Doc: Enhance the doc of scf_thr and scf_ene_thr (#7280)

* Doc: Enhance the doc of scf_thr and scf_ene_thr

* Doc: Update the doc

* Update source/source_io/module_parameter/read_input_item_elec_stru.cpp

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

* Update docs/parameters.yaml

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

* Update docs/advanced/input_files/input-main.md

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

---------

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Author: sunliang98

docs/advanced/input_files/input-main.md

@@ -1361,14 +1361,14 @@
 ### scf_thr
 
 - **Type**: Real
-- **Description**: It's the density threshold for electronic iteration. It represents the charge density error between two sequential densities from electronic iterations. Usually for local orbitals, usually 1e-6 may be accurate enough.
+- **Description**: It's the density threshold for electronic iteration. It represents the charge density error between two sequential densities from electronic iterations. This criterion is always enabled. If `scf_ene_thr` is set, its total-energy criterion is applied as an additional convergence check only after the charge-density criterion (`scf_thr`) has been satisfied, and only from the second SCF iteration onward (`iter > 1`). For local-orbital calculations, 1e-6 is usually accurate enough.
 - **Default**: 1.0e-9 (plane-wave basis), or 1.0e-7 (localized atomic orbital basis).
 - **Unit**: Ry if scf_thr_type=1, dimensionless if scf_thr_type=2
 
 ### scf_ene_thr
 
 - **Type**: Real
-- **Description**: It's the energy threshold for electronic iteration. It represents the total energy error between two sequential densities from electronic iterations.
+- **Description**: It's the energy threshold for electronic iteration. The compared quantity is the total-energy difference evaluated from the charge densities before and after the `Hpsi` operation in one SCF step. It is not the same as the screen-output `EDIFF`, which is the energy difference before `Hpsi` and after charge mixing (i.e., across both `Hpsi` and charge-mixing operations).
 - **Default**: -1.0. If the user does not set this parameter, it will not take effect.
 - **Unit**: eV
 

docs/parameters.yaml

@@ -823,15 +823,15 @@ parameters:
     category: Electronic structure
     type: Real
     description: |
-      It's the density threshold for electronic iteration. It represents the charge density error between two sequential densities from electronic iterations. Usually for local orbitals, usually 1e-6 may be accurate enough.
+      It's the density threshold for electronic iteration. It represents the charge density error between two sequential densities from electronic iterations. This criterion is always enabled. If `scf_ene_thr` is set, the total-energy criterion (`scf_ene_thr`) is evaluated conditionally after the charge-density criterion (`scf_thr`) is satisfied, and not on the first iteration. For local-orbital calculations, 1e-6 is usually accurate enough.
     default_value: "1.0e-9 (plane-wave basis), or 1.0e-7 (localized atomic orbital basis)."
     unit: "Ry if scf_thr_type=1, dimensionless if scf_thr_type=2"
     availability: ""
   - name: scf_ene_thr
     category: Electronic structure
     type: Real
     description: |
-      It's the energy threshold for electronic iteration. It represents the total energy error between two sequential densities from electronic iterations.
+      It's the energy threshold for electronic iteration. The compared quantity is the total-energy difference evaluated from the charge densities before and after the `Hpsi` operation in one SCF step. It is not the same as the screen-output `EDIFF`, which is the energy difference before `Hpsi` and after charge mixing (i.e., across both `Hpsi` and charge-mixing operations).
     default_value: "-1.0. If the user does not set this parameter, it will not take effect."
     unit: eV
     availability: ""

source/source_io/module_parameter/read_input_item_elec_stru.cpp

@@ -831,7 +831,7 @@ Note: If gamma_only is set to 1, the KPT file will be overwritten. So make sure
         item.annotation = "charge density error";
         item.category = "Electronic structure";
         item.type = "Real";
-        item.description = "It's the density threshold for electronic iteration. It represents the charge density error between two sequential densities from electronic iterations. Usually for local orbitals, usually 1e-6 may be accurate enough.";
+        item.description = "It's the density threshold for electronic iteration. It represents the charge density error between two sequential densities from electronic iterations. This criterion is always enabled. If scf_ene_thr is set, the total-energy criterion (scf_ene_thr) is additionally checked only after the first SCF iteration and only when the charge-density criterion (scf_thr) has already been satisfied. For local-orbital calculations, 1e-6 is usually accurate enough.";
         item.default_value = "1.0e-9 (plane-wave basis), or 1.0e-7 (localized atomic orbital basis).";
         item.unit = "Ry if scf_thr_type=1, dimensionless if scf_thr_type=2";
         item.availability = "";
@@ -865,7 +865,7 @@ Note: If gamma_only is set to 1, the KPT file will be overwritten. So make sure
         item.annotation = "total energy error threshold";
         item.category = "Electronic structure";
         item.type = "Real";
-        item.description = "It's the energy threshold for electronic iteration. It represents the total energy error between two sequential densities from electronic iterations.";
+        item.description = "It's the energy threshold for electronic iteration. The compared quantity is the total-energy difference evaluated from the charge densities before and after the Hpsi operation in one SCF step. It is not the same as the screen-output EDIFF, which is the energy difference before Hpsi and after charge mixing (i.e., across both Hpsi and charge-mixing operations).";
         item.default_value = "-1.0. If the user does not set this parameter, it will not take effect.";
         item.unit = "eV";
         item.availability = "";