修改拉曼输出文件布局

2024-12-22 15:53:11 +08:00
parent d584951fd7
commit f871c28768
31 changed files with 141 additions and 128 deletions
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -13,6 +13,7 @@ find_package(TBB REQUIRED)
 find_package(Matplot++ REQUIRED)
 find_package(biu REQUIRED)
 find_package(Threads REQUIRED)
+message("biu dir: ${biu_DIR}")

 add_executable(ufo src/fold.cpp src/unfold.cpp src/project-to-mode.cpp
  src/plot.cpp src/raman.cpp src/project-to-atom.cpp src/main.cpp)
@@ -42,11 +43,7 @@ add_test(NAME project-to-mode WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}/test/proje
  COMMAND ufo project-to-mode config.yaml)
 add_test(NAME raman-create-displacement WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}/test/raman-create-displacement
  COMMAND ufo raman-create-displacement config.yaml)
-set(OUTCAR_FILES)
-foreach(i RANGE 0 23)
-    list(APPEND OUTCAR_FILES job/${i}/OUTCAR)
-endforeach()
 add_test(NAME raman-extract WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}/test/raman-extract
-  COMMAND ufo raman-extract ${OUTCAR_FILES} job/origin/OUTCAR)
+  COMMAND ufo raman-extract .)
 add_test(NAME raman-apply-contribution WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}/test/raman-apply-contribution
  COMMAND ufo raman-apply-contribution config.yaml)
--- a/include/ufo.hpp
+++ b/include/ufo.hpp
@@ -99,6 +99,6 @@ namespace ufo
  void plot_band(std::string config_file);
  void plot_point(std::string config_file);
  void raman_create_displacement(std::string config_file);
-  void raman_extract(std::vector<std::string> files);
+  void raman_extract(std::string path);
  void raman_apply_contribution(std::string config_file);
 }
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -10,13 +10,7 @@ int main(int argc, const char** argv)
  else if (argv[1] == "project-to-atom"s) ufo::project_to_atom(argv[2]);
  else if (argv[1] == "project-to-mode"s) ufo::project_to_mode(argv[2]);
  else if (argv[1] == "raman-create-displacement"s) ufo::raman_create_displacement(argv[2]);
-  else if (argv[1] == "raman-extract"s) ufo::raman_extract
-  (
-    std::vector<const char*>(argv + 2, argv + argc)
-      | biu::toLvalue
-      | ranges::views::transform([](const char* arg) { return std::string(arg); })
-      | ranges::to_vector
-  );
+  else if (argv[1] == "raman-extract"s) ufo::raman_extract(argv[2]);
  else if (argv[1] == "raman-apply-contribution"s) ufo::raman_apply_contribution(argv[2]);
  else if (argv[1] == "plot-band"s) ufo::plot_band(argv[2]);
  else if (argv[1] == "plot-point"s) ufo::plot_point(argv[2]);
--- a/src/raman.cpp
+++ b/src/raman.cpp
@@ -1,18 +1,10 @@
-
 # include <ufo.hpp>

 namespace ufo
 {
  struct RamanData
  {
-    struct ModeType
-    {
-      std::size_t QpointIndex;
-      std::size_t ModeIndex;
-      double Ratio;
-      using serialize = zpp::bits::members<3>;
-    };
-    std::vector<ModeType> Mode;
+    std::map<std::pair<std::size_t, std::size_t>, double> ModeRatio;
    double MaxDisplacement;
    enum { Primative, Super } Cell;
    using serialize = zpp::bits::members<3>;
@@ -77,7 +69,6 @@ namespace ufo

    auto process = [&](auto& cell)
    {
-      std::size_t i_of_poscar = 0;
      auto mass = cell.AtomType
        | ranges::views::transform([&](auto&& atom)
          { return ranges::views::repeat_n(input.AtomMass[atom.first], atom.second); })
@@ -92,7 +83,7 @@ namespace ufo
          auto ratio = config.MaxDisplacement / atom_movement.rowwise().norm().maxCoeff();
          atom_movement *= ratio;
          // 输出
-          auto path = "{}/{}"_f(config.OutputPoscarDirectory, i_of_poscar);
+          auto path = "{}/{}/{}"_f(config.OutputPoscarDirectory, i_of_qpoint, i_of_mode);
          std::filesystem::create_directories(path);
          std::ofstream("{}/POSCAR"_f(path)) << generate_poscar
          (
@@ -100,9 +91,8 @@ namespace ufo
            cell.AtomPosition + atom_movement * cell.Cell.inverse(),
            cell.AtomType
          );
-          output.Mode.push_back({i_of_qpoint, i_of_mode, ratio});
+          output.ModeRatio[{i_of_qpoint, i_of_mode}] = ratio;
          log.debug("Write mode {} {} {}"_f(i_of_qpoint, i_of_mode, atom_movement.rowwise().norm().eval()));
-          i_of_poscar++;
        }
    };
    if (config.Cell == RamanData::Primative) process(input.Primative);
@@ -114,13 +104,12 @@ namespace ufo
    std::ofstream(config.OutputDataFile, std::ios::binary) << biu::serialize<char>(output);
  }

-  void raman_extract(std::vector<std::string> files)
+  void raman_extract(std::string path)
  {
-    biu::Logger::Guard log(files);
-    std::vector<Eigen::Matrix3d> electricity_tensors;
-
-    for (const auto& file : files)
+    biu::Logger::Guard log(path);
+    auto get_dielectric_tensor = [](std::filesystem::path file)
    {
+      biu::Logger::Guard log(file);
      auto in_stream = std::ifstream(file);
      std::string line;
      // search line containing: MACROSCOPIC STATIC DIELECTRIC TENSOR
@@ -131,28 +120,31 @@ namespace ufo
          log.debug("find in {}"_f(file));
          // skip 1 line
          std::getline(in_stream, line);
-          electricity_tensors.emplace_back();
+          Eigen::Matrix3d dielectric_tensor;
          for (std::size_t i = 0; i < 3; i++) for (std::size_t j = 0; j < 3; j++)
-            in_stream >> electricity_tensors.back()(i, j);
-          log.debug("read tensor {}"_f(electricity_tensors.back()));
-          break;
+            in_stream >> dielectric_tensor(i, j);
+          log.debug("read tensor {}"_f(dielectric_tensor));
+          return dielectric_tensor;
        }
      }
      // test if the file is read correctly
-      if (!in_stream) throw std::runtime_error("Error reading file: {}"_f(file));
-    }
-
-    // output the result
-    for (auto e: electricity_tensors) std::cout <<
-R"(- - [ {}, {}, {} ]
-  - [ {}, {}, {} ]
-  - [ {}, {}, {} ]
-)"_f
-      (
-        e(0, 0), e(0, 1), e(0, 2),
-        e(1, 0), e(1, 1), e(1, 2),
-        e(2, 0), e(2, 1), e(2, 2)
-      );
+      throw std::runtime_error("Error reading file: {}"_f(file));
+    };
+    auto search_path = [&](this auto self, std::size_t indent, std::string path) -> void
+    {
+      if (std::filesystem::exists(path + "/OUTCAR"))
+      {
+        auto e = get_dielectric_tensor(path + "/OUTCAR");
+        for (std::size_t i = 0; i < 3; i++) std::cout << "{}- [ {}, {}, {} ]\n"_f
+          (std::string(indent * 2, ' '), e(i, 0), e(i, 1), e(i, 2));
+      }
+      else for (auto entry : std::filesystem::directory_iterator(path)) if (entry.is_directory())
+      {
+        std::cout << "{}{}:\n"_f(std::string(indent * 2, ' '), entry.path().filename());
+        self(indent + 1, entry.path());
+      }
+    };
+    search_path(0, path);
  }

  void raman_apply_contribution(std::string config_file)
@@ -160,7 +152,7 @@ R"(- - [ {}, {}, {} ]
    struct Config
    {
      Eigen::Matrix3d OriginalSusceptibility;
-      std::vector<Eigen::Matrix3d> Susceptibility;
+      std::map<std::size_t, std::map<std::size_t, Eigen::Matrix3d>> Susceptibility;
      std::array<Eigen::Vector3d, 2> Polarization;
      std::string InputDataFile;
      std::string RamanInputDataFile;
@@ -177,17 +169,18 @@ R"(- - [ {}, {}, {} ]
    input.RamanPolarization = config.Polarization;
    auto process = [&](auto& cell)
    {
-      for (auto&& [i_of_mode, mode] : ranges::views::enumerate(raman_input.Mode))
+      for (auto&& [i, ratio] : raman_input.ModeRatio)
      {
-        auto&& _ = cell.Qpoint[mode.QpointIndex].Mode[mode.ModeIndex];
-        Eigen::Matrix3d raman_tensor = (config.Susceptibility[i_of_mode] - config.OriginalSusceptibility)
-          / mode.Ratio / raman_input.MaxDisplacement;
+        auto&& [i_of_qpoint, i_of_mode] = i;
+        auto&& _ = cell.Qpoint[i_of_qpoint].Mode[i_of_mode];
+        Eigen::Matrix3d raman_tensor = (config.Susceptibility[i_of_qpoint][i_of_mode] - config.OriginalSusceptibility)
+          / ratio / raman_input.MaxDisplacement;
        _.RamanTensor = raman_tensor | biu::fromEigen;
        _.WeightOnRaman = config.Polarization[0].transpose() * raman_tensor * config.Polarization[1];
        log.info("{}:{:.2f}:{}:{:.2f} {}"_f
        (
-          mode.QpointIndex, fmt::join(cell.Qpoint[mode.QpointIndex].Qpoint, ", "),
-          mode.ModeIndex, _.Frequency, *_.WeightOnRaman
+          i_of_qpoint, fmt::join(cell.Qpoint[i_of_qpoint].Qpoint, ", "),
+          i_of_mode, _.Frequency, *_.WeightOnRaman
        ));
      }
    };
--- a/test/raman-apply-contribution/config.yaml
+++ b/test/raman-apply-contribution/config.yaml
@@ -3,78 +3,107 @@ OriginalSusceptibility:
  - [ -3.4e-05, 7.002539, -2.4e-05 ]
  - [ -3e-06, -1.2e-05, 7.303458 ]
 Susceptibility:
-  - - [ 7.006379, -5e-06, -2e-06 ]
-    - [ -1.6e-05, 7.002547, -3e-05 ]
-    - [ -1.1e-05, -6e-06, 7.303627 ]
-  - - [ 7.007683, 5e-06, -5.3e-05 ]
-    - [ -0, 7.003913, 5e-06 ]
-    - [ -4e-05, 2.8e-05, 7.307388 ]
-  - - [ 7.018886, 1.8e-05, -5e-05 ]
-    - [ 2.7e-05, 7.015141, -3e-05 ]
-    - [ -5e-05, -1.7e-05, 7.307471 ]
-  - - [ 7.008862, 4.9e-05, -8.8e-05 ]
-    - [ 4.8e-05, 7.011172, -0.00086 ]
-    - [ -7.8e-05, -0.000845, 7.305162 ]
-  - - [ 7.015066, -4.3e-05, -0.000838 ]
-    - [ -4.5e-05, 7.005147, -2.9e-05 ]
-    - [ -0.000841, -9e-06, 7.305197 ]
-  - - [ 6.981143, 1.4e-05, -5.8e-05 ]
-    - [ 1.1e-05, 7.038724, 4.3e-05 ]
-    - [ -5.7e-05, 5.9e-05, 7.306158 ]
-  - - [ 7.014582, -0.027613, 1.6e-05 ]
-    - [ -0.027632, 7.005279, -7.1e-05 ]
-    - [ 4e-06, -6.7e-05, 7.306158 ]
-  - - [ 7.032791, 2.6e-05, -4.1e-05 ]
-    - [ 3.2e-05, 7.028882, -1.7e-05 ]
-    - [ -3.6e-05, -2e-06, 7.250185 ]
-  - - [ 7.007262, 1.3e-05, 1.3e-05 ]
-    - [ 9e-06, 7.013971, -5.9e-05 ]
-    - [ 7e-06, -4.6e-05, 7.305084 ]
-  - - [ 7.015281, 0.002384, -0 ]
-    - [ 0.002373, 7.005685, -4.4e-05 ]
-    - [ -4e-06, -2.8e-05, 7.3058 ]
-  - - [ 7.017108, 0.000122, -0.023832 ]
-    - [ 0.00013, 7.006382, -5.6e-05 ]
-    - [ -0.02384, -3.4e-05, 7.306937 ]
-  - - [ 7.006331, 7e-06, 1.6e-05 ]
-    - [ 2e-06, 7.002539, -1.9e-05 ]
-    - [ 1.7e-05, -3e-06, 7.303612 ]
-  - - [ 7.010335, 7.8e-05, -4.6e-05 ]
-    - [ 8.4e-05, 7.013598, 0.023664 ]
-    - [ -4.1e-05, 0.023683, 7.307236 ]
-  - - [ 7.008517, 2.9e-05, -1.6e-05 ]
-    - [ 2.5e-05, 7.004613, -9.3e-05 ]
-    - [ -1.8e-05, -7.1e-05, 7.324773 ]
-  - - [ 7.012128, 1e-05, 1.8e-05 ]
-    - [ 1e-06, 7.008401, -1e-05 ]
-    - [ 1.3e-05, -1e-06, 7.322152 ]
-  - - [ 7.010873, -5.9e-05, -3.8e-05 ]
-    - [ -7.8e-05, 7.007166, -3.6e-05 ]
-    - [ -4.3e-05, -2.5e-05, 7.319279 ]
-  - - [ 7.006421, -8e-06, -4e-05 ]
-    - [ -1.5e-05, 7.002682, -6.7e-05 ]
-    - [ -3.9e-05, -4.5e-05, 7.303477 ]
-  - - [ 7.007563, -0.001516, 5e-06 ]
-    - [ -0.001515, 7.00316, -5.5e-05 ]
-    - [ 0, -2.9e-05, 7.305665 ]
-  - - [ 7.005528, 1.8e-05, 4.1e-05 ]
-    - [ 1.2e-05, 7.005511, -3.7e-05 ]
-    - [ 3.7e-05, -1.5e-05, 7.30606 ]
-  - - [ 7.011048, 8e-05, -2.7e-05 ]
-    - [ 8.6e-05, 7.000001, 6e-06 ]
-    - [ -2.6e-05, 4.1e-05, 7.30555 ]
-  - - [ 7.00768, 0.004054, 1e-06 ]
-    - [ 0.004046, 7.003291, -4e-05 ]
-    - [ -1e-06, -1.7e-05, 7.305554 ]
-  - - [ 7.010948, -8.3e-05, -0.007718 ]
-    - [ -8e-05, 7.004814, -3.4e-05 ]
-    - [ -0.00772, -1.5e-05, 7.3101 ]
-  - - [ 7.008787, 7.2e-05, -1.8e-05 ]
-    - [ 7.4e-05, 7.007313, 0.007694 ]
-    - [ -2.4e-05, 0.007696, 7.310191 ]
-  - - [ 7.007532, -4.7e-05, -6e-06 ]
-    - [ -4.8e-05, 7.003828, -9e-06 ]
-    - [ -4e-06, 4e-06, 7.307759 ]
+  0:
+    0:
+      - [ 7.006379, -5e-06, -2e-06 ]
+      - [ -1.6e-05, 7.002547, -3e-05 ]
+      - [ -1.1e-05, -6e-06, 7.303627 ]
+    1:
+      - [ 7.006331, 7e-06, 1.6e-05 ]
+      - [ 2e-06, 7.002539, -1.9e-05 ]
+      - [ 1.7e-05, -3e-06, 7.303612 ]
+    10:
+      - [ 7.00768, 0.004054, 1e-06 ]
+      - [ 0.004046, 7.003291, -4e-05 ]
+      - [ -1e-06, -1.7e-05, 7.305554 ]
+    107:
+      - [ 7.007532, -4.7e-05, -6e-06 ]
+      - [ -4.8e-05, 7.003828, -9e-06 ]
+      - [ -4e-06, 4e-06, 7.307759 ]
+    115:
+      - [ 7.007683, 5e-06, -5.3e-05 ]
+      - [ -0, 7.003913, 5e-06 ]
+      - [ -4e-05, 2.8e-05, 7.307388 ]
+    15:
+      - [ 7.010948, -8.3e-05, -0.007718 ]
+      - [ -8e-05, 7.004814, -3.4e-05 ]
+      - [ -0.00772, -1.5e-05, 7.3101 ]
+    16:
+      - [ 7.008787, 7.2e-05, -1.8e-05 ]
+      - [ 7.4e-05, 7.007313, 0.007694 ]
+      - [ -2.4e-05, 0.007696, 7.310191 ]
+    185:
+      - [ 7.018886, 1.8e-05, -5e-05 ]
+      - [ 2.7e-05, 7.015141, -3e-05 ]
+      - [ -5e-05, -1.7e-05, 7.307471 ]
+    2:
+      - [ 7.006421, -8e-06, -4e-05 ]
+      - [ -1.5e-05, 7.002682, -6.7e-05 ]
+      - [ -3.9e-05, -4.5e-05, 7.303477 ]
+    251:
+      - [ 7.008862, 4.9e-05, -8.8e-05 ]
+      - [ 4.8e-05, 7.011172, -0.00086 ]
+      - [ -7.8e-05, -0.000845, 7.305162 ]
+    252:
+      - [ 7.015066, -4.3e-05, -0.000838 ]
+      - [ -4.5e-05, 7.005147, -2.9e-05 ]
+      - [ -0.000841, -9e-06, 7.305197 ]
+    281:
+      - [ 6.981143, 1.4e-05, -5.8e-05 ]
+      - [ 1.1e-05, 7.038724, 4.3e-05 ]
+      - [ -5.7e-05, 5.9e-05, 7.306158 ]
+    282:
+      - [ 7.014582, -0.027613, 1.6e-05 ]
+      - [ -0.027632, 7.005279, -7.1e-05 ]
+      - [ 4e-06, -6.7e-05, 7.306158 ]
+    287:
+      - [ 7.032791, 2.6e-05, -4.1e-05 ]
+      - [ 3.2e-05, 7.028882, -1.7e-05 ]
+      - [ -3.6e-05, -2e-06, 7.250185 ]
+    292:
+      - [ 7.007262, 1.3e-05, 1.3e-05 ]
+      - [ 9e-06, 7.013971, -5.9e-05 ]
+      - [ 7e-06, -4.6e-05, 7.305084 ]
+    293:
+      - [ 7.015281, 0.002384, -0 ]
+      - [ 0.002373, 7.005685, -4.4e-05 ]
+      - [ -4e-06, -2.8e-05, 7.3058 ]
+    311:
+      - [ 7.017108, 0.000122, -0.023832 ]
+      - [ 0.00013, 7.006382, -5.6e-05 ]
+      - [ -0.02384, -3.4e-05, 7.306937 ]
+    312:
+      - [ 7.010335, 7.8e-05, -4.6e-05 ]
+      - [ 8.4e-05, 7.013598, 0.023664 ]
+      - [ -4.1e-05, 0.023683, 7.307236 ]
+    327:
+      - [ 7.008517, 2.9e-05, -1.6e-05 ]
+      - [ 2.5e-05, 7.004613, -9.3e-05 ]
+      - [ -1.8e-05, -7.1e-05, 7.324773 ]
+    378:
+      - [ 7.012128, 1e-05, 1.8e-05 ]
+      - [ 1e-06, 7.008401, -1e-05 ]
+      - [ 1.3e-05, -1e-06, 7.322152 ]
+    379:
+      - [ 7.010873, -5.9e-05, -3.8e-05 ]
+      - [ -7.8e-05, 7.007166, -3.6e-05 ]
+      - [ -4.3e-05, -2.5e-05, 7.319279 ]
+    5:
+      - [ 7.007563, -0.001516, 5e-06 ]
+      - [ -0.001515, 7.00316, -5.5e-05 ]
+      - [ 0, -2.9e-05, 7.305665 ]
+    6:
+      - [ 7.005528, 1.8e-05, 4.1e-05 ]
+      - [ 1.2e-05, 7.005511, -3.7e-05 ]
+      - [ 3.7e-05, -1.5e-05, 7.30606 ]
+    9:
+      - [ 7.011048, 8e-05, -2.7e-05 ]
+      - [ 8.6e-05, 7.000001, 6e-06 ]
+      - [ -2.6e-05, 4.1e-05, 7.30555 ]
+origin:
+  - [ 7.006328, -3.3e-05, -2e-06 ]
+  - [ -3.4e-05, 7.002539, -2.4e-05 ]
+  - [ -3e-06, -1.2e-05, 7.303458 ]
 Polarization:
  - [ 0, 1, 0 ]
  - [ 0, 1, 0 ]
--- a/test/raman-extract/job/.gitattributes
+++ b/test/raman-extract/job/.gitattributes
--- a/test/raman-extract/job/0/OUTCAR
+++ b/test/raman-extract/job/0/OUTCAR
--- a/test/raman-extract/job/1/OUTCAR
+++ b/test/raman-extract/job/1/OUTCAR
--- a/test/raman-extract/job/6/OUTCAR
+++ b/test/raman-extract/job/6/OUTCAR
--- a/test/raman-extract/0/107/OUTCAR
+++ b/test/raman-extract/0/107/OUTCAR
--- a/test/raman-extract/job/10/OUTCAR
+++ b/test/raman-extract/job/10/OUTCAR
--- a/test/raman-extract/job/7/OUTCAR
+++ b/test/raman-extract/job/7/OUTCAR
--- a/test/raman-extract/job/8/OUTCAR
+++ b/test/raman-extract/job/8/OUTCAR
--- a/test/raman-extract/job/11/OUTCAR
+++ b/test/raman-extract/job/11/OUTCAR
--- a/test/raman-extract/job/2/OUTCAR
+++ b/test/raman-extract/job/2/OUTCAR
--- a/test/raman-extract/job/12/OUTCAR
+++ b/test/raman-extract/job/12/OUTCAR
--- a/test/raman-extract/job/13/OUTCAR
+++ b/test/raman-extract/job/13/OUTCAR
--- a/test/raman-extract/job/14/OUTCAR
+++ b/test/raman-extract/job/14/OUTCAR
--- a/test/raman-extract/job/15/OUTCAR
+++ b/test/raman-extract/job/15/OUTCAR
--- a/test/raman-extract/job/16/OUTCAR
+++ b/test/raman-extract/job/16/OUTCAR
--- a/test/raman-extract/job/17/OUTCAR
+++ b/test/raman-extract/job/17/OUTCAR
--- a/test/raman-extract/job/18/OUTCAR
+++ b/test/raman-extract/job/18/OUTCAR
--- a/test/raman-extract/job/19/OUTCAR
+++ b/test/raman-extract/job/19/OUTCAR
--- a/test/raman-extract/job/20/OUTCAR
+++ b/test/raman-extract/job/20/OUTCAR
--- a/test/raman-extract/job/21/OUTCAR
+++ b/test/raman-extract/job/21/OUTCAR
--- a/test/raman-extract/job/22/OUTCAR
+++ b/test/raman-extract/job/22/OUTCAR
--- a/test/raman-extract/job/23/OUTCAR
+++ b/test/raman-extract/job/23/OUTCAR
--- a/test/raman-extract/job/3/OUTCAR
+++ b/test/raman-extract/job/3/OUTCAR
--- a/test/raman-extract/job/4/OUTCAR
+++ b/test/raman-extract/job/4/OUTCAR
--- a/test/raman-extract/job/5/OUTCAR
+++ b/test/raman-extract/job/5/OUTCAR
--- a/test/raman-extract/job/origin/OUTCAR
+++ b/test/raman-extract/job/origin/OUTCAR