merge deepmodeling/Reconstruction to abacusmodeling/develop

.devcontainer/devcontainer.json

@@ -1,32 +1,5 @@
-// For format details, see https://aka.ms/devcontainer.json. For config options, see the README at:
-// https://github.com/microsoft/vscode-dev-containers/tree/v0.183.0/containers/docker-existing-dockerfile
+// For format details, see https://aka.ms/devcontainer.json.
 {
-	"name": "Existing Dockerfile",
-
-	// Sets the run context to one level up instead of the .devcontainer folder.
-	"context": "..",
-
-	// Update the 'dockerFile' property if you aren't using the standard 'Dockerfile' filename.
-	"dockerFile": "Dockerfile",
-
-	// Set *default* container specific settings.json values on container create.
-	"settings": {},
-
-	// Add the IDs of extensions you want installed when the container is created.
-	"extensions": []
-
-	// Use 'forwardPorts' to make a list of ports inside the container available locally.
-	// "forwardPorts": [],
-
-	// Uncomment the next line to run commands after the container is created - for example installing curl.
-	// "postCreateCommand": "apt-get update && apt-get install -y curl",
-
-	// Uncomment when using a ptrace-based debugger like C++, Go, and Rust
-	// "runArgs": [ "--cap-add=SYS_PTRACE", "--security-opt", "seccomp=unconfined" ],
-
-	// Uncomment to use the Docker CLI from inside the container. See https://aka.ms/vscode-remote/samples/docker-from-docker.
-	// "mounts": [ "source=/var/run/docker.sock,target=/var/run/docker.sock,type=bind" ],
-
-	// Uncomment to connect as a non-root user if you've added one. See https://aka.ms/vscode-remote/containers/non-root.
-	// "remoteUser": "vscode"
-}
+	"image":"ghcr.io/deepmodeling/abacus-development-kit:gnu",
+	"extensions": ["ms-vscode.cpptools-extension-pack"]
+}

.github/workflows/container.yml

@@ -6,27 +6,31 @@ on:
       - develop
       - reconstruction
 
-env:
-  CONTAINER: ghcr.io/${{ github.repository_owner }}/abacus-development-kit:gnu
-
 jobs:
   build_container_and_push:
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        dockerfile: ["gnu","intel","cuda"]
     steps:
       - name: Checkout
         uses: actions/checkout@v2
+
       - name: Setup Docker Buildx
         uses: docker/setup-buildx-action@v1
+
       - name: Login to GitHub Container Registry
         uses: docker/login-action@v1
         with:
           registry: ghcr.io
-          username: ${{ secrets.OWNER }}
-          password: ${{ secrets.PAT }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
       - name: Build and Push Container
         uses: docker/build-push-action@v2
         with:
-          tags: ${{ env.CONTAINER }}
-          cache-from: type=registry,ref=${{ env.CONTAINER }}
+          tags: ghcr.io/${{ github.repository_owner }}/abacus-development-kit:${{matrix.dockerfile}}
+          file: Dockerfile.${{matrix.dockerfile}}
+          cache-from: type=registry,ref=ghcr.io/${{ github.repository_owner }}/abacus-development-kit:${{matrix.dockerfile}}
           cache-to: type=inline
           push: true

.github/workflows/hosted_test.yml

@@ -0,0 +1,23 @@
+name: Test
+
+on:
+  push:
+    branches:
+      - develop
+      - reconstruction
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        dockerfile: ["gnu","intel","cuda"]
+    container: ghcr.io/${{ github.repository_owner }}/abacus-development-kit:${{ matrix.dockerfile }}
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+      - name: Build
+        run: |
+          cmake -B build -DBUILD_TESTING=ON
+          cmake --build build -j4
+          cmake --install build

.github/workflows/test.yml

@@ -48,7 +48,7 @@ jobs:
           cmake -B build -DBUILD_TESTING=ON
           cmake --build build -j16
           cmake --install build
-          ctest --test-dir build --verbose
+          cmake --build build --target test ARGS="-V"
   stop-runner:
     name: Stop self-hosted EC2 runner
     needs:

CMakeLists.txt

@@ -198,11 +198,11 @@ else()
   )
 endif()
 
-# if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
+if(CMAKE_COMPILER_IS_GNUCXX)
 target_link_libraries(${ABACUS_BIN_NAME}
   -lgfortran
 )
-# endif()
+endif()
 
 if(ENABLE_DEEPKS)
   target_link_libraries(${ABACUS_BIN_NAME}

Dockerfile.cuda

@@ -0,0 +1,6 @@
+FROM ghcr.io/deepmodeling/abacus-development-kit:gnu
+
+RUN wget https://developer.download.nvidia.com/compute/cuda/11.4.2/local_installers/cuda_11.4.2_470.57.02_linux.run --no-check-certificate --quiet \
+	&& sh cuda_11.4.2_470.57.02_linux.run --toolkit --silent \
+	&& rm cuda_11.4.2_470.57.02_linux.run
+ENV PATH=/usr/local/cuda/bin:$PATH

Dockerfile → Dockerfile.gnu

@@ -1,16 +1,10 @@
 FROM debian:bullseye-slim
 
-RUN apt-get update && apt-get install -y --no-install-recommends git gfortran libboost-dev libssl-dev make cmake ssh vim wget bc \
+RUN apt-get update && apt-get install -y --no-install-recommends git gfortran libssl-dev make cmake vim wget bc unzip \
     && apt-get install -y --no-install-recommends mpich libmpich-dev
 
 ENV GIT_SSL_NO_VERIFY 1
 
-RUN cd /tmp \
-    && wget https://cmake.org/files/v3.20/cmake-3.20.5.tar.gz --no-check-certificate \
-    && tar xf cmake-3.20.5.tar.gz cmake-3.20.5/ && cd cmake-3.20.5 \
-    && ./configure && make -j8 && make install \
-    && cd /tmp && rm -rf cmake-3.20.5
-
 RUN cd /tmp \
     && git clone https://github.com/USCiLab/cereal.git \
     && cp -r cereal/include /usr/local \
@@ -30,7 +24,7 @@ RUN cd /tmp \
     && git clone https://github.com/darelbeida/elpa.git -b ELPA_2016.05.004-openblas --single-branch --depth=1 \
     && cd elpa && mkdir build && cd build \
     && ../configure CFLAGS="-O3 -march=native -mavx2 -mfma -funsafe-loop-optimizations -funsafe-math-optimizations -ftree-vect-loop-version -ftree-vectorize" \
-        FCFLAGS="-O2 -mavx" \
+    FCFLAGS="-O2 -mavx" \
     && make -j8 && make PREFIX=/usr/local install \
     && ln -s /usr/local/include/elpa-2016.05.004/elpa /usr/local/include/ \
     && cd /tmp && rm -rf elpa
@@ -43,21 +37,17 @@ RUN cd /tmp \
     && make -j8 && make PREFIX=/usr/local install \
     && cd /tmp && rm -rf fftw-3.3.9 && rm fftw-3.3.9.tar.gz
 
-ENV LD_LIBRARY_PATH /usr/local/lib
-
-RUN apt-get install -y unzip
-
 RUN cd /tmp \
-    && wget https://download.pytorch.org/libtorch/cpu/libtorch-shared-with-deps-1.9.0%2Bcpu.zip --no-check-certificate \
+    && wget https://download.pytorch.org/libtorch/cpu/libtorch-shared-with-deps-1.9.0%2Bcpu.zip --no-check-certificate --quiet \
     && unzip libtorch-shared-with-deps-1.9.0+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 \
-    && tar xvzf libxc-5.1.5.tar.gz \
+    && 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 \

Dockerfile.intel

@@ -0,0 +1,49 @@
+FROM debian:bullseye-slim
+
+RUN apt-get update && apt-get install -y bc cmake git gnupg gcc g++ sudo wget vim unzip
+
+# Following steps by https://software.intel.com/content/www/us/en/develop/documentation/installation-guide-for-intel-oneapi-toolkits-linux/top/installation/install-using-package-managers/apt.html .
+RUN cd /tmp && \
+	wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB && \
+	apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB && \
+	rm GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB && \
+	echo "deb https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list
+
+# To save disk space, only install the required components, but not the whole intel-hpckit.
+RUN apt-get update --allow-unauthenticated \
+	&& apt-get install -y  \
+		intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic \
+		intel-oneapi-compiler-fortran \
+		intel-oneapi-mkl-devel \
+		intel-oneapi-mpi-devel
+
+# These environment variables are the most essential part generated by `source /opt/intel/oneapi/setvars.sh`.
+# It is recommended to do it again if this docker image is used for development.
+ENV I_MPI_ROOT=/opt/intel/oneapi/mpi/latest \
+	LIBRARY_PATH=/opt/intel/oneapi/tbb/latest/env/../lib/intel64/gcc4.8:/opt/intel/oneapi/mpi/latest//libfabric/lib:/opt/intel/oneapi/mpi/latest//lib/release:/opt/intel/oneapi/mpi/latest//lib:/opt/intel/oneapi/mkl/latest/lib/intel64:/opt/intel/oneapi/compiler/latest/linux/compiler/lib/intel64_lin:/opt/intel/oneapi/compiler/latest/linux/lib \
+	LD_LIBRARY_PATH=/opt/intel/oneapi/tbb/latest/env/../lib/intel64/gcc4.8:/opt/intel/oneapi/mpi/latest//libfabric/lib:/opt/intel/oneapi/mpi/latest//lib/release:/opt/intel/oneapi/mpi/latest//lib:/opt/intel/oneapi/mkl/latest/lib/intel64:/opt/intel/oneapi/debugger/10.1.2/gdb/intel64/lib:/opt/intel/oneapi/debugger/10.1.2/libipt/intel64/lib:/opt/intel/oneapi/debugger/10.1.2/dep/lib:/opt/intel/oneapi/compiler/latest/linux/lib:/opt/intel/oneapi/compiler/latest/linux/lib/x64:/opt/intel/oneapi/compiler/latest/linux/lib/emu:/opt/intel/oneapi/compiler/latest/linux/compiler/lib/intel64_lin \
+	PATH=/opt/intel/oneapi/mpi/latest//libfabric/bin:/opt/intel/oneapi/mpi/latest//bin:/opt/intel/oneapi/mkl/latest/bin/intel64:/opt/intel/oneapi/dev-utilities/latest/bin:/opt/intel/oneapi/debugger/10.1.2/gdb/intel64/bin:/opt/intel/oneapi/compiler/latest/linux/bin/intel64:/opt/intel/oneapi/compiler/latest/linux/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin \
+	MKLROOT=/opt/intel/oneapi/mkl/latest \
+	I_MPI_ROOT=/opt/intel/oneapi/mpi/latest
+
+# Using the Intel Compilers with mpi wrapper.
+# Further test on oneAPI Compilers needed: icx, icpx, ifx
+ENV CC=/opt/intel/oneapi/mpi/latest/bin/mpiicc \
+	CXX=/opt/intel/oneapi/mpi/latest/bin/mpiicpc \
+	FC=/opt/intel/oneapi/mpi/latest/bin/mpiifort
+
+SHELL ["/bin/bash", "-c"]
+RUN source /opt/intel/oneapi/setvars.sh \
+	&& cd /tmp \
+	&& git clone https://github.com/darelbeida/elpa.git -b ELPA_2016.05.004-openblas --single-branch --depth=1 \
+	&& cd elpa && mkdir build && cd build \
+	&& ../configure FCFLAGS="-mkl=cluster" \
+	&& make -j8 \
+	&& make PREFIX=/usr/local install \
+	&& ln -s /usr/local/include/elpa-2016.05.004/elpa /usr/local/include/ \
+	&& cd /tmp && rm -rf elpa
+
+RUN cd /tmp \
+	&& git clone https://github.com/USCiLab/cereal.git \
+	&& cp -r cereal/include /usr/local \
+	&& rm -rf cereal

doc/input-main.md

@@ -47,8 +47,6 @@
 
     - [DFT+U correction](#DFT_U-correction)
 
-    -[Start magnetization](#Start-magnetization)
-
     - [VdW correction](#vdw-correction)
 
         [vdw_method](#vdw-method) | [vdw_s6](#vdw-s6) | [vdw_s8](#vdw-s8) | [vdw_a1](#vdw-a1) | [vdw_a2](#vdw-a2) | [vdw_d](#vdw-d) | [vdw_abc](#vdw-abc) | [vdw_C6_file](#vdw-C6-file) | [vdw_C6_unit](#vdw-C6-unit) | [vdw_R0_file](#vdw-R0-file) | [vdw_R0_unit](#vdw-R0-unit) | [vdw_model](#vdw-model) | [vdw_radius](#vdw-radius) | [vdw_radius_unit](#vdw-radius-unit) | [vdw_cn_radius](#vdw-cn-radius) | [vdw_cn_radius_unit](#vdw-cn-radius-unit) | [vdw_period](#vdw-period)
@@ -1210,13 +1208,6 @@ This part of variables are used to control DFT+U correlated parameters
 
     [back to top](#input-file)
 
-### Start magnetization
-- magmom
-    - *Type*: Real
-    - *Description*: This set the start magnetization for each atom. The input magmom should be seperated by space and in the same order of STRU file. Different atoms with same magetic moment could be abbreviated as n\*magmom(NOTICE:No space before and after '\*').If one set the start magnetization here, they MUST NOT be specified again in STRU file(In STRU file, one could only set magnetic moment for each type of atom, but here setting different magnetic moment for the same kind of atom is allowed).
-    - *Default*: 0.0
-    [back to top](#input-file)
-
 
 ### VdW correction
 This part of variables are used to control vdW-corrected related parameters.

doc/input-stru.md

@@ -55,11 +55,13 @@ Direct //Cartesian or Direct coordinate.
 Si // Element type
 0.0 // magnetism
 2 // number of atoms
-0.00 0.00 0.00 0 0 0
+0.00 0.00 0.00 0 0 0//the position of atoms and other parameter specify by key word
 0.25 0.25 0.25 1 1 1
 ```
 The LATTICE_VECTORS section is removed.
 
+
+
 [back to top](#stru-file)
 
 
@@ -194,8 +196,24 @@ information that comes below.
 
     This section specifies the positions and other information of individual atoms. The first line signifies whether atom positions are given in `Cartesian` or `Direct` coordinates.
 
-    The following three lines tells the elemental type (`Si`), the initial magnetic moment (`0.0`), and the number of atoms for this particular element (`2`) repsectively.
+    The following three lines tells the elemental type (`Si`), the initial magnetic moment (`0.0`), and the number of atoms for this particular element (`2`) repsectively. Notice this  magnetic moment will be a default value for every atom of this type but will be overrided if one define it for each atom by keyword(see below).
 
-    The last two lines in this example are the coordinates of atomic positions. There are six numbers in each line: the first three specifies the atomic positions and the last three control how the atom move in geometry relaxation calculations. The numbers `0 0 0` following the coordinates of the first atom means this atom are *not allowed* to move in all three directions, and the numbers `1 1 1` following the coordinates of the second atom means this atom *can* move in all three directions.
+    The last two lines in this example are the coordinates of atomic positions. There are three numbers in each line, which specifies the atomic positions, following by other parameters marked by keywords.
+
+    Several other parameters could be defined after the atom position using key word :
+    - `m` or NO key word: three numbers, which take value in 0 or 1, control how the atom move in geometry relaxation calculations. The numbers `0 0 0` following the coordinates of the first atom means this atom are *not allowed* to move in all three directions, and the numbers `1 1 1` following the coordinates of the second atom means this atom *can* move in all three directions.  
+    - `v` or `vel` or `velocity`: set the three components of initial velocity of atoms in geometry relaxation calculations.
+    - `mag` or `magmom` : set the start magnetization for each atom. In colinear case only one number should be given. In non-colinear case one have two choice:either set one number for the norm of magnetization here and specify two polar angle later, or set three number for the xyz commponent of magnetization here.
+    - `angle1`: in non-colinear case, specify the angle between c-axis and real spin, in angle measure instead of radian measure
+    - `angle2`: in non-colinear case, specify angle between a-axis and real spin in projection in ab-plane , in angle measure instead of radian measure
+
+    e.g.:
+    ```
+    Fe
+    1
+    2
+    0.0 0.0 0.0 0 0 0 angle1 90 angle2 0
+    0.5 0.5 0.5 0 0 0 angle1 90 angle2 180
+    ```
 
 [back to top](#stru-file)

source/Makefile.Objects

@@ -310,6 +310,7 @@ symmetry_rho.o \
 symm_other.o \
 eximport.o \
 mulliken_charge.o\
+setup_nonlocal.o\
 
 OBJS_PDIAG=pdgseps.o \
 pzgseps.o \

source/input.cpp

@@ -510,7 +510,6 @@ bool Input::Read(const std::string &fn)
     }
 
     ifs.rdstate();
-	input_mag=false;
     while (ifs.good())
     {
         ifs >> word1;
@@ -1712,7 +1711,7 @@ bool Input::Read(const std::string &fn)
 		{
 			read_value(ifs, soc_lambda);
 		}
-		else if (strcmp("angle1", word) == 0)
+/*		else if (strcmp("angle1", word) == 0)
 		{
 			angle1.resize(ntype);
 			for(auto &i:angle1)
@@ -1723,7 +1722,7 @@ bool Input::Read(const std::string &fn)
 			angle2.resize(ntype);
 			for (auto &i : angle2)
 				read_value(ifs, i);
-		}
+		}*/
         //else if (strcmp("epsilon0_choice", word) == 0)
         //{
         //    read_value(ifs, epsilon0_choice);
@@ -1742,6 +1741,7 @@ bool Input::Read(const std::string &fn)
 		}
 //---------------
 //start magnetic
+/*
 #ifndef __CMD
 		else if (strcmp("magmom", word) == 0)
 		{
@@ -1810,11 +1810,10 @@ bool Input::Read(const std::string &fn)
 				atom_mag[i]=mags[n_m];
 				cout<<"atom_mag"<<atom_mag[i];
 			}	
-	input_mag=true;
 	}
 
 #endif
-
+*/		
 //--------------
 //----------------------------------------------------------------------------------
 //         Xin Qu added on 2020-10-29 for DFT+U

source/input.h

@@ -349,7 +349,6 @@ class Input
 	//double  ocp_kb[10000];
 	int     lcao_box[3];           // the scale for searching the existence of the overlap <i,0|j,R>
 	int    mulliken;//qifeng add 2019-9-10
-	bool input_mag;
 	double* atom_mag;
 	int n_mag_at;
 	//added by zhengdy-soc

source/input_conv.cpp

@@ -42,6 +42,7 @@ void Input_Conv::Convert(void)
 	GlobalC::ucell.ntype = INPUT.ntype;
 	GlobalC::ucell.lmaxmax = INPUT.lmaxmax;
 	GlobalC::ucell.set_vel = INPUT.set_vel;
+	GlobalV::out_descriptor = INPUT.out_descriptor;
 
     GlobalV::NBANDS = INPUT.nbands;
 	GlobalC::wf.seed = INPUT.seed;
@@ -319,11 +320,11 @@ void Input_Conv::Convert(void)
 			GlobalC::dftu.J = INPUT.hund_j;               //Hund exchange parameter J(ev)
 		}
 	}
+	/*
 #ifndef __CMD
-	GlobalC::ucell.input_mag=INPUT.input_mag;
 	GlobalC::ucell.n_mag_at=INPUT.n_mag_at;
 	GlobalC::ucell.atom_mag=INPUT.atom_mag;
-#endif
+#endif*/
 //--------------------------------------------
 // added by zhengdy-soc
 //--------------------------------------------
@@ -347,6 +348,7 @@ void Input_Conv::Convert(void)
 			GlobalV::DOMAG_Z = true;
 		}
 		GlobalV::LSPINORB = INPUT.lspinorb;
+		GlobalV::soc_lambda = INPUT.soc_lambda;
 
 		delete[] GlobalC::ucell.magnet.m_loc_;
 		delete[] GlobalC::ucell.magnet.angle1_;