Merge branch 'develop' into dmr

Author: dzzz2001

.gitignore

@@ -21,4 +21,6 @@ time.json
 *.pyc
 __pycache__
 abacus.json
-*.npy
+*.npy
+toolchain/install/
+toolchain/abacus_env.sh

CMakeLists.txt

@@ -352,9 +352,19 @@ if(USE_CUDA)
     endif()
     if (ENABLE_CUSOLVERMP)
       add_compile_definitions(__CUSOLVERMP)
+      find_library(CAL_LIBRARY
+          NAMES cal
+          PATHS ${CAL_CUSOLVERMP_PATH}
+          NO_DEFAULT_PATH
+      )
+      find_library(CUSOLVERMP_LIBRARY
+          NAMES cusolverMp
+          PATHS ${CAL_CUSOLVERMP_PATH}
+          NO_DEFAULT_PATH
+      )
       target_link_libraries(${ABACUS_BIN_NAME}
-          cal
-          cusolverMp
+          ${CAL_LIBRARY}
+          ${CUSOLVERMP_LIBRARY}
       )
     endif()
   endif()

Dockerfile.intel

@@ -44,6 +44,9 @@ RUN source /opt/intel/oneapi/setvars.sh && \
     ln -s /usr/local/include/elpa_openmp-$ELPA_VER/elpa /usr/local/include/ && \
     cd /tmp && rm -rf elpa-$ELPA_VER
 
+RUN cd /tmp && git clone https://github.com/Tencent/rapidjson.git && cp -r rapidjson/include/rapidjson /usr/include/ \
+    && rm -rf rapidjson
+
 RUN wget https://download.pytorch.org/libtorch/cpu/libtorch-cxx11-abi-shared-with-deps-2.0.0%2Bcpu.zip \
         --no-check-certificate --quiet -O libtorch.zip && \
     unzip -q libtorch.zip -d /opt  && rm libtorch.zip

docs/advanced/input_files/input-main.md

@@ -153,6 +153,7 @@
     - [out\_mat\_t](#out_mat_t)
     - [out\_mat\_dh](#out_mat_dh)
     - [out\_mat\_xc](#out_mat_xc)
+    - [out\_mat\_xc2](#out_mat_xc2)
     - [out\_eband\_terms](#out_eband_terms)
     - [out\_hr\_npz/out\_dm\_npz](#out_hr_npzout_dm_npz)
     - [dm\_to\_rho](#dm_to_rho)
@@ -1799,6 +1800,13 @@ These variables are used to control the output of properties.
 The band (KS orbital) energy for each (k-point, spin, band) will be printed in the file `OUT.${suffix}/vxc_out.dat`. If EXX is calculated, the local and EXX part of band energy will also be printed in `OUT.${suffix}/vxc_local_out.dat`and `OUT.${suffix}/vxc_exx_out.dat`, respectively. All the `vxc*_out.dat` files contains 3 integers (nk, nspin, nband) followed by nk\*nspin\*nband lines of energy Hartree and eV.
 - **Default**: False
 
+### out_mat_xc2
+
+- **Type**: Boolean
+- **Availability**: Numerical atomic orbital (NAO) basis
+- **Description**: Whether to print the exchange-correlation matrices in **numerical orbital representation** (unit: Ry): $\braket{\phi_i|V_\text{xc}^\text{(semi-)local}+V_\text{exx}+V_\text{DFTU}|\phi_j}(\mathbf{R})$ in CSR format (the same format as [out_mat_hs2](../elec_properties/hs_matrix.md#out_mat_hs2)) in the directory `OUT.${suffix}`. (Note that currently DeePKS term is not included. ) The files are named `Vxc_R_spin$s`.
+- **Default**: False
+
 ### out_eband_terms
 
 - **Type**: Boolean

docs/index.rst

@@ -7,7 +7,7 @@
 ABACUS Documentation
 =================================================
 
-ABACUS (**A**tomic-orbital **B**ased **A**b-initio **C**omputation at **US**tc) is
+ABACUS (Atomic-orbital Based Ab-initio Computation at UStc) is
 an open-source computer code package based on density functional
 theory (DFT). The package utilizes both plane wave and numerical
 atomic basis sets with the usage of pseudopotentials

docs/quick_start/easy_install.md

@@ -106,7 +106,7 @@ Here, 'build' is the path for building ABACUS; and '-D' is used for setting up s
 - `CMAKE_INSTALL_PREFIX`: the path of ABACUS binary to install; `/usr/local/bin/abacus` by default
 - Compilers
   - `CMAKE_CXX_COMPILER`: C++ compiler; usually `g++`(GNU C++ compiler) or `icpx`(Intel C++ compiler). Can also set from environment variable `CXX`. It is OK to use MPI compiler here.
-  - `MPI_CXX_COMPILER`: MPI wrapper for C++ compiler; usually `mpicxx` or `mpiicpc`(for Intel MPI).
+  - `MPI_CXX_COMPILER`: MPI wrapper for C++ compiler; usually `mpicxx` or `mpiicpx`(for Intel toolkits) or `mpiicpc`(for classic Intel Compiler Classic MPI before 2024.0).
 - Requirements: Unless indicated, CMake will try to find under default paths.
   - `MKLROOT`: If environment variable `MKLROOT` exists, `cmake` will take MKL as a preference, i.e. not using `LAPACK`, `ScaLAPACK` and `FFTW`. To disable MKL, unset environment variable `MKLROOT`, or pass `-DMKLROOT=OFF` to `cmake`.
   - `LAPACK_DIR`: Path to OpenBLAS library `libopenblas.so`(including BLAS and LAPACK)
@@ -136,7 +136,7 @@ Here, 'build' is the path for building ABACUS; and '-D' is used for setting up s
 Here is an example:
 
 ```bash
-CXX=mpiicpc cmake -B build -DCMAKE_INSTALL_PREFIX=~/abacus -DELPA_DIR=~/elpa-2016.05.004/build -DCEREAL_INCLUDE_DIR=~/cereal/include
+CXX=mpiicpx cmake -B build -DCMAKE_INSTALL_PREFIX=~/abacus -DELPA_DIR=~/elpa-2025.01.001/build -DCEREAL_INCLUDE_DIR=~/cereal/include
 ```
 
 ## Build and Install

docs/quick_start/output.md

@@ -14,7 +14,7 @@ For a complete list of input parameters, please consult this [instruction](../ad
 
 `running_scf.log` contains information on nearly all function calls made during the execution of ABACUS.
 
-## *KPT*
+## *KPT.info*
 
 This file contains the information of all generated k-points, as well as the list of k-points actually used for calculations after considering symmetry.
 
@@ -39,4 +39,4 @@ ABACUS generates a `.cif` format structure file based on the input file `STRU`,
 
 ## *warning.log*
 
-The file contains all the warning messages generated during the ABACUS run.
+The file contains all the warning messages generated during the ABACUS run.

python/pyabacus/CONTRIBUTING.md

@@ -190,8 +190,10 @@ list(APPEND _diago
     ${HSOLVER_PATH}/diag_const_nums.cpp
     ${HSOLVER_PATH}/diago_iter_assist.cpp
     ${HSOLVER_PATH}/kernels/dngvd_op.cpp
+    ${HSOLVER_PATH}/kernels/bpcg_kernel_op.cpp
     ${BASE_PATH}/kernels/math_kernel_op.cpp
-    ${BASE_PATH}/kernels/math_op.cpp
+    ${BASE_PATH}/kernels/math_kernel_op_vec.cpp
+    ${BASE_PATH}/kernels/math_ylm_op.cpp
     ${BASE_PATH}/module_device/device.cpp
     ${BASE_PATH}/module_device/memory_op.cpp
     ${PSI_PATH}/psi.cpp

python/pyabacus/src/ModuleBase/CMakeLists.txt

@@ -1,7 +1,8 @@
 list(APPEND pymodule_base
     ${PROJECT_SOURCE_DIR}/src/ModuleBase/py_base_math.cpp
-    ${BASE_PATH}/kernels/math_op.cpp
+    ${BASE_PATH}/kernels/math_ylm_op.cpp
     ${BASE_PATH}/kernels/math_kernel_op.cpp
+    ${BASE_PATH}/kernels/math_kernel_op_vec.cpp
     ${BASE_PATH}/module_device/memory_op.cpp
     ${BASE_PATH}/module_device/device.cpp
     )

python/pyabacus/src/ModuleNAO/CMakeLists.txt

@@ -13,8 +13,9 @@ list(APPEND _naos
     ${NAO_PATH}/two_center_integrator.cpp
     ${NAO_PATH}/two_center_table.cpp
     # dependency
-    ${ABACUS_SOURCE_DIR}/module_base/kernels/math_op.cpp
+    ${ABACUS_SOURCE_DIR}/module_base/kernels/math_ylm_op.cpp
     ${ABACUS_SOURCE_DIR}/module_base/kernels/math_kernel_op.cpp
+    ${ABACUS_SOURCE_DIR}/module_base/kernels/math_kernel_op_vec.cpp
     # ${ABACUS_SOURCE_DIR}/module_psi/kernels/psi_memory_op.cpp
     ${ABACUS_SOURCE_DIR}/module_base/module_device/memory_op.cpp
     ${ABACUS_SOURCE_DIR}/module_base/module_device/device.cpp