Merge branch 'develop' into refactor

Author: ErjieWu

.github/workflows/test.yml

@@ -132,12 +132,12 @@ jobs:
         run: |
           cmake --build build --target test ARGS="-V --timeout 1700 -R 03_NAO_multik"
 
-      - name: 04_LJ_DP Test
+      - name: 04_FF Test
         env:
           GTEST_COLOR: 'yes'
           OMP_NUM_THREADS: '2'
         run: |
-          cmake --build build --target test ARGS="-V --timeout 1700 -R 04_LJ_DP"
+          cmake --build build --target test ARGS="-V --timeout 1700 -R 04_FF"
 
       - name: 05_rtTDDFT Test
         env:
@@ -186,4 +186,4 @@ jobs:
           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|12_NAO_Gamma_GPU|13_NAO_multik_GPU|15_rtTDDFT_GPU|16_SDFT_GPU|MODULE_BASE|MODULE_IO|MODULE_HSOLVER|MODULE_CELL|MODULE_MD|source_psi|MODULE_RI'"
+          cmake --build build --target test ARGS="-V --timeout 1700 -E 'integrate_test|01_PW|02_NAO_Gamma|03_NAO_multik|04_FF|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|source_psi|MODULE_RI'"

.gitignore

@@ -23,4 +23,5 @@ __pycache__
 abacus.json
 *.npy
 toolchain/install/
-toolchain/abacus_env.sh
+toolchain/abacus_env.sh
+.trae

CMakeLists.txt

@@ -654,6 +654,15 @@ if(DEFINED DeePMD_DIR)
   endif()
 endif()
 
+if(DEFINED NEP_DIR)
+  find_package(NEP REQUIRED)
+
+  if(NEP_FOUND)
+    add_compile_definitions(__NEP)
+    target_link_libraries(${ABACUS_BIN_NAME} NEP::nep)
+  endif()
+endif()
+
 if(DEFINED TensorFlow_DIR)
   find_package(TensorFlow REQUIRED)
   include_directories(${TensorFlow_DIR}/include)

cmake/FindNEP.cmake

@@ -0,0 +1,49 @@
+###############################################################################
+# - Find NEP
+# Finds the NEP header and library.
+#
+# This module will search for the NEP library, looking for a hint
+# from the NEP_DIR environment variable or CMake variable.
+#
+# This module defines the following variables:
+#
+#  NEP_FOUND        - True if the NEP library and headers were found.
+#  NEP_INCLUDE_DIR  - The directory where nep.h is located.
+#  NEP_LIBRARY      - The full path to the NEP library.
+#
+# It also defines the following imported target:
+#
+#  NEP::nep     - The NEP library target.
+#
+###############################################################################
+# Note: Currently only CPU version is supported, Since the NEP interface with GPU support is not available yet.
+#       In feature, if available, we can use USE_CUDA to switch between CPU and GPU version.
+
+find_path(NEP_INCLUDE_DIR nep.h
+    HINTS ${NEP_DIR}
+    PATH_SUFFIXES "include"
+    )
+
+find_library(NEP_LIBRARY
+    NAMES nep
+    HINTS ${NEP_DIR}
+    PATH_SUFFIXES "lib"
+    )
+
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(NEP
+    DEFAULT_MSG
+    NEP_LIBRARY NEP_INCLUDE_DIR)
+
+if(NEP_FOUND)
+    if(NOT TARGET NEP::nep)
+        add_library(NEP::nep UNKNOWN IMPORTED)
+        set_target_properties(NEP::nep PROPERTIES
+            IMPORTED_LINK_INTERFACE_LANGUAGES "C"
+            IMPORTED_LOCATION "${NEP_LIBRARY}"
+            INTERFACE_INCLUDE_DIRECTORIES "${NEP_INCLUDE_DIR}"
+        )
+    endif()
+endif()
+
+mark_as_advanced(NEP_INCLUDE_DIR NEP_LIBRARY)

docs/advanced/input_files/input-main.md

@@ -535,6 +535,7 @@ These variables are used to control general system parameters.
   - tddft: real-time time-dependent density functional theory (TDDFT)
   - lj: Leonard Jones potential
   - dp: DeeP potential, see details in [md.md](../md.md#dpmd)
+  - nep: Neuroevolution Potential, see details in [md.md](../md.md#nep)
   - ks-lr: Kohn-Sham density functional theory + LR-TDDFT (Under Development Feature)
   - lr: LR-TDDFT with given KS orbitals (Under Development Feature)
 - **Default**: ksdft
@@ -2310,7 +2311,7 @@ Warning: this function is not robust enough for the current version. Please try
   - 0: Don't include bandgap label
   - 1: Include target bandgap label (see [deepks\_band\_range](#deepks_band_range) for more details)
   - 2: Include multiple bandgap label (see [deepks\_band\_range](#deepks_band_range) for more details)
-  - 3: For systems containing H atoms only, HOMO is defined as the max occupation expect H atoms and the bandgap label is the energy between HOMO and (HOMO + 1)
+  - 3: Used for systems containing H atoms. Here HOMO is defined as the max occupation except H atoms and the bandgap label is the energy between HOMO and (HOMO + 1)
 - **Default**: 0
 
 ### deepks_band_range
@@ -3327,7 +3328,7 @@ These variables are used to control molecular dynamics calculations. For more in
 ### pot_file
 
 - **Type**: String
-- **Description**: The filename of DP potential files, see [md.md](../md.md#dpmd) in detail.
+- **Description**: The filename of DP/NEP potential files, see [md.md](../md.md#dpmd) in detail.
 - **Default**: graph.pb
 
 ### dp_rescaling

docs/advanced/install.md

@@ -55,6 +55,17 @@ Similarly, DeePMD-kit supports PyTorch backend but its libraries are placed at a
 cmake -B build -DDeePMD_DIR=/dir_to_deepmd-kit -DTorch_DIR=/dir_to_pytorch
 ```
 
+## Build with NEP
+This interface enables running MD simulations with the NEP model. It requires the [NEP_CPU](https://github.com/brucefan1983/NEP_CPU) library, which can be easily installed using toolchain as shown below:
+```bash
+./install_abacus_toolchain.sh --with-nep=install
+```
+
+To build ABACUS:
+```bash
+cmake -B build -DNEP_DIR=/path/to/nep_cpu
+```
+
 ## Build with LibRI and LibComm
 
 The new EXX implementation depends on two external libraries:

docs/advanced/md.md

@@ -87,4 +87,8 @@ ABACUS performs the [Multi-Scale Shock Technique (MSST) integration](https://jou
 Compiling ABACUS with [DeePMD-kit](https://github.com/deepmodeling/deepmd-kit), MD calculations based on machine learning DP model is enabled.
 
 To employ DPMD calculations, [esolver_type](./input_files/input-main.md#esolver_type) should be set to `dp`.
-And the filename of DP model is specified by keyword [pot_file](./input_files/input-main.md#pot_file).
+And the filename of DP model is specified by keyword [pot_file](./input_files/input-main.md#pot_file).
+
+## NEP
+
+If ABACUS is compiled with the Neuroevolution Potential ([NEP](https://gpumd.org/potentials/nep.html)), MD simulations using  NEP models are enabled. To use this feature, set [esolver_type](./input_files/input-main.md#esolver_type) to `nep` and specify the potential file path with the [pot_file](./input_files/input-main.md#pot_file) keyword in your INPUT file.

source/Makefile.Objects

@@ -250,6 +250,7 @@ OBJS_ELECSTAT=elecstate.o\
     read_pseudo.o\
     cal_wfc.o\
     setup_estate_pw.o\
+    update_pot.o\
 
 OBJS_ELECSTAT_LCAO=elecstate_lcao.o\
       elecstate_lcao_cal_tau.o\
@@ -267,12 +268,12 @@ OBJS_ESOLVER=esolver.o\
     esolver_sdft_pw.o\
     esolver_lj.o\
     esolver_dp.o\
+    esolver_nep.o\
     esolver_of.o\
     esolver_of_tddft.o\
     esolver_of_tool.o\
     esolver_of_interface.o\
     pw_others.o\
-    pw_setup.o\
 
 OBJS_ESOLVER_LCAO=esolver_ks_lcao.o\
       esolver_ks_lcao_tddft.o\
@@ -545,7 +546,7 @@ OBJS_IO=input_conv.o\
     cal_test.o\
     write_dos_pw.o\
     nscf_fermi_surf.o\
-    nscf_band.o\
+    write_bands.o\
     cal_dos.o\
     cal_pdos_gamma.o\
     cal_pdos_multik.o\
@@ -578,6 +579,7 @@ OBJS_IO=input_conv.o\
     write_elecstat_pot.o\
     write_elf.o\
     write_dipole.o\
+    write_init.o\
     td_current_io.o\
     write_libxc_r.o\
     output_log.o\
@@ -723,6 +725,7 @@ OBJS_SRCPW=H_Ewald_pw.o\
     fp_energy.o\
     setup_pot.o\
     setup_pwrho.o\
+    setup_pwwfc.o\
     forces.o\
     forces_us.o\
     forces_nl.o\
@@ -764,6 +767,7 @@ OBJS_SRCPW=H_Ewald_pw.o\
     of_stress_pw.o\
     symmetry_rho.o\
     symmetry_rhog.o\
+    setup_psi.o\
     psi_init.o\
     elecond.o\
     sto_tool.o\

source/source_cell/module_neighbor/test/prepare_unitcell.h

@@ -98,7 +98,7 @@ class UcellTestPrepare
 		}
 		//lattice info
 		ucell->lat0 = this->lat0;
-		ucell->lat0_angstrom = ucell->lat0 * 0.529177;
+		ucell->lat0_angstrom = ucell->lat0 * ModuleBase::BOHR_TO_A;
 		ucell->tpiba = ModuleBase::TWO_PI/ucell->lat0;
 		ucell->tpiba2 = ucell->tpiba * ucell->tpiba;
 		ucell->latvec.e11 = this->latvec[0];

source/source_cell/read_atom_species.cpp

@@ -150,7 +150,7 @@ bool read_lattice_constant(std::ifstream& ifa,
         {
             ModuleBase::WARNING_QUIT("read_atom_species","Lattice constant <= 0.0");
         }
-        lat0_angstrom = lat0 * 0.529177;
+        lat0_angstrom = lat0 * ModuleBase::BOHR_TO_A;
         ModuleBase::GlobalFunc::OUT(ofs_running,"Lattice constant (Bohr)",lat0);
         ModuleBase::GlobalFunc::OUT(ofs_running,"Lattice constant (Angstrom)",lat0_angstrom);
         lat.tpiba  = ModuleBase::TWO_PI / lat0;