selector.cpp
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Created: Fri, May 17, 21:23

selector.cpp
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	/*-------------------------------------------------------

	- Module : database
	- File : selector.cpp
	- Author : Fabien Georget

	Copyright (c) 2014, Fabien Georget <fabieng@princeton.edu>, Princeton University
	All rights reserved.

	Redistribution and use in source and binary forms, with or without
	modification, are permitted provided that the following conditions are met:
	* Redistributions of source code must retain the above copyright
	notice, this list of conditions and the following disclaimer.
	* Redistributions in binary form must reproduce the above copyright
	notice, this list of conditions and the following disclaimer in the
	documentation and/or other materials provided with the distribution.
	* Neither the name of the Princeton University nor the
	names of its contributors may be used to endorse or promote products
	derived from this software without specific prior written permission.

	THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
	ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
	WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
	DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
	ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
	(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
	LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
	ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
	(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
	SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

	---------------------------------------------------------*/

	#include "selector.hpp"

	#include <iostream>

	namespace specmicp {
	namespace database {


	void DatabaseSelector::remove_component(const std::vector<index_t>& id_component_to_remove)
	{
	analyse_component(id_component_to_remove);
	select_aqueous(id_component_to_remove);
	select_minerals(id_component_to_remove);
	select_minerals_kinetic(id_component_to_remove);
	if (data->nb_gas() != 0) select_gas(id_component_to_remove);
	select_sorbed(id_component_to_remove);
	select_components();
	}

	void DatabaseSelector::analyse_component(const std::vector<index_t>& id_component_to_remove)
	{
	for (auto it: id_component_to_remove)
	{
	m_is_component_to_remove[it] = true;
	}
	m_nb_component_to_keep = data->nb_component() - id_component_to_remove.size();
	}

	void DatabaseSelector::select_secondary(
	ReactiveSpeciesList* toselect,
	const std::vector<index_t>& id_component_to_remove
	)
	{
	// first we select which aqueous species we should remove
	std::vector<bool> to_remove(toselect->size(), false);
	for (index_t j: toselect->range())
	{
	for (const auto& it: id_component_to_remove)
	{
	if (toselect->nu_ji(j, it) != 0.0)
	{
	to_remove[j] = true;
	break;
	}
	}
	}
	// then we remove them, in two steps
	const auto nb_to_keep = std::count(to_remove.cbegin(), to_remove.cend(), false);
	auto new_j = 0;
	// 1) first we copy data in the beginning of the arrays
	for (index_t j: toselect->range())
	{
	if (to_remove[j]) continue;
	toselect->move_erase(j, new_j, m_is_component_to_remove);
	++new_j;
	}
	specmicp_assert(new_j == nb_to_keep);
	// 2) then we resize the arrays
	toselect->resize(nb_to_keep, nb_component_to_keep());
	toselect->set_valid();
	// By doing in this order, we avoid bulk copy of arrays
	}

	void DatabaseSelector::select_aqueous(const std::vector<index_t>& id_component_to_remove)
	{
	select_secondary(&(data->aqueous), id_component_to_remove);
	}

	void DatabaseSelector::select_minerals(const std::vector<index_t>& id_component_to_remove)
	{
	select_secondary(&(data->minerals), id_component_to_remove);
	}

	void DatabaseSelector::select_minerals_kinetic(const std::vector<index_t>& id_component_to_remove)
	{
	select_secondary(&(data->minerals_kinetic), id_component_to_remove);
	}


	void DatabaseSelector::select_gas(const std::vector<index_t>& id_component_to_remove)
	{
	select_secondary(&(data->gas), id_component_to_remove);
	}

	void DatabaseSelector::select_sorbed(const std::vector<index_t>& id_component_to_remove)
	{
	select_secondary(&(data->sorbed), id_component_to_remove);
	}

	void DatabaseSelector::select_components()
	{
	uindex_t new_i = 0;
	for (index_t i: data->range_component())
	{
	if (is_component_to_remove(i)) continue;
	data->components.move_erase(i, new_i);
	++new_i;
	}
	specmicp_assert(new_i == nb_component_to_keep());
	data->components.resize(nb_component_to_keep());
	data->components.set_valid();
	}

	void DatabaseSelector::keep_only_component(const std::vector<index_t>& id_to_keep)
	{
	// First build the list of components to remove
	std::vector<index_t> id_to_remove;
	id_to_remove.reserve(data->nb_component() - id_to_keep.size());
	for (index_t id: data->range_component())
	{
	auto search = std::find(id_to_keep.begin(), id_to_keep.end(), id);
	if (search == id_to_keep.end())
	id_to_remove.push_back(id);
	}
	// Then remove them
	remove_component(id_to_remove);
	}

	void DatabaseSelector::remove_all_gas()
	{
	data->gas = GasList(0, data->nb_component());
	}

	void DatabaseSelector::remove_all_sorbed()
	{
	data->sorbed = SorbedList(0, data->nb_component());
	}

	//! \brief Remove some specific aqueous species
	void DatabaseSelector::remove_aqueous(const std::vector<index_t>& id_aqueous)
	{
	const index_t new_nb_aqueous = data->nb_aqueous() - id_aqueous.size();

	index_t new_id = 0;
	for (index_t aqueous: data->range_aqueous())
	{
	auto it = std::find(id_aqueous.cbegin(), id_aqueous.cend(), aqueous);
	if (it == id_aqueous.end()) // if we need to keep the species
	{
	if (*it == aqueous)
	{
	++new_id;
	continue; // nothing to change
	}
	data->aqueous.move_erase(aqueous, new_id);
	++new_id;
	}
	}
	specmicp_assert(new_id == new_nb_aqueous);
	data->aqueous.resize(new_nb_aqueous);

	}

	// -------------------
	//
	// Oxydo-reduction
	//
	// -------------------

	//void DatabaseSelector::remove_half_cells_reactions()
	//{
	// remove_half_cells_aqueous();
	// remove_half_cells_sorbed();
	// remove_half_cells_mineral();
	// remove_half_cells_mineral_kinetic();
	//}

	void DatabaseSelector::remove_half_cells_aqueous()
	{
	index_t new_id {0};

	// reorganize the data
	for (index_t aqueous: data->range_aqueous())
	{
	// if (not data->is_half_cell_reaction(aqueous))
	// {
	// data->aqueous.move_erase(aqueous, new_id);
	// ++new_id;
	// }
	}
	data->aqueous.resize(new_id);
	}

	void DatabaseSelector::remove_half_cells_sorbed()
	{
	// index_t new_id {0};
	// // reorganizing
	// for (index_t sorbed: data->range_sorbed())
	// {
	// if (data->is_sorbed_half_cell_reaction(sorbed))
	// {
	// data->nu_sorbed.row(new_id) = data->nu_sorbed.row(sorbed);
	// data->logk_sorbed(new_id) = data->logk_sorbed(sorbed);
	// data->labels_sorbed[new_id] = data->labels_sorbed[sorbed];

	// ++new_id;
	// }
	// }

	// data->nb_sorbed = new_id;
	// // resizing
	// data->labels_sorbed.resize(new_id);
	// data->nu_sorbed.conservativeResize(new_id, Eigen::NoChange);
	// data->logk_sorbed.conservativeResize(new_id);
	}

	void DatabaseSelector::remove_half_cells_gas()
	{
	// index_t new_id {0};
	// // reorganizing
	// for (index_t gas: data->range_gas())
	// {
	// if (data->is_gas_half_cell_reaction(gas))
	// {
	// data->nu_gas.row(new_id) = data->nu_gas.row(gas);
	// data->logk_gas(new_id) = data->logk_gas(gas);
	// data->labels_gas[new_id] = data->labels_gas[gas];

	// ++new_id;
	// }
	// }

	// data->nb_gas = new_id;
	// // resizing
	// data->labels_gas.resize(new_id);
	// data->nu_gas.conservativeResize(new_id, Eigen::NoChange);
	// data->logk_gas.conservativeResize(new_id);
	}

	//void DatabaseSelector::remove_half_cells_mineral()
	//{
	// index_t new_id {0};
	// // reorganizing
	// for (index_t mineral: data->range_mineral())
	// {
	// if (data->is_mineral_half_cell_reaction(mineral))
	// {
	// data->nu_mineral.row(new_id) = data->nu_mineral.row(mineral);
	// data->logk_mineral(new_id) = data->logk_mineral(mineral);
	// data->labels_minerals[new_id] = data->labels_minerals[mineral];
	// data->_molar_volume_mineral(new_id) = data->_molar_volume_mineral(mineral);

	// ++new_id;
	// }
	// }

	// data->nb_mineral = new_id;
	// //resizing
	// data->labels_minerals.resize(new_id);
	// data->nu_mineral.conservativeResize(new_id, Eigen::NoChange);
	// data->logk_mineral.conservativeResize(new_id);
	// data->_molar_volume_mineral.conservativeResize(new_id);
	//}

	//void DatabaseSelector::remove_half_cells_mineral_kinetic()
	//{
	// index_t new_id {0};
	// // reorganizing
	// for (index_t mineral: data->range_mineral_kinetic())
	// {
	// if (data->is_mineral_kinetic_half_cell_reaction(mineral))
	// {
	// data->nu_mineral_kinetic.row(new_id) = data->nu_mineral_kinetic.row(mineral);
	// data->logk_mineral_kinetic(new_id) = data->logk_mineral_kinetic(mineral);
	// data->labels_minerals_kinetic[new_id] = data->labels_minerals_kinetic[mineral];
	// data->_molar_volume_mineral_kinetic(new_id) = data->_molar_volume_mineral_kinetic(mineral);

	// ++new_id;
	// }
	// }

	// data->nb_mineral_kinetic = new_id;
	// //resizing
	// data->labels_minerals_kinetic.resize(new_id);
	// data->nu_mineral_kinetic.conservativeResize(new_id, Eigen::NoChange);
	// data->logk_mineral_kinetic.conservativeResize(new_id);
	// data->_molar_volume_mineral_kinetic.conservativeResize(new_id);
	//}
	} // end namespace database
	} // end namespace specmicp

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