docs: preserve generated INPUT metadata

Author: zhubonan

.readthedocs.yaml

@@ -42,7 +42,7 @@ build:
         -DGIT_SUBMODULE=OFF
         -DMKLROOT=OFF
       - cmake --build build-rtd-docs --target abacus_pw_ser --parallel 2
-      - ./build-rtd-docs/abacus_pw_ser --generate-parameters-yaml > docs/parameters.yaml
+      - ./build-rtd-docs/source/abacus_pw_ser --generate-parameters-yaml > docs/parameters.yaml
 
 # Build documentation in the "docs/" directory with Sphinx
 sphinx:

docs/advanced/input_files/input-main.md

@@ -336,6 +336,12 @@
     - [rpa\_ccp\_rmesh\_times](#rpa_ccp_rmesh_times)
     - [exx\_symmetry\_realspace](#exx_symmetry_realspace)
     - [out\_ri\_cv](#out_ri_cv)
+    - [out\_unshrinked\_v](#out_unshrinked_v)
+    - [exx\_coul\_moment](#exx_coul_moment)
+    - [exx\_rotate\_abfs](#exx_rotate_abfs)
+    - [exx\_multip\_moments\_threshold](#exx_multip_moments_threshold)
+    - [shrink\_abfs\_pca\_thr](#shrink_abfs_pca_thr)
+    - [shrink\_lu\_inv\_thr](#shrink_lu_inv_thr)
   - [Exact Exchange (PW)](#exact-exchange-pw)
     - [exxace](#exxace)
     - [exx\_gamma\_extrapolation](#exx_gamma_extrapolation)
@@ -2247,23 +2253,23 @@
 
 - **Type**: Boolean
 - **Availability**: *Numerical atomic orbital basis (not gamma-only algorithm)*
-- **Description**: Whether to print Hamiltonian matrices H(R) in npz format. This feature does not work for gamma-only calculations.
+- **Description**: Whether to print Hamiltonian matrices H(R) in npz format. The output files are named output_HR0.npz, output_HR1.npz, and so on according to spin channel. This feature requires ABACUS to be built with CNPY.
 - **Default**: False
 - **Unit**: Ry
 
 ### out_hsr_npz
 
 - **Type**: Boolean
 - **Availability**: *Numerical atomic orbital basis (not gamma-only algorithm)*
-- **Description**: Whether to print Hamiltonian matrices H(R) and overlap matrix S(R) in npz format. This feature does not work for gamma-only calculations.
+- **Description**: Whether to print Hamiltonian matrices H(R) and overlap matrix S(R) in npz format. The output files are named output_SR.npz, output_HR0.npz, output_HR1.npz, and so on according to spin channel. This feature requires ABACUS to be built with CNPY.
 - **Default**: False
 - **Unit**: Ry
 
 ### out_dm_npz
 
 - **Type**: Boolean
 - **Availability**: *Numerical atomic orbital basis (not gamma-only algorithm)*
-- **Description**: Whether to print density matrices DM(R) in npz format. This feature does not work for gamma-only calculations.
+- **Description**: Whether to print density matrices DM(R) in npz format. The output files are named output_DM0.npz, output_DM1.npz, and so on according to spin channel. This feature requires ABACUS to be built with CNPY.
 - **Default**: False
 
 ### out_mul
@@ -3295,6 +3301,42 @@
 - **Description**: Whether to output the coefficient tensor C(R) and ABFs-representation Coulomb matrix V(R) for each atom pair and cell in real space.
 - **Default**: false
 
+### out_unshrinked_v
+
+- **Type**: Boolean
+- **Description**: Whether to output the large Vq matrix in the unshrinked auxiliary basis.
+- **Default**: false
+
+### exx_coul_moment
+
+- **Type**: Boolean
+- **Description**: Whether to use the moment method for Coulomb calculation.
+- **Default**: false
+
+### exx_rotate_abfs
+
+- **Type**: Boolean
+- **Description**: Whether to rotate the auxiliary basis for Coulomb calculation.
+- **Default**: false
+
+### exx_multip_moments_threshold
+
+- **Type**: Real
+- **Description**: Threshold to screen multipole moments in Coulomb calculation.
+- **Default**: 1e-10
+
+### shrink_abfs_pca_thr
+
+- **Type**: Real
+- **Description**: Threshold to shrink the auxiliary basis for GW/RPA calculations.
+- **Default**: -1
+
+### shrink_lu_inv_thr
+
+- **Type**: Real
+- **Description**: Threshold for obtaining the inverse of the overlap matrix by LU decomposition in the auxiliary-basis representation.
+- **Default**: 1e-6
+
 [back to top](#full-list-of-input-keywords)
 
 ## Exact Exchange (PW)
@@ -3377,6 +3419,7 @@
   - berendsen: Berendsen thermostat, see md_nraise in detail.
   - rescaling: velocity Rescaling method 1, see md_tolerance in detail.
   - rescale_v: velocity Rescaling method 2, see md_nraise in detail.
+  - csvr: Canonical Sampling through Velocity Rescaling, see md_csvr_tau in detail.
 - **Default**: nhc
 
 ### md_tfirst

docs/parameters.yaml

@@ -1399,6 +1399,7 @@ parameters:
       * berendsen: Berendsen thermostat, see md_nraise in detail.
       * rescaling: velocity Rescaling method 1, see md_tolerance in detail.
       * rescale_v: velocity Rescaling method 2, see md_nraise in detail.
+      * csvr: Canonical Sampling through Velocity Rescaling, see md_csvr_tau in detail.
     default_value: nhc
     unit: ""
     availability: ""
@@ -3321,23 +3322,23 @@ parameters:
     category: Output information
     type: Boolean
     description: |
-      Whether to print Hamiltonian matrices H(R) in npz format. This feature does not work for gamma-only calculations.
+      Whether to print Hamiltonian matrices H(R) in npz format. The output files are named output_HR0.npz, output_HR1.npz, and so on according to spin channel. This feature requires ABACUS to be built with CNPY.
     default_value: "False"
     unit: Ry
     availability: Numerical atomic orbital basis (not gamma-only algorithm)
   - name: out_hsr_npz
     category: Output information
     type: Boolean
     description: |
-      Whether to print Hamiltonian matrices H(R) and overlap matrix S(R) in npz format. This feature does not work for gamma-only calculations.
+      Whether to print Hamiltonian matrices H(R) and overlap matrix S(R) in npz format. The output files are named output_SR.npz, output_HR0.npz, output_HR1.npz, and so on according to spin channel. This feature requires ABACUS to be built with CNPY.
     default_value: "False"
     unit: Ry
     availability: Numerical atomic orbital basis (not gamma-only algorithm)
   - name: out_dm_npz
     category: Output information
     type: Boolean
     description: |
-      Whether to print density matrices DM(R) in npz format. This feature does not work for gamma-only calculations.
+      Whether to print density matrices DM(R) in npz format. The output files are named output_DM0.npz, output_DM1.npz, and so on according to spin channel. This feature requires ABACUS to be built with CNPY.
     default_value: "False"
     unit: ""
     availability: Numerical atomic orbital basis (not gamma-only algorithm)
@@ -4314,6 +4315,54 @@ parameters:
     default_value: "false"
     unit: ""
     availability: ""
+  - name: out_unshrinked_v
+    category: Exact Exchange (LCAO)
+    type: Boolean
+    description: |
+      Whether to output the large Vq matrix in the unshrinked auxiliary basis.
+    default_value: "false"
+    unit: ""
+    availability: ""
+  - name: exx_coul_moment
+    category: Exact Exchange (LCAO)
+    type: Boolean
+    description: |
+      Whether to use the moment method for Coulomb calculation.
+    default_value: "false"
+    unit: ""
+    availability: ""
+  - name: exx_rotate_abfs
+    category: Exact Exchange (LCAO)
+    type: Boolean
+    description: |
+      Whether to rotate the auxiliary basis for Coulomb calculation.
+    default_value: "false"
+    unit: ""
+    availability: ""
+  - name: exx_multip_moments_threshold
+    category: Exact Exchange (LCAO)
+    type: Real
+    description: |
+      Threshold to screen multipole moments in Coulomb calculation.
+    default_value: "1e-10"
+    unit: ""
+    availability: ""
+  - name: shrink_abfs_pca_thr
+    category: Exact Exchange (LCAO)
+    type: Real
+    description: |
+      Threshold to shrink the auxiliary basis for GW/RPA calculations.
+    default_value: "-1"
+    unit: ""
+    availability: ""
+  - name: shrink_lu_inv_thr
+    category: Exact Exchange (LCAO)
+    type: Real
+    description: |
+      Threshold for obtaining the inverse of the overlap matrix by LU decomposition in the auxiliary-basis representation.
+    default_value: "1e-6"
+    unit: ""
+    availability: ""
   - name: dft_plus_u
     category: DFT+U correction
     type: Integer

source/source_io/module_parameter/read_input_item_exx_dftu.cpp

@@ -567,36 +567,72 @@ void ReadInput::item_exx()
     {
         Input_Item item("out_unshrinked_v");
         item.annotation = "whether to output the large Vq matrix in unshrinked auxiliary basis";
+        item.category = "Exact Exchange (LCAO)";
+        item.type = "Boolean";
+        item.description = "Whether to output the large Vq matrix in the unshrinked auxiliary basis.";
+        item.default_value = "false";
+        item.unit = "";
+        item.availability = "";
         read_sync_bool(input.out_unshrinked_v);
         this->add_item(item);
     }
     {
         Input_Item item("exx_coul_moment");
         item.annotation = "whether to use moment method for Coulomb calculation";
+        item.category = "Exact Exchange (LCAO)";
+        item.type = "Boolean";
+        item.description = "Whether to use the moment method for Coulomb calculation.";
+        item.default_value = "false";
+        item.unit = "";
+        item.availability = "";
         read_sync_bool(input.exx_coul_moment);
         this->add_item(item);
     }
     {
         Input_Item item("exx_rotate_abfs");
         item.annotation = "whether to rotate auxiliary basis for Coulomb calculation";
+        item.category = "Exact Exchange (LCAO)";
+        item.type = "Boolean";
+        item.description = "Whether to rotate the auxiliary basis for Coulomb calculation.";
+        item.default_value = "false";
+        item.unit = "";
+        item.availability = "";
         read_sync_bool(input.exx_rotate_abfs);
         this->add_item(item);
     }
     {
         Input_Item item("exx_multip_moments_threshold");
         item.annotation = "threshold to screen multipole moments in Coulomb calculation";
+        item.category = "Exact Exchange (LCAO)";
+        item.type = "Real";
+        item.description = "Threshold to screen multipole moments in Coulomb calculation.";
+        item.default_value = "1e-10";
+        item.unit = "";
+        item.availability = "";
         read_sync_double(input.exx_multip_moments_threshold);
         this->add_item(item);
     }
     {
         Input_Item item("shrink_abfs_pca_thr");
         item.annotation = "threshold to shrink auxiliary basis for GW/RPA";
+        item.category = "Exact Exchange (LCAO)";
+        item.type = "Real";
+        item.description = "Threshold to shrink the auxiliary basis for GW/RPA calculations.";
+        item.default_value = "-1";
+        item.unit = "";
+        item.availability = "";
         read_sync_double(input.shrink_abfs_pca_thr);
         this->add_item(item);
     }
     {
         Input_Item item("shrink_lu_inv_thr");
         item.annotation = "threshold to get inverse of overlap matrix by LU decomposition in auxiliary basis representation";
+        item.category = "Exact Exchange (LCAO)";
+        item.type = "Real";
+        item.description = "Threshold for obtaining the inverse of the overlap matrix by LU decomposition in the auxiliary-basis representation.";
+        item.default_value = "1e-6";
+        item.unit = "";
+        item.availability = "";
         read_sync_double(input.shrink_LU_inv_thr);
         this->add_item(item);
     }

source/source_io/module_parameter/read_input_item_md.cpp

@@ -83,7 +83,8 @@ void ReadInput::item_md()
 * anderson: Anderson thermostat, see md_nraise in detail.
 * berendsen: Berendsen thermostat, see md_nraise in detail.
 * rescaling: velocity Rescaling method 1, see md_tolerance in detail.
-* rescale_v: velocity Rescaling method 2, see md_nraise in detail.)";
+* rescale_v: velocity Rescaling method 2, see md_nraise in detail.
+* csvr: Canonical Sampling through Velocity Rescaling, see md_csvr_tau in detail.)";
         item.default_value = "nhc";
         item.unit = "";
         item.availability = "";

source/source_io/module_parameter/read_input_item_output.cpp

@@ -1187,7 +1187,7 @@ The circle order of the charge density on real space grids is: x is the outer lo
         item.annotation = "output H(R) matrix in npz format";
         item.category = "Output information";
         item.type = "Boolean";
-        item.description = "Whether to print Hamiltonian matrices H(R) in npz format. This feature does not work for gamma-only calculations.";
+        item.description = "Whether to print Hamiltonian matrices H(R) in npz format. The output files are named output_HR0.npz, output_HR1.npz, and so on according to spin channel. This feature requires ABACUS to be built with CNPY.";
         item.default_value = "False";
         item.unit = "Ry";
         item.availability = "Numerical atomic orbital basis (not gamma-only algorithm)";
@@ -1209,7 +1209,7 @@ The circle order of the charge density on real space grids is: x is the outer lo
         item.annotation = "output H(R) and S(R) matrices in npz format";
         item.category = "Output information";
         item.type = "Boolean";
-        item.description = "Whether to print Hamiltonian matrices H(R) and overlap matrix S(R) in npz format. This feature does not work for gamma-only calculations.";
+        item.description = "Whether to print Hamiltonian matrices H(R) and overlap matrix S(R) in npz format. The output files are named output_SR.npz, output_HR0.npz, output_HR1.npz, and so on according to spin channel. This feature requires ABACUS to be built with CNPY.";
         item.default_value = "False";
         item.unit = "Ry";
         item.availability = "Numerical atomic orbital basis (not gamma-only algorithm)";
@@ -1231,7 +1231,7 @@ The circle order of the charge density on real space grids is: x is the outer lo
         item.annotation = "output DM(R) matrix in npz format";
         item.category = "Output information";
         item.type = "Boolean";
-        item.description = "Whether to print density matrices DM(R) in npz format. This feature does not work for gamma-only calculations.";
+        item.description = "Whether to print density matrices DM(R) in npz format. The output files are named output_DM0.npz, output_DM1.npz, and so on according to spin channel. This feature requires ABACUS to be built with CNPY.";
         item.default_value = "False";
         item.unit = "";
         item.availability = "Numerical atomic orbital basis (not gamma-only algorithm)";