Merge branch 'develop' into io_libxc

Conflicts:
	source/module_esolver/esolver_fp.cpp
	source/module_hamilt_general/module_xc/xc_functional_gradcorr.cpp
	source/module_hamilt_general/module_xc/xc_functional_libxc.h
	source/module_hamilt_general/module_xc/xc_functional_libxc_tools.cpp
	source/module_hamilt_general/module_xc/xc_functional_libxc_vxc.cpp
	source/module_hamilt_general/module_xc/xc_functional_libxc_wrapper_gcxc.cpp
	source/module_hamilt_general/module_xc/xc_functional_libxc_wrapper_tauxc.cpp
	source/module_hamilt_general/module_xc/xc_functional_vxc.cpp
	source/module_io/cube_io.h
	source/module_io/write_cube.cpp

Author: PeizeLin

.github/workflows/coverage.yml

@@ -15,10 +15,10 @@ jobs:
         uses: actions/checkout@v4
       - name: Install Requirements for Coverage Testing
         run: |
-          apt update && apt install -y lcov
+          apt update && apt install -y lcov gpg
       - name: Building
         run: |
-          cmake -B build -DENABLE_DEEPKS=ON -DENABLE_LIBXC=ON -DBUILD_TESTING=ON -DENABLE_COVERAGE=ON
+          cmake -B build -DENABLE_COVERAGE=ON -DBUILD_TESTING=ON -DENABLE_DEEPKS=ON -DENABLE_LIBXC=ON -DENABLE_LIBRI=ON -DENABLE_PAW=ON -DENABLE_GOOGLEBENCH=ON -DENABLE_RAPIDJSON=ON
           cmake --build build -j`nproc`
           cmake --install build
       - name: Testing

.github/workflows/test.yml

@@ -39,7 +39,7 @@ jobs:
             --from-ref ${{ github.event.pull_request.base.sha }}
               --to-ref ${{ github.event.pull_request.head.sha }}
         continue-on-error: true
-      - uses: pre-commit-ci/lite-action@v1.0.2
+      - uses: pre-commit-ci/lite-action@v1.1.0
 
       - name: Build
         run: |

docs/advanced/acceleration/cuda.md

@@ -29,12 +29,14 @@ To compile and use ABACUS in CUDA mode, you currently need to have an NVIDIA GPU
 
 Check the [Advanced Installation Options](https://abacus-rtd.readthedocs.io/en/latest/advanced/install.html#build-with-cuda-support) for the installation of CUDA version support.
 
-When the compilation parameter USE_ELPA is ON (which is the default value) and USE_CUDA is also set to ON, the ELPA library needs to [enable GPU support](https://github.com/marekandreas/elpa/blob/master/documentation/INSTALL.md) at compile time.
+Setting both USE_ELPA and USE_CUDA to ON does not automatically enable ELPA to run on GPUs. ELPA support for GPUs needs to be enabled when ELPA is compiled. [enable GPU support](https://github.com/marekandreas/elpa/blob/master/documentation/INSTALL.md).
+
+The ABACUS program will automatically determine whether the current ELPA supports GPU based on the elpa/elpa_configured_options.h header file. Users can also check this header file to determine the GPU support of ELPA in their environment. ELPA introduced a new API elpa_setup_gpu in version 2023.11.001. So if you want to enable ELPA GPU in ABACUS, the ELPA version must be greater than or equal to 2023.11.001.
 
 ## Run with the GPU support by editing the INPUT script:
 
 In `INPUT` file we need to set the input parameter [device](../input_files/input-main.md#device) to `gpu`. If this parameter is not set, ABACUS will try to determine if there are available GPUs.
-- Set `ks_solver`: For the PW basis, CG, BPCG and Davidson methods are supported on GPU; set the input parameter [ks_solver](../input_files/input-main.md#ks_solver) to `cg`, `bpcg` or `dav`. For the LCAO basis, `cusolver` and `elpa` is supported on GPU.
+- Set `ks_solver`: For the PW basis, CG, BPCG and Davidson methods are supported on GPU; set the input parameter [ks_solver](../input_files/input-main.md#ks_solver) to `cg`, `bpcg` or `dav`. For the LCAO basis, `cusolver`, `cusolvermp` and `elpa` is supported on GPU.
 - **multi-card**: ABACUS allows for multi-GPU acceleration. If you have multiple GPU cards, you can run ABACUS with several MPI processes, and each process will utilize one GPU card. For example, the command `mpirun -n 2 abacus` will by default launch two GPUs for computation. If you only have one card, this command will only start one GPU. 
 
 ## Examples

docs/advanced/input_files/input-main.md

@@ -161,6 +161,7 @@
     - [nbands\_istate](#nbands_istate)
     - [bands\_to\_print](#bands_to_print)
     - [if\_separate\_k](#if_separate_k)
+    - [out\_elf](#out_elf)
   - [Density of states](#density-of-states)
     - [dos\_edelta\_ev](#dos_edelta_ev)
     - [dos\_sigma](#dos_sigma)
@@ -245,6 +246,7 @@
     - [exx\_real\_number](#exx_real_number)
     - [exx\_symmetry\_realspace](#exx_symmetry_realspace)
     - [rpa\_ccp\_rmesh\_times](#rpa_ccp_rmesh_times)
+    - [out\_ri\_cv](#out_ri_cv)
   - [Molecular dynamics](#molecular-dynamics)
     - [md\_type](#md_type)
     - [md\_nstep](#md_nstep)
@@ -424,6 +426,8 @@
     - [abs\_wavelen\_range](#abs_wavelen_range)
     - [out\_wfc\_lr](#out_wfc_lr)
     - [abs\_broadening](#abs_broadening)
+    - [ri\_hartree\_benchmark](#ri_hartree_benchmark)
+    - [aims_nbasis](#aims_nbasis)
 
 [back to top](#full-list-of-input-keywords)
 ## System variables
@@ -663,6 +667,7 @@ These variables are used to control parameters related to input files.
 - **Type**: String
 - **Description**: the name of the structure file
   - Containing various information about atom species, including pseudopotential files, local orbitals files, cell information, atom positions, and whether atoms should be allowed to move.
+  - When [calculation](#calculation) is set to `md` and [md_restart](#md_restart) is set to `true`, this keyword will NOT work.
   - Refer to [Doc](https://github.com/deepmodeling/abacus-develop/blob/develop/docs/advanced/input_files/stru.md)
 - **Default**: STRU
 
@@ -928,6 +933,8 @@ calculations.
   - **genelpa**: This method should be used if you choose localized orbitals.
   - **scalapack_gvx**: Scalapack can also be used for localized orbitals.
   - **cusolver**: This method needs building with CUDA and at least one gpu is available.
+  - **cusolvermp**: This method supports multi-GPU acceleration and needs building with CUDA。 Note that when using cusolvermp, you should set the number of MPI processes to be equal to the number of GPUs.
+  - **elpa**: The ELPA solver supports both CPU and GPU. By setting the `device` to GPU, you can launch the ELPA solver with GPU acceleration (provided that you have installed a GPU-supported version of ELPA, which requires you to manually compile and install ELPA, and the ABACUS should be compiled with -DUSE_ELPA=ON and -DUSE_CUDA=ON). The ELPA solver also supports multi-GPU acceleration.
 
   If you set ks_solver=`genelpa` for basis_type=`pw`, the program will be stopped with an error message:
 
@@ -936,7 +943,13 @@ calculations.
   ```
 
   Then the user has to correct the input file and restart the calculation.
-- **Default**: cg (plane-wave basis), or genelpa (localized atomic orbital basis, if compiling option `USE_ELPA` has been set),lapack (localized atomic orbital basis, if compiling option `ENABLE_MPI` has not been set), scalapack_gvx, (localized atomic orbital basis, if compiling option `USE_ELPA` has not been set and if compiling option `ENABLE_MPI` has been set)
+- **Default**: 
+  - **PW basis**: cg.
+  - **LCAO basis**:
+    - genelpa (if compiling option `USE_ELPA` has been set)
+    - lapack (if compiling option `ENABLE_MPI` has not been set)
+    - scalapack_gvx (if compiling option `USE_ELPA` has not been set and compiling option `ENABLE_MPI` has been set)
+    - cusolver (if compiling option `USE_CUDA` has been set)
 
 ### nbands
 
@@ -1517,7 +1530,7 @@ These variables are used to control the output of properties.
 - **Type**: Integer \[Integer\](optional)
 - **Description**: 
   The first integer controls whether to output the charge density on real space grids:
-  - 1. Output the charge density (in Bohr^-3) on real space grids into the density files in the folder `OUT.${suffix}`. The files are named as:
+  - 1: Output the charge density (in Bohr^-3) on real space grids into the density files in the folder `OUT.${suffix}`. The files are named as:
     - nspin = 1: SPIN1_CHG.cube;
     - nspin = 2: SPIN1_CHG.cube, and SPIN2_CHG.cube;
     - nspin = 4: SPIN1_CHG.cube, SPIN2_CHG.cube, SPIN3_CHG.cube, and SPIN4_CHG.cube.
@@ -1797,6 +1810,23 @@ The band (KS orbital) energy for each (k-point, spin, band) will be printed in t
 - **Description**: Specifies whether to write the partial charge densities for all k-points to individual files or merge them. **Warning**: Enabling symmetry may produce incorrect results due to incorrect k-point weights. Therefore, when calculating partial charge densities, it is strongly recommended to set `symmetry = -1`.
 - **Default**: false
 
+### out_elf
+
+- **Type**: Integer \[Integer\](optional)
+- **Availability**: Only for Kohn-Sham DFT and Orbital Free DFT.
+- **Description**: Whether to output the electron localization function (ELF) in the folder `OUT.${suffix}`. The files are named as 
+    - nspin = 1:
+      - ELF.cube: ${\rm{ELF}} = \frac{1}{1+\chi^2}$, $\chi = \frac{\frac{1}{2}\sum_{i}{f_i |\nabla\psi_{i}|^2} - \frac{|\nabla\rho|^2}{8\rho}}{\frac{3}{10}(3\pi^2)^{2/3}\rho^{5/3}}$;
+    - nspin = 2:
+      - ELF_SPIN1.cube, ELF_SPIN2.cube: ${\rm{ELF}}_\sigma = \frac{1}{1+\chi_\sigma^2}$, $\chi_\sigma = \frac{\frac{1}{2}\sum_{i}{f_i |\nabla\psi_{i,\sigma}|^2} - \frac{|\nabla\rho_\sigma|^2}{8\rho_\sigma}}{\frac{3}{10}(6\pi^2)^{2/3}\rho_\sigma^{5/3}}$;
+      - ELF.cube: ${\rm{ELF}} = \frac{1}{1+\chi^2}$, $\chi = \frac{\frac{1}{2}\sum_{i,\sigma}{f_i |\nabla\psi_{i,\sigma}|^2} - \sum_{\sigma}{\frac{|\nabla\rho_\sigma|^2}{8\rho_\sigma}}}{\sum_{\sigma}{\frac{3}{10}(6\pi^2)^{2/3}\rho_\sigma^{5/3}}}$;
+
+  The second integer controls the precision of the kinetic energy density output, if not given, will use `3` as default. For purpose restarting from this file and other high-precision involved calculation, recommend to use `10`.
+
+  ---
+  In molecular dynamics calculations, the output frequency is controlled by [out_interval](#out_interval).
+- **Default**: 0 3
+
 [back to top](#full-list-of-input-keywords)
 
 ## Density of states
@@ -2436,6 +2466,12 @@ These variables are relevant when using hybrid functionals.
   - True: rotate both D(k) and Hexx(R) to accelerate both diagonalization and EXX calculation
 - **Default**: True
 
+### out_ri_cv
+
+- **Type**: Boolean
+- **Description**: Whether to output the coefficient tensor C(R) and ABFs-representation Coulomb matrix V(R) for each atom pair and cell in real space.
+- **Default**: false
+
 [back to top](#full-list-of-input-keywords)
 
 ## Molecular dynamics
@@ -3946,4 +3982,21 @@ The output files are `OUT.${suffix}/Excitation_Energy.dat` and `OUT.${suffix}/Ex
 - **Description**: The broadening factor $\eta$ for the absorption spectrum calculation.
 - **Default**: 0.01
 
+### ri_hartree_benchmark
+- **Type**: String
+- **Description**: Whether to use the localized resolution-of-identity (LRI) approximation for the **Hartree** term of kernel in the $A$ matrix of LR-TDDFT for benchmark (with FHI-aims or another ABACUS calculation). Now it only supports molecular systems running with a single processor, and a large enough supercell should be used to make LRI C, V tensors contain only the R=(0 0 0) cell. 
+  - `aims`: The `OUT.${suffix}`directory should contain the FHI-aims output files: RI-LVL tensors`Cs_data_0.txt` and `coulomb_mat_0.txt`, and KS eigenstates from FHI-aims: `band_out`and `KS_eigenvectors.out`. The Casida equation will be constructed under FHI-aims' KS eigenpairs.
+    - LRI tensor files (`Cs_data_0.txt` and `coulomb_mat_0.txt`)and Kohn-Sham eigenvalues (`bands_out`): run FHI-aims with periodic boundary conditions and with `total_energy_method rpa` and `output librpa`.
+    - Kohn-Sham eigenstates under aims NAOs (`KS_eigenvectors.out`): run FHI-aims with `output eigenvectors`.
+    - If the number of atomic orbitals of any atom type in FHI-aims is different from that in ABACUS, the `aims_nbasis` should be set.
+  - `abacus`: The `OUT.${suffix}`directory should contain the RI-LVL tensors `Cs` and `Vs` (written by setting `out_ri_cv` to 1). The Casida equation will be constructed under ABACUS' KS eigenpairs, with the only difference that the Hartree term is constructed with RI approximation.
+  - `none`: Construct the Hartree term by Poisson equation and grid integration as usual.
+- **Default**: none
+
+### aims_nbasis
+- **Type**: A number(ntype) of Integers
+- **Availability**: `ri_hartree_benchmark` = `aims`
+- **Description**: Atomic basis set size for each atom type (with the same order as in `STRU`) in FHI-aims.
+- **Default**: {} (empty list, where ABACUS use its own basis set size)
+
 [back to top](#full-list-of-input-keywords)

docs/advanced/install.md

@@ -93,9 +93,9 @@ cmake -B build -DUSE_CUDA=1 -DCMAKE_CUDA_COMPILER=${path to cuda toolkit}/bin/nv
 
 ## Build math library from source
 
-> Note: This flag is **enabled by default**. It will get better performance than the standard implementation on `gcc` and `clang`. But it **will be disabled** when using `Intel Compiler` since the math functions will get wrong results and the performance is also unexpectly poor.
+> Note: We recommend using the latest available compiler sets, since they offer faster implementations of math functions.
 
-To build math functions from source code, instead of using c++ standard implementation, define `USE_ABACUS_LIBM` flag.
+This flag is disabled by default. To build math functions from source code, define `USE_ABACUS_LIBM` flag. It is expected to get a better performance on legacy versions of `gcc` and `clang`.
 
 Currently supported math functions:
  `sin`, `cos`, `sincos`, `exp`, `cexp`

examples/lr-tddft/H2-RI-J-aims-benchmark/INPUT

@@ -0,0 +1,39 @@
+INPUT_PARAMETERS
+#Parameters (1.General)
+suffix                 aims-benchmark-tdhf
+pseudo_dir              /home/fortneu49/LR-TDDFT/abacus-develop/tests/PP_ORB
+orbital_dir                 /home/fortneu49/LR-TDDFT/abacus-develop/tests/PP_ORB
+calculation             scf
+nbands                4
+symmetry               	0
+
+#Parameters (2.Iteration)
+ecutwfc                 50
+scf_thr                     1e-6
+scf_nmax                   100
+
+#Parameters (3.Basis)
+basis_type              lcao 
+gamma_only              1
+nspin 2
+
+#Parameters (4.Smearing)
+smearing_method                gaussian
+smearing_sigma                   0.02
+
+#Parameters (5.Mixing)
+mixing_type             pulay
+mixing_beta             0.4
+mixing_gg0 0.0
+
+
+exx_real_number 1
+lr_nstates 3
+nvirt 3
+xc_kernel hf
+lr_solver lapack
+
+esolver_type lr
+ri_hartree_benchmark aims
+aims_nbasis 5
+read_file_dir aims-files

examples/lr-tddft/H2-RI-J-aims-benchmark/KPT

@@ -0,0 +1,4 @@
+K_POINTS
+0
+Gamma
+1 1 1 0 0 0

examples/lr-tddft/H2-RI-J-aims-benchmark/STRU

@@ -0,0 +1,22 @@
+ATOMIC_SPECIES
+H 1.008 H_ONCV_PBE-1.0.upf
+
+NUMERICAL_ORBITAL
+H_gga_8au_60Ry_2s1p.orb
+
+LATTICE_CONSTANT
+1.889725989
+
+LATTICE_VECTORS
+30 0 0
+0 30 0
+0 0  30
+
+ATOMIC_POSITIONS
+Cartesian
+
+H
+0
+2 
+0 0 10.37 0 0 0
+0 0 9.63 0 0 0