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On the road to a better scheme for handling the deletion of

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multispecies phases.
This commit is contained in:
Harry Moffat 2008-08-18 23:17:18 +00:00
parent 180b693de5
commit d2358f1818
6 changed files with 214 additions and 128 deletions
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6
Cantera/src/equil/vcs_VolPhase.cpp
View file

@ -635,9 +635,9 @@ namespace VCSnonideal {
// This is where we will start to store a better approximation
// for the mole fractions, when the phase doesn't exist.
// This is currently unimplemented.
for (int k = 0; k < m_numSpecies; k++) {
Xmol[k] = 1.0 / m_numSpecies;
}
//for (int k = 0; k < m_numSpecies; k++) {
// Xmol[k] = 1.0 / m_numSpecies;
//}
m_existence = VCS_PHASE_EXIST_NO;
}
/*

78
Cantera/src/equil/vcs_elem.cpp
View file

@ -74,52 +74,54 @@ namespace VCSnonideal {
* Require 12 digits of accuracy on non-zero constraints.
*/
for (i = 0; i < top; ++i) {
if (fabs(m_elemAbundances[i] - m_elemAbundancesGoal[i]) > (fabs(m_elemAbundancesGoal[i]) * 1.0e-12)) {
/*
* This logic is for charge neutrality condition
*/
if (m_elType[i] == VCS_ELEM_TYPE_CHARGENEUTRALITY) {
AssertThrowVCS(m_elemAbundancesGoal[i] == 0.0, "vcs_elabcheck");
}
if (m_elemAbundancesGoal[i] == 0.0 || (m_elType[i] == VCS_ELEM_TYPE_ELECTRONCHARGE)) {
scale = VCS_DELETE_MINORSPECIES_CUTOFF;
if (m_elementActive[i]) {
if (fabs(m_elemAbundances[i] - m_elemAbundancesGoal[i]) > (fabs(m_elemAbundancesGoal[i]) * 1.0e-12)) {
/*
* Find out if the constraint is a multisign constraint.
* If it is, then we have to worry about roundoff error
* in the addition of terms. We are limited to 13
* digits of finite arithmetic accuracy.
* This logic is for charge neutrality condition
*/
numNonZero = 0;
multisign = false;
for (int kspec = 0; kspec < m_numSpeciesTot; kspec++) {
eval = m_formulaMatrix[i][kspec];
if (eval < 0.0) {
multisign = true;
}
if (eval != 0.0) {
scale = MAX(scale, fabs(eval * m_molNumSpecies_old[kspec]));
numNonZero++;
}
if (m_elType[i] == VCS_ELEM_TYPE_CHARGENEUTRALITY) {
AssertThrowVCS(m_elemAbundancesGoal[i] == 0.0, "vcs_elabcheck");
}
if (multisign) {
if (fabs(m_elemAbundances[i] - m_elemAbundancesGoal[i]) > 1e-11 * scale) {
return FALSE;
if (m_elemAbundancesGoal[i] == 0.0 || (m_elType[i] == VCS_ELEM_TYPE_ELECTRONCHARGE)) {
scale = VCS_DELETE_MINORSPECIES_CUTOFF;
/*
* Find out if the constraint is a multisign constraint.
* If it is, then we have to worry about roundoff error
* in the addition of terms. We are limited to 13
* digits of finite arithmetic accuracy.
*/
numNonZero = 0;
multisign = false;
for (int kspec = 0; kspec < m_numSpeciesTot; kspec++) {
eval = m_formulaMatrix[i][kspec];
if (eval < 0.0) {
multisign = true;
}
if (eval != 0.0) {
scale = MAX(scale, fabs(eval * m_molNumSpecies_old[kspec]));
numNonZero++;
}
}
if (multisign) {
if (fabs(m_elemAbundances[i] - m_elemAbundancesGoal[i]) > 1e-11 * scale) {
return FALSE;
}
} else {
if (fabs(m_elemAbundances[i] - m_elemAbundancesGoal[i]) > VCS_DELETE_MINORSPECIES_CUTOFF) {
return FALSE;
}
}
} else {
if (fabs(m_elemAbundances[i] - m_elemAbundancesGoal[i]) > VCS_DELETE_MINORSPECIES_CUTOFF) {
/*
* For normal element balances, we require absolute compliance
* even for rediculously small numbers.
*/
if (m_elType[i] == VCS_ELEM_TYPE_ABSPOS) {
return FALSE;
} else {
return FALSE;
}
}
} else {
/*
* For normal element balances, we require absolute compliance
* even for rediculously small numbers.
*/
if (m_elType[i] == VCS_ELEM_TYPE_ABSPOS) {
return FALSE;
} else {
return FALSE;
}
}
}
}

6
Cantera/src/equil/vcs_rxnadj.cpp
View file

@ -303,8 +303,8 @@ namespace VCSnonideal {
if (k == kspec) {
m_rxnStatus[irxn] = VCS_SPECIES_ZEROEDSS;
if (m_SSPhase[kspec] != 1) {
printf("we shouldn't be here!\n");
exit(-1);
printf("vcs_RxnStepSizes:: we shouldn't be here!\n");
std::exit(-1);
}
}
#ifdef DEBUG_MODE
@ -586,7 +586,7 @@ namespace VCSnonideal {
double diag = hessianDiag_Ideal;
double hessActCoef = vcs_Hessian_actCoeff_diag(irxn);
if (hessianDiag_Ideal <= 0.0) {
plogf("We shouldn't be here\n");
plogf("vcs_Hessian_diag_adj::We shouldn't be here\n");
exit(-1);
}
if (hessActCoef >= 0.0) {

20
Cantera/src/equil/vcs_solve.cpp
View file

@ -62,6 +62,7 @@ namespace VCSnonideal {
}
// Initialize the sizes within the VCS_SOLVE object
/*
* This resizes all of the internal arrays within the object. This routine
* operates in two modes. If all of the parameters are the same as it
@ -691,7 +692,7 @@ namespace VCSnonideal {
m_elementActive.resize(nelements, 1);
/*
* Copy over the element names
* Copy over the element names and types
*/
for (i = 0; i < nelements; i++) {
m_elementName[i] = pub->ElName[i];
@ -705,6 +706,23 @@ namespace VCSnonideal {
}
}
}
for (i = 0; i < nelements; i++) {
if (m_elType[i] == VCS_ELEM_TYPE_CHARGENEUTRALITY) {
if (m_elemAbundancesGoal[i] != 0.0) {
if (fabs(m_elemAbundancesGoal[i]) > 1.0E-9) {
plogf("Charge neutrality condition %s is signicantly nonzero, %g. Giving up\n",
m_elementName[i].c_str(), m_elemAbundancesGoal[i]);
std::exit(-1);
} else {
plogf("Charge neutrality condition %s not zero, %g. Setting it zero\n",
m_elementName[i].c_str(), m_elemAbundancesGoal[i]);
m_elemAbundancesGoal[i] = 0.0;
}
}
}
}
/*
* Copy over the species names

7
Cantera/src/equil/vcs_solve.h
View file

@ -507,7 +507,9 @@ public:
* Reconciles Phase existence flags with total moles in each phase.
*/
double vcs_tmoles();
#ifdef DEBUG_MODE
void check_tmoles() const;
#endif
//! This subroutine calculates reaction free energy changes for
//! all noncomponent formation reactions.
@ -1415,7 +1417,6 @@ public:
*
* length = [nspecies0][nelements0]
*/
//DoubleStarStar sc;
DoubleStarStar m_stoichCoeffRxnMatrix;
//! Absolute size of the stoichiometric coefficients
@ -1718,7 +1719,7 @@ public:
//! Species string name for the kth species
/*!
* SpName[k] = Species string name for the kth species
* Species string name for the kth species
*/
std::vector<std::string> m_speciesName;

225
Cantera/src/equil/vcs_solve_TP.cpp
View file

@ -404,7 +404,7 @@ namespace VCSnonideal {
if (uptodate_minors == FALSE) {
vcs_setFlagsVolPhases(false, VCS_STATECALC_OLD);
vcs_dfe(VCS_STATECALC_OLD, 1, 0, m_numSpeciesRdc);
vcs_deltag(1, false, VCS_STATECALC_NEW);
vcs_deltag(1, false, VCS_STATECALC_OLD);
}
uptodate_minors = TRUE;
} else {
@ -422,7 +422,15 @@ namespace VCSnonideal {
plogf(" (only major species)\n");
}
}
/*
* Calculate the total moles in each phase -> old solution
* -> Needed for numerical stability when phases disappear.
* -> the phase moles tend to drift off without this step.
*/
#ifdef DEBUG_MODE
check_tmoles();
#endif
vcs_tmoles();
/*
* Copy the old solution into the new solution as an initial guess
*/
@ -431,6 +439,7 @@ namespace VCSnonideal {
vcs_dcopy(VCS_DATA_PTR(m_actCoeffSpecies_new),
VCS_DATA_PTR(m_actCoeffSpecies_old), m_numSpeciesRdc);
vcs_dcopy(VCS_DATA_PTR(m_deltaGRxn_new), VCS_DATA_PTR(m_deltaGRxn_old), m_numRxnRdc);
/* Go find a new reaction adjustment ->
* i.e., change in extent of reaction for each reaction.
@ -1278,25 +1287,32 @@ namespace VCSnonideal {
if (m_tPhaseMoles_old[iph] != 0.0 &&
m_tPhaseMoles_old[iph]/m_totalMolNum <= VCS_DELETE_PHASE_CUTOFF) {
soldel = 1;
for (kspec = 0; kspec < m_numSpeciesRdc; kspec++) {
if (m_phaseID[kspec] == iph && m_molNumSpecies_old[kspec] > 0.0) {
irxn = kspec - m_numComponents;
if (kspec < m_numComponents) {
if (m_molNumSpecies_old[kspec] > VCS_RELDELETE_SPECIES_CUTOFF) {
soldel = 0;
break;
}
} else {
for (k = 0; k < m_numComponents; k++) {
if (m_stoichCoeffRxnMatrix[irxn][k] != 0.0) {
if (m_molNumSpecies_old[kspec]/m_molNumSpecies_old[k] >
VCS_DELETE_PHASE_CUTOFF) {
soldel = 0;
break;
}
}
}
}
// Both of these conditions are false and should be discarded.
// I think a proper special case would be if a species in a small phase
// had a significant contribution to total element total of a single
// element constraint. That's it.
// if (kspec < m_numComponents) {
// if (m_molNumSpecies_old[kspec] > VCS_RELDELETE_SPECIES_CUTOFF) {
//soldel = 0;
//break;
//}
//} else {
//for (k = 0; k < m_numComponents; k++) {
//if (m_stoichCoeffRxnMatrix[irxn][k] != 0.0) {
// if (m_molNumSpecies_old[kspec]/m_molNumSpecies_old[k] >
//VCS_DELETE_PHASE_CUTOFF) {
// soldel = 0;
// break;
// }
//}
//}
//}
}
}
if (soldel) {
@ -1323,23 +1339,19 @@ namespace VCSnonideal {
retn = vcs_basopt(FALSE, VCS_DATA_PTR(aw), VCS_DATA_PTR(sa),
VCS_DATA_PTR(sm), VCS_DATA_PTR(ss), test,
&usedZeroedSpecies);
if (retn != VCS_SUCCESS) return retn;
if (retn != VCS_SUCCESS) {
#ifdef DEBUG_MODE
plogf(" --- BASOPT returned with an error condition\n");
#endif
std::exit(-1);
}
vcs_setFlagsVolPhases(false, VCS_STATECALC_OLD);
vcs_dfe(VCS_STATECALC_OLD, 0, 0, m_numSpeciesRdc);
vcs_deltag(0, true, VCS_STATECALC_OLD);
uptodate_minors = TRUE;
if (conv) {
/*
* HKM -> I don't understand why the code would just give
* up here in some cases.
* This should probably be taken out
*/
plogf(" DELETION OF MULTISPECIES PHASE. ");
plogf("Convergence to number of positive n(i) less than C.\n");
plogf("Check results to follow carefully. \n");
plogendl();
goto L_RETURN_BLOCK;
}
iti = 0;
goto L_MAINLOOP_ALL_SPECIES ;
}
/*************************************************************************/
/***************** CHECK FOR ELEMENT ABUNDANCE****************************/
@ -2418,7 +2430,7 @@ namespace VCSnonideal {
/*
* When they are deleted, all of their species become active
* species, even though their mole numbers are set to zero.
* The routine does not make the decision to eliminate multiphases.
* This routine does not make the decision to eliminate multiphases.
*
* Note, species in phases with zero mole numbers are still
* considered active. Whether the phase pops back into
@ -2441,23 +2453,17 @@ namespace VCSnonideal {
plogf(" --- delete_multiphase %d, %s\n", iph, Vphase->PhaseName.c_str());
}
#endif
/*
* Zero out the total moles counters for the phase
*/
m_tPhaseMoles_old[iph] = 0.0;
m_tPhaseMoles_new[iph] = 0.0;
m_deltaPhaseMoles[iph] = 0.0;
/*
* Loop over all of the active species in the phase.
* Loop over all of the active noncomponent species in the phase.
*/
for (kspec = 0; kspec < m_numSpeciesRdc; ++kspec) {
for (kspec = m_numComponents; kspec < m_numSpeciesRdc; ++kspec) {
if (m_phaseID[kspec] == iph) {
if (m_speciesUnknownType[kspec] != VCS_SPECIES_TYPE_INTERFACIALVOLTAGE) {
irxn = kspec - m_numComponents;
if (irxn >= 0) {
/*
* calculate an extent of rxn, dx, that zeroes out the species.
*/
@ -2493,40 +2499,66 @@ namespace VCSnonideal {
* zeroed phase
*/
m_rxnStatus[irxn] = VCS_SPECIES_ZEROEDMS;
/*
* Changed the component mole numbers to account for the
* final extent of reaction. Make sure to keep component
* mole numbers above zero
*
*/
// for (j = 0; j < m_numComponents; ++j) {
// m_molNumSpecies_old[j] += m_stoichCoeffRxnMatrix[irxn][j] * dx;
//if (m_speciesUnknownType[j] == VCS_SPECIES_TYPE_MOLNUM) {
//if (m_molNumSpecies_old[j] < 0.0) {
// m_molNumSpecies_old[j] = 0.0;
//}
//}
//}
}
else {
#ifdef DEBUG_MODE
if (m_debug_print_lvl >= 2) {
plogf(" --- delete_multiphase One of the species is a component %d - %s with mole number %g\n",
kspec, m_speciesName[kspec].c_str(), m_molNumSpecies_old[kspec]);
}
#endif
if (m_molNumSpecies_old[kspec] > VCS_RELDELETE_SPECIES_CUTOFF * VCS_DELETE_PHASE_CUTOFF ) {
plogf(" --- delete_multiphase unknown situation error exit");
plogendl();
std::exit(-1);
} else {
m_molNumSpecies_old[kspec] = 0.0;
m_molNumSpecies_new[kspec] = 0.0;
}
}
}
}
}
int jcomp;
double deltaLarge, dj, dxWant, dxPerm, dxPerm2;
for (int kcomp = 0; kcomp < m_numComponents; ++kcomp) {
if (m_phaseID[kcomp] == iph) {
#ifdef DEBUG_MODE
if (m_debug_print_lvl >= 2) {
plogf(" --- delete_multiphase One of the species is a component %d - %s with mole number %g\n",
kcomp, m_speciesName[kcomp].c_str(), m_molNumSpecies_old[kcomp]);
}
#endif
if (m_molNumSpecies_old[kcomp] != 0.0) {
deltaLarge = 0.0;
for (kspec = m_numComponents; kspec < m_numSpeciesRdc; ++kspec) {
irxn = kspec - m_numComponents;
if (m_phaseID[kspec] != iph) {
if (m_stoichCoeffRxnMatrix[irxn][kcomp] != 0.0) {
dxWant = -m_molNumSpecies_old[kcomp] / m_stoichCoeffRxnMatrix[irxn][kcomp];
if (dxWant + m_molNumSpecies_old[kspec] < 0.0) {
dxPerm = -m_molNumSpecies_old[kspec];
}
for (jcomp = 0; kcomp < m_numComponents; ++kcomp) {
if (jcomp != kcomp) {
if (m_phaseID[jcomp] == iph) {
dxPerm = 0.0;
} else {
dj = dxWant * m_stoichCoeffRxnMatrix[irxn][jcomp];
if (dj + m_molNumSpecies_old[kcomp] < 0.0) {
dxPerm2 = -m_molNumSpecies_old[kcomp] / m_stoichCoeffRxnMatrix[irxn][jcomp];
}
if (fabs(dxPerm2) < fabs(dxPerm)) {
dxPerm = dxPerm2;
}
}
}
}
}
if (dxPerm != 0.0) {
delta_species(kspec, &dxPerm);
}
}
}
}
if (m_molNumSpecies_old[kcomp] != 0.0) {
#ifdef DEBUG_MODE
if (m_debug_print_lvl >= 2) {
plogf(" --- delete_multiphase One of the species is a component %d - %s still with mole number %g\n",
kcomp, m_speciesName[kcomp].c_str(), m_molNumSpecies_old[kcomp]);
plogf(" --- zeroing it \n");
}
#endif
m_molNumSpecies_old[kcomp] = 0.0;
}
}
}
/*
* Loop over all of the inactive species in the phase:
* Right now we reinstate all species in a deleted multiphase.
@ -2561,12 +2593,18 @@ namespace VCSnonideal {
}
}
}
/*
* Zero out the total moles counters for the phase
*/
m_tPhaseMoles_old[iph] = 0.0;
m_tPhaseMoles_new[iph] = 0.0;
m_deltaPhaseMoles[iph] = 0.0;
/*
* Upload the state to the VP object
*/
Vphase->setMolesFromVCSCheck(VCS_STATECALC_OLD,
VCS_DATA_PTR(m_molNumSpecies_old),
VCS_DATA_PTR(m_tPhaseMoles_old));
Vphase->setTotalMoles(0.0);
return successful;
}
/**********************************************************************************/
@ -3275,8 +3313,8 @@ namespace VCSnonideal {
ncTrial = m_numComponents;
int numPreDeleted = m_numRxnTot - m_numRxnRdc;
if (numPreDeleted != (m_numSpeciesTot - m_numSpeciesRdc)) {
plogf("we shouldn't be here\n");
exit(-1);
plogf("vcs_basopt:: we shouldn't be here\n");
std::exit(-1);
}
m_numRxnTot = m_numSpeciesTot - ncTrial;
m_numRxnRdc = m_numRxnTot - numPreDeleted;
@ -4434,6 +4472,33 @@ namespace VCSnonideal {
m_totalMolNum = sum;
return m_totalMolNum;
}
#ifdef DEBUG_MODE
void VCS_SOLVE::check_tmoles() const {
int i;
double sum, m_tPhaseMoles_old_a;
//vcs_VolPhase *Vphase;
for (i = 0; i < m_numPhases; i++) {
m_tPhaseMoles_old_a = TPhInertMoles[i];
for (int k = 0; k < m_numSpeciesTot; k++) {
if (m_speciesUnknownType[k] == VCS_SPECIES_TYPE_MOLNUM) {
if (m_phaseID[k] == i) {
m_tPhaseMoles_old_a += m_molNumSpecies_old[k];
}
}
}
sum += m_tPhaseMoles_old_a;
double denom = m_tPhaseMoles_old[i]+ m_tPhaseMoles_old_a + 1.0E-19;
if (!vcs_doubleEqual(m_tPhaseMoles_old[i]/denom, m_tPhaseMoles_old_a/denom)) {
plogf("check_tmoles: we have found a problem with phase %d: %20.15g, %20.15g\n",
i, m_tPhaseMoles_old[i], m_tPhaseMoles_old_a);
//std::exit(-1);
}
}
}
#endif
/*****************************************************************************/
// This routine uploads the state of the system into all of the
@ -5052,8 +5117,8 @@ namespace VCSnonideal {
// If it isn't, we don't know what's happening
if (m_molNumSpecies_old[kspec] != 0.0) {
w_kspec = 0.0;
plogf("we shouldn't be here\n");
exit(-1);
plogf("vcs_birthGuess:: we shouldn't be here\n");
std::exit(-1);
}
#endif
int ss = m_SSPhase[kspec];