Merge branch 'develop' of github.com:deepmodeling/abacus-develop into HSolver

Author: dyzheng

.github/workflows/performance.yml

@@ -26,7 +26,7 @@ jobs:
           cmake --install build
       - name: Test
         run: |
-          . /opt/intel/oneapi/setvars.sh 2> /dev/null || :
+          test -e /opt/intel/oneapi/setvars.sh && . /opt/intel/oneapi/setvars.sh
           cd examples/performance/
           bash run.sh
       - name: Show Result

CMakeLists.txt

@@ -1,11 +1,11 @@
 ########################################
 # CMake build system
 # This file is part of ABACUS
-cmake_minimum_required(VERSION 3.18)
+cmake_minimum_required(VERSION 3.16)
 ########################################
 
 project(ABACUS
-    VERSION 2.2.0
+    VERSION 2.2.3
     DESCRIPTION "ABACUS is an electronic structure package based on DFT."
     HOMEPAGE_URL "https://github.com/deepmodeling/abacus-develop"
     LANGUAGES CXX
@@ -22,14 +22,16 @@ option(BUILD_TESTING "Build ABACUS unit tests" OFF)
 option(GENERATE_TEST_REPORTS "Enable test report generation" OFF)
 
 set(ABACUS_BIN_NAME abacus)
-set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/modules)
+list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/modules)
 set(ABACUS_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/source)
 set(ABACUS_TEST_DIR ${CMAKE_CURRENT_SOURCE_DIR}/tests)
 set(ABACUS_BIN_PATH ${CMAKE_CURRENT_BINARY_DIR}/${ABACUS_BIN_NAME})
 include_directories(${ABACUS_SOURCE_DIR})
 add_executable(${ABACUS_BIN_NAME} source/main.cpp)
+set(CMAKE_CXX_STANDARD 11)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
 add_compile_options(-O2 -g)
-SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-write-strings" )
+add_compile_options(-Wno-write-strings)
 
 find_package(Cereal REQUIRED)
 include_directories(${Cereal_INCLUDE_DIR})
@@ -52,10 +54,9 @@ if(USE_OPENMP)
   find_package(OpenMP REQUIRED)
   target_link_libraries(${ABACUS_BIN_NAME} OpenMP::OpenMP_CXX)
   add_compile_options(${OpenMP_CXX_FLAGS})
-  #add_compile_definitions(_OPENMP)
+  add_link_options(${OpenMP_CXX_LIBRARIES})
 endif()
 
-set(CMAKE_CXX_STANDARD 11)
 include(CheckLanguage)
 check_language(CUDA)
 if(CMAKE_CUDA_COMPILER)
@@ -71,7 +72,7 @@ if(CMAKE_CUDA_COMPILER)
     endif()
   else()
     if(NOT USE_CUDA AND NOT USE_CUSOLVER_LCAO)
-      message(WARNING "CUDA components detected, but both USE_CUDA and USE_CUSOLVER_LCAO set to OFF. \nNOT building CUDA version of ABACUS.")
+      message(STATUS "CUDA components detected, but both USE_CUDA and USE_CUSOLVER_LCAO set to OFF. NOT building CUDA version of ABACUS.")
     elseif (USE_CUDA AND USE_CUSOLVER_LCAO)
       message(FATAL_ERROR "USE_CUDA and USE_CUSOLVER_LCAO set, but now they not allowed to coexist.")
     endif()
@@ -85,10 +86,10 @@ else() # CUDA not found
 endif()
 
 if(USE_CUDA OR USE_CUSOLVER_LCAO)
+  cmake_minimum_required(VERSION 3.18) # required by `CUDA_ARCHITECTURES` below
   set(CMAKE_CXX_STANDARD 14)
   set(CMAKE_CXX_EXTENSIONS ON)
-  set(CMAKE_CXX_STANDARD_REQUIRED ON)
-  set(CMAKE_CUDA_STANDARD 14)
+  set(CMAKE_CUDA_STANDARD ${CMAKE_CXX_STANDARD})
   set(CMAKE_CUDA_STANDARD_REQUIRED ON)
   set(CMAKE_CUDA_HOST_COMPILER ${CMAKE_CXX_COMPILER})
   enable_language(CUDA)
@@ -119,9 +120,7 @@ endif()
 # Warning: CMake add support to HIP in version 3.21. This is rather a new version.
 # Use cmake with AMD-ROCm: https://rocmdocs.amd.com/en/latest/Installation_Guide/Using-CMake-with-AMD-ROCm.html
 if(USE_ROCM)
-  set(CMAKE_CXX_STANDARD 11)
-  SET(CMAKE_HIP_STANDARD 11)
-  # set(CMAKE_CXX_STANDARD_REQUIRED True)
+  SET(CMAKE_HIP_STANDARD ${CMAKE_CXX_STANDARD})
   list(APPEND CMAKE_PREFIX_PATH /opt/rocm/hip /opt/rocm)
   list(APPEND CMAKE_SYSTEM_PREFIX_PATH "/opt/rocm/hip")
 
@@ -144,6 +143,9 @@ if(USE_ROCM)
 endif()
 
 if(ENABLE_ASAN)
+  if (CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
+    message(FATAL_ERROR "Address Sanitizer is not supported on Intel compiler.")
+  endif()
   add_compile_options(
     -fsanitize=address
     -fno-omit-frame-pointer
@@ -205,13 +207,16 @@ if(ENABLE_DEEPKS)
     FetchContent_Declare(
       libnpy
       GIT_REPOSITORY https://github.com/llohse/libnpy.git
+      GIT_SHALLOW TRUE
+      GIT_PROGRESS TRUE
     )
     FetchContent_MakeAvailable(libnpy)
   endif()
   include_directories(${libnpy_SOURCE_DIR}/include)
   add_compile_definitions(__DEEPKS)
 endif()
 
+list(APPEND math_libs m)
 target_link_libraries(${ABACUS_BIN_NAME} ${math_libs})
 
 if(DEFINED Libxc_DIR)
@@ -243,17 +248,18 @@ add_compile_definitions(
 )
 
 IF (BUILD_TESTING)
+  set(CMAKE_CXX_STANDARD 14) # Required in orbital
   include(CTest)
   enable_testing()
-  find_package(Threads)
-  set(CMAKE_CXX_STANDARD_REQUIRED ON)
   find_package(GTest HINTS /usr/local/lib/ ${GTEST_DIR})
   if(NOT ${GTest_FOUND})
     include(FetchContent)
     FetchContent_Declare(
       googletest
       GIT_REPOSITORY https://github.com/google/googletest.git
       GIT_TAG "origin/main"
+      GIT_SHALLOW TRUE
+      GIT_PROGRESS TRUE
     )
     FetchContent_MakeAvailable(googletest)
   endif()
@@ -266,8 +272,11 @@ IF (BUILD_TESTING)
     add_executable(${UT_TARGET} ${UT_SOURCES})
     #dependencies & link library
     target_link_libraries(${UT_TARGET} ${UT_LIBS}
-      OpenMP::OpenMP_CXX pthread GTest::gtest_main GTest::gmock_main)
-    install(TARGETS ${UT_TARGET} DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/../../../tests )
+      Threads::Threads GTest::gtest_main GTest::gmock_main)
+    if(USE_OPENMP)
+      target_link_libraries(${UT_TARGET} OpenMP::OpenMP_CXX)
+    endif()
+    install(TARGETS ${UT_TARGET} DESTINATION ${CMAKE_BINARY_DIR}/tests )
     add_test(NAME ${UT_TARGET}
       COMMAND ${UT_TARGET}
       WORKING_DIRECTORY $<TARGET_FILE_DIR:${UT_TARGET}>
@@ -289,6 +298,7 @@ target_link_libraries(${ABACUS_BIN_NAME}
     io
     ions
     lcao
+    gint
     parallel
     mrrr
     pdiag
@@ -301,7 +311,6 @@ target_link_libraries(${ABACUS_BIN_NAME}
     hamilt
     psi
     esolver
-    -lm
 )
 
 install(PROGRAMS ${ABACUS_BIN_PATH}

Dockerfile

@@ -1,4 +1,5 @@
-# To build this docker file, run `docker build -t abacus - < Dockerfile`.
+# To build this Dockerfile, run `docker build -t abacus - < Dockerfile`.
+# Pull image with `docker pull ghcr.io/deepmodeling/abacus:latest`.
 FROM ubuntu:latest
 RUN apt update && apt install -y --no-install-recommends libopenblas-dev liblapack-dev libscalapack-mpi-dev libelpa-dev libfftw3-dev libcereal-dev libxc-dev g++ make cmake bc time sudo vim git
 # If you wish to use the LLVM compiler, replace 'g++' above with 'clang libomp-dev'.

Dockerfile.gnu

@@ -1,9 +1,9 @@
 FROM debian:bullseye-slim
 
-RUN apt-get update && apt-get install -y --no-install-recommends git g++ gfortran libssl-dev make cmake vim wget bc unzip \
+RUN apt-get update && apt-get install -y --no-install-recommends git g++ gfortran libssl-dev make cmake vim wget bc unzip python3-numpy\
     && apt-get install -y --no-install-recommends mpich libmpich-dev
 
-ENV GIT_SSL_NO_VERIFY 1
+ENV GIT_SSL_NO_VERIFY=1 TERM=xterm-256color
 
 RUN cd /tmp \
     && git clone https://github.com/USCiLab/cereal.git \

docs/CONTRIBUTING.md

@@ -6,7 +6,6 @@ This file provides a guideline for it.
 ## Table of Contents
 
 - [Got a question?](#got-a-question)
-- [Before getting started](#before-getting-started)
 - [Structure of the package](#structure-of-the-package)
 - [Submitting an Issue](#submitting-an-issue)
 - [Comment Style for documentation](#comment-style-for-documentation)
@@ -23,6 +22,7 @@ If you would like to implement a new feature, please submit an issue with a prop
 
 ## Structure of the package
 
+Please refer to [our instructions](./install.md) on how to installing ABACUS.
 The source code of ABACUS is based on several modules. Under the ABACUS root directory, there are the following folders:
 
 - `cmake`: relevant files for finding required packages when compiling the code with cmake;

docs/input-main.md

@@ -24,7 +24,11 @@
 
 - [Electronic structure](#electronic-structure)
 
-    [basis_type](#basis-type) | [ks_solver](#ks-solver) | [nbands](#nbands) | [nbands_sto](#nbands_sto) | [nbands_istate](#nbands-istate) | [nspin](#nspin) | [occupations](#occupations) | [smearing_method](#smearing_method) | [smearing_sigma](#smearing_sigma) | [mixing_type](#mixing-type) | [mixing_beta](#mixing-beta) | [mixing_ndim](#mixing-ndim) | [mixing_gg0](#mixing-gg0) | [gamma_only](#gamma-only) | [printe](#printe) | [scf_nmax](#scf_nmax) | [scf_thr](#scf_thr) | [chg_extrap](#chg_extrap) | [nche_sto](#nche_sto) | [emin_sto](#emin_sto) | [emax_sto](#emax_sto) | [seed_sto](#seed_sto)
+    [basis_type](#basis-type) | [ks_solver](#ks-solver) | [nbands](#nbands) | [nbands_istate](#nbands-istate) | [nspin](#nspin) | [occupations](#occupations) | [smearing_method](#smearing_method) | [smearing_sigma](#smearing_sigma) | [mixing_type](#mixing-type) | [mixing_beta](#mixing-beta) | [mixing_ndim](#mixing-ndim) | [mixing_gg0](#mixing-gg0) | [gamma_only](#gamma-only) | [printe](#printe) | [scf_nmax](#scf_nmax) | [scf_thr](#scf_thr) | [chg_extrap](#chg_extrap)
+
+- [Electronic structure (SDFT)](#electronic-structure-sdft)
+
+    [nbands_sto](#nbands_sto) | [nche_sto](#nche_sto) | [emin_sto](#emin_sto) | [emax_sto](#emax_sto) | [seed_sto](#seed_sto)
 
 - [Geometry relaxation](#geometry-relaxation)
 
@@ -72,7 +76,7 @@
 
 - [Electric field and dipole correction](#Electric-field-and-dipole-correction)
 
-    [efield](#efield) | [dipole](#dipole) | [edir](#edir) | [emaxpos](#emaxpos) | [eopreg](#eopreg) | [eamp](#eamp)
+    [efield_flag](#efield_flag) | [dip_cor_flag](#dip_cor_flag) | [efield_dir](#efield_dir) | [efield_pos_max](#efield_pos_max) | [efield_pos_dec](#efield_pos_dec) | [efield_amp ](#efield_amp )
 
 [back to main page](../README.md)
 
@@ -464,14 +468,6 @@ calculations.
   - nspin=1: 1.2\*occupied_bands, occupied_bands+10)
   - nspin=2: max(1.2\*nelec, nelec+20)
 
-#### nbands_sto
-
-- **Type**: Integer
-- **Description**: 
-  - nbands_sto>0: Number of stochastic orbitals to calculate in stochastic DFT (SDFT) or mix stochastic-deterministic (MDFT). More bands obtain more precise results or smaller stochastic errors ($ \propto 1/\sqrt{N_{\chi}}$); 
-  - nbands_sto=0: Complete basis will be used to replace stochastic orbitals with the Chebyshev method (CT) and it will get the results the same as KSDFT without stochastic errors.
-- **Default**: 0
-
 #### nbands_istate
 
 - **Type**: Integer
@@ -570,6 +566,21 @@ calculations.
   - second-order: second-order extrapolation
 - **Default**:atomic
 
+ by time(NULL).
+- **Default**:0
+
+### Electronic structure (SDFT)
+
+This part of variables are used to control the parameters of stochastic DFT (SDFT),  mix stochastic-deterministic DFT (MDFT), or complete-basis Chebyshev method (CT).
+
+#### nbands_sto
+
+- **Type**: Integer
+- **Description**: 
+  - nbands_sto>0: Number of stochastic orbitals to calculate in SDFT and MDFT.  More bands obtain more precise results or smaller stochastic errors ($ \propto 1/\sqrt{N_{\chi}}$); 
+  - nbands_sto=0: Complete basis will be used to replace stochastic orbitals with the Chebyshev method (CT) and it will get the results the same as KSDFT without stochastic errors.
+- **Default**: 0
+
 #### nche_sto
 
 - **Type**: Integer
@@ -593,8 +604,7 @@ calculations.
 - **Type**: Integer
 - **Description**: The random seed to generate stochastic orbitals.
   - seed_sto>=0: Stochastic orbitals have the form of $\exp(i2\pi\theta(G))$, where $\theta$ is a uniform distribution in $(0,1)$. If seed_sto=0, the seed is decided by time(NULL).
-  - seed_sto<=-1: Stochastic orbitals have the form of $\pm1$ with the equal probability. If seed_sto=-1, the seed is decided by time(NULL).
-- **Default**:0
+  - seed_sto<=-1: Stochastic orbitals have the form of $\pm1$ with the equal probability. If seed_sto=-1, the seed is decided
 
 ### Geometry relaxation
 
@@ -918,42 +928,42 @@ Warning: this function is not robust enough for version 2.2.0. Please try these
 
 This part of variables are relevant to electric field and dipole correction
 
-#### efield
+#### efield_flag
 
 - **Type**: Boolean
 - **Description**: If set to true, a saw-like potential simulating an electric field
 is added to the bare ionic potential. 
 - **Default**: false
 
-#### dipole
+#### dip_cor_flag
 
 - **Type**: Boolean
-- **Description**: If dipole == true and efield == true,  a dipole correction is also
-added to the bare ionic potential. If you want no electric field, parameter eamp should be zero. Must be used ONLY in a slab geometry for surface calculations, with the discontinuity FALLING IN THE EMPTY SPACE.
+- **Description**: If dip_cor_flag == true and efield_flag == true,  a dipole correction is also
+added to the bare ionic potential. If you want no electric field, parameter efield_amp  should be zero. Must be used ONLY in a slab geometry for surface calculations, with the discontinuity FALLING IN THE EMPTY SPACE.
 - **Default**: false
 
-#### edir
+#### efield_dir
 
 - **Type**: Integer
-- **Description**: The direction of the electric field or dipole correction is parallel to the reciprocal lattice vector, so the potential is constant in planes defined by FFT grid points, edir = 0, 1 or 2. Used only if efield == true.
+- **Description**: The direction of the electric field or dipole correction is parallel to the reciprocal lattice vector, so the potential is constant in planes defined by FFT grid points, efield_dir = 0, 1 or 2. Used only if efield_flag == true.
 - **Default**: 2
 
-#### emaxpos
+#### efield_pos_max
 
 - **Type**: Real
-- **Description**: Position of the maximum of the saw-like potential along crystal axis edir, within the  unit cell, 0 < emaxpos < 1. Used only if efield == true.
+- **Description**: Position of the maximum of the saw-like potential along crystal axis efield_dir, within the  unit cell, 0 < efield_pos_max < 1. Used only if efield_flag == true.
 - **Default**: 0.5
 
-#### eopreg
+#### efield_pos_dec
 
 - **Type**: Real
-- **Description**: Zone in the unit cell where the saw-like potential decreases, 0 < eopreg < 1. Used only if efield == true.
+- **Description**: Zone in the unit cell where the saw-like potential decreases, 0 < efield_pos_dec < 1. Used only if efield_flag == true.
 - **Default**: 0.1
 
-#### eamp
+#### efield_amp 
 
 - **Type**: Real
-- **Description**: Amplitude of the electric field, in ***Hartree*** a.u.; 1 a.u. = 51.4220632*10^10 V/m. Used only if efield == true. The saw-like potential increases with slope eamp in the region from (emaxpos+eopreg-1) to (emaxpos), then decreases until (emaxpos+eopreg), in units of the crystal vector edir. Important: the change of slope of this potential must be located in the empty region, or else unphysical forces will result.
+- **Description**: Amplitude of the electric field, in ***Hartree*** a.u.; 1 a.u. = 51.4220632*10^10 V/m. Used only if efield_flag == true. The saw-like potential increases with slope efield_amp  in the region from (efield_pos_max+efield_pos_dec-1) to (efield_pos_max), then decreases until (efield_pos_max+efield_pos_dec), in units of the crystal vector efield_dir. Important: the change of slope of this potential must be located in the empty region, or else unphysical forces will result.
 - **Default**: 0.0
 
 ### Exact Exchange