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Remove duplication of string identifiers in Phase #724

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Remove duplication of string identifiers in Phase #724

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ea65ba6
[Thermo] deprecate name/id support in Phase::speciesIndex
Oct 7, 2019
3c98504
[Equil] replace references to Phase::name by Phase::id
ischoegl Oct 7, 2019
5bf6357
[Thermo] replace remaining references to Phase::name by Phase::id
ischoegl Oct 7, 2019
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4 changes: 2 additions & 2 deletions include/cantera/equil/MultiPhase.h
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Expand Up @@ -670,8 +670,8 @@ inline std::ostream& operator<<(std::ostream& s, MultiPhase& x)
{
x.updatePhases();
for (size_t ip = 0; ip < x.nPhases(); ip++) {
if (x.phase(ip).name() != "") {
s << "*************** " << x.phase(ip).name() << " *****************" << std::endl;
if (x.phase(ip).id() != "") {
s << "*************** " << x.phase(ip).id() << " *****************" << std::endl;
} else {
s << "*************** Phase " << ip << " *****************" << std::endl;
}
Expand Down
11 changes: 7 additions & 4 deletions include/cantera/equil/vcs_VolPhase.h
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Expand Up @@ -92,11 +92,11 @@ class vcs_VolPhase
/*!
* @param phaseNum index of the phase in the vcs problem
* @param numSpecies Number of species in the phase
* @param phaseName String name for the phase
* @param phaseID String identifier for the phase
* @param molesInert kmoles of inert in the phase (defaults to zero)
*/
void resize(const size_t phaseNum, const size_t numSpecies,
const size_t numElem, const char* const phaseName,
const size_t numElem, const char* const phaseID,
const double molesInert = 0.0);

void elemResize(const size_t numElemConstraints);
Expand Down Expand Up @@ -623,10 +623,13 @@ class vcs_VolPhase
size_t m_numSpecies;

public:
//! String name for the phase
std::string PhaseName;
//! String identifier for the phase
std::string PhaseID();

private:
//! String identifier of the phase
std::string m_phaseID;

//! Total moles of inert in the phase
double m_totalMolesInert;

Expand Down
4 changes: 2 additions & 2 deletions include/cantera/equil/vcs_solve.h
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Expand Up @@ -527,7 +527,7 @@ class VCS_SOLVE
* in the private data structure. All references to the species
* properties must employ the ind[] index vector.
* 4. Initialization of arrays to zero.
* 5. Check to see if the problem is well posed (If all the element
* 5. Check to see if the problem is well posed (If all the element
* abundances are zero, the algorithm will fail)
*
* @param printLvl Print level of the routine
Expand Down Expand Up @@ -1354,7 +1354,7 @@ class VCS_SOLVE
vector_int m_speciesStatus;

//! Mapping from the species number to the phase number
std::vector<size_t> m_phaseID;
std::vector<size_t> m_phaseNum;

//! Boolean indicating whether a species belongs to a single-species phase
// vector<bool> can't be used here because it doesn't work with std::swap
Expand Down
14 changes: 5 additions & 9 deletions include/cantera/thermo/Phase.h
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Expand Up @@ -66,15 +66,11 @@ namespace Cantera
* operate on a state vector, which is in general of length (2 + nSpecies()).
* The first two entries of the state vector are temperature and density.
*
* A species name may be referred to via three methods:
*
* - "speciesName"
* - "PhaseId:speciesName"
* - "phaseName:speciesName"
* .
*
* The first two methods of naming may not yield a unique species within
* complicated assemblies of %Cantera Phases.
* A species name is referred to via "speciesName", which is unique within a
* given phase. Note that within multiphase mixtures ("MultiPhase"), both a
* phase name/index as well as species name are required to access information
* about a species in a particular phase. For surfaces, the species names are
* unique among the phases.
*
* @todo
* - Make the concept of saving state vectors more general, so that it can
Expand Down
2 changes: 1 addition & 1 deletion interfaces/cython/cantera/test/test_thermo.py
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Expand Up @@ -304,14 +304,14 @@ def test_name(self):

self.phase.name = 'something'
self.assertEqual(self.phase.name, 'something')
self.assertIn('something', self.phase.report())

def test_ID(self):
self.assertEqual(self.phase.ID, 'ohmech')

self.phase.ID = 'something'
self.assertEqual(self.phase.ID, 'something')
self.assertEqual(self.phase.name, 'ohmech')
self.assertIn('something', self.phase.report())

def test_badLength(self):
X = np.zeros(5)
Expand Down
4 changes: 2 additions & 2 deletions src/clib/ct.cpp
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Expand Up @@ -287,7 +287,7 @@ extern "C" {
int thermo_getName(int n, size_t lennm, char* nm)
{
try {
return static_cast<int>(copyString(ThermoCabinet::item(n).name(), nm, lennm));
return static_cast<int>(copyString(ThermoCabinet::item(n).id(), nm, lennm));
} catch (...) {
return handleAllExceptions(-1, ERR);
}
Expand All @@ -296,7 +296,7 @@ extern "C" {
int thermo_setName(int n, const char* nm)
{
try {
ThermoCabinet::item(n).setName(nm);
ThermoCabinet::item(n).setID(nm);
return 0;
} catch (...) {
return handleAllExceptions(-1, ERR);
Expand Down
2 changes: 1 addition & 1 deletion src/equil/MultiPhase.cpp
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Expand Up @@ -55,7 +55,7 @@ void MultiPhase::addPhase(ThermoPhase* p, doublereal moles)

if (!p->compatibleWithMultiPhase()) {
throw CanteraError("MultiPhase::addPhase", "Phase '{}'' is not "
"compatible with MultiPhase equilibrium solver", p->name());
"compatible with MultiPhase equilibrium solver", p->id());
}

// save the pointer to the phase object
Expand Down
10 changes: 5 additions & 5 deletions src/equil/MultiPhaseEquil.cpp
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Expand Up @@ -706,7 +706,7 @@ void MultiPhaseEquil::reportCSV(const std::string& reportFile)
ThermoPhase& tref = m_mix->phase(iphase);
ThermoPhase* tp = &tref;
tp->getMoleFractions(&mf[istart]);
string phaseName = tref.name();
string phaseID = tref.id();
double TMolesPhase = phaseMoles(iphase);
size_t nSpecies = tref.nSpecies();
activity.resize(nSpecies, 0.0);
Expand All @@ -733,7 +733,7 @@ void MultiPhaseEquil::reportCSV(const std::string& reportFile)
tp->getChemPotentials(mu.data());

if (iphase == 0) {
fprintf(FP," Name, Phase, PhaseMoles, Mole_Fract, "
fprintf(FP," Name, PhaseID, PhaseMoles, Mole_Fract, "
"Molalities, ActCoeff, Activity,"
"ChemPot_SS0, ChemPot, mole_num, PMVol, Phase_Volume\n");

Expand All @@ -746,15 +746,15 @@ void MultiPhaseEquil::reportCSV(const std::string& reportFile)
fprintf(FP,"%12s, %11s, %11.3e, %11.3e, %11.3e, %11.3e, %11.3e,"
"%11.3e, %11.3e, %11.3e, %11.3e, %11.3e\n",
sName.c_str(),
phaseName.c_str(), TMolesPhase,
phaseID.c_str(), TMolesPhase,
mf[istart + k], molalities[k], ac[k], activity[k],
mu0[k]*1.0E-6, mu[k]*1.0E-6,
mf[istart + k] * TMolesPhase,
VolPM[k], VolPhaseVolumes);
}
} else {
if (iphase == 0) {
fprintf(FP," Name, Phase, PhaseMoles, Mole_Fract, "
fprintf(FP," Name, PhaseID, PhaseMoles, Mole_Fract, "
"Molalities, ActCoeff, Activity,"
" ChemPotSS0, ChemPot, mole_num, PMVol, Phase_Volume\n");

Expand All @@ -770,7 +770,7 @@ void MultiPhaseEquil::reportCSV(const std::string& reportFile)
fprintf(FP,"%12s, %11s, %11.3e, %11.3e, %11.3e, %11.3e, %11.3e, "
"%11.3e, %11.3e,% 11.3e, %11.3e, %11.3e\n",
sName.c_str(),
phaseName.c_str(), TMolesPhase,
phaseID.c_str(), TMolesPhase,
mf[istart + k], molalities[k], ac[k],
activity[k], mu0[k]*1.0E-6, mu[k]*1.0E-6,
mf[istart + k] * TMolesPhase,
Expand Down
2 changes: 1 addition & 1 deletion src/equil/vcs_Gibbs.cpp
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Expand Up @@ -42,7 +42,7 @@ double VCS_SOLVE::vcs_GibbsPhase(size_t iphase, const double* const w,
double g = 0.0;
double phaseMols = 0.0;
for (size_t kspec = 0; kspec < m_numSpeciesRdc; ++kspec) {
if (m_phaseID[kspec] == iphase && m_speciesUnknownType[kspec] != VCS_SPECIES_TYPE_INTERFACIALVOLTAGE) {
if (m_phaseNum[kspec] == iphase && m_speciesUnknownType[kspec] != VCS_SPECIES_TYPE_INTERFACIALVOLTAGE) {
g += w[kspec] * fe[kspec];
phaseMols += w[kspec];
}
Expand Down
12 changes: 6 additions & 6 deletions src/equil/vcs_MultiPhaseEquil.cpp
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Expand Up @@ -469,7 +469,7 @@ int vcs_MultiPhaseEquil::equilibrate_TP(int estimateEquil,
} else {
plogf(" %15.3e %15.3e ", m_mix->speciesMoles(i), m_mix->moleFraction(i));
if (m_mix->speciesMoles(i) <= 0.0) {
size_t iph = m_vsolve.m_phaseID[i];
size_t iph = m_vsolve.m_phaseNum[i];
vcs_VolPhase* VPhase = m_vsolve.m_VolPhaseList[iph].get();
if (VPhase->nSpecies() > 1) {
plogf(" -1.000e+300\n");
Expand Down Expand Up @@ -533,7 +533,7 @@ void vcs_MultiPhaseEquil::reportCSV(const std::string& reportFile)

for (size_t iphase = 0; iphase < nphase; iphase++) {
ThermoPhase& tref = m_mix->phase(iphase);
string phaseName = tref.name();
string phaseID = tref.id();
vcs_VolPhase* volP = m_vsolve.m_VolPhaseList[iphase].get();
double TMolesPhase = volP->totalMoles();
size_t nSpecies = tref.nSpecies();
Expand Down Expand Up @@ -562,7 +562,7 @@ void vcs_MultiPhaseEquil::reportCSV(const std::string& reportFile)
tref.getChemPotentials(&mu[0]);

if (iphase == 0) {
fprintf(FP," Name, Phase, PhaseMoles, Mole_Fract, "
fprintf(FP," Name, PhaseID, PhaseMoles, Mole_Fract, "
"Molalities, ActCoeff, Activity,"
"ChemPot_SS0, ChemPot, mole_num, PMVol, Phase_Volume\n");

Expand All @@ -575,15 +575,15 @@ void vcs_MultiPhaseEquil::reportCSV(const std::string& reportFile)
fprintf(FP,"%12s, %11s, %11.3e, %11.3e, %11.3e, %11.3e, %11.3e,"
"%11.3e, %11.3e, %11.3e, %11.3e, %11.3e\n",
sName.c_str(),
phaseName.c_str(), TMolesPhase,
phaseID.c_str(), TMolesPhase,
tref.moleFraction(k), molalities[k], ac[k], activity[k],
mu0[k]*1.0E-6, mu[k]*1.0E-6,
tref.moleFraction(k) * TMolesPhase,
VolPM[k], VolPhaseVolumes);
}
} else {
if (iphase == 0) {
fprintf(FP," Name, Phase, PhaseMoles, Mole_Fract, "
fprintf(FP," Name, PhaseID, PhaseMoles, Mole_Fract, "
"Molalities, ActCoeff, Activity,"
" ChemPotSS0, ChemPot, mole_num, PMVol, Phase_Volume\n");

Expand All @@ -599,7 +599,7 @@ void vcs_MultiPhaseEquil::reportCSV(const std::string& reportFile)
fprintf(FP,"%12s, %11s, %11.3e, %11.3e, %11.3e, %11.3e, %11.3e, "
"%11.3e, %11.3e,% 11.3e, %11.3e, %11.3e\n",
sName.c_str(),
phaseName.c_str(), TMolesPhase,
phaseID.c_str(), TMolesPhase,
tref.moleFraction(k), molalities[k], ac[k],
activity[k], mu0[k]*1.0E-6, mu[k]*1.0E-6,
tref.moleFraction(k) * TMolesPhase,
Expand Down
22 changes: 14 additions & 8 deletions src/equil/vcs_VolPhase.cpp
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Expand Up @@ -28,6 +28,7 @@ vcs_VolPhase::vcs_VolPhase(VCS_SOLVE* owningSolverObject) :
m_numElemConstraints(0),
m_elemGlobalIndex(0),
m_numSpecies(0),
m_phaseID("<phase-id>"),
m_totalMolesInert(0.0),
m_isIdealSoln(false),
m_existence(VCS_PHASE_EXIST_NO),
Expand Down Expand Up @@ -58,8 +59,13 @@ vcs_VolPhase::~vcs_VolPhase()
}
}

std::string vcs_VolPhase::PhaseID()
{
return m_phaseID;
}

void vcs_VolPhase::resize(const size_t phaseNum, const size_t nspecies,
const size_t numElem, const char* const phaseName,
const size_t numElem, const char* const phaseID,
const double molesInert)
{
AssertThrowMsg(nspecies > 0, "vcs_VolPhase::resize", "nspecies Error");
Expand All @@ -68,17 +74,17 @@ void vcs_VolPhase::resize(const size_t phaseNum, const size_t nspecies,
m_phiVarIndex = npos;

if (phaseNum == VP_ID_) {
if (strcmp(PhaseName.c_str(), phaseName)) {
if (strcmp(m_phaseID.c_str(), phaseID)) {
throw CanteraError("vcs_VolPhase::resize",
"Strings are different: " + PhaseName + " " +
phaseName + " :unknown situation");
"Strings are different: " + m_phaseID + " " +
phaseID + " :unknown situation");
}
} else {
VP_ID_ = phaseNum;
if (!phaseName) {
PhaseName = fmt::format("Phase_{}", VP_ID_);
if (!phaseID) {
m_phaseID = fmt::format("Phase_{}", VP_ID_);
} else {
PhaseName = phaseName;
m_phaseID = phaseID;
}
}
if (nspecies > 1) {
Expand Down Expand Up @@ -589,7 +595,7 @@ void vcs_VolPhase::setPtrThermoPhase(ThermoPhase* tp_ptr)
if (m_numSpecies != 0) {
plogf("Warning Nsp != NVolSpeces: %d %d \n", nsp, m_numSpecies);
}
resize(VP_ID_, nsp, nelem, PhaseName.c_str());
resize(VP_ID_, nsp, nelem, m_phaseID.c_str());
}
TP_ptr->getMoleFractions(&Xmol_[0]);
creationMoleNumbers_ = Xmol_;
Expand Down
2 changes: 1 addition & 1 deletion src/equil/vcs_elem.cpp
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Expand Up @@ -87,7 +87,7 @@ void VCS_SOLVE::vcs_elabPhase(size_t iphase, double* const elemAbundPhase)
for (size_t j = 0; j < m_nelem; ++j) {
elemAbundPhase[j] = 0.0;
for (size_t i = 0; i < m_nsp; ++i) {
if (m_speciesUnknownType[i] != VCS_SPECIES_TYPE_INTERFACIALVOLTAGE && m_phaseID[i] == iphase) {
if (m_speciesUnknownType[i] != VCS_SPECIES_TYPE_INTERFACIALVOLTAGE && m_phaseNum[i] == iphase) {
elemAbundPhase[j] += m_formulaMatrix(i,j) * m_molNumSpecies_old[i];
}
}
Expand Down
6 changes: 3 additions & 3 deletions src/equil/vcs_inest.cpp
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Expand Up @@ -83,7 +83,7 @@ void VCS_SOLVE::vcs_inest(double* const aw, double* const sa, double* const sm,
}
for (size_t kspec = 0; kspec < m_numComponents; ++kspec) {
if (m_speciesUnknownType[kspec] == VCS_SPECIES_TYPE_MOLNUM) {
m_tPhaseMoles_new[m_phaseID[kspec]] += m_molNumSpecies_old[kspec];
m_tPhaseMoles_new[m_phaseNum[kspec]] += m_molNumSpecies_old[kspec];
}
}
double TMolesMultiphase = 0.0;
Expand All @@ -103,7 +103,7 @@ void VCS_SOLVE::vcs_inest(double* const aw, double* const sa, double* const sm,
for (size_t kspec = 0; kspec < m_numComponents; ++kspec) {
if (m_speciesUnknownType[kspec] == VCS_SPECIES_TYPE_MOLNUM) {
if (! m_SSPhase[kspec]) {
size_t iph = m_phaseID[kspec];
size_t iph = m_phaseNum[kspec];
m_feSpecies_new[kspec] += log(m_molNumSpecies_new[kspec] / m_tPhaseMoles_old[iph]);
}
} else {
Expand Down Expand Up @@ -140,7 +140,7 @@ void VCS_SOLVE::vcs_inest(double* const aw, double* const sa, double* const sm,
// the phase exists, it stays. If it doesn't exist in the estimate, it
// doesn't come into existence here.
if (! m_SSPhase[kspec]) {
size_t iph = m_phaseID[kspec];
size_t iph = m_phaseNum[kspec];
if (m_deltaGRxn_new[irxn] > xtphMax[iph]) {
m_deltaGRxn_new[irxn] = 0.8 * xtphMax[iph];
}
Expand Down
12 changes: 6 additions & 6 deletions src/equil/vcs_phaseStability.cpp
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Expand Up @@ -125,7 +125,7 @@ size_t VCS_SOLVE::vcs_popPhaseID(std::vector<size_t> & phasePopPhaseIDs)
if (existence > 0) {
if (m_debug_print_lvl >= 2) {
plogf(" --- %18s %5d NA %11.3e\n",
Vphase->PhaseName, existence, m_tPhaseMoles_old[iph]);
Vphase->PhaseID(), existence, m_tPhaseMoles_old[iph]);
}
} else {
if (Vphase->m_singleSpecies) {
Expand Down Expand Up @@ -154,7 +154,7 @@ size_t VCS_SOLVE::vcs_popPhaseID(std::vector<size_t> & phasePopPhaseIDs)

if (m_debug_print_lvl >= 2) {
plogf(" --- %18s %5d %10.3g %10.3g %s\n",
Vphase->PhaseName, existence, Fephase,
Vphase->PhaseID(), existence, Fephase,
m_tPhaseMoles_old[iph], anote);
}
} else {
Expand All @@ -171,13 +171,13 @@ size_t VCS_SOLVE::vcs_popPhaseID(std::vector<size_t> & phasePopPhaseIDs)
}
if (m_debug_print_lvl >= 2) {
plogf(" --- %18s %5d %11.3g %11.3g\n",
Vphase->PhaseName, existence, Fephase,
Vphase->PhaseID(), existence, Fephase,
m_tPhaseMoles_old[iph]);
}
} else {
if (m_debug_print_lvl >= 2) {
plogf(" --- %18s %5d blocked %11.3g\n",
Vphase->PhaseName,
Vphase->PhaseID(),
existence, m_tPhaseMoles_old[iph]);
}
}
Expand Down Expand Up @@ -215,7 +215,7 @@ int VCS_SOLVE::vcs_popPhaseRxnStepSizes(const size_t iphasePop)
"called for a phase that exists!");
if (m_debug_print_lvl >= 2) {
plogf(" --- vcs_popPhaseRxnStepSizes() called to pop phase %s %d into existence\n",
Vphase->PhaseName, iphasePop);
Vphase->PhaseID(), iphasePop);
}
// Section for a single-species phase
if (Vphase->m_singleSpecies) {
Expand Down Expand Up @@ -307,7 +307,7 @@ int VCS_SOLVE::vcs_popPhaseRxnStepSizes(const size_t iphasePop)
}
} else {
if (m_elType[j] == VCS_ELEM_TYPE_ABSPOS) {
size_t jph = m_phaseID[j];
size_t jph = m_phaseNum[j];
if ((jph != iphasePop) && (!m_SSPhase[j])) {
double fdeltaJ = fabs(deltaJ);
if (m_molNumSpecies_old[j] > 0.0) {
Expand Down
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