{"id":6906,"date":"2026-04-10T14:43:39","date_gmt":"2026-04-10T05:43:39","guid":{"rendered":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/?p=6906"},"modified":"2026-04-10T17:11:46","modified_gmt":"2026-04-10T08:11:46","slug":"cp2k-2026-1-installation","status":"publish","type":"post","link":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/2026\/04\/10\/cp2k-2026-1-installation\/","title":{"rendered":"CP2K (2026.1) Installation"},"content":{"rendered":"\n

Source: https:\/\/ccportal.ims.ac.jp\/en\/node\/3927<\/a><\/p>\n\n\n\n

Environment: AlmaLinux 8<\/p>\n\n\n\n

Compilation (SHARED_LIB=ON)<\/h2>\n\n\n\n
cd /usr/local/cp2k\nsudo wget https://github.com/cp2k/cp2k/releases/download/v2026.1/cp2k-2026.1.tar.bz2\nsudo tar xvjf cp2k-2026.1.tar.bz2\nsudo cd cp2k-2026.1/tools/toolchain\nscl enable gcc-toolset-13 bash\nINSTDIR=/usr/local/cp2k/2026.1\nsudo mv cp2k-2026.1 2026.1\ncd 2026.1/tools/toolchain\n\nsudo ./install_cp2k_toolchain.sh --mpi-mode=openmpi \\\n--math-mode=openblas \\\n--with-gcc=system \\\n--with-cmake=system \\\n--with-openmpi=system \\\n--with-mpich=no \\\n--with-intelmpi=no \\\n--with-libxc=install \\\n--with-libint=install \\\n--with-fftw=install \\\n--with-acml=no \\\n--with-mkl=no \\\n--with-openblas=install \\\n--with-scalapack=install \\\n--with-libxsmm=install \\\n--with-elpa=install \\\n--with-deepmd=no \\\n--with-plumed=install \\\n--with-sirius=install \\\n--with-gsl=install \\\n--with-libvdwxc=install \\\n--with-spglib=install \\\n--with-hdf5=install \\\n--with-spfft=install \\\n--with-spla=install \\\n--with-cosma=install \\\n--with-libvori=install \\\n--with-libtorch=no \\\n--with-libsmeagol=install \\\n--with-dftd4=install \\\n--with-tblite=install \\\n--with-trexio=install \\\n--with-greenx=install \\\n--with-gmp=install \\\n--with-ace=install \\\n-j 37\n\n# ==================== Installing SIRIUS ====================\n# CMake Error at CMakeLists.txt:16 (cmake_policy):\n#  Policy "CMP0144" is not known to this version of CMake.\n\ncmake --version\n# cmake version 3.26.5\nexport PATH=/usr/local/cmake/4.1.0/bin:$PATH \n\nsudo ./install_cp2k_toolchain.sh --mpi-mode=openmpi \\\n--math-mode=openblas \\\n--with-gcc=system \\\n--with-cmake=system \\\n--with-openmpi=system \\\n--with-mpich=no \\\n--with-intelmpi=no \\\n--with-libxc=install \\\n--with-libint=install \\\n--with-fftw=install \\\n--with-acml=no \\\n--with-mkl=no \\\n--with-openblas=install \\\n--with-scalapack=install \\\n--with-libxsmm=install \\\n--with-elpa=install \\\n--with-deepmd=no \\\n--with-plumed=install \\\n--with-sirius=install \\\n--with-gsl=install \\\n--with-libvdwxc=install \\\n--with-spglib=install \\\n--with-hdf5=install \\\n--with-spfft=install \\\n--with-spla=install \\\n--with-cosma=install \\\n--with-libvori=install \\\n--with-libtorch=no \\\n--with-libsmeagol=install \\\n--with-dftd4=install \\\n--with-tblite=install \\\n--with-trexio=install \\\n--with-greenx=install \\\n--with-gmp=install \\\n--with-ace=install \\\n-j 37\n\nldd install/trexio-2.6.0/lib/libtrexio.so | grep hdf5\n# libhdf5.so.103 => /lib64/libhdf5.so.103 (0x0000148fd384e000)\nsudo rm -rf install/trexio-2.6.0/\n\nHDF5_VER=1.14.6\nTREXIO_VER=2.6.0\nINSTALLDIR="${PWD}/install"\n\ncd build/trexio-${TREXIO_VER}\nsudo make distclean \n\nsudo ./configure \\\n  --prefix="${INSTALLDIR}/trexio-${TREXIO_VER}" \\\n  --with-hdf5="${INSTALLDIR}/hdf5-${HDF5_VER}" \\\n  CPPFLAGS="-I${INSTALLDIR}/hdf5-${HDF5_VER}/include" \\\n  LDFLAGS="-L${INSTALLDIR}/hdf5-${HDF5_VER}/lib -Wl,-rpath,${INSTALLDIR}/hdf5-${HDF5_VER}/lib"\n\nsudo make -j 37\nsudo make install\n\ncd ../fftw-3.3.10\nsudo make distclean\nsudo ./configure \\\n    --prefix=/usr/local/cp2k/2026.1/tools/toolchain/install/fftw-3.3.10 \\\n    --enable-mpi \\\n    --enable-openmp \\\n    --enable-shared \\\n    --enable-sse2 \\\n    --enable-avx \\\n    --enable-avx2 \\\n    --enable-avx512 \n\nsudo make -j 37\nsudo make install\n\ncd ../../\nldd install/trexio-2.6.0/lib/libtrexio.so | grep hdf5\n#\tlibhdf5.so.310 => /usr/local/cp2k-2026.1/tools/toolchain/install/hdf5-1.14.6/lib/libhdf5.so.310 (0x00001503c3617000)\n\nsource install/setup\ncd ../../\nsudo rm -rf build\nsudo mkdir build\ncd build\nsudo cmake .. \\\n    -DCMAKE_BUILD_TYPE=Release \\\n    -DCMAKE_INSTALL_PREFIX=${INSTDIR} \\\n    -DBUILD_SHARED_LIBS=ON \\\n    -DCP2K_USE_ACCEL=NONE \\\n    -DCP2K_ENABLE_DBM_GPU=OFF \\\n    -DCP2K_ENABLE_GRID_GPU=OFF \\\n    -DCP2K_ENABLE_PW_GPU=OFF \\\n    -DCP2K_USE_MPI=ON \\\n    -DCP2K_USE_MPI_F08=ON \\\n    -DCP2K_USE_COSMA=ON \\\n    -DCP2K_USE_ELPA=ON \\\n    -DCP2K_ENABLE_ELPA_OPENMP_SUPPORT=ON \\\n    -DCP2K_USE_SPLA=ON \\\n    -DCP2K_USE_SPLA_GEMM_OFFLOADING=OFF \\\n    -DCP2K_USE_LIBXSMM=ON \\\n    -DCP2K_USE_FFTW3=ON \\\n    -DCP2K_USE_LIBXC=ON \\\n    -DCP2K_USE_LIBINT2=ON \\\n    -DCP2K_USE_LIBVDWXC=ON \\\n    -DCP2K_USE_DFTD4=ON \\\n    -DCP2K_USE_TBLITE=ON \\\n    -DCP2K_USE_SIRIUS=ON \\\n    -DCP2K_USE_SIRIUS_DFTD4=ON \\\n    -DCP2K_USE_SIRIUS_VCSQNM=ON \\\n    -DCP2K_USE_SIRIUS_NLCG=ON \\\n    -DCP2K_USE_ACE=OFF \\\n    -DCP2K_USE_DEEPMD=OFF \\\n    -DCP2K_USE_PLUMED=ON \\\n    -DCP2K_USE_PEXSI=OFF \\\n    -DCP2K_USE_LIBSMEAGOL=ON \\\n    -DCP2K_USE_GREENX=ON \\\n    -DCP2K_USE_HDF5=ON \\\n    -DCP2K_USE_SPGLIB=ON \\\n    -DCP2K_USE_VORI=ON \\\n    -DCP2K_USE_TREXIO=ON \\\n    -DCMAKE_INSTALL_RPATH="/usr/local/cp2k/2026.1/lib64" \\\n    -DCMAKE_INSTALL_RPATH_USE_LINK_PATH=ON\n\nsudo cmake --build . -j 37\nsudo cmake --build . --target install -j 37<\/pre>\n\n\n\n
Running<\/h2>\n\n\n\n
Energy (B3LYP\/6-31G(d))<\/h3>\n\n\n\n
methane.xyz<\/p>\n\n\n\n
5\nMethane\n  H      0.5288      0.1610      0.9359\n  C      0.0000      0.0000      0.0000\n  H      0.2051      0.8240     -0.6786\n  H      0.3345     -0.9314     -0.4496\n  H     -1.0685     -0.0537      0.1921<\/pre>\n\n\n\n
CH4_energy.inp<\/p>\n\n\n\n
&GLOBAL\n  PROJECT methane_b3lyp\n  RUN_TYPE ENERGY\n  PRINT_LEVEL MEDIUM\n&END GLOBAL\n\n&FORCE_EVAL\n  METHOD Quickstep\n\n  &DFT\n    BASIS_SET_FILE_NAME EMSL_BASIS_SETS\n    POTENTIAL_FILE_NAME POTENTIAL\n\n    CHARGE 0\n    MULTIPLICITY 1\n\n    &MGRID\n      CUTOFF 400\n      REL_CUTOFF 60\n      NGRIDS 5\n    &END MGRID\n\n    &QS\n      METHOD GAPW\n      EPS_DEFAULT 1.0E-12\n    &END QS\n\n    &XC\n      &XC_FUNCTIONAL B3LYP\n      &END XC_FUNCTIONAL\n      &XC_GRID\n        XC_SMOOTH_RHO NN50\n        XC_DERIV NN50_SMOOTH\n      &END XC_GRID\n    &END XC\n\n    &SCF\n      SCF_GUESS ATOMIC\n      MAX_SCF 100\n      EPS_SCF 1.0E-8\n      &OT ON\n        MINIMIZER DIIS\n        PRECONDITIONER FULL_ALL\n      &END OT\n      &OUTER_SCF ON\n        MAX_SCF 20\n        EPS_SCF 1.0E-8\n      &END OUTER_SCF\n      &PRINT\n        &RESTART OFF\n        &END RESTART\n      &END PRINT\n    &END SCF\n\n    &PRINT\n      &MO_CUBES OFF\n      &END MO_CUBES\n      &MULLIKEN ON\n      &END MULLIKEN\n      &HIRSHFELD ON\n      &END HIRSHFELD\n    &END PRINT\n\n  &END DFT\n\n  &SUBSYS\n    &CELL\n      ABC 10.0 10.0 10.0\n      PERIODIC NONE\n    &END CELL\n\n    &TOPOLOGY\n      COORD_FILE_NAME methane.xyz\n      COORDINATE XYZ\n      CONNECTIVITY OFF\n    &END TOPOLOGY\n\n    &KIND C\n      BASIS_SET 6-31G*\n      POTENTIAL ALL\n    &END KIND\n\n    &KIND H\n      BASIS_SET 6-31G*\n      POTENTIAL ALL\n    &END KIND\n\n  &END SUBSYS\n\n&END FORCE_EVAL<\/pre>\n\n\n\n
$ /usr/local/cp2k/2026.1/bin/cp2k.psmp -i CH4_energy.inp -o CH4_energy.out\n$ grep "Total energy:" CH4_energy.out \n  Total energy:                                               -40.47812358217958<\/pre>\n\n\n\n
Structural optimization (energy minimization)<\/h3>\n\n\n\n
CH4_minimization.inp<\/p>\n\n\n\n
&GLOBAL\n  PROJECT methane_b3lyp_opt\n  RUN_TYPE GEO_OPT\n  PRINT_LEVEL MEDIUM\n&END GLOBAL\n\n&MOTION\n  &GEO_OPT\n    TYPE MINIMIZATION\n    OPTIMIZER BFGS\n    MAX_ITER 200\n    MAX_FORCE 4.5E-4\n    RMS_FORCE 3.0E-4\n    MAX_DR    3.0E-3\n    RMS_DR    1.5E-3\n    &BFGS\n      TRUST_RADIUS 0.3\n    &END BFGS\n  &END GEO_OPT\n\n  &PRINT\n    &TRAJECTORY\n      FORMAT XYZ\n      &EACH\n        GEO_OPT 1\n      &END EACH\n    &END TRAJECTORY\n    &VELOCITIES OFF\n    &END VELOCITIES\n    &FORCES ON\n      &EACH\n        GEO_OPT 1\n      &END EACH\n    &END FORCES\n    &RESTART_HISTORY\n      &EACH\n        GEO_OPT 5\n      &END EACH\n    &END RESTART_HISTORY\n    &RESTART ON\n    &END RESTART\n  &END PRINT\n&END MOTION\n\n&FORCE_EVAL\n  METHOD Quickstep\n\n  &DFT\n    BASIS_SET_FILE_NAME EMSL_BASIS_SETS\n    POTENTIAL_FILE_NAME POTENTIAL\n    CHARGE 0\n    MULTIPLICITY 1\n\n    &MGRID\n      CUTOFF 400\n      REL_CUTOFF 60\n      NGRIDS 5\n    &END MGRID\n\n    &QS\n      METHOD GAPW\n      EPS_DEFAULT 1.0E-12\n    &END QS\n\n    &XC\n      &XC_FUNCTIONAL B3LYP\n      &END XC_FUNCTIONAL\n      &XC_GRID\n        XC_SMOOTH_RHO NN50\n        XC_DERIV NN50_SMOOTH\n      &END XC_GRID\n    &END XC\n\n    &SCF\n      SCF_GUESS ATOMIC\n      MAX_SCF 100\n      EPS_SCF 1.0E-8\n      &OT ON\n        MINIMIZER DIIS\n        PRECONDITIONER FULL_ALL\n      &END OT\n      &OUTER_SCF ON\n        MAX_SCF 20\n        EPS_SCF 1.0E-8\n      &END OUTER_SCF\n      &PRINT\n        &RESTART OFF\n        &END RESTART\n      &END PRINT\n    &END SCF\n\n    &PRINT\n      &MO_CUBES OFF\n      &END MO_CUBES\n      &MULLIKEN ON\n        &EACH\n          GEO_OPT 1\n        &END EACH\n      &END MULLIKEN\n      &HIRSHFELD ON\n        &EACH\n          GEO_OPT 1\n        &END EACH\n      &END HIRSHFELD\n    &END PRINT\n\n  &END DFT\n\n  &SUBSYS\n    &CELL\n      ABC 10.0 10.0 10.0\n      PERIODIC NONE\n    &END CELL\n\n    &TOPOLOGY\n      COORD_FILE_NAME methane.xyz\n      COORDINATE XYZ\n      CONNECTIVITY OFF\n    &END TOPOLOGY\n\n    &KIND C\n      BASIS_SET 6-31G*\n      POTENTIAL ALL\n    &END KIND\n\n    &KIND H\n      BASIS_SET 6-31G*\n      POTENTIAL ALL\n    &END KIND\n\n  &END SUBSYS\n\n&END FORCE_EVAL<\/pre>\n\n\n\n
$ export OMP_NUM_THREADS=1\n$ mpirun -np 4 /usr/local/cp2k/2026.1/bin/cp2k.psmp -i CH4_minimization.inp -o CH4_minimization.out\n$ grep "Total energy:" CH4_minimization.out \n  Total energy:                                               -40.47812358218015\n  Total energy:                                               -40.47825251290585\n  Total energy:                                               -40.47826101039904\n  Total energy:                                               -40.47826104637182\n  Total energy:                                               -40.47826104636347\n<\/pre>\n\n\n\n
GROMACS + CP2K Installation (MPI, double precision)<\/h2>\n\n\n\n
Source: https:\/\/ccportal.ims.ac.jp\/en\/node\/3916<\/a><\/p>\n\n\n\n
scl enable devtoolset-13 bash\nINSTALL_PREFIX=/usr/local/gromacs/2026.1_mpi_d_cp2k\nCP2KROOT=/usr/local/cp2k/2026.1\nCP2KROOT_TC=/usr/local/cp2k/2026.1/tools/toolchain\nHDF5_ROOT=/usr/local/cp2k/2026.1/tools/toolchain/install/hdf5-1.14.6\n\nsource /usr/local/cp2k/2026.1/tools/toolchain/install/setup\nmkdir build_cp2k\ncd build_cp2k\n/usr/local/cmake/4.1.0/bin/ccmake .. \\\n  -DCMAKE_PREFIX_PATH="${CP2KROOT_TC}/install/fftw-3.3.10" \\\n  -DGMX_DEFAULT_SUFFIX=OFF \\\n  -DGMX_BINARY_SUFFIX=_mpi_d_cp2k \\\n  -DGMX_LIBS_SUFFIX=_mpi_d_cp2k \\\n  -DCMAKE_INSTALL_PREFIX=${INSTALL_PREFIX} \\\n  -DCMAKE_C_COMPILER=mpicc \\\n  -DCMAKE_CXX_COMPILER=mpicxx \\\n  -DGMX_MPI=ON \\\n  -DGMX_GPU=OFF \\\n  -DGMX_DOUBLE=ON \\\n  -DGMX_THREAD_MPI=OFF \\\n  -DGMX_CP2K=ON \\\n  -DBUILD_SHARED_LIBS=OFF \\\n  -DGMXAPI=OFF \\\n  -DGMX_INSTALL_NBLIB_API=OFF \\\n  -DCP2K_DIR=${CP2KROOT}/lib64 \\\n  -DGMX_FFT_LIBRARY=fftw3 \\\n  -DGMX_EXTERNAL_BLAS=ON \\\n  -DGMX_BLAS_USER=${CP2KROOT_TC}/install/openblas-0.3.30/lib/libopenblas.so \\\n  -DGMX_EXTERNAL_LAPACK=ON \\\n  -DGMX_LAPACK_USER=${CP2KROOT_TC}/install/openblas-0.3.30/lib/libopenblas.so \\\n  -DGMX_USE_PLUMED=ON \\\n  -DGMX_NNPOT=OFF \\\n  -DHDF5_ROOT=${HDF5_ROOT} \\\n  -DHDF5_C_LIBRARY_hdf5=${HDF5_ROOT}/lib/libhdf5.so \\\n  -DHDF5_C_INCLUDE_DIR=${HDF5_ROOT}/include \\\n  -DCMAKE_PREFIX_PATH=${HDF5_ROOT}\n\ngrep -i hdf5 CMakeCache.txt | grep -i library\nmake -j 37\nunset OMP_NUM_THREADS\nmake check -j 37\n#The following tests FAILED:\n#\t  9 - QMMMAppliedForcesUnitTest (Failed)                GTest UnitTest\nsudo make install\n\ngmx_mpi_d_cp2k --version\n          :-) GROMACS - gmx_mpi_d_cp2k, 2026.1 (double precision) (-:\n\nExecutable:   /usr/local/gromacs/2026.1_mpi_d_cp2k/bin/gmx_mpi_d_cp2k\nData prefix:  /usr/local/gromacs/2026.1_mpi_d_cp2k\nWorking dir:  /home/user/data/CP2K/gromacs-2022-cp2k-tutorial/nma\nCommand line:\n  gmx_mpi_d_cp2k --version\n\nGROMACS version:     2026.1\nPrecision:           double\nMemory model:        64 bit\nMPI library:         MPI\nMPI version:         Open MPI v4.1.8, package: Open MPI user@mas-i9wx Distribution, ident: 4.1.8, repo rev: v4.1.8, Feb 04, 2025\nOpenMP support:      enabled (GMX_OPENMP_MAX_THREADS = 128)\nGPU support:         disabled\nSIMD instructions:   AVX_512\nCPU FFT library:     fftw-3.3.10-sse2-avx-avx2-avx2_128-avx512\nGPU FFT library:     none\nMulti-GPU FFT:       none\nRDTSCP:              enabled\nTNG support:         enabled\nHwloc support:       disabled\nTracing support:     disabled\nColvars support:     enabled (version 2025-10-13)\nCP2K support:        enabled (version CP2K version 2026.1)\nTorch support:       disabled\nPlumed support:      enabled\nC compiler:          /usr/local/open-mpi/4.1.8/bin/mpicc GNU 13.3.1\nC compiler flags:    -fexcess-precision=fast -funroll-all-loops -march=skylake-avx512 -Wno-missing-field-initializers -O3 -DNDEBUG\nC++ compiler:        /usr/local/open-mpi/4.1.8/bin/mpicxx GNU 13.3.1\nC++ compiler flags:  -fexcess-precision=fast -funroll-all-loops -march=skylake-avx512 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict SHELL:-fopenmp -O3 -DNDEBUG\nBLAS library:        External - user-supplied\nLAPACK library:      External - user-supplied\n<\/pre>\n\n\n\n
Test (N<\/em>-methylalanine in vacuum)<\/h3>\n\n\n\n
Source: https:\/\/zenn.dev\/meguru_compchem\/articles\/72044145e092b3<\/a> and https:\/\/github.com\/bioexcel\/gromacs-2022-cp2k-tutorial<\/a><\/p>\n\n\n\n
source /usr/local/gromacs/2026.1_mpi_d_cp2k/bin/GMXRC\ngit clone https://github.com/bioexcel/gromacs-2022-cp2k-tutorial.git\ncd gromacs-2022-cp2k-tutorial/nma\ngmx_mpi_d_cp2k pdb2gmx -f nma.pdb <<EOF \n1\n1\nEOF\ngmx_mpi_d_cp2k grompp -f em.mdp -p topol.top -c conf.gro -o nma-em\ntime gmx_mpi_d_cp2k mdrun -v -deffnm nma-em -ntomp 8\n# real\t13m25.061s (100 steps)\ntime mpirun -np 8 gmx_mpi_d_cp2k mdrun -v -deffnm nma-em -ntomp 1\n# real\t10m32.998s (100 steps)\ntime mpirun -np 16 gmx_mpi_d_cp2k mdrun -v -deffnm nma-em -ntomp 1\n# real\t8m52.430s (100 steps)\ngmx_mpi_d_cp2k grompp -f md-nvt.mdp -o nma-nvt\ntime mpirun -np 16 gmx_mpi_d_cp2k mdrun -v -deffnm nma-nvt -ntomp 1\n\n               Core t (s)   Wall t (s)        (%)\n       Time:     7807.185      487.949     1600.0\n                 (ns/day)    (hour/ns)    (ms/step)  (Matom*steps/s) \nPerformance:        0.018     1341.994     4831.180            0.000 \n<\/pre>\n\n\n\n
Test (EGFP protein in water)<\/h3>\n\n\n\n
cd gromacs-2022-cp2k-tutorial/egfp\ngmx_mpi_d_cp2k pdb2gmx -f 4eul.pdb  <<EOF \n1\n1\nEOF\ngmx_mpi_d_cp2k editconf -f conf.gro -o box.gro -bt cubic -d 1\ngmx_mpi_d_cp2k solvate -cp box.gro -o solv.gro -p topol.top\ngmx_mpi_d_cp2k grompp -f em.mdp -c solv.gro -o egfp-genion -maxwarn 2\ngmx_mpi_d_cp2k genion -s egfp-genion -p topol.top -o ions.gro -neutral -pname NA -nname CL  <<EOF \n13\nEOF\ngmx_mpi_d_cp2k grompp -f em.mdp -c ions.gro -o egfp-em\ngmx_mpi_d_cp2k mdrun -v -deffnm egfp-em -ntomp 9\ngmx_mpi_d_cp2k grompp -f md-mm-nvt.mdp -c egfp-em.gro -o egfp-mm-nvt\n\n/usr/local/gromacs/2026.1_cuda_torchcu128/bin/gmx mdrun -v -deffnm egfp-mm-nvt -ntmpi 1 -ntomp 9\n# 226.825 ns/day\ngmx_mpi_d_cp2k make_ndx -f ions.gro <<EOF\na 938-956\nname 17 QMatoms\nq\nEOF\ngmx_mpi_d_cp2k grompp -f md-qmmm-nvt.mdp -c egfp-mm-nvt.gro -t egfp-mm-nvt.cpt -n index.ndx -o egfp-qmmm-nvt -maxwarn 1\nmpirun -np 16 gmx_mpi_d_cp2k mdrun -v -deffnm egfp-qmmm-nvt -ntomp 1\n\n               Core t (s)   Wall t (s)        (%)\n       Time:    15669.242      979.328     1600.0\n                 (ns/day)    (hour/ns)    (ms/step)  (Matom*steps/s) \nPerformance:        0.009     2693.421     9696.315            0.005 \n<\/pre>\n","protected":false},"excerpt":{"rendered":"
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