A general purpose classical simulation package that can be used for the simulation of molecules in gases, fluids, zeolites, aluminosilicates, metal-organic frameworks, carbon nanotubes and external fields.
Like any other software library, RASPA2 should be installed through a package manager. This can be done through pip.
pip install RASPA2
There are currently two ways to use RASPA: through configuration files in the command line, or through Python functions.
This approach uses RASPA script files and a set of directories to load structures, gases, and forcefield files. It outputs a set of folders and files which contain data about the simulation run. This is the original designed use of RASPA, and can be used in conjunction with shell scripts for small sets of long-running simulations. To see the help, type:
To write and configure simulation input files, read Docs/raspa.pdf.
The previous approach is useful for long-running jobs, but can become cumbersome when you want to manage a large number of simulations. In this use case, the Python wrapper provides a streamlined workflow.
RASPA’s full functionality can be accessed in a Python script, which enables simulation runs to be “glued” together with auxiliary workflow steps. For example, to run a set of simulations across a logarithmic range of pressures, parse the outputs for uptake data, and plot the results, use:
import RASPA2 # Set up gas = "CO2" pressures = [1e4 * 10**(0.1 * i) for i in range(21)] # Run results = [RASPA2.run(my_structure, gas, temperature=298, pressure=pressure) for pressure in pressures] # Parse uptakes = [r["Number of molecules"][gas] ["Average loading absolute [cm^3 (STP)/cm^3 framework]"] for r in results] # Plot plot(pressures, uptakes)
When used in conjunction with supercomputer interfaces such as the IPython Notebook and chemical data handling libraries such as open babel, it is possible to completely automate job distribution, cif formatting, charge estimation, and more in a single script.
For more examples, read the workflow wiki.
In order to edit the RASPA forcefields, you need to access the associated .def
files. The current path of the .def files can be discovered by typing
raspa-dir into a terminal. In order to change your terminal directory to
this, you can chain commands:
Edit the files here, and then re-run your simulations. If you make any improvements to the existing force fields, molecules, or structures, you should consider contributing them back to RASPA by issuing a pull request.