Extend BinarySolutionTabulatedThermo by tabulated partial molar volumes #1072

dschmider-HSOG · 2021-07-16T09:22:08Z

Enable to consider non-constant partial molar volumes provided by tabular data, since the partial molar volume of typical battery intercalation materials shows strong dependency on e.g. lithium stoichiometry. The tabular data is included in the same table as enthalpy and entropy data.

-implement optional partialMolarVolume keyword in table(thermo)
-BinarySolutionTabulatedThermo::interpolate is adjusted to be more general and also interpolate partial molar volume
-BinarySolutionTabulatedThermo::integrate is added since partial molar volumes are often needed in integrated form (integrated over lithium stoichiometry)
-BinarySolutionTabulatedThermo::calcDensity is adjusted since density is not constant anymore and changes with varying partial molar volumes

Checklist

The pull request includes a clear description of this code change
Commit messages have short titles and reference relevant issues
Build passes (scons build & scons test) and unit tests address code coverage
Style & formatting of contributed code follows contributing guidelines
The pull request is ready for review

bryanwweber

Hi! Thank you for submitting these changes, the functionality looks like it will be useful. I have several formatting/style comments, if you can please implement them while the technical review is ongoing. Can you also please add a test for this new functionality? If any of my comments are not clear, please post a comment and ask about it, I am more than happy to help. Thank you!

bryanwweber · 2021-07-16T13:29:49Z

include/cantera/thermo/BinarySolutionTabulatedThermo.h

+    void getIntegratedPartialMolarVolumes(doublereal* vbar);
+    void getPartialMolarVolumes(doublereal* vbar) const;


Please avoid using doublereal in new code, preferring the standard double instead.

bryanwweber · 2021-07-16T13:30:34Z

include/cantera/thermo/BinarySolutionTabulatedThermo.h

 protected:
    //! If the compositions have changed, update the tabulated thermo lookup
    virtual void compositionChanged();

    //! Species thermodynamics interpolation functions
-    std::pair<double,double> interpolate(double x) const;
+    double interpolate(double x,const vector_fp& molefrac,const vector_fp& inputData) const;


Function definitions should please have one space after a comma. I'm not sure exactly how long this line is, but we prefer to keep line lengths to 88 characters or less, if possible.

In other words:

Suggested change

double interpolate(double x,const vector_fp& molefrac,const vector_fp& inputData) const;

double interpolate(double x, const vector_fp& molefrac,

const vector_fp& inputData) const;

There is a similar issue on line 162 (next declaration)

bryanwweber · 2021-07-16T13:31:48Z

interfaces/cython/cantera/cti2yaml.py

@@ -1357,18 +1357,21 @@ def get_yaml(self, out):

 class table:
    """User provided thermo table for BinarySolutionTabulatedThermo"""
-    def __init__(self, moleFraction=([],''), enthalpy=([],''), entropy=([],'')):
+    def __init__(self, moleFraction=([],''), enthalpy=([],''), entropy=([],''), partialMolarVolume=([],'')):


Since the CTI/XML formats are going to be removed in the next few versions, we are preferring to add new features only to the YAML format. Unless there is already a significant userbase for this feature who are using CTI/XML files, we'd prefer to not change any of the converters.

bryanwweber · 2021-07-16T13:32:41Z

src/thermo/BinarySolutionTabulatedThermo.cpp

+        else{
+        	vbar.resize(x.size());
+        	for(size_t i=0; i<N; i++){
+        		vbar[i]=m_speciesMolarVolume[0];


Please only use spaces for indentation, with 4 spaces per indent.

@dschmider-HSOG Depending on what code editor you are using, you can likely set this as a preference, so that a tab automatically inserts 4 spaces.

bryanwweber · 2021-07-16T13:33:05Z

src/thermo/BinarySolutionTabulatedThermo.cpp

+        // Check for partialMolarVolume tag in tabulatedThermo table, take m_speciesMolarVolume[0] if false (for backward compatibility)
+        if (table.hasKey("partialMolarVolume")){
+        	vbar = table.convertVector("partialMolarVolume", "m3/kmol", N);
+        	for(size_t i=0; i<N; i++){


Following the style elsewhere, there should be spaces around the = and <. Also, one space before {. This occurs in a few places.

bryanwweber · 2021-07-16T13:34:23Z

src/thermo/BinarySolutionTabulatedThermo.cpp

@@ -90,26 +91,50 @@ void BinarySolutionTabulatedThermo::initThermo()
        size_t N = x.size();
        vector_fp h = table.convertVector("enthalpy", "J/kmol", N);
        vector_fp s = table.convertVector("entropy", "J/kmol/K", N);
+        vector_fp vbar;
+        // Check for partialMolarVolume tag in tabulatedThermo table, take m_speciesMolarVolume[0] if false (for backward compatibility)
+        if (table.hasKey("partialMolarVolume")){


Suggested change

if (table.hasKey("partialMolarVolume")){

if (table.hasKey("partialMolarVolume")) {

bryanwweber · 2021-07-16T13:35:10Z

src/thermo/BinarySolutionTabulatedThermo.cpp

+        if (table.hasKey("partialMolarVolume")){
+        	vbar = table.convertVector("partialMolarVolume", "m3/kmol", N);
+        	for(size_t i=0; i<N; i++){
+        		vbar[i]+=m_speciesMolarVolume[1];


Please make sure there is one space on each side of the +=.

bryanwweber · 2021-07-16T13:35:21Z

src/thermo/BinarySolutionTabulatedThermo.cpp

+        	}
+        }
+        else{
+        	vbar.resize(x.size());


Why not use N here?

bryanwweber · 2021-07-16T13:36:32Z

src/thermo/BinarySolutionTabulatedThermo.cpp

@@ -161,29 +186,51 @@ void BinarySolutionTabulatedThermo::initThermoXML(XML_Node& phaseNode, const std
            getFloatArray(dataNode, h, true, "J/kmol", "enthalpy");
            getFloatArray(dataNode, s, true, "J/kmol/K", "entropy");

+            // Check for partialMolarVolume tag in tabulatedThermo table, take m_speciesMolarVolume[0] if false (for backward compatibility)


As I mentioned earlier, unless there is a substantial existing userbase for this feature, there's no need to add it to the XML reader.

bryanwweber · 2021-07-16T13:40:25Z

src/thermo/BinarySolutionTabulatedThermo.cpp

+		if (i==0 and moleFraction[0]==0){
+			integratedData[i]=0;
+		}
+		else if (i==0 and moleFraction[0]>0){
+			integratedData[i]=moleFraction[i]*inputData[0];
+		}


I think you can avoid this conditional by doing the first element outside the loop and starting the loop at 1 instead of 0. Also, these two conditions are identical, since if moleFraction[i] == 0 is true, then moleFraction[i]*inputData[i] will also be 0. There's no need to have the condition, I think you can just do the multiplication.

decaluwe · 2021-07-21T12:35:57Z

Hi, @dschmider-HSOG , I'll echo @bryanwweber's comments - many thanks for this excellent contribution!

In addition to @bryanwweber's comments on the coding style, there are a few places where a little bit more documentation will help a user understand some of this functionality.

To second @bryanwweber's comment, please add a test to test/thermo/BinarySolutionTabulatedThermo_Test.cpp which will test to make sure that no future changes to Cantera break this functionality. Ideally, load the phase and test the results at a few compositions, comparing to hand-calculations of what you know the answer should be.
The documentation at the top of the header file include/cantera/thermo/BinarySolutionTabulatedThermo.h should also be edited to reflect (and explain) this new capability.
In the same file, a small comment explaining for users what getIntegratedPartialMolarVolumes is for, either in-line where the function is declared, or also at the top of this file.

Other than that, I'll leave a few small comments here and there, and like Bryan, am happy to help get this across the finish line, as needed. It is really quite close to ready, though. Thanks again!

decaluwe · 2021-07-21T12:51:34Z

src/thermo/BinarySolutionTabulatedThermo.cpp

+
+void BinarySolutionTabulatedThermo::calcDensity()
+{
+	// Fallback to IdealSolidSolnPhase::calcDensity() if called before m_integrated_partial_molar_volume_tab is initialized


I understand why you cannot use the other routine if m_integrated_partial_molar_volume_tab is initialized, but wouldn't this still be an erroneous value?

Is there a specific case where this will be called before the table is initialized, during setup of the class, or is it possible that a user will call it before the initialization is complete? If the latter, I'd rather find a way for this call to trigger the initialization, or throw an informative error message, rather than returning an incorrect value.

That is sort of a workaround. When I implemented the calcDensity() function, the code crashed because the calcDensity() routine got invoked when m_integrated_partial_molar_volume_tab was still empty.
I wondered how this is possible because actually m_integrated_partial_molar_volume_tab is initialized at the end of void BinarySolutionTabulatedThermo::initThermo(), but I could not track down, which function called calcDensity() before initThermo() initialized the phase. So that was the only solution I could come up with.

dschmider-HSOG · 2021-08-02T12:20:39Z

Hi,
thank you very much @decaluwe and @bryanwweber, I really appreciate your comments.
I have just returned from holiday and will be working on the requested changes throughout this week. Since this is my first ever pull request, I have a rather general question:
Should I amend the previous commit to include all the changes or do you prefer follow-up commits to address the requested changes?

bryanwweber · 2021-08-02T13:39:09Z

HI @dschmider-HSOG Welcome back! It's up to you whether to amend the previous commit or add new ones. I usually try to keep a logical unit of work per commit.

dschmider-HSOG · 2021-08-06T13:07:42Z

Hi,
I hope I got all the formatting issues fixed now.
Regarding the test I might need some help. Can I just extend the existing BinarySolutionTabulatedThermo.yaml in the test data by a partial molar volume entry in the table and add test cases in BinarySolutionTabulatedThermo_Test.cpp or should I generate a separate data file?
Furthermore I will edit the documentation in the header file and also add some comments on the functions in a follow-up commit.

bryanwweber · 2021-08-07T23:34:15Z

Regarding the test I might need some help. Can I just extend the existing BinarySolutionTabulatedThermo.yaml in the test data by a partial molar volume entry in the table and add test cases in BinarySolutionTabulatedThermo_Test.cpp or should I generate a separate data file?

Hi @dschmider-HSOG Sure, editing that same file should be fine. Thanks!

bryanwweber · 2022-02-20T13:43:20Z

@dschmider-HSOG are you able to finish this pull request up? It looks like a neat function that'd be great to have merged. Please let me know if you have any questions!

dschmider-HSOG · 2022-02-21T08:05:41Z

Hi @bryanwweber, thanks for asking. I was occupied with other topics in the meantime, but should soon be able to complete the commit.

Enable to consider non-constant partial molar volumes provided by tabular data, since the partial molar volume of typical battery intercalation materials shows strong dependency on e.g. lithium stoichiometry. The tabular data is included in the same table as enthalpy and entropy data. -implement optional partialMolarVolume keyword in table(thermo) -BinarySolutionTabulatedThermo::interpolate is adjusted to be more general and also interpolate partial molar volume -BinarySolutionTabulatedThermo::integrate is added since partial molar volumes are often needed in integrated form (integrated over lithium stoichiometry) -BinarySolutionTabulatedThermo::calcDensity is adjusted since density is not constant anymore and changes with varying partial molar volumes

- Correct several formatting/style issues - Revert changes introduced in XML converters

- Change the implementation to provided molar volumes instead of partial molar volumes - Extend BinarySolutionTabulatedThermo_Test.cpp to test for added functionality - Add molarVolume data to BinarySolutionTabulatedThermo.yaml - Edit documentation in header file

dschmider-HSOG · 2022-04-07T09:01:54Z

Hi,
finally I pushed my recent changes. Since it has been quite some time since the last commit I also rebased my changes on the latest version of the main branch. I hope this was the correct way of doing it.

codecov · 2022-04-07T11:24:32Z

Codecov Report

Merging #1072 (e350553) into main (01b1a4b) will decrease coverage by 0.00%.
The diff coverage is 65.90%.

@@            Coverage Diff             @@
##             main    #1072      +/-   ##
==========================================
- Coverage   65.47%   65.47%   -0.01%     
==========================================
  Files         327      327              
  Lines       46350    46416      +66     
  Branches    19688    19718      +30     
==========================================
+ Hits        30349    30391      +42     
- Misses      13476    13496      +20     
- Partials     2525     2529       +4

Impacted Files	Coverage Δ
...ude/cantera/thermo/BinarySolutionTabulatedThermo.h	`100.00% <ø> (ø)`
include/cantera/thermo/IdealSolidSolnPhase.h	`78.94% <ø> (ø)`
src/thermo/BinarySolutionTabulatedThermo.cpp	`59.09% <65.11%> (+0.44%)`	⬆️
src/thermo/IdealSolidSolnPhase.cpp	`62.03% <100.00%> (+0.12%)`	⬆️
src/thermo/Phase.cpp	`81.48% <0.00%> (+0.35%)`	⬆️

📣 Codecov can now indicate which changes are the most critical in Pull Requests. Learn more

Stale

speth · 2022-04-11T01:18:55Z

include/cantera/thermo/BinarySolutionTabulatedThermo.h

+    //! Numerical derivation of the molar volume table
+    /*!
+     *  Tabulated values are only interpolated within the limits of the provided mole
+     *  fraction. If these limits are exceeded, the values are capped at the lower or
+     *  the upper limit.
+     */
+    void derive(vector_fp& inputData, vector_fp& derivedData,
+                vector_fp& moleFraction);


A few comments on this function:

This is the numerical derivative of the molar volume

I think diff would be a better name for this function is used, the mole fraction vector is m_molefrac_tab

I don't think the moleFraction argument is needed -- the only way this function is called,

The usual order of arguments would be to have the input arguments (inputData and moleFraction first, followed by the output argument.

The input arguments should be marked as const

The function itself is can be const as well.

speth · 2022-04-11T01:25:57Z

include/cantera/thermo/BinarySolutionTabulatedThermo.h

+    //! Species thermodynamics linear interpolation function
+    /*!
+     *  Tabulated values are only interpolated within the limits of the provided mole
+     *  fraction. If these limits are exceeded, the values are capped at the lower or
+     *  the upper limit.
+     */
+    double interpolate(double x, const vector_fp& molefrac,
+                       const vector_fp& inputData) const;


I don't think the molefrac vector needs to be an input argument -- it is always the m_molefrac_tab variable which is available in this function as well.

It would be useful to document the input and output arguments in the method docstring, e.g. with @param x (some description and @returns the value of ....

speth · 2022-04-11T01:44:35Z

include/cantera/thermo/ThermoPhase.h

+    //@}
+    /// @name Properties of the Standard State of the Species in the Solution
+    //@{


This change should be reverted - the lines containing @{ and @} need to be Doxygen comment lines (starting with //! or ///, as they were.

speth · 2022-04-11T01:50:30Z

test/data/BinarySolutionTabulatedThermo.yaml

@@ -43,6 +43,16 @@ phases:
      19.2971, 19.2977, 16.2213, 19.298, 19.2978, 19.2945, 19.2899, 19.2877,
      19.2882, 19.2882, 19.2882, 19.2882, 19.2882, 19.2885, 19.2876, 19.2837,
      19.2769, 19.285, 19.31, 19.3514]
+    molarVolume: [34.582988, 34.677730, 34.776275, 34.875760, 34.973980, 35.069268,


In the YAML format, we generally use lowercase words separated by spaces, so this should be molar-volume.

speth

Thanks for providing these updates. I appreciated the detailed description of the additions in the class docstring.

Besides the handful of comments above and below*, I found an alternative to duplicating the implementation of addSpecies from IdealSolidSolnPhase, which I've pushed to my fork (https://github.com/speth/cantera/tree/tabulated_partial_molar_volumes). You can either cherry-pick that commit onto your branch here, or if you want I can push that change to this branch.

*sorry, something funny happened with the GitHub plugin for VS Code and it posted part of this before I was finished reviewing -- please take a look at the comments from the prior review as well.

speth · 2022-04-11T01:52:13Z

src/thermo/BinarySolutionTabulatedThermo.cpp

+{
+    {
+        double vmol = interpolate(Phase::moleFraction(m_kk_tab), m_molefrac_tab,


There's an extra, unnecessary layer of braces and indentation around the body of this function.

Also, I don't think the Phase:: qualifier is needed before calling moleFraction (here or anywhere else in this class).

speth · 2022-04-11T01:54:05Z

src/thermo/BinarySolutionTabulatedThermo.cpp

+    }
+}
+
+void BinarySolutionTabulatedThermo::getPartialMolarVolumes(doublereal* vbar) const


There's a rogue doublereal here that should just be double (likewise for this method in the header file).

I saw that in the generation of the doxygen file, the information that this function is reimplemented from the parent class is lost if I change to double. Therefore I thought it would be better to keep doublereal. But sure I can change this to double.

Interesting. I thought Doxygen was smart enough to see through the typedef and know that these methods were the same. I'd suggest changing it to double anyways. We'll get around to eliminating doublereal on a wider scale eventually.

speth · 2022-04-11T01:57:28Z

src/thermo/BinarySolutionTabulatedThermo.cpp

+    }
+    else {


A minor formatting suggestion:

Suggested change

}

else {

} else {

dschmider-HSOG · 2022-04-12T07:06:21Z

Thanks @speth for reviewing. I've implemented your suggestions.

Regarding addSpecies: I think it should be possible to drop the call for calcDensity in IdealSolidSolnPhase::addSpecies completely. I think there is no need to calculate the density at this point, since calcDensity is invoked in the end of setupPhase or importPhase. All tests pass without errors if I simply remove it.

speth · 2022-04-12T15:26:56Z

Regarding addSpecies: I think it should be possible to drop the call for calcDensity in IdealSolidSolnPhase::addSpecies completely. I think there is no need to calculate the density at this point, since calcDensity is invoked in the end of setupPhase or importPhase. All tests pass without errors if I simply remove it.

That's true in most cases, but not if you add species to the phase after the fact (which is of course not allowed in the case of BinarySolutionTabulatedThermo, but could be for IdealSolidSolnPhase. So I think this call needs to remain to keep the phase in a consistent state.

speth · 2022-04-12T15:28:18Z

Hi @dschmider-HSOG, I think you haven't yet pushed the updates to this branch.

dschmider-HSOG · 2022-04-13T07:16:03Z

That's true in most cases, but not if you add species to the phase after the fact (which is of course not allowed in the case of BinarySolutionTabulatedThermo, but could be for IdealSolidSolnPhase. So I think this call needs to remain to keep the phase in a consistent state.

I see. But wouldn't the implementation with the ready() function that you proposed in your fork also result in the fact that calcDensity() will never get called from within IdealSolidSolnPhase::addSpecies? m_molefrac_tab would always be empty for an IdealSolidSolnPhase.
If it is possible to add species after the fact, I guess it is even more important that BinarySolutionTabulatedThermo gets its own addSpecies method two prevent adding more than two species. This is checked during initThermo() but shouldn't it then also be checked in addSpecies?

speth · 2022-04-13T12:36:09Z

I see. But wouldn't the implementation with the ready() function that you proposed in your fork also result in the fact that calcDensity() will never get called from within IdealSolidSolnPhase::addSpecies? m_molefrac_tab would always be empty for an IdealSolidSolnPhase.

ready() is a virtual function, which means that the implementation in BinarySolutionTabulatedThermo will be called only if the object is actually a BinarySolutionTabulatedThermo. Otherwise, the base class method (in this case, Phase::ready()) will be called, and that returns true as long as there are any species in the phase.

If it is possible to add species after the fact, I guess it is even more important that BinarySolutionTabulatedThermo gets its own addSpecies method two prevent adding more than two species. This is checked during initThermo() but shouldn't it then also be checked in addSpecies?

Yes, that's a good point. But this can be a pretty minimal implementation, which just checks that condition an then calls IdealSolidSolnPhase::addSpecies to avoid any code duplication.

- Edit method docstrings in header file - Change minor formatting issues

dschmider-HSOG · 2022-04-13T13:14:40Z

ready() is a virtual function, which means that the implementation in BinarySolutionTabulatedThermo will be called only if the object is actually a BinarySolutionTabulatedThermo. Otherwise, the base class method (in this case, Phase::ready()) will be called, and that returns true as long as there are any species in the phase.

Sorry, I somehow overlooked the fact that Phase::ready() exists. You're absolutely right.

Yes, that's a good point. But this can be a pretty minimal implementation, which just checks that condition an then calls IdealSolidSolnPhase::addSpecies to avoid any code duplication.

I changed my last commit to incorporate the ready() method and also check the condition of max. 2 species.

speth

Thanks, all of these changes look good to me. One other small thing that I forgot to mention is that there should be an update to doc/sphinx/yaml/phases.rst to describe the additional parameter in the YAML API documentation. This file is used to populate the information that ends up here on the Cantera website.

- Add description for molar-volume parameter to doc/sphinx/yaml/phases.rst in binary-solution-tabulated

dschmider-HSOG · 2022-04-19T08:05:50Z

Thank you @decaluwe, @bryanwweber and @speth for helping me finish my very first pull request. I really appreciated your constructive feedback.

Best regards,
David

decaluwe · 2022-04-20T02:28:26Z

Congrats, @dschmider-HSOG - so excited for your contribution!

bryanwweber previously requested changes Jul 16, 2021

View reviewed changes

decaluwe reviewed Jul 21, 2021

View reviewed changes

dschmider-HSOG and others added 3 commits April 6, 2022 15:35

Extend BinarySolutionTabulatedThermo by tabulated partial molar volumes

fad7cd9

- Correct several formatting/style issues - Revert changes introduced in XML converters

dschmider-HSOG force-pushed the tabulated_partial_molar_volumes branch from 8782ea6 to 1fc652f Compare April 7, 2022 08:55

bryanwweber requested a review from speth April 7, 2022 13:19

speth reviewed Apr 11, 2022

View reviewed changes

speth requested changes Apr 11, 2022

View reviewed changes

dschmider-HSOG force-pushed the tabulated_partial_molar_volumes branch from 22c2045 to 3e3ab4d Compare April 13, 2022 07:35

Extend BinarySolutionTabulatedThermo by tabulated molar volumes

9fd67db

- Edit method docstrings in header file - Change minor formatting issues

dschmider-HSOG force-pushed the tabulated_partial_molar_volumes branch from 3e3ab4d to 9fd67db Compare April 13, 2022 13:07

speth reviewed Apr 13, 2022

View reviewed changes

Extend BinarySolutionTabulatedThermo by tabulated molar volumes

e350553

- Add description for molar-volume parameter to doc/sphinx/yaml/phases.rst in binary-solution-tabulated

speth approved these changes Apr 14, 2022

View reviewed changes

speth merged commit e7b931b into Cantera:main Apr 14, 2022

dschmider-HSOG deleted the tabulated_partial_molar_volumes branch May 2, 2022 09:31

speth mentioned this pull request May 3, 2022

Increase rtol in thermoToYaml for ppcle64/aarch64 systems #1271

Closed

5 tasks

		void getIntegratedPartialMolarVolumes(doublereal* vbar);
		void getPartialMolarVolumes(doublereal* vbar) const;

	double interpolate(double x,const vector_fp& molefrac,const vector_fp& inputData) const;
	double interpolate(double x, const vector_fp& molefrac,
	const vector_fp& inputData) const;

	if (table.hasKey("partialMolarVolume")){
	if (table.hasKey("partialMolarVolume")) {

Extend BinarySolutionTabulatedThermo by tabulated partial molar volumes #1072

Extend BinarySolutionTabulatedThermo by tabulated partial molar volumes #1072

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dschmider-HSOG commented Jul 16, 2021 • edited Loading

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dschmider-HSOG commented Apr 12, 2022

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