merge the latest abacus

Author: JGHan7

.github/workflows/coverage.yml

@@ -25,7 +25,7 @@ jobs:
         env:
           OMP_NUM_THREADS: 1
         run: |
-          cmake --build build --target test ARGS="-V --timeout 21600"
+          cmake --build build --target test ARGS="-V --timeout 21600" || exit 0
       - name: Upload Coverage to Codecov
         uses: codecov/codecov-action@v4
         if: ${{ ! cancelled() }}

.gitmodules

@@ -1,11 +1,3 @@
-[submodule "deps/LibRI"]
-	path = deps/LibRI
-	url = https://github.com/abacusmodeling/LibRI.git
-	branch = master
-[submodule "deps/LibComm"]
-	path = deps/LibComm
-	url = https://github.com/abacusmodeling/LibComm.git
-	branch = master
 [submodule "deps/libpaw_interface"]
 	path = deps/libpaw_interface
 	url = https://github.com/wenfei-li/libpaw_interface

CMakeLists.txt

@@ -538,13 +538,10 @@ endif()
 if(ENABLE_LIBRI)
   set_if_higher(CMAKE_CXX_STANDARD 14)
   if(LIBRI_DIR)
-    include_directories(${LIBRI_DIR}/include)
-  elseif(GIT_SUBMODULE)
-    git_submodule_update()
-    include_directories(${CMAKE_CURRENT_SOURCE_DIR}/deps/LibRI/include)
   else()
-    message(FATAL_ERROR "Must provide LIBRI_DIR for RI related features.")
+    find_package(LibRI REQUIRED)
   endif()
+  include_directories(${LIBRI_DIR}/include)
   target_link_libraries(${ABACUS_BIN_NAME} ri module_exx_symmetry)
   add_compile_definitions(__EXX EXX_DM=3 EXX_H_COMM=2 TEST_EXX_LCAO=0
                           TEST_EXX_RADIAL=1)
@@ -555,13 +552,10 @@ if(ENABLE_LIBRI OR DEFINED LIBCOMM_DIR)
 endif()
 if(ENABLE_LIBCOMM)
   if(LIBCOMM_DIR)
-    include_directories(${LIBCOMM_DIR}/include)
-  elseif(GIT_SUBMODULE)
-    git_submodule_update()
-    include_directories(${CMAKE_CURRENT_SOURCE_DIR}/deps/LibComm/include)
   else()
-    message(FATAL_ERROR "Must provide LIBCOMM_DIR for RI related features.")
+    find_package(LibComm REQUIRED)
   endif()
+  include_directories(${LIBCOMM_DIR}/include)
 endif()
 
 if(ENABLE_PAW)

cmake/FindLibComm.cmake

@@ -0,0 +1,30 @@
+###############################################################################
+# - Find LibComm
+# Find the native LibComm files.
+#
+#  LIBCOMM_FOUND - True if LibComm is found.
+#  LIBCOMM_DIR - Where to find LibComm files.
+
+find_path(LIBCOMM_DIR
+    include/Comm/Comm_Tools.h
+    HINTS ${LIBCOMM_DIR}
+    HINTS ${LibComm_DIR}
+    HINTS ${libcomm_DIR}
+)
+
+if(NOT LIBCOMM_DIR)
+    include(FetchContent)
+    FetchContent_Declare(
+        LibComm
+        URL https://github.com/abacusmodeling/LibComm/archive/refs/tags/v0.1.1.tar.gz
+    )
+    FetchContent_Populate(LibComm)
+    set(LIBCOMM_DIR ${libcomm_SOURCE_DIR})
+endif()
+# Handle the QUIET and REQUIRED arguments and
+# set LIBCOMM_FOUND to TRUE if all variables are non-zero.
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(LibComm DEFAULT_MSG LIBCOMM_DIR)
+
+# Copy the results to the output variables and target.
+mark_as_advanced(LIBCOMM_DIR)

cmake/FindLibRI.cmake

@@ -0,0 +1,30 @@
+###############################################################################
+# - Find LibRI
+# Find the native LibRI files.
+#
+#  LIBRI_FOUND - True if LibRI is found.
+#  LIBRI_DIR - Where to find LibRI files.
+
+find_path(LIBRI_DIR
+    include/RI/version.h
+    HINTS ${LIBRI_DIR}
+    HINTS ${LibRI_DIR}
+    HINTS ${libri_DIR}
+)
+
+if(NOT LIBRI_DIR)
+    include(FetchContent)
+    FetchContent_Declare(
+        LibRI
+        URL https://github.com/abacusmodeling/LibRI/archive/refs/tags/v0.2.1.1.tar.gz
+    )
+    FetchContent_Populate(LibRI)
+    set(LIBRI_DIR ${libri_SOURCE_DIR})
+endif()
+# Handle the QUIET and REQUIRED arguments and
+# set LIBRI_FOUND to TRUE if all variables are non-zero.
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(LibRI DEFAULT_MSG LIBRI_DIR)
+
+# Copy the results to the output variables and target.
+mark_as_advanced(LIBRI_DIR)

deps/LibComm

@@ -88,6 +88,9 @@
     - [scf\_thr](#scf_thr)
     - [scf\_ene\_thr](#scf_ene_thr)
     - [scf\_thr\_type](#scf_thr_type)
+    - [scf\_os\_stop](#scf_os_stop)
+    - [scf\_os\_thr](#scf_os_thr)
+    - [scf\_os\_ndim](#scf_os_ndim)
     - [chg\_extrap](#chg_extrap)
     - [lspinorb](#lspinorb)
     - [noncolin](#noncolin)
@@ -1176,7 +1179,7 @@ Note: In new angle mixing, you should set `mixing_beta_mag >> mixing_beta`. The
 
 - **Type**: Integer
 - **Description**: Print out energy for each band for every printe step
-- **Default**: 100
+- **Default**: `scf_nmax`
 
 ### scf_nmax
 
@@ -1208,6 +1211,29 @@ Note: In new angle mixing, you should set `mixing_beta_mag >> mixing_beta`. The
 
 - **Default**: 1 (plane-wave basis), or 2 (localized atomic orbital basis).
 
+### scf_os_stop
+
+- **Type**: bool
+- **Description**: For systems that are difficult to converge, the SCF process may exhibit oscillations in charge density, preventing further progress toward the specified convergence criteria and resulting in continuous oscillation until the maximum number of steps is reached; this greatly wastes computational resources. To address this issue, this function allows ABACUS to terminate the SCF process early upon detecting oscillations, thus reducing subsequent meaningless calculations. The detection of oscillations is based on the slope of the logarithm of historical drho values.. To this end, Least Squares Method is used to calculate the slope of the logarithmically taken drho for the previous `scf_os_ndim` iterations. If the calculated slope is larger than `scf_os_thr`, stop the SCF.
+
+  - **0**: The SCF will continue to run regardless of whether there is oscillation or not. 
+  - **1**: If the calculated slope is larger than `scf_os_thr`, stop the SCF.
+
+- **Default**: false
+
+### scf_os_thr
+
+- **Type**: double
+- **Description**: The slope threshold to determine if the SCF is stuck in a charge density oscillation. If the calculated slope is larger than `scf_os_thr`, stop the SCF.
+
+- **Default**: -0.01
+
+### scf_os_ndim
+
+- **Type**: int
+- **Description**: To determine the number of old iterations' `drho` used in slope calculations.
+- **Default**: `mixing_ndim`
+
 ### chg_extrap
 
 - **Type**: String

deps/LibRI

@@ -3,8 +3,13 @@ INPUT_PARAMETERS
 pseudo_dir              ../../../tests/PP_ORB	
 calculation		scf
 #Parameters (Accuracy)
-ecutwfc			50
+ecutwfc			 60 ###Energy cutoff needs to be tested to ensure your calculation is reliable.[1]
 scf_thr         	1e-8
 scf_nmax		20
 basis_type		pw
 latname			fcc
+
+
+### [1] Energy cutoff determines the quality of numerical quadratures in your calculations.
+###     So it is strongly recommended to test whether your result (such as converged SCF energies) is
+###     converged with respect to the energy cutoff.

docs/advanced/input_files/input-main.md

@@ -3,9 +3,14 @@ INPUT_PARAMETERS
 pseudo_dir              ../../../tests/PP_ORB	
 calculation             scf
 #Parameters (Accuracy)
-ecutwfc			50
+ecutwfc			 60 ###Energy cutoff needs to be tested to ensure your calculation is reliable.[1]
 scf_thr         	1e-8
 scf_nmax		20
 smearing_sigma		0.002
 basis_type		pw
 latname			hexagonal
+
+
+### [1] Energy cutoff determines the quality of numerical quadratures in your calculations.
+###     So it is strongly recommended to test whether your result (such as converged SCF energies) is
+###     converged with respect to the energy cutoff.