Merge branch 'master' of https://github.com/sunliang98/abacus-develop into ML_KEDF_merge

Author: sunliang98

.github/pull_request_template.md

@@ -1,11 +1,15 @@
 ### Reminder
 - [ ] Have you linked an issue with this pull request?
+- [ ] Have you added adequate unit tests and/or case tests for your pull request?
 - [ ] Have you noticed possible changes of behavior below or in the linked issue?
 - [ ] Have you explained the changes of codes in core modules of ESolver, HSolver, ElecState, Hamilt, Operator or Psi? (ignore if not applicable)
 
 ### Linked Issue
 Fix #...
 
+### Unit Tests and/or Case Tests for my changes
+- A unit test is added for each new feature or bug fix.
+
 ### What's changed?
 - Example: My changes might affect the performance of the application under certain conditions, and I have tested the impact on various scenarios...
 

.github/workflows/pytest.yml

@@ -0,0 +1,26 @@
+name: Pyabacus Build and Test
+
+on:
+  pull_request:
+
+jobs:
+  test:
+    name: PyTest
+    runs-on: ubuntu-latest
+    container:
+      image: ghcr.io/deepmodeling/abacus-gnu
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+            python-version: 3.8
+      - name: Build Pyabacus
+        run: |
+          cd python/pyabacus
+          python -m pip install -v .[test]
+      - name: Test Pyabacus
+        run: |
+          cd python/pyabacus/tests
+          pytest -v

CMakeLists.txt

@@ -397,19 +397,9 @@ if(MKLROOT)
     list(APPEND math_libs -lifcore)
   endif()
 else()
-  # In compatibility to builtin FindLAPACK.cmake before v3.5.4
-  if(DEFINED LAPACK_DIR)
-    string(APPEND CMAKE_PREFIX_PATH ";${LAPACK_DIR}")
-  endif()
-  if(DEFINED LAPACK_LIBRARY)
-    set(LAPACK_LIBRARIES ${LAPACK_LIBRARY})
-  endif()
-  if(DEFINED BLAS_DIR)
-    string(APPEND CMAKE_PREFIX_PATH ";${BLAS_DIR}")
-  endif()
 
   find_package(FFTW3 REQUIRED)
-  find_package(LAPACK REQUIRED)
+  find_package(Lapack REQUIRED)
   include_directories(${FFTW3_INCLUDE_DIRS})
   list(APPEND math_libs FFTW3::FFTW3 LAPACK::LAPACK BLAS::BLAS)
 

Dockerfile.cuda

@@ -17,7 +17,7 @@ ADD https://api.github.com/repos/deepmodeling/abacus-develop/git/refs/heads/deve
 
 RUN git clone https://github.com/deepmodeling/abacus-develop.git --depth 1 && \
     cd abacus-develop && \
-    cmake -B build -DUSE_CUDA=ON && \
+    cmake -B build -DUSE_CUDA=ON -DENABLE_RAPIDJSON=ON && \
     cmake --build build -j`nproc` && \
     cmake --install build && \
     rm -rf build && \

Dockerfile.gnu

@@ -21,7 +21,7 @@ ADD https://api.github.com/repos/deepmodeling/abacus-develop/git/refs/heads/deve
 
 RUN git clone https://github.com/deepmodeling/abacus-develop.git --depth 1 && \
     cd abacus-develop && \
-    cmake -B build -DENABLE_DEEPKS=ON -DENABLE_LIBXC=ON -DENABLE_LIBRI=ON && \
+    cmake -B build -DENABLE_DEEPKS=ON -DENABLE_LIBXC=ON -DENABLE_LIBRI=ON -DENABLE_RAPIDJSON=ON && \
     cmake --build build -j`nproc` && \
     cmake --install build && \
     rm -rf build && \

Dockerfile.intel

@@ -56,7 +56,7 @@ ADD https://api.github.com/repos/deepmodeling/abacus-develop/git/refs/heads/deve
 RUN source /opt/intel/oneapi/setvars.sh && \
     git clone https://github.com/deepmodeling/abacus-develop.git --depth 1 && \
     cd abacus-develop && \
-    cmake -B build -DENABLE_DEEPKS=ON -DENABLE_LIBXC=ON -DENABLE_LIBRI=ON && \
+    cmake -B build -DENABLE_DEEPKS=ON -DENABLE_LIBXC=ON -DENABLE_LIBRI=ON -DENABLE_RAPIDJSON=ON && \
     cmake --build build -j`nproc` && \
     cmake --install build && \
     rm -rf build && \

cmake/FindBlas.cmake

@@ -0,0 +1,15 @@
+if(DEFINED BLAS_DIR)
+    string(APPEND CMAKE_PREFIX_PATH ";${BLAS_DIR}")
+endif()
+if(DEFINED BLAS_LIBRARY)
+    set(BLAS_LIBRARIES ${BLAS_LIBRARY})
+endif()
+
+find_package(BLAS REQUIRED)
+
+if(NOT TARGET BLAS::BLAS)
+    add_library(BLAS::BLAS UNKNOWN IMPORTED)
+    set_target_properties(BLAS::BLAS PROPERTIES
+        IMPORTED_LINK_INTERFACE_LANGUAGES "C"
+	IMPORTED_LOCATION "${BLAS_LIBRARIES}")
+endif()

cmake/FindLapack.cmake

@@ -0,0 +1,17 @@
+# In compatibility to builtin FindLAPACK.cmake before v3.5.4
+if(DEFINED LAPACK_DIR)
+  string(APPEND CMAKE_PREFIX_PATH ";${LAPACK_DIR}")
+endif()
+if(DEFINED LAPACK_LIBRARY)
+  set(LAPACK_LIBRARIES ${LAPACK_LIBRARY})
+endif()
+
+find_package(Blas REQUIRED)
+find_package(LAPACK REQUIRED)
+
+if(NOT TARGET LAPACK::LAPACK)
+    add_library(LAPACK::LAPACK UNKNOWN IMPORTED)
+    set_target_properties(LAPACK::LAPACK PROPERTIES
+        IMPORTED_LINK_INTERFACE_LANGUAGES "C"
+        IMPORTED_LOCATION "${LAPACK_LIBRARIES}")
+endif()

cmake/FindLibxc.cmake

@@ -11,7 +11,7 @@ endif()
 find_package(PkgConfig)
 if(PKG_CONFIG_FOUND)
   pkg_search_module(Libxc IMPORTED_TARGET GLOBAL libxc)
-  find_package_handle_standard_args(Libxc DEFAULT_MSG Libxc_LINK_LIBRARIES Libxc_INCLUDE_DIRS)
+  find_package_handle_standard_args(Libxc DEFAULT_MSG Libxc_LINK_LIBRARIES Libxc_FOUND)
 endif()
 if(NOT Libxc_FOUND)
   find_package(Libxc REQUIRED HINTS

docs/advanced/input_files/input-main.md

@@ -276,6 +276,7 @@
     - [hubbard\_u](#hubbard_u)
     - [yukawa\_potential](#yukawa_potential)
     - [yukawa\_lambda](#yukawa_lambda)
+    - [uramping](#uramping)
     - [omc](#omc)
     - [onsite\_radius](#onsite_radius)
   - [vdW correction](#vdw-correction)
@@ -338,8 +339,8 @@
     - [td\_trigo\_amp](#td_trigo_amp)
     - [td\_heavi\_t0](#td_heavi_t0)
     - [td\_heavi\_amp](#td_heavi_amp)
-    - [td\_out\_dipole](#td_out_dipole)
-    - [td\_out\_efield](#td_out_efield)
+    - [out\_dipole](#out_dipole)
+    - [out\_efield](#out_efield)
     - [ocp](#ocp)
     - [ocp\_set](#ocp_set)
   - [Variables useful for debugging](#variables-useful-for-debugging)
@@ -441,8 +442,9 @@ These variables are used to control general system parameters.
   - 0: Only time reversal symmetry would be considered in symmetry operations, which implied k point and -k point would be treated as a single k point with twice the weight.
   - 1: Symmetry analysis will be performed to determine the type of Bravais lattice and associated symmetry operations. (point groups, space groups, primitive cells, and irreducible k-points)
 - **Default**: 
-  - -1: if (*[dft_fuctional](#dft_functional)==hse/hf/pbe0/scan0/opt_orb* or *[rpa](#rpa)==True*) and *[calculation](#calculation)!=nscf*. Currently symmetry is not supported in EXX (exact exchange) calculation.
-  - 0: if *[calculation](#calculation)==md/nscf/get_pchg/get_wf/get_S* or *[gamma_only]==True*
+  - 0:
+    - if *[calculation](#calculation)==md/nscf/get_pchg/get_wf/get_S* or *[gamma_only]==True*;  
+    - If (*[dft_fuctional](#dft_functional)==hse/hf/pbe0/scan0/opt_orb* or *[rpa](#rpa)==True*). Currently *symmetry==1* is not supported in EXX (exact exchange) calculation.
   - 1: else
 
 ### symmetry_prec
@@ -1452,6 +1454,8 @@ These variables are used to control the output of properties.
   - npsin = 4: SPIN1_CHG.cube, SPIN2_CHG.cube, SPIN3_CHG.cube, and SPIN4_CHG.cube.
 
   The circle order of the charge density on real space grids is: x is the outer loop, then y and finally z (z is moving fastest).
+
+  If EXX(exact exchange) is calculated, (i.e. *[dft_fuctional](#dft_functional)==hse/hf/pbe0/scan0/opt_orb* or *[rpa](#rpa)==True*), the Hexx(R) files will be output in the folder `OUT.${suffix}` too, which can be read in NSCF calculation.
 - **Default**: False
 
 ### out_pot
@@ -1655,16 +1659,20 @@ These variables are used to control the output of properties.
 
 - **Type**: Boolean
 - **Availability**: Numerical atomic orbital basis
-- **Description**: Whether to save charge density files and Hamiltonian matrix files per ionic step, which are used to restart calculations. According to the value of [read_file_dir](#read_file_dir):
+- **Description**: Whether to save charge density files per ionic step, which are used to restart calculations. According to the value of [read_file_dir](#read_file_dir):
   - auto: These files are saved in folder `OUT.${suffix}/restart/`;
   - other: These files are saved in folder `${read_file_dir}/restart/`.
+  
+  If EXX(exact exchange) is calculated (i.e. *[dft_fuctional](#dft_functional)==hse/hf/pbe0/scan0/opt_orb* or *[rpa](#rpa)==True*), the Hexx(k) files for each k-point will also be saved in the above folder, which can be read in EXX calculation with *[restart_load](#restart_load)==True*.
 - **Default**: False
 
 ### restart_load
 
 - **Type**: Boolean
 - **Availability**: Numerical atomic orbital basis
-- **Description**: If [restart_save](#restart_save) is set to true and an electronic iteration is finished, calculations can be restarted from the charge density file and Hamiltonian matrix file, which are saved in the former calculation. Please ensure [read_file_dir](#read_file_dir) is correct, and  the charge density file and Hamiltonian matrix file exist.
+- **Description**: If [restart_save](#restart_save) is set to true and an electronic iteration is finished, calculations can be restarted from the charge density file, which are saved in the former calculation. Please ensure [read_file_dir](#read_file_dir) is correct, and  the charge density file exist.
+
+  If EXX(exact exchange) is calculated (i.e. *[dft_fuctional](#dft_functional)==hse/hf/pbe0/scan0/opt_orb* or *[rpa](#rpa)==True*), the Hexx(k) files in the same folder for each k-point will also be read.
 - **Default**: False
 
 ### rpa
@@ -2603,6 +2611,14 @@ These variables are used to control DFT+U correlated parameters
 - **Description**: The screen length of Yukawa potential. If left to default, the screen length will be calculated as an average of the entire system. It's better to stick to the default setting unless there is a very good reason.
 - **Default**: Calculated on the fly.
 
+### uramping
+
+- **Type**: Real
+- **Unit**: eV
+- **Availability**: DFT+U calculations with `mixing_restart > 0`.
+- **Description**: Once `uramping` > 0.15 eV. DFT+U calculations will start SCF with U = 0 eV, namely normal LDA/PBE calculations. Once SCF restarts when `drho<mixing_restart`, U value will increase by `uramping` eV. SCF will repeat above calcuations until U values reach target defined in `hubbard_u`. As for `uramping=1.0 eV`, the recommendations of `mixing_restart` is around `5e-4`.  
+- **Default**: -1.0.
+
 ### omc
 
 - **Type**: Integer
@@ -3170,18 +3186,18 @@ These variables are used to control berry phase and wannier90 interface paramete
   E = 0.0 , t>t0
 - **Default**: 2.74
 
-### td_out_dipole
+### out_dipole
 
 - **Type**: Boolean
 - **Description**:
   - True: output dipole.
   - False: do not output dipole.
 - **Default**: False
 
-### td_out_efield
+### out_efield
 
 - **Type**: Boolean
-- **Description**: The unit of output file is atomic unit (1 a.u. = 1 Ry/(bohr $\cdot$ e) = 51.422 V/Angstrom).
+- **Description**: output TDDFT Efield or not(V/Angstrom)
   - True: output efield.
   - False: do not output efield.
 - **Default**: False