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Workflow Trajectory Properties

Purpose: Serial-workflow trajectory/configurational property subsections

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classDiagram
    class ConfigurationalProperty
    class FreeEnergyCalculations
    class Pressures
    class RadiiOfGyration
    class SerialWorkflowResults
    class Temperatures
    ConfigurationalProperty <|-- FreeEnergyCalculations
    ConfigurationalProperty <|-- Pressures
    ConfigurationalProperty <|-- RadiiOfGyration
    ConfigurationalProperty <|-- Temperatures
    SerialWorkflowResults *-- FreeEnergyCalculations : free_energy_calculations
    SerialWorkflowResults *-- Pressures : pressures
    SerialWorkflowResults *-- RadiiOfGyration : radii_of_gyration
    SerialWorkflowResults *-- Temperatures : temperatures

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inheritance (is-a)
composition (has-a)

Quantities by Key Sections

SerialWorkflowResults

Section Description MetaInfo
SerialWorkflowResults Open in MetaInfo browser

This section has no direct quantities.

ConfigurationalProperty

Section Description MetaInfo
ConfigurationalProperty Abstract base section for observables calculated and stored at each individual frame of a trajectory. Open in MetaInfo browser
Quantity Type Description
n_frames m_int32(int) Number of frames for which the observable is stored.
frames m_int32(int32) (shape: ['n_frames']) Frames for which the observable is stored.
times m_float64(float64) (shape: ['n_frames']) Times for which the observable is stored.

Temperatures

Section Description MetaInfo
Temperatures Temperature as a function of time. Open in MetaInfo browser
Quantity Type Description
value m_float64(float64) (shape: ['*']) Specifies the temperature over a series of frames/steps.

Pressures

Section Description MetaInfo
Pressures Pressure as a function of time. Open in MetaInfo browser
Quantity Type Description
value m_float64(float64) (shape: ['*']) Specifies the pressure over a series of frames/steps.

RadiiOfGyration

Section Description MetaInfo
RadiiOfGyration Section containing information about the calculation of radius of gyration (Rg). Open in MetaInfo browser
Quantity Type Description
value m_float64(float64) (shape: ['n_frames']) Values of the property.

FreeEnergyCalculations

Section Description MetaInfo
FreeEnergyCalculations Section containing information regarding the instantaneous (i.e., for a single configuration) values of free energies calculated via thermodynamic perturbation. Open in MetaInfo browser
Quantity Type Description
method_ref Reference Links the free energy results with the method parameters.
lambda_index m_int32(int) Index of the lambda state for the present simulation within the free energy calculation workflow. I.e., lambda = method_ref.lambdas.values[lambda_index]
n_states m_int32(int) Number of states defined for the interpolation of the system, as indicate in method_ref.
value_total_energy_magnitude HDF5Dataset Value of the total energy for the present lambda state. The expected dimensions are ["n_frames"]. This quantity is a reference to the data (file+path), which is stored in an HDF5 file for efficiency.
value_PV_energy_magnitude HDF5Dataset Value of the pressure-volume energy (i.e., P*V) for the present lambda state. The expected dimensions are ["n_frames"]. This quantity is a reference to the data (file+path), which is stored in an HDF5 file for efficiency.
value_total_energy_differences_magnitude HDF5Dataset
Values correspond to the difference in total energy between each specified lambd...Values correspond to the difference in total energy between each specified lambda state
and the reference state, which corresponds to the value of lambda of the current simulation.
The expected dimensions are ["n_frames", "n_states"].
This quantity is a reference to the data (file+path), which is stored in an HDF5 file for efficiency.
value_total_energy_derivative_magnitude HDF5Dataset Value of the derivative of the total energy with respect to lambda, evaluated for the current lambda state. The expected dimensions are ["n_frames"]. This quantity is a reference to the data (file+path), which is stored in an HDF5 file for efficiency.