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Implement Integrated electrolyte conductivity #1188

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merged 112 commits into from
Nov 4, 2020
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Merged

Implement Integrated electrolyte conductivity #1188

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92de548
#884 added integrated conductivity model
brosaplanella Apr 22, 2020
e5d7c14
#884 debugging new submodel
brosaplanella May 16, 2020
fb667b3
#884 added integrated conductivity model
brosaplanella Apr 22, 2020
7899fdd
#884 debugging new submodel
brosaplanella May 16, 2020
7b3df30
Merge branch 'issue-884-electrolyte-integrated-conductivity' of https…
brosaplanella May 19, 2020
573db34
#884 added integrated conductivity model
brosaplanella Apr 22, 2020
eec8354
#884 debugging new submodel
brosaplanella May 16, 2020
5d7ca5d
Merge branch 'issue-884-electrolyte-integrated-conductivity' of https…
brosaplanella May 20, 2020
334dd17
flake8
brosaplanella May 20, 2020
3eb9c68
#884 added integrated conductivity model
brosaplanella Apr 22, 2020
4a3ebf7
#884 debugging new submodel
brosaplanella May 16, 2020
5c5b7fa
flake8
brosaplanella May 20, 2020
00bfd7c
added tab parameters (set to zero) so thermal model runs
brosaplanella May 21, 2020
a8496db
debugged conductivity
brosaplanella May 26, 2020
34b94f3
added new SPMe model
brosaplanella May 26, 2020
e439182
fix merge conflict
brosaplanella May 26, 2020
3ebae0b
flake8
brosaplanella May 26, 2020
5548930
#884 added integrated conductivity model
brosaplanella Apr 22, 2020
4c10748
#884 debugging new submodel
brosaplanella May 16, 2020
7e3c823
flake8
brosaplanella May 20, 2020
3f76b27
debugged conductivity
brosaplanella May 26, 2020
577f5fc
added new SPMe model
brosaplanella May 26, 2020
a39ac10
flake8
brosaplanella May 26, 2020
9d30d37
solved merge conflict
brosaplanella May 28, 2020
e7897be
#884 added integrated conductivity model
brosaplanella Apr 22, 2020
428e4aa
#884 debugging new submodel
brosaplanella May 16, 2020
e30ddf9
flake8
brosaplanella May 20, 2020
f5bef85
debugged conductivity
brosaplanella May 26, 2020
7ebf86a
added new SPMe model
brosaplanella May 26, 2020
f0aa087
flake8
brosaplanella May 26, 2020
57c856b
Merge branch 'issue-884-electrolyte-integrated-conductivity' of https…
brosaplanella Jun 10, 2020
320804b
#884 fixed the new SPMe model to work with the new geometry
brosaplanella Jun 11, 2020
bf92330
#884 added integrated conductivity model
brosaplanella Apr 22, 2020
44bdd41
#884 debugging new submodel
brosaplanella May 16, 2020
a0d17b5
flake8
brosaplanella May 20, 2020
90eb3ee
#884 added integrated conductivity model
brosaplanella Apr 22, 2020
bef6b8c
flake8
brosaplanella May 20, 2020
80dc52d
debugged conductivity
brosaplanella May 26, 2020
3866e20
added new SPMe model
brosaplanella May 26, 2020
a5c51cd
flake8
brosaplanella May 26, 2020
7b55d57
#884 debugging new submodel
brosaplanella May 16, 2020
06674fa
debugged conductivity
brosaplanella May 26, 2020
a923ca7
#884 fixed the new SPMe model to work with the new geometry
brosaplanella Jun 11, 2020
593ddd4
Merge branch 'issue-884-electrolyte-integrated-conductivity' of https…
brosaplanella Jun 22, 2020
764fcec
#884 cleaned code
brosaplanella Jun 22, 2020
96eb696
#884 added integrated conductivity model
brosaplanella Apr 22, 2020
183a765
#884 debugging new submodel
brosaplanella May 16, 2020
c0448ca
flake8
brosaplanella May 20, 2020
d790866
debugged conductivity
brosaplanella May 26, 2020
c135494
added new SPMe model
brosaplanella May 26, 2020
1cee889
flake8
brosaplanella May 26, 2020
a92fcf8
#884 fixed the new SPMe model to work with the new geometry
brosaplanella Jun 11, 2020
8dc661f
#884 added integrated conductivity model
brosaplanella Apr 22, 2020
40b12c3
flake8
brosaplanella May 20, 2020
fb4f6d9
#884 debugging new submodel
brosaplanella May 16, 2020
9e0d807
debugged conductivity
brosaplanella May 26, 2020
71d7a03
#884 cleaned code
brosaplanella Jun 22, 2020
d8108e8
#884 renamed model
brosaplanella Jun 23, 2020
4e47666
Merge branch 'issue-884-electrolyte-integrated-conductivity' of https…
brosaplanella Jun 23, 2020
6ec5ce6
#884 added integrated conductivity model
brosaplanella Apr 22, 2020
4a6874f
#884 debugging new submodel
brosaplanella May 16, 2020
b6626c0
flake8
brosaplanella May 20, 2020
93eefae
debugged conductivity
brosaplanella May 26, 2020
679ffbe
added new SPMe model
brosaplanella May 26, 2020
0a6dfd9
flake8
brosaplanella May 26, 2020
51f71c4
#884 fixed the new SPMe model to work with the new geometry
brosaplanella Jun 11, 2020
02ee792
#884 added integrated conductivity model
brosaplanella Apr 22, 2020
2b77066
flake8
brosaplanella May 20, 2020
a91053d
#884 debugging new submodel
brosaplanella May 16, 2020
7e6de9d
debugged conductivity
brosaplanella May 26, 2020
466e502
#884 cleaned code
brosaplanella Jun 22, 2020
d11e266
#884 debugging new submodel
brosaplanella May 16, 2020
a15c8d5
debugged conductivity
brosaplanella May 26, 2020
1521a3f
#884 added integrated conductivity model
brosaplanella Apr 22, 2020
73a5bfa
flake8
brosaplanella May 20, 2020
85c77e7
#884 debugging new submodel
brosaplanella May 16, 2020
3904114
debugged conductivity
brosaplanella May 26, 2020
1ae86bb
#884 cleaned code
brosaplanella Jun 22, 2020
62c52ea
#884 renamed model
brosaplanella Jun 23, 2020
9999775
Merge branch 'issue-884-electrolyte-integrated-conductivity' of https…
brosaplanella Jun 23, 2020
b55ede7
Merge branch 'develop' into issue-884-electrolyte-integrated-conducti…
brosaplanella Sep 15, 2020
dd8e174
Merge branch 'develop' into issue-884-electrolyte-integrated-conducti…
brosaplanella Oct 7, 2020
f4ba84e
#884 tidy up for merge
brosaplanella Oct 13, 2020
cf39650
#884 removed SPME_FBP (for development only)
brosaplanella Oct 13, 2020
756e093
#884 add preliminary citation
brosaplanella Oct 13, 2020
9d08f5e
#884 add test
brosaplanella Oct 13, 2020
0d19dbc
#884 removed activation energy from Nyman2008
brosaplanella Oct 13, 2020
48ca85c
Merge branch 'develop' into issue-884-electrolyte-integrated-conducti…
brosaplanella Oct 14, 2020
5eee5be
Merge branch 'develop' into issue-884-electrolyte-integrated-conducti…
brosaplanella Oct 19, 2020
e615e4a
#884 update CHANGELOG
brosaplanella Oct 19, 2020
08d191c
#884 add docs
brosaplanella Oct 19, 2020
6a89b7d
#884 removed arrhenius term
brosaplanella Oct 20, 2020
3f04c15
#884 included docstring reference
brosaplanella Oct 20, 2020
86051b9
#884 removed redundant right boundary integrals
brosaplanella Oct 20, 2020
a019e6b
#884 added SPMe tests
brosaplanella Oct 20, 2020
8341306
flake8
brosaplanella Oct 20, 2020
4890bab
#884 fixed typo in docs
brosaplanella Oct 20, 2020
f35dd26
#884 fix documentation
brosaplanella Oct 20, 2020
30ab27c
#884 added options to set integrated conductivity
brosaplanella Oct 22, 2020
6aa1bb3
#884 #1207 implemented option to choose electrolyte conductivity and …
brosaplanella Oct 23, 2020
0308466
#1207 update CHANGELOG
brosaplanella Oct 23, 2020
ddb5ac5
Merge branch 'develop' into issue-884-electrolyte-integrated-conducti…
brosaplanella Oct 23, 2020
006dc25
#884 set SPMe surface form to NotImplemented for the moment
brosaplanella Oct 23, 2020
480765f
#884 update CHANGELOG
brosaplanella Oct 23, 2020
9818f21
flake8
brosaplanella Oct 23, 2020
3afea4e
#884 removed SPMe from test_compare_outputs for surface form
brosaplanella Oct 23, 2020
8672eff
Merge branch 'develop' into issue-884-electrolyte-integrated-conducti…
brosaplanella Oct 24, 2020
e286ce0
Merge branch 'develop' into issue-884-electrolyte-integrated-conducti…
brosaplanella Oct 27, 2020
c301814
#884 fix typo CITATIONS.txt
brosaplanella Oct 27, 2020
f67357b
#884 add test citation Brosa Planella 2020
brosaplanella Nov 3, 2020
5d4bd51
#884 update citation TSPMe
brosaplanella Nov 4, 2020
49fa413
Merge branch 'develop' into issue-884-electrolyte-integrated-conducti…
brosaplanella Nov 4, 2020
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flake8
@brosaplanella
brosaplanella committed Jun 23, 2020

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commit c0448cae0fd44b266254c3540689c286df8e1360
44 changes: 28 additions & 16 deletions pybamm/models/submodels/electrolyte_conductivity/integrated_conductivity.py
View file
Original file line number Diff line number Diff line change
@@ -43,7 +43,7 @@ def get_coupled_variables(self, variables):

tor_n = variables["Negative electrolyte tortuosity"]
tor_s = variables["Separator tortuosity"]
tor_p = variables["Positive electrolyte tortuosity"]
tor_p = variables["Positive electrolyte tortuosity"]

T_av = variables["X-averaged cell temperature"]
T_av_n = pybamm.PrimaryBroadcast(T_av, "negative electrode")
@@ -77,23 +77,37 @@ def get_coupled_variables(self, variables):
# i_e_edge = pybamm.Concatenation(i_e_n_edge, i_e_s_edge, i_e_p_edge)

# electrolyte potential
indef_integral_n = pybamm.IndefiniteIntegral(
i_e_n_edge / (param.kappa_e(c_e_n, T_av_n) * tor_n), x_n
) * param.C_e / param.gamma_e
indef_integral_s = pybamm.IndefiniteIntegral(
i_e_s_edge / (param.kappa_e(c_e_s, T_av_s) * tor_s), x_s
) * param.C_e / param.gamma_e
indef_integral_p = pybamm.IndefiniteIntegral(
i_e_p_edge / (param.kappa_e(c_e_p, T_av_p) * tor_p), x_p
) * param.C_e / param.gamma_e

indef_integral_n = (
pybamm.IndefiniteIntegral(
i_e_n_edge / (param.kappa_e(c_e_n, T_av_n) * tor_n), x_n
)
* param.C_e
/ param.gamma_e
)
indef_integral_s = (
pybamm.IndefiniteIntegral(
i_e_s_edge / (param.kappa_e(c_e_s, T_av_s) * tor_s), x_s
)
* param.C_e
/ param.gamma_e
)
indef_integral_p = (
pybamm.IndefiniteIntegral(
i_e_p_edge / (param.kappa_e(c_e_p, T_av_p) * tor_p), x_p
)
* param.C_e
/ param.gamma_e
)

integral_n = indef_integral_n - pybamm.boundary_value(indef_integral_n, "left")
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left boundary value of an indefinite integral should always be zero by definition (and implementation) but worth checking

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I checked, and maybe it evaluates to zero (actually it should), but is not zero by definition. The definition is

<bound method UnaryOperator.evaluate of BoundaryValue(-0x33bf8d7889aadb3a, boundary value, children=["* integrated w.r.t x_n on ['negative electrode'](3.0 * x_n ** 2.0)"], domain=['current collector'], auxiliary_domains={})>

integral_s = (
indef_integral_s - pybamm.boundary_value(indef_integral_s, "left")
indef_integral_s
- pybamm.boundary_value(indef_integral_s, "left")
+ pybamm.boundary_value(integral_n, "right")
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pybamm.Integral(a) should give the same value as pybamm.boundary_value(pybamm.IndefiniteIntegral(a), "right") while building a smaller tree

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but maybe it automatically gets simplified down to the same tree anyway

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How can I check if they reduce to the same tree? In any case, I think that if they are equivalent, using pybamm.Integral(a) and removing the boundary values on the left should result in a much more readable code.

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Just tried replacing the boundary value at the "right" by Integral and I get a very long error (see below) which basically looks like a dimension mismatch. So I guess they are not the same object...

Traceback (most recent call last):
  File "/home/ferranbrosa/PyBaMM/pybamm/discretisations/discretisation.py", line 817, in process_symbol
    return self._discretised_symbols[symbol.id]
KeyError: 1041553401910644705

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/ferranbrosa/PyBaMM/pybamm/discretisations/discretisation.py", line 817, in process_symbol
    return self._discretised_symbols[symbol.id]
KeyError: 2459353937759019131

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/ferranbrosa/PyBaMM/pybamm/discretisations/discretisation.py", line 817, in process_symbol
    return self._discretised_symbols[symbol.id]
KeyError: 4130260032263747209

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/ferranbrosa/PyBaMM/pybamm/discretisations/discretisation.py", line 817, in process_symbol
    return self._discretised_symbols[symbol.id]
KeyError: 7060176036539492958

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/ferranbrosa/PyBaMM/pybamm/discretisations/discretisation.py", line 817, in process_symbol
    return self._discretised_symbols[symbol.id]
KeyError: 8911840126246680561

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/ferranbrosa/PyBaMM/pybamm/discretisations/discretisation.py", line 817, in process_symbol
    return self._discretised_symbols[symbol.id]
KeyError: -7919469058354380383

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/ferranbrosa/PyBaMM/pybamm/expression_tree/symbol.py", line 594, in evaluate_for_shape
    return self._saved_evaluate_for_shape
AttributeError: 'MatrixMultiplication' object has no attribute '_saved_evaluate_for_shape'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/ferranbrosa/PyBaMM/pybamm/expression_tree/symbol.py", line 801, in test_shape
    self.shape_for_testing
  File "/home/ferranbrosa/PyBaMM/pybamm/expression_tree/symbol.py", line 785, in shape_for_testing
    evaluated_self = self.evaluate_for_shape()
  File "/home/ferranbrosa/PyBaMM/pybamm/expression_tree/symbol.py", line 596, in evaluate_for_shape
    self._saved_evaluate_for_shape = self._evaluate_for_shape()
  File "/home/ferranbrosa/PyBaMM/pybamm/expression_tree/binary_operators.py", line 201, in _evaluate_for_shape
    return self._binary_evaluate(left, right)
  File "/home/ferranbrosa/PyBaMM/pybamm/expression_tree/binary_operators.py", line 497, in _binary_evaluate
    return left @ right
  File "/home/ferranbrosa/coding/reduced-TEC/env/lib/python3.7/site-packages/scipy/sparse/base.py", line 564, in __matmul__
    return self.__mul__(other)
  File "/home/ferranbrosa/coding/reduced-TEC/env/lib/python3.7/site-packages/scipy/sparse/base.py", line 502, in __mul__
    raise ValueError('dimension mismatch')
ValueError: dimension mismatch

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/ferranbrosa/miniconda3/lib/python3.7/runpy.py", line 193, in _run_module_as_main
    "__main__", mod_spec)
  File "/home/ferranbrosa/miniconda3/lib/python3.7/runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "/home/ferranbrosa/.vscode-server/extensions/ms-python.python-2020.9.114305/pythonFiles/lib/python/debugpy/__main__.py", line 45, in <module>
    cli.main()
  File "/home/ferranbrosa/.vscode-server/extensions/ms-python.python-2020.9.114305/pythonFiles/lib/python/debugpy/../debugpy/server/cli.py", line 430, in main
    run()
  File "/home/ferranbrosa/.vscode-server/extensions/ms-python.python-2020.9.114305/pythonFiles/lib/python/debugpy/../debugpy/server/cli.py", line 267, in run_file
    runpy.run_path(options.target, run_name=compat.force_str("__main__"))
  File "/home/ferranbrosa/miniconda3/lib/python3.7/runpy.py", line 263, in run_path
    pkg_name=pkg_name, script_name=fname)
  File "/home/ferranbrosa/miniconda3/lib/python3.7/runpy.py", line 96, in _run_module_code
    mod_name, mod_spec, pkg_name, script_name)
  File "/home/ferranbrosa/miniconda3/lib/python3.7/runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "/home/ferranbrosa/coding/reduced-TEC/TSPMe_compare_DFN.py", line 91, in <module>
    sim.solve([0, 3700 / Crate])
  File "/home/ferranbrosa/PyBaMM/pybamm/simulation.py", line 338, in solve
    self.build(check_model=check_model)
  File "/home/ferranbrosa/PyBaMM/pybamm/simulation.py", line 291, in build
    self._model_with_set_params, inplace=False, check_model=check_model
  File "/home/ferranbrosa/PyBaMM/pybamm/discretisations/discretisation.py", line 173, in process_model
    self.set_internal_boundary_conditions(model)
  File "/home/ferranbrosa/PyBaMM/pybamm/discretisations/discretisation.py", line 419, in set_internal_boundary_conditions
    rbc = (boundary_gradient(first_orphan, next_orphan), "Neumann")
  File "/home/ferranbrosa/PyBaMM/pybamm/discretisations/discretisation.py", line 399, in boundary_gradient
    right_symbol_disc = self.process_symbol(right_symbol)
  File "/home/ferranbrosa/PyBaMM/pybamm/discretisations/discretisation.py", line 819, in process_symbol
    discretised_symbol = self._process_symbol(symbol)
  File "/home/ferranbrosa/PyBaMM/pybamm/discretisations/discretisation.py", line 853, in _process_symbol
    disc_right = self.process_symbol(right)
  File "/home/ferranbrosa/PyBaMM/pybamm/discretisations/discretisation.py", line 819, in process_symbol
    discretised_symbol = self._process_symbol(symbol)
  File "/home/ferranbrosa/PyBaMM/pybamm/discretisations/discretisation.py", line 853, in _process_symbol
    disc_right = self.process_symbol(right)
  File "/home/ferranbrosa/PyBaMM/pybamm/discretisations/discretisation.py", line 819, in process_symbol
    discretised_symbol = self._process_symbol(symbol)
  File "/home/ferranbrosa/PyBaMM/pybamm/discretisations/discretisation.py", line 862, in _process_symbol
    disc_child = self.process_symbol(child)
  File "/home/ferranbrosa/PyBaMM/pybamm/discretisations/discretisation.py", line 819, in process_symbol
    discretised_symbol = self._process_symbol(symbol)
  File "/home/ferranbrosa/PyBaMM/pybamm/discretisations/discretisation.py", line 852, in _process_symbol
    disc_left = self.process_symbol(left)
  File "/home/ferranbrosa/PyBaMM/pybamm/discretisations/discretisation.py", line 819, in process_symbol
    discretised_symbol = self._process_symbol(symbol)
  File "/home/ferranbrosa/PyBaMM/pybamm/discretisations/discretisation.py", line 852, in _process_symbol
    disc_left = self.process_symbol(left)
  File "/home/ferranbrosa/PyBaMM/pybamm/discretisations/discretisation.py", line 821, in process_symbol
    discretised_symbol.test_shape()
  File "/home/ferranbrosa/PyBaMM/pybamm/expression_tree/symbol.py", line 803, in test_shape
    raise pybamm.ShapeError("Cannot find shape (original error: {})".format(e))

)
integral_p = (
indef_integral_p - pybamm.boundary_value(indef_integral_p, "left")
indef_integral_p
- pybamm.boundary_value(indef_integral_p, "left")
+ pybamm.boundary_value(integral_s, "right")
)

@@ -153,9 +167,7 @@ def get_coupled_variables(self, variables):
)

# average electrolyte ohmic losses
delta_phi_e_av = - (
pybamm.x_average(integral_p) - pybamm.x_average(integral_n)
)
delta_phi_e_av = -(pybamm.x_average(integral_p) - pybamm.x_average(integral_n))

variables.update(
self._get_standard_potential_variables(phi_e_n, phi_e_s, phi_e_p)