Merge pull request deepmodeling#2 from abacusmodeling/develop

merge from abacusmodeling/abacus-develop branch develop

CMakeLists.txt

@@ -12,15 +12,19 @@ project(ABACUS
 )
 
 option(ENABLE_DEEPKS "Enable DeePKS functionality" OFF)
+option(ENABLE_LIBXC "Enable LibXC functionality" OFF)
+
 option(ENABLE_ASAN "Enable AddressSanitizer" OFF)
-option(BUILD_TESTING "Build ABACUS unit tests" ON)
+option(BUILD_UNIT_TESTS "Build ABACUS unit tests" ON)
 option(GENERATE_TEST_REPORTS "Enable test report generation" OFF)
 
+
 if(ENABLE_DEEPKS)
   set(CMAKE_CXX_STANDARD 14)
 else()
   set(CMAKE_CXX_STANDARD 11)
 endif()
+
 if(ENABLE_ASAN)
   add_compile_options(
     -O1
@@ -44,7 +48,6 @@ set(ABACUS_BIN_PATH ${CMAKE_CURRENT_BINARY_DIR}/${ABACUS_BIN_NAME})
 
 include_directories(${ABACUS_SOURCE_DIR})
 
-find_package(Boost REQUIRED)
 find_package(Cereal REQUIRED)
 find_package(ELPA REQUIRED)
 find_package(MPI REQUIRED)
@@ -59,7 +62,6 @@ include(FetchContent)
 
 include_directories(
   ${Cereal_INCLUDE_DIRS}
-  ${Boost_INCLUDE_DIRS}
   ${MPI_CXX_INCLUDE_PATH}
 )
 
@@ -78,6 +80,22 @@ if(ENABLE_DEEPKS)
   add_definitions(-D__DEEPKS)
 endif()
 
+if(DEFINED Libxc_DIR)
+  set(ENABLE_LIBXC ON)
+endif()
+if(ENABLE_LIBXC)
+  find_package(Libxc)
+  if(${Libxc_FOUND})
+    message("Using Libxc.")
+    add_compile_definitions(USE_LIBXC)
+    # applying -DUSING_Libxc definition
+    # target_compile_definitions(${ABACUS_BIN_NAME} PRIVATE $<TARGET_PROPERTY:Libxc::xc,INTERFACE_COMPILE_DEFINITIONS>)
+    include_directories(${Libxc_INCLUDE_DIRS})
+  else()
+    message(WARNING "Will not use Libxc.")
+  endif()
+endif()
+
 if(DEFINED MKL_DIR_CACHE)
   find_package(IntelMKL REQUIRED)
   add_definitions(-D__MKL -DMKL_ILP64)
@@ -89,20 +107,20 @@ else()
   include_directories(${FFTW3_INCLUDE_DIRS})
 endif()
 
-add_definitions(
-    -D__EXX
-    -D__FFTW3
-    -D__FP
-    -D__MPI
-    -D__OPENMP
-    -D__SELINV
-    -D__LCAO
-    -DMETIS
-    -DEXX_DM=3
-    -DEXX_H_COMM=2
-    -DTEST_EXX_LCAO=0
-    -DTEST_EXX_RADIAL=1
-    -DUSE_CEREAL_SERIALIZATION
+add_compile_definitions(
+  __EXX
+  __FFTW3
+  __FP
+  __MPI
+  __OPENMP
+  __SELINV
+  __LCAO
+  METIS
+  EXX_DM=3
+  EXX_H_COMM=2
+  TEST_EXX_LCAO=0
+  TEST_EXX_RADIAL=1
+  USE_CEREAL_SERIALIZATION
 )
 
 add_subdirectory(source)
@@ -162,6 +180,10 @@ if(ENABLE_DEEPKS)
   )
 endif()
 
+if(${Libxc_FOUND})
+  target_link_libraries(${ABACUS_BIN_NAME} Libxc::xc)
+endif()
+
 install(PROGRAMS ${ABACUS_BIN_PATH}
     TYPE BIN
     #DESTINATION ${CMAKE_INSTALL_BINDIR}

doc/input-main.md

@@ -3,15 +3,15 @@
 - [List of keywords](#list-of-keywords)
     - [System variables](#system-variables)
 
-        [suffix](#suffix) | [ntype](#ntype) | [calculation](#calculation) | [dft_functional](#dft-functional) | [pseudo_type](#pseudo-type) | [npool](#npool) | [symmetry](#symmetry) | [pseudo_rcut](#pseudo-rcut) | [renormwithmesh](#renormwithmesh) | [nelec](#nelec) | [tot_magnetization](#tot-magnetization) | [mem_saver](#mem-saver) | [latname](#latname) | [start_wfc](#start-wfc) | [start_charge](#start-charge) | [start_pot](#start-pot) | [set_vel](#set_vel) | [diago_proc](#diago_proc) 
+        [suffix](#suffix) | [ntype](#ntype) | [calculation](#calculation) | [dft_functional](#dft-functional) | [pseudo_type](#pseudo-type) | [npool](#npool) | [symmetry](#symmetry) | [pseudo_rcut](#pseudo-rcut) | [renormwithmesh](#renormwithmesh) | [nelec](#nelec) | [tot_magnetization](#tot-magnetization) | [mem_saver](#mem-saver) | [latname](#latname) | [start_wfc](#start-wfc) | [seed](#seed) | [start_charge](#start-charge) | [start_pot](#start-pot) | [set_vel](#set_vel) | [diago_proc](#diago_proc) 
 
     - [Variables related to input files](#variables-related-to-input-files)
 
-        [atom_file](#atom-file) | [kpoint_file](#kpoint-file) | [pseudo_dir](#pseudo-dir) | [read_file_dir](#read-file-dir)
+        [atom_file](#atom-file) | [kpoint_file](#kpoint-file) | [pseudo_dir](#pseudo-dir) | [orbital_dir](#orbital-dir) | [read_file_dir](#read-file-dir)
 
     - [Plane wave related variables](#plane-wave-related-variables)
 
-        [ecutwfc](#ecutwfc)| [nx,ny,nz](#nx) | [ethr](#ethr) | [diago_cg_maxiter](#diago-cg-maxiter) | [diago_david_ndim](#diago-david-ndim)
+        [ecutwfc](#ecutwfc) | [nx,ny,nz](#nx) | [ethr](#ethr) | [diago_cg_maxiter](#diago-cg-maxiter) | [diago_david_ndim](#diago-david-ndim)
 
     - [Numerical atomic orbitals related variables](#numerical-atomic-orbitals-related-variables)
 
@@ -249,10 +249,20 @@ This part of variables are used to control general system parameters.
 
 - start_wfc<a id="start-wfc"></a>
     - *Type*: String
-    - *Description*: Only useful for plane wave basis only now. It is the name of the starting wave functions. In the future we should also make this         variable available for localized orbitals set.
-            - atomic:
-            - file:
-    - *Default*:atomic
+    - *Description*: Only useful for plane wave basis only now. It is the name of the starting wave functions. In the future we should also make this         variable available for localized orbitals set. 
+    Available options are:
+        - "atomic": from atomic pseudo wave functions. If they are not enough, other wave functions are initialized with random numbers.
+        - "atomic+random": add small random numbers on atomic pseudo-wavefunctions
+        - "file": from file
+        - "random": random numbers
+    - *Default*:"atomic"
+
+    [back to top](#input-file)
+
+- seed<a id="seed"></a>
+    - *Type*: Integer
+    - *Description*: Only useful for plane wave basis only now. It is the random seed to initialize wave functions. Only positive integers are avilable.
+    - *Default*:0
 
     [back to top](#input-file)
 
@@ -308,6 +318,13 @@ This part of variables are used to control input files related parameters.
 
     [back to top](#input-file)
 
+- orbital_dir<a id="orbital-dir"></a>
+    - *Type*: String
+    - *Description*: This parameter specifies orbital file directory.
+    - *Default*: ./
+
+    [back to top](#input-file)
+
 - read_file_dir<a id="read-file-dir"></a>
     - *Type*: String
     - *Description*: when the program needs to read files such as electron density(`SPIN1_CHG`) as a starting point, this variables tells the location of the files. For example, './' means the file is located in the working directory.
@@ -737,7 +754,7 @@ This part of variables are used to control the output of properties.
     [back to top](#input-file)
 - out_wf<a id="out-wf"></a>
     - *Type*: Integer
-    - *Description*: Only used in **planewave basis** set. When set this variable to 1, it outputs the coefficients of wave functions. The file names are WAVEFUNC.dat$K.txt, where $K is the index of k point.
+    - *Description*: Only used in **planewave basis** set. When set this variable to 1, it outputs the coefficients of wave functions into text files. The file names are WAVEFUNC$K.txt, where $K is the index of k point. When set this variable to 2, results are stored in binary files. The file names are WAVEFUNC$K.dat.
     - *Default*: 0
 
     [back to top](#input-file)

doc/install.md

@@ -31,6 +31,8 @@ FFTW3;
 
 ### Build and install ABACUS with CMake
 
+#### Configure
+
 We recommend building ABACUS with `cmake` to avoid dependency issues.
 ABACUS requires a minimum `cmake` version of `3.18`. Check the version of `cmake`  on your machine with:
 
@@ -52,10 +54,24 @@ For example:
 cmake -B build -DFFTW3_ROOT=/opt/fftw3 -DBOOST_INCLUDEDIR=/usr/include/boost
 ```
 
+You can also choose to build with which components.
+
+```bash
+cmake -B build -DUSE_LIBXC=1
+```
+
+If Libxc is not installed in standard path (i.e. installed with a custom prefix path), you may add the installation prefix of `FindLibxc.cmake` to `CMAKE_MODULE_PATH` environment variable, or set `Libxc_DIR` to the directory containing the file.
+
+```bash
+cmake -B build -DLibxc_DIR=~/libxc
+```
+
+#### Build and Install
+
 After configuring, start build and install by:
 
 ```bash
-cmake --build build
+cmake --build build -j9
 cmake --install build
 ```
 

source/Makefile.Objects

@@ -288,6 +288,7 @@ diago_cg.o\
 output.o  \
 run_md_classic.o\
 LJ_potential.o\
+cmd_neighbor.o\
 dos.o \
 inverse_matrix.o \
 energy.o \

source/driver.cpp

@@ -1,14 +1,16 @@
 #include "driver.h"
-#include "run_pw.h"
 #include "input.h"
 #include "input_conv.h"
+#include "run_pw.h"
+#include "src_pw/global.h"
 #ifdef __LCAO
 #include "run_lcao.h"
 #include "src_lcao/global_fp.h"
 #endif
-#include "src_pw/global.h"
 #include "src_io/cal_test.h"
 #include "src_io/winput.h"
+#include "src_io/print_info.h"
+#include "module_base/timer.h"
 
 Driver::Driver(){}
 
@@ -20,13 +22,20 @@ void Driver::init()
 {
 	TITLE("Driver","init");
 
+	time_t time_start = std::time(NULL);
+	timer::start();
+
 	// (1) read the input parameters.
 	this->reading();
 
 	// (2) welcome to the atomic world!
 	this->atomic_world();
 
-	// (3) close all of the running logs 
+	// (3) output information
+	time_t	time_finish= std::time(NULL);
+	Print_Info::print_time(time_start, time_finish);
+
+	// (4) close all of the running logs 
 	INPUT.close_log();
 
 	return;
@@ -46,11 +55,11 @@ void Driver::reading(void)
 	// (3) define the 'DIAGONALIZATION' world in MPI
 	Parallel_Global::split_diag_world(GlobalV::DIAGO_PROC);
 	Parallel_Global::split_grid_world(GlobalV::DIAGO_PROC);
-	OUT(GlobalV::ofs_running,"DRANK",GlobalV::DRANK+1);
-	OUT(GlobalV::ofs_running,"DSIZE",GlobalV::DSIZE);
-	OUT(GlobalV::ofs_running,"DCOLOR",GlobalV::DCOLOR+1);
-	OUT(GlobalV::ofs_running,"GRANK",GlobalV::GRANK+1);
-	OUT(GlobalV::ofs_running,"GSIZE",GlobalV::GSIZE);
+	ModuleBase::GlobalFunc::OUT(GlobalV::ofs_running,"DRANK",GlobalV::DRANK+1);
+	ModuleBase::GlobalFunc::OUT(GlobalV::ofs_running,"DSIZE",GlobalV::DSIZE);
+	ModuleBase::GlobalFunc::OUT(GlobalV::ofs_running,"DCOLOR",GlobalV::DCOLOR+1);
+	ModuleBase::GlobalFunc::OUT(GlobalV::ofs_running,"GRANK",GlobalV::GRANK+1);
+	ModuleBase::GlobalFunc::OUT(GlobalV::ofs_running,"GSIZE",GlobalV::GSIZE);
 
 #ifdef __MPI
     // (4)  divide the GlobalV::NPROC processors into GlobalV::NPOOL for k-points parallelization.
@@ -64,7 +73,7 @@ void Driver::reading(void)
     std::stringstream ss1;
     ss1 << GlobalV::global_out_dir << GlobalV::global_in_card;
     INPUT.Print( ss1.str() );
-    //DONE(GlobalV::ofs_running,"READING CARDS");
+    //ModuleBase::GlobalFunc::DONE(GlobalV::ofs_running,"READING CARDS");
 
 	timer::tick("Driver","reading");
 	return;