Merge branch 'develop' into refactor/hegvd_op

Author: Cstandardlib

.gitignore

@@ -23,4 +23,5 @@ __pycache__
 abacus.json
 *.npy
 toolchain/install/
-toolchain/abacus_env.sh
+toolchain/abacus_env.sh
+.trae

toolchain/README.md

@@ -151,21 +151,21 @@ Mix online and offline packages as needed - the toolchain automatically detects
 ## Supported Toolchains
 
 ### GNU Toolchain
-- **Compilers**: System GCC (≥5.0)
+- **Compilers**: System GCC (≥5.0) or installed GCC
 - **MPI**: OpenMPI or MPICH
 - **Math**: OpenBLAS + ScaLAPACK
 - **Features**: Most stable, widely compatible
 
 ### Intel Toolchain
-- **Compilers**: Intel OneAPI (icx/icpx/ifx or classic icc/icpc/ifort)
+- **Compilers**: Intel OneAPI (icx/icpx/ifx or classic icc/icpc/ifort) with system/installed GCC (≥5.0) 
 - **MPI**: Intel MPI
 - **Math**: Intel MKL
-- **Features**: Optimized performance, EXX support
+- **Features**: Optimized performance for Intel Machine
 
 ### AMD Toolchain
-- **Compilers**: AMD AOCC or GCC
+- **Compilers**: AMD AOCC or system/installed GCC
 - **Math**: AMD AOCL (Optimized math libraries)
-- **Features**: AMD processor optimization
+- **Features**: AMD processor optimization (e.g., Zen3+)
 
 ## Dependencies
 
@@ -193,7 +193,7 @@ Mix online and offline packages as needed - the toolchain automatically detects
 | LibComm | master | EXX calculations | GPL-3.0 | Install |
 | LibTorch | 2.1.2 / 1.12.1 | MLALGO support | BSD-3-Clause | Optional |
 | LibNPY | 1.0.1 / 1.0.1 | NumPy I/O | MIT | Optional |
-| NEP | main | Neural network potential | MIT | Optional |
+| NEP | main | Neuroevolution potential | MIT | Optional |
 
 Also, [Intel-oneAPI](https://www.intel.cn/content/www/cn/zh/developer/tools/oneapi/toolkits.html) and AMD [AOCC](https://www.amd.com/zh-cn/developer/aocc.html) and [AOCL](https://www.amd.com/zh-cn/developer/aocl.html) are supported in toolchain by setting them to system option, but one should install them manually by server administrator.
 

toolchain/install_abacus_toolchain.sh

@@ -1,30 +1,11 @@
 #!/bin/bash -e
 
-# TODO: Review and if possible fix shellcheck errors.
+# TODO: Remove this deprecated script in the future.
 # shellcheck disable=all
 
 [ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=$0
 SCRIPT_DIR="$(cd "$(dirname "$SCRIPT_NAME")" && pwd -P)"
 
-# +---------------------------------------------------------------------------+
-# |   ABACUS: (Atomic-orbital Based Ab-initio Computation at UStc)            |
-# |   -- an open-source package based on density functional theory(DFT)       |
-# |   Copyright 2004-2022 ABACUS developers group                             |
-# |   <https://github.com/deepmodeling/abacus-develop>                        |
-# |                                                                           |
-# |   SPDX-License-Identifier: GPL-2.0-or-later                               |
-# +---------------------------------------------------------------------------+
-#
-#
-# *****************************************************************************
-#> \brief    This script will compile and install or link existing tools and
-#>           libraries ABACUS depends on and generate setup files that
-#>           can be used to compile and use ABACUS
-#> \history  Created on Friday, 2023/08/18
-#            Update for Intel (18.08.2023, MK)
-#> \author   Zhaoqing Liu (Quantum Misaka) [email protected]
-# *****************************************************************************
-
 # ------------------------------------------------------------------------
 # Work directories and used files
 # ------------------------------------------------------------------------

toolchain/install_abacus_toolchain_new.sh

@@ -1,15 +1,14 @@
 #!/bin/bash -e
 
 # ============================================================================
-# ABACUS Toolchain Installation Script (New Version - Enhanced UI)
+# ABACUS Toolchain Installation Script (New refractored version)
 # ============================================================================
 # This is the new refactored version of the ABACUS toolchain installation script.
-# It provides the same functionality as the original script but with improved
-# modularity, maintainability, extensibility, and beautiful terminal output.
+# It provides the most main functionality as the original script but with 
+# improved modularity, maintainability, extensibility, and beautiful terminal output.
 #
 # Author: Quantum Misaka by Trae SOLO
 # Date: 2025-10-16
-# Enhanced: Beautiful terminal UI with harmonious color scheme
 # ============================================================================
 
 # Set script name for error reporting

toolchain/scripts/lib/user_interface.sh

@@ -690,6 +690,15 @@ ui_show_summary() {
     echo "   ├─ Kernel: $(uname -r)"
     echo "   ├─ glibc: $(ui_get_glibc_version)"
     echo "   ├─ CPU Cores: $(nproc 2>/dev/null || echo "unknown")"
+    # CPU model detection
+    local cpu_model="unknown"
+    if command -v lscpu &> /dev/null; then
+        cpu_model=$(LC_ALL=C lscpu | awk -F: '/^Model name/{print $2}' | sed 's/^[[:space:]]*//')
+    fi
+    if [[ -z "$cpu_model" || "$cpu_model" == "unknown" ]] && [[ -r /proc/cpuinfo ]]; then
+        cpu_model=$(awk -F: '/model name|Hardware|Processor/{print $2; exit}' /proc/cpuinfo | sed 's/^[[:space:]]*//')
+    fi
+    echo "   ├─ CPU Model: ${cpu_model}"
     if command -v free &> /dev/null; then
         local mem_gb=$(free -g | awk '/^Mem:/ {print $2}')
         echo "   ├─ Memory: ${mem_gb}GB"

toolchain/scripts/stage2/install_aocl.sh

@@ -80,9 +80,9 @@ export AOCL_ROOT="${pkg_install_dir}"
 export AOCL_CFLAGS="${AOCL_CFLAGS}"
 export AOCL_LDFLAGS="${AOCL_LDFLAGS}"
 export AOCL_LIBS="${AOCL_LIBS}"
-export FAST_MATH_CFLAGS="\${FAST_MATH_CFLAGS} ${AOCL_CFLAGS}"
-export FAST_MATH_LDFLAGS="\${FAST_MATH_LDFLAGS} ${AOCL_LDFLAGS}"
-export FAST_MATH_LIBS="\${FAST_MATH_LIBS} ${AOCL_LIBS}"
+export MATH_CFLAGS="\${MATH_CFLAGS} ${AOCL_CFLAGS}"
+export MATH_LDFLAGS="\${MATH_LDFLAGS} ${AOCL_LDFLAGS}"
+export MATH_LIBS="\${MATH_LIBS} ${AOCL_LIBS}"
 EOF
 fi
 

toolchain/scripts/tool_kit.sh

@@ -956,6 +956,7 @@ download_pkg_from_url() {
     "strict")
       echo "Downloading with strict certificate validation: $__url"
       if ! wget ${DOWNLOADER_FLAGS} "$__url" -O "$__filename"; then
+        rm -f "$__filename"
         report_error "failed to download $__url (strict certificate validation)"
         recommend_offline_installation "$__filename" "$__url"
         if [ "${PACK_RUN}" != "__TRUE__" ]; then
@@ -966,6 +967,7 @@ download_pkg_from_url() {
     "skip")
       echo "Downloading with certificate validation disabled: $__url"
       if ! wget ${DOWNLOADER_FLAGS} "$__url" -O "$__filename" --no-check-certificate; then
+        rm -f "$__filename"
         report_error "failed to download $__url"
         recommend_offline_installation "$__filename" "$__url"
         if [ "${PACK_RUN}" != "__TRUE__" ]; then
@@ -981,6 +983,7 @@ download_pkg_from_url() {
       else
         echo "Certificate validation failed, retrying without certificate check..."
         if ! wget ${DOWNLOADER_FLAGS} "$__url" -O "$__filename" --no-check-certificate; then
+          rm -f "$__filename"
           report_error "failed to download $__url (both secure and insecure attempts failed)"
           recommend_offline_installation "$__filename" "$__url"
           if [ "${PACK_RUN}" != "__TRUE__" ]; then

toolchain/toolchain_aocc-aocl.sh

@@ -39,9 +39,9 @@ WITH_RAPIDJSON="install"
 WITH_LIBRI="install"
 WITH_LIBCOMM="install"
 
-# Optional Features (DeepKS support)
-WITH_LIBTORCH="no"  # Set to "install" for DeepKS support
-WITH_LIBNPY="no"    # Set to "install" for DeepKS support
+# Optional Features (MLALGO support)
+WITH_LIBTORCH="no"
+WITH_LIBNPY="no"
 WITH_NEP="no"
 
 # AMD Compiler Options
@@ -71,7 +71,10 @@ CMAKE_VERSION="main"        # main=3.31.7, alt=3.30.5
 OPENMPI_VERSION="main"      # main=5.0.8, alt=4.1.6
 ELPA_VERSION="main"         # main=2025.06.001, alt=2024.05.001
 LIBXC_VERSION="main"        # main=7.0.0, alt=6.2.2
+# Optional Libraries
 LIBTORCH_VERSION="main"     # main=2.1.2, alt=1.12.1 (use alt for older GLIBC)
+# Note: main(2.1.2) version of LibTorch need glibc > 2.27
+# Note: alt(1.12.1) version of LibTorch cannot support DeePMD-Torch for DPA
 
 # Note: AOCC-AOCL toolchain uses AOCL for math libraries (FFTW, ScaLAPACK)
 # so OpenBLAS and ScaLAPACK version selections are not applicable

toolchain/toolchain_gcc-aocl.sh

@@ -68,7 +68,10 @@ CMAKE_VERSION="main"        # main=3.31.7, alt=3.30.5
 OPENMPI_VERSION="main"      # main=5.0.8, alt=4.1.6
 ELPA_VERSION="main"         # main=2025.06.001, alt=2024.05.001
 LIBXC_VERSION="main"        # main=7.0.0, alt=6.2.2
+# Optional Libraries
 LIBTORCH_VERSION="main"     # main=2.1.2, alt=1.12.1 (use alt for older GLIBC)
+# Note: main(2.1.2) version of LibTorch need glibc > 2.27
+# Note: alt(1.12.1) version of LibTorch cannot support DeePMD-Torch for DPA
 
 # Note: GCC-AOCL toolchain uses AOCL for math libraries (FFTW, ScaLAPACK)
 # so OpenBLAS and ScaLAPACK version selections are not applicable

toolchain/toolchain_gnu.sh

@@ -72,6 +72,8 @@ LIBXC_VERSION="main"        # main=7.0.0, alt=6.2.2
 SCALAPACK_VERSION="main"    # main=2.2.2, alt=2.2.1
 # Optional Libraries
 LIBTORCH_VERSION="main"     # main=2.1.2, alt=1.12.1 (use alt for older GLIBC)
+# Note: main(2.1.2) version of LibTorch need glibc > 2.27
+# Note: alt(1.12.1) version of LibTorch cannot support DeePMD-Torch for DPA
 
 # ============================================================================
 # Execute Installation (DO NOT MODIFY BELOW THIS LINE)