mdadash.backend.analyses.energies

Widgets for various simulation energies

Classes

AbsoluteTemperature()	Absolute Temperature
AnglesEnergy()	Angles Energy
BondsEnergy()	Bonds Energy
CoulombInteractionEnergy()	Coulomb Interaction Energy
DihedralsEnergy()	Dihedrals Energy
EnergyWidgetBase()	Base class for Energy Widgets
ImproperDihedralsEnergy()	Improper Dihedrals Energy
PotentialEnergy()	Potential energy
TotalEnergy()	Total Energy
VanDerWaalsEnergy()	Van Der Waals Energy

class mdadash.backend.analyses.energies.AbsoluteTemperature

Bases: EnergyWidgetBase, WidgetBase

Absolute Temperature

See EnergyWidgetBase for more details.

data_key = 'temperature'

description = 'Plot of Absolute Temperature'

name = 'Absolute Temperature'

y_label = 'Temperature ( K )'

class mdadash.backend.analyses.energies.AnglesEnergy

Bases: EnergyWidgetBase, WidgetBase

Angles Energy

See EnergyWidgetBase for more details.

data_key = 'angles_energy'

description = 'Plot of Angles Energy'

name = 'Angles Energy'

class mdadash.backend.analyses.energies.BondsEnergy

Bases: EnergyWidgetBase, WidgetBase

Bonds Energy

See EnergyWidgetBase for more details.

data_key = 'bonds_energy'

description = 'Plot of Bonds Energy'

name = 'Bonds Energy'

class mdadash.backend.analyses.energies.CoulombInteractionEnergy

Bases: EnergyWidgetBase, WidgetBase

Coulomb Interaction Energy

See EnergyWidgetBase for more details.

data_key = 'coulomb_energy'

description = 'Plot of Coulomb Interaction Energy'

name = 'Coulomb Interaction Energy'

class mdadash.backend.analyses.energies.DihedralsEnergy

Bases: EnergyWidgetBase, WidgetBase

Dihedrals Energy

See EnergyWidgetBase for more details.

data_key = 'dihedrals_energy'

description = 'Plot of Dihedrals Energy'

name = 'Dihedrals Energy'

class mdadash.backend.analyses.energies.EnergyWidgetBase

Bases: object

Base class for Energy Widgets

This is the base class for all Energy widgets.

Energy values are extracted from MDAnalysis.coordinates.timestep.Timestep.data.

The following keys are used for their respective plots:

• temperature - Absolute Temperature

• total_energy - Total Energy

• potential_energy - Potential Energy

• coulomb_energy - Coulomb Interaction Energy

• bonds_energy - Bonds Energy

• angles_energy - Angles Energy

• dihedrals_energy - Dihedrals Energy

• improper_dihedrals_energy - Improper Dihedrals Energy

• van_der_walls_energy - Van Der Waals Energy

Note

Energies are only available in the timestep data for streaming trajectories. The simulation engine must also be explicitly configured to send them

Inputs

Max values

Max values to show in plot

Default: 100

Title

Title for the plot

Default: ‘’

X-axis

X-axis value - time or step

Default: time

Outputs

Here is an example output plot of the Absolute Temperature widget:

Here is an example output plot of the Total Energy widget:

data_key = ''

name = ''

on_input_change(attribute, _old_value, new_value)

on_input_change handler

on_post_create()

on_post_create handler

run_every_frame()

every-frame run handler

y_label = 'Energy ( kJ / mol )'

class mdadash.backend.analyses.energies.ImproperDihedralsEnergy

Bases: EnergyWidgetBase, WidgetBase

Improper Dihedrals Energy

See EnergyWidgetBase for more details.

data_key = 'improper_dihedrals_energy'

description = 'Plot of Improper Dihedrals Energy'

name = 'Improper Dihedrals Energy'

class mdadash.backend.analyses.energies.PotentialEnergy

Bases: EnergyWidgetBase, WidgetBase

Potential energy

See EnergyWidgetBase for more details.

data_key = 'potential_energy'

description = 'Plot of Potential Energy'

name = 'Potential energy'

class mdadash.backend.analyses.energies.TotalEnergy

Bases: EnergyWidgetBase, WidgetBase

Total Energy

See EnergyWidgetBase for more details.

data_key = 'total_energy'

description = 'Plot of Total Energy'

name = 'Total Energy'

class mdadash.backend.analyses.energies.VanDerWaalsEnergy

Bases: EnergyWidgetBase, WidgetBase

Van Der Waals Energy

See EnergyWidgetBase for more details.

data_key = 'van_der_walls_energy'

description = 'Plot of Van Der Waals Energy'

name = 'Van Der Waals Energy'