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Quaternion formalism in the core and range check #3748

Merged
merged 7 commits into from
Jun 5, 2020
Merged

Quaternion formalism in the core and range check #3748

merged 7 commits into from
Jun 5, 2020

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jngrad
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@jngrad jngrad commented Jun 5, 2020

Partial fix for #3713

Description of changes:

  • document quaternion formalism in the core
  • add an assertion to catch invalid square roots
  • explain that force capping doesn't affect torques
  • use vector operations

jngrad added 6 commits June 4, 2020 11:26
@jngrad
core: Fix literature references
e165a4b
@jngrad
core: Document quaternion formalism
6cd8681
@jngrad
core: Catch incorrect quaternion derivatives
798c3c0 
Pull out the content of the square root and check that it is
positive with an assertion. Explain in the documentation that
it can happen for very high angular velocities.
@jngrad
core: Use vector operations
ae6d7f4
@jngrad
core: Remove duplicated docs
1324b78
@jngrad
docs: Force capping limitation and alternative
b6743a5 
Force capping ignores torques while steepest descent includes them.
@jngrad jngrad added this to the Espresso 4.1.3 milestone Jun 5, 2020
@jngrad jngrad requested a review from RudolfWeeber June 5, 2020 11:42
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codecov bot commented Jun 5, 2020 •
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Codecov Report

Merging #3748 into python will decrease coverage by 0%.
The diff coverage is 100%.

Impacted file tree graph

@@          Coverage Diff           @@
##           python   #3748   +/-   ##
======================================
- Coverage      89%     89%   -1%     
======================================
  Files         552     552           
  Lines       24513   24511    -2     
======================================
- Hits        21842   21831   -11     
- Misses       2671    2680    +9
Impacted Files Coverage Δ
src/core/rotation.hpp 100% <ø> (ø)
src/core/rotation.cpp 100% <100%> (ø)
src/core/polymer.cpp 92% <0%> (-7%) ⬇️
src/core/electrostatics_magnetostatics/p3m.cpp 87% <0%> (-1%) ⬇️
src/core/particle_data.cpp 96% <0%> (-1%) ⬇️

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@RudolfWeeber
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LGTM. Except that steepest descent does not cap the forces/torques but the maximum displacement in position and orientation.

RudolfWeeber
RudolfWeeber previously approved these changes Jun 5, 2020
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jngrad commented Jun 5, 2020

Except that steepest descent does not cap the forces/torques

good point, I'll correct the sentence

@jngrad jngrad added the automerge Merge with kodiak label Jun 5, 2020
@kodiakhq kodiakhq bot merged commit 9fe28fe into espressomd:python Jun 5, 2020
@jngrad jngrad deleted the fixp-3713 branch January 18, 2022 12:13
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@RudolfWeeber RudolfWeeber RudolfWeeber approved these changes

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