From d584951fd71867f37aca6ba50e276591ce7d3451 Mon Sep 17 00:00:00 2001 From: chn Date: Wed, 4 Dec 2024 15:16:49 +0800 Subject: [PATCH] fix raman, add test --- CMakeLists.txt | 10 +++ src/raman.cpp | 8 +-- test/raman-apply-contribution/.gitignore | 1 + test/raman-apply-contribution/config.yaml | 83 ++++++++++++++++++++++ test/raman-apply-contribution/data.zpp | 3 + test/raman-apply-contribution/raman.zpp | 3 + test/raman-create-displacement/.gitignore | 2 + test/raman-create-displacement/config.yaml | 7 ++ test/raman-create-displacement/data.zpp | 3 + test/raman-extract/job/.gitattributes | 1 + test/raman-extract/job/0/OUTCAR | 3 + test/raman-extract/job/1/OUTCAR | 3 + test/raman-extract/job/10/OUTCAR | 3 + test/raman-extract/job/11/OUTCAR | 3 + test/raman-extract/job/12/OUTCAR | 3 + test/raman-extract/job/13/OUTCAR | 3 + test/raman-extract/job/14/OUTCAR | 3 + test/raman-extract/job/15/OUTCAR | 3 + test/raman-extract/job/16/OUTCAR | 3 + test/raman-extract/job/17/OUTCAR | 3 + test/raman-extract/job/18/OUTCAR | 3 + test/raman-extract/job/19/OUTCAR | 3 + test/raman-extract/job/2/OUTCAR | 3 + test/raman-extract/job/20/OUTCAR | 3 + test/raman-extract/job/21/OUTCAR | 3 + test/raman-extract/job/22/OUTCAR | 3 + test/raman-extract/job/23/OUTCAR | 3 + test/raman-extract/job/3/OUTCAR | 3 + test/raman-extract/job/4/OUTCAR | 3 + test/raman-extract/job/5/OUTCAR | 3 + test/raman-extract/job/6/OUTCAR | 3 + test/raman-extract/job/7/OUTCAR | 3 + test/raman-extract/job/8/OUTCAR | 3 + test/raman-extract/job/9/OUTCAR | 3 + test/raman-extract/job/origin/OUTCAR | 3 + 35 files changed, 192 insertions(+), 4 deletions(-) create mode 100644 test/raman-apply-contribution/.gitignore create mode 100644 test/raman-apply-contribution/config.yaml create mode 100644 test/raman-apply-contribution/data.zpp create mode 100644 test/raman-apply-contribution/raman.zpp create mode 100644 test/raman-create-displacement/.gitignore create mode 100644 test/raman-create-displacement/config.yaml create mode 100644 test/raman-create-displacement/data.zpp create mode 100644 test/raman-extract/job/.gitattributes create mode 100644 test/raman-extract/job/0/OUTCAR create mode 100644 test/raman-extract/job/1/OUTCAR create mode 100644 test/raman-extract/job/10/OUTCAR create mode 100644 test/raman-extract/job/11/OUTCAR create mode 100644 test/raman-extract/job/12/OUTCAR create mode 100644 test/raman-extract/job/13/OUTCAR create mode 100644 test/raman-extract/job/14/OUTCAR create mode 100644 test/raman-extract/job/15/OUTCAR create mode 100644 test/raman-extract/job/16/OUTCAR create mode 100644 test/raman-extract/job/17/OUTCAR create mode 100644 test/raman-extract/job/18/OUTCAR create mode 100644 test/raman-extract/job/19/OUTCAR create mode 100644 test/raman-extract/job/2/OUTCAR create mode 100644 test/raman-extract/job/20/OUTCAR create mode 100644 test/raman-extract/job/21/OUTCAR create mode 100644 test/raman-extract/job/22/OUTCAR create mode 100644 test/raman-extract/job/23/OUTCAR create mode 100644 test/raman-extract/job/3/OUTCAR create mode 100644 test/raman-extract/job/4/OUTCAR create mode 100644 test/raman-extract/job/5/OUTCAR create mode 100644 test/raman-extract/job/6/OUTCAR create mode 100644 test/raman-extract/job/7/OUTCAR create mode 100644 test/raman-extract/job/8/OUTCAR create mode 100644 test/raman-extract/job/9/OUTCAR create mode 100644 test/raman-extract/job/origin/OUTCAR diff --git a/CMakeLists.txt b/CMakeLists.txt index 3008a16..eabe2b7 100644 --- a/CMakeLists.txt +++ b/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) diff --git a/src/raman.cpp b/src/raman.cpp index d833981..16335b4 100644 --- a/src/raman.cpp +++ b/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> 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(output); } @@ -160,7 +160,7 @@ R"(- - [ {}, {}, {} ] struct Config { Eigen::Matrix3d OriginalSusceptibility; - std::vector Susceptibilities; + std::vector Susceptibility; std::array 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]; diff --git a/test/raman-apply-contribution/.gitignore b/test/raman-apply-contribution/.gitignore new file mode 100644 index 0000000..765eecc --- /dev/null +++ b/test/raman-apply-contribution/.gitignore @@ -0,0 +1 @@ +output.zpp \ No newline at end of file diff --git a/test/raman-apply-contribution/config.yaml b/test/raman-apply-contribution/config.yaml new file mode 100644 index 0000000..b926c5e --- /dev/null +++ b/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 diff --git a/test/raman-apply-contribution/data.zpp b/test/raman-apply-contribution/data.zpp new file mode 100644 index 0000000..321c74e --- /dev/null +++ b/test/raman-apply-contribution/data.zpp @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:ee28fae9b62c0c1f754294a662ba81e7de0e32cd09b8c60db1aae274b8522765 +size 2921536 diff --git a/test/raman-apply-contribution/raman.zpp b/test/raman-apply-contribution/raman.zpp new file mode 100644 index 0000000..2222cec --- /dev/null +++ b/test/raman-apply-contribution/raman.zpp @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:f8f5d3c9eea71e2c1531261524ede1289497e586944a29df4ee71b90327c7992 +size 592 diff --git a/test/raman-create-displacement/.gitignore b/test/raman-create-displacement/.gitignore new file mode 100644 index 0000000..95ffa16 --- /dev/null +++ b/test/raman-create-displacement/.gitignore @@ -0,0 +1,2 @@ +POSCAR +output.zpp diff --git a/test/raman-create-displacement/config.yaml b/test/raman-create-displacement/config.yaml new file mode 100644 index 0000000..8c09b08 --- /dev/null +++ b/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 diff --git a/test/raman-create-displacement/data.zpp b/test/raman-create-displacement/data.zpp new file mode 100644 index 0000000..321c74e --- /dev/null +++ b/test/raman-create-displacement/data.zpp @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:ee28fae9b62c0c1f754294a662ba81e7de0e32cd09b8c60db1aae274b8522765 +size 2921536 diff --git a/test/raman-extract/job/.gitattributes b/test/raman-extract/job/.gitattributes new file mode 100644 index 0000000..6465f73 --- /dev/null +++ b/test/raman-extract/job/.gitattributes @@ -0,0 +1 @@ +OUTCAR filter=lfs diff=lfs merge=lfs -text diff --git a/test/raman-extract/job/0/OUTCAR b/test/raman-extract/job/0/OUTCAR new file mode 100644 index 0000000..442cefc --- /dev/null +++ b/test/raman-extract/job/0/OUTCAR @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:e3df2575c5473787e79f7444a68a3b11bf1bc2525aaed91c791bbba142d36f26 +size 438525 diff --git a/test/raman-extract/job/1/OUTCAR b/test/raman-extract/job/1/OUTCAR new file mode 100644 index 0000000..7d5e8a4 --- /dev/null +++ b/test/raman-extract/job/1/OUTCAR @@ -0,0 +1,3 @@ +version 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