7.20. TRZ trajectory I/O — MDAnalysis.coordinates.TRZ
¶
7.20.1. Classes¶
-
class
MDAnalysis.coordinates.TRZ.
Timestep
(n_atoms, **kwargs)[source]¶ TRZ custom Timestep
Create a Timestep, representing a frame of a trajectory
Parameters: - n_atoms (int) – The total number of atoms this Timestep describes
- positions (bool, optional) – Whether this Timestep has position information [
True
] - velocities (bool (optional)) – Whether this Timestep has velocity information [
False
] - forces (bool (optional)) – Whether this Timestep has force information [
False
] - reader (Reader (optional)) – A weak reference to the owning Reader. Used for when attributes require trajectory manipulation (e.g. dt)
- dt (float (optional)) – The time difference between frames (ps). If
time
is set, then dt will be ignored. - time_offset (float (optional)) – The starting time from which to calculate time (in ps)
Changed in version 0.11.0: Added keywords for positions, velocities and forces. Can add and remove position/velocity/force information by using the
has_*
attribute.-
frame
¶ Index of current frame number (0 based)
-
time
¶ Current system time in ps
-
n_atoms
¶ Number of atoms in the frame (will be constant throughout trajectory)
-
pressure
¶ System pressure in pascals
-
pressure_tensor
¶ Array containing pressure tensors in order: xx, xy, yy, xz, yz, zz
-
total_energy
¶ Hamiltonian for the system in kJ/mol
-
potential_energy
¶ Potential energy of the system in kJ/mol
-
kinetic_energy
¶ Kinetic energy of the system in kJ/mol
-
temperature
¶ Temperature of the system in Kelvin
-
dimensions
¶ Unit cell dimensions
[A,B,C,alpha,beta,gamma]
.
-
class
MDAnalysis.coordinates.TRZ.
TRZReader
(trzfilename, n_atoms=None, **kwargs)[source]¶ Reads an IBIsCO or YASP trajectory file
Note
Binary TRZ trajectories are always assumed to be written in little-endian byte order and are read as such.
Changed in version 0.11.0: Frames now 0-based instead of 1-based. Extra data (Temperature, Energies, Pressures, etc) now read into ts.data dictionary. Now passes a weakref of self to ts (ts._reader).
Creates a TRZ Reader
Parameters: -
Writer
(filename, n_atoms=None)[source]¶ A trajectory writer with the same properties as this trajectory.
-
delta
¶ MD integration timestep
-
n_atoms
¶ Number of atoms in a frame
-
n_frames
¶ Total number of frames in a trajectory
-
skip_timestep
¶ Timesteps between trajectory frames
-
-
class
MDAnalysis.coordinates.TRZ.
TRZWriter
(filename, n_atoms, title='TRZ', convert_units=None)[source]¶ Writes a TRZ format trajectory.
Note
Binary TRZ trajectories are always written in little-endian byte order.
Create a TRZWriter
Parameters: - filename (str) – name of output file
- n_atoms (int) – number of atoms in trajectory
- title (str (optional)) – title of the trajectory; the title must be 80 characters or shorter, a longer title raises a ValueError exception.
- convert_units (bool (optional)) – units are converted to the MDAnalysis base format;
None
selects the value ofMDAnalysis.core.flags
[‘convert_lengths’]. (see Flags)
-
class
MDAnalysis.coordinates.TRZ.
TRZReader
(trzfilename, n_atoms=None, **kwargs)[source] Reads an IBIsCO or YASP trajectory file
-
ts
TRZ.Timestep –
Timestep
object containing coordinates of current frame
Note
Binary TRZ trajectories are always assumed to be written in little-endian byte order and are read as such.
Changed in version 0.11.0: Frames now 0-based instead of 1-based. Extra data (Temperature, Energies, Pressures, etc) now read into ts.data dictionary. Now passes a weakref of self to ts (ts._reader).
Creates a TRZ Reader
Parameters: -
Writer
(filename, n_atoms=None)[source] A trajectory writer with the same properties as this trajectory.
-
close
()[source] Close trz file if it was open
-
delta
MD integration timestep
-
n_atoms
Number of atoms in a frame
-
n_frames
Total number of frames in a trajectory
-
open_trajectory
()[source] Open the trajectory file
-
skip_timestep
Timesteps between trajectory frames
-
-
class
MDAnalysis.coordinates.TRZ.
TRZWriter
(filename, n_atoms, title='TRZ', convert_units=None)[source] Writes a TRZ format trajectory.
Note
Binary TRZ trajectories are always written in little-endian byte order.
Create a TRZWriter
Parameters: - filename (str) – name of output file
- n_atoms (int) – number of atoms in trajectory
- title (str (optional)) – title of the trajectory; the title must be 80 characters or shorter, a longer title raises a ValueError exception.
- convert_units (bool (optional)) – units are converted to the MDAnalysis base format;
None
selects the value ofMDAnalysis.core.flags
[‘convert_lengths’]. (see Flags)
-
close
()[source] Close if it was open
-
class
MDAnalysis.coordinates.TRZ.
Timestep
(n_atoms, **kwargs)[source] TRZ custom Timestep
Create a Timestep, representing a frame of a trajectory
Parameters: - n_atoms (int) – The total number of atoms this Timestep describes
- positions (bool, optional) – Whether this Timestep has position information [
True
] - velocities (bool (optional)) – Whether this Timestep has velocity information [
False
] - forces (bool (optional)) – Whether this Timestep has force information [
False
] - reader (Reader (optional)) – A weak reference to the owning Reader. Used for when attributes require trajectory manipulation (e.g. dt)
- dt (float (optional)) – The time difference between frames (ps). If
time
is set, then dt will be ignored. - time_offset (float (optional)) – The starting time from which to calculate time (in ps)
Changed in version 0.11.0: Added keywords for positions, velocities and forces. Can add and remove position/velocity/force information by using the
has_*
attribute.-
dimensions
Unit cell dimensions
[A,B,C,alpha,beta,gamma]
.