fix INPUT problem

Author: Fei Yang

.github/workflows/test.yml

@@ -17,11 +17,17 @@ jobs:
       volumes:
         - /tmp/ccache:/github/home/.ccache
     steps:
-      - name: Checkout
+      - name: Checkout repository
         uses: actions/checkout@v5
         with:
-          submodules: recursive
           fetch-depth: 0
+          # We will handle submodules manually after fixing ownership
+          submodules: 'false'
+
+      - name: Take ownership of the workspace and update submodules
+        run: |
+          sudo chown -R $(whoami) .
+          git submodule update --init --recursive
 
       - name: Install CI tools
         run: |

docs/advanced/elec_properties/Mulliken.md

@@ -1,7 +1,7 @@
 # Mulliken Charge Analysis
 
 From version 2.1.0, ABACUS has the function of Mulliken population analysis. The example can be found in [examples/mulliken](https://github.com/deepmodeling/abacus-develop/tree/develop/examples/mulliken). \
-To use this function, set [out_mul](./input-main.md#out_mul) to `1` in the INPUT file. After calculation, there will be an output file named `mulliken.txt` in the output directory. In MD calculations, the output interval is controlled by the keyword [out_interval](./input-main.md#out_interval). In the file, there are contents like (`nspin 1`):
+To use this function, set [out_mul](./input-main.md#out_mul) to `1` in the INPUT file. After calculation, there will be an output file named `mulliken.txt` in the output directory. In MD calculations, the output interval is controlled by the keyword [out_freq_ion](./input-main.md#out_freq_ion). In the file, there are contents like (`nspin 1`):
 
 ```
 STEP: 0

docs/advanced/elec_properties/hs_matrix.md

@@ -45,7 +45,7 @@ The CSR format stores a sparse m × n matrix M in row form using three (one-dime
   - The arrays V and COL_INDEX are of length NNZ, and contain the non-zero values and the column indices of those values respectively.
   - The array ROW_INDEX is of length m + 1 and encodes the index in V and COL_INDEX where the given row starts. This is equivalent to ROW_INDEX[j] encoding the total number of nonzeros above row j. The last element is NNZ , i.e., the fictitious index in V immediately after the last valid index NNZ - 1.
 
-For calculations involving ionic movements, the output frequency of the matrix is controlled by [out_interval](../input_files/input-main.md#out_interval) and [out_app_flag](../input_files/input-main.md#out_app_flag). 
+For calculations involving ionic movements, the output frequency of the matrix is controlled by [out_freq_ion](../input_files/input-main.md#out_freq_ion) and [out_app_flag](../input_files/input-main.md#out_app_flag). 
 
 ## get_s
 We also offer the option of only calculating the overlap matrix without running SCF. For that purpose, in `INPUT` file we need to set the value keyword [calculation](../input_files/input-main.md#calculation) to be `get_s`.

docs/advanced/elec_properties/position_matrix.md

@@ -18,7 +18,7 @@ Each file or each section of the appended file starts with "STEP: " followed by
 
 Each block here contains the matrix for the corresponding cell. There are three columns in each block, giving the matrix elements in x, y, z directions, respectively. There are altogether nbasis * nbasis lines in each block, which emulates the matrix elements.
 
-In molecular dynamics (MD) calculations, if [out_app_flag](../input_files/input-main.md#out_app_flag) is set to true, then `data-rR-tr` is written in an append manner. Otherwise, output files will be put in a separate directory, `matrix`, and named as `$x`_data-rR-tr, where `$x` is the number of MD step. In addition, the output frequency is controlled by [out_interval](../input_files/input-main.md#out_interval). For example, if we are running a 10-step MD with out_interval = 3, then `$x` will be 0, 3, 6, and 9.
+In molecular dynamics (MD) calculations, if [out_app_flag](../input_files/input-main.md#out_app_flag) is set to true, then `data-rR-tr` is written in an append manner. Otherwise, output files will be put in a separate directory, `matrix`, and named as `$x`_data-rR-tr, where `$x` is the number of MD step. In addition, the output frequency is controlled by [out_freq_ion](../input_files/input-main.md#out_freq_ion). For example, if we are running a 10-step MD with out_freq_ion = 3, then `$x` will be 0, 3, 6, and 9.
 
 ## get_s
 We also offer the option of only calculating the position matrix without running SCF. For that purpose, in `INPUT` file we need to set the keyword [calculation](../input_files/input-main.md#calculation) to `get_s`, and [out_mat_r](../input_files/input-main.md#out_mat_r) to `true`.

docs/advanced/input_files/input-main.md

@@ -8,7 +8,7 @@ ecutwfc			10
 scf_nmax		20
 
 basis_type		pw
-relax_nmax      5
+relax_nmax      4
 
 cal_stress      1
 stress_thr      1e-6
@@ -25,18 +25,23 @@ relax_method    lbfgs
 pseudo_dir      ../../../tests/PP_ORB	
 orbital_dir	    ../../../tests/PP_ORB
 
-nspin           2
+nspin           4
+
+out_freq_ion    1
+#out_freq_elec   0 
+
+out_chg         1  # chg.txt g
+out_pot         1  # pot.txt g
+out_wfc_pw      1  # wfkx_pw.txt g
+out_dos         1  # dos.txt g
+out_elf         1  # elf.txt
+out_band        1  # eig.txt
+out_stru        1  # g
+out_bandgap     1
 
-out_chg         1
-out_pot         1
-out_wfc_pw      1
-out_dos         1
-out_stru        1
 out_app_flag    0
 
-out_interval    1
-kpar            2
+kpar            1
 symmetry        -1
 
-#out_freq_elec   2
-#out_band        1
+

examples/relax/pw_output/INPUT

@@ -2,3 +2,4 @@ K_POINTS
 0
 Gamma
 2 2 2 0 0 0
+

examples/relax/pw_output/KPT

@@ -189,7 +189,7 @@ list(APPEND _diago
     ${HSOLVER_PATH}/diago_david.cpp
     ${HSOLVER_PATH}/diag_const_nums.cpp
     ${HSOLVER_PATH}/diago_iter_assist.cpp
-    ${HSOLVER_PATH}/kernels/dngvd_op.cpp
+    ${HSOLVER_PATH}/kernels/hegvd_op.cpp
     ${HSOLVER_PATH}/kernels/bpcg_kernel_op.cpp
     ${BASE_PATH}/kernels/math_kernel_op.cpp
     ${BASE_PATH}/kernels/math_kernel_op_vec.cpp

python/pyabacus/CONTRIBUTING.md

@@ -9,7 +9,7 @@ list(APPEND _diago
     ${HSOLVER_PATH}/diago_pxxxgvx.cpp
 
 
-    ${HSOLVER_PATH}/kernels/dngvd_op.cpp
+    ${HSOLVER_PATH}/kernels/hegvd_op.cpp
     ${HSOLVER_PATH}/kernels/bpcg_kernel_op.cpp
     # dependency
     ${BASE_PATH}/kernels/math_kernel_op.cpp

python/pyabacus/src/hsolver/CMakeLists.txt

@@ -145,7 +145,7 @@ class PyDiagoCG
             std::copy(hpsi_ptr, hpsi_ptr + nvec * ld_psi, hpsi_out.data<std::complex<double>>());
         };
 
-        auto subspace_func = [] (const ct::Tensor& psi_in, ct::Tensor& psi_out) { /*do nothing*/ };
+        auto subspace_func = [](const ct::Tensor& psi_in, ct::Tensor& psi_out, const bool S_orth) { /*do nothing*/ };
 
         auto spsi_func = [this] (const ct::Tensor& psi_in, ct::Tensor& spsi_out) {
             const auto ndim = psi_in.shape().ndim();