SolutionArray truncates negative values

[DavidAkinpelu]

For SolutionArray/FlameBase, importers are not currently creating the same states. Negative values are truncated to zero which makes it impossible to have the same states initially stored in the SolutionArray or FlameBase object.

Quick example:

Operating system: Windows 10
Python Version: 3.9.2
Cantera version: 2.6.0a1

In [1]: import cantera as ct
   ...: gas = ct.Solution('h2o2.yaml')
   ...: gas.set_unnormalized_mole_fractions(gas.X - 1e-16)
   ...: arr = ct.SolutionArray(gas, 5)
   
In [2]: arr.X
Out[2]: 
array([[ 1.e+00, -1.e-16, -1.e-16, -1.e-16, -1.e-16, -1.e-16, -1.e-16,
        -1.e-16, -1.e-16, -1.e-16],
       [ 1.e+00, -1.e-16, -1.e-16, -1.e-16, -1.e-16, -1.e-16, -1.e-16,
        -1.e-16, -1.e-16, -1.e-16],
       [ 1.e+00, -1.e-16, -1.e-16, -1.e-16, -1.e-16, -1.e-16, -1.e-16,
        -1.e-16, -1.e-16, -1.e-16],
       [ 1.e+00, -1.e-16, -1.e-16, -1.e-16, -1.e-16, -1.e-16, -1.e-16,
        -1.e-16, -1.e-16, -1.e-16],
       [ 1.e+00, -1.e-16, -1.e-16, -1.e-16, -1.e-16, -1.e-16, -1.e-16,
        -1.e-16, -1.e-16, -1.e-16]])
In [3]: arr.write_hdf('test.h5') # save to HDF
Out[3]: 'group0'
   
In [4]: gas_new = ct.Solution('h2o2.yaml')
   ...: arr_new = ct.SolutionArray(gas_new)
In [5]: arr_new.read_hdf('test.h5') # load from HDF
   ...: arr_new.X
Out[5]: 
array([[1., 0., 0., 0., 0., 0., 0., 0., 0., 0.],
       [1., 0., 0., 0., 0., 0., 0., 0., 0., 0.],
       [1., 0., 0., 0., 0., 0., 0., 0., 0., 0.],
       [1., 0., 0., 0., 0., 0., 0., 0., 0., 0.],
       [1., 0., 0., 0., 0., 0., 0., 0., 0., 0.]])

Also, SolutionArray does not have set_unnormalized_mole_fractions() or set_unnormalized_mass_fractions() methods like a Solution object which I think should be applicable to SolutionArray too.

In [6]: arr_new.set_unnormalized_mole_fractions(arr.X - 1e-16)
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
<ipython-input-14-22b735859e09> in <module>
----> 1 arr_new.set_unnormalized_mole_fractions(arr.X - 1e-16)
~/.pyenv/versions/miniconda3-latest/envs/cantera-2.5.1/lib/python3.8/site-packages/cantera/composite.py in __getattr__(self, name)
    604             super().__getattr__(name)
    605         else:
--> 606             raise AttributeError("'{}' object has no attribute '{}'".format(
    607                 self.__class__.__name__, name))
    608 
AttributeError: 'SolutionArray' object has no attribute 'set_unnormalized_mole_fractions'

A proposed fix for the two issues raised above would be to implement set_unnormalized_mass_fractions and set_unnormalized_mole_fractions for SolutionArray objects.

Another related issue which I think would be fixed together with the above raise issues is

In [7]: states = ct.SolutionArray(gas)
   ...: states.append(T=600., P=ct.one_atm, X=[0.1, 0.3, 0.3, -0.4, 0.25, 0.15, -0.2, 0.1, 0, 0])
   ...: states.X            
Out[7]:
    array([[0.08333333, 0.25      , 0.25      , 0.        , 0.20833333,
            0.125     , 0.        , 0.08333333, 0.        , 0.        ]])

[ischoegl]

@DavidAkinpelu ... thank you for reporting. I believe you know how to fix the issue, so feel free to submit a PR.

[DavidAkinpelu]

Okay