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[Kinetics] Deprecate reacting phase not in first position

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Standardize on the behavior implemented by the newSolution and
newInterface constructors.
This commit is contained in:
Ray Speth
2023-04-17 22:45:25 -04:00
committed by Ingmar Schoegl
parent e82f932119
commit 707c569a3d
17 changed files with 62 additions and 34 deletions
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1
include/cantera/clib/ct.h
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@@ -122,6 +122,7 @@ extern "C" {
CANTERA_CAPI int thermo_setState_Psat(int n, double p, double x);
CANTERA_CAPI int thermo_setState_Tsat(int n, double t, double x);
//! @since Starting in Cantera 3.0, the "phasename" argument should be blank
CANTERA_CAPI int kin_newFromFile(const char* filename, const char* phasename,
int reactingPhase, int neighbor1, int neighbor2,
int neighbor3, int neighbor4);

3
include/cantera/kinetics/InterfaceKinetics.h
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@@ -133,7 +133,8 @@ public:
//! Add a thermo phase to the kinetics manager object.
/*!
* This must be done before the function init() is called or
* before any reactions are input.
* before any reactions are input. The lowest dimensional phase, where reactions
* occur, must be added first.
*
* This function calls Kinetics::addPhase(). It also sets the following
* fields:

3
include/cantera/kinetics/Kinetics.h
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@@ -216,6 +216,9 @@ public:
* phase with the smallest spatial dimension (1, 2, or 3) among the list
* of phases. If there is more than one, the index of the first one is
* returned. For homogeneous mechanisms, the value 0 is returned.
*
* @deprecated Starting in Cantera 3.0, the reacting phase will always be the
* first phase in the InterfaceKinetics object. To be removed after Cantera 3.1.
*/
size_t reactionPhaseIndex() const {
return m_rxnphase;

7
include/cantera/kinetics/KineticsFactory.h
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@@ -82,10 +82,15 @@ unique_ptr<Kinetics> newKinetics(const std::vector<ThermoPhase*>& phases,
* the reactions occur. Searches the Cantera data for this file.
* @param phase_name The name of the reacting phase in the input file (that is, the
* name of the first phase in the `phases` vector)
* @deprecated The 'phase_name' argument is deprecated and will be removed after
* Cantera 3.0.
* @since Starting with Cantera 3.0, if the reacting phase is not the first item in the
* `phases` vector, a deprecation warning will be issued. In Cantera 3.1, this
* warning will become an error.
*/
shared_ptr<Kinetics> newKinetics(const vector<shared_ptr<ThermoPhase>>& phases,
const string& filename,
const string& phase_name);
const string& phase_name="");
//! @copydoc newKinetics(const vector<shared_ptr<ThermoPhase>>&, const string&, const string&)
//! @deprecated To be removed after Cantera 3.0;

9
interfaces/cython/cantera/kinetics.pyx
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@@ -111,7 +111,14 @@ cdef class Kinetics(_SolutionBase):
return self.kinetics.nPhases()
property reaction_phase_index:
"""The index of the phase where the reactions occur."""
"""
The index of the phase where the reactions occur.
.. deprecated:: 3.0
After Cantera 3.0, the reacting phase is always the first phase associated
with the Kinetics object. This method will be removed after Cantera 3.1.
"""
def __get__(self):
return self.kinetics.reactionPhaseIndex()

4
src/fortran/cantera_funcs.f90
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@@ -24,7 +24,7 @@ module cantera_funcs
self = ctthermo_newFromFile(src)
end if
call ctkin_newFromFile(self, src, id)
call ctkin_newFromFile(self, src, '')
if (present(loglevel)) then
self%tran_id = trans_newdefault(self%thermo_id, loglevel)
@@ -52,7 +52,7 @@ module cantera_funcs
self%bulk = bulk
end if
self%gas = gas
call ctkin_newFromFile(self%surf, src, id, gas, bulk)
call ctkin_newFromFile(self%surf, src, '', gas, bulk)
ctfunc_importInterface = self
return

5
src/kinetics/Kinetics.cpp
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@@ -596,6 +596,11 @@ void Kinetics::addThermo(shared_ptr<ThermoPhase> thermo)
// the phase with lowest dimensionality is assumed to be the
// phase/interface at which reactions take place
if (thermo->nDim() <= m_mindim) {
if (!m_thermo.empty()) {
warn_deprecated("Kinetics::addThermo", "The reacting (lowest dimensional) "
"phase should be added first. This warning will become an error after "
"Cantera 3.0.");
}
m_mindim = thermo->nDim();
m_rxnphase = nPhases();
}

8
src/kinetics/KineticsFactory.cpp
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@@ -137,8 +137,14 @@ shared_ptr<Kinetics> newKinetics(const vector<shared_ptr<ThermoPhase>>& phases,
const string& filename,
const string& phase_name)
{
if (phase_name != "") {
warn_deprecated("newKinetics", "After Cantera 3.0, the 'phase_name' argument "
"will be removed and an exception will be thrown if the reacting phase is "
"not the first phase in the 'phases' vector.");
}
string reaction_phase = (phase_name.empty()) ? phases.at(0)->name() : phase_name;
AnyMap root = AnyMap::fromYamlFile(filename);
AnyMap& phaseNode = root["phases"].getMapWhere("name", phase_name);
AnyMap& phaseNode = root["phases"].getMapWhere("name", reaction_phase);
return newKinetics(phases, phaseNode, root);
}

2
test/clib/test_clib.cpp
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@@ -175,7 +175,7 @@ TEST(ct, thermo)
TEST(ct, kinetics)
{
int thermo = thermo_newFromFile("gri30.yaml", "gri30");
int kin = kin_newFromFile("gri30.yaml", "gri30", thermo, -1, -1, -1, -1);
int kin = kin_newFromFile("gri30.yaml", "", thermo, -1, -1, -1, -1);
ASSERT_GE(kin, 0);
size_t nr = kin_nReactions(kin);

4
test/clib/test_ctonedim.cpp
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@@ -102,7 +102,7 @@ TEST(ctonedim, reacting_surface_from_parts)
int gas = thermo_newFromFile("ptcombust.yaml", "gas");
int surf = thermo_newFromFile("ptcombust.yaml", "Pt_surf");
int kin = kin_newFromFile("ptcombust.yaml", "Pt_surf", surf, gas, -1, -1, -1);
int kin = kin_newFromFile("ptcombust.yaml", "", surf, gas, -1, -1, -1);
ASSERT_GE(kin, 0);
int ret = reactingsurf_setkineticsmgr(index, kin);
@@ -117,7 +117,7 @@ TEST(ctonedim, catcomb_stack)
int trans = soln_transport(sol);
int surf = thermo_newFromFile("ptcombust.yaml", "Pt_surf");
int surf_kin = kin_newFromFile("ptcombust.yaml", "Pt_surf", surf, gas, -1, -1, -1);
int surf_kin = kin_newFromFile("ptcombust.yaml", "", surf, gas, -1, -1, -1);
// inlet
int inlet = inlet_new();

4
test/clib/test_ctreactor.cpp
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@@ -11,7 +11,7 @@ using namespace Cantera;
TEST(ctreactor, reactor_objects)
{
int thermo = thermo_newFromFile("gri30.yaml", "gri30");
int kin = kin_newFromFile("gri30.yaml", "gri30", thermo, -1, -1, -1, -1);
int kin = kin_newFromFile("gri30.yaml", "", thermo, -1, -1, -1, -1);
int reactor = reactor_new("IdealGasReactor");
ASSERT_GT(reactor, 0);
@@ -64,7 +64,7 @@ TEST(ctreactor, reactor_from_parts)
string X = "CH4:1.0, O2:2.0, N2:7.52";
int thermo = thermo_newFromFile("gri30.yaml", "gri30");
int kin = kin_newFromFile("gri30.yaml", "gri30", thermo, -1, -1, -1, -1);
int kin = kin_newFromFile("gri30.yaml", "", thermo, -1, -1, -1, -1);
thermo_setMoleFractionsByName(thermo, X.c_str());
thermo_setTemperature(thermo, T);
thermo_setPressure(thermo, P);

4
test/general/test_serialization.cpp
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@@ -281,7 +281,7 @@ TEST(YamlWriter, Interface)
shared_ptr<ThermoPhase> gas1(newThermo("ptcombust.yaml", "gas"));
shared_ptr<ThermoPhase> surf1(newThermo("ptcombust.yaml", "Pt_surf"));
vector<shared_ptr<ThermoPhase>> phases1{surf1, gas1};
shared_ptr<Kinetics> kin1 = newKinetics(phases1, "ptcombust.yaml", "Pt_surf");
shared_ptr<Kinetics> kin1 = newKinetics(phases1, "ptcombust.yaml");
double T = 900;
double P = OneAtm;
@@ -301,7 +301,7 @@ TEST(YamlWriter, Interface)
shared_ptr<ThermoPhase> gas2(newThermo("generated-ptcombust.yaml", "gas"));
shared_ptr<ThermoPhase> surf2(newThermo("generated-ptcombust.yaml", "Pt_surf"));
vector<shared_ptr<ThermoPhase>> phases2{surf2, gas2};
shared_ptr<Kinetics> kin2 = newKinetics(phases2, "generated-ptcombust.yaml", "Pt_surf");
shared_ptr<Kinetics> kin2 = newKinetics(phases2, "generated-ptcombust.yaml");
auto iface1 = std::dynamic_pointer_cast<SurfPhase>(surf1);
auto iface2 = std::dynamic_pointer_cast<SurfPhase>(surf2);

6
test/kinetics/kineticsFromScratch.cpp
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@@ -27,7 +27,7 @@ public:
{
vector<shared_ptr<ThermoPhase>> th;
th.push_back(pp_ref);
kin_ref = newKinetics(th, "../data/kineticsfromscratch.yaml", "ohmech");
kin_ref = newKinetics(th, "../data/kineticsfromscratch.yaml");
kin.addThermo(pp);
kin.init();
@@ -519,7 +519,7 @@ public:
, surf(newThermo("sofc.yaml", "metal_surface"))
, surf_ref(newThermo("sofc.yaml", "metal_surface"))
{
kin_ref = newKinetics({surf_ref, gas_ref}, "sofc.yaml", "metal_surface");
kin_ref = newKinetics({surf_ref, gas_ref}, "sofc.yaml");
kin.addThermo(surf);
kin.addThermo(gas);
}
@@ -602,7 +602,7 @@ public:
p = make_shared<IdealGasPhase>();
vector<shared_ptr<ThermoPhase>> th;
th.push_back(pp_ref);
kin_ref = newKinetics(th, "../data/kineticsfromscratch.yaml", "ohmech");
kin_ref = newKinetics(th, "../data/kineticsfromscratch.yaml");
kin.addThermo(p);
std::vector<shared_ptr<Species>> S = getSpecies(

2
test/kinetics/rates.cpp
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@@ -16,7 +16,7 @@ public:
FracCoeffTest() :
therm(newThermo("frac.yaml", "gas"))
{
kin = newKinetics({therm}, "frac.yaml", "gas");
kin = newKinetics({therm}, "frac.yaml");
therm->setState_TPX(2000, 4*OneAtm,
"H2O:0.5, OH:.05, H:0.1, O2:0.15, H2:0.2");
kH2O = therm->speciesIndex("H2O");

3
test_problems/diamondSurf/runDiamond.cpp
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@@ -28,8 +28,7 @@ int main(int argc, char** argv)
size_t nsp_d100 = diamond100->nSpecies();
cout << "Number of species in diamond_100 = " << nsp_d100 << endl;
auto kin = newKinetics({gas, diamond, diamond100},
"diamond.yaml", "diamond_100");
auto kin = newKinetics({diamond100, gas, diamond}, "diamond.yaml");
InterfaceKinetics& ikin = dynamic_cast<InterfaceKinetics&>(*kin);
size_t nr = kin->nReactions();
cout << "Number of reactions = " << nr << endl;

8
test_problems/surfSolverTest/results2_blessed.txt
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@@ -1,6 +1,6 @@
Gas Temperature = 1.4e+03
Gas Pressure = 1.01e+05
Gas Phase: gas (0)
Gas Phase: gas (2)
Name Conc MoleF SrcRate
(kmol/m^3) (kmol/m^2/s)
0 H 8.69602e-05 0.00999001 -2.365619e-03
@@ -15,7 +15,7 @@ Gas Phase: gas (0)
9 O2 8.69602e-06 0.000999001 -9.060640e-07
Sum of gas mole fractions= 1
Bulk Phase: soot (10)
Bulk Phase: soot (11)
Bulk Temperature = 1.4e+03
Bulk Pressure = 1.01e+05
Name Conc MoleF SrcRate
@@ -28,14 +28,14 @@ Density of bulk phase = 3.52e+03 kg / m^3
= 3.52 gm / cm^3
Sum of bulk mole fractions= 1
Surface Phase: soot_interface (11)
Surface Phase: soot_interface (0)
Surface Temperature = 1.4e+03
Surface Pressure = 1.01e+05
Name Coverage SrcRate
0 Csoot-* 0.0184677 0.000000e+00
1 Csoot-H 0.981532 0.000000e+00
Sum of coverages = 1
Surface Phase: soot_interface (11)
Surface Phase: soot_interface (0)
Surface Temperature = 1.4e+03
Surface Pressure = 1.01e+05
Name Coverage SrcRate

23
test_problems/surfSolverTest/surfaceSolver2.cpp
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@@ -26,14 +26,15 @@ void printGas(ostream& oooo, shared_ptr<ThermoPhase> gasTP,
double x[MSSIZE];
double C[MSSIZE];
oooo.precision(3);
string gasPhaseName = "gas";
string gasPhaseName = "gas";
gasTP->getMoleFractions(x);
gasTP->getConcentrations(C);
double Temp = gasTP->temperature();
double p = gasTP->pressure();
oooo << "Gas Temperature = " << Temp << endl;
oooo << "Gas Pressure = " << p << endl;
size_t kstart = iKin_ptr->kineticsSpeciesIndex(0, 0);
size_t nGas = iKin_ptr->phaseIndex(gasPhaseName);
size_t kstart = iKin_ptr->kineticsSpeciesIndex(0, nGas);
oooo << "Gas Phase: " << gasPhaseName << " "
<< "(" << kstart << ")" << endl;
oooo << " Name "
@@ -43,7 +44,7 @@ void printGas(ostream& oooo, shared_ptr<ThermoPhase> gasTP,
double sum = 0.0;
size_t nspGas = gasTP->nSpecies();
for (size_t k = 0; k < nspGas; k++) {
kstart = iKin_ptr->kineticsSpeciesIndex(k, 0);
kstart = iKin_ptr->kineticsSpeciesIndex(k, nGas);
fmt::print(oooo, "{:4d} {:>24s} {:14g} {:14g} {:14e}\n",
k, gasTP->speciesName(k), C[k], x[k], src[kstart]);
sum += x[k];
@@ -63,7 +64,8 @@ void printBulk(ostream& oooo, shared_ptr<ThermoPhase> bulkPhaseTP,
string bulkParticlePhaseName = bulkPhaseTP->name();
bulkPhaseTP->getMoleFractions(x);
bulkPhaseTP->getConcentrations(C);
size_t kstart = iKin_ptr->kineticsSpeciesIndex(0, 1);
size_t nBulk = iKin_ptr->phaseIndex(bulkParticlePhaseName);
size_t kstart = iKin_ptr->kineticsSpeciesIndex(0, nBulk);
double dens = bulkPhaseTP->density();
oooo << "Bulk Phase: " << bulkParticlePhaseName << " "
<< "(" << kstart << ")" << endl;
@@ -80,7 +82,7 @@ void printBulk(ostream& oooo, shared_ptr<ThermoPhase> bulkPhaseTP,
const vector_fp& molecW = bulkPhaseTP->molecularWeights();
size_t nspBulk = bulkPhaseTP->nSpecies();
for (size_t k = 0; k < nspBulk; k++) {
kstart = iKin_ptr->kineticsSpeciesIndex(k, 1);
kstart = iKin_ptr->kineticsSpeciesIndex(k, nBulk);
fmt::print(oooo, "{:4d} {:>24s} {:14g} {:14g} {:14e}\n",
k, bulkPhaseTP->speciesName(k), C[k], x[k], src[kstart]);
sum += x[k];
@@ -105,7 +107,8 @@ void printSurf(ostream& oooo, shared_ptr<ThermoPhase> surfPhaseTP,
oooo.precision(3);
string surfParticlePhaseName = surfPhaseTP->name();
surfPhaseTP->getMoleFractions(x);
size_t kstart = iKin_ptr->kineticsSpeciesIndex(0, 2);
size_t nSurf = iKin_ptr->phaseIndex(surfParticlePhaseName);
size_t kstart = iKin_ptr->kineticsSpeciesIndex(0, nSurf);
oooo << "Surface Phase: " << surfParticlePhaseName
<< " (" << kstart << ")" << endl;
double Temp = surfPhaseTP->temperature();
@@ -117,7 +120,7 @@ void printSurf(ostream& oooo, shared_ptr<ThermoPhase> surfPhaseTP,
double sum = 0.0;
size_t nspSurf = surfPhaseTP->nSpecies();
for (size_t k = 0; k < nspSurf; k++) {
kstart = iKin_ptr->kineticsSpeciesIndex(0, 2);
kstart = iKin_ptr->kineticsSpeciesIndex(k, nSurf);
double srcK = src[kstart];
if (fabs(srcK) < 1.0E-8) {
srcK = 0.0;
@@ -152,8 +155,7 @@ int main(int argc, char** argv)
cout << "Number of species in surface phase, " << surfParticlePhaseName
<< " = " << nsp_d100 << endl;
auto kin = newKinetics({gasTP, bulkPhaseTP, surfPhaseTP},
infile, surfParticlePhaseName);
auto kin = newKinetics({surfPhaseTP, gasTP, bulkPhaseTP}, infile);
auto iKin_ptr = dynamic_pointer_cast<InterfaceKinetics>(kin);
size_t nr = iKin_ptr->nReactions();
cout << "Number of reactions = " << nr << endl;
@@ -170,8 +172,7 @@ int main(int argc, char** argv)
// create the second InterfaceKinetics object based on the
// second surface phase.
auto kin2 = newKinetics({gasTP, bulkPhaseTP, surfPhaseTP2},
infile, surfParticlePhaseName);
auto kin2 = newKinetics({surfPhaseTP2, gasTP, bulkPhaseTP}, infile);
auto iKin2_ptr = dynamic_pointer_cast<InterfaceKinetics>(kin2);
nr = iKin_ptr->nReactions();
cout << "Number of reactions = " << nr << endl;