Make: Update Makefile, and compile documents.

Author: sunliang98

docs/CITATIONS.md

@@ -33,3 +33,9 @@ The following references are required to be cited when using ABACUS. Specificall
     Peize Lin, Xinguo Ren, and Lixin He. "Efficient Hybrid Density Functional Calculations for Large Periodic Systems Using Numerical Atomic Orbitals." Journal of Chemical Theory and Computation 2021, 17(1), 222–239.
 
     Peize Lin, Xinguo Ren, and Lixin He. "Accuracy of Localized Resolution of the Identity in Periodic Hybrid Functional Calculations with Numerical Atomic Orbitals." Journal of Physical Chemistry Letters 2020, 11, 3082-3088.
+
+- **If ML-KEDF is used:**
+
+    Sun, Liang, and Mohan Chen. "Machine learning based nonlocal kinetic energy density functional for simple metals and alloys." Physical Review B 109.11 (2024): 115135.
+
+    Sun, Liang, and Mohan Chen. "Multi-channel machine learning based nonlocal kinetic energy density functional for semiconductors." Electronic Structure 6.4 (2024): 045006.

docs/advanced/install.md

@@ -31,6 +31,21 @@ cmake -B build -DENABLE_DEEPKS=1 -DTorch_DIR=~/libtorch/share/cmake/Torch/ -Dlib
 
 > CMake will try to download Libnpy if it cannot be found locally.
 
+## Build with ML-KEDF
+
+If machine learning based kinetic energy density functional (ML-KEDF) is required for OFDFT calculation, the following prerequisites and steps are needed:
+
+- C++ compiler, supporting **C++14** (GCC >= 5 is sufficient)
+- CMake >= 3.18
+- [LibTorch](https://pytorch.org/) with cxx11 ABI supporting CPU or GPU
+- [Libnpy](https://github.com/llohse/libnpy/)
+
+```bash
+cmake -B build -DENABLE_MLKEDF=1 -DTorch_DIR=~/libtorch/share/cmake/Torch/ -Dlibnpy_INCLUDE_DIR=~/libnpy/include
+```
+
+> CMake will try to download Libnpy if it cannot be found locally.
+
 ## Build with DeePMD-kit
 
 > Note: This part is only required if you want to load a trained DeeP Potential and run molecular dynamics with that. To train the DeeP Potential with DP-GEN, no extra prerequisite is needed and please refer to [this page](http://abacus.deepmodeling.com/en/latest/advanced/interface/dpgen.html) for ABACUS interface with DP-GEN.
@@ -141,7 +156,7 @@ CXX = mpiicpc
 # icpc:      compile intel sequential version
 # make: ELPA_DIR, ELPA_INCLUDE_DIR, CEREAL_DIR must also be set.
 # make pw: nothing need to be set except LIBXC_DIR
-#
+# 
 # mpicxx:    compile gnu parallel version
 # g++:       compile gnu sequential version
 # make: FFTW_DIR, OPENBLAS_LIB_DIR, SCALAPACK_LIB_DIR, ELPA_DIR, ELPA_INCLUDE_DIR, CEREAL_DIR must also be set.
@@ -150,6 +165,10 @@ CXX = mpiicpc
 # GPU = OFF  #We do not support GPU yet
 # OFF:  do not use GPU
 # CUDA: use CUDA
+OPENMP = OFF
+# the default is not to use OPENMP to accelerate. 
+# Change OPENMP to ON to use OPENMP.
+
 #======================================================================
 
 
@@ -167,7 +186,7 @@ CEREAL_DIR    = /usr/local/include/cereal
 
 ##-------------------  FOR GNU COMPILER  ------------------------------
 ## FFTW_DIR          should contain lib/libfftw3.a.
-## OPENBLAS_LIB_DIR  should contain libopenblas.a.
+## OPENBLAS_LIB_DIR  should contain libopenblas.a. 
 ## SCALAPACK_LIB_DIR should contain libscalapack.a
 ## All three above will only be used when CXX=mpicxx or g++
 ## ELPA_DIR          should contain an include folder and lib/libelpa.a
@@ -185,14 +204,18 @@ CEREAL_DIR    = /usr/local/include/cereal
 
 
 ##-------------------  OPTIONAL LIBS  ---------------------------------
-## To use DEEPKS: set LIBTORCH_DIR and LIBNPY_DIR
+## To use DEEPKS: set ENABLE_DEEPKS = ON, and set LIBTORCH_DIR and LIBNPY_DIR
+## To use MLKEDF: set ENABLE_MLKEDF = ON, and set LIBTORCH_DIR and LIBNPY_DIR
 ## To use LIBXC:  set LIBXC_DIR which contains include and lib/libxc.a (>5.1.7)
-## To use DeePMD: set DeePMD_DIR and TensorFlow_DIR
+## To use DeePMD: set DeePMD_DIR LIBTORCH_DIR and TensorFlow_DIR
 ## To use LibRI:  set LIBRI_DIR and LIBCOMM_DIR
+## To use PEXSI: set PEXSI_DIR DSUPERLU_DIR and PARMETIS_DIR
 ##---------------------------------------------------------------------
 
 # LIBTORCH_DIR  = /usr/local
 # LIBNPY_DIR    = /usr/local
+ENABLE_DEEPKS   = OFF
+ENABLE_MLKEDF   = OFF
 
 # LIBXC_DIR    		= /public/soft/libxc
 
@@ -202,6 +225,10 @@ CEREAL_DIR    = /usr/local/include/cereal
 # LIBRI_DIR     = /public/software/LibRI
 # LIBCOMM_DIR   = /public/software/LibComm
 
+# PEXSI_DIR = /public/software/pexsi
+# DSUPERLU_DIR = /public/software/superlu_dist
+# PARMETIS_DIR    = /public/software/parmetis
+
 ##---------------------------------------------------------------------
 # NP = 14 # It is not supported. use make -j14 or make -j to parallelly compile
 # DEBUG = OFF
@@ -247,20 +274,6 @@ CEREAL_DIR=/public/soft/cereal
 
 ABACUS now support full version and pw version. Use `make` or `make abacus` to compile full version which supports LCAO calculations. Use `make pw` to compile pw version which only supports pw calculations. For pw version, `make pw CXX=mpiicpc`, you do not need to provide any libs. For `make pw CXX=mpicxx`, you need provide `FFTW_DIR` and `OPENBLAS_LIB_DIR`.
 
-Besides, libxc and deepks are optional libs to compile abacus.
-They will be used when `LIBXC_DIR` is defined like
-
-```makefile
-LIBXC_DIR = /public/soft/libxc
-```
-
-or `LIBTORCH_DIR` and `LIBNPY_DIR` like
-
-```makefile
-LIBTORCH_DIR  = /usr/local
-LIBNPY_DIR    = /usr/local
-```
-
 After modifying the `Makefile.vars` file, execute `make` or `make -j12` to build the program.
 
 After the compilation finishes without error messages (except perhaps for some warnings), an executable program `ABACUS.mpi` will be created in directory `bin/`.
@@ -279,10 +292,20 @@ directly.
 
 ### Add DeePKS Support
 
-To compile ABACUS with DEEPKS, you need to define `LIBTORCH_DIR` and `LIBNPY_DIR` in the file `Makefile.vars` or use
+To compile ABACUS with DEEPKS, you need to set `ENABLE_DEEPKS = ON`, and define `LIBTORCH_DIR` and `LIBNPY_DIR` in the file `Makefile.vars` or use
+
+```makefile
+make ENABLE_DEEPKS=ON LIBTORCH_DIR=/opt/libtorch/ LIBNPY_DIR=/opt/libnpy/
+```
+
+directly.
+
+### Add ML-KEDF Support
+
+To compile ABACUS with ML-KEDF, you need to set `ENABLE_MLKEDF = ON`, and define `LIBTORCH_DIR` and `LIBNPY_DIR` in the file `Makefile.vars` or use
 
 ```makefile
-make LIBTORCH_DIR=/opt/libtorch/ LIBNPY_DIR=/opt/libnpy/
+make ENABLE_MLKEDF=ON LIBTORCH_DIR=/opt/libtorch/ LIBNPY_DIR=/opt/libnpy/
 ```
 
 directly.

source/Makefile.vars

@@ -55,7 +55,8 @@ CEREAL_DIR    = /usr/local/include/cereal
 
 
 ##-------------------  OPTIONAL LIBS  ---------------------------------
-## To use DEEPKS: set LIBTORCH_DIR and LIBNPY_DIR
+## To use DEEPKS: set ENABLE_DEEPKS = ON, and define LIBTORCH_DIR and LIBNPY_DIR
+## To use MLKEDF: set ENABLE_MLKEDF = ON, and define LIBTORCH_DIR and LIBNPY_DIR
 ## To use LIBXC:  set LIBXC_DIR which contains include and lib/libxc.a (>5.1.7)
 ## To use DeePMD: set DeePMD_DIR LIBTORCH_DIR and TensorFlow_DIR
 ## To use LibRI:  set LIBRI_DIR and LIBCOMM_DIR
@@ -64,8 +65,8 @@ CEREAL_DIR    = /usr/local/include/cereal
 
 # LIBTORCH_DIR  = /usr/local
 # LIBNPY_DIR    = /usr/local
-ENABLE_DEEPKS   = OFF
-ENABLE_MLKEDF   = OFF
+ENABLE_DEEPKS   ?= OFF
+ENABLE_MLKEDF   ?= OFF
 
 # LIBXC_DIR    		= /public/soft/libxc