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Fix polymer generation #3484

Merged
merged 6 commits into from
Feb 14, 2020
Merged

Fix polymer generation #3484

merged 6 commits into from
Feb 14, 2020

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fweik
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@fweik fweik commented Feb 14, 2020

Fixes #3483.

Description of changes:

  • Obey minimum image convention
  • To not falsely pre-populate all positions with the zero vector
  • Refactored generation loop to make it more redable
  • Check for constraint violations between starting positions

@fweik fweik requested a review from jngrad February 14, 2020 15:15
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codecov bot commented Feb 14, 2020 •
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Codecov Report

Merging #3484 into python will increase coverage by <1%.
The diff coverage is 92%.

Impacted file tree graph

@@           Coverage Diff           @@
##           python   #3484    +/-   ##
=======================================
+ Coverage      87%     87%   +<1%     
=======================================
  Files         537     537            
  Lines       24460   24449    -11     
=======================================
- Hits        21291   21284     -7     
+ Misses       3169    3165     -4
Impacted Files Coverage Δ
src/core/polymer.cpp 95% <92%> (+5%) ⬆️
src/core/particle_data.cpp 97% <0%> (-1%) ⬇️

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jngrad
jngrad requested changes Feb 14, 2020
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jngrad commented Feb 14, 2020

This is a lot better! The polymer_linear.py test doesn't fail anymore, even with a different seed at each execution. This isn't the first time that a bug is ignored by setting a magic seed in the test script...

@jngrad jngrad added this to the Espresso 4.1.3 milestone Feb 14, 2020
@fweik @jngrad
Fixed typos
e98e913 
Co-Authored-By: Jean-Noël Grad <[email protected]>
@jngrad jngrad added the automerge Merge with kodiak label Feb 14, 2020
@kodiakhq kodiakhq bot merged commit 9c2c70d into espressomd:python Feb 14, 2020
@fweik fweik deleted the polymer branch February 14, 2020 20:26
@jngrad jngrad mentioned this pull request Feb 17, 2020
Merged
kodiakhq bot added a commit that referenced this pull request Feb 17, 2020
@kodiakhq
Remove infinite loop in linear polymer (#3491)
f9ae0e8 
Description of changes:
- fix infinite loop in `draw_polymer_positions()` (regression from #3484)
- remove fixed seed in the `polymer_linear.py` test that used to hide a bug in the previous implementation of `draw_polymer_positions()`
@KaiSzuttor KaiSzuttor mentioned this pull request Feb 18, 2020
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jngrad added a commit to jngrad/espresso that referenced this pull request Feb 19, 2020
@jngrad
Fix electrophoresis sample test
c68c018 
The two values changed after the polymer refactoring in espressomd#3484.
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Polymer generation does not obey minimum image convention
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@fweik @jngrad