structfact.cpp

/**
 * structure factor tool
 * @author Tobias Weber <tweber@ill.fr>
 * @date Dec-2018
 * @license GPLv3, see 'LICENSE' file
 * @desc The present version was forked on 28-Dec-2018 from my privately developed "misc" project (https://github.com/t-weber/misc).
 *
 * ----------------------------------------------------------------------------
 * mag-core (part of the Takin software suite)
 * Copyright (C) 2018-2021  Tobias WEBER (Institut Laue-Langevin (ILL),
 *                          Grenoble, France).
 * "misc" project
 * Copyright (C) 2017-2021  Tobias WEBER (privately developed).
 *
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, version 3 of the License.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 * ----------------------------------------------------------------------------
 */

#include "structfact.h"

#include <QtCore/QDir>
#include <QtWidgets/QApplication>
#include <QtWidgets/QGridLayout>
#include <QtWidgets/QHeaderView>
#include <QtWidgets/QTabWidget>
#include <QtWidgets/QLabel>
#include <QtWidgets/QToolButton>
#include <QtWidgets/QFileDialog>
#include <QtWidgets/QMessageBox>

#include <iostream>
#include <fstream>
#include <random>
#include <chrono>
#include <tuple>

#include <boost/version.hpp>
#include <boost/config.hpp>
#include <boost/property_tree/ptree.hpp>
#include <boost/property_tree/xml_parser.hpp>
#include <boost/algorithm/string.hpp>
#include <boost/algorithm/string/replace.hpp>
namespace algo = boost::algorithm;
namespace pt = boost::property_tree;

#include "loadcif.h"
#include "tlibs2/libs/algos.h"
#include "tlibs2/libs/helper.h"


using namespace tl2_ops;


constexpr t_real g_eps = 1e-6;
constexpr int g_prec = 6;

std::vector<std::string> StructFactDlg::g_default_colours
{{
	"#ff0000", "#0000ff", "#00ff00", "#000000",
}};


enum : int
{
	COL_NAME = 0,
	COL_SCATLEN_RE,
	COL_SCATLEN_IM,
	COL_X, COL_Y, COL_Z,
	COL_RAD,
	COL_COL,

	NUM_COLS
};


struct PowderLine
{
	t_real Q{};
	t_real I{};
	std::size_t num_peaks = 0;
	std::string peaks;
};


// ----------------------------------------------------------------------------
StructFactDlg::StructFactDlg(QWidget* pParent) : QDialog{pParent},
	m_sett{new QSettings{"takin", "structfact"}}
{
	setWindowTitle("Nuclear Structure Factors");
	setSizeGripEnabled(true);
	setFont(QFontDatabase::systemFont(QFontDatabase::GeneralFont));


	auto tabs = new QTabWidget(this);


	{ // nuclei panel
		QWidget *nucleipanel = new QWidget(this);

		m_nuclei = new QTableWidget(nucleipanel);
		m_nuclei->setShowGrid(true);
		m_nuclei->setSortingEnabled(true);
		m_nuclei->setMouseTracking(true);
		m_nuclei->setSelectionBehavior(QTableWidget::SelectRows);
		m_nuclei->setSelectionMode(QTableWidget::ContiguousSelection);
		m_nuclei->setContextMenuPolicy(Qt::CustomContextMenu);

		m_nuclei->verticalHeader()->setDefaultSectionSize(fontMetrics().lineSpacing() + 4);
		m_nuclei->verticalHeader()->setVisible(false);

		m_nuclei->setColumnCount(NUM_COLS);
		m_nuclei->setHorizontalHeaderItem(COL_NAME, new QTableWidgetItem{"Name"});
		m_nuclei->setHorizontalHeaderItem(COL_SCATLEN_RE, new QTableWidgetItem{"Re{b} (fm)"});
		m_nuclei->setHorizontalHeaderItem(COL_SCATLEN_IM, new QTableWidgetItem{"Im{b} (fm)"});
		m_nuclei->setHorizontalHeaderItem(COL_X, new QTableWidgetItem{"x (frac.)"});
		m_nuclei->setHorizontalHeaderItem(COL_Y, new QTableWidgetItem{"y (frac.)"});
		m_nuclei->setHorizontalHeaderItem(COL_Z, new QTableWidgetItem{"z (frac.)"});
		m_nuclei->setHorizontalHeaderItem(COL_RAD, new QTableWidgetItem{"Radius"});
		m_nuclei->setHorizontalHeaderItem(COL_COL, new QTableWidgetItem{"Colour"});

		m_nuclei->setColumnWidth(COL_NAME, 90);
		m_nuclei->setColumnWidth(COL_SCATLEN_RE, 75);
		m_nuclei->setColumnWidth(COL_SCATLEN_IM, 75);
		m_nuclei->setColumnWidth(COL_X, 75);
		m_nuclei->setColumnWidth(COL_Y, 75);
		m_nuclei->setColumnWidth(COL_Z, 75);
		m_nuclei->setColumnWidth(COL_RAD, 75);
		m_nuclei->setColumnWidth(COL_COL, 75);

		QToolButton *pTabBtnAdd = new QToolButton(nucleipanel);
		QToolButton *pTabBtnDel = new QToolButton(nucleipanel);
		QToolButton *pTabBtnUp = new QToolButton(nucleipanel);
		QToolButton *pTabBtnDown = new QToolButton(nucleipanel);
		QToolButton *pTabBtnSG = new QToolButton(nucleipanel);

		m_nuclei->setSizePolicy(QSizePolicy{QSizePolicy::Expanding, QSizePolicy::Expanding});
		pTabBtnAdd->setSizePolicy(QSizePolicy{QSizePolicy::Expanding, QSizePolicy::Fixed});
		pTabBtnDel->setSizePolicy(QSizePolicy{QSizePolicy::Expanding, QSizePolicy::Fixed});
		pTabBtnUp->setSizePolicy(QSizePolicy{QSizePolicy::Expanding, QSizePolicy::Fixed});
		pTabBtnDown->setSizePolicy(QSizePolicy{QSizePolicy::Expanding, QSizePolicy::Fixed});
		pTabBtnSG->setSizePolicy(QSizePolicy{QSizePolicy::Expanding, QSizePolicy::Fixed});

		pTabBtnAdd->setText("Add Nucleus");
		pTabBtnDel->setText("Delete Nuclei");
		pTabBtnUp->setText("Move Nuclei Up");
		pTabBtnDown->setText("Move Nuclei Down");
		pTabBtnSG->setText("Generate");

		m_editA = new QLineEdit("5", nucleipanel);
		m_editB = new QLineEdit("5", nucleipanel);
		m_editC = new QLineEdit("5", nucleipanel);
		m_editAlpha = new QLineEdit("90", nucleipanel);
		m_editBeta = new QLineEdit("90", nucleipanel);
		m_editGamma = new QLineEdit("90", nucleipanel);

		m_comboSG = new QComboBox(nucleipanel);


		// get space groups and symops
		for(auto [sgnum, descr, ops] : get_sgs<t_mat>())
		{
			m_comboSG->addItem(descr.c_str(), m_comboSG->count());
			m_SGops.emplace_back(std::move(ops));
		}


		auto pTabGrid = new QGridLayout(nucleipanel);
		pTabGrid->setSpacing(2);
		pTabGrid->setContentsMargins(4,4,4,4);
		int y=0;
		//pTabGrid->addWidget(m_plot.get(), y,0,1,4);
		pTabGrid->addWidget(m_nuclei, y,0,1,4);
		pTabGrid->addWidget(pTabBtnAdd, ++y,0,1,1);
		pTabGrid->addWidget(pTabBtnDel, y,1,1,1);
		pTabGrid->addWidget(pTabBtnUp, y,2,1,1);
		pTabGrid->addWidget(pTabBtnDown, y,3,1,1);

		pTabGrid->addWidget(new QLabel("Space Groups:"), ++y,0,1,1);
		pTabGrid->addWidget(m_comboSG, y,1,1,2);
		pTabGrid->addWidget(pTabBtnSG, y,3,1,1);


		auto sep1 = new QFrame(nucleipanel); sep1->setFrameStyle(QFrame::HLine);
		pTabGrid->addWidget(sep1, ++y,0, 1,4);

		pTabGrid->addWidget(new QLabel("Lattice (A):"), ++y,0,1,1);
		pTabGrid->addWidget(m_editA, y,1,1,1);
		pTabGrid->addWidget(m_editB, y,2,1,1);
		pTabGrid->addWidget(m_editC, y,3,1,1);
		pTabGrid->addWidget(new QLabel("Angles (deg):"), ++y,0,1,1);
		pTabGrid->addWidget(m_editAlpha, y,1,1,1);
		pTabGrid->addWidget(m_editBeta, y,2,1,1);
		pTabGrid->addWidget(m_editGamma, y,3,1,1);


		// table CustomContextMenu
		m_pTabContextMenu = new QMenu(m_nuclei);
		m_pTabContextMenu->addAction("Add Nucleus Before", this, [this]() { this->AddTabItem(-2); });
		m_pTabContextMenu->addAction("Add Nucleus After", this, [this]() { this->AddTabItem(-3); });
		m_pTabContextMenu->addAction("Clone Nucleus", this, [this]() { this->AddTabItem(-4); });
		m_pTabContextMenu->addAction("Delete Nucleus", this, [this]() { StructFactDlg::DelTabItem(); });


		// table CustomContextMenu in case nothing is selected
		m_pTabContextMenuNoItem = new QMenu(m_nuclei);
		m_pTabContextMenuNoItem->addAction("Add Nucleus", this, [this]() { this->AddTabItem(); });
		m_pTabContextMenuNoItem->addAction("Delete Nucleus", this, [this]() { StructFactDlg::DelTabItem(); });
		//m_pTabContextMenuNoItem->addSeparator();


		// signals
		for(auto* edit : std::vector<QLineEdit*>{{ m_editA, m_editB, m_editC, m_editAlpha, m_editBeta, m_editGamma }})
			connect(edit, &QLineEdit::textEdited, this, [this]() { this->CalcB(); });

		connect(pTabBtnAdd, &QToolButton::clicked, this, [this]() { this->AddTabItem(-1); });
		connect(pTabBtnDel, &QToolButton::clicked, this, [this]() { StructFactDlg::DelTabItem(); });
		connect(pTabBtnUp, &QToolButton::clicked, this, &StructFactDlg::MoveTabItemUp);
		connect(pTabBtnDown, &QToolButton::clicked, this, &StructFactDlg::MoveTabItemDown);
		connect(pTabBtnSG, &QToolButton::clicked, this, &StructFactDlg::GenerateFromSG);

		connect(m_nuclei, &QTableWidget::currentCellChanged, this, &StructFactDlg::TableCurCellChanged);
		connect(m_nuclei, &QTableWidget::entered, this, &StructFactDlg::TableCellEntered);
		connect(m_nuclei, &QTableWidget::itemChanged, this, &StructFactDlg::TableItemChanged);
		connect(m_nuclei, &QTableWidget::customContextMenuRequested, this, &StructFactDlg::ShowTableContextMenu);

		tabs->addTab(nucleipanel, "Nuclei");
	}


	{	// structure factors panel
		auto sfactpanel = new QWidget(this);
		auto pGrid = new QGridLayout(sfactpanel);
		pGrid->setSpacing(4);
		pGrid->setContentsMargins(4,4,4,4);

		m_structfacts = new QPlainTextEdit(sfactpanel);
		m_structfacts->setReadOnly(true);
		m_structfacts->setFont(QFontDatabase::systemFont(QFontDatabase::FixedFont));

		m_maxBZ = new QSpinBox(sfactpanel);
		m_maxBZ->setMinimum(0);
		m_maxBZ->setMaximum(99);
		m_maxBZ->setValue(4);

		m_RemoveZeroes = new QCheckBox("Remove Zeroes", sfactpanel);
		m_RemoveZeroes->setChecked(true);


		pGrid->addWidget(m_structfacts, 0,0, 1,4);
		pGrid->addWidget(new QLabel("Max. Order:"), 1,0,1,1);
		pGrid->addWidget(m_maxBZ, 1,1, 1,1);
		pGrid->addWidget(m_RemoveZeroes, 1,2, 1,2);


		// signals
		connect(m_maxBZ, static_cast<void (QSpinBox::*)(int)>(&QSpinBox::valueChanged), this, [this]() { this->Calc(); });
		connect(m_RemoveZeroes, static_cast<void (QCheckBox::*)(int)>(&QCheckBox::stateChanged), this, [this]() { this->Calc(); });

		tabs->addTab(sfactpanel, "Structure Factors");
	}


	{	// powder lines panel
		auto powderpanel = new QWidget(this);
		auto pGrid = new QGridLayout(powderpanel);
		pGrid->setSpacing(4);
		pGrid->setContentsMargins(4,4,4,4);

		m_powderlines = new QPlainTextEdit(powderpanel);
		m_powderlines->setReadOnly(true);
		m_powderlines->setFont(QFontDatabase::systemFont(QFontDatabase::FixedFont));
		m_powderlines->setLineWrapMode(QPlainTextEdit::NoWrap);

		pGrid->addWidget(m_powderlines, 0,0, 1,4);

		tabs->addTab(powderpanel, "Powder Lines");
	}


	{ // find space group panel
		auto findsgpanel = new QWidget(this);

		m_nuclei_FindSG = new QTableWidget(findsgpanel);
		m_nuclei_FindSG->setShowGrid(true);
		m_nuclei_FindSG->setSortingEnabled(true);
		m_nuclei_FindSG->setMouseTracking(true);
		m_nuclei_FindSG->setSelectionBehavior(QTableWidget::SelectRows);
		m_nuclei_FindSG->setSelectionMode(QTableWidget::ContiguousSelection);
		m_nuclei_FindSG->setContextMenuPolicy(Qt::CustomContextMenu);

		m_nuclei_FindSG->verticalHeader()->setDefaultSectionSize(fontMetrics().lineSpacing() + 4);
		m_nuclei_FindSG->verticalHeader()->setVisible(false);

		m_nuclei_FindSG->setColumnCount(3);
		m_nuclei_FindSG->setHorizontalHeaderItem(0, new QTableWidgetItem{"x (frac.)"});
		m_nuclei_FindSG->setHorizontalHeaderItem(1, new QTableWidgetItem{"y (frac.)"});
		m_nuclei_FindSG->setHorizontalHeaderItem(2, new QTableWidgetItem{"z (frac.)"});

		m_nuclei_FindSG->setColumnWidth(0, 200);
		m_nuclei_FindSG->setColumnWidth(1, 200);
		m_nuclei_FindSG->setColumnWidth(2, 200);

		m_sgmatches = new QPlainTextEdit(findsgpanel);
		m_sgmatches->setReadOnly(true);
		m_sgmatches->setFont(QFontDatabase::systemFont(QFontDatabase::FixedFont));


		QToolButton *pTabBtnAdd = new QToolButton(findsgpanel);
		QToolButton *pTabBtnDel = new QToolButton(findsgpanel);
		QToolButton *pTabBtnUp = new QToolButton(findsgpanel);
		QToolButton *pTabBtnDown = new QToolButton(findsgpanel);
		QToolButton *pBtnCalc = new QToolButton(findsgpanel);

		m_nuclei_FindSG->setSizePolicy(QSizePolicy{QSizePolicy::Expanding, QSizePolicy::Expanding});
		pTabBtnAdd->setSizePolicy(QSizePolicy{QSizePolicy::Expanding, QSizePolicy::Fixed});
		pTabBtnDel->setSizePolicy(QSizePolicy{QSizePolicy::Expanding, QSizePolicy::Fixed});
		pTabBtnUp->setSizePolicy(QSizePolicy{QSizePolicy::Expanding, QSizePolicy::Fixed});
		pTabBtnDown->setSizePolicy(QSizePolicy{QSizePolicy::Expanding, QSizePolicy::Fixed});
		pBtnCalc->setSizePolicy(QSizePolicy{QSizePolicy::Expanding, QSizePolicy::Fixed});

		pTabBtnAdd->setText("Add Nucleus");
		pTabBtnDel->setText("Delete Nuclei");
		pTabBtnUp->setText("Move Nuclei Up");
		pTabBtnDown->setText("Move Nuclei Down");
		pBtnCalc->setText("Find Matching Space Groups");


		auto pTabGrid = new QGridLayout(findsgpanel);
		pTabGrid->setSpacing(2);
		pTabGrid->setContentsMargins(4,4,4,4);
		int y=0;
		pTabGrid->addWidget(m_nuclei_FindSG, y,0,1,4);
		pTabGrid->addWidget(m_sgmatches, ++y,0,1,4);
		pTabGrid->addWidget(pTabBtnAdd, ++y,0,1,1);
		pTabGrid->addWidget(pTabBtnDel, y,1,1,1);
		pTabGrid->addWidget(pTabBtnUp, y,2,1,1);
		pTabGrid->addWidget(pTabBtnDown, y,3,1,1);
		pTabGrid->addWidget(pBtnCalc, ++y,2,1,2);


		// table CustomContextMenu
		m_pTabContextMenu_FindSG = new QMenu(m_nuclei_FindSG);
		m_pTabContextMenu_FindSG->addAction("Add Nucleus Before", this, [this]() { this->AddTabItem_FindSG(-2); });
		m_pTabContextMenu_FindSG->addAction("Add Nucleus After", this, [this]() { this->AddTabItem_FindSG(-3); });
		m_pTabContextMenu_FindSG->addAction("Clone Nucleus", this, [this]() { this->AddTabItem_FindSG(-4); });
		m_pTabContextMenu_FindSG->addAction("Delete Nucleus", this, [this]() { StructFactDlg::DelTabItem_FindSG(); });


		// table CustomContextMenu in case nothing is selected
		m_pTabContextMenuNoItem_FindSG = new QMenu(m_nuclei_FindSG);
		m_pTabContextMenuNoItem_FindSG->addAction("Add Nucleus", this, [this]() { this->AddTabItem_FindSG(); });
		m_pTabContextMenuNoItem_FindSG->addAction("Delete Nucleus", this, [this]() { StructFactDlg::DelTabItem_FindSG(); });


		// signals
		connect(pTabBtnAdd, &QToolButton::clicked, this, [this]() { this->AddTabItem_FindSG(-1); });
		connect(pTabBtnDel, &QToolButton::clicked, this, [this]() { StructFactDlg::DelTabItem_FindSG(); });
		connect(pTabBtnUp, &QToolButton::clicked, this, &StructFactDlg::MoveTabItemUp_FindSG);
		connect(pTabBtnDown, &QToolButton::clicked, this, &StructFactDlg::MoveTabItemDown_FindSG);
		connect(pBtnCalc, &QToolButton::clicked, this, &StructFactDlg::FindSG);

		connect(m_nuclei_FindSG, &QTableWidget::itemChanged, this, &StructFactDlg::TableItemChanged_FindSG);
		connect(m_nuclei_FindSG, &QTableWidget::customContextMenuRequested, this, &StructFactDlg::ShowTableContextMenu_FindSG);

		tabs->addTab(findsgpanel, "Match Space Group");
	}


	{	// info panel
		auto infopanel = new QWidget(this);
		auto pGrid = new QGridLayout(infopanel);
		pGrid->setSpacing(4);
		pGrid->setContentsMargins(4,4,4,4);

		// table grid
		for(int i=0; i<4; ++i)
		{
			m_labelGlInfos[i] = new QLabel("", infopanel);
			m_labelGlInfos[i]->setSizePolicy(QSizePolicy::Ignored, m_labelGlInfos[i]->sizePolicy().verticalPolicy());
		}

		auto sep1 = new QFrame(infopanel); sep1->setFrameStyle(QFrame::HLine);
		auto sep2 = new QFrame(infopanel); sep2->setFrameStyle(QFrame::HLine);
		auto sep3 = new QFrame(infopanel); sep3->setFrameStyle(QFrame::HLine);

		std::string strBoost = BOOST_LIB_VERSION;
		algo::replace_all(strBoost, "_", ".");

		auto labelTitle = new QLabel("Nuclear Structure Factor Calculator", infopanel);
		auto fontTitle = labelTitle->font();
		fontTitle.setBold(true);
		labelTitle->setFont(fontTitle);
		labelTitle->setAlignment(Qt::AlignHCenter);

		auto labelAuthor = new QLabel("Written by Tobias Weber <tweber@ill.fr>.", infopanel);
		labelAuthor->setAlignment(Qt::AlignHCenter);

		auto labelDate = new QLabel("December 2018.", infopanel);
		labelDate->setAlignment(Qt::AlignHCenter);

		int y = 0;
		pGrid->addWidget(labelTitle, y++,0, 1,1);
		pGrid->addWidget(labelAuthor, y++,0, 1,1);
		pGrid->addWidget(labelDate, y++,0, 1,1);
		pGrid->addItem(new QSpacerItem(16,16, QSizePolicy::Minimum, QSizePolicy::Fixed), y++,0, 1,1);
		pGrid->addWidget(sep1, y++,0, 1,1);
		pGrid->addWidget(new QLabel(QString("Compiler: ") + QString(BOOST_COMPILER) + ".", infopanel), y++,0, 1,1);
		pGrid->addWidget(new QLabel(QString("C++ Library: ") + QString(BOOST_STDLIB) + ".", infopanel), y++,0, 1,1);
		pGrid->addWidget(new QLabel(QString("Build Date: ") + QString(__DATE__) + ", " + QString(__TIME__) + ".", infopanel), y++,0, 1,1);
		pGrid->addWidget(sep2, y++,0, 1,1);
		pGrid->addWidget(new QLabel(QString("Qt Version: ") + QString(QT_VERSION_STR) + ".", infopanel), y++,0, 1,1);
		pGrid->addWidget(new QLabel(QString("Boost Version: ") + strBoost.c_str() + ".", infopanel), y++,0, 1,1);
		pGrid->addWidget(sep3, y++,0, 1,1);
		for(int i=0; i<4; ++i)
			pGrid->addWidget(m_labelGlInfos[i], y++,0, 1,1);
		pGrid->addItem(new QSpacerItem(16,16, QSizePolicy::Minimum, QSizePolicy::Expanding), y++,0, 1,1);

		tabs->addTab(infopanel, "Infos");
	}


	// main grid
	auto pmainGrid = new QGridLayout(this);
	pmainGrid->setSpacing(4);
	pmainGrid->setContentsMargins(4,4,4,4);
	pmainGrid->addWidget(tabs, 0,0, 1,1);


	// menu bar
	{
		m_menu = new QMenuBar(this);
		m_menu->setNativeMenuBar(m_sett ? m_sett->value("native_gui", false).toBool() : false);

		auto menuFile = new QMenu("File", m_menu);
		auto menuView = new QMenu("View", m_menu);

		auto acNew = new QAction("New", menuFile);
		auto acLoad = new QAction("Load...", menuFile);
		auto acSave = new QAction("Save...", menuFile);
		auto acImportCIF = new QAction("Import CIF...", menuFile);
		auto acImportTAZ = new QAction("Import TAZ...", menuFile);
		auto acExportTAZ = new QAction("Export TAZ...", menuFile);
		auto acExit = new QAction("Quit", menuFile);
		auto ac3DView = new QAction("3D View...", menuFile);

		menuFile->addAction(acNew);
		menuFile->addSeparator();
		menuFile->addAction(acLoad);
		menuFile->addAction(acSave);
		menuFile->addSeparator();
		menuFile->addAction(acImportCIF);
		menuFile->addSeparator();
		menuFile->addAction(acImportTAZ);
		menuFile->addAction(acExportTAZ);
		menuFile->addSeparator();
		menuFile->addAction(acExit);
		menuView->addAction(ac3DView);

		connect(acNew, &QAction::triggered, this,  [this]()
		{
			// clear old table
			DelTabItem(-1);

			// set some defaults
			m_comboSG->setCurrentIndex(0);
			m_editA->setText("5");
			m_editB->setText("5");
			m_editC->setText("5");
			m_editAlpha->setText("90");
			m_editBeta->setText("90");
			m_editGamma->setText("90");
		});
		connect(acLoad, &QAction::triggered, this, &StructFactDlg::Load);
		connect(acSave, &QAction::triggered, this, &StructFactDlg::Save);
		connect(acImportCIF, &QAction::triggered, this, &StructFactDlg::ImportCIF);
		connect(acImportTAZ, &QAction::triggered, this, &StructFactDlg::ImportTAZ);
		connect(acExportTAZ, &QAction::triggered, this, &StructFactDlg::ExportTAZ);
		connect(acExit, &QAction::triggered, this, &QDialog::close);
		connect(ac3DView, &QAction::triggered, this, [this]()
		{
			// plot widget
			if(!m_dlgPlot)
			{
				m_dlgPlot = new QDialog(this);
				m_dlgPlot->setWindowTitle("Unit Cell - 3D View");

				m_plot = std::make_shared<tl2::GlPlot>(this);
				m_plot->GetRenderer()->SetLight(0, tl2::create<t_vec3_gl>({ 5, 5, 5 }));
				m_plot->GetRenderer()->SetLight(1, tl2::create<t_vec3_gl>({ -5, -5, -5 }));
				m_plot->GetRenderer()->SetCoordMax(1.);
				m_plot->GetRenderer()->SetCamBase(tl2::create<t_mat_gl>({1,0,0,0,  0,0,1,0,  0,-1,0,-1.5,  0,0,0,1}),
					tl2::create<t_vec_gl>({1,0,0,0}), tl2::create<t_vec_gl>({0,0,1,0}));


				auto labCoordSys = new QLabel("Coordinate System:", /*m_dlgPlot*/ this);
				auto comboCoordSys = new QComboBox(/*m_dlgPlot*/ this);
				m_status3D = new QLabel(/*m_dlgPlot*/ this);

				comboCoordSys->addItem("Fractional Units (rlu)");
				comboCoordSys->addItem("Lab Units (A)");


				m_plot->setSizePolicy(QSizePolicy{QSizePolicy::Expanding, QSizePolicy::Expanding});
				labCoordSys->setSizePolicy(QSizePolicy{QSizePolicy::Fixed, QSizePolicy::Fixed});

				auto grid = new QGridLayout(m_dlgPlot);
				grid->setSpacing(2);
				grid->setContentsMargins(4,4,4,4);
				grid->addWidget(m_plot.get(), 0,0,1,2);
				grid->addWidget(labCoordSys, 1,0,1,1);
				grid->addWidget(comboCoordSys, 1,1,1,1);
				grid->addWidget(m_status3D, 2,0,1,2);


				connect(m_plot.get(), &tl2::GlPlot::AfterGLInitialisation, this, &StructFactDlg::AfterGLInitialisation);
				connect(m_plot->GetRenderer(), &tl2::GlPlotRenderer::PickerIntersection, this, &StructFactDlg::PickerIntersection);
				connect(m_plot.get(), &tl2::GlPlot::MouseDown, this, &StructFactDlg::PlotMouseDown);
				connect(m_plot.get(), &tl2::GlPlot::MouseUp, this, &StructFactDlg::PlotMouseUp);
				connect(comboCoordSys, static_cast<void (QComboBox::*)(int)>(&QComboBox::currentIndexChanged), this, [this](int val)
				{
					if(this->m_plot)
						this->m_plot->GetRenderer()->SetCoordSys(val);
				});


				if(m_sett && m_sett->contains("geo_3dview"))
					m_dlgPlot->restoreGeometry(m_sett->value("geo_3dview").toByteArray());
				else
					m_dlgPlot->resize(500,500);
			}

			m_dlgPlot->show();
			m_dlgPlot->raise();
			m_dlgPlot->focusWidget();
		});

		m_menu->addMenu(menuFile);
		m_menu->addMenu(menuView);
		pmainGrid->setMenuBar(m_menu);
	}


	// restore window size and position
	if(m_sett && m_sett->contains("geo"))
		restoreGeometry(m_sett->value("geo").toByteArray());
	else
		resize(600, 500);


	m_ignoreChanges = 0;
}



// ============================================================================
// functions for nuclei tab

// ----------------------------------------------------------------------------

void StructFactDlg::AddTabItem(int row,
	const std::string& name, t_real bRe, t_real bIm, t_real x, t_real y, t_real z, t_real scale, const std::string& col)
{
	bool bclone = 0;
	m_ignoreChanges = 1;

	if(row == -1)	// append to end of table
		row = m_nuclei->rowCount();
	else if(row == -2 && m_iCursorRow >= 0)	// use row from member variable
		row = m_iCursorRow;
	else if(row == -3 && m_iCursorRow >= 0)	// use row from member variable +1
		row = m_iCursorRow + 1;
	else if(row == -4 && m_iCursorRow >= 0)	// use row from member variable +1
	{
		row = m_iCursorRow + 1;
		bclone = 1;
	}

	//bool sorting = m_nuclei->isSortingEnabled();
	m_nuclei->setSortingEnabled(false);
	m_nuclei->insertRow(row);

	if(bclone)
	{
		for(int thecol=0; thecol<NUM_COLS; ++thecol)
			m_nuclei->setItem(row, thecol, m_nuclei->item(m_iCursorRow, thecol)->clone());
	}
	else
	{
		m_nuclei->setItem(row, COL_NAME, new QTableWidgetItem(name.c_str()));
		m_nuclei->setItem(row, COL_SCATLEN_RE, new NumericTableWidgetItem<t_real>(bRe));
		m_nuclei->setItem(row, COL_SCATLEN_IM, new NumericTableWidgetItem<t_real>(bIm));
		m_nuclei->setItem(row, COL_X, new NumericTableWidgetItem<t_real>(x));
		m_nuclei->setItem(row, COL_Y, new NumericTableWidgetItem<t_real>(y));
		m_nuclei->setItem(row, COL_Z, new NumericTableWidgetItem<t_real>(z));
		m_nuclei->setItem(row, COL_RAD, new NumericTableWidgetItem<t_real>(scale));
		m_nuclei->setItem(row, COL_COL, new QTableWidgetItem(col.c_str()));
	}

	Add3DItem(row);

	m_nuclei->scrollToItem(m_nuclei->item(row, 0));
	m_nuclei->setCurrentCell(row, 0);

	m_nuclei->setSortingEnabled(/*sorting*/ true);

	m_ignoreChanges = 0;
	Calc();
}


/**
 * add 3d object
 */
void StructFactDlg::Add3DItem(int row)
{
	if(!m_plot) return;

	// add all items
	if(row < 0)
	{
		for(int row=0; row<m_nuclei->rowCount(); ++row)
			Add3DItem(row);
		return;
	}

	auto *itemName = m_nuclei->item(row, COL_NAME);
	auto *itemx = m_nuclei->item(row, COL_X);
	auto *itemy = m_nuclei->item(row, COL_Y);
	auto *itemz = m_nuclei->item(row, COL_Z);
	auto *itemsc = m_nuclei->item(row, COL_RAD);
	auto *itemCol = m_nuclei->item(row, COL_COL);

	t_real_gl posx=0, posy=0, posz=0, scale=1;
	std::istringstream{itemx->text().toStdString()} >> posx;
	std::istringstream{itemy->text().toStdString()} >> posy;
	std::istringstream{itemz->text().toStdString()} >> posz;
	std::istringstream{itemsc->text().toStdString()} >> scale;

	qreal r=1, g=1, b=1;
	QColor col{itemCol->text()};
	col.getRgbF(&r, &g, &b);

	auto obj = m_plot->GetRenderer()->AddLinkedObject(m_sphere, 0,0,0, r,g,b,1);
	//auto obj = m_plot->GetRenderer()->AddSphere(0.05, 0,0,0, r,g,b,1);
	m_plot->GetRenderer()->SetObjectMatrix(obj, tl2::hom_translation<t_mat_gl>(posx, posy, posz)*tl2::hom_scaling<t_mat_gl>(scale,scale,scale));
	m_plot->GetRenderer()->SetObjectLabel(obj, itemName->text().toStdString());
	m_plot->update();

	m_nuclei->item(row, COL_NAME)->setData(Qt::UserRole, unsigned(obj));
}


void StructFactDlg::DelTabItem(int begin, int end)
{
	m_ignoreChanges = 1;

	// if nothing is selected, clear all items
	if(begin == -1 || m_nuclei->selectedItems().count() == 0)
	{
		if(m_plot)
		{
			for(int row=0; row<m_nuclei->rowCount(); ++row)
				if(std::size_t obj = m_nuclei->item(row, COL_NAME)->data(Qt::UserRole).toUInt(); obj)
					m_plot->GetRenderer()->RemoveObject(obj);
			m_plot->update();
		}

		m_nuclei->clearContents();
		m_nuclei->setRowCount(0);
	}
	else if(begin == -2)	// clear selected
	{
		for(int row : GetSelectedRows(true))
		{
			// remove 3d object
			if(m_plot)
			{
				if(std::size_t obj = m_nuclei->item(row, COL_NAME)->data(Qt::UserRole).toUInt(); obj)
					m_plot->GetRenderer()->RemoveObject(obj);
				m_plot->update();
			}

			m_nuclei->removeRow(row);
		}
	}
	else if(begin >= 0 && end >= 0)		// clear given range
	{
		for(int row=end-1; row>=begin; --row)
		{
			// remove 3d object
			if(m_plot)
			{
				if(std::size_t obj = m_nuclei->item(row, COL_NAME)->data(Qt::UserRole).toUInt(); obj)
					m_plot->GetRenderer()->RemoveObject(obj);
				m_plot->update();
			}

			m_nuclei->removeRow(row);
		}
	}

	m_ignoreChanges = 0;
	Calc();
}


void StructFactDlg::MoveTabItemUp()
{
	m_ignoreChanges = 1;
	m_nuclei->setSortingEnabled(false);

	auto selected = GetSelectedRows(false);
	for(int row : selected)
	{
		if(row == 0)
			continue;

		auto *item = m_nuclei->item(row, 0);
		if(!item || !item->isSelected())
			continue;

		m_nuclei->insertRow(row-1);
		for(int col=0; col<m_nuclei->columnCount(); ++col)
			m_nuclei->setItem(row-1, col, m_nuclei->item(row+1, col)->clone());
		m_nuclei->removeRow(row+1);
	}

	for(int row=0; row<m_nuclei->rowCount(); ++row)
	{
		if(auto *item = m_nuclei->item(row, 0);
			item && std::find(selected.begin(), selected.end(), row+1) != selected.end())
		{
			for(int col=0; col<m_nuclei->columnCount(); ++col)
				m_nuclei->item(row, col)->setSelected(true);
		}
	}

	m_ignoreChanges = 0;
}


void StructFactDlg::MoveTabItemDown()
{
	m_ignoreChanges = 1;
	m_nuclei->setSortingEnabled(false);

	auto selected = GetSelectedRows(true);
	for(int row : selected)
	{
		if(row == m_nuclei->rowCount()-1)
			continue;

		auto *item = m_nuclei->item(row, 0);
		if(!item || !item->isSelected())
			continue;

		m_nuclei->insertRow(row+2);
		for(int col=0; col<m_nuclei->columnCount(); ++col)
			m_nuclei->setItem(row+2, col, m_nuclei->item(row, col)->clone());
		m_nuclei->removeRow(row);
	}

	for(int row=0; row<m_nuclei->rowCount(); ++row)
	{
		if(auto *item = m_nuclei->item(row, 0);
			item && std::find(selected.begin(), selected.end(), row-1) != selected.end())
		{
			for(int col=0; col<m_nuclei->columnCount(); ++col)
				m_nuclei->item(row, col)->setSelected(true);
		}
	}

	m_ignoreChanges = 0;
}
// ----------------------------------------------------------------------------




// ----------------------------------------------------------------------------
std::vector<int> StructFactDlg::GetSelectedRows(bool sort_reversed) const
{
	std::vector<int> vec;
	vec.reserve(m_nuclei->selectedItems().size());

	for(int row=0; row<m_nuclei->rowCount(); ++row)
	{
		if(auto *item = m_nuclei->item(row, 0); item && item->isSelected())
			vec.push_back(row);
	}

	if(sort_reversed)
	{
		std::stable_sort(vec.begin(), vec.end(), [](int row1, int row2)
		{ return row1 > row2; });
	}

	return vec;
}


/**
 * selected a new row
 */
void StructFactDlg::TableCurCellChanged(int rowNew, int colNew, int rowOld, int colOld)
{
}


/**
 * hovered over new row
 */
void StructFactDlg::TableCellEntered(const QModelIndex& idx)
{
}


/**
 * item contents changed
 */
void StructFactDlg::TableItemChanged(QTableWidgetItem *item)
{
	// update associated 3d object
	if(item && m_plot)
	{
		int row = item->row();
		if(std::size_t obj = m_nuclei->item(row, COL_NAME)->data(Qt::UserRole).toUInt(); obj)
		{
			auto *itemName = m_nuclei->item(row, COL_NAME);
			auto *itemx = m_nuclei->item(row, COL_X);
			auto *itemy = m_nuclei->item(row, COL_Y);
			auto *itemz = m_nuclei->item(row, COL_Z);
			auto *itemsc = m_nuclei->item(row, COL_RAD);
			auto *itemCol = m_nuclei->item(row, COL_COL);

			t_real_gl posx=0, posy=0, posz=0, scale=1;
			std::istringstream{itemx->text().toStdString()} >> posx;
			std::istringstream{itemy->text().toStdString()} >> posy;
			std::istringstream{itemz->text().toStdString()} >> posz;
			std::istringstream{itemsc->text().toStdString()} >> scale;

			qreal r=1, g=1, b=1;
			QColor col{itemCol->text()};
			col.getRgbF(&r, &g, &b);

			m_plot->GetRenderer()->SetObjectMatrix(obj, tl2::hom_translation<t_mat_gl>(posx, posy, posz)*tl2::hom_scaling<t_mat_gl>(scale,scale,scale));
			m_plot->GetRenderer()->SetObjectCol(obj, r, g, b, 1);
			m_plot->GetRenderer()->SetObjectLabel(obj, itemName->text().toStdString());
			m_plot->update();
		}
	}

	if(!m_ignoreChanges)
		Calc();
}


void StructFactDlg::ShowTableContextMenu(const QPoint& pt)
{
	auto ptGlob = m_nuclei->mapToGlobal(pt);

	if(const auto* item = m_nuclei->itemAt(pt); item)
	{
		m_iCursorRow = item->row();
		ptGlob.setY(ptGlob.y() + m_pTabContextMenu->sizeHint().height()/2);
		m_pTabContextMenu->popup(ptGlob);
	}
	else
	{
		ptGlob.setY(ptGlob.y() + m_pTabContextMenuNoItem->sizeHint().height()/2);
		m_pTabContextMenuNoItem->popup(ptGlob);
	}
}
// ----------------------------------------------------------------------------
// ============================================================================




// ============================================================================
// functions for space group finder tab

// ----------------------------------------------------------------------------

void StructFactDlg::AddTabItem_FindSG(int row, t_real x, t_real y, t_real z)
{
	bool bclone = 0;

	if(row == -1)	// append to end of table
		row = m_nuclei_FindSG->rowCount();
	else if(row == -2 && m_iCursorRow_FindSG >= 0)	// use row from member variable
		row = m_iCursorRow_FindSG;
	else if(row == -3 && m_iCursorRow_FindSG >= 0)	// use row from member variable +1
		row = m_iCursorRow_FindSG + 1;
	else if(row == -4 && m_iCursorRow_FindSG >= 0)	// use row from member variable +1
	{
		row = m_iCursorRow_FindSG + 1;
		bclone = 1;
	}

	m_nuclei_FindSG->setSortingEnabled(false);
	m_nuclei_FindSG->insertRow(row);

	if(bclone)
	{
		for(int thecol=0; thecol<3; ++thecol)
			m_nuclei_FindSG->setItem(row, thecol, m_nuclei_FindSG->item(m_iCursorRow_FindSG, thecol)->clone());
	}
	else
	{
		m_nuclei_FindSG->setItem(row, 0, new NumericTableWidgetItem<t_real>(x));
		m_nuclei_FindSG->setItem(row, 1, new NumericTableWidgetItem<t_real>(y));
		m_nuclei_FindSG->setItem(row, 2, new NumericTableWidgetItem<t_real>(z));
	}

	m_nuclei_FindSG->scrollToItem(m_nuclei_FindSG->item(row, 0));
	m_nuclei_FindSG->setCurrentCell(row, 0);
	m_nuclei_FindSG->setSortingEnabled(true);

	//FindSG();
}



void StructFactDlg::DelTabItem_FindSG(int begin, int end)
{
	// if nothing is selected, clear all items
	if(begin == -1 || m_nuclei_FindSG->selectedItems().count() == 0)
	{
		m_nuclei_FindSG->clearContents();
		m_nuclei_FindSG->setRowCount(0);
	}
	else if(begin == -2)	// clear selected
	{
		for(int row : GetSelectedRows_FindSG(true))
			m_nuclei_FindSG->removeRow(row);
	}
	else if(begin >= 0 && end >= 0)		// clear given range
	{
		for(int row=end-1; row>=begin; --row)
			m_nuclei_FindSG->removeRow(row);
	}

	//FindSG();
}


void StructFactDlg::MoveTabItemUp_FindSG()
{
	m_nuclei_FindSG->setSortingEnabled(false);

	auto selected = GetSelectedRows_FindSG(false);
	for(int row : selected)
	{
		if(row == 0)
			continue;

		auto *item = m_nuclei_FindSG->item(row, 0);
		if(!item || !item->isSelected())
			continue;

		m_nuclei_FindSG->insertRow(row-1);
		for(int col=0; col<m_nuclei_FindSG->columnCount(); ++col)
			m_nuclei_FindSG->setItem(row-1, col, m_nuclei_FindSG->item(row+1, col)->clone());
		m_nuclei_FindSG->removeRow(row+1);
	}

	for(int row=0; row<m_nuclei_FindSG->rowCount(); ++row)
	{
		if(auto *item = m_nuclei_FindSG->item(row, 0);
		   item && std::find(selected.begin(), selected.end(), row+1) != selected.end())
		   {
			   for(int col=0; col<m_nuclei_FindSG->columnCount(); ++col)
				   m_nuclei_FindSG->item(row, col)->setSelected(true);
		   }
	}
}


void StructFactDlg::MoveTabItemDown_FindSG()
{
	m_nuclei_FindSG->setSortingEnabled(false);

	auto selected = GetSelectedRows_FindSG(true);
	for(int row : selected)
	{
		if(row == m_nuclei_FindSG->rowCount()-1)
			continue;

		auto *item = m_nuclei_FindSG->item(row, 0);