amep.base.BaseFrame#

class amep.base.BaseFrame(reader, index)#

Bases: object

Per particle simulation data at one time step (a single frame).

__init__(reader, index)#

Basic data frame containing simulation data of particle-based simulations for one time step.

Parameters:

reader – AMEP reader object.
index (int) – Frame index.

Return type:

None.

Methods

`__init__`(reader, index)	Basic data frame containing simulation data of particle-based simulations for one time step.
`add_data`(key, data)	Adds new data to the frame.
`angmom`(**kwargs)	Returns the angular momentum of all particles or of all particles of a specific type.
`coords`(**kwargs)	All coordinates of all particles or of all particles of a specific particle type.
`data`(*args[, ptype, zerofill, return_keys])	Returns the entire data frame for all particles or for all particles of a specific particle type.
`density`([ptype])	Returns the number density.
`forces`(**kwargs)	Returns the forces acting on each particle or on particles of a specific particle type.
`ids`(**kwargs)	Returns the particle indices of all particles or of all particles of a specific particle type.
`mass`(**kwargs)	Returns the mass of all particles or of all particles of a specific type.
`n`([ptype])	Total number of particles.
`nojump_coords`(**kwargs)	Returns the nojump coordinates of all particles or of all particles of a specific particle type.
`omegas`(**kwargs)	Returns the angular velocities of all particles or of all particles of a specific particle type.
`orientations`(**kwargs)	Returns the orientation vectors of all particles or of all particles of a specific particle type.
`radius`(**kwargs)	Returns the radius of all particles or of all particles of a specific type.
`torque`(**kwargs)	Returns the torque acting on each particle or on each particle of a specific particle type.
`types`(**kwargs)	Returns the particle type of each or of each particle of a specific type.
`unwrapped_coords`(**kwargs)	Returns the unwrapped coordinates of all particles or of all particles of a specific particle type.
`velocities`(**kwargs)	Returns the velocities of all particles or of all particles of a specific particle type.

Attributes

`box`	Box boundary.
`center`	Center of the simulation box.
`dim`	Spatial dimension of the simnulation.
`keys`	Returns a list of all available data keys.
`ptypes`	Array of all particle types.
`step`	Time step of the frame.
`time`	The physical time of the frame.
`volume`	Returns the volume (for self.__dim=3) / area (for self.__dim=2) of the simulation box.

add_data(key: str, data: ndarray) → None#

Adds new data to the frame.

Parameters:

key (str) – Name of the data.
data (np.ndarray) – Data array of shape (N,x) with N being the total number of particles.

Return type:

None.

angmom(**kwargs) → ndarray#

Returns the angular momentum of all particles or of all particles of a specific type.

Parameters:: ptype (int, optional) – Particle type. The default is None.
Returns:: Array of particle angular momenta.
Return type:: np.ndarray

property box#: Box boundary.

property center#

Center of the simulation box.

Returns:: x – Center of the simulation box.
Return type:: np.ndarray

coords(**kwargs)#

All coordinates of all particles or of all particles of a specific particle type.

Parameters:: ptype (int, optional) – Particle type. The default is None.
Returns:: Coordinate frame of particle coordinates.
Return type:: np.ndarray

data(*args, ptype: int | None = None, zerofill: bool = False, return_keys: bool = False) → tuple[list, ndarray]#

Returns the entire data frame for all particles or for all particles of a specific particle type.

Notes

One can use _one_ wildcard character asterisk (“*”) to load all data sets matching that name. For example, “name*” returns all datasets that start with “name”, “value[*]” returns all datasets with any number of characters in between the square brackets i.e. “value[1]”, “value[2]”, …, “value[any text with any length]”.

Parameters:

*args (str) – Parameter keys. One wildcard character asterisk can be used, see note above.
ptype (int | list, optional) – Particle type. Is internally converted to a list and all matching ptypes are returned. The default is None.
zerofill (bool, optional) – If True, empty strings are replaced by a column of zeros in the returned data array. The default is False.
returnkeys (bool, optional) – If True, a list of the data keys is returned together with the data. The default is False.

Returns:

datakeys (list) – List of str containing the column keys/names. This is only returned if returnkeys=True.
data (np.ndarray) – Data array of shape (N, len(keys)).

density(ptype=None)#: Returns the number density.

property dim#

Spatial dimension of the simnulation.

Returns:: x – Spatial dimension.
Return type:: int

forces(**kwargs) → ndarray#

Returns the forces acting on each particle or on particles of a specific particle type.

Parameters:: ptype (int, optional) – Particle type. The default is None.
Returns:: Coordinate frame of particle forces.
Return type:: np.ndarray

ids(**kwargs) → ndarray#

Returns the particle indices of all particles or of all particles of a specific particle type.

Parameters:: ptype (int, optional) – Particle type. The default is None.
Returns:: Particle indices.
Return type:: np.ndarray

property keys: list#

Returns a list of all available data keys.

Returns:: datakeys – List of str containing all available data keys.
Return type:: list

mass(**kwargs) → ndarray#

Returns the mass of all particles or of all particles of a specific type.

Parameters:: ptype (int, optional) – Particle type. The default is None.
Returns:: Array of particle masses.
Return type:: np.ndarray

n(ptype=None)#

Total number of particles.

Parameters:: ptype (int, optional) – Particle type. The default is None (all particles).
Returns:: Total particle number of the given particle type.
Return type:: int

nojump_coords(**kwargs)#

Returns the nojump coordinates of all particles or of all particles of a specific particle type. These coordinates are only available, when the nojump method of the trajectory which contains the frames was called.

Parameters:: ptype (int, optional) – Particle type. The default is None.
Returns:: Coordinate frame of particle coordinates.
Return type:: np.ndarray

omegas(**kwargs) → ndarray#

Returns the angular velocities of all particles or of all particles of a specific particle type.

Parameters:: ptype (int, optional) – Particle type. The default is None.
Returns:: Coordinate frame of particle angular velocity vectors.
Return type:: np.ndarray

orientations(**kwargs) → ndarray#

Returns the orientation vectors of all particles or of all particles of a specific particle type.

Parameters:: ptype (int, optional) – Particle type. The default is None.
Returns:: Coordinate frame of particle orientation vectors.
Return type:: np.ndarray

property ptypes#: Array of all particle types.

radius(**kwargs) → ndarray#

Returns the radius of all particles or of all particles of a specific type.

Parameters:: ptype (int, optional) – Particle type. The default is None.
Returns:: Array of particle radii.
Return type:: np.ndarray

property step#

Time step of the frame.

Returns:: Time step of the frames.
Return type:: int

property time: float#: The physical time of the frame.

torque(**kwargs) → ndarray#

Returns the torque acting on each particle or on each particle of a specific particle type.

Parameters:: ptype (int, optional) – Particle type. The default is None.
Returns:: Coordinate frame of particle torque vectors.
Return type:: np.ndarray

types(**kwargs) → ndarray#

Returns the particle type of each or of each particle of a specific type.

Parameters:: ptype (int, optional) – Particle type. The default is None.
Returns:: Array of particle types.
Return type:: np.ndarray

unwrapped_coords(**kwargs) → ndarray#

Returns the unwrapped coordinates of all particles or of all particles of a specific particle type.

Parameters:: ptype (int, optional) – Particle type. The default is None.
Returns:: Coordinate frame of unwrapped particle coordinates.
Return type:: np.ndarray

velocities(**kwargs) → ndarray#

Returns the velocities of all particles or of all particles of a specific particle type.

Parameters:: ptype (int, optional) – Particle type. The default is None.
Returns:: Coordinate frame of particle velocities.
Return type:: np.ndarray

property volume#: Returns the volume (for self.__dim=3) / area (for self.__dim=2) of the simulation box.