Update output formats, prepare for ABACUS 3.11 version (#6522)

* add iter and itep into the output wave function file name in pw basis, change out_interval to out_freq_ion

* fix bugs, default value of out_freq_ion is 0, if one needs out_freq_elec, he/she should first turn on out_freq_ion

* fix bug in read_input_ptest

* fix bug in read_input_item_test.cpp

* read_wfc

* update output file names of command out_wfc_pw

* update description for out_wfc_pw

* add inp into lcao_after_scf

* update out_chg and out_pot

* update elf

* chagne eigs1.txt to eig.txt, change eig.txt to eig_occ.txt

* update output of pw documents

* update output of pw basis set

* update dos and eig and eig_occ to adapt to g index

* fix bugs in pw outputs

* change chgs1 to chg

* update file names and fix small bugs

* out_dos update

* update and fix band.txt

* fix bug

* update catch_properties, can deal with nspin=2 case to print wave function in pw basis

* fix bug in 072_PW_ELF

* fix 054 056 057 examples in 01_PW

* fix 01_PW 100

* fix mulliken charge output

* fix bugs in 02_NAO_Gamma

* fix bugs in 03_NAO_multik

* update to fix bugs in 03_NAO_multik

* remove k in hkk1.txt skk1.txt tkk1.txt

* update output formats

* do not output ks_pw dos when performing SDFT calculations

* add parameter in 007_PW_OW_GPU

* update result.ref

* fix some chg files

* delete out_interval in INPUT

* update documents

* update 01_PW/203 example

* update chage step -1

* fix bugs

* fix bug in 23 example

* fix bug

* fix OFDFT example

* fix bug in EXX

Author: mohanchen

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

@@ -133,9 +133,9 @@
     - [fixed\_atoms](#fixed_atoms)
     - [cell\_factor](#cell_factor)
   - [Output Variables](#variables-related-to-output-information)
+    - [out\_freq\_ion](#out_freq_ion)
     - [out\_freq\_elec](#out_freq_elec)
     - [out\_chg](#out_chg)
-    - [out\_xc\_r](#out_xc_r)
     - [out\_pot](#out_pot)
     - [out\_dm](#out_dmk)
     - [out\_dm1](#out_dmr)
@@ -159,12 +159,12 @@
     - [out\_mat\_xc](#out_mat_xc)
     - [out\_mat\_xc2](#out_mat_xc2)
     - [out\_mat\_l](#out_mat_l)
+    - [out\_xc\_r](#out_xc_r)
     - [out\_eband\_terms](#out_eband_terms)
     - [dm\_to\_rho](#dm_to_rho)
     - [out\_mul](#out_mul)
     - [out\_app\_flag](#out_app_flag)
     - [out\_ndigits](#out_ndigits)
-    - [out\_interval](#out_interval)
     - [out\_element\_info](#out_element_info)
     - [restart\_save](#restart_save)
     - [rpa](#rpa)
@@ -1636,6 +1636,13 @@ These variables are used to control the geometry relaxation.
 
 These variables are used to control the output of properties.
 
+### out_freq_ion
+
+- **Type**: Integer
+- **Description**: After self-consistent-field calculations, control the interval of ionic movements for printing properties. These properties cover charge density, local potential, electrostatic potential, Hamiltonian matrix, overlap matrix, density matrix, Mulliken population analysis and so on.
+- **Default**: 0
+- **Note**: If you want to use out_freq_elec, please set out_freq_ion to 1, otherwise out_freq_elec is useless 
+
 ### out_freq_elec
 
 - **Type**: Integer
@@ -1665,29 +1672,10 @@ These variables are used to control the output of properties.
 
   In EXX(exact exchange) calculations, (i.e. *[dft_fuctional](#dft_functional)==hse/hf/pbe0/scan0* or *[rpa](#rpa)==True*), the Hexx(R) files will be output in the folder `OUT.${suffix}` too, which can be read in NSCF calculation.
 
-  In molecular dynamics simulations, the output frequency is controlled by [out_interval](#out_interval).
+  In molecular dynamics simulations, the output frequency is controlled by [out_freq_ion](#out_freq_ion).
 - **Default**: 0 3
 - **Note**: In the 3.10-LTS version, the file names are SPIN1_CHG.cube and SPIN1_CHG_INI.cube, etc. 
 
-### out_xc_r
-
-- **Type**: Integer \[Integer\](optional)
-- **Description**: 
-  The first integer controls whether to output the exchange-correlation (in Bohr^-3) on real space grids using Libxc to folder `OUT.${suffix}`:
-  - 0: rho, amag, sigma, exc
-  - 1: vrho, vsigma
-  - 2: v2rho2, v2rhosigma, v2sigma2
-  - 3: v3rho3, v3rho2sigma, v3rhosigma2, v3sigma3
-  - 4: v4rho4, v4rho3sigma, v4rho2sigma2, v4rhosigma3, v4sigma4
-  The meaning of the files is presented in [Libxc](https://libxc.gitlab.io/manual/libxc-5.1.x/)
-
-  The second integer controls the precision of the charge density output, if not given, will use `3` as default.
-
-  ---
-  The circle order of the charge density on real space grids is: x is the outer loop, then y and finally z (z is moving fastest).
-
-- **Default**: -1 3
-
 ### out_pot
 
 - **Type**: Integer
@@ -1703,7 +1691,7 @@ These variables are used to control the output of properties.
     - nspin = 2: `pots1_ini.cube` and `pots2_ini.cube`; 
     - nspin = 4: `pots1_ini.cube`, `pots2_ini.cube`, `pots3_ini.cube`, and `pots4_ini.cube`
 
-  In molecular dynamics calculations, the output frequency is controlled by [out_interval](#out_interval).
+  In molecular dynamics calculations, the output frequency is controlled by [out_freq_ion](#out_freq_ion).
 - **Default**: 0
 - **Note**: In the 3.10-LTS version, the file names are SPIN1_POT.cube and SPIN1_POT_INI.cube, etc. 
 
@@ -1735,14 +1723,18 @@ These variables are used to control the output of properties.
 
 - **Type**: Integer
 - **Availability**: Output electronic wave functions in plane wave basis, or transform the real-space electronic wave function into plane wave basis (see get_wf option in [calculation](#calculation) with NAO basis)
-- **Description**: Whether to output the electronic wavefunction coefficients into files and store them in the folder `OUT.${suffix}`. The files are named as `wf{s}{spin index}{k}{k-point index}{_pw} + {".txt"/".dat"}`. Here, 's' refers to spin, where s1 means spin up channel while s2 means spin down channel, and 's12' refer to spinor wave functions that contains both spin channels with spin-orbital coupling or noncollinear calculations enabled.
+- **Description**: Whether to output the electronic wavefunction coefficients into files and store them in the folder `OUT.${suffix}`. The files are named as `wf{k}{k-point index}{s}{spin index}{g}{geometry index}{e}{electronic iteration index}{_pw} + {".txt"/".dat"}`. Here, the s index refers to spin but the label will not show up for non-spin-polarized calculations, where s1 means spin up channel while s2 means spin down channel, and s4 refers to spinor wave functions that contains both spin channels with spin-orbital coupling or noncollinear calculations enabled. For scf or nscf calculations, g index will not appear, but the g index appears for geometry relaxation and molecular dynamics, where one can use the [out_freq_ion](#out_freq_ion) command to control. To print out the electroinc wave functions every few SCF iterations, use the [out_freq_elec](#out_freq_elec) command and the e index will appear in the file name.
   - 0: no output
   - 1: (txt format)
-    - non-gamma-only: `wfs1k1_pw.txt` or `wfs1k2_pw.txt`, ...;
+    - non-gamma-only with nspin=1: `wfk1_pw.txt`, `wfk2_pw.txt`, ...;
+    - non-gamma-only with nspin=2: `wfk1s1_pw.txt`, `wfk1s2_pw.txt`, `wfk2s1_pw.txt`, `wfk2s2_pw.txt`, ...;
+    - non-gamma-only with nspin=4: `wfk1s4_pw.txt`, `wfk2s4_pw.txt`, ...;
   - 2: (binary format)
-    - non-gamma-only: `wfs1k1_pw.dat` or `wfs1k2_pw.dat`, ....
+    - non-gamma-only with nspin=1: `wfk1_pw.dat`, `wfk2_pw.dat`, ...;
+    - non-gamma-only with nspin=2: `wfk1s1_pw.dat`, `wfk1s2_pw.dat`, `wfk2s1_pw.dat`, `wfk2s2_pw.dat`, ...;
+    - non-gamma-only with nspin=4: `wfk1s4_pw.dat`, `wfk2s4_pw.dat`, ...;
 - **Default**: 0
-- **Note**: In the 3.10-LTS version, the file names are WAVEFUNC1.dat, WAVEFUNC2.dat, etc. 
+- **Note**: In the 3.10-LTS version, the file names are `WAVEFUNC1.dat`, `WAVEFUNC2.dat`, etc. 
 
 ### out_wfc_lcao
 
@@ -1759,7 +1751,7 @@ These variables are used to control the output of properties.
 
   The corresponding sequence of the orbitals can be seen in [Basis Set](../pp_orb.md#basis-set).
 
-  Also controled by [out_interval](#out_interval) and [out_app_flag](#out_app_flag).
+  Also controled by [out_freq_ion](#out_freq_ion) and [out_app_flag](#out_app_flag).
 - **Default**: False
 - **Note**: In the 3.10-LTS version, the file names are WFC_NAO_GAMMA1_ION1.txt and WFC_NAO_K1_ION1.txt, etc.
 
@@ -1789,7 +1781,7 @@ These variables are used to control the output of properties.
 
 - **Type**: Boolean \[Integer\](optional)
 - **Description**: Whether to output the eigenvalues of the Hamiltonian matrix (in eV) into the running log during electronic iterations and into a file at the end of calculations. The former can be used with the 'out_freq_elec' parameter while the latter option allows the output precision to be set via a second parameter, with a default value of 8. The output file names are:
-    - nspin = 1 or 4: `eigs1.txt`;
+    - nspin = 1 or 4: `eig.txt`;
     - nspin = 2: `eigs1.txt` and `eigs2.txt`;
     - For more information, refer to the [band.md](../elec_properties/band.md)
 - **Default**: False
@@ -1836,7 +1828,7 @@ These variables are used to control the output of properties.
 
 - **Type**: Boolean \[Integer\](optional)
 - **Availability**: Numerical atomic orbital basis
-- **Description**: Whether to print the upper triangular part of the Hamiltonian matrices and overlap matrices for each k-point into files in the directory `OUT.${suffix}`. The second number controls precision. For more information, please refer to [hs_matrix.md](../elec_properties/hs_matrix.md#out_mat_hs). Also controled by [out_interval](#out_interval) and [out_app_flag](#out_app_flag).
+- **Description**: Whether to print the upper triangular part of the Hamiltonian matrices and overlap matrices for each k-point into files in the directory `OUT.${suffix}`. The second number controls precision. For more information, please refer to [hs_matrix.md](../elec_properties/hs_matrix.md#out_mat_hs). Also controled by [out_freq_ion](#out_freq_ion) and [out_app_flag](#out_app_flag).
   - For gamma only case:
     - nspin = 1: `hks1_nao.txt` for the Hamiltonian matrix and `sks1_nao.txt` for the overlap matrix;
     - nspin = 2: `hks1_nao.txt` and `hks2_nao.txt` for the Hamiltonian matrix and `sks1_nao.txt` for the overlap matrix. Note that the code will not output `sks2_nao.txt` because it is the same as `sks1_nao.txt`;
@@ -1880,7 +1872,7 @@ These variables are used to control the output of properties.
 
 - **Type**: Boolean
 - **Availability**: Numerical atomic orbital basis (not gamma-only algorithm)
-- **Description**: Generate files containing the kinetic energy matrix $T(R)$. The format will be the same as the Hamiltonian matrix $H(R)$ and overlap matrix $S(R)$ as mentioned in [out_mat_hs2](#out_mat_hs2). The name of the files will be `trs1_nao.csr` and so on. Also controled by [out_interval](#out_interval) and [out_app_flag](#out_app_flag).
+- **Description**: Generate files containing the kinetic energy matrix $T(R)$. The format will be the same as the Hamiltonian matrix $H(R)$ and overlap matrix $S(R)$ as mentioned in [out_mat_hs2](#out_mat_hs2). The name of the files will be `trs1_nao.csr` and so on. Also controled by [out_freq_ion](#out_freq_ion) and [out_app_flag](#out_app_flag).
 - **Default**: False
 - **Unit**: Ry
 - **Note**: In the 3.10-LTS version, the file name is data-TR-sparse_SPIN0.csr. 
@@ -1889,7 +1881,7 @@ These variables are used to control the output of properties.
 
 - **Type**: Boolean
 - **Availability**: Numerical atomic orbital basis (not gamma-only algorithm)
-- **Description**: Whether to print files containing the derivatives of the Hamiltonian matrix. The format will be the same as the Hamiltonian matrix $H(R)$ and overlap matrix $S(R)$ as mentioned in [out_mat_hs2](#out_mat_hs2). The name of the files will be `dhrxs1_nao.csr`, `dhrys1_nao.csr`, `dhrzs1_nao.csr` and so on. Also controled by [out_interval](#out_interval) and [out_app_flag](#out_app_flag).
+- **Description**: Whether to print files containing the derivatives of the Hamiltonian matrix. The format will be the same as the Hamiltonian matrix $H(R)$ and overlap matrix $S(R)$ as mentioned in [out_mat_hs2](#out_mat_hs2). The name of the files will be `dhrxs1_nao.csr`, `dhrys1_nao.csr`, `dhrzs1_nao.csr` and so on. Also controled by [out_freq_ion](#out_freq_ion) and [out_app_flag](#out_app_flag).
 - **Default**: False
 - **Unit**: Ry/Bohr
 - **Note**: In the 3.10-LTS version, the file name is data-dHRx-sparse_SPIN0.csr and so on.
@@ -1898,7 +1890,7 @@ These variables are used to control the output of properties.
 
 - **Type**: Boolean
 - **Availability**: Numerical atomic orbital basis (not gamma-only algorithm)
-- **Description**: Whether to print files containing the derivatives of the overlap matrix. The format will be the same as the overlap matrix $dH(R)$ as mentioned in [out_mat_dh](#out_mat_dh). The name of the files will be `dsrxs1.csr` and so on. Also controled by [out_interval](#out_interval) and [out_app_flag](#out_app_flag). This feature can be used with `calculation get_s`.
+- **Description**: Whether to print files containing the derivatives of the overlap matrix. The format will be the same as the overlap matrix $dH(R)$ as mentioned in [out_mat_dh](#out_mat_dh). The name of the files will be `dsrxs1.csr` and so on. Also controled by [out_freq_ion](#out_freq_ion) and [out_app_flag](#out_app_flag). This feature can be used with `calculation get_s`.
 - **Default**: False
 - **Unit**: Ry/Bohr
 - **Note**: In the 3.10-LTS version, the file name is data-dSRx-sparse_SPIN0.csr and so on.
@@ -1928,6 +1920,25 @@ These variables are used to control the output of properties.
 - **Description**: Whether to print the expectation value of the angular momentum operator $\hat{L}_x$, $\hat{L}_y$, and $\hat{L}_z$ in the basis of the localized atomic orbitals. The files are named `OUT.${suffix}/${suffix}_Lx.dat`, `OUT.${suffix}/${suffix}_Ly.dat`, and `OUT.${suffix}/${suffix}_Lz.dat`. The second integer controls the precision of the output.
 - **Default**: False 8
 
+### out_xc_r
+
+- **Type**: Integer \[Integer\](optional)
+- **Description**: 
+  The first integer controls whether to output the exchange-correlation (in Bohr^-3) on real space grids using Libxc to folder `OUT.${suffix}`:
+  - 0: rho, amag, sigma, exc
+  - 1: vrho, vsigma
+  - 2: v2rho2, v2rhosigma, v2sigma2
+  - 3: v3rho3, v3rho2sigma, v3rhosigma2, v3sigma3
+  - 4: v4rho4, v4rho3sigma, v4rho2sigma2, v4rhosigma3, v4sigma4
+  The meaning of the files is presented in [Libxc](https://libxc.gitlab.io/manual/libxc-5.1.x/)
+
+  The second integer controls the precision of the charge density output, if not given, will use `3` as default.
+
+  ---
+  The circle order of the charge density on real space grids is: x is the outer loop, then y and finally z (z is moving fastest).
+
+- **Default**: -1 3
+
 ### out_eband_terms
 
 - **Type**: Boolean
@@ -1946,7 +1957,7 @@ These variables are used to control the output of properties.
 
 - **Type**: Boolean
 - **Availability**: Numerical atomic orbital basis
-- **Description**: Whether to print the Mulliken population analysis result into `OUT.${suffix}/mulliken.txt`. In molecular dynamics calculations, the output frequency is controlled by [out_interval](#out_interval).
+- **Description**: Whether to print the Mulliken population analysis result into `OUT.${suffix}/mulliken.txt`. In molecular dynamics calculations, the output frequency is controlled by [out_freq_ion](#out_freq_ion).
 - **Default**: False
 
 ### out_app_flag
@@ -1963,12 +1974,6 @@ These variables are used to control the output of properties.
 - **Description**: Controls the length of decimal part of output data, such as charge density, Hamiltonian matrix, Overlap matrix and so on.
 - **Default**: 8
 
-### out_interval
-
-- **Type**: Integer
-- **Description**: After self-consistent-field calculations, control the interval of ionic movements for printing properties. These properties cover charge density, local potential, electrostatic potential, Hamiltonian matrix, overlap matrix, density matrix, Mulliken population analysis and so on.
-- **Default**: 1
-
 ### out_element_info
 
 - **Type**: Boolean
@@ -2035,7 +2040,7 @@ These variables are used to control the output of properties.
   The second integer controls the precision of the kinetic energy density output, if not given, will use `3` as default. For purpose restarting from this file and other high-precision involved calculation, recommend to use `10`.
 
   ---
-  In molecular dynamics calculations, the output frequency is controlled by [out_interval](#out_interval).
+  In molecular dynamics calculations, the output frequency is controlled by [out_freq_ion](#out_freq_ion).
 - **Default**: 0 3
 
 ### out_spillage

examples/relax/pw_output/INPUT

@@ -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/KPT

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