6.23. FHI-AIMS file format — MDAnalysis.coordinates.FHIAIMS

Classes to read and write FHI-AIMS coordinate files.

The cell vectors are specified by the (optional) lines with the lattice_vector tag:

lattice_vector x  y  z

where x, y, and z are expressed in ångström (Å).

Note

In the original FHI-AIMS format, up to three lines with lattice_vector are allowed (order matters) where the absent line implies no periodicity in that direction. In MDAnalysis, only the case of no lattice_vector or three lattice_vector lines are allowed.

Atomic positions and names are specified either by the atom or by the atom_frac tags:

atom           x  y  z  name
atom_frac      nx ny nz name

where x, y, and z are expressed in ångström, and nx, ny and nz are real numbers in [0, 1] and are used to compute the atomic positions in units of the basic cell.

Atomic velocities can be added on the line right after the corresponding atom in units of Å/ps using the velocity tag:

velocity      vx vy vz

The field name is a string identifying the atomic species. See also the specifications in the official FHI-AIMS format.

6.23.1. Classes

class MDAnalysis.coordinates.FHIAIMS.Timestep(n_atoms, **kwargs)[source]

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.

copy()[source]

Make an independent (“deep”) copy of the whole Timestep.

copy_slice(sel)[source]

Make a new Timestep containing a subset of the original Timestep.

Parameters:sel (array_like or slice) – The underlying position, velocity, and force arrays are sliced using a list, slice, or any array-like.
Returns:A Timestep object of the same type containing all header information and all atom information relevant to the selection.
Return type:Timestep

Note

The selection must be a 0 based slice or array of the atom indices in this Timestep

Example

Using a Python slice object:

new_ts = ts.copy_slice(slice(start, stop, step))

Using a list of indices:

new_ts = ts.copy_slice([0, 2, 10, 20, 23])

New in version 0.8.

Changed in version 0.11.0: Reworked to follow new Timestep API. Now will strictly only copy official attributes of the Timestep.

dimensions

unitcell dimensions (A, B, C, alpha, beta, gamma)

dt

The time difference in ps between timesteps

Note

This defaults to 1.0 ps in the absence of time data

New in version 0.11.0.

forces

A record of the forces of all atoms in this Timestep

Setting this attribute will add forces to the Timestep if they weren’t originally present.

Returns:forces – force data of shape (n_atoms, 3) for all atoms
Return type:numpy.ndarray with dtype numpy.float32
Raises:MDAnalysis.exceptions.NoDataError – if the Timestep has no force data

New in version 0.11.0.

classmethod from_coordinates(positions=None, velocities=None, forces=None, **kwargs)[source]

Create an instance of this Timestep, from coordinate data

Can pass position, velocity and force data to form a Timestep.

New in version 0.11.0.

classmethod from_timestep(other, **kwargs)[source]

Create a copy of another Timestep, in the format of this Timestep

New in version 0.11.0.

has_forces

A boolean of whether this Timestep has force data

This can be changed to True or False to allocate space for or remove the data.

New in version 0.11.0.

has_positions

A boolean of whether this Timestep has position data

This can be changed to True or False to allocate space for or remove the data.

New in version 0.11.0.

has_velocities

A boolean of whether this Timestep has velocity data

This can be changed to True or False to allocate space for or remove the data.

New in version 0.11.0.

n_atoms

A read only view of the number of atoms this Timestep has

Changed in version 0.11.0: Changed to read only property

positions

A record of the positions of all atoms in this Timestep

Setting this attribute will add positions to the Timestep if they weren’t originally present.

Returns:positions – position data of shape (n_atoms, 3) for all atoms
Return type:numpy.ndarray with dtype numpy.float32
Raises:MDAnalysis.exceptions.NoDataError – if the Timestep has no position data

Changed in version 0.11.0: Now can raise NoDataError when no position data present

time

The time in ps of this timestep

This is calculated as:

time = ts.data['time_offset'] + ts.time

Or, if the trajectory doesn’t provide time information:

time = ts.data['time_offset'] + ts.frame * ts.dt

New in version 0.11.0.

triclinic_dimensions

The unitcell dimensions represented as triclinic vectors

Returns:A (3, 3) numpy.ndarray of unit cell vectors
Return type:numpy.ndarray

Examples

The unitcell for a given system can be queried as either three vectors lengths followed by their respective angle, or as three triclinic vectors.

>>> ts.dimensions
array([ 13.,  14.,  15.,  90.,  90.,  90.], dtype=float32)
>>> ts.triclinic_dimensions
array([[ 13.,   0.,   0.],
       [  0.,  14.,   0.],
       [  0.,   0.,  15.]], dtype=float32)

Setting the attribute also works:

>>> ts.triclinic_dimensions = [[15, 0, 0], [5, 15, 0], [5, 5, 15]]
>>> ts.dimensions
array([ 15.        ,  15.81138802,  16.58312416,  67.58049774,
        72.45159912,  71.56504822], dtype=float32)

See also

MDAnalysis.lib.mdamath.triclinic_vectors()

New in version 0.11.0.

velocities

A record of the velocities of all atoms in this Timestep

Setting this attribute will add velocities to the Timestep if they weren’t originally present.

Returns:velocities – velocity data of shape (n_atoms, 3) for all atoms
Return type:numpy.ndarray with dtype numpy.float32
Raises:MDAnalysis.exceptions.NoDataError – if the Timestep has no velocity data

New in version 0.11.0.

volume

volume of the unitcell

class MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader(filename, convert_units=True, n_atoms=None, **kwargs)[source]

Reader for the FHIAIMS geometry format.

Single frame reader for the FHI-AIMS input file format. Reads geometry (3D and molecules only), positions (absolut or fractional), velocities if given, all according to the FHI-AIMS format specifications

OtherWriter(filename, **kwargs)

Returns a writer appropriate for filename.

Sets the default keywords start, step and dt (if available). n_atoms is always set from Reader.n_atoms.

See also

Reader.Writer()

Writer(filename, n_atoms=None, **kwargs)[source]

Returns a FHIAIMSWriter for filename.

Parameters:filename (str) – filename of the output FHI-AIMS file
Returns:
Return type:FHIAIMSWriter
add_auxiliary(auxname, auxdata, format=None, **kwargs)

Add auxiliary data to be read alongside trajectory.

Auxiliary data may be any data timeseries from the trajectory additional to that read in by the trajectory reader. auxdata can be an AuxReader instance, or the data itself as e.g. a filename; in the latter case an appropriate AuxReader is guessed from the data/file format. An appropriate format may also be directly provided as a key word argument.

On adding, the AuxReader is initially matched to the current timestep of the trajectory, and will be updated when the trajectory timestep changes (through a call to next() or jumping timesteps with trajectory[i]).

The representative value(s) of the auxiliary data for each timestep (as calculated by the AuxReader) are stored in the current timestep in the ts.aux namespace under auxname; e.g. to add additional pull force data stored in pull-force.xvg:

u = MDAnalysis.Universe(PDB, XTC)
u.trajectory.add_auxiliary('pull', 'pull-force.xvg')

The representative value for the current timestep may then be accessed as u.trajectory.ts.aux.pull or u.trajectory.ts.aux['pull'].

See also

remove_auxiliary()

Note

Auxiliary data is assumed to be time-ordered, with no duplicates. See the Auxiliary API.

add_transformations(*transformations)

Add all transformations to be applied to the trajectory.

This function take as list of transformations as an argument. These transformations are functions that will be called by the Reader and given a Timestep object as argument, which will be transformed and returned to the Reader. The transformations can be part of the transformations module, or created by the user, and are stored as a list transformations. This list can only be modified once, and further calls of this function will raise an exception.

u = MDAnalysis.Universe(topology, coordinates)
workflow = [some_transform, another_transform, this_transform]
u.trajectory.add_transformations(*workflow)
Parameters:transform_list (list) – list of all the transformations that will be applied to the coordinates

See also

MDAnalysis.transformations

aux_list

Lists the names of added auxiliary data.

check_slice_indices(start, stop, step)

Check frame indices are valid and clip to fit trajectory.

The usage follows standard Python conventions for range() but see the warning below.

Parameters:
  • start (int or None) – Starting frame index (inclusive). None corresponds to the default of 0, i.e., the initial frame.
  • stop (int or None) – Last frame index (exclusive). None corresponds to the default of n_frames, i.e., it includes the last frame of the trajectory.
  • step (int or None) – step size of the slice, None corresponds to the default of 1, i.e, include every frame in the range start, stop.
Returns:

start, stop, step – Integers representing the slice
Return type:

tuple (int, int, int)

Warning

The returned values start, stop and step give the expected result when passed in range() but gives unexpected behavior when passed in a slice when stop=None and step=-1

This can be a problem for downstream processing of the output from this method. For example, slicing of trajectories is implemented by passing the values returned by check_slice_indices() to range()

range(start, stop, step)

and using them as the indices to randomly seek to. On the other hand, in MDAnalysis.analysis.base.AnalysisBase the values returned by check_slice_indices() are used to splice the trajectory by creating a slice instance

slice(start, stop, step)

This creates a discrepancy because these two lines are not equivalent:

range(10, -1, -1)             # [10, 9, 8, 7, 6, 5, 4, 3, 2, 1, 0]
range(10)[slice(10, -1, -1)]  # []
close()

Close the trajectory file.

convert_forces_from_native(force, inplace=True)

Conversion of forces array force from native to base units

Parameters:
  • force (array_like) – Forces to transform
  • inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input force is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.

New in version 0.7.7.

convert_forces_to_native(force, inplace=True)

Conversion of force array force from base to native units.

Parameters:
  • force (array_like) – Forces to transform
  • inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input force is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.

New in version 0.7.7.

convert_pos_from_native(x, inplace=True)

Conversion of coordinate array x from native units to base units.

Parameters:
  • x (array_like) – Positions to transform
  • inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input x is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.

Changed in version 0.7.5: Keyword inplace can be set to False so that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.

convert_pos_to_native(x, inplace=True)

Conversion of coordinate array x from base units to native units.

Parameters:
  • x (array_like) – Positions to transform
  • inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input x is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.

Changed in version 0.7.5: Keyword inplace can be set to False so that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.

convert_time_from_native(t, inplace=True)

Convert time t from native units to base units.

Parameters:
  • t (array_like) – Time values to transform
  • inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input t is modified in place and also returned (although note that scalar values t are passed by value in Python and hence an in-place modification has no effect on the caller.) In-place operations improve performance because allocating new arrays is avoided.

Changed in version 0.7.5: Keyword inplace can be set to False so that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.

convert_time_to_native(t, inplace=True)

Convert time t from base units to native units.

Parameters:
  • t (array_like) – Time values to transform
  • inplace (bool, optional) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input t is modified in place and also returned. (Also note that scalar values t are passed by value in Python and hence an in-place modification has no effect on the caller.)

Changed in version 0.7.5: Keyword inplace can be set to False so that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.

convert_velocities_from_native(v, inplace=True)

Conversion of velocities array v from native to base units

Parameters:
  • v (array_like) – Velocities to transform
  • inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input v is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.

New in version 0.7.5.

convert_velocities_to_native(v, inplace=True)

Conversion of coordinate array v from base to native units

Parameters:
  • v (array_like) – Velocities to transform
  • inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input v is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.

New in version 0.7.5.

copy()

Return independent copy of this Reader.

New Reader will have its own file handle and can seek/iterate independently of the original.

Will also copy the current state of the Timestep held in the original Reader

dt

Time between two trajectory frames in picoseconds.

frame

Frame number of the current time step.

This is a simple short cut to Timestep.frame.

get_aux_attribute(auxname, attrname)

Get the value of attrname from the auxiliary auxname

Parameters:
  • auxname (str) – Name of the auxiliary to get value for
  • attrname (str) – Name of gettable attribute in the auxiliary reader

See also

set_aux_attribute()

get_aux_descriptions(auxnames=None)

Get descriptions to allow reloading the specified auxiliaries.

If no auxnames are provided, defaults to the full list of added auxiliaries.

Passing the resultant description to add_auxiliary() will allow recreation of the auxiliary. e.g., to duplicate all auxiliaries into a second trajectory:

descriptions = trajectory_1.get_aux_descriptions()
for aux in descriptions:
    trajectory_2.add_auxiliary(**aux)
Returns:List of dictionaries of the args/kwargs describing each auxiliary.
Return type:list

See also

MDAnalysis.auxiliary.base.AuxReader.get_description()

iter_as_aux(auxname)

Iterate through timesteps for which there is at least one assigned step from the auxiliary auxname within the cutoff specified in auxname.

See also

next_as_aux(), iter_auxiliary()

iter_auxiliary(auxname, start=None, stop=None, step=None, selected=None)

Iterate through the auxiliary auxname independently of the trajectory.

Will iterate over the specified steps of the auxiliary (defaults to all steps). Allows to access all values in an auxiliary, including those out of the time range of the trajectory, without having to also iterate through the trajectory.

After interation, the auxiliary will be repositioned at the current step.

Parameters:
  • auxname (str) – Name of the auxiliary to iterate over.
  • stop, step) ((start,) – Options for iterating over a slice of the auxiliary.
  • selected (lst | ndarray, optional) – List of steps to iterate over.
Yields:

AuxStep object

See also

iter_as_aux()

next()

Forward one step to next frame.

next_as_aux(auxname)

Move to the next timestep for which there is at least one step from the auxiliary auxname within the cutoff specified in auxname.

This allows progression through the trajectory without encountering NaN representative values (unless these are specifically part of the auxiliary data).

If the auxiliary cutoff is not set, where auxiliary steps are less frequent (auxiliary.dt > trajectory.dt), this allows progression at the auxiliary pace (rounded to nearest timestep); while if the auxiliary steps are more frequent, this will work the same as calling next().

See the Auxiliary API.

See also

iter_as_aux()

classmethod parse_n_atoms(filename, **kwargs)

Read the coordinate file and deduce the number of atoms

Returns:n_atoms – the number of atoms in the coordinate file
Return type:int
Raises:NotImplementedError – when the number of atoms can’t be deduced
remove_auxiliary(auxname)

Clear data and close the AuxReader for the auxiliary auxname.

See also

add_auxiliary()

rename_aux(auxname, new)

Change the name of the auxiliary auxname to new.

Provided there is not already an auxiliary named new, the auxiliary name will be changed in ts.aux namespace, the trajectory’s list of added auxiliaries, and in the auxiliary reader itself.

Parameters:
  • auxname (str) – Name of the auxiliary to rename
  • new (str) – New name to try set
Raises:

ValueError – If the name new is already in use by an existing auxiliary.
rewind()

Position at beginning of trajectory

set_aux_attribute(auxname, attrname, new)

Set the value of attrname in the auxiliary auxname.

Parameters:
  • auxname (str) – Name of the auxiliary to alter
  • attrname (str) – Name of settable attribute in the auxiliary reader
  • new – New value to try set attrname to

See also

get_aux_attribute(), rename_aux()

time

Time of the current frame in MDAnalysis time units (typically ps).

This is either read straight from the Timestep, or calculated as time = Timestep.frame * Timestep.dt

totaltime

Total length of the trajectory

The time is calculated as (n_frames - 1) * dt, i.e., we assume that the first frame no time as elapsed. Thus, a trajectory with two frames will be considered to have a length of a single time step dt and a “trajectory” with a single frame will be reported as length 0.

transformations

Returns the list of transformations

class MDAnalysis.coordinates.FHIAIMS.FHIAIMSWriter(filename, convert_units=True, n_atoms=None, **kwargs)[source]

FHI-AIMS Writer.

Single frame writer for the FHI-AIMS format. Writes geometry (3D and molecules only), positions (absolut only), velocities if given, all according to the FHI-AIMS format specifications.

If no atom names are given, it will set each atom name to “X”.

Set up the FHI-AIMS Writer

Parameters:
  • filename (str) – output filename
  • n_atoms (int (optional)) – number of atoms
close()

Close the trajectory file.

convert_dimensions_to_unitcell(ts, inplace=True)

Read dimensions from timestep ts and return appropriate unitcell.

The default is to return [A,B,C,alpha,beta,gamma]; if this is not appropriate then this method has to be overriden.

convert_forces_from_native(force, inplace=True)

Conversion of forces array force from native to base units

Parameters:
  • force (array_like) – Forces to transform
  • inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input force is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.

New in version 0.7.7.

convert_forces_to_native(force, inplace=True)

Conversion of force array force from base to native units.

Parameters:
  • force (array_like) – Forces to transform
  • inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input force is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.

New in version 0.7.7.

convert_pos_from_native(x, inplace=True)

Conversion of coordinate array x from native units to base units.

Parameters:
  • x (array_like) – Positions to transform
  • inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input x is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.

Changed in version 0.7.5: Keyword inplace can be set to False so that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.

convert_pos_to_native(x, inplace=True)

Conversion of coordinate array x from base units to native units.

Parameters:
  • x (array_like) – Positions to transform
  • inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input x is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.

Changed in version 0.7.5: Keyword inplace can be set to False so that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.

convert_time_from_native(t, inplace=True)

Convert time t from native units to base units.

Parameters:
  • t (array_like) – Time values to transform
  • inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input t is modified in place and also returned (although note that scalar values t are passed by value in Python and hence an in-place modification has no effect on the caller.) In-place operations improve performance because allocating new arrays is avoided.

Changed in version 0.7.5: Keyword inplace can be set to False so that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.

convert_time_to_native(t, inplace=True)

Convert time t from base units to native units.

Parameters:
  • t (array_like) – Time values to transform
  • inplace (bool, optional) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input t is modified in place and also returned. (Also note that scalar values t are passed by value in Python and hence an in-place modification has no effect on the caller.)

Changed in version 0.7.5: Keyword inplace can be set to False so that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.

convert_velocities_from_native(v, inplace=True)

Conversion of velocities array v from native to base units

Parameters:
  • v (array_like) – Velocities to transform
  • inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input v is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.

New in version 0.7.5.

convert_velocities_to_native(v, inplace=True)

Conversion of coordinate array v from base to native units

Parameters:
  • v (array_like) – Velocities to transform
  • inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input v is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.

New in version 0.7.5.

fmt = {'box_triclinic': 'lattice_vector {box[0]:12.8f} {box[1]:12.8f} {box[2]:12.8f}\nlattice_vector {box[3]:12.8f} {box[4]:12.8f} {box[5]:12.8f}\nlattice_vector {box[6]:12.8f} {box[7]:12.8f} {box[8]:12.8f}\n', 'vel': 'velocity {vel[0]:12.8f} {vel[1]:12.8f} {vel[2]:12.8f}\n', 'xyz': 'atom {pos[0]:12.8f} {pos[1]:12.8f} {pos[2]:12.8f} {name:<3s}\n'}

format strings for the FHI-AIMS file (all include newline)

has_valid_coordinates(criteria, x)

Returns True if all values are within limit values of their formats.

Due to rounding, the test is asymmetric (and min is supposed to be negative):

min < x <= max
Parameters:
  • criteria (dict) – dictionary containing the max and min values in native units
  • x (numpy.ndarray) – (x, y, z) coordinates of atoms selected to be written out
Returns:
Return type:

bool
write(obj)

Write current timestep, using the supplied obj.

Parameters:obj (AtomGroup or Universe) – write coordinate information associate with obj

Note

The size of the obj must be the same as the number of atoms provided when setting up the trajectory.

Deprecated since version 1.0.0: Deprecated the use of Timestep as arguments to write. Use either an AtomGroup or Universe. To be removed in version 2.0.

write_next_timestep(obj)

Write current timestep, using the supplied obj.

Parameters:obj (AtomGroup or Universe) – write coordinate information associated with obj

Deprecated since version 1.0.0: Deprecated, use write() instead

6.23.2. Developer notes: FHIAIMSWriter format strings

The FHIAIMSWriter class has a FHIAIMSWriter.fmt attribute, which is a dictionary of different strings for writing lines in .in files. These are as follows:

xyz

An atom line without velocities. Requires that the name and pos keys be supplied. E.g.:

fmt['xyz'].format(pos=(0.0, 1.0, 2.0), name='O')
vel

An line that specifies velocities:

fmt['xyz'].format(vel=(0.1, 0.2, 0.3))
box_triclinic
The (optional) initial lines of the file which gives box dimensions. Requires the box keyword, as a length 9 vector. This is a flattened version of the (3, 3) triclinic vector representation of the unit cell.