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canonicalizer.cpp
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Sat, Nov 16, 04:11

canonicalizer.cpp
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/*-------------------------------------------------------
- Module : database
- File : canonicalizer.cpp
- Author : Fabien Georget
Copyright (c) 2014, Fabien Georget, Princeton University
---------------------------------------------------------*/
#include "canonicalizer.hpp"
#include "utils/log.hpp"
namespace specmicp {
namespace database {
void DatabaseCanonicalizer::make_canonical() {
if (data->is_canonical == true)
{
WARNING << "Database already in canonical form, aborting";
return;
}
make_aqueous_canonical();
make_mineral_canonical();
make_mineral_kinetic_canonical();
if (data->nb_gas != 0) make_gas_canonical();
data->is_canonical = true;
}
void DatabaseCanonicalizer::make_aqueous_canonical()
{
if (data->nu_aqueous.cols() == data->nb_component)
{
INFO << "Database already in canonical form";
return;
}
if (data->nu_aqueous.cols() != data->nb_component + data->nb_aqueous)
{
CRITICAL << "Canonicalization : invalid size for stoichiometric coefficients of aqueous species - abort";
throw invalid_database("Invalid size for stoichiometric coefficients of aqueous species");
}
for (int i=1; i<data->nb_aqueous; ++i)
{
for (int j=0; j<i; ++j)
{
const double stoech = data->nu_aqueous(i, data->nb_component+j);
if (stoech != 0)
{
data->nu_aqueous.row(i) += stoech*data->nu_aqueous.row(j);
data->logk_aqueous(i) += stoech*data->logk_aqueous(j);
data->nu_aqueous(i, data->nb_component+j) = 0;
}
}
}
data->nu_aqueous.conservativeResize(Eigen::NoChange_t(), data->nb_component);
}
void DatabaseCanonicalizer::make_mineral_canonical()
{
if (data->nu_mineral.cols() == data->nb_component)
{
INFO << "Database already in canonical form";
return;
}
if (data->nu_mineral.cols() != data->nb_component + data->nb_aqueous)
{
CRITICAL << "Canonicalization : invalid size for stoichiometric coefficients of mineral species - abort";
throw invalid_database("Invalid size for stoichiometric coefficients of mineral species");
}
for (int i=1; i<data->nb_mineral; ++i)
{
for (int j=0; j<data->nb_aqueous; ++j)
{
const double stoech = data->nu_mineral(i, data->nb_component+j);
if (stoech != 0)
{
data->nu_mineral.block(i, 0, 1, data->nb_component) +=
stoech*data->nu_aqueous.row(j);
data->logk_mineral(i) += stoech*data->logk_aqueous(j);
data->nu_mineral(i, data->nb_component+j) = 0;
}
}
}
data->nu_mineral.conservativeResize(Eigen::NoChange_t(), data->nb_component);
}
void DatabaseCanonicalizer::make_mineral_kinetic_canonical()
{
if (data->nu_mineral_kinetic.cols() == data->nb_component)
{
INFO << "Database already in canonical form";
return;
}
if (data->nu_mineral_kinetic.cols() != data->nb_component + data->nb_aqueous)
{
CRITICAL << "Canonicalization : invalid size for stoichiometric coefficients of mineral species - abort";
throw invalid_database("Invalid size for stoichiometric coefficients of mineral species");
}
for (int i=1; i<data->nb_mineral_kinetic; ++i)
{
for (int j=0; j<data->nb_aqueous; ++j)
{
const double stoech = data->nu_mineral_kinetic(i, data->nb_component+j);
if (stoech != 0)
{
data->nu_mineral_kinetic.block(i, 0, 1, data->nb_component) +=
stoech*data->nu_aqueous.row(j);
data->logk_mineral_kinetic(i) += stoech*data->logk_aqueous(j);
data->nu_mineral_kinetic(i, data->nb_component+j) = 0;
}
}
}
data->nu_mineral_kinetic.conservativeResize(Eigen::NoChange_t(), data->nb_component);
}
void DatabaseCanonicalizer::make_gas_canonical()
{
if (data->nu_gas.cols() == data->nb_component)
{
INFO << "Database already in canonical form";
return;
}
if (data->nu_gas.cols() != data->nb_component + data->nb_aqueous)
{
CRITICAL << "Canonicalization : invalid size for stoichiometric coefficients of gas species - abort";
throw invalid_database("Invalid size for stoichiometric coefficients of gas species");
}
for (int i=1; i<data->nb_gas; ++i)
{
for (int j=0; j<i; ++j)
{
const double stoech = data->nu_gas(i, data->nb_component+j);
if (stoech != 0)
{
data->nu_gas.row(i) += stoech*data->nu_gas.row(j);
data->logk_gas(i) += stoech*data->logk_gas(j);
data->nu_gas(i, data->nb_component+j) = 0;
}
}
}
data->nu_gas.conservativeResize(Eigen::NoChange_t(), data->nb_component);
}
} // end namespace database
} // end namespace specmicp

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