Merge branch 'deepmodeling:develop' into refactor

Author: ErjieWu

CMakeLists.txt

@@ -711,17 +711,17 @@ target_link_libraries(
   esolver
   vdw
   device
-  container)
+  container
+  dftu
+  deltaspin)
 if(ENABLE_LCAO)
   target_link_libraries(
     ${ABACUS_BIN_NAME}
     hamilt_lcao
     tddft
     orb
     gint
-    dftu
     hcontainer
-    deltaspin
     numerical_atomic_orbitals
     lr
     rdmft)

docs/advanced/input_files/input-main.md

@@ -1235,6 +1235,12 @@ Note: In new angle mixing, you should set `mixing_beta_mag >> mixing_beta`. The
 - **Description**: To determine the number of old iterations' `drho` used in slope calculations.
 - **Default**: `mixing_ndim`
 
+### sc_os_ndim
+
+- **Type**: int
+- **Description**: To determine the number of old iterations to judge oscillation, it occured,  more accurate lambda with DeltaSpin method would be calculated, only for PW base.
+- **Default**: 5
+
 ### chg_extrap
 
 - **Type**: String

docs/advanced/interface/Wannier90.md

@@ -2,11 +2,11 @@
 
 [Wannier90](http://www.wannier.org/) is a useful package to generating the maximally-localized Wannier functions (MLWFs), which can be used to compute advanced electronic properties. Some post-processing tools (such as WannierTools, etc.) will use MLWFs for further analysis and calculations. 
 
-Currently ABACUS provides an interface to Wannier90 package. The users are assumed to be familiar with the use of Wannier90. The ABACUS-Wannier90 interface is only suitable for nspin=1 or 2, not for nspin=4 or spin-orbit coupling (SOC). 
+Currently ABACUS provides an interface to Wannier90 package. The users are assumed to be familiar with the use of Wannier90. The ABACUS-Wannier90 interface is suitable for nspin=1, 2, 4 (including lspinorb=1).
 
 To construct the MLWFs using the wave functions of ABACUS generally requires four steps. Here we use the diamond as an example which can be found in [examples/interface_wannier90/](https://github.com/abacusmodeling/abacus-develop/tree/develop/examples/interface_wannier90).
 
-1. Enter the `ABACUS_towannier90/` folder, prepare a Wannier90 input file `diamond.win`, which is the main input file for Wannier90. Then To generate `diamond.nnkp` file by running Wannier90,  which ABACUS will read later: 
+1. Enter the `ABACUS_towannier90_pw/` folder, prepare a Wannier90 input file `diamond.win`, which is the main input file for Wannier90. Then To generate `diamond.nnkp` file by running Wannier90,  which ABACUS will read later: 
 
     ```
     wannier90 -pp diamond.win
@@ -73,17 +73,22 @@ To construct the MLWFs using the wave functions of ABACUS generally requires fou
     ```
     INPUT_PARAMETERS
 
+    pseudo_dir              ../../../tests/PP_ORB
+    orbital_dir             ../../../tests/PP_ORB
     ntype                   1
     ecutwfc                 50
     nbands                  4
+    smearing_method         fixed
     calculation             nscf
     scf_nmax                50
     pw_diag_thr             1.0e-12
-    scf_thr                 1.0e-15
+    scf_thr                 1.0e-13
     init_chg                file
-    symmetry                0
+    symmetry                -1
     towannier90             1
     nnkpfile                diamond.nnkp
+    basis_type              pw
+    out_wannier_unk         0
     ```
 
     There are seven interface-related parameters in the `INPUT` file:
@@ -97,7 +102,7 @@ To construct the MLWFs using the wave functions of ABACUS generally requires fou
     - [out_wannier_unk](../input_files/input-main.md#out_wannier_unk): control whether to output the "UNK.*" file.
     - [out_wannier_wvfn_formatted](../input_files/input-main.md#out_wannier_wvfn_formatted): control what format of the Wannier function file to output, `true`: output the formatted text file; `false`: output the binary file. Note that the `wvfn_formatted` option in `*.win` file (input file of Wannier90) has to be set accordingly with this option.
 
-    Note: You need to turn off the symmetry during the entire nscf calculation.
+    **Note: You need to turn off the symmetry during the entire nscf calculation.**
 
     To setup the `KPT` file according to the `diamond.win` file, which is similar to "begin kpoints ..." in the `diamond.win` file: 
 

docs/quick_start/easy_install.md

@@ -1,6 +1,17 @@
 # Easy Installation
 
-This guide helps you install ABACUS with basic features. **For DeePKS, DeePMD and Libxc support, or building with `make`, please refer to [the advanced installation guide](../advanced/install.md)** after going through this page. We recommend building ABACUS with `cmake` to avoid dependency issues. We recommend compiling ABACUS(and possibly its requirements) from the source code using the latest compiler for the best performace. You can also deploy ABACUS **without building** by [Docker](#container-deployment) or [conda](#install-by-conda). Please note that ABACUS only supports Linux; for Windows users, please consider using [WSL](https://learn.microsoft.com/en-us/windows/wsl/) or docker.
+This guide helps you install ABACUS with basic features. **For DeePKS, DeePMD and Libxc support, or building with `make`, please refer to [the advanced installation guide](../advanced/install.md)** after going through this page. We recommend building ABACUS with `cmake` to avoid dependency issues. We recommend compiling ABACUS(and possibly its requirements) from the source code using the latest compiler for the best performace. You can try [toolchain](#install-requirements-by-toolchain) to install ABACUS and dependencies in a source-code compilation way with convience. You can also deploy ABACUS **without building** by [Docker](#container-deployment) or [conda](#install-by-conda). Please note that ABACUS only supports Linux; for Windows users, please consider using [WSL](https://learn.microsoft.com/en-us/windows/wsl/) or docker.
+
+## Get ABACUS source code
+
+ABACUS source code can be obtained via one of the following choices:
+
+- Clone the whole repo with git: `git clone https://github.com/deepmodeling/abacus-develop.git`
+- Clone the minimum required part of repo: `git clone https://github.com/deepmodeling/abacus-develop.git --depth=1`
+- Download the latest source code without git: `wget https://github.com/deepmodeling/abacus-develop/archive/refs/heads/develop.zip`
+- Get the source code of a stable version [here](https://github.com/deepmodeling/abacus-develop/releases)
+- If you have connection issues accessing GitHub, please try out our official [Gitee repo](https://gitee.com/deepmodeling/abacus-develop/): e.g. `git clone https://gitee.com/deepmodeling/abacus-develop.git`. This Gitee repo is updated synchronously with GitHub.
+
 
 ## Prerequisites
 
@@ -43,32 +54,22 @@ Please refer to our [guide](https://github.com/deepmodeling/abacus-develop/wiki/
 
 We offer a set of [toolchain](https://github.com/deepmodeling/abacus-develop/tree/develop/toolchain)
 scripts to compile and install all the requirements
-automatically and suitable for machine characteristic in an online or offline way.
-The toolchain can be downloaded with ABACUS repo, which is easily used and can
-have a convenient installation under HPC environment in both `GNU` or `Intel-oneAPI` toolchain.
-Sometimes, ABACUS by toolchain installation may have highly efficient performance.
-A Tutorial for using this toolchain can be accessed in [bohrium-notebook](https://nb.bohrium.dp.tech/detail/5215742477)
-
-> Notice: the toolchain is under development, please let me know if you encounter any problem in using this toolchain.
+automatically and suitable for machine characteristic in an online or offline way. 
+The toolchain can be downloaded with ABACUS repo, and users can easily compile the requirements by running *toolchain_[gnu,intel].sh* and ABACUS itself by running *build_abacus_[gnu,intel].sh* script in the toolchain directory in both `GNU` and `Intel-oneAPI` toolchain.
+Sometimes, ABACUS by toolchain installation may have better efficient performance due to the suitable compiled dependencies.
 
+Users should read the README in toolchain directory for most of the information before use, and a tutorial for using this toolchain can be accessed in [bohrium-notebook](https://nb.bohrium.dp.tech/detail/5215742477) as reference.
 
-## Get ABACUS source code
-
-Of course a copy of ABACUS source code is required, which can be obtained via one of the following choices:
+> Notice: the toolchain is under development, please let we know if you encounter any problem in using this toolchain by raising issue or contacting us.
 
-- Clone the whole repo with git: `git clone https://github.com/deepmodeling/abacus-develop.git`
-- Clone the minimum required part of repo: `git clone https://github.com/deepmodeling/abacus-develop.git --depth=1`
-- Download the latest source code without git: `wget https://github.com/deepmodeling/abacus-develop/archive/refs/heads/develop.zip`
-- Get the source code of a stable version [here](https://github.com/deepmodeling/abacus-develop/releases)
-- If you have connection issues accessing GitHub, please try out our official [Gitee repo](https://gitee.com/deepmodeling/abacus-develop/): e.g. `git clone https://gitee.com/deepmodeling/abacus-develop.git`
 
-### Update to latest release
+## Update to latest release by git
 
 Please check the [release page](https://github.com/deepmodeling/abacus-develop/releases) for the release note of a new version.
 
 It is OK to download the new source code from beginning following the previous step.
 
-To update your cloned git repo in-place:
+You can update your cloned git repo (from Github or Gitee) in-place with the following commands:
 
 ```bash
 git remote -v
@@ -78,7 +79,7 @@ git remote -v
 
 # Replace "origin" with "upstream" or the remote name corresponding to deepmodeling/abacus-develop if necessary
 git fetch origin
-git checkout v3.2.0 # Replace the tag with the latest version
+git checkout v3.8.4 # Replace the tag with the latest version
 git describe --tags # Verify if the tag has been successfully checked out
 ```
 
@@ -158,6 +159,12 @@ If ABACUS is installed into a custom directory using `CMAKE_INSTALL_PREFIX`, ple
 export PATH=/my-install-dir/:$PATH
 ```
 
+If ABACUS is installed by toolchain, there will be an environment script in the toolchain directory named as *abacus_env.sh*. You can source it to set the environment variables.
+
+```bash
+source /path/to/abacus/toolchain/abacus_env.sh
+```
+
 Please set OpenMP threads by setting environment variable:
 
 ```bash

examples/interface_wannier90/ABACUS_towannier90_lcao/INPUT-nscf

@@ -10,9 +10,9 @@ scf_nmax                50
 pw_diag_thr             1.0e-12
 scf_thr                 1.0e-13
 init_chg                file
-symmetry                0
+symmetry                -1
 towannier90             1
 nnkpfile                diamond.nnkp
-basis_type		        lcao
+basis_type              lcao
 wannier_method          2
 out_wannier_unk         0

examples/interface_wannier90/ABACUS_towannier90_lcao_in_pw/INPUT-nscf

@@ -10,7 +10,7 @@ scf_nmax                50
 pw_diag_thr             1.0e-12
 scf_thr                 1.0e-13
 init_chg                file
-symmetry                0
+symmetry                -1
 towannier90             1
 nnkpfile                diamond.nnkp
 basis_type              lcao

examples/interface_wannier90/ABACUS_towannier90_pw/INPUT-nscf

@@ -11,8 +11,8 @@ scf_nmax                50
 pw_diag_thr             1.0e-12
 scf_thr                 1.0e-13
 init_chg                file
-symmetry                0
+symmetry                -1
 towannier90             1
 nnkpfile                diamond.nnkp
-basis_type		        pw
+basis_type              pw
 out_wannier_unk         0

python/pyabacus/src/ModuleNAO/CMakeLists.txt

@@ -12,7 +12,6 @@ list(APPEND _naos
     ${NAO_PATH}/two_center_bundle.cpp
     ${NAO_PATH}/two_center_integrator.cpp
     ${NAO_PATH}/two_center_table.cpp
-    ${NAO_PATH}/projgen.cpp
     # dependency
     ${ABACUS_SOURCE_DIR}/module_base/kernels/math_op.cpp
     # ${ABACUS_SOURCE_DIR}/module_psi/kernels/psi_memory_op.cpp

python/pyabacus/src/hsolver/py_diago_cg.hpp

@@ -114,13 +114,13 @@ class PyDiagoCG
         );
     }
 
-    void diag(
-        std::function<py::array_t<std::complex<double>>(py::array_t<std::complex<double>>)> mm_op,
-        int diag_ndim,
-        double tol,
-        bool need_subspace,
-        bool scf_type,
-        int nproc_in_pool = 1
+    void diag(std::function<py::array_t<std::complex<double>>(py::array_t<std::complex<double>>)> mm_op,
+              int diag_ndim,
+              double tol,
+              const std::vector<double>& diag_ethr,
+              bool need_subspace,
+              bool scf_type,
+              int nproc_in_pool = 1
     ) {
         const std::string basis_type = "pw";
         const std::string calculation = scf_type ? "scf" : "nscf";
@@ -171,7 +171,7 @@ class PyDiagoCG
             nproc_in_pool
         );
 
-        cg->diag(hpsi_func, spsi_func, *psi, *eig, *prec);
+        cg->diag(hpsi_func, spsi_func, *psi, *eig, diag_ethr, *prec);
     }
 
 private:

python/pyabacus/src/hsolver/py_hsolver.cpp

@@ -158,7 +158,9 @@ void bind_hsolver(py::module& m)
             for invoking this class is a function defined in _hsolver.py, 
             which uses this class to perform the calculations.
         )pbdoc")
-        .def("diag", &py_hsolver::PyDiagoCG::diag, R"pbdoc(
+        .def("diag",
+             &py_hsolver::PyDiagoCG::diag,
+             R"pbdoc(
             Diagonalize the linear operator using the Conjugate Gradient Method.
 
             Parameters
@@ -179,6 +181,7 @@ void bind_hsolver(py::module& m)
         "mm_op"_a,
         "max_iter"_a,
         "tol"_a,
+        "diag_ethr"_a,  
         "need_subspace"_a,
         "scf_type"_a,
         "nproc_in_pool"_a)