cleanups

.gitignore

@@ -32,6 +32,7 @@ data/**
 res/**
 tlibs
 tlibs2
+pathslib
 data
 
 # Temporary files

tools/structfact/CMakeLists.txt

@@ -24,6 +24,12 @@
 
 cmake_minimum_required(VERSION 3.0)
 project(structfact)
+enable_language(CXX)
+
+list(APPEND CMAKE_MODULE_PATH
+	"${PROJECT_SOURCE_DIR}"
+	"${PROJECT_SOURCE_DIR}/../../tlibs2/cmake"
+)
 
 set(CMAKE_VERBOSE_MAKEFILE TRUE)
 option(BUILD_LIB "build as dynamic library" FALSE)
@@ -40,6 +46,12 @@ endif()
 
 find_package(Boost REQUIRED)
 find_package(Qt5 REQUIRED COMPONENTS Core Gui Widgets)
+find_package(Qhull)
+
+if(Qhull_FOUND)
+	add_definitions(-DUSE_QHULL)
+	include_directories("${Qhull_INCLUDE_DIRS}")
+endif()
 
 set(CMAKE_AUTOUIC TRUE)
 set(CMAKE_AUTOMOC TRUE)
@@ -61,12 +73,18 @@ if(BUILD_LIB)
 
 	add_definitions(-DBUILD_LIB)
 	add_library(takin_structfact SHARED
-		structfact.cpp structfact.h
+		structfact.cpp structfact_file.cpp
+		structfact_structplot.cpp structfact_main.cpp
+		structfact_findsg.cpp structfact_nuclei.cpp
+		structfact.h
 		../../tlibs2/libs/qt/gl.cpp ../../tlibs2/libs/qt/gl.h
 		../../tlibs2/libs/qt/glplot.cpp ../../tlibs2/libs/qt/glplot.h)
 else()
 	add_executable(takin_structfact
-		structfact.cpp structfact.h
+		structfact.cpp structfact_file.cpp
+		structfact_structplot.cpp structfact_main.cpp
+		structfact_findsg.cpp structfact_nuclei.cpp
+		structfact.h
 		../../tlibs2/libs/qt/gl.cpp ../../tlibs2/libs/qt/gl.h
 		../../tlibs2/libs/qt/glplot.cpp ../../tlibs2/libs/qt/glplot.h)
 endif()
@@ -78,4 +96,8 @@ if(CMAKE_SYSTEM_NAME STREQUAL "Darwin")
 	)
 endif()
 
-target_link_libraries(takin_structfact ${Boost_LIBRARIES} Qt5::Core Qt5::Gui Qt5::Widgets)
+target_link_libraries(takin_structfact
+	${Boost_LIBRARIES}
+	${Qhull_LIBRARIES}
+	Qt5::Core Qt5::Gui Qt5::Widgets
+)

tools/structfact/structfact.h

@@ -64,6 +64,23 @@ using t_vec_gl = tl2::t_vec_gl;
 using t_mat_gl = tl2::t_mat_gl;
 
 
+constexpr t_real g_eps = 1e-6;
+constexpr int g_prec = 6;
+
+
+enum : int
+{
+	COL_NAME = 0,
+	COL_SCATLEN_RE,
+	COL_SCATLEN_IM,
+	COL_X, COL_Y, COL_Z,
+	COL_RAD,
+	COL_COL,
+
+	NUM_COLS
+};
+
+
 struct NuclPos
 {
 	std::string name;
@@ -78,6 +95,7 @@ public:
 	StructFactDlg(QWidget* pParent = nullptr);
 	~StructFactDlg() = default;
 
+
 protected:
 	QSettings *m_sett = nullptr;
 	QMenuBar *m_menu = nullptr;
@@ -116,6 +134,7 @@ protected:
 	t_mat m_crystA = tl2::unit<t_mat>(3);
 	t_mat m_crystB = tl2::unit<t_mat>(3);
 
+
 protected:
 	// for nuclei tab
 	void AddTabItem(int row=-1, const std::string& name="n/a", t_real bRe=0., t_real bIm=0.,
@@ -124,15 +143,11 @@ protected:
 	void MoveTabItemUp();
 	void MoveTabItemDown();
 
-	void Add3DItem(int row=-1);
-	void Set3DStatusMsg(const std::string& msg);
-
 	void TableCurCellChanged(int rowNew, int colNew, int rowOld, int colOld);
 	void TableCellEntered(const QModelIndex& idx);
 	void TableItemChanged(QTableWidgetItem *item);
 	void ShowTableContextMenu(const QPoint& pt);
 
-
 	void Load();
 	void Save();
 	void ImportCIF();
@@ -144,6 +159,10 @@ protected:
 	void CalcB(bool bFullRecalc=true);
 	void Calc();
 
+	void Add3DItem(int row=-1);
+	void Set3DStatusMsg(const std::string& msg);
+
+	void ShowStructPlot();
 	void PlotMouseDown(bool left, bool mid, bool right);
 	void PlotMouseUp(bool left, bool mid, bool right);
 	void PickerIntersection(const t_vec3_gl* pos, std::size_t objIdx, const t_vec3_gl* posSphere);
@@ -164,6 +183,7 @@ protected:
 
 	virtual void closeEvent(QCloseEvent *evt) override;
 
+
 private:
 	int m_iCursorRow = -1;
 	bool m_ignoreChanges = 1;
@@ -175,6 +195,7 @@ private:
 
 	static std::vector<std::string> g_default_colours;
 
+
 private:
 	std::vector<int> GetSelectedRows(bool sort_reversed = false) const;
 	std::vector<int> GetSelectedRows_FindSG(bool sort_reversed = false) const;

tools/structfact/structfact_file.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 <QtWidgets/QFileDialog>
+#include <QtWidgets/QMessageBox>
+
+#include <iostream>
+#include <fstream>
+#include <random>
+
+#include <boost/property_tree/ptree.hpp>
+#include <boost/property_tree/xml_parser.hpp>
+namespace pt = boost::property_tree;
+
+#include "loadcif.h"
+#include "tlibs2/libs/maths.h"
+#include "tlibs2/libs/algos.h"
+
+using namespace tl2_ops;
+
+
+std::vector<std::string> StructFactDlg::g_default_colours
+{{
+	"#ff0000", "#0000ff", "#00ff00", "#000000",
+}};
+
+
+void StructFactDlg::Load()
+{
+	m_ignoreCalc = 1;
+
+	try
+	{
+		QString dirLast = m_sett->value("dir", "").toString();
+		QString filename = QFileDialog::getOpenFileName(this, "Load File", dirLast, "XML Files (*.xml *.XML)");
+		if(filename=="" || !QFile::exists(filename))
+			return;
+		m_sett->setValue("dir", QFileInfo(filename).path());
+
+
+		pt::ptree node;
+
+		std::ifstream ifstr{filename.toStdString()};
+		pt::read_xml(ifstr, node);
+
+		// check signature
+		if(auto opt = node.get_optional<std::string>("sfact.meta.info"); !opt || *opt!=std::string{"sfact_tool"})
+		{
+			QMessageBox::critical(this, "Structure Factors", "Unrecognised file format.");
+			return;
+		}
+
+
+		// clear old nuclei
+		DelTabItem(-1);
+
+		if(auto opt = node.get_optional<t_real>("sfact.xtal.a"); opt)
+		{
+			std::ostringstream ostr; ostr.precision(g_prec); ostr << *opt;
+			m_editA->setText(ostr.str().c_str());
+		}
+		if(auto opt = node.get_optional<t_real>("sfact.xtal.b"); opt)
+		{
+			std::ostringstream ostr; ostr.precision(g_prec); ostr << *opt;
+			m_editB->setText(ostr.str().c_str());
+		}
+		if(auto opt = node.get_optional<t_real>("sfact.xtal.c"); opt)
+		{
+			std::ostringstream ostr; ostr.precision(g_prec); ostr << *opt;
+			m_editC->setText(ostr.str().c_str());
+		}
+		if(auto opt = node.get_optional<t_real>("sfact.xtal.alpha"); opt)
+		{
+			std::ostringstream ostr; ostr.precision(g_prec); ostr << *opt;
+			m_editAlpha->setText(ostr.str().c_str());
+		}
+		if(auto opt = node.get_optional<t_real>("sfact.xtal.beta"); opt)
+		{
+			std::ostringstream ostr; ostr.precision(g_prec); ostr << *opt;
+			m_editBeta->setText(ostr.str().c_str());
+		}
+		if(auto opt = node.get_optional<t_real>("sfact.xtal.gamma"); opt)
+		{
+			std::ostringstream ostr; ostr.precision(g_prec); ostr << *opt;
+			m_editGamma->setText(ostr.str().c_str());
+		}
+		if(auto opt = node.get_optional<int>("sfact.order"); opt)
+		{
+			m_maxBZ->setValue(*opt);
+		}
+		if(auto opt = node.get_optional<int>("sfact.removezeroes"); opt)
+		{
+			m_RemoveZeroes->setChecked(*opt != 0);
+		}
+		if(auto opt = node.get_optional<int>("sfact.sg_idx"); opt)
+		{
+			m_comboSG->setCurrentIndex(*opt);
+		}
+
+
+		// nuclei
+		if(auto nuclei = node.get_child_optional("sfact.nuclei"); nuclei)
+		{
+			std::size_t nucIdx = 0;
+			for(const auto &nucl : *nuclei)
+			{
+				auto optName = nucl.second.get<std::string>("name", "n/a");
+				auto optbRe = nucl.second.get<t_real>("b_Re", 0.);
+				auto optbIm = nucl.second.get<t_real>("b_Im", 0.);
+				auto optX = nucl.second.get<t_real>("x", 0.);
+				auto optY = nucl.second.get<t_real>("y", 0.);
+				auto optZ = nucl.second.get<t_real>("z", 0.);
+				auto optRad = nucl.second.get<t_real>("rad", 1.);
+				auto optCol = nucl.second.get<std::string>("col", g_default_colours[nucIdx%g_default_colours.size()]);
+
+				AddTabItem(-1, optName, optbRe, optbIm, optX,  optY, optZ, optRad, optCol);
+				++nucIdx;
+			}
+		}
+	}
+	catch(const std::exception& ex)
+	{
+		QMessageBox::critical(this, "Structure Factors", ex.what());
+	}
+
+
+	m_ignoreCalc = 0;
+	CalcB(false);
+	Calc();
+}
+
+
+void StructFactDlg::Save()
+{
+	QString dirLast = m_sett->value("dir", "").toString();
+	QString filename = QFileDialog::getSaveFileName(this, "Save File", dirLast, "XML Files (*.xml *.XML)");
+	if(filename=="")
+		return;
+	m_sett->setValue("dir", QFileInfo(filename).path());
+
+
+	pt::ptree node;
+	node.put<std::string>("sfact.meta.info", "sfact_tool");
+	node.put<std::string>("sfact.meta.date", tl2::epoch_to_str<t_real>(tl2::epoch<t_real>()));
+
+
+	// lattice
+	t_real a,b,c, alpha,beta,gamma;
+	std::istringstream{m_editA->text().toStdString()} >> a;
+	std::istringstream{m_editB->text().toStdString()} >> b;
+	std::istringstream{m_editC->text().toStdString()} >> c;
+	std::istringstream{m_editAlpha->text().toStdString()} >> alpha;
+	std::istringstream{m_editBeta->text().toStdString()} >> beta;
+	std::istringstream{m_editGamma->text().toStdString()} >> gamma;
+
+	node.put<t_real>("sfact.xtal.a", a);
+	node.put<t_real>("sfact.xtal.b", b);
+	node.put<t_real>("sfact.xtal.c", c);
+	node.put<t_real>("sfact.xtal.alpha", alpha);
+	node.put<t_real>("sfact.xtal.beta", beta);
+	node.put<t_real>("sfact.xtal.gamma", gamma);
+	node.put<int>("sfact.order", m_maxBZ->value());
+	node.put<int>("sfact.removezeroes", m_RemoveZeroes->isChecked());
+	node.put<int>("sfact.sg_idx", m_comboSG->currentIndex());
+
+	// nucleus list
+	for(int row=0; row<m_nuclei->rowCount(); ++row)
+	{
+		t_real bRe{},bIm{}, x{},y{},z{}, scale{};
+		std::istringstream{m_nuclei->item(row, COL_SCATLEN_RE)->text().toStdString()} >> bRe;
+		std::istringstream{m_nuclei->item(row, COL_SCATLEN_IM)->text().toStdString()} >> bIm;
+		std::istringstream{m_nuclei->item(row, COL_X)->text().toStdString()} >> x;
+		std::istringstream{m_nuclei->item(row, COL_Y)->text().toStdString()} >> y;
+		std::istringstream{m_nuclei->item(row, COL_Z)->text().toStdString()} >> z;
+		std::istringstream{m_nuclei->item(row, COL_RAD)->text().toStdString()} >> scale;
+
+		pt::ptree itemNode;
+		itemNode.put<std::string>("name", m_nuclei->item(row, COL_NAME)->text().toStdString());
+		itemNode.put<t_real>("b_Re", bRe);
+		itemNode.put<t_real>("b_Im", bIm);
+		itemNode.put<t_real>("x", x);
+		itemNode.put<t_real>("y", y);
+		itemNode.put<t_real>("z", z);
+		itemNode.put<t_real>("rad", scale);
+		itemNode.put<std::string>("col", m_nuclei->item(row, COL_COL)->text().toStdString());
+
+		node.add_child("sfact.nuclei.nucleus", itemNode);
+	}
+
+	std::ofstream ofstr{filename.toStdString()};
+	if(!ofstr)
+	{
+		QMessageBox::critical(this, "Structure Factors", "Cannot open file for writing.");
+		return;
+	}
+	ofstr.precision(g_prec);
+	pt::write_xml(ofstr, node, pt::xml_writer_make_settings('\t', 1, std::string{"utf-8"}));
+}
+
+
+/**
+ * load a TAZ file
+ */
+void StructFactDlg::ImportTAZ()
+{
+	m_ignoreCalc = 1;
+
+	try
+	{
+		QString dirLast = m_sett->value("dir_taz", "").toString();
+		QString filename = QFileDialog::getOpenFileName(this, "Load File", dirLast, "TAZ Files (*.taz *.TAZ)");
+		if(filename=="" || !QFile::exists(filename))
+			return;
+		m_sett->setValue("dir_taz", QFileInfo(filename).path());
+
+
+		pt::ptree node;
+
+		std::ifstream ifstr{filename.toStdString()};
+		pt::read_xml(ifstr, node);
+
+		// clear old nuclei
+		DelTabItem(-1);
+
+		if(auto opt = node.get_optional<t_real>("taz.sample.a"); opt)
+		{
+			std::ostringstream ostr; ostr.precision(g_prec); ostr << *opt;
+			m_editA->setText(ostr.str().c_str());
+		}
+		if(auto opt = node.get_optional<t_real>("taz.sample.b"); opt)
+		{
+			std::ostringstream ostr; ostr.precision(g_prec); ostr << *opt;
+			m_editB->setText(ostr.str().c_str());
+		}
+		if(auto opt = node.get_optional<t_real>("taz.sample.c"); opt)
+		{
+			std::ostringstream ostr; ostr.precision(g_prec); ostr << *opt;
+			m_editC->setText(ostr.str().c_str());
+		}
+		if(auto opt = node.get_optional<t_real>("taz.sample.alpha"); opt)
+		{
+			std::ostringstream ostr; ostr.precision(g_prec); ostr << *opt;
+			m_editAlpha->setText(ostr.str().c_str());
+		}
+		if(auto opt = node.get_optional<t_real>("taz.sample.beta"); opt)
+		{
+			std::ostringstream ostr; ostr.precision(g_prec); ostr << *opt;
+			m_editBeta->setText(ostr.str().c_str());
+		}
+		if(auto opt = node.get_optional<t_real>("taz.sample.gamma"); opt)
+		{
+			std::ostringstream ostr; ostr.precision(g_prec); ostr << *opt;
+			m_editGamma->setText(ostr.str().c_str());
+		}
+		if(auto opt = node.get_optional<std::string>("taz.sample.spacegroup"); opt)
+		{
+			// TODO
+			//std::cout << *opt << std::endl;
+		}
+
+		// nuclei
+		if(auto opt = node.get_optional<std::size_t>("taz.sample.atoms.num"); opt)
+		{
+			std::size_t numAtoms = *opt;
+			for(std::size_t atomIdx=0; atomIdx<numAtoms; ++atomIdx)
+			{
+				std::string strNum = tl2::var_to_str(atomIdx);
+
+				std::string name = node.get<std::string>("taz.sample.atoms."+strNum+".name", "n/a");
+				t_real x = node.get<t_real>("taz.sample.atoms."+strNum+".x", 0.);
+				t_real y = node.get<t_real>("taz.sample.atoms."+strNum+".y", 0.);
+				t_real z = node.get<t_real>("taz.sample.atoms."+strNum+".z", 0.);
+
+				// TODO
+				t_real bRe = 0.;
+				t_real bIm = 0.;
+
+				t_real rad = 1.;
+				std::string col = g_default_colours[atomIdx%g_default_colours.size()];
+
+				AddTabItem(-1, name, bRe, bIm, x, y, z, rad, col);
+			}
+		}
+	}
+	catch(const std::exception& ex)
+	{
+		QMessageBox::critical(this, "Structure Factors", ex.what());
+	}
+
+	m_ignoreCalc = 0;
+	GenerateFromSG();
+	CalcB(false);
+	Calc();
+}
+
+
+/**
+ * save a TAZ file
+ */
+void StructFactDlg::ExportTAZ()
+{
+	QString dirLast = m_sett->value("dir_taz", "").toString();
+	QString filename = QFileDialog::getSaveFileName(this, "Export TAZ", dirLast, "TAZ Files (*.taz *.TAZ)");
+	if(filename=="" || !QFile::exists(filename))
+		return;
+	m_sett->setValue("dir_taz", QFileInfo(filename).path());
+
+	std::ofstream ofstr{filename.toStdString()};
+	if(!ofstr)
+	{
+		QMessageBox::critical(this, "Structure Factors", "Cannot open file for writing.");
+		return;
+	}
+	ofstr.precision(g_prec);
+
+	ofstr << "<taz>\n";
+	ofstr << "\t<meta><info>Exported from Takin/Structfact.</info></meta>\n";
+
+	// sample infos
+	ofstr << "\t<sample>\n";
+	ofstr << "\t\t<a>" << m_editA->text().toStdString() << "</a>\n";
+	ofstr << "\t\t<b>" << m_editB->text().toStdString() << "</b>\n";
+	ofstr << "\t\t<c>" << m_editC->text().toStdString() << "</c>\n";
+	ofstr << "\t\t<alpha>" << m_editAlpha->text().toStdString() << "</alpha>\n";
+	ofstr << "\t\t<beta>" << m_editBeta->text().toStdString() << "</beta>\n";
+	ofstr << "\t\t<gamma>" << m_editGamma->text().toStdString() << "</gamma>\n";
+
+	// P1 only has the identity trafo, so we can directly output all raw nucleus positions
+	ofstr << "\t\t<spacegroup>P1</spacegroup>\n";
+
+	// nucleus list
+	ofstr << "\t\t<atoms>\n";
+	ofstr << "\t\t\t<num>" << m_nuclei->rowCount() << "</num>\n";
+	for(int row=0; row<m_nuclei->rowCount(); ++row)
+	{
+		ofstr << "\t\t\t<" << row << ">\n";
+		ofstr << "\t\t\t\t<name>" << m_nuclei->item(row, COL_NAME)->text().toStdString() << "</name>\n";
+		ofstr << "\t\t\t\t<x>" << m_nuclei->item(row, COL_X)->text().toStdString() << "</x>\n";
+		ofstr << "\t\t\t\t<y>" << m_nuclei->item(row, COL_Y)->text().toStdString() << "</y>\n";
+		ofstr << "\t\t\t\t<z>" << m_nuclei->item(row, COL_Z)->text().toStdString() << "</z>\n";
+		ofstr << "\t\t\t</" << row << ">\n";
+	}
+
+	ofstr << "\t\t</atoms>\n";
+	ofstr << "\t</sample>\n";
+
+	ofstr << "</taz>\n";
+}
+
+
+/**
+ * load a CIF
+ */
+void StructFactDlg::ImportCIF()
+{
+	m_ignoreCalc = 1;
+
+	try
+	{
+		QString dirLast = m_sett->value("dir_cif", "").toString();
+		QString filename = QFileDialog::getOpenFileName(this, "Import CIF", dirLast, "CIF Files (*.cif *.CIF)");
+		if(filename=="" || !QFile::exists(filename))
+			return;
+		m_sett->setValue("dir_cif", QFileInfo(filename).path());
+
+		auto [errstr, atoms, generatedatoms, atomnames, lattice, symops] =
+			load_cif<t_vec, t_mat>(filename.toStdString(), g_eps);
+		if(errstr != "")
+		{
+			QMessageBox::critical(this, "Structure Factors", errstr.c_str());
+			return;
+		}
+
+
+		// clear old nuclei
+		DelTabItem(-1);
+
+		// lattice
+		{
+			std::ostringstream ostr; ostr.precision(g_prec); ostr << lattice.a;
+			m_editA->setText(ostr.str().c_str());
+		}
+		{
+			std::ostringstream ostr; ostr.precision(g_prec); ostr << lattice.b;
+			m_editB->setText(ostr.str().c_str());
+		}
+		{
+			std::ostringstream ostr; ostr.precision(g_prec); ostr << lattice.c;
+			m_editC->setText(ostr.str().c_str());
+		}
+		{
+			std::ostringstream ostr; ostr.precision(g_prec); ostr << lattice.alpha;
+			m_editAlpha->setText(ostr.str().c_str());
+		}
+		{
+			std::ostringstream ostr; ostr.precision(g_prec); ostr << lattice.beta;
+			m_editBeta->setText(ostr.str().c_str());
+		}
+		{
+			std::ostringstream ostr; ostr.precision(g_prec); ostr << lattice.gamma;
+			m_editGamma->setText(ostr.str().c_str());
+		}
+
+
+		// atoms
+		std::mt19937 gen{tl2::epoch<unsigned int>()};
+		for(std::size_t atomnum=0; atomnum<atoms.size(); ++atomnum)
+		{
+			// random colour
+			std::ostringstream ostrcol;
+			std::uniform_int_distribution<int> dist{0, 255};
+			ostrcol << "#" << std::hex << std::setw(2) << std::setfill('0') << dist(gen)
+				<< std::setw(2) << std::setfill('0') << dist(gen)
+				<< std::setw(2) << std::setfill('0') << dist(gen);
+
+			for(std::size_t symnr=0; symnr<generatedatoms[atomnum].size(); ++symnr)
+			{
+				AddTabItem(-1, atomnames[atomnum], 0, 0,
+					generatedatoms[atomnum][symnr][0],  generatedatoms[atomnum][symnr][1], generatedatoms[atomnum][symnr][2],
+					1, ostrcol.str());
+			}
+		}
+	}