Merge branch 'deepmodeling:develop' into test

Author: ErjieWu

.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)

README.md

@@ -12,7 +12,9 @@
 
 # About ABACUS
 
-ABACUS (Atomic-orbital Based Ab-initio Computation at UStc) is an open-source package based on density functional theory (DFT). The package utilizes both plane wave and numerical atomic basis sets with the usage of norm-conserving pseudopotentials to describe the interactions between nuclear ions and valence electrons. ABACUS supports LDA, GGA, meta-GGA, and hybrid functionals. Apart from single-point calculations, the package allows geometry optimizations and ab-initio molecular dynamics with various ensembles. The package also provides a variety of advanced functionalities for simulating materials, including the DFT+U, VdW corrections, and implicit solvation model, etc. In addition, ABACUS strives to provide a general infrastructure to facilitate the developments and applications of novel machine-learning-assisted DFT methods (DeePKS, DP-GEN, DeepH, etc.) in molecular and material simulations.
+ABACUS (Atomic-orbital Based Ab-initio Computation at UStc) is an open-source package based on density functional theory (DFT). The package utilizes both plane wave and numerical atomic basis sets with the usage of norm-conserving pseudopotentials to describe the interactions between nuclear ions and valence electrons. ABACUS supports LDA, GGA, meta-GGA, and hybrid functionals. Apart from single-point calculations, the package allows geometry optimizations and ab-initio molecular dynamics with various ensembles. The package also provides a variety of advanced functionalities for simulating materials, including the DFT+U, VdW corrections, and implicit solvation model, etc. In addition, ABACUS strives to provide a general infrastructure to facilitate the developments and applications of novel machine-learning-assisted DFT methods (DeePKS, DP-GEN, DeepH, DeePTB etc.) in molecular and material simulations.
 
 # Online Documentation
 For detailed documentation, please refer to [our documentation website](https://abacus.deepmodeling.com/).
+
+See our [Github Pages](https://mcresearch.github.io/abacus-user-guide/) for more tutorials and developer guides.

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

@@ -26,7 +26,7 @@ The following references are required to be cited when using ABACUS. Specificall
 
 - **If DeePKS is used:**
 
-    Wenfei Li, Qi Ou, et al. "DeePKS+ABACUS as a Bridge between Expensive Quantum Mechanical Models and Machine Learning Potentials." <https://arxiv.org/abs/2206.10093>.
+    Wenfei Li, Qi Ou, et al. "DeePKS+ABACUS as a Bridge between Expensive Quantum Mechanical Models and Machine Learning Potentials." J. Phys. Chem. A 126.49 (2022): 9154-9164.
 
 - **If hybrid functional is used:**
 

deps/LibRI

@@ -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)
@@ -243,8 +246,8 @@
     - [exx\_opt\_orb\_ecut](#exx_opt_orb_ecut)
     - [exx\_opt\_orb\_tolerence](#exx_opt_orb_tolerence)
     - [exx\_real\_number](#exx_real_number)
-    - [exx\_symmetry\_realspace](#exx_symmetry_realspace)
     - [rpa\_ccp\_rmesh\_times](#rpa_ccp_rmesh_times)
+    - [exx\_symmetry\_realspace](#exx_symmetry_realspace)
     - [out\_ri\_cv](#out_ri_cv)
   - [Molecular dynamics](#molecular-dynamics)
     - [md\_type](#md_type)
@@ -273,6 +276,9 @@
     - [lj\_epsilon](#lj_epsilon)
     - [lj\_sigma](#lj_sigma)
     - [pot\_file](#pot_file)
+    - [dp\_rescaling](#dp_rescaling)
+    - [dp\_fparam](#dp_fparam)
+    - [dp\_aparam](#dp_aparam)
     - [msst\_direction](#msst_direction)
     - [msst\_vel](#msst_vel)
     - [msst\_vis](#msst_vis)
@@ -422,11 +428,12 @@
     - [nocc](#nocc)
     - [nvirt](#nvirt)
     - [lr\_nstates](#lr_nstates)
+    - [lr\_unrestricted](#lr_unrestricted)
     - [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)
+    - [aims\_nbasis](#aims_nbasis)
 
 [back to top](#full-list-of-input-keywords)
 ## System variables
@@ -728,7 +735,7 @@ These variables are used to control the plane wave related parameters.
 
 - **Type**: Real
 - **Description**: Energy cutoff for plane wave functions, the unit is **Rydberg**. Note that even for localized orbitals basis, you still need to setup an energy cutoff for this system. Because our local pseudopotential parts and the related force are calculated from plane wave basis set, etc. Also, because our orbitals are generated by matching localized orbitals to a chosen set of wave functions from a certain energy cutoff, this set of localize orbitals is most accurate under this same plane wave energy cutoff.
-- **Default**: 50
+- **Default**: 50 Ry (PW basis), 100 Ry (LCAO basis)
 
 ### ecutrho
 
@@ -1201,6 +1208,29 @@ 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
@@ -2908,46 +2938,38 @@ These variables are used to control vdW-corrected related parameters.
 - **Type**: String
 - **Description**: Specifies the method used for Van der Waals (VdW) correction. Available options are:
   - `d2`: [Grimme's D2](https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20495) dispersion correction method
-  - `d3_0`: [Grimme's DFT-D3(0)](https://aip.scitation.org/doi/10.1063/1.3382344) dispersion correction method
-  - `d3_bj`: [Grimme's DFTD3(BJ)](https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.21759) dispersion correction method
+  - `d3_0`: [Grimme's DFT-D3(0)](https://aip.scitation.org/doi/10.1063/1.3382344) dispersion correction method (zero-damping)
+  - `d3_bj`: [Grimme's DFTD3(BJ)](https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.21759) dispersion correction method (BJ-damping)
   - `none`: no vdW correction
 - **Default**: none
+- **Note**: ABACUS supports automatic setting on DFT-D3 parameters for common functionals after version 3.8.3 (and several develop versions earlier). To benefit from this feature, please specify the parameter `dft_functional` explicitly (for more details on this parameter, please see [dft_functional](#dft_functional)), otherwise the autoset procedure will crash with error message like `cannot find DFT-D3 parameter for XC(***)`. If not satisfied with those in-built parameters, any manually setting on `vdw_s6`, `vdw_s8`, `vdw_a1` and `vdw_a2` will overwrite. 
+- **Special**: There are special cases for functional family wB97 (Omega-B97): if want to use the functional wB97X-D3BJ, one needs to specify the `dft_functional` as `HYB_GGA_WB97X_V` and `vdw_method` as `d3_bj`. If want to use the functional wB97X-D3, specify `dft_functional` as `HYB_GGA_WB97X_D3` and `vdw_method` as `d3_0`.
 
 ### vdw_s6
 
 - **Type**: Real
 - **Availability**: `vdw_method` is set to `d2`, `d3_0`, or `d3_bj`
-- **Description**: This scale factor is used to optimize the interaction energy deviations in van der Waals (vdW) corrected calculations. The recommended values of this parameter are dependent on the chosen vdW correction method and the DFT functional being used. For DFT-D2, the recommended values are 0.75 (PBE), 1.2 (BLYP), 1.05 (B-P86), 1.0 (TPSS), and 1.05 (B3LYP). For DFT-D3, recommended values with different DFT functionals can be found on the [here](https://www.chemiebn.uni-bonn.de/pctc/mulliken-center/software/dft-d3/dft-d3). The default value of this parameter in ABACUS is set to be the recommended value for PBE.
+- **Description**: This scale factor is used to optimize the interaction energy deviations in van der Waals (vdW) corrected calculations. The recommended values of this parameter are dependent on the chosen vdW correction method and the DFT functional being used. For DFT-D2, the recommended values are 0.75 (PBE), 1.2 (BLYP), 1.05 (B-P86), 1.0 (TPSS), and 1.05 (B3LYP). If not set, will use values of PBE functional. For DFT-D3, recommended values with different DFT functionals can be found on the [here](https://github.com/dftd3/simple-dftd3/blob/main/assets/parameters.toml). If not set, will search in ABACUS built-in dataset based on the `dft_functional` keywords. User set value will overwrite the searched value.
 - **Default**:
   - 0.75: if `vdw_method` is set to `d2`
-  - 1.0: if `vdw_method` is set to `d3_0` or `d3_bj`
 
 ### vdw_s8
 
 - **Type**: Real
 - **Availability**: `vdw_method` is set to `d3_0` or `d3_bj`
-- **Description**: This scale factor is relevant for D3(0) and D3(BJ) van der Waals (vdW) correction methods. The recommended values of this parameter with different DFT functionals can be found on the [webpage](https://www.chemiebn.uni-bonn.de/pctc/mulliken-center/software/dft-d3/dft-d3). The default value of this parameter in ABACUS is set to be the recommended value for PBE.
-- **Default**:
-  - 0.722: if `vdw_method` is set to `d3_0`
-  - 0.7875: if `vdw_method` is set to `d3_bj`
+- **Description**: This scale factor is relevant for D3(0) and D3(BJ) van der Waals (vdW) correction methods. The recommended values of this parameter with different DFT functionals can be found on the [webpage](https://github.com/dftd3/simple-dftd3/blob/main/assets/parameters.toml). If not set, will search in ABACUS built-in dataset based on the `dft_functional` keywords. User set value will overwrite the searched value.
 
 ### vdw_a1
 
 - **Type**: Real
 - **Availability**: `vdw_method` is set to `d3_0` or `d3_bj`
-- **Description**: This damping function parameter is relevant for D3(0) and D3(BJ) van der Waals (vdW) correction methods. The recommended values of this parameter with different DFT functionals can be found on the [webpage](https://www.chemiebn.uni-bonn.de/pctc/mulliken-center/software/dft-d3/dft-d3). The default value of this parameter in ABACUS is set to be the recommended value for PBE.
-- **Default**:
-  - 1.217: if `vdw_method` is set to `d3_0`
-  - 0.4289: if `vdw_method` is set to `d3_bj`
+- **Description**: This damping function parameter is relevant for D3(0) and D3(BJ) van der Waals (vdW) correction methods. The recommended values of this parameter with different DFT functionals can be found on the [webpage](https://github.com/dftd3/simple-dftd3/blob/main/assets/parameters.toml). If not set, will search in ABACUS built-in dataset based on the `dft_functional` keywords. User set value will overwrite the searched value.
 
 ### vdw_a2
 
 - **Type**: Real
 - **Availability**: `vdw_method` is set to `d3_0` or `d3_bj`
-- **Description**: This damping function parameter is only relevant for D3(0) and D3(BJ) van der Waals (vdW) correction methods. The recommended values of this parameter with different DFT functionals can be found on the [webpage](https://www.chemiebn.uni-bonn.de/pctc/mulliken-center/software/dft-d3/dft-d3). The default value of this parameter in ABACUS is set to be the recommended value for PBE.
-- **Default**:
-  - 1.0: if `vdw_method` is set to `d3_0`
-  - 4.4407: if `vdw_method` is set to `d3_bj`
+- **Description**: This damping function parameter is only relevant for D3(0) and D3(BJ) van der Waals (vdW) correction methods. The recommended values of this parameter with different DFT functionals can be found on the [webpage](https://github.com/dftd3/simple-dftd3/blob/main/assets/parameters.toml). If not set, will search in ABACUS built-in dataset based on the `dft_functional` keywords. User set value will overwrite the searched value.
 
 ### vdw_d
 
@@ -3925,7 +3947,7 @@ Currently supported: `RPA`, `LDA`, `PBE`, `HSE`, `HF`.
 
 - **Type**: String
 - **Description**: The method to solve the Casida equation $AX=\Omega X$ in LR-TDDFT under Tamm-Dancoff approximation (TDA), where $A_{ai,bj}=(\epsilon_a-\epsilon_i)\delta_{ij}\delta_{ab}+(ai|f_{Hxc}|bj)+\alpha_{EX}(ab|ij)$ is the particle-hole excitation matrix and $X$ is the transition amplitude.
-  - `dav`: Construct $AX$ and diagonalize the Hamiltonian matrix iteratively with Davidson algorithm.
+  - `dav`/`dav_subspace`/ `cg`: Construct $AX$ and diagonalize the Hamiltonian matrix iteratively with Davidson/Non-ortho-Davidson/CG algorithm.
   - `lapack`: Construct the full $A$ matrix and directly diagonalize with LAPACK.
   - `spectrum`: Calculate absorption spectrum only without solving Casida equation. The `OUT.${suffix}/` directory should contain the
   files for LR-TDDFT eigenstates and eigenvalues, i.e. `Excitation_Energy.dat` and `Excitation_Amplitude_${processor_rank}.dat`