diff --git a/.gitignore b/.gitignore index fa41609..9ae3fb0 100644 --- a/.gitignore +++ b/.gitignore @@ -12,3 +12,7 @@ test/* !test/14.2.2.5.plot.yaml !test/14.2.4.4.unfold.yaml !test/14.2.4.4.plot.yaml +!test/14.2.5.5.unfold.yaml +!test/14.2.5.5.plot.yaml +!test/14.2.6.4.unfold.yaml +!test/14.2.6.4.plot.yaml diff --git a/include/ufo/fold.hpp b/include/ufo/fold.hpp index 4179737..7da8e38 100644 --- a/include/ufo/fold.hpp +++ b/include/ufo/fold.hpp @@ -8,7 +8,6 @@ namespace ufo public: struct InputType { - Eigen::Matrix3d PrimativeCell; Eigen::Vector SuperCellMultiplier; std::optional> SuperCellDeformation; std::vector Qpoints; @@ -18,7 +17,7 @@ namespace ufo }; struct OutputType { - std::vector QPoints; + std::vector Qpoints; void write(std::string filename) const; }; protected: @@ -27,7 +26,12 @@ namespace ufo public: FoldSolver(std::string config_file); FoldSolver& operator()() override; - static Eigen::Vector3d fold(Eigen::Vector3d qpoint, Eigen::Vector super_cell_multiplier, - std::optional> super_cell_deformation); + // return value: QpointInReciprocalSuperCellByReciprocalSuperCell + static Eigen::Vector3d fold + ( + Eigen::Vector3d qpoint_in_reciprocal_primitive_cell_by_reciprocal_primitive_cell, + Eigen::Vector super_cell_multiplier, + std::optional> super_cell_deformation + ); }; } \ No newline at end of file diff --git a/include/ufo/plot.hpp b/include/ufo/plot.hpp index 33012fd..3117322 100644 --- a/include/ufo/plot.hpp +++ b/include/ufo/plot.hpp @@ -36,17 +36,17 @@ namespace ufo PlotSolver& operator()() override; // 根据 q 点路径, 搜索要使用的 q 点 - static std::vector> search_qpoints + static std::vector> search_qpoints ( const std::pair& path, - const decltype(InputType::SourceType::QPointData)& available_qpoints, + const decltype(InputType::SourceType::QpointData)& available_qpoints, double threshold, bool exclude_endpoint = false ); // 根据搜索到的 q 点, 计算每个点的数值 static std::vector> calculate_values ( const std::vector>& path, - const std::vector>>& qpoints, + const std::vector>>& qpoints, const decltype(InputType::FigureConfigType::Resolution)& resolution, const decltype(InputType::FigureConfigType::Range)& range ); diff --git a/include/ufo/unfold.hpp b/include/ufo/unfold.hpp index edf7d84..4a75d58 100644 --- a/include/ufo/unfold.hpp +++ b/include/ufo/unfold.hpp @@ -41,16 +41,16 @@ namespace ufo // 从哪个文件读入 AtomPosition, 以及这个文件的格式, 格式可选值包括 "yaml" InputOutputFile AtomPositionInputFile; - // 从哪个文件读入 QPointData, 以及这个文件的格式, 格式可选值包括 "yaml" 和 "hdf5" - InputOutputFile QPointDataInputFile; + // 从哪个文件读入 QpointData, 以及这个文件的格式, 格式可选值包括 "yaml" 和 "hdf5" + InputOutputFile QpointDataInputFile; // 超胞中原子的坐标，每行表示一个原子的坐标，单位为埃 Eigen::MatrixX3d AtomPosition; // 关于各个 Q 点的数据 - struct QPointDataType + struct QpointDataType { // Q 点的坐标，单位为超胞的倒格矢 - Eigen::Vector3d QPoint; + Eigen::Vector3d Qpoint; // 关于这个 Q 点上各个模式的数据 struct ModeDataType @@ -65,14 +65,14 @@ namespace ufo }; std::vector ModeData; }; - std::vector QPointData; + std::vector QpointData; // 输出到哪些文件, 以及使用怎样的格式, 格式可选值包括: // yaml: 使用 yaml 格式输出 // yaml-human-readable: 使用 yaml 格式输出, 但是输出的结果更适合人类阅读, // 包括合并相近的模式, 去除权重过小的模式, 限制输出的小数位数. // zpp: 使用 zpp-bits 序列化, 可以直接被 plot.cpp 读取 - std::vector QPointDataOutputFile; + std::vector QpointDataOutputFile; // 从文件中读取输入 (包括一个较小的配置文件, 和一个 hdf5 或者一个 yaml 文件), 文件中应当包含: // 单胞的格矢: PrimativeCell 单位为埃 直接从 phonopy 的输出中复制 @@ -90,10 +90,10 @@ namespace ufo struct OutputType { // 关于各个 Q 点的数据 - struct QPointDataType + struct QpointDataType { // Q 点的坐标，单位为单胞的倒格矢 - Eigen::Vector3d QPoint; + Eigen::Vector3d Qpoint; // 来源于哪个 Q 点, 单位为超胞的倒格矢 Eigen::Vector3d Source; @@ -109,9 +109,9 @@ namespace ufo }; std::vector ModeData; }; - std::vector QPointData; + std::vector QpointData; - void write(decltype(InputType::QPointDataOutputFile) output_files) const; + void write(decltype(InputType::QpointDataOutputFile) output_files) const; void write(std::string filename, std::string format, unsigned percision = 10) const; using serialize = zpp::bits::members<1>; @@ -153,7 +153,7 @@ namespace ufo ( const BasisType& basis, const std::vector>& mode_data, + (InputType::QpointDataType::ModeDataType::AtomMovement)>>& mode_data, std::atomic& number_of_finished_modes ); @@ -162,9 +162,9 @@ namespace ufo const decltype(InputType::SuperCellMultiplier)& super_cell_multiplier, const decltype(InputType::SuperCellDeformation)& super_cell_deformation, const std::vector>& qpoint, + (InputType::QpointDataType::Qpoint)>>& qpoint, const std::vector>>& frequency, + (InputType::QpointDataType::ModeDataType::Frequency)>>>& frequency, const ProjectionCoefficientType_& projection_coefficient ); }; diff --git a/src/fold.cpp b/src/fold.cpp index 8f30e82..bb6958a 100644 --- a/src/fold.cpp +++ b/src/fold.cpp @@ -5,9 +5,6 @@ namespace ufo FoldSolver::InputType::InputType(std::string config_file) { auto input = YAML::LoadFile(config_file); - for (unsigned i = 0; i < 3; i++) - for (unsigned j = 0; j < 3; j++) - PrimativeCell(i, j) = input["PrimativeCell"][i][j].as(); for (unsigned i = 0; i < 3; i++) SuperCellMultiplier(i) = input["SuperCellMultiplier"][i].as(); if (input["SuperCellDeformation"]) @@ -27,8 +24,8 @@ namespace ufo std::ofstream(filename) << [&] { std::stringstream print; - print << "QPoints:\n"; - for (auto& qpoint : QPoints) + print << "Qpoints:\n"; + for (auto& qpoint : Qpoints) print << fmt::format(" - [ {:.8f}, {:.8f}, {:.8f} ]\n", qpoint(0), qpoint(1), qpoint(2)); return print.str(); }(); @@ -41,7 +38,7 @@ namespace ufo { Output_.emplace(); for (auto& qpoint : Input_.Qpoints) - Output_->QPoints.push_back(fold + Output_->Qpoints.push_back(fold ( qpoint, Input_.SuperCellMultiplier, Input_.SuperCellDeformation @@ -53,13 +50,15 @@ namespace ufo Eigen::Vector3d FoldSolver::fold ( - Eigen::Vector3d qpoint, Eigen::Vector super_cell_multiplier, + Eigen::Vector3d qpoint_in_reciprocal_primitive_cell_by_reciprocal_primitive_cell, + Eigen::Vector super_cell_multiplier, std::optional> super_cell_deformation ) { - // 首先需要将 q 点转移到超胞的倒格子中 + // 首先需要将 q 点转移到 ModifiedSuperCell 的倒格子中 // 将 q 点坐标扩大, 然后取小数部分, 就可以了 - auto qpoint_by_reciprocal_modified_super_cell = super_cell_multiplier.cast().asDiagonal() * qpoint; + auto qpoint_by_reciprocal_modified_super_cell = super_cell_multiplier.cast().asDiagonal() + * qpoint_in_reciprocal_primitive_cell_by_reciprocal_primitive_cell; auto qpoint_in_reciprocal_modified_super_cell_by_reciprocal_modified_super_cell = (qpoint_by_reciprocal_modified_super_cell.array() - qpoint_by_reciprocal_modified_super_cell.array().floor()) .matrix(); diff --git a/src/plot.cpp b/src/plot.cpp index 3a28437..c1bf9fd 100644 --- a/src/plot.cpp +++ b/src/plot.cpp @@ -58,7 +58,7 @@ namespace ufo for (auto& figure : Input_.Figures) { // 外层表示不同的线段的端点，内层表示这个线段上的 q 点 - std::vector>> qpoints; + std::vector>> qpoints; std::vector> lines; for (auto& path : figure.Qpoints) for (unsigned i = 0; i < path.size() - 1; i++) @@ -66,7 +66,7 @@ namespace ufo lines.emplace_back(path[i], path[i + 1]); qpoints.push_back(search_qpoints ( - lines.back(), Input_.Source.QPointData, + lines.back(), Input_.Source.QpointData, 0.001, i != path.size() - 2 )); } @@ -76,27 +76,27 @@ namespace ufo return *this; } - std::vector> PlotSolver::search_qpoints + std::vector> PlotSolver::search_qpoints ( const std::pair& path, - const decltype(InputType::SourceType::QPointData)& available_qpoints, + const decltype(InputType::SourceType::QpointData)& available_qpoints, double threshold, bool exclude_endpoint ) { - std::multimap> selected_qpoints; + std::multimap> selected_qpoints; // 对于 output 中的每一个点, 检查这个点是否在路径上. 如果在, 把它加入到 selected_qpoints 中 for (auto& qpoint : available_qpoints) { // 计算三点围成的三角形的面积的两倍 - auto area = (path.second - path.first).cross(qpoint.QPoint - path.first).norm(); + auto area = (path.second - path.first).cross(qpoint.Qpoint - path.first).norm(); // 计算这个点到前两个点所在直线的距离 auto distance = area / (path.second - path.first).norm(); // 如果这个点到前两个点所在直线的距离小于阈值, 则认为这个点在路径上 if (distance < threshold) { // 计算这个点到前两个点的距离, 两个距离都应该小于两点之间的距离 - auto distance1 = (qpoint.QPoint - path.first).norm(); - auto distance2 = (qpoint.QPoint - path.second).norm(); + auto distance1 = (qpoint.Qpoint - path.first).norm(); + auto distance2 = (qpoint.Qpoint - path.second).norm(); auto distance3 = (path.second - path.first).norm(); if (distance1 < distance3 + threshold && distance2 < distance3 + threshold) // 如果这个点不在终点处, 或者不排除终点, 则加入 @@ -117,7 +117,7 @@ namespace ufo } if (selected_qpoints.empty()) throw std::runtime_error("No q points found"); - std::vector> result; + std::vector> result; for (auto& qpoint : selected_qpoints) result.push_back(qpoint.second); return result; @@ -126,18 +126,18 @@ namespace ufo std::vector> PlotSolver::calculate_values ( const std::vector>& path, - const std::vector>>& qpoints, + const std::vector>>& qpoints, const decltype(InputType::FigureConfigType::Resolution)& resolution, const decltype(InputType::FigureConfigType::Range)& range ) { // 整理输入 - std::map> qpoints_with_distance; + std::map> qpoints_with_distance; double total_distance = 0; for (unsigned i = 0; i < path.size(); i++) { for (auto& _ : qpoints[i]) - qpoints_with_distance.emplace(total_distance + (_.get().QPoint - path[i].first).norm(), _); + qpoints_with_distance.emplace(total_distance + (_.get().Qpoint - path[i].first).norm(), _); total_distance += (path[i].second - path[i].first).norm(); } @@ -145,8 +145,8 @@ namespace ufo std::vector> values; auto blend = [] ( - const UnfoldSolver::OutputType::QPointDataType& a, - const UnfoldSolver::OutputType::QPointDataType& b, + const UnfoldSolver::OutputType::QpointDataType& a, + const UnfoldSolver::OutputType::QpointDataType& b, double ratio, unsigned resolution, std::pair range ) -> std::vector { diff --git a/src/unfold.cpp b/src/unfold.cpp index 942ceea..4806351 100644 --- a/src/unfold.cpp +++ b/src/unfold.cpp @@ -52,32 +52,32 @@ namespace ufo if (!std::set{"yaml"}.contains(AtomPositionInputFile.Format)) throw std::runtime_error(fmt::format ("Unknown AtomPositionInputFile.Format: {}, should be \"yaml\".", AtomPositionInputFile.Format)); - read_file_config(node["QPointDataInputFile"], QPointDataInputFile); - if (!std::set{"yaml", "hdf5"}.contains(QPointDataInputFile.Format)) + read_file_config(node["QpointDataInputFile"], QpointDataInputFile); + if (!std::set{"yaml", "hdf5"}.contains(QpointDataInputFile.Format)) throw std::runtime_error(fmt::format - ("Unknown QPointDataInputFile.Format: {}, should be \"yaml\" or \"hdf5\".", QPointDataInputFile.Format)); - if (auto value = node["QPointDataOutputFile"]) + ("Unknown QpointDataInputFile.Format: {}, should be \"yaml\" or \"hdf5\".", QpointDataInputFile.Format)); + if (auto value = node["QpointDataOutputFile"]) { - QPointDataOutputFile.resize(value.size()); + QpointDataOutputFile.resize(value.size()); for (unsigned i = 0; i < value.size(); i++) { - read_file_config(value[i], QPointDataOutputFile[i]); + read_file_config(value[i], QpointDataOutputFile[i]); if ( - QPointDataOutputFile[i].ExtraParameters.contains("SameAsConfigFile") - && std::any_cast(QPointDataOutputFile[i].ExtraParameters["SameAsConfigFile"]) + QpointDataOutputFile[i].ExtraParameters.contains("SameAsConfigFile") + && std::any_cast(QpointDataOutputFile[i].ExtraParameters["SameAsConfigFile"]) ) - throw std::runtime_error("QPointDataOutputFile.SameAsConfigFile should not be set."); + throw std::runtime_error("QpointDataOutputFile.SameAsConfigFile should not be set."); if ( !std::set{"yaml", "yaml-human-readable", "zpp", "hdf5"} - .contains(QPointDataOutputFile[i].Format) + .contains(QpointDataOutputFile[i].Format) ) throw std::runtime_error(fmt::format ( - "Unknown QPointDataOutputFile[{}].Format: {}, should be " + "Unknown QpointDataOutputFile[{}].Format: {}, should be " "\"yaml\", \"yaml-human-readable\", \"zpp\" or \"hdf5\".", - i, QPointDataOutputFile[i].Format + i, QpointDataOutputFile[i].Format )); } } @@ -99,20 +99,20 @@ namespace ufo * SuperCellMultiplier.cast().asDiagonal() * PrimativeCell).eval(); AtomPosition = atom_position_to_super_cell * super_cell; } - if (QPointDataInputFile.Format == "yaml") + if (QpointDataInputFile.Format == "yaml") { - auto node = YAML::LoadFile(QPointDataInputFile.FileName); + auto node = YAML::LoadFile(QpointDataInputFile.FileName); auto phonon = node["phonon"].as>(); - QPointData.resize(phonon.size()); + QpointData.resize(phonon.size()); for (unsigned i = 0; i < phonon.size(); i++) { for (unsigned j = 0; j < 3; j++) - QPointData[i].QPoint(j) = phonon[i]["q-position"][j].as(); + QpointData[i].Qpoint(j) = phonon[i]["q-position"][j].as(); auto band = phonon[i]["band"].as>(); - QPointData[i].ModeData.resize(band.size()); + QpointData[i].ModeData.resize(band.size()); for (unsigned j = 0; j < band.size(); j++) { - QPointData[i].ModeData[j].Frequency = band[j]["frequency"].as(); + QpointData[i].ModeData[j].Frequency = band[j]["frequency"].as(); auto eigenvector_vectors = band[j]["eigenvector"] .as>>>(); Eigen::MatrixX3cd eigenvectors(AtomPosition.rows(), 3); @@ -122,18 +122,18 @@ namespace ufo = eigenvector_vectors[k][l][0] + 1i * eigenvector_vectors[k][l][1]; // 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) // 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) - auto& AtomMovement = QPointData[i].ModeData[j].AtomMovement; + auto& AtomMovement = QpointData[i].ModeData[j].AtomMovement; // AtomMovement = eigenvectors.array().colwise() * (-2 * std::numbers::pi_v * 1i - // * (atom_position_to_super_cell * input.QPointData[i].QPoint)).array().exp(); + // * (atom_position_to_super_cell * input.QpointData[i].Qpoint)).array().exp(); // AtomMovement /= AtomMovement.norm(); // phonopy 似乎已经进行了相位的转换！为什么？ AtomMovement = eigenvectors / eigenvectors.norm(); } } } - else if (QPointDataInputFile.Format == "hdf5") + else if (QpointDataInputFile.Format == "hdf5") { - HighFive::File file(QPointDataInputFile.FileName, HighFive::File::ReadOnly); + HighFive::File file(QpointDataInputFile.FileName, HighFive::File::ReadOnly); auto size = file.getDataSet("/frequency").getDimensions(); auto frequency = file.getDataSet("/frequency") .read>>>(); @@ -141,28 +141,28 @@ namespace ufo .read>>>>(); auto path = file.getDataSet("/path") .read>>>(); - QPointData.resize(size[0] * size[1]); + QpointData.resize(size[0] * size[1]); for (unsigned i = 0; i < size[0]; i++) for (unsigned j = 0; j < size[1]; j++) { - QPointData[i * size[1] + j].QPoint = Eigen::Vector3d(path[i][j].data()); - QPointData[i * size[1] + j].ModeData.resize(size[2]); + QpointData[i * size[1] + j].Qpoint = Eigen::Vector3d(path[i][j].data()); + QpointData[i * size[1] + j].ModeData.resize(size[2]); for (unsigned k = 0; k < size[2]; k++) { - QPointData[i * size[1] + j].ModeData[k].Frequency = frequency[i][j][k]; + QpointData[i * size[1] + j].ModeData[k].Frequency = frequency[i][j][k]; Eigen::MatrixX3cd eigenvectors(AtomPosition.rows(), 3); for (unsigned l = 0; l < AtomPosition.rows(); l++) for (unsigned m = 0; m < 3; m++) eigenvectors(l, m) = eigenvector_vector[i][j][l * 3 + m][k].r + eigenvector_vector[i][j][l * 3 + m][k].i * 1i; - QPointData[i * size[1] + j].ModeData[k].AtomMovement = eigenvectors / eigenvectors.norm(); + QpointData[i * size[1] + j].ModeData[k].AtomMovement = eigenvectors / eigenvectors.norm(); } } } } void UnfoldSolver::OutputType::write - (decltype(InputType::QPointDataOutputFile) output_files) const + (decltype(InputType::QpointDataOutputFile) output_files) const { for (auto& output_file : output_files) write(output_file.FileName, output_file.Format); @@ -173,11 +173,11 @@ namespace ufo std::ofstream(filename) << [&] { std::stringstream print; - print << "QPointData:\n"; - for (auto& qpoint: QPointData) + print << "QpointData:\n"; + for (auto& qpoint: QpointData) { - print << fmt::format(" - QPoint: [ {1:.{0}f}, {2:.{0}f}, {3:.{0}f} ]\n", - percision, qpoint.QPoint[0], qpoint.QPoint[1], qpoint.QPoint[2]); + print << fmt::format(" - Qpoint: [ {1:.{0}f}, {2:.{0}f}, {3:.{0}f} ]\n", + percision, qpoint.Qpoint[0], qpoint.Qpoint[1], qpoint.Qpoint[2]); print << fmt::format(" Source: [ {1:.{0}f}, {2:.{0}f}, {3:.{0}f} ]\n", percision, qpoint.Source[0], qpoint.Source[1], qpoint.Source[2]); print << " ModeData:\n"; @@ -190,9 +190,9 @@ namespace ufo else if (format == "yaml-human-readable") { std::remove_cvref_t output; - std::map> + std::map> meta_qpoint_to_sub_qpoint_iterators; - for (auto it = QPointData.begin(); it != QPointData.end(); it++) + for (auto it = QpointData.begin(); it != QpointData.end(); it++) meta_qpoint_to_sub_qpoint_iterators[it->SourceIndex_].push_back(it); for (auto [meta_qpoint_index, sub_qpoint_iterators] : meta_qpoint_to_sub_qpoint_iterators) for (auto& qpoint : sub_qpoint_iterators) @@ -218,8 +218,8 @@ namespace ufo frequency_to_weight[frequency_sum / weight_sum] = weight_sum; } } - auto& _ = output.QPointData.emplace_back(); - _.QPoint = qpoint->QPoint; + auto& _ = output.QpointData.emplace_back(); + _.Qpoint = qpoint->Qpoint; _.Source = qpoint->Source; _.SourceIndex_ = qpoint->SourceIndex_; for (auto [frequency, weight] : frequency_to_weight) @@ -247,9 +247,9 @@ namespace ufo std::vector> Source; std::vector> Frequency; std::vector> Weight; - for (auto& qpoint : QPointData) + for (auto& qpoint : QpointData) { - Qpoint.emplace_back(qpoint.QPoint.data(), qpoint.QPoint.data() + 3); + Qpoint.emplace_back(qpoint.Qpoint.data(), qpoint.Qpoint.data() + 3); Source.emplace_back(qpoint.Source.data(), qpoint.Source.data() + 3); Frequency.emplace_back(); Weight.emplace_back(); @@ -262,7 +262,7 @@ namespace ufo HighFive::File file(filename, HighFive::File::ReadWrite | HighFive::File::Create | HighFive::File::Truncate); - file.createDataSet("QPoint", + file.createDataSet("Qpoint", HighFive::DataSpace::From(Qpoint)).write(Qpoint); file.createDataSet("Source", HighFive::DataSpace::From(Source)).write(Source); @@ -298,8 +298,8 @@ namespace ufo { std::clog << "Calculating projection coefficient... " << std::flush; std::vector> mode_data; - for (auto& qpoint : Input_.QPointData) + (InputType::QpointDataType::ModeDataType::AtomMovement)>> mode_data; + for (auto& qpoint : Input_.QpointData) for (auto& mode : qpoint.ModeData) mode_data.emplace_back(mode.AtomMovement); std::atomic number_of_finished_modes(0); @@ -321,12 +321,12 @@ namespace ufo std::clog << "\33[2K\rCalculating projection coefficient... Done." << std::endl; std::clog << "Constructing output... " << std::flush; - std::vector> qpoint; + std::vector> qpoint; std::vector>> frequency; - for (auto& qpoint_data : Input_.QPointData) + decltype(InputType::QpointDataType::ModeDataType::Frequency)>>> frequency; + for (auto& qpoint_data : Input_.QpointData) { - qpoint.emplace_back(qpoint_data.QPoint); + qpoint.emplace_back(qpoint_data.Qpoint); frequency.emplace_back(); for (auto& mode_data : qpoint_data.ModeData) frequency.back().emplace_back(mode_data.Frequency); @@ -339,7 +339,7 @@ namespace ufo std::clog << "Done." << std::endl; } std::clog << "Writing output... " << std::flush; - Output_->write(Input_.QPointDataOutputFile); + Output_->write(Input_.QpointDataOutputFile); std::clog << "Done." << std::endl; return *this; } @@ -380,7 +380,7 @@ namespace ufo ( const BasisType& basis, const std::vector>& mode_data, + (InputType::QpointDataType::ModeDataType::AtomMovement)>>& mode_data, std::atomic& number_of_finished_modes ) { @@ -418,16 +418,16 @@ namespace ufo const decltype(InputType::SuperCellMultiplier)& super_cell_multiplier, const decltype(InputType::SuperCellDeformation)& super_cell_deformation, const std::vector>& qpoint, + (InputType::QpointDataType::Qpoint)>>& qpoint, const std::vector>>& frequency, + (InputType::QpointDataType::ModeDataType::Frequency)>>>& frequency, const ProjectionCoefficientType_& projection_coefficient ) { OutputType output; for (unsigned i_of_qpoint = 0, num_of_mode_manipulated = 0; i_of_qpoint < qpoint.size(); i_of_qpoint++) { - // 当 SuperCellDeformation 不是单位矩阵时, input.QPointData[i_of_qpoint].QPoint 不一定在 reciprocal_primative_cell 中 + // 当 SuperCellDeformation 不是单位矩阵时, input.QpointData[i_of_qpoint].Qpoint 不一定在 reciprocal_primative_cell 中 // 需要首先将 q 点平移数个周期, 进入不包含 SuperCellDeformation 的超胞 (称为 ModifiedSupreCell) 的倒格子中 auto qpoint_by_reciprocal_modified_super_cell_in_reciprocal_modified_super_cell = !super_cell_deformation ? qpoint[i_of_qpoint].get() : [&] @@ -483,7 +483,7 @@ namespace ufo 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& _ = output.QpointData.emplace_back(); /* SubQpointByReciprocalModifiedSuperCell = XyzOfDiffOfSubQpointByReciprocalModifiedSuperCell + QpointInReciprocalModifiedSuperCellByReciprocalModifiedSuperCell; @@ -497,7 +497,7 @@ namespace ufo (XyzOfDiffOfSubQpointByReciprocalModifiedSuperCell + QpointInReciprocalModifiedSuperCellByReciprocalModifiedSuperCell); */ - _.QPoint = super_cell_multiplier.cast().cwiseInverse().asDiagonal() + _.Qpoint = super_cell_multiplier.cast().cwiseInverse().asDiagonal() * (xyz_of_diff_of_sub_qpoint_by_reciprocal_modified_super_cell.cast() + qpoint_by_reciprocal_modified_super_cell_in_reciprocal_modified_super_cell); _.Source = qpoint[i_of_qpoint]; diff --git a/test/14.2.5.5.plot.yaml b/test/14.2.5.5.plot.yaml new file mode 100644 index 0000000..ad219e2 --- /dev/null +++ b/test/14.2.5.5.plot.yaml @@ -0,0 +1,14 @@ +PrimativeCell: +- [ 1.548010265167714, -2.681232429908652, 0.000000000000000 ] # a +- [ 1.548010265167714, 2.681232429908652, 0.000000000000000 ] # b +- [ 0.000000000000000, 0.000000000000000, 5.061224103556595 ] # c +SourceFilename: ./test/14.2.5.5.result.zpp +Figures: +- Qpoints: + - - [ 0, 0, 0 ] + - [ 0.5, 0, 0 ] + - [ 0.3333333, 0.3333333, 0 ] + - [ 0, 0, 0 ] + Resolution: [ 1024, 400 ] + Range: [ -5, 35 ] + Filename: ./test/14.2.5.5.png diff --git a/test/14.2.5.5.unfold.yaml b/test/14.2.5.5.unfold.yaml new file mode 100644 index 0000000..18e4824 --- /dev/null +++ b/test/14.2.5.5.unfold.yaml @@ -0,0 +1,18 @@ +PrimativeCell: +- [ 1.548010265167714, -2.681232429908652, 0.000000000000000 ] # a +- [ 1.548010265167714, 2.681232429908652, 0.000000000000000 ] # b +- [ 0.000000000000000, 0.000000000000000, 5.061224103556595 ] # c +SuperCellMultiplier: [ 1, 2, 1 ] +SuperCellDeformation: +- [ 1, 0, 0] +- [ 1, 1, 0] +- [ 0, 0, 1] +PrimativeCellBasisNumber: [ 8, 8, 8 ] +AtomPositionInputFile: + FileName: "/home/chn/Documents/lammps-SiC/14/14.2/14.2.5/14.2.5.5/phonopy.yaml" + Format: "yaml" +QPointDataInputFile: { FileName: "/home/chn/Documents/lammps-SiC/14/14.2/14.2.5/14.2.5.5/band.hdf5", Format: "hdf5" } +QPointDataOutputFile: +- { FileName: "test/14.2.5.5.result.yaml", Format: "yaml" } +- { FileName: "test/14.2.5.5.result.human-readable.yaml", Format: "yaml-human-readable" } +- { FileName: "test/14.2.5.5.result.zpp", Format: "zpp" } diff --git a/test/14.2.6.4.plot.yaml b/test/14.2.6.4.plot.yaml new file mode 100644 index 0000000..80ff172 --- /dev/null +++ b/test/14.2.6.4.plot.yaml @@ -0,0 +1,14 @@ +PrimativeCell: +- [ 1.548010265167714, -2.681232429908652, 0.000000000000000 ] # a +- [ 1.548010265167714, 2.681232429908652, 0.000000000000000 ] # b +- [ 0.000000000000000, 0.000000000000000, 5.061224103556595 ] # c +SourceFilename: ./test/14.2.6.4.result.zpp +Figures: +- Qpoints: + - - [ 0, 0, 0 ] + - [ 0.5, 0, 0 ] + - [ 0.3333333, 0.3333333, 0 ] + - [ 0, 0, 0 ] + Resolution: [ 1024, 400 ] + Range: [ -5, 35 ] + Filename: ./test/14.2.6.4.png diff --git a/test/14.2.6.4.unfold.yaml b/test/14.2.6.4.unfold.yaml new file mode 100644 index 0000000..72f8793 --- /dev/null +++ b/test/14.2.6.4.unfold.yaml @@ -0,0 +1,18 @@ +PrimativeCell: +- [ 1.548010265167714, -2.681232429908652, 0.000000000000000 ] # a +- [ 1.548010265167714, 2.681232429908652, 0.000000000000000 ] # b +- [ 0.000000000000000, 0.000000000000000, 5.061224103556595 ] # c +SuperCellMultiplier: [ 4, 8, 1 ] +SuperCellDeformation: +- [ 1, 0, 0] +- [ 1, 1, 0] +- [ 0, 0, 1] +PrimativeCellBasisNumber: [ 8, 8, 8 ] +AtomPositionInputFile: + FileName: "/home/chn/Documents/lammps-SiC/14/14.2/14.2.6/14.2.6.4/phonopy.yaml" + Format: "yaml" +QPointDataInputFile: { FileName: "/home/chn/Documents/lammps-SiC/14/14.2/14.2.6/14.2.6.4/band.hdf5", Format: "hdf5" } +QPointDataOutputFile: +- { FileName: "test/14.2.6.4.result.yaml", Format: "yaml" } +- { FileName: "test/14.2.6.4.result.human-readable.yaml", Format: "yaml-human-readable" } +- { FileName: "test/14.2.6.4.result.zpp", Format: "zpp" }