Merge branch 'develop' into 2026-08-10

Author: mohanchen

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}")

docs/advanced/elec_properties/hs_matrix.md

@@ -18,7 +18,7 @@ Use [out_hsk](../input_files/input-main.md#out_hsk) to print the upper triangula
 | --- | --- |
 | `0` | Disabled |
 | `1` | Text; an optional second value controls precision, for example `out_hsk 1 12` |
-| `2` | Reserved for future binary output; not implemented |
+| `2` | Native binary `.dat` output |
 | `3` | Reserved for H(k)/S(k) NPZ output; not implemented |
 
 The legacy keyword `out_mat_hs 1 [precision]` remains supported as an alias for `out_hsk 1 [precision]`. If both names are present, `out_hsk` takes precedence.
@@ -45,6 +45,18 @@ Each output block starts with a comment header containing the one-based ionic-st
 
 For multi-k calculations, the matrices are Hermitian and each matrix element is written as `(real,imag)`. For gamma-only calculations, the matrices are symmetric and the matrix elements are written as real numbers.
 
+### Native Binary Format
+
+For `out_hsk 2`, the filenames in the table above use `.dat` instead of `.txt`. Each matrix record is written without padding or a self-describing header:
+
+1. the matrix dimension as a native C++ `int`;
+2. the upper-triangular elements in row-major order, from `(0,0)` through `(0,N-1)`, then `(1,1)` through `(1,N-1)`, and so on;
+3. each gamma-only element as one native `double`, or each multi-k/spinor element as two consecutive native `double` values containing the real and imaginary parts.
+
+The file therefore contains `sizeof(int) + N(N+1)/2 * sizeof(double)` bytes for a gamma-only record and `sizeof(int) + N(N+1) * sizeof(double)` bytes for a multi-k or spinor record. The format uses the host integer representation and byte order and is intended for readers using a compatible ABI.
+
+When `out_app_flag` is true, the first ionic step truncates the shared file and every later step appends another complete record. When it is false, each ionic step has a separate filename containing `g${step}` before `_nao`.
+
 ## out_hsr
 
 The output of $H(R)$ and $S(R)$ matrices is controlled by [out_hsr](../input_files/input-main.md#out_hsr). It is available for both gamma-only and multi-k LCAO calculations:

docs/advanced/input_files/input-main.md

@@ -2003,7 +2003,7 @@
 - **Description**: Output the upper triangular part of the Hamiltonian and overlap matrices in reciprocal space for each k-point into files in the directory OUT.${suffix}. The first integer selects the format:
   - 0: disabled;
   - 1: text output; the optional second integer controls precision and defaults to 8;
-  - 2: reserved for binary output, which is not implemented yet;
+  - 2: binary output in the native ABACUS .dat format;
   - 3: NPZ output, which is not implemented for H(k)/S(k).
 
   The output is also controlled by out_freq_ion and out_app_flag. For more information, refer to hs_matrix.md.
@@ -2014,6 +2014,8 @@
   - Multi-k, nspin = 1: hk1_nao.txt for the Hamiltonian matrix and sk1_nao.txt for the overlap matrix at the first k-point.
   - Multi-k, nspin = 2: hk1s1_nao.txt and hk1s2_nao.txt for the two spin channels of the Hamiltonian matrix, and sk1_nao.txt for the overlap matrix at the first k-point. Only one overlap matrix is written because it is identical for both spin channels.
   - Multi-k, nspin = 4: hk1s4_nao.txt for the spinor Hamiltonian matrix and sk1_nao.txt for the spinor overlap matrix at the first k-point.
+  For binary output, the same names use the .dat suffix. Each native binary record contains the matrix dimension as an int followed by the row-major upper triangle. Gamma-only elements are doubles; multi-k and spinor elements are pairs of doubles containing the real and imaginary parts. Native integer representation and byte order are used.
+  When out_app_flag is true, the first ionic step truncates the file and later steps append complete records.
   When out_app_flag is false, g followed by the one-based ionic-step index is inserted before _nao, for example hk1s1g1_nao.txt.
 
   > Note: In the 3.10-LTS version, the file names are data-0-H and data-0-S, etc.

docs/parameters.yaml

@@ -3112,7 +3112,7 @@ parameters:
       Output the upper triangular part of the Hamiltonian and overlap matrices in reciprocal space for each k-point into files in the directory OUT.${suffix}. The first integer selects the format:
       * 0: disabled;
       * 1: text output; the optional second integer controls precision and defaults to 8;
-      * 2: reserved for binary output, which is not implemented yet;
+      * 2: binary output in the native ABACUS .dat format;
       * 3: NPZ output, which is not implemented for H(k)/S(k).
 
       The output is also controlled by out_freq_ion and out_app_flag. For more information, refer to hs_matrix.md.
@@ -3122,6 +3122,8 @@ parameters:
       * Multi-k, nspin = 1: hk1_nao.txt for the Hamiltonian matrix and sk1_nao.txt for the overlap matrix at the first k-point.
       * Multi-k, nspin = 2: hk1s1_nao.txt and hk1s2_nao.txt for the two spin channels of the Hamiltonian matrix, and sk1_nao.txt for the overlap matrix at the first k-point. Only one overlap matrix is written because it is identical for both spin channels.
       * Multi-k, nspin = 4: hk1s4_nao.txt for the spinor Hamiltonian matrix and sk1_nao.txt for the spinor overlap matrix at the first k-point.
+      For binary output, the same names use the .dat suffix. Each native binary record contains the matrix dimension as an int followed by the row-major upper triangle. Gamma-only elements are doubles; multi-k and spinor elements are pairs of doubles containing the real and imaginary parts. Native integer representation and byte order are used.
+      When out_app_flag is true, the first ionic step truncates the file and later steps append complete records.
       When out_app_flag is false, g followed by the one-based ionic-step index is inserted before _nao, for example hk1s1g1_nao.txt.
 
       [NOTE] In the 3.10-LTS version, the file names are data-0-H and data-0-S, etc.

interfaces/ASE_interface/abacuslite/xtest.sh

@@ -67,6 +67,7 @@ set(_abacus_feature_definitions
   $<$<BOOL:${ENABLE_LIBRI}>:TEST_EXX_RADIAL=1>
   $<$<BOOL:${ENABLE_EXX_DEV}>:__EXX_DEV>
   $<$<BOOL:${ENABLE_LIBXC}>:__LIBXC>
+  $<$<BOOL:${ENABLE_DFTD4}>:__DFTD4>
   $<$<BOOL:${MATH_INFO}>:GATHER_INFO>)
 
 if(ABACUS_COMMIT_INFO_INCLUDE_DIR)