fix raman, add test

CMakeLists.txt

@@ -40,3 +40,13 @@ add_test(NAME zpp-to-yaml WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}/test/zpp-to-ya
   COMMAND sh -c "${CMAKE_BINARY_DIR}/ufo zpp-to-yaml < data.zpp > data.yaml")
 add_test(NAME project-to-mode WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}/test/project-to-mode
   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)
+add_test(NAME raman-apply-contribution WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}/test/raman-apply-contribution
+  COMMAND ufo raman-apply-contribution config.yaml)

src/raman.cpp

@@ -24,7 +24,7 @@ namespace ufo
     {
       // 要计算的是原胞还是超胞
       decltype(RamanData::Cell) Cell;
-      // 要计算的模式，总是假定是 gamma 点的模式
+      // 要计算哪个 q 点的哪些模式，总是假定是 gamma 点的模式
       std::map<std::size_t, std::set<std::size_t>> SelectedModes;
       // 原子最大位移大小，单位为埃
       double MaxDisplacement;
@@ -109,7 +109,7 @@ namespace ufo
     else process(input.Super);
 
     std::filesystem::create_directories("{}/{}"_f(config.OutputPoscarDirectory, "origin"));
-    std::ofstream("{}/origin/POSCAR"_f(config.OutputDataFile)) << generate_poscar
+    std::ofstream("{}/origin/POSCAR"_f(config.OutputPoscarDirectory)) << generate_poscar
       (input.Super.Cell, input.Super.AtomPosition, input.Super.AtomType);
     std::ofstream(config.OutputDataFile, std::ios::binary) << biu::serialize<char>(output);
   }
@@ -160,7 +160,7 @@ R"(- - [ {}, {}, {} ]
     struct Config
     {
       Eigen::Matrix3d OriginalSusceptibility;
-      std::vector<Eigen::Matrix3d> Susceptibilities;
+      std::vector<Eigen::Matrix3d> Susceptibility;
       std::array<Eigen::Vector3d, 2> Polarization;
       std::string InputDataFile;
       std::string RamanInputDataFile;
@@ -180,7 +180,7 @@ R"(- - [ {}, {}, {} ]
       for (auto&& [i_of_mode, mode] : ranges::views::enumerate(raman_input.Mode))
       {
         auto&& _ = cell.Qpoint[mode.QpointIndex].Mode[mode.ModeIndex];
-        Eigen::Matrix3d raman_tensor = (config.Susceptibilities[i_of_mode] - config.OriginalSusceptibility)
+        Eigen::Matrix3d raman_tensor = (config.Susceptibility[i_of_mode] - config.OriginalSusceptibility)
           / mode.Ratio / raman_input.MaxDisplacement;
         _.RamanTensor = raman_tensor | biu::fromEigen;
         _.WeightOnRaman = config.Polarization[0].transpose() * raman_tensor * config.Polarization[1];

test/raman-apply-contribution/.gitignore

@@ -0,0 +1 @@
+output.zpp

test/raman-apply-contribution/config.yaml

@@ -0,0 +1,83 @@
+OriginalSusceptibility:
+  - [ 7.006328, -3.3e-05, -2e-06 ]
+  - [ -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 ]
+Polarization:
+  - [ 0, 1, 0 ]
+  - [ 0, 1, 0 ]
+InputDataFile: data.zpp
+RamanInputDataFile: raman.zpp
+OutputDataFile: output.zpp

test/raman-create-displacement/.gitignore

@@ -0,0 +1,2 @@
+POSCAR
+output.zpp

test/raman-create-displacement/config.yaml

@@ -0,0 +1,7 @@
+Cell: Super
+SelectedModes: 
+  0: [ 0, 1, 2, 5, 6, 9, 10, 15, 16, 107, 115, 185, 251, 252, 281, 282, 287, 292, 293, 311, 312, 327, 378, 379 ]
+MaxDisplacement: 0.02
+OutputPoscarDirectory: POSCAR
+InputDataFile: data.zpp
+OutputDataFile: output.zpp

test/raman-extract/job/.gitattributes

@@ -0,0 +1 @@
+OUTCAR filter=lfs diff=lfs merge=lfs -text