Update out_chg 2 and out_pot 3, and elf (#7379)

* update 18_md examples

* update out_chg 2

* update out_pot function

* feat(module_io): 优化初始电荷密度/势能输出，支持 out_freq_ion 控制和动态文件名

- 添加 gen_ini_filename() 辅助函数，统一生成初始电荷密度/势能文件名
- out_freq_ion=0 时输出单个固定名称文件（不带 g#）
- out_freq_ion>0 时每个几何步输出独立文件（带 g#）
- 更新文档，说明两种模式的区别

修改文件：
- docs/advanced/output_files/output-specification.md
- source/source_io/module_chgpot/write_init.cpp
- source/source_io/module_chgpot/write_init.h
- source/source_io/module_parameter/read_input_item_output.cpp

* fix(module_io): 修正 out_freq_ion=0 时初始电荷密度/势能输出逻辑

- out_freq_ion=0 时，每个几何步都输出（覆盖同一个文件）
- out_freq_ion>0 时，只在 istep 是 out_freq_ion 倍数时输出
- 更新所有相关文档和注释

修改文件：
- docs/advanced/output_files/output-specification.md
- source/source_io/module_chgpot/write_init.cpp
- source/source_io/module_chgpot/write_init.h
- source/source_io/module_parameter/read_input_item_output.cpp

* fix a bug about out_pot

* fix bugs

* update

* update ELF and add openmp parallel

* update elf

* update elf

* update example reference data

* enable elf for rt-tddft, but results are wrong

* fix elf test

* fix elf test in 03_NAO_multik

* fix output of write_elf

* fix bug

* update potential file, fix bug

* fix elf test in ofdft

* fix: Move write_pot_init to ElecState::init_scf for correct timing

The write_pot_init was being called in ESolver_FP::before_scf before the
effective potential was computed. This caused pot_ini.cube to contain:
- All zeros for calculation=scf / first ionic step (istep=0)
- Converged potential from previous ionic step for relax/md with istep>0

The fix moves write_pot_init to ElecState::init_scf, which is called after
pot->init_pot(charge) computes the effective potential from the initial
charge density. This ensures pot_ini.cube correctly contains the effective
potential corresponding to the initial charge density.

Changes:
- Modified ElecState::init_scf signature to accept istep, out_dir, inp parameters
- Added write_pot_init call after pot->init_pot() in init_scf
- Updated pw::setup_pot to pass through the new parameters
- Updated all callers (LCAO and PW) to provide the new parameters
- Removed the premature write_pot_init call from ESolver_FP::before_scf

* Remove unused parameters from ElecState::init_scf

- Removed unused 'symm' and 'wfcpw' parameters from init_scf function
- Updated all call sites to match the new signature
- Simplified function interface by removing parameters not used in implementation

* Fix missing io_basic library link in elecstate tests

- Added io_basic library dependency to MODULE_ESTATE_elecstate_base test
- Added io_basic library dependency to MODULE_ESTATE_elecstate_pw test
- Fixes undefined reference to ModuleIO::write_pot_init

* update init_scf

* fix

* fix bug

* remove dependence of parameter for write_cube.cpp

* fix bugs

* fix bug

* add a new file init_scf

* update estate tests

* delete useless inclusion

---------

Co-authored-by: abacus_fixer <mohanchen@pku.eud.cn>

Author: mohanchen

docs/advanced/output_files/output-specification.md

@@ -49,11 +49,18 @@ All output file naming conventions can be found in the online documentation (wit
 | `s12` | Non-collinear spin calculation |
 | `k#` | k-point index (e.g., `k1`, `k2`) |
 | `g#` | Ionic step index for relax/md (e.g., `g1`, `g2`) |
+| `ini` | Initial state (before electronic iteration), used before or after `g#` |
 
 **Important:**
 - All index numbers start from 1 (not 0)
 - For Gamma-only algorithm in LCAO, no `k` index is included
 - Overlap matrix `s` does not distinguish spin, so only one matrix is output
+- For initial charge density output (`out_chg = 2`):
+  - `out_freq_ion = 0`: `chg_ini.cube` (nspin=1) or `chgs{#}_ini.cube` (nspin=2/4) - output at every step (overwrite same file)
+  - `out_freq_ion > 0`: `chgg{#}_ini.cube` (nspin=1) or `chgs{#}g{#}_ini.cube` (nspin=2/4) - output every out_freq_ion steps
+- For initial potential output (`out_pot = 3`):
+  - `out_freq_ion = 0`: `pot_ini.cube` (nspin=1) or `pots{#}_ini.cube` (nspin=2/4) - output at every step (overwrite same file)
+  - `out_freq_ion > 0`: `potg{#}_ini.cube` (nspin=1) or `pots{#}g{#}_ini.cube` (nspin=2/4) - output every out_freq_ion steps
 
 ### 2.2 Examples
 
@@ -62,7 +69,22 @@ All output file naming conventions can be found in the online documentation (wit
 | `chgs1.cube` | Charge density, spin 1 |
 | `chgs2.cube` | Charge density, spin 2 |
 | `chgs3.cube` | Charge density, spin 3 (non-collinear with SOC) |
+| `chg_ini.cube` | Initial charge density (out_freq_ion=0, nspin=1) |
+| `chgs1_ini.cube` | Initial charge density (out_freq_ion=0, spin 1, nspin=2/4) |
+| `chgg1_ini.cube` | Initial charge density, geometry step 1 (nspin=1) |
+| `chgs1g1_ini.cube` | Initial charge density, spin 1, geometry step 1 (nspin=2/4) |
+| `pot_ini.cube` | Initial potential (out_freq_ion=0, nspin=1) |
+| `pots1_ini.cube` | Initial potential (out_freq_ion=0, spin 1, nspin=2/4) |
+| `potg1_ini.cube` | Initial potential, geometry step 1 (nspin=1) |
+| `pots1g1_ini.cube` | Initial potential, spin 1, geometry step 1 (nspin=2/4) |
 | `pots1.cube` | Local potential, spin 1 |
+| `elftot.cube` | ELF, total (nspin=1/4) |
+| `elfs1.cube` | ELF, spin 1 (nspin=2) |
+| `elfs2.cube` | ELF, spin 2 (nspin=2) |
+| `elftot.cube` | ELF, total (nspin=2) |
+| `elftotg1.cube` | ELF, total, geometry step 1 (nspin=1/4) |
+| `elfs1g1.cube` | ELF, spin 1, geometry step 1 (nspin=2) |
+| `elftotg1.cube` | ELF, total, geometry step 1 (nspin=2) |
 | `eig_occ.txt` | Eigenvalues and occupations |
 | `doss1g1_nao.txt` | DOS, spin 1, geometry step 1, NAO basis |
 | `wf_pw.dat` | Wavefunction, plane wave basis |
@@ -79,8 +101,25 @@ All output file naming conventions can be found in the online documentation (wit
 | `band.txt` | Band structure |
 | `chgs1.cube`, `chgs2.cube` | Charge density (spin 1, spin 2) |
 | `chg.cube` | Total charge density |
+| Initial charge density (out_chg=2) | |
+| `chg_ini.cube` | Initial charge density (out_freq_ion=0, nspin=1) |
+| `chgs{#}_ini.cube` | Initial charge density (out_freq_ion=0, spin {#}, nspin=2/4) |
+| `chgg{#}_ini.cube` | Initial charge density (out_freq_ion>0, geometry step {#}, nspin=1) |
+| `chgs{#}g{#}_ini.cube` | Initial charge density (out_freq_ion>0, spin {#}, geometry step {#}, nspin=2/4) |
+| Initial potential (out_pot=3) | |
+| `pot_ini.cube` | Initial potential (out_freq_ion=0, nspin=1) |
+| `pots{#}_ini.cube` | Initial potential (out_freq_ion=0, spin {#}, nspin=2/4) |
+| `potg{#}_ini.cube` | Initial potential (out_freq_ion>0, geometry step {#}, nspin=1) |
+| `pots{#}g{#}_ini.cube` | Initial potential (out_freq_ion>0, spin {#}, geometry step {#}, nspin=2/4) |
 | `taus1.cube`, `taus2.cube` | Kinetic energy density (tau) |
 | `pots1.cube`, `pots2.cube` | Local potential |
+| ELF (out_elf) | |
+| `elftot.cube` | ELF, total (nspin=1/4) |
+| `elfs1.cube`, `elfs2.cube` | ELF, spin 1/2 (nspin=2) |
+| `elftot.cube` | ELF, total (nspin=2) |
+| `elftotg{#}.cube` | ELF, total, geometry step {#} (nspin=1/4) |
+| `elfs{#}g{#}.cube` | ELF, spin {#}, geometry step {#} (nspin=2) |
+| `elftotg{#}.cube` | ELF, total, geometry step {#} (nspin=2) |
 
 ## 3. File Format Standards