[Espressomd-maintainer] [espresso] Galilei transform (#68)

[jdegraaf]

This commit updates the following elements of ESPResSo.
1) It removes the Tcl functions: stop_particles, stopParticles, system_com, system_com_vel, and galileiTransformParticles, which were in the auxiliary.tcl script.
2) It replaces these with MPI functions: kill_particle_motion, kill_particle_forces, system_CMS, system_CMS_velocity, and galilei_transform (respectively). These new functions are incorporated in a new feature called 'GALILEI'.
3) It changes the Hat-potential entry in the user guide to be more clear on what the cut-off radius is and what the radial dependence is.
4) It updates the reaction code with two options:
(a) Letting each reactant interact only with one catalyst particle during each time step. This enables the creation of catalytic surfaces comprised of catalyst particles (with arbitrary density), yet maintaining a surface-density-independent reaction rate near the surface.
(b) A print option is given to the reaction command, such that the specific input parameters can be returned to the Tcl level.
5) All the necessary updates are made in the user guide.

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You can merge this Pull Request by running

  git pull https://github.com/jdegraaf/espresso galilei_transform

Or view, comment on, or merge it at:

  https://github.com/espressomd/espresso/pull/68

Commit Summary

• testing
• galilei is all finished up, must still work on the reactions
• This commit updates the following elements of ESPResSo.
• Merge branches 'galilei' and 'galilei_transform' into galilei_transform
• Also included the files I missed earlier.

File Changes

• M doc/ug/aux.tex (28)
• M doc/ug/features.tex (1)
• M doc/ug/inter.tex (23)
• M doc/ug/run.tex (14)
• M doc/ug/setup.tex (91)
• M scripts/auxiliary.tcl (208)
• M src/Makefile.am (2)
• M src/communication.c (183)
• M src/communication.h (18)
• M src/features.def (1)
• A src/galilei.c (235)
• A src/galilei.h (52)
• M src/initialize.c (1)
• M src/particle_data.c (4)
• M src/particle_data.h (4)
• M src/reaction.c (70)
• M src/reaction.h (3)
• A src/tcl/galilei_tcl.c (216)
• A src/tcl/galilei_tcl.h (45)
• M src/tcl/initialize_interpreter.c (8)
• M src/tcl/reaction_tcl.c (118)

Patch Links:

• https://github.com/espressomd/espresso/pull/68.patch
• https://github.com/espressomd/espresso/pull/68.diff