Remove useless and outdated write_psi_r_1 interface and improve related docs and examples

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).

docs/advanced/input_files/input-main.md

@@ -1703,7 +1703,7 @@ These variables are used to control the output of properties.
 
 - **Type**: Boolean
 - **Availability**: Numerical atomic orbital basis (multi-k points)
-- **Description**: Whether to output the density matrix with Bravias lattice vector R index into files in the folder `OUT.${suffix}`. The files are named as `dmr{s}{spin index}{g}{geometry index}{_nao} + {".csr"}`. Here, 's' refers to spin, where s1 means spin up channel while s2 means spin down channel, and the sparse matrix format 'csr' is mentioned in [out_mat_hs2](#out_mat_hs2). Finally, if [out_app_flag](#out_app_flag) is set to false, the file name contains the optinal 'g' index for each ionic step that may have different geometries, and if [out_app_flag](#out_app_flag) is set to true, the density matrix with respect to Bravias lattice vector R accumulates during ionic steps:
+- **Description**: Whether to output the density matrix with Bravias lattice vector R index into files in the folder `OUT.${suffix}`. The files are named as `dmr{s}{spin index}{g}{geometry index}{_nao} + {".csr"}`. Here, 's' refers to spin, where s1 means spin up channel while s2 means spin down channel, and the sparse matrix format 'csr' is mentioned in [out_mat_hs2](#out_mat_hs2). Finally, if [out_app_flag](#out_app_flag) is set to false, the file name contains the optional 'g' index for each ionic step that may have different geometries, and if [out_app_flag](#out_app_flag) is set to true, the density matrix with respect to Bravias lattice vector R accumulates during ionic steps:
   - nspin = 1: `dmrs1_nao.csr`;
   - nspin = 2: `dmrs1_nao.csr` and `dmrs2_nao.csr` for the two spin channels.
 - **Default**: False
@@ -1726,7 +1726,7 @@ These variables are used to control the output of properties.
 
 - **Type**: Integer
 - **Availability**: Numerical atomic orbital basis
-- **Description**: Whether to output the electronic wavefunction coefficients into files and store them in the folder `OUT.${suffix}`. The files are named as `wf{s}{spin index}{k(optinal)}{k-point index}{g(optional)}{geometry index1}{_nao} + {".txt"/".dat"}`. Here, 's' refers to spin, where s1 means spin up channel while s2 means spin down channel, and 's12' refer to spinor wave functions that contains both spin channels with spin-orbital coupling or noncollinear calculations enabled. In addition, if 'gamma_only' is set to 0, then the optinoal k-point sampling index appears with the k-point index attached to the electronic wave function file names. Finally, if [out_app_flag](#out_app_flag) is set to false, the file name contains the optinal 'g' index for each ionic step that may have different geometries, and if [out_app_flag](#out_app_flag) is set to true, the wave functions accumulate during ionic steps.
+- **Description**: Whether to output the electronic wavefunction coefficients into files and store them in the folder `OUT.${suffix}`. The files are named as `wf{s}{spin index}{k(optional)}{k-point index}{g(optional)}{geometry index1}{_nao} + {".txt"/".dat"}`. Here, 's' refers to spin, where s1 means spin up channel while s2 means spin down channel, and 's12' refer to spinor wave functions that contains both spin channels with spin-orbital coupling or noncollinear calculations enabled. In addition, if 'gamma_only' is set to 0, then the optinoal k-point sampling index appears with the k-point index attached to the electronic wave function file names. Finally, if [out_app_flag](#out_app_flag) is set to false, the file name contains the optional 'g' index for each ionic step that may have different geometries, and if [out_app_flag](#out_app_flag) is set to true, the wave functions accumulate during ionic steps.
   - 0: no output
   - 1: (txt format) 
     - gamma-only: `wfs1_nao.txt` or `wfs2_nao.txt`, ...;

examples/08_charge_density/lcao_nspin1_Si2/INPUT

@@ -1,16 +1,16 @@
 INPUT_PARAMETERS
-#Parameters     (General)
+#Parameters (General)
 pseudo_dir                      ../../../tests/PP_ORB
 orbital_dir                     ../../../tests/PP_ORB
-calculation                     scf     
+calculation                     scf
 nbands                          8
-#Parameters (Methos)
+#Parameters (Methods)
 basis_type                      lcao
-symmetry                        0       
+symmetry                        0
 #Parameters (Accuracy)
-ecutwfc                          60 ###Energy cutoff needs to be tested to ensure your calculation is reliable.[1]
+ecutwfc                         60 ###Energy cutoff needs to be tested to ensure your calculation is reliable.[1]
 scf_thr                         1.0e-7  // about iteration
-scf_nmax			100
+scf_nmax                        100
 #Parameters (File)
 out_chg                         1
 

examples/08_charge_density/pw_nspin1_Al/INPUT

@@ -1,15 +1,15 @@
 INPUT_PARAMETERS
-#Parameters     (General)
+#Parameters (General)
 pseudo_dir                      ../../../tests/PP_ORB
-calculation                     scf    
+calculation                     scf
 symmetry                        0
-#Parameters (Methos)
+#Parameters (Methods)
 basis_type                      pw
-ecutwfc                          60 ###Energy cutoff needs to be tested to ensure your calculation is reliable.[1]
+ecutwfc                         60 ###Energy cutoff needs to be tested to ensure your calculation is reliable.[1]
 scf_thr                         1.0e-8  // about iteration
-scf_nmax			100
-smearing_method         	gauss
-smearing_sigma          	0.01
+scf_nmax                        100
+smearing_method                 gauss
+smearing_sigma                  0.01
 #Parameters (File)
 out_chg                         1
 

examples/09_density_matrix/lcao_nspin1_Si2/INPUT

@@ -1,18 +1,18 @@
 INPUT_PARAMETERS
-#Parameters     (General)
+#Parameters (General)
 pseudo_dir                      ../../../tests/PP_ORB
 orbital_dir                     ../../../tests/PP_ORB
-calculation                     scf      
+calculation                     scf
 nbands                          16
-#Parameters (Methos)
+#Parameters (Methods)
 basis_type                      lcao
-symmetry                        0       
+symmetry                        0
 #Parameters (Accuracy)
-ecutwfc                          60 ###Energy cutoff needs to be tested to ensure your calculation is reliable.[1]
+ecutwfc                         60 ###Energy cutoff needs to be tested to ensure your calculation is reliable.[1]
 scf_thr                         1.0e-7  // about iteration
-scf_nmax			100
+scf_nmax                        100
 #Parameters (File)
-gamma_only			1
+gamma_only                      1
 out_dmk                         1
 
 

examples/11_wfc/README

@@ -1,16 +1,16 @@
-These examples show how to output the wavefunction in G space.
-For PW basis:
-	- set 'out_wfc_pw' to '1'
-The wave function is output in a file called 'WAVEFUNC1.txt'
+These examples demonstrate how to output wave functions in G-space and real space.
 
-For LCAO basis:
-	- set 'out_wfc_lcao' to '1'
-Several `WFC_NAO_K#.txt` files will be output in multi-k calculation and 
-`WFC_NAO_GAMMA1.txt` in gamma-only calculation.
+For Plane-Wave (PW) Basis:
+	- Set `out_wfc_pw = 1`.
+The wave functions will be output to a series of files named `wfs[spin]k[kpoint]_pw.txt`.
 
+For LCAO Basis:
+	- Set `out_wfc_lcao = 1`.
+In multi-k calculations, multiple files named `wfs[spin]k[kpoint]_nao.txt` will be generated.
+In gamma-only calculations, `wfs[spin]_nao.txt` instead.
 
-For the wave functions in Real Space:
-	- set 'out_wfc_r' to '1'
-The wave function is output in files OUT.${suffix}/wfc_realspace/wfc_realspace_$K_$B, 
-where $K and $B is the index of k point and band respectively.
-Note, it is only used in planewave basis and get_wf calculation in localized orbitals set
+For Wave Functions in Real Space:
+	- Set either `out_wfc_norm` or `out_wfc_re_im` to a space-separated string of 0s and 1s.
+    - E.g.: `1 0 0 0 0 1 1 1 1 1 0`, or `1 4*0 5*1 0` for short.
+The wave functions will be output to files named `wfi[state]s[spin]k[kpoint][re/im].cube`.
+Note, it is only supported for PW basis and `get_wf` calculation under LCAO basis.

examples/11_wfc/lcao_ienvelope_Si2/INPUT1

@@ -1,16 +1,16 @@
 INPUT_PARAMETERS
-#Parameters     (General)
+#Parameters (General)
 pseudo_dir                      ../../../tests/PP_ORB
 orbital_dir                     ../../../tests/PP_ORB
 calculation                     scf
 ntype                           1       
 nbands                          8
-#Parameters (Methos)
+#Parameters (Methods)
 basis_type                      lcao
 symmetry                        0       
 #Parameters (Accuracy)
 ecutwfc                         50
 scf_thr                         1.0e-7  // about iteration
-scf_nmax			100
+scf_nmax                        100
 #Parameters (File)
-out_wfc_lcao				1
+out_wfc_lcao                    1

examples/11_wfc/lcao_ienvelope_Si2/INPUT2

@@ -1,14 +1,14 @@
 INPUT_PARAMETERS
-#Parameters     (General)
+#Parameters (General)
 pseudo_dir                      ../../../tests/PP_ORB
 orbital_dir                     ../../../tests/PP_ORB
 calculation                     get_wf
 nbands                          8
-#Parameters (Methos)
+#Parameters (Methods)
 basis_type                      lcao
 symmetry                        0       
 #Parameters (Accuracy)
 ecutwfc                         50
 #Parameters (File)
-init_wfc			file
-out_wfc_r			1
+init_wfc                        file
+out_wfc_norm                    4*1

examples/11_wfc/lcao_ienvelope_Si2/run.sh

@@ -15,8 +15,8 @@ if [[ ! -f scf.output ]] ||
    [[ ! -f get_wf.output ]] || 
    [[ ! -f OUT.ABACUS/running_scf.log ]] ||
    [[ ! -f OUT.ABACUS/running_get_wf.log ]] ||
-   [[ ! -f OUT.ABACUS/WFC_NAO_K1.txt ]] ||
-   [[ ! -f OUT.ABACUS/WFC_NAO_K36.txt ]] ||
+   [[ ! -f OUT.ABACUS/wfs1k1_nao.txt ]] ||
+   [[ ! -f OUT.ABACUS/wfs1k36_nao.txt ]] ||
    [[ ! ( "$(tail -1 OUT.ABACUS/running_scf.log)" == " Total  Time  :"* ) ]] ||
    [[ ! ( "$(tail -1 OUT.ABACUS/running_get_wf.log)" == " Total  Time  :"* ) ]] 
 then

examples/11_wfc/lcao_scf_Si2/INPUT

@@ -1,18 +1,18 @@
 INPUT_PARAMETERS
-#Parameters     (General)
+#Parameters (General)
 pseudo_dir                      ../../../tests/PP_ORB
 orbital_dir                     ../../../tests/PP_ORB
 calculation                     scf    
 nbands                          8
-#Parameters (Methos)
+#Parameters (Methods)
 basis_type                      lcao
 symmetry                        0       
 #Parameters (Accuracy)
-ecutwfc                          60 ###Energy cutoff needs to be tested to ensure your calculation is reliable.[1]
+ecutwfc                         60 ###Energy cutoff needs to be tested to ensure your calculation is reliable.[1]
 scf_thr                         1.0e-7  // about iteration
-scf_nmax			100
+scf_nmax                        100
 #Parameters (File)
-out_wfc_lcao                         1
+out_wfc_lcao                    1
 
 
 ### [1] Energy cutoff determines the quality of numerical quadratures in your calculations.

examples/11_wfc/lcao_scf_Si2/run.sh

@@ -8,8 +8,8 @@ OMP_NUM_THREADS=${ABACUS_THREADS} mpirun -np ${ABACUS_NPROCS} ${ABACUS_PATH} | t
 
 if [[ ! -f output ]] ||
    [[ ! -f OUT.ABACUS/running_scf.log ]] ||
-   [[ ! -f OUT.ABACUS/WFC_NAO_K1.txt ]] ||
-   [[ ! -f OUT.ABACUS/WFC_NAO_K36.txt ]] ||
+   [[ ! -f OUT.ABACUS/wfs1k1_nao.txt ]] ||
+   [[ ! -f OUT.ABACUS/wfs1k36_nao.txt ]] ||
    [[ ! ( "$(tail -1 OUT.ABACUS/running_scf.log)" == " Total  Time  :"* ) ]] 
 then
 	echo "job failed!"

examples/11_wfc/pw_scf_Al/INPUT

@@ -1,18 +1,18 @@
 INPUT_PARAMETERS
-#Parameters     (General)
+#Parameters (General)
 pseudo_dir                      ../../../tests/PP_ORB
 calculation                     scf    
 symmetry                        0
-#Parameters (Methos)
+#Parameters (Methods)
 basis_type                      pw
-ecutwfc                          60 ###Energy cutoff needs to be tested to ensure your calculation is reliable.[1]
+ecutwfc                         60 ###Energy cutoff needs to be tested to ensure your calculation is reliable.[1]
 scf_thr                         1.0e-8  // about iteration
-scf_nmax			100
-smearing_method         	gauss
-smearing_sigma          	0.01
+scf_nmax                        100
+smearing_method                 gauss
+smearing_sigma                  0.01
 #Parameters (File)
-out_wfc_pw                         1
-out_wfc_r			1
+out_wfc_pw                      1
+out_wfc_norm                    1*1
 
 
 ### [1] Energy cutoff determines the quality of numerical quadratures in your calculations.

examples/12_band/lcao_Si2/INPUT1

@@ -1,16 +1,16 @@
 INPUT_PARAMETERS
-#Parameters     (General)
+#Parameters (General)
 pseudo_dir                      ../../../tests/PP_ORB
 orbital_dir                     ../../../tests/PP_ORB
 calculation                     scf
-ntype                           1       
+ntype                           1
 nbands                          8
-#Parameters (Methos)
+#Parameters (Methods)
 basis_type                      lcao
-symmetry                        0       
+symmetry                        0
 #Parameters (Accuracy)
 ecutwfc                         50
 scf_thr                         1.0e-7  // about iteration
-scf_nmax			100
+scf_nmax                        100
 #Parameters (File)
 out_chg                         1

examples/12_band/lcao_Si2/INPUT2

@@ -1,16 +1,16 @@
 INPUT_PARAMETERS
 #Parameters (General)
-kpoint_file             KLINES
-pseudo_dir              ../../../tests/PP_ORB
-orbital_dir             ../../../tests/PP_ORB
-calculation             nscf
-ntype                   1
-nbands                  8 
-symmetry                0
-#Parameters (Methos)
-basis_type              lcao
+kpoint_file                     KLINES
+pseudo_dir                      ../../../tests/PP_ORB
+orbital_dir                     ../../../tests/PP_ORB
+calculation                     nscf
+ntype                           1
+nbands                          8
+symmetry                        0
+#Parameters (Methods)
+basis_type                      lcao
 #Parameters (Accuracy)
-ecutwfc                 50
+ecutwfc                         50
 #Parameters (File)
-init_chg                file
-out_band                1
+init_chg                        file
+out_band                        1

examples/12_band/pw_Al/INPUT1

@@ -1,15 +1,15 @@
 INPUT_PARAMETERS
-#Parameters     (General)
+#Parameters (General)
 pseudo_dir                      ../../../tests/PP_ORB
 calculation                     scf
-ntype                           1       
+ntype                           1
 symmetry                        0
-#Parameters (Methos)
+#Parameters (Methods)
 basis_type                      pw
 ecutwfc                         50
 scf_thr                         1.0e-8  // about iteration
-scf_nmax			100
-smearing_method         	gauss
-smearing_sigma          	0.01
+scf_nmax                        100
+smearing_method                 gauss
+smearing_sigma                  0.01
 #Parameters (File)
 out_chg                         1

examples/12_band/pw_Al/INPUT2

@@ -1,18 +1,18 @@
 INPUT_PARAMETERS
 #Parameters (General)
-kpoint_file             KLINES
-pseudo_dir              ../../../tests/PP_ORB
-calculation             nscf
-ntype                   1
-symmetry                0
-#Parameters (Methos)
-ecutwfc                 50
-basis_type              pw
-pw_diag_thr		1e-10
-pw_diag_nmax		100
+kpoint_file                     KLINES
+pseudo_dir                      ../../../tests/PP_ORB
+calculation                     nscf
+ntype                           1
+symmetry                        0
+#Parameters (Methods)
+ecutwfc                         50
+basis_type                      pw
+pw_diag_thr                     1e-10
+pw_diag_nmax                    100
 #Parameters (Accuracy)
-smearing_method         gauss
-smearing_sigma          0.01
+smearing_method                 gauss
+smearing_sigma                  0.01
 #Parameters (File)
-init_chg                file
-out_band                1
+init_chg                        file
+out_band                        1

examples/13_dos/lcao_Si2/INPUT1

@@ -1,16 +1,16 @@
 INPUT_PARAMETERS
-#Parameters     (General)
+#Parameters (General)
 pseudo_dir                      ../../../tests/PP_ORB
 orbital_dir                     ../../../tests/PP_ORB
 calculation                     scf
 ntype                           1       
 nbands                          8
-#Parameters (Methos)
+#Parameters (Methods)
 basis_type                      lcao
 symmetry                        0       
 #Parameters (Accuracy)
 ecutwfc                         50
 scf_thr                         1.0e-7  // about iteration
-scf_nmax			            100
+scf_nmax                        100
 #Parameters (File)
 out_chg                         1