插件	AiiDA	Python
2.0.0
1.1.0

aiida-zeopp

AiiDA插件用于Zeo++

安装

pip install aiida-zeopp
reentry scan
verdi quicksetup  # better to set up a new profile
verdi calculation plugins  # should now show your calclulation plugins

功能

• 添加CIF格式的输入结构

CifData = DataFactory('cif')
inputs['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')
inputs['parameters'] = NetworkParameters(dict=d)

• NetworkParameters使用voluptuous验证命令行选项。了解支持选项

NetworkParameters = DataFactory('zeopp.parameters')
print(NetworkParameters.schema)

• 添加替代原子半径文件

SinglefileData = DataFactory('singlefile')
inputs['atomic_radii'] = SinglefileData(file='/path/to/file')

示例

查看examples文件夹以获取设置计算的完整示例。

verdi daemon start         # make sure the daemon is running
cd examples
verdi run examples/example_01.py  # runs test calculatio

测试

aiida_zeopp包含一些在每次提交时运行的测试。

以下将发现并运行所有单元测试

pip install -e .[testing]
pytest

分析输出

$ verdi process 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 calcjob 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 calcjob outputls 88
_scheduler-stderr.txt
_scheduler-stdout.txt
out.chan
out.cssr
out.sa
out.volpo

$ verdi calcjob 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

MIT

联系

leopold.talirz@gmail.com

致谢

本工作得到以下机构的支持：

• 由瑞士国家竞争力研究中心（MARVEL）资助的瑞士国家科学基金会（SNSF）；
• 瑞士大学P-5项目“材料云”。