merged so far privately developed and owned magtools project into in20tools

libs/_cxx20/magsg.h

+/**
+ * future math library, developed from scratch to eventually replace tlibs(2)
+ * magnetic space group library
+ * @author Tobias Weber <tweber@ill.fr>
+ * @date 7-apr-18
+ * @license GPLv3, see 'LICENSE' file
+ * @desc The present version was forked on 8-Nov-2018 from the privately developed "magtools" project (https://github.com/t-weber/magtools).
+ */
+
+#ifndef __MAG_SG_H__
+#define __MAG_SG_H__
+
+#include <string>
+#include <vector>
+#include <memory>
+#include <iostream>
+
+#include "math_algos.h"
+
+#include <boost/algorithm/string.hpp>
+#include <boost/property_tree/ptree.hpp>
+#include <boost/property_tree/info_parser.hpp>
+#include <boost/property_tree/xml_parser.hpp>
+namespace ptree = boost::property_tree;
+
+
+
+// ----------------------------------------------------------------------------
+/**
+ * forward declarations
+ */
+template<class t_mat, class t_vec>
+requires m::is_mat<t_mat> && m::is_vec<t_vec>
+class Spacegroups;
+// ----------------------------------------------------------------------------
+
+
+
+
+// ----------------------------------------------------------------------------
+/**
+ * Symmetry operations
+ */
+template<class t_mat, class t_vec>
+requires m::is_mat<t_mat> && m::is_vec<t_vec>
+class Symmetry
+{
+	friend class Spacegroups<t_mat, t_vec>;
+
+private:
+	// rotations
+	std::vector<t_mat> m_rot;
+
+	// translations
+	std::vector<t_vec> m_trans;
+
+	// time inversions
+	std::vector<typename t_mat::value_type> m_inv;
+
+public:
+	Symmetry() = default;
+	~Symmetry() = default;
+
+	const std::vector<t_mat>& GetRotations() const { return m_rot; }
+	const std::vector<t_vec>& GetTranslations() const { return m_trans; }
+	const std::vector<typename t_mat::value_type>& GetInversions() const { return m_inv; }
+};
+// ----------------------------------------------------------------------------
+
+
+
+
+// ----------------------------------------------------------------------------
+/**
+ * Wyckoff positions
+ */
+template<class t_mat, class t_vec>
+requires m::is_mat<t_mat> && m::is_vec<t_vec>
+class WycPositions
+{
+	friend class Spacegroups<t_mat, t_vec>;
+
+private:
+	std::string m_letter;
+
+	// multiplicity
+	int m_mult = 0;
+
+	// structural & magnetic rotations
+	std::vector<t_mat> m_rot, m_rotMag;
+
+	// translations
+	std::vector<t_vec> m_trans;
+
+public:
+	WycPositions() = default;
+	~WycPositions() = default;
+
+	const std::string& GetLetter() const { return m_letter; }
+	int GetMultiplicity() const { return m_mult; }
+	std::string GetName() const { return std::to_string(m_mult) + m_letter; }
+
+	const std::vector<t_mat>& GetRotations() const { return m_rot; }
+	const std::vector<t_mat>& GetRotationsMag() const { return m_rotMag; }
+	const std::vector<t_vec>& GetTranslations() const { return m_trans; }
+};
+// ----------------------------------------------------------------------------
+
+
+
+
+// ----------------------------------------------------------------------------
+/**
+ * a magnetic space group
+ */
+template<class t_mat, class t_vec>
+requires m::is_mat<t_mat> && m::is_vec<t_vec>
+class Spacegroup
+{
+	friend class Spacegroups<t_mat, t_vec>;
+
+private:
+	std::string m_nameBNS, m_nameOG;
+	std::string m_nrBNS, m_nrOG;
+	int m_sgnrStruct = -1, m_sgnrMag = -1;
+
+	// lattice definition
+	std::shared_ptr<std::vector<t_vec>> m_latticeBNS;
+	std::shared_ptr<std::vector<t_vec>> m_latticeOG;
+
+	// symmetry operations
+	std::shared_ptr<Symmetry<t_mat, t_vec>> m_symBNS;
+	std::shared_ptr<Symmetry<t_mat, t_vec>> m_symOG;
+
+	// Wyckoff positions
+	std::shared_ptr<std::vector<WycPositions<t_mat, t_vec>>> m_wycBNS;
+	std::shared_ptr<std::vector<WycPositions<t_mat, t_vec>>> m_wycOG;
+
+	// BNS to OG trafo
+	t_mat m_rotBNS2OG;
+	t_vec m_transBNS2OG;
+
+public:
+	Spacegroup() = default;
+	~Spacegroup() = default;
+
+	const std::string& GetName(bool bBNS=1) const
+	{ return bBNS ? m_nameBNS : m_nameOG; }
+
+	const std::string& GetNumber(bool bBNS=1) const
+	{ return bBNS ? m_nrBNS : m_nrOG; }
+
+	// structural and magnetic space group number
+	int GetStructNumber() const { return m_sgnrStruct; }
+	int GetMagNumber() const { return m_sgnrMag; }
+
+	const std::vector<t_vec>* GetLattice(bool bBNS=true) const
+	{ return bBNS ? m_latticeBNS.get() : m_latticeOG.get(); }
+
+	const Symmetry<t_mat, t_vec>* GetSymmetries(bool bBNS=true) const
+	{ return bBNS ? m_symBNS.get() : m_symOG.get(); }
+
+	const std::vector<WycPositions<t_mat, t_vec>>* GetWycPositions(bool bBNS=true) const
+	{ return bBNS ? m_wycBNS.get() : m_wycOG.get(); }
+};
+// ----------------------------------------------------------------------------
+
+
+
+
+// ----------------------------------------------------------------------------
+/**
+ * a collection of magnetic space groups
+ */
+template<class t_mat, class t_vec>
+requires m::is_mat<t_mat> && m::is_vec<t_vec>
+class Spacegroups
+{
+private:
+	std::vector<Spacegroup<t_mat, t_vec>> m_sgs;
+
+public:
+	Spacegroups() = default;
+	~Spacegroups() = default;
+
+	bool Load(const std::string& strFile);
+
+	const std::vector<Spacegroup<t_mat, t_vec>>* GetSpacegroups() const
+	{ return &m_sgs; }
+
+	const Spacegroup<t_mat, t_vec>* GetSpacegroupByNumber(int iStruc, int iMag) const
+	{
+		auto iter = std::find_if(m_sgs.begin(), m_sgs.end(),
+			[iStruc, iMag](const auto& sg) -> bool
+			{
+				return  (sg.GetStructNumber()==iStruc && sg.GetMagNumber()==iMag);
+			});
+
+		if(iter == m_sgs.end())
+			return nullptr;
+		return &*iter;
+	}
+};
+// ----------------------------------------------------------------------------
+
+
+
+
+// ----------------------------------------------------------------------------
+// Loader
+
+
+template<class t_mat, class t_vec>
+bool Spacegroups<t_mat, t_vec>::Load(const std::string& strFile)
+{
+	using t_real = typename t_mat::value_type;
+
+	// load xml database
+	ptree::ptree prop;
+	try
+	{
+		//ptree::read_xml(strFile, prop);
+		ptree::read_info(strFile, prop);
+	}
+	catch(const std::exception& ex)
+	{
+		std::cerr << ex.what() << std::endl;
+		return false;
+	}
+
+
+	// iterate space groups
+	const auto& groups = prop.get_child_optional("mag_groups");
+	if(!groups)
+	{
+		std::cerr << "No space groups defined." << std::endl;
+		return false;
+	}
+
+
+	for(const auto& group : *groups)
+	{
+		// --------------------------------------------------------------------
+		auto nameBNS = group.second.get_optional<std::string>("bns.id");
+		auto nrBNS = group.second.get_optional<std::string>("bns.nr");
+		const auto& lattBNS = group.second.get_child_optional("bns.lat");
+		const auto& opsBNS = group.second.get_child_optional("bns.ops");
+		const auto& wycBNS = group.second.get_child_optional("bns.wyc");
+
+		auto nameOG = group.second.get_optional<std::string>("og.id");
+		auto nrOG = group.second.get_optional<std::string>("og.nr");
+		const auto& lattOG = group.second.get_child_optional("og.lat");
+		const auto& opsOG = group.second.get_child_optional("og.ops");
+		const auto& wycOG = group.second.get_child_optional("og.wyc");
+
+		const auto& bns2og = group.second.get_child_optional("bns2og");
+		// --------------------------------------------------------------------
+
+
+		// --------------------------------------------------------------------
+		Spacegroup<t_mat, t_vec> sg;
+
+		sg.m_nameBNS = *nameBNS; boost::trim(sg.m_nameBNS);
+		sg.m_nameOG = *nameOG; boost::trim(sg.m_nameOG);
+		sg.m_nrBNS = *nrBNS; boost::trim(sg.m_nrBNS);
+		sg.m_nrOG = *nrOG; boost::trim(sg.m_nrOG);
+
+		// split BNS space group number in structural and magnetic part
+		std::vector<std::string> vecNumbers;
+		boost::split(vecNumbers, sg.m_nrBNS, [](auto c)->bool {return c=='.';}, boost::token_compress_on);
+		if(vecNumbers.size() < 2)
+		{	// purely-structural space group
+			std::cerr << "Non-magnetic space group: " << sg.m_nrBNS << std::endl;
+		}
+		else if(vecNumbers.size() > 2)
+		{	// unknown
+			std::cerr << "Unknown space group number: " << sg.m_nrBNS << std::endl;
+		}
+		else
+		{	// magnetic space group
+			sg.m_sgnrStruct = std::stoi(vecNumbers[0]);
+			sg.m_sgnrMag = std::stoi(vecNumbers[1]);
+		}
+		// --------------------------------------------------------------------
+
+
+
+		// --------------------------------------------------------------------
+		// reads in a vector
+		auto get_vec = [](const std::string& str) -> t_vec
+		{
+			t_vec vec = m::zero<t_vec>(3);
+
+			// abbreviations
+			if(str == "0")
+				;
+			else if(str == "x")
+				vec = m::create<t_vec>({1,0,0});
+			else if(str == "y")
+				vec = m::create<t_vec>({0,1,0});
+			else if(str == "z")
+				vec = m::create<t_vec>({0,0,1});
+			else if(str == "-x")
+				vec = m::create<t_vec>({-1,0,0});
+			else if(str == "-y")
+				vec = m::create<t_vec>({0,-1,0});
+			else if(str == "-z")
+				vec = m::create<t_vec>({0,0,-1});
+			else
+			{
+				// read vector
+				std::istringstream istr(str);
+				for(std::size_t i=0; i<vec.size(); ++i)
+					istr >> vec[i];
+			}
+
+			return vec;
+		};
+
+		// reads in a matrix
+		auto get_mat = [](const std::string& str) -> t_mat
+		{
+			t_mat mat = m::zero<t_mat>(3,3);
+
+			// abbreviations
+			if(str == "0")
+				;
+			else if(str == "1")
+				mat = m::unit<t_mat>(3);
+			else
+			{
+				// read matrix
+				std::istringstream istr(str);
+				for(std::size_t i=0; i<mat.size1(); ++i)
+					for(std::size_t j=0; j<mat.size2(); ++j)
+						istr >> mat(i,j);
+			}
+
+			return mat;
+		};
+
+		// transforms a BNS vector to OG
+		// TODO: check!
+		auto calc_bns2og = [](const auto& rotBNS2OG, const auto& transBNS2OG, auto *vecs) -> void
+		{
+			for(auto& vec : *vecs)
+				vec = rotBNS2OG*vec + transBNS2OG;
+		};
+		// --------------------------------------------------------------------
+
+
+
+		// --------------------------------------------------------------------
+		// BNS to OG trafo
+		if(bns2og)
+		{
+			auto opBNS2OGTrafo = bns2og->get_optional<std::string>("R");
+			auto opBNS2OGTrans = bns2og->get_optional<std::string>("v");
+			auto opBNS2OGdiv = bns2og->get_optional<t_real>("d");
+
+			sg.m_rotBNS2OG = opBNS2OGTrafo ? get_mat(*opBNS2OGTrafo) : m::unit<t_mat>(3,3);
+			sg.m_transBNS2OG = opBNS2OGTrans ? get_vec(*opBNS2OGTrans) : m::zero<t_vec>(3);
+			t_real divBNS2OG = opBNS2OGdiv ? *opBNS2OGdiv : t_real(1);
+			sg.m_transBNS2OG /= divBNS2OG;
+		}
+		// --------------------------------------------------------------------
+
+
+
+		// --------------------------------------------------------------------
+		// iterate symmetry trafos
+		auto load_ops = [&get_vec, &get_mat](const decltype(opsBNS)& ops)
+		-> std::tuple<std::vector<t_mat>, std::vector<t_vec>, std::vector<t_real>>
+		{
+			std::vector<t_mat> rotations;
+			std::vector<t_vec> translations;
+			std::vector<t_real> inversions;
+
+			for(std::size_t iOp=1; true; ++iOp)
+			{
+				std::string strOp = std::to_string(iOp);
+				std::string nameTrafo = "R" + strOp;
+				std::string nameTrans = "v" + strOp;
+				std::string nameDiv = "d" + strOp;
+				std::string nameInv = "t" + strOp;
+
+				auto opTrafo = ops->get_optional<std::string>(nameTrafo);
+				auto opTrans = ops->get_optional<std::string>(nameTrans);
+				auto opdiv = ops->get_optional<t_real>(nameDiv);
+				auto opinv = ops->get_optional<t_real>(nameInv);
+
+				if(!opTrafo)
+					break;
+
+				t_real div = opdiv ? *opdiv : t_real(1);
+				t_real inv = opinv ? *opinv : t_real(1);
+				t_mat rot = opTrafo ? get_mat(*opTrafo) : m::unit<t_mat>(3,3);
+				t_vec trans = opTrans ? get_vec(*opTrans) : m::zero<t_vec>(3);
+				trans /= div;
+
+				rotations.emplace_back(std::move(rot));
+				translations.emplace_back(std::move(trans));
+				inversions.push_back(inv);
+			}
+
+			return std::make_tuple(std::move(rotations), std::move(translations), std::move(inversions));
+		};
+
+		if(opsBNS)
+		{
+			sg.m_symBNS = std::make_shared<Symmetry<t_mat, t_vec>>();
+			std::tie(sg.m_symBNS->m_rot, sg.m_symBNS->m_trans, sg.m_symBNS->m_inv) = std::move(load_ops(opsBNS));
+		}
+		if(opsOG)
+		{
+			sg.m_symOG = std::make_shared<Symmetry<t_mat, t_vec>>();
+			std::tie(sg.m_symOG->m_rot, sg.m_symOG->m_trans, sg.m_symOG->m_inv) = std::move(load_ops(opsOG));
+		}
+		else
+		{
+			if(!bns2og)
+			{
+				// if neither OG nor BNS to OG trafo are defined, OG is identical to BNS
+				sg.m_symOG = sg.m_symBNS;
+			}
+			else
+			{
+				// calculate OG from BNS using trafo
+				sg.m_symOG = std::make_shared<Symmetry<t_mat, t_vec>>(*sg.m_symBNS);
+				calc_bns2og(sg.m_rotBNS2OG, sg.m_transBNS2OG, &sg.m_symOG->m_trans);
+
+				//std::cout << "bns2og trafo for sg " << sg.GetNumber() << std::endl;
+			}
+		}
+		// --------------------------------------------------------------------
+
+
+
+		// --------------------------------------------------------------------
+		// iterate over lattice vectors
+		auto load_latt = [&get_vec](const decltype(lattBNS)& latt)
+			-> std::vector<t_vec>
+		{
+			std::vector<t_vec> vectors;
+
+			for(std::size_t iVec=1; true; ++iVec)
+			{
+				std::string strVec = std::to_string(iVec);
+				std::string nameVec = "v" + strVec;
+				std::string nameDiv = "d" + strVec;
+
+				auto opVec = latt->get_optional<std::string>(nameVec);
+				auto opdiv = latt->get_optional<t_real>(nameDiv);
+
+				if(!opVec)
+					break;
+
+				t_real div = opdiv ? *opdiv : t_real(1);
+				t_vec vec = opVec ? get_vec(*opVec) : m::zero<t_vec>(3);
+				vec /= div;
+
+				vectors.emplace_back(std::move(vec));
+			}
+
+			return std::move(vectors);
+		};
+
+		if(lattBNS)
+		{
+			sg.m_latticeBNS = std::make_shared<std::vector<t_vec>>();
+			*sg.m_latticeBNS = std::move(load_latt(lattBNS));
+		}
+		if(lattOG)
+		{
+			sg.m_latticeOG = std::make_shared<std::vector<t_vec>>();
+			*sg.m_latticeOG = std::move(load_latt(lattOG));
+		}
+		else
+		{
+			if(!bns2og)
+			{
+				// if neither OG nor BNS to OG trafo are defined, OG is identical to BNS
+				sg.m_latticeOG = sg.m_latticeBNS;
+			}
+			else
+			{
+				// calculate OG from BNS using trafo
+				sg.m_latticeOG = std::make_shared<std::vector<t_vec>>(*sg.m_latticeBNS);
+				calc_bns2og(sg.m_rotBNS2OG, sg.m_transBNS2OG, sg.m_latticeOG.get());
+			}
+		}
+		// --------------------------------------------------------------------
+
+
+		// --------------------------------------------------------------------
+		// iterate wyckoff positions
+		auto load_wyc = [&get_vec, &get_mat](const decltype(wycBNS)& wycs)
+		-> std::vector<WycPositions<t_mat, t_vec>>
+		{
+			std::vector<WycPositions<t_mat, t_vec>> vecWyc;
+
+			for(std::size_t iWyc=1; true; ++iWyc)
+			{
+				std::string nameSite = "s" + std::to_string(iWyc);
+				auto wyc = wycs->get_child_optional(nameSite);
+				if(!wyc) break;
+
+				WycPositions<t_mat, t_vec> wycpos;
+
+				auto opLetter = wyc->get_optional<std::string>("l");
+				auto opMult = wyc->get_optional<int>("m");
+				if(opLetter) wycpos.m_letter = *opLetter;
+				wycpos.m_mult = opMult ? *opMult : 0;
+
+
+				for(std::size_t iPos=1; true; ++iPos)
+				{
+					std::string strPos = std::to_string(iPos);
+					std::string nameRot = "R" + strPos;
+					std::string nameRotMag = "M" + strPos;
+					std::string nameTrans = "v" + strPos;
+					std::string nameDiv = "d" + strPos;
+
+					auto opRot = wyc->get_optional<std::string>(nameRot);
+					auto opRotMag = wyc->get_optional<std::string>(nameRotMag);
+					auto opTrans = wyc->get_optional<std::string>(nameTrans);
+					auto opdiv = wyc->get_optional<t_real>(nameDiv);
+
+					if(!opRot)
+						break;
+
+					t_real div = opdiv ? *opdiv : t_real(1);
+					t_mat rot = opRot ? get_mat(*opRot) : m::unit<t_mat>(3,3);
+					t_mat rotMag = opRotMag ? get_mat(*opRotMag) : rot;
+					t_vec trans = opTrans ? get_vec(*opTrans) : m::zero<t_vec>(3);
+					trans /= div;
+
+					wycpos.m_rot.emplace_back(std::move(rot));
+					wycpos.m_rotMag.emplace_back(std::move(rotMag));
+					wycpos.m_trans.emplace_back(std::move(trans));
+				}
+
+				vecWyc.emplace_back(std::move(wycpos));
+			}
+
+			return std::move(vecWyc);
+		};
+
+
+		if(wycBNS)
+		{
+			sg.m_wycBNS = std::make_shared<std::vector<WycPositions<t_mat, t_vec>>>();
+			*sg.m_wycBNS = std::move(load_wyc(wycBNS));
+		}
+		if(wycOG)
+		{
+			sg.m_wycOG = std::make_shared<std::vector<WycPositions<t_mat, t_vec>>>();
+			*sg.m_wycOG = std::move(load_wyc(wycOG));
+		}
+		else
+		{
+			if(!bns2og)
+			{
+				// if neither OG nor BNS to OG trafo are defined, OG is identical to BNS
+				sg.m_wycOG = sg.m_wycBNS;
+			}
+			else
+			{
+				// calculate OG from BNS using trafo
+				sg.m_wycOG = std::make_shared<std::vector<WycPositions<t_mat, t_vec>>>(*sg.m_wycBNS);
+
+				for(auto& wycpos : *sg.m_wycOG)
+					calc_bns2og(sg.m_rotBNS2OG, sg.m_transBNS2OG, &wycpos.m_trans);
+			}
+		}
+		// --------------------------------------------------------------------
+
+
+		m_sgs.emplace_back(std::move(sg));
+	}
+
+
+	return true;
+}
+// ----------------------------------------------------------------------------
+
+
+#endif

libs/fit.h

@@ -23,9 +23,6 @@
 #include <algorithm>
 #include <limits>
 
-#include <boost/numeric/ublas/vector.hpp>
-#include <boost/math/special_functions/binomial.hpp>
-
 #include "math.h"
 #include "log.h"
 #include "traits.h"

tools/browser/CMakeLists.txt

+#
+# @author Tobias Weber
+# @date Apr-2018
+# @license GPLv3, see 'LICENSE' file
+# @desc The present version was forked on 8-Nov-2018 from the privately developed "magtools" project (https://github.com/t-weber/magtools).
+#
+project(sgbrowser)
+cmake_minimum_required(VERSION 3.0)