Merge remote-tracking branch 'origin/develop' into fix/dmk-dmr-fourier-sign

Conflict resolutions (build fixes required by the merged tree):
- module_operator_lcao/test/CMakeLists.txt: ORB_atomic_lm.cpp ->
  orb_atomic_lm.cpp, matching develop's filename normalization (#7797)
  in the dm_trace test target sources.
- module_lr/utils/exciton_plotter.cpp: add missing 'template' keyword
  for the dependent-template call eval_wfc_bloch<T> (upstream BSE
  module, #7718) that fails to compile with the standard C++11 rule.

Author: dyzheng

CMakeLists.txt

@@ -184,71 +184,52 @@ if(COMMIT_INFO)
   endif()
 endif()
 
-# Different exe files of ABACUS
-unset(ABACUS_BIN_NAME CACHE)
+# Determine the ABACUS executable name.
+if(NOT ENABLE_LCAO)
+  set(_abacus_bin_level "pw")
+# TODO: Not well-defined now.
+elseif(ENABLE_LIBRI AND ENABLE_MLALGO)
+  set(_abacus_bin_level "max")
+elseif(ENABLE_LIBRI)
+  set(_abacus_bin_level "std")
+# TODO: Not well-defined now.
+elseif(ENABLE_MLALGO)
+  set(_abacus_bin_level "ml")
+else()
+  set(_abacus_bin_level "basic")
+endif()
 
-# Case : LCAO or PW
-if(ENABLE_LCAO)
-  # Case: CUDA is enabled (suffix with 'g' for GPU)
-  if(USE_CUDA)
-    if(ENABLE_MPI)
-      if(NOT ENABLE_LIBRI AND NOT ENABLE_MLALGO)
-        set(ABACUS_BIN_NAME abacus_basic_gpu)
-      elseif(ENABLE_LIBRI AND NOT ENABLE_MLALGO)
-        set(ABACUS_BIN_NAME abacus_std_gpu)
-      elseif(NOT ENABLE_LIBRI AND ENABLE_MLALGO)
-        set(ABACUS_BIN_NAME abacus_ml_gpu)
-      elseif(ENABLE_LIBRI AND ENABLE_MLALGO)
-        set(ABACUS_BIN_NAME abacus_max_gpu)
-      endif()
-    endif()
-  # Case: CPU is enabled (suffix with 'p' for parallel) 
-  else()
-    if(ENABLE_MPI)
-      if(NOT ENABLE_LIBRI AND NOT ENABLE_MLALGO)
-        set(ABACUS_BIN_NAME abacus_basic_para)
-      elseif(ENABLE_LIBRI AND NOT ENABLE_MLALGO)
-        set(ABACUS_BIN_NAME abacus_std_para)
-      elseif(NOT ENABLE_LIBRI AND ENABLE_MLALGO)
-        set(ABACUS_BIN_NAME abacus_ml_para)
-      elseif(ENABLE_LIBRI AND ENABLE_MLALGO)
-        set(ABACUS_BIN_NAME abacus_max_para)
-      endif()
-    else()
-      if(NOT ENABLE_LIBRI AND NOT ENABLE_MLALGO)
-        set(ABACUS_BIN_NAME abacus_basic_ser)
-      elseif(ENABLE_LIBRI AND NOT ENABLE_MLALGO)
-        set(ABACUS_BIN_NAME abacus_std_ser)
-      elseif(NOT ENABLE_LIBRI AND ENABLE_MLALGO)
-        set(ABACUS_BIN_NAME abacus_ml_ser)
-      elseif(ENABLE_LIBRI AND ENABLE_MLALGO)
-        set(ABACUS_BIN_NAME abacus_max_ser)
-      endif()
-    endif()
-  endif()
-# Case : PW only
+if(ENABLE_MPI)
+  set(_abacus_bin_para "para")
+elseif(ENABLE_OPENMP)
+  set(_abacus_bin_para "omp")
 else()
-  if(USE_CUDA)
-    if(ENABLE_MPI)
-      set(ABACUS_BIN_NAME abacus_pw_gpu)
-    endif()
-  else()
-    if(ENABLE_MPI)
-      set(ABACUS_BIN_NAME abacus_pw_para)
-    else()
-      set(ABACUS_BIN_NAME abacus_pw_ser)
-    endif()
-  endif()
+  set(_abacus_bin_para "ser")
+endif()
+
+if(USE_CUDA OR USE_ROCM)
+  set(_abacus_bin_device "gpu")
+elseif(USE_CUDA_ON_DCU)
+  set(_abacus_bin_device "dcu")
+elseif(USE_DSP)
+  set(_abacus_bin_device "dsp")
+elseif(USE_SW)
+  set(_abacus_bin_device "sw")
 endif()
 
+# if(USE_KML)
+#  set(_abacus_bin_device "kp")
+# endif()
+
+if(_abacus_bin_device)
+  set(ABACUS_BIN_NAME "abacus_${_abacus_bin_level}_${_abacus_bin_device}")
+else()
+  set(ABACUS_BIN_NAME "abacus_${_abacus_bin_level}_${_abacus_bin_para}")
+endif()
 
 # Use DSP hardware
-if (USE_DSP)
-  if(ENABLE_ELPA)
-    message(WARNING USE_DSP is incompatible with ELPA; switching off ENABLE_ELPA)
-    set(ENABLE_ELPA OFF)
-  endif()
-  set(ABACUS_BIN_NAME abacus_dsp)
+if(USE_DSP AND ENABLE_ELPA)
+  message(FATAL_ERROR "USE_DSP is incompatible with ELPA.")
 endif()
 
 list(APPEND CMAKE_MODULE_PATH
@@ -499,6 +480,9 @@ endif()
 # version. Use cmake with AMD-ROCm:
 # https://rocmdocs.amd.com/en/latest/Installation_Guide/Using-CMake-with-AMD-ROCm.html
 if(USE_ROCM)
+  message(
+    DEPRECATION
+    "Option USE_ROCM is deprecated and will be ignored in a future release. ")
   cmake_minimum_required(VERSION 3.18)
   if(NOT DEFINED ROCM_PATH)
     set(ROCM_PATH

cmake/CollectBuildInfoVars.cmake

@@ -187,6 +187,12 @@ else()
     set(ABACUS_LIBXC_VERSION "no")
 endif()
 
+if(ENABLE_DFTD4)
+    set(ABACUS_DFTD4_VERSION "yes (v${dftd4_VERSION})")
+else()
+    set(ABACUS_DFTD4_VERSION "no")
+endif()
+
 # Accelerators
 if(USE_CUDA AND CUDAToolkit_VERSION)
     set(ABACUS_CUDA_VERSION "yes (v${CUDAToolkit_VERSION})")
@@ -451,6 +457,7 @@ message("                     LibRI          = ${ABACUS_LIBRI_VERSION}")
 if(ENABLE_EXX_DEV)
   message("                                      (EXX developing features enabled)")
 endif()
+message("                     DFT-D4         = ${ABACUS_DFTD4_VERSION}")
 message("                     RAPIDJSON      = ${ABACUS_RAPIDJSON_VERSION}")
 message("                     PEXSI          = ${ABACUS_PEXSI_VERSION}")
 message("                     CNPY           = ${ABACUS_CNPY_VERSION}")

cmake/modules/FindLibRI.cmake

@@ -16,7 +16,7 @@ if(NOT LIBRI_DIR)
     include(FetchContent)
     FetchContent_Declare(
         LibRI
-        URL https://codeload.github.com/abacusmodeling/LibRI/tar.gz/e6d78e0
+        URL https://codeload.github.com/abacusmodeling/LibRI/tar.gz/b0eff7a
     )
     FetchContent_Populate(LibRI)
     set(LIBRI_DIR ${libri_SOURCE_DIR})

docs/CONTRIBUTING.md

@@ -172,9 +172,12 @@ An practical example is class [LCAO_Deepks](https://github.com/deepmodeling/abac
 
 ## Documenting INPUT Parameters
 
-ABACUS includes a built-in help system that allows users to query INPUT parameters directly from the command line (e.g., `abacus -h ecutwfc`). Parameter metadata is defined inline in the C++ source files (`source/source_io/module_parameter/read_input_item_*.cpp`) using `Input_Item` registrations.
+ABACUS includes a built-in help system that allows users to query INPUT parameters directly from the command line (e.g., `abacus -h ecutwfc`). Parameter metadata is defined inline in the C++ source files under `source/source_io/module_parameter/` using `Input_Item` registrations.
 
-A checked-in file `docs/parameters.yaml` contains a YAML dump of all parameter metadata, generated from the binary itself. This file is used by Sphinx to produce the online documentation page `input-main.md`.
+The C++ `Input_Item` registrations are the source of truth for parameter metadata. The checked-in `docs/parameters.yaml` and `docs/advanced/input_files/input-main.md` files are generated artifacts: do not edit either file manually. `parameters.yaml` is generated from the binary and is used by Sphinx to produce `input-main.md`.
+
+Availability expressions follow the grammar and invariants in
+[`developers_guide/input_availability.md`](developers_guide/input_availability.md).
 
 ### When to Update `docs/parameters.yaml`
 
@@ -198,13 +201,13 @@ Then verify the YAML is valid:
 python3 -c "import yaml; d=yaml.safe_load(open('docs/parameters.yaml')); print(len(d['parameters']), 'parameters')"
 ```
 
-You can also regenerate the markdown documentation locally:
+Then regenerate the markdown documentation locally:
 
 ```bash
 python3 docs/generate_input_main.py docs/parameters.yaml --output docs/advanced/input_files/input-main.md
 ```
 
-**Important:** Include the updated `docs/parameters.yaml` and `input-main.md` in your commit when submitting a PR that modifies INPUT parameters. Reviewers should verify the YAML changes match the C++ source changes and the `input-main.md` is updated.
+**Important:** Include the updated `docs/parameters.yaml` and `input-main.md` in your commit when submitting a PR that modifies INPUT parameters. CI regenerates both files from the built binary and rejects any mismatch. Do not fix a documentation mismatch by editing either generated file; update the C++ `Input_Item` registration and regenerate them instead.
 
 ### Parameter Documentation Format
 
@@ -218,7 +221,7 @@ When adding or modifying INPUT parameters in C++ source, set the following field
     item.description = "Description of what this parameter does.";
     item.default_value = "0";
     item.unit = "Ry";          // Optional, empty string if no unit
-    item.availability = "";    // Optional, empty string if always available
+    item.set_availability("basis_type==pw"); // Optional; omit if always available
     // ... read_value, reset_value, check_value functions ...
     this->add_item(item);
 }

docs/advanced/elec_properties/hs_matrix.md

@@ -65,12 +65,12 @@ The output of $H(R)$ and $S(R)$ matrices is controlled by [out_hsr](../input_fil
 | --- | --- |
 | `0` | Disabled |
 | `1` | Text CSR; an optional second value controls precision, for example `out_hsr 1 12` |
-| `2` | Reserved for future binary output; not implemented |
+| `2` | Native binary CSR using `.dat` files |
 | `3` | NPZ: `hrs1_nao.npz`, `hrs2_nao.npz` when needed, and `sr_nao.npz` |
 
 The legacy keywords `out_mat_hs2 1 [precision]` and `out_hsr_npz 1` remain supported as aliases for text and NPZ output respectively. If `out_hsr` is present together with either legacy keyword, `out_hsr` takes precedence.
 
-For a multi-k calculation, the files contain the individual real-space blocks stored for the Bravais lattice vectors $R$. For a gamma-only calculation, ABACUS stores the real-space contributions in a folded representation. Both text CSR and NPZ output write this internal representation directly: all stored $R$-space contributions are summed into a single block labelled `R = (0, 0, 0)`.
+For a multi-k calculation, the files contain the individual real-space blocks stored for the Bravais lattice vectors $R$. For a gamma-only calculation, ABACUS stores the real-space contributions in a folded representation. Text CSR, native binary, and NPZ output write this internal representation directly: all stored $R$-space contributions are summed into a single block labelled `R = (0, 0, 0)`.
 
 The folded gamma-only output is sufficient to inspect the matrix used by the gamma-only real-space container, but it does not retain the original lattice-vector resolution and cannot be used to interpolate matrices at arbitrary k points. Terms that are added only while constructing $H(k)$, rather than stored in the internal $H(R)$ container, are not guaranteed to be present. Use [out_hsk](../input_files/input-main.md#out_hsk) when the final $H(\Gamma)$ and $S(\Gamma)$ matrices are required.
 
@@ -89,6 +89,22 @@ In gamma-only mode, every generated file reports one Bravais lattice vector and
 # representation: gamma-only folded matrix; stored R-space contributions are summed into R = (0, 0, 0)
 ```
 
+### Native Binary CSR Format
+
+Set `out_hsr 2` to write the same H(R) and S(R) matrix sets with a `.dat` suffix. For example, an `nspin = 2` calculation writes `hrs1_nao.dat`, `hrs2_nao.dat`, and `sr_nao.dat`. When `out_app_flag` is false, the one-based ionic step is included before `_nao`, for example `hrs1g1_nao.dat` and `srg1_nao.dat`.
+
+Each ionic step is a complete record with no padding or self-describing header:
+
+1. Native `int`: zero-based ionic step, matrix dimension, number of R blocks.
+2. For every R block in lexicographic `(Rx, Ry, Rz)` order, four native `int` values: `Rx`, `Ry`, `Rz`, and `nnz`.
+3. `nnz` matrix values in CSR order. Real matrices use one native `double`; complex matrices use consecutive real and imaginary `double` values.
+4. `nnz` native `int` column indices.
+5. `dimension + 1` native `long long` row pointers.
+
+All R blocks stored by the internal HContainer are present, including blocks with zero nonzero values. The sparse threshold is `1e-10`, matching text CSR output. The format uses the host integer representation and byte order and therefore requires a compatible ABI. It does not contain unit-cell, spin, or matrix-label metadata; those are determined by the calculation input and filename.
+
+When `out_app_flag` is true, the first ionic step truncates the shared file and later ionic steps append complete records. Otherwise every ionic step is written to its own file.
+
 ### NPZ Format
 
 Set `out_hsr 3` to write `hrs1_nao.npz`, `hrs2_nao.npz` when a second spin channel is present, and `sr_nao.npz`. Matrix entry names include the atom-pair indices and the three components of $R$. Multi-k calculations retain the stored $R$ blocks, while gamma-only calculations contain only matrix entry names ending in `_0_0_0`.
@@ -125,7 +141,7 @@ The CSR format stores a sparse m × n matrix M in row form using three arrays (v
 
 ### Precision Control
 
-Use `out_hsr 1 12` to output text CSR files with 12-digit precision (default is 8). Precision is ignored for NPZ output.
+Use `out_hsr 1 12` to output text CSR files with 12-digit precision (default is 8). Precision is ignored for native binary and NPZ output.
 
 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).