Coding day 2016 functional tests

Stage 1

 * analysis.tcl (Only stage 1 analysis routines. The tests uses canned data sotred in a block file.)

Drop

 * kinetic.tcl (not sure, what this tests)

Not implemented in python yet

 * correlation_checkpoint.tcl

Done

 * correlation.tcl
 * observable.tcl

Stage 1

 * Test integration and compare against stored data. These two tests probably share most of their code
 * intpbc.tcl
 * intppbc.tcl
 * layered.tcl
 * nsquare.tcl
 * npt.tcl
 * langevin_per_particle.tcl
 * langevin.tcl (do we depend on scipy or do we impleement our own moment calculation?)
 * These two can probably be merged
 * mass-and-rinertia.tcl (Merge with mass_and_rinerita_per_particle)
 * mass.tcl
 * lees_edwards.tcl (#1140)
 * minimize_energy_rotation.tcl
 * rotation_per_particle.tcl (See #1288)

Stage 2

 * rotation.tcl (Uses Gay Bernes potential. It's unclear whether that's correctly implemented)

Drop

 * nve_pe.tcl (no idea,what that tests)

No python support yet

 * dpd.tcl
 * ghmc.tcl
 * comfixed.tcl
 * comforce.tcl

Done

 * mass_and_rinertia_per_particle
 * minimize_energy.tcl

Stage 1

 * virtual-sites-rotation.tcl

Done

 * virtual-sites.tcl (pr #1299)

Stage 1

 * These two share nearly all code:
 * p3m_gpu_simple_noncubic.tcl
 * p3m_simple_noncubic.tcl
 * Merge dipolar open boundary tests into one
 * dawaanr-and-dds-gpu.tcl
 * scafacos-dipoles-non-periodic.tcl
 * Merge tests for dipolar 3d periodic
 * p3m_magnetostatics2.tcl
 * p3m_magnetostatics.tcl
 * scafacos-dipoles.tcl
 * Merge tests for dipolar 2d periodic into one
 * scafacos-dipoles-1d-and-2d-periodic.tcl
 * mdlc.tcl

Stage 2 (If you use one in your simulations, feel free to move up)

 * dielectric.tcl
 * el2d_die.tcl
 * el2d_nonneutral.tcl
 * el2d.tcl
 * iccp3m.tcl
 * dh.tcl
 * mmm1dgpu.tcl
 * mmm1d.tcl
 * madelung.tcl
 * p3m.tcl
 * p3m_tuning.tcl

Done

 * coulomb_cloud_wall.tcl
 * p3m_gpu.tcl (done)
 * ewaldgpu.tcl

No Python support

 * maggs.tcl
 * maggs_varying_epsilon.tcl

Interaction potentials
In addition to existing tests based on stored data, we'd like to add unit tests for the add_pair_force and add_pair_energy functions of each potential on the c++-level.

Stage 1

 * These two share most of their code
 * fene.tcl
 * harm.tcl
 * angle.tcl

Stage 2

 * bonded_coulomb.tcl
 * dihedral.tcl
 * gb.tcl (No python interface and possibly broken)
 * Shared code
 * lj.tcl
 * lj-cos.tcl (no py support yet)
 * lj-generic.tcl
 * tabulated.tcl

No python support yet

 * quartic.tcl

Done

 * exclusions.tcl

No py support yet

 * external_potential.tcl
 * constraints_reflecting.tcl
 * constraints_rhomboid.tcl
 * constraints.tcl

Done

 * magnetic-field.tcl

No py support yet
See (github RudolfWeeber py_collision_detection)
 * collision-detection-angular.tcl
 * collision-detection-centers.tcl
 * collision-detection-glue.tcl
 * collision-detection-poc.tcl

Electrokinetics

 * Merge
 * ek_electrostatics_coupling_x.tcl
 * ek_electrostatics_coupling_y.tcl
 * ek_electrostatics_coupling_z.tcl
 * ek_reaction.tcl

Done

 * ek_eof_one_species_x_nonlinear.tcl
 * ek_eof_one_species_x.tcl
 * ek_eof_one_species_y_nonlinear.tcl
 * ek_eof_one_species_y.tcl
 * ek_eof_one_species_z_nonlinear.tcl
 * ek_eof_one_species_z.tcl

Done

 * engine_langevin.tcl
 * Merge
 * engine_lbgpu.tcl
 * engine_lb.tcl

Lattice Boltzmann

 * Merge
 * lb_fluid_coupling_gpu.tcl
 * lb_fluid_coupling.tcl
 * Merge
 * lb_gpu.tcl
 * lb.tcl
 * Merge
 * lb_planar_embedded_particles_gpu.tcl
 * lb_planar_embedded_particles.tcl
 * Merge
 * lb_planar_gpu.tcl
 * lb_planar.tcl
 * Merge
 * lb_stokes_sphere_gpu.tcl
 * lb_stokes_sphere.tcl
 * sc_fluid_gpu.tcl
 * sc_affinity_gpu.tcl

Drop

 * sd_ewald.tcl
 * sd_thermalization.tcl
 * sd_two_spheres.tcl

No py support yet

 * immersed_boundary_gpu.tcl
 * immersed_boundary.tcl
 * object_in_fluid_gpu.tcl
 * object_in_fluid.tcl

No py support yet

 * rotate-system-dipoles.tcl
 * rotate-system.tcl
 * uwerr.tcl
 * tunable_slip.tcl
 * slitpore.tcl
 * pdb_parser.tcl
 * pe_micelle.tcl

Drop

 * command_syntax.tcl