mammoth module

This module provides the base classes for setting up a calculation with Mammoth and manage mammoth input parameters.

Mammoth

Model for Atomic Molecular Mechanics On The Hub

The Mammoth class

class mammoth.Mammoth(controls)

Mammoth class to master the Mammoth

Set up the mammoth to run the desired calculations

Parameters:controls (MammothControls) – The MammothConrols object that contains all the control parameters

main()

Run the FF calculation

setup_molecule()

Setup a the molecule object from a QM results

The MammothControls class

class mammoth.MammothControls(*args, **kwargs)

A convenient container of all Mammoth control paramters

classmethod default_parameters()

All default parameters as a dict that can be used to set up a MammothConrols object. The filename is empty.

classmethod from_file(inputfile='input.mmt', encoding='utf8')

read in inputfile and load all parameters in a new instance

get_md_params()

return a dict with the needed parameters for the MD run

get_qm2ff_params()

return a dict with the needed parameters for the QM2FF class

update([E, ]**F) → None. Update D from dict/iterable E and F.

If E is present and has a .keys() method, then does: for k in E: D[k] = E[k] If E is present and lacks a .keys() method, then does: for k, v in E: D[k] = v In either case, this is followed by: for k in F: D[k] = F[k]