Revised sphinx documentation

[KonradBreitsprecher]

Introducing a much more structured sphinx documentation and layout.

TODO (Needs doc, probably python interface):

• Introduction

  • Available simulation methods (Update)

• Particles

  • Grand canonical feature (compare against Creteria-based particle selection #1672; rename; mark critical combination of features)

• Non-bonded interactions

  • Membrane-collision interaction (OIF)
  • Affinity interaction (OIF)

• Bonded interactions

  • Quartic bond
  • Bonded coulomb
  • Subtracted Lennard-Jones bond

• Electrostatics

  • Coulomb Ewald GPU (status/fate unclear)
  • Tuning Alpha Ewald GPU (status/fate unclear)

• Magnetostatics / Dipolar interactions (needs doc)

  • Dipolar interaction
  • Dipolar P3M
  • Tuning dipolar P3M
  • Dipolar Layer Correction (DLC)
  • Dipolar all-with-all and no replicas (DAWAANR)
  • Magnetic Dipolar Direct Sum (MDDS) on CPU

• System manipulation (find better name)

  • Fixing the center of mass

• Single particle forces (constraints)

  • Setting the minimal distance to a constraint

• Analysis

  • Direct analysis routines (Remove TCL reference and update)
  • Temperature of the LB fluid
  • Energies (Extend doc)

• Chains (status/fate unclear)

  • Internal distances
  • Internal distances II (specific monomer)
  • Bond lengths
  • Form factor

• Observables and correlators

  • Accumulators (Not documented)
  • Available observables (links and examples)
  • The correlation algorithm: multiple tau correlator (status, fate unclear)

• Input and Output (status/fate unclear; David?)

  • Writing VTF files
  • writevsf: Writing the topology
  • writevcf: Writing the coordinates
  • vtfpid: Translating particles ids to VMD particle ids
  • Parsing PDB Files (see Top ten reasons why you should be parsing PDB. #1441, extend doc)

• Advanced Methods

  • Immersed Boundary Method for soft elastic objects (OIF)
  • Object-in-fluid (OIF)

• Appendix

  • Reaction Ensemble (add examples; highlight that doc is in class description; move to Advanced methods)
  • Electrokinetics (shift from purely physical doc to python doc; move to Advanced methods)

Commented out (Keep in core for now, don't expose to user):

• System

  • GHMC thermostat

• Particles

  • Cross-linking polymers
  • Virtual sites in the center of mass of a molecule
  • (Virtual Sites) Additional features

• Non-bonded interactions

  • Directional Lennard-Jones interaction

• Electrostatics

  • Maxwell Equation Molecular Dynamics (MEMD)

• Lattice Boltzmann

  • The Shan Chen bicomponent fluid
  • SC as a thermostat
  • SC component-dependent interactions between particles

• Analysis

  • Radial density map
  • Van-Hove autocorrelation function
  • Aggregation
  • Finding holes

• Advanced methods:

  • nemd: Setting up non-equilibrium MD

Removed (Not supported anymore):

• Setting up an icosaeder

Announced in / fixes #1778

[KonradBreitsprecher]

ICP GitLab CI link down for some reason...

[mkuron]

Try to amend the commit so it gets a new hash and then push again. It seems like the CI never got notified.

[KaiSzuttor]

Maybe the webserver had been down when the pr was opened, i can trigger the webhook manually

[KaiSzuttor]

didnt help, will have a look

[hmenke]

Removed (Not supported anymore):

• Parsing PDB Files

What about #1441?

[KonradBreitsprecher]

@hmenke Yes I missed that. But the doc could be extended.

[codecov]

Codecov Report

Merging #1785 into python will increase coverage by <1%.
The diff coverage is n/a.

@@           Coverage Diff           @@
##           python   #1785    +/-   ##
=======================================
+ Coverage      58%     58%   +<1%     
=======================================
  Files         416     417     +1     
  Lines       29268   29413   +145     
=======================================
+ Hits        17162   17277   +115     
- Misses      12106   12136    +30

Impacted Files	Coverage Δ
src/core/observables/ProfileObservable.hpp	33% <0%> (-17%)	⬇️
src/core/observables/CylindricalDensityProfile.hpp	85% <0%> (-7%)	⬇️
...core/observables/CylindricalFluxDensityProfile.hpp	65% <0%> (-4%)	⬇️
...ndricalLBFluxDensityProfileAtParticlePositions.cpp	76% <0%> (-4%)	⬇️
src/core/p3m.cpp	82% <0%> (-1%)	⬇️
src/core/observables/LBRadialVelocityProfile.hpp	0% <0%> (ø)	⬆️
src/core/utils/coordinate_transformation.hpp	100% <0%> (ø)
src/core/observables/ForceDensityProfile.hpp	95% <0%> (ø)	⬆️
...rc/core/observables/CylindricalVelocityProfile.hpp	95% <0%> (ø)	⬆️
src/core/observables/FluxDensityProfile.hpp	94% <0%> (ø)	⬆️
... and 3 more

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[KaiSzuttor]

gitlab webhook does not work because you deleted your python branch on github

[KaiSzuttor]

i just fixed it, but still you may have deleted your branch unintentionally @KonradBreitsprecher

[KonradBreitsprecher]

That happened while cleaning my github.. thanks @KaiSzuttor.

[fweik]

So the plan is to merge this now and then work on the docs on Friday? Or does anybody wants to still discuss the structure?