Atom Generation

Generate Atoms

nufeb_tools.generate_atom.clean()

Remove old NUFEB runs

nufeb_tools.generate_atom.main(args)

Wrapper function to generate new NUFEB simulation conditions

Parameters

args (List[str]) – command line parameters as list of strings

nufeb_tools.generate_atom.parse_args(args)

Parse command line parameters

Parameters

args (List[str]) – command line parameters as list of strings (for example ["--help"]).

Returns

command line parameters namespace

Return type

argparse.Namespace

nufeb_tools.generate_atom.run()

Calls main() passing the CLI arguments extracted from sys.argv

This function can be used as entry point to create console scripts with setuptools.

nufeb_tools.generate_atom.setup_logging(loglevel)

Setup basic logging

Parameters

loglevel (int) – minimum loglevel for emitting messages

Generate Atoms (development version)

This is a script to seed NUFEB simulations

class nufeb_tools.generate_atom_dev.Cell(Species, Group, idx, args, Info={'cyano': {'Decay': 0, 'Density': 370, 'Diameter': 1e-06, 'GrowthRate': 1.67e-05, 'Inertia': {'ixx': 0, 'ixy': 0, 'ixz': 0, 'iyy': 0, 'iyz': 0, 'izz': 9.2e-23}, 'K_s': {'co2': 0.000138, 'light': 0.00035, 'o2': 0.0002, 'suc': 0.01}, 'Maintenance': 0, 'Yield': 0.55, 'max_length': 5e-06, 'min_length': 1e-06}, 'ecw': {'Decay': 2e-05, 'Density': 236, 'Diameter': 7.3e-07, 'GrowthRate': 0.00027, 'Inertia': {'ixx': 0, 'ixy': 0, 'ixz': 0, 'iyy': 0, 'iyz': 0, 'izz': 9.2e-23}, 'K_s': {'co2': 0.05, 'light': 0, 'o2': 0.001, 'suc': 3.6}, 'Maintenance': 9.5e-07, 'Yield': 0.43, 'max_length': 2.72e-06, 'min_length': 1.94e-06}})

Bacteria object class

Atom()

Function to return atom (cell) positions to render atom.in file

Bacillus()

Function to return rod shape (bacillus) parameters to render atom.in file

Check()

Return cell position, orientation, and size

Report()

Return cell position, orientation, and size

rotate(z_dim=False)

Randomly generate cell orientation displacements based on input angle

class nufeb_tools.generate_atom_dev.Culture(args)

Create a collection of cells with defined positions, lengths, and orientations

Check()

Check initial positions of each cell and move one of them if there is a collision

class nufeb_tools.generate_atom_dev.Nutrient(c, d, mw, state, bc)

Nutrient class to define the chemicals present in the simulation volume, their concentrations, and their properties

nufeb_tools.generate_atom_dev.main(args)

Wrapper function to generate new NUFEB simulation conditions

Parameters

args (List[str]) – command line parameters as list of strings

nufeb_tools.generate_atom_dev.parse_args(args)

Parse command line parameters

Parameters

args (List[str]) – command line parameters as list of strings (for example ["--help"]).

Returns

command line parameters namespace

Return type

argparse.Namespace

nufeb_tools.generate_atom_dev.run()

Calls main() passing the CLI arguments extracted from sys.argv

This function can be used as entry point to create console scripts with setuptools.

nufeb_tools.generate_atom_dev.setup_logging(loglevel)

Setup basic logging

Parameters

loglevel (int) – minimum loglevel for emitting messages