Prelude to YAML serialization by speth · Pull Request #795 · Cantera/cantera

speth · 2020-01-14T23:33:37Z

Checklist

There is a clear use-case for this code change
The commit message has a short title & references relevant issues
Build passes (scons build & scons test) and unit tests address code coverage
The pull request is ready for review

To make the upcoming PR which implements serialization to the YAML format a bit smaller and more manageable, I have extracted a number of commits which resolve some issues that I encountered and interface additions that I found were needed while implementing serialization, which can be considered separately.

Changes proposed in this pull request

Some additions to the AnyMap class, including:
- equality comparisons
- improved handling for entries which can be either single maps or lists of maps
- a clear() method
- automatic skipping of "hidden" fields (e.g. __file__) when iterating
- generalization of handling for metadata applicable to an AnyMap tree
Fix a bug in the pure fluid models where calculating c_p and other similar properties slightly changes the state
Make instantiating phase types which reference other phase definitions possible when using a YAML input string (rather than an input file)
Implement Option 4 in Revise YAML species definitions to support multiple thermo models enhancements#20
- Reorganize Debye-Huckel input data
- Allow the equation-of-state field to allow multiple model options
Provide a way of determining the "canonical" name used by factories for instantiating an object, and make the names used in the YAML format canonical
Update pure fluid names to match YAML naming style
Fix adding YAML-defined reactions to CTI/XML-defined surface phases

codecov · 2020-01-15T00:05:08Z

Codecov Report

Merging #795 into master will increase coverage by 0.1%.
The diff coverage is 86.31%.

@@            Coverage Diff            @@
##           master     #795     +/-   ##
=========================================
+ Coverage   71.44%   71.54%   +0.1%     
=========================================
  Files         372      372             
  Lines       43952    44348    +396     
=========================================
+ Hits        31400    31730    +330     
- Misses      12552    12618     +66

Impacted Files	Coverage Δ
src/thermo/VPStandardStateTP.cpp	`81.63% <ø> (-0.25%)`	⬇️
src/tpx/CarbonDioxide.h	`100% <100%> (ø)`	⬆️
src/thermo/HMWSoln.cpp	`71.57% <100%> (-0.02%)`	⬇️
src/kinetics/KineticsFactory.cpp	`95% <100%> (ø)`	⬆️
src/tpx/Heptane.h	`100% <100%> (ø)`	⬆️
test/thermo/thermoFromYaml.cpp	`100% <100%> (ø)`	⬆️
src/tpx/Sub.cpp	`86.57% <100%> (+0.08%)`	⬆️
src/thermo/Species.cpp	`100% <100%> (ø)`	⬆️
src/thermo/IdealSolidSolnPhase.cpp	`60.16% <100%> (+0.08%)`	⬆️
include/cantera/base/AnyMap.h	`100% <100%> (ø)`	⬆️
... and 17 more

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For entries that are lists of maps in the general case but often only contain one item, it is convenient to allow them to be provided as just a map. This modifies methods used to work with vectors of AnyMap objects to handle the case where the child object is just a map.

…ions

This allows for error checking at the time of adding the alias, as well as providing a public interface for adding aliases.

The first phase in a Kinetics object is not necessarily the reacting phase for Kinetics objects loaded from CTI/XML files, but is for YAML files.

include/cantera/base/FactoryBase.h

data/liquidvapor.yaml

src/base/AnyMap.cpp

Didn't mean to request/submit review

Ensure that the name returned by Sub::name() is a name that can be used to reconstruct a substance of the same type. Make phase names in liquidvapor.yaml match the substance model names.

After calculating properties using finite differences (e.g. cp), the fluid was returned to its original state by setting the state in terms of pressure and temperature. However, because setting the state using these variables is an iterative calculation with some error tolerance, the state was not restored exactly. By restoring the state based on the initial temperature and density, the restored state is identical to the initial state.

bryanwweber

Looks good to me, other than a few copy-editing things.

bryanwweber · 2020-01-20T13:56:04Z

doc/sphinx/yaml/phases.rst

+    One of ``solvent``, ``charged-species``, ``weak-acid-associated``,
+    ``strong-acid-associated``, ``polar-neutral``, or ``nonpolar-neutral``.
+    The types ``solvent``, ``charged-species``, and ``nonpolar-neutral`` can be
+    inferred automatically.


Can you add something here about how these types are automatically inferred?

bryanwweber · 2020-01-20T13:56:18Z

doc/sphinx/yaml/phases.rst

+    inferred automatically.
+
+``weak-acid-charge``
+    Charge to use for species can break apart into charged species.


Suggested change

Charge to use for species can break apart into charged species.

Charge to use for species that can break apart into charged species.

bryanwweber · 2020-01-20T13:57:37Z

doc/sphinx/yaml/species.rst

-    the ``ideal-gas`` model is assumed.
+    A mapping or list of mappings. Each mapping contains an equation of state
+    model specification for the species, any parameters for that model, and any
+    parameters for interactions with other species. :ref:`sec-yaml-species-eos`.


Is the reference intended to be a complete sentence here?

speth added 12 commits January 14, 2020 21:09

[Input] Allow 'equation-of-state' field to contain multiple model opt…

6b051c0

…ions

[Input] Skip over hidden keys when iterating over AnyMap

902a4ec

Make canonical names of factory-registered types accessible

e89a4ea

Add functions for factory alias management

a5ce147

This allows for error checking at the time of adding the alias, as well as providing a public interface for adding aliases.

[Input] Make YAML designated names canonical for factories

26edb23

Implement equality comparisons for AnyValue / AnyMap

8f07ebc

Handle equality comparisons for types converted by AnyValue

0a89f21

[Kinetics] Fix creation of surface reactions depending on phase order

972330b

The first phase in a Kinetics object is not necessarily the reacting phase for Kinetics objects loaded from CTI/XML files, but is for YAML files.

Make use of AnyValue equality comparisons

e9c936a

[Input] Fix reading of long integers in YAML files

b8c3f7c

Add 'clear' method to AnyMap

e1c12c2

speth force-pushed the yaml-serialization-prep branch from 5579ea4 to 8772272 Compare January 15, 2020 02:10

bryanwweber reviewed Jan 15, 2020

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include/cantera/base/FactoryBase.h Show resolved Hide resolved

bryanwweber reviewed Jan 15, 2020

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data/liquidvapor.yaml Show resolved Hide resolved

speth force-pushed the yaml-serialization-prep branch from 8772272 to 5545939 Compare January 15, 2020 18:46

bryanwweber reviewed Jan 15, 2020

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src/base/AnyMap.cpp Show resolved Hide resolved

bryanwweber self-requested a review January 15, 2020 19:37

bryanwweber previously approved these changes Jan 15, 2020

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speth added 6 commits January 15, 2020 15:40

[Input] Use more general data structure for AnyMap metadata

78fc3b1

Standardize names used for pure substance models

8662f3c

Ensure that the name returned by Sub::name() is a name that can be used to reconstruct a substance of the same type. Make phase names in liquidvapor.yaml match the substance model names.

[Input] Move Debye-Huckel species parameters to their own sub-field

2d2c1e2

[Input] Make string-based instantiation of IonsFromNeutral possible

2b5fe59

[Input] Make string-based instantiation of LatticeSolid possible

89b5ca2

speth force-pushed the yaml-serialization-prep branch from 5545939 to cdef8c7 Compare January 15, 2020 20:44

bryanwweber approved these changes Jan 20, 2020

View reviewed changes

[Doc] Small improvements to YAML API docs

4447096

speth merged commit b7591cb into Cantera:master Jan 21, 2020

speth deleted the yaml-serialization-prep branch January 22, 2020 15:59

speth mentioned this pull request Jun 24, 2020

Implementation of Peng-Robinson EoS #641

Closed

bryanwweber mentioned this pull request Apr 5, 2021

Revise YAML species definitions to support multiple thermo models Cantera/enhancements#20

Closed

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Prelude to YAML serialization#795

Prelude to YAML serialization#795
speth merged 19 commits intoCantera:masterfrom
speth:yaml-serialization-prep

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	Charge to use for species can break apart into charged species.
	Charge to use for species that can break apart into charged species.

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