janus

driver

This is the qmmm driver module

janus.driver.run_janus(filename='input.json')

Drives the janus program. Creates an instance of the Initializer class and feeds wrappers to either run_simulation() or run_single_point()

Parameters:filename (str) – Filename from which to read input parameters
janus.driver.run_simulation(md_sim_wrapper, qmmm_wrapper)

Drives QM/MM with MD time step integration

Parameters:
  • md_sim_wrapper (MMWrapper) – A child class of MMWrapper that drives MD simulation
  • qmmm_wrapper (QMMM) – A QMMM or AQMMM wrapper that drives the QM/MM computations
janus.driver.run_single_point(ll_wrapper, qmmm_wrapper)

Drives single QM/MM computation

Parameters:
  • ll_wrapper (MMWrapper) – A child class of MMWrapper that contains MM information on the whole system
  • qmmm_wrapper (QMMM) – A QMMM or AQMMM wrapper that drives the QM/MM computations

system

class janus.system.System(qm_indices, qm_residues, run_ID, partition_ID='qm')

Bases: object

A class that stores system information. Holds information such as energy, forces, and positions for a QM/MM partition. Stores qmmm and aqmmm information as well.

Parameters:
  • indices (qm) – indices of the atoms of the QM region
  • run_ID (int) – the current step of the MD simulation
  • partition_ID – An identifier for the specfic partition in aqmmm computations, default is ‘qm’
compute_scale_factor_g(mm, link)

Computes scale factor g for link atom, RC, and RCD schemes. The equation used to compute g is:

rac{R_{qm} + R_{link}}{R_{qm} + R_{mm}}

where R is the pyykko covalent radius of an atom.

qm : str
element symbol of the QM atom involved in broken bond
mm : str
element symbol of the MM atom involved in broken bond
link : str
element symbol for link atom
float
g, the scaling factor
>>> compute_scale_factor_g('C', 'C', 'H')
class janus.system.Buffer(ID)

Bases: object

A class to store information for buffer groups from aqmmm computations. This includes the atom indicies contained in the buffer group, the switching function, COM coordinates, etc.

Parameters:ID – the identifer for the buffer group

Initializer

class janus.initializer.Initializer(parameters, as_file=True)

Bases: object

Class that initializes the initial parameters and necessary wrapppers.

Parameters:
  • paramaters (str) – filename of a json input file; if as_file is False, param is a dict
  • as_file – param is a file if True, dict if False
get_wrappers()

Determines what type of wrapper object to instantiate based on input parameters

initialize_wrappers()

Instantiates wrapper objects based on input parameters. Create instances of appropriate wrappers for low and high level computations, QM/MM or adaptive QM/MM computations, as well as MD simulations.

Returns:
load_param(fname)

Converts a json file into a dictionary

Parameters:fname (str) – name of json file
Returns:parameters contained in filename
Return type:dict
set_attributes(dictionary, obj)

Sets values in the dicionary to be an attribute of the object given. The key of the dictionary will be set as an attribute of the object given.

Parameters:
  • dictionary (dict) – Dictionary with relevant parameters
  • obj (obj) – Object to have attributes set to.
Returns:
Return type:

None

Examples

>>> set_attributes({'aqmmm' : False}, self)

This sets self.aqmmm to be False.