Merge pull request #15 from stanfordbshan/dev

HTMACat1.0.2更新
更新内容如下：
1.为了更好的反馈问题和提供建议，提供了issues模板
2.添加了SML标识各物种以SMILES形式读取
3.添加了workflow，实现每次push到master分支时都会自动编译wheel并发布到release

.github/ISSUE_TEMPLATE/bug.md

@@ -0,0 +1,29 @@
+---
+name: 问题模板
+about: 如发现Bug，请按此模板提交issues，不按模板提交的问题将直接关闭。提交问题务必描述清楚、附上日志，描述不清导致无法理解和分析的问题也可能会被直接关闭。
+---
+
+## 你使用的 HTMACat 是什么版本，什么环境？
+
+> HTMACat 版本: x.x.x
+>
+> 环境: python x.x in windows or linux, install_requires
+>
+
+## 你遇到什么问题了？
+
+> 描述一下你遇到的问题
+
+## 是否已经浏览过Issues仍无法解决？
+
+> 请搜索Issues列表、查看wiki跟TG公众号的更新说明，已经解释过的问题不要重复提问
+
+
+## 你期望的结果
+
+> 描述以下你期望的结果
+
+## 给出程序界面截图、后台运行日志或配置文件
+
+> 请提供截图及配置文件截图
+> 其它问题提供后台日志

.github/ISSUE_TEMPLATE/feature.md

@@ -0,0 +1,19 @@
+---
+name: 功能需求模板
+about: 如有新功能需要需要提交，请按此模板创建issues
+---
+
+## 你使用的 HTMACat 是什么版本，什么环境？
+
+> HTMACat 版本: x.x.x
+>
+> 环境: python x.x in windows or linux, install_requires
+>
+
+## 你想要新增或者改进什么功能？
+
+> 你想要新增或者改进什么功能？
+
+## 这个功能有什么可以参考的资料吗？
+
+> 这个功能有什么可以参考的资料吗？是否可以列举一些，不要引用同类但商业化软件的任何内容.

.github/workflows/auto_gen_whl.yml

@@ -0,0 +1,49 @@
+name: Python package
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+    types:
+      - ready_for_review
+      - review_requested
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    permissions: write-all
+    steps:
+      - uses: actions/checkout@v2
+      - name: Publish Python Package
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.8
+          publish-package: true
+
+      - name: Build wheel and source distribution
+        run: |
+          cd src
+          pip install setuptools wheel
+          python setup.py sdist bdist_wheel
+
+      - name: Release version
+        id: release_version
+        run: |
+          cd src
+          app_version=$(cat setup.py | grep version | sed "s/version='\([0-9]\+\.[0-9]\+\.[0-9]\+\)',/\1/" | sed s/[[:space:]]//g)
+          echo "app_version=$app_version" >> $GITHUB_ENV
+          echo "app_version=$app_version"
+
+      - name: Upload binaries to release
+        uses: svenstaro/upload-release-action@v2
+        with:
+          repo_token: ${{ secrets.GITHUB_TOKEN }}
+          file: src/dist/*.whl
+          tag: v${{env.app_version}}
+          release_name: v${{env.app_version}}
+          overwrite: true
+          file_glob: true
+          body: ${{github.event.head_commit.message}}

.gitignore

@@ -22,6 +22,8 @@ wheels/
 *.vasp
 MANIFEST
 script/
+dist/
+.vscode/
 
 # PyInstaller
 #  Usually these files are written by a python script from a template
@@ -99,4 +101,6 @@ venv.bak/
 # mypy
 .mypy_cache/
 
-# custom
+# custom
+example/backup*
+example/zjwang*

README.md

@@ -19,14 +19,23 @@ download the install script:[install_wheel.bat](https://raw.githubusercontent.co
 ```shell
 ./install_wheel.bat # Windows 
 ./install_wheel.sh # linux
-pip install HTMACat.whl # [download from releases](https://github.com/stanfordbshan/HTMACat-kit/releases/latest)
 ```
 ### 2) Manual installation
+
 ```shell
+# windows
+pip install ase numpy==1.23.5 scikit-learn
+pip install https://raw.githubusercontent.com/stanfordbshan/HTMACat-kit/master/requires_wheel/FireWorks-2.0.3-py3-none-any.whl
+pip install https://raw.githubusercontent.com/stanfordbshan/HTMACat-kit/master/requires_wheel/CatKit-0.5.4-py3-none-any.requires_wheel
+for /f "tokens=1,* delims=:" %%A in ('curl -ks https://api.github.com/repos/stanfordbshan/HTMACat-kit/releases/latest ^| find "browser_download_url"') do (
+    pip install -U %%B
+)
+
+#linux
 pip install ase numpy==1.23.5 scikit-learn
 pip install https://raw.githubusercontent.com/stanfordbshan/HTMACat-kit/master/requires_wheel/FireWorks-2.0.3-py3-none-any.whl
 pip install https://raw.githubusercontent.com/stanfordbshan/HTMACat-kit/master/requires_wheel/CatKit-0.5.4-py3-none-any.whl
-pip install HTMACat.whl # [download from releases](https://github.com/stanfordbshan/HTMACat-kit/releases/latest)
+pip install --upgrade $(curl -s https://api.github.com/repos/stanfordbshan/HTMACat-kit/releases/latest | grep "browser_download_url.*\.whl" | cut -d : -f 2,3 | tr -d \")
 ```
 
 # Getting started
@@ -45,11 +54,11 @@ pip install HTMACat.whl # [download from releases](https://github.com/stanfordbs
 
     ```shell
     Cu # Doping elements
-    0 1 1L 2 3 b1 # Doping type
-    H NH2 NO N2 N2O O2 H2O # Adsorption species
-    1 1 1 2 2 1 # Adsorption type
+    b1 # Doping type
+    SML C(=O)O # Adsorption species (SMILES of formic acid)
+    1 2 # Adsorption type
     ```
-    Where the first line of the file is the doping element and the second line is the doping type, 0 corresponds to no doping, 1, 2 and 3 correspond to surface layers doped with 1, 2 and 3 atoms, respectively, and 1L and b1 represent surface layer substitution and bulk equivalent proportional substitution. Users can modify the corresponding parameters to achieve customized modeling according to their research needs.
+    Where the first line of the file is the doping element and the second line is the doping type, 0 corresponds to no doping, 1, 2 and 3 correspond to surface layers doped with 1, 2 and 3 atoms, respectively, and 1L and b1 represent surface layer substitution and bulk equivalent proportional substitution. The third and fourth lines respectively represent the adsorbate species and the adsorption types. <b>Please note that the adsorbates should be declared by their SMILES expressions if the third line starts with 'SML'!</b> If no 'SML' at the beginning of this line, the species are represented in their chemical formula. <b>To avoid ambiguity, it is recommended that SMILES be used when declaring complex species.</b> Users can modify the corresponding parameters to achieve customized modeling according to their research needs.
 
     (2) run script
 
@@ -63,11 +72,11 @@ pip install HTMACat.whl # [download from releases](https://github.com/stanfordbs
 
     ```shell
     Cu # Doping elements
-    1 1L 2 3 # Doping type
-    NH2 H2O;NH H2O;N H2O;NH2 H;NH H;N H # Co-adsorption species
-    1 1;1 1;1 1;1 1;1 1;1 1 # Adsorption type
+    3 # Doping type
+    SML N [O];[NH2] [OH];[N] [N];[N] [O];[N] [N]=O # Co-adsorption species
+    1 1;1 1;1 1;1 1;1 1 # Adsorption type
     ```
-    The first line represents the dopant element, the second line represents the dopant type, the third and fourth lines respectively represent the co-adsorbate species and the co-adsorption type. Different co-adsorption combinations are separated by ";".
+    The first line represents the dopant element, the second line represents the dopant type, the third and fourth lines respectively represent the co-adsorbate species (also in SMILES format) and the co-adsorption type. Different co-adsorption combinations are separated by ";".
 
     (2) run script
 
@@ -82,4 +91,10 @@ pip install HTMACat.whl # [download from releases](https://github.com/stanfordbs
 
 * Jiaqiang Yang email:[jqyang_hust@hust.edu.cn](mailto:jqyang_hust@hust.edu.cn)
 * Feifeng Wu email:[wufeifeng_hust@163.com](wufeifeng_hust@163.com)
-* Bin Shan email:[bshan@mail.hust.edu.cn](bshan@mail.hust.edu.cn)
+* Bin Shan email:[bshan@mail.hust.edu.cn](bshan@mail.hust.edu.cn)
+
+‍
+
+# Links
+
+* Materials Design and Nano-Manufacturing Center@HUST:http://www.materialssimulation.com/

example/Formic_acid_ads-SML/Model

@@ -0,0 +1,4 @@
+Cu
+b1
+SML C(=O)O
+1

example/Formic_acid_ads/Model

@@ -0,0 +1,4 @@
+Cu
+b1
+HCOOH
+1

example/coads-SML/Model

@@ -0,0 +1,4 @@
+Cu
+3
+SML N [O];[NH2] [OH];[N] [N];[N] [O];[N] [N]=O
+1 1;1 1;1 1;1 1;1 1

example/coads-SML/StrucInfo

@@ -0,0 +1 @@
+Au fcc 4.16 111

example/coads/StrucInfo

@@ -0,0 +1 @@
+Au fcc 4.16 111

install_wheel.bat

@@ -1,3 +1,6 @@
 pip install ase numpy==1.23.5 scikit-learn
 pip install https://raw.githubusercontent.com/stanfordbshan/HTMACat-kit/master/requires_wheel/FireWorks-2.0.3-py3-none-any.whl
-pip install https://raw.githubusercontent.com/stanfordbshan/HTMACat-kit/master/requires_wheel/CatKit-0.5.4-py3-none-any.whl
+pip install https://raw.githubusercontent.com/stanfordbshan/HTMACat-kit/master/requires_wheel/CatKit-0.5.4-py3-none-any.requires_wheel
+for /f "tokens=1,* delims=:" %%A in ('curl -ks https://api.github.com/repos/stanfordbshan/HTMACat-kit/releases/latest ^| find "browser_download_url"') do (
+    pip install -U %%B
+)

install_wheel.sh

@@ -1,4 +1,5 @@
 #!/bin/bash
 pip install ase numpy==1.23.5 scikit-learn
 pip install https://raw.githubusercontent.com/stanfordbshan/HTMACat-kit/master/requires_wheel/FireWorks-2.0.3-py3-none-any.whl
-pip install https://raw.githubusercontent.com/stanfordbshan/HTMACat-kit/master/requires_wheel/CatKit-0.5.4-py3-none-any.whl
+pip install https://raw.githubusercontent.com/stanfordbshan/HTMACat-kit/master/requires_wheel/CatKit-0.5.4-py3-none-any.whl
+pip install --upgrade $(curl -s https://api.github.com/repos/stanfordbshan/HTMACat-kit/releases/latest | grep "browser_download_url.*\.whl" | cut -d : -f 2,3 | tr -d \")

src/HTMACat/model/Construct_Coadsorption.py

@@ -9,6 +9,12 @@ def Construct_coadsorption(Path_Info,Model,spec_ads_stable):
     Ele_dop=model.readline().split()
     Natom_dop=model.readline().split()
     Ads=model.readline().split(';')
+    SML = False
+    if 'SML' == Ads[0].split()[0]:
+       SML = True
+       Ads[0] = Ads[0][3:]
+    else:
+       pass
     Index=model.readline().split(';')
     model.close()
     LatInfo = open(Path_Info,"r+")
@@ -41,11 +47,11 @@ def Construct_coadsorption(Path_Info,Model,spec_ads_stable):
                    ads=ads.strip() 
                    ads_symb='_'.join(ads.split(' '))
                    if Index[k].strip() == '1 1':
-                      slabs_ads=Construct_coadsorption_11(slabs,ads,dis_inter,spec_ads_stable) 
+                      slabs_ads=Construct_coadsorption_11(slabs,ads,dis_inter,spec_ads_stable,SML) 
                    elif Index[k].strip() == '1 2':
-                      slabs_ads=Construct_coadsorption_12(slabs,ads,dis_inter)
+                      slabs_ads=Construct_coadsorption_12(slabs,ads,dis_inter,SML)
                    elif Index[k].strip() == '2 2':
-                      slabs_ads=Construct_coadsorption_22(slabs,ads,dis_inter)
+                      slabs_ads=Construct_coadsorption_22(slabs,ads,dis_inter,SML)
                    #view(slabs_ads) 
                    for m,slab_ad in enumerate(slabs_ads):
                       #write_vasp("%s_%s_%s_%s_%s.vasp" %(mname,mfacet,natom_dop,ads_symb,m), slab_ad, direct=True, sort=[''], vasp5=True)
@@ -59,11 +65,11 @@ def Construct_coadsorption(Path_Info,Model,spec_ads_stable):
                    ads=ads.strip()
                    ads_symb='_'.join(ads.split(' '))
                    if Index[k].strip() == '1 1':
-                      slabs_ads=Construct_coadsorption_11(slabs,ads,dis_inter,spec_ads_stable)
+                      slabs_ads=Construct_coadsorption_11(slabs,ads,dis_inter,spec_ads_stable,SML)
                    elif Index[k].strip() == '1 2':
-                      slabs_ads=Construct_coadsorption_12(slabs,ads,dis_inter)
+                      slabs_ads=Construct_coadsorption_12(slabs,ads,dis_inter,SML)
                    elif Index[k].strip() == '2 2':
-                      slabs_ads=Construct_coadsorption_22(slabs,ads,dis_inter)
+                      slabs_ads=Construct_coadsorption_22(slabs,ads,dis_inter,SML)
                    for m,slab_ad in enumerate(slabs_ads):
                       write_vasp("%s_%s_%s_b1_%s.vasp" %(mname,mfacet,ads_symb,m), slab_ad, direct=True, sort=[''], vasp5=True)
                    print("%s %s adsorption on b1 doped systemare finished!" %(ads_symb,m+1))
@@ -76,11 +82,11 @@ def Construct_coadsorption(Path_Info,Model,spec_ads_stable):
                    ads=ads.strip() 
                    ads_symb='_'.join(ads.split(' '))
                    if Index[k].strip() == '1 1':
-                      slabs_ads=Construct_coadsorption_11(slabs_dop,ads,dis_inter,spec_ads_stable)
+                      slabs_ads=Construct_coadsorption_11(slabs_dop,ads,dis_inter,spec_ads_stable,SML)
                    elif Index[k].strip() == '1 2':
-                      slabs_ads=Construct_coadsorption_12(slabs_dop,ads,dis_inter)
+                      slabs_ads=Construct_coadsorption_12(slabs_dop,ads,dis_inter,SML)
                    elif Index[k].strip() == '2 2':
-                      slabs_ads=Construct_coadsorption_22(slabs_dop,ads,dis_inter)
+                      slabs_ads=Construct_coadsorption_22(slabs_dop,ads,dis_inter,SML)
                    #view(slabs_ads)
                    for m,slab_ad in enumerate(slabs_ads):
                       write_vasp("%s_%s_%s_%s_%s_%s.vasp" %(mname,ele_dop,mfacet,natom_dop,ads_symb,m), slab_ad, direct=True, sort=[''], vasp5=True)
@@ -94,11 +100,11 @@ def Construct_coadsorption(Path_Info,Model,spec_ads_stable):
                    ads=ads.strip()
                    ads_symb='_'.join(ads.split(' '))
                    if Index[k].strip() == '1 1':
-                      slabs_ads=Construct_coadsorption_11(slabs_dop,ads,dis_inter,spec_ads_stable)
+                      slabs_ads=Construct_coadsorption_11(slabs_dop,ads,dis_inter,spec_ads_stable,SML)
                    elif Index[k].strip() == '1 2':
-                      slabs_ads=Construct_coadsorption_12(slabs_dop,ads,dis_inter)
+                      slabs_ads=Construct_coadsorption_12(slabs_dop,ads,dis_inter,SML)
                    elif Index[k].strip() == '2 2':
-                      slabs_ads=Construct_coadsorption_22(slabs_dop,ads,dis_inter)
+                      slabs_ads=Construct_coadsorption_22(slabs_dop,ads,dis_inter,SML)
                    ## To choose the config whose neighbor list includes the doped atoms
                    slabs_ads_near=[]
                    for slb in slabs_ads: