XYZ trajectory files

class XYZTrajectoryFile(filename, mode='r', fileobject=None, ntap=None)

Class representing an XYZ file containing a molecular trajectory

An instance of this class has the following attributes:

• file_object – A Python file object, referring to the actual XYZ file

• position – The frame to which the cursor is currently pointing in the XYZ file

• mode – Designates whether the file is in read or write mode (‘r’ or ‘w’)

• ntap – The number of atoms in the molecular system (needs to be constant throughout)

• elements – The elements of the atoms in the system (needs to be constant throughout)

An XYZTrajectoryFile object behaves very similar to a regular file object. It has read and write methods (read_next() and write_next()) that read and write from/to the position of the cursor in the file_object attribute. If the file is in read mode, an additional method read_frame() can be used that moves the cursor to any frame in the file and reads from there. The amount of information stored in memory is kept to a minimum, as only information from the current frame is ever stored.

Reading and writing to and from the files can be done as follows:

>>> from scm.plams import XYZTrajectoryFile

>>> xyz = XYZTrajectoryFile('old.xyz')
>>> mol = xyz.get_plamsmol()

>>> xyzout = XYZTrajectoryFile('new.xyz',mode='w')

>>> for i in range(xyz.get_length()) :
>>>     crd,cell = xyz.read_frame(i,molecule=mol)
>>>     xyzout.write_next(molecule=mol)

The above script reads information from the XYZ file old.xyz into the Molecule object mol in a step-by-step manner. The Molecule object is then passed to the write_next() method of the new XYZTrajectoryFile object corresponding to the new xyz file new.xyz.

The exact same result can also be achieved by iterating over the instance as a callable

>>> xyz = XYZTrajectoryFile('old.xyz')
>>> mol = xyz.get_plamsmol()

>>> xyzout = XYZTrajectoryFile('new.xyz',mode='w')

>>> for crd,cell in xyz(mol) :
>>>     xyzout.write_next(molecule=mol)

This procedure requires all coordinate information to be passed to and from the Molecule object for each frame, which can be time-consuming. It is therefore also possible to bypass the Molecule object when reading through the frames:

>>> xyz = XYZTrajectoryFile('old.xyz')

>>> xyzout = XYZTrajectoryFile('new.xyz',mode='w')
>>> xyzout.set_elements(xyz.get_elements())

>>> for crd,cell in xyz :
>>>     xyzout.write_next(coords=crd)
>>> xyzout.close()

By default the write mode will create a minimal version of the XYZ file, containing only elements and coordinates. Additional information can be written to the file by supplying additional arguments to the write_next() method. The additional keywords step and energy trigger the writing of a remark containing the molecule name, the step number, the energy, and the lattice vectors.

>>> mol = Molecule('singleframe.xyz')

>>> xyzout = XYZTrajectoryFile('new.xyz',mode='w')
>>> xyzout.set_name('MyMol')

>>> xyzout.write_next(molecule=mol, step=0, energy=5.)

__init__(filename, mode='r', fileobject=None, ntap=None)

Initiates an XYZTrajectoryFile object

• filename – The path to the XYZ file

• mode – The mode in which to open the XYZ file (‘r’ or ‘w’)

• fileobject – Optionally, a file object can be passed instead (filename needs to be set to None)

• ntap – If the file is in write mode, the number of atoms needs to be passed here

store_historydata()

Additional data should be read from/written to file

set_name(name)

Sets the name of the system, in case an extensive write is requested

• name – A string containing the name of the molecule

read_next(molecule=None, read=True)

Reads coordinates from the current position of the cursor and returns it

• molecule – Molecule object in which the new coordinates need to be stored

• read – If set to False the cursor will move to the next frame without reading

write_next(coords=None, molecule=None, cell=[0.0, 0.0, 0.0], conect=None, historydata=None)

Write frame to next position in trajectory file

• coords – A list or numpy array of (ntap,3) containing the system coordinates

• molecule – A molecule object to read the molecular data from

• cell – A set of lattice vectors or cell diameters

• conect – A dictionary containing connectivity info (not used)

• historydata – A dictionary containing additional variables to be written to the comment line

The historydata dictionary can contain for example: (‘Step’,’Energy’), the frame number and the energy respectively

Note

Either coords or molecule are mandatory arguments

__call__(molecule=None, read=True)

Magic method that makes an instance of this class into a callable

_move_cursor_to_append_pos()

Get file ready to append

close()

Close the file

property connection_table

Symmetrize the connection table and remove bond orders

get_elements()

Get the elements attribute

get_length()

Get the number of frames in the file

get_plamsmol()

Extracts a PLAMS molecule object from the XYZ trajectory file

property molecule

Returns the current molecule, which exists only when the object is used as an iterator

read_frame(frame, molecule=None)

Reads the relevant info from frame frame and returns it, or stores it in molecule

• frame – The frame number to be read from the file

• molecule – Molecule object in which the new coordinates need to be stored

read_last_frame(molecule=None)

Reads the last frame from the file

rewind(nframes=None)

Rewind the file either by nframes or to the first frame

• nframes – The number of frames to rewind

set_elements(elements)

Sets the elements attribute (needed in write mode).

• elements – A list containing the element symbol of each atom

XYZ history files

This subsection describes the API of the XYZHistoryFile class, which can read and write the results from simulations with changing numbers of atoms. The majority of molecular simulations explore a subspace of the canonical, micro-canonical, or isothermal-isobaric ensembles, in which the number of atoms \(N\) remains constant. However, a Grand Canonical Monte Carlo simulation is one of the exceptions in which the number of atoms in the system does change. The XYZTrajectoryFile object cannot read and write the resulting simulation history, and the derived class XYZHistoryFile was developed to handle these atypical trajectories. While the methods in this class will be slower than the ones in the parent class, the API is nearly identical. The only exception is the write_next() method, which has an additional argument elements.

class XYZHistoryFile(filename, mode='r', fileobject=None, ntap=None)

Class representing an XYZ file containing a molecular simulation history with varying numbers of atoms

An instance of this class has the following attributes:

• file_object – A Python file object, referring to the actual XYZ file

• position – The frame to which the cursor is currently pointing in the XYZ file

• mode – Designates whether the file is in read or write mode (‘r’ or ‘w’)

• elements – The elements of the atoms in the system at the current frame

An XYZHistoryFile object behaves very similar to a regular file object. It has read and write methods (read_next() and write_next()) that read and write from/to the position of the cursor in the file_object attribute. If the file is in read mode, an additional method read_frame() can be used that moves the cursor to any frame in the file and reads from there. The amount of information stored in memory is kept to a minimum, as only information from the current frame is ever stored.

Reading and writing to and from the files can be done as follows:

>>> from scm.plams import XYZHistoryFile

>>> xyz = XYZHistoryFile('old.xyz')
>>> mol = xyz.get_plamsmol()

>>> xyzout = XYZHistoryFile('new.xyz',mode='w')

>>> for i in range(xyz.get_length()) :
>>>     crd,cell = xyz.read_frame(i,molecule=mol)
>>>     xyzout.write_next(molecule=mol)

The above script reads information from the XYZ file old.xyz into the Molecule object mol in a step-by-step manner. The Molecule object is then passed to the write_next() method of the new XYZHistoryFile object corresponding to the new xyz file new.xyz.

The exact same result can also be achieved by iterating over the instance as a callable

>>> xyz = XYZHistoryFile('old.xyz')
>>> mol = xyz.get_plamsmol()

>>> xyzout = XYZHistoryFile('new.xyz',mode='w')

>>> for crd,cell in xyz(mol) :
>>>     xyzout.write_next(molecule=mol)

This procedure requires all coordinate information to be passed to and from the Molecule object for each frame, which can be time-consuming. It is therefore also possible to bypass the Molecule object when reading through the frames:

>>> xyz = XYZHistoryFile('old.xyz')

>>> xyzout = XYZHistoryFile('new.xyz',mode='w')

>>> for crd,cell in xyz :
>>>     xyzout.write_next(coords=crd,elements=xyz.elements)

By default the write mode will create a minimal version of the XYZ file, containing only elements and coordinates. Additional information can be written to the file by supplying additional arguments to the write_next() method. The additional keywords step and energy trigger the writing of a remark containing the molecule name, the step number, the energy, and the lattice vectors.

>>> mol = Molecule('singleframe.xyz')

>>> xyzout = XYZHistoryFile('new.xyz',mode='w')
>>> xyzout.set_name('MyMol')

>>> xyzout.write_next(molecule=mol, step=0, energy=5.)

__init__(filename, mode='r', fileobject=None, ntap=None)

Initiates an XYZHistoryFile object

• filename – The path to the XYZ file

• mode – The mode in which to open the XYZ file (‘r’ or ‘w’)

• fileobject – Optionally, a file object can be passed instead (filename needs to be set to None)

• ntap – If the file is in write mode, the number of atoms can be passed here

write_next(coords=None, molecule=None, elements=None, cell=[0.0, 0.0, 0.0], conect=None, historydata=None)

Write frame to next position in trajectory file

• coords – A list or numpy array of (ntap,3) containing the system coordinates

• molecule – A molecule object to read the molecular data from

• elements – The element symbols of the atoms in the system

• cell – A set of lattice vectors or cell diameters

• energy – An energy value to be written to the remark line

• conect – A dictionary containing connectivity info (not used)

• historydata – A dictionary containing additional variables to be written to the comment line

The historydata dictionary can contain for example: (‘Step’,’Energy’), the frame number and the energy respectively

Note

Either coords and elements or molecule are mandatory arguments