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5.6. LAMMPS DCD trajectory I/O — MDAnalysis.coordinates.LAMMPS

Classes to read and write LAMMPS DCD binary trajectories. Trajectories can be read regardless of system-endianness as this is auto-detected.

LAMMPS can write DCD trajectories but unlike a CHARMM trajectory (which is often called a DCD even though CHARMM itself calls them “trj”) the time unit is not fixed to be the AKMA time unit (20 AKMA is 0.978 picoseconds or 1 AKMA = 4.888821e-14 s) but can depend on settings in LAMMPS. The most common case appears to be that the time step is actually recorded in picoseconds. Other cases are unit-less Lennard-Jones time units.

This presents a problem for MDAnalysis because it cannot autodetect the unit from the file. By default we are assuming that the unit for length is the ångström and for the time is the picosecond. If this is not true then the user should supply the appropriate units in the as keywords timeunit and/or lengthunit to DCDWriter and DCDReader.

Note

Lennard-Jones units are not implemented. See MDAnalysis.core.units for other recognized values.

See also

For further discussion follow the reports for Issue 84 and Issue 64.

5.6.1. Classes

class MDAnalysis.coordinates.LAMMPS.Timestep(arg, **kwargs)[source]

LAMMPS trajectory time step

copy()

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

copy_slice(sel)

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

ts.copy_slice(slice(start, stop, skip)) ts.copy_slice([list of indices])

Returns:A Timestep object of the same type containing all header information and all atom information relevent to the selection.

Note

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

New in version 0.8.

dimensions

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

lengths A, B, C are in the MDAnalysis length unit (Å), and angles are in degrees.

dimensions is read-only because it transforms the actual format of the unitcell (which differs between different trajectory formats) to the representation described here, which is used everywhere in MDAnalysis.

The ordering of the angles in the unitcell is the same as in recent versions of VMD’s DCDplugin (2013), namely the X-PLOR DCD format: The original unitcell is read as [A, gamma, B, beta, alpha, C] from the DCD file (actually, the direction cosines are stored instead of the angles but the underlying C code already does this conversion); if any of these values are < 0 or if any of the angles are > 180 degrees then it is assumed it is a new-style CHARMM unitcell (at least since c36b2) in which box vectors were recorded.

Warning

The DCD format is not well defined. Check your unit cell dimensions carefully, especially when using triclinic boxes. Different software packages implement different conventions and MDAnalysis is currently implementing the newer NAMD/VMD convention and tries to guess the new CHARMM one. Old CHARMM trajectories might give wrong unitcell values. For more details see Issue 187.

Changed in version 0.9.0: Unitcell is now interpreted in the newer NAMD DCD format as [A, gamma, B, beta, alpha, C] instead of the old MDAnalysis/CHARMM ordering [A, alpha, B, beta, gamma, C]. We attempt to detect the new CHARMM DCD unitcell format (see Issue 187 for a discussion).

volume

volume of the unitcell

class MDAnalysis.coordinates.LAMMPS.DCDReader(dcdfilename, **kwargs)[source]

Read a LAMMPS DCD trajectory.

The units can be set from the constructor with the keyword arguments timeunit and lengthunit. The defaults are “ps” and “Angstrom”. See MDAnalysis.core.units for other recognized values.

OtherWriter(filename, **kwargs)

Returns a writer appropriate for filename.

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

See also

Reader.Writer() and MDAnalysis.Writer()

Writer(filename, **kwargs)

Returns a DCDWriter for filename with the same parameters as this DCD.

All values can be changed through keyword arguments.

Arguments:
filename

filename of the output DCD trajectory

Keywords:
numatoms

number of atoms

start

number of the first recorded MD step

step

indicate that step MD steps (!) make up one trajectory frame

delta

MD integrator time step (!), in AKMA units

dt

Override step and delta so that the DCD records that dt ps lie between two frames. (It sets step = 1 and delta = AKMA(dt).) The default is None, in which case step and delta are used.

remarks

string that is stored in the DCD header [XXX – max length?]

Returns:

DCDWriter

Note

The keyword arguments set the low-level attributes of the DCD according to the CHARMM format. The time between two frames would be delta * step !

See also

DCDWriter has detailed argument description

close_trajectory()

Specific implementation of trajectory closing.

convert_forces_from_native(force, inplace=True)

In-place conversion of forces array force from native units to base units.

By default, the input force is modified in place and also returned.

New in version 0.7.7.

convert_forces_to_native(force, inplace=True)

In-place conversion of force array force from base units to native units.

By default, the input force is modified in place and also returned.

New in version 0.7.7.

convert_pos_from_native(x, inplace=True)

In-place conversion of coordinate array x from native units to base units.

By default, the input x is modified in place and also returned.

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.

By default, the input x is modified in place and also returned.

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.

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.)

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.

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)

In-place conversion of velocities array v from native units to base units.

By default, the input v is modified in place and also returned.

New in version 0.7.5.

convert_velocities_to_native(v, inplace=True)

In-place conversion of coordinate array v from base units to native units.

By default, the input v is modified in place and also returned.

New in version 0.7.5.

correl(timeseries, start=0, stop=-1, skip=1)

Populate a TimeseriesCollection object with timeseries computed from the trajectory

Arguments:
timeseries

MDAnalysis.core.Timeseries.TimeseriesCollection

start, stop, skip

subset of trajectory to use, with start and stop being inclusive

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.

next()

Forward one step to next frame.

rewind()

Position at beginning of trajectory

time

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

time = Timestep.frame * Reader.dt

timeseries(asel, start=0, stop=-1, skip=1, format='afc')

Return a subset of coordinate data for an AtomGroup

Arguments:
asel

AtomGroup object

start, stop, skip

range of trajectory to access, start and stop are inclusive

format

the order/shape of the return data array, corresponding to (a)tom, (f)rame, (c)oordinates all six combinations of ‘a’, ‘f’, ‘c’ are allowed ie “fac” - return array where the shape is (frame, number of atoms, coordinates)

totaltime

Total length of the trajectory numframes * dt.

class MDAnalysis.coordinates.LAMMPS.DCDWriter(*args, **kwargs)[source]

Write a LAMMPS DCD trajectory.

The units can be set from the constructor with the keyword arguments timeunit and lengthunit. The defaults are “ps” and “Angstrom”. See MDAnalysis.core.units for other recognized values.

close()

Close trajectory and flush buffers.

close_trajectory()

Specific implementation of trajectory closing.

convert_dimensions_to_unitcell(ts, _ts_order=[0, 2, 5, 4, 3, 1])

Read dimensions from timestep ts and return appropriate native unitcell.

convert_forces_from_native(force, inplace=True)

In-place conversion of forces array force from native units to base units.

By default, the input force is modified in place and also returned.

New in version 0.7.7.

convert_forces_to_native(force, inplace=True)

In-place conversion of force array force from base units to native units.

By default, the input force is modified in place and also returned.

New in version 0.7.7.

convert_pos_from_native(x, inplace=True)

In-place conversion of coordinate array x from native units to base units.

By default, the input x is modified in place and also returned.

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.

By default, the input x is modified in place and also returned.

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.

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.)

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.

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)

In-place conversion of velocities array v from native units to base units.

By default, the input v is modified in place and also returned.

New in version 0.7.5.

convert_velocities_to_native(v, inplace=True)

In-place conversion of coordinate array v from base units to native units.

By default, the input v is modified in place and also returned.

New in version 0.7.5.

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
Arguments:
criteria

dictionary containing the max and min values in native units

x

numpy.ndarray of (x, y, z) coordinates of atoms selected to be written out.

Returns:

boolean

write(obj)

Write current timestep, using the supplied obj.

The argument should be a AtomGroup or a Universe or a Timestep instance.

Note

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

write_next_timestep(ts=None)

write a new timestep to the dcd file

ts - timestep object containing coordinates to be written to dcd file

Changed in version 0.7.5: Raises ValueError instead of generic Exception if wrong number of atoms supplied and NoDataError if no coordinates to be written.

class MDAnalysis.coordinates.LAMMPS.DATAReader(pdbfilename, numatoms=None, convert_units=None, **kwargs)[source]

Reads a single frame of coordinate information from a LAMMPS DATA file.

New in version 0.9.0.

OtherWriter(filename, **kwargs)

Returns a writer appropriate for filename.

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

See also

Reader.Writer() and MDAnalysis.Writer()

Writer(filename, **kwargs)

Returns a trajectory writer with the same properties as this trajectory.

close()

Close the trajectory file.

close_trajectory()

Specific implementation of trajectory closing.

convert_forces_from_native(force, inplace=True)

In-place conversion of forces array force from native units to base units.

By default, the input force is modified in place and also returned.

New in version 0.7.7.

convert_forces_to_native(force, inplace=True)

In-place conversion of force array force from base units to native units.

By default, the input force is modified in place and also returned.

New in version 0.7.7.

convert_pos_from_native(x, inplace=True)

In-place conversion of coordinate array x from native units to base units.

By default, the input x is modified in place and also returned.

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.

By default, the input x is modified in place and also returned.

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.

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.)

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.

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)

In-place conversion of velocities array v from native units to base units.

By default, the input v is modified in place and also returned.

New in version 0.7.5.

convert_velocities_to_native(v, inplace=True)

In-place conversion of coordinate array v from base units to native units.

By default, the input v is modified in place and also returned.

New in version 0.7.5.

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.

next()

Forward one step to next frame.

rewind()

Position at beginning of trajectory

time

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

time = Timestep.frame * Reader.dt

totaltime

Total length of the trajectory numframes * dt.