) (DONE)
 * energy (DONE)
 * mindist (done)
 * momentum (DONE)
 * rdf (DONE)
 * ???temperature
 * structurefactor (DONE)
 * re (DONE)
 *  (DONE)
 * rg (DONE)
 *  (DONE)

==Stage 2
 * angularmomentum (done)
 * centermass (done)
 * distto (done)
 * gyration_tensor
 * local_stress_tensor (done)
 * momentofinertiamatrix
 * nbhood (done)
 * radial_density_map (broken?)
 * (done)
 * rdfchain
 *  (done)
 * stress_tensor (Done, Rudolf)
 * Vkappa

==Stage 3
 * aggregation
 * bilayer_density_profile
 * 
 * bond_dist
 * 
 * bond_l
 * distribution
 * find_principal_axis
 * formfactor
 * 
 * g123
 * 
 * 
 * get_folded_positions
 * holes
 * 
 * internal_dist
 * modes2d
 * necklace
 * rh
 * 
 * vanhove
 * vel_distr
 * vel_distr

==In danger of being removed due to lack of documentation
 * bins
 * cell_gpb
 * check_mol
 * cluster_size_dist
 * configtemp
 * current
 * cwvac
 * 
 * 
 * dipmom_mol
 * dipmom_normal
 * energy_kinetic
 * energy_kinetic_mol
 * get_lipid_orients
 * lipid_orient_order
 * mol
 * MSD
 * deprecate p_IK1
 * p_inst
 * pressure_mol
 * wallstuff