/*
* The Cl- species is special in the sense that its single ion
* molality-based activity coefficient is used in the specification
* of the pH scale for single ions. Therefore, we need to know
* what species index Cl- is. If the species isn't in the species
* list then this routine returns -1, and we can't use the NBS
* pH scale.
*
* Right now we use a restrictive interpretation. The species
* must be named "Cl-". It must consist of exactly one Cl and one E
* atom.
*/
size_t MolalityVPSSTP::findCLMIndex() const
{
size_t indexCLM = npos;
size_t eCl = npos;
size_t eE = npos;
size_t ne = nElements();
string sn;
for (size_t e = 0; e < ne; e++) {
sn = elementName(e);
if (sn == "Cl" || sn == "CL") {
eCl = e;
break;
}
}
// We have failed if we can't find the Cl element index
if (eCl == npos) {
return npos;
}
for (size_t e = 0; e < ne; e++) {
sn = elementName(e);
if (sn == "E" || sn == "e") {
eE = e;
break;
}
}
// We have failed if we can't find the E element index
if (eE == npos) {
return npos;
}
for (size_t k = 1; k < m_kk; k++) {
doublereal nCl = nAtoms(k, eCl);
if (nCl != 1.0) {
continue;
}
doublereal nE = nAtoms(k, eE);
if (nE != 1.0) {
continue;
}
for (size_t e = 0; e < ne; e++) {
if (e != eE && e != eCl) {
doublereal nA = nAtoms(k, e);
if (nA != 0.0) {
continue;
}
}
}
sn = speciesName(k);
if (sn != "Cl-" && sn != "CL-") {
continue;
}
indexCLM = k;
break;
}
return indexCLM;
}
void MineralEQ3::convertDGFormation() {
/*
* Ok let's get the element compositions and conversion factors.
*/
int ne = nElements();
doublereal na;
doublereal ge;
string ename;
doublereal totalSum = 0.0;
for (int m = 0; m < ne; m++) {
na = nAtoms(0, m);
if (na > 0.0) {
ename = elementName(m);
ge = LookupGe(ename);
totalSum += na * ge;
}
}
// Add in the charge
// if (m_charge_j != 0.0) {
// ename = "H";
// ge = LookupGe(ename);
// totalSum -= m_charge_j * ge;
//}
// Ok, now do the calculation. Convert to joules kmol-1
doublereal dg = m_deltaG_formation_pr_tr * 4.184 * 1.0E3;
//! Store the result into an internal variable.
m_Mu0_pr_tr = dg + totalSum;
}
void MineralEQ3::convertDGFormation()
{
// Ok let's get the element compositions and conversion factors.
doublereal totalSum = 0.0;
for (size_t m = 0; m < nElements(); m++) {
double na = nAtoms(0, m);
if (na > 0.0) {
totalSum += na * LookupGe(elementName(m));
}
}
// Ok, now do the calculation. Convert to joules kmol-1
doublereal dg = m_deltaG_formation_pr_tr * toSI("cal/gmol");
//! Store the result into an internal variable.
m_Mu0_pr_tr = dg + totalSum;
double Hcalc = m_Mu0_pr_tr + 298.15 * m_Entrop_pr_tr * toSI("cal/gmol");
double DHjmol = m_deltaH_formation_pr_tr * toSI("kal/gmol");
// If the discrepancy is greater than 100 cal gmol-1, print an error
if (fabs(Hcalc -DHjmol) > 100 * toSI("cal/gmol")) {
throw CanteraError("installMinEQ3asShomateThermoFromXML()",
"DHjmol is not consistent with G and S: {} vs {}",
Hcalc, DHjmol);
}
}
void System::writeToXYZ(const std::string& filename)
{
std::ofstream ofile(filename);
// Header
ofile << nAtoms() << std::endl;
ofile << "Comment" << std::endl;
// Atoms
for (Atom *atom : m_atoms) {
ofile << atom->getIndex() << " ";
for (uint i = 0; i < 3; i++) {
ofile << atom->getPosition()[i] << " ";
}
for (uint i = 0; i < 3; i++) {
ofile << atom->getVelocity()[i] << " ";
}
for (uint i = 0; i < 3; i++) {
ofile << atom->getForce()[i] << " ";
}
ofile << atom->getVelocity().length() << " ";
ofile << atom->getForce().length() << " ";
ofile << std::endl;
}
}
doublereal Phase::elementalMoleFraction(const size_t m) const
{
checkElementIndex(m);
double denom = 0;
for (size_t k = 0; k < m_kk; k++) {
double atoms = 0;
for (size_t j = 0; j < nElements(); j++) {
atoms += nAtoms(k, j);
}
denom += atoms * moleFraction(k);
}
doublereal numerator = 0.0;
for (size_t k = 0; k != m_kk; ++k) {
numerator += nAtoms(k, m) * moleFraction(k);
}
return numerator / denom;
}
doublereal Phase::elementalMassFraction(const size_t m) const
{
checkElementIndex(m);
doublereal Z_m = 0.0;
for (size_t k = 0; k != m_kk; ++k) {
Z_m += nAtoms(k, m) * atomicWeight(m) / molecularWeight(k)
* massFraction(k);
}
return Z_m;
}
void IdealSolidSolnPhase::setToEquilState(const doublereal* lambda_RT)
{
const vector_fp& grt = gibbs_RT_ref();
// set the pressure and composition to be consistent with
// the temperature,
doublereal pres = 0.0;
for (size_t k = 0; k < m_kk; k++) {
m_pp[k] = -grt[k];
for (size_t m = 0; m < nElements(); m++) {
m_pp[k] += nAtoms(k,m)*lambda_RT[m];
}
m_pp[k] = m_Pref * exp(m_pp[k]);
pres += m_pp[k];
}
setState_PX(pres, &m_pp[0]);
}
void System::writeToXYZWithBoxID(const std::string& filename)
{
std::ofstream ofile(filename);
if (!ofile.is_open())
{
std::cout << "Error: Couldn't open file \"" << filename << "\" for writing." << std::endl;
}
else
{
// Header
ofile << nAtoms() << std::endl;
ofile << "Comment" << std::endl;
// Atoms
for (const NeighborList& list : m_integrator->getNeighborLists())
{
for (const Atom *atom : list.getAtoms())
{
ofile << atom->getIndex() << " ";
for (uint i = 0; i < 3; i++) {
ofile << atom->getPosition()[i] << " ";
}
for (uint i = 0; i < 3; i++) {
ofile << atom->getVelocity()[i] << " ";
}
for (uint i = 0; i < 3; i++) {
ofile << atom->getForce()[i] << " ";
}
ofile << atom->getVelocity().length() << " ";
ofile << atom->getForce().length() << " ";
ofile << list.getLinearIndex() << " ";
ofile << std::endl;
}
}
}
}
