Merge remote-tracking branch 'upstream/develop' into develop

Author: Flying-dragon-boxing

CMakeLists.txt

@@ -252,8 +252,8 @@ if(ENABLE_LCAO)
     add_compile_definitions(__PEXSI)
     set(CMAKE_CXX_STANDARD 14)
   endif()
-  if(NEW_GINT)
-    add_compile_definitions(__NEW_GINT)
+  if(OLD_GINT)
+    add_compile_definitions(__OLD_GINT)
   endif()
 else()
   set(ENABLE_MLALGO OFF)
@@ -735,9 +735,9 @@ target_link_libraries(
   hsolver
   elecstate
   hamilt_general
-  hamilt_pwdft
-  hamilt_ofdft
-  hamilt_stodft
+  module_pwdft
+  module_ofdft
+  module_stodft
   psi
   psi_initializer
   psi_overall_init

docs/CONTRIBUTING.md

@@ -54,38 +54,36 @@ For those who are interested in the source code, the following figure shows the
 |   |-- module_neighbor         The module for finding the neighbors of each atom in the unit cell.
 |   |-- module_paw              The module for performing PAW calculations.
 |   |-- module_symmetry         The module for finding the symmetry operations of the unit cell.
-|-- source_estate            The module for defining the electronic state and its operations.
+|-- source_estate               The module for defining the electronic state and its operations.
 |   |-- module_charge           The module for calculating the charge density, charge mixing
 |   |-- potentials              The module for calculating the potentials, including Hartree, exchange-correlation, local pseudopotential, etc.
 |-- source_esolver              The module defining task-specific driver of corresponding workflow for evaluating energies, forces, etc., including lj, dp, ks, sdft, ofdft, etc.
 |   |                           TDDFT, Orbital-free DFT, etc.
-|-- source_hamilt       The module for defining general Hamiltonian that can be used both in PW and LCAO calculations.
+|-- source_hamilt               The module for defining general Hamiltonian that can be used both in PW and LCAO calculations.
 |   |-- module_ewald            The module for calculating the Ewald summation.
 |   |-- module_surchem          The module for calculating the surface charge correction.
 |   |-- module_vdw              The module for calculating the van der Waals correction.
 |   |-- module_xc               The module for calculating the exchange-correlation energy and potential.
-|-- module_hamilt_lcao          The module for defining the Hamiltonian in LCAO calculations.
+|-- source_lcao                 The module for defining the Hamiltonian in LCAO calculations.
 |   |-- hamilt_lcaodft          The module for defining the Hamiltonian in LCAO-DFT calculations.
 |   |   |-- operator_lcao       The module for defining the operators in LCAO-DFT calculations.
 |   |-- module_deepks           The module for defining the Hamiltonian in DeepKS calculations.
 |   |-- module_dftu             The module for defining the Hamiltonian in DFT+U calculations.
 |   |-- module_gint             The module for performing grid integral in LCAO calculations.
 |   |-- module_hcontainer       The module for storing the Hamiltonian matrix in LCAO calculations.
-|   `-- module_tddft            The module for defining the Hamiltonian in TDDFT calculations.
-|-- source_pw            The module for defining the Hamiltonian in PW calculations.
-|   |-- hamilt_ofdft            The module for defining the Hamiltonian in OFDFT calculations.
-|   |-- hamilt_pwdft            The module for defining the Hamiltonian in PW-DFT calculations.
+|   |-- module_rt               The module for defining the Hamiltonian in TDDFT calculations.
+|   `-- module_ri               The module for performing RI calculations.
+|-- source_pw                   The module for defining the Hamiltonian in PW calculations.
+|   |-- module_ofdft            The module for defining the Hamiltonian in OFDFT calculations.
+|   |-- module_pwdft            The module for defining the Hamiltonian in PW-DFT calculations.
 |   |   |-- operator_pw         The module for defining the operators in PW-DFT calculations.
-|   `-- hamilt_stodft           The module for defining the Hamiltonian in STODFT calculations.
+|   `-- module_stodft           The module for defining the Hamiltonian in STODFT calculations.
 |-- source_hsolver              The module for solving the Hamiltonian with different diagonalization methods, including CG, Davidson in PW
 |   |                           calculations, and scalapack and genelpa in LCAO calculations.
-|-- module_io                   The module for reading of INPUT files and output properties including band structure, density of states, charge density, etc.
-|-- module_md                   The module for performing molecular dynamics.
+|-- source_io                   The module for reading of INPUT files and output properties including band structure, density of states, charge density, etc.
+|-- source_md                   The module for performing molecular dynamics.
 |-- source_psi                  The module for defining the wave function and its operations.
-|-- module_relax                The module for performing structural optimization.
-|   |-- relax_new               The module for performing structural optimization with new algorithm, optimized for cell and ion simultaneously.
-|   `-- relax_old               The module for performing structural optimization with old algorithm, optimized for cell and ion separately.
-|-- module_ri                   The module for performing RI calculations.
+`-- source_relax                The module for performing structural optimization, optimized for cell and ion simultaneously.
 ```
 
 ## Submitting an Issue
@@ -101,7 +99,7 @@ For comments that need to be shown in documents, these formats should be used --
 
 A helpful VS Code extension -- [Doxygen Documentation Generator](https://marketplace.visualstudio.com/items?itemName=cschlosser.doxdocgen), can help you formating comments.
 
-An practical example is class [LCAO_Deepks](https://github.com/deepmodeling/abacus-develop/blob/deepks/source/module_hamilt_lcao/module_deepks/LCAO_deepks.h), the effects can be seen on [readthedocs page](https://abacus-deepks.readthedocs.io/en/latest/DeePKS_API/classLCAO__Descriptor.html#exhale-class-classLCAO-Descriptor)
+An practical example is class [LCAO_Deepks](https://github.com/deepmodeling/abacus-develop/blob/deepks/source/source_lcao/module_deepks/LCAO_deepks.h), the effects can be seen on [readthedocs page](https://abacus-deepks.readthedocs.io/en/latest/DeePKS_API/classLCAO__Descriptor.html#exhale-class-classLCAO-Descriptor)
 
 - Tips
   - Only comments in .h file will be visible in generated  by Doxygen + Sphinx;

docs/advanced/elec_properties/wfc.md

@@ -1,14 +1,18 @@
 # Extracting Wave Functions
 
-ABACUS is able to output electron wave functions in both PW and LCAO basis calculations. One can find the examples in [examples/wfc](https://github.com/deepmodeling/abacus-develop/tree/develop/examples/wfc).
+ABACUS is able to output electron wave functions in both PW and LCAO basis calculations. One can find the examples in [examples/11_wfc](https://github.com/deepmodeling/abacus-develop/tree/develop/examples/11_wfc).
 
-## wave function in G space
-For the wave function in G space, one only needs to do a ground-state energy calculation with one additional keyword in the INPUT file: '***[out_wfc_pw](https://abacus-rtd.readthedocs.io/en/latest/advanced/input_files/input-main.html#out-wfc-pw)***' for PW basis calculation, and '***[out_wfc_lcao](https://abacus-rtd.readthedocs.io/en/latest/advanced/input_files/input-main.html#out-wfc-lcao)***' for LCAO basis calculation.
-In the PW basis case, the wave function is output in a file called `WAVEFUNC${k}.txt`, where `${k}` is the index of K point. \
-In the LCAO basis case, several `WFC_NAO_K${k}.dat` files will be output in multi-k calculation and `WFC_NAO_GAMMA1.dat` in gamma-only calculation. 
+## Wave Function in G-Space
 
-## wave function in real space
+To output wave functions in G-space, add one of the following keywords to the `INPUT` file while performing SCF calculation:
+- **PW basis**: Set [`out_wfc_pw`](https://abacus-rtd.readthedocs.io/en/latest/advanced/input_files/input-main.html#out-wfc-pw) to `1`. Output file format: `wfs[spin]k[kpoint]_pw.txt`, where `[spin]` is the spin channel index, and `[kpoint]` the k-point index.
 
-One can also choose to output real-space wave function in PW basis calculation with the key word ***[out_wfc_norm](https://abacus-rtd.readthedocs.io/en/latest/advanced/input_files/input-main.html#out-wfc-norm)***.
+- **LCAO basis**: Set [`out_wfc_lcao`](https://abacus-rtd.readthedocs.io/en/latest/advanced/input_files/input-main.html#out-wfc-lcao) to `1`.  
+  - **Multi-k calculations**: Generates multiple files `wfs[spin]k[kpoint]_nao.txt`.
+  - **Gamma-only calculations**: `wfs[spin]_nao.txt` instead.
 
-Notice: when the ***[basis_type](https://abacus-rtd.readthedocs.io/en/latest/advanced/input_files/input-main.html#basis_type)*** is `lcao`, only `get_wf` ***[calculation](https://abacus-rtd.readthedocs.io/en/latest/advanced/input_files/input-main.html#calculation)*** is effective. An example is [examples/wfc/lcao_ienvelope_Si2](https://github.com/deepmodeling/abacus-develop/tree/develop/examples/wfc/lcao_ienvelope_Si2). 
+## Wave Function in Real Space
+
+One can also choose to output real-space wave functions with the keyword [`out_wfc_norm`](https://abacus-rtd.readthedocs.io/en/latest/advanced/input_files/input-main.html#out-wfc-norm) or [`out_wfc_re_im`](https://abacus-rtd.readthedocs.io/en/latest/advanced/input_files/input-main.html#out-wfc-re-im).
+
+Notice: When the [`basis_type`](https://abacus-rtd.readthedocs.io/en/latest/advanced/input_files/input-main.html#basis-type) is `lcao`, only `get_wf` [`calculation`](https://abacus-rtd.readthedocs.io/en/latest/advanced/input_files/input-main.html#calculation) is effective. An example is [examples/11_wfc/lcao_ienvelope_Si2](https://github.com/deepmodeling/abacus-develop/tree/develop/examples/11_wfc/lcao_ienvelope_Si2).