ConfigurationDataContainer

class ConfigurationDataContainer(path=None, group_name=None)

Constructor for the ConfigurationDataContainer that contains the different configurations.

Parameters:

• path (str | None) – The path to the HDF5 file. If the path is None then all data will be stored in memory and no file will be written.
  Default: None

• group_name (str | None) – The name of the HDF5 group to store the data in. If the value is None then a new group will be automatically made.
  Default: None

allCoordinates()

Returns:

The Cartesian coordinates of all images. A MxNx3 array is returned where M is the number of images and N is the number of atoms per image.

Return type:

list of PhysicalQuantity of type length

calculator()

Returns:

The calculator if one is available, otherwise None.

Return type:

Calculator | None

cell(idx)

Parameters:

idx (int) – The index to return.

Returns:

The cell vectors of images with index idx or None if the trajectory length is zero or the configuration is a MoleculeConfiguration.

Return type:

PhysicalQuantity of type length | None

coordinates(idx)

Parameters:

idx (int) – The index to return.

Returns:

The Cartesian coordinates of the images or None if the trajectory length is zero.

Return type:

PhysicalQuantity of type length | None

elements(idx)

Parameters:

idx (int) – The index to return.

Returns:

The elements of the images as a list of length n or None if the trajectory length is zero.

Return type:

list of type PeriodicTableElement

forces(idx=None)

Parameters:

idx (int | None) – The index to return.

Returns:

The forces of the image. If the trajectory length is zero or the forces were not written then None is returned.

Return type:

PhysicalQuantity of type energy/length | list of PhysicalQuantity of type energy/length | None

image(image_index, set_calculator=True, set_velocities=True, ignore_cache=False)

Parameters:

• image_index (int) – The index of the configuration that should be extracted.

• set_calculator (bool) – If True, the calculator is set on the returned image. This can be disabled to increase the performance when iterating over images, because the overhead of copying and setting up a new calculator can be large.
  Default: True

• set_velocities (bool) – DEPRECATED, only kept for compatibility. The velocities are always set on the configuration.

• ignore_cache – If True, the image is not read from the cache.

Returns:

A copy of the configuration with the image_index.

Return type:

BulkConfiguration | MoleculeConfiguration

imageEnergy(idx=Ellipsis)

Parameters:

idx (int | slice) – The index or slice to return.
Default: All indices

Returns:

The potential energies of the images or None the trajectory length is zero.

Return type:

PhysicalQuantity of type energy | None

imageForces(idx=None)

Parameters:

idx (int | None) – The index to return.

Returns:

The forces of the image. If the trajectory length is zero or the forces were not written then None is returned.

Return type:

PhysicalQuantity of type energy/length | list of PhysicalQuantity of type energy/length | None

imageStress(idx=None)

Parameters:

idx (int | None) – The index to return.

Returns:

The stresses of the image. If the trajectory length is zero or the stresses were not written then None is returned. None is also returned if the configuration is a MoleculeConfiguration.

Return type:

PhysicalQuantity of type energy/length | list of PhysicalQuantity of type energy/length | None

images(set_calculator=True, set_velocities=True, ignore_cache=False)

Parameters:

• set_calculator (bool) – If True, the calculator is set on the returned image. This can be disabled to increase the performance when iterating over images, because the overhead of copying and setting up a new calculator can be large.
  Default: True.

• set_velocities (bool) – If True, the velocities are set on the returned image. This can be disabled to increase performance.
  Default: True.

Returns:

All the configurations in the trajectory.

Return type:

list of MoleculeConfiguration | BulkConfiguration | DeviceConfiguration | SurfaceConfiguration

kineticEnergies(idx=Ellipsis)

Parameters:

idx (int | slice) – The index or slice to return.
Default: All indices

Returns:

The kinetic energies of the images or None the trajectory length is zero.

Return type:

PhysicalQuantity of type energy | None

lastImage()

Returns:

The last image in the trajectory with the calculator attached.

Return type:

BulkConfiguration | MoleculeConfiguration

lastStep()

Returns:

The step number of the last step.

Return type:

int

lastTime()

Returns:

The time associated with the last step.

Return type:

PhysicalQuantity of type time

length()

Returns:

The number of images in the trajectory.

Return type:

int

masses(idx)

Parameters:

idx (int) – The index to return.

Returns:

The masses of the atoms of image with index idx with shape (num_atoms,) or None if the trajectory length is zero.

Return type:

PhysicalQuantity of type mass

measurement(name, idx=Ellipsis)

Parameters:

• name (str) – The name of the measurement.

• idx (int | slice) – The index or slice to return.
  Default: All indices

Returns:

A 2-tuple of the time and the measurement.

Return type:

tuple

measurementNames()

Returns:

The names of the measurements.

Return type:

list of type str

metatext()

Returns:

The metatext of the object or None if no metatext is set.

Return type:

str | None

nlinfo()

Returns:

The trajectory information.

Return type:

dict

nlprint(stream=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)

Write a text description of the trajectory to the stream.

Parameters:

stream (file-like object) – The stream to write to.
Default: sys.stdout

numberOfAtoms(idx)

Parameters:

idx (int) – The index to return.

Returns:

The number of atoms in the system.

Return type:

int

partialCharges(idx)

Parameters:

idx (int) – The index to return.

Returns:

The partial charges of the atoms with shape (num_atoms,) or None if the trajectory length is zero.

Return type:

PhysicalQuantity of type mass

potentialEnergies(idx=Ellipsis)

Parameters:

idx (int | slice) – The index or slice to return.
Default: All indices

Returns:

The potential energies of the images or None the trajectory length is zero.

Return type:

PhysicalQuantity of type energy | None

pressure(idx)

Parameters:

idx (int) – The index to return.

Returns:

The pressure value of the image with index idx or None if the trajectory length is zero.

Return type:

PhysicalQuantity of type pressure | None

pressureTensor(idx)

Parameters:

idx (int) – The index to return.

Returns:

The pressure tensor of the image as a vector with shape (1, 3, 3) or None if the trajectory length is zero.

Return type:

PhysicalQuantity of type pressure | None

pressures()

Returns:

The pressure values of all images as a vector with shape (m) or None if the trajectory length is zero.

Return type:

PhysicalQuantity of type pressure | None

reservoirPressures(idx=Ellipsis)

Parameters:

idx (int | slice) – The index or slice to return.
Default: All indices

Returns:

The reservoir pressure of the MD barostat. If the trajectory length is zero or this trajectory was not generated from a NPT simulation then None is returned. NaN is returned for indices for which no temperature data is available.

Return type:

PhysicalQuantity of type temperature

reservoirTemperatures(idx=Ellipsis)

Parameters:

idx (int | slice) – The index or slice to return.
Default: All indices

Returns:

The reservoir temperature of the MD thermostat. If the trajectory length is zero or this trajectory was generated from a NVE simulation then None is returned. NaN is returned for indices for which no temperature data is available.

Return type:

PhysicalQuantity of type temperature

setMetatext(text)

Set a given metatext string on the object.

Parameters:

text (str | None) – The metatext string that should be set. A value of “None” can be given to remove the current metatext.

steps(idx=Ellipsis)

Parameters:

idx (int | slice) – The index or slice to return.
Default: All indices

Returns:

The step numbers of the images or None if the trajectory length is zero.

Return type:

array of type int | None

stresses(idx=None)

Parameters:

idx (int | None) – The index to return.

Returns:

The stresses of the image. If the trajectory length is zero or the stresses were not written then None is returned. None is also returned if the configuration is a MoleculeConfiguration.

Return type:

PhysicalQuantity of type energy/length | list of PhysicalQuantity of type energy/length | None

tagData(idx)

Parameters:

idx (int) – The index to return.

Returns:

The tag data of the image or None if the trajectory length is zero or the tags are not stored in the trajectory.

Return type:

ndarray of type int | None

temperatures(idx=Ellipsis)

Parameters:

idx (int | slice) – The index to return.
Default: All indices

Returns:

The instantaneous kinetic temperatures of the images. If the trajectory length is zero or the temperatures were not written during the MolecularDynamics run then None is returned. NaN is returned for indices for which no temperature data is available.

Return type:

PhysicalQuantity of type temperature

timeInterval()

Returns:

The time interval between two images.

Return type:

PhysicalQuantity of type time

timeStep()

Returns:

The time step of the simulation.

Return type:

PhysicalQuantity of type time or None if times are not available.

times(idx=Ellipsis)

Parameters:

idx (int | slice) – The index or slice to return.
Default: All indices

Returns:

The simulation times of the images or None if the trajectory length is zero.

Return type:

PhysicalQuantity of type time | None

trajectoryInterval()

Returns:

The interval at which snapshots are saved.

Return type:

int

uniqueElements(idx=None)

Parameters:

idx (int | None) – The index to return. If None, all images are considered.

Returns:

The unique elements of the images, sorted after their atomic numbers or None if the trajectory length is zero.

Return type:

list of type PeriodicTableElement

velocities(idx)

Parameters:

idx (int) – The index to return.

Returns:

The velocities of the images. If the trajectory length is zero or the velocities were not written during the MolecularDynamics run then None is returned.

Return type:

PhysicalQuantity of type length/time

volume(idx)

Parameters:

idx (int) – The index to return.

Returns:

The volume of the unit cell of index idx. If this was a simulation of molecules, then None will be returned.

Return type:

PhysicalQuantity of type length**3 | None

volumes()

Returns:

The volume of all unit cells. If this was a simulation of molecules, then None will be returned.

Return type:

PhysicalQuantity of type length**3 | None

Notes

The MDTrajectory format is very efficient but does not support storage of heterogeneous data such as configurations with different numbers and types of atoms. The ConfigurationDataContainer format is designed to overcome this limitation. However, it does so in a more efficient way than Trajectory which stores every configuration as an individual image.