Issue 1582 concentration #1866

valentinsulzer · 2021-12-19T17:34:02Z

Description

Make initial concentration a function of r as well as x.
This prompted a few changes to the internal representation of function parameters, averaging, etc

Fixes #1582

Type of change

Please add a line in the relevant section of CHANGELOG.md to document the change (include PR #) - note reverse order of PR #s. If necessary, also add to the list of breaking changes.

New feature (non-breaking change which adds functionality)
Optimization (back-end change that speeds up the code)
Bug fix (non-breaking change which fixes an issue)

Key checklist:

No style issues: $ flake8
All tests pass: $ python run-tests.py --unit
The documentation builds: $ cd docs and then $ make clean; make html

You can run all three at once, using $ python run-tests.py --quick.

Further checks:

Code is commented, particularly in hard-to-understand areas
Tests added that prove fix is effective or that feature works

codecov · 2021-12-21T18:25:38Z

Codecov Report

Merging #1866 (6f636bd) into develop (bac27fd) will increase coverage by 0.00%.
The diff coverage is 99.55%.

❗ Current head 6f636bd differs from pull request most recent head 21b84ba. Consider uploading reports for the commit 21b84ba to get more accurate results

@@            Coverage Diff            @@
##           develop    #1866    +/-   ##
=========================================
  Coverage    99.32%   99.32%            
=========================================
  Files          346      346            
  Lines        19124    18981   -143     
=========================================
- Hits         18995    18853   -142     
+ Misses         129      128     -1

Impacted Files	Coverage Δ
pybamm/__init__.py	`100.00% <ø> (ø)`
pybamm/meshes/meshes.py	`97.77% <ø> (-0.17%)`	⬇️
pybamm/util.py	`100.00% <ø> (ø)`
pybamm/expression_tree/scalar.py	`96.77% <75.00%> (ø)`
pybamm/expression_tree/symbol.py	`98.54% <98.57%> (-0.21%)`	⬇️
pybamm/discretisations/discretisation.py	`99.79% <100.00%> (+<0.01%)`	⬆️
pybamm/expression_tree/array.py	`100.00% <100.00%> (ø)`
pybamm/expression_tree/averages.py	`100.00% <100.00%> (ø)`
pybamm/expression_tree/binary_operators.py	`99.54% <100.00%> (-0.01%)`	⬇️
pybamm/expression_tree/broadcasts.py	`100.00% <100.00%> (ø)`
... and 46 more

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Δ = absolute <relative> (impact), ø = not affected, ? = missing data
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valentinsulzer · 2022-01-21T00:22:33Z

Benchmarks are still failing, but only just, and it's only setup, and I can't figure out how to bring them down

rtimms

thanks @tinosulzer looks great! much prefer just having a single domains dict

rtimms · 2022-01-25T09:54:03Z

pybamm/expression_tree/array.py

@@ -25,6 +25,11 @@ class Array(pybamm.Symbol):
        list of domains the parameter is valid over, defaults to empty list
    auxiliary_domainds : dict, optional


wasn't you, but there is a typo in auxiliary_domains

rtimms · 2022-01-25T09:58:29Z

pybamm/expression_tree/independent_variable.py

@@ -20,18 +20,25 @@ class IndependentVariable(pybamm.Symbol):
        name of the node
    domain : iterable of str
        list of domains that this variable is valid over
+    auxiliary_domainds : dict, optional


"domainds" again

rtimms · 2022-01-25T10:22:14Z

test.json

@@ -0,0 +1 @@
+{"c": [1.0, 0.9798027714409646, 0.960006460477965, 0.9406095788204055, 0.9216020347741102, 0.9029823702003188, 0.8847366581852026, 0.8668601056564101, 0.8493459377424136, 0.832186662408666, 0.8153749778386046, 0.7989034974265092, 0.782764985023561, 0.7669526757329163, 0.751460238142306, 0.7362803334995669, 0.7214067595017163, 0.7068339060218576, 0.692555361502903, 0.6785650429748535, 0.664857083100717, 0.6514259326371419, 0.6382661109279633, 0.625372202374782, 0.6127383975890887, 0.600359805229227, 0.5882313786270565, 0.5763482045504048, 0.5647049769256993, 0.5532968734428519, 0.5421193144470962, 0.5311677011174264, 0.5204374421815062, 0.5099238253787153, 0.49962263026903947, 0.48952957667911157, 0.47964047942244703, 0.4699510980498083, 0.4604574329920214, 0.4511555543059014, 0.4420416052186034, 0.4331116685232906, 0.4243618878176341, 0.41578879237242733, 0.4073888417395631, 0.39915858160714324, 0.3910946437994791, 0.3831937462770909, 0.37545269003839876, 0.3678681114226823], "d": 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can this file be deleted?

valentinsulzer added 18 commits August 5, 2021 13:50

#1582 allow initial concentration to depend on r

18ac674

#1582 flake8

dc0dd72

Merge branch 'develop' into issue-1582-concentration

1bee8cc

#1582 fix tests

c6daef5

#1582 merge develop

611219f

#1582 merge develop

cbfdbea

Merge branch 'develop' into issue-1582-concentration

a7eb9b9

#1582 fixing tests

eb2042b

Merge branch 'develop' into issue-1582-concentration

569f814

#1582 merge develop

de6bce4

Merge branch 'issue-1816-domain-error' into issue-1582-concentration

4e046fe

#1582 fix compare_lithium_ion

b69d1d0

#1582 merge #1781

8e79d8c

#1582 fix tests

d6b08cb

#1582 merge averages-class

2ae4d5c

#1582 merge develop

8ea7dc7

Merge branch 'develop' into issue-1582-concentration

9d8cd09

#1582 fix some tests

1d86579

valentinsulzer marked this pull request as draft December 19, 2021 17:34

valentinsulzer added 5 commits December 19, 2021 12:39

#1582 remove accidental duplicate files

2bda121

#1582 reduce if statements

d00ffb5

#1582 revert examples

40e2681

#1582 fix test

038d3f9

merge develop

c3ffef2

valentinsulzer added 5 commits December 29, 2021 09:28

#1582 fixing tests

647540a

Merge branch 'develop' into issue-1582-concentration

556490d

flake8

cdde52a

#1582 fix dfn tests

be7f4a8

#1582 revert examples

966f3a3

valentinsulzer added 14 commits January 12, 2022 13:03

#1582 replacing auxiliary_domains with domains

d4d044a

merge develop

c36c0b4

#1582 fix tests except save/load

7b8d60b

remove gif

6d4371a

#1582 fix save/load

6c8d7aa

#1582 benchmark test

20e6f41

#1582 more tests and benchmarks

f6ce7bd

#1582 flake8

31a30fb

#1582 fix tests

8fda417

#1582 fix docs

a2cb799

#1582 flake8

13e25c8

#1582 merge develop

5eb20f7

#158 coverage

434a544

#1582 coverage and benchmarks

a050d8d

valentinsulzer marked this pull request as ready for review January 21, 2022 00:22

valentinsulzer requested review from brosaplanella and rtimms January 21, 2022 00:22

valentinsulzer added 3 commits January 21, 2022 14:17

Merge branch 'develop' into issue-1582-concentration

d0af13b

#1582 merge develop

ba9a4d0

#1582 test for benchmarks

79e330d

rtimms approved these changes Jan 25, 2022

View reviewed changes

valentinsulzer added 6 commits February 1, 2022 14:10

Merge branch 'develop' into issue-1582-concentration

9b0aa46

#1582 test benchmarks

f1a644a

#1582 more benchmarking

a9acb6b

#1582 deprecate domain setter and fix tests

7cc0d9f

#1582 changelog

6f636bd

#1582 remove test.json

21b84ba

valentinsulzer merged commit 4e028e0 into develop Feb 2, 2022

valentinsulzer deleted the issue-1582-concentration branch February 2, 2022 17:27

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Issue 1582 concentration #1866

Issue 1582 concentration #1866

valentinsulzer commented Dec 19, 2021

codecov bot commented Dec 21, 2021 •

edited

valentinsulzer commented Jan 21, 2022

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rtimms Jan 25, 2022

		@@ -25,6 +25,11 @@ class Array(pybamm.Symbol):
		list of domains the parameter is valid over, defaults to empty list
		auxiliary_domainds : dict, optional

Issue 1582 concentration #1866

Issue 1582 concentration #1866

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valentinsulzer commented Dec 19, 2021

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codecov bot commented Dec 21, 2021 • edited

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codecov bot commented Dec 21, 2021 •

edited