Merge pull request #166 from deepmodeling/develop

v2.3.1

Author: dyzheng

.github/workflows/static.yaml

@@ -22,7 +22,7 @@ jobs:
         run: |
           git diff -U0 HEAD^ | clang-tidy-diff -p1 -path build -export-fixes fixes.yml
       - name: Pull request comments from clang-tidy reports
-        uses: platisd/clang-tidy-pr-comments@1.1.6
+        uses: platisd/clang-tidy-pr-comments@master
         with:
           # The GitHub token (or a personal access token)
           github_token: ${{ secrets.GITHUB_TOKEN }}
@@ -35,3 +35,4 @@ jobs:
           # to avoid GitHub API timeouts for heavily loaded
           # pull requests
           suggestions_per_comment: 10
+          repo_path_prefix: /__w

.github/workflows/test.yml

@@ -22,5 +22,6 @@ jobs:
       - name: Test
         env:
           GTEST_COLOR: 'yes'
+          OMP_NUM_THREADS: '2'
         run: |
           cmake --build build --target test ARGS="-V"

CMakeLists.txt

@@ -30,11 +30,25 @@ 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)
 add_compile_options(-Wno-write-strings)
+set(FETCHCONTENT_QUIET FALSE) # Notify user when cloning git repo
+
+find_program(CCACHE ccache)
+if (CCACHE)
+  set (CMAKE_CXX_COMPILER_LAUNCHER ${CCACHE} ${CMAKE_CXX_COMPILER_LAUNCHER})
+  set (CMAKE_C_COMPILER_LAUNCHER ${CCACHE} ${CMAKE_C_COMPILER_LAUNCHER})
+endif()
+
+# Select 'Release' configuration for best performance;
+#   this will disable all assertions.
+# Other default configurations are also available, see:
+# https://cmake.org/cmake/help/latest/manual/cmake-buildsystem.7.html#default-and-custom-configurations
+if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
+  add_compile_options(-O2 -g) # default flag
+endif()
 
 find_package(Cereal REQUIRED)
-include_directories(${Cereal_INCLUDE_DIR})
+include_directories(${CEREAL_INCLUDE_DIR})
 add_compile_definitions(USE_CEREAL_SERIALIZATION)
 
 find_package(ELPA REQUIRED)

Dockerfile

@@ -1,11 +1,20 @@
 # 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
+FROM ubuntu:22.04
+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'.
-RUN GIT_SSL_NO_VERIFY=true git clone https://github.com/deepmodeling/abacus-develop.git --depth 1 && cd abacus-develop && cmake -B build && cmake --build build -j`nproc` && cmake --install build && cd .. && rm -rf abacus-develop
+
+ENV GIT_SSL_NO_VERIFY=true TERM=xterm-256color \
+    OMPI_ALLOW_RUN_AS_ROOT=1 OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 OMPI_MCA_btl_vader_single_copy_mechanism=none
+RUN git clone https://github.com/deepmodeling/abacus-develop.git --depth 1 && \
+    cd abacus-develop && \
+    cmake -B build && \
+    cmake --build build -j`nproc` && \
+    cmake --install build && \
+    cd .. && rm -rf abacus-develop
 # If you have trouble cloning repo, replace "github.com" with "gitee.com".
-ENV OMPI_ALLOW_RUN_AS_ROOT=1 OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 OMPI_MCA_btl_vader_single_copy_mechanism=none
 CMD mpirun --use-hwthread-cpus abacus
 
 # To run ABACUS built by this image with all available threads, execute `docker run -v <host>:<wd> -w <wd/input> abacus`.

Dockerfile.gnu

@@ -1,59 +1,18 @@
-FROM debian:bullseye-slim
-
-RUN apt-get update && apt-get install -y --no-install-recommends libopenblas-dev liblapack-dev libscalapack-mpi-dev git g++ gfortran libssl-dev make cmake vim wget bc unzip python3-numpy
-ENV OMPI_ALLOW_RUN_AS_ROOT=1 OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 OMPI_MCA_btl_vader_single_copy_mechanism=none
-
-ENV GIT_SSL_NO_VERIFY=1 TERM=xterm-256color
-
-RUN cd /tmp \
-    && git clone https://github.com/USCiLab/cereal.git \
-    && cp -r cereal/include /usr/local \
-    && rm -rf cereal
-
-RUN cd /tmp \
-    && wget https://elpa.mpcdf.mpg.de/software/tarball-archive/Releases/2021.05.002/elpa-2021.05.002.tar.gz --no-check-certificate --quiet \
-    && tar xzf elpa-2021.05.002.tar.gz && rm elpa-2021.05.002.tar.gz \
-    && cd elpa-2021.05.002 && mkdir build && cd build \
-    && ../configure CFLAGS="-O3 -march=native -funsafe-loop-optimizations -funsafe-math-optimizations -ftree-vect-loop-version -ftree-vectorize" \
-    FCFLAGS="-O2 -mavx" --disable-avx512 \
-    && make -j8 && make PREFIX=/usr/local install \
-    && ln -s /usr/local/include/elpa-2021.05.002/elpa /usr/local/include/ \
-    && cd /tmp && rm -rf elpa-2021.05.002
-
-RUN cd /tmp \
-    && wget http://www.fftw.org/fftw-3.3.9.tar.gz --no-check-certificate --quiet \
-    && tar zxvf fftw-3.3.9.tar.gz \
-    && cd fftw-3.3.9 \
-    && ./configure --enable-mpi-fortran --enable-orterun-prefix-by-default FC=gfortran \
-    && make -j8 && make PREFIX=/usr/local install \
-    && cd /tmp && rm -rf fftw-3.3.9 && rm fftw-3.3.9.tar.gz
-
-RUN cd /tmp \
-    && wget https://download.pytorch.org/libtorch/cpu/libtorch-cxx11-abi-shared-with-deps-1.9.1%2Bcpu.zip --no-check-certificate --quiet \
-    && unzip libtorch-cxx11-abi-shared-with-deps-1.9.1+cpu.zip \
-    && cp -r libtorch/include /usr/local \
-    && cp -r libtorch/lib /usr/local \
-    && cp -r libtorch/share /usr/local \
-    && rm -rf libtorch
-
-RUN cd /tmp \
-    && wget https://gitlab.com/libxc/libxc/-/archive/5.1.5/libxc-5.1.5.tar.gz --no-check-certificate --quiet \
-    && tar xzf libxc-5.1.5.tar.gz \
-    && cd libxc-5.1.5 \
-    && mkdir build \
-    && cmake -B build -DBUILD_TESTING=OFF \
-    && cmake --build build \
-    && cmake --install build \
-    && cd /tmp \
-    && rm -rf libxc-5.1.5 \
-    && rm libxc-5.1.5.tar.gz
-
-RUN cd /tmp \
-    && git clone https://github.com/llohse/libnpy.git \
-    && cp libnpy/include/npy.hpp /usr/local/include \
-    && rm -rf libnpy
-
-RUN cd /tmp \
-    && git clone https://github.com/google/googletest.git \
-    && cd googletest && cmake . && make install \
-    && rm -rf googletest
+FROM ubuntu:22.04
+RUN apt update && apt install -y --no-install-recommends \
+    libopenblas-dev liblapack-dev libscalapack-mpi-dev libelpa-dev libfftw3-dev libcereal-dev \
+    libxc-dev libgtest-dev libgmock-dev python3-numpy \
+    bc cmake git g++ make bc time sudo unzip vim wget
+
+ENV GIT_SSL_NO_VERIFY=true TERM=xterm-256color \
+    OMPI_ALLOW_RUN_AS_ROOT=1 OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 OMPI_MCA_btl_vader_single_copy_mechanism=none
+
+RUN git clone https://github.com/llohse/libnpy.git && \
+    cp libnpy/include/npy.hpp /usr/local/include && \
+    rm -r libnpy
+
+RUN wget https://download.pytorch.org/libtorch/cpu/libtorch-cxx11-abi-shared-with-deps-1.9.1%2Bcpu.zip \
+        --no-check-certificate --quiet -O libtorch.zip && \
+    unzip -q libtorch.zip && rm libtorch.zip && \
+    cd libtorch && cp -r . /usr/local && \
+    cd .. && rm -r libtorch

README.md

@@ -17,6 +17,7 @@ ABACUS is an electronic structure package based on density functional theory(DFT
 Please refer to our [GitHub repository](https://github.com/deepmodeling/abacus-develop) for more information and support.
 # Table of contents
 
+- [Table of contents](#table-of-contents)
 - [Features](#features)
 - [Download and install](#download-and-install)
 - [Quickstart guide](#quickstart-guide)
@@ -27,6 +28,7 @@ Please refer to our [GitHub repository](https://github.com/deepmodeling/abacus-d
 - [Citations](#citations)
 - [Development team](#development-team)
 - [Communicating and making contributions](#communicating-and-making-contributions)
+- [Miscellaneous](#miscellaneous)
 
 # Features
 
@@ -139,7 +141,7 @@ The following provides basic sample jobs in ABACUS. More can be found in the dir
 - [Basic electronic structure calculation with PW basis set](docs/examples/basic-pw.md)
 - [Basic electronic structure calculation with LCAO basis set](docs/examples/basic-lcao.md)
 - [DFT + dispersion calculations](docs/examples/dispersion.md)
-- [DOS, wave functions](docs/examples/dos.md)
+- [Density of states](docs/examples/dos.md)
 - [Band structure](docs/examples/band-struc.md)
 - [Magnetic properties](docs/examples/magnetic.md)
 - [Force calculation and structure relaxation](docs/examples/force.md)
@@ -153,6 +155,8 @@ The following provides basic sample jobs in ABACUS. More can be found in the dir
 - [Hybrid functional](docs/examples/hybrid.md)
 - [Electric field and dipole correction](docs/examples/electric_dipole.md)
 - [Stochastic DFT and mix stochastic-deterministic DFT](docs/examples/stochastic.md)
+- [Wave functions](docs/examples/wavefunction.md)
+- [BSSE for molecular formation energy](docs/examples/BSSE.md)
 
 [back to top](#readme-top)
 

docs/examples/BSSE.md

@@ -0,0 +1,171 @@
+# BSSE
+
+[back to main page](../../README.md)
+
+An empty atom is defined in the `STRU` file when an element name contains the "empty" suffix, such as "H_empty" in the following example: calculating the molecular formation energy of H$_2$O by using the BSSE (Basis Set Superposition Errors) method.
+
+$$
+\Delta E(\text{H}_2\text{O}) = E(\text{H}_2\text{O}) - E(\text{O}) - E(\text{H}^1) - E(\text{H}^2)
+$$
+
+## $E(\text{H}_2\text{O})$
+
+```
+ntype   2
+```
+```
+ATOMIC_SPECIES
+H	1.008	H_ONCV_PBE-1.0.upf
+O	15.9994	O_ONCV_PBE-1.0.upf
+
+NUMERICAL_ORBITAL
+H_gga_8au_60Ry_2s1p.orb
+O_gga_6au_60Ry_2s2p1d.orb
+
+LATTICE_CONSTANT
+1.889725989
+
+LATTICE_VECTORS
+20 0 0
+0 20 0
+0 0 20
+
+ATOMIC_POSITIONS
+Cartesian    # Cartesian(Unit is LATTICE_CONSTANT)
+
+H
+0.5
+2
+0.9584	0.0000	0.0000	0 0 0
+-0.2392	0.9281	0.0000	0 0 0
+
+O
+0.5
+1
+0.0000 0.0000 0.0000 0 0 0
+```
+
+## $E(\text{O})$
+
+```
+ntype   2
+```
+```
+ATOMIC_SPECIES
+H_empty	1.008	H_ONCV_PBE-1.0.upf
+O		15.9994	O_ONCV_PBE-1.0.upf
+
+NUMERICAL_ORBITAL
+H_gga_8au_60Ry_2s1p.orb
+O_gga_6au_60Ry_2s2p1d.orb
+
+LATTICE_CONSTANT
+1.889725989
+
+LATTICE_VECTORS
+20 0 0
+0 20 0
+0 0 20
+
+ATOMIC_POSITIONS
+Cartesian    # Cartesian(Unit is LATTICE_CONSTANT)
+
+H_empty
+0.5
+2
+0.9584	0.0000	0.0000	0 0 0
+-0.2392	0.9281	0.0000	0 0 0
+
+O
+0.5
+1
+0.0000 0.0000 0.0000 0 0 0
+```
+
+## $E(\text{H}^1)$
+
+```
+ntype   3
+```
+```
+ATOMIC_SPECIES
+H			1.008	H_ONCV_PBE-1.0.upf
+H_empty_2	1.008	H_ONCV_PBE-1.0.upf
+O_empty		15.9994	O_ONCV_PBE-1.0.upf
+
+NUMERICAL_ORBITAL
+H_gga_8au_60Ry_2s1p.orb
+H_gga_8au_60Ry_2s1p.orb
+O_gga_6au_60Ry_2s2p1d.orb
+
+LATTICE_CONSTANT
+1.889725989
+
+LATTICE_VECTORS
+20 0 0
+0 20 0
+0 0 20
+
+ATOMIC_POSITIONS
+Cartesian    # Cartesian(Unit is LATTICE_CONSTANT)
+
+H
+0.5
+1
+0.9584	0.0000	0.0000	0 0 0
+
+H_empty_2
+0.5
+1
+-0.2392	0.9281	0.0000	0 0 0
+
+O_empty
+0.5
+1
+0.0000 0.0000 0.0000 0 0 0
+```
+
+## $E(\text{H}^2)$
+
+```
+ntype   3
+```
+```
+ATOMIC_SPECIES
+H_empty_1	1.008	H_ONCV_PBE-1.0.upf
+H			1.008	H_ONCV_PBE-1.0.upf
+O_empty		15.9994	O_ONCV_PBE-1.0.upf
+
+NUMERICAL_ORBITAL
+H_gga_8au_60Ry_2s1p.orb
+H_gga_8au_60Ry_2s1p.orb
+O_gga_6au_60Ry_2s2p1d.orb
+
+LATTICE_CONSTANT
+1.889725989
+
+LATTICE_VECTORS
+20 0 0
+0 20 0
+0 0 20
+
+ATOMIC_POSITIONS
+Cartesian    # Cartesian(Unit is LATTICE_CONSTANT)
+
+H_empty_1
+0.5
+1
+0.9584	0.0000	0.0000	0 0 0
+
+H
+0.5
+1
+-0.2392	0.9281	0.0000	0 0 0
+
+O_empty
+0.5
+1
+0.0000 0.0000 0.0000 0 0 0
+```
+
+[back to top](#BSSE)

docs/examples/dos.md

@@ -1,8 +1,10 @@
-# DOS, wave functions
+# Density_of_states
 
 [back to main page](../../README.md)
 
-The main task of this example is to calculate the density of states (DOS) of the system. At first, do a ground-state energy calculation as in [this example](#basic-lcao.md) ***with one additional keyword in the INPUT file***:
+# DOS
+
+The main task of this example is to calculate the density of states (DOS) of the system. At first, do a ground-state energy calculation ***with one additional keyword in the INPUT file***:
 
 ```
 out_chg              1
@@ -72,6 +74,8 @@ Gamma
 ```
 Run the program, and you will see a file named DOS1_smearing.dat in the output directory. The first two columns in the file are the energy and DOS, respectively.Plot file DOS1_smearing.dat with graphing software, and you’ll get the DOS.
 
+# PDOS
+
 Along with the DOS1_smearing.dat file, we also produce the projected density of states (PDOS) in a file called PDOS.
 
 The PDOS file starts with number of atomic orbitals in the system, then a list of energy values, such as:
@@ -102,4 +106,4 @@ The rest of the fileis arranged in sections, each section with a header such as
 ```
 which tells the atom and symmetry of the current atomic orbital, and followed by the PDOS values. The values can thus be plotted against the energies.
 
-[back to top](#dos,-wave-functions)
+[back to top](#Density_of_states)