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Fix ELC sample #3468

Merged
merged 6 commits into from
Feb 11, 2020
Merged

Fix ELC sample #3468

merged 6 commits into from
Feb 11, 2020

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jngrad
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@jngrad jngrad commented Feb 10, 2020

Fixes #3453

Description of changes:

  • remove ELC from P3M sample
  • create a stand-alone ELC sample with a gap and walls
  • update documentation of electrostatics/magnetostatics methods

The script was not correct. The ELC method requires a gap region
with solid walls to block periodicity along the z-direction.
This recycles the recently deleted visualization_mmm2d.py sample.
This recycles the recently deleted documentation for MMM2D.
Move documentation of class constructor arguments from the reSt
files to the corresponding classes docstrings in electrostatics
and magnetostatics methods. Add links to Python classes in reSt
files and add links to reSt files in the Python docstrings.
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jngrad commented Feb 10, 2020

This could be reviewed by @biermanncarl.

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codecov bot commented Feb 10, 2020

Codecov Report

Merging #3468 into python will increase coverage by <1%.
The diff coverage is 97%.

Impacted file tree graph

@@           Coverage Diff           @@
##           python   #3468    +/-   ##
=======================================
+ Coverage      86%     86%   +<1%     
=======================================
  Files         537     537            
  Lines       24730   24659    -71     
=======================================
- Hits        21340   21333     -7     
+ Misses       3390    3326    -64
Impacted Files Coverage Δ
src/core/statistics.hpp 87% <ø> (ø) ⬆️
src/core/shapes/Ellipsoid.cpp 100% <ø> (ø) ⬆️
src/core/dpd.hpp 100% <ø> (ø) ⬆️
src/core/bonded_interactions/thermalized_bond.cpp 83% <ø> (+1%) ⬆️
src/core/shapes/Stomatocyte.cpp 0% <ø> (ø) ⬆️
src/core/statistics.cpp 75% <ø> (+11%) ⬆️
...ore/grid_based_algorithms/lb_particle_coupling.cpp 98% <ø> (ø) ⬆️
src/core/dpd.cpp 91% <100%> (-2%) ⬇️
src/core/observables/TotalForce.hpp 100% <100%> (ø)
src/core/integrators/langevin_inline.hpp 100% <100%> (ø) ⬆️
... and 11 more

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@biermanncarl biermanncarl left a comment

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I put a just a few suggestions on the content of the documentation in my comments. Everything else seems good to me.

doc/sphinx/under_the_hood.rst Outdated Show resolved Hide resolved
doc/sphinx/under_the_hood.rst Outdated Show resolved Hide resolved
src/core/energy.hpp Show resolved Hide resolved
src/core/forces.hpp Show resolved Hide resolved
src/core/pressure.cpp Show resolved Hide resolved
src/python/espressomd/magnetostatics.pyx Show resolved Hide resolved
doc/sphinx/electrostatics.rst Show resolved Hide resolved
doc/sphinx/electrostatics.rst Show resolved Hide resolved
samples/visualization_elc.py Show resolved Hide resolved
@jngrad jngrad added the automerge Merge with kodiak label Feb 11, 2020
@kodiakhq kodiakhq bot merged commit 722e65a into espressomd:python Feb 11, 2020
@jngrad jngrad deleted the fix-3453 branch January 18, 2022 12:07
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ELC sample is missing the gap region
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