499 lines
22 KiB
C++
499 lines
22 KiB
C++
# include <ufo/unfold.hpp>
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namespace ufo
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{
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UnfoldSolver::InputType::InputType(std::string filename)
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{
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// read main input file
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{
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auto node = YAML::LoadFile(filename);
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for (unsigned i = 0; i < 3; i++)
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for (unsigned j = 0; j < 3; j++)
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PrimativeCell(i, j) = node["PrimativeCell"][i][j].as<double>();
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for (unsigned i = 0; i < 3; i++)
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SuperCellMultiplier(i) = node["SuperCellMultiplier"][i].as<int>();
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if (auto value = node["SuperCellDeformation"])
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{
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SuperCellDeformation.emplace();
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for (unsigned i = 0; i < 3; i++)
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for (unsigned j = 0; j < 3; j++)
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(*SuperCellDeformation)(i, j) = value[i][j].as<double>();
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}
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for (unsigned i = 0; i < 3; i++)
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PrimativeCellBasisNumber(i) = node["PrimativeCellBasisNumber"][i].as<int>();
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auto read_file_config = [filename](YAML::Node source, InputOutputFile& config)
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{
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if (auto _ = source["SameAsConfigFile"])
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{
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auto __ = _.as<bool>();
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config.ExtraParameters["SameAsConfigFile"] = __;
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if (__)
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{
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config.FileName = filename;
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config.Format = "yaml";
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return;
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}
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}
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config.FileName = source["FileName"].as<std::string>();
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config.Format = source["Format"].as<std::string>();
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if (auto _ = source["RelativeToConfigFile"])
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{
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auto __ = _.as<bool>();
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config.ExtraParameters["RelativeToConfigFile"] = __;
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if (__)
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config.FileName = std::filesystem::path(filename).parent_path() / config.FileName;
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}
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};
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read_file_config(node["AtomPositionInputFile"], AtomPositionInputFile);
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if (!std::set<std::string>{"yaml"}.contains(AtomPositionInputFile.Format))
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throw std::runtime_error(fmt::format
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("Unknown AtomPositionInputFile.Format: {}, should be \"yaml\".", AtomPositionInputFile.Format));
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read_file_config(node["QPointDataInputFile"], QPointDataInputFile);
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if (!std::set<std::string>{"yaml", "hdf5"}.contains(QPointDataInputFile.Format))
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throw std::runtime_error(fmt::format
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("Unknown QPointDataInputFile.Format: {}, should be \"yaml\" or \"hdf5\".", QPointDataInputFile.Format));
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if (auto value = node["QPointDataOutputFile"])
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{
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QPointDataOutputFile.resize(value.size());
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for (unsigned i = 0; i < value.size(); i++)
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{
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read_file_config(value[i], QPointDataOutputFile[i]);
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if
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(
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QPointDataOutputFile[i].ExtraParameters.contains("SameAsConfigFile")
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&& std::any_cast<bool>(QPointDataOutputFile[i].ExtraParameters["SameAsConfigFile"])
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)
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throw std::runtime_error("QPointDataOutputFile.SameAsConfigFile should not be set.");
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if
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(
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!std::set<std::string>{"yaml", "yaml-human-readable", "zpp"}
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.contains(QPointDataOutputFile[i].Format)
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)
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throw std::runtime_error(fmt::format
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(
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"Unknown QPointDataOutputFile[{}].Format: {}, should be \"yaml\", \"yaml-human-readable\" or \"zpp\".",
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i, QPointDataOutputFile[i].Format
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));
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}
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}
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}
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if (AtomPositionInputFile.Format == "yaml")
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{
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auto node = YAML::LoadFile(AtomPositionInputFile.FileName);
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std::vector<YAML::Node> points;
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if (auto _ = node["points"])
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points = _.as<std::vector<YAML::Node>>();
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else
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points = node["unit_cell"]["points"].as<std::vector<YAML::Node>>();
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auto atom_position_to_super_cell = Eigen::MatrixX3d(points.size(), 3);
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for (unsigned i = 0; i < points.size(); i++)
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for (unsigned j = 0; j < 3; j++)
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atom_position_to_super_cell(i, j) = points[i]["coordinates"][j].as<double>();
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auto super_cell = (SuperCellDeformation.value_or(Eigen::Matrix3d::Identity())
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* SuperCellMultiplier.cast<double>().asDiagonal() * PrimativeCell).eval();
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AtomPosition = atom_position_to_super_cell * super_cell;
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}
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if (QPointDataInputFile.Format == "yaml")
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{
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auto node = YAML::LoadFile(QPointDataInputFile.FileName);
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auto phonon = node["phonon"].as<std::vector<YAML::Node>>();
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QPointData.resize(phonon.size());
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for (unsigned i = 0; i < phonon.size(); i++)
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{
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for (unsigned j = 0; j < 3; j++)
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QPointData[i].QPoint(j) = phonon[i]["q-position"][j].as<double>();
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auto band = phonon[i]["band"].as<std::vector<YAML::Node>>();
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QPointData[i].ModeData.resize(band.size());
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for (unsigned j = 0; j < band.size(); j++)
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{
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QPointData[i].ModeData[j].Frequency = band[j]["frequency"].as<double>();
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auto eigenvector_vectors = band[j]["eigenvector"]
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.as<std::vector<std::vector<std::vector<double>>>>();
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Eigen::MatrixX3cd eigenvectors(AtomPosition.rows(), 3);
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for (unsigned k = 0; k < AtomPosition.rows(); k++)
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for (unsigned l = 0; l < 3; l++)
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eigenvectors(k, l)
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= eigenvector_vectors[k][l][0] + 1i * eigenvector_vectors[k][l][1];
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// 需要对读入的原子运动状态作相位转换, 使得它们与我们的约定一致(对超胞周期性重复)
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// 这里还要需要做归一化处理 (指将数据简单地作为向量处理的归一化)
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auto& AtomMovement = QPointData[i].ModeData[j].AtomMovement;
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// AtomMovement = eigenvectors.array().colwise() * (-2 * std::numbers::pi_v<double> * 1i
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// * (atom_position_to_super_cell * input.QPointData[i].QPoint)).array().exp();
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// AtomMovement /= AtomMovement.norm();
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// phonopy 似乎已经进行了相位的转换！为什么？
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AtomMovement = eigenvectors / eigenvectors.norm();
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}
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}
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}
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else if (QPointDataInputFile.Format == "hdf5")
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{
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HighFive::File file(QPointDataInputFile.FileName, HighFive::File::ReadOnly);
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auto size = file.getDataSet("/frequency").getDimensions();
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auto frequency = file.getDataSet("/frequency")
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.read<std::vector<std::vector<std::vector<double>>>>();
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auto eigenvector_vector = file.getDataSet("/eigenvector")
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.read<std::vector<std::vector<std::vector<std::vector<PhonopyComplex>>>>>();
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auto path = file.getDataSet("/path")
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.read<std::vector<std::vector<std::vector<double>>>>();
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QPointData.resize(size[0] * size[1]);
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for (unsigned i = 0; i < size[0]; i++)
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for (unsigned j = 0; j < size[1]; j++)
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{
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QPointData[i * size[1] + j].QPoint = Eigen::Vector3d(path[i][j].data());
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QPointData[i * size[1] + j].ModeData.resize(size[2]);
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for (unsigned k = 0; k < size[2]; k++)
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{
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QPointData[i * size[1] + j].ModeData[k].Frequency = frequency[i][j][k];
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Eigen::MatrixX3cd eigenvectors(AtomPosition.rows(), 3);
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for (unsigned l = 0; l < AtomPosition.rows(); l++)
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for (unsigned m = 0; m < 3; m++)
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eigenvectors(l, m)
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= eigenvector_vector[i][j][l * 3 + m][k].r + eigenvector_vector[i][j][l * 3 + m][k].i * 1i;
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QPointData[i * size[1] + j].ModeData[k].AtomMovement = eigenvectors / eigenvectors.norm();
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}
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}
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}
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}
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void UnfoldSolver::OutputType::write
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(decltype(InputType::QPointDataOutputFile) output_files) const
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{
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for (auto& output_file : output_files)
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write(output_file.FileName, output_file.Format);
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}
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void UnfoldSolver::OutputType::write(std::string filename, std::string format, unsigned percision) const
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{
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if (format == "yaml")
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std::ofstream(filename) << [&]
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{
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std::stringstream print;
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print << "QPointData:\n";
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for (auto& qpoint: QPointData)
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{
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print << fmt::format(" - QPoint: [ {1:.{0}f}, {2:.{0}f}, {3:.{0}f} ]\n",
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percision, qpoint.QPoint[0], qpoint.QPoint[1], qpoint.QPoint[2]);
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print << fmt::format(" Source: [ {1:.{0}f}, {2:.{0}f}, {3:.{0}f} ]\n",
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percision, qpoint.Source[0], qpoint.Source[1], qpoint.Source[2]);
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print << " ModeData:\n";
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for (auto& mode: qpoint.ModeData)
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print << fmt::format(" - {{ Frequency: {1:.{0}f}, Weight: {2:.{0}f} }}\n",
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percision, mode.Frequency, mode.Weight);
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}
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return print.str();
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}();
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else if (format == "yaml-human-readable")
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{
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std::remove_cvref_t<decltype(*this)> output;
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std::map<unsigned, std::vector<decltype(QPointData)::const_iterator>>
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meta_qpoint_to_sub_qpoint_iterators;
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for (auto it = QPointData.begin(); it != QPointData.end(); it++)
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meta_qpoint_to_sub_qpoint_iterators[it->SourceIndex_].push_back(it);
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for (auto [meta_qpoint_index, sub_qpoint_iterators] : meta_qpoint_to_sub_qpoint_iterators)
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for (auto& qpoint : sub_qpoint_iterators)
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{
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std::map<double, double> frequency_to_weight;
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for (unsigned i_of_mode = 0; i_of_mode < qpoint->ModeData.size(); i_of_mode++)
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{
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auto frequency = qpoint->ModeData[i_of_mode].Frequency;
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auto weight = qpoint->ModeData[i_of_mode].Weight;
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auto it_lower = frequency_to_weight.lower_bound(frequency - 0.1);
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auto it_upper = frequency_to_weight.upper_bound(frequency + 0.1);
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if (it_lower == it_upper)
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frequency_to_weight[frequency] = weight;
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else
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{
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auto frequency_sum = std::accumulate(it_lower, it_upper, 0.,
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[](const auto& a, const auto& b) { return a + b.first * b.second; });
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auto weight_sum = std::accumulate(it_lower, it_upper, 0.,
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[](const auto& a, const auto& b) { return a + b.second; });
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frequency_sum += frequency * weight;
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weight_sum += weight;
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frequency_to_weight.erase(it_lower, it_upper);
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frequency_to_weight[frequency_sum / weight_sum] = weight_sum;
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}
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}
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auto& _ = output.QPointData.emplace_back();
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_.QPoint = qpoint->QPoint;
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_.Source = qpoint->Source;
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_.SourceIndex_ = qpoint->SourceIndex_;
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for (auto [frequency, weight] : frequency_to_weight)
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if (weight > 0.1)
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{
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auto& __ = _.ModeData.emplace_back();
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__.Frequency = frequency;
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__.Weight = weight;
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}
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}
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output.write(filename, "yaml", 3);
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}
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else if (format == "zpp")
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{
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auto [data, out] = zpp::bits::data_out();
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out(*this).or_throw();
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static_assert(sizeof(char) == sizeof(std::byte));
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std::ofstream file(filename, std::ios::binary | std::ios::out);
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file.exceptions(std::ios::badbit | std::ios::failbit);
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file.write(reinterpret_cast<const char*>(data.data()), data.size());
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}
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}
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UnfoldSolver::UnfoldSolver(std::string config_file) : Input_([&]
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{
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std::clog << "Reading input file... " << std::flush;
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return config_file;
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}())
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{
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std::clog << "Done." << std::endl;
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}
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UnfoldSolver& UnfoldSolver::operator()()
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{
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if (!Basis_)
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{
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std::clog << "Constructing basis... " << std::flush;
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Basis_ = construct_basis
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(
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Input_.PrimativeCell, Input_.SuperCellMultiplier,
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Input_.PrimativeCellBasisNumber, Input_.AtomPosition
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);
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std::clog << "Done." << std::endl;
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}
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if (!Output_)
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{
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std::clog << "Calculating projection coefficient... " << std::flush;
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std::vector<std::reference_wrapper<const decltype
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(InputType::QPointDataType::ModeDataType::AtomMovement)>> mode_data;
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for (auto& qpoint : Input_.QPointData)
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for (auto& mode : qpoint.ModeData)
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mode_data.emplace_back(mode.AtomMovement);
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std::atomic<unsigned> number_of_finished_modes(0);
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std::thread print_thread([&]
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{
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unsigned n;
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while ((n = number_of_finished_modes) < mode_data.size())
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{
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std::osyncstream(std::cerr) << fmt::format("\rCalculating projection coefficient... ({}/{})",
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number_of_finished_modes, mode_data.size()) << std::flush;
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std::this_thread::sleep_for(100ms);
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number_of_finished_modes.wait(n);
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}
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});
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auto projection_coefficient = construct_projection_coefficient
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(*Basis_, mode_data, number_of_finished_modes);
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number_of_finished_modes = mode_data.size();
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print_thread.join();
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std::clog << "\rCalculating projection coefficient... Done." << std::endl;
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std::clog << "Constructing output... " << std::flush;
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std::vector<std::reference_wrapper<const decltype(InputType::QPointDataType::QPoint)>> qpoint;
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std::vector<std::vector<std::reference_wrapper<const
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decltype(InputType::QPointDataType::ModeDataType::Frequency)>>> frequency;
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for (auto& qpoint_data : Input_.QPointData)
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{
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qpoint.emplace_back(qpoint_data.QPoint);
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frequency.emplace_back();
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for (auto& mode_data : qpoint_data.ModeData)
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frequency.back().emplace_back(mode_data.Frequency);
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}
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Output_ = construct_output
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(
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Input_.PrimativeCell, Input_.SuperCellMultiplier,
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Input_.SuperCellDeformation, qpoint, frequency, projection_coefficient
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);
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std::clog << "Done." << std::endl;
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}
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std::clog << "Writing output... " << std::flush;
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Output_->write(Input_.QPointDataOutputFile);
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std::clog << "Done." << std::endl;
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return *this;
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}
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UnfoldSolver::BasisType UnfoldSolver::construct_basis
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(
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const decltype(InputType::PrimativeCell)& primative_cell,
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const decltype(InputType::SuperCellMultiplier)& super_cell_multiplier,
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const decltype(InputType::PrimativeCellBasisNumber)& primative_cell_basis_number,
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const decltype(InputType::AtomPosition)& atom_position
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)
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{
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BasisType basis(super_cell_multiplier.prod());
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// 每个 q 点对应的一组 sub qpoint。不同的 q 点所对应的 sub qpoint 是不一样的，但 sub qpoint 与 q 点的相对位置一致。
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// 这里 xyz_of_diff_of_sub_qpoint 即表示这个相对位置，单位为超胞的倒格矢
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for (auto [xyz_of_diff_of_sub_qpoint_by_reciprocal_modified_super_cell, i_of_sub_qpoint]
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: triplet_sequence(super_cell_multiplier))
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{
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basis[i_of_sub_qpoint].resize(primative_cell_basis_number.prod());
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for (auto [xyz_of_basis, i_of_basis] : triplet_sequence(primative_cell_basis_number))
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{
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// 计算 q 点的坐标, 单位为单胞的倒格矢
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auto diff_of_sub_qpoint_by_reciprocal_primative_cell = xyz_of_basis.cast<double>()
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+ super_cell_multiplier.cast<double>().cwiseInverse().asDiagonal()
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* xyz_of_diff_of_sub_qpoint_by_reciprocal_modified_super_cell.cast<double>();
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// 将 q 点坐标转换为埃^-1
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auto qpoint = (diff_of_sub_qpoint_by_reciprocal_primative_cell.transpose()
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* (primative_cell.transpose().inverse())).transpose();
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// 计算基矢
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basis[i_of_sub_qpoint][i_of_basis]
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= (2i * std::numbers::pi_v<double> * (atom_position * qpoint)).array().exp();
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}
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}
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return basis;
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}
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std::vector<std::vector<double>> UnfoldSolver::construct_projection_coefficient
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(
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const BasisType& basis,
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const std::vector<std::reference_wrapper<const decltype
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(InputType::QPointDataType::ModeDataType::AtomMovement)>>& mode_data,
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std::atomic<unsigned>& number_of_finished_modes
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)
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{
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// 第一层下标对应不同模式, 第二层下标对应这个模式在反折叠后的 q 点(sub qpoint)
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std::vector<std::vector<double>> projection_coefficient(mode_data.size());
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// 对每个模式并行
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std::transform
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(
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std::execution::par, mode_data.begin(), mode_data.end(), projection_coefficient.begin(),
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[&](const auto& mode_data)
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{
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// 这里, mode_data 和 projection_coefficient 均指对应于一个模式的数据
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std::vector<double> projection_coefficient(basis.size());
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for (unsigned i_of_sub_qpoint = 0; i_of_sub_qpoint < basis.size(); i_of_sub_qpoint++)
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// 对于 basis 中, 对应于单胞倒格子的部分, 以及对应于不同方向的部分, 分别求内积, 然后求模方和
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for (unsigned i_of_basis = 0; i_of_basis < basis[i_of_sub_qpoint].size(); i_of_basis++)
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projection_coefficient[i_of_sub_qpoint] +=
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(basis[i_of_sub_qpoint][i_of_basis].transpose().conjugate() * mode_data.get())
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.array().abs2().sum();
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// 如果是严格地将向量分解到一组完备的基矢上, 那么不需要对计算得到的权重再做归一化处理
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// 但这里并不是这样一个严格的概念. 因此对分解到各个 sub qpoint 上的权重做归一化处理
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auto sum = std::accumulate
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(projection_coefficient.begin(), projection_coefficient.end(), 0.);
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for (auto& _ : projection_coefficient)
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_ /= sum;
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number_of_finished_modes++;
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return projection_coefficient;
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}
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);
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return projection_coefficient;
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}
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UnfoldSolver::OutputType UnfoldSolver::construct_output
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(
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const decltype(InputType::PrimativeCell)& primative_cell,
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const decltype(InputType::SuperCellMultiplier)& super_cell_multiplier,
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const decltype(InputType::SuperCellDeformation)& super_cell_deformation,
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const std::vector<std::reference_wrapper<const decltype
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(InputType::QPointDataType::QPoint)>>& qpoint,
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const std::vector<std::vector<std::reference_wrapper<const decltype
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(InputType::QPointDataType::ModeDataType::Frequency)>>>& frequency,
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const ProjectionCoefficientType_& projection_coefficient
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)
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{
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OutputType output;
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for (unsigned i_of_qpoint = 0, num_of_mode_in_all_qpoint = 0; i_of_qpoint < qpoint.size(); i_of_qpoint++)
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{
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// 当 SuperCellDeformation 不是单位矩阵时, input.QPointData[i_of_qpoint].QPoint 不一定在 reciprocal_primative_cell 中
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// 需要首先将 q 点平移数个周期, 进入不包含 SuperCellDeformation 的超胞的倒格子中
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auto qpoint_by_reciprocal_modified_super_cell_in_modified_reciprocal_super_cell
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= !super_cell_deformation ? qpoint[i_of_qpoint].get() : [&]
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{
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auto current_qpoint = qpoint[i_of_qpoint].get();
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// 给一个 q 点打分
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// 计算这个 q 点以 modified_reciprocal_supre_cell 为单位的坐标, 依次考虑每个维度, 总分为每个维度之和.
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// 如果这个坐标大于 0 小于 1, 则打 0 分.
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// 如果这个坐标小于 0, 则打这个坐标的相反数分.
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// 如果这个坐标大于 1, 则打这个坐标减去 1 的分.
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auto score = [&](Eigen::Vector3d qpoint_by_reciprocal_super_cell)
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{
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// SuperCell = SuperCellDeformation * SuperCellMultiplier.asDiagonal() * PrimativeCell
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// ModifiedSuperCell = SuperCellMultiplier.asDiagonal() * PrimativeCell
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// ReciprocalSuperCell = SuperCell.inverse().transpose()
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// ReciprocalModifiedSuperCell = ModifiedSuperCell.inverse().transpose()
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// qpoint.transpose() = qpoint_by_reciprocal_super_cell.transpose() * ReciprocalSuperCell
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// qpoint.transpose() = qpoint_by_reciprocal_modified_super_cell.transpose() * ReciprocalModifiedSuperCell
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auto qpoint_by_reciprocal_modified_super_cell =
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(super_cell_deformation->inverse() * qpoint_by_reciprocal_super_cell).eval();
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double score = 0;
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for (unsigned i = 0; i < 3; i++)
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{
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auto coordinate = qpoint_by_reciprocal_modified_super_cell[i];
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if (coordinate < 0)
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score -= coordinate;
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else if (coordinate > 1)
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score += coordinate - 1;
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}
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return score;
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};
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while (score(current_qpoint) > 0)
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{
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double min_score = std::numeric_limits<double>::max();
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Eigen::Vector3d min_score_qpoint;
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for (int x = -1; x <= 1; x++)
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for (int y = -1; y <= 1; y++)
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|
for (int z = -1; z <= 1; z++)
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|
{
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auto this_qpoint = current_qpoint
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+ Eigen::Matrix<int, 3, 1>{{x}, {y}, {z}}.cast<double>();
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|
auto this_score = score(this_qpoint);
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|
if (this_score < min_score)
|
|
{
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|
min_score = this_score;
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|
min_score_qpoint = this_qpoint;
|
|
}
|
|
}
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|
current_qpoint = min_score_qpoint;
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|
}
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|
return super_cell_deformation->inverse() * current_qpoint;
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|
}();
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|
for (auto [xyz_of_diff_of_sub_qpoint_by_reciprocal_modified_super_cell, i_of_sub_qpoint]
|
|
: triplet_sequence(super_cell_multiplier))
|
|
{
|
|
auto& _ = output.QPointData.emplace_back();
|
|
auto reciprocal_modified_super_cell =
|
|
(super_cell_multiplier.cast<double>().asDiagonal() * primative_cell).inverse().transpose();
|
|
// sub qpoint 的坐标，单位为埃^-1
|
|
auto sub_qpoint = ((xyz_of_diff_of_sub_qpoint_by_reciprocal_modified_super_cell.cast<double>()
|
|
+ qpoint_by_reciprocal_modified_super_cell_in_modified_reciprocal_super_cell)
|
|
.transpose() * reciprocal_modified_super_cell).transpose();
|
|
// 将坐标转换为相对于单胞的倒格矢的坐标并写入
|
|
// 由 sub_qpoint.transpose() = sub_qpoint_by_reciprocal_primative_cell.transpose()
|
|
// * PrimativeCell.transpose().inverse()
|
|
// 得到 sub_qpoint_by_reciprocal_primative_cell = PrimativeCell * sub_qpoint
|
|
_.QPoint = primative_cell * sub_qpoint;
|
|
_.Source = qpoint[i_of_qpoint];
|
|
_.SourceIndex_ = i_of_qpoint;
|
|
for (unsigned i_of_mode = 0; i_of_mode < frequency[i_of_qpoint].size(); i_of_mode++, num_of_mode_in_all_qpoint++)
|
|
{
|
|
auto& __ = _.ModeData.emplace_back();
|
|
__.Frequency = frequency[i_of_qpoint][i_of_mode];
|
|
__.Weight = projection_coefficient[num_of_mode_in_all_qpoint][i_of_sub_qpoint];
|
|
}
|
|
}
|
|
}
|
|
return output;
|
|
}
|
|
}
|
|
|
|
// inline Output::Output(std::string filename)
|
|
// {
|
|
// auto input = std::ifstream(filename, std::ios::binary | std::ios::in);
|
|
// input.exceptions(std::ios::badbit | std::ios::failbit);
|
|
// std::vector<std::byte> data;
|
|
// {
|
|
// std::vector<char> string(std::istreambuf_iterator<char>(input), {});
|
|
// data.assign
|
|
// (
|
|
// reinterpret_cast<std::byte*>(string.data()),
|
|
// reinterpret_cast<std::byte*>(string.data() + string.size())
|
|
// );
|
|
// }
|
|
// auto in = zpp::bits::in(data);
|
|
// in(*this).or_throw();
|
|
// }
|
|
|