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

Author: dyzheng

.github/workflows/cuda.yml

@@ -0,0 +1,74 @@
+name: CUDA Test
+
+on:
+  workflow_dispatch:
+
+jobs:
+  start-runner:
+    name: Start self-hosted EC2 runner
+    runs-on: ubuntu-latest
+    outputs:
+      label: ${{ steps.start-ec2-runner.outputs.label }}
+      ec2-instance-id: ${{ steps.start-ec2-runner.outputs.ec2-instance-id }}
+    steps:
+      - name: Configure AWS credentials
+        uses: aws-actions/configure-aws-credentials@v1
+        with:
+          aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }}
+          aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+          aws-region: us-east-2
+      - name: Start EC2 runner
+        id: start-ec2-runner
+        uses: machulav/ec2-github-runner@v2
+        with:
+          mode: start
+          github-token: ${{ secrets.PAT }}
+          ec2-image-id: ami-04cd9fec4a7a39019
+          ec2-instance-type: g4dn.xlarge
+          subnet-id: subnet-72d3e53e
+          security-group-id: sg-06b0c93122c08aeab
+
+  test:
+    name: Do the job on the runner
+    needs: start-runner # required to start the main job when the runner is ready
+    runs-on: ${{ needs.start-runner.outputs.label }} # run the job on the newly created runner
+    container: 
+      image: ghcr.io/deepmodeling/abacus-development-kit:cuda
+      options: --gpus all
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Build cuSolver
+        run: |
+          nvidia-smi
+          cmake -B build -DUSE_CUSOLVER_LCAO=ON
+          cmake --build build -j4
+          cmake --install build
+      - name: Test
+        run: |
+          export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/usr/local/cuda/lib64
+          cd tests/integrate
+          echo "ks_solver cusolver" >> ./270_NO_MD_2O/INPUT
+          ./Autotest.sh -r 270_NO_MD_2O
+
+  stop-runner:
+    name: Stop self-hosted EC2 runner
+    needs:
+      - start-runner # required to get output from the start-runner job
+      - test # required to wait when the main job is done
+    runs-on: ubuntu-latest
+    if: ${{ always() }} # required to stop the runner even if the error happened in the previous jobs
+    steps:
+      - name: Configure AWS credentials
+        uses: aws-actions/configure-aws-credentials@v1
+        with:
+          aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }}
+          aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+          aws-region: us-east-2
+      - name: Stop EC2 runner
+        uses: machulav/ec2-github-runner@v2
+        with:
+          mode: stop
+          github-token: ${{ secrets.PAT }}
+          label: ${{ needs.start-runner.outputs.label }}
+          ec2-instance-id: ${{ needs.start-runner.outputs.ec2-instance-id }}

.github/workflows/container.yml renamed to .github/workflows/devcontainer.yml

@@ -8,6 +8,7 @@ on:
 jobs:
   build_container_and_push:
     runs-on: ubuntu-latest
+    if: github.repository_owner == 'deepmodeling'
     strategy:
       matrix:
         dockerfile: ["gnu","intel","cuda"]
@@ -25,10 +26,19 @@ jobs:
           username: ${{ github.actor }}
           password: ${{ secrets.GITHUB_TOKEN }}
 
+      - name: Login to Aliyun Registry
+        uses: docker/login-action@v1
+        with:
+          registry: ${{ secrets.DP_HARBOR_REGISTRY }}
+          username: ${{ secrets.DP_HARBOR_USERNAME }}
+          password: ${{ secrets.DP_HARBOR_PASSWORD }}
+
       - name: Build and Push Container
         uses: docker/build-push-action@v2
         with:
-          tags: ghcr.io/${{ github.repository_owner }}/abacus-development-kit:${{ matrix.dockerfile }}
+          tags: |
+            ghcr.io/${{ github.repository_owner }}/abacus-development-kit:${{ matrix.dockerfile }}
+            ${{ secrets.DP_HARBOR_REGISTRY }}/dplc/abacus-${{ matrix.dockerfile }}:latest
           file: Dockerfile.${{ matrix.dockerfile }}
           cache-from: type=registry,ref=ghcr.io/${{ github.repository_owner }}/abacus-development-kit:${{matrix.dockerfile}}
           cache-to: type=inline

.github/workflows/image.yml

@@ -0,0 +1,42 @@
+name: Build Image
+
+on:
+  push:
+    branches:
+      - develop
+
+jobs:
+  build_container_and_push:
+    runs-on: ubuntu-latest
+    if: github.repository_owner == 'deepmodeling'
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - 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: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Login to Aliyun Registry
+        uses: docker/login-action@v1
+        with:
+          registry: ${{ secrets.DP_HARBOR_REGISTRY }}
+          username: ${{ secrets.DP_HARBOR_USERNAME }}
+          password: ${{ secrets.DP_HARBOR_PASSWORD }}
+
+      - name: Build and Push Container
+        uses: docker/build-push-action@v2
+        with:
+          tags: |
+            ghcr.io/${{ github.repository_owner }}/abacus:latest
+            ${{ secrets.DP_HARBOR_REGISTRY }}/dplc/abacus:latest
+          file: Dockerfile
+          cache-from: type=registry,ref=ghcr.io/${{ github.repository_owner }}/abacus:latest
+          cache-to: type=inline
+          push: true

.github/workflows/performance.yml

@@ -0,0 +1,34 @@
+name: Performance test
+
+on:
+  workflow_dispatch:
+
+jobs:
+  test:
+    name: Performance test
+    runs-on: self-hosted
+    strategy:
+      matrix:
+        tag: ["gnu", "intel"]
+    if: github.repository_owner == 'deepmodeling'
+    container: ghcr.io/${{ github.repository_owner }}/abacus-development-kit:${{ matrix.tag }}
+    timeout-minutes: 2880
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Install Requirements
+        run: |
+          apt install -y time
+      - name: Build
+        run: |
+          cmake -B build -DENABLE_LIBXC=ON
+          cmake --build build -j16
+          cmake --install build
+      - name: Test
+        run: |
+          . /opt/intel/oneapi/setvars.sh 2> /dev/null || :
+          cd examples/performance/
+          bash run.sh
+      - name: Show Result
+        run: |
+          cat examples/performance/sumall.dat

.github/workflows/test.yml

@@ -16,7 +16,7 @@ jobs:
           ref: "refs/pull/${{ github.event.number }}/merge"
       - name: Build
         run: |
-          cmake -B build -DBUILD_TESTING=ON -DENABLE_DEEPKS=ON
+          cmake -B build -DBUILD_TESTING=ON -DENABLE_DEEPKS=ON -DENABLE_LIBXC=ON
           cmake --build build -j8
           cmake --install build
       - name: Test

CMakeLists.txt

@@ -282,6 +282,7 @@ target_link_libraries(${ABACUS_BIN_NAME}
     cell
     symmetry
     md
+    planewave
     surchem
     neighbor
     orb

Dockerfile

@@ -0,0 +1,16 @@
+# To build this docker file, run `docker build -t abacus - < Dockerfile`.
+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'.
+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
+# 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`.
+# Replace '<host>' with the path to all files(including pseudopotential files), '<wd>' with a path to working directory, and '<wd/input>' with the path to input folder(containing 'INPUT', 'STRU', etc.).
+# e.g. after clone the repo to `$HOME` and pulled this image, execute `docker run -v ~/abacus-develop/tests/integrate:/workspace -w /workspace/101_PW_15_f_pseudopots abacus`.
+# To run ABACUS with a given MPI process number, execute `docker run -v <host>:<wd> -w <wd/input> -it --entrypoint mpirun abacus -np <processes> abacus`. Note: the first "abacus" is the name of the image, the second "abacus" is the name of the executable file. Do not use '--cpus' flag of 'docker run' to specify the number of processes.
+
+# To use this image as developing environment, execute `docker run -it --entrypoint /bin/bash abacus`.
+# Please refer to https://docs.docker.com/engine/reference/commandline/run/ for more details.

Dockerfile.cuda

@@ -1,6 +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
+RUN wget https://developer.download.nvidia.com/compute/cuda/11.7.0/local_installers/cuda_11.7.0_515.43.04_linux.run --no-check-certificate --quiet \
+	&& sh cuda_11.7.0_515.43.04_linux.run --toolkit --silent \
+	&& rm cuda_11.7.0_515.43.04_linux.run
 ENV PATH=/usr/local/cuda/bin:$PATH

docs/input-main.md

@@ -70,6 +70,10 @@
 
     [deepks_out_labels](#out-descriptor) | [deepks_descriptor_lmax](#lmax-descriptor) | [deepks_scf](#deepks-scf) | [deepks_model](#model-file)
 
+- [Electric field and dipole correction](#Electric-field-and-dipole-correction)
+
+    [efield](#efield) | [dipole](#dipole) | [edir](#edir) | [emaxpos](#emaxpos) | [eopreg](#eopreg) | [eamp](#eamp)
+
 [back to main page](../README.md)
 
 ## Structure of the file
@@ -910,6 +914,48 @@ Warning: this function is not robust enough for version 2.2.0. Please try these
 - **Description**: the path of the trained, traced NN model file (generated by deepks-kit). used when deepks_scf is set to 1.
 - **Default**: None
 
+### Electric field and dipole correction
+
+This part of variables are relevant to electric field and dipole correction
+
+#### efield
+
+- **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
+
+- **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.
+- **Default**: false
+
+#### edir
+
+- **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.
+- **Default**: 2
+
+#### emaxpos
+
+- **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.
+- **Default**: 0.5
+
+#### eopreg
+
+- **Type**: Real
+- **Description**: Zone in the unit cell where the saw-like potential decreases, 0 < eopreg < 1. Used only if efield == true.
+- **Default**: 0.1
+
+#### eamp
+
+- **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.
+- **Default**: 0.0
+
 ### Exact Exchange
 
 This part of variables are relevant when using hybrid functionals