variables.cpp
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	#include "variables.hpp"

	#include "dfpm/meshes/mesh1d.hpp"

	namespace specmicp {
	namespace reactmicp {
	namespace systems {
	namespace satdiff {

	SaturatedVariables::SaturatedVariables(mesh::Mesh1DPtr the_mesh,
	RawDatabasePtr the_database):
	m_mesh(the_mesh),
	m_database(the_database)
	{}

	Vector SaturatedVariables::total_concentrations(index_t node) {

	Vector total_conc = porosity(node)*displacement().segment(offset_aqueous_concentration(node), nb_component())
	+ displacement().segment(offset_solid_concentration(node), nb_component());
	for (index_t r=0; r<total_conc.rows(); ++r)
	{
	if (std::abs(total_conc(r)) < 1e-10)
	total_conc(r) = 0.0;
	}
	return total_conc;
	}


	} // end namespace satdiff
	} // end namespace systems
	} // end namespace reactmicp
	} // end namespace specmicp