Reaction Ensemble refactor and unit testing #4164

jngrad · 2021-03-17T12:08:42Z

Description of changes:

make SingleReaction class self-contained
make RE methods and arguments const whenever possible
write unit tests for the acceptance probability of all RE classes
write integration tests to increase code coverage of RE to 90%

This way the methods can be unit tested.

src/core/reaction_ensemble.hpp

src/core/unit_tests/reaction_ensemble_classes_test.cpp

Also do some cosmetic changes.

Move the Wang-Landau output files checks to an interface test. The statistical test runs the Monte Carlo algorithm until convergence.

Sample at a pH farther away from the pKa, shorten warmup phase, run with 1 MPI rank to remove large overhead from communication.

src/core/unit_tests/reaction_ensemble_classes_test.cpp

Separate the formatting code from the file opening code. Helps with unit testing.

KaiSzuttor

Overall looks good, it's just not the prettiest neighbourhood of espresso :P

src/core/reaction_ensemble.cpp

src/core/unit_tests/reaction_ensemble_classes_test.cpp

testsuite/python/constant_pH_stats.py

jngrad added 9 commits March 11, 2021 15:59

core: Move SingleReaction constructor

7add1c6

core: ReactionEnsemble: make everything const

b62a88c

tests: Unit test ReactionEnsemble classes

974e8e9

tests: Check factorial expression

3191b97

core: Make acceptance probability methods protected

acf5786

This way the methods can be unit tested.

tests: Check acceptance probability methods

3d22a1d

core: Remove prototype without implementation

b032021

core: Add missing includes

62cdcb5

core: Fix -Wconversion

959b426

jngrad added Testcase CodeQuality labels Mar 17, 2021

KaiSzuttor reviewed Mar 17, 2021

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src/core/reaction_ensemble.hpp Outdated Show resolved Hide resolved

KaiSzuttor reviewed Mar 17, 2021

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src/core/unit_tests/reaction_ensemble_classes_test.cpp Show resolved Hide resolved

jngrad added 8 commits March 18, 2021 10:16

tests: Check Wang-Landau CV and histogram

b32e086

core: Improve documentation of RE classes

989395b

test: Improve clarity of RE unit tests

a8d0bd5

core: Simplify RE code

3d282f8

tests: Rename Reaction Ensemble statistical tests

ccfd290

Also do some cosmetic changes.

tests: Split Wang-Landau test

f40d61e

Move the Wang-Landau output files checks to an interface test. The statistical test runs the Monte Carlo algorithm until convergence.

tests: Create a faster constant pH test

ce04cc6

Sample at a pH farther away from the pKa, shorten warmup phase, run with 1 MPI rank to remove large overhead from communication.

tests: Remove UB in unit test

76332ae

jngrad added the Core label Mar 18, 2021

KaiSzuttor reviewed Mar 23, 2021

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src/core/unit_tests/reaction_ensemble_classes_test.cpp Outdated Show resolved Hide resolved

jngrad added 2 commits March 23, 2021 15:24

core: Refactor Wang-Landau write function

a942d87

Separate the formatting code from the file opening code. Helps with unit testing.

tests: Simplify code

ebb8ab7

jngrad changed the title ~~Reaction Ensemble unit tests~~ Reaction Ensemble refactor and unit testing Mar 23, 2021

KaiSzuttor reviewed Mar 24, 2021

View reviewed changes

jngrad added 3 commits March 24, 2021 13:37

core: Simplify file I/O operations

ead37ef

core: Refactor Wang-Landau Collective Variable

28eea67

core: Use std::accumulate

3090ff7

tests: Remove WidomInsertion unit test

b3e6d4f

KaiSzuttor approved these changes Mar 24, 2021

View reviewed changes

jngrad added the automerge Merge with kodiak label Mar 24, 2021

Merge branch 'python' into re_unit_tests

d06d823

kodiakhq bot merged commit b6fa1a9 into espressomd:python Mar 24, 2021

jngrad deleted the re_unit_tests branch March 24, 2021 16:15

jngrad added this to the Espresso 4.2 milestone Jun 27, 2022

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Reaction Ensemble refactor and unit testing #4164

Reaction Ensemble refactor and unit testing #4164

jngrad commented Mar 17, 2021 •

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Reaction Ensemble refactor and unit testing #4164

Reaction Ensemble refactor and unit testing #4164

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jngrad commented Mar 17, 2021 •

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