2. Perform geometric analysis of one MOF

Use the zeo++ code to analyze the structure, such as the volume inside the MOF that is accessible to methane.

• To make things simple, start with one MOF: DSoLANSUKYIH.cif

• Set up the Deneb computer at EPFL

  • Import the deneb-molsim computer and its codes into AiiDA

    $ verdi import {{ "/assets/2018_EPFL_molsim/deneb-molsim.aiida" | absolute_url }} 
    $ verdi computer list -a  # should show 'deneb-molsim'
    $ verdi code list -A   # should show 'zeopp@deneb-molsim', 'raspa@deneb-molsim'
    

  • Generate an SSH key pair for passwordless connection

    $ ssh-keygen
    
    Generating public/private rsa key pair. 
    Enter file in which to save the key (/home/max/.ssh/id_rsa): <Enter> 
    Enter passphrase (empty for no passphrase): <Enter> 
    Enter same passphrase again: <Enter> 
    Your identification has been savedin /home/max/.ssh/id_rsa. 
    Your public key has been saved in /home/max/.ssh/id_rsa.pub. 
    The key fingerprint is: ... 
    The key's randomart image is: ... 
    

    $ ssh-copy-id <user>@deneb1.epfl.ch 
    $ ssh <user>@deneb1.epfl.ch  # should now work without password
    

  • configure your personal access to the deneb-molsim computer

    $ verdi computer configure deneb-molsim
    
    Configuring computer 'deneb-molsim' for the AiiDA user '<your-aiida-user>@epfl.ch' 
    Computer deneb-molsim has transport of type ssh 
    Note: to leave a field unconfigured, leave it empty and press [Enter] 
    => username = <your-epfl-username> 
    => port = 22 
    => look_for_keys = 
    => key_filename = 
    => timeout = 60 
    => allow_agent = 
    => proxy_command = 
    => compress = True 
    => gss_auth = no 
    => gss_kex = no  
    => gss_deleg_creds = no 
    => gss_host = deneb1.epfl.ch 
    => load_system_host_keys = True 
    => key_policy = AutoAddPolicy 
    Configuration stored for your user on computer 'deneb-molsim'.
    

  • Finally, test your new computer

    $ verdi computer test deneb-molsim
    

• Compute the density, accessible volume and accessible surface area using zeo++.

  Use the zeo++ web site to figure out what the -ha, -res, -sa, -volpo command line options do.

  What is an appropriate value for the probe radius r?

  code = Code.get_from_string("zeopp@deneb-molsim") 
  calc = code.new_calc()
  
  # computational resources for calculation 
  calc.set_withmpi(False)
  calc.set_resources( {"num_machines": 1, "tot_num_mpiprocs":} )
  calc.set_max_wallclock_seconds(30*60) \# 30 minutes
  calc.set_max_memory_kb(2e6)
  
  # zeo++ command line parameters
  NetworkParameters = DataFactory('zeopp.parameters') d={
      'ha': True,
      'res': True,
      'sa': [<r (Angstrom)>, <r (Angstrom)>, 1000], 
      'volpo': [<r (Angstrom)>, <r (Angstrom)>, 1000],
  }
  parameters = NetworkParameters(dict=d)
  calc.use_parameters(parameters)
  
  # Load the cif node from the database, e.g. by PK
  # cif = load_node(<PK>)
  calc.use_structure(cif)
  
  # This places files in a subfolder "submit_test" instead of submitting.
  calc.submit_test()
  # Uncomment lines below when the script runs through
  # calc.store_all()
  # calc.submit()
  # print(calc)  # prints UUID and PK
  

Remember: Use verdi run <script.py> to run python scripts in the same environment as in the verdi shell.