Zeo支持插件++
aiida-zeopp的Python项目详细描述
艾伊达•泽普
用于Zeo++
的aiida插件安装
git clone https://github.com/ltalirz/aiida-zeopp aiida-zeopp cd aiida-zeopp pip install -e . # also installs aiida, if missing (but not postgres) reentry scan verdi quicksetup # better to set up a new profile verdi calculation plugins # should now show your calclulation plugins
功能
- 以CIF格式添加输入结构
CifData=DataFactory('cif')calc.use_structure(CifData(file='/path/to/file'))
- 使用python字典和
NetworkParameters指定命令行选项
d={'sa':[1.82,1.82,1000],'volpo':[1.82,1.82,1000],'chan':1.2}NetworkParameters=DataFactory('zeopp.parameters')calc.use_parameters(NetworkParameters(dict=d))
NetworkParameters使用voluptuous验证命令行选项。 了解支持的选项：
NetworkParameters=DataFactory('zeopp.parameters')print(NetworkParameters.schema)
- 添加备用原子半径文件
SinglefileData=DataFactory('singlefile')calc.use_atomic_radii(SinglefileData(file='/path/to/file'))
示例
有关设置计算或工作流的完整示例，请参见examples文件夹。
verdi daemon start # make sure the daemon is runningcd examples verdi run submit.py # submit test calculation verdi calculation list -a # check status of calculation
测试
aiida_zeopp附带了许多在每次提交时运行的测试。
下面将发现并运行所有单元测试：
pip install -e .[testing] python manage.py
分析输出
$ verdi calculation show 88 ----------- ------------------------------------------------------------------------------ type NetworkCalculation pk 88 uuid deb63433-4dcd-4ca1-9165-cb97877496b3 label aiida_zeopp example calculation description Converts .cif to .cssr format, computes surface area, pore volume and channels ctime 2018-11-19 09:12:55.259776+00:00 mtime 2018-11-19 09:15:15.708275+00:00 computer [1] localhost code network ----------- ------------------------------------------------------------------------------ ##### INPUTS: Link label PK Type ------------ ---- ----------------- parameters 87 NetworkParameters structure 86 CifData ##### OUTPUTS: Link label PK Type ----------------- ---- -------------- remote_folder 89 RemoteData retrieved 90 FolderData structure_cssr 91 SinglefileData output_parameters 92 ParameterData $ verdi calculation res 88{"ASA_A^2": 3532.09, "ASA_m^2/cm^3": 1932.13, "ASA_m^2/g": 2197.86, "Channel_surface_area_A^2": 3532.09, "Channels": {"Dimensionalities": [3], "Largest_free_spheres": [6.74621 ], "Largest_included_free_spheres": [13.1994 ], "Largest_included_spheres": [13.1994 ]}, "Density": 0.879097, "Input_chan": 1.2, "Input_cssr": true, "Input_sa": [1.82, 1.82, 1000], "Input_structure_filename": "HKUST-1.cif", "Input_volpo": [1.82, 1.82, 1000], "NASA_A^2": 0.0, "NASA_m^2/cm^3": 0.0, "NASA_m^2/g": 0.0, "Number_of_channels": 1, "Number_of_pockets": 0, "POAV_A^3": 9049.01, "POAV_Volume_fraction": 0.495, "POAV_cm^3/g": 0.563078, "PONAV_A^3": 0.0, "PONAV_Volume_fraction": 0.0, "PONAV_cm^3/g": 0.0, "Pocket_surface_area_A^2": 0.0, "Unitcell_volume": 18280.8 } $ verdi calculation outputls 88 _scheduler-stderr.txt _scheduler-stdout.txt out.chan out.cssr out.sa out.volpo $ verdi calculation outputcat 88 -p out.sa @ out.sa Unitcell_volume: 18280.8 Density: 0.879097 ASA_A^2: 3532.09 ASA_m^2/cm^3: 1932.13 ASA_m^2/g: 2197.86 NASA_A^2: 0 NASA_m^2/cm^3: 0 NASA_m^2/g: 0 Number_of_channels: 1 Channel_surface_area_A^2: 3532.09 Number_of_pockets: 0 Pocket_surface_area_A^2:
许可证
麻省理工学院
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