Merge branch 'deepmodeling:develop' into develop

Author: 1041176461

.github/workflows/build_test_cmake.yml

@@ -17,7 +17,7 @@ jobs:
             name: "Build with Intel toolchain"
 
           - tag: gnu
-            build_args: "-DENABLE_LIBXC=1 -DENABLE_DEEPKS=1 -DENABLE_MLKEDF=1 -DENABLE_LIBRI=1 -DENABLE_PAW=1"
+            build_args: "-DENABLE_LIBXC=1 -DENABLE_DEEPKS=1 -DENABLE_MLKEDF=1 -DENABLE_LIBRI=1"
             name: "Build extra components with GNU toolchain"
           - tag: intel
             build_args: "-DENABLE_LIBXC=1 -DENABLE_DEEPKS=1 -DENABLE_MLKEDF=1 -DENABLE_LIBRI=1"

.github/workflows/coverage.yml

@@ -18,7 +18,7 @@ jobs:
           apt update && apt install -y lcov gpg curl jq ca-certificates
       - name: Building
         run: |
-          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 -B build -DENABLE_COVERAGE=ON -DBUILD_TESTING=ON -DENABLE_DEEPKS=ON -DENABLE_LIBXC=ON -DENABLE_LIBRI=ON -DENABLE_GOOGLEBENCH=ON -DENABLE_RAPIDJSON=ON
           cmake --build build -j`nproc`
           cmake --install build
       - name: Testing

.github/workflows/test.yml

@@ -31,7 +31,7 @@ jobs:
 
       - name: Configure
         run: |
-          cmake -B build -DBUILD_TESTING=ON -DENABLE_DEEPKS=ON -DENABLE_MLKEDF=ON -DENABLE_LIBXC=ON -DENABLE_LIBRI=ON -DENABLE_PAW=ON -DENABLE_GOOGLEBENCH=ON -DENABLE_RAPIDJSON=ON  -DCMAKE_EXPORT_COMPILE_COMMANDS=1
+          cmake -B build -DBUILD_TESTING=ON -DENABLE_DEEPKS=ON -DENABLE_MLKEDF=ON -DENABLE_LIBXC=ON -DENABLE_LIBRI=ON -DENABLE_GOOGLEBENCH=ON -DENABLE_RAPIDJSON=ON  -DCMAKE_EXPORT_COMPILE_COMMANDS=1 -DENABLE_FLOAT_FFTW=ON
 
 # Temporarily removed because no one maintains this now.
 # And it will break the CI test workflow.
@@ -49,13 +49,62 @@ jobs:
           cmake --build build -j8
           cmake --install build
 
-      - name: Integrated Test
+      - name: Integrated Tests Preparation
         env:
           GTEST_COLOR: 'yes'
           OMP_NUM_THREADS: '2'
         run: |
           cmake --build build --target test ARGS="-V --timeout 1700 -R integrated_test"
 
+      - name: Module_Base Unittests
+        env:
+          GTEST_COLOR: 'yes'
+          OMP_NUM_THREADS: '2'
+        run: |
+          cmake --build build --target test ARGS="-V --timeout 1700 -R MODULE_BASE"
+      
+      - name: Module_IO Unittests
+        env:
+          GTEST_COLOR: 'yes'
+          OMP_NUM_THREADS: '2'
+        run: |
+          cmake --build build --target test ARGS="-V --timeout 1700 -R MODULE_IO"
+
+      - name: Module_HSolver Unittests
+        env:
+          GTEST_COLOR: 'yes'
+          OMP_NUM_THREADS: '2'
+        run: |
+          cmake --build build --target test ARGS="-V --timeout 1700 -R MODULE_HSOLVER"
+      
+      - name: Module_Cell Unittests
+        env:
+          GTEST_COLOR: 'yes'
+          OMP_NUM_THREADS: '2'
+        run: |
+          cmake --build build --target test ARGS="-V --timeout 1700 -R MODULE_CELL"
+      
+      - name: Module_MD Unittests
+        env:
+          GTEST_COLOR: 'yes'
+          OMP_NUM_THREADS: '2'
+        run: |
+          cmake --build build --target test ARGS="-V --timeout 1700 -R MODULE_MD"
+      
+      - name: Module_Psi Unittests
+        env:
+          GTEST_COLOR: 'yes'
+          OMP_NUM_THREADS: '2'
+        run: |
+          cmake --build build --target test ARGS="-V --timeout 1700 -R MODULE_PSI"
+      
+      - name: Module_RI Unittests
+        env:
+          GTEST_COLOR: 'yes'
+          OMP_NUM_THREADS: '2'
+        run: |
+          cmake --build build --target test ARGS="-V --timeout 1700 -R MODULE_RI"
+
       - name: 01_PW Test
         env:
           GTEST_COLOR: 'yes'
@@ -126,16 +175,9 @@ jobs:
         run: |
           cmake --build build --target test ARGS="-V --timeout 1700 -R 10_others"
 
-      - name: Module Base Unit Test
-        env:
-          GTEST_COLOR: 'yes'
-          OMP_NUM_THREADS: '2'
-        run: |
-          cmake --build build --target test ARGS="-V --timeout 1700 -R MODULE_BASE"
-
-      - name: Unit Test
+      - name: Other Unittests
         env:
           GTEST_COLOR: 'yes'
           OMP_NUM_THREADS: '2'
         run: |
-          cmake --build build --target test ARGS="-V --timeout 1700 -E 'integrate_test|01_PW|02_NAO_Gamma|03_NAO_multik|04_LJ_DP|05_rtTDDFT|06_SDFT|07_OFDFT|08_EXX|09_DeePKS|10_others|11_PW_GPU|16_SDFT_GPU'"
+          cmake --build build --target test ARGS="-V --timeout 1700 -E 'integrate_test|01_PW|02_NAO_Gamma|03_NAO_multik|04_LJ_DP|05_rtTDDFT|06_SDFT|07_OFDFT|08_EXX|09_DeePKS|10_others|11_PW_GPU|12_NAO_Gamma_GPU|13_NAO_multik_GPU|15_rtTDDFT_GPU|16_SDFT_GPU|MODULE_BASE|MODULE_IO|MODULE_HSOLVER|MODULE_CELL|MODULE_MD|MODULE_PSI|MODULE_RI'"

.gitignore

@@ -23,4 +23,4 @@ __pycache__
 abacus.json
 *.npy
 toolchain/install/
-toolchain/abacus_env.sh
+toolchain/abacus_env.sh

CMakeLists.txt

@@ -37,8 +37,6 @@ option(INFO "Enable gathering math library information" OFF)
 option(ENABLE_COVERAGE "Enable coverage build" OFF)
 option(GIT_SUBMODULE "Check submodules during build" ON)
 
-option(ENABLE_PAW "Enable PAW method" OFF)
-
 # Do not enable it if generated code will run on different CPUs
 option(ENABLE_NATIVE_OPTIMIZATION
        "Enable compilation optimization for the native machine's CPU type" OFF)
@@ -271,6 +269,7 @@ if(ENABLE_MPI)
   list(APPEND math_libs MPI::MPI_CXX)
 endif()
 
+
 if (USE_DSP)
   add_compile_definitions(__DSP)
   target_link_libraries(${ABACUS_BIN_NAME} ${OMPI_LIBRARY1})
@@ -611,18 +610,7 @@ if(ENABLE_LIBCOMM)
   include_directories(${LIBCOMM_DIR}/include)
 endif()
 
-if(ENABLE_PAW)
-  if(LIBPAW_DIR)
-    add_subdirectory(${LIBPAW_DIR})
-  elseif(GIT_SUBMODULE)
-    git_submodule_update()
-    add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/deps/libpaw_interface)
-  else()
-    message(FATAL_ERROR "Must provide LIBPAW_DIR for PAW related features.")
-  endif()
-  target_link_libraries(${ABACUS_BIN_NAME} paw)
-  add_compile_definitions(USE_PAW)
-endif()
+
 
 list(APPEND math_libs m)
 target_link_libraries(${ABACUS_BIN_NAME} ${math_libs})

docs/advanced/elec_properties/band.md

@@ -1,41 +1,40 @@
 # Extracting Band Structure
 
-ABACUS can calculate the energy band structure, and the examples can be found in [examples/band](https://github.com/deepmodeling/abacus-develop/tree/develop/examples/band).
-Similar to the [DOS case](https://abacus-rtd.readthedocs.io/en/latest/advanced/elec_properties/dos.html), we first, do a ground-state energy calculation ***with one additional keyword "[out_chg](https://abacus-rtd.readthedocs.io/en/latest/advanced/input_files/input-main.html#out-chg)" in the INPUT file***:
+In ABACUS, in order to obtain the eigenvalues of Hamiltonian, or generally called band structure, examples can be found in [examples/band](https://github.com/deepmodeling/abacus-develop/tree/develop/examples/band).
+Similar to the [DOS case](https://abacus-rtd.readthedocs.io/en/latest/advanced/elec_properties/dos.html), one first needs to perform a ground-state energy calculation ***with one additional keyword "[out_chg](https://abacus-rtd.readthedocs.io/en/latest/advanced/input_files/input-main.html#out-chg)" in the INPUT file***:
 
 ```
-out_chg             1
+out_chg 1
 ```
 
-This will produce the converged charge density, which is contained in the file SPIN1_CHG.cube.
-Then, use the same `STRU` file, pseudopotential file and atomic orbital file (and the local density matrix file onsite.dm if DFT+U is used) to do a non-self-consistent calculation. In this example, the potential is constructed from the ground-state charge density from the proceeding calculation. Now the INPUT file is like:
+With this input parameter, the converged charge density will be output in the files such as `chgs1.cube`, `chgs2.cube`, etc.
+Then, one can use the same `STRU` file, pseudopotential files and atomic orbital files (and the local density matrix file onsite.dm if DFT+U is used) to do a non-self-consistent (NSCF) calculation. In this example, the potential is constructed from the ground-state charge density from the proceeding calculation. Now the INPUT file is like:
 
 ```
 INPUT_PARAMETERS
 #Parameters (General)
-ntype 1
-nbands 8
-calculation nscf
-basis_type lcao
-read_file_dir   ./
+nbands        8
+calculation   nscf
+basis_type    lcao
+read_file_dir ./
 
 #Parameters (Accuracy)
-ecutwfc 60
-scf_nmax 50
-scf_thr 1.0e-9
-pw_diag_thr 1.0e-7
+ecutwfc       60
+scf_nmax      50
+scf_thr       1.0e-9
+pw_diag_thr   1.0e-7
 
 #Parameters (File)
-init_chg file
-out_band 1
+init_chg      file
+out_band      1
 out_proj_band 1
 
 #Parameters (Smearing)
 smearing_method gaussian
-smearing_sigma 0.02
+smearing_sigma  0.02
 ```
 
-Here the the relevant k-point file KPT looks like,
+Here is a relevant k-point file KPT (in LINE mode):
 
 ```
 K_POINTS # keyword for start
@@ -49,16 +48,16 @@ Line # line-mode
 0.0 0.0 0.0 1 # G
 ```
 
-This means we are using:
+This means we are using the following k-points:
 
-- 6 number of k points, here means 6 k points:
+- 6 k points, here means 6 k points:
   (0.5, 0.0, 0.5) (0.0, 0.0, 0.0) (0.5, 0.5, 0.5) (0.5, 0.25, 0.75) (0.375, 0.375, 0.75) (0.0, 0.0,
   0.0)
 - 20/1 number of k points along the segment line, which is constructed by two adjacent k
   points.
 
-Run the program, and you will see a file named BANDS_1.dat in the output directory. Plot it
-to get energy band structure.
+Next, run ABACUS and you will see a file named `eigs1.txt` in the output directory. 
+Plot it and you will obtain the energy band structure!
 
 If "out_proj_band" set 1, it will also produce the projected band structure in a file called PBAND_1 in xml format.
 
@@ -77,8 +76,8 @@ The rest of the files arranged in sections, each section with a header such as b
 
 ```
 <orbital
- index="                                       1"
- atom_index="                                       1"
+ index="                                   1"
+ atom_index="                              1"
  species="Si"
  l="                                       0"
  m="                                       0"

docs/advanced/elec_properties/hs_matrix.md

@@ -12,7 +12,7 @@ and
 
 ## out_mat_hs
 
-Users may set the keyword [out_mat_hs](../input_files/input-main.md#out_mat_hs) to true for outputting the upper triangular part of the Hamiltonian matrices and overlap matrices for each k point into files in the directory `OUT.${suffix}`. It is available for both gamma_only and multi-k calculations. 
+Users can set the keyword [out_mat_hs](../input_files/input-main.md#out_mat_hs) to true for outputting the upper triangular part of the Hamiltonian matrices and overlap matrices for each k point into files in the directory `OUT.${suffix}`. It is available for both gamma_only and multi-k calculations. 
 
 The files are named `data-$k-H` and `data-$k-S`, where `$k` is a composite index consisting of the k point index as well as the spin index. The corresponding sequence of the orbitals can be seen in [Basis Set](../pp_orb.md#basis-set).
 
@@ -35,7 +35,7 @@ The rest of the file contains the upper triangular part of the specified matrice
 
 The output of R-space matrices is controlled by the keyword [out_mat_hs2](../input_files/input-main.md#out_mat_hs2). This functionality is not available for gamma_only calculations. To generate such matrices for gamma only calculations, users should turn off [gamma_only](../input_files/input-main.md#gamma_only), and explicitly specify that gamma point is the only k point in the KPT file.
 
-For single-point SCF calculations, if nspin = 1 or nspin = 4, two files `data-HR-sparse_SPIN0.csr` and `data-SR-sparse_SPIN0.csr` are generated, which contain the Hamiltonian matrix $H(R)$ and overlap matrix $S(R)$ respectively. For nspin = 2, three files `data-HR-sparse_SPIN0.csr` and `data-HR-sparse_SPIN1.csr` and `data-SR-sparse_SPIN0.csr` are created, where the first two contain $H(R)$ for spin up and spin down, respectively.
+For single-point SCF calculations, if nspin = 1 or nspin = 4, two files `hrs1_nao.csr` and `sr_nao.csr` are generated, which contain the Hamiltonian matrix $H(R)$ and overlap matrix $S(R)$ respectively. For nspin = 2, three files `hrs1_nao.csr` and `hrs2_nao.csr` and `sr_nao.csr` are created, where the first two files correspodn to $H(R)$ for spin up and spin down, respectively.
 
 As for molecular dynamics calculations, the format is controlled by [out_interval](../input_files/input-main.md#out_interval) and [out_app_flag](../input_files/input-main.md#out_app_flag) in the same manner as the position matrix as detailed in [out_mat_r](../input_files/input-main.md#out_mat_r).
 
@@ -74,4 +74,4 @@ We provide [examples](https://github.com/deepmodeling/abacus-develop/tree/develo
 - out_hs_multik : writing H(k) and S(k) for multi-k calculation
 - out_s_multik : running get_S for multi-k calculation
 
-Reference output files are provided in each directory.
+Reference output files are provided in each directory.

docs/advanced/elec_properties/wfc.md

@@ -9,8 +9,6 @@ In the LCAO basis case, several `WFC_NAO_K${k}.dat` files will be output in mult
 
 ## wave function in real space
 
-One can also choose to output real-space wave function in PW basis calculation with the key word ***[out_wfc_r](https://abacus-rtd.readthedocs.io/en/latest/advanced/input_files/input-main.html#out_wfc_r)***.
-
-After calculation, an additional directory named `wfc_realspace` will appear in the `OUT.${system}` directory.
+One can also choose to output real-space wave function in PW basis calculation with the key word ***[out_wfc_norm](https://abacus-rtd.readthedocs.io/en/latest/advanced/input_files/input-main.html#out-wfc-norm)***.
 
 Notice: when the ***[basis_type](https://abacus-rtd.readthedocs.io/en/latest/advanced/input_files/input-main.html#basis_type)*** is `lcao`, only `get_wf` ***[calculation](https://abacus-rtd.readthedocs.io/en/latest/advanced/input_files/input-main.html#calculation)*** is effective. An example is [examples/wfc/lcao_ienvelope_Si2](https://github.com/deepmodeling/abacus-develop/tree/develop/examples/wfc/lcao_ienvelope_Si2).