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Fix problems in ThermoPhase and Kinetics classes for the experimental Matlab toolbox #1586

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merged 10 commits into from
Oct 18, 2023
Merged

Fix problems in ThermoPhase and Kinetics classes for the experimental Matlab toolbox #1586

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dc598cc
Added ctRoot to gitignore
ssun30 Aug 11, 2023
6e41a7c
Added Cantera error identifiers.
ssun30 May 25, 2023
5e3a71a
Changed how ThermoPhase is printed.
ssun30 May 25, 2023
9999041
Fixed Kinetics class so all tests pass
ssun30 Aug 11, 2023
30deaf9
Fixed issues in ThermoPhase to pass more tests
ssun30 Aug 11, 2023
c71c936
Removed unnecessary variable `root_dir`
ssun30 Sep 23, 2023
0e65e3d
Added error handling for out of bounds indices
ssun30 Sep 26, 2023
cf75bec
Fixed setter errors with unit conversions
ssun30 Oct 3, 2023
f526c4a
Updated documentation for stoich coeff methods
ssun30 Oct 13, 2023
e213360
Density/specific volume are now basis dependent
ssun30 Oct 13, 2023
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2 changes: 1 addition & 1 deletion .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@ include/cantera/base/system.h.gch
include/cantera/ext/
interfaces/matlab/ctpath.m
interfaces/matlab/Contents.m
interfaces/matlab_experimental/ctRoot.m
interfaces/matlab_experimental/Utility/ctRoot.m
src/extensions/delegator.h
stage/
.sconsign.dblite
Expand Down
117 changes: 85 additions & 32 deletions interfaces/matlab_experimental/Base/Kinetics.m
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Original file line number Diff line number Diff line change
Expand Up @@ -163,12 +163,15 @@ function delete(kin)
% >> n = kin.kineticsSpeciesIndex(name, phase)
%
% :param name:
% String name of the species.
% String name or integer index of the species.
% :param phase:
% String name of the phase.
% String name or integer index of the phase.
% :return:
% Index of the species.

if nargin == 2
phase = '';
end
n = ctFunc('kin_speciesIndex', kin.kinID, name, phase) + 1;
end

Expand Down Expand Up @@ -231,21 +234,23 @@ function delete(kin)
% >> n = kin.reactantStoichCoeffs(species, rxns)
%
% :param species:
% Species indices for which reactant stoichiometric
% coefficients should be retrieved. Optional argument; if
% specified, ``rxns`` must be specified as well.
% Species indices or names for which reactant stoichiometric
% coefficients should be retrieved.
% Optional argument; if specified, ``rxns`` must be specified as well.
% :param rxns:
% Reaction indices for which reactant stoichiometric
% coefficients should be retrieved. Optional argument; if
% specified, ``species`` must be specified as well.
% :return:
% Returns a sparse matrix of all reactant stoichiometric
% coefficients. The matrix elements ``nu(k, i)`` is the
% stoichiometric coefficient of species k as a reactant in
% reaction i. If ``species`` and ``rxns`` are specified, the
% matrix will contain only entries for the specified species
% and reactions. For example, ``stoich_p(a, 3, [1, 3, 5,
% 7])`` returns a sparse matrix containing only the
% coefficients if there are more than 1 species or reactions,
% otherwise returns an integer.
% The matrix elements ``nu(k, i)`` is the stoichiometric
% coefficient of species k as a reactant in reaction i.
% If ``species`` and ``rxns`` are specified, the matrix
% will contain only entries for the specified species
% and reactions. For example, ``kin.reactantStoichCoeffs(3,
% [1, 3, 5, 7])`` returns a sparse matrix containing only the
% coefficients for species 3 in reactions 1, 3, 5, and 7.

nsp = kin.nTotalSpecies;
Expand All @@ -256,7 +261,11 @@ function delete(kin)
krange = 1:nsp;
irange = 1:nr;
elseif nargin == 3
krange = species;
if ischar(species)
krange = {species};
else
krange = species;
end
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irange = rxns;
else
error('stoichReactant requires 1 or 3 arguments.')
Expand All @@ -265,17 +274,29 @@ function delete(kin)
for k = krange

for i = irange
t = ctFunc('kin_reactantStoichCoeff', kin.kinID, k - 1, i - 1);
if iscell(k)
kk = kin.kineticsSpeciesIndex(k{:});
elseif ischar(k)
kk = kin.kineticsSpeciesIndex(k);
else
kk = k;
end

t = ctFunc('kin_reactantStoichCoeff', kin.kinID, kk - 1, i - 1);

if t ~= 0.0
temp(k, i) = t;
temp(kk, i) = t;
end

end

end

n = temp;
if length(krange) > 1 || length(irange) > 1
n = temp;
else
n = sum(full(temp), 'all');
end
end

function n = productStoichCoeffs(kin, species, rxns)
Expand All @@ -284,16 +305,24 @@ function delete(kin)
% >> n = kin.productStoichCoeffs(species, rxns)
%
% :param species:
% Species indices for which product stoichiometric
% coefficients should be retrieved. Optional argument; if
% specified, ``rxns`` must be specified as well.
% Species indices or names for which product stoichiometric
% coefficients should be retrieved.
% Optional argument; if specified, ``rxns`` must be specified as well.
% :param rxns:
% Reaction indices for which product stoichiometric
% coefficients should be retrieved. Optional argument; if
% specified, ``species`` must be specified as well.
% :return:
% Returns a sparse matrix of all product stoichiometric
% coefficients.
% coefficients if there are more than 1 species or reactions,
% otherwise returns an integer.
% The matrix elements ``nu(k, i)`` is the stoichiometric
% coefficient of species k as a product in reaction i.
% If ``species`` and ``rxns`` are specified, the matrix
% will contain only entries for the specified species
% and reactions. For example, ``kin.productStoichCoeffs(3,
% [1, 3, 5, 7])`` returns a sparse matrix containing only the
% coefficients for species 3 in reactions 1, 3, 5, and 7.

nsp = kin.nTotalSpecies;
nr = kin.nReactions;
Expand All @@ -303,7 +332,11 @@ function delete(kin)
krange = 1:nsp;
irange = 1:nr;
elseif nargin == 3
krange = species;
if ischar(species)
krange = {species};
else
krange = species;
end
irange = rxns;
else
error('stoichProduct requires 1 or 3 arguments.')
Expand All @@ -312,17 +345,28 @@ function delete(kin)
for k = krange

for i = irange
t = ctFunc('kin_productStoichCoeff', kin.kinID, k - 1, i - 1);

if iscell(k)
kk = kin.kineticsSpeciesIndex(k{:});
else
kk = k;
end

t = ctFunc('kin_productStoichCoeff', kin.kinID, kk - 1, i - 1);

if t ~= 0.0
temp(k, i) = t;
temp(kk, i) = t;
end

end

end

n = temp;
if length(krange) > 1 || length(irange) > 1
n = temp;
else
n = sum(full(temp), 'all');
end
end

function n = netStoichCoeffs(kin, species, rxns)
Expand All @@ -331,21 +375,30 @@ function delete(kin)
% >> n = kin.netStoichCoeffs(species, rxns)
%
% :param species:
% Species indices for which net stoichiometric coefficients
% should be retrieved. Optional argument; if specified,
% "rxns" must be specified as well.
% Species indices or names for which net stoichiometric
% coefficients should be retrieved.
% Optional argument; if specified, ``rxns`` must be specified as well.
% :param rxns:
% Reaction indices for which net stoichiometric
% coefficients should be retrieved. Optional argument; if
% specified, "species" must be specified as well.
% specified, ``species`` must be specified as well.
% :return:
% A sparse matrix of all net stoichiometric coefficients.
% Returns a sparse matrix of all net stoichiometric
% coefficients if there are more than 1 species or reactions,
% otherwise returns an integer.
% The matrix elements ``nu(k, i)`` is the stoichiometric
% coefficient of species k as a product in reaction i.
% If ``species`` and ``rxns`` are specified, the matrix
% will contain only entries for the specified species
% and reactions. For example, ``kin.netStoichCoeffs(3,
% [1, 3, 5, 7])`` returns a sparse matrix containing only the
% coefficients for species 3 in reactions 1, 3, 5, and 7.

if nargin == 1
n = kin.stoichProduct - kin.stoichReactant;
n = kin.productStoichCoeffs - kin.reactantStoichCoeffs;
elseif nargin == 3
n = kin.stoichProduct(species, rxns) - ...
kin.stoichReactant(species, rxns);
n = kin.productStoichCoeffs(species, rxns) - ...
kin.reactantStoichCoeffs(species, rxns);
else
error('stoichNet requires 1 or 3 arguments.');
end
Expand Down Expand Up @@ -378,7 +431,7 @@ function delete(kin)
% :return:
% True if reaction number i is reversible. false if irreversible.

n = boolean(ctFunc('kin_isReversible', kin.kinID, i));
n = boolean(ctFunc('kin_isReversible', kin.kinID, i - 1));
end

function wdot = get.netProdRates(kin)
Expand Down
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