Merge branch 'develop' of https://github.com/1041176461/abacus-develop into develop

Author: jiyuang

.github/ISSUE_TEMPLATE/bug-report.md

@@ -2,25 +2,33 @@
 name: Bug Report
 about: Create a report for problems with ABACUS
 title: ''
-labels: bug
+labels: Bug
 assignees: dyzheng
 
 ---
 
 ## Describe the Bug
-A clear and concise description of what the bug is.
+A clear and concise description of what the bug is. 
+The bug may results in:
+- abnormal interruption of the program,
+- systematic or randomized numerical error, or
+- relatively low efficiency.
+
+## Expected behavior
+A clear and concise description of what you expected to happen.
 
 ## To Reproduce
 Steps to reproduce the behavior:
 1. [e.g. clone the source code from ...]
 2. [e.g. configure CMake with options ...]
 3. [e.g. build ABACUS with ...]
 4. [e.g. run ABACUS with ...]
+It is recommended to attach your calculation case here for the developers to reproduce the bug.
 
 ## Environment
-- OS: [e.g. CentOS 7.6]
-- Compiler: [e.g. Intel LLVM 2021.1]
-- Optional Dependencies: [e.g. Intel MKL]
+- OS: [e.g. Ubuntu 20.04]
+- Compiler: [e.g. gcc 5.1.0]
+- Dependencies: [e.g. Intel MKL, OpenBLAS]
 
 ## Additional Context
 Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature-request.md

@@ -0,0 +1,17 @@
+---
+name: Feature Request
+about: Suggest something more for ABACUS to do
+title: ''
+labels: Feature
+assignees: mohanchen
+
+---
+
+## Background
+A clear and concise description of why this new feature is important.
+
+## Describe the solution you'd like
+A clear and concise description of what you want to happen.
+
+## Additional context
+Add any other context or screenshots about the feature request here.

.github/ISSUE_TEMPLATE/help-wanted.md

@@ -0,0 +1,10 @@
+---
+name: Help Wanted
+about: For general questions or assistance.
+title: ''
+labels: Help wanted
+assignees: caic99
+
+---
+
+Want to use ABACUS for certain system? Facing problems when installing ABACUS? Don't know how to choose a good parameter? Feel free to reach us, and we'll do our best to help!

.github/ISSUE_TEMPLATE/software-enhancements.md

@@ -2,14 +2,16 @@
 name: Software Enhancements
 about: Suggest an idea to make ABACUS more robust and organized
 title: ''
-labels: enhancement
+labels: Refactor
 assignees: caic99
 
 ---
 
 ## Describe Current Status and Possible Solution
 
-A clear and concise description of why this enhancement is important. If you have some ideas about how to achieve it, please also describe.
+A clear and concise description of why this enhancement is important. 
+Describing the current situation of ABACUS is preferred.
+If you have some ideas about how to achieve it, please feel free to comment.
 
 ## Additional Context
 

.github/workflows/build_test.yml

@@ -23,7 +23,7 @@ jobs:
     container: ghcr.io/${{ github.repository_owner }}/abacus-development-kit:${{ matrix.tag }}
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
       - name: Build
         run: |
           cmake -B build -DBUILD_TESTING=ON ${{ matrix.build_args }}

.github/workflows/container.yml

@@ -4,8 +4,6 @@ on:
   push:
     branches:
       - develop
-      - reconstruction
-      - newelpa
 
 jobs:
   build_container_and_push:
@@ -15,7 +13,7 @@ jobs:
         dockerfile: ["gnu","intel","cuda"]
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Setup Docker Buildx
         uses: docker/setup-buildx-action@v1
@@ -30,8 +28,8 @@ jobs:
       - name: Build and Push Container
         uses: docker/build-push-action@v2
         with:
-          tags: ghcr.io/${{ github.repository_owner }}/abacus-development-kit:${{matrix.dockerfile}}
-          file: Dockerfile.${{matrix.dockerfile}}
+          tags: ghcr.io/${{ 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/dynamic.yml

@@ -4,31 +4,29 @@ on:
   schedule:
     - cron: '0 3 * * *'
   workflow_dispatch:
-    inputs:
-      name:
-        description: 'Number of Cores to Run ABACUS'
-        required: false
-        default: '2'
 
 jobs:
   test:
-    name: Do the job on the runner
+    name: Dynamic analysis
     runs-on: self-hosted
     if: github.repository_owner == 'deepmodeling'
     container: ghcr.io/deepmodeling/abacus-development-kit:gnu
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
-      - name: Build and Test
+        uses: actions/checkout@v3
+      - name: Building
         run: |
           cmake -B build -DENABLE_ASAN=1 -DBUILD_TESTING=ON -DENABLE_DEEPKS=1
           cmake --build build -j16
           cmake --install build
+      - name: Testing
+        run: |
           cmake --build build --target test ARGS="-V"
       - name: Publish Report to Dashboard
         uses: crazy-max/ghaction-github-pages@v2
+        if: ${{ ! cancelled() }}
         with:
           target_branch: dashboard
-          build_dir: html
+          build_dir: tests/html
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/static.yaml

@@ -1,41 +1,36 @@
 name: Static Analysis
 
 on:
-  workflow_dispatch:
+  pull_request:
 
 jobs:
   clang-tidy:
-    runs-on: self-hosted
-    if: github.repository_owner == 'deepmodeling'
+    runs-on: ubuntu-latest
     container: ghcr.io/deepmodeling/abacus-development-kit:gnu
     steps:
       - name: Checkout Pull Request
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
-          ref: ${{ github.event.pull_request.head.sha }}
+          fetch-depth: 2
       - name: Setup clang-tidy
         run: |
           apt-get update && apt-get install -y --no-install-recommends clang-format clang-tidy
       - name: Generate Build Commands
         run: |
           cmake -B build -DCMAKE_EXPORT_COMPILE_COMMANDS=1
-      - name: Checkout Changed Files
-        id: files
-        uses: deepmodeling/get-changed-files@master
       - name: Run clang-tidy
         run: |
-          printf "%s\n" ${{ steps.files.outputs.added_modified }} | grep -E "^.*\.(cpp|h)$" > cppfiles.txt
-          clang-tidy -p=build --export-fixes=diagnostics.yaml `cat cppfiles.txt`
-      - name: Run clang-tidy-pr-comments action
-        uses: deepmodeling/abacus-code-reviewer@master
+          git diff -U0 HEAD^ | clang-tidy-diff -p1 -path build -export-fixes fixes.yml
+      - name: Pull request comments from clang-tidy reports
+        uses: platisd/[email protected]
         with:
           # The GitHub token (or a personal access token)
           github_token: ${{ secrets.GITHUB_TOKEN }}
           # The path to the clang-tidy fixes generated previously
-          clang_tidy_fixes: diagnostics.yaml
+          clang_tidy_fixes: fixes.yml
           # Optionally set to true if you want the Action to request
           # changes in case warnings are found
-          request_changes: true
+          request_changes: false
           # Optionally set the number of comments per review
           # to avoid GitHub API timeouts for heavily loaded
           # pull requests

.github/workflows/test.yml

@@ -1,33 +1,26 @@
 name: Integration Test and Unit Test
 
 on:
-  pull_request_target:
-    branches:
-      - develop
-      - tryEigen
-      - update_MD
-      - ABACUS_2.2.0_beta
-      - deepks
-      - planewave
-      - pw_refactor
-      - TDDFT
+  pull_request:
 
 jobs:
   test:
-    name: Do the job on the runner
+    name: Test
     runs-on: self-hosted
     if: github.repository_owner == 'deepmodeling'
     container: ghcr.io/deepmodeling/abacus-development-kit:gnu
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
-          ref: ${{ github.event.pull_request.head.sha }}
-      - name: Build and Test
-        env:
-          GTEST_COLOR: 'yes'
+          ref: "refs/pull/${{ github.event.number }}/merge"
+      - name: Build
         run: |
           cmake -B build -DBUILD_TESTING=ON -DENABLE_DEEPKS=ON
           cmake --build build -j8
           cmake --install build
+      - name: Test
+        env:
+          GTEST_COLOR: 'yes'
+        run: |
           cmake --build build --target test ARGS="-V"

.gitignore

@@ -5,8 +5,10 @@ obj
 OUT.*
 log.txt
 result.out
+*.dat
 .DS_Store
 .cache
 .vscode
 html
-run.log
+*.log
+STRU_READIN_ADJUST.cif