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Add species alias#714

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speth merged 3 commits intoCantera:masterfrom
ischoegl:add-species-alias
Oct 30, 2019
Merged

Add species alias#714
speth merged 3 commits intoCantera:masterfrom
ischoegl:add-species-alias

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@ischoegl ischoegl commented Sep 24, 2019 •
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This PR adds utility functions that facilitate selection of species and isomers. Functions are defined in the C++ layer and broken out using the Cython interface.

Changes proposed in this pull request:

  • add_species_alias allows for alternate species names/shorthands
  • find_isomers returns a list of isomers for a given composition

Usage:

In [1]: import cantera as ct

In [2]: gas = ct.Solution('nDodecane_Reitz.yaml')

In [3]: gas.find_isomers({'C':4, 'H':9, 'O':2})
Out[3]: ['c4h8ooh', 'c4h9o2']

In [4]: gas.find_isomers({'C':7, 'H':16})
Out[4]: []

In [5]: gas.find_isomers('C:1, H:4')
Out[5]: ['ch4']

In [6]: gas.add_species_alias('ch4', 'Methane')

In [7]: gas.species_index('Methane') == gas.species_index('ch4')
Out[7]: True

In [8]: gas.X = 'Methane:1.'

In [9]: gas.X[gas.species_index('ch4')]
Out[9]: 1.0

PS: the implementation of findIsomers is analogous to #635; this PR explicitly does not address the overloading of speciesIndex (which could be simplified based on this PR).

speth
speth requested changes Oct 29, 2019
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The addition of findIsomers makes sense to me.

I don't see much of a direct use case for addSpeciesAlias, but I can imagine ways of using it if you had some extra data in your input file, e.g. the SMILES corresponding to each species, so adding some underlying infrastructure for this kind of feature seems fine.

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ischoegl commented Oct 30, 2019

I don't see much of a direct use case for addSpeciesAlias [...]

Sometimes I find large molecules with non-intuitive species names, and keep having to remind myself what they actually are. Those names are also not consistent among groups; as m_speciesIndices is already a map, it's pretty simple to add this feature.

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codecov bot commented Oct 30, 2019 •
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Codecov Report

Merging #714 into master will increase coverage by 0.01%.
The diff coverage is 100%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master     #714      +/-   ##
==========================================
+ Coverage   70.85%   70.86%   +0.01%     
==========================================
  Files         374      374              
  Lines       43668    43683      +15     
==========================================
+ Hits        30939    30954      +15     
  Misses      12729    12729
Impacted Files Coverage Δ
include/cantera/thermo/Phase.h 100% <ø> (ø) ⬆️
src/thermo/Phase.cpp 82.24% <100%> (+0.58%) ⬆️
src/transport/GasTransport.cpp 90.58% <0%> (ø) ⬆️

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@speth speth merged commit 54c12fc into Cantera:master Oct 30, 2019
@ischoegl ischoegl mentioned this pull request Nov 2, 2019
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@bryanwweber bryanwweber mentioned this pull request Dec 10, 2019
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@ischoegl ischoegl deleted the add-species-alias branch December 16, 2019 15:56
@bryanwweber bryanwweber mentioned this pull request Jun 29, 2020
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@ischoegl @speth